Query psy18119
Match_columns 263
No_of_seqs 157 out of 1130
Neff 8.0
Searched_HMMs 46136
Date Fri Aug 16 22:59:41 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy18119.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/18119hhsearch_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 1.1E-52 2.3E-57 362.9 30.6 228 3-233 2-229 (230)
2 PRK03983 exosome complex exonu 100.0 2.2E-52 4.7E-57 364.0 31.0 234 2-238 7-240 (244)
3 KOG1068|consensus 100.0 3.7E-51 8E-56 345.0 21.9 239 1-241 5-243 (245)
4 PRK00173 rph ribonuclease PH; 100.0 2.1E-48 4.5E-53 337.6 28.8 219 11-231 1-237 (238)
5 TIGR01966 RNasePH ribonuclease 100.0 2.9E-47 6.3E-52 330.1 29.1 217 12-230 1-235 (236)
6 COG0689 Rph RNase PH [Translat 100.0 1.8E-47 3.9E-52 324.0 24.9 224 4-230 3-229 (230)
7 PRK04282 exosome complex RNA-b 100.0 2.7E-44 5.9E-49 317.6 26.5 219 8-231 21-270 (271)
8 TIGR03591 polynuc_phos polyrib 100.0 1.4E-43 3.1E-48 345.9 29.4 252 2-258 303-571 (684)
9 PRK11824 polynucleotide phosph 100.0 1.7E-42 3.7E-47 339.0 28.6 252 2-258 307-574 (693)
10 COG2123 RNase PH-related exori 100.0 2.3E-41 5E-46 289.5 26.2 222 5-231 17-271 (272)
11 TIGR02696 pppGpp_PNP guanosine 100.0 9.5E-42 2.1E-46 328.4 25.8 251 2-258 328-598 (719)
12 KOG1069|consensus 100.0 1.2E-40 2.5E-45 271.9 19.0 207 20-236 4-214 (217)
13 PLN00207 polyribonucleotide nu 100.0 9.4E-40 2E-44 320.4 29.0 252 2-258 431-705 (891)
14 KOG1614|consensus 100.0 1.7E-38 3.7E-43 265.9 24.1 226 7-240 18-279 (291)
15 TIGR03591 polynuc_phos polyrib 100.0 1.7E-32 3.6E-37 268.3 27.7 207 22-236 5-220 (684)
16 PRK11824 polynucleotide phosph 100.0 5.7E-32 1.2E-36 265.0 27.7 206 21-234 13-227 (693)
17 KOG1612|consensus 100.0 4.8E-30 1E-34 216.3 25.3 225 7-235 17-279 (288)
18 KOG1613|consensus 100.0 2.1E-30 4.6E-35 216.9 15.3 215 9-227 34-297 (298)
19 PF01138 RNase_PH: 3' exoribon 100.0 3E-29 6.6E-34 198.5 17.0 131 20-150 1-132 (132)
20 PLN00207 polyribonucleotide nu 100.0 9.4E-28 2E-32 236.1 23.7 207 22-236 89-304 (891)
21 KOG1067|consensus 99.9 1.1E-25 2.4E-30 207.3 13.9 241 9-257 356-616 (760)
22 COG1185 Pnp Polyribonucleotide 99.9 8E-25 1.7E-29 207.4 16.1 247 9-258 310-572 (692)
23 TIGR02696 pppGpp_PNP guanosine 99.9 1.4E-20 3E-25 182.3 22.2 207 22-234 17-248 (719)
24 COG1185 Pnp Polyribonucleotide 99.8 2.3E-18 4.9E-23 163.8 18.8 211 22-241 14-233 (692)
25 KOG1067|consensus 99.7 2.1E-16 4.4E-21 146.6 12.3 207 20-235 54-269 (760)
26 PF03725 RNase_PH_C: 3' exorib 99.3 2.2E-11 4.7E-16 85.2 8.1 65 153-218 1-68 (68)
27 PF02575 YbaB_DNA_bd: YbaB/Ebf 51.5 88 0.0019 22.4 8.2 45 177-222 26-74 (93)
28 PF12651 RHH_3: Ribbon-helix-h 44.6 45 0.00096 20.8 3.6 35 202-236 8-42 (44)
29 PF01402 RHH_1: Ribbon-helix-h 42.1 35 0.00076 20.1 2.8 33 203-235 6-38 (39)
30 PHA01623 hypothetical protein 33.5 63 0.0014 21.3 3.2 36 202-237 19-54 (56)
31 COG3625 PhnH Uncharacterized e 30.2 2.6E+02 0.0057 23.3 6.8 96 102-199 18-143 (196)
32 PRK00153 hypothetical protein; 29.2 2.4E+02 0.0052 20.9 8.0 46 175-221 32-81 (104)
33 PF03333 PapB: Adhesin biosynt 28.0 77 0.0017 23.3 3.1 34 200-233 20-53 (91)
34 PF06519 TolA: TolA C-terminal 27.9 2E+02 0.0043 21.2 5.4 57 94-151 13-79 (96)
35 KOG0257|consensus 26.3 5.5E+02 0.012 24.3 9.0 109 96-219 73-205 (420)
36 PRK14627 hypothetical protein; 25.6 2.8E+02 0.0061 20.5 6.7 47 175-222 30-80 (100)
37 PRK14629 hypothetical protein; 24.0 3E+02 0.0066 20.4 5.7 46 175-221 32-81 (99)
38 PRK14628 hypothetical protein; 24.0 3.4E+02 0.0073 20.9 6.9 49 175-224 48-98 (118)
39 TIGR00103 DNA_YbaB_EbfC DNA-bi 22.2 3.3E+02 0.0072 20.2 6.5 45 175-220 34-81 (102)
40 PF03764 EFG_IV: Elongation fa 21.1 3.5E+02 0.0077 20.0 8.5 54 95-148 58-120 (120)
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=1.1e-52 Score=362.89 Aligned_cols=228 Identities=41% Similarity=0.686 Sum_probs=212.9
Q ss_pred cccCCCCCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCc
Q psy18119 3 LLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTG 82 (263)
Q Consensus 3 ~~~~~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~ 82 (263)
+|++ +|+|+|||.++|+|++++++|++++++|||++++|+|+|+|+|+||.+.+......++++.|+|+|+++||++.
T Consensus 2 ~~~~--~~~R~DGR~~~e~R~~~~~~g~~~~a~GSa~~~~G~T~Vl~~V~gp~e~~~~~~~~~~~~~l~v~~~~~~~a~~ 79 (230)
T TIGR02065 2 LILE--DGVRLDGRKPDELRPIKIEAGVLKNADGSAYVEFGGTKIIAAVYGPREMHPRHLQLPDRAVLRVRYHMAPFSTD 79 (230)
T ss_pred cccC--CCcCCCCCCcccccCeEEEECCCCCCCeEEEEEECCcEEEEEEeCCCccccccccCCCceEEEEEEEeCCcccC
Confidence 4566 99999999999999999999999999999999999999999999998865543456889999999999999886
Q ss_pred cccCCCCCCcchHHHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCCccCceeEEEEEe
Q psy18119 83 ERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASL 162 (263)
Q Consensus 83 ~~~~~~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp~~~~~~avt~~~ 162 (263)
++++ +.+++++.+++++|+++|+++++++.||++.|+|+|+||++||++++|++||+++||+|+||||+++++++|+++
T Consensus 80 ~~~~-~~~~~~~~~~s~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~DG~~~~aai~aa~lAL~dagIp~~~~v~avtv~~ 158 (230)
T TIGR02065 80 ERKR-PGPSRREIEISKVIREALEPAILLEQFPRTAIDVFIEVLQADAGTRCAGLTAASLALADAGIPMRDLVVGVAVGK 158 (230)
T ss_pred CccC-CCCCccHHHHHHHHHHHHHHHhChhhcCCeEEEEEEEEEEcCCCHHHHHHHHHHHHHHHcCCccccceeeEEEEE
Confidence 5543 346788899999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCeeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEecccCChhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy18119 163 AGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQH 233 (263)
Q Consensus 163 ~~~~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G~i~~~~l~~~i~~A~~~~~~i~~~i~~~l~~~ 233 (263)
+++.+++|||..||..+.+.++|++++..++|+++++.|.++++++.++++.|.++|+.++++++++|+++
T Consensus 159 ~~~~~v~Dpt~~Ee~~~~~~l~va~~~~~~~i~~i~~~g~~~~e~~~~~l~~a~~~~~~l~~~~~~~l~~~ 229 (230)
T TIGR02065 159 VDGVVVLDLNEEEDMYGEADMPVAMMPKLGEITLLQLDGDMTPDEFRQALDLAVKGIKIIYQIQREALKNK 229 (230)
T ss_pred ECCeEEECCCHHHhhcCCCceEEEEeCCCCCEEEEEEecCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 99999999999999999999999998778999999999999999999999999999999999999999876
No 2
>PRK03983 exosome complex exonuclease Rrp41; Provisional
Probab=100.00 E-value=2.2e-52 Score=363.97 Aligned_cols=234 Identities=41% Similarity=0.687 Sum_probs=217.0
Q ss_pred ccccCCCCCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCC
Q psy18119 2 DLLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFST 81 (263)
Q Consensus 2 e~~~~~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~ 81 (263)
+++++ +|+|+|||.++|+|++++++|++++++|||++++|+|+|+|+|+||.+........++++.++|+++++||++
T Consensus 7 ~~~~~--~~~R~DGR~~~~~R~i~i~~G~l~~a~GSa~v~~G~T~Vl~~V~gp~e~~~~~~~~~~~~~l~v~~~~~p~~~ 84 (244)
T PRK03983 7 KLILE--DGLRLDGRKPDELRPIKIEVGVLKNADGSAYLEWGNNKIIAAVYGPREMHPRHLQLPDRAVLRVRYNMAPFSV 84 (244)
T ss_pred hhhcc--CCCCCCCCCcCcccceEEEeCCCCCCCeEEEEEECCeEEEEEEecCCccccccccCCCcEEEEEEEEcCCCcc
Confidence 45676 9999999999999999999999999999999999999999999999887654345688999999999999998
Q ss_pred ccccCCCCCCcchHHHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCCccCceeEEEEE
Q psy18119 82 GERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSAS 161 (263)
Q Consensus 82 ~~~~~~~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp~~~~~~avt~~ 161 (263)
.++. +..+++++.+++++|+++|+++++++.||++.|+|+++||++|||+++|++||+++||+|+||||+++++++|++
T Consensus 85 ~~~~-~~~~~~~~~~~s~~l~~~l~~~i~~~~~p~~~I~I~i~VL~~DG~~~~aai~Aa~lAL~dagIp~~~~v~avtv~ 163 (244)
T PRK03983 85 DERK-RPGPDRRSIEISKVIREALEPAIMLELFPRTVIDVFIEVLQADAGTRVAGITAASLALADAGIPMRDLVAGCAVG 163 (244)
T ss_pred cccc-CCCCChhHHHHHHHHHHHHHHhccHHhCCCeEEEEEEEEEECCCCHHHHHHHHHHHHHHhcCCccccceeEEEEE
Confidence 6554 334677889999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ecCCeeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEecccCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy18119 162 LAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKVA 238 (263)
Q Consensus 162 ~~~~~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G~i~~~~l~~~i~~A~~~~~~i~~~i~~~l~~~~~~~~ 238 (263)
++++.+++|||..||+.+++.++|+++++.++|+++++.|.++.+++.++++.|.++|++++++|+++|+++..+..
T Consensus 164 ~~~~~~i~DPt~~Ee~~~~~~l~va~~~~~~~I~~l~~~G~~~~~~~~~~i~~A~~~~~~i~~~i~~~l~~~~~~~~ 240 (244)
T PRK03983 164 KVDGVIVLDLNKEEDNYGEADMPVAIMPRLGEITLLQLDGNLTREEFLEALELAKKGIKRIYQLQREALKSKYGEIA 240 (244)
T ss_pred EECCEEEECCCHHHhccCCceEEEEEECCCCCEEEEEEecCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 99999999999999999999999999777899999999999999999999999999999999999999998877543
No 3
>KOG1068|consensus
Probab=100.00 E-value=3.7e-51 Score=345.03 Aligned_cols=239 Identities=52% Similarity=0.841 Sum_probs=228.1
Q ss_pred CccccCCCCCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCC
Q psy18119 1 MDLLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFS 80 (263)
Q Consensus 1 ~e~~~~~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~ 80 (263)
|+++++ +|+|.|||.++|.|+|..++|++.+++|||++++|||||+|.|+||++++..+...++++.++|.|..+.|+
T Consensus 5 ~~~~se--eg~r~dgRr~~elR~i~~~~g~~~~a~GSay~E~GnTKVl~aV~GPre~~~~~~~~~~~a~lnc~~~~a~Fs 82 (245)
T KOG1068|consen 5 YETLSE--EGLRTDGRRPNELRRIYARIGVLTQADGSAYMEQGNTKVLCAVYGPREIRGKSARRPDKAVLNCEVSSAQFS 82 (245)
T ss_pred ccccCc--cccccCCCChhHhhhhhhhcCccccCCccchhhcCCeEEEEEEeCCcccccccccccccceEEEEEeeeccc
Confidence 578999 999999999999999999999999999999999999999999999999887655578899999999999999
Q ss_pred CccccCCCCCCcchHHHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCCccCceeEEEE
Q psy18119 81 TGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSA 160 (263)
Q Consensus 81 ~~~~~~~~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp~~~~~~avt~ 160 (263)
+..+++++..+.++++++.+|+++|+++|.++.||+++|+|+|+||++||+.+++|+||+.+||.|+||||+|+++++|+
T Consensus 83 t~~r~~~~~~~rr~~e~s~~L~~afe~~I~~~lyPrsqIDI~v~VleddG~~laa~inaatlAL~daGI~m~D~i~~~t~ 162 (245)
T KOG1068|consen 83 TGDRKKRPKGDRREKELSLMLQQAFEPVILLELYPRSQIDIYVQVLEDDGSNLAAAINAATLALADAGIPMYDLITACTA 162 (245)
T ss_pred cchhccCCCccHHHHHHHHHHHHHHHHHHHhhhCccccceEEEEEEECCCccHHHHHHHHHHHHHHcCCChhhhhhhcee
Confidence 99988878889999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EecCCeeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEecccCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q psy18119 161 SLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKVAGA 240 (263)
Q Consensus 161 ~~~~~~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G~i~~~~l~~~i~~A~~~~~~i~~~i~~~l~~~~~~~~~~ 240 (263)
++.++.+++||+..||......+||++.+..++|..+++.+.++.+.|...++.|..+|+++.+.++.++.+++.++...
