Query 033397
Match_columns 120
No_of_seqs 116 out of 194
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 13:24:29 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033397.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033397hhsearch_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 2.9E-47 6.3E-52 300.8 7.3 114 1-117 1-120 (215)
2 PRK13149 H/ACA RNA-protein com 100.0 2.2E-28 4.8E-33 165.6 7.7 63 50-114 1-64 (73)
3 PF04410 Gar1: Gar1/Naf1 RNA b 99.9 2.4E-23 5.1E-28 156.2 6.1 77 40-116 13-92 (154)
4 COG3277 GAR1 RNA-binding prote 99.9 4.8E-23 1.1E-27 147.8 7.3 67 50-116 1-67 (98)
5 KOG2236 Uncharacterized conser 98.4 1.9E-07 4.1E-12 82.2 2.4 65 49-113 207-272 (483)
6 PTZ00146 fibrillarin; Provisio 93.3 0.48 1E-05 39.8 7.8 16 71-88 81-96 (293)
7 PF05239 PRC: PRC-barrel domai 92.8 0.23 5E-06 31.9 4.2 34 76-109 10-46 (79)
8 KOG3973 Uncharacterized conser 92.3 0.26 5.6E-06 43.5 4.9 6 28-33 370-375 (465)
9 PTZ00146 fibrillarin; Provisio 88.5 0.78 1.7E-05 38.5 4.5 6 54-59 66-71 (293)
10 TIGR02273 16S_RimM 16S rRNA pr 77.9 5.1 0.00011 30.0 4.6 33 75-107 100-132 (165)
11 PF05918 API5: Apoptosis inhib 77.1 0.76 1.7E-05 41.8 0.0 7 3-9 517-523 (556)
12 KOG0921 Dosage compensation co 76.9 3.3 7.1E-05 40.8 4.1 6 8-13 1233-1238(1282)
13 PRK00122 rimM 16S rRNA-process 69.3 10 0.00022 28.6 4.5 33 75-107 105-137 (172)
14 PRK14592 rimM 16S rRNA-process 68.3 11 0.00023 28.5 4.4 32 76-107 98-129 (165)
15 PRK13828 rimM 16S rRNA-process 65.6 14 0.00031 27.7 4.6 33 75-107 85-117 (161)
16 PF02470 MCE: mce related prot 60.1 24 0.00052 22.9 4.4 36 75-111 16-53 (81)
17 PF08669 GCV_T_C: Glycine clea 57.3 17 0.00036 24.2 3.3 34 68-101 27-61 (95)
18 PRK13829 rimM 16S rRNA-process 56.1 23 0.00051 26.7 4.3 34 76-110 95-128 (162)
19 PRK14591 rimM 16S rRNA-process 55.1 23 0.00051 26.8 4.2 32 76-107 106-137 (169)
20 KOG3262 H/ACA small nucleolar 52.9 20 0.00043 29.3 3.6 6 9-14 15-20 (215)
21 cd04479 RPA3 RPA3: A subfamily 51.9 55 0.0012 22.8 5.4 49 48-100 16-66 (101)
22 COG0806 RimM RimM protein, req 46.3 37 0.0008 26.5 4.2 32 76-107 107-138 (174)
23 PRK14590 rimM 16S rRNA-process 46.1 44 0.00096 25.5 4.5 32 76-107 103-135 (171)
24 PRK14594 rimM 16S rRNA-process 40.9 55 0.0012 24.7 4.3 31 76-107 103-133 (166)
25 smart00652 eIF1a eukaryotic tr 40.5 43 0.00093 23.0 3.3 27 83-112 3-29 (83)
26 PF13953 PapC_C: PapC C-termin 39.4 34 0.00074 22.0 2.6 27 67-93 4-30 (68)
27 PF01176 eIF-1a: Translation i 38.5 92 0.002 20.1 4.5 28 83-113 1-28 (65)
28 PF10246 MRP-S35: Mitochondria 36.1 47 0.001 24.5 3.1 27 42-68 17-43 (104)
29 COG1873 Protein implicated in 35.9 36 0.00078 23.7 2.4 20 75-94 11-30 (87)
30 COG0311 PDX2 Predicted glutami 33.4 58 0.0012 26.4 3.5 55 58-117 115-173 (194)
31 TIGR00008 infA translation ini 31.1 1.2E+02 0.0025 20.5 4.2 26 86-114 6-31 (68)
32 COG3881 PRC-barrel domain cont 30.7 70 0.0015 25.6 3.5 36 75-110 7-44 (176)
33 PF05284 DUF736: Protein of un 28.8 1E+02 0.0022 22.1 3.8 38 71-110 38-78 (107)
34 cd04717 BAH_polybromo BAH, or 25.1 1.4E+02 0.003 20.9 4.0 55 49-104 2-66 (121)
35 cd04716 BAH_plantDCM_I BAH, or 24.6 1.4E+02 0.0031 21.8 4.0 10 88-97 22-31 (122)
36 PRK12442 translation initiatio 24.6 1.6E+02 0.0035 20.9 4.2 24 87-113 9-32 (87)
37 PF11705 RNA_pol_3_Rpc31: DNA- 23.4 49 0.0011 26.1 1.5 9 71-79 66-74 (233)
38 PRK04012 translation initiatio 22.6 1.3E+02 0.0028 21.5 3.4 26 83-111 19-44 (100)
39 cd00226 PRCH Photosynthetic re 22.3 73 0.0016 26.6 2.3 34 75-108 148-184 (246)
40 cd08689 C2_fungal_Pkc1p C2 dom 21.4 61 0.0013 24.0 1.5 20 96-115 20-39 (109)
41 PF08770 SoxZ: Sulphur oxidati 20.9 1.1E+02 0.0025 21.5 2.8 55 55-109 20-76 (100)
