Query 036294
Match_columns 833
No_of_seqs 329 out of 1021
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 11:15:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036294.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036294hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1990 Poly(A)-specific exori 100.0 9.7E-80 2.1E-84 694.3 20.3 521 214-774 3-528 (564)
2 PRK10343 RNA-binding protein Y 99.9 2.7E-25 5.8E-30 202.5 13.3 88 629-720 2-89 (97)
3 PRK10343 RNA-binding protein Y 99.9 2.3E-25 5E-30 202.9 12.4 88 225-312 2-89 (97)
4 PF01985 CRS1_YhbY: CRS1 / Yhb 99.9 1.7E-25 3.8E-30 197.8 10.2 84 226-309 1-84 (84)
5 TIGR00253 RNA_bind_YhbY putati 99.9 5.4E-25 1.2E-29 199.8 13.1 87 630-720 1-87 (95)
6 TIGR00253 RNA_bind_YhbY putati 99.9 5.4E-25 1.2E-29 199.8 12.2 87 226-312 1-87 (95)
7 PF01985 CRS1_YhbY: CRS1 / Yhb 99.9 3.4E-24 7.3E-29 189.6 10.7 84 630-717 1-84 (84)
8 COG1534 Predicted RNA-binding 99.9 8.9E-24 1.9E-28 192.2 12.2 96 629-729 1-96 (97)
9 COG1534 Predicted RNA-binding 99.9 3.3E-23 7.2E-28 188.5 11.3 85 225-309 1-85 (97)
10 KOG1990 Poly(A)-specific exori 98.6 4.9E-08 1.1E-12 112.7 5.5 265 221-512 170-480 (564)
11 PF04931 DNA_pol_phi: DNA poly 74.6 5.4 0.00012 48.9 6.2 38 731-770 596-633 (784)
12 PF10446 DUF2457: Protein of u 52.3 14 0.0003 43.1 3.7 8 755-762 38-45 (458)
13 PF15237 PTRF_SDPR: PTRF/SDPR 51.6 26 0.00057 38.1 5.3 66 447-514 54-121 (246)
14 KOG1832 HIV-1 Vpr-binding prot 43.6 16 0.00034 46.0 2.5 37 473-509 1060-1096(1516)
15 COG1623 Predicted nucleic-acid 35.5 1.4E+02 0.0031 33.7 8.0 71 683-765 104-174 (349)
16 KOG3130 Uncharacterized conser 35.5 22 0.00047 41.2 1.9 26 804-829 282-307 (514)
17 PF14812 PBP1_TM: Transmembran 33.5 14 0.0003 34.1 0.0 16 798-813 31-46 (81)
18 PF06524 NOA36: NOA36 protein; 31.9 49 0.0011 36.7 3.7 13 685-697 159-171 (314)
19 PF07412 Geminin: Geminin; In 31.4 50 0.0011 35.1 3.6 32 735-768 116-147 (200)
20 PF10369 ALS_ss_C: Small subun 28.6 1E+02 0.0023 27.4 4.6 35 673-715 6-40 (75)
21 KOG3130 Uncharacterized conser 26.6 36 0.00077 39.6 1.7 13 635-647 142-154 (514)
22 KOG3064 RNA-binding nuclear pr 26.6 30 0.00065 38.1 1.1 33 773-805 218-250 (303)
23 PF06524 NOA36: NOA36 protein; 25.9 74 0.0016 35.3 3.8 6 666-671 104-109 (314)
24 PF11702 DUF3295: Protein of u 25.4 35 0.00076 40.5 1.4 19 804-822 308-327 (507)
25 PF15249 GLTSCR1: Glioma tumor 25.2 28 0.00061 33.0 0.5 24 400-423 13-44 (109)
26 PF12207 DUF3600: Domain of un 24.6 13 0.00028 37.9 -2.0 92 591-682 27-132 (162)
27 PF04472 DUF552: Protein of un 23.8 4.8E+02 0.01 22.9 7.8 56 257-313 12-70 (73)
28 PF15337 Vasculin: Vascular pr 23.4 40 0.00086 32.1 1.1 41 419-460 34-74 (97)
29 PF04871 Uso1_p115_C: Uso1 / p 23.0 1.1E+02 0.0024 30.3 4.1 26 747-772 85-110 (136)
30 PF04931 DNA_pol_phi: DNA poly 22.5 63 0.0014 39.9 2.9 21 469-489 335-355 (784)
31 PF10205 KLRAQ: Predicted coil 22.2 2E+02 0.0043 27.9 5.4 39 731-771 34-72 (102)
No 1
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=100.00 E-value=9.7e-80 Score=694.35 Aligned_cols=521 Identities=45% Similarity=0.644 Sum_probs=487.2
Q ss_pred ccCCCCcccccCCCHHHHHHHHHcccCCCceEecCCCCCCHHHHHHHHHHHHhCCeEEEEecCCchHhHHHHHHHHHHHh
Q 036294 214 RRMKAPTLAELTIEDEELRRLRRNGMYLRERINVPKAGLTQDVMRKIHDKWRKDELVRLKFHEVLATDMKTAHEIVERRT 293 (833)
Q Consensus 214 ~~~~~ps~AEltLt~kErr~LR~lAh~LkpvV~IGK~GVTd~VVeeIh~awk~hELVKVKvl~~~~~dmk~~~e~LEekT 293 (833)
+... |++||+++.+.++.+||..|..+...+ +++|+|+.+++.|++.|+.+|+++++|....+.+|.+++++++..|
T Consensus 3 ~~~~-~~~~~~~~~~~~~~~l~~~~~~~~~~~--~~~~~~~~~~~~~y~k~k~~~~~~~~~q~~~~~~~~~~~~~~~~~~ 79 (564)
T KOG1990|consen 3 NFES-LSLAELTVDEADLRRLRLVATGMTSAP--WKAGSTFDTVEAIYLKWKDNEEVYLKFQFGLCLFMKRSHEALEMST 79 (564)
T ss_pred cccc-hhHHHhhcCHHHHHHHhhhhccceecc--cccccchhhhHHHHHHHHhhhhhheeeccccchhHHHhhhHhhccC
Confidence 3444 999999999999999999999998887 9999999999999999999999999999999999999999999999
Q ss_pred CC-eEEEEECcEEEEeccCCCCCCCCCCCCCCCCCCCccccCCCCCCCCCcccccccCCccccccCCCCCCChHHHhhhh
Q 036294 294 GG-LVIWRAGSVMVVYRGNNYAGPSSKPQPLDGDGDTLFVPHVSSTDGSTARSVDEKSEVPVRILDHSKPMTEEEAECNS 372 (833)
Q Consensus 294 Gg-eVVqrIG~viVLYRg~nY~~p~~~~~~~~~~~~~l~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~e~e~e~n~ 372 (833)
|| .+||+.|.+...|++..|..|..-..+ .. ..+....+++++.+.+.