T Consensus 163 ~l~~~~~l~Dl~~~eesa~~~~ltVa~l~~~~~i~~l~~~~~~~~d~l~~vl~~a~~~c~~v~~~l~~~l~~~l~~~~~~ 242 (245)
T KOG1068|consen 163 GLADGTPLLDLTSLEESARAPGLTVAALPNREEIALLQLDERLHCDHLETVLELAIAGCKRVYERLRLVLREHLKNAESA 242 (245)
T ss_pred eecCCccccccccchhhccCCceEEEEecCcceEEEEEecCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 99999999999999999999899999998889999999999999999999999999999999999999999998876654
Q ss_pred C
Q psy18119 241 R 241 (263)
Q Consensus 241 ~ 241 (263)
+
T Consensus 243 ~ 243 (245)
T KOG1068|consen 243 L 243 (245)
T ss_pred c
Confidence 3
No 4
>PRK00173 rph ribonuclease PH; Reviewed
Probab=100.00 E-value=2.1e-48 Score=337.63 Aligned_cols=219 Identities=27% Similarity=0.381 Sum_probs=200.0
Q ss_pred ccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCccccCC---
Q psy18119 11 LRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGERKTR--- 87 (263)
Q Consensus 11 ~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~~~~~--- 87 (263)
+|+|||+++|+|++++++|++++++|||++++|+|+|+|+|++|...+.. ...++++.|+|+|.++||++.++.++
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 59999999999999999999999999999999999999999987653321 23467899999999999998876433
Q ss_pred -CCCCcchHHHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHc-----------CCCccCce
Q psy18119 88 -PRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDA-----------GIPMREYV 155 (263)
Q Consensus 88 -~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~da-----------gIp~~~~~ 155 (263)
+++++++.+++++|+++|+++++++.||++.|+|+++||++|||+++|++||+++||+|+ ++||+++|
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 246677899999999999999999999998999999999999999999999999999999 99999999
Q ss_pred eEEEEEecCCeeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEecc---cCChhHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy18119 156 VACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQ---KLHLDHLPRVLDCALKGCADIHAILDTAIK 231 (263)
Q Consensus 156 ~avt~~~~~~~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G---~i~~~~l~~~i~~A~~~~~~i~~~i~~~l~ 231 (263)
+++|++++++.+|+|||..||..+++.++|++ +..++||++++.| +++.+++.+|++.|.+++++++++++++|+
T Consensus 160 ~~vt~~~~~~~~lvDpt~~Ee~~~~~~l~v~~-~~~~~i~~v~~~g~g~~~~~e~l~~~i~~A~~~~~~l~~~~~~~l~ 237 (238)
T PRK00173 160 AAVSVGIVDGEPVLDLDYEEDSAAETDMNVVM-TGSGGFVEVQGTAEGAPFSREELDALLDLAEKGIAELVALQKAALA 237 (238)
T ss_pred eEEEEEEECCEEEECCCHHHHhcCCceEEEEE-CCCCCEEEEEccCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 99999999999999999999999999999998 6788999999953 699999999999999999999999999885
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=2.9e-47 Score=330.12 Aligned_cols=217 Identities=29% Similarity=0.400 Sum_probs=196.3
Q ss_pred cCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCccccCC----
Q psy18119 12 RNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGERKTR---- 87 (263)
Q Consensus 12 R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~~~~~---- 87 (263)
|+|||+++|+|++++++|++++|+|||++++|+|+|+|+|+++.+.+.. ...++++.++|++.++|+++..+.++
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 8999999999999999999999999999999999999999976543321 12357899999999999998765222
Q ss_pred CCCCcchHHHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHc-----------CCCccCcee
Q psy18119 88 PRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDA-----------GIPMREYVV 156 (263)
Q Consensus 88 ~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~da-----------gIp~~~~~~ 156 (263)
++++.++.+++++|+++|+++++++.||++.|+|+|+||++|||+++||+||+++||+|+ +|||+++|+
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 234556889999999999999999999998999999999999999999999999999999 999999999
Q ss_pred EEEEEecCCeeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEec---ccCChhHHHHHHHHHHHHHHHHHHHHHHHH
Q psy18119 157 ACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELS---QKLHLDHLPRVLDCALKGCADIHAILDTAI 230 (263)
Q Consensus 157 avt~~~~~~~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~---G~i~~~~l~~~i~~A~~~~~~i~~~i~~~l 230 (263)
++|++++++.+|+|||..||..+++.+++++ +..++||++++. ++++++++.++++.|.+++++++++++++|
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 9999999999999999999999999999999 568999999995 369999999999999999999999999886
No 6
>COG0689 Rph RNase PH [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.8e-47 Score=324.00 Aligned_cols=224 Identities=37% Similarity=0.557 Sum_probs=209.9
Q ss_pred ccCCCCCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCcc
Q psy18119 4 LTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGE 83 (263)
Q Consensus 4 ~~~~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~ 83 (263)
..+ ++.|+|||.++|.|+|+++.|++++++||+++++|+|+|+|+|+||.++.+.+...++++.++++|.+.|+++.+
T Consensus 3 ~~~--~~~R~dgR~~delR~i~~~~~~~~~a~GS~~~~~G~tkVic~vsGp~e~~p~~l~~~~~g~~t~ey~m~p~sT~~ 80 (230)
T COG0689 3 ESE--DGMRPDGRKPDELRPIKITRGVLKHAEGSSLIEFGNTKVICTVSGPREPVPRFLRGTGKGWLTAEYGMLPRSTDE 80 (230)
T ss_pred Ccc--cCcCCCCCCcccccceEEEeccccCCCccEEEEeCCeEEEEEEecCCCCCChhhcCCCceEEEEEEecccccccc
Confidence 456 899999999999999999999999999999999999999999999998887666678999999999999999976
Q ss_pred ccCCCCCCc-chHHHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCCccCceeEEEEEe
Q psy18119 84 RKTRPRGDR-KTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASL 162 (263)
Q Consensus 84 ~~~~~~~~~-~~~~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp~~~~~~avt~~~ 162 (263)
+..+. .++ ++++++++|.++|+++++++.||++.|+|+|.|+++||+.+.|++||+++||+|+|+||+++++|+|+|+
T Consensus 81 R~~~~-~~~gR~~eisrli~~al~~~i~L~~~p~~~I~i~~dVlqaDggTrta~It~A~lAL~DAgipl~~~vaaiSvgi 159 (230)
T COG0689 81 RKKRE-ADRGRTKEISRLIGRALRAVIDLELLPESTIDIDCDVLQADGGTRTASITGASLALADAGIPLRDLVAAISVGI 159 (230)
T ss_pred ccccc-ccccchhHHHHHHHHHHHHHhhhhhcCccEEEEEEEEEECCCCeeeehhhHHHHHHHHcCCchhhheeEeEEEE
Confidence 65443 333 7899999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCeeEecCCchhhhcCCCeEEEEEeCCCC--cEEEEEecccCChhHHHHHHHHHHHHHHHHHHHHHHHH
Q psy18119 163 AGDTPLVDISHLEETLGGPNLTVAALPLSG--KVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAI 230 (263)
Q Consensus 163 ~~~~~lvDPt~~Ee~~~~~~l~v~~~~~~~--~i~~i~~~G~i~~~~l~~~i~~A~~~~~~i~~~i~~~l 230 (263)
+++.+++||+..|++.+...++|++..+.+ +|..++..|+|++++|.+++++|.++|+++++.++++|
T Consensus 160 ~~~~~~lDl~~~Eds~~~~d~~v~~~~~~~~~ei~~~~~~~~~~~del~~lL~la~~g~~~~~~~~~~al 229 (230)
T COG0689 160 VDGVIVLDLDYEEDSAAEADMNVVMTGNGGLVEIQGLAEDGPFTEDELLELLDLAIKGCNELRELQREAL 229 (230)
T ss_pred ECCceEecCcchhhcccccCceEEEEecCCeEEEEEEeccCCcCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 999999999999999999999999987777 79999999999999999999999999999999999987
No 7
>PRK04282 exosome complex RNA-binding protein Rrp42; Provisional
Probab=100.00 E-value=2.7e-44 Score=317.61 Aligned_cols=219 Identities=23% Similarity=0.294 Sum_probs=194.2
Q ss_pred CCCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCC-CCCCCCcCCCCeEEEEEEEeeCCCCCccccC
Q psy18119 8 GGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPR-PVRNKSIKVHGSVLINFQYSMAVFSTGERKT 86 (263)
Q Consensus 8 ~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~-~~~~~~~~~~~~~~l~v~~~~~~~~~~~~~~ 86 (263)
++|+|+|||+++|+|++++++|++++++|||++++|+|+|+|+|+++. ++.. ..|++|.++|++.++|++...+.
T Consensus 21 ~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~vl~~V~~~~~~p~~---~~~~~g~i~~~v~~~~~a~~~~~- 96 (271)
T PRK04282 21 KKGKRIDGRKLDEYRPIEIETGVIKKAEGSALVKLGNTQVLAGVKLEIGEPFP---DTPNEGVLIVNAELLPLASPTFE- 96 (271)
T ss_pred hcCCCCCCCCCccccCeEEEeCCccCCCcEEEEEECCCEEEEEEEEEEecCCC---CCCCCCEEEEEEEECCCcCcccc-
Confidence 389999999999999999999999999999999999999999999632 3332 24678999999999999876542
Q ss_pred CCCCCcchHHHHHHHHHHHHhh--hccCCC---C---ceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCC--------
Q psy18119 87 RPRGDRKTSEISLQLRQAVSAA--IMSEVH---P---RSQIDIFVEVLQADGGNFCACVNAATLALIDAGIP-------- 150 (263)
Q Consensus 87 ~~~~~~~~~~l~~~l~~~l~~~--i~l~~~---p---~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp-------- 150 (263)
.+++++++.+++++|+++|++. ++++.| | .|.|+|+|+||++|||++||+++|+++||+|+++|
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 3356778899999999999886 444444 3 47999999999999999999999999999999995
Q ss_pred ------------ccCceeEEEEEecCCeeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEecc--cCChhHHHHHHHHHH
Q psy18119 151 ------------MREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQ--KLHLDHLPRVLDCAL 216 (263)
Q Consensus 151 ------------~~~~~~avt~~~~~~~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G--~i~~~~l~~~i~~A~ 216 (263)
|+++|+++|++++++.+|+|||..||+.+++.++|++ +..|+|+++++.| +++.+++.++++.|.
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 9999999999999999999999999999999999999 5678999999874 699999999999999
Q ss_pred HHHHHHHHHHHHHHH
Q psy18119 217 KGCADIHAILDTAIK 231 (263)
Q Consensus 217 ~~~~~i~~~i~~~l~ 231 (263)
+++++++++++++|+
T Consensus 256 ~~~~~l~~~~~~~l~ 270 (271)
T PRK04282 256 EKAKELREKLKEALG 270 (271)
T ss_pred HHHHHHHHHHHHHhc
Confidence 999999999999874
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=1.4e-43 Score=345.94 Aligned_cols=252 Identities=23% Similarity=0.332 Sum_probs=223.7
Q ss_pred ccccCCCCCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEE-cCCCCCCCC--cCCCCeEEEEEEEeeCC
Q psy18119 2 DLLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVY-GPRPVRNKS--IKVHGSVLINFQYSMAV 78 (263)
Q Consensus 2 e~~~~~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~-gp~~~~~~~--~~~~~~~~l~v~~~~~~ 78 (263)
+++.+ +|+|+|||.++|+||+++++|+++++||||+|++|+|+|+|+|+ ||.+..+.. .....++.+.++|+++|
T Consensus 303 ~~il~--~g~R~DGR~~~e~Rpi~~~~g~l~~a~GSa~~~~G~Tqvl~~vt~g~~~~~~~~~~~~~~~~~~~~~~y~~~p 380 (684)
T TIGR03591 303 ERILK--EGKRIDGRDLDTIRPISIEVGVLPRTHGSALFTRGETQALVVTTLGTERDEQIIDDLEGEYRKRFMLHYNFPP 380 (684)
T ss_pred HHHhc--CCCCCCCCCCCCcCceEEEeCCCCCCCceEEEEeCCeEEEEEEecCCcccccCCcccCCCccEEEEEEEEcCC
Confidence 45677 99999999999999999999999999999999999999999995 876543211 11245789999999999
Q ss_pred CCCccccCCCCCCcchHHHHHHHHHHHHhhhcc-CCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCCccCceeE
Q psy18119 79 FSTGERKTRPRGDRKTSEISLQLRQAVSAAIMS-EVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVA 157 (263)
Q Consensus 79 ~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~i~l-~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp~~~~~~a 157 (263)
|+++++++.+++++++.+++++++++|++++++ +.||+ .|+|+++||++|||..+|+++|+++||+|+||||++.+++
T Consensus 381 fs~~e~~~~g~~~rrei~~~~l~~ral~~~i~~~~~~p~-tI~v~~~VLesdGs~~~Aai~aaslAL~dAgvP~~~~Vag 459 (684)
T TIGR03591 381 YSVGEVGRVGGPGRREIGHGALAERALKAVLPSEEEFPY-TIRVVSEILESNGSSSMASVCGGSLALMDAGVPIKAPVAG 459 (684)
T ss_pred CCCCCcCCCCCCChHHHHHHHHHHHHHHHhcCccccCCe-EEEEEEEEEeCCCChHHHHHHHHHHHHHhcCCCCcCCEEE
Confidence 999987765567889999999999999999986 78996 6999999999999999999999999999999999999999
Q ss_pred EEEEecCC-----eeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEeccc---CChhHHHHHHHHHHHHHHHHHHHHHHH
Q psy18119 158 CSASLAGD-----TPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQK---LHLDHLPRVLDCALKGCADIHAILDTA 229 (263)
Q Consensus 158 vt~~~~~~-----~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G~---i~~~~l~~~i~~A~~~~~~i~~~i~~~ 229 (263)
+|+|++++ .+++||+..|+..++..++|+. +..+ |+++++++. ++.+.|.++++.|.+++.+++++|+++
T Consensus 460 vs~gli~~~~~~~~il~D~~~~Ed~~~d~d~~va~-t~~g-I~~lq~d~k~~~i~~~~l~~al~~a~~~~~~I~~~m~~~ 537 (684)
T TIGR03591 460 IAMGLIKEGDERFAVLSDILGDEDHLGDMDFKVAG-TRDG-ITALQMDIKIDGITREIMEQALEQAKEGRLHILGEMNKV 537 (684)
T ss_pred EEEEEEcCCCcceEEEeCCChHHHhcCCceEEEEE-cCCc-eEEEEEEcCcCCcCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999952 5999999999999999999988 3444 999999754 699999999999999999999999999
Q ss_pred HHHHHHHhhccCC-----CCccccccceecCCcc
Q psy18119 230 IKQHLIKVAGARG-----LGRKFQLGQLTGKKKE 258 (263)
Q Consensus 230 l~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~ 258 (263)
+.++..+...+.+ .++....|.++|++|.
