Query 020486
Match_columns 325
No_of_seqs 122 out of 273
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 02:46:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020486.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020486hhsearch_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 1.9E-81 4.1E-86 597.7 14.0 232 62-304 1-236 (291)
2 KOG3925 Uncharacterized conser 100.0 1.5E-79 3.3E-84 590.9 11.5 256 57-317 64-326 (371)
3 COG2106 Uncharacterized conser 100.0 1.9E-56 4.1E-61 419.9 19.5 202 59-294 2-205 (272)
4 KOG4342 Alpha-mannosidase [Car 75.9 1.1 2.4E-05 48.4 0.8 33 290-322 72-107 (1078)
5 PF00588 SpoU_methylase: SpoU 48.5 16 0.00034 30.8 2.6 31 72-106 6-36 (142)
6 KOG2422 Uncharacterized conser 46.5 14 0.00029 39.9 2.3 48 2-49 48-98 (665)
7 TIGR02266 gmx_TIGR02266 Myxoco 42.9 28 0.00061 27.0 3.1 78 180-258 3-82 (96)
8 TIGR00050 rRNA_methyl_1 RNA me 41.2 21 0.00047 33.4 2.5 24 84-107 16-39 (233)
9 PF10646 Germane: Sporulation 39.3 75 0.0016 25.5 5.2 45 62-107 65-111 (117)
10 KOG2201 Pantothenate kinase Pa 35.0 40 0.00087 34.2 3.4 27 77-103 284-311 (371)
11 KOG2367 Alpha-isopropylmalate 34.6 22 0.00048 37.6 1.6 20 137-156 150-169 (560)
12 PRK15114 tRNA (cytidine/uridin 34.3 32 0.00069 32.6 2.6 23 84-106 17-39 (245)
13 TIGR00186 rRNA_methyl_3 rRNA m 29.8 42 0.00092 31.3 2.6 31 72-106 95-125 (237)
14 PF10246 MRP-S35: Mitochondria 28.1 2.2E+02 0.0048 24.2 6.2 47 176-225 21-73 (104)
15 PRK11181 23S rRNA (guanosine-2 27.7 48 0.001 31.2 2.6 31 72-106 100-130 (244)
16 PLN02726 dolichyl-phosphate be 25.5 1.6E+02 0.0035 26.4 5.5 45 59-108 7-51 (243)
17 TIGR00185 rRNA_methyl_2 rRNA m 25.4 57 0.0012 28.4 2.4 28 71-102 5-32 (153)
18 PRK10864 putative methyltransf 25.1 56 0.0012 32.8 2.6 21 84-104 211-231 (346)
19 PRK10433 putative RNA methyltr 25.0 58 0.0013 30.7 2.5 23 84-106 15-37 (228)
20 PF00575 S1: S1 RNA binding do 22.9 3.1E+02 0.0067 20.0 5.8 46 177-225 3-61 (74)
21 cd04455 S1_NusA S1_NusA: N-uti 22.0 2.8E+02 0.006 20.4 5.3 43 179-225 4-53 (67)
22 TIGR00008 infA translation ini 20.2 2.3E+02 0.005 22.1 4.6 50 182-238 7-66 (68)
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=1.9e-81 Score=597.71 Aligned_cols=232 Identities=51% Similarity=0.921 Sum_probs=155.6
Q ss_pred eEEEEecCccccCCCCHHHHHHHHHHHHHHHhhhcccEEEEEeCCCCCCccccccccccCCCCCCCcchHHHHHHHHhHh
Q 020486 62 TVSVAVPGSIIDNTQSLELATRLAGQIARAVTIFRIDEVVVFDNKSSSDNYSRSSAANRSNRSDENESGAAFLVRLLQYL 141 (325)
Q Consensus 62 tvSIAIP~SIlsnaqslelkT~~aGqIARAaaIF~VDEIVVydD~~~~~~~~~~~~~~~~~~~~~~~~~~~fLa~iLqYl 141 (325)
|||||||+|||+||||+|+|||+|||||||||||||||||||||+....+... ..........+++.||++|||||
