Query 020088
Match_columns 331
No_of_seqs 126 out of 274
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 06:55:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020088.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020088hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02598 Methyltrn_RNA_3: Puta 100.0 4.5E-85 9.8E-90 624.9 14.9 254 62-326 1-260 (291)
2 KOG3925 Uncharacterized conser 100.0 2.4E-83 5.2E-88 617.2 17.3 269 57-330 64-335 (371)
3 COG2106 Uncharacterized conser 100.0 1.5E-59 3.2E-64 441.1 20.5 223 58-314 1-226 (272)
4 PRK03958 tRNA 2'-O-methylase; 88.6 0.3 6.4E-06 44.6 2.3 70 248-321 52-129 (176)
5 TIGR00246 tRNA_RlmH_YbeA rRNA 72.5 2 4.3E-05 38.2 1.4 49 274-322 66-122 (153)
6 PRK00103 rRNA large subunit me 59.3 7.2 0.00016 34.8 2.4 49 273-321 67-124 (157)
7 PRK10433 putative RNA methyltr 54.5 24 0.00051 33.4 5.1 56 250-311 54-121 (228)
8 COG1576 Uncharacterized conser 52.8 6 0.00013 35.5 0.8 43 273-315 67-115 (155)
9 PF00588 SpoU_methylase: SpoU 46.4 18 0.00039 30.6 2.7 24 83-106 13-36 (142)
10 KOG2422 Uncharacterized conser 46.3 14 0.0003 39.8 2.3 15 2-16 48-62 (665)
11 PF02590 SPOUT_MTase: Predicte 43.5 8.7 0.00019 34.1 0.3 49 273-321 67-124 (155)
12 TIGR00050 rRNA_methyl_1 RNA me 43.5 43 0.00093 31.4 4.9 56 250-311 55-119 (233)
13 TIGR00050 rRNA_methyl_1 RNA me 41.2 25 0.00055 33.0 3.0 24 84-107 16-39 (233)
14 PRK15114 tRNA (cytidine/uridin 39.2 56 0.0012 31.0 5.0 61 254-320 60-133 (245)
15 KOG2201 Pantothenate kinase Pa 36.2 38 0.00081 34.3 3.4 27 77-103 284-311 (371)
16 PF00588 SpoU_methylase: SpoU 35.5 39 0.00084 28.5 3.1 56 254-315 58-114 (142)
17 PF10646 Germane: Sporulation 35.1 90 0.002 25.1 5.1 44 62-106 65-110 (117)
18 PRK15114 tRNA (cytidine/uridin 34.2 44 0.00096 31.7 3.5 23 84-106 17-39 (245)
19 COG0565 LasT rRNA methylase [T 34.1 51 0.0011 31.7 3.9 57 254-316 60-129 (242)
20 TIGR02266 gmx_TIGR02266 Myxoco 32.5 52 0.0011 25.5 3.1 62 196-258 19-82 (96)
21 KOG2367 Alpha-isopropylmalate 31.4 29 0.00063 36.6 1.9 20 137-156 150-169 (560)
22 TIGR00186 rRNA_methyl_3 rRNA m 27.8 48 0.001 31.0 2.6 23 83-105 102-124 (237)
23 PF09895 DUF2122: RecB-family 27.5 1.8E+02 0.0038 24.6 5.6 54 253-311 21-75 (106)
24 TIGR00186 rRNA_methyl_3 rRNA m 26.7 3.1E+02 0.0067 25.6 7.8 65 253-322 145-212 (237)
25 PRK11181 23S rRNA (guanosine-2 25.9 55 0.0012 30.9 2.6 22 84-105 108-129 (244)
26 PF10246 MRP-S35: Mitochondria 25.5 2.5E+02 0.0054 23.8 6.0 46 177-225 22-73 (104)
27 PLN02726 dolichyl-phosphate be 25.3 1.8E+02 0.0038 26.3 5.8 45 59-108 7-51 (243)
28 PRK10433 putative RNA methyltr 25.2 67 0.0014 30.4 3.0 23 84-106 15-37 (228)
29 PRK12703 tRNA 2'-O-methylase; 24.7 78 0.0017 31.8 3.5 53 249-306 52-107 (339)
30 TIGR00185 rRNA_methyl_2 rRNA m 24.7 60 0.0013 28.3 2.4 28 71-102 5-32 (153)
31 PRK10864 putative methyltransf 23.9 62 0.0013 32.6 2.6 21 84-104 211-231 (346)
32 PRK09756 PTS system N-acetylga 23.8 99 0.0021 27.5 3.7 49 84-153 16-65 (158)
33 COG0565 LasT rRNA methylase [T 22.9 79 0.0017 30.4 3.0 25 84-108 17-41 (242)
34 PRK00026 trmD tRNA (guanine-N( 21.7 69 0.0015 30.9 2.3 51 273-323 81-135 (244)
35 PF09936 Methyltrn_RNA_4: SAM- 21.3 1E+02 0.0022 28.5 3.3 40 82-142 27-66 (185)
36 PRK10714 undecaprenyl phosphat 20.3 2.5E+02 0.0054 27.3 6.0 46 59-109 4-50 (325)
No 1
>PF02598 Methyltrn_RNA_3: Putative RNA methyltransferase; InterPro: IPR003750 This entry describes proteins of unknown function.; PDB: 1K3R_B.
Probab=100.00 E-value=4.5e-85 Score=624.93 Aligned_cols=254 Identities=51% Similarity=0.904 Sum_probs=159.3
Q ss_pred eEEEEecCccccCCCCHHHHHHHHHHHHHHHhhhcccEEEEEcCCCCCCccccccccccCCCCCCCcchHHHHHHHHhhh
Q 020088 62 TVSVAVPGSIIDNTQSLELATRLAGQIARAVTIFRIDEVVVFDNKSSSDNYSRSSAANRSNRSDENESGAAFLVRLLQYL 141 (331)
Q Consensus 62 tvSIAIP~SIlsnaqslelkT~~agqIARAaaIF~VdEIVVydd~~~~~~~~~~~~~~~~~~~~~~~~~~~fL~~lLqYl 141 (331)
|||||||+|||+||||+|+|||+|||||||||||||||||||||+....+... ..........+++.||++|||||
T Consensus 1 tvSIaIP~Sil~n~~s~e~~T~~~gqIARaaaiF~VdEIvVydd~~~~~~~~~----~~~~~~~~~~~~~~~l~~lLqYl 76 (291)
T PF02598_consen 1 TVSIAIPGSILSNAQSLELKTYKAGQIARAAAIFRVDEIVVYDDSPKVQNNQD----GENEKGKSNRDDAEFLARLLQYL 76 (291)
T ss_dssp -EEEEEETTTTTT---HHHHHHHHHHHHHHHHHTT--EEEEEE---------------------SSS--HHHHHHHHHHH
T ss_pred CEEEEechHHhccCCCHHHHHHHHHHHHHHHHeecCcEEEEEccccccccccc----cccccccCCCCHHHHHHHHHHHh
