Query 037553
Match_columns 151
No_of_seqs 130 out of 1060
Neff 7.3
Searched_HMMs 46136
Date Fri Mar 29 13:26:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037553.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037553hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1068 Exosomal 3'-5' exoribo 100.0 3.1E-32 6.7E-37 213.0 10.0 119 33-151 9-132 (245)
2 TIGR02065 ECX1 archaeal exosom 100.0 1.1E-30 2.4E-35 205.3 15.7 119 33-151 4-126 (230)
3 PRK03983 exosome complex exonu 100.0 1.3E-30 2.8E-35 206.5 15.2 119 33-151 10-132 (244)
4 PRK00173 rph ribonuclease PH; 100.0 1.5E-29 3.2E-34 199.9 14.8 115 37-151 1-123 (238)
5 COG0689 Rph RNase PH [Translat 100.0 1.7E-29 3.6E-34 197.7 13.5 119 33-151 4-127 (230)
6 TIGR01966 RNasePH ribonuclease 100.0 2.1E-28 4.6E-33 193.1 14.6 114 38-151 1-122 (236)
7 PF01138 RNase_PH: 3' exoribon 99.9 2E-25 4.3E-30 160.8 14.2 106 46-151 1-111 (132)
8 PRK04282 exosome complex RNA-b 99.9 6.3E-26 1.4E-30 182.1 11.1 125 26-151 13-148 (271)
9 TIGR03591 polynuc_phos polyrib 99.9 2.6E-25 5.5E-30 197.7 15.1 118 33-151 306-432 (684)
10 PRK11824 polynucleotide phosph 99.9 3.3E-25 7.2E-30 197.3 15.3 118 33-151 310-436 (693)
11 COG2123 RNase PH-related exori 99.9 4.1E-25 8.8E-30 175.3 11.1 128 23-151 9-147 (272)
12 TIGR02696 pppGpp_PNP guanosine 99.9 1.5E-23 3.1E-28 185.5 12.9 118 33-151 331-457 (719)
13 PLN00207 polyribonucleotide nu 99.9 5.8E-23 1.2E-27 185.0 15.3 118 33-151 434-561 (891)
14 KOG1613 Exosomal 3'-5' exoribo 99.9 2.6E-23 5.6E-28 162.5 3.3 138 13-151 12-160 (298)
15 KOG1069 Exosomal 3'-5' exoribo 99.9 4.5E-22 9.7E-27 151.7 8.3 101 46-151 4-104 (217)
16 KOG1612 Exosomal 3'-5' exoribo 99.8 1.5E-20 3.3E-25 147.7 12.9 119 32-151 16-146 (288)
17 KOG1614 Exosomal 3'-5' exoribo 99.8 5E-19 1.1E-23 138.7 9.9 118 30-151 15-143 (291)
18 KOG1067 Predicted RNA-binding 99.7 6.9E-17 1.5E-21 138.6 7.1 116 34-151 355-479 (760)
19 TIGR03591 polynuc_phos polyrib 99.6 5E-15 1.1E-19 132.2 13.4 96 48-151 5-113 (684)
20 PRK11824 polynucleotide phosph 99.6 2.1E-14 4.5E-19 128.4 13.4 99 48-151 14-122 (693)
21 COG1185 Pnp Polyribonucleotide 99.4 1.3E-13 2.8E-18 121.0 5.6 117 34-151 309-434 (692)
22 PLN00207 polyribonucleotide nu 99.0 3E-09 6.4E-14 97.0 9.4 99 48-151 89-197 (891)
23 TIGR02696 pppGpp_PNP guanosine 98.4 1.2E-06 2.6E-11 78.7 8.5 99 48-151 17-126 (719)
24 COG1185 Pnp Polyribonucleotide 98.2 5.9E-06 1.3E-10 73.4 8.1 98 48-151 14-121 (692)
25 KOG1067 Predicted RNA-binding 96.7 0.00045 9.7E-09 60.7 0.5 100 46-151 54-163 (760)
26 PF03726 PNPase: Polyribonucle 64.5 2.5 5.4E-05 27.7 0.3 17 23-43 67-83 (83)
27 PF09866 DUF2093: Uncharacteri 21.6 82 0.0018 18.3 1.8 12 70-81 5-16 (42)
No 1
>KOG1068 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp41 and related exoribonucleases [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=3.1e-32 Score=213.03 Aligned_cols=119 Identities=39% Similarity=0.629 Sum_probs=110.8
Q ss_pred CCCCCCCCCCCCCCCcceEEEeCCcCCCCeEEEEEECCeEEEEEEEcCccccc-ccccCceeEEEEEEEecCCcccccC-
Q 037553 33 DVDWLRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSVFGPRESKK-AMMYSNIGRLNCNVSYTTFATPIRG- 110 (151)
Q Consensus 33 ~~~~~R~DGR~~~e~R~i~i~~g~l~~adGSa~v~~G~T~Vl~~V~gp~~~~~-~~~~~~~g~l~v~v~~~p~a~~~r~- 110 (151)
+++++|.|||+++|+|+|.+++|++++++||||+++|||||+|.|+||++... +...++++.++|.|.+.+|++.+|.
T Consensus 9 seeg~r~dgRr~~elR~i~~~~g~~~~a~GSay~E~GnTKVl~aV~GPre~~~~~~~~~~~a~lnc~~~~a~Fst~~r~~ 88 (245)
T KOG1068|consen 9 SEEGLRTDGRRPNELRRIYARIGVLTQADGSAYMEQGNTKVLCAVYGPREIRGKSARRPDKAVLNCEVSSAQFSTGDRKK 88 (245)
T ss_pred CccccccCCCChhHhhhhhhhcCccccCCccchhhcCCeEEEEEEeCCcccccccccccccceEEEEEeeeccccchhcc
Confidence 58999999999999999999999999999999999999999999999999764 2346899999999999999999764
Q ss_pred ---CCchHHHHHHHHHHHHHhhhccCCCCCcEEEEEEEEEecCC
Q 037553 111 ---QGSDHKDFSSMLHKALEGAIILETFPKTTVDVFALVLESGG 151 (151)
Q Consensus 111 ---~~~~~~~l~~~l~~~l~~~I~l~~~p~~~I~I~v~VL~~DG 151 (151)
.+.++++++.+|+++|+++|+++.|||++|+|+|+||+|||
T Consensus 89 ~~~~~rr~~e~s~~L~~afe~~I~~~lyPrsqIDI~v~VleddG 132 (245)
T KOG1068|consen 89 RPKGDRREKELSLMLQQAFEPVILLELYPRSQIDIYVQVLEDDG 132 (245)
T ss_pred CCCccHHHHHHHHHHHHHHHHHHHhhhCccccceEEEEEEECCC
Confidence 34589999999999999999999999999999999999998
No 2
>TIGR02065 ECX1 archaeal exosome-like complex exonuclease 1. This family contains the archaeal protein orthologous to the eukaryotic exosome protein Rrp41. It is somewhat more distantly related to the bacterial protein ribonuclease PH. An exosome-like complex has been demonstrated experimentally for the Archaea in Sulfolobus solfataricus, so members of this family are designated exosome complex exonuclease 1, after usage in SwissProt.
Probab=99.97 E-value=1.1e-30 Score=205.26 Aligned_cols=119 Identities=36% Similarity=0.571 Sum_probs=109.6
Q ss_pred CCCCCCCCCCCCCCCcceEEEeCCcCCCCeEEEEEECCeEEEEEEEcCccccc-ccccCceeEEEEEEEecCCcccccC-
Q 037553 33 DVDWLRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSVFGPRESKK-AMMYSNIGRLNCNVSYTTFATPIRG- 110 (151)
Q Consensus 33 ~~~~~R~DGR~~~e~R~i~i~~g~l~~adGSa~v~~G~T~Vl~~V~gp~~~~~-~~~~~~~g~l~v~v~~~p~a~~~r~- 110 (151)
+++++|+|||.++|+|++++++|++++|||||++++|+|+|+|+|+||++... ....+++|.|+|+|+++||++.++.
T Consensus 4 ~~~~~R~DGR~~~e~R~~~~~~g~~~~a~GSa~~~~G~T~Vl~~V~gp~e~~~~~~~~~~~~~l~v~~~~~~~a~~~~~~ 83 (230)
T TIGR02065 4 LEDGVRLDGRKPDELRPIKIEAGVLKNADGSAYVEFGGTKIIAAVYGPREMHPRHLQLPDRAVLRVRYHMAPFSTDERKR 83 (230)
T ss_pred cCCCcCCCCCCcccccCeEEEECCCCCCCeEEEEEECCcEEEEEEeCCCccccccccCCCceEEEEEEEeCCcccCCccC
Confidence 58999999999999999999999999999999999999999999999987543 3456899999999999999997542
Q ss_pred --CCchHHHHHHHHHHHHHhhhccCCCCCcEEEEEEEEEecCC
Q 037553 111 --QGSDHKDFSSMLHKALEGAIILETFPKTTVDVFALVLESGG 151 (151)
Q Consensus 111 --~~~~~~~l~~~l~~~l~~~I~l~~~p~~~I~I~v~VL~~DG 151 (151)
+++++.+++++|+++|+++|++++||++.|+|+|+||++||
T Consensus 84 ~~~~~~~~~~s~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~DG 126 (230)
T TIGR02065 84 PGPSRREIEISKVIREALEPAILLEQFPRTAIDVFIEVLQADA 126 (230)
T ss_pred CCCCccHHHHHHHHHHHHHHHhChhhcCCeEEEEEEEEEEcCC
Confidence 66789999999999999999999999999999999999998
No 3
>PRK03983 exosome complex exonuclease Rrp41; Provisional
Probab=99.97 E-value=1.3e-30 Score=206.51 Aligned_cols=119 Identities=35% Similarity=0.563 Sum_probs=109.8
Q ss_pred CCCCCCCCCCCCCCCcceEEEeCCcCCCCeEEEEEECCeEEEEEEEcCcccc-cccccCceeEEEEEEEecCCcccccC-
Q 037553 33 DVDWLRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSVFGPRESK-KAMMYSNIGRLNCNVSYTTFATPIRG- 110 (151)
Q Consensus 33 ~~~~~R~DGR~~~e~R~i~i~~g~l~~adGSa~v~~G~T~Vl~~V~gp~~~~-~~~~~~~~g~l~v~v~~~p~a~~~r~- 110 (151)
+++++|+|||.++++|++++++|++++|||||+|++|+|+|+|+|+||.+.. +....+++|.|.|++++.||++.++.
