Query 018178
Match_columns 360
No_of_seqs 123 out of 325
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 06:48:00 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018178.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018178hhsearch_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 1.5E-71 3.3E-76 540.6 15.4 318 1-347 1-321 (441)
2 PF04146 YTH: YT521-B-like dom 100.0 9.4E-52 2E-56 359.2 9.9 139 70-209 1-140 (140)
3 KOG1901 Uncharacterized high-g 100.0 1.6E-42 3.4E-47 351.2 10.5 149 68-221 296-451 (487)
4 PRK00809 hypothetical protein; 96.8 0.015 3.1E-07 51.9 10.5 128 72-204 2-143 (144)
5 PF01878 EVE: EVE domain; Int 85.5 1.7 3.6E-05 37.6 5.1 127 72-205 1-143 (143)
6 PRK02268 hypothetical protein; 73.7 37 0.0008 30.7 9.7 125 71-208 2-138 (141)
7 PF06199 Phage_tail_2: Phage m 31.1 1.1E+02 0.0024 25.7 5.1 43 91-133 67-109 (134)
8 PF00076 RRM_1: RNA recognitio 26.4 2.2E+02 0.0048 20.1 5.3 35 98-132 10-45 (70)
9 PF02407 Viral_Rep: Putative v 14.8 1.2E+02 0.0026 25.0 1.9 44 93-136 4-55 (86)
10 PF03439 Spt5-NGN: Early trans 9.7 5.2E+02 0.011 20.7 4.2 49 72-133 1-51 (84)
No 1
>KOG1902 consensus Putative signal transduction protein involved in RNA splicing [Signal transduction mechanisms; RNA processing and modification]
Probab=100.00 E-value=1.5e-71 Score=540.56 Aligned_cols=318 Identities=33% Similarity=0.416 Sum_probs=287.8
Q ss_pred CCcccccccceeecCceee-ecCCCCCCCCCCccCCCCCCCCcchhhhhhcCCCCCcCCCCccc-cCCCCCcceEEEEEe
Q 018178 1 MSSDTAKENASVVDSSVTE-KHDVGNSDDPESSSYKANEHRCPSLAKEAKAGHSNGQLENSTDN-NKGKLYNTRYFIIKS 78 (360)
Q Consensus 1 ~~~~~~~~~~~~~~~~v~~-~~~~~~~d~p~s~~y~~~~~~~~~~~~~~~~~~~~~q~~n~~~~-~~~~~~~aRFFIIKS 78 (360)
|.+||++|++++++.++|. ..+.+++++|++..|+..++.-+..++.++ +.+..|...-... .......+|||||||
T Consensus 1 ~~~dt~~~~~~~~~~~~t~~~q~l~~~~~~~~~~~rk~e~~~~~~v~~~~-~~s~~q~~s~~~~~ss~~~~~~rYFIiKS 79 (441)
T KOG1902|consen 1 NDYDTRSEASDSGSESVSFTDGSVRSGSGTDGSDEKKKERKRARGISPIS-GSSASESYADQTSKLKYVLQDARYFIIKS 79 (441)
T ss_pred CcccchhhhhhhcccccchhhhhhccCCCCCCCcccccccccccCCCccc-ccCccccchhhcccccccCCceEEEEEec
Confidence 6899999999999999999 999999999999999999999999988884 4777777543333 333578999999999
