Query psy8691
Match_columns 211
No_of_seqs 120 out of 322
Neff 4.7
Searched_HMMs 46136
Date Fri Aug 16 16:46:34 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8691.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8691hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04146 YTH: YT521-B-like dom 100.0 2.4E-44 5.2E-49 291.6 9.6 118 48-208 1-118 (140)
2 KOG1901|consensus 100.0 2.2E-42 4.7E-47 326.1 9.7 150 14-208 268-417 (487)
3 KOG1902|consensus 100.0 9.3E-41 2E-45 303.9 8.5 125 41-207 64-188 (441)
4 PRK00809 hypothetical protein; 96.4 0.035 7.5E-07 45.7 9.3 99 50-193 2-108 (144)
5 KOG1901|consensus 95.3 0.01 2.2E-07 57.7 2.2 96 90-200 299-401 (487)
6 PF01878 EVE: EVE domain; Int 87.3 1.3 2.9E-05 35.2 5.1 67 125-193 39-110 (143)
7 PF04146 YTH: YT521-B-like dom 69.4 4.6 0.0001 32.7 2.8 24 78-101 31-54 (140)
8 PRK02268 hypothetical protein; 51.9 49 0.0011 27.4 5.9 91 50-193 3-100 (141)
9 PF06199 Phage_tail_2: Phage m 51.1 40 0.00086 26.1 5.1 49 107-155 64-112 (134)
10 PF00076 RRM_1: RNA recognitio 47.6 69 0.0015 20.8 5.2 34 118-151 11-45 (70)
11 KOG1902|consensus 35.4 21 0.00046 34.2 1.5 28 87-114 69-96 (441)
No 1
>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=2.4e-44 Score=291.55 Aligned_cols=118 Identities=44% Similarity=0.752 Sum_probs=94.0
Q ss_pred cceEEEEecCChhhHHHHHHhCccccCchhHHHHHHHHHhccceEEEEecccccccccceeccccccCccchHHHHHHHh
Q psy8691 48 DARFFVIKSNNSENVDIAKSQGVWSTLPQNEQKLNQAYRESRDVLLIFSNYYVSNELNFKVYGVWSTLPQNEQKLNQAYR 127 (211)
Q Consensus 48 ~~rfFiIKS~~~~ni~~S~~~g~W~st~~~n~~L~~ay~~~~~~~~ifs~~~~~~~l~~i~~~vWaT~~~Ne~~L~~AF~ 127 (211)
++|||||||++++||++|+++|+|+|+++ |+++|++||+
T Consensus 1 ~~rfFiiKS~~~~ni~~s~~~gvW~t~~~-----------------------------------------~~~~L~~Af~ 39 (140)
T PF04146_consen 1 NARFFIIKSFNEENIHLSIKYGVWATQPK-----------------------------------------NEKKLNEAFK 39 (140)
T ss_dssp --EEEEEEESSCHHHHHHHHCTEEE--CC-----------------------------------------CHHHHHHHHH
T ss_pred CcEEEEEEECCHHHHHHHHhCCEEccccc-----------------------------------------chHHHHHHHH
Confidence 48999999999999999999988888887 7777777777
Q ss_pred cCCcEEEEEEECCCCceeEEEEeecCCCCCCCCccccCCCCCCCCccCCceeEEEEEeecCCcccccccccccCCCcccc
Q psy8691 128 ESRNVLLIFSVRESGKFSGFARLASEADHGVSPVKWVLPPGLSGKVLNGVFKIDWVSRKELPFTSTLHLYNSWNEGEWYN 207 (211)
Q Consensus 128 ~~~~V~LiFSVN~Sg~FqGyArM~S~~~~~~~~~~W~~~~g~~~~~~~g~F~I~Wl~~~dLPf~~~~HL~Np~NenkPV~ 207 (211)
++++||||||||+||+|||||+|+|+++.+.+...|... ....+|+|+|+|+||++++|||+.++||+||+|+|+||+
T Consensus 40 ~~~~V~L~FSvn~S~~F~G~A~M~s~~~~~~~~~~w~~~--~~~~~~~g~F~v~Wl~~~~lpf~~~~hl~n~~n~~~pV~ 117 (140)
T PF04146_consen 40 ESRNVYLFFSVNGSGHFQGYARMTSPIDPDSPKPFWQQD--SSSSKWGGPFRVEWLRVKDLPFSKLRHLRNPLNENKPVK 117 (140)
T ss_dssp HSS-EEEEEEETTTSEEEEEEEEECECCSSS------SS---SGCGG-SEEEEEEEE-S-EEHHHHTT-EETTTTTEETT
T ss_pred hCCCEEEEEeecCcceEEEEEEEccCCCCcccCcccccc--ccccccCCceEEEEEECCcCChHHhcccccccCCCcEEE
Confidence 789999999999999999999999999999888899532 235789999999999999999999999999999999998
Q ss_pred c
Q psy8691 208 S 208 (211)
Q Consensus 208 ~ 208 (211)
.
