Query 045479
Match_columns 482
No_of_seqs 129 out of 189
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 02:29:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045479.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045479hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF11955 PORR: Plant organelle 100.0 1E-112 2E-117 866.7 30.3 328 55-396 1-334 (335)
2 PF11955 PORR: Plant organelle 98.6 2.1E-07 4.6E-12 96.2 10.3 141 159-353 11-152 (335)
3 PF10446 DUF2457: Protein of u 86.9 0.54 1.2E-05 50.9 3.3 8 460-467 120-127 (458)
4 KOG1832 HIV-1 Vpr-binding prot 77.6 1.7 3.7E-05 50.9 2.9 135 173-314 1156-1302(1516)
5 KOG1832 HIV-1 Vpr-binding prot 66.3 4.4 9.6E-05 47.7 2.8 8 208-215 1099-1106(1516)
6 PLN03196 MOC1-like protein; Pr 64.5 13 0.00029 40.8 6.0 204 100-355 169-374 (487)
7 PHA02608 67 prohead core prote 57.9 11 0.00024 32.1 3.1 33 373-405 8-40 (80)
8 PF11705 RNA_pol_3_Rpc31: DNA- 55.6 12 0.00025 37.1 3.4 9 275-283 63-71 (233)
9 PF12872 OST-HTH: OST-HTH/LOTU 37.0 81 0.0017 24.9 4.9 49 74-125 7-66 (74)
10 PLN03196 MOC1-like protein; Pr 36.9 9.9 0.00022 41.8 -0.5 208 100-363 205-416 (487)
11 KOG1991 Nuclear transport rece 30.0 90 0.0019 37.5 5.6 15 72-86 522-536 (1010)
12 PF04931 DNA_pol_phi: DNA poly 29.7 39 0.00084 39.2 2.7 20 374-393 583-602 (784)
13 PF04931 DNA_pol_phi: DNA poly 28.4 39 0.00085 39.2 2.5 7 174-180 397-403 (784)
14 KOG3130 Uncharacterized conser 25.4 41 0.00089 36.7 1.8 15 213-227 119-133 (514)
15 PTZ00415 transmission-blocking 24.7 61 0.0013 41.3 3.2 10 382-391 134-143 (2849)
16 PF04340 DUF484: Protein of un 24.4 60 0.0013 31.7 2.6 50 107-161 9-60 (225)
17 KOG0526 Nucleosome-binding fac 20.1 77 0.0017 35.8 2.6 48 74-123 82-132 (615)
No 1
>PF11955 PORR: Plant organelle RNA recognition domain; InterPro: IPR021099 The plant organelle RNA recognition (PORR) domain, previously known as DUF860, is a component of group II intron ribonucleoprotein particles in maize chloroplasts. It is required for the splicing of the introns with which it associates, and promotes splicing in the context of a heterodimer with the RNase III-domain protein RNC1. Proteins containing this domain are predicted to localise to mitochondria or chloroplasts []. It seems likely that most PORR proteins function in organellar RNA metabolism [].
Probab=100.00 E-value=1.1e-112 Score=866.75 Aligned_cols=328 Identities=45% Similarity=0.749 Sum_probs=312.8
Q ss_pred cccCcchhhHHHHhcchhHHHHHHHHHhcCCCCeechhhhhhccccCCCCCcchHhHHHhhCCceeEEeccCCCCCCCCC
Q 045479 55 IVRSPSLDKHIVTHNRTRFVQKLKTLLLSKPKHYIPIHILSKCRSYLSLPKLKSIRSMIHRYPMIFEVFAVPMPPTPLNA 134 (482)
Q Consensus 55 ~vRD~~LD~~v~rek~lr~v~~lk~lI~s~P~~~lpl~~L~k~r~~LgL~~~~~v~~FlrrYP~iF~~f~~p~~~~P~~~ 134 (482)
|+||++||++|+++|++++|++|+++|+++|+++|||+.|++++++|||+ ++++++||+|||+||++|.++..
