Query 028091
Match_columns 214
No_of_seqs 151 out of 1137
Neff 8.3
Searched_HMMs 46136
Date Fri Mar 29 06:06:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028091.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028091hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR02065 ECX1 archaeal exosom 100.0 2.8E-53 6.2E-58 348.0 27.3 210 3-213 2-211 (230)
2 PRK03983 exosome complex exonu 100.0 1.1E-52 2.4E-57 347.3 26.5 211 2-213 7-217 (244)
3 KOG1068 Exosomal 3'-5' exoribo 100.0 4.7E-50 1E-54 321.6 17.2 212 1-212 5-216 (245)
4 PRK00173 rph ribonuclease PH; 100.0 1.8E-48 4E-53 320.8 25.3 203 9-213 1-221 (238)
5 TIGR01966 RNasePH ribonuclease 100.0 1.7E-47 3.6E-52 314.9 25.5 202 10-213 1-220 (236)
6 COG0689 Rph RNase PH [Translat 100.0 1.2E-46 2.6E-51 303.1 21.5 211 3-213 2-214 (230)
7 COG2123 RNase PH-related exori 100.0 1.3E-45 2.7E-50 300.1 23.2 206 4-213 18-255 (272)
8 PRK04282 exosome complex RNA-b 100.0 1.7E-45 3.6E-50 308.8 23.5 205 5-213 20-254 (271)
9 TIGR03591 polynuc_phos polyrib 100.0 1.3E-42 2.9E-47 321.4 26.0 209 2-213 303-523 (684)
10 PRK11824 polynucleotide phosph 100.0 1.9E-42 4E-47 321.1 25.7 209 2-213 307-526 (693)
11 KOG1614 Exosomal 3'-5' exoribo 100.0 2.4E-41 5.1E-46 269.3 19.5 202 5-213 18-254 (291)
12 TIGR02696 pppGpp_PNP guanosine 100.0 3.2E-40 7E-45 301.5 22.5 209 2-213 328-551 (719)
13 PLN00207 polyribonucleotide nu 100.0 3.9E-39 8.5E-44 299.8 25.1 209 2-213 431-657 (891)
14 KOG1069 Exosomal 3'-5' exoribo 100.0 5.7E-39 1.2E-43 249.2 16.1 187 18-214 4-194 (217)
15 KOG1612 Exosomal 3'-5' exoribo 100.0 1.7E-33 3.8E-38 225.5 21.4 205 5-213 17-259 (288)
16 TIGR03591 polynuc_phos polyrib 100.0 1.6E-31 3.5E-36 247.7 23.5 183 20-213 5-199 (684)
17 KOG1613 Exosomal 3'-5' exoribo 100.0 1.3E-32 2.8E-37 219.0 13.2 206 4-213 31-285 (298)
18 PF01138 RNase_PH: 3' exoribon 100.0 2.1E-31 4.5E-36 200.6 16.2 131 18-148 1-132 (132)
19 PRK11824 polynucleotide phosph 100.0 1.8E-30 4E-35 241.1 22.9 187 19-213 13-208 (693)
20 KOG1067 Predicted RNA-binding 99.9 2.1E-26 4.6E-31 201.8 12.8 204 3-214 352-570 (760)
21 PLN00207 polyribonucleotide nu 99.9 1.5E-25 3.3E-30 209.3 19.1 186 20-213 89-283 (891)
22 COG1185 Pnp Polyribonucleotide 99.9 9.7E-25 2.1E-29 196.4 12.2 208 3-213 306-524 (692)
23 TIGR02696 pppGpp_PNP guanosine 99.8 1.4E-18 3.1E-23 159.8 18.3 184 20-213 17-229 (719)
24 COG1185 Pnp Polyribonucleotide 99.7 6.9E-17 1.5E-21 146.1 16.4 182 19-212 13-206 (692)
25 KOG1067 Predicted RNA-binding 99.5 3.4E-14 7.3E-19 125.6 10.3 187 18-213 54-249 (760)
26 PF03725 RNase_PH_C: 3' exorib 99.3 4.7E-12 1E-16 84.3 6.8 62 151-213 1-65 (68)
27 PF06519 TolA: TolA C-terminal 50.1 53 0.0011 23.1 5.1 59 90-149 11-79 (96)
28 KOG2925 Predicted translation 39.8 9 0.0002 29.2 -0.1 44 162-205 64-107 (167)
29 PF09695 YtfJ_HI0045: Bacteria 39.6 53 0.0012 25.4 4.0 26 186-212 131-156 (160)
30 COG3625 PhnH Uncharacterized e 38.0 2.1E+02 0.0045 22.8 7.2 98 100-199 18-145 (196)
31 PF13098 Thioredoxin_2: Thiore 34.7 87 0.0019 21.6 4.4 28 182-210 85-112 (112)
32 PF03727 Hexokinase_2: Hexokin 31.3 1.2E+02 0.0026 24.9 5.2 40 95-140 202-241 (243)
33 PF14060 DUF4252: Domain of un 27.6 1.2E+02 0.0027 22.5 4.4 31 181-212 125-155 (155)
34 PF15645 Tox-PLDMTX: Dermonecr 25.8 2.3E+02 0.0049 21.3 5.4 31 144-177 38-69 (135)
35 PF14237 DUF4339: Domain of un 23.9 79 0.0017 18.5 2.2 17 196-212 9-25 (45)
36 PF04679 DNA_ligase_A_C: ATP d 21.2 1.6E+02 0.0035 20.2 3.7 33 179-211 6-40 (97)
37 PF13202 EF-hand_5: EF hand; P 21.1 51 0.0011 16.8 0.8 13 198-210 13-25 (25)
38 PF03764 EFG_IV: Elongation fa 20.6 3.2E+02 0.0068 19.3 7.0 54 93-146 58-120 (120)
39 PTZ00107 hexokinase; Provision 20.6 2E+02 0.0044 26.3 5.0 40 95-140 421-460 (464)
No 1
>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=2.8e-53 Score=347.96 Aligned_cols=210 Identities=47% Similarity=0.761 Sum_probs=198.0
Q ss_pred ccCCCCCcCCCCCCCCCcceEEEECCCCCCCeeEEEEeCCeEEEEEEECCccccccccCCCCceEEEEEEeecCCCcccc
Q 028091 3 FVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDR 82 (214)
Q Consensus 3 ~~~~~~~R~DgR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~V~~~V~gp~e~~~~~~~~~~~g~l~v~v~~~~~~~~~~ 82 (214)
+|+++++|+|||.++|+|++++++|++++++|||++++|+|+|+|+|+||.+.+.+..+.|++|.++|+++++||++.++
T Consensus 2 ~~~~~~~R~DGR~~~e~R~~~~~~g~~~~a~GSa~~~~G~T~Vl~~V~gp~e~~~~~~~~~~~~~l~v~~~~~~~a~~~~ 81 (230)
T TIGR02065 2 LILEDGVRLDGRKPDELRPIKIEAGVLKNADGSAYVEFGGTKIIAAVYGPREMHPRHLQLPDRAVLRVRYHMAPFSTDER 81 (230)
T ss_pred cccCCCcCCCCCCcccccCeEEEECCCCCCCeEEEEEECCcEEEEEEeCCCccccccccCCCceEEEEEEEeCCcccCCc
Confidence 67899999999999999999999999999999999999999999999999988776666789999999999999998765
Q ss_pred cCCCCCCcchHHHHHHHHHHHHHhhccCCCCCceEEEEEEEEecCCChHHHHHHHHHHHHHhCCCCCCCceEEEEEEeeC
Q 028091 83 MRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLN 162 (214)
Q Consensus 83 ~~~~~~~~~~~~l~~~l~~~l~~~i~~~~~p~~~i~i~v~Vl~~dG~l~~a~~~A~~~AL~~~gIp~~~~~~~vt~~~~~ 162 (214)
++ +.+++++.+++++|+++|++++.++.||++.|+|.++||++||++++|++||+++||.|+||||+++++++|+++++
T Consensus 82 ~~-~~~~~~~~~~s~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~DG~~~~aai~aa~lAL~dagIp~~~~v~avtv~~~~ 160 (230)
T TIGR02065 82 KR-PGPSRREIEISKVIREALEPAILLEQFPRTAIDVFIEVLQADAGTRCAGLTAASLALADAGIPMRDLVVGVAVGKVD 160 (230)
T ss_pred cC-CCCCccHHHHHHHHHHHHHHHhChhhcCCeEEEEEEEEEEcCCCHHHHHHHHHHHHHHHcCCccccceeeEEEEEEC
Confidence 43 44678888999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CeEEEeCChhhhhcCCCcEEEEEcCCCCcEEEEEEeeccCHHHHHHHHhcC
Q 028091 163 STPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQVCLKFSSSFFSLLISQR 213 (214)
Q Consensus 163 ~~~l~DPt~~Ee~~~~~~~tv~~~~~~~~i~~~~~~G~~~~~~~~~~~~~~ 213 (214)
+.+++|||.+||+.+.+.++|+++++.++|+++++.|.++.++++++++.|
T Consensus 161 ~~~v~Dpt~~Ee~~~~~~l~va~~~~~~~i~~i~~~g~~~~e~~~~~l~~a 211 (230)
T TIGR02065 161 GVVVLDLNEEEDMYGEADMPVAMMPKLGEITLLQLDGDMTPDEFRQALDLA 211 (230)
T ss_pred CeEEECCCHHHhhcCCCceEEEEeCCCCCEEEEEEecCcCHHHHHHHHHHH
Confidence 999999999999999999999988888999999999999999999999875
No 2
>PRK03983 exosome complex exonuclease Rrp41; Provisional
Probab=100.00 E-value=1.1e-52 Score=347.27 Aligned_cols=211 Identities=49% Similarity=0.801 Sum_probs=198.3
Q ss_pred cccCCCCCcCCCCCCCCCcceEEEECCCCCCCeeEEEEeCCeEEEEEEECCccccccccCCCCceEEEEEEeecCCCccc
Q 028091 2 EFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGD 81 (214)
Q Consensus 2 ~~~~~~~~R~DgR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~V~~~V~gp~e~~~~~~~~~~~g~l~v~v~~~~~~~~~ 81 (214)
++++++|+|+|||.++|+|++++++|++++++|||++++|+|+|+|+|+||.+...+..+.|++|.+.++++++||++.+
T Consensus 7 ~~~~~~~~R~DGR~~~~~R~i~i~~G~l~~a~GSa~v~~G~T~Vl~~V~gp~e~~~~~~~~~~~~~l~v~~~~~p~~~~~ 86 (244)
T PRK03983 7 KLILEDGLRLDGRKPDELRPIKIEVGVLKNADGSAYLEWGNNKIIAAVYGPREMHPRHLQLPDRAVLRVRYNMAPFSVDE 86 (244)
T ss_pred hhhccCCCCCCCCCcCcccceEEEeCCCCCCCeEEEEEECCeEEEEEEecCCccccccccCCCcEEEEEEEEcCCCcccc
Confidence 46788999999999999999999999999999999999999999999999999877766778999999999999999876
Q ss_pred ccCCCCCCcchHHHHHHHHHHHHHhhccCCCCCceEEEEEEEEecCCChHHHHHHHHHHHHHhCCCCCCCceEEEEEEee
Q 028091 82 RMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYL 161 (214)
Q Consensus 82 ~~~~~~~~~~~~~l~~~l~~~l~~~i~~~~~p~~~i~i~v~Vl~~dG~l~~a~~~A~~~AL~~~gIp~~~~~~~vt~~~~ 161 (214)
+.+ +.+++++.+++++|+++|+++++++.||++.|+|.++||++|||+++|++||+++||+|+||||+++++++|++++
T Consensus 87 ~~~-~~~~~~~~~~s~~l~~~l~~~i~~~~~p~~~I~I~i~VL~~DG~~~~aai~Aa~lAL~dagIp~~~~v~avtv~~~ 165 (244)
T PRK03983 87 RKR-PGPDRRSIEISKVIREALEPAIMLELFPRTVIDVFIEVLQADAGTRVAGITAASLALADAGIPMRDLVAGCAVGKV 165 (244)
T ss_pred ccC-CCCChhHHHHHHHHHHHHHHhccHHhCCCeEEEEEEEEEECCCCHHHHHHHHHHHHHHhcCCccccceeEEEEEEE
Confidence 543 3467788899999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCeEEEeCChhhhhcCCCcEEEEEcCCCCcEEEEEEeeccCHHHHHHHHhcC
Q 028091 162 NSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQVCLKFSSSFFSLLISQR 213 (214)
Q Consensus 162 ~~~~l~DPt~~Ee~~~~~~~tv~~~~~~~~i~~~~~~G~~~~~~~~~~~~~~ 213 (214)
++.+++|||..||+.+++.++|+++++.++|+++++.|.++.++++++++.|
T Consensus 166 ~~~~i~DPt~~Ee~~~~~~l~va~~~~~~~I~~l~~~G~~~~~~~~~~i~~A 217 (244)
T PRK03983 166 DGVIVLDLNKEEDNYGEADMPVAIMPRLGEITLLQLDGNLTREEFLEALELA 217 (244)
T ss_pred CCEEEECCCHHHhccCCceEEEEEECCCCCEEEEEEecCcCHHHHHHHHHHH
Confidence 9999999999999999999999987788999999999999999999999876
No 3
>KOG1068 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp41 and related exoribonucleases [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.7e-50 Score=321.55 Aligned_cols=212 Identities=53% Similarity=0.853 Sum_probs=202.8
Q ss_pred CcccCCCCCcCCCCCCCCCcceEEEECCCCCCCeeEEEEeCCeEEEEEEECCccccccccCCCCceEEEEEEeecCCCcc
Q 028091 1 MEFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTG 80 (214)
Q Consensus 1 ~~~~~~~~~R~DgR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~V~~~V~gp~e~~~~~~~~~~~g~l~v~v~~~~~~~~ 80 (214)
+++++++|.|.|||.++|+|+|..+.|++++++|||++++|||||+|.|+||+|++.....+++++.++|.|++++|++.
