Query gi|254780261|ref|YP_003064674.1| 50S ribosomal protein L3 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 221
No_of_seqs 143 out of 1792
Neff 5.6
Searched_HMMs 39220
Date Tue May 24 08:03:53 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780261.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK00001 rplC 50S ribosomal pr 100.0 0 0 609.0 20.8 211 1-213 1-211 (212)
2 CHL00143 rpl3 ribosomal protei 100.0 0 0 606.9 20.8 207 1-210 1-207 (207)
3 TIGR03625 L3_bact 50S ribosoma 100.0 0 0 595.4 19.4 202 4-207 1-202 (202)
4 COG0087 RplC Ribosomal protein 100.0 0 0 549.1 18.5 214 2-216 1-216 (218)
5 KOG3141 consensus 100.0 0 0 550.1 17.4 215 1-217 61-276 (310)
6 pfam00297 Ribosomal_L3 Ribosom 100.0 0 0 543.6 16.9 195 9-207 1-199 (199)
7 TIGR03626 L3_arch archaeal rib 100.0 0 0 380.4 18.2 212 3-216 36-316 (330)
8 PRK04231 rpl3p 50S ribosomal p 100.0 0 0 354.5 17.2 212 3-216 37-317 (333)
9 PTZ00103 60S ribosomal protein 100.0 0 0 310.7 16.6 209 3-215 44-346 (393)
10 KOG0746 consensus 99.9 1.7E-26 4.3E-31 176.0 6.1 204 3-210 31-332 (384)
11 PRK10737 FKBP-type peptidyl-pr 50.1 21 0.00054 16.8 3.9 18 178-197 108-125 (196)
12 TIGR01810 betA choline dehydro 47.3 14 0.00036 17.9 2.1 63 13-87 223-285 (540)
13 TIGR02013 rpoB DNA-directed RN 43.9 9 0.00023 19.0 0.7 23 27-49 1000-1025(1449)
14 KOG0482 consensus 43.0 11 0.00027 18.6 1.0 97 27-133 170-289 (721)
15 pfam11325 DUF3127 Protein of u 42.7 25 0.00063 16.4 2.8 29 94-122 43-72 (84)
16 cd00686 Terpene_cyclase_cis_tr 34.0 16 0.0004 17.6 0.7 40 120-160 158-198 (357)
17 pfam06003 SMN Survival motor n 31.7 42 0.0011 15.1 3.3 28 5-32 66-95 (264)
18 pfam06330 TRI5 Trichodiene syn 31.0 19 0.00049 17.1 0.7 40 120-160 158-198 (376)
19 TIGR02684 dnstrm_HI1420 probab 24.5 7 0.00018 19.6 -2.5 13 3-15 39-51 (91)
20 KOG1800 consensus 23.5 43 0.0011 15.0 1.4 24 43-66 106-129 (468)
21 cd05697 S1_Rrp5_repeat_hs5 S1_ 21.9 30 0.00077 15.9 0.4 29 76-104 29-57 (69)
22 KOG3181 consensus 21.2 48 0.0012 14.7 1.3 10 43-52 31-40 (244)
23 TIGR01628 PABP-1234 polyadenyl 21.1 41 0.001 15.1 0.9 21 95-120 113-133 (860)
24 cd06188 NADH_quinone_reductase 20.6 67 0.0017 13.9 2.1 13 102-114 128-140 (283)
No 1
>PRK00001 rplC 50S ribosomal protein L3; Validated
Probab=100.00 E-value=0 Score=608.98 Aligned_cols=211 Identities=52% Similarity=0.815 Sum_probs=206.0
Q ss_pred CCCCEEEEECCCCEEECCCCCEEEEEEEEECCCEEEEEEECCCCCCEEEEECCCCCCCCCCCCCHHHHHHHHCCCCCCEE
Q ss_conf 94426899658451698898792268999179789999706778861256405555643157101125764035634103
Q gi|254780261|r 1 MRSGVVARKLGMTCVYNIEGRRIPVTVLHLDNCQVVVHRTLDKNGYMAVQVGAGEAKVKNVSKPMRGFFSSVNVSPKKKL 80 (221)
Q Consensus 1 mr~Glig~KiGMT~if~e~G~~vpVTViev~~~~Vv~~kt~ekdGY~Avqvg~~~~k~k~~~Kp~~G~fkK~g~~pk~~l 80 (221)
|+.||||+|+||||+||+||.++||||||++||+|+|+||.|+|||+|+||||++.+++++|||++|||+|++++|+++|
T Consensus 1 M~~Glig~KiGMT~i~~~~G~~vpVTVl~v~p~~V~~~kt~ekdGY~avqlg~~~~k~~~~~Kp~~g~~~K~~~~p~~~l 80 (212)
T PRK00001 1 MMKGILGKKVGMTQIFTEDGESIPVTVIEAGPNVVTQVKTVEKDGYNAVQLGFGDKKEKRVNKPEAGHFAKAGVEPKRKL 80 (212)
T ss_pred CCCCEEEEECCCEEEECCCCCEEEEEEEEECCCEEEEEEEECCCCEEEEEEECEECCCCCCCHHHCCHHHHHCCCCCCEE
T ss_conf 96514599637718888999599879999689799999950579806899711013532258545013566154646228
Q ss_pred EEEECCCCHHHHHCCCCEEEEEECCCCEEEEEEEEECCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECC
Q ss_conf 65320651121100341000123025326578987534336405750442123335774543466655555675224226
Q gi|254780261|r 81 FEFRVQKDDDLLPVGSVFSPSYFTVGQLVDVTGMTIGKGFSGAMKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKN 160 (221)
Q Consensus 81 ~Efrv~~~~~~~~vG~~i~~~~F~~Gq~VDV~g~SkGKGFqGviKR~gf~g~~~sHG~sk~hR~~GsiG~~~~PgRV~kG 160 (221)
+|||++++ +.+++|++|++|+|++||+|||+|+||||||||+||||||+++|+|||+|++||+|||||+|++|||||||
T Consensus 81 ~Efrv~~~-~~~~~G~~i~~~~F~~Gq~VDV~g~SkGKGFqGvmKRh~F~g~~~sHG~s~~hR~~GSiG~~~~PgRV~kG 159 (212)
T PRK00001 81 KEFRVDEL-AEYEVGDEITVDIFEAGQKVDVTGTSKGKGFAGVMKRHNFSGGPASHGSSRSHRRPGSIGQRQTPGRVFKG 159 (212)
T ss_pred EEEEECCH-HHCCCCCEECHHHCCCCCEEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 99971561-20347872378885799768888877077542027750247887635688656178866667788867568
Q ss_pred CCCCCCCCCEEEEECCCEEEEEECCCCEEEEECCCCCCCCCEEEEEEECCCCC
Q ss_conf 76665237733365165899980768989997157458887099996031467
Q gi|254780261|r 161 KKMAGRMGGNRVTVKNLEVVSVDDKRGLILVKGCVPGAKKNSWILVRDSFKSA 213 (221)
Q Consensus 161 kkm~G~mG~~~~T~~nl~i~~id~e~n~i~vkGsVPG~~~~~~v~ir~a~k~~ 213 (221)
+|||||||++++|++||+|++||+|+|||||||||||| +|++|+||||+|+.
