Query 024240
Match_columns 270
No_of_seqs 115 out of 431
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 03:06:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024240.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024240hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3031 Protein required for b 100.0 2.1E-83 4.5E-88 575.5 14.8 262 1-268 1-268 (307)
2 COG5106 RPF2 Uncharacterized c 100.0 1.4E-64 2.9E-69 446.5 12.0 262 1-268 1-275 (316)
3 KOG2971 RNA-binding protein re 100.0 1.9E-47 4.1E-52 339.2 14.5 203 23-249 45-265 (299)
4 COG5154 BRX1 RNA-binding prote 100.0 4.4E-44 9.5E-49 311.1 13.5 205 26-249 29-251 (283)
5 PF04427 Brix: Brix domain; I 100.0 2.2E-42 4.8E-47 299.1 6.2 185 32-232 1-191 (191)
6 smart00879 Brix Brix domain. T 100.0 1.4E-36 3E-41 259.3 17.6 179 31-227 1-180 (180)
7 KOG2963 RNA-binding protein re 100.0 3.2E-27 6.9E-32 218.2 17.4 189 3-208 3-201 (405)
8 KOG2781 U3 small nucleolar rib 99.7 7.9E-16 1.7E-20 137.3 16.5 181 28-238 83-264 (290)
9 KOG2780 Ribosome biogenesis pr 99.5 4.2E-13 9.1E-18 121.2 14.9 180 28-235 97-277 (302)
10 PRK03972 ribosomal biogenesis 99.0 4.4E-08 9.4E-13 86.8 17.4 191 30-245 2-203 (208)
11 COG2136 IMP4 Predicted exosome 98.7 1.4E-06 3.1E-11 76.5 16.2 182 29-234 3-186 (191)
12 PRK00933 ribosomal biogenesis 94.4 1.7 3.7E-05 37.4 13.5 114 31-172 2-116 (165)
13 PF12249 AftA_C: Arabinofurano 41.9 25 0.00053 30.7 2.8 32 198-230 146-177 (178)
14 PRK15456 universal stress prot 38.2 23 0.00049 28.3 2.0 30 76-106 95-124 (142)
15 PHA02096 hypothetical protein 33.2 80 0.0017 24.3 4.1 52 139-191 22-74 (103)
16 cd01988 Na_H_Antiporter_C The 31.4 40 0.00087 25.8 2.4 23 76-98 84-106 (132)
17 cd01987 USP_OKCHK USP domain i 29.5 19 0.0004 27.8 0.1 32 76-107 75-106 (124)
18 PRK15005 universal stress prot 28.4 42 0.00091 26.5 2.0 20 76-95 97-116 (144)
19 PF05450 Nicastrin: Nicastrin; 27.0 80 0.0017 28.6 3.7 62 141-202 49-117 (234)
20 PF08616 SPA: Stabilization of 26.4 1.6E+02 0.0036 23.4 5.1 63 26-96 24-88 (113)
21 PRK00536 speE spermidine synth 22.4 70 0.0015 29.5 2.5 24 23-47 69-92 (262)
No 1
>KOG3031 consensus Protein required for biogenesis of the ribosomal 60S subunit [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.1e-83 Score=575.53 Aligned_cols=262 Identities=50% Similarity=0.781 Sum_probs=257.5
Q ss_pred CCCccCCCChhhhhHHHHhCCccccCCcEEEEEeCCCCCHhHHHHHHHHHhcccccceeccccCCCcCcCCCCCcchhhh
Q 024240 1 MLKVKTPKNPRVKRALEKRAPKLVETGKKTLILQGTKTSNTLNDVLTELYLLKKGSAIRYTRKNENIRPFESGGETSLEF 80 (270)
Q Consensus 1 ~~~~~k~kt~~~kr~l~~repk~~en~K~~L~l~g~~~s~~~~~ll~DL~~L~kP~a~~~~Kkn~~i~pFe~~~~~~le~ 80 (270)
|.++++||+++++|++.+|||+.+||.+.+||+.|..|++.+.++|.||++|++|.++.++|+|. |+||||. ++|||
T Consensus 1 m~rv~k~k~~~~kr~l~kr~~klve~~k~alf~~g~~~~~tl~~vm~dl~alKKp~~i~~~rkN~-i~pFEd~--sslef 77 (307)
T KOG3031|consen 1 MNRVVKPKNARAKRALVKREPKLVENHKDALFLPGMKTNKTLLDVMKDLYALKKPLEIRYNRKNN-IHPFEDP--SSLEF 77 (307)
T ss_pred CCceeecchhhhHHHHHhhchhhchhhhhhhccCchhhchHHHHHHHHHHHhccCceeeeccCCC-cccCCCC--chHHH
Confidence 78999999999999999999999999999999999999999999999999999999999999996 9999998 99999
Q ss_pred hhccCCCcEEEEeeeCCCCCCceEEEEccCCceeeeEEEEeeceeecccccCCCCCCCCCCCccEEEEeCCCCCChHHHH
Q 024240 81 FSLKTDCSIFIYGSTSKKRPDNLVIGRTYDHHIYDLVEVGVENFKPLNSFIYDKKLAPRVGSKPFICFVGEGFESVEELK 160 (270)
Q Consensus 81 la~k~dcslf~f~s~~KKrp~~L~igR~~~g~~LDm~ef~V~n~~~~~~~~~~~~~~~~~gskPllvF~g~~F~~~~~l~ 160 (270)
+++++||++|+++|||||||+||+|||+||+++|||+||+|+||+++++|+.+++ ..|++|+|+|+|+.|++++.|+
T Consensus 78 fseK~D~slfv~gs~sKKrp~nLv~gR~fd~~vlDMiElgI~~ykslsdF~~~k~---~~gtKP~l~f~G~~f~~~~~~k 154 (307)
T KOG3031|consen 78 FSEKNDCSLFVLGSHSKKRPNNLVIGRTFDYEVLDMIELGIENYKSLSDFKAAKI---TEGTKPMLIFQGAVFDQHPEYK 154 (307)
T ss_pred HhhhhhhhhhhhccccccCCCceEEEEecCchhhHHHHHhhhhhhhhhhhhccCC---CCCCCceEEEecchhccChHHH
Confidence 9999999999999999999999999999999999999999999999999999887 9999999999999999999999
Q ss_pred HHHHHHHhhCCCCCCCccccCCCcEEEEEEEecCCeEEEEEEEEEeecCCCCCCCeeEEeeccceeEEEEeeeCCCHHHH
Q 024240 161 HLKEVLVDLLRGEVIENLNLAGLDHAYVCTAVSSNRVFFTHCALRLKKSGTIVPRMELVEVGPCMDFVVRRHRLPNESLR 240 (270)
Q Consensus 161 ~lK~ll~d~F~~~~~~~i~l~~id~vi~ft~~d~~~I~~R~Y~I~~~~sg~~~p~v~L~EiGPr~dl~~~r~~~~~~~~~ 240 (270)
+|+|||+|||+|+.++.++|+|++|||+||+.|+..|+||+|.+.+++||+.+||+||+||||++||+++|++.||+|+|
T Consensus 155 rlknL~vDfFrge~vd~v~l~Gl~~v~vfta~~~~~v~~r~Y~lklkKs~~~~PRiELeE~GPsldf~irR~~~asddL~ 234 (307)
T KOG3031|consen 155 RLKNLFVDFFRGEKVDKVRLAGLEYVIVFTATEETNVLFRVYRLKLKKSGTRTPRIELEEMGPSLDFEIRRTKLASDDLY 234 (307)
T ss_pred HHHHHHHHHHcCCcccceeeccccEEEEEEeecCceeeeeeeeeeeeeccCCCCceehhhcCCceeEEEEeccCCCHHHH
Confidence 99999999999999999999999999999999988899999999999999999999999999999999999999999999
Q ss_pred HHHHhhhhhh--cCCCCcccccc----eeeeecc
Q 024240 241 KEAMKTAKDQ--SKKKVDSLDII----LLFHYMS 268 (270)
Q Consensus 241 k~A~k~pk~~--kk~KNi~~d~~----g~~h~~~ 268 (270)
|+|||+||++ |++|||++|.| ||||++.