42 PRK14593 rimM 16S rRNA-process 20.3 3E+02 0.0066 21.0 5.2 33 75-108 109-141 (184)
43 PF09939 DUF2171: Uncharacteri 20.2 1.2E+02 0.0025 20.6 2.6 20 77-96 5-24 (67)
No 1
>KOG3262 consensus H/ACA small nucleolar RNP component GAR1 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.9e-47 Score=300.75 Aligned_cols=114 Identities=65% Similarity=1.117 Sum_probs=93.2
Q ss_pred CCCCCCCCCCCCCCCCCCCCCC---CCCCCCCC---CCCCCCCCCCCCCCCCCcceEEeeeEEeeeCCcEEEeecCCCCC
Q 033397 1 MRPPRGGGGFRGGRDGGRGGRG---GGRFGGGG---RGGGGRGGFGFRDEGPPAEVVEVSSFLHACEGDAVTKLTNEKIP 74 (120)
Q Consensus 1 ~~~~~~~~~f~~~~~g~~gg~~---~~~~~ggg---rggrg~g~~~~~~~gPP~~v~elG~f~H~ce~~lV~k~t~~~VP 74 (120)
|+|||+++++++++ +-|++.+ .++|+++. |++++ ++..+|++||+||+||++|+|+||+|||||+++.+||
T Consensus 1 ~~~~rgggg~~g~~-gfRgg~ggg~~gg~rgg~g~grgg~~--~~~~~d~gpp~evvelg~flh~Cegd~Vck~~~~kIP 77 (215)
T KOG3262|consen 1 GGGPRGGGGGGGGG-GFRGGGGGGRGGGFRGGNGFGRGGRG--GRGFQDQGPPEEVVELGKFLHMCEGDLVCKLTNKKIP 77 (215)
T ss_pred CCCCcCCCCCCCCC-CcccCCCCCCCCCcccCcccccCCcc--cCCcccCCCchhhhhhhhhhhhcCCceEEeeccccCC
Confidence 78888877766665 2233221 23344443 33322 3456799999999999999999999999999999999
Q ss_pred ccCCeeEecCcceeeeeeEeeccCCcceEEEeeCCCcceeeeE
Q 033397 75 YFNAPIYLQNKTQIGKVDEIFGPINESVIFFGQNDGRYCCNFI 117 (120)
Q Consensus 75 yfNapVy~enK~~IGKVdEIFGPIn~~yfSVKl~~gv~AsSf~ 117 (120)
|||||||||||+||||||||||||||+||||||+|+|+||||-
T Consensus 78 yfNAPIylenk~qIGKVDEIfG~i~d~~fsIK~~dgv~assfk 120 (215)
T KOG3262|consen 78 YFNAPIYLENKEQIGKVDEIFGPINDVHFSIKPSDGVQASSFK 120 (215)
T ss_pred CCCCceeecchhhhcchhhhcccccccEEEEecCCCceeeccc
Confidence 9999999999999999999999999999999999999999984
No 2
>PRK13149 H/ACA RNA-protein complex component Gar1; Reviewed
Probab=99.95 E-value=2.2e-28 Score=165.61 Aligned_cols=63 Identities=24% Similarity=0.473 Sum_probs=60.8
Q ss_pred eEEeeeEEeee-CCcEEEeecCCCCCccCCeeEecCcceeeeeeEeeccCCcceEEEeeCCCccee
Q 033397 50 VVEVSSFLHAC-EGDAVTKLTNEKIPYFNAPIYLQNKTQIGKVDEIFGPINESVIFFGQNDGRYCC 114 (120)
Q Consensus 50 v~elG~f~H~c-e~~lV~k~t~~~VPyfNapVy~enK~~IGKVdEIFGPIn~~yfSVKl~~gv~As 114 (120)
|++||+|+|.| +++||||+ +++|+||++|||+|+++||||+|||||+++||||||+++++.|+
T Consensus 1 Mk~~G~~~h~~~~g~lI~~~--~~~P~~n~~V~~~~~~~IGkV~dIfGPV~~pY~~Vk~~~~~~~~ 64 (73)
T PRK13149 1 MKRLGKVLHYAPKGKLIIRL--DKQPPIGSVVYDKKLKKIGKVVDVFGPVKEPYVLVKPDKKDPPE 64 (73)
T ss_pred CcEeEEEEEEcCCCCEEEEc--CCCCCCCCEeECCCCCEeEEEEEEECCCCCcEEEEEeCCCCCcc
Confidence 57999999999 78999999 78999999999999999999999999999999999999999997
No 3
>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=99.88 E-value=2.4e-23 Score=156.23 Aligned_cols=77 Identities=31% Similarity=0.498 Sum_probs=65.4
Q ss_pred CCCCCCCCcceEEeeeEEeeeCCcEEEeecCC-CCCccCCeeEecCcceeeeeeEeeccCCcceEEEe--eCCCcceeee
Q 033397 40 GFRDEGPPAEVVEVSSFLHACEGDAVTKLTNE-KIPYFNAPIYLQNKTQIGKVDEIFGPINESVIFFG--QNDGRYCCNF 116 (120)
Q Consensus 40 ~~~~~gPP~~v~elG~f~H~ce~~lV~k~t~~-~VPyfNapVy~enK~~IGKVdEIFGPIn~~yfSVK--l~~gv~AsSf 116 (120)
...+..|++++++||+++|+|++.+|||++.. .||++|++||++|+++||||+|||||+++||+||| +++++++.++
T Consensus 13 ~~~~~~~~~~i~~lG~v~~i~~~~vVvk~~~~~~vl~~~s~v~~edr~~iG~V~eiFGpV~~P~y~Vr~~~~~~~~~~~~ 92 (154)
T PF04410_consen 13 PDVEIGPPEEIKPLGTVSHIVENLVVVKSTPSKQVLDFGSVVCLEDRTKIGKVDEIFGPVNNPYYSVRFNSSEGIKAKSL 92 (154)
T ss_dssp TT-B--TTSSEEEEEEEEEEETTEEEEEE-SS-CEEBTT-EEEETTSBEEEEEEEEESESSS-EEEEE-SCHHHHHHHCC
T ss_pred CCcccCCCceEEEeeeEEEEeCCcEEEEeCCCCcCCCCCCEEECCCCCEeEEEeeEeCCCCceEEEEEeCCccccccccc
Confidence 35678899999999999999999999999765 89999999999999999999999999999999999 7788877554
No 4
>COG3277 GAR1 RNA-binding protein involved in rRNA processing [Translation, ribosomal structure and biogenesis]
Probab=99.88 E-value=4.8e-23 Score=147.82 Aligned_cols=67 Identities=33% Similarity=0.582 Sum_probs=62.7