T Consensus 1 w~rd~~lD~~i~~~k~l~~v~~l~~~i~~~p~~~~pl~~l~k~~~~L~l~-~~~~~~flrkyP~iF~~~~~~~~------ 73 (335)
T PF11955_consen 1 WVRDPYLDKVIEREKRLRFVLRLKDLILSQPSHSLPLRDLSKLRRQLGLK-PRKVSRFLRKYPSIFEVFQHPSR------ 73 (335)
T ss_pred CCCchhHHHHHHhhhhHHHHHHHHHHHHcCCCCcccHHHHHHHHHhcCCC-cccHHHHHHhCCceEEEeccCCC------
Confidence 99999999999999999999999999999999999999999999999995 47999999999999999997543
Q ss_pred CCCCccceeecCHHHHHHHHHHHHHHHhhhHHHHHHHHHHHhccCCceechhhHHHhhhhCCCCchhhhccccCCCCCeE
Q 045479 135 TKSGYQQCVRLTPAAAALAAQEISLKSAISNTLANKLQKLLMLSSHRRLLLSKLVHLASDLGLLPNFRSRLCNDYPDKFK 214 (482)
Q Consensus 135 ~~~~~~~~vrLT~~A~~L~~eE~~v~~~~e~~~v~rLrKLLMMS~~rrLpL~kL~~lr~dLGLP~DF~~~lv~~yPd~Fr 214 (482)
+++||+||++|++|++||++|++++++++|+||+||||||++++|||++|+|++||||||+||+++++++|||+|+
T Consensus 74 ----~~~~~~LT~~a~~L~~eE~~~~~~~e~~~v~rL~KLLMMS~~~rlpL~ki~~l~~dLGLP~Df~~~lv~~yP~~Fr 149 (335)
T PF11955_consen 74 ----SVPWFRLTPEAEDLLREERRVREEMEPDLVERLRKLLMMSKDRRLPLSKIAHLRRDLGLPDDFRDSLVPKYPDYFR 149 (335)
T ss_pred ----CCceEEeCHHHHHHHHHHHHHHHhChHHHHHHHHHHhccCCCCcccHHHHHHHHHHcCCChhhccchhhhCCCCcE
Confidence 4669999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEec-CCCceEEEeecCCCCccChhhhhcc-----cCCccccCCCCCcccccccCcccchHHHHHHHhhccCCCCCCCCC
Q 045479 215 IVDT-SYGRALELVSWDPQLAVPMPCAETK-----SLGLIVDRPLKFRHLKLRKGLNLKRRHRNFLIKFGELPDVCPYNT 288 (482)
Q Consensus 215 vv~~-~~g~~LeLv~Wd~~LAVs~~e~r~~-----~~~~~i~~P~~Fp~~~~~rGf~l~k~~r~~L~~fQkLPYiSPYed 288 (482)
||+. +++.+||||+|||+||||++|.+.. ..+..+..|++|| ++||+||++++++++||++||+|||+|||+|
T Consensus 150 vv~~~~~~~~LeLv~Wd~~LAvs~~E~~~~~~~~~~~~~~~~~~~~Fp-~~fp~G~~l~k~~~~~l~~fQ~lPy~SPYed 228 (335)
T PF11955_consen 150 VVDLEDGGRYLELVSWDPELAVSALEKRAEKEYREKREDGFDRPLAFP-VSFPKGFRLKKKFREWLEEFQKLPYISPYED 228 (335)
T ss_pred EeecCCCCCEEEEeecCCccCcCccchhhhhccccccccccCCceeee-ecCCCCccccHHHHHHHHHHhcCCCCCCCCC
Confidence 9994 4458999999999999999988643 3456788999999 9999999999999999999999999999999
Q ss_pred CCCCCCcCChhhhHHHHHHHHHHhhcchhhHhhhhHHHhhHHhhCCcHHHHHHHhhCCCcEEEeecCCeeeEEeecccCC
Q 045479 289 SSEEFPKESLQAEKRACALVREVLGMMVEKQTLIDHLTHFRKDFGLSNNLRAMILRHPELFYVSPKGIRNSVQLVEEFDE 368 (482)
Q Consensus 289 ~~~~l~~~S~eaEKRaVaVlHELLSLTveKr~~v~~L~hFr~efgLp~k~~~~l~RHPgIFYvS~Kg~~~TVfLREAY~~ 368 (482)
++ +++++|+++|||||||+||||||||||||++++|+|||+|||||++|+++|+|||||||||+||+|+||||||||+
T Consensus 229 ~~-~l~~~s~~~EKRaVaVlHElLSLTveKr~~~~~L~~fr~ef~lp~k~~~~l~rHPgIFYvS~kg~~~TVfLrEAY~- 306 (335)
T PF11955_consen 229 AS-HLDPGSDEAEKRAVAVLHELLSLTVEKRTEVDHLTHFRKEFGLPQKFRRLLLRHPGIFYVSLKGKRHTVFLREAYD- 306 (335)
T ss_pred cc-CCCCCChHHHhHHHHHHHHHHHhhhhhhccHHHHHHHHHHhCCcHHHHHHHHhCCCeEEEeccCCceEEEEeeccC-
Confidence 98 6999999999999999999999999999999999999999999999999999999999999999999999999997
Q ss_pred CCCccccChhhHHHHHHHHHHHHhHHHH
Q 045479 369 KGVLLKRDETLLIKEKLMELVREGKKMR 396 (482)
Q Consensus 369 ~g~LIek~Pl~~iReK~~~Lm~~g~~~r 396 (482)
+|+||||||++.+|+||++||.+|+++|
T Consensus 307 ~~~Liek~Pl~~~r~k~~~Lm~~~~~~~ 334 (335)
T PF11955_consen 307 GGELIEKHPLVVIREKFLELMQEGRRKR 334 (335)
T ss_pred CCCCCCCCchHHHHHHHHHHHhhccccc
Confidence 5799999999999999999999998765
No 2
>PF11955 PORR: Plant organelle RNA recognition domain; InterPro: IPR021099 The plant organelle RNA recognition (PORR) domain, previously known as DUF860, is a component of group II intron ribonucleoprotein particles in maize chloroplasts. It is required for the splicing of the introns with which it associates, and promotes splicing in the context of a heterodimer with the RNase III-domain protein RNC1. Proteins containing this domain are predicted to localise to mitochondria or chloroplasts []. It seems likely that most PORR proteins function in organellar RNA metabolism [].