T Consensus 538 l~~~~~~~~~~~p~~~~~~I~~~kI~~vIG~gGk 571 (684)
T TIGR03591 538 ISEPRAELSPYAPRIETIKINPDKIRDVIGPGGK 571 (684)
T ss_pred HhhhhccccccCCeEEEEecCHHHHHhhcCCCcH
Confidence 9999988888877 3477778999999885
No 9
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=100.00 E-value=1.7e-42 Score=339.02 Aligned_cols=252 Identities=24% Similarity=0.351 Sum_probs=219.2
Q ss_pred ccccCCCCCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEE-cCCCCCCC--CcCCCCeEEEEEEEeeCC
Q psy18119 2 DLLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVY-GPRPVRNK--SIKVHGSVLINFQYSMAV 78 (263)
Q Consensus 2 e~~~~~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~-gp~~~~~~--~~~~~~~~~l~v~~~~~~ 78 (263)
++|.+ +|+|+|||.++|+|++++++|+++++||||+|++|+|+|+|+|+ ||..+.+. .....+++.+.++|+++|
T Consensus 307 ~~il~--~g~R~DGR~~~e~Rpi~~~~g~l~~a~GSal~~~G~T~Vl~~vt~g~~~~~~~~~~~~~~~~~~~~~~y~~~p 384 (693)
T PRK11824 307 RRILE--EGIRIDGRKLDEIRPISIEVGVLPRTHGSALFTRGETQALVVATLGTLRDEQIIDGLEGEYKKRFMLHYNFPP 384 (693)
T ss_pred HHHhc--CCCCCCCCCcCcccceEEEeCCCCCCCceEEEEECCeEEEEEEecCCCcccccccccCCCCcEEEEEEEEcCC
Confidence 46777 99999999999999999999999999999999999999999995 76432211 011236799999999999
Q ss_pred CCCccccCCCCCCcchHHHHHHHHHHHHhhhcc-CCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCCccCceeE
Q psy18119 79 FSTGERKTRPRGDRKTSEISLQLRQAVSAAIMS-EVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVA 157 (263)
Q Consensus 79 ~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~i~l-~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp~~~~~~a 157 (263)
|+++++++.+++++++.+++++++++|++++++ +.||+ .|+|+++||++|||.++|+++|+++||+|+||||++++++
T Consensus 385 fs~~e~~~~~~~~rre~~~~~li~ral~~vi~~~~~~p~-~I~v~~~VLe~dGs~~~Aai~aaslAL~dAgvP~~~~Va~ 463 (693)
T PRK11824 385 YSVGETGRVGSPGRREIGHGALAERALEPVLPSEEEFPY-TIRVVSEILESNGSSSMASVCGSSLALMDAGVPIKAPVAG 463 (693)
T ss_pred CCCCCcCCCCCCChhHHHHHHHHHHHHHHhcCcccCCCE-EEEEEEEEEecCCCHHHHHHHHHHHHHHhcCCCccCceeE
Confidence 999887665567889999999999999999998 68995 8999999999999999999999999999999999999999
Q ss_pred EEEEecCC----eeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEeccc---CChhHHHHHHHHHHHHHHHHHHHHHHHH
Q psy18119 158 CSASLAGD----TPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQK---LHLDHLPRVLDCALKGCADIHAILDTAI 230 (263)
Q Consensus 158 vt~~~~~~----~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G~---i~~~~l~~~i~~A~~~~~~i~~~i~~~l 230 (263)
+++|++++ .+++||+..|+..++..++|+. +..+ |++++++++ ++.+.+.++++.|.+++.+|++.|++++
T Consensus 464 vs~gli~~~~~~~il~D~~~~Ed~~~d~d~~va~-t~~g-i~~lq~d~k~~~i~~~~l~~al~~a~~g~~~I~~~M~~aI 541 (693)
T PRK11824 464 IAMGLIKEGDKYAVLTDILGDEDHLGDMDFKVAG-TRDG-ITALQMDIKIDGITREILEEALEQAKEGRLHILGKMNEAI 541 (693)
T ss_pred EEEEEEcCCCceEEEcCCChhhHhhCCceEEEEe-cCCc-eEEEEEecccCCcCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 99999953 4889999999999999999998 3444 999998754 6999999999999999999999999999
Q ss_pred HHHHHHhhccCCC-----CccccccceecCCcc
Q psy18119 231 KQHLIKVAGARGL-----GRKFQLGQLTGKKKE 258 (263)
Q Consensus 231 ~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~ 258 (263)
.+.........+. .+....|.++|.+|.
T Consensus 542 ~~~r~~~~~~ap~~~~~~I~~~kI~~vIG~gg~ 574 (693)
T PRK11824 542 SEPRAELSPYAPRIETIKIPPDKIRDVIGPGGK 574 (693)
T ss_pred cCChhhhcccCchheeecCCHHHHHHHhcCCch
Confidence 9888777766552 245557888888764
No 10
>COG2123 RNase PH-related exoribonuclease [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.3e-41 Score=289.54 Aligned_cols=222 Identities=23% Similarity=0.272 Sum_probs=189.9
Q ss_pred cCCCCCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCC-CCCCCCcCCCCeEEEEEEEeeCCCCCcc
Q psy18119 5 TEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPR-PVRNKSIKVHGSVLINFQYSMAVFSTGE 83 (263)
Q Consensus 5 ~~~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~-~~~~~~~~~~~~~~l~v~~~~~~~~~~~ 83 (263)
+.+++|+|+|||.++|+|++.|++|+++.++|||+|++|+|+|+|+|+... +|-+. .|++|.+.+++...|.++..
T Consensus 17 ~ll~~g~R~DGR~~~efR~ieI~~~vi~ka~GSa~VklG~Tqvv~gvK~eig~Pf~D---tP~eG~~~~n~El~Plas~~ 93 (272)
T COG2123 17 NLLKKGIRIDGRSFDEFRPLEIETGVIPKANGSALVKLGNTQVVVGVKAEIGEPFPD---TPNEGVLVVNVELSPLASPS 93 (272)
T ss_pred HHhccCcccCCCCcccccceEEEeCceecCCCcEEEEecCeEEEEEEEcccCCCCCC---CCCCceEEeeeeeecccccc
Confidence 335699999999999999999999999999999999999999999999732 22221 34566555565555655544
Q ss_pred ccCCCCCCcchHHHHHHHHHHHHh--hhccCCCC------ceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCC-----
Q psy18119 84 RKTRPRGDRKTSEISLQLRQAVSA--AIMSEVHP------RSQIDIFVEVLQADGGNFCACVNAATLALIDAGIP----- 150 (263)
Q Consensus 84 ~~~~~~~~~~~~~l~~~l~~~l~~--~i~l~~~p------~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp----- 150 (263)
+... .+++.+.+++++++|.++. +++++.+. .|.+.++++||++|||++||++.|+++||+++++|
T Consensus 94 fE~G-ppde~aielsrvvdr~lr~s~aiDlekL~I~~g~kvwvv~vDv~vld~DGnl~Da~~lA~~aAL~~t~vP~~~~~ 172 (272)
T COG2123 94 FEPG-PPDELAIELSRVVDRGLRESKAIDLEKLCIEEGKKVWVVFVDVHVLDYDGNLIDAASLAAVAALLNTRVPKAVEV 172 (272)
T ss_pred ccCC-CCchhHHHHHHHHHHHHHhccCcchhheeEecCCEEEEEEEEEEEEcCCCCHHHHHHHHHHHHHHhcCCCceeec
Confidence 3322 3667889999999999998 46666542 38999999999999999999999999999999987
Q ss_pred -----------------ccCceeEEEEEecCCeeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEecc--cCChhHHHHH
Q psy18119 151 -----------------MREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQ--KLHLDHLPRV 211 (263)
Q Consensus 151 -----------------~~~~~~avt~~~~~~~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G--~i~~~~l~~~ 211 (263)
+.++|+++|++++++.+++|||.+||..+++.+||.+ ++.++|+.+++.| .+++..+.+|
T Consensus 173 ~~~~~v~~~~~~~~pl~~~~~pi~vt~a~ig~~lvvDPsleEe~v~d~~ltit~-~~~~~Iv~iqK~g~~~~~~~~~~~~ 251 (272)
T COG2123 173 GDGEIVIEVEEEPVPLPVSNPPISVTFAKIGNVLVVDPSLEEELVADGRLTITV-NEDGEIVAIQKVGGGSITESDLEKA 251 (272)
T ss_pred CCcceeecccCCCcccccCCCceEEEEEEECCEEEeCCCcchhhhcCceEEEEE-CCCCcEEEEEEcCCCcCCHHHHHHH
Confidence 5789999999999999999999999999999999999 6889999999985 6899999999
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q psy18119 212 LDCALKGCADIHAILDTAIK 231 (263)
Q Consensus 212 i~~A~~~~~~i~~~i~~~l~ 231 (263)
++.|.+.+.++.+.+.++|+
T Consensus 252 ~~~A~~~~~kl~~~~~~~L~ 271 (272)
T COG2123 252 LKTALSKAEKLREALKEALK 271 (272)
T ss_pred HHHHHHHHHHHHHHHHHhhc
Confidence 99999999999999988875
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=9.5e-42 Score=328.36 Aligned_cols=251 Identities=24% Similarity=0.323 Sum_probs=220.4
Q ss_pred ccccCCCCCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEc-CCCCCCC--CcCCCCeEEEEEEEeeCC
Q psy18119 2 DLLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYG-PRPVRNK--SIKVHGSVLINFQYSMAV 78 (263)
Q Consensus 2 e~~~~~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~g-p~~~~~~--~~~~~~~~~l~v~~~~~~ 78 (263)
+++.+ ++.|+|||.++++|++++++|++++++|||+++.|+|+|+|.+.. |.+..+. ....++...+.|+|+++|
T Consensus 328 ~~il~--~g~R~DGR~~~eiR~i~~~~g~l~~a~GSa~~~~G~Tqvl~~~tlG~~~~~q~~~~l~~~~~~~~~~~YnfpP 405 (719)
T TIGR02696 328 ERVLT--EGVRIDGRGVTDIRPLDAEVQVIPRVHGSALFERGETQILGVTTLNMLKMEQQIDSLSPETSKRYMHHYNFPP 405 (719)
T ss_pred HHHhc--CCCCCCCCCccccccceeecCCCCCCCceEEEEecCcEEEEEEeCCCchhhhhcccccccccceEEEEEeCCC
Confidence 56777 999999999999999999999999999999999999999999874 4332221 111245677789999999
Q ss_pred CCCccccCCCCCCcchHHHHHHHHHHHHhhhc-cCCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCCccCceeE
Q psy18119 79 FSTGERKTRPRGDRKTSEISLQLRQAVSAAIM-SEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVA 157 (263)
Q Consensus 79 ~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~i~-l~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp~~~~~~a 157 (263)
|+++++++...+++++.+++++++++|+++++ ++.||++ |.+.++||++||+...|++||+++||+||||||++++++
T Consensus 406 FSt~er~~~~~~~RReighg~La~rALe~vI~~~e~fP~T-IrvvseVLeSdGSss~AsIcaasLALmDAGVPmkd~VAg 484 (719)
T TIGR02696 406 YSTGETGRVGSPKRREIGHGALAERALVPVLPSREEFPYA-IRQVSEALGSNGSTSMGSVCASTLSLLNAGVPLKAPVAG 484 (719)
T ss_pred CcccCCCCCCCCCccHHHHHHHHHHHHHHhhCcHhhCCCE-EEEEEEeeccCCcHHHHHHHHHHHHHHHcCcchhheeeE
Confidence 99998887767788999999999999999997 6999996 889999999999999999999999999999999999999
Q ss_pred EEEEecCC--------eeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEecccC---ChhHHHHHHHHHHHHHHHHHHHH
Q psy18119 158 CSASLAGD--------TPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQKL---HLDHLPRVLDCALKGCADIHAIL 226 (263)
Q Consensus 158 vt~~~~~~--------~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G~i---~~~~l~~~i~~A~~~~~~i~~~i 226 (263)
+++|++++ .+++||+..|+...+..+.++. ..+.|++++++|++ +.+.+.+++++|.++|.+++++|
T Consensus 485 is~Gli~e~~~~~~~~~iL~Di~g~ED~~Gdmdfkvag--t~~gIt~lQmd~ki~gi~~e~l~~aL~~A~~g~~~Il~~m 562 (719)
T TIGR02696 485 IAMGLISDEVDGETRYVALTDILGAEDAFGDMDFKVAG--TSEFVTALQLDTKLDGIPASVLASALKQARDARLAILDVM 562 (719)
T ss_pred EEEEEeccccCCCcceeEEeCCCchhhhcCCceEEEEe--cCCCEEEEEEEeeECCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999943 2899999999999998888875 57999999999875 88999999999999999999999
Q ss_pred HHHHHHHHHHhhccCCCC-----ccccccceecCCcc
Q psy18119 227 DTAIKQHLIKVAGARGLG-----RKFQLGQLTGKKKE 258 (263)
Q Consensus 227 ~~~l~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~ 258 (263)
+++|... .+...+.+.. +....|.++|.+|.