T Consensus 235 k~A~k~PK~l~~K~kKNv~~D~~g~k~GriHm~k 268 (307)
T KOG3031|consen 235 KEALKKPKQLEKKKKKNVSKDAFGNKLGRIHMGK 268 (307)
T ss_pred HHHhcCchhcccccccccchhhhcCcceeEecCh
Confidence 9999999998 89999999999 9999974
No 2
>COG5106 RPF2 Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=1.4e-64 Score=446.48 Aligned_cols=262 Identities=37% Similarity=0.560 Sum_probs=251.4
Q ss_pred CCCccCCCChhhhhHHHHhCCccccCCcEEEEEeCCCCCHhHHHHHHHHHhcccccceeccccCCCcCcCCCCCcchhhh
Q 024240 1 MLKVKTPKNPRVKRALEKRAPKLVETGKKTLILQGTKTSNTLNDVLTELYLLKKGSAIRYTRKNENIRPFESGGETSLEF 80 (270)
Q Consensus 1 ~~~~~k~kt~~~kr~l~~repk~~en~K~~L~l~g~~~s~~~~~ll~DL~~L~kP~a~~~~Kkn~~i~pFe~~~~~~le~ 80 (270)
|.|.+|||++|.||+|.+|||+++|+.|.++|+.|..+++..-++|-|+.+|++|..+.+.++|. |+||||+ ++||+
T Consensus 1 M~r~vkpkNaR~kRAl~kRepklve~~k~AiF~pg~s~~k~lldvi~d~~alkkp~~i~f~rkn~-ihpfEd~--SplEf 77 (316)
T COG5106 1 MFRAVKPKNARVKRALHKREPKLVEAHKDAIFYPGMSERKTLLDVICDTEALKKPKEIGFIRKNT-IHPFEDT--SPLEF 77 (316)
T ss_pred CccccCCcchHHHHHHHhcCchhhhhhhheEeccCcccchhhhhhhcchhhhccchhhccccCCc-ccccccC--CHHHH
Confidence 78999999999999999999999999999999999999999999999999999999999999997 9999999 99999
Q ss_pred hhccCCCcEEEEeeeCCCCCCceEEEEccCCceeeeEEEEeeceeecccccCCCCCCCCCCCccEEEEeCCCCCChHHHH
Q 024240 81 FSLKTDCSIFIYGSTSKKRPDNLVIGRTYDHHIYDLVEVGVENFKPLNSFIYDKKLAPRVGSKPFICFVGEGFESVEELK 160 (270)
Q Consensus 81 la~k~dcslf~f~s~~KKrp~~L~igR~~~g~~LDm~ef~V~n~~~~~~~~~~~~~~~~~gskPllvF~g~~F~~~~~l~ 160 (270)
+++++||++.+.++|+|||+|||+|||+|+..++|||||+|.+|++++||..+.. ..|.+|+++|||..|+..|.|+
T Consensus 78 fseknd~~l~vl~ts~kKr~hnlt~~R~Fny~~~DMiEl~i~~yksvsdF~~~~~---~~g~Kpmv~fQg~~fd~hp~yr 154 (316)
T COG5106 78 FSEKNDKKLSVLFTSVKKRRHNLTIGRAFNYELIDMIELKINRYKSVSDFECAGP---ELGMKPMVVFQGINFDAHPTYR 154 (316)
T ss_pred HHHhhhhhhhhhhhhccccccceeEEeecchHHHHHHHHhhhhhhehhhhhccCC---ccCCceEEEEeccccccchHHH
Confidence 9999999999999999999999999999999999999999999999999987654 8999999999999999999999
Q ss_pred HHHHHHHhhCCCCCCCccccCCCcEEEEEEEec---C----CeEEEEEEEEEeecCCCCCCCeeEEeeccceeEEEEeee
Q 024240 161 HLKEVLVDLLRGEVIENLNLAGLDHAYVCTAVS---S----NRVFFTHCALRLKKSGTIVPRMELVEVGPCMDFVVRRHR 233 (270)
Q Consensus 161 ~lK~ll~d~F~~~~~~~i~l~~id~vi~ft~~d---~----~~I~~R~Y~I~~~~sg~~~p~v~L~EiGPr~dl~~~r~~ 233 (270)
+|+|||.|||+|...+....+|+.|||+-|+.. + +.+.||+|...+-++.+++|++||+|||||+||+++|++
T Consensus 155 ~iksLflDFFrges~~~ldsagls~Vi~~t~~g~~~d~~plp~v~fRVyk~k~~kt~~~lpr~elee~GPrldf~i~R~~ 234 (316)
T COG5106 155 RIKSLFLDFFRGESSKVLDSAGLSWVIARTEEGYVLDTYPLPLVVFRVYKTKLLKTKTNLPRLELEECGPRLDFEIVRSY 234 (316)
T ss_pred HHHHHHHHHHcCCchhhhhhcceeEEEEEecchhhhccccccceeeeeeecccccccCCCCceehhhcccceeeEEEeec
Confidence 999999999999999999999999999999862 2 348999999988899999999999999999999999999
Q ss_pred CCCHHHHHHHHhhhhhh--cCCCCcccccc----eeeeecc
Q 024240 234 LPNESLRKEAMKTAKDQ--SKKKVDSLDII----LLFHYMS 268 (270)
Q Consensus 234 ~~~~~~~k~A~k~pk~~--kk~KNi~~d~~----g~~h~~~ 268 (270)
.||+|+|++|+++|++. |.+||+..|.| ||+|+|-
T Consensus 235 ~~s~d~~~ealkkPk~~e~KpkKNv~~di~gdkiGriHidk 275 (316)
T COG5106 235 HCSDDLYKEALKKPKTQEPKPKKNVAKDIFGDKIGRIHIDK 275 (316)
T ss_pred CCChHHHHHHhcCccccCCCcccchhhhhhhccccceeech
Confidence 99999999999999988 99999999999 9999974
No 3
>KOG2971 consensus RNA-binding protein required for biogenesis of the ribosomal 60S subunit [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.9e-47 Score=339.25 Aligned_cols=203 Identities=16% Similarity=0.243 Sum_probs=184.3
Q ss_pred cccCCcEEEEEeCCCCCHhHHHHHHHHHhcccccceeccc----cCCCcCcCCCCCcchhhhhhccCCCcEEEEeeeCCC
Q 024240 23 LVETGKKTLILQGTKTSNTLNDVLTELYLLKKGSAIRYTR----KNENIRPFESGGETSLEFFSLKTDCSIFIYGSTSKK 98 (270)
Q Consensus 23 ~~en~K~~L~l~g~~~s~~~~~ll~DL~~L~kP~a~~~~K----kn~~i~pFe~~~~~~le~la~k~dcslf~f~s~~KK 98 (270)
.+.|++++|++++|++|.+.||||+||..|+ ||++..+| ++. ..|+++|+.++|+.++|++++|+
T Consensus 45 ~w~NK~rvlv~ssRgis~R~RhLm~di~~Ll-ph~k~dsk~d~~k~l----------~~lnel~elkncn~~lfFesrkr 113 (299)
T KOG2971|consen 45 KWKNKERVLVLSSRGISFRTRHLMKDISSLL-PHSKKDSKLDRKKKL----------GVLNELAELKNCNSCLFFESRKR 113 (299)
T ss_pred ccccceeEEEEecCCchHHHHHHHHHHHHhc-ccccccchhhhcchH----------HHHHHHHHHhcCCeEEEEEeecc
Confidence 4679999999999999999999999999998 99876543 332 89999999999999999999999
Q ss_pred CCCceEEEEccCCceeeeEEEEeeceeecccccCCCCCCCCCCCccEEEEeCCCCCChHHHHHHHHHHHhhCCCCCCCcc
Q 024240 99 RPDNLVIGRTYDHHIYDLVEVGVENFKPLNSFIYDKKLAPRVGSKPFICFVGEGFESVEELKHLKEVLVDLLRGEVIENL 178 (270)
Q Consensus 99 rp~~L~igR~~~g~~LDm~ef~V~n~~~~~~~~~~~~~~~~~gskPllvF~g~~F~~~~~l~~lK~ll~d~F~~~~~~~i 178 (270)
+..||||++.++||+ ++|.|+|.|||+|++++++ +++||||+|+|+.. ||+.|||+++|+||+++|+.|..|+.
T Consensus 114 ~DlYlWm~~~p~GpS---vkFlv~n~hTM~ElkmtgN--~lkgsrplLsFd~~-Fd~~pHlkl~Kell~q~fgiP~~hrk 187 (299)
T KOG2971|consen 114 KDLYLWMSNSPNGPS---VKFLVHNVHTMAELKMTGN--CLKGSRPLLSFDKA-FDELPHLKLLKELLEQIFGIPKHHRK 187 (299)
T ss_pred CceeEEEecCCCCCc---eEEehhhhhhHHHhCCccc--cccCCcceeecccc-cccchHHHHHHHHHHHHcCCCCCCcc
Confidence 999999999999997 7999999999999999842 49999999999996 99999999999999999999999999
Q ss_pred ccCCCcEEEEEEEecCCeEEEEEEEEEeecCCCCCCCeeEEeeccceeEEEEeeeC--------------CCHHHHHHHH
Q 024240 179 NLAGLDHAYVCTAVSSNRVFFTHCALRLKKSGTIVPRMELVEVGPCMDFVVRRHRL--------------PNESLRKEAM 244 (270)
Q Consensus 179 ~l~~id~vi~ft~~d~~~I~~R~Y~I~~~~sg~~~p~v~L~EiGPr~dl~~~r~~~--------------~~~~~~k~A~ 244 (270)
+.|++|||++||++|+. ||||+|||... ....|+||||||+|+++++.. .|++..+++.
