Query 003572
Match_columns 810
No_of_seqs 342 out of 1042
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 01:58:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003572.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003572hhsearch_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 6.6E-73 1.4E-77 637.2 21.6 523 238-807 3-530 (564)
2 PRK10343 RNA-binding protein Y 99.9 8.3E-25 1.8E-29 198.7 13.4 96 659-760 1-96 (97)
3 PF01985 CRS1_YhbY: CRS1 / Yhb 99.9 8.8E-25 1.9E-29 192.7 11.0 84 250-333 1-84 (84)
4 TIGR00253 RNA_bind_YhbY putati 99.9 2E-24 4.4E-29 195.6 13.2 87 661-751 1-87 (95)
5 PRK10343 RNA-binding protein Y 99.9 2.6E-24 5.7E-29 195.5 12.5 88 248-335 1-88 (97)
6 TIGR00253 RNA_bind_YhbY putati 99.9 6E-24 1.3E-28 192.5 12.4 86 250-335 1-86 (95)
7 PF01985 CRS1_YhbY: CRS1 / Yhb 99.9 1.1E-23 2.4E-28 185.8 10.7 84 661-748 1-84 (84)
8 COG1534 Predicted RNA-binding 99.9 3.1E-23 6.7E-28 188.2 12.3 97 660-761 1-97 (97)
9 COG1534 Predicted RNA-binding 99.9 4.6E-22 1E-26 180.6 11.9 85 249-333 1-85 (97)
10 KOG1990 Poly(A)-specific exori 98.7 2.3E-08 4.9E-13 115.1 7.1 283 247-541 172-480 (564)
11 KOG2769 Putative u4/u6 small n 52.1 21 0.00046 42.0 5.1 54 479-533 375-435 (522)
12 COG1623 Predicted nucleic-acid 29.3 1.4E+02 0.003 33.8 6.5 76 715-802 105-181 (349)
13 PF11211 DUF2997: Protein of u 28.9 75 0.0016 26.5 3.5 33 491-525 10-42 (48)
14 PF12207 DUF3600: Domain of un 28.3 7.6 0.00017 39.3 -2.8 93 622-714 27-133 (162)
15 KOG1257 NADP+-dependent malic 25.8 1.7E+02 0.0036 35.4 6.8 84 253-339 376-465 (582)
16 PF15249 GLTSCR1: Glioma tumor 23.7 30 0.00066 32.6 0.4 24 429-452 13-44 (109)
17 PF15237 PTRF_SDPR: PTRF/SDPR 23.2 1.4E+02 0.0031 32.5 5.3 65 476-542 54-120 (246)
18 PF03641 Lysine_decarbox: Poss 21.3 1.5E+02 0.0031 28.7 4.5 36 666-701 73-109 (133)
No 1
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=100.00 E-value=6.6e-73 Score=637.24 Aligned_cols=523 Identities=46% Similarity=0.647 Sum_probs=484.3
Q ss_pred cccchhhhhcCCCCHHHHHHHHHhhhcCCCeEEeCCCCCCHHHHHHHHHHhhhCCeEEEEecCCChHhHHHHHHHHHHHh
Q 003572 238 RRRSNTELAEKMIPEHELQRLRNISLRMLERTKVGSAGITQALVDSIHEKWKLDEVVKLKFEEPHSLQMKRTHEILERRT 317 (810)
Q Consensus 238 ~~~s~~~lae~tLT~kErr~LRklAh~LkpvV~IGK~GLTd~VVeeIh~awk~~ELVKVK~~~~~~~dmk~a~e~LEekT 317 (810)
+..+ +.+|++++.+.++.+||..|.++...+ +++|+|+++++.|++.|+.+|+++++|....+.+|.+.+++++..|
T Consensus 3 ~~~~-~~~~~~~~~~~~~~~l~~~~~~~~~~~--~~~~~~~~~~~~~y~k~k~~~~~~~~~q~~~~~~~~~~~~~~~~~~ 79 (564)
T KOG1990|consen 3 NFES-LSLAELTVDEADLRRLRLVATGMTSAP--WKAGSTFDTVEAIYLKWKDNEEVYLKFQFGLCLFMKRSHEALEMST 79 (564)
T ss_pred cccc-hhHHHhhcCHHHHHHHhhhhccceecc--cccccchhhhHHHHHHHHhhhhhheeeccccchhHHHhhhHhhccC
Confidence 4556 999999999999999999999998888 9999999999999999999999999999999999999999999999
Q ss_pred CC-eEEEEEccEEEEeecCCCCCCCcccccccccccccccccchhhcccCCCCCCCccccCCCCcccccccchHHHHhhH
Q 003572 318 GG-LVIWRSGSSVVLFRGMAYKLPCVQSFTKHNHTQQTQDVTNEVMRNVGEHPPRSAMESYVPDSANNLENLSKEELMDL 396 (810)
Q Consensus 318 Gg-~VVqrIG~viVLYRG~nY~~p~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~ee~~~~ 396 (810)
|| .+||+.|.....|++..|..|..-.... .+ ....... ....