T Consensus 563 ~~al~~p-~~~s~~aP~~~~~~I~~~ki~~vIG~gGk 598 (719)
T TIGR02696 563 AEAIDTP-DEMSPYAPRIITVKIPVDKIGEVIGPKGK 598 (719)
T ss_pred HHHHhCc-cccccCCCeeEEEEeChHHhhheeCCCcH
Confidence 9999999 6677766633 66778999998874
No 12
>KOG1069|consensus
Probab=100.00 E-value=1.2e-40 Score=271.94 Aligned_cols=207 Identities=28% Similarity=0.423 Sum_probs=189.3
Q ss_pred CCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCccccCCCCCCcchHHHHH
Q psy18119 20 ELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGERKTRPRGDRKTSEISL 99 (263)
Q Consensus 20 e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~~~~~~~~~~~~~~l~~ 99 (263)
..|++.++.|+++++|||+.|++|+|+|+|+|+||.+++.+ ++.+++..++|.+++...- ++..++.+++
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 RLRGIACEISILSRPDGSSEFSQGDTKVICSVYGPIDVKAR-QEDPEKATLEVIWRPKSGV---------NGTVEKVLER 73 (217)
T ss_pred hhhhhhhhhceecCCCCccceecCCcEEEEEeeCCcchhhc-ccCchhceEEEEEecccCc---------chHHHHHHHH
Confidence 68999999999999999999999999999999999998887 5789999999999865432 3456789999
Q ss_pred HHHHHHHhhhccCCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCCccCceeEEEEEecCC-eeEecCCchhhhc
Q psy18119 100 QLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLAGD-TPLVDISHLEETL 178 (263)
Q Consensus 100 ~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp~~~~~~avt~~~~~~-~~lvDPt~~Ee~~ 178 (263)
+|+++|+++|.++.||++.|+|.+||+++||+.+++|+|||++||.|+||||+++++++.+++.++ .+++|||..+|+.
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 999999999999999999999999999999999999999999999999999999999999999977 8999999999998
Q ss_pred CCCeEEEEEeC---CCCcEEEEEecccCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy18119 179 GGPNLTVAALP---LSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIK 236 (263)
Q Consensus 179 ~~~~l~v~~~~---~~~~i~~i~~~G~i~~~~l~~~i~~A~~~~~~i~~~i~~~l~~~~~~ 236 (263)
+.+..++++.. ...+++.++..|.++.+++..+++.|..++.+++.++++.+++..++
T Consensus 154 ~~~~~~lsf~~~~~~~~~vi~s~t~G~~~~d~lf~~le~a~~~~~~~f~f~r~~~q~~~s~ 214 (217)
T KOG1069|consen 154 STARATLSFEGGSLGEPKVIISETNGEKSEDQLFYVLELAQAAAQSLFPFYREVLQRKYSK 214 (217)
T ss_pred hhceEEEEEecCCCCCcceEEEeccCCCCHHHHHHHHHhhHHHHHHHHHHHHHHHHhhcCc
Confidence 87777777632 24689999999999999999999999999999999999999887654
No 13
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=100.00 E-value=9.4e-40 Score=320.35 Aligned_cols=252 Identities=23% Similarity=0.319 Sum_probs=220.9
Q ss_pred ccccCCCCCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEE-cCCCCCCCCcC---CCCeEEEEEEEeeC
Q psy18119 2 DLLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVY-GPRPVRNKSIK---VHGSVLINFQYSMA 77 (263)
Q Consensus 2 e~~~~~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~-gp~~~~~~~~~---~~~~~~l~v~~~~~ 77 (263)
++|++ +|.|+|||.++|.|+|.+++|.+++++|||+|++|+|+|+|+|+ ||.+..+..+. .+....+.++|+++
T Consensus 431 ~~i~~--~g~R~DGR~~~eiRpI~~e~G~Lp~A~GSAlf~~G~TqVLatVtlGp~~~~q~~d~l~~~~~~~~f~~~y~fP 508 (891)
T PLN00207 431 RRIVE--GGKRSDGRTPDEIRPINSSCGLLPRAHGSALFTRGETQALAVVTLGDKQMAQRIDNLVDADEVKRFYLQYSFP 508 (891)
T ss_pred HHHhc--CCCCCCCCCcCccceEEEEeCCcCCCCceEEEEECCeEEEEEEEecCccccccccccccccceeeEEEEEEcC
Confidence 45677 99999999999999999999999999999999999999999997 78754432111 13456677999999
Q ss_pred CCCCccccCCCCCCcchHHHHHHHHHHHHhhhccC-CCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCCccCcee
Q psy18119 78 VFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSE-VHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVV 156 (263)
Q Consensus 78 ~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~i~l~-~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp~~~~~~ 156 (263)
||+.+++++.+++++++.+++++++++|+++++.+ .||+ .|+|+++||++||+..+|++||+++||+|+||||+++++
T Consensus 509 Pfs~ge~~r~g~psrREi~hg~L~eRALrpvip~~~~fP~-tIrV~~~VLesDGSssmAaV~aaSLALmDAGIPmk~~VA 587 (891)
T PLN00207 509 PSCVGEVGRIGAPSRREIGHGMLAERALEPILPSEDDFPY-TIRVESTITESNGSSSMASVCGGCLALQDAGVPVKCPIA 587 (891)
T ss_pred CCCCccccCCCCCCHHHHHHHHHHHHHHHHhCCcccCCCE-EEEEEEEEEeCCCChHHHHHHHHHHHHHhcCCCccCcee
Confidence 99988877666678899999999999999999885 7995 899999999999999999999999999999999999999
Q ss_pred EEEEEec-C-------Ce--eEecCCchhhhcCCCeEEEEEeCCCCcEEEEEeccc---CChhHHHHHHHHHHHHHHHHH
Q psy18119 157 ACSASLA-G-------DT--PLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQK---LHLDHLPRVLDCALKGCADIH 223 (263)
Q Consensus 157 avt~~~~-~-------~~--~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G~---i~~~~l~~~i~~A~~~~~~i~ 223 (263)
++++|++ + +. +++||+..|+..++..|.|+. ..+.|++++++++ ++.+.|.++++.|.+++.+++
T Consensus 588 GvsvGli~d~~~~~~~g~~~IL~Dp~g~Ed~~gdmDfkVAg--T~~gIt~iqmd~k~~gis~e~l~eAL~~A~~g~~~Il 665 (891)
T PLN00207 588 GIAMGMVLDTEEFGGDGSPLILSDITGSEDASGDMDFKVAG--NEDGITAFQMDIKVGGITLPIMERALLQAKDGRKHIL 665 (891)
T ss_pred EEEEEEEecccccCCCCcEEEEeCCCHHHHhcCCceEEEEe--cccceEEEEEecccCCCCHHHHHHHHHHHHHHHHHHH
Confidence 9999999 2 23 567999999999999999997 4689999999864 589999999999999999999
Q ss_pred HHHHHHHHHHHHHhhccCCCC-----ccccccceecCCcc
Q psy18119 224 AILDTAIKQHLIKVAGARGLG-----RKFQLGQLTGKKKE 258 (263)
Q Consensus 224 ~~i~~~l~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~ 258 (263)
+.|++++.....+...+.+.. +....|.++|.+|.
T Consensus 666 ~~M~~~i~~pr~~~s~~aP~i~~~~i~~~ki~~vIG~GGk 705 (891)
T PLN00207 666 AEMSKCSPPPSKRLSKYAPLIHIMKVKPEKVNMIIGSGGK 705 (891)
T ss_pred HHHHHHHhhhhhhhcccCCeeEEEEcCHHHHHHHhcCCch
Confidence 999999999988888887743 77778889988774
No 14
>KOG1614|consensus
Probab=100.00 E-value=1.7e-38 Score=265.94 Aligned_cols=226 Identities=20% Similarity=0.227 Sum_probs=190.8
Q ss_pred CCCCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCCC-CCCCCcCCCCeEEEEEEEeeCCCCCcccc
Q psy18119 7 YGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRP-VRNKSIKVHGSVLINFQYSMAVFSTGERK 85 (263)
Q Consensus 7 ~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~~-~~~~~~~~~~~~~l~v~~~~~~~~~~~~~ 85 (263)
.|.|.|.|||++.|+|.+++++| .-.||+.+++|+|+|+|.|+.... |.. ..|.+|.+++...++|.+.+...
T Consensus 18 lk~g~R~DgR~l~efR~lei~fG---ke~gs~~vt~G~Tkvm~~vt~~ia~Py~---dRP~eG~~~I~telsPmA~~sfE 91 (291)
T KOG1614|consen 18 LKAGLRFDGRSLEEFRDLEIEFG---KEYGSVLVTMGNTKVMARVTAQIAQPYI---DRPHEGSFSIFTELSPMASPSFE 91 (291)
T ss_pred HHhcccccccchhhhhceEEEec---cccccEEEEecCeeEEEEeehhhcCccc---CCCCCCeeeeeeccccccccccC
Confidence 35899999999999999999999 478999999999999999997432 121 13455555555555555543322
Q ss_pred CCCCCCcchHHHHHHHHHHHHh--hhccCCCC------ceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCC-------
Q psy18119 86 TRPRGDRKTSEISLQLRQAVSA--AIMSEVHP------RSQIDIFVEVLQADGGNFCACVNAATLALIDAGIP------- 150 (263)
Q Consensus 86 ~~~~~~~~~~~l~~~l~~~l~~--~i~l~~~p------~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp------- 150 (263)
. ++.++.+.+++++|+++++. +||+|.++ .|.|++++++|+.|||++|||+.|+.+||++++-|
T Consensus 92 ~-Gr~~~~~v~l~Rliek~~R~S~aiD~EsLCI~aG~kvW~IRiDlhiLd~DGnlvDaA~iAviaaL~hFrrPdvTv~g~ 170 (291)
T KOG1614|consen 92 P-GRKGESEVELSRLIEKALRRSKAIDTESLCIRAGEKVWLIRIDLHILDHDGNLVDAACIAVIAALMHFRRPDVTVGGE 170 (291)
T ss_pred C-CCccchHHHHHHHHHHHHHhccccchHHHHhhhCCeEEEEEEEEEEEcCCCCeehhHHHHHHHHHHhcCCCCcccccc
Confidence 1 13457788999999999987 56666553 48999999999999999999999999999999933
Q ss_pred ----------------ccCceeEEEEEecC--CeeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEeccc--CChhHHHH
Q psy18119 151 ----------------MREYVVACSASLAG--DTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQK--LHLDHLPR 210 (263)
Q Consensus 151 ----------------~~~~~~avt~~~~~--~~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G~--i~~~~l~~ 210 (263)
|+|+|+|+||++++ +.+++|||..||...+|.++|++ |+.++||.+++.|. ++..++..
T Consensus 171 ev~ihp~eEr~PvPL~I~HmPIC~tf~ffnkG~ivviDpt~~Ee~~~dGs~vVt~-Nk~rEVc~i~k~G~~~~~~~~i~~ 249 (291)
T KOG1614|consen 171 EVIIHPVEEREPVPLSIHHMPICFTFGFFNKGEIVVIDPTEKEEAVMDGSMVVTM-NKNREVCAIQKSGGEILDESVIER 249 (291)
T ss_pred eeEecChhccCCcceeeeeccceEEEEEecCceEEEeCCcHHHHhccCceEEEEE-cCCccEEEEecCCCccccHHHHHH
Confidence 89999999999997 48899999999999999999999 78999999999985 58899999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q psy18119 211 VLDCALKGCADIHAILDTAIKQHLIKVAGA 240 (263)
Q Consensus 211 ~i~~A~~~~~~i~~~i~~~l~~~~~~~~~~ 240 (263)
|.+.|...+.++...+.++|+++..++..+
T Consensus 250 C~k~A~~~a~~vt~ii~e~l~~d~~~r~~~ 279 (291)
T KOG1614|consen 250 CYKLAKDRAVEVTGIILEALEEDQRERSAQ 279 (291)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 999999999999999999999998887766
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=100.00 E-value=1.7e-32 Score=268.25 Aligned_cols=207 Identities=17% Similarity=0.231 Sum_probs=181.6
Q ss_pred cceEEEeCCC-CCCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCcc-----ccCCCCCCcchH
Q psy18119 22 RKIRCRLGVF-SQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGE-----RKTRPRGDRKTS 95 (263)
Q Consensus 22 R~i~i~~g~l-~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~-----~~~~~~~~~~~~ 95 (263)
|++.+++|.+ ++|+|||++++|+|+|+|+|++|.++++. .+++.|+|+|...+++.+. .++.+++++++.
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 57999999999999999999999886653 5789999999987765542 233446888999
Q ss_pred HHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCChh-H-HHHHHHHHHHHHcCCCccCceeEEEEEecCCeeEecCCc
Q psy18119 96 EISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNF-C-ACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISH 173 (263)
Q Consensus 96 ~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~-~-a~i~Aa~~AL~dagIp~~~~~~avt~~~~~~~~lvDPt~ 173 (263)
+++++|+|.|+++++.. | .|.|+|+++||++||+.. + ||+||+++||++++|||++++++++++++++.+++|||.
