Query 006993
Match_columns 622
No_of_seqs 218 out of 671
Neff 3.5
Searched_HMMs 46136
Date Thu Mar 28 17:25:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/006993.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/006993hhsearch_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 1.3E-73 2.7E-78 622.4 19.2 461 3-534 75-540 (564)
2 PRK10343 RNA-binding protein Y 99.9 4.3E-25 9.3E-30 194.8 13.3 88 377-468 2-89 (97)
3 TIGR00253 RNA_bind_YhbY putati 99.9 7.8E-25 1.7E-29 192.4 13.1 87 378-468 1-87 (95)
4 PF01985 CRS1_YhbY: CRS1 / Yhb 99.9 1E-24 2.2E-29 186.3 10.4 84 378-465 1-84 (84)
5 COG1534 Predicted RNA-binding 99.9 4.8E-24 1E-28 188.1 12.2 96 377-477 1-96 (97)
6 PF01985 CRS1_YhbY: CRS1 / Yhb 99.6 4.9E-16 1.1E-20 133.0 8.3 84 165-249 1-84 (84)
7 TIGR00253 RNA_bind_YhbY putati 98.9 6E-09 1.3E-13 92.4 10.0 87 165-252 1-87 (95)
8 PRK10343 RNA-binding protein Y 98.6 3E-07 6.4E-12 82.1 9.7 88 164-252 2-89 (97)
9 COG1534 Predicted RNA-binding 98.3 5.3E-06 1.2E-10 74.4 9.2 85 164-249 1-85 (97)
10 KOG1990 Poly(A)-specific exori 98.1 2.6E-05 5.6E-10 87.4 12.7 246 164-472 13-268 (564)
11 PF15337 Vasculin: Vascular pr 63.0 3.3 7.2E-05 37.8 0.9 43 164-207 33-75 (97)
12 PF15249 GLTSCR1: Glioma tumor 52.1 5.6 0.00012 36.2 0.4 23 147-169 14-44 (109)
13 cd05797 Ribosomal_L10 Ribosoma 46.8 26 0.00056 33.1 4.0 27 164-190 29-55 (157)
14 PF07412 Geminin: Geminin; In 43.6 33 0.00072 35.1 4.4 42 482-525 115-156 (200)
15 PF12207 DUF3600: Domain of un 36.6 7.1 0.00015 38.4 -1.4 92 340-431 28-133 (162)
16 smart00271 DnaJ DnaJ molecular 34.4 48 0.001 25.7 3.2 51 152-204 2-53 (60)
17 PF04472 DUF552: Protein of un 31.1 2.2E+02 0.0047 24.0 6.7 55 409-468 12-69 (73)
18 cd06257 DnaJ DnaJ domain or J- 30.9 59 0.0013 24.7 3.1 33 153-187 2-35 (55)
19 TIGR00285 DNA-binding protein 29.3 1.6E+02 0.0034 26.8 5.8 66 395-461 2-67 (87)
20 PF10446 DUF2457: Protein of u 28.1 83 0.0018 35.8 4.7 10 596-605 119-128 (458)
21 PF04931 DNA_pol_phi: DNA poly 27.4 50 0.0011 39.2 3.2 25 479-503 596-620 (784)
22 PF03641 Lysine_decarbox: Poss 26.5 1E+02 0.0023 28.6 4.5 35 384-418 74-109 (133)
23 cd08775 DED_Caspase-like_repea 26.5 23 0.0005 31.1 0.2 49 152-200 1-49 (81)
24 COG1623 Predicted nucleic-acid 25.7 3.1E+02 0.0068 30.2 8.3 50 431-484 104-153 (349)
25 PHA03158 hypothetical protein; 24.7 64 0.0014 33.5 2.9 63 146-232 203-266 (273)
26 KOG3130 Uncharacterized conser 23.9 46 0.001 37.6 1.9 15 537-551 269-283 (514)
27 TIGR00730 conserved hypothetic 22.7 1E+02 0.0022 30.4 3.8 34 384-417 117-150 (178)
28 PRK04015 DNA/RNA-binding prote 22.2 3.5E+02 0.0075 24.8 6.7 68 394-462 4-71 (91)
29 PF00922 Phosphoprotein: Vesic 21.4 67 0.0015 34.5 2.4 56 527-584 43-105 (283)
30 cd08340 DED_c-FLIP_repeat2 Dea 20.1 34 0.00074 30.0 -0.0 48 152-199 1-48 (81)
No 1
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=100.00 E-value=1.3e-73 Score=622.40 Aligned_cols=461 Identities=46% Similarity=0.692 Sum_probs=430.5
Q ss_pred cceeeCc-EEEEecCCeEEEeeccCCCCcchhhhhhhhcccCCCCCCccccchhhhhhhhcccCCcchhhhccccCCCCC
Q 006993 3 YWRKTGG-LVIWRSGTAVSLYRGVSYEVPSVQLNKRIYKRNELPASSVSQATDKQIHKQISMSGNSLSAAADKTAQDPSN 81 (622)
Q Consensus 3 ~~rkTGG-LVIWRsGs~~vlYRG~~Y~~p~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (622)
++..||| +||||+|++++.|+|+.|..|.+-.+++ + +
T Consensus 75 ~~~~~~~n~~~~~~g~~~s~~~~~~~~~~~~~~~~~---~-~-------------------------------------- 112 (564)
T KOG1990|consen 75 LEMSTGGNFVVWSRGDSISSPEFLCQRSPVDFVARQ---Q-E-------------------------------------- 112 (564)
T ss_pred hhccCCCceeeeecCccccCCccceeecchhhhhhh---c-h--------------------------------------
Confidence 5788999 9999999999999999999986443321 0 0
Q ss_pred CCCccccccchhhhcccccccccccccccccHHHHHhhhcCcCCCcCCCCCCCCCCCCCCCCCCCCCCCCCCcccCCCCC
Q 006993 82 FDSYNNVHATQVNLETASEEQETDFVREVKYEDEVEKLLDGLGPRYTDWPGCDPLPVDADMLPGIVPGYQPPFRVLPYGV 161 (622)
Q Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~e~d~lLd~LGPRf~dW~g~~PlPVDaDlLP~~vpgyk~PfRlLP~gv 161 (622)
+.......++++|.+.+|+++||++.||||.+|+|+|+|+||+.||+|.+|||.||+|+
T Consensus 113 ---------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dl~~~~i~~~~~p~r~l~~~~ 171 (564)
T KOG1990|consen 113 ---------------------NQAGKWPSELEKEKNELLDSLGPELSDWGGSDRLSVDADLLPEKIPDYMRPFRTLPVGS 171 (564)
T ss_pred ---------------------hhhhhhHHHHHHHHHHHhhccCcccccCCCCCCccchhhhchhhhhcccChhccCCCCC
Confidence 00001134678999999999999999999999999999999999999999999999999
Q ss_pred CCcCCHHHHHHHHHhhhcCCCeeeeccccccchHHHHHHHHhhccceeEEeeccCCCcCchHHHHHHH--hhccCceEEe
Q 006993 162 RSTLARKEATNLQRLARVLPPHFALGRSRQLQGLAVAMIKLWEKSSIAKIALKRGVQLTTSERMVEDI--KKLTGGTLLS 239 (622)
Q Consensus 162 rp~LT~~E~t~Lrrlar~lp~hf~LGRn~~~qGLa~am~klWeks~i~KIa~KrGv~~td~e~ma~eL--k~LTGG~lLs 239 (622)
++.||..|++.+|+++.++|+||++|+++.+||++.+|+++|+++.++||+|+||++++..+.||.+| +.+|||+|++
T Consensus 172 ~~~l~~~~~~~~r~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~k~~~~k~~~~rg~~~~~~~~~a~~l~~~~~tg~~lv~ 251 (564)
T KOG1990|consen 172 PPLLTSIESTLLRRLGYKLPPHFALGRSRKLQGLAVAMVSFWEKHEFAKILIKRGVLETRKERMADELQELLLTGKVLVL 251 (564)
T ss_pred hhhhhhHHHHHHHHhcccccccceehhccccccchhHHHHHHHHHHHHHHHHHhcchhhhccchHHHHHHHHhcCCeEEe
Confidence 99999999999999999999999999999999999999999999999999999999999999999999 9999999999
Q ss_pred ecCcEEEEEecCCCCChhHHHHHHHHHHHHHhhhhHHHHHHhhhccccccccccccccCccchhHHHHhhhhhccCCCCc
Q 006993 240 RNKDFLVFYRGKNFLSPDVTEALQERERLAKSLQDEEEQARLRASAFVLPSIETIEKSGTAGTLKETLDANSRWGKRLDD 319 (622)
Q Consensus 240 r~k~~Iv~yRGkdflp~~V~~~l~eR~~~~~~~q~~Ee~aR~~a~~~~~~~~~~~~~~~~agtl~e~~~a~~~w~~~~~~ 319 (622)
||+.++++|||++|++ .|.++|.++.......++.++.+|+... .+. .....++|+.|+..+.++|+..+..
