Query 032083
Match_columns 147
No_of_seqs 132 out of 307
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 09:23:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032083.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032083hhsearch_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 4.9E-56 1.1E-60 357.6 9.6 139 1-140 1-143 (215)
2 PRK13149 H/ACA RNA-protein com 99.9 9E-28 2E-32 167.2 8.1 72 50-125 1-73 (73)
3 COG3277 GAR1 RNA-binding prote 99.9 2.9E-27 6.2E-32 173.7 8.5 92 50-141 1-92 (98)
4 PF04410 Gar1: Gar1/Naf1 RNA b 99.9 2E-26 4.4E-31 178.8 7.6 99 41-142 14-115 (154)
5 KOG1596 Fibrillarin and relate 99.4 2.4E-13 5.3E-18 115.2 6.6 72 45-131 79-162 (317)
6 PTZ00146 fibrillarin; Provisio 99.4 1.2E-12 2.6E-17 111.7 7.7 62 43-115 51-125 (293)
7 KOG2236 Uncharacterized conser 98.8 5.8E-09 1.3E-13 93.9 4.0 78 49-126 207-287 (483)
8 PF01269 Fibrillarin: Fibrilla 97.4 1.7E-05 3.7E-10 66.2 -1.9 52 57-115 3-66 (229)
9 COG1889 NOP1 Fibrillarin-like 96.2 0.0016 3.4E-08 54.5 0.8 50 59-115 11-69 (231)
10 PTZ00146 fibrillarin; Provisio 91.9 0.28 6E-06 42.4 4.7 16 52-67 64-80 (293)
11 PF05239 PRC: PRC-barrel domai 87.6 1.4 3E-05 29.3 4.5 33 76-108 10-45 (79)
12 PRK04266 fibrillarin; Provisio 78.5 1.7 3.7E-05 35.6 2.4 60 55-121 3-75 (226)
13 PF02470 MCE: mce related prot 76.6 19 0.00042 24.1 6.9 60 72-136 15-76 (81)
14 TIGR02273 16S_RimM 16S rRNA pr 63.7 9.6 0.00021 29.5 3.5 33 75-107 100-132 (165)
15 PRK00122 rimM 16S rRNA-process 56.7 16 0.00035 28.4 3.7 32 75-106 105-136 (172)
16 PRK14592 rimM 16S rRNA-process 55.5 17 0.00038 28.2 3.7 32 76-107 98-129 (165)
17 PRK13828 rimM 16S rRNA-process 53.9 18 0.00039 28.1 3.5 33 75-107 85-117 (161)
18 PRK13829 rimM 16S rRNA-process 53.1 21 0.00045 27.8 3.7 34 76-110 95-128 (162)
19 PRK14591 rimM 16S rRNA-process 48.4 24 0.00053 27.6 3.5 32 76-107 106-137 (169)
20 COG0809 QueA S-adenosylmethion 47.3 53 0.0011 29.5 5.7 59 61-127 52-113 (348)
21 PF08669 GCV_T_C: Glycine clea 40.6 1.2E+02 0.0025 20.7 6.0 54 69-125 28-82 (95)
22 COG0806 RimM RimM protein, req 39.9 38 0.00082 27.2 3.4 32 76-107 107-138 (174)
23 PF09939 DUF2171: Uncharacteri 39.8 65 0.0014 22.3 4.1 40 77-125 5-44 (67)
24 KOG1596 Fibrillarin and relate 38.8 57 0.0012 28.6 4.5 14 89-102 172-185 (317)
25 PF13953 PapC_C: PapC C-termin 38.4 36 0.00078 22.6 2.6 23 70-92 7-29 (68)
26 PRK14594 rimM 16S rRNA-process 35.9 52 0.0011 25.7 3.6 31 76-107 103-133 (166)
27 PRK14593 rimM 16S rRNA-process 34.8 1E+02 0.0022 24.4 5.1 33 75-108 109-141 (184)
28 PF14578 GTP_EFTU_D4: Elongati 34.8 1.1E+02 0.0025 21.7 4.9 72 46-124 3-81 (81)
29 PRK14590 rimM 16S rRNA-process 33.4 68 0.0015 25.2 3.9 31 76-106 103-134 (171)
30 cd03698 eRF3_II_like eRF3_II_l 30.1 97 0.0021 20.9 3.8 15 114-128 25-39 (83)
31 PRK12442 translation initiatio 28.9 1.1E+02 0.0024 22.3 4.0 21 89-112 11-31 (87)
32 cd04717 BAH_polybromo BAH, or 27.8 79 0.0017 22.9 3.2 20 86-105 21-41 (121)
33 COG1255 Uncharacterized protei 27.6 16 0.00034 28.4 -0.6 38 89-126 55-102 (129)
34 PF11705 RNA_pol_3_Rpc31: DNA- 26.8 38 0.00083 27.7 1.5 7 8-14 1-7 (233)
35 smart00652 eIF1a eukaryotic tr 26.6 1.3E+02 0.0028 21.2 4.0 27 83-112 3-29 (83)
36 COG3881 PRC-barrel domain cont 26.4 1E+02 0.0022 25.2 3.7 34 76-109 8-43 (176)
37 PF13865 FoP_duplication: C-te 25.5 83 0.0018 21.6 2.8 9 45-53 37-45 (74)
38 PRK00122 rimM 16S rRNA-process 25.0 1.2E+02 0.0027 23.5 4.0 86 47-132 4-95 (172)
39 PLN03138 Protein TOC75; Provis 23.6 73 0.0016 31.5 2.9 13 116-128 221-233 (796)
40 PHA02142 putative RNA ligase 23.4 50 0.0011 29.7 1.7 20 114-133 42-62 (366)
41 PHA01365 hypothetical protein 22.7 1.6E+02 0.0035 21.5 3.9 44 87-130 32-80 (91)
42 PF10246 MRP-S35: Mitochondria 22.6 85 0.0019 23.6 2.5 26 42-67 17-42 (104)
43 TIGR00008 infA translation ini 21.6 1.8E+02 0.0039 20.1 3.8 24 88-114 8-31 (68)
44 COG4353 Uncharacterized conser 20.3 45 0.00097 27.4 0.7 30 63-92 15-45 (192)
45 cd03694 GTPBP_II Domain II of 20.2 1E+02 0.0022 21.1 2.4 15 113-127 24-38 (87)
46 cd04716 BAH_plantDCM_I BAH, or 20.1 1.4E+02 0.003 22.5 3.2 11 88-98 22-32 (122)
47 cd04714 BAH_BAHCC1 BAH, or Bro 20.1 1.5E+02 0.0033 21.8 3.5 20 87-106 22-42 (121)
No 1
>KOG3262 consensus H/ACA small nucleolar RNP component GAR1 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.9e-56 Score=357.63 Aligned_cols=139 Identities=66% Similarity=1.136 Sum_probs=117.2
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCC---CCCCCCCCCCCCCC-CCCCCCCCCCceEEeceeeeeeeCCeEEEeccCCCCCCC
Q 032083 1 MRPPRGGGGFRGGRDGGRGGRGG---GRFGGGGRGGGGRG-GFGFRDEGPPAEVVEVSSFLHACEGDAVTKLTNEKIPYF 76 (147)