T Consensus 81 l~srlIdR~lrplfp~~-~-~~~i~V~~~VLs~Dg~~~~d~aai~aAsaAL~~s~IP~~~~v~av~vg~idg~~ildPt~ 158 (684)
T TIGR03591 81 LTSRLIDRPIRPLFPKG-F-RNEVQVVATVLSYDPENDPDILAIIGASAALAISGIPFNGPIAAVRVGYIDGQYVLNPTV 158 (684)
T ss_pred HHHHHHhhHHHHhcCCC-C-CceEEEEEEEEecCcCCchHHHHHHHHHHHHHhcCCCcCCCeEEEEEEEECCEEEEcCCH
Confidence 99999999999875422 2 268999999999999975 5 999999999999999999999999999999999999999
Q ss_pred hhhhcCCCeEEEEEeCCCCcEEEEEeccc-CChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy18119 174 LEETLGGPNLTVAALPLSGKVAVMELSQK-LHLDHLPRVLDCALKGCADIHAILDTAIKQHLIK 236 (263)
Q Consensus 174 ~Ee~~~~~~l~v~~~~~~~~i~~i~~~G~-i~~~~l~~~i~~A~~~~~~i~~~i~~~l~~~~~~ 236 (263)
.|++.++..++|+. ..+.+++++..+. ++.+++.++++.|.++++++.++++++++++...
T Consensus 159 ~E~~~s~~~l~va~--t~~~i~mie~~~~~i~e~~l~~al~~a~~~~~~i~~~~~~~~~~~~~~ 220 (684)
T TIGR03591 159 DELEKSDLDLVVAG--TKDAVLMVESEAKELSEEVMLGAIEFGHEEIQPVIEAIEELAEEAGKE 220 (684)
T ss_pred HHHhhCCceEEEEc--cCCcEEEEEcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC
Confidence 99999999999986 4568899998764 9999999999999999999999999999888754
No 16
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=100.00 E-value=5.7e-32 Score=265.04 Aligned_cols=206 Identities=17% Similarity=0.211 Sum_probs=181.3
Q ss_pred CcceEEEeCCCC-CCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCcc-----ccCCCCCCcch
Q psy18119 21 LRKIRCRLGVFS-QSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGE-----RKTRPRGDRKT 94 (263)
Q Consensus 21 ~R~i~i~~g~l~-~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~-----~~~~~~~~~~~ 94 (263)
-|++.+++|.++ +|+|||++++|+|+|+|+|++|.++++ ..+++.++|+|...+|+++. .++.+++++++
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 378999999995 699999999999999999999988654 35789999999987776542 22334678899
Q ss_pred HHHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCCh-hH-HHHHHHHHHHHHcCCCccCceeEEEEEecCCeeEecCC
Q psy18119 95 SEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGN-FC-ACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDIS 172 (263)
Q Consensus 95 ~~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~-~~-a~i~Aa~~AL~dagIp~~~~~~avt~~~~~~~~lvDPt 172 (263)
.+++++|+|.|+++++. .++|.|+|+++||++||+. .+ +|+||+++||++++|||++.+++|+++++++.+++|||
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 TLTSRLIDRPIRPLFPK--GFRNEVQVVATVLSVDPENDPDILAMIGASAALSISGIPFNGPIAAVRVGYIDGEFVLNPT 166 (693)
T ss_pred HHHHHHHhhhHHHhCCC--CCCeEEEEEEEEEeCCCCCcHHHHHHHHHHHHHHhcCCCcCCCeEEEEEEEECCEEEEcCC
Confidence 99999999999997642 2467999999999999976 55 89999999999999999999999999999999999999
Q ss_pred chhhhcCCCeEEEEEeCCCCcEEEEEecc-cCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy18119 173 HLEETLGGPNLTVAALPLSGKVAVMELSQ-KLHLDHLPRVLDCALKGCADIHAILDTAIKQHL 234 (263)
Q Consensus 173 ~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G-~i~~~~l~~~i~~A~~~~~~i~~~i~~~l~~~~ 234 (263)
..|++.++..++|+.. .+.+++++..| .++.+++.++++.|.++++++.+++++++++..
T Consensus 167 ~~E~~~s~~~l~va~t--~~~i~mie~~~~~l~e~~l~~al~~a~~~~~~i~~~~~~~~~~~~ 227 (693)
T PRK11824 167 VEELEESDLDLVVAGT--KDAVLMVESEAKELSEEVMLEAIEFGHEAIQELIDAQEELAAEAG 227 (693)
T ss_pred HHHHhhCcceEEEEEc--cCceEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 9999999999999983 45899999876 599999999999999999999999999888766
No 17
>KOG1612|consensus
Probab=99.98 E-value=4.8e-30 Score=216.34 Aligned_cols=225 Identities=20% Similarity=0.251 Sum_probs=182.8
Q ss_pred CCCCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCC-eEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCcccc
Q psy18119 7 YGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGN-TKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGERK 85 (263)
Q Consensus 7 ~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~-T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~~~ 85 (263)
+.+.+|+|||.++++|||.++++++++++|||+|++|. |.|+++|+.....+.. +.|.++.+.+.+.+.|.+++++.
T Consensus 17 ~e~~iR~DGR~~~~~Rpi~vetdVlp~tNGSaRVk~g~~tdiivgVKaEvg~~~~--~~p~egk~~~~VD~S~sasp~f~ 94 (288)
T KOG1612|consen 17 SEPDIRNDGRSCHQFRPIEVETDVLPGTNGSARVKLGDGTDIIVGVKAEVGSPDD--ETPVEGKYLFFVDCSPSASPQFQ 94 (288)
T ss_pred cCcccccCCcCccccceEEEEeccccCCCCcEEEEecCCceEEEEEeeeccCccc--cCCCCCeEEEEEEecCCcCcccc
Confidence 34889999999999999999999999999999999999 9999999985442221 23445556666666666665554
Q ss_pred CCCCCCcchHHHHHHHHHHHHh--h-hccCCC---C--ceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCC-------
Q psy18119 86 TRPRGDRKTSEISLQLRQAVSA--A-IMSEVH---P--RSQIDIFVEVLQADGGNFCACVNAATLALIDAGIP------- 150 (263)
Q Consensus 86 ~~~~~~~~~~~l~~~l~~~l~~--~-i~l~~~---p--~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp------- 150 (263)
+|+ .++...+|+..|+++|.+ + +++..+ | .|.|.|++.|++.|||++||...|+++||.++.+|
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 432 456667899999999987 1 333221 2 47999999999999999999999999999999987
Q ss_pred --------------------ccCceeEEEEEecCCeeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEecc--cCChhHH
Q psy18119 151 --------------------MREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQ--KLHLDHL 208 (263)
Q Consensus 151 --------------------~~~~~~avt~~~~~~~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G--~i~~~~l 208 (263)
...+|+-+|++.++..+++|||.+||.++...+.|.+ ++.+-+.++..-| .+.++.+
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 2347888999999999999999999999999999999 5667666666654 5889999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy18119 209 PRVLDCALKGCADIHAILDTAIKQHLI 235 (263)
Q Consensus 209 ~~~i~~A~~~~~~i~~~i~~~l~~~~~ 235 (263)
.+|++.+++-.+.++..+.+.|++.-.
T Consensus 253 ~~mle~~~~~~e~l~~~l~k~L~~~e~ 279 (288)
T KOG1612|consen 253 PEMLEQGKAVVETLAPDLVKSLENEED 279 (288)
T ss_pred HHHHHHHHHHHHhhhHHHHHHhhhhhh
Confidence 999999999999999988888876543
No 18
>KOG1613|consensus
Probab=99.97 E-value=2.1e-30 Score=216.95 Aligned_cols=215 Identities=21% Similarity=0.256 Sum_probs=175.0
Q ss_pred CCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCccccCCC
Q psy18119 9 GGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGERKTRP 88 (263)
Q Consensus 9 ~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~~~~~~ 88 (263)
+++|+|||+..|+|.+.++.|.++.+|||+.++.|+|.|+|+|++..-.+. +..|++|.+..+|.++|.++...+. +
T Consensus 34 e~~RpdgR~lgefRdt~in~g~IsTangSal~K~G~ttvi~~Ik~ei~eps--tdapdeg~Iv~n~~lpplcs~r~Rp-G 110 (298)
T KOG1613|consen 34 EGIRPDGRKLGEFRDTAINAGNISTANGSALLKSGKTTVICGIKAEIAEPS--TDAPDEGDIVPNYALPPLCSSRFRP-G 110 (298)
T ss_pred cccCcchhhhhHHhhhheecCceeccCcHHHHhcCCcEEEEEeeeeecccc--cCCCCCcceeecccCCcccccCCCC-C
Confidence 899999999999999999999999999999999999999999999543222 2467899999999999998765433 3
Q ss_pred CCCcchHHHHHHHHHHHHhh--hccCCC------CceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCCc---------
Q psy18119 89 RGDRKTSEISLQLRQAVSAA--IMSEVH------PRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPM--------- 151 (263)
Q Consensus 89 ~~~~~~~~l~~~l~~~l~~~--i~l~~~------p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp~--------- 151 (263)
++.+.++.+++.|...+.++ |+++.+ +-|.++.++.+|++||+++|+|++|.++||.+-.+|.
T Consensus 111 ~p~dea~viSq~LhdtIl~S~ii~~k~Lci~~gKaawvlYadIicLd~dG~~fDa~w~al~aAlknvklP~a~ide~~~~ 190 (298)
T KOG1613|consen 111 PPTDEAQVISQKLHDTILHSRIIPKKALCIKAGKAAWVLYADIICLDYDGPVFDACWNALMAALKNVKLPRAFIDERASD 190 (298)
T ss_pred CCchHHHHHHHHHHHHHHhcCCcchhhheeeccceeeEEEEEEEEEcCCCcHHHHHHHHHHHHHhcCCCceeeecccchh
Confidence 57788888999998887764 444332 3478888999999999999999999999999999882
Q ss_pred ----------------------cCcee-----EEEEE-ecCCe-eEecCCchhhhcCCCeEEEEEeCCCCcEEEEEeccc
Q psy18119 152 ----------------------REYVV-----ACSAS-LAGDT-PLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQK 202 (263)
Q Consensus 152 ----------------------~~~~~-----avt~~-~~~~~-~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G~ 202 (263)
...++ ..|.. ++++. ++.|||.+||..+++.+||+. ++.|+++.+.+.|.
T Consensus 191 ~~~t~e~~ic~~tlt~p~~ln~e~r~~~~~n~~fS~~~vl~~~li~adpT~eEE~l~~~~lTIvl-dss~n~v~l~k~GG 269 (298)
T KOG1613|consen 191 LRMTIEEIICDQTLTVPLMLNAENRAFASQNSDFSEEEVLDDVLIAADPTEEEETLITSTLTIVL-DSSGNYVQLTKVGG 269 (298)
T ss_pred hhhhHHHHHHhhhhcchhhhccccccccccCCCccHHHhhcceeEecCCCchhhhhhhceEEEEE-cCCCCEEEEEecCc
Confidence 01111 12222 44554 459999999999999999999 57899998888763
Q ss_pred ---CChhHHHHHHHHHHHHHHHHHHHHH
Q psy18119 203 ---LHLDHLPRVLDCALKGCADIHAILD 227 (263)
Q Consensus 203 ---i~~~~l~~~i~~A~~~~~~i~~~i~ 227 (263)
.+++.+++|+++|..+++++.+.+.
T Consensus 270 ~al~~~~~iK~c~elar~Rakelk~~~~ 297 (298)
T KOG1613|consen 270 GALITPEMIKRCLELARVRAKELKTRFN 297 (298)
T ss_pred ccccCHHHHHHHHHHHHHHHHHHHHHhc
Confidence 5779999999999999999987664
No 19
>PF01138 RNase_PH: 3' exoribonuclease family, domain 1 This Prosite family only includes Ribonuclease PH; InterPro: IPR001247 The PH (phosphorolytic) domain is responsible for 3'-5' exoribonuclease activity, although in some proteins this domain has lost its catalytic function. An active PH domain uses inorganic phosphate as a nucleophile, adding it across the phosphodiester bond between the end two nucleotides in order to release ribonucleoside 5'-diphosphate (rNDP) from the 3' end of the RNA substrate. PH domains can be found in bacterial/organelle RNases and PNPases (polynucleotide phosphorylases) [], as well as in archaeal and eukaryotic RNA exosomes [, ], the later acting as nano-compartments for the degradation or processing of RNA (including mRNA, rRNA, snRNA and snoRNA). Bacterial/organelle PNPases share a common barrel structure with RNA exosomes, consisting of a hexameric ring of PH domains that act as a degradation chamber, and an S1-domain/KH-domain containing cap that binds the RNA substrate (and sometimes accessory proteins) in order to regulate and restrict entry into the degradation chamber []. Unstructured RNA substrates feed in through the pore made by the S1 domains, are degraded by the PH domain ring, and exit as nucleotides via the PH pore at the opposite end of the barrel [, ]. This entry represents the phosphorolytic (PH) domain 1, which has a core 2-layer alpha/beta structure with a left-handed crossover, similar to that found in ribosomal protein S5. This domain is found in bacterial/organelle PNPases and in archaeal/eukaryotic exosomes []. More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; PDB: 2C38_G 2BR2_O 2C37_M 3L7Z_A 2JEB_A 2C39_A 2JEA_A 2JE6_A 3U1K_A 4AM3_B ....
