Query 024064
Match_columns 273
No_of_seqs 161 out of 1367
Neff 6.9
Searched_HMMs 46136
Date Fri Mar 29 08:41:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024064.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024064hhsearch_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 3.9E-46 8.5E-51 331.1 29.1 216 2-265 6-230 (230)
2 PRK03983 exosome complex exonu 100.0 1.7E-45 3.7E-50 329.7 28.5 219 2-268 12-239 (244)
3 KOG1069 Exosomal 3'-5' exoribo 100.0 2.2E-46 4.8E-51 317.9 20.9 213 13-269 4-216 (217)
4 PRK00173 rph ribonuclease PH; 100.0 1E-42 2.2E-47 310.7 28.1 210 4-263 1-238 (238)
5 TIGR01966 RNasePH ribonuclease 100.0 3.6E-42 7.8E-47 306.8 27.9 208 5-261 1-235 (236)
6 KOG1068 Exosomal 3'-5' exoribo 100.0 7E-42 1.5E-46 299.8 19.3 222 2-271 11-242 (245)
7 COG0689 Rph RNase PH [Translat 100.0 1.1E-40 2.3E-45 293.0 24.4 215 2-262 6-230 (230)
8 PRK04282 exosome complex RNA-b 100.0 2.8E-38 6.1E-43 287.0 27.3 211 2-262 22-270 (271)
9 TIGR03591 polynuc_phos polyrib 100.0 4.9E-36 1.1E-40 301.8 28.5 214 2-265 308-542 (684)
10 PRK11824 polynucleotide phosph 100.0 8.1E-36 1.8E-40 300.8 27.7 213 2-264 312-544 (693)
11 COG2123 RNase PH-related exori 100.0 2.3E-35 5E-40 262.2 25.7 211 2-262 21-271 (272)
12 TIGR02696 pppGpp_PNP guanosine 100.0 4.7E-34 1E-38 284.4 25.0 213 2-264 333-569 (719)
13 PLN00207 polyribonucleotide nu 100.0 1.9E-33 4.1E-38 285.1 28.0 213 2-264 436-675 (891)
14 KOG1614 Exosomal 3'-5' exoribo 100.0 2.8E-33 6E-38 244.2 23.2 213 2-267 20-275 (291)
15 TIGR03591 polynuc_phos polyrib 100.0 1.3E-29 2.8E-34 255.4 27.4 197 15-266 5-219 (684)
16 PRK11824 polynucleotide phosph 100.0 4.6E-29 1E-33 251.8 26.8 197 14-265 13-227 (693)
17 KOG1612 Exosomal 3'-5' exoribo 100.0 4.4E-26 9.6E-31 200.1 23.9 214 2-266 19-279 (288)
18 PF01138 RNase_PH: 3' exoribon 100.0 2E-27 4.3E-32 192.9 14.1 121 13-163 1-132 (132)
19 PLN00207 polyribonucleotide nu 99.9 2.2E-25 4.7E-30 226.6 23.6 197 15-266 89-303 (891)
20 KOG1613 Exosomal 3'-5' exoribo 99.9 2.4E-24 5.2E-29 188.0 15.1 207 2-257 34-296 (298)
21 KOG1067 Predicted RNA-binding 99.8 4.6E-20 9.9E-25 176.8 14.4 217 2-264 356-587 (760)
22 TIGR02696 pppGpp_PNP guanosine 99.8 5.8E-18 1.3E-22 169.6 22.8 206 15-262 17-245 (719)
23 COG1185 Pnp Polyribonucleotide 99.7 4.3E-16 9.2E-21 153.6 19.8 195 14-265 13-226 (692)
24 COG1185 Pnp Polyribonucleotide 99.7 1.1E-16 2.4E-21 157.6 14.4 215 2-266 310-544 (692)
25 KOG1067 Predicted RNA-binding 99.5 1.7E-13 3.7E-18 132.0 13.4 196 13-264 54-267 (760)
26 PF03725 RNase_PH_C: 3' exorib 98.9 6.1E-09 1.3E-13 75.1 8.3 65 166-249 1-68 (68)
27 PRK15031 5-carboxymethyl-2-hyd 42.7 1.4E+02 0.003 24.1 7.2 63 85-147 55-118 (126)
28 PF02962 CHMI: 5-carboxymethyl 37.4 1E+02 0.0022 24.8 5.6 58 84-142 53-110 (124)
29 PF01402 RHH_1: Ribbon-helix-h 34.3 23 0.0005 21.8 1.2 33 234-266 6-38 (39)
30 PF03764 EFG_IV: Elongation fa 33.7 2.2E+02 0.0048 21.9 7.4 55 107-161 57-120 (120)
31 PF03333 PapB: Adhesin biosynt 29.2 77 0.0017 24.2 3.4 34 230-263 19-52 (91)
32 PF12651 RHH_3: Ribbon-helix-h 25.1 82 0.0018 20.4 2.6 34 233-266 8-41 (44)
33 PF13541 ChlI: Subunit ChlI of 20.9 4.2E+02 0.009 21.1 6.4 73 100-175 15-90 (121)
34 PRK15215 fimbriae biosynthesis 20.2 1.4E+02 0.0031 23.2 3.4 34 230-263 27-60 (100)
35 CHL00079 rps9 ribosomal protei 20.0 4.8E+02 0.01 21.2 8.6 45 112-160 43-90 (130)
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=3.9e-46 Score=331.08 Aligned_cols=216 Identities=28% Similarity=0.417 Sum_probs=192.6
Q ss_pred CCCCCCCCCCCCCcccEEEeCCCCCCCceEEEEeCcccccccccccccceeeccccccccccCCCCcEEEEEEEcccCCC
Q 024064 2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGFRFIQTSHFYHFNLFVFTSKCYFCYWVGSGDTKVLAAVYGPKAGT 81 (273)
Q Consensus 2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~~~~~~~~~~~~~~~~~~~~~~g~~~~~~g~T~Vl~~V~gp~~~~ 81 (273)
+++|+|||+++|+|++++++|++++++|||++++| +|+|+|+|+||++.+
T Consensus 6 ~~~R~DGR~~~e~R~~~~~~g~~~~a~GSa~~~~G------------------------------~T~Vl~~V~gp~e~~ 55 (230)
T TIGR02065 6 DGVRLDGRKPDELRPIKIEAGVLKNADGSAYVEFG------------------------------GTKIIAAVYGPREMH 55 (230)
T ss_pred CCcCCCCCCcccccCeEEEECCCCCCCeEEEEEEC------------------------------CcEEEEEEeCCCccc
Confidence 68999999999999999999999999999999999 999999999999764
Q ss_pred C-CCCCCceEEEEEEE--ecCCC------CCCchHHHHHHHHHHHhhhhhhcCCCCCcEEEEEEEEEecCCCchhHHHHH
Q 024064 82 K-KNENPEKASIEVIW--KPRTG------QIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINA 152 (273)
Q Consensus 82 ~-~~~~~~~~~l~v~~--~p~~g------~~~~~~~~l~~~l~~~l~s~i~~~~~p~~~I~i~v~Vl~~dG~ll~a~inA 152 (273)
. ..+.|+++.++|++ .|+++ .+++.+++++++|+++|++++.++.||++.|+|+++||++||++++|++||
T Consensus 56 ~~~~~~~~~~~l~v~~~~~~~a~~~~~~~~~~~~~~~~s~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~DG~~~~aai~a 135 (230)
T TIGR02065 56 PRHLQLPDRAVLRVRYHMAPFSTDERKRPGPSRREIEISKVIREALEPAILLEQFPRTAIDVFIEVLQADAGTRCAGLTA 135 (230)
T ss_pred cccccCCCceEEEEEEEeCCcccCCccCCCCCccHHHHHHHHHHHHHHHhChhhcCCeEEEEEEEEEEcCCCHHHHHHHH
Confidence 3 34568888877666 47643 345678899999999999999999999999999999999999999999999
Q ss_pred HHHHHHhCCCCcccceeEEEEEEeeCCeEEeCCCHHHHhhccccEEEEecCCcccccCCCCccccCCccccceEEEEecC
Q 024064 153 ACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTHG 232 (273)
Q Consensus 153 a~lAL~dagIp~~~~~~avsv~~~~~~~~ilDPt~~Ee~~~~~~~~va~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~G 232 (273)
+++||.|+||||+++++++++++. ++.+++||+.+|++.+.+.+++++..+ ..++++++..|
T Consensus 136 a~lAL~dagIp~~~~v~avtv~~~-~~~~v~Dpt~~Ee~~~~~~l~va~~~~-----------------~~~i~~i~~~g 197 (230)
T TIGR02065 136 ASLALADAGIPMRDLVVGVAVGKV-DGVVVLDLNEEEDMYGEADMPVAMMPK-----------------LGEITLLQLDG 197 (230)
T ss_pred HHHHHHHcCCccccceeeEEEEEE-CCeEEECCCHHHhhcCCCceEEEEeCC-----------------CCCEEEEEEec
Confidence 999999999999999999999986 889999999999999999999988421 12344555789
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 024064 233 AMSVDDYFHCLERGRAASAKLSDFLRRSLQSKL 265 (273)
Q Consensus 233 ~~~~~~~~~~l~~A~~~~~~i~~~i~~~l~~~~ 265 (273)
.++++++++|++.|.++|++++++|+++|++++
T Consensus 198 ~~~~e~~~~~l~~a~~~~~~l~~~~~~~l~~~~ 230 (230)
T TIGR02065 198 DMTPDEFRQALDLAVKGIKIIYQIQREALKNKY 230 (230)
T ss_pred CcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 999999999999999999999999999998763
No 2
>PRK03983 exosome complex exonuclease Rrp41; Provisional
Probab=100.00 E-value=1.7e-45 Score=329.68 Aligned_cols=219 Identities=27% Similarity=0.415 Sum_probs=195.3
Q ss_pred CCCCCCCCCCCCCcccEEEeCCCCCCCceEEEEeCcccccccccccccceeeccccccccccCCCCcEEEEEEEcccCCC
Q 024064 2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGFRFIQTSHFYHFNLFVFTSKCYFCYWVGSGDTKVLAAVYGPKAGT 81 (273)
Q Consensus 2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~~~~~~~~~~~~~~~~~~~~~~g~~~~~~g~T~Vl~~V~gp~~~~ 81 (273)
+++|+|||+++|+|++++++|++++++|||++++| +|+|+|+|+||++..
T Consensus 12 ~~~R~DGR~~~~~R~i~i~~G~l~~a~GSa~v~~G------------------------------~T~Vl~~V~gp~e~~ 61 (244)
T PRK03983 12 DGLRLDGRKPDELRPIKIEVGVLKNADGSAYLEWG------------------------------NNKIIAAVYGPREMH 61 (244)
T ss_pred CCCCCCCCCcCcccceEEEeCCCCCCCeEEEEEEC------------------------------CeEEEEEEecCCccc
Confidence 68999999999999999999999999999999999 999999999999854
Q ss_pred C-CCCCCceEEEEEEE--ecCCC------CCCchHHHHHHHHHHHhhhhhhcCCCCCcEEEEEEEEEecCCCchhHHHHH
Q 024064 82 K-KNENPEKASIEVIW--KPRTG------QIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINA 152 (273)
Q Consensus 82 ~-~~~~~~~~~l~v~~--~p~~g------~~~~~~~~l~~~l~~~l~s~i~~~~~p~~~I~i~v~Vl~~dG~ll~a~inA 152 (273)
. ..+.|+++.++|++ .|+++ .+++++.+++++|+++|++++.++.||++.|+|+|+||++|||+++||+||
T Consensus 62 ~~~~~~~~~~~l~v~~~~~p~~~~~~~~~~~~~~~~~~s~~l~~~l~~~i~~~~~p~~~I~I~i~VL~~DG~~~~aai~A 141 (244)
T PRK03983 62 PRHLQLPDRAVLRVRYNMAPFSVDERKRPGPDRRSIEISKVIREALEPAIMLELFPRTVIDVFIEVLQADAGTRVAGITA 141 (244)
T ss_pred cccccCCCcEEEEEEEEcCCCccccccCCCCChhHHHHHHHHHHHHHHhccHHhCCCeEEEEEEEEEECCCCHHHHHHHH
Confidence 3 34568888776665 47653 245567899999999999999999999999999999999999999999999
Q ss_pred HHHHHHhCCCCcccceeEEEEEEeeCCeEEeCCCHHHHhhccccEEEEecCCcccccCCCCccccCCccccceEEEEecC
Q 024064 153 ACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTHG 232 (273)
Q Consensus 153 a~lAL~dagIp~~~~~~avsv~~~~~~~~ilDPt~~Ee~~~~~~~~va~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~G 232 (273)
+++||+|+||||++++++++++.. ++.+++||+..|++.+++.++++++.+ ...++.++..|
T Consensus 142 a~lAL~dagIp~~~~v~avtv~~~-~~~~i~DPt~~Ee~~~~~~l~va~~~~-----------------~~~I~~l~~~G 203 (244)
T PRK03983 142 ASLALADAGIPMRDLVAGCAVGKV-DGVIVLDLNKEEDNYGEADMPVAIMPR-----------------LGEITLLQLDG 203 (244)
T ss_pred HHHHHHhcCCccccceeEEEEEEE-CCEEEECCCHHHhccCCceEEEEEECC-----------------CCCEEEEEEec
Confidence 999999999999999999999986 889999999999999999999998631 12345556788
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCc
Q 024064 233 AMSVDDYFHCLERGRAASAKLSDFLRRSLQSKLPGD 268 (273)
Q Consensus 233 ~~~~~~~~~~l~~A~~~~~~i~~~i~~~l~~~~~~~ 268 (273)
.++.+++.+|++.|.++|++++++|+++|++++.+.
T Consensus 204 ~~~~~~~~~~i~~A~~~~~~i~~~i~~~l~~~~~~~ 239 (244)
T PRK03983 204 NLTREEFLEALELAKKGIKRIYQLQREALKSKYGEI 239 (244)
T ss_pred CcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 999999999999999999999999999999887654
No 3
>KOG1069 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp46 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.2e-46 Score=317.95 Aligned_cols=213 Identities=47% Similarity=0.721 Sum_probs=200.9
Q ss_pred CCcccEEEeCCCCCCCceEEEEeCcccccccccccccceeeccccccccccCCCCcEEEEEEEcccCCCCCCCCCceEEE
Q 024064 13 QLRPLACSCSILHRAHGSASWSQGFRFIQTSHFYHFNLFVFTSKCYFCYWVGSGDTKVLAAVYGPKAGTKKNENPEKASI 92 (273)
Q Consensus 13 e~R~i~i~~~~l~~a~GSa~v~~G~~~~~~~~~~~~~~~~~~~~~~g~~~~~~g~T~Vl~~V~gp~~~~~~~~~~~~~~l 92 (273)
.+|++.++.|+|+++|||+.|++| +|+|+|+|+||.+++.+++.|+++.+
T Consensus 4 ~lr~~~cei~iLsr~dGSs~fsqg------------------------------dT~V~c~V~GP~dvk~r~E~~~katl 53 (217)
T KOG1069|consen 4 RLRGIACEISILSRPDGSSEFSQG------------------------------DTKVICSVYGPIDVKARQEDPEKATL 53 (217)
T ss_pred hhhhhhhhhceecCCCCccceecC------------------------------CcEEEEEeeCCcchhhcccCchhceE
Confidence 789999999999999999999999 99999999999999999999999999
Q ss_pred EEEEecCCCCCCchHHHHHHHHHHHhhhhhhcCCCCCcEEEEEEEEEecCCCchhHHHHHHHHHHHhCCCCcccceeEEE
Q 024064 93 EVIWKPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLAVAIC 172 (273)
Q Consensus 93 ~v~~~p~~g~~~~~~~~l~~~l~~~l~s~i~~~~~p~~~I~i~v~Vl~~dG~ll~a~inAa~lAL~dagIp~~~~~~avs 172 (273)
+|.|+|..|.+++.++.+++.|+++|+++|.++.||++.|+|.+||+++||+++++|||||++||+|+||||+++++|++
T Consensus 54 eVi~rp~~G~~~~~eK~~e~iI~~tl~~~I~l~l~Prt~iqVsiqvv~ddgs~LacaINaAclALvDaGIpl~~mfcai~ 133 (217)
T KOG1069|consen 54 EVIWRPKSGVNGTVEKVLERIIRKTLSKAIILELYPRTTIQVSIQVVEDDGSTLACAINAACLALVDAGIPLRSMFCAIS 133 (217)
T ss_pred EEEEecccCcchHHHHHHHHHHHHHHHHhheeeecCCceEEEEEEEEecCCcchHHHHHHHHHHHHhcCCchHHhhhhce
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEeeCCeEEeCCCHHHHhhccccEEEEecCCcccccCCCCccccCCccccceEEEEecCCCCHHHHHHHHHHHHHHHHH
Q 024064 173 CCSAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAK 252 (273)
Q Consensus 173 v~~~~~~~~ilDPt~~Ee~~~~~~~~va~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~G~~~~~~~~~~l~~A~~~~~~ 252 (273)
+++.+++.+++||+..++..+++..++.|.... . + ..+++.+...|.++.++|+.+++.|..+++.