T Consensus 80 ~~n~~~~~~g~~~s~~~~~~~~~~~~~~~~~--------------------------~~--------~~~~~~~--~~~~ 123 (564)
T KOG1990|consen 80 GGNFVVWSRGDSISSPEFLCQRSPVDFVARQ--------------------------QE--------NQAGKWP--SELE 123 (564)
T ss_pred CCceeeeecCccccCCccceeecchhhhhhh--------------------------ch--------hhhhhhH--HHHH
Confidence 99 9999999999999999999884211000 00 0000101 1236
Q ss_pred hhhhhhhcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccCCCCCCCCCChHHHHHHHHhhhcCCCceEecccchhh
Q 003572 397 CELNYLLDELGPRFKDWPGREPLPVDADLLPPVVPDYKPPLRLLPYGIKPGLRDCETTEFRRLARKTPPHFALGRNRELQ 476 (810)
Q Consensus 397 ~E~n~LLD~LGPRf~dW~g~~PlPVDaDLLP~vvPgy~~PfRllP~gv~~~Ls~~E~t~LRk~ar~lpph~aLGRn~~~~ 476 (810)
++.+.++|++||+|.|||+.+|+|+|+||+|++||+|.+|||.+|+|++++|+..|++.+|++|..+||||++|+++.++
T Consensus 124 ~~~~~~~~~~~~~~~~~~~~~~~~~~~dl~~~~i~~~~~p~r~l~~~~~~~l~~~~~~~~r~~~~~~p~~~~~~~~~~~~ 203 (564)
T KOG1990|consen 124 KEKNELLDSLGPELSDWGGSDRLSVDADLLPEKIPDYMRPFRTLPVGSPPLLTSIESTLLRRLGYKLPPHFALGRSRKLQ 203 (564)
T ss_pred HHHHHHhhccCcccccCCCCCCccchhhhchhhhhcccChhccCCCCChhhhhhHHHHHHHHhcccccccceehhccccc
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhhCceeEEeecCCCCCCcHHHHHHHH--hhccCcEEEeeeCCeEEEEecCCCCChhhhhHHHHhhhhhhh
Q 003572 477 GLAKAMVKLWEKSAIAKIAIKRDVMNTRNERMAEEL--KKLTGGTLLCRNKDYIVFYRGNDFLPPVVTDAVKERSKLTDI 554 (810)
Q Consensus 477 gLa~aI~k~wek~~lakI~~K~gv~~T~~~~m~~eL--k~LTGgvLLSRnke~IVlYRGkdf~p~~Va~al~ERe~~~~~ 554 (810)
|++.+|+.+|++|+++++.|++|++.+..+.||.+| ..+||++|++||+.++|+|||++|++ .|.++|.++......
T Consensus 204 ~~~~~~~~~~~k~~~~k~~~~rg~~~~~~~~~a~~l~~~~~tg~~lv~hN~~~dv~y~~~~Fl~-~lp~~l~~f~~~~~~ 282 (564)
T KOG1990|consen 204 GLAVAMVSFWEKHEFAKILIKRGVLETRKERMADELQELLLTGKVLVLHNKLLDVMYRYKNFLS-PLPSTLEEFTDSSSM 282 (564)
T ss_pred cchhHHHHHHHHHHHHHHHHHhcchhhhccchHHHHHHHHhcCCeEEeeccceeeeeehhhccc-ccchhHHHhhhhhhh
Confidence 999999999999999999999999999999999999 99999999999999999999999999 999999999999888
Q ss_pred hhhHHHHhhhhhhHHHHhhccccccccccccHHHHHHHhhhccCCCChhHHH-HHHHhhhhHHHHHHHHHHHHHHHHHHH
Q 003572 555 RQDEEERARHVASALIELKAKGFVGSLVAGTLAETLAATSRWGRQPSYEDVE-KMMRDSTLSRHASLLRYLEQKLALAKR 633 (810)
Q Consensus 555 ~q~eEE~aR~~~~~~~~~~~~~~~~~~~aGtl~E~~~a~~~wg~~~~~~~~~-~~~~e~~~~~~~~~~k~~e~kL~~a~~ 633 (810)
.++.++.+|..... + ......+||+.|+..+.++|+......+.. .+..+......+...+.+.++++.+..
