Query 015740
Match_columns 401
No_of_seqs 126 out of 322
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 09:08:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015740.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015740hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1902 Putative signal transd 100.0 3.8E-69 8.3E-74 529.8 13.9 320 1-349 1-323 (441)
2 PF04146 YTH: YT521-B-like dom 100.0 3E-51 6.5E-56 359.7 10.3 139 70-209 1-140 (140)
3 KOG1901 Uncharacterized high-g 100.0 4.1E-43 9E-48 359.1 14.6 150 67-221 295-451 (487)
4 PRK00809 hypothetical protein; 96.8 0.016 3.4E-07 52.3 10.8 128 72-204 2-143 (144)
5 PF01878 EVE: EVE domain; Int 86.7 1.3 2.8E-05 38.7 5.0 127 72-205 1-143 (143)
6 PRK02268 hypothetical protein; 64.9 65 0.0014 29.6 9.5 124 72-208 3-138 (141)
7 PF06199 Phage_tail_2: Phage m 30.7 1.1E+02 0.0023 26.2 5.0 43 91-133 67-109 (134)
8 PF00076 RRM_1: RNA recognitio 22.5 2.8E+02 0.006 19.8 5.3 35 98-132 10-45 (70)
9 PF15343 DEPP: Decidual protei 20.1 72 0.0016 30.8 2.1 16 347-362 13-28 (188)
10 COG4957 Predicted transcriptio 12.6 1.9E+02 0.0041 27.0 2.8 49 292-359 84-134 (148)
No 1
>KOG1902 consensus Putative signal transduction protein involved in RNA splicing [Signal transduction mechanisms; RNA processing and modification]
Probab=100.00 E-value=3.8e-69 Score=529.80 Aligned_cols=320 Identities=33% Similarity=0.421 Sum_probs=284.2
Q ss_pred CCcccccccceeecccccc-cCCCCCCCCCCCccccccCCCCchhhhhhhcCCCCCccc-CCCCCCCCCCCCceEEEEEe
Q 015740 1 MSSDTAKENASVVDSSVTE-KHDVGNSDDPESSSYKANEHRCPSLAKEAKAGHSNGQLE-NSTDNNKGKLYNTRYFIIKS 78 (401)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~-~~d~g~~d~~~s~~yk~~e~~~~~~~~~~k~g~s~~q~~-~~~~~~~~~~~~aRFFIIKS 78 (401)
|++||++|++++++.++|. +.+.+++++|.+.+|+..++.++..+...... |..|.. .....+.....++|||||||
T Consensus 1 ~~~dt~~~~~~~~~~~~t~~~q~l~~~~~~~~~~~rk~e~~~~~~v~~~~~~-s~~q~~s~~~~~ss~~~~~~rYFIiKS 79 (441)
T KOG1902|consen 1 NDYDTRSEASDSGSESVSFTDGSVRSGSGTDGSDEKKKERKRARGISPISGS-SASESYADQTSKLKYVLQDARYFIIKS 79 (441)
T ss_pred CcccchhhhhhhcccccchhhhhhccCCCCCCCcccccccccccCCCccccc-CccccchhhcccccccCCceEEEEEec
Confidence 7899999999999999999 99999999999999999999999887666323 323333 33333444478999999999
Q ss_pred CChhHHHHHhhcCeeeeccCChHHHHHHHhcCCcEEEEEEecCCCceeEEEEeeccCCCCCCc-cccCCCCCCCCCCCce
Q 015740 79 LNHQNIQLSIEKEIWATQVMNEPILEEAFHNSGKVILIFSVNMSGFFQGYAQMMSSVGWRRDN-VWSQGNGKNNPWGRSF 157 (401)
