Query 043337
Match_columns 465
No_of_seqs 204 out of 1199
Neff 6.0
Searched_HMMs 46136
Date Fri Mar 29 04:02:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043337.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043337hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1614 Exosomal 3'-5' exoribo 100.0 3.3E-63 7.1E-68 472.2 30.1 286 6-294 1-286 (291)
2 COG2123 RNase PH-related exori 100.0 1E-54 2.2E-59 422.9 31.0 266 7-278 3-271 (272)
3 PRK04282 exosome complex RNA-b 100.0 6.7E-53 1.5E-57 418.7 33.2 261 10-278 7-270 (271)
4 KOG1613 Exosomal 3'-5' exoribo 100.0 1.2E-45 2.6E-50 351.5 16.6 268 5-274 14-297 (298)
5 PRK00173 rph ribonuclease PH; 100.0 1.4E-41 3.1E-46 332.0 28.4 227 27-278 1-237 (238)
6 PRK03983 exosome complex exonu 100.0 2.5E-40 5.4E-45 324.2 29.4 226 21-284 8-239 (244)
7 TIGR01966 RNasePH ribonuclease 100.0 2E-40 4.3E-45 323.5 28.4 225 28-277 1-235 (236)
8 TIGR02065 ECX1 archaeal exosom 100.0 1E-39 2.2E-44 317.3 28.3 220 23-280 4-229 (230)
9 KOG1612 Exosomal 3'-5' exoribo 100.0 1.8E-39 3.9E-44 311.5 26.1 269 8-279 2-276 (288)
10 TIGR03591 polynuc_phos polyrib 100.0 6.5E-33 1.4E-37 306.1 30.3 229 23-286 306-547 (684)
11 PRK11824 polynucleotide phosph 100.0 2.3E-32 4.9E-37 302.4 29.9 226 23-283 310-547 (693)
12 COG0689 Rph RNase PH [Translat 100.0 1.1E-30 2.4E-35 252.0 22.2 216 24-277 5-229 (230)
13 PRK11824 polynucleotide phosph 100.0 8.3E-31 1.8E-35 290.0 24.3 243 37-330 13-282 (693)
14 TIGR03591 polynuc_phos polyrib 100.0 1.8E-30 3.9E-35 286.8 26.4 243 38-330 5-275 (684)
15 KOG1068 Exosomal 3'-5' exoribo 100.0 3.5E-30 7.6E-35 248.1 19.2 224 24-285 10-240 (245)
16 PLN00207 polyribonucleotide nu 100.0 1.6E-28 3.4E-33 273.3 30.2 230 17-283 427-678 (891)
17 TIGR02696 pppGpp_PNP guanosine 99.9 5.4E-26 1.2E-30 248.6 25.4 224 21-280 329-569 (719)
18 KOG1067 Predicted RNA-binding 99.9 7.4E-27 1.6E-31 243.6 13.7 252 35-337 53-334 (760)
19 PLN00207 polyribonucleotide nu 99.9 1.1E-25 2.3E-30 250.8 21.4 243 38-330 89-358 (891)
20 TIGR02696 pppGpp_PNP guanosine 99.9 1.3E-23 2.7E-28 230.1 23.5 245 38-330 17-305 (719)
21 KOG1069 Exosomal 3'-5' exoribo 99.9 1.6E-23 3.5E-28 195.9 18.5 199 36-279 4-210 (217)
22 PF01138 RNase_PH: 3' exoribon 99.9 9.5E-24 2.1E-28 187.1 16.2 125 36-168 1-132 (132)
23 COG1185 Pnp Polyribonucleotide 99.8 1.7E-18 3.7E-23 186.6 18.3 243 37-331 13-283 (692)
24 KOG1067 Predicted RNA-binding 99.7 2.1E-16 4.6E-21 165.9 16.5 223 14-279 345-586 (760)
25 COG1185 Pnp Polyribonucleotide 99.4 3.1E-12 6.8E-17 138.6 14.8 230 23-289 308-551 (692)
26 PF03725 RNase_PH_C: 3' exorib 99.3 2.5E-11 5.4E-16 96.1 8.7 67 197-265 1-68 (68)
27 PF03726 PNPase: Polyribonucle 48.0 12 0.00026 30.6 1.7 11 23-33 73-83 (83)
28 PF02575 YbaB_DNA_bd: YbaB/Ebf 47.6 1.1E+02 0.0023 25.3 7.5 45 225-269 28-74 (93)
29 PF12075 KN_motif: KN motif; 25.9 27 0.00058 25.1 0.4 14 374-387 7-20 (39)
30 PRK00153 hypothetical protein; 20.3 2.8E+02 0.0061 23.6 5.7 44 224-267 35-80 (104)
No 1
>KOG1614 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp45 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.3e-63 Score=472.21 Aligned_cols=286 Identities=57% Similarity=0.932 Sum_probs=278.7
Q ss_pred cCCCcCCccHHHHHHHHHhcCCCCCCCCCCCCcceEEEecCCCceEEEEeCCeEEEEEEEeecccCCCCCCCcceEEEEE
Q 043337 6 ANTWRLTVNEKRFIETALSSGIRIDGRNPFEYRKLSIKFGREDGSSEVQLGQTHIMGFVTGQLVQPYRDRPNEGTLSIFT 85 (465)
Q Consensus 6 ~~~~~lS~~e~~fi~~~L~~giR~DGR~~~e~R~I~I~~G~AdGSA~V~~G~T~Vi~~V~~ei~~P~~~rp~eG~L~v~V 85 (465)
++.|.+|.+|+.|+.++|+.|.|.|||++.|||.+.|++|+..||+.|++|+|+|||.|+.++.+|+.+||.+|.+.+.+
T Consensus 1 ~r~~~~t~~e~~fvl~alk~g~R~DgR~l~efR~lei~fGke~gs~~vt~G~Tkvm~~vt~~ia~Py~dRP~eG~~~I~t 80 (291)
T KOG1614|consen 1 ARMWELTVNESKFVLNALKAGLRFDGRSLEEFRDLEIEFGKEYGSVLVTMGNTKVMARVTAQIAQPYIDRPHEGSFSIFT 80 (291)
T ss_pred CCccccccchHHHHHHHHHhcccccccchhhhhceEEEeccccccEEEEecCeeEEEEeehhhcCcccCCCCCCeeeeee
Confidence 35799999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EeCCCCCCCccCCCCChhHHHHHHHHHhhhccccccccccceeecCceeEEEEEEEEEEcCCCCHHHHHHHHHHHHHhhC
Q 043337 86 EFSPMADPSFETGRPSESAVELGRIVDRGLRESRAVDTESLCVLAGKLVWAIRIDLHILDNGGNLVDAANIAALASLLTF 165 (465)
Q Consensus 86 d~sp~as~~~~~g~~se~e~~lsrlL~r~Lr~s~~idlesLcI~pg~~~w~I~IdV~VL~~DGnllDaa~~Aa~aAL~da 165 (465)
+++|+|+++|++|+.++.+.+++|+|++++|.|++||+|+|||..|+.+|.|++|+++|+.|||++||+++|+.+||+++
T Consensus 81 elsPmA~~sfE~Gr~~~~~v~l~Rliek~~R~S~aiD~EsLCI~aG~kvW~IRiDlhiLd~DGnlvDaA~iAviaaL~hF 160 (291)
T KOG1614|consen 81 ELSPMASPSFEPGRKGESEVELSRLIEKALRRSKAIDTESLCIRAGEKVWLIRIDLHILDHDGNLVDAACIAVIAALMHF 160 (291)
T ss_pred ccccccccccCCCCccchHHHHHHHHHHHHHhccccchHHHHhhhCCeEEEEEEEEEEEcCCCCeehhHHHHHHHHHHhc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCcccCCCCCceeEeCCCCCCCCCccccccccEEEEEEEECCccEEEEcCCHHHHHcCcceEEEEEcCCCCEEEEEcc
Q 043337 166 RRPECSLGGEDDLEVIVHPPEEREPLPLIIHHLPIAVTFGFFSSESLLVIDPTHHEEAVMVGKMTATLNANGDVCAIQKP 245 (465)
Q Consensus 166 ~IP~v~~~~~dG~~v~i~~~~~~~~~pL~i~~lPiavT~gli~~~~~iLvDPT~~EE~~s~~~LtVa~~~~g~I~~i~k~ 245 (465)
+.|.+++.| .+++||+.++++|+||+|+|+|+|+|||+|+.|..+|+|||..||.++++.++|++|++.+||.+++.
T Consensus 161 rrPdvTv~g---~ev~ihp~eEr~PvPL~I~HmPIC~tf~ffnkG~ivviDpt~~Ee~~~dGs~vVt~Nk~rEVc~i~k~ 237 (291)
T KOG1614|consen 161 RRPDVTVGG---EEVIIHPVEEREPVPLSIHHMPICFTFGFFNKGEIVVIDPTEKEEAVMDGSMVVTMNKNREVCAIQKS 237 (291)
T ss_pred CCCCccccc---ceeEecChhccCCcceeeeeccceEEEEEecCceEEEeCCcHHHHhccCceEEEEEcCCccEEEEecC
Confidence 999999864 68999999999999999999999999999998779999999999999999999999999999999999
Q ss_pred CCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHhhhhccCCC
Q 043337 246 GGEGVLQSVIMQCLRLASRMASDITKKIKDAVETYNTERALRKIKRHPT 294 (465)
Q Consensus 246 Gg~~is~~~L~~~i~~A~~~a~~I~~~I~~~l~~~~~er~~~~~k~~~~ 294 (465)
|+..+++.++++|.++|...+.++...|.++|+++..+|..++.++++.
T Consensus 238 G~~~~~~~~i~~C~k~A~~~a~~vt~ii~e~l~~d~~~r~~~~~~~~~~ 286 (291)
T KOG1614|consen 238 GGEILDESVIERCYKLAKDRAVEVTGIILEALEEDQRERSAQKVKTAGT 286 (291)
T ss_pred CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhccccc
Confidence 9999999999999999999999999999999999999999999988765
No 2
>COG2123 RNase PH-related exoribonuclease [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1e-54 Score=422.89 Aligned_cols=266 Identities=43% Similarity=0.715 Sum_probs=249.4
Q ss_pred CCCcCCccHHHHHHHHHhcCCCCCCCCCCCCcceEEEec---CCCceEEEEeCCeEEEEEEEeecccCCCCCCCcceEEE
Q 043337 7 NTWRLTVNEKRFIETALSSGIRIDGRNPFEYRKLSIKFG---REDGSSEVQLGQTHIMGFVTGQLVQPYRDRPNEGTLSI 83 (465)
Q Consensus 7 ~~~~lS~~e~~fi~~~L~~giR~DGR~~~e~R~I~I~~G---~AdGSA~V~~G~T~Vi~~V~~ei~~P~~~rp~eG~L~v 83 (465)
..-.++...+.|+...|+.|+|+|||.++|||+|.|++| +|+|||+|++|+|+|+|+|+.++++|++++|++|.+.+
T Consensus 3 ~~~~~~~~~~~~i~~ll~~g~R~DGR~~~efR~ieI~~~vi~ka~GSa~VklG~Tqvv~gvK~eig~Pf~DtP~eG~~~~ 82 (272)
T COG2123 3 MSEIISEIKREYILNLLKKGIRIDGRSFDEFRPLEIETGVIPKANGSALVKLGNTQVVVGVKAEIGEPFPDTPNEGVLVV 82 (272)
T ss_pred cchhhhhhHHHHHHHHhccCcccCCCCcccccceEEEeCceecCCCcEEEEecCeEEEEEEEcccCCCCCCCCCCceEEe
Confidence 345678889999999999999999999999999999999 59999999999999999999999999999999999999
Q ss_pred EEEeCCCCCCCccCCCCChhHHHHHHHHHhhhccccccccccceeecCceeEEEEEEEEEEcCCCCHHHHHHHHHHHHHh
Q 043337 84 FTEFSPMADPSFETGRPSESAVELGRIVDRGLRESRAVDTESLCVLAGKLVWAIRIDLHILDNGGNLVDAANIAALASLL 163 (465)
Q Consensus 84 ~Vd~sp~as~~~~~g~~se~e~~lsrlL~r~Lr~s~~idlesLcI~pg~~~w~I~IdV~VL~~DGnllDaa~~Aa~aAL~ 163 (465)
|+++.|+|++.|++|++++.+++++|+++|.||.++.+|+++|||.+|+++|.|++|++||++|||++||+++|+++||+
T Consensus 83 n~El~Plas~~fE~Gppde~aielsrvvdr~lr~s~aiDlekL~I~~g~kvwvv~vDv~vld~DGnl~Da~~lA~~aAL~ 162 (272)
T COG2123 83 NVELSPLASPSFEPGPPDELAIELSRVVDRGLRESKAIDLEKLCIEEGKKVWVVFVDVHVLDYDGNLIDAASLAAVAALL 162 (272)
T ss_pred eeeeeccccccccCCCCchhHHHHHHHHHHHHHhccCcchhheeEecCCEEEEEEEEEEEEcCCCCHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hCCCCCcccCCCCCceeEeCCCCCCCCCccccccccEEEEEEEECCccEEEEcCCHHHHHcCcceEEEEEcCCCCEEEEE
Q 043337 164 TFRRPECSLGGEDDLEVIVHPPEEREPLPLIIHHLPIAVTFGFFSSESLLVIDPTHHEEAVMVGKMTATLNANGDVCAIQ 243 (465)
Q Consensus 164 da~IP~v~~~~~dG~~v~i~~~~~~~~~pL~i~~lPiavT~gli~~~~~iLvDPT~~EE~~s~~~LtVa~~~~g~I~~i~ 243 (465)
++++|+..+.++ | ..+....+ ++.||.+.++|+++||+++++ .+|+|||.+||..+++.++|.++++|+||+++
T Consensus 163 ~t~vP~~~~~~~-~--~~v~~~~~-~~~pl~~~~~pi~vt~a~ig~--~lvvDPsleEe~v~d~~ltit~~~~~~Iv~iq 236 (272)
T COG2123 163 NTRVPKAVEVGD-G--EIVIEVEE-EPVPLPVSNPPISVTFAKIGN--VLVVDPSLEEELVADGRLTITVNEDGEIVAIQ 236 (272)
T ss_pred hcCCCceeecCC-c--ceeecccC-CCcccccCCCceEEEEEEECC--EEEeCCCcchhhhcCceEEEEECCCCcEEEEE
Confidence 999998766532 2 22332233 778899999999999999998 99999999999999999999999999999999
Q ss_pred ccCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043337 244 KPGGEGVLQSVIMQCLRLASRMASDITKKIKDAVE 278 (465)
Q Consensus 244 k~Gg~~is~~~L~~~i~~A~~~a~~I~~~I~~~l~ 278 (465)
+.|+..+++..+.+|++.|...+.++...+.++|+
T Consensus 237 K~g~~~~~~~~~~~~~~~A~~~~~kl~~~~~~~L~ 271 (272)
T COG2123 237 KVGGGSITESDLEKALKTALSKAEKLREALKEALK 271 (272)
T ss_pred EcCCCcCCHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 99999999999999999999999999999998875
No 3
>PRK04282 exosome complex RNA-binding protein Rrp42; Provisional
Probab=100.00 E-value=6.7e-53 Score=418.74 Aligned_cols=261 Identities=39% Similarity=0.659 Sum_probs=245.3
Q ss_pred cCCccHHHHHHHHHhcCCCCCCCCCCCCcceEEEecC---CCceEEEEeCCeEEEEEEEeecccCCCCCCCcceEEEEEE
Q 043337 10 RLTVNEKRFIETALSSGIRIDGRNPFEYRKLSIKFGR---EDGSSEVQLGQTHIMGFVTGQLVQPYRDRPNEGTLSIFTE 86 (465)
Q Consensus 10 ~lS~~e~~fi~~~L~~giR~DGR~~~e~R~I~I~~G~---AdGSA~V~~G~T~Vi~~V~~ei~~P~~~rp~eG~L~v~Vd 86 (465)
.+|..|++|++++|++|+|+|||+++++|++.|++|. ++|||+|++|+|+|+|+|++++..|..++|++|.|.++|+
T Consensus 7 ~~~~~e~~~i~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~vl~~V~~~~~~p~~~~~~~g~i~~~v~ 86 (271)
T PRK04282 7 IIPEIKKDYILSLLKKGKRIDGRKLDEYRPIEIETGVIKKAEGSALVKLGNTQVLAGVKLEIGEPFPDTPNEGVLIVNAE 86 (271)
T ss_pred hhhHHHHHHHHHHHhcCCCCCCCCCccccCeEEEeCCccCCCcEEEEEECCCEEEEEEEEEEecCCCCCCCCCEEEEEEE
Confidence 3799999999999999999999999999999999994 9999999999999999999998888888899999999999
Q ss_pred eCCCCCCCccCCCCChhHHHHHHHHHhhhccccccccccceeecCceeEEEEEEEEEEcCCCCHHHHHHHHHHHHHhhCC
Q 043337 87 FSPMADPSFETGRPSESAVELGRIVDRGLRESRAVDTESLCVLAGKLVWAIRIDLHILDNGGNLVDAANIAALASLLTFR 166 (465)
Q Consensus 87 ~sp~as~~~~~g~~se~e~~lsrlL~r~Lr~s~~idlesLcI~pg~~~w~I~IdV~VL~~DGnllDaa~~Aa~aAL~da~ 166 (465)
++|++.+.|+.+++++.+++++++|+++|+++..+|+++|||+||+++|.|+|+|+||++|||++|||++|+++||+|++
T Consensus 87 ~~~~a~~~~~~~~~~~~~~~l~~~l~r~l~~~~~~dl~~L~I~~g~~~w~i~Vdv~VL~~dG~~~daa~~Aa~aAL~~~~ 166 (271)
T PRK04282 87 LLPLASPTFEPGPPDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWVVFIDVYVLDHDGNLLDASMLAAVAALLNTK 166 (271)
T ss_pred ECCCcCccccCCCCCHHHHHHHHHHHHHHhccCCccHHHcEEecCcEEEEEEEEEEEECCCCCHHHHHHHHHHHHHHhCC
Confidence 99999998888889999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCcccCCCCCceeEeCCCCCCCCCccccccccEEEEEEEECCccEEEEcCCHHHHHcCcceEEEEEcCCCCEEEEEccC
Q 043337 167 RPECSLGGEDDLEVIVHPPEEREPLPLIIHHLPIAVTFGFFSSESLLVIDPTHHEEAVMVGKMTATLNANGDVCAIQKPG 246 (465)
Q Consensus 167 IP~v~~~~~dG~~v~i~~~~~~~~~pL~i~~lPiavT~gli~~~~~iLvDPT~~EE~~s~~~LtVa~~~~g~I~~i~k~G 246 (465)
||.+.+.+++ + +. ++.+..||.|+++|+++|||++++ .+|+|||.+||+++++.++|+++++|+||++++.|
T Consensus 167 iP~~~~~~~~---~-~~--~~~~~~~l~~~~~p~~vt~~~~~~--~~v~Dpt~~Ee~~~~~~l~va~~~~g~i~~l~~~g 238 (271)
T PRK04282 167 VPAVEEGEDG---V-VD--KLGEDFPLPVNDKPVTVTFAKIGN--YLIVDPTLEEESVMDARITITTDEDGNIVAIQKSG 238 (271)
T ss_pred CCcEEEcCCc---e-ec--cCCCcccCCCCCeeEEEEEEEECC--EEEECCCHHHHhhcCceEEEEECCCCcEEEEEcCC
Confidence 9999886422 2 22 355678899999999999999987 89999999999999999999999999999999999
Q ss_pred CCccCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043337 247 GEGVLQSVIMQCLRLASRMASDITKKIKDAVE 278 (465)
Q Consensus 247 g~~is~~~L~~~i~~A~~~a~~I~~~I~~~l~ 278 (465)
+++++.++|.+|+++|.+++++|+++|++++.
