Query psy5527
Match_columns 269
No_of_seqs 114 out of 192
Neff 6.2
Searched_HMMs 46136
Date Fri Aug 16 19:49:33 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5527.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5527hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04821 TIMELESS: Timeless pr 100.0 7.9E-68 1.7E-72 483.0 20.3 221 21-248 1-226 (266)
2 KOG1974|consensus 100.0 1.9E-54 4.2E-59 444.6 17.1 234 1-236 1-243 (1229)
3 cd00020 ARM Armadillo/beta-cat 76.4 29 0.00064 25.9 8.9 101 61-210 3-105 (120)
4 KOG2734|consensus 49.8 2.4E+02 0.0051 28.5 11.1 143 53-230 102-258 (536)
5 PF10165 Ric8: Guanine nucleot 37.0 3.4E+02 0.0074 26.7 10.4 153 31-193 49-214 (446)
6 PF05804 KAP: Kinesin-associat 36.8 4E+02 0.0087 28.2 11.2 86 123-236 323-408 (708)
7 PF08625 Utp13: Utp13 specific 24.9 2E+02 0.0044 23.9 5.6 53 184-237 50-102 (141)
8 PF08158 NUC130_3NT: NUC130/3N 23.9 1.5E+02 0.0033 20.5 3.9 37 132-169 12-48 (52)
9 smart00185 ARM Armadillo/beta- 22.7 1.7E+02 0.0036 17.5 3.7 37 123-171 4-40 (41)
10 PF03224 V-ATPase_H_N: V-ATPas 17.5 4.7E+02 0.01 24.0 7.0 41 157-207 254-294 (312)
No 1
>PF04821 TIMELESS: Timeless protein; InterPro: IPR006906 The timeless gene in Drosophila melanogaster (Fruit fly) and its homologues in a number of other insects and mammals (including human) are involved in circadian rhythm control []. This family includes related proteins from a number of fungal species and from Arabidopsis thaliana.
Probab=100.00 E-value=7.9e-68 Score=483.00 Aligned_cols=221 Identities=33% Similarity=0.504 Sum_probs=209.3
Q ss_pred cCCcccCCchHHHHHHHHHHHHhhcCCCChHHHHHhhhhcccccCchhhhccccCChhHHHHHHHHHHhccccccccCCC
Q psy5527 21 EDETNITENDRVEVLQDIYNKLCFEDRTTRPFRRAIGFTQVVKKDLLPLLISTKDDSTTFDLCIKILMNLTIPVECLLPI 100 (269)
Q Consensus 21 e~~~Y~~g~dcl~~LkDL~R~Lr~dd~~~r~vrr~lg~~~iv~~DLiPIL~~~~~d~~l~~~~lrLLV~LT~P~~~~~~~ 100 (269)
|+++|++||||++|||||+||||+||++.|+|||+||+||||++||||||++|.+++++|++|+||||+||||++++ .
T Consensus 1 e~~~Y~~g~dcl~~LkdL~r~lr~dd~~~~~v~r~lg~~~iv~~DLiPiL~~~~~~~~l~~~~l~LLV~LT~P~~~~--~ 78 (266)
T PF04821_consen 1 EDGVYVKGDDCLECLKDLKRFLRRDDEDQRDVRRQLGEWNIVQKDLIPILISYKDDDKLFLACLRLLVNLTWPIELL--V 78 (266)
T ss_pred CCCceecCHhHHHHHHHHHHHHHHhCcchHHHHHHHHHhchhhhhHHHHHHhccCchHHHHHHHHHHHHhCCCHHHh--c
Confidence 68899999999999999999999999998899999999999999999999999999999999999999999999997 3
Q ss_pred CCccccccchhhHHHHHHHHHHHHHHhccchhHHHHHHHHHhhhcCccccCCChhhhhHHHHHHHHHHHhccccCCCC--
Q psy5527 101 DSLCKTDEGRNTIYELNWLLTSCKEAFLESKITRCIIEHIKKFTDNESETHVTARICDCINNCLVLLRNILHIPEVRG-- 178 (269)
Q Consensus 101 ~~~~~~~~~r~~~~el~~~l~~yK~afl~~~~~~~l~~~l~~~L~~~~~~~Rt~~d~~iI~liL~LiRNiL~Ip~~~~-- 178 (269)
+..|++.+++++|.++.++|+.||+||+++++|+++++++.++|++++ .+||++|+.+|++||+|||||||||+++.
