Query 022580
Match_columns 295
No_of_seqs 143 out of 394
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 04:37:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022580.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022580hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG3881 PRC-barrel domain cont 99.9 7.2E-26 1.6E-30 196.1 13.6 163 116-281 1-166 (176)
2 TIGR02888 spore_YlmC_YmxH spor 99.5 4.9E-14 1.1E-18 109.5 6.8 66 118-183 1-75 (76)
3 PF05239 PRC: PRC-barrel domai 99.2 3.2E-11 7E-16 91.3 7.3 71 115-186 2-76 (79)
4 COG1873 Protein implicated in 99.0 9.3E-10 2E-14 87.6 7.3 70 115-185 4-79 (87)
5 PF05239 PRC: PRC-barrel domai 99.0 1.9E-09 4.2E-14 81.6 7.2 74 196-272 5-78 (79)
6 TIGR02888 spore_YlmC_YmxH spor 98.9 2.2E-09 4.8E-14 83.5 6.3 71 197-267 2-75 (76)
7 COG1873 Protein implicated in 98.6 2.1E-07 4.6E-12 74.1 7.3 72 196-267 7-78 (87)
8 COG3881 PRC-barrel domain cont 97.3 0.001 2.2E-08 58.9 7.7 69 121-189 85-157 (176)
9 cd00226 PRCH Photosynthetic re 96.7 0.0069 1.5E-07 56.8 7.8 63 119-184 145-208 (246)
10 cd00226 PRCH Photosynthetic re 95.7 0.035 7.6E-07 52.2 7.4 63 196-267 144-207 (246)
11 COG0806 RimM RimM protein, req 91.5 0.46 9.9E-06 42.5 5.8 53 180-233 86-138 (174)
12 PRK13829 rimM 16S rRNA-process 91.0 0.61 1.3E-05 40.8 6.0 36 195-234 89-124 (162)
13 TIGR01150 puhA photosynthetic 91.0 0.69 1.5E-05 43.7 6.7 61 120-184 149-211 (252)
14 PRK14591 rimM 16S rRNA-process 90.7 0.64 1.4E-05 40.9 5.9 36 195-231 100-135 (169)
15 PRK13828 rimM 16S rRNA-process 89.7 0.75 1.6E-05 40.2 5.5 37 195-234 80-116 (161)
16 PRK14592 rimM 16S rRNA-process 89.7 0.6 1.3E-05 40.9 4.9 53 179-232 76-128 (165)
17 TIGR02273 16S_RimM 16S rRNA pr 89.3 0.86 1.9E-05 39.7 5.6 37 196-233 96-132 (165)
18 PRK00122 rimM 16S rRNA-process 89.2 0.66 1.4E-05 40.7 4.8 36 195-233 100-135 (172)
19 PRK14594 rimM 16S rRNA-process 88.5 1.5 3.4E-05 38.4 6.6 52 179-232 81-132 (166)
20 PRK14590 rimM 16S rRNA-process 85.6 1.6 3.5E-05 38.6 5.1 35 196-233 98-133 (171)
21 PRK13829 rimM 16S rRNA-process 83.0 6.6 0.00014 34.3 7.8 52 117-171 89-141 (162)
22 PRK14591 rimM 16S rRNA-process 81.6 3.7 8E-05 36.1 5.8 48 117-171 100-147 (169)
23 COG0806 RimM RimM protein, req 79.5 5.3 0.00012 35.8 6.1 51 117-172 101-151 (174)
24 PRK14593 rimM 16S rRNA-process 76.6 11 0.00025 33.5 7.3 62 116-183 103-175 (184)
25 PF13028 DUF3889: Protein of u 75.4 5.8 0.00013 32.6 4.7 29 206-234 67-95 (97)
26 PRK14592 rimM 16S rRNA-process 73.3 8.7 0.00019 33.5 5.6 62 117-183 92-158 (165)
27 PRK14594 rimM 16S rRNA-process 73.0 7.7 0.00017 34.0 5.2 46 117-170 97-142 (166)
28 PRK14593 rimM 16S rRNA-process 71.0 4.1 9E-05 36.3 3.1 35 195-233 104-138 (184)
29 PRK14590 rimM 16S rRNA-process 70.9 9.8 0.00021 33.6 5.5 51 116-172 96-147 (171)
30 TIGR02273 16S_RimM 16S rRNA pr 70.8 11 0.00024 32.7 5.7 58 115-177 93-152 (165)
31 PRK00122 rimM 16S rRNA-process 67.6 13 0.00029 32.5 5.5 63 115-183 98-165 (172)
32 PRK13149 H/ACA RNA-protein com 63.8 9.2 0.0002 29.4 3.4 27 199-226 24-50 (73)
33 TIGR01150 puhA photosynthetic 59.4 17 0.00037 34.5 4.9 39 197-235 148-186 (252)
34 COG3277 GAR1 RNA-binding prote 57.0 13 0.00028 30.7 3.2 23 198-220 24-46 (98)
35 PRK13828 rimM 16S rRNA-process 54.6 10 0.00022 33.0 2.5 67 116-187 79-150 (161)
36 PF09939 DUF2171: Uncharacteri 52.4 72 0.0016 24.6 6.5 55 124-184 5-60 (67)
37 PF08669 GCV_T_C: Glycine clea 46.5 50 0.0011 25.5 5.0 36 199-234 33-68 (95)
38 PF13670 PepSY_2: Peptidase pr 42.7 18 0.00039 27.7 1.9 27 201-231 56-82 (83)
39 cd02410 archeal_CPSF_KH The ar 42.1 16 0.00035 32.0 1.8 21 216-237 68-88 (145)
40 PRK06009 flgD flagellar basal 33.1 1E+02 0.0022 26.9 5.3 36 197-235 92-127 (140)
41 COG3798 Uncharacterized protei 31.6 59 0.0013 25.5 3.1 60 116-184 1-62 (75)
42 PF03413 PepSY: Peptidase prop 29.7 66 0.0014 22.3 3.0 18 214-231 46-63 (64)
43 PF13861 FLgD_tudor: FlgD Tudo 22.2 3E+02 0.0064 19.9 5.4 54 115-176 3-60 (61)
44 PF04410 Gar1: Gar1/Naf1 RNA b 21.3 2.4E+02 0.0052 24.4 5.5 46 166-219 22-68 (154)
45 PF09000 Cytotoxic: Cytotoxic; 21.1 1.1E+02 0.0023 24.8 3.0 53 172-229 9-74 (85)
46 PF15640 Tox-MPTase4: Metallop 20.1 61 0.0013 28.0 1.5 31 199-229 32-63 (132)
No 1
>COG3881 PRC-barrel domain containing protein [General function prediction only]
Probab=99.93 E-value=7.2e-26 Score=196.12 Aligned_cols=163 Identities=15% Similarity=0.162 Sum_probs=141.5
Q ss_pred eeeeccccCCeeEeccCcceeeeEeEEEEECCCCEEEEEEEcCCCCCCCceEEecccceeeC-cEEEEecCCccc-cccc
Q 022580 116 VMRRSNLLAKQVISIQSAMSLGFVSQLWVDTTSWVVLVVEVRPNLLSGEPERLLLEDICQVG-DVVLIEDESVME-NDFK 193 (295)
Q Consensus 116 m~r~SeLiGlpVIsi~tG~rLG~V~DL~vDp~~~rV~gLiV~~~~l~~~~~~Ip~e~I~~IG-DaIlV~~~~~v~-~~~~ 193 (295)
|+|..||.|.||++.+||++||.|.|+.+|++..+|.+|.+..++|+.+...+|+.+|.+|| |+||+.-+.... ..++
T Consensus 1 Mit~~EleG~pVys~~tg~~lg~V~Dvif~~~gdrvl~flvnkggwfh~h~~lp~~~i~Sig~k~Imi~vp~~~~~~~~n 80 (176)
T COG3881 1 MITSRELEGAPVYSTKTGEKLGAVDDVIFNFSGDRVLGFLVNKGGWFHKHCCLPVKNIVSIGSKMIMIYVPYKGSFIRFN 80 (176)
T ss_pred CccchhhcCCceEEecccccccceeeEEEecCCCeEEEEEEecCcEEeeeeeeeecceeeeccceEEEeccccceecccC
Confidence 78999999999999999999999999999999999999999999999999999999999999 999998754432 1223
Q ss_pred ccccccccCCEEEcCCCceeEEEEEEEEEcCCccEEEEEEcCCCccccCCCcccceeeehhhhhhccCcEEEEccchhh-
Q 022580 194 MVRLDTLVGYRVVTPGRQNIGKVRGYTFNINSGAVESLELDSFGISIIPSSLVSTYALLVEDVLEVVADIVVVHEAAAS- 272 (295)
Q Consensus 194 l~~~~~LiG~~ViTe~G~~LG~V~Dv~FD~~TG~I~~yels~~G~~~ip~~~~sr~~Lp~e~IvsiG~D~VIV~e~A~~- 272 (295)
.--+.-+.+.-+.|.+|+.||.|+|+|||+++|+|++||+|+ |. +++...+|..+++...+.+|+|.+||+.+..-
T Consensus 81 s~~ye~m~mk~~lt~dG~iLGmveDVyFdek~gkIvgyevS~-Gf--fADlt~gRkiira~~~v~vgKD~~ivs~~~~~~ 157 (176)
T COG3881 81 SFTYEIMNMKVILTYDGTILGMVEDVYFDEKTGKIVGYEVSR-GF--FADLTSGRKIIRAGNYVLVGKDLFIVSNDKNLS 157 (176)
T ss_pred chhhHhhcCceEeccCCcEeeeeeEEEEeccCCcEEEEEecC-ch--hhhccCCceEEECCCcEEecccEEEecCCcchh
Confidence 334567778888899999999999999999999999999999 86 78899999999999999999999999988443
Q ss_pred hhhhccccc
Q 022580 273 RVQRLTKVP 281 (295)
Q Consensus 273 ~L~q~~~GL 281 (295)
-..+...|.