Probab=99.97 E-value=3e-29 Score=198.47 Aligned_cols=131 Identities=37% Similarity=0.502 Sum_probs=116.0
Q ss_pred CCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCccccCCCCCCcchHHHHH
Q psy18119 20 ELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGERKTRPRGDRKTSEISL 99 (263)
Q Consensus 20 e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~~~~~~~~~~~~~~l~~ 99 (263)
|+|++.+++|++++++|||+|++|+|+|+|+|++|.+.++.....+..+.++|+++++|++....++.+.++..+.++++
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 78999999999999999999999999999999999877543221223478899999889887766544457788899999
Q ss_pred HHHHHHHhhhccCCCCceEEEEEEEEEeCCC-ChhHHHHHHHHHHHHHcCCC
Q psy18119 100 QLRQAVSAAIMSEVHPRSQIDIFVEVLQADG-GNFCACVNAATLALIDAGIP 150 (263)
Q Consensus 100 ~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG-~~~~a~i~Aa~~AL~dagIp 150 (263)
+|+++|++++.++.||+|.|+|+|+||++|| |++|+++||+++||+|+|||
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 20
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=99.96 E-value=9.4e-28 Score=236.08 Aligned_cols=207 Identities=18% Similarity=0.183 Sum_probs=181.4
Q ss_pred cceEEEeCCCC-CCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCccc-----cCCCCCCcchH
Q psy18119 22 RKIRCRLGVFS-QSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGER-----KTRPRGDRKTS 95 (263)
Q Consensus 22 R~i~i~~g~l~-~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~~-----~~~~~~~~~~~ 95 (263)
|.+.+++|.+. +|+||+.++.|+|.|+|+|....+++. ..+++.|.|+|....++.+.. ++.+++++++.
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 RHILVETGHIGRQASGSVTVTDGETIVYTSVCLADVPSE----PSDFFPLSVHYQERFSAAGRTSGGFFKREGRTKDHEV 164 (891)
T ss_pred EEEEEEhhHHHHhCCCcEEEEECCeEEEEEEEeccCCCC----CCCccceeEeeeeehhhcCccCCceeccCCCCChHHH
Confidence 47999999885 699999999999999999997555443 357899999998766665432 44557888999
Q ss_pred HHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCC--hhHHHHHHHHHHHHHcCCCccCceeEEEEEecCCeeEecCCc
Q psy18119 96 EISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGG--NFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISH 173 (263)
Q Consensus 96 ~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~--~~~a~i~Aa~~AL~dagIp~~~~~~avt~~~~~~~~lvDPt~ 173 (263)
.++++|+|.|+++++.+.||+++| .++||++||+ ...+|+|||++||+++||||++.++||++|++++.+|+|||.
T Consensus 165 L~sRlIdR~lRPlfp~~~~~etQI--~i~VLsaDg~~~pd~~AInAASaAL~~SgIP~~gpVaAVrVG~idg~~VlnPt~ 242 (891)
T PLN00207 165 LICRLIDRPLRPTMPKGFYHETQI--LSWVLSYDGLHSPDSLAVTAAGIAVALSEVPNLKAIAGVRVGLIGGKFIVNPTT 242 (891)
T ss_pred HHHHHHCccchhhccccCCCCcEE--EEEEEeeCCCCChhhHHHHHHHHHHHhhCCCccCceEEEEEEEECCEEEECCCH
Confidence 999999999999999999998665 4589999998 568999999999999999999999999999999999999999
Q ss_pred hhhhcCCCeEEEEEeCCCCcEEEEEeccc-CChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy18119 174 LEETLGGPNLTVAALPLSGKVAVMELSQK-LHLDHLPRVLDCALKGCADIHAILDTAIKQHLIK 236 (263)
Q Consensus 174 ~Ee~~~~~~l~v~~~~~~~~i~~i~~~G~-i~~~~l~~~i~~A~~~~~~i~~~i~~~l~~~~~~ 236 (263)
.|++.++..++|+. ..+.|++++..+. ++++++.++++.|.++++.+.++++++++++...
T Consensus 243 ~E~~~s~ldLvvag--t~~~IvMIE~~a~e~see~l~~Al~~a~~aik~i~~~~~el~~~~gk~ 304 (891)
T PLN00207 243 KEMEESELDLIMAG--TDSAILMIEGYCNFLPEEKLLEAVEVGQDAVRAICKEIEVLVKKCGKP 304 (891)
T ss_pred HHHhcCCeeEEEEE--cCCeEEEEEcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC
Confidence 99999999998887 3567999999886 5999999999999999999999999998887654
No 21
>KOG1067|consensus
Probab=99.93 E-value=1.1e-25 Score=207.33 Aligned_cols=241 Identities=24% Similarity=0.289 Sum_probs=199.7
Q ss_pred CCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCC-CCCC--CCcCCCCeE-EEEEEEeeCCCCCccc
Q psy18119 9 GGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPR-PVRN--KSIKVHGSV-LINFQYSMAVFSTGER 84 (263)
Q Consensus 9 ~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~-~~~~--~~~~~~~~~-~l~v~~~~~~~~~~~~ 84 (263)
+|.|.|||..++.|+|.|+.+.++..+||++|+.|.|+|+|+|+.-. +... ++-..++.+ .+-.+|.++|+++++.
T Consensus 356 ~gkR~DGR~ldelR~I~ce~~m~~~lHGSaLFqRGqTQvlctVtl~s~e~a~klD~l~~~~~~~~FmLhY~FPPyat~Ev 435 (760)
T KOG1067|consen 356 EGKRCDGRDLDELRNISCEVDMLKTLHGSALFQRGQTQVLCTVTLDSLESAQKLDSLIGPDNGINFMLHYEFPPYATNEV 435 (760)
T ss_pred cccccCCcchhhhcccceecCccccccchhhhhcCceeEEEEEEcCCHHHhhhhhhhccCccCceEEEEeccCCcccccc
Confidence 89999999999999999999999999999999999999999999622 2111 111122222 5667999999999998
Q ss_pred cCCCCCCcchHHHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCCccCceeEEEEEecC
Q psy18119 85 KTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLAG 164 (263)
Q Consensus 85 ~~~~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp~~~~~~avt~~~~~ 164 (263)
++.+..++++.-...+-+++|.++++ +.||. .|+|.-.||++||+.-.|++.+-++||+|+|+|++.-+++|.+|++-
T Consensus 436 gkig~~nRRE~GhgaLAEkaL~~vlP-~dfPf-tIRv~SeVleSnGSsSMASvCGGslALmDaGvPv~a~vAGvaiGlvt 513 (760)
T KOG1067|consen 436 GKIGGLNRRELGHGALAEKALLPVLP-EDFPF-TIRVTSEVLESNGSSSMASVCGGSLALMDAGVPVSAHVAGVAIGLVT 513 (760)
T ss_pred ccccCCcccccCchhHhhhhhhccCc-ccCce-EEEEeeeeeecCCcchHHhhhcchhhhhhcCCccccccceeEEEeEe
Confidence 88877888888778899999999998 78997 89999999999999999999999999999999999999999999873
Q ss_pred C-----------eeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEecccCChhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy18119 165 D-----------TPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQH 233 (263)
Q Consensus 165 ~-----------~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G~i~~~~l~~~i~~A~~~~~~i~~~i~~~l~~~ 233 (263)
+ .++.|....|+...+..+.|+. +++.|+++ .++.+-+.+.+..|..+-.+|.+.|.+.+...
T Consensus 514 ~td~e~g~i~dyriltDIlGiEd~~GDMDFKiAG--t~dGvTA~----gi~l~Iv~eal~~a~~ar~~Il~~m~k~i~~P 587 (760)
T KOG1067|consen 514 KTDPEKGEIEDYRILTDILGIEDYNGDMDFKIAG--TNDGVTAL----GIPLKIVMEALQKAREARLQILDIMEKNINSP 587 (760)
T ss_pred ccCcccCCcccceeehhhcchhhhcCCcceeecc--ccCcceec----CCcHHHHHHHHHhhhHHHHHHHHHHHhhcCCc
Confidence 2 6889999999999999999998 35667777 78889999999999999999999999888776
Q ss_pred HHHhhccCCC-----CccccccceecCCc
Q psy18119 234 LIKVAGARGL-----GRKFQLGQLTGKKK 257 (263)
Q Consensus 234 ~~~~~~~~~~-----~~~~~~~~~~~~~~ 257 (263)
.....++.+. ....++-+|+|-+|
T Consensus 588 r~~~~~y~P~~~tlkv~~sk~~~lIGp~G 616 (760)
T KOG1067|consen 588 RGSDKEYSPVLETLKVSPSKRATLIGPGG 616 (760)
T ss_pred ccCccccCceeeEEeecchhhheeecCcc
Confidence 6554444431 24444555665544
No 22
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=99.92 E-value=8e-25 Score=207.38 Aligned_cols=247 Identities=23% Similarity=0.314 Sum_probs=212.6
Q ss_pred CCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEc-CCCCCCCCc--CCCCeEEEEEEEeeCCCCCcccc
Q psy18119 9 GGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYG-PRPVRNKSI--KVHGSVLINFQYSMAVFSTGERK 85 (263)
Q Consensus 9 ~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~g-p~~~~~~~~--~~~~~~~l~v~~~~~~~~~~~~~ 85 (263)
.++|+|||..++.||+.++.|++++.|||+++..|.|+.++.++. +....+-.+ ..+..-.+-.+|+++||+.++.+
T Consensus 310 ~~vR~DGR~~~~VRpi~~ev~~lpr~HGS~LFtRGeTQal~v~TLG~~~d~Qvid~l~~e~~krfm~hYNFPp~SvGE~g 389 (692)
T COG1185 310 GKVRIDGRFGDEVRPIGIEVGVLPRTHGSALFTRGETQALVVVTLGTPRDAQVIDILEGEYKKRFLLHYNFPPFSVGETG 389 (692)
T ss_pred CCcccCCCCcceeeeeeEEecCCCCccchhhhccCCCcceEEEEcCCcchhhhhhhccchhhhheeeeccCCCCCccccC
Confidence 899999999999999999999999999999999999999988884 322111111 11123334468999999999988
Q ss_pred CCCCCCcchHHHHHHHHHHHHhhhc-cCCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCCccCceeEEEEEecC
Q psy18119 86 TRPRGDRKTSEISLQLRQAVSAAIM-SEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLAG 164 (263)
Q Consensus 86 ~~~~~~~~~~~l~~~l~~~l~~~i~-l~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp~~~~~~avt~~~~~ 164 (263)
+.+.+.+++.-..++-++++.++++ .+.||+ .|++.-.|++++|+-..|++++.++||+|+|+|++..++++..|++.
T Consensus 390 ~~g~p~RREiGHG~LA~Ral~~vlp~~e~fpy-tiRvVsEi~eSNGSsSmaSVCg~sLaLmdAGVPIk~pVAGIAMGLI~ 468 (692)
T COG1185 390 RMGSPGRREIGHGALAERALAPVLPSEEEFPY-TIRVVSEILESNGSSSMASVCGGSLALMDAGVPIKAPVAGIAMGLIK 468 (692)
T ss_pred CCCCCCcccccCchhhHHHHhhhCCchhcCCc-eeeeeehhhcccCcccchhhhhhHHHHHhCCCcccccccchhcccee
Confidence 8878888888888999999999998 578998 89999999999999999999999999999999999999999999985
Q ss_pred C----eeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEecc---cCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy18119 165 D----TPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQ---KLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKV 237 (263)
Q Consensus 165 ~----~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G---~i~~~~l~~~i~~A~~~~~~i~~~i~~~l~~~~~~~ 237 (263)
+ .++-|....|+...+..+-|+. ...-|++++++- .++.+.+.+++..|+.+..++...|.+++.+...+.
T Consensus 469 eg~~~~vLsDI~G~EDhlGDMDFKVAG--T~~GiTAlQMDiKi~Git~eim~~AL~QAk~aRlhIL~~M~~ai~~pr~el 546 (692)
T COG1185 469 EGDKYAVLSDILGDEDHLGDMDFKVAG--TDDGITALQMDIKIKGITKEIMKKALEQAKGARLHILIVMNEAISEPRKEL 546 (692)
T ss_pred cCCceEeeccccccccccCCceeEEec--CCCcceeeeeeeeecCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhh
Confidence 4 6889999999999999999997 467899999884 579999999999999999999999999999999888
Q ss_pred hccCCCC-----ccccccceecCCcc
Q psy18119 238 AGARGLG-----RKFQLGQLTGKKKE 258 (263)
Q Consensus 238 ~~~~~~~-----~~~~~~~~~~~~~~ 258 (263)
....++. +.-..++++|.+|.
T Consensus 547 s~~aPri~t~~i~~dKI~dvIG~gGk 572 (692)
T COG1185 547 SPYAPRIETIKIDPDKIRDVIGPGGK 572 (692)
T ss_pred hccCCceEEEccCHHHHhhccCCccc
Confidence 8888754 55567888888775
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=99.87 E-value=1.4e-20 Score=182.25 Aligned_cols=207 Identities=14% Similarity=0.143 Sum_probs=173.7
Q ss_pred cceEEEeCCCC-CCceeEEEEe-CCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCccc-----cCCCCCCcch
Q psy18119 22 RKIRCRLGVFS-QSDGSAYIEQ-GNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGER-----KTRPRGDRKT 94 (263)
Q Consensus 22 R~i~i~~g~l~-~a~GSa~v~~-G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~~-----~~~~~~~~~~ 94 (263)
|++.+++|.+. +|+||+.+++ |+|.|+|+|....+++. ..++++|.|+|....++.+.. +|.++|++++
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 47999999885 6999999999 99999999997555443 357899999998766665433 4455788889
Q ss_pred HHHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCChh--HHHHHHHHHHHHHcCCCccCceeEEEEEecCCeeEecCC
Q psy18119 95 SEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNF--CACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDIS 172 (263)
Q Consensus 95 ~~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~--~a~i~Aa~~AL~dagIp~~~~~~avt~~~~~~~~lvDPt 172 (263)
...+|+|+|.++|+++- .|.+ .++|.++||+.|+..- -.++|||++||.-++||+...+.+|.+|.+++++|++||
T Consensus 93 iL~sRliDR~iRPLFp~-~~~~-e~qi~~~vls~D~~~~pdvla~~~ASaAl~iSdiPf~gPv~~vrVg~i~g~~viNPt 170 (719)
T TIGR02696 93 ILTCRLIDRPLRPSFVK-GLRN-EVQVVVTVLSLNPDHLYDVVAINAASASTQLAGLPFSGPIGGVRVALIDGQWVAFPT 170 (719)
T ss_pred hHHHHhhCCCCccCCCC-CCCc-ceEEEEEEEEcCCCCChHHHHHHHHHHHHHhcCCCCCCceEEEEEEEECCEEEECcC
Confidence 99999999999999863 3333 6888999999998653 468999999999999999999999999999999999999
Q ss_pred chhhhcCCCeEEEEEeCC---CCcEEEEEe------------cc-cCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy18119 173 HLEETLGGPNLTVAALPL---SGKVAVMEL------------SQ-KLHLDHLPRVLDCALKGCADIHAILDTAIKQHL 234 (263)
Q Consensus 173 ~~Ee~~~~~~l~v~~~~~---~~~i~~i~~------------~G-~i~~~~l~~~i~~A~~~~~~i~~~i~~~l~~~~ 234 (263)
..|.+.++-.++|+.... .+.|++++. .+ .++++.+.+++..|.+..+.+.+++++..+...