T Consensus 252 hN~~~dv~y~~~~Fl~-~lp~~l~~f~~~~~~fp~~~~~~~~~~~---~~~----~~~~~~~t~~e~~~~~~~~~~~~~~ 323 (564)
T KOG1990|consen 252 HNKLLDVMYRYKNFLS-PLPSTLEEFTDSSSMFPNIEDTKRLAKL---SEY----QKLNLKATLLELARAKAKKEKEIER 323 (564)
T ss_pred eccceeeeeehhhccc-ccchhHHHhhhhhhhhhhhHHHHHhhcc---ccc----cchhhhhhHHHHHHHhcccccCccc
Confidence 9999999999999999 9999999999998889999999999862 221 2256899999999999999999876
Q ss_pred hhH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccCCCCCCCCCCCCCCHHHHHHHHHhccCCcceEe
Q 006993 320 SHK-ENLVREAEVRRHAYLVQKLEKKLARAERKLLRAERALSKVEESLKPAERQADPESITDEERFMFRKLGLRMKAFLL 398 (622)
Q Consensus 320 ~~~-~~m~~e~~~~~~~~~~~~~e~KL~~a~~K~~kae~~L~K~e~~~~P~e~~~d~E~LT~eERr~LRklGhkLKPvV~ 398 (622)
... ..+..+.+...+++..+.+.+|++.+++|+++++..|++++.+..|++..++++.+|.+++.+++++|.+|++++.
T Consensus 324 ~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~e~~t~ee~~~~~k~g~k~~~~~~ 403 (564)
T KOG1990|consen 324 RSISSRLKLEFEKASSEKLTEAIFHKLEKAKKKLASANRILAKLEDPKIPAELRYDPESITEEERLMLRKVGLKMKRRLL 403 (564)
T ss_pred ccccchhhhhhhccchhhHHHHHHHHHhhhhhhccchhhhhhcccccccccccccchhhcChHHHHHHHHHHHhhccccc
Confidence 553 4678899999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eCCCCCCHHHHHHHHHHHhhCCeEeEEEcCCCH-HHHHHHHHHHHHHhCCEEEeecccccCcEEEEEecCCCCCCCCCCC
Q 006993 399 LGRRGVFDGTVENMHLHWKYRELVKIIVKVKTF-DQAKKIALALEAESGGVLVSVDKISKGYAMVVYRGKDYQRPSTLRP 477 (622)
Q Consensus 399 IGK~GVTdgVVeeIh~Awk~hELVKVk~~~~~~-ed~keiAe~Lee~TGg~LVqV~kv~IG~tIILYRGkNYkrP~~l~P 477 (622)
+|++|+++|++.++|.||++||++||+|+.... .+++..|..++..+|+++|+++++..|+.|+.|||+||++|..++|
T Consensus 404 ~~rrg~f~g~i~n~~l~wk~~e~~k~i~~~~~~~~~~~~~a~~le~esg~~~v~~~~~~~~~ai~~yr~k~y~~p~~l~P 483 (564)
T KOG1990|consen 404 SGRRGVFDGVIENMHLHWKSRELVKVICKEKNLPSQVKQYASALERESGGILVSIDKNPKGYAIIAYRGKNYDRPTSLRP 483 (564)
T ss_pred cCCcccccceeecchhhhhhcccceeeeccccccHHHHHHHHHHHHHhCCceeeeccCCchhhHHHhhhhhccCCcccCc
Confidence 999999999999999999999999999998876 9999999999999999999999999999999999999999999999
Q ss_pred cccccHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCchHHHHH
Q 006993 478 KNLLTKRKALARSIELQRQEALLKHVATLESNAGRLRSEIEQMNSVKGTGDEQLYDK 534 (622)
Q Consensus 478 knlLTKrkAl~rS~e~qr~~~l~~~i~~l~k~i~~l~~~l~~~~~~~~~~~~~l~~~ 534 (622)
.++|+||+|+.+|+++|++++++.||..++.++++++.++..|...+.+.|.+.+.+
T Consensus 484 ~~~l~~~k~~~~~~~~~~~~a~~~~i~~~~~~~e~~~~~~~~~~~~~~~~d~~~en~ 540 (564)
T KOG1990|consen 484 RNLLSRRKALERSLEEQRKEALKSHISDLEQEIEQLQASVEAMPAINKKDDLEEENS 540 (564)
T ss_pred hhhhcccCCccccHHHHHHHHHhhhcchhhhhHHHhhcchhcccccccccchHHHhh
Confidence 999999999999999999999999999999999999999999999999999888888
No 2
>PRK10343 RNA-binding protein YhbY; Provisional
Probab=99.92 E-value=4.3e-25 Score=194.81 Aligned_cols=88 Identities=23% Similarity=0.423 Sum_probs=85.9
Q ss_pred CCCHHHHHHHHHhccCCcceEeeCCCCCCHHHHHHHHHHHhhCCeEeEEEcCCCHHHHHHHHHHHHHHhCCEEEeecccc
Q 006993 377 SITDEERFMFRKLGLRMKAFLLLGRRGVFDGTVENMHLHWKYRELVKIIVKVKTFDQAKKIALALEAESGGVLVSVDKIS 456 (622)
Q Consensus 377 ~LT~eERr~LRklGhkLKPvV~IGK~GVTdgVVeeIh~Awk~hELVKVk~~~~~~ed~keiAe~Lee~TGg~LVqV~kv~ 456 (622)
+||++||++||++||+|+|+|+||++|||++|+++|..+|++||||||++.+++.++++++++.|++.|||++||+
T Consensus 2 ~Lt~kqr~~LR~~ah~l~Pvv~IGk~Glt~~vi~ei~~aL~~hELIKvkv~~~~~~~~~e~~~~i~~~~~ae~Vq~---- 77 (97)
T PRK10343 2 NLSTKQKQHLKGLAHPLKPVVLLGSNGLTEGVLAEIEQALEHHELIKVKIATEDRETKTLIVEAIVRETGACNVQV---- 77 (97)
T ss_pred CCCHHHHHHHHHhcCCCCCeEEECCCCCCHHHHHHHHHHHHHCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEee----
Confidence 5999999999999999999999999999999999999999999999999999999999999999999999999996
Q ss_pred cCcEEEEEecCC
Q 006993 457 KGYAMVVYRGKD 468 (622)
Q Consensus 457 IG~tIILYRGkN 468 (622)
||+++||||++.