T Consensus 134 ~~~~~d~~lv~Dpt~~qek~~~~~~~lsf~~~~---~--------~---~~~vi~s~t~G~~~~d~lf~~le~a~~~~~~ 199 (217)
T KOG1069|consen 134 CALHEDGVLVLDPTAKQEKISTARATLSFEGGS---L--------G---EPKVIISETNGEKSEDQLFYVLELAQAAAQS 199 (217)
T ss_pred EEEecCccEEECCcHHhhhhhhceEEEEEecCC---C--------C---CcceEEEeccCCCCHHHHHHHHHhhHHHHHH
Confidence 999988999999999999988888888875421 1 1 3567788899999999999999999999999
Q ss_pred HHHHHHHHHhhhccCcC
Q 024064 253 LSDFLRRSLQSKLPGDL 269 (273)
Q Consensus 253 i~~~i~~~l~~~~~~~~ 269 (273)
+++|+|+.++++++++.
T Consensus 200 ~f~f~r~~~q~~~s~~~ 216 (217)
T KOG1069|consen 200 LFPFYREVLQRKYSKSE 216 (217)
T ss_pred HHHHHHHHHHhhcCccc
Confidence 99999999999988764
No 4
>PRK00173 rph ribonuclease PH; Reviewed
Probab=100.00 E-value=1e-42 Score=310.71 Aligned_cols=210 Identities=24% Similarity=0.309 Sum_probs=185.0
Q ss_pred CCCCCCCCCCCcccEEEeCCCCCCCceEEEEeCcccccccccccccceeeccccccccccCCCCcEEEEEEEcccCCCCC
Q 024064 4 DRADGRNPNQLRPLACSCSILHRAHGSASWSQGFRFIQTSHFYHFNLFVFTSKCYFCYWVGSGDTKVLAAVYGPKAGTKK 83 (273)
Q Consensus 4 ~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~~~~~~~~~~~~~~~~~~~~~~g~~~~~~g~T~Vl~~V~gp~~~~~~ 83 (273)
+|+|||+++|+|++++++|++++++|||++++| +|+|+|+|++|.+.++.
T Consensus 1 ~R~DGR~~~e~R~i~~~~g~~~~a~GSa~v~~G------------------------------~T~Vla~V~~~~~~p~~ 50 (238)
T PRK00173 1 MRPDGRAADQLRPVTITRNFTKHAEGSVLVEFG------------------------------DTKVLCTASVEEGVPRF 50 (238)
T ss_pred CCCCCCCcccccCeEEEeCCCCCCCeeEEEEec------------------------------CcEEEEEEEcCCCCCCc
Confidence 599999999999999999999999999999999 99999999998875543
Q ss_pred CCCCceEEEEEEE--ecCC-----------CCCCchHHHHHHHHHHHhhhhhhcCCCCCcEEEEEEEEEecCCCchhHHH
Q 024064 84 NENPEKASIEVIW--KPRT-----------GQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAI 150 (273)
Q Consensus 84 ~~~~~~~~l~v~~--~p~~-----------g~~~~~~~~l~~~l~~~l~s~i~~~~~p~~~I~i~v~Vl~~dG~ll~a~i 150 (273)
...++++.++|+| .|++ |++++.+++++++|+++|++++.++.||++.|+|+++||++|||+++||+
T Consensus 51 ~~~~~~g~l~v~~~~~p~a~~~~~~~~~~~g~~~~~~~~~sr~i~r~lr~~i~l~~l~~~~i~v~v~VL~~DG~~~~aai 130 (238)
T PRK00173 51 LKGQGQGWVTAEYGMLPRATHTRNDREAAKGKQGGRTQEIQRLIGRSLRAVVDLKALGERTITIDCDVIQADGGTRTASI 130 (238)
T ss_pred cCCCCcEEEEEEEecCCCCCcccccccccCCCCCccHHHHHHHHHHHHHHhcCHHHcCCeEEEEEEEEEeCCCCHHHHHH
Confidence 3456777766555 4653 33455678999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhC-----------CCCcccceeEEEEEEeeCCeEEeCCCHHHHhhccccEEEEecCCcccccCCCCccccCC
Q 024064 151 NAACAALVDA-----------GIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGE 219 (273)
Q Consensus 151 nAa~lAL~da-----------gIp~~~~~~avsv~~~~~~~~ilDPt~~Ee~~~~~~~~va~~~~~~~~~~~~~~~~~~~ 219 (273)
||+++||+|+ ++||+++|+++|++++ ++.+|+|||.+||+.+++.+++++++
T Consensus 131 ~Aa~~AL~da~~~~~~~~~~~~ip~~~~~~~vt~~~~-~~~~lvDpt~~Ee~~~~~~l~v~~~~---------------- 193 (238)
T PRK00173 131 TGAYVALADALNKLVARGKLKKNPLKDQVAAVSVGIV-DGEPVLDLDYEEDSAAETDMNVVMTG---------------- 193 (238)
T ss_pred HHHHHHHHHhhhhhhccCcccCCcccCceeEEEEEEE-CCEEEECCCHHHHhcCCceEEEEECC----------------
Confidence 9999999999 9999999999999987 88999999999999999999999863
Q ss_pred ccccceEEEE-ecC---CCCHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 024064 220 PMEHGIITSV-THG---AMSVDDYFHCLERGRAASAKLSDFLRRSLQS 263 (273)
Q Consensus 220 ~~~~~~v~~~-~~G---~~~~~~~~~~l~~A~~~~~~i~~~i~~~l~~ 263 (273)
.+.++.+ +.| .++++++.+|++.|++++++++++++++|++
T Consensus 194 ---~~~i~~v~~~g~g~~~~~e~l~~~i~~A~~~~~~l~~~~~~~l~~ 238 (238)
T PRK00173 194 ---SGGFVEVQGTAEGAPFSREELDALLDLAEKGIAELVALQKAALAD 238 (238)
T ss_pred ---CCCEEEEEccCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 2344444 422 7999999999999999999999999999864
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=3.6e-42 Score=306.80 Aligned_cols=208 Identities=25% Similarity=0.325 Sum_probs=180.7
Q ss_pred CCCCCCCCCCcccEEEeCCCCCCCceEEEEeCcccccccccccccceeeccccccccccCCCCcEEEEEEEcccCCCCCC
Q 024064 5 RADGRNPNQLRPLACSCSILHRAHGSASWSQGFRFIQTSHFYHFNLFVFTSKCYFCYWVGSGDTKVLAAVYGPKAGTKKN 84 (273)
Q Consensus 5 R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~~~~~~~~~~~~~~~~~~~~~~g~~~~~~g~T~Vl~~V~gp~~~~~~~ 84 (273)
|+|||+++|+|++++++|++++|+|||++++| +|+|+|+|+++.+.++..
T Consensus 1 R~DGR~~~e~R~i~i~~G~~~~A~GSa~v~~G------------------------------~T~Vla~V~~~~~~p~~~ 50 (236)
T TIGR01966 1 RPDGRKPDQLRPVSITRDFLKHAEGSVLIEFG------------------------------NTKVLCTASVEEKVPPFL 50 (236)
T ss_pred CCCCCCCCCccCeEEEeCCcCCCCceEEEEec------------------------------CCEEEEEEEccCccCCcc
Confidence 89999999999999999999999999999999 999999999877544333
Q ss_pred CCCceEEEE--EEEecCC-----------CCCCchHHHHHHHHHHHhhhhhhcCCCCCcEEEEEEEEEecCCCchhHHHH
Q 024064 85 ENPEKASIE--VIWKPRT-----------GQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAIN 151 (273)
Q Consensus 85 ~~~~~~~l~--v~~~p~~-----------g~~~~~~~~l~~~l~~~l~s~i~~~~~p~~~I~i~v~Vl~~dG~ll~a~in 151 (273)
..++++.+. +++.|++ |+++.++++++++|+++|+++|+++.||++.|+|+++||++|||+++||+|
T Consensus 51 ~~~~~g~l~v~~~~~p~a~~~~~~r~~~~g~~~~~~~e~~~~i~r~lr~~i~l~~l~~~~i~I~v~VL~~DG~~~~aai~ 130 (236)
T TIGR01966 51 RGSGEGWITAEYGMLPRATQTRNRRESAKGKQSGRTQEIQRLIGRALRAVVDLEALGERTIWIDCDVIQADGGTRTASIT 130 (236)
T ss_pred cCCCcEEEEEEEecCCCCCCCCccccccCCCCCccHHHHHHHHHHHHHHhcCHhhcCCeEEEEEEEEEeCCCCHHHHHHH
Confidence 335666554 5556753 333446789999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhC-----------CCCcccceeEEEEEEeeCCeEEeCCCHHHHhhccccEEEEecCCcccccCCCCccccCCc
Q 024064 152 AACAALVDA-----------GIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEP 220 (273)
Q Consensus 152 Aa~lAL~da-----------gIp~~~~~~avsv~~~~~~~~ilDPt~~Ee~~~~~~~~va~~~~~~~~~~~~~~~~~~~~ 220 (273)
|+++||.|+ ||||+++|+++|++++ ++.+|+|||.+||+.+++.++++++..
T Consensus 131 Aa~aAL~da~~~~~~~~~~~~ip~~~~~~~vt~~~~-~~~~v~Dpt~~Ee~~~~~~l~l~~~~~---------------- 193 (236)
T TIGR01966 131 GAFVALADAISKLHKRGILKESPIRDFVAAVSVGIV-DGEPVLDLDYEEDSAADVDMNVVMTGS---------------- 193 (236)
T ss_pred HHHHHHHHHHHhhhhcCcccCCCccCceeEEEEEEE-CCEEEECCChhHHhccCceEEEEEcCC----------------
Confidence 999999999 9999999999999987 789999999999999999999998742
Q ss_pred cccceEEEEec---CCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024064 221 MEHGIITSVTH---GAMSVDDYFHCLERGRAASAKLSDFLRRSL 261 (273)
Q Consensus 221 ~~~~~v~~~~~---G~~~~~~~~~~l~~A~~~~~~i~~~i~~~l 261 (273)
..++.++.. +.++++++.+|++.|.+++++++++|+++|
T Consensus 194 --~~i~~i~~~g~~~~~~~~~l~~~i~~a~~~~~~l~~~~~~~l 235 (236)
T TIGR01966 194 --GGFVEVQGTAEEGPFSRDELNKLLDLAKKGIRELIELQKQAL 235 (236)
T ss_pred --CCEEEEEecCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 223444442 479999999999999999999999999987
No 6
>KOG1068 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp41 and related exoribonucleases [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=7e-42 Score=299.85 Aligned_cols=222 Identities=33% Similarity=0.428 Sum_probs=194.1
Q ss_pred CCCCCCCCCCCCCcccEEEeCCCCCCCceEEEEeCcccccccccccccceeeccccccccccCCCCcEEEEEEEcccCCC
Q 024064 2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGFRFIQTSHFYHFNLFVFTSKCYFCYWVGSGDTKVLAAVYGPKAGT 81 (273)
Q Consensus 2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~~~~~~~~~~~~~~~~~~~~~~g~~~~~~g~T~Vl~~V~gp~~~~ 81 (273)
|++|.|||+++|+|++..+.|++.+++|||++++| ||||+|.|+||++.+
T Consensus 11 eg~r~dgRr~~elR~i~~~~g~~~~a~GSay~E~G------------------------------nTKVl~aV~GPre~~ 60 (245)
T KOG1068|consen 11 EGLRTDGRRPNELRRIYARIGVLTQADGSAYMEQG------------------------------NTKVLCAVYGPREIR 60 (245)
T ss_pred cccccCCCChhHhhhhhhhcCccccCCccchhhcC------------------------------CeEEEEEEeCCcccc
Confidence 78999999999999999999999999999999999 999999999999865
Q ss_pred CCC-CCCceEEEEEEE--ecCCC-------CCCchHHHHHHHHHHHhhhhhhcCCCCCcEEEEEEEEEecCCCchhHHHH
Q 024064 82 KKN-ENPEKASIEVIW--KPRTG-------QIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAIN 151 (273)
Q Consensus 82 ~~~-~~~~~~~l~v~~--~p~~g-------~~~~~~~~l~~~l~~~l~s~i~~~~~p~~~I~i~v~Vl~~dG~ll~a~in 151 (273)
... ..++++.+++.+ .+|.. +.+++++|++.+|+++|+++|.++.||+++|+|+|+|+++||+.+++|+|
T Consensus 61 ~~~~~~~~~a~lnc~~~~a~Fst~~r~~~~~~~rr~~e~s~~L~~afe~~I~~~lyPrsqIDI~v~VleddG~~laa~in 140 (245)
T KOG1068|consen 61 GKSARRPDKAVLNCEVSSAQFSTGDRKKRPKGDRREKELSLMLQQAFEPVILLELYPRSQIDIYVQVLEDDGSNLAAAIN 140 (245)
T ss_pred cccccccccceEEEEEeeeccccchhccCCCccHHHHHHHHHHHHHHHHHHHhhhCccccceEEEEEEECCCccHHHHHH
Confidence 432 357777666555 56532 23558899999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhCCCCcccceeEEEEEEeeCCeEEeCCCHHHHhhccccEEEEecCCcccccCCCCccccCCccccceEEEEec
Q 024064 152 AACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTH 231 (273)
Q Consensus 152 Aa~lAL~dagIp~~~~~~avsv~~~~~~~~ilDPt~~Ee~~~~~~~~va~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~ 231 (273)
|+.+||.|+||||+|+++++|+++. ++..++||+..||......++|++.-. .+.++.++..
T Consensus 141 aatlAL~daGI~m~D~i~~~t~~l~-~~~~l~Dl~~~eesa~~~~ltVa~l~~-----------------~~~i~~l~~~ 202 (245)
T KOG1068|consen 141 AATLALADAGIPMYDLITACTAGLA-DGTPLLDLTSLEESARAPGLTVAALPN-----------------REEIALLQLD 202 (245)
T ss_pred HHHHHHHHcCCChhhhhhhceeeec-CCccccccccchhhccCCceEEEEecC-----------------cceEEEEEec
Confidence 9999999999999999999999997 679999999999999887788877421 2334555678
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCcCCc
Q 024064 232 GAMSVDDYFHCLERGRAASAKLSDFLRRSLQSKLPGDLSK 271 (273)
Q Consensus 232 G~~~~~~~~~~l~~A~~~~~~i~~~i~~~l~~~~~~~~~~ 271 (273)
+.+..+.+...++.+..+|+++++.++..+.+.+.+...+
T Consensus 203 ~~~~~d~l~~vl~~a~~~c~~v~~~l~~~l~~~l~~~~~~ 242 (245)
T KOG1068|consen 203 ERLHCDHLETVLELAIAGCKRVYERLRLVLREHLKNAESA 242 (245)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 8999999999999999999999999999999887665544
No 7
>COG0689 Rph RNase PH [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.1e-40 Score=292.99 Aligned_cols=215 Identities=27% Similarity=0.391 Sum_probs=186.9
Q ss_pred CCCCCCCCCCCCCcccEEEeCCCCCCCceEEEEeCcccccccccccccceeeccccccccccCCCCcEEEEEEEcccCCC
Q 024064 2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGFRFIQTSHFYHFNLFVFTSKCYFCYWVGSGDTKVLAAVYGPKAGT 81 (273)
Q Consensus 2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~~~~~~~~~~~~~~~~~~~~~~g~~~~~~g~T~Vl~~V~gp~~~~ 81 (273)
++.|+|||+++|+|+++++.|++++++||+++++| +|||+|+|+||++..
T Consensus 6 ~~~R~dgR~~delR~i~~~~~~~~~a~GS~~~~~G------------------------------~tkVic~vsGp~e~~ 55 (230)
T COG0689 6 DGMRPDGRKPDELRPIKITRGVLKHAEGSSLIEFG------------------------------NTKVICTVSGPREPV 55 (230)
T ss_pred cCcCCCCCCcccccceEEEeccccCCCccEEEEeC------------------------------CeEEEEEEecCCCCC
Confidence 57899999999999999999999999999999999 999999999999865
Q ss_pred CCC-CCCceEEE--EEEEecCCC----CCC--c-hHHHHHHHHHHHhhhhhhcCCCCCcEEEEEEEEEecCCCchhHHHH
Q 024064 82 KKN-ENPEKASI--EVIWKPRTG----QIG--K-PEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAIN 151 (273)
Q Consensus 82 ~~~-~~~~~~~l--~v~~~p~~g----~~~--~-~~~~l~~~l~~~l~s~i~~~~~p~~~I~i~v~Vl~~dG~ll~a~in 151 (273)
++. ..++++.+ ++.+.|++. ++. + +++|++++|.++|+++|.++.||+..|+|+++|+++||+.+.|+||
T Consensus 56 p~~l~~~~~g~~t~ey~m~p~sT~~R~~~~~~~gR~~eisrli~~al~~~i~L~~~p~~~I~i~~dVlqaDggTrta~It 135 (230)
T COG0689 56 PRFLRGTGKGWLTAEYGMLPRSTDERKKREADRGRTKEISRLIGRALRAVIDLELLPESTIDIDCDVLQADGGTRTASIT 135 (230)
T ss_pred ChhhcCCCceEEEEEEecccccccccccccccccchhHHHHHHHHHHHHHhhhhhcCccEEEEEEEEEECCCCeeeehhh
Confidence 443 33555555 555568765 121 1 5789999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhCCCCcccceeEEEEEEeeCCeEEeCCCHHHHhhccccEEEEecCCcccccCCCCccccCCccccceEEEEec
Q 024064 152 AACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTH 231 (273)
Q Consensus 152 Aa~lAL~dagIp~~~~~~avsv~~~~~~~~ilDPt~~Ee~~~~~~~~va~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~ 231 (273)
|+++||+||||||+++++|+|+|+. ++.+++||+..|++.+...++|++...+.. ..+......
