Query 041729
Match_columns 744
No_of_seqs 284 out of 792
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 10:03:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041729.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041729hhsearch_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 1.6E-77 3.4E-82 669.5 19.2 494 114-690 2-524 (564)
2 PRK10343 RNA-binding protein Y 99.9 4.1E-26 8.9E-31 205.5 13.0 89 550-642 1-89 (97)
3 TIGR00253 RNA_bind_YhbY putati 99.9 1.1E-25 2.3E-30 202.1 12.8 87 552-642 1-87 (95)
4 PRK10343 RNA-binding protein Y 99.9 4.1E-25 8.8E-30 199.1 12.2 89 125-213 1-89 (97)
5 PF01985 CRS1_YhbY: CRS1 / Yhb 99.9 4E-25 8.6E-30 193.3 10.8 84 127-210 1-84 (84)
6 TIGR00253 RNA_bind_YhbY putati 99.9 2.8E-24 6.1E-29 193.0 12.8 86 127-212 1-86 (95)
7 PF01985 CRS1_YhbY: CRS1 / Yhb 99.9 1.5E-24 3.4E-29 189.6 10.4 84 552-639 1-84 (84)
8 COG1534 Predicted RNA-binding 99.9 2.7E-24 5.9E-29 193.4 11.8 96 551-651 1-96 (97)
9 COG1534 Predicted RNA-binding 99.9 1.1E-22 2.3E-27 183.2 11.4 86 126-211 1-86 (97)
10 KOG1990 Poly(A)-specific exori 97.3 0.00048 1E-08 79.4 7.8 238 339-645 13-267 (564)
11 PF15249 GLTSCR1: Glioma tumor 41.6 10 0.00022 35.4 0.5 24 321-344 13-44 (109)
12 PF04472 DUF552: Protein of un 23.9 4.5E+02 0.0097 22.7 7.6 56 158-214 12-70 (73)
13 TIGR02867 spore_II_P stage II 23.4 1E+02 0.0022 32.1 4.0 52 382-434 107-167 (196)
14 PF13604 AAA_30: AAA domain; P 22.2 3.3E+02 0.0071 27.4 7.4 71 551-626 1-73 (196)
No 1
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=100.00 E-value=1.6e-77 Score=669.50 Aligned_cols=494 Identities=42% Similarity=0.566 Sum_probs=446.6
Q ss_pred hhccccCcccccCCCHHHHHHHHHHhhcccceEEecCCCCCHHHHHHHHHHHHhCceEEEEecCCchhhHHHHHHHHHHH
Q 041729 114 MKKERMVTKAETMLDGELLERLKDEARKMRKWVKVKKAGVTESVVFEIRLAWRRNELAMVKFDVPLCRNMDRAREILELK 193 (744)
Q Consensus 114 ~~~~~~~s~AEl~L~~~ElrrLR~lA~~LkpvV~VGK~GVT~~VV~~Iheawk~~ELIKVKv~~~~~~dmk~v~e~LEek 193 (744)
.+.++ +++||+++++.++.+||..|..+...+ +++|+|+.+++.|++.|+.+|+++++|....+.+|++.+++++..
T Consensus 2 ~~~~~-~~~~~~~~~~~~~~~l~~~~~~~~~~~--~~~~~~~~~~~~~y~k~k~~~~~~~~~q~~~~~~~~~~~~~~~~~ 78 (564)
T KOG1990|consen 2 SNFES-LSLAELTVDEADLRRLRLVATGMTSAP--WKAGSTFDTVEAIYLKWKDNEEVYLKFQFGLCLFMKRSHEALEMS 78 (564)
T ss_pred Ccccc-hhHHHhhcCHHHHHHHhhhhccceecc--cccccchhhhHHHHHHHHhhhhhheeeccccchhHHHhhhHhhcc
Confidence 45667 999999999999999999999998888 999999999999999999999999999999999999999999999
Q ss_pred hCC-eEEEEeCCEEEEEecCCCCCCcccCCCCCCCCCCcccccccccccccccccccccccccccccccccCCCCCCCCc
Q 041729 194 TGG-LVIWTKKDAHVVYRGDGSKSSVKMCPRSADDQEAPLSKSTHLHLEKKVNVSWIKSNTATLDQNRSLKDGEENSLPT 272 (744)
Q Consensus 194 TGg-~VVqriG~viVLYRg~~Y~~p~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 272 (744)
