Query 005091
Match_columns 715
No_of_seqs 336 out of 963
Neff 4.1
Searched_HMMs 46136
Date Thu Mar 28 17:54:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/005091.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/005091hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1990 Poly(A)-specific exori 100.0 1.2E-46 2.7E-51 422.0 18.9 400 242-715 3-406 (564)
2 PF01985 CRS1_YhbY: CRS1 / Yhb 99.9 3.3E-25 7.2E-30 193.6 11.0 84 254-337 1-84 (84)
3 PRK10343 RNA-binding protein Y 99.9 9.5E-25 2.1E-29 196.2 12.9 89 252-340 1-89 (97)
4 TIGR00253 RNA_bind_YhbY putati 99.9 2.3E-24 4.9E-29 193.2 12.8 87 254-340 1-87 (95)
5 PRK10343 RNA-binding protein Y 99.9 4.3E-24 9.3E-29 192.0 12.5 90 477-567 1-90 (97)
6 TIGR00253 RNA_bind_YhbY putati 99.9 6.8E-24 1.5E-28 190.1 12.7 88 479-567 1-88 (95)
7 PF01985 CRS1_YhbY: CRS1 / Yhb 99.9 1.8E-23 3.8E-28 182.8 11.1 84 479-563 1-84 (84)
8 KOG1990 Poly(A)-specific exori 99.9 3.3E-24 7.1E-29 241.6 7.6 332 245-607 166-514 (564)
9 COG1534 Predicted RNA-binding 99.9 2.8E-22 6.1E-27 179.8 12.1 86 253-338 1-86 (97)
10 COG1534 Predicted RNA-binding 99.9 4.3E-22 9.2E-27 178.6 11.6 88 478-566 1-88 (97)
11 cd08619 PI-PLCXDc_plant Cataly 31.4 98 0.0021 33.9 5.9 68 505-572 92-174 (285)
12 PF04472 DUF552: Protein of un 25.0 4.3E+02 0.0092 22.7 7.6 55 285-340 12-69 (73)
13 PF15249 GLTSCR1: Glioma tumor 24.3 30 0.00065 32.2 0.5 19 462-480 15-41 (109)
14 cd08619 PI-PLCXDc_plant Cataly 23.4 1.8E+02 0.004 31.9 6.2 68 281-348 93-176 (285)
15 PF04472 DUF552: Protein of un 22.4 5E+02 0.011 22.3 7.6 51 510-561 12-65 (73)
16 PF12720 DUF3807: Protein of u 21.2 67 0.0015 32.7 2.3 35 472-527 43-77 (172)
17 PF03641 Lysine_decarbox: Poss 21.1 1.4E+02 0.003 28.4 4.3 39 482-520 71-110 (133)
18 TIGR00730 conserved hypothetic 20.5 1.5E+02 0.0033 29.9 4.6 58 483-545 115-177 (178)
No 1
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=100.00 E-value=1.2e-46 Score=422.01 Aligned_cols=400 Identities=43% Similarity=0.587 Sum_probs=364.2
Q ss_pred hccCccccccCCCCHHHHHHHHhhhcCCCCeEEeCCCCCCHHHHHHHHHHHHhCCeEEEEecCCChhhHHHHHHHHHHHh
Q 005091 242 RRSSRTSLAELTLPESELRRLRNLTFQTKSKTRIKGAGLTQAVVDIIHEKWKTSEIVRLKIEGAPALNMKRMHEILERKT 321 (715)
Q Consensus 242 ~k~~~p~~ae~~Lt~kErr~LR~lA~~Lkp~v~IGK~GlTd~Vv~~I~~awek~ELVKIK~~g~~~~dmk~~ae~Le~kT 321 (715)
++.+ +.++++++...++.+||..|..+.-.. +++|+|+.+++.|+..|+.+|+++++|....+.+|.+++++++..|
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 3456 999999999999999999999998887 9999999999999999999999999999989999999999999999
Q ss_pred CC-eEEEEECcEEEEeeCCCCCCchhhhhHHHhhhccCCccccccchhhhhhhhhccccCCcccccccccCCCCCCCCcc
Q 005091 322 GG-LVIWRSGTAVSLYRGVSYEVPSVQLNKRIYKRNELPASSVSQATDKQIHKQISMSGNSLSAAADKTAQDPSNFDSYN 400 (715)
Q Consensus 322 Gg-~VVqriG~~iVLYRGknY~~p~v~~~~~l~~r~e~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~s~~ 400 (715)
|| -+||+.|.....|++..|..|.+..++. ++ . +
T Consensus 80 ~~n~~~~~~g~~~s~~~~~~~~~~~~~~~~~----~~-----------~----~-------------------------- 114 (564)
T KOG1990|consen 80 GGNFVVWSRGDSISSPEFLCQRSPVDFVARQ----QE-----------N----Q-------------------------- 114 (564)
T ss_pred CCceeeeecCccccCCccceeecchhhhhhh----ch-----------h----h--------------------------
Confidence 99 9999999999999888888775433210 00 0 0
Q ss_pred cchhcchhhcccchhhhhhhHHhhhhHHHHHHHhhccCCCcCCCCCCCCCCCCCCCCCCCCCCCCCCcccCCCCCCccCC
Q 005091 401 NVHATQVNLETASEEQETDFVREVKYEDEVEKLLDGLGPRYTDWPGCDPLPVDADMLPGIVPGYQPPFRVLPYGVRSTLA 480 (715)
Q Consensus 401 e~~~~~~~~~~~~~~~~~~~~~~~~~e~e~d~LLd~LgpR~~dW~g~~plPVDadLLPa~vPgyk~PfR~lP~g~~e~LT 480 (715)
...-..+++++.+.+++++||++.+||+.+++|||+|++|+.||+|..|||.+|++++++|+
T Consensus 115 ------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dl~~~~i~~~~~p~r~l~~~~~~~l~ 176 (564)
T KOG1990|consen 115 ------------------AGKWPSELEKEKNELLDSLGPELSDWGGSDRLSVDADLLPEKIPDYMRPFRTLPVGSPPLLT 176 (564)
T ss_pred ------------------hhhhHHHHHHHHHHHhhccCcccccCCCCCCccchhhhchhhhhcccChhccCCCCChhhhh
Confidence 00012356789999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhccCCCCeEEeCCCCchHHHHHHHHHHHHhcCeeEEEEcCCCChhhHHHHHHHH--HHHhCCeEEEeeCCE
Q 005091 481 RKEATNLQRLARVLPPHFALGRSRQLQGLAVAMIKLWEKSSIAKIALKRGVQLTTSERMVEDI--KKLTGGTLLSRNKDF 558 (715)
Q Consensus 481 ~kEr~~LRklAh~LkPvv~LGknGvtdgvi~~I~~awekhELIKIkik~g~~~~~~~~mAeeL--~~~TGg~LVq~iG~~ 558 (715)
..+.+++|++|..++|||.+|.++..++++..|+.+|++|+.+|+.+++|.+.+....||.++ ...||+.||.+++..