T Consensus 118 ~ 118 (140)
T PF04146_consen 118 I 118 (140)
T ss_dssp S
T ss_pred E
Confidence 5
No 2
>KOG1901|consensus
Probab=100.00 E-value=2.2e-42 Score=326.15 Aligned_cols=150 Identities=28% Similarity=0.474 Sum_probs=136.0
Q ss_pred hhhhcccccccccCCCCCCccCccchhccccCCCcceEEEEecCChhhHHHHHHhCccccCchhHHHHHHHHHhccceEE
Q psy8691 14 EVKKARSAEKVTARPEKPTIRTYDYITKINYLFRDARFFVIKSNNSENVDIAKSQGVWSTLPQNEQKLNQAYRESRDVLL 93 (211)
Q Consensus 14 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rfFiIKS~~~~ni~~S~~~g~W~st~~~n~~L~~ay~~~~~~~~ 93 (211)
+...+...+.....+++.+|+..+|.++ ..++|||||||++|||||+|+||+|||||.+||+|||+|||+++.+
T Consensus 268 ~~~~~s~~~~~~~~~~~~~yn~~~f~~~----~~nAkfFVIKSySEDdVHkSIKY~vWsST~~GNKkLdaAYreak~~-- 341 (487)
T KOG1901|consen 268 EAGSASAPESNESVKRRDRYNPPDFLTD----YSNAKFFVIKSYSEDDVHKSIKYNVWSSTLNGNKKLDAAYREAKKK-- 341 (487)
T ss_pred hccccccccccccccChhhcCccccccc----cccceEEEEeccChhhhhhhcccceeecccCCchhhHHHHHHhhhc--
Confidence 3334444444457889999999999988 6799999999999999999999999999999999999999998731
Q ss_pred EEecccccccccceeccccccCccchHHHHHHHhcCCcEEEEEEECCCCceeEEEEeecCCCCCCCCccccCCCCCCCCc
Q psy8691 94 IFSNYYVSNELNFKVYGVWSTLPQNEQKLNQAYRESRNVLLIFSVRESGKFSGFARLASEADHGVSPVKWVLPPGLSGKV 173 (211)
Q Consensus 94 ifs~~~~~~~l~~i~~~vWaT~~~Ne~~L~~AF~~~~~V~LiFSVN~Sg~FqGyArM~S~~~~~~~~~~W~~~~g~~~~~ 173 (211)
...++|+||||||.||+|||+|+|+++++.+....+|+ +.+
T Consensus 342 ---------------------------------~~~cPvfLfFSVNaSGqFCGvAEMvgPVdfn~~~~~Wq------QDK 382 (487)
T KOG1901|consen 342 ---------------------------------SGKCPVFLFFSVNASGQFCGVAEMVGPVDFNKDMEYWQ------QDK 382 (487)
T ss_pred ---------------------------------cCCCCceEEEEEcCCccccceeeeccceecccccchhh------hcc
Confidence 35799999999999999999999999999999999997 589
Q ss_pred cCCceeEEEEEeecCCcccccccccccCCCccccc
Q psy8691 174 LNGVFKIDWVSRKELPFTSTLHLYNSWNEGEWYNS 208 (211)
Q Consensus 174 ~~g~F~I~Wl~~~dLPf~~~~HL~Np~NenkPV~~ 208 (211)
|.|.|.|+|+.|+|||+..++||+.+.|||||||+
T Consensus 383 W~G~FpVKWhiVKDVPNs~lrHI~LeNNeNKPVTn 417 (487)
T KOG1901|consen 383 WSGSFPVKWHIVKDVPNSQLRHIILENNENKPVTN 417 (487)
T ss_pred cceecceeeEEEeeCCccceeEEEeecCCCCCccc
Confidence 99999999999999999999999999999999996
No 3
>KOG1902|consensus
Probab=100.00 E-value=9.3e-41 Score=303.89 Aligned_cols=125 Identities=57% Similarity=1.035 Sum_probs=113.7
