Query 004185
Match_columns 770
No_of_seqs 380 out of 1173
Neff 4.4
Searched_HMMs 46136
Date Thu Mar 28 19:01:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004185.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/004185hhsearch_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 3.5E-63 7.7E-68 561.5 18.0 512 169-741 4-531 (564)
2 PRK10343 RNA-binding protein Y 99.9 3.3E-25 7.1E-30 200.8 12.9 95 593-693 2-96 (97)
3 TIGR00253 RNA_bind_YhbY putati 99.9 5.2E-25 1.1E-29 199.0 12.7 88 594-685 1-88 (95)
4 PF01985 CRS1_YhbY: CRS1 / Yhb 99.9 2.1E-24 4.5E-29 190.5 10.9 84 180-263 1-84 (84)
5 PRK10343 RNA-binding protein Y 99.9 7.2E-24 1.6E-28 192.1 12.8 89 178-266 1-89 (97)
6 COG1534 Predicted RNA-binding 99.9 5.8E-24 1.3E-28 192.0 11.9 96 593-693 1-96 (97)
7 TIGR00253 RNA_bind_YhbY putati 99.9 1.4E-23 3.1E-28 189.7 12.9 88 180-267 1-88 (95)
8 PF01985 CRS1_YhbY: CRS1 / Yhb 99.9 7.3E-24 1.6E-28 187.1 10.2 84 594-681 1-84 (84)
9 COG1534 Predicted RNA-binding 99.9 6.6E-22 1.4E-26 178.7 11.9 89 179-267 1-89 (97)
10 KOG1990 Poly(A)-specific exori 99.8 1.5E-19 3.2E-24 206.6 4.3 302 168-502 163-493 (564)
11 PF15337 Vasculin: Vascular pr 41.0 15 0.00033 34.3 1.4 41 399-440 34-74 (97)
12 PF12720 DUF3807: Protein of u 26.1 48 0.001 34.0 2.4 18 392-409 43-60 (172)
13 PF03641 Lysine_decarbox: Poss 25.2 1.1E+02 0.0025 29.3 4.6 37 598-634 72-109 (133)
14 PF04472 DUF552: Protein of un 24.8 2.5E+02 0.0054 24.4 6.3 56 625-685 12-70 (73)
15 PF09339 HTH_IclR: IclR helix- 24.6 49 0.0011 26.6 1.7 23 62-84 29-51 (52)
16 PF12207 DUF3600: Domain of un 23.7 14 0.0003 37.2 -1.9 100 554-653 25-139 (162)
17 TIGR00285 DNA-binding protein 22.8 2.7E+02 0.0058 25.9 6.2 65 611-676 2-66 (87)
18 PF12802 MarR_2: MarR family; 20.4 54 0.0012 26.5 1.2 25 62-86 32-56 (62)
No 1
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=100.00 E-value=3.5e-63 Score=561.53 Aligned_cols=512 Identities=44% Similarity=0.630 Sum_probs=443.3
Q ss_pred ccCCChhhhccCCHHHHHHHHhcccCCCCeEEeCCCCCCHHHHHHHHHHHHhCCeEEEEEcCCchhhHHHHHHHHHHHhC
Q 004185 169 EKEVPTLAELKLSGKELRRLRTLGIGLRKKLKIGKAGITEGIVNGIHERWRHAEVVKIVCEDLCRLNMKRTHDSLERKTG 248 (770)
Q Consensus 169 ~~~~p~~aE~~Lt~kE~r~LRklA~~Lkp~V~IGK~GlTe~Vv~eI~~~wk~~ELVKIKi~~~~~~dmk~~ae~Le~kTG 248 (770)
... |+.|++++..+++.+||..+..+.-.+ +++|+|+.+++.|+..|+.+|+++++|......+|.+++++++..||
T Consensus 4 ~~~-~~~~~~~~~~~~~~~l~~~~~~~~~~~--~~~~~~~~~~~~~y~k~k~~~~~~~~~q~~~~~~~~~~~~~~~~~~~ 80 (564)
T KOG1990|consen 4 FES-LSLAELTVDEADLRRLRLVATGMTSAP--WKAGSTFDTVEAIYLKWKDNEEVYLKFQFGLCLFMKRSHEALEMSTG 80 (564)
T ss_pred ccc-hhHHHhhcCHHHHHHHhhhhccceecc--cccccchhhhHHHHHHHHhhhhhheeeccccchhHHHhhhHhhccCC
Confidence 345 999999999999999999999998777 99999999999999999999999999998888899999999999999
Q ss_pred C-eEEEEECcEEEEEecCCCCCCccccCCCccCCCCCCCCCCcccccccccccccccCCCCCCCCCCCCCCchhhhhhhc
Q 004185 249 G-LVVWRSGSKIILYRGADYKYPYFLADESSTDGASSDDLPNQLVDDEGLDETKTHSSGADSAKPSGQSPTNKKVQQTLI 327 (770)
Q Consensus 249 g-~VV~riG~~iVLYRgkny~~p~~~~~~~~~~e~~~~~~q~~~~~~~~~~~~~~~~s~~~~~~~~g~~~~~~~~~~~l~ 327 (770)
| -+||+.|.....|++..|..|..-... . | + .....
