Query 002557
Match_columns 908
No_of_seqs 322 out of 992
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 02:23:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002557.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002557hhsearch_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 4.4E-82 9.4E-87 716.7 22.1 533 242-820 3-540 (564)
2 PRK10343 RNA-binding protein Y 99.9 6E-26 1.3E-30 208.2 12.7 89 252-340 1-89 (97)
3 TIGR00253 RNA_bind_YhbY putati 99.9 2.3E-25 5.1E-30 203.6 12.7 88 254-341 1-88 (95)
4 PF01985 CRS1_YhbY: CRS1 / Yhb 99.9 1.8E-25 4E-30 198.9 10.8 84 254-337 1-84 (84)
5 PRK10343 RNA-binding protein Y 99.9 1.2E-24 2.6E-29 199.7 13.2 88 663-754 2-89 (97)
6 TIGR00253 RNA_bind_YhbY putati 99.9 2.4E-24 5.2E-29 197.0 12.9 87 664-754 1-87 (95)
7 PF01985 CRS1_YhbY: CRS1 / Yhb 99.9 6E-24 1.3E-28 189.2 10.4 84 664-751 1-84 (84)
8 COG1534 Predicted RNA-binding 99.9 1.5E-23 3.3E-28 192.1 12.0 88 253-340 1-88 (97)
9 COG1534 Predicted RNA-binding 99.9 3.4E-23 7.3E-28 189.8 12.2 96 663-763 1-96 (97)
10 KOG1990 Poly(A)-specific exori 98.1 1.6E-06 3.5E-11 101.0 4.7 110 253-362 382-496 (564)
11 PF10446 DUF2457: Protein of u 45.2 32 0.00069 40.6 5.1 11 882-892 119-129 (458)
12 PF12207 DUF3600: Domain of un 39.3 6.3 0.00014 40.4 -1.4 93 625-717 27-133 (162)
13 PF15237 PTRF_SDPR: PTRF/SDPR 36.7 1E+02 0.0022 34.1 7.0 67 477-545 52-120 (246)
14 TIGR03321 alt_F1F0_F0_B altern 36.6 5.7E+02 0.012 27.5 15.0 34 537-570 23-56 (246)
15 PF07412 Geminin: Geminin; In 35.4 1.2E+02 0.0027 32.6 7.2 39 769-809 116-154 (200)
16 COG0488 Uup ATPase components 31.9 9.9E+02 0.022 29.1 14.7 101 639-757 133-237 (530)
17 KOG3653 Transforming growth fa 28.8 48 0.001 39.8 3.2 68 429-498 425-492 (534)
18 PF15249 GLTSCR1: Glioma tumor 27.1 25 0.00053 33.7 0.5 9 433-441 14-22 (109)
19 PRK14475 F0F1 ATP synthase sub 25.3 4.6E+02 0.01 26.6 9.1 34 538-571 29-62 (167)
20 KOG0994 Extracellular matrix g 24.6 6.1E+02 0.013 34.1 11.5 29 628-656 1583-1611(1758)
21 PF04472 DUF552: Protein of un 22.7 4.9E+02 0.011 23.1 7.7 56 285-341 12-70 (73)
22 PRK13455 F0F1 ATP synthase sub 22.6 6.7E+02 0.014 25.8 9.8 32 540-571 48-79 (184)
23 PF04931 DNA_pol_phi: DNA poly 22.1 71 0.0015 39.8 3.2 26 765-790 596-621 (784)
24 PRK00013 groEL chaperonin GroE 21.5 1.2E+03 0.025 28.4 12.9 75 451-527 226-303 (542)
25 TIGR00285 DNA-binding protein 21.1 2.4E+02 0.0051 27.0 5.6 67 681-748 2-68 (87)
No 1
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=100.00 E-value=4.4e-82 Score=716.68 Aligned_cols=533 Identities=46% Similarity=0.666 Sum_probs=499.5
Q ss_pred cccccccccccCCCHHHHHHHHhhhcCCCCeEEeCCCCCCHHHHHHHHHHHHhCCeEEEEecCCChhhHHHHHHHHHHHh
Q 002557 242 RRSSRTSLAELTLPESELRRLRNLTFQTKSKTRIKGAGLTQAVVDIIHEKWKTSEIVRLKIEGAPALNMKRMHEILERKT 321 (908)
Q Consensus 242 kk~s~pslAEltLT~kErr~LR~lAh~LkPvV~IGK~GLTd~VVeeIh~awk~hELVKVK~l~~~~~dmk~~ae~LEekT 321 (908)
++.+ +++|++++.+.++++||..|..+.-.+ +++|+|+.+++.|++.|+.+|+++++|....+.+|.+.+++++..|
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 999999999999999999999998888 9999999999999999999999999999999999999999999999
Q ss_pred CC-eEEEEEccEEEEeecCCCCCCccchhhhhhhccCCCCCCCCccchhhhhhcccccccccccccccccccccccchHH
Q 002557 322 GG-LVIWRSGTAVSLYRGVSYEVPSVQLNKRIYKRNELPASSVSQATDKQIHKQISMSVNLETASEEQETDFVREVKYED 400 (908)
Q Consensus 322 Gg-eVVqrIG~viVLYRgsnY~~p~~~~~~~~~~~~e~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~ 400 (908)
|+ .+||+.|.....|++..|..|..-.++. ++ +....-..+++.