T Consensus 239 ~~~~~~~~l~~~i~~A~~~~~~l~~~~~~~l~ 270 (271)
T PRK04282 239 IGSFTEEEVDKAIDIALEKAKELREKLKEALG 270 (271)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 88999999999999999999999999999874
No 4
>KOG1613 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp43 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.2e-45 Score=351.50 Aligned_cols=268 Identities=24% Similarity=0.452 Sum_probs=233.4
Q ss_pred ccCCCcCCccHHHHHHHHHhcCCCCCCCCCCCCcceEEEecC---CCceEEEEeCCeEEEEEEEeecccCCCCCCCcceE
Q 043337 5 LANTWRLTVNEKRFIETALSSGIRIDGRNPFEYRKLSIKFGR---EDGSSEVQLGQTHIMGFVTGQLVQPYRDRPNEGTL 81 (465)
Q Consensus 5 m~~~~~lS~~e~~fi~~~L~~giR~DGR~~~e~R~I~I~~G~---AdGSA~V~~G~T~Vi~~V~~ei~~P~~~rp~eG~L 81 (465)
|+++++-.+.|..|++++|.+++|+|||.+.+||.+.|..|. ||||++++.|+|.|+|+|++++.+|..+.|++|.|
T Consensus 14 f~p~~fkrI~Pe~~l~rhLse~~RpdgR~lgefRdt~in~g~IsTangSal~K~G~ttvi~~Ik~ei~epstdapdeg~I 93 (298)
T KOG1613|consen 14 FPPEVFKRISPELYLQRHLSEGIRPDGRKLGEFRDTAINAGNISTANGSALLKSGKTTVICGIKAEIAEPSTDAPDEGDI 93 (298)
T ss_pred cCHHHHhhcCHHHHHHHHhhcccCcchhhhhHHhhhheecCceeccCcHHHHhcCCcEEEEEeeeeecccccCCCCCcce
Confidence 667778889999999999999999999999999999999994 99999999999999999999999999999999999
Q ss_pred EEEEEeCCCCCCCccCCCCChhHHHHHHHHHhhhccccccccccceeecCceeEEEEEEEEEEcCCCCHHHHHHHHHHHH
Q 043337 82 SIFTEFSPMADPSFETGRPSESAVELGRIVDRGLRESRAVDTESLCVLAGKLVWAIRIDLHILDNGGNLVDAANIAALAS 161 (465)
Q Consensus 82 ~v~Vd~sp~as~~~~~g~~se~e~~lsrlL~r~Lr~s~~idlesLcI~pg~~~w~I~IdV~VL~~DGnllDaa~~Aa~aA 161 (465)
..+++++|.+++.|++|+|+++++.+++.|...|.+|++|+++.|||++|++.|.+|+||.||++||+++|+|++|+++|
T Consensus 94 v~n~~lpplcs~r~RpG~p~dea~viSq~LhdtIl~S~ii~~k~Lci~~gKaawvlYadIicLd~dG~~fDa~w~al~aA 173 (298)
T KOG1613|consen 94 VPNYALPPLCSSRFRPGPPTDEAQVISQKLHDTILHSRIIPKKALCIKAGKAAWVLYADIICLDYDGPVFDACWNALMAA 173 (298)
T ss_pred eecccCCcccccCCCCCCCchHHHHHHHHHHHHHHhcCCcchhhheeeccceeeEEEEEEEEEcCCCcHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhCCCCCcccCCCCCcee--Ee----CCCCCCCCCccccccccE-----EEEEE-EECCccEEEEcCCHHHHHcCcceE
Q 043337 162 LLTFRRPECSLGGEDDLEV--IV----HPPEEREPLPLIIHHLPI-----AVTFG-FFSSESLLVIDPTHHEEAVMVGKM 229 (465)
Q Consensus 162 L~da~IP~v~~~~~dG~~v--~i----~~~~~~~~~pL~i~~lPi-----avT~g-li~~~~~iLvDPT~~EE~~s~~~L 229 (465)
|.+.++|.+.|+. ++..+ ++ ++..-..+.-|+....++ ..++. ++++ ..++.|||.+||..+++.+
T Consensus 174 lknvklP~a~ide-~~~~~~~t~e~~ic~~tlt~p~~ln~e~r~~~~~n~~fS~~~vl~~-~li~adpT~eEE~l~~~~l 251 (298)
T KOG1613|consen 174 LKNVKLPRAFIDE-RASDLRMTIEEIICDQTLTVPLMLNAENRAFASQNSDFSEEEVLDD-VLIAADPTEEEETLITSTL 251 (298)
T ss_pred HhcCCCceeeecc-cchhhhhhHHHHHHhhhhcchhhhccccccccccCCCccHHHhhcc-eeEecCCCchhhhhhhceE
Confidence 9999999998874 33222 11 111111222333333333 33444 6665 2556999999999999999
Q ss_pred EEEEcCCCCEEEEEccCCCccCH-HHHHHHHHHHHHHHHHHHHHHH
Q 043337 230 TATLNANGDVCAIQKPGGEGVLQ-SVIMQCLRLASRMASDITKKIK 274 (465)
Q Consensus 230 tVa~~~~g~I~~i~k~Gg~~is~-~~L~~~i~~A~~~a~~I~~~I~ 274 (465)
+|++++.|++|.+.+.||+.+.. +.|.+|+++|..+++++-+.+.
T Consensus 252 TIvldss~n~v~l~k~GG~al~~~~~iK~c~elar~Rakelk~~~~ 297 (298)
T KOG1613|consen 252 TIVLDSSGNYVQLTKVGGGALITPEMIKRCLELARVRAKELKTRFN 297 (298)
T ss_pred EEEEcCCCCEEEEEecCcccccCHHHHHHHHHHHHHHHHHHHHHhc
Confidence 99999999999999999877665 8999999999999999877653
No 5
>PRK00173 rph ribonuclease PH; Reviewed
Probab=100.00 E-value=1.4e-41 Score=332.02 Aligned_cols=227 Identities=21% Similarity=0.271 Sum_probs=198.5
Q ss_pred CCCCCCCCCCCcceEEEec---CCCceEEEEeCCeEEEEEEEeecccCCC-CCCCcceEEEEEEeCCCCCCCcc-----C
Q 043337 27 IRIDGRNPFEYRKLSIKFG---REDGSSEVQLGQTHIMGFVTGQLVQPYR-DRPNEGTLSIFTEFSPMADPSFE-----T 97 (465)
Q Consensus 27 iR~DGR~~~e~R~I~I~~G---~AdGSA~V~~G~T~Vi~~V~~ei~~P~~-~rp~eG~L~v~Vd~sp~as~~~~-----~ 97 (465)
+|+|||+++++|++.|++| .|+|||+|++|+|+|+|+|++++..|.. ..+++|+|.|+|+++|++++.+. .
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 5999999999999999999 4999999999999999999999887754 34678999999999999988762 4
Q ss_pred CCCChhHHHHHHHHHhhhccccccccccceeecCceeEEEEEEEEEEcCCCCHHHHHHHHHHHHHhhCCCCCcccCCCCC
Q 043337 98 GRPSESAVELGRIVDRGLRESRAVDTESLCVLAGKLVWAIRIDLHILDNGGNLVDAANIAALASLLTFRRPECSLGGEDD 177 (465)
Q Consensus 98 g~~se~e~~lsrlL~r~Lr~s~~idlesLcI~pg~~~w~I~IdV~VL~~DGnllDaa~~Aa~aAL~da~IP~v~~~~~dG 177 (465)
|++++++++++++|+|+|++ +||++.| ++ ++|+|+++||++|||++|||++|+++||+|++++. . ++|
T Consensus 81 g~~~~~~~~~sr~i~r~lr~--~i~l~~l----~~--~~i~v~v~VL~~DG~~~~aai~Aa~~AL~da~~~~---~-~~~ 148 (238)
T PRK00173 81 GKQGGRTQEIQRLIGRSLRA--VVDLKAL----GE--RTITIDCDVIQADGGTRTASITGAYVALADALNKL---V-ARG 148 (238)
T ss_pred CCCCccHHHHHHHHHHHHHH--hcCHHHc----CC--eEEEEEEEEEeCCCCHHHHHHHHHHHHHHHhhhhh---h-ccC
Confidence 67788899999999999997 6999987 23 35666778899999999999999999999998541 1 111
Q ss_pred ceeEeCCCCCCCCCccccccccEEEEEEEECCccEEEEcCCHHHHHcCcceEEEEEcCCCCEEEEEccC-CCccCHHHHH
Q 043337 178 LEVIVHPPEEREPLPLIIHHLPIAVTFGFFSSESLLVIDPTHHEEAVMVGKMTATLNANGDVCAIQKPG-GEGVLQSVIM 256 (465)
Q Consensus 178 ~~v~i~~~~~~~~~pL~i~~lPiavT~gli~~~~~iLvDPT~~EE~~s~~~LtVa~~~~g~I~~i~k~G-g~~is~~~L~ 256 (465)
+..++.|+++|+++|||++++ .+|+|||.+||+++++.|+|++++.|+||++++.| +..++.++|.
T Consensus 149 -----------~~~~ip~~~~~~~vt~~~~~~--~~lvDpt~~Ee~~~~~~l~v~~~~~~~i~~v~~~g~g~~~~~e~l~ 215 (238)
T PRK00173 149 -----------KLKKNPLKDQVAAVSVGIVDG--EPVLDLDYEEDSAAETDMNVVMTGSGGFVEVQGTAEGAPFSREELD 215 (238)
T ss_pred -----------cccCCcccCceeEEEEEEECC--EEEECCCHHHHhcCCceEEEEECCCCCEEEEEccCCCCCcCHHHHH
Confidence 122345789999999999997 89999999999999999999999989999999954 5689999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 043337 257 QCLRLASRMASDITKKIKDAVE 278 (465)
Q Consensus 257 ~~i~~A~~~a~~I~~~I~~~l~ 278 (465)
+|+++|.+++++|+++++++|+
T Consensus 216 ~~i~~A~~~~~~l~~~~~~~l~ 237 (238)
T PRK00173 216 ALLDLAEKGIAELVALQKAALA 237 (238)
T ss_pred HHHHHHHHHHHHHHHHHHHHhc
Confidence 9999999999999999999875
No 6
>PRK03983 exosome complex exonuclease Rrp41; Provisional
Probab=100.00 E-value=2.5e-40 Score=324.16 Aligned_cols=226 Identities=20% Similarity=0.323 Sum_probs=200.4
Q ss_pred HHHhcCCCCCCCCCCCCcceEEEecC---CCceEEEEeCCeEEEEEEEeec--ccCCCCCCCcceEEEEEEeCCCCCCCc
Q 043337 21 TALSSGIRIDGRNPFEYRKLSIKFGR---EDGSSEVQLGQTHIMGFVTGQL--VQPYRDRPNEGTLSIFTEFSPMADPSF 95 (465)
Q Consensus 21 ~~L~~giR~DGR~~~e~R~I~I~~G~---AdGSA~V~~G~T~Vi~~V~~ei--~~P~~~rp~eG~L~v~Vd~sp~as~~~ 95 (465)
.++.+|+|+|||.++++|++.|++|. ++|||++++|+|+|+|+|+|+. ..|...+|++|.|.++++++|++...+
T Consensus 8 ~~~~~~~R~DGR~~~~~R~i~i~~G~l~~a~GSa~v~~G~T~Vl~~V~gp~e~~~~~~~~~~~~~l~v~~~~~p~~~~~~ 87 (244)
T PRK03983 8 LILEDGLRLDGRKPDELRPIKIEVGVLKNADGSAYLEWGNNKIIAAVYGPREMHPRHLQLPDRAVLRVRYNMAPFSVDER 87 (244)
T ss_pred hhccCCCCCCCCCcCcccceEEEeCCCCCCCeEEEEEECCeEEEEEEecCCccccccccCCCcEEEEEEEEcCCCccccc
Confidence 34778999999999999999999994 9999999999999999999864 345556788999999999999988655
Q ss_pred cCCCCChhHHHHHHHHHhhhccccccccccceeecCceeEEEEEEEEEEcCCCCHHHHHHHHHHHHHhhCCCCCcccCCC
Q 043337 96 ETGRPSESAVELGRIVDRGLRESRAVDTESLCVLAGKLVWAIRIDLHILDNGGNLVDAANIAALASLLTFRRPECSLGGE 175 (465)
Q Consensus 96 ~~g~~se~e~~lsrlL~r~Lr~s~~idlesLcI~pg~~~w~I~IdV~VL~~DGnllDaa~~Aa~aAL~da~IP~v~~~~~ 175 (465)
..+++++++++++++|+++|+++.++++ + +.|+|+|.|+||++|||++++|++|+++||.+++||
T Consensus 88 ~~~~~~~~~~~~s~~l~~~l~~~i~~~~-----~---p~~~I~I~i~VL~~DG~~~~aai~Aa~lAL~dagIp------- 152 (244)
T PRK03983 88 KRPGPDRRSIEISKVIREALEPAIMLEL-----F---PRTVIDVFIEVLQADAGTRVAGITAASLALADAGIP------- 152 (244)
T ss_pred cCCCCChhHHHHHHHHHHHHHHhccHHh-----C---CCeEEEEEEEEEECCCCHHHHHHHHHHHHHHhcCCc-------
Confidence 5556778899999999999998743333 2 468899999999999999999999999999999999
Q ss_pred CCceeEeCCCCCCCCCccccccccEEEEEEEECCccEEEEcCCHHHHHcCcceEEEEEc-CCCCEEEEEccCCCccCHHH
Q 043337 176 DDLEVIVHPPEEREPLPLIIHHLPIAVTFGFFSSESLLVIDPTHHEEAVMVGKMTATLN-ANGDVCAIQKPGGEGVLQSV 254 (465)
Q Consensus 176 dG~~v~i~~~~~~~~~pL~i~~lPiavT~gli~~~~~iLvDPT~~EE~~s~~~LtVa~~-~~g~I~~i~k~Gg~~is~~~ 254 (465)
|+++|+++|++++++ .+|+|||..||+.+++.++|+++ ..|+||++++.| .++.++
T Consensus 153 -------------------~~~~v~avtv~~~~~--~~i~DPt~~Ee~~~~~~l~va~~~~~~~I~~l~~~G--~~~~~~ 209 (244)
T PRK03983 153 -------------------MRDLVAGCAVGKVDG--VIVLDLNKEEDNYGEADMPVAIMPRLGEITLLQLDG--NLTREE 209 (244)
T ss_pred -------------------cccceeEEEEEEECC--EEEECCCHHHhccCCceEEEEEECCCCCEEEEEEec--CcCHHH
Confidence 356999999999987 89999999999999999999998 578999999987 699999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhHHH
Q 043337 255 IMQCLRLASRMASDITKKIKDAVETYNTER 284 (465)
Q Consensus 255 L~~~i~~A~~~a~~I~~~I~~~l~~~~~er 284 (465)
+.+|+++|.++|++|+++|+++++++..+.
