Query 025943
Match_columns 246
No_of_seqs 145 out of 1255
Neff 7.8
Searched_HMMs 46136
Date Fri Mar 29 11:19:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025943.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025943hhsearch_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 6.6E-51 1.4E-55 348.7 30.1 222 3-225 2-229 (230)
2 PRK03983 exosome complex exonu 100.0 1.7E-50 3.7E-55 349.0 29.8 223 2-225 7-235 (244)
3 KOG1068 Exosomal 3'-5' exoribo 100.0 1.5E-49 3.3E-54 333.4 21.2 226 1-226 5-236 (245)
4 COG0689 Rph RNase PH [Translat 100.0 1.1E-46 2.4E-51 317.2 24.6 219 3-222 2-229 (230)
5 PRK00173 rph ribonuclease PH; 100.0 1.2E-45 2.5E-50 317.8 27.8 213 9-223 1-237 (238)
6 TIGR01966 RNasePH ribonuclease 100.0 1.1E-44 2.3E-49 311.5 28.1 211 10-222 1-235 (236)
7 PRK04282 exosome complex RNA-b 100.0 3.9E-42 8.4E-47 301.2 25.7 215 5-223 20-270 (271)
8 TIGR03591 polynuc_phos polyrib 100.0 4.2E-40 9.1E-45 318.8 28.9 222 2-226 303-542 (684)
9 COG2123 RNase PH-related exori 100.0 7.6E-40 1.6E-44 278.6 26.0 216 4-223 18-271 (272)
10 PRK11824 polynucleotide phosph 100.0 4.7E-40 1E-44 319.1 28.0 221 2-225 307-544 (693)
11 TIGR02696 pppGpp_PNP guanosine 100.0 6.4E-39 1.4E-43 306.5 24.1 222 1-225 327-569 (719)
12 KOG1069 Exosomal 3'-5' exoribo 100.0 3.4E-38 7.3E-43 256.3 18.8 198 18-225 4-211 (217)
13 PLN00207 polyribonucleotide nu 100.0 2.4E-37 5.1E-42 301.2 27.3 222 2-226 431-676 (891)
14 KOG1614 Exosomal 3'-5' exoribo 100.0 3.3E-37 7.1E-42 257.0 22.5 222 5-233 18-280 (291)
15 TIGR03591 polynuc_phos polyrib 100.0 2.9E-30 6.3E-35 250.3 25.3 202 20-232 5-225 (684)
16 PF01138 RNase_PH: 3' exoribon 100.0 3.7E-30 8.1E-35 201.9 16.3 130 18-148 1-132 (132)
17 PRK11824 polynucleotide phosph 100.0 2.8E-29 6.1E-34 244.0 25.1 200 19-226 13-227 (693)
18 KOG1612 Exosomal 3'-5' exoribo 100.0 4E-28 8.7E-33 203.7 24.9 224 6-233 18-285 (288)
19 KOG1613 Exosomal 3'-5' exoribo 100.0 1.8E-28 3.9E-33 204.4 14.2 214 2-219 29-297 (298)
20 PLN00207 polyribonucleotide nu 99.9 6E-26 1.3E-30 221.7 21.7 204 20-231 89-308 (891)
21 KOG1067 Predicted RNA-binding 99.9 9.9E-25 2.2E-29 200.0 15.1 215 3-225 352-587 (760)
22 COG1185 Pnp Polyribonucleotide 99.9 1.1E-22 2.4E-27 191.6 15.5 221 3-226 306-543 (692)
23 TIGR02696 pppGpp_PNP guanosine 99.8 5E-19 1.1E-23 170.2 21.0 202 20-232 17-255 (719)
24 COG1185 Pnp Polyribonucleotide 99.8 7.4E-18 1.6E-22 159.2 19.2 204 19-234 13-235 (692)
25 KOG1067 Predicted RNA-binding 99.6 1.4E-14 3E-19 133.8 11.3 214 18-238 54-281 (760)
26 PF03725 RNase_PH_C: 3' exorib 98.4 1.1E-06 2.5E-11 60.7 6.9 60 151-210 1-68 (68)
27 PRK00153 hypothetical protein; 50.2 1E+02 0.0022 22.8 7.9 64 170-234 35-103 (104)
28 PF06519 TolA: TolA C-terminal 44.2 85 0.0019 23.0 5.7 60 89-149 10-79 (96)
29 PRK14624 hypothetical protein; 38.9 1.7E+02 0.0038 22.2 7.2 66 170-236 38-108 (115)
30 PRK14628 hypothetical protein; 37.8 1.8E+02 0.004 22.2 7.2 63 171-234 52-117 (118)
31 PF12651 RHH_3: Ribbon-helix-h 36.5 78 0.0017 19.5 3.8 34 194-227 8-41 (44)
32 PF01402 RHH_1: Ribbon-helix-h 34.2 55 0.0012 19.1 2.8 34 194-227 5-38 (39)
33 COG3040 Blc Bacterial lipocali 33.4 1.5E+02 0.0033 24.2 5.9 52 162-214 111-163 (174)
34 PF02575 YbaB_DNA_bd: YbaB/Ebf 28.7 2.1E+02 0.0046 20.2 7.8 58 171-229 28-90 (93)
35 PF03333 PapB: Adhesin biosynt 25.9 97 0.0021 22.6 3.3 32 192-223 20-51 (91)
36 PHA01623 hypothetical protein 23.8 1.3E+02 0.0029 19.6 3.4 35 194-228 19-53 (56)
37 PF09695 YtfJ_HI0045: Bacteria 23.8 2.6E+02 0.0057 22.6 5.7 30 179-209 130-159 (160)
38 PRK05463 hypothetical protein; 22.9 1.3E+02 0.0028 26.3 4.1 28 137-164 120-147 (262)
39 PRK14621 hypothetical protein; 22.1 3.5E+02 0.0076 20.4 6.6 65 170-235 36-103 (111)
40 PF02962 CHMI: 5-carboxymethyl 21.8 3.6E+02 0.0078 20.7 6.0 55 63-127 56-110 (124)
41 PRK14627 hypothetical protein; 21.0 3.5E+02 0.0076 19.9 7.8 60 170-230 33-97 (100)
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=6.6e-51 Score=348.75 Aligned_cols=222 Identities=46% Similarity=0.773 Sum_probs=207.4
Q ss_pred ccCCCCCCCCCCCCCCCcceEEEECCCCCCCeEEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCCcccc
Q 025943 3 FVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDR 82 (246)
Q Consensus 3 ~~~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~gp~e~~~~~~~~p~~g~l~v~v~~~~~s~~~~ 82 (246)
+|+++|+|+|||+++|+|++++++|++++++|||++++|+|+|+|+|+||.++..+....|++|.++|+++++||++.++
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 57899999999999999999999999999999999999999999999999998777667789999999999999998665
Q ss_pred ccCCCCCchHHHHHHHHHHHHhhhhhcCCCCCceEEEEEEEEecCCChHHHHHHHHHHHHHhCCCCCcCceeEEEEEEec
Q 025943 83 MRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLN 162 (246)
Q Consensus 83 ~~~~~~~~~~~~l~~~l~~~l~~~i~le~~p~~~I~i~v~VL~~dG~ll~a~i~aa~~AL~~a~Ip~~~~~~avs~~~~~ 162 (246)
++ +++++++++++++|+++|++++.++.||++.|+|.++||++||++++|++||+++||.|+||||+++++++|+++++
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 45788899999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CceeecC------CCCCeEEEEEcCCCCcEEEEEeecCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025943 163 STPLLDS------AGGPDVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVRKFL 225 (246)
Q Consensus 163 ~~~lvD~------~~~~~ltv~~~~~~~~i~~i~~~g~~~~~~l~~~l~~A~~~~~~i~~~i~~~l~~~ 225 (246)
+.+++|+ .+.++++|+++++.++|+++++.|.++++++.++++.|.++|+++.++|++++++.
T Consensus 161 ~~~v~Dpt~~Ee~~~~~~l~va~~~~~~~i~~i~~~g~~~~e~~~~~l~~a~~~~~~l~~~~~~~l~~~ 229 (230)
T TIGR02065 161 GVVVLDLNEEEDMYGEADMPVAMMPKLGEITLLQLDGDMTPDEFRQALDLAVKGIKIIYQIQREALKNK 229 (230)
T ss_pred CeEEECCCHHHhhcCCCceEEEEeCCCCCEEEEEEecCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 9999994 35678999888888999999999999999999999999999999999999998753
No 2
>PRK03983 exosome complex exonuclease Rrp41; Provisional
Probab=100.00 E-value=1.7e-50 Score=349.03 Aligned_cols=223 Identities=48% Similarity=0.802 Sum_probs=208.8
Q ss_pred cccCCCCCCCCCCCCCCCcceEEEECCCCCCCeEEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCCccc
Q 025943 2 EFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGD 81 (246)
Q Consensus 2 e~~~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~gp~e~~~~~~~~p~~g~l~v~v~~~~~s~~~ 81 (246)
+|++++|+|+|||+++|+|++++++|++++++|||++++|+|+|+|+|+||.++..+....|++|.+.|++++.|+++.+
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 57899999999999999999999999999999999999999999999999999887777789999999999999999866
Q ss_pred cccCCCCCchHHHHHHHHHHHHhhhhhcCCCCCceEEEEEEEEecCCChHHHHHHHHHHHHHhCCCCCcCceeEEEEEEe
Q 025943 82 RMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYL 161 (246)
Q Consensus 82 ~~~~~~~~~~~~~l~~~l~~~l~~~i~le~~p~~~I~i~v~VL~~dG~ll~a~i~aa~~AL~~a~Ip~~~~~~avs~~~~ 161 (246)
++ .+++++++.+++++|+++|++++.++.||++.|+|.++||++|||+++||+||+++||.|+||||++++++++++++
T Consensus 87 ~~-~~~~~~~~~~~s~~l~~~l~~~i~~~~~p~~~I~I~i~VL~~DG~~~~aai~Aa~lAL~dagIp~~~~v~avtv~~~ 165 (244)
T PRK03983 87 RK-RPGPDRRSIEISKVIREALEPAIMLELFPRTVIDVFIEVLQADAGTRVAGITAASLALADAGIPMRDLVAGCAVGKV 165 (244)
T ss_pred cc-CCCCChhHHHHHHHHHHHHHHhccHHhCCCeEEEEEEEEEECCCCHHHHHHHHHHHHHHhcCCccccceeEEEEEEE
Confidence 54 33577888899999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCceeecC------CCCCeEEEEEcCCCCcEEEEEeecCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025943 162 NSTPLLDS------AGGPDVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVRKFL 225 (246)
Q Consensus 162 ~~~~lvD~------~~~~~ltv~~~~~~~~i~~i~~~g~~~~~~l~~~l~~A~~~~~~i~~~i~~~l~~~ 225 (246)
++.+++|+ .+.+.++|+++++.++|+++++.|.++.+++.++++.|+++|++|.++|++++++.
T Consensus 166 ~~~~i~DPt~~Ee~~~~~~l~va~~~~~~~I~~l~~~G~~~~~~~~~~i~~A~~~~~~i~~~i~~~l~~~ 235 (244)
T PRK03983 166 DGVIVLDLNKEEDNYGEADMPVAIMPRLGEITLLQLDGNLTREEFLEALELAKKGIKRIYQLQREALKSK 235 (244)
T ss_pred CCEEEECCCHHHhccCCceEEEEEECCCCCEEEEEEecCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999993 35678999888788999999999999999999999999999999999999998875
No 3
>KOG1068 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp41 and related exoribonucleases [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.5e-49 Score=333.39 Aligned_cols=226 Identities=54% Similarity=0.869 Sum_probs=213.2
Q ss_pred CcccCCCCCCCCCCCCCCCcceEEEECCCCCCCeEEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCCcc
Q 025943 1 MEFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTG 80 (246)
Q Consensus 1 ~e~~~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~gp~e~~~~~~~~p~~g~l~v~v~~~~~s~~ 80 (246)
+|++.++|.|.|||.++|.|++..+.|++++++||||+++|||||+|.|+||+|+......+|+++.++|.+.+.+|+++
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 58899999999999999999999999999999999999999999999999999999877668999999999999999999
Q ss_pred ccccCCCCCchHHHHHHHHHHHHhhhhhcCCCCCceEEEEEEEEecCCChHHHHHHHHHHHHHhCCCCCcCceeEEEEEE
Q 025943 81 DRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGY 160 (246)
Q Consensus 81 ~~~~~~~~~~~~~~l~~~l~~~l~~~i~le~~p~~~I~i~v~VL~~dG~ll~a~i~aa~~AL~~a~Ip~~~~~~avs~~~ 160 (246)
+++++++.+.+++|++.+|+++|+++|.++.||+++|+|.|+||+|||+.+++|+||+.+||.|+||||+|+++++|.++
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 98766788899999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ecCceeecC------CCCCeEEEEEcCCCCcEEEEEeecCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025943 161 LNSTPLLDS------AGGPDVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVRKFLL 226 (246)
Q Consensus 161 ~~~~~lvD~------~~~~~ltv~~~~~~~~i~~i~~~g~~~~~~l~~~l~~A~~~~~~i~~~i~~~l~~~~ 226 (246)
.++.+++|. .....+||+++++.++|..+|+.+.++.+.+...++.|...|+++.+.++..+...+
T Consensus 165 ~~~~~l~Dl~~~eesa~~~~ltVa~l~~~~~i~~l~~~~~~~~d~l~~vl~~a~~~c~~v~~~l~~~l~~~l 236 (245)
T KOG1068|consen 165 ADGTPLLDLTSLEESARAPGLTVAALPNREEIALLQLDERLHCDHLETVLELAIAGCKRVYERLRLVLREHL 236 (245)
T ss_pred cCCccccccccchhhccCCceEEEEecCcceEEEEEecCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999992 223478999999999999999999999999999999999999999999999887763
No 4
>COG0689 Rph RNase PH [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.1e-46 Score=317.20 Aligned_cols=219 Identities=39% Similarity=0.621 Sum_probs=202.2
Q ss_pred ccCCCCCCCCCCCCCCCcceEEEECCCCCCCeEEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCCcccc
Q 025943 3 FVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDR 82 (246)
Q Consensus 3 ~~~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~gp~e~~~~~~~~p~~g~l~v~v~~~~~s~~~~ 82 (246)
...+++.|+|||.++|.|+++++.|++++++||+++++|+|||+|+|+||.|...+....+++|.++++|.+.|+++.++
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 35678999999999999999999999999999999999999999999999998888777778899999999999999665
Q ss_pred ccCCCCCc-hHHHHHHHHHHHHhhhhhcCCCCCceEEEEEEEEecCCChHHHHHHHHHHHHHhCCCCCcCceeEEEEEEe
Q 025943 83 MRKPKGDR-RSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYL 161 (246)
Q Consensus 83 ~~~~~~~~-~~~~l~~~l~~~l~~~i~le~~p~~~I~i~v~VL~~dG~ll~a~i~aa~~AL~~a~Ip~~~~~~avs~~~~ 161 (246)
..+ .+++ |++|++++|.++|+++|+++.||+++|+|++.|+++||+.+.|++||+++||.|+|+||.++++|+|+|+.