Confidence 79999999999999999999999999999999999999999999532222111 01112334567899999999999
Q ss_pred cCCchhhhhhcCCCCCccccCcCCCCCCCCCC-CCCCccCceeEEEeeccCCCCCceEEEeCCCceeeecc-cCCCCcEE
Q 020088 142 ETPQYLRKALFSMHSSLRFVGMLPPLDAPHHL-RKHEWAPFREGVTLKENAPNSVGTLVDVGLNKHVVVDQ-VLDPGVRV 219 (331)
Q Consensus 142 eTPpYLRK~LFP~~~~Lk~aGlLPPL~~PhH~-r~~~~~~yREGvvv~~~~~~g~~s~VdiGl~~~v~i~~-~l~~g~RV 219 (331)
||||||||+|||+|++|||||+||||++|||+ +.++|++||||||+++..+.++++|||||+.+++.++. .+++|+||
T Consensus 77 eTPpYLRK~lFp~~~~Lk~aGlLppL~~phH~~~~~~~~~yREGvv~~~~~~~~~~~~VdiGl~~~v~i~~~~l~~g~RV 156 (291)
T PF02598_consen 77 ETPPYLRKRLFPIHPDLKYAGLLPPLDAPHHMSRSDEWGPYREGVVVRKPSKGGKGSYVDIGLDKPVEIDKQELPPGTRV 156 (291)
T ss_dssp HS-HHHHHHHS---GGGCCGGGS-----TTS--SS--TT-EEEEEEEEE-SSS---EEEESSSSEEEESSS----SS-EE
T ss_pred cCCHHHHHhhcccCcccccccccCCCCCCccccCCccccceeEEEEEeCCCCCCceEEEEeCCCcEEeecccccCCCCEE
Confidence 99999999999999999999999999999999 88999999999999998767777999999999999999 99999999
Q ss_pred EEEecCCCCCCCCCCceecCCCCCCCCCcccceEEEEeCChHHHhhcCCCCCCCcEEEEeCCCCCCCCCCCCCCC--CCC
Q 020088 220 TVAMGTNRNLDADSPRQVVPPSKPKESGMYWGYKVRYAPNISSVFKNCSYKGGYDHLIGTSEHGDIVNSSDLTLP--TFR 297 (331)
Q Consensus 220 TV~l~~~~~~~~~~~~~vVsp~~P~~~G~YWGY~VR~a~sL~~vf~e~p~~~gYD~~IgTS~~G~~i~~~~~~l~--~~k 297 (331)
||+|++ ..|++|+|++|...|+||||+||+|+||++||++|||++|||++||||++|.++++.....+ +++
T Consensus 157 TV~~~~-------~~~~vVsp~~p~~~g~YwGY~VR~a~sl~~v~~~~~~~~GYd~~IgtS~~G~~~~~~~~~~~~~~~~ 229 (291)
T PF02598_consen 157 TVRIKS-------LKGKVVSPSEPREAGYYWGYSVRIASSLSEVFTECPYPEGYDLIIGTSERGEPISSSELEIKSSSFK 229 (291)
T ss_dssp EEEEEE-------SSS-EEEE---SS--S----EEEEECEHHHHHHHC------SEEEEE-TTS-BTTTSHHHHHHHT-S
T ss_pred EEEecC-------CcCCEeCcccCCcCCccCCeEEEEeCCHHHHHhcCCcccccceEEEECCCCeeCchhhcccccCCCC
Confidence 999994 35899999999439999999999999999999999999999999999999999987665554 899
Q ss_pred cEEEEEcCcccHHHHHhcCCCC--ccccccc
Q 020088 298 HLLIAFGGLAGLEESIEEDDGL--KVHYLLK 326 (331)
Q Consensus 298 hlLIVFGgp~GLe~~~~~D~~l--~~~~~~~ 326 (331)
|+|||||||.+++.+++.|+++ .+.++.+
T Consensus 230 ~~LiVFGg~~~~~~~~~~~~~~~~~~~~~~~ 260 (291)
T PF02598_consen 230 HLLIVFGGWSPLEGADEIDEKLFEGGEDAEE 260 (291)
T ss_dssp EEEEE-----SSS---S--------------
T ss_pred cEEEEEecCHHHhhccccccccccccccccc
Confidence 9999999999999999999954 4444433
No 2
>KOG3925 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=2.4e-83 Score=617.19 Aligned_cols=269 Identities=44% Similarity=0.783 Sum_probs=245.2
Q ss_pred CCCcceEEEEecCccccCCCCHHHHHHHHHHHHHHHhhhcccEEEEEcCCCCCCccccccccccCCCCCCCcchHHHHHH
Q 020088 57 PIEVPTVSVAVPGSIIDNTQSLELATRLAGQIARAVTIFRIDEVVVFDNKSSSDNYSRSSAANRSNRSDENESGAAFLVR 136 (331)
Q Consensus 57 ~~r~~tvSIAIP~SIlsnaqslelkT~~agqIARAaaIF~VdEIVVydd~~~~~~~~~~~~~~~~~~~~~~~~~~~fL~~ 136 (331)
.++.+|+|||||+|||+||||+||+|++||||||||++|+|||||||||.....+.+.. ...+.+..++|.||++
T Consensus 64 ~~~~~t~SIaiPgsil~n~~nlel~T~~a~QIAR~aslf~V~Eiivldd~~~~~~~~~~-----~~~~~~~~s~~~~L~~ 138 (371)
T KOG3925|consen 64 ESRPYTYSIAIPGSILNNAQNLELATYFAGQIARAASLFRVDEIIVLDDSEYVTNEQVN-----TSSDKENISGCKLLAR 138 (371)
T ss_pred CCCceEEEEEechHHHhhhhhhHHHHHHhhhhhhhheeecceeEEEecccchhhhhhhc-----ccccccccccHHHHHH
Confidence 67999999999999999999999999999999999999999999999998766554321 1123557789999999
Q ss_pred HHhhhcCCchhhhhhcCCCCCccccCcCCCCCCCCCCCCCCccCceeEEEeeccCCCCCceEEEeCCCceeeec-ccCC-
Q 020088 137 LLQYLETPQYLRKALFSMHSSLRFVGMLPPLDAPHHLRKHEWAPFREGVTLKENAPNSVGTLVDVGLNKHVVVD-QVLD- 214 (331)
Q Consensus 137 lLqYleTPpYLRK~LFP~~~~Lk~aGlLPPL~~PhH~r~~~~~~yREGvvv~~~~~~g~~s~VdiGl~~~v~i~-~~l~- 214 (331)
|||||||||||||+|||+|++|||||+|||||+|||++.+++++||||||+.+.++.|.+++|||||.+.+.|+ ..+.
T Consensus 139 lLqYfetPqyLRk~~Fp~~~~Lk~ag~lppLd~~hh~~q~e~~~YREGvvi~~~~~~g~~~~in~gL~k~v~I~~~~v~~ 218 (371)
T KOG3925|consen 139 LLQYFETPQYLRKTLFPKHPDLKYAGLLPPLDTPHHLRQDEKFRYREGVVIKRKSPAGHGYIINAGLKKEVYIDSKAVEA 218 (371)
T ss_pred HHhhccCcHHHHHhhccCCccccccccCCCCCchHHhhhhhhhccccceeeccCCCCCCcceecccceeeEEecchhhcC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999998 5566
Q ss_pred CCcEEEEEecCCCCCCCCCCceecCCCCC-CCCCcccceEEEEeCChHHHhhcCCCCCCCcEEEEeCCCCCCCCCCCCCC
Q 020088 215 PGVRVTVAMGTNRNLDADSPRQVVPPSKP-KESGMYWGYKVRYAPNISSVFKNCSYKGGYDHLIGTSEHGDIVNSSDLTL 293 (331)
Q Consensus 215 ~g~RVTV~l~~~~~~~~~~~~~vVsp~~P-~~~G~YWGY~VR~a~sL~~vf~e~p~~~gYD~~IgTS~~G~~i~~~~~~l 293 (331)
||+||||+|+...+....+.|+||||++| +++|+||||+||+|++|++||++|||++|||++||||.+|..|.+.+...