T Consensus 5 ~~~~seeg~r~dgRr~~elR~i~~~~g~~~~a~GSay~E~GnTKVl~aV~GPre~~~~~~~~~~~a~lnc~~~~a~Fst~ 84 (245)
T KOG1068|consen 5 YETLSEEGLRTDGRRPNELRRIYARIGVLTQADGSAYMEQGNTKVLCAVYGPREIRGKSARRPDKAVLNCEVSSAQFSTG 84 (245)
T ss_pred ccccCccccccCCCChhHhhhhhhhcCccccCCccchhhcCCeEEEEEEeCCcccccccccccccceEEEEEeeeccccc
Confidence 57889999999999999999999999999999999999999999999999999988876667899999999999999999
Q ss_pred cccCCCCCCcchHHHHHHHHHHHHHhhccCCCCCceEEEEEEEEecCCChHHHHHHHHHHHHHhCCCCCCCceEEEEEEe
Q 028091 81 DRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGY 160 (214)
Q Consensus 81 ~~~~~~~~~~~~~~l~~~l~~~l~~~i~~~~~p~~~i~i~v~Vl~~dG~l~~a~~~A~~~AL~~~gIp~~~~~~~vt~~~ 160 (214)
++.+++..+.+++|++.+|+++|+++|.++.||+++|+|.|+||+|||+.+.+|+||+.+||.|+||||+|+++++|+++
T Consensus 85 ~r~~~~~~~rr~~e~s~~L~~afe~~I~~~lyPrsqIDI~v~VleddG~~laa~inaatlAL~daGI~m~D~i~~~t~~l 164 (245)
T KOG1068|consen 85 DRKKRPKGDRREKELSLMLQQAFEPVILLELYPRSQIDIYVQVLEDDGSNLAAAINAATLALADAGIPMYDLITACTAGL 164 (245)
T ss_pred hhccCCCccHHHHHHHHHHHHHHHHHHHhhhCccccceEEEEEEECCCccHHHHHHHHHHHHHHcCCChhhhhhhceeee
Confidence 98777788899999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eCCeEEEeCChhhhhcCCCcEEEEEcCCCCcEEEEEEeeccCHHHHHHHHhc
Q 028091 161 LNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQVCLKFSSSFFSLLISQ 212 (214)
Q Consensus 161 ~~~~~l~DPt~~Ee~~~~~~~tv~~~~~~~~i~~~~~~G~~~~~~~~~~~~~ 212 (214)
.++..++||+..||+.....+||++++..++|..+|++++++.+.|+.+++-
T Consensus 165 ~~~~~l~Dl~~~eesa~~~~ltVa~l~~~~~i~~l~~~~~~~~d~l~~vl~~ 216 (245)
T KOG1068|consen 165 ADGTPLLDLTSLEESARAPGLTVAALPNREEIALLQLDERLHCDHLETVLEL 216 (245)
T ss_pred cCCccccccccchhhccCCceEEEEecCcceEEEEEecCCCCHHHHHHHHHH
Confidence 9999999999999999998999999999999999999999999999988864
No 4
>PRK00173 rph ribonuclease PH; Reviewed
Probab=100.00 E-value=1.8e-48 Score=320.84 Aligned_cols=203 Identities=32% Similarity=0.427 Sum_probs=185.0
Q ss_pred CcCCCCCCCCCcceEEEECCCCCCCeeEEEEeCCeEEEEEEECCccccccccCCCCceEEEEEEeecCCCcccccC----
Q 028091 9 LRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDRMR---- 84 (214)
Q Consensus 9 ~R~DgR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~V~~~V~gp~e~~~~~~~~~~~g~l~v~v~~~~~~~~~~~~---- 84 (214)
+|+|||+++|+|++++++|++++++|||++++|+|+|+|+|++|.+.+. ....+++|.++|+|+++||++.++.+
T Consensus 1 ~R~DGR~~~e~R~i~~~~g~~~~a~GSa~v~~G~T~Vla~V~~~~~~p~-~~~~~~~g~l~v~~~~~p~a~~~~~~~~~~ 79 (238)
T PRK00173 1 MRPDGRAADQLRPVTITRNFTKHAEGSVLVEFGDTKVLCTASVEEGVPR-FLKGQGQGWVTAEYGMLPRATHTRNDREAA 79 (238)
T ss_pred CCCCCCCcccccCeEEEeCCCCCCCeeEEEEecCcEEEEEEEcCCCCCC-ccCCCCcEEEEEEEecCCCCCccccccccc
Confidence 5999999999999999999999999999999999999999998765432 22346889999999999999987632
Q ss_pred CCCCCcchHHHHHHHHHHHHHhhccCCCCCceEEEEEEEEecCCChHHHHHHHHHHHHHhC-----------CCCCCCce
Q 028091 85 KPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDA-----------GIPMRDIV 153 (214)
Q Consensus 85 ~~~~~~~~~~l~~~l~~~l~~~i~~~~~p~~~i~i~v~Vl~~dG~l~~a~~~A~~~AL~~~-----------gIp~~~~~ 153 (214)
.|++++++.+++++|+++|+++++++.||++.|+|+++||++|||+++|++||+++||+|+ ++||+++|
T Consensus 80 ~g~~~~~~~~~sr~i~r~lr~~i~l~~l~~~~i~v~v~VL~~DG~~~~aai~Aa~~AL~da~~~~~~~~~~~~ip~~~~~ 159 (238)
T PRK00173 80 KGKQGGRTQEIQRLIGRSLRAVVDLKALGERTITIDCDVIQADGGTRTASITGAYVALADALNKLVARGKLKKNPLKDQV 159 (238)
T ss_pred CCCCCccHHHHHHHHHHHHHHhcCHHHcCCeEEEEEEEEEeCCCCHHHHHHHHHHHHHHHhhhhhhccCcccCCcccCce
Confidence 3456778899999999999999999999999999999999999999999999999999999 99999999
Q ss_pred EEEEEEeeCCeEEEeCChhhhhcCCCcEEEEEcCCCCcEEEEEEee---ccCHHHHHHHHhcC
Q 028091 154 TSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQVCL---KFSSSFFSLLISQR 213 (214)
Q Consensus 154 ~~vt~~~~~~~~l~DPt~~Ee~~~~~~~tv~~~~~~~~i~~~~~~G---~~~~~~~~~~~~~~ 213 (214)
+++|++++++.+|+|||.+||+.+++.++|++ ++.++||++++.| .++.+++.+|++.|
T Consensus 160 ~~vt~~~~~~~~lvDpt~~Ee~~~~~~l~v~~-~~~~~i~~v~~~g~g~~~~~e~l~~~i~~A 221 (238)
T PRK00173 160 AAVSVGIVDGEPVLDLDYEEDSAAETDMNVVM-TGSGGFVEVQGTAEGAPFSREELDALLDLA 221 (238)
T ss_pred eEEEEEEECCEEEECCCHHHHhcCCceEEEEE-CCCCCEEEEEccCCCCCcCHHHHHHHHHHH
Confidence 99999999999999999999999999999985 8889999999954 59999999999875
No 5
>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=1.7e-47 Score=314.87 Aligned_cols=202 Identities=34% Similarity=0.456 Sum_probs=182.1
Q ss_pred cCCCCCCCCCcceEEEECCCCCCCeeEEEEeCCeEEEEEEECCccccccccCCCCceEEEEEEeecCCCcccccC----C
Q 028091 10 RLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDRMR----K 85 (214)
Q Consensus 10 R~DgR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~V~~~V~gp~e~~~~~~~~~~~g~l~v~v~~~~~~~~~~~~----~ 85 (214)
|+|||+++|+|++++++|++++|+|||++++|+|+|+|+|+++.+.+.. ...+++|.++|++++.|+++.++.+ .
T Consensus 1 R~DGR~~~e~R~i~i~~G~~~~A~GSa~v~~G~T~Vla~V~~~~~~p~~-~~~~~~g~l~v~~~~~p~a~~~~~~r~~~~ 79 (236)
T TIGR01966 1 RPDGRKPDQLRPVSITRDFLKHAEGSVLIEFGNTKVLCTASVEEKVPPF-LRGSGEGWITAEYGMLPRATQTRNRRESAK 79 (236)
T ss_pred CCCCCCCCCccCeEEEeCCcCCCCceEEEEecCCEEEEEEEccCccCCc-ccCCCcEEEEEEEecCCCCCCCCccccccC
Confidence 8999999999999999999999999999999999999999976443322 2235789999999999999876522 2
Q ss_pred CCCCcchHHHHHHHHHHHHHhhccCCCCCceEEEEEEEEecCCChHHHHHHHHHHHHHhC-----------CCCCCCceE
Q 028091 86 PKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDA-----------GIPMRDIVT 154 (214)
Q Consensus 86 ~~~~~~~~~l~~~l~~~l~~~i~~~~~p~~~i~i~v~Vl~~dG~l~~a~~~A~~~AL~~~-----------gIp~~~~~~ 154 (214)
|.+++++.+++++|+|+|+++++++.||++.|+|+++||++|||+++|++||+++||+|+ +|||+++|+
T Consensus 80 g~~~~~~~e~~~~i~r~lr~~i~l~~l~~~~i~I~v~VL~~DG~~~~aai~Aa~aAL~da~~~~~~~~~~~~ip~~~~~~ 159 (236)
T TIGR01966 80 GKQSGRTQEIQRLIGRALRAVVDLEALGERTIWIDCDVIQADGGTRTASITGAFVALADAISKLHKRGILKESPIRDFVA 159 (236)
T ss_pred CCCCccHHHHHHHHHHHHHHhcCHhhcCCeEEEEEEEEEeCCCCHHHHHHHHHHHHHHHHHHhhhhcCcccCCCccCcee
Confidence 455567789999999999999999999999999999999999999999999999999999 999999999
Q ss_pred EEEEEeeCCeEEEeCChhhhhcCCCcEEEEEcCCCCcEEEEEEee---ccCHHHHHHHHhcC
Q 028091 155 SCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQVCL---KFSSSFFSLLISQR 213 (214)
Q Consensus 155 ~vt~~~~~~~~l~DPt~~Ee~~~~~~~tv~~~~~~~~i~~~~~~G---~~~~~~~~~~~~~~ 213 (214)
++|++++++.+++|||.+||+++++.+++++ ++.++||++++.| .++.+++.+|++.|
T Consensus 160 ~vt~~~~~~~~v~Dpt~~Ee~~~~~~l~l~~-~~~~~i~~i~~~g~~~~~~~~~l~~~i~~a 220 (236)
T TIGR01966 160 AVSVGIVDGEPVLDLDYEEDSAADVDMNVVM-TGSGGFVEVQGTAEEGPFSRDELNKLLDLA 220 (236)
T ss_pred EEEEEEECCEEEECCChhHHhccCceEEEEE-cCCCCEEEEEecCCCCCcCHHHHHHHHHHH
Confidence 9999999999999999999999999999985 7889999999953 69999999999875
No 6
>COG0689 Rph RNase PH [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.2e-46 Score=303.10 Aligned_cols=211 Identities=39% Similarity=0.572 Sum_probs=195.9
Q ss_pred ccCCCCCcCCCCCCCCCcceEEEECCCCCCCeeEEEEeCCeEEEEEEECCccccccccCCCCceEEEEEEeecCCCcccc
Q 028091 3 FVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDR 82 (214)
Q Consensus 3 ~~~~~~~R~DgR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~V~~~V~gp~e~~~~~~~~~~~g~l~v~v~~~~~~~~~~ 82 (214)
...+++.|+|||.++|+|+++++.|++++++||+++++|+|+|+|+|+||.|..+++...+++|+++++|.+.|+++.++
T Consensus 2 ~~~~~~~R~dgR~~delR~i~~~~~~~~~a~GS~~~~~G~tkVic~vsGp~e~~p~~l~~~~~g~~t~ey~m~p~sT~~R 81 (230)
T COG0689 2 LESEDGMRPDGRKPDELRPIKITRGVLKHAEGSSLIEFGNTKVICTVSGPREPVPRFLRGTGKGWLTAEYGMLPRSTDER 81 (230)
T ss_pred CCcccCcCCCCCCcccccceEEEeccccCCCccEEEEeCCeEEEEEEecCCCCCChhhcCCCceEEEEEEeccccccccc
Confidence 45678999999999999999999999999999999999999999999999998887777788999999999999999766
Q ss_pred cCCCCCCcchHHHHHHHHHHHHHhhccCCCCCceEEEEEEEEecCCChHHHHHHHHHHHHHhCCCCCCCceEEEEEEeeC
Q 028091 83 MRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLN 162 (214)
Q Consensus 83 ~~~~~~~~~~~~l~~~l~~~l~~~i~~~~~p~~~i~i~v~Vl~~dG~l~~a~~~A~~~AL~~~gIp~~~~~~~vt~~~~~ 162 (214)
.+++....|.+|++++|.++|++++++++||++.|+|++.|+++||+...|+++|+++||.|+|+||++++.++|+|+++
T Consensus 82 ~~~~~~~gR~~eisrli~~al~~~i~L~~~p~~~I~i~~dVlqaDggTrta~It~A~lAL~DAgipl~~~vaaiSvgi~~ 161 (230)
T COG0689 82 KKREADRGRTKEISRLIGRALRAVIDLELLPESTIDIDCDVLQADGGTRTASITGASLALADAGIPLRDLVAAISVGIVD 161 (230)
T ss_pred ccccccccchhHHHHHHHHHHHHHhhhhhcCccEEEEEEEEEECCCCeeeehhhHHHHHHHHcCCchhhheeEeEEEEEC
Confidence 44433224788999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CeEEEeCChhhhhcCCCcEEEEEcCCCC--cEEEEEEeeccCHHHHHHHHhcC
Q 028091 163 STPLLDLNYVEDSAGGPDVTVGILPTLD--KVTLLQVCLKFSSSFFSLLISQR 213 (214)
Q Consensus 163 ~~~l~DPt~~Ee~~~~~~~tv~~~~~~~--~i~~~~~~G~~~~~~~~~~~~~~ 213 (214)
+.+++|+++.|++.+...++|+++.+.+ +|..++.+|+++.++|.++++.|
T Consensus 162 ~~~~lDl~~~Eds~~~~d~~v~~~~~~~~~ei~~~~~~~~~~~del~~lL~la 214 (230)
T COG0689 162 GVIVLDLDYEEDSAAEADMNVVMTGNGGLVEIQGLAEDGPFTEDELLELLDLA 214 (230)
T ss_pred CceEecCcchhhcccccCceEEEEecCCeEEEEEEeccCCcCHHHHHHHHHHH
Confidence 9999999999999999999999877777 89999999999999999999865
No 7
>COG2123 RNase PH-related exoribonuclease [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.3e-45 Score=300.06 Aligned_cols=206 Identities=21% Similarity=0.279 Sum_probs=188.8
Q ss_pred cCCCCCcCCCCCCCCCcceEEEECCCCCCCeeEEEEeCCeEEEEEEECCccccccccCCCCceEEEEEEeecCCCccccc
Q 028091 4 VSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDRM 83 (214)
Q Consensus 4 ~~~~~~R~DgR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~V~~~V~gp~e~~~~~~~~~~~g~l~v~v~~~~~~~~~~~ 83 (214)
++++|+|+|||.++|+|+++|++|+++.++|||+|++|+|+|+|+|+ .++.+|+++.|++|.+.+++++.|.+++.+.