Q ss_pred ccccCCCcceEEEEecCChhhHHHHHHhCccccCchhHHHHHHHHHhccceEEEEecccccccccceeccccccCccchH
Q psy8691 41 KINYLFRDARFFVIKSNNSENVDIAKSQGVWSTLPQNEQKLNQAYRESRDVLLIFSNYYVSNELNFKVYGVWSTLPQNEQ 120 (211)
Q Consensus 41 ~~~~~~~~~rfFiIKS~~~~ni~~S~~~g~W~st~~~n~~L~~ay~~~~~~~~ifs~~~~~~~l~~i~~~vWaT~~~Ne~ 120 (211)
+......++|||||||.|.+||++|++.|||+||+. ||+
T Consensus 64 ~ss~~~~~~rYFIiKS~N~eN~elSvqkGiWaTq~s-----------------------------------------NE~ 102 (441)
T KOG1902|consen 64 KLKYVLQDARYFIIKSNNHENVELSVQKGVWSTQPS-----------------------------------------NEK 102 (441)
T ss_pred cccccCCceEEEEEecCCccceeeehhcceeccccc-----------------------------------------cHH
Confidence 344566789999999999999999998766555555 999
Q ss_pred HHHHHHhcCCcEEEEEEECCCCceeEEEEeecCCCCCCCCccccCCCCCCCCccCCceeEEEEEeecCCccccccccccc
Q psy8691 121 KLNQAYRESRNVLLIFSVRESGKFSGFARLASEADHGVSPVKWVLPPGLSGKVLNGVFKIDWVSRKELPFTSTLHLYNSW 200 (211)
Q Consensus 121 ~L~~AF~~~~~V~LiFSVN~Sg~FqGyArM~S~~~~~~~~~~W~~~~g~~~~~~~g~F~I~Wl~~~dLPf~~~~HL~Np~ 200 (211)
+|+.||.++..||||||||+||||||||+|+|+++....-..|..+.|++ +.||+.|+|+||++++|||+++.||+|||
T Consensus 103 kLn~AF~~s~~ViLIFSVn~SghFQG~ArMsS~IG~~~~q~~W~~~~G~~-a~~G~~FkVkWiRl~eLpFqkt~hL~NP~ 181 (441)
T KOG1902|consen 103 KLNLAFRSSRSVILIFSVNESGHFQGFARMSSEIGHGGSQIHWVLPAGMS-AMLGGVFKVKWIRLRELPFQKTAHLTNPW 181 (441)
T ss_pred HHHHHHhhcCcEEEEEEecccccchhhhhhcchhccCCCCccccccCCcc-cccCceeeEeEEeeccccchhhhhcCCcc
Confidence 99999999999999999999999999999999999988878999887764 68999999999999999999999999999
Q ss_pred CCCcccc
Q psy8691 201 NEGEWYN 207 (211)
Q Consensus 201 NenkPV~ 207 (211)
||||||.
T Consensus 182 NdnkpVK 188 (441)
T KOG1902|consen 182 NENKPVK 188 (441)
T ss_pred cccCcee
Confidence 9999995
No 4
>PRK00809 hypothetical protein; Provisional
Probab=96.36 E-value=0.035 Score=45.73 Aligned_cols=99 Identities=18% Similarity=0.297 Sum_probs=69.0
Q ss_pred eEEEEecCChhhHHHHHHhCccccCchhHHHHHHHHHhccceEEEEecccccccccceeccccccCccchHHHHHHHhcC
Q psy8691 50 RFFVIKSNNSENVDIAKSQGVWSTLPQNEQKLNQAYRESRDVLLIFSNYYVSNELNFKVYGVWSTLPQNEQKLNQAYRES 129 (211)
Q Consensus 50 rfFiIKS~~~~ni~~S~~~g~W~st~~~n~~L~~ay~~~~~~~~ifs~~~~~~~l~~i~~~vWaT~~~Ne~~L~~AF~~~ 129 (211)
+|.|+=+ ++||+....++|+|-..... -..|.+ -+.
