Query 001969
Match_columns 989
No_of_seqs 278 out of 552
Neff 3.7
Searched_HMMs 46136
Date Thu Mar 28 13:31:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001969.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001969hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF06507 Auxin_resp: Auxin res 100.0 2.3E-35 5.1E-40 265.9 8.5 83 258-341 1-83 (83)
2 PF02362 B3: B3 DNA binding do 99.8 4.6E-18 9.9E-23 153.0 10.7 98 132-234 1-100 (100)
3 KOG0644 Uncharacterized conser 99.5 2.2E-14 4.7E-19 168.1 5.6 149 210-367 874-1045(1113)
4 PF09217 EcoRII-N: Restriction 98.1 1.1E-05 2.3E-10 81.4 9.3 91 128-219 6-110 (156)
5 PF03754 DUF313: Domain of unk 97.8 2.9E-05 6.3E-10 75.1 6.2 80 127-207 19-114 (114)
6 KOG3598 Thyroid hormone recept 95.3 0.014 3.1E-07 74.1 4.0 43 175-218 1694-1741(2220)
7 PRK10737 FKBP-type peptidyl-pr 71.8 9.5 0.00021 40.7 6.4 104 209-326 2-114 (196)
8 KOG0644 Uncharacterized conser 69.2 3.7 8E-05 51.5 3.1 67 39-107 872-940 (1113)
9 PF10844 DUF2577: Protein of u 60.8 54 0.0012 31.3 8.6 29 204-232 71-99 (100)
10 smart00743 Agenet Tudor-like d 56.7 16 0.00034 31.1 3.8 28 296-326 2-29 (61)
11 PF09606 Med15: ARC105 or Med1 49.5 5.5 0.00012 50.1 0.0 7 317-323 39-45 (799)
12 PF04014 Antitoxin-MazE: Antid 49.0 19 0.00042 29.6 3.1 28 203-230 14-41 (47)
13 PF13163 DUF3999: Protein of u 41.0 1.9E+02 0.004 34.3 10.6 164 135-346 9-196 (429)
14 KOG4369 RTK signaling protein 39.6 10 0.00022 49.3 0.2 36 24-59 1026-1077(2131)
15 smart00333 TUDOR Tudor domain. 39.2 43 0.00093 27.7 3.8 53 296-365 2-54 (57)
16 KOG3207 Beta-tubulin folding c 38.2 37 0.00081 40.7 4.3 43 297-353 3-45 (505)
17 KOG4369 RTK signaling protein 37.8 13 0.00027 48.6 0.6 12 733-744 1972-1984(2131)
18 TIGR01439 lp_hng_hel_AbrB loop 35.8 43 0.00093 26.3 3.1 27 203-229 14-40 (43)
19 PF06003 SMN: Survival motor n 35.5 35 0.00076 37.9 3.5 57 295-366 67-123 (264)
20 PF06752 E_Pc_C: Enhancer of P 35.0 31 0.00068 37.9 2.9 15 589-603 5-19 (230)
21 COG1047 SlpA FKBP-type peptidy 33.6 1.5E+02 0.0032 31.7 7.4 105 209-326 2-115 (174)
22 PRK03760 hypothetical protein; 32.0 97 0.0021 30.6 5.5 48 171-221 62-117 (117)
23 PF11515 Cul7: Mouse developme 28.1 74 0.0016 30.0 3.7 70 285-365 7-76 (78)
24 PF05641 Agenet: Agenet domain 27.6 1.1E+02 0.0023 27.2 4.5 42 297-348 1-42 (68)
25 cd04491 SoSSB_OBF SoSSB_OBF: A 27.0 3.2E+02 0.0069 24.4 7.5 49 168-232 23-75 (82)
26 cd04451 S1_IF1 S1_IF1: Transla 25.8 2.6E+02 0.0056 24.3 6.5 38 171-221 15-52 (64)
27 PF01878 EVE: EVE domain; Int 25.2 74 0.0016 31.4 3.4 27 208-234 38-65 (143)
28 PF02513 Spin-Ssty: Spin/Ssty 23.0 1.2E+02 0.0027 26.5 3.8 31 299-329 1-31 (50)
29 smart00536 AXH domain in Ataxi 22.5 2E+02 0.0043 29.0 5.7 28 191-219 76-113 (116)
30 PF08922 DUF1905: Domain of un 20.4 3.2E+02 0.007 25.2 6.3 79 132-219 1-79 (80)
31 PF15057 DUF4537: Domain of un 20.0 4.4E+02 0.0095 26.3 7.6 79 213-325 1-82 (124)
No 1