T Consensus 136 ~A~lAL~DAgipl~~~vaaiSvgi~-~~~~~lDl~~~Eds~~~~d~~v~~~~~~~~---------------~ei~~~~~~ 199 (230)
T COG0689 136 GASLALADAGIPLRDLVAAISVGIV-DGVIVLDLDYEEDSAAEADMNVVMTGNGGL---------------VEIQGLAED 199 (230)
T ss_pred HHHHHHHHcCCchhhheeEeEEEEE-CCceEecCcchhhcccccCceEEEEecCCe---------------EEEEEEecc
Confidence 9999999999999999999999997 777999999999999999999998642110 012233457
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024064 232 GAMSVDDYFHCLERGRAASAKLSDFLRRSLQ 262 (273)
Q Consensus 232 G~~~~~~~~~~l~~A~~~~~~i~~~i~~~l~ 262 (273)
|.+++++|.++++.|+++|+++++.++++|.
T Consensus 200 ~~~~~del~~lL~la~~g~~~~~~~~~~al~ 230 (230)
T COG0689 200 GPFTEDELLELLDLAIKGCNELRELQREALA 230 (230)
T ss_pred CCcCHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 8999999999999999999999999999873
No 8
>PRK04282 exosome complex RNA-binding protein Rrp42; Provisional
Probab=100.00 E-value=2.8e-38 Score=286.99 Aligned_cols=211 Identities=22% Similarity=0.322 Sum_probs=178.3
Q ss_pred CCCCCCCCCCCCCcccEEEeCCCCCCCceEEEEeCcccccccccccccceeeccccccccccCCCCcEEEEEEEcccCCC
Q 024064 2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGFRFIQTSHFYHFNLFVFTSKCYFCYWVGSGDTKVLAAVYGPKAGT 81 (273)
Q Consensus 2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~~~~~~~~~~~~~~~~~~~~~~g~~~~~~g~T~Vl~~V~gp~~~~ 81 (273)
+++|+|||+++|+|++.+++|++++++|||++++| +|+|+|+|+++...
T Consensus 22 ~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G------------------------------~T~vl~~V~~~~~~- 70 (271)
T PRK04282 22 KGKRIDGRKLDEYRPIEIETGVIKKAEGSALVKLG------------------------------NTQVLAGVKLEIGE- 70 (271)
T ss_pred cCCCCCCCCCccccCeEEEeCCccCCCcEEEEEEC------------------------------CCEEEEEEEEEEec-
Confidence 68999999999999999999999999999999999 99999999965422
Q ss_pred CCCCCCceEE--EEEEEecCC------CCCCchHHHHHHHHHHHhhhhhhcC--------CCCCcEEEEEEEEEecCCCc
Q 024064 82 KKNENPEKAS--IEVIWKPRT------GQIGKPEKEYEIILKRTLQSICILT--------INPNTTTSVIIQVVHDDGAL 145 (273)
Q Consensus 82 ~~~~~~~~~~--l~v~~~p~~------g~~~~~~~~l~~~l~~~l~s~i~~~--------~~p~~~I~i~v~Vl~~dG~l 145 (273)
+..+.|+++. ++|++.|++ |++++.+++++++|+++|++....+ ....|.|+|+|+||++|||+
T Consensus 71 p~~~~~~~g~i~~~v~~~~~a~~~~~~~~~~~~~~~l~~~l~r~l~~~~~~dl~~L~I~~g~~~w~i~Vdv~VL~~dG~~ 150 (271)
T PRK04282 71 PFPDTPNEGVLIVNAELLPLASPTFEPGPPDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWVVFIDVYVLDHDGNL 150 (271)
T ss_pred CCCCCCCCCEEEEEEEECCCcCccccCCCCCHHHHHHHHHHHHHHhccCCccHHHcEEecCcEEEEEEEEEEEECCCCCH
Confidence 2334566655 566666764 4556678899999999998753333 22368999999999999999
Q ss_pred hhHHHHHHHHHHHhCCCC--------------------cccceeEEEEEEeeCCeEEeCCCHHHHhhccccEEEEecCCc
Q 024064 146 LPCAINAACAALVDAGIP--------------------MKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSI 205 (273)
Q Consensus 146 l~a~inAa~lAL~dagIp--------------------~~~~~~avsv~~~~~~~~ilDPt~~Ee~~~~~~~~va~~~~~ 205 (273)
++|+++|+++||.|++|| |+++|+++|+++. ++.+|+||+.+||..+++.+++++++.
T Consensus 151 ~daa~~Aa~aAL~~~~iP~~~~~~~~~~~~~~~~~~l~~~~~p~~vt~~~~-~~~~v~Dpt~~Ee~~~~~~l~va~~~~- 228 (271)
T PRK04282 151 LDASMLAAVAALLNTKVPAVEEGEDGVVDKLGEDFPLPVNDKPVTVTFAKI-GNYLIVDPTLEEESVMDARITITTDED- 228 (271)
T ss_pred HHHHHHHHHHHHHhCCCCcEEEcCCceeccCCCcccCCCCCeeEEEEEEEE-CCEEEECCCHHHHhhcCceEEEEECCC-
Confidence 999999999999999995 9999999999987 789999999999999999999999742
Q ss_pred ccccCCCCccccCCccccceEEEEec--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024064 206 LSVLPEGSSLVQGEPMEHGIITSVTH--GAMSVDDYFHCLERGRAASAKLSDFLRRSLQ 262 (273)
Q Consensus 206 ~~~~~~~~~~~~~~~~~~~~v~~~~~--G~~~~~~~~~~l~~A~~~~~~i~~~i~~~l~ 262 (273)
.+++.+... |.++.+++.+|++.|.+++++++++++++|+
T Consensus 229 -----------------g~i~~l~~~g~~~~~~~~l~~~i~~A~~~~~~l~~~~~~~l~ 270 (271)
T PRK04282 229 -----------------GNIVAIQKSGIGSFTEEEVDKAIDIALEKAKELREKLKEALG 270 (271)
T ss_pred -----------------CcEEEEEcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 123333433 4799999999999999999999999999984
No 9
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=100.00 E-value=4.9e-36 Score=301.83 Aligned_cols=214 Identities=20% Similarity=0.291 Sum_probs=185.0
Q ss_pred CCCCCCCCCCCCCcccEEEeCCCCCCCceEEEEeCcccccccccccccceeeccccccccccCCCCcEEEEEE-EcccCC
Q 024064 2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGFRFIQTSHFYHFNLFVFTSKCYFCYWVGSGDTKVLAAV-YGPKAG 80 (273)
Q Consensus 2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~~~~~~~~~~~~~~~~~~~~~~g~~~~~~g~T~Vl~~V-~gp~~~ 80 (273)
+++|+|||+++|+||+.+++|++++++|||+|++| +|+|+|+| .||.+.
T Consensus 308 ~g~R~DGR~~~e~Rpi~~~~g~l~~a~GSa~~~~G------------------------------~Tqvl~~vt~g~~~~ 357 (684)
T TIGR03591 308 EGKRIDGRDLDTIRPISIEVGVLPRTHGSALFTRG------------------------------ETQALVVTTLGTERD 357 (684)
T ss_pred CCCCCCCCCCCCcCceEEEeCCCCCCCceEEEEeC------------------------------CeEEEEEEecCCccc
Confidence 68999999999999999999999999999999999 99999999 598853
Q ss_pred CCCC-----CCCceEEEEEEEecCC-------CCCCchHHHHHHHHHHHhhhhhhc-CCCCCcEEEEEEEEEecCCCchh
Q 024064 81 TKKN-----ENPEKASIEVIWKPRT-------GQIGKPEKEYEIILKRTLQSICIL-TINPNTTTSVIIQVVHDDGALLP 147 (273)
Q Consensus 81 ~~~~-----~~~~~~~l~v~~~p~~-------g~~~~~~~~l~~~l~~~l~s~i~~-~~~p~~~I~i~v~Vl~~dG~ll~ 147 (273)
.... +...++.+++++.||+ |++++++.+++++++|+|++++.. +.|| |.|+|+++||++|||..+
T Consensus 358 ~~~~~~~~~~~~~~~~~~y~~~pfs~~e~~~~g~~~rrei~~~~l~~ral~~~i~~~~~~p-~tI~v~~~VLesdGs~~~ 436 (684)
T TIGR03591 358 EQIIDDLEGEYRKRFMLHYNFPPYSVGEVGRVGGPGRREIGHGALAERALKAVLPSEEEFP-YTIRVVSEILESNGSSSM 436 (684)
T ss_pred ccCCcccCCCccEEEEEEEEcCCCCCCCcCCCCCCChHHHHHHHHHHHHHHHhcCccccCC-eEEEEEEEEEeCCCChHH
Confidence 2111 1234577888888974 345678889999999999999985 6777 679999999999999999
Q ss_pred HHHHHHHHHHHhCCCCcccceeEEEEEEeeCC----eEEeCCCHHHHhhccccEEEEecCCcccccCCCCccccCCcccc
Q 024064 148 CAINAACAALVDAGIPMKHLAVAICCCSAESG----YCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEH 223 (273)
Q Consensus 148 a~inAa~lAL~dagIp~~~~~~avsv~~~~~~----~~ilDPt~~Ee~~~~~~~~va~~~~~~~~~~~~~~~~~~~~~~~ 223 (273)
|+++|+++||+||||||+++++++++|+..++ .+++||+..|+..++..++++.+. +
T Consensus 437 Aai~aaslAL~dAgvP~~~~Vagvs~gli~~~~~~~~il~D~~~~Ed~~~d~d~~va~t~-------------------~ 497 (684)
T TIGR03591 437 ASVCGGSLALMDAGVPIKAPVAGIAMGLIKEGDERFAVLSDILGDEDHLGDMDFKVAGTR-------------------D 497 (684)
T ss_pred HHHHHHHHHHHhcCCCCcCCEEEEEEEEEcCCCcceEEEeCCChHHHhcCCceEEEEEcC-------------------C
Confidence 99999999999999999999999999998432 599999999999999999988752 4
Q ss_pred ceEEEEecC---CCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 024064 224 GIITSVTHG---AMSVDDYFHCLERGRAASAKLSDFLRRSLQSKL 265 (273)
Q Consensus 224 ~~v~~~~~G---~~~~~~~~~~l~~A~~~~~~i~~~i~~~l~~~~ 265 (273)
+++.++.++ .++.+.+.+|++.|++++++|+++|+++|.+..
T Consensus 498 gI~~lq~d~k~~~i~~~~l~~al~~a~~~~~~I~~~m~~~l~~~~ 542 (684)
T TIGR03591 498 GITALQMDIKIDGITREIMEQALEQAKEGRLHILGEMNKVISEPR 542 (684)
T ss_pred ceEEEEEEcCcCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 555555533 589999999999999999999999999998764
No 10
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=100.00 E-value=8.1e-36 Score=300.78 Aligned_cols=213 Identities=20% Similarity=0.294 Sum_probs=183.4
Q ss_pred CCCCCCCCCCCCCcccEEEeCCCCCCCceEEEEeCcccccccccccccceeeccccccccccCCCCcEEEEEE-EcccC-
Q 024064 2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGFRFIQTSHFYHFNLFVFTSKCYFCYWVGSGDTKVLAAV-YGPKA- 79 (273)
Q Consensus 2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~~~~~~~~~~~~~~~~~~~~~~g~~~~~~g~T~Vl~~V-~gp~~- 79 (273)
++.|+|||+++|+||+++++|++++++|||+|++| +|+|+|+| .||..
T Consensus 312 ~g~R~DGR~~~e~Rpi~~~~g~l~~a~GSal~~~G------------------------------~T~Vl~~vt~g~~~~ 361 (693)
T PRK11824 312 EGIRIDGRKLDEIRPISIEVGVLPRTHGSALFTRG------------------------------ETQALVVATLGTLRD 361 (693)
T ss_pred CCCCCCCCCcCcccceEEEeCCCCCCCceEEEEEC------------------------------CeEEEEEEecCCCcc
Confidence 68999999999999999999999999999999999 99999999 58853
Q ss_pred CCCC----CCCCceEEEEEEEecCC-------CCCCchHHHHHHHHHHHhhhhhhc-CCCCCcEEEEEEEEEecCCCchh
Q 024064 80 GTKK----NENPEKASIEVIWKPRT-------GQIGKPEKEYEIILKRTLQSICIL-TINPNTTTSVIIQVVHDDGALLP 147 (273)
Q Consensus 80 ~~~~----~~~~~~~~l~v~~~p~~-------g~~~~~~~~l~~~l~~~l~s~i~~-~~~p~~~I~i~v~Vl~~dG~ll~ 147 (273)
.++. .+...++.+++++.|++ |++++++.+++++++|+|++++.. +.|| |.|+|+++||++|||..+
T Consensus 362 ~~~~~~~~~~~~~~~~~~y~~~pfs~~e~~~~~~~~rre~~~~~li~ral~~vi~~~~~~p-~~I~v~~~VLe~dGs~~~ 440 (693)
T PRK11824 362 EQIIDGLEGEYKKRFMLHYNFPPYSVGETGRVGSPGRREIGHGALAERALEPVLPSEEEFP-YTIRVVSEILESNGSSSM 440 (693)
T ss_pred cccccccCCCCcEEEEEEEEcCCCCCCCcCCCCCCChhHHHHHHHHHHHHHHhcCcccCCC-EEEEEEEEEEecCCCHHH
Confidence 2221 12234577788888964 235678889999999999999987 5777 799999999999999999
Q ss_pred HHHHHHHHHHHhCCCCcccceeEEEEEEeeCC---eEEeCCCHHHHhhccccEEEEecCCcccccCCCCccccCCccccc
Q 024064 148 CAINAACAALVDAGIPMKHLAVAICCCSAESG---YCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHG 224 (273)
Q Consensus 148 a~inAa~lAL~dagIp~~~~~~avsv~~~~~~---~~ilDPt~~Ee~~~~~~~~va~~~~~~~~~~~~~~~~~~~~~~~~ 224 (273)
|+++|+++||+||||||+++++++++|+..++ .+++||+..|+..++..++++.+. ++
T Consensus 441 Aai~aaslAL~dAgvP~~~~Va~vs~gli~~~~~~~il~D~~~~Ed~~~d~d~~va~t~-------------------~g 501 (693)
T PRK11824 441 ASVCGSSLALMDAGVPIKAPVAGIAMGLIKEGDKYAVLTDILGDEDHLGDMDFKVAGTR-------------------DG 501 (693)
T ss_pred HHHHHHHHHHHhcCCCccCceeEEEEEEEcCCCceEEEcCCChhhHhhCCceEEEEecC-------------------Cc
Confidence 99999999999999999999999999998543 489999999999999999998752 45
Q ss_pred eEEEEec---CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 024064 225 IITSVTH---GAMSVDDYFHCLERGRAASAKLSDFLRRSLQSK 264 (273)
Q Consensus 225 ~v~~~~~---G~~~~~~~~~~l~~A~~~~~~i~~~i~~~l~~~ 264 (273)
++.++.+ |.++.+.+.++++.|++++.+|++.|++++.+.