T Consensus 80 ~~n~~~~~~g~~~s~~~~~~~~~~~~~~~~---~~----------------------------~~~~~~~~~~~~~~~~~ 128 (564)
T KOG1990|consen 80 GGNFVVWSRGDSISSPEFLCQRSPVDFVAR---QQ----------------------------ENQAGKWPSELEKEKNE 128 (564)
T ss_pred CCceeeeecCccccCCccceeecchhhhhh---hc----------------------------hhhhhhhHHHHHHHHHH
Confidence 99 999999999999988888877532110 00 01222334778889999
Q ss_pred hhhccCCCcccccCCCCCCCCCCCCCCCCCCCCCCcccCCCCCCCCCCHHHHHHHHHhhhcCCCeeEecccchhhHHHHH
Q 036294 373 LLDSLGPRFQEWWGTGILPVDADLLPPKVDGYKTPFRLLPTGMRSRLTNAEMTDLRRLARSLPCHFALGRNRNHQGLAVA 452 (833)
Q Consensus 373 LLd~LGPRf~dW~g~~plPVDadLLp~~vpgyk~PfR~lP~Gvr~~Lt~~E~T~LRrlar~lPphfaLGRn~~~~gLA~a 452 (833)
+++++||+|.|||+.+++|||+||+|++||+|.+|||.+|+|++++||..|+|.+|++|..+||||+||+++.+||++.+
T Consensus 129 ~~~~~~~~~~~~~~~~~~~~~~dl~~~~i~~~~~p~r~l~~~~~~~l~~~~~~~~r~~~~~~p~~~~~~~~~~~~~~~~~ 208 (564)
T KOG1990|consen 129 LLDSLGPELSDWGGSDRLSVDADLLPEKIPDYMRPFRTLPVGSPPLLTSIESTLLRRLGYKLPPHFALGRSRKLQGLAVA 208 (564)
T ss_pred HhhccCcccccCCCCCCccchhhhchhhhhcccChhccCCCCChhhhhhHHHHHHHHhcccccccceehhccccccchhH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhcceEEEeeccCCCCCchHHHHHHH--hhccCceeeeecCCEEEEEecCCCCChhHHHHHHHHHHHHHhhhhHH
Q 036294 453 ILKLWEKSLVAKIAVKRGIQNTNNKLMAEEL--KSLTGGTLLQRNKFYIVLYRGKDFLPPNVASALAEREQCAKQIQDVE 530 (833)
Q Consensus 453 I~klWEk~~iaKIa~KrGvqnT~~e~MaeeL--K~LTGgvLLsRnke~IVlYRGkdFlp~~V~~al~eRe~~~~~~q~~E 530 (833)
|+++|++|++++|+|++|++++.++.||.+| +.+||++|++||+.++|+|||++|++ .|.++|.++.......|+.+
T Consensus 209 ~~~~~~k~~~~k~~~~rg~~~~~~~~~a~~l~~~~~tg~~lv~hN~~~dv~y~~~~Fl~-~lp~~l~~f~~~~~~fp~~~ 287 (564)
T KOG1990|consen 209 MVSFWEKHEFAKILIKRGVLETRKERMADELQELLLTGKVLVLHNKLLDVMYRYKNFLS-PLPSTLEEFTDSSSMFPNIE 287 (564)
T ss_pred HHHHHHHHHHHHHHHHhcchhhhccchHHHHHHHHhcCCeEEeeccceeeeeehhhccc-ccchhHHHhhhhhhhhhhhH
Confidence 9999999999999999999999999999999 99999999999999999999999999 99999999999888899999
Q ss_pred HHHhhccccCCCCCCCCCCCCCcchHHHHHHHHhhccccchHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 036294 531 EKVRSKTLEATPSGETEGQAPAGTLAEFYEAQKRWGREVSAEER-EKMVEEASKAKHARLVKRIEHKLAVSQAKKLRAER 609 (833)
Q Consensus 531 e~aR~~a~~~~~~~~~~~~~~aGtl~e~~~a~~~w~~~~~~~~~-~~~~~e~~~~~~~~~~k~~e~kL~~a~~K~~~ae~ 609 (833)
+.+|+.+++.... ...++|+.|+..+..+|+..+..... ..+..+......++..+.+.+++..+++|++.++.
T Consensus 288 ~~~~~~~~~~~~~-----~~~~~t~~e~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 362 (564)
T KOG1990|consen 288 DTKRLAKLSEYQK-----LNLKATLLELARAKAKKEKEIERRSISSRLKLEFEKASSEKLTEAIFHKLEKAKKKLASANR 362 (564)
T ss_pred HHHHhhccccccc-----hhhhhhHHHHHHHhcccccCcccccccchhhhhhhccchhhHHHHHHHHHhhhhhhccchhh
Confidence 9999988433111 46799999999999999998866654 47888999999999999999999999999999999
Q ss_pred HHHhhhccCCCCCCCccCCCCCHHHHHHHHHcccCCcceeeccCCCCCHHHHHHHHHHHhhCceEEEEecCCCH-HHHHH
Q 036294 610 LLAKIEASMVPSGPDYDQETITDEERAMFRRVGLRMKAFLPLGIRGVFDGVVENMHLHWKYRELVKLITKQKTL-AYVED 688 (833)
Q Consensus 610 ~L~Kle~~~~P~e~~~d~E~LT~eERk~LRklGhkLKPvV~IGKrGVtdgVIeeIh~awk~hELVKVkv~~~~~-ed~ke 688 (833)
.|++++....|++..++++.+|.+++.+++++|.+|++++.+|++|+|+|||.+||.||++||++||+|+.... .+++.
T Consensus 363 ~l~~~~~~~~~~~~~~~~e~~t~ee~~~~~k~g~k~~~~~~~~rrg~f~g~i~n~~l~wk~~e~~k~i~~~~~~~~~~~~ 442 (564)
T KOG1990|consen 363 ILAKLEDPKIPAELRYDPESITEEERLMLRKVGLKMKRRLLSGRRGVFDGVIENMHLHWKSRELVKVICKEKNLPSQVKQ 442 (564)
T ss_pred hhhcccccccccccccchhhcChHHHHHHHHHHHhhccccccCCcccccceeecchhhhhhcccceeeeccccccHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999876 99999
Q ss_pred HHHHHHHHhCCEEEEEeecCCCcEEEEEecCCCCCCCCCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 036294 689 TARLLEYESGGILIAIERVPKGFALIFYRGKNYRRPISLRPRNLLTKAKALKRSVAMQRHEALSQHISDLENTIEQMKKE 768 (833)
Q Consensus 689 iA~~Le~~SGg~LVqVI~~~kG~tiILYRgkNY~rP~~~~P~nlLtKrkAL~rS~~~Qr~esl~~~i~~lek~i~~l~~~ 768 (833)
.|..++.++|+++|+++++.+|+.|++||++||++|..++|.++|+||+|+.+++++|+.+++++||..++.++++++.+
T Consensus 443 ~a~~le~esg~~~v~~~~~~~~~ai~~yr~k~y~~p~~l~P~~~l~~~k~~~~~~~~~~~~a~~~~i~~~~~~~e~~~~~ 522 (564)
T KOG1990|consen 443 YASALERESGGILVSIDKNPKGYAIIAYRGKNYDRPTSLRPRNLLSRRKALERSLEEQRKEALKSHISDLEQEIEQLQAS 522 (564)
T ss_pred HHHHHHHHhCCceeeeccCCchhhHHHhhhhhccCCcccCchhhhcccCCccccHHHHHHHHHhhhcchhhhhHHHhhcc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hccccc
Q 036294 769 IGVSKD 774 (833)
Q Consensus 769 l~~~~~ 774 (833)
+....+
T Consensus 523 ~~~~~~ 528 (564)
T KOG1990|consen 523 VEAMPA 528 (564)
T ss_pred hhcccc
Confidence 866544
No 2
>PRK10343 RNA-binding protein YhbY; Provisional
Probab=99.93 E-value=2.7e-25 Score=202.51 Aligned_cols=88 Identities=17% Similarity=0.327 Sum_probs=86.4
Q ss_pred CCCHHHHHHHHHcccCCcceeeccCCCCCHHHHHHHHHHHhhCceEEEEecCCCHHHHHHHHHHHHHHhCCEEEEEeecC
Q 036294 629 TITDEERAMFRRVGLRMKAFLPLGIRGVFDGVVENMHLHWKYRELVKLITKQKTLAYVEDTARLLEYESGGILIAIERVP 708 (833)
Q Consensus 629 ~LT~eERk~LRklGhkLKPvV~IGKrGVtdgVIeeIh~awk~hELVKVkv~~~~~ed~keiA~~Le~~SGg~LVqVI~~~ 708 (833)
+||++||+|||++||+|+|+|+||++||||+||++++.+|++||||||++.+++.+++++++++||+.+||++||+|
T Consensus 2 ~Lt~kqr~~LR~~ah~l~Pvv~IGk~Glt~~vi~ei~~aL~~hELIKvkv~~~~~~~~~e~~~~i~~~~~ae~Vq~I--- 78 (97)
T PRK10343 2 NLSTKQKQHLKGLAHPLKPVVLLGSNGLTEGVLAEIEQALEHHELIKVKIATEDRETKTLIVEAIVRETGACNVQVI--- 78 (97)
T ss_pred CCCHHHHHHHHHhcCCCCCeEEECCCCCCHHHHHHHHHHHHHCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEeee---
Confidence 69999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcEEEEEecCC
Q 036294 709 KGFALIFYRGKN 720 (833)
Q Consensus 709 kG~tiILYRgkN 720 (833)
|+++||||++.