T Consensus 10 ~~~~~R~DGR~~~~~R~i~i~~G~l~~a~GSa~v~~G~T~Vl~~V~gp~e~~~~~~~~~~~~~l~v~~~~~p~~~~~~~~ 89 (244)
T PRK03983 10 LEDGLRLDGRKPDELRPIKIEVGVLKNADGSAYLEWGNNKIIAAVYGPREMHPRHLQLPDRAVLRVRYNMAPFSVDERKR 89 (244)
T ss_pred ccCCCCCCCCCcCcccceEEEeCCCCCCCeEEEEEECCeEEEEEEecCCccccccccCCCcEEEEEEEEcCCCccccccC
Confidence 5899999999999999999999999999999999999999999999998753 33467899999999999999987543
Q ss_pred --CCchHHHHHHHHHHHHHhhhccCCCCCcEEEEEEEEEecCC
Q 037553 111 --QGSDHKDFSSMLHKALEGAIILETFPKTTVDVFALVLESGG 151 (151)
Q Consensus 111 --~~~~~~~l~~~l~~~l~~~I~l~~~p~~~I~I~v~VL~~DG 151 (151)
+++++.+++++|+++|+++|+++.||++.|+|+|+||++||
T Consensus 90 ~~~~~~~~~~s~~l~~~l~~~i~~~~~p~~~I~I~i~VL~~DG 132 (244)
T PRK03983 90 PGPDRRSIEISKVIREALEPAIMLELFPRTVIDVFIEVLQADA 132 (244)
T ss_pred CCCChhHHHHHHHHHHHHHHhccHHhCCCeEEEEEEEEEECCC
Confidence 56789999999999999999999999999999999999998
No 4
>PRK00173 rph ribonuclease PH; Reviewed
Probab=99.97 E-value=1.5e-29 Score=199.91 Aligned_cols=115 Identities=24% Similarity=0.392 Sum_probs=106.2
Q ss_pred CCCCCCCCCCCcceEEEeCCcCCCCeEEEEEECCeEEEEEEEcCcccccccccCceeEEEEEEEecCCccccc-------
Q 037553 37 LRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSVFGPRESKKAMMYSNIGRLNCNVSYTTFATPIR------- 109 (151)
Q Consensus 37 ~R~DGR~~~e~R~i~i~~g~l~~adGSa~v~~G~T~Vl~~V~gp~~~~~~~~~~~~g~l~v~v~~~p~a~~~r------- 109 (151)
+|+|||+++++|++++++|++++|+|||+|++|+|+|+|+|++|.+.|.....+++|.|+|+|++.||++.++
T Consensus 1 ~R~DGR~~~e~R~i~~~~g~~~~a~GSa~v~~G~T~Vla~V~~~~~~p~~~~~~~~g~l~v~~~~~p~a~~~~~~~~~~~ 80 (238)
T PRK00173 1 MRPDGRAADQLRPVTITRNFTKHAEGSVLVEFGDTKVLCTASVEEGVPRFLKGQGQGWVTAEYGMLPRATHTRNDREAAK 80 (238)
T ss_pred CCCCCCCcccccCeEEEeCCCCCCCeeEEEEecCcEEEEEEEcCCCCCCccCCCCcEEEEEEEecCCCCCcccccccccC
Confidence 5999999999999999999999999999999999999999999988664445678999999999999999875
Q ss_pred C-CCchHHHHHHHHHHHHHhhhccCCCCCcEEEEEEEEEecCC
Q 037553 110 G-QGSDHKDFSSMLHKALEGAIILETFPKTTVDVFALVLESGG 151 (151)
Q Consensus 110 ~-~~~~~~~l~~~l~~~l~~~I~l~~~p~~~I~I~v~VL~~DG 151 (151)
| +++++.+++++|+++|+++|+++.||++.|+|+++||++||
T Consensus 81 g~~~~~~~~~sr~i~r~lr~~i~l~~l~~~~i~v~v~VL~~DG 123 (238)
T PRK00173 81 GKQGGRTQEIQRLIGRSLRAVVDLKALGERTITIDCDVIQADG 123 (238)
T ss_pred CCCCccHHHHHHHHHHHHHHhcCHHHcCCeEEEEEEEEEeCCC
Confidence 2 45679999999999999999999999999999999999998
No 5
>COG0689 Rph RNase PH [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=1.7e-29 Score=197.66 Aligned_cols=119 Identities=34% Similarity=0.487 Sum_probs=109.6
Q ss_pred CCCCCCCCCCCCCCCcceEEEeCCcCCCCeEEEEEECCeEEEEEEEcCccccc-ccccCceeEEEEEEEecCCcccccC-
Q 037553 33 DVDWLRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSVFGPRESKK-AMMYSNIGRLNCNVSYTTFATPIRG- 110 (151)
Q Consensus 33 ~~~~~R~DGR~~~e~R~i~i~~g~l~~adGSa~v~~G~T~Vl~~V~gp~~~~~-~~~~~~~g~l~v~v~~~p~a~~~r~- 110 (151)
..++.|+|||.++|+|+|.++.|++++++||+++++|+|||+|+|+||.+..+ +...+.+|+++++|.+.||++.+|.
T Consensus 4 ~~~~~R~dgR~~delR~i~~~~~~~~~a~GS~~~~~G~tkVic~vsGp~e~~p~~l~~~~~g~~t~ey~m~p~sT~~R~~ 83 (230)
T COG0689 4 SEDGMRPDGRKPDELRPIKITRGVLKHAEGSSLIEFGNTKVICTVSGPREPVPRFLRGTGKGWLTAEYGMLPRSTDERKK 83 (230)
T ss_pred cccCcCCCCCCcccccceEEEeccccCCCccEEEEeCCeEEEEEEecCCCCCChhhcCCCceEEEEEEeccccccccccc
Confidence 36789999999999999999999999999999999999999999999998543 5566889999999999999997664
Q ss_pred --CCc-hHHHHHHHHHHHHHhhhccCCCCCcEEEEEEEEEecCC
Q 037553 111 --QGS-DHKDFSSMLHKALEGAIILETFPKTTVDVFALVLESGG 151 (151)
Q Consensus 111 --~~~-~~~~l~~~l~~~l~~~I~l~~~p~~~I~I~v~VL~~DG 151 (151)
.+. +.+|++++|.++|+++|+|++||+.+|+|+++|||+||
T Consensus 84 ~~~~~gR~~eisrli~~al~~~i~L~~~p~~~I~i~~dVlqaDg 127 (230)
T COG0689 84 READRGRTKEISRLIGRALRAVIDLELLPESTIDIDCDVLQADG 127 (230)
T ss_pred ccccccchhHHHHHHHHHHHHHhhhhhcCccEEEEEEEEEECCC
Confidence 333 79999999999999999999999999999999999998
No 6
>TIGR01966 RNasePH ribonuclease PH. This bacterial enzyme, ribonuclease PH, performs the final 3'-trimming and modification of tRNA precursors. This model is restricted absolutely to bacteria. Related families outside the model include proteins described as probable exosome complex exonucleases (rRNA processing) and polyribonucleotide nucleotidyltransferases (mRNA degradation). The most divergent member within the family is RNase PH from Deinococcus radiodurans.