T Consensus 177 ~~~~~~~r~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~k~~~~k~~~~rg~~~~~~~~~a~~l~~~~~tg~~lv~hN~~~ 256 (564)
T KOG1990|consen 177 SIESTLLRRLGYKLPPHFALGRSRKLQGLAVAMVSFWEKHEFAKILIKRGVLETRKERMADELQELLLTGKVLVLHNKLL 256 (564)
T ss_pred hHHHHHHHHhcccccccceehhccccccchhHHHHHHHHHHHHHHHHHhcchhhhccchHHHHHHHHhcCCeEEeeccce
Confidence 999999999999999999999999999999999999999999999999999999999999999 999999999999999
Q ss_pred EEEEcCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHhhhhccccchhhhcccCccchhHHHHHHhhhcCCCCChhHH-H
Q 005091 559 LVFYRGKNFLSPDVTEALQERERLAKSLQDEEEQARLRASAFVLPSIETIEKSGTAGTLKETLDANSRWGKRLDDSHK-E 637 (715)
Q Consensus 559 IILYRgkn~~~p~v~n~L~kr~al~rs~q~~Ee~ar~~a~~~~~~~~~~~~~~~~agtl~e~~~a~~~~g~~~~~~~~-~ 637 (715)
+|+||+++|.+ .+..+|.+++++....++.++.+|+.++..+. .+..++|+.|+..+.++|+..+.-... .
T Consensus 257 dv~y~~~~Fl~-~lp~~l~~f~~~~~~fp~~~~~~~~~~~~~~~-------~~~~~~t~~e~~~~~~~~~~~~~~~~~~~ 328 (564)
T KOG1990|consen 257 DVMYRYKNFLS-PLPSTLEEFTDSSSMFPNIEDTKRLAKLSEYQ-------KLNLKATLLELARAKAKKEKEIERRSISS 328 (564)
T ss_pred eeeeehhhccc-ccchhHHHhhhhhhhhhhhHHHHHhhcccccc-------chhhhhhHHHHHHHhcccccCcccccccc
Confidence 99999999999 88889999999977789999999999743222 145799999999999999999865543 3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCCHHHHHHHHhhcccccccccCCC
Q 005091 638 NLVREAEVRRHAYLVQKLEKKLARAERKLLRAERALSKVEESLKPAERQADPESITDEERFMFRKLGLRMKAFLLLGK 715 (715)
Q Consensus 638 ~~~~e~~~~r~~~~~k~~e~kL~~a~~K~~kaek~L~kle~~~~P~~~~~d~E~iTeEER~mfRkiGLkMk~fLlLGR 715 (715)
.+..+.....+++..+.++++++.+..|++.|+..|++++....|++...|+|.||+|||+||+|+|++|+.|+++||
T Consensus 329 ~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~e~~t~ee~~~~~k~g~k~~~~~~~~r 406 (564)
T KOG1990|consen 329 RLKLEFEKASSEKLTEAIFHKLEKAKKKLASANRILAKLEDPKIPAELRYDPESITEEERLMLRKVGLKMKRRLLSGR 406 (564)
T ss_pred hhhhhhhccchhhHHHHHHHHHhhhhhhccchhhhhhcccccccccccccchhhcChHHHHHHHHHHHhhccccccCC
Confidence 678888999999999999999999999999999999999999999999999999999999999999999999999997
No 2
>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=3.3e-25 Score=193.58 Aligned_cols=84 Identities=32% Similarity=0.466 Sum_probs=75.7
Q ss_pred CCHHHHHHHHhhhcCCCCeEEeCCCCCCHHHHHHHHHHHHhCCeEEEEecCCChhhHHHHHHHHHHHhCCeEEEEECcEE
Q 005091 254 LPESELRRLRNLTFQTKSKTRIKGAGLTQAVVDIIHEKWKTSEIVRLKIEGAPALNMKRMHEILERKTGGLVIWRSGTAV 333 (715)
Q Consensus 254 Lt~kErr~LR~lA~~Lkp~v~IGK~GlTd~Vv~~I~~awek~ELVKIK~~g~~~~dmk~~ae~Le~kTGg~VVqriG~~i 333 (715)
||++|+++||++||+|+|+|+|||+|+|++|+++|+++|++||||||+|.+++..++++++++|+++|||++||++|+++
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 005091 334 SLYR 337 (715)
Q Consensus 334 VLYR 337 (715)
||||
T Consensus 81 vlyR 84 (84)
T PF01985_consen 81 VLYR 84 (84)
T ss_dssp EEEE
T ss_pred EEEC
Confidence 9998
No 3
>PRK10343 RNA-binding protein YhbY; Provisional
Probab=99.92 E-value=9.5e-25 Score=196.19 Aligned_cols=89 Identities=22% Similarity=0.349 Sum_probs=86.9
Q ss_pred CCCCHHHHHHHHhhhcCCCCeEEeCCCCCCHHHHHHHHHHHHhCCeEEEEecCCChhhHHHHHHHHHHHhCCeEEEEECc
Q 005091 252 LTLPESELRRLRNLTFQTKSKTRIKGAGLTQAVVDIIHEKWKTSEIVRLKIEGAPALNMKRMHEILERKTGGLVIWRSGT 331 (715)
Q Consensus 252 ~~Lt~kErr~LR~lA~~Lkp~v~IGK~GlTd~Vv~~I~~awek~ELVKIK~~g~~~~dmk~~ae~Le~kTGg~VVqriG~ 331 (715)
++||++|+++||++||+|+|+|+|||+|||++|+++|.++|++||||||++++++.++.++++++|+++||+++||.||+
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 36999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEeeCCC
Q 005091 332 AVSLYRGVS 340 (715)
Q Consensus 332 ~iVLYRGkn 340 (715)
++||||.+.