T Consensus 79 -G~~~vlYR~~~ 89 (97)
T PRK10343 79 -GKTLVLYRPTK 89 (97)
T ss_pred -CcEEEEEecCC
Confidence 99999999874
No 3
>PRK10343 RNA-binding protein YhbY; Provisional
Probab=99.93 E-value=2.3e-25 Score=202.94 Aligned_cols=88 Identities=20% Similarity=0.315 Sum_probs=86.4
Q ss_pred CCCHHHHHHHHHcccCCCceEecCCCCCCHHHHHHHHHHHHhCCeEEEEecCCchHhHHHHHHHHHHHhCCeEEEEECcE
Q 036294 225 TIEDEELRRLRRNGMYLRERINVPKAGLTQDVMRKIHDKWRKDELVRLKFHEVLATDMKTAHEIVERRTGGLVIWRAGSV 304 (833)
Q Consensus 225 tLt~kErr~LR~lAh~LkpvV~IGK~GVTd~VVeeIh~awk~hELVKVKvl~~~~~dmk~~~e~LEekTGgeVVqrIG~v 304 (833)
+||++|+++||++||+|+|+|+|||+|||++|+++|+++|++|||||||+++++.++.++++++|+++||+++||.||++
T Consensus 2 ~Lt~kqr~~LR~~ah~l~Pvv~IGk~Glt~~vi~ei~~aL~~hELIKvkv~~~~~~~~~e~~~~i~~~~~ae~Vq~IG~~ 81 (97)
T PRK10343 2 NLSTKQKQHLKGLAHPLKPVVLLGSNGLTEGVLAEIEQALEHHELIKVKIATEDRETKTLIVEAIVRETGACNVQVIGKT 81 (97)
T ss_pred CCCHHHHHHHHHhcCCCCCeEEECCCCCCHHHHHHHHHHHHHCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEeeeCcE
Confidence 69999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEeccCC
Q 036294 305 MVVYRGNN 312 (833)
Q Consensus 305 iVLYRg~n 312 (833)
+||||++.
T Consensus 82 ~vlYR~~~ 89 (97)
T PRK10343 82 LVLYRPTK 89 (97)
T ss_pred EEEEecCC
Confidence 99999974
No 4
>PF01985 CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR001890 The CRM domain is an ~100-amino acid RNA-binding domain. The name chloroplast RNA splicing and ribosome maturation (CRM) has been suggested to reflect the functions established for the four characterised members of the family: Zea mays (Maize) CRS1 (Q9FYT6 from SWISSPROT), CAF1 (Q84N49 from SWISSPROT) and CAF2 (Q84N48 from SWISSPROT) proteins and the Escherichia coli protein YhbY (P0AGK4 from SWISSPROT). The CRM domain is found in eubacteria, archaea, and plants. The CRM domain is represented as a stand-alone protein in archaea and bacteria, and in single- and multi-domain proteins in plants. It has been suggested that prokaryotic CRM proteins existed as ribosome-associated proteins prior to the divergence of archaea and bacteria, and that they were co-opted in the plant lineage as RNA binding modules by incorporation into diverse protein contexts. Plant CRM domains are predicted to reside not only in the chloroplast, but also in the mitochondrion and the nucleo/cytoplasmic compartment. The diversity of the CRM domain family in plants suggests a diverse set of RNA targets [, ]. The CRM domain is a compact alpha/beta domain consisting of a four-stranded beta sheet and three alpha helices with an alpha-beta-alpha-beta-alpha-beta-beta topology. The beta sheet face is basic, consistent with a role in RNA binding. Proximal to the basic beta sheet face is another moiety that could contribute to nucleic acid recognition. Connecting strand beta1 and helix alpha2 is a loop with a six amino acid motif, GxxG flanked by large aliphatic residues, within which one 'x' is typically a basic residue []. Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants []. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing []. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes []. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome [].; GO: 0003723 RNA binding; PDB: 1RQ8_A 1JO0_B 1LN4_A.
Probab=99.92 E-value=1.7e-25 Score=197.76 Aligned_cols=84 Identities=31% Similarity=0.453 Sum_probs=75.7
Q ss_pred CCHHHHHHHHHcccCCCceEecCCCCCCHHHHHHHHHHHHhCCeEEEEecCCchHhHHHHHHHHHHHhCCeEEEEECcEE
Q 036294 226 IEDEELRRLRRNGMYLRERINVPKAGLTQDVMRKIHDKWRKDELVRLKFHEVLATDMKTAHEIVERRTGGLVIWRAGSVM 305 (833)
Q Consensus 226 Lt~kErr~LR~lAh~LkpvV~IGK~GVTd~VVeeIh~awk~hELVKVKvl~~~~~dmk~~~e~LEekTGgeVVqrIG~vi 305 (833)
||++|+++||+.||+|+|+|+|||+|||++|+++|+++|++||||||||.+++..++++++++|+++|||+|||++|+++
T Consensus 1 Lt~ke~~~Lr~~a~~l~p~v~IGk~Glt~~vi~~i~~~l~~~eLvKVk~~~~~~~~~~~~~~~l~~~t~~~~V~~iG~~~ 80 (84)
T PF01985_consen 1 LTSKERKFLRKLAHHLKPVVQIGKNGLTDGVIEEIDDALEKHELVKVKVLGNCREDRKEIAEQLAEKTGAEVVQVIGRTI 80 (84)
T ss_dssp --HHHHHHHHHHHTTC--SEEE-TTSS-HHHHHHHHHHHHHHSEEEEEETT--HHHHHHHHHHHHHHHTEEEEEEETTEE
T ss_pred CCHHHHHHHHHHhcCCCCeEEECCCCCCHHHHHHHHHHHHhCCeeEEEEccCCHHHHHHHHHHHHHHhCCEEEEEECCEE
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEec
Q 036294 306 VVYR 309 (833)
Q Consensus 306 VLYR 309 (833)
||||
T Consensus 81 vlyR 84 (84)
T PF01985_consen 81 VLYR 84 (84)
T ss_dssp EEEE
T ss_pred EEEC
Confidence 9998
No 5
>TIGR00253 RNA_bind_YhbY putative RNA-binding protein, YhbY family. A combination of crystal structure, molecular modeling, and bioinformatic data together suggest that members of this family, including YhbY of E. coli, are RNA binding proteins.
Probab=99.92 E-value=5.4e-25 Score=199.85 Aligned_cols=87 Identities=21% Similarity=0.354 Sum_probs=85.4
Q ss_pred CCHHHHHHHHHcccCCcceeeccCCCCCHHHHHHHHHHHhhCceEEEEecCCCHHHHHHHHHHHHHHhCCEEEEEeecCC
Q 036294 630 ITDEERAMFRRVGLRMKAFLPLGIRGVFDGVVENMHLHWKYRELVKLITKQKTLAYVEDTARLLEYESGGILIAIERVPK 709 (833)
Q Consensus 630 LT~eERk~LRklGhkLKPvV~IGKrGVtdgVIeeIh~awk~hELVKVkv~~~~~ed~keiA~~Le~~SGg~LVqVI~~~k 709 (833)
||++||++||++||+|+|+|+||++||||+||++++++|++||||||++++++.++++++|++||+.+||++||+|
T Consensus 1 Lt~kqr~~Lr~~ah~l~p~v~IGK~Glt~~vi~ei~~aL~~hELIKVkvl~~~~~~~~e~a~~i~~~~~a~~Vq~i---- 76 (95)
T TIGR00253 1 LTGKQKRHLRGKAHHLKPVVLVGKNGLTEGVIKEIEQALEHRELIKVKVATEDREDKTLIAEALVKETGACNVQVI---- 76 (95)
T ss_pred CCHHHHHHHHHHhCCCCCeEEECCCCCCHHHHHHHHHHHHhCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEEEE----
Confidence 7999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcEEEEEecCC
Q 036294 710 GFALIFYRGKN 720 (833)
Q Consensus 710 G~tiILYRgkN 720 (833)
|+++||||++.
