Query 003706
Match_columns 801
No_of_seqs 343 out of 1051
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 04:29:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003706.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003706hhsearch_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 5.9E-73 1.3E-77 637.4 21.4 517 237-800 2-523 (564)
2 PRK10343 RNA-binding protein Y 99.9 4.1E-25 8.9E-30 200.6 13.4 96 659-760 1-96 (97)
3 TIGR00253 RNA_bind_YhbY putati 99.9 1E-24 2.3E-29 197.2 13.2 87 661-751 1-87 (95)
4 PF01985 CRS1_YhbY: CRS1 / Yhb 99.9 7.9E-25 1.7E-29 192.9 11.1 84 250-333 1-84 (84)
5 PRK10343 RNA-binding protein Y 99.9 3.4E-24 7.5E-29 194.6 12.6 89 248-336 1-89 (97)
6 TIGR00253 RNA_bind_YhbY putati 99.9 7.3E-24 1.6E-28 191.8 12.5 86 250-335 1-86 (95)
7 PF01985 CRS1_YhbY: CRS1 / Yhb 99.9 1E-23 2.2E-28 185.9 10.9 84 661-748 1-84 (84)
8 COG1534 Predicted RNA-binding 99.9 1.8E-23 4E-28 189.4 12.3 97 660-761 1-97 (97)
9 COG1534 Predicted RNA-binding 99.9 4.2E-22 9.1E-27 180.6 11.9 85 249-333 1-85 (97)
10 KOG1990 Poly(A)-specific exori 98.7 1.3E-08 2.7E-13 117.1 7.0 286 244-541 169-480 (564)
11 KOG2769 Putative u4/u6 small n 52.7 20 0.00044 42.1 5.0 54 479-533 375-435 (522)
12 PF11211 DUF2997: Protein of u 31.4 65 0.0014 26.8 3.5 32 492-525 11-42 (48)
13 KOG1257 NADP+-dependent malic 28.3 1.4E+02 0.0031 35.9 6.8 85 253-340 376-466 (582)
14 PF12207 DUF3600: Domain of un 26.4 8.5 0.00018 38.9 -2.8 93 622-714 27-133 (162)
15 PF15249 GLTSCR1: Glioma tumor 23.3 31 0.00068 32.5 0.4 24 429-452 13-44 (109)
16 PF03641 Lysine_decarbox: Poss 21.9 1.4E+02 0.003 28.8 4.5 37 665-701 72-109 (133)
17 PF04472 DUF552: Protein of un 21.8 5.3E+02 0.012 22.5 7.7 55 281-336 12-69 (73)
18 PF15237 PTRF_SDPR: PTRF/SDPR 21.3 1.9E+02 0.004 31.7 5.6 64 476-541 54-119 (246)
No 1
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=100.00 E-value=5.9e-73 Score=637.42 Aligned_cols=517 Identities=46% Similarity=0.653 Sum_probs=479.4
Q ss_pred ccccchhhhhcCCCCHHHHHHHHHhhhcCCCeEEeCCCCCCHHHHHHHHHHhhhCCeEEEEecCCChHhHHHHHHHHHHH
Q 003706 237 RRRRSNTELAEKMIPEHELQRLRNISLRMLERTKVGSAGITQALVDSIHEKWKLDEVVKLKFEEPHSLQMKRTHEILERR 316 (801)
Q Consensus 237 ~~~~s~psLAe~~LT~kErr~LRklAh~LkpvV~IGK~GVTd~VVeeIh~awk~hELVKVK~~~~~~~dm~~~~e~LEek 316 (801)
.+..+ +++|++++.+.++++||..|..+...+ +++|+|+++++.|++.|+.+|+++++|....+.+|.+.+++++..
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 34556 999999999999999999999998887 999999999999999999999999999999999999999999999
Q ss_pred hCC-eEEEEEccEEEEeecCCCCCCCccccccccccccccccccccccccCCCCCCCccccCCCCcccccccccHHHHhh
Q 003706 317 TGG-LVIWRSGSSVVLFRGMAYKLPCVQSFTKHNHTQQTQDVTNEVMRNVGEHPPRSAMESYVPDSANNLENLSKEELMD 395 (801)
Q Consensus 317 TGG-~VVqrIG~viVLYRGknY~~P~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~ee~~~ 395 (801)
||| .+||+.|.+...|++..|..|..-.... .+ ....+.. ...