Q ss_pred CChhhHHHHhhcCeeeeccCChHHHHHHHhcCCcEEEEEEecCCCceeEEEEeeccCCCCCCc-cccCCCCCCCCCCCce
Q 018178 79 LNHQNIQLSIEKEIWATQVMNEPILEEAFHNSGKVILIFSVNMSGFFQGYAQMMSSVGWRRDN-VWSQGNGKNNPWGRSF 157 (360)
Q Consensus 79 ~n~eNI~~Sik~GIWaTt~~NekkLn~AFk~s~~VyLIFSVN~Sg~FqGyArM~S~i~~~~~~-~W~~~~g~~~~wgg~F 157 (360)
+|++||.+|+++|||+||+.||++||.||+++..||||||||+||||||||+|+|+|++.+++ +|.++.|.++.||++|
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 999999999999999999999999999999999999999999999999999999999999986 8999888789999999
Q ss_pred eeEEEEeeeCCCCcccCccCCCCCCCCeeeCCCCcccChhHHHHHHHHhcCCCCccccccccccCCCCCCCCCCCCCCCC
Q 018178 158 KVKWLRLNTLPFQKTLHLKNPLNDYKPVKISRDCQELPQDIGEALCHLLDGKDDVDGIQTSFHRDDLPAKRPCIEPSCSL 237 (360)
Q Consensus 158 ~VeWL~v~dLPF~~~~HLrNplNenKPVk~sRDGQEIe~e~G~qLckLF~~~~~~~~l~~sf~~~~~~~~r~~~~~~~~~ 237 (360)
+|+||++++|||+++.||+|||||||||+|+||||||++++|+|||.||+..++.+ +++.-++++.+.++-+. | -
T Consensus 160 kVkWiRl~eLpFqkt~hL~NP~NdnkpVKISRD~QELep~VGEqL~~Ll~~~p~~e-l~~~s~~~~~kr~~~~A--p--~ 234 (441)
T KOG1902|consen 160 KVKWIRLRELPFQKTAHLTNPWNENKPVKISRDGQELEPEVGEQLCLLLPPDPSID-LYQVSHKMRHKRRMHSA--P--R 234 (441)
T ss_pred eEeEEeeccccchhhhhcCCcccccCceeecccccccChhHHHHHHHhcCCCcchh-hhhhhHHHHHhhhhhcC--C--c
Confidence 99999999999999999999999999999999999999999999999999999999 66766777777776666 4 4
Q ss_pred CCcccCCCCCcccCCCCCCCCCccccccCCCCCchhhhhccCCCCcccccCCCCccccceeeccCCCCCccccccCCCCC
Q 018178 238 GDEEYHKPPLHVPLGKTPMPYPSFLYQHQGGPSNFHLAQRCGGDAENLPFTSMSSKFSRIYHSRKGNLSNLQVDCDLSSR 317 (360)
Q Consensus 238 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 317 (360)
|+.| ||+++||.|++..|.++....+|| ++-+|.+++++++++++++ ++..+|..-|
T Consensus 235 sr~E--------p~~~~p~~~~~~~~ped~d~~~~~-~~p~G~~p~~~h~~Pg~~~--------------~~r~q~~~~r 291 (441)
T KOG1902|consen 235 SRGE--------PSRREPVRDVGRRRPEDYDIHNSR-KKPRGDYPPEFHQRPGYLK--------------DPRYQEVDRR 291 (441)
T ss_pred cCCC--------cccCCcccCccccCcccchhhhhh-hCCCCCCCcccccCCCcCC--------------Cccccccccc
Confidence 4544 999999999999999999999999 3455666999999999887 6777899999
Q ss_pred ccccccCCCCCCccCCCccccceeeeehhc
Q 018178 318 YDFWGLSADSPLASTITEDDFLEMVLVPVF 347 (360)
Q Consensus 318 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 347 (360)
+.-|+|.-++|++..+|.+||++|.--|+.