T Consensus 77 G~~~vlYR~~~ 87 (95)
T TIGR00253 77 GKTIVLYRPTK 87 (95)
T ss_pred ccEEEEEecCC
Confidence 99999999864
No 6
>TIGR00253 RNA_bind_YhbY putative RNA-binding protein, YhbY family. A combination of crystal structure, molecular modeling, and bioinformatic data together suggest that members of this family, including YhbY of E. coli, are RNA binding proteins.
Probab=99.92 E-value=5.4e-25 Score=199.85 Aligned_cols=87 Identities=25% Similarity=0.386 Sum_probs=85.4
Q ss_pred CCHHHHHHHHHcccCCCceEecCCCCCCHHHHHHHHHHHHhCCeEEEEecCCchHhHHHHHHHHHHHhCCeEEEEECcEE
Q 036294 226 IEDEELRRLRRNGMYLRERINVPKAGLTQDVMRKIHDKWRKDELVRLKFHEVLATDMKTAHEIVERRTGGLVIWRAGSVM 305 (833)
Q Consensus 226 Lt~kErr~LR~lAh~LkpvV~IGK~GVTd~VVeeIh~awk~hELVKVKvl~~~~~dmk~~~e~LEekTGgeVVqrIG~vi 305 (833)
||++|+++||++||+|+|+|+|||+|||++|+++|+++|++|||||||+++++..+.+++++.|+++|||++||.||+++
T Consensus 1 Lt~kqr~~Lr~~ah~l~p~v~IGK~Glt~~vi~ei~~aL~~hELIKVkvl~~~~~~~~e~a~~i~~~~~a~~Vq~iG~~~ 80 (95)
T TIGR00253 1 LTGKQKRHLRGKAHHLKPVVLVGKNGLTEGVIKEIEQALEHRELIKVKVATEDREDKTLIAEALVKETGACNVQVIGKTI 80 (95)
T ss_pred CCHHHHHHHHHHhCCCCCeEEECCCCCCHHHHHHHHHHHHhCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEEEEccEE
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEeccCC
Q 036294 306 VVYRGNN 312 (833)
Q Consensus 306 VLYRg~n 312 (833)
||||++.
T Consensus 81 vlYR~~~ 87 (95)
T TIGR00253 81 VLYRPTK 87 (95)
T ss_pred EEEecCC
Confidence 9999973
No 7
>PF01985 CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR001890 The CRM domain is an ~100-amino acid RNA-binding domain. The name chloroplast RNA splicing and ribosome maturation (CRM) has been suggested to reflect the functions established for the four characterised members of the family: Zea mays (Maize) CRS1 (Q9FYT6 from SWISSPROT), CAF1 (Q84N49 from SWISSPROT) and CAF2 (Q84N48 from SWISSPROT) proteins and the Escherichia coli protein YhbY (P0AGK4 from SWISSPROT). The CRM domain is found in eubacteria, archaea, and plants. The CRM domain is represented as a stand-alone protein in archaea and bacteria, and in single- and multi-domain proteins in plants. It has been suggested that prokaryotic CRM proteins existed as ribosome-associated proteins prior to the divergence of archaea and bacteria, and that they were co-opted in the plant lineage as RNA binding modules by incorporation into diverse protein contexts. Plant CRM domains are predicted to reside not only in the chloroplast, but also in the mitochondrion and the nucleo/cytoplasmic compartment. The diversity of the CRM domain family in plants suggests a diverse set of RNA targets [, ]. The CRM domain is a compact alpha/beta domain consisting of a four-stranded beta sheet and three alpha helices with an alpha-beta-alpha-beta-alpha-beta-beta topology. The beta sheet face is basic, consistent with a role in RNA binding. Proximal to the basic beta sheet face is another moiety that could contribute to nucleic acid recognition. Connecting strand beta1 and helix alpha2 is a loop with a six amino acid motif, GxxG flanked by large aliphatic residues, within which one 'x' is typically a basic residue []. Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants []. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing []. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes []. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome [].; GO: 0003723 RNA binding; PDB: 1RQ8_A 1JO0_B 1LN4_A.
Probab=99.91 E-value=3.4e-24 Score=189.60 Aligned_cols=84 Identities=25% Similarity=0.456 Sum_probs=75.6
Q ss_pred CCHHHHHHHHHcccCCcceeeccCCCCCHHHHHHHHHHHhhCceEEEEecCCCHHHHHHHHHHHHHHhCCEEEEEeecCC
Q 036294 630 ITDEERAMFRRVGLRMKAFLPLGIRGVFDGVVENMHLHWKYRELVKLITKQKTLAYVEDTARLLEYESGGILIAIERVPK 709 (833)
Q Consensus 630 LT~eERk~LRklGhkLKPvV~IGKrGVtdgVIeeIh~awk~hELVKVkv~~~~~ed~keiA~~Le~~SGg~LVqVI~~~k 709 (833)
||++||++||++||+|+|+|+||++|||++|+++|+++|++||||||+|.+++.++++++|+.|++.+||++||+|
T Consensus 1 Lt~ke~~~Lr~~a~~l~p~v~IGk~Glt~~vi~~i~~~l~~~eLvKVk~~~~~~~~~~~~~~~l~~~t~~~~V~~i---- 76 (84)
T PF01985_consen 1 LTSKERKFLRKLAHHLKPVVQIGKNGLTDGVIEEIDDALEKHELVKVKVLGNCREDRKEIAEQLAEKTGAEVVQVI---- 76 (84)
T ss_dssp --HHHHHHHHHHHTTC--SEEE-TTSS-HHHHHHHHHHHHHHSEEEEEETT--HHHHHHHHHHHHHHHTEEEEEEE----
T ss_pred CCHHHHHHHHHHhcCCCCeEEECCCCCCHHHHHHHHHHHHhCCeeEEEEccCCHHHHHHHHHHHHHHhCCEEEEEE----
Confidence 7999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcEEEEEe
Q 036294 710 GFALIFYR 717 (833)
Q Consensus 710 G~tiILYR 717 (833)
|+++||||
T Consensus 77 G~~~vlyR 84 (84)
T PF01985_consen 77 GRTIVLYR 84 (84)
T ss_dssp TTEEEEEE
T ss_pred CCEEEEEC
Confidence 99999998
No 8
>COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]
Probab=99.90 E-value=8.9e-24 Score=192.17 Aligned_cols=96 Identities=23% Similarity=0.411 Sum_probs=90.6
Q ss_pred CCCHHHHHHHHHcccCCcceeeccCCCCCHHHHHHHHHHHhhCceEEEEecCCCHHHHHHHHHHHHHHhCCEEEEEeecC
Q 036294 629 TITDEERAMFRRVGLRMKAFLPLGIRGVFDGVVENMHLHWKYRELVKLITKQKTLAYVEDTARLLEYESGGILIAIERVP 708 (833)
Q Consensus 629 ~LT~eERk~LRklGhkLKPvV~IGKrGVtdgVIeeIh~awk~hELVKVkv~~~~~ed~keiA~~Le~~SGg~LVqVI~~~ 708 (833)
+||++|+++||+.||+++|+|+||++|||++||.+|+.+|++||||||++.+++.++++++|+.|++.+||.+||+|