T Consensus 82 ~~~-~~~~gR~~eisrli~~al~~~i~L~~~p~~~I~i~~dVlqaDggTrta~It~A~lAL~DAgipl~~~vaaiSvgi~ 160 (230)
T COG0689 82 KKR-EADRGRTKEISRLIGRALRAVIDLELLPESTIDIDCDVLQADGGTRTASITGASLALADAGIPLRDLVAAISVGIV 160 (230)
T ss_pred ccc-cccccchhHHHHHHHHHHHHHhhhhhcCccEEEEEEEEEECCCCeeeehhhHHHHHHHHcCCchhhheeEeEEEEE
Confidence 433 2333 78999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCceeec------CCCCCeEEEEEcCCCC--cEEEEEeecCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025943 162 NSTPLLD------SAGGPDVTVGILPTLD--KVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVR 222 (246)
Q Consensus 162 ~~~~lvD------~~~~~~ltv~~~~~~~--~i~~i~~~g~~~~~~l~~~l~~A~~~~~~i~~~i~~~l 222 (246)
++.+++| +.+..+++|+++++.+ +|.+++.+|+++++++.+++++|+++|+++.+.++++|
T Consensus 161 ~~~~~lDl~~~Eds~~~~d~~v~~~~~~~~~ei~~~~~~~~~~~del~~lL~la~~g~~~~~~~~~~al 229 (230)
T COG0689 161 DGVIVLDLDYEEDSAAEADMNVVMTGNGGLVEIQGLAEDGPFTEDELLELLDLAIKGCNELRELQREAL 229 (230)
T ss_pred CCceEecCcchhhcccccCceEEEEecCCeEEEEEEeccCCcCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 9999999 3456788887777777 89999999999999999999999999999999999986
No 5
>PRK00173 rph ribonuclease PH; Reviewed
Probab=100.00 E-value=1.2e-45 Score=317.76 Aligned_cols=213 Identities=29% Similarity=0.391 Sum_probs=193.0
Q ss_pred CCCCCCCCCCCcceEEEECCCCCCCeEEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCCcccccc----
Q 025943 9 LRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDRMR---- 84 (246)
Q Consensus 9 ~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~gp~e~~~~~~~~p~~g~l~v~v~~~~~s~~~~~~---- 84 (246)
+|+|||+++|+|++++++|++++++|||++++|+|+|+|+|++|.+.+.. ...|++|.++|+|.++||++.++.+
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 MRPDGRAADQLRPVTITRNFTKHAEGSVLVEFGDTKVLCTASVEEGVPRF-LKGQGQGWVTAEYGMLPRATHTRNDREAA 79 (238)
T ss_pred CCCCCCCcccccCeEEEeCCCCCCCeeEEEEecCcEEEEEEEcCCCCCCc-cCCCCcEEEEEEEecCCCCCccccccccc
Confidence 59999999999999999999999999999999999999999988665432 2456899999999999999887632
Q ss_pred CCCCCchHHHHHHHHHHHHhhhhhcCCCCCceEEEEEEEEecCCChHHHHHHHHHHHHHhC-----------CCCCcCce
Q 025943 85 KPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDA-----------GIPMRDIV 153 (246)
Q Consensus 85 ~~~~~~~~~~l~~~l~~~l~~~i~le~~p~~~I~i~v~VL~~dG~ll~a~i~aa~~AL~~a-----------~Ip~~~~~ 153 (246)
.|++++++.+++++|+++|+++++++.||++.|+|+++||++|||+++||+||+++||+|+ ++||+++|
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 3467788899999999999999999999999999999999999999999999999999999 99999999
Q ss_pred eEEEEEEecCceeecC------CCCCeEEEEEcCCCCcEEEEEeec---CCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025943 154 TSCSAGYLNSTPLLDS------AGGPDVTVGILPTLDKVTLLQMDA---KLPTNTFEDVMQLAIEGCKAVANYIREVRK 223 (246)
Q Consensus 154 ~avs~~~~~~~~lvD~------~~~~~ltv~~~~~~~~i~~i~~~g---~~~~~~l~~~l~~A~~~~~~i~~~i~~~l~ 223 (246)
+++|++++++.+++|+ .+.+.++|+ +++.++||++++.| +++.+++.++++.|+++++++.+.++++++
T Consensus 160 ~~vt~~~~~~~~lvDpt~~Ee~~~~~~l~v~-~~~~~~i~~v~~~g~g~~~~~e~l~~~i~~A~~~~~~l~~~~~~~l~ 237 (238)
T PRK00173 160 AAVSVGIVDGEPVLDLDYEEDSAAETDMNVV-MTGSGGFVEVQGTAEGAPFSREELDALLDLAEKGIAELVALQKAALA 237 (238)
T ss_pred eEEEEEEECCEEEECCCHHHHhcCCceEEEE-ECCCCCEEEEEccCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 9999999999999993 356789995 57788999999953 699999999999999999999999999875
No 6
>TIGR01966 RNasePH ribonuclease PH. This bacterial enzyme, ribonuclease PH, performs the final 3'-trimming and modification of tRNA precursors. This model is restricted absolutely to bacteria. Related families outside the model include proteins described as probable exosome complex exonucleases (rRNA processing) and polyribonucleotide nucleotidyltransferases (mRNA degradation). The most divergent member within the family is RNase PH from Deinococcus radiodurans.
Probab=100.00 E-value=1.1e-44 Score=311.45 Aligned_cols=211 Identities=30% Similarity=0.429 Sum_probs=188.8
Q ss_pred CCCCCCCCCCcceEEEECCCCCCCeEEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCCcccccc----C
Q 025943 10 RLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDRMR----K 85 (246)
Q Consensus 10 R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~gp~e~~~~~~~~p~~g~l~v~v~~~~~s~~~~~~----~ 85 (246)
|+|||+++|+|++++++|++++|+|||++++|+|+|+|+|+++.+.+.+ ...|++|.++|++.+.|+++.++.+ .
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 8999999999999999999999999999999999999999976543322 2336899999999999999876522 2
Q ss_pred CCCCchHHHHHHHHHHHHhhhhhcCCCCCceEEEEEEEEecCCChHHHHHHHHHHHHHhC-----------CCCCcCcee
Q 025943 86 PKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDA-----------GIPMRDIVT 154 (246)
Q Consensus 86 ~~~~~~~~~l~~~l~~~l~~~i~le~~p~~~I~i~v~VL~~dG~ll~a~i~aa~~AL~~a-----------~Ip~~~~~~ 154 (246)
|++++++.+++++|+++|+++++++.||++.|+|+++||++|||+++||+||+++||.|+ +|||+++|+
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 456667889999999999999999999999999999999999999999999999999999 999999999
Q ss_pred EEEEEEecCceeecC------CCCCeEEEEEcCCCCcEEEEEee---cCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025943 155 SCSAGYLNSTPLLDS------AGGPDVTVGILPTLDKVTLLQMD---AKLPTNTFEDVMQLAIEGCKAVANYIREVR 222 (246)
Q Consensus 155 avs~~~~~~~~lvD~------~~~~~ltv~~~~~~~~i~~i~~~---g~~~~~~l~~~l~~A~~~~~~i~~~i~~~l 222 (246)
++|++++++.+++|+ .+.+.+++++ +..++||++++. +.++++++.++++.|+++++++.+.|++++
T Consensus 160 ~vt~~~~~~~~v~Dpt~~Ee~~~~~~l~l~~-~~~~~i~~i~~~g~~~~~~~~~l~~~i~~a~~~~~~l~~~~~~~l 235 (236)
T TIGR01966 160 AVSVGIVDGEPVLDLDYEEDSAADVDMNVVM-TGSGGFVEVQGTAEEGPFSRDELNKLLDLAKKGIRELIELQKQAL 235 (236)
T ss_pred EEEEEEECCEEEECCChhHHhccCceEEEEE-cCCCCEEEEEecCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 999999999999993 3456899964 667999999995 369999999999999999999999999876
No 7
>PRK04282 exosome complex RNA-binding protein Rrp42; Provisional
Probab=100.00 E-value=3.9e-42 Score=301.23 Aligned_cols=215 Identities=21% Similarity=0.316 Sum_probs=190.4
Q ss_pred CCCCCCCCCCCCCCCcceEEEECCCCCCCeEEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCCcccccc
Q 025943 5 SPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDRMR 84 (246)
Q Consensus 5 ~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~gp~e~~~~~~~~p~~g~l~v~v~~~~~s~~~~~~ 84 (246)
+++|+|+|||+++|+|++++++|.+++++|||++++|+|+|+|+|+++ +..|..++|++|.++|+++++|+++..+ +
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 468999999999999999999999999999999999999999999953 3344456789999999999999987654 4
Q ss_pred CCCCCchHHHHHHHHHHHHhhh--hhcCCC---CC---ceEEEEEEEEecCCChHHHHHHHHHHHHHhCCCC--------
Q 025943 85 KPKGDRRSTEISLVIRQTMEAC--ILTHLM---PR---SQIDIFVQVLQADGGTRSACINAATLALQDAGIP-------- 148 (246)
Q Consensus 85 ~~~~~~~~~~l~~~l~~~l~~~--i~le~~---p~---~~I~i~v~VL~~dG~ll~a~i~aa~~AL~~a~Ip-------- 148 (246)
.+++++++++++++|+++|+++ ++++.+ |+ |.|+|+++||++|||++|||++|+++||.|+++|
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 5677888899999999999987 455544 65 5999999999999999999999999999999995
Q ss_pred ------------CcCceeEEEEEEecCceeecC------CCCCeEEEEEcCCCCcEEEEEeec--CCCHHHHHHHHHHHH
Q 025943 149 ------------MRDIVTSCSAGYLNSTPLLDS------AGGPDVTVGILPTLDKVTLLQMDA--KLPTNTFEDVMQLAI 208 (246)
Q Consensus 149 ------------~~~~~~avs~~~~~~~~lvD~------~~~~~ltv~~~~~~~~i~~i~~~g--~~~~~~l~~~l~~A~ 208 (246)
|+++|+++|++++++.+++|+ .+.+.++|++ +..++|+++++.| +++.+++.++++.|.
T Consensus 177 ~~~~~~~~~~l~~~~~p~~vt~~~~~~~~v~Dpt~~Ee~~~~~~l~va~-~~~g~i~~l~~~g~~~~~~~~l~~~i~~A~ 255 (271)
T PRK04282 177 VVDKLGEDFPLPVNDKPVTVTFAKIGNYLIVDPTLEEESVMDARITITT-DEDGNIVAIQKSGIGSFTEEEVDKAIDIAL 255 (271)
T ss_pred eeccCCCcccCCCCCeeEEEEEEEECCEEEECCCHHHHhhcCceEEEEE-CCCCcEEEEEcCCCCCCCHHHHHHHHHHHH
Confidence 999999999999999999993 3568899975 6677999999974 599999999999999
Q ss_pred HHHHHHHHHHHHHHH
Q 025943 209 EGCKAVANYIREVRK 223 (246)
Q Consensus 209 ~~~~~i~~~i~~~l~ 223 (246)
+.++++.+.++++++
T Consensus 256 ~~~~~l~~~~~~~l~ 270 (271)
T PRK04282 256 EKAKELREKLKEALG 270 (271)
T ss_pred HHHHHHHHHHHHHhc
Confidence 999999999999873
No 8
>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=4.2e-40 Score=318.82 Aligned_cols=222 Identities=25% Similarity=0.395 Sum_probs=196.1
Q ss_pred cccCCCCCCCCCCCCCCCcceEEEECCCCCCCeEEEEEeCCeEEEEEE-EcCccccccccC--CCCceEEEEEEeecCCC
Q 025943 2 EFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAV-YGPREVQNKSQQ--MSDQALVRCEYSMANFS 78 (246)
Q Consensus 2 e~~~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V-~gp~e~~~~~~~--~p~~g~l~v~v~~~~~s 78 (246)
+|++++|.|+|||+++|+||+.+++|+++++||||+++.|+|+|+|+| .||.+..++.+. ..+++.+.++|+++|||
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 578999999999999999999999999999999999999999999999 598765443222 13578999999999999
Q ss_pred ccccccCCCCCchHHHHHHHHHHHHhhhhhc-CCCCCceEEEEEEEEecCCChHHHHHHHHHHHHHhCCCCCcCceeEEE
Q 025943 79 TGDRMRKPKGDRRSTEISLVIRQTMEACILT-HLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCS 157 (246)
Q Consensus 79 ~~~~~~~~~~~~~~~~l~~~l~~~l~~~i~l-e~~p~~~I~i~v~VL~~dG~ll~a~i~aa~~AL~~a~Ip~~~~~~avs 157 (246)
++++++.+.+++++.+++++++|+|++++++ +.||. +|+|+++||++|||..+|+++|+++||+|+||||.+.++++|
T Consensus 383 ~~e~~~~g~~~rrei~~~~l~~ral~~~i~~~~~~p~-tI~v~~~VLesdGs~~~Aai~aaslAL~dAgvP~~~~Vagvs 461 (684)
T TIGR03591 383 VGEVGRVGGPGRREIGHGALAERALKAVLPSEEEFPY-TIRVVSEILESNGSSSMASVCGGSLALMDAGVPIKAPVAGIA 461 (684)
T ss_pred CCCcCCCCCCChHHHHHHHHHHHHHHHhcCccccCCe-EEEEEEEEEeCCCChHHHHHHHHHHHHHhcCCCCcCCEEEEE
Confidence 9988767778899999999999999999986 78995 699999999999999999999999999999999999999999
Q ss_pred EEEec-C----ceeecC------CCCCeEEEEEcCCCCcEEEEEeecC---CCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025943 158 AGYLN-S----TPLLDS------AGGPDVTVGILPTLDKVTLLQMDAK---LPTNTFEDVMQLAIEGCKAVANYIREVRK 223 (246)
Q Consensus 158 ~~~~~-~----~~lvD~------~~~~~ltv~~~~~~~~i~~i~~~g~---~~~~~l~~~l~~A~~~~~~i~~~i~~~l~ 223 (246)
+|+++ + .+++|. .++++++|+ ++.+.|++++++++ ++.+.+.++++.|++++.+|.+.|++++.