T Consensus 219 p~~RvtV~l~aq~~~~~t~~g~IVSp~~pr~~tGlywGY~VR~assls~vf~~~P~~~GYD~~vg~s~rg~~I~s~~~~~ 298 (371)
T KOG3925|consen 219 PGTRVTVRLNAQTVTCDTLRGKIVSPQDPREETGLYWGYKVRLASSLSEVFSESPFKGGYDFVVGTSTRGSAIASLSLEA 298 (371)
T ss_pred CcceEEEecCCcCchhhhhcccccCCCCcccccCcccceeeehhhhHHHHhhcCCccCCcceEEEeccCCcccccccccc
Confidence 99999999995434555678999999999 99999999999999999999999999999999999999999998877777
Q ss_pred CCCCcEEEEEcCcccHHHHHhcCCCCccccccccccC
Q 020088 294 PTFRHLLIAFGGLAGLEESIEEDDGLKVHYLLKSYSL 330 (331)
Q Consensus 294 ~~~khlLIVFGgp~GLe~~~~~D~~l~~~~~~~~~~~ 330 (331)
+.+.|+|+|||||+||+.+|+.|+...+.+.--.+.+
T Consensus 299 ~t~~~iLlvfg~l~~l~~a~e~~~~~~~~~~~~~f~~ 335 (371)
T KOG3925|consen 299 ETPPHILLVFGGLAGLVRAFELDEQTTWRDSEDPFDV 335 (371)
T ss_pred CCCCcEEEEeechhhHHHHHHhccchhccccCCchhh
Confidence 8899999999999999999999999888877655544
No 3
>COG2106 Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=1.5e-59 Score=441.07 Aligned_cols=223 Identities=35% Similarity=0.634 Sum_probs=193.7
Q ss_pred CCcceEEEEecCccccCCCCHHHHHHHHHHHHHHHhhhcccEEEEEcCCCCCCccccccccccCCCCCCCcchHHHHHHH
Q 020088 58 IEVPTVSVAVPGSIIDNTQSLELATRLAGQIARAVTIFRIDEVVVFDNKSSSDNYSRSSAANRSNRSDENESGAAFLVRL 137 (331)
Q Consensus 58 ~r~~tvSIAIP~SIlsnaqslelkT~~agqIARAaaIF~VdEIVVydd~~~~~~~~~~~~~~~~~~~~~~~~~~~fL~~l 137 (331)
.|..++|||||+|++++|.|++++||++||||||||||||||||||+|+....+ ++.||+.|
T Consensus 1 ~~~~~~Sv~iP~Sll~~~~dl~~kT~Kvg~IARaaaiF~V~eIii~~D~~~~~~------------------~~~~i~~l 62 (272)
T COG2106 1 SRRVMLSVAIPTSLLSEENDLKLKTYKVGQIARAAAIFRVDEIIIYEDGDDVRR------------------DAKFITTL 62 (272)
T ss_pred CceeEEEEEcchHHhhccCCHHHhHHHHHHHHHHHHhhcccEEEEEeCCCCccc------------------hhHHHHHH
Confidence 367899999999999999999999999999999999999999999999854322 58999999
Q ss_pred HhhhcCCchhhhhhcCCCCCccccCcCCCCCCCCCCCC--CCccCceeEEEeeccCCCCCceEEEeCCCceeeecccCCC
Q 020088 138 LQYLETPQYLRKALFSMHSSLRFVGMLPPLDAPHHLRK--HEWAPFREGVTLKENAPNSVGTLVDVGLNKHVVVDQVLDP 215 (331)
Q Consensus 138 LqYleTPpYLRK~LFP~~~~Lk~aGlLPPL~~PhH~r~--~~~~~yREGvvv~~~~~~g~~s~VdiGl~~~v~i~~~l~~ 215 (331)
||||+|||||||++||++++|||||+||||++|||+.. +.+|+||||+|+.+. +++.+||||+++.+.+...+++
T Consensus 63 L~Y~~TPpyLRK~vFp~~~~LkyAg~lPPL~ip~h~~~~~~~~Ge~ReG~v~~~~---~~~~~v~iG~~~~~~l~~~~~~ 139 (272)
T COG2106 63 LEYFETPPYLRKRVFPIKRELKYAGLLPPLRIPSHTVSTSPKEGEYREGLVIRRG---KKGNLVDIGKDKLAKLSSPAPP 139 (272)
T ss_pred HHHhcCCHHHHhhhcCCCcccccccccCCCCCCCccCcCCccceeecceEEEEec---CCceEEEecCCcceeccCCCCC
Confidence 99999999999999999999999999999999999976 789999999999984 6779999999999999999999
Q ss_pred CcEEEEEecCCCCCCCCCCceecCCCCCCCCCcccceEEEEeCChHHHhhcCCCCCCCcEEEEeCCCCCCCCCCCCCCCC
Q 020088 216 GVRVTVAMGTNRNLDADSPRQVVPPSKPKESGMYWGYKVRYAPNISSVFKNCSYKGGYDHLIGTSEHGDIVNSSDLTLPT 295 (331)
Q Consensus 216 g~RVTV~l~~~~~~~~~~~~~vVsp~~P~~~G~YWGY~VR~a~sL~~vf~e~p~~~gYD~~IgTS~~G~~i~~~~~~l~~ 295 (331)
|+||||++.+.. ....|.|.+| .+ ||||+||.+++|.++++.. +.++.+|+||++| +++..+...+.
T Consensus 140 ~~RvTvri~~~~------~p~~~~~~~~--~~-YwGY~V~~~~~L~e~~~~~---~~~~vvi~tsr~g-~~~~~e~~~~~ 206 (272)
T COG2106 140 GARVTVRIISRS------SPLRVEPAEP--PD-YWGYKVRIAKSLNELLKGF---DLDVVVIATSRYG-PLDVRETEAPL 206 (272)
T ss_pred CceEEEEEEecc------CceeeecCCC--CC-cCcEEEEehhhHHHHhhcc---CCCceEEEecccC-cceeeeccccc
Confidence 999999998542 1223444544 23 9999999999999999854 3344789999999 66555566666
Q ss_pred CCcEEEEEcCc-ccHHHHHh
Q 020088 296 FRHLLIAFGGL-AGLEESIE 314 (331)
Q Consensus 296 ~khlLIVFGgp-~GLe~~~~ 314 (331)
...+++|||+| .||.++..
T Consensus 207 ~~~~~~~fg~P~~gv~~~~~ 226 (272)
T COG2106 207 KSKVTLVFGGPEKGVLEILK 226 (272)
T ss_pred CCcceEEecCcccChheecc
Confidence 67899999999 99998865
No 4
>PRK03958 tRNA 2'-O-methylase; Reviewed
Probab=88.63 E-value=0.3 Score=44.60 Aligned_cols=70 Identities=23% Similarity=0.264 Sum_probs=44.2
Q ss_pred cccc--eEEEEeCChHHHhhcCCCCCC-CcEEEEeCCCCCCCCCCCCCCC----CCCcEEEEEcCcccHHHHHh-cCCCC
Q 020088 248 MYWG--YKVRYAPNISSVFKNCSYKGG-YDHLIGTSEHGDIVNSSDLTLP----TFRHLLIAFGGLAGLEESIE-EDDGL 319 (331)
Q Consensus 248 ~YWG--Y~VR~a~sL~~vf~e~p~~~g-YD~~IgTS~~G~~i~~~~~~l~----~~khlLIVFGgp~GLe~~~~-~D~~l 319 (331)
-||| |.|+...|+.+++.+.. .+| .=.++.|+.+-.+ ...++. ..+.+|||||||+=-.++++ +|=+|
T Consensus 52 ~~WGg~fnv~~~~s~~~~i~~~k-~~G~vvhLtmyga~~~~---~~~~ir~~~~~~~p~LIvvGg~gvp~evye~aDynl 127 (176)
T PRK03958 52 ERWGGPFEVEVTKSWKKEIREWK-DGGIVVHLTMYGENIQD---VEPEIREAHRKGEPLLIVVGAEKVPREVYELADWNV 127 (176)
T ss_pred HhcCCceEEEEcCCHHHHHHHHH-hCCcEEEEEEecCCccc---hHHHHHHhhccCCcEEEEEcCCCCCHHHHhhCCEEe
Confidence 5897 67999999999999876 333 3345566554333 222221 25679999998855555554 45555
Q ss_pred cc
Q 020088 320 KV 321 (331)
Q Consensus 320 ~~ 321 (331)
.+
T Consensus 128 gv 129 (176)
T PRK03958 128 AV 129 (176)
T ss_pred cc
Confidence 33
No 5
>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=72.45 E-value=2 Score=38.19 Aligned_cols=49 Identities=18% Similarity=0.339 Sum_probs=36.4
Q ss_pred cEEEEeCCCCCCCCCCCCC--C----CCCCcEEEEEcCcccHHHHHhc--CCCCccc
Q 020088 274 DHLIGTSEHGDIVNSSDLT--L----PTFRHLLIAFGGLAGLEESIEE--DDGLKVH 322 (331)
Q Consensus 274 D~~IgTS~~G~~i~~~~~~--l----~~~khlLIVFGgp~GLe~~~~~--D~~l~~~ 322 (331)
|++|.-.++|+.+++.++. + -..+++.+|+||+.|+.+.+.+ |..|...