T Consensus 1 ~Lt~kq~~~Lrs~Ah~l~piv~IGk~Glte~vi~Ei~~aL~~reLIKVkvl~~~~edr~eia~~l~~~~~a~lVqvi--- 77 (97)
T COG1534 1 MLTGKQKRFLRSKAHHLKPIVQIGKNGLTEGVIKEIDRALEARELIKVKVLQNAREDKKEIAEALAEETGAELVQVI--- 77 (97)
T ss_pred CCcHHHHHHHHHhhccCCceEEecCCccCHHHHHHHHHHHHhCCcEEEEeeccchhhHHHHHHHHHHHhCCEEeeee---
Confidence 59999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcEEEEEecCCCCCCCCCCC
Q 036294 709 KGFALIFYRGKNYRRPISLRP 729 (833)
Q Consensus 709 kG~tiILYRgkNY~rP~~~~P 729 (833)
|+++|||| .+..++++..|
T Consensus 78 -G~~~vlyr-~~~e~~~i~l~ 96 (97)
T COG1534 78 -GKTLVLYR-ESKEKRKISLP 96 (97)
T ss_pred -eeEEEEEe-cCcccccccCC
Confidence 99999999 45566666555
No 9
>COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]
Probab=99.89 E-value=3.3e-23 Score=188.47 Aligned_cols=85 Identities=26% Similarity=0.425 Sum_probs=84.2
Q ss_pred CCCHHHHHHHHHcccCCCceEecCCCCCCHHHHHHHHHHHHhCCeEEEEecCCchHhHHHHHHHHHHHhCCeEEEEECcE
Q 036294 225 TIEDEELRRLRRNGMYLRERINVPKAGLTQDVMRKIHDKWRKDELVRLKFHEVLATDMKTAHEIVERRTGGLVIWRAGSV 304 (833)
Q Consensus 225 tLt~kErr~LR~lAh~LkpvV~IGK~GVTd~VVeeIh~awk~hELVKVKvl~~~~~dmk~~~e~LEekTGgeVVqrIG~v 304 (833)
+||++|+++||+.||+++|+|+|||+|||++|+++|+++|++||||||+|++++.++.+.+++.|++++|+.+||.||++
T Consensus 1 ~Lt~kq~~~Lrs~Ah~l~piv~IGk~Glte~vi~Ei~~aL~~reLIKVkvl~~~~edr~eia~~l~~~~~a~lVqviG~~ 80 (97)
T COG1534 1 MLTGKQKRFLRSKAHHLKPIVQIGKNGLTEGVIKEIDRALEARELIKVKVLQNAREDKKEIAEALAEETGAELVQVIGKT 80 (97)
T ss_pred CCcHHHHHHHHHhhccCCceEEecCCccCHHHHHHHHHHHHhCCcEEEEeeccchhhHHHHHHHHHHHhCCEEeeeeeeE
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEec
Q 036294 305 MVVYR 309 (833)
Q Consensus 305 iVLYR 309 (833)
+||||
T Consensus 81 ~vlyr 85 (97)
T COG1534 81 LVLYR 85 (97)
T ss_pred EEEEe
Confidence 99999
No 10
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=98.57 E-value=4.9e-08 Score=112.74 Aligned_cols=265 Identities=21% Similarity=0.293 Sum_probs=182.9
Q ss_pred ccccCCCHHHHHHHHHcccCCCceEecCCCCCCHHHHHHHHHHHHhCCeEEEEecCCchHhHHH-HHHHH--HHHhCCeE
Q 036294 221 LAELTIEDEELRRLRRNGMYLRERINVPKAGLTQDVMRKIHDKWRKDELVRLKFHEVLATDMKT-AHEIV--ERRTGGLV 297 (833)
Q Consensus 221 ~AEltLt~kErr~LR~lAh~LkpvV~IGK~GVTd~VVeeIh~awk~hELVKVKvl~~~~~dmk~-~~e~L--EekTGgeV 297 (833)
.-+..|+..+.-.+|.+|-...+.+.+|..+.-+++.-.+...|..|+..|+.+.......... ++.++ -..||+.|
T Consensus 170 ~~~~~l~~~~~~~~r~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~k~~~~k~~~~rg~~~~~~~~~a~~l~~~~~tg~~l 249 (564)
T KOG1990|consen 170 GSPPLLTSIESTLLRRLGYKLPPHFALGRSRKLQGLAVAMVSFWEKHEFAKILIKRGVLETRKERMADELQELLLTGKVL 249 (564)
T ss_pred CChhhhhhHHHHHHHHhcccccccceehhccccccchhHHHHHHHHHHHHHHHHHhcchhhhccchHHHHHHHHhcCCeE
Confidence 3345699999999999999999999999999999999999999999999998777665444433 67777 88999999
Q ss_pred EEEECcEEEEeccCCCCCCCCCCCCCCCCCCCccccC---------CCCCCCCCccc-------ccccCCccccccCCC-
Q 036294 298 IWRAGSVMVVYRGNNYAGPSSKPQPLDGDGDTLFVPH---------VSSTDGSTARS-------VDEKSEVPVRILDHS- 360 (833)
Q Consensus 298 VqrIG~viVLYRg~nY~~p~~~~~~~~~~~~~l~~~~---------~~s~~~~~~~~-------~~~~~~~~~~~~~~~- 360 (833)
|-+-|-..++||+++|-.+ .+..-......+--+|. .++.....+.. .......+.......
T Consensus 250 v~hN~~~dv~y~~~~Fl~~-lp~~l~~f~~~~~~fp~~~~~~~~~~~~~~~~~~~~~t~~e~~~~~~~~~~~~~~~~~~~ 328 (564)
T KOG1990|consen 250 VLHNKLLDVMYRYKNFLSP-LPSTLEEFTDSSSMFPNIEDTKRLAKLSEYQKLNLKATLLELARAKAKKEKEIERRSISS 328 (564)
T ss_pred Eeeccceeeeeehhhcccc-cchhHHHhhhhhhhhhhhHHHHHhhccccccchhhhhhHHHHHHHhcccccCcccccccc
Confidence 9999999999999999874 22110000000000110 00000000000 000000011111100
Q ss_pred ------CCCChHH-Hh---------------hhhhhhccCCCcccccCCCCCCCCCCCCCCCCCCCCCCcccCCCCCCCC
Q 036294 361 ------KPMTEEE-AE---------------CNSLLDSLGPRFQEWWGTGILPVDADLLPPKVDGYKTPFRLLPTGMRSR 418 (833)
Q Consensus 361 ------~~~~e~e-~e---------------~n~LLd~LGPRf~dW~g~~plPVDadLLp~~vpgyk~PfR~lP~Gvr~~ 418 (833)
...+.+. .+ .+..|..+..- .| |+-. +.+|..
T Consensus 329 ~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~--~~------~~~~--------------~~~~e~---- 382 (564)
T KOG1990|consen 329 RLKLEFEKASSEKLTEAIFHKLEKAKKKLASANRILAKLEDP--KI------PAEL--------------RYDPES---- 382 (564)
T ss_pred hhhhhhhccchhhHHHHHHHHHhhhhhhccchhhhhhccccc--cc------cccc--------------ccchhh----
Confidence 0111110 01 13333222211 11 1111 135655
Q ss_pred CCHHHHHHHHHhhhcCCCeeEecccchhhHHHHHHHHHHhhcceEEEeeccCCCCCchHHHHHHHhhccCceeeeec---
Q 036294 419 LTNAEMTDLRRLARSLPCHFALGRNRNHQGLAVAILKLWEKSLVAKIAVKRGIQNTNNKLMAEELKSLTGGTLLQRN--- 495 (833)
Q Consensus 419 Lt~~E~T~LRrlar~lPphfaLGRn~~~~gLA~aI~klWEk~~iaKIa~KrGvqnT~~e~MaeeLK~LTGgvLLsRn--- 495 (833)
+|++|...+++.+..+..-.-+||-|++.|+...|..+|..++.+|+-||-.-..+..+..|.+|..+.||++++=+
T Consensus 383 ~t~ee~~~~~k~g~k~~~~~~~~rrg~f~g~i~n~~l~wk~~e~~k~i~~~~~~~~~~~~~a~~le~esg~~~v~~~~~~ 462 (564)
T KOG1990|consen 383 ITEEERLMLRKVGLKMKRRLLSGRRGVFDGVIENMHLHWKSRELVKVICKEKNLPSQVKQYASALERESGGILVSIDKNP 462 (564)
T ss_pred cChHHHHHHHHHHHhhccccccCCcccccceeecchhhhhhcccceeeeccccccHHHHHHHHHHHHHhCCceeeeccCC
Confidence 99999999999999999999999999999999999999999999999999777778999999999999999999944
Q ss_pred CCE-EEEEecCCCCChhH
Q 036294 496 KFY-IVLYRGKDFLPPNV 512 (833)
Q Consensus 496 ke~-IVlYRGkdFlp~~V 512 (833)
+.| |++|||++|-=+..