T Consensus 2 ~yWi~~~-~~~~~~~~~~~gv~g~~~~~-----------------------------------------rn~lr~--Mk~ 37 (144)
T PRK00809 2 TYWLCIT-NEDNWEVIKDKNVWGVPERY-----------------------------------------KNTIEK--VKP 37 (144)
T ss_pred ceEEEec-CHHHHHHHHhCCEeecchhh-----------------------------------------hhHHhh--CCC
Confidence 5777766 89999999999998875541 111222 235
Q ss_pred CcEEEEEEEC------CCCceeEEEEeecCCCCCCCCccccCCCCCCCCccCCceeEEEEEeec--CCcccc
Q psy8691 130 RNVLLIFSVR------ESGKFSGFARLASEADHGVSPVKWVLPPGLSGKVLNGVFKIDWVSRKE--LPFTST 193 (211)
Q Consensus 130 ~~V~LiFSVN------~Sg~FqGyArM~S~~~~~~~~~~W~~~~g~~~~~~~g~F~I~Wl~~~d--LPf~~~ 193 (211)
+..+|||+-+ .-+.|-|.|++++..-++ ++..|..+..+....+--..+|+++...+ +|.+.+
T Consensus 38 GD~v~fYhs~~~~~~~~~~~ivgi~eV~~~~y~D-~t~~~p~~~~~~~~~~p~rvdV~~~~~~~~~v~l~~L 108 (144)
T PRK00809 38 GDKLIIYVSQEYGAERLPGKIVGIYEVVSEWYED-STPIFPAEPVRPKEIYPYRVKLKPVKIFEEPIDFKPL 108 (144)
T ss_pred CCEEEEEECCccCCCCCCceEEEEEEEecCcccC-CccCCCccccCCCCCceEEEEEEEeeecCCcccHHHH
Confidence 7778888887 578999999999987544 33556443333344455678899998888 887766
No 5
>KOG1901|consensus
Probab=95.30 E-value=0.01 Score=57.69 Aligned_cols=96 Identities=26% Similarity=0.379 Sum_probs=63.1
Q ss_pred ceEEEEecccccccccceeccccccCccchHHHHHHHhcCCcEEEEEEECCCCc---eeEEEEeecCCCCC----CCCcc
Q psy8691 90 DVLLIFSNYYVSNELNFKVYGVWSTLPQNEQKLNQAYRESRNVLLIFSVRESGK---FSGFARLASEADHG----VSPVK 162 (211)
Q Consensus 90 ~~~~ifs~~~~~~~l~~i~~~vWaT~~~Ne~~L~~AF~~~~~V~LiFSVN~Sg~---FqGyArM~S~~~~~----~~~~~ 162 (211)
+++||++++..++.=..|+|+||+..++-+++|+.||++... +++. |.=|-+=.|.--++ ..+..
T Consensus 299 AkfFVIKSySEDdVHkSIKY~vWsST~~GNKkLdaAYreak~--------~~~~cPvfLfFSVNaSGqFCGvAEMvgPVd 370 (487)
T KOG1901|consen 299 AKFFVIKSYSEDDVHKSIKYNVWSSTLNGNKKLDAAYREAKK--------KSGKCPVFLFFSVNASGQFCGVAEMVGPVD 370 (487)
T ss_pred ceEEEEeccChhhhhhhcccceeecccCCchhhHHHHHHhhh--------ccCCCCceEEEEEcCCccccceeeecccee
Confidence 589999999998888899999999999999999999999776 2221 11111111100000 01122
Q ss_pred ccCCCCCCCCccCCceeEEEEEeecCCccccccccccc
Q psy8691 163 WVLPPGLSGKVLNGVFKIDWVSRKELPFTSTLHLYNSW 200 (211)
Q Consensus 163 W~~~~g~~~~~~~g~F~I~Wl~~~dLPf~~~~HL~Np~ 200 (211)
... +..-|. +=+|.-.-.|-+..++|+-|..
