Query 022140
Match_columns 302
No_of_seqs 159 out of 1247
Neff 8.2
Searched_HMMs 46136
Date Fri Mar 29 08:20:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022140.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022140hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG2123 RNase PH-related exori 100.0 1.2E-61 2.6E-66 420.7 31.8 266 19-298 6-272 (272)
2 PRK04282 exosome complex RNA-b 100.0 1.9E-58 4.1E-63 416.4 34.2 260 23-297 11-270 (271)
3 KOG1614 Exosomal 3'-5' exoribo 100.0 5.5E-59 1.2E-63 394.3 26.6 266 21-301 7-274 (291)
4 KOG1613 Exosomal 3'-5' exoribo 100.0 1.4E-59 3.1E-64 397.0 20.9 291 1-293 1-297 (298)
5 KOG1612 Exosomal 3'-5' exoribo 100.0 6.5E-48 1.4E-52 328.8 25.6 264 24-300 9-278 (288)
6 PRK00173 rph ribonuclease PH; 100.0 4.2E-46 9.2E-51 329.6 29.1 231 36-298 1-238 (238)
7 TIGR01966 RNasePH ribonuclease 100.0 1.6E-44 3.6E-49 319.2 28.5 228 37-296 1-235 (236)
8 PRK03983 exosome complex exonu 100.0 3.6E-44 7.8E-49 318.6 28.7 224 31-299 9-235 (244)
9 TIGR02065 ECX1 archaeal exosom 100.0 1.5E-43 3.2E-48 312.1 28.5 223 32-299 4-229 (230)
10 TIGR03591 polynuc_phos polyrib 100.0 9.4E-37 2E-41 304.3 30.4 242 15-300 289-542 (684)
11 PRK11824 polynucleotide phosph 100.0 2.5E-36 5.5E-41 301.9 30.1 238 15-298 293-543 (693)
12 COG0689 Rph RNase PH [Translat 100.0 3.1E-35 6.8E-40 253.5 22.4 220 33-297 5-230 (230)
13 KOG1068 Exosomal 3'-5' exoribo 100.0 3.9E-33 8.6E-38 239.3 17.4 222 33-299 10-235 (245)
14 PLN00207 polyribonucleotide nu 100.0 3.1E-31 6.7E-36 265.5 30.4 236 17-298 419-674 (891)
15 TIGR02696 pppGpp_PNP guanosine 100.0 2.3E-29 4.9E-34 247.5 26.9 240 15-299 314-569 (719)
16 PRK11824 polynucleotide phosph 100.0 1.4E-29 3.1E-34 253.4 25.6 202 47-299 14-226 (693)
17 TIGR03591 polynuc_phos polyrib 100.0 1.8E-29 3.9E-34 252.1 25.3 202 47-299 5-217 (684)
18 KOG1069 Exosomal 3'-5' exoribo 100.0 2.8E-28 6.1E-33 202.1 17.9 201 45-298 4-210 (217)
19 PF01138 RNase_PH: 3' exoribon 100.0 8.2E-28 1.8E-32 194.1 15.6 128 45-180 1-132 (132)
20 PLN00207 polyribonucleotide nu 99.9 3.4E-22 7.4E-27 200.8 22.0 202 47-299 89-301 (891)
21 KOG1067 Predicted RNA-binding 99.9 1.4E-20 3.1E-25 176.5 17.3 233 14-298 336-586 (760)
22 TIGR02696 pppGpp_PNP guanosine 99.8 8.1E-18 1.8E-22 166.2 22.5 203 47-298 17-246 (719)
23 COG1185 Pnp Polyribonucleotide 99.7 8.7E-16 1.9E-20 148.8 16.4 236 16-299 292-542 (692)
24 COG1185 Pnp Polyribonucleotide 99.6 8E-15 1.7E-19 142.2 18.7 200 47-298 14-224 (692)
25 KOG1067 Predicted RNA-binding 99.5 4.8E-13 1E-17 126.4 13.0 203 45-299 54-267 (760)
26 PF03725 RNase_PH_C: 3' exorib 99.4 6.6E-13 1.4E-17 94.5 8.4 67 217-284 1-68 (68)
27 PF03726 PNPase: Polyribonucle 86.5 0.46 1E-05 34.7 1.8 29 14-42 55-83 (83)
28 PF02575 YbaB_DNA_bd: YbaB/Ebf 62.9 54 0.0012 24.0 7.4 41 242-283 27-69 (93)
29 PF07023 DUF1315: Protein of u 39.5 31 0.00068 25.8 2.6 35 12-52 6-41 (93)
30 PF09695 YtfJ_HI0045: Bacteria 37.3 74 0.0016 26.3 4.8 34 245-282 125-158 (160)
31 COG3139 Uncharacterized protei 34.0 35 0.00077 24.8 2.1 29 12-46 8-36 (90)
32 PRK00153 hypothetical protein; 32.8 1.6E+02 0.0034 22.3 5.7 44 241-285 34-79 (104)
33 PF12651 RHH_3: Ribbon-helix-h 22.7 92 0.002 19.7 2.4 31 267-298 8-38 (44)
34 KOG4690 Uncharacterized conser 20.5 1.6E+02 0.0034 23.8 3.7 79 18-99 9-98 (165)
35 COG3054 Predicted transcriptio 20.2 2.3E+02 0.005 23.4 4.7 49 230-282 128-180 (184)
36 PF09866 DUF2093: Uncharacteri 20.0 71 0.0015 20.1 1.4 11 69-79 5-15 (42)
No 1
>COG2123 RNase PH-related exoribonuclease [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.2e-61 Score=420.72 Aligned_cols=266 Identities=30% Similarity=0.532 Sum_probs=249.3
Q ss_pred HhhhChHHHHHHHHhcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeeccCCCCCCCcceEEEEEe
Q 022140 19 FRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSIDFH 98 (302)
Q Consensus 19 ~~~~~p~~f~~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~p~~~~p~~g~l~v~V~ 98 (302)
+-...++.|+.+.+++++|+|||+++|||++.|++|++++|+|||+|++|+|+|+|+||.++++|.+++|++|.+.+|++
T Consensus 6 ~~~~~~~~~i~~ll~~g~R~DGR~~~efR~ieI~~~vi~ka~GSa~VklG~Tqvv~gvK~eig~Pf~DtP~eG~~~~n~E 85 (272)
T COG2123 6 IISEIKREYILNLLKKGIRIDGRSFDEFRPLEIETGVIPKANGSALVKLGNTQVVVGVKAEIGEPFPDTPNEGVLVVNVE 85 (272)
T ss_pred hhhhhHHHHHHHHhccCcccCCCCcccccceEEEeCceecCCCcEEEEecCeEEEEEEEcccCCCCCCCCCCceEEeeee
Confidence 44556779999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCCCccCCCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHhhCC
Q 022140 99 MPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQ 178 (302)
Q Consensus 99 ~~~~~~~~~~~g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~~~~ 178 (302)
+.|.+++.|++|++++.+.++++++++.++.++.+|+++|||.+|+++|.+++|++||++|||++||+++|+++||++++
T Consensus 86 l~Plas~~fE~Gppde~aielsrvvdr~lr~s~aiDlekL~I~~g~kvwvv~vDv~vld~DGnl~Da~~lA~~aAL~~t~ 165 (272)
T COG2123 86 LSPLASPSFEPGPPDELAIELSRVVDRGLRESKAIDLEKLCIEEGKKVWVVFVDVHVLDYDGNLIDAASLAAVAALLNTR 165 (272)
T ss_pred eeccccccccCCCCchhHHHHHHHHHHHHHhccCcchhheeEecCCEEEEEEEEEEEEcCCCCHHHHHHHHHHHHHHhcC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcEEe-cCCceeecCccccccccCcCccccccccccCCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEEcCCCcE
Q 022140 179 IPTVSL-DDGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQL 257 (302)
Q Consensus 179 iP~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~~~g~i 257 (302)
+|+... +++..+. ..+.++.++.+.++|+++|++++++.+++|||.+||..+++.++|.++++|++
T Consensus 166 vP~~~~~~~~~~v~-------------~~~~~~~pl~~~~~pi~vt~a~ig~~lvvDPsleEe~v~d~~ltit~~~~~~I 232 (272)
T COG2123 166 VPKAVEVGDGEIVI-------------EVEEEPVPLPVSNPPISVTFAKIGNVLVVDPSLEEELVADGRLTITVNEDGEI 232 (272)
T ss_pred CCceeecCCcceee-------------cccCCCcccccCCCceEEEEEEECCEEEeCCCcchhhhcCceEEEEECCCCcE
Confidence 997766 4443222 12236777999999999999999999999999999999999999999999999
Q ss_pred EEEEccCCcccChHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 022140 258 VSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAISG 298 (302)
Q Consensus 258 ~~i~~~G~~~~~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~ 298 (302)
++++|.|+.+++.+. +.+|++.|.+.+.++.+.+.++|+.
T Consensus 233 v~iqK~g~~~~~~~~-~~~~~~~A~~~~~kl~~~~~~~L~~ 272 (272)
T COG2123 233 VAIQKVGGGSITESD-LEKALKTALSKAEKLREALKEALKE 272 (272)
T ss_pred EEEEEcCCCcCCHHH-HHHHHHHHHHHHHHHHHHHHHhhcC
Confidence 999999999999995 9999999999999999999998863
No 2
>PRK04282 exosome complex RNA-binding protein Rrp42; Provisional
Probab=100.00 E-value=1.9e-58 Score=416.39 Aligned_cols=260 Identities=34% Similarity=0.568 Sum_probs=244.5
Q ss_pred ChHHHHHHHHhcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeeccCCCCCCCcceEEEEEecCCC
Q 022140 23 FPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPI 102 (302)
Q Consensus 23 ~p~~f~~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~p~~~~p~~g~l~v~V~~~~~ 102 (302)
.+++|+++++++++|+|||+++|+|++.+++|.+++++|||+|++|+|+|+|+|++++..|..++|++|.+.++|+++|+
T Consensus 11 ~e~~~i~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~vl~~V~~~~~~p~~~~~~~g~i~~~v~~~~~ 90 (271)
T PRK04282 11 IKKDYILSLLKKGKRIDGRKLDEYRPIEIETGVIKKAEGSALVKLGNTQVLAGVKLEIGEPFPDTPNEGVLIVNAELLPL 90 (271)
T ss_pred HHHHHHHHHHhcCCCCCCCCCccccCeEEEeCCccCCCcEEEEEECCCEEEEEEEEEEecCCCCCCCCCEEEEEEEECCC
Confidence 45799999999999999999999999999999999999999999999999999999999888889999999999999999
Q ss_pred CCCCccCCCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHhhCCCCcE
Q 022140 103 CSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTV 182 (302)
Q Consensus 103 ~~~~~~~g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~~~~iP~~ 182 (302)
+.+.|+.|++++.++.++++|+++|+++..+|+++|||.||+++|.|+|+++||++|||++||+++|+++||+|+++|.+
T Consensus 91 a~~~~~~~~~~~~~~~l~~~l~r~l~~~~~~dl~~L~I~~g~~~w~i~Vdv~VL~~dG~~~daa~~Aa~aAL~~~~iP~~ 170 (271)
T PRK04282 91 ASPTFEPGPPDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWVVFIDVYVLDHDGNLLDASMLAAVAALLNTKVPAV 170 (271)
T ss_pred cCccccCCCCCHHHHHHHHHHHHHHhccCCccHHHcEEecCcEEEEEEEEEEEECCCCCHHHHHHHHHHHHHHhCCCCcE
Confidence 99888888888899999999999999989999999999999999999999999999999999999999999999999999
Q ss_pred EecCCceeecCccccccccCcCccccccccccCCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEEcCCCcEEEEEc
Q 022140 183 SLDDGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYK 262 (302)
Q Consensus 183 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~~~g~i~~i~~ 262 (302)
.+.++... .++.+..++.++++|+++||+++++.+|+|||.+||+++++.++|+++++|+++++++
T Consensus 171 ~~~~~~~~--------------~~~~~~~~l~~~~~p~~vt~~~~~~~~v~Dpt~~Ee~~~~~~l~va~~~~g~i~~l~~ 236 (271)
T PRK04282 171 EEGEDGVV--------------DKLGEDFPLPVNDKPVTVTFAKIGNYLIVDPTLEEESVMDARITITTDEDGNIVAIQK 236 (271)
T ss_pred EEcCCcee--------------ccCCCcccCCCCCeeEEEEEEEECCEEEECCCHHHHhhcCceEEEEECCCCcEEEEEc
Confidence 99443321 1245677899999999999999999999999999999999999999999999999999
Q ss_pred cCCcccChHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022140 263 PGGAVLAYTSAVQDCIALTRQRVKELHQILEEAIS 297 (302)
Q Consensus 263 ~G~~~~~~~~~l~~~i~~A~~~~~~l~~~l~~~l~ 297 (302)
.|+.+++.++ +.+|+++|.+++++++++++++|+
T Consensus 237 ~g~~~~~~~~-l~~~i~~A~~~~~~l~~~~~~~l~ 270 (271)
T PRK04282 237 SGIGSFTEEE-VDKAIDIALEKAKELREKLKEALG 270 (271)
T ss_pred CCCCCCCHHH-HHHHHHHHHHHHHHHHHHHHHHhc
Confidence 9988999996 999999999999999999999984
No 3
>KOG1614 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp45 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.5e-59 Score=394.26 Aligned_cols=266 Identities=26% Similarity=0.514 Sum_probs=253.2
Q ss_pred hhChHHHHHHHHhcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeeccCCCCCCCcceEEEEEecC
Q 022140 21 RLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMP 100 (302)
Q Consensus 21 ~~~p~~f~~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~p~~~~p~~g~l~v~V~~~ 100 (302)
.+++..|+.++|+.|.|.|||+++|||.+.|++|. ..||+.|++|+|+|+|.|++++.+|..++|.+|.+.+.++++
T Consensus 7 t~~e~~fvl~alk~g~R~DgR~l~efR~lei~fGk---e~gs~~vt~G~Tkvm~~vt~~ia~Py~dRP~eG~~~I~tels 83 (291)
T KOG1614|consen 7 TVNESKFVLNALKAGLRFDGRSLEEFRDLEIEFGK---EYGSVLVTMGNTKVMARVTAQIAQPYIDRPHEGSFSIFTELS 83 (291)
T ss_pred ccchHHHHHHHHHhcccccccchhhhhceEEEecc---ccccEEEEecCeeEEEEeehhhcCcccCCCCCCeeeeeeccc
Confidence 45789999999999999999999999999999995 899999999999999999999999999999999999999999
Q ss_pred CCCCCCccCCCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHhhCCCC
Q 022140 101 PICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIP 180 (302)
Q Consensus 101 ~~~~~~~~~g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~~~~iP 180 (302)
|++++.|++|+.++.+..++++|++.++.+++||+|+|||..|+++|.|++|+++|+.|||++||+++|+.+||++.|.|
T Consensus 84 PmA~~sfE~Gr~~~~~v~l~Rliek~~R~S~aiD~EsLCI~aG~kvW~IRiDlhiLd~DGnlvDaA~iAviaaL~hFrrP 163 (291)
T KOG1614|consen 84 PMASPSFEPGRKGESEVELSRLIEKALRRSKAIDTESLCIRAGEKVWLIRIDLHILDHDGNLVDAACIAVIAALMHFRRP 163 (291)
T ss_pred cccccccCCCCccchHHHHHHHHHHHHHhccccchHHHHhhhCCeEEEEEEEEEEEcCCCCeehhHHHHHHHHHHhcCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cEEecCCceeecCccccccccCcCccccccccccCCCccEEEEEEEEC--CEEEECCChHHHhcCCceEEEEEcCCCcEE
Q 022140 181 TVSLDDGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHK--NYILADPTSEEESIMETLVTVVLDSSNQLV 258 (302)
