Query 032119
Match_columns 147
No_of_seqs 141 out of 332
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 09:51:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032119.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032119hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3262 H/ACA small nucleolar 100.0 6.3E-55 1.4E-59 350.3 9.0 139 1-140 1-143 (215)
2 PRK13149 H/ACA RNA-protein com 99.9 4E-26 8.6E-31 158.7 6.4 72 50-125 1-73 (73)
3 COG3277 GAR1 RNA-binding prote 99.9 6.6E-26 1.4E-30 166.1 6.7 92 50-141 1-92 (98)
4 PF04410 Gar1: Gar1/Naf1 RNA b 99.9 5.5E-25 1.2E-29 170.6 6.2 99 41-142 14-115 (154)
5 KOG1596 Fibrillarin and relate 99.6 4.2E-16 9E-21 131.6 7.3 76 44-133 78-164 (317)
6 PTZ00146 fibrillarin; Provisio 99.5 4E-14 8.7E-19 120.6 8.1 78 43-132 51-139 (293)
7 KOG2236 Uncharacterized conser 98.5 9.7E-08 2.1E-12 85.9 4.0 79 49-127 207-288 (483)
8 PF01269 Fibrillarin: Fibrilla 98.4 4.4E-08 9.5E-13 81.4 -0.2 67 57-133 3-81 (229)
9 COG1889 NOP1 Fibrillarin-like 97.6 2.1E-05 4.6E-10 65.3 1.0 61 59-133 11-84 (231)
10 PTZ00146 fibrillarin; Provisio 93.4 0.14 3.1E-06 44.1 4.9 16 52-67 64-80 (293)
11 KOG3262 H/ACA small nucleolar 80.5 3.2 6.9E-05 34.4 4.5 11 115-125 107-117 (215)
12 PRK04266 fibrillarin; Provisio 77.4 1.7 3.6E-05 35.6 2.1 75 55-137 3-95 (226)
13 KOG4745 Metalloproteinase inhi 66.2 4.7 0.0001 31.7 2.1 58 90-147 10-73 (141)
14 PF05239 PRC: PRC-barrel domai 65.4 4.3 9.4E-05 26.8 1.6 33 76-108 10-45 (79)
15 PF02470 MCE: mce related prot 45.0 88 0.0019 20.8 5.5 61 71-136 14-76 (81)
16 PF10879 DUF2674: Protein of u 41.0 14 0.0003 25.2 0.9 47 81-130 11-65 (67)
17 PF13953 PapC_C: PapC C-termin 33.2 67 0.0015 21.2 3.3 34 71-108 8-41 (68)
18 PF11705 RNA_pol_3_Rpc31: DNA- 31.5 28 0.00061 28.4 1.5 7 8-14 1-7 (233)
19 TIGR02273 16S_RimM 16S rRNA pr 30.8 39 0.00084 26.0 2.1 32 76-107 101-132 (165)
20 PF14578 GTP_EFTU_D4: Elongati 30.5 94 0.002 22.1 3.8 72 46-124 3-81 (81)
21 PF13865 FoP_duplication: C-te 30.4 63 0.0014 22.2 2.9 9 45-53 37-45 (74)
22 PHA02809 hypothetical protein; 30.0 52 0.0011 24.6 2.5 50 76-132 8-68 (111)
23 PLN03138 Protein TOC75; Provis 29.7 48 0.001 32.6 2.9 14 115-128 220-233 (796)
24 PRK14592 rimM 16S rRNA-process 24.7 66 0.0014 24.9 2.4 32 76-107 98-129 (165)
25 KOG4307 RNA binding protein RB 23.0 1.1E+02 0.0024 30.3 3.9 11 62-74 866-876 (944)
26 PF10246 MRP-S35: Mitochondria 22.6 80 0.0017 23.7 2.4 26 42-67 17-42 (104)
27 PRK13828 rimM 16S rRNA-process 22.4 73 0.0016 24.6 2.2 32 76-107 86-117 (161)
28 PRK00122 rimM 16S rRNA-process 22.0 81 0.0017 24.5 2.4 31 76-106 106-136 (172)
29 PF06068 TIP49: TIP49 C-termin 21.9 28 0.0006 31.6 -0.2 34 111-144 166-215 (398)
30 COG4371 Predicted membrane pro 21.4 1.5E+02 0.0033 26.0 4.1 8 7-14 55-62 (334)
31 smart00652 eIF1a eukaryotic tr 20.5 1.4E+02 0.003 21.0 3.1 22 86-110 6-27 (83)
32 COG3881 PRC-barrel domain cont 20.1 85 0.0018 25.5 2.2 19 76-94 8-27 (176)
No 1
>KOG3262 consensus H/ACA small nucleolar RNP component GAR1 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=6.3e-55 Score=350.34 Aligned_cols=139 Identities=66% Similarity=1.136 Sum_probs=117.5
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCC---CCCCCCCCCCCCC-CCCCCCCCCCceEEecceeeeeeCCeEEEeccCCCcCCC
Q 032119 1 MRPPRGGGGFRGGRDGGRGGRGGG---RFGGGGRGGGGRG-GFGFRDEGPPAEVVEVSSFLHACEGDAVTKLTNEKIPYF 76 (147)
Q Consensus 1 ~~~~~~~~~~~~~~~g~~g~~~~~---~~~gg~~ggrgg~-~~g~~~~Gpp~~vielG~f~H~~eg~lV~K~t~~~VPyf 76 (147)
|+||||++++++++ +-|++++++ .|+++...||+++ .++++|++||++|+|||+|+|.||++||||+|+++||||
T Consensus 1 ~~~~rgggg~~g~~-gfRgg~ggg~~gg~rgg~g~grgg~~~~~~~d~gpp~evvelg~flh~Cegd~Vck~~~~kIPyf 79 (215)
T KOG3262|consen 1 GGGPRGGGGGGGGG-GFRGGGGGGRGGGFRGGNGFGRGGRGGRGFQDQGPPEEVVELGKFLHMCEGDLVCKLTNKKIPYF 79 (215)
T ss_pred CCCCcCCCCCCCCC-CcccCCCCCCCCCcccCcccccCCcccCCcccCCCchhhhhhhhhhhhcCCceEEeeccccCCCC
Confidence 78899987776665 334433322 2333322234432 234679999999999999999999999999999999999
Q ss_pred CCceeeccceeecccccccCcceeccEEEEecCcccccccccCCEEEecCCCeeecccccCCCC
Q 032119 77 NAPIYLQNKTQIGKVDEIFGPINESYFSVKMMEGIVATSYSLGDKFYIDPSKLLPLARFLPQPK 140 (147)
Q Consensus 77 Na~Vy~ekk~~IGkVdEIFGpi~e~yfsvKl~~gI~a~sfk~gdkiyI~p~KlLpl~rFlp~p~ 140 (147)
|||||+|||+|||||||||||++|++|||||+++|+|+|||++|+|||||+|||||+||||+|.
