Query 003851
Match_columns 791
No_of_seqs 330 out of 1043
Neff 3.8
Searched_HMMs 46136
Date Thu Mar 28 13:10:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003851.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003851hhsearch_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 2.6E-71 5.7E-76 623.0 20.3 504 238-788 3-511 (564)
2 PRK10343 RNA-binding protein Y 99.9 9.1E-26 2E-30 204.5 13.3 97 659-761 1-97 (97)
3 TIGR00253 RNA_bind_YhbY putati 99.9 2.1E-25 4.6E-30 201.5 13.0 95 661-760 1-95 (95)
4 PF01985 CRS1_YhbY: CRS1 / Yhb 99.9 6E-25 1.3E-29 193.3 11.0 84 250-333 1-84 (84)
5 PRK10343 RNA-binding protein Y 99.9 1.3E-24 2.8E-29 197.1 12.6 88 248-335 1-88 (97)
6 TIGR00253 RNA_bind_YhbY putati 99.9 4.1E-24 9E-29 193.1 12.6 86 250-335 1-86 (95)
7 COG1534 Predicted RNA-binding 99.9 3.8E-24 8.2E-29 193.6 12.1 97 660-761 1-97 (97)
8 PF01985 CRS1_YhbY: CRS1 / Yhb 99.9 7.6E-24 1.7E-28 186.4 10.7 84 661-748 1-84 (84)
9 COG1534 Predicted RNA-binding 99.9 2.3E-22 5.1E-27 182.0 11.9 85 249-333 1-85 (97)
10 KOG1990 Poly(A)-specific exori 98.7 2E-08 4.3E-13 115.3 7.1 284 246-541 171-480 (564)
11 KOG2769 Putative u4/u6 small n 53.2 20 0.00042 42.2 5.0 54 479-533 375-435 (522)
12 PF12207 DUF3600: Domain of un 42.8 3.1 6.6E-05 41.9 -2.9 94 622-715 27-134 (162)
13 PF11211 DUF2997: Protein of u 30.2 70 0.0015 26.6 3.5 32 492-525 11-42 (48)
14 KOG1257 NADP+-dependent malic 26.3 1.6E+02 0.0035 35.5 6.8 84 253-339 376-465 (582)
15 PF04472 DUF552: Protein of un 24.4 4.4E+02 0.0095 23.0 7.7 56 281-337 12-70 (73)
16 PF03641 Lysine_decarbox: Poss 24.3 1.2E+02 0.0025 29.3 4.5 36 666-701 73-109 (133)
17 PF15249 GLTSCR1: Glioma tumor 23.5 31 0.00067 32.5 0.4 24 429-452 13-44 (109)
18 PRK03979 ADP-specific phosphof 22.0 4.7E+02 0.01 31.0 9.5 110 634-749 247-356 (463)
No 1
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=100.00 E-value=2.6e-71 Score=623.01 Aligned_cols=504 Identities=45% Similarity=0.634 Sum_probs=466.6
Q ss_pred cccchhhhhcCCCCHHHHHHHHHhhccCCCeEEeCCCCCCHHHHHHHHHHhhhCCeEEEEecCCChHhHHHHHHHHHHHh
Q 003851 238 RRRSNTELAEKMIPEHELQRLRNISLRMLERTKVGSAGITQALVDSIHEKWKLDEVVKLKFEEPHSLQMKRTHEILERRT 317 (791)
Q Consensus 238 ~~~~~~~lae~tLT~kErr~LRklAh~LkpvV~IGK~GVTd~VVeeIh~awk~hELVKVK~~~~~~~dm~~~~e~LEekT 317 (791)
+..+ +.+|++++.+.++.+||..|..+...+ +++|+|+++++.|++.|+.+|+++++|....+.+|.+.+++++..|
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 999999999999999999999998887 9999999999999999999999999999999999999999999999
Q ss_pred CC-eEEEEEccEEEEeecCCCCCCCcccccccccccccccccchhhcccCCCCCCCccccCCCCcccccccchHHHHhhH
Q 003851 318 GG-LVIWRSGSSVVLFRGMAYKLPCVQSFTKHNHTQQTQDVTNEVMRNVGEHPPRSAMESYVPDSANNLENLSKEELMDL 396 (791)
Q Consensus 318 Gg-~VVqrIG~viVLYRG~NY~~p~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~ee~~~~ 396 (791)
|| .+||+.|.....|++..|..|..-.... .+ ....+.. ....