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 020486 142 ETPQYLRKALFSMHSSLRFVGMLPPLDAPHHL-RKHEWAPFREGVTLKENAPNSVGTLVDVGLNKHVVVDQ-VLDPGVRV 219 (325)
Q Consensus 142 ETPpYLRK~LFP~h~dLKyaGlLPPLd~PHH~-r~~e~~~yREGvVv~~~~~~g~gs~VdvGL~k~v~i~~-~l~~g~RV 219 (325)
||||||||+|||+|++|||||+||||++|||+ +.++|++||||||+++..+.+++++|||||.+++.++. .+++|+||
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 89999999999999998766677999999999999999 99999999
Q ss_pred EEEecCCCCCCCCCCceecCCCCCCCCCcccceEEEEcCChHHHhhcCCcCCCCceEEEeCCCCCCCCCCCCCCC--Ccc
Q 020486 220 TVAMGTNRNLDADSPRQVVPPSKPKESGMYWGYKVRYAPNISSVFKNCSYKGGYDHLIGTSEHGDIVNSSDLTLP--TFR 297 (325)
Q Consensus 220 TV~l~~~~~~~~~~~g~vVsp~~P~~~G~YWGY~VR~a~sLs~vf~~~p~~~gYD~~IgTSerG~~i~~~~~~lp--~fk 297 (325)
||+|+. ..|++|+|++|.+.|+||||+||+|+||++||++|||++|||++||||++|.++++....++ +|+
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 999984 36899999999439999999999999999999999999999999999999999988766665 999
Q ss_pred hhhhhhh
Q 020486 298 SMLGYAL 304 (325)
Q Consensus 298 H~Li~~~ 304 (325)
|+||-.|
T Consensus 230 ~~LiVFG 236 (291)
T PF02598_consen 230 HLLIVFG 236 (291)
T ss_dssp EEEEE--
T ss_pred cEEEEEe
Confidence 9999555
No 2
>KOG3925 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=1.5e-79 Score=590.94 Aligned_cols=256 Identities=43% Similarity=0.750 Sum_probs=232.5
Q ss_pred CCCcceEEEEecCccccCCCCHHHHHHHHHHHHHHHhhhcccEEEEEeCCCCCCccccccccccCCCCCCCcchHHHHHH
Q 020486 57 PIEVPTVSVAVPGSIIDNTQSLELATRLAGQIARAVTIFRIDEVVVFDNKSSSDNYSRSSAANRSNRSDENESGAAFLVR 136 (325)
Q Consensus 57 ~~r~~tvSIAIP~SIlsnaqslelkT~~aGqIARAaaIF~VDEIVVydD~~~~~~~~~~~~~~~~~~~~~~~~~~~fLa~ 136 (325)
.++.+|+|||||+|||+||||+||+|++||||||||++|+|||||||||.....+.++. ..+.....++|.||++
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 1123456788999999
Q ss_pred HHhHhcCCchhhhhhcCCCCCccccCcCCCCCCCCCCCCCCcccceEEEEeeccCCCCCceEEEeCCCceeeec-ccCC-
Q 020486 137 LLQYLETPQYLRKALFSMHSSLRFVGMLPPLDAPHHLRKHEWAPFREGVTLKENAPNSVGTLVDVGLNKHVVVD-QVLD- 214 (325)
Q Consensus 137 iLqYlETPpYLRK~LFP~h~dLKyaGlLPPLd~PHH~r~~e~~~yREGvVv~~~~~~g~gs~VdvGL~k~v~i~-~~l~- 214 (325)
|||||||||||||.|||+|++|||||+|||||+|||++.+++++||||||+.+.++.|+|++|||||.+.+.|+ ..+.
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-CCCCcccceEEEEcCChHHHhhcCCcCCCCceEEEeCCCCCCCCCCCCCC
Q 020486 215 PGVRVTVAMGTNRNLDADSPRQVVPPSKP-KESGMYWGYKVRYAPNISSVFKNCSYKGGYDHLIGTSEHGDIVNSSDLTL 293 (325)
Q Consensus 215 ~g~RVTV~l~~~~~~~~~~~g~vVsp~~P-~~~G~YWGY~VR~a~sLs~vf~~~p~~~gYD~~IgTSerG~~i~~~~~~l 293 (325)
||+||||+|+...+.+.++.|+||||++| +++|+||||+||+|++|++||++|||++|||++||||+||..|.+.++..