>PF06507 Auxin_resp: Auxin response factor; InterPro: IPR010525 This pattern represents a conserved region of auxin-responsive transcription factors. The plant hormone auxin (indole-3-acetic acid) can regulate the gene expression of several families, including Aux/IAA, GH3 and SAUR families. Two related families of proteins, Aux/IAA proteins (IPR003311 from INTERPRO) and the auxin response factors (ARF), are key regulators of auxin-modulated gene expression []. There are multiple ARF proteins, some of which activate, while others repress transcription. ARF proteins bind to auxin-responsive cis-acting promoter elements (AuxREs) using an N-terminal DNA-binding domain. It is thought that Aux/IAA proteins activate transcription by modifying ARF activity through the C-terminal protein-protein interaction domains (IPR011525 from INTERPRO) found in both Aux/IAA and ARF proteins. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0009725 response to hormone stimulus, 0005634 nucleus
Probab=100.00 E-value=2.3e-35 Score=265.85 Aligned_cols=83 Identities=67% Similarity=1.128 Sum_probs=81.6
Q ss_pred HHHHHhcCCcEEEEEcCCCCCCcceeehHHHHHHHhhCCCccCCeeeeeeeccCCCcceeeEEEEEeecCCCCCCCCCCc
Q 001969 258 AAHAAANNSPFTVFYNPRASPSEFVVPLAKYYKAVHSNQISLGMRFRMMFETEESGTRRYMGTITGISDLDPVRWKNSQW 337 (989)
Q Consensus 258 Aa~aaatgs~FtV~Y~PRas~sEFVVp~~kY~kA~~~~~ws~GMRFRM~FEtEDss~rry~GTItgi~d~DP~rWpnS~W 337 (989)
|+|||++|++|+|+||||++++|||||++||++|++ ++|++||||||.||+||+++++|+|||+||+|+||+|||+|+|
T Consensus 1 A~~aa~~~~~F~V~Y~PRa~~sEFVV~~~k~~~al~-~~~~~GmRfkM~fE~eds~~~~~~GtI~~v~~~dp~~w~~S~W 79 (83)
T PF06507_consen 1 AAHAAATGSPFEVFYYPRASPSEFVVPASKYDKALN-HPWSVGMRFKMRFETEDSSERRWQGTIVGVSDLDPIRWPGSKW 79 (83)
T ss_pred ChhHhhcCCeEEEEECCCCCCcceEEEHHHHHHHhc-CCCCCCcEEEEEeccCCCccceeeeEEeEeeccCCCCCCCCCc
Confidence 689999999999999999999999999999999998 9999999999999999999999999999999999999999999
Q ss_pred ceee
Q 001969 338 RNLQ 341 (989)
Q Consensus 338 R~Lq 341 (989)
||||
T Consensus 80 R~Lq 83 (83)
T PF06507_consen 80 RMLQ 83 (83)
T ss_pred ccCc
Confidence 9996
No 2
>PF02362 B3: B3 DNA binding domain; InterPro: IPR003340 Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana contain two distinct amino acid sequence domains found only in higher plant species. The N-terminal regions of RAV1 and RAV2 are homologous to the AP2 DNA-binding domain (see IPR001471 from INTERPRO) present in a family of transcription factors, while the C-terminal region exhibits homology to the highly conserved C-terminal domain, designated B3, of VP1/ABI3 transcription factors []. The AP2 and B3-like domains of RAV1 bind autonomously to the CAACA and CACCTG motifs, respectively, and together achieve a high affinity and specificity of binding. It has been suggested that the AP2 and B3-like domains of RAV1 are connected by a highly flexible structure enabling the two domains to bind to the CAACA and CACCTG motifs in various spacings and orientations [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1WID_A 1YEL_A.