Q ss_pred eEEeeeEEeeeCCcEEEeecCCCCCccCCeeEecCcceeeeeeEeeccCCcceEEEeeCCCcceeee
Q 033397 50 VVEVSSFLHACEGDAVTKLTNEKIPYFNAPIYLQNKTQIGKVDEIFGPINESVIFFGQNDGRYCCNF 116 (120)
Q Consensus 50 v~elG~f~H~ce~~lV~k~t~~~VPyfNapVy~enK~~IGKVdEIFGPIn~~yfSVKl~~gv~AsSf 116 (120)
|++||+++|.|+.++||..++.++|++||||||+|.++||+|+|||||++++|++||+++.+.++++
T Consensus 1 m~~lG~vlh~~~~g~vi~~~~~~iP~l~~~V~~~~~k~IG~V~dVfGPv~~PY~~Vkp~~~~~~~~~ 67 (98)
T COG3277 1 MKRLGKVLHVCGTGMVIVRDNDRIPPLNAPVYDANLKRIGKVVDVFGPVDEPYILVKPDDRDVKLES 67 (98)
T ss_pred CccceeEEEecCCceEEEeCCCCCCCCCCeeEecCCCEEEEEEEEEccCCCCEEEEecccccccccc
Confidence 5789999999999999999888999999999999999999999999999999999999999885554
No 5
>KOG2236 consensus Uncharacterized conserved protein [Function unknown]
Probab=98.36 E-value=1.9e-07 Score=82.17 Aligned_cols=65 Identities=18% Similarity=0.337 Sum_probs=59.2
Q ss_pred ceEEeeeEEeeeCCcEEEeecCCCCC-ccCCeeEecCcceeeeeeEeeccCCcceEEEeeCCCcce
Q 033397 49 EVVEVSSFLHACEGDAVTKLTNEKIP-YFNAPIYLQNKTQIGKVDEIFGPINESVIFFGQNDGRYC 113 (120)
Q Consensus 49 ~v~elG~f~H~ce~~lV~k~t~~~VP-yfNapVy~enK~~IGKVdEIFGPIn~~yfSVKl~~gv~A 113 (120)
++++||.++-+.+.++|++++.++.+ -+.+.+|+++.+-||+|+|||||+.++|+.|+....-.+
T Consensus 207 ~~~plG~V~svv~~~VII~s~~~~~vlde~Svlf~edR~~lG~I~EiFGpV~~P~YvvRFnS~~e~ 272 (483)
T KOG2236|consen 207 ELLPLGKVSSVVDQQVIIESTCNKEVLDEDSVLFLEDRTALGQIFEIFGPVKNPYYVVRFNSEEEI 272 (483)
T ss_pred ceechhHHHHHhhhceEEEeccCcccccccceEEeeccccchhhhhhhcccCCceEEEecCchhhh
Confidence 68899999999999999999888766 699999999999999999999999999999998765544
No 6
>PTZ00146 fibrillarin; Provisional
Probab=93.33 E-value=0.48 Score=39.75 Aligned_cols=16 Identities=13% Similarity=0.438 Sum_probs=8.0
Q ss_pred CCCCccCCeeEecCccee
Q 033397 71 EKIPYFNAPIYLQNKTQI 88 (120)
Q Consensus 71 ~~VPyfNapVy~enK~~I 88 (120)
+.+|- ..||.|..-.+
T Consensus 81 n~~pg--~~vygek~~~~ 96 (293)
T PTZ00146 81 NMVPG--ESVYGEKRISV 96 (293)
T ss_pred cCCCC--cccccceEEee
Confidence 34552 45666555333
No 7
>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=92.84 E-value=0.23 Score=31.95 Aligned_cols=34 Identities=21% Similarity=0.351 Sum_probs=25.6
Q ss_pred cCCeeEecCcceeeeeeEe-eccC-Ccc-eEEEeeCC
Q 033397 76 FNAPIYLQNKTQIGKVDEI-FGPI-NES-VIFFGQND 109 (120)
Q Consensus 76 fNapVy~enK~~IGKVdEI-FGPI-n~~-yfSVKl~~ 109 (120)
.+.+||+++.++||+|.|| |-+- .++ ++.|+...
T Consensus 10 ~g~~V~~~~G~~iG~V~di~id~~~~~i~~i~v~~~~ 46 (79)
T PF05239_consen 10 IGKEVIDRDGEKIGKVKDIVIDPKTGKIVGIVVSSGG 46 (79)
T ss_dssp TTSEEEETTSCEEEEEEEEEEETTTTEEEEEEEEETT
T ss_pred cCCEEEcCCCCEEEEEEEEEEeCCCCCEEEEEEcCCC
Confidence 5789999999999999999 7763 333 45555543
No 8
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=92.27 E-value=0.26 Score=43.51 Aligned_cols=6 Identities=100% Similarity=2.090 Sum_probs=2.5
Q ss_pred CCCCCC
Q 033397 28 GGGRGG 33 (120)
Q Consensus 28 gggrgg 33 (120)
|+||||
T Consensus 370 GgGRGg 375 (465)
T KOG3973|consen 370 GGGRGG 375 (465)
T ss_pred CCCCCC
Confidence 344443
No 9
>PTZ00146 fibrillarin; Provisional
Probab=88.53 E-value=0.78 Score=38.50 Aligned_cols=6 Identities=17% Similarity=0.445 Sum_probs=2.4
Q ss_pred eeEEee
Q 033397 54 SSFLHA 59 (120)
Q Consensus 54 G~f~H~ 59 (120)
|.|...
T Consensus 66 gv~~~~ 71 (293)
T PTZ00146 66 GVFIAK 71 (293)
T ss_pred CEEEee
Confidence 344433
No 10
>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=77.93 E-value=5.1 Score=29.99 Aligned_cols=33 Identities=18% Similarity=0.281 Sum_probs=29.2
Q ss_pred ccCCeeEecCcceeeeeeEeeccCCcceEEEee
Q 033397 75 YFNAPIYLQNKTQIGKVDEIFGPINESVIFFGQ 107 (120)
Q Consensus 75 yfNapVy~enK~~IGKVdEIFGPIn~~yfSVKl 107 (120)
.++-.|++++.+.+|+|.||+=.-.+..+.||.
