Query 009820
Match_columns 524
No_of_seqs 135 out of 183
Neff 4.3
Searched_HMMs 46136
Date Thu Mar 28 17:43:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009820.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009820hhsearch_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 3E-113 6E-118 878.5 31.2 332 85-421 1-334 (335)
2 PF11955 PORR: Plant organelle 98.9 2E-08 4.2E-13 104.7 13.0 140 177-379 10-152 (335)
3 KOG1832 HIV-1 Vpr-binding prot 87.8 0.51 1.1E-05 55.5 3.9 139 192-340 1156-1302(1516)
4 PLN03196 MOC1-like protein; Pr 86.6 0.38 8.3E-06 53.1 2.1 51 328-381 323-374 (487)
5 PF04931 DNA_pol_phi: DNA poly 85.6 0.82 1.8E-05 53.1 4.2 18 399-416 583-600 (784)
6 PF05285 SDA1: SDA1; InterPro 81.1 1 2.2E-05 47.3 2.4 14 464-477 111-124 (324)
7 PF06524 NOA36: NOA36 protein; 79.9 2.5 5.4E-05 43.8 4.5 12 305-316 115-126 (314)
8 PF11705 RNA_pol_3_Rpc31: DNA- 79.3 1.5 3.2E-05 43.8 2.7 31 280-310 34-71 (233)
9 PF10446 DUF2457: Protein of u 77.8 2 4.3E-05 47.2 3.3 10 487-496 120-129 (458)
10 PLN03196 MOC1-like protein; Pr 76.1 6.4 0.00014 43.7 6.7 51 331-386 361-414 (487)
11 KOG0943 Predicted ubiquitin-pr 74.7 2.4 5.2E-05 51.6 3.1 15 249-263 1388-1402(3015)
12 KOG1832 HIV-1 Vpr-binding prot 63.4 7 0.00015 46.6 3.7 12 50-61 962-973 (1516)
13 PF06524 NOA36: NOA36 protein; 62.6 9.3 0.0002 39.8 4.1 7 227-233 84-90 (314)
14 PF11705 RNA_pol_3_Rpc31: DNA- 61.0 12 0.00026 37.4 4.5 7 225-231 33-39 (233)
15 KOG2038 CAATT-binding transcri 54.1 11 0.00023 44.4 3.2 11 105-115 326-336 (988)
16 KOG1991 Nuclear transport rece 53.9 8.4 0.00018 46.1 2.3 17 101-117 521-537 (1010)
17 PF04147 Nop14: Nop14-like fam 53.1 17 0.00036 43.2 4.6 8 333-340 185-192 (840)
18 PF12872 OST-HTH: OST-HTH/LOTU 51.5 50 0.0011 26.4 5.9 49 104-155 7-66 (74)
19 PF15017 AF1Q: Drug resistance 44.9 17 0.00036 32.0 2.2 25 395-419 22-46 (87)
20 KOG3064 RNA-binding nuclear pr 40.4 13 0.00028 38.7 1.1 9 368-376 126-134 (303)
21 PF04147 Nop14: Nop14-like fam 38.6 34 0.00074 40.6 4.2 8 407-414 281-288 (840)
22 PHA02664 hypothetical protein; 37.6 43 0.00093 36.1 4.3 18 462-479 486-503 (534)
23 COG5593 Nucleic-acid-binding p 36.3 19 0.0004 41.1 1.5 44 437-480 679-726 (821)
24 PF04931 DNA_pol_phi: DNA poly 36.3 32 0.00069 40.3 3.5 7 468-474 676-682 (784)
25 COG5406 Nucleosome binding fac 34.6 21 0.00046 41.4 1.6 31 205-235 639-669 (1001)
26 PF11702 DUF3295: Protein of u 33.6 24 0.00051 39.8 1.7 19 466-484 310-329 (507)
27 PF09073 BUD22: BUD22; InterP 32.3 65 0.0014 35.3 4.8 12 448-459 208-220 (432)
28 KOG4364 Chromatin assembly fac 30.3 60 0.0013 37.9 4.2 48 403-450 476-536 (811)
29 PF05285 SDA1: SDA1; InterPro 29.8 21 0.00045 37.7 0.5 20 371-390 35-54 (324)
30 KOG1999 RNA polymerase II tran 28.9 53 0.0012 39.7 3.6 6 468-473 81-86 (1024)
31 PF02724 CDC45: CDC45-like pro 28.3 52 0.0011 37.9 3.4 31 382-415 96-126 (622)
32 PF06957 COPI_C: Coatomer (COP 26.9 21 0.00046 39.3 0.0 12 463-474 70-81 (422)
33 KOG2393 Transcription initiati 24.8 64 0.0014 36.7 3.1 40 438-477 242-296 (555)
34 KOG2652 RNA polymerase II tran 22.9 79 0.0017 34.1 3.3 9 304-312 135-143 (348)
35 PHA00458 single-stranded DNA-b 21.9 85 0.0018 32.1 3.1 23 381-403 121-143 (233)
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=2.6e-113 Score=878.45 Aligned_cols=332 Identities=50% Similarity=0.839 Sum_probs=313.9
Q ss_pred cccCCChhhHHHhhhhhhHHHHHHHHHhhCCCCcccHHHHhhcccccCCCccchHHHHHHhCCcceEEeecCce-eeeee
Q 009820 85 RRKELPFDNVIQRDKKLKLVSKIRKILVSQPDRIMSLKQLGRFRRDLGLTKKRRFIALLRKFPAVFEIIEEGVY-SLRFK 163 (524)
Q Consensus 85 w~kD~~LD~~i~rek~lr~vl~Lk~lI~s~P~~~lpl~~Lsk~r~~LgL~~~~~v~~FLrkYP~iF~vf~~~~~-~l~~r 163 (524)