Probab=99.75 E-value=4.6e-18 Score=152.99 Aligned_cols=98 Identities=29% Similarity=0.404 Sum_probs=74.8
Q ss_pred EEEEeccccCCCCCceeeecchhhhcCCCCCCCCCCCceEEEEEecCCCeEEEEEEEeCCCCceeecccchhhhccCCCC
Q 001969 132 FCKTLTASDTSTHGGFSVPRRAAEKIFPPLDFSMQPPAQELMARDLHDNIWTFRHIYRGQPKRHLLTTGWSLFVSGKRLF 211 (989)
Q Consensus 132 F~KtLT~SDVs~~GrfsVPkr~AE~~FPpLd~s~~~psq~Lvv~Dl~Gk~W~FR~iyrg~prRhlLTTGWs~FVr~KkL~ 211 (989)
|.|+|+++|+.+.++|.||++++++|. ++ ...+.++.++|..|++|++++.|++.+++++|++||..||++++|+
T Consensus 1 F~K~l~~s~~~~~~~l~iP~~f~~~~~--~~---~~~~~~v~l~~~~g~~W~v~~~~~~~~~~~~l~~GW~~Fv~~n~L~ 75 (100)
T PF02362_consen 1 FFKVLKPSDVSSSCRLIIPKEFAKKHG--GN---KRKSREVTLKDPDGRSWPVKLKYRKNSGRYYLTGGWKKFVRDNGLK 75 (100)
T ss_dssp EEEE--TTCCCCTT-EEE-HHHHTTTS-------SS--CEEEEEETTTEEEEEEEEEECCTTEEEEETTHHHHHHHCT--
T ss_pred CEEEEEccCcCCCCEEEeCHHHHHHhC--CC---cCCCeEEEEEeCCCCEEEEEEEEEccCCeEEECCCHHHHHHHcCCC
Confidence 899999999999999999999999972 11 1135689999999999999999998888899999999999999999
Q ss_pred CCCeEEEEEcc--CccEEEEEEecC
Q 001969 212 AGDSVLFIRDE--KQQLLLGIRRAN 234 (989)
Q Consensus 212 aGDsVVF~R~e--~GeL~VGIRRA~ 234 (989)
+||.|+|+... ..++.|.|+|+.
T Consensus 76 ~GD~~~F~~~~~~~~~~~v~i~~~~ 100 (100)
T PF02362_consen 76 EGDVCVFELIGNSNFTLKVHIFRKS 100 (100)
T ss_dssp TT-EEEEEE-SSSCE-EEEEEE---
T ss_pred CCCEEEEEEecCCCceEEEEEEECc
Confidence 99999999875 455699999873
No 3
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=99.48 E-value=2.2e-14 Score=168.09 Aligned_cols=149 Identities=22% Similarity=0.386 Sum_probs=121.5
Q ss_pred CCCCCeEEEEEccCccEEEEEEecCCCCCCC---------------------CCCcCCCCccccchHHHHHHHHhcCCcE
Q 001969 210 LFAGDSVLFIRDEKQQLLLGIRRANRQPANL---------------------SSSVLSSDSMHIGILAAAAHAAANNSPF 268 (989)
Q Consensus 210 L~aGDsVVF~R~e~GeL~VGIRRA~r~~~~~---------------------~ssv~ss~sm~~gvlaaAa~aaatgs~F 268 (989)
...||.|+++|....++.-.+|+.+...++. +.+.-+-=+|.+.|+.-|.++ -+..|
T Consensus 874 pQmgDEViyfrQghqeyl~~~~~n~~~~~~~~p~~~~~v~~~kv~kl~~~~y~~~~~s~c~m~l~~idp~s~~--~~k~F 951 (1113)
T KOG0644|consen 874 PQMGDEVIYFRQGHQEYLEAVRLNNIELNNKEPWNKMAVEICKVEKLVYITYPGSGDSCCKMKLAVIDPASKL--MDKSF 951 (1113)
T ss_pred ccccceeehhhhhhHHHHhhhhhccccccccCcccccchhhheeeeeeeeeccCCCcchheeeeeeecchhhh--hhccc