Probab=98.59 E-value=2.1e-07 Score=96.18 Aligned_cols=141 Identities=21% Similarity=0.392 Sum_probs=108.0
Q ss_pred HHHhhhHHHHHHHHHHHhccCCceechhhHHHhhhhCCCCchhhhccccCCCCCeEEEecCCCceEEEeecCCCCccChh
Q 045479 159 LKSAISNTLANKLQKLLMLSSHRRLLLSKLVHLASDLGLLPNFRSRLCNDYPDKFKIVDTSYGRALELVSWDPQLAVPMP 238 (482)
Q Consensus 159 v~~~~e~~~v~rLrKLLMMS~~rrLpL~kL~~lr~dLGLP~DF~~~lv~~yPd~Frvv~~~~g~~LeLv~Wd~~LAVs~~ 238 (482)
+..+.....|.+|+.+|--++++.||++.+...+..|||+.-=..+++.+||..|.+...+..
T Consensus 11 i~~~k~l~~v~~l~~~i~~~p~~~~pl~~l~k~~~~L~l~~~~~~~flrkyP~iF~~~~~~~~----------------- 73 (335)
T PF11955_consen 11 IEREKRLRFVLRLKDLILSQPSHSLPLRDLSKLRRQLGLKPRKVSRFLRKYPSIFEVFQHPSR----------------- 73 (335)
T ss_pred HHhhhhHHHHHHHHHHHHcCCCCcccHHHHHHHHHhcCCCcccHHHHHHhCCceEEEeccCCC-----------------
Confidence 444556678999999999999999999999999999999533335789999999999764211
Q ss_pred hhhcccCCccccCCCCCcccccccCcccchHHHHHHHhhccCCCCCCCCCCCCCCCcCChhhhHHHHHHHHHHhhcchhh
Q 045479 239 CAETKSLGLIVDRPLKFRHLKLRKGLNLKRRHRNFLIKFGELPDVCPYNTSSEEFPKESLQAEKRACALVREVLGMMVEK 318 (482)
Q Consensus 239 e~r~~~~~~~i~~P~~Fp~~~~~rGf~l~k~~r~~L~~fQkLPYiSPYed~~~~l~~~S~eaEKRaVaVlHELLSLTveK 318 (482)
.+ .-+++.....+-+.+ -.. + -.+.|--+|..+.-||.|+..+
T Consensus 74 ------------~~---------~~~~LT~~a~~L~~e------------E~~-~---~~~~e~~~v~rL~KLLMMS~~~ 116 (335)
T PF11955_consen 74 ------------SV---------PWFRLTPEAEDLLRE------------ERR-V---REEMEPDLVERLRKLLMMSKDR 116 (335)
T ss_pred ------------CC---------ceEEeCHHHHHHHHH------------HHH-H---HHhChHHHHHHHHHHhccCCCC
Confidence 11 112344444432211 000 0 0145678899999999999999
Q ss_pred HhhhhHHHhhHHhhCCcHHHHH-HHhhCCCcEEEee
Q 045479 319 QTLIDHLTHFRKDFGLSNNLRA-MILRHPELFYVSP 353 (482)
Q Consensus 319 r~~v~~L~hFr~efgLp~k~~~-~l~RHPgIFYvS~ 353 (482)
|+.+++|.|++.+||||..|+. ++-+||+.|=|..