||| .+||+.|.+...|++..|..|+.-.++. .+
T Consensus 79 ~~~n~~~~~~g~~~s~~~~~~~~~~~~~~~~~----------------------------------------~~------ 112 (564)
T KOG1990|consen 79 TGGNFVVWSRGDSISSPEFLCQRSPVDFVARQ----------------------------------------QE------ 112 (564)
T ss_pred CCCceeeeecCccccCCccceeecchhhhhhh----------------------------------------ch------
Confidence 999 9999999999999998887664321100 00
Q ss_pred ccccccccccchhhhhhhhhhhhccCCCCccCCCCCCCCCCCCCCCCcccCCCCCCcccCCCCCCCCCChHHHHHHHHhc
Q 041729 273 SIFMDKNLRIDKSLYEREGDRLLDGLGPRFVDWWMWKPLPVDGDLLPEVVPGFKPPFRLSPPDARSKLTDDELTYLRKLA 352 (744)
Q Consensus 273 s~~~~~~~~~~~~~~e~E~d~LLD~LGPRf~dW~g~~PlPVDaDLLP~vvpgyk~PfRllP~gvrp~Lt~~E~T~lRrla 352 (744)
.+......+++.|.+.+||++||||.|||+.+|+|||+||+|++||+|.+|||.||+|++++||..|+|.+|++|
T Consensus 113 -----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dl~~~~i~~~~~p~r~l~~~~~~~l~~~~~~~~r~~~ 187 (564)
T KOG1990|consen 113 -----NQAGKWPSELEKEKNELLDSLGPELSDWGGSDRLSVDADLLPEKIPDYMRPFRTLPVGSPPLLTSIESTLLRRLG 187 (564)
T ss_pred -----hhhhhhHHHHHHHHHHHhhccCcccccCCCCCCccchhhhchhhhhcccChhccCCCCChhhhhhHHHHHHHHhc
Confidence 011223467889999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCcEeecccccchhHHHHHHHHhhhcceeeeeeccCCCCCchHHHHHHH--HhhhcccCCCCcccccchhhcccccC
Q 041729 353 HPLPTHFVLGRNRGLQGLATAILKLWEKSLVAKITVKWGIPNTDNEQMANEL--KASLAKWKPNFKFSDDGVLLMQHLTG 430 (744)
Q Consensus 353 r~LPpHfaLGRNr~lqGLA~ai~KLWEks~iaKIavKrGvqnT~ne~MaeeL--K~~~~~~~~~~~f~~~~~~~~~~LTG 430 (744)
+.+||||++|+++.+||++.+|+++|++|+++||+|+||++++.++.||.++ + .+||
T Consensus 188 ~~~p~~~~~~~~~~~~~~~~~~~~~~~k~~~~k~~~~rg~~~~~~~~~a~~l~~~---------------------~~tg 246 (564)
T KOG1990|consen 188 YKLPPHFALGRSRKLQGLAVAMVSFWEKHEFAKILIKRGVLETRKERMADELQEL---------------------LLTG 246 (564)
T ss_pred ccccccceehhccccccchhHHHHHHHHHHHHHHHHHhcchhhhccchHHHHHHH---------------------HhcC
Confidence 9999999999999999999999999999999999999999999999999999 7 8999
Q ss_pred eeEEeeeCcEEEEEecCCCCCcchhhhHHHHHHHHHHhhhhhhhhhhhhhhcccCCCCcccccCcccchHHHHHHHhhhc
Q 041729 431 GVLLLRNKFLIILYRGKDFLPCGVENLIVERERELQICQNHEEGARLKAIETFHLPDEPLEKTSKAGTLSEFQNIQSDFG 510 (744)
Q Consensus 431 gvLLsRnke~Iv~yRGkDFlp~~V~~al~eRe~~~~~~q~~EE~aR~~a~~~~~~~~~~~~~~~~agtl~E~~~~~~~~~ 510 (744)
++|++||++++|+|||++|++ .|.++|.++.......|+.++.+|+.++... .....++|+.|+..+.++|+
T Consensus 247 ~~lv~hN~~~dv~y~~~~Fl~-~lp~~l~~f~~~~~~fp~~~~~~~~~~~~~~-------~~~~~~~t~~e~~~~~~~~~ 318 (564)
T KOG1990|consen 247 KVLVLHNKLLDVMYRYKNFLS-PLPSTLEEFTDSSSMFPNIEDTKRLAKLSEY-------QKLNLKATLLELARAKAKKE 318 (564)
T ss_pred CeEEeeccceeeeeehhhccc-ccchhHHHhhhhhhhhhhhHHHHHhhccccc-------cchhhhhhHHHHHHHhcccc
Confidence 999999999999999999999 9999999999998899999999999873221 23467899999999999999