Q Consensus 79 ~NeeNI~~Sik~GIWaTt~~NekkLneAFk~s~~VyLIFSVN~SG~FqGyArM~S~id~~~~~-iW~~~~g~~~~wgg~F 157 (401)
+|++||.+|+++|||+||+.||++||.||.++..||||||||+||||||||+|+|+|++.+.. +|.++.|.++.||++|
T Consensus 80 ~N~eN~elSvqkGiWaTq~sNE~kLn~AF~~s~~ViLIFSVn~SghFQG~ArMsS~IG~~~~q~~W~~~~G~~a~~G~~F 159 (441)
T KOG1902|consen 80 NNHENVELSVQKGVWSTQPSNEKKLNLAFRSSRSVILIFSVNESGHFQGFARMSSEIGHGGSQIHWVLPAGMSAMLGGVF 159 (441)
T ss_pred CCccceeeehhcceeccccccHHHHHHHHhhcCcEEEEEEecccccchhhhhhcchhccCCCCccccccCCcccccCcee
Confidence 999999999999999999999999999999999999999999999999999999999999875 8999888889999999
Q ss_pred EEEEEEeecCCCCccccccCCCCCCCCeeeCCCCcccChHHHHHHHHHhcCCCCccccccccccCCCCCCCCCCCCCCCC
Q 015740 158 KVKWLRLNTLPFQKTLHLKNPLNDYKPVKISRDCQELPQDIGEALCHLLDGKDDVDGIQTSFHRDDLPAKRPCIEPSCSL 237 (401)
Q Consensus 158 kVeWL~v~dLPF~~t~HLkNPlNeNKPVk~sRDGQEIepeiG~qLckLF~~~~~~~s~~~sf~~~D~~~~r~~~~~~~~~ 237 (401)
+|+||++++|||+++.||+||||+||||+|+||||||+|++|+|||.||+..++.+ +++..+.+|++-++.++ | ++.
T Consensus 160 kVkWiRl~eLpFqkt~hL~NP~NdnkpVKISRD~QELep~VGEqL~~Ll~~~p~~e-l~~~s~~~~~kr~~~~A-p-~sr 236 (441)
T KOG1902|consen 160 KVKWIRLRELPFQKTAHLTNPWNENKPVKISRDGQELEPEVGEQLCLLLPPDPSID-LYQVSHKMRHKRRMHSA-P-RSR 236 (441)
T ss_pred eEeEEeeccccchhhhhcCCcccccCceeecccccccChhHHHHHHHhcCCCcchh-hhhhhHHHHHhhhhhcC-C-ccC
Confidence 99999999999999999999999999999999999999999999999999999999 77778889999888888 3 333
Q ss_pred CCCCCCCCCCccccccCCCCCCccccccCCCCCccccccccCCCCccccccccCccceeeeeccCCCCCccccccccCcc
Q 015740 238 GDEEYHKPPLHVPLGKTPMPYPSFLYQHQGGPSNFHLAQRCGGDAENLPFTSMSSKFSRIYHSRKGNLSNLQVDCDLSSR 317 (401)
Q Consensus 238 ~~~~~~~~~~~~~~~~~p~~~~~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 317 (401)
+ + +|.++|+.|....|.++....+|| +.-.|.+++.+-...++++ +...+|..-|
T Consensus 237 ~--E--------p~~~~p~~~~~~~~ped~d~~~~~-~~p~G~~p~~~h~~Pg~~~--------------~~r~q~~~~r 291 (441)
T KOG1902|consen 237 G--E--------PSRREPVRDVGRRRPEDYDIHNSR-KKPRGDYPPEFHQRPGYLK--------------DPRYQEVDRR 291 (441)
T ss_pred C--C--------cccCCcccCccccCcccchhhhhh-hCCCCCCCcccccCCCcCC--------------Cccccccccc
Confidence 3 1 899999999999999999999999 3333444777777777655 3455688899
Q ss_pred ccccccCCCCCccccCCcchhhhhcHHHHHHH
Q 015740 318 YDFWGLSADSPLASTITEDDFLEMSYEEYLEA 349 (401)
Q Consensus 318 ~~~w~~~~~sp~~~~~~~~~~~~~~~~~~~~~ 349 (401)
+.-|+|.-++|++..++.++|++|.+++|++.