T Consensus 18 ll~~g~R~DGR~~~efR~ieI~~~vi~ka~GSa~VklG~Tqvv~gvK--~eig~Pf~DtP~eG~~~~n~El~Plas~~fE 95 (272)
T COG2123 18 LLKKGIRIDGRSFDEFRPLEIETGVIPKANGSALVKLGNTQVVVGVK--AEIGEPFPDTPNEGVLVVNVELSPLASPSFE 95 (272)
T ss_pred HhccCcccCCCCcccccceEEEeCceecCCCcEEEEecCeEEEEEEE--cccCCCCCCCCCCceEEeeeeeecccccccc
Confidence 45689999999999999999999999999999999999999999999 5788999999999999999999998876653
Q ss_pred CCCCCCcchHHHHHHHHHHHHHh--hccCCC---CC---ceEEEEEEEEecCCChHHHHHHHHHHHHHhCCCC-------
Q 028091 84 RKPKGDRRSTEISLVIRQTMEAC--ILTHLM---PR---SQIDIFVQVLQADGGTRSACINAATLALQDAGIP------- 148 (214)
Q Consensus 84 ~~~~~~~~~~~l~~~l~~~l~~~--i~~~~~---p~---~~i~i~v~Vl~~dG~l~~a~~~A~~~AL~~~gIp------- 148 (214)
.|.+++.+.+++++++|.++++ +|++.+ ++ |.+.+|++||++|||++||++.|+++||+++++|
T Consensus 96 -~Gppde~aielsrvvdr~lr~s~aiDlekL~I~~g~kvwvv~vDv~vld~DGnl~Da~~lA~~aAL~~t~vP~~~~~~~ 174 (272)
T COG2123 96 -PGPPDELAIELSRVVDRGLRESKAIDLEKLCIEEGKKVWVVFVDVHVLDYDGNLIDAASLAAVAALLNTRVPKAVEVGD 174 (272)
T ss_pred -CCCCchhHHHHHHHHHHHHHhccCcchhheeEecCCEEEEEEEEEEEEcCCCCHHHHHHHHHHHHHHhcCCCceeecCC
Confidence 5677888899999999999976 666654 33 7999999999999999999999999999999988
Q ss_pred ---------------CCCceEEEEEEeeCCeEEEeCChhhhhcCCCcEEEEEcCCCCcEEEEEEee--ccCHHHHHHHHh
Q 028091 149 ---------------MRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQVCL--KFSSSFFSLLIS 211 (214)
Q Consensus 149 ---------------~~~~~~~vt~~~~~~~~l~DPt~~Ee~~~~~~~tv~~~~~~~~i~~~~~~G--~~~~~~~~~~~~ 211 (214)
+.+.|+++|++++++.+++|||.+||..+++.+||. +++.|+|++++|.| .++.+.+.+|++
T Consensus 175 ~~~v~~~~~~~~pl~~~~~pi~vt~a~ig~~lvvDPsleEe~v~d~~ltit-~~~~~~Iv~iqK~g~~~~~~~~~~~~~~ 253 (272)
T COG2123 175 GEIVIEVEEEPVPLPVSNPPISVTFAKIGNVLVVDPSLEEELVADGRLTIT-VNEDGEIVAIQKVGGGSITESDLEKALK 253 (272)
T ss_pred cceeecccCCCcccccCCCceEEEEEEECCEEEeCCCcchhhhcCceEEEE-ECCCCcEEEEEEcCCCcCCHHHHHHHHH
Confidence 568999999999999999999999999999999998 59999999999986 489999999998
Q ss_pred cC
Q 028091 212 QR 213 (214)
Q Consensus 212 ~~ 213 (214)
+|
T Consensus 254 ~A 255 (272)
T COG2123 254 TA 255 (272)
T ss_pred HH
Confidence 86
No 8
>PRK04282 exosome complex RNA-binding protein Rrp42; Provisional
Probab=100.00 E-value=1.7e-45 Score=308.82 Aligned_cols=205 Identities=22% Similarity=0.288 Sum_probs=183.1
Q ss_pred CCCCCcCCCCCCCCCcceEEEECCCCCCCeeEEEEeCCeEEEEEEECCccccccccCCCCceEEEEEEeecCCCcccccC
Q 028091 5 SPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDRMR 84 (214)
Q Consensus 5 ~~~~~R~DgR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~V~~~V~gp~e~~~~~~~~~~~g~l~v~v~~~~~~~~~~~~ 84 (214)
+++++|+|||+++|+|++++++|++++++|||++++|+|+|+|+|+++ +..+..++|++|.+.++++++|+++..+ +
T Consensus 20 l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~vl~~V~~~--~~~p~~~~~~~g~i~~~v~~~~~a~~~~-~ 96 (271)
T PRK04282 20 LKKGKRIDGRKLDEYRPIEIETGVIKKAEGSALVKLGNTQVLAGVKLE--IGEPFPDTPNEGVLIVNAELLPLASPTF-E 96 (271)
T ss_pred HhcCCCCCCCCCccccCeEEEeCCccCCCcEEEEEECCCEEEEEEEEE--EecCCCCCCCCCEEEEEEEECCCcCccc-c
Confidence 368999999999999999999999999999999999999999999953 3334445789999999999999987664 3
Q ss_pred CCCCCcchHHHHHHHHHHHHHh--hccCCC---CC---ceEEEEEEEEecCCChHHHHHHHHHHHHHhCCCC--------
Q 028091 85 KPKGDRRSTEISLVIRQTMEAC--ILTHLM---PR---SQIDIFVQVLQADGGTRSACINAATLALQDAGIP-------- 148 (214)
Q Consensus 85 ~~~~~~~~~~l~~~l~~~l~~~--i~~~~~---p~---~~i~i~v~Vl~~dG~l~~a~~~A~~~AL~~~gIp-------- 148 (214)
.+++++++.+++++|+++|++. ++++.+ |+ |.|+|+++||++|||++||+++|+++||+|+++|
T Consensus 97 ~~~~~~~~~~l~~~l~r~l~~~~~~dl~~L~I~~g~~~w~i~Vdv~VL~~dG~~~daa~~Aa~aAL~~~~iP~~~~~~~~ 176 (271)
T PRK04282 97 PGPPDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWVVFIDVYVLDHDGNLLDASMLAAVAALLNTKVPAVEEGEDG 176 (271)
T ss_pred CCCCCHHHHHHHHHHHHHHhccCCccHHHcEEecCcEEEEEEEEEEEECCCCCHHHHHHHHHHHHHHhCCCCcEEEcCCc
Confidence 4567778889999999999886 445544 54 6999999999999999999999999999999995
Q ss_pred ------------CCCceEEEEEEeeCCeEEEeCChhhhhcCCCcEEEEEcCCCCcEEEEEEee--ccCHHHHHHHHhcC
Q 028091 149 ------------MRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQVCL--KFSSSFFSLLISQR 213 (214)
Q Consensus 149 ------------~~~~~~~vt~~~~~~~~l~DPt~~Ee~~~~~~~tv~~~~~~~~i~~~~~~G--~~~~~~~~~~~~~~ 213 (214)
|+++|+++|++++++.+++|||.+||+.+++.++|++ ++.|+|+++++.| +++.+++++++++|
T Consensus 177 ~~~~~~~~~~l~~~~~p~~vt~~~~~~~~v~Dpt~~Ee~~~~~~l~va~-~~~g~i~~l~~~g~~~~~~~~l~~~i~~A 254 (271)
T PRK04282 177 VVDKLGEDFPLPVNDKPVTVTFAKIGNYLIVDPTLEEESVMDARITITT-DEDGNIVAIQKSGIGSFTEEEVDKAIDIA 254 (271)
T ss_pred eeccCCCcccCCCCCeeEEEEEEEECCEEEECCCHHHHhhcCceEEEEE-CCCCcEEEEEcCCCCCCCHHHHHHHHHHH
Confidence 9999999999999999999999999999999999996 7788999999985 58999999999876
No 9
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=100.00 E-value=1.3e-42 Score=321.36 Aligned_cols=209 Identities=24% Similarity=0.385 Sum_probs=187.6
Q ss_pred cccCCCCCcCCCCCCCCCcceEEEECCCCCCCeeEEEEeCCeEEEEEE-ECCccccccccC--CCCceEEEEEEeecCCC
Q 028091 2 EFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAV-YGPREVQNKSQQ--MSDQALVRCEYSMANFS 78 (214)
Q Consensus 2 ~~~~~~~~R~DgR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~V~~~V-~gp~e~~~~~~~--~~~~g~l~v~v~~~~~~ 78 (214)
++++++|.|+|||+++|+|++.+++|++++++|||+|+.|+|+|+|+| .||.+..++.+. ..+++.+.++|+++||+
T Consensus 303 ~~il~~g~R~DGR~~~e~Rpi~~~~g~l~~a~GSa~~~~G~Tqvl~~vt~g~~~~~~~~~~~~~~~~~~~~~~y~~~pfs 382 (684)
T TIGR03591 303 ERILKEGKRIDGRDLDTIRPISIEVGVLPRTHGSALFTRGETQALVVTTLGTERDEQIIDDLEGEYRKRFMLHYNFPPYS 382 (684)
T ss_pred HHHhcCCCCCCCCCCCCcCceEEEeCCCCCCCceEEEEeCCeEEEEEEecCCcccccCCcccCCCccEEEEEEEEcCCCC
Confidence 468899999999999999999999999999999999999999999999 588765433211 23578999999999999
Q ss_pred cccccCCCCCCcchHHHHHHHHHHHHHhhcc-CCCCCceEEEEEEEEecCCChHHHHHHHHHHHHHhCCCCCCCceEEEE
Q 028091 79 TGDRMRKPKGDRRSTEISLVIRQTMEACILT-HLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCS 157 (214)
Q Consensus 79 ~~~~~~~~~~~~~~~~l~~~l~~~l~~~i~~-~~~p~~~i~i~v~Vl~~dG~l~~a~~~A~~~AL~~~gIp~~~~~~~vt 157 (214)
++++++.+.+++++.+++++++|+|++++++ +.|| |+|+|+++||++|||..+|+++|+++||+|+||||+++++++|
T Consensus 383 ~~e~~~~g~~~rrei~~~~l~~ral~~~i~~~~~~p-~tI~v~~~VLesdGs~~~Aai~aaslAL~dAgvP~~~~Vagvs 461 (684)
T TIGR03591 383 VGEVGRVGGPGRREIGHGALAERALKAVLPSEEEFP-YTIRVVSEILESNGSSSMASVCGGSLALMDAGVPIKAPVAGIA 461 (684)
T ss_pred CCCcCCCCCCChHHHHHHHHHHHHHHHhcCccccCC-eEEEEEEEEEeCCCChHHHHHHHHHHHHHhcCCCCcCCEEEEE
Confidence 9998777778889999999999999999986 7899 5799999999999999999999999999999999999999999
Q ss_pred EEeeCC-----eEEEeCChhhhhcCCCcEEEEEcCCCCcEEEEEEeec---cCHHHHHHHHhcC
Q 028091 158 AGYLNS-----TPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQVCLK---FSSSFFSLLISQR 213 (214)
Q Consensus 158 ~~~~~~-----~~l~DPt~~Ee~~~~~~~tv~~~~~~~~i~~~~~~G~---~~~~~~~~~~~~~ 213 (214)
+|++++ .+++||+..|+..+++.|+|+ .+..| |+++|++++ ++.+.|+++++||
T Consensus 462 ~gli~~~~~~~~il~D~~~~Ed~~~d~d~~va-~t~~g-I~~lq~d~k~~~i~~~~l~~al~~a 523 (684)
T TIGR03591 462 MGLIKEGDERFAVLSDILGDEDHLGDMDFKVA-GTRDG-ITALQMDIKIDGITREIMEQALEQA 523 (684)
T ss_pred EEEEcCCCcceEEEeCCChHHHhcCCceEEEE-EcCCc-eEEEEEEcCcCCcCHHHHHHHHHHH
Confidence 999952 499999999999999999998 35554 999999876 5999999999987
No 10
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=100.00 E-value=1.9e-42 Score=321.07 Aligned_cols=209 Identities=24% Similarity=0.398 Sum_probs=186.7
Q ss_pred cccCCCCCcCCCCCCCCCcceEEEECCCCCCCeeEEEEeCCeEEEEEE-ECCccccccccC--CCCceEEEEEEeecCCC
Q 028091 2 EFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAV-YGPREVQNKSQQ--MSDQALVRCEYSMANFS 78 (214)
Q Consensus 2 ~~~~~~~~R~DgR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~V~~~V-~gp~e~~~~~~~--~~~~g~l~v~v~~~~~~ 78 (214)
++++++|.|+|||.++|+|++++++|++++++|||+|++|+|+|+|+| .||....++.+. ..+++++.++|+++||+
T Consensus 307 ~~il~~g~R~DGR~~~e~Rpi~~~~g~l~~a~GSal~~~G~T~Vl~~vt~g~~~~~~~~~~~~~~~~~~~~~~y~~~pfs 386 (693)
T PRK11824 307 RRILEEGIRIDGRKLDEIRPISIEVGVLPRTHGSALFTRGETQALVVATLGTLRDEQIIDGLEGEYKKRFMLHYNFPPYS 386 (693)
T ss_pred HHHhcCCCCCCCCCcCcccceEEEeCCCCCCCceEEEEECCeEEEEEEecCCCcccccccccCCCCcEEEEEEEEcCCCC
Confidence 468899999999999999999999999999999999999999999999 587433222111 23679999999999999
Q ss_pred cccccCCCCCCcchHHHHHHHHHHHHHhhcc-CCCCCceEEEEEEEEecCCChHHHHHHHHHHHHHhCCCCCCCceEEEE
Q 028091 79 TGDRMRKPKGDRRSTEISLVIRQTMEACILT-HLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCS 157 (214)
Q Consensus 79 ~~~~~~~~~~~~~~~~l~~~l~~~l~~~i~~-~~~p~~~i~i~v~Vl~~dG~l~~a~~~A~~~AL~~~gIp~~~~~~~vt 157 (214)
++++++.+.+++++.+++++++|+|++++++ +.|| |+|+|+++||++|||..+|+++|+++||+|+||||++++++++
T Consensus 387 ~~e~~~~~~~~rre~~~~~li~ral~~vi~~~~~~p-~~I~v~~~VLe~dGs~~~Aai~aaslAL~dAgvP~~~~Va~vs 465 (693)
T PRK11824 387 VGETGRVGSPGRREIGHGALAERALEPVLPSEEEFP-YTIRVVSEILESNGSSSMASVCGSSLALMDAGVPIKAPVAGIA 465 (693)
T ss_pred CCCcCCCCCCChhHHHHHHHHHHHHHHhcCcccCCC-EEEEEEEEEEecCCCHHHHHHHHHHHHHHhcCCCccCceeEEE
Confidence 9998777778899999999999999999998 6899 6999999999999999999999999999999999999999999
Q ss_pred EEeeCC----eEEEeCChhhhhcCCCcEEEEEcCCCCcEEEEEEeec---cCHHHHHHHHhcC
Q 028091 158 AGYLNS----TPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQVCLK---FSSSFFSLLISQR 213 (214)
Q Consensus 158 ~~~~~~----~~l~DPt~~Ee~~~~~~~tv~~~~~~~~i~~~~~~G~---~~~~~~~~~~~~~ 213 (214)
+|++++ .+++||+..|+..+++.|+|+ .+.+| |+++|++|+ ++.+.|+++++||
T Consensus 466 ~gli~~~~~~~il~D~~~~Ed~~~d~d~~va-~t~~g-i~~lq~d~k~~~i~~~~l~~al~~a 526 (693)
T PRK11824 466 MGLIKEGDKYAVLTDILGDEDHLGDMDFKVA-GTRDG-ITALQMDIKIDGITREILEEALEQA 526 (693)
T ss_pred EEEEcCCCceEEEcCCChhhHhhCCceEEEE-ecCCc-eEEEEEecccCCcCHHHHHHHHHHH
Confidence 999953 388999999999999999998 45555 999998875 6999999999987
No 11
>KOG1614 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp45 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.4e-41 Score=269.32 Aligned_cols=202 Identities=22% Similarity=0.253 Sum_probs=179.4
Q ss_pred CCCCCcCCCCCCCCCcceEEEECCCCCCCeeEEEEeCCeEEEEEEECCccccccccCCCCceEEEEEEeecCCCcccccC
Q 028091 5 SPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDRMR 84 (214)
Q Consensus 5 ~~~~~R~DgR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~V~~~V~gp~e~~~~~~~~~~~g~l~v~v~~~~~~~~~~~~ 84 (214)
++.|.|.|||++.|+|.++|++|- -.||+.+++|+|+|+|.|. .++.+|+.++|.+|.+.+..+++|++++...