T Consensus 160 kkMaG~mG~~~~T~~Nl~V~~id~e~nli~vkGsVPG~-~~~~V~ir~aik~~ 211 (212)
T PRK00001 160 KKMAGHMGNERVTVQNLEVVKVDAERNLLLVKGAVPGA-KGSLVIIKPAVKAG 211 (212)
T ss_pred CCCCCCCCCEEEEECCCEEEEEECCCCEEEEEECCCCC-CCCEEEEEECEECC
T ss_conf 98798648716887487999996888989998468789-99899996140058
No 2
>CHL00143 rpl3 ribosomal protein L3; Validated
Probab=100.00 E-value=0 Score=606.91 Aligned_cols=207 Identities=43% Similarity=0.741 Sum_probs=202.5
Q ss_pred CCCCEEEEECCCCEEECCCCCEEEEEEEEECCCEEEEEEECCCCCCEEEEECCCCCCCCCCCCCHHHHHHHHCCCCCCEE
Q ss_conf 94426899658451698898792268999179789999706778861256405555643157101125764035634103
Q gi|254780261|r 1 MRSGVVARKLGMTCVYNIEGRRIPVTVLHLDNCQVVVHRTLDKNGYMAVQVGAGEAKVKNVSKPMRGFFSSVNVSPKKKL 80 (221)
Q Consensus 1 mr~Glig~KiGMT~if~e~G~~vpVTViev~~~~Vv~~kt~ekdGY~Avqvg~~~~k~k~~~Kp~~G~fkK~g~~pk~~l 80 (221)
|++||||+|+||||+|||+|.++||||||++||+|+|+||.|+|||+|+||||++.+++++|||++|||+|++++|++++
T Consensus 1 M~~Glig~KiGMt~if~~~G~~vpVTVl~v~~~~V~~~kt~e~dGY~Avqvg~~~~k~k~~~Kp~~G~f~Kagv~p~~~l 80 (207)
T CHL00143 1 MSIGILGTKIGMTQIFDESGNAIPVTIVKVGPCVITQIKTTSTDGYNAIQIGYGEVKEKKLNKPQLGHLQKSNIPPLKYL 80 (207)
T ss_pred CCCEEEEEECCCEEEECCCCCEEEEEEEEEECCEEEEEEECCCCCCEEEEEEEEECCCCCCCHHHHHHHHHCCCCCCEEE
T ss_conf 96337899637606578999499879999608799999813679947899956004643258535215876399865478
Q ss_pred EEEECCCCHHHHHCCCCEEEEEECCCCEEEEEEEEECCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECC
Q ss_conf 65320651121100341000123025326578987534336405750442123335774543466655555675224226
Q gi|254780261|r 81 FEFRVQKDDDLLPVGSVFSPSYFTVGQLVDVTGMTIGKGFSGAMKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKN 160 (221)
Q Consensus 81 ~Efrv~~~~~~~~vG~~i~~~~F~~Gq~VDV~g~SkGKGFqGviKR~gf~g~~~sHG~sk~hR~~GsiG~~~~PgRV~kG 160 (221)
+|||+++.+ .+++|++|++|+|++||+|||+|+|||||||||||||||+|+|+||| |++||+|||||+|++|||||||
T Consensus 81 ~Efrv~~~~-~~~vG~~l~v~~F~~Gq~VdVtg~SkGKGF~GvmKRh~F~gg~asHG-s~~hR~~GSiG~~~~PgRV~kG 158 (207)
T CHL00143 81 KEFRVESTE-EFEVGQQLTVESFEVGQKVNVSGKSIGKGFSGYQKRHNFSRGPMTHG-SKNHRQPGSIGAGTTPGRVYPG 158 (207)
T ss_pred EEECCCCCC-CCCCCCCCCHHHCCCCCEEEEEEEECCCCCCCCEEECCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCC
T ss_conf 998557743-24688640202257998399968876872466376525578987677-8877388446888978618589
Q ss_pred CCCCCCCCCEEEEECCCEEEEEECCCCEEEEECCCCCCCCCEEEEEEECC
Q ss_conf 76665237733365165899980768989997157458887099996031
Q gi|254780261|r 161 KKMAGRMGGNRVTVKNLEVVSVDDKRGLILVKGCVPGAKKNSWILVRDSF 210 (221)
Q Consensus 161 kkm~G~mG~~~~T~~nl~i~~id~e~n~i~vkGsVPG~~~~~~v~ir~a~ 210 (221)
||||||||++++|++||+|++||+|+|||||||||||+ +|++|+|+||.
T Consensus 159 kkM~G~mG~~~~Tv~nl~Vv~id~e~nli~vkG~VPG~-~g~~V~i~~ak 207 (207)
T CHL00143 159 KKMAGRLGNKKVTIKNLKIVQVDSDNNLLVLKGSVPGK-PGNLLSISPSK 207 (207)
T ss_pred CCCCCCCCCEEEEEECCEEEEEECCCCEEEEEECCCCC-CCCEEEEEECC
T ss_conf 86577568715888088999996778989997458789-99889998697
No 3
>TIGR03625 L3_bact 50S ribosomal protein L3, bacterial. This model describes bacterial (and mitochondrial and chloroplast) class of ribosomal protein L3. A separate model describes the archaeal form, where both belong to pfam00297. The name is phrased to meet the needs of bacterial genome annotation. Organellar forms typically will have transit peptides, N-terminal to the region modeled here.
Probab=100.00 E-value=0 Score=595.44 Aligned_cols=202 Identities=53% Similarity=0.848 Sum_probs=197.7
Q ss_pred CEEEEECCCCEEECCCCCEEEEEEEEECCCEEEEEEECCCCCCEEEEECCCCCCCCCCCCCHHHHHHHHCCCCCCEEEEE
Q ss_conf 26899658451698898792268999179789999706778861256405555643157101125764035634103653
Q gi|254780261|r 4 GVVARKLGMTCVYNIEGRRIPVTVLHLDNCQVVVHRTLDKNGYMAVQVGAGEAKVKNVSKPMRGFFSSVNVSPKKKLFEF 83 (221)
Q Consensus 4 Glig~KiGMT~if~e~G~~vpVTViev~~~~Vv~~kt~ekdGY~Avqvg~~~~k~k~~~Kp~~G~fkK~g~~pk~~l~Ef 83 (221)
||||+|+||||+||+||.++||||||++||+|+|+||.|+|||+|+||||++.+++++|||++|||+|++++|+++|+||
T Consensus 1 Glig~KiGMT~i~~~~G~~vPVTVl~v~~~~V~~~kt~e~dGY~avqlg~~~~k~k~~~Kp~~G~~~K~~~~~~~~l~Ef 80 (202)
T TIGR03625 1 GLLGKKVGMTQIFTEDGKAVPVTVIEVGPNVVTQVKTVEKDGYSAVQLGFGEKKEKRVNKPEAGHFAKAGVEPKRHLREF 80 (202)
T ss_pred CCCEEECCCEEEECCCCCEEEEEEEEECCCEEEEEEECCCCCCEEEEEEECCCCCCCCCHHHCCHHHHHCCCCCCEEEEE
T ss_conf 96289658807888999699879999589899999921689806889831224532228545110455135765237999
Q ss_pred ECCCCHHHHHCCCCEEEEEECCCCEEEEEEEEECCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCC
Q ss_conf 20651121100341000123025326578987534336405750442123335774543466655555675224226766
Q gi|254780261|r 84 RVQKDDDLLPVGSVFSPSYFTVGQLVDVTGMTIGKGFSGAMKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKM 163 (221)
Q Consensus 84 rv~~~~~~~~vG~~i~~~~F~~Gq~VDV~g~SkGKGFqGviKR~gf~g~~~sHG~sk~hR~~GsiG~~~~PgRV~kGkkm 163 (221)
|+++.+ .+++|++|++|+|++||+|||+|+||||||||+||||||+++|+|||+|++||+|||||+|++|||||||+||
T Consensus 81 rv~~~~-~~~~G~~l~v~~F~~Gq~VdV~g~skGKGFqGv~KR~~F~g~~~sHG~s~~hR~~GSiG~~~~PgrV~kGkkM 159 (202)
T TIGR03625 81 RVDDLD-GYEVGDEITVDIFEAGQKVDVTGTSKGKGFAGVMKRHNFSGGPASHGNSKSHRAPGSIGQRQTPGRVFKGKKM 159 (202)
T ss_pred EECCCC-CCCCCCEECHHHCCCCCEEEEEEEEECCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 716732-2468776458670788638888877066432017750247897535688777388867667888878578987
Q ss_pred CCCCCCEEEEECCCEEEEEECCCCEEEEECCCCCCCCCEEEEEE
Q ss_conf 65237733365165899980768989997157458887099996
Q gi|254780261|r 164 AGRMGGNRVTVKNLEVVSVDDKRGLILVKGCVPGAKKNSWILVR 207 (221)
Q Consensus 164 ~G~mG~~~~T~~nl~i~~id~e~n~i~vkGsVPG~~~~~~v~ir 207 (221)
|||||++++|++||+|++||+|+|||+|||||||| +|++|+||
T Consensus 160 aG~mG~~~~T~~nl~v~~id~e~nli~vkGsVPG~-~~~~v~ir 202 (202)
T TIGR03625 160 AGHMGNERVTVQNLEVVRVDAERNLLLVKGAVPGA-KGSLVLIK 202 (202)
T ss_pred CCCCCCCEEEECCCEEEEEECCCCEEEEEECCCCC-CCCEEEEC
T ss_conf 88758852887467899995888989997368789-99899969
No 4
>COG0087 RplC Ribosomal protein L3 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=0 Score=549.14 Aligned_cols=214 Identities=51% Similarity=0.795 Sum_probs=205.2
Q ss_pred CCCEEEEECCCCEEECCCCCEEEEEEEEECCCEEEEEEECCCCCCEEEEECCCCCCCCCCCCCHHHHHHHHCCCCCCEEE
Q ss_conf 44268996584516988987922689991797899997067788612564055556431571011257640356341036
Q gi|254780261|r 2 RSGVVARKLGMTCVYNIEGRRIPVTVLHLDNCQVVVHRTLDKNGYMAVQVGAGEAKVKNVSKPMRGFFSSVNVSPKKKLF 81 (221)
Q Consensus 2 r~Glig~KiGMT~if~e~G~~vpVTViev~~~~Vv~~kt~ekdGY~Avqvg~~~~k~k~~~Kp~~G~fkK~g~~pk~~l~ 81 (221)
+.||||+|+||||+|+++|.++||||||++||.|+|+||.|+|||+|+||+++++++++++||+.|||.|++++|+++|.