T Consensus 79 ~~~~~~~~~~~~~~~l~~~l~~yK~afl~~~~l~~~~~~l~~~l~~~~-~~rt~~d~~ii~lvL~LiRNlL~Ip~~~~~~ 157 (266)
T PF04821_consen 79 ESQPKDKNQRRNIPELLKYLQSYKEAFLDPRVLKALIRLLLPPLEKDW-EDRTERDNLIIELVLTLIRNLLAIPDPPSAS 157 (266)
T ss_pred cCCCCChHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHhHHhhccc-ccCCHHHHHHHHHHHHHHHHHhcCCCCcccc
Confidence 777788899999999999999999999999999999999999999999 79999999999999999999999998864
Q ss_pred ---CCCcchHHHHHHHHHhcChHHHHHHHHhccccccchhhhHHHHHHHHHcCCChHHHHHHhhhhccCCCCc
Q psy5527 179 ---GVTTSHHNQILWNLFTHGFDKVLTQLISQHHRHKLWSISVVQLIALMYKDQHVNTLQKLLNLWFETSPSE 248 (269)
Q Consensus 179 ---~~~~s~~~~ii~~l~~~~i~~lLl~l~s~~~e~~~~~~~ilEIi~ll~k~~~~~~L~~~~~~~~~~s~se 248 (269)
+.++++||++||+|+++||+++|++|++++++ ++|+++++||||+|||||+|++|++ ++.+++++|
T Consensus 158 ~~~~~~~~~~d~li~~l~~~~v~~lLL~l~s~~~~-~~f~~~lLEIi~ll~k~~~p~~L~~---~~~~~~~~e 226 (266)
T PF04821_consen 158 KRSDEDSSLHDQLIWALFESGVLDLLLTLASSPQE-SDFNLLLLEIIYLLFKGQDPESLAS---AQPQRSTSE 226 (266)
T ss_pred cccchhHHHHHHHHHHHHHcCHHHHHHHHHhCccc-cchhhHHHHHHHHHHcCCCHHHHhh---ccccccccc
Confidence 46788999999999999999999999999998 8999999999999999999999998 555666666
No 2
>KOG1974|consensus
Probab=100.00 E-value=1.9e-54 Score=444.62 Aligned_cols=234 Identities=34% Similarity=0.491 Sum_probs=224.0
Q ss_pred CcccccchhhHhHhhccCcccCCcccCCch-HHHHHHHHHHHHhhcCCCChHHHHHhhhhcccccCchhhhccccCChhH
Q psy5527 1 MEWVNLNPMILSTFGSLRVHEDETNITEND-RVEVLQDIYNKLCFEDRTTRPFRRAIGFTQVVKKDLLPLLISTKDDSTT 79 (269)
Q Consensus 1 m~~~~l~~~i~~~~saLG~~e~~~Y~~g~d-cl~~LkDL~R~Lr~dd~~~r~vrr~lg~~~iv~~DLiPIL~~~~~d~~l 79 (269)
|+|..|+++|.++|+||||+|+++|+..|| ||+|||||+||||.||++.|+||+++|.|+||++||||||++|.+|..+
T Consensus 1 m~l~~~~~~l~~a~saLGy~E~d~y~~~pdycLa~LKDL~RyLr~~Dd~~r~vr~~vg~~qiVt~DLiPIL~~~~~d~~l 80 (1229)
T KOG1974|consen 1 MDLLLMNPGLYSACSALGYPEGDTYVVEPDYCLACLKDLKRYLRYVDDTLRTVRRAVGAGQIVTSDLIPILIDWDKDDAL 80 (1229)
T ss_pred CcHHHHHHHHHHHHHhcCCCCCCeeecCchHHHHHHHHHHHHHHhcCchHHHHHHHHhhHhhhhhhhhhhhhhhccccHH
Confidence 899999999999999999999999999999 9999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhccccccccCCCCCccccccchhhHHHHHHHHHHHHHHhccchhHHHHHHHHHhhhcCccccCCChhhhhH