T Consensus 18 lk~g~R~DgR~l~efR~lei~fGk---e~gs~~vt~G~Tkvm~~vt--~~ia~Py~dRP~eG~~~I~telsPmA~~sfE- 91 (291)
T KOG1614|consen 18 LKAGLRFDGRSLEEFRDLEIEFGK---EYGSVLVTMGNTKVMARVT--AQIAQPYIDRPHEGSFSIFTELSPMASPSFE- 91 (291)
T ss_pred HHhcccccccchhhhhceEEEecc---ccccEEEEecCeeEEEEee--hhhcCcccCCCCCCeeeeeeccccccccccC-
Confidence 578999999999999999999995 7999999999999999999 5688899999999999999999999977653
Q ss_pred CCCCCcchHHHHHHHHHHHHHh--hccCCC----CC--ceEEEEEEEEecCCChHHHHHHHHHHHHHhCCCC--------
Q 028091 85 KPKGDRRSTEISLVIRQTMEAC--ILTHLM----PR--SQIDIFVQVLQADGGTRSACINAATLALQDAGIP-------- 148 (214)
Q Consensus 85 ~~~~~~~~~~l~~~l~~~l~~~--i~~~~~----p~--~~i~i~v~Vl~~dG~l~~a~~~A~~~AL~~~gIp-------- 148 (214)
.|..++...+|.++|+++++.+ ||+|.+ ++ |.|++++++|+.|||++||++.|+.+||+|++-|
T Consensus 92 ~Gr~~~~~v~l~Rliek~~R~S~aiD~EsLCI~aG~kvW~IRiDlhiLd~DGnlvDaA~iAviaaL~hFrrPdvTv~g~e 171 (291)
T KOG1614|consen 92 PGRKGESEVELSRLIEKALRRSKAIDTESLCIRAGEKVWLIRIDLHILDHDGNLVDAACIAVIAALMHFRRPDVTVGGEE 171 (291)
T ss_pred CCCccchHHHHHHHHHHHHHhccccchHHHHhhhCCeEEEEEEEEEEEcCCCCeehhHHHHHHHHHHhcCCCCcccccce
Confidence 3455677789999999999875 677654 33 8999999999999999999999999999999943
Q ss_pred ---------------CCCceEEEEEEeeC--CeEEEeCChhhhhcCCCcEEEEEcCCCCcEEEEEEeecc--CHHHHHHH
Q 028091 149 ---------------MRDIVTSCSAGYLN--STPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQVCLKF--SSSFFSLL 209 (214)
Q Consensus 149 ---------------~~~~~~~vt~~~~~--~~~l~DPt~~Ee~~~~~~~tv~~~~~~~~i~~~~~~G~~--~~~~~~~~ 209 (214)
|+|+|+|+||++++ +..++|||..||.+.++.++|+ ||++++||.++|.|++ ..+++..|
T Consensus 172 v~ihp~eEr~PvPL~I~HmPIC~tf~ffnkG~ivviDpt~~Ee~~~dGs~vVt-~Nk~rEVc~i~k~G~~~~~~~~i~~C 250 (291)
T KOG1614|consen 172 VIIHPVEEREPVPLSIHHMPICFTFGFFNKGEIVVIDPTEKEEAVMDGSMVVT-MNKNREVCAIQKSGGEILDESVIERC 250 (291)
T ss_pred eEecChhccCCcceeeeeccceEEEEEecCceEEEeCCcHHHHhccCceEEEE-EcCCccEEEEecCCCccccHHHHHHH
Confidence 78999999999997 5788999999999999999998 7999999999999974 77788777
Q ss_pred HhcC
Q 028091 210 ISQR 213 (214)
Q Consensus 210 ~~~~ 213 (214)
...|
T Consensus 251 ~k~A 254 (291)
T KOG1614|consen 251 YKLA 254 (291)
T ss_pred HHHH
Confidence 6544
No 12
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=100.00 E-value=3.2e-40 Score=301.51 Aligned_cols=209 Identities=27% Similarity=0.403 Sum_probs=186.7
Q ss_pred cccCCCCCcCCCCCCCCCcceEEEECCCCCCCeeEEEEeCCeEEEEEEE-CCcccccccc--CCCCceEEEEEEeecCCC
Q 028091 2 EFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVY-GPREVQNKSQ--QMSDQALVRCEYSMANFS 78 (214)
Q Consensus 2 ~~~~~~~~R~DgR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~V~~~V~-gp~e~~~~~~--~~~~~g~l~v~v~~~~~~ 78 (214)
+++++++.|+|||.++++|++++++|++++++|||+++.|+|+|+|.+. ||.+..+..+ ...+++.+.|+|+++||+
T Consensus 328 ~~il~~g~R~DGR~~~eiR~i~~~~g~l~~a~GSa~~~~G~Tqvl~~~tlG~~~~~q~~~~l~~~~~~~~~~~YnfpPFS 407 (719)
T TIGR02696 328 ERVLTEGVRIDGRGVTDIRPLDAEVQVIPRVHGSALFERGETQILGVTTLNMLKMEQQIDSLSPETSKRYMHHYNFPPYS 407 (719)
T ss_pred HHHhcCCCCCCCCCccccccceeecCCCCCCCceEEEEecCcEEEEEEeCCCchhhhhcccccccccceEEEEEeCCCCc
Confidence 5788999999999999999999999999999999999999999999876 4543333211 124568888999999999
Q ss_pred cccccCCCCCCcchHHHHHHHHHHHHHhhc-cCCCCCceEEEEEEEEecCCChHHHHHHHHHHHHHhCCCCCCCceEEEE
Q 028091 79 TGDRMRKPKGDRRSTEISLVIRQTMEACIL-THLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCS 157 (214)
Q Consensus 79 ~~~~~~~~~~~~~~~~l~~~l~~~l~~~i~-~~~~p~~~i~i~v~Vl~~dG~l~~a~~~A~~~AL~~~gIp~~~~~~~vt 157 (214)
++++++.+.+++|+.+++++++|+|+++++ ++.||++ |++..+||++||+...|++||+++||+||||||++++++++
T Consensus 408 t~er~~~~~~~RReighg~La~rALe~vI~~~e~fP~T-IrvvseVLeSdGSss~AsIcaasLALmDAGVPmkd~VAgis 486 (719)
T TIGR02696 408 TGETGRVGSPKRREIGHGALAERALVPVLPSREEFPYA-IRQVSEALGSNGSTSMGSVCASTLSLLNAGVPLKAPVAGIA 486 (719)
T ss_pred ccCCCCCCCCCccHHHHHHHHHHHHHHhhCcHhhCCCE-EEEEEEeeccCCcHHHHHHHHHHHHHHHcCcchhheeeEEE
Confidence 999887777788999999999999999997 6999976 88999999999999999999999999999999999999999
Q ss_pred EEeeCC----e----EEEeCChhhhhcCCCcEEEEEcCCCCcEEEEEEeecc---CHHHHHHHHhcC
Q 028091 158 AGYLNS----T----PLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQVCLKF---SSSFFSLLISQR 213 (214)
Q Consensus 158 ~~~~~~----~----~l~DPt~~Ee~~~~~~~tv~~~~~~~~i~~~~~~G~~---~~~~~~~~~~~~ 213 (214)
+|++++ . +++||+..|+..++..|.|+ ++.++|+++|.+|++ +.+.|+++|+||
T Consensus 487 ~Gli~e~~~~~~~~~iL~Di~g~ED~~Gdmdfkva--gt~~gIt~lQmd~ki~gi~~e~l~~aL~~A 551 (719)
T TIGR02696 487 MGLISDEVDGETRYVALTDILGAEDAFGDMDFKVA--GTSEFVTALQLDTKLDGIPASVLASALKQA 551 (719)
T ss_pred EEEeccccCCCcceeEEeCCCchhhhcCCceEEEE--ecCCCEEEEEEEeeECCCCHHHHHHHHHHH
Confidence 999943 2 89999999999999888886 567999999999986 899999999987
No 13
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=100.00 E-value=3.9e-39 Score=299.80 Aligned_cols=209 Identities=24% Similarity=0.402 Sum_probs=186.7
Q ss_pred cccCCCCCcCCCCCCCCCcceEEEECCCCCCCeeEEEEeCCeEEEEEEE-CCccccccccC---CCCceEEEEEEeecCC
Q 028091 2 EFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVY-GPREVQNKSQQ---MSDQALVRCEYSMANF 77 (214)
Q Consensus 2 ~~~~~~~~R~DgR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~V~~~V~-gp~e~~~~~~~---~~~~g~l~v~v~~~~~ 77 (214)
++|++++.|+|||.++|.|++.+++|++++++|||++++|+|+|+|+|+ ||.+..+..+. .+..+.+.++|+++||
T Consensus 431 ~~i~~~g~R~DGR~~~eiRpI~~e~G~Lp~A~GSAlf~~G~TqVLatVtlGp~~~~q~~d~l~~~~~~~~f~~~y~fPPf 510 (891)
T PLN00207 431 RRIVEGGKRSDGRTPDEIRPINSSCGLLPRAHGSALFTRGETQALAVVTLGDKQMAQRIDNLVDADEVKRFYLQYSFPPS 510 (891)
T ss_pred HHHhcCCCCCCCCCcCccceEEEEeCCcCCCCceEEEEECCeEEEEEEEecCccccccccccccccceeeEEEEEEcCCC
Confidence 4688999999999999999999999999999999999999999999995 88765543222 1356788899999999
Q ss_pred CcccccCCCCCCcchHHHHHHHHHHHHHhhccC-CCCCceEEEEEEEEecCCChHHHHHHHHHHHHHhCCCCCCCceEEE
Q 028091 78 STGDRMRKPKGDRRSTEISLVIRQTMEACILTH-LMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSC 156 (214)
Q Consensus 78 ~~~~~~~~~~~~~~~~~l~~~l~~~l~~~i~~~-~~p~~~i~i~v~Vl~~dG~l~~a~~~A~~~AL~~~gIp~~~~~~~v 156 (214)
+++++++.+.+++++.+++++++|+|++++..+ .|| |.|+|+++||++||+..+|++||+++||+|+||||++++.++
T Consensus 511 s~ge~~r~g~psrREi~hg~L~eRALrpvip~~~~fP-~tIrV~~~VLesDGSssmAaV~aaSLALmDAGIPmk~~VAGv 589 (891)
T PLN00207 511 CVGEVGRIGAPSRREIGHGMLAERALEPILPSEDDFP-YTIRVESTITESNGSSSMASVCGGCLALQDAGVPVKCPIAGI 589 (891)
T ss_pred CCccccCCCCCCHHHHHHHHHHHHHHHHhCCcccCCC-EEEEEEEEEEeCCCChHHHHHHHHHHHHHhcCCCccCceeEE
Confidence 998887777888898999999999999999885 899 699999999999999999999999999999999999999999
Q ss_pred EEEee-C-------Ce--EEEeCChhhhhcCCCcEEEEEcCCCCcEEEEEEeec---cCHHHHHHHHhcC
Q 028091 157 SAGYL-N-------ST--PLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQVCLK---FSSSFFSLLISQR 213 (214)
Q Consensus 157 t~~~~-~-------~~--~l~DPt~~Ee~~~~~~~tv~~~~~~~~i~~~~~~G~---~~~~~~~~~~~~~ 213 (214)
++|++ + +. +++||+..|+..++..|.|+ .+.+.|+++|.+++ ++.+.|+++|+||
T Consensus 590 svGli~d~~~~~~~g~~~IL~Dp~g~Ed~~gdmDfkVA--gT~~gIt~iqmd~k~~gis~e~l~eAL~~A 657 (891)
T PLN00207 590 AMGMVLDTEEFGGDGSPLILSDITGSEDASGDMDFKVA--GNEDGITAFQMDIKVGGITLPIMERALLQA 657 (891)
T ss_pred EEEEEecccccCCCCcEEEEeCCCHHHHhcCCceEEEE--ecccceEEEEEecccCCCCHHHHHHHHHHH
Confidence 99999 2 13 55799999999999999998 56689999999875 4999999999987
No 14
>KOG1069 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp46 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.7e-39 Score=249.22 Aligned_cols=187 Identities=27% Similarity=0.411 Sum_probs=167.3
Q ss_pred CCcceEEEECCCCCCCeeEEEEeCCeEEEEEEECCccccccccCCCCceEEEEEEeecCCCcccccCCCCCCcchHHHHH
Q 028091 18 EMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISL 97 (214)
Q Consensus 18 e~R~i~i~~g~l~~a~GSa~v~~G~T~V~~~V~gp~e~~~~~~~~~~~g~l~v~v~~~~~~~~~~~~~~~~~~~~~~l~~ 97 (214)
.+|++..+.|+++++|||+.|++|+|+|+|+|+||.+++.+. +.|++..++|.|+. . .|..+..++.+++
T Consensus 4 ~lr~~~cei~iLsr~dGSs~fsqgdT~V~c~V~GP~dvk~r~-E~~~katleVi~rp--~-------~G~~~~~eK~~e~ 73 (217)
T KOG1069|consen 4 RLRGIACEISILSRPDGSSEFSQGDTKVICSVYGPIDVKARQ-EDPEKATLEVIWRP--K-------SGVNGTVEKVLER 73 (217)
T ss_pred hhhhhhhhhceecCCCCccceecCCcEEEEEeeCCcchhhcc-cCchhceEEEEEec--c-------cCcchHHHHHHHH
Confidence 689999999999999999999999999999999999988764 56899999988873 2 2345567789999
Q ss_pred HHHHHHHHhhccCCCCCceEEEEEEEEecCCChHHHHHHHHHHHHHhCCCCCCCceEEEEEEeeCC-eEEEeCChhhhhc
Q 028091 98 VIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNS-TPLLDLNYVEDSA 176 (214)
Q Consensus 98 ~l~~~l~~~i~~~~~p~~~i~i~v~Vl~~dG~l~~a~~~A~~~AL~~~gIp~~~~~~~vt~~~~~~-~~l~DPt~~Ee~~ 176 (214)
.|+++|++.|.++.||++.|+|.+||+++||+++.+|+|||++||+|+||||+++++++.+++.++ .+++|||..+|+.
T Consensus 74 iI~~tl~~~I~l~l~Prt~iqVsiqvv~ddgs~LacaINaAclALvDaGIpl~~mfcai~~~~~~d~~lv~Dpt~~qek~ 153 (217)
T KOG1069|consen 74 IIRKTLSKAIILELYPRTTIQVSIQVVEDDGSTLACAINAACLALVDAGIPLRSMFCAISCALHEDGVLVLDPTAKQEKI 153 (217)
T ss_pred HHHHHHHHhheeeecCCceEEEEEEEEecCCcchHHHHHHHHHHHHhcCCchHHhhhhceEEEecCccEEECCcHHhhhh
Confidence 999999999999999999999999999999999999999999999999999999999999999976 8999999999997
Q ss_pred CCCcEEEEEcC---CCCcEEEEEEeeccCHHHHHHHHhcCC
Q 028091 177 GGPDVTVGILP---TLDKVTLLQVCLKFSSSFFSLLISQRP 214 (214)
Q Consensus 177 ~~~~~tv~~~~---~~~~i~~~~~~G~~~~~~~~~~~~~~~ 214 (214)
+.+..++++.. ...+++.++..|.++.+++..+++.|+
T Consensus 154 ~~~~~~lsf~~~~~~~~~vi~s~t~G~~~~d~lf~~le~a~ 194 (217)
T KOG1069|consen 154 STARATLSFEGGSLGEPKVIISETNGEKSEDQLFYVLELAQ 194 (217)
T ss_pred hhceEEEEEecCCCCCcceEEEeccCCCCHHHHHHHHHhhH
Confidence 76666665422 356899999999999999999998764
No 15
>KOG1612 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp42 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.7e-33 Score=225.52 Aligned_cols=205 Identities=18% Similarity=0.233 Sum_probs=172.0
Q ss_pred CCCCCcCCCCCCCCCcceEEEECCCCCCCeeEEEEeCC-eEEEEEEECCccccccccCCCCceEEEEEEeecCCCccccc
Q 028091 5 SPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGN-TKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDRM 83 (214)
Q Consensus 5 ~~~~~R~DgR~~~e~R~i~i~~g~l~~a~GSa~v~~G~-T~V~~~V~gp~e~~~~~~~~~~~g~l~v~v~~~~~~~~~~~ 83 (214)
.++.+|.|||.++++|||.++++++|+++|||+|++|+ |.|+++|+ .|+..+..+.|++|.+.+.|++.|.+++++.