T Consensus 81 ~n~~~~~~g~~~s~~~~~~~~~~~~~~~~----~------~--~-----------------------------~~~~~-- 117 (564)
T KOG1990|consen 81 GNFVVWSRGDSISSPEFLCQRSPVDFVAR----Q------Q--E-----------------------------NQAGK-- 117 (564)
T ss_pred CceeeeecCccccCCccceeecchhhhhh----h------c--h-----------------------------hhhhh--
Confidence 9 999999999999977777655322110 0 0 0 00000
Q ss_pred cccCCCCccccCCcchhhhHHHHHHHhhccCCCccCCCCCCCCCcCCCCCCcccCCCCCCcccCCCCCCCCCCHHHHHHH
Q 004185 328 HSVGSPDKLRYQLPGEAELVEEADRLLDGLGPRFTDWWGYDPQPVDADLLPATVPGYRRPFRLLPYGVQPKLTNDEMTTL 407 (770)
Q Consensus 328 ~~~~~~~~~~~~~~~E~~~~~e~~~LLd~LgpRf~dW~g~~PlPVdadLLP~~vpgy~~PfR~lP~g~~~~LT~~Er~~L 407 (770)
-...++.+.+.+++++||+|.+||+.+|+|+|+|++|++||+|.+|||.+|+++++.||..|.+++
T Consensus 118 --------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dl~~~~i~~~~~p~r~l~~~~~~~l~~~~~~~~ 183 (564)
T KOG1990|consen 118 --------------WPSELEKEKNELLDSLGPELSDWGGSDRLSVDADLLPEKIPDYMRPFRTLPVGSPPLLTSIESTLL 183 (564)
T ss_pred --------------hHHHHHHHHHHHhhccCcccccCCCCCCccchhhhchhhhhcccChhccCCCCChhhhhhHHHHHH
Confidence 023467789999999999999999999999999999999999999999999999999999999999
Q ss_pred HHcCCCCCceEEecCCcchHHHHHHHHHHHhcCcceEEEecCCCCcchHHHHHHHH--HhhhCCEEEEEeCCEEEEEcCC
Q 004185 408 RRLGRPLPCHFALGRNRNLQGLAAAIVKLWEKCEIAKIAVKRGAQNTNSEMMAQEL--KRLTGGTLLSRDREFIVFYRGK 485 (770)
Q Consensus 408 Rkla~~l~p~~~LGRnGv~~Gla~~I~~~we~~ELVKI~~K~gv~~td~~~ma~eL--k~lTGgvLVsr~~~~iIlYRGk 485 (770)
|++|..+||||++|+++..+|++.+|+.+|++|+.+++.+++|+..+..+.||..+ ...||++||++|+.++|+|||+
T Consensus 184 r~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~k~~~~k~~~~rg~~~~~~~~~a~~l~~~~~tg~~lv~hN~~~dv~y~~~ 263 (564)
T KOG1990|consen 184 RRLGYKLPPHFALGRSRKLQGLAVAMVSFWEKHEFAKILIKRGVLETRKERMADELQELLLTGKVLVLHNKLLDVMYRYK 263 (564)
T ss_pred HHhcccccccceehhccccccchhHHHHHHHHHHHHHHHHHhcchhhhccchHHHHHHHHhcCCeEEeeccceeeeeehh
Confidence 99999999999999999999999999999999999999999999999999999999 9999999999999999999999
Q ss_pred CCCChhhhhhHHHhhhhhccccCCCCCccccCCC--CCCCCCCCcccccc---ccc------cccchhhHHHHHHHHHHH
Q 004185 486 DFLPPAASSAIEERRKHEFSTSNDSKEEPELGNR--HDNSGDNTQDEFGC---TND------QKSTMHSEQKERRSAEVA 554 (770)
Q Consensus 486 d~~p~~v~~~l~eR~~~~~s~~~~~~~~~~~~~~--~~~~~~~t~~~~~~---~~~------~~~~~~~~~~~~~~~~~~ 554 (770)
+|++ .+..+|.++.+.....+............ +.....+|..++.. .++ ..+.....+.+....++.
T Consensus 264 ~Fl~-~lp~~l~~f~~~~~~fp~~~~~~~~~~~~~~~~~~~~~t~~e~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~ 342 (564)
T KOG1990|consen 264 NFLS-PLPSTLEEFTDSSSMFPNIEDTKRLAKLSEYQKLNLKATLLELARAKAKKEKEIERRSISSRLKLEFEKASSEKL 342 (564)
T ss_pred hccc-ccchhHHHhhhhhhhhhhhHHHHHhhccccccchhhhhhHHHHHHHhcccccCcccccccchhhhhhhccchhhH
Confidence 9999 99999999998633223211100000000 11122344443321 111 111011223344556778
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhcc-cCCCCccCCCCCCCHHHHHHHHhcccCCCceEEeccCCCCHHHHHHHHHHHh
Q 004185 555 IRRTNIRLSRVLEKKAEAEKLLAELEE-ERPEQYEVDKEGITEEERYMLRKVGLRMKAFLLMGRRGVFDGTVENMHLHWK 633 (770)
Q Consensus 555 ~k~~e~kL~~~~~K~~k~e~ll~kl~~-~~p~~~~~d~E~LT~eER~~LRkig~klkpvv~IGk~Gvtd~vIe~i~~alk 633 (770)
.+.++++++.+..|...++..+++++. ..|.+..+|+|.+|.+++.+++++|.+|++++.+|++|+|+|++.+||.||+
T Consensus 343 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~e~~t~ee~~~~~k~g~k~~~~~~~~rrg~f~g~i~n~~l~wk 422 (564)
T KOG1990|consen 343 TEAIFHKLEKAKKKLASANRILAKLEDPKIPAELRYDPESITEEERLMLRKVGLKMKRRLLSGRRGVFDGVIENMHLHWK 422 (564)
T ss_pred HHHHHHHHhhhhhhccchhhhhhcccccccccccccchhhcChHHHHHHHHHHHhhccccccCCcccccceeecchhhhh