T Consensus 188 Skpf~Dhvf~Fsi~D~~-IWfRnyqI~~~------ed~~L~EiGPRfvl~~ikif~gsFgG~~lYenp~yvspn~~r~~~ 260 (299)
T KOG2971|consen 188 SKPFVDHVFTFSILDGK-IWFRNYQISEE------EDKTLIEIGPRFVLNVIKIFEGSFGGPTLYENPKYVSPNMIRAVI 260 (299)
T ss_pred cCCccceEEEEEEecCe-EEEEEeEeccc------cCcceeeeccHHHHhHHHHHhccCCCceeecCccccCHHHHHHHH
Confidence 99999999999999997 99999999632 237899999999999999874 5888888888
Q ss_pred hhhhh
Q 024240 245 KTAKD 249 (270)
Q Consensus 245 k~pk~ 249 (270)
|+..+
T Consensus 261 k~~~a 265 (299)
T KOG2971|consen 261 KKQAA 265 (299)
T ss_pred HHHHH
Confidence 76654
No 4
>COG5154 BRX1 RNA-binding protein required for 60S ribosomal subunit biogenesis [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.4e-44 Score=311.07 Aligned_cols=205 Identities=17% Similarity=0.249 Sum_probs=185.0
Q ss_pred CCcEEEEEeCCCCCHhHHHHHHHHHhcccccceecc----ccCCCcCcCCCCCcchhhhhhccCCCcEEEEeeeCCCCCC
Q 024240 26 TGKKTLILQGTKTSNTLNDVLTELYLLKKGSAIRYT----RKNENIRPFESGGETSLEFFSLKTDCSIFIYGSTSKKRPD 101 (270)
Q Consensus 26 n~K~~L~l~g~~~s~~~~~ll~DL~~L~kP~a~~~~----Kkn~~i~pFe~~~~~~le~la~k~dcslf~f~s~~KKrp~ 101 (270)
+++++|++++|++|.+.||||+||..|+ ||+++.. |+|- .+|+++|+.++|+.++|++++|....
T Consensus 29 ~kq~~lilSsRGvsyr~RHL~~Dls~l~-phskke~KlD~kk~l----------~qLnelaelynCnn~lFFesrkr~Dl 97 (283)
T COG5154 29 PKQTSLILSSRGVSYRIRHLMKDLSRLV-PHSKKEQKLDMKKNL----------GQLNELAELYNCNNMLFFESRKRSDL 97 (283)
T ss_pred ccceEEEEecCCchHHHHHHHHHHHHhC-cccccccccchhhhH----------HHHHHHHHHhcCCceEEEeecccccc
Confidence 6899999999999999999999999998 9987543 4553 89999999999999999999999999
Q ss_pred ceEEEEccCCceeeeEEEEeeceeecccccCCCCCCCCCCCccEEEEeCCCCCChHHHHHHHHHHHhhCCCCCCCccccC
Q 024240 102 NLVIGRTYDHHIYDLVEVGVENFKPLNSFIYDKKLAPRVGSKPFICFVGEGFESVEELKHLKEVLVDLLRGEVIENLNLA 181 (270)
Q Consensus 102 ~L~igR~~~g~~LDm~ef~V~n~~~~~~~~~~~~~~~~~gskPllvF~g~~F~~~~~l~~lK~ll~d~F~~~~~~~i~l~ 181 (270)
|||++|.+|||+ ++|.++|.++|+++.+++ ++++||+|+|.|+.+ ||+.|||+.+|++|.+.|+.|.....+.|
T Consensus 98 yl~~ar~pnGpt---vkF~~~NlhTMdelNftg--N~lKgsrpvLsFdk~-Fe~~pHlk~~Kell~h~F~ip~~arrSkp 171 (283)
T COG5154 98 YLMGARIPNGPT---VKFRMHNLHTMDELNFTG--NSLKGSRPVLSFDKE-FEDIPHLKYAKELLEHIFGIPKGARRSKP 171 (283)
T ss_pred eeeeccCCCCCe---EEEEEeccchHhhcCCcc--ccccCCcceEeeccc-cccchHHHHHHHHHHHhccCCCccccccc
Confidence 999999999998 799999999999999984 259999999999997 99999999999999999999999999999
Q ss_pred CCcEEEEEEEecCCeEEEEEEEEEeecCCCCCCCeeEEeeccceeEEEEeee--------------CCCHHHHHHHHhhh
Q 024240 182 GLDHAYVCTAVSSNRVFFTHCALRLKKSGTIVPRMELVEVGPCMDFVVRRHR--------------LPNESLRKEAMKTA 247 (270)
Q Consensus 182 ~id~vi~ft~~d~~~I~~R~Y~I~~~~sg~~~p~v~L~EiGPr~dl~~~r~~--------------~~~~~~~k~A~k~p 247 (270)
++|||++|+++|++ ||+|+|.|.- ...++...|.|+||||||+|+++.+- +.|+.+.++|++++
T Consensus 172 fiD~v~~f~i~Dgk-IWvR~YeI~r-e~ed~~~dv~L~EIGPRfVmtvi~iLEgsFgGp~iYkn~~~vs~~~vra~ir~q 249 (283)
T COG5154 172 FIDKVLCFFILDGK-IWVRCYEIGR-ENEDKSKDVKLEEIGPRFVMTVIKILEGSFGGPAIYKNETFVSSTMVRAAIRNQ 249 (283)
T ss_pred chhheEEEEEecCe-EEEEEEeecc-ccccccccceeeeeccHHHHHHHHHHHhccCCceeeecccccchHHHHHHHHHH
Confidence 99999999999998 9999999962 34455566999999999999998764 36889999999865
Q ss_pred hh
Q 024240 248 KD 249 (270)
Q Consensus 248 k~ 249 (270)
.+
T Consensus 250 aa 251 (283)
T COG5154 250 AA 251 (283)
T ss_pred HH
Confidence 44
No 5
>PF04427 Brix: Brix domain; InterPro: IPR007109 The Brix domain is found in a number of eukaryotic proteins including some from Saccharomyces cerevisiae and Homo sapiens, Arabidopsis thaliana Peter Pan-like protein and several hypothetical proteins. There are six (one archaean and five eukaryotic) protein families which have a similar domain architecture with a central globular Brix domain. They have an optional N- and obligatory C-terminal segments, which both have charged low-complexity regions []. Proteins from the Imp4/Brix superfamily appear to be involved in ribosomal RNA processing, which essential for the functioning of all cells. The N- and C-terminal halves of a member of the superfamily, Mil, show significant structural similarity to one another. This suggests an origin by means of an ancestral duplication. Both halves have the same fold as the anticodon-binding domain of class IIa aminoacyl-tRNA synthetases, with greater conservation seen in the N-terminal half. Structural evidence suggests that the Imp4/Brix superfamily proteins could bind single-stranded segments of RNA along a concave surface formed by the N-terminal half of their beta-sheet and a central alpha-helix [].; PDB: 2CXH_A.