T Consensus 80 NAPIylenk~qIGKVDEIfG~i~d~~fsIK~~dgv~assfk~g~k~fi~p~KllPl~RFLP~p~ 143 (215)
T KOG3262|consen 80 NAPIYLENKEQIGKVDEIFGPINDVHFSIKPSDGVQASSFKPGDKLFIDPDKLLPLDRFLPQPV 143 (215)
T ss_pred CCceeecchhhhcchhhhcccccccEEEEecCCCceeecccCCCeEEecccccCcHhhcCCCCC
Confidence 9999999999999999999999999999999999999999999999999999999999999984
No 2
>PRK13149 H/ACA RNA-protein complex component Gar1; Reviewed
Probab=99.93 E-value=4e-26 Score=158.70 Aligned_cols=72 Identities=29% Similarity=0.560 Sum_probs=68.7
Q ss_pred EEecceeeeee-CCeEEEeccCCCcCCCCCceeeccceeecccccccCcceeccEEEEecCcccccccccCCEEEec
Q 032119 50 VVEVSSFLHAC-EGDAVTKLTNEKIPYFNAPIYLQNKTQIGKVDEIFGPINESYFSVKMMEGIVATSYSLGDKFYID 125 (147)
Q Consensus 50 vielG~f~H~~-eg~lV~K~t~~~VPyfNa~Vy~ekk~~IGkVdEIFGpi~e~yfsvKl~~gI~a~sfk~gdkiyI~ 125 (147)
|.++|+|+|.| ++++|||+ +++|+||++||+||+++||||+|||||++++||+||+++++.++ +++|++||.
T Consensus 1 Mk~~G~~~h~~~~g~lI~~~--~~~P~~n~~V~~~~~~~IGkV~dIfGPV~~pY~~Vk~~~~~~~~--~~g~k~yi~ 73 (73)
T PRK13149 1 MKRLGKVLHYAPKGKLIIRL--DKQPPIGSVVYDKKLKKIGKVVDVFGPVKEPYVLVKPDKKDPPE--LVGEKLYVR 73 (73)
T ss_pred CcEeEEEEEEcCCCCEEEEc--CCCCCCCCEeECCCCCEeEEEEEEECCCCCcEEEEEeCCCCCcc--ccCCEEEeC
Confidence 57899999999 89999999 68999999999999999999999999999999999999999997 889999984
No 3
>COG3277 GAR1 RNA-binding protein involved in rRNA processing [Translation, ribosomal structure and biogenesis]
Probab=99.92 E-value=6.6e-26 Score=166.12 Aligned_cols=92 Identities=38% Similarity=0.632 Sum_probs=87.8
Q ss_pred EEecceeeeeeCCeEEEeccCCCcCCCCCceeeccceeecccccccCcceeccEEEEecCcccccccccCCEEEecCCCe
Q 032119 50 VVEVSSFLHACEGDAVTKLTNEKIPYFNAPIYLQNKTQIGKVDEIFGPINESYFSVKMMEGIVATSYSLGDKFYIDPSKL 129 (147)
Q Consensus 50 vielG~f~H~~eg~lV~K~t~~~VPyfNa~Vy~ekk~~IGkVdEIFGpi~e~yfsvKl~~gI~a~sfk~gdkiyI~p~Kl 129 (147)
|++||+|+|.|+..+||..++..+|++|++||+++.++||+|+|||||++++|+.||+++.+...++.++|++||.++|+
T Consensus 1 m~~lG~vlh~~~~g~vi~~~~~~iP~l~~~V~~~~~k~IG~V~dVfGPv~~PY~~Vkp~~~~~~~~~~vg~~lYi~~~k~ 80 (98)
T COG3277 1 MKRLGKVLHVCGTGMVIVRDNDRIPPLNAPVYDANLKRIGKVVDVFGPVDEPYILVKPDDRDVKLESLVGDTLYIPPDKL 80 (98)
T ss_pred CccceeEEEecCCceEEEeCCCCCCCCCCeeEecCCCEEEEEEEEEccCCCCEEEEeccccccccccccceEEEeccccc
Confidence 47899999999999999988789999999999999999999999999999999999999999888899999999999999
Q ss_pred eecccccCCCCC
Q 032119 130 LPLARFLPQPKC 141 (147)
Q Consensus 130 Lpl~rFlp~p~~ 141 (147)
++.+||+|+++.
T Consensus 81 ~~~~r~~~~~k~ 92 (98)
T COG3277 81 IRKKRKLPRKKR 92 (98)
T ss_pred CcccccCccccc
Confidence 999999999885
No 4
>PF04410 Gar1: Gar1/Naf1 RNA binding region; InterPro: IPR007504 H/ACA ribonucleoprotein particles (RNPs) are a family of RNA pseudouridine synthases that specify modification sites through guide RNAs. More than 100 mammalian H/ACA RNAs form an equal number of ribonucleoproteins (RNPs) by associating with the same four core proteins: Cbf5, Gar1, Nhp2 and Nop10. The function of these H/ACA RNPs is essential for biogenesis of the ribosome, splicing of precursor mRNAs (pre-mRNAs), maintenance of telomeres and probably for additional cellular processes []. Recent crystal structures of archaeal H/ACA protein complexes show how the same four proteins accommodate >100 distinct but related H/ACA RNAs []. The complex contains a stable core composed of Cbf5 and Nop10, to which Gar1 and Nhp2 subsequently bind, the complex interacts with snoRNAs []. This entry represents Gar1 and Naf1. Naf1 is an RNA-binding protein required for the maturation of box H/ACA snoRNPs complex and ribosome biogenesis. During assembly of the H/ACA snoRNPs complex, it associates with the complex, disappearing during maturation of the complex being replaced by GAR1 to yield mature H/ACA snoRNPs complex. Naf1 reveals a striking structural homology with the core domain of archaeal Gar1 [].; GO: 0030515 snoRNA binding, 0031120 snRNA pseudouridine synthesis, 0042254 ribosome biogenesis; PDB: 2EY4_C 3MQK_C 2RFK_C 2HVY_B 3HAY_B 3U28_C 3UAI_C 2EQN_A 2V3M_F.