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 9999999999999999999884311000 00 0000101 1236
Q ss_pred hhhhhhhcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccCCCCCCCCCChHHHHHHHHhhhcCCCeEEecccchhh
Q 003851 397 CELNYLLDELGPRFKDWPGREPLPVDADLLPPVVPDYKPPLRLLPYGIKPGLRDCETTEFRRLARKTPPHFALGRNRELQ 476 (791)
Q Consensus 397 ~E~n~LLD~LGPRf~dW~g~~PlPVDaDLLP~vvPgy~~PfRllP~gv~~~Ls~~E~t~LRk~a~~lpph~aLGRn~~~~ 476 (791)
++.+.++|++||+|.|||+.+|+|+|+||+|++||+|.+|||.+|+|++++|+..|++.+|++|..+||||++|+++.++
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 003851 477 GLAKAMVKLWEKSAIAKIAIKRDVMNTRNERMAEEL--KKLTGGTLLCRNKDYIVFYRGNDFLPPVVTDAVKERSKLTDI 554 (791)
Q Consensus 477 gLa~aI~~~wek~~lakI~~K~gv~~T~~~~m~~eL--k~LTGgvLLSRnk~~IVlYRGkdf~p~~Va~al~ERe~~~~~ 554 (791)
|++.+|+.+|++|+++++.|++|++.+..+.||.+| ..+||++|++||+.++|+|||++|++ .|.++|.++......
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 hhhHHHHhhhhhhHHHHhhccccccccccchhHHHHHHhhhccCCCChhHHH-HHHHhhhHHHHHHHHHHHHHHHHHHHH
Q 003851 555 RQDEEERARHVASALIELKAKGFVGSLVAGTLAETLAATSRWGRQPSYEDVE-KMMRDSTLSRHASLLRYLEQKLALAKR 633 (791)
Q Consensus 555 ~q~eEE~aR~~~~~~~~~~~~~~~~~~~aGtl~E~~~a~~~wg~~~~~~~~~-~~~~e~~~~~~~~~~k~~e~kL~~a~~ 633 (791)
.++.++.+|....+ + ......+||+.|+..+.++|+......+.. .+..+......+...+.+.++++.+..
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 003851 634 KLKMADKALAKVQESLDPAELPSDLETITNEERFLLRKMGLSMKPYLLLGRRGIYDGTIENMHLHWKYRELVKIIVKGKS 713 (791)
Q Consensus 634 K~~rae~~LaKl~~~~~P~e~~~d~E~LT~eERk~LRklGhkLKPvV~IGK~GVtdgVIeeI~~ALk~hELVKIkv~~~~ 713 (791)
|+..++..|++++.+..|.+..+|++.+|.+++.+++++|.+|++++.+|++|+++|++.++|.||++||++|++|+...
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-HHHHHHHHHHHHHhCCeEEeeeecCCCcEEEEeccCCCCCCCccCCcccccHHHHHHHHHHHHhhhhhhhcccc
Q 003851 714 F-AQVKQIAISLEAESGGVLVSLDKTPKGIAIIVYRGKNYVRPLKLRPQNLLTRRQALARSVELQRRTKTSHLGLT 788 (791)
Q Consensus 714 ~-ed~keia~~Le~~SGg~LVqVIk~~iG~~iILYRgkNy~rP~illP~nlLtKrkAL~rSie~QR~esl~~h~l~ 788 (791)
. .+++..|..++.++|+++|+++++..|++|+.|||+||++|..+.|.|+|+||+|+.+|+++|+.+||++|+-.