|+||++||++|+++|++++|++|+++|+++|+++|||++|++++++||| .++++++||+|||+||++|.++.. .+||+
T Consensus 1 w~rd~~lD~~i~~~k~l~~v~~l~~~i~~~p~~~~pl~~l~k~~~~L~l-~~~~~~~flrkyP~iF~~~~~~~~~~~~~~ 79 (335)
T PF11955_consen 1 WVRDPYLDKVIEREKRLRFVLRLKDLILSQPSHSLPLRDLSKLRRQLGL-KPRKVSRFLRKYPSIFEVFQHPSRSVPWFR 79 (335)
T ss_pred CCCchhHHHHHHhhhhHHHHHHHHHHHHcCCCCcccHHHHHHHHHhcCC-CcccHHHHHHhCCceEEEeccCCCCCceEE
Confidence 9999999999999999999999999999999999999999999999999 457899999999999999997655 56999
Q ss_pred cCHHHHHHHHHHHHHHhhchHHHHHHHHHHhccccCccccHHHHHHHHHhcCCChhhhhhhcccCCCceEEEecC-CCCe
Q 009820 164 LTPEAERLYLEEVKVRNEMEDLLVTKLRKLLMMSLEKRILLEKIAHLKTDLGLPLEFRDTICHRYPQYFRVVATE-RGPA 242 (524)
Q Consensus 164 LT~~A~~L~~EE~~v~~e~e~~~V~rLrKLLMMS~~rrLpL~kL~~lr~dLGLP~DFr~slv~kyPd~Frvv~~~-~g~~ 242 (524)
||++|++|+.||+++++++++++|+||+||||||.+++|||++|+|++||||||+||++++|++|||||+||+.+ ++.+
T Consensus 80 LT~~a~~L~~eE~~~~~~~e~~~v~rL~KLLMMS~~~rlpL~ki~~l~~dLGLP~Df~~~lv~~yP~~Frvv~~~~~~~~ 159 (335)
T PF11955_consen 80 LTPEAEDLLREERRVREEMEPDLVERLRKLLMMSKDRRLPLSKIAHLRRDLGLPDDFRDSLVPKYPDYFRVVDLEDGGRY 159 (335)
T ss_pred eCHHHHHHHHHHHHHHHhChHHHHHHHHHHhccCCCCcccHHHHHHHHHHcCCChhhccchhhhCCCCcEEeecCCCCCE
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999954 4589
Q ss_pred eEecccCCCCcchHHHHHHHHhhhHhhhhccccccCCCCCCcccCCCCcccChhHHHHHhhhhcCCCCCCCCCCCCCCCC
Q 009820 243 LELTHWDPQLAVSAAELAAEENRIRELKEKDLIIDRPLKFNRVKLPKGLNLSKGETRRICQFRDMPYISPYSDFSGLRPG 322 (524)
Q Consensus 243 LELV~WdpeLAVSa~E~~ae~~r~~e~~e~~~~i~~plkF~~v~fP~Gf~l~k~~~~~L~~fQ~LPYiSPYed~s~l~~~ 322 (524)
||||+|||+||||++|++++.+.. ...+..+..+++| ||+||+||++++++++||++||+|||+|||+|+++++++
T Consensus 160 LeLv~Wd~~LAvs~~E~~~~~~~~---~~~~~~~~~~~~F-p~~fp~G~~l~k~~~~~l~~fQ~lPy~SPYed~~~l~~~ 235 (335)
T PF11955_consen 160 LELVSWDPELAVSALEKRAEKEYR---EKREDGFDRPLAF-PVSFPKGFRLKKKFREWLEEFQKLPYISPYEDASHLDPG 235 (335)
T ss_pred EEEeecCCccCcCccchhhhhccc---cccccccCCceee-eecCCCCccccHHHHHHHHHHhcCCCCCCCCCccCCCCC
Confidence 999999999999999998875411 1123345678899 599999999999999999999999999999999999999
Q ss_pred CchhhhHHHHHHHHHhhccchhhhhhhHHHHHHhhhCChHHHHHhhhhCCCeeEEEeeCCceeEEEeeccCCCCCccCCh
Q 009820 323 TPEKEKHACGIVHEILSLTVEKKTLVDHLTHFREEFRFSQQVRGMLIRHPDMFYVSLKGDRDSVFLREAYRDSQLIDKDR 402 (524)
Q Consensus 323 S~e~EKRaVaVlHELLSLTVEKr~~v~~L~hFR~efgLp~k~r~~L~RHPgIFYVS~Kg~~~TVfLREAY~~~~LIek~P 402 (524)
|+++|||||||+||||||||||||++++|+|||+|||||++|+++|+|||||||||+||+|+||||||||++|+||||||
T Consensus 236 s~~~EKRaVaVlHElLSLTveKr~~~~~L~~fr~ef~lp~k~~~~l~rHPgIFYvS~kg~~~TVfLrEAY~~~~Liek~P 315 (335)
T PF11955_consen 236 SDEAEKRAVAVLHELLSLTVEKRTEVDHLTHFRKEFGLPQKFRRLLLRHPGIFYVSLKGKRHTVFLREAYDGGELIEKHP 315 (335)
T ss_pred ChHHHhHHHHHHHHHHHhhhhhhccHHHHHHHHHHhCCcHHHHHHHHhCCCeEEEeccCCceEEEEeeccCCCCCCCCCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhHHHHHHHHHHcCCCcCC
Q 009820 403 LLVIKEKFRALVSVPRFPK 421 (524)
Q Consensus 403 L~~iReK~~~Lm~~~~~~~ 421 (524)
|+.+|+||++||..|++.+
T Consensus 316 l~~~r~k~~~Lm~~~~~~~ 334 (335)
T PF11955_consen 316 LVVIREKFLELMQEGRRKR 334 (335)
T ss_pred hHHHHHHHHHHHhhccccc
Confidence 9999999999999998744
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=98.87 E-value=2e-08 Score=104.71 Aligned_cols=140 Identities=23% Similarity=0.415 Sum_probs=108.6
Q ss_pred HHHhhchHHHHHHHHHHhccccCccccHHHHHHHHHhcCCChhhhhhhcccCCCceEEEecC-CC-CeeEecccCCCCcc
Q 009820 177 KVRNEMEDLLVTKLRKLLMMSLEKRILLEKIAHLKTDLGLPLEFRDTICHRYPQYFRVVATE-RG-PALELTHWDPQLAV 254 (524)
Q Consensus 177 ~v~~e~e~~~V~rLrKLLMMS~~rrLpL~kL~~lr~dLGLP~DFr~slv~kyPd~Frvv~~~-~g-~~LELV~WdpeLAV 254 (524)
.+..+.....|.+|+.+|--++++.||++.+...+..|||+.-=..+++.+||..|.+...+ .+ .++.|+.