T Consensus 292 f~g~~L~v~~Pg~~~~y~~~f~nm~p~p~~ 321 (441)
T KOG1902|consen 292 FSGVRLDVFLPGSYNDYVREFHNMGPPPPW 321 (441)
T ss_pred cCceecccccCcccccccchhhhcCCCccc
Confidence 999999999999999999999999765553
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=9.4e-52 Score=359.25 Aligned_cols=139 Identities=53% Similarity=0.888 Sum_probs=115.3
Q ss_pred cceEEEEEeCChhhHHHHhhcCeeeeccCChHHHHHHHhcCCcEEEEEEecCCCceeEEEEeeccCCCCC-CccccCCCC
Q 018178 70 NTRYFIIKSLNHQNIQLSIEKEIWATQVMNEPILEEAFHNSGKVILIFSVNMSGFFQGYAQMMSSVGWRR-DNVWSQGNG 148 (360)
Q Consensus 70 ~aRFFIIKS~n~eNI~~Sik~GIWaTt~~NekkLn~AFk~s~~VyLIFSVN~Sg~FqGyArM~S~i~~~~-~~~W~~~~g 148 (360)
++|||||||+|++||++|+++|||+|+++|+++|++||+++++||||||||+||+|||||+|+|+++... ...|..+.
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 NARFFIIKSFNEENIHLSIKYGVWATQPKNEKKLNEAFKESRNVYLFFSVNGSGHFQGYARMTSPIDPDSPKPFWQQDS- 79 (140)
T ss_dssp --EEEEEEESSCHHHHHHHHCTEEE--CCCHHHHHHHHHHSS-EEEEEEETTTSEEEEEEEEECECCSSS------SS--
T ss_pred CcEEEEEEECCHHHHHHHHhCCEEcccccchHHHHHHHHhCCCEEEEEeecCcceEEEEEEEccCCCCcccCccccccc-
Confidence 5899999999999999999999999999999999999999999999999999999999999999998885 47795431
Q ss_pred CCCCCCCceeeEEEEeeeCCCCcccCccCCCCCCCCeeeCCCCcccChhHHHHHHHHhcCC
Q 018178 149 KNNPWGRSFKVKWLRLNTLPFQKTLHLKNPLNDYKPVKISRDCQELPQDIGEALCHLLDGK 209 (360)
Q Consensus 149 ~~~~wgg~F~VeWL~v~dLPF~~~~HLrNplNenKPVk~sRDGQEIe~e~G~qLckLF~~~ 209 (360)
...+|+|.|+|+||++++|||+.++||+||+|+||||+++||||||++++|++||+||+++
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 2369999999999999999999999999999999999999999999999999999999863
No 3
>KOG1901 consensus Uncharacterized high-glucose-regulated protein [General function prediction only]
Probab=100.00 E-value=1.6e-42 Score=351.18 Aligned_cols=149 Identities=32% Similarity=0.577 Sum_probs=143.9
Q ss_pred CCcceEEEEEeCChhhHHHHhhcCeeeeccCChHHHHHHHhc------CCcEEEEEEecCCCceeEEEEeeccCCCCCC-
Q 018178 68 LYNTRYFIIKSLNHQNIQLSIEKEIWATQVMNEPILEEAFHN------SGKVILIFSVNMSGFFQGYAQMMSSVGWRRD- 140 (360)
Q Consensus 68 ~~~aRFFIIKS~n~eNI~~Sik~GIWaTt~~NekkLn~AFk~------s~~VyLIFSVN~Sg~FqGyArM~S~i~~~~~- 140 (360)
..++|||||||++++|||+||+|+|||+|.++|++|+.||++ .++||||||||.||+|||+|+|++++++.++
T Consensus 296 ~~nAkfFVIKSySEDdVHkSIKY~vWsST~~GNKkLdaAYreak~~~~~cPvfLfFSVNaSGqFCGvAEMvgPVdfn~~~ 375 (487)
T KOG1901|consen 296 YSNAKFFVIKSYSEDDVHKSIKYNVWSSTLNGNKKLDAAYREAKKKSGKCPVFLFFSVNASGQFCGVAEMVGPVDFNKDM 375 (487)
T ss_pred cccceEEEEeccChhhhhhhcccceeecccCCchhhHHHHHHhhhccCCCCceEEEEEcCCccccceeeeccceeccccc
Confidence 569999999999999999999999999999999999999986 3589999999999999999999999999986
Q ss_pred ccccCCCCCCCCCCCceeeEEEEeeeCCCCcccCccCCCCCCCCeeeCCCCcccChhHHHHHHHHhcCCCCccccccccc
Q 018178 141 NVWSQGNGKNNPWGRSFKVKWLRLNTLPFQKTLHLKNPLNDYKPVKISRDCQELPQDIGEALCHLLDGKDDVDGIQTSFH 220 (360)
Q Consensus 141 ~~W~~~~g~~~~wgg~F~VeWL~v~dLPF~~~~HLrNplNenKPVk~sRDGQEIe~e~G~qLckLF~~~~~~~~l~~sf~ 220 (360)
.+|+++ +|.|.|.|+|+.|+|||+..++||+.+.||||||+.+||+|||..+.|.++|+||..+...++||+||.