Probab=99.96 E-value=2.1e-28 Score=193.05 Aligned_cols=114 Identities=27% Similarity=0.364 Sum_probs=103.1
Q ss_pred CCCCCCCCCCcceEEEeCCcCCCCeEEEEEECCeEEEEEEEcCcccccccccCceeEEEEEEEecCCccccc-------C
Q 037553 38 RPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSVFGPRESKKAMMYSNIGRLNCNVSYTTFATPIR-------G 110 (151)
Q Consensus 38 R~DGR~~~e~R~i~i~~g~l~~adGSa~v~~G~T~Vl~~V~gp~~~~~~~~~~~~g~l~v~v~~~p~a~~~r-------~ 110 (151)
|+|||+++|+|++++++|++++|||||+|++|+|+|+|+|+++...+.....+++|.|+|++++.||++..+ |
T Consensus 1 R~DGR~~~e~R~i~i~~G~~~~A~GSa~v~~G~T~Vla~V~~~~~~p~~~~~~~~g~l~v~~~~~p~a~~~~~~r~~~~g 80 (236)
T TIGR01966 1 RPDGRKPDQLRPVSITRDFLKHAEGSVLIEFGNTKVLCTASVEEKVPPFLRGSGEGWITAEYGMLPRATQTRNRRESAKG 80 (236)
T ss_pred CCCCCCCCCccCeEEEeCCcCCCCceEEEEecCCEEEEEEEccCccCCcccCCCcEEEEEEEecCCCCCCCCccccccCC
Confidence 899999999999999999999999999999999999999998877554333468999999999999999854 2
Q ss_pred -CCchHHHHHHHHHHHHHhhhccCCCCCcEEEEEEEEEecCC
Q 037553 111 -QGSDHKDFSSMLHKALEGAIILETFPKTTVDVFALVLESGG 151 (151)
Q Consensus 111 -~~~~~~~l~~~l~~~l~~~I~l~~~p~~~I~I~v~VL~~DG 151 (151)
++.++.+++++|+++|+++|+++.||++.|+|+|+||++||
T Consensus 81 ~~~~~~~e~~~~i~r~lr~~i~l~~l~~~~i~I~v~VL~~DG 122 (236)
T TIGR01966 81 KQSGRTQEIQRLIGRALRAVVDLEALGERTIWIDCDVIQADG 122 (236)
T ss_pred CCCccHHHHHHHHHHHHHHhcCHhhcCCeEEEEEEEEEeCCC
Confidence 33468899999999999999999999999999999999998
No 7
>PF01138 RNase_PH: 3' exoribonuclease family, domain 1 This Prosite family only includes Ribonuclease PH; InterPro: IPR001247 The PH (phosphorolytic) domain is responsible for 3'-5' exoribonuclease activity, although in some proteins this domain has lost its catalytic function. An active PH domain uses inorganic phosphate as a nucleophile, adding it across the phosphodiester bond between the end two nucleotides in order to release ribonucleoside 5'-diphosphate (rNDP) from the 3' end of the RNA substrate. PH domains can be found in bacterial/organelle RNases and PNPases (polynucleotide phosphorylases) [], as well as in archaeal and eukaryotic RNA exosomes [, ], the later acting as nano-compartments for the degradation or processing of RNA (including mRNA, rRNA, snRNA and snoRNA). Bacterial/organelle PNPases share a common barrel structure with RNA exosomes, consisting of a hexameric ring of PH domains that act as a degradation chamber, and an S1-domain/KH-domain containing cap that binds the RNA substrate (and sometimes accessory proteins) in order to regulate and restrict entry into the degradation chamber []. Unstructured RNA substrates feed in through the pore made by the S1 domains, are degraded by the PH domain ring, and exit as nucleotides via the PH pore at the opposite end of the barrel [, ]. This entry represents the phosphorolytic (PH) domain 1, which has a core 2-layer alpha/beta structure with a left-handed crossover, similar to that found in ribosomal protein S5. This domain is found in bacterial/organelle PNPases and in archaeal/eukaryotic exosomes []. More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; PDB: 2C38_G 2BR2_O 2C37_M 3L7Z_A 2JEB_A 2C39_A 2JEA_A 2JE6_A 3U1K_A 4AM3_B ....
Probab=99.94 E-value=2e-25 Score=160.78 Aligned_cols=106 Identities=38% Similarity=0.595 Sum_probs=95.4
Q ss_pred CCcceEEEeCCcCCCCeEEEEEECCeEEEEEEEcCcccccccccC-ceeEEEEEEEecCCccccc---C-CCchHHHHHH
Q 037553 46 QCRPAFFRTGAVNSASGSAYAEFGNTKVIVSVFGPRESKKAMMYS-NIGRLNCNVSYTTFATPIR---G-QGSDHKDFSS 120 (151)
Q Consensus 46 e~R~i~i~~g~l~~adGSa~v~~G~T~Vl~~V~gp~~~~~~~~~~-~~g~l~v~v~~~p~a~~~r---~-~~~~~~~l~~ 120 (151)
|+|++.+++|+++++||||+|++|+|+|+|+|+||.+.++..+.+ .+|.++|+|++.|++..+. + ++..+.++++
T Consensus 1 e~R~i~i~~~~~~~a~GSa~v~~G~T~V~~~V~~~~~~~~~~~~~~~~g~~~v~v~~~~~~~~~~~~~~~~~~~~~~l~~ 80 (132)
T PF01138_consen 1 ELRPISIETGVLPRADGSARVSLGNTKVICSVKGPIEPPPSNERDDAEGRLTVEVEFSPFASPSFRRGGRPDEEERELSS 80 (132)
T ss_dssp CBEEEEEEESSSSSSSEEEEEEETTEEEEEEEEEEEEGCSCSTTSSSSEEEEEEEEECCCGSTSSSSSSSTHHHHHHHHH
T ss_pred CCccEEEEeCCCCCCCeEEEEEECCeEEEEEEEecccccchhcccCCCceEEEEEEeccccccccccccccchhHHHHHH
Confidence 799999999999999999999999999999999999874433323 3599999999999998754 2 5668999999
Q ss_pred HHHHHHHhhhccCCCCCcEEEEEEEEEecCC
Q 037553 121 MLHKALEGAIILETFPKTTVDVFALVLESGG 151 (151)
Q Consensus 121 ~l~~~l~~~I~l~~~p~~~I~I~v~VL~~DG 151 (151)
+|+++|+++++++.||+|.|+|+|+||++||
T Consensus 81 ~l~~~l~~~~~~~~~~~~~i~v~v~vl~~dG 111 (132)
T PF01138_consen 81 LLERALRSSILLEGYPRWQIHVDVQVLSDDG 111 (132)
T ss_dssp HHHHHHHHTBSTTTTSSEEEEEEEEEEECSS
T ss_pred HHhhhccccccccccCceEEEEEEEEEecCC
Confidence 9999999999999999999999999999998
No 8
>PRK04282 exosome complex RNA-binding protein Rrp42; Provisional
Probab=99.93 E-value=6.3e-26 Score=182.08 Aligned_cols=125 Identities=25% Similarity=0.294 Sum_probs=107.4
Q ss_pred cCcccCCCCCCCCCCCCCCCCCcceEEEeCCcCCCCeEEEEEECCeEEEEEEEcCcccccccccCceeEEEEEEEecCCc
Q 037553 26 PPIFSGSDVDWLRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSVFGPRESKKAMMYSNIGRLNCNVSYTTFA 105 (151)
Q Consensus 26 ~~~~~~~~~~~~R~DGR~~~e~R~i~i~~g~l~~adGSa~v~~G~T~Vl~~V~gp~~~~~~~~~~~~g~l~v~v~~~p~a 105 (151)
-+|+.+.+++++|+|||.++|+|++++++|++++++|||+|++|+|+|+|+|+++...+ ....+++|.|+|+|+++||+
T Consensus 13 ~~~i~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~vl~~V~~~~~~p-~~~~~~~g~i~~~v~~~~~a 91 (271)
T PRK04282 13 KDYILSLLKKGKRIDGRKLDEYRPIEIETGVIKKAEGSALVKLGNTQVLAGVKLEIGEP-FPDTPNEGVLIVNAELLPLA 91 (271)
T ss_pred HHHHHHHHhcCCCCCCCCCccccCeEEEeCCccCCCcEEEEEECCCEEEEEEEEEEecC-CCCCCCCCEEEEEEEECCCc
Confidence 34666667899999999999999999999999999999999999999999999765433 34568999999999999999
Q ss_pred cccc--C-CCchHHHHHHHHHHHHHhh--hccCCC---CC---cEEEEEEEEEecCC
Q 037553 106 TPIR--G-QGSDHKDFSSMLHKALEGA--IILETF---PK---TTVDVFALVLESGG 151 (151)
Q Consensus 106 ~~~r--~-~~~~~~~l~~~l~~~l~~~--I~l~~~---p~---~~I~I~v~VL~~DG 151 (151)
++.+ + +++++.+++++|+++|++. ++++.| |+ |.|+|+|+||++||