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 99999999996545566789999999999 99999999999999999999999999999999999999999999988889
Q ss_pred CCcchhhh----hhheeeeeeecceeee
Q 020486 294 PTFRSMLG----YALYYWVIASVDCFWW 317 (325)
Q Consensus 294 p~fkH~Li----~~~~~~~~~~~~~~~~ 317 (325)
|.|.|+|+ .+++.|-+..++..=|
T Consensus 299 ~t~~~iLlvfg~l~~l~~a~e~~~~~~~ 326 (371)
T KOG3925|consen 299 ETPPHILLVFGGLAGLVRAFELDEQTTW 326 (371)
T ss_pred CCCCcEEEEeechhhHHHHHHhccchhc
Confidence 99999988 5667788877765444
No 3
>COG2106 Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=1.9e-56 Score=419.91 Aligned_cols=202 Identities=36% Similarity=0.659 Sum_probs=176.4
Q ss_pred CcceEEEEecCccccCCCCHHHHHHHHHHHHHHHhhhcccEEEEEeCCCCCCccccccccccCCCCCCCcchHHHHHHHH
Q 020486 59 EVPTVSVAVPGSIIDNTQSLELATRLAGQIARAVTIFRIDEVVVFDNKSSSDNYSRSSAANRSNRSDENESGAAFLVRLL 138 (325)
Q Consensus 59 r~~tvSIAIP~SIlsnaqslelkT~~aGqIARAaaIF~VDEIVVydD~~~~~~~~~~~~~~~~~~~~~~~~~~~fLa~iL 138 (325)
|..++|||||+|++++|.|++++||++||||||||||+|||||||+|+....+ ++.||+.||
T Consensus 2 ~~~~~Sv~iP~Sll~~~~dl~~kT~Kvg~IARaaaiF~V~eIii~~D~~~~~~------------------~~~~i~~lL 63 (272)
T COG2106 2 RRVMLSVAIPTSLLSEENDLKLKTYKVGQIARAAAIFRVDEIIIYEDGDDVRR------------------DAKFITTLL 63 (272)
T ss_pred ceeEEEEEcchHHhhccCCHHHhHHHHHHHHHHHHhhcccEEEEEeCCCCccc------------------hhHHHHHHH
Confidence 67899999999999999999999999999999999999999999999854322 489999999
Q ss_pred hHhcCCchhhhhhcCCCCCccccCcCCCCCCCCCCCC--CCcccceEEEEeeccCCCCCceEEEeCCCceeeecccCCCC
Q 020486 139 QYLETPQYLRKALFSMHSSLRFVGMLPPLDAPHHLRK--HEWAPFREGVTLKENAPNSVGTLVDVGLNKHVVVDQVLDPG 216 (325)
Q Consensus 139 qYlETPpYLRK~LFP~h~dLKyaGlLPPLd~PHH~r~--~e~~~yREGvVv~~~~~~g~gs~VdvGL~k~v~i~~~l~~g 216 (325)
|||+|||||||++||+.++|||||+||||++|||+.. +..|+||||+|+.+. +++.+||||+++.+.+...+++|
T Consensus 64 ~Y~~TPpyLRK~vFp~~~~LkyAg~lPPL~ip~h~~~~~~~~Ge~ReG~v~~~~---~~~~~v~iG~~~~~~l~~~~~~~ 140 (272)
T COG2106 64 EYFETPPYLRKRVFPIKRELKYAGLLPPLRIPSHTVSTSPKEGEYREGLVIRRG---KKGNLVDIGKDKLAKLSSPAPPG 140 (272)
T ss_pred HHhcCCHHHHhhhcCCCcccccccccCCCCCCCccCcCCccceeecceEEEEec---CCceEEEecCCcceeccCCCCCC
Confidence 9999999999999999999999999999999999875 789999999999985 67799999999999999999999
Q ss_pred cEEEEEecCCCCCCCCCCceecCCCCCCCCCcccceEEEEcCChHHHhhcCCcCCCCceEEEeCCCCCCCCCCCCCCC
Q 020486 217 VRVTVAMGTNRNLDADSPRQVVPPSKPKESGMYWGYKVRYAPNISSVFKNCSYKGGYDHLIGTSEHGDIVNSSDLTLP 294 (325)
Q Consensus 217 ~RVTV~l~~~~~~~~~~~g~vVsp~~P~~~G~YWGY~VR~a~sLs~vf~~~p~~~gYD~~IgTSerG~~i~~~~~~lp 294 (325)
+||||++.+.. ....|.|.+|.+ ||||+||.+++|.++++.. +.++.+|+||++| +++..+...|
T Consensus 141 ~RvTvri~~~~------~p~~~~~~~~~~---YwGY~V~~~~~L~e~~~~~---~~~~vvi~tsr~g-~~~~~e~~~~ 205 (272)
T COG2106 141 ARVTVRIISRS------SPLRVEPAEPPD---YWGYKVRIAKSLNELLKGF---DLDVVVIATSRYG-PLDVRETEAP 205 (272)