T Consensus 10 ~i~~~k~l~~v~~l~~~i~~~p~~~~pl~~l~k~~~~L~l~~~~~~~flrkyP~iF~~~~~~~~~~~~~~LT~------- 82 (335)
T PF11955_consen 10 VIEREKRLRFVLRLKDLILSQPSHSLPLRDLSKLRRQLGLKPRKVSRFLRKYPSIFEVFQHPSRSVPWFRLTP------- 82 (335)
T ss_pred HHHhhhhHHHHHHHHHHHHcCCCCcccHHHHHHHHHhcCCCcccHHHHHHhCCceEEEeccCCCCCceEEeCH-------
Confidence 35556667789999999999999999999999999999994333357899999999998742 22 4555532
Q ss_pred hHHHHHHHHhhhHhhhhccccccCCCCCCcccCCCCcccChhHHHHHhhhhcCCCCCCCCCCCCCCCCCchhhhHHHHHH
Q 009820 255 SAAELAAEENRIRELKEKDLIIDRPLKFNRVKLPKGLNLSKGETRRICQFRDMPYISPYSDFSGLRPGTPEKEKHACGIV 334 (524)
Q Consensus 255 Sa~E~~ae~~r~~e~~e~~~~i~~plkF~~v~fP~Gf~l~k~~~~~L~~fQ~LPYiSPYed~s~l~~~S~e~EKRaVaVl 334 (524)
.|.+...+|.++ -.+.|--+|..+
T Consensus 83 ~a~~L~~eE~~~--------------------------------------------------------~~~~e~~~v~rL 106 (335)
T PF11955_consen 83 EAEDLLREERRV--------------------------------------------------------REEMEPDLVERL 106 (335)
T ss_pred HHHHHHHHHHHH--------------------------------------------------------HHhChHHHHHHH
Confidence 222222222211 122345678899
Q ss_pred HHHhhccchhhhhhhHHHHHHhhhCChHHHHHh-hhhCCCeeEEEe
Q 009820 335 HEILSLTVEKKTLVDHLTHFREEFRFSQQVRGM-LIRHPDMFYVSL 379 (524)
Q Consensus 335 HELLSLTVEKr~~v~~L~hFR~efgLp~k~r~~-L~RHPgIFYVS~ 379 (524)
.-||+|+..+|+.+.+|.|++.+||||..|+.- +-+||+.|=|..
T Consensus 107 ~KLLMMS~~~rlpL~ki~~l~~dLGLP~Df~~~lv~~yP~~Frvv~ 152 (335)
T PF11955_consen 107 RKLLMMSKDRRLPLSKIAHLRRDLGLPDDFRDSLVPKYPDYFRVVD 152 (335)
T ss_pred HHHhccCCCCcccHHHHHHHHHHcCCChhhccchhhhCCCCcEEee
Confidence 999999999999999999999999999999986 699999998877
No 3
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=87.81 E-value=0.51 Score=55.53 Aligned_cols=139 Identities=17% Similarity=0.163 Sum_probs=73.8
Q ss_pred HHhccccCccccHHHHHHHHHhcCCChhhhhhhcccCC--CceEEEecCCCCeeEecccCCCCcchHHHHHHHHhhhHhh
Q 009820 192 KLLMMSLEKRILLEKIAHLKTDLGLPLEFRDTICHRYP--QYFRVVATERGPALELTHWDPQLAVSAAELAAEENRIREL 269 (524)
Q Consensus 192 KLLMMS~~rrLpL~kL~~lr~dLGLP~DFr~slv~kyP--d~Frvv~~~~g~~LELV~WdpeLAVSa~E~~ae~~r~~e~ 269 (524)
-++..|..-+=||..|+.+..-+|--+-|...=+.+|. -.||++.+....++- +|-+ .-+.++..--. -....