T Consensus 78 IG~~~vlYR~~~ 89 (97)
T PRK10343 78 IGKTLVLYRPTK 89 (97)
T ss_pred eCcEEEEEecCC
Confidence 999999999874
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=99.92 E-value=7.8e-25 Score=192.38 Aligned_cols=87 Identities=28% Similarity=0.461 Sum_probs=84.9
Q ss_pred CCHHHHHHHHHhccCCcceEeeCCCCCCHHHHHHHHHHHhhCCeEeEEEcCCCHHHHHHHHHHHHHHhCCEEEeeccccc
Q 006993 378 ITDEERFMFRKLGLRMKAFLLLGRRGVFDGTVENMHLHWKYRELVKIIVKVKTFDQAKKIALALEAESGGVLVSVDKISK 457 (622)
Q Consensus 378 LT~eERr~LRklGhkLKPvV~IGK~GVTdgVVeeIh~Awk~hELVKVk~~~~~~ed~keiAe~Lee~TGg~LVqV~kv~I 457 (622)
||++||++||++||+|+|+|+|||+|||++||++|+.+|++||||||++.+++.++++++|+.|++.|||++||+ |
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 799999999999999999999999999999999999999999999999999999999999999999999999996 9
Q ss_pred CcEEEEEecCC
Q 006993 458 GYAMVVYRGKD 468 (622)
Q Consensus 458 G~tIILYRGkN 468 (622)
|+++||||++.
T Consensus 77 G~~~vlYR~~~ 87 (95)
T TIGR00253 77 GKTIVLYRPTK 87 (95)
T ss_pred ccEEEEEecCC
Confidence 99999999864
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=1e-24 Score=186.26 Aligned_cols=84 Identities=33% Similarity=0.529 Sum_probs=75.2
Q ss_pred CCHHHHHHHHHhccCCcceEeeCCCCCCHHHHHHHHHHHhhCCeEeEEEcCCCHHHHHHHHHHHHHHhCCEEEeeccccc
Q 006993 378 ITDEERFMFRKLGLRMKAFLLLGRRGVFDGTVENMHLHWKYRELVKIIVKVKTFDQAKKIALALEAESGGVLVSVDKISK 457 (622)
Q Consensus 378 LT~eERr~LRklGhkLKPvV~IGK~GVTdgVVeeIh~Awk~hELVKVk~~~~~~ed~keiAe~Lee~TGg~LVqV~kv~I 457 (622)
||++|+++||++||+|+|+|+|||+|||++|+++|+.+|++||||||+|.+++..+++++++.|++.|||++||+ +
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 799999999999999999999999999999999999999999999999999999999999999999999999995 9
Q ss_pred CcEEEEEe
Q 006993 458 GYAMVVYR 465 (622)
Q Consensus 458 G~tIILYR 465 (622)
|+++||||
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 5
>COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]
Probab=99.91 E-value=4.8e-24 Score=188.12 Aligned_cols=96 Identities=27% Similarity=0.475 Sum_probs=90.8
Q ss_pred CCCHHHHHHHHHhccCCcceEeeCCCCCCHHHHHHHHHHHhhCCeEeEEEcCCCHHHHHHHHHHHHHHhCCEEEeecccc
Q 006993 377 SITDEERFMFRKLGLRMKAFLLLGRRGVFDGTVENMHLHWKYRELVKIIVKVKTFDQAKKIALALEAESGGVLVSVDKIS 456 (622)
Q Consensus 377 ~LT~eERr~LRklGhkLKPvV~IGK~GVTdgVVeeIh~Awk~hELVKVk~~~~~~ed~keiAe~Lee~TGg~LVqV~kv~ 456 (622)
+||++|+++||+.||+++|+|+|||+|||++||.+|+.+|++||||||++.+++.++.+++|+.|++.+||.+||+
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 5999999999999999999999999999999999999999999999999999999999999999999999999996
Q ss_pred cCcEEEEEecCCCCCCCCCCC
Q 006993 457 KGYAMVVYRGKDYQRPSTLRP 477 (622)
Q Consensus 457 IG~tIILYRGkNYkrP~~l~P 477 (622)
||+++|||| .++.++.+..|
T Consensus 77 iG~~~vlyr-~~~e~~~i~l~ 96 (97)
T COG1534 77 IGKTLVLYR-ESKEKRKISLP 96 (97)
T ss_pred eeeEEEEEe-cCcccccccCC
Confidence 999999999 56666666555
No 6
>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=99.64 E-value=4.9e-16 Score=132.99 Aligned_cols=84 Identities=24% Similarity=0.372 Sum_probs=75.1
Q ss_pred CCHHHHHHHHHhhhcCCCeeeeccccccchHHHHHHHHhhccceeEEeeccCCCcCchHHHHHHHhhccCceEEeecCcE
Q 006993 165 LARKEATNLQRLARVLPPHFALGRSRQLQGLAVAMIKLWEKSSIAKIALKRGVQLTTSERMVEDIKKLTGGTLLSRNKDF 244 (622)
Q Consensus 165 LT~~E~t~Lrrlar~lp~hf~LGRn~~~qGLa~am~klWeks~i~KIa~KrGv~~td~e~ma~eLk~LTGG~lLsr~k~~ 244 (622)
||.+|..+||++|..++|++.+|+||..++++.+|..+|++++++||.|. +.+..+++.||++|.+.|||.++++.+.+
T Consensus 1 Lt~ke~~~Lr~~a~~l~p~v~IGk~Glt~~vi~~i~~~l~~~eLvKVk~~-~~~~~~~~~~~~~l~~~t~~~~V~~iG~~ 79 (84)
T PF01985_consen 1 LTSKERKFLRKLAHHLKPVVQIGKNGLTDGVIEEIDDALEKHELVKVKVL-GNCREDRKEIAEQLAEKTGAEVVQVIGRT 79 (84)
T ss_dssp --HHHHHHHHHHHTTC--SEEE-TTSS-HHHHHHHHHHHHHHSEEEEEET-T--HHHHHHHHHHHHHHHTEEEEEEETTE
T ss_pred CCHHHHHHHHHHhcCCCCeEEECCCCCCHHHHHHHHHHHHhCCeeEEEEc-cCCHHHHHHHHHHHHHHhCCEEEEEECCE
Confidence 79999999999999999999999999999999999999999999999997 89999999999999999999999999999
Q ss_pred EEEEe
Q 006993 245 LVFYR 249 (622)
Q Consensus 245 Iv~yR 249 (622)
+||||
T Consensus 80 ~vlyR 84 (84)
T PF01985_consen 80 IVLYR 84 (84)
T ss_dssp EEEEE
T ss_pred EEEEC
Confidence 99998
No 7
>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=98.93 E-value=6e-09 Score=92.39 Aligned_cols=87 Identities=20% Similarity=0.271 Sum_probs=82.1
Q ss_pred CCHHHHHHHHHhhhcCCCeeeeccccccchHHHHHHHHhhccceeEEeeccCCCcCchHHHHHHHhhccCceEEeecCcE
Q 006993 165 LARKEATNLQRLARVLPPHFALGRSRQLQGLAVAMIKLWEKSSIAKIALKRGVQLTTSERMVEDIKKLTGGTLLSRNKDF 244 (622)
Q Consensus 165 LT~~E~t~Lrrlar~lp~hf~LGRn~~~qGLa~am~klWeks~i~KIa~KrGv~~td~e~ma~eLk~LTGG~lLsr~k~~ 244 (622)
||.++..+||.+|..|.|.+.+|+||..+++...|...|+.++++||.+- .-+..+-..+|++|.+.||+.++..-|..
T Consensus 1 Lt~kqr~~Lr~~ah~l~p~v~IGK~Glt~~vi~ei~~aL~~hELIKVkvl-~~~~~~~~e~a~~i~~~~~a~~Vq~iG~~ 79 (95)
T TIGR00253 1 LTGKQKRHLRGKAHHLKPVVLVGKNGLTEGVIKEIEQALEHRELIKVKVA-TEDREDKTLIAEALVKETGACNVQVIGKT 79 (95)
T ss_pred CCHHHHHHHHHHhCCCCCeEEECCCCCCHHHHHHHHHHHHhCCcEEEEec-CCChhHHHHHHHHHHHHHCCEEEEEEccE
Confidence 79999999999999999999999999999999999999999999999995 66667788899999999999999999999
Q ss_pred EEEEecCC
Q 006993 245 LVFYRGKN 252 (622)
Q Consensus 245 Iv~yRGkd 252 (622)
++|||.+.