T ss_pred ceEEEEEEecc------CceeeecCCCCC---cCcEEEEehhhHHHHhhcc---CCCceEEEecccC-cceeeecccc
Confidence 99999998542 123355555532 9999999999999999865 3445789999999 6665555554
No 4
>KOG4342 consensus Alpha-mannosidase [Carbohydrate transport and metabolism]
Probab=75.89 E-value=1.1 Score=48.41 Aligned_cols=33 Identities=27% Similarity=0.660 Sum_probs=20.0
Q ss_pred CCCCCCcchhhhhhheeeeeeeccee---eeeeecc
Q 020486 290 DLTLPTFRSMLGYALYYWVIASVDCF---WWTCWFG 322 (325)
Q Consensus 290 ~~~lp~fkH~Li~~~~~~~~~~~~~~---~~~~~~~ 322 (325)
....|+|+.++.---.--+..-.|+| ||||||-
T Consensus 72 p~~rPs~~e~v~rdk~~e~a~~~d~FGPsW~T~WF~ 107 (1078)
T KOG4342|consen 72 PERRPSYQEAVQRDKRPEQAGINDSFGPSWWTCWFR 107 (1078)
T ss_pred cccCccHHHHhccccchhhcccCCCCCCcceeEEEE
Confidence 34678888776622222222335777 9999995
No 5
>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=48.53 E-value=16 Score=30.85 Aligned_cols=31 Identities=29% Similarity=0.486 Sum_probs=23.8
Q ss_pred ccCCCCHHHHHHHHHHHHHHHhhhcccEEEEEeCC
Q 020486 72 IDNTQSLELATRLAGQIARAVTIFRIDEVVVFDNK 106 (325)
Q Consensus 72 lsnaqslelkT~~aGqIARAaaIF~VDEIVVydD~ 106 (325)
|++.+++ .=+|-|+|+|.-|+++.|++-+..
T Consensus 6 l~~~~~p----~NlG~i~Rta~afG~~~v~l~~~~ 36 (142)
T PF00588_consen 6 LDNVQDP----GNLGAIIRTAAAFGVDGVILVGPR 36 (142)
T ss_dssp EES-SSH----HHHHHHHHHHHHTTESEEEEESSS
T ss_pred EeCCCCc----CcHHHHHHHHHHhCCchhheeccc
Confidence 3444553 468999999999999999998643
No 6
>KOG2422 consensus Uncharacterized conserved protein [Function unknown]
Probab=46.50 E-value=14 Score=39.87 Aligned_cols=48 Identities=40% Similarity=0.385 Sum_probs=22.8
Q ss_pred CCcccCCCCchhhhh--hhcCCCCcccccccc-ccCCCcccchHHHHhhhh
Q 020486 2 GNKKKRGGLEPELKE--AATGENHESQNELSL-ANGDSSSCDNKKKKKRKR 49 (325)
Q Consensus 2 ~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~ 49 (325)
++-.|-||--+|--| ++.+|.|+.-+.+.- +...++..|||||||+++
T Consensus 48 ~~l~kd~~~~nee~e~~~~~ee~de~~~~~es~~~~~~~~sk~k~KKK~kr 98 (665)
T KOG2422|consen 48 NNLRKDGGQMNEEDEEAAIAEERDEPSVGQESRITLASKSSKNKKKKKKKR 98 (665)
T ss_pred ccccccccccchhhHHhhhhhcccCcccCCcccccccchhhccccchhhhh
Confidence 444455655444333 333444444444443 555555555554444443
No 7
>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=42.88 E-value=28 Score=27.00 Aligned_cols=78 Identities=15% Similarity=0.153 Sum_probs=45.9
Q ss_pred cceEEEEeeccCCCCCceEEEeCCCce-eeecccCCCCcEEEEEecCCCCC-CCCCCceecCCCCCCCCCcccceEEEEc
Q 020486 180 PFREGVTLKENAPNSVGTLVDVGLNKH-VVVDQVLDPGVRVTVAMGTNRNL-DADSPRQVVPPSKPKESGMYWGYKVRYA 257 (325)
Q Consensus 180 ~yREGvVv~~~~~~g~gs~VdvGL~k~-v~i~~~l~~g~RVTV~l~~~~~~-~~~~~g~vVsp~~P~~~G~YWGY~VR~a 257 (325)
+++-.+.+......-.+...|+..+-. +..+..+++|++|.|++.-.... .-...|+||.-......+ ..||-|++.