T Consensus 463 ~~~ai~~yr~k~y~~p~~ 480 (564)
T KOG1990|consen 463 KGYAIIAYRGKNYDRPTS 480 (564)
T ss_pred chhhHHHhhhhhccCCcc
Confidence 445 99999999987665
No 11
>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=74.63 E-value=5.4 Score=48.85 Aligned_cols=38 Identities=26% Similarity=0.442 Sum_probs=28.7
Q ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 036294 731 NLLTKAKALKRSVAMQRHEALSQHISDLENTIEQMKKEIG 770 (833)
Q Consensus 731 nlLtKrkAL~rS~~~Qr~esl~~~i~~lek~i~~l~~~l~ 770 (833)
.||++.++|-|.+..|=-+++-.||.. ..++.|-..|.
T Consensus 596 slls~~s~llR~~~~~vf~~~~~~~t~--~~l~~ll~vl~ 633 (784)
T PF04931_consen 596 SLLSQPSALLRKVSEQVFEAFCPHLTE--SGLQLLLDVLD 633 (784)
T ss_pred HHHhCcchHHHHHHHHHHHHHHhhcCH--HHHHHHHHHhc
Confidence 578999999999999998888877653 44555555553
No 12
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=52.30 E-value=14 Score=43.09 Aligned_cols=8 Identities=25% Similarity=0.314 Sum_probs=3.0
Q ss_pred HHHHHHHH
Q 036294 755 ISDLENTI 762 (833)
Q Consensus 755 i~~lek~i 762 (833)
|.+|-++.
T Consensus 38 IRkLgeEa 45 (458)
T PF10446_consen 38 IRKLGEEA 45 (458)
T ss_pred HhhhhHHH
Confidence 33333333
No 13
>PF15237 PTRF_SDPR: PTRF/SDPR family
Probab=51.57 E-value=26 Score=38.07 Aligned_cols=66 Identities=26% Similarity=0.369 Sum_probs=54.2
Q ss_pred hHHHHHHHHHHhhcceEEEeeccCCCCCchHHHHHHHhhc--cCceeeeecCCEEEEEecCCCCChhHHH
Q 036294 447 QGLAVAILKLWEKSLVAKIAVKRGIQNTNNKLMAEELKSL--TGGTLLQRNKFYIVLYRGKDFLPPNVAS 514 (833)
Q Consensus 447 ~gLA~aI~klWEk~~iaKIa~KrGvqnT~~e~MaeeLK~L--TGgvLLsRnke~IVlYRGkdFlp~~V~~ 514 (833)
.+-+.++-||.||+.=|-+.+| --....++=|..+|+| +-+-||-||++.++||-+..=.|+.+..
T Consensus 54 ~~TsnTV~KLLeK~RKVS~~vk--~Vr~r~ekQ~~qVkklE~n~~eLL~Rn~FkVlI~Qee~eiPa~~~~ 121 (246)
T PF15237_consen 54 STTSNTVNKLLEKTRKVSVNVK--EVRERLEKQAAQVKKLEANHAELLKRNKFKVLIFQEENEIPASVFV 121 (246)
T ss_pred ccHHHHHHHHHHHHHHhhhhHH--HHHHHHHHHHHHHhhhhccHHHHhhccCceEEeccccccCCCcccc
Confidence 3456789999999998888887 3345677888888875 6688999999999999999999988654
No 14
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=43.60 E-value=16 Score=45.98 Aligned_cols=37 Identities=22% Similarity=0.275 Sum_probs=26.8
Q ss_pred CCchHHHHHHHhhccCceeeeecCCEEEEEecCCCCC
Q 036294 473 NTNNKLMAEELKSLTGGTLLQRNKFYIVLYRGKDFLP 509 (833)
Q Consensus 473 nT~~e~MaeeLK~LTGgvLLsRnke~IVlYRGkdFlp 509 (833)
|.+...--.||-..-|||-=.|-+.+.||-|=++|..
T Consensus 1060 N~t~Rl~~rel~~~y~gV~g~~~dr~~IFSRFr~w~~ 1096 (1516)
T KOG1832|consen 1060 NMTGRLGTRELQSFYSGVHGNRRDRQFIFSRFRSWRS 1096 (1516)
T ss_pred hhhhcccchhhcCcccccccCcccchhhHhhcccchh
Confidence 4444555667888888888888888888888776654
No 15
>COG1623 Predicted nucleic-acid-binding protein (contains the HHH domain) [General function prediction only]
Probab=35.54 E-value=1.4e+02 Score=33.74 Aligned_cols=71 Identities=21% Similarity=0.295 Sum_probs=45.5
Q ss_pred HHHHHHHHHHHHHHhCCEEEEEeecCCCcEEEEEecCCCCCCCCCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 036294 683 LAYVEDTARLLEYESGGILIAIERVPKGFALIFYRGKNYRRPISLRPRNLLTKAKALKRSVAMQRHEALSQHISDLENTI 762 (833)
Q Consensus 683 ~ed~keiA~~Le~~SGg~LVqVI~~~kG~tiILYRgkNY~rP~~~~P~nlLtKrkAL~rS~~~Qr~esl~~~i~~lek~i 762 (833)
...++.+|+..+..||..||+|- ..-++|.||.+ |++.-- .-+..+||| ..|.++.|..+-..|.+.+
T Consensus 104 tGtRHRTAER~AkqTG~~VIaiS--~rrNvITlY~~-~~ky~L-~d~~~il~r--------anQAi~TLEkYk~~Ld~~~ 171 (349)
T COG1623 104 TGTRHRTAERVAKQTGNPVIAIS--ERRNVITLYVG-NLKYVL-KDSAFILSR--------ANQAIQTLEKYKTVLDRVL 171 (349)
T ss_pred CccccchHHHHHHHhCCeEEEEe--cccceEEEEec-Ceeeee-cChHHHHHH--------HHHHHHHHHHHHHHHHHHh
Confidence 34578899999999999999987 34678999987 444321 124455555 3455555555555555544
Q ss_pred HHH
Q 036294 763 EQM 765 (833)
Q Consensus 763 ~~l 765 (833)
..|
T Consensus 172 ~~L 174 (349)
T COG1623 172 NQL 174 (349)
T ss_pred hhh
Confidence 443
No 16
>KOG3130 consensus Uncharacterized conserved protein [Function unknown]
Probab=35.47 E-value=22 Score=41.22 Aligned_cols=26 Identities=23% Similarity=0.364 Sum_probs=16.1
Q ss_pred cCcccCCCcccccccccccccCCccc
Q 036294 804 VSDEDFDSEADEDSELSSFESDDNDL 829 (833)
Q Consensus 804 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 829 (833)
|+||++..++++|+.....-+.||-+
T Consensus 282 dDdeeN~ddd~~d~d~e~~~v~dN~~ 307 (514)
T KOG3130|consen 282 DDDEENIDDDDGDNDHEALGVGDNSI 307 (514)
T ss_pred cchhhcccccccccchhhhccCCCcC
Confidence 44556666667766666666666654
No 17
>PF14812 PBP1_TM: Transmembrane domain of transglycosylase PBP1 at N-terminal; PDB: 3FWL_A 3VMA_A.
Probab=33.52 E-value=14 Score=34.12 Aligned_cols=16 Identities=31% Similarity=0.312 Sum_probs=0.0
Q ss_pred CCCCcccCcccCCCcc
Q 036294 798 NEDDDYVSDEDFDSEA 813 (833)
Q Consensus 798 ~~~~~~~~~~~~~~~~ 813 (833)
|+||++++++|+|.++
T Consensus 31 DDDD~ddd~~DDD~dD 46 (81)
T PF14812_consen 31 DDDDYDDDYEDDDDDD 46 (81)
T ss_dssp ----------------
T ss_pred chhccccccccccccc
Confidence 3333334444444333
No 18
>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=31.91 E-value=49 Score=36.66 Aligned_cols=13 Identities=23% Similarity=0.330 Sum_probs=7.5
Q ss_pred HHHHHHHHHHHHh
Q 036294 685 YVEDTARLLEYES 697 (833)
Q Consensus 685 d~keiA~~Le~~S 697 (833)
+-++..+.|+.++
T Consensus 159 EHQAsCQvLe~E~ 171 (314)
T PF06524_consen 159 EHQASCQVLESET 171 (314)
T ss_pred hhhhhhhhhhccc
Confidence 3355566666654
No 19
>PF07412 Geminin: Geminin; InterPro: IPR022786 This family contains the eukaryotic protein geminin (approximately 200 residues long). Geminin inhibits DNA replication by preventing the incorporation of MCM complex into prereplication complex, and is degraded during the mitotic phase of the cell cycle. It has been proposed that geminin inhibits DNA replication during S, G2, and M phases and that geminin destruction at the metaphase-anaphase transition permits replication in the succeeding cell cycle []. ; GO: 0008156 negative regulation of DNA replication; PDB: 1T6F_B 2LP0_B 1UII_B 2WVR_B 2ZXX_B.