Confidence 899999999999999999999999998 8899988999999999999999999999999999999999999999999999
Q ss_pred ccceEEEEecCCCH-HHHHHHHHHHHHHhCCEEEEeeecccCcEEEEEccCCCCCCCcCCCcccccHHHHHHHhHHHHHH
Q 004185 634 HRELVKIISKQRKI-EAALQEARTLEVESGGILVAVERVNKGYAIILYRGKNYERPACLRPKTLLTKREAMKRSLEAQRR 712 (770)
Q Consensus 634 ~rELIKV~v~~~~~-~d~~eia~~L~~~sgg~lVqv~k~~iG~~iILYRgkny~rP~~~~P~~lLtK~~Al~rs~e~qr~ 712 (770)
+||++|++|+.... .++++.|..++.++|+++|+++++..|++|+.|||+||++|..+.|.++|+||+|+.+|+++|++
T Consensus 423 ~~e~~k~i~~~~~~~~~~~~~a~~le~esg~~~v~~~~~~~~~ai~~yr~k~y~~p~~l~P~~~l~~~k~~~~~~~~~~~ 502 (564)
T KOG1990|consen 423 SRELVKVICKEKNLPSQVKQYASALERESGGILVSIDKNPKGYAIIAYRGKNYDRPTSLRPRNLLSRRKALERSLEEQRK 502 (564)
T ss_pred hcccceeeeccccccHHHHHHHHHHHHHhCCceeeeccCCchhhHHHhhhhhccCCcccCchhhhcccCCccccHHHHHH
Confidence 99999999999777 99999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhhcCc
Q 004185 713 QSLKLHVLELTRNIEKLKLQLVKDKEANS 741 (770)
Q Consensus 713 ~~l~~~i~~l~~~i~~l~~~l~~~~~~~~ 741 (770)
++++.||..++.++++++.++..+...|.
T Consensus 503 ~a~~~~i~~~~~~~e~~~~~~~~~~~~~~ 531 (564)
T KOG1990|consen 503 EALKSHISDLEQEIEQLQASVEAMPAINK 531 (564)
T ss_pred HHHhhhcchhhhhHHHhhcchhccccccc
Confidence 99999999999999999999877555553
No 2
>PRK10343 RNA-binding protein YhbY; Provisional
Probab=99.92 E-value=3.3e-25 Score=200.84 Aligned_cols=95 Identities=21% Similarity=0.376 Sum_probs=89.4
Q ss_pred CCCHHHHHHHHhcccCCCceEEeccCCCCHHHHHHHHHHHhccceEEEEecCCCHHHHHHHHHHHHHHhCCEEEEeeecc
Q 004185 593 GITEEERYMLRKVGLRMKAFLLMGRRGVFDGTVENMHLHWKHRELVKIISKQRKIEAALQEARTLEVESGGILVAVERVN 672 (770)
Q Consensus 593 ~LT~eER~~LRkig~klkpvv~IGk~Gvtd~vIe~i~~alk~rELIKV~v~~~~~~d~~eia~~L~~~sgg~lVqv~k~~ 672 (770)
+||++||+|||++||+++|+|+||++|||++|+.+++++|++||||||++++++.++++++|.+||+.+||++||+
T Consensus 2 ~Lt~kqr~~LR~~ah~l~Pvv~IGk~Glt~~vi~ei~~aL~~hELIKvkv~~~~~~~~~e~~~~i~~~~~ae~Vq~---- 77 (97)
T PRK10343 2 NLSTKQKQHLKGLAHPLKPVVLLGSNGLTEGVLAEIEQALEHHELIKVKIATEDRETKTLIVEAIVRETGACNVQV---- 77 (97)
T ss_pred CCCHHHHHHHHHhcCCCCCeEEECCCCCCHHHHHHHHHHHHHCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEee----
Confidence 4999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCcEEEEEccCCCCCCCcCCC
Q 004185 673 KGYAIILYRGKNYERPACLRP 693 (770)
Q Consensus 673 iG~~iILYRgkny~rP~~~~P 693 (770)
||+++||||+++. |...+|
T Consensus 78 IG~~~vlYR~~~~--~~i~lp 96 (97)
T PRK10343 78 IGKTLVLYRPTKE--RKISLP 96 (97)
T ss_pred eCcEEEEEecCCC--ccCCCC
Confidence 9999999999853 444444
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=99.92 E-value=5.2e-25 Score=198.96 Aligned_cols=88 Identities=28% Similarity=0.451 Sum_probs=86.0
Q ss_pred CCHHHHHHHHhcccCCCceEEeccCCCCHHHHHHHHHHHhccceEEEEecCCCHHHHHHHHHHHHHHhCCEEEEeeeccc
Q 004185 594 ITEEERYMLRKVGLRMKAFLLMGRRGVFDGTVENMHLHWKHRELVKIISKQRKIEAALQEARTLEVESGGILVAVERVNK 673 (770)
Q Consensus 594 LT~eER~~LRkig~klkpvv~IGk~Gvtd~vIe~i~~alk~rELIKV~v~~~~~~d~~eia~~L~~~sgg~lVqv~k~~i 673 (770)
||++||++||++||+|+|+|+||++|||++||+++++||++||||||+++++++++++++|.+||+.+||++||+ |
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 LTGKQKRHLRGKAHHLKPVVLVGKNGLTEGVIKEIEQALEHRELIKVKVATEDREDKTLIAEALVKETGACNVQV----I 76 (95)
T ss_pred CCHHHHHHHHHHhCCCCCeEEECCCCCCHHHHHHHHHHHHhCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEEE----E
Confidence 799999999999999999999999999999999999999999999999999999999999999999999999999 9
Q ss_pred CcEEEEEccCCC
Q 004185 674 GYAIILYRGKNY 685 (770)
Q Consensus 674 G~~iILYRgkny 685 (770)
|+++||||+++.