Q psy5527 80 FDLCIKILMNLTIPVECLLPIDSLCKTDEGRNTIYELNWLLTSCKEAFLESKITRCIIEHIKKFTDNESETHVTARICDC 159 (269)
Q Consensus 80 ~~~~lrLLV~LT~P~~~~~~~~~~~~~~~~r~~~~el~~~l~~yK~afl~~~~~~~l~~~l~~~L~~~~~~~Rt~~d~~i 159 (269)
|++++|+|||||+|+++++..+.++.+..++++|++|.++|++||.||+..+.++++...+..+|..-+ +.|+++|+.+
T Consensus 81 ~~~~ir~lvnlt~pv~~t~~~k~~~~~~~~v~~~~~L~~~l~~~K~Ait~~~~~~vi~~~l~~~l~~~~-e~r~erd~~~ 159 (1229)
T KOG1974|consen 81 FDNVIRLLVNLTQPVELTFSDKVMPRTRVGVHMIWELLEYLQTSKNAITSAKSFKVIVEYLKHLLESLD-EKRSERDCLL 159 (1229)
T ss_pred HHHHHHHhcccccccccccCCcccccchhhhHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHhccc-cccCHHHHHH
Confidence 999999999999999999986668888899999999999999999999999999999999999887546 7999999999
Q ss_pred HHHHHHHHHHhccccCCCC--------CCCcchHHHHHHHHHhcChHHHHHHHHhccccccchhhhHHHHHHHHHcCCCh
Q psy5527 160 INNCLVLLRNILHIPEVRG--------GVTTSHHNQILWNLFTHGFDKVLTQLISQHHRHKLWSISVVQLIALMYKDQHV 231 (269)
Q Consensus 160 I~liL~LiRNiL~Ip~~~~--------~~~~s~~~~ii~~l~~~~i~~lLl~l~s~~~e~~~~~~~ilEIi~ll~k~~~~ 231 (269)
|++||+|||||||||+... +..+|+|+++||+++.+|++++|++|++++.+ .+|+++++|||++|+|||+|
T Consensus 160 I~~vlLLirnil~Ip~d~~~~k~~~~~~~~~s~~d~il~~~~~s~idk~ll~I~t~p~~-~~~~v~lleIiali~k~q~~ 238 (1229)
T KOG1974|consen 160 IELVLLLIRNILHIPEDHAHCKMPQSTPHGASMHDQILINLKISGIDKILLYIATLPEE-EHDDVTLLEIIALILKGQHP 238 (1229)
T ss_pred HHHHHHHHHHHHhCCCcchhhhcccccccccccchHHHHHHHHhhhHhHhhhhccCChh-hhcceeHHHHHHHHHccCCH
Confidence 9999999999999999843 56789999999999999999999999999998 99999999999999999999
Q ss_pred HHHHH
Q psy5527 232 NTLQK 236 (269)
Q Consensus 232 ~~L~~ 236 (269)
+.++.
T Consensus 239 e~la~ 243 (1229)
T KOG1974|consen 239 ELLAG 243 (1229)
T ss_pred HHhcC
Confidence 98886
No 3
>cd00020 ARM Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model.
Probab=76.42 E-value=29 Score=25.89 Aligned_cols=101 Identities=21% Similarity=0.206 Sum_probs=63.3
Q ss_pred ccccCchhhhcc--ccCChhHHHHHHHHHHhccccccccCCCCCccccccchhhHHHHHHHHHHHHHHhccchhHHHHHH
Q psy5527 61 VVKKDLLPLLIS--TKDDSTTFDLCIKILMNLTIPVECLLPIDSLCKTDEGRNTIYELNWLLTSCKEAFLESKITRCIIE 138 (269)
Q Consensus 61 iv~~DLiPIL~~--~~~d~~l~~~~lrLLV~LT~P~~~~~~~~~~~~~~~~r~~~~el~~~l~~yK~afl~~~~~~~l~~ 138 (269)
+++.+++|.|+. .++++++...++..+.+++--. -.++..|.+.++++.++.