T Consensus 117 rlpL~ki~~l~~dLGLP~Df~~~lv~~yP~~Frvv~ 152 (335)
T PF11955_consen 117 RLPLSKIAHLRRDLGLPDDFRDSLVPKYPDYFRVVD 152 (335)
T ss_pred cccHHHHHHHHHHcCCChhhccchhhhCCCCcEEee
Confidence 9999999999999999999988 5999999999987
No 3
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=86.91 E-value=0.54 Score=50.94 Aligned_cols=8 Identities=38% Similarity=0.875 Sum_probs=5.7
Q ss_pred cccceeee
Q 045479 460 ENGELWTA 467 (482)
Q Consensus 460 ~~~~~~~~ 467 (482)
..-+||+-
T Consensus 120 sd~~~WtP 127 (458)
T PF10446_consen 120 SDYEFWTP 127 (458)
T ss_pred ccceeecc
Confidence 45579987
No 4
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=77.59 E-value=1.7 Score=50.92 Aligned_cols=135 Identities=21% Similarity=0.165 Sum_probs=72.2
Q ss_pred HHHhccCCceechhhHHHhhhhCCCCchhhhccccCCC--CCeEEEecCCCce-EEEeecCCCC-c-cChhhhhcccCCc
Q 045479 173 KLLMLSSHRRLLLSKLVHLASDLGLLPNFRSRLCNDYP--DKFKIVDTSYGRA-LELVSWDPQL-A-VPMPCAETKSLGL 247 (482)
Q Consensus 173 KLLMMS~~rrLpL~kL~~lr~dLGLP~DF~~~lv~~yP--d~Frvv~~~~g~~-LeLv~Wd~~L-A-Vs~~e~r~~~~~~ 247 (482)
-++..|..-.=||..|+.+..-+|--.-|...=+.++. -.||++.+..... |-=+.=...| . .+-.-...++...
T Consensus 1156 s~~Ltsss~S~PlsaLW~~~s~~~~~Hsf~ed~~vkFsn~~q~r~~gt~~d~a~~YDvqT~~~l~tylt~~~~~~y~~n~ 1235 (1516)
T KOG1832|consen 1156 STQLTSSSSSSPLSALWDASSTGGPRHSFDEDKAVKFSNSLQFRALGTEADDALLYDVQTCSPLQTYLTDTVTSSYSNNL 1235 (1516)
T ss_pred ceeeeeccccCchHHHhccccccCccccccccceeehhhhHHHHHhcccccceEEEecccCcHHHHhcCcchhhhhhccc
Confidence 34555667778999999999999988888866555654 4577776643211 1111110000 0 0000000111111
Q ss_pred cccCCCCCcccccccCcccchHHHHHHHhhccCCCCCCCCCCCCCCC-------cCChhhhHHHHHHHHHHhhc
Q 045479 248 IVDRPLKFRHLKLRKGLNLKRRHRNFLIKFGELPDVCPYNTSSEEFP-------KESLQAEKRACALVREVLGM 314 (482)
Q Consensus 248 ~i~~P~~Fp~~~~~rGf~l~k~~r~~L~~fQkLPYiSPYed~~~~l~-------~~S~eaEKRaVaVlHELLSL 314 (482)
+--.|- = .+-|-.|.=++.+..+.+..|.++- =|--. ++. .+|..-+-|+.-.+|-+=+|
T Consensus 1236 a~FsP~-D-~LIlndGvLWDvR~~~aIh~FD~ft---~~~~G--~FHP~g~eVIINSEIwD~RTF~lLh~VP~L 1302 (1516)
T KOG1832|consen 1236 AHFSPC-D-TLILNDGVLWDVRIPEAIHRFDQFT---DYGGG--GFHPSGNEVIINSEIWDMRTFKLLHSVPSL 1302 (1516)
T ss_pred cccCCC-c-ceEeeCceeeeeccHHHHhhhhhhe---ecccc--cccCCCceEEeechhhhhHHHHHHhcCccc
Confidence 111110 0 1445578877777778888888876 22221 233 34455677777777776665
No 5
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=66.35 E-value=4.4 Score=47.74 Aligned_cols=8 Identities=25% Similarity=0.239 Sum_probs=3.3
Q ss_pred CCCCCeEE
Q 045479 208 DYPDKFKI 215 (482)
Q Consensus 208 ~yPd~Frv 215 (482)
.+-..|.-
T Consensus 1099 d~~~~fTc 1106 (1516)
T KOG1832|consen 1099 DETALFTC 1106 (1516)
T ss_pred ccccceee
Confidence 33344443
No 6
>PLN03196 MOC1-like protein; Provisional
Probab=64.49 E-value=13 Score=40.77 Aligned_cols=204 Identities=15% Similarity=0.231 Sum_probs=109.7
Q ss_pred cCCCCCcchHhHHHhhCCceeEEeccCCCCCCCCCCCCCccceeecCHHHHHHHHHHHHHHHhhhHHHHHHHHHHHhccC
Q 045479 100 YLSLPKLKSIRSMIHRYPMIFEVFAVPMPPTPLNATKSGYQQCVRLTPAAAALAAQEISLKSAISNTLANKLQKLLMLSS 179 (482)
Q Consensus 100 ~LgL~~~~~v~~FlrrYP~iF~~f~~p~~~~P~~~~~~~~~~~vrLT~~A~~L~~eE~~v~~~~e~~~v~rLrKLLMMS~ 179 (482)
.+|+.. ..+.+.|.+||.++..-... .|.+...-|. +.-+-...-..++.+--.||.++.
