Query 028058
Match_columns 214
No_of_seqs 104 out of 188
Neff 3.3
Searched_HMMs 46136
Date Fri Mar 29 05:35:11 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028058.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028058hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR02888 spore_YlmC_YmxH spor 99.9 2.5E-22 5.4E-27 149.4 6.8 67 118-184 1-76 (76)
2 COG1873 Protein implicated in 99.5 1.4E-13 2.9E-18 104.8 6.7 70 115-185 4-79 (87)
3 PF05239 PRC: PRC-barrel domai 99.3 3.7E-12 8E-17 90.4 5.9 72 115-187 2-77 (79)
4 COG3881 PRC-barrel domain cont 98.0 1.4E-05 3.1E-10 68.4 7.1 68 121-188 85-156 (176)
5 COG3881 PRC-barrel domain cont 97.7 0.00011 2.4E-09 63.1 6.7 73 116-189 1-75 (176)
6 cd00226 PRCH Photosynthetic re 94.0 0.22 4.7E-06 45.1 7.3 61 120-183 146-207 (246)
7 PRK13829 rimM 16S rRNA-process 74.3 18 0.00039 29.9 7.4 51 117-170 89-140 (162)
8 KOG0918 Selenium-binding prote 62.7 8.1 0.00018 38.1 3.5 76 57-151 342-440 (476)
9 COG0806 RimM RimM protein, req 58.5 27 0.00059 29.9 5.6 51 117-172 101-151 (174)
10 TIGR01150 puhA photosynthetic 47.9 31 0.00067 31.8 4.5 36 121-157 150-185 (252)
11 PRK14592 rimM 16S rRNA-process 47.3 88 0.0019 25.9 6.8 64 117-185 92-160 (165)
12 TIGR02273 16S_RimM 16S rRNA pr 46.8 53 0.0012 26.9 5.4 50 116-171 94-144 (165)
13 smart00652 eIF1a eukaryotic tr 43.6 1E+02 0.0022 23.4 6.0 48 132-187 4-57 (83)
14 PRK14591 rimM 16S rRNA-process 41.7 48 0.0011 27.6 4.4 48 117-171 100-147 (169)
15 PRK04012 translation initiatio 41.0 1.1E+02 0.0024 24.1 6.1 57 123-187 11-73 (100)
16 PRK14594 rimM 16S rRNA-process 40.5 61 0.0013 26.9 4.9 46 117-170 97-142 (166)
17 PRK14593 rimM 16S rRNA-process 40.5 1.3E+02 0.0029 25.3 6.9 57 117-176 104-165 (184)
18 PRK00122 rimM 16S rRNA-process 39.0 72 0.0016 26.4 5.0 64 116-185 99-167 (172)
19 PLN00208 translation initiatio 33.9 1.3E+02 0.0029 25.5 5.9 56 124-187 23-84 (145)
20 PRK13828 rimM 16S rRNA-process 32.6 2.8E+02 0.0062 22.8 7.6 67 117-188 80-151 (161)
21 PTZ00329 eukaryotic translatio 30.3 1.9E+02 0.004 24.9 6.2 55 125-187 24-84 (155)
22 PF13028 DUF3889: Protein of u 29.4 95 0.0021 24.7 4.0 28 130-157 68-95 (97)
23 TIGR00523 eIF-1A eukaryotic/ar 29.0 1.9E+02 0.0042 22.7 5.7 54 122-183 8-67 (99)
24 PF05523 FdtA: WxcM-like, C-te 29.0 1.1E+02 0.0023 24.5 4.4 56 117-187 56-112 (131)
25 PF03413 PepSY: Peptidase prop 28.4 60 0.0013 21.3 2.4 14 140-153 49-62 (64)
26 PF06115 DUF956: Domain of unk 26.6 39 0.00084 27.9 1.5 15 167-181 47-62 (118)
27 PF13861 FLgD_tudor: FlgD Tudo 25.6 82 0.0018 21.9 2.8 53 115-176 3-60 (61)
28 cd04456 S1_IF1A_like S1_IF1A_l 25.3 2.6E+02 0.0056 21.0 5.6 38 142-187 15-52 (78)
29 PF00122 E1-E2_ATPase: E1-E2 A 24.5 50 0.0011 27.2 1.8 25 164-189 43-67 (230)
30 PF07533 BRK: BRK domain; Int 23.2 50 0.0011 22.8 1.3 12 126-137 9-20 (46)
31 PRK14590 rimM 16S rRNA-process 23.1 1.6E+02 0.0035 24.7 4.5 37 117-155 97-134 (171)
32 cd05793 S1_IF1A S1_IF1A: Trans 22.4 3E+02 0.0065 20.5 5.4 38 142-187 15-52 (77)
33 smart00592 BRK domain in trans 21.1 51 0.0011 22.6 1.0 12 126-137 7-18 (45)
34 PF01176 eIF-1a: Translation i 20.9 1.5E+02 0.0033 21.0 3.4 47 133-187 3-55 (65)
No 1
>TIGR02888 spore_YlmC_YmxH sporulation protein, YlmC/YmxH family. Members of this family belong to the broader family of PRC-barrel domain proteins (see Pfam model pfam05239), but are found only in endospore-forming bacteria of the Firmicutes lineage. Most such species have exactly two members of this family and all have at least one; the function is unknown. One of two members from Bacillus subtilis, YmxH, is strongly induced by the mother cell-specific sigma-E factor.
Probab=99.87 E-value=2.5e-22 Score=149.41 Aligned_cols=67 Identities=25% Similarity=0.410 Sum_probs=60.5
Q ss_pred EeccccCceeEeccCcceeeee--eeEEEECCCCEEEEEEECCC-----CCCCCC-eEEeccccceec-cEEEEec
Q 028058 118 RRSNLLAKQVISIQSAMSLGFV--SQLWVDTTSWVVLVVEVRPN-----LLSGEP-ERLLLEDICQVG-DVVLIED 184 (214)
Q Consensus 118 r~SeL~~KEVINi~dG~RLG~V--~DL~VD~~sG~V~AIiVp~~-----~f~ge~-~~IPWe~IkKIG-DVILVe~ 184 (214)
|+|||++|||||++||+|||+| .|+++|+++|+|.||++|++ ||+++. ..|||++|+||| |+|||+.
T Consensus 1 r~seL~~keVIni~~G~~lG~v~~~Dl~iD~~~G~I~aiIi~~~~~~~~~~~~~~~~~Ipw~~I~kIG~DvIlV~~ 76 (76)
T TIGR02888 1 RLSDLRGKEIINVNDGERLGVIGNIDLEIDEEDGRILSLIIPGKGKKFGLFSKGEEIEIPWDAIKKIGSDVILVDV 76 (76)
T ss_pred CHHHccCCCEEECCCCcEeeccccceEEEECCCCEEEEEEEeCCCcEEEeecCCcEEEEEhhhccEECCCEEEEeC
Confidence 5899999999999999999999 79999999999999999973 455544 579999999999 9999984
No 2
>COG1873 Protein implicated in RNA metabolism, contains PRC-barrel domain [General function prediction only]
Probab=99.46 E-value=1.4e-13 Score=104.83 Aligned_cols=70 Identities=29% Similarity=0.386 Sum_probs=59.6
Q ss_pred ceeEeccccCceeEeccCcceeeeeeeEEEECCCCEEEEEEECCC---CC--CCC-CeEEeccccceeccEEEEecC
Q 028058 115 QVMRRSNLLAKQVISIQSAMSLGFVSQLWVDTTSWVVLVVEVRPN---LL--SGE-PERLLLEDICQVGDVVLIEDE 185 (214)
Q Consensus 115 qmmr~SeL~~KEVINi~dG~RLG~V~DL~VD~~sG~V~AIiVp~~---~f--~ge-~~~IPWe~IkKIGDVILVe~~ 185 (214)
.||++|+|.+|+|+|. +|++||.|+|+.+|.++|+|.++.|.++ +| +++ ...|||+.|++|||.|||...