T Consensus 3 ~~~~~~i~~l~~~l~~~~~~~~~~a~~~l~~l~~~~--------------------------~~~~~~~~~~~~i~~l~~ 56 (120)
T cd00020 3 VIQAGGLPALVSLLSSSDENVQREAAWALSNLSAGN--------------------------NDNIQAVVEAGGLPALVQ 56 (120)
T ss_pred HHHcCChHHHHHHHHcCCHHHHHHHHHHHHHHhcCC--------------------------HHHHHHHHHCCChHHHHH
Confidence 345566666663 2334567777777777766421 013334445566666665
Q ss_pred HHHhhhcCccccCCChhhhhHHHHHHHHHHHhccccCCCCCCCcchHHHHHHHHHhcChHHHHHHHHhcccc
Q psy5527 139 HIKKFTDNESETHVTARICDCINNCLVLLRNILHIPEVRGGVTTSHHNQILWNLFTHGFDKVLTQLISQHHR 210 (269)
Q Consensus 139 ~l~~~L~~~~~~~Rt~~d~~iI~liL~LiRNiL~Ip~~~~~~~~s~~~~ii~~l~~~~i~~lLl~l~s~~~e 210 (269)
.+.. .|..+.+.++..++|+...++. ....+.+.|+...|+.+.+..+.
T Consensus 57 ~l~~------------~~~~v~~~a~~~L~~l~~~~~~-----------~~~~~~~~g~l~~l~~~l~~~~~ 105 (120)
T cd00020 57 LLKS------------EDEEVVKAALWALRNLAAGPED-----------NKLIVLEAGGVPKLVNLLDSSNE 105 (120)
T ss_pred HHhC------------CCHHHHHHHHHHHHHHccCcHH-----------HHHHHHHCCChHHHHHHHhcCCH
Confidence 5432 2567888999999999876542 44455678888888888876543
No 4
>KOG2734|consensus
Probab=49.77 E-value=2.4e+02 Score=28.50 Aligned_cols=143 Identities=17% Similarity=0.320 Sum_probs=83.7
Q ss_pred HHHhhhhccccc--Cchhhhccc-----------cCChhHHHHHHHHHHhccccccccCCCCCccccccchhhHHHHHHH
Q psy5527 53 RRAIGFTQVVKK--DLLPLLIST-----------KDDSTTFDLCIKILMNLTIPVECLLPIDSLCKTDEGRNTIYELNWL 119 (269)
Q Consensus 53 rr~lg~~~iv~~--DLiPIL~~~-----------~~d~~l~~~~lrLLV~LT~P~~~~~~~~~~~~~~~~r~~~~el~~~ 119 (269)
.-.+-+.++|-+ ||.|+|+.- .++.+|+.+++.|+--||=- +..+...++ --.|.
T Consensus 102 hd~IQ~mhvlAt~PdLYp~lveln~V~slL~LLgHeNtDI~iavvdLLqELTD~-------Dv~~es~eg---AevLi-- 169 (536)
T KOG2734|consen 102 HDIIQEMHVLATMPDLYPILVELNAVQSLLELLGHENTDIAIAVVDLLQELTDE-------DVLYESEEG---AEVLI-- 169 (536)
T ss_pred HHHHHHHHhhhcChHHHHHHHHhccHHHHHHHhcCCCchhHHHHHHHHHHhhhh-------ccccccccc---HHHHH--
Confidence 334445555543 888888753 25788999999999999851 222222222 11222
Q ss_pred HHHHHHHhccchhHHHHHHHHHhhhcCccccCCChhhhhHHHHHHHHHHHhccccCCCCCCCcchHHHHHHHHHhcChHH
Q psy5527 120 LTSCKEAFLESKITRCIIEHIKKFTDNESETHVTARICDCINNCLVLLRNILHIPEVRGGVTTSHHNQILWNLFTHGFDK 199 (269)
Q Consensus 120 l~~yK~afl~~~~~~~l~~~l~~~L~~~~~~~Rt~~d~~iI~liL~LiRNiL~Ip~~~~~~~~s~~~~ii~~l~~~~i~~ 199 (269)
.|..++.++.-++.-+.+.= +--+++..-+...|..+-|++.+.+. +-..--++|...