Q Consensus 1 ~~~~~~~~~~~~~~~g~~g~~~~---g~~~gg~~ggrgg~-~~~~~~~Gpp~~vielG~f~H~ceg~lV~K~t~~~VP~f 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 78899987776664 22333222 23333332234332 234579999999999999999999999999999999999
Q ss_pred CCceeeccccccceeeEeeCCCCcceEEEEecCCccccccCCCCEEEEcCCCcccccccCCCCC
Q 032083 77 NAPIYLQNKTQIGKVDEIFGPINESYFSVKMMEGIVATSYSLGDKFYIDPSKLLPLARFLPQPK 140 (147)
Q Consensus 77 Na~Vy~enK~~IGKVdEIFGPi~~~yfsVKl~~gi~a~sfk~gdk~yI~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=99.95 E-value=9e-28 Score=167.17 Aligned_cols=72 Identities=29% Similarity=0.560 Sum_probs=68.9
Q ss_pred EEeceeeeeee-CCeEEEeccCCCCCCCCCceeeccccccceeeEeeCCCCcceEEEEecCCccccccCCCCEEEEc
Q 032083 50 VVEVSSFLHAC-EGDAVTKLTNEKIPYFNAPIYLQNKTQIGKVDEIFGPINESYFSVKMMEGIVATSYSLGDKFYID 125 (147)
Q Consensus 50 vielG~f~H~c-eg~lV~K~t~~~VP~fNa~Vy~enK~~IGKVdEIFGPi~~~yfsVKl~~gi~a~sfk~gdk~yI~ 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 78999999 78999999999999999999999999999999999999999997 899999984
No 3
>COG3277 GAR1 RNA-binding protein involved in rRNA processing [Translation, ribosomal structure and biogenesis]
Probab=99.94 E-value=2.9e-27 Score=173.66 Aligned_cols=92 Identities=38% Similarity=0.631 Sum_probs=88.2
Q ss_pred EEeceeeeeeeCCeEEEeccCCCCCCCCCceeeccccccceeeEeeCCCCcceEEEEecCCccccccCCCCEEEEcCCCc
Q 032083 50 VVEVSSFLHACEGDAVTKLTNEKIPYFNAPIYLQNKTQIGKVDEIFGPINESYFSVKMMEGIVATSYSLGDKFYIDPSKL 129 (147)
Q Consensus 50 vielG~f~H~ceg~lV~K~t~~~VP~fNa~Vy~enK~~IGKVdEIFGPi~~~yfsVKl~~gi~a~sfk~gdk~yI~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 46899999999999999988789999999999999999999999999999999999999999988899999999999999
Q ss_pred ccccccCCCCCC
Q 032083 130 LPLARFLPQPKI 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 999999999886
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=99.93 E-value=2e-26 Score=178.75 Aligned_cols=99 Identities=43% Similarity=0.745 Sum_probs=82.3
Q ss_pred CCCCCCCceEEeceeeeeeeCCeEEEeccCC-CCCCCCCceeeccccccceeeEeeCCCCcceEEEE--ecCCccccccC
Q 032083 41 FRDEGPPAEVVEVSSFLHACEGDAVTKLTNE-KIPYFNAPIYLQNKTQIGKVDEIFGPINESYFSVK--MMEGIVATSYS 117 (147)
Q Consensus 41 ~~~~Gpp~~vielG~f~H~ceg~lV~K~t~~-~VP~fNa~Vy~enK~~IGKVdEIFGPi~~~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 CCCEEEEcCCCcccccccCCCCCCC
Q 032083 118 LGDKFYIDPSKLLPLARFLPQPKIV 142 (147)
Q Consensus 118 ~gdk~yI~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 9999999999 999999988754
No 5
>KOG1596 consensus Fibrillarin and related nucleolar RNA-binding proteins [RNA processing and modification]
Probab=99.42 E-value=2.4e-13 Score=115.23 Aligned_cols=72 Identities=31% Similarity=0.570 Sum_probs=63.5
Q ss_pred CCCceEEeceeeeeeeCCeEEEec------cCCCCCCCCCceeecccccc----ceee-EeeCCCCcceEEEEecCCccc
Q 032083 45 GPPAEVVEVSSFLHACEGDAVTKL------TNEKIPYFNAPIYLQNKTQI----GKVD-EIFGPINESYFSVKMMEGIVA 113 (147)
Q Consensus 45 Gpp~~vielG~f~H~ceg~lV~K~------t~~~VP~fNa~Vy~enK~~I----GKVd-EIFGPi~~~yfsVKl~~gi~a 113 (147)
+..+.++|. |.+.+++|+|. |.|.|| ++.||.|++..+ +||+ +||+| |++||+++|..
T Consensus 79 gG~~v~vEP----HRh~GVfi~rgkeDaLvTkNlvp--ge~vYgEkRisv~~~~~kvEyRVWnP-----frSKLAA~I~g 147 (317)
T KOG1596|consen 79 GGSKVLVEP----HRHAGVFIARGKEDALVTKNLVP--GESVYGEKRISVENEDGKVEYRVWNP-----FRSKLAAGILG 147 (317)
T ss_pred CCceEEecc----ccccceEEEcCchhheeecccCC--cccccCceEEEeecCCCcEEEEEeCh-----HHHHHHHHhhc
Confidence 467778887 99999999995 889999 999999999987 7898 99999 99999999999
Q ss_pred cccCCCCEEEEcC-CCccc
Q 032083 114 TSYSLGDKFYIDP-SKLLP 131 (147)
Q Consensus 114 ~sfk~gdk~yI~p-~klLP 131 (147)
.. |.+||.| .|+|=
T Consensus 148 Gv----dnihikpGsKVLY 162 (317)
T KOG1596|consen 148 GV----DNIHIKPGSKVLY 162 (317)
T ss_pred Cc----cceeecCCceEEE
Confidence 88 9999988 45553
No 6
>PTZ00146 fibrillarin; Provisional
Probab=99.37 E-value=1.2e-12 Score=111.71 Aligned_cols=62 Identities=23% Similarity=0.515 Sum_probs=50.6
Q ss_pred CCCCCceEEeceeeeeeeCCeEEEe------ccCCCCCCCCCceeeccccccc------eee-EeeCCCCcceEEEEecC
Q 032083 43 DEGPPAEVVEVSSFLHACEGDAVTK------LTNEKIPYFNAPIYLQNKTQIG------KVD-EIFGPINESYFSVKMME 109 (147)
Q Consensus 43 ~~Gpp~~vielG~f~H~ceg~lV~K------~t~~~VP~fNa~Vy~enK~~IG------KVd-EIFGPi~~~yfsVKl~~ 109 (147)
..++.+.+++. |.+++.++++ +|.|++| +.+||.|+..++. +++ ++|+| |++||++
T Consensus 51 ~~~~~~~~~~~----~~~~gv~~~~~~~~~l~t~n~~p--g~~vygek~~~~~~~~~~~~~eyR~w~p-----~rSKlaa 119 (293)
T PTZ00146 51 GGGPGKVIVVP----HRFPGVFIAKGKSDALVTKNMVP--GESVYGEKRISVEDAEGGEKIEYRVWNP-----FRSKLAA 119 (293)
T ss_pred CCCCCceEEee----eeecCEEEeecCCceeEeecCCC--CcccccceEEeeccCCCCCcceeeeeCC-----cccHHHH
Confidence 33456777766 8899999997 3889999 9999999998876 555 99999 9999998
Q ss_pred Cccccc
Q 032083 110 GIVATS 115 (147)
Q Consensus 110 gi~a~s 115 (147)
+|....
