Query 002966
Match_columns 862
No_of_seqs 331 out of 980
Neff 4.0
Searched_HMMs 46136
Date Thu Mar 28 14:21:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002966.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002966hhsearch_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 3.7E-78 8.1E-83 686.9 23.3 533 242-848 3-540 (564)
2 PRK10343 RNA-binding protein Y 99.9 1E-24 2.2E-29 199.7 12.7 89 252-340 1-89 (97)
3 PRK10343 RNA-binding protein Y 99.9 2.6E-24 5.7E-29 197.0 13.3 89 690-782 1-89 (97)
4 PF01985 CRS1_YhbY: CRS1 / Yhb 99.9 1.4E-24 3.1E-29 193.2 10.8 84 254-337 1-84 (84)
5 TIGR00253 RNA_bind_YhbY putati 99.9 2.9E-24 6.2E-29 196.1 12.4 87 692-782 1-87 (95)
6 TIGR00253 RNA_bind_YhbY putati 99.9 5E-24 1.1E-28 194.6 12.6 87 254-340 1-87 (95)
7 PF01985 CRS1_YhbY: CRS1 / Yhb 99.9 6.4E-24 1.4E-28 189.1 10.4 84 692-779 1-84 (84)
8 COG1534 Predicted RNA-binding 99.9 3.7E-23 8E-28 188.9 12.1 96 691-791 1-96 (97)
9 KOG1990 Poly(A)-specific exori 99.9 1.3E-23 2.8E-28 241.0 6.4 328 244-605 165-512 (564)
10 COG1534 Predicted RNA-binding 99.9 5.1E-22 1.1E-26 181.5 12.0 87 253-339 1-87 (97)
11 PF04472 DUF552: Protein of un 25.7 2.4E+02 0.0052 24.9 6.4 56 723-783 12-70 (73)
12 PF12207 DUF3600: Domain of un 25.4 15 0.00034 37.4 -1.2 93 654-748 28-136 (162)
13 COG1623 Predicted nucleic-acid 24.7 1.4E+02 0.0029 34.0 5.6 50 745-798 104-153 (349)
14 PF15337 Vasculin: Vascular pr 24.5 67 0.0014 30.7 2.7 43 478-521 33-75 (97)
15 PF15249 GLTSCR1: Glioma tumor 24.0 30 0.00066 33.0 0.5 17 460-476 13-37 (109)
16 PF04472 DUF552: Protein of un 22.8 4.6E+02 0.0099 23.1 7.6 55 285-340 12-69 (73)
17 PF07820 TraC: TraC-like prote 22.4 1E+02 0.0022 29.4 3.6 37 815-851 2-54 (92)
No 1
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=100.00 E-value=3.7e-78 Score=686.91 Aligned_cols=533 Identities=46% Similarity=0.674 Sum_probs=496.2
Q ss_pred ccccccccccCCCCHHHHHHHHhhhcCCCCeEEeCCCCcCHHHHHHHHHHHHhCCeEEEEecCCChhhHHHHHHHHHHHh
Q 002966 242 RRSSRTSLAELTLPESELRRLRNLTFQTKSKTRIKGAGLTQAVVDIIHEKWKTSEIVRLKIEGAPALNMKRMHEILERKT 321 (862)
Q Consensus 242 ~~~~~p~~ae~tLt~kErr~LR~lAh~LkpvV~IGK~GlTq~Vv~eI~~awe~~ELVKIKv~g~~~~dmk~~ae~Le~kT 321 (862)
+..+ +.+|++++...++.+||..|..+...+ +++|+|+.+++.|+..|+.+|+++++|....+.+|.+++++++..|
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 999999999999999999999998777 9999999999999999999999999999999999999999999999
Q ss_pred CC-eEEEEECcEEEEeeCCCCCCchhhhhHHHhhhccCCCCcccchhhhhhhhhhccccCCcccccccccCCCCCCCCcc
Q 002966 322 GG-LVIWRSGTAVSLYRGVSYEVPSVQLNKRIYKRNELPASSVSQATDKQIHKQISMSGNSLSAAADKTAQDPSNFDSYN 400 (862)
Q Consensus 322 Gg-eVIqrIG~~iVLYRg~~Y~~P~v~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 400 (862)
|| .+||+.|.++..|++..|..|.+..+ ++++ .+
T Consensus 80 ~~n~~~~~~g~~~s~~~~~~~~~~~~~~~----~~~~-----------~~------------------------------ 114 (564)
T KOG1990|consen 80 GGNFVVWSRGDSISSPEFLCQRSPVDFVA----RQQE-----------NQ------------------------------ 114 (564)
T ss_pred CCceeeeecCccccCCccceeecchhhhh----hhch-----------hh------------------------------