T Consensus 1156 s~~Ltsss~S~PlsaLW~~~s~~~~~Hsf~ed~~vkFsn~~q~r~~gt~~d~a~~---YDvq-T~~~l~tylt~-~~~~~ 1230 (1516)
T KOG1832|consen 1156 STQLTSSSSSSPLSALWDASSTGGPRHSFDEDKAVKFSNSLQFRALGTEADDALL---YDVQ-TCSPLQTYLTD-TVTSS 1230 (1516)
T ss_pred ceeeeeccccCchHHHhccccccCccccccccceeehhhhHHHHHhcccccceEE---Eecc-cCcHHHHhcCc-chhhh
Confidence 45566677788999999999999999999976666664 468888775432110 0100 11111110000 00000
Q ss_pred hhccccccCCCCCCc---ccCCCCcccChhHHHHHhhhhcCC-CCCCCCCCC--CCCCCCchhhhHHHHHHHHHhhc
Q 009820 270 KEKDLIIDRPLKFNR---VKLPKGLNLSKGETRRICQFRDMP-YISPYSDFS--GLRPGTPEKEKHACGIVHEILSL 340 (524)
Q Consensus 270 ~e~~~~i~~plkF~~---v~fP~Gf~l~k~~~~~L~~fQ~LP-YiSPYed~s--~l~~~S~e~EKRaVaVlHELLSL 340 (524)
.+++ .-.|+| +-|-.|.=-..+..+.+..|-++- |++----.+ .+--+|..-+-|+.-.+|-+=+|
T Consensus 1231 y~~n-----~a~FsP~D~LIlndGvLWDvR~~~aIh~FD~ft~~~~G~FHP~g~eVIINSEIwD~RTF~lLh~VP~L 1302 (1516)
T KOG1832|consen 1231 YSNN-----LAHFSPCDTLILNDGVLWDVRIPEAIHRFDQFTDYGGGGFHPSGNEVIINSEIWDMRTFKLLHSVPSL 1302 (1516)
T ss_pred hhcc-----ccccCCCcceEeeCceeeeeccHHHHhhhhhheecccccccCCCceEEeechhhhhHHHHHHhcCccc
Confidence 0111 123443 334556544444556777777665 222111111 13335666777888888876665
No 4
>PLN03196 MOC1-like protein; Provisional
Probab=86.55 E-value=0.38 Score=53.07 Aligned_cols=51 Identities=24% Similarity=0.371 Sum_probs=39.3
Q ss_pred hHHHHHHHHHhhccchhhhhhhHHHHHHhhhCChH-HHHHhhhhCCCeeEEEeeC
Q 009820 328 KHACGIVHEILSLTVEKKTLVDHLTHFREEFRFSQ-QVRGMLIRHPDMFYVSLKG 381 (524)
Q Consensus 328 KRaVaVlHELLSLTVEKr~~v~~L~hFR~efgLp~-k~r~~L~RHPgIFYVS~Kg 381 (524)
.++|.-+-.+|++..+| ...++..|++ +|++. .+..|+.++|.++-.|.+.
T Consensus 323 ~~~v~k~P~il~lSe~k--l~~kvefL~~-~Gls~edI~~mv~k~P~lL~~S~~~ 374 (487)
T PLN03196 323 GRVIEKLPQIVSLNRNV--ALKHVEFLRG-RGFSAQDVAKMVVRCPQILALNLEI 374 (487)
T ss_pred HHHHHhcchhhcccHHH--HHHHHHHHHH-cCCCHHHHHHHHHhCCceeeccHHH
Confidence 34566667888888764 3467888875 99985 8889999999999999843
No 5
>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=85.57 E-value=0.82 Score=53.09 Aligned_cols=18 Identities=22% Similarity=0.219 Sum_probs=10.0
Q ss_pred cCChHhHHHHHHHHHHcC
Q 009820 399 DKDRLLVIKEKFRALVSV 416 (524)
Q Consensus 399 ek~PL~~iReK~~~Lm~~ 416 (524)
|++++..+=|=++.|+..
T Consensus 583 e~~~~~vlveiLLslls~ 600 (784)
T PF04931_consen 583 EPEWSEVLVEILLSLLSQ 600 (784)
T ss_pred CccHHHHHHHHHHHHHhC
Confidence 456666665555555543
No 6
>PF05285 SDA1: SDA1; InterPro: IPR007949 This domain consists of several SDA1 protein homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localised in the nucleus [].
Probab=81.08 E-value=1 Score=47.26 Aligned_cols=14 Identities=36% Similarity=0.881 Sum_probs=8.2
Q ss_pred CCCCCCCCCCCCCC
Q 009820 464 DDGNEDDWSDEDDD 477 (524)
Q Consensus 464 ~~~~~~~~~~~~~~ 477 (524)
|+|++++|.+++++
T Consensus 111 d~Dd~~e~idv~~d 124 (324)
T PF05285_consen 111 DSDDEGEWIDVESD 124 (324)
T ss_pred cccccCCcccccch
Confidence 33446777777555
No 7
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=79.87 E-value=2.5 Score=43.83 Aligned_cols=12 Identities=17% Similarity=0.224 Sum_probs=5.7
Q ss_pred hcCCCCCCCCCC
Q 009820 305 RDMPYISPYSDF 316 (524)
Q Consensus 305 Q~LPYiSPYed~ 316 (524)
+......|..|+
T Consensus 115 ~~HaC~Cpl~da 126 (314)
T PF06524_consen 115 STHACTCPLQDA 126 (314)
T ss_pred ccccccCcCCCc
Confidence 344455555444
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=79.25 E-value=1.5 Score=43.78 Aligned_cols=31 Identities=32% Similarity=0.436 Sum_probs=16.1
Q ss_pred CCCCcccCCCCcccChhHHH-------HHhhhhcCCCC
Q 009820 280 LKFNRVKLPKGLNLSKGETR-------RICQFRDMPYI 310 (524)
Q Consensus 280 lkF~~v~fP~Gf~l~k~~~~-------~L~~fQ~LPYi 310 (524)
+-|+++.+|.-..+...... -...|+..||-
T Consensus 34 ~lfP~~~~P~~~~~t~~E~~~v~~~~~lr~~~~~sPyy 71 (233)