Q Consensus 181 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~--~~~l~DPt~~Ee~~~~~~l~i~~~~~g~i~ 258 (302)
.+++....+..++ +.++++.||+|+|+|+|+||++++ +..++|||..||.+.++.++|++++++++|
T Consensus 164 dvTv~g~ev~ihp-----------~eEr~PvPL~I~HmPIC~tf~ffnkG~ivviDpt~~Ee~~~dGs~vVt~Nk~rEVc 232 (291)
T KOG1614|consen 164 DVTVGGEEVIIHP-----------VEEREPVPLSIHHMPICFTFGFFNKGEIVVIDPTEKEEAVMDGSMVVTMNKNREVC 232 (291)
T ss_pred CcccccceeEecC-----------hhccCCcceeeeeccceEEEEEecCceEEEeCCcHHHHhccCceEEEEEcCCccEE
Confidence 9999665666554 346889999999999999999998 689999999999999999999999999999
Q ss_pred EEEccCCcccChHHHHHHHHHHHHHHHHHHHHHHHHHhhcccC
Q 022140 259 SLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAISGMEI 301 (302)
Q Consensus 259 ~i~~~G~~~~~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~~~~ 301 (302)
.++|.||..+...+ +..|.+.|..++.++...+.++|++.++
T Consensus 233 ~i~k~G~~~~~~~~-i~~C~k~A~~~a~~vt~ii~e~l~~d~~ 274 (291)
T KOG1614|consen 233 AIQKSGGEILDESV-IERCYKLAKDRAVEVTGIILEALEEDQR 274 (291)
T ss_pred EEecCCCccccHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999996 9999999999999999999999998764
No 4
>KOG1613 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp43 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.4e-59 Score=397.04 Aligned_cols=291 Identities=37% Similarity=0.619 Sum_probs=255.4
Q ss_pred CCCCCCCccccccccHHHHhhhChHHHHHHHHhcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeee
Q 022140 1 MGLPNASEDLSSEMEVDAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEV 80 (302)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~p~~f~~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v 80 (302)
||.|.+....+.+|++++|+|+.|..|++++|++++|+|||++.+||.+.|+.|.++++|||+.++.|+|.|+|+|++++
T Consensus 1 ~~~~~aa~~~~~~f~p~~fkrI~Pe~~l~rhLse~~RpdgR~lgefRdt~in~g~IsTangSal~K~G~ttvi~~Ik~ei 80 (298)
T KOG1613|consen 1 STTLEAAGIHPITFPPEVFKRISPELYLQRHLSEGIRPDGRKLGEFRDTAINAGNISTANGSALLKSGKTTVICGIKAEI 80 (298)
T ss_pred CcccccccccccccCHHHHhhcCHHHHHHHHhhcccCcchhhhhHHhhhheecCceeccCcHHHHhcCCcEEEEEeeeee
Confidence 68899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCCCCCcceEEEEEecCCCCCCCccCCCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCC
Q 022140 81 MTPSLESPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADG 160 (302)
Q Consensus 81 ~~p~~~~p~~g~l~v~V~~~~~~~~~~~~g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG 160 (302)
.+|..+.|++|.+..++.++|.|++.||+|+++++++.+|+.|.+.+.++++|+++.|||.+||++|.+|.|+.||++||
T Consensus 81 ~epstdapdeg~Iv~n~~lpplcs~r~RpG~p~dea~viSq~LhdtIl~S~ii~~k~Lci~~gKaawvlYadIicLd~dG 160 (298)
T KOG1613|consen 81 AEPSTDAPDEGDIVPNYALPPLCSSRFRPGPPTDEAQVISQKLHDTILHSRIIPKKALCIKAGKAAWVLYADIICLDYDG 160 (298)
T ss_pred cccccCCCCCcceeecccCCcccccCCCCCCCchHHHHHHHHHHHHHHhcCCcchhhheeeccceeeEEEEEEEEEcCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CHHHHHHHHHHHHHhhCCCCcEEecC-CceeecCcccccccc---CcCccccccccccCCCccEEEEEEEECC-EEEECC
Q 022140 161 ALFDAALLSAVAAFSNLQIPTVSLDD-GKIVMLPEEQKEENS---EKEPVNKEKRKLTLGGIPFSLTCILHKN-YILADP 235 (302)
Q Consensus 161 ~l~da~~~A~~~AL~~~~iP~~~~~~-~~~~~~~~~~~~~~~---~~~~~~~~~~~l~i~~~p~~vt~~~~~~-~~l~DP 235 (302)
++||+|++|+++||++.++|.+.+++ +...........-+. .....+.+.+++..++.+.+.+. ++++ .++.||
T Consensus 161 ~~fDa~w~al~aAlknvklP~a~ide~~~~~~~t~e~~ic~~tlt~p~~ln~e~r~~~~~n~~fS~~~-vl~~~li~adp 239 (298)
T KOG1613|consen 161 PVFDACWNALMAALKNVKLPRAFIDERASDLRMTIEEIICDQTLTVPLMLNAENRAFASQNSDFSEEE-VLDDVLIAADP 239 (298)
T ss_pred cHHHHHHHHHHHHHhcCCCceeeecccchhhhhhHHHHHHhhhhcchhhhccccccccccCCCccHHH-hhcceeEecCC
Confidence 99999999999999999999999943 322211100000000 00112445556666666666554 4455 455999
Q ss_pred ChHHHhcCCceEEEEEcCCCcEEEEEccCCcccCh-HHHHHHHHHHHHHHHHHHHHHHH
Q 022140 236 TSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLAY-TSAVQDCIALTRQRVKELHQILE 293 (302)
Q Consensus 236 t~~Ee~~~~~~l~i~~~~~g~i~~i~~~G~~~~~~-~~~l~~~i~~A~~~~~~l~~~l~ 293 (302)
|.+||..+.+.++|+++++|+++.+.|.||..+.. + .+++|+++|+.+++++.+.+.
T Consensus 240 T~eEE~l~~~~lTIvldss~n~v~l~k~GG~al~~~~-~iK~c~elar~Rakelk~~~~ 297 (298)
T KOG1613|consen 240 TEEEETLITSTLTIVLDSSGNYVQLTKVGGGALITPE-MIKRCLELARVRAKELKTRFN 297 (298)
T ss_pred CchhhhhhhceEEEEEcCCCCEEEEEecCcccccCHH-HHHHHHHHHHHHHHHHHHHhc
Confidence 99999999999999999999999999999988755 6 799999999999999988764
No 5
>KOG1612 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp42 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=6.5e-48 Score=328.80 Aligned_cols=264 Identities=26% Similarity=0.402 Sum_probs=234.7
Q ss_pred hHHHHHHHHhcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCC-eEEEEEEEeeeccCCCCCCCcceEEEEEecCCC
Q 022140 24 PLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGS-TTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPI 102 (302)
Q Consensus 24 p~~f~~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~-T~Vi~~V~~~v~~p~~~~p~~g~l~v~V~~~~~ 102 (302)
+.-|+..+.++.+|+|||+++|||++.+++++++++||||+|++|. |.|+++||+|++.|+.+.|++|.+.+.|+++|.
T Consensus 9 e~~~~i~g~e~~iR~DGR~~~~~Rpi~vetdVlp~tNGSaRVk~g~~tdiivgVKaEvg~~~~~~p~egk~~~~VD~S~s 88 (288)
T KOG1612|consen 9 EKLYIITGSEPDIRNDGRSCHQFRPIEVETDVLPGTNGSARVKLGDGTDIIVGVKAEVGSPDDETPVEGKYLFFVDCSPS 88 (288)
T ss_pred ceeEEecccCcccccCCcCccccceEEEEeccccCCCCcEEEEecCCceEEEEEeeeccCccccCCCCCeEEEEEEecCC
Confidence 4467778889999999999999999999999999999999999998 899999999999999999999999999999999
Q ss_pred CCCCccCCCC-CCcHHHHHHHHHHHhhcCCC-cccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHhhCCCC
Q 022140 103 CSPLVRPGRP-AEAAPVVAKQLSDTISSSGM-INLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIP 180 (302)
Q Consensus 103 ~~~~~~~g~~-~~~~~~ls~~l~~~l~~~~~-i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~~~~iP 180 (302)
++++|. ||. ++...+|+..|+++|..-.. +|+..|++-|| ++|.||||+.|++.|||++||..+|+++||.++++|
T Consensus 89 asp~f~-gRggde~~~eltsaLq~~l~~~~sgv~ls~L~lt~~-~~W~i~VDvlVi~s~gn~~dAiS~Ai~~AL~~T~lP 166 (288)
T KOG1612|consen 89 ASPQFQ-GRGGDELVEELTSALQRVLNSLGSGVDLSKLQLTPG-YCWKIYVDVLVISSDGNLLDAISIAIYAALNNTRLP 166 (288)
T ss_pred cCcccc-CCChhhHHHHHHHHHHHHHhCcCcccchhheeccCC-eeEEEEEeEEEEecCCCHHHHHHHHHHHHHhcccCC
Confidence 999985 554 46788999999999987444 99999999998 799999999999999999999999999999999999
Q ss_pred cEEe--c-CCceeecCccccccccCcCccccccccccCCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEEcCCCcE
Q 022140 181 TVSL--D-DGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQL 257 (302)
Q Consensus 181 ~~~~--~-~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~~~g~i 257 (302)
++.+ + ++++.....++ ..+-..+....+|+.+|++.++..+++|||.+||.++.+.+.|.+++.|-+
T Consensus 167 kv~v~~dd~~~~~i~~s~~----------~Yd~~~~~~~~~P~ivtlskIG~~~lVD~T~eEe~~a~s~l~Isv~a~giv 236 (288)
T KOG1612|consen 167 KVIVAFDDDGEVEILLSDE----------EYDLMVKLVENVPLIVTLSKIGTNMLVDPTAEEESVANSGLLISVSAGGIV 236 (288)
T ss_pred ccccccccCCceeeccCcc----------cchhhhhhcccCCEEEEEEeecceEEccCCccHHHhhhcceEEEEecCcce
Confidence 9998 3 44444322211 122233456789999999999999999999999999999999999999988
Q ss_pred EEEEccCCcccChHHHHHHHHHHHHHHHHHHHHHHHHHhhccc
Q 022140 258 VSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAISGME 300 (302)
Q Consensus 258 ~~i~~~G~~~~~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~~~ 300 (302)
.++++.|++.+.++. +.+|++.+++..+.++..+.+.|+++|
T Consensus 237 s~~r~VG~G~l~~s~-i~~mle~~~~~~e~l~~~l~k~L~~~e 278 (288)
T KOG1612|consen 237 SCTRSVGLGDLDPSS-IPEMLEQGKAVVETLAPDLVKSLENEE 278 (288)
T ss_pred EEEEEecCCCCChhh-HHHHHHHHHHHHHhhhHHHHHHhhhhh
Confidence 889999987799995 999999999999999999999998876
No 6
>PRK00173 rph ribonuclease PH; Reviewed
Probab=100.00 E-value=4.2e-46 Score=329.63 Aligned_cols=231 Identities=22% Similarity=0.340 Sum_probs=203.6
Q ss_pred CCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeeccCCC-CCCCcceEEEEEecCCCCCCCcc-----C
Q 022140 36 IRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSL-ESPDEGCVSIDFHMPPICSPLVR-----P 109 (302)
Q Consensus 36 ~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~p~~-~~p~~g~l~v~V~~~~~~~~~~~-----~ 109 (302)
+|+|||+++++|++.+++|++++++|||+|++|+|+|+|+|++++..|.. ..|++|.++++++++|++++.++ .
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 59999999999999999999999999999999999999999999988854 45788999999999999988762 4
Q ss_pred CCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHhhCCCCcEEecCCce
Q 022140 110 GRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDGKI 189 (302)
Q Consensus 110 g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~~~~iP~~~~~~~~~ 189 (302)
|++++.+.+++++|++.|++ .+|++.| ++. .++|+++||++|||++||+++|+++||+|++++.. +.
T Consensus 81 g~~~~~~~~~sr~i~r~lr~--~i~l~~l----~~~--~i~v~v~VL~~DG~~~~aai~Aa~~AL~da~~~~~--~~--- 147 (238)
T PRK00173 81 GKQGGRTQEIQRLIGRSLRA--VVDLKAL----GER--TITIDCDVIQADGGTRTASITGAYVALADALNKLV--AR--- 147 (238)
T ss_pred CCCCccHHHHHHHHHHHHHH--hcCHHHc----CCe--EEEEEEEEEeCCCCHHHHHHHHHHHHHHHhhhhhh--cc---
Confidence 66778899999999999996 8999887 343 46667778999999999999999999999985411 11
Q ss_pred eecCccccccccCcCccccccccccCCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEEcCCCcEEEEEccC-Cccc
Q 022140 190 VMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPG-GAVL 268 (302)
Q Consensus 190 ~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~~~g~i~~i~~~G-~~~~ 268 (302)
.+..++.++++|+++|++++++.+|+|||.+||+++++.++|++++.|+||++++.| |..+
T Consensus 148 ------------------~~~~~ip~~~~~~~vt~~~~~~~~lvDpt~~Ee~~~~~~l~v~~~~~~~i~~v~~~g~g~~~ 209 (238)
T PRK00173 148 ------------------GKLKKNPLKDQVAAVSVGIVDGEPVLDLDYEEDSAAETDMNVVMTGSGGFVEVQGTAEGAPF 209 (238)
T ss_pred ------------------CcccCCcccCceeEEEEEEECCEEEECCCHHHHhcCCceEEEEECCCCCEEEEEccCCCCCc
Confidence 122346689999999999999999999999999999999999999999999999965 5689
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 022140 269 AYTSAVQDCIALTRQRVKELHQILEEAISG 298 (302)
Q Consensus 269 ~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~ 298 (302)
+.++ +.+|+++|.+.+++|+++++++|++
T Consensus 210 ~~e~-l~~~i~~A~~~~~~l~~~~~~~l~~ 238 (238)
T PRK00173 210 SREE-LDALLDLAEKGIAELVALQKAALAD 238 (238)
T ss_pred CHHH-HHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 9996 9999999999999999999999864
No 7
>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=100.00 E-value=1.6e-44 Score=319.21 Aligned_cols=228 Identities=18% Similarity=0.326 Sum_probs=200.0
Q ss_pred CCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeeccCCCCC-CCcceEEEEEecCCCCCCCc---c--CC
Q 022140 37 RPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLES-PDEGCVSIDFHMPPICSPLV---R--PG 110 (302)
Q Consensus 37 R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~p~~~~-p~~g~l~v~V~~~~~~~~~~---~--~g 110 (302)
|+|||+++|+|++++++|++++|+|||+|++|+|+|+|+|+++...|...+ |++|.+.+++++.|++++.+ . .|
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 899999999999999999999999999999999999999999887776554 57899999999999998755 1 35
Q ss_pred CCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHhhCCCCcEEecCCcee
Q 022140 111 RPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDGKIV 190 (302)
Q Consensus 111 ~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~~~~iP~~~~~~~~~~ 190 (302)
++++.+.++++++++.+++ .|+++.| ++ +.|+|+++||++|||++|||++|+++||+|++++....