T Consensus 120 ~i~~g~ 125 (293)
T PTZ00146 120 AIIGGV 125 (293)
T ss_pred HHHCCc
Confidence 876553
No 7
>KOG2236 consensus Uncharacterized conserved protein [Function unknown]
Probab=98.76 E-value=5.8e-09 Score=93.86 Aligned_cols=78 Identities=22% Similarity=0.484 Sum_probs=70.6
Q ss_pred eEEeceeeeeeeCCeEEEeccCCCCC-CCCCceeeccccccceeeEeeCCCCcceEEEEecCCcccc--ccCCCCEEEEc
Q 032083 49 EVVEVSSFLHACEGDAVTKLTNEKIP-YFNAPIYLQNKTQIGKVDEIFGPINESYFSVKMMEGIVAT--SYSLGDKFYID 125 (147)
Q Consensus 49 ~vielG~f~H~ceg~lV~K~t~~~VP-~fNa~Vy~enK~~IGKVdEIFGPi~~~yfsVKl~~gi~a~--sfk~gdk~yI~ 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 68889999999999999999888655 6899999999999999999999999999999998877766 66789999998
Q ss_pred C
Q 032083 126 P 126 (147)
Q Consensus 126 p 126 (147)
|
T Consensus 287 p 287 (483)
T KOG2236|consen 287 P 287 (483)
T ss_pred C
Confidence 8
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=97.40 E-value=1.7e-05 Score=66.25 Aligned_cols=52 Identities=19% Similarity=0.404 Sum_probs=37.8
Q ss_pred ee-eeCCeEEEe------ccCCCCCCCCCceeeccccccce-----eeEeeCCCCcceEEEEecCCccccc
Q 032083 57 LH-ACEGDAVTK------LTNEKIPYFNAPIYLQNKTQIGK-----VDEIFGPINESYFSVKMMEGIVATS 115 (147)
Q Consensus 57 ~H-~ceg~lV~K------~t~~~VP~fNa~Vy~enK~~IGK-----VdEIFGPi~~~yfsVKl~~gi~a~s 115 (147)
.| .+++.++++ +|.|++| +.+||.|+...+.. -+++|+| |++||+++|....
T Consensus 3 ~h~~~~gvy~~~~~~~~l~T~n~~p--g~~vYGEk~i~~~~~~~~~eYR~W~P-----~RSKLaAai~~Gl 66 (229)
T PF01269_consen 3 PHERFEGVYIARGKGDALATKNLVP--GESVYGEKRISVEGEGKKVEYRVWNP-----FRSKLAAAILKGL 66 (229)
T ss_dssp EEESSTTEEEEETTSTEEEEE-SST--T--SSSSEEEEETTE---EEEEEE-T-----TT-HHHHHHHTT-
T ss_pred ceeeecCEEEEecCCCeEEEecCCC--CCcccCceeEeecCCCCccceeecCc-----hhhHHHHHHHcCc
Confidence 47 788888887 3788999 99999999988744 3499999 9999999887654
No 9
>COG1889 NOP1 Fibrillarin-like rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=96.23 E-value=0.0016 Score=54.53 Aligned_cols=50 Identities=16% Similarity=0.272 Sum_probs=40.2
Q ss_pred eeCCeEEEec--------cCCCCCCCCCceeecccccccee-eEeeCCCCcceEEEEecCCccccc
Q 032083 59 ACEGDAVTKL--------TNEKIPYFNAPIYLQNKTQIGKV-DEIFGPINESYFSVKMMEGIVATS 115 (147)
Q Consensus 59 ~ceg~lV~K~--------t~~~VP~fNa~Vy~enK~~IGKV-dEIFGPi~~~yfsVKl~~gi~a~s 115 (147)
..++..+++. |.|.+| +.+||.|+..++.-- +++|+| +++||+++|....
T Consensus 11 ~~~gvy~~~~~dg~~~l~T~nl~p--g~~VYGE~ii~~~~~eYR~Wnp-----~RSKLaAaIl~Gl 69 (231)
T COG1889 11 RFEGVYIVRFKDGSDRLATKNLVP--GERVYGERIIKVEGEEYREWNP-----RRSKLAAAILKGL 69 (231)
T ss_pred ccCCeEEEEcccccceeeeecCCC--CccccCceeEEecCcceeeeCc-----chhHHHHHHHcCc
Confidence 3556555542 678899 999999999999666 699999 9999999888653
No 10
>PTZ00146 fibrillarin; Provisional
Probab=91.92 E-value=0.28 Score=42.41 Aligned_cols=16 Identities=25% Similarity=0.194 Sum_probs=7.5
Q ss_pred eceeeeeeeC-CeEEEe
Q 032083 52 EVSSFLHACE-GDAVTK 67 (147)
Q Consensus 52 elG~f~H~ce-g~lV~K 67 (147)
.-|.|..... +.|+.+
T Consensus 64 ~~gv~~~~~~~~~l~t~ 80 (293)
T PTZ00146 64 FPGVFIAKGKSDALVTK 80 (293)
T ss_pred ecCEEEeecCCceeEee
Confidence 4455655432 334444
No 11
>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=87.61 E-value=1.4 Score=29.26 Aligned_cols=33 Identities=21% Similarity=0.288 Sum_probs=24.8
Q ss_pred CCCceeeccccccceeeEe-eCCCC-cc-eEEEEec
Q 032083 76 FNAPIYLQNKTQIGKVDEI-FGPIN-ES-YFSVKMM 108 (147)
Q Consensus 76 fNa~Vy~enK~~IGKVdEI-FGPi~-~~-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 77743 33 3455544
No 12
>PRK04266 fibrillarin; Provisional
Probab=78.53 E-value=1.7 Score=35.58 Aligned_cols=60 Identities=18% Similarity=0.221 Sum_probs=42.6
Q ss_pred eeeeeeCCeEEEec--------cCCCCCCCCCceeecccccc-ceeeEeeCCCCcceEEEEecCCccc----cccCCCCE
Q 032083 55 SFLHACEGDAVTKL--------TNEKIPYFNAPIYLQNKTQI-GKVDEIFGPINESYFSVKMMEGIVA----TSYSLGDK 121 (147)
Q Consensus 55 ~f~H~ceg~lV~K~--------t~~~VP~fNa~Vy~enK~~I-GKVdEIFGPi~~~yfsVKl~~gi~a----~sfk~gdk 121 (147)
+.+|.+++.++++. |.+.+| +..+|.+.-... +.-..+|-| ++.|++..+.+ -.++++++
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~g~~~~~~~~~~~~~~~~-----~r~~~~~~ll~~~~~l~i~~g~~ 75 (226)
T PRK04266 3 KKKEIFEGVYEVEFEDGSKRLATKNLVP--GKRVYGERLIKWEGVEYREWNP-----RRSKLAAAILKGLKNFPIKKGSK 75 (226)