T Consensus 81 ~~vlYR~~~ 89 (97)
T PRK10343 81 TLVLYRPTK 89 (97)
T ss_pred EEEEEecCC
Confidence 999999985
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=99.91 E-value=2.3e-24 Score=193.16 Aligned_cols=87 Identities=23% Similarity=0.356 Sum_probs=85.5
Q ss_pred CCHHHHHHHHhhhcCCCCeEEeCCCCCCHHHHHHHHHHHHhCCeEEEEecCCChhhHHHHHHHHHHHhCCeEEEEECcEE
Q 005091 254 LPESELRRLRNLTFQTKSKTRIKGAGLTQAVVDIIHEKWKTSEIVRLKIEGAPALNMKRMHEILERKTGGLVIWRSGTAV 333 (715)
Q Consensus 254 Lt~kErr~LR~lA~~Lkp~v~IGK~GlTd~Vv~~I~~awek~ELVKIK~~g~~~~dmk~~ae~Le~kTGg~VVqriG~~i 333 (715)
||++|+++||++||+|+|+|+|||+|||++|+++|+++|++||||||++..++..+.++++++|++.||+++||.||+++
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 EEeeCCC
Q 005091 334 SLYRGVS 340 (715)
Q Consensus 334 VLYRGkn 340 (715)
||||++.
T Consensus 81 vlYR~~~ 87 (95)
T TIGR00253 81 VLYRPTK 87 (95)
T ss_pred EEEecCC
Confidence 9999975
No 5
>PRK10343 RNA-binding protein YhbY; Provisional
Probab=99.91 E-value=4.3e-24 Score=191.99 Aligned_cols=90 Identities=24% Similarity=0.311 Sum_probs=86.1
Q ss_pred ccCCHHHHHHHHHhccCCCCeEEeCCCCchHHHHHHHHHHHHhcCeeEEEEcCCCChhhHHHHHHHHHHHhCCeEEEeeC
Q 005091 477 STLARKEATNLQRLARVLPPHFALGRSRQLQGLAVAMIKLWEKSSIAKIALKRGVQLTTSERMVEDIKKLTGGTLLSRNK 556 (715)
Q Consensus 477 e~LT~kEr~~LRklAh~LkPvv~LGknGvtdgvi~~I~~awekhELIKIkik~g~~~~~~~~mAeeL~~~TGg~LVq~iG 556 (715)
++||++|++|||++||+|+|+|+||++|++++|+++|..+|++||||||++.+ ++.++++++|++|++.||+++||+||
T Consensus 1 m~Lt~kqr~~LR~~ah~l~Pvv~IGk~Glt~~vi~ei~~aL~~hELIKvkv~~-~~~~~~~e~~~~i~~~~~ae~Vq~IG 79 (97)
T PRK10343 1 MNLSTKQKQHLKGLAHPLKPVVLLGSNGLTEGVLAEIEQALEHHELIKVKIAT-EDRETKTLIVEAIVRETGACNVQVIG 79 (97)
T ss_pred CCCCHHHHHHHHHhcCCCCCeEEECCCCCCHHHHHHHHHHHHHCCcEEEEecC-CChhHHHHHHHHHHHHHCCEEEeeeC
Confidence 36999999999999999999999999999999999999999999999999975 68899999999999999999999999
Q ss_pred CEEEEEcCCCC
Q 005091 557 DFLVFYRGKNF 567 (715)
Q Consensus 557 ~~IILYRgkn~ 567 (715)
+++||||.++.
T Consensus 80 ~~~vlYR~~~~ 90 (97)
T PRK10343 80 KTLVLYRPTKE 90 (97)
T ss_pred cEEEEEecCCC
Confidence 99999999864
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=6.8e-24 Score=190.07 Aligned_cols=88 Identities=19% Similarity=0.257 Sum_probs=84.8
Q ss_pred CCHHHHHHHHHhccCCCCeEEeCCCCchHHHHHHHHHHHHhcCeeEEEEcCCCChhhHHHHHHHHHHHhCCeEEEeeCCE
Q 005091 479 LARKEATNLQRLARVLPPHFALGRSRQLQGLAVAMIKLWEKSSIAKIALKRGVQLTTSERMVEDIKKLTGGTLLSRNKDF 558 (715)
Q Consensus 479 LT~kEr~~LRklAh~LkPvv~LGknGvtdgvi~~I~~awekhELIKIkik~g~~~~~~~~mAeeL~~~TGg~LVq~iG~~ 558 (715)
||++|+++||++||+|+|+|+||++|++++|+++|+.+|++||||||++.+ ++.++++++|++|++.|||++||+||++
T Consensus 1 Lt~kqr~~Lr~~ah~l~p~v~IGK~Glt~~vi~ei~~aL~~hELIKVkvl~-~~~~~~~e~a~~i~~~~~a~~Vq~iG~~ 79 (95)
T TIGR00253 1 LTGKQKRHLRGKAHHLKPVVLVGKNGLTEGVIKEIEQALEHRELIKVKVAT-EDREDKTLIAEALVKETGACNVQVIGKT 79 (95)
T ss_pred CCHHHHHHHHHHhCCCCCeEEECCCCCCHHHHHHHHHHHHhCCcEEEEecC-CChhHHHHHHHHHHHHHCCEEEEEEccE
Confidence 799999999999999999999999999999999999999999999999976 5788999999999999999999999999
Q ss_pred EEEEcCCCC
Q 005091 559 LVFYRGKNF 567 (715)
Q Consensus 559 IILYRgkn~ 567 (715)
+||||+++.