T Consensus 80 ~~n~~~~~~g~~~s~~~~~~~~~~~~~~~~~-----------------------------~~------~~~~~~~~~~~~ 124 (564)
T KOG1990|consen 80 GGNFVVWSRGDSISSPEFLCQRSPVDFVARQ-----------------------------QE------NQAGKWPSELEK 124 (564)
T ss_pred CCceeeeecCccccCCccceeecchhhhhhh-----------------------------ch------hhhhhhHHHHHH
Confidence 99 9999999999999999998875432211 00 000111467899
Q ss_pred HHHhhhcCCCCcccCCCCCCCCCCCCCCCCCcCCCCCCCcccCCCCCCccCCHHHHHHHHHhcccCCCeEEecccchhhH
Q 002557 401 EVEKLLDGLGPRYTDWPGCDPLPVDADMLPGIVPGYQPPFRVLPYGVRSTLARKEATNLQRLARVLPPHFALGRSRQLQG 480 (908)
Q Consensus 401 E~d~LLD~LGPRf~dW~g~~PlPVDaDLLP~vVpgyk~PfRllP~Gvr~~Lt~~E~T~LRrLar~lPpHfaLGRNr~lqG 480 (908)
|.+.+||++||+|.|||+.+|+|||+||||++||+|.+|||.+|+|++++|+..|+|.+|++|+.+||||+||+++.+||
T Consensus 125 ~~~~~~~~~~~~~~~~~~~~~~~~~~dl~~~~i~~~~~p~r~l~~~~~~~l~~~~~~~~r~~~~~~p~~~~~~~~~~~~~ 204 (564)
T KOG1990|consen 125 EKNELLDSLGPELSDWGGSDRLSVDADLLPEKIPDYMRPFRTLPVGSPPLLTSIESTLLRRLGYKLPPHFALGRSRKLQG 204 (564)
T ss_pred HHHHHhhccCcccccCCCCCCccchhhhchhhhhcccChhccCCCCChhhhhhHHHHHHHHhcccccccceehhcccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhhhcceeeeeeccCCCCCchHHHHHHH--hhcccceeeeccCCeEEEEecCCCCcHHHHHHHHHHHHHHHhh
Q 002557 481 LAVAMIKLWEKSSIAKIALKRGVQLTTSERMVEDI--KKLTGGTLLSRNKDFLVFYRGKNFLSPDVTEALQERERLAKSL 558 (908)
Q Consensus 481 LA~AIvKLWEKs~IAKIaiKrGvqnT~ne~MaeEL--K~LTGGvLLsRnk~~IV~YRGKDFLp~~Va~al~eRe~~~~~~ 558 (908)
||.+|+++|++|+++||+|+||+++|.++.||.+| +.+||++|++||+.++|+|||++||+ .|.++|.++.......
T Consensus 205 ~~~~~~~~~~k~~~~k~~~~rg~~~~~~~~~a~~l~~~~~tg~~lv~hN~~~dv~y~~~~Fl~-~lp~~l~~f~~~~~~f 283 (564)
T KOG1990|consen 205 LAVAMVSFWEKHEFAKILIKRGVLETRKERMADELQELLLTGKVLVLHNKLLDVMYRYKNFLS-PLPSTLEEFTDSSSMF 283 (564)
T ss_pred chhHHHHHHHHHHHHHHHHHhcchhhhccchHHHHHHHHhcCCeEEeeccceeeeeehhhccc-ccchhHHHhhhhhhhh
Confidence 99999999999999999999999999999999999 99999999999999999999999999 9999999999998899
Q ss_pred hhHHHHHHhhhhcccccccccccccCccchhHHHHHhhhccccCCChhHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002557 559 QDEEEQARLRASAFVLPSIETIEKSGTAGTLKETLDANSRWGKRLDDSHK-ENLVREAEVRRHAYLVQKLEKKLARAERK 637 (908)
Q Consensus 559 q~~EE~aR~~a~~~~~~~~~~~~~~~~aGtl~e~~~a~~~~g~~~~~~~~-~~~~~e~~~~r~~~~~k~~e~kL~~a~~K 637 (908)
++.++.+|+.+.... .....++|+.|+..+.++|+..+.-... ..+..+.++..+++..+.+.++++.+++|
T Consensus 284 p~~~~~~~~~~~~~~-------~~~~~~~t~~e~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~ 356 (564)
T KOG1990|consen 284 PNIEDTKRLAKLSEY-------QKLNLKATLLELARAKAKKEKEIERRSISSRLKLEFEKASSEKLTEAIFHKLEKAKKK 356 (564)
T ss_pred hhhHHHHHhhccccc-------cchhhhhhHHHHHHHhcccccCcccccccchhhhhhhccchhhHHHHHHHHHhhhhhh
Confidence 999999999983311 1246899999999999999999975543 46788899999999999999999999999
Q ss_pred HHHHHHHHHhhhccCCCCCCCCCCCCCCHHHHHHHHhhccCCcceEEeCCCCCCHHHHHHHHHHHHhCCeEEEEEcCCCH
Q 002557 638 LLRAERALSKVEESLKPAERQADPESITDEERFMFRKLGLRMKAFLLLGRRGVFDGTVENMHLHWKYRELVKIIVKVKTF 717 (908)
Q Consensus 638 ~~rae~~L~K~e~~~~p~~~~~d~E~LT~eER~~LRklAhkLKPvV~IGKrGVTdgVIeeIh~hwk~hELVKVkv~~~~~ 717 (908)
+.++++.|++++....|++...|++.+|.+++.+++++|.+|++++.+|++|+++|+|.+||+||++||++||+|+....