T Consensus 210 ~~~~i~~A~~~~~~i~~~i~~~l~~~~~~~ 239 (244)
T PRK03983 210 FLEALELAKKGIKRIYQLQREALKSKYGEI 239 (244)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 999999999999999999999999865543
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=2e-40 Score=323.47 Aligned_cols=225 Identities=23% Similarity=0.283 Sum_probs=195.6
Q ss_pred CCCCCCCCCCcceEEEec---CCCceEEEEeCCeEEEEEEEeecccCCCCC-CCcceEEEEEEeCCCCCCCc---c--CC
Q 043337 28 RIDGRNPFEYRKLSIKFG---REDGSSEVQLGQTHIMGFVTGQLVQPYRDR-PNEGTLSIFTEFSPMADPSF---E--TG 98 (465)
Q Consensus 28 R~DGR~~~e~R~I~I~~G---~AdGSA~V~~G~T~Vi~~V~~ei~~P~~~r-p~eG~L~v~Vd~sp~as~~~---~--~g 98 (465)
|+|||+++|+|++.|++| .|+|||+|++|+|+|+|+|+++...|...+ +++|.|.|++++.|++++.+ . .|
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 899999999999999999 499999999999999999999887776554 57899999999999998755 1 35
Q ss_pred CCChhHHHHHHHHHhhhccccccccccceeecCceeEEEEEEEEEEcCCCCHHHHHHHHHHHHHhhCCCCCcccCCCCCc
Q 043337 99 RPSESAVELGRIVDRGLRESRAVDTESLCVLAGKLVWAIRIDLHILDNGGNLVDAANIAALASLLTFRRPECSLGGEDDL 178 (465)
Q Consensus 99 ~~se~e~~lsrlL~r~Lr~s~~idlesLcI~pg~~~w~I~IdV~VL~~DGnllDaa~~Aa~aAL~da~IP~v~~~~~dG~ 178 (465)
++++.+.+++++|+|+|++ +||++.|+ .++|+|+++||++|||++|||+||+++||+|+.++... .+
T Consensus 81 ~~~~~~~e~~~~i~r~lr~--~i~l~~l~------~~~i~I~v~VL~~DG~~~~aai~Aa~aAL~da~~~~~~----~~- 147 (236)
T TIGR01966 81 KQSGRTQEIQRLIGRALRA--VVDLEALG------ERTIWIDCDVIQADGGTRTASITGAFVALADAISKLHK----RG- 147 (236)
T ss_pred CCCccHHHHHHHHHHHHHH--hcCHhhcC------CeEEEEEEEEEeCCCCHHHHHHHHHHHHHHHHHHhhhh----cC-
Confidence 6666788999999999997 68998872 24788889999999999999999999999999664210 00
Q ss_pred eeEeCCCCCCCCCccccccccEEEEEEEECCccEEEEcCCHHHHHcCcceEEEEEcCCCCEEEEEccC-CCccCHHHHHH
Q 043337 179 EVIVHPPEEREPLPLIIHHLPIAVTFGFFSSESLLVIDPTHHEEAVMVGKMTATLNANGDVCAIQKPG-GEGVLQSVIMQ 257 (465)
Q Consensus 179 ~v~i~~~~~~~~~pL~i~~lPiavT~gli~~~~~iLvDPT~~EE~~s~~~LtVa~~~~g~I~~i~k~G-g~~is~~~L~~ 257 (465)
... .+.|+++|+++|||++++ .+|+|||.+||+++++.+++++++.++||++++.| +..+++++|.+
T Consensus 148 --------~~~--~ip~~~~~~~vt~~~~~~--~~v~Dpt~~Ee~~~~~~l~l~~~~~~~i~~i~~~g~~~~~~~~~l~~ 215 (236)
T TIGR01966 148 --------ILK--ESPIRDFVAAVSVGIVDG--EPVLDLDYEEDSAADVDMNVVMTGSGGFVEVQGTAEEGPFSRDELNK 215 (236)
T ss_pred --------ccc--CCCccCceeEEEEEEECC--EEEECCChhHHhccCceEEEEEcCCCCEEEEEecCCCCCcCHHHHHH
Confidence 111 244789999999999997 89999999999999999999999999999999964 57899999999
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 043337 258 CLRLASRMASDITKKIKDAV 277 (465)
Q Consensus 258 ~i~~A~~~a~~I~~~I~~~l 277 (465)
|+++|.+++++|+++|+++|
T Consensus 216 ~i~~a~~~~~~l~~~~~~~l 235 (236)
T TIGR01966 216 LLDLAKKGIRELIELQKQAL 235 (236)
T ss_pred HHHHHHHHHHHHHHHHHHHh
Confidence 99999999999999999876
No 8
>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=1e-39 Score=317.27 Aligned_cols=220 Identities=24% Similarity=0.341 Sum_probs=194.7
Q ss_pred HhcCCCCCCCCCCCCcceEEEec---CCCceEEEEeCCeEEEEEEEeecc--cCCCCCCCcceEEEEEEeCCCCCCCccC
Q 043337 23 LSSGIRIDGRNPFEYRKLSIKFG---REDGSSEVQLGQTHIMGFVTGQLV--QPYRDRPNEGTLSIFTEFSPMADPSFET 97 (465)
Q Consensus 23 L~~giR~DGR~~~e~R~I~I~~G---~AdGSA~V~~G~T~Vi~~V~~ei~--~P~~~rp~eG~L~v~Vd~sp~as~~~~~ 97 (465)
+.+|+|+|||.++++|++.+++| .++|||++++|+|+|+|+|+++.. .+....|++|.|.++++++|++...+..
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 56899999999999999999999 499999999999999999999643 3444568889999999999998865555
Q ss_pred CCCChhHHHHHHHHHhhhccccccccccceeecCceeEEEEEEEEEEcCCCCHHHHHHHHHHHHHhhCCCCCcccCCCCC
Q 043337 98 GRPSESAVELGRIVDRGLRESRAVDTESLCVLAGKLVWAIRIDLHILDNGGNLVDAANIAALASLLTFRRPECSLGGEDD 177 (465)
Q Consensus 98 g~~se~e~~lsrlL~r~Lr~s~~idlesLcI~pg~~~w~I~IdV~VL~~DGnllDaa~~Aa~aAL~da~IP~v~~~~~dG 177 (465)
+.+++++++++++|+++|+++.+ ++. + +.++|+|.++||++||++++|+++|+++||.|++||
T Consensus 84 ~~~~~~~~~~s~~l~~~l~~~i~--~~~---~---p~~~i~i~v~vl~~DG~~~~aai~aa~lAL~dagIp--------- 146 (230)
T TIGR02065 84 PGPSRREIEISKVIREALEPAIL--LEQ---F---PRTAIDVFIEVLQADAGTRCAGLTAASLALADAGIP--------- 146 (230)
T ss_pred CCCCccHHHHHHHHHHHHHHHhC--hhh---c---CCeEEEEEEEEEEcCCCHHHHHHHHHHHHHHHcCCc---------
Confidence 66788999999999999998733 332 2 256788888999999999999999999999999999
Q ss_pred ceeEeCCCCCCCCCccccccccEEEEEEEECCccEEEEcCCHHHHHcCcceEEEEEc-CCCCEEEEEccCCCccCHHHHH
Q 043337 178 LEVIVHPPEEREPLPLIIHHLPIAVTFGFFSSESLLVIDPTHHEEAVMVGKMTATLN-ANGDVCAIQKPGGEGVLQSVIM 256 (465)
Q Consensus 178 ~~v~i~~~~~~~~~pL~i~~lPiavT~gli~~~~~iLvDPT~~EE~~s~~~LtVa~~-~~g~I~~i~k~Gg~~is~~~L~ 256 (465)
|+++|+++|++++++ .+|+|||.+||+.+.+.++|++. ..++|+++++.| .++++++.
T Consensus 147 -----------------~~~~v~avtv~~~~~--~~v~Dpt~~Ee~~~~~~l~va~~~~~~~i~~i~~~g--~~~~e~~~ 205 (230)
T TIGR02065 147 -----------------MRDLVVGVAVGKVDG--VVVLDLNEEEDMYGEADMPVAMMPKLGEITLLQLDG--DMTPDEFR 205 (230)
T ss_pred -----------------cccceeeEEEEEECC--eEEECCCHHHhhcCCCceEEEEeCCCCCEEEEEEec--CcCHHHHH
Confidence 356899999999987 89999999999999999999985 578999999886 69999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHh
Q 043337 257 QCLRLASRMASDITKKIKDAVETY 280 (465)
Q Consensus 257 ~~i~~A~~~a~~I~~~I~~~l~~~ 280 (465)
+|+++|.++|+.|+++|+++++++
T Consensus 206 ~~l~~a~~~~~~l~~~~~~~l~~~ 229 (230)
T TIGR02065 206 QALDLAVKGIKIIYQIQREALKNK 229 (230)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhh
Confidence 999999999999999999999874
No 9
>KOG1612 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp42 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.8e-39 Score=311.46 Aligned_cols=269 Identities=28% Similarity=0.419 Sum_probs=240.2
Q ss_pred CCcCCccHHHHHHHHHhcCCCCCCCCCCCCcceEEEecC---CCceEEEEeCC-eEEEEEEEeecccCCCCCCCcceEEE
Q 043337 8 TWRLTVNEKRFIETALSSGIRIDGRNPFEYRKLSIKFGR---EDGSSEVQLGQ-THIMGFVTGQLVQPYRDRPNEGTLSI 83 (465)
Q Consensus 8 ~~~lS~~e~~fi~~~L~~giR~DGR~~~e~R~I~I~~G~---AdGSA~V~~G~-T~Vi~~V~~ei~~P~~~rp~eG~L~v 83 (465)
.+.+|..|+-|+..+.+..+|.|||.+++||+|.+++|. ++|||+|++|+ |.|+++|+++++.|..+.|++|.+.+
T Consensus 2 ~~~ls~~e~~~~i~g~e~~iR~DGR~~~~~Rpi~vetdVlp~tNGSaRVk~g~~tdiivgVKaEvg~~~~~~p~egk~~~ 81 (288)
T KOG1612|consen 2 SVSLSEKEKLYIITGSEPDIRNDGRSCHQFRPIEVETDVLPGTNGSARVKLGDGTDIIVGVKAEVGSPDDETPVEGKYLF 81 (288)
T ss_pred cccccccceeEEecccCcccccCCcCccccceEEEEeccccCCCCcEEEEecCCceEEEEEeeeccCccccCCCCCeEEE
Confidence 357889999999999999999999999999999999994 99999999999 99999999999999999999999999
Q ss_pred EEEeCCCCCCCccCCCCChhHHHHHHHHHhhhcccc-ccccccceeecCceeEEEEEEEEEEcCCCCHHHHHHHHHHHHH
Q 043337 84 FTEFSPMADPSFETGRPSESAVELGRIVDRGLRESR-AVDTESLCVLAGKLVWAIRIDLHILDNGGNLVDAANIAALASL 162 (465)
Q Consensus 84 ~Vd~sp~as~~~~~g~~se~e~~lsrlL~r~Lr~s~-~idlesLcI~pg~~~w~I~IdV~VL~~DGnllDaa~~Aa~aAL 162 (465)
+||++|.+.|.|..-...+...+|+..|+++|.... .+|+..||+.++ |+|.|+||+.|++.|||++||..+|+.+||
T Consensus 82 ~VD~S~sasp~f~gRggde~~~eltsaLq~~l~~~~sgv~ls~L~lt~~-~~W~i~VDvlVi~s~gn~~dAiS~Ai~~AL 160 (288)
T KOG1612|consen 82 FVDCSPSASPQFQGRGGDELVEELTSALQRVLNSLGSGVDLSKLQLTPG-YCWKIYVDVLVISSDGNLLDAISIAIYAAL 160 (288)
T ss_pred EEEecCCcCccccCCChhhHHHHHHHHHHHHHhCcCcccchhheeccCC-eeEEEEEeEEEEecCCCHHHHHHHHHHHHH
Confidence 999999999998632234677899999999999844 499999999998 999999999999999999999999999999
Q ss_pred hhCCCCCcccCCCCCceeEeCCC-CCCCCCccccccccEEEEEEEECCccEEEEcCCHHHHHcCcceEEEEEcCCCCEEE
Q 043337 163 LTFRRPECSLGGEDDLEVIVHPP-EEREPLPLIIHHLPIAVTFGFFSSESLLVIDPTHHEEAVMVGKMTATLNANGDVCA 241 (465)
Q Consensus 163 ~da~IP~v~~~~~dG~~v~i~~~-~~~~~~pL~i~~lPiavT~gli~~~~~iLvDPT~~EE~~s~~~LtVa~~~~g~I~~ 241 (465)
.+++||++.+..+++.+++++.. ++++..-+....+|+.+|++.++. .+|+|||.+||+++...+.|.+++.|-+.+
T Consensus 161 ~~T~lPkv~v~~dd~~~~~i~~s~~~Yd~~~~~~~~~P~ivtlskIG~--~~lVD~T~eEe~~a~s~l~Isv~a~givs~ 238 (288)
T KOG1612|consen 161 NNTRLPKVIVAFDDDGEVEILLSDEEYDLMVKLVENVPLIVTLSKIGT--NMLVDPTAEEESVANSGLLISVSAGGIVSC 238 (288)
T ss_pred hcccCCccccccccCCceeeccCcccchhhhhhcccCCEEEEEEeecc--eEEccCCccHHHhhhcceEEEEecCcceEE
Confidence 99999999887765556666543 334434455678999999999997 899999999999999999999999998888
Q ss_pred EEccCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043337 242 IQKPGGEGVLQSVIMQCLRLASRMASDITKKIKDAVET 279 (465)
Q Consensus 242 i~k~Gg~~is~~~L~~~i~~A~~~a~~I~~~I~~~l~~ 279 (465)
+...|.+.+.++-+.+|++.+.+....+...+.+.|++
T Consensus 239 ~r~VG~G~l~~s~i~~mle~~~~~~e~l~~~l~k~L~~ 276 (288)
T KOG1612|consen 239 TRSVGLGDLDPSSIPEMLEQGKAVVETLAPDLVKSLEN 276 (288)
T ss_pred EEEecCCCCChhhHHHHHHHHHHHHHhhhHHHHHHhhh
Confidence 88888777999999999999999999999988888876
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=6.5e-33 Score=306.13 Aligned_cols=229 Identities=20% Similarity=0.285 Sum_probs=196.2
Q ss_pred HhcCCCCCCCCCCCCcceEEEec---CCCceEEEEeCCeEEEEEEE-eeccc--CC--CCCCCcceEEEEEEeCCCCCCC
Q 043337 23 LSSGIRIDGRNPFEYRKLSIKFG---REDGSSEVQLGQTHIMGFVT-GQLVQ--PY--RDRPNEGTLSIFTEFSPMADPS 94 (465)
Q Consensus 23 L~~giR~DGR~~~e~R~I~I~~G---~AdGSA~V~~G~T~Vi~~V~-~ei~~--P~--~~rp~eG~L~v~Vd~sp~as~~ 94 (465)
|.+|+|+|||+++++|+|.|++| .++|||++++|+|+|+|+|+ |+... +. .....+|++.++++|+||+++.