T Consensus 292 f~g~~L~v~~Pg~~~~y~~~f~nm~p~p~~~g 323 (441)
T KOG1902|consen 292 FSGVRLDVFLPGSYNDYVREFHNMGPPPPWQG 323 (441)
T ss_pred cCceecccccCcccccccchhhhcCCCccccC
Confidence 99999999999999999999999999999987
No 2
>PF04146 YTH: YT521-B-like domain; InterPro: IPR007275 A protein of the YTH family has been shown to selectively remove transcripts of meiosis-specific genes expressed in mitotic cells []. It has been speculated that in higher eukaryotic YTH-family members may be involved in similar mechanaisms to suppress gene regulation during gametogenesis or general silencing. The rat protein YT521-B, Q9QY02 from SWISSPROT, is a tyrosine-phosphorylated nuclear protein, that interacts with the nuclear transcriptosomal component scaffold attachment factor B, and the 68kDa Src substrate associated during mitosis, Sam68. In vivo splicing assays demonstrated that YT521-B modulates alternative splice site selection in a concentration-dependent manner []. The domain is predicted to have four alpha helices and six beta strands []. In plant cells environmental stimuli, which light, pathogens, hormones, and abiotic stresses, elicit changes in the cytosolic Ca levels but little is known of the cytosolic-nuclear Ca-signaling pathway; where gene regulation occurs to respond appropriately to the stress. It has been demonstrated that two novel Arabidopsis thaliana (Mouse-ear cress) proteins, (ECT1 and ECT2), specifically associated with Calcineurin B-Like-Interacting Protein Kinase1 (CIPK1), a member of Ser/Thr protein kinases that interact with the calcineurin B-like Ca-binding proteins. These two proteins contain a very similar C-terminal region (180 amino acids in length, 81% similarity), which is required and sufficient for both interaction with CIPK1 and translocation to the nucleus. This domain, the YTH-domain, is conserved across all eukaryotes and suggests that the conserved C-terminal region plays a critical role in relaying the cytosolic Ca-signals to the nucleus, thereby regulating gene expression [].; PDB: 2YUD_A 2YU6_A.
Probab=100.00 E-value=3e-51 Score=359.68 Aligned_cols=139 Identities=53% Similarity=0.887 Sum_probs=115.4
Q ss_pred CceEEEEEeCChhHHHHHhhcCeeeeccCChHHHHHHHhcCCcEEEEEEecCCCceeEEEEeeccCCCCC-CccccCCCC
Q 015740 70 NTRYFIIKSLNHQNIQLSIEKEIWATQVMNEPILEEAFHNSGKVILIFSVNMSGFFQGYAQMMSSVGWRR-DNVWSQGNG 148 (401)
Q Consensus 70 ~aRFFIIKS~NeeNI~~Sik~GIWaTt~~NekkLneAFk~s~~VyLIFSVN~SG~FqGyArM~S~id~~~-~~iW~~~~g 148 (401)
++|||||||+|++||++|+++|||+|+++|+++|++||+++++||||||||+||+|||||+|+|+++... ..+|.++ .