T Consensus 77 G~~~vlYR~~~~ 88 (95)
T TIGR00253 77 GKTIVLYRPTKE 88 (95)
T ss_pred ccEEEEEecCCc
Confidence 999999999753
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=2.1e-24 Score=190.54 Aligned_cols=84 Identities=37% Similarity=0.580 Sum_probs=75.7
Q ss_pred CCHHHHHHHHhcccCCCCeEEeCCCCCCHHHHHHHHHHHHhCCeEEEEEcCCchhhHHHHHHHHHHHhCCeEEEEECcEE
Q 004185 180 LSGKELRRLRTLGIGLRKKLKIGKAGITEGIVNGIHERWRHAEVVKIVCEDLCRLNMKRTHDSLERKTGGLVVWRSGSKI 259 (770)
Q Consensus 180 Lt~kE~r~LRklA~~Lkp~V~IGK~GlTe~Vv~eI~~~wk~~ELVKIKi~~~~~~dmk~~ae~Le~kTGg~VV~riG~~i 259 (770)
||++|+++||+.||+|+|+|+|||+|+|++|+++|+++|++||||||+|.+++..|++++|+.|+++|||++||++|+++
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 004185 260 ILYR 263 (770)
Q Consensus 260 VLYR 263 (770)
||||
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=99.91 E-value=7.2e-24 Score=192.14 Aligned_cols=89 Identities=27% Similarity=0.428 Sum_probs=87.2
Q ss_pred ccCCHHHHHHHHhcccCCCCeEEeCCCCCCHHHHHHHHHHHHhCCeEEEEEcCCchhhHHHHHHHHHHHhCCeEEEEECc
Q 004185 178 LKLSGKELRRLRTLGIGLRKKLKIGKAGITEGIVNGIHERWRHAEVVKIVCEDLCRLNMKRTHDSLERKTGGLVVWRSGS 257 (770)
Q Consensus 178 ~~Lt~kE~r~LRklA~~Lkp~V~IGK~GlTe~Vv~eI~~~wk~~ELVKIKi~~~~~~dmk~~ae~Le~kTGg~VV~riG~ 257 (770)
|+||++|+++||++||+|+|+|+|||+|+|++|+++|.+++++||||||++.+++.++.++++++|++.||+++||+||+
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 004185 258 KIILYRGAD 266 (770)
Q Consensus 258 ~iVLYRgkn 266 (770)
++||||.+.
T Consensus 81 ~~vlYR~~~ 89 (97)
T PRK10343 81 TLVLYRPTK 89 (97)
T ss_pred EEEEEecCC
Confidence 999999975
No 6
>COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]
Probab=99.91 E-value=5.8e-24 Score=191.95 Aligned_cols=96 Identities=27% Similarity=0.443 Sum_probs=90.5
Q ss_pred CCCHHHHHHHHhcccCCCceEEeccCCCCHHHHHHHHHHHhccceEEEEecCCCHHHHHHHHHHHHHHhCCEEEEeeecc
Q 004185 593 GITEEERYMLRKVGLRMKAFLLMGRRGVFDGTVENMHLHWKHRELVKIISKQRKIEAALQEARTLEVESGGILVAVERVN 672 (770)
Q Consensus 593 ~LT~eER~~LRkig~klkpvv~IGk~Gvtd~vIe~i~~alk~rELIKV~v~~~~~~d~~eia~~L~~~sgg~lVqv~k~~ 672 (770)
+||++|+++||+.||+++|+|+||++|||++||.+|+++|++||||||++.+++.++.+++|+.||+.+||.+||+
T Consensus 1 ~Lt~kq~~~Lrs~Ah~l~piv~IGk~Glte~vi~Ei~~aL~~reLIKVkvl~~~~edr~eia~~l~~~~~a~lVqv---- 76 (97)
T COG1534 1 MLTGKQKRFLRSKAHHLKPIVQIGKNGLTEGVIKEIDRALEARELIKVKVLQNAREDKKEIAEALAEETGAELVQV---- 76 (97)
T ss_pred CCcHHHHHHHHHhhccCCceEEecCCccCHHHHHHHHHHHHhCCcEEEEeeccchhhHHHHHHHHHHHhCCEEeee----
Confidence 6999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCcEEEEEccCCCCCCCcCCC
Q 004185 673 KGYAIILYRGKNYERPACLRP 693 (770)
Q Consensus 673 iG~~iILYRgkny~rP~~~~P 693 (770)
||+++|||| .+..++++.+|
T Consensus 77 iG~~~vlyr-~~~e~~~i~l~ 96 (97)
T COG1534 77 IGKTLVLYR-ESKEKRKISLP 96 (97)
T ss_pred eeeEEEEEe-cCcccccccCC
Confidence 999999999 44456666555
No 7
>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=99.90 E-value=1.4e-23 Score=189.69 Aligned_cols=88 Identities=31% Similarity=0.472 Sum_probs=86.0
Q ss_pred CCHHHHHHHHhcccCCCCeEEeCCCCCCHHHHHHHHHHHHhCCeEEEEEcCCchhhHHHHHHHHHHHhCCeEEEEECcEE
Q 004185 180 LSGKELRRLRTLGIGLRKKLKIGKAGITEGIVNGIHERWRHAEVVKIVCEDLCRLNMKRTHDSLERKTGGLVVWRSGSKI 259 (770)
Q Consensus 180 Lt~kE~r~LRklA~~Lkp~V~IGK~GlTe~Vv~eI~~~wk~~ELVKIKi~~~~~~dmk~~ae~Le~kTGg~VV~riG~~i 259 (770)
||++|+++||++||+|+|.|+|||+|+|++|+++|+++|++||||||++.+++..+.+++|++|++.||+++|+.+|+++
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 004185 260 ILYRGADY 267 (770)
Q Consensus 260 VLYRgkny 267 (770)
||||+++.