Confidence 4579999999987777776666665543221 122222336899999988864 45689
Q ss_pred EEEEcCCCCCCcceeehHHHHHHHhhCCCccCCeeeeeee--ccCCCcceeeEEEEEeecCCCCCCCCCCcceeeecccc
Q 001969 269 TVFYNPRASPSEFVVPLAKYYKAVHSNQISLGMRFRMMFE--TEESGTRRYMGTITGISDLDPVRWKNSQWRNLQVGWDE 346 (989)
Q Consensus 269 tV~Y~PRas~sEFVVp~~kY~kA~~~~~ws~GMRFRM~FE--tEDss~rry~GTItgi~d~DP~rWpnS~WR~LqV~WDE 346 (989)
.+.|......+||+|.+..|++|+. ++|..|+|||..+. +||. .+||.|+|.++.+..| .+|+|+|+|+.|+||.
T Consensus 952 ~ltlpdlv~fpDFlV~rsrYd~AiQ-rnW~~~d~crvwwrda~~e~-g~WWeG~ils~~pksp-~fpdSpwery~v~~~~ 1028 (1113)
T KOG0644|consen 952 KLTLPDLVTFPDFLVERSRYDAAIQ-RNWTCRDKCRVWWRDAGEED-GAWWEGRILSVKPKSP-DFPDSPWERYIVRYDN 1028 (1113)
T ss_pred eeecccccCcchhhhhhhhHHHHHh-hccccccceeEEEccCCCcC-CceeeeeeeeccCCCC-CCCCCcceeEEEEecC
Confidence 9999999999999999999999998 99999999999993 3332 3899999999999988 9999999999999999
Q ss_pred CCCCCCCCccccCcccccCCC
Q 001969 347 STAGEKRNRVSIWEIEPVTAP 367 (989)
Q Consensus 347 ~~~~~~~~RVSPWEIEpv~~~ 367 (989)
.+. +.-||||.|++..-
T Consensus 1029 ~e~----~~~spwe~~~i~de 1045 (1113)
T KOG0644|consen 1029 TET----ELHSPWEMEPIPDE 1045 (1113)
T ss_pred Ccc----cccCccccCCCccc
Confidence 974 78899999999863
No 4
>PF09217 EcoRII-N: Restriction endonuclease EcoRII, N-terminal; InterPro: IPR023372 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry represents the N-terminal effector-binding domain of the type II restriction endonuclease EcoRII, which has a DNA recognition fold, allowing for binding to 5'-CCWGG sequences. It assumes a structure composed of an eight-stranded beta-sheet with the strands in the order of b2, b5, b4, b3, b7, b6, b1 and b8. They are mostly antiparallel to each other except that b3 is parallel to b7. Alternatively, it may also be viewed as consisting of two mini beta-sheets of four antiparallel beta-strands, sheet I from beta-strands b2, b5, b4, b3 and sheet II from strands b7, b6, b1, b8, folded into an open mixed beta-barrel with a novel topology. Sheet I has a simple Greek key motif while sheet II does not []. The domain represented by this entry is only found in bacterial proteins.; PDB: 3HQF_A 1NA6_A.