T Consensus 462 ~gli~~~~~~~~il~D~~~~Ed~~~d~d~~va--~t~~gI~~lq~d~k~~~i~~~~l~~al~~a~~~~~~I~~~m~~~l~ 539 (684)
T TIGR03591 462 MGLIKEGDERFAVLSDILGDEDHLGDMDFKVA--GTRDGITALQMDIKIDGITREIMEQALEQAKEGRLHILGEMNKVIS 539 (684)
T ss_pred EEEEcCCCcceEEEeCCChHHHhcCCceEEEE--EcCCceEEEEEEcCcCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 99995 2 377893 456777773 44555999999754 79999999999999999999999999998
Q ss_pred HHH
Q 025943 224 FLL 226 (246)
Q Consensus 224 ~~~ 226 (246)
+..
T Consensus 540 ~~~ 542 (684)
T TIGR03591 540 EPR 542 (684)
T ss_pred hhh
Confidence 873
No 9
>COG2123 RNase PH-related exoribonuclease [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=7.6e-40 Score=278.64 Aligned_cols=216 Identities=21% Similarity=0.315 Sum_probs=195.5
Q ss_pred cCCCCCCCCCCCCCCCcceEEEECCCCCCCeEEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCCccccc
Q 025943 4 VSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDRM 83 (246)
Q Consensus 4 ~~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~gp~e~~~~~~~~p~~g~l~v~v~~~~~s~~~~~ 83 (246)
.++.|+|+|||.++|+|++.+++|++++++|||++++|+|+|+|+|+ .++.+|++++|++|.+.+++.+.|.+++.+
T Consensus 18 ll~~g~R~DGR~~~efR~ieI~~~vi~ka~GSa~VklG~Tqvv~gvK--~eig~Pf~DtP~eG~~~~n~El~Plas~~f- 94 (272)
T COG2123 18 LLKKGIRIDGRSFDEFRPLEIETGVIPKANGSALVKLGNTQVVVGVK--AEIGEPFPDTPNEGVLVVNVELSPLASPSF- 94 (272)
T ss_pred HhccCcccCCCCcccccceEEEeCceecCCCcEEEEecCeEEEEEEE--cccCCCCCCCCCCceEEeeeeeeccccccc-
Confidence 35689999999999999999999999999999999999999999999 688999999999999999999999987654
Q ss_pred cCCCCCchHHHHHHHHHHHHhhh--hhcCCC---CC---ceEEEEEEEEecCCChHHHHHHHHHHHHHhCCCC-------
Q 025943 84 RKPKGDRRSTEISLVIRQTMEAC--ILTHLM---PR---SQIDIFVQVLQADGGTRSACINAATLALQDAGIP------- 148 (246)
Q Consensus 84 ~~~~~~~~~~~l~~~l~~~l~~~--i~le~~---p~---~~I~i~v~VL~~dG~ll~a~i~aa~~AL~~a~Ip------- 148 (246)
.+|.+++.+.+++++++|.++.+ ++++++ ++ |.+++|++||++|||++||+..|+.+||+++++|
T Consensus 95 E~Gppde~aielsrvvdr~lr~s~aiDlekL~I~~g~kvwvv~vDv~vld~DGnl~Da~~lA~~aAL~~t~vP~~~~~~~ 174 (272)
T COG2123 95 EPGPPDELAIELSRVVDRGLRESKAIDLEKLCIEEGKKVWVVFVDVHVLDYDGNLIDAASLAAVAALLNTRVPKAVEVGD 174 (272)
T ss_pred cCCCCchhHHHHHHHHHHHHHhccCcchhheeEecCCEEEEEEEEEEEEcCCCCHHHHHHHHHHHHHHhcCCCceeecCC
Confidence 56788888999999999999876 666654 33 6899999999999999999999999999999988
Q ss_pred ---------------CcCceeEEEEEEecCceeecCC------CCCeEEEEEcCCCCcEEEEEeec--CCCHHHHHHHHH
Q 025943 149 ---------------MRDIVTSCSAGYLNSTPLLDSA------GGPDVTVGILPTLDKVTLLQMDA--KLPTNTFEDVMQ 205 (246)
Q Consensus 149 ---------------~~~~~~avs~~~~~~~~lvD~~------~~~~ltv~~~~~~~~i~~i~~~g--~~~~~~l~~~l~ 205 (246)
+.+.|.++|++++++..++|++ +++.+||. +++.++|++++|.| +++++.+.+|++
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 5789999999999999999943 56788985 68999999999985 699999999999
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 025943 206 LAIEGCKAVANYIREVRK 223 (246)
Q Consensus 206 ~A~~~~~~i~~~i~~~l~ 223 (246)
.|.+.+.++.+.+.++|+
T Consensus 254 ~A~~~~~kl~~~~~~~L~ 271 (272)
T COG2123 254 TALSKAEKLREALKEALK 271 (272)
T ss_pred HHHHHHHHHHHHHHHhhc
Confidence 999999999999988875
No 10
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=100.00 E-value=4.7e-40 Score=319.09 Aligned_cols=221 Identities=25% Similarity=0.409 Sum_probs=193.9
Q ss_pred cccCCCCCCCCCCCCCCCcceEEEECCCCCCCeEEEEEeCCeEEEEEE-EcCccccccccC--CCCceEEEEEEeecCCC
Q 025943 2 EFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAV-YGPREVQNKSQQ--MSDQALVRCEYSMANFS 78 (246)
Q Consensus 2 e~~~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V-~gp~e~~~~~~~--~p~~g~l~v~v~~~~~s 78 (246)
++|+++|.|+|||+++|+||+.+++|+++++||||+++.|+|+|+|+| .||....++.+. ..+++.+.++|+++|||
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 589999999999999999999999999999999999999999999999 587543332111 12679999999999999
Q ss_pred ccccccCCCCCchHHHHHHHHHHHHhhhhhc-CCCCCceEEEEEEEEecCCChHHHHHHHHHHHHHhCCCCCcCceeEEE
Q 025943 79 TGDRMRKPKGDRRSTEISLVIRQTMEACILT-HLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCS 157 (246)
Q Consensus 79 ~~~~~~~~~~~~~~~~l~~~l~~~l~~~i~l-e~~p~~~I~i~v~VL~~dG~ll~a~i~aa~~AL~~a~Ip~~~~~~avs 157 (246)
++++++.+.+++++.+++++++|+|++++++ +.|| |+|+|+++||++|||.++|+++|+++||+|+||||.+++++++
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 9988777778899999999999999999998 6899 5899999999999999999999999999999999999999999
Q ss_pred EEEecC----ceeecC------CCCCeEEEEEcCCCCcEEEEEeec---CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025943 158 AGYLNS----TPLLDS------AGGPDVTVGILPTLDKVTLLQMDA---KLPTNTFEDVMQLAIEGCKAVANYIREVRKF 224 (246)
Q Consensus 158 ~~~~~~----~~lvD~------~~~~~ltv~~~~~~~~i~~i~~~g---~~~~~~l~~~l~~A~~~~~~i~~~i~~~l~~ 224 (246)
+|++++ .+++|. .++++++|+ ++.+.|+++|+++ .++.+.+.++++.|++++.+|.+.|++++..
T Consensus 466 ~gli~~~~~~~il~D~~~~Ed~~~d~d~~va--~t~~gi~~lq~d~k~~~i~~~~l~~al~~a~~g~~~I~~~M~~aI~~ 543 (693)
T PRK11824 466 MGLIKEGDKYAVLTDILGDEDHLGDMDFKVA--GTRDGITALQMDIKIDGITREILEEALEQAKEGRLHILGKMNEAISE 543 (693)
T ss_pred EEEEcCCCceEEEcCCChhhHhhCCceEEEE--ecCCceEEEEEecccCCcCHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 999953 267782 456778873 4444599999875 4799999999999999999999999999876
Q ss_pred H
Q 025943 225 L 225 (246)
Q Consensus 225 ~ 225 (246)
.
T Consensus 544 ~ 544 (693)
T PRK11824 544 P 544 (693)
T ss_pred C
Confidence 5
No 11
>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=6.4e-39 Score=306.55 Aligned_cols=222 Identities=26% Similarity=0.401 Sum_probs=194.7
Q ss_pred CcccCCCCCCCCCCCCCCCcceEEEECCCCCCCeEEEEEeCCeEEEEEEE-cCcccccccc--CCCCceEEEEEEeecCC
Q 025943 1 MEFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVY-GPREVQNKSQ--QMSDQALVRCEYSMANF 77 (246)
Q Consensus 1 ~e~~~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~-gp~e~~~~~~--~~p~~g~l~v~v~~~~~ 77 (246)
+|++++++.|+|||+++|+|++.+++|++++++|||+++.|+|+|+|.+. ||.+..+..+ ..++++.+.|+|+++||
T Consensus 327 r~~il~~g~R~DGR~~~eiR~i~~~~g~l~~a~GSa~~~~G~Tqvl~~~tlG~~~~~q~~~~l~~~~~~~~~~~YnfpPF 406 (719)
T TIGR02696 327 RERVLTEGVRIDGRGVTDIRPLDAEVQVIPRVHGSALFERGETQILGVTTLNMLKMEQQIDSLSPETSKRYMHHYNFPPY 406 (719)
T ss_pred HHHHhcCCCCCCCCCccccccceeecCCCCCCCceEEEEecCcEEEEEEeCCCchhhhhcccccccccceEEEEEeCCCC
Confidence 36899999999999999999999999999999999999999999999877 4443332211 12456889999999999
Q ss_pred CccccccCCCCCchHHHHHHHHHHHHhhhhh-cCCCCCceEEEEEEEEecCCChHHHHHHHHHHHHHhCCCCCcCceeEE
Q 025943 78 STGDRMRKPKGDRRSTEISLVIRQTMEACIL-THLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSC 156 (246)
Q Consensus 78 s~~~~~~~~~~~~~~~~l~~~l~~~l~~~i~-le~~p~~~I~i~v~VL~~dG~ll~a~i~aa~~AL~~a~Ip~~~~~~av 156 (246)
|++++++.+.++.|+.+++++++|+|+++|. ++.||++ |.+.++||++||+...|++||+++||+||||||+++++|+
T Consensus 407 St~er~~~~~~~RReighg~La~rALe~vI~~~e~fP~T-IrvvseVLeSdGSss~AsIcaasLALmDAGVPmkd~VAgi 485 (719)
T TIGR02696 407 STGETGRVGSPKRREIGHGALAERALVPVLPSREEFPYA-IRQVSEALGSNGSTSMGSVCASTLSLLNAGVPLKAPVAGI 485 (719)
T ss_pred cccCCCCCCCCCccHHHHHHHHHHHHHHhhCcHhhCCCE-EEEEEEeeccCCcHHHHHHHHHHHHHHHcCcchhheeeEE
Confidence 9999877777788999999999999999997 6999977 8888999999999999999999999999999999999999
Q ss_pred EEEEecC----c----eeec------CCCCCeEEEEEcCCCCcEEEEEeecCC---CHHHHHHHHHHHHHHHHHHHHHHH
Q 025943 157 SAGYLNS----T----PLLD------SAGGPDVTVGILPTLDKVTLLQMDAKL---PTNTFEDVMQLAIEGCKAVANYIR 219 (246)
Q Consensus 157 s~~~~~~----~----~lvD------~~~~~~ltv~~~~~~~~i~~i~~~g~~---~~~~l~~~l~~A~~~~~~i~~~i~ 219 (246)
++|++++ . +++| +.+++++.+ +++.++|+++|.+|++ +.+.+.+++++|+++|..|++.|+
T Consensus 486 s~Gli~e~~~~~~~~~iL~Di~g~ED~~Gdmdfkv--agt~~gIt~lQmd~ki~gi~~e~l~~aL~~A~~g~~~Il~~m~ 563 (719)
T TIGR02696 486 AMGLISDEVDGETRYVALTDILGAEDAFGDMDFKV--AGTSEFVTALQLDTKLDGIPASVLASALKQARDARLAILDVMA 563 (719)
T ss_pred EEEEeccccCCCcceeEEeCCCchhhhcCCceEEE--EecCCCEEEEEEEeeECCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999943 2 6889 234555655 6788999999999875 899999999999999999999999
Q ss_pred HHHHHH
Q 025943 220 EVRKFL 225 (246)
Q Consensus 220 ~~l~~~ 225 (246)
+++.+.