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 357889999999999999999988888899986
No 11
>PF05918 API5: Apoptosis inhibitory protein 5 (API5); InterPro: IPR008383 This family consists of apoptosis inhibitory protein 5 (API5) sequences from several organisms. Apoptosis or programmed cell death is a physiological form of cell death that occurs in embryonic development and organ formation. It is characterised by biochemical and morphological changes such as DNA fragmentation and cell volume shrinkage. API5 is an anti apoptosis gene located in Homo sapiens chromosome 11, whose expression prevents the programmed cell death that occurs upon the deprivation of growth factors [,].; PDB: 3U0R_A 3V6A_A.
Probab=77.13 E-value=0.76 Score=41.78 Aligned_cols=7 Identities=43% Similarity=0.805 Sum_probs=0.0
Q ss_pred CCCCCCC
Q 033397 3 PPRGGGG 9 (120)
Q Consensus 3 ~~~~~~~ 9 (120)
||++..+
T Consensus 517 ~p~~k~s 523 (556)
T PF05918_consen 517 PPSGKYS 523 (556)
T ss_dssp -------
T ss_pred CCCCCCc
Confidence 5666433
No 12
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=76.90 E-value=3.3 Score=40.79 Aligned_cols=6 Identities=67% Similarity=1.426 Sum_probs=2.5
Q ss_pred CCCCCC
Q 033397 8 GGFRGG 13 (120)
Q Consensus 8 ~~f~~~ 13 (120)
++||+-
T Consensus 1233 gGfrnn 1238 (1282)
T KOG0921|consen 1233 GGFRNN 1238 (1282)
T ss_pred CccccC
Confidence 344443
No 13
>PRK00122 rimM 16S rRNA-processing protein RimM; Provisional
Probab=69.28 E-value=10 Score=28.58 Aligned_cols=33 Identities=15% Similarity=0.266 Sum_probs=28.0
Q ss_pred ccCCeeEecCcceeeeeeEeeccCCcceEEEee
Q 033397 75 YFNAPIYLQNKTQIGKVDEIFGPINESVIFFGQ 107 (120)
Q Consensus 75 yfNapVy~enK~~IGKVdEIFGPIn~~yfSVKl 107 (120)
.++..|++++.+.+|+|.+|+=.-.+..+.||.
T Consensus 105 LiG~~V~d~~g~~lG~V~~v~~~~a~dll~I~~ 137 (172)
T PRK00122 105 LIGLEVVDEDGEELGKVTDILETGANDVLVVLK 137 (172)
T ss_pred hCCcEEEeCCCcEEEEEEEEccCCCceEEEEEC
Confidence 367899999999999999999877777788863
No 14
>PRK14592 rimM 16S rRNA-processing protein RimM; Provisional
Probab=68.35 E-value=11 Score=28.47 Aligned_cols=32 Identities=16% Similarity=0.228 Sum_probs=27.2
Q ss_pred cCCeeEecCcceeeeeeEeeccCCcceEEEee
Q 033397 76 FNAPIYLQNKTQIGKVDEIFGPINESVIFFGQ 107 (120)
Q Consensus 76 fNapVy~enK~~IGKVdEIFGPIn~~yfSVKl 107 (120)
.+..|++++.+.+|+|.||+=.-.+-.+.|+.
T Consensus 98 iG~~V~~~~g~~lG~V~~v~~~ga~dvlvI~~ 129 (165)
T PRK14592 98 IGMEVKLEDNTIYGYIKKIYNFGSCDIIEISL 129 (165)
T ss_pred CCcEEEcCCCCEEEEEEEEccCCCccEEEEEE
Confidence 57789999999999999999877666688883
No 15
>PRK13828 rimM 16S rRNA-processing protein RimM; Provisional
Probab=65.60 E-value=14 Score=27.73 Aligned_cols=33 Identities=6% Similarity=0.070 Sum_probs=26.9
Q ss_pred ccCCeeEecCcceeeeeeEeeccCCcceEEEee
Q 033397 75 YFNAPIYLQNKTQIGKVDEIFGPINESVIFFGQ 107 (120)
Q Consensus 75 yfNapVy~enK~~IGKVdEIFGPIn~~yfSVKl 107 (120)
..+..|++++.+.+|+|.+|+=.-.+-.+.||.
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 356789999999999999999866555578884
No 16
>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=60.12 E-value=24 Score=22.91 Aligned_cols=36 Identities=17% Similarity=0.244 Sum_probs=28.3
Q ss_pred ccCCeeEecCcceeeeeeEe-e-ccCCcceEEEeeCCCc
Q 033397 75 YFNAPIYLQNKTQIGKVDEI-F-GPINESVIFFGQNDGR 111 (120)
Q Consensus 75 yfNapVy~enK~~IGKVdEI-F-GPIn~~yfSVKl~~gv 111 (120)
..++||.. +.-+||+|++| | -.-+.+.+++++++..
T Consensus 16 ~~gs~V~~-~Gv~VG~V~~i~l~~~~~~v~v~~~i~~~~ 53 (81)
T PF02470_consen 16 SVGSPVRY-RGVEVGKVTSIELDPDGNRVRVTLRIDPDY 53 (81)
T ss_pred CCcCEEEE-CCEEEEEEEEEEEcCCCCEEEEEEEEcCCc
Confidence 45689988 57899999999 4 4456788888888876
No 17
>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=57.30 E-value=17 Score=24.24 Aligned_cols=34 Identities=21% Similarity=0.419 Sum_probs=24.7
Q ss_pred ecCCCCCccCCeeEecCcceeeeeeEe-eccCCcc
Q 033397 68 LTNEKIPYFNAPIYLQNKTQIGKVDEI-FGPINES 101 (120)
Q Consensus 68 ~t~~~VPyfNapVy~enK~~IGKVdEI-FGPIn~~ 101 (120)
++....|.-+++||.+|.++||.|-.. +.|..+-
T Consensus 27 ~~~~~~~~~g~~v~~~~g~~vG~vTS~~~sp~~~~ 61 (95)
T PF08669_consen 27 LDGDAPPRGGEPVYDEDGKPVGRVTSGAYSPTLGK 61 (95)
T ss_dssp ESSSS--STTCEEEETTTEEEEEEEEEEEETTTTE
T ss_pred ECCccCCCCCCEEEECCCcEEeEEEEEeECCCCCc
Confidence 344568899999999999999999875 6665433
No 18
>PRK13829 rimM 16S rRNA-processing protein RimM; Provisional
Probab=56.08 E-value=23 Score=26.66 Aligned_cols=34 Identities=15% Similarity=0.345 Sum_probs=27.1
Q ss_pred cCCeeEecCcceeeeeeEeeccCCcceEEEeeCCC
Q 033397 76 FNAPIYLQNKTQIGKVDEIFGPINESVIFFGQNDG 110 (120)
Q Consensus 76 fNapVy~enK~~IGKVdEIFGPIn~~yfSVKl~~g 110 (120)
.+-.|+ ++.+.+|+|.+|+=.-.+-++.||..++
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 456788 8999999999999866666678886554
No 19
>PRK14591 rimM 16S rRNA-processing protein RimM; Provisional
Probab=55.14 E-value=23 Score=26.79 Aligned_cols=32 Identities=16% Similarity=0.200 Sum_probs=26.7
Q ss_pred cCCeeEecCcceeeeeeEeeccCCcceEEEee
Q 033397 76 FNAPIYLQNKTQIGKVDEIFGPINESVIFFGQ 107 (120)
Q Consensus 76 fNapVy~enK~~IGKVdEIFGPIn~~yfSVKl 107 (120)
.+-.|++++.+.+|+|.||+=.-.+..+.||.