T Consensus 1 ~~rfFiiKS~~~~ni~~s~~~gvW~t~~~~~~~L~~Af~~~~~V~L~FSvn~S~~F~G~A~M~s~~~~~~~~~~w~~~-~ 79 (140)
T PF04146_consen 1 NARFFIIKSFNEENIHLSIKYGVWATQPKNEKKLNEAFKESRNVYLFFSVNGSGHFQGYARMTSPIDPDSPKPFWQQD-S 79 (140)
T ss_dssp --EEEEEEESSCHHHHHHHHCTEEE--CCCHHHHHHHHHHSS-EEEEEEETTTSEEEEEEEEECECCSSS------SS--
T ss_pred CcEEEEEEECCHHHHHHHHhCCEEcccccchHHHHHHHHhCCCEEEEEeecCcceEEEEEEEccCCCCcccCcccccc-c
Confidence 5899999999999999999999999999999999999999999999999999999999999999998885 5788543 1
Q ss_pred CCCCCCCceEEEEEEeecCCCCccccccCCCCCCCCeeeCCCCcccChHHHHHHHHHhcCC
Q 015740 149 KNNPWGRSFKVKWLRLNTLPFQKTLHLKNPLNDYKPVKISRDCQELPQDIGEALCHLLDGK 209 (401)
Q Consensus 149 ~~~~wgg~FkVeWL~v~dLPF~~t~HLkNPlNeNKPVk~sRDGQEIepeiG~qLckLF~~~ 209 (401)
...+|+|.|+|+||++++|||+.++||+||+|+||||+++||||||++++|++||+||+++
T Consensus 80 ~~~~~~g~F~v~Wl~~~~lpf~~~~hl~n~~n~~~pV~~~rDgqEi~~~~G~~l~~~f~~~ 140 (140)
T PF04146_consen 80 SSSKWGGPFRVEWLRVKDLPFSKLRHLRNPLNENKPVKISRDGQEIEPEIGEQLLKIFDNQ 140 (140)
T ss_dssp SGCGG-SEEEEEEEE-S-EEHHHHTT-EETTTTTEETTS--TTEEE-CCHHHHHHHHCGT-
T ss_pred cccccCCceEEEEEECCcCChHHhcccccccCCCcEEEECCCCEEeCHHHHHHHHHHHhhC
Confidence 2479999999999999999999999999999999999999999999999999999999863
No 3
>KOG1901 consensus Uncharacterized high-glucose-regulated protein [General function prediction only]
Probab=100.00 E-value=4.1e-43 Score=359.14 Aligned_cols=150 Identities=31% Similarity=0.581 Sum_probs=144.3
Q ss_pred CCCCceEEEEEeCChhHHHHHhhcCeeeeccCChHHHHHHHhcC------CcEEEEEEecCCCceeEEEEeeccCCCCCC
Q 015740 67 KLYNTRYFIIKSLNHQNIQLSIEKEIWATQVMNEPILEEAFHNS------GKVILIFSVNMSGFFQGYAQMMSSVGWRRD 140 (401)
Q Consensus 67 ~~~~aRFFIIKS~NeeNI~~Sik~GIWaTt~~NekkLneAFk~s------~~VyLIFSVN~SG~FqGyArM~S~id~~~~ 140 (401)
++.++|||||||++++|||+||+|+||++|.++|++|+.||++. ++||||||||.||+|||+|+|++++++.++
T Consensus 295 ~~~nAkfFVIKSySEDdVHkSIKY~vWsST~~GNKkLdaAYreak~~~~~cPvfLfFSVNaSGqFCGvAEMvgPVdfn~~ 374 (487)
T KOG1901|consen 295 DYSNAKFFVIKSYSEDDVHKSIKYNVWSSTLNGNKKLDAAYREAKKKSGKCPVFLFFSVNASGQFCGVAEMVGPVDFNKD 374 (487)
T ss_pred ccccceEEEEeccChhhhhhhcccceeecccCCchhhHHHHHHhhhccCCCCceEEEEEcCCccccceeeeccceecccc
Confidence 46799999999999999999999999999999999999999963 489999999999999999999999999985
Q ss_pred -ccccCCCCCCCCCCCceEEEEEEeecCCCCccccccCCCCCCCCeeeCCCCcccChHHHHHHHHHhcCCCCcccccccc
Q 015740 141 -NVWSQGNGKNNPWGRSFKVKWLRLNTLPFQKTLHLKNPLNDYKPVKISRDCQELPQDIGEALCHLLDGKDDVDGIQTSF 219 (401)
Q Consensus 141 -~iW~~~~g~~~~wgg~FkVeWL~v~dLPF~~t~HLkNPlNeNKPVk~sRDGQEIepeiG~qLckLF~~~~~~~s~~~sf 219 (401)
.+|++ ++|.|.|+|+|+.|+|||+..++||+.+.||||||+++||+|||..+.|.++|+||......+++|+||
T Consensus 375 ~~~WqQ-----DKW~G~FpVKWhiVKDVPNs~lrHI~LeNNeNKPVTnSRDTQEV~leqGievlkIfk~y~~~TSiLDDf 449 (487)
T KOG1901|consen 375 MEYWQQ-----DKWSGSFPVKWHIVKDVPNSQLRHIILENNENKPVTNSRDTQEVPLEQGIEVLKIFKSYAAKTSILDDF 449 (487)
T ss_pred cchhhh-----cccceecceeeEEEeeCCccceeEEEeecCCCCCcccccccceecHHHHHHHHHHHHhhcceeeecccc
Confidence 89998 599999999999999999999999999999999999999999999999999999999999999999988
Q ss_pred cc
Q 015740 220 HR 221 (401)
Q Consensus 220 ~~ 221 (401)
..