T Consensus 79 ~~~n~~~~~~g~~~s~~~~~~~~~~~~~~~~~--------------------------~~--------~~~~~~~--~~~ 122 (564)
T KOG1990|consen 79 TGGNFVVWSRGDSISSPEFLCQRSPVDFVARQ--------------------------QE--------NQAGKWP--SEL 122 (564)
T ss_pred CCCceeeeecCccccCCccceeecchhhhhhh--------------------------ch--------hhhhhhH--HHH
Confidence 999 9999999999999999999884311000 00 0000101 224
Q ss_pred HhhhhhhhcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccCCCCCCCCCChHHHHHHHHhhhcCCCeEEecccchh
Q 003706 396 LCELNYLLDELGPRFKDWPGREPLPVDADLLPPVVPDYKPPLRLLPYGIKPGLRDCETTEFRRLARKTPPHFALGRNREL 475 (801)
Q Consensus 396 ~~E~n~lLD~LGPRf~dW~g~~PlPVDaDLLP~vvPgy~~PfRllP~gv~~~Ls~~E~t~LRk~ar~lpph~aLGRn~~~ 475 (801)
.++.+.++|++||+|.|||+.+|+|+|+||+|++||+|.+|||.+|+|++++|+..|++.+|++|..+||||++|+++.+
T Consensus 123 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~dl~~~~i~~~~~p~r~l~~~~~~~l~~~~~~~~r~~~~~~p~~~~~~~~~~~ 202 (564)
T KOG1990|consen 123 EKEKNELLDSLGPELSDWGGSDRLSVDADLLPEKIPDYMRPFRTLPVGSPPLLTSIESTLLRRLGYKLPPHFALGRSRKL 202 (564)
T ss_pred HHHHHHHhhccCcccccCCCCCCccchhhhchhhhhcccChhccCCCCChhhhhhHHHHHHHHhcccccccceehhcccc
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHhhCceeEEeecCCCCCCcHHHHHHHH--hhccCcEEEeeeCCeEEEEecCCCCChhhhhHHHHhhhhhh
Q 003706 476 QGLAKAMVKLWEKSAIAKIAIKRDVMNTRNERMAEEL--KKLTGGTLLCRNKDYIVFYRGNDFLPPVVTDAVKERSKLTD 553 (801)
Q Consensus 476 ~gLa~aI~k~wek~~lakI~~K~gv~~T~~~~m~~eL--k~LTGgvLLSRnke~IVlYRGkdf~p~~V~~al~ERe~~~~ 553 (801)
+|++.+|+.+|++|+++++.|++|++.+..+.||.+| ..+||++|++||+.++|+|||++|++ .|.++|.++.....
T Consensus 203 ~~~~~~~~~~~~k~~~~k~~~~rg~~~~~~~~~a~~l~~~~~tg~~lv~hN~~~dv~y~~~~Fl~-~lp~~l~~f~~~~~ 281 (564)
T KOG1990|consen 203 QGLAVAMVSFWEKHEFAKILIKRGVLETRKERMADELQELLLTGKVLVLHNKLLDVMYRYKNFLS-PLPSTLEEFTDSSS 281 (564)
T ss_pred ccchhHHHHHHHHHHHHHHHHHhcchhhhccchHHHHHHHHhcCCeEEeeccceeeeeehhhccc-ccchhHHHhhhhhh
Confidence 9999999999999999999999999999999999999 99999999999999999999999999 99999999999988
Q ss_pred hhhhHHHHhhhhhhHHHHhhccccccccccccHHHHHHHhhhccCCCChhHHH-HHHHhhhHHHHHHHHHHHHHHHHHHH
Q 003706 554 IRQDEEERARHVASALIELKAKGFVGSLVAGTLAETLAATSRWGRQPSYEDVE-KMMRDSTLSRHASLLRYLEQKLALAK 632 (801)
Q Consensus 554 ~~q~eEE~aR~~a~~~~~~~~~~~~~~~~aGtl~E~~~a~~~wg~~~~~~~~~-~~~~e~~~~~~~~l~k~~e~kL~~a~ 632 (801)
..++.++.+|..... + ......+||+.|+..+.++|+......+.. .+..+......+...+.+.++++.+.
T Consensus 282 ~fp~~~~~~~~~~~~---~----~~~~~~~~t~~e~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~ 354 (564)
T KOG1990|consen 282 MFPNIEDTKRLAKLS---E----YQKLNLKATLLELARAKAKKEKEIERRSISSRLKLEFEKASSEKLTEAIFHKLEKAK 354 (564)
T ss_pred hhhhhHHHHHhhccc---c----ccchhhhhhHHHHHHHhcccccCcccccccchhhhhhhccchhhHHHHHHHHHhhhh
Confidence 999999999966611 1 112357899999999999999999877653 67888889999999999999999999
Q ss_pred HHHHHHHHHHHhhcccCCCCCCCCCCCCCCHHHHHHHHHcccCCCceEeeCCCCCCHHHHHHHHHHHHhcceEEEEEcCC
Q 003706 633 RKLKMADKALAKVQESLDPAELPSDLETITNEERFLLRKMGLSMKPYLLLGRRGIYDGTIENMHLHWKYRELVKIIVKGK 712 (801)
Q Consensus 633 ~K~~rae~~L~K~~~~~~P~e~~~d~E~LT~eERk~LRklGhkLKPvV~IGK~GVtdgVIeeI~~aLk~hELVKVkv~~~ 712 (801)
.|+..+...|++++.+..|.+..+|++.+|.+++.+++++|.+|++++.+|++|+++|+|.+||.||++||++|++|+..