T Consensus 357 ~~~~~~~l~~~~~~~~~~~~~~~~e~~t~ee~~~~~k~g~k~~~~~~~~rrg~f~g~i~n~~l~wk~~e~~k~i~~~~~~ 436 (564)
T KOG1990|consen 357 LASANRILAKLEDPKIPAELRYDPESITEEERLMLRKVGLKMKRRLLSGRRGVFDGVIENMHLHWKSRELVKVICKEKNL 436 (564)
T ss_pred ccchhhhhhcccccccccccccchhhcChHHHHHHHHHHHhhccccccCCcccccceeecchhhhhhcccceeeeccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999998766
Q ss_pred -HHHHHHHHHHHHHhCCEEEeccccccccEEEEEecCCCCCCCCCCCCccccHHHHHHHhHHHHHHHHHHHHHHHHHHHH
Q 002557 718 -DQAKKIALALEAESGGVLVSVDKISKGYAMVVYRGKDYQRPSTLRPKNLLTKRKALARSIELQRQEALLKHVATLESNA 796 (908)
Q Consensus 718 -~d~keiAe~Le~~SGg~LVqV~k~~IG~tiILYRgkNY~rP~~l~PknlLTKrkAl~rS~e~qr~~~l~~hI~~l~~~i 796 (908)
.+++..|..++.++|+++|.|+++..|+.|+.|||+||++|..++|.++|+||+|+.+++++|++++++.||..+..++
T Consensus 437 ~~~~~~~a~~le~esg~~~v~~~~~~~~~ai~~yr~k~y~~p~~l~P~~~l~~~k~~~~~~~~~~~~a~~~~i~~~~~~~ 516 (564)
T KOG1990|consen 437 PSQVKQYASALERESGGILVSIDKNPKGYAIIAYRGKNYDRPTSLRPRNLLSRRKALERSLEEQRKEALKSHISDLEQEI 516 (564)
T ss_pred cHHHHHHHHHHHHHhCCceeeeccCCchhhHHHhhhhhccCCcccCchhhhcccCCccccHHHHHHHHHhhhcchhhhhH
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhhcccCCCcHHHHHh
Q 002557 797 GRLRSEIEQMNSVKGTGDEQLYDK 820 (908)
Q Consensus 797 ~~l~~~l~~~~~~~~~~d~~ly~~ 820 (908)
++++.+++.|.......|.+.|++
T Consensus 517 e~~~~~~~~~~~~~~~~d~~~en~ 540 (564)
T KOG1990|consen 517 EQLQASVEAMPAINKKDDLEEENS 540 (564)
T ss_pred HHhhcchhcccccccccchHHHhh
Confidence 999999999999988999999998
No 2
>PRK10343 RNA-binding protein YhbY; Provisional
Probab=99.93 E-value=6e-26 Score=208.22 Aligned_cols=89 Identities=22% Similarity=0.349 Sum_probs=87.2
Q ss_pred cCCCHHHHHHHHhhhcCCCCeEEeCCCCCCHHHHHHHHHHHHhCCeEEEEecCCChhhHHHHHHHHHHHhCCeEEEEEcc
Q 002557 252 LTLPESELRRLRNLTFQTKSKTRIKGAGLTQAVVDIIHEKWKTSEIVRLKIEGAPALNMKRMHEILERKTGGLVIWRSGT 331 (908)
Q Consensus 252 ltLT~kErr~LR~lAh~LkPvV~IGK~GLTd~VVeeIh~awk~hELVKVK~l~~~~~dmk~~ae~LEekTGgeVVqrIG~ 331 (908)
|+||++|+++||++||+|+|+|+|||+|||++|+++|+++|++|||||||+++++.++.++++++|+++||+++||.||+
T Consensus 1 m~Lt~kqr~~LR~~ah~l~Pvv~IGk~Glt~~vi~ei~~aL~~hELIKvkv~~~~~~~~~e~~~~i~~~~~ae~Vq~IG~ 80 (97)
T PRK10343 1 MNLSTKQKQHLKGLAHPLKPVVLLGSNGLTEGVLAEIEQALEHHELIKVKIATEDRETKTLIVEAIVRETGACNVQVIGK 80 (97)
T ss_pred CCCCHHHHHHHHHhcCCCCCeEEECCCCCCHHHHHHHHHHHHHCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEeeeCc
Confidence 46999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEeecCC
Q 002557 332 AVSLYRGVS 340 (908)
Q Consensus 332 viVLYRgsn 340 (908)
++||||+++
T Consensus 81 ~~vlYR~~~ 89 (97)
T PRK10343 81 TLVLYRPTK 89 (97)
T ss_pred EEEEEecCC
Confidence 999999985
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=2.3e-25 Score=203.61 Aligned_cols=88 Identities=23% Similarity=0.342 Sum_probs=86.1
Q ss_pred CCHHHHHHHHhhhcCCCCeEEeCCCCCCHHHHHHHHHHHHhCCeEEEEecCCChhhHHHHHHHHHHHhCCeEEEEEccEE
Q 002557 254 LPESELRRLRNLTFQTKSKTRIKGAGLTQAVVDIIHEKWKTSEIVRLKIEGAPALNMKRMHEILERKTGGLVIWRSGTAV 333 (908)
Q Consensus 254 LT~kErr~LR~lAh~LkPvV~IGK~GLTd~VVeeIh~awk~hELVKVK~l~~~~~dmk~~ae~LEekTGgeVVqrIG~vi 333 (908)
||++|+++||++||+|+|+|+|||+|||++||++|+++|++|||||||+++++..+.++++++|+++|||++||.||+++
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 EEeecCCC
Q 002557 334 SLYRGVSY 341 (908)
Q Consensus 334 VLYRgsnY 341 (908)
||||+++.