Confidence 99 99999999999998888887765321 1100 00
Q ss_pred ccccchhhhccccchhhhhhhhhhchHHHHHHHhhccCCCCCCCCCCCCCCccCCCCCCCCCCCCCCcccCCCCCCCCCC
Q 002966 401 NVHATQVNLETASEEQETDFVREVKYEDEVEKLLDGLGPRYTDWPGCDPLPVDADMLPGIVPGYQPPFRVLPYGVRSTLA 480 (862)
Q Consensus 401 ~~~~~~l~~~~~~~~~~~~~l~e~~~e~e~~kLLd~LGPRf~dW~g~~PlPVDADLLP~~VPgyk~PfRllP~gvr~~LT 480 (862)
... -..+++++.+.++++|||++.||||.+|+|||+||+|..||+|.+|||.||+|++++||
T Consensus 115 ----------------~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dl~~~~i~~~~~p~r~l~~~~~~~l~ 176 (564)
T KOG1990|consen 115 ----------------AGK--WPSELEKEKNELLDSLGPELSDWGGSDRLSVDADLLPEKIPDYMRPFRTLPVGSPPLLT 176 (564)
T ss_pred ----------------hhh--hHHHHHHHHHHHhhccCcccccCCCCCCccchhhhchhhhhcccChhccCCCCChhhhh
Confidence 000 01456789999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhhhcCCCeeeecccchhhHHHHHHHHHHhhhceeeeeeccCCCcchHHHHHHHH--HhhcCCeEEeecccE
Q 002966 481 RKEATNLQRLARVLPPHFALGRSRQLQGLAVAMIKLWEKSSIAKIALKRGVQLTTSERMVEDI--KKLTGGTLLSRNKDF 558 (862)
Q Consensus 481 deE~t~lRkLar~lp~hfaLGRnr~lqGLa~am~klWEkseIvKIavKrGvqnt~~e~mA~eL--k~LTGGvLLSrnK~~ 558 (862)
..|+|++|+||...||||+||+++.+||++.+|+++|++++++||++++|++++.++.||.+| ..+|||+||++|+++
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 EEEEecCCCCChHHHHHHHHHHHHHHHHhhHHHHHHHhhhcccccCcccccccCcccchHHHHhhhhccCCCCChhHH-H
Q 002966 559 LVFYRGKNFLSPDVTEALQERERLAKSLQDEEEQARLRASAFVLPSIETIEKSGTAGTLKETLDANSRWGKRLDDSHK-E 637 (862)
Q Consensus 559 II~YRGKDFlpp~V~~~L~eReal~rs~q~~EE~aR~~a~~~~~~~~~~~~~~~~aGTl~e~~ea~~~~g~~~~~~~~-~ 637 (862)
+|+||||+|++ .+..+|.+++++....++.++.+|+.++... .....++|+.|+..+.++|+.++.-... .
T Consensus 257 dv~y~~~~Fl~-~lp~~l~~f~~~~~~fp~~~~~~~~~~~~~~-------~~~~~~~t~~e~~~~~~~~~~~~~~~~~~~ 328 (564)
T KOG1990|consen 257 DVMYRYKNFLS-PLPSTLEEFTDSSSMFPNIEDTKRLAKLSEY-------QKLNLKATLLELARAKAKKEKEIERRSISS 328 (564)
T ss_pred eeeeehhhccc-ccchhHHHhhhhhhhhhhhHHHHHhhccccc-------cchhhhhhHHHHHHHhcccccCcccccccc
Confidence 99999999999 9999999999998888999999999983211 1256899999999999999999975543 4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccCCCCCCCCCCCCCHHHHHHHHhhccCCCceEEeCCCC
Q 002966 638 NLVREAEVRRHAYLVQKLEKKLARAERKLLRAERALSKVEESLKPAERQADPESITDEERFMFRKLGLRMKAFLLLGRRG 717 (862)
Q Consensus 638 ~~~~e~~~~r~~~~~k~~e~kL~~a~~K~~~ae~~L~Kle~~~~p~~~~~d~e~LT~eER~~LRklahkmKpvV~IGK~G 717 (862)
.+..+.....+++..+.+.++++.+.+|+.++++.|++++....|++.+.|++.+|.+++.+++++|.+|++++.+|++|
T Consensus 329 ~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~e~~t~ee~~~~~k~g~k~~~~~~~~rrg 408 (564)
T KOG1990|consen 329 RLKLEFEKASSEKLTEAIFHKLEKAKKKLASANRILAKLEDPKIPAELRYDPESITEEERLMLRKVGLKMKRRLLSGRRG 408 (564)
T ss_pred hhhhhhhccchhhHHHHHHHHHhhhhhhccchhhhhhcccccccccccccchhhcChHHHHHHHHHHHhhccccccCCcc
Confidence 67888999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCHHHHHHHHHHHHhCCeEEEEEcCCCH-HHHHHHHHHHHHHhCCEEEeccccccCcEEEEEecCCCCCCCCCCCCCccc
Q 002966 718 VFDGTVENMHLHWKYRELVKIIVKVKTF-DQAKKIALALEAESGGVLVSVDKISKGYAMVVYRGKDYQRPSTLRPKNLLT 796 (862)