T PF11705_consen 34 PLFPPLNLPVPLPLTEEERYLVALKRELRERMRDSPYY 71 (233)
T ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHhCCCc
Confidence 44555556655555543322 12467777763
No 9
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=77.79 E-value=2 Score=47.23 Aligned_cols=10 Identities=0% Similarity=-0.114 Sum_probs=5.9
Q ss_pred cceeeecccc
Q 009820 487 GTVKIGENKS 496 (524)
Q Consensus 487 ~~~~~~~~~~ 496 (524)
+...||.-.+
T Consensus 120 sd~~~WtP~~ 129 (458)
T PF10446_consen 120 SDYEFWTPGA 129 (458)
T ss_pred ccceeecccc
Confidence 3566776553
No 10
>PLN03196 MOC1-like protein; Provisional
Probab=76.09 E-value=6.4 Score=43.69 Aligned_cols=51 Identities=22% Similarity=0.331 Sum_probs=38.2
Q ss_pred HHHHHHHhhccchhhhhhhHHHHHHhhhCChHHHHHhhhhCCCeeEEEeeCC---ceeE
Q 009820 331 CGIVHEILSLTVEKKTLVDHLTHFREEFRFSQQVRGMLIRHPDMFYVSLKGD---RDSV 386 (524)
Q Consensus 331 VaVlHELLSLTVEKr~~v~~L~hFR~efgLp~k~r~~L~RHPgIFYVS~Kg~---~~TV 386 (524)
|.-.=-+|++.+ .....++.-|.+++|++. +.+.++|.+|-.|+..+ ||.|
T Consensus 361 v~k~P~lL~~S~--~~l~~k~dFlvneMg~~~---~~Iv~fP~~LsySLEkRI~PR~~~ 414 (487)
T PLN03196 361 VVRCPQILALNL--EIMKPSLEFFKKEMKRPL---KELVEFPAYFTYGLESRIKPRYER 414 (487)
T ss_pred HHhCCceeeccH--HHHHHHHHHHHHHhCCCH---HHHHhChHHhccChhhhhHHHHHH
Confidence 333445677776 455788999999999994 44899999998888755 4665
No 11
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=74.73 E-value=2.4 Score=51.62 Aligned_cols=15 Identities=27% Similarity=0.381 Sum_probs=10.4
Q ss_pred CCCCcchHHHHHHHH
Q 009820 249 DPQLAVSAAELAAEE 263 (524)
Q Consensus 249 dpeLAVSa~E~~ae~ 263 (524)
.|.+|.+++|.--..
T Consensus 1388 PPkFAk~ALEqcckd 1402 (3015)
T KOG0943|consen 1388 PPKFAKLALEQCCKD 1402 (3015)
T ss_pred CchHHHHHHHHHHHH
Confidence 467888999874433
No 12
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=63.37 E-value=7 Score=46.63 Aligned_cols=12 Identities=8% Similarity=0.066 Sum_probs=5.2
Q ss_pred cccccccccccC
Q 009820 50 SQFWGKGLVLHK 61 (524)
Q Consensus 50 ~~fl~~~~~~~~ 61 (524)
+.|.+.+++-++
T Consensus 962 s~l~~~~~p~re 973 (1516)
T KOG1832|consen 962 SELRDSSVPGRE 973 (1516)
T ss_pred ccccCccccccc
Confidence 344444444443
No 13
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=62.63 E-value=9.3 Score=39.78 Aligned_cols=7 Identities=29% Similarity=0.610 Sum_probs=4.2
Q ss_pred cCCCceE
Q 009820 227 RYPQYFR 233 (524)
Q Consensus 227 kyPd~Fr 233 (524)
+||..|.
T Consensus 84 kH~g~~~ 90 (314)
T PF06524_consen 84 KHPGVFT 90 (314)
T ss_pred ecCceee
Confidence 6666654
No 14
>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=61.04 E-value=12 Score=37.43 Aligned_cols=7 Identities=14% Similarity=0.292 Sum_probs=3.9
Q ss_pred cccCCCc
Q 009820 225 CHRYPQY 231 (524)
Q Consensus 225 v~kyPd~ 231 (524)
.+-||.+
T Consensus 33 ~~lfP~~ 39 (233)
T PF11705_consen 33 PPLFPPL 39 (233)
T ss_pred CCCCCCC
Confidence 3456666
No 15
>KOG2038 consensus CAATT-binding transcription factor/60S ribosomal subunit biogenesis protein [Translation, ribosomal structure and biogenesis; Transcription]
Probab=54.05 E-value=11 Score=44.40 Aligned_cols=11 Identities=27% Similarity=0.597 Sum_probs=4.6
Q ss_pred HHHHHHHhhCC
Q 009820 105 SKIRKILVSQP 115 (524)
Q Consensus 105 l~Lk~lI~s~P 115 (524)
-.|.++|-++|
T Consensus 326 ~ti~~lL~~kP 336 (988)
T KOG2038|consen 326 KTIYDLLTNKP 336 (988)
T ss_pred HHHHHHHhCCc
Confidence 33344444444
No 16
>KOG1991 consensus Nuclear transport receptor RANBP7/RANBP8 (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=53.90 E-value=8.4 Score=46.09 Aligned_cols=17 Identities=6% Similarity=0.198 Sum_probs=12.3
Q ss_pred hhHHHHHHHHHhhCCCC
Q 009820 101 LKLVSKIRKILVSQPDR 117 (524)
Q Consensus 101 lr~vl~Lk~lI~s~P~~ 117 (524)
+-.++.|+.+|.+++..