T ss_pred ccccccCCEEEEecCCCcceEeeecCCC--CCCCCCceEEecCCcEEEEECC-----CccchHHHHHhhHhhCCCCCCCE
Confidence 35688888888873 778999 888888666544 444589998 67788887776 33445554
No 13
>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=76.58 E-value=19 Score=24.11 Aligned_cols=60 Identities=17% Similarity=0.215 Sum_probs=43.7
Q ss_pred CCCCCCCceeeccccccceeeEe-e-CCCCcceEEEEecCCccccccCCCCEEEEcCCCcccccccC
Q 032083 72 KIPYFNAPIYLQNKTQIGKVDEI-F-GPINESYFSVKMMEGIVATSYSLGDKFYIDPSKLLPLARFL 136 (147)
Q Consensus 72 ~VP~fNa~Vy~enK~~IGKVdEI-F-GPi~~~yfsVKl~~gi~a~sfk~gdk~yI~p~klLPl~rFl 136 (147)
..+ +++|.. +-.+||+|++| | -.-+.+.+++++++... ..+..+.++-|....+| =+.|+
T Consensus 15 L~~--gs~V~~-~Gv~VG~V~~i~l~~~~~~v~v~~~i~~~~~-~~i~~~s~a~i~~~~ll-G~~~i 76 (81)
T PF02470_consen 15 LSV--GSPVRY-RGVEVGKVTSIELDPDGNRVRVTLRIDPDYW-HRIPDDSRASIRSSGLL-GEKYI 76 (81)
T ss_pred CCC--cCEEEE-CCEEEEEEEEEEEcCCCCEEEEEEEEcCCcc-eecCCCcEEEEEeCCch-hheEE
Confidence 455 888888 67899999988 3 44466788888888762 24566788888887777 44443
No 14
>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=63.69 E-value=9.6 Score=29.45 Aligned_cols=33 Identities=18% Similarity=0.271 Sum_probs=29.0
Q ss_pred CCCCceeeccccccceeeEeeCCCCcceEEEEe
Q 032083 75 YFNAPIYLQNKTQIGKVDEIFGPINESYFSVKM 107 (147)
Q Consensus 75 ~fNa~Vy~enK~~IGKVdEIFGPi~~~yfsVKl 107 (147)
.++..|++++...+|+|.||+-.-.+..+.||.
T Consensus 100 LiG~~V~d~~~~~lG~V~~v~~~~a~dll~V~~ 132 (165)
T TIGR02273 100 LIGLEVVTEEGEELGKVVEILETGANDVLVVRS 132 (165)
T ss_pred hCCcEEEcCCCcEEEEEEEEecCCCccEEEEEE
Confidence 367899999989999999999988888899986
No 15
>PRK00122 rimM 16S rRNA-processing protein RimM; Provisional
Probab=56.72 E-value=16 Score=28.41 Aligned_cols=32 Identities=16% Similarity=0.251 Sum_probs=27.5
Q ss_pred CCCCceeeccccccceeeEeeCCCCcceEEEE
Q 032083 75 YFNAPIYLQNKTQIGKVDEIFGPINESYFSVK 106 (147)
Q Consensus 75 ~fNa~Vy~enK~~IGKVdEIFGPi~~~yfsVK 106 (147)
.++..||+++...+|+|.+|+-.-.+..+.||
T Consensus 105 LiG~~V~d~~g~~lG~V~~v~~~~a~dll~I~ 136 (172)
T PRK00122 105 LIGLEVVDEDGEELGKVTDILETGANDVLVVL 136 (172)
T ss_pred hCCcEEEeCCCcEEEEEEEEccCCCceEEEEE
Confidence 36889999988999999999987777778887
No 16
>PRK14592 rimM 16S rRNA-processing protein RimM; Provisional
Probab=55.48 E-value=17 Score=28.23 Aligned_cols=32 Identities=13% Similarity=0.264 Sum_probs=27.3
Q ss_pred CCCceeeccccccceeeEeeCCCCcceEEEEe
Q 032083 76 FNAPIYLQNKTQIGKVDEIFGPINESYFSVKM 107 (147)
Q Consensus 76 fNa~Vy~enK~~IGKVdEIFGPi~~~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 57899999999999999999877666688883
No 17
>PRK13828 rimM 16S rRNA-processing protein RimM; Provisional
Probab=53.91 E-value=18 Score=28.09 Aligned_cols=33 Identities=6% Similarity=0.055 Sum_probs=27.2
Q ss_pred CCCCceeeccccccceeeEeeCCCCcceEEEEe
Q 032083 75 YFNAPIYLQNKTQIGKVDEIFGPINESYFSVKM 107 (147)
Q Consensus 75 ~fNa~Vy~enK~~IGKVdEIFGPi~~~yfsVKl 107 (147)
.++..|++++...+|+|.+|+-.-.+-.+.||.
T Consensus 85 LiG~~V~d~~g~~lG~V~~V~~~ga~dvlvV~~ 117 (161)
T PRK13828 85 LIGLAAVDTGGALLGRVKAVHNFGAGDILEIAP 117 (161)
T ss_pred ccCCEEEeCCCCEEEEEEEEccCCCccEEEEEE
Confidence 357899999999999999999866556678884
No 18
>PRK13829 rimM 16S rRNA-processing protein RimM; Provisional
Probab=53.09 E-value=21 Score=27.84 Aligned_cols=34 Identities=15% Similarity=0.369 Sum_probs=27.3
Q ss_pred CCCceeeccccccceeeEeeCCCCcceEEEEecCC
Q 032083 76 FNAPIYLQNKTQIGKVDEIFGPINESYFSVKMMEG 110 (147)
Q Consensus 76 fNa~Vy~enK~~IGKVdEIFGPi~~~yfsVKl~~g 110 (147)
.+..|| ++...+|+|.+|+-.-.+-++.||..++
T Consensus 95 iG~~V~-~~g~~lG~V~~v~~~ga~dvlvV~~~~~ 128 (162)
T PRK13829 95 RGLPVY-VDGEPLGEVVDVEDAGAQDLLVIRHVGG 128 (162)
T ss_pred cCeEEE-ECCEeeEEEEEEecCCCceEEEEEeCCC
Confidence 577899 8888999999999876666678886543
No 19
>PRK14591 rimM 16S rRNA-processing protein RimM; Provisional
Probab=48.38 E-value=24 Score=27.56 Aligned_cols=32 Identities=16% Similarity=0.148 Sum_probs=26.7
Q ss_pred CCCceeeccccccceeeEeeCCCCcceEEEEe
Q 032083 76 FNAPIYLQNKTQIGKVDEIFGPINESYFSVKM 107 (147)
Q Consensus 76 fNa~Vy~enK~~IGKVdEIFGPi~~~yfsVKl 107 (147)
++..||+++...+|+|.+|+-.-.+..+.||.