T Consensus 81 ~~~~~~~e~~~~i~r~lr~--~i~l~~l----~~--~~i~I~v~VL~~DG~~~~aai~Aa~aAL~da~~~~~~~------ 146 (236)
T TIGR01966 81 KQSGRTQEIQRLIGRALRA--VVDLEAL----GE--RTIWIDCDVIQADGGTRTASITGAFVALADAISKLHKR------ 146 (236)
T ss_pred CCCccHHHHHHHHHHHHHH--hcCHhhc----CC--eEEEEEEEEEeCCCCHHHHHHHHHHHHHHHHHHhhhhc------
Confidence 6666788999999999996 7998877 23 36788888999999999999999999999996642100
Q ss_pred ecCccccccccCcCccccccccccCCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEEcCCCcEEEEEccC-CcccC
Q 022140 191 MLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPG-GAVLA 269 (302)
Q Consensus 191 ~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~~~g~i~~i~~~G-~~~~~ 269 (302)
.....+.|+++|+++|++++++.+|+|||.+||+++++.++++++.+++||++++.| +..++
T Consensus 147 -----------------~~~~~ip~~~~~~~vt~~~~~~~~v~Dpt~~Ee~~~~~~l~l~~~~~~~i~~i~~~g~~~~~~ 209 (236)
T TIGR01966 147 -----------------GILKESPIRDFVAAVSVGIVDGEPVLDLDYEEDSAADVDMNVVMTGSGGFVEVQGTAEEGPFS 209 (236)
T ss_pred -----------------CcccCCCccCceeEEEEEEECCEEEECCChhHHhccCceEEEEEcCCCCEEEEEecCCCCCcC
Confidence 011236689999999999999999999999999999999999999999999999965 56899
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 022140 270 YTSAVQDCIALTRQRVKELHQILEEAI 296 (302)
Q Consensus 270 ~~~~l~~~i~~A~~~~~~l~~~l~~~l 296 (302)
.++ +.+|+++|.+++++++++++++|
T Consensus 210 ~~~-l~~~i~~a~~~~~~l~~~~~~~l 235 (236)
T TIGR01966 210 RDE-LNKLLDLAKKGIRELIELQKQAL 235 (236)
T ss_pred HHH-HHHHHHHHHHHHHHHHHHHHHHh
Confidence 996 99999999999999999999987
No 8
>PRK03983 exosome complex exonuclease Rrp41; Provisional
Probab=100.00 E-value=3.6e-44 Score=318.64 Aligned_cols=224 Identities=21% Similarity=0.290 Sum_probs=199.9
Q ss_pred HHhcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeee--ccCCCCCCCcceEEEEEecCCCCCCCcc
Q 022140 31 HLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEV--MTPSLESPDEGCVSIDFHMPPICSPLVR 108 (302)
Q Consensus 31 ~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v--~~p~~~~p~~g~l~v~V~~~~~~~~~~~ 108 (302)
++++++|+|||+++++|++++++|++++++|||++++|+|+|+|+|+|+. ..|....|++|.+.++++++|+++..++
T Consensus 9 ~~~~~~R~DGR~~~~~R~i~i~~G~l~~a~GSa~v~~G~T~Vl~~V~gp~e~~~~~~~~~~~~~l~v~~~~~p~~~~~~~ 88 (244)
T PRK03983 9 ILEDGLRLDGRKPDELRPIKIEVGVLKNADGSAYLEWGNNKIIAAVYGPREMHPRHLQLPDRAVLRVRYNMAPFSVDERK 88 (244)
T ss_pred hccCCCCCCCCCcCcccceEEEeCCCCCCCeEEEEEECCeEEEEEEecCCccccccccCCCcEEEEEEEEcCCCcccccc
Confidence 46889999999999999999999999999999999999999999999854 4455667899999999999999886544
Q ss_pred CCCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHhhCCCCcEEecCCc
Q 022140 109 PGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDGK 188 (302)
Q Consensus 109 ~g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~~~~iP~~~~~~~~ 188 (302)
.+.+++++.+++++|++.|++. +.++. +| .|.|+|.++||++|||+++|+++|+++||.|+++|
T Consensus 89 ~~~~~~~~~~~s~~l~~~l~~~--i~~~~---~p---~~~I~I~i~VL~~DG~~~~aai~Aa~lAL~dagIp-------- 152 (244)
T PRK03983 89 RPGPDRRSIEISKVIREALEPA--IMLEL---FP---RTVIDVFIEVLQADAGTRVAGITAASLALADAGIP-------- 152 (244)
T ss_pred CCCCChhHHHHHHHHHHHHHHh--ccHHh---CC---CeEEEEEEEEEECCCCHHHHHHHHHHHHHHhcCCc--------
Confidence 4456778899999999999975 33332 34 47899999999999999999999999999999998
Q ss_pred eeecCccccccccCcCccccccccccCCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEEc-CCCcEEEEEccCCcc
Q 022140 189 IVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLD-SSNQLVSLYKPGGAV 267 (302)
Q Consensus 189 ~~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~-~~g~i~~i~~~G~~~ 267 (302)
++++|.++|++++++.+++|||.+||+++++.++|+++ ..|+|+++++.| .
T Consensus 153 --------------------------~~~~v~avtv~~~~~~~i~DPt~~Ee~~~~~~l~va~~~~~~~I~~l~~~G--~ 204 (244)
T PRK03983 153 --------------------------MRDLVAGCAVGKVDGVIVLDLNKEEDNYGEADMPVAIMPRLGEITLLQLDG--N 204 (244)
T ss_pred --------------------------cccceeEEEEEEECCEEEECCCHHHhccCCceEEEEEECCCCCEEEEEEec--C
Confidence 57899999999999999999999999999999999998 578999999988 6
Q ss_pred cChHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 022140 268 LAYTSAVQDCIALTRQRVKELHQILEEAISGM 299 (302)
Q Consensus 268 ~~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~~ 299 (302)
++.++ +.+|+++|.+.+++|+++|+++|+++
T Consensus 205 ~~~~~-~~~~i~~A~~~~~~i~~~i~~~l~~~ 235 (244)
T PRK03983 205 LTREE-FLEALELAKKGIKRIYQLQREALKSK 235 (244)
T ss_pred cCHHH-HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 78886 99999999999999999999999864
No 9
>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=100.00 E-value=1.5e-43 Score=312.10 Aligned_cols=223 Identities=22% Similarity=0.305 Sum_probs=198.0
Q ss_pred HhcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeee--ccCCCCCCCcceEEEEEecCCCCCCCccC
Q 022140 32 LAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEV--MTPSLESPDEGCVSIDFHMPPICSPLVRP 109 (302)
Q Consensus 32 l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v--~~p~~~~p~~g~l~v~V~~~~~~~~~~~~ 109 (302)
+.+++|+|||+++|+|++.+++|++++++|||++++|+|+|+|+|+|+. ..+....|++|.+.++++++|+++..++.
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 5789999999999999999999999999999999999999999999954 34445668899999999999998865544
Q ss_pred CCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHhhCCCCcEEecCCce
Q 022140 110 GRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDGKI 189 (302)
Q Consensus 110 g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~~~~iP~~~~~~~~~ 189 (302)
+.+++++.+++++|++.+++. +.++. +|+ +.|+|.++||++||++++|+++|+++||.|++||
T Consensus 84 ~~~~~~~~~~s~~l~~~l~~~--i~~~~---~p~---~~i~i~v~vl~~DG~~~~aai~aa~lAL~dagIp--------- 146 (230)
T TIGR02065 84 PGPSRREIEISKVIREALEPA--ILLEQ---FPR---TAIDVFIEVLQADAGTRCAGLTAASLALADAGIP--------- 146 (230)
T ss_pred CCCCccHHHHHHHHHHHHHHH--hChhh---cCC---eEEEEEEEEEEcCCCHHHHHHHHHHHHHHHcCCc---------
Confidence 557788999999999999974 44442 342 5677788899999999999999999999999998
Q ss_pred eecCccccccccCcCccccccccccCCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEEc-CCCcEEEEEccCCccc
Q 022140 190 VMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLD-SSNQLVSLYKPGGAVL 268 (302)
Q Consensus 190 ~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~-~~g~i~~i~~~G~~~~ 268 (302)
|++++.++|++++++.+++|||.+||+.+.+.++|++. ..++++++++.| .+
T Consensus 147 -------------------------~~~~v~avtv~~~~~~~v~Dpt~~Ee~~~~~~l~va~~~~~~~i~~i~~~g--~~ 199 (230)
T TIGR02065 147 -------------------------MRDLVVGVAVGKVDGVVVLDLNEEEDMYGEADMPVAMMPKLGEITLLQLDG--DM 199 (230)
T ss_pred -------------------------cccceeeEEEEEECCeEEECCCHHHhhcCCCceEEEEeCCCCCEEEEEEec--Cc
Confidence 57899999999999999999999999999999999985 478999999988 68
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 022140 269 AYTSAVQDCIALTRQRVKELHQILEEAISGM 299 (302)
Q Consensus 269 ~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~~ 299 (302)
++++ +.+|++.|.+++++++++++++|+++
T Consensus 200 ~~e~-~~~~l~~a~~~~~~l~~~~~~~l~~~ 229 (230)
T TIGR02065 200 TPDE-FRQALDLAVKGIKIIYQIQREALKNK 229 (230)
T ss_pred CHHH-HHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 8886 99999999999999999999999875
No 10
>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=100.00 E-value=9.4e-37 Score=304.26 Aligned_cols=242 Identities=17% Similarity=0.181 Sum_probs=206.2
Q ss_pred cHHHHhhhChHHHHHHHHhcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEE-eeeccCCC----CCCC
Q 022140 15 EVDAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIK-MEVMTPSL----ESPD 89 (302)
Q Consensus 15 ~~~~~~~~~p~~f~~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~-~~v~~p~~----~~p~ 89 (302)
-.++|..+.-..+-+-.+.+++|+|||+++|+|++.+++|.+++++|||+++.|+|+|+|+|+ |+...... ....
T Consensus 289 ~~~~~~~~~~~~~r~~il~~g~R~DGR~~~e~Rpi~~~~g~l~~a~GSa~~~~G~Tqvl~~vt~g~~~~~~~~~~~~~~~ 368 (684)
T TIGR03591 289 IKEAFKDLEKKIVRERILKEGKRIDGRDLDTIRPISIEVGVLPRTHGSALFTRGETQALVVTTLGTERDEQIIDDLEGEY 368 (684)
T ss_pred HHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCcCceEEEeCCCCCCCceEEEEeCCeEEEEEEecCCcccccCCcccCCCc
Confidence 445666666666666667899999999999999999999999999999999999999999997 43211100 1124
Q ss_pred cceEEEEEecCCCCCCCcc-CCCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHH
Q 022140 90 EGCVSIDFHMPPICSPLVR-PGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALL 168 (302)
Q Consensus 90 ~g~l~v~V~~~~~~~~~~~-~g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~ 168 (302)
.|.+.++++++||+++.++ .|++++++..+++++++.|++ .+++ .+.+.|+|+|+++||++|||..+|+++
T Consensus 369 ~~~~~~~y~~~pfs~~e~~~~g~~~rrei~~~~l~~ral~~--~i~~------~~~~p~tI~v~~~VLesdGs~~~Aai~ 440 (684)
T TIGR03591 369 RKRFMLHYNFPPYSVGEVGRVGGPGRREIGHGALAERALKA--VLPS------EEEFPYTIRVVSEILESNGSSSMASVC 440 (684)
T ss_pred cEEEEEEEEcCCCCCCCcCCCCCCChHHHHHHHHHHHHHHH--hcCc------cccCCeEEEEEEEEEeCCCChHHHHHH
Confidence 6899999999999988765 567788999999999999987 4542 245679999999999999999999999
Q ss_pred HHHHHHhhCCCCcEEecCCceeecCccccccccCcCccccccccccCCCccEEEEEEEEC-C----EEEECCChHHHhcC
Q 022140 169 SAVAAFSNLQIPTVSLDDGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHK-N----YILADPTSEEESIM 243 (302)
Q Consensus 169 A~~~AL~~~~iP~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~-~----~~l~DPt~~Ee~~~ 243 (302)
|+++||+|+++| +.+++.++|+|+++ + .+++||+.+|+..+
T Consensus 441 aaslAL~dAgvP----------------------------------~~~~Vagvs~gli~~~~~~~~il~D~~~~Ed~~~ 486 (684)
T TIGR03591 441 GGSLALMDAGVP----------------------------------IKAPVAGIAMGLIKEGDERFAVLSDILGDEDHLG 486 (684)
T ss_pred HHHHHHHhcCCC----------------------------------CcCCEEEEEEEEEcCCCcceEEEeCCChHHHhcC
Confidence 999999999999 45678999999985 1 59999999999999
Q ss_pred CceEEEEEcCCCcEEEEEccC-CcccChHHHHHHHHHHHHHHHHHHHHHHHHHhhccc
Q 022140 244 ETLVTVVLDSSNQLVSLYKPG-GAVLAYTSAVQDCIALTRQRVKELHQILEEAISGME 300 (302)
Q Consensus 244 ~~~l~i~~~~~g~i~~i~~~G-~~~~~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~~~ 300 (302)
+..++|+.+.+| |+++++.+ +..++.+. |.+|++.|.+++++|++.|++++.++-
T Consensus 487 d~d~~va~t~~g-I~~lq~d~k~~~i~~~~-l~~al~~a~~~~~~I~~~m~~~l~~~~ 542 (684)
T TIGR03591 487 DMDFKVAGTRDG-ITALQMDIKIDGITREI-MEQALEQAKEGRLHILGEMNKVISEPR 542 (684)
T ss_pred CceEEEEEcCCc-eEEEEEEcCcCCcCHHH-HHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 999999999887 99999954 35689995 999999999999999999999998763
No 11
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=100.00 E-value=2.5e-36 Score=301.86 Aligned_cols=238 Identities=18% Similarity=0.216 Sum_probs=201.6
Q ss_pred cHHHHhhhChHHHHHHHHhcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeeccCCCC-------C
Q 022140 15 EVDAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLE-------S 87 (302)
Q Consensus 15 ~~~~~~~~~p~~f~~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~p~~~-------~ 87 (302)
-.++|..+.-..+-+..+.+++|+|||+++|+|++.+++|.+++++|||+++.|+|+|+|+|+. ++|... .