T Consensus 4 ~~~~~s~l~gk~V~~~-~G~~vG~V~dv~ld~~~g~i~~l~v~~~~~~l~~~~k~~~v~IP~~~V~aIGd~III~~~ 79 (87)
T COG1873 4 EMMRLSELLGKEVITN-DGKYVGTVSDVVLDIKEGKITGLLVIPTNKGLFLFGKGKEVIVPYEYVKAIGDIIIIKDV 79 (87)
T ss_pred hhheHHHhcCcEEEcC-CCeEEEEEEeEEEEccCCcEEEEEEecCCccccccCCCcEEEEehhHeEEecCEEEEech
Confidence 4789999999999999 9999999999999999999999999754 44 333 346999999999966666543
No 3
>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=99.31 E-value=3.7e-12 Score=90.36 Aligned_cols=72 Identities=19% Similarity=0.379 Sum_probs=62.9
Q ss_pred ceeEeccccCceeEeccCcceeeeeeeEEEECCCCEEEEEEECCC-CCC--CCCeEEeccccceec-cEEEEecCCc
Q 028058 115 QVMRRSNLLAKQVISIQSAMSLGFVSQLWVDTTSWVVLVVEVRPN-LLS--GEPERLLLEDICQVG-DVVLIEDESV 187 (214)
Q Consensus 115 qmmr~SeL~~KEVINi~dG~RLG~V~DL~VD~~sG~V~AIiVp~~-~f~--ge~~~IPWe~IkKIG-DVILVe~~~~ 187 (214)
.+++.|||.+++|+|.+ |+++|.|.|+.+|+.+|+|.++++..+ +|+ ++...|||+++.++| |.|+|+....
T Consensus 2 ~~~~~s~l~g~~V~~~~-G~~iG~V~di~id~~~~~i~~i~v~~~~~~~~~~~~~~iP~~~~v~~~~~~i~v~~~~~ 77 (79)
T PF05239_consen 2 DEFRLSELIGKEVIDRD-GEKIGKVKDIVIDPKTGKIVGIVVSSGGFFGIGGKKVLIPWDQIVDIGGDRIIVDPPKE 77 (79)
T ss_dssp CHGCHHHHTTSEEEETT-SCEEEEEEEEEEETTTTEEEEEEEEETTSTCSSSEEEEEEGGEEEEECTTEEEESSSTG
T ss_pred CeEEhHHccCCEEEcCC-CCEEEEEEEEEEeCCCCCEEEEEEcCCCccCcCCcEEEEcCeEeEEecCCEEEEcCCCC
Confidence 46889999999999998 999999999999999999999999876 332 344579999888888 9999998754
No 4
>COG3881 PRC-barrel domain containing protein [General function prediction only]
Probab=98.04 E-value=1.4e-05 Score=68.44 Aligned_cols=68 Identities=16% Similarity=0.331 Sum_probs=60.7
Q ss_pred cccCceeEeccCcceeeeeeeEEEECCCCEEEEEEECCCCCC---CCCeEEeccccceec-cEEEEecCCcc
Q 028058 121 NLLAKQVISIQSAMSLGFVSQLWVDTTSWVVLVVEVRPNLLS---GEPERLLLEDICQVG-DVVLIEDESVM 188 (214)
Q Consensus 121 eL~~KEVINi~dG~RLG~V~DL~VD~~sG~V~AIiVp~~~f~---ge~~~IPWe~IkKIG-DVILVe~~~~~ 188 (214)
++++.++++-.+|.+||.|.|+.+|.++|+|+|..+..+||+ +....|+=.+-.++| |.++|..+...
T Consensus 85 e~m~mk~~lt~dG~iLGmveDVyFdek~gkIvgyevS~GffADlt~gRkiira~~~v~vgKD~~ivs~~~~~ 156 (176)
T COG3881 85 EIMNMKVILTYDGTILGMVEDVYFDEKTGKIVGYEVSRGFFADLTSGRKIIRAGNYVLVGKDLFIVSNDKNL 156 (176)
T ss_pred HhhcCceEeccCCcEeeeeeEEEEeccCCcEEEEEecCchhhhccCCceEEECCCcEEecccEEEecCCcch
Confidence 567778888999999999999999999999999999999995 346689999999999 99999887654
No 5
>COG3881 PRC-barrel domain containing protein [General function prediction only]
Probab=97.69 E-value=0.00011 Score=63.11 Aligned_cols=73 Identities=18% Similarity=0.179 Sum_probs=64.2
Q ss_pred eeEeccccCceeEeccCcceeeeeeeEEEECCCCEEEEEEECCC-CCCCCCeEEeccccceec-cEEEEecCCccc
Q 028058 116 VMRRSNLLAKQVISIQSAMSLGFVSQLWVDTTSWVVLVVEVRPN-LLSGEPERLLLEDICQVG-DVVLIEDESVME 189 (214)
Q Consensus 116 mmr~SeL~~KEVINi~dG~RLG~V~DL~VD~~sG~V~AIiVp~~-~f~ge~~~IPWe~IkKIG-DVILVe~~~~~e 189 (214)
|++--||.+.+|++.+||++||.|.|+.+|.+.++|.++.+-.+ +| ..-..+|..+|.-|| |.|+...+...-
T Consensus 1 Mit~~EleG~pVys~~tg~~lg~V~Dvif~~~gdrvl~flvnkggwf-h~h~~lp~~~i~Sig~k~Imi~vp~~~~ 75 (176)
T COG3881 1 MITSRELEGAPVYSTKTGEKLGAVDDVIFNFSGDRVLGFLVNKGGWF-HKHCCLPVKNIVSIGSKMIMIYVPYKGS 75 (176)
T ss_pred CccchhhcCCceEEecccccccceeeEEEecCCCeEEEEEEecCcEE-eeeeeeeecceeeeccceEEEeccccce
Confidence 56677999999999999999999999999999999999999765 44 455689999999999 999998877644
No 6
>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=93.99 E-value=0.22 Score=45.14 Aligned_cols=61 Identities=23% Similarity=0.258 Sum_probs=50.0
Q ss_pred ccccCceeEeccCcceeeeeeeEEEECCCCEEEEEEECCCCCCCCCeEEeccccceec-cEEEEe
Q 028058 120 SNLLAKQVISIQSAMSLGFVSQLWVDTTSWVVLVVEVRPNLLSGEPERLLLEDICQVG-DVVLIE 183 (214)
Q Consensus 120 SeL~~KEVINi~dG~RLG~V~DL~VD~~sG~V~AIiVp~~~f~ge~~~IPWe~IkKIG-DVILVe 183 (214)
.|+++..|+.. ||+.+|.|.|+|+|..+|.|.-++|-.+. ++++.-|| -.+.+|- +.|.|+
T Consensus 146 ~DprGl~V~g~-DGevvGtV~Dv~vD~~e~~iRYLeVdtg~-~gkkVLLP-i~~~rId~~~V~V~ 207 (246)
T cd00226 146 VDPRGLPVVGA-DGEVAGKVTDLWVDRPEQLFRYLEVELAG-GGRTVLLP-MGFAKVKSDRVKVT 207 (246)
T ss_pred CCCCCCEeEcC-CCcEeEEEEEEEEcCCcceEEEEEEEcCC-CCCEEEEE-eEEEEecCCEEEEe
Confidence 57999999998 99999999999999999999999997654 34555577 5556776 888887
No 7
>PRK13829 rimM 16S rRNA-processing protein RimM; Provisional