T Consensus 81 vlYR~~~~ 88 (95)
T TIGR00253 81 VLYRPTKE 88 (95)
T ss_pred EEEecCCc
Confidence 99999754
No 8
>PF01985 CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR001890 The CRM domain is an ~100-amino acid RNA-binding domain. The name chloroplast RNA splicing and ribosome maturation (CRM) has been suggested to reflect the functions established for the four characterised members of the family: Zea mays (Maize) CRS1 (Q9FYT6 from SWISSPROT), CAF1 (Q84N49 from SWISSPROT) and CAF2 (Q84N48 from SWISSPROT) proteins and the Escherichia coli protein YhbY (P0AGK4 from SWISSPROT). The CRM domain is found in eubacteria, archaea, and plants. The CRM domain is represented as a stand-alone protein in archaea and bacteria, and in single- and multi-domain proteins in plants. It has been suggested that prokaryotic CRM proteins existed as ribosome-associated proteins prior to the divergence of archaea and bacteria, and that they were co-opted in the plant lineage as RNA binding modules by incorporation into diverse protein contexts. Plant CRM domains are predicted to reside not only in the chloroplast, but also in the mitochondrion and the nucleo/cytoplasmic compartment. The diversity of the CRM domain family in plants suggests a diverse set of RNA targets [, ]. The CRM domain is a compact alpha/beta domain consisting of a four-stranded beta sheet and three alpha helices with an alpha-beta-alpha-beta-alpha-beta-beta topology. The beta sheet face is basic, consistent with a role in RNA binding. Proximal to the basic beta sheet face is another moiety that could contribute to nucleic acid recognition. Connecting strand beta1 and helix alpha2 is a loop with a six amino acid motif, GxxG flanked by large aliphatic residues, within which one 'x' is typically a basic residue []. Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants []. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing []. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes []. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome [].; GO: 0003723 RNA binding; PDB: 1RQ8_A 1JO0_B 1LN4_A.
Probab=99.90 E-value=7.3e-24 Score=187.09 Aligned_cols=84 Identities=32% Similarity=0.493 Sum_probs=75.5
Q ss_pred CCHHHHHHHHhcccCCCceEEeccCCCCHHHHHHHHHHHhccceEEEEecCCCHHHHHHHHHHHHHHhCCEEEEeeeccc
Q 004185 594 ITEEERYMLRKVGLRMKAFLLMGRRGVFDGTVENMHLHWKHRELVKIISKQRKIEAALQEARTLEVESGGILVAVERVNK 673 (770)
Q Consensus 594 LT~eER~~LRkig~klkpvv~IGk~Gvtd~vIe~i~~alk~rELIKV~v~~~~~~d~~eia~~L~~~sgg~lVqv~k~~i 673 (770)
||++|+++||++||+|+|+|+||++|||++|+++|+++|++||||||+|.+++.++++++|..|++.+||++|++ +
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 LTSKERKFLRKLAHHLKPVVQIGKNGLTDGVIEEIDDALEKHELVKVKVLGNCREDRKEIAEQLAEKTGAEVVQV----I 76 (84)
T ss_dssp --HHHHHHHHHHHTTC--SEEE-TTSS-HHHHHHHHHHHHHHSEEEEEETT--HHHHHHHHHHHHHHHTEEEEEE----E
T ss_pred CCHHHHHHHHHHhcCCCCeEEECCCCCCHHHHHHHHHHHHhCCeeEEEEccCCHHHHHHHHHHHHHHhCCEEEEE----E
Confidence 799999999999999999999999999999999999999999999999999999999999999999999999998 9
Q ss_pred CcEEEEEc
Q 004185 674 GYAIILYR 681 (770)
Q Consensus 674 G~~iILYR 681 (770)
|+++||||
T Consensus 77 G~~~vlyR 84 (84)
T PF01985_consen 77 GRTIVLYR 84 (84)
T ss_dssp TTEEEEEE
T ss_pred CCEEEEEC
Confidence 99999998
No 9
>COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]
Probab=99.87 E-value=6.6e-22 Score=178.70 Aligned_cols=89 Identities=30% Similarity=0.478 Sum_probs=85.7
Q ss_pred cCCHHHHHHHHhcccCCCCeEEeCCCCCCHHHHHHHHHHHHhCCeEEEEEcCCchhhHHHHHHHHHHHhCCeEEEEECcE
Q 004185 179 KLSGKELRRLRTLGIGLRKKLKIGKAGITEGIVNGIHERWRHAEVVKIVCEDLCRLNMKRTHDSLERKTGGLVVWRSGSK 258 (770)
Q Consensus 179 ~Lt~kE~r~LRklA~~Lkp~V~IGK~GlTe~Vv~eI~~~wk~~ELVKIKi~~~~~~dmk~~ae~Le~kTGg~VV~riG~~ 258 (770)
+||++|+++||+.||+++|+|+|||+|+|++|+.+|.++|++||||||++.+++.+|.+++|+.|++.||+.+|+++|++
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 EEEEecCCC
Q 004185 259 IILYRGADY 267 (770)
Q Consensus 259 iVLYRgkny 267 (770)
+||||.+..