T Consensus 293 ~~~~~~~~~~~~~r~~il~~g~R~DGR~~~e~Rpi~~~~g~l~~a~GSal~~~G~T~Vl~~vt~--g~~~~~~~~~~~~~ 370 (693)
T PRK11824 293 IKEAFKKLEKKIVRRRILEEGIRIDGRKLDEIRPISIEVGVLPRTHGSALFTRGETQALVVATL--GTLRDEQIIDGLEG 370 (693)
T ss_pred HHHHHHHHHHHHHHHHHhcCCCCCCCCCcCcccceEEEeCCCCCCCceEEEEECCeEEEEEEec--CCCcccccccccCC
Confidence 3445666655555555568899999999999999999999999999999999999999999972 222221 1
Q ss_pred CCcceEEEEEecCCCCCCCc-cCCCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHH
Q 022140 88 PDEGCVSIDFHMPPICSPLV-RPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAA 166 (302)
Q Consensus 88 p~~g~l~v~V~~~~~~~~~~-~~g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~ 166 (302)
.++|.+.++++++|+++..+ +.|++++++..+++++++.|++ ++++ ++++.|+|+|+++||++|||..+|+
T Consensus 371 ~~~~~~~~~y~~~pfs~~e~~~~~~~~rre~~~~~li~ral~~--vi~~------~~~~p~~I~v~~~VLe~dGs~~~Aa 442 (693)
T PRK11824 371 EYKKRFMLHYNFPPYSVGETGRVGSPGRREIGHGALAERALEP--VLPS------EEEFPYTIRVVSEILESNGSSSMAS 442 (693)
T ss_pred CCcEEEEEEEEcCCCCCCCcCCCCCCChhHHHHHHHHHHHHHH--hcCc------ccCCCEEEEEEEEEEecCCCHHHHH
Confidence 26799999999999998766 3566788999999999999987 4443 2456799999999999999999999
Q ss_pred HHHHHHHHhhCCCCcEEecCCceeecCccccccccCcCccccccccccCCCccEEEEEEEECC----EEEECCChHHHhc
Q 022140 167 LLSAVAAFSNLQIPTVSLDDGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKN----YILADPTSEEESI 242 (302)
Q Consensus 167 ~~A~~~AL~~~~iP~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~----~~l~DPt~~Ee~~ 242 (302)
++|+++||+|+++| +.+++.++++|++++ .+++||+..|+..
T Consensus 443 i~aaslAL~dAgvP----------------------------------~~~~Va~vs~gli~~~~~~~il~D~~~~Ed~~ 488 (693)
T PRK11824 443 VCGSSLALMDAGVP----------------------------------IKAPVAGIAMGLIKEGDKYAVLTDILGDEDHL 488 (693)
T ss_pred HHHHHHHHHhcCCC----------------------------------ccCceeEEEEEEEcCCCceEEEcCCChhhHhh
Confidence 99999999999999 467889999999853 4899999999999
Q ss_pred CCceEEEEEcCCCcEEEEEccCC-cccChHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 022140 243 METLVTVVLDSSNQLVSLYKPGG-AVLAYTSAVQDCIALTRQRVKELHQILEEAISG 298 (302)
Q Consensus 243 ~~~~l~i~~~~~g~i~~i~~~G~-~~~~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~ 298 (302)
++..++|+.+.+| |++++..|. ..++.+. |.+|++.|.+.+++|++.|++++..
T Consensus 489 ~d~d~~va~t~~g-i~~lq~d~k~~~i~~~~-l~~al~~a~~g~~~I~~~M~~aI~~ 543 (693)
T PRK11824 489 GDMDFKVAGTRDG-ITALQMDIKIDGITREI-LEEALEQAKEGRLHILGKMNEAISE 543 (693)
T ss_pred CCceEEEEecCCc-eEEEEEecccCCcCHHH-HHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 9999999999887 999995432 1578885 9999999999999999999999864
No 12
>COG0689 Rph RNase PH [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.1e-35 Score=253.48 Aligned_cols=220 Identities=21% Similarity=0.348 Sum_probs=189.6
Q ss_pred hcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeecc-C-CCCCCCcceEEEEEecCCCCCCCccCC
Q 022140 33 AESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMT-P-SLESPDEGCVSIDFHMPPICSPLVRPG 110 (302)
Q Consensus 33 ~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~-p-~~~~p~~g~l~v~V~~~~~~~~~~~~g 110 (302)
..+.|+|||+++|.|++.++.|++++++||+++++|+|+|+|+|+|+... | ....+.+|++++.+.+.|+++......
T Consensus 5 ~~~~R~dgR~~delR~i~~~~~~~~~a~GS~~~~~G~tkVic~vsGp~e~~p~~l~~~~~g~~t~ey~m~p~sT~~R~~~ 84 (230)
T COG0689 5 EDGMRPDGRKPDELRPIKITRGVLKHAEGSSLIEFGNTKVICTVSGPREPVPRFLRGTGKGWLTAEYGMLPRSTDERKKR 84 (230)
T ss_pred ccCcCCCCCCcccccceEEEeccccCCCccEEEEeCCeEEEEEEecCCCCCChhhcCCCceEEEEEEecccccccccccc
Confidence 45899999999999999999999999999999999999999999986532 2 234456799999999999987332111
Q ss_pred CCCC-cHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHhhCCCCcEEecCCce
Q 022140 111 RPAE-AAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDGKI 189 (302)
Q Consensus 111 ~~~~-~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~~~~iP~~~~~~~~~ 189 (302)
.+.+ +.++++++|.++|++ +++++. +|. -+|+|++.|+++||+...|+++|+..||.|+++|
T Consensus 85 ~~~~gR~~eisrli~~al~~--~i~L~~---~p~---~~I~i~~dVlqaDggTrta~It~A~lAL~DAgip--------- 147 (230)
T COG0689 85 EADRGRTKEISRLIGRALRA--VIDLEL---LPE---STIDIDCDVLQADGGTRTASITGASLALADAGIP--------- 147 (230)
T ss_pred cccccchhHHHHHHHHHHHH--Hhhhhh---cCc---cEEEEEEEEEECCCCeeeehhhHHHHHHHHcCCc---------
Confidence 1223 689999999999986 677754 454 4899999999999999999999999999999988
Q ss_pred eecCccccccccCcCccccccccccCCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEEcCCCc---EEEEEccCCc
Q 022140 190 VMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQ---LVSLYKPGGA 266 (302)
Q Consensus 190 ~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~~~g~---i~~i~~~G~~ 266 (302)
+.++..++|+|++++.+++|++.+|++.+.+.++|++..+|+ |.+++..|
T Consensus 148 -------------------------l~~~vaaiSvgi~~~~~~lDl~~~Eds~~~~d~~v~~~~~~~~~ei~~~~~~~-- 200 (230)
T COG0689 148 -------------------------LRDLVAAISVGIVDGVIVLDLDYEEDSAAEADMNVVMTGNGGLVEIQGLAEDG-- 200 (230)
T ss_pred -------------------------hhhheeEeEEEEECCceEecCcchhhcccccCceEEEEecCCeEEEEEEeccC--
Confidence 456788999999999999999999999999999999988775 77777766
Q ss_pred ccChHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022140 267 VLAYTSAVQDCIALTRQRVKELHQILEEAIS 297 (302)
Q Consensus 267 ~~~~~~~l~~~i~~A~~~~~~l~~~l~~~l~ 297 (302)
+++.++ +.+++++|.+.++++++.++++|.
T Consensus 201 ~~~~de-l~~lL~la~~g~~~~~~~~~~al~ 230 (230)
T COG0689 201 PFTEDE-LLELLDLAIKGCNELRELQREALA 230 (230)
T ss_pred CcCHHH-HHHHHHHHHHHHHHHHHHHHHHhC
Confidence 789998 999999999999999999999873
No 13
>KOG1068 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp41 and related exoribonucleases [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.9e-33 Score=239.32 Aligned_cols=222 Identities=21% Similarity=0.221 Sum_probs=189.0
Q ss_pred hcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeeccCC--CCCCCcceEEEEEecCCCCCCCccC-
Q 022140 33 AESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPS--LESPDEGCVSIDFHMPPICSPLVRP- 109 (302)
Q Consensus 33 ~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~p~--~~~p~~g~l~v~V~~~~~~~~~~~~- 109 (302)
.++.|.|||.+++.|++....|++.+++|||+++.|||+|+|.|+||-.... ..+|+.+.++|.+.+.+|....++.
T Consensus 10 eeg~r~dgRr~~elR~i~~~~g~~~~a~GSay~E~GnTKVl~aV~GPre~~~~~~~~~~~a~lnc~~~~a~Fst~~r~~~ 89 (245)
T KOG1068|consen 10 EEGLRTDGRRPNELRRIYARIGVLTQADGSAYMEQGNTKVLCAVYGPREIRGKSARRPDKAVLNCEVSSAQFSTGDRKKR 89 (245)
T ss_pred ccccccCCCChhHhhhhhhhcCccccCCccchhhcCCeEEEEEEeCCcccccccccccccceEEEEEeeeccccchhccC
Confidence 5799999999999999999999999999999999999999999999754321 2357889999999998887655432
Q ss_pred CCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHhhCCCCcEEecCCce
Q 022140 110 GRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDGKI 189 (302)
Q Consensus 110 g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~~~~iP~~~~~~~~~ 189 (302)
-+.+.++.+++.+|++++.+ +|.++ ++|. .+|+|.|+||++||+.+.+|+||+.+||.|++||
T Consensus 90 ~~~~rr~~e~s~~L~~afe~--~I~~~---lyPr---sqIDI~v~VleddG~~laa~inaatlAL~daGI~--------- 152 (245)
T KOG1068|consen 90 PKGDRREKELSLMLQQAFEP--VILLE---LYPR---SQIDIYVQVLEDDGSNLAAAINAATLALADAGIP--------- 152 (245)
T ss_pred CCccHHHHHHHHHHHHHHHH--HHHhh---hCcc---ccceEEEEEEECCCccHHHHHHHHHHHHHHcCCC---------
Confidence 12346788999999999986 45443 4674 5999999999999999999999999999999998
Q ss_pred eecCccccccccCcCccccccccccCCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEEcCC-CcEEEEEccCCccc
Q 022140 190 VMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSS-NQLVSLYKPGGAVL 268 (302)
Q Consensus 190 ~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~~~-g~i~~i~~~G~~~~ 268 (302)
|.++..++|.++.++.+++||+..||......++|++-.+ +++..+++.+ .+
T Consensus 153 -------------------------m~D~i~~~t~~l~~~~~l~Dl~~~eesa~~~~ltVa~l~~~~~i~~l~~~~--~~ 205 (245)
T KOG1068|consen 153 -------------------------MYDLITACTAGLADGTPLLDLTSLEESARAPGLTVAALPNREEIALLQLDE--RL 205 (245)
T ss_pred -------------------------hhhhhhhceeeecCCccccccccchhhccCCceEEEEecCcceEEEEEecC--CC
Confidence 5788889999999999999999999999988999987654 4688888887 45
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 022140 269 AYTSAVQDCIALTRQRVKELHQILEEAISGM 299 (302)
Q Consensus 269 ~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~~ 299 (302)
+.+. |...++.|...|+++++.++..+.++
T Consensus 206 ~~d~-l~~vl~~a~~~c~~v~~~l~~~l~~~ 235 (245)
T KOG1068|consen 206 HCDH-LETVLELAIAGCKRVYERLRLVLREH 235 (245)
T ss_pred CHHH-HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6774 99999999999999999888877653
No 14
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=100.00 E-value=3.1e-31 Score=265.49 Aligned_cols=236 Identities=15% Similarity=0.190 Sum_probs=195.3
Q ss_pred HHHhhhChHHHHHHHHhcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEE-eeeccC-CCC----CCCc
Q 022140 17 DAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIK-MEVMTP-SLE----SPDE 90 (302)
Q Consensus 17 ~~~~~~~p~~f~~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~-~~v~~p-~~~----~p~~ 90 (302)
.+|..+.-..+.+..+.++.|+|||++++.|++.+++|.+++++|||+++.|+|+|+|+|+ |+...+ ..+ .+..
T Consensus 419 ~~~~~~~k~~~R~~i~~~g~R~DGR~~~eiRpI~~e~G~Lp~A~GSAlf~~G~TqVLatVtlGp~~~~q~~d~l~~~~~~ 498 (891)
T PLN00207 419 LVFKEVTSKFLRRRIVEGGKRSDGRTPDEIRPINSSCGLLPRAHGSALFTRGETQALAVVTLGDKQMAQRIDNLVDADEV 498 (891)
T ss_pred HHHHHHHHHHHHHHHhcCCCCCCCCCcCccceEEEEeCCcCCCCceEEEEECCeEEEEEEEecCccccccccccccccce
Confidence 4556665555555567889999999999999999999999999999999999999999997 442111 111 2456
Q ss_pred ceEEEEEecCCCCCCCc-cCCCCCCcHHHHHHHHHHHhhcCCCcccccceeecCe--eeEEEEEEEEEecCCCCHHHHHH
Q 022140 91 GCVSIDFHMPPICSPLV-RPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGK--AAWMVYLDIYCLDADGALFDAAL 167 (302)
Q Consensus 91 g~l~v~V~~~~~~~~~~-~~g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~--~~w~i~v~v~Vl~~dG~l~da~~ 167 (302)
+.+.+++.++|++.... +.|++++++..+++++++.|++ . +|++ +.|.|+|+++||++||+...|++
T Consensus 499 ~~f~~~y~fPPfs~ge~~r~g~psrREi~hg~L~eRALrp--v--------ip~~~~fP~tIrV~~~VLesDGSssmAaV 568 (891)
T PLN00207 499 KRFYLQYSFPPSCVGEVGRIGAPSRREIGHGMLAERALEP--I--------LPSEDDFPYTIRVESTITESNGSSSMASV 568 (891)
T ss_pred eeEEEEEEcCCCCCccccCCCCCCHHHHHHHHHHHHHHHH--h--------CCcccCCCEEEEEEEEEEeCCCChHHHHH
Confidence 88999999999986543 4567788899999999999997 2 3433 67999999999999999999999
Q ss_pred HHHHHHHhhCCCCcEEecCCceeecCccccccccCcCccccccccccCCCccEEEEEEEE-C--------CE-EEECCCh
Q 022140 168 LSAVAAFSNLQIPTVSLDDGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILH-K--------NY-ILADPTS 237 (302)
Q Consensus 168 ~A~~~AL~~~~iP~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~-~--------~~-~l~DPt~ 237 (302)
+|+++||+|+++| |+++..++++|++ + .. +++||+.