Probab=31.37 E-value=50 Score=35.08 Aligned_cols=32 Identities=25% Similarity=0.464 Sum_probs=19.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 036294 735 KAKALKRSVAMQRHEALSQHISDLENTIEQMKKE 768 (833)
Q Consensus 735 KrkAL~rS~~~Qr~esl~~~i~~lek~i~~l~~~ 768 (833)
+|+||.-++++-+. |..-|..++.+|..|+.+
T Consensus 116 RR~AL~eaL~ENe~--Lh~~ie~~~eEi~~lk~e 147 (200)
T PF07412_consen 116 RRKALEEALEENEK--LHKEIEQKDEEIAKLKEE 147 (200)
T ss_dssp HHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHH
Confidence 67888888775443 444466666666666644
No 20
>PF10369 ALS_ss_C: Small subunit of acetolactate synthase; InterPro: IPR019455 This entry represents the C-terminal domain of the small subunit of acetolactate synthase (the N-terminal domain being an ACT domain). Acetolactate synthase is a tetrameric enzyme, composed of two large and two small subunits, which catalyses the first step in branched-chain amino acid biosynthesis. This reaction is sensitive to certain herbicides []. ; PDB: 2F1F_B 2FGC_A 2PC6_A.
Probab=28.59 E-value=1e+02 Score=27.38 Aligned_cols=35 Identities=11% Similarity=0.191 Sum_probs=0.0
Q ss_pred eEEEEecCCCHHHHHHHHHHHHHHhCCEEEEEeecCCCcEEEE
Q 036294 673 LVKLITKQKTLAYVEDTARLLEYESGGILIAIERVPKGFALIF 715 (833)
Q Consensus 673 LVKVkv~~~~~ed~keiA~~Le~~SGg~LVqVI~~~kG~tiIL 715 (833)
||||.+......++.++++. .+|.+|.+- ..++|+
T Consensus 6 LiKV~~~~~~r~ei~~l~~~----f~a~ivd~~----~~~~ii 40 (75)
T PF10369_consen 6 LIKVKATPENRSEILQLAEI----FRARIVDVS----PDSIII 40 (75)
T ss_dssp EEEEE-SCHHHHHHHHHHHH----TT-EEEEEE----TTEEEE
T ss_pred EEEEECCccCHHHHHHHHHH----hCCEEEEEC----CCEEEE
No 21
>KOG3130 consensus Uncharacterized conserved protein [Function unknown]
Probab=26.61 E-value=36 Score=39.59 Aligned_cols=13 Identities=8% Similarity=-0.033 Sum_probs=5.7
Q ss_pred HHHHHHcccCCcc
Q 036294 635 RAMFRRVGLRMKA 647 (833)
Q Consensus 635 Rk~LRklGhkLKP 647 (833)
..++-+.-.+++|
T Consensus 142 ~~f~a~hr~~~~~ 154 (514)
T KOG3130|consen 142 FEFKAKHRIAHKP 154 (514)
T ss_pred HHHHHHHHhhhcc
Confidence 4444444444444
No 22
>KOG3064 consensus RNA-binding nuclear protein (MAK16) containing a distinct C4 Zn-finger [RNA processing and modification]
Probab=26.56 E-value=30 Score=38.12 Aligned_cols=33 Identities=18% Similarity=0.034 Sum_probs=15.5
Q ss_pred cccccccccCCCCCcccccccCCCCCCCCcccC
Q 036294 773 KDEEDGNIRCSGDLKQFDHVSVLPQNEDDDYVS 805 (833)
Q Consensus 773 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 805 (833)
+.+.......|++.+.....+...+++|+++|+
T Consensus 218 D~e~e~~e~~D~E~~~~~~~~~~~~~s~~d~d~ 250 (303)
T KOG3064|consen 218 DGELEAEETDDSEDWDGDDDSDESDDSDEDSDS 250 (303)
T ss_pred Ccccccccccchhhhcccchhhhhhhccccccc
Confidence 444444455555555555544444444444333
No 23
>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=25.88 E-value=74 Score=35.32 Aligned_cols=6 Identities=17% Similarity=0.501 Sum_probs=2.6
Q ss_pred HHHhhC
Q 036294 666 LHWKYR 671 (833)
Q Consensus 666 ~awk~h 671 (833)
+||--|
T Consensus 104 EawvCH 109 (314)
T PF06524_consen 104 EAWVCH 109 (314)
T ss_pred hhheec
Confidence 445433
No 24
>PF11702 DUF3295: Protein of unknown function (DUF3295); InterPro: IPR021711 This family is conserved in fungi but the function is not known.
Probab=25.37 E-value=35 Score=40.53 Aligned_cols=19 Identities=32% Similarity=0.267 Sum_probs=11.8
Q ss_pred cCcccCCC-ccccccccccc
Q 036294 804 VSDEDFDS-EADEDSELSSF 822 (833)
Q Consensus 804 ~~~~~~~~-~~~~~~~~~~~ 822 (833)
|+|+|.|| |+.||+|-|+.
T Consensus 308 DDDDssDWEDSveESG~sSv 327 (507)
T PF11702_consen 308 DDDDSSDWEDSVEESGKSSV 327 (507)
T ss_pred CCccchhhhhccccccCCCc
Confidence 44566677 55677776654
No 25
>PF15249 GLTSCR1: Glioma tumor suppressor candidate region
Probab=25.23 E-value=28 Score=33.00 Aligned_cols=24 Identities=42% Similarity=0.570 Sum_probs=14.8
Q ss_pred CCCCCCCCc--------ccCCCCCCCCCCHHH
Q 036294 400 KVDGYKTPF--------RLLPTGMRSRLTNAE 423 (833)
Q Consensus 400 ~vpgyk~Pf--------R~lP~Gvr~~Lt~~E 423 (833)
.-|.|++|| |||||.|=......+
T Consensus 13 ~~PD~~tPF~s~~DA~~RLLPYHv~~~~~~~~ 44 (109)
T PF15249_consen 13 LNPDYKTPFRSLEDAVERLLPYHVFQEPEEDE 44 (109)
T ss_pred hCCCcCCCCCCHHHHHHHhcchhhhcCCCCCh
Confidence 347889999 566766554444333
No 26
>PF12207 DUF3600: Domain of unknown function (DUF3600); InterPro: IPR022019 This family of proteins is found in bacteria. Proteins in this family are approximately 230 amino acids in length. This domain is the C-terminal of the putative ecf-type sigma factor negative effector. ; PDB: 3FGG_A 3FH3_A.
Probab=24.60 E-value=13 Score=37.90 Aligned_cols=92 Identities=17% Similarity=0.246 Sum_probs=57.2
Q ss_pred HHHHHHHHHHHHHHHHH-----HHHHHhhhc---cCCCCCCCccCCCCCHHHHHHHHHcccCCcceee-c-----cCCCC
Q 036294 591 KRIEHKLAVSQAKKLRA-----ERLLAKIEA---SMVPSGPDYDQETITDEERAMFRRVGLRMKAFLP-L-----GIRGV 656 (833)
Q Consensus 591 k~~e~kL~~a~~K~~~a-----e~~L~Kle~---~~~P~e~~~d~E~LT~eERk~LRklGhkLKPvV~-I-----GKrGV 656 (833)
-+++.||+.|+.++-.. .++|.+|-. ..--+.-..|.+.|+..++..++++...|.|++- | -|.=+
T Consensus 27 ~~~eaKLqqAK~~lgeeEfeef~~lLK~lt~~kLkygD~NGnidye~ls~~eqee~k~~~~eLqPYFdKLN~~~SsK~vl 106 (162)
T PF12207_consen 27 LRLEAKLQQAKGELGEEEFEEFKELLKKLTNAKLKYGDKNGNIDYEKLSKEEQEEYKKLTMELQPYFDKLNGHKSSKEVL 106 (162)
T ss_dssp HHHHHHHHHHHHCS-HHHHHHHHHHHHHHHHHHHHHB-TTS-B-GGGS-HHHHHHHHHHHHHHHHHHHHHTT---HHHHS
T ss_pred HHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHhHHhhcccCCCcCHHhCCHHHHHHHHHHHHhcchHHHHhcCCcchhhhc
Confidence 35666777665443222 233333322 1122345678999999999999999999999873 2 34445
Q ss_pred CHHHHHHHHHHHhhCceEEEEecCCC
Q 036294 657 FDGVVENMHLHWKYRELVKLITKQKT 682 (833)
Q Consensus 657 tdgVIeeIh~awk~hELVKVkv~~~~ 682 (833)
++.-.+.--.||-.+|.|+|++.-..