T Consensus 81 ~vlyr~~~e 89 (97)
T COG1534 81 LVLYRESKE 89 (97)
T ss_pred EEEEecCcc
Confidence 999994433
No 10
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=99.77 E-value=1.5e-19 Score=206.57 Aligned_cols=302 Identities=21% Similarity=0.278 Sum_probs=216.9
Q ss_pred hccCCChhhhccCCHHHHHHHHhcccCCCCeEEeCCCCCCHHHHHHHHHHHHhCCeEEEEEc-CCchhhHHHHHHHH--H
Q 004185 168 KEKEVPTLAELKLSGKELRRLRTLGIGLRKKLKIGKAGITEGIVNGIHERWRHAEVVKIVCE-DLCRLNMKRTHDSL--E 244 (770)
Q Consensus 168 k~~~~p~~aE~~Lt~kE~r~LRklA~~Lkp~V~IGK~GlTe~Vv~eI~~~wk~~ELVKIKi~-~~~~~dmk~~ae~L--e 244 (770)
-....|.+.+..|+..+...+|+++...+++|.+|.++.-+++.-.+...|.+|+.+|+.+. +.+......++.++ -
T Consensus 163 p~r~l~~~~~~~l~~~~~~~~r~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~k~~~~k~~~~rg~~~~~~~~~a~~l~~~ 242 (564)
T KOG1990|consen 163 PFRTLPVGSPPLLTSIESTLLRRLGYKLPPHFALGRSRKLQGLAVAMVSFWEKHEFAKILIKRGVLETRKERMADELQEL 242 (564)
T ss_pred hhccCCCCChhhhhhHHHHHHHHhcccccccceehhccccccchhHHHHHHHHHHHHHHHHHhcchhhhccchHHHHHHH
Confidence 34577888899999999999999999999999999999999999999999999999998886 77788888999999 8
Q ss_pred HHhCCeEEEEECcEEEEEecCCCCCCccccCCCccCCCCCCCCCCcccccccccccccccCCCCCCCCCCCCCCchhhhh
Q 004185 245 RKTGGLVVWRSGSKIILYRGADYKYPYFLADESSTDGASSDDLPNQLVDDEGLDETKTHSSGADSAKPSGQSPTNKKVQQ 324 (770)
Q Consensus 245 ~kTGg~VV~riG~~iVLYRgkny~~p~~~~~~~~~~e~~~~~~q~~~~~~~~~~~~~~~~s~~~~~~~~g~~~~~~~~~~ 324 (770)
..||+.||.++|-..++||+++|.. +... +...........++.++...... ..+ .......++..+...+..
T Consensus 243 ~~tg~~lv~hN~~~dv~y~~~~Fl~-~lp~-~l~~f~~~~~~fp~~~~~~~~~~----~~~-~~~~~~~~t~~e~~~~~~ 315 (564)
T KOG1990|consen 243 LLTGKVLVLHNKLLDVMYRYKNFLS-PLPS-TLEEFTDSSSMFPNIEDTKRLAK----LSE-YQKLNLKATLLELARAKA 315 (564)
T ss_pred HhcCCeEEeeccceeeeeehhhccc-ccch-hHHHhhhhhhhhhhhHHHHHhhc----ccc-ccchhhhhhHHHHHHHhc
Confidence 9999999999999999999999976 3222 22111111112222111111111 011 111123344445555555
Q ss_pred hhccccCCCCcc-ccCCcchh----hhH--------------HHHHHHhhccCCCccCCCCCCCCCcCCCCCCcccCCCC
Q 004185 325 TLIHSVGSPDKL-RYQLPGEA----ELV--------------EEADRLLDGLGPRFTDWWGYDPQPVDADLLPATVPGYR 385 (770)
Q Consensus 325 ~l~~~~~~~~~~-~~~~~~E~----~~~--------------~e~~~LLd~LgpRf~dW~g~~PlPVdadLLP~~vpgy~ 385 (770)
.|..++...+.. ...++.+. +.. ..++..|++++ ....|+.
T Consensus 316 ~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~---------------~~~~~~~----- 375 (564)
T KOG1990|consen 316 KKEKEIERRSISSRLKLEFEKASSEKLTEAIFHKLEKAKKKLASANRILAKLE---------------DPKIPAE----- 375 (564)
T ss_pred ccccCcccccccchhhhhhhccchhhHHHHHHHHHhhhhhhccchhhhhhccc---------------ccccccc-----
Confidence 555444333221 11112111 111 11333333322 2222221
Q ss_pred CCcccCCCCCCCCCCHHHHHHHHHcCCCCCceEEecCCcchHHHHHHHHHHHhcCcceEEEecCCCCcchHHHHHHHHHh
Q 004185 386 RPFRLLPYGVQPKLTNDEMTTLRRLGRPLPCHFALGRNRNLQGLAAAIVKLWEKCEIAKIAVKRGAQNTNSEMMAQELKR 465 (770)
Q Consensus 386 ~PfR~lP~g~~~~LT~~Er~~LRkla~~l~p~~~LGRnGv~~Gla~~I~~~we~~ELVKI~~K~gv~~td~~~ma~eLk~ 465 (770)
++.+.+.+|++|+.++++.|..++..+.+||.|+++|++.++|.||+++|++|+.|+........+..|..++.