T Consensus 80 ~vlYR~~~~ 88 (95)
T TIGR00253 80 IVLYRPTKE 88 (95)
T ss_pred EEEEecCCc
Confidence 999999864
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=1.8e-23 Score=182.77 Aligned_cols=84 Identities=23% Similarity=0.341 Sum_probs=74.9
Q ss_pred CCHHHHHHHHHhccCCCCeEEeCCCCchHHHHHHHHHHHHhcCeeEEEEcCCCChhhHHHHHHHHHHHhCCeEEEeeCCE
Q 005091 479 LARKEATNLQRLARVLPPHFALGRSRQLQGLAVAMIKLWEKSSIAKIALKRGVQLTTSERMVEDIKKLTGGTLLSRNKDF 558 (715)
Q Consensus 479 LT~kEr~~LRklAh~LkPvv~LGknGvtdgvi~~I~~awekhELIKIkik~g~~~~~~~~mAeeL~~~TGg~LVq~iG~~ 558 (715)
||++|+++||++||+|+|+|.||++|+|++|+++|+.+|++||||||+|.. ++.++.+++|++|++.|||++|+++|++
T Consensus 1 Lt~ke~~~Lr~~a~~l~p~v~IGk~Glt~~vi~~i~~~l~~~eLvKVk~~~-~~~~~~~~~~~~l~~~t~~~~V~~iG~~ 79 (84)
T PF01985_consen 1 LTSKERKFLRKLAHHLKPVVQIGKNGLTDGVIEEIDDALEKHELVKVKVLG-NCREDRKEIAEQLAEKTGAEVVQVIGRT 79 (84)
T ss_dssp --HHHHHHHHHHHTTC--SEEE-TTSS-HHHHHHHHHHHHHHSEEEEEETT---HHHHHHHHHHHHHHHTEEEEEEETTE
T ss_pred CCHHHHHHHHHHhcCCCCeEEECCCCCCHHHHHHHHHHHHhCCeeEEEEcc-CCHHHHHHHHHHHHHHhCCEEEEEECCE
Confidence 799999999999999999999999999999999999999999999999976 7899999999999999999999999999
Q ss_pred EEEEc
Q 005091 559 LVFYR 563 (715)
Q Consensus 559 IILYR 563 (715)
+||||
T Consensus 80 ~vlyR 84 (84)
T PF01985_consen 80 IVLYR 84 (84)
T ss_dssp EEEEE
T ss_pred EEEEC
Confidence 99998
No 8
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=99.90 E-value=3.3e-24 Score=241.62 Aligned_cols=332 Identities=17% Similarity=0.206 Sum_probs=259.3
Q ss_pred CccccccCCCCHHHHHHHHhhhcCCCCeEEeCCCCCCHHHHHHHHHHHHhCCeEEEEec-CCChhhHHHHHHHH--HHHh
Q 005091 245 SRTSLAELTLPESELRRLRNLTFQTKSKTRIKGAGLTQAVVDIIHEKWKTSEIVRLKIE-GAPALNMKRMHEIL--ERKT 321 (715)
Q Consensus 245 ~~p~~ae~~Lt~kErr~LR~lA~~Lkp~v~IGK~GlTd~Vv~~I~~awek~ELVKIK~~-g~~~~dmk~~ae~L--e~kT 321 (715)
..|-.....|+..+...+|.+|..++++|.+|.++.-+++.-.++..|.+|+.+|+.|. +.+......++.++ ...|
T Consensus 166 ~l~~~~~~~l~~~~~~~~r~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~k~~~~k~~~~rg~~~~~~~~~a~~l~~~~~t 245 (564)
T KOG1990|consen 166 TLPVGSPPLLTSIESTLLRRLGYKLPPHFALGRSRKLQGLAVAMVSFWEKHEFAKILIKRGVLETRKERMADELQELLLT 245 (564)
T ss_pred cCCCCChhhhhhHHHHHHHHhcccccccceehhccccccchhHHHHHHHHHHHHHHHHHhcchhhhccchHHHHHHHHhc
Confidence 45667777899999999999999999999999999999999999999999999999998 88888888999999 9999
Q ss_pred CCeEEEEECcEEEEeeCCCCCCchhhhhHHHhhhccCCccccccchhhhhhhhhccccCCcccccccccCCCCCCCCccc
Q 005091 322 GGLVIWRSGTAVSLYRGVSYEVPSVQLNKRIYKRNELPASSVSQATDKQIHKQISMSGNSLSAAADKTAQDPSNFDSYNN 401 (715)
Q Consensus 322 Gg~VVqriG~~iVLYRGknY~~p~v~~~~~l~~r~e~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~s~~e 401 (715)
|+.||.++|-..|+||+++|.. ++.++ +.++.+. ....+...+ + ..+.. ++... .....++..+
T Consensus 246 g~~lv~hN~~~dv~y~~~~Fl~-~lp~~--l~~f~~~-~~~fp~~~~-~----~~~~~--~~~~~-----~~~~~~t~~e 309 (564)
T KOG1990|consen 246 GKVLVLHNKLLDVMYRYKNFLS-PLPST--LEEFTDS-SSMFPNIED-T----KRLAK--LSEYQ-----KLNLKATLLE 309 (564)
T ss_pred CCeEEeeccceeeeeehhhccc-ccchh--HHHhhhh-hhhhhhhHH-H----HHhhc--ccccc-----chhhhhhHHH
Confidence 9999999999999999999999 67665 5555443 222322222 1 11111 00000 0112334444
Q ss_pred chhcchhhcccch-----hhhhhhHHhhhhHHHHHHHhhccCC--CcCCCCCCCCCCCCCCCCCCCCCCCCCCcccCCCC
Q 005091 402 VHATQVNLETASE-----EQETDFVREVKYEDEVEKLLDGLGP--RYTDWPGCDPLPVDADMLPGIVPGYQPPFRVLPYG 474 (715)
Q Consensus 402 ~~~~~~~~~~~~~-----~~~~~~~~~~~~e~e~d~LLd~Lgp--R~~dW~g~~plPVDadLLPa~vPgyk~PfR~lP~g 474 (715)
.......|+.... .....+......+...+.+.+.+.. ++..|.......++....|+. ++.