T Consensus 355 ~~~~~~~~~l~~~~~~~~~~~~~~~~e~~t~ee~~~~~k~g~k~~~~~~~~rrg~f~g~i~n~~l~wk~~e~~k~i~~~~ 434 (564)
T KOG1990|consen 355 KKLASANRILAKLEDPKIPAELRYDPESITEEERLMLRKVGLKMKRRLLSGRRGVFDGVIENMHLHWKSRELVKVICKEK 434 (564)
T ss_pred hhccchhhhhhcccccccccccccchhhcChHHHHHHHHHHHhhccccccCCcccccceeecchhhhhhcccceeeeccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred CH-HHHHHHHHHHHHHhCCEEEEeeecCCCcEEEEEccCCCCCCCcCCccccccHHHHHHHhHHHHHhhhhhHHHHHHHH
Q 003706 713 SF-AQVKQIAISLEAESGGVLVSLDKTPKGIAIIVYRGKNYVRPLKLRPQNLLTRRQALARSVELQRREGLKHHILDLQE 791 (801)
Q Consensus 713 ~~-~d~keiA~~Le~~SGg~LVqVIk~~iG~tIILYRgkNY~rP~~l~P~nlLtKrkAL~rs~e~qr~esl~~~i~~l~~ 791 (801)
.. .+++..|..++.++|+++|+++++..|++|+.|||+||++|..+.|.|+|+||+|+.+|+++|+.++++.||..++.
T Consensus 435 ~~~~~~~~~a~~le~esg~~~v~~~~~~~~~ai~~yr~k~y~~p~~l~P~~~l~~~k~~~~~~~~~~~~a~~~~i~~~~~ 514 (564)
T KOG1990|consen 435 NLPSQVKQYASALERESGGILVSIDKNPKGYAIIAYRGKNYDRPTSLRPRNLLSRRKALERSLEEQRKEALKSHISDLEQ 514 (564)
T ss_pred cccHHHHHHHHHHHHHhCCceeeeccCCchhhHHHhhhhhccCCcccCchhhhcccCCccccHHHHHHHHHhhhcchhhh
Confidence 76 99999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhh
Q 003706 792 RIELVKSEL 800 (801)
Q Consensus 792 ~i~~l~~~l 800 (801)
++++++.++
T Consensus 515 ~~e~~~~~~ 523 (564)
T KOG1990|consen 515 EIEQLQASV 523 (564)
T ss_pred hHHHhhcch
Confidence 999998765
No 2
>PRK10343 RNA-binding protein YhbY; Provisional
Probab=99.92 E-value=4.1e-25 Score=200.58 Aligned_cols=96 Identities=20% Similarity=0.381 Sum_probs=90.0
Q ss_pred CCCCHHHHHHHHHcccCCCceEeeCCCCCCHHHHHHHHHHHHhcceEEEEEcCCCHHHHHHHHHHHHHHhCCEEEEeeec
Q 003706 659 ETITNEERFLLRKMGLSMKPYLLLGRRGIYDGTIENMHLHWKYRELVKIIVKGKSFAQVKQIAISLEAESGGVLVSLDKT 738 (801)
Q Consensus 659 E~LT~eERk~LRklGhkLKPvV~IGK~GVtdgVIeeI~~aLk~hELVKVkv~~~~~~d~keiA~~Le~~SGg~LVqVIk~ 738 (801)
++||++||++||++||+|+|+|+||++||||+|+++++.+|++||||||++.+++.+++++++++|++.+||++||+|
T Consensus 1 m~Lt~kqr~~LR~~ah~l~Pvv~IGk~Glt~~vi~ei~~aL~~hELIKvkv~~~~~~~~~e~~~~i~~~~~ae~Vq~I-- 78 (97)
T PRK10343 1 MNLSTKQKQHLKGLAHPLKPVVLLGSNGLTEGVLAEIEQALEHHELIKVKIATEDRETKTLIVEAIVRETGACNVQVI-- 78 (97)
T ss_pred CCCCHHHHHHHHHhcCCCCCeEEECCCCCCHHHHHHHHHHHHHCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEeee--
Confidence 469999999999999999999999999999999999999999999999999999999999999999999999999987
Q ss_pred CCCcEEEEEccCCCCCCCcCCc
Q 003706 739 PKGIAIIVYRGKNYVRPLKLRP 760 (801)
Q Consensus 739 ~iG~tIILYRgkNY~rP~~l~P 760 (801)
|+++||||++. .|.+.+|
T Consensus 79 --G~~~vlYR~~~--~~~i~lp 96 (97)
T PRK10343 79 --GKTLVLYRPTK--ERKISLP 96 (97)
T ss_pred --CcEEEEEecCC--CccCCCC
Confidence 99999999875 3445455
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=1e-24 Score=197.24 Aligned_cols=87 Identities=29% Similarity=0.472 Sum_probs=85.2
Q ss_pred CCHHHHHHHHHcccCCCceEeeCCCCCCHHHHHHHHHHHHhcceEEEEEcCCCHHHHHHHHHHHHHHhCCEEEEeeecCC
Q 003706 661 ITNEERFLLRKMGLSMKPYLLLGRRGIYDGTIENMHLHWKYRELVKIIVKGKSFAQVKQIAISLEAESGGVLVSLDKTPK 740 (801)
Q Consensus 661 LT~eERk~LRklGhkLKPvV~IGK~GVtdgVIeeI~~aLk~hELVKVkv~~~~~~d~keiA~~Le~~SGg~LVqVIk~~i 740 (801)
||++||++||++||+|+|+|+||++|||++||++++++|++||||||++.+++.++++++|++|++.|||++||+|
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 7999999999999999999999999999999999999999999999999999999999999999999999999987
Q ss_pred CcEEEEEccCC
Q 003706 741 GIAIIVYRGKN 751 (801)
Q Consensus 741 G~tIILYRgkN 751 (801)
|+++||||++.