T Consensus 92 ~~~~~~~~~~~~~~~l~~~l~r~l~~~~~~dl~~L~I~~g~~~w~i~Vdv~VL~~dG 148 (271)
T PRK04282 92 SPTFEPGPPDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWVVFIDVYVLDHDG 148 (271)
T ss_pred CccccCCCCCHHHHHHHHHHHHHHhccCCccHHHcEEecCcEEEEEEEEEEEECCCC
Confidence 8854 3 6678999999999999985 566655 43 68999999999998
No 9
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=99.93 E-value=2.6e-25 Score=197.72 Aligned_cols=118 Identities=23% Similarity=0.353 Sum_probs=104.6
Q ss_pred CCCCCCCCCCCCCCCcceEEEeCCcCCCCeEEEEEECCeEEEEEE-EcCccccc---ccccCceeEEEEEEEecCCcccc
Q 037553 33 DVDWLRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSV-FGPRESKK---AMMYSNIGRLNCNVSYTTFATPI 108 (151)
Q Consensus 33 ~~~~~R~DGR~~~e~R~i~i~~g~l~~adGSa~v~~G~T~Vl~~V-~gp~~~~~---~~~~~~~g~l~v~v~~~p~a~~~ 108 (151)
+++++|+|||+++|+|+++|++|+++++||||+|++|+|+|+|+| .||.+... .....+++++.++|+|+|||+++
T Consensus 306 l~~g~R~DGR~~~e~Rpi~~~~g~l~~a~GSa~~~~G~Tqvl~~vt~g~~~~~~~~~~~~~~~~~~~~~~y~~~pfs~~e 385 (684)
T TIGR03591 306 LKEGKRIDGRDLDTIRPISIEVGVLPRTHGSALFTRGETQALVVTTLGTERDEQIIDDLEGEYRKRFMLHYNFPPYSVGE 385 (684)
T ss_pred hcCCCCCCCCCCCCcCceEEEeCCCCCCCceEEEEeCCeEEEEEEecCCcccccCCcccCCCccEEEEEEEEcCCCCCCC
Confidence 479999999999999999999999999999999999999999999 59875321 22335689999999999999997
Q ss_pred cC----CCchHHHHHHHHHHHHHhhhcc-CCCCCcEEEEEEEEEecCC
Q 037553 109 RG----QGSDHKDFSSMLHKALEGAIIL-ETFPKTTVDVFALVLESGG 151 (151)
Q Consensus 109 r~----~~~~~~~l~~~l~~~l~~~I~l-~~~p~~~I~I~v~VL~~DG 151 (151)
++ +++++.+++++++++|+++|++ +.||+ +|+|+++||++||
T Consensus 386 ~~~~g~~~rrei~~~~l~~ral~~~i~~~~~~p~-tI~v~~~VLesdG 432 (684)
T TIGR03591 386 VGRVGGPGRREIGHGALAERALKAVLPSEEEFPY-TIRVVSEILESNG 432 (684)
T ss_pred cCCCCCCChHHHHHHHHHHHHHHHhcCccccCCe-EEEEEEEEEeCCC
Confidence 54 6778999999999999999986 78885 6999999999998
No 10
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=99.93 E-value=3.3e-25 Score=197.27 Aligned_cols=118 Identities=24% Similarity=0.360 Sum_probs=104.0
Q ss_pred CCCCCCCCCCCCCCCcceEEEeCCcCCCCeEEEEEECCeEEEEEE-EcCcccc-c--ccccCceeEEEEEEEecCCcccc
Q 037553 33 DVDWLRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSV-FGPRESK-K--AMMYSNIGRLNCNVSYTTFATPI 108 (151)
Q Consensus 33 ~~~~~R~DGR~~~e~R~i~i~~g~l~~adGSa~v~~G~T~Vl~~V-~gp~~~~-~--~~~~~~~g~l~v~v~~~p~a~~~ 108 (151)
+++++|+|||+++|+|+++|++|++++|||||+|++|+|+|+|+| .||.... . .....+++++.++|+++|||+++
T Consensus 310 l~~g~R~DGR~~~e~Rpi~~~~g~l~~a~GSal~~~G~T~Vl~~vt~g~~~~~~~~~~~~~~~~~~~~~~y~~~pfs~~e 389 (693)
T PRK11824 310 LEEGIRIDGRKLDEIRPISIEVGVLPRTHGSALFTRGETQALVVATLGTLRDEQIIDGLEGEYKKRFMLHYNFPPYSVGE 389 (693)
T ss_pred hcCCCCCCCCCcCcccceEEEeCCCCCCCceEEEEECCeEEEEEEecCCCcccccccccCCCCcEEEEEEEEcCCCCCCC
Confidence 379999999999999999999999999999999999999999999 5885321 1 12234789999999999999997
Q ss_pred cC----CCchHHHHHHHHHHHHHhhhcc-CCCCCcEEEEEEEEEecCC
Q 037553 109 RG----QGSDHKDFSSMLHKALEGAIIL-ETFPKTTVDVFALVLESGG 151 (151)
Q Consensus 109 r~----~~~~~~~l~~~l~~~l~~~I~l-~~~p~~~I~I~v~VL~~DG 151 (151)
++ +++++.+++++++++|+++|++ ++|| |+|+|+++||++||
T Consensus 390 ~~~~~~~~rre~~~~~li~ral~~vi~~~~~~p-~~I~v~~~VLe~dG 436 (693)
T PRK11824 390 TGRVGSPGRREIGHGALAERALEPVLPSEEEFP-YTIRVVSEILESNG 436 (693)
T ss_pred cCCCCCCChhHHHHHHHHHHHHHHhcCcccCCC-EEEEEEEEEEecCC
Confidence 64 6778999999999999999998 6888 58999999999998
No 11
>COG2123 RNase PH-related exoribonuclease [Translation, ribosomal structure and biogenesis]
Probab=99.92 E-value=4.1e-25 Score=175.31 Aligned_cols=128 Identities=30% Similarity=0.335 Sum_probs=113.1
Q ss_pred CCCcCcccCCCCCCCCCCCCCCCCCcceEEEeCCcCCCCeEEEEEECCeEEEEEEEcCcccccccccCceeEEEEEEEec
Q 037553 23 KTRPPIFSGSDVDWLRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSVFGPRESKKAMMYSNIGRLNCNVSYT 102 (151)
Q Consensus 23 ~~~~~~~~~~~~~~~R~DGR~~~e~R~i~i~~g~l~~adGSa~v~~G~T~Vl~~V~gp~~~~~~~~~~~~g~l~v~v~~~ 102 (151)
..+.+|+.+.+..++|+|||.++|+|++++++|+++.|+|||+|++|+|+|+|+|+.....| ..+.|++|.+.+++++.
T Consensus 9 ~~~~~~i~~ll~~g~R~DGR~~~efR~ieI~~~vi~ka~GSa~VklG~Tqvv~gvK~eig~P-f~DtP~eG~~~~n~El~ 87 (272)
T COG2123 9 EIKREYILNLLKKGIRIDGRSFDEFRPLEIETGVIPKANGSALVKLGNTQVVVGVKAEIGEP-FPDTPNEGVLVVNVELS 87 (272)
T ss_pred hhHHHHHHHHhccCcccCCCCcccccceEEEeCceecCCCcEEEEecCeEEEEEEEcccCCC-CCCCCCCceEEeeeeee
Confidence 34455666677899999999999999999999999999999999999999999999998765 46789999999999999
Q ss_pred CCcccc--cC-CCchHHHHHHHHHHHHHh--hhccCCC----CC--cEEEEEEEEEecCC
Q 037553 103 TFATPI--RG-QGSDHKDFSSMLHKALEG--AIILETF----PK--TTVDVFALVLESGG 151 (151)
Q Consensus 103 p~a~~~--r~-~~~~~~~l~~~l~~~l~~--~I~l~~~----p~--~~I~I~v~VL~~DG 151 (151)
|.|++. .| +++...++++++.+.++. +|++++| ++ |.+.++++||++||
T Consensus 88 Plas~~fE~Gppde~aielsrvvdr~lr~s~aiDlekL~I~~g~kvwvv~vDv~vld~DG 147 (272)
T COG2123 88 PLASPSFEPGPPDELAIELSRVVDRGLRESKAIDLEKLCIEEGKKVWVVFVDVHVLDYDG 147 (272)
T ss_pred ccccccccCCCCchhHHHHHHHHHHHHHhccCcchhheeEecCCEEEEEEEEEEEEcCCC
Confidence 999994 45 677889999999999987 7888887 22 67899999999998
No 12
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=99.90 E-value=1.5e-23 Score=185.51 Aligned_cols=118 Identities=19% Similarity=0.247 Sum_probs=103.1
Q ss_pred CCCCCCCCCCCCCCCcceEEEeCCcCCCCeEEEEEECCeEEEEEEE-cCccccc---ccccCceeEEEEEEEecCCcccc
Q 037553 33 DVDWLRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSVF-GPRESKK---AMMYSNIGRLNCNVSYTTFATPI 108 (151)
Q Consensus 33 ~~~~~R~DGR~~~e~R~i~i~~g~l~~adGSa~v~~G~T~Vl~~V~-gp~~~~~---~~~~~~~g~l~v~v~~~p~a~~~ 108 (151)
+++++|+|||+++++|+++|++|+++++||||+|+.|+|+|+|.+. ||..... .....+++.+.|||+|+|||+.+
T Consensus 331 l~~g~R~DGR~~~eiR~i~~~~g~l~~a~GSa~~~~G~Tqvl~~~tlG~~~~~q~~~~l~~~~~~~~~~~YnfpPFSt~e 410 (719)
T TIGR02696 331 LTEGVRIDGRGVTDIRPLDAEVQVIPRVHGSALFERGETQILGVTTLNMLKMEQQIDSLSPETSKRYMHHYNFPPYSTGE 410 (719)
T ss_pred hcCCCCCCCCCccccccceeecCCCCCCCceEEEEecCcEEEEEEeCCCchhhhhcccccccccceEEEEEeCCCCcccC