T Consensus 107 t~~E~d~y~eALm~~e~v~vk~~~~~ 132 (162)
T PF12207_consen 107 TQEEYDQYIEALMTYETVRVKTKSSG 132 (162)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHCT-SS
T ss_pred CHHHHHHHHHHHhhhheeeeeccCCC
Confidence 66667777788999999999887544
No 27
>PF04472 DUF552: Protein of unknown function (DUF552); InterPro: IPR007561 This entry represents a cell division protein, designated SepF, which is conserved in Gram-positive bacteria. SepF accumulates at the cell division site in an FtsZ-dependent manner and is required for proper septum formation []. Mutants are viable but the formation of the septum is much slower and occurs with a very abnormal morphology. This entry also includes archaeal related proteins of unknown function.; GO: 0000917 barrier septum formation; PDB: 3P04_A.
Probab=23.76 E-value=4.8e+02 Score=22.88 Aligned_cols=56 Identities=11% Similarity=0.164 Sum_probs=37.8
Q ss_pred HHHHHHHHHhCCeEEEEecCCchHhHHHHHHHHHH---HhCCeEEEEECcEEEEeccCCC
Q 036294 257 MRKIHDKWRKDELVRLKFHEVLATDMKTAHEIVER---RTGGLVIWRAGSVMVVYRGNNY 313 (833)
Q Consensus 257 VeeIh~awk~hELVKVKvl~~~~~dmk~~~e~LEe---kTGgeVVqrIG~viVLYRg~nY 313 (833)
+.+|-++++....|=|.+..-.....+++.+.|.. ..+|.+.+. |..++||=+.+.
T Consensus 12 ~~~i~~~l~~g~~Vivnl~~l~~~~~~Ri~Dfl~G~~~al~G~i~~i-~~~~~l~~P~~V 70 (73)
T PF04472_consen 12 AREIVDALREGKIVIVNLENLDDEEAQRILDFLSGAVYALDGDIQKI-SEKVFLLTPKGV 70 (73)
T ss_dssp HHHHHHHHHTT--EEEE-TTS-HHHHHHHHHHHHHHHHHTT-EEEEE-ETTEEEEE----
T ss_pred HHHHHHHHHcCCEEEEECCCCCHHHHHHHHHHHhchheeeCCEEEEE-cCCEEEEECCCc
Confidence 45688999999999999999888899998888865 678887766 666777655554
No 28
>PF15337 Vasculin: Vascular protein family Vasculin-like 1
Probab=23.43 E-value=40 Score=32.12 Aligned_cols=41 Identities=20% Similarity=0.418 Sum_probs=34.7
Q ss_pred CCHHHHHHHHHhhhcCCCeeEecccchhhHHHHHHHHHHhhc
Q 036294 419 LTNAEMTDLRRLARSLPCHFALGRNRNHQGLAVAILKLWEKS 460 (833)
Q Consensus 419 Lt~~E~T~LRrlar~lPphfaLGRn~~~~gLA~aI~klWEk~ 460 (833)
||.+|+.++--...+|- ---+||||.+|++..++-.-|...
T Consensus 34 lTEDElkEF~~kseQlr-rNGf~kngfl~~rs~slf~pWr~t 74 (97)
T PF15337_consen 34 LTEDELKEFQVKSEQLR-RNGFGKNGFLQSRSLSLFSPWRST 74 (97)
T ss_pred CcHHHHHHHHHHHHHHH-Hccccccchhhhhhhhcccccccc
Confidence 99999999988887777 567899999999888877777654
No 29
>PF04871 Uso1_p115_C: Uso1 / p115 like vesicle tethering protein, C terminal region; InterPro: IPR006955 This domain identifies a group of proteins, which are described as: General vesicular transport factor, Transcytosis associate protein (TAP) and Vesicle docking protein. This myosin-shaped molecule consists of an N-terminal globular head region, a coiled-coil tail which mediates dimerisation, and a short C-terminal acidic region []. p115 tethers COP1 vesicles to the Golgi by binding the coiled coil proteins giantin (on the vesicles) and GM130 (on the Golgi), via its C-terminal acidic region. It is required for intercisternal transport in the Golgi stack. This domain is found in the acidic C-terminal region, which binds to the golgins giantin and GM130. p115 is thought to juxtapose two membranes by binding giantin with one acidic region, and GM130 with another [].; GO: 0008565 protein transporter activity, 0006886 intracellular protein transport, 0005737 cytoplasm, 0016020 membrane
Probab=23.04 E-value=1.1e+02 Score=30.33 Aligned_cols=26 Identities=19% Similarity=0.239 Sum_probs=18.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhccc
Q 036294 747 RHEALSQHISDLENTIEQMKKEIGVS 772 (833)
Q Consensus 747 r~esl~~~i~~lek~i~~l~~~l~~~ 772 (833)
-++=|=--...++..+..||..|...
T Consensus 85 EldDLL~ll~Dle~K~~kyk~rLk~L 110 (136)
T PF04871_consen 85 ELDDLLVLLGDLEEKRKKYKERLKEL 110 (136)
T ss_pred hHHHHHHHHHhHHHHHHHHHHHHHHc
Confidence 34556666778888888888887443
No 30
>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=22.53 E-value=63 Score=39.94 Aligned_cols=21 Identities=14% Similarity=0.120 Sum_probs=9.4
Q ss_pred cCCCCCchHHHHHHHhhccCc
Q 036294 469 RGIQNTNNKLMAEELKSLTGG 489 (833)
Q Consensus 469 rGvqnT~~e~MaeeLK~LTGg 489 (833)
.|.|+.+.-.+--.+..++..
T Consensus 335 ~g~q~fd~~t~~k~i~~il~~ 355 (784)
T PF04931_consen 335 LGNQNFDQITKTKTIEQILLS 355 (784)
T ss_pred ccchHHHHHHHHHHHHHHHhc
Confidence 344544444444444444443
No 31
>PF10205 KLRAQ: Predicted coiled-coil domain-containing protein; InterPro: IPR019343 This entry represents a N-terminal 100 residues long domain, which contains a conserved KLRAQ motif. This domain is found in a family of coiled-coil domain-containing proteins that are conserved from nematodes to humans. These proteins also contain a C-terminal TTKRSYEDQ motif domain (IPR019348 from INTERPRO). The function of these proteins is not known.
Probab=22.18 E-value=2e+02 Score=27.86 Aligned_cols=39 Identities=23% Similarity=0.375 Sum_probs=32.6
Q ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Q 036294 731 NLLTKAKALKRSVAMQRHEALSQHISDLENTIEQMKKEIGV 771 (833)
Q Consensus 731 nlLtKrkAL~rS~~~Qr~esl~~~i~~lek~i~~l~~~l~~ 771 (833)
.|-.|-++|.++ +|-++||.++=.+|+++++.|+.+|..
T Consensus 34 ~Lk~ke~~LRk~--eqE~dSL~FrN~QL~kRV~~LQ~El~~ 72 (102)
T PF10205_consen 34 QLKEKEQALRKL--EQENDSLTFRNQQLTKRVEVLQEELEE 72 (102)
T ss_pred HHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345666777765 678999999999999999999999974
Done!