T Consensus 502 i~~lq~d~k~~~i~~~~l~~al~~a~~g~~~I~~~M~~aI~~~ 544 (693)
T PRK11824 502 ITALQMDIKIDGITREILEEALEQAKEGRLHILGKMNEAISEP 544 (693)
T ss_pred eEEEEEecccCCcCHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 4445544 468999999999999999999999999999754
No 11
>COG2123 RNase PH-related exoribonuclease [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.3e-35 Score=262.23 Aligned_cols=211 Identities=24% Similarity=0.356 Sum_probs=183.3
Q ss_pred CCCCCCCCCCCCCcccEEEeCCCCCCCceEEEEeCcccccccccccccceeeccccccccccCCCCcEEEEEEEcccCCC
Q 024064 2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGFRFIQTSHFYHFNLFVFTSKCYFCYWVGSGDTKVLAAVYGPKAGT 81 (273)
Q Consensus 2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~~~~~~~~~~~~~~~~~~~~~~g~~~~~~g~T~Vl~~V~gp~~~~ 81 (273)
++.|.|||.++|+|++.|++|+++.++|||+|++| +|+|+|+|+... .+
T Consensus 21 ~g~R~DGR~~~efR~ieI~~~vi~ka~GSa~VklG------------------------------~Tqvv~gvK~ei-g~ 69 (272)
T COG2123 21 KGIRIDGRSFDEFRPLEIETGVIPKANGSALVKLG------------------------------NTQVVVGVKAEI-GE 69 (272)
T ss_pred cCcccCCCCcccccceEEEeCceecCCCcEEEEec------------------------------CeEEEEEEEccc-CC
Confidence 57899999999999999999999999999999999 999999998766 44
Q ss_pred CCCCCCceEE--EEEEEecC------CCCCCchHHHHHHHHHHHhhh--------hhhcCCCCCcEEEEEEEEEecCCCc
Q 024064 82 KKNENPEKAS--IEVIWKPR------TGQIGKPEKEYEIILKRTLQS--------ICILTINPNTTTSVIIQVVHDDGAL 145 (273)
Q Consensus 82 ~~~~~~~~~~--l~v~~~p~------~g~~~~~~~~l~~~l~~~l~s--------~i~~~~~p~~~I~i~v~Vl~~dG~l 145 (273)
|..+.|+++. +++++.|. .|+++..+.+++++++|.++. +|+..+...|.+.++++||++|||+
T Consensus 70 Pf~DtP~eG~~~~n~El~Plas~~fE~Gppde~aielsrvvdr~lr~s~aiDlekL~I~~g~kvwvv~vDv~vld~DGnl 149 (272)
T COG2123 70 PFPDTPNEGVLVVNVELSPLASPSFEPGPPDELAIELSRVVDRGLRESKAIDLEKLCIEEGKKVWVVFVDVHVLDYDGNL 149 (272)
T ss_pred CCCCCCCCceEEeeeeeeccccccccCCCCchhHHHHHHHHHHHHHhccCcchhheeEecCCEEEEEEEEEEEEcCCCCH
Confidence 5677888864 57888884 467777788999999999865 4555566789999999999999999
Q ss_pred hhHHHHHHHHHHHhCCCC----------------------cccceeEEEEEEeeCCeEEeCCCHHHHhhccccEEEEecC
Q 024064 146 LPCAINAACAALVDAGIP----------------------MKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPN 203 (273)
Q Consensus 146 l~a~inAa~lAL~dagIp----------------------~~~~~~avsv~~~~~~~~ilDPt~~Ee~~~~~~~~va~~~ 203 (273)
+||++.|+++||.++++| +.++|.++|++.. ++.+++|||.+||..+++.+++.+++
T Consensus 150 ~Da~~lA~~aAL~~t~vP~~~~~~~~~~v~~~~~~~~pl~~~~~pi~vt~a~i-g~~lvvDPsleEe~v~d~~ltit~~~ 228 (272)
T COG2123 150 IDAASLAAVAALLNTRVPKAVEVGDGEIVIEVEEEPVPLPVSNPPISVTFAKI-GNVLVVDPSLEEELVADGRLTITVNE 228 (272)
T ss_pred HHHHHHHHHHHHHhcCCCceeecCCcceeecccCCCcccccCCCceEEEEEEE-CCEEEeCCCcchhhhcCceEEEEECC
Confidence 999999999999999988 4578899999987 89999999999999999999999875
Q ss_pred CcccccCCCCccccCCccccceEEEEe--cCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024064 204 SILSVLPEGSSLVQGEPMEHGIITSVT--HGAMSVDDYFHCLERGRAASAKLSDFLRRSLQ 262 (273)
Q Consensus 204 ~~~~~~~~~~~~~~~~~~~~~~v~~~~--~G~~~~~~~~~~l~~A~~~~~~i~~~i~~~l~ 262 (273)
+ ..++.++. .|.++++.+++|++.|.+.+.++.+.+.++|+
T Consensus 229 ~------------------~~Iv~iqK~g~~~~~~~~~~~~~~~A~~~~~kl~~~~~~~L~ 271 (272)
T COG2123 229 D------------------GEIVAIQKVGGGSITESDLEKALKTALSKAEKLREALKEALK 271 (272)
T ss_pred C------------------CcEEEEEEcCCCcCCHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 3 22344443 34899999999999999999999999999886
No 12
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=100.00 E-value=4.7e-34 Score=284.38 Aligned_cols=213 Identities=17% Similarity=0.214 Sum_probs=182.4
Q ss_pred CCCCCCCCCCCCCcccEEEeCCCCCCCceEEEEeCcccccccccccccceeeccccccccccCCCCcEEEEEEE-cccCC
Q 024064 2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGFRFIQTSHFYHFNLFVFTSKCYFCYWVGSGDTKVLAAVY-GPKAG 80 (273)
Q Consensus 2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~~~~~~~~~~~~~~~~~~~~~~g~~~~~~g~T~Vl~~V~-gp~~~ 80 (273)
++.|+|||.++|+|++.+++|++++++|||+++.| +|+|+|.+. ||.+.
T Consensus 333 ~g~R~DGR~~~eiR~i~~~~g~l~~a~GSa~~~~G------------------------------~Tqvl~~~tlG~~~~ 382 (719)
T TIGR02696 333 EGVRIDGRGVTDIRPLDAEVQVIPRVHGSALFERG------------------------------ETQILGVTTLNMLKM 382 (719)
T ss_pred CCCCCCCCCccccccceeecCCCCCCCceEEEEec------------------------------CcEEEEEEeCCCchh
Confidence 57899999999999999999999999999999999 999999976 44432
Q ss_pred CCCC-----CCCceEEEEEEEecCCC-------CCCchHHHHHHHHHHHhhhhhh-cCCCCCcEEEEEEEEEecCCCchh
Q 024064 81 TKKN-----ENPEKASIEVIWKPRTG-------QIGKPEKEYEIILKRTLQSICI-LTINPNTTTSVIIQVVHDDGALLP 147 (273)
Q Consensus 81 ~~~~-----~~~~~~~l~v~~~p~~g-------~~~~~~~~l~~~l~~~l~s~i~-~~~~p~~~I~i~v~Vl~~dG~ll~ 147 (273)
.... +...++.++++|.||+. .+++++.+++++++|+|+++|. ++.||++ |.+..+||++||+...
T Consensus 383 ~q~~~~l~~~~~~~~~~~YnfpPFSt~er~~~~~~~RReighg~La~rALe~vI~~~e~fP~T-IrvvseVLeSdGSss~ 461 (719)
T TIGR02696 383 EQQIDSLSPETSKRYMHHYNFPPYSTGETGRVGSPKRREIGHGALAERALVPVLPSREEFPYA-IRQVSEALGSNGSTSM 461 (719)
T ss_pred hhhcccccccccceEEEEEeCCCCcccCCCCCCCCCccHHHHHHHHHHHHHHhhCcHhhCCCE-EEEEEEeeccCCcHHH
Confidence 2111 12234678899999862 3467899999999999999998 6999988 8888999999999999
Q ss_pred HHHHHHHHHHHhCCCCcccceeEEEEEEeeC---Ce----EEeCCCHHHHhhccccEEEEecCCcccccCCCCccccCCc
Q 024064 148 CAINAACAALVDAGIPMKHLAVAICCCSAES---GY----CILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEP 220 (273)
Q Consensus 148 a~inAa~lAL~dagIp~~~~~~avsv~~~~~---~~----~ilDPt~~Ee~~~~~~~~va~~~~~~~~~~~~~~~~~~~~ 220 (273)
|++||+++||+||||||+++++|+++|+..+ +. +++||+..|+...+..+.++.+
T Consensus 462 AsIcaasLALmDAGVPmkd~VAgis~Gli~e~~~~~~~~~iL~Di~g~ED~~Gdmdfkvagt------------------ 523 (719)
T TIGR02696 462 GSVCASTLSLLNAGVPLKAPVAGIAMGLISDEVDGETRYVALTDILGAEDAFGDMDFKVAGT------------------ 523 (719)
T ss_pred HHHHHHHHHHHHcCcchhheeeEEEEEEeccccCCCcceeEEeCCCchhhhcCCceEEEEec------------------
Confidence 9999999999999999999999999998744 33 8999999999998877777654
Q ss_pred cccceEEEEecCC---CCHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 024064 221 MEHGIITSVTHGA---MSVDDYFHCLERGRAASAKLSDFLRRSLQSK 264 (273)
Q Consensus 221 ~~~~~v~~~~~G~---~~~~~~~~~l~~A~~~~~~i~~~i~~~l~~~ 264 (273)
.+++..++.+|. ++.+.+.+++++|.+++.+|+++|+++|...
T Consensus 524 -~~gIt~lQmd~ki~gi~~e~l~~aL~~A~~g~~~Il~~m~~al~~p 569 (719)
T TIGR02696 524 -SEFVTALQLDTKLDGIPASVLASALKQARDARLAILDVMAEAIDTP 569 (719)
T ss_pred -CCCEEEEEEEeeECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhCc
Confidence 245555666664 5999999999999999999999999999987
No 13
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=100.00 E-value=1.9e-33 Score=285.14 Aligned_cols=213 Identities=23% Similarity=0.327 Sum_probs=182.8
Q ss_pred CCCCCCCCCCCCCcccEEEeCCCCCCCceEEEEeCcccccccccccccceeeccccccccccCCCCcEEEEEEE-cccCC
Q 024064 2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGFRFIQTSHFYHFNLFVFTSKCYFCYWVGSGDTKVLAAVY-GPKAG 80 (273)
Q Consensus 2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~~~~~~~~~~~~~~~~~~~~~~g~~~~~~g~T~Vl~~V~-gp~~~ 80 (273)
++.|+|||+++|+|++.+++|++++++|||+|++| +|+|+|+|+ ||++.
T Consensus 436 ~g~R~DGR~~~eiRpI~~e~G~Lp~A~GSAlf~~G------------------------------~TqVLatVtlGp~~~ 485 (891)
T PLN00207 436 GGKRSDGRTPDEIRPINSSCGLLPRAHGSALFTRG------------------------------ETQALAVVTLGDKQM 485 (891)
T ss_pred CCCCCCCCCcCccceEEEEeCCcCCCCceEEEEEC------------------------------CeEEEEEEEecCccc
Confidence 68999999999999999999999999999999999 999999995 88854
Q ss_pred CCCCC------CCceEEEEEEEecCC-------CCCCchHHHHHHHHHHHhhhhhhcC-CCCCcEEEEEEEEEecCCCch
Q 024064 81 TKKNE------NPEKASIEVIWKPRT-------GQIGKPEKEYEIILKRTLQSICILT-INPNTTTSVIIQVVHDDGALL 146 (273)
Q Consensus 81 ~~~~~------~~~~~~l~v~~~p~~-------g~~~~~~~~l~~~l~~~l~s~i~~~-~~p~~~I~i~v~Vl~~dG~ll 146 (273)
....+ ...++.++++|.|++ |++++++.+++++++|+|+++|..+ .|| |.|+|+++||++||+..
T Consensus 486 ~q~~d~l~~~~~~~~f~~~y~fPPfs~ge~~r~g~psrREi~hg~L~eRALrpvip~~~~fP-~tIrV~~~VLesDGSss 564 (891)
T PLN00207 486 AQRIDNLVDADEVKRFYLQYSFPPSCVGEVGRIGAPSRREIGHGMLAERALEPILPSEDDFP-YTIRVESTITESNGSSS 564 (891)
T ss_pred cccccccccccceeeEEEEEEcCCCCCccccCCCCCCHHHHHHHHHHHHHHHHhCCcccCCC-EEEEEEEEEEeCCCChH
Confidence 32211 234577899999965 2346778889999999999999885 788 79999999999999999
Q ss_pred hHHHHHHHHHHHhCCCCcccceeEEEEEEeeC-------Ce--EEeCCCHHHHhhccccEEEEecCCcccccCCCCcccc
Q 024064 147 PCAINAACAALVDAGIPMKHLAVAICCCSAES-------GY--CILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQ 217 (273)
Q Consensus 147 ~a~inAa~lAL~dagIp~~~~~~avsv~~~~~-------~~--~ilDPt~~Ee~~~~~~~~va~~~~~~~~~~~~~~~~~ 217 (273)
.|++||+++||+||||||+++++++++|+..+ +. +++||+..|+..++..+.++.+
T Consensus 565 mAaV~aaSLALmDAGIPmk~~VAGvsvGli~d~~~~~~~g~~~IL~Dp~g~Ed~~gdmDfkVAgT--------------- 629 (891)
T PLN00207 565 MASVCGGCLALQDAGVPVKCPIAGIAMGMVLDTEEFGGDGSPLILSDITGSEDASGDMDFKVAGN--------------- 629 (891)
T ss_pred HHHHHHHHHHHHhcCCCccCceeEEEEEEEecccccCCCCcEEEEeCCCHHHHhcCCceEEEEec---------------
Confidence 99999999999999999999999999999732 23 5679999999999888888754
Q ss_pred CCccccceEEEEecC---CCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 024064 218 GEPMEHGIITSVTHG---AMSVDDYFHCLERGRAASAKLSDFLRRSLQSK 264 (273)
Q Consensus 218 ~~~~~~~~v~~~~~G---~~~~~~~~~~l~~A~~~~~~i~~~i~~~l~~~ 264 (273)
.++++.++..+ .++.+.+.++++.|++++.+|.+.|++++...