T Consensus 283 fp~~~~~~~~~~~~---~----~~~~~~~~t~~e~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~ 355 (564)
T KOG1990|consen 283 FPNIEDTKRLAKLS---E----YQKLNLKATLLELARAKAKKEKEIERRSISSRLKLEFEKASSEKLTEAIFHKLEKAKK 355 (564)
T ss_pred hhhhHHHHHhhccc---c----ccchhhhhhHHHHHHHhcccccCcccccccchhhhhhhccchhhHHHHHHHHHhhhhh
Confidence 89999999966511 1 112357899999999999999999877653 678888999999999999999999999
Q ss_pred HHHHHHHHHHhhcccCCCCCCCCCCCCCCHHHHHHHHHcccCCCceEeeCCCCCCHHHHHHHHHHHHhCceEEEEEcCCC
Q 003572 634 KLKMADKALAKVQESLDPAELPSDLETITNEERFLLRKMGLSMKPYLLLGRRGIYDGTIENMHLHWKYRELVKIIVKGKS 713 (810)
Q Consensus 634 K~~rae~~L~K~~~~~~P~e~~~d~E~LT~eQRk~LRkiGhkLkPvV~IGK~GVtdgVIeeIh~aLk~hELVKVkv~~~~ 713 (810)
|+..+...|++++.+..|.+..+|++.+|.+++.+++++|.+|++++.+|++|+++|+|.++|.||++||++|++|+...
T Consensus 356 ~~~~~~~~l~~~~~~~~~~~~~~~~e~~t~ee~~~~~k~g~k~~~~~~~~rrg~f~g~i~n~~l~wk~~e~~k~i~~~~~ 435 (564)
T KOG1990|consen 356 KLASANRILAKLEDPKIPAELRYDPESITEEERLMLRKVGLKMKRRLLSGRRGVFDGVIENMHLHWKSRELVKVICKEKN 435 (564)
T ss_pred hccchhhhhhcccccccccccccchhhcChHHHHHHHHHHHhhccccccCCcccccceeecchhhhhhcccceeeecccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999987
Q ss_pred H-HHHHHHHHHHHHHhCCEEEEeeecCCCcEEEEEccCCCCCCccCCCcccccHHHHHHHhHHHHHhhhhhHHHHHHHHH
Q 003572 714 F-AQVKQIAISLEAESGGVLVSLDKTPKGIAIIVYRGKNYVRPLKLRPQNLLTRRQALARSVELQRREGLKHHILDLQER 792 (810)
Q Consensus 714 ~-ed~keiA~~Le~~SGgeLVqvik~~iG~tIILYRgkNY~rP~~l~P~nlLtKrkAl~rs~e~qr~~sl~~~i~~l~~~ 792 (810)
. .+++..|..++..+|+++|+++++..|++|+.|||+||++|..+.|.|+|+|++|+.+|+++|++++++.||..++.+
T Consensus 436 ~~~~~~~~a~~le~esg~~~v~~~~~~~~~ai~~yr~k~y~~p~~l~P~~~l~~~k~~~~~~~~~~~~a~~~~i~~~~~~ 515 (564)
T KOG1990|consen 436 LPSQVKQYASALERESGGILVSIDKNPKGYAIIAYRGKNYDRPTSLRPRNLLSRRKALERSLEEQRKEALKSHISDLEQE 515 (564)
T ss_pred ccHHHHHHHHHHHHHhCCceeeeccCCchhhHHHhhhhhccCCcccCchhhhcccCCccccHHHHHHHHHhhhcchhhhh
Confidence 6 999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhcCC
Q 003572 793 IELVKSELEEIEGGK 807 (810)
Q Consensus 793 i~~l~~~l~~~~~~~ 807 (810)
+++++.++..|...+
T Consensus 516 ~e~~~~~~~~~~~~~ 530 (564)
T KOG1990|consen 516 IEQLQASVEAMPAIN 530 (564)
T ss_pred HHHhhcchhcccccc
Confidence 999999998876554
No 2
>PRK10343 RNA-binding protein YhbY; Provisional
Probab=99.92 E-value=8.3e-25 Score=198.74 Aligned_cols=96 Identities=20% Similarity=0.381 Sum_probs=89.6
Q ss_pred CCCCHHHHHHHHHcccCCCceEeeCCCCCCHHHHHHHHHHHHhCceEEEEEcCCCHHHHHHHHHHHHHHhCCEEEEeeec
Q 003572 659 ETITNEERFLLRKMGLSMKPYLLLGRRGIYDGTIENMHLHWKYRELVKIIVKGKSFAQVKQIAISLEAESGGVLVSLDKT 738 (810)
Q Consensus 659 E~LT~eQRk~LRkiGhkLkPvV~IGK~GVtdgVIeeIh~aLk~hELVKVkv~~~~~ed~keiA~~Le~~SGgeLVqvik~ 738 (810)
++||++||++||++||+|+|+|+||++||||+|+++|+++|++||||||++.+++.+++++++++|++.+||++||+|
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 469999999999999999999999999999999999999999999999999999999999999999999999999986
Q ss_pred CCCcEEEEEccCCCCCCccCCC
Q 003572 739 PKGIAIIVYRGKNYVRPLKLRP 760 (810)