Probab=74.29 E-value=18 Score=29.95 Aligned_cols=51 Identities=20% Similarity=0.095 Sum_probs=37.6
Q ss_pred eEeccccCceeEeccCcceeeeeeeEEEECCCCEEEEEEECCC-CCCCCCeEEec
Q 028058 117 MRRSNLLAKQVISIQSAMSLGFVSQLWVDTTSWVVLVVEVRPN-LLSGEPERLLL 170 (214)
Q Consensus 117 mr~SeL~~KEVINi~dG~RLG~V~DL~VD~~sG~V~AIiVp~~-~f~ge~~~IPW 170 (214)
.-..||.+-+|+ .+|..||.|.++ ++.-.+.|..|..+++ +++.+..-||+
T Consensus 89 yY~~dLiG~~V~--~~g~~lG~V~~v-~~~ga~dvlvV~~~~~~~~~~k~~LIP~ 140 (162)
T PRK13829 89 YYYHELRGLPVY--VDGEPLGEVVDV-EDAGAQDLLVIRHVGGSLRARATYFVPL 140 (162)
T ss_pred EEehhccCeEEE--ECCEeeEEEEEE-ecCCCceEEEEEeCCCCCccCceEEEcc
Confidence 779999999999 799999999997 5655666766654544 33334446887
No 8
>KOG0918 consensus Selenium-binding protein [Inorganic ion transport and metabolism]
Probab=62.68 E-value=8.1 Score=38.07 Aligned_cols=76 Identities=22% Similarity=0.217 Sum_probs=43.5
Q ss_pred CCCCCccccccccceeeeeeccccCCchhhhhHhhhhhhhhccCCCCCC-cccccccccceeEeccccCceeEeccCcce
Q 028058 57 PPSKNQELFDELGFKDKFSVNSAEENSREIAEVKEEKREEEKDGSDGSS-EKVKLRRGRQVMRRSNLLAKQVISIQSAMS 135 (214)
Q Consensus 57 ~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~e~~~~~~~~-~~~~~~~~~qmmr~SeL~~KEVINi~dG~R 135 (214)
-+++|+.+=||+-.---+.-+ + ..-++++ ++++...|-+- --...||++|||.+|- ||+|
T Consensus 342 sDP~n~kLtgQi~lGG~i~~~---s---~vkvl~~---e~~~~~~ea~~vKGrkl~GGPQMlQLSL----------DGKR 402 (476)
T KOG0918|consen 342 SDPKNPKLTGQIFLGGSIQKG---S---PVKVLEE---EGLKKQPEALYVKGRKLRGGPQMLQLSL----------DGKR 402 (476)
T ss_pred CCCCCcceEEEEEECcEeecC---C---ceEEecc---ccccCCCccceecCccccCCceeEEecc----------CCcE
Confidence 577888777774322111111 1 1222222 13333333222 3456799999999984 7888
Q ss_pred e----------------------eeeeeEEEECCCCEE
Q 028058 136 L----------------------GFVSQLWVDTTSWVV 151 (214)
Q Consensus 136 L----------------------G~V~DL~VD~~sG~V 151 (214)
| |.+-+++||+..|.+
T Consensus 403 LYVt~SLys~WD~QFYPE~v~~G~~miqidvdt~~g~~ 440 (476)
T KOG0918|consen 403 LYVTNSLYSAWDRQFYPELVSKGSHMIQIDVDTVKGGL 440 (476)
T ss_pred EEEEchhhhhhHhhhCHHHHhcCceEEEEeeeccCCce
Confidence 7 566778888877754
No 9
>COG0806 RimM RimM protein, required for 16S rRNA processing [Translation, ribosomal structure and biogenesis]
Probab=58.46 E-value=27 Score=29.94 Aligned_cols=51 Identities=22% Similarity=0.307 Sum_probs=39.6
Q ss_pred eEeccccCceeEeccCcceeeeeeeEEEECCCCEEEEEEECCCCCCCCCeEEeccc
Q 028058 117 MRRSNLLAKQVISIQSAMSLGFVSQLWVDTTSWVVLVVEVRPNLLSGEPERLLLED 172 (214)
Q Consensus 117 mr~SeL~~KEVINi~dG~RLG~V~DL~VD~~sG~V~AIiVp~~~f~ge~~~IPWe~ 172 (214)
.-..||.+-+|+|.. |+.||.|.++ +++-.+.|..|..+. +++...||.-+
T Consensus 101 fY~~DLiG~~V~~~~-g~~lG~V~~i-~~~Ga~Dvl~V~~~~---~~k~~LIPf~~ 151 (174)
T COG0806 101 FYYHDLIGLEVVTED-GELLGKVTEI-LETGANDVLVVKAKG---GKKERLIPFVD 151 (174)
T ss_pred EEeEeecCcEEEcCC-CcEEEEEEEE-eeCCCccEEEEEecC---CCcEEEecchH
Confidence 779999999999998 9999999997 788888888777622 12334566654
No 10
>TIGR01150 puhA photosynthetic reaction center, subunit H, bacterial. This model describes the photosynthetic reaction center H subunit in non-oxygenic photosynthetic bacteria. The reaction center is an integral membrane pigment-protein that carries out light-driven electron transfer reactions. At the core of reaction center is a collection light-harvesting cofactors and closely associated polypeptides. The core protein complex is made of L, M and H subunits. The common cofactors include bacterichlorophyll, bacteriopheophytins, ubiquinone and no-heme ferrous iron. The net result of electron tranfer reactions is the establishment of proton electrochemical gradient and production of reducing equivalents in the form of NADH. Ultimately, the process results in the reduction of C02 to carbohydrates(C6H12O6) In non-oxygenic organisms, the electron donor is an organic acid rather than water. Much of our current functional understanding of photosynthesis comes from the structural determination
Probab=47.85 E-value=31 Score=31.79 Aligned_cols=36 Identities=25% Similarity=0.346 Sum_probs=30.9
Q ss_pred cccCceeEeccCcceeeeeeeEEEECCCCEEEEEEEC
Q 028058 121 NLLAKQVISIQSAMSLGFVSQLWVDTTSWVVLVVEVR 157 (214)
Q Consensus 121 eL~~KEVINi~dG~RLG~V~DL~VD~~sG~V~AIiVp 157 (214)
|-+++.|+-- ||..-|.|+|+|||.-.-.|.-+.|.