T Consensus 170 -----daLvdg~vlaLLvqnveRLd------Esvkeea~gv~~~L~vveNlv~~r~~-----------~~~~~~e~~ll~ 227 (536)
T KOG2734|consen 170 -----DALVDGQVLALLVQNVERLD------ESVKEEADGVHNTLAVVENLVEVRPA-----------ICTEIVEQGLLS 227 (536)
T ss_pred -----HHHHhccHHHHHHHHHHHhh------hcchhhhhhhHHHHHHHHHHHhccHH-----------HHHHHHHhhHHH
Confidence 24567887777666655443 23366677788999999999988664 333333446666
Q ss_pred HHHH-HHhccccccchhhhHHHHHHHHHcCCC
Q psy5527 200 VLTQ-LISQHHRHKLWSISVVQLIALMYKDQH 230 (269)
Q Consensus 200 lLl~-l~s~~~e~~~~~~~ilEIi~ll~k~~~ 230 (269)
.||+ +..-... ..-.+...||.+.++-+-+
T Consensus 228 WLL~rl~~k~~f-~aNk~YasEiLaillq~s~ 258 (536)
T KOG2734|consen 228 WLLKRLKGKAAF-DANKQYASEILAILLQNSD 258 (536)
T ss_pred HHHHHHhcccCc-chhHHHHHHHHHHHhccCc
Confidence 6665 3222111 2222445566666655544
No 5
>PF10165 Ric8: Guanine nucleotide exchange factor synembryn; InterPro: IPR019318 Ric8 is involved in the EGL-30 neurotransmitter signalling pathway []. It is a guanine nucleotide exchange factor [] that regulates neurotransmitter secretion.
Probab=37.03 E-value=3.4e+02 Score=26.75 Aligned_cols=153 Identities=18% Similarity=0.131 Sum_probs=75.2
Q ss_pred HHHHHHHHHHHHhhcCCCChHHHHHhhhhcccccCchhhhccccC---ChhHHHHHHHHHHhccc-cccccCCCCCcccc
Q psy5527 31 RVEVLQDIYNKLCFEDRTTRPFRRAIGFTQVVKKDLLPLLISTKD---DSTTFDLCIKILMNLTI-PVECLLPIDSLCKT 106 (269)
Q Consensus 31 cl~~LkDL~R~Lr~dd~~~r~vrr~lg~~~iv~~DLiPIL~~~~~---d~~l~~~~lrLLV~LT~-P~~~~~~~~~~~~~ 106 (269)
..|.||=|...+-.. ...|..+...+...+ |+..|..+.+ +.++...+.|||..+|- +.+.. .+.-++
T Consensus 49 ~~EALKCL~N~lf~s----~~aR~~~~~~~~~~~-l~~~Lk~~~~~~~~~d~~Fl~~RLLFLlTa~~~~~~---~~L~~e 120 (446)
T PF10165_consen 49 SREALKCLCNALFLS----PSARQIFVDLGLAEK-LCERLKNYSDSSQPSDVEFLDSRLLFLLTALRPDDR---KKLIEE 120 (446)
T ss_pred HHHHHHHHHHHHhCC----HHHHHHHHHcCcHHH-HHHHHHcccccCCChhHHHHHHHHHHHHhcCChhHH---HHHHHH
Confidence 456666665555322 345566666666654 7888887643 45666779999999994 22221 111111
Q ss_pred ccchhh-HHHHHHHHHHHHHHhc-----cchhHHHHHHHHHhhhc--CccccCCC-hhhhhHHHHHHHHHHHhccccCCC