T Consensus 436 ~~~~~~~~a~~le~esg~~~v~~~~~~~~~ai~~yr~k~y~~p~~l~P~~~l~~~k~~~~~~~~~~~~a~~~~i~~ 511 (564)
T KOG1990|consen 436 LPSQVKQYASALERESGGILVSIDKNPKGYAIIAYRGKNYDRPTSLRPRNLLSRRKALERSLEEQRKEALKSHISD 511 (564)
T ss_pred ccHHHHHHHHHHHHHhCCceeeeccCCchhhHHHhhhhhccCCcccCchhhhcccCCccccHHHHHHHHHhhhcch
Confidence 6 99999999999999999999999999999999999999999999999999999999999999999999999853
No 2
>PRK10343 RNA-binding protein YhbY; Provisional
Probab=99.93 E-value=9.1e-26 Score=204.51 Aligned_cols=97 Identities=20% Similarity=0.371 Sum_probs=91.3
Q ss_pred CCCCHHHHHHHHHccCCCCceEeeCCCCCCHHHHHHHHHHHHhcceEEEEecCCCHHHHHHHHHHHHHHhCCeEEeeeec
Q 003851 659 ETITNEERFLLRKMGLSMKPYLLLGRRGIYDGTIENMHLHWKYRELVKIIVKGKSFAQVKQIAISLEAESGGVLVSLDKT 738 (791)
Q Consensus 659 E~LT~eERk~LRklGhkLKPvV~IGK~GVtdgVIeeI~~ALk~hELVKIkv~~~~~ed~keia~~Le~~SGg~LVqVIk~ 738 (791)
++||++||++||++||+|+|+|+||++||||+|++++++||++||||||++.+++.+++++++++|++.+||++||+|
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 369999999999999999999999999999999999999999999999999999999999999999999999999987
Q ss_pred CCCcEEEEeccCCCCCCCccCCc
Q 003851 739 PKGIAIIVYRGKNYVRPLKLRPQ 761 (791)
Q Consensus 739 ~iG~~iILYRgkNy~rP~illP~ 761 (791)
|+++||||+++. |.+.+|+
T Consensus 79 --G~~~vlYR~~~~--~~i~lp~ 97 (97)
T PRK10343 79 --GKTLVLYRPTKE--RKISLPR 97 (97)
T ss_pred --CcEEEEEecCCC--ccCCCCC
Confidence 999999999753 5676763
No 3
>TIGR00253 RNA_bind_YhbY putative RNA-binding protein, YhbY family. A combination of crystal structure, molecular modeling, and bioinformatic data together suggest that members of this family, including YhbY of E. coli, are RNA binding proteins.
Probab=99.93 E-value=2.1e-25 Score=201.45 Aligned_cols=95 Identities=28% Similarity=0.449 Sum_probs=89.0
Q ss_pred CCHHHHHHHHHccCCCCceEeeCCCCCCHHHHHHHHHHHHhcceEEEEecCCCHHHHHHHHHHHHHHhCCeEEeeeecCC
Q 003851 661 ITNEERFLLRKMGLSMKPYLLLGRRGIYDGTIENMHLHWKYRELVKIIVKGKSFAQVKQIAISLEAESGGVLVSLDKTPK 740 (791)
Q Consensus 661 LT~eERk~LRklGhkLKPvV~IGK~GVtdgVIeeI~~ALk~hELVKIkv~~~~~ed~keia~~Le~~SGg~LVqVIk~~i 740 (791)
||++||++||++||+|+|+|+|||+||||+||+++++||++||||||++++++.++++++|++|++.|||++||+|
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 CcEEEEeccCCCCCCCccCC
Q 003851 741 GIAIIVYRGKNYVRPLKLRP 760 (791)
Q Consensus 741 G~~iILYRgkNy~rP~illP 760 (791)
|+++||||+++. .|.+.+|
T Consensus 77 G~~~vlYR~~~~-~~~i~l~ 95 (95)
T TIGR00253 77 GKTIVLYRPTKE-RKIIELP 95 (95)
T ss_pred ccEEEEEecCCc-cCCcCCC
Confidence 999999999754 2445554
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=6e-25 Score=193.34 Aligned_cols=84 Identities=25% Similarity=0.417 Sum_probs=75.7
Q ss_pred CCHHHHHHHHHhhccCCCeEEeCCCCCCHHHHHHHHHHhhhCCeEEEEecCCChHhHHHHHHHHHHHhCCeEEEEEccEE
Q 003851 250 IPEHELQRLRNISLRMLERTKVGSAGITQALVDSIHEKWKLDEVVKLKFEEPHSLQMKRTHEILERRTGGLVIWRSGSSV 329 (791)