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~diS~gG~~~~~~~~~~~g~~v~l~l~l~~~~~~i~~~g~Vv~~~~~~~~~-~~~~Gv~F~ 81 (96)
T TIGR02266 3 PARLKVDFRTDSEFLRDYSINLSKGGLFIRTRKPLAVGTRVELKLTLPGGERPVELKGVVAWVRPAADGG-PPGMGVRFE 81 (96)
T ss_pred cEEEEEEECChhhHHHHHhhhcCCceEEEecCCCcCCCCEEEEEEEcCCCCeEEEEEEEEEEeCCCCCCC-CCeeEEEec
Confidence 344445554321112345677777665 44577899999999998532211 112468888765444444 348888887
Q ss_pred C
Q 020486 258 P 258 (325)
Q Consensus 258 ~ 258 (325)
+
T Consensus 82 ~ 82 (96)
T TIGR02266 82 D 82 (96)
T ss_pred c
Confidence 5
No 8
>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=41.16 E-value=21 Score=33.39 Aligned_cols=24 Identities=33% Similarity=0.457 Sum_probs=21.3
Q ss_pred HHHHHHHHHhhhcccEEEEEeCCC
Q 020486 84 LAGQIARAVTIFRIDEVVVFDNKS 107 (325)
Q Consensus 84 ~aGqIARAaaIF~VDEIVVydD~~ 107 (325)
=+|-|||++.-|+++.+++-+...
T Consensus 16 NiGaiaR~~~~fG~~~l~lv~p~~ 39 (233)
T TIGR00050 16 NIGSIARAMKNMGLTELCLVNPKS 39 (233)
T ss_pred CHHHHHHHHHhCCCCEEEEeCCCc
Confidence 479999999999999999997653
No 9
>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=39.26 E-value=75 Score=25.49 Aligned_cols=45 Identities=18% Similarity=0.270 Sum_probs=36.5
Q ss_pred eEEEEecCccccCCCCHHHHHHHHHHHHHHHh-hhc-ccEEEEEeCCC
Q 020486 62 TVSVAVPGSIIDNTQSLELATRLAGQIARAVT-IFR-IDEVVVFDNKS 107 (325)
Q Consensus 62 tvSIAIP~SIlsnaqslelkT~~aGqIARAaa-IF~-VDEIVVydD~~ 107 (325)
++.|=+..+++.. .+......+++||..+++ -|. |++|.|+=|+.
T Consensus 65 ~~~Vd~s~~~~~~-~~~~~~~~~~~~i~~Tl~~~~~~v~~V~i~vdG~ 111 (117)
T PF10646_consen 65 TLTVDFSSEFLNF-LGSSQEALLLAQIVNTLTEQFPGVKKVQILVDGK 111 (117)
T ss_pred EEEEECCHHHhhc-CChHHHHHHHHHHHHHHHHhcCCccEEEEEECCE
Confidence 5666667767665 666677899999999999 999 99999997764
No 10
>KOG2201 consensus Pantothenate kinase PanK and related proteins [Coenzyme transport and metabolism]
Probab=34.99 E-value=40 Score=34.16 Aligned_cols=27 Identities=26% Similarity=0.141 Sum_probs=22.3
Q ss_pred CHHHHHHHHHHHHHHHh-hhcccEEEEE
Q 020486 77 SLELATRLAGQIARAVT-IFRIDEVVVF 103 (325)
Q Consensus 77 slelkT~~aGqIARAaa-IF~VDEIVVy 103 (325)
.+...|+-+|||||-+| +++|++|++=
T Consensus 284 lL~mIsnNIGqiAyl~A~~~ni~rV~Fg 311 (371)
T KOG2201|consen 284 LLRMISNNIGQIAYLCALNENIKRVYFG 311 (371)
T ss_pred HHHHHHhhHHHHHHHHHHHhCccEEEEe
Confidence 45678899999999865 7999999764
No 11
>KOG2367 consensus Alpha-isopropylmalate synthase/homocitrate synthase [Amino acid transport and metabolism]
Probab=34.60 E-value=22 Score=37.56 Aligned_cols=20 Identities=10% Similarity=0.164 Sum_probs=17.3
Q ss_pred HHhHhcCCchhhhhhcCCCC
Q 020486 137 LLQYLETPQYLRKALFSMHS 156 (325)
Q Consensus 137 iLqYlETPpYLRK~LFP~h~ 156 (325)
|.-|+-|-+++||+.|.+..