T Consensus 564 ~al~~p 569 (719)
T TIGR02696 564 EAIDTP 569 (719)
T ss_pred HHHhCc
Confidence 999877
No 12
>KOG1069 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp46 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.4e-38 Score=256.30 Aligned_cols=198 Identities=28% Similarity=0.438 Sum_probs=175.1
Q ss_pred CCcceEEEECCCCCCCeEEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCCccccccCCCCCchHHHHHH
Q 025943 18 EMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISL 97 (246)
Q Consensus 18 e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~gp~e~~~~~~~~p~~g~l~v~v~~~~~s~~~~~~~~~~~~~~~~l~~ 97 (246)
.+|++.++.|+++++|||+.|++|+|+|+|+|+||.+++.++ +.|++..++|-++ |.+ |.+...++.+++
T Consensus 4 ~lr~~~cei~iLsr~dGSs~fsqgdT~V~c~V~GP~dvk~r~-E~~~katleVi~r--p~~-------G~~~~~eK~~e~ 73 (217)
T KOG1069|consen 4 RLRGIACEISILSRPDGSSEFSQGDTKVICSVYGPIDVKARQ-EDPEKATLEVIWR--PKS-------GVNGTVEKVLER 73 (217)
T ss_pred hhhhhhhhhceecCCCCccceecCCcEEEEEeeCCcchhhcc-cCchhceEEEEEe--ccc-------CcchHHHHHHHH
Confidence 689999999999999999999999999999999999998874 6789999988877 443 345677889999
Q ss_pred HHHHHHhhhhhcCCCCCceEEEEEEEEecCCChHHHHHHHHHHHHHhCCCCCcCceeEEEEEEecC-ceeecCC------
Q 025943 98 VIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNS-TPLLDSA------ 170 (246)
Q Consensus 98 ~l~~~l~~~i~le~~p~~~I~i~v~VL~~dG~ll~a~i~aa~~AL~~a~Ip~~~~~~avs~~~~~~-~~lvD~~------ 170 (246)
.|+++|++.|.++.||++.|+|.++|+++||+++++|+|||++||+|+||||+++++|+++++.++ .+++|+.
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 999999999999999999999999999999999999999999999999999999999999999876 6778942
Q ss_pred --CCCeEEEEE-cCCCCcEEEEEeecCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025943 171 --GGPDVTVGI-LPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVRKFL 225 (246)
Q Consensus 171 --~~~~ltv~~-~~~~~~i~~i~~~g~~~~~~l~~~l~~A~~~~~~i~~~i~~~l~~~ 225 (246)
+...+++.. .....+++..+..|.++.+++..+++.|...+++++.++|+.+..-
T Consensus 154 ~~~~~~lsf~~~~~~~~~vi~s~t~G~~~~d~lf~~le~a~~~~~~~f~f~r~~~q~~ 211 (217)
T KOG1069|consen 154 STARATLSFEGGSLGEPKVIISETNGEKSEDQLFYVLELAQAAAQSLFPFYREVLQRK 211 (217)
T ss_pred hhceEEEEEecCCCCCcceEEEeccCCCCHHHHHHHHHhhHHHHHHHHHHHHHHHHhh
Confidence 223444422 2346789999999999999999999999999999999999987654
No 13
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=100.00 E-value=2.4e-37 Score=301.23 Aligned_cols=222 Identities=24% Similarity=0.384 Sum_probs=195.5
Q ss_pred cccCCCCCCCCCCCCCCCcceEEEECCCCCCCeEEEEEeCCeEEEEEEE-cCccccccccC---CCCceEEEEEEeecCC
Q 025943 2 EFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVY-GPREVQNKSQQ---MSDQALVRCEYSMANF 77 (246)
Q Consensus 2 e~~~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~-gp~e~~~~~~~---~p~~g~l~v~v~~~~~ 77 (246)
++|+++|.|+|||+++|.|++.+++|.+++++|||+++.|+|+|+|+|+ ||.+..+..+. .+..+.+.++|+++|+
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 5789999999999999999999999999999999999999999999996 88766544222 1356788899999999
Q ss_pred CccccccCCCCCchHHHHHHHHHHHHhhhhhcC-CCCCceEEEEEEEEecCCChHHHHHHHHHHHHHhCCCCCcCceeEE
Q 025943 78 STGDRMRKPKGDRRSTEISLVIRQTMEACILTH-LMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSC 156 (246)
Q Consensus 78 s~~~~~~~~~~~~~~~~l~~~l~~~l~~~i~le-~~p~~~I~i~v~VL~~dG~ll~a~i~aa~~AL~~a~Ip~~~~~~av 156 (246)
+.+++++.+++++++.+++++++|+|++++..+ .|| +.|+|+++||++||+..+|++||+++||+|+||||++.++++
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 998887777888999999999999999999885 799 589999999999999999999999999999999999999999
Q ss_pred EEEEe-c-------Cc--eeec------CCCCCeEEEEEcCCCCcEEEEEeecC---CCHHHHHHHHHHHHHHHHHHHHH
Q 025943 157 SAGYL-N-------ST--PLLD------SAGGPDVTVGILPTLDKVTLLQMDAK---LPTNTFEDVMQLAIEGCKAVANY 217 (246)
Q Consensus 157 s~~~~-~-------~~--~lvD------~~~~~~ltv~~~~~~~~i~~i~~~g~---~~~~~l~~~l~~A~~~~~~i~~~ 217 (246)
++|++ + +. +++| ..+++++.| +++.+.|+++|.+++ ++.+.+.++++.|++++..|.+.
T Consensus 590 svGli~d~~~~~~~g~~~IL~Dp~g~Ed~~gdmDfkV--AgT~~gIt~iqmd~k~~gis~e~l~eAL~~A~~g~~~Il~~ 667 (891)
T PLN00207 590 AMGMVLDTEEFGGDGSPLILSDITGSEDASGDMDFKV--AGNEDGITAFQMDIKVGGITLPIMERALLQAKDGRKHILAE 667 (891)
T ss_pred EEEEEecccccCCCCcEEEEeCCCHHHHhcCCceEEE--EecccceEEEEEecccCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 99999 2 23 4458 345566666 477889999999864 69999999999999999999999
Q ss_pred HHHHHHHHH
Q 025943 218 IREVRKFLL 226 (246)
Q Consensus 218 i~~~l~~~~ 226 (246)
|++++.+..
T Consensus 668 M~~~i~~pr 676 (891)
T PLN00207 668 MSKCSPPPS 676 (891)
T ss_pred HHHHHhhhh
Confidence 999998773
No 14
>KOG1614 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp45 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.3e-37 Score=257.01 Aligned_cols=222 Identities=22% Similarity=0.257 Sum_probs=196.0
Q ss_pred CCCCCCCCCCCCCCCcceEEEECCCCCCCeEEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCCcccccc
Q 025943 5 SPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDRMR 84 (246)
Q Consensus 5 ~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~gp~e~~~~~~~~p~~g~l~v~v~~~~~s~~~~~~ 84 (246)
++.|+|.|||++.|+|.+.+++|. ..||+.+++|+|+|+|.|. .+..+|+.++|.+|.+++...++|++++.. .
T Consensus 18 lk~g~R~DgR~l~efR~lei~fGk---e~gs~~vt~G~Tkvm~~vt--~~ia~Py~dRP~eG~~~I~telsPmA~~sf-E 91 (291)
T KOG1614|consen 18 LKAGLRFDGRSLEEFRDLEIEFGK---EYGSVLVTMGNTKVMARVT--AQIAQPYIDRPHEGSFSIFTELSPMASPSF-E 91 (291)
T ss_pred HHhcccccccchhhhhceEEEecc---ccccEEEEecCeeEEEEee--hhhcCcccCCCCCCeeeeeecccccccccc-C
Confidence 578999999999999999999995 7899999999999999999 688899999999999999999999997654 4
Q ss_pred CCCCCchHHHHHHHHHHHHhhh--hhcCCC----CC--ceEEEEEEEEecCCChHHHHHHHHHHHHHhCC----------
Q 025943 85 KPKGDRRSTEISLVIRQTMEAC--ILTHLM----PR--SQIDIFVQVLQADGGTRSACINAATLALQDAG---------- 146 (246)
Q Consensus 85 ~~~~~~~~~~l~~~l~~~l~~~--i~le~~----p~--~~I~i~v~VL~~dG~ll~a~i~aa~~AL~~a~---------- 146 (246)
+|+.++.+.+|.++|+++++.+ |++|.+ ++ |.|++|+++|+.|||++|||+.|+.+||+|++
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 5667788889999999999875 677764 33 79999999999999999999999999999999
Q ss_pred -------------CCCcCceeEEEEEEec--CceeecC------CCCCeEEEEEcCCCCcEEEEEeecC--CCHHHHHHH
Q 025943 147 -------------IPMRDIVTSCSAGYLN--STPLLDS------AGGPDVTVGILPTLDKVTLLQMDAK--LPTNTFEDV 203 (246)
Q Consensus 147 -------------Ip~~~~~~avs~~~~~--~~~lvD~------~~~~~ltv~~~~~~~~i~~i~~~g~--~~~~~l~~~ 203 (246)
+.|+|+|+|+|+++++ +..++|+ ..++.++| .+++++++|.++|.|. ++..++..|
T Consensus 172 v~ihp~eEr~PvPL~I~HmPIC~tf~ffnkG~ivviDpt~~Ee~~~dGs~vV-t~Nk~rEVc~i~k~G~~~~~~~~i~~C 250 (291)
T KOG1614|consen 172 VIIHPVEEREPVPLSIHHMPICFTFGFFNKGEIVVIDPTEKEEAVMDGSMVV-TMNKNREVCAIQKSGGEILDESVIERC 250 (291)
T ss_pred eEecChhccCCcceeeeeccceEEEEEecCceEEEeCCcHHHHhccCceEEE-EEcCCccEEEEecCCCccccHHHHHHH
Confidence 3389999999999997 3457793 35788999 5899999999999985 789999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhccccc
Q 025943 204 MQLAIEGCKAVANYIREVRKFLLIAVDIVG 233 (246)
Q Consensus 204 l~~A~~~~~~i~~~i~~~l~~~~~~~~~~~ 233 (246)
.+.|...+.++...+.+++++...-+.-++
T Consensus 251 ~k~A~~~a~~vt~ii~e~l~~d~~~r~~~~ 280 (291)
T KOG1614|consen 251 YKLAKDRAVEVTGIILEALEEDQRERSAQK 280 (291)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence 999999999999999999999966665544
No 15
>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=2.9e-30 Score=250.33 Aligned_cols=202 Identities=23% Similarity=0.372 Sum_probs=173.5
Q ss_pred cceEEEECCC-CCCCeEEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCCccc-----cccCCCCCchHH
Q 025943 20 RQLRAEIGNV-AKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGD-----RMRKPKGDRRST 93 (246)
Q Consensus 20 R~i~i~~g~l-~~a~GSa~v~~G~T~Vl~~V~gp~e~~~~~~~~p~~g~l~v~v~~~~~s~~~-----~~~~~~~~~~~~ 93 (246)
|++.+++|.+ ++|+|||++++|+|+|+|+|+||.+++.. .+..+++|+|...+++.+. .++.|++++++.
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 RTLTLETGKIARQADGAVVVRYGDTVVLVTVVAAKEAKEG----QDFFPLTVNYQEKFYAAGKIPGGFFKREGRPSEKET 80 (684)
T ss_pred ccEEEEECCcCCCCCeEEEEEECCeEEEEEEEcCCCCCCC----CceEeEEEEEEehhhhccCCCCCcccCCCCCCHHHH
Confidence 8999999999 57999999999999999999999875432 2567899999987766542 345678899999
Q ss_pred HHHHHHHHHHhhhhhcCCCCC---ceEEEEEEEEecCCChH-H-HHHHHHHHHHHhCCCCCcCceeEEEEEEecCceeec
Q 025943 94 EISLVIRQTMEACILTHLMPR---SQIDIFVQVLQADGGTR-S-ACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLD 168 (246)
Q Consensus 94 ~l~~~l~~~l~~~i~le~~p~---~~I~i~v~VL~~dG~ll-~-a~i~aa~~AL~~a~Ip~~~~~~avs~~~~~~~~lvD 168 (246)
+++++|+|+|+++ ||+ +.|+|+++||++||+.. + ||+||+++||.+++||++++++|+++|++++.+++|
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 9999999999984 777 78999999999999974 4 999999999999999999999999999999999999
Q ss_pred C------CCCCeEEEEEcCCCCcEEEEEeecC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-Hhhcccc
Q 025943 169 S------AGGPDVTVGILPTLDKVTLLQMDAK-LPTNTFEDVMQLAIEGCKAVANYIREVRKFL-LIAVDIV 232 (246)
Q Consensus 169 ~------~~~~~ltv~~~~~~~~i~~i~~~g~-~~~~~l~~~l~~A~~~~~~i~~~i~~~l~~~-~~~~~~~ 232 (246)
+ .++.+++| .++.+.+++++..+. ++++++.++++.|.++++++.+.+++.+++. +..+++.