T Consensus 66 ~~~i~LDe~Gk~~sS~~fA~~l~~~~~~g~~i~FvIGGa~G~~~~v~~~a~~~lSLS 122 (153)
T TIGR00246 66 AHVVTLDIPGKPWTTPQLADTLEKWKTDGRDVTLLIGGPEGLSPTCKAAAEQSWSLS 122 (153)
T ss_pred CeEEEEcCCCCcCCHHHHHHHHHHHhccCCeEEEEEcCCCcCCHHHHHhcCceEEee
Confidence 7899999999999875432 1 1235799999999999999854 5545443
No 6
>PRK00103 rRNA large subunit methyltransferase; Provisional
Probab=59.26 E-value=7.2 Score=34.76 Aligned_cols=49 Identities=22% Similarity=0.436 Sum_probs=35.9
Q ss_pred CcEEEEeCCCCCCCCCCCCC--C-----CCCCcEEEEEcCcccHHHHHhc--CCCCcc
Q 020088 273 YDHLIGTSEHGDIVNSSDLT--L-----PTFRHLLIAFGGLAGLEESIEE--DDGLKV 321 (331)
Q Consensus 273 YD~~IgTS~~G~~i~~~~~~--l-----~~~khlLIVFGgp~GLe~~~~~--D~~l~~ 321 (331)
-|++|.-.++|+.+++.++. + .....+.+|+||+.|+.+.+.+ |..|..
T Consensus 67 ~~~~i~LDe~Gk~~sS~~fA~~l~~~~~~g~~~i~F~IGGa~G~~~~v~~~a~~~lSL 124 (157)
T PRK00103 67 GARVIALDERGKQLSSEEFAQELERWRDDGRSDVAFVIGGADGLSPAVKKRADQSLSL 124 (157)
T ss_pred CCEEEEEcCCCCcCCHHHHHHHHHHHHhcCCccEEEEEcCccccCHHHHHhcCceEEe
Confidence 57889999999999875432 1 1224799999999999998854 444443
No 7
>PRK10433 putative RNA methyltransferase; Provisional
Probab=54.49 E-value=24 Score=33.36 Aligned_cols=56 Identities=14% Similarity=0.195 Sum_probs=36.0
Q ss_pred cceEEEEeCChHHHhhcCCCCCCCcEEEEeCCCCCCCCCCCCC----------CCC-CCcEEEEEcCc-ccHHH
Q 020088 250 WGYKVRYAPNISSVFKNCSYKGGYDHLIGTSEHGDIVNSSDLT----------LPT-FRHLLIAFGGL-AGLEE 311 (331)
Q Consensus 250 WGY~VR~a~sL~~vf~e~p~~~gYD~~IgTS~~G~~i~~~~~~----------l~~-~khlLIVFGgp-~GLe~ 311 (331)
|==.+++.++|.+.+.+| +++||||.+.......... ... ...+.||||.= .||-.
T Consensus 54 ~L~~a~v~~tL~eAl~d~------~~vigttar~~~~~~~~~~p~~~~~~l~~~~~~~~~~alvfG~E~~Gl~~ 121 (228)
T PRK10433 54 ILDNAKVFDTLAEALHDV------DFTVATTARSRAKFHYYATPAELVPLLEEKSSWMSHAALVFGREDSGLTN 121 (228)
T ss_pred HhcCceEECCHHHHHHhC------CeEEEEccCCCCCCCcccCHHHHHHHHHhhhcccCCEEEEECCCCCCCCH
Confidence 333577778999999865 7899999764422111000 111 25799999987 88754
No 8
>COG1576 Uncharacterized conserved protein [Function unknown]
Probab=52.80 E-value=6 Score=35.52 Aligned_cols=43 Identities=21% Similarity=0.349 Sum_probs=33.3
Q ss_pred CcEEEEeCCCCCCCCCCCCC--C----CCCCcEEEEEcCcccHHHHHhc
Q 020088 273 YDHLIGTSEHGDIVNSSDLT--L----PTFRHLLIAFGGLAGLEESIEE 315 (331)
Q Consensus 273 YD~~IgTS~~G~~i~~~~~~--l----~~~khlLIVFGgp~GLe~~~~~ 315 (331)
-+++|.-..+|+.+++..+. + -..+++.+++||+.||.+.+.+
T Consensus 67 ~~~vi~Ld~~Gk~~sSe~fA~~l~~~~~~G~~i~f~IGG~~Gl~~~~~~ 115 (155)
T COG1576 67 GSYVVLLDIRGKALSSEEFADFLERLRDDGRDISFLIGGADGLSEAVKA 115 (155)
T ss_pred CCeEEEEecCCCcCChHHHHHHHHHHHhcCCeEEEEEeCcccCCHHHHH
Confidence 35788889999999875432 1 1237899999999999998875
No 9
>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=46.40 E-value=18 Score=30.60 Aligned_cols=24 Identities=25% Similarity=0.458 Sum_probs=20.4
Q ss_pred HHHHHHHHHHhhhcccEEEEEcCC
Q 020088 83 RLAGQIARAVTIFRIDEVVVFDNK 106 (331)
Q Consensus 83 ~~agqIARAaaIF~VdEIVVydd~ 106 (331)
.=+|-|+|+|.-|+|+.|++-+..
T Consensus 13 ~NlG~i~Rta~afG~~~v~l~~~~ 36 (142)
T PF00588_consen 13 GNLGAIIRTAAAFGVDGVILVGPR 36 (142)
T ss_dssp HHHHHHHHHHHHTTESEEEEESSS
T ss_pred CcHHHHHHHHHHhCCchhheeccc
Confidence 458999999999999999997643
No 10
>KOG2422 consensus Uncharacterized conserved protein [Function unknown]
Probab=46.35 E-value=14 Score=39.75 Aligned_cols=15 Identities=40% Similarity=0.474 Sum_probs=7.2
Q ss_pred CCcccCCCCchhhhh
Q 020088 2 GNKKKRGGLEPELKE 16 (331)
Q Consensus 2 ~~~~~~~~~~~~~~~ 16 (331)
++-.|-||--+|--|
T Consensus 48 ~~l~kd~~~~nee~e 62 (665)
T KOG2422|consen 48 NNLRKDGGQMNEEDE 62 (665)
T ss_pred ccccccccccchhhH
Confidence 344455555454433
No 11
>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=43.54 E-value=8.7 Score=34.15 Aligned_cols=49 Identities=24% Similarity=0.422 Sum_probs=29.1
Q ss_pred CcEEEEeCCCCCCCCCCCCC-------CCCCCcEEEEEcCcccHHHHHh--cCCCCcc
Q 020088 273 YDHLIGTSEHGDIVNSSDLT-------LPTFRHLLIAFGGLAGLEESIE--EDDGLKV 321 (331)
Q Consensus 273 YD~~IgTS~~G~~i~~~~~~-------l~~~khlLIVFGgp~GLe~~~~--~D~~l~~ 321 (331)
-+++|.-.++|+.+++.++. ..+..++.+++||+.|+.+.+. +|..|..