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 46799999999999999999999 59999999999999999996 44311 11 0112368999999999999987
Q ss_pred cc-CCCCChhHHHHHHHHHhhhccccccccccceeecCceeEEEEEEEEEEcCCCCHHHHHHHHHHHHHhhCCCCCcccC
Q 043337 95 FE-TGRPSESAVELGRIVDRGLRESRAVDTESLCVLAGKLVWAIRIDLHILDNGGNLVDAANIAALASLLTFRRPECSLG 173 (465)
Q Consensus 95 ~~-~g~~se~e~~lsrlL~r~Lr~s~~idlesLcI~pg~~~w~I~IdV~VL~~DGnllDaa~~Aa~aAL~da~IP~v~~~ 173 (465)
++ .++++++++.++++++|+|++. |++ .+.+.|.|+|+++||++|||..+|+++|+++||+|+++|.
T Consensus 386 ~~~~g~~~rrei~~~~l~~ral~~~--i~~------~~~~p~tI~v~~~VLesdGs~~~Aai~aaslAL~dAgvP~---- 453 (684)
T TIGR03591 386 VGRVGGPGRREIGHGALAERALKAV--LPS------EEEFPYTIRVVSEILESNGSSSMASVCGGSLALMDAGVPI---- 453 (684)
T ss_pred cCCCCCCChHHHHHHHHHHHHHHHh--cCc------cccCCeEEEEEEEEEeCCCChHHHHHHHHHHHHHhcCCCC----
Confidence 76 4778899999999999999983 432 2567899999999999999999999999999999999993
Q ss_pred CCCCceeEeCCCCCCCCCccccccccEEEEEEEECCc---cEEEEcCCHHHHHcCcceEEEEEcCCCCEEEEEcc-CCCc
Q 043337 174 GEDDLEVIVHPPEEREPLPLIIHHLPIAVTFGFFSSE---SLLVIDPTHHEEAVMVGKMTATLNANGDVCAIQKP-GGEG 249 (465)
Q Consensus 174 ~~dG~~v~i~~~~~~~~~pL~i~~lPiavT~gli~~~---~~iLvDPT~~EE~~s~~~LtVa~~~~g~I~~i~k~-Gg~~ 249 (465)
.++|+++++|+++++ +.+|+||+..|+..++..++|+.+.+| |+++++. ++.+
T Consensus 454 ----------------------~~~Vagvs~gli~~~~~~~~il~D~~~~Ed~~~d~d~~va~t~~g-I~~lq~d~k~~~ 510 (684)
T TIGR03591 454 ----------------------KAPVAGIAMGLIKEGDERFAVLSDILGDEDHLGDMDFKVAGTRDG-ITALQMDIKIDG 510 (684)
T ss_pred ----------------------cCCEEEEEEEEEcCCCcceEEEeCCChHHHhcCCceEEEEEcCCc-eEEEEEEcCcCC
Confidence 357899999999643 369999999999999999999999887 9999984 4467
Q ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHh
Q 043337 250 VLQSVIMQCLRLASRMASDITKKIKDAVETYNTERAL 286 (465)
Q Consensus 250 is~~~L~~~i~~A~~~a~~I~~~I~~~l~~~~~er~~ 286 (465)
++.+.|.+|++.|.+++.+|++.|++++.++..+...
T Consensus 511 i~~~~l~~al~~a~~~~~~I~~~m~~~l~~~~~~~~~ 547 (684)
T TIGR03591 511 ITREIMEQALEQAKEGRLHILGEMNKVISEPRAELSP 547 (684)
T ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccccc
Confidence 9999999999999999999999999999986554333
No 11
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=100.00 E-value=2.3e-32 Score=302.38 Aligned_cols=226 Identities=22% Similarity=0.329 Sum_probs=192.3
Q ss_pred HhcCCCCCCCCCCCCcceEEEec---CCCceEEEEeCCeEEEEEEE-eecccCCC-C---CCCcceEEEEEEeCCCCCCC
Q 043337 23 LSSGIRIDGRNPFEYRKLSIKFG---REDGSSEVQLGQTHIMGFVT-GQLVQPYR-D---RPNEGTLSIFTEFSPMADPS 94 (465)
Q Consensus 23 L~~giR~DGR~~~e~R~I~I~~G---~AdGSA~V~~G~T~Vi~~V~-~ei~~P~~-~---rp~eG~L~v~Vd~sp~as~~ 94 (465)
|.+|+|+|||.++++|+|.+++| .++|||++++|+|+|+|+|+ ++...... + ..++|++.++++|+||+++.
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 36899999999999999999999 59999999999999999996 43211000 1 12679999999999999877
Q ss_pred c-cCCCCChhHHHHHHHHHhhhccccccccccceeecCceeEEEEEEEEEEcCCCCHHHHHHHHHHHHHhhCCCCCcccC
Q 043337 95 F-ETGRPSESAVELGRIVDRGLRESRAVDTESLCVLAGKLVWAIRIDLHILDNGGNLVDAANIAALASLLTFRRPECSLG 173 (465)
Q Consensus 95 ~-~~g~~se~e~~lsrlL~r~Lr~s~~idlesLcI~pg~~~w~I~IdV~VL~~DGnllDaa~~Aa~aAL~da~IP~v~~~ 173 (465)
+ +.++++++++.++++++|+|++. |++ .+.+.|+|+|+++||++|||.++|+++|+++||+|+++|.
T Consensus 390 ~~~~~~~~rre~~~~~li~ral~~v--i~~------~~~~p~~I~v~~~VLe~dGs~~~Aai~aaslAL~dAgvP~---- 457 (693)
T PRK11824 390 TGRVGSPGRREIGHGALAERALEPV--LPS------EEEFPYTIRVVSEILESNGSSSMASVCGSSLALMDAGVPI---- 457 (693)
T ss_pred cCCCCCCChhHHHHHHHHHHHHHHh--cCc------ccCCCEEEEEEEEEEecCCCHHHHHHHHHHHHHHhcCCCc----
Confidence 6 35678899999999999999983 332 1457899999999999999999999999999999999993
Q ss_pred CCCCceeEeCCCCCCCCCccccccccEEEEEEEECCc--cEEEEcCCHHHHHcCcceEEEEEcCCCCEEEEEccCC-Ccc
Q 043337 174 GEDDLEVIVHPPEEREPLPLIIHHLPIAVTFGFFSSE--SLLVIDPTHHEEAVMVGKMTATLNANGDVCAIQKPGG-EGV 250 (465)
Q Consensus 174 ~~dG~~v~i~~~~~~~~~pL~i~~lPiavT~gli~~~--~~iLvDPT~~EE~~s~~~LtVa~~~~g~I~~i~k~Gg-~~i 250 (465)
.+++.++++|+++++ +.+|+||+..|+..++..++|+.+.+| |++++..|. .++
T Consensus 458 ----------------------~~~Va~vs~gli~~~~~~~il~D~~~~Ed~~~d~d~~va~t~~g-i~~lq~d~k~~~i 514 (693)
T PRK11824 458 ----------------------KAPVAGIAMGLIKEGDKYAVLTDILGDEDHLGDMDFKVAGTRDG-ITALQMDIKIDGI 514 (693)
T ss_pred ----------------------cCceeEEEEEEEcCCCceEEEcCCChhhHhhCCceEEEEecCCc-eEEEEEecccCCc
Confidence 458899999999642 358999999999999999999998887 999995532 268
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHH
Q 043337 251 LQSVIMQCLRLASRMASDITKKIKDAVETYNTE 283 (465)
Q Consensus 251 s~~~L~~~i~~A~~~a~~I~~~I~~~l~~~~~e 283 (465)
+.+.|.+|++.|.+++.+|++.|++++.....+
T Consensus 515 ~~~~l~~al~~a~~g~~~I~~~M~~aI~~~r~~ 547 (693)
T PRK11824 515 TREILEEALEQAKEGRLHILGKMNEAISEPRAE 547 (693)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHhcCChhh
Confidence 999999999999999999999999999874443
No 12
>COG0689 Rph RNase PH [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=1.1e-30 Score=251.99 Aligned_cols=216 Identities=24% Similarity=0.392 Sum_probs=183.0
Q ss_pred hcCCCCCCCCCCCCcceEEEec---CCCceEEEEeCCeEEEEEEEeeccc-C-CCCCCCcceEEEEEEeCCCCCCCccCC
Q 043337 24 SSGIRIDGRNPFEYRKLSIKFG---REDGSSEVQLGQTHIMGFVTGQLVQ-P-YRDRPNEGTLSIFTEFSPMADPSFETG 98 (465)
Q Consensus 24 ~~giR~DGR~~~e~R~I~I~~G---~AdGSA~V~~G~T~Vi~~V~~ei~~-P-~~~rp~eG~L~v~Vd~sp~as~~~~~g 98 (465)
..++|+|||.+++.|+|.++.| +++|||++++|+|+|+|+|+|+... | ....+..|++.+.+.+.|+++.....-
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 3689999999999999999999 4999999999999999999987532 2 222356688888888889987332111
Q ss_pred CCCh-hHHHHHHHHHhhhccccccccccceeecCceeEEEEEEEEEEcCCCCHHHHHHHHHHHHHhhCCCCCcccCCCCC
Q 043337 99 RPSE-SAVELGRIVDRGLRESRAVDTESLCVLAGKLVWAIRIDLHILDNGGNLVDAANIAALASLLTFRRPECSLGGEDD 177 (465)
Q Consensus 99 ~~se-~e~~lsrlL~r~Lr~s~~idlesLcI~pg~~~w~I~IdV~VL~~DGnllDaa~~Aa~aAL~da~IP~v~~~~~dG 177 (465)
.+.. +.++++++|.++|++. ++++.| ...+|+|++.|+++||+.+.|+++|++.||+|+++|.
T Consensus 85 ~~~~gR~~eisrli~~al~~~--i~L~~~------p~~~I~i~~dVlqaDggTrta~It~A~lAL~DAgipl-------- 148 (230)
T COG0689 85 EADRGRTKEISRLIGRALRAV--IDLELL------PESTIDIDCDVLQADGGTRTASITGASLALADAGIPL-------- 148 (230)
T ss_pred cccccchhHHHHHHHHHHHHH--hhhhhc------CccEEEEEEEEEECCCCeeeehhhHHHHHHHHcCCch--------
Confidence 1222 6799999999999974 777664 3569999999999999999999999999999999983
Q ss_pred ceeEeCCCCCCCCCccccccccEEEEEEEECCccEEEEcCCHHHHHcCcceEEEEEcCCCC---EEEEEccCCCccCHHH
Q 043337 178 LEVIVHPPEEREPLPLIIHHLPIAVTFGFFSSESLLVIDPTHHEEAVMVGKMTATLNANGD---VCAIQKPGGEGVLQSV 254 (465)
Q Consensus 178 ~~v~i~~~~~~~~~pL~i~~lPiavT~gli~~~~~iLvDPT~~EE~~s~~~LtVa~~~~g~---I~~i~k~Gg~~is~~~ 254 (465)
.++..++++|++++ .+++|+++.|++.+...++|++..++. |.+++..| ++++++
T Consensus 149 ------------------~~~vaaiSvgi~~~--~~~lDl~~~Eds~~~~d~~v~~~~~~~~~ei~~~~~~~--~~~~de 206 (230)
T COG0689 149 ------------------RDLVAAISVGIVDG--VIVLDLDYEEDSAAEADMNVVMTGNGGLVEIQGLAEDG--PFTEDE 206 (230)
T ss_pred ------------------hhheeEeEEEEECC--ceEecCcchhhcccccCceEEEEecCCeEEEEEEeccC--CcCHHH
Confidence 34779999999998 799999999999999999999987766 67776655 799999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 043337 255 IMQCLRLASRMASDITKKIKDAV 277 (465)
Q Consensus 255 L~~~i~~A~~~a~~I~~~I~~~l 277 (465)
|.+++++|.+.|+++++.++++|
T Consensus 207 l~~lL~la~~g~~~~~~~~~~al 229 (230)
T COG0689 207 LLELLDLAIKGCNELRELQREAL 229 (230)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHh
Confidence 99999999999999999999886
No 13
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=99.97 E-value=8.3e-31 Score=289.96 Aligned_cols=243 Identities=16% Similarity=0.225 Sum_probs=200.9
Q ss_pred CcceEEEecC----CCceEEEEeCCeEEEEEEEeecccCCCCCCCcceEEEEEEeCCCC--CC----Cc--cCCCCChhH
Q 043337 37 YRKLSIKFGR----EDGSSEVQLGQTHIMGFVTGQLVQPYRDRPNEGTLSIFTEFSPMA--DP----SF--ETGRPSESA 104 (465)
Q Consensus 37 ~R~I~I~~G~----AdGSA~V~~G~T~Vi~~V~~ei~~P~~~rp~eG~L~v~Vd~sp~a--s~----~~--~~g~~se~e 104 (465)
-|++.+++|. |+|||+|++|+|+|+|+|+++.. | ++..++++++|+|.+.+ ++ .| +.|+|++.+
T Consensus 13 ~r~i~~e~G~ia~qAdGSa~v~~G~T~VlatV~~~~~-~---~~~~df~pL~v~y~e~~~A~gkiP~~f~kreg~pse~e 88 (693)
T PRK11824 13 GRTLTLETGKLARQANGAVLVRYGDTVVLVTVVASKE-P---KEGQDFFPLTVDYEEKTYAAGKIPGGFFKREGRPSEKE 88 (693)
T ss_pred CccEEEEECCcCCCCCeEEEEEECCeEEEEEEEcCCC-C---CCCCCeeeeEEEEEehhhhccCCCcccccCCCCCChHH
Confidence 3789999993 99999999999999999999874 4 35678999999998754 22 34 458899999
Q ss_pred HHHHHHHHhhhccccccccccceeecCceeEEEEEEEEEEcCCCCH-HH-HHHHHHHHHHhhCCCCCcccCCCCCceeEe
Q 043337 105 VELGRIVDRGLRESRAVDTESLCVLAGKLVWAIRIDLHILDNGGNL-VD-AANIAALASLLTFRRPECSLGGEDDLEVIV 182 (465)
Q Consensus 105 ~~lsrlL~r~Lr~s~~idlesLcI~pg~~~w~I~IdV~VL~~DGnl-lD-aa~~Aa~aAL~da~IP~v~~~~~dG~~v~i 182 (465)
++++|+|+|.||++ +|+.++|.|+|+++||++||+. +| +|+||+++||++++||.
T Consensus 89 il~srlIdR~lrpl----------fp~~~~~~i~I~~~VL~~Dg~~~~d~aai~aAsaAL~~s~IP~------------- 145 (693)
T PRK11824 89 TLTSRLIDRPIRPL----------FPKGFRNEVQVVATVLSVDPENDPDILAMIGASAALSISGIPF------------- 145 (693)
T ss_pred HHHHHHHhhhHHHh----------CCCCCCeEEEEEEEEEeCCCCCcHHHHHHHHHHHHHHhcCCCc-------------
Confidence 99999999999985 8889999999999999999965 67 78899999999999993
Q ss_pred CCCCCCCCCccccccccEEEEEEEECCccEEEEcCCHHHHHcCcceEEEEEcCCCCEEEEEccCCCccCHHHHHHHHHHH
Q 043337 183 HPPEEREPLPLIIHHLPIAVTFGFFSSESLLVIDPTHHEEAVMVGKMTATLNANGDVCAIQKPGGEGVLQSVIMQCLRLA 262 (465)
Q Consensus 183 ~~~~~~~~~pL~i~~lPiavT~gli~~~~~iLvDPT~~EE~~s~~~LtVa~~~~g~I~~i~k~Gg~~is~~~L~~~i~~A 262 (465)
.+++.+||+|++++ .+|+|||.+|++.++..|+|+.+.+ .|++++ .|+..++.++|.+|++.|
T Consensus 146 -------------~~~v~av~vg~i~g--~~ivdPt~~E~~~s~~~l~va~t~~-~i~mie-~~~~~l~e~~l~~al~~a 208 (693)
T PRK11824 146 -------------NGPIAAVRVGYIDG--EFVLNPTVEELEESDLDLVVAGTKD-AVLMVE-SEAKELSEEVMLEAIEFG 208 (693)
T ss_pred -------------CCCeEEEEEEEECC--EEEEcCCHHHHhhCcceEEEEEccC-ceEEEE-CCCCCCCHHHHHHHHHHH
Confidence 34789999999997 8999999999999999999998765 577776 455679999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhhHHHHhhhhccCCCcc------ee---cce----eeecccccCCCcchhhHHHHHHhhhccc
Q 043337 263 SRMASDITKKIKDAVETYNTERALRKIKRHPTSI------TL---DGS----VNLKEKLNEPSGHNVVNELSRKHLEKPR 329 (465)
Q Consensus 263 ~~~a~~I~~~I~~~l~~~~~er~~~~~k~~~~~~------~~---~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 329 (465)
.+++++|+++++++++++. .|+..... .. .++ -..-..++|..|++++++|+.++++++.