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 56789999999999999999876655577884
No 20
>KOG3262 consensus H/ACA small nucleolar RNP component GAR1 [Translation, ribosomal structure and biogenesis]
Probab=52.88 E-value=20 Score=29.34 Aligned_cols=6 Identities=83% Similarity=1.691 Sum_probs=2.4
Q ss_pred CCCCCC
Q 033397 9 GFRGGR 14 (120)
Q Consensus 9 ~f~~~~ 14 (120)
+||+++
T Consensus 15 gfRgg~ 20 (215)
T KOG3262|consen 15 GFRGGG 20 (215)
T ss_pred CcccCC
Confidence 344443
No 21
>cd04479 RPA3 RPA3: A subfamily of OB folds similar to human RPA3 (also called RPA14). RPA3 is the smallest subunit of Replication protein A (RPA). RPA is a nuclear ssDNA binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA3 is believed to have a structural role in assembly of the RPA heterotrimer.
Probab=51.94 E-value=55 Score=22.79 Aligned_cols=49 Identities=14% Similarity=0.174 Sum_probs=34.3
Q ss_pred cceEEeeeEEeeeCCcEEEeecCC-CCC-ccCCeeEecCcceeeeeeEeeccCCc
Q 033397 48 AEVVEVSSFLHACEGDAVTKLTNE-KIP-YFNAPIYLQNKTQIGKVDEIFGPINE 100 (120)
Q Consensus 48 ~~v~elG~f~H~ce~~lV~k~t~~-~VP-yfNapVy~enK~~IGKVdEIFGPIn~ 100 (120)
..|..+|++.+.-.+.++.++++. .|- .+|.|. ..+++++.||-|-.++
T Consensus 16 k~V~ivGkV~~~~~~~~~~~~~Dg~~v~v~l~~~~----~~~~~~~vEViG~V~~ 66 (101)
T cd04479 16 KTVRIVGKVEKVDGDSLTLISSDGVNVTVELNRPL----DLPISGYVEVIGKVSP 66 (101)
T ss_pred CEEEEEEEEEEecCCeEEEEcCCCCEEEEEeCCCC----CcccCCEEEEEEEECC
Confidence 578999999988766677777543 333 344443 4577888999886654
No 22
>COG0806 RimM RimM protein, required for 16S rRNA processing [Translation, ribosomal structure and biogenesis]
Probab=46.28 E-value=37 Score=26.48 Aligned_cols=32 Identities=19% Similarity=0.294 Sum_probs=27.8
Q ss_pred cCCeeEecCcceeeeeeEeeccCCcceEEEee
Q 033397 76 FNAPIYLQNKTQIGKVDEIFGPINESVIFFGQ 107 (120)
Q Consensus 76 fNapVy~enK~~IGKVdEIFGPIn~~yfSVKl 107 (120)
....||+++.+.+|||.||+=+=++-.+-||.
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 46689999999999999999988766688886
No 23
>PRK14590 rimM 16S rRNA-processing protein RimM; Provisional
Probab=46.06 E-value=44 Score=25.48 Aligned_cols=32 Identities=6% Similarity=0.148 Sum_probs=24.6
Q ss_pred cCCeeEecCcceee-eeeEeeccCCcceEEEee
Q 033397 76 FNAPIYLQNKTQIG-KVDEIFGPINESVIFFGQ 107 (120)
Q Consensus 76 fNapVy~enK~~IG-KVdEIFGPIn~~yfSVKl 107 (120)
.+-.|++++.+.+| +|.||.=.-.+..+.|+.
T Consensus 103 iG~~V~d~~g~~lGG~V~~v~~~~a~dllvV~~ 135 (171)
T PRK14590 103 IGLQAIDETGKPLNWKLTDVQDNPAHPILVFIK 135 (171)
T ss_pred cCcEEEeCCCCEeeeEEEEEecCCCceEEEEEC
Confidence 56789999999998 999998666544456543
No 24
>PRK14594 rimM 16S rRNA-processing protein RimM; Provisional
Probab=40.89 E-value=55 Score=24.74 Aligned_cols=31 Identities=16% Similarity=0.221 Sum_probs=25.7
Q ss_pred cCCeeEecCcceeeeeeEeeccCCcceEEEee
Q 033397 76 FNAPIYLQNKTQIGKVDEIFGPINESVIFFGQ 107 (120)
Q Consensus 76 fNapVy~enK~~IGKVdEIFGPIn~~yfSVKl 107 (120)
.+-.|+++ ...+|+|.+|+=.-.+..+.||.
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 46688986 78899999999877777788984
No 25
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=40.52 E-value=43 Score=23.03 Aligned_cols=27 Identities=19% Similarity=0.331 Sum_probs=19.8
Q ss_pred cCcceeeeeeEeeccCCcceEEEeeCCCcc
Q 033397 83 QNKTQIGKVDEIFGPINESVIFFGQNDGRY 112 (120)
Q Consensus 83 enK~~IGKVdEIFGPIn~~yfSVKl~~gv~ 112 (120)
++.+.+|+|.+.+| +-.|.|++.+|..
