Query 016426
Match_columns 390
No_of_seqs 55 out of 57
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 06:45:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016426.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016426hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04003 Utp12: Dip2/Utp12 Fam 96.3 0.021 4.7E-07 47.2 7.7 91 275-387 13-105 (110)
2 PF09384 UTP15_C: UTP15 C term 76.2 11 0.00024 33.9 7.1 84 280-387 64-147 (148)
3 PRK07194 fliG flagellar motor 61.8 1.9E+02 0.0041 29.4 14.2 207 74-300 39-257 (334)
4 cd07609 BAR_SIP3_fungi The Bin 55.9 36 0.00079 32.7 6.6 76 80-158 25-101 (214)
5 cd01055 Nonheme_Ferritin nonhe 54.3 67 0.0014 27.9 7.5 85 289-389 49-143 (156)
6 PF07899 Frigida: Frigida-like 42.8 2.8E+02 0.0061 27.9 10.7 118 60-208 100-220 (290)
7 smart00544 MA3 Domain in DAP-5 41.9 47 0.001 27.4 4.4 38 67-104 51-88 (113)
8 PF15365 PNRC: Proline-rich nu 36.3 40 0.00086 26.5 2.9 20 41-60 12-31 (58)
9 PF02845 CUE: CUE domain; Int 32.9 66 0.0014 22.8 3.4 25 179-203 3-27 (42)
10 PRK15338 type III secretion sy 32.5 4.2E+02 0.009 28.1 10.3 78 127-208 55-137 (372)
11 PF13929 mRNA_stabil: mRNA sta 31.5 1.5E+02 0.0032 30.3 6.8 147 57-208 82-253 (292)
12 KOG0310 Conserved WD40 repeat- 30.9 1.9E+02 0.004 31.6 7.7 86 280-389 396-481 (487)
13 PF07035 Mic1: Colon cancer-as 30.1 2.3E+02 0.0051 26.4 7.4 79 86-188 5-85 (167)
14 KOG3380 Actin-related protein 29.1 58 0.0012 30.4 3.2 24 280-303 91-114 (152)
15 PF04699 P16-Arc: ARP2/3 compl 28.7 53 0.0011 30.3 2.9 24 280-303 91-114 (152)
16 smart00546 CUE Domain that may 28.7 82 0.0018 22.3 3.3 24 179-202 4-27 (43)
17 PF04938 SIP1: Survival motor 25.5 1E+02 0.0023 29.0 4.4 69 280-374 138-206 (233)
18 PF13565 HTH_32: Homeodomain-l 24.8 1.2E+02 0.0026 23.2 3.9 45 299-348 2-47 (77)
19 PF02847 MA3: MA3 domain; Int 23.2 1.4E+02 0.0029 24.5 4.1 36 69-104 53-88 (113)
20 cd04756 Commd8 COMM_Domain con 22.0 62 0.0014 30.1 2.1 36 272-307 61-96 (176)
21 PF08064 UME: UME (NUC010) dom 21.5 4.7E+02 0.01 22.1 7.2 40 86-131 5-44 (107)
22 PF04192 Utp21: Utp21 specific 20.6 6.4E+02 0.014 24.6 8.7 59 289-371 156-217 (237)
No 1
>PF04003 Utp12: Dip2/Utp12 Family; InterPro: IPR007148 A large ribonuclear protein complex is required for the processing of the small-ribosomal-subunit rRNA - the small-subunit (SSU) processome [, ]. This preribosomal complex contains the U3 snoRNA and at least 40 proteins, which have the following properties: They are nucleolar. They are able to coimmunoprecipitate with the U3 snoRNA and Mpp10 (a protein specific to the SSU processome). They are required for 18S rRNA biogenesis. There appears to be a linkage between polymerase I transcription and the formation of the SSU processome; as some, but not all, of the SSU processome components are required for pre-rRNA transcription initiation. These SSU processome components have been termed t-Utps. They form a pre-complex with pre-18S rRNA in the absence of snoRNA U3 and other SSU processome components. It has been proposed that the t-Utp complex proteins are both rDNA and rRNA binding proteins that are involved in the initiation of pre18S rRNA transcription. Initially binding to rDNA then associating with the 5' end of the nascent pre18S rRNA. The t-Utpcomplex forms the nucleus around which the rest of the SSU processome components, including snoRNA U3, assemble []. From electron microscopy the SSU processome may correspond to the terminal knobs visualized at the 5' ends of nascent 18S rRNA. This domain is found at the C terminus of proteins containing WD40 repeats. These proteins are part of the U3 ribonucleoprotein. In yeast, these proteins are called Utp5, Utp1 or Pwp2, Utp12 or DIP2 Q12220 from SWISSPROT. They interact with snoRNA U3 and with MPP10 []. Pwp2 is an essential Saccharomyces cerevisiae (Baker's yeast) protein involved in cell separation.
Probab=96.27 E-value=0.021 Score=47.18 Aligned_cols=91 Identities=19% Similarity=0.222 Sum_probs=77.2
Q ss_pred CchhhHhhhhccCChHHHHHHHHHHHHHHHHhccCCCCCCCCCcccccCCCcCCCCCChHHHHHHHHHHhhcccceeeec
Q 016426 275 IDEVILSSSISKLNGKELMGLIRYLGKWLKKFERFPQAGPCPEASFGLGLKACDWVPKLEVIVQCLGLVLDENFSSLVLL 354 (390)
Q Consensus 275 ~De~~Llp~LkdL~~~ev~~lLrYL~kW~~kys~~~~~~pcp~a~s~pgl~~~~~vPtl~qI~dWi~LlLDahFT~lVm~ 354 (390)
+|...+--.++.||...+..||+|+..|+.+- ..|..+-.+.|+-.+|-.|.+.+.-.