T Consensus 81 vlYR~~~~ 88 (95)
T TIGR00253 81 VLYRPTKE 88 (95)
T ss_pred EEEecCCc
Confidence 99999853
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=1.8e-25 Score=198.89 Aligned_cols=84 Identities=32% Similarity=0.466 Sum_probs=75.7
Q ss_pred CCHHHHHHHHhhhcCCCCeEEeCCCCCCHHHHHHHHHHHHhCCeEEEEecCCChhhHHHHHHHHHHHhCCeEEEEEccEE
Q 002557 254 LPESELRRLRNLTFQTKSKTRIKGAGLTQAVVDIIHEKWKTSEIVRLKIEGAPALNMKRMHEILERKTGGLVIWRSGTAV 333 (908)
Q Consensus 254 LT~kErr~LR~lAh~LkPvV~IGK~GLTd~VVeeIh~awk~hELVKVK~l~~~~~dmk~~ae~LEekTGgeVVqrIG~vi 333 (908)
||++|+++||++||+|+|+|+|||+|||++|+++|+++|++||||||||.+++..+++++++.|+++|||+|||+||+++
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 002557 334 SLYR 337 (908)
Q Consensus 334 VLYR 337 (908)
||||
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=1.2e-24 Score=199.74 Aligned_cols=88 Identities=22% Similarity=0.406 Sum_probs=86.2
Q ss_pred CCCHHHHHHHHhhccCCcceEEeCCCCCCHHHHHHHHHHHHhCCeEEEEEcCCCHHHHHHHHHHHHHHhCCEEEeccccc
Q 002557 663 SITDEERFMFRKLGLRMKAFLLLGRRGVFDGTVENMHLHWKYRELVKIIVKVKTFDQAKKIALALEAESGGVLVSVDKIS 742 (908)
Q Consensus 663 ~LT~eER~~LRklAhkLKPvV~IGKrGVTdgVIeeIh~hwk~hELVKVkv~~~~~~d~keiAe~Le~~SGg~LVqV~k~~ 742 (908)
+||++||++||++||+|+|+|+||+.||||+||++|..+|++||||||++.+++.+++++++++||+.|||++|| +
T Consensus 2 ~Lt~kqr~~LR~~ah~l~Pvv~IGk~Glt~~vi~ei~~aL~~hELIKvkv~~~~~~~~~e~~~~i~~~~~ae~Vq----~ 77 (97)
T PRK10343 2 NLSTKQKQHLKGLAHPLKPVVLLGSNGLTEGVLAEIEQALEHHELIKVKIATEDRETKTLIVEAIVRETGACNVQ----V 77 (97)
T ss_pred CCCHHHHHHHHHhcCCCCCeEEECCCCCCHHHHHHHHHHHHHCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEe----e
Confidence 699999999999999999999999999999999999999999999999999999999999999999999999999 7
Q ss_pred cccEEEEEecCC
Q 002557 743 KGYAMVVYRGKD 754 (908)
Q Consensus 743 IG~tiILYRgkN 754 (908)
||+++||||++.
T Consensus 78 IG~~~vlYR~~~ 89 (97)
T PRK10343 78 IGKTLVLYRPTK 89 (97)
T ss_pred eCcEEEEEecCC
Confidence 999999999874
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=2.4e-24 Score=197.01 Aligned_cols=87 Identities=26% Similarity=0.445 Sum_probs=85.1
Q ss_pred CCHHHHHHHHhhccCCcceEEeCCCCCCHHHHHHHHHHHHhCCeEEEEEcCCCHHHHHHHHHHHHHHhCCEEEecccccc
Q 002557 664 ITDEERFMFRKLGLRMKAFLLLGRRGVFDGTVENMHLHWKYRELVKIIVKVKTFDQAKKIALALEAESGGVLVSVDKISK 743 (908)
Q Consensus 664 LT~eER~~LRklAhkLKPvV~IGKrGVTdgVIeeIh~hwk~hELVKVkv~~~~~~d~keiAe~Le~~SGg~LVqV~k~~I 743 (908)
||++||++||++||+|+|+|+||++||||+||++|+.+|++||||||++++++.++++++|++||+.|||++|| .|
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 79
Q ss_pred ccEEEEEecCC
Q 002557 744 GYAMVVYRGKD 754 (908)
Q Consensus 744 G~tiILYRgkN 754 (908)
|+++||||++.
T Consensus 77 G~~~vlYR~~~ 87 (95)
T TIGR00253 77 GKTIVLYRPTK 87 (95)
T ss_pred ccEEEEEecCC
Confidence 99999999864
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=6e-24 Score=189.23 Aligned_cols=84 Identities=32% Similarity=0.512 Sum_probs=75.5
Q ss_pred CCHHHHHHHHhhccCCcceEEeCCCCCCHHHHHHHHHHHHhCCeEEEEEcCCCHHHHHHHHHHHHHHhCCEEEecccccc
Q 002557 664 ITDEERFMFRKLGLRMKAFLLLGRRGVFDGTVENMHLHWKYRELVKIIVKVKTFDQAKKIALALEAESGGVLVSVDKISK 743 (908)
Q Consensus 664 LT~eER~~LRklAhkLKPvV~IGKrGVTdgVIeeIh~hwk~hELVKVkv~~~~~~d~keiAe~Le~~SGg~LVqV~k~~I 743 (908)
||++||++||++||+|+|+|+|||+|||++|+++|+.+|++||||||+|.+++..+++++|+.|++.|||++|+ ++
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 002557 744 GYAMVVYR 751 (908)
Q Consensus 744 G~tiILYR 751 (908)
|+++||||
T Consensus 77 G~~~vlyR 84 (84)
T PF01985_consen 77 GRTIVLYR 84 (84)
T ss_dssp TTEEEEEE
T ss_pred CCEEEEEC
Confidence 99999998
No 8
>COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]
Probab=99.90 E-value=1.5e-23 Score=192.15 Aligned_cols=88 Identities=25% Similarity=0.368 Sum_probs=85.4
Q ss_pred CCCHHHHHHHHhhhcCCCCeEEeCCCCCCHHHHHHHHHHHHhCCeEEEEecCCChhhHHHHHHHHHHHhCCeEEEEEccE
Q 002557 253 TLPESELRRLRNLTFQTKSKTRIKGAGLTQAVVDIIHEKWKTSEIVRLKIEGAPALNMKRMHEILERKTGGLVIWRSGTA 332 (908)
Q Consensus 253 tLT~kErr~LR~lAh~LkPvV~IGK~GLTd~VVeeIh~awk~hELVKVK~l~~~~~dmk~~ae~LEekTGgeVVqrIG~v 332 (908)
+||++|+++||+.||+++|+|+|||+|||++|+.+|+++|++||||||++++++.++.+.+++.|++++|+.+||.||++
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 EEEeecCC
Q 002557 333 VSLYRGVS 340 (908)
Q Consensus 333 iVLYRgsn 340 (908)
+||||.+.