Q ss_pred ccccCch-HHHHHHHHHHHHHHHHHHHHHHhhcC----------------------CCCCccCCCCHHHHHHHHhhcccC
Q 041729 511 DLKMGNR-EFELQLEAEIEDLERELRKQERKLLL----------------------EQDPDLEMITEEERQCLHKIGMKI 567 (744)
Q Consensus 511 ~~~~~~~-~~~~~~ea~~~k~e~~l~~~E~kl~~----------------------~~~~d~e~LT~eQR~~LRklghkL 567 (744)
....... ...+..+.++...++..+.+.+++.. +...|++.+|.+++.+++++|.+|
T Consensus 319 ~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~e~~t~ee~~~~~k~g~k~ 398 (564)
T KOG1990|consen 319 KEIERRSISSRLKLEFEKASSEKLTEAIFHKLEKAKKKLASANRILAKLEDPKIPAELRYDPESITEEERLMLRKVGLKM 398 (564)
T ss_pred cCcccccccchhhhhhhccchhhHHHHHHHHHhhhhhhccchhhhhhcccccccccccccchhhcChHHHHHHHHHHHhh
Confidence 8875432 22344555666666555555555432 566999999999999999999999
Q ss_pred cceeeeCCCCCCHHHHHHHHHHhhhCCeEEEEecCCCH-HHHHHHHHHHHHHhCCEEEeecccCcCcEEEEecCCCCCCC
Q 041729 568 NSNLLLGRRGVFDGVIEGLHQHWKYREVARVITKQKLF-AQVIYTAKSLVAESGGILISVDKLKEGHAIIIYRGKNYRRP 646 (744)
Q Consensus 568 KPvV~IGKrGVtdgVIeeIh~aLk~hELVKVkv~~~~~-~d~keiA~~Le~~SGg~LVqV~k~~IG~tiILYRgknY~rP 646 (744)
++++.+|++|+|+|+|.+||.||++||++||+|+.... .++++.|..++.++|+++|+++++..|++|+.||++||++|
T Consensus 399 ~~~~~~~rrg~f~g~i~n~~l~wk~~e~~k~i~~~~~~~~~~~~~a~~le~esg~~~v~~~~~~~~~ai~~yr~k~y~~p 478 (564)
T KOG1990|consen 399 KRRLLSGRRGVFDGVIENMHLHWKSRELVKVICKEKNLPSQVKQYASALERESGGILVSIDKNPKGYAIIAYRGKNYDRP 478 (564)
T ss_pred ccccccCCcccccceeecchhhhhhcccceeeeccccccHHHHHHHHHHHHHhCCceeeeccCCchhhHHHhhhhhccCC
Confidence 99999999999999999999999999999999999776 99999999999999999999999999999999999999999
Q ss_pred ccccccccccHHHHHHHHHHHHHhhhhhhccc--ccchhhhhhhcc
Q 041729 647 LKLMTQNLLSKRQALRRSLEMQRLGSLKFFRI--PETAGHLQFENQ 690 (744)
Q Consensus 647 ~~l~pknlLtKrkAl~rs~~~Qr~~sl~~~i~--~~~i~~l~~~~~ 690 (744)
..++|.++|+||+|+.+|+++|+.+|+++||. +.++++++....
T Consensus 479 ~~l~P~~~l~~~k~~~~~~~~~~~~a~~~~i~~~~~~~e~~~~~~~ 524 (564)
T KOG1990|consen 479 TSLRPRNLLSRRKALERSLEEQRKEALKSHISDLEQEIEQLQASVE 524 (564)
T ss_pred cccCchhhhcccCCccccHHHHHHHHHhhhcchhhhhHHHhhcchh
Confidence 99999999999999999999999999999998 899999887654
No 2
>PRK10343 RNA-binding protein YhbY; Provisional
Probab=99.94 E-value=4.1e-26 Score=205.52 Aligned_cols=89 Identities=20% Similarity=0.384 Sum_probs=86.8
Q ss_pred CCCCHHHHHHHHhhcccCcceeeeCCCCCCHHHHHHHHHHhhhCCeEEEEecCCCHHHHHHHHHHHHHHhCCEEEeeccc
Q 041729 550 EMITEEERQCLHKIGMKINSNLLLGRRGVFDGVIEGLHQHWKYREVARVITKQKLFAQVIYTAKSLVAESGGILISVDKL 629 (744)
Q Consensus 550 e~LT~eQR~~LRklghkLKPvV~IGKrGVtdgVIeeIh~aLk~hELVKVkv~~~~~~d~keiA~~Le~~SGg~LVqV~k~ 629 (744)
++||++||+|||++||+|+|+|+||++||||+||++++++|++||||||++.+++.+++++++++||+.|||++||+
T Consensus 1 m~Lt~kqr~~LR~~ah~l~Pvv~IGk~Glt~~vi~ei~~aL~~hELIKvkv~~~~~~~~~e~~~~i~~~~~ae~Vq~--- 77 (97)