T Consensus 1 ~~G~~G~KvGMT~vf~~~g~~vPVTVie~~p~~V~~vkt~e~~Gy~a~qv~~~~~k~~~~~k~~~g~~~k~~~~~k~~l~ 80 (218)
T COG0087 1 MLGFLGYKVGMTHVFDERGISVPVTVIEVPPNVVVQVKTYETDGYRAVQVGAGDRKAKRVNKPLVGHFAKAGVKPKRHLA 80 (218)
T ss_pred CCCCCEEECCCEEEECCCCCEEEEEEEECCCCEEEEEEEECCCCCEEEEEEECCEEEEHHCCCEEEEECCCCCCCCCEEE
T ss_conf 95411684176699842895887899982895899999402588189997406203201043123541336787787279
Q ss_pred EEECCCCH--HHHHCCCCEEEEEECCCCEEEEEEEEECCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEC
Q ss_conf 53206511--2110034100012302532657898753433640575044212333577454346665555567522422
Q gi|254780261|r 82 EFRVQKDD--DLLPVGSVFSPSYFTVGQLVDVTGMTIGKGFSGAMKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFK 159 (221)
Q Consensus 82 Efrv~~~~--~~~~vG~~i~~~~F~~Gq~VDV~g~SkGKGFqGviKR~gf~g~~~sHG~sk~hR~~GsiG~~~~PgRV~k 159 (221)
|||+.+.+ +.+++|++|++|+|++||+|||+|+||||||||+||||||+++|+|||++.+||++||||++|+|+||||
T Consensus 81 E~rv~~~~~~~~~e~g~ei~~dvF~~g~~VDV~gvTKGKGF~G~~KR~gf~~~p~sHg~~~~hR~~GSiG~~~~P~rV~~ 160 (218)
T COG0087 81 EFRVGGGDVAEKFEVGQEITVDVFKEGELVDVTGVTKGKGFQGVMKRWGFKGGPASHGSSLSHRRPGSIGQRQTPGRVFK 160 (218)
T ss_pred EEEECCCCCCCCCCHHHHHCHHHCCCCCEEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEC
T ss_conf 99715876421031366514633358887999988636564110554124668764578866657734689898976627
Q ss_pred CCCCCCCCCCEEEEECCCEEEEEECCCCEEEEECCCCCCCCCEEEEEEECCCCCCCC
Q ss_conf 676665237733365165899980768989997157458887099996031467785
Q gi|254780261|r 160 NKKMAGRMGGNRVTVKNLEVVSVDDKRGLILVKGCVPGAKKNSWILVRDSFKSAVNC 216 (221)
Q Consensus 160 Gkkm~G~mG~~~~T~~nl~i~~id~e~n~i~vkGsVPG~~~~~~v~ir~a~k~~~~~ 216 (221)
|++||||||+++||+|||+|++||.|+|||||||||||| ++++|.||+|+|+....
T Consensus 161 g~kmaG~mG~~~vTvqNl~Vv~id~e~~~ilVkGaVPG~-~k~~v~vr~a~k~~~~~ 216 (218)
T COG0087 161 GKKMAGHMGNERVTVQNLEVVKVDVENNLILVKGAVPGA-KKRLVVVRPAVKAKKKT 216 (218)
T ss_pred CCCCCCCCCCCEEEEEEEEEEEECCCCCEEEEECCCCCC-CCCEEEEEHHHCCCCCC
T ss_conf 974575678845888755999983778889996246788-88569985122267767
No 5
>KOG3141 consensus
Probab=100.00 E-value=0 Score=550.08 Aligned_cols=215 Identities=47% Similarity=0.755 Sum_probs=207.8
Q ss_pred CCCCEEEEECCCCEEECCCCCEEEEEEEEECCCEEEEEEECC-CCCCEEEEECCCCCCCCCCCCCHHHHHHHHCCCCCCE
Q ss_conf 944268996584516988987922689991797899997067-7886125640555564315710112576403563410
Q gi|254780261|r 1 MRSGVVARKLGMTCVYNIEGRRIPVTVLHLDNCQVVVHRTLD-KNGYMAVQVGAGEAKVKNVSKPMRGFFSSVNVSPKKK 79 (221)
Q Consensus 1 mr~Glig~KiGMT~if~e~G~~vpVTViev~~~~Vv~~kt~e-kdGY~Avqvg~~~~k~k~~~Kp~~G~fkK~g~~pk~~ 79 (221)
-|+|+|+.|+||+.+||+||+++||||||+++|.|+++++.| ++||.|+||||+.+++++++|+++|||.++|+.||++
T Consensus 61 ~R~GvI~~K~GMmp~w~k~G~ri~~TiL~v~d~~Vi~~~t~E~~~g~~avqVG~g~~~p~kltk~~~g~f~~~gv~pK~~ 140 (310)
T KOG3141 61 RRVGVIARKLGMMPLWDKDGERIPVTILQVDDNHVIKYITPEAKGGYFAVQVGYGTVKPKKLTKAELGHFRSAGVPPKRH 140 (310)
T ss_pred CCCEEEEEECCCCHHHCCCCCEEEEEEEEEECCEEEEEECHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 63106988325741010579787789999824468998552115976899966663785776088887898738975553
Q ss_pred EEEEECCCCHHHHHCCCCEEEEEECCCCEEEEEEEEECCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEC
Q ss_conf 36532065112110034100012302532657898753433640575044212333577454346665555567522422
Q gi|254780261|r 80 LFEFRVQKDDDLLPVGSVFSPSYFTVGQLVDVTGMTIGKGFSGAMKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFK 159 (221)
Q Consensus 80 l~Efrv~~~~~~~~vG~~i~~~~F~~Gq~VDV~g~SkGKGFqGviKR~gf~g~~~sHG~sk~hR~~GsiG~~~~PgRV~k 159 (221)
|+||||+ ++++++.|+.|.++||++||||||+|+|+||||||+||||||+|+|||||+|++||++||+|++++||||||
T Consensus 141 l~eF~Vt-~~al~~pGt~l~~~hFk~GqyVDV~g~TigkGFqGvmKR~GFkG~pasHG~sksHR~~GS~G~~~~pgRV~p 219 (310)
T KOG3141 141 LREFRVT-EEALLPPGTPLFARHFKPGQYVDVTGKTIGKGFQGVMKRHGFKGGPASHGTSKSHRRPGSIGQGTTPGRVWP 219 (310)
T ss_pred HHEEEEC-HHCCCCCCCCCCHHHCCCCCEEEEEEEEECCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 1057505-300479996632531478754887745715554200320344678666674201447755568888764136
Q ss_pred CCCCCCCCCCEEEEECCCEEEEEECCCCEEEEECCCCCCCCCEEEEEEECCCCCCCCC
Q ss_conf 6766652377333651658999807689899971574588870999960314677853
Q gi|254780261|r 160 NKKMAGRMGGNRVTVKNLEVVSVDDKRGLILVKGCVPGAKKNSWILVRDSFKSAVNCK 217 (221)
Q Consensus 160 Gkkm~G~mG~~~~T~~nl~i~~id~e~n~i~vkGsVPG~~~~~~v~ir~a~k~~~~~k 217 (221)
|+||||||||++||++||+|++||.|+|+|||||||||+ +|++|+|+||+.+..+..
T Consensus 220 GrKMpGhMG~~~rtik~LkV~kId~~~nvi~VkGsVpG~-~g~~V~I~Da~~~~~~i~ 276 (310)
T KOG3141 220 GRKMPGHMGNEWRTIKGLKVWKIDTELNVIWVKGSVPGP-KGNLVKIKDAILPTVDIP 276 (310)
T ss_pred CCCCCCCCCCCEEEEEEEEEEEECCCCEEEEEECCCCCC-CCCEEEEEECCCCCCCCC
T ss_conf 872776457623787323999985873289993545799-897799874123357766
No 6
>pfam00297 Ribosomal_L3 Ribosomal protein L3.