Probab=99.91 E-value=5.5e-25 Score=170.64 Aligned_cols=99 Identities=43% Similarity=0.748 Sum_probs=82.2
Q ss_pred CCCCCCCceEEecceeeeeeCCeEEEeccCC-CcCCCCCceeeccceeecccccccCcceeccEEEE--ecCcccccccc
Q 032119 41 FRDEGPPAEVVEVSSFLHACEGDAVTKLTNE-KIPYFNAPIYLQNKTQIGKVDEIFGPINESYFSVK--MMEGIVATSYS 117 (147)
Q Consensus 41 ~~~~Gpp~~vielG~f~H~~eg~lV~K~t~~-~VPyfNa~Vy~ekk~~IGkVdEIFGpi~e~yfsvK--l~~gI~a~sfk 117 (147)
..+.+|+.++++||+|+|.|++.+|||++.+ .||++|+.||+|+++.||+|+|||||++++||+|| +++.+.+.+++
T Consensus 14 ~~~~~~~~~i~~lG~v~~i~~~~vVvk~~~~~~vl~~~s~v~~edr~~iG~V~eiFGpV~~P~y~Vr~~~~~~~~~~~~~ 93 (154)
T PF04410_consen 14 DVEIGPPEEIKPLGTVSHIVENLVVVKSTPSKQVLDFGSVVCLEDRTKIGKVDEIFGPVNNPYYSVRFNSSEGIKAKSLK 93 (154)
T ss_dssp T-B--TTSSEEEEEEEEEEETTEEEEEE-SS-CEEBTT-EEEETTSBEEEEEEEEESESSS-EEEEE-SCHHHHHHHCCC
T ss_pred CcccCCCceEEEeeeEEEEeCCcEEEEeCCCCcCCCCCCEEECCCCCEeEEEeeEeCCCCceEEEEEeCCcccccccccc
Confidence 4577899999999999999999999999877 89999999999999999999999999999999999 88999999999
Q ss_pred cCCEEEecCCCeeecccccCCCCCC
Q 032119 118 LGDKFYIDPSKLLPLARFLPQPKCS 142 (147)
Q Consensus 118 ~gdkiyI~p~KlLpl~rFlp~p~~~ 142 (147)
++++||+++. |+++|||+|+.+
T Consensus 94 ~g~~vy~~~~---~~~~~~~~~~~~ 115 (154)
T PF04410_consen 94 VGDKVYYDPD---PTSRFLPEPLKR 115 (154)
T ss_dssp TTSEEEEECC----GGGG-------
T ss_pred ccceEEECCC---chheeccccccc
Confidence 9999999998 999999988754
No 5
>KOG1596 consensus Fibrillarin and related nucleolar RNA-binding proteins [RNA processing and modification]
Probab=99.64 E-value=4.2e-16 Score=131.58 Aligned_cols=76 Identities=26% Similarity=0.423 Sum_probs=68.2
Q ss_pred CCCCceEEecceeeeeeCCeEEEe------ccCCCcCCCCCceeeccceeecccccccCcceec----cEEEEecCcccc
Q 032119 44 EGPPAEVVEVSSFLHACEGDAVTK------LTNEKIPYFNAPIYLQNKTQIGKVDEIFGPINES----YFSVKMMEGIVA 113 (147)
Q Consensus 44 ~Gpp~~vielG~f~H~~eg~lV~K------~t~~~VPyfNa~Vy~ekk~~IGkVdEIFGpi~e~----yfsvKl~~gI~a 113 (147)
.+..+.++|+ |+|.+++|+| +|+|+|| +++||+|++..|..-|+ +.|| +|++||+++|..
T Consensus 78 ~gG~~v~vEP----HRh~GVfi~rgkeDaLvTkNlvp--ge~vYgEkRisv~~~~~----kvEyRVWnPfrSKLAA~I~g 147 (317)
T KOG1596|consen 78 KGGSKVLVEP----HRHAGVFIARGKEDALVTKNLVP--GESVYGEKRISVENEDG----KVEYRVWNPFRSKLAAGILG 147 (317)
T ss_pred cCCceEEecc----ccccceEEEcCchhheeecccCC--cccccCceEEEeecCCC----cEEEEEeChHHHHHHHHhhc
Confidence 3467788887 9999999999 5999999 99999999999866653 8888 999999999999
Q ss_pred cccccCCEEEecCC-Ceeecc
Q 032119 114 TSYSLGDKFYIDPS-KLLPLA 133 (147)
Q Consensus 114 ~sfk~gdkiyI~p~-KlLpl~ 133 (147)
. .|.|||.|+ |+|||-
T Consensus 148 G----vdnihikpGsKVLYLG 164 (317)
T KOG1596|consen 148 G----VDNIHIKPGSKVLYLG 164 (317)
T ss_pred C----ccceeecCCceEEEee
Confidence 9 999999999 999985
No 6
>PTZ00146 fibrillarin; Provisional
Probab=99.51 E-value=4e-14 Score=120.60 Aligned_cols=78 Identities=24% Similarity=0.396 Sum_probs=62.4
Q ss_pred CCCCCceEEecceeeeeeCCeEEEe------ccCCCcCCCCCceeeccceeecccccccCcceec----cEEEEecCccc
Q 032119 43 DEGPPAEVVEVSSFLHACEGDAVTK------LTNEKIPYFNAPIYLQNKTQIGKVDEIFGPINES----YFSVKMMEGIV 112 (147)
Q Consensus 43 ~~Gpp~~vielG~f~H~~eg~lV~K------~t~~~VPyfNa~Vy~ekk~~IGkVdEIFGpi~e~----yfsvKl~~gI~ 112 (147)
..++.+.+++. |+++++++++ +|.|++| +.+||.|++.++...++ +...|| +|++||+++|.