Q Consensus 718 VtdgVIeeIh~hwk~hELVKVkv~~~~~-~d~~eiae~Le~~SGg~lVqV~k~~IG~~iILYRgknY~~P~~l~P~~lLt 796 (862)
+++|+|.+||.||++||++||+|+.... .++++.|..++..+|+++|+|+++..|+.|++|||+||++|..|+|.++|+
T Consensus 409 ~f~g~i~n~~l~wk~~e~~k~i~~~~~~~~~~~~~a~~le~esg~~~v~~~~~~~~~ai~~yr~k~y~~p~~l~P~~~l~ 488 (564)
T KOG1990|consen 409 VFDGVIENMHLHWKSRELVKVICKEKNLPSQVKQYASALERESGGILVSIDKNPKGYAIIAYRGKNYDRPTSLRPRNLLS 488 (564)
T ss_pred cccceeecchhhhhhcccceeeeccccccHHHHHHHHHHHHHhCCceeeeccCCchhhHHHhhhhhccCCcccCchhhhc
Confidence 9999999999999999999999998766 999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCchHHHHh
Q 002966 797 KRKALARSIELQRQEALLKHVATLESNAGRLRSEIEQMNSVKGTGDEQLYDK 848 (862)
Q Consensus 797 KrkAl~rs~~~qr~~~l~~~i~~l~~~i~~l~~~l~~~~~~~~~~d~~~~~~ 848 (862)
||+|+.+++++|+.++++.||..+..++++++.+++.|.....+.|.+.|++
T Consensus 489 ~~k~~~~~~~~~~~~a~~~~i~~~~~~~e~~~~~~~~~~~~~~~~d~~~en~ 540 (564)
T KOG1990|consen 489 RRKALERSLEEQRKEALKSHISDLEQEIEQLQASVEAMPAINKKDDLEEENS 540 (564)
T ss_pred ccCCccccHHHHHHHHHhhhcchhhhhHHHhhcchhcccccccccchHHHhh
Confidence 9999999999999999999999999999999999999999999999999997
No 2
>PRK10343 RNA-binding protein YhbY; Provisional
Probab=99.92 E-value=1e-24 Score=199.65 Aligned_cols=89 Identities=22% Similarity=0.349 Sum_probs=87.2
Q ss_pred CCCCHHHHHHHHhhhcCCCCeEEeCCCCcCHHHHHHHHHHHHhCCeEEEEecCCChhhHHHHHHHHHHHhCCeEEEEECc
Q 002966 252 LTLPESELRRLRNLTFQTKSKTRIKGAGLTQAVVDIIHEKWKTSEIVRLKIEGAPALNMKRMHEILERKTGGLVIWRSGT 331 (862)
Q Consensus 252 ~tLt~kErr~LR~lAh~LkpvV~IGK~GlTq~Vv~eI~~awe~~ELVKIKv~g~~~~dmk~~ae~Le~kTGgeVIqrIG~ 331 (862)
|+||++|+++||++||+|+|+|+|||+|||++|+++|+++|++||||||+|++++..+.++++++|+++||+++||.||+
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 57999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEeeCCC
Q 002966 332 AVSLYRGVS 340 (862)
Q Consensus 332 ~iVLYRg~~ 340 (862)
++||||+++
T Consensus 81 ~~vlYR~~~ 89 (97)
T PRK10343 81 TLVLYRPTK 89 (97)
T ss_pred EEEEEecCC
Confidence 999999985
No 3
>PRK10343 RNA-binding protein YhbY; Provisional
Probab=99.91 E-value=2.6e-24 Score=196.99 Aligned_cols=89 Identities=21% Similarity=0.394 Sum_probs=86.4
Q ss_pred CCCCHHHHHHHHhhccCCCceEEeCCCCCCHHHHHHHHHHHHhCCeEEEEEcCCCHHHHHHHHHHHHHHhCCEEEecccc
Q 002966 690 ESITDEERFMFRKLGLRMKAFLLLGRRGVFDGTVENMHLHWKYRELVKIIVKVKTFDQAKKIALALEAESGGVLVSVDKI 769 (862)
Q Consensus 690 e~LT~eER~~LRklahkmKpvV~IGK~GVtdgVIeeIh~hwk~hELVKVkv~~~~~~d~~eiae~Le~~SGg~lVqV~k~ 769 (862)
++||++||++||++||+|+|+|+||++||||+|+++|+.+|++||||||++.+++.+++++++++||+.|||++||
T Consensus 1 m~Lt~kqr~~LR~~ah~l~Pvv~IGk~Glt~~vi~ei~~aL~~hELIKvkv~~~~~~~~~e~~~~i~~~~~ae~Vq---- 76 (97)
T PRK10343 1 MNLSTKQKQHLKGLAHPLKPVVLLGSNGLTEGVLAEIEQALEHHELIKVKIATEDRETKTLIVEAIVRETGACNVQ---- 76 (97)
T ss_pred CCCCHHHHHHHHHhcCCCCCeEEECCCCCCHHHHHHHHHHHHHCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEe----
Confidence 3699999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCcEEEEEecCC
Q 002966 770 SKGYAMVVYRGKD 782 (862)
Q Consensus 770 ~IG~~iILYRgkn 782 (862)
.||+++||||++.