T Consensus 156 Pt~~E~~~s~~~l~v--a~t~~~i~mie~~~~~i~e~~l~~al~~a~~~~~~i~~~~~~~~~~~~~~k~~~~ 225 (684)
T TIGR03591 156 PTVDELEKSDLDLVV--AGTKDAVLMVESEAKELSEEVMLGAIEFGHEEIQPVIEAIEELAEEAGKEKWEFV 225 (684)
T ss_pred CCHHHHhhCCceEEE--EccCCcEEEEEcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCC
Confidence 4 34566666 466678999998865 9999999999999999999999999998887 3435444
No 16
>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=99.97 E-value=3.7e-30 Score=201.95 Aligned_cols=130 Identities=38% Similarity=0.536 Sum_probs=117.8
Q ss_pred CCcceEEEECCCCCCCeEEEEEeCCeEEEEEEEcCccccccccCCC-CceEEEEEEeecCCCccccccCCCCCchHHHHH
Q 025943 18 EMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMS-DQALVRCEYSMANFSTGDRMRKPKGDRRSTEIS 96 (246)
Q Consensus 18 e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~gp~e~~~~~~~~p-~~g~l~v~v~~~~~s~~~~~~~~~~~~~~~~l~ 96 (246)
|+|++.+++|++++++|||+|++|+|+|+|+|+||.+.+.. .+.+ .+|.+++++++.|++..+.++.+.++.++.+++
T Consensus 1 e~R~i~i~~~~~~~a~GSa~v~~G~T~V~~~V~~~~~~~~~-~~~~~~~g~~~v~v~~~~~~~~~~~~~~~~~~~~~~l~ 79 (132)
T PF01138_consen 1 ELRPISIETGVLPRADGSARVSLGNTKVICSVKGPIEPPPS-NERDDAEGRLTVEVEFSPFASPSFRRGGRPDEEERELS 79 (132)
T ss_dssp CBEEEEEEESSSSSSSEEEEEEETTEEEEEEEEEEEEGCSC-STTSSSSEEEEEEEEECCCGSTSSSSSSSTHHHHHHHH
T ss_pred CCccEEEEeCCCCCCCeEEEEEECCeEEEEEEEecccccch-hcccCCCceEEEEEEeccccccccccccccchhHHHHH
Confidence 78999999999999999999999999999999999887432 2323 359999999999999877655567788888999
Q ss_pred HHHHHHHhhhhhcCCCCCceEEEEEEEEecCC-ChHHHHHHHHHHHHHhCCCC
Q 025943 97 LVIRQTMEACILTHLMPRSQIDIFVQVLQADG-GTRSACINAATLALQDAGIP 148 (246)
Q Consensus 97 ~~l~~~l~~~i~le~~p~~~I~i~v~VL~~dG-~ll~a~i~aa~~AL~~a~Ip 148 (246)
++|+++|++++.++.||+|.|+|+++||++|| |++|+|+||+++||+|+|||
T Consensus 80 ~~l~~~l~~~~~~~~~~~~~i~v~v~vl~~dG~~~~~a~~~A~~~AL~~~~iP 132 (132)
T PF01138_consen 80 SLLERALRSSILLEGYPRWQIHVDVQVLSDDGGNLLDAAINAACLALLDAGIP 132 (132)
T ss_dssp HHHHHHHHHTBSTTTTSSEEEEEEEEEEECSSSSHHHHHHHHHHHHHHHHTCS
T ss_pred HHHhhhccccccccccCceEEEEEEEEEecCCCCHHHHHHHHHHHHHHhcCCC
Confidence 99999999999999999999999999999999 99999999999999999998
No 17
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=99.97 E-value=2.8e-29 Score=243.96 Aligned_cols=200 Identities=21% Similarity=0.326 Sum_probs=169.4
Q ss_pred CcceEEEECCCC-CCCeEEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCCccc-----cccCCCCCchH
Q 025943 19 MRQLRAEIGNVA-KADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGD-----RMRKPKGDRRS 92 (246)
Q Consensus 19 ~R~i~i~~g~l~-~a~GSa~v~~G~T~Vl~~V~gp~e~~~~~~~~p~~g~l~v~v~~~~~s~~~-----~~~~~~~~~~~ 92 (246)
-|++.+++|.+. +|+|||++++|+|+|+|+|++|.+++.. .+...++|+|...+++++. .++.|++++++
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 GRTLTLETGKLARQANGAVLVRYGDTVVLVTVVASKEPKEG----QDFFPLTVDYEEKTYAAGKIPGGFFKREGRPSEKE 88 (693)
T ss_pred CccEEEEECCcCCCCCeEEEEEECCeEEEEEEEcCCCCCCC----CCeeeeEEEEEehhhhccCCCcccccCCCCCChHH
Confidence 379999999995 6999999999999999999999875321 2567899999988876542 23557889999
Q ss_pred HHHHHHHHHHHhhhhhcCCCCCceEEEEEEEEecCCCh-HH-HHHHHHHHHHHhCCCCCcCceeEEEEEEecCceeecC-
Q 025943 93 TEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGT-RS-ACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDS- 169 (246)
Q Consensus 93 ~~l~~~l~~~l~~~i~le~~p~~~I~i~v~VL~~dG~l-l~-a~i~aa~~AL~~a~Ip~~~~~~avs~~~~~~~~lvD~- 169 (246)
.+++++|+|+|+++.. ..++|.++|+++||++||+. .| +|+||+++||.+++||+++.++|+++|++++.+++|+
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 9999999999999522 12258999999999999976 55 8999999999999999999999999999999999994
Q ss_pred -----CCCCeEEEEEcCCCCcEEEEEeec-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025943 170 -----AGGPDVTVGILPTLDKVTLLQMDA-KLPTNTFEDVMQLAIEGCKAVANYIREVRKFLL 226 (246)
Q Consensus 170 -----~~~~~ltv~~~~~~~~i~~i~~~g-~~~~~~l~~~l~~A~~~~~~i~~~i~~~l~~~~ 226 (246)
.++.+++| .++.+.+++++..| .++++++.++++.|.++++++.+.+++.+++.-
T Consensus 167 ~~E~~~s~~~l~v--a~t~~~i~mie~~~~~l~e~~l~~al~~a~~~~~~i~~~~~~~~~~~~ 227 (693)
T PRK11824 167 VEELEESDLDLVV--AGTKDAVLMVESEAKELSEEVMLEAIEFGHEAIQELIDAQEELAAEAG 227 (693)
T ss_pred HHHHhhCcceEEE--EEccCceEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 34556665 35556899999876 499999999999999999999999999887764
No 18
>KOG1612 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp42 [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=4e-28 Score=203.71 Aligned_cols=224 Identities=16% Similarity=0.209 Sum_probs=184.8
Q ss_pred CCCCCCCCCCCCCCcceEEEECCCCCCCeEEEEEeCC-eEEEEEEEcCccccccccCCCCceEEEEEEeecCCCcccccc
Q 025943 6 PEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGN-TKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDRMR 84 (246)
Q Consensus 6 ~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~-T~Vl~~V~gp~e~~~~~~~~p~~g~l~v~v~~~~~s~~~~~~ 84 (246)
+.++|+|||.++++|||.+++|++++++|||++++|+ |.|+++|+ .|+..|..+.|++|.+.++|+++|.++++...
T Consensus 18 e~~iR~DGR~~~~~Rpi~vetdVlp~tNGSaRVk~g~~tdiivgVK--aEvg~~~~~~p~egk~~~~VD~S~sasp~f~g 95 (288)
T KOG1612|consen 18 EPDIRNDGRSCHQFRPIEVETDVLPGTNGSARVKLGDGTDIIVGVK--AEVGSPDDETPVEGKYLFFVDCSPSASPQFQG 95 (288)
T ss_pred CcccccCCcCccccceEEEEeccccCCCCcEEEEecCCceEEEEEe--eeccCccccCCCCCeEEEEEEecCCcCccccC
Confidence 5789999999999999999999999999999999999 99999999 57777778889999999999999998876533
Q ss_pred CCCCCchHHHHHHHHHHHHhh--h-hhcCC---CCC--ceEEEEEEEEecCCChHHHHHHHHHHHHHhCCCC--------
Q 025943 85 KPKGDRRSTEISLVIRQTMEA--C-ILTHL---MPR--SQIDIFVQVLQADGGTRSACINAATLALQDAGIP-------- 148 (246)
Q Consensus 85 ~~~~~~~~~~l~~~l~~~l~~--~-i~le~---~p~--~~I~i~v~VL~~dG~ll~a~i~aa~~AL~~a~Ip-------- 148 (246)
+ ..++...+|...++++|.+ + +++.. -|+ |.|+||+.||+.|||++||...|+.+||.+.++|
T Consensus 96 R-ggde~~~eltsaLq~~l~~~~sgv~ls~L~lt~~~~W~i~VDvlVi~s~gn~~dAiS~Ai~~AL~~T~lPkv~v~~dd 174 (288)
T KOG1612|consen 96 R-GGDELVEELTSALQRVLNSLGSGVDLSKLQLTPGYCWKIYVDVLVISSDGNLLDAISIAIYAALNNTRLPKVIVAFDD 174 (288)
T ss_pred C-ChhhHHHHHHHHHHHHHhCcCcccchhheeccCCeeEEEEEeEEEEecCCCHHHHHHHHHHHHHhcccCCcccccccc
Confidence 3 2456667899999999987 1 34432 243 7999999999999999999999999999999998
Q ss_pred -------------------CcCceeEEEEEEecCceeecC------CCCCeEEEEEcCCCCcEEEEEee--cCCCHHHHH
Q 025943 149 -------------------MRDIVTSCSAGYLNSTPLLDS------AGGPDVTVGILPTLDKVTLLQMD--AKLPTNTFE 201 (246)
Q Consensus 149 -------------------~~~~~~avs~~~~~~~~lvD~------~~~~~ltv~~~~~~~~i~~i~~~--g~~~~~~l~ 201 (246)
...+|.=++++.++..+++|+ .+...+.|++ ++.+-+.++.+- |.+.++.+.
T Consensus 175 ~~~~~i~~s~~~Yd~~~~~~~~~P~ivtlskIG~~~lVD~T~eEe~~a~s~l~Isv-~a~givs~~r~VG~G~l~~s~i~ 253 (288)
T KOG1612|consen 175 DGEVEILLSDEEYDLMVKLVENVPLIVTLSKIGTNMLVDPTAEEESVANSGLLISV-SAGGIVSCTRSVGLGDLDPSSIP 253 (288)
T ss_pred CCceeeccCcccchhhhhhcccCCEEEEEEeecceEEccCCccHHHhhhcceEEEE-ecCcceEEEEEecCCCCChhhHH
Confidence 234667778888888999993 2345677765 444444444443 358999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhccccc
Q 025943 202 DVMQLAIEGCKAVANYIREVRKFLLIAVDIVG 233 (246)
Q Consensus 202 ~~l~~A~~~~~~i~~~i~~~l~~~~~~~~~~~ 233 (246)
++++.+++..+.++..+.+.|++..+.-++.+
T Consensus 254 ~mle~~~~~~e~l~~~l~k~L~~~e~~~~~~~ 285 (288)
T KOG1612|consen 254 EMLEQGKAVVETLAPDLVKSLENEEDILSFKG 285 (288)
T ss_pred HHHHHHHHHHHhhhHHHHHHhhhhhhccCccc
Confidence 99999999999999999999999988777766
No 19
>KOG1613 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp43 [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=1.8e-28 Score=204.40 Aligned_cols=214 Identities=22% Similarity=0.305 Sum_probs=173.8
Q ss_pred cccCCCCCCCCCCCCCCCcceEEEECCCCCCCeEEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCCccc
Q 025943 2 EFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGD 81 (246)
Q Consensus 2 e~~~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~gp~e~~~~~~~~p~~g~l~v~v~~~~~s~~~ 81 (246)
+.++.+++|+|||+..|+|.+.++.|.++++|||+.++.|+|.|+|+|++ |+..|+.+.|++|.+..+|.++|.++.
T Consensus 29 ~rhLse~~RpdgR~lgefRdt~in~g~IsTangSal~K~G~ttvi~~Ik~--ei~epstdapdeg~Iv~n~~lpplcs~- 105 (298)
T KOG1613|consen 29 QRHLSEGIRPDGRKLGEFRDTAINAGNISTANGSALLKSGKTTVICGIKA--EIAEPSTDAPDEGDIVPNYALPPLCSS- 105 (298)
T ss_pred HHHhhcccCcchhhhhHHhhhheecCceeccCcHHHHhcCCcEEEEEeee--eecccccCCCCCcceeecccCCccccc-
Confidence 45678999999999999999999999999999999999999999999995 677788889999999999999999975
Q ss_pred cccCCCCCchHHHHHHHHHHHHhhh--hhcCC---CCC---ceEEEEEEEEecCCChHHHHHHHHHHHHHhCCCCCc---
Q 025943 82 RMRKPKGDRRSTEISLVIRQTMEAC--ILTHL---MPR---SQIDIFVQVLQADGGTRSACINAATLALQDAGIPMR--- 150 (246)
Q Consensus 82 ~~~~~~~~~~~~~l~~~l~~~l~~~--i~le~---~p~---~~I~i~v~VL~~dG~ll~a~i~aa~~AL~~a~Ip~~--- 150 (246)
+.++|++++.++-+++.|..++.++ |+++. .++ |.++.++.+|+.||+++|+|.+|..+||.+-.+|..
T Consensus 106 r~RpG~p~dea~viSq~LhdtIl~S~ii~~k~Lci~~gKaawvlYadIicLd~dG~~fDa~w~al~aAlknvklP~a~id 185 (298)
T KOG1613|consen 106 RFRPGPPTDEAQVISQKLHDTILHSRIIPKKALCIKAGKAAWVLYADIICLDYDGPVFDACWNALMAALKNVKLPRAFID 185 (298)
T ss_pred CCCCCCCchHHHHHHHHHHHHHHhcCCcchhhheeeccceeeEEEEEEEEEcCCCcHHHHHHHHHHHHHhcCCCceeeec
Confidence 4567889999999999998888765 34333 344 589999999999999999999999999999999921
Q ss_pred C-------------------cee--------------EEEEE-EecCcee-ecC------CCCCeEEEEEcCCCCcEEEE
Q 025943 151 D-------------------IVT--------------SCSAG-YLNSTPL-LDS------AGGPDVTVGILPTLDKVTLL 189 (246)
Q Consensus 151 ~-------------------~~~--------------avs~~-~~~~~~l-vD~------~~~~~ltv~~~~~~~~i~~i 189 (246)
. .+. ..|.. ++++.++ .|+ ...+.+|| +++..|+++.+
T Consensus 186 e~~~~~~~t~e~~ic~~tlt~p~~ln~e~r~~~~~n~~fS~~~vl~~~li~adpT~eEE~l~~~~lTI-vldss~n~v~l 264 (298)
T KOG1613|consen 186 ERASDLRMTIEEIICDQTLTVPLMLNAENRAFASQNSDFSEEEVLDDVLIAADPTEEEETLITSTLTI-VLDSSGNYVQL 264 (298)
T ss_pred ccchhhhhhHHHHHHhhhhcchhhhccccccccccCCCccHHHhhcceeEecCCCchhhhhhhceEEE-EEcCCCCEEEE
Confidence 0 000 11111 2233344 342 23467888 68999999999
Q ss_pred EeecC---CCHHHHHHHHHHHHHHHHHHHHHHH
Q 025943 190 QMDAK---LPTNTFEDVMQLAIEGCKAVANYIR 219 (246)
Q Consensus 190 ~~~g~---~~~~~l~~~l~~A~~~~~~i~~~i~ 219 (246)
.+.|. .+++.+++|+++|..+++++.+.+.