T Consensus 51 ~~~~~~~~~~~----~~~~gv~~~~~~~~~l~t~n~~p--g~~vygek~~~~~~~~~--~~~~eyR~w~p~rSKlaa~i~ 122 (293)
T PTZ00146 51 GGGPGKVIVVP----HRFPGVFIAKGKSDALVTKNMVP--GESVYGEKRISVEDAEG--GEKIEYRVWNPFRSKLAAAII 122 (293)
T ss_pred CCCCCceEEee----eeecCEEEeecCCceeEeecCCC--CcccccceEEeeccCCC--CCcceeeeeCCcccHHHHHHH
Confidence 33456777776 9999999998 5899999 99999999999875542 135577 99999999998
Q ss_pred ccccccCCEEEecCC-Ceeec
Q 032119 113 ATSYSLGDKFYIDPS-KLLPL 132 (147)
Q Consensus 113 a~sfk~gdkiyI~p~-KlLpl 132 (147)
.. .+.|+|.|+ +||.|
T Consensus 123 ~g----~~~l~IkpG~~VLDL 139 (293)
T PTZ00146 123 GG----VANIPIKPGSKVLYL 139 (293)
T ss_pred CC----cceeccCCCCEEEEe
Confidence 77 777888877 77765
No 7
>KOG2236 consensus Uncharacterized conserved protein [Function unknown]
Probab=98.49 E-value=9.7e-08 Score=85.91 Aligned_cols=79 Identities=22% Similarity=0.503 Sum_probs=70.1
Q ss_pred eEEecceeeeeeCCeEEEeccCCC-cCCCCCceeeccceeecccccccCcceeccEEEEecCccccc--ccccCCEEEec
Q 032119 49 EVVEVSSFLHACEGDAVTKLTNEK-IPYFNAPIYLQNKTQIGKVDEIFGPINESYFSVKMMEGIVAT--SYSLGDKFYID 125 (147)
Q Consensus 49 ~vielG~f~H~~eg~lV~K~t~~~-VPyfNa~Vy~ekk~~IGkVdEIFGpi~e~yfsvKl~~gI~a~--sfk~gdkiyI~ 125 (147)
++++||.++-+.+...|+++|.++ |--+.+.+|+|+++-||.|+|||||+.++||.||....-.+. .++.++++|+-
T Consensus 207 ~~~plG~V~svv~~~VII~s~~~~~vlde~Svlf~edR~~lG~I~EiFGpV~~P~YvvRFnS~~e~~~~gi~ig~~vy~a 286 (483)
T KOG2236|consen 207 ELLPLGKVSSVVDQQVIIESTCNKEVLDEDSVLFLEDRTALGQIFEIFGPVKNPYYVVRFNSEEEISFLGICIGEKVYYA 286 (483)
T ss_pred ceechhHHHHHhhhceEEEeccCcccccccceEEeeccccchhhhhhhcccCCceEEEecCchhhhhhhccccCCeeEec
Confidence 688999999999999999998885 446999999999999999999999999999999998876655 66779999999
Q ss_pred CC
Q 032119 126 PS 127 (147)
Q Consensus 126 p~ 127 (147)
|.
T Consensus 287 p~ 288 (483)
T KOG2236|consen 287 PD 288 (483)
T ss_pred Cc
Confidence 83
No 8
>PF01269 Fibrillarin: Fibrillarin; InterPro: IPR000692 Fibrillarin is a component of a nucleolar small nuclear ribonucleoprotein (SnRNP), functioning in vivo in ribosomal RNA processing [, ]. It is associated with U3, U8 and U13 small nuclear RNAs in mammals [] and is similar to the yeast NOP1 protein []. Fibrillarin has a well conserved sequence of around 320 amino acids, and contains 3 domains, an N-terminal Gly/Arg-rich region; a central domain resembling other RNA-binding proteins and containing an RNP-2-like consensus sequence; and a C-terminal alpha-helical domain. An evolutionarily related pre-rRNA processing protein, which lacks the Gly/Arg-rich domain, has been found in various archaebacteria.; GO: 0003723 RNA binding, 0008168 methyltransferase activity, 0006364 rRNA processing, 0008033 tRNA processing; PDB: 3PLA_E 3ID6_C 3ID5_B 1NT2_A 3NVK_J 2NNW_B 3NVM_B 3NMU_J 1PRY_A 1G8A_A ....
Probab=98.42 E-value=4.4e-08 Score=81.43 Aligned_cols=67 Identities=24% Similarity=0.364 Sum_probs=48.6
Q ss_pred ee-eeCCeEEEe------ccCCCcCCCCCceeeccceeecccccccCcceec----cEEEEecCcccccccccCCEEEec
Q 032119 57 LH-ACEGDAVTK------LTNEKIPYFNAPIYLQNKTQIGKVDEIFGPINES----YFSVKMMEGIVATSYSLGDKFYID 125 (147)
Q Consensus 57 ~H-~~eg~lV~K------~t~~~VPyfNa~Vy~ekk~~IGkVdEIFGpi~e~----yfsvKl~~gI~a~sfk~gdkiyI~ 125 (147)
.| .+++.++++ +|.|++| +.+||+|++..+... +...|| +|++||+++|..+ .|.++|.
T Consensus 3 ~h~~~~gvy~~~~~~~~l~T~n~~p--g~~vYGEk~i~~~~~----~~~~eYR~W~P~RSKLaAai~~G----l~~~~ik 72 (229)
T PF01269_consen 3 PHERFEGVYIARGKGDALATKNLVP--GESVYGEKRISVEGE----GKKVEYRVWNPFRSKLAAAILKG----LENIPIK 72 (229)
T ss_dssp EEESSTTEEEEETTSTEEEEE-SST--T--SSSSEEEEETTE-------EEEEEE-TTT-HHHHHHHTT-----S--S--
T ss_pred ceeeecCEEEEecCCCeEEEecCCC--CCcccCceeEeecCC----CCccceeecCchhhHHHHHHHcC----ccccCCC
Confidence 48 889999997 5889999 999999999998554 457777 9999999999988 8999999
Q ss_pred CC-Ceeecc
Q 032119 126 PS-KLLPLA 133 (147)
Q Consensus 126 p~-KlLpl~ 133 (147)
|+ |+|||-
T Consensus 73 ~gskVLYLG 81 (229)
T PF01269_consen 73 PGSKVLYLG 81 (229)
T ss_dssp TT-EEEEET
T ss_pred CCCEEEEec
Confidence 99 999985
No 9
>COG1889 NOP1 Fibrillarin-like rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=97.60 E-value=2.1e-05 Score=65.35 Aligned_cols=61 Identities=21% Similarity=0.259 Sum_probs=50.9
Q ss_pred eeCCeEEEe--------ccCCCcCCCCCceeeccceeecccccccCcceec----cEEEEecCcccccccccCCEEEecC
Q 032119 59 ACEGDAVTK--------LTNEKIPYFNAPIYLQNKTQIGKVDEIFGPINES----YFSVKMMEGIVATSYSLGDKFYIDP 126 (147)
Q Consensus 59 ~~eg~lV~K--------~t~~~VPyfNa~Vy~ekk~~IGkVdEIFGpi~e~----yfsvKl~~gI~a~sfk~gdkiyI~p 126 (147)
.++++++++ +|.|.+| +.+||+|+.++++.. || ++++||+++|..+ -+.+.|.+
T Consensus 11 ~~~gvy~~~~~dg~~~l~T~nl~p--g~~VYGE~ii~~~~~--------eYR~Wnp~RSKLaAaIl~G----l~~~pi~~ 76 (231)
T COG1889 11 RFEGVYIVRFKDGSDRLATKNLVP--GERVYGERIIKVEGE--------EYREWNPRRSKLAAAILKG----LKNFPIKE 76 (231)
T ss_pred ccCCeEEEEcccccceeeeecCCC--CccccCceeEEecCc--------ceeeeCcchhHHHHHHHcC----cccCCcCC
Confidence 467777776 4778999 999999999987332 44 7899999999988 78899999
Q ss_pred C-Ceeecc
Q 032119 127 S-KLLPLA 133 (147)
Q Consensus 127 ~-KlLpl~ 133 (147)
+ |+|||-
T Consensus 77 g~~VLYLG 84 (231)
T COG1889 77 GSKVLYLG 84 (231)
T ss_pred CCEEEEee
Confidence 9 999984
No 10
>PTZ00146 fibrillarin; Provisional
Probab=93.35 E-value=0.14 Score=44.07 Aligned_cols=16 Identities=25% Similarity=0.194 Sum_probs=7.2
Q ss_pred ecceeeeeeC-CeEEEe
Q 032119 52 EVSSFLHACE-GDAVTK 67 (147)
Q Consensus 52 elG~f~H~~e-g~lV~K 67 (147)
.-|.|..... +.|+-|
T Consensus 64 ~~gv~~~~~~~~~l~t~ 80 (293)
T PTZ00146 64 FPGVFIAKGKSDALVTK 80 (293)
T ss_pred ecCEEEeecCCceeEee
Confidence 4455555432 334444
No 11
>KOG3262 consensus H/ACA small nucleolar RNP component GAR1 [Translation, ribosomal structure and biogenesis]
Probab=80.46 E-value=3.2 Score=34.42 Aligned_cols=11 Identities=18% Similarity=0.045 Sum_probs=5.7
Q ss_pred ccccCCEEEec
Q 032119 115 SYSLGDKFYID 125 (147)
Q Consensus 115 sfk~gdkiyI~ 125 (147)
|+|..|-|+..