T Consensus 3 ~e~q~~g~V~~~lG---~~~~~V~~~dG~~ 29 (83)
T smart00652 3 EDGQEIAQVVKMLG---NGRLEVMCADGKE 29 (83)
T ss_pred CCCcEEEEEEEEcC---CCEEEEEECCCCE
Confidence 56778888888888 4457788777754
No 26
>PF13953 PapC_C: PapC C-terminal domain; PDB: 3L48_E 2XET_A 3RFZ_E 2KT6_A.
Probab=39.39 E-value=34 Score=22.02 Aligned_cols=27 Identities=22% Similarity=0.261 Sum_probs=17.4
Q ss_pred eecCCCCCccCCeeEecCcceeeeeeE
Q 033397 67 KLTNEKIPYFNAPIYLQNKTQIGKVDE 93 (120)
Q Consensus 67 k~t~~~VPyfNapVy~enK~~IGKVdE 93 (120)
+..+.+.+-|.|.|++++.+.+|-|.+
T Consensus 4 ~~~~G~~lPfGA~v~~~~g~~~g~Vg~ 30 (68)
T PF13953_consen 4 RDADGKPLPFGASVSDEDGNNIGIVGQ 30 (68)
T ss_dssp EETTSEE--TT-EEEETTSSEEEEB-G
T ss_pred EcCCCCcCCCCcEEEcCCCCEEEEEcC
Confidence 333445667999999999999987754
No 27
>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.
Probab=38.50 E-value=92 Score=20.05 Aligned_cols=28 Identities=25% Similarity=0.437 Sum_probs=21.3
Q ss_pred cCcceeeeeeEeeccCCcceEEEeeCCCcce
Q 033397 83 QNKTQIGKVDEIFGPINESVIFFGQNDGRYC 113 (120)
Q Consensus 83 enK~~IGKVdEIFGPIn~~yfSVKl~~gv~A 113 (120)
|+.+.+|+|-+.+| .-+|.|+++++..-
T Consensus 1 ee~e~~~~V~~~lG---~~~~~V~~~dg~~~ 28 (65)
T PF01176_consen 1 EEGEVIGRVTEMLG---NNLFEVECEDGEER 28 (65)
T ss_dssp STTEEEEEEEEEES---SSEEEEEETTSEEE
T ss_pred CCcEEEEEEEEECC---CCEEEEEeCCCCEE
Confidence 45678899999998 44588888887653
No 28
>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=36.14 E-value=47 Score=24.46 Aligned_cols=27 Identities=15% Similarity=0.343 Sum_probs=23.2
Q ss_pred CCCCCCcceEEeeeEEeeeCCcEEEee
Q 033397 42 RDEGPPAEVVEVSSFLHACEGDAVTKL 68 (120)
Q Consensus 42 ~~~gPP~~v~elG~f~H~ce~~lV~k~ 68 (120)
-+.|+|+--+-+|++.|..+++|-+--
T Consensus 17 i~lG~~~gk~V~G~I~hvv~ddLYIDf 43 (104)
T PF10246_consen 17 IQLGDPEGKIVIGKIFHVVDDDLYIDF 43 (104)
T ss_pred hhcCCccCCEEEEEEEEEecCceEEEe
Confidence 467899999999999999999986654
No 29
>COG1873 Protein implicated in RNA metabolism, contains PRC-barrel domain [General function prediction only]
Probab=35.93 E-value=36 Score=23.66 Aligned_cols=20 Identities=10% Similarity=0.373 Sum_probs=17.2
Q ss_pred ccCCeeEecCcceeeeeeEe
Q 033397 75 YFNAPIYLQNKTQIGKVDEI 94 (120)
Q Consensus 75 yfNapVy~enK~~IGKVdEI 94 (120)
.+.-.||+.|.+.+|+|.||
T Consensus 11 l~gk~V~~~~G~~vG~V~dv 30 (87)
T COG1873 11 LLGKEVITNDGKYVGTVSDV 30 (87)
T ss_pred hcCcEEEcCCCeEEEEEEeE
Confidence 35668999999999999987
No 30
>COG0311 PDX2 Predicted glutamine amidotransferase involved in pyridoxine biosynthesis [Coenzyme metabolism]
Probab=33.39 E-value=58 Score=26.40 Aligned_cols=55 Identities=15% Similarity=0.281 Sum_probs=39.8
Q ss_pred eeeCCcEEEeecCC--CCC--ccCCeeEecCcceeeeeeEeeccCCcceEEEeeCCCcceeeeE
Q 033397 58 HACEGDAVTKLTNE--KIP--YFNAPIYLQNKTQIGKVDEIFGPINESVIFFGQNDGRYCCNFI 117 (120)
Q Consensus 58 H~ce~~lV~k~t~~--~VP--yfNapVy~enK~~IGKVdEIFGPIn~~yfSVKl~~gv~AsSf~ 117 (120)
-++|.++-++-... .+| ++-||+..+ +|+-.+++...++..+.+|.. ++-|+||-
T Consensus 115 dSFe~~~di~~~~~~~~~~avFIRAP~I~~----vg~~V~vLa~l~~~iVav~qg-n~LatsFH 173 (194)
T COG0311 115 DSFETELDIEGFGLPFPFPAVFIRAPVIEE----VGDGVEVLATLDGRIVAVKQG-NILATSFH 173 (194)
T ss_pred ccceeeEEeecccCCCcceEEEEEcceeeh----hcCcceEeeeeCCEEEEEEeC-CEEEEecC
Confidence 34556666664222 254 678898864 455578999999999999987 99999983
No 31
>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=31.10 E-value=1.2e+02 Score=20.53 Aligned_cols=26 Identities=19% Similarity=0.217 Sum_probs=17.9
Q ss_pred ceeeeeeEeeccCCcceEEEeeCCCccee
Q 033397 86 TQIGKVDEIFGPINESVIFFGQNDGRYCC 114 (120)
Q Consensus 86 ~~IGKVdEIFGPIn~~yfSVKl~~gv~As 114 (120)
+-.|+|.|.++ +-+|.|++++|...-
T Consensus 6 e~~G~V~e~L~---~~~f~V~l~ng~~vl 31 (68)
T TIGR00008 6 EMEGKVTESLP---NAMFRVELENGHEVL 31 (68)
T ss_pred EEEEEEEEECC---CCEEEEEECCCCEEE
Confidence 34577888877 446788888776543
No 32
>COG3881 PRC-barrel domain containing protein [General function prediction only]
Probab=30.66 E-value=70 Score=25.56 Aligned_cols=36 Identities=31% Similarity=0.528 Sum_probs=26.4
Q ss_pred ccCCeeEecC-cceeeeeeEe-eccCCcceEEEeeCCC
Q 033397 75 YFNAPIYLQN-KTQIGKVDEI-FGPINESVIFFGQNDG 110 (120)
Q Consensus 75 yfNapVy~en-K~~IGKVdEI-FGPIn~~yfSVKl~~g 110 (120)
...+|||.+. .+++|.|+|| |-+--+...-++.+++
T Consensus 7 leG~pVys~~tg~~lg~V~Dvif~~~gdrvl~flvnkg 44 (176)
T COG3881 7 LEGAPVYSTKTGEKLGAVDDVIFNFSGDRVLGFLVNKG 44 (176)
T ss_pred hcCCceEEecccccccceeeEEEecCCCeEEEEEEecC
Confidence 3578999876 9999999985 6665555566666655
No 33
>PF05284 DUF736: Protein of unknown function (DUF736); InterPro: IPR007948 This family consists of several uncharacterised bacterial proteins of unknown function.