T Consensus 77 ~IG~~~vlYR~~~ 89 (97)
T PRK10343 77 VIGKTLVLYRPTK 89 (97)
T ss_pred eeCcEEEEEecCC
Confidence 6999999999864
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=99.91 E-value=1.4e-24 Score=193.24 Aligned_cols=84 Identities=32% Similarity=0.466 Sum_probs=75.7
Q ss_pred CCHHHHHHHHhhhcCCCCeEEeCCCCcCHHHHHHHHHHHHhCCeEEEEecCCChhhHHHHHHHHHHHhCCeEEEEECcEE
Q 002966 254 LPESELRRLRNLTFQTKSKTRIKGAGLTQAVVDIIHEKWKTSEIVRLKIEGAPALNMKRMHEILERKTGGLVIWRSGTAV 333 (862)
Q Consensus 254 Lt~kErr~LR~lAh~LkpvV~IGK~GlTq~Vv~eI~~awe~~ELVKIKv~g~~~~dmk~~ae~Le~kTGgeVIqrIG~~i 333 (862)
||++|+++||++||+++|+|+|||+|+|++|+++|+++|++||||||+|.+++..++++++++|+++|||++||++|+++
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 002966 334 SLYR 337 (862)
Q Consensus 334 VLYR 337 (862)
||||
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
>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=2.9e-24 Score=196.13 Aligned_cols=87 Identities=26% Similarity=0.445 Sum_probs=84.9
Q ss_pred CCHHHHHHHHhhccCCCceEEeCCCCCCHHHHHHHHHHHHhCCeEEEEEcCCCHHHHHHHHHHHHHHhCCEEEecccccc
Q 002966 692 ITDEERFMFRKLGLRMKAFLLLGRRGVFDGTVENMHLHWKYRELVKIIVKVKTFDQAKKIALALEAESGGVLVSVDKISK 771 (862)
Q Consensus 692 LT~eER~~LRklahkmKpvV~IGK~GVtdgVIeeIh~hwk~hELVKVkv~~~~~~d~~eiae~Le~~SGg~lVqV~k~~I 771 (862)
||++||++||++||+|+|+|+||++||||+||++|+.+|++||||||++.+++.++++++|++||+.|||++|| .|
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 LTGKQKRHLRGKAHHLKPVVLVGKNGLTEGVIKEIEQALEHRELIKVKVATEDREDKTLIAEALVKETGACNVQ----VI 76 (95)
T ss_pred CCHHHHHHHHHHhCCCCCeEEECCCCCCHHHHHHHHHHHHhCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEE----EE
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999 69
Q ss_pred CcEEEEEecCC
Q 002966 772 GYAMVVYRGKD 782 (862)
Q Consensus 772 G~~iILYRgkn 782 (862)
|+++||||++.
T Consensus 77 G~~~vlYR~~~ 87 (95)
T TIGR00253 77 GKTIVLYRPTK 87 (95)
T ss_pred ccEEEEEecCC
Confidence 99999999863
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=5e-24 Score=194.55 Aligned_cols=87 Identities=23% Similarity=0.356 Sum_probs=85.6
Q ss_pred CCHHHHHHHHhhhcCCCCeEEeCCCCcCHHHHHHHHHHHHhCCeEEEEecCCChhhHHHHHHHHHHHhCCeEEEEECcEE
Q 002966 254 LPESELRRLRNLTFQTKSKTRIKGAGLTQAVVDIIHEKWKTSEIVRLKIEGAPALNMKRMHEILERKTGGLVIWRSGTAV 333 (862)
Q Consensus 254 Lt~kErr~LR~lAh~LkpvV~IGK~GlTq~Vv~eI~~awe~~ELVKIKv~g~~~~dmk~~ae~Le~kTGgeVIqrIG~~i 333 (862)
||++|+++||++||+|+|+|+|||+|||++|+++|+++|++||||||+|++++..+.++++++|+++||+++||.||+++
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 002966 334 SLYRGVS 340 (862)
Q Consensus 334 VLYRg~~ 340 (862)
||||+++
T Consensus 81 vlYR~~~ 87 (95)
T TIGR00253 81 VLYRPTK 87 (95)
T ss_pred EEEecCC
Confidence 9999985
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=6.4e-24 Score=189.05 Aligned_cols=84 Identities=32% Similarity=0.512 Sum_probs=75.4
Q ss_pred CCHHHHHHHHhhccCCCceEEeCCCCCCHHHHHHHHHHHHhCCeEEEEEcCCCHHHHHHHHHHHHHHhCCEEEecccccc
Q 002966 692 ITDEERFMFRKLGLRMKAFLLLGRRGVFDGTVENMHLHWKYRELVKIIVKVKTFDQAKKIALALEAESGGVLVSVDKISK 771 (862)
Q Consensus 692 LT~eER~~LRklahkmKpvV~IGK~GVtdgVIeeIh~hwk~hELVKVkv~~~~~~d~~eiae~Le~~SGg~lVqV~k~~I 771 (862)