T Consensus 107 sIK~~dgv~as 117 (215)
T KOG3262|consen 107 SIKPSDGVQAS 117 (215)
T ss_pred EEecCCCceee
Confidence 45556655443
No 12
>PRK04266 fibrillarin; Provisional
Probab=77.38 E-value=1.7 Score=35.58 Aligned_cols=75 Identities=15% Similarity=0.165 Sum_probs=46.3
Q ss_pred eeeeeeCCeEEEe--------ccCCCcCCCCCceeeccceeecccccccCc--ceeccEEEEecCcccc----cccccCC
Q 032119 55 SFLHACEGDAVTK--------LTNEKIPYFNAPIYLQNKTQIGKVDEIFGP--INESYFSVKMMEGIVA----TSYSLGD 120 (147)
Q Consensus 55 ~f~H~~eg~lV~K--------~t~~~VPyfNa~Vy~ekk~~IGkVdEIFGp--i~e~yfsvKl~~gI~a----~sfk~gd 120 (147)
+.+|++++.+++| +|.|++| +..+|++.-... .+. ..-.+++.|+++.+.+ -.+++++
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~g~~~~~~------~~~~~~~~~~~r~~~~~~ll~~~~~l~i~~g~ 74 (226)
T PRK04266 3 KKKEIFEGVYEVEFEDGSKRLATKNLVP--GKRVYGERLIKW------EGVEYREWNPRRSKLAAAILKGLKNFPIKKGS 74 (226)
T ss_pred ccccccCCEEEEecCCCcceEeeecCCC--CCCCCCceEEec------CCcEEEEECCCccchHHHHHhhHhhCCCCCCC
Confidence 4679999999998 4889999 899998655332 111 0111467888888876 3344554
Q ss_pred E-EEec--CC-CeeecccccC
Q 032119 121 K-FYID--PS-KLLPLARFLP 137 (147)
Q Consensus 121 k-iyI~--p~-KlLpl~rFlp 137 (147)
+ +.+. ++ .+++|++..+
T Consensus 75 ~VlD~G~G~G~~~~~la~~v~ 95 (226)
T PRK04266 75 KVLYLGAASGTTVSHVSDIVE 95 (226)
T ss_pred EEEEEccCCCHHHHHHHHhcC
Confidence 3 3333 33 4566665543
No 13
>KOG4745 consensus Metalloproteinase inhibitor TIMP and related proteins [General function prediction only]
Probab=66.18 E-value=4.7 Score=31.66 Aligned_cols=58 Identities=24% Similarity=0.405 Sum_probs=42.3
Q ss_pred ccccccCcceeccEEEEecCc-----ccccccccCCEEEe-cCCCeeecccccCCCCCCCCccC
Q 032119 90 KVDEIFGPINESYFSVKMMEG-----IVATSYSLGDKFYI-DPSKLLPLARFLPQPKCSVSHWY 147 (147)
Q Consensus 90 kVdEIFGpi~e~yfsvKl~~g-----I~a~sfk~gdkiyI-~p~KlLpl~rFlp~p~~~~~~~~ 147 (147)
.+++|+-|..|.-.=+|++.+ +.|+++.-++++|| --+-++|.+|-.-.-...++|||
T Consensus 10 ~~~~i~Tp~~es~CG~~l~~~~~keYLlaGrv~~dg~l~itlC~~v~pwd~ls~~qre~~~~~y 73 (141)
T KOG4745|consen 10 DPEFIYTPADESACGLKLDVGGKKEYLLAGRVEGDGKLLITLCDFVVPWDRLSLTQREGLNHWY 73 (141)
T ss_pred CcceecCcccccccceeeecCCcEEEEEeeeecCCCcEEEEeeceEeechhcchHHhcccccee
Confidence 456777788887777777777 56777776888998 45578888876655567778887
No 14
>PF05239 PRC: PRC-barrel domain; InterPro: IPR007903 The PRC-barrel is an all beta barrel domain found in photosynthetic reaction centre subunit H of the purple bacteria. PRC-barrels are approximately 80 residues long, and found widely represented in bacteria, archaea and plants. This domain is also present at the C terminus of the pan-bacterial protein RimM, which is involved in ribosomal maturation and processing of 16S rRNA. A family of small proteins conserved in all known euryarchaea are composed entirely of a single stand-alone copy of the domain [].; PDB: 2QGG_A 3H9N_A 2WJN_H 2PRC_H 5PRC_H 2X5V_H 1DXR_H 1R2C_H 3G7F_H 1PRC_H ....
Probab=65.43 E-value=4.3 Score=26.81 Aligned_cols=33 Identities=21% Similarity=0.268 Sum_probs=24.0
Q ss_pred CCCceeeccceeecccccc-cCccee-c-cEEEEec
Q 032119 76 FNAPIYLQNKTQIGKVDEI-FGPINE-S-YFSVKMM 108 (147)
Q Consensus 76 fNa~Vy~ekk~~IGkVdEI-FGpi~e-~-yfsvKl~ 108 (147)
.+.+||+++-+++|+|+|| |-+... + ++.++..