T Consensus 80 ~vlYR~~~ 87 (95)
T TIGR00253 80 IVLYRPTK 87 (95)
T ss_pred EEEEecCC
Confidence 99999863
No 8
>PRK10343 RNA-binding protein YhbY; Provisional
Probab=98.59 E-value=3e-07 Score=82.15 Aligned_cols=88 Identities=25% Similarity=0.335 Sum_probs=83.1
Q ss_pred cCCHHHHHHHHHhhhcCCCeeeeccccccchHHHHHHHHhhccceeEEeeccCCCcCchHHHHHHHhhccCceEEeecCc
Q 006993 164 TLARKEATNLQRLARVLPPHFALGRSRQLQGLAVAMIKLWEKSSIAKIALKRGVQLTTSERMVEDIKKLTGGTLLSRNKD 243 (622)
Q Consensus 164 ~LT~~E~t~Lrrlar~lp~hf~LGRn~~~qGLa~am~klWeks~i~KIa~KrGv~~td~e~ma~eLk~LTGG~lLsr~k~ 243 (622)
.||..+..+||.+|..|.|.|-+|++|...++...|-..-+.+++.||.+- +-+..+-+.+|++|.+.||+.++..=|.
T Consensus 2 ~Lt~kqr~~LR~~ah~l~Pvv~IGk~Glt~~vi~ei~~aL~~hELIKvkv~-~~~~~~~~e~~~~i~~~~~ae~Vq~IG~ 80 (97)
T PRK10343 2 NLSTKQKQHLKGLAHPLKPVVLLGSNGLTEGVLAEIEQALEHHELIKVKIA-TEDRETKTLIVEAIVRETGACNVQVIGK 80 (97)
T ss_pred CCCHHHHHHHHHhcCCCCCeEEECCCCCCHHHHHHHHHHHHHCCcEEEEec-CCChhHHHHHHHHHHHHHCCEEEeeeCc
Confidence 489999999999999999999999999999999999999999999999985 7777788899999999999999999999
Q ss_pred EEEEEecCC
Q 006993 244 FLVFYRGKN 252 (622)
Q Consensus 244 ~Iv~yRGkd 252 (622)
.+||||=+.
T Consensus 81 ~~vlYR~~~ 89 (97)
T PRK10343 81 TLVLYRPTK 89 (97)
T ss_pred EEEEEecCC
Confidence 999999763
No 9
>COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]
Probab=98.26 E-value=5.3e-06 Score=74.38 Aligned_cols=85 Identities=21% Similarity=0.302 Sum_probs=80.1
Q ss_pred cCCHHHHHHHHHhhhcCCCeeeeccccccchHHHHHHHHhhccceeEEeeccCCCcCchHHHHHHHhhccCceEEeecCc
Q 006993 164 TLARKEATNLQRLARVLPPHFALGRSRQLQGLAVAMIKLWEKSSIAKIALKRGVQLTTSERMVEDIKKLTGGTLLSRNKD 243 (622)
Q Consensus 164 ~LT~~E~t~Lrrlar~lp~hf~LGRn~~~qGLa~am~klWeks~i~KIa~KrGv~~td~e~ma~eLk~LTGG~lLsr~k~ 243 (622)
.||.++...||.+|..+-|.|-+|+||...|+...|-..-+.++++||.+= +=+--|-.-+|++|.+.||+.++..-+.
T Consensus 1 ~Lt~kq~~~Lrs~Ah~l~piv~IGk~Glte~vi~Ei~~aL~~reLIKVkvl-~~~~edr~eia~~l~~~~~a~lVqviG~ 79 (97)
T COG1534 1 MLTGKQKRFLRSKAHHLKPIVQIGKNGLTEGVIKEIDRALEARELIKVKVL-QNAREDKKEIAEALAEETGAELVQVIGK 79 (97)
T ss_pred CCcHHHHHHHHHhhccCCceEEecCCccCHHHHHHHHHHHHhCCcEEEEee-ccchhhHHHHHHHHHHHhCCEEeeeeee
Confidence 489999999999999999999999999999999999999999999999994 5566677889999999999999999999
Q ss_pred EEEEEe
Q 006993 244 FLVFYR 249 (622)
Q Consensus 244 ~Iv~yR 249 (622)
.+|+||
T Consensus 80 ~~vlyr 85 (97)
T COG1534 80 TLVLYR 85 (97)
T ss_pred EEEEEe
Confidence 999999
No 10
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=98.10 E-value=2.6e-05 Score=87.42 Aligned_cols=246 Identities=21% Similarity=0.244 Sum_probs=163.8
Q ss_pred cCCHHHHHHHHHhhhcCCCeeeeccccccchHHHHHHHHhhccceeEEeeccCCCcCchHHHHHHHhhccCc-eEEeecC
Q 006993 164 TLARKEATNLQRLARVLPPHFALGRSRQLQGLAVAMIKLWEKSSIAKIALKRGVQLTTSERMVEDIKKLTGG-TLLSRNK 242 (622)
Q Consensus 164 ~LT~~E~t~Lrrlar~lp~hf~LGRn~~~qGLa~am~klWeks~i~KIa~KrGv~~td~e~ma~eLk~LTGG-~lLsr~k 242 (622)
.+-..|...||.-+-.+ -++.++.+..+....+|..-|+.++++++.|--|+ ..+|.++-+-++.-||| ..+-|.+
T Consensus 13 ~~~~~~~~~l~~~~~~~--~~~~~~~~~~~~~~~~~y~k~k~~~~~~~~~q~~~-~~~~~~~~~~~~~~~~~n~~~~~~g 89 (564)
T KOG1990|consen 13 TVDEADLRRLRLVATGM--TSAPWKAGSTFDTVEAIYLKWKDNEEVYLKFQFGL-CLFMKRSHEALEMSTGGNFVVWSRG 89 (564)
T ss_pred hcCHHHHHHHhhhhccc--eecccccccchhhhHHHHHHHHhhhhhheeecccc-chhHHHhhhHhhccCCCceeeeecC
Confidence 44455555666555433 23348889999999999999999999999997555 56888899999999999 6666668
Q ss_pred cEEEEEecCCCCChhHHHHHHHHH-HHHHh---hhhHHHHHHhhhccccccccccccccCccchhHHHHhhhhhccCCCC
Q 006993 243 DFLVFYRGKNFLSPDVTEALQERE-RLAKS---LQDEEEQARLRASAFVLPSIETIEKSGTAGTLKETLDANSRWGKRLD 318 (622)
Q Consensus 243 ~~Iv~yRGkdflp~~V~~~l~eR~-~~~~~---~q~~Ee~aR~~a~~~~~~~~~~~~~~~~agtl~e~~~a~~~w~~~~~ 318 (622)
..+..|+|-.|..+-+.. -|+ ..... .+-+.++..+.- ++.+ +...-||...-
T Consensus 90 ~~~s~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~--~~~~------------------~~~~~~~~~~~ 146 (564)
T KOG1990|consen 90 DSISSPEFLCQRSPVDFV---ARQQENQAGKWPSELEKEKNELLD--SLGP------------------ELSDWGGSDRL 146 (564)
T ss_pred ccccCCccceeecchhhh---hhhchhhhhhhHHHHHHHHHHHhh--ccCc------------------ccccCCCCCCc
Confidence 888888777766653321 111 00000 111111111110 0010 01112222221
Q ss_pred chhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccCCCCC--CCCCCCCCCHHHHHHHHHhccCCcce
Q 006993 319 DSHKENLVREAEVRRHAYLVQKLEKKLARAERKLLRAERALSKVEESLKPAE--RQADPESITDEERFMFRKLGLRMKAF 396 (622)
Q Consensus 319 ~~~~~~m~~e~~~~~~~~~~~~~e~KL~~a~~K~~kae~~L~K~e~~~~P~e--~~~d~E~LT~eERr~LRklGhkLKPv 396 (622)
+...... +.+|..-+.|.. +...+..|+..+.-++|.+|-...|+
T Consensus 147 ~~~~dl~---------------------------------~~~i~~~~~p~r~l~~~~~~~l~~~~~~~~r~~~~~~p~~ 193 (564)
T KOG1990|consen 147 SVDADLL---------------------------------PEKIPDYMRPFRTLPVGSPPLLTSIESTLLRRLGYKLPPH 193 (564)
T ss_pred cchhhhc---------------------------------hhhhhcccChhccCCCCChhhhhhHHHHHHHHhccccccc
Confidence 1111111 112222223322 23556779999999999999999999
Q ss_pred EeeCCCCCCHHHHHHHHHHHhhCCeEeEEEcCCC-HHHHHHHHHHH--HHHhCCEEEeecccccCcEEEEEecCCCCCC
Q 006993 397 LLLGRRGVFDGTVENMHLHWKYRELVKIIVKVKT-FDQAKKIALAL--EAESGGVLVSVDKISKGYAMVVYRGKDYQRP 472 (622)
Q Consensus 397 V~IGK~GVTdgVVeeIh~Awk~hELVKVk~~~~~-~ed~keiAe~L--ee~TGg~LVqV~kv~IG~tIILYRGkNYkrP 472 (622)