T Consensus 450 ~~ 451 (487)
T KOG1901|consen 450 GF 451 (487)
T ss_pred cc
Confidence 75
No 4
>PRK00809 hypothetical protein; Provisional
Probab=96.78 E-value=0.016 Score=52.29 Aligned_cols=128 Identities=13% Similarity=0.236 Sum_probs=86.1
Q ss_pred eEEEEEeCChhHHHHHhhcCeeeeccCChHHHHHHHhcCCcEEEEEEec------CCCceeEEEEeeccCCCCCCccccC
Q 015740 72 RYFIIKSLNHQNIQLSIEKEIWATQVMNEPILEEAFHNSGKVILIFSVN------MSGFFQGYAQMMSSVGWRRDNVWSQ 145 (401)
Q Consensus 72 RFFIIKS~NeeNI~~Sik~GIWaTt~~NekkLneAFk~s~~VyLIFSVN------~SG~FqGyArM~S~id~~~~~iW~~ 145 (401)
+|+|+=+ |.+|+..++++|+|-.....-.-|.+ -+.+..+|||+-+ .-+.|.|.|++++..-...+.+|.+
T Consensus 2 ~yWi~~~-~~~~~~~~~~~gv~g~~~~~rn~lr~--Mk~GD~v~fYhs~~~~~~~~~~~ivgi~eV~~~~y~D~t~~~p~ 78 (144)
T PRK00809 2 TYWLCIT-NEDNWEVIKDKNVWGVPERYKNTIEK--VKPGDKLIIYVSQEYGAERLPGKIVGIYEVVSEWYEDSTPIFPA 78 (144)
T ss_pred ceEEEec-CHHHHHHHHhCCEeecchhhhhHHhh--CCCCCEEEEEECCccCCCCCCceEEEEEEEecCcccCCccCCCc
Confidence 6777765 99999999999999997654444444 4557888888877 5799999999998864444455532
Q ss_pred CC-CCCCCCCCceEEEEEEeec--CCCCcc----ccccCCCCCCCCe-eeCCCCcccChHHHHHHHH
Q 015740 146 GN-GKNNPWGRSFKVKWLRLNT--LPFQKT----LHLKNPLNDYKPV-KISRDCQELPQDIGEALCH 204 (401)
Q Consensus 146 ~~-g~~~~wgg~FkVeWL~v~d--LPF~~t----~HLkNPlNeNKPV-k~sRDGQEIepeiG~qLck 204 (401)
.. ....++--..+|+++...+ ||+..+ .-|+|.-.=...+ ..++ .||+.+-.+.|++
T Consensus 79 ~~~~~~~~~p~rvdV~~~~~~~~~v~l~~L~~~L~fik~~~~w~~~l~R~~~--~~I~~~d~~~I~~ 143 (144)
T PRK00809 79 EPVRPKEIYPYRVKLKPVKIFEEPIDFKPLIPKLKFIENKKQWSGHLRNRAM--RPIPEEDYKLIEE 143 (144)
T ss_pred cccCCCCCceEEEEEEEeeecCCcccHHHHHhhhhhhhcccccchhhhcCCC--ccCCHHHHHHHhc
Confidence 11 1123444678999998888 777765 2224432211333 5566 8888877766653
No 5
>PF01878 EVE: EVE domain; InterPro: IPR002740 The EVE domain is part of the wider PUA domain superfamily. The function of this domain is not known but, given the structural similarities to PUA, is likely to involve RNA binding []. ; PDB: 2G2X_B 2AR1_A 3EOP_A 2EVE_A 2HD9_A 2ZBN_A 1WMM_A 2P5D_A 2GBS_A 1ZCE_A.