T Consensus 13 ~~~~~I~~tv~~Lp~~~~~~LL~~l~~~l~~~----------------------~~~~~e~~l~Wl~~ll~~H~~~l~~~ 70 (110)
T PF04003_consen 13 IPPSDIENTVRSLPFSYAERLLQFLSERLQTR----------------------KSPHVEFLLRWLKALLKTHGSYLSSS 70 (110)
T ss_pred CCHHHHHHHHHhCCHHHHHHHHHHHHHHhccc----------------------CCCchhHHHHHHHHHHHHHHHHHHhc
Confidence 45777888889999999999999999997522 23677889999999999999999999
Q ss_pred -hhhHHHHHHHHHHHHHHHHHHHhhccHH-HHHHH
Q 016426 355 -PEFQEELRSIEGVVSTLASEARYCCSLA-NVVKR 387 (390)
Q Consensus 355 -peake~L~~l~~~Vksq~~~~~~~~~~~-~~~~~ 387 (390)
|+....|+.+++.+++.....+..+..- +-++-
T Consensus 71 ~~~~~~~L~~L~~~l~~~~~~l~~l~~~n~~~L~~ 105 (110)
T PF04003_consen 71 SPELRPVLRSLQKILRERLQNLSKLLDLNLGRLDY 105 (110)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHH
Confidence 9999999999999999888888777665 55443
No 2
>PF09384 UTP15_C: UTP15 C terminal; InterPro: IPR018983 This entry represents the C-terminal domain of the U3 small nucleolar RNA-associated protein 15 (UTP15). This protein is involved in nucleolar processing of pre-18S ribosomal RNA, and is required for optimal pre-ribosomal RNA transcription by RNA polymerase I together with a subset of U3 proteins required for transcription (t-UTPs). UTP15 is a component of the ribosomal small subunit (SSU) processome, which is a large ribonucleoprotein (RNP) required for processing of precursors to the small subunit RNA, the 18S, of the ribosome [, ]. This domain is found C-terminal to the WD40 repeat (IPR001680 from INTERPRO). UTP15 associates with U3 snoRNA, which is ubiquitous in eukaryotes and is required for nucleolar processing of pre-18S ribosomal RNA []. ; GO: 0006364 rRNA processing, 0005730 nucleolus
Probab=76.17 E-value=11 Score=33.87 Aligned_cols=84 Identities=14% Similarity=0.241 Sum_probs=66.2
Q ss_pred HhhhhccCChHHHHHHHHHHHHHHHHhccCCCCCCCCCcccccCCCcCCCCCChHHHHHHHHHHhhcccceeeechhhHH
Q 016426 280 LSSSISKLNGKELMGLIRYLGKWLKKFERFPQAGPCPEASFGLGLKACDWVPKLEVIVQCLGLVLDENFSSLVLLPEFQE 359 (390)
Q Consensus 280 Llp~LkdL~~~ev~~lLrYL~kW~~kys~~~~~~pcp~a~s~pgl~~~~~vPtl~qI~dWi~LlLDahFT~lVm~peake 359 (390)
|-.+|++.+..++..+|+|+.+++.. +. -.+-+++++..+||--=.++.-.|+..+
T Consensus 64 L~~AL~~Rde~~L~piL~Fl~k~i~~----pr--------------------~~~~l~~v~~~ildiY~~~~~~s~~v~~ 119 (148)
T PF09384_consen 64 LRAALAGRDEESLEPILKFLIKNITD----PR--------------------YTRILVDVANIILDIYSPVIGQSPEVDK 119 (148)
T ss_pred HHHHHHhCCHHHHHHHHHHHHHhCCC----cc--------------------cHHHHHHHHHHHHHHHHHHhcccHHHHH
Confidence 45667788888888888888877531 11 1344678888999976666666778999
Q ss_pred HHHHHHHHHHHHHHHHHhhccHHHHHHH
Q 016426 360 ELRSIEGVVSTLASEARYCCSLANVVKR 387 (390)
Q Consensus 360 ~L~~l~~~Vksq~~~~~~~~~~~~~~~~ 387 (390)
.++.|+.-|++-+.-.+....+.|.++-
T Consensus 120 ~~~~L~~~v~~E~~~~~~l~~l~G~ld~ 147 (148)
T PF09384_consen 120 LFQKLQRKVQEELQLQKELLELQGMLDM 147 (148)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhHHhh
Confidence 9999999999999999999999998874
No 3
>PRK07194 fliG flagellar motor switch protein G; Reviewed
Probab=61.76 E-value=1.9e+02 Score=29.38 Aligned_cols=207 Identities=14% Similarity=0.144 Sum_probs=107.5
Q ss_pred HHHhhhcCCCCCChHHHHHHhHHHHHhhhhhccccccccCCCCchhHHHHHH-hhcchhHHHHHHHHHhhcchhhHHHHH
Q 016426 74 KLKRKLKDTNNFDKDEFIGILNPYLQKIGEKVGISTRINRSDSGYTQGLIEK-VGFLMGRDVASLVLEACISLRIWELVE 152 (390)
Q Consensus 74 ~lk~~l~~~~~~~~~~~~~~l~~fl~~~~~~~~~~~~~~~s~~~~~~~~i~~-~~~~ig~~v~~lv~r~~~~~~fw~~L~ 152 (390)
+|.+.....++.++++....|..|.+.+...-|+..| +..|.+.++++ +|+--..-+..-+. +.....-|+.|.
T Consensus 39 ~l~~~m~~l~~v~~~~~~~vl~eF~~~~~~~~~~~~g----~~~~~~~~L~~alg~~~a~~il~~i~-~~~~~~~~~~L~ 113 (334)
T PRK07194 39 RLSQKMARLSGIKVDQARQVLQRFFDDYREQSGINGA----SRSYLQRTLNKALGGDIAKSLINSIY-GDEIRHRMQRLQ 113 (334)
T ss_pred HHHHHHHhCCCCCHHHHHHHHHHHHHHHHhcCCcccc----hHHHHHHHHHHHcCHHHHHHHHHHHh-ccccCchHHHHH
Confidence 3445666778899999999999999998776555444 12366666654 34322222211111 122335665543
Q ss_pred HHHHhCCCC--CCCchHHHHHHHhcCChhHHHHHHhhCCCCChHHHHHHHHHhhCCCccchhhhhhHHHHHHHHHHHHHH
Q 016426 153 TLIVHGLVD--HSSYSNLVTRLATEKRSDLLCLCVKYSPDLGSSELLCILKYFLCPPKDAYGSMGSVRMEWESQALLAIE 230 (390)
Q Consensus 153 ~Li~~g~Ls--~S~cP~Lv~~llEk~d~~LLqlcL~qfpDI~es~~~AcLK~FLs~~d~~~~~m~sV~~~w~e~a~na~~ 230 (390)
.+=-..+.. -.-+|+-++.++-+=+.+----.|.++| +.+.-.+.+..-....-+.+.++.|....++...+...