T PRK10343 1 MNLSTKQKQHLKGLAHPLKPVVLLGSNGLTEGVLAEIEQALEHHELIKVKIATEDRETKTLIVEAIVRETGACNVQV--- 77 (97)
T ss_pred CCCCHHHHHHHHHhcCCCCCeEEECCCCCCHHHHHHHHHHHHHCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEee---
Confidence 36999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred CcCcEEEEecCCC
Q 041729 630 KEGHAIIIYRGKN 642 (744)
Q Consensus 630 ~IG~tiILYRgkn 642 (744)
||+++||||+++
T Consensus 78 -IG~~~vlYR~~~ 89 (97)
T PRK10343 78 -IGKTLVLYRPTK 89 (97)
T ss_pred -eCcEEEEEecCC
Confidence 899999999975
No 3
>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=99.93 E-value=1.1e-25 Score=202.11 Aligned_cols=87 Identities=25% Similarity=0.443 Sum_probs=85.4
Q ss_pred CCHHHHHHHHhhcccCcceeeeCCCCCCHHHHHHHHHHhhhCCeEEEEecCCCHHHHHHHHHHHHHHhCCEEEeecccCc
Q 041729 552 ITEEERQCLHKIGMKINSNLLLGRRGVFDGVIEGLHQHWKYREVARVITKQKLFAQVIYTAKSLVAESGGILISVDKLKE 631 (744)
Q Consensus 552 LT~eQR~~LRklghkLKPvV~IGKrGVtdgVIeeIh~aLk~hELVKVkv~~~~~~d~keiA~~Le~~SGg~LVqV~k~~I 631 (744)
||++||++||++||+|+|+|+||++||||+||++++++|++||||||++.++++++++++|++||+.|||++||+ |
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 LTGKQKRHLRGKAHHLKPVVLVGKNGLTEGVIKEIEQALEHRELIKVKVATEDREDKTLIAEALVKETGACNVQV----I 76 (95)
T ss_pred CCHHHHHHHHHHhCCCCCeEEECCCCCCHHHHHHHHHHHHhCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEEE----E
Confidence 799999999999999999999999999999999999999999999999999999999999999999999999998 8
Q ss_pred CcEEEEecCCC
Q 041729 632 GHAIIIYRGKN 642 (744)
Q Consensus 632 G~tiILYRgkn 642 (744)
|+++||||+++
T Consensus 77 G~~~vlYR~~~ 87 (95)
T TIGR00253 77 GKTIVLYRPTK 87 (95)
T ss_pred ccEEEEEecCC
Confidence 99999999975
No 4
>PRK10343 RNA-binding protein YhbY; Provisional
Probab=99.92 E-value=4.1e-25 Score=199.10 Aligned_cols=89 Identities=25% Similarity=0.227 Sum_probs=87.0
Q ss_pred cCCCHHHHHHHHHHhhcccceEEecCCCCCHHHHHHHHHHHHhCceEEEEecCCchhhHHHHHHHHHHHhCCeEEEEeCC
Q 041729 125 TMLDGELLERLKDEARKMRKWVKVKKAGVTESVVFEIRLAWRRNELAMVKFDVPLCRNMDRAREILELKTGGLVIWTKKD 204 (744)
Q Consensus 125 l~L~~~ElrrLR~lA~~LkpvV~VGK~GVT~~VV~~Iheawk~~ELIKVKv~~~~~~dmk~v~e~LEekTGg~VVqriG~ 204 (744)
|+||.+|+++||++||+|+|+|+|||+|||++|+++|+++|++||||||||+++|.++.+++++.|+++||+++||+||+
T Consensus 1 m~Lt~kqr~~LR~~ah~l~Pvv~IGk~Glt~~vi~ei~~aL~~hELIKvkv~~~~~~~~~e~~~~i~~~~~ae~Vq~IG~ 80 (97)
T PRK10343 1 MNLSTKQKQHLKGLAHPLKPVVLLGSNGLTEGVLAEIEQALEHHELIKVKIATEDRETKTLIVEAIVRETGACNVQVIGK 80 (97)
T ss_pred CCCCHHHHHHHHHhcCCCCCeEEECCCCCCHHHHHHHHHHHHHCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEeeeCc
Confidence 57999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEEecCC
Q 041729 205 AHVVYRGDG 213 (744)
Q Consensus 205 viVLYRg~~ 213 (744)
++||||.+.