Q Consensus 739 ~iG~tIILYRgkNY~rP~~l~P 760 (810)
|+++||||.++ .|.+.+|
T Consensus 79 --G~~~vlYR~~~--~~~i~lp 96 (97)
T PRK10343 79 --GKTLVLYRPTK--ERKISLP 96 (97)
T ss_pred --CcEEEEEecCC--CccCCCC
Confidence 99999999875 2444455
No 3
>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=8.8e-25 Score=192.74 Aligned_cols=84 Identities=25% Similarity=0.417 Sum_probs=75.7
Q ss_pred CCHHHHHHHHHhhhcCCCeEEeCCCCCCHHHHHHHHHHhhhCCeEEEEecCCChHhHHHHHHHHHHHhCCeEEEEEccEE
Q 003572 250 IPEHELQRLRNISLRMLERTKVGSAGITQALVDSIHEKWKLDEVVKLKFEEPHSLQMKRTHEILERRTGGLVIWRSGSSV 329 (810)
Q Consensus 250 LT~kErr~LRklAh~LkpvV~IGK~GLTd~VVeeIh~awk~~ELVKVK~~~~~~~dmk~a~e~LEekTGg~VVqrIG~vi 329 (810)
||++|+++||++||+|+|+|+|||+|||++|+++|+++|++||||||+|.+++..+++++++.|+++|||++||++|+++
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 003572 330 VLFR 333 (810)
Q Consensus 330 VLYR 333 (810)
||||
T Consensus 81 vlyR 84 (84)
T PF01985_consen 81 VLYR 84 (84)
T ss_dssp EEEE
T ss_pred EEEC
Confidence 9998
No 4
>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=2e-24 Score=195.55 Aligned_cols=87 Identities=29% Similarity=0.472 Sum_probs=85.0
Q ss_pred CCHHHHHHHHHcccCCCceEeeCCCCCCHHHHHHHHHHHHhCceEEEEEcCCCHHHHHHHHHHHHHHhCCEEEEeeecCC
Q 003572 661 ITNEERFLLRKMGLSMKPYLLLGRRGIYDGTIENMHLHWKYRELVKIIVKGKSFAQVKQIAISLEAESGGVLVSLDKTPK 740 (810)
Q Consensus 661 LT~eQRk~LRkiGhkLkPvV~IGK~GVtdgVIeeIh~aLk~hELVKVkv~~~~~ed~keiA~~Le~~SGgeLVqvik~~i 740 (810)
||++||++||++||+|+|+|+||++||||+||++++++|++||||||++.+++.++++++|.+|++.+||++||+|
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 7999999999999999999999999999999999999999999999999999999999999999999999999986
Q ss_pred CcEEEEEccCC
Q 003572 741 GIAIIVYRGKN 751 (810)
Q Consensus 741 G~tIILYRgkN 751 (810)
|+++||||+++
T Consensus 77 G~~~vlYR~~~ 87 (95)
T TIGR00253 77 GKTIVLYRPTK 87 (95)
T ss_pred ccEEEEEecCC
Confidence 99999999864
No 5
>PRK10343 RNA-binding protein YhbY; Provisional
Probab=99.91 E-value=2.6e-24 Score=195.48 Aligned_cols=88 Identities=20% Similarity=0.322 Sum_probs=86.3
Q ss_pred CCCCHHHHHHHHHhhhcCCCeEEeCCCCCCHHHHHHHHHHhhhCCeEEEEecCCChHhHHHHHHHHHHHhCCeEEEEEcc
Q 003572 248 KMIPEHELQRLRNISLRMLERTKVGSAGITQALVDSIHEKWKLDEVVKLKFEEPHSLQMKRTHEILERRTGGLVIWRSGS 327 (810)
Q Consensus 248 ~tLT~kErr~LRklAh~LkpvV~IGK~GLTd~VVeeIh~awk~~ELVKVK~~~~~~~dmk~a~e~LEekTGg~VVqrIG~ 327 (810)
|+||++|+++||++||+|+|+|+|||+|||++|+++|.++|++||||||++++++.++.+++++.|+++||+++||.||+
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 46999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEeecC
Q 003572 328 SVVLFRGM 335 (810)
Q Consensus 328 viVLYRG~ 335 (810)
++||||.+
T Consensus 81 ~~vlYR~~ 88 (97)
T PRK10343 81 TLVLYRPT 88 (97)
T ss_pred EEEEEecC
Confidence 99999986
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=6e-24 Score=192.48 Aligned_cols=86 Identities=21% Similarity=0.339 Sum_probs=84.7
Q ss_pred CCHHHHHHHHHhhhcCCCeEEeCCCCCCHHHHHHHHHHhhhCCeEEEEecCCChHhHHHHHHHHHHHhCCeEEEEEccEE