Probab=98.13 E-value=1.1e-05 Score=81.38 Aligned_cols=91 Identities=25% Similarity=0.370 Sum_probs=59.0
Q ss_pred cceEEEEEeccccCCCCC----ceeeecchhhhcCCCCCC-CCCCCceEEEEEecCC--CeEEEEEEEeCC------CCc
Q 001969 128 QTEFFCKTLTASDTSTHG----GFSVPRRAAEKIFPPLDF-SMQPPAQELMARDLHD--NIWTFRHIYRGQ------PKR 194 (989)
Q Consensus 128 ~~~~F~KtLT~SDVs~~G----rfsVPkr~AE~~FPpLd~-s~~~psq~Lvv~Dl~G--k~W~FR~iyrg~------prR 194 (989)
....|+|.|++.|++..| |+.|||..++..||.+.. ....|...|.+++..| ..|+||++|.|+ ++.
T Consensus 6 ~~~~~~K~LSaNDtGaTGgHQaGiyIpk~~~~~lFp~~~~~~~~Np~~~~~~~~~s~~~~~~~~r~iYYnn~~~~gTRNE 85 (156)
T PF09217_consen 6 SWAIYCKRLSANDTGATGGHQAGIYIPKSAAELLFPSINHTKEENPDIWLKARWQSHFVTDSQVRFIYYNNRLFGGTRNE 85 (156)
T ss_dssp SEEEEEEE--CCCCTTTSSS--EEEE-HHHHHHH-GGG-SSSSSS-EEEEEEEETTTT---EEEEEEEE-CCCTTSS--E
T ss_pred ceEEEEEEccCCCCCCcCcccceeEecccHHHHhCCCCCcccccCCceeEEEEECCCCccceeEEEEEEcccccCCCcCc
Confidence 446799999999999874 799999999999997655 4456889999999887 679999999975 677
Q ss_pred eeecccchhhhc-cCCCCCCCeEEEE
Q 001969 195 HLLTTGWSLFVS-GKRLFAGDSVLFI 219 (989)
Q Consensus 195 hlLTTGWs~FVr-~KkL~aGDsVVF~ 219 (989)
+.|| +|...-. .+.=..||.+||.
T Consensus 86 ~RIT-~~G~~~~~~~~~~tGaL~vla 110 (156)
T PF09217_consen 86 YRIT-RFGRGFPLQNPENTGALLVLA 110 (156)
T ss_dssp EEEE----TTSGGG-GGGTT-EEEEE
T ss_pred eEEe-eecCCCccCCccccccEEEEE
Confidence 8885 3433222 1112478988887
No 5
>PF03754 DUF313: Domain of unknown function (DUF313) ; InterPro: IPR005508 This is a family of proteins from Arabidopsis thaliana (Mouse-ear cress) with uncharacterised function.
Probab=97.84 E-value=2.9e-05 Score=75.10 Aligned_cols=80 Identities=21% Similarity=0.239 Sum_probs=63.1
Q ss_pred CcceEEEEEeccccCCCC-CceeeecchhhhcCCCCCC------------CCCCCceEEEEEecCCCeEEEEEEEeCC--
Q 001969 127 PQTEFFCKTLTASDTSTH-GGFSVPRRAAEKIFPPLDF------------SMQPPAQELMARDLHDNIWTFRHIYRGQ-- 191 (989)
Q Consensus 127 ~~~~~F~KtLT~SDVs~~-GrfsVPkr~AE~~FPpLd~------------s~~~psq~Lvv~Dl~Gk~W~FR~iyrg~-- 191 (989)
.....|+|+|+.||+..+ .||+||-..... ...|.. .....++.+.+.|..++.|..++..|..