T Consensus 81 ~~vlYR~~~ 89 (97)
T PRK10343 81 TLVLYRPTK 89 (97)
T ss_pred EEEEEecCC
Confidence 999999963
No 5
>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=4e-25 Score=193.30 Aligned_cols=84 Identities=29% Similarity=0.301 Sum_probs=75.6
Q ss_pred CCHHHHHHHHHHhhcccceEEecCCCCCHHHHHHHHHHHHhCceEEEEecCCchhhHHHHHHHHHHHhCCeEEEEeCCEE
Q 041729 127 LDGELLERLKDEARKMRKWVKVKKAGVTESVVFEIRLAWRRNELAMVKFDVPLCRNMDRAREILELKTGGLVIWTKKDAH 206 (744)
Q Consensus 127 L~~~ElrrLR~lA~~LkpvV~VGK~GVT~~VV~~Iheawk~~ELIKVKv~~~~~~dmk~v~e~LEekTGg~VVqriG~vi 206 (744)
||.+|+++||++||+++|+|+|||+|||++|+++|+++|++||||||||.+++..|++++++.|+++|||++||++|+++
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 78999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEe
Q 041729 207 VVYR 210 (744)
Q Consensus 207 VLYR 210 (744)
||||
T Consensus 81 vlyR 84 (84)
T PF01985_consen 81 VLYR 84 (84)
T ss_dssp EEEE
T ss_pred EEEC
Confidence 9998
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=99.91 E-value=2.8e-24 Score=193.01 Aligned_cols=86 Identities=29% Similarity=0.319 Sum_probs=84.7
Q ss_pred CCHHHHHHHHHHhhcccceEEecCCCCCHHHHHHHHHHHHhCceEEEEecCCchhhHHHHHHHHHHHhCCeEEEEeCCEE
Q 041729 127 LDGELLERLKDEARKMRKWVKVKKAGVTESVVFEIRLAWRRNELAMVKFDVPLCRNMDRAREILELKTGGLVIWTKKDAH 206 (744)
Q Consensus 127 L~~~ElrrLR~lA~~LkpvV~VGK~GVT~~VV~~Iheawk~~ELIKVKv~~~~~~dmk~v~e~LEekTGg~VVqriG~vi 206 (744)
||.+|+++||++||+|+|+|+|||+|||++|+++|+++|++||||||||++++..|.+++++.|+++|||++||.||+++
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 78999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEecC
Q 041729 207 VVYRGD 212 (744)
Q Consensus 207 VLYRg~ 212 (744)
||||++
T Consensus 81 vlYR~~ 86 (95)
T TIGR00253 81 VLYRPT 86 (95)
T ss_pred EEEecC
Confidence 999996
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=1.5e-24 Score=189.58 Aligned_cols=84 Identities=26% Similarity=0.467 Sum_probs=75.4
Q ss_pred CCHHHHHHHHhhcccCcceeeeCCCCCCHHHHHHHHHHhhhCCeEEEEecCCCHHHHHHHHHHHHHHhCCEEEeecccCc
Q 041729 552 ITEEERQCLHKIGMKINSNLLLGRRGVFDGVIEGLHQHWKYREVARVITKQKLFAQVIYTAKSLVAESGGILISVDKLKE 631 (744)
Q Consensus 552 LT~eQR~~LRklghkLKPvV~IGKrGVtdgVIeeIh~aLk~hELVKVkv~~~~~~d~keiA~~Le~~SGg~LVqV~k~~I 631 (744)
||++||++||++||+|+|+|+||++||||+|+++|+++|++||||||+|.+++.++++++|++|++.|||++||+ +
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 LTSKERKFLRKLAHHLKPVVQIGKNGLTDGVIEEIDDALEKHELVKVKVLGNCREDRKEIAEQLAEKTGAEVVQV----I 76 (84)
T ss_dssp --HHHHHHHHHHHTTC--SEEE-TTSS-HHHHHHHHHHHHHHSEEEEEETT--HHHHHHHHHHHHHHHTEEEEEE----E
T ss_pred CCHHHHHHHHHHhcCCCCeEEECCCCCCHHHHHHHHHHHHhCCeeEEEEccCCHHHHHHHHHHHHHHhCCEEEEE----E
Confidence 799999999999999999999999999999999999999999999999999999999999999999999999998 8
Q ss_pred CcEEEEec
Q 041729 632 GHAIIIYR 639 (744)
Q Consensus 632 G~tiILYR 639 (744)
|+++||||
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=99.91 E-value=2.7e-24 Score=193.36 Aligned_cols=96 Identities=22% Similarity=0.394 Sum_probs=90.0
Q ss_pred CCCHHHHHHHHhhcccCcceeeeCCCCCCHHHHHHHHHHhhhCCeEEEEecCCCHHHHHHHHHHHHHHhCCEEEeecccC