T Consensus 630 ----~~gIt~iqmd~k~~gis~e~l~eAL~~A~~g~~~Il~~M~~~i~~p 675 (891)
T PLN00207 630 ----EDGITAFQMDIKVGGITLPIMERALLQAKDGRKHILAEMSKCSPPP 675 (891)
T ss_pred ----ccceEEEEEecccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 24555555543 57999999999999999999999999998654
No 14
>KOG1614 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp45 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.8e-33 Score=244.16 Aligned_cols=213 Identities=22% Similarity=0.336 Sum_probs=184.5
Q ss_pred CCCCCCCCCCCCCcccEEEeCCCCCCCceEEEEeCcccccccccccccceeeccccccccccCCCCcEEEEEEEcccCCC
Q 024064 2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGFRFIQTSHFYHFNLFVFTSKCYFCYWVGSGDTKVLAAVYGPKAGT 81 (273)
Q Consensus 2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~~~~~~~~~~~~~~~~~~~~~~g~~~~~~g~T~Vl~~V~gp~~~~ 81 (273)
.++|.|||++.|+|.+.+++|- -.||+.+++| +|+|+|.|+... .+
T Consensus 20 ~g~R~DgR~l~efR~lei~fGk---e~gs~~vt~G------------------------------~Tkvm~~vt~~i-a~ 65 (291)
T KOG1614|consen 20 AGLRFDGRSLEEFRDLEIEFGK---EYGSVLVTMG------------------------------NTKVMARVTAQI-AQ 65 (291)
T ss_pred hcccccccchhhhhceEEEecc---ccccEEEEec------------------------------CeeEEEEeehhh-cC
Confidence 4789999999999999999984 5688888888 999999999876 55
Q ss_pred CCCCCCceE--EEEEEEecCC------CCCCchHHHHHHHHHHHh--------hhhhhcCCCCCcEEEEEEEEEecCCCc
Q 024064 82 KKNENPEKA--SIEVIWKPRT------GQIGKPEKEYEIILKRTL--------QSICILTINPNTTTSVIIQVVHDDGAL 145 (273)
Q Consensus 82 ~~~~~~~~~--~l~v~~~p~~------g~~~~~~~~l~~~l~~~l--------~s~i~~~~~p~~~I~i~v~Vl~~dG~l 145 (273)
|..++|+++ .|.++++|++ |+.+..+.++.++|++++ |++|+......|.|++++++|+.|||+
T Consensus 66 Py~dRP~eG~~~I~telsPmA~~sfE~Gr~~~~~v~l~Rliek~~R~S~aiD~EsLCI~aG~kvW~IRiDlhiLd~DGnl 145 (291)
T KOG1614|consen 66 PYIDRPHEGSFSIFTELSPMASPSFEPGRKGESEVELSRLIEKALRRSKAIDTESLCIRAGEKVWLIRIDLHILDHDGNL 145 (291)
T ss_pred cccCCCCCCeeeeeeccccccccccCCCCccchHHHHHHHHHHHHHhccccchHHHHhhhCCeEEEEEEEEEEEcCCCCe
Confidence 677889886 4678888864 566777889999999997 567888888899999999999999999
Q ss_pred hhHHHHHHHHHHHhCC-----------------------CCcccceeEEEEEEeeCC-eEEeCCCHHHHhhccccEEEEe
Q 024064 146 LPCAINAACAALVDAG-----------------------IPMKHLAVAICCCSAESG-YCILDPTKLEEQKMKGFAYLVF 201 (273)
Q Consensus 146 l~a~inAa~lAL~dag-----------------------Ip~~~~~~avsv~~~~~~-~~ilDPt~~Ee~~~~~~~~va~ 201 (273)
+|||+.|+++||++.+ +-|+|+|+|++|+++.+| .+++|||..||..+++.+++++
T Consensus 146 vDaA~iAviaaL~hFrrPdvTv~g~ev~ihp~eEr~PvPL~I~HmPIC~tf~ffnkG~ivviDpt~~Ee~~~dGs~vVt~ 225 (291)
T KOG1614|consen 146 VDAACIAVIAALMHFRRPDVTVGGEEVIIHPVEEREPVPLSIHHMPICFTFGFFNKGEIVVIDPTEKEEAVMDGSMVVTM 225 (291)
T ss_pred ehhHHHHHHHHHHhcCCCCcccccceeEecChhccCCcceeeeeccceEEEEEecCceEEEeCCcHHHHhccCceEEEEE
Confidence 9999999999999999 337899999999999654 7899999999999999999999
Q ss_pred cCCcccccCCCCccccCCccccceEEEE-ecC--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccC
Q 024064 202 PNSILSVLPEGSSLVQGEPMEHGIITSV-THG--AMSVDDYFHCLERGRAASAKLSDFLRRSLQSKLPG 267 (273)
Q Consensus 202 ~~~~~~~~~~~~~~~~~~~~~~~~v~~~-~~G--~~~~~~~~~~l~~A~~~~~~i~~~i~~~l~~~~~~ 267 (273)
++ +++||.+ +.| .++..+++.|.+.|.+.+.++...+.++|+++..+
T Consensus 226 Nk-------------------~rEVc~i~k~G~~~~~~~~i~~C~k~A~~~a~~vt~ii~e~l~~d~~~ 275 (291)
T KOG1614|consen 226 NK-------------------NREVCAIQKSGGEILDESVIERCYKLAKDRAVEVTGIILEALEEDQRE 275 (291)
T ss_pred cC-------------------CccEEEEecCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 74 4556554 445 67899999999999999999999999999876543
No 15
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=99.97 E-value=1.3e-29 Score=255.44 Aligned_cols=197 Identities=19% Similarity=0.205 Sum_probs=167.5
Q ss_pred cccEEEeCCC-CCCCceEEEEeCcccccccccccccceeeccccccccccCCCCcEEEEEEEcccCCCCCCCCCceEEEE
Q 024064 15 RPLACSCSIL-HRAHGSASWSQGFRFIQTSHFYHFNLFVFTSKCYFCYWVGSGDTKVLAAVYGPKAGTKKNENPEKASIE 93 (273)
Q Consensus 15 R~i~i~~~~l-~~a~GSa~v~~G~~~~~~~~~~~~~~~~~~~~~~g~~~~~~g~T~Vl~~V~gp~~~~~~~~~~~~~~l~ 93 (273)
|++.+++|.+ ++|+|||++++| +|+|+|+|+||+++++ ..+.+.++
T Consensus 5 R~i~ie~G~la~~AdGSa~v~~G------------------------------~T~VlatV~~~~~~~~---~~df~pL~ 51 (684)
T TIGR03591 5 RTLTLETGKIARQADGAVVVRYG------------------------------DTVVLVTVVAAKEAKE---GQDFFPLT 51 (684)
T ss_pred ccEEEEECCcCCCCCeEEEEEEC------------------------------CeEEEEEEEcCCCCCC---CCceEeEE
Confidence 7999999999 579999999999 9999999999987432 34678888
Q ss_pred EEEecC--------------CCCCCchHHHHHHHHHHHhhhhhhcCCCCCcEEEEEEEEEecCCCch-h-HHHHHHHHHH
Q 024064 94 VIWKPR--------------TGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALL-P-CAINAACAAL 157 (273)
Q Consensus 94 v~~~p~--------------~g~~~~~~~~l~~~l~~~l~s~i~~~~~p~~~I~i~v~Vl~~dG~ll-~-a~inAa~lAL 157 (273)
|+|.+. .|++++++.+++++|+|+|++++... | .|.|+|+++||++||+.. + ||+|||++||
T Consensus 52 vey~e~~~A~gkipg~f~kReg~p~~~eil~srlIdR~lrplfp~~-~-~~~i~V~~~VLs~Dg~~~~d~aai~aAsaAL 129 (684)
T TIGR03591 52 VNYQEKFYAAGKIPGGFFKREGRPSEKETLTSRLIDRPIRPLFPKG-F-RNEVQVVATVLSYDPENDPDILAIIGASAAL 129 (684)
T ss_pred EEEEehhhhccCCCCCcccCCCCCCHHHHHHHHHHhhHHHHhcCCC-C-CceEEEEEEEEecCcCCchHHHHHHHHHHHH
Confidence 998742 25677788899999999999964322 1 299999999999999985 4 9999999999
Q ss_pred HhCCCCcccceeEEEEEEeeCCeEEeCCCHHHHhhccccEEEEecCCcccccCCCCccccCCccccceEEEEecC-CCCH
Q 024064 158 VDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTHG-AMSV 236 (273)
Q Consensus 158 ~dagIp~~~~~~avsv~~~~~~~~ilDPt~~Ee~~~~~~~~va~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~G-~~~~ 236 (273)
.+++|||+++++|+++|+. +|.+++|||.+|++.++..++++.+ .+.++++...| .+++
T Consensus 130 ~~s~IP~~~~v~av~vg~i-dg~~ildPt~~E~~~s~~~l~va~t-------------------~~~i~mie~~~~~i~e 189 (684)
T TIGR03591 130 AISGIPFNGPIAAVRVGYI-DGQYVLNPTVDELEKSDLDLVVAGT-------------------KDAVLMVESEAKELSE 189 (684)
T ss_pred HhcCCCcCCCeEEEEEEEE-CCEEEEcCCHHHHhhCCceEEEEcc-------------------CCcEEEEEcCCCCCCH
Confidence 9999999999999999987 8999999999999999988888743 12344444444 6999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Q 024064 237 DDYFHCLERGRAASAKLSDFLRRSLQSKLP 266 (273)
Q Consensus 237 ~~~~~~l~~A~~~~~~i~~~i~~~l~~~~~ 266 (273)
+++.++++.|+++++++.+++++.+++...
T Consensus 190 ~~l~~al~~a~~~~~~i~~~~~~~~~~~~~ 219 (684)
T TIGR03591 190 EVMLGAIEFGHEEIQPVIEAIEELAEEAGK 219 (684)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 999999999999999999999998876653
No 16
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=99.97 E-value=4.6e-29 Score=251.83 Aligned_cols=197 Identities=20% Similarity=0.198 Sum_probs=169.1
Q ss_pred CcccEEEeCCCC-CCCceEEEEeCcccccccccccccceeeccccccccccCCCCcEEEEEEEcccCCCCCCCCCceEEE
Q 024064 14 LRPLACSCSILH-RAHGSASWSQGFRFIQTSHFYHFNLFVFTSKCYFCYWVGSGDTKVLAAVYGPKAGTKKNENPEKASI 92 (273)
Q Consensus 14 ~R~i~i~~~~l~-~a~GSa~v~~G~~~~~~~~~~~~~~~~~~~~~~g~~~~~~g~T~Vl~~V~gp~~~~~~~~~~~~~~l 92 (273)
-|++.+++|.+. +|+|||++++| +|+|+|+|++|++++ ...+.+.+
T Consensus 13 ~r~i~~e~G~ia~qAdGSa~v~~G------------------------------~T~VlatV~~~~~~~---~~~df~pL 59 (693)
T PRK11824 13 GRTLTLETGKLARQANGAVLVRYG------------------------------DTVVLVTVVASKEPK---EGQDFFPL 59 (693)
T ss_pred CccEEEEECCcCCCCCeEEEEEEC------------------------------CeEEEEEEEcCCCCC---CCCCeeee
Confidence 489999999995 69999999999 999999999999742 23567888
Q ss_pred EEEEecC--------------CCCCCchHHHHHHHHHHHhhhhhhcCCCCCcEEEEEEEEEecCCCc-hh-HHHHHHHHH
Q 024064 93 EVIWKPR--------------TGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGAL-LP-CAINAACAA 156 (273)
Q Consensus 93 ~v~~~p~--------------~g~~~~~~~~l~~~l~~~l~s~i~~~~~p~~~I~i~v~Vl~~dG~l-l~-a~inAa~lA 156 (273)
+|+|.+. .|++++++.+++++|+|+|++++. ..++|.|+|+++||++||+. .+ ||+|||++|
T Consensus 60 ~v~y~e~~~A~gkiP~~f~kreg~pse~eil~srlIdR~lrplfp--~~~~~~i~I~~~VL~~Dg~~~~d~aai~aAsaA 137 (693)
T PRK11824 60 TVDYEEKTYAAGKIPGGFFKREGRPSEKETLTSRLIDRPIRPLFP--KGFRNEVQVVATVLSVDPENDPDILAMIGASAA 137 (693)
T ss_pred EEEEEehhhhccCCCcccccCCCCCChHHHHHHHHHhhhHHHhCC--CCCCeEEEEEEEEEeCCCCCcHHHHHHHHHHHH
Confidence 8888742 256777889999999999999754 33589999999999999976 44 899999999
Q ss_pred HHhCCCCcccceeEEEEEEeeCCeEEeCCCHHHHhhccccEEEEecCCcccccCCCCccccCCccccceEEEEecC-CCC
Q 024064 157 LVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTHG-AMS 235 (273)
Q Consensus 157 L~dagIp~~~~~~avsv~~~~~~~~ilDPt~~Ee~~~~~~~~va~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~G-~~~ 235 (273)
|.++||||+++++|+++|+. ++.+++|||.+|++.++..++++.+. ..++++...| .++
T Consensus 138 L~~s~IP~~~~v~av~vg~i-~g~~ivdPt~~E~~~s~~~l~va~t~-------------------~~i~mie~~~~~l~ 197 (693)
T PRK11824 138 LSISGIPFNGPIAAVRVGYI-DGEFVLNPTVEELEESDLDLVVAGTK-------------------DAVLMVESEAKELS 197 (693)
T ss_pred HHhcCCCcCCCeEEEEEEEE-CCEEEEcCCHHHHhhCcceEEEEEcc-------------------CceEEEECCCCCCC
Confidence 99999999999999999987 88999999999999999999888752 2333334444 699
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 024064 236 VDDYFHCLERGRAASAKLSDFLRRSLQSKL 265 (273)
Q Consensus 236 ~~~~~~~l~~A~~~~~~i~~~i~~~l~~~~ 265 (273)
++++.++++.|+++++++.+++++.+++.-
T Consensus 198 e~~l~~al~~a~~~~~~i~~~~~~~~~~~~ 227 (693)
T PRK11824 198 EEVMLEAIEFGHEAIQELIDAQEELAAEAG 227 (693)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 999999999999999999999999887655
No 17
>KOG1612 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp42 [Translation, ribosomal structure and biogenesis]
Probab=99.95 E-value=4.4e-26 Score=200.10 Aligned_cols=214 Identities=24% Similarity=0.301 Sum_probs=169.8
Q ss_pred CCCCCCCCCCCCCcccEEEeCCCCCCCceEEEEeCcccccccccccccceeeccccccccccCCCCcEEEEEEEcccCCC
Q 024064 2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGFRFIQTSHFYHFNLFVFTSKCYFCYWVGSGDTKVLAAVYGPKAGT 81 (273)
Q Consensus 2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~~~~~~~~~~~~~~~~~~~~~~g~~~~~~g~T~Vl~~V~gp~~~~ 81 (273)
+.+|.|||.++++|||.++++++++++|||+|++|. .|.|+++|+.... .
T Consensus 19 ~~iR~DGR~~~~~Rpi~vetdVlp~tNGSaRVk~g~-----------------------------~tdiivgVKaEvg-~ 68 (288)
T KOG1612|consen 19 PDIRNDGRSCHQFRPIEVETDVLPGTNGSARVKLGD-----------------------------GTDIIVGVKAEVG-S 68 (288)
T ss_pred cccccCCcCccccceEEEEeccccCCCCcEEEEecC-----------------------------CceEEEEEeeecc-C
Confidence 478999999999999999999999999999999991 4999999998774 3
Q ss_pred CCCCCCceEE--EEEEEecC-----CCCCCc-hHHHHHHHHHHHhhh---------hhhcCCCCCcEEEEEEEEEecCCC
Q 024064 82 KKNENPEKAS--IEVIWKPR-----TGQIGK-PEKEYEIILKRTLQS---------ICILTINPNTTTSVIIQVVHDDGA 144 (273)
Q Consensus 82 ~~~~~~~~~~--l~v~~~p~-----~g~~~~-~~~~l~~~l~~~l~s---------~i~~~~~p~~~I~i~v~Vl~~dG~ 144 (273)
+..+.|+++. +.|++.|. .||.+. ...++...|+++|.+ +.+.+. .+|.|.|++.||+.|||
T Consensus 69 ~~~~~p~egk~~~~VD~S~sasp~f~gRggde~~~eltsaLq~~l~~~~sgv~ls~L~lt~~-~~W~i~VDvlVi~s~gn 147 (288)
T KOG1612|consen 69 PDDETPVEGKYLFFVDCSPSASPQFQGRGGDELVEELTSALQRVLNSLGSGVDLSKLQLTPG-YCWKIYVDVLVISSDGN 147 (288)
T ss_pred ccccCCCCCeEEEEEEecCCcCccccCCChhhHHHHHHHHHHHHHhCcCcccchhheeccCC-eeEEEEEeEEEEecCCC
Confidence 4456666544 56777764 345433 235777777887766 122233 57999999999999999
Q ss_pred chhHHHHHHHHHHHhCCCCcc---------------------------cceeEEEEEEeeCCeEEeCCCHHHHhhccccE
Q 024064 145 LLPCAINAACAALVDAGIPMK---------------------------HLAVAICCCSAESGYCILDPTKLEEQKMKGFA 197 (273)
Q Consensus 145 ll~a~inAa~lAL~dagIp~~---------------------------~~~~avsv~~~~~~~~ilDPt~~Ee~~~~~~~ 197 (273)
+++|...|+.+||.+..+|-. .+|.-++++.. +..+++|||.+||.++.+.+
T Consensus 148 ~~dAiS~Ai~~AL~~T~lPkv~v~~dd~~~~~i~~s~~~Yd~~~~~~~~~P~ivtlskI-G~~~lVD~T~eEe~~a~s~l 226 (288)
T KOG1612|consen 148 LLDAISIAIYAALNNTRLPKVIVAFDDDGEVEILLSDEEYDLMVKLVENVPLIVTLSKI-GTNMLVDPTAEEESVANSGL 226 (288)
T ss_pred HHHHHHHHHHHHHhcccCCccccccccCCceeeccCcccchhhhhhcccCCEEEEEEee-cceEEccCCccHHHhhhcce
Confidence 999999999999999998832 13444566644 78999999999999999998
Q ss_pred EEEecCCcccccCCCCccccCCccccceEEEE---ecCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Q 024064 198 YLVFPNSILSVLPEGSSLVQGEPMEHGIITSV---THGAMSVDDYFHCLERGRAASAKLSDFLRRSLQSKLP 266 (273)
Q Consensus 198 ~va~~~~~~~~~~~~~~~~~~~~~~~~~v~~~---~~G~~~~~~~~~~l~~A~~~~~~i~~~i~~~l~~~~~ 266 (273)
.+.+.+ .+++++. ..|.+.++-+.+|++.++.-.+.++..+.+.|++.-.
T Consensus 227 ~Isv~a-------------------~givs~~r~VG~G~l~~s~i~~mle~~~~~~e~l~~~l~k~L~~~e~ 279 (288)
T KOG1612|consen 227 LISVSA-------------------GGIVSCTRSVGLGDLDPSSIPEMLEQGKAVVETLAPDLVKSLENEED 279 (288)
T ss_pred EEEEec-------------------CcceEEEEEecCCCCChhhHHHHHHHHHHHHHhhhHHHHHHhhhhhh
Confidence 888864 3455554 3567999999999999999999999999988876543
No 18
>PF01138 RNase_PH: 3' exoribonuclease family, domain 1 This Prosite family only includes Ribonuclease PH; InterPro: IPR001247 The PH (phosphorolytic) domain is responsible for 3'-5' exoribonuclease activity, although in some proteins this domain has lost its catalytic function. An active PH domain uses inorganic phosphate as a nucleophile, adding it across the phosphodiester bond between the end two nucleotides in order to release ribonucleoside 5'-diphosphate (rNDP) from the 3' end of the RNA substrate. PH domains can be found in bacterial/organelle RNases and PNPases (polynucleotide phosphorylases) [], as well as in archaeal and eukaryotic RNA exosomes [, ], the later acting as nano-compartments for the degradation or processing of RNA (including mRNA, rRNA, snRNA and snoRNA). Bacterial/organelle PNPases share a common barrel structure with RNA exosomes, consisting of a hexameric ring of PH domains that act as a degradation chamber, and an S1-domain/KH-domain containing cap that binds the RNA substrate (and sometimes accessory proteins) in order to regulate and restrict entry into the degradation chamber []. Unstructured RNA substrates feed in through the pore made by the S1 domains, are degraded by the PH domain ring, and exit as nucleotides via the PH pore at the opposite end of the barrel [, ]. This entry represents the phosphorolytic (PH) domain 1, which has a core 2-layer alpha/beta structure with a left-handed crossover, similar to that found in ribosomal protein S5. This domain is found in bacterial/organelle PNPases and in archaeal/eukaryotic exosomes []. More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; PDB: 2C38_G 2BR2_O 2C37_M 3L7Z_A 2JEB_A 2C39_A 2JEA_A 2JE6_A 3U1K_A 4AM3_B ....