T Consensus 371 fn~----~~~~Wq---QDKW~G~FpVKWhiVKDVPNs~ 401 (487)
T KOG1901|consen 371 FNK----DMEYWQ---QDKWSGSFPVKWHIVKDVPNSQ 401 (487)
T ss_pred ccc----ccchhh---hcccceecceeeEEEeeCCccc
Confidence 221 123444 5589888889999999987764
No 6
>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=87.34 E-value=1.3 Score=35.23 Aligned_cols=67 Identities=10% Similarity=0.103 Sum_probs=35.5
Q ss_pred HHhcCCcEEEEEEEC-CCCceeEEEEeecCCCCCCCCccccCCCCCCCCc--cCCceeEEEEEeec--CCcccc
Q psy8691 125 AYRESRNVLLIFSVR-ESGKFSGFARLASEADHGVSPVKWVLPPGLSGKV--LNGVFKIDWVSRKE--LPFTST 193 (211)
Q Consensus 125 AF~~~~~V~LiFSVN-~Sg~FqGyArM~S~~~~~~~~~~W~~~~g~~~~~--~~g~F~I~Wl~~~d--LPf~~~ 193 (211)
..+. +.-+|||.-+ +.+.|.|.|+.++..-.+.. ..+..+...+.+. .....+|+++..-+ |+...+
T Consensus 39 ~mk~-GD~vifY~s~~~~~~ivai~~V~~~~~~d~~-~~~~~~~~~~~~~~~~~~~v~v~~~~~~~~pi~l~~L 110 (143)
T PF01878_consen 39 RMKP-GDKVIFYHSGCKERGIVAIGEVVSEPYPDPT-AFDPDSPYYDPKSNPKPYRVDVEYVKIFEKPIPLKEL 110 (143)
T ss_dssp C--T-T-EEEEEETSSSS-EEEEEEEEEEEEEE-GG-GTSTTSTTBTTTSCSSSEEEEEEEEEEEEEEEEHHHH
T ss_pred cCCC-CCEEEEEEcCCCCCEEEEEEEEeccccCCCc-cccccccCcCCccCCCeeEEEEEEEEecCCCcCHHHH
Confidence 3344 4555567666 67899999999998643322 2122111112222 45677888887555 443555
No 7
>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=69.39 E-value=4.6 Score=32.72 Aligned_cols=24 Identities=50% Similarity=0.696 Sum_probs=19.1
Q ss_pred HHHHHHHHHhccceEEEEeccccc
Q psy8691 78 EQKLNQAYRESRDVLLIFSNYYVS 101 (211)
Q Consensus 78 n~~L~~ay~~~~~~~~ifs~~~~~ 101 (211)
+++|++||++.+.++|||+-+...
T Consensus 31 ~~~L~~Af~~~~~V~L~FSvn~S~ 54 (140)
T PF04146_consen 31 EKKLNEAFKESRNVYLFFSVNGSG 54 (140)
T ss_dssp HHHHHHHHHHSS-EEEEEEETTTS
T ss_pred hHHHHHHHHhCCCEEEEEeecCcc
Confidence 037999999999999999977654
No 8
>PRK02268 hypothetical protein; Provisional
Probab=51.85 E-value=49 Score=27.45 Aligned_cols=91 Identities=11% Similarity=0.251 Sum_probs=54.8
Q ss_pred eEEEEecCChhhHHHHHHhCccccCchhHHHHHHHHHhccceEEEEecccccccccceeccccccCccchHHHHHHHhcC
Q psy8691 50 RFFVIKSNNSENVDIAKSQGVWSTLPQNEQKLNQAYRESRDVLLIFSNYYVSNELNFKVYGVWSTLPQNEQKLNQAYRES 129 (211)
Q Consensus 50 rfFiIKS~~~~ni~~S~~~g~W~st~~~n~~L~~ay~~~~~~~~ifs~~~~~~~l~~i~~~vWaT~~~Ne~~L~~AF~~~ 129 (211)
+|.|.= -+.||+.+.++.|+|-. .+|.+ ..|.+- +.