Confidence 4789999999999999999999999999999999999999999986 4443222 12235678999999999999997
Q ss_pred cC----CCchHHHHHHHHHHHHHhhhc-cCCCCCcEEEEEEEEEecCC
Q 037553 109 RG----QGSDHKDFSSMLHKALEGAII-LETFPKTTVDVFALVLESGG 151 (151)
Q Consensus 109 r~----~~~~~~~l~~~l~~~l~~~I~-l~~~p~~~I~I~v~VL~~DG 151 (151)
++ ++.++.+++.+++++|+++|+ ++.||++ |.+.++||++||
T Consensus 411 r~~~~~~~RReighg~La~rALe~vI~~~e~fP~T-IrvvseVLeSdG 457 (719)
T TIGR02696 411 TGRVGSPKRREIGHGALAERALVPVLPSREEFPYA-IRQVSEALGSNG 457 (719)
T ss_pred CCCCCCCCccHHHHHHHHHHHHHHhhCcHhhCCCE-EEEEEEeeccCC
Confidence 65 467899999999999999997 7999987 888999999998
No 13
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=99.90 E-value=5.8e-23 Score=184.97 Aligned_cols=118 Identities=24% Similarity=0.272 Sum_probs=103.6
Q ss_pred CCCCCCCCCCCCCCCcceEEEeCCcCCCCeEEEEEECCeEEEEEEE-cCcccccccc----cCceeEEEEEEEecCCccc
Q 037553 33 DVDWLRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSVF-GPRESKKAMM----YSNIGRLNCNVSYTTFATP 107 (151)
Q Consensus 33 ~~~~~R~DGR~~~e~R~i~i~~g~l~~adGSa~v~~G~T~Vl~~V~-gp~~~~~~~~----~~~~g~l~v~v~~~p~a~~ 107 (151)
+.+++|+|||+++|+|+|.|++|++++|||||+|++|+|+|+|+|+ ||.+.....+ ....+.+.++|+++||+++
T Consensus 434 ~~~g~R~DGR~~~eiRpI~~e~G~Lp~A~GSAlf~~G~TqVLatVtlGp~~~~q~~d~l~~~~~~~~f~~~y~fPPfs~g 513 (891)
T PLN00207 434 VEGGKRSDGRTPDEIRPINSSCGLLPRAHGSALFTRGETQALAVVTLGDKQMAQRIDNLVDADEVKRFYLQYSFPPSCVG 513 (891)
T ss_pred hcCCCCCCCCCcCccceEEEEeCCcCCCCceEEEEECCeEEEEEEEecCccccccccccccccceeeEEEEEEcCCCCCc
Confidence 4789999999999999999999999999999999999999999995 8875432211 1457889999999999987
Q ss_pred ccC----CCchHHHHHHHHHHHHHhhhccC-CCCCcEEEEEEEEEecCC
Q 037553 108 IRG----QGSDHKDFSSMLHKALEGAIILE-TFPKTTVDVFALVLESGG 151 (151)
Q Consensus 108 ~r~----~~~~~~~l~~~l~~~l~~~I~l~-~~p~~~I~I~v~VL~~DG 151 (151)
+++ +++++.+++++++++|+++|+.+ .|| +.|+|+++||++||
T Consensus 514 e~~r~g~psrREi~hg~L~eRALrpvip~~~~fP-~tIrV~~~VLesDG 561 (891)
T PLN00207 514 EVGRIGAPSRREIGHGMLAERALEPILPSEDDFP-YTIRVESTITESNG 561 (891)
T ss_pred cccCCCCCCHHHHHHHHHHHHHHHHhCCcccCCC-EEEEEEEEEEeCCC
Confidence 543 57789999999999999999986 889 58999999999998
No 14
>KOG1613 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp43 [Translation, ribosomal structure and biogenesis]
Probab=99.87 E-value=2.6e-23 Score=162.51 Aligned_cols=138 Identities=20% Similarity=0.234 Sum_probs=123.6
Q ss_pred cccccCCCCCCCCcCcccCCCCCCCCCCCCCCCCCcceEEEeCCcCCCCeEEEEEECCeEEEEEEEcCcccccccccCce
Q 037553 13 ATYSPIDPTRKTRPPIFSGSDVDWLRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSVFGPRESKKAMMYSNI 92 (151)
Q Consensus 13 ~~~~~~~~~~~~~~~~~~~~~~~~~R~DGR~~~e~R~i~i~~g~l~~adGSa~v~~G~T~Vl~~V~gp~~~~~~~~~~~~ 92 (151)
..|.|++++++++..||++++.+++|+|||+..|+|.+.++.|.++++|||+.++.|+|.|+|+|++++..| ....|++
T Consensus 12 ~~f~p~~fkrI~Pe~~l~rhLse~~RpdgR~lgefRdt~in~g~IsTangSal~K~G~ttvi~~Ik~ei~ep-stdapde 90 (298)
T KOG1613|consen 12 ITFPPEVFKRISPELYLQRHLSEGIRPDGRKLGEFRDTAINAGNISTANGSALLKSGKTTVICGIKAEIAEP-STDAPDE 90 (298)
T ss_pred cccCHHHHhhcCHHHHHHHHhhcccCcchhhhhHHhhhheecCceeccCcHHHHhcCCcEEEEEeeeeeccc-ccCCCCC
Confidence 679999999999999999999999999999999999999999999999999999999999999999999865 4567999
Q ss_pred eEEEEEEEecCCccccc--C-CCchHHHHHHHHHHHHHh--hhccCCC----CC--cEEEEEEEEEecCC
Q 037553 93 GRLNCNVSYTTFATPIR--G-QGSDHKDFSSMLHKALEG--AIILETF----PK--TTVDVFALVLESGG 151 (151)
Q Consensus 93 g~l~v~v~~~p~a~~~r--~-~~~~~~~l~~~l~~~l~~--~I~l~~~----p~--~~I~I~v~VL~~DG 151 (151)
|.|..+|.++|.|++.. | +++.++.+++.|..++.+ +|+++.+ +| |..+.++.||+.||
T Consensus 91 g~Iv~n~~lpplcs~r~RpG~p~dea~viSq~LhdtIl~S~ii~~k~Lci~~gKaawvlYadIicLd~dG 160 (298)
T KOG1613|consen 91 GDIVPNYALPPLCSSRFRPGPPTDEAQVISQKLHDTILHSRIIPKKALCIKAGKAAWVLYADIICLDYDG 160 (298)
T ss_pred cceeecccCCcccccCCCCCCCchHHHHHHHHHHHHHHhcCCcchhhheeeccceeeEEEEEEEEEcCCC
Confidence 99999999999999853 4 677899999999888876 5666655 34 56788899999998
No 15
>KOG1069 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp46 [Translation, ribosomal structure and biogenesis]
Probab=99.87 E-value=4.5e-22 Score=151.67 Aligned_cols=101 Identities=30% Similarity=0.389 Sum_probs=91.4
Q ss_pred CCcceEEEeCCcCCCCeEEEEEECCeEEEEEEEcCcccccccccCceeEEEEEEEecCCcccccCCCchHHHHHHHHHHH
Q 037553 46 QCRPAFFRTGAVNSASGSAYAEFGNTKVIVSVFGPRESKKAMMYSNIGRLNCNVSYTTFATPIRGQGSDHKDFSSMLHKA 125 (151)
Q Consensus 46 e~R~i~i~~g~l~~adGSa~v~~G~T~Vl~~V~gp~~~~~~~~~~~~g~l~v~v~~~p~a~~~r~~~~~~~~l~~~l~~~ 125 (151)
++|++.++.|+++++||||.|++|+|+|+|+|+||.+.+.+.+.+++..|.|-++ |.+.. .+..++.++++|+++
T Consensus 4 ~lr~~~cei~iLsr~dGSs~fsqgdT~V~c~V~GP~dvk~r~E~~~katleVi~r--p~~G~---~~~~eK~~e~iI~~t 78 (217)
T KOG1069|consen 4 RLRGIACEISILSRPDGSSEFSQGDTKVICSVYGPIDVKARQEDPEKATLEVIWR--PKSGV---NGTVEKVLERIIRKT 78 (217)
T ss_pred hhhhhhhhhceecCCCCccceecCCcEEEEEeeCCcchhhcccCchhceEEEEEe--cccCc---chHHHHHHHHHHHHH
Confidence 7899999999999999999999999999999999999887788899998855554 55433 456789999999999
Q ss_pred HHhhhccCCCCCcEEEEEEEEEecCC
Q 037553 126 LEGAIILETFPKTTVDVFALVLESGG 151 (151)
Q Consensus 126 l~~~I~l~~~p~~~I~I~v~VL~~DG 151 (151)
|+++|.++.||+..|+|.+||+++||
T Consensus 79 l~~~I~l~l~Prt~iqVsiqvv~ddg 104 (217)
T KOG1069|consen 79 LSKAIILELYPRTTIQVSIQVVEDDG 104 (217)
T ss_pred HHHhheeeecCCceEEEEEEEEecCC
Confidence 99999999999999999999999998
No 16
>KOG1612 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp42 [Translation, ribosomal structure and biogenesis]
Probab=99.85 E-value=1.5e-20 Score=147.74 Aligned_cols=119 Identities=27% Similarity=0.321 Sum_probs=102.2
Q ss_pred CCCCCCCCCCCCCCCCcceEEEeCCcCCCCeEEEEEECC-eEEEEEEEcCcccccccccCceeEEEEEEEecCCccccc-
Q 037553 32 SDVDWLRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGN-TKVIVSVFGPRESKKAMMYSNIGRLNCNVSYTTFATPIR- 109 (151)
Q Consensus 32 ~~~~~~R~DGR~~~e~R~i~i~~g~l~~adGSa~v~~G~-T~Vl~~V~gp~~~~~~~~~~~~g~l~v~v~~~p~a~~~r- 109 (151)
-.+..+|+|||.++++|+|.++++++++++|||+|++|+ |.|+++|+.+...+ ..+.|++|.+.+.|+++|-++++.