T Consensus 376 ------~~~~~e~~t~ee~~~~~k~g~k~~~~~~~~rrg~f~g~i~n~~l~wk~~e~~k~i~~~~~~~~~~~~~a~~le~ 449 (564)
T KOG1990|consen 376 ------LRYDPESITEEERLMLRKVGLKMKRRLLSGRRGVFDGVIENMHLHWKSRELVKVICKEKNLPSQVKQYASALER 449 (564)
T ss_pred ------cccchhhcChHHHHHHHHHHHhhccccccCCcccccceeecchhhhhhcccceeeeccccccHHHHHHHHHHHH
Confidence 22466789999999999999999999999999999999999999999999999999987677999999999999
Q ss_pred hhCCEEEEEeC----CEEEEEcCCCCCChhh---hhhHHHhhhh
Q 004185 466 LTGGTLLSRDR----EFIVFYRGKDFLPPAA---SSAIEERRKH 502 (770)
Q Consensus 466 lTGgvLVsr~~----~~iIlYRGkd~~p~~v---~~~l~eR~~~ 502 (770)
+.||++|+.+. +.|++|||++|..|.. -+.|.+|.++
T Consensus 450 esg~~~v~~~~~~~~~ai~~yr~k~y~~p~~l~P~~~l~~~k~~ 493 (564)
T KOG1990|consen 450 ESGGILVSIDKNPKGYAIIAYRGKNYDRPTSLRPRNLLSRRKAL 493 (564)
T ss_pred HhCCceeeeccCCchhhHHHhhhhhccCCcccCchhhhcccCCc
Confidence 99999999976 5589999999999886 2344444433
No 11
>PF15337 Vasculin: Vascular protein family Vasculin-like 1
Probab=40.99 E-value=15 Score=34.32 Aligned_cols=41 Identities=24% Similarity=0.419 Sum_probs=33.0
Q ss_pred CCHHHHHHHHHcCCCCCceEEecCCcchHHHHHHHHHHHhcC
Q 004185 399 LTNDEMTTLRRLGRPLPCHFALGRNRNLQGLAAAIVKLWEKC 440 (770)
Q Consensus 399 LT~~Er~~LRkla~~l~p~~~LGRnGv~~Gla~~I~~~we~~ 440 (770)
||.+|.++|--+.-.|+ ---+||||++++..-++-..|...
T Consensus 34 lTEDElkEF~~kseQlr-rNGf~kngfl~~rs~slf~pWr~t 74 (97)
T PF15337_consen 34 LTEDELKEFQVKSEQLR-RNGFGKNGFLQSRSLSLFSPWRST 74 (97)
T ss_pred CcHHHHHHHHHHHHHHH-Hccccccchhhhhhhhcccccccc
Confidence 99999999988775555 456899999999888877777653
No 12
>PF12720 DUF3807: Protein of unknown function (DUF3807); InterPro: IPR024526 This is a family of conserved fungal proteins of unknown function.
Probab=26.14 E-value=48 Score=34.04 Aligned_cols=18 Identities=33% Similarity=0.698 Sum_probs=17.3
Q ss_pred CCCCCCCCCHHHHHHHHH
Q 004185 392 PYGVQPKLTNDEMTTLRR 409 (770)
Q Consensus 392 P~g~~~~LT~~Er~~LRk 409 (770)
|.||+-+||++|..+||+
T Consensus 43 pDGVKRTLTDEQI~IFRH 60 (172)
T PF12720_consen 43 PDGVKRTLTDEQIEIFRH 60 (172)
T ss_pred CCCCcccccHHHHHHHHH
Confidence 899999999999999997
No 13
>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=25.17 E-value=1.1e+02 Score=29.32 Aligned_cols=37 Identities=22% Similarity=0.330 Sum_probs=31.1
Q ss_pred HHHHHHhcccCCC-ceEEeccCCCCHHHHHHHHHHHhc
Q 004185 598 ERYMLRKVGLRMK-AFLLMGRRGVFDGTVENMHLHWKH 634 (770)
Q Consensus 598 ER~~LRkig~klk-pvv~IGk~Gvtd~vIe~i~~alk~ 634 (770)
+--.+.++|.+-+ |++.++.+|.|+.+++.++.....
T Consensus 72 ~~~~~~~l~~~~~~Piil~~~~g~w~~l~~~l~~~~~~ 109 (133)
T PF03641_consen 72 EALTLMQLGRHNKVPIILLNIDGFWDPLLEFLDRMIEE 109 (133)
T ss_dssp HHHHHHHTTSSTS-EEEEEECGGCCHHHHHHHHHHHHT
T ss_pred HHHHHHhhccccCCCEEEeCCcchHHHHHHHHHHHHHC
Confidence 5566788998888 999999999999999999755443
No 14
>PF04472 DUF552: Protein of unknown function (DUF552); InterPro: IPR007561 This entry represents a cell division protein, designated SepF, which is conserved in Gram-positive bacteria. SepF accumulates at the cell division site in an FtsZ-dependent manner and is required for proper septum formation []. Mutants are viable but the formation of the septum is much slower and occurs with a very abnormal morphology. This entry also includes archaeal related proteins of unknown function.; GO: 0000917 barrier septum formation; PDB: 3P04_A.
Probab=24.85 E-value=2.5e+02 Score=24.38 Aligned_cols=56 Identities=13% Similarity=0.060 Sum_probs=39.8
Q ss_pred HHHHHHHHhccceEEEEecCCCHHHHHHHHHHHHH---HhCCEEEEeeecccCcEEEEEccCCC
Q 004185 625 VENMHLHWKHRELVKIISKQRKIEAALQEARTLEV---ESGGILVAVERVNKGYAIILYRGKNY 685 (770)
Q Consensus 625 Ie~i~~alk~rELIKV~v~~~~~~d~~eia~~L~~---~sgg~lVqv~k~~iG~~iILYRgkny 685 (770)
+.++-++++....|=+.+..-+.++.+.+...|+. ..+|.+..+ |..+++|=+++.