T Consensus 169 ~lGvs~-~~i~~~l~r~P~LL~~~~e~-----------------~l~p~v~fL~--~lGvs~~~i~~il~~~P~iL~~sv 228 (487)
T PLN03196 169 GLDVKR-QDIPRVLERYPELLGFKLEG-----------------TMSTSVAYLV--SIGVAPRDIGPMLTRFPEILGMRV 228 (487)
T ss_pred HcCCCH-HHHHHHHHhCchhhcCCHHH-----------------HHHHHHHHHH--HcCCCHHHHHHHHHhCcHHhhcCh
Confidence 589985 57899999999997643211 1223333222 112222333346666667888888
Q ss_pred CceechhhHHHhhhhCCCCchhhhccccCCCCCeEEEecCC-CceEEEeecCCCCccChhhhhcccCCccccCCCCCccc
Q 045479 180 HRRLLLSKLVHLASDLGLLPNFRSRLCNDYPDKFKIVDTSY-GRALELVSWDPQLAVPMPCAETKSLGLIVDRPLKFRHL 258 (482)
Q Consensus 180 ~rrLpL~kL~~lr~dLGLP~DF~~~lv~~yPd~Frvv~~~~-g~~LeLv~Wd~~LAVs~~e~r~~~~~~~i~~P~~Fp~~ 258 (482)
++.| ..+++-++ ++|++.+=...++.++|.+|..--... -..++.. .++.|+.... ...+ ..+|.+
T Consensus 229 e~~i-~P~v~fL~-~lGv~~~~I~~il~~~P~iL~~sle~~lkp~v~~L---~elGv~~~~i-----~~lI---~~~P~i 295 (487)
T PLN03196 229 GNNI-KPKVDYLE-SLGLPRLAVARILEKRPYILGFDLEETVKPNVECL---LEFGVRKEAL-----PSVI---AQYPDI 295 (487)
T ss_pred hhhH-HHHHHHHH-HcCCCHHHHHHHHHhCCceeEcCHHHhHHHHHHHH---HHcCCCHHHH-----HHHH---HhCCce
Confidence 7754 34566665 799999888889999999987631100 0000000 0111111000 0001 112211
Q ss_pred ccccCcccchHHHHHHHhhccCCCCCCCCCCCCCCCcCChhhhHHHHHHHHHHhhcchhhHhhhhHHHhhHHhhCCc-HH
Q 045479 259 KLRKGLNLKRRHRNFLIKFGELPDVCPYNTSSEEFPKESLQAEKRACALVREVLGMMVEKQTLIDHLTHFRKDFGLS-NN 337 (482)
Q Consensus 259 ~~~rGf~l~k~~r~~L~~fQkLPYiSPYed~~~~l~~~S~eaEKRaVaVlHELLSLTveKr~~v~~L~hFr~efgLp-~k 337 (482)
=|+.++++....+.-+++ .. ++++ +.=.++|.-+-.+|++..+| ...++..|++ +|++ +.
T Consensus 296 ---L~~s~e~kl~~~~~fL~~---------~l-G~s~---e~i~~~v~k~P~il~lSe~k--l~~kvefL~~-~Gls~ed 356 (487)
T PLN03196 296 ---LGLDLKAKLAEQQYWLTS---------KL-KIDP---EDFGRVIEKLPQIVSLNRNV--ALKHVEFLRG-RGFSAQD 356 (487)
T ss_pred ---eEecHHHhhhHHHHHHHH---------hh-CCCH---HHHHHHHHhcchhhcccHHH--HHHHHHHHHH-cCCCHHH
Confidence 123345444443322221 11 2332 22234555566778877654 3456777764 8888 55
Q ss_pred HHHHHhhCCCcEEEeecC
Q 045479 338 LRAMILRHPELFYVSPKG 355 (482)
Q Consensus 338 ~~~~l~RHPgIFYvS~Kg 355 (482)
+..|+.++|.++-.|.+.
T Consensus 357 I~~mv~k~P~lL~~S~~~ 374 (487)
T PLN03196 357 VAKMVVRCPQILALNLEI 374 (487)
T ss_pred HHHHHHhCCceeeccHHH
Confidence 677889999998888643
No 7
>PHA02608 67 prohead core protein; Provisional
Probab=57.93 E-value=11 Score=32.11 Aligned_cols=33 Identities=15% Similarity=0.208 Sum_probs=23.1
Q ss_pred cccChhhHHHHHHHHHHHHhHHHHHHhhhcCcc
Q 045479 373 LKRDETLLIKEKLMELVREGKKMRRERRKQSIF 405 (482)
Q Consensus 373 Iek~Pl~~iReK~~~Lm~~g~~~r~~r~~~g~~ 405 (482)
|.-+-|+.+|..|...|..-..-.++.++..+.
T Consensus 8 IKS~DLV~akK~F~~~Me~rt~~li~e~k~eIA 40 (80)
T PHA02608 8 IKSGDLVEAKKEFASIMEARTEALIEEEKVEIA 40 (80)
T ss_pred HhcCcHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344778999999999998766555555554444
No 8
>PF11705 RNA_pol_3_Rpc31: DNA-directed RNA polymerase III subunit Rpc31; InterPro: IPR024661 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 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA polymerase III-specific, and form the functionally distinct groups: (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in Saccharomyces cerevisiae and Homo sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain []. This entry represents the Rpc31 subunit.