T Consensus 67 ~~~~i~Ld~~Gk~~sS~~fA~~l~~~~~~g~~~i~F~IGG~~G~~~~~~~~a~~~lSL 124 (155)
T PF02590_consen 67 NDYVILLDERGKQLSSEEFAKKLERWMNQGKSDIVFIIGGADGLSEEVRKRADEKLSL 124 (155)
T ss_dssp TSEEEEE-TTSEE--HHHHHHHHHHHHHTTS-EEEEEE-BTTB--HHHHHH-SEEEES
T ss_pred CCEEEEEcCCCccCChHHHHHHHHHHHhcCCceEEEEEecCCCCCHHHHhhcCceEEE
Confidence 46788889999999875432 1235599999999999988765 4444443
No 12
>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=43.47 E-value=43 Score=31.44 Aligned_cols=56 Identities=21% Similarity=0.367 Sum_probs=35.7
Q ss_pred cceEEEEeCChHHHhhcCCCCCCCcEEEEeCCCCCCCCCCCCC--------CCCCCcEEEEEcCc-ccHHH
Q 020088 250 WGYKVRYAPNISSVFKNCSYKGGYDHLIGTSEHGDIVNSSDLT--------LPTFRHLLIAFGGL-AGLEE 311 (331)
Q Consensus 250 WGY~VR~a~sL~~vf~e~p~~~gYD~~IgTS~~G~~i~~~~~~--------l~~~khlLIVFGgp-~GLe~ 311 (331)
|--.+++.++|.+.+.+| +++||||.+...+...... ......+.||||.= .||-.
T Consensus 55 ~l~~~~v~~~l~eal~~~------~~vv~tt~~~~~~~~~~~~~~~~~~~~~~~~~~~aLvFG~E~~GL~~ 119 (233)
T TIGR00050 55 ILDNAKVVDDLDEALDDC------DLVVGTSARSRNLQRPLLTPRELAPKLVAYKGKIAIVFGREDSGLTN 119 (233)
T ss_pred hhccCEEECCHHHHHhcC------CEEEEECCCcCCCCCCcCCHHHHHHHHHhhcCCEEEEECCCCCCCCH
Confidence 333456677899999854 5799999765443321110 01134799999986 88854
No 13
>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=41.17 E-value=25 Score=32.98 Aligned_cols=24 Identities=33% Similarity=0.457 Sum_probs=21.2
Q ss_pred HHHHHHHHHhhhcccEEEEEcCCC
Q 020088 84 LAGQIARAVTIFRIDEVVVFDNKS 107 (331)
Q Consensus 84 ~agqIARAaaIF~VdEIVVydd~~ 107 (331)
=+|-|||+|.-|+++.+++-+...
T Consensus 16 NiGaiaR~~~~fG~~~l~lv~p~~ 39 (233)
T TIGR00050 16 NIGSIARAMKNMGLTELCLVNPKS 39 (233)
T ss_pred CHHHHHHHHHhCCCCEEEEeCCCc
Confidence 379999999999999999997653
No 14
>PRK15114 tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ; Provisional
Probab=39.20 E-value=56 Score=31.03 Aligned_cols=61 Identities=15% Similarity=0.233 Sum_probs=36.4
Q ss_pred EEEeCChHHHhhcCCCCCCCcEEEEeCCCCCCCCCCCC----------CCCCCCcEEEEEcCc-ccHHHHH--hcCCCCc
Q 020088 254 VRYAPNISSVFKNCSYKGGYDHLIGTSEHGDIVNSSDL----------TLPTFRHLLIAFGGL-AGLEESI--EEDDGLK 320 (331)
Q Consensus 254 VR~a~sL~~vf~e~p~~~gYD~~IgTS~~G~~i~~~~~----------~l~~~khlLIVFGgp-~GLe~~~--~~D~~l~ 320 (331)
+++.++|.+++..| +++||||-++..+..... .......+.||||.= .||.... ..|..+.
T Consensus 60 a~i~~~l~eal~~~------~~vvatt~r~~~~~~~~~~~~~~~~~~~~~~~~~~~alVFG~E~~GLs~e~l~~cd~~v~ 133 (245)
T PRK15114 60 ATIVDTLDEALAGC------SLVVGTSARSRTLPWPMLDPRECGLKSVAEAANAPVALVFGRERVGLTNDELQKCHYHVA 133 (245)
T ss_pred CeEecCHHHHHhcC------CEEEEEcCCccCCcccccCHHHHHHHHHhhccCCCEEEEECCCCCCCCHHHHHhCCeEEE
Confidence 34456899988865 569999977643221100 001234699999996 8886533 3444443
No 15
>KOG2201 consensus Pantothenate kinase PanK and related proteins [Coenzyme transport and metabolism]
Probab=36.24 E-value=38 Score=34.27 Aligned_cols=27 Identities=26% Similarity=0.141 Sum_probs=22.5
Q ss_pred CHHHHHHHHHHHHHHHh-hhcccEEEEE
Q 020088 77 SLELATRLAGQIARAVT-IFRIDEVVVF 103 (331)
Q Consensus 77 slelkT~~agqIARAaa-IF~VdEIVVy 103 (331)
.|...|+-+|||||-+| +++|++|+.=
T Consensus 284 lL~mIsnNIGqiAyl~A~~~ni~rV~Fg 311 (371)
T KOG2201|consen 284 LLRMISNNIGQIAYLCALNENIKRVYFG 311 (371)
T ss_pred HHHHHHhhHHHHHHHHHHHhCccEEEEe
Confidence 46678899999999876 7999999764
No 16
>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=35.53 E-value=39 Score=28.53 Aligned_cols=56 Identities=23% Similarity=0.480 Sum_probs=40.2
Q ss_pred EEEeCChHHHhhcCCCCCCCcEEEEeCCCCCCCCCCCCCCCCCCcEEEEEcCc-ccHHHHHhc
Q 020088 254 VRYAPNISSVFKNCSYKGGYDHLIGTSEHGDIVNSSDLTLPTFRHLLIAFGGL-AGLEESIEE 315 (331)
Q Consensus 254 VR~a~sL~~vf~e~p~~~gYD~~IgTS~~G~~i~~~~~~l~~~khlLIVFGgp-~GLe~~~~~ 315 (331)
++...++.+.+.++... ||. +++++..++++.+. ..+ +++++|||+= .||-+.+.+
T Consensus 58 ~~~~~~~~~~l~~~~~~-g~~-i~~~~~~~~~~~~~--~~~--~~~~lv~G~E~~Gls~~~~~ 114 (142)
T PF00588_consen 58 IRRVDDLEEALKDLKEN-GYT-IVATSPGATPLYEL--DFP--KKVALVFGNESRGLSEEVLE 114 (142)
T ss_dssp EEEESSHHHHHHHHHHT-TEE-EEEESTTSCEGGGS--HTT--SSEEEEEEBTTTBS-HHHHH
T ss_pred eeeeehhhhhccccccc-ccc-cceeeecccccccc--ccc--cceEEEEcCcCCCCCccccc
Confidence 67777899998877654 565 58888877766532 333 6899999998 998776543
No 17
>PF10646 Germane: Sporulation and spore germination; InterPro: IPR019606 The GerMN domain is a region of approximately 100 residues that is found, duplicated, in the Bacillus GerM protein and is implicated in both sporulation and spore germination. It is also found in lipoprotein LpqB. The domain is present in a number of different bacterial species both alone and in association with other domains such as Gmad1 and Gmad2. It is predicted to have a novel alpha-beta fold.