T Consensus 158 ~~~~~~~~~ 166 (176)
T COG3881 158 FVRVFHSIS 166 (176)
T ss_pred hhhhccCcc
Confidence 334444433
No 2
>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=99.49 E-value=4.9e-14 Score=109.53 Aligned_cols=66 Identities=26% Similarity=0.413 Sum_probs=59.7
Q ss_pred eeccccCCeeEeccCcceeeeE--eEEEEECCCCEEEEEEEcC-CCCC-----CCceEEecccceeeC-cEEEEe
Q 022580 118 RRSNLLAKQVISIQSAMSLGFV--SQLWVDTTSWVVLVVEVRP-NLLS-----GEPERLLLEDICQVG-DVVLIE 183 (295)
Q Consensus 118 r~SeLiGlpVIsi~tG~rLG~V--~DL~vDp~~~rV~gLiV~~-~~l~-----~~~~~Ip~e~I~~IG-DaIlV~ 183 (295)
|+|||.+++||++++|++||.| .|+.+|+++|+|.|++++. +.|+ .+...|||++|.+|| |+|+|+
T Consensus 1 r~seL~~keVIni~~G~~lG~v~~~Dl~iD~~~G~I~aiIi~~~~~~~~~~~~~~~~~Ipw~~I~kIG~DvIlV~ 75 (76)
T TIGR02888 1 RLSDLRGKEIINVNDGERLGVIGNIDLEIDEEDGRILSLIIPGKGKKFGLFSKGEEIEIPWDAIKKIGSDVILVD 75 (76)
T ss_pred CHHHccCCCEEECCCCcEeeccccceEEEECCCCEEEEEEEeCCCcEEEeecCCcEEEEEhhhccEECCCEEEEe
Confidence 5899999999999999999999 8999999999999999987 3332 456799999999999 999996
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=99.22 E-value=3.2e-11 Score=91.32 Aligned_cols=71 Identities=20% Similarity=0.348 Sum_probs=64.0
Q ss_pred ceeeeccccCCeeEeccCcceeeeEeEEEEECCCCEEEEEEEcCCCCC---CCceEEecccceeeC-cEEEEecCC
Q 022580 115 QVMRRSNLLAKQVISIQSAMSLGFVSQLWVDTTSWVVLVVEVRPNLLS---GEPERLLLEDICQVG-DVVLIEDES 186 (295)
Q Consensus 115 ~m~r~SeLiGlpVIsi~tG~rLG~V~DL~vDp~~~rV~gLiV~~~~l~---~~~~~Ip~e~I~~IG-DaIlV~~~~ 186 (295)
+++++|+|+|+||++.+ |+++|+|.|+++|+.++++.++++..+.|+ .+...+||+++..++ |.|+|+...
T Consensus 2 ~~~~~s~l~g~~V~~~~-G~~iG~V~di~id~~~~~i~~i~v~~~~~~~~~~~~~~iP~~~~v~~~~~~i~v~~~~ 76 (79)
T PF05239_consen 2 DEFRLSELIGKEVIDRD-GEKIGKVKDIVIDPKTGKIVGIVVSSGGFFGIGGKKVLIPWDQIVDIGGDRIIVDPPK 76 (79)
T ss_dssp CHGCHHHHTTSEEEETT-SCEEEEEEEEEEETTTTEEEEEEEEETTSTCSSSEEEEEEGGEEEEECTTEEEESSST
T ss_pred CeEEhHHccCCEEEcCC-CCEEEEEEEEEEeCCCCCEEEEEEcCCCccCcCCcEEEEcCeEeEEecCCEEEEcCCC
Confidence 56889999999999977 999999999999999999999999998874 367899999888888 999998654
No 4
>COG1873 Protein implicated in RNA metabolism, contains PRC-barrel domain [General function prediction only]
Probab=99.01 E-value=9.3e-10 Score=87.63 Aligned_cols=70 Identities=30% Similarity=0.387 Sum_probs=60.7
Q ss_pred ceeeeccccCCeeEeccCcceeeeEeEEEEECCCCEEEEEEEcCC--CC--CCC--ceEEecccceeeCcEEEEecC
Q 022580 115 QVMRRSNLLAKQVISIQSAMSLGFVSQLWVDTTSWVVLVVEVRPN--LL--SGE--PERLLLEDICQVGDVVLIEDE 185 (295)
Q Consensus 115 ~m~r~SeLiGlpVIsi~tG~rLG~V~DL~vDp~~~rV~gLiV~~~--~l--~~~--~~~Ip~e~I~~IGDaIlV~~~ 185 (295)
.||++|+|.|++|++. +|+++|+|.|+.+|.+++.+.++.+.+. .| +++ .-.+||+.|.+|||-|+|...
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 4789999999999997 9999999999999999999999999876 23 333 669999999999987777653
No 5
>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=98.97 E-value=1.9e-09 Score=81.57 Aligned_cols=74 Identities=20% Similarity=0.336 Sum_probs=62.5
Q ss_pred ccccccCCEEEcCCCceeEEEEEEEEEcCCccEEEEEEcCCCccccCCCcccceeeehhhhhhccCcEEEEccchhh
Q 022580 196 RLDTLVGYRVVTPGRQNIGKVRGYTFNINSGAVESLELDSFGISIIPSSLVSTYALLVEDVLEVVADIVVVHEAAAS 272 (295)
Q Consensus 196 ~~~~LiG~~ViTe~G~~LG~V~Dv~FD~~TG~I~~yels~~G~~~ip~~~~sr~~Lp~e~IvsiG~D~VIV~e~A~~ 272 (295)
..++|+|++|+|.+|+.+|+|.|++||+++|+|.++.++..+...+ -...+.||++.+++++.|+|+|...+++
T Consensus 5 ~~s~l~g~~V~~~~G~~iG~V~di~id~~~~~i~~i~v~~~~~~~~---~~~~~~iP~~~~v~~~~~~i~v~~~~~~ 78 (79)
T PF05239_consen 5 RLSELIGKEVIDRDGEKIGKVKDIVIDPKTGKIVGIVVSSGGFFGI---GGKKVLIPWDQIVDIGGDRIIVDPPKEQ 78 (79)
T ss_dssp CHHHHTTSEEEETTSCEEEEEEEEEEETTTTEEEEEEEEETTSTCS---SSEEEEEEGGEEEEECTTEEEESSSTG-
T ss_pred EhHHccCCEEEcCCCCEEEEEEEEEEeCCCCCEEEEEEcCCCccCc---CCcEEEEcCeEeEEecCCEEEEcCCCCC
Confidence 5678999999999999999999999999999999999998432111 2246799999999999999999877653
No 6
>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=98.93 E-value=2.2e-09 Score=83.53 Aligned_cols=71 Identities=15% Similarity=0.235 Sum_probs=58.3
Q ss_pred cccccCCEEEc-CCCceeEEE--EEEEEEcCCccEEEEEEcCCCccccCCCcccceeeehhhhhhccCcEEEEc
Q 022580 197 LDTLVGYRVVT-PGRQNIGKV--RGYTFNINSGAVESLELDSFGISIIPSSLVSTYALLVEDVLEVVADIVVVH 267 (295)
Q Consensus 197 ~~~LiG~~ViT-e~G~~LG~V--~Dv~FD~~TG~I~~yels~~G~~~ip~~~~sr~~Lp~e~IvsiG~D~VIV~ 267 (295)
+++|.+++|++ .+|+.||.| .|+.||+++|+|.++.+...|..+--..-...+.+|+++|..+|.|+|+|.