T Consensus 150 DPrG~pV~g~-Dg~v~GtV~D~WVDr~E~~iRYlEVe 185 (252)
T TIGR01150 150 DPRGLPVVAA-DGEVAGKVTDLWVDRPEQYFRYLEVE 185 (252)
T ss_pred CCCCCeeEcC-CCceeeEEEEEEEcCccceeeEEEEE
Confidence 5678888875 99999999999999998888887774
No 11
>PRK14592 rimM 16S rRNA-processing protein RimM; Provisional
Probab=47.34 E-value=88 Score=25.86 Aligned_cols=64 Identities=9% Similarity=0.222 Sum_probs=42.8
Q ss_pred eEeccccCceeEeccCcceeeeeeeEEEECCCCEEEEEEECCCCCCCCCeEEeccc--cceec---cEEEEecC
Q 028058 117 MRRSNLLAKQVISIQSAMSLGFVSQLWVDTTSWVVLVVEVRPNLLSGEPERLLLED--ICQVG---DVVLIEDE 185 (214)
Q Consensus 117 mr~SeL~~KEVINi~dG~RLG~V~DL~VD~~sG~V~AIiVp~~~f~ge~~~IPWe~--IkKIG---DVILVe~~ 185 (214)
.-..||.+-+|++. +|..||.|.++ ++.-.+.|..|..+.. +++..||+-+ |.+|= -.|.|+..
T Consensus 92 ~y~~dLiG~~V~~~-~g~~lG~V~~v-~~~ga~dvlvI~~~~~---~ke~LIP~v~~~V~~IDle~k~I~v~~p 160 (165)
T PRK14592 92 FYQSDLIGMEVKLE-DNTIYGYIKKI-YNFGSCDIIEISLTST---KKSTMLPFTKEIFPHINVKERYIILVPP 160 (165)
T ss_pred EEHHHcCCcEEEcC-CCCEEEEEEEE-ccCCCccEEEEEECCC---CcEEEEecchhcccEEECCCCEEEEECc
Confidence 67899999999997 57889999997 5666666766653221 2334577743 44442 45666553
No 12
>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=46.75 E-value=53 Score=26.90 Aligned_cols=50 Identities=20% Similarity=0.263 Sum_probs=35.8
Q ss_pred eeEeccccCceeEeccCcceeeeeeeEEEECCCCEEEEEEE-CCCCCCCCCeEEecc
Q 028058 116 VMRRSNLLAKQVISIQSAMSLGFVSQLWVDTTSWVVLVVEV-RPNLLSGEPERLLLE 171 (214)
Q Consensus 116 mmr~SeL~~KEVINi~dG~RLG~V~DL~VD~~sG~V~AIiV-p~~~f~ge~~~IPWe 171 (214)
-.-..||.+.+|++ .+|..||.|.|+ ++.-.+.+..|.. ++ +++..||+.
T Consensus 94 e~y~~dLiG~~V~d-~~~~~lG~V~~v-~~~~a~dll~V~~~~~----~ke~liP~~ 144 (165)
T TIGR02273 94 EYYWTDLIGLEVVT-EEGEELGKVVEI-LETGANDVLVVRSKKG----KKEVLIPFV 144 (165)
T ss_pred CEEhhHhCCcEEEc-CCCcEEEEEEEE-ecCCCccEEEEEECCC----CcEEEEECc
Confidence 37799999999999 467889999997 5655566666654 22 234458874
No 13
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=43.63 E-value=1e+02 Score=23.38 Aligned_cols=48 Identities=15% Similarity=0.167 Sum_probs=32.1
Q ss_pred Ccceeeeeee------EEEECCCCEEEEEEECCCCCCCCCeEEeccccceeccEEEEecCCc
Q 028058 132 SAMSLGFVSQ------LWVDTTSWVVLVVEVRPNLLSGEPERLLLEDICQVGDVVLIEDESV 187 (214)
Q Consensus 132 dG~RLG~V~D------L~VD~~sG~V~AIiVp~~~f~ge~~~IPWe~IkKIGDVILVe~~~~ 187 (214)
.|.-+|.|.+ +.|-+..|...-..+|+.| +...+| +.||.|+|+..+.
T Consensus 4 e~q~~g~V~~~lG~~~~~V~~~dG~~~la~ipgK~--Rk~iwI------~~GD~VlVe~~~~ 57 (83)
T smart00652 4 DGQEIAQVVKMLGNGRLEVMCADGKERLARIPGKM--RKKVWI------RRGDIVLVDPWDF 57 (83)
T ss_pred CCcEEEEEEEEcCCCEEEEEECCCCEEEEEEchhh--cccEEE------cCCCEEEEEecCC
Confidence 5566677755 4566667877777888886 233333 4589999987654
No 14
>PRK14591 rimM 16S rRNA-processing protein RimM; Provisional
Probab=41.73 E-value=48 Score=27.57 Aligned_cols=48 Identities=21% Similarity=0.249 Sum_probs=34.5
Q ss_pred eEeccccCceeEeccCcceeeeeeeEEEECCCCEEEEEEECCCCCCCCCeEEecc
Q 028058 117 MRRSNLLAKQVISIQSAMSLGFVSQLWVDTTSWVVLVVEVRPNLLSGEPERLLLE 171 (214)
Q Consensus 117 mr~SeL~~KEVINi~dG~RLG~V~DL~VD~~sG~V~AIiVp~~~f~ge~~~IPWe 171 (214)
.-..||.+-+|++. +|..||.|.++ ++.-.+.+..|. + + +++..||+-
T Consensus 100 ~Y~~dLiG~~V~d~-~g~~lG~V~~v-~~~ga~dll~I~-~-~---~ke~LIP~~ 147 (169)
T PRK14591 100 VYFKDLIGCSVKNI-NNDSFGVVVDI-IETGANEVLVCK-E-D---NSEYLIPYV 147 (169)
T ss_pred EEeeeecCcEEEeC-CCCEEEEEEEE-eecCCceEEEEE-c-C---CeEEEEeCh
Confidence 77999999999995 78899999997 566566666543 2 1 333457763
No 15
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=40.97 E-value=1.1e+02 Score=24.12 Aligned_cols=57 Identities=16% Similarity=0.154 Sum_probs=39.1
Q ss_pred cCceeEeccCcceeeeeee------EEEECCCCEEEEEEECCCCCCCCCeEEeccccceeccEEEEecCCc
Q 028058 123 LAKQVISIQSAMSLGFVSQ------LWVDTTSWVVLVVEVRPNLLSGEPERLLLEDICQVGDVVLIEDESV 187 (214)
Q Consensus 123 ~~KEVINi~dG~RLG~V~D------L~VD~~sG~V~AIiVp~~~f~ge~~~IPWe~IkKIGDVILVe~~~~ 187 (214)
..+++..-..|.-+|.|.+ +.|-+..|...-.-+|+.| +...+| +.||.|+|+..+.