T Consensus 16 g~e~~iR~DGR~~~~~Rpi~vetdVlp~tNGSaRVk~g~~tdiivgVKaEvg~~-~~~~p~egk~~~~VD~S~sasp~f~ 94 (288)
T KOG1612|consen 16 GSEPDIRNDGRSCHQFRPIEVETDVLPGTNGSARVKLGDGTDIIVGVKAEVGSP-DDETPVEGKYLFFVDCSPSASPQFQ 94 (288)
T ss_pred ccCcccccCCcCccccceEEEEeccccCCCCcEEEEecCCceEEEEEeeeccCc-cccCCCCCeEEEEEEecCCcCcccc
Confidence 456889999999999999999999999999999999999 99999999999865 457799999999999999998754
Q ss_pred --CCCchHHHHHHHHHHHHHh---hhccCCC---CC--cEEEEEEEEEecCC
Q 037553 110 --GQGSDHKDFSSMLHKALEG---AIILETF---PK--TTVDVFALVLESGG 151 (151)
Q Consensus 110 --~~~~~~~~l~~~l~~~l~~---~I~l~~~---p~--~~I~I~v~VL~~DG 151 (151)
+.++...++++.|+++|.+ .+++.++ |+ |.|+|++.||++||
T Consensus 95 gRggde~~~eltsaLq~~l~~~~sgv~ls~L~lt~~~~W~i~VDvlVi~s~g 146 (288)
T KOG1612|consen 95 GRGGDELVEELTSALQRVLNSLGSGVDLSKLQLTPGYCWKIYVDVLVISSDG 146 (288)
T ss_pred CCChhhHHHHHHHHHHHHHhCcCcccchhheeccCCeeEEEEEeEEEEecCC
Confidence 3445688999999999987 2555544 44 67888889999997
No 17
>KOG1614 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp45 [Translation, ribosomal structure and biogenesis]
Probab=99.79 E-value=5e-19 Score=138.69 Aligned_cols=118 Identities=24% Similarity=0.292 Sum_probs=105.2
Q ss_pred cCCCCCCCCCCCCCCCCCcceEEEeCCcCCCCeEEEEEECCeEEEEEEEcCcccccccccCceeEEEEEEEecCCccc--
Q 037553 30 SGSDVDWLRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSVFGPRESKKAMMYSNIGRLNCNVSYTTFATP-- 107 (151)
Q Consensus 30 ~~~~~~~~R~DGR~~~e~R~i~i~~g~l~~adGSa~v~~G~T~Vl~~V~gp~~~~~~~~~~~~g~l~v~v~~~p~a~~-- 107 (151)
-+.++.|+|.|||+..|+|.+++++|- -.||+.|++|+|+|+|.|..++..| ..++|.+|.+++..+++|++.+
T Consensus 15 l~alk~g~R~DgR~l~efR~lei~fGk---e~gs~~vt~G~Tkvm~~vt~~ia~P-y~dRP~eG~~~I~telsPmA~~sf 90 (291)
T KOG1614|consen 15 LNALKAGLRFDGRSLEEFRDLEIEFGK---EYGSVLVTMGNTKVMARVTAQIAQP-YIDRPHEGSFSIFTELSPMASPSF 90 (291)
T ss_pred HHHHHhcccccccchhhhhceEEEecc---ccccEEEEecCeeEEEEeehhhcCc-ccCCCCCCeeeeeecccccccccc
Confidence 445689999999999999999999995 6999999999999999999988654 5688999999999999999988
Q ss_pred ccC-CCchHHHHHHHHHHHHHh--hhccCCC----C--CcEEEEEEEEEecCC
Q 037553 108 IRG-QGSDHKDFSSMLHKALEG--AIILETF----P--KTTVDVFALVLESGG 151 (151)
Q Consensus 108 ~r~-~~~~~~~l~~~l~~~l~~--~I~l~~~----p--~~~I~I~v~VL~~DG 151 (151)
+.| .++.+.++.++|+++++. +|++|.+ + -|.|++++++|+.||
T Consensus 91 E~Gr~~~~~v~l~Rliek~~R~S~aiD~EsLCI~aG~kvW~IRiDlhiLd~DG 143 (291)
T KOG1614|consen 91 EPGRKGESEVELSRLIEKALRRSKAIDTESLCIRAGEKVWLIRIDLHILDHDG 143 (291)
T ss_pred CCCCccchHHHHHHHHHHHHHhccccchHHHHhhhCCeEEEEEEEEEEEcCCC
Confidence 445 667899999999999987 8898887 2 389999999999998
No 18
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=99.68 E-value=6.9e-17 Score=138.57 Aligned_cols=116 Identities=26% Similarity=0.319 Sum_probs=100.7
Q ss_pred CCCCCCCCCCCCCCcceEEEeCCcCCCCeEEEEEECCeEEEEEEEcCc-cccc---ccccCcee-EEEEEEEecCCcccc
Q 037553 34 VDWLRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSVFGPR-ESKK---AMMYSNIG-RLNCNVSYTTFATPI 108 (151)
Q Consensus 34 ~~~~R~DGR~~~e~R~i~i~~g~l~~adGSa~v~~G~T~Vl~~V~gp~-~~~~---~~~~~~~g-~l~v~v~~~p~a~~~ 108 (151)
..++|-|||..+++|+|.|+.+.++..|||++|+-|+|+|+|+|..-. +... +...+++| .+..||+|+|+|+++
T Consensus 355 ~~gkR~DGR~ldelR~I~ce~~m~~~lHGSaLFqRGqTQvlctVtl~s~e~a~klD~l~~~~~~~~FmLhY~FPPyat~E 434 (760)
T KOG1067|consen 355 EEGKRCDGRDLDELRNISCEVDMLKTLHGSALFQRGQTQVLCTVTLDSLESAQKLDSLIGPDNGINFMLHYEFPPYATNE 434 (760)
T ss_pred hcccccCCcchhhhcccceecCccccccchhhhhcCceeEEEEEEcCCHHHhhhhhhhccCccCceEEEEeccCCccccc
Confidence 689999999999999999999999999999999999999999997432 2111 22344554 899999999999997
Q ss_pred cC----CCchHHHHHHHHHHHHHhhhccCCCCCcEEEEEEEEEecCC
Q 037553 109 RG----QGSDHKDFSSMLHKALEGAIILETFPKTTVDVFALVLESGG 151 (151)
Q Consensus 109 r~----~~~~~~~l~~~l~~~l~~~I~l~~~p~~~I~I~v~VL~~DG 151 (151)
-| .+.+|..+..+.+++|.+++. +.|| ++|+|.-.||++||
T Consensus 435 vgkig~~nRRE~GhgaLAEkaL~~vlP-~dfP-ftIRv~SeVleSnG 479 (760)
T KOG1067|consen 435 VGKIGGLNRRELGHGALAEKALLPVLP-EDFP-FTIRVTSEVLESNG 479 (760)
T ss_pred cccccCCcccccCchhHhhhhhhccCc-ccCc-eEEEEeeeeeecCC
Confidence 54 677999999999999999987 8898 89999999999998
No 19
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=99.62 E-value=5e-15 Score=132.16 Aligned_cols=96 Identities=27% Similarity=0.409 Sum_probs=81.9
Q ss_pred cceEEEeCCc-CCCCeEEEEEECCeEEEEEEEcCcccccccccCceeEEEEEEEecCCcccc-------c-C-CCchHHH
Q 037553 48 RPAFFRTGAV-NSASGSAYAEFGNTKVIVSVFGPRESKKAMMYSNIGRLNCNVSYTTFATPI-------R-G-QGSDHKD 117 (151)
Q Consensus 48 R~i~i~~g~l-~~adGSa~v~~G~T~Vl~~V~gp~~~~~~~~~~~~g~l~v~v~~~p~a~~~-------r-~-~~~~~~~ 117 (151)
|++.+++|.+ ++|||||+|++|+|+|+|+|+||.+.+. ..+...|+|+|...+||.++ | | +++++.+
T Consensus 5 R~i~ie~G~la~~AdGSa~v~~G~T~VlatV~~~~~~~~---~~df~pL~vey~e~~~A~gkipg~f~kReg~p~~~eil 81 (684)
T TIGR03591 5 RTLTLETGKIARQADGAVVVRYGDTVVLVTVVAAKEAKE---GQDFFPLTVNYQEKFYAAGKIPGGFFKREGRPSEKETL 81 (684)
T ss_pred ccEEEEECCcCCCCCeEEEEEECCeEEEEEEEcCCCCCC---CCceEeEEEEEEehhhhccCCCCCcccCCCCCCHHHHH
Confidence 7999999999 5799999999999999999999987432 24677888898887776651 2 3 6788999
Q ss_pred HHHHHHHHHHhhhccCCCCC---cEEEEEEEEEecCC