T Consensus 2 ~seL~~keVIni~~G~~lG~v~~~Dl~iD~~~G~I~aiIi~~~~~~~~~~~~~~~~~Ipw~~I~kIG~DvIlV~ 75 (76)
T TIGR02888 2 LSDLRGKEIINVNDGERLGVIGNIDLEIDEEDGRILSLIIPGKGKKFGLFSKGEEIEIPWDAIKKIGSDVILVD 75 (76)
T ss_pred HHHccCCCEEECCCCcEeeccccceEEEECCCCEEEEEEEeCCCcEEEeecCCcEEEEEhhhccEECCCEEEEe
Confidence 56889999999 799999999 899999999999999998744322000112348999999999999999984
No 7
>COG1873 Protein implicated in RNA metabolism, contains PRC-barrel domain [General function prediction only]
Probab=98.56 E-value=2.1e-07 Score=74.14 Aligned_cols=72 Identities=19% Similarity=0.237 Sum_probs=59.4
Q ss_pred ccccccCCEEEcCCCceeEEEEEEEEEcCCccEEEEEEcCCCccccCCCcccceeeehhhhhhccCcEEEEc
Q 022580 196 RLDTLVGYRVVTPGRQNIGKVRGYTFNINSGAVESLELDSFGISIIPSSLVSTYALLVEDVLEVVADIVVVH 267 (295)
Q Consensus 196 ~~~~LiG~~ViTe~G~~LG~V~Dv~FD~~TG~I~~yels~~G~~~ip~~~~sr~~Lp~e~IvsiG~D~VIV~ 267 (295)
...+|.|++|+|.+|+.+|+|.|+.||.++|+|+++.+...+..+....-.....+|++.|..+|.+.||..
T Consensus 7 ~~s~l~gk~V~~~~G~~vG~V~dv~ld~~~g~i~~l~v~~~~~~l~~~~k~~~v~IP~~~V~aIGd~III~~ 78 (87)
T COG1873 7 RLSELLGKEVITNDGKYVGTVSDVVLDIKEGKITGLLVIPTNKGLFLFGKGKEVIVPYEYVKAIGDIIIIKD 78 (87)
T ss_pred eHHHhcCcEEEcCCCeEEEEEEeEEEEccCCcEEEEEEecCCccccccCCCcEEEEehhHeEEecCEEEEec
Confidence 467899999999999999999999999999999999999742222222211368999999999999988874
No 8
>COG3881 PRC-barrel domain containing protein [General function prediction only]
Probab=97.29 E-value=0.001 Score=58.86 Aligned_cols=69 Identities=16% Similarity=0.329 Sum_probs=60.2
Q ss_pred cccCCeeEeccCcceeeeEeEEEEECCCCEEEEEEEcCCCC---CCCceEEecccceeeC-cEEEEecCCccc
Q 022580 121 NLLAKQVISIQSAMSLGFVSQLWVDTTSWVVLVVEVRPNLL---SGEPERLLLEDICQVG-DVVLIEDESVME 189 (295)
Q Consensus 121 eLiGlpVIsi~tG~rLG~V~DL~vDp~~~rV~gLiV~~~~l---~~~~~~Ip~e~I~~IG-DaIlV~~~~~v~ 189 (295)
|++...++..++|..||.|.|+.||+.+++|+|..+..+.| .+.++.+|-.+...+| |.+.|....++.
T Consensus 85 e~m~mk~~lt~dG~iLGmveDVyFdek~gkIvgyevS~GffADlt~gRkiira~~~v~vgKD~~ivs~~~~~~ 157 (176)
T COG3881 85 EIMNMKVILTYDGTILGMVEDVYFDEKTGKIVGYEVSRGFFADLTSGRKIIRAGNYVLVGKDLFIVSNDKNLS 157 (176)
T ss_pred HhhcCceEeccCCcEeeeeeEEEEeccCCcEEEEEecCchhhhccCCceEEECCCcEEecccEEEecCCcchh
Confidence 56677777789999999999999999999999999999987 3458899999999999 999998866554
No 9
>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=96.66 E-value=0.0069 Score=56.84 Aligned_cols=63 Identities=22% Similarity=0.272 Sum_probs=52.8
Q ss_pred eccccCCeeEeccCcceeeeEeEEEEECCCCEEEEEEEcCCCCCCCceEEecccceeeC-cEEEEec
Q 022580 119 RSNLLAKQVISIQSAMSLGFVSQLWVDTTSWVVLVVEVRPNLLSGEPERLLLEDICQVG-DVVLIED 184 (295)
Q Consensus 119 ~SeLiGlpVIsi~tG~rLG~V~DL~vDp~~~rV~gLiV~~~~l~~~~~~Ip~e~I~~IG-DaIlV~~ 184 (295)
-.|+.|++|+.. +|+.+|+|+|+|+|..++.+.-|.|+.+. ++++..||+ ....|. +.|.|+.
T Consensus 145 ~~DprGl~V~g~-DGevvGtV~Dv~vD~~e~~iRYLeVdtg~-~gkkVLLPi-~~~rId~~~V~V~~ 208 (246)
T cd00226 145 DVDPRGLPVVGA-DGEVAGKVTDLWVDRPEQLFRYLEVELAG-GGRTVLLPM-GFAKVKSDRVKVTA 208 (246)
T ss_pred CCCCCCCEeEcC-CCcEeEEEEEEEEcCCcceEEEEEEEcCC-CCCEEEEEe-EEEEecCCEEEEec
Confidence 468999999975 89999999999999989999999998866 566778884 446667 7899974
No 10
>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=95.75 E-value=0.035 Score=52.21 Aligned_cols=63 Identities=22% Similarity=0.110 Sum_probs=48.1
Q ss_pred ccccccCCEEEcCCCceeEEEEEEEEEcCCccEEEEEEcCCCccccCCCcccce-eeehhhhhhccCcEEEEc
Q 022580 196 RLDTLVGYRVVTPGRQNIGKVRGYTFNINSGAVESLELDSFGISIIPSSLVSTY-ALLVEDVLEVVADIVVVH 267 (295)
Q Consensus 196 ~~~~LiG~~ViTe~G~~LG~V~Dv~FD~~TG~I~~yels~~G~~~ip~~~~sr~-~Lp~e~IvsiG~D~VIV~ 267 (295)
+-.++.|++|+..+|+.+|+|.|++||..++.|-.+|++..+ .++. .|| -....+..++|.|.
T Consensus 144 ~~~DprGl~V~g~DGevvGtV~Dv~vD~~e~~iRYLeVdtg~--------~gkkVLLP-i~~~rId~~~V~V~ 207 (246)
T cd00226 144 GDVDPRGLPVVGADGEVAGKVTDLWVDRPEQLFRYLEVELAG--------GGRTVLLP-MGFAKVKSDRVKVT 207 (246)
T ss_pred CCCCCCCCEeEcCCCcEeEEEEEEEEcCCcceEEEEEEEcCC--------CCCEEEEE-eEEEEecCCEEEEe
Confidence 368999999999999999999999999999999999998721 1122 233 33344556788885
No 11
>COG0806 RimM RimM protein, required for 16S rRNA processing [Translation, ribosomal structure and biogenesis]
Probab=91.50 E-value=0.46 Score=42.55 Aligned_cols=53 Identities=19% Similarity=0.299 Sum_probs=37.1
Q ss_pred EEEecCCcccccccccccccccCCEEEcCCCceeEEEEEEEEEcCCccEEEEEE
Q 022580 180 VLIEDESVMENDFKMVRLDTLVGYRVVTPGRQNIGKVRGYTFNINSGAVESLEL 233 (295)
Q Consensus 180 IlV~~~~~v~~~~~l~~~~~LiG~~ViTe~G~~LG~V~Dv~FD~~TG~I~~yel 233 (295)
|.|..+.......+-.-+++|+|++|+|++|+.||+|.++ ++.-.+.|--+..
T Consensus 86 i~v~~~~~p~l~EdEfY~~DLiG~~V~~~~g~~lG~V~~i-~~~Ga~Dvl~V~~ 138 (174)
T COG0806 86 IFVDRSELPELEEDEFYYHDLIGLEVVTEDGELLGKVTEI-LETGANDVLVVKA 138 (174)
T ss_pred EEEEHHHCCCCCCCcEEeEeecCcEEEcCCCcEEEEEEEE-eeCCCccEEEEEe
Confidence 4454433322122334579999999999999999999999 7766666666555
No 12
>PRK13829 rimM 16S rRNA-processing protein RimM; Provisional
Probab=91.00 E-value=0.61 Score=40.79 Aligned_cols=36 Identities=22% Similarity=0.266 Sum_probs=27.8
Q ss_pred cccccccCCEEEcCCCceeEEEEEEEEEcCCccEEEEEEc
Q 022580 195 VRLDTLVGYRVVTPGRQNIGKVRGYTFNINSGAVESLELD 234 (295)
Q Consensus 195 ~~~~~LiG~~ViTe~G~~LG~V~Dv~FD~~TG~I~~yels 234 (295)
.-+.+|+|++|+ ++|+.||+|.|+ ++ ||.=.-|++.