T Consensus 114 ~~~~~~la~~l~~EhPQ~iAiiL~~L~~e~AA~VL~~Lp---e~~~~~v~~ria~l~~Vs~e~~~~V~e~l~~~~~~~~~ 190 (334)
T PRK07194 114 WVDPQQLARLIANEHLQMQAVFLAFLPPESAAAVLKYLP---EDRQDDILYRIAQLDDVDRDVVDELDELIERCLAVLSE 190 (334)
T ss_pred CCCHHHHHHHHHccCHHHHHHHHHhcCHHHHHHHHHhCC---HHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHhhhh
Confidence 331111111 1223666666666666666666666655 34444445555555555555555554222333222111
Q ss_pred HhhhhhhhhhhHHHHHHHHHHHHHHhcCCChhhHHHHHHhhcCCCchhhHhh---------hhccCChHHHHHHHHHHH
Q 016426 231 KASDENLSRKKLCLAKEASILLMVAHDGFSVSELCLHYLLASSNIDEVILSS---------SISKLNGKELMGLIRYLG 300 (390)
Q Consensus 231 ~~~~k~l~~K~~~~AkrAAlL~~va~d~fs~~elCLH~L~aS~~~De~~Llp---------~LkdL~~~ev~~lLrYL~ 300 (390)
. .. . ......+.|.++|-+- + +. +..+..|= ..|+..+.. .|.+++.+-+..+|+|+.
T Consensus 191 ~-~~--~--~~~G~~~aa~ILn~l~--~-~~-~~il~~L~---~~dp~~a~~Ir~~mF~FedL~~~~~qtia~iL~~v~ 257 (334)
T PRK07194 191 Q-SH--T--KVIGVKQAADIINRFP--G-DR-QQLMEMLK---EHDEEVVNEIEDNMYDFFILSRQSEETLQRLMDEVP 257 (334)
T ss_pred c-cc--c--cCCCHHHHHHHHHhCc--h-hH-HHHHHHHH---hhCHHHHHHHHHhcCCHHHHhcCCHHHHHHHHHhCC
Confidence 0 00 0 0112223456777743 1 22 44555543 245566655 777888888888888775
No 4
>cd07609 BAR_SIP3_fungi The Bin/Amphiphysin/Rvs (BAR) domain of fungal Snf1p-interacting protein 3. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. This group is composed of mostly uncharacterized fungal proteins with similarity to Saccharomyces cerevisiae Snf1p-interacting protein 3 (SIP3). These proteins contain an N-terminal BAR domain followed by a Pleckstrin Homology (PH) domain. SIP3 interacts with SNF1 protein kinase and activates transcription when anchored to DNA. It may function in the SNF1 pathway. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=55.87 E-value=36 Score=32.73 Aligned_cols=76 Identities=13% Similarity=0.144 Sum_probs=50.4
Q ss_pred cCCCCCChHHHHHHhHHHHHhhhhhccccccccCCCCchhHHHHHHhhcchhHHHHHHHHHhhcchhhH-HHHHHHHHhC
Q 016426 80 KDTNNFDKDEFIGILNPYLQKIGEKVGISTRINRSDSGYTQGLIEKVGFLMGRDVASLVLEACISLRIW-ELVETLIVHG 158 (390)
Q Consensus 80 ~~~~~~~~~~~~~~l~~fl~~~~~~~~~~~~~~~s~~~~~~~~i~~~~~~ig~~v~~lv~r~~~~~~fw-~~L~~Li~~g 158 (390)
+...+ +..+|....++||..+.....++.++- +..||+.++++.|..+-....+++.-..-....+ ++|..++...
T Consensus 25 ~k~~~-~~~~~e~~~nsfl~~~~p~~~~s~~vi--dqdYT~~al~~f~~~l~e~~~~ll~~~~~~~~~~~~pL~~f~k~~ 101 (214)
T cd07609 25 KKLYS-SLDELERVINSFLSHLLPPLLVSGGVI--DQDYTPLALKRFGDGLKDFWGGVLSALKGNDSLILDPLRSFVKSD 101 (214)
T ss_pred HHHHH-HHHHHHHHHHHHHHhcCCccccccchh--CchhHHHHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHH
Confidence 33443 678999999999999877333555543 3559999999998887777666655555444444 5555555443
No 5
>cd01055 Nonheme_Ferritin nonheme-containing ferritins. Nonheme Ferritin domain, found in archaea and bacteria, is a member of a broad superfamily of ferritin-like diiron-carboxylate proteins. The ferritin protein shell is composed of 24 protein subunits arranged in 432 symmetry. Each protein subunit, a four-helix bundle with a fifth short terminal helix, contains a dinuclear ferroxidase center (H type). Unique to this group of proteins is a third metal site in the ferroxidase center. Iron storage involves the uptake of iron (II) at the protein shell, its oxidation by molecular oxygen at the ferroxidase centers, and the movement of iron (III) into the cavity for deposition as ferrihydrite.
Probab=54.29 E-value=67 Score=27.94 Aligned_cols=85 Identities=12% Similarity=0.126 Sum_probs=57.8
Q ss_pred hHHHHHHHHHHHHHHHHhccCCCCCCCCCcccccCCCcCCCCC-ChHHHHHHHHHHhhcccceeeechhhHHHHH-----
Q 016426 289 GKELMGLIRYLGKWLKKFERFPQAGPCPEASFGLGLKACDWVP-KLEVIVQCLGLVLDENFSSLVLLPEFQEELR----- 362 (390)
Q Consensus 289 ~~ev~~lLrYL~kW~~kys~~~~~~pcp~a~s~pgl~~~~~vP-tl~qI~dWi~LlLDahFT~lVm~peake~L~----- 362 (390)
..|+..+++|+.+. .+.++..+.| .+| ....+.+++-..|+.--.+..+.+++.+.=+
T Consensus 49 ~~HA~~l~~~i~~~----gg~~~~~~~~------------~~~~~~~~~~~~l~~al~~E~~~~~~~~~l~~~A~~~~D~ 112 (156)
T cd01055 49 REHAMKFFDYLNDR----GGRVELPAIE------------APPSEFESLLEVFEAALEHEQKVTESINNLVDLALEEKDY 112 (156)
T ss_pred HHHHHHHHHHHHHC----CCCeeCCCCC------------CCCcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCH
Confidence 47788999998877 3333332322 122 3456778888888776667777777766543
Q ss_pred ----HHHHHHHHHHHHHHhhccHHHHHHHhc
Q 016426 363 ----SIEGVVSTLASEARYCCSLANVVKRFG 389 (390)
Q Consensus 363 ----~l~~~Vksq~~~~~~~~~~~~~~~~~~ 389 (390)
-++.|++.|+.+.+....+.+.+++++
T Consensus 113 ~~~~~l~~~l~~q~e~~~~~~~~l~~l~~~g 143 (156)
T cd01055 113 ATFNFLQWFVKEQVEEEALARDILDKLKLAG 143 (156)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 356788888888888888888888775
No 6
>PF07899 Frigida: Frigida-like protein; InterPro: IPR012474 This family is composed of plant proteins that are similar to FRIGIDA protein expressed by Arabidopsis thaliana (Mouse-ear cress) (Q9FDW0 from SWISSPROT). This protein is probably nuclear and is required for the regulation of flowering time in the late-flowering phenotype. It is known to increase RNA levels of flowering locus C. Allelic variation at the FRIGIDA locus is a major determinant of natural variation in flowering time [].