T Consensus 150 Vh~~~aTSd~~rey~~~ksk 169 (560)
T KOG2367|consen 150 VHVFIATSDIHREYKLKKSK 169 (560)
T ss_pred EEEEecccHHHHHHHhcccH
Confidence 66788999999999999864
No 12
>PRK15114 tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ; Provisional
Probab=34.27 E-value=32 Score=32.60 Aligned_cols=23 Identities=17% Similarity=0.312 Sum_probs=20.8
Q ss_pred HHHHHHHHHhhhcccEEEEEeCC
Q 020486 84 LAGQIARAVTIFRIDEVVVFDNK 106 (325)
Q Consensus 84 ~aGqIARAaaIF~VDEIVVydD~ 106 (325)
=+|-|||+|.-|+++++++-...
T Consensus 17 NiGaiaRa~~~fG~~~l~lv~p~ 39 (245)
T PRK15114 17 NMGSVARAMKTMGLTNLWLVNPL 39 (245)
T ss_pred cHHHHHHHHHhcCCCEEEEeCCC
Confidence 47999999999999999998664
No 13
>TIGR00186 rRNA_methyl_3 rRNA methylase, putative, group 3. this is part of the trmH (spoU) family of rRNA methylases
Probab=29.84 E-value=42 Score=31.32 Aligned_cols=31 Identities=23% Similarity=0.400 Sum_probs=23.6
Q ss_pred ccCCCCHHHHHHHHHHHHHHHhhhcccEEEEEeCC
Q 020486 72 IDNTQSLELATRLAGQIARAVTIFRIDEVVVFDNK 106 (325)
Q Consensus 72 lsnaqslelkT~~aGqIARAaaIF~VDEIVVydD~ 106 (325)
|++.+++ .=+|-|.|+|.-|+|+.||+=+..
T Consensus 95 Ld~v~dp----~NlGaI~Rta~afG~~~vil~~~~ 125 (237)
T TIGR00186 95 LDEITDP----HNLGAILRTAEAFGVDGVILPKRR 125 (237)
T ss_pred EcCCCCC----ccHHHHHHHHHHcCCCEEEECCCC
Confidence 4555553 358999999999999999776543
No 14
>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=28.11 E-value=2.2e+02 Score=24.20 Aligned_cols=47 Identities=17% Similarity=0.150 Sum_probs=35.1
Q ss_pred CCcccceEEEEeeccCCCCCceEEEeCCCceeeecc------cCCCCcEEEEEecC
Q 020486 176 HEWAPFREGVTLKENAPNSVGTLVDVGLNKHVVVDQ------VLDPGVRVTVAMGT 225 (325)
Q Consensus 176 ~e~~~yREGvVv~~~~~~g~gs~VdvGL~k~v~i~~------~l~~g~RVTV~l~~ 225 (325)
+..+..=.|-|...- +.--|||.|..=++.+.+ .+..|+||.|+++.