Q Consensus 250 LT~kErr~LRklAh~LkpvV~IGK~GVTd~VVeeIh~awk~hELVKVK~~~~~~~dm~~~~e~LEekTGg~VVqrIG~vi 329 (791)
||++|+++||++||+|+|+|+|||+|||++|+++|+++|++||||||+|.+++..+++++++.|+++|||++||++|+++
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 003851 330 VLFR 333 (791)
Q Consensus 330 VLYR 333 (791)
||||
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=99.92 E-value=1.3e-24 Score=197.09 Aligned_cols=88 Identities=20% Similarity=0.322 Sum_probs=86.3
Q ss_pred CCCCHHHHHHHHHhhccCCCeEEeCCCCCCHHHHHHHHHHhhhCCeEEEEecCCChHhHHHHHHHHHHHhCCeEEEEEcc
Q 003851 248 KMIPEHELQRLRNISLRMLERTKVGSAGITQALVDSIHEKWKLDEVVKLKFEEPHSLQMKRTHEILERRTGGLVIWRSGS 327 (791)
Q Consensus 248 ~tLT~kErr~LRklAh~LkpvV~IGK~GVTd~VVeeIh~awk~hELVKVK~~~~~~~dm~~~~e~LEekTGg~VVqrIG~ 327 (791)
|+||++|+++||++||+|+|+|+|||+|||++|+++|.++|++||||||++.+++.++.+++++.|+++||+++||+||+
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 EEEEeecC
Q 003851 328 SVVLFRGM 335 (791)
Q Consensus 328 viVLYRG~ 335 (791)
++||||.+
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=4.1e-24 Score=193.09 Aligned_cols=86 Identities=21% Similarity=0.339 Sum_probs=84.7
Q ss_pred CCHHHHHHHHHhhccCCCeEEeCCCCCCHHHHHHHHHHhhhCCeEEEEecCCChHhHHHHHHHHHHHhCCeEEEEEccEE
Q 003851 250 IPEHELQRLRNISLRMLERTKVGSAGITQALVDSIHEKWKLDEVVKLKFEEPHSLQMKRTHEILERRTGGLVIWRSGSSV 329 (791)
Q Consensus 250 LT~kErr~LRklAh~LkpvV~IGK~GVTd~VVeeIh~awk~hELVKVK~~~~~~~dm~~~~e~LEekTGg~VVqrIG~vi 329 (791)
||++|+++||++||+|+|+|+|||+|||++|+++|+++|++||||||++.+++..+.+++++.|+++||+++||.||+++
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 003851 330 VLFRGM 335 (791)
Q Consensus 330 VLYRG~ 335 (791)
||||++
T Consensus 81 vlYR~~ 86 (95)
T TIGR00253 81 VLYRPT 86 (95)
T ss_pred EEEecC
Confidence 999985
No 7
>COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]
Probab=99.91 E-value=3.8e-24 Score=193.63 Aligned_cols=97 Identities=27% Similarity=0.458 Sum_probs=91.7
Q ss_pred CCCHHHHHHHHHccCCCCceEeeCCCCCCHHHHHHHHHHHHhcceEEEEecCCCHHHHHHHHHHHHHHhCCeEEeeeecC
Q 003851 660 TITNEERFLLRKMGLSMKPYLLLGRRGIYDGTIENMHLHWKYRELVKIIVKGKSFAQVKQIAISLEAESGGVLVSLDKTP 739 (791)
Q Consensus 660 ~LT~eERk~LRklGhkLKPvV~IGK~GVtdgVIeeI~~ALk~hELVKIkv~~~~~ed~keia~~Le~~SGg~LVqVIk~~ 739 (791)
+||++|+++||++||+++|+|+||++|||++||.+|+++|++||||||++.+++.++++++|+.|++++||.+||+|
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 69999999999999999999999999999999999999999999999999999999999999999999999999987
Q ss_pred CCcEEEEeccCCCCCCCccCCc
Q 003851 740 KGIAIIVYRGKNYVRPLKLRPQ 761 (791)
Q Consensus 740 iG~~iILYRgkNy~rP~illP~ 761 (791)
|+++||||. +..++++.+|+
T Consensus 78 -G~~~vlyr~-~~e~~~i~l~~ 97 (97)
T COG1534 78 -GKTLVLYRE-SKEKRKISLPR 97 (97)
T ss_pred -eeEEEEEec-CcccccccCCC
Confidence 999999994 44557887874
No 8