T Consensus 3 ~yWI~v-~s~~hv~~g~~~gf~qv-~hgK~----------------------------------------apl~Rm--kp 38 (141)
T PRK02268 3 RYWIGV-VSAEHVRRGVEGGFMQV-CHGKA----------------------------------------APLRRM--KP 38 (141)
T ss_pred ceEEEE-ccHHHHHHHHhCCEEEe-CCCcc----------------------------------------chhhcC--CC
Confidence 445443 45899999999999955 44322 112111 34
Q ss_pred CcEEEEEEEC-------CCCceeEEEEeecCCCCCCCCccccCCCCCCCCccCCceeEEEEEeecCCcccc
Q psy8691 130 RNVLLIFSVR-------ESGKFSGFARLASEADHGVSPVKWVLPPGLSGKVLNGVFKIDWVSRKELPFTST 193 (211)
Q Consensus 130 ~~V~LiFSVN-------~Sg~FqGyArM~S~~~~~~~~~~W~~~~g~~~~~~~g~F~I~Wl~~~dLPf~~~ 193 (211)
+.-+++||=. .=.+|-|.+++++.-- |+.. |......=..+|+|+...++|++-+
T Consensus 39 GD~ivyYsp~~~~~~~~~~qaftAig~V~~~~~-------Yq~~--m~~~f~P~Rr~v~~~~~~e~pi~pL 100 (141)
T PRK02268 39 GDWIIYYSPKTTFGGKDKLQAFTAIGKVKDDEP-------YQVE--MAPGFIPWRRDVDYYPCAETPIRPL 100 (141)
T ss_pred CCEEEEEeceEecCCCcccceEEEEEEEcCCce-------Eecc--cCCCceeEEEEeeEeecCccchHHh
Confidence 6666777732 2367999999887621 2111 1111222367899999999998844
No 9
>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=51.15 E-value=40 Score=26.14 Aligned_cols=49 Identities=16% Similarity=0.215 Sum_probs=41.1
Q ss_pred eeccccccCccchHHHHHHHhcCCcEEEEEEECCCCceeEEEEeecCCC
Q psy8691 107 KVYGVWSTLPQNEQKLNQAYRESRNVLLIFSVRESGKFSGFARLASEAD 155 (211)
Q Consensus 107 i~~~vWaT~~~Ne~~L~~AF~~~~~V~LiFSVN~Sg~FqGyArM~S~~~ 155 (211)
...|+|.........|.+||.....|.+-+.+...+.|.|.+.+++--.
T Consensus 64 s~~g~~~~~d~~~~~l~~a~~~~~~~~~~v~~~~~~~~~g~~~vts~~~ 112 (134)
T PF06199_consen 64 SGEGLFDPDDASYDALEDAFDNGEPVEWRVTKPDGGKYEGKFFVTSLEE 112 (134)
T ss_pred EEEEEEecCchHHHHHHHHHHCCCcEEEEEEECCCCEEEEEEEEEECcc
Confidence 4467887666788999999999999998888899999999999877543
No 10
>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=47.60 E-value=69 Score=20.84 Aligned_cols=34 Identities=21% Similarity=0.339 Sum_probs=26.3
Q ss_pred chHHHHHHHhcCCcE-EEEEEECCCCceeEEEEee
Q psy8691 118 NEQKLNQAYRESRNV-LLIFSVRESGKFSGFARLA 151 (211)
Q Consensus 118 Ne~~L~~AF~~~~~V-~LiFSVN~Sg~FqGyArM~ 151 (211)
.++.|.+.|...+.| .+.+..+.++..+|||-+.
T Consensus 11 t~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~a~V~ 45 (70)
T PF00076_consen 11 TEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVE 45 (70)
T ss_dssp SHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEE
T ss_pred CHHHHHHHHHHhhhcccccccccccccccceEEEE
Confidence 678899999998888 4444445889999998654
No 11
>KOG1902|consensus
Probab=35.39 E-value=21 Score=34.16 Aligned_cols=28 Identities=25% Similarity=0.182 Sum_probs=23.3
Q ss_pred hccceEEEEecccccccccceecccccc
Q psy8691 87 ESRDVLLIFSNYYVSNELNFKVYGVWST 114 (211)
Q Consensus 87 ~~~~~~~ifs~~~~~~~l~~i~~~vWaT 114 (211)
...-+|||.+++-.+|..-+.+.|||||
T Consensus 69 ~~~~rYFIiKS~N~eN~elSvqkGiWaT 96 (441)
T KOG1902|consen 69 LQDARYFIIKSNNHENVELSVQKGVWST 96 (441)
T ss_pred CCceEEEEEecCCccceeeehhcceecc
Confidence 3445899999999998777788999998
Done!