T Consensus 569 ~aaSLALmDAGIP----------------------------------mk~~VAGvsvGli~d~~~~~~~g~~~IL~Dp~g 614 (891)
T PLN00207 569 CGGCLALQDAGVP----------------------------------VKCPIAGIAMGMVLDTEEFGGDGSPLILSDITG 614 (891)
T ss_pred HHHHHHHHhcCCC----------------------------------ccCceeEEEEEEEecccccCCCCcEEEEeCCCH
Confidence 9999999999999 5677889999998 2 23 5679999
Q ss_pred HHHhcCCceEEEEEcCCCcEEEEEccCCc-ccChHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 022140 238 EEESIMETLVTVVLDSSNQLVSLYKPGGA-VLAYTSAVQDCIALTRQRVKELHQILEEAISG 298 (302)
Q Consensus 238 ~Ee~~~~~~l~i~~~~~g~i~~i~~~G~~-~~~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~ 298 (302)
.|+..++..+.|+.+.+ .|++++..+.. .++.+. |.+++++|.+.+..|++.|++++..
T Consensus 615 ~Ed~~gdmDfkVAgT~~-gIt~iqmd~k~~gis~e~-l~eAL~~A~~g~~~Il~~M~~~i~~ 674 (891)
T PLN00207 615 SEDASGDMDFKVAGNED-GITAFQMDIKVGGITLPI-MERALLQAKDGRKHILAEMSKCSPP 674 (891)
T ss_pred HHHhcCCceEEEEeccc-ceEEEEEecccCCCCHHH-HHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 99999999999997764 58898875532 478885 9999999999999999999999864
No 15
>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=99.97 E-value=2.3e-29 Score=247.46 Aligned_cols=240 Identities=16% Similarity=0.183 Sum_probs=198.9
Q ss_pred cHHHHhhhChHHHHHHHHhcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEe-eecc-CCC---CCCC
Q 022140 15 EVDAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKM-EVMT-PSL---ESPD 89 (302)
Q Consensus 15 ~~~~~~~~~p~~f~~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~-~v~~-p~~---~~p~ 89 (302)
-..+|..+....+.+..++++.|+|||+++++|++.+++|.+++++|||+++.|+|+|+|.+++ +... ... ...+
T Consensus 314 i~~~~~~~~k~~~r~~il~~g~R~DGR~~~eiR~i~~~~g~l~~a~GSa~~~~G~Tqvl~~~tlG~~~~~q~~~~l~~~~ 393 (719)
T TIGR02696 314 ISAAYRAVTKKLVRERVLTEGVRIDGRGVTDIRPLDAEVQVIPRVHGSALFERGETQILGVTTLNMLKMEQQIDSLSPET 393 (719)
T ss_pred HHHHHHHHHHHHHHHHHhcCCCCCCCCCccccccceeecCCCCCCCceEEEEecCcEEEEEEeCCCchhhhhcccccccc
Confidence 3456777888888888889999999999999999999999999999999999999999998774 1100 001 1245
Q ss_pred cceEEEEEecCCCCCCCcc-CCCCCCcHHHHHHHHHHHhhcCCCcc-cccceeecCeeeEEEEEEEEEecCCCCHHHHHH
Q 022140 90 EGCVSIDFHMPPICSPLVR-PGRPAEAAPVVAKQLSDTISSSGMIN-LKELSLVGGKAAWMVYLDIYCLDADGALFDAAL 167 (302)
Q Consensus 90 ~g~l~v~V~~~~~~~~~~~-~g~~~~~~~~ls~~l~~~l~~~~~i~-~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~ 167 (302)
.+.+.+++.|+||+....+ .+.++.++..++++++++|++ +++ ++. +| .+|.+...||++||+...|++
T Consensus 394 ~~~~~~~YnfpPFSt~er~~~~~~~RReighg~La~rALe~--vI~~~e~---fP----~TIrvvseVLeSdGSss~AsI 464 (719)
T TIGR02696 394 SKRYMHHYNFPPYSTGETGRVGSPKRREIGHGALAERALVP--VLPSREE---FP----YAIRQVSEALGSNGSTSMGSV 464 (719)
T ss_pred cceEEEEEeCCCCcccCCCCCCCCCccHHHHHHHHHHHHHH--hhCcHhh---CC----CEEEEEEEeeccCCcHHHHHH
Confidence 6889999999999876543 344567889999999999986 454 333 44 358888899999999999999
Q ss_pred HHHHHHHhhCCCCcEEecCCceeecCccccccccCcCccccccccccCCCccEEEEEEEECC--------EEEECCChHH
Q 022140 168 LSAVAAFSNLQIPTVSLDDGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKN--------YILADPTSEE 239 (302)
Q Consensus 168 ~A~~~AL~~~~iP~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~--------~~l~DPt~~E 239 (302)
+|+++||+|+++| |+++..++++|++++ .+|+||+..|
T Consensus 465 caasLALmDAGVP----------------------------------mkd~VAgis~Gli~e~~~~~~~~~iL~Di~g~E 510 (719)
T TIGR02696 465 CASTLSLLNAGVP----------------------------------LKAPVAGIAMGLISDEVDGETRYVALTDILGAE 510 (719)
T ss_pred HHHHHHHHHcCcc----------------------------------hhheeeEEEEEEeccccCCCcceeEEeCCCchh
Confidence 9999999999999 578888999999843 2899999999
Q ss_pred HhcCCceEEEEEcCCCcEEEEEccCCc-ccChHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 022140 240 ESIMETLVTVVLDSSNQLVSLYKPGGA-VLAYTSAVQDCIALTRQRVKELHQILEEAISGM 299 (302)
Q Consensus 240 e~~~~~~l~i~~~~~g~i~~i~~~G~~-~~~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~~ 299 (302)
+...+..+.++.+. +.+++++..|.. .++.+. +.+++++|.+.+..|++.|+++|..-
T Consensus 511 D~~Gdmdfkvagt~-~gIt~lQmd~ki~gi~~e~-l~~aL~~A~~g~~~Il~~m~~al~~p 569 (719)
T TIGR02696 511 DAFGDMDFKVAGTS-EFVTALQLDTKLDGIPASV-LASALKQARDARLAILDVMAEAIDTP 569 (719)
T ss_pred hhcCCceEEEEecC-CCEEEEEEEeeECCCCHHH-HHHHHHHHHHHHHHHHHHHHHHHhCc
Confidence 99999999997665 569999987743 368885 99999999999999999999998753
No 16
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=99.97 E-value=1.4e-29 Score=253.36 Aligned_cols=202 Identities=20% Similarity=0.233 Sum_probs=174.9
Q ss_pred cceEEEeCCcc-CCCeeEEEEeCCeEEEEEEEeeeccCCCCCCCcceEEEEEecCCCCC--C----Cc--cCCCCCCcHH
Q 022140 47 RNTTISMGAVA-SADGSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPICS--P----LV--RPGRPAEAAP 117 (302)
Q Consensus 47 R~i~i~~g~l~-~a~GSa~v~~G~T~Vi~~V~~~v~~p~~~~p~~g~l~v~V~~~~~~~--~----~~--~~g~~~~~~~ 117 (302)
|++.+++|.++ +|+|||+|++|+|+|+|+|+++.. | ++..+++.++|+|.+.+. . .| +.|++++.+.
T Consensus 14 r~i~~e~G~ia~qAdGSa~v~~G~T~VlatV~~~~~-~---~~~~df~pL~v~y~e~~~A~gkiP~~f~kreg~pse~ei 89 (693)
T PRK11824 14 RTLTLETGKLARQANGAVLVRYGDTVVLVTVVASKE-P---KEGQDFFPLTVDYEEKTYAAGKIPGGFFKREGRPSEKET 89 (693)
T ss_pred ccEEEEECCcCCCCCeEEEEEECCeEEEEEEEcCCC-C---CCCCCeeeeEEEEEehhhhccCCCcccccCCCCCChHHH
Confidence 79999999996 699999999999999999999765 3 355788889999876542 2 23 5688999999
Q ss_pred HHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCH-HH-HHHHHHHHHHhhCCCCcEEecCCceeecCcc
Q 022140 118 VVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGAL-FD-AALLSAVAAFSNLQIPTVSLDDGKIVMLPEE 195 (302)
Q Consensus 118 ~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l-~d-a~~~A~~~AL~~~~iP~~~~~~~~~~~~~~~ 195 (302)
.+++++++.|++ ++|+.++|.++|+++||++||+. .| ||++|+++||.++++|
T Consensus 90 l~srlIdR~lrp----------lfp~~~~~~i~I~~~VL~~Dg~~~~d~aai~aAsaAL~~s~IP--------------- 144 (693)
T PRK11824 90 LTSRLIDRPIRP----------LFPKGFRNEVQVVATVLSVDPENDPDILAMIGASAALSISGIP--------------- 144 (693)
T ss_pred HHHHHHhhhHHH----------hCCCCCCeEEEEEEEEEeCCCCCcHHHHHHHHHHHHHHhcCCC---------------
Confidence 999999999997 27888899999999999999965 67 7999999999999999
Q ss_pred ccccccCcCccccccccccCCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEEcCCCcEEEEEccCCcccChHHHHH
Q 022140 196 QKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLAYTSAVQ 275 (302)
Q Consensus 196 ~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~~~g~i~~i~~~G~~~~~~~~~l~ 275 (302)
+.+++.++++|++++.+++|||.+|++.++..++|+.+.+ .++.++ .|+..++.++ +.
T Consensus 145 -------------------~~~~v~av~vg~i~g~~ivdPt~~E~~~s~~~l~va~t~~-~i~mie-~~~~~l~e~~-l~ 202 (693)
T PRK11824 145 -------------------FNGPIAAVRVGYIDGEFVLNPTVEELEESDLDLVVAGTKD-AVLMVE-SEAKELSEEV-ML 202 (693)
T ss_pred -------------------cCCCeEEEEEEEECCEEEEcCCHHHHhhCcceEEEEEccC-ceEEEE-CCCCCCCHHH-HH
Confidence 3567889999999999999999999999999999998765 455554 5656799996 99
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcc
Q 022140 276 DCIALTRQRVKELHQILEEAISGM 299 (302)
Q Consensus 276 ~~i~~A~~~~~~l~~~l~~~l~~~ 299 (302)
+|+++|++.++++++++++.+++.
T Consensus 203 ~al~~a~~~~~~i~~~~~~~~~~~ 226 (693)
T PRK11824 203 EAIEFGHEAIQELIDAQEELAAEA 226 (693)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhc
Confidence 999999999999999999988754
No 17
>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=99.97 E-value=1.8e-29 Score=252.13 Aligned_cols=202 Identities=17% Similarity=0.212 Sum_probs=172.8
Q ss_pred cceEEEeCCc-cCCCeeEEEEeCCeEEEEEEEeeeccCCCCCCCcceEEEEEecCCCCC--C----Cc--cCCCCCCcHH
Q 022140 47 RNTTISMGAV-ASADGSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPICS--P----LV--RPGRPAEAAP 117 (302)
Q Consensus 47 R~i~i~~g~l-~~a~GSa~v~~G~T~Vi~~V~~~v~~p~~~~p~~g~l~v~V~~~~~~~--~----~~--~~g~~~~~~~ 117 (302)
|++.+++|.+ ++|+|||++++|+|+|+|+|+++.. | ++..+++.++|+|.+.++ . .| +.|++++.+.
T Consensus 5 R~i~ie~G~la~~AdGSa~v~~G~T~VlatV~~~~~-~---~~~~df~pL~vey~e~~~A~gkipg~f~kReg~p~~~ei 80 (684)
T TIGR03591 5 RTLTLETGKIARQADGAVVVRYGDTVVLVTVVAAKE-A---KEGQDFFPLTVNYQEKFYAAGKIPGGFFKREGRPSEKET 80 (684)
T ss_pred ccEEEEECCcCCCCCeEEEEEECCeEEEEEEEcCCC-C---CCCCceEeEEEEEEehhhhccCCCCCcccCCCCCCHHHH
Confidence 7999999999 4799999999999999999999753 2 344678888888876442 2 22 5688999999
Q ss_pred HHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHH-H-HHHHHHHHHHhhCCCCcEEecCCceeecCcc
Q 022140 118 VVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALF-D-AALLSAVAAFSNLQIPTVSLDDGKIVMLPEE 195 (302)
Q Consensus 118 ~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~-d-a~~~A~~~AL~~~~iP~~~~~~~~~~~~~~~ 195 (302)
.+++++++.+++ .+|++++|.|+|+++||++||+.. | ||++|+++||.++++|
T Consensus 81 l~srlIdR~lrp----------lfp~~~~~~i~V~~~VLs~Dg~~~~d~aai~aAsaAL~~s~IP--------------- 135 (684)
T TIGR03591 81 LTSRLIDRPIRP----------LFPKGFRNEVQVVATVLSYDPENDPDILAIIGASAALAISGIP--------------- 135 (684)
T ss_pred HHHHHHhhHHHH----------hcCCCCCceEEEEEEEEecCcCCchHHHHHHHHHHHHHhcCCC---------------
Confidence 999999999986 388889999999999999999974 6 9999999999999999
Q ss_pred ccccccCcCccccccccccCCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEEcCCCcEEEEEccCCcccChHHHHH
Q 022140 196 QKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLAYTSAVQ 275 (302)
Q Consensus 196 ~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~~~g~i~~i~~~G~~~~~~~~~l~ 275 (302)
+++++.+++++++++.+++|||.+|++.++..++++.+.+ .++.+ +.|+..++.++ +.