T Consensus 21 ~~~gk~V~G~I~hvv---~ddLYIDfG~KFhcVc~rp~~~~~~y~~G~rV~lrLkd 73 (104)
T PF10246_consen 21 DPEGKIVIGKIFHVV---DDDLYIDFGGKFHCVCKRPAVNGEKYVRGSRVRLRLKD 73 (104)
T ss_pred CccCCEEEEEEEEEe---cCceEEEeCCceeEEEecccccccccccCCEEEEEECC
Confidence 345666677776653 568899999987766643 48899999999984
No 15
>PRK11181 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional
Probab=27.74 E-value=48 Score=31.18 Aligned_cols=31 Identities=16% Similarity=0.253 Sum_probs=23.7
Q ss_pred ccCCCCHHHHHHHHHHHHHHHhhhcccEEEEEeCC
Q 020486 72 IDNTQSLELATRLAGQIARAVTIFRIDEVVVFDNK 106 (325)
Q Consensus 72 lsnaqslelkT~~aGqIARAaaIF~VDEIVVydD~ 106 (325)
|++.|++ .=+|-|.|+|..|+|+.||+-.+.
T Consensus 100 Ld~v~dp----~NlGai~Rta~a~G~~~vi~~~~~ 130 (244)
T PRK11181 100 LDGVTDP----HNLGACLRSADAAGVHAVIVPKDR 130 (244)
T ss_pred EcCCCCc----chHHHHHHHHHHcCCCEEEECCCC
Confidence 4455554 358999999999999999885543
No 16
>PLN02726 dolichyl-phosphate beta-D-mannosyltransferase
Probab=25.51 E-value=1.6e+02 Score=26.44 Aligned_cols=45 Identities=20% Similarity=0.229 Sum_probs=27.5
Q ss_pred CcceEEEEecCccccCCCCHHHHHHHHHHHHHHHhhhcccEEEEEeCCCC
Q 020486 59 EVPTVSVAVPGSIIDNTQSLELATRLAGQIARAVTIFRIDEVVVFDNKSS 108 (325)
Q Consensus 59 r~~tvSIAIP~SIlsnaqslelkT~~aGqIARAaaIF~VDEIVVydD~~~ 108 (325)
..+.|||.||. .+++.+++ ..+..|.+.+.-+.=-||||.||++.
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 23344544443332349999999753
No 17
>TIGR00185 rRNA_methyl_2 rRNA methylase, putative, group 2. this is part of the trmH (spoU) family of rRNA methylases
Probab=25.42 E-value=57 Score=28.45 Aligned_cols=28 Identities=14% Similarity=0.159 Sum_probs=20.6
Q ss_pred cccCCCCHHHHHHHHHHHHHHHhhhcccEEEE
Q 020486 71 IIDNTQSLELATRLAGQIARAVTIFRIDEVVV 102 (325)
Q Consensus 71 IlsnaqslelkT~~aGqIARAaaIF~VDEIVV 102 (325)
+|++.|++ .=+|-|+|+|..|+|+-|++
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 44555664 35899999999999965555
No 18
>PRK10864 putative methyltransferase; Provisional
Probab=25.12 E-value=56 Score=32.84 Aligned_cols=21 Identities=38% Similarity=0.477 Sum_probs=18.8
Q ss_pred HHHHHHHHHhhhcccEEEEEe
Q 020486 84 LAGQIARAVTIFRIDEVVVFD 104 (325)
Q Consensus 84 ~aGqIARAaaIF~VDEIVVyd 104 (325)
=+|-|.|+|..|+|+.||+-+
T Consensus 211 NlGaIiRTA~afGv~~Vil~~ 231 (346)
T PRK10864 211 NLGGIMRSCAHFGVKGVVVQD 231 (346)
T ss_pred cHHHHHHHHHHhCCCEEEECC
Confidence 479999999999999998854
No 19
>PRK10433 putative RNA methyltransferase; Provisional
Probab=24.96 E-value=58 Score=30.75 Aligned_cols=23 Identities=26% Similarity=0.423 Sum_probs=20.8
Q ss_pred HHHHHHHHHhhhcccEEEEEeCC
Q 020486 84 LAGQIARAVTIFRIDEVVVFDNK 106 (325)
Q Consensus 84 ~aGqIARAaaIF~VDEIVVydD~ 106 (325)
=+|-||||+.-|+++++++-+..
T Consensus 15 NiGaiaRam~nfG~~~L~lV~p~ 37 (228)
T PRK10433 15 NVGAAARAMKTMGFSELRIVDSQ 37 (228)
T ss_pred cHHHHHHHHHHCCCCEEEEeCCC
Confidence 58999999999999999999654
No 20
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 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 [, ]. The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....