T Consensus 17 ~e~~iR~DGR~~~~~Rpi~vetdVlp~tNGSaRVk~g~~tdiivgVK--aEvg~~~~~~p~egk~~~~VD~S~sasp~f~ 94 (288)
T KOG1612|consen 17 SEPDIRNDGRSCHQFRPIEVETDVLPGTNGSARVKLGDGTDIIVGVK--AEVGSPDDETPVEGKYLFFVDCSPSASPQFQ 94 (288)
T ss_pred cCcccccCCcCccccceEEEEeccccCCCCcEEEEecCCceEEEEEe--eeccCccccCCCCCeEEEEEEecCCcCcccc
Confidence 35789999999999999999999999999999999998 99999999 5677777778999999999999998886654
Q ss_pred CCCCCCcchHHHHHHHHHHHHHh---hccCC---CCC--ceEEEEEEEEecCCChHHHHHHHHHHHHHhCCCC-------
Q 028091 84 RKPKGDRRSTEISLVIRQTMEAC---ILTHL---MPR--SQIDIFVQVLQADGGTRSACINAATLALQDAGIP------- 148 (214)
Q Consensus 84 ~~~~~~~~~~~l~~~l~~~l~~~---i~~~~---~p~--~~i~i~v~Vl~~dG~l~~a~~~A~~~AL~~~gIp------- 148 (214)
.++ .++...+|.+.|+++|++. +++.. -|+ |.|+||+.|++.|||++||+..|+++||.++.+|
T Consensus 95 gRg-gde~~~eltsaLq~~l~~~~sgv~ls~L~lt~~~~W~i~VDvlVi~s~gn~~dAiS~Ai~~AL~~T~lPkv~v~~d 173 (288)
T KOG1612|consen 95 GRG-GDELVEELTSALQRVLNSLGSGVDLSKLQLTPGYCWKIYVDVLVISSDGNLLDAISIAIYAALNNTRLPKVIVAFD 173 (288)
T ss_pred CCC-hhhHHHHHHHHHHHHHhCcCcccchhheeccCCeeEEEEEeEEEEecCCCHHHHHHHHHHHHHhcccCCccccccc
Confidence 332 3445567888888888771 34432 243 8999999999999999999999999999999998
Q ss_pred --------------------CCCceEEEEEEeeCCeEEEeCChhhhhcCCCcEEEEEcCCCCcEEEEEEee--ccCHHHH
Q 028091 149 --------------------MRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQVCL--KFSSSFF 206 (214)
Q Consensus 149 --------------------~~~~~~~vt~~~~~~~~l~DPt~~Ee~~~~~~~tv~~~~~~~~i~~~~~~G--~~~~~~~ 206 (214)
...+|+-++++.++...++|||.+||.++...+.|++ ++.|-+..+.+-| ...++.+
T Consensus 174 d~~~~~i~~s~~~Yd~~~~~~~~~P~ivtlskIG~~~lVD~T~eEe~~a~s~l~Isv-~a~givs~~r~VG~G~l~~s~i 252 (288)
T KOG1612|consen 174 DDGEVEILLSDEEYDLMVKLVENVPLIVTLSKIGTNMLVDPTAEEESVANSGLLISV-SAGGIVSCTRSVGLGDLDPSSI 252 (288)
T ss_pred cCCceeeccCcccchhhhhhcccCCEEEEEEeecceEEccCCccHHHhhhcceEEEE-ecCcceEEEEEecCCCCChhhH
Confidence 2247899999999999999999999999999999996 6666555555544 4888999
Q ss_pred HHHHhcC
Q 028091 207 SLLISQR 213 (214)
Q Consensus 207 ~~~~~~~ 213 (214)
.+||+|+
T Consensus 253 ~~mle~~ 259 (288)
T KOG1612|consen 253 PEMLEQG 259 (288)
T ss_pred HHHHHHH
Confidence 9999875
No 16
>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=1.6e-31 Score=247.67 Aligned_cols=183 Identities=23% Similarity=0.338 Sum_probs=159.8
Q ss_pred cceEEEECCC-CCCCeeEEEEeCCeEEEEEEECCccccccccCCCCceEEEEEEeecCCCcc-----cccCCCCCCcchH
Q 028091 20 RQLRAEIGNV-AKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTG-----DRMRKPKGDRRST 93 (214)
Q Consensus 20 R~i~i~~g~l-~~a~GSa~v~~G~T~V~~~V~gp~e~~~~~~~~~~~g~l~v~v~~~~~~~~-----~~~~~~~~~~~~~ 93 (214)
|++.+++|.+ ++|+|||++++|+|+|+|+|++|.+.+. ..+...++|+|...+|+.+ ..++.|++++++.
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 RTLTLETGKIARQADGAVVVRYGDTVVLVTVVAAKEAKE----GQDFFPLTVNYQEKFYAAGKIPGGFFKREGRPSEKET 80 (684)
T ss_pred ccEEEEECCcCCCCCeEEEEEECCeEEEEEEEcCCCCCC----CCceEeEEEEEEehhhhccCCCCCcccCCCCCCHHHH
Confidence 8999999999 5799999999999999999999976332 1345778888887676554 2345678889999
Q ss_pred HHHHHHHHHHHHhhccCCCCC---ceEEEEEEEEecCCChH-H-HHHHHHHHHHHhCCCCCCCceEEEEEEeeCCeEEEe
Q 028091 94 EISLVIRQTMEACILTHLMPR---SQIDIFVQVLQADGGTR-S-ACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLD 168 (214)
Q Consensus 94 ~l~~~l~~~l~~~i~~~~~p~---~~i~i~v~Vl~~dG~l~-~-a~~~A~~~AL~~~gIp~~~~~~~vt~~~~~~~~l~D 168 (214)
+++++|+|.|++. ||+ |.|+|+++||++||+.. | +++||+++||++++||+++++.++++|++++.+++|
T Consensus 81 l~srlIdR~lrpl-----fp~~~~~~i~V~~~VLs~Dg~~~~d~aai~aAsaAL~~s~IP~~~~v~av~vg~idg~~ild 155 (684)
T TIGR03591 81 LTSRLIDRPIRPL-----FPKGFRNEVQVVATVLSYDPENDPDILAIIGASAALAISGIPFNGPIAAVRVGYIDGQYVLN 155 (684)
T ss_pred HHHHHHhhHHHHh-----cCCCCCceEEEEEEEEecCcCCchHHHHHHHHHHHHHhcCCCcCCCeEEEEEEEECCEEEEc
Confidence 9999999999884 777 79999999999999974 5 999999999999999999999999999999999999
Q ss_pred CChhhhhcCCCcEEEEEcCCCCcEEEEEEeec-cCHHHHHHHHhcC
Q 028091 169 LNYVEDSAGGPDVTVGILPTLDKVTLLQVCLK-FSSSFFSLLISQR 213 (214)
Q Consensus 169 Pt~~Ee~~~~~~~tv~~~~~~~~i~~~~~~G~-~~~~~~~~~~~~~ 213 (214)
||.+|++.++..++|+ .+.+.+++++..|+ ++.++|.++++.|
T Consensus 156 Pt~~E~~~s~~~l~va--~t~~~i~mie~~~~~i~e~~l~~al~~a 199 (684)
T TIGR03591 156 PTVDELEKSDLDLVVA--GTKDAVLMVESEAKELSEEVMLGAIEFG 199 (684)
T ss_pred CCHHHHhhCCceEEEE--ccCCcEEEEEcCCCCCCHHHHHHHHHHH
Confidence 9999999999999997 45678999998876 9999999999875
No 17
>KOG1613 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp43 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.3e-32 Score=219.02 Aligned_cols=206 Identities=21% Similarity=0.253 Sum_probs=172.0
Q ss_pred cCCCCCcCCCCCCCCCcceEEEECCCCCCCeeEEEEeCCeEEEEEEECCccccccccCCCCceEEEEEEeecCCCccccc
Q 028091 4 VSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDRM 83 (214)
Q Consensus 4 ~~~~~~R~DgR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~V~~~V~gp~e~~~~~~~~~~~g~l~v~v~~~~~~~~~~~ 83 (214)
++.+++|+|||+..|+|.+.|+.|.++.+|||+.++.|+|.|+|+|++ |+-.|+.+.|++|.+..++.++|.++...
T Consensus 31 hLse~~RpdgR~lgefRdt~in~g~IsTangSal~K~G~ttvi~~Ik~--ei~epstdapdeg~Iv~n~~lpplcs~r~- 107 (298)
T KOG1613|consen 31 HLSEGIRPDGRKLGEFRDTAINAGNISTANGSALLKSGKTTVICGIKA--EIAEPSTDAPDEGDIVPNYALPPLCSSRF- 107 (298)
T ss_pred HhhcccCcchhhhhHHhhhheecCceeccCcHHHHhcCCcEEEEEeee--eecccccCCCCCcceeecccCCcccccCC-
Confidence 456999999999999999999999999999999999999999999995 56677778899999999999999998654
Q ss_pred CCCCCCcchHHHHHHHHHHHHHh--hccCC---CCC---ceEEEEEEEEecCCChHHHHHHHHHHHHHhCCCCCC-----
Q 028091 84 RKPKGDRRSTEISLVIRQTMEAC--ILTHL---MPR---SQIDIFVQVLQADGGTRSACINAATLALQDAGIPMR----- 150 (214)
Q Consensus 84 ~~~~~~~~~~~l~~~l~~~l~~~--i~~~~---~p~---~~i~i~v~Vl~~dG~l~~a~~~A~~~AL~~~gIp~~----- 150 (214)
+.|++.+.+.-++..|..++.++ |+++. .++ |.++.++.+|++||+++|+|++|.++||.+..+|..
T Consensus 108 RpG~p~dea~viSq~LhdtIl~S~ii~~k~Lci~~gKaawvlYadIicLd~dG~~fDa~w~al~aAlknvklP~a~ide~ 187 (298)
T KOG1613|consen 108 RPGPPTDEAQVISQKLHDTILHSRIIPKKALCIKAGKAAWVLYADIICLDYDGPVFDACWNALMAALKNVKLPRAFIDER 187 (298)
T ss_pred CCCCCchHHHHHHHHHHHHHHhcCCcchhhheeeccceeeEEEEEEEEEcCCCcHHHHHHHHHHHHHhcCCCceeeeccc
Confidence 57788888888898888888765 34433 343 799999999999999999999999999999999820
Q ss_pred --------------------------CceE-----EEEEE-eeCC-eEEEeCChhhhhcCCCcEEEEEcCCCCcEEEEEE
Q 028091 151 --------------------------DIVT-----SCSAG-YLNS-TPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQV 197 (214)
Q Consensus 151 --------------------------~~~~-----~vt~~-~~~~-~~l~DPt~~Ee~~~~~~~tv~~~~~~~~i~~~~~ 197 (214)
..++ ..|.. ++++ .++.|||.+||....+.+||. +++.|+++.+.|
T Consensus 188 ~~~~~~t~e~~ic~~tlt~p~~ln~e~r~~~~~n~~fS~~~vl~~~li~adpT~eEE~l~~~~lTIv-ldss~n~v~l~k 266 (298)
T KOG1613|consen 188 ASDLRMTIEEIICDQTLTVPLMLNAENRAFASQNSDFSEEEVLDDVLIAADPTEEEETLITSTLTIV-LDSSGNYVQLTK 266 (298)
T ss_pred chhhhhhHHHHHHhhhhcchhhhccccccccccCCCccHHHhhcceeEecCCCchhhhhhhceEEEE-EcCCCCEEEEEe
Confidence 1111 12222 3344 455999999999999999997 799999999999
Q ss_pred eec---cCHHHHHHHHhcC
Q 028091 198 CLK---FSSSFFSLLISQR 213 (214)
Q Consensus 198 ~G~---~~~~~~~~~~~~~ 213 (214)
.|+ .+++.+++|++.|
T Consensus 267 ~GG~al~~~~~iK~c~ela 285 (298)
T KOG1613|consen 267 VGGGALITPEMIKRCLELA 285 (298)
T ss_pred cCcccccCHHHHHHHHHHH
Confidence 874 5789999999865
No 18
>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=99.98 E-value=2.1e-31 Score=200.57 Aligned_cols=131 Identities=38% Similarity=0.533 Sum_probs=117.0
Q ss_pred CCcceEEEECCCCCCCeeEEEEeCCeEEEEEEECCccccccccCCCCceEEEEEEeecCCCcccccCCCCCCcchHHHHH
Q 028091 18 EMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISL 97 (214)
Q Consensus 18 e~R~i~i~~g~l~~a~GSa~v~~G~T~V~~~V~gp~e~~~~~~~~~~~g~l~v~v~~~~~~~~~~~~~~~~~~~~~~l~~ 97 (214)
|+|++++++|++++++|||+|++|+|+|+|+|+||.+.+...+..+.+|.+.++|+++|++....++.+.++.++.++++
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 78999999999999999999999999999999999876322221223599999999999998776555667778889999
Q ss_pred HHHHHHHHhhccCCCCCceEEEEEEEEecCC-ChHHHHHHHHHHHHHhCCCC
Q 028091 98 VIRQTMEACILTHLMPRSQIDIFVQVLQADG-GTRSACINAATLALQDAGIP 148 (214)
Q Consensus 98 ~l~~~l~~~i~~~~~p~~~i~i~v~Vl~~dG-~l~~a~~~A~~~AL~~~gIp 148 (214)
+|+++|+++++++.||+|.|+|+++||++|| |++|+++||+++||+|+|||
T Consensus 81 ~l~~~l~~~~~~~~~~~~~i~v~v~vl~~dG~~~~~a~~~A~~~AL~~~~iP 132 (132)
T PF01138_consen 81 LLERALRSSILLEGYPRWQIHVDVQVLSDDGGNLLDAAINAACLALLDAGIP 132 (132)
T ss_dssp HHHHHHHHTBSTTTTSSEEEEEEEEEEECSSSSHHHHHHHHHHHHHHHHTCS
T ss_pred HHhhhccccccccccCceEEEEEEEEEecCCCCHHHHHHHHHHHHHHhcCCC
Confidence 9999999999999999999999999999999 99999999999999999998
No 19
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=99.97 E-value=1.8e-30 Score=241.15 Aligned_cols=187 Identities=21% Similarity=0.290 Sum_probs=158.5
Q ss_pred CcceEEEECCCC-CCCeeEEEEeCCeEEEEEEECCccccccccCCCCceEEEEEEeecCCCcc-----cccCCCCCCcch
Q 028091 19 MRQLRAEIGNVA-KADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTG-----DRMRKPKGDRRS 92 (214)
Q Consensus 19 ~R~i~i~~g~l~-~a~GSa~v~~G~T~V~~~V~gp~e~~~~~~~~~~~g~l~v~v~~~~~~~~-----~~~~~~~~~~~~ 92 (214)
-|++.+++|.+. +|+|||++++|+|+|+|+|++|.+.+. ..+...++|+|...+|+.+ ..++.|++++++
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 GRTLTLETGKLARQANGAVLVRYGDTVVLVTVVASKEPKE----GQDFFPLTVDYEEKTYAAGKIPGGFFKREGRPSEKE 88 (693)
T ss_pred CccEEEEECCcCCCCCeEEEEEECCeEEEEEEEcCCCCCC----CCCeeeeEEEEEehhhhccCCCcccccCCCCCChHH
Confidence 389999999995 799999999999999999999976321 1345678888887777644 233457888999
Q ss_pred HHHHHHHHHHHHHhhccCCCCCceEEEEEEEEecCCCh-HH-HHHHHHHHHHHhCCCCCCCceEEEEEEeeCCeEEEeCC
Q 028091 93 TEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGT-RS-ACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLN 170 (214)
Q Consensus 93 ~~l~~~l~~~l~~~i~~~~~p~~~i~i~v~Vl~~dG~l-~~-a~~~A~~~AL~~~gIp~~~~~~~vt~~~~~~~~l~DPt 170 (214)
.+++++|+|.|++++. ...+|.++|+++||++||+. .| +|+||+++||++++||+++++.++++|++++.+++|||
T Consensus 89 il~srlIdR~lrplfp--~~~~~~i~I~~~VL~~Dg~~~~d~aai~aAsaAL~~s~IP~~~~v~av~vg~i~g~~ivdPt 166 (693)
T PRK11824 89 TLTSRLIDRPIRPLFP--KGFRNEVQVVATVLSVDPENDPDILAMIGASAALSISGIPFNGPIAAVRVGYIDGEFVLNPT 166 (693)