T Consensus 11 ~~~~~~~p~e~e~~g~V~~~lG~~~~~V~~~dG~~~la~i~GK~--Rk~IwI------~~GD~VlVe~~~~ 73 (100)
T PRK04012 11 TRVRLPMPEEGEVFGVVEQMLGANRVRVRCMDGVERMGRIPGKM--KKRMWI------REGDVVIVAPWDF 73 (100)
T ss_pred eeEEccCCCCCEEEEEEEEEcCCCEEEEEeCCCCEEEEEEchhh--cccEEe------cCCCEEEEEeccc
Confidence 3455666678888888876 4566667777777788876 233333 4589999987665
No 16
>PRK14594 rimM 16S rRNA-processing protein RimM; Provisional
Probab=40.54 E-value=61 Score=26.95 Aligned_cols=46 Identities=15% Similarity=0.127 Sum_probs=34.9
Q ss_pred eEeccccCceeEeccCcceeeeeeeEEEECCCCEEEEEEECCCCCCCCCeEEec
Q 028058 117 MRRSNLLAKQVISIQSAMSLGFVSQLWVDTTSWVVLVVEVRPNLLSGEPERLLL 170 (214)
Q Consensus 117 mr~SeL~~KEVINi~dG~RLG~V~DL~VD~~sG~V~AIiVp~~~f~ge~~~IPW 170 (214)
.-..||.+-+|++ . |..||.|.++ +++-.+-+..|. + .+++..|||
T Consensus 97 ~Y~~dLiG~~V~~-~-g~~lG~V~~v-~~~ga~dll~V~-~----~~ke~LIPf 142 (166)
T PRK14594 97 YYFGKLIGYAIVN-D-GKELGEVVSF-FECLNSVLLEVK-V----GIKLFFVPF 142 (166)
T ss_pred EeHhHccCeEEEE-C-CEEEEEEEEE-eeCCCcEEEEEE-e----CCEEEEEeC
Confidence 7799999999999 4 8999999997 566666666555 2 233446887
No 17
>PRK14593 rimM 16S rRNA-processing protein RimM; Provisional
Probab=40.49 E-value=1.3e+02 Score=25.32 Aligned_cols=57 Identities=18% Similarity=0.184 Sum_probs=36.8
Q ss_pred eEeccccCceeEeccCcceeeeeeeEEEECCCCEEEEEEECCCCC-C--CCCeEEeccc--ccee
Q 028058 117 MRRSNLLAKQVISIQSAMSLGFVSQLWVDTTSWVVLVVEVRPNLL-S--GEPERLLLED--ICQV 176 (214)
Q Consensus 117 mr~SeL~~KEVINi~dG~RLG~V~DL~VD~~sG~V~AIiVp~~~f-~--ge~~~IPWe~--IkKI 176 (214)
.-..||.+-+|++ +|..||.|.++ +++-.+.|..|.-....- . +++..||+-+ |.+|
T Consensus 104 yY~~dLiGl~V~~--~g~~lG~V~~v-~~~ga~dvlvV~~~~~~~~~~~~ke~LIP~~~~~V~~V 165 (184)
T PRK14593 104 FFYCDLVGLSVVE--ENEILGKVIEI-QRISQTDYFMVETTLSLVEKGLAKIFLIPYRDFYIQEI 165 (184)
T ss_pred EEeehccCcEEEE--CCEEeEEEEEE-ccCCCceEEEEEeccccccCCCCcEEEEeChhhhhceE
Confidence 6799999999997 49999999997 355455555544221111 1 2345699944 4444
No 18
>PRK00122 rimM 16S rRNA-processing protein RimM; Provisional
Probab=39.03 E-value=72 Score=26.38 Aligned_cols=64 Identities=19% Similarity=0.242 Sum_probs=41.7
Q ss_pred eeEeccccCceeEeccCcceeeeeeeEEEECCCCEEEEEEECCCCCCCCCeEEeccc--cceec---cEEEEecC
Q 028058 116 VMRRSNLLAKQVISIQSAMSLGFVSQLWVDTTSWVVLVVEVRPNLLSGEPERLLLED--ICQVG---DVVLIEDE 185 (214)
Q Consensus 116 mmr~SeL~~KEVINi~dG~RLG~V~DL~VD~~sG~V~AIiVp~~~f~ge~~~IPWe~--IkKIG---DVILVe~~ 185 (214)
-.-..||.+-+|++- +|..||.|.++ .+.-.+.+..|. .. ++++..||+-+ |.+|= -.|.|+..
T Consensus 99 e~y~~dLiG~~V~d~-~g~~lG~V~~v-~~~~a~dll~I~-~~---~~~e~liP~~~~~V~~iD~~~~~I~v~~p 167 (172)
T PRK00122 99 EYYWHDLIGLEVVDE-DGEELGKVTDI-LETGANDVLVVL-KD---KKEERLIPFVEEVVKEVDLEAKRITVDWP 167 (172)
T ss_pred CEEHHHhCCcEEEeC-CCcEEEEEEEE-ccCCCceEEEEE-CC---CCCEEEEecChhhCCEEECCCCEEEEeCC
Confidence 377999999999995 68899999997 566566665554 21 13344688842 23332 45555543
No 19
>PLN00208 translation initiation factor (eIF); Provisional
Probab=33.90 E-value=1.3e+02 Score=25.47 Aligned_cols=56 Identities=11% Similarity=0.119 Sum_probs=37.6
Q ss_pred CceeEeccCcceeeeeee------EEEECCCCEEEEEEECCCCCCCCCeEEeccccceeccEEEEecCCc
Q 028058 124 AKQVISIQSAMSLGFVSQ------LWVDTTSWVVLVVEVRPNLLSGEPERLLLEDICQVGDVVLIEDESV 187 (214)
Q Consensus 124 ~KEVINi~dG~RLG~V~D------L~VD~~sG~V~AIiVp~~~f~ge~~~IPWe~IkKIGDVILVe~~~~ 187 (214)
.++++--..|.-+|.|.. +.|-+..|...-.-+|+.| +...+| +.||.|||++.+.