Q 003572 250 IPEHELQRLRNISLRMLERTKVGSAGITQALVDSIHEKWKLDEVVKLKFEEPHSLQMKRTHEILERRTGGLVIWRSGSSV 329 (810)
Q Consensus 250 LT~kErr~LRklAh~LkpvV~IGK~GLTd~VVeeIh~awk~~ELVKVK~~~~~~~dmk~a~e~LEekTGg~VVqrIG~vi 329 (810)
||++|+++||++||+|+|+|+|||+|||++|+++|+++|++||||||++++++..+.+++++.|+++||+++||.||+++
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 003572 330 VLFRGM 335 (810)
Q Consensus 330 VLYRG~ 335 (810)
||||++
T Consensus 81 vlYR~~ 86 (95)
T TIGR00253 81 VLYRPT 86 (95)
T ss_pred EEEecC
Confidence 999986
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=1.1e-23 Score=185.81 Aligned_cols=84 Identities=36% Similarity=0.584 Sum_probs=75.2
Q ss_pred CCHHHHHHHHHcccCCCceEeeCCCCCCHHHHHHHHHHHHhCceEEEEEcCCCHHHHHHHHHHHHHHhCCEEEEeeecCC
Q 003572 661 ITNEERFLLRKMGLSMKPYLLLGRRGIYDGTIENMHLHWKYRELVKIIVKGKSFAQVKQIAISLEAESGGVLVSLDKTPK 740 (810)
Q Consensus 661 LT~eQRk~LRkiGhkLkPvV~IGK~GVtdgVIeeIh~aLk~hELVKVkv~~~~~ed~keiA~~Le~~SGgeLVqvik~~i 740 (810)
||++|+++||++||+|+|+|+|||+|||++|+++|+++|++||||||+|.+++.++++++|+.|++.|||++|+++
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 7999999999999999999999999999999999999999999999999999999999999999999999999986
Q ss_pred CcEEEEEc
Q 003572 741 GIAIIVYR 748 (810)
Q Consensus 741 G~tIILYR 748 (810)
|+++||||
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=3.1e-23 Score=188.16 Aligned_cols=97 Identities=27% Similarity=0.465 Sum_probs=91.2
Q ss_pred CCCHHHHHHHHHcccCCCceEeeCCCCCCHHHHHHHHHHHHhCceEEEEEcCCCHHHHHHHHHHHHHHhCCEEEEeeecC
Q 003572 660 TITNEERFLLRKMGLSMKPYLLLGRRGIYDGTIENMHLHWKYRELVKIIVKGKSFAQVKQIAISLEAESGGVLVSLDKTP 739 (810)
Q Consensus 660 ~LT~eQRk~LRkiGhkLkPvV~IGK~GVtdgVIeeIh~aLk~hELVKVkv~~~~~ed~keiA~~Le~~SGgeLVqvik~~ 739 (810)
+||++|+++||+.||+++|+|+||++|||++||.+|+++|++||||||++.+++.++++++|+.|++.+||.+||+|
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 59999999999999999999999999999999999999999999999999999999999999999999999999986
Q ss_pred CCcEEEEEccCCCCCCccCCCc
Q 003572 740 KGIAIIVYRGKNYVRPLKLRPQ 761 (810)
Q Consensus 740 iG~tIILYRgkNY~rP~~l~P~ 761 (810)
|+++|||| .+..++.+.+|+
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=4.6e-22 Score=180.55 Aligned_cols=85 Identities=22% Similarity=0.381 Sum_probs=84.1
Q ss_pred CCCHHHHHHHHHhhhcCCCeEEeCCCCCCHHHHHHHHHHhhhCCeEEEEecCCChHhHHHHHHHHHHHhCCeEEEEEccE
Q 003572 249 MIPEHELQRLRNISLRMLERTKVGSAGITQALVDSIHEKWKLDEVVKLKFEEPHSLQMKRTHEILERRTGGLVIWRSGSS 328 (810)
Q Consensus 249 tLT~kErr~LRklAh~LkpvV~IGK~GLTd~VVeeIh~awk~~ELVKVK~~~~~~~dmk~a~e~LEekTGg~VVqrIG~v 328 (810)
+||++|+++||+.||+++|+|+|||+|||++|+.+|.++|++||||||++.+++.+|.+.+++.|++++|+.+||+||++
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 003572 329 VVLFR 333 (810)
Q Consensus 329 iVLYR 333 (810)
+||||
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=98.69 E-value=2.3e-08 Score=115.10 Aligned_cols=283 Identities=18% Similarity=0.247 Sum_probs=182.6