T ss_pred HHHHHHHhhhHHHhCC--CCCCeEEEEEEEEEeCCCCCcHHHHHHHHHHHHHHhcCCCcCCCeEEEEEEEECCEEEEcCC
Confidence 9999999999999521 12358999999999999976 56 89999999999999999999999999999999999999
Q ss_pred hhhhhcCCCcEEEEEcCCCCcEEEEEEeec-cCHHHHHHHHhcC
Q 028091 171 YVEDSAGGPDVTVGILPTLDKVTLLQVCLK-FSSSFFSLLISQR 213 (214)
Q Consensus 171 ~~Ee~~~~~~~tv~~~~~~~~i~~~~~~G~-~~~~~~~~~~~~~ 213 (214)
.+|++.++..++|+. + .+.|++++..|+ ++.++|.++++.|
T Consensus 167 ~~E~~~s~~~l~va~-t-~~~i~mie~~~~~l~e~~l~~al~~a 208 (693)
T PRK11824 167 VEELEESDLDLVVAG-T-KDAVLMVESEAKELSEEVMLEAIEFG 208 (693)
T ss_pred HHHHhhCcceEEEEE-c-cCceEEEECCCCCCCHHHHHHHHHHH
Confidence 999999999999983 4 458999998875 9999999999865
No 20
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=99.94 E-value=2.1e-26 Score=201.83 Aligned_cols=204 Identities=25% Similarity=0.349 Sum_probs=176.6
Q ss_pred ccCCCCCcCCCCCCCCCcceEEEECCCCCCCeeEEEEeCCeEEEEEEE-CCccccccccC--CCCce-EEEEEEeecCCC
Q 028091 3 FVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVY-GPREVQNKSQQ--MSDQA-LVRCEYSMANFS 78 (214)
Q Consensus 3 ~~~~~~~R~DgR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~V~~~V~-gp~e~~~~~~~--~~~~g-~l~v~v~~~~~~ 78 (214)
.+.+.++|.|||..++.|+|.++.+.++..+||+.|+-|.|+|+|+|+ +..+..++.+. .++++ .|..+|+|+|++
T Consensus 352 ~i~~~gkR~DGR~ldelR~I~ce~~m~~~lHGSaLFqRGqTQvlctVtl~s~e~a~klD~l~~~~~~~~FmLhY~FPPya 431 (760)
T KOG1067|consen 352 RILEEGKRCDGRDLDELRNISCEVDMLKTLHGSALFQRGQTQVLCTVTLDSLESAQKLDSLIGPDNGINFMLHYEFPPYA 431 (760)
T ss_pred HHHhcccccCCcchhhhcccceecCccccccchhhhhcCceeEEEEEEcCCHHHhhhhhhhccCccCceEEEEeccCCcc
Confidence 356789999999999999999999999999999999999999999997 33333322222 24444 899999999999
Q ss_pred cccccCCCCCCcchHHHHHHHHHHHHHhhccCCCCCceEEEEEEEEecCCChHHHHHHHHHHHHHhCCCCCCCceEEEEE
Q 028091 79 TGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSA 158 (214)
Q Consensus 79 ~~~~~~~~~~~~~~~~l~~~l~~~l~~~i~~~~~p~~~i~i~v~Vl~~dG~l~~a~~~A~~~AL~~~gIp~~~~~~~vt~ 158 (214)
+++.++.|..++|+.--..+-+|+|.+++. +.|| .+|+|.-.||+.||+.-.|++++.++||+|+|||++.-+.+|.+
T Consensus 432 t~Evgkig~~nRRE~GhgaLAEkaL~~vlP-~dfP-ftIRv~SeVleSnGSsSMASvCGGslALmDaGvPv~a~vAGvai 509 (760)
T KOG1067|consen 432 TNEVGKIGGLNRRELGHGALAEKALLPVLP-EDFP-FTIRVTSEVLESNGSSSMASVCGGSLALMDAGVPVSAHVAGVAI 509 (760)
T ss_pred ccccccccCCcccccCchhHhhhhhhccCc-ccCc-eEEEEeeeeeecCCcchHHhhhcchhhhhhcCCccccccceeEE
Confidence 999988888888877667788999998876 7788 69999999999999999999999999999999999999999999
Q ss_pred EeeC----------C-eEEEeCChhhhhcCCCcEEEEEcCCCCcEEEEEEeeccCHHHHHHHHhcCC
Q 028091 159 GYLN----------S-TPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQVCLKFSSSFFSLLISQRP 214 (214)
Q Consensus 159 ~~~~----------~-~~l~DPt~~Ee~~~~~~~tv~~~~~~~~i~~~~~~G~~~~~~~~~~~~~~~ 214 (214)
|++- + .++.|-...|....+..|.|| .+++.|+++ +++.+.+.+++.||+
T Consensus 510 Glvt~td~e~g~i~dyriltDIlGiEd~~GDMDFKiA--Gt~dGvTA~----gi~l~Iv~eal~~a~ 570 (760)
T KOG1067|consen 510 GLVTKTDPEKGEIEDYRILTDILGIEDYNGDMDFKIA--GTNDGVTAL----GIPLKIVMEALQKAR 570 (760)
T ss_pred EeEeccCcccCCcccceeehhhcchhhhcCCcceeec--cccCcceec----CCcHHHHHHHHHhhh
Confidence 9862 1 488999999999999999998 667778887 889999999998874
No 21
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=99.94 E-value=1.5e-25 Score=209.29 Aligned_cols=186 Identities=18% Similarity=0.194 Sum_probs=159.3
Q ss_pred cceEEEECCCC-CCCeeEEEEeCCeEEEEEEECCccccccccCCCCceEEEEEEeecCCCccc-----ccCCCCCCcchH
Q 028091 20 RQLRAEIGNVA-KADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGD-----RMRKPKGDRRST 93 (214)
Q Consensus 20 R~i~i~~g~l~-~a~GSa~v~~G~T~V~~~V~gp~e~~~~~~~~~~~g~l~v~v~~~~~~~~~-----~~~~~~~~~~~~ 93 (214)
|.+.+++|.+. +|+||+.+++|+|.|+|+|....+.+.. .+-..|.|+|.-..++.+. .+|.|++++++.
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 RHILVETGHIGRQASGSVTVTDGETIVYTSVCLADVPSEP----SDFFPLSVHYQERFSAAGRTSGGFFKREGRTKDHEV 164 (891)
T ss_pred EEEEEEhhHHHHhCCCcEEEEECCeEEEEEEEeccCCCCC----CCccceeEeeeeehhhcCccCCceeccCCCCChHHH
Confidence 57999999995 8999999999999999999853332221 2446788888776666543 345688889999
Q ss_pred HHHHHHHHHHHHhhccCCCCCceEEEEEEEEecCCC--hHHHHHHHHHHHHHhCCCCCCCceEEEEEEeeCCeEEEeCCh
Q 028091 94 EISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGG--TRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNY 171 (214)
Q Consensus 94 ~l~~~l~~~l~~~i~~~~~p~~~i~i~v~Vl~~dG~--l~~a~~~A~~~AL~~~gIp~~~~~~~vt~~~~~~~~l~DPt~ 171 (214)
.++++|+|.|++.+..+.||+.+|.+ +||++||+ ...+++|||++||++++|||++++.||++|++++.+++|||.
T Consensus 165 L~sRlIdR~lRPlfp~~~~~etQI~i--~VLsaDg~~~pd~~AInAASaAL~~SgIP~~gpVaAVrVG~idg~~VlnPt~ 242 (891)
T PLN00207 165 LICRLIDRPLRPTMPKGFYHETQILS--WVLSYDGLHSPDSLAVTAAGIAVALSEVPNLKAIAGVRVGLIGGKFIVNPTT 242 (891)
T ss_pred HHHHHHCccchhhccccCCCCcEEEE--EEEeeCCCCChhhHHHHHHHHHHHhhCCCccCceEEEEEEEECCEEEECCCH
Confidence 99999999999999999999887755 89999998 568999999999999999999999999999999999999999
Q ss_pred hhhhcCCCcEEEEEcCCCCcEEEEEEeecc-CHHHHHHHHhcC
Q 028091 172 VEDSAGGPDVTVGILPTLDKVTLLQVCLKF-SSSFFSLLISQR 213 (214)
Q Consensus 172 ~Ee~~~~~~~tv~~~~~~~~i~~~~~~G~~-~~~~~~~~~~~~ 213 (214)
.|+..++..+.|+. ..+.|++++..|+. +.++|.++|+.|
T Consensus 243 ~E~~~s~ldLvvag--t~~~IvMIE~~a~e~see~l~~Al~~a 283 (891)
T PLN00207 243 KEMEESELDLIMAG--TDSAILMIEGYCNFLPEEKLLEAVEVG 283 (891)
T ss_pred HHHhcCCeeEEEEE--cCCeEEEEEcCCCCCCHHHHHHHHHHH
Confidence 99999988888873 45679999999975 999999999754
No 22
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=99.92 E-value=9.7e-25 Score=196.45 Aligned_cols=208 Identities=25% Similarity=0.394 Sum_probs=181.1
Q ss_pred ccCCCCCcCCCCCCCCCcceEEEECCCCCCCeeEEEEeCCeEEEEEEE-CCccccccccCC--CCceEEEEEEeecCCCc
Q 028091 3 FVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVY-GPREVQNKSQQM--SDQALVRCEYSMANFST 79 (214)
Q Consensus 3 ~~~~~~~R~DgR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~V~~~V~-gp~e~~~~~~~~--~~~g~l~v~v~~~~~~~ 79 (214)
.|++.++|+|||..++.|++.++.|++|+++||+.+..|.|+.++.++ |+....+-.+.. +..-++-.+|+|+||+.
T Consensus 306 ~Il~~~vR~DGR~~~~VRpi~~ev~~lpr~HGS~LFtRGeTQal~v~TLG~~~d~Qvid~l~~e~~krfm~hYNFPp~Sv 385 (692)
T COG1185 306 LILEGKVRIDGRFGDEVRPIGIEVGVLPRTHGSALFTRGETQALVVVTLGTPRDAQVIDILEGEYKKRFLLHYNFPPFSV 385 (692)
T ss_pred HHhcCCcccCCCCcceeeeeeEEecCCCCccchhhhccCCCcceEEEEcCCcchhhhhhhccchhhhheeeeccCCCCCc
Confidence 577899999999999999999999999999999999999999998885 543323322221 12347788999999999
Q ss_pred ccccCCCCCCcchHHHHHHHHHHHHHhhc-cCCCCCceEEEEEEEEecCCChHHHHHHHHHHHHHhCCCCCCCceEEEEE
Q 028091 80 GDRMRKPKGDRRSTEISLVIRQTMEACIL-THLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSA 158 (214)
Q Consensus 80 ~~~~~~~~~~~~~~~l~~~l~~~l~~~i~-~~~~p~~~i~i~v~Vl~~dG~l~~a~~~A~~~AL~~~gIp~~~~~~~vt~ 158 (214)
++.++.+.+.+|+.--.++=+|++...+. .+.|| +.|++.-.|++.+|+.-.|.+++.++||+++|+|++..+.++..
T Consensus 386 GE~g~~g~p~RREiGHG~LA~Ral~~vlp~~e~fp-ytiRvVsEi~eSNGSsSmaSVCg~sLaLmdAGVPIk~pVAGIAM 464 (692)
T COG1185 386 GETGRMGSPGRREIGHGALAERALAPVLPSEEEFP-YTIRVVSEILESNGSSSMASVCGGSLALMDAGVPIKAPVAGIAM 464 (692)
T ss_pred cccCCCCCCCcccccCchhhHHHHhhhCCchhcCC-ceeeeeehhhcccCcccchhhhhhHHHHHhCCCcccccccchhc
Confidence 99988888888888777888999999887 57799 69999999999999999999999999999999999999999999
Q ss_pred EeeCC----eEEEeCChhhhhcCCCcEEEEEcCCCCcEEEEEEeec---cCHHHHHHHHhcC
Q 028091 159 GYLNS----TPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQVCLK---FSSSFFSLLISQR 213 (214)
Q Consensus 159 ~~~~~----~~l~DPt~~Ee~~~~~~~tv~~~~~~~~i~~~~~~G~---~~~~~~~~~~~~~ 213 (214)
|++.+ .++-|-...|....+..|.|+ .+..-|+++|++-+ ++.+.+++++.||
T Consensus 465 GLI~eg~~~~vLsDI~G~EDhlGDMDFKVA--GT~~GiTAlQMDiKi~Git~eim~~AL~QA 524 (692)
T COG1185 465 GLIKEGDKYAVLSDILGDEDHLGDMDFKVA--GTDDGITALQMDIKIKGITKEIMKKALEQA 524 (692)
T ss_pred cceecCCceEeeccccccccccCCceeEEe--cCCCcceeeeeeeeecCCCHHHHHHHHHHH
Confidence 99854 578899999999999999998 67788999999974 6999999999997
No 23
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=99.81 E-value=1.4e-18 Score=159.78 Aligned_cols=184 Identities=15% Similarity=0.180 Sum_probs=151.1
Q ss_pred cceEEEECCCC-CCCeeEEEEe-CCeEEEEEEECCccccccccCCCCceEEEEEEeecCCCccc-----ccCCCCCCcch
Q 028091 20 RQLRAEIGNVA-KADGSAVFEM-GNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGD-----RMRKPKGDRRS 92 (214)
Q Consensus 20 R~i~i~~g~l~-~a~GSa~v~~-G~T~V~~~V~gp~e~~~~~~~~~~~g~l~v~v~~~~~~~~~-----~~~~~~~~~~~ 92 (214)
|++.+++|.+. +|+||+.+++ |+|.|+|+|....+.+. ..+-..|.|+|.-..++.+. .+|.|++++++
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 RTIRFETGRLARQAAGSVVAYLDDETMLLSATTASKQPKD----QFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDA 92 (719)
T ss_pred EEEEEEcchhHhhCCceEEEEecCCeEEEEEEEecCCCCC----CCCCcceeEeeeehhhhcCccCCceeccCCCCChhh
Confidence 47999999995 8999999999 99999999984332221 12446788998776666554 34567888998
Q ss_pred HHHHHHHHHHHHHhhccCCCCC---ceEEEEEEEEecCCCh--HHHHHHHHHHHHHhCCCCCCCceEEEEEEeeCCeEEE
Q 028091 93 TEISLVIRQTMEACILTHLMPR---SQIDIFVQVLQADGGT--RSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLL 167 (214)
Q Consensus 93 ~~l~~~l~~~l~~~i~~~~~p~---~~i~i~v~Vl~~dG~l--~~a~~~A~~~AL~~~gIp~~~~~~~vt~~~~~~~~l~ 167 (214)
...+|+++|.+++ +||+ ..++|.++||+.|+.. --.++||+++||.-++||+...+.+|.+|+++|.+++
T Consensus 93 iL~sRliDR~iRP-----LFp~~~~~e~qi~~~vls~D~~~~pdvla~~~ASaAl~iSdiPf~gPv~~vrVg~i~g~~vi 167 (719)
T TIGR02696 93 ILTCRLIDRPLRP-----SFVKGLRNEVQVVVTVLSLNPDHLYDVVAINAASASTQLAGLPFSGPIGGVRVALIDGQWVA 167 (719)
T ss_pred hHHHHhhCCCCcc-----CCCCCCCcceEEEEEEEEcCCCCChHHHHHHHHHHHHHhcCCCCCCceEEEEEEEECCEEEE
Confidence 8999999999998 5665 3788899999999864 3478999999999999999999999999999999999
Q ss_pred eCChhhhhcCCCcEEEEEcCC----CCcEEEEEE------------eec-cCHHHHHHHHhcC
Q 028091 168 DLNYVEDSAGGPDVTVGILPT----LDKVTLLQV------------CLK-FSSSFFSLLISQR 213 (214)
Q Consensus 168 DPt~~Ee~~~~~~~tv~~~~~----~~~i~~~~~------------~G~-~~~~~~~~~~~~~ 213 (214)
+||.+|...++-.++|+- +. .+.|++++. .++ ++.+.|.+++.-|
T Consensus 168 NPt~~~~~~s~ldLvvag-t~~~~~~~~i~MiE~~a~~~~~~~~~~~a~e~~e~~~~~Ai~~a 229 (719)