T Consensus 89 yY~~dLiG~~V~-~~g~~lG~V~~v-~~--~ga~dvlvV~ 124 (162)
T PRK13829 89 YYYHELRGLPVY-VDGEPLGEVVDV-ED--AGAQDLLVIR 124 (162)
T ss_pred EEehhccCeEEE-ECCEeeEEEEEE-ec--CCCceEEEEE
Confidence 357899999999 999999999999 44 4544444554
No 13
>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=91.00 E-value=0.69 Score=43.65 Aligned_cols=61 Identities=23% Similarity=0.304 Sum_probs=46.9
Q ss_pred ccccCCeeEeccCcceeeeEeEEEEECCCCEEEEEEEcCCCCCC-CceEEecccceeeC-cEEEEec
Q 022580 120 SNLLAKQVISIQSAMSLGFVSQLWVDTTSWVVLVVEVRPNLLSG-EPERLLLEDICQVG-DVVLIED 184 (295)
Q Consensus 120 SeLiGlpVIsi~tG~rLG~V~DL~vDp~~~rV~gLiV~~~~l~~-~~~~Ip~e~I~~IG-DaIlV~~ 184 (295)
-|-.|+||+. .+|+..|+|.|+|||..+..|..+.|+-+ .+ +...+|..-. .|. +.|.|+.
T Consensus 149 ~DPrG~pV~g-~Dg~v~GtV~D~WVDr~E~~iRYlEVel~--~~~~~vLlP~~f~-~i~~~~V~v~a 211 (252)
T TIGR01150 149 VDPRGLPVVA-ADGEVAGKVTDLWVDRPEQYFRYLEVELA--GGARTALLPMGMC-KVKSDRVVVNS 211 (252)
T ss_pred CCCCCCeeEc-CCCceeeEEEEEEEcCccceeeEEEEEec--CCCceEEecccce-eccCCcEEEEE
Confidence 3578999996 67999999999999999998988887642 23 3456676644 446 7888875
No 14
>PRK14591 rimM 16S rRNA-processing protein RimM; Provisional
Probab=90.67 E-value=0.64 Score=40.88 Aligned_cols=36 Identities=19% Similarity=0.254 Sum_probs=28.0
Q ss_pred cccccccCCEEEcCCCceeEEEEEEEEEcCCccEEEE
Q 022580 195 VRLDTLVGYRVVTPGRQNIGKVRGYTFNINSGAVESL 231 (295)
Q Consensus 195 ~~~~~LiG~~ViTe~G~~LG~V~Dv~FD~~TG~I~~y 231 (295)
.-+.+|+|++|++++|+.||+|.|+ ++.-.+.+.-+
T Consensus 100 ~Y~~dLiG~~V~d~~g~~lG~V~~v-~~~ga~dll~I 135 (169)
T PRK14591 100 VYFKDLIGCSVKNINNDSFGVVVDI-IETGANEVLVC 135 (169)
T ss_pred EEeeeecCcEEEeCCCCEEEEEEEE-eecCCceEEEE
Confidence 3578999999999999999999999 55434444433
No 15
>PRK13828 rimM 16S rRNA-processing protein RimM; Provisional
Probab=89.74 E-value=0.75 Score=40.15 Aligned_cols=37 Identities=30% Similarity=0.453 Sum_probs=28.1
Q ss_pred cccccccCCEEEcCCCceeEEEEEEEEEcCCccEEEEEEc
Q 022580 195 VRLDTLVGYRVVTPGRQNIGKVRGYTFNINSGAVESLELD 234 (295)
Q Consensus 195 ~~~~~LiG~~ViTe~G~~LG~V~Dv~FD~~TG~I~~yels 234 (295)
.-+.+|+|++|++++|+.||+|.|+. +||.=.=|++.
T Consensus 80 ~y~~dLiG~~V~d~~g~~lG~V~~V~---~~ga~dvlvV~ 116 (161)
T PRK13828 80 FYHADLIGLAAVDTGGALLGRVKAVH---NFGAGDILEIA 116 (161)
T ss_pred EEhhhccCCEEEeCCCCEEEEEEEEc---cCCCccEEEEE
Confidence 35789999999999999999999993 34533334443
No 16
>PRK14592 rimM 16S rRNA-processing protein RimM; Provisional
Probab=89.70 E-value=0.6 Score=40.85 Aligned_cols=53 Identities=13% Similarity=0.197 Sum_probs=34.1
Q ss_pred EEEEecCCcccccccccccccccCCEEEcCCCceeEEEEEEEEEcCCccEEEEE
Q 022580 179 VVLIEDESVMENDFKMVRLDTLVGYRVVTPGRQNIGKVRGYTFNINSGAVESLE 232 (295)
Q Consensus 179 aIlV~~~~~v~~~~~l~~~~~LiG~~ViTe~G~~LG~V~Dv~FD~~TG~I~~ye 232 (295)
.|+|+.+....-+.+-.-+.+|+|++|++++|+.+|+|.|+ ++.-.+.+--++
T Consensus 76 ~l~v~~~~lp~l~e~e~y~~dLiG~~V~~~~g~~lG~V~~v-~~~ga~dvlvI~ 128 (165)
T PRK14592 76 KLYVERSKLPNLNEDEFYQSDLIGMEVKLEDNTIYGYIKKI-YNFGSCDIIEIS 128 (165)
T ss_pred EEEEEHHHCCCCCCCCEEHHHcCCcEEEcCCCCEEEEEEEE-ccCCCccEEEEE
Confidence 55665433211112233578999999999999999999999 443334444444
No 17
>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=89.33 E-value=0.86 Score=39.66 Aligned_cols=37 Identities=24% Similarity=0.337 Sum_probs=28.9
Q ss_pred ccccccCCEEEcCCCceeEEEEEEEEEcCCccEEEEEE
Q 022580 196 RLDTLVGYRVVTPGRQNIGKVRGYTFNINSGAVESLEL 233 (295)
Q Consensus 196 ~~~~LiG~~ViTe~G~~LG~V~Dv~FD~~TG~I~~yel 233 (295)
-+.+|+|++|++++|+.+|+|.|+ ++...+.+--+..
T Consensus 96 y~~dLiG~~V~d~~~~~lG~V~~v-~~~~a~dll~V~~ 132 (165)
T TIGR02273 96 YWTDLIGLEVVTEEGEELGKVVEI-LETGANDVLVVRS 132 (165)
T ss_pred EhhHhCCcEEEcCCCcEEEEEEEE-ecCCCccEEEEEE
Confidence 568999999999999999999999 4444445555544
No 18
>PRK00122 rimM 16S rRNA-processing protein RimM; Provisional
Probab=89.24 E-value=0.66 Score=40.68 Aligned_cols=36 Identities=22% Similarity=0.408 Sum_probs=28.0
Q ss_pred cccccccCCEEEcCCCceeEEEEEEEEEcCCccEEEEEE
Q 022580 195 VRLDTLVGYRVVTPGRQNIGKVRGYTFNINSGAVESLEL 233 (295)
Q Consensus 195 ~~~~~LiG~~ViTe~G~~LG~V~Dv~FD~~TG~I~~yel 233 (295)
.-+.+|+|++|++++|..+|+|.|+ ++.-.+ .-|++
T Consensus 100 ~y~~dLiG~~V~d~~g~~lG~V~~v-~~~~a~--dll~I 135 (172)
T PRK00122 100 YYWHDLIGLEVVDEDGEELGKVTDI-LETGAN--DVLVV 135 (172)
T ss_pred EEHHHhCCcEEEeCCCcEEEEEEEE-ccCCCc--eEEEE
Confidence 4568999999999999999999999 443344 44455
No 19
>PRK14594 rimM 16S rRNA-processing protein RimM; Provisional
Probab=88.49 E-value=1.5 Score=38.40 Aligned_cols=52 Identities=17% Similarity=0.364 Sum_probs=32.6
Q ss_pred EEEEecCCcccccccccccccccCCEEEcCCCceeEEEEEEEEEcCCccEEEEE
Q 022580 179 VVLIEDESVMENDFKMVRLDTLVGYRVVTPGRQNIGKVRGYTFNINSGAVESLE 232 (295)
Q Consensus 179 aIlV~~~~~v~~~~~l~~~~~LiG~~ViTe~G~~LG~V~Dv~FD~~TG~I~~ye 232 (295)
.++|+.+....-..+-.-+++|+|++|+++ |..+|+|.|+ ++.-.+.+--+.