Probab=100.00 E-value=0 Score=543.61 Aligned_cols=195 Identities=41% Similarity=0.645 Sum_probs=187.9
Q ss_pred ECCCCEEECCC-CCEEEEEEEEECCCEEEEEEECCC--CCCEEEEECCCCCCCCCCCCCHHHHHHHHCCCCCCEEEEEEC
Q ss_conf 65845169889-879226899917978999970677--886125640555564315710112576403563410365320
Q gi|254780261|r 9 KLGMTCVYNIE-GRRIPVTVLHLDNCQVVVHRTLDK--NGYMAVQVGAGEAKVKNVSKPMRGFFSSVNVSPKKKLFEFRV 85 (221)
Q Consensus 9 KiGMT~if~e~-G~~vpVTViev~~~~Vv~~kt~ek--dGY~Avqvg~~~~k~k~~~Kp~~G~fkK~g~~pk~~l~Efrv 85 (221)
|+||||+||++ |.++||||||++||.|+|+||.|+ |||+|+||||++.++++++||++|||+|++++|+++|+|||+
T Consensus 1 KiGMT~if~~~~G~~vPVTVle~~p~~V~~vkt~e~~~dGy~Avqlg~~~~k~~~~~K~~~gh~~k~~~~~k~~l~Efrv 80 (199)
T pfam00297 1 KAGMTHIFTEKKGVLEPVTVIEVPPMVVVQVKTYEETNDGYKAIQVGLESIKKYRVVKRVLGHTQKRGTPPKAHVMEFRV 80 (199)
T ss_pred CCCCCEEECCCCCEEEEEEEEEECCCEEEEEEEEECCCCCHHHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCCEEEEEEC
T ss_conf 99874077289998998899991896999998462079953543402032343355565666664326877720699961
Q ss_pred CCCHHHHHCCCCEEE-EEECCCCEEEEEEEEECCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCC
Q ss_conf 651121100341000-1230253265789875343364057504421233357745434666555556752242267666
Q gi|254780261|r 86 QKDDDLLPVGSVFSP-SYFTVGQLVDVTGMTIGKGFSGAMKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKMA 164 (221)
Q Consensus 86 ~~~~~~~~vG~~i~~-~~F~~Gq~VDV~g~SkGKGFqGviKR~gf~g~~~sHG~sk~hR~~GsiG~~~~PgRV~kGkkm~ 164 (221)
++++ .+++|++|++ |+|++||+|||+|+||||||||+||||||+++|+||| |++||+|||||+ ++|||||||+|||
T Consensus 81 ~~~~-~~~~G~~i~v~~~F~~Gq~VDV~g~skGKGFqGv~KR~gf~g~p~sHG-~~~hR~~GSiG~-~~PgRV~kgkkm~ 157 (199)
T pfam00297 81 NGGE-EFEPGQTIAVSDVFREGEYVDVTGVTKGKGFQGVMKRWGFKRLPRKHG-RGYHRKPGSIGA-WHPGRVFPGVKMA 157 (199)
T ss_pred CCHH-CCCCCCEEEHHHHCCCCCEEEEEEEECCCCCCCCEEECCCCCCCCCCC-CCCCCCCCCCCC-CCCCCEECCCCCC
T ss_conf 5333-045673887789336998899998745873566557767678997568-988878940489-8997531686247
Q ss_pred CCCCCEEEEECCCEEEEEECCCCEEEEECCCCCCCCCEEEEEE
Q ss_conf 5237733365165899980768989997157458887099996
Q gi|254780261|r 165 GRMGGNRVTVKNLEVVSVDDKRGLILVKGCVPGAKKNSWILVR 207 (221)
Q Consensus 165 G~mG~~~~T~~nl~i~~id~e~n~i~vkGsVPG~~~~~~v~ir 207 (221)
||||++++|++||+|++||+|+|||||||||||| ++++|+||
T Consensus 158 G~mG~~~~T~~Nl~V~~id~~~nli~vkGsVPG~-~~~~v~ir 199 (199)
T pfam00297 158 GQMGNHHRTEQNLKIYRIDQENNLLLVKGSVPGP-KKRLVTIR 199 (199)
T ss_pred CCCCCCEEEEECCEEEEEECCCCEEEEEECCCCC-CCCEEEEC
T ss_conf 7559825988377999980879989998558579-99889869
No 7
>TIGR03626 L3_arch archaeal ribosomal protein L3. This model describes exclusively the archaeal class of ribosomal protein L3. A separate model (TIGR03625) describes the bacterial/organelle form, and both belong to pfam00297. Eukaryotic proteins are excluded from this model.
Probab=100.00 E-value=0 Score=380.43 Aligned_cols=212 Identities=29% Similarity=0.413 Sum_probs=171.6
Q ss_pred CCEEEEECCCCEEECCCCC----------EEEEEEEEECCCEEEEEEECCCCC--CEEEEECCCCCC----CCCCCCCHH
Q ss_conf 4268996584516988987----------922689991797899997067788--612564055556----431571011
Q gi|254780261|r 3 SGVVARKLGMTCVYNIEGR----------RIPVTVLHLDNCQVVVHRTLDKNG--YMAVQVGAGEAK----VKNVSKPMR 66 (221)
Q Consensus 3 ~Glig~KiGMT~if~e~G~----------~vpVTViev~~~~Vv~~kt~ekdG--Y~Avqvg~~~~k----~k~~~Kp~~ 66 (221)
.||+|||+||||++.+|.. .+||||||+||+.|+.++.+..+. +.++.-.|-+.. .++++.+..
T Consensus 36 ~gF~GYKAGMTHv~~~ddrp~S~~~gkEi~~pVTViEtPPm~V~gvr~Y~~t~~Gl~~l~evwa~~l~~e~~Rr~~~~k~ 115 (330)
T TIGR03626 36 QGFAGYKAGMTHVIMVDDRKNSPTEGKEISVPVTVLEAPPLRVAAIRAYGKDPYGLKVLTEVWANNLDKELSRKITLPKN 115 (330)
T ss_pred EEEEEECCCCEEEEEECCCCCCCCCCCEEEEEEEEEECCCEEEEEEEEEEECCCCCEEEEEEECCCCCHHHHHHCCCCCC
T ss_conf 78735415765999955889987689378876777506985999998776679986888999714778777750144545
Q ss_pred HHHHH---------------------------HCCCCCC-EEEEEECCCC--HHHH-----HCCCCEEE-EEECCCCEEE
Q ss_conf 25764---------------------------0356341-0365320651--1211-----00341000-1230253265
Q gi|254780261|r 67 GFFSS---------------------------VNVSPKK-KLFEFRVQKD--DDLL-----PVGSVFSP-SYFTVGQLVD 110 (221)
Q Consensus 67 G~fkK---------------------------~g~~pk~-~l~Efrv~~~--~~~~-----~vG~~i~~-~~F~~Gq~VD 110 (221)
...++ .+++-|+ ++.|+++... ++.+ -+|++|++ |+|++||+||
T Consensus 116 ~~~~~~~e~~~~~~~~~~~~vRvi~~Tqp~~~~g~~kKkp~imEi~v~Ggs~~~k~~~a~~~LgKeI~v~dvF~~g~~vD 195 (330)
T TIGR03626 116 YDVEEKLEKIEELLENDADDVRLIVHTQPKLVTGVPKKKPEIMEIRIGGGSVEERFEYALSILGKEISVSDVFKEGQLVD 195 (330)
T ss_pred CCHHHHHHHHHHHHHCCCCEEEEEEEECHHHCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHCCEEEHHHHCCCCCEEE
T ss_conf 57578899998775377618999997252212686556762899950689989999999998488672467026885689
Q ss_pred EEEEEECCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCEEEEECCCEEEEEECC-----
Q ss_conf 789875343364057504421233357745434666555556752242267666523773336516589998076-----
Q gi|254780261|r 111 VTGMTIGKGFSGAMKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKMAGRMGGNRVTVKNLEVVSVDDK----- 185 (221)
Q Consensus 111 V~g~SkGKGFqGviKR~gf~g~~~sHG~sk~hR~~GsiG~~~~PgRV~kGkkm~G~mG~~~~T~~nl~i~~id~e----- 185 (221)
|+|+||||||||+||||||+++|++||+|+.||++||||+ |+|+||+++++||||||+++||++|++|++|+.+
T Consensus 196 v~gvTKGKGfqG~vkR~g~~~~~~~h~~~k~~R~~gsiG~-~~p~rV~~~v~~aGq~G~h~rT~~Nk~I~kig~~~~~It 274 (330)
T TIGR03626 196 VIAVTKGKGFQGVVKRWGVKLLPRKHKRRKGGRHIGTLGP-WTPSRVRWTVPQAGQMGYHQRTEYNKRILKIGEDGDEIT 274 (330)
T ss_pred EEEEECCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCC-CCCCCEECCCCCCCCCCCCEEEEECCEEEEECCCCCCCC
T ss_conf 9975304542111575243457741346656545763378-888634437776876787445774338999768886035
Q ss_pred ------------CCEEEEECCCCCCCCCEEEEEEECCCCCCCC
Q ss_conf ------------8989997157458887099996031467785
Q gi|254780261|r 186 ------------RGLILVKGCVPGAKKNSWILVRDSFKSAVNC 216 (221)
Q Consensus 186 ------------~n~i~vkGsVPG~~~~~~v~ir~a~k~~~~~ 216 (221)
+|+|+||||||||.|+ +|.+|+|+++....