T TIGR02696 168 FPTHEQLEGAVFDMVVAG-RVLENGDVAIMMVEAEATEKTWDLVKGGAEAPTEEVVAEGLEAA 229 (719)
T ss_pred CcCHHHHhhCeeeEEEEe-eecCCCCccEEEEecCCccccccccccCCCCCCHHHHHHHHHHH
Confidence 999999999988899983 33 348999997 444 7999999988643
No 24
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=99.74 E-value=6.9e-17 Score=146.07 Aligned_cols=182 Identities=21% Similarity=0.334 Sum_probs=153.9
Q ss_pred CcceEEEECCCC-CCCeeEEEEeCCeEEEEEEECCccccccccCCCCceEEEEEEeecCCCccc-----ccCCCCCCcch
Q 028091 19 MRQLRAEIGNVA-KADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGD-----RMRKPKGDRRS 92 (214)
Q Consensus 19 ~R~i~i~~g~l~-~a~GSa~v~~G~T~V~~~V~gp~e~~~~~~~~~~~g~l~v~v~~~~~~~~~-----~~~~~~~~~~~ 92 (214)
-|++.+++|.+. +|+|++.+++|+|.|++++.+.. .+ ..-|-..|.|+|.-.-|+.+. .+|.|++++++
T Consensus 13 ~~~l~~etg~~A~qa~gav~~~~gdt~vl~t~~~~~-~~----~~~dF~PLtV~y~Ek~yaaGkiPGgf~kREGrpse~e 87 (692)
T COG1185 13 GRTLTLETGKIARQANGAVLVRYGDTVVLATVVASK-PK----EGQDFFPLTVNYEEKTYAAGKIPGGFFKREGRPSEKE 87 (692)
T ss_pred CeeEEEEcchhhhhcCccEEEEECCeEEEEEEeecC-CC----CCCCccceeEeeeeehhccCcCCCcccccCCCCCccc
Confidence 389999999995 89999999999999999998753 22 123556889999877777654 34568889999
Q ss_pred HHHHHHHHHHHHHhhccCCCCC---ceEEEEEEEEecCCCh--HHHHHHHHHHHHHhCCCCCCCceEEEEEEeeCCeEEE
Q 028091 93 TEISLVIRQTMEACILTHLMPR---SQIDIFVQVLQADGGT--RSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLL 167 (214)
Q Consensus 93 ~~l~~~l~~~l~~~i~~~~~p~---~~i~i~v~Vl~~dG~l--~~a~~~A~~~AL~~~gIp~~~~~~~vt~~~~~~~~l~ 167 (214)
...+|+|+|-+++ .||+ .-++|..+|++.|+.. .-.+++++++||.-++||+.....++.+|++++.+++
T Consensus 88 ~L~sRLIDRpiRP-----lFp~g~~~evqIv~tvls~D~~~~pdi~a~~gaSaAl~is~iPf~gpi~~vrvg~idg~~vl 162 (692)
T COG1185 88 ILTSRLIDRPIRP-----LFPKGFRNEVQIVNTVLSVDPENDPDILAMVGASAALSLSGIPFLGPIGAVRVGYIDGIFVL 162 (692)
T ss_pred hhhhhhccccccc-----ccchhhccceEEEEEEEEECCCCCHHHHHHHHHHHHHhccCCCccCccceEEEEEECCEEEE
Confidence 9999999999888 4664 3788899999999976 3478999999999999999999999999999999999
Q ss_pred eCChhhhhcCCCcEEEEEcCCCCcEEEEEEeec-cCHHHHHHHHhc
Q 028091 168 DLNYVEDSAGGPDVTVGILPTLDKVTLLQVCLK-FSSSFFSLLISQ 212 (214)
Q Consensus 168 DPt~~Ee~~~~~~~tv~~~~~~~~i~~~~~~G~-~~~~~~~~~~~~ 212 (214)
+||.+|...+.-.++|+ .+...|.+++.+.. ++.+.+.+++.-
T Consensus 163 NPt~~e~~~s~lDlvVA--GT~~aV~MVE~~a~~l~E~~ml~Av~f 206 (692)
T COG1185 163 NPTLEELEESKLDLVVA--GTKDAVNMVESEADELDEEVMLEAVEF 206 (692)
T ss_pred CCChHHhhhcceeeEec--CChhhhheeecccccCCHHHHHHHHHH
Confidence 99999999988888887 67778999999985 688888888753
No 25
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=99.54 E-value=3.4e-14 Score=125.65 Aligned_cols=187 Identities=19% Similarity=0.233 Sum_probs=143.2
Q ss_pred CCcceEEEECCCC-CCCeeEEEEeCCeEEEEEEECCccccccccCCCCceEEEEEEeecCCCccc-----ccCCCCCCcc
Q 028091 18 EMRQLRAEIGNVA-KADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGD-----RMRKPKGDRR 91 (214)
Q Consensus 18 e~R~i~i~~g~l~-~a~GSa~v~~G~T~V~~~V~gp~e~~~~~~~~~~~g~l~v~v~~~~~~~~~-----~~~~~~~~~~ 91 (214)
--|.+.+++|.+. .|+||+.+..|+|.|+++|... ..+.+ +.--.+.|+|.....+.+. .+|.+.+.++
T Consensus 54 GnR~i~~etGklaRfAngsvvv~~GeT~Vm~Tv~~a-~~PSp----~qFlPL~VdYqeK~aAvGRip~~fmRREg~tkdk 128 (760)
T KOG1067|consen 54 GNREILFETGKLARFANGSVVVQMGETAVMTTVVLA-DKPSP----PQFLPLVVDYQEKFAAVGRIPGNFMRREGRTKDK 128 (760)
T ss_pred CCeEEEEecchhhhhcCCcEEEccCCeEEEEEEEec-CCCCc----cccceEEEehhhhhhhhccCCCcccccccCCcch
Confidence 5699999999996 6999999999999999999742 22222 2234678888654444332 2345566666
Q ss_pred hHHHHHHHHHHHHHhhccCCCCCceEEEEEEEEecCCChH--HHHHHHHHHHHHhCCCCCCCceEEEEEEeeCCeEEEeC
Q 028091 92 STEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTR--SACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDL 169 (214)
Q Consensus 92 ~~~l~~~l~~~l~~~i~~~~~p~~~i~i~v~Vl~~dG~l~--~a~~~A~~~AL~~~gIp~~~~~~~vt~~~~~~~~l~DP 169 (214)
+....++++|.+++......| ...++-..+|..||-.- --++||+++||..+.||+.....++.+|++++.++++|
T Consensus 129 EiL~~rLidrsirplfp~g~~--~etqi~~n~Ls~dG~~~pdvlainaas~Al~lsdvpw~gpig~vRigLi~Ge~vVNP 206 (760)
T KOG1067|consen 129 EILTGRLIDRPIRPLFPKGFY--HETQILCNVLSSDGVHDPDVLAINAASAALSLSDVPWNGPIGAVRIGLIDGEFVVNP 206 (760)
T ss_pred hheeeeccccccccCCcccch--hHHHHHhhheecccccCchHHHHhHHHHHhhhccCCCCCceeeeEeeeecceEEeCc
Confidence 666778888887774222212 24455667888898642 35799999999999999999999999999999999999
Q ss_pred ChhhhhcCCCcEEEEEcCCCCcEEEEEEeec-cCHHHHHHHHhcC
Q 028091 170 NYVEDSAGGPDVTVGILPTLDKVTLLQVCLK-FSSSFFSLLISQR 213 (214)
Q Consensus 170 t~~Ee~~~~~~~tv~~~~~~~~i~~~~~~G~-~~~~~~~~~~~~~ 213 (214)
|..|.+.+.-.+.++ ....++++++..+. +..+.|-+++.++
T Consensus 207 T~kEmssS~Lnlvva--gt~~~~vmle~~s~~i~qqdl~~Aikvg 249 (760)
T KOG1067|consen 207 TRKEMSSSQLNLVVA--GTKSQTVMLEGSSNNILQQDLLHAIKVG 249 (760)
T ss_pred chhhhhhccceeEEE--eccceEEEEEcccccccHHHHHHHHHhc
Confidence 999999988888888 45889999998885 6889998888764
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=99.33 E-value=4.7e-12 Score=84.32 Aligned_cols=62 Identities=16% Similarity=0.173 Sum_probs=51.5
Q ss_pred CceEEEEEEeeCCeEEEeCChhhhhcCCCcEEEEEcCCCCcEEEEEE-eec--cCHHHHHHHHhcC
Q 028091 151 DIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQV-CLK--FSSSFFSLLISQR 213 (214)
Q Consensus 151 ~~~~~vt~~~~~~~~l~DPt~~Ee~~~~~~~tv~~~~~~~~i~~~~~-~G~--~~~~~~~~~~~~~ 213 (214)
|+|+++|++++++.+++|||.+||+.+++.+++++ +.+++++.+++ .|. ++.+++.++++.|
T Consensus 1 ~~~~avt~~~i~~~~v~Dpt~~Ee~~~~~~l~~~~-~~~~~~~~~~~~~g~~~~~~~~l~~~i~~A 65 (68)
T PF03725_consen 1 DPPVAVTVGIIDGELVVDPTAEEESLSDSSLTLAV-DGTGNICTLQKSGGGSELSEDQLEEAIELA 65 (68)
T ss_dssp SEEEEEEEEEETTEEEES--HHHHHHSSEEEEEEE-ETTSSEEEEEEEEESSEEEHHHHHHHHHHH
T ss_pred CCeEEEEEEEECCEEEECCCHHHHhhcCCcEEEEE-ECCCCEEEEEEcCCCCCCCHHHHHHHHHHH
Confidence 68999999999999999999999999999999997 55666655554 455 9999999999876
No 27
>PF06519 TolA: TolA C-terminal; InterPro: IPR014161 TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cut-offs are based largely on conserved operon structure. The Tol-Pal complex is required for maintaining outer membrane integrity, and is also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins OmpC, PhoE and LamB.; GO: 0005215 transporter activity, 0006810 transport, 0016020 membrane; PDB: 2X9A_D 3QDP_A 3QDR_A 1TOL_A 1S62_A.
Probab=50.10 E-value=53 Score=23.05 Aligned_cols=59 Identities=19% Similarity=0.227 Sum_probs=30.9
Q ss_pred cchHHHHHHHHHHHHHhhc-cCCCCCceEEEEEEEEecCCChH--------HHHHHHHHHHHHh-CCCCC
Q 028091 90 RRSTEISLVIRQTMEACIL-THLMPRSQIDIFVQVLQADGGTR--------SACINAATLALQD-AGIPM 149 (214)
Q Consensus 90 ~~~~~l~~~l~~~l~~~i~-~~~~p~~~i~i~v~Vl~~dG~l~--------~a~~~A~~~AL~~-~gIp~ 149 (214)
.+...+...|++.+++-+. -+.|-++...|.+. |..||.+. .+.+.|+..|... +.+|+
T Consensus 11 ~ev~~Y~~~I~~~Iq~~l~~~~~y~GK~C~v~i~-l~~dG~v~~v~~~~GD~~lC~aa~~Ai~k~~~~P~ 79 (96)
T PF06519_consen 11 SEVSRYAAQIKQAIQRNLYDDESYKGKECRVRIR-LAPDGLVLSVTVESGDPALCRAAKSAIAKAAKFPP 79 (96)
T ss_dssp HHHHHHHHHHHHHHHTTTTTGGGGTT--EEEEEE-EETTSEEEEEEEEEE-HHHHHHHHHH-HCCS----
T ss_pred HHHHHHHHHHHHHHHHhcCCccccCCCEEEEEEE-ECCCCcEEEeeecCCCHHHHHHHHHHHHHhcCCCC
Confidence 3334566778888876543 34565554444444 56677642 4567777777454 45763
No 28
>KOG2925 consensus Predicted translation initiation factor related to eIF-1A [Translation, ribosomal structure and biogenesis]
Probab=39.76 E-value=9 Score=29.20 Aligned_cols=44 Identities=23% Similarity=0.176 Sum_probs=27.8
Q ss_pred CCeEEEeCChhhhhcCCCcEEEEEcCCCCcEEEEEEeeccCHHH
Q 028091 162 NSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQVCLKFSSSF 205 (214)
Q Consensus 162 ~~~~l~DPt~~Ee~~~~~~~tv~~~~~~~~i~~~~~~G~~~~~~ 205 (214)
++.+|+||+.+|++...-.-+|.|.=-..++..+++.|..+..-
T Consensus 64 g~FvvVdpiee~~~g~KVkgeI~yVl~~d~vr~lqk~g~WPe~F 107 (167)
T KOG2925|consen 64 GSFVVVDPIEEEKSGSKVKGEICYVLFFDQVRLLQKSGEWPEIF 107 (167)
T ss_pred CCEEEEccccccccCCccceEEEEEEccHHHHHHHHcCCcchhh
Confidence 45788999998876554333333322345677778888765543
No 29
>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=39.61 E-value=53 Score=25.40 Aligned_cols=26 Identities=19% Similarity=0.070 Sum_probs=22.4
Q ss_pred cCCCCcEEEEEEeeccCHHHHHHHHhc
Q 028091 186 LPTLDKVTLLQVCLKFSSSFFSLLISQ 212 (214)
Q Consensus 186 ~~~~~~i~~~~~~G~~~~~~~~~~~~~ 212 (214)
+++.|+|.+ -++|.++.+++++.++.
T Consensus 131 lDK~G~V~F-~k~G~Ls~~Ev~qVi~L 156 (160)
T PF09695_consen 131 LDKQGKVQF-VKEGALSPAEVQQVIAL 156 (160)
T ss_pred EcCCccEEE-EECCCCCHHHHHHHHHH
Confidence 589998887 68999999999998863
No 30
>COG3625 PhnH Uncharacterized enzyme of phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=37.96 E-value=2.1e+02 Score=22.79 Aligned_cols=98 Identities=10% Similarity=0.047 Sum_probs=56.4
Q ss_pred HHHHHHhhccCCCCCceEEEEEEEEecCCChHHHHHHHHHHHHHhCCCC-----------------------CCCceEEE
Q 028091 100 RQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIP-----------------------MRDIVTSC 156 (214)
Q Consensus 100 ~~~l~~~i~~~~~p~~~i~i~v~Vl~~dG~l~~a~~~A~~~AL~~~gIp-----------------------~~~~~~~v 156 (214)
+++|+..++--.+|+....++-. -..=--+..+.-|++++|+|...| +...+--.
T Consensus 18 Q~~FR~ll~a~A~PG~v~~l~~~--~~~p~pL~~At~Av~LtL~D~dTpvWL~~~l~~~~v~~wL~FHtgaplt~~~~~A 95 (196)
T COG3625 18 QRVFRALLDAMARPGVVVPLDRA--AAPPAPLNPATGAVCLTLCDNDTPVWLDPALSSSAVRAWLRFHTGAPLTETPEEA 95 (196)
T ss_pred HHHHHHHHHhhcCCCceeecccc--cCCCcCCCHHHHHHHHHHhcCCCceeecccccchhhhhhhhhccCCcccCCcccc
Confidence 45566666555788755544311 112234788899999999999766 33445555
Q ss_pred EEEeeCCe------EEEeCChhhhhcCCCcEEEEEcC-CCCcEEEEEEee
Q 028091 157 SAGYLNST------PLLDLNYVEDSAGGPDVTVGILP-TLDKVTLLQVCL 199 (214)
Q Consensus 157 t~~~~~~~------~l~DPt~~Ee~~~~~~~tv~~~~-~~~~i~~~~~~G 199 (214)
.||++++. -..+|-..|--..+.++.|=+-+ +.|.-+.+...|
T Consensus 96 ~FAv~~~~~~~~~l~~f~~Gt~eyPdrStTLiiQV~sl~~G~~l~l~GPG 145 (196)
T COG3625 96 RFAVVDDGAALPQLSGFAPGTAEYPDRSTTLIIQVASLEGGRPLRLTGPG 145 (196)
T ss_pred eEEEecCcccchhhcccCCCcccCCCcceEEEEEecccCCCCceEeECCC
Confidence 67776542 33555555554455566664422 345555555444
No 31
>PF13098 Thioredoxin_2: Thioredoxin-like domain; PDB: 1T3B_A 2L57_A 1EEJ_B 1TJD_A 1JZD_B 1JZO_A 1G0T_B 3GV1_A 1V58_A 2H0H_A ....