T Consensus 106 iG~~V~d~~g~~lG~V~~v~~~ga~dll~I~~ 137 (169)
T PRK14591 106 IGCSVKNINNDSFGVVVDIIETGANEVLVCKE 137 (169)
T ss_pred cCcEEEeCCCCEEEEEEEEeecCCceEEEEEc
Confidence 57899999999999999999877666677874
No 20
>COG0809 QueA S-adenosylmethionine:tRNA-ribosyltransferase-isomerase (queuine synthetase) [Translation, ribosomal structure and biogenesis]
Probab=47.33 E-value=53 Score=29.46 Aligned_cols=59 Identities=24% Similarity=0.258 Sum_probs=38.1
Q ss_pred CCeEEEeccCCCCCCCCCceeeccccccceee---EeeCCCCcceEEEEecCCccccccCCCCEEEEcCC
Q 032083 61 EGDAVTKLTNEKIPYFNAPIYLQNKTQIGKVD---EIFGPINESYFSVKMMEGIVATSYSLGDKFYIDPS 127 (147)
Q Consensus 61 eg~lV~K~t~~~VP~fNa~Vy~enK~~IGKVd---EIFGPi~~~yfsVKl~~gi~a~sfk~gdk~yI~p~ 127 (147)
++|++|-....-+| |.+|..+...-++|+ +=+=..|..-..+|++. .+|+||+||...+
T Consensus 52 ~GD~LVfNdTrVIp---ARl~G~k~~~g~~vEvll~~~~~~~~w~al~~~~k-----r~k~G~~i~f~~~ 113 (348)
T COG0809 52 PGDLLVFNDTRVIP---ARLFGRKHESGGKVEVLLERRLDDNRWLALIKPSK-----RLKAGDEIYFGDG 113 (348)
T ss_pred CCCEEEEecCeeec---hheeeccCCCCceEEEEEEeecCCCcEEEEecccc-----CCCCCCEEEeCCC
Confidence 35566644333344 888887766778877 22334466667888665 5677899998875
No 21
>PF08669 GCV_T_C: Glycine cleavage T-protein C-terminal barrel domain; InterPro: IPR013977 This entry shows glycine cleavage T-proteins, part of the glycine cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes. GCV catalyses the catabolism of glycine in eukaryotes. The T-protein is an aminomethyl transferase. ; PDB: 3ADA_A 1VRQ_A 1X31_A 3AD9_A 3AD8_A 3AD7_A 3GIR_A 1WOO_A 1WOS_A 1WOR_A ....
Probab=40.58 E-value=1.2e+02 Score=20.73 Aligned_cols=54 Identities=13% Similarity=0.332 Sum_probs=35.8
Q ss_pred cCCCCCCCCCceeeccccccceee-EeeCCCCcceEEEEecCCccccccCCCCEEEEc
Q 032083 69 TNEKIPYFNAPIYLQNKTQIGKVD-EIFGPINESYFSVKMMEGIVATSYSLGDKFYID 125 (147)
Q Consensus 69 t~~~VP~fNa~Vy~enK~~IGKVd-EIFGPi~~~yfsVKl~~gi~a~sfk~gdk~yI~ 125 (147)
+.+..|.-+++||.++.++||.|. -.|.|..+-.+.+=+-+ .....+|+.+.|+
T Consensus 28 ~~~~~~~~g~~v~~~~g~~vG~vTS~~~sp~~~~~Iala~v~---~~~~~~g~~l~v~ 82 (95)
T PF08669_consen 28 DGDAPPRGGEPVYDEDGKPVGRVTSGAYSPTLGKNIALAYVD---REYAEPGTELEVE 82 (95)
T ss_dssp SSSS--STTCEEEETTTEEEEEEEEEEEETTTTEEEEEEEEE---GGGGSTTSEEEEE
T ss_pred CCccCCCCCCEEEECCCcEEeEEEEEeECCCCCceEEEEEEC---HHHcCCCCEEEEE
Confidence 444678889999999999999999 67888755433322211 2344667888886
No 22
>COG0806 RimM RimM protein, required for 16S rRNA processing [Translation, ribosomal structure and biogenesis]
Probab=39.92 E-value=38 Score=27.19 Aligned_cols=32 Identities=22% Similarity=0.302 Sum_probs=27.9
Q ss_pred CCCceeeccccccceeeEeeCCCCcceEEEEe
Q 032083 76 FNAPIYLQNKTQIGKVDEIFGPINESYFSVKM 107 (147)
Q Consensus 76 fNa~Vy~enK~~IGKVdEIFGPi~~~yfsVKl 107 (147)
++..||+++...+|+|.||+-+-++-.+-||.
T Consensus 107 iG~~V~~~~g~~lG~V~~i~~~Ga~Dvl~V~~ 138 (174)
T COG0806 107 IGLEVVTEDGELLGKVTEILETGANDVLVVKA 138 (174)
T ss_pred cCcEEEcCCCcEEEEEEEEeeCCCccEEEEEe
Confidence 47889999999999999999998766678886
No 23
>PF09939 DUF2171: Uncharacterized protein conserved in bacteria (DUF2171); InterPro: IPR018684 This family of various hypothetical prokaryotic proteins has no known function.
Probab=39.78 E-value=65 Score=22.32 Aligned_cols=40 Identities=20% Similarity=0.369 Sum_probs=29.2
Q ss_pred CCceeeccccccceeeEeeCCCCcceEEEEecCCccccccCCCCEEEEc
Q 032083 77 NAPIYLQNKTQIGKVDEIFGPINESYFSVKMMEGIVATSYSLGDKFYID 125 (147)
Q Consensus 77 Na~Vy~enK~~IGKVdEIFGPi~~~yfsVKl~~gi~a~sfk~gdk~yI~ 125 (147)
...|+..+...||+||.+=|. +|||...-.. ..+..-||+
T Consensus 5 hmeVi~sdG~~vGtVDhveGd------~IKLtk~d~~---~~g~HH~IP 44 (67)
T PF09939_consen 5 HMEVIGSDGVHVGTVDHVEGD------RIKLTKDDSG---HDGQHHYIP 44 (67)
T ss_pred CCEEEeCCCCEEEEEeeEeCC------EEEEeccCCC---CCCcceEEe
Confidence 457888999999999999897 8898764321 234556654
No 24
>KOG1596 consensus Fibrillarin and related nucleolar RNA-binding proteins [RNA processing and modification]
Probab=38.77 E-value=57 Score=28.65 Aligned_cols=14 Identities=36% Similarity=0.653 Sum_probs=7.1
Q ss_pred ceeeEeeCCCCcce
Q 032083 89 GKVDEIFGPINESY 102 (147)
Q Consensus 89 GKVdEIFGPi~~~y 102 (147)
-.|.||-||.--+|
T Consensus 172 SHvSDiVGpeG~VY 185 (317)
T KOG1596|consen 172 SHVSDIVGPEGCVY 185 (317)
T ss_pred ehhhcccCCCceEE
Confidence 34556666544443
No 25
>PF13953 PapC_C: PapC C-terminal domain; PDB: 3L48_E 2XET_A 3RFZ_E 2KT6_A.