T Consensus 521 VeAalALq~fI~~~~~~ 537 (1010)
T KOG1991|consen 521 VEAALALQSFISNQEQA 537 (1010)
T ss_pred hHHHHHHHHHHhcchhh
Confidence 34688888888887743
No 17
>PF04147 Nop14: Nop14-like family ; InterPro: IPR007276 Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production [].
Probab=53.13 E-value=17 Score=43.17 Aligned_cols=8 Identities=25% Similarity=0.605 Sum_probs=3.8
Q ss_pred HHHHHhhc
Q 009820 333 IVHEILSL 340 (524)
Q Consensus 333 VlHELLSL 340 (524)
|+.|+..=
T Consensus 185 vm~EiIaK 192 (840)
T PF04147_consen 185 VMEEIIAK 192 (840)
T ss_pred HHHHHHHH
Confidence 44454443
No 18
>PF12872 OST-HTH: OST-HTH/LOTUS domain; PDB: 2KPM_A 3S93_B 3RCO_A 2KZV_A.
Probab=51.54 E-value=50 Score=26.40 Aligned_cols=49 Identities=39% Similarity=0.539 Sum_probs=33.8
Q ss_pred HHHHHHHHhhCCC--CcccHHHHhhc---------ccccCCCccchHHHHHHhCCcceEEeec
Q 009820 104 VSKIRKILVSQPD--RIMSLKQLGRF---------RRDLGLTKKRRFIALLRKFPAVFEIIEE 155 (524)
Q Consensus 104 vl~Lk~lI~s~P~--~~lpl~~Lsk~---------r~~LgL~~~~~v~~FLrkYP~iF~vf~~ 155 (524)
.-.|+++|.+.++ +.+++..|... -+.+|+. ++..||+..|.+|++-..
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 3456777756654 37888888544 2456665 589999999999999433
No 19
>PF15017 AF1Q: Drug resistance and apoptosis regulator
Probab=44.91 E-value=17 Score=32.01 Aligned_cols=25 Identities=20% Similarity=0.163 Sum_probs=15.4
Q ss_pred CCCccCChHhHHHHHHHHHHcCCCc
Q 009820 395 SQLIDKDRLLVIKEKFRALVSVPRF 419 (524)
Q Consensus 395 ~~LIek~PL~~iReK~~~Lm~~~~~ 419 (524)
+.+-=++||-.|=.-+++|+.+...
T Consensus 22 sF~fWR~PlP~id~~~lEll~~~~~ 46 (87)
T PF15017_consen 22 SFLFWRNPLPDIDLELLELLGLDKS 46 (87)
T ss_pred ceeeccCCCCCCCHHHHhhhccccc
Confidence 3444567777776677777754433
No 20
>KOG3064 consensus RNA-binding nuclear protein (MAK16) containing a distinct C4 Zn-finger [RNA processing and modification]
Probab=40.39 E-value=13 Score=38.65 Aligned_cols=9 Identities=11% Similarity=0.010 Sum_probs=3.4
Q ss_pred hhhCCCeeE
Q 009820 368 LIRHPDMFY 376 (524)
Q Consensus 368 L~RHPgIFY 376 (524)
-+||-.--|
T Consensus 126 alr~~q~~~ 134 (303)
T KOG3064|consen 126 ALRGRQKKL 134 (303)
T ss_pred HhccCceEE
Confidence 344333333
No 21
>PF04147 Nop14: Nop14-like family ; InterPro: IPR007276 Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production [].
Probab=38.61 E-value=34 Score=40.63 Aligned_cols=8 Identities=38% Similarity=0.567 Sum_probs=3.7
Q ss_pred HHHHHHHH
Q 009820 407 KEKFRALV 414 (524)
Q Consensus 407 ReK~~~Lm 414 (524)
++|+-.|=
T Consensus 281 ~erLeklE 288 (840)
T PF04147_consen 281 KERLEKLE 288 (840)
T ss_pred HHHHHHHH
Confidence 44444443
No 22
>PHA02664 hypothetical protein; Provisional
Probab=37.64 E-value=43 Score=36.15 Aligned_cols=18 Identities=39% Similarity=0.713 Sum_probs=11.4
Q ss_pred CCCCCCCCCCCCCCCCCC
Q 009820 462 DVDDGNEDDWSDEDDDMP 479 (524)
Q Consensus 462 ~~~~~~~~~~~~~~~~~~ 479 (524)
|++|..+|.|.|+.|.+-
T Consensus 486 de~ds~ddswgd~sdsgi 503 (534)
T PHA02664 486 DESDSADDSWGDESDSGI 503 (534)
T ss_pred ccccccccccccccccCc
Confidence 344455788988866543
No 23
>COG5593 Nucleic-acid-binding protein possibly involved in ribosomal biogenesis [Translation, ribosomal structure and biogenesis]
Probab=36.26 E-value=19 Score=41.10 Aligned_cols=44 Identities=30% Similarity=0.395 Sum_probs=28.3
Q ss_pred CCCCCCCCCCCccc--ccc--ccccCCCCCCCCCCCCCCCCCCCCCCC
Q 009820 437 EPEEGSGEDGEDWS--IDD--YMTDGQFDDVDDGNEDDWSDEDDDMPP 480 (524)
Q Consensus 437 ~~~~~~~~~~~~~~--~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~ 480 (524)
-|+|+|-+++|-|+ |+. =++++.++.+=|..+||.+|-+.|++|