T Consensus 10 ~g~~V~~~~G~~iG~V~di~id~~~~~i~~i~v~~~ 45 (79)
T PF05239_consen 10 IGKEVIDRDGEKIGKVKDIVIDPKTGKIVGIVVSSG 45 (79)
T ss_dssp TTSEEEETTSCEEEEEEEEEEETTTTEEEEEEEEET
T ss_pred cCCEEEcCCCCEEEEEEEEEEeCCCCCEEEEEEcCC
Confidence 4789999999999999999 554232 2 4555544
No 15
>PF02470 MCE: mce related protein; InterPro: IPR003399 This domain is found in all 24 mce genes associated with the four mammalian cell entry (mce) operons of Mycobacterium tuberculosis and their homologs in other Actinomycetales [, ]. The archetype (mce1A, Rv0169), was isolated as being necessary for colonisation of, and survival within, the macrophage []. The domain is also found in: Chloroplast Ycf22 and related cyanobacterial homologs, the majority of which have an N-terminal transmembrane domain and are putative ABC transporters. Proteobacterial homologs, which include YrbD, YebT, VpsC and Ttg2C, the latter being annotated as a toluene tolerance proteins, belong to the periplasmic substrate-binding ABC transporter superfamily.
Probab=45.02 E-value=88 Score=20.80 Aligned_cols=61 Identities=16% Similarity=0.207 Sum_probs=40.2
Q ss_pred CCcCCCCCceeeccceeecccccc-c-CcceeccEEEEecCcccccccccCCEEEecCCCeeeccccc
Q 032119 71 EKIPYFNAPIYLQNKTQIGKVDEI-F-GPINESYFSVKMMEGIVATSYSLGDKFYIDPSKLLPLARFL 136 (147)
Q Consensus 71 ~~VPyfNa~Vy~ekk~~IGkVdEI-F-Gpi~e~yfsvKl~~gI~a~sfk~gdkiyI~p~KlLpl~rFl 136 (147)
...+ +++|.. +-.+||+|++| | -..+.+.+++++++... ..+..+.++-|....+| -+.|+
T Consensus 14 GL~~--gs~V~~-~Gv~VG~V~~i~l~~~~~~v~v~~~i~~~~~-~~i~~~s~a~i~~~~ll-G~~~i 76 (81)
T PF02470_consen 14 GLSV--GSPVRY-RGVEVGKVTSIELDPDGNRVRVTLRIDPDYW-HRIPDDSRASIRSSGLL-GEKYI 76 (81)
T ss_pred CCCC--cCEEEE-CCEEEEEEEEEEEcCCCCEEEEEEEEcCCcc-eecCCCcEEEEEeCCch-hheEE
Confidence 3566 888887 67899999987 2 33444677777777662 23455777777776666 44443
No 16
>PF10879 DUF2674: Protein of unknown function (DUF2674); InterPro: IPR024246 This family of proteins with unknown function appears to be restricted to Rickettsia spp.
Probab=40.97 E-value=14 Score=25.23 Aligned_cols=47 Identities=23% Similarity=0.462 Sum_probs=24.8
Q ss_pred eeccceeecccccccCcceeccEEEEecCccc-------ccccccCCEEEecCC-Cee
Q 032119 81 YLQNKTQIGKVDEIFGPINESYFSVKMMEGIV-------ATSYSLGDKFYIDPS-KLL 130 (147)
Q Consensus 81 y~ekk~~IGkVdEIFGpi~e~yfsvKl~~gI~-------a~sfk~gdkiyI~p~-KlL 130 (147)
|.|.|..|..+.. .+.|-+.-|||..+-. .-|-.+.+.+||.|. |+|
T Consensus 11 fsehkadierikk---~ieegwaivklvpn~~rfigllekis~~~detiyipprkkii 65 (67)
T PF10879_consen 11 FSEHKADIERIKK---SIEEGWAIVKLVPNKDRFIGLLEKISHAEDETIYIPPRKKII 65 (67)
T ss_pred hhhhhhhHHHHHH---HHhcCeEEEEEccCCcceehhhhhhcCcccCeEecCCccccc
Confidence 4455555544432 3444456666654321 012334889999998 443
No 17
>PF13953 PapC_C: PapC C-terminal domain; PDB: 3L48_E 2XET_A 3RFZ_E 2KT6_A.
Probab=33.22 E-value=67 Score=21.18 Aligned_cols=34 Identities=24% Similarity=0.166 Sum_probs=22.2
Q ss_pred CCcCCCCCceeeccceeecccccccCcceeccEEEEec
Q 032119 71 EKIPYFNAPIYLQNKTQIGKVDEIFGPINESYFSVKMM 108 (147)
Q Consensus 71 ~~VPyfNa~Vy~ekk~~IGkVdEIFGpi~e~yfsvKl~ 108 (147)
.+.+-|++.|++++...+|-|. .--..|++.-..
T Consensus 8 G~~lPfGA~v~~~~g~~~g~Vg----~~G~vyl~~~~~ 41 (68)
T PF13953_consen 8 GKPLPFGASVSDEDGNNIGIVG----QDGQVYLSGLPP 41 (68)
T ss_dssp SEE--TT-EEEETTSSEEEEB-----GCGEEEEEEE-T
T ss_pred CCcCCCCcEEEcCCCCEEEEEc----CCCEEEEECCCC
Confidence 3444599999999999998885 456677766543
No 18
>PF11705 RNA_pol_3_Rpc31: DNA-directed RNA polymerase III subunit Rpc31; InterPro: IPR024661 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA polymerase III-specific, and form the functionally distinct groups: (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in Saccharomyces cerevisiae and Homo sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain []. This entry represents the Rpc31 subunit.
Probab=31.54 E-value=28 Score=28.41 Aligned_cols=7 Identities=43% Similarity=0.411 Sum_probs=3.3
Q ss_pred CCCCCCC
Q 032119 8 GGFRGGR 14 (147)
Q Consensus 8 ~~~~~~~ 14 (147)
|++||||
T Consensus 1 MSgRGgg 7 (233)
T PF11705_consen 1 MSGRGGG 7 (233)
T ss_pred CCCCCCC
Confidence 4445444
No 19
>TIGR02273 16S_RimM 16S rRNA processing protein RimM. This family consists of the bacterial protein RimM (YfjA, 21K), a 30S ribosomal subunit-binding protein implicated in 16S ribsomal RNA processing. It has been partially characterized in Escherichia coli, is found with other translation-associated genes such as trmD. It is broadly distributed among bacteria, including some minimal genomes such the aphid endosymbiont Buchnera aphidicola. The protein contains a PRC-barrel domain that it shares with other protein families (pfam05239) and a unique domain (pfam01782). This model describes the full-length protein. A member from Arabidopsis (plant) has additional N-terminal sequence likely to represent a chloroplast transit peptide.
Probab=30.76 E-value=39 Score=26.03 Aligned_cols=32 Identities=19% Similarity=0.280 Sum_probs=26.8
Q ss_pred CCCceeeccceeecccccccCcceeccEEEEe
Q 032119 76 FNAPIYLQNKTQIGKVDEIFGPINESYFSVKM 107 (147)
Q Consensus 76 fNa~Vy~ekk~~IGkVdEIFGpi~e~yfsvKl 107 (147)
+|-.|++++...+|+|.||+-.-....+.||.