Probab=35.13 E-value=90 Score=25.08 Aligned_cols=44 Identities=18% Similarity=0.275 Sum_probs=35.6
Q ss_pred eEEEEecCccccCCCCHHHHHHHHHHHHHHHh-hhc-ccEEEEEcCC
Q 020088 62 TVSVAVPGSIIDNTQSLELATRLAGQIARAVT-IFR-IDEVVVFDNK 106 (331)
Q Consensus 62 tvSIAIP~SIlsnaqslelkT~~agqIARAaa-IF~-VdEIVVydd~ 106 (331)
++.|=+..++... .+......++.||..+++ -|. |++|.|+=|+
T Consensus 65 ~~~Vd~s~~~~~~-~~~~~~~~~~~~i~~Tl~~~~~~v~~V~i~vdG 110 (117)
T PF10646_consen 65 TLTVDFSSEFLNF-LGSSQEALLLAQIVNTLTEQFPGVKKVQILVDG 110 (117)
T ss_pred EEEEECCHHHhhc-CChHHHHHHHHHHHHHHHHhcCCccEEEEEECC
Confidence 5666666666655 666677899999999999 999 9999999775
No 18
>PRK15114 tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ; Provisional
Probab=34.25 E-value=44 Score=31.70 Aligned_cols=23 Identities=17% Similarity=0.312 Sum_probs=20.7
Q ss_pred HHHHHHHHHhhhcccEEEEEcCC
Q 020088 84 LAGQIARAVTIFRIDEVVVFDNK 106 (331)
Q Consensus 84 ~agqIARAaaIF~VdEIVVydd~ 106 (331)
=+|-|||+|.-|+++++++-...
T Consensus 17 NiGaiaRa~~~fG~~~l~lv~p~ 39 (245)
T PRK15114 17 NMGSVARAMKTMGLTNLWLVNPL 39 (245)
T ss_pred cHHHHHHHHHhcCCCEEEEeCCC
Confidence 47999999999999999998664
No 19
>COG0565 LasT rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=34.14 E-value=51 Score=31.70 Aligned_cols=57 Identities=19% Similarity=0.269 Sum_probs=35.4
Q ss_pred EEEeCChHHHhhcCCCCCCCcEEEEeCCCCCCCCCCCC-------CCC-C--CCcEEEEEcCc-ccH--HHHHhcC
Q 020088 254 VRYAPNISSVFKNCSYKGGYDHLIGTSEHGDIVNSSDL-------TLP-T--FRHLLIAFGGL-AGL--EESIEED 316 (331)
Q Consensus 254 VR~a~sL~~vf~e~p~~~gYD~~IgTS~~G~~i~~~~~-------~l~-~--~khlLIVFGgp-~GL--e~~~~~D 316 (331)
.++.++|.+.+.+| |++||||-+-........ .+. . ..++.||||.= .|| |++...|
T Consensus 60 A~i~~tL~eAl~d~------~~v~aTtar~r~~~~~~~~P~e~~~~l~~~~~~~~vAlvFGRE~~GLtNeEl~~c~ 129 (242)
T COG0565 60 AKIVDTLEEALADC------DLVVATTARSRDLLRPLRTPREAAPELLEKAKGGKVALVFGRERVGLTNEELALCD 129 (242)
T ss_pred CeeecCHHHHhcCC------CEEEEeccccCcccccccCHHHHHHHHHHHhcCCCeEEEECCccCCCCHHHHHhhh
Confidence 46667899999865 899999944332221100 011 1 36999999977 776 4444444
No 20
>TIGR02266 gmx_TIGR02266 Myxococcus xanthus paralogous domain TIGR02266. This domain is related to Type IV pilus assembly protein PilZ (Pfam model pfam07238). It is found in at least 12 copies in Myxococcus xanthus DK 1622.
Probab=32.54 E-value=52 Score=25.53 Aligned_cols=62 Identities=15% Similarity=0.139 Sum_probs=38.4
Q ss_pred ceEEEeCCCce-eeecccCCCCcEEEEEecCCCCC-CCCCCceecCCCCCCCCCcccceEEEEeC
Q 020088 196 GTLVDVGLNKH-VVVDQVLDPGVRVTVAMGTNRNL-DADSPRQVVPPSKPKESGMYWGYKVRYAP 258 (331)
Q Consensus 196 ~s~VdiGl~~~-v~i~~~l~~g~RVTV~l~~~~~~-~~~~~~~vVsp~~P~~~G~YWGY~VR~a~ 258 (331)
+...|+..... +..+..+++|++|.|.+.-.... .-...++||.-......+ +.||-|++.+
T Consensus 19 ~~~~diS~gG~~~~~~~~~~~g~~v~l~l~l~~~~~~i~~~g~Vv~~~~~~~~~-~~~~Gv~F~~ 82 (96)
T TIGR02266 19 DYSINLSKGGLFIRTRKPLAVGTRVELKLTLPGGERPVELKGVVAWVRPAADGG-PPGMGVRFED 82 (96)
T ss_pred HHhhhcCCceEEEecCCCcCCCCEEEEEEEcCCCCeEEEEEEEEEEeCCCCCCC-CCeeEEEecc
Confidence 44567777665 34567799999999998532111 112357888655333333 4488888874
No 21
>KOG2367 consensus Alpha-isopropylmalate synthase/homocitrate synthase [Amino acid transport and metabolism]
Probab=31.40 E-value=29 Score=36.65 Aligned_cols=20 Identities=10% Similarity=0.164 Sum_probs=17.2
Q ss_pred HHhhhcCCchhhhhhcCCCC
Q 020088 137 LLQYLETPQYLRKALFSMHS 156 (331)
Q Consensus 137 lLqYleTPpYLRK~LFP~~~ 156 (331)
|.-|+-|-+++||+.|.+..
T Consensus 150 Vh~~~aTSd~~rey~~~ksk 169 (560)
T KOG2367|consen 150 VHVFIATSDIHREYKLKKSK 169 (560)
T ss_pred EEEEecccHHHHHHHhcccH
Confidence 56688999999999999864
No 22
>TIGR00186 rRNA_methyl_3 rRNA methylase, putative, group 3. this is part of the trmH (spoU) family of rRNA methylases
Probab=27.83 E-value=48 Score=31.00 Aligned_cols=23 Identities=26% Similarity=0.413 Sum_probs=19.6
Q ss_pred HHHHHHHHHHhhhcccEEEEEcC
Q 020088 83 RLAGQIARAVTIFRIDEVVVFDN 105 (331)
Q Consensus 83 ~~agqIARAaaIF~VdEIVVydd 105 (331)
.=+|-|+|+|.-|+|+.||+=+.
T Consensus 102 ~NlGaI~Rta~afG~~~vil~~~ 124 (237)
T TIGR00186 102 HNLGAILRTAEAFGVDGVILPKR 124 (237)
T ss_pred ccHHHHHHHHHHcCCCEEEECCC
Confidence 35899999999999999977644
No 23
>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=27.54 E-value=1.8e+02 Score=24.63 Aligned_cols=54 Identities=17% Similarity=0.212 Sum_probs=33.5
Q ss_pred EEEEeCChHHHhhcCCCCCCCcEEEEeCCCCCCCCCCCCCCCCCCcEEEEEcCc-ccHHH
Q 020088 253 KVRYAPNISSVFKNCSYKGGYDHLIGTSEHGDIVNSSDLTLPTFRHLLIAFGGL-AGLEE 311 (331)
Q Consensus 253 ~VR~a~sL~~vf~e~p~~~gYD~~IgTS~~G~~i~~~~~~l~~~khlLIVFGgp-~GLe~ 311 (331)
++-+..+|.++.+=. +.|.++..|+.|...... ..+...++++|||+|- .|+..