T Consensus 265 ~k~GG~al~~~~~iK~c~elar~Rakelk~~~~ 297 (298)
T KOG1613|consen 265 TKVGGGALITPEMIKRCLELARVRAKELKTRFN 297 (298)
T ss_pred EecCcccccCHHHHHHHHHHHHHHHHHHHHHhc
Confidence 99853 6779999999999999999987653
No 20
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=99.94 E-value=6e-26 Score=221.73 Aligned_cols=204 Identities=18% Similarity=0.218 Sum_probs=174.3
Q ss_pred cceEEEECCCC-CCCeEEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCCcccc-----ccCCCCCchHH
Q 025943 20 RQLRAEIGNVA-KADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDR-----MRKPKGDRRST 93 (246)
Q Consensus 20 R~i~i~~g~l~-~a~GSa~v~~G~T~Vl~~V~gp~e~~~~~~~~p~~g~l~v~v~~~~~s~~~~-----~~~~~~~~~~~ 93 (246)
|++.+++|.+. +|+||+.++.|+|.|+|+|....+++.. .|..+|+|+|+-..++.+.. ++.|++++.+.
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 57999999986 8999999999999999999864443332 25678999998877776543 45688999999
Q ss_pred HHHHHHHHHHhhhhhcCCCCCceEEEEEEEEecCCC--hHHHHHHHHHHHHHhCCCCCcCceeEEEEEEecCceeecC--
Q 025943 94 EISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGG--TRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDS-- 169 (246)
Q Consensus 94 ~l~~~l~~~l~~~i~le~~p~~~I~i~v~VL~~dG~--ll~a~i~aa~~AL~~a~Ip~~~~~~avs~~~~~~~~lvD~-- 169 (246)
.++++|+|.|++.+..+.||+.+|.+ +||++||+ ...+|+||+++||++++|||.+.++||++|++++.+++|+
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 99999999999999999999888855 99999998 6699999999999999999999999999999999999993
Q ss_pred ----CCCCeEEEEEcCCCCcEEEEEeecC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-Hhhccc
Q 025943 170 ----AGGPDVTVGILPTLDKVTLLQMDAK-LPTNTFEDVMQLAIEGCKAVANYIREVRKFL-LIAVDI 231 (246)
Q Consensus 170 ----~~~~~ltv~~~~~~~~i~~i~~~g~-~~~~~l~~~l~~A~~~~~~i~~~i~~~l~~~-~~~~~~ 231 (246)
.++.++.| .++.+.|++++..+. ++++++.++++.|.++++.+.+++++.++.. +..+++
T Consensus 243 ~E~~~s~ldLvv--agt~~~IvMIE~~a~e~see~l~~Al~~a~~aik~i~~~~~el~~~~gk~k~~~ 308 (891)
T PLN00207 243 KEMEESELDLIM--AGTDSAILMIEGYCNFLPEEKLLEAVEVGQDAVRAICKEIEVLVKKCGKPKMLD 308 (891)
T ss_pred HHHhcCCeeEEE--EEcCCeEEEEEcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccC
Confidence 34555654 456678999999986 5999999999999999999999999988877 333444
No 21
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=99.92 E-value=9.9e-25 Score=200.00 Aligned_cols=215 Identities=24% Similarity=0.325 Sum_probs=184.0
Q ss_pred ccCCCCCCCCCCCCCCCcceEEEECCCCCCCeEEEEEeCCeEEEEEEEc-Ccccccccc--CCCCce-EEEEEEeecCCC
Q 025943 3 FVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYG-PREVQNKSQ--QMSDQA-LVRCEYSMANFS 78 (246)
Q Consensus 3 ~~~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~g-p~e~~~~~~--~~p~~g-~l~v~v~~~~~s 78 (246)
.|..+|.|.|||..+|+|+|.|+.+.++..+||++|+-|+|+|+|+|+- ..+...+.+ ..|++| .+..+|.|+|++
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 5678999999999999999999999999999999999999999999983 333222221 235555 899999999999
Q ss_pred ccccccCCCCCchHHHHHHHHHHHHhhhhhcCCCCCceEEEEEEEEecCCChHHHHHHHHHHHHHhCCCCCcCceeEEEE
Q 025943 79 TGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSA 158 (246)
Q Consensus 79 ~~~~~~~~~~~~~~~~l~~~l~~~l~~~i~le~~p~~~I~i~v~VL~~dG~ll~a~i~aa~~AL~~a~Ip~~~~~~avs~ 158 (246)
+++..+.|..++|+.....+-+++|.+.+. +.|| ..|+|.-.||+.||+...|.+.+.++||+|+|+|++.-++++++
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 999888888889988888999999999887 6688 69999999999999999999999999999999999999999999
Q ss_pred EEecC----------c-eeec------CCCCCeEEEEEcCCCCcEEEEEeecCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025943 159 GYLNS----------T-PLLD------SAGGPDVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREV 221 (246)
Q Consensus 159 ~~~~~----------~-~lvD------~~~~~~ltv~~~~~~~~i~~i~~~g~~~~~~l~~~l~~A~~~~~~i~~~i~~~ 221 (246)
|+.-+ + ++-| ..+++++.| +++++.|.++ .++.+.+.++++.|..+-.+|...|.+.
T Consensus 510 Glvt~td~e~g~i~dyriltDIlGiEd~~GDMDFKi--AGt~dGvTA~----gi~l~Iv~eal~~a~~ar~~Il~~m~k~ 583 (760)
T KOG1067|consen 510 GLVTKTDPEKGEIEDYRILTDILGIEDYNGDMDFKI--AGTNDGVTAL----GIPLKIVMEALQKAREARLQILDIMEKN 583 (760)
T ss_pred EeEeccCcccCCcccceeehhhcchhhhcCCcceee--ccccCcceec----CCcHHHHHHHHHhhhHHHHHHHHHHHhh
Confidence 98621 2 3345 355677776 5888888887 7889999999999999999999999988
Q ss_pred HHHH
Q 025943 222 RKFL 225 (246)
Q Consensus 222 l~~~ 225 (246)
+...
T Consensus 584 i~~P 587 (760)
T KOG1067|consen 584 INSP 587 (760)
T ss_pred cCCc
Confidence 7665
No 22
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=99.89 E-value=1.1e-22 Score=191.56 Aligned_cols=221 Identities=23% Similarity=0.360 Sum_probs=187.8
Q ss_pred ccCCCCCCCCCCCCCCCcceEEEECCCCCCCeEEEEEeCCeEEEEEEE-cCccccccccCCCC--ceEEEEEEeecCCCc
Q 025943 3 FVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVY-GPREVQNKSQQMSD--QALVRCEYSMANFST 79 (246)
Q Consensus 3 ~~~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~-gp~e~~~~~~~~p~--~g~l~v~v~~~~~s~ 79 (246)
.|...++|+|||..++.||+.++.|+++++|||+++..|.|+.++.++ |+....+-.+.... .-.+-.+|+|+|||.
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 577899999999999999999999999999999999999999999886 44332222112112 236778999999999
Q ss_pred cccccCCCCCchHHHHHHHHHHHHhhhhh-cCCCCCceEEEEEEEEecCCChHHHHHHHHHHHHHhCCCCCcCceeEEEE
Q 025943 80 GDRMRKPKGDRRSTEISLVIRQTMEACIL-THLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSA 158 (246)
Q Consensus 80 ~~~~~~~~~~~~~~~l~~~l~~~l~~~i~-le~~p~~~I~i~v~VL~~dG~ll~a~i~aa~~AL~~a~Ip~~~~~~avs~ 158 (246)
++.++.+.+.+|+.-..++-+|++.+.+. .+.|| ..|++.-.|++.+|+-..|.+.+.++||+++|+|++..++++..
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 99888888888988889999999999887 46788 68999999999999999999999999999999999999999999
Q ss_pred EEecC--c--eeec------CCCCCeEEEEEcCCCCcEEEEEeec---CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025943 159 GYLNS--T--PLLD------SAGGPDVTVGILPTLDKVTLLQMDA---KLPTNTFEDVMQLAIEGCKAVANYIREVRKFL 225 (246)
Q Consensus 159 ~~~~~--~--~lvD------~~~~~~ltv~~~~~~~~i~~i~~~g---~~~~~~l~~~l~~A~~~~~~i~~~i~~~l~~~ 225 (246)
|++.+ . ++-| +..++++.| .++.+.|+++|++- .++.+.+.+++..|+.+..+|...|.+++++.
T Consensus 465 GLI~eg~~~~vLsDI~G~EDhlGDMDFKV--AGT~~GiTAlQMDiKi~Git~eim~~AL~QAk~aRlhIL~~M~~ai~~p 542 (692)
T COG1185 465 GLIKEGDKYAVLSDILGDEDHLGDMDFKV--AGTDDGITALQMDIKIKGITKEIMKKALEQAKGARLHILIVMNEAISEP 542 (692)
T ss_pred cceecCCceEeeccccccccccCCceeEE--ecCCCcceeeeeeeeecCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 98843 2 2334 456777786 58899999999984 58999999999999999999999999998877
Q ss_pred H
Q 025943 226 L 226 (246)
Q Consensus 226 ~ 226 (246)
.
T Consensus 543 r 543 (692)
T COG1185 543 R 543 (692)
T ss_pred h
Confidence 3
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=99.83 E-value=5e-19 Score=170.22 Aligned_cols=202 Identities=15% Similarity=0.199 Sum_probs=165.6
Q ss_pred cceEEEECCCC-CCCeEEEEEe-CCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCCcccc-----ccCCCCCchH
Q 025943 20 RQLRAEIGNVA-KADGSAVFEM-GNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDR-----MRKPKGDRRS 92 (246)
Q Consensus 20 R~i~i~~g~l~-~a~GSa~v~~-G~T~Vl~~V~gp~e~~~~~~~~p~~g~l~v~v~~~~~s~~~~-----~~~~~~~~~~ 92 (246)
|++.+++|.+. +|+||+.+++ |+|.|+|+|....+++.. .|..+|+|+|+-..++.+.. ++.|+|++++
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 RTIRFETGRLARQAAGSVVAYLDDETMLLSATTASKQPKDQ----FDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDA 92 (719)
T ss_pred EEEEEEcchhHhhCCceEEEEecCCeEEEEEEEecCCCCCC----CCCcceeEeeeehhhhcCccCCceeccCCCCChhh
Confidence 47999999996 8999999999 999999999854433321 25678999999877776654 4568899999
Q ss_pred HHHHHHHHHHHhhhhhcCCCCC---ceEEEEEEEEecCCCh--HHHHHHHHHHHHHhCCCCCcCceeEEEEEEecCceee
Q 025943 93 TEISLVIRQTMEACILTHLMPR---SQIDIFVQVLQADGGT--RSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLL 167 (246)
Q Consensus 93 ~~l~~~l~~~l~~~i~le~~p~---~~I~i~v~VL~~dG~l--l~a~i~aa~~AL~~a~Ip~~~~~~avs~~~~~~~~lv 167 (246)
...+|+|+|.+|| +||+ ..++|.++||+.|+.. --.++||+++||.-++||+.+.+.|+.+|.++|++++
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 9999999999999 5665 3788889999999864 4679999999999999999999999999999999999
Q ss_pred cC------CCCCeEEEEEcCCC-----CcEEEEEe------------ec-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025943 168 DS------AGGPDVTVGILPTL-----DKVTLLQM------------DA-KLPTNTFEDVMQLAIEGCKAVANYIREVRK 223 (246)
Q Consensus 168 D~------~~~~~ltv~~~~~~-----~~i~~i~~------------~g-~~~~~~l~~~l~~A~~~~~~i~~~i~~~l~ 223 (246)
+| .++.+++|+ ++. +.|++++. .+ .++++++.+++..|.+..+.+.+.+++..+
T Consensus 168 NPt~~~~~~s~ldLvva--gt~~~~~~~~i~MiE~~a~~~~~~~~~~~a~e~~e~~~~~Ai~~a~~~i~~~~~~~~~l~~ 245 (719)
T TIGR02696 168 FPTHEQLEGAVFDMVVA--GRVLENGDVAIMMVEAEATEKTWDLVKGGAEAPTEEVVAEGLEAAKPFIKVLCRAQADLAE 245 (719)
T ss_pred CcCHHHHhhCeeeEEEE--eeecCCCCccEEEEecCCccccccccccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 94 345566663 443 48999997 33 389999999999999999999999999777
Q ss_pred HH-Hhhcccc
Q 025943 224 FL-LIAVDIV 232 (246)
Q Consensus 224 ~~-~~~~~~~ 232 (246)
.. +..+.+.
T Consensus 246 ~~gk~k~~~~ 255 (719)
T TIGR02696 246 KAAKPTGEFP 255 (719)
T ss_pred HhCCCccccC
Confidence 66 3334444
No 24
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=99.79 E-value=7.4e-18 Score=159.23 Aligned_cols=204 Identities=22% Similarity=0.337 Sum_probs=172.5
Q ss_pred CcceEEEECCCC-CCCeEEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCCcccc-----ccCCCCCchH
Q 025943 19 MRQLRAEIGNVA-KADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDR-----MRKPKGDRRS 92 (246)
Q Consensus 19 ~R~i~i~~g~l~-~a~GSa~v~~G~T~Vl~~V~gp~e~~~~~~~~p~~g~l~v~v~~~~~s~~~~-----~~~~~~~~~~ 92 (246)
-|++.+++|.+. +|+|++++++|+|.|++++.+.. ++. .-|..+++|+|.-..++.+.. ++.|+|++++
T Consensus 13 ~~~l~~etg~~A~qa~gav~~~~gdt~vl~t~~~~~-~~~----~~dF~PLtV~y~Ek~yaaGkiPGgf~kREGrpse~e 87 (692)
T COG1185 13 GRTLTLETGKIARQANGAVLVRYGDTVVLATVVASK-PKE----GQDFFPLTVNYEEKTYAAGKIPGGFFKREGRPSEKE 87 (692)
T ss_pred CeeEEEEcchhhhhcCccEEEEECCeEEEEEEeecC-CCC----CCCccceeEeeeeehhccCcCCCcccccCCCCCccc
Confidence 489999999996 89999999999999999999755 222 236778999998877777654 4568899999
Q ss_pred HHHHHHHHHHHhhhhhcCCCCC---ceEEEEEEEEecCCCh--HHHHHHHHHHHHHhCCCCCcCceeEEEEEEecCceee
Q 025943 93 TEISLVIRQTMEACILTHLMPR---SQIDIFVQVLQADGGT--RSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLL 167 (246)
Q Consensus 93 ~~l~~~l~~~l~~~i~le~~p~---~~I~i~v~VL~~dG~l--l~a~i~aa~~AL~~a~Ip~~~~~~avs~~~~~~~~lv 167 (246)
...+|+|+|.++| .||+ .-++|..+|++.|+.. --.+++++++||.-++||+...+.++.+|++++.+++
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 9999999999999 4554 3688899999999976 4589999999999999999999999999999999999
Q ss_pred cC------CCCCeEEEEEcCCCCcEEEEEeec-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-Hhhccccce
Q 025943 168 DS------AGGPDVTVGILPTLDKVTLLQMDA-KLPTNTFEDVMQLAIEGCKAVANYIREVRKFL-LIAVDIVGL 234 (246)
Q Consensus 168 D~------~~~~~ltv~~~~~~~~i~~i~~~g-~~~~~~l~~~l~~A~~~~~~i~~~i~~~l~~~-~~~~~~~~~ 234 (246)
++ .+..+++| .++...|.+++... .++++++.+++..+.+..+.+.+++++..... +..|+|...