T Consensus 19 d~kli~~K~L~~tDv~~~qsRLsmP~~qi~~-~dFLt~eE~~~i~~~~~~~~~~~Gv~V~lvdp~~~~~~m~lkkW~mg~ 97 (114)
T PF03754_consen 19 DPKLIIEKTLFKTDVDPHQSRLSMPFNQIID-NDFLTEEEKRIIKEEKKNNDKKKGVEVILVDPSLRKWTMRLKKWNMGN 97 (114)
T ss_pred CCeEEEeeeecccCCCCCCceeeccHHHhcc-cccCCHHHHHHHHHhhccCcccCCceEEEECCcCcEEEEEEEEecccC
Confidence 457899999999999986 899999876633 222311 1234578899999999999999999964
Q ss_pred -CCceeecccchhhhcc
Q 001969 192 -PKRHLLTTGWSLFVSG 207 (989)
Q Consensus 192 -prRhlLTTGWs~FVr~ 207 (989)
...|+|++||..+|++
T Consensus 98 ~~~~YvL~~gWn~VV~~ 114 (114)
T PF03754_consen 98 GTSNYVLNSGWNKVVED 114 (114)
T ss_pred CceEEEEEcChHhhccC
Confidence 5579999999999864
No 6
>KOG3598 consensus Thyroid hormone receptor-associated protein complex, subunit TRAP230 [Transcription]
Probab=95.28 E-value=0.014 Score=74.11 Aligned_cols=43 Identities=28% Similarity=0.321 Sum_probs=22.5
Q ss_pred EecCCC-eEEEEEEEeCCCCceeec----ccchhhhccCCCCCCCeEEE
Q 001969 175 RDLHDN-IWTFRHIYRGQPKRHLLT----TGWSLFVSGKRLFAGDSVLF 218 (989)
Q Consensus 175 ~Dl~Gk-~W~FR~iyrg~prRhlLT----TGWs~FVr~KkL~aGDsVVF 218 (989)
.|..|+ .=.|--|+.+. ..++.| .-|-.|--.|.+..|-.--|
T Consensus 1694 idtkgnkiagFdsi~kK~-Glqvstkqk~spwdlFEg~k~~aplsW~wF 1741 (2220)
T KOG3598|consen 1694 IDTKGNKIAGFDSIEKKN-GLQVSTKQKKSPWDLFEGTKHLAPLSWKWF 1741 (2220)
T ss_pred cccccceeccchhhhhhc-CceeccccccCcchhhccCCCCCCccceee
Confidence 355553 34455555422 224444 34777777777766554443
No 7
>PRK10737 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=71.84 E-value=9.5 Score=40.75 Aligned_cols=104 Identities=20% Similarity=0.207 Sum_probs=61.9
Q ss_pred CCCCCCeEEEE---EccCccEEEEEEecCCCCCCCCCCcCCCCccccchHHHHHHHHhcCCcEEEEEcCCCCCC------
Q 001969 209 RLFAGDSVLFI---RDEKQQLLLGIRRANRQPANLSSSVLSSDSMHIGILAAAAHAAANNSPFTVFYNPRASPS------ 279 (989)
Q Consensus 209 kL~aGDsVVF~---R~e~GeL~VGIRRA~r~~~~~~ssv~ss~sm~~gvlaaAa~aaatgs~FtV~Y~PRas~s------ 279 (989)
++..|++|.|. |.++|+++-.-+ . ..|..++--...-+--|.+|..-...|..|+|..-|-....