Probab=28.76 E-value=1e+02 Score=22.15 Aligned_cols=38 Identities=13% Similarity=0.203 Sum_probs=28.8
Q ss_pred CCCCccCCeeEecC--cceeeeeeEeeccC-CcceEEEeeCCC
Q 033397 71 EKIPYFNAPIYLQN--KTQIGKVDEIFGPI-NESVIFFGQNDG 110 (120)
Q Consensus 71 ~~VPyfNapVy~en--K~~IGKVdEIFGPI-n~~yfSVKl~~g 110 (120)
++.|-+ .||..+ ..+||-.=+=.+.. ...|+||||++-
T Consensus 38 e~aPdy--RV~~~~~~~~EvGaaW~~~~~~tg~~Ylsl~LddP 78 (107)
T PF05284_consen 38 ENAPDY--RVYAGPRGGVEVGAAWKKTSKDTGRDYLSLKLDDP 78 (107)
T ss_pred CCCCCE--EEEecCCCCCceeeeehhhccccCCceEEEEEcCC
Confidence 456633 566664 77888888888877 799999999975
No 34
>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=25.14 E-value=1.4e+02 Score=20.94 Aligned_cols=55 Identities=9% Similarity=0.082 Sum_probs=27.6
Q ss_pred ceEEeeeEEeeeCC-----cEEEeec-----CCCCCccCCeeEecCcceeeeeeEeeccCCcceEE
Q 033397 49 EVVEVSSFLHACEG-----DAVTKLT-----NEKIPYFNAPIYLQNKTQIGKVDEIFGPINESVIF 104 (120)
Q Consensus 49 ~v~elG~f~H~ce~-----~lV~k~t-----~~~VPyfNapVy~enK~~IGKVdEIFGPIn~~yfS 104 (120)
.+.++|.+.+++.. ..|++.. .+..++|++.-|..-.+-...-...|. .|++|+|
T Consensus 2 ~~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~~~~Wf~rP~et~~~~~~~~~-~~Evfls 66 (121)
T cd04717 2 LQYRVGDCVYVANPEDPSKPIIFRIERLWKDEDGEKFFFGCWFYRPEETFHEPTRKFY-KNEVFKS 66 (121)
T ss_pred CEEECCCEEEEeCCCCCCCCEEEEEeEEEECCCCCEEEEEEEEeChHHccCCCccccc-cCceEEc
Confidence 35667777666632 1233321 123566777777654443332233443 3666665
No 35
>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=24.62 E-value=1.4e+02 Score=21.80 Aligned_cols=10 Identities=40% Similarity=0.584 Sum_probs=6.2
Q ss_pred eeeeeEeecc
Q 033397 88 IGKVDEIFGP 97 (120)
Q Consensus 88 IGKVdEIFGP 97 (120)
||||.+|+=.
T Consensus 22 i~rI~~i~e~ 31 (122)
T cd04716 22 ICKITEFFEG 31 (122)
T ss_pred EEEEEEEEEc
Confidence 6666666643
No 36
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=24.56 E-value=1.6e+02 Score=20.94 Aligned_cols=24 Identities=25% Similarity=0.243 Sum_probs=14.8
Q ss_pred eeeeeeEeeccCCcceEEEeeCCCcce
Q 033397 87 QIGKVDEIFGPINESVIFFGQNDGRYC 113 (120)
Q Consensus 87 ~IGKVdEIFGPIn~~yfSVKl~~gv~A 113 (120)
..|+|.|+|+ +-.|.|+|+++..-
T Consensus 9 ~~G~V~e~Lp---~~~frV~LenG~~v 32 (87)
T PRK12442 9 LDGIVDEVLP---DSRFRVTLENGVEV 32 (87)
T ss_pred EEEEEEEECC---CCEEEEEeCCCCEE
Confidence 4567777766 33567777766543
No 37
>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=23.37 E-value=49 Score=26.14 Aligned_cols=9 Identities=22% Similarity=0.759 Sum_probs=4.1
Q ss_pred CCCCccCCe
Q 033397 71 EKIPYFNAP 79 (120)
Q Consensus 71 ~~VPyfNap 79 (120)
..-||+-..
T Consensus 66 ~~sPyy~~~ 74 (233)
T PF11705_consen 66 RDSPYYTES 74 (233)
T ss_pred HhCCCcccc
Confidence 345654433
No 38
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=22.58 E-value=1.3e+02 Score=21.55 Aligned_cols=26 Identities=19% Similarity=0.351 Sum_probs=13.9
Q ss_pred cCcceeeeeeEeeccCCcceEEEeeCCCc
Q 033397 83 QNKTQIGKVDEIFGPINESVIFFGQNDGR 111 (120)
Q Consensus 83 enK~~IGKVdEIFGPIn~~yfSVKl~~gv 111 (120)
++.+.+|+|.+.+| +-.|.|+++++.