T Consensus 23 ~~el~~p~egq~~g~V~~~lGn~~~~V~c~dG~~rLa~IpGKm--RKrIWI------~~GD~VlVel~~~ 84 (145)
T PLN00208 23 KRELIFKEDGQEYAQVLRMLGNGRCEALCIDGTKRLCHIRGKM--RKKVWI------AAGDIILVGLRDY 84 (145)
T ss_pred eeecccCCCCcEEEEEEEEcCCCEEEEEECCCCEEEEEEeccc--eeeEEe------cCCCEEEEEccCC
Confidence 356666678888999876 4565556777777788876 222222 4588888886665
No 20
>PRK13828 rimM 16S rRNA-processing protein RimM; Provisional
Probab=32.64 E-value=2.8e+02 Score=22.83 Aligned_cols=67 Identities=13% Similarity=0.159 Sum_probs=42.6
Q ss_pred eEeccccCceeEeccCcceeeeeeeEEEECCCCEEEEEEECCCCCCCCCeEEeccc--cceec---cEEEEecCCcc
Q 028058 117 MRRSNLLAKQVISIQSAMSLGFVSQLWVDTTSWVVLVVEVRPNLLSGEPERLLLED--ICQVG---DVVLIEDESVM 188 (214)
Q Consensus 117 mr~SeL~~KEVINi~dG~RLG~V~DL~VD~~sG~V~AIiVp~~~f~ge~~~IPWe~--IkKIG---DVILVe~~~~~ 188 (214)
+-..||.+-+|++. +|..||.|.++ +++-.+-|..|.-.. .++..-||+-. |.+|= -.|.|+..+-+
T Consensus 80 ~y~~dLiG~~V~d~-~g~~lG~V~~V-~~~ga~dvlvV~~~~---~~ke~LIP~v~~~V~~VDl~~~~I~v~~peGL 151 (161)
T PRK13828 80 FYHADLIGLAAVDT-GGALLGRVKAV-HNFGAGDILEIAPPG---GGPTLLLPFTRAVVPTVDLAAGRVVADPPAEI 151 (161)
T ss_pred EEhhhccCCEEEeC-CCCEEEEEEEE-ccCCCccEEEEEECC---CCcEEEEeccccccCeEECCCCEEEEeCCccc
Confidence 67999999999986 67889999997 344344454443211 12334588744 44552 56777766543
No 21
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=30.27 E-value=1.9e+02 Score=24.93 Aligned_cols=55 Identities=13% Similarity=0.203 Sum_probs=37.0
Q ss_pred ceeEeccCcceeeeeee------EEEECCCCEEEEEEECCCCCCCCCeEEeccccceeccEEEEecCCc
Q 028058 125 KQVISIQSAMSLGFVSQ------LWVDTTSWVVLVVEVRPNLLSGEPERLLLEDICQVGDVVLIEDESV 187 (214)
Q Consensus 125 KEVINi~dG~RLG~V~D------L~VD~~sG~V~AIiVp~~~f~ge~~~IPWe~IkKIGDVILVe~~~~ 187 (214)
++++--..|.-+|.|.. +.|-+..|...---+|+.| +...+| +.||.|||++.+.
T Consensus 24 rel~~~eegq~~g~V~~~LGn~~f~V~c~dG~~rLa~I~GKm--RK~IWI------~~GD~VlVel~~y 84 (155)
T PTZ00329 24 RELVFKEEGQEYAQVLRMLGNGRLEAYCFDGVKRLCHIRGKM--RKRVWI------NIGDIILVSLRDF 84 (155)
T ss_pred eeeccCCCCcEEEEEEEEcCCCEEEEEECCCCEEEEEeeccc--eeeEEe------cCCCEEEEeccCC
Confidence 45555568888999976 4665566777777778876 222222 4589999987665
No 22
>PF13028 DUF3889: Protein of unknown function (DUF3889)
Probab=29.45 E-value=95 Score=24.67 Aligned_cols=28 Identities=7% Similarity=0.192 Sum_probs=25.3
Q ss_pred ccCcceeeeeeeEEEECCCCEEEEEEEC
Q 028058 130 IQSAMSLGFVSQLWVDTTSWVVLVVEVR 157 (214)
Q Consensus 130 i~dG~RLG~V~DL~VD~~sG~V~AIiVp 157 (214)
..+|+..|+..++..|+.|.+|.+|.+.
T Consensus 68 ~~~~kefgV~v~V~f~p~T~ki~~I~~~ 95 (97)
T PF13028_consen 68 REGGKEFGVFVTVSFNPKTEKIISINVE 95 (97)
T ss_pred EcCCeEEEEEEEEEEeCCCCcEEEEEEE
Confidence 4689999999999999999999999874
No 23
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=29.00 E-value=1.9e+02 Score=22.70 Aligned_cols=54 Identities=17% Similarity=0.197 Sum_probs=35.2
Q ss_pred ccCceeEeccCcceeeeeee------EEEECCCCEEEEEEECCCCCCCCCeEEeccccceeccEEEEe
Q 028058 122 LLAKQVISIQSAMSLGFVSQ------LWVDTTSWVVLVVEVRPNLLSGEPERLLLEDICQVGDVVLIE 183 (214)
Q Consensus 122 L~~KEVINi~dG~RLG~V~D------L~VD~~sG~V~AIiVp~~~f~ge~~~IPWe~IkKIGDVILVe 183 (214)
....++.+-..|.-+|.|.+ +.|-+..|...-.-+|+.| +...+| +.||.|||.
T Consensus 8 ~~~~~~p~~~e~e~~g~V~~~lG~~~~~V~~~dG~~~la~i~GK~--Rk~iwI------~~GD~VlVs 67 (99)
T TIGR00523 8 QIRVRLPRKEEGEILGVIEQMLGAGRVKVRCLDGKTRLGRIPGKL--KKRIWI------REGDVVIVK 67 (99)
T ss_pred cceeeCCCCCCCEEEEEEEEEcCCCEEEEEeCCCCEEEEEEchhh--cccEEe------cCCCEEEEE
Confidence 34455555567888888866 4566667777777788876 223333 458888884
No 24
>PF05523 FdtA: WxcM-like, C-terminal ; InterPro: IPR008894 This entry includes FdtA (Q6T1W8 from SWISSPROT) from Aneurinibacillus thermoaerophilus, which has been characterised as a dTDP-6-deoxy-3,4-keto-hexulose isomerase []. It also includes WxcM (Q93S92 from SWISSPROT) from Xanthomonas campestris pv campestris) []. ; PDB: 2PAK_A 2PAE_A 2PA7_B 2PAM_A.
Probab=29.00 E-value=1.1e+02 Score=24.51 Aligned_cols=56 Identities=14% Similarity=0.101 Sum_probs=31.9
Q ss_pred eEeccccCceeEeccCcceeeeeeeEEEECCCCEEEEEEECCCCCCCCCeEEeccccceec-cEEEEecCCc
Q 028058 117 MRRSNLLAKQVISIQSAMSLGFVSQLWVDTTSWVVLVVEVRPNLLSGEPERLLLEDICQVG-DVVLIEDESV 187 (214)
Q Consensus 117 mr~SeL~~KEVINi~dG~RLG~V~DL~VD~~sG~V~AIiVp~~~f~ge~~~IPWe~IkKIG-DVILVe~~~~ 187 (214)
..+-=+.++=.|.+.+|+.- ..+.+|..+ .+|.||++. |..+...+ |.||+-..+.