Q 041729 551 MITEEERQCLHKIGMKINSNLLLGRRGVFDGVIEGLHQHWKYREVARVITKQKLFAQVIYTAKSLVAESGGILISVDKLK 630 (744)
Q Consensus 551 ~LT~eQR~~LRklghkLKPvV~IGKrGVtdgVIeeIh~aLk~hELVKVkv~~~~~~d~keiA~~Le~~SGg~LVqV~k~~ 630 (744)
+||++|+++||+.||+++|+|+||++|||++||.+|+++|++||||||++.+++.++++++|+.||+++||.+||+
T Consensus 1 ~Lt~kq~~~Lrs~Ah~l~piv~IGk~Glte~vi~Ei~~aL~~reLIKVkvl~~~~edr~eia~~l~~~~~a~lVqv---- 76 (97)
T COG1534 1 MLTGKQKRFLRSKAHHLKPIVQIGKNGLTEGVIKEIDRALEARELIKVKVLQNAREDKKEIAEALAEETGAELVQV---- 76 (97)
T ss_pred CCcHHHHHHHHHhhccCCceEEecCCccCHHHHHHHHHHHHhCCcEEEEeeccchhhHHHHHHHHHHHhCCEEeee----
Confidence 6999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred cCcEEEEecCCCCCCCccccc
Q 041729 631 EGHAIIIYRGKNYRRPLKLMT 651 (744)
Q Consensus 631 IG~tiILYRgknY~rP~~l~p 651 (744)
||+++||||. +..++.+.+|
T Consensus 77 iG~~~vlyr~-~~e~~~i~l~ 96 (97)
T COG1534 77 IGKTLVLYRE-SKEKRKISLP 96 (97)
T ss_pred eeeEEEEEec-CcccccccCC
Confidence 8999999994 5555555555
No 9
>COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]
Probab=99.88 E-value=1.1e-22 Score=183.16 Aligned_cols=86 Identities=29% Similarity=0.349 Sum_probs=84.5
Q ss_pred CCCHHHHHHHHHHhhcccceEEecCCCCCHHHHHHHHHHHHhCceEEEEecCCchhhHHHHHHHHHHHhCCeEEEEeCCE
Q 041729 126 MLDGELLERLKDEARKMRKWVKVKKAGVTESVVFEIRLAWRRNELAMVKFDVPLCRNMDRAREILELKTGGLVIWTKKDA 205 (744)
Q Consensus 126 ~L~~~ElrrLR~lA~~LkpvV~VGK~GVT~~VV~~Iheawk~~ELIKVKv~~~~~~dmk~v~e~LEekTGg~VVqriG~v 205 (744)
+|+.+|+++||+.||+++|+|+|||+|||++|+.+|+++|++||||||||.+++.+|.+++++.|++.||+.+||+||++
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 EEEEec
Q 041729 206 HVVYRG 211 (744)
Q Consensus 206 iVLYRg 211 (744)
+||||.
T Consensus 81 ~vlyr~ 86 (97)
T COG1534 81 LVLYRE 86 (97)
T ss_pred EEEEec
Confidence 999993
No 10
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=97.32 E-value=0.00048 Score=79.45 Aligned_cols=238 Identities=17% Similarity=0.160 Sum_probs=160.8
Q ss_pred CCChHHHHHHHHhcCCCCCcEeecccccchhHHHHHHHHhhhcceeeeeeccCCCCCchHHHHHHHHhhhcccCCCCccc
Q 041729 339 KLTDDELTYLRKLAHPLPTHFVLGRNRGLQGLATAILKLWEKSLVAKITVKWGIPNTDNEQMANELKASLAKWKPNFKFS 418 (744)
Q Consensus 339 ~Lt~~E~T~lRrlar~LPpHfaLGRNr~lqGLA~ai~KLWEks~iaKIavKrGvqnT~ne~MaeeLK~~~~~~~~~~~f~ 418 (744)
.+-..|+-.||.-|-.+- ++.++-+..|+.+.+|-.-|..++++++=| ++.-.++-.++-+-+.
T Consensus 13 ~~~~~~~~~l~~~~~~~~--~~~~~~~~~~~~~~~~y~k~k~~~~~~~~~-q~~~~~~~~~~~~~~~------------- 76 (564)
T KOG1990|consen 13 TVDEADLRRLRLVATGMT--SAPWKAGSTFDTVEAIYLKWKDNEEVYLKF-QFGLCLFMKRSHEALE------------- 76 (564)
T ss_pred hcCHHHHHHHhhhhccce--ecccccccchhhhHHHHHHHHhhhhhheee-ccccchhHHHhhhHhh-------------
Confidence 344455556666554432 333788889999999999999999999999 6777788888877777
Q ss_pred ccchhhcccccCee-EEeeeCcEEEEEecCCCCCcchhhhHHHHHHHHHHhhhhhhhhhhhhhhcccCCCCcccccCccc
Q 041729 419 DDGVLLMQHLTGGV-LLLRNKFLIILYRGKDFLPCGVENLIVERERELQICQNHEEGARLKAIETFHLPDEPLEKTSKAG 497 (744)
Q Consensus 419 ~~~~~~~~~LTGgv-LLsRnke~Iv~yRGkDFlp~~V~~al~eRe~~~~~~q~~EE~aR~~a~~~~~~~~~~~~~~~~ag 497 (744)
.=|||. .+-|....+..|+|-.+..+ -...-|+ |+ + ....