T Consensus 21 ~livlpdl~DAiEvl----~p~~V~~i~~~~~~~~~~-~~~~~~~rvllVf~G~d~gfsk 75 (106)
T PF09895_consen 21 SLIVLPDLKDAIEVL----KPDVVYLISRSGEEEEKL-EFLKIEGRVLLVFSGSDPGFSK 75 (106)
T ss_pred cEEEeCCHHHHHHhc----CCcEEEEEcCcccccccc-cccCcCCcEEEEEeCCCCCCCh
Confidence 455555666655422 368888888777655331 2233466899999998 66543
No 24
>TIGR00186 rRNA_methyl_3 rRNA methylase, putative, group 3. this is part of the trmH (spoU) family of rRNA methylases
Probab=26.72 E-value=3.1e+02 Score=25.58 Aligned_cols=65 Identities=17% Similarity=0.240 Sum_probs=39.8
Q ss_pred EEEEeCChHHHhhcCCCCCCCcEEEEeCCCCCCCCCCCCCCCCCCcEEEEEcCc-ccHHHHHh--cCCCCccc
Q 020088 253 KVRYAPNISSVFKNCSYKGGYDHLIGTSEHGDIVNSSDLTLPTFRHLLIAFGGL-AGLEESIE--EDDGLKVH 322 (331)
Q Consensus 253 ~VR~a~sL~~vf~e~p~~~gYD~~IgTS~~G~~i~~~~~~l~~~khlLIVFGgp-~GLe~~~~--~D~~l~~~ 322 (331)
.++...++.+.+..+. ..|| .+++|+..|.... .+....+.++||||+= .||-+.+. .|..+...
T Consensus 145 ~~~~~~~~~~~l~~l~-~~g~-~i~~~~~~~~~~~---~~~~~~~~~~lv~GnE~~Gls~~~l~~~d~~v~IP 212 (237)
T TIGR00186 145 PLARVTNLSRTITKLK-ESGF-WTVGTDLDAQDTL---YQVKLTKPLALVVGNEGEGVSRLIKENCDFLIKIP 212 (237)
T ss_pred EEEEeCCHHHHHHHHH-HCCC-EEEEEecCCCccc---cccccCCCEEEEECCCCCCcCHHHHHhCCEEEEEC
Confidence 3555567888877553 2355 4788887766431 1122245799999999 99877654 44444433
No 25
>PRK11181 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional
Probab=25.93 E-value=55 Score=30.87 Aligned_cols=22 Identities=18% Similarity=0.214 Sum_probs=19.2
Q ss_pred HHHHHHHHHhhhcccEEEEEcC
Q 020088 84 LAGQIARAVTIFRIDEVVVFDN 105 (331)
Q Consensus 84 ~agqIARAaaIF~VdEIVVydd 105 (331)
=+|-|+|+|.-|+|+.||+-.+
T Consensus 108 NlGai~Rta~a~G~~~vi~~~~ 129 (244)
T PRK11181 108 NLGACLRSADAAGVHAVIVPKD 129 (244)
T ss_pred hHHHHHHHHHHcCCCEEEECCC
Confidence 4899999999999999988544
No 26
>PF10246 MRP-S35: Mitochondrial ribosomal protein MRP-S35; InterPro: IPR019375 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This is a family of short mitochondrial ribosomal proteins, less than 200 amino acids long. MRP-S35 was proposed as a more appropriate name to this group of proteins [].
Probab=25.51 E-value=2.5e+02 Score=23.82 Aligned_cols=46 Identities=17% Similarity=0.152 Sum_probs=33.7
Q ss_pred CccCceeEEEeeccCCCCCceEEEeCCCceeeec------ccCCCCcEEEEEecC
Q 020088 177 EWAPFREGVTLKENAPNSVGTLVDVGLNKHVVVD------QVLDPGVRVTVAMGT 225 (331)
Q Consensus 177 ~~~~yREGvvv~~~~~~g~~s~VdiGl~~~v~i~------~~l~~g~RVTV~l~~ 225 (331)
..+..=.|-+... .+.--|||+|..=+..+. +.+..|+||.|+++.
T Consensus 22 ~~gk~V~G~I~hv---v~ddLYIDfG~KFhcVc~rp~~~~~~y~~G~rV~lrLkd 73 (104)
T PF10246_consen 22 PEGKIVIGKIFHV---VDDDLYIDFGGKFHCVCKRPAVNGEKYVRGSRVRLRLKD 73 (104)
T ss_pred ccCCEEEEEEEEE---ecCceEEEeCCceeEEEecccccccccccCCEEEEEECC
Confidence 4555556666655 356789999998776664 348899999999984
No 27
>PLN02726 dolichyl-phosphate beta-D-mannosyltransferase
Probab=25.32 E-value=1.8e+02 Score=26.30 Aligned_cols=45 Identities=20% Similarity=0.229 Sum_probs=27.7
Q ss_pred CcceEEEEecCccccCCCCHHHHHHHHHHHHHHHhhhcccEEEEEcCCCC
Q 020088 59 EVPTVSVAVPGSIIDNTQSLELATRLAGQIARAVTIFRIDEVVVFDNKSS 108 (331)
Q Consensus 59 r~~tvSIAIP~SIlsnaqslelkT~~agqIARAaaIF~VdEIVVydd~~~ 108 (331)
..+.|||.||. .+++.+++ ..+..|.+.+.-+.=-||||.||.+.
T Consensus 7 ~~~~vsVvIp~--yne~~~l~---~~l~~l~~~~~~~~~~eiivvDdgS~ 51 (243)
T PLN02726 7 GAMKYSIIVPT--YNERLNIA---LIVYLIFKALQDVKDFEIIVVDDGSP 51 (243)
T ss_pred CCceEEEEEcc--CCchhhHH---HHHHHHHHHhccCCCeEEEEEeCCCC
Confidence 45679999996 35555543 23444555443332349999998754
No 28
>PRK10433 putative RNA methyltransferase; Provisional
Probab=25.22 E-value=67 Score=30.37 Aligned_cols=23 Identities=26% Similarity=0.423 Sum_probs=20.7
Q ss_pred HHHHHHHHHhhhcccEEEEEcCC
Q 020088 84 LAGQIARAVTIFRIDEVVVFDNK 106 (331)
Q Consensus 84 ~agqIARAaaIF~VdEIVVydd~ 106 (331)
=+|-||||+.-|+++++++-+..