T Consensus 209 ~~~~~~i~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~r~~~~~~~~~~~~~~~~ 281 (693)
T PRK11824 209 HEAIQELIDAQEELAAEAG-------PKWEWQPPEVDEELKAAVKELAEAKLKEAYQITDKQEREAALDAIKEEVLEALA 281 (693)
T ss_pred HHHHHHHHHHHHHHHHhcC-------CCcccCCCCCCHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHHhh
Confidence 9999999999999999854 33332211 00 111 0111135899999999999999999886
Q ss_pred c
Q 043337 330 L 330 (465)
Q Consensus 330 ~ 330 (465)
+
T Consensus 282 ~ 282 (693)
T PRK11824 282 A 282 (693)
T ss_pred h
Confidence 4
No 14
>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-30 Score=286.76 Aligned_cols=243 Identities=17% Similarity=0.223 Sum_probs=200.5
Q ss_pred cceEEEecC----CCceEEEEeCCeEEEEEEEeecccCCCCCCCcceEEEEEEeCCCCC--C----Cc--cCCCCChhHH
Q 043337 38 RKLSIKFGR----EDGSSEVQLGQTHIMGFVTGQLVQPYRDRPNEGTLSIFTEFSPMAD--P----SF--ETGRPSESAV 105 (465)
Q Consensus 38 R~I~I~~G~----AdGSA~V~~G~T~Vi~~V~~ei~~P~~~rp~eG~L~v~Vd~sp~as--~----~~--~~g~~se~e~ 105 (465)
|++.|++|. |+|||+|++|+|+|+|+|+++.. | ++..++++++|+|.+.+. + .| +.|+|++.++
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 799999993 99999999999999999999763 3 245679999999986442 2 34 4588999999
Q ss_pred HHHHHHHhhhccccccccccceeecCceeEEEEEEEEEEcCCCCHH-H-HHHHHHHHHHhhCCCCCcccCCCCCceeEeC
Q 043337 106 ELGRIVDRGLRESRAVDTESLCVLAGKLVWAIRIDLHILDNGGNLV-D-AANIAALASLLTFRRPECSLGGEDDLEVIVH 183 (465)
Q Consensus 106 ~lsrlL~r~Lr~s~~idlesLcI~pg~~~w~I~IdV~VL~~DGnll-D-aa~~Aa~aAL~da~IP~v~~~~~dG~~v~i~ 183 (465)
+++|+|+|.||++ +|++++|.|+|+++||++||+.. | +|+||+++||++++||
T Consensus 81 l~srlIdR~lrpl----------fp~~~~~~i~V~~~VLs~Dg~~~~d~aai~aAsaAL~~s~IP--------------- 135 (684)
T TIGR03591 81 LTSRLIDRPIRPL----------FPKGFRNEVQVVATVLSYDPENDPDILAIIGASAALAISGIP--------------- 135 (684)
T ss_pred HHHHHHhhHHHHh----------cCCCCCceEEEEEEEEecCcCCchHHHHHHHHHHHHHhcCCC---------------
Confidence 9999999999985 89999999999999999999964 7 8889999999999999
Q ss_pred CCCCCCCCccccccccEEEEEEEECCccEEEEcCCHHHHHcCcceEEEEEcCCCCEEEEEccCCCccCHHHHHHHHHHHH
Q 043337 184 PPEEREPLPLIIHHLPIAVTFGFFSSESLLVIDPTHHEEAVMVGKMTATLNANGDVCAIQKPGGEGVLQSVIMQCLRLAS 263 (465)
Q Consensus 184 ~~~~~~~~pL~i~~lPiavT~gli~~~~~iLvDPT~~EE~~s~~~LtVa~~~~g~I~~i~k~Gg~~is~~~L~~~i~~A~ 263 (465)
|++++.+|++|++++ .+|+|||.+|++.++..|+|+.+.+ .+++++ .|+..++.++|.+|+++|.
T Consensus 136 -----------~~~~v~av~vg~idg--~~ildPt~~E~~~s~~~l~va~t~~-~i~mie-~~~~~i~e~~l~~al~~a~ 200 (684)
T TIGR03591 136 -----------FNGPIAAVRVGYIDG--QYVLNPTVDELEKSDLDLVVAGTKD-AVLMVE-SEAKELSEEVMLGAIEFGH 200 (684)
T ss_pred -----------cCCCeEEEEEEEECC--EEEEcCCHHHHhhCCceEEEEccCC-cEEEEE-cCCCCCCHHHHHHHHHHHH
Confidence 235889999999987 8999999999999999999986543 466665 5566899999999999999
Q ss_pred HHHHHHHHHHHHHHHHhhHHHHhhhhccCCCcce--e----cce-eee-------cccccCCCcchhhHHHHHHhhhccc
Q 043337 264 RMASDITKKIKDAVETYNTERALRKIKRHPTSIT--L----DGS-VNL-------KEKLNEPSGHNVVNELSRKHLEKPR 329 (465)
Q Consensus 264 ~~a~~I~~~I~~~l~~~~~er~~~~~k~~~~~~~--~----~~~-~~~-------~~~~~~~~~~~~~~~~~~~~~~~~~ 329 (465)
+++++|++++++++++ .++.|+...... . .+. ... -..++|..|++++++|+.+.++++.
T Consensus 201 ~~~~~i~~~~~~~~~~------~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~r~~~~~~~~~~~~~~~~ 274 (684)
T TIGR03591 201 EEIQPVIEAIEELAEE------AGKEKWEFVAPEVDEELKAKVKELAYEAGLKEAYQITEKQERYAALDAIKEEVLEALA 274 (684)
T ss_pred HHHHHHHHHHHHHHHH------hCCCCccCCCCCCCHHHHHHHHHHhhhHHHHHHhhccchHHHHHHHHHHHHHHHHHhh
Confidence 9999999999999988 556665543221 1 011 100 1235899999999999999999885
Q ss_pred c
Q 043337 330 L 330 (465)
Q Consensus 330 ~ 330 (465)
+
T Consensus 275 ~ 275 (684)
T TIGR03591 275 E 275 (684)
T ss_pred h
Confidence 4
No 15
>KOG1068 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp41 and related exoribonucleases [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=3.5e-30 Score=248.09 Aligned_cols=224 Identities=21% Similarity=0.250 Sum_probs=190.6
Q ss_pred hcCCCCCCCCCCCCcceEEEec---CCCceEEEEeCCeEEEEEEEeecccCC--CCCCCcceEEEEEEeCCCCCCCccC-
Q 043337 24 SSGIRIDGRNPFEYRKLSIKFG---REDGSSEVQLGQTHIMGFVTGQLVQPY--RDRPNEGTLSIFTEFSPMADPSFET- 97 (465)
Q Consensus 24 ~~giR~DGR~~~e~R~I~I~~G---~AdGSA~V~~G~T~Vi~~V~~ei~~P~--~~rp~eG~L~v~Vd~sp~as~~~~~- 97 (465)
.+|+|.|||++++.|+|...+| .++||||+++|||+|+|.|+||...-. ..++++++++|.+.+.+|....++.
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 4799999999999999999999 399999999999999999999863221 2257788999999999887766543
Q ss_pred CCCChhHHHHHHHHHhhhccccccccccceeecCceeEEEEEEEEEEcCCCCHHHHHHHHHHHHHhhCCCCCcccCCCCC
Q 043337 98 GRPSESAVELGRIVDRGLRESRAVDTESLCVLAGKLVWAIRIDLHILDNGGNLVDAANIAALASLLTFRRPECSLGGEDD 177 (465)
Q Consensus 98 g~~se~e~~lsrlL~r~Lr~s~~idlesLcI~pg~~~w~I~IdV~VL~~DGnllDaa~~Aa~aAL~da~IP~v~~~~~dG 177 (465)
...+.++.+++.+|.++|.+. |.++- + +..+|+|.|+||++||+.+.+|+||+.+||.|++||
T Consensus 90 ~~~~rr~~e~s~~L~~afe~~--I~~~l---y---PrsqIDI~v~VleddG~~laa~inaatlAL~daGI~--------- 152 (245)
T KOG1068|consen 90 PKGDRREKELSLMLQQAFEPV--ILLEL---Y---PRSQIDIYVQVLEDDGSNLAAAINAATLALADAGIP--------- 152 (245)
T ss_pred CCccHHHHHHHHHHHHHHHHH--HHhhh---C---ccccceEEEEEEECCCccHHHHHHHHHHHHHHcCCC---------
Confidence 234457899999999999875 33322 3 467999999999999999999999999999999999
Q ss_pred ceeEeCCCCCCCCCccccccccEEEEEEEECCccEEEEcCCHHHHHcCcceEEEEEcCC-CCEEEEEccCCCccCHHHHH
Q 043337 178 LEVIVHPPEEREPLPLIIHHLPIAVTFGFFSSESLLVIDPTHHEEAVMVGKMTATLNAN-GDVCAIQKPGGEGVLQSVIM 256 (465)
Q Consensus 178 ~~v~i~~~~~~~~~pL~i~~lPiavT~gli~~~~~iLvDPT~~EE~~s~~~LtVa~~~~-g~I~~i~k~Gg~~is~~~L~ 256 (465)
|+++..++|+|+.++ .+++||+..||......+||++-.+ ++|..++..+ .++.+.|.
T Consensus 153 -----------------m~D~i~~~t~~l~~~--~~l~Dl~~~eesa~~~~ltVa~l~~~~~i~~l~~~~--~~~~d~l~ 211 (245)
T KOG1068|consen 153 -----------------MYDLITACTAGLADG--TPLLDLTSLEESARAPGLTVAALPNREEIALLQLDE--RLHCDHLE 211 (245)
T ss_pred -----------------hhhhhhhceeeecCC--ccccccccchhhccCCceEEEEecCcceEEEEEecC--CCCHHHHH
Confidence 457889999999998 7999999999999988888887543 4688888876 68999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhHHHH
Q 043337 257 QCLRLASRMASDITKKIKDAVETYNTERA 285 (465)
Q Consensus 257 ~~i~~A~~~a~~I~~~I~~~l~~~~~er~ 285 (465)
..++.|...|+++++.++..+.++...+.
T Consensus 212 ~vl~~a~~~c~~v~~~l~~~l~~~l~~~~ 240 (245)
T KOG1068|consen 212 TVLELAIAGCKRVYERLRLVLREHLKNAE 240 (245)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 99999999999999999999998765544
No 16
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=99.97 E-value=1.6e-28 Score=273.26 Aligned_cols=230 Identities=21% Similarity=0.288 Sum_probs=190.5
Q ss_pred HHHHHH-HhcCCCCCCCCCCCCcceEEEec---CCCceEEEEeCCeEEEEEEE-eecccC-C----CCCCCcceEEEEEE
Q 043337 17 RFIETA-LSSGIRIDGRNPFEYRKLSIKFG---REDGSSEVQLGQTHIMGFVT-GQLVQP-Y----RDRPNEGTLSIFTE 86 (465)
Q Consensus 17 ~fi~~~-L~~giR~DGR~~~e~R~I~I~~G---~AdGSA~V~~G~T~Vi~~V~-~ei~~P-~----~~rp~eG~L~v~Vd 86 (465)
.++++. +.+|+|+|||.+++.|+|.+++| .|+|||++++|+|+|+|+|+ |+...+ . ...+..+.+.++++
T Consensus 427 ~~~R~~i~~~g~R~DGR~~~eiRpI~~e~G~Lp~A~GSAlf~~G~TqVLatVtlGp~~~~q~~d~l~~~~~~~~f~~~y~ 506 (891)
T PLN00207 427 KFLRRRIVEGGKRSDGRTPDEIRPINSSCGLLPRAHGSALFTRGETQALAVVTLGDKQMAQRIDNLVDADEVKRFYLQYS 506 (891)
T ss_pred HHHHHHHhcCCCCCCCCCcCccceEEEEeCCcCCCCceEEEEECCeEEEEEEEecCccccccccccccccceeeEEEEEE
Confidence 334443 45799999999999999999999 49999999999999999997 443111 1 11234578889999
Q ss_pred eCCCCCCCc-cCCCCChhHHHHHHHHHhhhccccccccccceeecCc--eeEEEEEEEEEEcCCCCHHHHHHHHHHHHHh
Q 043337 87 FSPMADPSF-ETGRPSESAVELGRIVDRGLRESRAVDTESLCVLAGK--LVWAIRIDLHILDNGGNLVDAANIAALASLL 163 (465)
Q Consensus 87 ~sp~as~~~-~~g~~se~e~~lsrlL~r~Lr~s~~idlesLcI~pg~--~~w~I~IdV~VL~~DGnllDaa~~Aa~aAL~ 163 (465)
|+|++...+ +.++++++++.++++++|+|++. +|.. |.|.|+|+++||++||+...|+++|+++||+
T Consensus 507 fPPfs~ge~~r~g~psrREi~hg~L~eRALrpv----------ip~~~~fP~tIrV~~~VLesDGSssmAaV~aaSLALm 576 (891)
T PLN00207 507 FPPSCVGEVGRIGAPSRREIGHGMLAERALEPI----------LPSEDDFPYTIRVESTITESNGSSSMASVCGGCLALQ 576 (891)
T ss_pred cCCCCCccccCCCCCCHHHHHHHHHHHHHHHHh----------CCcccCCCEEEEEEEEEEeCCCChHHHHHHHHHHHHH
Confidence 999987554 45778899999999999999984 5543 7899999999999999999999999999999
Q ss_pred hCCCCCcccCCCCCceeEeCCCCCCCCCccccccccEEEEEEEECC-------ccE-EEEcCCHHHHHcCcceEEEEEcC
Q 043337 164 TFRRPECSLGGEDDLEVIVHPPEEREPLPLIIHHLPIAVTFGFFSS-------ESL-LVIDPTHHEEAVMVGKMTATLNA 235 (465)
Q Consensus 164 da~IP~v~~~~~dG~~v~i~~~~~~~~~pL~i~~lPiavT~gli~~-------~~~-iLvDPT~~EE~~s~~~LtVa~~~ 235 (465)
+++|| |++++.+|++|++.+ +.. +|+||+..|+..++..+.|+.+.
T Consensus 577 DAGIP--------------------------mk~~VAGvsvGli~d~~~~~~~g~~~IL~Dp~g~Ed~~gdmDfkVAgT~ 630 (891)
T PLN00207 577 DAGVP--------------------------VKCPIAGIAMGMVLDTEEFGGDGSPLILSDITGSEDASGDMDFKVAGNE 630 (891)
T ss_pred hcCCC--------------------------ccCceeEEEEEEEecccccCCCCcEEEEeCCCHHHHhcCCceEEEEecc
Confidence 99999 356889999999921 223 66799999999999999999876
Q ss_pred CCCEEEEEccCC-CccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHH
Q 043337 236 NGDVCAIQKPGG-EGVLQSVIMQCLRLASRMASDITKKIKDAVETYNTE 283 (465)
Q Consensus 236 ~g~I~~i~k~Gg-~~is~~~L~~~i~~A~~~a~~I~~~I~~~l~~~~~e 283 (465)
+ .|++++..+. ..++.+.|.++++.|.+++..|++.|++++.....+
T Consensus 631 ~-gIt~iqmd~k~~gis~e~l~eAL~~A~~g~~~Il~~M~~~i~~pr~~ 678 (891)
T PLN00207 631 D-GITAFQMDIKVGGITLPIMERALLQAKDGRKHILAEMSKCSPPPSKR 678 (891)
T ss_pred c-ceEEEEEecccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhh
Confidence 5 5899987542 368999999999999999999999999999875443
No 17
>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=99.95 E-value=5.4e-26 Score=248.62 Aligned_cols=224 Identities=24% Similarity=0.312 Sum_probs=184.7
Q ss_pred HHHhcCCCCCCCCCCCCcceEEEec---CCCceEEEEeCCeEEEEEEEee-c-ccCCCC---CCCcceEEEEEEeCCCCC
Q 043337 21 TALSSGIRIDGRNPFEYRKLSIKFG---REDGSSEVQLGQTHIMGFVTGQ-L-VQPYRD---RPNEGTLSIFTEFSPMAD 92 (465)
Q Consensus 21 ~~L~~giR~DGR~~~e~R~I~I~~G---~AdGSA~V~~G~T~Vi~~V~~e-i-~~P~~~---rp~eG~L~v~Vd~sp~as 92 (465)
..|.+++|+|||.++++|+|.+++| .++|||+++.|+|+|+|.++.- . .....+ ..+.+.+.|++.|+||+.