Probab=55.62 E-value=12 Score=37.07 Aligned_cols=9 Identities=11% Similarity=0.183 Sum_probs=6.1
Q ss_pred HhhccCCCC
Q 045479 275 IKFGELPDV 283 (482)
Q Consensus 275 ~~fQkLPYi 283 (482)
..|+..||-
T Consensus 63 ~~~~~sPyy 71 (233)
T PF11705_consen 63 ERMRDSPYY 71 (233)
T ss_pred HHHHhCCCc
Confidence 467777763
No 9
>PF12872 OST-HTH: OST-HTH/LOTUS domain; PDB: 2KPM_A 3S93_B 3RCO_A 2KZV_A.
Probab=37.02 E-value=81 Score=24.87 Aligned_cols=49 Identities=16% Similarity=0.271 Sum_probs=33.6
Q ss_pred HHHHHHHHhcCCC--Ceechhhhhhc---------cccCCCCCcchHhHHHhhCCceeEEecc
Q 045479 74 VQKLKTLLLSKPK--HYIPIHILSKC---------RSYLSLPKLKSIRSMIHRYPMIFEVFAV 125 (482)
Q Consensus 74 v~~lk~lI~s~P~--~~lpl~~L~k~---------r~~LgL~~~~~v~~FlrrYP~iF~~f~~ 125 (482)
...|+.+|.+.++ +.+++..|... -+.+|+. ++..||+..|.+|++-..
T Consensus 7 ~~~l~~ll~~~~~~~g~v~ls~l~~~~~~~~~~f~~~~yG~~---~l~~ll~~~~~~~~i~~~ 66 (74)
T PF12872_consen 7 KKLLRELLESQKGEDGWVSLSQLGQEYKKKYPDFDPRDYGFS---SLSELLESLPDVVEIEER 66 (74)
T ss_dssp HHHHHHHHHHTCTTTSSEEHHHHHHHHHHHHTT--TCCTTSS---SHHHHHHT-TTTEEEEEE
T ss_pred HHHHHHHHHhCcCCCceEEHHHHHHHHHHHCCCCCccccCCC---cHHHHHHhCCCeEEEeee
Confidence 3456777755554 47898877643 1455776 789999999999999443
No 10
>PLN03196 MOC1-like protein; Provisional
Probab=36.87 E-value=9.9 Score=41.78 Aligned_cols=208 Identities=13% Similarity=0.191 Sum_probs=107.8
Q ss_pred cCCCCCcchHhHHHhhCCceeEEeccCCCCCCCCCCCCCccceeecCHHHHHHHHHHHHHHHhhhHHHHHHHHHHHhccC
Q 045479 100 YLSLPKLKSIRSMIHRYPMIFEVFAVPMPPTPLNATKSGYQQCVRLTPAAAALAAQEISLKSAISNTLANKLQKLLMLSS 179 (482)
Q Consensus 100 ~LgL~~~~~v~~FlrrYP~iF~~f~~p~~~~P~~~~~~~~~~~vrLT~~A~~L~~eE~~v~~~~e~~~v~rLrKLLMMS~ 179 (482)
.+|++. ..+...|.+||.|+...... .+.|...-|.. .-+-.+.-..++.+-=.+|++|.