Q ss_pred cCCCCHHHHHHHHHhhhcCCCeEEeCCCCCCHHHHHHHHHHhhhCCeEEEEecCCChH-hHHHHHHHH--HHHhCCeEEE
Q 003572 247 EKMIPEHELQRLRNISLRMLERTKVGSAGITQALVDSIHEKWKLDEVVKLKFEEPHSL-QMKRTHEIL--ERRTGGLVIW 323 (810)
Q Consensus 247 e~tLT~kErr~LRklAh~LkpvV~IGK~GLTd~VVeeIh~awk~~ELVKVK~~~~~~~-dmk~a~e~L--EekTGg~VVq 323 (810)
...|+..+.-.+|.+|-...+.+.+|..+.-+++.-.+...|..|+..|+-+...... .-..++.++ -..||+.+|-
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 3458999999999999999999999999999999999999999999999777654433 334577777 8899999999
Q ss_pred EEccEEEEeecCCCCCCCcccc-ccccc-ccccccccchhhcc--cCCCC--CCCccccCC---------CCcccccccc
Q 003572 324 RSGSSVVLFRGMAYKLPCVQSF-TKHNH-TQQTQDVTNEVMRN--VGEHP--PRSAMESYV---------PDSANNLENL 388 (810)
Q Consensus 324 rIG~viVLYRG~nY~~p~~~~~-~k~~~-~~~~~~~~~~~~~~--~~~~~--~~~~~~~~~---------p~~~~~~~~~ 388 (810)
+-|-..++||++||-.| ..+. ....+ ...-++........ ....+ +..+..+.. +....+...+
T Consensus 252 hN~~~dv~y~~~~Fl~~-lp~~l~~f~~~~~~fp~~~~~~~~~~~~~~~~~~~~~t~~e~~~~~~~~~~~~~~~~~~~~~ 330 (564)
T KOG1990|consen 252 HNKLLDVMYRYKNFLSP-LPSTLEEFTDSSSMFPNIEDTKRLAKLSEYQKLNLKATLLELARAKAKKEKEIERRSISSRL 330 (564)
T ss_pred eccceeeeeehhhcccc-cchhHHHhhhhhhhhhhhHHHHHhhccccccchhhhhhHHHHHHHhcccccCcccccccchh
Confidence 99999999999999884 3321 10000 00000000000000 01111 111110000 0000111011
Q ss_pred hHH-HHhhHh---hhhhhhcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccCCCCCCCCCChHHHHHHHHhhhcCC
Q 003572 389 SKE-ELMDLC---ELNYLLDELGPRFKDWPGREPLPVDADLLPPVVPDYKPPLRLLPYGIKPGLRDCETTEFRRLARKTP 464 (810)
Q Consensus 389 ~~e-e~~~~~---E~n~LLD~LGPRf~dW~g~~PlPVDaDLLP~vvPgy~~PfRllP~gv~~~Ls~~E~t~LRk~ar~lp 464 (810)
..+ +.+... +........|-++.-|- .+.=+.+-+.-.|.=. +.+| ..+|++|..++++.+.++-
T Consensus 331 ~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~l~~~~~~~~~~~~---~~~~----e~~t~ee~~~~~k~g~k~~ 399 (564)
T KOG1990|consen 331 KLEFEKASSEKLTEAIFHKLEKAKKKLASA----NRILAKLEDPKIPAEL---RYDP----ESITEEERLMLRKVGLKMK 399 (564)
T ss_pred hhhhhccchhhHHHHHHHHHhhhhhhccch----hhhhhccccccccccc---ccch----hhcChHHHHHHHHHHHhhc
Confidence 110 010000 00000011111111110 0000000000011000 1344 7799999999999999999
Q ss_pred CceEecccchhhHHHHHHHHHHhhCceeEEeecCCCCCCcHHHHHHHHhhccCcEEEeeeC---Ce-EEEEecCCCCChh
Q 003572 465 PHFALGRNRELQGLAKAMVKLWEKSAIAKIAIKRDVMNTRNERMAEELKKLTGGTLLCRNK---DY-IVFYRGNDFLPPV 540 (810)
Q Consensus 465 ph~aLGRn~~~~gLa~aI~k~wek~~lakI~~K~gv~~T~~~~m~~eLk~LTGgvLLSRnk---e~-IVlYRGkdf~p~~ 540 (810)
.-.-+||=|+..|+.-.++.||..++.+++-||..-.....++.|..|..+.||++++=++ .| |++|||++|.=+.
T Consensus 400 ~~~~~~rrg~f~g~i~n~~l~wk~~e~~k~i~~~~~~~~~~~~~a~~le~esg~~~v~~~~~~~~~ai~~yr~k~y~~p~ 479 (564)
T KOG1990|consen 400 RRLLSGRRGVFDGVIENMHLHWKSRELVKVICKEKNLPSQVKQYASALERESGGILVSIDKNPKGYAIIAYRGKNYDRPT 479 (564)
T ss_pred cccccCCcccccceeecchhhhhhcccceeeeccccccHHHHHHHHHHHHHhCCceeeeccCCchhhHHHhhhhhccCCc
Confidence 9999999999999999999999999999999998888899999999999999999998655 44 8999999998666
Q ss_pred h
Q 003572 541 V 541 (810)
Q Consensus 541 V 541 (810)
.