+.+|.++.-.++...|..+|+.|+..|+-++..- ......++..+ -..+|+.||. +-|..+++||++|+-.|
T Consensus 194 ~~~~~~~~~~~~~~~~~~~~~k~~~~k~~~~rg~~~~~~~~~a~~l~~~~~tg~~lv~----hN~~~dv~y~~~~Fl~~ 268 (564)
T KOG1990|consen 194 FALGRSRKLQGLAVAMVSFWEKHEFAKILIKRGVLETRKERMADELQELLLTGKVLVL----HNKLLDVMYRYKNFLSP 268 (564)
T ss_pred ceehhccccccchhHHHHHHHHHHHHHHHHHhcchhhhccchHHHHHHHHhcCCeEEe----eccceeeeeehhhcccc
Confidence 9999999999999999999999999998876543 33445677777 8899999999 68899999999997774
No 11
>PF15337 Vasculin: Vascular protein family Vasculin-like 1
Probab=62.96 E-value=3.3 Score=37.81 Aligned_cols=43 Identities=19% Similarity=0.359 Sum_probs=37.7
Q ss_pred cCCHHHHHHHHHhhhcCCCeeeeccccccchHHHHHHHHhhccc
Q 006993 164 TLARKEATNLQRLARVLPPHFALGRSRQLQGLAVAMIKLWEKSS 207 (622)
Q Consensus 164 ~LT~~E~t~Lrrlar~lp~hf~LGRn~~~qGLa~am~klWeks~ 207 (622)
+||.+|+.++-.++.+|. ---+||||++|++..++..-|...-
T Consensus 33 PlTEDElkEF~~kseQlr-rNGf~kngfl~~rs~slf~pWr~t~ 75 (97)
T PF15337_consen 33 PLTEDELKEFQVKSEQLR-RNGFGKNGFLQSRSLSLFSPWRSTC 75 (97)
T ss_pred cCcHHHHHHHHHHHHHHH-Hccccccchhhhhhhhccccccccc
Confidence 489999999999999988 5679999999999999888897654
No 12
>PF15249 GLTSCR1: Glioma tumor suppressor candidate region
Probab=52.12 E-value=5.6 Score=36.20 Aligned_cols=23 Identities=43% Similarity=0.818 Sum_probs=16.8
Q ss_pred CCCCCCCc--------ccCCCCCCCcCCHHH
Q 006993 147 VPGYQPPF--------RVLPYGVRSTLARKE 169 (622)
Q Consensus 147 vpgyk~Pf--------RlLP~gvrp~LT~~E 169 (622)
-|.|++|| |||||.|=.....++
T Consensus 14 ~PD~~tPF~s~~DA~~RLLPYHv~~~~~~~~ 44 (109)
T PF15249_consen 14 NPDYKTPFRSLEDAVERLLPYHVFQEPEEDE 44 (109)
T ss_pred CCCcCCCCCCHHHHHHHhcchhhhcCCCCCh
Confidence 48899999 699998766544333
No 13
>cd05797 Ribosomal_L10 Ribosomal protein L10 family, L10 subfamily; composed of bacterial 50S ribosomal protein and eukaryotic mitochondrial 39S ribosomal protein, L10. L10 occupies the L7/L12 stalk of the ribosome. The N-terminal domain (NTD) of L10 interacts with L11 protein and forms the base of the L7/L12 stalk, while the extended C-terminal helix binds to two or three dimers of the NTD of L7/L12 (L7 and L12 are identical except for an acetylated N-terminus). The L7/L12 stalk is known to contain the binding site for elongation factors G and Tu (EF-G and EF-Tu, respectively); however, there is disagreement as to whether or not L10 is involved in forming the binding site. The stalk is believed to be associated with GTPase activities in protein synthesis. In a neuroblastoma cell line, L10 has been shown to interact with the SH3 domain of Src and to activate the binding of the Nck1 adaptor protein with skeletal proteins such as the Wiskott-Aldrich Syndrome Protein (WASP) and the WASP-in
Probab=46.83 E-value=26 Score=33.09 Aligned_cols=27 Identities=15% Similarity=0.144 Sum_probs=24.8
Q ss_pred cCCHHHHHHHHHhhhcCCCeeeecccc
Q 006993 164 TLARKEATNLQRLARVLPPHFALGRSR 190 (622)
Q Consensus 164 ~LT~~E~t~Lrrlar~lp~hf~LGRn~ 190 (622)
+||..+++.||+..+....+|.+++|.
T Consensus 29 gl~~~~~~~lR~~lr~~~~~~~V~KNt 55 (157)
T cd05797 29 GLTVAQLTELRKELREAGVKLKVVKNT 55 (157)
T ss_pred CCcHHHHHHHHHHHHHcCCEEEEehhH
Confidence 799999999999999998899999984
No 14
>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=43.57 E-value=33 Score=35.11 Aligned_cols=42 Identities=24% Similarity=0.437 Sum_probs=26.7
Q ss_pred cHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCC
Q 006993 482 TKRKALARSIELQRQEALLKHVATLESNAGRLRSEIEQMNSVKG 525 (622)
Q Consensus 482 TKrkAl~rS~e~qr~~~l~~~i~~l~k~i~~l~~~l~~~~~~~~ 525 (622)
-||+||.-+++.-+. |..-|..++.+|..|+.+......+-+
T Consensus 115 ~RR~AL~eaL~ENe~--Lh~~ie~~~eEi~~lk~en~~L~elae 156 (200)
T PF07412_consen 115 ERRKALEEALEENEK--LHKEIEQKDEEIAKLKEENEELKELAE 156 (200)
T ss_dssp HHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHCCHHHHH
T ss_pred HHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 367788777665443 555577777777777776665554433
No 15
>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=36.62 E-value=7.1 Score=38.41 Aligned_cols=92 Identities=17% Similarity=0.202 Sum_probs=58.8
Q ss_pred HHHHHHHHHHHH-----HHHHHHHHhhhh---ccCCCCCCCCCCCCCCHHHHHHHHHhccCCcceEe------eCCCCCC
Q 006993 340 KLEKKLARAERK-----LLRAERALSKVE---ESLKPAERQADPESITDEERFMFRKLGLRMKAFLL------LGRRGVF 405 (622)
Q Consensus 340 ~~e~KL~~a~~K-----~~kae~~L~K~e---~~~~P~e~~~d~E~LT~eERr~LRklGhkLKPvV~------IGK~GVT 405 (622)
+++.||+.|+.. .+.-.+.|+++- ...--+....|.+-||..++..++++...|.|++- --|.=+|
T Consensus 28 ~~eaKLqqAK~~lgeeEfeef~~lLK~lt~~kLkygD~NGnidye~ls~~eqee~k~~~~eLqPYFdKLN~~~SsK~vlt 107 (162)
T PF12207_consen 28 RLEAKLQQAKGELGEEEFEEFKELLKKLTNAKLKYGDKNGNIDYEKLSKEEQEEYKKLTMELQPYFDKLNGHKSSKEVLT 107 (162)
T ss_dssp HHHHHHHHHHHCS-HHHHHHHHHHHHHHHHHHHHHB-TTS-B-GGGS-HHHHHHHHHHHHHHHHHHHHHTT---HHHHS-
T ss_pred HHHHHHHHHHHhhhHHHHHHHHHHHHHHHHhHHhhcccCCCcCHHhCCHHHHHHHHHHHHhcchHHHHhcCCcchhhhcC
Confidence 567777777633 233334444432 22334566788999999999999999999999872 2333466
Q ss_pred HHHHHHHHHHHhhCCeEeEEEcCCCH
Q 006993 406 DGTVENMHLHWKYRELVKIIVKVKTF 431 (622)
Q Consensus 406 dgVVeeIh~Awk~hELVKVk~~~~~~ 431 (622)
+.-.+.--.||-.+|.|+|+......