T Consensus 81 ~vlyr~~~ 88 (97)
T COG1534 81 LVLYRESK 88 (97)
T ss_pred EEEEecCc
Confidence 99999433
No 9
>COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]
Probab=99.89 E-value=3.4e-23 Score=189.85 Aligned_cols=96 Identities=26% Similarity=0.460 Sum_probs=89.8
Q ss_pred CCCHHHHHHHHhhccCCcceEEeCCCCCCHHHHHHHHHHHHhCCeEEEEEcCCCHHHHHHHHHHHHHHhCCEEEeccccc
Q 002557 663 SITDEERFMFRKLGLRMKAFLLLGRRGVFDGTVENMHLHWKYRELVKIIVKVKTFDQAKKIALALEAESGGVLVSVDKIS 742 (908)
Q Consensus 663 ~LT~eER~~LRklAhkLKPvV~IGKrGVTdgVIeeIh~hwk~hELVKVkv~~~~~~d~keiAe~Le~~SGg~LVqV~k~~ 742 (908)
+||++|+++||+.||+++|+|+||+.|||++||.+|..+|++||||||++.+++.++++++|+.|++++||.+|| +
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 7
Q ss_pred cccEEEEEecCCCCCCCCCCC
Q 002557 743 KGYAMVVYRGKDYQRPSTLRP 763 (908)
Q Consensus 743 IG~tiILYRgkNY~rP~~l~P 763 (908)
||+++|||| .+..++....|
T Consensus 77 iG~~~vlyr-~~~e~~~i~l~ 96 (97)
T COG1534 77 IGKTLVLYR-ESKEKRKISLP 96 (97)
T ss_pred eeeEEEEEe-cCcccccccCC
Confidence 999999999 45555555544
No 10
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=98.15 E-value=1.6e-06 Score=100.98 Aligned_cols=110 Identities=23% Similarity=0.423 Sum_probs=98.2
Q ss_pred CCCHHHHHHHHhhhcCCCCeEEeCCCCCCHHHHHHHHHHHHhCCeEEEEecCCCh-hhHHHHHHHHHHHhCCeEEEEEcc
Q 002557 253 TLPESELRRLRNLTFQTKSKTRIKGAGLTQAVVDIIHEKWKTSEIVRLKIEGAPA-LNMKRMHEILERKTGGLVIWRSGT 331 (908)
Q Consensus 253 tLT~kErr~LR~lAh~LkPvV~IGK~GLTd~VVeeIh~awk~hELVKVK~l~~~~-~dmk~~ae~LEekTGgeVVqrIG~ 331 (908)
.+|.+++..+++++..+++.+.+|..|+-++++.++|.+|+.+|++||.|..-.. ..++..+..++..+|+.+|..+..
T Consensus 382 ~~t~ee~~~~~k~g~k~~~~~~~~rrg~f~g~i~n~~l~wk~~e~~k~i~~~~~~~~~~~~~a~~le~esg~~~v~~~~~ 461 (564)
T KOG1990|consen 382 SITEEERLMLRKVGLKMKRRLLSGRRGVFDGVIENMHLHWKSRELVKVICKEKNLPSQVKQYASALERESGGILVSIDKN 461 (564)
T ss_pred hcChHHHHHHHHHHHhhccccccCCcccccceeecchhhhhhcccceeeeccccccHHHHHHHHHHHHHhCCceeeeccC
Confidence 5899999999999999999999999999999999999999999999999999887 899999999999999999997765
Q ss_pred E----EEEeecCCCCCCccchhhhhhhccCCCCCC
Q 002557 332 A----VSLYRGVSYEVPSVQLNKRIYKRNELPASS 362 (908)
Q Consensus 332 v----iVLYRgsnY~~p~~~~~~~~~~~~e~~~~s 362 (908)
. ++.||+.+|+.|....+...+.++.+...+
T Consensus 462 ~~~~ai~~yr~k~y~~p~~l~P~~~l~~~k~~~~~ 496 (564)
T KOG1990|consen 462 PKGYAIIAYRGKNYDRPTSLRPRNLLSRRKALERS 496 (564)
T ss_pred CchhhHHHhhhhhccCCcccCchhhhcccCCcccc
Confidence 4 699999999999887776666555454443
No 11
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=45.16 E-value=32 Score=40.64 Aligned_cols=11 Identities=27% Similarity=0.271 Sum_probs=7.1
Q ss_pred ccceeeeeeee
Q 002557 882 DSESEAYTVHS 892 (908)
Q Consensus 882 ~~~~~~~~~~~ 892 (908)
.|.|..||--.
T Consensus 119 ~sd~~~WtP~~ 129 (458)
T PF10446_consen 119 GSDYEFWTPGA 129 (458)
T ss_pred cccceeecccc
Confidence 46777777543
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=39.33 E-value=6.3 Score=40.39 Aligned_cols=93 Identities=19% Similarity=0.223 Sum_probs=59.6
Q ss_pred HHHHHHHHHHHHHHHHHH-----HHHHhh---hccCCCCCCCCCCCCCCHHHHHHHHhhccCCcceE------EeCCCCC
Q 002557 625 QKLEKKLARAERKLLRAE-----RALSKV---EESLKPAERQADPESITDEERFMFRKLGLRMKAFL------LLGRRGV 690 (908)
Q Consensus 625 k~~e~kL~~a~~K~~rae-----~~L~K~---e~~~~p~~~~~d~E~LT~eER~~LRklAhkLKPvV------~IGKrGV 690 (908)
-+++.||+.|+.++-..| +.|.+| ...---++-..|.+.|+..++..++++...|.|++ +--|.=+
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 367888888875433222 233332 22222356689999999999999999999999986 2334456
Q ss_pred CHHHHHHHHHHHHhCCeEEEEEcCCCH
Q 002557 691 FDGTVENMHLHWKYRELVKIIVKVKTF 717 (908)
Q Consensus 691 TdgVIeeIh~hwk~hELVKVkv~~~~~ 717 (908)
|+.-.+.--.||-..|.|+|+......