T Consensus 171 ~~~~~~s~ldLvvagt~~~~~~~~i~MiE~~a~~~~~~~~~~~a~e~~e~~~~~Ai~~a~~~i~~~~~~~~~l~~~~g 248 (719)
T TIGR02696 171 HEQLEGAVFDMVVAGRVLENGDVAIMMVEAEATEKTWDLVKGGAEAPTEEVVAEGLEAAKPFIKVLCRAQADLAEKAA 248 (719)
T ss_pred HHHHhhCeeeEEEEeeecCCCCccEEEEecCCccccccccccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 999999999999998321 348999997 33 489999999999999999999999988655444
No 24
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=99.80 E-value=2.3e-18 Score=163.76 Aligned_cols=211 Identities=17% Similarity=0.183 Sum_probs=179.6
Q ss_pred cceEEEeCCCC-CCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCccc-----cCCCCCCcchH
Q psy18119 22 RKIRCRLGVFS-QSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGER-----KTRPRGDRKTS 95 (263)
Q Consensus 22 R~i~i~~g~l~-~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~~-----~~~~~~~~~~~ 95 (263)
|++.+++|.+. +|+|++++++|+|.|++++.+.. ++. ..++++|.|+|....++.+.. ++.++|++++.
T Consensus 14 ~~l~~etg~~A~qa~gav~~~~gdt~vl~t~~~~~-~~~----~~dF~PLtV~y~Ek~yaaGkiPGgf~kREGrpse~e~ 88 (692)
T COG1185 14 RTLTLETGKIARQANGAVLVRYGDTVVLATVVASK-PKE----GQDFFPLTVNYEEKTYAAGKIPGGFFKREGRPSEKEI 88 (692)
T ss_pred eeEEEEcchhhhhcCccEEEEECCeEEEEEEeecC-CCC----CCCccceeEeeeeehhccCcCCCcccccCCCCCccch
Confidence 88999999885 69999999999999999999966 332 358999999998777666543 44557889999
Q ss_pred HHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCChh--HHHHHHHHHHHHHcCCCccCceeEEEEEecCCeeEecCCc
Q psy18119 96 EISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNF--CACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISH 173 (263)
Q Consensus 96 ~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~--~a~i~Aa~~AL~dagIp~~~~~~avt~~~~~~~~lvDPt~ 173 (263)
..+|+|+|-+++.++.. |- ..++|.++|++.|+... -.+++++++||.-++||+...+.++++|++++.+++.||.
T Consensus 89 L~sRLIDRpiRPlFp~g-~~-~evqIv~tvls~D~~~~pdi~a~~gaSaAl~is~iPf~gpi~~vrvg~idg~~vlNPt~ 166 (692)
T COG1185 89 LTSRLIDRPIRPLFPKG-FR-NEVQIVNTVLSVDPENDPDILAMVGASAALSLSGIPFLGPIGAVRVGYIDGIFVLNPTL 166 (692)
T ss_pred hhhhhcccccccccchh-hc-cceEEEEEEEEECCCCCHHHHHHHHHHHHHhccCCCccCccceEEEEEECCEEEECCCh
Confidence 99999999999887532 32 26889999999999764 4789999999999999999999999999999999999999
Q ss_pred hhhhcCCCeEEEEEeCCCCcEEEEEecc-cCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccC
Q psy18119 174 LEETLGGPNLTVAALPLSGKVAVMELSQ-KLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKVAGAR 241 (263)
Q Consensus 174 ~Ee~~~~~~l~v~~~~~~~~i~~i~~~G-~i~~~~l~~~i~~A~~~~~~i~~~i~~~l~~~~~~~~~~~ 241 (263)
.|-+.+.-.++|+. +...|.+++... .++++++.+++..+.+..+.+.+++++.......+.+.+.
T Consensus 167 ~e~~~s~lDlvVAG--T~~aV~MVE~~a~~l~E~~ml~Av~fg~~~~~~~~~~qe~l~~~~g~~~~~~~ 233 (692)
T COG1185 167 EELEESKLDLVVAG--TKDAVNMVESEADELDEEVMLEAVEFGHEAIQSVINAQEELALEVGKKKWELE 233 (692)
T ss_pred HHhhhcceeeEecC--ChhhhheeecccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccccc
Confidence 99999999999987 355899999876 5789999999999999999999999998877765555554
No 25
>KOG1067|consensus
Probab=99.69 E-value=2.1e-16 Score=146.55 Aligned_cols=207 Identities=18% Similarity=0.196 Sum_probs=168.2
Q ss_pred CCcceEEEeCCCCC-CceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCcc-----ccCCCCCCcc
Q psy18119 20 ELRKIRCRLGVFSQ-SDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGE-----RKTRPRGDRK 93 (263)
Q Consensus 20 e~R~i~i~~g~l~~-a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~-----~~~~~~~~~~ 93 (263)
--|.+.+++|.+.+ |+||+.+..|+|.|+++|..-..|.+ +.+..+.|+|.....+.+. .++..++.++
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 56999999999975 99999999999999999998555554 2478999999754433322 1233345566
Q ss_pred hHHHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCChh--HHHHHHHHHHHHHcCCCccCceeEEEEEecCCeeEecC
Q psy18119 94 TSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNF--CACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDI 171 (263)
Q Consensus 94 ~~~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~--~a~i~Aa~~AL~dagIp~~~~~~avt~~~~~~~~lvDP 171 (263)
+....++|++.+++......|. ..++-+.+|..||-.- --++|++++||.-+.||+...+.++.+|+++++++++|
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 6666788888888776544343 3556677899999654 35899999999999999999999999999999999999
Q ss_pred CchhhhcCCCeEEEEEeCCCCcEEEEEecc-cCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy18119 172 SHLEETLGGPNLTVAALPLSGKVAVMELSQ-KLHLDHLPRVLDCALKGCADIHAILDTAIKQHLI 235 (263)
Q Consensus 172 t~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G-~i~~~~l~~~i~~A~~~~~~i~~~i~~~l~~~~~ 235 (263)
|..|.+.+.-.+.++. ...++++++-.+ .+..+++.++++++.+.+.++...+....+++..
T Consensus 207 T~kEmssS~Lnlvvag--t~~~~vmle~~s~~i~qqdl~~Aikvg~~~~q~~i~~i~~L~k~~Gk 269 (760)
T KOG1067|consen 207 TRKEMSSSQLNLVVAG--TKSQTVMLEGSSNNILQQDLLHAIKVGVKEAQQIIQGIERLAKKYGK 269 (760)
T ss_pred chhhhhhccceeEEEe--ccceEEEEEcccccccHHHHHHHHHhccHHHHHHHHHHHHHHHHhCc
Confidence 9999999999999998 388999999887 4789999999999999999999988887777644
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=99.27 E-value=2.2e-11 Score=85.22 Aligned_cols=65 Identities=25% Similarity=0.294 Sum_probs=54.3
Q ss_pred CceeEEEEEecCCeeEecCCchhhhcCCCeEEEEEeCCCCcEE-EEEeccc--CChhHHHHHHHHHHHH
Q psy18119 153 EYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVA-VMELSQK--LHLDHLPRVLDCALKG 218 (263)
Q Consensus 153 ~~~~avt~~~~~~~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~-~i~~~G~--i~~~~l~~~i~~A~~~ 218 (263)
|+|+++|++++++.+++|||..||..+++.+++++. .+++++ .++..|. ++++++.++++.|.++
T Consensus 1 ~~~~avt~~~i~~~~v~Dpt~~Ee~~~~~~l~~~~~-~~~~~~~~~~~~g~~~~~~~~l~~~i~~A~~~ 68 (68)
T PF03725_consen 1 DPPVAVTVGIIDGELVVDPTAEEESLSDSSLTLAVD-GTGNICTLQKSGGGSELSEDQLEEAIELAKKA 68 (68)
T ss_dssp SEEEEEEEEEETTEEEES--HHHHHHSSEEEEEEEE-TTSSEEEEEEEEESSEEEHHHHHHHHHHHHHH
T ss_pred CCeEEEEEEEECCEEEECCCHHHHhhcCCcEEEEEE-CCCCEEEEEEcCCCCCCCHHHHHHHHHHHhcC
Confidence 689999999999999999999999999999999996 456665 4445554 9999999999999875
No 27
>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=51.45 E-value=88 Score=22.41 Aligned_cols=45 Identities=22% Similarity=0.256 Sum_probs=31.7
Q ss_pred hcCCCeEEEEEeCCCCcEEEEEecc----cCChhHHHHHHHHHHHHHHHH
Q psy18119 177 TLGGPNLTVAALPLSGKVAVMELSQ----KLHLDHLPRVLDCALKGCADI 222 (263)
Q Consensus 177 ~~~~~~l~v~~~~~~~~i~~i~~~G----~i~~~~l~~~i~~A~~~~~~i 222 (263)
.+.++.++|.+ +..|+|..++.+- +.+++.|.+++-.|...+..-
T Consensus 26 ~s~~g~V~V~v-~g~g~v~~i~i~~~~~~~~~~~~L~~~I~~A~n~A~~~ 74 (93)
T PF02575_consen 26 TSGDGLVTVTV-NGNGEVVDIEIDPSALRPLDPEELEDLIVEAVNDAQKK 74 (93)
T ss_dssp EETCCTEEEEE-ETTS-EEEEEE-GGGGCTS-HHHHHHHHHHHHHHHHHH
T ss_pred EECCCEEEEEE-ecCceEEEEEEehHhhccCCHHHHHHHHHHHHHHHHHH
Confidence 45678899999 5799999999873 367788888887776666543
No 28
>PF12651 RHH_3: Ribbon-helix-helix domain
Probab=44.62 E-value=45 Score=20.79 Aligned_cols=35 Identities=14% Similarity=0.140 Sum_probs=31.2
Q ss_pred cCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy18119 202 KLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIK 236 (263)
Q Consensus 202 ~i~~~~l~~~i~~A~~~~~~i~~~i~~~l~~~~~~ 236 (263)
.++.+.+.++-++|.+......++++++++....+
T Consensus 8 ~l~~el~~~L~~ls~~t~i~~S~Ll~eAle~~l~k 42 (44)
T PF12651_consen 8 SLDKELYEKLKELSEETGIPKSKLLREALEDYLEK 42 (44)
T ss_pred ecCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHh
Confidence 57888999999999999999999999999988764
No 29
>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=42.13 E-value=35 Score=20.12 Aligned_cols=33 Identities=18% Similarity=0.107 Sum_probs=28.3
Q ss_pred CChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy18119 203 LHLDHLPRVLDCALKGCADIHAILDTAIKQHLI 235 (263)
Q Consensus 203 i~~~~l~~~i~~A~~~~~~i~~~i~~~l~~~~~ 235 (263)
++.+....+=++|.+......++++.++.++..
T Consensus 6 l~~~~~~~l~~~a~~~g~s~s~~ir~ai~~~l~ 38 (39)
T PF01402_consen 6 LPDELYERLDELAKELGRSRSELIREAIREYLE 38 (39)
T ss_dssp EEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHH
T ss_pred eCHHHHHHHHHHHHHHCcCHHHHHHHHHHHHHh
Confidence 567788888888999999999999999988865
No 30
>PHA01623 hypothetical protein
Probab=33.53 E-value=63 Score=21.31 Aligned_cols=36 Identities=22% Similarity=0.195 Sum_probs=30.6
Q ss_pred cCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy18119 202 KLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKV 237 (263)
Q Consensus 202 ~i~~~~l~~~i~~A~~~~~~i~~~i~~~l~~~~~~~ 237 (263)
.++.+.+.++-.+|.+.-....++++++++.++.+.
T Consensus 19 rldeel~~~Ld~y~~~~g~~rSe~IreAI~~yL~~~ 54 (56)
T PHA01623 19 YMDKDLKTRLKVYCAKNNLQLTQAIEEAIKEYLQKR 54 (56)
T ss_pred EeCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHc
Confidence 467888889989999988889999999999888653
No 31
>COG3625 PhnH Uncharacterized enzyme of phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=30.18 E-value=2.6e+02 Score=23.34 Aligned_cols=96 Identities=14% Similarity=0.098 Sum_probs=55.0
Q ss_pred HHHHHhhhccCCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCC-----------------------ccCceeEE
Q psy18119 102 RQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIP-----------------------MREYVVAC 158 (263)
Q Consensus 102 ~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp-----------------------~~~~~~av 158 (263)
+++|+.+++--.+|.....++ -.-..=--+..+.-|++++|+|...| +..-+--.