T Consensus 275 P~GGF~hYG~V~~~~ilikGsvpGp~Kr-~i~lr~~irp~~~~ 316 (330)
T TIGR03626 275 PKGGFVNYGLVRNDYVLIKGSVPGPSKR-LIRLRDAIRPPKPP 316 (330)
T ss_pred CCCCCCCCCEECCCEEEEECCCCCCCCC-EEEEECCCCCCCCC
T ss_conf 6788654525637789997256887661-38960013688765
No 8
>PRK04231 rpl3p 50S ribosomal protein L3P; Reviewed
Probab=100.00 E-value=0 Score=354.50 Aligned_cols=212 Identities=31% Similarity=0.436 Sum_probs=167.9
Q ss_pred CCEEEEECCCCEEECCCCC----------EEEEEEEEECCCEEEEEEECCCCCCEEEEECCCCC---C---CCCCCCCHH
Q ss_conf 4268996584516988987----------92268999179789999706778861256405555---6---431571011
Q gi|254780261|r 3 SGVVARKLGMTCVYNIEGR----------RIPVTVLHLDNCQVVVHRTLDKNGYMAVQVGAGEA---K---VKNVSKPMR 66 (221)
Q Consensus 3 ~Glig~KiGMT~if~e~G~----------~vpVTViev~~~~Vv~~kt~ekdGY~Avqvg~~~~---k---~k~~~Kp~~ 66 (221)
.||+|||+||||++..|.. .+||||||+||+.|+.++.+..+-|---.++.-+. . .++++.+..
T Consensus 37 ~gF~GYKAGMTHvv~~dd~p~S~~~gkEi~~pVTViEtPPm~V~gvr~Y~~tp~Gl~~l~evwa~~l~~el~Rri~~~k~ 116 (333)
T PRK04231 37 LGFAGYKAGMTHVIMIDDRPNSPTEGKEIFVPVTVLETPPLRVAGIRAYEKDPYGLKALTEVWADDLDKELSRRITLPKK 116 (333)
T ss_pred EEEEEECCCCEEEEEECCCCCCCCCCCEEEEEEEEEECCCEEEEEEEEEEECCCCCEEEEEEECCCCCHHHHHHCCCCCC
T ss_conf 68736425775999964889997689378876677506986999999988879986898999404678888741045555
Q ss_pred H----HHHH-----------------------HCCCCCC-EEEEEECCCCH--HHH-----HCCCCEEE-EEECCCCEEE
Q ss_conf 2----5764-----------------------0356341-03653206511--211-----00341000-1230253265
Q gi|254780261|r 67 G----FFSS-----------------------VNVSPKK-KLFEFRVQKDD--DLL-----PVGSVFSP-SYFTVGQLVD 110 (221)
Q Consensus 67 G----~fkK-----------------------~g~~pk~-~l~Efrv~~~~--~~~-----~vG~~i~~-~~F~~Gq~VD 110 (221)
. .+++ .+++-|+ ++.|.++...+ +.+ -+|.+|++ |+|++||+||
T Consensus 117 ~~~~~~~~k~~~~~~~~~~~vRvIv~Tqp~~~~g~~kKkp~imEi~i~GGsi~~kl~~a~~~LgKei~v~dvF~~g~~vD 196 (333)
T PRK04231 117 DDKEKALEKLEELLDGKVVDVRVIVHTQPKLVTGVPKKKPEIMEIRIGGGSVEERLEYAKELLGKEVSISDVFKEGQLVD 196 (333)
T ss_pred CCHHHHHHHHHHHHHCCCEEEEEEEEECHHHCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHCCEECHHHHHCCCCEEE
T ss_conf 56577799998765256228999998350003587667874999941799989999999998478022667314794688
Q ss_pred EEEEEECCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCEEEEECCCEEEEEEC------
Q ss_conf 78987534336405750442123335774543466655555675224226766652377333651658999807------
Q gi|254780261|r 111 VTGMTIGKGFSGAMKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKMAGRMGGNRVTVKNLEVVSVDD------ 184 (221)
Q Consensus 111 V~g~SkGKGFqGviKR~gf~g~~~sHG~sk~hR~~GsiG~~~~PgRV~kGkkm~G~mG~~~~T~~nl~i~~id~------ 184 (221)
|+|+||||||||+||||||+.+|++|++++.||++||||+ |+|+||+++++||||||+++||++|++|++|..
T Consensus 197 v~gvTKGkGfqG~vkR~g~~~~~~kh~~~k~~R~~g~iG~-~~p~rV~~~v~~aGq~G~h~Rte~Nk~i~~ig~~~~~It 275 (333)
T PRK04231 197 VIAVTKGKGFQGVVKRWGVKLLPRKHKRRKGSRRVGTLGP-WHPSRVMWTVPQAGQMGFHQRTEYNKRILKIGDNGEEIT 275 (333)
T ss_pred EEEEECCCCCCCCEEECCEECCCCCCCCCCCCCCCCCCCC-CCCCCEEECCCCCCCCCCCEEEEEEEEEEEECCCCCCCC
T ss_conf 8875203554321576010015521356666435652378-888734545654776787447786428999558986035
Q ss_pred -----------CCCEEEEECCCCCCCCCEEEEEEECCCCCCCC
Q ss_conf -----------68989997157458887099996031467785
Q gi|254780261|r 185 -----------KRGLILVKGCVPGAKKNSWILVRDSFKSAVNC 216 (221)
Q Consensus 185 -----------e~n~i~vkGsVPG~~~~~~v~ir~a~k~~~~~ 216 (221)
.+++|+||||||||.|+ +|.+|+++++....
T Consensus 276 P~GGF~~YG~Vkndyi~ikGsvpGp~KR-~i~lR~~irp~~~~ 317 (333)
T PRK04231 276 PKGGFLHYGLVRNDYVLIKGSVPGPAKR-LIRLRPPIRPPEKK 317 (333)
T ss_pred CCCCCCCCCEECCCEEEEECCCCCCCCC-EEEECCCCCCCCCC
T ss_conf 6788653425637779997046887761-38970003588565
No 9
>PTZ00103 60S ribosomal protein L3; Provisional
Probab=100.00 E-value=0 Score=310.66 Aligned_cols=209 Identities=22% Similarity=0.281 Sum_probs=158.8
Q ss_pred CCEEEEECCCCEEECCCCC----------EEEEEEEEECCCEEEEEEECCCCCCEEEEECCCC---CC---CCCC-----
Q ss_conf 4268996584516988987----------9226899917978999970677886125640555---56---4315-----
Q gi|254780261|r 3 SGVVARKLGMTCVYNIEGR----------RIPVTVLHLDNCQVVVHRTLDKNGYMAVQVGAGE---AK---VKNV----- 61 (221)
Q Consensus 3 ~Glig~KiGMT~if~e~G~----------~vpVTViev~~~~Vv~~kt~ekdGY~Avqvg~~~---~k---~k~~----- 61 (221)
.||+|||+||||++.+|.. .+||||||+||+.|+.++-+..+-|.--.++.-+ .. .+++
T Consensus 44 ~gF~GYKAGMTHvv~~ddrp~S~~~gkEi~~pVTViEtPPm~V~gvrgY~~tp~Gl~~l~evwa~~l~~e~~rr~~kn~~ 123 (393)
T PTZ00103 44 TAFMGYKAGMTHIVRDVDRPGSKLNKKEVVEAVTIIEAPPMVVVGIVGYRETPVGLRTLTTVWAHHTSVEFRRRFYKNWY 123 (393)
T ss_pred EEEEEECCCCEEEEEECCCCCCCCCCCEEEEEEEEEECCCEEEEEEEEEEECCCCCEEEEEEEHHCCCHHHHHHHHCCHH
T ss_conf 78601125765999934899986679658844789876985999999875669986687888530076888765410011
Q ss_pred -------CC----C--------HHHHHH---------------HHCCCCC-CEEEEEECCCCH--HHH-----HCCCCEE
Q ss_conf -------71----0--------112576---------------4035634-103653206511--211-----0034100
Q gi|254780261|r 62 -------SK----P--------MRGFFS---------------SVNVSPK-KKLFEFRVQKDD--DLL-----PVGSVFS 99 (221)
Q Consensus 62 -------~K----p--------~~G~fk---------------K~g~~pk-~~l~Efrv~~~~--~~~-----~vG~~i~ 99 (221)
++ . .+..++ +.+++.| .++.|.++...+ +.+ -+|++|+
T Consensus 124 ~skkka~~k~~k~~~~~~~~e~~l~~~~~~~~viRvI~~Tqp~~~~l~~Kkp~imEi~v~GGsi~ekl~~a~~~lgkei~ 203 (393)
T PTZ00103 124 QSKKKAFTKYKKFAATKTAEERTLKRIAKYASVIRVIAHTQLSKLRLGQKKAHVMEIQVNGGTVAEKVDFAKSLLEKEVP 203 (393)
T ss_pred HHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCEEEEEEECCHHHCCCCCCCCEEEEEEECCCCHHHHHHHHHHHHCCCCC
T ss_conf 23334432210133530568999998764062899998637432488877761799850689989999999998468214
Q ss_pred E-EEECCCCEEEEEEEEECCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCEEEEECCCE
Q ss_conf 0-123025326578987534336405750442123335774543466655555675224226766652377333651658
Q gi|254780261|r 100 P-SYFTVGQLVDVTGMTIGKGFSGAMKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKMAGRMGGNRVTVKNLE 178 (221)
Q Consensus 100 ~-~~F~~Gq~VDV~g~SkGKGFqGviKR~gf~g~~~sHG~sk~hR~~GsiG~~~~PgRV~kGkkm~G~mG~~~~T~~nl~ 178 (221)
+ |+|++||+|||+|+|||||||||+||||.+.+|..| ++..|++||||+ |+|+||.....||||||+++||++|.+
T Consensus 204 v~dVF~~ge~iDvigVTKGKG~qGvvkRwGvk~lprK~--~kg~Rkvg~iG~-whP~rV~~tVpraGQ~GyH~RTE~NKr 280 (393)
T PTZ00103 204 VDSVFQQNEAIDVIGVTKGHGFEGVVKRWGVACLPRKT--HRGLRKVACIGA-WHPARVQYTVARAGQHGYHHRTELNKK 280 (393)
T ss_pred HHHHCCCCCEEEEEEEECCCCCCCCEEEECEECCCCCC--CCCCCCCCCCCC-CCCCCEEEECCCCCCCCCCCEEEECCE
T ss_conf 66822688458999853156754433550101045433--345312454357-677516664134766775212210307
Q ss_pred EEEEE------------------------------CCCCEEEEECCCCCCCCCEEEEEEECCCCCCC
Q ss_conf 99980------------------------------76898999715745888709999603146778
Q gi|254780261|r 179 VVSVD------------------------------DKRGLILVKGCVPGAKKNSWILVRDSFKSAVN 215 (221)
Q Consensus 179 i~~id------------------------------~e~n~i~vkGsVPG~~~~~~v~ir~a~k~~~~ 215 (221)
|++|- ..+++|+||||||||.|+ +|.+|+|+++...