T Consensus 108 ~~E~d~y~eALm~~e~v~vk~~~~~~ 133 (162)
T PF12207_consen 108 QEEYDQYIEALMTYETVRVKTKSSGG 133 (162)
T ss_dssp HHHHHHHHHHHHHHHHHHHHCT-SS-
T ss_pred HHHHHHHHHHHhhhheeeeeccCCCC
Confidence 66667777799999999998875443
No 16
>smart00271 DnaJ DnaJ molecular chaperone homology domain.
Probab=34.37 E-value=48 Score=25.71 Aligned_cols=51 Identities=18% Similarity=0.235 Sum_probs=34.4
Q ss_pred CCcccCCCCCCCcCCHHHH-HHHHHhhhcCCCeeeeccccccchHHHHHHHHhh
Q 006993 152 PPFRVLPYGVRSTLARKEA-TNLQRLARVLPPHFALGRSRQLQGLAVAMIKLWE 204 (622)
Q Consensus 152 ~PfRlLP~gvrp~LT~~E~-t~Lrrlar~lp~hf~LGRn~~~qGLa~am~klWe 204 (622)
.||.+| |+.+..|.+|+ ...|++++..-|-..-|......-....|..+|+
T Consensus 2 ~~y~vL--gl~~~~~~~~ik~ay~~l~~~~HPD~~~~~~~~~~~~~~~l~~Ay~ 53 (60)
T smart00271 2 DYYEIL--GVPRDASLDEIKKAYRKLALKYHPDKNPGDKEEAEEKFKEINEAYE 53 (60)
T ss_pred CHHHHc--CCCCCCCHHHHHHHHHHHHHHHCcCCCCCchHHHHHHHHHHHHHHH
Confidence 477777 88999999998 6789999998887665532222333344445554
No 17
>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=31.05 E-value=2.2e+02 Score=24.03 Aligned_cols=55 Identities=11% Similarity=0.067 Sum_probs=39.7
Q ss_pred HHHHHHHHhhCCeEeEEEcCCCHHHHHHHHHHHHH---HhCCEEEeecccccCcEEEEEecCC
Q 006993 409 VENMHLHWKYRELVKIIVKVKTFDQAKKIALALEA---ESGGVLVSVDKISKGYAMVVYRGKD 468 (622)
Q Consensus 409 VeeIh~Awk~hELVKVk~~~~~~ed~keiAe~Lee---~TGg~LVqV~kv~IG~tIILYRGkN 468 (622)
+.++-.+++....|=|.+.....+..+.+...|.. ..+|.+.. +|+.++++=+++
T Consensus 12 ~~~i~~~l~~g~~Vivnl~~l~~~~~~Ri~Dfl~G~~~al~G~i~~-----i~~~~~l~~P~~ 69 (73)
T PF04472_consen 12 AREIVDALREGKIVIVNLENLDDEEAQRILDFLSGAVYALDGDIQK-----ISEKVFLLTPKG 69 (73)
T ss_dssp HHHHHHHHHTT--EEEE-TTS-HHHHHHHHHHHHHHHHHTT-EEEE-----EETTEEEEE---
T ss_pred HHHHHHHHHcCCEEEEECCCCCHHHHHHHHHHHhchheeeCCEEEE-----EcCCEEEEECCC
Confidence 34588899999999999999998888988888875 67999999 588888887654
No 18
>cd06257 DnaJ DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification.
Probab=30.92 E-value=59 Score=24.70 Aligned_cols=33 Identities=21% Similarity=0.299 Sum_probs=27.4
Q ss_pred CcccCCCCCCCcCCHHHH-HHHHHhhhcCCCeeeec
Q 006993 153 PFRVLPYGVRSTLARKEA-TNLQRLARVLPPHFALG 187 (622)
Q Consensus 153 PfRlLP~gvrp~LT~~E~-t~Lrrlar~lp~hf~LG 187 (622)
||.+| |+.+..|.+++ ...|++++..-|.-.-+
T Consensus 2 ~y~vL--gl~~~~~~~~ik~~y~~l~~~~HPD~~~~ 35 (55)
T cd06257 2 YYDIL--GVPPDASDEEIKKAYRKLALKYHPDKNPD 35 (55)
T ss_pred hHHHc--CCCCCCCHHHHHHHHHHHHHHHCcCCCCC
Confidence 67787 78899999998 67899999988877655
No 19
>TIGR00285 DNA-binding protein Alba. This protein appears so far only in the Archaea, but may be universal there. There is a single member in three of the first four completed archaeal genomes, and a second copy in A. fulgidus. In Sulfolobus shibatae there is a tandem second copy that is poorly conserved and scores below the trusted cutoff; all other members of the family are conserved at greater than 50 % pairwise identity.
Probab=29.30 E-value=1.6e+02 Score=26.84 Aligned_cols=66 Identities=14% Similarity=0.120 Sum_probs=53.2
Q ss_pred ceEeeCCCCCCHHHHHHHHHHHhhCCeEeEEEcCCCHHHHHHHHHHHHHHhCCEEEeecccccCcEE
Q 006993 395 AFLLLGRRGVFDGTVENMHLHWKYRELVKIIVKVKTFDQAKKIALALEAESGGVLVSVDKISKGYAM 461 (622)
Q Consensus 395 PvV~IGK~GVTdgVVeeIh~Awk~hELVKVk~~~~~~ed~keiAe~Lee~TGg~LVqV~kv~IG~tI 461 (622)
.++.||+.++..-|++-+.+--+...=|.|+-.+..-...=.+|+.|..+.... +++.++.+|---
T Consensus 2 ~~i~vG~KPvmnYVlavlt~fn~g~~eV~iKarG~aIskAVdvaeiik~r~~~~-v~v~~I~i~te~ 67 (87)
T TIGR00285 2 NVVYIGNKPVMNYVLAVLTQLNSGADEVIIKARGRAISRAVDVAEIVRNRFIPD-IKIKKIKIGTEE 67 (87)
T ss_pred CEEEEcCCcHHHHHHHHHHHHhCCCCeEEEEEecchhhhHHHHHHHHHHhccCC-ceEEEEEeccEE
Confidence 578999999999999998876555677888888988888888999999987654 577666677543
No 20
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=28.10 E-value=83 Score=35.84 Aligned_cols=10 Identities=30% Similarity=0.262 Sum_probs=6.4
Q ss_pred ccceeeeeee
Q 006993 596 DSESEAYTVH 605 (622)
Q Consensus 596 ~~~~~~~~~~ 605 (622)
.|.|..||--
T Consensus 119 ~sd~~~WtP~ 128 (458)
T PF10446_consen 119 GSDYEFWTPG 128 (458)
T ss_pred cccceeeccc
Confidence 4677777654
No 21
>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=27.40 E-value=50 Score=39.17 Aligned_cols=25 Identities=36% Similarity=0.446 Sum_probs=20.8
Q ss_pred ccccHHHHHHHhHHHHHHHHHHHHH
Q 006993 479 NLLTKRKALARSIELQRQEALLKHV 503 (622)
Q Consensus 479 nlLTKrkAl~rS~e~qr~~~l~~~i 503 (622)
.+|++..+|=|++-.|--+++--||
T Consensus 596 slls~~s~llR~~~~~vf~~~~~~~ 620 (784)
T PF04931_consen 596 SLLSQPSALLRKVSEQVFEAFCPHL 620 (784)
T ss_pred HHHhCcchHHHHHHHHHHHHHHhhc
Confidence 3678888999999988888887776
No 22
>PF03641 Lysine_decarbox: Possible lysine decarboxylase; InterPro: IPR005269 This entry represents a cytokinin-activating enzyme working in the direct activation pathway. It is a phosphoribohydrolase that converts inactive cytokinin nucleotides to the biologically active free-base forms [, ]. The proteins in this entry belong to the LOG family of proteins.; PDB: 1YDH_B 2Q4D_A 1RCU_C 1WEH_B 3SBX_F 3BQ9_B 2PMB_D 3GH1_D 1WEK_C 3QUA_A ....