Probab=99.95 E-value=2e-27 Score=192.93 Aligned_cols=121 Identities=43% Similarity=0.640 Sum_probs=108.1
Q ss_pred CCcccEEEeCCCCCCCceEEEEeCcccccccccccccceeeccccccccccCCCCcEEEEEEEcccCCCCCCCCC---ce
Q 024064 13 QLRPLACSCSILHRAHGSASWSQGFRFIQTSHFYHFNLFVFTSKCYFCYWVGSGDTKVLAAVYGPKAGTKKNENP---EK 89 (273)
Q Consensus 13 e~R~i~i~~~~l~~a~GSa~v~~G~~~~~~~~~~~~~~~~~~~~~~g~~~~~~g~T~Vl~~V~gp~~~~~~~~~~---~~ 89 (273)
|+|++.+++|++++++|||+|++| +|+|+|+|+||.+.+++.+.+ ..
T Consensus 1 e~R~i~i~~~~~~~a~GSa~v~~G------------------------------~T~V~~~V~~~~~~~~~~~~~~~~g~ 50 (132)
T PF01138_consen 1 ELRPISIETGVLPRADGSARVSLG------------------------------NTKVICSVKGPIEPPPSNERDDAEGR 50 (132)
T ss_dssp CBEEEEEEESSSSSSSEEEEEEET------------------------------TEEEEEEEEEEEEGCSCSTTSSSSEE
T ss_pred CCccEEEEeCCCCCCCeEEEEEEC------------------------------CeEEEEEEEecccccchhcccCCCce
Confidence 799999999999999999999999 999999999999875444422 33
Q ss_pred EEEEEEEecCC-------CCCCchHHHHHHHHHHHhhhhhhcCCCCCcEEEEEEEEEecCC-CchhHHHHHHHHHHHhCC
Q 024064 90 ASIEVIWKPRT-------GQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDG-ALLPCAINAACAALVDAG 161 (273)
Q Consensus 90 ~~l~v~~~p~~-------g~~~~~~~~l~~~l~~~l~s~i~~~~~p~~~I~i~v~Vl~~dG-~ll~a~inAa~lAL~dag 161 (273)
+.++|++.|++ |.++..+++++++|+++|++++.++.||+|.|+|+|+||++|| |+++|++||+++||+|+|
T Consensus 51 ~~v~v~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~i~v~v~vl~~dG~~~~~a~~~A~~~AL~~~~ 130 (132)
T PF01138_consen 51 LTVEVEFSPFASPSFRRGGRPDEEERELSSLLERALRSSILLEGYPRWQIHVDVQVLSDDGGNLLDAAINAACLALLDAG 130 (132)
T ss_dssp EEEEEEECCCGSTSSSSSSSTHHHHHHHHHHHHHHHHHTBSTTTTSSEEEEEEEEEEECSSSSHHHHHHHHHHHHHHHHT
T ss_pred EEEEEEeccccccccccccccchhHHHHHHHHhhhccccccccccCceEEEEEEEEEecCCCCHHHHHHHHHHHHHHhcC
Confidence 66778888865 3445678899999999999999999999999999999999999 999999999999999999
Q ss_pred CC
Q 024064 162 IP 163 (273)
Q Consensus 162 Ip 163 (273)
||
T Consensus 131 iP 132 (132)
T PF01138_consen 131 IP 132 (132)
T ss_dssp CS
T ss_pred CC
Confidence 98
No 19
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=99.94 E-value=2.2e-25 Score=226.64 Aligned_cols=197 Identities=17% Similarity=0.153 Sum_probs=169.7
Q ss_pred cccEEEeCCC-CCCCceEEEEeCcccccccccccccceeeccccccccccCCCCcEEEEEEEcccCCCCCCCCCceEEEE
Q 024064 15 RPLACSCSIL-HRAHGSASWSQGFRFIQTSHFYHFNLFVFTSKCYFCYWVGSGDTKVLAAVYGPKAGTKKNENPEKASIE 93 (273)
Q Consensus 15 R~i~i~~~~l-~~a~GSa~v~~G~~~~~~~~~~~~~~~~~~~~~~g~~~~~~g~T~Vl~~V~gp~~~~~~~~~~~~~~l~ 93 (273)
|++.+++|-+ .+|+||+.+++| +|.|+|+|....+. .+..+.+.|.
T Consensus 89 ~~~~~etG~~a~qA~gav~v~~g------------------------------~t~vl~t~~~~~~~---~~~~dF~PLt 135 (891)
T PLN00207 89 RHILVETGHIGRQASGSVTVTDG------------------------------ETIVYTSVCLADVP---SEPSDFFPLS 135 (891)
T ss_pred EEEEEEhhHHHHhCCCcEEEEEC------------------------------CeEEEEEEEeccCC---CCCCCcccee
Confidence 4799999988 579999999999 99999999765432 2345778899
Q ss_pred EEEec--------------CCCCCCchHHHHHHHHHHHhhhhhhcCCCCCcEEEEEEEEEecCCC--chhHHHHHHHHHH
Q 024064 94 VIWKP--------------RTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGA--LLPCAINAACAAL 157 (273)
Q Consensus 94 v~~~p--------------~~g~~~~~~~~l~~~l~~~l~s~i~~~~~p~~~I~i~v~Vl~~dG~--ll~a~inAa~lAL 157 (273)
|+|.. +.|+++..+..++++|+|+|++++..+.||+++|.+ +||++||+ ...+|+|||++||
T Consensus 136 V~y~Ek~~AaGkipggf~kREgrp~d~eiL~sRlIdR~lRPlfp~~~~~etQI~i--~VLsaDg~~~pd~~AInAASaAL 213 (891)
T PLN00207 136 VHYQERFSAAGRTSGGFFKREGRTKDHEVLICRLIDRPLRPTMPKGFYHETQILS--WVLSYDGLHSPDSLAVTAAGIAV 213 (891)
T ss_pred EeeeeehhhcCccCCceeccCCCCChHHHHHHHHHCccchhhccccCCCCcEEEE--EEEeeCCCCChhhHHHHHHHHHH
Confidence 99963 236778889999999999999999999999987755 99999998 6799999999999
Q ss_pred HhCCCCcccceeEEEEEEeeCCeEEeCCCHHHHhhccccEEEEecCCcccccCCCCccccCCccccceEEEEecC-CCCH
Q 024064 158 VDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTHG-AMSV 236 (273)
Q Consensus 158 ~dagIp~~~~~~avsv~~~~~~~~ilDPt~~Ee~~~~~~~~va~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~G-~~~~ 236 (273)
+++||||+++++|+++|+. +|.+|+|||..|++.++..++++.+. .++++++..| .+++
T Consensus 214 ~~SgIP~~gpVaAVrVG~i-dg~~VlnPt~~E~~~s~ldLvvagt~-------------------~~IvMIE~~a~e~se 273 (891)
T PLN00207 214 ALSEVPNLKAIAGVRVGLI-GGKFIVNPTTKEMEESELDLIMAGTD-------------------SAILMIEGYCNFLPE 273 (891)
T ss_pred HhhCCCccCceEEEEEEEE-CCEEEECCCHHHHhcCCeeEEEEEcC-------------------CeEEEEEcCCCCCCH
Confidence 9999999999999999986 99999999999999998888777642 3455566666 5699
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Q 024064 237 DDYFHCLERGRAASAKLSDFLRRSLQSKLP 266 (273)
Q Consensus 237 ~~~~~~l~~A~~~~~~i~~~i~~~l~~~~~ 266 (273)
++|.++++.|+++++++++++++.+++...
T Consensus 274 e~l~~Al~~a~~aik~i~~~~~el~~~~gk 303 (891)
T PLN00207 274 EKLLEAVEVGQDAVRAICKEIEVLVKKCGK 303 (891)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 999999999999999999999998876553
No 20
>KOG1613 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp43 [Translation, ribosomal structure and biogenesis]
Probab=99.92 E-value=2.4e-24 Score=187.99 Aligned_cols=207 Identities=22% Similarity=0.272 Sum_probs=160.9
Q ss_pred CCCCCCCCCCCCCcccEEEeCCCCCCCceEEEEeCcccccccccccccceeeccccccccccCCCCcEEEEEEEcccCCC
Q 024064 2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGFRFIQTSHFYHFNLFVFTSKCYFCYWVGSGDTKVLAAVYGPKAGT 81 (273)
Q Consensus 2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~~~~~~~~~~~~~~~~~~~~~~g~~~~~~g~T~Vl~~V~gp~~~~ 81 (273)
|++|+|||+..|+|.+.+..|.++++|||+.++.| +|.|+|+|.+....
T Consensus 34 e~~RpdgR~lgefRdt~in~g~IsTangSal~K~G------------------------------~ttvi~~Ik~ei~e- 82 (298)
T KOG1613|consen 34 EGIRPDGRKLGEFRDTAINAGNISTANGSALLKSG------------------------------KTTVICGIKAEIAE- 82 (298)
T ss_pred cccCcchhhhhHHhhhheecCceeccCcHHHHhcC------------------------------CcEEEEEeeeeecc-
Confidence 68999999999999999999999999999999999 99999999998843
Q ss_pred CCCCCCceEEE--EEEEecC------CCCCCchHHHHHHHHHHHhhh--------hhhcCCCCCcEEEEEEEEEecCCCc
Q 024064 82 KKNENPEKASI--EVIWKPR------TGQIGKPEKEYEIILKRTLQS--------ICILTINPNTTTSVIIQVVHDDGAL 145 (273)
Q Consensus 82 ~~~~~~~~~~l--~v~~~p~------~g~~~~~~~~l~~~l~~~l~s--------~i~~~~~p~~~I~i~v~Vl~~dG~l 145 (273)
+....|+++.| ++.+.|- .|+++..+.-++..|..++++ +|+..+.-.|.++.+|.+|++||++
T Consensus 83 pstdapdeg~Iv~n~~lpplcs~r~RpG~p~dea~viSq~LhdtIl~S~ii~~k~Lci~~gKaawvlYadIicLd~dG~~ 162 (298)
T KOG1613|consen 83 PSTDAPDEGDIVPNYALPPLCSSRFRPGPPTDEAQVISQKLHDTILHSRIIPKKALCIKAGKAAWVLYADIICLDYDGPV 162 (298)
T ss_pred cccCCCCCcceeecccCCcccccCCCCCCCchHHHHHHHHHHHHHHhcCCcchhhheeeccceeeEEEEEEEEEcCCCcH
Confidence 34567888765 5555563 466667777777777777654 3344444569999999999999999
Q ss_pred hhHHHHHHHHHHHhCCCCccc--------------cee----------------------EEEEE-EeeCCeEEeCCCHH
Q 024064 146 LPCAINAACAALVDAGIPMKH--------------LAV----------------------AICCC-SAESGYCILDPTKL 188 (273)
Q Consensus 146 l~a~inAa~lAL~dagIp~~~--------------~~~----------------------avsv~-~~~~~~~ilDPt~~ 188 (273)
+|+|.+|+++||..-.+|... ..+ ..|.. ++.+..++.|||.+
T Consensus 163 fDa~w~al~aAlknvklP~a~ide~~~~~~~t~e~~ic~~tlt~p~~ln~e~r~~~~~n~~fS~~~vl~~~li~adpT~e 242 (298)
T KOG1613|consen 163 FDACWNALMAALKNVKLPRAFIDERASDLRMTIEEIICDQTLTVPLMLNAENRAFASQNSDFSEEEVLDDVLIAADPTEE 242 (298)
T ss_pred HHHHHHHHHHHHhcCCCceeeecccchhhhhhHHHHHHhhhhcchhhhccccccccccCCCccHHHhhcceeEecCCCch
Confidence 999999999999999988321 000 11111 22234566999999
Q ss_pred HHhhccccEEEEecCCcccccCCCCccccCCccccceEEEEe--cC-CCCHHHHHHHHHHHHHHHHHHHHHH
Q 024064 189 EEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVT--HG-AMSVDDYFHCLERGRAASAKLSDFL 257 (273)
Q Consensus 189 Ee~~~~~~~~va~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~--~G-~~~~~~~~~~l~~A~~~~~~i~~~i 257 (273)
||..+++.++++++.+ .+.+.... +| ...++.++.|++.|+.+++++.+.+
T Consensus 243 EE~l~~~~lTIvldss------------------~n~v~l~k~GG~al~~~~~iK~c~elar~Rakelk~~~ 296 (298)
T KOG1613|consen 243 EETLITSTLTIVLDSS------------------GNYVQLTKVGGGALITPEMIKRCLELARVRAKELKTRF 296 (298)
T ss_pred hhhhhhceEEEEEcCC------------------CCEEEEEecCcccccCHHHHHHHHHHHHHHHHHHHHHh
Confidence 9999999999999864 33444443 22 5677999999999999999998765
No 21
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=99.83 E-value=4.6e-20 Score=176.78 Aligned_cols=217 Identities=22% Similarity=0.340 Sum_probs=170.9
Q ss_pred CCCCCCCCCCCCCcccEEEeCCCCCCCceEEEEeCcccccccccccccceeeccccccccccCCCCcEEEEEEEc-ccCC
Q 024064 2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGFRFIQTSHFYHFNLFVFTSKCYFCYWVGSGDTKVLAAVYG-PKAG 80 (273)
Q Consensus 2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~~~~~~~~~~~~~~~~~~~~~~g~~~~~~g~T~Vl~~V~g-p~~~ 80 (273)
+++|.|||..+|+|+|.|+.+.++..+||+.|+-| +|+|+|+|+. ..+.
T Consensus 356 ~gkR~DGR~ldelR~I~ce~~m~~~lHGSaLFqRG------------------------------qTQvlctVtl~s~e~ 405 (760)
T KOG1067|consen 356 EGKRCDGRDLDELRNISCEVDMLKTLHGSALFQRG------------------------------QTQVLCTVTLDSLES 405 (760)
T ss_pred cccccCCcchhhhcccceecCccccccchhhhhcC------------------------------ceeEEEEEEcCCHHH
Confidence 58999999999999999999999999999999999 9999999974 3322
Q ss_pred CCC-C--CCC---ceEEEEEEEecCC----C---CCCchHHHHHHHHHHHhhhhhhcCCCCCcEEEEEEEEEecCCCchh
Q 024064 81 TKK-N--ENP---EKASIEVIWKPRT----G---QIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLP 147 (273)
Q Consensus 81 ~~~-~--~~~---~~~~l~v~~~p~~----g---~~~~~~~~l~~~l~~~l~s~i~~~~~p~~~I~i~v~Vl~~dG~ll~ 147 (273)
..+ + ..+ -++.++++|.|.+ | ..++++.-...+-+++|.+++. +.|| +.|+|+-.||+.||+---
T Consensus 406 a~klD~l~~~~~~~~FmLhY~FPPyat~Evgkig~~nRRE~GhgaLAEkaL~~vlP-~dfP-ftIRv~SeVleSnGSsSM 483 (760)
T KOG1067|consen 406 AQKLDSLIGPDNGINFMLHYEFPPYATNEVGKIGGLNRRELGHGALAEKALLPVLP-EDFP-FTIRVTSEVLESNGSSSM 483 (760)
T ss_pred hhhhhhhccCccCceEEEEeccCCccccccccccCCcccccCchhHhhhhhhccCc-ccCc-eEEEEeeeeeecCCcchH
Confidence 111 1 112 2578999998853 3 3456777788889999999887 6677 889999999999999999
Q ss_pred HHHHHHHHHHHhCCCCcccceeEEEEEEeeCCeEEeCCCHHHHhhccccEEEEecCC-cccccCCCCccccCCccccceE
Q 024064 148 CAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNS-ILSVLPEGSSLVQGEPMEHGII 226 (273)
Q Consensus 148 a~inAa~lAL~dagIp~~~~~~avsv~~~~~~~~ilDPt~~Ee~~~~~~~~va~~~~-~~~~~~~~~~~~~~~~~~~~~v 226 (273)
|++.+-++||+|||+|++-.++++.+|+..+ .||...|.+...-. .+.. ....+.+|+|++.|. ++|+.
T Consensus 484 ASvCGGslALmDaGvPv~a~vAGvaiGlvt~----td~e~g~i~dyril----tDIlGiEd~~GDMDFKiAGt--~dGvT 553 (760)
T KOG1067|consen 484 ASVCGGSLALMDAGVPVSAHVAGVAIGLVTK----TDPEKGEIEDYRIL----TDILGIEDYNGDMDFKIAGT--NDGVT 553 (760)
T ss_pred HhhhcchhhhhhcCCccccccceeEEEeEec----cCcccCCcccceee----hhhcchhhhcCCcceeeccc--cCcce
Confidence 9999999999999999999999999998633 56666666654322 1211 134556677777775 34432
Q ss_pred EEEecCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 024064 227 TSVTHGAMSVDDYFHCLERGRAASAKLSDFLRRSLQSK 264 (273)
Q Consensus 227 ~~~~~G~~~~~~~~~~l~~A~~~~~~i~~~i~~~l~~~ 264 (273)
.. .++.+.+++.+..|..+-.+|.+.|.+.+...