T Consensus 281 I~kIG~~~~~~~~~t~~D~tek~ItP~GGF~hYG~VkndyimiKGsvpGp~KR-li~lR~~irp~~~ 346 (393)
T PTZ00103 281 IYRIGRAVEPNQATTEADLTEKTITPMGGFPHYGTVRNDFLMLKGCVVGPKKR-VITLRKSLVPQTS 346 (393)
T ss_pred EEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCEEEEECCCCCCCCC-EEEECCCCCCCCC
T ss_conf 89944766656553334555751267888765633658779996467886640-2872023266766
No 10
>KOG0746 consensus
Probab=99.93 E-value=1.7e-26 Score=175.96 Aligned_cols=204 Identities=23% Similarity=0.317 Sum_probs=138.5
Q ss_pred CCEEEEECCCCEEECCC---CC-------EEEEEEEEECCCEEEEEEECCC--CCCEEE------EECCCCCC-------
Q ss_conf 42689965845169889---87-------9226899917978999970677--886125------64055556-------
Q gi|254780261|r 3 SGVVARKLGMTCVYNIE---GR-------RIPVTVLHLDNCQVVVHRTLDK--NGYMAV------QVGAGEAK------- 57 (221)
Q Consensus 3 ~Glig~KiGMT~if~e~---G~-------~vpVTViev~~~~Vv~~kt~ek--dGY~Av------qvg~~~~k------- 57 (221)
++|||||.|||+|.-|- |. .-+|||||.||+.|+.+--+.+ .|..++ .|+-+..+
T Consensus 31 T~FlgYKAGMThivRe~drpgsK~~kkEv~eAVTi~etPpmvVvgvvgyv~Tp~Glr~l~tv~A~hlSde~~Rrfyknw~ 110 (384)
T KOG0746 31 TAFLGYKAGMTHIVREVDRPGSKVNKKEVVEAVTIVETPPMVVVGIVGYVETPRGLRTLKTVWAEHLSDECKRRFYKNWH 110 (384)
T ss_pred EEEECCCCCCHHHHHHHCCCCCCCCHHHHEEEEEEECCCCEEEEEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 65510124421111230476430030330356787427987999875665467316677799999866999999977555
Q ss_pred ---CCCCCCCHHHHHHHHC---C----------------------------CCCCEEEEEECCCCH--HHHH-----CCC
Q ss_conf ---4315710112576403---5----------------------------634103653206511--2110-----034
Q gi|254780261|r 58 ---VKNVSKPMRGFFSSVN---V----------------------------SPKKKLFEFRVQKDD--DLLP-----VGS 96 (221)
Q Consensus 58 ---~k~~~Kp~~G~fkK~g---~----------------------------~pk~~l~Efrv~~~~--~~~~-----vG~ 96 (221)
.+-.++....++...+ + ..+.||.|..++... +.+. .-+
T Consensus 111 kskkkaft~~~k~~~~~~gk~~~~~~~~~~kky~~virv~ahtq~~~~~l~qkkahlmeiqvngGtia~KvdwA~~~lEk 190 (384)
T KOG0746 111 KSKKKAFTKYCKKWQDEDGKKQLEKDFSSMKKYCQVIRVIAHTQMRLLPLRQKKAHLMEIQVNGGTVAEKVDWARERLEK 190 (384)
T ss_pred HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHEEEEEEECHHHHHHHHHHHHHHHEEEECCCCHHHHHHHHHHHHHC
T ss_conf 55567777875334332041056789999985442676522102223123454423303431477377776777764320
Q ss_pred CEEE-EEECCCCEEEEEEEEECCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCEEEEEC
Q ss_conf 1000-123025326578987534336405750442123335774543466655555675224226766652377333651
Q gi|254780261|r 97 VFSP-SYFTVGQLVDVTGMTIGKGFSGAMKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKMAGRMGGNRVTVK 175 (221)
Q Consensus 97 ~i~~-~~F~~Gq~VDV~g~SkGKGFqGviKR~gf~g~~~sHG~sk~hR~~GsiG~~~~PgRV~kGkkm~G~mG~~~~T~~ 175 (221)
++.+ .+|...+.+|+.|+|+|+||.|+..||+-..+|... ++..|...+||+ |+|+||-.-..+|||.|++.+|..
T Consensus 191 qv~v~~vF~qdemId~IgvtkGkGykGvt~rw~tkklprkt--hrglrkvaciga-whpa~V~~sVaRaGqkgyHhrTei 267 (384)
T KOG0746 191 QVPVNQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKLPRKT--HRGLRKVACIGA-WHPARVAFSVARAGQKGYHHRTEI 267 (384)
T ss_pred CCCHHHCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCHH--CCCCHHEEECCC-CCCHHEEEEEEECCCCCCCHHHHH
T ss_conf 36611113543321125444224434320123433476010--033011110145-552120122010534463034343
Q ss_pred CCEEEEEEC-------------------------------CCCEEEEECCCCCCCCCEEEEEEECC
Q ss_conf 658999807-------------------------------68989997157458887099996031
Q gi|254780261|r 176 NLEVVSVDD-------------------------------KRGLILVKGCVPGAKKNSWILVRDSF 210 (221)
Q Consensus 176 nl~i~~id~-------------------------------e~n~i~vkGsVPG~~~~~~v~ir~a~ 210 (221)
|.+|++|-- .++++++||+|+|+.+. ++.+|.+.
T Consensus 268 NkkiY~ig~g~~~~~nastdyDlt~k~itpmggf~hYG~V~ndfvM~kgcvvg~kKr-v~TLrksl 332 (384)
T KOG0746 268 NKKIYRIGQGKLIKNNASTDYDLTEKSITPMGGFPHYGEVINDFVMLKGCVVGPKKR-VVTLRKSL 332 (384)
T ss_pred HHHEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECHHEEECCCCCCCCCC-CCCHHHHH
T ss_conf 110142265420124566675431001466788650314402010111332586433-33014333
No 11
>PRK10737 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=50.14 E-value=21 Score=16.83 Aligned_cols=18 Identities=28% Similarity=0.401 Sum_probs=7.4
Q ss_pred EEEEEECCCCEEEEECCCCC
Q ss_conf 89998076898999715745
Q gi|254780261|r 178 EVVSVDDKRGLILVKGCVPG 197 (221)
Q Consensus 178 ~i~~id~e~n~i~vkGsVPG 197 (221)
+|+.|+. +-+.|-+.=|=
T Consensus 108 ~V~eV~~--~~VtvD~NHPL 125 (196)
T PRK10737 108 EITAVED--DHVVVDGNHML 125 (196)
T ss_pred EEEEECC--CEEEEECCCCC
T ss_conf 9999779--98999589877
No 12
>TIGR01810 betA choline dehydrogenase; InterPro: IPR011533 Choline dehydrogenase catalyzes the conversion of exogenously supplied choline into the intermediate glycine betaine aldehyde, as part of a two-step oxidative reaction leading to the formation of osmoprotectant betaine. This enzymatic system can be found in both Gram-positive and Gram-negative bacteria. As in Escherichia coli , Staphylococcus xylosus , and Sinorhizobium meliloti , this enzyme is found associated in a transcriptionally co-induced gene cluster with betaine aldehyde dehydrogenase, the second catalytic enzyme in this reaction. Other Gram-positive organisms have been shown to employ a different enzymatic system, utilising a soluble choline oxidase or type III alcohol dehydrogenase instead of choline dehydrogenase . This enzyme is a member of the GMC oxidoreductase family, sharing a common evolutionary origin and enzymatic reaction with alcohol dehydrogenase . Out grouping from this model, Caulobacter crescentus shares sequence homology with choline dehydrogenase, yet other genes participating in this enzymatic reaction have not currently been identified. ; GO: 0008812 choline dehydrogenase activity, 0019285 glycine betaine biosynthetic process from choline.