Probab=100.00 E-value=2.2e-42 Score=299.12 Aligned_cols=185 Identities=33% Similarity=0.534 Sum_probs=72.1
Q ss_pred EEeCCCCCHhHHHHHHHHHhcccccceeccccCC-CcCcCCCCCcchhhhhhccCCCcEEEEeeeCCCCCCceEEEEccC
Q 024240 32 ILQGTKTSNTLNDVLTELYLLKKGSAIRYTRKNE-NIRPFESGGETSLEFFSLKTDCSIFIYGSTSKKRPDNLVIGRTYD 110 (270)
Q Consensus 32 ~l~g~~~s~~~~~ll~DL~~L~kP~a~~~~Kkn~-~i~pFe~~~~~~le~la~k~dcslf~f~s~~KKrp~~L~igR~~~ 110 (270)
|++|+++|+.++++++||+.|++|+|++++|++. .+. +.+|+.+.+++|++++|++++| +|++|||||+|+
T Consensus 1 i~ts~~~s~~~~~l~~DL~~l~~p~s~~~~r~~~~~l~-------~~~~~~~~~~~~~l~~~~~~~k-~p~~L~i~r~~~ 72 (191)
T PF04427_consen 1 ITTSRKPSKRLRQLMKDLRSLFPPNSKKLNRKKKNSLK-------DLLEFAKQKNCTSLFVFGEHKK-NPNNLWIGRLPN 72 (191)
T ss_dssp -EESSS--HHHHHHHHHHHTTS-TTEEE---TT---HH-------HHHHHHHHTTEEEEEEEEEETT-EEEEEEEEE-SS
T ss_pred cCCCCCCCHHHHHHHHHHHHHcCCCeEEEeCCCCCchH-------HHHHHHHHCCCCEEEEEEEeCC-CcceEEEEecCC
Confidence 6789999999999999999999899999987764 232 4566666666668888988876 999999999999
Q ss_pred CceeeeEEEEeeceeecccccCCCCCCCCCCCccEEEEeCCCCCChHHHHHHHHHHHhhCCCCCCCccccCCCcEEEEEE
Q 024240 111 HHIYDLVEVGVENFKPLNSFIYDKKLAPRVGSKPFICFVGEGFESVEELKHLKEVLVDLLRGEVIENLNLAGLDHAYVCT 190 (270)
Q Consensus 111 g~~LDm~ef~V~n~~~~~~~~~~~~~~~~~gskPllvF~g~~F~~~~~l~~lK~ll~d~F~~~~~~~i~l~~id~vi~ft 190 (270)
||++ +|+|++|++++|++.... ...|++|+|+|+|..|+.+++++++++||+|+|+++.++.++++++|||++|+
T Consensus 73 gptl---~f~I~~~~~~~~~~~~~~--~~~~~~P~lif~g~~~~~~~~~~~ik~~l~~lF~~~~~~~~~~~~~~rvi~f~ 147 (191)
T PF04427_consen 73 GPTL---EFSIENYKLMKDIKSSSK--RPKGSRPLLIFNGFFFELDPELKLIKELLQDLFPGPNVDSIPLPGIDRVISFS 147 (191)
T ss_dssp --EE---EEEEEEEE-HHHHT---------S---EEEEE-----------------------------------------
T ss_pred CCCE---EEEEEeEEEhhHhccccc--CCCCCCeEEEEEecccccccccccccccccccccccccccccccccccccccc
Confidence 9996 999999999999986521 14589999999998777779999999999999999999999999999999999
Q ss_pred EecCCeEEEEEEEEEeecCCCCC-----CCeeEEeeccceeEEEEee
Q 024240 191 AVSSNRVFFTHCALRLKKSGTIV-----PRMELVEVGPCMDFVVRRH 232 (270)
Q Consensus 191 ~~d~~~I~~R~Y~I~~~~sg~~~-----p~v~L~EiGPr~dl~~~r~ 232 (270)
+.++..|||||| | .+++++. |.++|+||||||+|+++|+
T Consensus 148 ~~~d~~I~fR~Y-i--~~~~~~~~~~~~~~v~L~EiGPr~~l~l~kI 191 (191)
T PF04427_consen 148 NQRDFVIFFRHY-I--FKSGSKNPKKLLPRVELVEIGPRFTLKLRKI 191 (191)
T ss_dssp -----------------------------------------------
T ss_pred cccccccccccc-c--cccccccccccccccccccccccccccccCC
Confidence 987756999999 7 4445554 4489999999999999985
No 6
>smart00879 Brix Brix domain. The Brix domain is found in a number of eukaryotic proteins including SSF proteins from yeast and humans, Arabidopsis thaliana Peter Pan-like protein and several hypothetical proteins.
Probab=100.00 E-value=1.4e-36 Score=259.25 Aligned_cols=179 Identities=30% Similarity=0.372 Sum_probs=149.9
Q ss_pred EEEeCCCCCHhHHHHHHHHHhcccccceeccccCCCcCcCCCCCcchhhhhhcc-CCCcEEEEeeeCCCCCCceEEEEcc
Q 024240 31 LILQGTKTSNTLNDVLTELYLLKKGSAIRYTRKNENIRPFESGGETSLEFFSLK-TDCSIFIYGSTSKKRPDNLVIGRTY 109 (270)
Q Consensus 31 L~l~g~~~s~~~~~ll~DL~~L~kP~a~~~~Kkn~~i~pFe~~~~~~le~la~k-~dcslf~f~s~~KKrp~~L~igR~~ 109 (270)
||++|+++|+.++++++||+.++.|+++...++++ + . +.+|+++.+ .+|+++++++++|++|++||+||+|
T Consensus 1 lit~sr~~s~~~r~~~~dL~~~~~~~~~~~r~~~~-~-----~--~~~e~~~~~~~~~~i~v~e~~~k~~p~~L~i~~~~ 72 (180)
T smart00879 1 LITTSRKPSKRTRQLAKDLRRLFPPSTKINRGKNK-L-----N--ELLEFASEKGNTDLLVVFESSSKGRPLNLTIYRLP 72 (180)
T ss_pred CEEcCCCCCHHHHHHHHHHHHHCCCcEeecccCcc-H-----H--HHHHHHHHcCCccEEEEecccCCCCCceEEEEECC
Confidence 58899999999999999999999444443344443 3 1 577777777 6668888888889999999999999
Q ss_pred CCceeeeEEEEeeceeecccccCCCCCCCCCCCccEEEEeCCCCCChHHHHHHHHHHHhhCCCCCCCccccCCCcEEEEE
Q 024240 110 DHHIYDLVEVGVENFKPLNSFIYDKKLAPRVGSKPFICFVGEGFESVEELKHLKEVLVDLLRGEVIENLNLAGLDHAYVC 189 (270)
Q Consensus 110 ~g~~LDm~ef~V~n~~~~~~~~~~~~~~~~~gskPllvF~g~~F~~~~~l~~lK~ll~d~F~~~~~~~i~l~~id~vi~f 189 (270)
+||++||.+++|..++.+..+...++ ..+++|+|+|+|..|+.. ++++++|+++|+++.++.++++++|||++|
T Consensus 73 ~gp~l~f~i~~v~~~~~~~~~~~~~~---~~~~~P~li~~~~~~~~~---~~~k~~l~~~F~~~~~~~~~~~~~~rvi~f 146 (180)
T smart00879 73 NGPTLDFKILNVSLRKELKGFKTGNC---LTGSRPLLIFNNFFTELG---KLIKELFQDLFPGPPEHKKSLPGLRRVVTF 146 (180)
T ss_pred CCCcEEEEEECcccHhhhhhhhcCCC---cCCCccEEEECCCCCchH---HHHHHHHHHHCCCCCccccccCCCCEEEEE
Confidence 99999888877777777666643444 889999999999644433 789999999999999999999999999999
Q ss_pred EEecCCeEEEEEEEEEeecCCCCCCCeeEEeeccceeE
Q 024240 190 TAVSSNRVFFTHCALRLKKSGTIVPRMELVEVGPCMDF 227 (270)
Q Consensus 190 t~~d~~~I~~R~Y~I~~~~sg~~~p~v~L~EiGPr~dl 227 (270)
++.++. ||||||+|.. +.+.++++|.||||||+|
T Consensus 147 ~~~~~~-I~~R~y~i~~---~~~~~~v~l~eiGPr~~l 180 (180)
T smart00879 147 SNQDDY-IFFRHYRIKF---GKKKPRVELQEIGPRFTL 180 (180)
T ss_pred EecCCE-EEEEEEEEEc---cCCCCceEEEEecCCccC
Confidence 999885 9999999975 567888999999999986
No 7
>KOG2963 consensus RNA-binding protein required for 60S ribosomal subunit biogenesis [Translation, ribosomal structure and biogenesis]
Probab=99.95 E-value=3.2e-27 Score=218.21 Aligned_cols=189 Identities=13% Similarity=0.187 Sum_probs=152.1
Q ss_pred CccCCCChhhhhHHHHhCCccccCCcEEEEEeCCCCCHhHHHHHHHHHhcccccc-eec--cccCCCcCcCCCCCcchhh
Q 024240 3 KVKTPKNPRVKRALEKRAPKLVETGKKTLILQGTKTSNTLNDVLTELYLLKKGSA-IRY--TRKNENIRPFESGGETSLE 79 (270)
Q Consensus 3 ~~~k~kt~~~kr~l~~repk~~en~K~~L~l~g~~~s~~~~~ll~DL~~L~kP~a-~~~--~Kkn~~i~pFe~~~~~~le 79 (270)
+.+++|+++++- ....+....++ ..++++..+-+...+++|-.||+.||.||+ .++ .|+|. |++|..+
T Consensus 3 k~r~kK~~~aq~-~~~~e~~i~~~-ph~~v~~rgla~~~~~~L~~DlR~iMeP~TA~~LkerK~N~-iKDfv~~------ 73 (405)
T KOG2963|consen 3 KRRHKKRTHAQF-TPEQEIEIAKS-PHIRVGHRGLAGRSLKQLTLDLRRIMEPHTASNLKERKRNK-LKDFVVM------ 73 (405)
T ss_pred cccchhhhhhhc-CccchhhcccC-ceEEEEecccccccHHHHHHHHHHhhCcchhhHHHHHhhhh-hhhHHhh------
Confidence 344555444332 22333333333 344555555667899999999999999995 555 58897 9999998