Probab=42.78 E-value=2.8e+02 Score=27.90 Aligned_cols=118 Identities=19% Similarity=0.203 Sum_probs=70.0
Q ss_pred chhhHHHhhhHHHHHHHhhhcCCCCCChHHHHHHhHHHHHhhhhhccccccccCCCCchhHHHHHHhhcchhHHHHHHHH
Q 016426 60 VDTYLIDSGKKFHAKLKRKLKDTNNFDKDEFIGILNPYLQKIGEKVGISTRINRSDSGYTQGLIEKVGFLMGRDVASLVL 139 (390)
Q Consensus 60 ~d~~~~~~~~~f~~~lk~~l~~~~~~~~~~~~~~l~~fl~~~~~~~~~~~~~~~s~~~~~~~~i~~~~~~ig~~v~~lv~ 139 (390)
-.+.+-+-|++.+...|.++.+.++-+.-++.+.| .||.. .||+..-+ ..++..++..++.+
T Consensus 100 is~~vke~A~~lA~~WK~~l~~~~~~~~lea~gFL-~lla~----fgi~s~Fd---~del~~Lv~~va~~---------- 161 (290)
T PF07899_consen 100 ISPEVKEEAKKLAEEWKSKLDGVNNENSLEALGFL-QLLAA----FGIVSEFD---EDELLKLVVSVARR---------- 161 (290)
T ss_pred CCHHHHHHHHHHHHHHHHHHHhcccCCCHHHHHHH-HHHHH----cCCccccC---HHHHHHHHHHhcch----------
Confidence 36788999999999999999655556666766654 34444 47777743 34555555444432
Q ss_pred HhhcchhhHHHHHHHHHhCCCCCCCchHHHHHHHhcCChhHHHHHHhhCC--C-CChHHHHHHHHHhhCCCc
Q 016426 140 EACISLRIWELVETLIVHGLVDHSSYSNLVTRLATEKRSDLLCLCVKYSP--D-LGSSELLCILKYFLCPPK 208 (390)
Q Consensus 140 r~~~~~~fw~~L~~Li~~g~Ls~S~cP~Lv~~llEk~d~~LLqlcL~qfp--D-I~es~~~AcLK~FLs~~d 208 (390)
.--..|-..--+.+-. ||+|..++.+|+.-.-=-+.+-|- | +|+ ..+||.+|..++
T Consensus 162 ---------~~a~~L~~sLgl~~k~-~d~V~~LI~~g~~ieAv~fi~~f~L~dkfpP---v~lLk~yl~~~k 220 (290)
T PF07899_consen 162 ---------KQAPELCRSLGLSDKM-PDIVEKLIKKGKQIEAVRFIYAFGLVDKFPP---VPLLKSYLEDSK 220 (290)
T ss_pred ---------HhhHHHHHHcCchhhh-HHHHHHHHHCCCccchHHHHHHHcCCCCCCC---HHHHHHHHHHHH
Confidence 1122233333344443 999999999988654333333221 1 333 346777776543
No 7
>smart00544 MA3 Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains Ponting (TIBS) "Novel eIF4G domain homologues" in press
Probab=41.93 E-value=47 Score=27.37 Aligned_cols=38 Identities=16% Similarity=0.168 Sum_probs=30.0
Q ss_pred hhhHHHHHHHhhhcCCCCCChHHHHHHhHHHHHhhhhh
Q 016426 67 SGKKFHAKLKRKLKDTNNFDKDEFIGILNPYLQKIGEK 104 (390)
Q Consensus 67 ~~~~f~~~lk~~l~~~~~~~~~~~~~~l~~fl~~~~~~ 104 (390)
.-++++++|=..|-+.+.+++..|...+..+++.+.+-
T Consensus 51 ~~~~~~~~Ll~~L~~~~~~~~~~~~~~f~~~~~~l~dl 88 (113)
T smart00544 51 TYREMYSVLLSRLCQANVISTKQFEKGFWRLLEDIEDL 88 (113)
T ss_pred cHHHHHHHHHHHHHHcCCcCHHHHHHHHHHHHhhChhh
Confidence 34556666666777777799999999999999998775
No 8
>PF15365 PNRC: Proline-rich nuclear receptor coactivator
Probab=36.32 E-value=40 Score=26.50 Aligned_cols=20 Identities=30% Similarity=0.381 Sum_probs=16.7
Q ss_pred CCCCCCCCCCCCCCcccCcc
Q 016426 41 EGASAASLVNPVSGWQISEV 60 (390)
Q Consensus 41 ~~~~~~~l~~p~s~w~~s~~ 60 (390)
+.|.+|+|+.|..-|.-...
T Consensus 12 ~sP~PssLP~P~f~~~~~~~ 31 (58)
T PF15365_consen 12 NSPSPSSLPLPPFHWKSSPS 31 (58)
T ss_pred CCCChhhcCCCCcccccCcc
Confidence 58899999999999985544
No 9
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=32.90 E-value=66 Score=22.77 Aligned_cols=25 Identities=16% Similarity=0.226 Sum_probs=19.3
Q ss_pred hHHHHHHhhCCCCChHHHHHHHHHh
Q 016426 179 DLLCLCVKYSPDLGSSELLCILKYF 203 (390)
Q Consensus 179 ~LLqlcL~qfpDI~es~~~AcLK~F 203 (390)
+.++-...-|||+++.+|..+|+..