T Consensus 163 NPt~~e~~~s~lDlvV--AGT~~aV~MVE~~a~~l~E~~ml~Av~fg~~~~~~~~~~qe~l~~~~g~~~~~~~~~ 235 (692)
T COG1185 163 NPTLEELEESKLDLVV--AGTKDAVNMVESEADELDEEVMLEAVEFGHEAIQSVINAQEELALEVGKKKWELEPP 235 (692)
T ss_pred CCChHHhhhcceeeEe--cCChhhhheeecccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccccccc
Confidence 83 33455665 68888899999986 48999999999999999999999999987777 577777643
No 25
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=99.57 E-value=1.4e-14 Score=133.82 Aligned_cols=214 Identities=17% Similarity=0.230 Sum_probs=166.5
Q ss_pred CCcceEEEECCCC-CCCeEEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCCcccc-----ccCCCCCch
Q 025943 18 EMRQLRAEIGNVA-KADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDR-----MRKPKGDRR 91 (246)
Q Consensus 18 e~R~i~i~~g~l~-~a~GSa~v~~G~T~Vl~~V~gp~e~~~~~~~~p~~g~l~v~v~~~~~s~~~~-----~~~~~~~~~ 91 (246)
-.|.+.+++|.+. .|+||+.+..|+|+|+++|.....+.. |+.-++.|+|+....+.+.. ++.+.+.++
T Consensus 54 GnR~i~~etGklaRfAngsvvv~~GeT~Vm~Tv~~a~~PSp-----~qFlPL~VdYqeK~aAvGRip~~fmRREg~tkdk 128 (760)
T KOG1067|consen 54 GNREILFETGKLARFANGSVVVQMGETAVMTTVVLADKPSP-----PQFLPLVVDYQEKFAAVGRIPGNFMRREGRTKDK 128 (760)
T ss_pred CCeEEEEecchhhhhcCCcEEEccCCeEEEEEEEecCCCCc-----cccceEEEehhhhhhhhccCCCcccccccCCcch
Confidence 5799999999997 689999999999999999985332221 34568999998765554322 455667777
Q ss_pred HHHHHHHHHHHHhhhhhcCCCCCceEEEEEEEEecCCCh--HHHHHHHHHHHHHhCCCCCcCceeEEEEEEecCceeecC
Q 025943 92 STEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGT--RSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDS 169 (246)
Q Consensus 92 ~~~l~~~l~~~l~~~i~le~~p~~~I~i~v~VL~~dG~l--l~a~i~aa~~AL~~a~Ip~~~~~~avs~~~~~~~~lvD~ 169 (246)
+....++|++.+++......|. ..++-+.+|..||-. ---++|++++||..+.||+...+.++.+|++++++++++
T Consensus 129 EiL~~rLidrsirplfp~g~~~--etqi~~n~Ls~dG~~~pdvlainaas~Al~lsdvpw~gpig~vRigLi~Ge~vVNP 206 (760)
T KOG1067|consen 129 EILTGRLIDRPIRPLFPKGFYH--ETQILCNVLSSDGVHDPDVLAINAASAALSLSDVPWNGPIGAVRIGLIDGEFVVNP 206 (760)
T ss_pred hheeeeccccccccCCcccchh--HHHHHhhheecccccCchHHHHhHHHHHhhhccCCCCCceeeeEeeeecceEEeCc
Confidence 7778899999888843322222 345566888889865 346899999999999999999999999999999999993
Q ss_pred ----CCCCeEEEEEcCCCCcEEEEEeec-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HhhccccceeEEE
Q 025943 170 ----AGGPDVTVGILPTLDKVTLLQMDA-KLPTNTFEDVMQLAIEGCKAVANYIREVRKFL-LIAVDIVGLCLVI 238 (246)
Q Consensus 170 ----~~~~~ltv~~~~~~~~i~~i~~~g-~~~~~~l~~~l~~A~~~~~~i~~~i~~~l~~~-~~~~~~~~~~~~~ 238 (246)
.+.+.+.+.+..++.++++++-.+ .+.++++.+++..+.+.++.+...|....++. ++.+....+++.+
T Consensus 207 T~kEmssS~Lnlvvagt~~~~vmle~~s~~i~qqdl~~Aikvg~~~~q~~i~~i~~L~k~~Gk~Kr~~~~~~~p~ 281 (760)
T KOG1067|consen 207 TRKEMSSSQLNLVVAGTKSQTVMLEGSSNNILQQDLLHAIKVGVKEAQQIIQGIERLAKKYGKQKREPQKLFLPD 281 (760)
T ss_pred chhhhhhccceeEEEeccceEEEEEcccccccHHHHHHHHHhccHHHHHHHHHHHHHHHHhCccccchhhhcCCC
Confidence 233344433456799999999886 48999999999999999999999998887777 7777777776543
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=98.41 E-value=1.1e-06 Score=60.68 Aligned_cols=60 Identities=18% Similarity=0.294 Sum_probs=46.8
Q ss_pred CceeEEEEEEecCceeecC------CCCCeEEEEEcCCCCcEEEEEeecC--CCHHHHHHHHHHHHHH
Q 025943 151 DIVTSCSAGYLNSTPLLDS------AGGPDVTVGILPTLDKVTLLQMDAK--LPTNTFEDVMQLAIEG 210 (246)
Q Consensus 151 ~~~~avs~~~~~~~~lvD~------~~~~~ltv~~~~~~~~i~~i~~~g~--~~~~~l~~~l~~A~~~ 210 (246)
|+|+++|++++++.+++|+ .+.+.+++++.++.+.+..++..|. ++++++.+++++|+++
T Consensus 1 ~~~~avt~~~i~~~~v~Dpt~~Ee~~~~~~l~~~~~~~~~~~~~~~~~g~~~~~~~~l~~~i~~A~~~ 68 (68)
T PF03725_consen 1 DPPVAVTVGIIDGELVVDPTAEEESLSDSSLTLAVDGTGNICTLQKSGGGSELSEDQLEEAIELAKKA 68 (68)
T ss_dssp SEEEEEEEEEETTEEEES--HHHHHHSSEEEEEEEETTSSEEEEEEEEESSEEEHHHHHHHHHHHHHH
T ss_pred CCeEEEEEEEECCEEEECCCHHHHhhcCCcEEEEEECCCCEEEEEEcCCCCCCCHHHHHHHHHHHhcC
Confidence 6799999999999999994 3567899977554444444455555 9999999999999874
No 27
>PRK00153 hypothetical protein; Validated
Probab=50.18 E-value=1e+02 Score=22.75 Aligned_cols=64 Identities=20% Similarity=0.214 Sum_probs=43.7
Q ss_pred CCCCeEEEEEcCCCCcEEEEEeec----CCCHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHhhccccce
Q 025943 170 AGGPDVTVGILPTLDKVTLLQMDA----KLPTNTFEDVMQLAIEGCKA-VANYIREVRKFLLIAVDIVGL 234 (246)
Q Consensus 170 ~~~~~ltv~~~~~~~~i~~i~~~g----~~~~~~l~~~l~~A~~~~~~-i~~~i~~~l~~~~~~~~~~~~ 234 (246)
+..+.++| +++..+++..++-+- +-+.+.+.+++-.|...+.+ +.+...+.+....-...+.||
T Consensus 35 s~~G~V~V-~v~G~~~v~~i~Id~~ll~~~d~e~LedlI~~A~n~A~~~~~~~~~e~m~~~~gg~~~pgl 103 (104)
T PRK00153 35 AGGGLVKV-TMTGKKEVKRVKIDPSLVDPEDVEMLEDLILAAFNDALRKAEETMKEKMGKLTGGLLPPGF 103 (104)
T ss_pred ECCCeEEE-EEecCceEEEEEECHHHcCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCC
Confidence 34566777 578999999998873 24678888888777666553 444456666666666665565
No 28
>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=44.22 E-value=85 Score=22.99 Aligned_cols=60 Identities=18% Similarity=0.202 Sum_probs=32.0
Q ss_pred CchHHHHHHHHHHHHhhhh-hcCCCCCceEEEEEEEEecCCChH--------HHHHHHHHHHHHh-CCCCC
Q 025943 89 DRRSTEISLVIRQTMEACI-LTHLMPRSQIDIFVQVLQADGGTR--------SACINAATLALQD-AGIPM 149 (246)
Q Consensus 89 ~~~~~~l~~~l~~~l~~~i-~le~~p~~~I~i~v~VL~~dG~ll--------~a~i~aa~~AL~~-a~Ip~ 149 (246)
..+...+...|++.+++-+ +-+.|-++...|.+. |..||.+. .+.+.|+..|+.. +.+|+
T Consensus 10 ~~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 10 GSEVSRYAAQIKQAIQRNLYDDESYKGKECRVRIR-LAPDGLVLSVTVESGDPALCRAAKSAIAKAAKFPP 79 (96)
T ss_dssp CHHHHHHHHHHHHHHHTTTTTGGGGTT--EEEEEE-EETTSEEEEEEEEEE-HHHHHHHHHH-HCCS----
T ss_pred hHHHHHHHHHHHHHHHHhcCCccccCCCEEEEEEE-ECCCCcEEEeeecCCCHHHHHHHHHHHHHhcCCCC
Confidence 3444567788888886644 345676655555444 45555432 5677777777554 46774
No 29
>PRK14624 hypothetical protein; Provisional
Probab=38.89 E-value=1.7e+02 Score=22.22 Aligned_cols=66 Identities=17% Similarity=0.104 Sum_probs=46.5
Q ss_pred CCCCeEEEEEcCCCCcEEEEEeecC-C---CHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHhhccccceeE
Q 025943 170 AGGPDVTVGILPTLDKVTLLQMDAK-L---PTNTFEDVMQLAIEGCKAVA-NYIREVRKFLLIAVDIVGLCL 236 (246)
Q Consensus 170 ~~~~~ltv~~~~~~~~i~~i~~~g~-~---~~~~l~~~l~~A~~~~~~i~-~~i~~~l~~~~~~~~~~~~~~ 236 (246)
++.+.++| .++.++++..++-+-. + +.+.+++++-.|...+.+=. +...+.+...+.+..+.||++
T Consensus 38 sGgG~VkV-~~nG~~~i~~i~Idp~lld~eD~E~LeDLI~aAvNdA~~k~~e~~~e~m~~~tgGm~lPGl~~ 108 (115)
T PRK14624 38 AGAGMVTV-TATGEGQITNVFINKQLFDADDNKMLEDLVMAATNDALKKAKEATAYEFQNASGGLDFSEISK 108 (115)
T ss_pred ECCcEEEE-EEEcCccEEEEEECHHHcCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCchHH
Confidence 34556777 5788999999988742 3 56778888888877665433 334556777777888888776
No 30
>PRK14628 hypothetical protein; Provisional
Probab=37.77 E-value=1.8e+02 Score=22.18 Aligned_cols=63 Identities=17% Similarity=0.225 Sum_probs=43.7
Q ss_pred CCCeEEEEEcCCCCcEEEEEeecC-C-CHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHhhccccce
Q 025943 171 GGPDVTVGILPTLDKVTLLQMDAK-L-PTNTFEDVMQLAIEGCKAVANYI-REVRKFLLIAVDIVGL 234 (246)
Q Consensus 171 ~~~~ltv~~~~~~~~i~~i~~~g~-~-~~~~l~~~l~~A~~~~~~i~~~i-~~~l~~~~~~~~~~~~ 234 (246)
+.+.++| .++.++++..++-+-. + +.+.+++++-.|...+.+=.+.. .+.+...+.+..+.||
T Consensus 52 ggG~VkV-~~nG~~ei~~I~Idp~~l~D~E~LeDLIiaA~NdA~~ka~~~~~~~m~~~tggm~lPGl 117 (118)
T PRK14628 52 GGGAVRI-VATCDRRVKDIEIDEDLKEDFETLKDLLIAGMNEVMEKIEKRREEEMSKITQQFGIPGL 117 (118)
T ss_pred cCceEEE-EEEcCceEEEEEECHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCC
Confidence 3556777 5688999999988743 3 67888888888887776655543 3446666666666664
No 31
>PF12651 RHH_3: Ribbon-helix-helix domain
Probab=36.49 E-value=78 Score=19.55 Aligned_cols=34 Identities=21% Similarity=0.224 Sum_probs=30.4
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 025943 194 KLPTNTFEDVMQLAIEGCKAVANYIREVRKFLLI 227 (246)
Q Consensus 194 ~~~~~~l~~~l~~A~~~~~~i~~~i~~~l~~~~~ 227 (246)
.++.+.+.++-++|.+......+.++++++..+.