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 QRVFRALLDAMARPGVVVPLD--RAAAPPAPLNPATGAVCLTLCDNDTPVWLDPALSSSAVRAWLRFHTGAPLTETPEEA 95 (196)
T ss_pred HHHHHHHHHhhcCCCceeecc--cccCCCcCCCHHHHHHHHHHhcCCCceeecccccchhhhhhhhhccCCcccCCcccc
Confidence 456777666556787433333 11122234678889999999998654 55566667
Q ss_pred EEEecCCe------eEecCCchhhhcCCCeEEEEEeC-CCCcEEEEEe
Q psy18119 159 SASLAGDT------PLVDISHLEETLGGPNLTVAALP-LSGKVAVMEL 199 (263)
Q Consensus 159 t~~~~~~~------~lvDPt~~Ee~~~~~~l~v~~~~-~~~~i~~i~~ 199 (263)
.|+++++. -..+|-..|--....++.|=+.+ +.|.-+.+.-
T Consensus 96 ~FAv~~~~~~~~~l~~f~~Gt~eyPdrStTLiiQV~sl~~G~~l~l~G 143 (196)
T COG3625 96 RFAVVDDGAALPQLSGFAPGTAEYPDRSTTLIIQVASLEGGRPLRLTG 143 (196)
T ss_pred eEEEecCcccchhhcccCCCcccCCCcceEEEEEecccCCCCceEeEC
Confidence 78887651 23445555554455555555521 2355444443
No 32
>PRK00153 hypothetical protein; Validated
Probab=29.18 E-value=2.4e+02 Score=20.88 Aligned_cols=46 Identities=15% Similarity=0.197 Sum_probs=34.2
Q ss_pred hhhcCCCeEEEEEeCCCCcEEEEEecc----cCChhHHHHHHHHHHHHHHH
Q psy18119 175 EETLGGPNLTVAALPLSGKVAVMELSQ----KLHLDHLPRVLDCALKGCAD 221 (263)
Q Consensus 175 Ee~~~~~~l~v~~~~~~~~i~~i~~~G----~i~~~~l~~~i~~A~~~~~~ 221 (263)
|.++.++.++|.+ +..++|..++.+- +-+++.+.+++-.|...+.+
T Consensus 32 ~~~s~~G~V~V~v-~G~~~v~~i~Id~~ll~~~d~e~LedlI~~A~n~A~~ 81 (104)
T PRK00153 32 EGEAGGGLVKVTM-TGKKEVKRVKIDPSLVDPEDVEMLEDLILAAFNDALR 81 (104)
T ss_pred EEEECCCeEEEEE-ecCceEEEEEECHHHcCCcCHHHHHHHHHHHHHHHHH
Confidence 4456678899998 6789999999874 23577788888777766653
No 33
>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=27.99 E-value=77 Score=23.27 Aligned_cols=34 Identities=18% Similarity=0.138 Sum_probs=24.3
Q ss_pred cccCChhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy18119 200 SQKLHLDHLPRVLDCALKGCADIHAILDTAIKQH 233 (263)
Q Consensus 200 ~G~i~~~~l~~~i~~A~~~~~~i~~~i~~~l~~~ 233 (263)
.|.+++++|.-+++++.-++..+..++++.|-.-
T Consensus 20 pG~vs~e~F~lLl~ls~IrS~kiI~AL~dyLV~G 53 (91)
T PF03333_consen 20 PGKVSEEHFWLLLELSSIRSEKIIAALRDYLVDG 53 (91)
T ss_dssp TT-S-HHHHHHHHHHS----HHHHHHHHHHHTT-
T ss_pred CCCcCHHHHHHHHHHCCCCcHHHHHHHHHHHHcC
Confidence 4889999999999999999999999999988544
No 34
>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=27.91 E-value=2e+02 Score=21.18 Aligned_cols=57 Identities=25% Similarity=0.262 Sum_probs=28.6
Q ss_pred hHHHHHHHHHHHHhhh-ccCCCCceEEEEEEEEEeCCCChh--------HHHHHHHHHHHHH-cCCCc
Q psy18119 94 TSEISLQLRQAVSAAI-MSEVHPRSQIDIFVEVLQADGGNF--------CACVNAATLALID-AGIPM 151 (263)
Q Consensus 94 ~~~l~~~l~~~l~~~i-~l~~~p~~~I~v~v~VL~~dG~~~--------~a~i~Aa~~AL~d-agIp~ 151 (263)
-..+...|+..+..-+ +.+.|-...+.|.+. |..||.+. .+.+.|+..|+.. +.+|+
T Consensus 13 v~~Y~~~I~~~Iq~~l~~~~~y~GK~C~v~i~-l~~dG~v~~v~~~~GD~~lC~aa~~Ai~k~~~~P~ 79 (96)
T PF06519_consen 13 VSRYAAQIKQAIQRNLYDDESYKGKECRVRIR-LAPDGLVLSVTVESGDPALCRAAKSAIAKAAKFPP 79 (96)
T ss_dssp HHHHHHHHHHHHHTTTTTGGGGTT--EEEEEE-EETTSEEEEEEEEEE-HHHHHHHHHH-HCCS----
T ss_pred HHHHHHHHHHHHHHhcCCccccCCCEEEEEEE-ECCCCcEEEeeecCCCHHHHHHHHHHHHHhcCCCC
Confidence 3455667777776643 335565444444443 56677652 3566777777554 45764
No 35
>KOG0257|consensus
Probab=26.35 E-value=5.5e+02 Score=24.33 Aligned_cols=109 Identities=17% Similarity=0.206 Sum_probs=59.8
Q ss_pred HHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCCc-----------------cCceeEE
Q psy18119 96 EISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPM-----------------REYVVAC 158 (263)
Q Consensus 96 ~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp~-----------------~~~~~av 158 (263)
+|...|.+.++...-....|...|-|. +|.- .++..+.++|++.|..+ -..|+.+
T Consensus 73 ~L~~aL~k~~se~~~~~~~~~~eVlVT------~GA~--~ai~~~~~~l~~~GDeVii~eP~fd~Y~~~~~maG~tpv~v 144 (420)
T KOG0257|consen 73 QLRKALAKAYSEFYGGLLDPDDEVLVT------AGAN--EAISSALLGLLNPGDEVIVFEPFFDCYIPQVVMAGGTPVFV 144 (420)
T ss_pred HHHHHHHHHHHHHhccccCCcccEEEe------cCch--HHHHHHHHHHcCCCCEEEEecCcchhhhhHHhhcCCcceee
Confidence 566677777776333344565445444 3542 23566778999999531 1123333
Q ss_pred EEEec-----CCeeEecCCchhhhcCCCe-EEEEEeCCCCcEEEEEeccc-CChhHHHHHHHHHHHHH
Q psy18119 159 SASLA-----GDTPLVDISHLEETLGGPN-LTVAALPLSGKVAVMELSQK-LHLDHLPRVLDCALKGC 219 (263)
Q Consensus 159 t~~~~-----~~~~lvDPt~~Ee~~~~~~-l~v~~~~~~~~i~~i~~~G~-i~~~~l~~~i~~A~~~~ 219 (263)
+...- .+.+.+||-..|-+...-+ +.|...|++ ..|+ ++.++|.++.++|+++-
T Consensus 145 ~~~~~~g~~~s~~~~~D~~~le~~~t~kTk~Ii~ntPhN-------PtGkvfsReeLe~ia~l~~k~~ 205 (420)
T KOG0257|consen 145 PLKPKEGNVSSSDWTLDPEELESKITEKTKAIILNTPHN-------PTGKVFSREELERIAELCKKHG 205 (420)
T ss_pred ccccccccccCccccCChHHHHhhccCCccEEEEeCCCC-------CcCcccCHHHHHHHHHHHHHCC
Confidence 32211 1256777766665533222 222221211 1364 69999999999999875
No 36
>PRK14627 hypothetical protein; Provisional
Probab=25.64 E-value=2.8e+02 Score=20.54 Aligned_cols=47 Identities=23% Similarity=0.316 Sum_probs=33.4
Q ss_pred hhhcCCCeEEEEEeCCCCcEEEEEeccc-C---ChhHHHHHHHHHHHHHHHH
Q psy18119 175 EETLGGPNLTVAALPLSGKVAVMELSQK-L---HLDHLPRVLDCALKGCADI 222 (263)
Q Consensus 175 Ee~~~~~~l~v~~~~~~~~i~~i~~~G~-i---~~~~l~~~i~~A~~~~~~i 222 (263)
|-.+..+.++|.+ +..++|..++.+-. + +.+.+.+++-.|...+..-
T Consensus 30 eg~sggG~VkV~~-~G~~~v~~i~Idp~ll~~ed~e~LeDLI~aA~N~A~~k 80 (100)
T PRK14627 30 EGTAGGGAITVKM-NGHREVQSITISPEVVDPDDVEMLQDLLLVAINDASRK 80 (100)
T ss_pred EEEEcCCeEEEEE-EcCccEEEEEECHHHcCcccHHHHHHHHHHHHHHHHHH
Confidence 3445678888888 67899999988742 3 4567888888777766543
No 37
>PRK14629 hypothetical protein; Provisional
Probab=24.02 E-value=3e+02 Score=20.43 Aligned_cols=46 Identities=11% Similarity=0.144 Sum_probs=31.6
Q ss_pred hhhcCCCeEEEEEeCCCCcEEEEEeccc-C---ChhHHHHHHHHHHHHHHH
Q psy18119 175 EETLGGPNLTVAALPLSGKVAVMELSQK-L---HLDHLPRVLDCALKGCAD 221 (263)
Q Consensus 175 Ee~~~~~~l~v~~~~~~~~i~~i~~~G~-i---~~~~l~~~i~~A~~~~~~ 221 (263)
|.....+.++|.+ +..++|..++.+-. + +.+.+++++-.|...+..
T Consensus 32 eg~aggGlVkV~~-nG~~~v~~i~Idp~lld~eD~e~LeDLI~aAvNdA~~ 81 (99)
T PRK14629 32 CGRAGSDVVVVEM-NGEFNVKKVSIKEEFFDDLDNEALEHMIKSAFNDAVS 81 (99)
T ss_pred EEEecCCEEEEEE-EcCccEEEEEECHHHcCcccHHHHHHHHHHHHHHHHH
Confidence 3445567788887 67889998887743 3 466777877777665543
No 38
>PRK14628 hypothetical protein; Provisional
Probab=23.97 E-value=3.4e+02 Score=20.86 Aligned_cols=49 Identities=16% Similarity=0.323 Sum_probs=34.7
Q ss_pred hhhcCCCeEEEEEeCCCCcEEEEEeccc-C-ChhHHHHHHHHHHHHHHHHHH
Q psy18119 175 EETLGGPNLTVAALPLSGKVAVMELSQK-L-HLDHLPRVLDCALKGCADIHA 224 (263)
Q Consensus 175 Ee~~~~~~l~v~~~~~~~~i~~i~~~G~-i-~~~~l~~~i~~A~~~~~~i~~ 224 (263)
|-.+..+.++|.+ +-.++|..++.+-. + +.+.+++++-.|...+..-.+
T Consensus 48 ~g~sggG~VkV~~-nG~~ei~~I~Idp~~l~D~E~LeDLIiaA~NdA~~ka~ 98 (118)
T PRK14628 48 EASVGGGAVRIVA-TCDRRVKDIEIDEDLKEDFETLKDLLIAGMNEVMEKIE 98 (118)
T ss_pred EEEecCceEEEEE-EcCceEEEEEECHHHcCCHHHHHHHHHHHHHHHHHHHH
Confidence 3345567888888 67889999887643 2 677888888887776654443
No 39
>TIGR00103 DNA_YbaB_EbfC DNA-binding protein, YbaB/EbfC family. The function of this protein is unknown, but it has been expressed and crystallized. Its gene nearly always occurs next to recR and/or dnaX. It is restricted to Bacteria and the plant 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 member is present even in the minimal gene complement of Mycoplasm genitalium.
Probab=22.24 E-value=3.3e+02 Score=20.15 Aligned_cols=45 Identities=16% Similarity=0.144 Sum_probs=31.7
Q ss_pred hhhcCCCeEEEEEeCCCCcEEEEEeccc---CChhHHHHHHHHHHHHHH
Q psy18119 175 EETLGGPNLTVAALPLSGKVAVMELSQK---LHLDHLPRVLDCALKGCA 220 (263)
Q Consensus 175 Ee~~~~~~l~v~~~~~~~~i~~i~~~G~---i~~~~l~~~i~~A~~~~~ 220 (263)
|..+..+.++|.+ +..++|..++.+-. -+.+.+.+++-.|...+.
T Consensus 34 ~g~sggGlV~V~~-~G~~~v~~v~Id~~~l~~d~e~LedlI~~A~N~A~ 81 (102)
T TIGR00103 34 TGKSGAGLVTVTI-NGNLELKSIEIDPSLLEEDKEALEDMITEALNDAV 81 (102)
T ss_pred EEEECCCEEEEEE-EcCceEEEEEECHHHHhCCHHHHHHHHHHHHHHHH
Confidence 3445677888888 57889988887632 356677777777766654
No 40
>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=21.12 E-value=3.5e+02 Score=20.04 Aligned_cols=54 Identities=19% Similarity=0.131 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHHhhhc---cCCCCceEEEEEEEEEeCC------CChhHHHHHHHHHHHHHcC
Q psy18119 95 SEISLQLRQAVSAAIM---SEVHPRSQIDIFVEVLQAD------GGNFCACVNAATLALIDAG 148 (263)
Q Consensus 95 ~~l~~~l~~~l~~~i~---l~~~p~~~I~v~v~VL~~d------G~~~~a~i~Aa~~AL~dag 148 (263)
.++...|.+-|+.+.. +-.||-..+.|.++=.+.. +....|+-.|...||..|+
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 4566677777777663 2346765555555444422 2245677777788887764
Done!