T Consensus 329 ~il~~g~R~DGR~~~eiR~i~~~~g~l~~a~GSa~~~~G~Tqvl~~~tlG~~~~~q~~~~l~~~~~~~~~~~YnfpPFSt 408 (719)
T TIGR02696 329 RVLTEGVRIDGRGVTDIRPLDAEVQVIPRVHGSALFERGETQILGVTTLNMLKMEQQIDSLSPETSKRYMHHYNFPPYST 408 (719)
T ss_pred HHhcCCCCCCCCCccccccceeecCCCCCCCceEEEEecCcEEEEEEeCCCchhhhhcccccccccceEEEEEeCCCCcc
Confidence 3467789999999999999999999 4999999999999999988741 1 001111 234578889999999997
Q ss_pred CCcc-CCCCChhHHHHHHHHHhhhccccccc-cccceeecCceeEEEEEEEEEEcCCCCHHHHHHHHHHHHHhhCCCCCc
Q 043337 93 PSFE-TGRPSESAVELGRIVDRGLRESRAVD-TESLCVLAGKLVWAIRIDLHILDNGGNLVDAANIAALASLLTFRRPEC 170 (465)
Q Consensus 93 ~~~~-~g~~se~e~~lsrlL~r~Lr~s~~id-lesLcI~pg~~~w~I~IdV~VL~~DGnllDaa~~Aa~aAL~da~IP~v 170 (465)
.... .+.++.+++.++++++|+|++. |+ ++ .|.+.|++...||++||+...|+++|+++||+|++||
T Consensus 409 ~er~~~~~~~RReighg~La~rALe~v--I~~~e-------~fP~TIrvvseVLeSdGSss~AsIcaasLALmDAGVP-- 477 (719)
T TIGR02696 409 GETGRVGSPKRREIGHGALAERALVPV--LPSRE-------EFPYAIRQVSEALGSNGSTSMGSVCASTLSLLNAGVP-- 477 (719)
T ss_pred cCCCCCCCCCccHHHHHHHHHHHHHHh--hCcHh-------hCCCEEEEEEEeeccCCcHHHHHHHHHHHHHHHcCcc--
Confidence 6543 3456678999999999999974 33 22 2335588889999999999999999999999999999
Q ss_pred ccCCCCCceeEeCCCCCCCCCccccccccEEEEEEEECC------ccEEEEcCCHHHHHcCcceEEEEEcCCCCEEEEEc
Q 043337 171 SLGGEDDLEVIVHPPEEREPLPLIIHHLPIAVTFGFFSS------ESLLVIDPTHHEEAVMVGKMTATLNANGDVCAIQK 244 (465)
Q Consensus 171 ~~~~~dG~~v~i~~~~~~~~~pL~i~~lPiavT~gli~~------~~~iLvDPT~~EE~~s~~~LtVa~~~~g~I~~i~k 244 (465)
|++++.+|++|++.+ .+.+|+||+..|+...+..+.|+.+. +.|+.++.
T Consensus 478 ------------------------mkd~VAgis~Gli~e~~~~~~~~~iL~Di~g~ED~~Gdmdfkvagt~-~gIt~lQm 532 (719)
T TIGR02696 478 ------------------------LKAPVAGIAMGLISDEVDGETRYVALTDILGAEDAFGDMDFKVAGTS-EFVTALQL 532 (719)
T ss_pred ------------------------hhheeeEEEEEEeccccCCCcceeEEeCCCchhhhcCCceEEEEecC-CCEEEEEE
Confidence 457889999999954 23589999999999999989987764 56999988
Q ss_pred cCC-CccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 043337 245 PGG-EGVLQSVIMQCLRLASRMASDITKKIKDAVETY 280 (465)
Q Consensus 245 ~Gg-~~is~~~L~~~i~~A~~~a~~I~~~I~~~l~~~ 280 (465)
.|. .+++.+.|.+++++|.+.|.+|++.+++++...
T Consensus 533 d~ki~gi~~e~l~~aL~~A~~g~~~Il~~m~~al~~p 569 (719)
T TIGR02696 533 DTKLDGIPASVLASALKQARDARLAILDVMAEAIDTP 569 (719)
T ss_pred EeeECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhCc
Confidence 763 247999999999999999999999999999985
No 18
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=99.94 E-value=7.4e-27 Score=243.62 Aligned_cols=252 Identities=22% Similarity=0.319 Sum_probs=208.0
Q ss_pred CCCcceEEEecC----CCceEEEEeCCeEEEEEEEeecccCCCCCCCcceEEEEEEeCCCCCC------Cc--cCCCCCh
Q 043337 35 FEYRKLSIKFGR----EDGSSEVQLGQTHIMGFVTGQLVQPYRDRPNEGTLSIFTEFSPMADP------SF--ETGRPSE 102 (465)
Q Consensus 35 ~e~R~I~I~~G~----AdGSA~V~~G~T~Vi~~V~~ei~~P~~~rp~eG~L~v~Vd~sp~as~------~~--~~g~~se 102 (465)
...|.|.+++|. |+||+.|+.|+|.||++|...- .|+ |.. |+++.|+|....++ .| +.|++.+
T Consensus 53 fGnR~i~~etGklaRfAngsvvv~~GeT~Vm~Tv~~a~-~PS---p~q-FlPL~VdYqeK~aAvGRip~~fmRREg~tkd 127 (760)
T KOG1067|consen 53 FGNREILFETGKLARFANGSVVVQMGETAVMTTVVLAD-KPS---PPQ-FLPLVVDYQEKFAAVGRIPGNFMRREGRTKD 127 (760)
T ss_pred cCCeEEEEecchhhhhcCCcEEEccCCeEEEEEEEecC-CCC---ccc-cceEEEehhhhhhhhccCCCcccccccCCcc
Confidence 367999999995 9999999999999999999853 454 333 99999999764332 23 3478899
Q ss_pred hHHHHHHHHHhhhccccccccccceeecCceeEEEEEEEEEEcCCC-CHHHH-HHHHHHHHHhhCCCCCcccCCCCCcee
Q 043337 103 SAVELGRIVDRGLRESRAVDTESLCVLAGKLVWAIRIDLHILDNGG-NLVDA-ANIAALASLLTFRRPECSLGGEDDLEV 180 (465)
Q Consensus 103 ~e~~lsrlL~r~Lr~s~~idlesLcI~pg~~~w~I~IdV~VL~~DG-nllDa-a~~Aa~aAL~da~IP~v~~~~~dG~~v 180 (465)
.+++..|+|+|.||+. +|..|+.-.++-..+|..|| +-.|+ ++||+++||....+| |++
T Consensus 128 kEiL~~rLidrsirpl----------fp~g~~~etqi~~n~Ls~dG~~~pdvlainaas~Al~lsdvp---w~g------ 188 (760)
T KOG1067|consen 128 KEILTGRLIDRPIRPL----------FPKGFYHETQILCNVLSSDGVHDPDVLAINAASAALSLSDVP---WNG------ 188 (760)
T ss_pred hhheeeeccccccccC----------CcccchhHHHHHhhheecccccCchHHHHhHHHHHhhhccCC---CCC------
Confidence 9999999999999985 77766664444445566666 34564 569999999999999 653
Q ss_pred EeCCCCCCCCCccccccccEEEEEEEECCccEEEEcCCHHHHHcCcceEEEEEcCCCCEEEEEccCCCccCHHHHHHHHH
Q 043337 181 IVHPPEEREPLPLIIHHLPIAVTFGFFSSESLLVIDPTHHEEAVMVGKMTATLNANGDVCAIQKPGGEGVLQSVIMQCLR 260 (465)
Q Consensus 181 ~i~~~~~~~~~pL~i~~lPiavT~gli~~~~~iLvDPT~~EE~~s~~~LtVa~~~~g~I~~i~k~Gg~~is~~~L~~~i~ 260 (465)
...++.+|++++ .+|++||+.|.+.++.+|+|+.+ ..++++++.. +..|.+++|.++|+
T Consensus 189 -----------------pig~vRigLi~G--e~vVNPT~kEmssS~Lnlvvagt-~~~~vmle~~-s~~i~qqdl~~Aik 247 (760)
T KOG1067|consen 189 -----------------PIGAVRIGLIDG--EFVVNPTRKEMSSSQLNLVVAGT-KSQTVMLEGS-SNNILQQDLLHAIK 247 (760)
T ss_pred -----------------ceeeeEeeeecc--eEEeCcchhhhhhccceeEEEec-cceEEEEEcc-cccccHHHHHHHHH
Confidence 557899999998 89999999999999999999998 6689999877 46899999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHhhHHHHhhhhccCCCcc-------ee---cce------eeecccccCCCcchhhHHHHHHh
Q 043337 261 LASRMASDITKKIKDAVETYNTERALRKIKRHPTSI-------TL---DGS------VNLKEKLNEPSGHNVVNELSRKH 324 (465)
Q Consensus 261 ~A~~~a~~I~~~I~~~l~~~~~er~~~~~k~~~~~~-------~~---~~~------~~~~~~~~~~~~~~~~~~~~~~~ 324 (465)
++.+.++.++..|..+.++ .+|.||.+... .+ +++ ||+|.+|||++||+|+|+||.+.
T Consensus 248 vg~~~~q~~i~~i~~L~k~------~Gk~Kr~~~~~~~p~pel~K~v~~la~erl~~vftd~shdK~sR~eAvn~i~~~~ 321 (760)
T KOG1067|consen 248 VGVKEAQQIIQGIERLAKK------YGKQKREPQKLFLPDPELVKHVHKLAMERLYAVFTDYSHDKISRDEAVNKIRLDD 321 (760)
T ss_pred hccHHHHHHHHHHHHHHHH------hCccccchhhhcCCCHHHHHHHHHHHHHHHHHHhcccccccchhhhHHhhhccch
Confidence 9999999999999999999 67777766554 11 222 99999999999999999999999
Q ss_pred hhccccccccccC
Q 043337 325 LEKPRLASAENAS 337 (465)
Q Consensus 325 ~~~~~~~~~~~~~ 337 (465)
++++++.--|+..
T Consensus 322 e~~~~e~~pe~e~ 334 (760)
T KOG1067|consen 322 EDKVKEEFPEQEP 334 (760)
T ss_pred HHHHHhhcCCccH
Confidence 9999988777644
No 19
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=99.94 E-value=1.1e-25 Score=250.81 Aligned_cols=243 Identities=17% Similarity=0.161 Sum_probs=196.0
Q ss_pred cceEEEecC----CCceEEEEeCCeEEEEEEEeecccCCCCCCCcceEEEEEEeCCCCCC------Cc--cCCCCChhHH
Q 043337 38 RKLSIKFGR----EDGSSEVQLGQTHIMGFVTGQLVQPYRDRPNEGTLSIFTEFSPMADP------SF--ETGRPSESAV 105 (465)
Q Consensus 38 R~I~I~~G~----AdGSA~V~~G~T~Vi~~V~~ei~~P~~~rp~eG~L~v~Vd~sp~as~------~~--~~g~~se~e~ 105 (465)
|.|.+++|+ |+||+.|++|+|.|+|+|+..- .|. +..+|+++.|+|.....+ .| +.|+|++.++
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-VPS---EPSDFFPLSVHYQERFSAAGRTSGGFFKREGRTKDHEV 164 (891)
T ss_pred EEEEEEhhHHHHhCCCcEEEEECCeEEEEEEEecc-CCC---CCCCccceeEeeeeehhhcCccCCceeccCCCCChHHH
Confidence 478999995 9999999999999999999743 232 345799999999765332 24 3589999999
Q ss_pred HHHHHHHhhhccccccccccceeecCceeEEEEEEEEEEcCCCC--HHHHHHHHHHHHHhhCCCCCcccCCCCCceeEeC
Q 043337 106 ELGRIVDRGLRESRAVDTESLCVLAGKLVWAIRIDLHILDNGGN--LVDAANIAALASLLTFRRPECSLGGEDDLEVIVH 183 (465)
Q Consensus 106 ~lsrlL~r~Lr~s~~idlesLcI~pg~~~w~I~IdV~VL~~DGn--llDaa~~Aa~aAL~da~IP~v~~~~~dG~~v~i~ 183 (465)
+++|+|+|.||+. |+..++....|.++||++||+ ...+|+|||++||++++||
T Consensus 165 L~sRlIdR~lRPl----------fp~~~~~etQI~i~VLsaDg~~~pd~~AInAASaAL~~SgIP--------------- 219 (891)
T PLN00207 165 LICRLIDRPLRPT----------MPKGFYHETQILSWVLSYDGLHSPDSLAVTAAGIAVALSEVP--------------- 219 (891)
T ss_pred HHHHHHCccchhh----------ccccCCCCcEEEEEEEeeCCCCChhhHHHHHHHHHHHhhCCC---------------
Confidence 9999999999985 666666777777899999997 4467789999999999999
Q ss_pred CCCCCCCCccccccccEEEEEEEECCccEEEEcCCHHHHHcCcceEEEEEcCCCCEEEEEccCCCccCHHHHHHHHHHHH
Q 043337 184 PPEEREPLPLIIHHLPIAVTFGFFSSESLLVIDPTHHEEAVMVGKMTATLNANGDVCAIQKPGGEGVLQSVIMQCLRLAS 263 (465)
Q Consensus 184 ~~~~~~~~pL~i~~lPiavT~gli~~~~~iLvDPT~~EE~~s~~~LtVa~~~~g~I~~i~k~Gg~~is~~~L~~~i~~A~ 263 (465)
|.+++.+|++|++++ .+|+|||..|++.++..|+|+.+.. .|+||+.. +..++.++|.++|++|.