T Consensus 77 --------~~~~~n~~~~~~g~~~s~~~~~~~~~~---~~~~~~~------~~--~--------------------~~~~ 117 (564)
T KOG1990|consen 77 --------MSTGGNFVVWSRGDSISSPEFLCQRSP---VDFVARQ------QE--N--------------------QAGK 117 (564)
T ss_pred --------ccCCCceeeeecCccccCCccceeecc---hhhhhhh------ch--h--------------------hhhh
Confidence 667873 22232666666644444332 2222222 11 0 0011
Q ss_pred chHHHHHHHhhhcccc-------------cCchHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCccCCCCHHHHHHHHhhc
Q 041729 498 TLSEFQNIQSDFGDLK-------------MGNREFELQLEAEIEDLERELRKQERKLLLEQDPDLEMITEEERQCLHKIG 564 (744)
Q Consensus 498 tl~E~~~~~~~~~~~~-------------~~~~~~~~~~ea~~~k~e~~l~~~E~kl~~~~~~d~e~LT~eQR~~LRklg 564 (744)
.+.+...+...|-.-. +....+.+ ..+....+....-+...+..+|..+..++|.+|
T Consensus 118 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dl~~----------~~i~~~~~p~r~l~~~~~~~l~~~~~~~~r~~~ 187 (564)
T KOG1990|consen 118 WPSELEKEKNELLDSLGPELSDWGGSDRLSVDADLLP----------EKIPDYMRPFRTLPVGSPPLLTSIESTLLRRLG 187 (564)
T ss_pred hHHHHHHHHHHHhhccCcccccCCCCCCccchhhhch----------hhhhcccChhccCCCCChhhhhhHHHHHHHHhc
Confidence 1233333333332221 11221111 122233333344677778889999999999999
Q ss_pred ccCcceeeeCCCCCCHHHHHHHHHHhhhCCeEEEEecCCCH-HHHHHHHHHH--HHHhCCEEEeecccCcCcEEEEecCC
Q 041729 565 MKINSNLLLGRRGVFDGVIEGLHQHWKYREVARVITKQKLF-AQVIYTAKSL--VAESGGILISVDKLKEGHAIIIYRGK 641 (744)
Q Consensus 565 hkLKPvV~IGKrGVtdgVIeeIh~aLk~hELVKVkv~~~~~-~d~keiA~~L--e~~SGg~LVqV~k~~IG~tiILYRgk 641 (744)
-...+++.+|..+...++.-.|.++|+.|+..|+.+...-. .....+|..+ -..+|+.||.- -|...++||++
T Consensus 188 ~~~p~~~~~~~~~~~~~~~~~~~~~~~k~~~~k~~~~rg~~~~~~~~~a~~l~~~~~tg~~lv~h----N~~~dv~y~~~ 263 (564)
T KOG1990|consen 188 YKLPPHFALGRSRKLQGLAVAMVSFWEKHEFAKILIKRGVLETRKERMADELQELLLTGKVLVLH----NKLLDVMYRYK 263 (564)
T ss_pred ccccccceehhccccccchhHHHHHHHHHHHHHHHHHhcchhhhccchHHHHHHHHhcCCeEEee----ccceeeeeehh
Confidence 99999999999999999999999999999999987776433 3445677777 78899999994 79999999999
Q ss_pred CCCC
Q 041729 642 NYRR 645 (744)
Q Consensus 642 nY~r 645 (744)
++-.
T Consensus 264 ~Fl~ 267 (564)
T KOG1990|consen 264 NFLS 267 (564)
T ss_pred hccc
Confidence 9887
No 11
>PF15249 GLTSCR1: Glioma tumor suppressor candidate region
Probab=41.58 E-value=10 Score=35.41 Aligned_cols=24 Identities=38% Similarity=0.677 Sum_probs=16.2
Q ss_pred ccCCCCCCc--------ccCCCCCCCCCChHH
Q 041729 321 VVPGFKPPF--------RLSPPDARSKLTDDE 344 (744)
Q Consensus 321 vvpgyk~Pf--------RllP~gvrp~Lt~~E 344 (744)
.-|.|++|| |||||.|=.....++
T Consensus 13 ~~PD~~tPF~s~~DA~~RLLPYHv~~~~~~~~ 44 (109)
T PF15249_consen 13 LNPDYKTPFRSLEDAVERLLPYHVFQEPEEDE 44 (109)
T ss_pred hCCCcCCCCCCHHHHHHHhcchhhhcCCCCCh
Confidence 457899999 577777655444333
No 12
>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=23.87 E-value=4.5e+02 Score=22.72 Aligned_cols=56 Identities=16% Similarity=0.127 Sum_probs=37.9
Q ss_pred HHHHHHHHHhCceEEEEecCCchhhHHHHHHHHHH---HhCCeEEEEeCCEEEEEecCCC
Q 041729 158 VFEIRLAWRRNELAMVKFDVPLCRNMDRAREILEL---KTGGLVIWTKKDAHVVYRGDGS 214 (744)
Q Consensus 158 V~~Iheawk~~ELIKVKv~~~~~~dmk~v~e~LEe---kTGg~VVqriG~viVLYRg~~Y 214 (744)
+.+|-++++....|=+.+..-...+.+++.+.|.- ..+|.+.+. |..++||=+.+.