Probab=34.72 E-value=87 Score=21.56 Aligned_cols=28 Identities=14% Similarity=0.058 Sum_probs=18.9
Q ss_pred EEEEcCCCCcEEEEEEeeccCHHHHHHHH
Q 028091 182 TVGILPTLDKVTLLQVCLKFSSSFFSLLI 210 (214)
Q Consensus 182 tv~~~~~~~~i~~~~~~G~~~~~~~~~~~ 210 (214)
|+.+++.+|+++.. ..|-.+.++|.++|
T Consensus 85 t~~~~d~~G~~v~~-~~G~~~~~~l~~~L 112 (112)
T PF13098_consen 85 TIVFLDKDGKIVYR-IPGYLSPEELLKML 112 (112)
T ss_dssp EEEECTTTSCEEEE-EESS--HHHHHHHH
T ss_pred EEEEEcCCCCEEEE-ecCCCCHHHHHhhC
Confidence 44446778888854 56889999998875
No 32
>PF03727 Hexokinase_2: Hexokinase; InterPro: IPR022673 Hexokinase is an important enzyme that catalyses the ATP-dependent conversion of aldo- and keto-hexose sugars to the hexose-6-phosphate (H6P). The enzyme can catalyse this reaction on glucose, fructose, sorbitol and glucosamine, and as such is the first step in a number of metabolic pathways []. The addition of a phosphate group to the sugar acts to trap it in a cell, since the negatively charged phosphate cannot easily traverse the plasma membrane. The enzyme is widely distributed in eukaryotes. There are three isozymes of hexokinase in yeast (PI, PII and glucokinase): isozymes PI and PII phosphorylate both aldo- and keto-sugars; glucokinase is specific for aldo-hexoses. All three isozymes contain two domains []. Structural studies of yeast hexokinase reveal a well-defined catalytic pocket that binds ATP and hexose, allowing easy transfer of the phosphate from ATP to the sugar []. Vertebrates contain four hexokinase isozymes, designated I to IV, where types I to III contain a duplication of the two-domain yeast-type hexokinases. Both the N- and C-terminal halves bind hexose and H6P, though in types I an III only the C-terminal half supports catalysis, while both halves support catalysis in type II. The N-terminal half is the regulatory region. Type IV hexokinase is similar to the yeast enzyme in containing only the two domains, and is sometimes incorrectly referred to as glucokinase. The different vertebrate isozymes differ in their catalysis, localisation and regulation, thereby contributing to the different patterns of glucose metabolism in different tissues []. Whereas types I to III can phosphorylate a variety of hexose sugars and are inhibited by glucose-6-phosphate (G6P), type IV is specific for glucose and shows no G6P inhibition. Type I enzyme may have a catabolic function, producing H6P for energy production in glycolysis; it is bound to the mitochondrial membrane, which enables the coordination of glycolysis with the TCA cycle. Types II and III enzyme may have anabolic functions, providing H6P for glycogen or lipid synthesis. Type IV enzyme is found in the liver and pancreatic beta-cells, where it is controlled by insulin (activation) and glucagon (inhibition). In pancreatic beta-cells, type IV enzyme acts as a glucose sensor to modify insulin secretion. Mutations in type IV hexokinase have been associated with diabetes mellitus. Hexokinase (2.7.1.1 from EC), a fructose and glucose phosphorylating enzyme, contains two structurally similar domains represented by this family and PF00349 from PFAM. Some members of the family have two copies of each of these domains. This entry represents the more C-terminal domain.; GO: 0005524 ATP binding, 0016773 phosphotransferase activity, alcohol group as acceptor, 0005975 carbohydrate metabolic process; PDB: 4DHY_A 3ID8_A 4DCH_A 3FGU_A 3QIC_A 3A0I_X 3VEY_A 3IDH_A 3VEV_A 3VF6_A ....
Probab=31.30 E-value=1.2e+02 Score=24.88 Aligned_cols=40 Identities=20% Similarity=0.286 Sum_probs=24.4
Q ss_pred HHHHHHHHHHHhhccCCCCCceEEEEEEEEecCCChHHHHHHHHHH
Q 028091 95 ISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATL 140 (214)
Q Consensus 95 l~~~l~~~l~~~i~~~~~p~~~i~i~v~Vl~~dG~l~~a~~~A~~~ 140 (214)
+...+++.++....-+ ...+ .+ ++.+||+..-|++.|+.+
T Consensus 202 f~~~l~~~l~~L~~~~---~~~v--~~-~~~~dgsg~GAAi~AA~a 241 (243)
T PF03727_consen 202 FRERLQEALDELLPEE---GCKV--EF-VLSEDGSGVGAAIAAAVA 241 (243)
T ss_dssp HHHHHHHHHHHHSTT----CEEE--EE-EE-SSTHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhcccc---cceE--EE-EEecCchHHHHHHHHHHh
Confidence 5556666666632211 2343 33 577999999999988865
No 33
>PF14060 DUF4252: Domain of unknown function (DUF4252)
Probab=27.59 E-value=1.2e+02 Score=22.54 Aligned_cols=31 Identities=13% Similarity=0.178 Sum_probs=25.0
Q ss_pred EEEEEcCCCCcEEEEEEeeccCHHHHHHHHhc
Q 028091 181 VTVGILPTLDKVTLLQVCLKFSSSFFSLLISQ 212 (214)
Q Consensus 181 ~tv~~~~~~~~i~~~~~~G~~~~~~~~~~~~~ 212 (214)
+.+.. ...++.+.++-.|.++++++.+++.+
T Consensus 125 lvi~~-~~~~e~~~v~i~G~i~~~~I~~l~~s 155 (155)
T PF14060_consen 125 LVILV-SDKDEFVVVRIKGDIDPEDISKLIKS 155 (155)
T ss_pred EEEEE-eCCCcEEEEEEeCCCCHHHHHHHHcC
Confidence 44432 45889999999999999999998753
No 34
>PF15645 Tox-PLDMTX: Dermonecrotoxin of the Papain-like fold
Probab=25.81 E-value=2.3e+02 Score=21.27 Aligned_cols=31 Identities=16% Similarity=0.100 Sum_probs=20.5
Q ss_pred hCCCCCCCceEEEEEEeeCC-eEEEeCChhhhhcC
Q 028091 144 DAGIPMRDIVTSCSAGYLNS-TPLLDLNYVEDSAG 177 (214)
Q Consensus 144 ~~gIp~~~~~~~vt~~~~~~-~~l~DPt~~Ee~~~ 177 (214)
....|+.|.++- +.++| .+++|||..+-...
T Consensus 38 ~~~~p~NH~vv~---~k~~g~eyV~D~Ta~QF~~~ 69 (135)
T PF15645_consen 38 NDDSPTNHFVVV---AKKNGKEYVFDPTAHQFSNK 69 (135)
T ss_pred CccCCcceEEEE---EEECCEEEEEeCcHHHhhcc
Confidence 345678887533 44444 79999999876443
No 35
>PF14237 DUF4339: Domain of unknown function (DUF4339)
Probab=23.93 E-value=79 Score=18.47 Aligned_cols=17 Identities=35% Similarity=0.155 Sum_probs=14.3
Q ss_pred EEeeccCHHHHHHHHhc
Q 028091 196 QVCLKFSSSFFSLLISQ 212 (214)
Q Consensus 196 ~~~G~~~~~~~~~~~~~ 212 (214)
++.|.++.++++++++.
T Consensus 9 ~~~GP~s~~el~~l~~~ 25 (45)
T PF14237_consen 9 QQQGPFSLEELRQLISS 25 (45)
T ss_pred eEECCcCHHHHHHHHHc
Confidence 46789999999998865
No 36
>PF04679 DNA_ligase_A_C: ATP dependent DNA ligase C terminal region ; InterPro: IPR012309 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalysing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase, one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC), the latter being restricted to eubacteria. Eukaryotic, archaebacterial, viral and some eubacterial DNA ligases are ATP-dependent. The first step in the ligation reaction is the formation of a covalent enzyme-AMP complex. The co-factor ATP is cleaved to pyrophosphate and AMP, with the AMP being covalently joined to a highly conserved lysine residue in the active site of the ligase. The activated AMP residue is then transferred to the 5'phosphate of the nick, before the nick is sealed by phosphodiester-bond formation and AMP elimination [,]. Vertebrate cells encode three well-characterised DNA ligases (DNA ligases I, III and IV), all of which are related in structure and sequence. With the exception of the atypically small PBCV-1 viral enzyme, two regions of primary sequence are common to all members of the family. The catalytic region comprises six conserved sequence motifs (I, III, IIIa, IV, V-VI), motif I includes the lysine residue that is adenylated in the first step of the ligation reaction. The function of the second, less well-conserved region is unknown. When folded, each protein comprises of two distinct sub-domains: a large amino-terminal sub-domain ('domain 1') and a smaller carboxy-terminal sub-domain ('domain 2'). The ATP-binding site of the enzyme lies in the cleft between the two sub-domains. Domain 1 consists of two antiparallel beta sheets flanked by alpha helices, whereas domain 2 consists of a five-stranded beta barrel and a single alpha helix, which form the oligonucleotide-binding fold [, ]. This region is found in many but not all ATP-dependent DNA ligase enzymes (6.5.1.1 from EC). It is thought to constitute part of the catalytic core of ATP dependent DNA ligase []. ; GO: 0003910 DNA ligase (ATP) activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 3RR5_A 2CFM_A 1X9N_A 1VS0_B 3GDE_A 2HIX_A 2HIV_A 3L2P_A 4EQ5_A.
Probab=21.21 E-value=1.6e+02 Score=20.17 Aligned_cols=33 Identities=12% Similarity=0.116 Sum_probs=23.1
Q ss_pred CcEEEEEcCCC-CcEEEEEEee-ccCHHHHHHHHh
Q 028091 179 PDVTVGILPTL-DKVTLLQVCL-KFSSSFFSLLIS 211 (214)
Q Consensus 179 ~~~tv~~~~~~-~~i~~~~~~G-~~~~~~~~~~~~ 211 (214)
+.+.+++.+.. +++.++-+-| +++.++++++.+
T Consensus 6 ~slllg~~d~~~~~l~~vg~vgtG~~~~~~~~l~~ 40 (97)
T PF04679_consen 6 GSLLLGVYDPDSGRLVYVGKVGTGFSDEELRELRE 40 (97)
T ss_dssp EEEEEEEEETTTTEEEEEEEE-SS--HHHHHHHHH
T ss_pred ceEEEEEEcCCCCcEEEEEEECCCCCHHHHHHHHH
Confidence 45777776655 8999998887 599999888765
No 37
>PF13202 EF-hand_5: EF hand; PDB: 3DD4_A 2Q4U_A 2BE4_A 1UHJ_B 1UHI_A 1UHH_B 1EJ3_B 1UHK_A 2ZFD_A 1UHN_A ....
Probab=21.06 E-value=51 Score=16.76 Aligned_cols=13 Identities=31% Similarity=0.115 Sum_probs=9.5
Q ss_pred eeccCHHHHHHHH
Q 028091 198 CLKFSSSFFSLLI 210 (214)
Q Consensus 198 ~G~~~~~~~~~~~ 210 (214)
+|.++.++|++++
T Consensus 13 DG~is~~E~~~~~ 25 (25)
T PF13202_consen 13 DGKISFEEFQRLV 25 (25)
T ss_dssp SSEEEHHHHHHHH
T ss_pred CCcCCHHHHHHHC
Confidence 5778888887754
No 38
>PF03764 EFG_IV: Elongation factor G, domain IV; InterPro: IPR005517 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. Elongation factor EF2 (EF-G) is a G-protein. It brings about the translocation of peptidyl-tRNA and mRNA through a ratchet-like mechanism: the binding of GTP-EF2 to the ribosome causes a counter-clockwise rotation in the small ribosomal subunit; the hydrolysis of GTP to GDP by EF2 and the subsequent release of EF2 causes a clockwise rotation of the small subunit back to the starting position [, ]. This twisting action destabilises tRNA-ribosome interactions, freeing the tRNA to translocate along the ribosome upon GTP-hydrolysis by EF2. EF2 binding also affects the entry and exit channel openings for the mRNA, widening it when bound to enable the mRNA to translocate along the ribosome. EF2 has five domains. This entry represents domain IV found in EF2 (or EF-G) of both prokaryotes and eukaryotes. The EF2-GTP-ribosome complex undergoes extensive structural rearrangement for tRNA-mRNA movement to occur. Domain IV, which extends from the 'body' of the EF2 molecule much like a lever arm, appears to be essential for the structural transition to take place. More information about these proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005525 GTP binding; PDB: 3J0E_H 1FNM_A 3IZP_E 2OM7_L 1KTV_A 2J7K_A 2BM1_A 2BM0_A 2BV3_A 1ZM3_E ....
Probab=20.63 E-value=3.2e+02 Score=19.28 Aligned_cols=54 Identities=20% Similarity=0.249 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHHhhccC---CCCCceEEEEEEEEecC------CChHHHHHHHHHHHHHhCC
Q 028091 93 TEISLVIRQTMEACILTH---LMPRSQIDIFVQVLQAD------GGTRSACINAATLALQDAG 146 (214)
Q Consensus 93 ~~l~~~l~~~l~~~i~~~---~~p~~~i~i~v~Vl~~d------G~l~~a~~~A~~~AL~~~g 146 (214)
.++...|.+-|+.....- .||=..+.|.+.=.+.. +....|+-.|...||..++
T Consensus 58 ~~~~~ai~~G~~~a~~~Gpl~g~pv~~v~v~l~~~~~~~~~s~~~a~~~aa~~a~~~al~~A~ 120 (120)
T PF03764_consen 58 KEFQDAIEEGFQSALSSGPLCGYPVTDVKVTLTDGEYHEVDSSPGAFRAAARRAFREALKKAG 120 (120)
T ss_dssp GGGHHHHHHHHHHHHCSSTTTSSEB-SEEEEEEEEEC-TTTBSHHHHHHHHHHHHHHHHHHS-
T ss_pred HHHHHHHhhhhhheecccccCCCceEEEEEEEEEeeecCCcCCHHHHHHHHHHHHHHHHHhcC
Confidence 456677777777765322 24533444444433321 2245677777777777664
No 39
>PTZ00107 hexokinase; Provisional
Probab=20.56 E-value=2e+02 Score=26.26 Aligned_cols=40 Identities=18% Similarity=0.286 Sum_probs=25.3
Q ss_pred HHHHHHHHHHHhhccCCCCCceEEEEEEEEecCCChHHHHHHHHHH
Q 028091 95 ISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATL 140 (214)
Q Consensus 95 l~~~l~~~l~~~i~~~~~p~~~i~i~v~Vl~~dG~l~~a~~~A~~~ 140 (214)
+...+++.|+..+.-+ ...| + .++.+||+..-|++.|+++
T Consensus 421 f~~~~~~~l~~ll~~~---~~~v--~-l~~a~DGSg~GAAl~AA~~ 460 (464)
T PTZ00107 421 FRRLLQEYINSILGPD---AGNV--V-FYLADDGSGKGAAIIAAMV 460 (464)
T ss_pred HHHHHHHHHHHHhCCC---CCcE--E-EEEccCchHHHHHHHHHHh
Confidence 4455666666543211 1233 3 3588999999999988875
Done!