Probab=86.71 E-value=1.3 Score=38.75 Aligned_cols=127 Identities=12% Similarity=0.206 Sum_probs=62.4
Q ss_pred eEEEEEeC----ChhHH---HHHhhcCeeeeccCChHHHHHHHhcCCcEEEEEEec-CCCceeEEEEeeccCCCCCCcc-
Q 015740 72 RYFIIKSL----NHQNI---QLSIEKEIWATQVMNEPILEEAFHNSGKVILIFSVN-MSGFFQGYAQMMSSVGWRRDNV- 142 (401)
Q Consensus 72 RFFIIKS~----NeeNI---~~Sik~GIWaTt~~NekkLneAFk~s~~VyLIFSVN-~SG~FqGyArM~S~id~~~~~i- 142 (401)
+|+|+|+. ..+++ ......|+|-.+..+ ..+..+. +.-+|||.-+ +.+.|.|.|++++..-......
T Consensus 1 ~YWl~~~~P~~~~~~~~~~~~~~~~~gv~~~~~~~---~l~~mk~-GD~vifY~s~~~~~~ivai~~V~~~~~~d~~~~~ 76 (143)
T PF01878_consen 1 RYWLLKANPENFSIDDLEHWGVTVWDGVRNYQARK---NLKRMKP-GDKVIFYHSGCKERGIVAIGEVVSEPYPDPTAFD 76 (143)
T ss_dssp -EEEEEEBTTTSHHHHHHHHSEEECHTEEEHHHHH---HHHC--T-T-EEEEEETSSSS-EEEEEEEEEEEEEE-GGGTS
T ss_pred CEEEEEeCCcccCHHHhcccceEEEcCEeehhhhh---hhhcCCC-CCEEEEEEcCCCCCEEEEEEEEeccccCCCcccc
Confidence 69999987 65555 223334444433332 2223333 4555666555 6799999999998753322211
Q ss_pred ----ccCCCCCCCCCCCceEEEEEEeec--CCCCccccccCCCCCCCCeeeCC-CCcccChHHHHHHHHH
Q 015740 143 ----WSQGNGKNNPWGRSFKVKWLRLNT--LPFQKTLHLKNPLNDYKPVKISR-DCQELPQDIGEALCHL 205 (401)
Q Consensus 143 ----W~~~~g~~~~wgg~FkVeWL~v~d--LPF~~t~HLkNPlNeNKPVk~sR-DGQEIepeiG~qLckL 205 (401)
|-.. .........+|+++..-+ |+...++.. ..+.+..-++..| --.+|+++.-..|++|
T Consensus 77 ~~~~~~~~--~~~~~~~~v~v~~~~~~~~pi~l~~Lk~~-~~l~~l~~i~~~r~s~~~it~~~~~~I~~~ 143 (143)
T PF01878_consen 77 PDSPYYDP--KSNPKPYRVDVEYVKIFEKPIPLKELKAE-PELENLSFIRNKRLSVFPITEEDFEAIMEM 143 (143)
T ss_dssp TTSTTBTT--TSCSSSEEEEEEEEEEEEEEEEHHHHHC--GGGTTSHHHHTTT-SEEEE-HHHHHHHHHH
T ss_pred ccccCcCC--ccCCCeeEEEEEEEEecCCCcCHHHHhcC-CccccChhhhcCCcCeEEECHHHHHHHHhC
Confidence 1111 011234568888887544 444555321 0011112222222 2356777777777764
No 6
>PRK02268 hypothetical protein; Provisional
Probab=64.89 E-value=65 Score=29.57 Aligned_cols=124 Identities=12% Similarity=0.097 Sum_probs=80.8