T Consensus 81 ~l~v~~~~lp~l~edE~Y~~dLiG~~V~~~-g~~lG~V~~v-~~~ga~dll~V~ 132 (166)
T PRK14594 81 ELWVDDELASKLEEGEYYFGKLIGYAIVND-GKELGEVVSF-FECLNSVLLEVK 132 (166)
T ss_pred EEEEEHHHCCCCCCCcEeHhHccCeEEEEC-CEEEEEEEEE-eeCCCcEEEEEE
Confidence 455554332111112235689999999995 9999999999 554344444433
No 20
>PRK14590 rimM 16S rRNA-processing protein RimM; Provisional
Probab=85.59 E-value=1.6 Score=38.60 Aligned_cols=35 Identities=14% Similarity=0.224 Sum_probs=27.0
Q ss_pred ccccccCCEEEcCCCceeE-EEEEEEEEcCCccEEEEEE
Q 022580 196 RLDTLVGYRVVTPGRQNIG-KVRGYTFNINSGAVESLEL 233 (295)
Q Consensus 196 ~~~~LiG~~ViTe~G~~LG-~V~Dv~FD~~TG~I~~yel 233 (295)
-+++|+|++|++++|+.+| +|.|+ ++ +|.=.=|++
T Consensus 98 y~~dLiG~~V~d~~g~~lGG~V~~v-~~--~~a~dllvV 133 (171)
T PRK14590 98 YSEDLIGLQAIDETGKPLNWKLTDV-QD--NPAHPILVF 133 (171)
T ss_pred EhHHccCcEEEeCCCCEeeeEEEEE-ec--CCCceEEEE
Confidence 4689999999999999997 99999 33 443333444
No 21
>PRK13829 rimM 16S rRNA-processing protein RimM; Provisional
Probab=82.98 E-value=6.6 Score=34.30 Aligned_cols=52 Identities=19% Similarity=0.105 Sum_probs=35.2
Q ss_pred eeeccccCCeeEeccCcceeeeEeEEEEECCCCEEEEEEEcCCCC-CCCceEEecc
Q 022580 117 MRRSNLLAKQVISIQSAMSLGFVSQLWVDTTSWVVLVVEVRPNLL-SGEPERLLLE 171 (295)
Q Consensus 117 ~r~SeLiGlpVIsi~tG~rLG~V~DL~vDp~~~rV~gLiV~~~~l-~~~~~~Ip~e 171 (295)
.=..||+|++|+ .+|..+|+|.++ ++...+-|.-+....+.. ..+...||+-
T Consensus 89 yY~~dLiG~~V~--~~g~~lG~V~~v-~~~ga~dvlvV~~~~~~~~~~k~~LIP~v 141 (162)
T PRK13829 89 YYYHELRGLPVY--VDGEPLGEVVDV-EDAGAQDLLVIRHVGGSLRARATYFVPLQ 141 (162)
T ss_pred EEehhccCeEEE--ECCEeeEEEEEE-ecCCCceEEEEEeCCCCCccCceEEEccc
Confidence 568899999999 789999999998 444455565443222221 1245688873
No 22
>PRK14591 rimM 16S rRNA-processing protein RimM; Provisional
Probab=81.64 E-value=3.7 Score=36.07 Aligned_cols=48 Identities=17% Similarity=0.176 Sum_probs=35.0
Q ss_pred eeeccccCCeeEeccCcceeeeEeEEEEECCCCEEEEEEEcCCCCCCCceEEecc
Q 022580 117 MRRSNLLAKQVISIQSAMSLGFVSQLWVDTTSWVVLVVEVRPNLLSGEPERLLLE 171 (295)
Q Consensus 117 ~r~SeLiGlpVIsi~tG~rLG~V~DL~vDp~~~rV~gLiV~~~~l~~~~~~Ip~e 171 (295)
.-..||+|++|++ .+|..+|+|.++ ++...+-|. .++.+ ++...||+-
T Consensus 100 ~Y~~dLiG~~V~d-~~g~~lG~V~~v-~~~ga~dll--~I~~~---~ke~LIP~~ 147 (169)
T PRK14591 100 VYFKDLIGCSVKN-INNDSFGVVVDI-IETGANEVL--VCKED---NSEYLIPYV 147 (169)
T ss_pred EEeeeecCcEEEe-CCCCEEEEEEEE-eecCCceEE--EEEcC---CeEEEEeCh
Confidence 5689999999998 578899999998 455556564 34432 346678874
No 23
>COG0806 RimM RimM protein, required for 16S rRNA processing [Translation, ribosomal structure and biogenesis]
Probab=79.48 E-value=5.3 Score=35.79 Aligned_cols=51 Identities=22% Similarity=0.258 Sum_probs=37.6
Q ss_pred eeeccccCCeeEeccCcceeeeEeEEEEECCCCEEEEEEEcCCCCCCCceEEeccc
Q 022580 117 MRRSNLLAKQVISIQSAMSLGFVSQLWVDTTSWVVLVVEVRPNLLSGEPERLLLED 172 (295)
Q Consensus 117 ~r~SeLiGlpVIsi~tG~rLG~V~DL~vDp~~~rV~gLiV~~~~l~~~~~~Ip~e~ 172 (295)
.=..||+|+.|++.+ |+.||.|.++ +++..+-|..+.. ....+...||+-+
T Consensus 101 fY~~DLiG~~V~~~~-g~~lG~V~~i-~~~Ga~Dvl~V~~---~~~~k~~LIPf~~ 151 (174)
T COG0806 101 FYYHDLIGLEVVTED-GELLGKVTEI-LETGANDVLVVKA---KGGKKERLIPFVD 151 (174)
T ss_pred EEeEeecCcEEEcCC-CcEEEEEEEE-eeCCCccEEEEEe---cCCCcEEEecchH
Confidence 457899999999877 9999999997 4776666755443 1223467888876
No 24
>PRK14593 rimM 16S rRNA-processing protein RimM; Provisional
Probab=76.62 E-value=11 Score=33.46 Aligned_cols=62 Identities=15% Similarity=0.077 Sum_probs=41.3
Q ss_pred eeeeccccCCeeEeccCcceeeeEeEEEEECCCCEEEEEEEcC------CCCCCCceEEeccc--ceeeC-c--EEEEe
Q 022580 116 VMRRSNLLAKQVISIQSAMSLGFVSQLWVDTTSWVVLVVEVRP------NLLSGEPERLLLED--ICQVG-D--VVLIE 183 (295)
Q Consensus 116 m~r~SeLiGlpVIsi~tG~rLG~V~DL~vDp~~~rV~gLiV~~------~~l~~~~~~Ip~e~--I~~IG-D--aIlV~ 183 (295)
-.=..||+|+.|++ +|..||+|.++. +...+-|. +++. .+. .+...||+-+ |..|- + .|+|+
T Consensus 103 EyY~~dLiGl~V~~--~g~~lG~V~~v~-~~ga~dvl--vV~~~~~~~~~~~-~ke~LIP~~~~~V~~VDle~k~I~v~ 175 (184)
T PRK14593 103 EFFYCDLVGLSVVE--ENEILGKVIEIQ-RISQTDYF--MVETTLSLVEKGL-AKIFLIPYRDFYIQEILLQDKKITTH 175 (184)
T ss_pred cEEeehccCcEEEE--CCEEeEEEEEEc-cCCCceEE--EEEeccccccCCC-CcEEEEeChhhhhceEecCCCEEEEe
Confidence 35588999999996 489999999984 55445554 4432 111 3577999854 55665 2 55554
No 25
>PF13028 DUF3889: Protein of unknown function (DUF3889)
Probab=75.42 E-value=5.8 Score=32.55 Aligned_cols=29 Identities=17% Similarity=0.375 Sum_probs=26.0
Q ss_pred EcCCCceeEEEEEEEEEcCCccEEEEEEc
Q 022580 206 VTPGRQNIGKVRGYTFNINSGAVESLELD 234 (295)
Q Consensus 206 iTe~G~~LG~V~Dv~FD~~TG~I~~yels 234 (295)
+.++|+.-|...+++||+.|++|..+.+-
T Consensus 67 l~~~~kefgV~v~V~f~p~T~ki~~I~~~ 95 (97)
T PF13028_consen 67 LREGGKEFGVFVTVSFNPKTEKIISINVE 95 (97)
T ss_pred EEcCCeEEEEEEEEEEeCCCCcEEEEEEE
Confidence 35889999999999999999999998764
No 26
>PRK14592 rimM 16S rRNA-processing protein RimM; Provisional
Probab=73.27 E-value=8.7 Score=33.55 Aligned_cols=62 Identities=10% Similarity=0.263 Sum_probs=40.3