T Consensus 376 ~~WqQD-----KW~G~FpVKWhiVKDVPNs~lrHI~LeNNeNKPVTnSRDTQEV~leqGievlkIfk~y~~~TSiLDDf~ 450 (487)
T KOG1901|consen 376 EYWQQD-----KWSGSFPVKWHIVKDVPNSQLRHIILENNENKPVTNSRDTQEVPLEQGIEVLKIFKSYAAKTSILDDFG 450 (487)
T ss_pred chhhhc-----ccceecceeeEEEeeCCccceeEEEeecCCCCCcccccccceecHHHHHHHHHHHHhhcceeeeccccc
Confidence 799985 999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred c
Q 018178 221 R 221 (360)
Q Consensus 221 ~ 221 (360)
-
T Consensus 451 ~ 451 (487)
T KOG1901|consen 451 F 451 (487)
T ss_pred c
Confidence 4
No 4
>PRK00809 hypothetical protein; Provisional
Probab=96.79 E-value=0.015 Score=51.87 Aligned_cols=128 Identities=13% Similarity=0.236 Sum_probs=86.5
Q ss_pred eEEEEEeCChhhHHHHhhcCeeeeccCChHHHHHHHhcCCcEEEEEEec------CCCceeEEEEeeccCCCCCCccccC
Q 018178 72 RYFIIKSLNHQNIQLSIEKEIWATQVMNEPILEEAFHNSGKVILIFSVN------MSGFFQGYAQMMSSVGWRRDNVWSQ 145 (360)
Q Consensus 72 RFFIIKS~n~eNI~~Sik~GIWaTt~~NekkLn~AFk~s~~VyLIFSVN------~Sg~FqGyArM~S~i~~~~~~~W~~ 145 (360)
+|.|+=+ +.+|+..++++|+|......-.-|.+ -+.+..+|||+-+ .-+.|.|.|++++..-...+.+|.+
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 6777777 89999999999999997665555554 4567888888887 5799999999998764444455532
Q ss_pred CC-CCCCCCCCceeeEEEEeee--CCCCcc----cCccCCCCCCCCe-eeCCCCcccChhHHHHHHH
Q 018178 146 GN-GKNNPWGRSFKVKWLRLNT--LPFQKT----LHLKNPLNDYKPV-KISRDCQELPQDIGEALCH 204 (360)
Q Consensus 146 ~~-g~~~~wgg~F~VeWL~v~d--LPF~~~----~HLrNplNenKPV-k~sRDGQEIe~e~G~qLck 204 (360)
.. ....++--..+|+++...+ ||++.+ .-|+|.-.=...+ ..++ .||+.+-.+.|++
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 10 0113444678899998888 777765 2224431111333 5666 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=85.51 E-value=1.7 Score=37.58 Aligned_cols=127 Identities=10% Similarity=0.182 Sum_probs=62.1
Q ss_pred eEEEEEeC----ChhhH---HHHhhcCeeeeccCChHHHHHHHhcCCcEEEEEEec-CCCceeEEEEeeccCCCCCCcc-
Q 018178 72 RYFIIKSL----NHQNI---QLSIEKEIWATQVMNEPILEEAFHNSGKVILIFSVN-MSGFFQGYAQMMSSVGWRRDNV- 142 (360)
Q Consensus 72 RFFIIKS~----n~eNI---~~Sik~GIWaTt~~NekkLn~AFk~s~~VyLIFSVN-~Sg~FqGyArM~S~i~~~~~~~- 142 (360)
+|+|+|+. ..+++ ......|+|-.+..+ ..+..+. +.-+|||.-+ +.+.|.|.|++++.........