T Consensus 3 ~~v~~L~~mFP~~~~~~I~~~L~~~ 27 (42)
T PF02845_consen 3 EMVQQLQEMFPDLDREVIEAVLQAN 27 (42)
T ss_dssp HHHHHHHHHSSSS-HHHHHHHHHHT
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHc
Confidence 4566667789999999999999753
No 10
>PRK15338 type III secretion system regulator InvE; Provisional
Probab=32.51 E-value=4.2e+02 Score=28.07 Aligned_cols=78 Identities=14% Similarity=0.185 Sum_probs=53.2
Q ss_pred hcchhHHHHHHHHHhhcchh---hHHHHHHHHHhCCCCCCCchHHHHHHHhc--CChhHHHHHHhhCCCCChHHHHHHHH
Q 016426 127 GFLMGRDVASLVLEACISLR---IWELVETLIVHGLVDHSSYSNLVTRLATE--KRSDLLCLCVKYSPDLGSSELLCILK 201 (390)
Q Consensus 127 ~~~ig~~v~~lv~r~~~~~~---fw~~L~~Li~~g~Ls~S~cP~Lv~~llEk--~d~~LLqlcL~qfpDI~es~~~AcLK 201 (390)
.--|+-.++..+-|+-.+-+ .|+.....++.+.---- -.|+..+=-+ +.-++++-.+++||| +||+...|+
T Consensus 55 ~deMsml~aqf~rRr~~~kk~~~~s~~~erILed~aDeKl--~~l~~~Lk~~~~~~~~ll~~arq~FpD--~SDl~~aLr 130 (372)
T PRK15338 55 TDEMSAALAQFRNRRDYEKKSSNLSDSFERVLEDEALPKA--KQILKLISVHGGALEEFLRQARKLFPD--PSDLVLVLR 130 (372)
T ss_pred hhHHHHHHHHHHhhcchhhcccccchHHHHHhccchHHHH--HHHHHHHHhcCCCHHHHHHHHHHhCCC--HHHHHHHHH
Confidence 44688888888888877744 68766666655432211 1233333101 456899999999995 899999999
Q ss_pred HhhCCCc
Q 016426 202 YFLCPPK 208 (390)
Q Consensus 202 ~FLs~~d 208 (390)
..|-..+
T Consensus 131 eLl~r~k 137 (372)
T PRK15338 131 ELLRRKQ 137 (372)
T ss_pred HHHhCcc
Confidence 9997553
No 11
>PF13929 mRNA_stabil: mRNA stabilisation
Probab=31.48 E-value=1.5e+02 Score=30.32 Aligned_cols=147 Identities=12% Similarity=0.128 Sum_probs=88.0
Q ss_pred cCcchhhHHHhhhHHHHHHHhhhcCCCCCChHHHHHHhHHHHHhhhhhc-----cccccccCCCCchhHH---HHH----
Q 016426 57 ISEVDTYLIDSGKKFHAKLKRKLKDTNNFDKDEFIGILNPYLQKIGEKV-----GISTRINRSDSGYTQG---LIE---- 124 (390)
Q Consensus 57 ~s~~d~~~~~~~~~f~~~lk~~l~~~~~~~~~~~~~~l~~fl~~~~~~~-----~~~~~~~~s~~~~~~~---~i~---- 124 (390)
+-.+||+..+.-.+|-..++.|-..-..+++++|+++|+--.+++...= ++-.. ...+-. +++
T Consensus 82 Ln~~~p~~y~~~~~~~DYf~lK~s~g~~Lt~~Dli~FL~~~i~~~~~~k~~~Y~~LVk~-----N~~Vv~aL~L~~~~~~ 156 (292)
T PF13929_consen 82 LNIADPQNYSVRRFINDYFLLKKSMGCELTKEDLISFLKLVIINLSSNKSFNYWDLVKR-----NKIVVEALKLYDGLNP 156 (292)
T ss_pred HhhcCcccCCHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhccccccchHHHHHHHh-----hHHHHHHHHHhhccCc
Confidence 6788888887776666555555555555899999999888777654330 00000 001111 111
Q ss_pred -----HhhcchhHHHHHHHH-HhhcchhhHHHHHHHHHh--CCCCCCCchHHHHHHHhcCChhHH-HHHHhhCCC----C
Q 016426 125 -----KVGFLMGRDVASLVL-EACISLRIWELVETLIVH--GLVDHSSYSNLVTRLATEKRSDLL-CLCVKYSPD----L 191 (390)
Q Consensus 125 -----~~~~~ig~~v~~lv~-r~~~~~~fw~~L~~Li~~--g~Ls~S~cP~Lv~~llEk~d~~LL-qlcL~qfpD----I 191 (390)
.-+..|...+-.++. +..--.++||++.-++.+ |.++-..-=..+..+.|.++..-+ +.--++.+. -
T Consensus 157 ~~~Ii~d~evislLL~sMv~~~~~~l~alYEvV~~l~~t~~~~l~~~vi~~Il~~L~~~~dW~kl~~fW~~~~~~~~~~~ 236 (292)
T PF13929_consen 157 DESIIFDEEVISLLLKSMVIDENTKLNALYEVVDFLVSTFSKSLTRNVIISILEILAESRDWNKLFQFWEQCIPNSVPGN 236 (292)
T ss_pred ccceeeChHHHHHHHHHHHhccccchhhHHHHHHHHHhccccCCChhHHHHHHHHHHhcccHHHHHHHHHHhcccCCCCC
Confidence 123345555566666 455558899999999988 777776666778888888887644 433444444 2
Q ss_pred ChHHHHHHHHHhhCCCc
Q 016426 192 GSSELLCILKYFLCPPK 208 (390)
Q Consensus 192 ~es~~~AcLK~FLs~~d 208 (390)
+.-.+-.-+|.+..-+|
T Consensus 237 D~rpW~~FI~li~~sgD 253 (292)
T PF13929_consen 237 DPRPWAEFIKLIVESGD 253 (292)
T ss_pred CCchHHHHHHHHHHcCC
Confidence 23334555555555444
No 12
>KOG0310 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=30.88 E-value=1.9e+02 Score=31.56 Aligned_cols=86 Identities=17% Similarity=0.263 Sum_probs=67.6
Q ss_pred HhhhhccCChHHHHHHHHHHHHHHHHhccCCCCCCCCCcccccCCCcCCCCCChHHHHHHHHHHhhcccceeeechhhHH
Q 016426 280 LSSSISKLNGKELMGLIRYLGKWLKKFERFPQAGPCPEASFGLGLKACDWVPKLEVIVQCLGLVLDENFSSLVLLPEFQE 359 (390)
Q Consensus 280 Llp~LkdL~~~ev~~lLrYL~kW~~kys~~~~~~pcp~a~s~pgl~~~~~vPtl~qI~dWi~LlLDahFT~lVm~peake 359 (390)
+.-+|.+.+-.+...||.+|.+-+.+ +=..+-.|.|++.+||--=-.+-..|++.+
T Consensus 396 l~~AL~grde~eL~~lLnfl~~~l~~------------------------~rf~~~L~~~~~~iLd~Y~~~i~~s~~l~k 451 (487)
T KOG0310|consen 396 LRRALAGRDESELAPLLNFLVKNLTV------------------------VRFASILMEVVSVILDLYARDIEGSPMLAK 451 (487)
T ss_pred HHHHhcCccHHHHHHHHHHHHhhccc------------------------hhhHHHHHHHHHHHHHHHHhhhccCHHHHH
Confidence 45667777788888887777654321 112345789999999988888999999999
Q ss_pred HHHHHHHHHHHHHHHHHhhccHHHHHHHhc
Q 016426 360 ELRSIEGVVSTLASEARYCCSLANVVKRFG 389 (390)
Q Consensus 360 ~L~~l~~~Vksq~~~~~~~~~~~~~~~~~~ 389 (390)
.+.+|.+.|..-+..-+..-.+.+.++-|.