T Consensus 8 ~l~~el~~~L~~ls~~t~i~~S~Ll~eAle~~l~ 41 (44)
T PF12651_consen 8 SLDKELYEKLKELSEETGIPKSKLLREALEDYLE 41 (44)
T ss_pred ecCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 5789999999999999999999999999988754
No 32
>PF01402 RHH_1: Ribbon-helix-helix protein, copG family; InterPro: IPR002145 CopG, also known as RepA, is responsible for the regulation of plasmid copy number. It binds to the repAB promoter and controls synthesis of the plasmid replication initiator protein RepB. Many bacterial transcription regulation proteins bind DNA through a 'helix-turn-helix' motif, nevertheless CopG displays a fully defined HTH-motif structure that is involved not in DNA-binding, but in the maintenance of the intrinsic dimeric functional structure and cooperativity [, ].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2BJ3_B 2BJ8_A 2BJ1_A 2BJ9_A 2BJ7_B 1EA4_L 2CPG_C 1B01_B 2BA3_A 2K9I_B ....
Probab=34.22 E-value=55 Score=19.12 Aligned_cols=34 Identities=29% Similarity=0.376 Sum_probs=28.4
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 025943 194 KLPTNTFEDVMQLAIEGCKAVANYIREVRKFLLI 227 (246)
Q Consensus 194 ~~~~~~l~~~l~~A~~~~~~i~~~i~~~l~~~~~ 227 (246)
.++.+..+.+=++|.+......++|+.++.+...
T Consensus 5 ~l~~~~~~~l~~~a~~~g~s~s~~ir~ai~~~l~ 38 (39)
T PF01402_consen 5 RLPDELYERLDELAKELGRSRSELIREAIREYLE 38 (39)
T ss_dssp EEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHH
T ss_pred EeCHHHHHHHHHHHHHHCcCHHHHHHHHHHHHHh
Confidence 3568888889999999999999999999877643
No 33
>COG3040 Blc Bacterial lipocalin [Cell envelope biogenesis, outer membrane]
Probab=33.40 E-value=1.5e+02 Score=24.24 Aligned_cols=52 Identities=12% Similarity=0.028 Sum_probs=37.7
Q ss_pred cCceeecCCCCCeEEEEEcCCCCcEEEEEeecC-CCHHHHHHHHHHHHHHHHHH
Q 025943 162 NSTPLLDSAGGPDVTVGILPTLDKVTLLQMDAK-LPTNTFEDVMQLAIEGCKAV 214 (246)
Q Consensus 162 ~~~~lvD~~~~~~ltv~~~~~~~~i~~i~~~g~-~~~~~l~~~l~~A~~~~~~i 214 (246)
+++.+++.+.+....| +.+.+.+-+.+-...+ ++.+.++++++.|++..-.+
T Consensus 111 g~Y~Vl~~d~eYs~ai-VgsPdr~ylWlLsRtP~~s~~~~~~ml~~ak~~Gfdv 163 (174)
T COG3040 111 GDYWVLALDPEYSWAI-VGSPDREYLWLLSRTPTLSQETLKRMLEIAKRRGFDV 163 (174)
T ss_pred ccEEEEEECCCccEEE-EeCCCcceEEEEecCCCCCHHHHHHHHHHHHHcCCCc
Confidence 4455666444455655 4577788888888887 99999999999998765433
No 34
>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=28.67 E-value=2.1e+02 Score=20.17 Aligned_cols=58 Identities=21% Similarity=0.212 Sum_probs=35.6
Q ss_pred CCCeEEEEEcCCCCcEEEEEeec----CCCHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHhhc
Q 025943 171 GGPDVTVGILPTLDKVTLLQMDA----KLPTNTFEDVMQLAIEGCKA-VANYIREVRKFLLIAV 229 (246)
Q Consensus 171 ~~~~ltv~~~~~~~~i~~i~~~g----~~~~~~l~~~l~~A~~~~~~-i~~~i~~~l~~~~~~~ 229 (246)
.++.++| .++..+++..++.+. +.+++++.+++-.|...+.. ..+..++.+....-..
T Consensus 28 ~~g~V~V-~v~g~g~v~~i~i~~~~~~~~~~~~L~~~I~~A~n~A~~~a~~~~~~~~~~~~g~~ 90 (93)
T PF02575_consen 28 GDGLVTV-TVNGNGEVVDIEIDPSALRPLDPEELEDLIVEAVNDAQKKAREKAQEEMAELTGGL 90 (93)
T ss_dssp TCCTEEE-EEETTS-EEEEEE-GGGGCTS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred CCCEEEE-EEecCceEEEEEEehHhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 4556777 568999999999873 36778888877776665543 3344555555554433
No 35
>PF03333 PapB: Adhesin biosynthesis transcription regulatory protein; InterPro: IPR004356 P pili, or fimbriae, are ~68A in diameter and 1 micron in length, the bulk of which is a fibre composed of the main structural protein PapA []. At its tip, the pilus is terminated by a fibrillum consisting of repeating units of the PapE protein. This, in turn, is topped by the adhesins, PapF and PapG, both of which are needed for receptor binding. The tip fibrillum is anchored to the main PapA fibre by the PapK pilus-adaptor protein. PapH, an outer membrane protein, then anchors the entire rod in the bacterial envelope []. A cytoplasmic chaperone (PapD) assists in assembling the monomers of the macromolecule in the membrane. All of the functional pap genes are arranged in a cluster (operon) on the Escherichia coli genome. It is believed that selective pressure exerted by the host's urinal and intestinal tract isoreceptors forced the spread of this operon to other strains via lateral transfer []. PapB, encoded within the cluster, acts as a transcriptional regulator of the functional pap genes and is located in the bacterial cytoplasm []. Its mechanism involves differential binding to separate sites in the cluster, suggesting that this protein is both an activator and repressor of pilus-adhesion transcription. The protein shares similarity with other E. coli fimbrial- adhesion transcription regulators, such as AfaA, DaaA and FanB. ; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 3M8J_A.
Probab=25.87 E-value=97 Score=22.61 Aligned_cols=32 Identities=13% Similarity=0.171 Sum_probs=23.0
Q ss_pred ecCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025943 192 DAKLPTNTFEDVMQLAIEGCKAVANYIREVRK 223 (246)
Q Consensus 192 ~g~~~~~~l~~~l~~A~~~~~~i~~~i~~~l~ 223 (246)
.|.+++++|.-+++++.-....+...+++++-
T Consensus 20 pG~vs~e~F~lLl~ls~IrS~kiI~AL~dyLV 51 (91)
T PF03333_consen 20 PGKVSEEHFWLLLELSSIRSEKIIAALRDYLV 51 (91)
T ss_dssp TT-S-HHHHHHHHHHS----HHHHHHHHHHHT
T ss_pred CCCcCHHHHHHHHHHCCCCcHHHHHHHHHHHH
Confidence 47899999999999999999999999988753
No 36
>PHA01623 hypothetical protein
Probab=23.81 E-value=1.3e+02 Score=19.65 Aligned_cols=35 Identities=11% Similarity=0.012 Sum_probs=29.1
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 025943 194 KLPTNTFEDVMQLAIEGCKAVANYIREVRKFLLIA 228 (246)
Q Consensus 194 ~~~~~~l~~~l~~A~~~~~~i~~~i~~~l~~~~~~ 228 (246)
.++.+...++-.+|.+......++|+++++..+..
T Consensus 19 rldeel~~~Ld~y~~~~g~~rSe~IreAI~~yL~~ 53 (56)
T PHA01623 19 YMDKDLKTRLKVYCAKNNLQLTQAIEEAIKEYLQK 53 (56)
T ss_pred EeCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHH
Confidence 47788888888999998888899999998887543
No 37
>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=23.80 E-value=2.6e+02 Score=22.62 Aligned_cols=30 Identities=20% Similarity=0.311 Sum_probs=23.6
Q ss_pred EcCCCCcEEEEEeecCCCHHHHHHHHHHHHH
Q 025943 179 ILPTLDKVTLLQMDAKLPTNTFEDVMQLAIE 209 (246)
Q Consensus 179 ~~~~~~~i~~i~~~g~~~~~~l~~~l~~A~~ 209 (246)
+.+..|.|.+ -++|.++++++++.+++-.+
T Consensus 130 VlDK~G~V~F-~k~G~Ls~~Ev~qVi~Ll~~ 159 (160)
T PF09695_consen 130 VLDKQGKVQF-VKEGALSPAEVQQVIALLKK 159 (160)
T ss_pred EEcCCccEEE-EECCCCCHHHHHHHHHHHhc
Confidence 4677777766 46899999999999887553
No 38
>PRK05463 hypothetical protein; Provisional
Probab=22.94 E-value=1.3e+02 Score=26.31 Aligned_cols=28 Identities=29% Similarity=0.398 Sum_probs=22.2
Q ss_pred HHHHHHHhCCCCCcCceeEEEEEEecCc
Q 025943 137 AATLALQDAGIPMRDIVTSCSAGYLNST 164 (246)
Q Consensus 137 aa~~AL~~a~Ip~~~~~~avs~~~~~~~ 164 (246)
.-=-||+.+|||++|+-.+.++.++...
T Consensus 120 SFE~AL~~aGip~Rhi~~g~nVpMYrTn 147 (262)
T PRK05463 120 SFEHALLEAGIPVRHIEEGRNVPMYRTN 147 (262)
T ss_pred cHHHHHHHCCCCcccccCCCccCcEecC
Confidence 3345899999999999988888877543
No 39
>PRK14621 hypothetical protein; Provisional
Probab=22.10 E-value=3.5e+02 Score=20.37 Aligned_cols=65 Identities=15% Similarity=0.121 Sum_probs=45.7
Q ss_pred CCCCeEEEEEcCCCCcEEEEEeecC-C-CHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHhhcccccee
Q 025943 170 AGGPDVTVGILPTLDKVTLLQMDAK-L-PTNTFEDVMQLAIEGCKAVA-NYIREVRKFLLIAVDIVGLC 235 (246)
Q Consensus 170 ~~~~~ltv~~~~~~~~i~~i~~~g~-~-~~~~l~~~l~~A~~~~~~i~-~~i~~~l~~~~~~~~~~~~~ 235 (246)
++.+.++| .++.++++..++-+-. + +.+.+++++-.|...+.+=. +...+.+...+.+..+.|+|
T Consensus 36 sGgG~VkV-~~~G~~~i~~i~Idp~lldD~e~LeDLI~aA~NdA~~ka~~~~~e~m~~~tgGm~~p~~~ 103 (111)
T PRK14621 36 AGGGMVKA-SVNGKQKLLSLAIDPEIMDDVEMVQDLVVAAVNSALEESAKLAQEEISKVAGGMMNPADI 103 (111)
T ss_pred ECCceEEE-EEEcCceEEEEEECHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHH
Confidence 34566777 5788999999988743 3 67888888888776665433 44556677777777777754
No 40
>PF02962 CHMI: 5-carboxymethyl-2-hydroxymuconate isomerase; InterPro: IPR004220 5-carboxymethyl-2-hydroxymuconate isomerase transforms 5-carboxymethyl-2-hydroxy-muconic acid into 5-oxo-pent-3-ene-1,2,5-tricarboxylic acid during the third step of the homoprotocatechuate catabolic pathway []. Homoprotocatechuate (HPC; 3,4-dihydroxyphenylacetate) is catabolized to Krebs cycle intermediates via extradiol (meta-) cleavage and the necessary enzymes are chromosomally encoded in a variety of bacteria []. 5-carboxymethyl-2-hydroxymuconate isomerase is probably a dimer of two identical subunits []. A comparison of the N-terminal half of the isomerase/decarboxylase sequence from the pathway (both encoded by the gene hpcE), with the second half showed significant similarity. This suggests that a duplication may have occurred to produce a bifunctional gene [].; PDB: 3E6Q_H 1OTG_B.
Probab=21.78 E-value=3.6e+02 Score=20.73 Aligned_cols=55 Identities=15% Similarity=0.319 Sum_probs=30.8
Q ss_pred CCceEEEEEEeecCCCccccccCCCCCchHHHHHHHHHHHHhhhhhcCCCCCceEEEEEEEEecC
Q 025943 63 SDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQAD 127 (246)
Q Consensus 63 p~~g~l~v~v~~~~~s~~~~~~~~~~~~~~~~l~~~l~~~l~~~i~le~~p~~~I~i~v~VL~~d 127 (246)
++.+++.+.+++.+ |+..+.-+.++..|-.+++.-. -..+.+..+.+.+.|.+-|
T Consensus 56 ~~~~FvHv~l~il~---------GRs~e~k~~l~~~l~~~l~~~~-~~~~~~~~~~LsvEi~E~~ 110 (124)
T PF02962_consen 56 PDDAFVHVTLRILA---------GRSEEQKKALSEALLAVLKAHL-APLFAQRYLQLSVEIREMD 110 (124)
T ss_dssp S-EEEEEEEEEEET---------T--HHHHHHHHHHHHHHHHHHC-CCHCCHSEEEEEEEEEEE-
T ss_pred CCCcEEEEEeeecC---------CCCHHHHHHHHHHHHHHHHHHh-hHhhcCCeeEEEEEEEEcC
Confidence 46789999888754 2233344466666666666532 1234445667777776655
No 41
>PRK14627 hypothetical protein; Provisional
Probab=20.95 E-value=3.5e+02 Score=19.90 Aligned_cols=60 Identities=20% Similarity=0.273 Sum_probs=39.3
Q ss_pred CCCCeEEEEEcCCCCcEEEEEeecC-C---CHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHhhcc
Q 025943 170 AGGPDVTVGILPTLDKVTLLQMDAK-L---PTNTFEDVMQLAIEGCKAVANY-IREVRKFLLIAVD 230 (246)
Q Consensus 170 ~~~~~ltv~~~~~~~~i~~i~~~g~-~---~~~~l~~~l~~A~~~~~~i~~~-i~~~l~~~~~~~~ 230 (246)
++.+.++| .++..+++..++-+-. + +.+.+++++-.|...+..=.+. ..+.+.....+..
T Consensus 33 sggG~VkV-~~~G~~~v~~i~Idp~ll~~ed~e~LeDLI~aA~N~A~~k~~~~~~~~m~~~tgg~~ 97 (100)
T PRK14627 33 AGGGAITV-KMNGHREVQSITISPEVVDPDDVEMLQDLLLVAINDASRKAQQLAEERMQPLTGGLK 97 (100)
T ss_pred EcCCeEEE-EEEcCccEEEEEECHHHcCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Confidence 34566777 5788999999998732 3 4677888888887766654433 4445555554433
Done!