Q psy5527 107 DEGRNT-IYELNWLLTSCKEAFL-----ESKITRCIIEHIKKFTD--NESETHVT-ARICDCINNCLVLLRNILHIPEVR 177 (269)
Q Consensus 107 ~~~r~~-~~el~~~l~~yK~afl-----~~~~~~~l~~~l~~~L~--~~~~~~Rt-~~d~~iI~liL~LiRNiL~Ip~~~ 177 (269)
..+-.. ...+..++..+...-. .+.-..++.+.|+-.+. ... .... +++...+..++.++|.++ .+..+
T Consensus 121 ~~~~~~l~~~L~~~l~~~~~~~~~~~~~~~~~~~~l~EiLKllFNit~~~-~~~~~~~~~~~~~~l~~il~~~l-~~~~~ 198 (446)
T PF10165_consen 121 HHGVELLTEALERHLKVKSKSSQEPTAPSPMDEEALSEILKLLFNITLHY-PKSVPEEFSPSIPHLVSILRRLL-PPPPS 198 (446)
T ss_pred hhhHHHHHHHHHHHHhcccccccccCCCCcchHHHHHHHHHHHHHhhhcc-CcccchhhhHHHHHHHHHHHHHh-ccCCC
Confidence 111111 1222223222111111 11233444554444332 122 2333 488889999999999997 33332
Q ss_pred CCCCcchHHHHHHHHH
Q psy5527 178 GGVTTSHHNQILWNLF 193 (269)
Q Consensus 178 ~~~~~s~~~~ii~~l~ 193 (269)
..+....+..+|.+|-
T Consensus 199 ~~~l~~~~~~~in~L~ 214 (446)
T PF10165_consen 199 SPPLDPPHSHAINALL 214 (446)
T ss_pred CCcchhhHHHHHHHHh
Confidence 2222333444444443
No 6
>PF05804 KAP: Kinesin-associated protein (KAP)
Probab=36.83 E-value=4e+02 Score=28.24 Aligned_cols=86 Identities=20% Similarity=0.269 Sum_probs=49.5
Q ss_pred HHHHhccchhHHHHHHHHHhhhcCccccCCChhhhhHHHHHHHHHHHhccccCCCCCCCcchHHHHHHHHHhcChHHHHH
Q psy5527 123 CKEAFLESKITRCIIEHIKKFTDNESETHVTARICDCINNCLVLLRNILHIPEVRGGVTTSHHNQILWNLFTHGFDKVLT 202 (269)
Q Consensus 123 yK~afl~~~~~~~l~~~l~~~L~~~~~~~Rt~~d~~iI~liL~LiRNiL~Ip~~~~~~~~s~~~~ii~~l~~~~i~~lLl 202 (269)
.|..+...+++..+.+.+ . . ++..+.+..|.++-|+-.-++ +-..+-+.|+..-|.
T Consensus 323 NK~~m~~~giV~kL~kLl----~--s------~~~~l~~~aLrlL~NLSfd~~------------~R~~mV~~GlIPkLv 378 (708)
T PF05804_consen 323 NKDEMAESGIVEKLLKLL----P--S------ENEDLVNVALRLLFNLSFDPE------------LRSQMVSLGLIPKLV 378 (708)
T ss_pred HHHHHHHcCCHHHHHHHh----c--C------CCHHHHHHHHHHHHHhCcCHH------------HHHHHHHCCCcHHHH
Confidence 355555566666555544 2 1 123578888888888866544 344666777777777
Q ss_pred HHHhccccccchhhhHHHHHHHHHcCCChHHHHH
Q psy5527 203 QLISQHHRHKLWSISVVQLIALMYKDQHVNTLQK 236 (269)
Q Consensus 203 ~l~s~~~e~~~~~~~ilEIi~ll~k~~~~~~L~~ 236 (269)
.+..+++ +....+-|+|+|=.+-.....+.