T Consensus 136 -------------------~~~~v~av~vg~idg~~ildPt~~E~~~s~~~l~va~t~~-~i~mi-e~~~~~i~e~~-l~ 193 (684)
T TIGR03591 136 -------------------FNGPIAAVRVGYIDGQYVLNPTVDELEKSDLDLVVAGTKD-AVLMV-ESEAKELSEEV-ML 193 (684)
T ss_pred -------------------cCCCeEEEEEEEECCEEEEcCCHHHHhhCCceEEEEccCC-cEEEE-EcCCCCCCHHH-HH
Confidence 4678899999999999999999999999999998875432 35444 55666799996 99
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcc
Q 022140 276 DCIALTRQRVKELHQILEEAISGM 299 (302)
Q Consensus 276 ~~i~~A~~~~~~l~~~l~~~l~~~ 299 (302)
+|+++|++.+++++++++++++++
T Consensus 194 ~al~~a~~~~~~i~~~~~~~~~~~ 217 (684)
T TIGR03591 194 GAIEFGHEEIQPVIEAIEELAEEA 217 (684)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHh
Confidence 999999999999999999988764
No 18
>KOG1069 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp46 [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=2.8e-28 Score=202.14 Aligned_cols=201 Identities=19% Similarity=0.344 Sum_probs=169.0
Q ss_pred CCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeecc-CCCCCCCcceEEEEEecCCCCCCCccCCCCCCcHHHHHHHH
Q 022140 45 RARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMT-PSLESPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQL 123 (302)
Q Consensus 45 e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~-p~~~~p~~g~l~v~V~~~~~~~~~~~~g~~~~~~~~ls~~l 123 (302)
+.|++.++.|.|+++|||+.+++|+|+|+|+|+||... .+.+.|++..+++.+ .|.+ |.....++.++++|
T Consensus 4 ~lr~~~cei~iLsr~dGSs~fsqgdT~V~c~V~GP~dvk~r~E~~~katleVi~--rp~~------G~~~~~eK~~e~iI 75 (217)
T KOG1069|consen 4 RLRGIACEISILSRPDGSSEFSQGDTKVICSVYGPIDVKARQEDPEKATLEVIW--RPKS------GVNGTVEKVLERII 75 (217)
T ss_pred hhhhhhhhhceecCCCCccceecCCcEEEEEeeCCcchhhcccCchhceEEEEE--eccc------CcchHHHHHHHHHH
Confidence 68999999999999999999999999999999998753 335566666666655 4543 44455678999999
Q ss_pred HHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHhhCCCCcEEecCCceeecCccccccccCc
Q 022140 124 SDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDGKIVMLPEEQKEENSEK 203 (302)
Q Consensus 124 ~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~~~~iP~~~~~~~~~~~~~~~~~~~~~~~ 203 (302)
.++|.+ +|.+ -++|.+ .|.|.++|+++||+.+.+|+||+++||.|+|+|
T Consensus 76 ~~tl~~--~I~l---~l~Prt---~iqVsiqvv~ddgs~LacaINaAclALvDaGIp----------------------- 124 (217)
T KOG1069|consen 76 RKTLSK--AIIL---ELYPRT---TIQVSIQVVEDDGSTLACAINAACLALVDAGIP----------------------- 124 (217)
T ss_pred HHHHHH--hhee---eecCCc---eEEEEEEEEecCCcchHHHHHHHHHHHHhcCCc-----------------------
Confidence 999975 4443 246754 799999999999999999999999999999999
Q ss_pred CccccccccccCCCccEEEEEEEECC-EEEECCChHHHhcCCceEEEEEc----CCCcEEEEEccCCcccChHHHHHHHH
Q 022140 204 EPVNKEKRKLTLGGIPFSLTCILHKN-YILADPTSEEESIMETLVTVVLD----SSNQLVSLYKPGGAVLAYTSAVQDCI 278 (302)
Q Consensus 204 ~~~~~~~~~l~i~~~p~~vt~~~~~~-~~l~DPt~~Ee~~~~~~l~i~~~----~~g~i~~i~~~G~~~~~~~~~l~~~i 278 (302)
++++++++.+++.++ .+++|||..+|+.+.+..++++- ..-+++.+...| .++.+| |..++
T Consensus 125 -----------l~~mfcai~~~~~~d~~lv~Dpt~~qek~~~~~~~lsf~~~~~~~~~vi~s~t~G--~~~~d~-lf~~l 190 (217)
T KOG1069|consen 125 -----------LRSMFCAISCALHEDGVLVLDPTAKQEKISTARATLSFEGGSLGEPKVIISETNG--EKSEDQ-LFYVL 190 (217)
T ss_pred -----------hHHhhhhceEEEecCccEEECCcHHhhhhhhceEEEEEecCCCCCcceEEEeccC--CCCHHH-HHHHH
Confidence 578999999998875 89999999999988888777763 234799999988 668887 99999
Q ss_pred HHHHHHHHHHHHHHHHHhhc
Q 022140 279 ALTRQRVKELHQILEEAISG 298 (302)
Q Consensus 279 ~~A~~~~~~l~~~l~~~l~~ 298 (302)
+.|...+++++.++++.+++
T Consensus 191 e~a~~~~~~~f~f~r~~~q~ 210 (217)
T KOG1069|consen 191 ELAQAAAQSLFPFYREVLQR 210 (217)
T ss_pred HhhHHHHHHHHHHHHHHHHh
Confidence 99999999999999999875
No 19
>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=99.96 E-value=8.2e-28 Score=194.12 Aligned_cols=128 Identities=32% Similarity=0.544 Sum_probs=113.3
Q ss_pred CCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeecc-CCCCCC-CcceEEEEEecCCCCCCCccC-CCCCCcHHHHHH
Q 022140 45 RARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMT-PSLESP-DEGCVSIDFHMPPICSPLVRP-GRPAEAAPVVAK 121 (302)
Q Consensus 45 e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~-p~~~~p-~~g~l~v~V~~~~~~~~~~~~-g~~~~~~~~ls~ 121 (302)
|+|++.+++|.+++++|||+|++|+|+|+|+|++++.. |..+++ .+|.+.++|+++|++...++. +.+++.+..+++
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 79999999999999999999999999999999999987 555434 358999999999999877653 556678889999
Q ss_pred HHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCC-CHHHHHHHHHHHHHhhCCCC
Q 022140 122 QLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADG-ALFDAALLSAVAAFSNLQIP 180 (302)
Q Consensus 122 ~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG-~l~da~~~A~~~AL~~~~iP 180 (302)
+|+++|++... .+++++|+|+|+++||++|| |++||+++|+++||+|+++|
T Consensus 81 ~l~~~l~~~~~--------~~~~~~~~i~v~v~vl~~dG~~~~~a~~~A~~~AL~~~~iP 132 (132)
T PF01138_consen 81 LLERALRSSIL--------LEGYPRWQIHVDVQVLSDDGGNLLDAAINAACLALLDAGIP 132 (132)
T ss_dssp HHHHHHHHTBS--------TTTTSSEEEEEEEEEEECSSSSHHHHHHHHHHHHHHHHTCS
T ss_pred HHhhhcccccc--------ccccCceEEEEEEEEEecCCCCHHHHHHHHHHHHHHhcCCC
Confidence 99999987432 36777899999999999999 99999999999999999998
No 20
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=99.90 E-value=3.4e-22 Score=200.76 Aligned_cols=202 Identities=15% Similarity=0.166 Sum_probs=168.4
Q ss_pred cceEEEeCCcc-CCCeeEEEEeCCeEEEEEEEeeeccCCCCCCCcceEEEEEecCCCCCC------Cc--cCCCCCCcHH
Q 022140 47 RNTTISMGAVA-SADGSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPICSP------LV--RPGRPAEAAP 117 (302)
Q Consensus 47 R~i~i~~g~l~-~a~GSa~v~~G~T~Vi~~V~~~v~~p~~~~p~~g~l~v~V~~~~~~~~------~~--~~g~~~~~~~ 117 (302)
|++.+++|.+. +|+||+.++.|+|.|+|+|...- .| ++..+++.+.|+|....+. .| |.|++++.+.
T Consensus 89 ~~~~~etG~~a~qA~gav~v~~g~t~vl~t~~~~~-~~---~~~~dF~PLtV~y~Ek~~AaGkipggf~kREgrp~d~ei 164 (891)
T PLN00207 89 RHILVETGHIGRQASGSVTVTDGETIVYTSVCLAD-VP---SEPSDFFPLSVHYQERFSAAGRTSGGFFKREGRTKDHEV 164 (891)
T ss_pred EEEEEEhhHHHHhCCCcEEEEECCeEEEEEEEecc-CC---CCCCCccceeEeeeeehhhcCccCCceeccCCCCChHHH
Confidence 47999999998 59999999999999999998632 22 2345789999999754332 12 4688999999
Q ss_pred HHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCC--HHHHHHHHHHHHHhhCCCCcEEecCCceeecCcc
Q 022140 118 VVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGA--LFDAALLSAVAAFSNLQIPTVSLDDGKIVMLPEE 195 (302)
Q Consensus 118 ~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~--l~da~~~A~~~AL~~~~iP~~~~~~~~~~~~~~~ 195 (302)
.+++++++.|++ . +|..++....|.++||++||+ ...+|++|+++||.+++||
T Consensus 165 L~sRlIdR~lRP--l--------fp~~~~~etQI~i~VLsaDg~~~pd~~AInAASaAL~~SgIP--------------- 219 (891)
T PLN00207 165 LICRLIDRPLRP--T--------MPKGFYHETQILSWVLSYDGLHSPDSLAVTAAGIAVALSEVP--------------- 219 (891)
T ss_pred HHHHHHCccchh--h--------ccccCCCCcEEEEEEEeeCCCCChhhHHHHHHHHHHHhhCCC---------------
Confidence 999999999997 2 444444567778899999998 5678999999999999999
Q ss_pred ccccccCcCccccccccccCCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEEcCCCcEEEEEccCCcccChHHHHH
Q 022140 196 QKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLAYTSAVQ 275 (302)
Q Consensus 196 ~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~~~g~i~~i~~~G~~~~~~~~~l~ 275 (302)
++++..+|++|.+++.+++|||.+|++.++..|.|+.+.+ .|++++..| ..++.++ +.
T Consensus 220 -------------------~~gpVaAVrVG~idg~~VlnPt~~E~~~s~ldLvvagt~~-~IvMIE~~a-~e~see~-l~ 277 (891)
T PLN00207 220 -------------------NLKAIAGVRVGLIGGKFIVNPTTKEMEESELDLIMAGTDS-AILMIEGYC-NFLPEEK-LL 277 (891)
T ss_pred -------------------ccCceEEEEEEEECCEEEECCCHHHHhcCCeeEEEEEcCC-eEEEEEcCC-CCCCHHH-HH
Confidence 5677889999999999999999999999999998887754 588887654 4578886 99
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcc
Q 022140 276 DCIALTRQRVKELHQILEEAISGM 299 (302)
Q Consensus 276 ~~i~~A~~~~~~l~~~l~~~l~~~ 299 (302)
+++++|++.++.+.+++++.++++
T Consensus 278 ~Al~~a~~aik~i~~~~~el~~~~ 301 (891)
T PLN00207 278 EAVEVGQDAVRAICKEIEVLVKKC 301 (891)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHh
Confidence 999999999999999999988764
No 21
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=99.86 E-value=1.4e-20 Score=176.54 Aligned_cols=233 Identities=18% Similarity=0.257 Sum_probs=186.4
Q ss_pred ccHHHHhhhChHHHHHHHHhcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeeccC-----CCCCC
Q 022140 14 MEVDAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTP-----SLESP 88 (302)
Q Consensus 14 ~~~~~~~~~~p~~f~~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~p-----~~~~p 88 (302)
--.+.|..+.-+.|-...++.+.|.|||.+++.|+|.++.+.++..+||++++-|.|+|+|+|+..-.+. +...|
T Consensus 336 ~i~~~fn~vskkv~Rs~i~~~gkR~DGR~ldelR~I~ce~~m~~~lHGSaLFqRGqTQvlctVtl~s~e~a~klD~l~~~ 415 (760)
T KOG1067|consen 336 EIIESFNTVSKKVFRSRILEEGKRCDGRDLDELRNISCEVDMLKTLHGSALFQRGQTQVLCTVTLDSLESAQKLDSLIGP 415 (760)
T ss_pred HHHHHHHHHHHHHHHHHHHhcccccCCcchhhhcccceecCccccccchhhhhcCceeEEEEEEcCCHHHhhhhhhhccC
Confidence 3456788888999999999999999999999999999999999999999999999999999999731110 01133
Q ss_pred Cc-ceEEEEEecCCCCCCCc-cCCCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHH
Q 022140 89 DE-GCVSIDFHMPPICSPLV-RPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAA 166 (302)
Q Consensus 89 ~~-g~l~v~V~~~~~~~~~~-~~g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~ 166 (302)
++ +.+.++++|+|.+...- +-|..+.++.--..+-++.|.+ ++|..+.|+|+|.-.||+.+|+--.|.
T Consensus 416 ~~~~~FmLhY~FPPyat~Evgkig~~nRRE~GhgaLAEkaL~~----------vlP~dfPftIRv~SeVleSnGSsSMAS 485 (760)
T KOG1067|consen 416 DNGINFMLHYEFPPYATNEVGKIGGLNRRELGHGALAEKALLP----------VLPEDFPFTIRVTSEVLESNGSSSMAS 485 (760)
T ss_pred ccCceEEEEeccCCccccccccccCCcccccCchhHhhhhhhc----------cCcccCceEEEEeeeeeecCCcchHHh
Confidence 44 49999999999987643 2244455555566677777754 467778899999999999999999999
Q ss_pred HHHHHHHHhhCCCCcEEecCCceeecCccccccccCcCccccccccccCCCccEEEEEEEE-----------CCEEEECC
Q 022140 167 LLSAVAAFSNLQIPTVSLDDGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILH-----------KNYILADP 235 (302)
Q Consensus 167 ~~A~~~AL~~~~iP~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~-----------~~~~l~DP 235 (302)
..+-++||+|+++|.-.... .|.+|+. +..++.|.
T Consensus 486 vCGGslALmDaGvPv~a~vA----------------------------------GvaiGlvt~td~e~g~i~dyriltDI 531 (760)
T KOG1067|consen 486 VCGGSLALMDAGVPVSAHVA----------------------------------GVAIGLVTKTDPEKGEIEDYRILTDI 531 (760)
T ss_pred hhcchhhhhhcCCccccccc----------------------------------eeEEEeEeccCcccCCcccceeehhh
Confidence 99999999999999432211 2222322 23689999
Q ss_pred ChHHHhcCCceEEEEEcCCCcEEEEEccCCcccChHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 022140 236 TSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAISG 298 (302)
Q Consensus 236 t~~Ee~~~~~~l~i~~~~~g~i~~i~~~G~~~~~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~ 298 (302)
...|....+..+.|+-++.| ++.+ | ++.+ +++++++.|..+..+|.+.|.+.+..