T Consensus 220 -----------~~gpVaAVrVG~idg--~~VlnPt~~E~~~s~ldLvvagt~~-~IvMIE~~-a~e~see~l~~Al~~a~ 284 (891)
T PLN00207 220 -----------NLKAIAGVRVGLIGG--KFIVNPTTKEMEESELDLIMAGTDS-AILMIEGY-CNFLPEEKLLEAVEVGQ 284 (891)
T ss_pred -----------ccCceEEEEEEEECC--EEEECCCHHHHhcCCeeEEEEEcCC-eEEEEEcC-CCCCCHHHHHHHHHHHH
Confidence 345889999999987 8999999999999999998888754 59999865 46789999999999999
Q ss_pred HHHHHHHHHHHHHHHHhhHHHHhhhhccCCCcc------ee---cce----eeecccccCCCcchhhHHHHHHhhhcccc
Q 043337 264 RMASDITKKIKDAVETYNTERALRKIKRHPTSI------TL---DGS----VNLKEKLNEPSGHNVVNELSRKHLEKPRL 330 (465)
Q Consensus 264 ~~a~~I~~~I~~~l~~~~~er~~~~~k~~~~~~------~~---~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 330 (465)
++++.|++++++++++ .++.|+..... .. ..+ ...-...+|..|+.++++|+.++++.|.+
T Consensus 285 ~aik~i~~~~~el~~~------~gk~k~~~~~~~~~~~l~~~v~~~~~~~~~~~~~~~~K~~R~~~~~~~~~~~~~~~~~ 358 (891)
T PLN00207 285 DAVRAICKEIEVLVKK------CGKPKMLDAIKLPPPELYKHVKEIAGDELVKALQIRGKIPRRKALSSLEEKVLSILTE 358 (891)
T ss_pred HHHHHHHHHHHHHHHH------hCCCCccCCCCCCCHHHHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHHhhc
Confidence 9999999999999988 55555443322 11 111 01111238899999999999999998844
No 20
>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=99.92 E-value=1.3e-23 Score=230.15 Aligned_cols=245 Identities=20% Similarity=0.184 Sum_probs=200.6
Q ss_pred cceEEEecC----CCceEEEEe-CCeEEEEEEEeecccCCCCCCCcceEEEEEEeCCCCCC------Cc--cCCCCChhH
Q 043337 38 RKLSIKFGR----EDGSSEVQL-GQTHIMGFVTGQLVQPYRDRPNEGTLSIFTEFSPMADP------SF--ETGRPSESA 104 (465)
Q Consensus 38 R~I~I~~G~----AdGSA~V~~-G~T~Vi~~V~~ei~~P~~~rp~eG~L~v~Vd~sp~as~------~~--~~g~~se~e 104 (465)
|.+.+++|+ |+||+++++ |+|.|+|+|...- .|. +..+|+++.|+|.....+ .| +.|+|++.+
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-QPK---DQFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDA 92 (719)
T ss_pred EEEEEEcchhHhhCCceEEEEecCCeEEEEEEEecC-CCC---CCCCCcceeEeeeehhhhcCccCCceeccCCCCChhh
Confidence 479999995 999999999 9999999998642 222 445799999999765432 23 358999999
Q ss_pred HHHHHHHHhhhccccccccccceeecCceeEEEEEEEEEEcCCC-CHHHH-HHHHHHHHHhhCCCCCcccCCCCCceeEe
Q 043337 105 VELGRIVDRGLRESRAVDTESLCVLAGKLVWAIRIDLHILDNGG-NLVDA-ANIAALASLLTFRRPECSLGGEDDLEVIV 182 (465)
Q Consensus 105 ~~lsrlL~r~Lr~s~~idlesLcI~pg~~~w~I~IdV~VL~~DG-nllDa-a~~Aa~aAL~da~IP~v~~~~~dG~~v~i 182 (465)
++.+|+|||.|||. ||..|++-+.|.++||++|+ |..|. ++|||++||+-++|| |+
T Consensus 93 iL~sRliDR~iRPL----------Fp~~~~~e~qi~~~vls~D~~~~pdvla~~~ASaAl~iSdiP---f~--------- 150 (719)
T TIGR02696 93 ILTCRLIDRPLRPS----------FVKGLRNEVQVVVTVLSLNPDHLYDVVAINAASASTQLAGLP---FS--------- 150 (719)
T ss_pred hHHHHhhCCCCccC----------CCCCCCcceEEEEEEEEcCCCCChHHHHHHHHHHHHHhcCCC---CC---------
Confidence 99999999999995 99999999999999999988 46775 569999999999999 43
Q ss_pred CCCCCCCCCccccccccEEEEEEEECCccEEEEcCCHHHHHcCcceEEEEEcC----CCCEEEEEcc-----------CC
Q 043337 183 HPPEEREPLPLIIHHLPIAVTFGFFSSESLLVIDPTHHEEAVMVGKMTATLNA----NGDVCAIQKP-----------GG 247 (465)
Q Consensus 183 ~~~~~~~~~pL~i~~lPiavT~gli~~~~~iLvDPT~~EE~~s~~~LtVa~~~----~g~I~~i~k~-----------Gg 247 (465)
.+..+|++|++++ .+|++||..|.+.++..|+|+.+. ++.|+|++.. |+
T Consensus 151 --------------gPv~~vrVg~i~g--~~viNPt~~~~~~s~ldLvvagt~~~~~~~~i~MiE~~a~~~~~~~~~~~a 214 (719)
T TIGR02696 151 --------------GPIGGVRVALIDG--QWVAFPTHEQLEGAVFDMVVAGRVLENGDVAIMMVEAEATEKTWDLVKGGA 214 (719)
T ss_pred --------------CceEEEEEEEECC--EEEECcCHHHHhhCeeeEEEEeeecCCCCccEEEEecCCccccccccccCC
Confidence 3678999999998 899999999999999999999986 4479999862 67
Q ss_pred CccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHhhhhccCCC-cc--ee-------cce----eeecccccCCCc
Q 043337 248 EGVLQSVIMQCLRLASRMASDITKKIKDAVETYNTERALRKIKRHPT-SI--TL-------DGS----VNLKEKLNEPSG 313 (465)
Q Consensus 248 ~~is~~~L~~~i~~A~~~a~~I~~~I~~~l~~~~~er~~~~~k~~~~-~~--~~-------~~~----~~~~~~~~~~~~ 313 (465)
..++.+++.++|..|.+.++.++++++++.+. .+|.|+... .. .. ... -..-...+|..|
T Consensus 215 ~e~~e~~~~~Ai~~a~~~i~~~~~~~~~l~~~------~gk~k~~~~~~~~~~~~l~~~v~~~~~~~~~~~~~~~~K~~R 288 (719)
T TIGR02696 215 EAPTEEVVAEGLEAAKPFIKVLCRAQADLAEK------AAKPTGEFPLFPDYQDDVYEAVEGAVKDELSAALTIAGKQER 288 (719)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH------hCCCccccCCCCCCCHHHHHHHHHHHHHHHHHHHhccchHHH
Confidence 78999999999999999999999999998877 666766544 11 11 011 011112389999
Q ss_pred chhhHHHHHHhhhcccc
Q 043337 314 HNVVNELSRKHLEKPRL 330 (465)
Q Consensus 314 ~~~~~~~~~~~~~~~~~ 330 (465)
++++++|+.++++.+.+
T Consensus 289 ~~~~~~~~~~~~~~~~~ 305 (719)
T TIGR02696 289 EEALDEVKALVAAKLAE 305 (719)
T ss_pred HHHHHHHHHHHHHHhhc
Confidence 99999999999998854
No 21
>KOG1069 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp46 [Translation, ribosomal structure and biogenesis]
Probab=99.91 E-value=1.6e-23 Score=195.94 Aligned_cols=199 Identities=20% Similarity=0.315 Sum_probs=164.2
Q ss_pred CCcceEEEec---CCCceEEEEeCCeEEEEEEEeecccC-CCCCCCcceEEEEEEeCCCCCCCccCCCCChhHHHHHHHH
Q 043337 36 EYRKLSIKFG---REDGSSEVQLGQTHIMGFVTGQLVQP-YRDRPNEGTLSIFTEFSPMADPSFETGRPSESAVELGRIV 111 (465)
Q Consensus 36 e~R~I~I~~G---~AdGSA~V~~G~T~Vi~~V~~ei~~P-~~~rp~eG~L~v~Vd~sp~as~~~~~g~~se~e~~lsrlL 111 (465)
..|.+.++.| ++|||+.+.+|+|+|+|+|+||...- ..+.|+ ...+.|-+.|+. |-.+..+..++++|
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 RLRGIACEISILSRPDGSSEFSQGDTKVICSVYGPIDVKARQEDPE--KATLEVIWRPKS------GVNGTVEKVLERII 75 (217)
T ss_pred hhhhhhhhhceecCCCCccceecCCcEEEEEeeCCcchhhcccCch--hceEEEEEeccc------CcchHHHHHHHHHH
Confidence 5677888877 59999999999999999999997432 233454 456666677764 44455678999999
Q ss_pred HhhhccccccccccceeecCceeEEEEEEEEEEcCCCCHHHHHHHHHHHHHhhCCCCCcccCCCCCceeEeCCCCCCCCC
Q 043337 112 DRGLRESRAVDTESLCVLAGKLVWAIRIDLHILDNGGNLVDAANIAALASLLTFRRPECSLGGEDDLEVIVHPPEEREPL 191 (465)
Q Consensus 112 ~r~Lr~s~~idlesLcI~pg~~~w~I~IdV~VL~~DGnllDaa~~Aa~aAL~da~IP~v~~~~~dG~~v~i~~~~~~~~~ 191 (465)
.++|.+...+ .=.++..|.|.++|+++||+.+.+|+|||++||.|++||
T Consensus 76 ~~tl~~~I~l--------~l~Prt~iqVsiqvv~ddgs~LacaINaAclALvDaGIp----------------------- 124 (217)
T KOG1069|consen 76 RKTLSKAIIL--------ELYPRTTIQVSIQVVEDDGSTLACAINAACLALVDAGIP----------------------- 124 (217)
T ss_pred HHHHHHhhee--------eecCCceEEEEEEEEecCCcchHHHHHHHHHHHHhcCCc-----------------------
Confidence 9998764222 223567999999999999999999999999999999999
Q ss_pred ccccccccEEEEEEEECCccEEEEcCCHHHHHcCcceEEEEEc----CCCCEEEEEccCCCccCHHHHHHHHHHHHHHHH
Q 043337 192 PLIIHHLPIAVTFGFFSSESLLVIDPTHHEEAVMVGKMTATLN----ANGDVCAIQKPGGEGVLQSVIMQCLRLASRMAS 267 (465)
Q Consensus 192 pL~i~~lPiavT~gli~~~~~iLvDPT~~EE~~s~~~LtVa~~----~~g~I~~i~k~Gg~~is~~~L~~~i~~A~~~a~ 267 (465)
|+++++++.+++..++ .+++|||..++..+.+..++++. ..-+|+.+...| .++.++|..|+++|...++
T Consensus 125 ---l~~mfcai~~~~~~d~-~lv~Dpt~~qek~~~~~~~lsf~~~~~~~~~vi~s~t~G--~~~~d~lf~~le~a~~~~~ 198 (217)
T KOG1069|consen 125 ---LRSMFCAISCALHEDG-VLVLDPTAKQEKISTARATLSFEGGSLGEPKVIISETNG--EKSEDQLFYVLELAQAAAQ 198 (217)
T ss_pred ---hHHhhhhceEEEecCc-cEEECCcHHhhhhhhceEEEEEecCCCCCcceEEEeccC--CCCHHHHHHHHHhhHHHHH
Confidence 4578999999999986 89999999999998888777763 233688888776 7999999999999999999
Q ss_pred HHHHHHHHHHHH
Q 043337 268 DITKKIKDAVET 279 (465)
Q Consensus 268 ~I~~~I~~~l~~ 279 (465)
+++.++++.+++
T Consensus 199 ~~f~f~r~~~q~ 210 (217)
T KOG1069|consen 199 SLFPFYREVLQR 210 (217)
T ss_pred HHHHHHHHHHHh
Confidence 999999999986
No 22
>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=99.91 E-value=9.5e-24 Score=187.12 Aligned_cols=125 Identities=44% Similarity=0.710 Sum_probs=110.5
Q ss_pred CCcceEEEec---CCCceEEEEeCCeEEEEEEEeeccc-CCCCCC-CcceEEEEEEeCCCCCCCccC-CCCChhHHHHHH
Q 043337 36 EYRKLSIKFG---REDGSSEVQLGQTHIMGFVTGQLVQ-PYRDRP-NEGTLSIFTEFSPMADPSFET-GRPSESAVELGR 109 (465)
Q Consensus 36 e~R~I~I~~G---~AdGSA~V~~G~T~Vi~~V~~ei~~-P~~~rp-~eG~L~v~Vd~sp~as~~~~~-g~~se~e~~lsr 109 (465)
|+|++.|++| .++|||+|++|+|+|+|+|++++.. |..+++ .+|.+.++|+++|++...++. +++++.+.++++
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 7899999999 4999999999999999999999877 554433 358999999999999887754 667788999999
Q ss_pred HHHhhhccccccccccceeecCceeEEEEEEEEEEcCCC-CHHHHHHHHHHHHHhhCCCC
Q 043337 110 IVDRGLRESRAVDTESLCVLAGKLVWAIRIDLHILDNGG-NLVDAANIAALASLLTFRRP 168 (465)
Q Consensus 110 lL~r~Lr~s~~idlesLcI~pg~~~w~I~IdV~VL~~DG-nllDaa~~Aa~aAL~da~IP 168 (465)
+|+++|+++.. ++++++|+|+|+|+||++|| |++|+|++|+++||+|++||
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 99999987632 36678999999999999999 99999999999999999998
No 23
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=99.79 E-value=1.7e-18 Score=186.56 Aligned_cols=243 Identities=16% Similarity=0.221 Sum_probs=191.7
Q ss_pred CcceEEEecC----CCceEEEEeCCeEEEEEEEeecccCCCCCCCcceEEEEEEeCCCCC------CCc--cCCCCChhH
Q 043337 37 YRKLSIKFGR----EDGSSEVQLGQTHIMGFVTGQLVQPYRDRPNEGTLSIFTEFSPMAD------PSF--ETGRPSESA 104 (465)
Q Consensus 37 ~R~I~I~~G~----AdGSA~V~~G~T~Vi~~V~~ei~~P~~~rp~eG~L~v~Vd~sp~as------~~~--~~g~~se~e 104 (465)
-|++.+++|. |+|++++++|+|.|+++|++.- + ++...|++++|+|.-... ..| +.|+|++.+
T Consensus 13 ~~~l~~etg~~A~qa~gav~~~~gdt~vl~t~~~~~--~---~~~~dF~PLtV~y~Ek~yaaGkiPGgf~kREGrpse~e 87 (692)
T COG1185 13 GRTLTLETGKIARQANGAVLVRYGDTVVLATVVASK--P---KEGQDFFPLTVNYEEKTYAAGKIPGGFFKREGRPSEKE 87 (692)
T ss_pred CeeEEEEcchhhhhcCccEEEEECCeEEEEEEeecC--C---CCCCCccceeEeeeeehhccCcCCCcccccCCCCCccc
Confidence 3889999994 9999999999999999999864 2 245679999999965432 123 459999999
Q ss_pred HHHHHHHHhhhccccccccccceeecCceeEEEEEEEEEEcCCCCH-HH-HHHHHHHHHHhhCCCCCcccCCCCCceeEe
Q 043337 105 VELGRIVDRGLRESRAVDTESLCVLAGKLVWAIRIDLHILDNGGNL-VD-AANIAALASLLTFRRPECSLGGEDDLEVIV 182 (465)
Q Consensus 105 ~~lsrlL~r~Lr~s~~idlesLcI~pg~~~w~I~IdV~VL~~DGnl-lD-aa~~Aa~aAL~da~IP~v~~~~~dG~~v~i 182 (465)
++.+|+|||.+||. ||..+..-++|-.+|++.|+.. .| .+++++++||.-++|| +
T Consensus 88 ~L~sRLIDRpiRPl----------Fp~g~~~evqIv~tvls~D~~~~pdi~a~~gaSaAl~is~iP---f---------- 144 (692)
T COG1185 88 ILTSRLIDRPIRPL----------FPKGFRNEVQIVNTVLSVDPENDPDILAMVGASAALSLSGIP---F---------- 144 (692)
T ss_pred hhhhhhcccccccc----------cchhhccceEEEEEEEEECCCCCHHHHHHHHHHHHHhccCCC---c----------
Confidence 99999999999995 8888888999999999998864 56 4569999999999999 2
Q ss_pred CCCCCCCCCccccccccEEEEEEEECCccEEEEcCCHHHHHcCcceEEEEEcCCCCEEEEEccCCCccCHHHHHHHHHHH
Q 043337 183 HPPEEREPLPLIIHHLPIAVTFGFFSSESLLVIDPTHHEEAVMVGKMTATLNANGDVCAIQKPGGEGVLQSVIMQCLRLA 262 (465)
Q Consensus 183 ~~~~~~~~~pL~i~~lPiavT~gli~~~~~iLvDPT~~EE~~s~~~LtVa~~~~g~I~~i~k~Gg~~is~~~L~~~i~~A 262 (465)
..+..++++|++++ .++++||..|.+.+...++|+.+.+ .|.|++ .|...++.+++..++..|
T Consensus 145 -------------~gpi~~vrvg~idg--~~vlNPt~~e~~~s~lDlvVAGT~~-aV~MVE-~~a~~l~E~~ml~Av~fg 207 (692)
T COG1185 145 -------------LGPIGAVRVGYIDG--IFVLNPTLEELEESKLDLVVAGTKD-AVNMVE-SEADELDEEVMLEAVEFG 207 (692)
T ss_pred -------------cCccceEEEEEECC--EEEECCChHHhhhcceeeEecCChh-hhheee-cccccCCHHHHHHHHHHH
Confidence 23668999999998 9999999999999999999998766 577776 557789999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhhHHHHhhhhccCCCcc---ee-----------cceeeecccccCCCcchhhHHHHHHhhhcc
Q 043337 263 SRMASDITKKIKDAVETYNTERALRKIKRHPTSI---TL-----------DGSVNLKEKLNEPSGHNVVNELSRKHLEKP 328 (465)
Q Consensus 263 ~~~a~~I~~~I~~~l~~~~~er~~~~~k~~~~~~---~~-----------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 328 (465)
.+..+.++++++++..... +.+...... .. .+. ..-.-++|.-|+.++++++.+..+.|
T Consensus 208 ~~~~~~~~~~qe~l~~~~g------~~~~~~~~~~~~~~l~~~i~~~~~~~l~-~a~~i~~K~eR~~~~~~~~~~i~~~~ 280 (692)
T COG1185 208 HEAIQSVINAQEELALEVG------KKKWELEPPSLDEELEAKVRDLAEDELK-EAVGIREKQERSAALDAIKEKIEEEL 280 (692)
T ss_pred HHHHHHHHHHHHHHHHHhC------CccccccccCccHHHHHHHHHHhHHHHH-HHhcccchhhhhhhHHHHHHHHHHHH
Confidence 9999999999999998844 222111100 00 111 11122346668888888887777777
Q ss_pred ccc
Q 043337 329 RLA 331 (465)
Q Consensus 329 ~~~ 331 (465)
...