T Consensus 480 ~ 480 (564)
T KOG1990|consen 480 S 480 (564)
T ss_pred c
Confidence 4
No 11
>KOG2769 consensus Putative u4/u6 small nuclear ribonucleoprotein [RNA processing and modification]
Probab=52.10 E-value=21 Score=42.00 Aligned_cols=54 Identities=24% Similarity=0.330 Sum_probs=39.4
Q ss_pred HHHHHHHHhhC-ceeEEeecCCCCCCcHHHHHHHHh------hccCcEEEeeeCCeEEEEec
Q 003572 479 AKAMVKLWEKS-AIAKIAIKRDVMNTRNERMAEELK------KLTGGTLLCRNKDYIVFYRG 533 (810)
Q Consensus 479 a~aI~k~wek~-~lakI~~K~gv~~T~~~~m~~eLk------~LTGgvLLSRnke~IVlYRG 533 (810)
+++++++||.. -.|.+-| .++.+..+...=++++ .|||++++.++.+.||+=-|
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 5555555554444444 69999999999999998833
No 12
>COG1623 Predicted nucleic-acid-binding protein (contains the HHH domain) [General function prediction only]
Probab=29.27 E-value=1.4e+02 Score=33.82 Aligned_cols=76 Identities=18% Similarity=0.232 Sum_probs=50.4
Q ss_pred HHHHHHHHHHHHHhCCEEEEeeecCCCcEEEEEccCCCCCCccCCCcccccHHHHHHHhHHHHHhhhhhHHHHHHHHHHH
Q 003572 715 AQVKQIAISLEAESGGVLVSLDKTPKGIAIIVYRGKNYVRPLKLRPQNLLTRRQALARSVELQRREGLKHHILDLQERIE 794 (810)
Q Consensus 715 ed~keiA~~Le~~SGgeLVqvik~~iG~tIILYRgkNY~rP~~l~P~nlLtKrkAl~rs~e~qr~~sl~~~i~~l~~~i~ 794 (810)
..+...|+-.|..||..||+|- .--++|.||.+ |++.- .-=+-.+|||. -|-++.|..+-..|.+-+.
T Consensus 105 GtRHRTAER~AkqTG~~VIaiS--~rrNvITlY~~-~~ky~-L~d~~~il~ra--------nQAi~TLEkYk~~Ld~~~~ 172 (349)
T COG1623 105 GTRHRTAERVAKQTGNPVIAIS--ERRNVITLYVG-NLKYV-LKDSAFILSRA--------NQAIQTLEKYKTVLDRVLN 172 (349)
T ss_pred ccccchHHHHHHHhCCeEEEEe--cccceEEEEec-Ceeee-ecChHHHHHHH--------HHHHHHHHHHHHHHHHHhh
Confidence 4578899999999999999986 34579999986 55442 11234556653 4555666666666666666
Q ss_pred HHHH-HHHH
Q 003572 795 LVKS-ELEE 802 (810)
Q Consensus 795 ~l~~-~l~~ 802 (810)
.|.. |+++
T Consensus 173 ~L~~lEled 181 (349)
T COG1623 173 QLNLLELED 181 (349)
T ss_pred hhhhHHHhh
Confidence 5543 4433
No 13
>PF11211 DUF2997: Protein of unknown function (DUF2997); InterPro: IPR021375 This family of proteins has no known function.
Probab=28.91 E-value=75 Score=26.51 Aligned_cols=33 Identities=9% Similarity=0.087 Sum_probs=28.7
Q ss_pred eeEEeecCCCCCCcHHHHHHHHhhccCcEEEeeeC
Q 003572 491 IAKIAIKRDVMNTRNERMAEELKKLTGGTLLCRNK 525 (810)
Q Consensus 491 lakI~~K~gv~~T~~~~m~~eLk~LTGgvLLSRnk 525 (810)
-|.+.++ |+.|.++..+...|+++.|.|. +|+.
T Consensus 10 ~V~~~v~-G~~G~~C~~~t~~lE~~LG~v~-~~e~ 42 (48)
T PF11211_consen 10 RVEEEVE-GFKGSSCLEATAALEEALGTVT-SREL 42 (48)
T ss_pred EEEEEEE-eccChhHHHHHHHHHHHhCcee-eeec
Confidence 3677885 9999999999999999999998 7764
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=28.32 E-value=7.6 Score=39.30 Aligned_cols=93 Identities=20% Similarity=0.233 Sum_probs=59.3
Q ss_pred HHHHHHHHHHHHHHHHHH-----HHHHhhcc---cCCCCCCCCCCCCCCHHHHHHHHHcccCCCceE------eeCCCCC
Q 003572 622 RYLEQKLALAKRKLKMAD-----KALAKVQE---SLDPAELPSDLETITNEERFLLRKMGLSMKPYL------LLGRRGI 687 (810)
Q Consensus 622 k~~e~kL~~a~~K~~rae-----~~L~K~~~---~~~P~e~~~d~E~LT~eQRk~LRkiGhkLkPvV------~IGK~GV 687 (810)
-++|.||+.|+.++-..| +.|.++-. ..--+.-..|.+-||..++..++++...|.|++ +--|.=+
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 358888888887544333 33333311 122334456889999999999999999999986 2334456
Q ss_pred CHHHHHHHHHHHHhCceEEEEEcCCCH
Q 003572 688 YDGTIENMHLHWKYRELVKIIVKGKSF 714 (810)
Q Consensus 688 tdgVIeeIh~aLk~hELVKVkv~~~~~ 714 (810)
++.-.+.--.||-..|.|+|+......