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 69999997 54444 233344455444322 2223333 5566666666 6799999999998753322221
Q ss_pred ----ccCCCCCCCCCCCceeeEEEEeee--CCCCcccCccCCCCCCCCeeeC-CCCcccChhHHHHHHHH
Q 018178 143 ----WSQGNGKNNPWGRSFKVKWLRLNT--LPFQKTLHLKNPLNDYKPVKIS-RDCQELPQDIGEALCHL 205 (360)
Q Consensus 143 ----W~~~~g~~~~wgg~F~VeWL~v~d--LPF~~~~HLrNplNenKPVk~s-RDGQEIe~e~G~qLckL 205 (360)
|-... .+......+|+++..-+ |+...++.. ..+.+..-++.. .--.+|+++.-..|++|
T Consensus 77 ~~~~~~~~~--~~~~~~~v~v~~~~~~~~pi~l~~Lk~~-~~l~~l~~i~~~r~s~~~it~~~~~~I~~~ 143 (143)
T PF01878_consen 77 PDSPYYDPK--SNPKPYRVDVEYVKIFEKPIPLKELKAE-PELENLSFIRNKRLSVFPITEEDFEAIMEM 143 (143)
T ss_dssp TTSTTBTTT--SCSSSEEEEEEEEEEEEEEEEHHHHHC--GGGTTSHHHHTTT-SEEEE-HHHHHHHHHH
T ss_pred ccccCcCCc--cCCCeeEEEEEEEEecCCCcCHHHHhcC-CccccChhhhcCCcCeEEECHHHHHHHHhC
Confidence 11110 11234567888887555 444555321 001111222222 22356777777777664
No 6
>PRK02268 hypothetical protein; Provisional
Probab=73.71 E-value=37 Score=30.66 Aligned_cols=125 Identities=12% Similarity=0.087 Sum_probs=82.4
Q ss_pred ceEEEEEeCChhhHHHHhhcCeeeeccCChHHHHHHHhcCCcEEEEEEe-------cCCCceeEEEEeeccCCCCCCccc
Q 018178 71 TRYFIIKSLNHQNIQLSIEKEIWATQVMNEPILEEAFHNSGKVILIFSV-------NMSGFFQGYAQMMSSVGWRRDNVW 143 (360)
Q Consensus 71 aRFFIIKS~n~eNI~~Sik~GIWaTt~~NekkLn~AFk~s~~VyLIFSV-------N~Sg~FqGyArM~S~i~~~~~~~W 143 (360)
.+|.|.=. +.+|+...++.|+|-+--....-|.+- +.+.-+++||= ..=..|-|.+++++.--++.. .
T Consensus 2 ~~yWI~v~-s~~hv~~g~~~gf~qv~hgK~apl~Rm--kpGD~ivyYsp~~~~~~~~~~qaftAig~V~~~~~Yq~~--m 76 (141)
T PRK02268 2 MRYWIGVV-SAEHVRRGVEGGFMQVCHGKAAPLRRM--KPGDWIIYYSPKTTFGGKDKLQAFTAIGKVKDDEPYQVE--M 76 (141)
T ss_pred cceEEEEc-cHHHHHHHHhCCEEEeCCCccchhhcC--CCCCEEEEEeceEecCCCcccceEEEEEEEcCCceEecc--c
Confidence 35666555 799999999999998864444444442 34677888882 245789999999876322211 0
Q ss_pred cCCCCCCCCCCCceeeEEEEeeeCCCCcc----cCccCCCCCCCCeeeCCCC-cccChhHHHHHHHHhcC
Q 018178 144 SQGNGKNNPWGRSFKVKWLRLNTLPFQKT----LHLKNPLNDYKPVKISRDC-QELPQDIGEALCHLLDG 208 (360)
Q Consensus 144 ~~~~g~~~~wgg~F~VeWL~v~dLPF~~~----~HLrNplNenKPVk~sRDG-QEIe~e~G~qLckLF~~ 208 (360)
.. ....-..+|+|+...++|++.+ +.++|+-+=.... |=| -||+.+-.+.+.+.+..