Probab=47.27 E-value=14 Score=17.86 Aligned_cols=63 Identities=14% Similarity=0.122 Sum_probs=38.3
Q ss_pred CEEECCCCCEEEEEEEEECCCEEEEEEECCCCCCEEEEECCCCCCCCCCCCCHHHHHHHHCCCCCCEEEEEECCC
Q ss_conf 516988987922689991797899997067788612564055556431571011257640356341036532065
Q gi|254780261|r 13 TCVYNIEGRRIPVTVLHLDNCQVVVHRTLDKNGYMAVQVGAGEAKVKNVSKPMRGFFSSVNVSPKKKLFEFRVQK 87 (221)
Q Consensus 13 T~if~e~G~~vpVTViev~~~~Vv~~kt~ekdGY~Avqvg~~~~k~k~~~Kp~~G~fkK~g~~pk~~l~Efrv~~ 87 (221)
++|.-|.++++-||..+=+.......+ .+|. |.|..+. +|-|++ +..+|+-+-.+|+||-+..
T Consensus 223 ~ki~feg~ratGVe~~~ggst~~e~~~-ankE----Vilsaga-----inSPql--L~lSGiG~aehL~e~gI~~ 285 (540)
T TIGR01810 223 DKIVFEGKRATGVEFKKGGSTIKERVK-ANKE----VILSAGA-----INSPQL--LQLSGIGDAEHLKELGIEL 285 (540)
T ss_pred EEEEECCCEEEEEEEECCCCCCCCEEC-CCCE----EEEECCH-----HHHHHH--HHHCCCCCHHHHHHCCCCE
T ss_conf 000330883799888228973300001-2445----7883341-----213589--9762897179998558960
No 13
>TIGR02013 rpoB DNA-directed RNA polymerase, beta subunit; InterPro: IPR010243 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This entry describes orthologues of the beta subunit of bacterial RNA polymerase. The core enzyme consists of two alpha chains, one beta chain, and one beta' subunit.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006350 transcription.
Probab=43.90 E-value=9 Score=18.99 Aligned_cols=23 Identities=13% Similarity=0.167 Sum_probs=15.1
Q ss_pred EEEECC---CEEEEEEECCCCCCEEE
Q ss_conf 999179---78999970677886125
Q gi|254780261|r 27 VLHLDN---CQVVVHRTLDKNGYMAV 49 (221)
Q Consensus 27 Viev~~---~~Vv~~kt~ekdGY~Av 49 (221)
=|.||| -+|+.+|-..+.||..-
T Consensus 1000 SL~vP~G~~G~ViDVkvF~R~g~~K~ 1025 (1449)
T TIGR02013 1000 SLRVPPGVEGTVIDVKVFSREGKEKD 1025 (1449)
T ss_pred CCCCCCCCCEEEEEEEEECCCCCCCC
T ss_conf 63057997207998688540123330
No 14
>KOG0482 consensus
Probab=43.03 E-value=11 Score=18.59 Aligned_cols=97 Identities=22% Similarity=0.280 Sum_probs=53.5
Q ss_pred EEEECCCEEEEEEECCCCCCEEEEECCCCCCCCCCCC---CHHHHHHHHCCC----------CCCEEEEEECCCCHHHHH
Q ss_conf 9991797899997067788612564055556431571---011257640356----------341036532065112110
Q gi|254780261|r 27 VLHLDNCQVVVHRTLDKNGYMAVQVGAGEAKVKNVSK---PMRGFFSSVNVS----------PKKKLFEFRVQKDDDLLP 93 (221)
Q Consensus 27 Viev~~~~Vv~~kt~ekdGY~Avqvg~~~~k~k~~~K---p~~G~fkK~g~~----------pk~~l~Efrv~~~~~~~~ 93 (221)
+-+|-|+.++..-|.|..||+--| ++...-++- +--..+...... .+-+..|....+-.+..|
T Consensus 170 ~S~VKP~m~VatYtCd~CGaE~yQ----eV~s~~F~pl~~CpS~eC~~n~~~G~L~lqtRgSKFikfQe~kmQEls~qVP 245 (721)
T KOG0482 170 VSDVKPSMVVATYTCDQCGAETYQ----EVNSRTFTPLSECPSEECRTNKAGGRLYLQTRGSKFIKFQEVKMQELSDQVP 245 (721)
T ss_pred CCCCCCCEEEEEEECCCCCHHHHC----CCCCCCCCCHHHCCHHHHHHCCCCCEEEEEECCCCCCHHHHHHHHHHHCCCC
T ss_conf 034566349999852654576600----0457654654339848864324588189983211130345656988745588
Q ss_pred CCCC---EE-------EEEECCCCEEEEEEEEECCCCCCEEEECCCCCCC
Q ss_conf 0341---00-------0123025326578987534336405750442123
Q gi|254780261|r 94 VGSV---FS-------PSYFTVGQLVDVTGMTIGKGFSGAMKRHNFGGLR 133 (221)
Q Consensus 94 vG~~---i~-------~~~F~~Gq~VDV~g~SkGKGFqGviKR~gf~g~~ 133 (221)
+|.. ++ ...-.+|+.|+|+|+=- ++-++||+-..
T Consensus 246 vG~IPRsltv~~~ge~tr~~~PGDvV~vsGiFL------P~pytGfr~~~ 289 (721)
T KOG0482 246 VGHIPRSLTVHVYGEMTRKCQPGDVVVVSGIFL------PIPYTGFRALK 289 (721)
T ss_pred CCCCCCEEEEEEECCCCEECCCCCEEEEEEEEC------CCCHHHHHHHH
T ss_conf 776675158997300001058998799966551------66135379987
No 15
>pfam11325 DUF3127 Protein of unknown function (DUF3127). This bacterial family of proteins has no known function.
Probab=42.69 E-value=25 Score=16.41 Aligned_cols=29 Identities=24% Similarity=0.316 Sum_probs=23.5
Q ss_pred CCCCEEE-EEECCCCEEEEEEEEECCCCCC
Q ss_conf 0341000-1230253265789875343364
Q gi|254780261|r 94 VGSVFSP-SYFTVGQLVDVTGMTIGKGFSG 122 (221)
Q Consensus 94 vG~~i~~-~~F~~Gq~VDV~g~SkGKGFqG 122 (221)
.++.++. +-|.+||.|.|+-.-.|+=|+|
T Consensus 43 ~~dk~~~~~~~~vGd~V~V~fnl~gREw~g 72 (84)
T pfam11325 43 WGDKIDLLDSLNVGDEVKVSFDLEGREWNG 72 (84)
T ss_pred ECCCHHHHCCCCCCCEEEEEEEEECCEECC
T ss_conf 836756770689999899999825368154
No 16
>cd00686 Terpene_cyclase_cis_trans_C1 Cis, Trans, Terpene Cyclases, Class 1. This CD includes the terpenoid cyclase, trichodiene synthase, which catalyzes the cyclization of farnesyl diphosphate (FPP) to trichodiene using a cis-trans pathway, and is the first committed step in the biosynthesis of trichothecene toxins and antibiotics. As with other enzymes with the 'terpenoid synthase fold', this enzyme has two conserved metal binding motifs that coordinate Mg2+ ion-bridged binding of the diphosphate moiety of FPP. Metal-triggered substrate ionization initiates catalysis, and the alpha-barrel active site serves as a template to channel and stabilize the conformations of reactive carbocation intermediates through a complex cyclization cascade. These enzymes function as homodimers and are found in several genera of fungi.
Probab=33.96 E-value=16 Score=17.56 Aligned_cols=40 Identities=23% Similarity=0.447 Sum_probs=29.5
Q ss_pred CCCE-EEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECC
Q ss_conf 3640-5750442123335774543466655555675224226
Q gi|254780261|r 120 FSGA-MKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKN 160 (221)
Q Consensus 120 FqGv-iKR~gf~g~~~sHG~sk~hR~~GsiG~~~~PgRV~kG 160 (221)
|||. |.-|||+|-|-||---.+.|+.-.+|.|-. |-.||-
T Consensus 158 FeGCWIEQ~NF~GypGs~~yPgFLRRlNgLG~~vg-~sl~P~ 198 (357)
T cd00686 158 FEGCWIEQYNFGGFPGSHDYPQFLRRMNGLGHCVG-ASLWPK 198 (357)
T ss_pred HCCCCEEECCCCCCCCCCCCHHHHHHHCCCCCCCC-CCCCCH
T ss_conf 51201033256898885436089998426544025-453765
No 17
>pfam06003 SMN Survival motor neuron protein (SMN). This family consists of several eukaryotic survival motor neuron (SMN) proteins. The Survival of Motor Neurons (SMN) protein, the product of the spinal muscular atrophy-determining gene, is part of a large macromolecular complex (SMN complex) that functions in the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs). The SMN complex functions as a specificity factor essential for the efficient assembly of Sm proteins on U snRNAs and likely protects cells from illicit, and potentially deleterious, non-specific binding of Sm proteins to RNAs.