T Consensus 310 ~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~-----------~~~ 378 (564)
T KOG1990|consen 310 LARAKAKKEKEIERRSISSRLKLEFEKASSEKLTEAIFHKLEKAKKKLASANRILAKLEDPKIPAE-----------LRY 378 (564)
T ss_pred HHHHhcccccCcccccccchhhhhhhccchhhHHHHHHHHHhhhhhhccchhhhhhcccccccccc-----------ccc
Confidence 4444444432211 1233344445555566666666655 677788777888888888887 336
Q ss_pred CCccCCHHHHHHHHHhccCCCCeEEeCCCCchHHHHHHHHHHHHhcCeeEEEEcCCCChhhHHHHHHHHHHHhCCeEEEe
Q 005091 475 VRSTLARKEATNLQRLARVLPPHFALGRSRQLQGLAVAMIKLWEKSSIAKIALKRGVQLTTSERMVEDIKKLTGGTLLSR 554 (715)
Q Consensus 475 ~~e~LT~kEr~~LRklAh~LkPvv~LGknGvtdgvi~~I~~awekhELIKIkik~g~~~~~~~~mAeeL~~~TGg~LVq~ 554 (715)
+++.+|.+++.+++++|.++++.+.+|++|+++|++.+||.||+++|++||.|+........+..|..++.++|+++|++
T Consensus 379 ~~e~~t~ee~~~~~k~g~k~~~~~~~~rrg~f~g~i~n~~l~wk~~e~~k~i~~~~~~~~~~~~~a~~le~esg~~~v~~ 458 (564)
T KOG1990|consen 379 DPESITEEERLMLRKVGLKMKRRLLSGRRGVFDGVIENMHLHWKSRELVKVICKEKNLPSQVKQYASALERESGGILVSI 458 (564)
T ss_pred chhhcChHHHHHHHHHHHhhccccccCCcccccceeecchhhhhhcccceeeeccccccHHHHHHHHHHHHHhCCceeee
Confidence 88999999999999999999999999999999999999999999999999999886666899999999999999999999
Q ss_pred eC----CEEEEEcCCCCCChhHH---HHHHHHHHHHHHHHHHHHHHHHhhhhccccchhh
Q 005091 555 NK----DFLVFYRGKNFLSPDVT---EALQERERLAKSLQDEEEQARLRASAFVLPSIET 607 (715)
Q Consensus 555 iG----~~IILYRgkn~~~p~v~---n~L~kr~al~rs~q~~Ee~ar~~a~~~~~~~~~~ 607 (715)
+. +.|++|||++|..|..+ +.|++|+++.+++..+ +.+|...+++..+.
T Consensus 459 ~~~~~~~ai~~yr~k~y~~p~~l~P~~~l~~~k~~~~~~~~~----~~~a~~~~i~~~~~ 514 (564)
T KOG1990|consen 459 DKNPKGYAIIAYRGKNYDRPTSLRPRNLLSRRKALERSLEEQ----RKEALKSHISDLEQ 514 (564)
T ss_pred ccCCchhhHHHhhhhhccCCcccCchhhhcccCCccccHHHH----HHHHHhhhcchhhh
Confidence 87 45899999999998884 9999999999998887 66666655554433
No 9
>COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]
Probab=99.88 E-value=2.8e-22 Score=179.76 Aligned_cols=86 Identities=26% Similarity=0.380 Sum_probs=84.5
Q ss_pred CCCHHHHHHHHhhhcCCCCeEEeCCCCCCHHHHHHHHHHHHhCCeEEEEecCCChhhHHHHHHHHHHHhCCeEEEEECcE
Q 005091 253 TLPESELRRLRNLTFQTKSKTRIKGAGLTQAVVDIIHEKWKTSEIVRLKIEGAPALNMKRMHEILERKTGGLVIWRSGTA 332 (715)
Q Consensus 253 ~Lt~kErr~LR~lA~~Lkp~v~IGK~GlTd~Vv~~I~~awek~ELVKIK~~g~~~~dmk~~ae~Le~kTGg~VVqriG~~ 332 (715)
+||++|+++||+.||+++|+|+|||+|||++|+++|.++|++||||||++.+++..+.+++|+.|++.+|+.+||.||++
T Consensus 1 ~Lt~kq~~~Lrs~Ah~l~piv~IGk~Glte~vi~Ei~~aL~~reLIKVkvl~~~~edr~eia~~l~~~~~a~lVqviG~~ 80 (97)
T COG1534 1 MLTGKQKRFLRSKAHHLKPIVQIGKNGLTEGVIKEIDRALEARELIKVKVLQNAREDKKEIAEALAEETGAELVQVIGKT 80 (97)
T ss_pred CCcHHHHHHHHHhhccCCceEEecCCccCHHHHHHHHHHHHhCCcEEEEeeccchhhHHHHHHHHHHHhCCEEeeeeeeE
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEeeC
Q 005091 333 VSLYRG 338 (715)
Q Consensus 333 iVLYRG 338 (715)
+||||.