Q 037553 118 FSSMLHKALEGAIILETFPK---TTVDVFALVLESGG 151 (151)
Q Consensus 118 l~~~l~~~l~~~I~l~~~p~---~~I~I~v~VL~~DG 151 (151)
++++|.++|+++ ||+ +.|+|+++||++||
T Consensus 82 ~srlIdR~lrpl-----fp~~~~~~i~V~~~VLs~Dg 113 (684)
T TIGR03591 82 TSRLIDRPIRPL-----FPKGFRNEVQVVATVLSYDP 113 (684)
T ss_pred HHHHHhhHHHHh-----cCCCCCceEEEEEEEEecCc
Confidence 999999999985 666 88999999999998
No 20
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=99.59 E-value=2.1e-14 Score=128.43 Aligned_cols=99 Identities=23% Similarity=0.311 Sum_probs=82.2
Q ss_pred cceEEEeCCcC-CCCeEEEEEECCeEEEEEEEcCcccccccccCceeEEEEEEEecCCcccc-------c-C-CCchHHH
Q 037553 48 RPAFFRTGAVN-SASGSAYAEFGNTKVIVSVFGPRESKKAMMYSNIGRLNCNVSYTTFATPI-------R-G-QGSDHKD 117 (151)
Q Consensus 48 R~i~i~~g~l~-~adGSa~v~~G~T~Vl~~V~gp~~~~~~~~~~~~g~l~v~v~~~p~a~~~-------r-~-~~~~~~~ 117 (151)
|++.+++|.+. +|||||+|++|+|+|+|+|++|.+.+ ...+...|+|+|...+||.++ | | +++++.+
T Consensus 14 r~i~~e~G~ia~qAdGSa~v~~G~T~VlatV~~~~~~~---~~~df~pL~v~y~e~~~A~gkiP~~f~kreg~pse~eil 90 (693)
T PRK11824 14 RTLTLETGKLARQANGAVLVRYGDTVVLVTVVASKEPK---EGQDFFPLTVDYEEKTYAAGKIPGGFFKREGRPSEKETL 90 (693)
T ss_pred ccEEEEECCcCCCCCeEEEEEECCeEEEEEEEcCCCCC---CCCCeeeeEEEEEehhhhccCCCcccccCCCCCChHHHH
Confidence 78999999995 69999999999999999999998732 234667788888887777551 2 3 6788999
Q ss_pred HHHHHHHHHHhhhccCCCCCcEEEEEEEEEecCC
Q 037553 118 FSSMLHKALEGAIILETFPKTTVDVFALVLESGG 151 (151)
Q Consensus 118 l~~~l~~~l~~~I~l~~~p~~~I~I~v~VL~~DG 151 (151)
++++|.++|++++. ..++|.|+|+++||++||
T Consensus 91 ~srlIdR~lrplfp--~~~~~~i~I~~~VL~~Dg 122 (693)
T PRK11824 91 TSRLIDRPIRPLFP--KGFRNEVQVVATVLSVDP 122 (693)
T ss_pred HHHHHhhhHHHhCC--CCCCeEEEEEEEEEeCCC
Confidence 99999999999632 334689999999999998
No 21
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=99.43 E-value=1.3e-13 Score=121.00 Aligned_cols=117 Identities=25% Similarity=0.321 Sum_probs=99.5
Q ss_pred CCCCCCCCCCCCCCcceEEEeCCcCCCCeEEEEEECCeEEEEEEE-cCcccc---cccccCceeEEEEEEEecCCccccc
Q 037553 34 VDWLRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSVF-GPRESK---KAMMYSNIGRLNCNVSYTTFATPIR 109 (151)
Q Consensus 34 ~~~~R~DGR~~~e~R~i~i~~g~l~~adGSa~v~~G~T~Vl~~V~-gp~~~~---~~~~~~~~g~l~v~v~~~p~a~~~r 109 (151)
..+.|+|||..++.|++.++.|+++++|||++|..|.|+.++.+. |+.... ...+....-.+..||+|+||+.++.
T Consensus 309 ~~~vR~DGR~~~~VRpi~~ev~~lpr~HGS~LFtRGeTQal~v~TLG~~~d~Qvid~l~~e~~krfm~hYNFPp~SvGE~ 388 (692)
T COG1185 309 EGKVRIDGRFGDEVRPIGIEVGVLPRTHGSALFTRGETQALVVVTLGTPRDAQVIDILEGEYKKRFLLHYNFPPFSVGET 388 (692)
T ss_pred cCCcccCCCCcceeeeeeEEecCCCCccchhhhccCCCcceEEEEcCCcchhhhhhhccchhhhheeeeccCCCCCcccc
Confidence 688999999999999999999999999999999999999999995 553321 1223334567889999999998875
Q ss_pred C----CCchHHHHHHHHHHHHHhhhc-cCCCCCcEEEEEEEEEecCC
Q 037553 110 G----QGSDHKDFSSMLHKALEGAII-LETFPKTTVDVFALVLESGG 151 (151)
Q Consensus 110 ~----~~~~~~~l~~~l~~~l~~~I~-l~~~p~~~I~I~v~VL~~DG 151 (151)
+ ++.++..+..+-++++..++. .+.|| +.|++...|++++|
T Consensus 389 g~~g~p~RREiGHG~LA~Ral~~vlp~~e~fp-ytiRvVsEi~eSNG 434 (692)
T COG1185 389 GRMGSPGRREIGHGALAERALAPVLPSEEEFP-YTIRVVSEILESNG 434 (692)
T ss_pred CCCCCCCcccccCchhhHHHHhhhCCchhcCC-ceeeeeehhhcccC
Confidence 4 677999999999999999988 66778 78999999999987
No 22
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=98.96 E-value=3e-09 Score=97.00 Aligned_cols=99 Identities=22% Similarity=0.190 Sum_probs=81.7
Q ss_pred cceEEEeCCcC-CCCeEEEEEECCeEEEEEEEcCcccccccccCceeEEEEEEEecCCcccc-------c-C-CCchHHH
Q 037553 48 RPAFFRTGAVN-SASGSAYAEFGNTKVIVSVFGPRESKKAMMYSNIGRLNCNVSYTTFATPI-------R-G-QGSDHKD 117 (151)
Q Consensus 48 R~i~i~~g~l~-~adGSa~v~~G~T~Vl~~V~gp~~~~~~~~~~~~g~l~v~v~~~p~a~~~-------r-~-~~~~~~~ 117 (151)
|.+.+++|-+. +|+||+.+++|+|.|+|+|..-.+.+ +..+.-.|+|+|.-.-+|.+. | | +++.+..
T Consensus 89 ~~~~~etG~~a~qA~gav~v~~g~t~vl~t~~~~~~~~---~~~dF~PLtV~y~Ek~~AaGkipggf~kREgrp~d~eiL 165 (891)
T PLN00207 89 RHILVETGHIGRQASGSVTVTDGETIVYTSVCLADVPS---EPSDFFPLSVHYQERFSAAGRTSGGFFKREGRTKDHEVL 165 (891)
T ss_pred EEEEEEhhHHHHhCCCcEEEEECCeEEEEEEEeccCCC---CCCCccceeEeeeeehhhcCccCCceeccCCCCChHHHH
Confidence 46899999885 79999999999999999998654322 224567799999877777663 2 2 7788999
Q ss_pred HHHHHHHHHHhhhccCCCCCcEEEEEEEEEecCC
Q 037553 118 FSSMLHKALEGAIILETFPKTTVDVFALVLESGG 151 (151)
Q Consensus 118 l~~~l~~~l~~~I~l~~~p~~~I~I~v~VL~~DG 151 (151)
++++|.+.|+++++.+.||+++|.+ +||++||
T Consensus 166 ~sRlIdR~lRPlfp~~~~~etQI~i--~VLsaDg 197 (891)
T PLN00207 166 ICRLIDRPLRPTMPKGFYHETQILS--WVLSYDG 197 (891)
T ss_pred HHHHHCccchhhccccCCCCcEEEE--EEEeeCC
Confidence 9999999999999999999988855 9999998
No 23
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=98.40 E-value=1.2e-06 Score=78.69 Aligned_cols=99 Identities=21% Similarity=0.294 Sum_probs=76.8
Q ss_pred cceEEEeCCcC-CCCeEEEEEE-CCeEEEEEEEcCcccccccccCceeEEEEEEEecCCcccc-------c-C-CCchHH
Q 037553 48 RPAFFRTGAVN-SASGSAYAEF-GNTKVIVSVFGPRESKKAMMYSNIGRLNCNVSYTTFATPI-------R-G-QGSDHK 116 (151)
Q Consensus 48 R~i~i~~g~l~-~adGSa~v~~-G~T~Vl~~V~gp~~~~~~~~~~~~g~l~v~v~~~p~a~~~-------r-~-~~~~~~ 116 (151)
+.+.+++|-+. +||||+.+++ |+|.|||+|..-.+.+ ...+.-.|+|+|.-..+|.++ | | +++.+.