T Consensus 679 ~d~d~emde~eiw~alv~srp~~e~d~ddse~d~~e~d~sd~~sd~e~ 726 (821)
T COG5593 679 FDSDDEMDENEIWSALVKSRPDVEDDSDDSELDFAEDDFSDSTSDDEP 726 (821)
T ss_pred cCccccccHHHHHHHHhccCCccccCccccccchhhccccccCCCccc
Confidence 46677778888898 777 345554444444567788877555444
No 24
>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=36.25 E-value=32 Score=40.30 Aligned_cols=7 Identities=71% Similarity=0.777 Sum_probs=3.0
Q ss_pred CCCCCCC
Q 009820 468 EDDWSDE 474 (524)
Q Consensus 468 ~~~~~~~ 474 (524)
++|++++
T Consensus 676 e~d~e~~ 682 (784)
T PF04931_consen 676 EDDDEDE 682 (784)
T ss_pred ccccccc
Confidence 3444444
No 25
>COG5406 Nucleosome binding factor SPN, SPT16 subunit [Transcription / DNA replication, recombination, and repair / Chromatin structure and dynamics]
Probab=34.56 E-value=21 Score=41.37 Aligned_cols=31 Identities=13% Similarity=-0.070 Sum_probs=19.3
Q ss_pred HHHHHHHHhcCCChhhhhhhcccCCCceEEE
Q 009820 205 EKIAHLKTDLGLPLEFRDTICHRYPQYFRVV 235 (524)
Q Consensus 205 ~kL~~lr~dLGLP~DFr~slv~kyPd~Frvv 235 (524)
+....+-+-+|.|+-|-+..+.-.|+-=|++
T Consensus 639 eqdKlie~k~~rt~~~~~~~vRp~~d~KR~p 669 (1001)
T COG5406 639 EQDKLIERKLSRTDVYMKTDVRPGSDGKRKP 669 (1001)
T ss_pred hhhhhhhccccccchhhhcccccCCCcCccC
Confidence 3344556778888888777666555544443
No 26
>PF11702 DUF3295: Protein of unknown function (DUF3295); InterPro: IPR021711 This family is conserved in fungi but the function is not known.
Probab=33.56 E-value=24 Score=39.78 Aligned_cols=19 Identities=26% Similarity=0.669 Sum_probs=9.7
Q ss_pred CCCCCCCCC-CCCCCCCCCC
Q 009820 466 GNEDDWSDE-DDDMPPDFDE 484 (524)
Q Consensus 466 ~~~~~~~~~-~~~~~~~~~~ 484 (524)
|+++||+|- +|.|.+.-||
T Consensus 310 DDssDWEDSveESG~sSvde 329 (507)
T PF11702_consen 310 DDSSDWEDSVEESGKSSVDE 329 (507)
T ss_pred ccchhhhhccccccCCCccc
Confidence 336788443 4444444444
No 27
>PF09073 BUD22: BUD22; InterPro: IPR015158 BUD22 has been shown in yeast to be a nuclear protein involved in bud-site selection. It plays a role in positioning the proximal bud pole signal [].
Probab=32.27 E-value=65 Score=35.28 Aligned_cols=12 Identities=25% Similarity=0.412 Sum_probs=6.6
Q ss_pred ccc-cccccccCC
Q 009820 448 DWS-IDDYMTDGQ 459 (524)
Q Consensus 448 ~~~-~~~~~~~~~ 459 (524)
+.. .|+++-+++
T Consensus 208 ~~~q~d~~l~~Ss 220 (432)
T PF09073_consen 208 DLSQYDGLLASSS 220 (432)
T ss_pred hhhhhhccccCCc
Confidence 344 667775443
No 28
>KOG4364 consensus Chromatin assembly factor-I [Chromatin structure and dynamics]
Probab=30.33 E-value=60 Score=37.91 Aligned_cols=48 Identities=19% Similarity=0.059 Sum_probs=27.6
Q ss_pred HhHHHHHHHHHHcCCCcCCCCC-------------CCCCCCCCCCCCCCCCCCCCCCCccc
Q 009820 403 LLVIKEKFRALVSVPRFPKRGA-------------PQKDDHYSDRTDEPEEGSGEDGEDWS 450 (524)
Q Consensus 403 L~~iReK~~~Lm~~~~~~~r~~-------------~~~~~~~~~g~~~~~~~~~~~~~~~~ 450 (524)
-+.+|-||++...--|..|=|- ........=..|.|+++|+++.|+..
T Consensus 476 ~r~mKaKlLqF~~NrRP~YyGTWrKKS~~VsarrPlAq~~llDYEVdSDeEWEEEepGESl 536 (811)
T KOG4364|consen 476 SRRMKAKLLQFDKNRRPGYYGTWRKKSQVVSARRPLAQDPLLDYEVDSDEEWEEEEPGESL 536 (811)
T ss_pred cchhHHHHhhhccccCCcccccccccccccccCCcccccccccccccCcccccccCCCccc
Confidence 3448889999886433333221 11111112246778888888888775
No 29
>PF05285 SDA1: SDA1; InterPro: IPR007949 This domain consists of several SDA1 protein homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localised in the nucleus [].
Probab=29.76 E-value=21 Score=37.70 Aligned_cols=20 Identities=10% Similarity=0.233 Sum_probs=10.5
Q ss_pred CCCeeEEEeeCCceeEEEee
Q 009820 371 HPDMFYVSLKGDRDSVFLRE 390 (524)
Q Consensus 371 HPgIFYVS~Kg~~~TVfLRE 390 (524)
+|.+.-=.-+|+..+.-++.