T Consensus 101 iG~~V~d~~~~~lG~V~~v~~~~a~dll~V~~ 132 (165)
T TIGR02273 101 IGLEVVTEEGEELGKVVEILETGANDVLVVRS 132 (165)
T ss_pred CCcEEEcCCCcEEEEEEEEecCCCccEEEEEE
Confidence 57889999889999999998866666788885
No 20
>PF14578 GTP_EFTU_D4: Elongation factor Tu domain 4; PDB: 1G7R_A 1G7S_A 1G7T_A 1XE1_A.
Probab=30.50 E-value=94 Score=22.05 Aligned_cols=72 Identities=15% Similarity=0.228 Sum_probs=34.8
Q ss_pred CCceEEecceeeeeeCCeEEEeccCCCcCCCCCceeeccceeecccccccCcceec-------cEEEEecCccccccccc
Q 032119 46 PPAEVVEVSSFLHACEGDAVTKLTNEKIPYFNAPIYLQNKTQIGKVDEIFGPINES-------YFSVKMMEGIVATSYSL 118 (147)
Q Consensus 46 pp~~vielG~f~H~~eg~lV~K~t~~~VPyfNa~Vy~ekk~~IGkVdEIFGpi~e~-------yfsvKl~~gI~a~sfk~ 118 (147)
||..+.-|=.+.....+.+|.++. .-+-+.|.++ +-..||.|..|==..+++ -+.++++..+ .+++
T Consensus 3 ~p~ki~Ilp~~vFr~~~~IvG~V~-~G~ik~G~~l---~G~~iG~I~sIe~~~k~v~~A~~G~eVai~Ieg~~---~i~e 75 (81)
T PF14578_consen 3 RPGKIRILPVCVFRQSDAIVGEVL-EGIIKPGYPL---DGRKIGRIKSIEDNGKNVDEAKKGDEVAISIEGPT---QIKE 75 (81)
T ss_dssp -SEEEEEEEEEEECTCCEEEEEEE-EEEEETT-EE---CSSCEEEEEEEEETTEEESEEETT-EEEEEEET-----TB-T
T ss_pred CceEEEECCcCEEecCCeEEEEEe-eeEEeCCCcc---CCEEEEEEEEeEECCcCccccCCCCEEEEEEeCCc---cCCC
Confidence 566666554444444444444331 1233447777 334488876441111111 5677777644 6778
Q ss_pred CCEEEe
Q 032119 119 GDKFYI 124 (147)
Q Consensus 119 gdkiyI 124 (147)
+|.||+
T Consensus 76 GDiLyV 81 (81)
T PF14578_consen 76 GDILYV 81 (81)
T ss_dssp T-EEEE
T ss_pred CCEEeC
Confidence 888885
No 21
>PF13865 FoP_duplication: C-terminal duplication domain of Friend of PRMT1
Probab=30.35 E-value=63 Score=22.19 Aligned_cols=9 Identities=33% Similarity=0.637 Sum_probs=4.1
Q ss_pred CCCceEEec
Q 032119 45 GPPAEVVEV 53 (147)
Q Consensus 45 Gpp~~viel 53 (147)
-||....+|
T Consensus 37 ~~~kT~EeL 45 (74)
T PF13865_consen 37 KPPKTAEEL 45 (74)
T ss_pred CCCCCHHHH
Confidence 444444444
No 22
>PHA02809 hypothetical protein; Provisional
Probab=29.96 E-value=52 Score=24.65 Aligned_cols=50 Identities=22% Similarity=0.305 Sum_probs=26.5
Q ss_pred CCCceeeccceeecccccccCcce---------eccEEEEecCccccccc--ccCCEEEecCCCeeec
Q 032119 76 FNAPIYLQNKTQIGKVDEIFGPIN---------ESYFSVKMMEGIVATSY--SLGDKFYIDPSKLLPL 132 (147)
Q Consensus 76 fNa~Vy~ekk~~IGkVdEIFGpi~---------e~yfsvKl~~gI~a~sf--k~gdkiyI~p~KlLpl 132 (147)
||.++|. ++++| +|||.++ +.-+.+|+...-. .| ..=|.=||.|.|+-+-
T Consensus 8 Fnvsl~s-knQkI----~VmGSvpti~e~~P~IDIRI~~K~~~~~~--n~~d~~ydEnfIkP~kv~~d 68 (111)
T PHA02809 8 FNISLNT-TKQKI----EVMGSVPTIDGKDPSIDIRIVSKPNKEKN--NFLDNGYDESFIKPNKVSYD 68 (111)
T ss_pred ceeEeec-ccceE----EEeecCCCCCCCCCceEEEEEEeccCCCC--ccccCcccccccCccccCcc
Confidence 8889998 77776 4555332 2344445433211 22 1134567777775443
No 23
>PLN03138 Protein TOC75; Provisional
Probab=29.73 E-value=48 Score=32.63 Aligned_cols=14 Identities=14% Similarity=0.064 Sum_probs=7.0
Q ss_pred ccccCCEEEecCCC
Q 032119 115 SYSLGDKFYIDPSK 128 (147)
Q Consensus 115 sfk~gdkiyI~p~K 128 (147)
+|+++++..|+.-+
T Consensus 220 ~i~Eg~~~~I~~I~ 233 (796)
T PLN03138 220 SFTESTWQSADSFR 233 (796)
T ss_pred EEEeCCceeeeeee
Confidence 45555555554444
No 24
>PRK14592 rimM 16S rRNA-processing protein RimM; Provisional
Probab=24.66 E-value=66 Score=24.92 Aligned_cols=32 Identities=13% Similarity=0.264 Sum_probs=25.4
Q ss_pred CCCceeeccceeecccccccCcceeccEEEEe
Q 032119 76 FNAPIYLQNKTQIGKVDEIFGPINESYFSVKM 107 (147)
Q Consensus 76 fNa~Vy~ekk~~IGkVdEIFGpi~e~yfsvKl 107 (147)
++-.|++++...+|+|.||+=.-.+-.+.|++
T Consensus 98 iG~~V~~~~g~~lG~V~~v~~~ga~dvlvI~~ 129 (165)
T PRK14592 98 IGMEVKLEDNTIYGYIKKIYNFGSCDIIEISL 129 (165)
T ss_pred CCcEEEcCCCCEEEEEEEEccCCCccEEEEEE
Confidence 57889999989999999998755555577873
No 25
>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]
Probab=23.05 E-value=1.1e+02 Score=30.34 Aligned_cols=11 Identities=27% Similarity=0.495 Sum_probs=6.4
Q ss_pred CeEEEeccCCCcC
Q 032119 62 GDAVTKLTNEKIP 74 (147)
Q Consensus 62 g~lV~K~t~~~VP 74 (147)
+--|++| +.+|
T Consensus 866 Gp~V~~~--~n~P 876 (944)
T KOG4307|consen 866 GPRVLSC--NNFP 876 (944)
T ss_pred CCeEEEe--cCCC
Confidence 4446666 5667
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=22.62 E-value=80 Score=23.69 Aligned_cols=26 Identities=15% Similarity=0.331 Sum_probs=22.1
Q ss_pred CCCCCCceEEecceeeeeeCCeEEEe
Q 032119 42 RDEGPPAEVVEVSSFLHACEGDAVTK 67 (147)
Q Consensus 42 ~~~Gpp~~vielG~f~H~~eg~lV~K 67 (147)
-+.|+|+-.+-+|++.|..++++-+-
T Consensus 17 i~lG~~~gk~V~G~I~hvv~ddLYID 42 (104)
T PF10246_consen 17 IQLGDPEGKIVIGKIFHVVDDDLYID 42 (104)
T ss_pred hhcCCccCCEEEEEEEEEecCceEEE
Confidence 46788999999999999999877654
No 27
>PRK13828 rimM 16S rRNA-processing protein RimM; Provisional
Probab=22.43 E-value=73 Score=24.65 Aligned_cols=32 Identities=6% Similarity=0.056 Sum_probs=25.5
Q ss_pred CCCceeeccceeecccccccCcceeccEEEEe
Q 032119 76 FNAPIYLQNKTQIGKVDEIFGPINESYFSVKM 107 (147)
Q Consensus 76 fNa~Vy~ekk~~IGkVdEIFGpi~e~yfsvKl 107 (147)
++-.|++++...+|+|.+|+-.-.+-.+.||.