Probab=31.73 E-value=42 Score=15.09 Aligned_cols=28 Identities=18% Similarity=0.386 Sum_probs=22.2
Q ss_pred EEEEECCCC--EEECCCCCEEEEEEEEECC
Q ss_conf 689965845--1698898792268999179
Q gi|254780261|r 5 VVARKLGMT--CVYNIEGRRIPVTVLHLDN 32 (221)
Q Consensus 5 lig~KiGMT--~if~e~G~~vpVTViev~~ 32 (221)
+.-+|+|=. .+|+|||..-|.||+.+..
T Consensus 66 ~~~wkVGD~C~A~yseDG~~YeAtI~SId~ 95 (264)
T pfam06003 66 LKEWQVGDSCNAVWSEDGNLYTATITSIDQ 95 (264)
T ss_pred CCEEECCCEEEEEECCCCCCCEEEEEEECC
T ss_conf 420111885676652578520136777526
No 18
>pfam06330 TRI5 Trichodiene synthase (TRI5). This family consists of several fungal trichodiene synthase proteins (EC:4.2.3.6). TRI5 encodes the enzyme trichodiene synthase, which has been shown to catalyse the first step in the trichothecene pathways of Fusarium and Trichothecium species.
Probab=30.97 E-value=19 Score=17.09 Aligned_cols=40 Identities=23% Similarity=0.451 Sum_probs=29.6
Q ss_pred CCCE-EEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECC
Q ss_conf 3640-5750442123335774543466655555675224226
Q gi|254780261|r 120 FSGA-MKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKN 160 (221)
Q Consensus 120 FqGv-iKR~gf~g~~~sHG~sk~hR~~GsiG~~~~PgRV~kG 160 (221)
|+|. |.-|||+|-|-||---.+.|+.-.+|.|-. |-.||-
T Consensus 158 FeGCWIEQ~NF~G~pGs~~yPgFLRRlNgLG~~vg-~sl~P~ 198 (376)
T pfam06330 158 FEGCWIEQYNFGGFPGSDDYPQFLRRMNGLGHCVG-GSLWPK 198 (376)
T ss_pred HCCCCEEECCCCCCCCCCCCHHHHHHHCCCCCCCC-CCCCCH
T ss_conf 51201033256898885435389998336554125-454765
No 19
>TIGR02684 dnstrm_HI1420 probable addiction module antidote protein; InterPro: IPR014057 Members of this strictly bacterial protein family are small, at roughly 100 amino acids. The gene is almost invariably the downstream member of a gene pair. It is a predicted DNA-binding protein from a clade within the helix-turn-helix family IPR001387 from INTERPRO. These gene pairs, when found on the bacterial chromosome, are located often with prophage regions, but also both in integrated plasmid regions and in housekeeping gene regions. Analysis suggests that the gene pair may serve as an addiction module..
Probab=24.52 E-value=7 Score=19.63 Aligned_cols=13 Identities=54% Similarity=0.726 Sum_probs=11.0
Q ss_pred CCEEEEECCCCEE
Q ss_conf 4268996584516
Q gi|254780261|r 3 SGVVARKLGMTCV 15 (221)
Q Consensus 3 ~Glig~KiGMT~i 15 (221)
.|.|++.-||||+
T Consensus 39 LG~iArArGMtql 51 (91)
T TIGR02684 39 LGVIARARGMTQL 51 (91)
T ss_pred HHHHHHHCCHHHH
T ss_conf 8899865165789
No 20
>KOG1800 consensus
Probab=23.53 E-value=43 Score=15.03 Aligned_cols=24 Identities=21% Similarity=0.306 Sum_probs=19.7
Q ss_pred CCCCEEEEECCCCCCCCCCCCCHH
Q ss_conf 788612564055556431571011
Q gi|254780261|r 43 KNGYMAVQVGAGEAKVKNVSKPMR 66 (221)
Q Consensus 43 kdGY~Avqvg~~~~k~k~~~Kp~~ 66 (221)
.|.|+|+.|+||...++++.-|-.
T Consensus 106 ~~~ydavvLaYGa~~dR~L~IPGe 129 (468)
T KOG1800 106 TDNYDAVVLAYGADGDRRLDIPGE 129 (468)
T ss_pred HHCCCEEEEEECCCCCCCCCCCCC
T ss_conf 621667999715888740689874
No 21
>cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=21.88 E-value=30 Score=15.90 Aligned_cols=29 Identities=14% Similarity=0.248 Sum_probs=15.1
Q ss_pred CCCEEEEEECCCCHHHHHCCCCEEEEEEC
Q ss_conf 34103653206511211003410001230
Q gi|254780261|r 76 PKKKLFEFRVQKDDDLLPVGSVFSPSYFT 104 (221)
Q Consensus 76 pk~~l~Efrv~~~~~~~~vG~~i~~~~F~ 104 (221)
|..++.+.++.+..+.+.+|+++.+.+++
T Consensus 29 ~~s~lsd~~v~~p~~~fk~G~~Vk~rVl~ 57 (69)
T cd05697 29 PPMHLADVRLKHPEKKFKPGLKVKCRVLS 57 (69)
T ss_pred EHHHHCCCCCCCHHHCCCCCCEEEEEEEE
T ss_conf 78990865206988908999999999999
No 22
>KOG3181 consensus
Probab=21.17 E-value=48 Score=14.71 Aligned_cols=10 Identities=40% Similarity=0.813 Sum_probs=4.4
Q ss_pred CCCCEEEEEC
Q ss_conf 7886125640
Q gi|254780261|r 43 KNGYMAVQVG 52 (221)
Q Consensus 43 kdGY~Avqvg 52 (221)
.|||+.+.|-
T Consensus 31 edGySgvEvR 40 (244)
T KOG3181 31 EDGYSGVEVR 40 (244)
T ss_pred HCCCCCEEEE
T ss_conf 6476742899
No 23
>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family; InterPro: IPR006515 These eukaryotic proteins recognize the poly-A of mRNA and consist of four tandem RNA recognition domains at the N terminus followed by a PABP-specific domain at the C terminus. The protein is involved in the transport of mRNAs from the nucleus to the cytoplasm . There are four paralogs in Homo sapiens which are expressed in testis , platelets (Q13310 from SWISSPROT ), broadly expressed (P11940 from SWISSPROT ) and of unknown tissue range (Q15097 from SWISSPROT). ; GO: 0003723 RNA binding.
Probab=21.08 E-value=41 Score=15.13 Aligned_cols=21 Identities=33% Similarity=0.559 Sum_probs=13.8
Q ss_pred CCCEEEEEECCCCEEEEEEEEECCCC
Q ss_conf 34100012302532657898753433
Q gi|254780261|r 95 GSVFSPSYFTVGQLVDVTGMTIGKGF 120 (221)
Q Consensus 95 G~~i~~~~F~~Gq~VDV~g~SkGKGF 120 (221)
|..|++-+ ..|..|.|||+||
T Consensus 113 G~IlSCKV-----a~dE~GkSrGYgF 133 (860)
T TIGR01628 113 GNILSCKV-----ATDENGKSRGYGF 133 (860)
T ss_pred CCEEEEEE-----EECCCCCCCCCCE
T ss_conf 86577887-----7626860035413
No 24
>cd06188 NADH_quinone_reductase Na+-translocating NADH:quinone oxidoreductase (Na+-NQR) FAD/NADH binding domain. (Na+-NQR) provides a means of storing redox reaction energy via the transmembrane translocation of Na2+ ions. The C-terminal domain resembles ferredoxin:NADP+ oxidoreductase, and has NADH and FAD binding sites. (Na+-NQR) is distinct from H+-translocating NADH:quinone oxidoreductases and noncoupled NADH:quinone oxidoreductases. The NAD(P) binding domain of ferredoxin reductase-like proteins catalyze electron transfer between an NAD(P)-binding domain of the alpha/beta class and a discrete (usually N-terminal) domain which vary in orientation with respect to the NAD(P) binding domain. The N-terminal domain of this group typically contains an iron-sulfur cluster binding domain.
Probab=20.61 E-value=67 Score=13.86 Aligned_cols=13 Identities=23% Similarity=0.347 Sum_probs=8.8
Q ss_pred EECCCCEEEEEEE
Q ss_conf 2302532657898
Q gi|254780261|r 102 YFTVGQLVDVTGM 114 (221)
Q Consensus 102 ~F~~Gq~VDV~g~ 114 (221)
.+++|+.|.|.|=
T Consensus 128 ~lk~Gd~v~i~gP 140 (283)
T cd06188 128 NLKPGDKVTASGP 140 (283)
T ss_pred CCCCCCEEEEECC
T ss_conf 4999998999646
Done!