Probab=38.40 E-value=36 Score=22.56 Aligned_cols=23 Identities=26% Similarity=0.291 Sum_probs=14.9
Q ss_pred CCCCCCCCCceeeccccccceee
Q 032083 70 NEKIPYFNAPIYLQNKTQIGKVD 92 (147)
Q Consensus 70 ~~~VP~fNa~Vy~enK~~IGKVd 92 (147)
..+.+.|+|.|++++...+|-|.
T Consensus 7 ~G~~lPfGA~v~~~~g~~~g~Vg 29 (68)
T PF13953_consen 7 DGKPLPFGASVSDEDGNNIGIVG 29 (68)
T ss_dssp TSEE--TT-EEEETTSSEEEEB-
T ss_pred CCCcCCCCcEEEcCCCCEEEEEc
Confidence 34445699999999988887665
No 26
>PRK14594 rimM 16S rRNA-processing protein RimM; Provisional
Probab=35.95 E-value=52 Score=25.65 Aligned_cols=31 Identities=23% Similarity=0.352 Sum_probs=25.8
Q ss_pred CCCceeeccccccceeeEeeCCCCcceEEEEe
Q 032083 76 FNAPIYLQNKTQIGKVDEIFGPINESYFSVKM 107 (147)
Q Consensus 76 fNa~Vy~enK~~IGKVdEIFGPi~~~yfsVKl 107 (147)
++..|+++ ...+|+|.+|+-.-.+..+.||.
T Consensus 103 iG~~V~~~-g~~lG~V~~v~~~ga~dll~V~~ 133 (166)
T PRK14594 103 IGYAIVND-GKELGEVVSFFECLNSVLLEVKV 133 (166)
T ss_pred cCeEEEEC-CEEEEEEEEEeeCCCcEEEEEEe
Confidence 57789986 77899999999977777788984
No 27
>PRK14593 rimM 16S rRNA-processing protein RimM; Provisional
Probab=34.83 E-value=1e+02 Score=24.37 Aligned_cols=33 Identities=24% Similarity=0.296 Sum_probs=25.3
Q ss_pred CCCCceeeccccccceeeEeeCCCCcceEEEEec
Q 032083 75 YFNAPIYLQNKTQIGKVDEIFGPINESYFSVKMM 108 (147)
Q Consensus 75 ~fNa~Vy~enK~~IGKVdEIFGPi~~~yfsVKl~ 108 (147)
.++..||++ ...+|+|.+|+-.-.+-.+.|+..
T Consensus 109 LiGl~V~~~-g~~lG~V~~v~~~ga~dvlvV~~~ 141 (184)
T PRK14593 109 LVGLSVVEE-NEILGKVIEIQRISQTDYFMVETT 141 (184)
T ss_pred ccCcEEEEC-CEEeEEEEEEccCCCceEEEEEec
Confidence 357889986 577999999998666556788754
No 28
>PF14578 GTP_EFTU_D4: Elongation factor Tu domain 4; PDB: 1G7R_A 1G7S_A 1G7T_A 1XE1_A.
Probab=34.78 E-value=1.1e+02 Score=21.68 Aligned_cols=72 Identities=15% Similarity=0.228 Sum_probs=35.3
Q ss_pred CCceEEeceeeeeeeCCeEEEeccCCCCCCCCCceeeccccccceeeEeeCCCCcc-------eEEEEecCCccccccCC
Q 032083 46 PPAEVVEVSSFLHACEGDAVTKLTNEKIPYFNAPIYLQNKTQIGKVDEIFGPINES-------YFSVKMMEGIVATSYSL 118 (147)
Q Consensus 46 pp~~vielG~f~H~ceg~lV~K~t~~~VP~fNa~Vy~enK~~IGKVdEIFGPi~~~-------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 455555554444333343333221 1133347777 444599888664432222 1667777644 6788
Q ss_pred CCEEEE
Q 032083 119 GDKFYI 124 (147)
Q Consensus 119 gdk~yI 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 999986
No 29
>PRK14590 rimM 16S rRNA-processing protein RimM; Provisional
Probab=33.37 E-value=68 Score=25.22 Aligned_cols=31 Identities=3% Similarity=0.027 Sum_probs=24.6
Q ss_pred CCCceeeccccccc-eeeEeeCCCCcceEEEE
Q 032083 76 FNAPIYLQNKTQIG-KVDEIFGPINESYFSVK 106 (147)
Q Consensus 76 fNa~Vy~enK~~IG-KVdEIFGPi~~~yfsVK 106 (147)
.+..|++++...+| +|.+|+-.-.+..+.|+
T Consensus 103 iG~~V~d~~g~~lGG~V~~v~~~~a~dllvV~ 134 (171)
T PRK14590 103 IGLQAIDETGKPLNWKLTDVQDNPAHPILVFI 134 (171)
T ss_pred cCcEEEeCCCCEeeeEEEEEecCCCceEEEEE
Confidence 57889999999997 99999876655556665
No 30
>cd03698 eRF3_II_like eRF3_II_like: domain similar to domain II of the eukaryotic class II release factor (eRF3). In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribsome. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM
Probab=30.13 E-value=97 Score=20.88 Aligned_cols=15 Identities=40% Similarity=0.556 Sum_probs=9.0
Q ss_pred cccCCCCEEEEcCCC
Q 032083 114 TSYSLGDKFYIDPSK 128 (147)
Q Consensus 114 ~sfk~gdk~yI~p~k 128 (147)
.++++||+++|.|..
T Consensus 25 G~i~~Gd~v~i~P~~ 39 (83)
T cd03698 25 GSIQKGDTLLVMPSK 39 (83)
T ss_pred eEEeCCCEEEEeCCC
Confidence 455666777666643
No 31
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=28.86 E-value=1.1e+02 Score=22.29 Aligned_cols=21 Identities=38% Similarity=0.676 Sum_probs=14.1
Q ss_pred ceeeEeeCCCCcceEEEEecCCcc
Q 032083 89 GKVDEIFGPINESYFSVKMMEGIV 112 (147)
Q Consensus 89 GKVdEIFGPi~~~yfsVKl~~gi~ 112 (147)
|+|.|++. +-.|.|+|+++..