Q ss_pred hhhccCCCcEEEEeeeCCCCCCceEEEEccCCceeeeEEEEeeceeecccccCC----CCCCCCCCCccEEEEeCCCCCC
Q 024240 80 FFSLKTDCSIFIYGSTSKKRPDNLVIGRTYDHHIYDLVEVGVENFKPLNSFIYD----KKLAPRVGSKPFICFVGEGFES 155 (270)
Q Consensus 80 ~la~k~dcslf~f~s~~KKrp~~L~igR~~~g~~LDm~ef~V~n~~~~~~~~~~----~~~~~~~gskPllvF~g~~F~~ 155 (270)
|+..|+++|++.|.+.. ..+|.++|+|.||+| .|.|..|....|.... .+.+-...+.||||+|| |++
T Consensus 74 --~gplGVTH~l~lskt~~-nlslki~R~PqGPTL---tFkV~qYsLardV~~~qkrp~~~~~~Fk~pPLlVmNg--Fg~ 145 (405)
T KOG2963|consen 74 --SGPLGVTHLLMLSKTET-NLSLKIARTPQGPTL---TFKVHQYSLARDVVSLQKRPKSPNDLFKSPPLLVLNG--FGT 145 (405)
T ss_pred --cccccceEEEEEecccC-ceeEEEEecCCCCce---EEEeeehhhHHHHHHHHhCCCCchhhccCCCEEEEcc--CCC
Confidence 99999998888887655 668999999999995 9999999998888542 34444788999999999 998
Q ss_pred h--HHHHHHHHHHHhhCCCCCCCccccCCCcEEEEEEEe-cCCeEEEEEEEEEeec
Q 024240 156 V--EELKHLKEVLVDLLRGEVIENLNLAGLDHAYVCTAV-SSNRVFFTHCALRLKK 208 (270)
Q Consensus 156 ~--~~l~~lK~ll~d~F~~~~~~~i~l~~id~vi~ft~~-d~~~I~~R~Y~I~~~~ 208 (270)
+ +|++++-.||++||++.+++.++|..|+||+.|+|. |++.|.||||.|...+
T Consensus 146 ~~~~HlkL~~t~FQNmFPsInv~tvnlntikRcllinyn~dt~eIdmRHysI~vvp 201 (405)
T KOG2963|consen 146 SGRKHLKLMTTMFQNMFPSINVATVNLNTIKRCLLINYNRDTGEIDMRHYSIRVVP 201 (405)
T ss_pred CcchhHHHHHHHHHHcCCCcCcceeeccceeEEEEEecCCCCCeeeeeeeEEEEEe
Confidence 6 899999999999999999999999999999999995 6677999999998764
No 8
>KOG2781 consensus U3 small nucleolar ribonucleoprotein (snoRNP) component [RNA processing and modification]
Probab=99.70 E-value=7.9e-16 Score=137.28 Aligned_cols=181 Identities=19% Similarity=0.162 Sum_probs=152.1
Q ss_pred cEEEEEeCCCCCHhHHHHHHHHHhcccccceeccccCCCcCcCCCCCcchhhhhhccCCC-cEEEEeeeCCCCCCceEEE
Q 024240 28 KKTLILQGTKTSNTLNDVLTELYLLKKGSAIRYTRKNENIRPFESGGETSLEFFSLKTDC-SIFIYGSTSKKRPDNLVIG 106 (270)
Q Consensus 28 K~~L~l~g~~~s~~~~~ll~DL~~L~kP~a~~~~Kkn~~i~pFe~~~~~~le~la~k~dc-slf~f~s~~KKrp~~L~ig 106 (270)
-++|+--|+.-|..+.+.+++|.-+. |+|.++++-|.. + .+|-+-|..+|. .++++.+|+ =.|..|+++
T Consensus 83 PKimvTTSR~PSsrL~~FaKelkLvf-PNaqr~nRG~~~------~--~~lv~a~ra~~~Td~iivHEhR-G~PdgL~vs 152 (290)
T KOG2781|consen 83 PKIMVTTSRDPSSRLKMFAKELKLVF-PNAQRLNRGNYV------V--GELVDAARANGVTDLIIVHEHR-GIPDGLVVS 152 (290)
T ss_pred CcEEEEeCCCchHHHHHHHHhheEec-cChhhhccccee------H--HHHHHHHHHCCCceEEEEeccC-CCCCceEEE
Confidence 35688889999999999999999886 999999988762 2 788899999999 677888874 559999999
Q ss_pred EccCCceeeeEEEEeeceeecccccCCCCCCCCCCCccEEEEeCCCCCChHHHHHHHHHHHhhCCCCCCCccccCCCcEE
Q 024240 107 RTYDHHIYDLVEVGVENFKPLNSFIYDKKLAPRVGSKPFICFVGEGFESVEELKHLKEVLVDLLRGEVIENLNLAGLDHA 186 (270)
Q Consensus 107 R~~~g~~LDm~ef~V~n~~~~~~~~~~~~~~~~~gskPllvF~g~~F~~~~~l~~lK~ll~d~F~~~~~~~i~l~~id~v 186 (270)
-+|=||+ .-|.+.|+..=.|+...+. ..-.+|-|+|++ |.+. -=++++++|-.+|++|..+ -.||
T Consensus 153 hlPfGPT---a~Fsl~nvVmRhdip~~G~---msE~~phlIfdN--f~t~-lG~Rv~~iLkhLFP~pk~d------s~Rv 217 (290)
T KOG2781|consen 153 HLPFGPT---AFFSLHNVVMRHDIPDIGT---MSEQKPHLIFDN--FTTK-LGKRVKTILKHLFPVPKDD------SKRV 217 (290)
T ss_pred ecCCCCc---eEeeeeeeeeccccccccc---ccccCceEEecc--ccch-HHHHHHHHHHHhCCCCcCC------cccE
Confidence 9999998 5999999999999976554 566699999999 9764 3458999999999987654 5899
Q ss_pred EEEEEecCCeEEEEEEEEEeecCCCCCCCeeEEeeccceeEEEEeeeCCCHH
Q 024240 187 YVCTAVSSNRVFFTHCALRLKKSGTIVPRMELVEVGPCMDFVVRRHRLPNES 238 (270)
Q Consensus 187 i~ft~~d~~~I~~R~Y~I~~~~sg~~~p~v~L~EiGPr~dl~~~r~~~~~~~ 238 (270)
|+|...+|- |.||||.+.-. + -..++|.|+||||+|.+=-+.+..-|
T Consensus 218 vtf~N~~Dy-IsFRhhvy~~~--~--~k~vel~evGPRfelklyeIrlGTlE 264 (290)
T KOG2781|consen 218 VTFANRNDY-ISFRHHVYKKT--D--GKEVELTEVGPRFELKLYEIRLGTLE 264 (290)
T ss_pred EEEecCCce-EEEEEEEEecC--C--CceEEEeeccccceeeeeeeeeccee
Confidence 999999997 99999988521 1 13589999999999999988876655
No 9
>KOG2780 consensus Ribosome biogenesis protein RPF1, contains IMP4 domain [RNA processing and modification]
Probab=99.51 E-value=4.2e-13 Score=121.21 Aligned_cols=180 Identities=16% Similarity=0.193 Sum_probs=141.7
Q ss_pred cEEEEEeCCCCCHhHHHHHHHHHhcccccceeccccCCCcCcCCCCCcchhhhhhccCCCcEE-EEeeeCCCCCCceEEE
Q 024240 28 KKTLILQGTKTSNTLNDVLTELYLLKKGSAIRYTRKNENIRPFESGGETSLEFFSLKTDCSIF-IYGSTSKKRPDNLVIG 106 (270)
Q Consensus 28 K~~L~l~g~~~s~~~~~ll~DL~~L~kP~a~~~~Kkn~~i~pFe~~~~~~le~la~k~dcslf-~f~s~~KKrp~~L~ig 106 (270)
-++||--....+.....++..|..+. ||+.-..+.|.. + .++-+.|.+.+.+-+ ++.+.+ |.|+.|.|+
T Consensus 97 pKvlITt~~~~~~~t~~~~~eL~~ii-PNs~~~~R~~~~------v--k~i~~~a~~~eftdlvvV~edR-kk~n~L~ii 166 (302)
T KOG2780|consen 97 PKVLITTSKNPKRTTYKFASELLDII-PNSTVKKRDNYT------V--KSIVEIAIKREFTDLVVVNEDR-KKPNGLKII 166 (302)
T ss_pred ccEEEEcCCCCcccHHHHHHHHHHhC-CCceEEecCCch------H--HHHHHHHHHhcCCceEEEecCc-CCccceEEE
Confidence 46677777788889999999999997 997544343532 2 788888999999544 555554 559999999
Q ss_pred EccCCceeeeEEEEeeceeecccccCCCCCCCCCCCccEEEEeCCCCCChHHHHHHHHHHHhhCCCCCCCccccCCCcEE
Q 024240 107 RTYDHHIYDLVEVGVENFKPLNSFIYDKKLAPRVGSKPFICFVGEGFESVEELKHLKEVLVDLLRGEVIENLNLAGLDHA 186 (270)
Q Consensus 107 R~~~g~~LDm~ef~V~n~~~~~~~~~~~~~~~~~gskPllvF~g~~F~~~~~l~~lK~ll~d~F~~~~~~~i~l~~id~v 186 (270)
-.|+||+ +.|.+.+|..-+|++.-+. .-+..|=|++++ |.+.-.+ .+..||+.+|+-++. .. -++|
T Consensus 167 hlP~GPT---~~Fkls~~~~~kdi~k~g~---~t~h~PElIlNN--FtTrlG~-~v~r~f~sLfp~~p~----f~-gRrv 232 (302)
T KOG2780|consen 167 HLPNGPT---AYFKLSNVVLTKDIKKHGR---PTSHIPELILNN--FTTRLGM-TVGRLFASLFPHDPQ----FT-GRRV 232 (302)
T ss_pred ecCCCCc---eEEEeecccchhhhhhcCC---cccccchhhhhc--ccchhhH-HHHHHHHHhCCCCcc----cc-ceeE
Confidence 9999998 6999999999999876543 456688899998 9775444 688999999987652 12 2789
Q ss_pred EEEEEecCCeEEEEEEEEEeecCCCCCCCeeEEeeccceeEEEEeeeCC
Q 024240 187 YVCTAVSSNRVFFTHCALRLKKSGTIVPRMELVEVGPCMDFVVRRHRLP 235 (270)
Q Consensus 187 i~ft~~d~~~I~~R~Y~I~~~~sg~~~p~v~L~EiGPr~dl~~~r~~~~ 235 (270)
+.|+..-| -|+||||++..+..+ -.+-|.|+||||+|.+++.|..