>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=7.6e-24 Score=186.37 Aligned_cols=84 Identities=36% Similarity=0.584 Sum_probs=75.2
Q ss_pred CCHHHHHHHHHccCCCCceEeeCCCCCCHHHHHHHHHHHHhcceEEEEecCCCHHHHHHHHHHHHHHhCCeEEeeeecCC
Q 003851 661 ITNEERFLLRKMGLSMKPYLLLGRRGIYDGTIENMHLHWKYRELVKIIVKGKSFAQVKQIAISLEAESGGVLVSLDKTPK 740 (791)
Q Consensus 661 LT~eERk~LRklGhkLKPvV~IGK~GVtdgVIeeI~~ALk~hELVKIkv~~~~~ed~keia~~Le~~SGg~LVqVIk~~i 740 (791)
||++||++||++||+|+|+|+|||+|+|++|+++|+++|++||||||+|.+++.++++++++.|++.|||++|++|
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 7999999999999999999999999999999999999999999999999999999999999999999999999977
Q ss_pred CcEEEEec
Q 003851 741 GIAIIVYR 748 (791)
Q Consensus 741 G~~iILYR 748 (791)
|+++||||
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 9
>COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]
Probab=99.88 E-value=2.3e-22 Score=182.03 Aligned_cols=85 Identities=22% Similarity=0.381 Sum_probs=84.1
Q ss_pred CCCHHHHHHHHHhhccCCCeEEeCCCCCCHHHHHHHHHHhhhCCeEEEEecCCChHhHHHHHHHHHHHhCCeEEEEEccE
Q 003851 249 MIPEHELQRLRNISLRMLERTKVGSAGITQALVDSIHEKWKLDEVVKLKFEEPHSLQMKRTHEILERRTGGLVIWRSGSS 328 (791)
Q Consensus 249 tLT~kErr~LRklAh~LkpvV~IGK~GVTd~VVeeIh~awk~hELVKVK~~~~~~~dm~~~~e~LEekTGg~VVqrIG~v 328 (791)
+||++|+++||+.||+++|+|+|||+|||++|+.+|.++|++||||||++.+++.++.+++++.|++++|+.+||+||++
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 003851 329 VVLFR 333 (791)
Q Consensus 329 iVLYR 333 (791)
+||||
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=98.70 E-value=2e-08 Score=115.35 Aligned_cols=284 Identities=17% Similarity=0.235 Sum_probs=183.6
Q ss_pred hcCCCCHHHHHHHHHhhccCCCeEEeCCCCCCHHHHHHHHHHhhhCCeEEEEecCCChH-hHHHHHHHH--HHHhCCeEE
Q 003851 246 AEKMIPEHELQRLRNISLRMLERTKVGSAGITQALVDSIHEKWKLDEVVKLKFEEPHSL-QMKRTHEIL--ERRTGGLVI 322 (791)
Q Consensus 246 ae~tLT~kErr~LRklAh~LkpvV~IGK~GVTd~VVeeIh~awk~hELVKVK~~~~~~~-dm~~~~e~L--EekTGg~VV 322 (791)
-...|+..+.-.+|.+|-...+.+.+|..+.-+++.-.+...|..|+..|+-+...... .-..++.++ -..||+.+|
T Consensus 171 ~~~~l~~~~~~~~r~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~k~~~~k~~~~rg~~~~~~~~~a~~l~~~~~tg~~lv 250 (564)
T KOG1990|consen 171 SPPLLTSIESTLLRRLGYKLPPHFALGRSRKLQGLAVAMVSFWEKHEFAKILIKRGVLETRKERMADELQELLLTGKVLV 250 (564)
T ss_pred ChhhhhhHHHHHHHHhcccccccceehhccccccchhHHHHHHHHHHHHHHHHHhcchhhhccchHHHHHHHHhcCCeEE
Confidence 34458999999999999999999999999999999999999999999999877765433 334577888 889999999
Q ss_pred EEEccEEEEeecCCCCCCCcccc-ccccc-ccccccccchhhcc--cCCCC--CCCccccCC---------CCccccccc
Q 003851 323 WRSGSSVVLFRGMAYKLPCVQSF-TKHNH-TQQTQDVTNEVMRN--VGEHP--PRSAMESYV---------PDSANNLEN 387 (791)
Q Consensus 323 qrIG~viVLYRG~NY~~p~~~~~-~k~~~-~~~~~~~~~~~~~~--~~~~~--~~~~~~~~~---------p~~~~~~~~ 387 (791)
-+-|-..++|||+||-. +..+. ....+ ...-++........ ....+ +..+..+.. +....+...