T Consensus 205 ~lGvs~-~~i~~il~~~P~iL~~sve~-----------------~i~P~v~fL~~--lGv~~~~I~~il~~~P~iL~~sl 264 (487)
T PLN03196 205 SIGVAP-RDIGPMLTRFPEILGMRVGN-----------------NIKPKVDYLES--LGLPRLAVARILEKRPYILGFDL 264 (487)
T ss_pred HcCCCH-HHHHHHHHhCcHHhhcChhh-----------------hHHHHHHHHHH--cCCCHHHHHHHHHhCCceeEcCH
Confidence 479985 68999999999998653211 12333333321 11111111223333334666666
Q ss_pred CceechhhHHHhhhhCCCCchhhhccccCCCCCeEEEecCC-CceEEEeecCCCCccChhhhhcccCCccccCCCCCccc
Q 045479 180 HRRLLLSKLVHLASDLGLLPNFRSRLCNDYPDKFKIVDTSY-GRALELVSWDPQLAVPMPCAETKSLGLIVDRPLKFRHL 258 (482)
Q Consensus 180 ~rrLpL~kL~~lr~dLGLP~DF~~~lv~~yPd~Frvv~~~~-g~~LeLv~Wd~~LAVs~~e~r~~~~~~~i~~P~~Fp~~ 258 (482)
+++| -.++..++ ++|++.+=...++.+||..+...-... ...++... ..+.++..+.. ..-.++|++
T Consensus 265 e~~l-kp~v~~L~-elGv~~~~i~~lI~~~P~iL~~s~e~kl~~~~~fL~--~~lG~s~e~i~--------~~v~k~P~i 332 (487)
T PLN03196 265 EETV-KPNVECLL-EFGVRKEALPSVIAQYPDILGLDLKAKLAEQQYWLT--SKLKIDPEDFG--------RVIEKLPQI 332 (487)
T ss_pred HHhH-HHHHHHHH-HcCCCHHHHHHHHHhCCceeEecHHHhhhHHHHHHH--HhhCCCHHHHH--------HHHHhcchh
Confidence 5443 23556665 899999988999999998876421100 00000000 01111110000 001122211
Q ss_pred ccccCcccchHHHHHHHhhccCCCCCCCCCCCCCCCcCChhhhHHHHHHHHHHhhcchhhHhhhhHHHhhHHhhCCcHHH
Q 045479 259 KLRKGLNLKRRHRNFLIKFGELPDVCPYNTSSEEFPKESLQAEKRACALVREVLGMMVEKQTLIDHLTHFRKDFGLSNNL 338 (482)
Q Consensus 259 ~~~rGf~l~k~~r~~L~~fQkLPYiSPYed~~~~l~~~S~eaEKRaVaVlHELLSLTveKr~~v~~L~hFr~efgLp~k~ 338 (482)
=++.. .+++.+++=++++ |++. +.=-++|.-.=-+|++.+ .....++.-|.+++|+|
T Consensus 333 ---l~lSe-~kl~~kvefL~~~-----------Gls~---edI~~mv~k~P~lL~~S~--~~l~~k~dFlvneMg~~--- 389 (487)
T PLN03196 333 ---VSLNR-NVALKHVEFLRGR-----------GFSA---QDVAKMVVRCPQILALNL--EIMKPSLEFFKKEMKRP--- 389 (487)
T ss_pred ---hcccH-HHHHHHHHHHHHc-----------CCCH---HHHHHHHHhCCceeeccH--HHHHHHHHHHHHHhCCC---
Confidence 01111 1222222222211 2332 111133444446788887 44588899999999999
Q ss_pred HHHHhhCCCcEEEeecCC---eeeEEee
Q 045479 339 RAMILRHPELFYVSPKGI---RNSVQLV 363 (482)
Q Consensus 339 ~~~l~RHPgIFYvS~Kg~---~~TVfLR 363 (482)
.+.+.++|.+|-.|+..+ ||.| |+
T Consensus 390 ~~~Iv~fP~~LsySLEkRI~PR~~~-L~ 416 (487)
T PLN03196 390 LKELVEFPAYFTYGLESRIKPRYER-VA 416 (487)
T ss_pred HHHHHhChHHhccChhhhhHHHHHH-HH
Confidence 556899999999998765 6765 44
No 11
>KOG1991 consensus Nuclear transport receptor RANBP7/RANBP8 (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=29.97 E-value=90 Score=37.52 Aligned_cols=15 Identities=7% Similarity=0.208 Sum_probs=9.3
Q ss_pred hHHHHHHHHHhcCCC
Q 045479 72 RFVQKLKTLLLSKPK 86 (482)
Q Consensus 72 r~v~~lk~lI~s~P~ 86 (482)
-.++.|+.+|.+++.
T Consensus 522 eAalALq~fI~~~~~ 536 (1010)
T KOG1991|consen 522 EAALALQSFISNQEQ 536 (1010)
T ss_pred HHHHHHHHHHhcchh
Confidence 456666666666653
No 12
>PF04931 DNA_pol_phi: DNA polymerase phi; InterPro: IPR007015 Proteins of this family are predominantly nucleolar. The majority are described as transcription factor transactivators. The family also includes the fifth essential DNA polymerase (Pol5p) of Schizosaccharomyces pombe (Fission yeast) and Saccharomyces cerevisiae (Baker's yeast) (2.7.7.7 from EC). Pol5p is localized exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=29.74 E-value=39 Score=39.25 Aligned_cols=20 Identities=15% Similarity=0.245 Sum_probs=13.7
Q ss_pred ccChhhHHHHHHHHHHHHhH
Q 045479 374 KRDETLLIKEKLMELVREGK 393 (482)
Q Consensus 374 ek~Pl~~iReK~~~Lm~~g~ 393 (482)
|++++.++=|=++.|+....