T Consensus 77 G~~~vlYR~~~ 87 (95)
T TIGR00253 77 GKTIVLYRPTK 87 (95)
T ss_pred ccEEEEEecCC
Confidence 99999999874
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=7.9e-25 Score=192.91 Aligned_cols=84 Identities=25% Similarity=0.417 Sum_probs=75.7
Q ss_pred CCHHHHHHHHHhhhcCCCeEEeCCCCCCHHHHHHHHHHhhhCCeEEEEecCCChHhHHHHHHHHHHHhCCeEEEEEccEE
Q 003706 250 IPEHELQRLRNISLRMLERTKVGSAGITQALVDSIHEKWKLDEVVKLKFEEPHSLQMKRTHEILERRTGGLVIWRSGSSV 329 (801)
Q Consensus 250 LT~kErr~LRklAh~LkpvV~IGK~GVTd~VVeeIh~awk~hELVKVK~~~~~~~dm~~~~e~LEekTGG~VVqrIG~vi 329 (801)
||++|+++||++||+|+|+|+|||+|||++|+++|+++|++||||||+|.+++..+++++++.|+++|||++||++|+++
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 EEee
Q 003706 330 VLFR 333 (801)
Q Consensus 330 VLYR 333 (801)
||||
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
>PRK10343 RNA-binding protein YhbY; Provisional
Probab=99.91 E-value=3.4e-24 Score=194.57 Aligned_cols=89 Identities=20% Similarity=0.317 Sum_probs=86.6
Q ss_pred CCCCHHHHHHHHHhhhcCCCeEEeCCCCCCHHHHHHHHHHhhhCCeEEEEecCCChHhHHHHHHHHHHHhCCeEEEEEcc
Q 003706 248 KMIPEHELQRLRNISLRMLERTKVGSAGITQALVDSIHEKWKLDEVVKLKFEEPHSLQMKRTHEILERRTGGLVIWRSGS 327 (801)
Q Consensus 248 ~~LT~kErr~LRklAh~LkpvV~IGK~GVTd~VVeeIh~awk~hELVKVK~~~~~~~dm~~~~e~LEekTGG~VVqrIG~ 327 (801)
|+||++|+++||++||+|+|+|+|||+|||++|+++|.++|++||||||++.+++.++.+++++.|+++||+++||+||+
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 47999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEeecCC
Q 003706 328 SVVLFRGMA 336 (801)
Q Consensus 328 viVLYRGkn 336 (801)
++||||.+.
T Consensus 81 ~~vlYR~~~ 89 (97)
T PRK10343 81 TLVLYRPTK 89 (97)
T ss_pred EEEEEecCC
Confidence 999999863
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=7.3e-24 Score=191.77 Aligned_cols=86 Identities=21% Similarity=0.339 Sum_probs=84.7
Q ss_pred CCHHHHHHHHHhhhcCCCeEEeCCCCCCHHHHHHHHHHhhhCCeEEEEecCCChHhHHHHHHHHHHHhCCeEEEEEccEE
Q 003706 250 IPEHELQRLRNISLRMLERTKVGSAGITQALVDSIHEKWKLDEVVKLKFEEPHSLQMKRTHEILERRTGGLVIWRSGSSV 329 (801)
Q Consensus 250 LT~kErr~LRklAh~LkpvV~IGK~GVTd~VVeeIh~awk~hELVKVK~~~~~~~dm~~~~e~LEekTGG~VVqrIG~vi 329 (801)
||++|+++||++||+|+|+|+|||+|||++|+++|+++|++||||||++.+++..+.+++++.|+++||+++||+||+++
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 EEeecC
Q 003706 330 VLFRGM 335 (801)
Q Consensus 330 VLYRGk 335 (801)
||||.+
T Consensus 81 vlYR~~ 86 (95)
T TIGR00253 81 VLYRPT 86 (95)
T ss_pred EEEecC
Confidence 999985
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=99.90 E-value=1e-23 Score=185.92 Aligned_cols=84 Identities=36% Similarity=0.584 Sum_probs=75.3
Q ss_pred CCHHHHHHHHHcccCCCceEeeCCCCCCHHHHHHHHHHHHhcceEEEEEcCCCHHHHHHHHHHHHHHhCCEEEEeeecCC
Q 003706 661 ITNEERFLLRKMGLSMKPYLLLGRRGIYDGTIENMHLHWKYRELVKIIVKGKSFAQVKQIAISLEAESGGVLVSLDKTPK 740 (801)
Q Consensus 661 LT~eERk~LRklGhkLKPvV~IGK~GVtdgVIeeI~~aLk~hELVKVkv~~~~~~d~keiA~~Le~~SGg~LVqVIk~~i 740 (801)
||++||++||++||+|+|+++||++|||++|+++|+++|++||||||+|.+++.++++++|+.|++.|||++|+++
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 7999999999999999999999999999999999999999999999999999999999999999999999999987