Q ss_pred eeeccccCCeeEeccCcceeeeEeEEEEECCCCEEEEEEEcCCCCCCCceEEeccc--ceeeC-c--EEEEe
Q 022580 117 MRRSNLLAKQVISIQSAMSLGFVSQLWVDTTSWVVLVVEVRPNLLSGEPERLLLED--ICQVG-D--VVLIE 183 (295)
Q Consensus 117 ~r~SeLiGlpVIsi~tG~rLG~V~DL~vDp~~~rV~gLiV~~~~l~~~~~~Ip~e~--I~~IG-D--aIlV~ 183 (295)
.=..||+|+.|++ .+|..+|+|.++ ++...+-|.-+....+ ++...||+-. |..|- + .|+|+
T Consensus 92 ~y~~dLiG~~V~~-~~g~~lG~V~~v-~~~ga~dvlvI~~~~~---~ke~LIP~v~~~V~~IDle~k~I~v~ 158 (165)
T PRK14592 92 FYQSDLIGMEVKL-EDNTIYGYIKKI-YNFGSCDIIEISLTST---KKSTMLPFTKEIFPHINVKERYIILV 158 (165)
T ss_pred EEHHHcCCcEEEc-CCCCEEEEEEEE-ccCCCccEEEEEECCC---CcEEEEecchhcccEEECCCCEEEEE
Confidence 4578999999997 467899999999 4554555644432122 3567888743 44554 2 55554
No 27
>PRK14594 rimM 16S rRNA-processing protein RimM; Provisional
Probab=73.01 E-value=7.7 Score=34.02 Aligned_cols=46 Identities=17% Similarity=0.179 Sum_probs=33.9
Q ss_pred eeeccccCCeeEeccCcceeeeEeEEEEECCCCEEEEEEEcCCCCCCCceEEec
Q 022580 117 MRRSNLLAKQVISIQSAMSLGFVSQLWVDTTSWVVLVVEVRPNLLSGEPERLLL 170 (295)
Q Consensus 117 ~r~SeLiGlpVIsi~tG~rLG~V~DL~vDp~~~rV~gLiV~~~~l~~~~~~Ip~ 170 (295)
.=..||+|+.|++ + |..+|+|.++ ++...+-+. .++. .++...||+
T Consensus 97 ~Y~~dLiG~~V~~-~-g~~lG~V~~v-~~~ga~dll--~V~~---~~ke~LIPf 142 (166)
T PRK14594 97 YYFGKLIGYAIVN-D-GKELGEVVSF-FECLNSVLL--EVKV---GIKLFFVPF 142 (166)
T ss_pred EeHhHccCeEEEE-C-CEEEEEEEEE-eeCCCcEEE--EEEe---CCEEEEEeC
Confidence 5688999999998 5 9999999999 455455554 4442 235678887
No 28
>PRK14593 rimM 16S rRNA-processing protein RimM; Provisional
Probab=71.03 E-value=4.1 Score=36.26 Aligned_cols=35 Identities=23% Similarity=0.227 Sum_probs=26.4
Q ss_pred cccccccCCEEEcCCCceeEEEEEEEEEcCCccEEEEEE
Q 022580 195 VRLDTLVGYRVVTPGRQNIGKVRGYTFNINSGAVESLEL 233 (295)
Q Consensus 195 ~~~~~LiG~~ViTe~G~~LG~V~Dv~FD~~TG~I~~yel 233 (295)
.-+.+|+|++|+++ |+.||+|.|+ + +||.=.-|.+
T Consensus 104 yY~~dLiGl~V~~~-g~~lG~V~~v-~--~~ga~dvlvV 138 (184)
T PRK14593 104 FFYCDLVGLSVVEE-NEILGKVIEI-Q--RISQTDYFMV 138 (184)
T ss_pred EEeehccCcEEEEC-CEEeEEEEEE-c--cCCCceEEEE
Confidence 35789999999985 9999999999 3 4555333444
No 29
>PRK14590 rimM 16S rRNA-processing protein RimM; Provisional
Probab=70.95 E-value=9.8 Score=33.61 Aligned_cols=51 Identities=18% Similarity=0.264 Sum_probs=34.5
Q ss_pred eeeeccccCCeeEeccCcceee-eEeEEEEECCCCEEEEEEEcCCCCCCCceEEeccc
Q 022580 116 VMRRSNLLAKQVISIQSAMSLG-FVSQLWVDTTSWVVLVVEVRPNLLSGEPERLLLED 172 (295)
Q Consensus 116 m~r~SeLiGlpVIsi~tG~rLG-~V~DL~vDp~~~rV~gLiV~~~~l~~~~~~Ip~e~ 172 (295)
-.=..||+|++|++ .+|..+| +|.++. +...+-+.-+. +.. ++...||+-.
T Consensus 96 e~y~~dLiG~~V~d-~~g~~lGG~V~~v~-~~~a~dllvV~-~~~---~ke~LiP~v~ 147 (171)
T PRK14590 96 EFYSEDLIGLQAID-ETGKPLNWKLTDVQ-DNPAHPILVFI-KGE---GEEILIPFLN 147 (171)
T ss_pred CEEhHHccCcEEEe-CCCCEeeeEEEEEe-cCCCceEEEEE-CCC---CCEEEEechH
Confidence 34578999999998 6788997 999984 44455554332 222 2456788643
No 30
>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=70.76 E-value=11 Score=32.67 Aligned_cols=58 Identities=17% Similarity=0.234 Sum_probs=38.5
Q ss_pred ceeeeccccCCeeEeccCcceeeeEeEEEEECCCCEEEEEEEcCCCCCCCceEEecc--cceeeC
Q 022580 115 QVMRRSNLLAKQVISIQSAMSLGFVSQLWVDTTSWVVLVVEVRPNLLSGEPERLLLE--DICQVG 177 (295)
Q Consensus 115 ~m~r~SeLiGlpVIsi~tG~rLG~V~DL~vDp~~~rV~gLiV~~~~l~~~~~~Ip~e--~I~~IG 177 (295)
.-.-..||+|+.|++ .+|..+|+|.++. +...+-+.-+...++ ++...||+. -|..|-
T Consensus 93 ~e~y~~dLiG~~V~d-~~~~~lG~V~~v~-~~~a~dll~V~~~~~---~ke~liP~~~~fv~~ID 152 (165)
T TIGR02273 93 DEYYWTDLIGLEVVT-EEGEELGKVVEIL-ETGANDVLVVRSKKG---KKEVLIPFVEEIVKEID 152 (165)
T ss_pred CCEEhhHhCCcEEEc-CCCcEEEEEEEEe-cCCCccEEEEEECCC---CcEEEEECchhhCCEEe
Confidence 346688999999997 6688999999994 544555544432112 346688874 234554
No 31
>PRK00122 rimM 16S rRNA-processing protein RimM; Provisional
Probab=67.57 E-value=13 Score=32.49 Aligned_cols=63 Identities=17% Similarity=0.289 Sum_probs=40.9
Q ss_pred ceeeeccccCCeeEeccCcceeeeEeEEEEECCCCEEEEEEEcCCCCCCCceEEeccc--ceeeC-c--EEEEe
Q 022580 115 QVMRRSNLLAKQVISIQSAMSLGFVSQLWVDTTSWVVLVVEVRPNLLSGEPERLLLED--ICQVG-D--VVLIE 183 (295)
Q Consensus 115 ~m~r~SeLiGlpVIsi~tG~rLG~V~DL~vDp~~~rV~gLiV~~~~l~~~~~~Ip~e~--I~~IG-D--aIlV~ 183 (295)
...-..||+|+.|++ .+|..+|+|.++ ++...+-+. .++.. .++...||+-. |..|- + .|.|+
T Consensus 98 ~e~y~~dLiG~~V~d-~~g~~lG~V~~v-~~~~a~dll--~I~~~--~~~e~liP~~~~~V~~iD~~~~~I~v~ 165 (172)
T PRK00122 98 DEYYWHDLIGLEVVD-EDGEELGKVTDI-LETGANDVL--VVLKD--KKEERLIPFVEEVVKEVDLEAKRITVD 165 (172)
T ss_pred CCEEHHHhCCcEEEe-CCCcEEEEEEEE-ccCCCceEE--EEECC--CCCEEEEecChhhCCEEECCCCEEEEe
Confidence 346789999999997 568899999998 455455553 33221 23457888843 33444 2 55554
No 32
>PRK13149 H/ACA RNA-protein complex component Gar1; Reviewed
Probab=63.84 E-value=9.2 Score=29.41 Aligned_cols=27 Identities=26% Similarity=0.253 Sum_probs=21.5
Q ss_pred cccCCEEEcCCCceeEEEEEEEEEcCCc
Q 022580 199 TLVGYRVVTPGRQNIGKVRGYTFNINSG 226 (295)
Q Consensus 199 ~LiG~~ViTe~G~~LG~V~Dv~FD~~TG 226 (295)
.-+|..|++++++++|+|.|+ |=|-+.