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 34588899999999999999999999999988876 789999985 777888876653
No 15
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=24.59 E-value=49 Score=26.60 Aligned_cols=23 Identities=26% Similarity=0.361 Sum_probs=20.0
Q ss_pred CCCCcHHHHHHHHHHhcCCcccC
Q 004185 62 NDTTSAIQRIADKLRSLGIVEQT 84 (770)
Q Consensus 62 ~~~~s~~~ri~~klr~~g~~~~~ 84 (770)
.+|.|++.||+.-|...||++.+
T Consensus 29 gl~~stv~r~L~tL~~~g~v~~d 51 (52)
T PF09339_consen 29 GLPKSTVHRLLQTLVEEGYVERD 51 (52)
T ss_dssp TS-HHHHHHHHHHHHHTTSEEEC
T ss_pred CcCHHHHHHHHHHHHHCcCeecC
Confidence 47899999999999999999765
No 16
>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=23.68 E-value=14 Score=37.22 Aligned_cols=100 Identities=14% Similarity=0.155 Sum_probs=67.3
Q ss_pred HHHHHHHHHHHHHHHH---H--HHHHHHhhhcc----cCCCCccCCCCCCCHHHHHHHHhcccCCCceEE------eccC
Q 004185 554 AIRRTNIRLSRVLEKK---A--EAEKLLAELEE----ERPEQYEVDKEGITEEERYMLRKVGLRMKAFLL------MGRR 618 (770)
Q Consensus 554 ~~k~~e~kL~~~~~K~---~--k~e~ll~kl~~----~~p~~~~~d~E~LT~eER~~LRkig~klkpvv~------IGk~ 618 (770)
.--+++.||+.|+-.. + .=..+|+++-. ..-+.-..|.|.||..++..++++...+.|++- --|.
T Consensus 25 ~Y~~~eaKLqqAK~~lgeeEfeef~~lLK~lt~~kLkygD~NGnidye~ls~~eqee~k~~~~eLqPYFdKLN~~~SsK~ 104 (162)
T PF12207_consen 25 DYLRLEAKLQQAKGELGEEEFEEFKELLKKLTNAKLKYGDKNGNIDYEKLSKEEQEEYKKLTMELQPYFDKLNGHKSSKE 104 (162)
T ss_dssp HHHHHHHHHHHHHHCS-HHHHHHHHHHHHHHHHHHHHHB-TTS-B-GGGS-HHHHHHHHHHHHHHHHHHHHHTT---HHH
T ss_pred HHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHhHHhhcccCCCcCHHhCCHHHHHHHHHHHHhcchHHHHhcCCcchhh
Confidence 4467899999998542 2 22346666643 456677889999999999999999999999873 3445
Q ss_pred CCCHHHHHHHHHHHhccceEEEEecCCCHHHHHHH
Q 004185 619 GVFDGTVENMHLHWKHRELVKIISKQRKIEAALQE 653 (770)
Q Consensus 619 Gvtd~vIe~i~~alk~rELIKV~v~~~~~~d~~ei 653 (770)
=+++.=.+.--.||-..|.|+|+........+.++
T Consensus 105 vlt~~E~d~y~eALm~~e~v~vk~~~~~~~~ve~v 139 (162)
T PF12207_consen 105 VLTQEEYDQYIEALMTYETVRVKTKSSGGITVEEV 139 (162)
T ss_dssp HS-HHHHHHHHHHHHHHHHHHHHCT-SS---GGGS
T ss_pred hcCHHHHHHHHHHHhhhheeeeeccCCCCCcHHhc
Confidence 56777777788899999999998886554444333
No 17
>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=22.77 E-value=2.7e+02 Score=25.95 Aligned_cols=65 Identities=14% Similarity=0.164 Sum_probs=53.9
Q ss_pred ceEEeccCCCCHHHHHHHHHHHhccceEEEEecCCCHHHHHHHHHHHHHHhCCEEEEeeecccCcE
Q 004185 611 AFLLMGRRGVFDGTVENMHLHWKHRELVKIISKQRKIEAALQEARTLEVESGGILVAVERVNKGYA 676 (770)
Q Consensus 611 pvv~IGk~Gvtd~vIe~i~~alk~rELIKV~v~~~~~~d~~eia~~L~~~sgg~lVqv~k~~iG~~ 676 (770)
.++.||+.++..=|+.-+.+--+.-.=|.|+-.+..-...-++|+.|....... +++.++++|--
T Consensus 2 ~~i~vG~KPvmnYVlavlt~fn~g~~eV~iKarG~aIskAVdvaeiik~r~~~~-v~v~~I~i~te 66 (87)
T TIGR00285 2 NVVYIGNKPVMNYVLAVLTQLNSGADEVIIKARGRAISRAVDVAEIVRNRFIPD-IKIKKIKIGTE 66 (87)
T ss_pred CEEEEcCCcHHHHHHHHHHHHhCCCCeEEEEEecchhhhHHHHHHHHHHhccCC-ceEEEEEeccE
Confidence 578999999999999999876565677888888998899999999999987655 57777777754
No 18
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=20.44 E-value=54 Score=26.51 Aligned_cols=25 Identities=28% Similarity=0.492 Sum_probs=20.1
Q ss_pred CCCCcHHHHHHHHHHhcCCcccCCC
Q 004185 62 NDTTSAIQRIADKLRSLGIVEQTTS 86 (770)
Q Consensus 62 ~~~~s~~~ri~~klr~~g~~~~~~~ 86 (770)
..+++++.+++.+|.+.||++-..+
T Consensus 32 ~~~~~~vs~~v~~L~~~Glv~r~~~ 56 (62)
T PF12802_consen 32 GISKSTVSRIVKRLEKKGLVERERD 56 (62)
T ss_dssp TS-HHHHHHHHHHHHHTTSEEEEE-
T ss_pred CcCHHHHHHHHHHHHHCCCEEEeCC
Confidence 4678999999999999999975543
Done!