T Consensus 583 e~~~~~vlveiLLslls~~s 602 (784)
T PF04931_consen 583 EPEWSEVLVEILLSLLSQPS 602 (784)
T ss_pred CccHHHHHHHHHHHHHhCcc
Confidence 56777777777777765443
No 13
>PF04931 DNA_pol_phi: DNA polymerase phi; InterPro: IPR007015 Proteins of this family are predominantly nucleolar. The majority are described as transcription factor transactivators. The family also includes the fifth essential DNA polymerase (Pol5p) of Schizosaccharomyces pombe (Fission yeast) and Saccharomyces cerevisiae (Baker's yeast) (2.7.7.7 from EC). Pol5p is localized exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=28.45 E-value=39 Score=39.19 Aligned_cols=7 Identities=43% Similarity=0.468 Sum_probs=2.6
Q ss_pred HHhccCC
Q 045479 174 LLMLSSH 180 (482)
Q Consensus 174 LLMMS~~ 180 (482)
++.+..+
T Consensus 397 ll~lir~ 403 (784)
T PF04931_consen 397 LLSLIRN 403 (784)
T ss_pred HHHHHhc
Confidence 3333333
No 14
>KOG3130 consensus Uncharacterized conserved protein [Function unknown]
Probab=25.39 E-value=41 Score=36.74 Aligned_cols=15 Identities=27% Similarity=0.545 Sum_probs=7.0
Q ss_pred eEEEecCCCceEEEe
Q 045479 213 FKIVDTSYGRALELV 227 (482)
Q Consensus 213 Frvv~~~~g~~LeLv 227 (482)
|.=+....|.-+|+|
T Consensus 119 f~~~s~~~Gd~VeIv 133 (514)
T KOG3130|consen 119 FQKMSDAAGDIVEIV 133 (514)
T ss_pred HhhccCCCCCeehhH
Confidence 333333445556655
No 15
>PTZ00415 transmission-blocking target antigen s230; Provisional
Probab=24.70 E-value=61 Score=41.35 Aligned_cols=10 Identities=20% Similarity=0.381 Sum_probs=4.3
Q ss_pred HHHHHHHHHH
Q 045479 382 KEKLMELVRE 391 (482)
Q Consensus 382 ReK~~~Lm~~ 391 (482)
|++.-+|..+
T Consensus 134 ~~~~r~l~ee 143 (2849)
T PTZ00415 134 RRRARHLAEE 143 (2849)
T ss_pred hHHhhccchh
Confidence 4444444443
No 16
>PF04340 DUF484: Protein of unknown function, DUF484; InterPro: IPR007435 This family consists of several proteins of uncharacterised function.; PDB: 3E98_B.
Probab=24.44 E-value=60 Score=31.67 Aligned_cols=50 Identities=14% Similarity=0.142 Sum_probs=15.1
Q ss_pred chHhHHHhhCCceeEEeccCCC--CCCCCCCCCCccceeecCHHHHHHHHHHHHHHH
Q 045479 107 KSIRSMIHRYPMIFEVFAVPMP--PTPLNATKSGYQQCVRLTPAAAALAAQEISLKS 161 (482)
Q Consensus 107 ~~v~~FlrrYP~iF~~f~~p~~--~~P~~~~~~~~~~~vrLT~~A~~L~~eE~~v~~ 161 (482)
..|.+||+++|..|..+..--. .+|. +. .-.+.|.+...+.++++.+-++
T Consensus 9 ~~V~~yL~~~PdFf~~~~~ll~~l~~ph---~~--~~avSL~erQ~~~LR~~~~~L~ 60 (225)
T PF04340_consen 9 EDVAAYLRQHPDFFERHPELLAELRLPH---PS--GGAVSLVERQLERLRERNRQLE 60 (225)
T ss_dssp -------------------------------------HHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHhCcHHHHhCHHHHHHcCCCC---CC--CCcccHHHHHHHHHHHHHHHHH
Confidence 3678888888888877642111 1222 11 1267888888888887776654
No 17
>KOG0526 consensus Nucleosome-binding factor SPN, POB3 subunit [Transcription; Replication, recombination and repair; Chromatin structure and dynamics]
Probab=20.06 E-value=77 Score=35.84 Aligned_cols=48 Identities=21% Similarity=0.068 Sum_probs=26.6
Q ss_pred HHHHHHHHhcCCCCeechhhhhh---ccccCCCCCcchHhHHHhhCCceeEEe
Q 045479 74 VQKLKTLLLSKPKHYIPIHILSK---CRSYLSLPKLKSIRSMIHRYPMIFEVF 123 (482)
Q Consensus 74 v~~lk~lI~s~P~~~lpl~~L~k---~r~~LgL~~~~~v~~FlrrYP~iF~~f 123 (482)
+-+|+++++++=+..|--+.|+- ...+.++.. ..+.|...--.||++-
T Consensus 82 ~~~L~~ff~~~~~~~i~qkel~ikGwNwGea~~~G--~~l~F~~~skpiFEIP 132 (615)
T KOG0526|consen 82 LEKLKSFFSSNFSITIEQKELSIKGWNWGEADFKG--QELVFDVNSKPIFEIP 132 (615)
T ss_pred HHHHHHHHHHhhccchhhheeeecccccccccccC--cEEEEeeCCceeEEee
Confidence 34677777765444444443331 223445553 4567777777777763
Done!