Q ss_pred CcEEEEEc
Q 003706 741 GIAIIVYR 748 (801)
Q Consensus 741 G~tIILYR 748 (801)
|+++||||
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=1.8e-23 Score=189.43 Aligned_cols=97 Identities=27% Similarity=0.465 Sum_probs=91.1
Q ss_pred CCCHHHHHHHHHcccCCCceEeeCCCCCCHHHHHHHHHHHHhcceEEEEEcCCCHHHHHHHHHHHHHHhCCEEEEeeecC
Q 003706 660 TITNEERFLLRKMGLSMKPYLLLGRRGIYDGTIENMHLHWKYRELVKIIVKGKSFAQVKQIAISLEAESGGVLVSLDKTP 739 (801)
Q Consensus 660 ~LT~eERk~LRklGhkLKPvV~IGK~GVtdgVIeeI~~aLk~hELVKVkv~~~~~~d~keiA~~Le~~SGg~LVqVIk~~ 739 (801)
+||++|+++||+.||+++|+|+||++|||++||.+|+++|++||||||++.+++.++++++|+.|++.+||.+||+|
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 59999999999999999999999999999999999999999999999999999999999999999999999999987
Q ss_pred CCcEEEEEccCCCCCCCcCCcc
Q 003706 740 KGIAIIVYRGKNYVRPLKLRPQ 761 (801)
Q Consensus 740 iG~tIILYRgkNY~rP~~l~P~ 761 (801)
|+++|||| .+..++.+.+|+
T Consensus 78 -G~~~vlyr-~~~e~~~i~l~~ 97 (97)
T COG1534 78 -GKTLVLYR-ESKEKRKISLPR 97 (97)
T ss_pred -eeEEEEEe-cCcccccccCCC
Confidence 99999999 555666666663
No 9
>COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]
Probab=99.87 E-value=4.2e-22 Score=180.64 Aligned_cols=85 Identities=22% Similarity=0.381 Sum_probs=84.1
Q ss_pred CCCHHHHHHHHHhhhcCCCeEEeCCCCCCHHHHHHHHHHhhhCCeEEEEecCCChHhHHHHHHHHHHHhCCeEEEEEccE
Q 003706 249 MIPEHELQRLRNISLRMLERTKVGSAGITQALVDSIHEKWKLDEVVKLKFEEPHSLQMKRTHEILERRTGGLVIWRSGSS 328 (801)
Q Consensus 249 ~LT~kErr~LRklAh~LkpvV~IGK~GVTd~VVeeIh~awk~hELVKVK~~~~~~~dm~~~~e~LEekTGG~VVqrIG~v 328 (801)
+||++|+++||+.||+++|+|+|||+|||++|+.+|.++|++||||||++.+++.++.+.+++.|++++|+.+||+||++
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 EEEee
Q 003706 329 VVLFR 333 (801)
Q Consensus 329 iVLYR 333 (801)
+||||
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=98.74 E-value=1.3e-08 Score=117.13 Aligned_cols=286 Identities=17% Similarity=0.215 Sum_probs=184.5
Q ss_pred hhhcCCCCHHHHHHHHHhhhcCCCeEEeCCCCCCHHHHHHHHHHhhhCCeEEEEecCCChH-hHHHHHHHH--HHHhCCe
Q 003706 244 ELAEKMIPEHELQRLRNISLRMLERTKVGSAGITQALVDSIHEKWKLDEVVKLKFEEPHSL-QMKRTHEIL--ERRTGGL 320 (801)
Q Consensus 244 sLAe~~LT~kErr~LRklAh~LkpvV~IGK~GVTd~VVeeIh~awk~hELVKVK~~~~~~~-dm~~~~e~L--EekTGG~ 320 (801)
---...|+..+.-.+|.+|-...+.+.+|..+.-+++.-.+...|..|+..|+-+...... .-..++.++ -..||+.
T Consensus 169 ~~~~~~l~~~~~~~~r~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~k~~~~k~~~~rg~~~~~~~~~a~~l~~~~~tg~~ 248 (564)
T KOG1990|consen 169 VGSPPLLTSIESTLLRRLGYKLPPHFALGRSRKLQGLAVAMVSFWEKHEFAKILIKRGVLETRKERMADELQELLLTGKV 248 (564)
T ss_pred CCChhhhhhHHHHHHHHhcccccccceehhccccccchhHHHHHHHHHHHHHHHHHhcchhhhccchHHHHHHHHhcCCe
Confidence 3334558999999999999999999999999999999999999999999999877764433 334577777 8899999
Q ss_pred EEEEEccEEEEeecCCCCCCCccccc--ccc-ccccccccccccccc-cCCCC--CCCccccCC---------CCccccc
Q 003706 321 VIWRSGSSVVLFRGMAYKLPCVQSFT--KHN-HTQQTQDVTNEVMRN-VGEHP--PRSAMESYV---------PDSANNL 385 (801)
Q Consensus 321 VVqrIG~viVLYRGknY~~P~~~~~~--k~~-~~~~~~~~~~~~~~~-~~~~~--~~~~~~~~~---------p~~~~~~ 385 (801)
+|.+-|-..++|||+||-. +.++.. ... ...++..+....... ....+ +..+..+.. +......