T Consensus 251 ~hN~~~dv~y~~~~Fl~-~lp~~l~~f~~~~~~fp~~~~~~~~~~~~~~~~~~~~~t~~e~~~~~~~~~~~~~~~~~~~~ 329 (564)
T KOG1990|consen 251 LHNKLLDVMYRYKNFLS-PLPSTLEEFTDSSSMFPNIEDTKRLAKLSEYQKLNLKATLLELARAKAKKEKEIERRSISSR 329 (564)
T ss_pred eeccceeeeeehhhccc-ccchhHHHhhhhhhhhhhhHHHHHhhccccccchhhhhhHHHHHHHhcccccCcccccccch
Confidence 99999999999999988 44321 10000 00000000000000 01111 111110000 000011001
Q ss_pred chHH-HHhhHh---hhhhhhcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccCCCCCCCCCChHHHHHHHHhhhcC
Q 003851 388 LSKE-ELMDLC---ELNYLLDELGPRFKDWPGREPLPVDADLLPPVVPDYKPPLRLLPYGIKPGLRDCETTEFRRLARKT 463 (791)
Q Consensus 388 ~~~e-e~~~~~---E~n~LLD~LGPRf~dW~g~~PlPVDaDLLP~vvPgy~~PfRllP~gv~~~Ls~~E~t~LRk~a~~l 463 (791)
+..+ +.+... +........|-++.-|- .+.=+.+-+.-.|.=. +.+| ..+|++|..++++.+.++
T Consensus 330 ~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~l~~~~~~~~~~~~---~~~~----e~~t~ee~~~~~k~g~k~ 398 (564)
T KOG1990|consen 330 LKLEFEKASSEKLTEAIFHKLEKAKKKLASA----NRILAKLEDPKIPAEL---RYDP----ESITEEERLMLRKVGLKM 398 (564)
T ss_pred hhhhhhccchhhHHHHHHHHHhhhhhhccch----hhhhhccccccccccc---ccch----hhcChHHHHHHHHHHHhh
Confidence 1110 010000 00000011111111110 0000000000111000 1344 779999999999999999
Q ss_pred CCeEEecccchhhHHHHHHHHHHhhCceeEEeecCCCCCCcHHHHHHHHhhccCcEEEeeeC---Ce-EEEEecCCCCCh
Q 003851 464 PPHFALGRNRELQGLAKAMVKLWEKSAIAKIAIKRDVMNTRNERMAEELKKLTGGTLLCRNK---DY-IVFYRGNDFLPP 539 (791)
Q Consensus 464 pph~aLGRn~~~~gLa~aI~~~wek~~lakI~~K~gv~~T~~~~m~~eLk~LTGgvLLSRnk---~~-IVlYRGkdf~p~ 539 (791)
-.-.-+||=|+..|+.-.++.||..++.+++-||..-.....++.|..|..+.||++++=++ .| |++|||++|.=+
T Consensus 399 ~~~~~~~rrg~f~g~i~n~~l~wk~~e~~k~i~~~~~~~~~~~~~a~~le~esg~~~v~~~~~~~~~ai~~yr~k~y~~p 478 (564)
T KOG1990|consen 399 KRRLLSGRRGVFDGVIENMHLHWKSRELVKVICKEKNLPSQVKQYASALERESGGILVSIDKNPKGYAIIAYRGKNYDRP 478 (564)
T ss_pred ccccccCCcccccceeecchhhhhhcccceeeeccccccHHHHHHHHHHHHHhCCceeeeccCCchhhHHHhhhhhccCC
Confidence 99999999999999999999999999999999998888899999999999999999998655 44 899999999766
Q ss_pred hh
Q 003851 540 VV 541 (791)
Q Consensus 540 ~V 541 (791)
..
T Consensus 479 ~~ 480 (564)
T KOG1990|consen 479 TS 480 (564)
T ss_pred cc
Confidence 64
No 11
>KOG2769 consensus Putative u4/u6 small nuclear ribonucleoprotein [RNA processing and modification]
Probab=53.23 E-value=20 Score=42.16 Aligned_cols=54 Identities=24% Similarity=0.330 Sum_probs=39.5
Q ss_pred HHHHHHHHhhC-ceeEEeecCCCCCCcHHHHHHHHh------hccCcEEEeeeCCeEEEEec
Q 003851 479 AKAMVKLWEKS-AIAKIAIKRDVMNTRNERMAEELK------KLTGGTLLCRNKDYIVFYRG 533 (791)
Q Consensus 479 a~aI~~~wek~-~lakI~~K~gv~~T~~~~m~~eLk------~LTGgvLLSRnk~~IVlYRG 533 (791)
+++++++||.. -.|.+-| .++.+..+...=++++ .|||++++.++.+.||+=-|
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 4565555554444444 69999999999999998833
No 12
>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=42.80 E-value=3.1 Score=41.91 Aligned_cols=94 Identities=20% Similarity=0.213 Sum_probs=60.8
Q ss_pred HHHHHHHHHHHHHHHHHH-----HHHHhh---cccCCCCCCCCCcCCCCHHHHHHHHHccCCCCceEe------eCCCCC
Q 003851 622 RYLEQKLALAKRKLKMAD-----KALAKV---QESLDPAELPSDLETITNEERFLLRKMGLSMKPYLL------LGRRGI 687 (791)
Q Consensus 622 k~~e~kL~~a~~K~~rae-----~~LaKl---~~~~~P~e~~~d~E~LT~eERk~LRklGhkLKPvV~------IGK~GV 687 (791)
-++|.||+.|+.++-..| +.|.++ .-..--+.-..|.+.||..++..++++...|.|++- --|.=+
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 358888888887554444 333333 222333444578999999999999999999999872 234456
Q ss_pred CHHHHHHHHHHHHhcceEEEEecCCCHH
Q 003851 688 YDGTIENMHLHWKYRELVKIIVKGKSFA 715 (791)
Q Consensus 688 tdgVIeeI~~ALk~hELVKIkv~~~~~e 715 (791)
++.-.+.--.||-..|.|+|+.......