T Consensus 15 NiGaiaRam~nfG~~~L~lV~p~ 37 (228)
T PRK10433 15 NVGAAARAMKTMGFSELRIVDSQ 37 (228)
T ss_pred cHHHHHHHHHHCCCCEEEEeCCC
Confidence 48999999999999999999654
No 29
>PRK12703 tRNA 2'-O-methylase; Reviewed
Probab=24.72 E-value=78 Score=31.82 Aligned_cols=53 Identities=13% Similarity=0.231 Sum_probs=41.1
Q ss_pred ccc--eEEEEeCChHHHhhcCCCCCCCcEEEEeCCCCCCCCCCCCCCC-CCCcEEEEEcCc
Q 020088 249 YWG--YKVRYAPNISSVFKNCSYKGGYDHLIGTSEHGDIVNSSDLTLP-TFRHLLIAFGGL 306 (331)
Q Consensus 249 YWG--Y~VR~a~sL~~vf~e~p~~~gYD~~IgTS~~G~~i~~~~~~l~-~~khlLIVFGgp 306 (331)
-|| |.|+...+....+.++ +| .+|--+=+|.++++...+++ ..+.+|||.|+-
T Consensus 52 ~~gg~f~~~~~~~~~~~~~~~---~g--~vvhltmyg~~~~~~~~~i~~~~~~~~~vvg~~ 107 (339)
T PRK12703 52 NFGGSFEIKTGIEWKSEFKKF---HG--IRVHLTMYGRPIEDVIDEIRESGKDVMVLVGSE 107 (339)
T ss_pred hcCCCeEEEeccCHHHHHHhc---CC--EEEEEecCCCchHHHHHHHhccCCCEEEEECCC
Confidence 455 6799998999999987 44 56666689999987666666 457899999985
No 30
>TIGR00185 rRNA_methyl_2 rRNA methylase, putative, group 2. this is part of the trmH (spoU) family of rRNA methylases
Probab=24.67 E-value=60 Score=28.32 Aligned_cols=28 Identities=14% Similarity=0.159 Sum_probs=20.2
Q ss_pred cccCCCCHHHHHHHHHHHHHHHhhhcccEEEE
Q 020088 71 IIDNTQSLELATRLAGQIARAVTIFRIDEVVV 102 (331)
Q Consensus 71 IlsnaqslelkT~~agqIARAaaIF~VdEIVV 102 (331)
+|++.|++ .=+|-|+|+|..|+|+-|++
T Consensus 5 vL~~v~dP----~NlG~iiRta~afGv~~vi~ 32 (153)
T TIGR00185 5 VLYEPEIP----PNTGNIARTCAATGTRLHLI 32 (153)
T ss_pred EEcCCCCC----ChHHHHHHHHHHhCCEEEEE
Confidence 34555553 35899999999999965544
No 31
>PRK10864 putative methyltransferase; Provisional
Probab=23.90 E-value=62 Score=32.57 Aligned_cols=21 Identities=38% Similarity=0.477 Sum_probs=18.8
Q ss_pred HHHHHHHHHhhhcccEEEEEc
Q 020088 84 LAGQIARAVTIFRIDEVVVFD 104 (331)
Q Consensus 84 ~agqIARAaaIF~VdEIVVyd 104 (331)
=+|-|+|+|..|+|+.||+-+
T Consensus 211 NlGaIiRTA~afGv~~Vil~~ 231 (346)
T PRK10864 211 NLGGIMRSCAHFGVKGVVVQD 231 (346)
T ss_pred cHHHHHHHHHHhCCCEEEECC
Confidence 479999999999999998853
No 32
>PRK09756 PTS system N-acetylgalactosamine-specific transporter subunit IIB; Provisional
Probab=23.85 E-value=99 Score=27.50 Aligned_cols=49 Identities=14% Similarity=0.215 Sum_probs=33.9
Q ss_pred HHHHHH-HHHhhhcccEEEEEcCCCCCCccccccccccCCCCCCCcchHHHHHHHHhhhcCCchhhhhhcC
Q 020088 84 LAGQIA-RAVTIFRIDEVVVFDNKSSSDNYSRSSAANRSNRSDENESGAAFLVRLLQYLETPQYLRKALFS 153 (331)
Q Consensus 84 ~agqIA-RAaaIF~VdEIVVydd~~~~~~~~~~~~~~~~~~~~~~~~~~~fL~~lLqYleTPpYLRK~LFP 153 (331)
+=||++ +++.-++++.|||-+|.-.. ..|...+|.-..+|+=..=.++.
T Consensus 16 IHGQV~~~W~~~~~~~~IiVvdD~vA~---------------------D~~~k~~lkma~~P~gvk~~i~s 65 (158)
T PRK09756 16 VHGQVGVTWTSTIGANLLVVVDDVVAN---------------------DDIQQKLMGITAETYGFGIRFFT 65 (158)
T ss_pred hhHHHHHhhhcccCCCEEEEEcchhcC---------------------CHHHHHHHHhcCCCCCCEEEEEE
Confidence 348977 99999999999999987431 23677777766556654433443
No 33
>COG0565 LasT rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=22.90 E-value=79 Score=30.41 Aligned_cols=25 Identities=24% Similarity=0.462 Sum_probs=22.2
Q ss_pred HHHHHHHHHhhhcccEEEEEcCCCC
Q 020088 84 LAGQIARAVTIFRIDEVVVFDNKSS 108 (331)
Q Consensus 84 ~agqIARAaaIF~VdEIVVydd~~~ 108 (331)
=+|-+|||..-|+.+|+++.+....
T Consensus 17 NIG~vARaMKNfGl~eL~LV~Pr~~ 41 (242)
T COG0565 17 NIGSVARAMKNFGLSELRLVNPRAG 41 (242)
T ss_pred cHHHHHHHHHhCCcceEEEECCCCC
Confidence 4899999999999999999987653
No 34
>PRK00026 trmD tRNA (guanine-N(1)-)-methyltransferase; Reviewed
Probab=21.66 E-value=69 Score=30.89 Aligned_cols=51 Identities=22% Similarity=0.351 Sum_probs=39.9
Q ss_pred CcEEEEeCCCCCCCCCCCC-CCCCCCcEEEEEcCcccHHHHHh---cCCCCcccc
Q 020088 273 YDHLIGTSEHGDIVNSSDL-TLPTFRHLLIAFGGLAGLEESIE---EDDGLKVHY 323 (331)
Q Consensus 273 YD~~IgTS~~G~~i~~~~~-~l~~~khlLIVFGgp~GLe~~~~---~D~~l~~~~ 323 (331)
...+|..|-.|..+++... ++...+|++++-|=-.|+.+-+- .|+.+.+.|
T Consensus 81 ~~~vi~lsP~G~~f~Q~~a~~ls~~~~lillCGrYEGiDeRv~~~~vdeeiSiGD 135 (244)
T PRK00026 81 KAKVILLSPQGKPFTQADARELAKEEHLILLCGRYEGIDERVIEHYVDEEISIGD 135 (244)
T ss_pred CCeEEEECCCCCcCCHHHHHHHhCCCCEEEEeccccChHHHHHhhhCcEEEeecc
Confidence 4579999999999987543 35567899999999999998874 377776655
No 35
>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=21.35 E-value=1e+02 Score=28.53 Aligned_cols=40 Identities=13% Similarity=0.143 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHhhhcccEEEEEcCCCCCCccccccccccCCCCCCCcchHHHHHHHHhhhc
Q 020088 82 TRLAGQIARAVTIFRIDEVVVFDNKSSSDNYSRSSAANRSNRSDENESGAAFLVRLLQYLE 142 (331)
Q Consensus 82 T~~agqIARAaaIF~VdEIVVydd~~~~~~~~~~~~~~~~~~~~~~~~~~~fL~~lLqYle 142 (331)
.+=+..|||+|..|+|..-+|-..-. +-..+..+||.|-.
T Consensus 27 NlDlHDIAR~~rTYgv~~yyiVtPl~---------------------~Q~~l~~ril~hW~ 66 (185)
T PF09936_consen 27 NLDLHDIARSARTYGVKGYYIVTPLE---------------------AQRELAERILGHWQ 66 (185)
T ss_dssp HHHHHHHHHHHHHTT-SEEEEE---H---------------------HHHHHHHHHHHHHH
T ss_pred cccHHhhhhhhhccCCcCEEEecchH---------------------HHHHHHHHHHHhcc
Confidence 35579999999999999999985431 12567888888754
No 36
>PRK10714 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional
Probab=20.26 E-value=2.5e+02 Score=27.33 Aligned_cols=46 Identities=26% Similarity=0.371 Sum_probs=26.0
Q ss_pred CcceEEEEecCccccCCCCHHHHHHHHHHHHHHHh-hhcccEEEEEcCCCCC
Q 020088 59 EVPTVSVAVPGSIIDNTQSLELATRLAGQIARAVT-IFRIDEVVVFDNKSSS 109 (331)
Q Consensus 59 r~~tvSIAIP~SIlsnaqslelkT~~agqIARAaa-IF~VdEIVVydd~~~~ 109 (331)
+...+||.||. .+++.+++ .++..+..++. ++.--||||.||.+.+
T Consensus 4 ~~~~vSVVIP~--yNE~~~i~---~~l~~l~~~~~~~~~~~EIIvVDDgS~D 50 (325)
T PRK10714 4 PIKKVSVVIPV--YNEQESLP---ELIRRTTAACESLGKEYEILLIDDGSSD 50 (325)
T ss_pred CCCeEEEEEcc--cCchhhHH---HHHHHHHHHHHhCCCCEEEEEEeCCCCC
Confidence 44569999993 44445443 22233333222 2334599999997643
Done!