Probab=26.51 E-value=1e+02 Score=28.56 Aligned_cols=35 Identities=23% Similarity=0.323 Sum_probs=29.4
Q ss_pred HHHHHhccCCc-ceEeeCCCCCCHHHHHHHHHHHhh
Q 006993 384 FMFRKLGLRMK-AFLLLGRRGVFDGTVENMHLHWKY 418 (622)
Q Consensus 384 r~LRklGhkLK-PvV~IGK~GVTdgVVeeIh~Awk~ 418 (622)
-.+.++|.+-+ |++.++.+|.++.+++.++...+.
T Consensus 74 ~~~~~l~~~~~~Piil~~~~g~w~~l~~~l~~~~~~ 109 (133)
T PF03641_consen 74 LTLMQLGRHNKVPIILLNIDGFWDPLLEFLDRMIEE 109 (133)
T ss_dssp HHHHHTTSSTS-EEEEEECGGCCHHHHHHHHHHHHT
T ss_pred HHHHhhccccCCCEEEeCCcchHHHHHHHHHHHHHC
Confidence 45688888888 999999999999999999755444
No 23
>cd08775 DED_Caspase-like_repeat2 Death effector domain, repeat 2, of initator caspase-like proteins. Death Effector Domain (DED), second repeat, found in initator caspase-like proteins like caspase-8, -10 and c-FLIP. Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. Initiator caspases are the first to be activated following death- or inflammation-inducing signals. Caspase-8 and -10 are the initiators of death receptor mediated apoptosis. Together with FADD and the pseudo-caspase c-FLIP, they form the death-inducing signaling complex (DISC), whose formation is triggered by the activation of type 1 tumor necrosis factor (TNF) receptors such as Fas, TNF receptor 1, and TRAIL receptor. Caspase-8 and -10 also play important functions in cell adhesion and motility. c-FLIP is a catalytically inactive homolog of the initator procaspases-8 and -10. It negatively influences apoptotic signaling by interfering with the efficient formation of DISC.
Probab=26.50 E-value=23 Score=31.09 Aligned_cols=49 Identities=22% Similarity=0.323 Sum_probs=40.8
Q ss_pred CCcccCCCCCCCcCCHHHHHHHHHhhhcCCCeeeeccccccchHHHHHH
Q 006993 152 PPFRVLPYGVRSTLARKEATNLQRLARVLPPHFALGRSRQLQGLAVAMI 200 (622)
Q Consensus 152 ~PfRlLP~gvrp~LT~~E~t~Lrrlar~lp~hf~LGRn~~~qGLa~am~ 200 (622)
+|||.+=+.+.-.||.+|...|.=+|+...|...+-.+.-.-.|...|-
T Consensus 1 S~yr~lL~~Ise~L~~~dl~~lkFL~~d~i~~~kle~~~s~ldlf~~Le 49 (81)
T cd08775 1 SAYRVMLYQVSEELSRSELRSLKFLLQEEISSCKLDDDMNFLDIVIEME 49 (81)
T ss_pred ChHHHHHHHHHHhcCHHHHHHHHHHCccccccccccccCCHHHHHHHHH
Confidence 5899888889999999999999999999888888887765555655554
No 24
>COG1623 Predicted nucleic-acid-binding protein (contains the HHH domain) [General function prediction only]
Probab=25.75 E-value=3.1e+02 Score=30.23 Aligned_cols=50 Identities=10% Similarity=0.274 Sum_probs=34.7
Q ss_pred HHHHHHHHHHHHHHhCCEEEeecccccCcEEEEEecCCCCCCCCCCCcccccHH
Q 006993 431 FDQAKKIALALEAESGGVLVSVDKISKGYAMVVYRGKDYQRPSTLRPKNLLTKR 484 (622)
Q Consensus 431 ~ed~keiAe~Lee~TGg~LVqV~kv~IG~tIILYRGkNYkrP~~l~PknlLTKr 484 (622)
..-+...|+..+..||..||+|- .--++|.||.+ |++.-.. -+-.+|+|.
T Consensus 104 tGtRHRTAER~AkqTG~~VIaiS--~rrNvITlY~~-~~ky~L~-d~~~il~ra 153 (349)
T COG1623 104 TGTRHRTAERVAKQTGNPVIAIS--ERRNVITLYVG-NLKYVLK-DSAFILSRA 153 (349)
T ss_pred CccccchHHHHHHHhCCeEEEEe--cccceEEEEec-Ceeeeec-ChHHHHHHH
Confidence 34578899999999999999985 34578999986 4444221 234455553
No 25
>PHA03158 hypothetical protein; Provisional
Probab=24.72 E-value=64 Score=33.46 Aligned_cols=63 Identities=22% Similarity=0.367 Sum_probs=40.2
Q ss_pred CCCCCCCCcccCCCCCCCcCCHHHHHHHHHhhhcCCCeeeeccccccchHHHHHHHHhhccceeEEeeccCCCcCch-HH
Q 006993 146 IVPGYQPPFRVLPYGVRSTLARKEATNLQRLARVLPPHFALGRSRQLQGLAVAMIKLWEKSSIAKIALKRGVQLTTS-ER 224 (622)
Q Consensus 146 ~vpgyk~PfRlLP~gvrp~LT~~E~t~Lrrlar~lp~hf~LGRn~~~qGLa~am~klWeks~i~KIa~KrGv~~td~-e~ 224 (622)
.|-||+.=||-||+ +-|++|.-||-|.+-..- -.-+...++|.=++ +|| |+.. ..