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 45688999999999999988888888999999874 788988776 555677655544
No 13
>TIGR02867 spore_II_P stage II sporulation protein P. Stage II sporulation protein P is a protein of the endospore formation program in a number of lineages in the Firmicutes (low-GC Gram-positive bacteria). It is expressed in the mother cell compartment, under control of Sigma-E. SpoIIP, along with SpoIIM and SpoIID, is one of three major proteins involved in engulfment of the forespore by the mother cell. This protein family is named for the single member in Bacillus subtilis, although most sporulating bacteria have two members.
Probab=23.36 E-value=1e+02 Score=32.08 Aligned_cols=52 Identities=38% Similarity=0.484 Sum_probs=37.6
Q ss_pred ceeeeeeccCCCCC---chHHHHHHHHhhhcccCCCCc---cc---ccchhhcccccCeeEE
Q 041729 382 LVAKITVKWGIPNT---DNEQMANELKASLAKWKPNFK---FS---DDGVLLMQHLTGGVLL 434 (744)
Q Consensus 382 ~iaKIavKrGvqnT---~ne~MaeeLK~~~~~~~~~~~---f~---~~~~~~~~~LTGgvLL 434 (744)
.+|||..=-|-+|. .|..+|..|.+.+-.+.|.++ |. ..+.++ |+|+++-||
T Consensus 107 ~~Aki~fVvG~~np~~~~N~~fA~~l~~~~~~~yPgl~rgi~~k~~~~~~YN-Qdl~~~alL 167 (196)
T TIGR02867 107 SVAKVMFVIGKNNPHFEKNLQLANKLHAKLEKKYPGLSRGIFYKDYGNGVYN-QDLSPNAIL 167 (196)
T ss_pred EEEEEEEEEcCCCCCHHHHHHHHHHHHHHHHhhCCCcccceEEccCCCCccc-ccCCCCeEE
Confidence 45788777777888 789999999999988888776 22 223333 677766654
No 14
>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A.
Probab=22.16 E-value=3.3e+02 Score=27.44 Aligned_cols=71 Identities=21% Similarity=0.206 Sum_probs=48.4
Q ss_pred CCCHHHHHHHHhhcccCcceeee-CCCCCCHHH-HHHHHHHhhhCCeEEEEecCCCHHHHHHHHHHHHHHhCCEEEee
Q 041729 551 MITEEERQCLHKIGMKINSNLLL-GRRGVFDGV-IEGLHQHWKYREVARVITKQKLFAQVIYTAKSLVAESGGILISV 626 (744)
Q Consensus 551 ~LT~eQR~~LRklghkLKPvV~I-GKrGVtdgV-IeeIh~aLk~hELVKVkv~~~~~~d~keiA~~Le~~SGg~LVqV 626 (744)
.||++|+..++.+-..-+.++.| |..|.--.. +..+..+|..+. .+|.+.... ...+..|...+|....-|
T Consensus 1 ~L~~~Q~~a~~~~l~~~~~~~~l~G~aGtGKT~~l~~~~~~~~~~g-~~v~~~apT----~~Aa~~L~~~~~~~a~Ti 73 (196)
T PF13604_consen 1 TLNEEQREAVRAILTSGDRVSVLQGPAGTGKTTLLKALAEALEAAG-KRVIGLAPT----NKAAKELREKTGIEAQTI 73 (196)
T ss_dssp -S-HHHHHHHHHHHHCTCSEEEEEESTTSTHHHHHHHHHHHHHHTT---EEEEESS----HHHHHHHHHHHTS-EEEH
T ss_pred CCCHHHHHHHHHHHhcCCeEEEEEECCCCCHHHHHHHHHHHHHhCC-CeEEEECCc----HHHHHHHHHhhCcchhhH
Confidence 48999999999997666665555 999976654 677899999987 777777655 345566777777554444
Done!