T Consensus 379 ~LL~d~~----~~~val~iLy~LS~dd~~r~~f~ 408 (708)
T PF05804_consen 379 ELLKDPN----FREVALKILYNLSMDDEARSMFA 408 (708)
T ss_pred HHhCCCc----hHHHHHHHHHHhccCHhhHHHHh
Confidence 6666533 22345566666655544444443
No 7
>PF08625 Utp13: Utp13 specific WD40 associated domain; InterPro: IPR013934 A large ribonuclear protein complex is required for the processing of the small-ribosomal-subunit rRNA - the small-subunit (SSU) processome [, ]. This preribosomal complex contains the U3 snoRNA and at least 40 proteins, which have the following properties: They are nucleolar. They are able to coimmunoprecipitate with the U3 snoRNA and Mpp10 (a protein specific to the SSU processome). They are required for 18S rRNA biogenesis. There appears to be a linkage between polymerase I transcription and the formation of the SSU processome; as some, but not all, of the SSU processome components are required for pre-rRNA transcription initiation. These SSU processome components have been termed t-Utps. They form a pre-complex with pre-18S rRNA in the absence of snoRNA U3 and other SSU processome components. It has been proposed that the t-Utp complex proteins are both rDNA and rRNA binding proteins that are involved in the initiation of pre18S rRNA transcription. Initially binding to rDNA then associating with the 5' end of the nascent pre18S rRNA. The t-Utpcomplex forms the nucleus around which the rest of the SSU processome components, including snoRNA U3, assemble []. From electron microscopy the SSU processome may correspond to the terminal knobs visualized at the 5' ends of nascent 18S rRNA. Utp13 is a nucleolar protein and component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA []. Upt13 is also a component of the Pwp2 complex that forms part of a stable particle subunit independent of the U3 small nucleolar ribonucleoprotein that is essential for the initial assembly steps of the 90S pre-ribosome []. Components of the Pwp2 complex are: Utp1 (Pwp2), Utp6, Utp12 (Dip2), Utp13, Utp18, and Utp21. The relationship between the Pwp2 complex and the t-Utps complex [] that also associates with the 5' end of nascent pre-18S rRNA is unclear. ; GO: 0006364 rRNA processing, 0032040 small-subunit processome
Probab=24.89 E-value=2e+02 Score=23.85 Aligned_cols=53 Identities=13% Similarity=0.160 Sum_probs=37.6
Q ss_pred hHHHHHHHHHhcChHHHHHHHHhccccccchhhhHHHHHHHHHcCCChHHHHHH
Q psy5527 184 HHNQILWNLFTHGFDKVLTQLISQHHRHKLWSISVVQLIALMYKDQHVNTLQKL 237 (269)
Q Consensus 184 ~~~~ii~~l~~~~i~~lLl~l~s~~~e~~~~~~~ilEIi~ll~k~~~~~~L~~~ 237 (269)
.-+.+|..|....+..+|-++..=... ..++...=-+++.+||..+|+.|.+.
T Consensus 50 ~l~~~i~~L~~~~l~~LL~~ir~WNTN-sr~~~vAQ~vL~~il~~~~~~~L~~~ 102 (141)
T PF08625_consen 50 ELDEVIKKLDDEQLEKLLRFIRDWNTN-SRTSHVAQRVLNAILKSHPPEELLKI 102 (141)
T ss_pred HHHHHHHhcCHHHHHHHHHHHHHhhcc-cccHHHHHHHHHHHHHhCCHHHHHcc
Confidence 345688888888888777776542222 34445555578899999999999874
No 8
>PF08158 NUC130_3NT: NUC130/3NT domain; InterPro: IPR012977 This N-terminal domain is found in a novel nucleolar protein family defined by NUC130/133 [].
Probab=23.92 E-value=1.5e+02 Score=20.52 Aligned_cols=37 Identities=22% Similarity=0.254 Sum_probs=23.9
Q ss_pred hHHHHHHHHHhhhcCccccCCChhhhhHHHHHHHHHHH
Q psy5527 132 ITRCIIEHIKKFTDNESETHVTARICDCINNCLVLLRN 169 (269)
Q Consensus 132 ~~~~l~~~l~~~L~~~~~~~Rt~~d~~iI~liL~LiRN 169 (269)
.++.+-..+.+.|.... ....++-..-+=..|.|+||
T Consensus 12 ~~~~Fp~~L~~lL~~~~-~~L~p~lR~~lv~aLiLLRn 48 (52)
T PF08158_consen 12 ETKDFPQELIDLLRNHH-TVLDPDLRMKLVKALILLRN 48 (52)
T ss_pred HHHHHHHHHHHHHHhcc-ccCCHHHHHHHHHHHHHHHc
Confidence 45555556666665444 45667777777777888887
No 9
>smart00185 ARM Armadillo/beta-catenin-like repeats. Approx. 40 amino acid repeat. Tandem repeats form superhelix of helices that is proposed to mediate interaction of beta-catenin with its ligands. Involved in transducing the Wingless/Wnt signal. In plakoglobin arm repeats bind alpha-catenin and N-cadherin.