T Consensus 452 ~i~~L~~~V~~Ev~~q~ellr~~G~ldmL~ 481 (487)
T KOG0310|consen 452 LIQALRGKVEQEVRVQKELLRLIGMLDMLG 481 (487)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 999999999999998888888888777654
No 13
>PF07035 Mic1: Colon cancer-associated protein Mic1-like; InterPro: IPR009755 This entry represents the C terminus (approximately 160 residues) of a number of proteins that resemble colon cancer-associated protein Mic1.
Probab=30.08 E-value=2.3e+02 Score=26.41 Aligned_cols=79 Identities=15% Similarity=0.260 Sum_probs=53.0
Q ss_pred ChHHHHHHhHHHHHhhhhhccccccccCCCCchhHHHHHHhhcchhHHHHHHHHHhhcchhhHHHHHHHHHhCCCCCCCc
Q 016426 86 DKDEFIGILNPYLQKIGEKVGISTRINRSDSGYTQGLIEKVGFLMGRDVASLVLEACISLRIWELVETLIVHGLVDHSSY 165 (390)
Q Consensus 86 ~~~~~~~~l~~fl~~~~~~~~~~~~~~~s~~~~~~~~i~~~~~~ig~~v~~lv~r~~~~~~fw~~L~~Li~~g~Ls~S~c 165 (390)
+..=++.++-.|+..+.+. |++.+ +-+-.++++.++..+-|+.|.||++.|++.-|.
T Consensus 5 ~~~yli~vllEYirSl~~~-~i~~~---------------------~~L~~lli~lLi~~~~~~~L~qllq~~Vi~DSk- 61 (167)
T PF07035_consen 5 DPRYLIAVLLEYIRSLNQH-NIPVQ---------------------HELYELLIDLLIRNGQFSQLHQLLQYHVIPDSK- 61 (167)
T ss_pred cHHHHHHHHHHHHHHHHHc-CCCCC---------------------HHHHHHHHHHHHHcCCHHHHHHHHhhcccCCcH-
Confidence 3344667777888877665 44433 557778888888888899999999999998776
Q ss_pred hHHHHHHHhc--CChhHHHHHHhhC
Q 016426 166 SNLVTRLATE--KRSDLLCLCVKYS 188 (390)
Q Consensus 166 P~Lv~~llEk--~d~~LLqlcL~qf 188 (390)
.+.-.+++. .....-|+++--+
T Consensus 62 -~lA~~LLs~~~~~~~~~Ql~lDML 85 (167)
T PF07035_consen 62 -PLACQLLSLGNQYPPAYQLGLDML 85 (167)
T ss_pred -HHHHHHHHhHccChHHHHHHHHHH
Confidence 344444444 3344555554433
No 14
>KOG3380 consensus Actin-related protein Arp2/3 complex, subunit ARPC5 [Cytoskeleton]
Probab=29.13 E-value=58 Score=30.36 Aligned_cols=24 Identities=25% Similarity=0.463 Sum_probs=20.1
Q ss_pred HhhhhccCChHHHHHHHHHHHHHH
Q 016426 280 LSSSISKLNGKELMGLIRYLGKWL 303 (390)
Q Consensus 280 Llp~LkdL~~~ev~~lLrYL~kW~ 303 (390)
.-..+++|+.+++-.||+|+||=+
T Consensus 91 I~~~v~~Ls~e~~DiLmKYiYkGm 114 (152)
T KOG3380|consen 91 IEAAVKKLSTEEIDILMKYIYKGM 114 (152)
T ss_pred HHHHHHHhhHHHHHHHHHHHHHHh
Confidence 345678999999999999999854
No 15
>PF04699 P16-Arc: ARP2/3 complex 16 kDa subunit (p16-Arc); InterPro: IPR006789 The Arp2/3 protein complex has been implicated in the control of actin polymerisation. The human complex consists of seven subunits which include the actin related proteins Arp2 and Arp3, and five others referred to as p41-Arc, p34-Arc, p21-Arc, p20-Arc, and p16-Arc. The precise function of p16-Arc is currently unknown. Its structure consists of a single domain containing a bundle of seven alpha helices [, ].; GO: 0030833 regulation of actin filament polymerization, 0005856 cytoskeleton; PDB: 3DWL_G 1TYQ_G 1U2V_G 2P9U_G 2P9L_G 1K8K_G 3DXM_G 2P9N_G 3DXK_G 2P9I_G ....