T Consensus 107 t~~E~d~y~eALm~~e~v~vk~~~~~~ 133 (162)
T PF12207_consen 107 TQEEYDQYIEALMTYETVRVKTKSSGG 133 (162)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHCT-SS-
T ss_pred CHHHHHHHHHHHhhhheeeeeccCCCC
Confidence 777777777899999999999875443
No 13
>PF15237 PTRF_SDPR: PTRF/SDPR family
Probab=36.73 E-value=1e+02 Score=34.07 Aligned_cols=67 Identities=25% Similarity=0.310 Sum_probs=52.8
Q ss_pred hhhHHHHHHHHHhhhcceeeeeeccCCCCCchHHHHHHHhhc--ccceeeeccCCeEEEEecCCCCcHHHH
Q 002557 477 QLQGLAVAMIKLWEKSSIAKIALKRGVQLTTSERMVEDIKKL--TGGTLLSRNKDFLVFYRGKNFLSPDVT 545 (908)
Q Consensus 477 ~lqGLA~AIvKLWEKs~IAKIaiKrGvqnT~ne~MaeELK~L--TGGvLLsRnk~~IV~YRGKDFLp~~Va 545 (908)
.|.+-+.++-||.||+.=+-+.+|- | ..+.++=|.-+|+| +-+-||-||++.++||.+..=+|+.|.
T Consensus 52 ~H~~TsnTV~KLLeK~RKVS~~vk~-V-r~r~ekQ~~qVkklE~n~~eLL~Rn~FkVlI~Qee~eiPa~~~ 120 (246)
T PF15237_consen 52 SHSTTSNTVNKLLEKTRKVSVNVKE-V-RERLEKQAAQVKKLEANHAELLKRNKFKVLIFQEENEIPASVF 120 (246)
T ss_pred hcccHHHHHHHHHHHHHHhhhhHHH-H-HHHHHHHHHHHhhhhccHHHHhhccCceEEeccccccCCCccc
Confidence 4556678899999999877777753 2 24566677777765 668899999999999999999998765
No 14
>TIGR03321 alt_F1F0_F0_B alternate F1F0 ATPase, F0 subunit B. CC and in principle may run in either direction. This model represents the F0 subunit B of this apparent second ATP synthase.
Probab=36.60 E-value=5.7e+02 Score=27.55 Aligned_cols=34 Identities=21% Similarity=0.330 Sum_probs=24.7
Q ss_pred CCCCcHHHHHHHHHHHHHHHhhhhHHHHHHhhhh
Q 002557 537 KNFLSPDVTEALQERERLAKSLQDEEEQARLRAS 570 (908)
Q Consensus 537 KDFLp~~Va~al~eRe~~~~~~q~~EE~aR~~a~ 570 (908)
+=|+-+.|..+|.+|++......+.-|+++..|-
T Consensus 23 ~kfl~kPi~~~l~~R~~~I~~~l~~Ae~~~~eA~ 56 (246)
T TIGR03321 23 KRFLYRPILDAMDAREKKIAGELADADTKKREAE 56 (246)
T ss_pred HHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3477788999999999977766666566555543
No 15
>PF07412 Geminin: Geminin; InterPro: IPR022786 This family contains the eukaryotic protein geminin (approximately 200 residues long). Geminin inhibits DNA replication by preventing the incorporation of MCM complex into prereplication complex, and is degraded during the mitotic phase of the cell cycle. It has been proposed that geminin inhibits DNA replication during S, G2, and M phases and that geminin destruction at the metaphase-anaphase transition permits replication in the succeeding cell cycle []. ; GO: 0008156 negative regulation of DNA replication; PDB: 1T6F_B 2LP0_B 1UII_B 2WVR_B 2ZXX_B.
Probab=35.35 E-value=1.2e+02 Score=32.59 Aligned_cols=39 Identities=26% Similarity=0.481 Sum_probs=26.2
Q ss_pred HHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 002557 769 KRKALARSIELQRQEALLKHVATLESNAGRLRSEIEQMNSV 809 (908)
Q Consensus 769 KrkAl~rS~e~qr~~~l~~hI~~l~~~i~~l~~~l~~~~~~ 809 (908)
||+||.-+++.-+. |..-|..++..|..|+.+...+..+
T Consensus 116 RR~AL~eaL~ENe~--Lh~~ie~~~eEi~~lk~en~~L~el 154 (200)
T PF07412_consen 116 RRKALEEALEENEK--LHKEIEQKDEEIAKLKEENEELKEL 154 (200)
T ss_dssp HHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHCCHHH
T ss_pred HHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 78888887765544 5555777777777777766544443
No 16
>COG0488 Uup ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]
Probab=31.92 E-value=9.9e+02 Score=29.14 Aligned_cols=101 Identities=21% Similarity=0.113 Sum_probs=73.6
Q ss_pred HHHHHHHHhhhccCCCCCCCCCCCCCCHHHHHHH-HhhccCCcceEEe---CCCCCCHHHHHHHHHHHHhCCeEEEEEcC
Q 002557 639 LRAERALSKVEESLKPAERQADPESITDEERFMF-RKLGLRMKAFLLL---GRRGVFDGTVENMHLHWKYRELVKIIVKV 714 (908)
Q Consensus 639 ~rae~~L~K~e~~~~p~~~~~d~E~LT~eER~~L-RklAhkLKPvV~I---GKrGVTdgVIeeIh~hwk~hELVKVkv~~ 714 (908)
.+++..|..|.-.. + +..+..|++-||..+ =..++-.+|-++| --+-|--..|+=+...|+.++= -|++-.