T Consensus 233 vtFhnQrD-~IfFRhhRY~Fkee~---~kvglqElGPrfTLrL~~lq~G 277 (302)
T KOG2780|consen 233 VTFHNQRD-YIFFRHHRYEFKEEE---IKVGLQELGPRFTLRLRRLQKG 277 (302)
T ss_pred EEEEecCc-eEEEEEEEEeecccc---cccchhhcCCceeeeehhhhhc
Confidence 99988666 499999999988755 3467999999999999998853
No 10
>PRK03972 ribosomal biogenesis protein; Validated
Probab=98.98 E-value=4.4e-08 Score=86.76 Aligned_cols=191 Identities=14% Similarity=0.071 Sum_probs=137.8
Q ss_pred EEEEeCCCCCHhHHHHHHHHHhcccccceeccccCCCcCcCCCCCcchhhhhhccCCCc-EEEEeeeCCCCCCceEEEEc
Q 024240 30 TLILQGTKTSNTLNDVLTELYLLKKGSAIRYTRKNENIRPFESGGETSLEFFSLKTDCS-IFIYGSTSKKRPDNLVIGRT 108 (270)
Q Consensus 30 ~L~l~g~~~s~~~~~ll~DL~~L~kP~a~~~~Kkn~~i~pFe~~~~~~le~la~k~dcs-lf~f~s~~KKrp~~L~igR~ 108 (270)
+||=.|+..|+.++++++||..+. |++..+++.+..+ +.|-+.|..+|.+ ++++.++ ++.|+.|++.-+
T Consensus 2 iLITTSr~PS~rtr~F~keL~~v~-Pns~~i~RGk~~l--------kel~~~A~~~g~TdLIVV~E~-rg~P~~L~i~hL 71 (208)
T PRK03972 2 MLITTSHRPTRRTRSFGHDLERVF-PNSLYLTRGKKTI--------QDLLMEAYDRGYERLLIINVW-KGNPLKMTFIKV 71 (208)
T ss_pred EEEECCCCccHHHHHHHHHHHHhC-CCCEEEecCCccH--------HHHHHHHHHCCCCeEEEEecC-CCcCCeEEEEcC
Confidence 456678899999999999999998 9999887655322 5666678788885 5555555 778999999999
Q ss_pred cCCceeeeEEEEeeceeeccccc--CCCCCCCCCCCccEEEEeCCCCCChHHHHHHHHHHHhhCCCCCCCc--cccC---
Q 024240 109 YDHHIYDLVEVGVENFKPLNSFI--YDKKLAPRVGSKPFICFVGEGFESVEELKHLKEVLVDLLRGEVIEN--LNLA--- 181 (270)
Q Consensus 109 ~~g~~LDm~ef~V~n~~~~~~~~--~~~~~~~~~gskPllvF~g~~F~~~~~l~~lK~ll~d~F~~~~~~~--i~l~--- 181 (270)
++||--....|.+.|+..-+|+. ..+. .....|++|..+ |..++.+...-..+..-++.+-+.. .++.
T Consensus 72 P~gP~GPTa~FkLsnV~l~~ei~~~~~~~---~s~~~p~iItts--~kt~~g~~~~Ak~lA~eLgi~yV~R~k~Sl~~L~ 146 (208)
T PRK03972 72 GPEDWGYLGYLYLHGIKLQREMGFRNLRP---IREDMPLVITTA--KRVGLDHMAFAQVFAELTGGKFVPRGGKSLQDIA 146 (208)
T ss_pred CCCCCCceEEEEEccEEEHHHcccCCCCC---ccccccEEEEcC--CCCCHHHHHHHHHHHHHhCCceeCcCCcCHHHHH
Confidence 86663333799999999999993 3433 567899999887 8888856444444666677765654 4533
Q ss_pred ---CCcEEEEEEEecCCeEEEEEEEEEeecCCCCCCCeeEEeeccceeEEEEeeeCCCHHHHHHHHh
Q 024240 182 ---GLDHAYVCTAVSSNRVFFTHCALRLKKSGTIVPRMELVEVGPCMDFVVRRHRLPNESLRKEAMK 245 (270)
Q Consensus 182 ---~id~vi~ft~~d~~~I~~R~Y~I~~~~sg~~~p~v~L~EiGPr~dl~~~r~~~~~~~~~k~A~k 245 (270)
+.|.|+++.----. .-+-.|+....+ -..+||.+-..+=+..-.-.=.||+|+.
T Consensus 147 ~~~~~d~vLVV~~~~~~-~~~~~~~~~~~~---------~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 203 (208)
T PRK03972 147 DKYNTDVLGVIERHPRG-MAVNFYRLDVTK---------ERPVGPLIFVKIWIMEDGRRWDYKEALG 203 (208)
T ss_pred hhhcCceEEEEecCCCc-eEEEEEEecccc---------ccccCCcEEEEEEEeccCcccchhhhhc
Confidence 44888887554444 677778775432 2567999988877776555556777763
No 11
>COG2136 IMP4 Predicted exosome subunit/U3 small nucleolar ribonucleoprotein (snoRNP) component, contains IMP4 domain [Translation, ribosomal structure and biogenesis / RNA processing and modification]
Probab=98.67 E-value=1.4e-06 Score=76.47 Aligned_cols=182 Identities=15% Similarity=0.140 Sum_probs=126.7
Q ss_pred EEEEEeCCCCCHhHHHHHHHHHhcccccceeccccCCCcCcCCCCCcchhhhhhccCCCcEEEEeeeCCCCCCceEEEEc
Q 024240 29 KTLILQGTKTSNTLNDVLTELYLLKKGSAIRYTRKNENIRPFESGGETSLEFFSLKTDCSIFIYGSTSKKRPDNLVIGRT 108 (270)
Q Consensus 29 ~~L~l~g~~~s~~~~~ll~DL~~L~kP~a~~~~Kkn~~i~pFe~~~~~~le~la~k~dcslf~f~s~~KKrp~~L~igR~ 108 (270)
++|+-.|++-|.+++++.+||.... |++....+-+.++ ..+-+-|-..+.+-+++..-.+..|..|++--.