T Consensus 107 t~~E~d~y~eALm~~e~v~vk~~~~~~~ 134 (162)
T PF12207_consen 107 TQEEYDQYIEALMTYETVRVKTKSSGGI 134 (162)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHCT-SS--
T ss_pred CHHHHHHHHHHHhhhheeeeeccCCCCC
Confidence 6777777778999999999988755443
No 13
>PF11211 DUF2997: Protein of unknown function (DUF2997); InterPro: IPR021375 This family of proteins has no known function.
Probab=30.18 E-value=70 Score=26.57 Aligned_cols=32 Identities=9% Similarity=0.115 Sum_probs=28.4
Q ss_pred eEEeecCCCCCCcHHHHHHHHhhccCcEEEeeeC
Q 003851 492 AKIAIKRDVMNTRNERMAEELKKLTGGTLLCRNK 525 (791)
Q Consensus 492 akI~~K~gv~~T~~~~m~~eLk~LTGgvLLSRnk 525 (791)
|.+.++ |+.|.++..+.+.|+++.|.|. +|+.
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 14
>KOG1257 consensus NADP+-dependent malic enzyme [Energy production and conversion]
Probab=26.26 E-value=1.6e+02 Score=35.46 Aligned_cols=84 Identities=20% Similarity=0.285 Sum_probs=63.5
Q ss_pred HHHHHHHHhhccCCCeEEeCCCCC----CHHHHHHHHHHhhhCCeEEEEecCCChHhHHHHHHHHHHHhCCeEEEEEccE
Q 003851 253 HELQRLRNISLRMLERTKVGSAGI----TQALVDSIHEKWKLDEVVKLKFEEPHSLQMKRTHEILERRTGGLVIWRSGSS 328 (791)
Q Consensus 253 kErr~LRklAh~LkpvV~IGK~GV----Td~VVeeIh~awk~hELVKVK~~~~~~~dm~~~~e~LEekTGg~VVqrIG~v 328 (791)
++.+-|-..-..+||-|.||-.|+ |+.|++.++.. +|==-|=-+.|++..+.-.+++.=.-|+|.+|...|+-
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 77777777755 44444555678888888899999999999999999985
Q ss_pred E--EEeecCCCCC
Q 003851 329 V--VLFRGMAYKL 339 (791)
Q Consensus 329 i--VLYRG~NY~~ 339 (791)
+ |-|-|+-|..
T Consensus 453 F~pV~~~gK~~~p 465 (582)
T KOG1257|consen 453 FPPVEYNGKVYVP 465 (582)
T ss_pred CCCceeCCcEecc
Confidence 3 3344444443
No 15
>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=24.43 E-value=4.4e+02 Score=22.96 Aligned_cols=56 Identities=14% Similarity=0.170 Sum_probs=38.0
Q ss_pred HHHHHHHhhhCCeEEEEecCCChHhHHHHHHHHHH---HhCCeEEEEEccEEEEeecCCC
Q 003851 281 VDSIHEKWKLDEVVKLKFEEPHSLQMKRTHEILER---RTGGLVIWRSGSSVVLFRGMAY 337 (791)
Q Consensus 281 VeeIh~awk~hELVKVK~~~~~~~dm~~~~e~LEe---kTGg~VVqrIG~viVLYRG~NY 337 (791)
+.+|-++++....|-+.+..-.....+++.+.|.. ..+|.+.+. |..++||=+.+.