T Consensus 532 lGiEd~~GDMDFKiAGt~dG-vTA~---g---i~l~-Iv~eal~~a~~ar~~Il~~m~k~i~~ 586 (760)
T KOG1067|consen 532 LGIEDYNGDMDFKIAGTNDG-VTAL---G---IPLK-IVMEALQKAREARLQILDIMEKNINS 586 (760)
T ss_pred cchhhhcCCcceeeccccCc-ceec---C---CcHH-HHHHHHHhhhHHHHHHHHHHHhhcCC
Confidence 99999999999999998887 6666 3 4567 69999999999999999999987653
No 22
>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=99.80 E-value=8.1e-18 Score=166.21 Aligned_cols=203 Identities=17% Similarity=0.167 Sum_probs=168.8
Q ss_pred cceEEEeCCcc-CCCeeEEEEe-CCeEEEEEEEeeeccCCCCCCCcceEEEEEecCCCCCC------Cc--cCCCCCCcH
Q 022140 47 RNTTISMGAVA-SADGSALAKI-GSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPICSP------LV--RPGRPAEAA 116 (302)
Q Consensus 47 R~i~i~~g~l~-~a~GSa~v~~-G~T~Vi~~V~~~v~~p~~~~p~~g~l~v~V~~~~~~~~------~~--~~g~~~~~~ 116 (302)
|++.+++|.+. +|+||+.+++ |+|.|+|++...- +| ++..+++.+.|+|....+. .| |.|+|++.+
T Consensus 17 ~~~~~etG~~A~qA~Gav~v~~~G~t~vl~t~~~~~-~~---~~~~dF~PLtV~y~Ek~yA~GkiPggf~kREgrps~~e 92 (719)
T TIGR02696 17 RTIRFETGRLARQAAGSVVAYLDDETMLLSATTASK-QP---KDQFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDA 92 (719)
T ss_pred EEEEEEcchhHhhCCceEEEEecCCeEEEEEEEecC-CC---CCCCCCcceeEeeeehhhhcCccCCceeccCCCCChhh
Confidence 47999999998 5999999999 9999999998631 22 2346789999999765432 12 468899999
Q ss_pred HHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCC-HHH-HHHHHHHHHHhhCCCCcEEecCCceeecCc
Q 022140 117 PVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGA-LFD-AALLSAVAAFSNLQIPTVSLDDGKIVMLPE 194 (302)
Q Consensus 117 ~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~-l~d-a~~~A~~~AL~~~~iP~~~~~~~~~~~~~~ 194 (302)
...+++++|.+|+ ++|..++..++|.++||++|+. ..| .+++|+++||.-+.||
T Consensus 93 iL~sRliDR~iRP----------LFp~~~~~e~qi~~~vls~D~~~~pdvla~~~ASaAl~iSdiP-------------- 148 (719)
T TIGR02696 93 ILTCRLIDRPLRP----------SFVKGLRNEVQVVVTVLSLNPDHLYDVVAINAASASTQLAGLP-------------- 148 (719)
T ss_pred hHHHHhhCCCCcc----------CCCCCCCcceEEEEEEEEcCCCCChHHHHHHHHHHHHHhcCCC--------------
Confidence 9999999999997 4888888899999999999985 345 5789999999999998
Q ss_pred cccccccCcCccccccccccCCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEEcC----CCcEEEEEcc-------
Q 022140 195 EQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDS----SNQLVSLYKP------- 263 (302)
Q Consensus 195 ~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~~----~g~i~~i~~~------- 263 (302)
++....+|.+|.+++.+++.||.+|-+.++-.|+|+-++ ++.+++++..
T Consensus 149 --------------------f~gPv~~vrVg~i~g~~viNPt~~~~~~s~ldLvvagt~~~~~~~~i~MiE~~a~~~~~~ 208 (719)
T TIGR02696 149 --------------------FSGPIGGVRVALIDGQWVAFPTHEQLEGAVFDMVVAGRVLENGDVAIMMVEAEATEKTWD 208 (719)
T ss_pred --------------------CCCceEEEEEEEECCEEEECcCHHHHhhCeeeEEEEeeecCCCCccEEEEecCCcccccc
Confidence 355567899999999999999999999988889998876 4478888852
Q ss_pred ----CCcccChHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 022140 264 ----GGAVLAYTSAVQDCIALTRQRVKELHQILEEAISG 298 (302)
Q Consensus 264 ----G~~~~~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~ 298 (302)
|+..++.++ |.++|.+|++..+.+.+++++..+.
T Consensus 209 ~~~~~a~e~~e~~-~~~Ai~~a~~~i~~~~~~~~~l~~~ 246 (719)
T TIGR02696 209 LVKGGAEAPTEEV-VAEGLEAAKPFIKVLCRAQADLAEK 246 (719)
T ss_pred ccccCCCCCCHHH-HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 556788886 9999999999999999998886543
No 23
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=99.68 E-value=8.7e-16 Score=148.84 Aligned_cols=236 Identities=17% Similarity=0.179 Sum_probs=183.7
Q ss_pred HHHHhhhChHHHHHHHHhcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeeccCCC-------CCC
Q 022140 16 VDAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSL-------ESP 88 (302)
Q Consensus 16 ~~~~~~~~p~~f~~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~p~~-------~~p 88 (302)
.+.|..+.+..-.+..++.++|+|||..++.|++.++.|.+++++||+++..|.|+.++.++. +.+.. ..+
T Consensus 292 ~~~~~~l~~~~vR~~Il~~~vR~DGR~~~~VRpi~~ev~~lpr~HGS~LFtRGeTQal~v~TL--G~~~d~Qvid~l~~e 369 (692)
T COG1185 292 KAILEKLEKKPVRRLILEGKVRIDGRFGDEVRPIGIEVGVLPRTHGSALFTRGETQALVVVTL--GTPRDAQVIDILEGE 369 (692)
T ss_pred HHHHHHHhHHHHHHHHhcCCcccCCCCcceeeeeeEEecCCCCccchhhhccCCCcceEEEEc--CCcchhhhhhhccch
Confidence 456888888888888889999999999999999999999999999999999999999988886 22221 122
Q ss_pred CcceEEEEEecCCCCCCC-ccCCCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHH
Q 022140 89 DEGCVSIDFHMPPICSPL-VRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAAL 167 (302)
Q Consensus 89 ~~g~l~v~V~~~~~~~~~-~~~g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~ 167 (302)
...++..++.|+|++... .+-|.|+.++.--.++-++++.+ .++. ..++.++|++--.|++.+|+--.|.+
T Consensus 370 ~~krfm~hYNFPp~SvGE~g~~g~p~RREiGHG~LA~Ral~~--vlp~------~e~fpytiRvVsEi~eSNGSsSmaSV 441 (692)
T COG1185 370 YKKRFLLHYNFPPFSVGETGRMGSPGRREIGHGALAERALAP--VLPS------EEEFPYTIRVVSEILESNGSSSMASV 441 (692)
T ss_pred hhhheeeeccCCCCCccccCCCCCCCcccccCchhhHHHHhh--hCCc------hhcCCceeeeeehhhcccCcccchhh
Confidence 346789999999998533 23355555666666667777764 2221 12456899999999999999999999
Q ss_pred HHHHHHHhhCCCCcEEecCCceeecCccccccccCcCccccccccccCCCccEEEEEEEEC----CEEEECCChHHHhcC
Q 022140 168 LSAVAAFSNLQIPTVSLDDGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHK----NYILADPTSEEESIM 243 (302)
Q Consensus 168 ~A~~~AL~~~~iP~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~----~~~l~DPt~~Ee~~~ 243 (302)
++..+||+++++|.- .....+..|++. ..++.|....|....
T Consensus 442 Cg~sLaLmdAGVPIk----------------------------------~pVAGIAMGLI~eg~~~~vLsDI~G~EDhlG 487 (692)
T COG1185 442 CGGSLALMDAGVPIK----------------------------------APVAGIAMGLIKEGDKYAVLSDILGDEDHLG 487 (692)
T ss_pred hhhHHHHHhCCCccc----------------------------------ccccchhccceecCCceEeeccccccccccC
Confidence 999999999999942 222223344432 257899999999999
Q ss_pred CceEEEEEcCCCcEEEEEc---cCCcccChHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 022140 244 ETLVTVVLDSSNQLVSLYK---PGGAVLAYTSAVQDCIALTRQRVKELHQILEEAISGM 299 (302)
Q Consensus 244 ~~~l~i~~~~~g~i~~i~~---~G~~~~~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~~ 299 (302)
+..+-|+-+..| ++.++. .. .++.+ +|.+++..|+.+..++...|.+++...
T Consensus 488 DMDFKVAGT~~G-iTAlQMDiKi~--Git~e-im~~AL~QAk~aRlhIL~~M~~ai~~p 542 (692)
T COG1185 488 DMDFKVAGTDDG-ITALQMDIKIK--GITKE-IMKKALEQAKGARLHILIVMNEAISEP 542 (692)
T ss_pred CceeEEecCCCc-ceeeeeeeeec--CCCHH-HHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 999999998888 666653 33 35777 699999999999999999999998764
No 24
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=99.65 E-value=8e-15 Score=142.22 Aligned_cols=200 Identities=20% Similarity=0.195 Sum_probs=164.2
Q ss_pred cceEEEeCCcc-CCCeeEEEEeCCeEEEEEEEeeeccCCCCCCCcceEEEEEecCCCCCC------Cc--cCCCCCCcHH
Q 022140 47 RNTTISMGAVA-SADGSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPICSP------LV--RPGRPAEAAP 117 (302)
Q Consensus 47 R~i~i~~g~l~-~a~GSa~v~~G~T~Vi~~V~~~v~~p~~~~p~~g~l~v~V~~~~~~~~------~~--~~g~~~~~~~ 117 (302)
|++.+++|.+. +|+|++.+++|+|.|++++.+.- + ++..+++.+.|+|.-.... .| |.|+|++.+.
T Consensus 14 ~~l~~etg~~A~qa~gav~~~~gdt~vl~t~~~~~--~---~~~~dF~PLtV~y~Ek~yaaGkiPGgf~kREGrpse~e~ 88 (692)
T COG1185 14 RTLTLETGKIARQANGAVLVRYGDTVVLATVVASK--P---KEGQDFFPLTVNYEEKTYAAGKIPGGFFKREGRPSEKEI 88 (692)
T ss_pred eeEEEEcchhhhhcCccEEEEECCeEEEEEEeecC--C---CCCCCccceeEeeeeehhccCcCCCcccccCCCCCccch
Confidence 79999999998 69999999999999999999853 2 2356788888888643221 12 5799999999
Q ss_pred HHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHH-H-HHHHHHHHHHhhCCCCcEEecCCceeecCcc
Q 022140 118 VVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALF-D-AALLSAVAAFSNLQIPTVSLDDGKIVMLPEE 195 (302)
Q Consensus 118 ~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~-d-a~~~A~~~AL~~~~iP~~~~~~~~~~~~~~~ 195 (302)
..++++++-+++ ++|..+..-++|..+|+++|+... | .+++|+++||.-+++|.
T Consensus 89 L~sRLIDRpiRP----------lFp~g~~~evqIv~tvls~D~~~~pdi~a~~gaSaAl~is~iPf-------------- 144 (692)
T COG1185 89 LTSRLIDRPIRP----------LFPKGFRNEVQIVNTVLSVDPENDPDILAMVGASAALSLSGIPF-------------- 144 (692)
T ss_pred hhhhhccccccc----------ccchhhccceEEEEEEEEECCCCCHHHHHHHHHHHHHhccCCCc--------------
Confidence 999999998886 477667778999999999998653 3 67899999999999884
Q ss_pred ccccccCcCccccccccccCCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEEcCCCcEEEEEccCCcccChHHHHH
Q 022140 196 QKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLAYTSAVQ 275 (302)
Q Consensus 196 ~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~~~g~i~~i~~~G~~~~~~~~~l~ 275 (302)
.....++++|++++.+++.||.+|-+.++-.++|+-+++ .|.+++. |...++.++ +.
T Consensus 145 --------------------~gpi~~vrvg~idg~~vlNPt~~e~~~s~lDlvVAGT~~-aV~MVE~-~a~~l~E~~-ml 201 (692)
T COG1185 145 --------------------LGPIGAVRVGYIDGIFVLNPTLEELEESKLDLVVAGTKD-AVNMVES-EADELDEEV-ML 201 (692)
T ss_pred --------------------cCccceEEEEEECCEEEECCChHHhhhcceeeEecCChh-hhheeec-ccccCCHHH-HH
Confidence 455568999999999999999999998888888876665 4666654 556788775 99
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhc
Q 022140 276 DCIALTRQRVKELHQILEEAISG 298 (302)
Q Consensus 276 ~~i~~A~~~~~~l~~~l~~~l~~ 298 (302)
+++..+++..+.+.+++++....
T Consensus 202 ~Av~fg~~~~~~~~~~qe~l~~~ 224 (692)
T COG1185 202 EAVEFGHEAIQSVINAQEELALE 224 (692)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999998887654
No 25
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=99.47 E-value=4.8e-13 Score=126.38 Aligned_cols=203 Identities=19% Similarity=0.225 Sum_probs=155.2
Q ss_pred CCcceEEEeCCccC-CCeeEEEEeCCeEEEEEEEeeeccCCCCCCCcceEEEEEecCCCCCC------Cc--cCCCCCCc
Q 022140 45 RARNTTISMGAVAS-ADGSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPICSP------LV--RPGRPAEA 115 (302)
Q Consensus 45 e~R~i~i~~g~l~~-a~GSa~v~~G~T~Vi~~V~~~v~~p~~~~p~~g~l~v~V~~~~~~~~------~~--~~g~~~~~ 115 (302)
--|.+.+++|.+.+ |+||+.++.|+|.|+++|.+.- .|. |.+ ++.+.|+|.-..+. .| |.|++++.
T Consensus 54 GnR~i~~etGklaRfAngsvvv~~GeT~Vm~Tv~~a~-~PS---p~q-FlPL~VdYqeK~aAvGRip~~fmRREg~tkdk 128 (760)
T KOG1067|consen 54 GNREILFETGKLARFANGSVVVQMGETAVMTTVVLAD-KPS---PPQ-FLPLVVDYQEKFAAVGRIPGNFMRREGRTKDK 128 (760)
T ss_pred CCeEEEEecchhhhhcCCcEEEccCCeEEEEEEEecC-CCC---ccc-cceEEEehhhhhhhhccCCCcccccccCCcch
Confidence 46899999999996 9999999999999999998742 232 223 88889988754321 11 45777888
Q ss_pred HHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCH-HH-HHHHHHHHHHhhCCCCcEEecCCceeecC
Q 022140 116 APVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGAL-FD-AALLSAVAAFSNLQIPTVSLDDGKIVMLP 193 (302)
Q Consensus 116 ~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l-~d-a~~~A~~~AL~~~~iP~~~~~~~~~~~~~ 193 (302)
+....+++.+.+++ .+|.-++....+-..+|..||-. -| .+++|+.+||.-..+|
T Consensus 129 EiL~~rLidrsirp----------lfp~g~~~etqi~~n~Ls~dG~~~pdvlainaas~Al~lsdvp------------- 185 (760)
T KOG1067|consen 129 EILTGRLIDRPIRP----------LFPKGFYHETQILCNVLSSDGVHDPDVLAINAASAALSLSDVP------------- 185 (760)
T ss_pred hheeeecccccccc----------CCcccchhHHHHHhhheecccccCchHHHHhHHHHHhhhccCC-------------
Confidence 88888989888876 24444444455556677888843 23 4789999999998888
Q ss_pred ccccccccCcCccccccccccCCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEEcCCCcEEEEEccCCcccChHHH
Q 022140 194 EEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLAYTSA 273 (302)
Q Consensus 194 ~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~~~g~i~~i~~~G~~~~~~~~~ 273 (302)
++....++.+|++++.++++||..|.+.++-.+.++.+ ..+++.++..+. .+..++
T Consensus 186 ---------------------w~gpig~vRigLi~Ge~vVNPT~kEmssS~Lnlvvagt-~~~~vmle~~s~-~i~qqd- 241 (760)
T KOG1067|consen 186 ---------------------WNGPIGAVRIGLIDGEFVVNPTRKEMSSSQLNLVVAGT-KSQTVMLEGSSN-NILQQD- 241 (760)
T ss_pred ---------------------CCCceeeeEeeeecceEEeCcchhhhhhccceeEEEec-cceEEEEEcccc-cccHHH-
Confidence 23444578999999999999999999998888888877 557888876654 456665
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcc
Q 022140 274 VQDCIALTRQRVKELHQILEEAISGM 299 (302)
Q Consensus 274 l~~~i~~A~~~~~~l~~~l~~~l~~~ 299 (302)
+.++++.+...++++..-+....+++
T Consensus 242 l~~Aikvg~~~~q~~i~~i~~L~k~~ 267 (760)
T KOG1067|consen 242 LLHAIKVGVKEAQQIIQGIERLAKKY 267 (760)
T ss_pred HHHHHHhccHHHHHHHHHHHHHHHHh
Confidence 99999999999999988877766553
No 26
>PF03725 RNase_PH_C: 3' exoribonuclease family, domain 2 This Prosite family only includes Ribonuclease PH; InterPro: IPR015847 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 2, which has a core 3-layer alpha/beta/alpha structure. 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 [].; GO: 0003723 RNA binding, 0006396 RNA processing; PDB: 1E3H_A 1E3P_A 2NN6_E 2WNR_A 3U1K_B 2BA0_H 2BA1_H 3M85_G 3M7N_H 3H1C_K ....