T Consensus 249 lv~hN~~~dv~y~~~~Fl~-~lp~~l~~f~~~~~~fp~~~~~~~~~~~~~~~~~~~~~t~~e~~~~~~~~~~~~~~~~~~ 327 (564)
T KOG1990|consen 249 LVLHNKLLDVMYRYKNFLS-PLPSTLEEFTDSSSMFPNIEDTKRLAKLSEYQKLNLKATLLELARAKAKKEKEIERRSIS 327 (564)
T ss_pred EEeeccceeeeeehhhccc-ccchhHHHhhhhhhhhhhhHHHHHhhccccccchhhhhhHHHHHHHhcccccCccccccc
Confidence 9999999999999999998 444221 000 001110000000000 01111 111110000 0000111
Q ss_pred ccccHH-HHhhHh---hhhhhhcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccCCCCCCCCCChHHHHHHHHhhh
Q 003706 386 ENLSKE-ELMDLC---ELNYLLDELGPRFKDWPGREPLPVDADLLPPVVPDYKPPLRLLPYGIKPGLRDCETTEFRRLAR 461 (801)
Q Consensus 386 ~~~~~e-e~~~~~---E~n~lLD~LGPRf~dW~g~~PlPVDaDLLP~vvPgy~~PfRllP~gv~~~Ls~~E~t~LRk~ar 461 (801)
..+..+ +.+... +........|-++.-|- .+.=+.+-+.-.|.=. +.+| ..+|++|..++++.+.
T Consensus 328 ~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~l~~~~~~~~~~~~---~~~~----e~~t~ee~~~~~k~g~ 396 (564)
T KOG1990|consen 328 SRLKLEFEKASSEKLTEAIFHKLEKAKKKLASA----NRILAKLEDPKIPAEL---RYDP----ESITEEERLMLRKVGL 396 (564)
T ss_pred chhhhhhhccchhhHHHHHHHHHhhhhhhccch----hhhhhccccccccccc---ccch----hhcChHHHHHHHHHHH
Confidence 011110 000000 00000011111111110 0000000000011000 1344 7799999999999999
Q ss_pred cCCCeEEecccchhhHHHHHHHHHHhhCceeEEeecCCCCCCcHHHHHHHHhhccCcEEEeeeC---Ce-EEEEecCCCC
Q 003706 462 KTPPHFALGRNRELQGLAKAMVKLWEKSAIAKIAIKRDVMNTRNERMAEELKKLTGGTLLCRNK---DY-IVFYRGNDFL 537 (801)
Q Consensus 462 ~lpph~aLGRn~~~~gLa~aI~k~wek~~lakI~~K~gv~~T~~~~m~~eLk~LTGgvLLSRnk---e~-IVlYRGkdf~ 537 (801)
++-.-.-+||=|+..|+.-.++.||..++.+++-||..-.....++.|..|..+.||++++=++ .| |++|||++|.
T Consensus 397 k~~~~~~~~rrg~f~g~i~n~~l~wk~~e~~k~i~~~~~~~~~~~~~a~~le~esg~~~v~~~~~~~~~ai~~yr~k~y~ 476 (564)
T KOG1990|consen 397 KMKRRLLSGRRGVFDGVIENMHLHWKSRELVKVICKEKNLPSQVKQYASALERESGGILVSIDKNPKGYAIIAYRGKNYD 476 (564)
T ss_pred hhccccccCCcccccceeecchhhhhhcccceeeeccccccHHHHHHHHHHHHHhCCceeeeccCCchhhHHHhhhhhcc
Confidence 9999999999999999999999999999999999998888899999999999999999998655 44 8999999997
Q ss_pred Chhh
Q 003706 538 PPVV 541 (801)
Q Consensus 538 p~~V 541 (801)
=+..
T Consensus 477 ~p~~ 480 (564)
T KOG1990|consen 477 RPTS 480 (564)
T ss_pred CCcc
Confidence 6664
No 11
>KOG2769 consensus Putative u4/u6 small nuclear ribonucleoprotein [RNA processing and modification]
Probab=52.72 E-value=20 Score=42.10 Aligned_cols=54 Identities=24% Similarity=0.330 Sum_probs=39.6
Q ss_pred HHHHHHHHhhC-ceeEEeecCCCCCCcHHHHHHHHh------hccCcEEEeeeCCeEEEEec
Q 003706 479 AKAMVKLWEKS-AIAKIAIKRDVMNTRNERMAEELK------KLTGGTLLCRNKDYIVFYRG 533 (801)
Q Consensus 479 a~aI~k~wek~-~lakI~~K~gv~~T~~~~m~~eLk------~LTGgvLLSRnke~IVlYRG 533 (801)
+++++++||.. -.|.+-| .++.+..+...=++++ .|||++++.++.+.||+=-|
T Consensus 375 eKk~rKl~ED~st~v~~~V-~r~K~l~~p~~rFKve~NAkql~ltG~~vl~~d~~vvVvEGg 435 (522)
T KOG2769|consen 375 EKKERKLFEDPSTGVHCSV-YRIKNLQNPKKRFKVEMNAKQLQLTGVCVLHRDMNVVVVEGG 435 (522)
T ss_pred HHHHhhhccCCCceEEEEE-EEEecccCCccceeeeechhhhceeeeEEEecCCcEEEEecC
Confidence 46788999987 6666666 5565555554444444 69999999999999998833
No 12
>PF11211 DUF2997: Protein of unknown function (DUF2997); InterPro: IPR021375 This family of proteins has no known function.