T Consensus 77 ~~-----~f~P~Rr~v~~~~~~e~pi~pLi~~L~Fi~~k~~Wg~~f---r~g~~eI~e~Df~~I~~am~~ 138 (141)
T PRK02268 77 AP-----GFIPWRRDVDYYPCAETPIRPLLDHLDFTEDRKNWGYQF---RFGHFEISKHDFETIASAMTV 138 (141)
T ss_pred CC-----CceeEEEEeeEeecCccchHHhhcccceeeCcchhhHhh---cCCcEecCHHHHHHHHHHhcc
Confidence 00 1222357899999999999854 6677754433333 334 78988888888777654
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=31.07 E-value=1.1e+02 Score=25.74 Aligned_cols=43 Identities=21% Similarity=0.228 Sum_probs=35.7
Q ss_pred CeeeeccCChHHHHHHHhcCCcEEEEEEecCCCceeEEEEeec
Q 018178 91 EIWATQVMNEPILEEAFHNSGKVILIFSVNMSGFFQGYAQMMS 133 (360)
Q Consensus 91 GIWaTt~~NekkLn~AFk~s~~VyLIFSVN~Sg~FqGyArM~S 133 (360)
|+|.........|.+||.+...|.+-+.+...+.|.|.+-+++
T Consensus 67 g~~~~~d~~~~~l~~a~~~~~~~~~~v~~~~~~~~~g~~~vts 109 (134)
T PF06199_consen 67 GLFDPDDASYDALEDAFDNGEPVEWRVTKPDGGKYEGKFFVTS 109 (134)
T ss_pred EEEecCchHHHHHHHHHHCCCcEEEEEEECCCCEEEEEEEEEE
Confidence 4565556677899999999999988888888899999999775
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=26.37 E-value=2.2e+02 Score=20.05 Aligned_cols=35 Identities=31% Similarity=0.391 Sum_probs=26.1
Q ss_pred CChHHHHHHHhcCCcE-EEEEEecCCCceeEEEEee
Q 018178 98 MNEPILEEAFHNSGKV-ILIFSVNMSGFFQGYAQMM 132 (360)
Q Consensus 98 ~NekkLn~AFk~s~~V-yLIFSVN~Sg~FqGyArM~ 132 (360)
-.++.|.++|...+.| .+.+..+.+++..|||-+.
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 3568899999998877 3444444789999998764
No 9
>PF02407 Viral_Rep: Putative viral replication protein; InterPro: IPR003365 Proteins in this entry are essential for the replication of viral ssDNA. The closed circular ssDNA genome is first converted to a superhelical dsDNA. Rep and/or Rep' binds a specific hairpin at the genome origin of replication introducing an endonucleolytic nick within the conserved sequence 5'-AGTATTAC-3'. This initiates rolling circle replication (RCR). Following cleavage, the protein binds covalently to the 5'-phosphate of DNA as a tyrosyl ester. The cleavage gives rise to a free 3'-OH that serves as a primer for the cellular DNA polymerase. The polymerase synthesizes the (+) strand DNA by rolling circle mechanism. After one round of replication, a Rep-catalyzed nucleotidyl transfer reaction releases a circular single-stranded virus genome, thereby terminating the replication.; GO: 0016779 nucleotidyltransferase activity, 0016888 endodeoxyribonuclease activity, producing 5'-phosphomonoesters, 0042624 ATPase activity, uncoupled, 0006260 DNA replication, 0018142 protein-DNA covalent cross-linking; PDB: 2HW0_A 2HWT_A.