T Consensus 81 ~vlyr~ 86 (97)
T COG1534 81 LVLYRE 86 (97)
T ss_pred EEEEec
Confidence 999993
No 10
>COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]
Probab=99.87 E-value=4.3e-22 Score=178.61 Aligned_cols=88 Identities=20% Similarity=0.302 Sum_probs=84.4
Q ss_pred cCCHHHHHHHHHhccCCCCeEEeCCCCchHHHHHHHHHHHHhcCeeEEEEcCCCChhhHHHHHHHHHHHhCCeEEEeeCC
Q 005091 478 TLARKEATNLQRLARVLPPHFALGRSRQLQGLAVAMIKLWEKSSIAKIALKRGVQLTTSERMVEDIKKLTGGTLLSRNKD 557 (715)
Q Consensus 478 ~LT~kEr~~LRklAh~LkPvv~LGknGvtdgvi~~I~~awekhELIKIkik~g~~~~~~~~mAeeL~~~TGg~LVq~iG~ 557 (715)
+||++|+.+||++||+++|+|+||++|++++|+++|..+|++||||||++.+ ++.++.+++|+.|++.+|+.+||+||+
T Consensus 1 ~Lt~kq~~~Lrs~Ah~l~piv~IGk~Glte~vi~Ei~~aL~~reLIKVkvl~-~~~edr~eia~~l~~~~~a~lVqviG~ 79 (97)
T COG1534 1 MLTGKQKRFLRSKAHHLKPIVQIGKNGLTEGVIKEIDRALEARELIKVKVLQ-NAREDKKEIAEALAEETGAELVQVIGK 79 (97)
T ss_pred CCcHHHHHHHHHhhccCCceEEecCCccCHHHHHHHHHHHHhCCcEEEEeec-cchhhHHHHHHHHHHHhCCEEeeeeee
Confidence 5999999999999999999999999999999999999999999999999987 688899999999999999999999999
Q ss_pred EEEEEcCCC
Q 005091 558 FLVFYRGKN 566 (715)
Q Consensus 558 ~IILYRgkn 566 (715)
++||||.+.
T Consensus 80 ~~vlyr~~~ 88 (97)
T COG1534 80 TLVLYRESK 88 (97)
T ss_pred EEEEEecCc
Confidence 999999543
No 11
>cd08619 PI-PLCXDc_plant Catalytic domain of phosphatidylinositol-specific phospholipase C, X domain containing proteins found in plants. The CD corresponds to the catalytic domain present in uncharacterized plant phosphatidylinositol-specific phospholipase C, X domain containing proteins (PI-PLCXD). The typical eukaryotic phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11) has a multidomain organization that consists of a PLC catalytic core domain, and various regulatory domains. The catalytic core domain is assembled from two highly conserved X- and Y-regions split by a divergent linker sequence. In contrast, plant PI-PLCXDs contain a single TIM-barrel type catalytic domain, X domain, and are more closely related to bacterial PI-PLCs, which participate in Ca2+-independent PI metabolism, hydrolyzing the membrane lipid phosphatidylinositol (PI) to produce phosphorylated myo-inositol and diacylglycerol (DAG). Although the biological function of plant PI-PLCXDs still remains u
Probab=31.41 E-value=98 Score=33.94 Aligned_cols=68 Identities=7% Similarity=0.185 Sum_probs=51.1
Q ss_pred chHHHHHHHHHHHHhc--CeeEEEEcCCCChhhHHHHHHHHHHHhCCeEEEee-------------CCEEEEEcCCCCCC
Q 005091 505 QLQGLAVAMIKLWEKS--SIAKIALKRGVQLTTSERMVEDIKKLTGGTLLSRN-------------KDFLVFYRGKNFLS 569 (715)
Q Consensus 505 vtdgvi~~I~~awekh--ELIKIkik~g~~~~~~~~mAeeL~~~TGg~LVq~i-------------G~~IILYRgkn~~~ 569 (715)
.++.|+.+|..-+..| |+|-+.++.-...++..+....|.+..|..++... +.+||+|+...|..
T Consensus 92 ~~~dvL~~i~~FL~~hp~EvVIL~~k~ey~~~~~~~~~~~li~~lGd~l~~~~~~~~~~TL~eL~~krVIviy~~~~~~~ 171 (285)
T cd08619 92 PVDVVLNDIKRFLSETKSEFVILEIRTEYGHEDPPQFDLWLVEQLGDHLIHQDDSVFSKTLAELLPKRVICIWKPRKSPA 171 (285)
T ss_pred cHHHHHHHHHHHHHHCCCeEEEEEEeecccCCCchHHHHHHHHHhcchhccCCCccccccHHHHhCCcEEEEEcCCCCCc
Confidence 5788999999999777 99999997643344444566777888898888663 25799999987765
Q ss_pred hhH
Q 005091 570 PDV 572 (715)
Q Consensus 570 p~v 572 (715)
|.+
T Consensus 172 ~~~ 174 (285)
T cd08619 172 PAV 174 (285)
T ss_pred cCC
Confidence 544
No 12
>PF04472 DUF552: Protein of unknown function (DUF552); InterPro: IPR007561 This entry represents a cell division protein, designated SepF, which is conserved in Gram-positive bacteria. SepF accumulates at the cell division site in an FtsZ-dependent manner and is required for proper septum formation []. Mutants are viable but the formation of the septum is much slower and occurs with a very abnormal morphology. This entry also includes archaeal related proteins of unknown function.; GO: 0000917 barrier septum formation; PDB: 3P04_A.