Probab=22.88 E-value=3.1e+02 Score=19.99 Aligned_cols=46 Identities=22% Similarity=0.247 Sum_probs=33.1
Q ss_pred CcccceEEEEeeccCCCCCceEEEeCCCceeeec-------------ccCCCCcEEEEEecC
Q 020486 177 EWAPFREGVTLKENAPNSVGTLVDVGLNKHVVVD-------------QVLDPGVRVTVAMGT 225 (325)
Q Consensus 177 e~~~yREGvVv~~~~~~g~gs~VdvGL~k~v~i~-------------~~l~~g~RVTV~l~~ 225 (325)
..++.-+|.|..-. ..|.+|++|..-...++ ..+.+|.+|.|++..
T Consensus 3 ~~G~iv~g~V~~v~---~~g~~V~l~~~~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~v~~ 61 (74)
T PF00575_consen 3 KEGDIVEGKVTSVE---DFGVFVDLGNGIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIK 61 (74)
T ss_dssp STTSEEEEEEEEEE---TTEEEEEESTSSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEE
T ss_pred CCCCEEEEEEEEEE---CCEEEEEECCcEEEEEEeehhcCccccccccccCCCCEEEEEEEE
Confidence 45666789888774 58999999955444331 347789999998864
No 21
>cd04455 S1_NusA S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three RNA binding domains (RBD's). The RBD's include one S1 domain and two KH domains that form an RNA binding surface. DNA transcription by RNA polymerase (RNAP) includes three phases - initiation, elongation, and termination. During initiation, sigma factors bind RNAP and target RNAP to specific promoters. During elongation, N-utilization substances (NusA, B, E, and G) replace sigma factors and regulate pausing, termination, and antitermination. NusA is cold-shock-inducible.
Probab=22.05 E-value=2.8e+02 Score=20.45 Aligned_cols=43 Identities=16% Similarity=0.321 Sum_probs=29.9
Q ss_pred ccceEEEEeeccCCCCCceEEEeCCCceeeec-------ccCCCCcEEEEEecC
Q 020486 179 APFREGVTLKENAPNSVGTLVDVGLNKHVVVD-------QVLDPGVRVTVAMGT 225 (325)
Q Consensus 179 ~~yREGvVv~~~~~~g~gs~VdvGL~k~v~i~-------~~l~~g~RVTV~l~~ 225 (325)
+..=+|.|+... .++.+||+|- ....++ ..+.+|.+|.|-+..
T Consensus 4 g~iV~G~V~~~~---~~~~~vdig~-~eg~lp~~e~~~~~~~~~Gd~v~v~v~~ 53 (67)
T cd04455 4 GEIVTGIVKRVD---RGNVIVDLGK-VEAILPKKEQIPGESYRPGDRIKAYVLE 53 (67)
T ss_pred CCEEEEEEEEEc---CCCEEEEcCC-eEEEeeHHHCCCCCcCCCCCEEEEEEEE
Confidence 344578887764 5789999986 433332 347899999988864
No 22
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=20.22 E-value=2.3e+02 Score=22.15 Aligned_cols=50 Identities=16% Similarity=0.205 Sum_probs=30.0
Q ss_pred eEEEEeeccCCCCCceE-E--EeCCCceeeeccc-------CCCCcEEEEEecCCCCCCCCCCceec
Q 020486 182 REGVTLKENAPNSVGTL-V--DVGLNKHVVVDQV-------LDPGVRVTVAMGTNRNLDADSPRQVV 238 (325)
Q Consensus 182 REGvVv~~~~~~g~gs~-V--dvGL~k~v~i~~~-------l~~g~RVTV~l~~~~~~~~~~~g~vV 238 (325)
-+|+|+..- +++.| | +-|....+.+..+ +-+|.+|+|.+..-+ ..+|.+|
T Consensus 7 ~~G~V~e~L---~~~~f~V~l~ng~~vla~i~GKmr~~rI~I~~GD~V~Ve~spyd----~tkgrIi 66 (68)
T TIGR00008 7 MEGKVTESL---PNAMFRVELENGHEVLAHISGKIRMHYIRILPGDKVKVELSPYD----LTRGRIT 66 (68)
T ss_pred EEEEEEEEC---CCCEEEEEECCCCEEEEEecCcchhccEEECCCCEEEEEECccc----CCcEeEE
Confidence 478888764 33433 3 3444444455442 679999999997532 1246665
Done!