Probab=14.78 E-value=1.2e+02 Score=24.98 Aligned_cols=44 Identities=18% Similarity=0.239 Sum_probs=27.2
Q ss_pred eeeccCChHH---HHHHHhcCCcEEEEEE--ec---CCCceeEEEEeeccCC
Q 018178 93 WATQVMNEPI---LEEAFHNSGKVILIFS--VN---MSGFFQGYAQMMSSVG 136 (360)
Q Consensus 93 WaTt~~Nekk---Ln~AFk~s~~VyLIFS--VN---~Sg~FqGyArM~S~i~ 136 (360)
|+.|-.|... +...+....-.|+++- +- +.-|+|||..+..+..
T Consensus 4 WcFTlNn~~~~~~~~~~~~~~~~~Y~i~~~E~g~~tGt~HlQgyv~~~~~~r 55 (86)
T PF02407_consen 4 WCFTLNNPTEEDEIISLLENEDVKYAIGQEEVGPSTGTPHLQGYVEFKNRKR 55 (86)
T ss_dssp EEEEEES--HHHHCCHTS-GCCECEEEEEEEE-STTSSEEEEEEEEESSSB-
T ss_pred EEEEEeCCCcchhhhhhhccccceEEEEEEeecCCCCCCcEEEEEEecCCcc
Confidence 6666555543 3333444566788887 33 7789999999987754
No 10
>PF03439 Spt5-NGN: Early transcription elongation factor of RNA pol II, NGN section; InterPro: IPR005100 Spt5p and prokaryotic NusG are shown to contain a novel 'NGN' domain. The combined NGN and KOW motif regions of Spt5 form the binding domain with Spt4 []. Spt5 complexes with Spt4 as a 1:1 heterodimer snf this Spt5-Spt4 complex regulates early transcription elongation by RNA polymerase II and has an imputed role in pre-mRNA processing via its physical association with mRNA capping enzymes. The Schizosaccharomyces pombe core Spt5-Spt4 complex is a heterodimer bearing a trypsin-resistant Spt4-binding domain within the Spt5 subunit []. ; PDB: 3H7H_B 3QQC_D 3P8B_B 2EXU_A.
Probab=9.74 E-value=5.2e+02 Score=20.67 Aligned_cols=49 Identities=16% Similarity=0.316 Sum_probs=27.1
Q ss_pred eEEEEEeC--ChhhHHHHhhcCeeeeccCChHHHHHHHhcCCcEEEEEEecCCCceeEEEEeec
Q 018178 72 RYFIIKSL--NHQNIQLSIEKEIWATQVMNEPILEEAFHNSGKVILIFSVNMSGFFQGYAQMMS 133 (360)
Q Consensus 72 RFFIIKS~--n~eNI~~Sik~GIWaTt~~NekkLn~AFk~s~~VyLIFSVN~Sg~FqGyArM~S 133 (360)
++|.+|+. .|.++..++.. +.++.+... + .-||||-...++.||--..+
T Consensus 1 ~iw~Vkc~~G~E~~v~~~l~~----------k~~~~~~~~--~-l~I~Si~~~~~lkGyIyVEA 51 (84)
T PF03439_consen 1 KIWAVKCKPGQEREVAISLMN----------KAEDLAKKN--N-LNIYSIFAPDSLKGYIYVEA 51 (84)
T ss_dssp EEEEEEE-TTTHHHHHHHHHH----------HHHHHHHHS--T-----EEEE-TTSTSEEEEEE
T ss_pred CEEEEEeCCChHHHHHHHHHH----------HHHHhhhcC--C-CceEEEEEeCCCceEEEEEe
Confidence 46667665 45666666543 333333333 3 88899999999999988765
Done!