T Consensus 3 ~~liTTSRkPS~Rtr~Fak~L~~~l-p~~~~~~rg~~~~--------~el~~~a~~~g~~~l~iv~E~rGnP~~L~f~d~ 73 (191)
T COG2136 3 KMLLTTSRKPSRRTRSFAKDLSRVL-PNAYFLRRGKKSI--------IELSEEAIARGATDLLIVGERRGNPARLTFYDL 73 (191)
T ss_pred cEEEEecCCccHHHHHHHHHHHHhC-CcceEEecCccch--------hHHHHHHHhcCCceEEEEEEecCCCcEEEEEEe
Confidence 5688899999999999999999998 9988775422212 566677888888655555545777999999877
Q ss_pred -cCCceeeeEEEEeeceeecccccCCCCCCCCCCCccEEEEeCCCCCChHHHHHHHHHHHhhCCCCCCCccccCCCcEEE
Q 024240 109 -YDHHIYDLVEVGVENFKPLNSFIYDKKLAPRVGSKPFICFVGEGFESVEELKHLKEVLVDLLRGEVIENLNLAGLDHAY 187 (270)
Q Consensus 109 -~~g~~LDm~ef~V~n~~~~~~~~~~~~~~~~~gskPllvF~g~~F~~~~~l~~lK~ll~d~F~~~~~~~i~l~~id~vi 187 (270)
+.|+. +-|.+.++++..++...+. ....+-|.+++++ |.+.-+++...++|.++-....+. -+..++-.
T Consensus 74 ~~~~~~---~~f~l~~v~l~re~~~~~~--~~~~~~~~~I~~~--~~~~~g~~~~~~~~~~~~~~~f~~---~~~~~~~~ 143 (191)
T COG2136 74 EPEGLT---FSFKLSGVKLRREIPVLGP--KSRLHGPELIFNN--FTTLLGFLKVAEAFSELLLVKFVP---NPAWEHEL 143 (191)
T ss_pred cCCCce---EEEEEecceEEEeccccCC--cccCCCCceeeec--ccccccchhhHHHHHhhccccccc---Ccccceee
Confidence 77776 5899999999999976532 1356789999998 988888889999999993221111 11233333
Q ss_pred EEEEe-cCCeEEEEEEEEEeecCCCCCCCeeEEeeccceeEEEEeeeC
Q 024240 188 VCTAV-SSNRVFFTHCALRLKKSGTIVPRMELVEVGPCMDFVVRRHRL 234 (270)
Q Consensus 188 ~ft~~-d~~~I~~R~Y~I~~~~sg~~~p~v~L~EiGPr~dl~~~r~~~ 234 (270)
+++.. .+.-+.+|.+.-.... ..+.+.|+||+|.+.+-|.+.
T Consensus 144 v~~~~~~~~f~~~~~~~~~~~~-----~~~~~~~vgp~~~~r~~~~~~ 186 (191)
T COG2136 144 VATGANKGDFKSLRRHRRVFEE-----DGIGLEEVGPRLTLRLWRMED 186 (191)
T ss_pred eeeccccceEEEEEeeeeEeee-----eeeeEEEeCceeeeehhhhhh
Confidence 33322 2222444443322211 347799999999999888754
No 12
>PRK00933 ribosomal biogenesis protein; Validated
Probab=94.43 E-value=1.7 Score=37.42 Aligned_cols=114 Identities=15% Similarity=0.146 Sum_probs=72.5
Q ss_pred EEEeCCCCCHhHHHHHHHHHhcccccceeccccCCCcCcCCCCCcchhhhhhccCCC-cEEEEeeeCCCCCCceEEEEcc
Q 024240 31 LILQGTKTSNTLNDVLTELYLLKKGSAIRYTRKNENIRPFESGGETSLEFFSLKTDC-SIFIYGSTSKKRPDNLVIGRTY 109 (270)
Q Consensus 31 L~l~g~~~s~~~~~ll~DL~~L~kP~a~~~~Kkn~~i~pFe~~~~~~le~la~k~dc-slf~f~s~~KKrp~~L~igR~~ 109 (270)
+|=.|++.|+.++++.++|.... ++....++ . .+++++++..+. .++++.++ |+.|+.|.+-+.-
T Consensus 2 IITTSrkPs~~t~~fAkeLa~~l--n~~yv~Rg-k----------~Sl~eL~~~~~~~~llVV~E~-kg~P~~L~iyd~~ 67 (165)
T PRK00933 2 IITTSRKPSQRTRSLVKDLARFL--NCKYVNRG-K----------MSLQELLEECEARYLLIIGEY-KGNPGALKFYDVE 67 (165)
T ss_pred EEECCCCCCHHHHHHHHHHHHHh--CCEEEccC-C----------ccHHHHHHHhccCcEEEEECC-CCCCceEEEEECC
Confidence 34457899999999999999886 55444443 3 577777765445 45556665 7889999999888
Q ss_pred CCceeeeEEEEeeceeecccccCCCCCCCCCCCccEEEEeCCCCCChHHHHHHHHHHHhhCCC
Q 024240 110 DHHIYDLVEVGVENFKPLNSFIYDKKLAPRVGSKPFICFVGEGFESVEELKHLKEVLVDLLRG 172 (270)
Q Consensus 110 ~g~~LDm~ef~V~n~~~~~~~~~~~~~~~~~gskPllvF~g~~F~~~~~l~~lK~ll~d~F~~ 172 (270)
+.+.+- +-++| .++ .+... ....+.+|.+.=.+. .-..+.++|..+...
T Consensus 68 ~~~~~~-~~~~v-~~~--~~~~~----~~~~~~~p~~~~~~~------~~~~~~e~f~~~l~~ 116 (165)
T PRK00933 68 GNKLLS-YRLSV-KLQ--REISG----PVFKNRRPIKSAFDV------GGDELAELFDYFLFY 116 (165)
T ss_pred CCEEEE-EEEEe-eee--cccCc----ceeecCCCcccchhh------HHHHHHHHHHHHHhh
Confidence 788763 34444 221 22222 136777786543332 134566777776643
No 13
>PF12249 AftA_C: Arabinofuranosyltransferase A C terminal; InterPro: IPR020959 The arabinofuranosyltransferase enzyme AftA is involved in cell wall arabinan biosynthesis in bacteria []. It catalyses the addition of the first key arabinofuranosyl residue from the sugar donor beta-D-arabinofuranosyl-1-monophosphoryldecaprenol to the galactan domain of the cell wall, thus priming the galactan for further elaboration by the arabinofuranosyltransferases. As this enzyme is important for cell growth and is found in some important pathogens, such as Mycobacterium tuberculosis, it represents a potential target for the devlopment of new antibacterial drugs. This entry represents the C-terminal domain of AftA.; GO: 0016757 transferase activity, transferring glycosyl groups, 0044038 cell wall macromolecule biosynthetic process, 0005886 plasma membrane, 0016021 integral to membrane
Probab=41.89 E-value=25 Score=30.73 Aligned_cols=32 Identities=25% Similarity=0.379 Sum_probs=23.9
Q ss_pred EEEEEEEEeecCCCCCCCeeEEeeccceeEEEE
Q 024240 198 FFTHCALRLKKSGTIVPRMELVEVGPCMDFVVR 230 (270)
Q Consensus 198 ~~R~Y~I~~~~sg~~~p~v~L~EiGPr~dl~~~ 230 (270)
.+|.|.|.+.++--.-|+.++.+|||-. +.+|
T Consensus 146 NVr~~~V~F~~~~Fd~p~f~v~~vGPFv-vvvR 177 (178)
T PF12249_consen 146 NVRRYTVTFDPEVFDDPRFTVTQVGPFV-VVVR 177 (178)
T ss_pred CceeeeeeeCHHHcCCCCCeEeeeCCeE-EEEe
Confidence 4678888877766667889999999954 4444
No 14
>PRK15456 universal stress protein UspG; Provisional
Probab=38.21 E-value=23 Score=28.29 Aligned_cols=30 Identities=10% Similarity=0.249 Sum_probs=22.5
Q ss_pred chhhhhhccCCCcEEEEeeeCCCCCCceEEE
Q 024240 76 TSLEFFSLKTDCSIFIYGSTSKKRPDNLVIG 106 (270)
Q Consensus 76 ~~le~la~k~dcslf~f~s~~KKrp~~L~ig 106 (270)
..|.++|+.++|+++++|+|.+ ....+++|
T Consensus 95 ~~I~~~a~~~~~DLIVmG~~g~-~~~~~llG 124 (142)
T PRK15456 95 DEVNELAEELGADVVVIGSRNP-SISTHLLG 124 (142)
T ss_pred HHHHHHHhhcCCCEEEEcCCCC-CccceecC
Confidence 5788899999999999999853 23334444
No 15
>PHA02096 hypothetical protein
Probab=33.22 E-value=80 Score=24.30 Aligned_cols=52 Identities=19% Similarity=0.211 Sum_probs=45.7
Q ss_pred CCCCccEEEEeCCCCCC-hHHHHHHHHHHHhhCCCCCCCccccCCCcEEEEEEE
Q 024240 139 RVGSKPFICFVGEGFES-VEELKHLKEVLVDLLRGEVIENLNLAGLDHAYVCTA 191 (270)
Q Consensus 139 ~~gskPllvF~g~~F~~-~~~l~~lK~ll~d~F~~~~~~~i~l~~id~vi~ft~ 191 (270)
+.|+--=++|..+ ||. +..++..|+-+..+..|..+-+.+|=|.--++++.-
T Consensus 22 l~g~~~gv~fh~s-we~a~~~~~~ak~~i~eylkgt~vikkrlfg~ptiv~ink 74 (103)
T PHA02096 22 LHGAFGGVMFHDS-WEEADVSLKNAKKSIEEYLKGTTVIKKRLFGPPTIVSVNK 74 (103)
T ss_pred ccccccceEEecc-HHHhhhHHHHHHHHHHHHhcccchhhhhhcCCCeEEEecC
Confidence 7888888899986 988 568999999999999999999999999998888764
No 16
>cd01988 Na_H_Antiporter_C The C-terminal domain of a subfamily of Na+ /H+ antiporter existed in bacteria and archea . Na+/H+ exchange proteins eject protons from cells, effectively eliminating excess acid from actively metabolising cells. Na+ /H+ exchange activity is also crucial for the regulation of cell volume, and for the reabsorption of NaCl across renal, intestinal, and other epithelia. These antiports exchange Na+ for H+ in an electroneutral manner, and this activity is carried out by a family of Na+ /H+ exchangers, or NHEs, which are known to be present in both prokaryotic and eukaryotic cells. These exchangers are highly-regulated (glyco)phosphoproteins, which, based on their primary structure, appear to contain 10-12 membrane-spanning regions (M) at the N-terminus and a large cytoplasmic region at the C-terminus. The transmembrane regions M3-M12 share identity wit h other members of the family. The M6 and M7 regions are highly conserved. Thus, this is thought to be the regio
Probab=31.40 E-value=40 Score=25.82 Aligned_cols=23 Identities=9% Similarity=0.141 Sum_probs=19.9
Q ss_pred chhhhhhccCCCcEEEEeeeCCC
Q 024240 76 TSLEFFSLKTDCSIFIYGSTSKK 98 (270)
Q Consensus 76 ~~le~la~k~dcslf~f~s~~KK 98 (270)
..|.++|+..+|+++++|++.+.