||++||++||++||+|+|+|+||++|||++|+++|+++|++||||||+|.+++.++++++|+.|++.|||++|| .+
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 LTSKERKFLRKLAHHLKPVVQIGKNGLTDGVIEEIDDALEKHELVKVKVLGNCREDRKEIAEQLAEKTGAEVVQ----VI 76 (84)
T ss_dssp --HHHHHHHHHHHTTC--SEEE-TTSS-HHHHHHHHHHHHHHSEEEEEETT--HHHHHHHHHHHHHHHTEEEEE----EE
T ss_pred CCHHHHHHHHHHhcCCCCeEEECCCCCCHHHHHHHHHHHHhCCeeEEEEccCCHHHHHHHHHHHHHHhCCEEEE----EE
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999 79
Q ss_pred CcEEEEEe
Q 002966 772 GYAMVVYR 779 (862)
Q Consensus 772 G~~iILYR 779 (862)
|+++||||
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=99.89 E-value=3.7e-23 Score=188.91 Aligned_cols=96 Identities=26% Similarity=0.460 Sum_probs=89.1
Q ss_pred CCCHHHHHHHHhhccCCCceEEeCCCCCCHHHHHHHHHHHHhCCeEEEEEcCCCHHHHHHHHHHHHHHhCCEEEeccccc
Q 002966 691 SITDEERFMFRKLGLRMKAFLLLGRRGVFDGTVENMHLHWKYRELVKIIVKVKTFDQAKKIALALEAESGGVLVSVDKIS 770 (862)
Q Consensus 691 ~LT~eER~~LRklahkmKpvV~IGK~GVtdgVIeeIh~hwk~hELVKVkv~~~~~~d~~eiae~Le~~SGg~lVqV~k~~ 770 (862)
+||++|+++||+.||+++|+|+||++|||++||.+|+.+|++||||||++.+++.++.+++|+.|++++||.+|| +
T Consensus 1 ~Lt~kq~~~Lrs~Ah~l~piv~IGk~Glte~vi~Ei~~aL~~reLIKVkvl~~~~edr~eia~~l~~~~~a~lVq----v 76 (97)
T COG1534 1 MLTGKQKRFLRSKAHHLKPIVQIGKNGLTEGVIKEIDRALEARELIKVKVLQNAREDKKEIAEALAEETGAELVQ----V 76 (97)
T ss_pred CCcHHHHHHHHHhhccCCceEEecCCccCHHHHHHHHHHHHhCCcEEEEeeccchhhHHHHHHHHHHHhCCEEee----e
Confidence 699999999999999999999999999999999999999999999999999999999999999999999999999 6
Q ss_pred cCcEEEEEecCCCCCCCCCCC
Q 002966 771 KGYAMVVYRGKDYQRPSTLRP 791 (862)
Q Consensus 771 IG~~iILYRgknY~~P~~l~P 791 (862)
||+++|||| .+..++....|
T Consensus 77 iG~~~vlyr-~~~e~~~i~l~ 96 (97)
T COG1534 77 IGKTLVLYR-ESKEKRKISLP 96 (97)
T ss_pred eeeEEEEEe-cCcccccccCC
Confidence 999999999 45555544333
No 9
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=99.88 E-value=1.3e-23 Score=240.98 Aligned_cols=328 Identities=18% Similarity=0.235 Sum_probs=230.0
Q ss_pred ccccccccCCCCHHHHHHHHhhhcCCCCeEEeCCCCcCHHHHHHHHHHHHhCCeEEEEec-CCChhhHHHHHHHH--HHH
Q 002966 244 SSRTSLAELTLPESELRRLRNLTFQTKSKTRIKGAGLTQAVVDIIHEKWKTSEIVRLKIE-GAPALNMKRMHEIL--ERK 320 (862)
Q Consensus 244 ~~~p~~ae~tLt~kErr~LR~lAh~LkpvV~IGK~GlTq~Vv~eI~~awe~~ELVKIKv~-g~~~~dmk~~ae~L--e~k 320 (862)
+..|...+..|+..+...+|.++..++++|.+|..+.-+++.-.+...|..|+.+|+.+. +.+......++.++ ...
T Consensus 165 r~l~~~~~~~l~~~~~~~~r~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~k~~~~k~~~~rg~~~~~~~~~a~~l~~~~~ 244 (564)
T KOG1990|consen 165 RTLPVGSPPLLTSIESTLLRRLGYKLPPHFALGRSRKLQGLAVAMVSFWEKHEFAKILIKRGVLETRKERMADELQELLL 244 (564)
T ss_pred ccCCCCChhhhhhHHHHHHHHhcccccccceehhccccccchhHHHHHHHHHHHHHHHHHhcchhhhccchHHHHHHHHh
Confidence 356777788899999999999999999999999999999999999999999999999998 88888889999999 999
Q ss_pred hCCeEEEEECcEEEEeeCCCCCCchhhhhHHHhhhccCCCCcccchhhhhhhhhhccccC-CcccccccccCCCC--CCC
Q 002966 321 TGGLVIWRSGTAVSLYRGVSYEVPSVQLNKRIYKRNELPASSVSQATDKQIHKQISMSGN-SLSAAADKTAQDPS--NFD 397 (862)
Q Consensus 321 TGgeVIqrIG~~iVLYRg~~Y~~P~v~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~--~~~ 397 (862)
||+.||.|+|-..|+||+++|.. ++..+.. ..+ .. ....|+..+......+....+ ....+...+..... ...