T Consensus 24 P~~n~~V~~~~~~~IGkV~dI-fGPV~~ 50 (73)
T PRK13149 24 PPIGSVVYDKKLKKIGKVVDV-FGPVKE 50 (73)
T ss_pred CCCCCEeECCCCCEeEEEEEE-ECCCCC
Confidence 346899999999999999999 444333
No 33
>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=59.41 E-value=17 Score=34.50 Aligned_cols=39 Identities=21% Similarity=0.124 Sum_probs=34.1
Q ss_pred cccccCCEEEcCCCceeEEEEEEEEEcCCccEEEEEEcC
Q 022580 197 LDTLVGYRVVTPGRQNIGKVRGYTFNINSGAVESLELDS 235 (295)
Q Consensus 197 ~~~LiG~~ViTe~G~~LG~V~Dv~FD~~TG~I~~yels~ 235 (295)
-.+..|++|+-.||+..|+|.|+-.|..--.|-.||++-
T Consensus 148 d~DPrG~pV~g~Dg~v~GtV~D~WVDr~E~~iRYlEVel 186 (252)
T TIGR01150 148 DVDPRGLPVVAADGEVAGKVTDLWVDRPEQYFRYLEVEL 186 (252)
T ss_pred CCCCCCCeeEcCCCceeeEEEEEEEcCccceeeEEEEEe
Confidence 478899999999999999999999998777777877743
No 34
>COG3277 GAR1 RNA-binding protein involved in rRNA processing [Translation, ribosomal structure and biogenesis]
Probab=56.97 E-value=13 Score=30.67 Aligned_cols=23 Identities=22% Similarity=0.114 Sum_probs=19.8
Q ss_pred ccccCCEEEcCCCceeEEEEEEE
Q 022580 198 DTLVGYRVVTPGRQNIGKVRGYT 220 (295)
Q Consensus 198 ~~LiG~~ViTe~G~~LG~V~Dv~ 220 (295)
.--+|.+|+|++++.+|.|.|++
T Consensus 24 iP~l~~~V~~~~~k~IG~V~dVf 46 (98)
T COG3277 24 IPPLNAPVYDANLKRIGKVVDVF 46 (98)
T ss_pred CCCCCCeeEecCCCEEEEEEEEE
Confidence 33468999999999999999993
No 35
>PRK13828 rimM 16S rRNA-processing protein RimM; Provisional
Probab=54.64 E-value=10 Score=33.02 Aligned_cols=67 Identities=15% Similarity=0.171 Sum_probs=43.0
Q ss_pred eeeeccccCCeeEeccCcceeeeEeEEEEECCCCEEEEEEEcCCCCCCCceEEeccc--ceeeC---cEEEEecCCc
Q 022580 116 VMRRSNLLAKQVISIQSAMSLGFVSQLWVDTTSWVVLVVEVRPNLLSGEPERLLLED--ICQVG---DVVLIEDESV 187 (295)
Q Consensus 116 m~r~SeLiGlpVIsi~tG~rLG~V~DL~vDp~~~rV~gLiV~~~~l~~~~~~Ip~e~--I~~IG---DaIlV~~~~~ 187 (295)
-.=..||+|+.|++ .+|..||+|.++.= ...+-| |+|+... .++...||+-. |..|- ..|+|+-..-
T Consensus 79 e~y~~dLiG~~V~d-~~g~~lG~V~~V~~-~ga~dv--lvV~~~~-~~ke~LIP~v~~~V~~VDl~~~~I~v~~peG 150 (161)
T PRK13828 79 EFYHADLIGLAAVD-TGGALLGRVKAVHN-FGAGDI--LEIAPPG-GGPTLLLPFTRAVVPTVDLAAGRVVADPPAE 150 (161)
T ss_pred CEEhhhccCCEEEe-CCCCEEEEEEEEcc-CCCccE--EEEEECC-CCcEEEEeccccccCeEECCCCEEEEeCCcc
Confidence 35588999999997 57789999999853 334444 3444200 13567888744 55565 3677765443
No 36
>PF09939 DUF2171: Uncharacterized protein conserved in bacteria (DUF2171); InterPro: IPR018684 This family of various hypothetical prokaryotic proteins has no known function.
Probab=52.43 E-value=72 Score=24.58 Aligned_cols=55 Identities=16% Similarity=0.125 Sum_probs=38.0
Q ss_pred CCeeEeccCcceeeeEeEEEEECCCCEEEEEEEcCCCCCCCceEEecccceeeC-cEEEEec
Q 022580 124 AKQVISIQSAMSLGFVSQLWVDTTSWVVLVVEVRPNLLSGEPERLLLEDICQVG-DVVLIED 184 (295)
Q Consensus 124 GlpVIsi~tG~rLG~V~DL~vDp~~~rV~gLiV~~~~l~~~~~~Ip~e~I~~IG-DaIlV~~ 184 (295)
+++||. ..|..+|+|..+.= .+|. |+-..+.=.++..|||++.|..+- +.|....
T Consensus 5 hmeVi~-sdG~~vGtVDhveG----d~IK-Ltk~d~~~~g~HH~IPls~V~~Vd~~~V~L~~ 60 (67)
T PF09939_consen 5 HMEVIG-SDGVHVGTVDHVEG----DRIK-LTKDDSGHDGQHHYIPLSWVDSVDDDKVHLSK 60 (67)
T ss_pred CCEEEe-CCCCEEEEEeeEeC----CEEE-EeccCCCCCCcceEEehhHheeEcCCEEEEcC
Confidence 679995 88999999988752 2331 221111113567899999999999 6777654
No 37
>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=46.51 E-value=50 Score=25.50 Aligned_cols=36 Identities=17% Similarity=0.159 Sum_probs=29.0
Q ss_pred cccCCEEEcCCCceeEEEEEEEEEcCCccEEEEEEc
Q 022580 199 TLVGYRVVTPGRQNIGKVRGYTFNINSGAVESLELD 234 (295)
Q Consensus 199 ~LiG~~ViTe~G~~LG~V~Dv~FD~~TG~I~~yels 234 (295)
-.-|.+|+.++|+.+|+|.-..|.+..|+-.++=+=
T Consensus 33 ~~~g~~v~~~~g~~vG~vTS~~~sp~~~~~Iala~v 68 (95)
T PF08669_consen 33 PRGGEPVYDEDGKPVGRVTSGAYSPTLGKNIALAYV 68 (95)
T ss_dssp -STTCEEEETTTEEEEEEEEEEEETTTTEEEEEEEE
T ss_pred CCCCCEEEECCCcEEeEEEEEeECCCCCceEEEEEE
Confidence 345677777899999999999999999977766544
No 38
>PF13670 PepSY_2: Peptidase propeptide and YPEB domain This Prosite motif covers only the active site. This is family M4 in the peptidase classification.
Probab=42.73 E-value=18 Score=27.72 Aligned_cols=27 Identities=7% Similarity=-0.068 Sum_probs=19.8
Q ss_pred cCCEEEcCCCceeEEEEEEEEEcCCccEEEE
Q 022580 201 VGYRVVTPGRQNIGKVRGYTFNINSGAVESL 231 (295)
Q Consensus 201 iG~~ViTe~G~~LG~V~Dv~FD~~TG~I~~y 231 (295)
...++.+.+|+ ..++++|+.||+|+.-
T Consensus 56 yev~~~~~dG~----~~ev~vD~~tG~V~~~ 82 (83)
T PF13670_consen 56 YEVEARDKDGK----KVEVYVDPATGEVVKE 82 (83)
T ss_pred EEEEEEECCCC----EEEEEEcCCCCeEeec
Confidence 33445666655 5699999999999763
No 39
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=42.08 E-value=16 Score=32.04 Aligned_cols=21 Identities=24% Similarity=0.439 Sum_probs=15.6
Q ss_pred EEEEEEEcCCccEEEEEEcCCC
Q 022580 216 VRGYTFNINSGAVESLELDSFG 237 (295)
Q Consensus 216 V~Dv~FD~~TG~I~~yels~~G 237 (295)
|.|++||++||+|. ++....|
T Consensus 68 i~di~Fd~~tGEV~-IeaeKPG 88 (145)
T cd02410 68 ITDIYFDDDTGEVI-IEAEKPG 88 (145)
T ss_pred ceeeEecCCCcEEE-EEEcCCe
Confidence 79999999999875 3444334
No 40
>PRK06009 flgD flagellar basal body rod modification protein; Reviewed
Probab=33.12 E-value=1e+02 Score=26.89 Aligned_cols=36 Identities=22% Similarity=0.289 Sum_probs=26.9
Q ss_pred cccccCCEEEcCCCceeEEEEEEEEEcCCccEEEEEEcC
Q 022580 197 LDTLVGYRVVTPGRQNIGKVRGYTFNINSGAVESLELDS 235 (295)
Q Consensus 197 ~~~LiG~~ViTe~G~~LG~V~Dv~FD~~TG~I~~yels~ 235 (295)
...|+|+.|...+|..-|.|+-+.|.. |.+ .+.+.+
T Consensus 92 a~slIGk~V~~~~~~~~G~V~sV~~~~--~~~-~~~~~d 127 (140)
T PRK06009 92 AEGLIGRTVTSADGSITGVVKSVTVYS--DGV-IATLED 127 (140)
T ss_pred HHHhcCCEEEecCCcEEEEEEEEEEeC--Cce-EEEEEC
Confidence 468999999999998889999888863 333 344544
No 41
>COG3798 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.57 E-value=59 Score=25.52 Aligned_cols=60 Identities=20% Similarity=0.190 Sum_probs=38.3
Q ss_pred eeeeccccC-CeeEeccCcceeeeEeEEEEECCCCEEEEEEEcCCCCCCCceEEecccceeeCc-EEEEec
Q 022580 116 VMRRSNLLA-KQVISIQSAMSLGFVSQLWVDTTSWVVLVVEVRPNLLSGEPERLLLEDICQVGD-VVLIED 184 (295)
Q Consensus 116 m~r~SeLiG-lpVIsi~tG~rLG~V~DL~vDp~~~rV~gLiV~~~~l~~~~~~Ip~e~I~~IGD-aIlV~~ 184 (295)
||+++++.. +||+ ..+|+.+|+|..+. ..++. |.= .=.++..+||+++|..+.+ +|+...