T Consensus 56 ~~~~~l~Gs~~v~~~d~~~~---~~~~L~~~~---~~L~Ippg~---------w~~~~~~s~~svlLv~as~ 112 (131)
T PF05523_consen 56 QWFIVLSGSFKVVLDDGREE---EEFILDEPN---KGLYIPPGV---------WHGIKNFSEDSVLLVLASE 112 (131)
T ss_dssp EEEEEEES-EEEEEE-SS-E---EEEEE--TT---EEEEE-TT----------EEEEE---TT-EEEEEESS
T ss_pred EEEEEEeCEEEEEEecCCCc---EEEEECCCC---eEEEECCch---------hhHhhccCCCcEEEEEcCC
Confidence 34555667777777777654 667777666 678899987 99999999 7777765554
No 25
>PF03413 PepSY: Peptidase propeptide and YPEB domain This Prosite motif covers only the active site. This is family M4 in the peptidase classification. ; InterPro: IPR005075 This signature, PepSY, is found in the propeptide of members of the MEROPS peptidase family M4 (clan MA(E)), which contains the thermostable thermolysins (3.4.24.27 from EC), and related thermolabile neutral proteases (bacillolysins) (3.4.24.28 from EC) from various species of Bacillus. It is also in many non-peptidase proteins, including Bacillus subtilis YpeB protein - a regulator of SleB spore cortex lytic enzyme - and a large number of eubacterial and archaeal cell wall-associated and secreted proteins which are mostly annotated as 'hypothetical protein'. Many extracellular bacterial proteases are produced as proenzymes. The propeptides usually have a dual function, i.e. they function as an intramolecular chaperone required for the folding of the polypeptide and as an inhibitor preventing premature activation of the enzyme. Analysis of the propeptide region of the M4 family of peptidases reveals two regions of conservation, the PepSY domain and a second domain, proximate to the N terminus, the FTP domain (IPR011096 from INTERPRO), which is also found in isolation in the propeptide of eukaryotic peptidases belong to MEROPS peptidase family M36. Propeptide domain swapping experiments, for example swapping the propeptide domain of PA protease with that of vibrolysin, both propeptides contain the FTP and PepSY domains, allows the PA protease domain to fold correctly and inhibits the C-terminal autoprocessing activity. However, swapping the propeptide of PA protease for the thermolysin propeptide, does not facilitate the correct folding nor the processing of the chimaeric protein into an active peptidase []. Mutational analysis of the Pseudomonas aeruginosa elastase gene revealed two mutations in the propeptide which resulted in the loss of inhibitory activity but not chaperone activity: A-15V and T-153I (where +1 is defined as the first residue of the mature peptidase). Both mutations resulted in peptidase activity, the T-153V mutation being much less effective than the A-15I mutation [] in activating peptidase activity. The T-153V mutation lies N-terminal to the FTP domain while the A-15I mutation is C-terminal to the PepSY domain. Given the diverse range of other proteins, both domains occur in in isolation, the exact function of each is still unclear; though it has been proposed that the PepSY domain primarily has inhibitory activity and in conjunction with the FTP domain in chaperone activity. ; GO: 0008237 metallopeptidase activity, 0008270 zinc ion binding, 0006508 proteolysis, 0005576 extracellular region; PDB: 2GU3_A 3NQZ_A 3NQY_A 2KGY_A.
Probab=28.38 E-value=60 Score=21.26 Aligned_cols=14 Identities=21% Similarity=0.339 Sum_probs=10.0
Q ss_pred eeEEEECCCCEEEE
Q 028058 140 SQLWVDTTSWVVLV 153 (214)
Q Consensus 140 ~DL~VD~~sG~V~A 153 (214)
-++.||..||+|+.
T Consensus 49 ~~v~VDa~tG~Il~ 62 (64)
T PF03413_consen 49 YEVYVDAYTGEILS 62 (64)
T ss_dssp EEEEEETTT--EEE
T ss_pred EEEEEECCCCeEEE
Confidence 56779999999986
No 26
>PF06115 DUF956: Domain of unknown function (DUF956); InterPro: IPR010360 This is a family of bacterial sequences with undetermined function.
Probab=26.61 E-value=39 Score=27.94 Aligned_cols=15 Identities=27% Similarity=0.235 Sum_probs=13.3
Q ss_pred EEeccccceec-cEEE
Q 028058 167 RLLLEDICQVG-DVVL 181 (214)
Q Consensus 167 ~IPWe~IkKIG-DVIL 181 (214)
.|||+.|..|+ +|.+
T Consensus 47 QIPW~eI~~V~a~V~f 62 (118)
T PF06115_consen 47 QIPWEEIDYVIASVSF 62 (118)
T ss_pred EeChhheeEEEEEEEE
Confidence 59999999999 8874
No 27
>PF13861 FLgD_tudor: FlgD Tudor-like domain; PDB: 3OSV_A 3C12_A.
Probab=25.62 E-value=82 Score=21.90 Aligned_cols=53 Identities=25% Similarity=0.323 Sum_probs=33.0
Q ss_pred ceeEeccccCceeEeccCcceeeeeeeEEEEC-CCCEEEEEEECCC--C--CCCCCeEEecccccee
Q 028058 115 QVMRRSNLLAKQVISIQSAMSLGFVSQLWVDT-TSWVVLVVEVRPN--L--LSGEPERLLLEDICQV 176 (214)
Q Consensus 115 qmmr~SeL~~KEVINi~dG~RLG~V~DL~VD~-~sG~V~AIiVp~~--~--f~ge~~~IPWe~IkKI 176 (214)
|++..+.|.+|+|.-- ..+...+ ..|+|.++...++ . +++....+|..+|++|
T Consensus 3 q~lqa~~lIGk~V~~~---------~~~~~~~~~~g~V~sV~~~~g~~~L~l~~~~~~v~l~~V~~v 60 (61)
T PF13861_consen 3 QMLQAASLIGKEVLVP---------KSVAATTLVSGRVESVTFSGGGPMLNLGGGGSTVPLSDVTEV 60 (61)
T ss_dssp HHHHTTCTTTSEEEEE---------EEEEE-EEEEEEEEEEEEETTEEEEEETTTCEEEECCCB-B-
T ss_pred HHHHHHHhcCCEEEEC---------CcEeeeeEEEEEEEEEEEcCCeEEEEEecCCcEEEHHHeEEe
Confidence 5666777888887654 3333333 3588888888765 2 2344556999999876
No 28
>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=25.29 E-value=2.6e+02 Score=20.98 Aligned_cols=38 Identities=13% Similarity=0.139 Sum_probs=25.0
Q ss_pred EEEECCCCEEEEEEECCCCCCCCCeEEeccccceeccEEEEecCCc
Q 028058 142 LWVDTTSWVVLVVEVRPNLLSGEPERLLLEDICQVGDVVLIEDESV 187 (214)
Q Consensus 142 L~VD~~sG~V~AIiVp~~~f~ge~~~IPWe~IkKIGDVILVe~~~~ 187 (214)
+.|-+..|...-.-+|+.| +...+| +.||.|+|+..+.
T Consensus 15 ~~V~~~dg~~~l~~i~gK~--Rk~iwI------~~GD~VlV~~~~~ 52 (78)
T cd04456 15 HEVECADGQRRLVSIPGKL--RKNIWI------KRGDFLIVDPIEE 52 (78)
T ss_pred EEEEECCCCEEEEEEchhh--ccCEEE------cCCCEEEEEeccc
Confidence 4555566777777888886 223333 4589999987665
No 29
>PF00122 E1-E2_ATPase: E1-E2 ATPase p-type cation-transporting ATPase superfamily signature H+-transporting ATPase (proton pump) signature sodium/potassium-transporting ATPase signature; InterPro: IPR008250 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. P-ATPases (sometime known as E1-E2 ATPases) (3.6.3.- from EC) are found in bacteria and in a number of eukaryotic plasma membranes and organelles []. P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, each of which transports a specific type of ion: H+, Na+, K+, Mg2+, Ca2+, Ag+ and Ag2+, Zn2+, Co2+, Pb2+, Ni2+, Cd2+, Cu+ and Cu2+. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2. This entry represents the actuator (A) domain, and some transmembrane helices found in P-type ATPases []. It contains the TGES-loop which is essential for the metal ion binding which results in tight association between the A and P (phosphorylation) domains []. It does not contain the phosphorylation site. It is thought that the large movement of the actuator domain, which is transmitted to the transmembrane helices, is essential to the long distance coupling between formation/decomposition of the acyl phosphate in the cytoplasmic P-domain and the changes in the ion-binding sites buried deep in the membranous region []. This domain has a modulatory effect on the phosphoenzyme processing steps through its nucleotide binding [],[]. P-type (or E1-E2-type) ATPases that form an aspartyl phosphate intermediate in the course of ATP hydrolysis, can be divided into 4 major groups []: (1) Ca2+-transporting ATPases; (2) Na+/K+- and gastric H+/K+-transporting ATPases; (3) plasma membrane H+-transporting ATPases (proton pumps) of plants, fungi and lower eukaryotes; and (4) all bacterial P-type ATPases, except the g2+-ATPase of Salmonella typhimurium, which is more similar to the eukaryotic sequences. However, great variety of sequence analysis methods results in diversity of classification. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0000166 nucleotide binding, 0046872 metal ion binding; PDB: 2XZB_A 1MHS_B 3TLM_A 3A3Y_A 2ZXE_A 3NAL_A 3NAM_A 3NAN_A 2YJ6_B 2IYE_A ....