T Consensus 133 ~~~~~~L~gLg~~~---~-~~~~~~LSGG~r~Rv~LA~aL~~~pDlLLLDEPTNHLD~~~i~WLe~~L~~~~g-tviiVS 207 (530)
T COG0488 133 ARAEEALLGLGFPD---E-DRPVSSLSGGWRRRVALARALLEEPDLLLLDEPTNHLDLESIEWLEDYLKRYPG-TVIVVS 207 (530)
T ss_pred HHHHHHHhcCCCCc---c-cCchhhcCHHHHHHHHHHHHHhcCCCEEEEcCCCcccCHHHHHHHHHHHHhCCC-cEEEEe
Confidence 56667777776542 2 666788999887665 5777888888888 6678888999999999988776 455555
Q ss_pred CCHHHHHHHHHHHHHHhCCEEEeccccccccEEEEEecCCCCC
Q 002557 715 KTFDQAKKIALALEAESGGVLVSVDKISKGYAMVVYRGKDYQR 757 (908)
Q Consensus 715 ~~~~d~keiAe~Le~~SGg~LVqV~k~~IG~tiILYRgkNY~r 757 (908)
.++...+++|..|.....| .+..|.| ||..
T Consensus 208 HDR~FLd~V~t~I~~ld~g------------~l~~y~G-ny~~ 237 (530)
T COG0488 208 HDRYFLDNVATHILELDRG------------KLTPYKG-NYSS 237 (530)
T ss_pred CCHHHHHHHhhheEEecCC------------ceeEecC-CHHH
Confidence 5788888888876554444 5666888 7765
No 17
>KOG3653 consensus Transforming growth factor beta/activin receptor subfamily of serine/threonine kinases [Signal transduction mechanisms]
Probab=28.83 E-value=48 Score=39.76 Aligned_cols=68 Identities=24% Similarity=0.370 Sum_probs=57.2
Q ss_pred CCCcCCCCCCCcccCCCCCCccCCHHHHHHHHHhcccCCCeEEecccchhhHHHHHHHHHhhhcceeeee
Q 002557 429 LPGIVPGYQPPFRVLPYGVRSTLARKEATNLQRLARVLPPHFALGRSRQLQGLAVAMIKLWEKSSIAKIA 498 (908)
Q Consensus 429 LP~vVpgyk~PfRllP~Gvr~~Lt~~E~T~LRrLar~lPpHfaLGRNr~lqGLA~AIvKLWEKs~IAKIa 498 (908)
-|..||.|+.||.. =-|..|+|-..+....|+.+|+.-|-+-++- -.+++|-..|-.-|--..=|++-
T Consensus 425 ~~~~vp~Yqlpfe~-evG~hPt~e~mq~~VV~kK~RP~~p~~W~~h-~~~~~l~et~EeCWDhDaeARLT 492 (534)
T KOG3653|consen 425 DPGPVPEYQLPFEA-EVGNHPTLEEMQELVVRKKQRPKIPDAWRKH-AGMAVLCETIEECWDHDAEARLT 492 (534)
T ss_pred cCCCCCcccCchhH-HhcCCCCHHHHHHHHHhhccCCCChhhhhcC-ccHHHHHHHHHHHcCCchhhhhh
Confidence 35778999999985 3588999999999999999999998887776 88999999999999887766653
No 18
>PF15249 GLTSCR1: Glioma tumor suppressor candidate region
Probab=27.11 E-value=25 Score=33.67 Aligned_cols=9 Identities=56% Similarity=1.265 Sum_probs=6.6
Q ss_pred CCCCCCCcc
Q 002557 433 VPGYQPPFR 441 (908)
Q Consensus 433 Vpgyk~PfR 441 (908)
-|.|++||+
T Consensus 14 ~PD~~tPF~ 22 (109)
T PF15249_consen 14 NPDYKTPFR 22 (109)
T ss_pred CCCcCCCCC
Confidence 367888884
No 19
>PRK14475 F0F1 ATP synthase subunit B; Provisional
Probab=25.29 E-value=4.6e+02 Score=26.63 Aligned_cols=34 Identities=24% Similarity=0.235 Sum_probs=29.4
Q ss_pred CCCcHHHHHHHHHHHHHHHhhhhHHHHHHhhhhc
Q 002557 538 NFLSPDVTEALQERERLAKSLQDEEEQARLRASA 571 (908)
Q Consensus 538 DFLp~~Va~al~eRe~~~~~~q~~EE~aR~~a~~ 571 (908)
=||++.|..+|.+|+.......++-|++|..|..
T Consensus 29 k~l~~pi~~~le~R~~~I~~~l~~Ae~~k~eAe~ 62 (167)
T PRK14475 29 KVLPKALAGALDAYAAKIQAELDEAQRLREEAQA 62 (167)
T ss_pred HHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5899999999999999988888888888877755
No 20
>KOG0994 consensus Extracellular matrix glycoprotein Laminin subunit beta [Extracellular structures]
Probab=24.64 E-value=6.1e+02 Score=34.13 Aligned_cols=29 Identities=31% Similarity=0.441 Sum_probs=21.3
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhccCCCCC
Q 002557 628 EKKLARAERKLLRAERALSKVEESLKPAE 656 (908)
Q Consensus 628 e~kL~~a~~K~~rae~~L~K~e~~~~p~~ 656 (908)
+.-+..|.+-++-|+..|.|++..+-++|
T Consensus 1583 ~~ai~~a~~~~~~a~~~l~kv~~~t~~aE 1611 (1758)
T KOG0994|consen 1583 QDAIQGADRDIRLAQQLLAKVQEETAAAE 1611 (1758)
T ss_pred HHHHHhhHHHHHHHHHHHHHHHHHHHHHH
Confidence 33355577778888888888888877766
No 21
>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=22.66 E-value=4.9e+02 Score=23.10 Aligned_cols=56 Identities=16% Similarity=0.150 Sum_probs=38.0
Q ss_pred HHHHHHHHHhCCeEEEEecCCChhhHHHHHHHHHH---HhCCeEEEEEccEEEEeecCCC
Q 002557 285 VDIIHEKWKTSEIVRLKIEGAPALNMKRMHEILER---KTGGLVIWRSGTAVSLYRGVSY 341 (908)
Q Consensus 285 VeeIh~awk~hELVKVK~l~~~~~dmk~~ae~LEe---kTGgeVVqrIG~viVLYRgsnY 341 (908)
+.+|-++++....|=|.+..-.....+++.+.|.- ..+|.+.+. |..++|+=+++.