Probab=28.72 E-value=53 Score=30.28 Aligned_cols=24 Identities=17% Similarity=0.360 Sum_probs=20.0
Q ss_pred HhhhhccCChHHHHHHHHHHHHHH
Q 016426 280 LSSSISKLNGKELMGLIRYLGKWL 303 (390)
Q Consensus 280 Llp~LkdL~~~ev~~lLrYL~kW~ 303 (390)
+...++.|+.+|.-.||+|+||=+
T Consensus 91 I~~~v~~L~~~~~D~LMKYiYkg~ 114 (152)
T PF04699_consen 91 IENAVKSLDSDQQDILMKYIYKGM 114 (152)
T ss_dssp HHHHHCCS-HHHHHHHHHHHHHHT
T ss_pred HHHHHHhCCHHHHhHHHHHHHHhc
Confidence 557889999999999999998853
No 16
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=28.70 E-value=82 Score=22.27 Aligned_cols=24 Identities=17% Similarity=0.199 Sum_probs=19.4
Q ss_pred hHHHHHHhhCCCCChHHHHHHHHH
Q 016426 179 DLLCLCVKYSPDLGSSELLCILKY 202 (390)
Q Consensus 179 ~LLqlcL~qfpDI~es~~~AcLK~ 202 (390)
+.+.....-|||+++..+..||+.
T Consensus 4 ~~v~~L~~mFP~l~~~~I~~~L~~ 27 (43)
T smart00546 4 EALHDLKDMFPNLDEEVIKAVLEA 27 (43)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHH
Confidence 345556677999999999999985
No 17
>PF04938 SIP1: Survival motor neuron (SMN) interacting protein 1 (SIP1); PDB: 3S6N_2.
Probab=25.54 E-value=1e+02 Score=28.99 Aligned_cols=69 Identities=28% Similarity=0.385 Sum_probs=42.7
Q ss_pred HhhhhccCChHHHHHHHHHHHHHHHHhccCCCCCCCCCcccccCCCcCCCCCChHHHHHHHHHHhhcccceeeechhhHH
Q 016426 280 LSSSISKLNGKELMGLIRYLGKWLKKFERFPQAGPCPEASFGLGLKACDWVPKLEVIVQCLGLVLDENFSSLVLLPEFQE 359 (390)
Q Consensus 280 Llp~LkdL~~~ev~~lLrYL~kW~~kys~~~~~~pcp~a~s~pgl~~~~~vPtl~qI~dWi~LlLDahFT~lVm~peake 359 (390)
.+..+..|+..++..+|+|+..|+... ++ .+.+.+=+=.+++.||.. +.||...
T Consensus 138 ~l~~l~~l~~~~v~~Ll~~~~~w~~~~----------------~~-----~~~~~~WlyaLLa~ld~p-----L~~d~~s 191 (233)
T PF04938_consen 138 TLSILLQLDQVTVSQLLEYLTEWLEEE----------------GL-----SPNLSQWLYALLARLDKP-----LDADTCS 191 (233)
T ss_dssp -HHHHTTS-HHHHHHHHHHHHHGGGTS------------------------HHHHHHHHHHHHH--SS-------HHHHH
T ss_pred hHHHHHhCCHHHHHHHHHHHHHHHhcc----------------cC-----chHHHHHHHHHHHHhCCC-----CCHHHHH
Confidence 445677899999999999999993211 22 233444444456667865 5689999
Q ss_pred HHHHHHHHHHHHHHH
Q 016426 360 ELRSIEGVVSTLASE 374 (390)
Q Consensus 360 ~L~~l~~~Vksq~~~ 374 (390)
.||+|-+--.++-+.
T Consensus 192 ~LR~LaR~C~~lR~~ 206 (233)
T PF04938_consen 192 SLRSLARKCAKLRAK 206 (233)
T ss_dssp HHHHHHHHHHHHGGG
T ss_pred HHHHHHHHHHHHHHh
Confidence 999988776665443
No 18
>PF13565 HTH_32: Homeodomain-like domain
Probab=24.78 E-value=1.2e+02 Score=23.19 Aligned_cols=45 Identities=16% Similarity=0.127 Sum_probs=29.0
Q ss_pred HHHHHHHhccCCCCCCCCC-cccccCCCcCCCCCChHHHHHHHHHHhhccc
Q 016426 299 LGKWLKKFERFPQAGPCPE-ASFGLGLKACDWVPKLEVIVQCLGLVLDENF 348 (390)
Q Consensus 299 L~kW~~kys~~~~~~pcp~-a~s~pgl~~~~~vPtl~qI~dWi~LlLDahF 348 (390)
+++|+.+|.+.+..|.-+. ...-+| ++++-.++.++|.-++..|-
T Consensus 2 v~rw~~ry~~~G~~gL~~~~~~~~~G-----rp~~~~e~~~~i~~~~~~~p 47 (77)
T PF13565_consen 2 VYRWLKRYREEGLEGLKDRKRRPRPG-----RPRKDPEQRERIIALIEEHP 47 (77)
T ss_pred HHHHHHHHHhhCchhhhcccccCCCC-----CCCCcHHHHHHHHHHHHhCC
Confidence 5789999999775544321 112244 34453566699999988885
No 19
>PF02847 MA3: MA3 domain; InterPro: IPR003891 This entry represents the MI domain (after MA-3 and eIF4G), it is a protein-protein interaction module of ~130 amino acids [, , ]. It appears in several translation factors and is found in: One copy in plant and animal eIF4G 1 and 2 (DAP-5/NAT1/p97) Two copies in the animal programmed cell death protein 4 (PDCD4) or MA-3 that is induced during programmed cell death and inhibits neoplastic transformation Four tandem-repeated copies in a group of uncharacterised plant proteins The MI domain consists of seven alpha-helices, which pack into a globular form. The packing arrangement consists of repeating pairs of antiparallel helices packed one upon the other such that a superhelical axis is generated perpendicular to the alpha-helical axes []. The MI domain has also been named MA3 domain.; PDB: 2ION_A 2IOL_B 2NSZ_A 3EIQ_C 2HM8_A 2KZT_B 2IOS_A 2RG8_B 2ZU6_E 3EIJ_A ....