Probab=24.46 E-value=50 Score=27.24 Aligned_cols=25 Identities=8% Similarity=0.422 Sum_probs=18.7
Q ss_pred CCeEEeccccceeccEEEEecCCccc
Q 028058 164 EPERLLLEDICQVGDVVLIEDESVME 189 (214)
Q Consensus 164 e~~~IPWe~IkKIGDVILVe~~~~~e 189 (214)
....+||++++. ||+|+++..+...
T Consensus 43 ~~~~i~~~~L~~-GDiI~l~~g~~vP 67 (230)
T PF00122_consen 43 RWQKIPSSELVP-GDIIILKAGDIVP 67 (230)
T ss_dssp EEEEEEGGGT-T-TSEEEEETTEBES
T ss_pred ccccchHhhccc-eeeeecccccccc
Confidence 345699999987 9999998777554
No 30
>PF07533 BRK: BRK domain; InterPro: IPR006576 BRK is a domain of unknown function found only in the metazoa and in association with CHROMO domain (IPR000953 from INTERPRO) and DEAD/DEAH box helicase domain (IPR011545 from INTERPRO).; GO: 0005515 protein binding, 0016817 hydrolase activity, acting on acid anhydrides; PDB: 2DL6_A 2CKA_A 2V0F_A 2V0E_A 2CKC_A.
Probab=23.22 E-value=50 Score=22.76 Aligned_cols=12 Identities=25% Similarity=0.293 Sum_probs=9.4
Q ss_pred eeEeccCcceee
Q 028058 126 QVISIQSAMSLG 137 (214)
Q Consensus 126 EVINi~dG~RLG 137 (214)
.|||+.||++|.
T Consensus 9 ~Vi~~~tGk~l~ 20 (46)
T PF07533_consen 9 PVINRKTGKRLT 20 (46)
T ss_dssp -EEETTTTEEE-
T ss_pred EeEECCCCCCcc
Confidence 589999999985
No 31
>PRK14590 rimM 16S rRNA-processing protein RimM; Provisional
Probab=23.13 E-value=1.6e+02 Score=24.71 Aligned_cols=37 Identities=19% Similarity=0.312 Sum_probs=28.7
Q ss_pred eEeccccCceeEeccCcceee-eeeeEEEECCCCEEEEEE
Q 028058 117 MRRSNLLAKQVISIQSAMSLG-FVSQLWVDTTSWVVLVVE 155 (214)
Q Consensus 117 mr~SeL~~KEVINi~dG~RLG-~V~DL~VD~~sG~V~AIi 155 (214)
.-.+||.+-+|+| .+|..|| .|.++ .+.-.+.+..|.
T Consensus 97 ~y~~dLiG~~V~d-~~g~~lGG~V~~v-~~~~a~dllvV~ 134 (171)
T PRK14590 97 FYSEDLIGLQAID-ETGKPLNWKLTDV-QDNPAHPILVFI 134 (171)
T ss_pred EEhHHccCcEEEe-CCCCEeeeEEEEE-ecCCCceEEEEE
Confidence 6689999999999 5888897 99997 455555565443
No 32
>cd05793 S1_IF1A S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A in archaea, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=22.43 E-value=3e+02 Score=20.53 Aligned_cols=38 Identities=18% Similarity=0.185 Sum_probs=24.6
Q ss_pred EEEECCCCEEEEEEECCCCCCCCCeEEeccccceeccEEEEecCCc
Q 028058 142 LWVDTTSWVVLVVEVRPNLLSGEPERLLLEDICQVGDVVLIEDESV 187 (214)
Q Consensus 142 L~VD~~sG~V~AIiVp~~~f~ge~~~IPWe~IkKIGDVILVe~~~~ 187 (214)
+.|-.+.|...---+|+.| +...+| +.||.|+|+..+.
T Consensus 15 ~~V~~~~g~~~la~i~gK~--rk~iwI------~~GD~V~Ve~~~~ 52 (77)
T cd05793 15 LEVRCFDGKKRLCRIRGKM--RKRVWI------NEGDIVLVAPWDF 52 (77)
T ss_pred EEEEECCCCEEEEEEchhh--cccEEE------cCCCEEEEEeccc
Confidence 4455556777667778875 222233 4589999997766
No 33
>smart00592 BRK domain in transcription and CHROMO domain helicases.
Probab=21.14 E-value=51 Score=22.62 Aligned_cols=12 Identities=25% Similarity=0.307 Sum_probs=10.0
Q ss_pred eeEeccCcceee
Q 028058 126 QVISIQSAMSLG 137 (214)
Q Consensus 126 EVINi~dG~RLG 137 (214)
.|||..||++|+
T Consensus 7 ~vi~~~tG~~l~ 18 (45)
T smart00592 7 PVINRETGKKLT 18 (45)
T ss_pred EeeccCCccEec
Confidence 589999999884
No 34
>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=20.88 E-value=1.5e+02 Score=21.03 Aligned_cols=47 Identities=17% Similarity=0.203 Sum_probs=27.2
Q ss_pred cceeeeeee------EEEECCCCEEEEEEECCCCCCCCCeEEeccccceeccEEEEecCCc
Q 028058 133 AMSLGFVSQ------LWVDTTSWVVLVVEVRPNLLSGEPERLLLEDICQVGDVVLIEDESV 187 (214)
Q Consensus 133 G~RLG~V~D------L~VD~~sG~V~AIiVp~~~f~ge~~~IPWe~IkKIGDVILVe~~~~ 187 (214)
+.-+|.|.+ +.|.+..|+..-..+|+. | .... | .+.||.|+|+..+.
T Consensus 3 ~e~~~~V~~~lG~~~~~V~~~dg~~~l~~i~gK-~-r~~i---w---I~~GD~V~V~~~~~ 55 (65)
T PF01176_consen 3 GEVIGRVTEMLGNNLFEVECEDGEERLARIPGK-F-RKRI---W---IKRGDFVLVEPSPY 55 (65)
T ss_dssp TEEEEEEEEEESSSEEEEEETTSEEEEEEE-HH-H-HTCC---------TTEEEEEEESTT
T ss_pred cEEEEEEEEECCCCEEEEEeCCCCEEEEEeccc-e-eeeE---e---cCCCCEEEEEeccc
Confidence 344555544 556666777777777776 3 1122 2 24589999998665
Done!