Q ss_pred eEEEEEeCChhHHHHHhhcCeeeeccCChHHHHHHHhcCCcEEEEEEe-------cCCCceeEEEEeeccCCCCCCcccc
Q 015740 72 RYFIIKSLNHQNIQLSIEKEIWATQVMNEPILEEAFHNSGKVILIFSV-------NMSGFFQGYAQMMSSVGWRRDNVWS 144 (401)
Q Consensus 72 RFFIIKS~NeeNI~~Sik~GIWaTt~~NekkLneAFk~s~~VyLIFSV-------N~SG~FqGyArM~S~id~~~~~iW~ 144 (401)
+|.|. ..+.+|+...++.|+|-.--....-|.+- +.+.-+|+||= ..=..|-|++++++.--++.. ..
T Consensus 3 ~yWI~-v~s~~hv~~g~~~gf~qv~hgK~apl~Rm--kpGD~ivyYsp~~~~~~~~~~qaftAig~V~~~~~Yq~~--m~ 77 (141)
T PRK02268 3 RYWIG-VVSAEHVRRGVEGGFMQVCHGKAAPLRRM--KPGDWIIYYSPKTTFGGKDKLQAFTAIGKVKDDEPYQVE--MA 77 (141)
T ss_pred ceEEE-EccHHHHHHHHhCCEEEeCCCccchhhcC--CCCCEEEEEeceEecCCCcccceEEEEEEEcCCceEecc--cC
Confidence 56654 37899999999999998754444444442 34577777872 245789999999876222211 00
Q ss_pred CCCCCCCCCCCceEEEEEEeecCCCCcc----ccccCCCCCCCCeeeCCCC-cccChHHHHHHHHHhcC
Q 015740 145 QGNGKNNPWGRSFKVKWLRLNTLPFQKT----LHLKNPLNDYKPVKISRDC-QELPQDIGEALCHLLDG 208 (401)
Q Consensus 145 ~~~g~~~~wgg~FkVeWL~v~dLPF~~t----~HLkNPlNeNKPVk~sRDG-QEIepeiG~qLckLF~~ 208 (401)
.....-..+|+|+...++|++.+ ..++|.-+=.... |=| -||+.+-.+.|.+.+..
T Consensus 78 -----~~f~P~Rr~v~~~~~~e~pi~pLi~~L~Fi~~k~~Wg~~f---r~g~~eI~e~Df~~I~~am~~ 138 (141)
T PRK02268 78 -----PGFIPWRRDVDYYPCAETPIRPLLDHLDFTEDRKNWGYQF---RFGHFEISKHDFETIASAMTV 138 (141)
T ss_pred -----CCceeEEEEeeEeecCccchHHhhcccceeeCcchhhHhh---cCCcEecCHHHHHHHHHHhcc
Confidence 11222367899999999999854 6666654433333 334 78888877777777654
No 7
>PF06199 Phage_tail_2: Phage major tail protein 2; InterPro: IPR011855 This entry describes the major tail protein (MTP) of the Siphoviridae and MTP genes in prophage regions of bacterial genomes. Homologues are also found in Gene Transfer Agents (GTA) [], including ORFg9 (RCAP_rcc01691) of the GTA of Rhodobacter capsulatus (Rhodopseudomonas capsulata) [see Fig.1, in ].