T Consensus 554 A~----gi~l~Iv~eal~~a~~ar~~Il~~m~k~i~~P 587 (760)
T KOG1067|consen 554 AL----GIPLKIVMEALQKAREARLQILDIMEKNINSP 587 (760)
T ss_pred ec----CCcHHHHHHHHHhhhHHHHHHHHHHHhhcCCc
Confidence 22 68999999999999999999999999888643
No 22
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=99.80 E-value=5.8e-18 Score=169.57 Aligned_cols=206 Identities=16% Similarity=0.058 Sum_probs=162.8
Q ss_pred cccEEEeCCC-CCCCceEEEEe-CcccccccccccccceeeccccccccccCCCCcEEEEEEEcccCCCCCCCCCceEEE
Q 024064 15 RPLACSCSIL-HRAHGSASWSQ-GFRFIQTSHFYHFNLFVFTSKCYFCYWVGSGDTKVLAAVYGPKAGTKKNENPEKASI 92 (273)
Q Consensus 15 R~i~i~~~~l-~~a~GSa~v~~-G~~~~~~~~~~~~~~~~~~~~~~g~~~~~~g~T~Vl~~V~gp~~~~~~~~~~~~~~l 92 (273)
|++.+++|-+ .+|+||+.+++ | +|.|+|+|...++. .+..+.++|
T Consensus 17 ~~~~~etG~~A~qA~Gav~v~~~G------------------------------~t~vl~t~~~~~~~---~~~~dF~PL 63 (719)
T TIGR02696 17 RTIRFETGRLARQAAGSVVAYLDD------------------------------ETMLLSATTASKQP---KDQFDFFPL 63 (719)
T ss_pred EEEEEEcchhHhhCCceEEEEecC------------------------------CeEEEEEEEecCCC---CCCCCCcce
Confidence 4799999988 57999999999 9 99999999754432 334577899
Q ss_pred EEEEec--------------CCCCCCchHHHHHHHHHHHhhhhhhcCCCCCcEEEEEEEEEecCCCc--hhHHHHHHHHH
Q 024064 93 EVIWKP--------------RTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGAL--LPCAINAACAA 156 (273)
Q Consensus 93 ~v~~~p--------------~~g~~~~~~~~l~~~l~~~l~s~i~~~~~p~~~I~i~v~Vl~~dG~l--l~a~inAa~lA 156 (273)
.|+|+. +.|+|+..+...+|+|+|.|++++.... +..+||.++||+.|+.. --.++|||++|
T Consensus 64 tV~y~Ek~yA~GkiPggf~kREgrps~~eiL~sRliDR~iRPLFp~~~--~~e~qi~~~vls~D~~~~pdvla~~~ASaA 141 (719)
T TIGR02696 64 TVDVEERMYAAGRIPGSFFRREGRPSTDAILTCRLIDRPLRPSFVKGL--RNEVQVVVTVLSLNPDHLYDVVAINAASAS 141 (719)
T ss_pred eEeeeehhhhcCccCCceeccCCCCChhhhHHHHhhCCCCccCCCCCC--CcceEEEEEEEEcCCCCChHHHHHHHHHHH
Confidence 999963 2467888899999999999999887543 46788899999988853 55899999999
Q ss_pred HHhCCCCcccceeEEEEEEeeCCeEEeCCCHHHHhhccccEEEEecCC---c-ccccCCCCccccCCccccceEEEEecC
Q 024064 157 LVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNS---I-LSVLPEGSSLVQGEPMEHGIITSVTHG 232 (273)
Q Consensus 157 L~dagIp~~~~~~avsv~~~~~~~~ilDPt~~Ee~~~~~~~~va~~~~---~-~~~~~~~~~~~~~~~~~~~~v~~~~~G 232 (273)
|.-++||+...++|+.+|.. +|.++++||.+|.+.++..++++-+.+ . ..+|.|+....+-+ . .....+
T Consensus 142 l~iSdiPf~gPv~~vrVg~i-~g~~viNPt~~~~~~s~ldLvvagt~~~~~~~~i~MiE~~a~~~~~-----~-~~~~~a 214 (719)
T TIGR02696 142 TQLAGLPFSGPIGGVRVALI-DGQWVAFPTHEQLEGAVFDMVVAGRVLENGDVAIMMVEAEATEKTW-----D-LVKGGA 214 (719)
T ss_pred HHhcCCCCCCceEEEEEEEE-CCEEEECcCHHHHhhCeeeEEEEeeecCCCCccEEEEecCCccccc-----c-ccccCC
Confidence 99999999999999999986 999999999999999999999887642 1 33444321111000 0 000122
Q ss_pred -CCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024064 233 -AMSVDDYFHCLERGRAASAKLSDFLRRSLQ 262 (273)
Q Consensus 233 -~~~~~~~~~~l~~A~~~~~~i~~~i~~~l~ 262 (273)
.++++++.++++.|++.++.+.+++.+..+
T Consensus 215 ~e~~e~~~~~Ai~~a~~~i~~~~~~~~~l~~ 245 (719)
T TIGR02696 215 EAPTEEVVAEGLEAAKPFIKVLCRAQADLAE 245 (719)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 799999999999999999999999988543
No 23
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=99.72 E-value=4.3e-16 Score=153.55 Aligned_cols=195 Identities=21% Similarity=0.192 Sum_probs=165.0
Q ss_pred CcccEEEeCCC-CCCCceEEEEeCcccccccccccccceeeccccccccccCCCCcEEEEEEEcccCCCCCCCCCceEEE
Q 024064 14 LRPLACSCSIL-HRAHGSASWSQGFRFIQTSHFYHFNLFVFTSKCYFCYWVGSGDTKVLAAVYGPKAGTKKNENPEKASI 92 (273)
Q Consensus 14 ~R~i~i~~~~l-~~a~GSa~v~~G~~~~~~~~~~~~~~~~~~~~~~g~~~~~~g~T~Vl~~V~gp~~~~~~~~~~~~~~l 92 (273)
-|++.+++|.+ .+|+|++.+++| +|.|+++|.+.+ . .+..|.+.+
T Consensus 13 ~~~l~~etg~~A~qa~gav~~~~g------------------------------dt~vl~t~~~~~-~---~~~~dF~PL 58 (692)
T COG1185 13 GRTLTLETGKIARQANGAVLVRYG------------------------------DTVVLATVVASK-P---KEGQDFFPL 58 (692)
T ss_pred CeeEEEEcchhhhhcCccEEEEEC------------------------------CeEEEEEEeecC-C---CCCCCccce
Confidence 48999999988 579999999999 999999998766 2 344688889
Q ss_pred EEEEe---------c-----CCCCCCchHHHHHHHHHHHhhhhhhcCCCCCcEEEEEEEEEecCCCc--hhHHHHHHHHH
Q 024064 93 EVIWK---------P-----RTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGAL--LPCAINAACAA 156 (273)
Q Consensus 93 ~v~~~---------p-----~~g~~~~~~~~l~~~l~~~l~s~i~~~~~p~~~I~i~v~Vl~~dG~l--l~a~inAa~lA 156 (273)
.|+|. | +.|+|+..+...+++|+|.+++++.... +..++|..+|++.|+.. .-.+++++++|
T Consensus 59 tV~y~Ek~yaaGkiPGgf~kREGrpse~e~L~sRLIDRpiRPlFp~g~--~~evqIv~tvls~D~~~~pdi~a~~gaSaA 136 (692)
T COG1185 59 TVNYEEKTYAAGKIPGGFFKREGRPSEKEILTSRLIDRPIRPLFPKGF--RNEVQIVNTVLSVDPENDPDILAMVGASAA 136 (692)
T ss_pred eEeeeeehhccCcCCCcccccCCCCCccchhhhhhcccccccccchhh--ccceEEEEEEEEECCCCCHHHHHHHHHHHH
Confidence 99984 2 2478889999999999999999876433 57789999999999865 45899999999
Q ss_pred HHhCCCCcccceeEEEEEEeeCCeEEeCCCHHHHhhccccEEEEecCCcccccCCCCccccCCccccceEEEEecC--CC
Q 024064 157 LVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTHG--AM 234 (273)
Q Consensus 157 L~dagIp~~~~~~avsv~~~~~~~~ilDPt~~Ee~~~~~~~~va~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~G--~~ 234 (273)
|.-++||+...++++.+|+. +|.++++|+.+|.+.++..++++-++ . -|.++..| .+
T Consensus 137 l~is~iPf~gpi~~vrvg~i-dg~~vlNPt~~e~~~s~lDlvVAGT~-------------------~-aV~MVE~~a~~l 195 (692)
T COG1185 137 LSLSGIPFLGPIGAVRVGYI-DGIFVLNPTLEELEESKLDLVVAGTK-------------------D-AVNMVESEADEL 195 (692)
T ss_pred HhccCCCccCccceEEEEEE-CCEEEECCChHHhhhcceeeEecCCh-------------------h-hhheeecccccC
Confidence 99999999999999999987 99999999999999999888887653 2 23334333 78
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 024064 235 SVDDYFHCLERGRAASAKLSDFLRRSLQSKL 265 (273)
Q Consensus 235 ~~~~~~~~l~~A~~~~~~i~~~i~~~l~~~~ 265 (273)
+++++.+.+..+++..+.+.+++.+.....-
T Consensus 196 ~E~~ml~Av~fg~~~~~~~~~~qe~l~~~~g 226 (692)
T COG1185 196 DEEVMLEAVEFGHEAIQSVINAQEELALEVG 226 (692)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 8999999999999999999999988776544
No 24
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=99.71 E-value=1.1e-16 Score=157.64 Aligned_cols=215 Identities=21% Similarity=0.296 Sum_probs=169.9
Q ss_pred CCCCCCCCCCCCCcccEEEeCCCCCCCceEEEEeCcccccccccccccceeeccccccccccCCCCcEEEEEEE-ccc-C
Q 024064 2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGFRFIQTSHFYHFNLFVFTSKCYFCYWVGSGDTKVLAAVY-GPK-A 79 (273)
Q Consensus 2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~~~~~~~~~~~~~~~~~~~~~~g~~~~~~g~T~Vl~~V~-gp~-~ 79 (273)
.+.|+|||..++.||+.++.+++++++||+.|+.| .|..++.++ |+. +
T Consensus 310 ~~vR~DGR~~~~VRpi~~ev~~lpr~HGS~LFtRG------------------------------eTQal~v~TLG~~~d 359 (692)
T COG1185 310 GKVRIDGRFGDEVRPIGIEVGVLPRTHGSALFTRG------------------------------ETQALVVVTLGTPRD 359 (692)
T ss_pred CCcccCCCCcceeeeeeEEecCCCCccchhhhccC------------------------------CCcceEEEEcCCcch
Confidence 47899999999999999999999999999999999 888888775 332 3
Q ss_pred CCCC----CCCCceEEEEEEEecCC-------CCCCchHHHHHHHHHHHhhhhhhc-CCCCCcEEEEEEEEEecCCCchh
Q 024064 80 GTKK----NENPEKASIEVIWKPRT-------GQIGKPEKEYEIILKRTLQSICIL-TINPNTTTSVIIQVVHDDGALLP 147 (273)
Q Consensus 80 ~~~~----~~~~~~~~l~v~~~p~~-------g~~~~~~~~l~~~l~~~l~s~i~~-~~~p~~~I~i~v~Vl~~dG~ll~ 147 (273)
.+.- .+...++.++++|.|++ |.++++++-..++-+|++.+++.. +.|| +.|++.-.|++.+|+--.
T Consensus 360 ~Qvid~l~~e~~krfm~hYNFPp~SvGE~g~~g~p~RREiGHG~LA~Ral~~vlp~~e~fp-ytiRvVsEi~eSNGSsSm 438 (692)
T COG1185 360 AQVIDILEGEYKKRFLLHYNFPPFSVGETGRMGSPGRREIGHGALAERALAPVLPSEEEFP-YTIRVVSEILESNGSSSM 438 (692)
T ss_pred hhhhhhccchhhhheeeeccCCCCCccccCCCCCCCcccccCchhhHHHHhhhCCchhcCC-ceeeeeehhhcccCcccc
Confidence 3221 12345688899999986 246778888999999999999884 4555 889999999999999999
Q ss_pred HHHHHHHHHHHhCCCCcccceeEEEEEEeeCC---eEEeCCCHHHHhhccccEEEEecCCcccccCCCCccccCCccccc
Q 024064 148 CAINAACAALVDAGIPMKHLAVAICCCSAESG---YCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHG 224 (273)
Q Consensus 148 a~inAa~lAL~dagIp~~~~~~avsv~~~~~~---~~ilDPt~~Ee~~~~~~~~va~~~~~~~~~~~~~~~~~~~~~~~~ 224 (273)
|++++.++||+|||+|++..++++..|+..++ .++-|-.-.|....+-.+=|+ |. ..|
T Consensus 439 aSVCg~sLaLmdAGVPIk~pVAGIAMGLI~eg~~~~vLsDI~G~EDhlGDMDFKVA-----------------GT--~~G 499 (692)
T COG1185 439 ASVCGGSLALMDAGVPIKAPVAGIAMGLIKEGDKYAVLSDILGDEDHLGDMDFKVA-----------------GT--DDG 499 (692)
T ss_pred hhhhhhHHHHHhCCCcccccccchhccceecCCceEeeccccccccccCCceeEEe-----------------cC--CCc
Confidence 99999999999999999999999999987553 345555555533333333333 32 345
Q ss_pred eEEEEe---cCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Q 024064 225 IITSVT---HGAMSVDDYFHCLERGRAASAKLSDFLRRSLQSKLP 266 (273)
Q Consensus 225 ~v~~~~---~G~~~~~~~~~~l~~A~~~~~~i~~~i~~~l~~~~~ 266 (273)
+...++ -..++.+.+.+++..|+.+..++...|.+++.+.-.
T Consensus 500 iTAlQMDiKi~Git~eim~~AL~QAk~aRlhIL~~M~~ai~~pr~ 544 (692)
T COG1185 500 ITALQMDIKIKGITKEIMKKALEQAKGARLHILIVMNEAISEPRK 544 (692)
T ss_pred ceeeeeeeeecCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence 545543 357899999999999999999999999999987643
No 25
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=99.51 E-value=1.7e-13 Score=132.01 Aligned_cols=196 Identities=19% Similarity=0.206 Sum_probs=153.5
Q ss_pred CCcccEEEeCCCCC-CCceEEEEeCcccccccccccccceeeccccccccccCCCCcEEEEEEEcccCCCCCCCCCceEE
Q 024064 13 QLRPLACSCSILHR-AHGSASWSQGFRFIQTSHFYHFNLFVFTSKCYFCYWVGSGDTKVLAAVYGPKAGTKKNENPEKAS 91 (273)
Q Consensus 13 e~R~i~i~~~~l~~-a~GSa~v~~G~~~~~~~~~~~~~~~~~~~~~~g~~~~~~g~T~Vl~~V~gp~~~~~~~~~~~~~~ 91 (273)
--|.+.+++|.+.+ |+||+.+..| +|+|+++|..-..+. -+....