Probab=23.25 E-value=1.4e+02 Score=24.50 Aligned_cols=36 Identities=17% Similarity=0.300 Sum_probs=26.7
Q ss_pred hHHHHHHHhhhcCCCCCChHHHHHHhHHHHHhhhhh
Q 016426 69 KKFHAKLKRKLKDTNNFDKDEFIGILNPYLQKIGEK 104 (390)
Q Consensus 69 ~~f~~~lk~~l~~~~~~~~~~~~~~l~~fl~~~~~~ 104 (390)
+.++++|=..|-+.+.++++.|...+..+++.+.+-
T Consensus 53 r~~~~~Ll~~L~~~~~~~~~~~~~gf~~~l~~l~Dl 88 (113)
T PF02847_consen 53 REYYSKLLSHLCKRKLISKEQFQEGFEDLLESLEDL 88 (113)
T ss_dssp HHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhcCCCCHHHHHHHHHHHHhHhhhc
Confidence 345555556666677789999999999999998765
No 20
>cd04756 Commd8 COMM_Domain containing protein 8. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=21.99 E-value=62 Score=30.06 Aligned_cols=36 Identities=11% Similarity=0.197 Sum_probs=31.1
Q ss_pred cCCCchhhHhhhhccCChHHHHHHHHHHHHHHHHhc
Q 016426 272 SSNIDEVILSSSISKLNGKELMGLIRYLGKWLKKFE 307 (390)
Q Consensus 272 S~~~De~~Llp~LkdL~~~ev~~lLrYL~kW~~kys 307 (390)
..|+++.-+..+|.+|+..+...+++=+..|...-.
T Consensus 61 ~~~l~~~~l~~~L~~L~~~~~~a~~~~~~~~~~ei~ 96 (176)
T cd04756 61 GKNSNDEEAKAQLSDLSSSHQEALLKCVKSRKEEIR 96 (176)
T ss_pred ccCCCHHHHHHHHhcCCHHHHHHHHHHHHHhhHHHH
Confidence 567889999999999999999999999998866533
No 21
>PF08064 UME: UME (NUC010) domain; InterPro: IPR012993 This domain is characteristic of UVSB PI-3 kinase, MEI-41 and ESR1 [].; GO: 0004674 protein serine/threonine kinase activity
Probab=21.46 E-value=4.7e+02 Score=22.12 Aligned_cols=40 Identities=13% Similarity=0.216 Sum_probs=25.1
Q ss_pred ChHHHHHHhHHHHHhhhhhccccccccCCCCchhHHHHHHhhcchh
Q 016426 86 DKDEFIGILNPYLQKIGEKVGISTRINRSDSGYTQGLIEKVGFLMG 131 (390)
Q Consensus 86 ~~~~~~~~l~~fl~~~~~~~~~~~~~~~s~~~~~~~~i~~~~~~ig 131 (390)
=++.|.++++.|=+++-+.-| . ..-.+-+..|+.++.+|-
T Consensus 5 L~~~~Lgil~~f~~~l~d~~~-~-----~~~~ek~~~l~si~~lI~ 44 (107)
T PF08064_consen 5 LQPHILGILTRFSDVLNDLRG-K-----KPIPEKKRALRSIEELIK 44 (107)
T ss_pred HHHHHHHHHHHHHHHHhcccc-C-----CCHHHHHHHHHHHHHHHH
Confidence 357888999999888777311 1 123455666777666654
No 22
>PF04192 Utp21: Utp21 specific WD40 associated putative domain ; InterPro: IPR007319 A large ribonuclear protein complex is required for the processing of the small-ribosomal-subunit rRNA - the small-subunit (SSU) processome [, ]. This preribosomal complex contains the U3 snoRNA and at least 40 proteins, which have the following properties: They are nucleolar. They are able to coimmunoprecipitate with the U3 snoRNA and Mpp10 (a protein specific to the SSU processome). They are required for 18S rRNA biogenesis. There appears to be a linkage between polymerase I transcription and the formation of the SSU processome; as some, but not all, of the SSU processome components are required for pre-rRNA transcription initiation. These SSU processome components have been termed t-Utps. They form a pre-complex with pre-18S rRNA in the absence of snoRNA U3 and other SSU processome components. It has been proposed that the t-Utp complex proteins are both rDNA and rRNA binding proteins that are involved in the initiation of pre18S rRNA transcription. Initially binding to rDNA then associating with the 5' end of the nascent pre18S rRNA. The t-Utpcomplex forms the nucleus around which the rest of the SSU processome components, including snoRNA U3, assemble []. From electron microscopy the SSU processome may correspond to the terminal knobs visualized at the 5' ends of nascent 18S rRNA. Utp21 is a component of the SSU processome, which is required for pre-18S rRNA processing. It interacts with Utp18 [].; GO: 0006364 rRNA processing, 0032040 small-subunit processome
Probab=20.56 E-value=6.4e+02 Score=24.58 Aligned_cols=59 Identities=20% Similarity=0.294 Sum_probs=46.1
Q ss_pred hHHHHHHHHHHHHHHHHhccCCCCCCCCCcccccCCCcCCCCCChHHHHHHHHHHhhcccceeeechh---hHHHHHHHH
Q 016426 289 GKELMGLIRYLGKWLKKFERFPQAGPCPEASFGLGLKACDWVPKLEVIVQCLGLVLDENFSSLVLLPE---FQEELRSIE 365 (390)
Q Consensus 289 ~~ev~~lLrYL~kW~~kys~~~~~~pcp~a~s~pgl~~~~~vPtl~qI~dWi~LlLDahFT~lVm~pe---ake~L~~l~ 365 (390)
.+++..|++||..+++.-.- +.-|-.|+++.|=.|-.+++-.++ .++.|..+.
T Consensus 156 ~~~l~~Fl~~l~~~L~~~~d------------------------fElvQa~l~vFLk~Hgd~i~~~~~~~~L~~~l~~l~ 211 (237)
T PF04192_consen 156 YEELVSFLRFLTYRLKSRRD------------------------FELVQAYLSVFLKVHGDVIMESEEEEELREALEELR 211 (237)
T ss_pred HHHHHHHHHHHHHHHHcCCC------------------------HHHHHHHHHHHHHHHHHHHHcCCchHHHHHHHHHHH
Confidence 78889999999998874332 455778999999999999999999 677766666
Q ss_pred HHHHHH
Q 016426 366 GVVSTL 371 (390)
Q Consensus 366 ~~Vksq 371 (390)
...++.
T Consensus 212 ~~q~~~ 217 (237)
T PF04192_consen 212 EAQESE 217 (237)
T ss_pred HHHHHH
Confidence 655543
Done!