T Consensus 86 iG~~V~d~~g~~lG~V~~V~~~ga~dvlvV~~ 117 (161)
T PRK13828 86 IGLAAVDTGGALLGRVKAVHNFGAGDILEIAP 117 (161)
T ss_pred cCCEEEeCCCCEEEEEEEEccCCCccEEEEEE
Confidence 57899999989999999998755445568874
No 28
>PRK00122 rimM 16S rRNA-processing protein RimM; Provisional
Probab=22.00 E-value=81 Score=24.47 Aligned_cols=31 Identities=16% Similarity=0.259 Sum_probs=24.7
Q ss_pred CCCceeeccceeecccccccCcceeccEEEE
Q 032119 76 FNAPIYLQNKTQIGKVDEIFGPINESYFSVK 106 (147)
Q Consensus 76 fNa~Vy~ekk~~IGkVdEIFGpi~e~yfsvK 106 (147)
+|-.|++++...+|+|.+|+=.-.+..+.||
T Consensus 106 iG~~V~d~~g~~lG~V~~v~~~~a~dll~I~ 136 (172)
T PRK00122 106 IGLEVVDEDGEELGKVTDILETGANDVLVVL 136 (172)
T ss_pred CCcEEEeCCCcEEEEEEEEccCCCceEEEEE
Confidence 5788999988899999998775555567776
No 29
>PF06068 TIP49: TIP49 C-terminus; InterPro: IPR010339 This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins. The N-terminal domain contains the AAA ATPase, central region IPR003959 from INTERPRO domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway []. TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities. TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases [].; GO: 0003678 DNA helicase activity, 0005524 ATP binding; PDB: 2XSZ_E 2CQA_A 2C9O_C.
Probab=21.92 E-value=28 Score=31.65 Aligned_cols=34 Identities=32% Similarity=0.639 Sum_probs=19.2
Q ss_pred ccccccccCCEEEecCC--Ce--------------eecccccCCCCCCCC
Q 032119 111 IVATSYSLGDKFYIDPS--KL--------------LPLARFLPQPKCSVS 144 (147)
Q Consensus 111 I~a~sfk~gdkiyI~p~--Kl--------------Lpl~rFlp~p~~~~~ 144 (147)
+....+++||.|||+.. ++ ++-++|.|-|+|.|.
T Consensus 166 l~kekV~~GDVI~Id~~tG~V~k~Grs~~~~~~~D~~~~~~V~~P~Gev~ 215 (398)
T PF06068_consen 166 LQKEKVRVGDVIYIDKNTGRVKKVGRSDSYAKDYDLEATKFVPCPKGEVH 215 (398)
T ss_dssp HHHTT--TTCEEEEETTTTEEEEEEEECCCS-TTSECCTTEE---SS-SE
T ss_pred HHHhCCccCcEEEEECCCCeEEEEecccchhhccccccceEeeCCCCcce
Confidence 33446778999999876 22 455678888888763
No 30
>COG4371 Predicted membrane protein [Function unknown]
Probab=21.36 E-value=1.5e+02 Score=26.00 Aligned_cols=8 Identities=50% Similarity=0.999 Sum_probs=4.1
Q ss_pred CCCCCCCC
Q 032119 7 GGGFRGGR 14 (147)
Q Consensus 7 ~~~~~~~~ 14 (147)
+++||...
T Consensus 55 GgSfraps 62 (334)
T COG4371 55 GGSFRAPS 62 (334)
T ss_pred CCCCCCCC
Confidence 45555544
No 31
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=20.48 E-value=1.4e+02 Score=21.01 Aligned_cols=22 Identities=23% Similarity=0.484 Sum_probs=9.3
Q ss_pred eeecccccccCcceeccEEEEecCc
Q 032119 86 TQIGKVDEIFGPINESYFSVKMMEG 110 (147)
Q Consensus 86 ~~IGkVdEIFGpi~e~yfsvKl~~g 110 (147)
+.+++|.+.+| +-.|.|+++++
T Consensus 6 q~~g~V~~~lG---~~~~~V~~~dG 27 (83)
T smart00652 6 QEIAQVVKMLG---NGRLEVMCADG 27 (83)
T ss_pred cEEEEEEEEcC---CCEEEEEECCC
Confidence 44444444433 22344444443
No 32
>COG3881 PRC-barrel domain containing protein [General function prediction only]
Probab=20.08 E-value=85 Score=25.52 Aligned_cols=19 Identities=32% Similarity=0.690 Sum_probs=15.8
Q ss_pred CCCceeecc-ceeecccccc
Q 032119 76 FNAPIYLQN-KTQIGKVDEI 94 (147)
Q Consensus 76 fNa~Vy~ek-k~~IGkVdEI 94 (147)
.+.|||.++ -.++|.|+||
T Consensus 8 eG~pVys~~tg~~lg~V~Dv 27 (176)
T COG3881 8 EGAPVYSTKTGEKLGAVDDV 27 (176)
T ss_pred cCCceEEecccccccceeeE
Confidence 388999988 7899999874
Done!