T Consensus 54 GnR~i~~etGklaRfAngsvvv~~G------------------------------eT~Vm~Tv~~a~~PS----p~qFlP 99 (760)
T KOG1067|consen 54 GNREILFETGKLARFANGSVVVQMG------------------------------ETAVMTTVVLADKPS----PPQFLP 99 (760)
T ss_pred CCeEEEEecchhhhhcCCcEEEccC------------------------------CeEEEEEEEecCCCC----ccccce
Confidence 35888899998864 8899988888 999999997543221 134677
Q ss_pred EEEEEecC--------------CCCCCchHHHHHHHHHHHhhhhhhcCCCCCcEEEEEEEEEecCCC--chhHHHHHHHH
Q 024064 92 IEVIWKPR--------------TGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGA--LLPCAINAACA 155 (273)
Q Consensus 92 l~v~~~p~--------------~g~~~~~~~~l~~~l~~~l~s~i~~~~~p~~~I~i~v~Vl~~dG~--ll~a~inAa~l 155 (273)
+.|.|.-. .|++...|....++|+|.+++.+....| ...++-..+|..||- .-.-++||+++
T Consensus 100 L~VdYqeK~aAvGRip~~fmRREg~tkdkEiL~~rLidrsirplfp~g~~--~etqi~~n~Ls~dG~~~pdvlainaas~ 177 (760)
T KOG1067|consen 100 LVVDYQEKFAAVGRIPGNFMRREGRTKDKEILTGRLIDRPIRPLFPKGFY--HETQILCNVLSSDGVHDPDVLAINAASA 177 (760)
T ss_pred EEEehhhhhhhhccCCCcccccccCCcchhheeeeccccccccCCcccch--hHHHHHhhheecccccCchHHHHhHHHH
Confidence 88888531 2344556677788899999988765544 344566677888884 35578999999
Q ss_pred HHHhCCCCcccceeEEEEEEeeCCeEEeCCCHHHHhhccccEEEEecCCcccccCCCCccccCCccccceEEEEecC-CC
Q 024064 156 ALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTHG-AM 234 (273)
Q Consensus 156 AL~dagIp~~~~~~avsv~~~~~~~~ilDPt~~Ee~~~~~~~~va~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~G-~~ 234 (273)
||.-+.||+...+.++.+|+. +|+++++||..|.+.++..++++.+. ..++++...+ .+
T Consensus 178 Al~lsdvpw~gpig~vRigLi-~Ge~vVNPT~kEmssS~Lnlvvagt~-------------------~~~vmle~~s~~i 237 (760)
T KOG1067|consen 178 ALSLSDVPWNGPIGAVRIGLI-DGEFVVNPTRKEMSSSQLNLVVAGTK-------------------SQTVMLEGSSNNI 237 (760)
T ss_pred HhhhccCCCCCceeeeEeeee-cceEEeCcchhhhhhccceeEEEecc-------------------ceEEEEEcccccc
Confidence 999999999999999999987 99999999999999999888887752 3455566544 78
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 024064 235 SVDDYFHCLERGRAASAKLSDFLRRSLQSK 264 (273)
Q Consensus 235 ~~~~~~~~l~~A~~~~~~i~~~i~~~l~~~ 264 (273)
.+++|.++++.+...++++..-|....+++
T Consensus 238 ~qqdl~~Aikvg~~~~q~~i~~i~~L~k~~ 267 (760)
T KOG1067|consen 238 LQQDLLHAIKVGVKEAQQIIQGIERLAKKY 267 (760)
T ss_pred cHHHHHHHHHhccHHHHHHHHHHHHHHHHh
Confidence 999999999999999999998887666543
No 26
>PF03725 RNase_PH_C: 3' exoribonuclease family, domain 2 This Prosite family only includes Ribonuclease PH; InterPro: IPR015847 The PH (phosphorolytic) domain is responsible for 3'-5' exoribonuclease activity, although in some proteins this domain has lost its catalytic function. An active PH domain uses inorganic phosphate as a nucleophile, adding it across the phosphodiester bond between the end two nucleotides in order to release ribonucleoside 5'-diphosphate (rNDP) from the 3' end of the RNA substrate. PH domains can be found in bacterial/organelle RNases and PNPases (polynucleotide phosphorylases) [], as well as in archaeal and eukaryotic RNA exosomes [, ], the later acting as nano-compartments for the degradation or processing of RNA (including mRNA, rRNA, snRNA and snoRNA). Bacterial/organelle PNPases share a common barrel structure with RNA exosomes, consisting of a hexameric ring of PH domains that act as a degradation chamber, and an S1-domain/KH-domain containing cap that binds the RNA substrate (and sometimes accessory proteins) in order to regulate and restrict entry into the degradation chamber []. Unstructured RNA substrates feed in through the pore made by the S1 domains, are degraded by the PH domain ring, and exit as nucleotides via the PH pore at the opposite end of the barrel [, ]. This entry represents the phosphorolytic (PH) domain 2, which has a core 3-layer alpha/beta/alpha structure. This domain is found in bacterial/organelle PNPases and in archaeal/eukaryotic exosomes []. More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding, 0006396 RNA processing; PDB: 1E3H_A 1E3P_A 2NN6_E 2WNR_A 3U1K_B 2BA0_H 2BA1_H 3M85_G 3M7N_H 3H1C_K ....
Probab=98.93 E-value=6.1e-09 Score=75.08 Aligned_cols=65 Identities=25% Similarity=0.253 Sum_probs=51.4
Q ss_pred cceeEEEEEEeeCCeEEeCCCHHHHhhccccEEEEecCCcccccCCCCccccCCccccceEEEE-ecCC--CCHHHHHHH
Q 024064 166 HLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSV-THGA--MSVDDYFHC 242 (273)
Q Consensus 166 ~~~~avsv~~~~~~~~ilDPt~~Ee~~~~~~~~va~~~~~~~~~~~~~~~~~~~~~~~~~v~~~-~~G~--~~~~~~~~~ 242 (273)
|+|+++|++++ ++.+++|||.+||+.+++.+++++..+ .+.+.+. ..|. ++++++.+|
T Consensus 1 ~~~~avt~~~i-~~~~v~Dpt~~Ee~~~~~~l~~~~~~~------------------~~~~~~~~~~g~~~~~~~~l~~~ 61 (68)
T PF03725_consen 1 DPPVAVTVGII-DGELVVDPTAEEESLSDSSLTLAVDGT------------------GNICTLQKSGGGSELSEDQLEEA 61 (68)
T ss_dssp SEEEEEEEEEE-TTEEEES--HHHHHHSSEEEEEEEETT------------------SSEEEEEEEEESSEEEHHHHHHH
T ss_pred CCeEEEEEEEE-CCEEEECCCHHHHhhcCCcEEEEEECC------------------CCEEEEEEcCCCCCCCHHHHHHH
Confidence 57999999998 889999999999999999999999742 2333333 3443 999999999
Q ss_pred HHHHHHH
Q 024064 243 LERGRAA 249 (273)
Q Consensus 243 l~~A~~~ 249 (273)
++.|.++
T Consensus 62 i~~A~~~ 68 (68)
T PF03725_consen 62 IELAKKA 68 (68)
T ss_dssp HHHHHHH
T ss_pred HHHHhcC
Confidence 9999874
No 27
>PRK15031 5-carboxymethyl-2-hydroxymuconate delta-isomerase; Provisional
Probab=42.66 E-value=1.4e+02 Score=24.12 Aligned_cols=63 Identities=13% Similarity=0.068 Sum_probs=40.8
Q ss_pred CCCceEEEEEEEecCCCCCCchHHHHHHHHHHHhhhhhhcCC-CCCcEEEEEEEEEecCCCchh
Q 024064 85 ENPEKASIEVIWKPRTGQIGKPEKEYEIILKRTLQSICILTI-NPNTTTSVIIQVVHDDGALLP 147 (273)
Q Consensus 85 ~~~~~~~l~v~~~p~~g~~~~~~~~l~~~l~~~l~s~i~~~~-~p~~~I~i~v~Vl~~dG~ll~ 147 (273)
+.++.+.|++.++=..||....-++++..|-.+++..+.... .+...+.+.|.-++..++..-
T Consensus 55 g~~~~~Fihv~l~i~~GRs~e~k~~l~~~l~~~l~~~~~~~~~~~~~~LS~Ei~d~d~~~s~k~ 118 (126)
T PRK15031 55 GKHDYAFVHMTLKIGAGRSLESRQEVGEMLFALIKAHFAALMESRYLALSFEIEELHPTLNFKQ 118 (126)
T ss_pred CCCCCcEEEEEeeecCCCCHHHHHHHHHHHHHHHHHHhhhhhcccceEEEEEEEEcCCccChhh
Confidence 445678888888888898776667777777777766544321 122556666666666655443
No 28
>PF02962 CHMI: 5-carboxymethyl-2-hydroxymuconate isomerase; InterPro: IPR004220 5-carboxymethyl-2-hydroxymuconate isomerase transforms 5-carboxymethyl-2-hydroxy-muconic acid into 5-oxo-pent-3-ene-1,2,5-tricarboxylic acid during the third step of the homoprotocatechuate catabolic pathway []. Homoprotocatechuate (HPC; 3,4-dihydroxyphenylacetate) is catabolized to Krebs cycle intermediates via extradiol (meta-) cleavage and the necessary enzymes are chromosomally encoded in a variety of bacteria []. 5-carboxymethyl-2-hydroxymuconate isomerase is probably a dimer of two identical subunits []. A comparison of the N-terminal half of the isomerase/decarboxylase sequence from the pathway (both encoded by the gene hpcE), with the second half showed significant similarity. This suggests that a duplication may have occurred to produce a bifunctional gene [].; PDB: 3E6Q_H 1OTG_B.
Probab=37.42 E-value=1e+02 Score=24.80 Aligned_cols=58 Identities=14% Similarity=0.190 Sum_probs=37.3
Q ss_pred CCCCceEEEEEEEecCCCCCCchHHHHHHHHHHHhhhhhhcCCCCCcEEEEEEEEEecC
Q 024064 84 NENPEKASIEVIWKPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDD 142 (273)
Q Consensus 84 ~~~~~~~~l~v~~~p~~g~~~~~~~~l~~~l~~~l~s~i~~~~~p~~~I~i~v~Vl~~d 142 (273)
.+.++.+.|+|.++=..||....-+.++..|-.+|+.-+ ...+.+..+++.+.|.+-|
T Consensus 53 dg~~~~~FvHv~l~il~GRs~e~k~~l~~~l~~~l~~~~-~~~~~~~~~~LsvEi~E~~ 110 (124)
T PF02962_consen 53 DGQPDDAFVHVTLRILAGRSEEQKKALSEALLAVLKAHL-APLFAQRYLQLSVEIREMD 110 (124)
T ss_dssp TSSS-EEEEEEEEEEETT--HHHHHHHHHHHHHHHHHHC-CCHCCHSEEEEEEEEEEE-
T ss_pred cCCCCCcEEEEEeeecCCCCHHHHHHHHHHHHHHHHHHh-hHhhcCCeeEEEEEEEEcC
Confidence 344678889999988888876666777777777777753 2344555677777776654
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=34.33 E-value=23 Score=21.80 Aligned_cols=33 Identities=15% Similarity=0.213 Sum_probs=27.0
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Q 024064 234 MSVDDYFHCLERGRAASAKLSDFLRRSLQSKLP 266 (273)
Q Consensus 234 ~~~~~~~~~l~~A~~~~~~i~~~i~~~l~~~~~ 266 (273)
++.+.+..+-+.|...-....++++.+|.+++.
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 567788888888888888889999999987753
No 30
>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=33.67 E-value=2.2e+02 Score=21.88 Aligned_cols=55 Identities=29% Similarity=0.242 Sum_probs=36.5
Q ss_pred HHHHHHHHHHHhhhhhh---cCCCCCcEEEEEEEEEecC------CCchhHHHHHHHHHHHhCC
Q 024064 107 EKEYEIILKRTLQSICI---LTINPNTTTSVIIQVVHDD------GALLPCAINAACAALVDAG 161 (273)
Q Consensus 107 ~~~l~~~l~~~l~s~i~---~~~~p~~~I~i~v~Vl~~d------G~ll~a~inAa~lAL~dag 161 (273)
-+++...|.+.++..+. +-.||-..+.|.|+=++.. +.+..|+-.|...||..|+
T Consensus 57 ~~~~~~ai~~G~~~a~~~Gpl~g~pv~~v~v~l~~~~~~~~~s~~~a~~~aa~~a~~~al~~A~ 120 (120)
T PF03764_consen 57 PKEFQDAIEEGFQSALSSGPLCGYPVTDVKVTLTDGEYHEVDSSPGAFRAAARRAFREALKKAG 120 (120)
T ss_dssp GGGGHHHHHHHHHHHHCSSTTTSSEB-SEEEEEEEEEC-TTTBSHHHHHHHHHHHHHHHHHHS-
T ss_pred cHHHHHHHhhhhhheecccccCCCceEEEEEEEEEeeecCCcCCHHHHHHHHHHHHHHHHHhcC
Confidence 35666777777777664 3457888888888766643 2357788888888887764
No 31
>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=29.21 E-value=77 Score=24.22 Aligned_cols=34 Identities=26% Similarity=0.318 Sum_probs=24.5
Q ss_pred ecCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 024064 230 THGAMSVDDYFHCLERGRAASAKLSDFLRRSLQS 263 (273)
Q Consensus 230 ~~G~~~~~~~~~~l~~A~~~~~~i~~~i~~~l~~ 263 (273)
..|.+++++|.-+++.+.-+++++..++++.|-.
T Consensus 19 ~pG~vs~e~F~lLl~ls~IrS~kiI~AL~dyLV~ 52 (91)
T PF03333_consen 19 IPGKVSEEHFWLLLELSSIRSEKIIAALRDYLVD 52 (91)
T ss_dssp -TT-S-HHHHHHHHHHS----HHHHHHHHHHHTT
T ss_pred CCCCcCHHHHHHHHHHCCCCcHHHHHHHHHHHHc
Confidence 4799999999999999999999999999988754
No 32
>PF12651 RHH_3: Ribbon-helix-helix domain
Probab=25.11 E-value=82 Score=20.44 Aligned_cols=34 Identities=21% Similarity=0.242 Sum_probs=28.5
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Q 024064 233 AMSVDDYFHCLERGRAASAKLSDFLRRSLQSKLP 266 (273)
Q Consensus 233 ~~~~~~~~~~l~~A~~~~~~i~~~i~~~l~~~~~ 266 (273)
.++.+.+.++-+.|.+......++++++|+..+.
T Consensus 8 ~l~~el~~~L~~ls~~t~i~~S~Ll~eAle~~l~ 41 (44)
T PF12651_consen 8 SLDKELYEKLKELSEETGIPKSKLLREALEDYLE 41 (44)
T ss_pred ecCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 4788888888888988888889999999987654
No 33
>PF13541 ChlI: Subunit ChlI of Mg-chelatase
Probab=20.93 E-value=4.2e+02 Score=21.06 Aligned_cols=73 Identities=18% Similarity=0.104 Sum_probs=42.5
Q ss_pred CCCCCchHHHHHHHHHHHhhhhhhcCCCCCcEEEEEEEE--EecCCCchhHHHHHHHHHHHhCCCCcc-cceeEEEEEE
Q 024064 100 TGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQV--VHDDGALLPCAINAACAALVDAGIPMK-HLAVAICCCS 175 (273)
Q Consensus 100 ~g~~~~~~~~l~~~l~~~l~s~i~~~~~p~~~I~i~v~V--l~~dG~ll~a~inAa~lAL~dagIp~~-~~~~avsv~~ 175 (273)
.|.++..-+|-..-++.+++. ..-.+|...|.|.+.- +.-.|.-+|.++-++.++- ...+|.. +.++.--+++
T Consensus 15 vGl~~~av~esr~Rv~~al~~--~g~~~p~~~i~VNlap~~l~k~g~~~DLaIA~ailsa-~~~~~~~~~~~~~GEl~L 90 (121)
T PF13541_consen 15 VGLPDTAVKESRERVRSALKN--SGFPFPNQDITVNLAPADLKKEGPAFDLAIAIAILSA-FGQIPIPEDTVFIGELGL 90 (121)
T ss_pred ecCchHHHHHHHHHHHHHHHh--cCCCCCcceeeeEEEeCCEEEeeeeehHHHHHHHHHh-CCCcccCCCEEEEEEecC
Confidence 355555555666667777777 2345677767676642 5667888887775555432 3446654 3444334444
No 34
>PRK15215 fimbriae biosynthesis regulatory protein; Provisional
Probab=20.19 E-value=1.4e+02 Score=23.17 Aligned_cols=34 Identities=15% Similarity=0.167 Sum_probs=30.6
Q ss_pred ecCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 024064 230 THGAMSVDDYFHCLERGRAASAKLSDFLRRSLQS 263 (273)
Q Consensus 230 ~~G~~~~~~~~~~l~~A~~~~~~i~~~i~~~l~~ 263 (273)
..|.+++++|.-++|.+--+++++..++++.|-.
T Consensus 27 ~pG~v~eehF~LLieIS~IrS~KvI~AL~dyLV~ 60 (100)
T PRK15215 27 IPAKVNEEHFWLLIGISSIHSEKIIQALRDYLVF 60 (100)
T ss_pred cCCccCHHHHHHHHHHcccchHHHHHHHHHHHHc
Confidence 4789999999999999999999999999988753
No 35
>CHL00079 rps9 ribosomal protein S9
Probab=20.01 E-value=4.8e+02 Score=21.16 Aligned_cols=45 Identities=18% Similarity=0.230 Sum_probs=29.8
Q ss_pred HHHHHHhhhhhhcCCCCCcEEEEEEEEEecCCCc---hhHHHHHHHHHHHhC
Q 024064 112 IILKRTLQSICILTINPNTTTSVIIQVVHDDGAL---LPCAINAACAALVDA 160 (273)
Q Consensus 112 ~~l~~~l~s~i~~~~~p~~~I~i~v~Vl~~dG~l---l~a~inAa~lAL~da 160 (273)
...+.+++++.+.+...+ ++|.+.| ..|+. -.|+-.|+.-||+..
T Consensus 43 ~~~~~v~~Pl~~~~~~~~--~Di~i~V--~GGG~sgQa~Air~aIaraLv~~ 90 (130)
T CHL00079 43 NYLNAIKAPLKLLGLENK--YDIIVKV--KGGGLTGQAEAIRLGLARALCKI 90 (130)
T ss_pred HHHHHHHHHHHHhCcCCc--eeEEEEE--EcCChhHHHHHHHHHHHHHHHHH
Confidence 345778899888876544 4444444 45655 557777888888765
Done!