T Consensus 203 ~vnG~~V~y~sLpf-------------~ERl~Rs~pPWCv~t~~E-K~~~~kQllka~kk------c~~----~s~~~~~ 258 (273)
T PHA03158 203 NINGKHVRFDDLPF-------------MERIKRSGPPWCIKTAKE-KAAILKQLLKAAKK------CCK----NSEHEKE 258 (273)
T ss_pred EecCEEEEeccCcH-------------HHHHhccCCCcEeecHHH-hHHHHHHHHHHHHH------Hhc----chHHHHH
Confidence 47888888888885 678999999999997431 22334444444333 354 3333 34
Q ss_pred HHHHHhhc
Q 006993 225 MVEDIKKL 232 (622)
Q Consensus 225 ma~eLk~L 232 (622)
+-+||++|
T Consensus 259 leeei~el 266 (273)
T PHA03158 259 LEEEIEEL 266 (273)
T ss_pred HHHHHHHH
Confidence 66777765
No 26
>KOG3130 consensus Uncharacterized conserved protein [Function unknown]
Probab=23.90 E-value=46 Score=37.57 Aligned_cols=15 Identities=47% Similarity=0.942 Sum_probs=8.2
Q ss_pred hhcCCCCCCCcccch
Q 006993 537 SAYATEDDDSEDEGD 551 (622)
Q Consensus 537 ~~~~~~~~~~e~e~~ 551 (622)
+.|++||+|.+|+||
T Consensus 269 ss~~edD~Dddd~dD 283 (514)
T KOG3130|consen 269 SSYHEDDDDDDDDDD 283 (514)
T ss_pred CCccccccccccccc
Confidence 356666655555543
No 27
>TIGR00730 conserved hypothetical protein, DprA/Smf-related, family 2. This model represents one branch of a subfamily of proteins of unknown function. Both PSI-BLAST and weak hits by this model show a low level of similarity to and suggest an evolutionary relationship of the subfamily to the DprA/Smf family of DNA-processing proteins involved in chromosomal transformation with foreign DNA. Both Aquifex aeolicus and Mycobacterium leprae have one member in each of two branches of this subfamily, suggesting that the branches may have distinct functions.
Probab=22.71 E-value=1e+02 Score=30.42 Aligned_cols=34 Identities=29% Similarity=0.577 Sum_probs=28.8
Q ss_pred HHHHHhccCCcceEeeCCCCCCHHHHHHHHHHHh
Q 006993 384 FMFRKLGLRMKAFLLLGRRGVFDGTVENMHLHWK 417 (622)
Q Consensus 384 r~LRklGhkLKPvV~IGK~GVTdgVVeeIh~Awk 417 (622)
-.+.++|.+-||++.++-+|.++.+++-++...+
T Consensus 117 ~~~~qlg~~~kPiil~n~~g~~~~l~~~l~~~~~ 150 (178)
T TIGR00730 117 LTWAQLGIHQKPIILFNVNGHFDGLVEWLKYSIQ 150 (178)
T ss_pred HHHHHcCCCCCCEEEECCcchHHHHHHHHHHHHH
Confidence 4568889999999999999999999998884443
No 28
>PRK04015 DNA/RNA-binding protein albA; Provisional
Probab=22.19 E-value=3.5e+02 Score=24.79 Aligned_cols=68 Identities=16% Similarity=0.168 Sum_probs=53.7
Q ss_pred cceEeeCCCCCCHHHHHHHHHHHhhCCeEeEEEcCCCHHHHHHHHHHHHHHhCCEEEeecccccCcEEE
Q 006993 394 KAFLLLGRRGVFDGTVENMHLHWKYRELVKIIVKVKTFDQAKKIALALEAESGGVLVSVDKISKGYAMV 462 (622)
Q Consensus 394 KPvV~IGK~GVTdgVVeeIh~Awk~hELVKVk~~~~~~ed~keiAe~Lee~TGg~LVqV~kv~IG~tII 462 (622)
...+.||+.++..-|+.-+.+--+.-.=|.|+-.+..-...=.+|+.|.++...- |++.++.+|.-.+
T Consensus 4 en~i~Ig~kpvmnYV~~~~~~l~~g~~eV~iKa~G~aIskAV~vaEilk~r~~~~-v~v~~I~i~se~i 71 (91)
T PRK04015 4 ENVVLVGKKPVMNYVLAVLTQFNQGAKEVVIKARGRAISKAVDVAEIVRNRFLPD-VEIKEIKIGTEEV 71 (91)
T ss_pred CCEEEEcCCcHHHHHHHHHHHHhCCCCeEEEEEeccccchhhhHHHHHHHhccCC-eEEEEEEeccEEe
Confidence 4689999999998888888764446677888888888888888999999987644 7776777877655
No 29
>PF00922 Phosphoprotein: Vesiculovirus phosphoprotein; InterPro: IPR000224 This entry contains phosphoprotein from vesiculoviruses, which are ssRNA negative-strand rhabdoviruses. It is known as the phosphoprotein or P protein [, ]. This protein may be part of the RNA dependent RNA polymerase complex []. The phosphorylation states of this protein may regulate the transcription and replication complexes [].; GO: 0003968 RNA-directed RNA polymerase activity; PDB: 2K47_A 3PMK_R 2FQM_F 3HHZ_C 3HHW_D.
Probab=21.38 E-value=67 Score=34.52 Aligned_cols=56 Identities=21% Similarity=0.302 Sum_probs=0.8
Q ss_pred CchHHHHHhhhhcCCCCCCCcc-------cchhHHHHHhhCCCCCCccccccccccccccCCCCC
Q 006993 527 GDEQLYDKLDSAYATEDDDSED-------EGDEAYLEMYAGGNDNEDEIDNSTHNLEMESDFPYH 584 (622)
Q Consensus 527 ~~~~l~~~~d~~~~~~~~~~e~-------e~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 584 (622)
.-..-|.+.+..-++.+++.|| ......++.|..+.+++.++|+. .++++++.|+.
T Consensus 43 ~~PsYY~~~e~~e~~~e~~~ed~~~~~~~~~~~~~VE~y~~~~~d~~~Ddd~--~V~F~~~~~Wk 105 (283)
T PF00922_consen 43 SSPSYYQAEEDDESDEEDSEEDDDSLNTELPPPPEVEGYEEEPEDEYIDDDV--QVVFTSDQPWK 105 (283)
T ss_dssp ---------------------------------------------------------------S-
T ss_pred CCchhhhhhhccccccCCcccccccccccCCCchhccccccCcchhcccccc--eEEeccccccc
Confidence 4455677755544433333233 12345678888887777666654 78888888884
No 30
>cd08340 DED_c-FLIP_repeat2 Death Effector Domain, repeat 2, of cellular FLICE-Inhibitory Protein. Death Effector Domain (DED), repeat 2, similar to that found in cellular FLICE-inhibitory protein (c-FLIP/CASH, also known as Casper/iFLICE/FLAME-1/CLARP/MRIT/usurpin). c-FLIP is a catalytically inactive homolog of the initator procaspases-8 and -10. It negatively influences apoptotic signaling by interfering with the efficient formation of the Death Inducing Signalling Complex (DISC). At low levels, c-FLIP has been shown to enhance apoptotic signaling by allosterically activating caspase-8. As a modulator of the initiator caspases, c-FLIP regulates life and death in various types of cells and tissues. All members contain two N-terminal DEDs and a C-terminal pseudo-caspase domain. DEDs comprise a subfamily of the Death Domain (DD) superfamily. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-as
Probab=20.12 E-value=34 Score=29.96 Aligned_cols=48 Identities=21% Similarity=0.300 Sum_probs=38.4
Q ss_pred CCcccCCCCCCCcCCHHHHHHHHHhhhcCCCeeeeccccccchHHHHH
Q 006993 152 PPFRVLPYGVRSTLARKEATNLQRLARVLPPHFALGRSRQLQGLAVAM 199 (622)
Q Consensus 152 ~PfRlLP~gvrp~LT~~E~t~Lrrlar~lp~hf~LGRn~~~qGLa~am 199 (622)
+|||.+=+.+.-.||.+|...|+=+|+...|...+-++.-.-.|...|
T Consensus 1 s~yr~lL~~Ise~L~~~dl~~lkFL~~d~i~~~kle~~~s~l~lf~~L 48 (81)
T cd08340 1 SDYRVLMVEVGEELDKSDLRSLIFLLKDLMPSGSKAKDKSFLELVLEL 48 (81)
T ss_pred CcHHHHHHHHHHHcCHHHHHHHHHHhhcccccccccccCCHHHHHHHH
Confidence 588888888999999999999999999888877777765444444444
Done!