T Consensus 245 tg~~lv~hN~~~dv~y~~~~Fl~-~lp~~l~-~f~-~~-~~~fp~~~~~~~~~~~~~~~~~~~~~t~~e~~~~~~~~~~~ 320 (564)
T KOG1990|consen 245 TGKVLVLHNKLLDVMYRYKNFLS-PLPSTLE-EFT-DS-SSMFPNIEDTKRLAKLSEYQKLNLKATLLELARAKAKKEKE 320 (564)
T ss_pred cCCeEEeeccceeeeeehhhccc-ccchhHH-Hhh-hh-hhhhhhhHHHHHhhccccccchhhhhhHHHHHHHhcccccC
Confidence 99999999999999999999998 6766543 222 11 334444322211111111111 00000000000000 000
Q ss_pred Ccccccc--chhhhccccchhhhhhh----hh-hchHHHHHHHhhccCCCCCCCCCCCCCCccCCCCCCCCCCCCCCccc
Q 002966 398 SYNNVHA--TQVNLETASEEQETDFV----RE-VKYEDEVEKLLDGLGPRYTDWPGCDPLPVDADMLPGIVPGYQPPFRV 470 (862)
Q Consensus 398 ~~~~~~~--~~l~~~~~~~~~~~~~l----~e-~~~e~e~~kLLd~LGPRf~dW~g~~PlPVDADLLP~~VPgyk~PfRl 470 (862)
....... ..+.......+.....+ .. -.-+...+..|..++. ..-|+ -
T Consensus 321 ~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~---------------~~~~~----~------ 375 (564)
T KOG1990|consen 321 IERRSISSRLKLEFEKASSEKLTEAIFHKLEKAKKKLASANRILAKLED---------------PKIPA----E------ 375 (564)
T ss_pred cccccccchhhhhhhccchhhHHHHHHHHHhhhhhhccchhhhhhcccc---------------ccccc----c------
Confidence 0000000 00000000000000000 00 0001223344433331 11111 1
Q ss_pred CCCCCCCCCCHHHHHHHHHhhhcCCCeeeecccchhhHHHHHHHHHHhhhceeeeeeccCCCcchHHHHHHHHHhhcCCe
Q 002966 471 LPYGVRSTLARKEATNLQRLARVLPPHFALGRSRQLQGLAVAMIKLWEKSSIAKIALKRGVQLTTSERMVEDIKKLTGGT 550 (862)
Q Consensus 471 lP~gvr~~LTdeE~t~lRkLar~lp~hfaLGRnr~lqGLa~am~klWEkseIvKIavKrGvqnt~~e~mA~eLk~LTGGv 550 (862)
++..++.+|++|+.+++++|..|..++.+||+|+|+||+.|||+||++++.+|++||....-...+..|.+|+.++||+
T Consensus 376 -~~~~~e~~t~ee~~~~~k~g~k~~~~~~~~rrg~f~g~i~n~~l~wk~~e~~k~i~~~~~~~~~~~~~a~~le~esg~~ 454 (564)
T KOG1990|consen 376 -LRYDPESITEEERLMLRKVGLKMKRRLLSGRRGVFDGVIENMHLHWKSRELVKVICKEKNLPSQVKQYASALERESGGI 454 (564)
T ss_pred -cccchhhcChHHHHHHHHHHHhhccccccCCcccccceeecchhhhhhcccceeeeccccccHHHHHHHHHHHHHhCCc
Confidence 1134589999999999999999999999999999999999999999999999999997755589999999999999999
Q ss_pred EEeecc----cEEEEEecCCCCChHHH---HHHHHHHHHHHHHhhHHHHHHHhhhcccccCc
Q 002966 551 LLSRNK----DFLVFYRGKNFLSPDVT---EALQERERLAKSLQDEEEQARLRASAFVLPSI 605 (862)
Q Consensus 551 LLSrnK----~~II~YRGKDFlpp~V~---~~L~eReal~rs~q~~EE~aR~~a~~~~~~~~ 605 (862)
+++.++ |+|++||||+|..|..+ +.|.+|.++.+++..+ +.+|...+++..
T Consensus 455 ~v~~~~~~~~~ai~~yr~k~y~~p~~l~P~~~l~~~k~~~~~~~~~----~~~a~~~~i~~~ 512 (564)
T KOG1990|consen 455 LVSIDKNPKGYAIIAYRGKNYDRPTSLRPRNLLSRRKALERSLEEQ----RKEALKSHISDL 512 (564)
T ss_pred eeeeccCCchhhHHHhhhhhccCCcccCchhhhcccCCccccHHHH----HHHHHhhhcchh
Confidence 999888 88999999999888764 8999999999998776 778877777554
No 10
>COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]
Probab=99.87 E-value=5.1e-22 Score=181.47 Aligned_cols=87 Identities=25% Similarity=0.372 Sum_probs=84.9
Q ss_pred CCCHHHHHHHHhhhcCCCCeEEeCCCCcCHHHHHHHHHHHHhCCeEEEEecCCChhhHHHHHHHHHHHhCCeEEEEECcE
Q 002966 253 TLPESELRRLRNLTFQTKSKTRIKGAGLTQAVVDIIHEKWKTSEIVRLKIEGAPALNMKRMHEILERKTGGLVIWRSGTA 332 (862)
Q Consensus 253 tLt~kErr~LR~lAh~LkpvV~IGK~GlTq~Vv~eI~~awe~~ELVKIKv~g~~~~dmk~~ae~Le~kTGgeVIqrIG~~ 332 (862)
+||++|+++||+.||+++|+|+|||+|||++|+++|+++|++||||||+|.+++..+.+.+|+.|++.||+.+||+||++
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 EEEeeCC
Q 002966 333 VSLYRGV 339 (862)
Q Consensus 333 iVLYRg~ 339 (862)
+||||.+
T Consensus 81 ~vlyr~~ 87 (97)
T COG1534 81 LVLYRES 87 (97)
T ss_pred EEEEecC
Confidence 9999933
No 11
>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=25.73 E-value=2.4e+02 Score=24.86 Aligned_cols=56 Identities=11% Similarity=0.059 Sum_probs=38.9
Q ss_pred HHHHHHHHHhCCeEEEEEcCCCHHHHHHHHHHHHH---HhCCEEEeccccccCcEEEEEecCCC
Q 002966 723 VENMHLHWKYRELVKIIVKVKTFDQAKKIALALEA---ESGGVLVSVDKISKGYAMVVYRGKDY 783 (862)
Q Consensus 723 IeeIh~hwk~hELVKVkv~~~~~~d~~eiae~Le~---~SGg~lVqV~k~~IG~~iILYRgknY 783 (862)
+.+|-++++....|-|.+..-..+..+.+.+.|.. ..+|.+.. +|..+++|=+++.