T Consensus 11 G~V~e~Lp---~~~frV~LenG~~ 31 (87)
T PRK12442 11 GIVDEVLP---DSRFRVTLENGVE 31 (87)
T ss_pred EEEEEECC---CCEEEEEeCCCCE
Confidence 77777765 3457777776654
No 32
>cd04717 BAH_polybromo BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human polybromo protein (BAF180) is a component of the SWI/SNF chromatin-remodeling complex PBAF. It is thought that polybromo participates in transcriptional regulation. Saccharomyces cerevisiae RSC1 and RSC2 are part of the 15-subunit nucleosome remodeling RSC complex. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=27.79 E-value=79 Score=22.94 Aligned_cols=20 Identities=15% Similarity=0.300 Sum_probs=11.7
Q ss_pred cccceeeEeeCCC-CcceEEE
Q 032083 86 TQIGKVDEIFGPI-NESYFSV 105 (147)
Q Consensus 86 ~~IGKVdEIFGPi-~~~yfsV 105 (147)
..|++|++||=-. ++.+|.+
T Consensus 21 ~~i~~I~~i~~~~~g~~~~~~ 41 (121)
T cd04717 21 PIIFRIERLWKDEDGEKFFFG 41 (121)
T ss_pred CEEEEEeEEEECCCCCEEEEE
Confidence 3477777777654 3444443
No 33
>COG1255 Uncharacterized protein conserved in archaea [Function unknown]
Probab=27.60 E-value=16 Score=28.45 Aligned_cols=38 Identities=26% Similarity=0.466 Sum_probs=28.0
Q ss_pred ceeeEeeCCCCcce------EEEEecCCcccccc----CCCCEEEEcC
Q 032083 89 GKVDEIFGPINESY------FSVKMMEGIVATSY----SLGDKFYIDP 126 (147)
Q Consensus 89 GKVdEIFGPi~~~y------fsVKl~~gi~a~sf----k~gdk~yI~p 126 (147)
.-+||||+|.-..| |||++-..+....+ +.+-.+||.|
T Consensus 55 ~v~DDitnP~~~iY~~A~lIYSiRpppEl~~~ildva~aVga~l~I~p 102 (129)
T COG1255 55 FVVDDITNPNISIYEGADLIYSIRPPPELQSAILDVAKAVGAPLYIKP 102 (129)
T ss_pred EEEccCCCccHHHhhCccceeecCCCHHHHHHHHHHHHhhCCCEEEEe
Confidence 34899999987777 88888777665432 4467788876
No 34
>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=26.79 E-value=38 Score=27.66 Aligned_cols=7 Identities=43% Similarity=0.411 Sum_probs=3.1
Q ss_pred CCCCCCC
Q 032083 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 4444443
No 35
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=26.57 E-value=1.3e+02 Score=21.19 Aligned_cols=27 Identities=19% Similarity=0.358 Sum_probs=17.8
Q ss_pred ccccccceeeEeeCCCCcceEEEEecCCcc
Q 032083 83 QNKTQIGKVDEIFGPINESYFSVKMMEGIV 112 (147)
Q Consensus 83 enK~~IGKVdEIFGPi~~~yfsVKl~~gi~ 112 (147)
++.+.+|+|.+.+|- -.|.|+++++..
T Consensus 3 ~e~q~~g~V~~~lG~---~~~~V~~~dG~~ 29 (83)
T smart00652 3 EDGQEIAQVVKMLGN---GRLEVMCADGKE 29 (83)
T ss_pred CCCcEEEEEEEEcCC---CEEEEEECCCCE
Confidence 355667788877773 446777776654
No 36
>COG3881 PRC-barrel domain containing protein [General function prediction only]
Probab=26.45 E-value=1e+02 Score=25.19 Aligned_cols=34 Identities=24% Similarity=0.440 Sum_probs=23.9
Q ss_pred CCCceeecc-ccccceeeE-eeCCCCcceEEEEecC
Q 032083 76 FNAPIYLQN-KTQIGKVDE-IFGPINESYFSVKMME 109 (147)
Q Consensus 76 fNa~Vy~en-K~~IGKVdE-IFGPi~~~yfsVKl~~ 109 (147)
.++|||.++ ..++|.|+| ||.+--+..--++..+
T Consensus 8 eG~pVys~~tg~~lg~V~Dvif~~~gdrvl~flvnk 43 (176)
T COG3881 8 EGAPVYSTKTGEKLGAVDDVIFNFSGDRVLGFLVNK 43 (176)
T ss_pred cCCceEEecccccccceeeEEEecCCCeEEEEEEec
Confidence 488999988 789999995 6777555544444443
No 37
>PF13865 FoP_duplication: C-terminal duplication domain of Friend of PRMT1
Probab=25.54 E-value=83 Score=21.62 Aligned_cols=9 Identities=33% Similarity=0.637 Sum_probs=4.3
Q ss_pred CCCceEEec
Q 032083 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 455554444
No 38
>PRK00122 rimM 16S rRNA-processing protein RimM; Provisional
Probab=25.03 E-value=1.2e+02 Score=23.46 Aligned_cols=86 Identities=15% Similarity=0.169 Sum_probs=46.2
Q ss_pred CceEEeceeee--eeeCCeEEEeccCCCCC-CCC-Cceeecccccc--ceeeEeeCCCCcceEEEEecCCccccccCCCC
Q 032083 47 PAEVVEVSSFL--HACEGDAVTKLTNEKIP-YFN-APIYLQNKTQI--GKVDEIFGPINESYFSVKMMEGIVATSYSLGD 120 (147)
Q Consensus 47 p~~vielG~f~--H~ceg~lV~K~t~~~VP-~fN-a~Vy~enK~~I--GKVdEIFGPi~~~yfsVKl~~gi~a~sfk~gd 120 (147)
.++.+.+|++. |=..+++-+++..+..- ++. ..+|.+.+... =+|.++.---+.+.++.+=-+.+.+..-..|.
T Consensus 4 ~~~~v~iG~i~~~hGlkGevkv~~~td~p~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~lvkf~gi~~~~~Ae~l~g~ 83 (172)
T PRK00122 4 PEDLLVVGKIVSAHGIKGEVKVKSFTDFPERIFDYGPWLLGKGGEWQEVEIESGRFHKGFLIVKFEGVDDRNAAEALKGC 83 (172)
T ss_pred ccceEEEEEEECCCcccEEEEEEEecCCHHHHcCcCcEEEccCCceEEEEEEEEEEECCEEEEEECCCCCHHHHHHhCCC
Confidence 35688999887 55568998887444222 222 23454332111 13444442222223333333444444446689
Q ss_pred EEEEcCCCcccc
Q 032083 121 KFYIDPSKLLPL 132 (147)
Q Consensus 121 k~yI~p~klLPl 132 (147)
.+||+.+.+-++
T Consensus 84 ~l~i~~~~lp~l 95 (172)
T PRK00122 84 ELFVPRSQLPEL 95 (172)
T ss_pred EEEEEHHHCCCC
Confidence 999998876554
No 39
>PLN03138 Protein TOC75; Provisional
Probab=23.55 E-value=73 Score=31.48 Aligned_cols=13 Identities=8% Similarity=0.013 Sum_probs=6.4
Q ss_pred cCCCCEEEEcCCC
Q 032083 116 YSLGDKFYIDPSK 128 (147)
Q Consensus 116 fk~gdk~yI~p~k 128 (147)
|.++++.+|+.-+
T Consensus 221 i~Eg~~~~I~~I~ 233 (796)
T PLN03138 221 FTESTWQSADSFR 233 (796)
T ss_pred EEeCCceeeeeee
Confidence 4455555554444
No 40
>PHA02142 putative RNA ligase
Probab=23.42 E-value=50 Score=29.65 Aligned_cols=20 Identities=30% Similarity=0.687 Sum_probs=17.4
Q ss_pred cccCCCCE-EEEcCCCccccc
Q 032083 114 TSYSLGDK-FYIDPSKLLPLA 133 (147)
Q Consensus 114 ~sfk~gdk-~yI~p~klLPl~ 133 (147)
..|++||. +||.++.+||+.