Probab=25.02 E-value=4.3e+02 Score=22.72 Aligned_cols=55 Identities=18% Similarity=0.169 Sum_probs=37.2
Q ss_pred HHHHHHHHHhCCeEEEEecCCChhhHHHHHHHHHH---HhCCeEEEEECcEEEEeeCCC
Q 005091 285 VDIIHEKWKTSEIVRLKIEGAPALNMKRMHEILER---KTGGLVIWRSGTAVSLYRGVS 340 (715)
Q Consensus 285 v~~I~~awek~ELVKIK~~g~~~~dmk~~ae~Le~---kTGg~VVqriG~~iVLYRGkn 340 (715)
+.+|-++++...+|=|.+........+++.+.|.. ..+|.+.+...+ ++||=+++
T Consensus 12 ~~~i~~~l~~g~~Vivnl~~l~~~~~~Ri~Dfl~G~~~al~G~i~~i~~~-~~l~~P~~ 69 (73)
T PF04472_consen 12 AREIVDALREGKIVIVNLENLDDEEAQRILDFLSGAVYALDGDIQKISEK-VFLLTPKG 69 (73)
T ss_dssp HHHHHHHHHTT--EEEE-TTS-HHHHHHHHHHHHHHHHHTT-EEEEEETT-EEEEE---
T ss_pred HHHHHHHHHcCCEEEEECCCCCHHHHHHHHHHHhchheeeCCEEEEEcCC-EEEEECCC
Confidence 45688999999999999998888888999888874 679998777555 55554443
No 13
>PF15249 GLTSCR1: Glioma tumor suppressor candidate region
Probab=24.31 E-value=30 Score=32.24 Aligned_cols=19 Identities=47% Similarity=0.950 Sum_probs=12.5
Q ss_pred CCCCCCc--------ccCCCCCCccCC
Q 005091 462 PGYQPPF--------RVLPYGVRSTLA 480 (715)
Q Consensus 462 Pgyk~Pf--------R~lP~g~~e~LT 480 (715)
|.|++|| |||||++=-...
T Consensus 15 PD~~tPF~s~~DA~~RLLPYHv~~~~~ 41 (109)
T PF15249_consen 15 PDYKTPFRSLEDAVERLLPYHVFQEPE 41 (109)
T ss_pred CCcCCCCCCHHHHHHHhcchhhhcCCC
Confidence 6777888 577877654433
No 14
>cd08619 PI-PLCXDc_plant Catalytic domain of phosphatidylinositol-specific phospholipase C, X domain containing proteins found in plants. The CD corresponds to the catalytic domain present in uncharacterized plant phosphatidylinositol-specific phospholipase C, X domain containing proteins (PI-PLCXD). The typical eukaryotic phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11) has a multidomain organization that consists of a PLC catalytic core domain, and various regulatory domains. The catalytic core domain is assembled from two highly conserved X- and Y-regions split by a divergent linker sequence. In contrast, plant PI-PLCXDs contain a single TIM-barrel type catalytic domain, X domain, and are more closely related to bacterial PI-PLCs, which participate in Ca2+-independent PI metabolism, hydrolyzing the membrane lipid phosphatidylinositol (PI) to produce phosphorylated myo-inositol and diacylglycerol (DAG). Although the biological function of plant PI-PLCXDs still remains u
Probab=23.42 E-value=1.8e+02 Score=31.90 Aligned_cols=68 Identities=16% Similarity=0.214 Sum_probs=50.5
Q ss_pred CHHHHHHHHHHHHhC--CeEEEEecCCCh-hhHHHHHHHHHHHhCCeEEEEE-------------CcEEEEeeCCCCCCc
Q 005091 281 TQAVVDIIHEKWKTS--EIVRLKIEGAPA-LNMKRMHEILERKTGGLVIWRS-------------GTAVSLYRGVSYEVP 344 (715)
Q Consensus 281 Td~Vv~~I~~awek~--ELVKIK~~g~~~-~dmk~~ae~Le~kTGg~VVqri-------------G~~iVLYRGknY~~p 344 (715)
-+.|+++|..-+..| |+|=+.|+.... .+.......|.+..|..++.+. ..+||+|+...|..|
T Consensus 93 ~~dvL~~i~~FL~~hp~EvVIL~~k~ey~~~~~~~~~~~li~~lGd~l~~~~~~~~~~TL~eL~~krVIviy~~~~~~~~ 172 (285)
T cd08619 93 VDVVLNDIKRFLSETKSEFVILEIRTEYGHEDPPQFDLWLVEQLGDHLIHQDDSVFSKTLAELLPKRVICIWKPRKSPAP 172 (285)
T ss_pred HHHHHHHHHHHHHHCCCeEEEEEEeecccCCCchHHHHHHHHHhcchhccCCCccccccHHHHhCCcEEEEEcCCCCCcc
Confidence 478999999999876 999999973322 2222455677778888888663 357999999999877
Q ss_pred hhhh
Q 005091 345 SVQL 348 (715)
Q Consensus 345 ~v~~ 348 (715)
.+..