Probab=31.40 E-value=65 Score=26.82 Aligned_cols=32 Identities=9% Similarity=0.115 Sum_probs=28.4
Q ss_pred eEEeecCCCCCCcHHHHHHHHhhccCcEEEeeeC
Q 003706 492 AKIAIKRDVMNTRNERMAEELKKLTGGTLLCRNK 525 (801)
Q Consensus 492 akI~~K~gv~~T~~~~m~~eLk~LTGgvLLSRnk 525 (801)
|.+.++ |+.|.++..+.+.|+++.|.+. +|+.
T Consensus 11 V~~~v~-G~~G~~C~~~t~~lE~~LG~v~-~~e~ 42 (48)
T PF11211_consen 11 VEEEVE-GFKGSSCLEATAALEEALGTVT-SREL 42 (48)
T ss_pred EEEEEE-eccChhHHHHHHHHHHHhCcee-eeec
Confidence 677885 9999999999999999999998 7764
No 13
>KOG1257 consensus NADP+-dependent malic enzyme [Energy production and conversion]
Probab=28.32 E-value=1.4e+02 Score=35.95 Aligned_cols=85 Identities=20% Similarity=0.276 Sum_probs=64.3
Q ss_pred HHHHHHHHhhhcCCCeEEeCCCCC----CHHHHHHHHHHhhhCCeEEEEecCCChHhHHHHHHHHHHHhCCeEEEEEccE
Q 003706 253 HELQRLRNISLRMLERTKVGSAGI----TQALVDSIHEKWKLDEVVKLKFEEPHSLQMKRTHEILERRTGGLVIWRSGSS 328 (801)
Q Consensus 253 kErr~LRklAh~LkpvV~IGK~GV----Td~VVeeIh~awk~hELVKVK~~~~~~~dm~~~~e~LEekTGG~VVqrIG~v 328 (801)
++.+-|-..-..+||.|.||-.|+ |+.|++.++.+ +|==-|--+-+++..+.-++++.=.-|+|.+|...|+-
T Consensus 376 ~~~~~L~e~V~~vKPtvLiG~S~~~g~Fteevl~~Ma~~---~erPiIFalSNPT~~aECtae~ay~~t~Gr~ifaSGSP 452 (582)
T KOG1257|consen 376 EEIKDLEEAVKEVKPTVLIGASGVGGAFTEEVLRAMAKS---NERPIIFALSNPTSKAECTAEQAYKWTKGRAIFASGSP 452 (582)
T ss_pred hHHHHHHHHHHhcCCcEEEecccCCccCCHHHHHHHHhc---CCCceEEecCCCccccccCHHHHhhhcCCcEEEecCCC
Confidence 455578888889999999999986 77788877765 44444555678888888899999999999999999974
Q ss_pred E--EEeecCCCCCC
Q 003706 329 V--VLFRGMAYKLP 340 (801)
Q Consensus 329 i--VLYRGknY~~P 340 (801)
+ |-|-|+-|...
T Consensus 453 F~pV~~~gK~~~pg 466 (582)
T KOG1257|consen 453 FPPVEYNGKVYVPG 466 (582)
T ss_pred CCCceeCCcEeccc
Confidence 3 44445544433
No 14
>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=26.39 E-value=8.5 Score=38.92 Aligned_cols=93 Identities=20% Similarity=0.233 Sum_probs=59.0
Q ss_pred HHHHHHHHHHHHHHHHHH-----HHHHhhcc---cCCCCCCCCCCCCCCHHHHHHHHHcccCCCceE------eeCCCCC
Q 003706 622 RYLEQKLALAKRKLKMAD-----KALAKVQE---SLDPAELPSDLETITNEERFLLRKMGLSMKPYL------LLGRRGI 687 (801)
Q Consensus 622 k~~e~kL~~a~~K~~rae-----~~L~K~~~---~~~P~e~~~d~E~LT~eERk~LRklGhkLKPvV------~IGK~GV 687 (801)
-++|.||+.|+.++-..| +.|.++-. ..--+.-..|.+-|+..++..++++...|.|++ +--|.=+
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 358888888887544433 33333311 122334456888999999999999999999986 2234446
Q ss_pred CHHHHHHHHHHHHhcceEEEEEcCCCH
Q 003706 688 YDGTIENMHLHWKYRELVKIIVKGKSF 714 (801)
Q Consensus 688 tdgVIeeI~~aLk~hELVKVkv~~~~~ 714 (801)
++.=.+.--.||-.+|.|+|+......