T Consensus 42 g~f~~GD~~vY~eiDS~lP~~ 62 (366)
T PHA02142 42 GEFRVGDDCVYFEIDSLLPTD 62 (366)
T ss_pred cccccCCeEEEecccccccCC
Confidence 47899885 899999999986
No 41
>PHA01365 hypothetical protein
Probab=22.66 E-value=1.6e+02 Score=21.48 Aligned_cols=44 Identities=25% Similarity=0.403 Sum_probs=30.2
Q ss_pred ccceeeEeeCCCCcceEEEEecCCcc----ccccCCCC-EEEEcCCCcc
Q 032083 87 QIGKVDEIFGPINESYFSVKMMEGIV----ATSYSLGD-KFYIDPSKLL 130 (147)
Q Consensus 87 ~IGKVdEIFGPi~~~yfsVKl~~gi~----a~sfk~gd-k~yI~p~klL 130 (147)
.+-+-+=||=|+.+.|--+-+.++|+ |.....|. .+|.+|.|=.
T Consensus 32 dv~~KYiif~r~s~~y~G~~vvdGiqIPFiAev~lngk~~iYLyP~KDF 80 (91)
T PHA01365 32 SPHKKYMIIDPESKYYIGYILTDGIKIPFIAEVWHNNTTRIYLDPRKDF 80 (91)
T ss_pred CccccEEEEEEecceEEEEEEEcceeccEEeeeeeCCeEEEEEccccce
Confidence 34445556888889998888888887 33334443 6888887743
No 42
>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=22.57 E-value=85 Score=23.61 Aligned_cols=26 Identities=15% Similarity=0.331 Sum_probs=21.7
Q ss_pred CCCCCCceEEeceeeeeeeCCeEEEe
Q 032083 42 RDEGPPAEVVEVSSFLHACEGDAVTK 67 (147)
Q Consensus 42 ~~~Gpp~~vielG~f~H~ceg~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 43
>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=21.60 E-value=1.8e+02 Score=20.07 Aligned_cols=24 Identities=29% Similarity=0.403 Sum_probs=17.6
Q ss_pred cceeeEeeCCCCcceEEEEecCCcccc
Q 032083 88 IGKVDEIFGPINESYFSVKMMEGIVAT 114 (147)
Q Consensus 88 IGKVdEIFGPi~~~yfsVKl~~gi~a~ 114 (147)
.|+|.|.++ +-+|.|+++++...-
T Consensus 8 ~G~V~e~L~---~~~f~V~l~ng~~vl 31 (68)
T TIGR00008 8 EGKVTESLP---NAMFRVELENGHEVL 31 (68)
T ss_pred EEEEEEECC---CCEEEEEECCCCEEE
Confidence 388888876 357899998876633
No 44
>COG4353 Uncharacterized conserved protein [Function unknown]
Probab=20.28 E-value=45 Score=27.36 Aligned_cols=30 Identities=30% Similarity=0.428 Sum_probs=19.3
Q ss_pred eEEEeccCCCCC-CCCCceeeccccccceee
Q 032083 63 DAVTKLTNEKIP-YFNAPIYLQNKTQIGKVD 92 (147)
Q Consensus 63 ~lV~K~t~~~VP-~fNa~Vy~enK~~IGKVd 92 (147)
.+++|......- -||-.++++|..+++++.
T Consensus 15 kl~vk~~qgrfkeef~~dl~Le~ge~l~~l~ 45 (192)
T COG4353 15 KLVVKNLQGRFKEEFNFDLLLENGEQLGKLK 45 (192)
T ss_pred eeeeeccccccceeeeeEEeecCCceeeEEE
Confidence 455554333322 467888888888888765
No 45
>cd03694 GTPBP_II Domain II of the GP-1 family of GTPase. This group includes proteins similar to GTPBP1 and GTPBP2. GTPB1 is structurally, related to elongation factor 1 alpha, a key component of protein biosynthesis machinery. Immunohistochemical analyses on mouse tissues revealed that GTPBP1 is expressed in some neurons and smooth muscle cells of various organs as well as macrophages. Immunofluorescence analyses revealed that GTPBP1 is localized exclusively in cytoplasm and shows a diffuse granular network forming a gradient from the nucleus to the periphery of the cells in smooth muscle cell lines and macrophages. No significant difference was observed in the immune response to protein antigen between mutant mice and wild-type mice, suggesting normal function of antigen-presenting cells of the mutant mice. The absence of an eminent phenotype in GTPBP1-deficient mice may be due to functional compensation by GTPBP2, which is similar to GTPBP1 in structure and tissue distribution.
Probab=20.18 E-value=1e+02 Score=21.13 Aligned_cols=15 Identities=27% Similarity=0.556 Sum_probs=10.4
Q ss_pred ccccCCCCEEEEcCC
Q 032083 113 ATSYSLGDKFYIDPS 127 (147)
Q Consensus 113 a~sfk~gdk~yI~p~ 127 (147)
...+++||++++-|.
T Consensus 24 ~G~v~~g~~v~~~P~ 38 (87)
T cd03694 24 KGVIRLGDTLLLGPD 38 (87)
T ss_pred cCEEeCCCEEEECCC
Confidence 346677788887775
No 46
>cd04716 BAH_plantDCM_I BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5)-methyltransferases (DCM) from plants. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=20.09 E-value=1.4e+02 Score=22.49 Aligned_cols=11 Identities=36% Similarity=0.513 Sum_probs=7.0
Q ss_pred cceeeEeeCCC
Q 032083 88 IGKVDEIFGPI 98 (147)
Q Consensus 88 IGKVdEIFGPi 98 (147)
||+|.+||=..
T Consensus 22 i~rI~~i~e~~ 32 (122)
T cd04716 22 ICKITEFFEGT 32 (122)
T ss_pred EEEEEEEEEcC
Confidence 67777777543
No 47
>cd04714 BAH_BAHCC1 BAH, or Bromo Adjacent Homology domain, as present in mammalian BAHCC1 and similar proteins. BAHCC1 stands for BAH domain and coiled-coil containing 1. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=20.06 E-value=1.5e+02 Score=21.79 Aligned_cols=20 Identities=10% Similarity=0.305 Sum_probs=12.6
Q ss_pred ccceeeEeeCCC-CcceEEEE
Q 032083 87 QIGKVDEIFGPI-NESYFSVK 106 (147)
Q Consensus 87 ~IGKVdEIFGPi-~~~yfsVK 106 (147)
-||+|.+||-.. .+.|+++.
T Consensus 22 yIgrI~~i~e~~~g~~~~~v~ 42 (121)
T cd04714 22 YVARIESLWEDPEGNMVVRVK 42 (121)
T ss_pred EEEEEEEEEEcCCCCEEEEEE
Confidence 478888888644 34555554
Done!