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 45688999999999999999999999999888875 678887766 666666655543
No 22
>PRK13455 F0F1 ATP synthase subunit B; Provisional
Probab=22.62 E-value=6.7e+02 Score=25.77 Aligned_cols=32 Identities=19% Similarity=0.162 Sum_probs=26.1
Q ss_pred CcHHHHHHHHHHHHHHHhhhhHHHHHHhhhhc
Q 002557 540 LSPDVTEALQERERLAKSLQDEEEQARLRASA 571 (908)
Q Consensus 540 Lp~~Va~al~eRe~~~~~~q~~EE~aR~~a~~ 571 (908)
+|+.|...|.+|+.......++-|+++..|..
T Consensus 48 ~~~~v~~~L~~R~~~I~~~l~~Ae~~~~eA~~ 79 (184)
T PRK13455 48 VPGMIGGMLDKRAEGIRSELEEARALREEAQT 79 (184)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 58899999999999888777777777776654
No 23
>PF04931 DNA_pol_phi: DNA polymerase phi; InterPro: IPR007015 Proteins of this family are predominantly nucleolar. The majority are described as transcription factor transactivators. The family also includes the fifth essential DNA polymerase (Pol5p) of Schizosaccharomyces pombe (Fission yeast) and Saccharomyces cerevisiae (Baker's yeast) (2.7.7.7 from EC). Pol5p is localized exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=22.06 E-value=71 Score=39.82 Aligned_cols=26 Identities=35% Similarity=0.437 Sum_probs=22.1
Q ss_pred ccccHHHHHHHhHHHHHHHHHHHHHH
Q 002557 765 NLLTKRKALARSIELQRQEALLKHVA 790 (908)
Q Consensus 765 nlLTKrkAl~rS~e~qr~~~l~~hI~ 790 (908)
.+|++..+|=|.+-.|--+++-.||.
T Consensus 596 slls~~s~llR~~~~~vf~~~~~~~t 621 (784)
T PF04931_consen 596 SLLSQPSALLRKVSEQVFEAFCPHLT 621 (784)
T ss_pred HHHhCcchHHHHHHHHHHHHHHhhcC
Confidence 35778999999999999999888873
No 24
>PRK00013 groEL chaperonin GroEL; Reviewed
Probab=21.51 E-value=1.2e+03 Score=28.36 Aligned_cols=75 Identities=24% Similarity=0.349 Sum_probs=45.3
Q ss_pred CCH-HHHHH-HHHhcccCCCeEEecccchhhHHHHHHH-HHhhhcceeeeeeccCCCCCchHHHHHHHhhcccceeeecc
Q 002557 451 LAR-KEATN-LQRLARVLPPHFALGRSRQLQGLAVAMI-KLWEKSSIAKIALKRGVQLTTSERMVEDIKKLTGGTLLSRN 527 (908)
Q Consensus 451 Lt~-~E~T~-LRrLar~lPpHfaLGRNr~lqGLA~AIv-KLWEKs~IAKIaiKrGvqnT~ne~MaeELK~LTGGvLLsRn 527 (908)
|++ +++.. +..+...-.|.+... ..+.++|-+.+ +.+-+.-+..+|||+---+...+..-+.|-.+|||++++++
T Consensus 226 i~~~~~l~~~l~~i~~~g~~lvi~~--~~I~~~al~~l~~~~~~g~~~i~avr~~~~~~~r~~~l~~ia~~tG~~~i~~~ 303 (542)
T PRK00013 226 ISNIQDLLPVLEQVAQSGKPLLIIA--EDVEGEALATLVVNKLRGTLKVVAVKAPGFGDRRKAMLEDIAILTGGTVISEE 303 (542)
T ss_pred cCCHHHHHHHHHHHHHhCCCEEEEC--CCCcHHHHHHHHHcCCcccceEEEEecCCcccchhhhHHHHHHHcCCEEeccc
Confidence 444 45444 555655555666654 45788887755 44444455577776532223334456677789999999963
No 25
>TIGR00285 DNA-binding protein Alba. This protein appears so far only in the Archaea, but may be universal there. There is a single member in three of the first four completed archaeal genomes, and a second copy in A. fulgidus. In Sulfolobus shibatae there is a tandem second copy that is poorly conserved and scores below the trusted cutoff; all other members of the family are conserved at greater than 50 % pairwise identity.
Probab=21.10 E-value=2.4e+02 Score=26.96 Aligned_cols=67 Identities=13% Similarity=0.133 Sum_probs=52.9
Q ss_pred ceEEeCCCCCCHHHHHHHHHHHHhCCeEEEEEcCCCHHHHHHHHHHHHHHhCCEEEeccccccccEEE
Q 002557 681 AFLLLGRRGVFDGTVENMHLHWKYRELVKIIVKVKTFDQAKKIALALEAESGGVLVSVDKISKGYAMV 748 (908)
Q Consensus 681 PvV~IGKrGVTdgVIeeIh~hwk~hELVKVkv~~~~~~d~keiAe~Le~~SGg~LVqV~k~~IG~tiI 748 (908)
.++.||+.++..=|+.-+.+--+-..=|.|+-.+..-...=.+|+.|..+...- ++|.++.||.--+
T Consensus 2 ~~i~vG~KPvmnYVlavlt~fn~g~~eV~iKarG~aIskAVdvaeiik~r~~~~-v~v~~I~i~te~~ 68 (87)
T TIGR00285 2 NVVYIGNKPVMNYVLAVLTQLNSGADEVIIKARGRAISRAVDVAEIVRNRFIPD-IKIKKIKIGTEEI 68 (87)
T ss_pred CEEEEcCCcHHHHHHHHHHHHhCCCCeEEEEEecchhhhHHHHHHHHHHhccCC-ceEEEEEeccEEe
Confidence 579999999999999988876555677778888877777778999999988655 5777778875433
Done!