T Consensus 35 ~P~lL~kkdRGr~~~~~~~~ 54 (324)
T PF05285_consen 35 NPELLHKKDRGRPAEMGAKP 54 (324)
T ss_pred CHHhcCchhcCCcchhhhhc
Confidence 45554445566655555543
No 30
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=28.87 E-value=53 Score=39.67 Aligned_cols=6 Identities=33% Similarity=0.546 Sum_probs=2.3
Q ss_pred CCCCCC
Q 009820 468 EDDWSD 473 (524)
Q Consensus 468 ~~~~~~ 473 (524)
+|+|.|
T Consensus 81 dd~~~e 86 (1024)
T KOG1999|consen 81 DDDDEE 86 (1024)
T ss_pred ccchhc
Confidence 333333
No 31
>PF02724 CDC45: CDC45-like protein; InterPro: IPR003874 CDC45 is an essential gene required for initiation of DNA replication in Saccharomyces cerevisiae (cell division control protein 45), forming a complex with MCM5/CDC46. Homologs of CDC45 have been identified in human [], mouse and the smut fungus, Melampsora spp., (tsd2 protein) among others.; GO: 0006270 DNA-dependent DNA replication initiation
Probab=28.28 E-value=52 Score=37.87 Aligned_cols=31 Identities=10% Similarity=0.209 Sum_probs=14.5
Q ss_pred CceeEEEeeccCCCCCccCChHhHHHHHHHHHHc
Q 009820 382 DRDSVFLREAYRDSQLIDKDRLLVIKEKFRALVS 415 (524)
Q Consensus 382 ~~~TVfLREAY~~~~LIek~PL~~iReK~~~Lm~ 415 (524)
..+.|++-++....+|- +.-.-++-|..+..
T Consensus 96 ~~~v~v~ddg~~~~~l~---~~~~~~~a~~~l~~ 126 (622)
T PF02724_consen 96 NDQVIVFDDGDIEEELQ---EEPEYRDAYEALEE 126 (622)
T ss_pred CCcEEEEECCChhhhcc---hhhhhHHHHHHhhh
Confidence 44555555544433322 12223666666664
No 32
>PF06957 COPI_C: Coatomer (COPI) alpha subunit C-terminus; InterPro: IPR010714 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the C terminus (approximately 500 residues) of the eukaryotic coatomer alpha subunit [, ]. This domain is found along with the IPR006692 from INTERPRO domain. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0005515 protein binding, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030126 COPI vesicle coat; PDB: 3MKR_B 3MV2_E 3MKQ_B 3MV3_A.
Probab=26.94 E-value=21 Score=39.32 Aligned_cols=12 Identities=25% Similarity=0.659 Sum_probs=0.0
Q ss_pred CCCCCCCCCCCC
Q 009820 463 VDDGNEDDWSDE 474 (524)
Q Consensus 463 ~~~~~~~~~~~~ 474 (524)
+++++++.|.-+
T Consensus 70 ~~~~e~~gWD~d 81 (422)
T PF06957_consen 70 EDEDEEGGWDLD 81 (422)
T ss_dssp ------------
T ss_pred cccccccccccc
Confidence 344556778553
No 33
>KOG2393 consensus Transcription initiation factor IIF, large subunit (RAP74) [Transcription]
Probab=24.77 E-value=64 Score=36.73 Aligned_cols=40 Identities=23% Similarity=0.298 Sum_probs=23.4
Q ss_pred CCCCCCCCCCcccc--cccc-------------ccCCCCCCCCCCCCCCCCCCCC
Q 009820 438 PEEGSGEDGEDWSI--DDYM-------------TDGQFDDVDDGNEDDWSDEDDD 477 (524)
Q Consensus 438 ~~~~~~~~~~~~~~--~~~~-------------~~~~~~~~~~~~~~~~~~~~~~ 477 (524)
.++.++++++.|-. ++=. -.-+.||++-+.+|||++++..
T Consensus 242 ~~d~~d~e~e~~~kk~~~~kkk~~~~~~~~krkkk~d~Dd~a~eesdd~d~e~~E 296 (555)
T KOG2393|consen 242 SEDKKDGEVERWKKKHLDNKKKTTTAKGATKRKKKKDVDDEAFEESDDGDNEGRE 296 (555)
T ss_pred hcccccccchhhhhccccccccccccccccccccccCCcccccccCCCccccccc
Confidence 56677778888874 2211 1112345555668888887543
No 34
>KOG2652 consensus RNA polymerase II transcription initiation factor TFIIA, large chain [Transcription]
Probab=22.87 E-value=79 Score=34.15 Aligned_cols=9 Identities=33% Similarity=0.674 Sum_probs=6.0
Q ss_pred hhcCCCCCC
Q 009820 304 FRDMPYISP 312 (524)
Q Consensus 304 fQ~LPYiSP 312 (524)
+|--|+.+|
T Consensus 135 ~q~~p~~~p 143 (348)
T KOG2652|consen 135 TQPVPALSP 143 (348)
T ss_pred cCCCcCcCc
Confidence 566666666
No 35
>PHA00458 single-stranded DNA-binding protein
Probab=21.94 E-value=85 Score=32.15 Aligned_cols=23 Identities=17% Similarity=0.291 Sum_probs=10.7
Q ss_pred CCceeEEEeeccCCCCCccCChH
Q 009820 381 GDRDSVFLREAYRDSQLIDKDRL 403 (524)
Q Consensus 381 g~~~TVfLREAY~~~~LIek~PL 403 (524)
|+..+..|+=-=.+|..|.+.|.
T Consensus 121 Ge~~~i~l~v~DskGK~l~~vp~ 143 (233)
T PHA00458 121 GENKPIVLRVVDSKGKRIEDVPA 143 (233)
T ss_pred CcccccceeEEcCCCcCcCcCcc
Confidence 44444444332234555555554
Done!