T Consensus 281 ~~~ 283 (692)
T COG1185 281 SGE 283 (692)
T ss_pred hhh
Confidence 654
No 24
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=99.70 E-value=2.1e-16 Score=165.92 Aligned_cols=223 Identities=22% Similarity=0.299 Sum_probs=180.8
Q ss_pred cHHHHHHHHHhcCCCCCCCCCCCCcceEEEec---CCCceEEEEeCCeEEEEEEEeecccCC--CC---C-CCcceEEEE
Q 043337 14 NEKRFIETALSSGIRIDGRNPFEYRKLSIKFG---REDGSSEVQLGQTHIMGFVTGQLVQPY--RD---R-PNEGTLSIF 84 (465)
Q Consensus 14 ~e~~fi~~~L~~giR~DGR~~~e~R~I~I~~G---~AdGSA~V~~G~T~Vi~~V~~ei~~P~--~~---r-p~eG~L~v~ 84 (465)
.-+.|-...+..|.|.|||.+++.|+|.++.+ ..+||++++.|+|.|+|+|+..-.+.. .+ . ++.+.+.++
T Consensus 345 skkv~Rs~i~~~gkR~DGR~ldelR~I~ce~~m~~~lHGSaLFqRGqTQvlctVtl~s~e~a~klD~l~~~~~~~~FmLh 424 (760)
T KOG1067|consen 345 SKKVFRSRILEEGKRCDGRDLDELRNISCEVDMLKTLHGSALFQRGQTQVLCTVTLDSLESAQKLDSLIGPDNGINFMLH 424 (760)
T ss_pred HHHHHHHHHHhcccccCCcchhhhcccceecCccccccchhhhhcCceeEEEEEEcCCHHHhhhhhhhccCccCceEEEE
Confidence 34556667789999999999999999999998 399999999999999999997432111 11 1 333488999
Q ss_pred EEeCCCCCCCc-cCCCCChhHHHHHHHHHhhhccccccccccceeecCceeEEEEEEEEEEcCCCCHHHHHHHHHHHHHh
Q 043337 85 TEFSPMADPSF-ETGRPSESAVELGRIVDRGLRESRAVDTESLCVLAGKLVWAIRIDLHILDNGGNLVDAANIAALASLL 163 (465)
Q Consensus 85 Vd~sp~as~~~-~~g~~se~e~~lsrlL~r~Lr~s~~idlesLcI~pg~~~w~I~IdV~VL~~DGnllDaa~~Aa~aAL~ 163 (465)
++|+|.|.... +.|.++.++.--..+-+++|.+ ++|..|.|.|+|.-.||+.+|+---|.+.+-++||+
T Consensus 425 Y~FPPyat~Evgkig~~nRRE~GhgaLAEkaL~~----------vlP~dfPftIRv~SeVleSnGSsSMASvCGGslALm 494 (760)
T KOG1067|consen 425 YEFPPYATNEVGKIGGLNRRELGHGALAEKALLP----------VLPEDFPFTIRVTSEVLESNGSSSMASVCGGSLALM 494 (760)
T ss_pred eccCCccccccccccCCcccccCchhHhhhhhhc----------cCcccCceEEEEeeeeeecCCcchHHhhhcchhhhh
Confidence 99999987654 3466777777778888888865 578889999999999999999988888899999999
Q ss_pred hCCCCCcccCCCCCceeEeCCCCCCCCCccccccccEEEEEEEECC---------ccEEEEcCCHHHHHcCcceEEEEEc
Q 043337 164 TFRRPECSLGGEDDLEVIVHPPEEREPLPLIIHHLPIAVTFGFFSS---------ESLLVIDPTHHEEAVMVGKMTATLN 234 (465)
Q Consensus 164 da~IP~v~~~~~dG~~v~i~~~~~~~~~pL~i~~lPiavT~gli~~---------~~~iLvDPT~~EE~~s~~~LtVa~~ 234 (465)
|+++|. ...+.+|.+|++-+ .+.+|.|-...|....+..+-|+.+
T Consensus 495 DaGvPv--------------------------~a~vAGvaiGlvt~td~e~g~i~dyriltDIlGiEd~~GDMDFKiAGt 548 (760)
T KOG1067|consen 495 DAGVPV--------------------------SAHVAGVAIGLVTKTDPEKGEIEDYRILTDILGIEDYNGDMDFKIAGT 548 (760)
T ss_pred hcCCcc--------------------------ccccceeEEEeEeccCcccCCcccceeehhhcchhhhcCCcceeeccc
Confidence 999992 12345566666632 2568999999999999999999998
Q ss_pred CCCCEEEEEccCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043337 235 ANGDVCAIQKPGGEGVLQSVIMQCLRLASRMASDITKKIKDAVET 279 (465)
Q Consensus 235 ~~g~I~~i~k~Gg~~is~~~L~~~i~~A~~~a~~I~~~I~~~l~~ 279 (465)
.+| |..+ .|+.+.+++++..|..+-.+|.+.+.+.+..
T Consensus 549 ~dG-vTA~------gi~l~Iv~eal~~a~~ar~~Il~~m~k~i~~ 586 (760)
T KOG1067|consen 549 NDG-VTAL------GIPLKIVMEALQKAREARLQILDIMEKNINS 586 (760)
T ss_pred cCc-ceec------CCcHHHHHHHHHhhhHHHHHHHHHHHhhcCC
Confidence 887 6665 3888999999999999999999998877665
No 25
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=99.40 E-value=3.1e-12 Score=138.60 Aligned_cols=230 Identities=19% Similarity=0.261 Sum_probs=178.0
Q ss_pred HhcCCCCCCCCCCCCcceEEEecC---CCceEEEEeCCeEEEEEEEeecccCCCC-------CCCcceEEEEEEeCCCCC
Q 043337 23 LSSGIRIDGRNPFEYRKLSIKFGR---EDGSSEVQLGQTHIMGFVTGQLVQPYRD-------RPNEGTLSIFTEFSPMAD 92 (465)
Q Consensus 23 L~~giR~DGR~~~e~R~I~I~~G~---AdGSA~V~~G~T~Vi~~V~~ei~~P~~~-------rp~eG~L~v~Vd~sp~as 92 (465)
+..++|+|||..++.|+|.++.|. ++||+++..|.|..++.++.- .+... ....-++-++++|+|++.
T Consensus 308 l~~~vR~DGR~~~~VRpi~~ev~~lpr~HGS~LFtRGeTQal~v~TLG--~~~d~Qvid~l~~e~~krfm~hYNFPp~Sv 385 (692)
T COG1185 308 LEGKVRIDGRFGDEVRPIGIEVGVLPRTHGSALFTRGETQALVVVTLG--TPRDAQVIDILEGEYKKRFLLHYNFPPFSV 385 (692)
T ss_pred hcCCcccCCCCcceeeeeeEEecCCCCccchhhhccCCCcceEEEEcC--CcchhhhhhhccchhhhheeeeccCCCCCc
Confidence 456899999999999999999984 999999999999999888863 22211 112335778999999985
Q ss_pred CCc-cCCCCChhHHHHHHHHHhhhccccccccccceeecCceeEEEEEEEEEEcCCCCHHHHHHHHHHHHHhhCCCCCcc
Q 043337 93 PSF-ETGRPSESAVELGRIVDRGLRESRAVDTESLCVLAGKLVWAIRIDLHILDNGGNLVDAANIAALASLLTFRRPECS 171 (465)
Q Consensus 93 ~~~-~~g~~se~e~~lsrlL~r~Lr~s~~idlesLcI~pg~~~w~I~IdV~VL~~DGnllDaa~~Aa~aAL~da~IP~v~ 171 (465)
..- +.|.|+.+++--.++-+|++.+. ++. ...+.|.|++--.|++..|+---|.+.+.++||+++++|.
T Consensus 386 GE~g~~g~p~RREiGHG~LA~Ral~~v--lp~------~e~fpytiRvVsEi~eSNGSsSmaSVCg~sLaLmdAGVPI-- 455 (692)
T COG1185 386 GETGRMGSPGRREIGHGALAERALAPV--LPS------EEEFPYTIRVVSEILESNGSSSMASVCGGSLALMDAGVPI-- 455 (692)
T ss_pred cccCCCCCCCcccccCchhhHHHHhhh--CCc------hhcCCceeeeeehhhcccCcccchhhhhhHHHHHhCCCcc--
Confidence 432 34666677777788888888763 221 1246789999999999999988888899999999999992
Q ss_pred cCCCCCceeEeCCCCCCCCCccccccccEEEEEEEECCc--cEEEEcCCHHHHHcCcceEEEEEcCCCCEEEEEcc-CCC
Q 043337 172 LGGEDDLEVIVHPPEEREPLPLIIHHLPIAVTFGFFSSE--SLLVIDPTHHEEAVMVGKMTATLNANGDVCAIQKP-GGE 248 (465)
Q Consensus 172 ~~~~dG~~v~i~~~~~~~~~pL~i~~lPiavT~gli~~~--~~iLvDPT~~EE~~s~~~LtVa~~~~g~I~~i~k~-Gg~ 248 (465)
+.++..+-.|++.++ +.++-|-.-.|....+..+-|+.+..| |..++.. --.
T Consensus 456 ------------------------k~pVAGIAMGLI~eg~~~~vLsDI~G~EDhlGDMDFKVAGT~~G-iTAlQMDiKi~ 510 (692)
T COG1185 456 ------------------------KAPVAGIAMGLIKEGDKYAVLSDILGDEDHLGDMDFKVAGTDDG-ITALQMDIKIK 510 (692)
T ss_pred ------------------------cccccchhccceecCCceEeeccccccccccCCceeEEecCCCc-ceeeeeeeeec
Confidence 335556777877543 457888888898899999999998887 5555532 012
Q ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHhhhh
Q 043337 249 GVLQSVIMQCLRLASRMASDITKKIKDAVETYNTERALRKI 289 (465)
Q Consensus 249 ~is~~~L~~~i~~A~~~a~~I~~~I~~~l~~~~~er~~~~~ 289 (465)
.++.+.+.+++..|..+..+|...+.+++.....+.....+
T Consensus 511 Git~eim~~AL~QAk~aRlhIL~~M~~ai~~pr~els~~aP 551 (692)
T COG1185 511 GITKEIMKKALEQAKGARLHILIVMNEAISEPRKELSPYAP 551 (692)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhccCC
Confidence 48999999999999999999999999999987665555444
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=99.26 E-value=2.5e-11 Score=96.14 Aligned_cols=67 Identities=31% Similarity=0.626 Sum_probs=60.1
Q ss_pred cccEEEEEEEECCccEEEEcCCHHHHHcCcceEEEEEcCCCCEEEEEccCCCc-cCHHHHHHHHHHHHHH
Q 043337 197 HLPIAVTFGFFSSESLLVIDPTHHEEAVMVGKMTATLNANGDVCAIQKPGGEG-VLQSVIMQCLRLASRM 265 (465)
Q Consensus 197 ~lPiavT~gli~~~~~iLvDPT~~EE~~s~~~LtVa~~~~g~I~~i~k~Gg~~-is~~~L~~~i~~A~~~ 265 (465)
++|+++|++++++ .+|+|||.+||.++++.++++++.++++|.+.+.|+.. +++++|.+|+++|.++
T Consensus 1 ~~~~avt~~~i~~--~~v~Dpt~~Ee~~~~~~l~~~~~~~~~~~~~~~~~g~~~~~~~~l~~~i~~A~~~ 68 (68)
T PF03725_consen 1 DPPVAVTVGIIDG--ELVVDPTAEEESLSDSSLTLAVDGTGNICTLQKSGGGSELSEDQLEEAIELAKKA 68 (68)
T ss_dssp SEEEEEEEEEETT--EEEES--HHHHHHSSEEEEEEEETTSSEEEEEEEEESSEEEHHHHHHHHHHHHHH
T ss_pred CCeEEEEEEEECC--EEEECCCHHHHhhcCCcEEEEEECCCCEEEEEEcCCCCCCCHHHHHHHHHHHhcC
Confidence 4899999999998 79999999999999999999999999999888888776 9999999999999864
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=48.01 E-value=12 Score=30.59 Aligned_cols=11 Identities=73% Similarity=1.226 Sum_probs=8.2
Q ss_pred HhcCCCCCCCC
Q 043337 23 LSSGIRIDGRN 33 (465)
Q Consensus 23 L~~giR~DGR~ 33 (465)
|..|+|+|||+
T Consensus 73 l~~~~R~DGR~ 83 (83)
T PF03726_consen 73 LEEGIRIDGRK 83 (83)
T ss_dssp HCTSBTTTS-B
T ss_pred HCCCCCCCCCC
Confidence 46789999995
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=47.61 E-value=1.1e+02 Score=25.28 Aligned_cols=45 Identities=22% Similarity=0.158 Sum_probs=30.7
Q ss_pred CcceEEEEEcCCCCEEEEEccCCC--ccCHHHHHHHHHHHHHHHHHH
Q 043337 225 MVGKMTATLNANGDVCAIQKPGGE--GVLQSVIMQCLRLASRMASDI 269 (465)
Q Consensus 225 s~~~LtVa~~~~g~I~~i~k~Gg~--~is~~~L~~~i~~A~~~a~~I 269 (465)
.++.++|.++.+|+|..|...... ..+++.|..+|-.|...|..-
T Consensus 28 ~~g~V~V~v~g~g~v~~i~i~~~~~~~~~~~~L~~~I~~A~n~A~~~ 74 (93)
T PF02575_consen 28 GDGLVTVTVNGNGEVVDIEIDPSALRPLDPEELEDLIVEAVNDAQKK 74 (93)
T ss_dssp TCCTEEEEEETTS-EEEEEE-GGGGCTS-HHHHHHHHHHHHHHHHHH
T ss_pred CCCEEEEEEecCceEEEEEEehHhhccCCHHHHHHHHHHHHHHHHHH
Confidence 456799999999999988765332 267788888877776655543
No 29
>PF12075 KN_motif: KN motif; InterPro: IPR021939 This small motif is found at the N terminus of Kank proteins and has been called the KN (for Kank N-terminal) motif. This protein is found in eukaryotes. Proteins in this family are typically between 413 to 1202 amino acids in length. This protein is found associated with PF00023 from PFAM. This protein has two conserved sequence motifs: TPYG and LDLDF. Kank1 was obtained by positional cloning of a tumor suppressor gene in renal cell carcinoma, while the other members were found by homology search. The family is involved in the regulation of actin polymerisation and cell motility through signaling pathways containing PI3K/Akt and/or unidentified modulators/effectors [].
Probab=25.86 E-value=27 Score=25.11 Aligned_cols=14 Identities=43% Similarity=0.757 Sum_probs=12.8
Q ss_pred ccccCCChhhhhhh
Q 043337 374 PYSRGVDSDFLKAS 387 (465)
Q Consensus 374 ~~~~~~~~~~~~~~ 387 (465)
||--++|+||||--
T Consensus 7 PYGyhiDLDFvkyv 20 (39)
T PF12075_consen 7 PYGYHIDLDFVKYV 20 (39)
T ss_pred CcceeecchHHHHH
Confidence 99999999999964
No 30
>PRK00153 hypothetical protein; Validated
Probab=20.30 E-value=2.8e+02 Score=23.65 Aligned_cols=44 Identities=11% Similarity=-0.030 Sum_probs=29.5
Q ss_pred cCcceEEEEEcCCCCEEEEEccCCC--ccCHHHHHHHHHHHHHHHH
Q 043337 224 VMVGKMTATLNANGDVCAIQKPGGE--GVLQSVIMQCLRLASRMAS 267 (465)
Q Consensus 224 ~s~~~LtVa~~~~g~I~~i~k~Gg~--~is~~~L~~~i~~A~~~a~ 267 (465)
..++.++|+++.+++|..|.-.-.. +.+++.|..+|-.|...|.
T Consensus 35 s~~G~V~V~v~G~~~v~~i~Id~~ll~~~d~e~LedlI~~A~n~A~ 80 (104)
T PRK00153 35 AGGGLVKVTMTGKKEVKRVKIDPSLVDPEDVEMLEDLILAAFNDAL 80 (104)
T ss_pred ECCCeEEEEEecCceEEEEEECHHHcCCcCHHHHHHHHHHHHHHHH
Confidence 3457799999999999988754211 2356667777666655554
Done!