T Consensus 1 m~~~sqikEhmeVv-~aDG~hvGtVDh~d----G~~ik-lak---ddsgkHH~ipLs~Ve~vD~~~v~l~v 62 (75)
T COG3798 1 MMDTSQIKEHMEVV-GADGKHVGTVDHLD----GEYIK-LAK---DDSGKHHYIPLSAVEHVDEHKVLLSV 62 (75)
T ss_pred CcchHhhhhcceee-cCCCcEeccEeecc----CcEEE-Eee---ccCCCceeEehhHhhhccCeeEEEec
Confidence 455555543 6777 58899999998652 22331 111 1134678999999999984 555543
No 42
>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=29.73 E-value=66 Score=22.31 Aligned_cols=18 Identities=17% Similarity=0.124 Sum_probs=12.3
Q ss_pred EEEEEEEEEcCCccEEEE
Q 022580 214 GKVRGYTFNINSGAVESL 231 (295)
Q Consensus 214 G~V~Dv~FD~~TG~I~~y 231 (295)
|..-+|++|..||+|...
T Consensus 46 ~~~~~v~VDa~tG~Il~~ 63 (64)
T PF03413_consen 46 GGEYEVYVDAYTGEILSS 63 (64)
T ss_dssp TEEEEEEEETTT--EEEE
T ss_pred CCEEEEEEECCCCeEEEe
Confidence 334788899999999875
No 43
>PF13861 FLgD_tudor: FlgD Tudor-like domain; PDB: 3OSV_A 3C12_A.
Probab=22.20 E-value=3e+02 Score=19.87 Aligned_cols=54 Identities=19% Similarity=0.325 Sum_probs=31.4
Q ss_pred ceeeeccccCCeeEe----ccCcceeeeEeEEEEECCCCEEEEEEEcCCCCCCCceEEecccceee
Q 022580 115 QVMRRSNLLAKQVIS----IQSAMSLGFVSQLWVDTTSWVVLVVEVRPNLLSGEPERLLLEDICQV 176 (295)
Q Consensus 115 ~m~r~SeLiGlpVIs----i~tG~rLG~V~DL~vDp~~~rV~gLiV~~~~l~~~~~~Ip~e~I~~I 176 (295)
|++....|+|+.|.- -.+..-.|+|..+.++ .+.. -|.+ .+....+|+++|.+|
T Consensus 3 q~lqa~~lIGk~V~~~~~~~~~~~~~g~V~sV~~~--~g~~-~L~l-----~~~~~~v~l~~V~~v 60 (61)
T PF13861_consen 3 QMLQAASLIGKEVLVPKSVAATTLVSGRVESVTFS--GGGP-MLNL-----GGGGSTVPLSDVTEV 60 (61)
T ss_dssp HHHHTTCTTTSEEEEEEEEEE-EEEEEEEEEEEEE--TTEE-EEEE-----TTTCEEEECCCB-B-
T ss_pred HHHHHHHhcCCEEEECCcEeeeeEEEEEEEEEEEc--CCeE-EEEE-----ecCCcEEEHHHeEEe
Confidence 456678899999976 3344555666666666 2333 2332 123345999998875
No 44
>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=21.32 E-value=2.4e+02 Score=24.38 Aligned_cols=46 Identities=22% Similarity=0.261 Sum_probs=29.4
Q ss_pred eEEecccceeeC-cEEEEecCCcccccccccccccccCCEEEcCCCceeEEEEEE
Q 022580 166 ERLLLEDICQVG-DVVLIEDESVMENDFKMVRLDTLVGYRVVTPGRQNIGKVRGY 219 (295)
Q Consensus 166 ~~Ip~e~I~~IG-DaIlV~~~~~v~~~~~l~~~~~LiG~~ViTe~G~~LG~V~Dv 219 (295)
...++-.|..+= +.|+|+.... ...--.|..|++++++.||+|.|+
T Consensus 22 ~i~~lG~v~~i~~~~vVvk~~~~--------~~vl~~~s~v~~edr~~iG~V~ei 68 (154)
T PF04410_consen 22 EIKPLGTVSHIVENLVVVKSTPS--------KQVLDFGSVVCLEDRTKIGKVDEI 68 (154)
T ss_dssp SEEEEEEEEEEETTEEEEEE-SS---------CEEBTT-EEEETTSBEEEEEEEE
T ss_pred eEEEeeeEEEEeCCcEEEEeCCC--------CcCCCCCCEEECCCCCEeEEEeeE
Confidence 455555555554 5566665433 122336788999999999999998
No 45
>PF09000 Cytotoxic: Cytotoxic; InterPro: IPR009105 Colicins are plasmid-encoded protein antibiotics, or bacteriocins, produced by strains of Escherichia coli that kill closely related bacteria. Colicins are classified according to the cell-surface receptor they bind to, colicin E3 binding to the BtuB receptor involved in vitamin B12 uptake. The lethal action of colicin E3 arises from its ability to inactivate the ribosome by site-specific RNase cleavage of the 16S ribosomal RNA, which is carried out by the catalytic, or ribonuclease domain. Colicin E3 is comprised of three domains, each domain being involved in a different stage of infection: receptor binding, translocation and cytotoxicity. Colicin E3 is a Y-shaped molecule with the receptor-binding middle domain forming the stalk, the N-terminal translocation domain forming the two globular heads (IPR003058 from INTERPRO), and the C-terminal catalytic domain forming the two globular arms. To neutralise the toxic effects of colicin E3, the host cell produces an immunity protein, which binds to the C-terminal end of the ribonuclease domain and effectively suppresses its activity. This entry represents the ribonuclease domain (also called catalytic or cytotoxic domain) found in various colicins. This domain confers cytotoxic activity to proteins, enabling the formation of nucleolytic breaks in 16S ribosomal RNA. The structure of the domain reveals a highly twisted central beta-sheet elaborated with a short N-terminal alpha-helix [, ]. ; GO: 0003723 RNA binding, 0016788 hydrolase activity, acting on ester bonds, 0043022 ribosome binding, 0009405 pathogenesis; PDB: 2B5U_C 1JCH_A 1E44_B 2XFZ_Y.
Probab=21.13 E-value=1.1e+02 Score=24.79 Aligned_cols=53 Identities=19% Similarity=0.276 Sum_probs=26.9
Q ss_pred cceeeCcEEEEecCCcccccc------------cccccccccC-CEEEcCCCceeEEEEEEEEEcCCccEE
Q 022580 172 DICQVGDVVLIEDESVMENDF------------KMVRLDTLVG-YRVVTPGRQNIGKVRGYTFNINSGAVE 229 (295)
Q Consensus 172 ~I~~IGDaIlV~~~~~v~~~~------------~l~~~~~LiG-~~ViTe~G~~LG~V~Dv~FD~~TG~I~ 229 (295)
.|.+++|+..+.....++... ..+.+.+..| .+|++..|+-||. ||+.||+.+
T Consensus 9 ~i~g~~~l~~~k~ktp~~gg~~~r~rw~~~kG~kiYewDsqHG~lEvy~~~GkHLGe-----~Dp~TGe~~ 74 (85)
T PF09000_consen 9 DIPGFPDLKKAKPKTPVQGGGGKRKRWKDKKGRKIYEWDSQHGELEVYNKRGKHLGE-----FDPKTGEQI 74 (85)
T ss_dssp G--SSSSEEEE---SB-SSSSSB--EEEETTTTEEEEEETTTTEEEEEETT-BEEEE-----E-TTTS-EE
T ss_pred cccCchhhhhccccCccccCCccccceEcCCCCEEEEEcCCCCeEEEEcCCCcCccc-----ccCCcccCc
Confidence 566777887777766665311 1222223333 5788888888885 888888654
No 46
>PF15640 Tox-MPTase4: Metallopeptidase toxin 4
Probab=20.14 E-value=61 Score=28.05 Aligned_cols=31 Identities=13% Similarity=0.246 Sum_probs=24.7
Q ss_pred cccCCEE-EcCCCceeEEEEEEEEEcCCccEE
Q 022580 199 TLVGYRV-VTPGRQNIGKVRGYTFNINSGAVE 229 (295)
Q Consensus 199 ~LiG~~V-iTe~G~~LG~V~Dv~FD~~TG~I~ 229 (295)
.-.|.+| +++.|..|..=.---||+.||+|.
T Consensus 32 ~~~gIkV~Idkk~kilP~n~aagFd~~tg~I~ 63 (132)
T PF15640_consen 32 GKRGIKVKIDKKDKILPENKAAGFDPETGEIY 63 (132)
T ss_pred HhCCcEEEECCccCCCCccccccCCCCCCcEE
Confidence 4467777 778888888877888999999884
Done!