Probab=30.73 E-value=1.1e+02 Score=26.16 Aligned_cols=43 Identities=21% Similarity=0.228 Sum_probs=35.6
Q ss_pred CeeeeccCChHHHHHHHhcCCcEEEEEEecCCCceeEEEEeec
Q 015740 91 EIWATQVMNEPILEEAFHNSGKVILIFSVNMSGFFQGYAQMMS 133 (401)
Q Consensus 91 GIWaTt~~NekkLneAFk~s~~VyLIFSVN~SG~FqGyArM~S 133 (401)
|+|.........|.+||.+...|.+-+.+...+.|.|.+-+++
T Consensus 67 g~~~~~d~~~~~l~~a~~~~~~~~~~v~~~~~~~~~g~~~vts 109 (134)
T PF06199_consen 67 GLFDPDDASYDALEDAFDNGEPVEWRVTKPDGGKYEGKFFVTS 109 (134)
T ss_pred EEEecCchHHHHHHHHHHCCCcEEEEEEECCCCEEEEEEEEEE
Confidence 4555555677899999999999888888889999999999775
No 8
>PF00076 RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....
Probab=22.49 E-value=2.8e+02 Score=19.83 Aligned_cols=35 Identities=31% Similarity=0.391 Sum_probs=25.9
Q ss_pred CChHHHHHHHhcCCcE-EEEEEecCCCceeEEEEee
Q 015740 98 MNEPILEEAFHNSGKV-ILIFSVNMSGFFQGYAQMM 132 (401)
Q Consensus 98 ~NekkLneAFk~s~~V-yLIFSVN~SG~FqGyArM~ 132 (401)
-.++.|.++|...+.| .+.+..+.++...|||-+.
T Consensus 10 ~t~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~a~V~ 45 (70)
T PF00076_consen 10 VTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVE 45 (70)
T ss_dssp SSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEE
T ss_pred CCHHHHHHHHHHhhhcccccccccccccccceEEEE
Confidence 3567899999998877 4444445889999998765
No 9
>PF15343 DEPP: Decidual protein induced by progesterone family
Probab=20.09 E-value=72 Score=30.77 Aligned_cols=16 Identities=44% Similarity=0.578 Sum_probs=13.6
Q ss_pred HHHHHHHHHHhcCCCC
Q 015740 347 LEAHSRSIKQLCHPVG 362 (401)
Q Consensus 347 ~~~~~~~~~~l~~~~~ 362 (401)
|++|+|+|.||--|.+
T Consensus 13 LdDYvrSIcqLAQPTs 28 (188)
T PF15343_consen 13 LDDYVRSICQLAQPTS 28 (188)
T ss_pred HHHHHHHHHHHcCCCc
Confidence 6788999999977776
No 10
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=12.58 E-value=1.9e+02 Score=26.95 Aligned_cols=49 Identities=31% Similarity=0.508 Sum_probs=36.4
Q ss_pred ccceeeeeccCCCCCcccccccc-Cccc-cccccCCCCCccccCCcchhhhhcHHHHHHHHHHHHHHhcC
Q 015740 292 SKFSRIYHSRKGNLSNLQVDCDL-SSRY-DFWGLSADSPLASTITEDDFLEMSYEEYLEAHSRSIKQLCH 359 (401)
Q Consensus 292 ~~~~~~~~~~~~~~~~~~~~~~~-~~~~-~~w~~~~~sp~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ 359 (401)
-++.+|||- |.++.+| +..| +-|+|++|-| |++..|-++-|+--|++|+
T Consensus 84 kkfKSLKRH-------L~t~~gmTPd~YR~KW~LP~dYP------------MvAPnYAa~RS~LAK~mGL 134 (148)
T COG4957 84 KKFKSLKRH-------LTTHYGLTPDEYRAKWGLPPDYP------------MVAPNYAAARSQLAKAMGL 134 (148)
T ss_pred cchHHHHHH-------HhcccCCCHHHHHHhcCCCCCCC------------ccchHHHHHHHHHHHHhCc
Confidence 445555543 3455666 4444 5699999988 8899999999999999885
Done!