T Consensus 19 ~e~e~~g~V~~~lG---~~~~~V~~~dG~ 44 (100)
T PRK04012 19 EEGEVFGVVEQMLG---ANRVRVRCMDGV 44 (100)
T ss_pred CCCEEEEEEEEEcC---CCEEEEEeCCCC
Confidence 44555666666665 224555555543
No 39
>cd00226 PRCH Photosynthetic reaction center (RC) complex, subunit H; RC is an integral membrane protein-pigment complex which catalyzes light-induced reduction of ubiquinone to ubiquinol, generating a transmembrane electrochemical gradient of protons used to produce ATP by ATP synthase. Subunit H is positioned mainly in the cytoplasm with one transmembrane alpha helix. Provides proton transfer pathway (water channels) connecting the terminal quinone electron acceptor of RC, to the aqueous phase. Found in photosynthetic bacteria: alpha, beta, and gamma proteobacteria.
Probab=22.28 E-value=73 Score=26.57 Aligned_cols=34 Identities=12% Similarity=0.008 Sum_probs=24.6
Q ss_pred ccCCeeEecCcceeeeeeEeeccC---CcceEEEeeC
Q 033397 75 YFNAPIYLQNKTQIGKVDEIFGPI---NESVIFFGQN 108 (120)
Q Consensus 75 yfNapVy~enK~~IGKVdEIFGPI---n~~yfSVKl~ 108 (120)
--.-+||..+.++||+|.|++==. .==|+-|.+.
T Consensus 148 prGl~V~g~DGevvGtV~Dv~vD~~e~~iRYLeVdtg 184 (246)
T cd00226 148 PRGLPVVGADGEVAGKVTDLWVDRPEQLFRYLEVELA 184 (246)
T ss_pred CCCCEeEcCCCcEeEEEEEEEEcCCcceEEEEEEEcC
Confidence 355689999999999999997311 1137777763
No 40
>cd08689 C2_fungal_Pkc1p C2 domain found in protein kinase C (Pkc1p) in Saccharomyces cerevisiae. This family is named after the protein kinase C in Saccharomyces cerevisiae, Pkc1p. Protein kinase C is a member of a family of Ser/Thr phosphotransferases that are involved in many cellular signaling pathways. PKC has two antiparallel coiled-coiled regions (ACC finger domain) (AKA PKC homology region 1 (HR1)/ Rho binding domain) upstream of the C2 domain and two C1 domains downstream. The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains, like those of PKC, are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that
Probab=21.45 E-value=61 Score=23.96 Aligned_cols=20 Identities=10% Similarity=-0.016 Sum_probs=15.6
Q ss_pred ccCCcceEEEeeCCCcceee
Q 033397 96 GPINESVIFFGQNDGRYCCN 115 (120)
Q Consensus 96 GPIn~~yfSVKl~~gv~AsS 115 (120)
.---++|++||.++.++|.+
T Consensus 20 ~~~~etyV~IKved~~kaRT 39 (109)
T cd08689 20 SKRPETYVSIKVEDVERART 39 (109)
T ss_pred ccCCCcEEEEEECCEEEEec
Confidence 33568999999999877743
No 41
>PF08770 SoxZ: Sulphur oxidation protein SoxZ; InterPro: IPR014880 SoxZ forms an anti parallel beta structure and forms a complex with SoxY. Sulphur oxidation occurs at the thiol of a conserved cysteine residue of the SoxY subunit []. ; PDB: 1V8H_B 2OX5_E 2OXG_E 2OXH_C.
Probab=20.94 E-value=1.1e+02 Score=21.47 Aligned_cols=55 Identities=15% Similarity=0.065 Sum_probs=26.8
Q ss_pred eEEeeeCCcEEEeecCCCCC--ccCCeeEecCcceeeeeeEeeccCCcceEEEeeCC
Q 033397 55 SFLHACEGDAVTKLTNEKIP--YFNAPIYLQNKTQIGKVDEIFGPINESVIFFGQND 109 (120)
Q Consensus 55 ~f~H~ce~~lV~k~t~~~VP--yfNapVy~enK~~IGKVdEIFGPIn~~yfSVKl~~ 109 (120)
-++|+-+.=|.--.+-..+| |++.....-|.+++=..|==..=-.+|||+.++..
T Consensus 20 li~HPMetGl~~d~tg~~iPa~~I~~v~v~~ng~~v~~~~~~~siS~NP~l~F~~~~ 76 (100)
T PF08770_consen 20 LISHPMETGLRKDQTGKYIPAHFIEEVEVTYNGKPVFRADWGPSISENPYLRFSFKG 76 (100)
T ss_dssp EE----B-S-BB-TTS-BB--B-EEEEEEEETTEEEEEEEE-TTB-SS-EEEEEEEE
T ss_pred EEECCCccccccCCCCCCCChHheEEEEEEECCEEEEEEEeCCcccCCCcEEEEEec
Confidence 35666665443322334477 77777777788887776644443377888777654
No 42
>PRK14593 rimM 16S rRNA-processing protein RimM; Provisional
Probab=20.27 E-value=3e+02 Score=21.00 Aligned_cols=33 Identities=15% Similarity=0.140 Sum_probs=24.3
Q ss_pred ccCCeeEecCcceeeeeeEeeccCCcceEEEeeC
Q 033397 75 YFNAPIYLQNKTQIGKVDEIFGPINESVIFFGQN 108 (120)
Q Consensus 75 yfNapVy~enK~~IGKVdEIFGPIn~~yfSVKl~ 108 (120)
.++-.|+++ .+.+|+|.||+=.-.+-.+.||..
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 356788886 588999999997555555677753
No 43
>PF09939 DUF2171: Uncharacterized protein conserved in bacteria (DUF2171); InterPro: IPR018684 This family of various hypothetical prokaryotic proteins has no known function.
Probab=20.15 E-value=1.2e+02 Score=20.61 Aligned_cols=20 Identities=20% Similarity=0.411 Sum_probs=18.1
Q ss_pred CCeeEecCcceeeeeeEeec
Q 033397 77 NAPIYLQNKTQIGKVDEIFG 96 (120)
Q Consensus 77 NapVy~enK~~IGKVdEIFG 96 (120)
..+|+..+...||+||.+=|
T Consensus 5 hmeVi~sdG~~vGtVDhveG 24 (67)
T PF09939_consen 5 HMEVIGSDGVHVGTVDHVEG 24 (67)
T ss_pred CCEEEeCCCCEEEEEeeEeC
Confidence 45789999999999999988
Done!