T Consensus 12 ~~~i~~~l~~g~~Vivnl~~l~~~~~~Ri~Dfl~G~~~al~G~i~~-----i~~~~~l~~P~~V 70 (73)
T PF04472_consen 12 AREIVDALREGKIVIVNLENLDDEEAQRILDFLSGAVYALDGDIQK-----ISEKVFLLTPKGV 70 (73)
T ss_dssp HHHHHHHHHTT--EEEE-TTS-HHHHHHHHHHHHHHHHHTT-EEEE-----EETTEEEEE----
T ss_pred HHHHHHHHHcCCEEEEECCCCCHHHHHHHHHHHhchheeeCCEEEE-----EcCCEEEEECCCc
Confidence 34588899999999999988888888888888765 77999999 5888888876553
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=25.43 E-value=15 Score=37.41 Aligned_cols=93 Identities=18% Similarity=0.204 Sum_probs=58.2
Q ss_pred HHHHHHHHHHHHHHH-----HHHHHH-----hhhcccCCCCCCCCCCCCCHHHHHHHHhhccCCCceE------EeCCCC
Q 002966 654 KLEKKLARAERKLLR-----AERALS-----KVEESLKPAERQADPESITDEERFMFRKLGLRMKAFL------LLGRRG 717 (862)
Q Consensus 654 ~~e~kL~~a~~K~~~-----ae~~L~-----Kle~~~~p~~~~~d~e~LT~eER~~LRklahkmKpvV------~IGK~G 717 (862)
+++.||+.|+.++-. -.+.|. ||.-. -+.-..|.+-||..++..++++...|.|++ +--|.=
T Consensus 28 ~~eaKLqqAK~~lgeeEfeef~~lLK~lt~~kLkyg--D~NGnidye~ls~~eqee~k~~~~eLqPYFdKLN~~~SsK~v 105 (162)
T PF12207_consen 28 RLEAKLQQAKGELGEEEFEEFKELLKKLTNAKLKYG--DKNGNIDYEKLSKEEQEEYKKLTMELQPYFDKLNGHKSSKEV 105 (162)
T ss_dssp HHHHHHHHHHHCS-HHHHHHHHHHHHHHHHHHHHHB---TTS-B-GGGS-HHHHHHHHHHHHHHHHHHHHHTT---HHHH
T ss_pred HHHHHHHHHHHhhhHHHHHHHHHHHHHHHHhHHhhc--ccCCCcCHHhCCHHHHHHHHHHHHhcchHHHHhcCCcchhhh
Confidence 478888888763222 222233 33333 234578999999999999999999999976 233445
Q ss_pred CCHHHHHHHHHHHHhCCeEEEEEcCCCHHHH
Q 002966 718 VFDGTVENMHLHWKYRELVKIIVKVKTFDQA 748 (862)
Q Consensus 718 VtdgVIeeIh~hwk~hELVKVkv~~~~~~d~ 748 (862)
+++.-.+.--.||-.+|.|+|+........+
T Consensus 106 lt~~E~d~y~eALm~~e~v~vk~~~~~~~~v 136 (162)
T PF12207_consen 106 LTQEEYDQYIEALMTYETVRVKTKSSGGITV 136 (162)
T ss_dssp S-HHHHHHHHHHHHHHHHHHHHCT-SS---G
T ss_pred cCHHHHHHHHHHHhhhheeeeeccCCCCCcH
Confidence 6666677777899999999999875544333
No 13
>COG1623 Predicted nucleic-acid-binding protein (contains the HHH domain) [General function prediction only]
Probab=24.74 E-value=1.4e+02 Score=34.04 Aligned_cols=50 Identities=10% Similarity=0.266 Sum_probs=35.8
Q ss_pred HHHHHHHHHHHHHHhCCEEEeccccccCcEEEEEecCCCCCCCCCCCCCcccHH
Q 002966 745 FDQAKKIALALEAESGGVLVSVDKISKGYAMVVYRGKDYQRPSTLRPKNLLTKR 798 (862)
Q Consensus 745 ~~d~~eiae~Le~~SGg~lVqV~k~~IG~~iILYRgknY~~P~~l~P~~lLtKr 798 (862)
...++..|+-.+..||..||+|-. --++|.||.+ |++.-- .-+-.+|||.