Probab=99.43 E-value=6.6e-13 Score=94.54 Aligned_cols=67 Identities=27% Similarity=0.509 Sum_probs=60.6
Q ss_pred CccEEEEEEEECCEEEECCChHHHhcCCceEEEEEcCCCcEEEEEccCCcc-cChHHHHHHHHHHHHHH
Q 022140 217 GIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAV-LAYTSAVQDCIALTRQR 284 (302)
Q Consensus 217 ~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~~~g~i~~i~~~G~~~-~~~~~~l~~~i~~A~~~ 284 (302)
++|+++|++++++.+++|||.+||+++++.++++++++++++.+.+.|+.. +++++ +.+|+++|+++
T Consensus 1 ~~~~avt~~~i~~~~v~Dpt~~Ee~~~~~~l~~~~~~~~~~~~~~~~~g~~~~~~~~-l~~~i~~A~~~ 68 (68)
T PF03725_consen 1 DPPVAVTVGIIDGELVVDPTAEEESLSDSSLTLAVDGTGNICTLQKSGGGSELSEDQ-LEEAIELAKKA 68 (68)
T ss_dssp SEEEEEEEEEETTEEEES--HHHHHHSSEEEEEEEETTSSEEEEEEEEESSEEEHHH-HHHHHHHHHHH
T ss_pred CCeEEEEEEEECCEEEECCCHHHHhhcCCcEEEEEECCCCEEEEEEcCCCCCCCHHH-HHHHHHHHhcC
Confidence 579999999999999999999999999999999999999999999998876 99996 99999999864
No 27
>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=86.49 E-value=0.46 Score=34.69 Aligned_cols=29 Identities=34% Similarity=0.243 Sum_probs=20.8
Q ss_pred ccHHHHhhhChHHHHHHHHhcCCCCCCCC
Q 022140 14 MEVDAFRRLFPLRYFERHLAESIRPDARS 42 (302)
Q Consensus 14 ~~~~~~~~~~p~~f~~~~l~~~~R~DGR~ 42 (302)
.-..+|..+.-...-...|..++|+|||+
T Consensus 55 ~i~~~~~~l~k~~vR~~Il~~~~R~DGR~ 83 (83)
T PF03726_consen 55 EIKEAFEELEKKIVREMILEEGIRIDGRK 83 (83)
T ss_dssp HHHHHHHHHHHHHHHHHHHCTSBTTTS-B
T ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCCCCC
Confidence 34456777777777777788899999995
No 28
>PF02575 YbaB_DNA_bd: YbaB/EbfC DNA-binding family; InterPro: IPR004401 The function of this protein is unknown. It is restricted to bacteria and a few plants, such as Arabidopsis. The plant form contains an additional N-terminal region that may serve as a transit peptide and shows a close relationship to the cyanobacterial member, suggesting that it is a chloroplast protein. Members of this family are found in a single copy per bacterial genome, but are broadly distributed. A crystal structure of one member, YbaB from Haemophilus influenzae, revealed a core structure consisting of two layers, alpha/beta; YbaB forms a tight dimer with a 3-layer structure, beta/alpha/beta []. YbaB is co-transcribed with RecR, which appears to protect DNA strands of the replilcation fork when it is blocked by DNA damage. A deletion of the YbaB operon resulted in increased sensitivity to DNA-damaging agents compared with the wild-type strain.; PDB: 1PUG_B 3F42_B 1YBX_B 1J8B_A.
Probab=62.88 E-value=54 Score=24.01 Aligned_cols=41 Identities=22% Similarity=0.254 Sum_probs=26.3
Q ss_pred cCCceEEEEEcCCCcEEEEEccCCcc--cChHHHHHHHHHHHHH
Q 022140 242 IMETLVTVVLDSSNQLVSLYKPGGAV--LAYTSAVQDCIALTRQ 283 (302)
Q Consensus 242 ~~~~~l~i~~~~~g~i~~i~~~G~~~--~~~~~~l~~~i~~A~~ 283 (302)
..++.++|.++.+|++..+....... .+++. |.++|-.|.+
T Consensus 27 s~~g~V~V~v~g~g~v~~i~i~~~~~~~~~~~~-L~~~I~~A~n 69 (93)
T PF02575_consen 27 SGDGLVTVTVNGNGEVVDIEIDPSALRPLDPEE-LEDLIVEAVN 69 (93)
T ss_dssp ETCCTEEEEEETTS-EEEEEE-GGGGCTS-HHH-HHHHHHHHHH
T ss_pred ECCCEEEEEEecCceEEEEEEehHhhccCCHHH-HHHHHHHHHH
Confidence 45678999999999999998655322 56664 6665555543
No 29
>PF07023 DUF1315: Protein of unknown function (DUF1315); InterPro: IPR009749 This family consists of several bacterial proteins of around 90 residues in length. The function of this family is unknown.
Probab=39.50 E-value=31 Score=25.81 Aligned_cols=35 Identities=20% Similarity=0.458 Sum_probs=27.0
Q ss_pred ccccHHHHhhhChHHHHHHHHhcCCCCCCCCCCC-CcceEEE
Q 022140 12 SEMEVDAFRRLFPLRYFERHLAESIRPDARSLSR-ARNTTIS 52 (302)
Q Consensus 12 ~~~~~~~~~~~~p~~f~~~~l~~~~R~DGR~~~e-~R~i~i~ 52 (302)
..|++++|.| ++.+++-|.-+|||.+.+ -|..+++
T Consensus 6 ~~mtPevY~r------L~~AVElGKWpDG~~LT~eQre~~mQ 41 (93)
T PF07023_consen 6 DSMTPEVYER------LKQAVELGKWPDGRALTPEQRESCMQ 41 (93)
T ss_pred HhCCHHHHHH------HHHHHHhCcCCCCCCCCHHHHHHHHH
Confidence 4688888874 678899999999999876 5555544
No 30
>PF09695 YtfJ_HI0045: Bacterial protein of unknown function (YtfJ_HI0045); InterPro: IPR006513 These are sequences from gammaproteobacteria that are related to the Escherichia coli protein, YtfJ.
Probab=37.32 E-value=74 Score=26.33 Aligned_cols=34 Identities=32% Similarity=0.458 Sum_probs=26.5
Q ss_pred ceEEEEEcCCCcEEEEEccCCcccChHHHHHHHHHHHH
Q 022140 245 TLVTVVLDSSNQLVSLYKPGGAVLAYTSAVQDCIALTR 282 (302)
Q Consensus 245 ~~l~i~~~~~g~i~~i~~~G~~~~~~~~~l~~~i~~A~ 282 (302)
+...|+++++|+|..+ +.| .+++++ +++.+++-+
T Consensus 125 ~SaiiVlDK~G~V~F~-k~G--~Ls~~E-v~qVi~Ll~ 158 (160)
T PF09695_consen 125 SSAIIVLDKQGKVQFV-KEG--ALSPAE-VQQVIALLK 158 (160)
T ss_pred CceEEEEcCCccEEEE-ECC--CCCHHH-HHHHHHHHh
Confidence 4567788999998877 457 789998 888887643
No 31
>COG3139 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.01 E-value=35 Score=24.79 Aligned_cols=29 Identities=17% Similarity=0.375 Sum_probs=22.3
Q ss_pred ccccHHHHhhhChHHHHHHHHhcCCCCCCCCCCCC
Q 022140 12 SEMEVDAFRRLFPLRYFERHLAESIRPDARSLSRA 46 (302)
Q Consensus 12 ~~~~~~~~~~~~p~~f~~~~l~~~~R~DGR~~~e~ 46 (302)
+.|.|++|.| +..+++-|.-+|||.+.+.
T Consensus 8 n~mtPEiYQr------L~~AvElGKWPdG~~Ltqe 36 (90)
T COG3139 8 NSMTPEIYQR------LSTAVELGKWPDGVALTQE 36 (90)
T ss_pred HhcCHHHHHH------HHHHHHhcCCCCCCcCCHH
Confidence 4577787765 4567788999999998764
No 32
>PRK00153 hypothetical protein; Validated
Probab=32.83 E-value=1.6e+02 Score=22.31 Aligned_cols=44 Identities=11% Similarity=0.037 Sum_probs=28.7
Q ss_pred hcCCceEEEEEcCCCcEEEEEccCCc--ccChHHHHHHHHHHHHHHH
Q 022140 241 SIMETLVTVVLDSSNQLVSLYKPGGA--VLAYTSAVQDCIALTRQRV 285 (302)
Q Consensus 241 ~~~~~~l~i~~~~~g~i~~i~~~G~~--~~~~~~~l~~~i~~A~~~~ 285 (302)
.+.++.++|.++.++++..+.-.-.. +-+++ .|.++|-.|.+.+
T Consensus 34 ~s~~G~V~V~v~G~~~v~~i~Id~~ll~~~d~e-~LedlI~~A~n~A 79 (104)
T PRK00153 34 EAGGGLVKVTMTGKKEVKRVKIDPSLVDPEDVE-MLEDLILAAFNDA 79 (104)
T ss_pred EECCCeEEEEEecCceEEEEEECHHHcCCcCHH-HHHHHHHHHHHHH
Confidence 34568899999999999999754321 12455 3666665554433
No 33
>PF12651 RHH_3: Ribbon-helix-helix domain
Probab=22.70 E-value=92 Score=19.65 Aligned_cols=31 Identities=16% Similarity=0.150 Sum_probs=24.1
Q ss_pred ccChHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 022140 267 VLAYTSAVQDCIALTRQRVKELHQILEEAISG 298 (302)
Q Consensus 267 ~~~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~ 298 (302)
.++.+ ++.++=++|.+......++++++|+.
T Consensus 8 ~l~~e-l~~~L~~ls~~t~i~~S~Ll~eAle~ 38 (44)
T PF12651_consen 8 SLDKE-LYEKLKELSEETGIPKSKLLREALED 38 (44)
T ss_pred ecCHH-HHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence 56777 58888889988887777777777764
No 34
>KOG4690 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.49 E-value=1.6e+02 Score=23.76 Aligned_cols=79 Identities=27% Similarity=0.434 Sum_probs=54.3
Q ss_pred HHhhhChHHHHHHHH-----hcCCCCCCCCCCCCcceEEEeCCccCCCe-eEEEEeC-CeEEEEEEEeeeccCCCCCCC-
Q 022140 18 AFRRLFPLRYFERHL-----AESIRPDARSLSRARNTTISMGAVASADG-SALAKIG-STTMLAAIKMEVMTPSLESPD- 89 (302)
Q Consensus 18 ~~~~~~p~~f~~~~l-----~~~~R~DGR~~~e~R~i~i~~g~l~~a~G-Sa~v~~G-~T~Vi~~V~~~v~~p~~~~p~- 89 (302)
.+-++.|..|+.+++ .++.-.|--++.+.|...+..+.+..-+- ++.-.+| .++.+++|..+ |.++.|.
T Consensus 9 l~~~~~~~r~~tr~~~L~~~fe~~~q~~~~~~~e~~~~V~~~~~E~~p~~~~S~~~~N~~kk~~GV~VP---PkPEEP~n 85 (165)
T KOG4690|consen 9 LLYRIYPVRRFTRYSRLDMTFEGNTQDISTSVEERMTTVFGGRLEGEPPRSTSRVLSNGTKKIAGVQVP---PKPEEPDN 85 (165)
T ss_pred hhHhhhhHHHHhhhcchhhhhccccCCCCchHHhhcCceeeeeecCCCchhhhhhccCCceeeeeeeCC---CCCCCccc
Confidence 456788888888875 35777888888898888888876654322 2333344 48999999864 6666664
Q ss_pred ---cceEEEEEec
Q 022140 90 ---EGCVSIDFHM 99 (302)
Q Consensus 90 ---~g~l~v~V~~ 99 (302)
.|.+.|-.++
T Consensus 86 CC~SGCv~CVWDV 98 (165)
T KOG4690|consen 86 CCMSGCVNCVWDV 98 (165)
T ss_pred chhhccceeehHh
Confidence 3777776653
No 35
>COG3054 Predicted transcriptional regulator [General function prediction only]
Probab=20.15 E-value=2.3e+02 Score=23.40 Aligned_cols=49 Identities=27% Similarity=0.343 Sum_probs=33.7
Q ss_pred EEEECCChHHHh----cCCceEEEEEcCCCcEEEEEccCCcccChHHHHHHHHHHHH
Q 022140 230 YILADPTSEEES----IMETLVTVVLDSSNQLVSLYKPGGAVLAYTSAVQDCIALTR 282 (302)
Q Consensus 230 ~~l~DPt~~Ee~----~~~~~l~i~~~~~g~i~~i~~~G~~~~~~~~~l~~~i~~A~ 282 (302)
.+++|-...--. ...+...|++++.|++..+ +.| .++..+ +++.+.+-.
T Consensus 128 q~vlD~~gvak~AWqL~e~~SaivVlDk~G~Vkfv-keG--aLt~ae-vQ~Vi~ll~ 180 (184)
T COG3054 128 QFVLDSNGVAKNAWQLKEESSAVVVLDKDGRVKFV-KEG--ALTQAE-VQQVIDLLQ 180 (184)
T ss_pred eeEEccchhhhhhhccccccceEEEEcCCCcEEEE-ecC--CccHHH-HHHHHHHHH
Confidence 467776653221 1245788999999999887 456 678887 888877643
No 36
>PF09866 DUF2093: Uncharacterized protein conserved in bacteria (DUF2093); InterPro: IPR018661 This family of various hypothetical prokaryotic proteins has no known function.
Probab=20.01 E-value=71 Score=20.13 Aligned_cols=11 Identities=9% Similarity=0.105 Sum_probs=9.6
Q ss_pred CeEEEEEEEee
Q 022140 69 STTMLAAIKME 79 (302)
Q Consensus 69 ~T~Vi~~V~~~ 79 (302)
++.|+|+|+|+
T Consensus 5 G~~V~CAVTg~ 15 (42)
T PF09866_consen 5 GSFVRCAVTGQ 15 (42)
T ss_pred CCEEEEEeeCC
Confidence 67899999995
Done!