T Consensus 12 ~~~i~~~l~~g~~Vivnl~~l~~~~~~Ri~Dfl~G~~~al~G~i~~i-~~~~~l~~P~~V 70 (73)
T PF04472_consen 12 AREIVDALREGKIVIVNLENLDDEEAQRILDFLSGAVYALDGDIQKI-SEKVFLLTPKGV 70 (73)
T ss_dssp HHHHHHHHHTT--EEEE-TTS-HHHHHHHHHHHHHHHHHTT-EEEEE-ETTEEEEE----
T ss_pred HHHHHHHHHcCCEEEEECCCCCHHHHHHHHHHHhchheeeCCEEEEE-cCCEEEEECCCc
Confidence 45688999999999999999888889999888876 568887766 666777755543
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=24.35 E-value=1.2e+02 Score=29.25 Aligned_cols=36 Identities=25% Similarity=0.376 Sum_probs=29.7
Q ss_pred HHHHHHccCCCC-ceEeeCCCCCCHHHHHHHHHHHHh
Q 003851 666 RFLLRKMGLSMK-PYLLLGRRGIYDGTIENMHLHWKY 701 (791)
Q Consensus 666 Rk~LRklGhkLK-PvV~IGK~GVtdgVIeeI~~ALk~ 701 (791)
--.+.++|.+-+ |++.++.+|.++.+++.++.....
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 345678888888 999999999999999999755544
No 17
>PF15249 GLTSCR1: Glioma tumor suppressor candidate region
Probab=23.50 E-value=31 Score=32.50 Aligned_cols=24 Identities=46% Similarity=0.823 Sum_probs=16.2
Q ss_pred CCCCCCCCc--------ccCCCCCCCCCChHH
Q 003851 429 VVPDYKPPL--------RLLPYGIKPGLRDCE 452 (791)
Q Consensus 429 vvPgy~~Pf--------RllP~gv~~~Ls~~E 452 (791)
.-|.|++|| |||||.|=......+
T Consensus 13 ~~PD~~tPF~s~~DA~~RLLPYHv~~~~~~~~ 44 (109)
T PF15249_consen 13 LNPDYKTPFRSLEDAVERLLPYHVFQEPEEDE 44 (109)
T ss_pred hCCCcCCCCCCHHHHHHHhcchhhhcCCCCCh
Confidence 346788888 678887765555444
No 18
>PRK03979 ADP-specific phosphofructokinase; Provisional
Probab=21.99 E-value=4.7e+02 Score=31.03 Aligned_cols=110 Identities=18% Similarity=0.168 Sum_probs=76.9
Q ss_pred HHHHHHHHHHhhcccCCCCCCCCCcCCCCHHHHHHHHHccCCCCceEeeCCCCCCHHHHHHHHHHHHhcceEEEEecCCC
Q 003851 634 KLKMADKALAKVQESLDPAELPSDLETITNEERFLLRKMGLSMKPYLLLGRRGIYDGTIENMHLHWKYRELVKIIVKGKS 713 (791)
Q Consensus 634 K~~rae~~LaKl~~~~~P~e~~~d~E~LT~eERk~LRklGhkLKPvV~IGK~GVtdgVIeeI~~ALk~hELVKIkv~~~~ 713 (791)
.++++...+..+.+ .|.+.+.--|.=+-..+..++.+...+=| .+---|+.+.=+.++...+.+.+|-.=.+..+.
T Consensus 247 ~l~r~~~~i~~L~~--~~~~i~iH~E~As~~~~~ir~~i~~~ilp--~vDSlGmNE~ELa~l~~~lg~~~l~~~i~~~~~ 322 (463)
T PRK03979 247 YLKRAKEDIKLLKK--KNKDIKIHVEFASIQNREIRKKIITYILP--HVDSVGMDETEIANILNVLGYEELSERILKESR 322 (463)
T ss_pred HHHHHHHHHHHHhh--CCCCceEEEEeccccCHHHHHHHHHhhcc--ccccccCCHHHHHHHHHHhcCcchhhhhhcccc
Confidence 34455555444432 34455555554444445555666656555 345568888888888888888887776666667
Q ss_pred HHHHHHHHHHHHHHhCCeEEeeeecCCCcEEEEecc
Q 003851 714 FAQVKQIAISLEAESGGVLVSLDKTPKGIAIIVYRG 749 (791)
Q Consensus 714 ~ed~keia~~Le~~SGg~LVqVIk~~iG~~iILYRg 749 (791)
.+++-+.+..|.+++|-+.|+|. +.|..+.+.+.
T Consensus 323 i~~v~~a~~~L~~~~~leri~vH--T~~y~l~i~~~ 356 (463)
T PRK03979 323 IEDVIEGAKILLDELNLERVQVH--TLYYIMYICKK 356 (463)
T ss_pred HHHHHHHHHHHHHHcCCCEEEEE--ecceeeEEecc
Confidence 89999999999999999999999 66777777763
Done!