Probab=22.66 E-value=1.7e+02 Score=17.55 Aligned_cols=37 Identities=16% Similarity=0.208 Sum_probs=24.9
Q ss_pred HHHHhccchhHHHHHHHHHhhhcCccccCCChhhhhHHHHHHHHHHHhc
Q psy5527 123 CKEAFLESKITRCIIEHIKKFTDNESETHVTARICDCINNCLVLLRNIL 171 (269)
Q Consensus 123 yK~afl~~~~~~~l~~~l~~~L~~~~~~~Rt~~d~~iI~liL~LiRNiL 171 (269)
.|+++.+.+.++.++..+. ..|..+++-.+..+||+.
T Consensus 4 ~~~~i~~~g~i~~L~~ll~------------~~~~~i~~~a~~aL~nl~ 40 (41)
T smart00185 4 QKQAVVDAGGLPALVELLK------------SEDEEVVKEAAWALSNLS 40 (41)
T ss_pred HHHHHHHCCCHHHHHHHHc------------CCCHHHHHHHHHHHHHHc
Confidence 4556666676666655542 235678888889999885
No 10
>PF03224 V-ATPase_H_N: V-ATPase subunit H; InterPro: IPR004908 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. V-ATPases (also known as V1V0-ATPase or vacuolar ATPase) (3.6.3.14 from EC) are found in the eukaryotic endomembrane system, and in the plasma membrane of prokaryotes and certain specialised eukaryotic cells. V-ATPases hydrolyse ATP to drive a proton pump, and are involved in a variety of vital intra- and inter-cellular processes such as receptor mediated endocytosis, protein trafficking, active transport of metabolites, homeostasis and neurotransmitter release []. V-ATPases are composed of two linked complexes: the V1 complex (subunits A-H) contains the catalytic core that hydrolyses ATP, while the V0 complex (subunits a, c, c', c'', d) forms the membrane-spanning pore. V-ATPases may have an additional role in membrane fusion through binding to t-SNARE proteins []. This entry represents subunit H (also known as Vma13p) found in the V1 complex of V-ATPases. This subunit has a regulatory function, being responsible for activating ATPase activity and coupling ATPase activity to proton flow []. The yeast enzyme contains five motifs similar to the HEAT or Armadillo repeats seen in the importins, and can be divided into two distinct domains: a large N-terminal domain consisting of stacked alpha helices, and a smaller C-terminal alpha-helical domain with a similar superhelical topology to an armadillo repeat []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0046961 proton-transporting ATPase activity, rotational mechanism, 0015991 ATP hydrolysis coupled proton transport, 0000221 vacuolar proton-transporting V-type ATPase, V1 domain; PDB: 1HO8_A.
Probab=17.54 E-value=4.7e+02 Score=24.05 Aligned_cols=41 Identities=22% Similarity=0.246 Sum_probs=32.5
Q ss_pred hhHHHHHHHHHHHhccccCCCCCCCcchHHHHHHHHHhcChHHHHHHHHhc
Q psy5527 157 CDCINNCLVLLRNILHIPEVRGGVTTSHHNQILWNLFTHGFDKVLTQLISQ 207 (269)
Q Consensus 157 ~~iI~liL~LiRNiL~Ip~~~~~~~~s~~~~ii~~l~~~~i~~lLl~l~s~ 207 (269)
+.+++.++..+||++..++.. ++..|-..|+.+++-.|...
T Consensus 254 EKvvRv~la~l~Nl~~~~~~~----------~~~~mv~~~~l~~l~~L~~r 294 (312)
T PF03224_consen 254 EKVVRVSLAILRNLLSKAPKS----------NIELMVLCGLLKTLQNLSER 294 (312)
T ss_dssp HHHHHHHHHHHHHTTSSSSTT----------HHHHHHHH-HHHHHHHHHSS
T ss_pred chHHHHHHHHHHHHHhccHHH----------HHHHHHHccHHHHHHHHhcC
Confidence 479999999999999887642 77788888888888777653
Done!