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 666677777899999999999885443
No 15
>KOG1257 consensus NADP+-dependent malic enzyme [Energy production and conversion]
Probab=25.78 E-value=1.7e+02 Score=35.38 Aligned_cols=84 Identities=20% Similarity=0.285 Sum_probs=63.3
Q ss_pred HHHHHHHHhhhcCCCeEEeCCCCC----CHHHHHHHHHHhhhCCeEEEEecCCChHhHHHHHHHHHHHhCCeEEEEEccE
Q 003572 253 HELQRLRNISLRMLERTKVGSAGI----TQALVDSIHEKWKLDEVVKLKFEEPHSLQMKRTHEILERRTGGLVIWRSGSS 328 (810)
Q Consensus 253 kErr~LRklAh~LkpvV~IGK~GL----Td~VVeeIh~awk~~ELVKVK~~~~~~~dmk~a~e~LEekTGg~VVqrIG~v 328 (810)
++.+-|-..-..+||.|.||-.|+ |+.|++.++.. +|==-|=-+-|++..+.-+++..=.-|+|.+|...|+-
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 345578888889999999999986 77788877765 44444455668888888899999999999999999985
Q ss_pred E--EEeecCCCCC
Q 003572 329 V--VLFRGMAYKL 339 (810)
Q Consensus 329 i--VLYRG~nY~~ 339 (810)
+ |-|-|+-|..
T Consensus 453 F~pV~~~gK~~~p 465 (582)
T KOG1257|consen 453 FPPVEYNGKVYVP 465 (582)
T ss_pred CCCceeCCcEecc
Confidence 3 3344444443
No 16
>PF15249 GLTSCR1: Glioma tumor suppressor candidate region
Probab=23.71 E-value=30 Score=32.65 Aligned_cols=24 Identities=46% Similarity=0.823 Sum_probs=16.3
Q ss_pred CCCCCCCCc--------ccCCCCCCCCCChHH
Q 003572 429 VVPDYKPPL--------RLLPYGIKPGLRDCE 452 (810)
Q Consensus 429 vvPgy~~Pf--------RllP~gv~~~Ls~~E 452 (810)
.-|.|++|| |||||.|=......+
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 17
>PF15237 PTRF_SDPR: PTRF/SDPR family
Probab=23.23 E-value=1.4e+02 Score=32.55 Aligned_cols=65 Identities=29% Similarity=0.423 Sum_probs=52.0
Q ss_pred hHHHHHHHHHHhhCceeEEeecCCCCCCcHHHHHHHHhhc--cCcEEEeeeCCeEEEEecCCCCChhhh
Q 003572 476 QGLAKAMVKLWEKSAIAKIAIKRDVMNTRNERMAEELKKL--TGGTLLCRNKDYIVFYRGNDFLPPVVT 542 (810)
Q Consensus 476 ~gLa~aI~k~wek~~lakI~~K~gv~~T~~~~m~~eLk~L--TGgvLLSRnke~IVlYRGkdf~p~~Va 542 (810)
.+-+.++-+|.+|+.=|-+++| -| ....++=|...|+| +-+-||-||++.+++|-+..=+|..+.
T Consensus 54 ~~TsnTV~KLLeK~RKVS~~vk-~V-r~r~ekQ~~qVkklE~n~~eLL~Rn~FkVlI~Qee~eiPa~~~ 120 (246)
T PF15237_consen 54 STTSNTVNKLLEKTRKVSVNVK-EV-RERLEKQAAQVKKLEANHAELLKRNKFKVLIFQEENEIPASVF 120 (246)
T ss_pred ccHHHHHHHHHHHHHHhhhhHH-HH-HHHHHHHHHHHhhhhccHHHHhhccCceEEeccccccCCCccc
Confidence 3456889999999998888886 33 34566677777765 567899999999999999999998853
No 18
>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=21.30 E-value=1.5e+02 Score=28.70 Aligned_cols=36 Identities=25% Similarity=0.376 Sum_probs=29.4
Q ss_pred HHHHHHcccCCC-ceEeeCCCCCCHHHHHHHHHHHHh
Q 003572 666 RFLLRKMGLSMK-PYLLLGRRGIYDGTIENMHLHWKY 701 (810)
Q Consensus 666 Rk~LRkiGhkLk-PvV~IGK~GVtdgVIeeIh~aLk~ 701 (810)
--.+.++|.+-+ |++.++.+|.++.+++.++.....
T Consensus 73 ~~~~~~l~~~~~~Piil~~~~g~w~~l~~~l~~~~~~ 109 (133)
T PF03641_consen 73 ALTLMQLGRHNKVPIILLNIDGFWDPLLEFLDRMIEE 109 (133)
T ss_dssp HHHHHHTTSSTS-EEEEEECGGCCHHHHHHHHHHHHT
T ss_pred HHHHHhhccccCCCEEEeCCcchHHHHHHHHHHHHHC
Confidence 345677888888 999999999999999999755443
Done!