T Consensus 104 tGtRHRTAER~AkqTG~~VIaiS~--rrNvITlY~~-~~ky~L-~d~~~il~ra 153 (349)
T COG1623 104 TGTRHRTAERVAKQTGNPVIAISE--RRNVITLYVG-NLKYVL-KDSAFILSRA 153 (349)
T ss_pred CccccchHHHHHHHhCCeEEEEec--ccceEEEEec-Ceeeee-cChHHHHHHH
Confidence 356789999999999999999733 3378999986 555522 2345667664
No 14
>PF15337 Vasculin: Vascular protein family Vasculin-like 1
Probab=24.53 E-value=67 Score=30.75 Aligned_cols=43 Identities=19% Similarity=0.359 Sum_probs=36.1
Q ss_pred CCCHHHHHHHHHhhhcCCCeeeecccchhhHHHHHHHHHHhhhc
Q 002966 478 TLARKEATNLQRLARVLPPHFALGRSRQLQGLAVAMIKLWEKSS 521 (862)
Q Consensus 478 ~LTdeE~t~lRkLar~lp~hfaLGRnr~lqGLa~am~klWEkse 521 (862)
-||++|+-.|.-..-+|. -==+|+||.+|++..++-..|.-.-
T Consensus 33 PlTEDElkEF~~kseQlr-rNGf~kngfl~~rs~slf~pWr~t~ 75 (97)
T PF15337_consen 33 PLTEDELKEFQVKSEQLR-RNGFGKNGFLQSRSLSLFSPWRSTC 75 (97)
T ss_pred cCcHHHHHHHHHHHHHHH-Hccccccchhhhhhhhccccccccc
Confidence 489999999888777777 5568999999999999888997543
No 15
>PF15249 GLTSCR1: Glioma tumor suppressor candidate region
Probab=24.02 E-value=30 Score=32.95 Aligned_cols=17 Identities=53% Similarity=1.116 Sum_probs=12.8
Q ss_pred CCCCCCCCc--------ccCCCCCC
Q 002966 460 IVPGYQPPF--------RVLPYGVR 476 (862)
Q Consensus 460 ~VPgyk~Pf--------RllP~gvr 476 (862)
.-|.|++|| |||||.|=
T Consensus 13 ~~PD~~tPF~s~~DA~~RLLPYHv~ 37 (109)
T PF15249_consen 13 LNPDYKTPFRSLEDAVERLLPYHVF 37 (109)
T ss_pred hCCCcCCCCCCHHHHHHHhcchhhh
Confidence 347899999 57787773
No 16
>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=22.82 E-value=4.6e+02 Score=23.13 Aligned_cols=55 Identities=16% Similarity=0.159 Sum_probs=37.3
Q ss_pred HHHHHHHHHhCCeEEEEecCCChhhHHHHHHHHHH---HhCCeEEEEECcEEEEeeCCC
Q 002966 285 VDIIHEKWKTSEIVRLKIEGAPALNMKRMHEILER---KTGGLVIWRSGTAVSLYRGVS 340 (862)
Q Consensus 285 v~eI~~awe~~ELVKIKv~g~~~~dmk~~ae~Le~---kTGgeVIqrIG~~iVLYRg~~ 340 (862)
+.+|-++++...+|=|.+........+++.+.|.. ..+|.+.+. |..++||=+++
T Consensus 12 ~~~i~~~l~~g~~Vivnl~~l~~~~~~Ri~Dfl~G~~~al~G~i~~i-~~~~~l~~P~~ 69 (73)
T PF04472_consen 12 AREIVDALREGKIVIVNLENLDDEEAQRILDFLSGAVYALDGDIQKI-SEKVFLLTPKG 69 (73)
T ss_dssp HHHHHHHHHTT--EEEE-TTS-HHHHHHHHHHHHHHHHHTT-EEEEE-ETTEEEEE---
T ss_pred HHHHHHHHHcCCEEEEECCCCCHHHHHHHHHHHhchheeeCCEEEEE-cCCEEEEECCC
Confidence 45688999999999999998888889999988875 568887776 44455554443
No 17
>PF07820 TraC: TraC-like protein; InterPro: IPR012930 The members of this family are sequences that are similar to TraC (Q84HT8 from SWISSPROT) from Rhizobium etli. The gene encoding this protein is one of a group of genes found on plasmid p42a of Rhizobium etli (strain CFN 42/ATCC 51251) that are thought to be involved in the process of plasmid self-transmission. Mobilisation of plasmid p42a is of importance as it is required for transfer of plasmid p42d, the symbiotic plasmid which carries most of the genes required for nodulation and nitrogen fixation by this symbiotic bacterium. The predicted protein products of p42a are similar to known transfer proteins of Agrobacterium tumefaciens plasmid pTiC58 []. ; GO: 0000746 conjugation
Probab=22.44 E-value=1e+02 Score=29.36 Aligned_cols=37 Identities=14% Similarity=0.293 Sum_probs=24.8
Q ss_pred HHHHHHHHHHHHHHHHHHHhhh----------------ccCCCchHHHHhhhh
Q 002966 815 KHVATLESNAGRLRSEIEQMNS----------------VKGTGDEQLYDKLDS 851 (862)
Q Consensus 815 ~~i~~l~~~i~~l~~~l~~~~~----------------~~~~~d~~~~~~~~~ 851 (862)
.+++++..+|++||.+|.+++. .=++.|.+|+.-++.
T Consensus 2 k~~s~I~~eIekLqe~lk~~e~keaERigr~AlKaGL~eieI~d~eL~~~Fee 54 (92)
T PF07820_consen 2 KSSSKIREEIEKLQEQLKQAETKEAERIGRIALKAGLGEIEISDAELQAAFEE 54 (92)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccCCHHHHHHHHHH
Confidence 4567777777777777776654 225577778776653
Done!