T Consensus 17 ~~~~~etG~~A~qA~Gav~v~~~G~t~vl~t~~~~~~~~---~~~dF~PLtV~y~Ek~yA~GkiPggf~kREgrps~~ei 93 (719)
T TIGR02696 17 RTIRFETGRLARQAAGSVVAYLDDETMLLSATTASKQPK---DQFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDAI 93 (719)
T ss_pred EEEEEEcchhHhhCCceEEEEecCCeEEEEEEEecCCCC---CCCCCcceeEeeeehhhhcCccCCceeccCCCCChhhh
Confidence 46999999985 7999999999 9999999998544322 224567899999877777663 2 2 778899
Q ss_pred HHHHHHHHHHHhhhccCCCCCcEEEEEEEEEecCC
Q 037553 117 DFSSMLHKALEGAIILETFPKTTVDVFALVLESGG 151 (151)
Q Consensus 117 ~l~~~l~~~l~~~I~l~~~p~~~I~I~v~VL~~DG 151 (151)
..+++|.|.|++..+ +.| +..++|.++||+.|+
T Consensus 94 L~sRliDR~iRPLFp-~~~-~~e~qi~~~vls~D~ 126 (719)
T TIGR02696 94 LTCRLIDRPLRPSFV-KGL-RNEVQVVVTVLSLNP 126 (719)
T ss_pred HHHHhhCCCCccCCC-CCC-CcceEEEEEEEEcCC
Confidence 999999999998632 111 246899999999986
No 24
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=98.20 E-value=5.9e-06 Score=73.42 Aligned_cols=98 Identities=20% Similarity=0.283 Sum_probs=78.1
Q ss_pred cceEEEeCCcC-CCCeEEEEEECCeEEEEEEEcCcccccccccCceeEEEEEEEecCCcccc-------c-C-CCchHHH
Q 037553 48 RPAFFRTGAVN-SASGSAYAEFGNTKVIVSVFGPRESKKAMMYSNIGRLNCNVSYTTFATPI-------R-G-QGSDHKD 117 (151)
Q Consensus 48 R~i~i~~g~l~-~adGSa~v~~G~T~Vl~~V~gp~~~~~~~~~~~~g~l~v~v~~~p~a~~~-------r-~-~~~~~~~ 117 (151)
|.+.+++|.+. +|+||+++++|+|.|+++|.+.. .+ +..+.-.|+|+|.-.-||.++ | | +++.+..
T Consensus 14 ~~l~~etg~~A~qa~gav~~~~gdt~vl~t~~~~~-~~---~~~dF~PLtV~y~Ek~yaaGkiPGgf~kREGrpse~e~L 89 (692)
T COG1185 14 RTLTLETGKIARQANGAVLVRYGDTVVLATVVASK-PK---EGQDFFPLTVNYEEKTYAAGKIPGGFFKREGRPSEKEIL 89 (692)
T ss_pred eeEEEEcchhhhhcCccEEEEECCeEEEEEEeecC-CC---CCCCccceeEeeeeehhccCcCCCcccccCCCCCccchh
Confidence 78999999985 79999999999999999999886 22 235777899999887777773 2 2 7788999
Q ss_pred HHHHHHHHHHhhhccCCCCCcEEEEEEEEEecCC
Q 037553 118 FSSMLHKALEGAIILETFPKTTVDVFALVLESGG 151 (151)
Q Consensus 118 l~~~l~~~l~~~I~l~~~p~~~I~I~v~VL~~DG 151 (151)
.+++|.+-+++... +--+..++|.++|++.|+
T Consensus 90 ~sRLIDRpiRPlFp--~g~~~evqIv~tvls~D~ 121 (692)
T COG1185 90 TSRLIDRPIRPLFP--KGFRNEVQIVNTVLSVDP 121 (692)
T ss_pred hhhhcccccccccc--hhhccceEEEEEEEEECC
Confidence 99999998888532 111246899999999885
No 25
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=96.74 E-value=0.00045 Score=60.69 Aligned_cols=100 Identities=19% Similarity=0.231 Sum_probs=66.8
Q ss_pred CCcceEEEeCCcC-CCCeEEEEEECCeEEEEEEEcCcccccccccCceeEEEEEEEecCCcccc-------c-C-CCchH
Q 037553 46 QCRPAFFRTGAVN-SASGSAYAEFGNTKVIVSVFGPRESKKAMMYSNIGRLNCNVSYTTFATPI-------R-G-QGSDH 115 (151)
Q Consensus 46 e~R~i~i~~g~l~-~adGSa~v~~G~T~Vl~~V~gp~~~~~~~~~~~~g~l~v~v~~~p~a~~~-------r-~-~~~~~ 115 (151)
--|.+.+++|.+. .|+||+.+..|+|.|+++|..-.. ++ -+..-.|.|+|.....|.+. | + +.+.|
T Consensus 54 GnR~i~~etGklaRfAngsvvv~~GeT~Vm~Tv~~a~~--PS--p~qFlPL~VdYqeK~aAvGRip~~fmRREg~tkdkE 129 (760)
T KOG1067|consen 54 GNREILFETGKLARFANGSVVVQMGETAVMTTVVLADK--PS--PPQFLPLVVDYQEKFAAVGRIPGNFMRREGRTKDKE 129 (760)
T ss_pred CCeEEEEecchhhhhcCCcEEEccCCeEEEEEEEecCC--CC--ccccceEEEehhhhhhhhccCCCcccccccCCcchh
Confidence 4589999999997 489999999999999999975532 11 13466788888765555442 2 1 55667
Q ss_pred HHHHHHHHHHHHhhhccCCCCCcEEEEEEEEEecCC
Q 037553 116 KDFSSMLHKALEGAIILETFPKTTVDVFALVLESGG 151 (151)
Q Consensus 116 ~~l~~~l~~~l~~~I~l~~~p~~~I~I~v~VL~~DG 151 (151)
....++|.+.+++...-..| +..+|-+.+|..||
T Consensus 130 iL~~rLidrsirplfp~g~~--~etqi~~n~Ls~dG 163 (760)
T KOG1067|consen 130 ILTGRLIDRPIRPLFPKGFY--HETQILCNVLSSDG 163 (760)
T ss_pred heeeeccccccccCCcccch--hHHHHHhhheeccc
Confidence 77788888877775332112 23444455555555
No 26
>PF03726 PNPase: Polyribonucleotide nucleotidyltransferase, RNA binding domain; InterPro: IPR015848 The PH (phosphorolytic) domain is responsible for 3'-5' exoribonuclease activity, although in some proteins this domain has lost its catalytic function. An active PH domain uses inorganic phosphate as a nucleophile, adding it across the phosphodiester bond between the end two nucleotides in order to release ribonucleoside 5'-diphosphate (rNDP) from the 3' end of the RNA substrate. PH domains can be found in bacterial/organelle RNases and PNPases (polynucleotide phosphorylases) [], as well as in archaeal and eukaryotic RNA exosomes [, ], the later acting as nano-compartments for the degradation or processing of RNA (including mRNA, rRNA, snRNA and snoRNA). Bacterial/organelle PNPases share a common barrel structure with RNA exosomes, consisting of a hexameric ring of PH domains that act as a degradation chamber, and an S1-domain/KH-domain containing cap that binds the RNA substrate (and sometimes accessory proteins) in order to regulate and restrict entry into the degradation chamber []. Unstructured RNA substrates feed in through the pore made by the S1 domains, are degraded by the PH domain ring, and exit as nucleotides via the PH pore at the opposite end of the barrel [, ]. This entry represents an RNA-binding phosphorolytic (PH) domain found in bacterial and organelle PNPases, but not in exosomes. It usually occurs in combination with PH domain 1 (IPR001247 from INTERPRO) and PH domain 2 (IPR015847 from INTERPRO), both of which are found in PNPases and exosomes. The core structure of the RNA-binding PH domain consists of a DNA/RNA-binding 3-helical bundle. More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0000175 3'-5'-exoribonuclease activity, 0003723 RNA binding, 0006396 RNA processing; PDB: 1E3H_A 1E3P_A 3U1K_B 3GCM_A 3GLL_A 3GME_A 4AM3_B 4AID_C 4AIM_A 1WHU_A ....
Probab=64.51 E-value=2.5 Score=27.68 Aligned_cols=17 Identities=29% Similarity=0.317 Sum_probs=11.7
Q ss_pred CCCcCcccCCCCCCCCCCCCC
Q 037553 23 KTRPPIFSGSDVDWLRPDSRG 43 (151)
Q Consensus 23 ~~~~~~~~~~~~~~~R~DGR~ 43 (151)
..|..++ .+++|+|||.
T Consensus 67 ~vR~~Il----~~~~R~DGR~ 83 (83)
T PF03726_consen 67 IVREMIL----EEGIRIDGRK 83 (83)
T ss_dssp HHHHHHH----CTSBTTTS-B
T ss_pred HHHHHHH----CCCCCCCCCC
Confidence 3455566 7899999995
No 27
>PF09866 DUF2093: Uncharacterized protein conserved in bacteria (DUF2093); InterPro: IPR018661 This family of various hypothetical prokaryotic proteins has no known function.
Probab=21.62 E-value=82 Score=18.31 Aligned_cols=12 Identities=25% Similarity=0.207 Sum_probs=10.0
Q ss_pred CeEEEEEEEcCc
Q 037553 70 NTKVIVSVFGPR 81 (151)
Q Consensus 70 ~T~Vl~~V~gp~ 81 (151)
++-|+|+|.|..
T Consensus 5 G~~V~CAVTg~~ 16 (42)
T PF09866_consen 5 GSFVRCAVTGQP 16 (42)
T ss_pred CCEEEEEeeCCc
Confidence 578999999875
Done!