T Consensus 107 t~~E~d~y~eALm~~e~v~vk~~~~~~ 133 (162)
T PF12207_consen 107 TQEEYDQYIEALMTYETVRVKTKSSGG 133 (162)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHCT-SS-
T ss_pred CHHHHHHHHHHHhhhheeeeeccCCCC
Confidence 666677777899999999998875443
No 15
>PF15249 GLTSCR1: Glioma tumor suppressor candidate region
Probab=23.33 E-value=31 Score=32.53 Aligned_cols=24 Identities=46% Similarity=0.823 Sum_probs=16.3
Q ss_pred CCCCCCCCc--------ccCCCCCCCCCChHH
Q 003706 429 VVPDYKPPL--------RLLPYGIKPGLRDCE 452 (801)
Q Consensus 429 vvPgy~~Pf--------RllP~gv~~~Ls~~E 452 (801)
.-|.|++|| |||||.|=......+
T Consensus 13 ~~PD~~tPF~s~~DA~~RLLPYHv~~~~~~~~ 44 (109)
T PF15249_consen 13 LNPDYKTPFRSLEDAVERLLPYHVFQEPEEDE 44 (109)
T ss_pred hCCCcCCCCCCHHHHHHHhcchhhhcCCCCCh
Confidence 357788888 678887766555444
No 16
>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=21.86 E-value=1.4e+02 Score=28.83 Aligned_cols=37 Identities=27% Similarity=0.398 Sum_probs=30.2
Q ss_pred HHHHHHHcccCCC-ceEeeCCCCCCHHHHHHHHHHHHh
Q 003706 665 ERFLLRKMGLSMK-PYLLLGRRGIYDGTIENMHLHWKY 701 (801)
Q Consensus 665 ERk~LRklGhkLK-PvV~IGK~GVtdgVIeeI~~aLk~ 701 (801)
+--.+.++|.+-+ |++.++.+|.++.+++.++...+.
T Consensus 72 ~~~~~~~l~~~~~~Piil~~~~g~w~~l~~~l~~~~~~ 109 (133)
T PF03641_consen 72 EALTLMQLGRHNKVPIILLNIDGFWDPLLEFLDRMIEE 109 (133)
T ss_dssp HHHHHHHTTSSTS-EEEEEECGGCCHHHHHHHHHHHHT
T ss_pred HHHHHHhhccccCCCEEEeCCcchHHHHHHHHHHHHHC
Confidence 4455678888888 999999999999999999755443
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=21.78 E-value=5.3e+02 Score=22.49 Aligned_cols=55 Identities=15% Similarity=0.180 Sum_probs=37.3
Q ss_pred HHHHHHHhhhCCeEEEEecCCChHhHHHHHHHHHH---HhCCeEEEEEccEEEEeecCC
Q 003706 281 VDSIHEKWKLDEVVKLKFEEPHSLQMKRTHEILER---RTGGLVIWRSGSSVVLFRGMA 336 (801)
Q Consensus 281 VeeIh~awk~hELVKVK~~~~~~~dm~~~~e~LEe---kTGG~VVqrIG~viVLYRGkn 336 (801)
+.+|-++++....|-+.+..-.....+++.+.|.- ..+|.+.+. |..++||=..|
T Consensus 12 ~~~i~~~l~~g~~Vivnl~~l~~~~~~Ri~Dfl~G~~~al~G~i~~i-~~~~~l~~P~~ 69 (73)
T PF04472_consen 12 AREIVDALREGKIVIVNLENLDDEEAQRILDFLSGAVYALDGDIQKI-SEKVFLLTPKG 69 (73)
T ss_dssp HHHHHHHHHTT--EEEE-TTS-HHHHHHHHHHHHHHHHHTT-EEEEE-ETTEEEEE---
T ss_pred HHHHHHHHHcCCEEEEECCCCCHHHHHHHHHHHhchheeeCCEEEEE-cCCEEEEECCC
Confidence 45688999999999999999888888888888764 678888776 55566665444
No 18
>PF15237 PTRF_SDPR: PTRF/SDPR family
Probab=21.25 E-value=1.9e+02 Score=31.71 Aligned_cols=64 Identities=30% Similarity=0.441 Sum_probs=51.4
Q ss_pred hHHHHHHHHHHhhCceeEEeecCCCCCCcHHHHHHHHhhc--cCcEEEeeeCCeEEEEecCCCCChhh
Q 003706 476 QGLAKAMVKLWEKSAIAKIAIKRDVMNTRNERMAEELKKL--TGGTLLCRNKDYIVFYRGNDFLPPVV 541 (801)
Q Consensus 476 ~gLa~aI~k~wek~~lakI~~K~gv~~T~~~~m~~eLk~L--TGgvLLSRnke~IVlYRGkdf~p~~V 541 (801)
.+-+.++-++.+|+.=|-+++| -| ....++=|...|+| +-+-||-||++.+++|-+..=+|..+
T Consensus 54 ~~TsnTV~KLLeK~RKVS~~vk-~V-r~r~ekQ~~qVkklE~n~~eLL~Rn~FkVlI~Qee~eiPa~~ 119 (246)
T PF15237_consen 54 STTSNTVNKLLEKTRKVSVNVK-EV-RERLEKQAAQVKKLEANHAELLKRNKFKVLIFQEENEIPASV 119 (246)
T ss_pred ccHHHHHHHHHHHHHHhhhhHH-HH-HHHHHHHHHHHhhhhccHHHHhhccCceEEeccccccCCCcc
Confidence 3456889999999998888886 33 34566667777765 56789999999999999999999884
Done!