T Consensus 173 ~~~~ 176 (285)
T cd08619 173 AVGS 176 (285)
T ss_pred CCCC
Confidence 7653
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=22.43 E-value=5e+02 Score=22.29 Aligned_cols=51 Identities=10% Similarity=0.257 Sum_probs=35.6
Q ss_pred HHHHHHHHHhcCeeEEEEcCCCChhhHHHHHHHHHH---HhCCeEEEeeCCEEEE
Q 005091 510 AVAMIKLWEKSSIAKIALKRGVQLTTSERMVEDIKK---LTGGTLLSRNKDFLVF 561 (715)
Q Consensus 510 i~~I~~awekhELIKIkik~g~~~~~~~~mAeeL~~---~TGg~LVq~iG~~IIL 561 (715)
+.+|..+++...+|=|.+. ....+..+++.+.|+- ..+|.+..+-.+++++
T Consensus 12 ~~~i~~~l~~g~~Vivnl~-~l~~~~~~Ri~Dfl~G~~~al~G~i~~i~~~~~l~ 65 (73)
T PF04472_consen 12 AREIVDALREGKIVIVNLE-NLDDEEAQRILDFLSGAVYALDGDIQKISEKVFLL 65 (73)
T ss_dssp HHHHHHHHHTT--EEEE-T-TS-HHHHHHHHHHHHHHHHHTT-EEEEEETTEEEE
T ss_pred HHHHHHHHHcCCEEEEECC-CCCHHHHHHHHHHHhchheeeCCEEEEEcCCEEEE
Confidence 4558889999999999994 4677788888888874 7899998886665543
No 16
>PF12720 DUF3807: Protein of unknown function (DUF3807); InterPro: IPR024526 This is a family of conserved fungal proteins of unknown function.
Probab=21.19 E-value=67 Score=32.71 Aligned_cols=35 Identities=20% Similarity=0.296 Sum_probs=30.4
Q ss_pred CCCCCccCCHHHHHHHHHhccCCCCeEEeCCCCchHHHHHHHHHHHHhcCeeEEEE
Q 005091 472 PYGVRSTLARKEATNLQRLARVLPPHFALGRSRQLQGLAVAMIKLWEKSSIAKIAL 527 (715)
Q Consensus 472 P~g~~e~LT~kEr~~LRklAh~LkPvv~LGknGvtdgvi~~I~~awekhELIKIki 527 (715)
|+|++-+||++|+.+||. .+|+.++..+|+.+..-
T Consensus 43 pDGVKRTLTDEQI~IFRH---------------------SEI~aL~Rere~~~e~~ 77 (172)
T PF12720_consen 43 PDGVKRTLTDEQIEIFRH---------------------SEIQALRRERELREEAE 77 (172)
T ss_pred CCCCcccccHHHHHHHHH---------------------HHHHHHHHHHHHHHHhh
Confidence 999999999999999986 58888888888877765
No 17
>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=21.06 E-value=1.4e+02 Score=28.44 Aligned_cols=39 Identities=23% Similarity=0.166 Sum_probs=33.1
Q ss_pred HHHHHHHHhccCCC-CeEEeCCCCchHHHHHHHHHHHHhc
Q 005091 482 KEATNLQRLARVLP-PHFALGRSRQLQGLAVAMIKLWEKS 520 (715)
Q Consensus 482 kEr~~LRklAh~Lk-Pvv~LGknGvtdgvi~~I~~awekh 520 (715)
-+.-.+.+++.+-+ |++.++.+|-++++++.|....+..
T Consensus 71 ~~~~~~~~l~~~~~~Piil~~~~g~w~~l~~~l~~~~~~g 110 (133)
T PF03641_consen 71 FEALTLMQLGRHNKVPIILLNIDGFWDPLLEFLDRMIEEG 110 (133)
T ss_dssp HHHHHHHHTTSSTS-EEEEEECGGCCHHHHHHHHHHHHTT
T ss_pred HHHHHHHhhccccCCCEEEeCCcchHHHHHHHHHHHHHCC
Confidence 36677889998899 9999999999999999997666543
No 18
>TIGR00730 conserved hypothetical protein, DprA/Smf-related, family 2. This model represents one branch of a subfamily of proteins of unknown function. Both PSI-BLAST and weak hits by this model show a low level of similarity to and suggest an evolutionary relationship of the subfamily to the DprA/Smf family of DNA-processing proteins involved in chromosomal transformation with foreign DNA. Both Aquifex aeolicus and Mycobacterium leprae have one member in each of two branches of this subfamily, suggesting that the branches may have distinct functions.
Probab=20.55 E-value=1.5e+02 Score=29.93 Aligned_cols=58 Identities=12% Similarity=0.241 Sum_probs=41.7
Q ss_pred HHHHHHHhccCCCCeEEeCCCCchHHHHHHHHHHHHhc-----CeeEEEEcCCCChhhHHHHHHHHHH
Q 005091 483 EATNLQRLARVLPPHFALGRSRQLQGLAVAMIKLWEKS-----SIAKIALKRGVQLTTSERMVEDIKK 545 (715)
Q Consensus 483 Er~~LRklAh~LkPvv~LGknGvtdgvi~~I~~awekh-----ELIKIkik~g~~~~~~~~mAeeL~~ 545 (715)
|.-.+.+++.+-+|++.++-+|.++.+++-|+...+.. .+-.|.+ -++.+++.+.|+.
T Consensus 115 e~~~~~qlg~~~kPiil~n~~g~~~~l~~~l~~~~~~gfi~~~~~~~~~~-----~d~~~e~~~~i~~ 177 (178)
T TIGR00730 115 EVLTWAQLGIHQKPIILFNVNGHFDGLVEWLKYSIQEGFISESHLKLIHV-----VSRPDELIEQVQN 177 (178)
T ss_pred HHHHHHHcCCCCCCEEEECCcchHHHHHHHHHHHHHCCCCCHHHcCcEEE-----cCCHHHHHHHHHh
Confidence 56668899999999999999999999999888555542 2222333 2456777776643
Done!