T Consensus 84 ~~I~~~a~~~~~dlIV~G~~~~~ 106 (132)
T cd01988 84 SGILRTAKERQADLIIMGWHGST 106 (132)
T ss_pred HHHHHHHHhcCCCEEEEecCCCC
Confidence 57888999999999999998544
No 17
>cd01987 USP_OKCHK USP domain is located between the N-terminal sensor domain and C-terminal catalytic domain of this Osmosensitive K+ channel histidine kinase family. The family of KdpD sensor kinase proteins regulates the kdpFABC operon responsible for potassium transport. The USP domain is homologous to the universal stress protein Usp Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general "stress endurance" activity.
Probab=29.49 E-value=19 Score=27.84 Aligned_cols=32 Identities=16% Similarity=0.301 Sum_probs=24.7
Q ss_pred chhhhhhccCCCcEEEEeeeCCCCCCceEEEE
Q 024240 76 TSLEFFSLKTDCSIFIYGSTSKKRPDNLVIGR 107 (270)
Q Consensus 76 ~~le~la~k~dcslf~f~s~~KKrp~~L~igR 107 (270)
+.|.+.|+.++|+++++|++.+.....+++|.
T Consensus 75 ~~I~~~~~~~~~dllviG~~~~~~~~~~~~Gs 106 (124)
T cd01987 75 EAIVEFAREHNVTQIVVGKSRRSRWRELFRGS 106 (124)
T ss_pred HHHHHHHHHcCCCEEEeCCCCCchHHHHhccc
Confidence 67889999999999999998655444445443
No 18
>PRK15005 universal stress protein F; Provisional
Probab=28.43 E-value=42 Score=26.48 Aligned_cols=20 Identities=15% Similarity=0.152 Sum_probs=18.1
Q ss_pred chhhhhhccCCCcEEEEeee
Q 024240 76 TSLEFFSLKTDCSIFIYGST 95 (270)
Q Consensus 76 ~~le~la~k~dcslf~f~s~ 95 (270)
..|.++|+.++|+++++|++
T Consensus 97 ~~I~~~a~~~~~DLIV~Gs~ 116 (144)
T PRK15005 97 DRILELAKKIPADMIIIASH 116 (144)
T ss_pred HHHHHHHHHcCCCEEEEeCC
Confidence 56888999999999999987
No 19
>PF05450 Nicastrin: Nicastrin; InterPro: IPR008710 Nicastrin and presenilin are two major components of the gamma-secretase complex, which executes the intramembrane proteolysis of type I integral membrane proteins such as the amyloid precursor protein (APP) and Notch. Nicastrin is synthesised in fibroblasts and neurons as an endoglycosidase-H-sensitive glycosylated precursor protein (immature nicastrin) and is then modified by complex glycosylation in the Golgi apparatus and by sialylation in the trans-Golgi network (mature nicastrin) [].; GO: 0016485 protein processing, 0016021 integral to membrane
Probab=27.01 E-value=80 Score=28.56 Aligned_cols=62 Identities=15% Similarity=0.207 Sum_probs=47.3
Q ss_pred CCccEE--EEeCCCCCChHHHHHHHHHHHhhCC--CCCCCccccCCCcEEEEEEEec---CCeEEEEEE
Q 024240 141 GSKPFI--CFVGEGFESVEELKHLKEVLVDLLR--GEVIENLNLAGLDHAYVCTAVS---SNRVFFTHC 202 (270)
Q Consensus 141 gskPll--vF~g~~F~~~~~l~~lK~ll~d~F~--~~~~~~i~l~~id~vi~ft~~d---~~~I~~R~Y 202 (270)
..|+++ .|+||.|+---.=+.+..|-...|+ .-...++++..||.+|.+--+. +..+|+-.+
T Consensus 49 ~~knV~F~~F~GEs~dYiGS~R~vyDm~~~~f~~~~~~~~~i~~~~I~~~IElgqvg~~~~~~l~~Hvd 117 (234)
T PF05450_consen 49 LNKNVLFAFFNGESFDYIGSSRFVYDMQNGNFPSDSLQFQPISLDNIDSVIELGQVGLSNSSGLYAHVD 117 (234)
T ss_pred ccCcEEEEEecCccccccchHHHHHHHHcCcCcccccccccccHHHCCEEEEeeccCCCCCCCEEEEec
Confidence 456664 8899999987777778888888887 3345679999999999998763 222777755
No 20
>PF08616 SPA: Stabilization of polarity axis
Probab=26.39 E-value=1.6e+02 Score=23.40 Aligned_cols=63 Identities=16% Similarity=0.272 Sum_probs=43.7
Q ss_pred CCcEEEEEeCCCCCHhHHHHHHHHHhcccccce--eccccCCCcCcCCCCCcchhhhhhccCCCcEEEEeeeC
Q 024240 26 TGKKTLILQGTKTSNTLNDVLTELYLLKKGSAI--RYTRKNENIRPFESGGETSLEFFSLKTDCSIFIYGSTS 96 (270)
Q Consensus 26 n~K~~L~l~g~~~s~~~~~ll~DL~~L~kP~a~--~~~Kkn~~i~pFe~~~~~~le~la~k~dcslf~f~s~~ 96 (270)
-.|+++|+........+.+.+.=|.+|..|... .+. +. .+||-+. +.++.+.+.-+ ++.|.+|
T Consensus 24 ~~krivv~s~~~~~~~~s~~Vlal~~Li~p~~~~~~~~--~~-~~PY~~i--~~~~~l~~~~~---~I~GvtN 88 (113)
T PF08616_consen 24 LGKRIVVYSPSPSAGEVSEFVLALCSLISPGQDLRYFS--NR-YFPYFTI--SDLDELKSCPG---YIAGVTN 88 (113)
T ss_pred hCCCEEEECCCCCHHHHHHHHHHHHHHHCcccchhccc--cc-ccceeec--hhhhhhccCCC---EEEEeCC
Confidence 468888888777777789999999999977221 121 22 6899887 56665555444 7777765
No 21
>PRK00536 speE spermidine synthase; Provisional
Probab=22.44 E-value=70 Score=29.48 Aligned_cols=24 Identities=17% Similarity=0.202 Sum_probs=19.9
Q ss_pred cccCCcEEEEEeCCCCCHhHHHHHH
Q 024240 23 LVETGKKTLILQGTKTSNTLNDVLT 47 (270)
Q Consensus 23 ~~en~K~~L~l~g~~~s~~~~~ll~ 47 (270)
.+.|||++||+.| |-...+|.+++
T Consensus 69 ~h~~pk~VLIiGG-GDGg~~REvLk 92 (262)
T PRK00536 69 TKKELKEVLIVDG-FDLELAHQLFK 92 (262)
T ss_pred hCCCCCeEEEEcC-CchHHHHHHHC
Confidence 4579999999988 67888888876
Done!