T Consensus 2 kI~~~~vV~l~Y~l~~~dG~v~dst~-~-----~~Pl~~~~G~g~lipglE~aL~G~~~Gd~~~v~l~peeAyGe~d~~l 75 (196)
T PRK10737 2 KVAKDLVVSLAYQVRTEDGVLVDESP-V-----SAPLDYLHGHGSLISGLETALEGHEVGDKFDVAVGANDAYGQYDENL 75 (196)
T ss_pred ccCCCCEEEEEEEEEeCCCCEEEecC-C-----CCCeEEEeCCCcchHHHHHHHcCCCCCCEEEEEEChHHhcCCCChHH
Confidence 34567777763 346676533221 1 12323332222223346677777788889999976654332
Q ss_pred cceeehHHHHHHHhhCCCccCCeeeeeeeccCCCcceeeEEEEEeec
Q 001969 280 EFVVPLAKYYKAVHSNQISLGMRFRMMFETEESGTRRYMGTITGISD 326 (989)
Q Consensus 280 EFVVp~~kY~kA~~~~~ws~GMRFRM~FEtEDss~rry~GTItgi~d 326 (989)
-+.||++.|... ....+||||.+ ++++. .+.++|+.|.+
T Consensus 76 V~~vpr~~F~~~---~~l~~G~~~~~--~~~~G---~~~~~V~ev~~ 114 (196)
T PRK10737 76 VQRVPKDVFMGV---DELQVGMRFLA--ETDQG---PVPVEITAVED 114 (196)
T ss_pred EEEecHHHCCCc---cCCCCCCEEEE--eCCCC---cEEEEEEEEcC
Confidence 356787776432 24789999886 44553 36889999975
No 8
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=69.20 E-value=3.7 Score=51.49 Aligned_cols=67 Identities=24% Similarity=0.397 Sum_probs=46.1
Q ss_pred CCCCCCCeEEEecCCchhhhhccccccccCCCCCC--CCCCCcceEEEEEEeeccCCCCcceeeeeeeecC
Q 001969 39 NLPAAGTHVVYFPQGHSEQVAASMKKDIDGQIPNY--PNLPSKLLCILLNVTLHADTETDEVYAQMTLQPV 107 (989)
Q Consensus 39 ~lP~vGs~V~YFPQGH~Eq~~as~~~~~~~~~p~~--~~lP~~i~C~V~~V~L~AD~~TDEVyAqitL~P~ 107 (989)
.||.+|..|.||-|||-|-+.+....+.+ .-++ -++=..=+|.|..+..--=+....-..+|+|.=+
T Consensus 872 yipQmgDEViyfrQghqeyl~~~~~n~~~--~~~~~p~~~~~v~~~kv~kl~~~~y~~~~~s~c~m~l~~i 940 (1113)
T KOG0644|consen 872 YIPQMGDEVIYFRQGHQEYLEAVRLNNIE--LNNKEPWNKMAVEICKVEKLVYITYPGSGDSCCKMKLAVI 940 (1113)
T ss_pred ccccccceeehhhhhhHHHHhhhhhcccc--ccccCcccccchhhheeeeeeeeeccCCCcchheeeeeee
Confidence 68999999999999999999986543332 1121 1333456788888776666666666666666543
No 9
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=60.75 E-value=54 Score=31.29 Aligned_cols=29 Identities=24% Similarity=0.320 Sum_probs=23.7
Q ss_pred hhccCCCCCCCeEEEEEccCccEEEEEEe
Q 001969 204 FVSGKRLFAGDSVLFIRDEKQQLLLGIRR 232 (989)
Q Consensus 204 FVr~KkL~aGDsVVF~R~e~GeL~VGIRR 232 (989)
|.-...|++||.|..+|.++|..++=+-|
T Consensus 71 i~~~~~Lk~GD~V~ll~~~~gQ~yiVlDk 99 (100)
T PF10844_consen 71 ITFTDGLKVGDKVLLLRVQGGQKYIVLDK 99 (100)
T ss_pred EEEecCCcCCCEEEEEEecCCCEEEEEEe
Confidence 66778899999999999988877665544
No 10
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=56.73 E-value=16 Score=31.12 Aligned_cols=28 Identities=14% Similarity=0.274 Sum_probs=23.9
Q ss_pred CCccCCeeeeeeeccCCCcceeeEEEEEeec
Q 001969 296 QISLGMRFRMMFETEESGTRRYMGTITGISD 326 (989)
Q Consensus 296 ~ws~GMRFRM~FEtEDss~rry~GTItgi~d 326 (989)
.|++|+++...|+.++ .||.|+|+.+..
T Consensus 2 ~~~~G~~Ve~~~~~~~---~W~~a~V~~~~~ 29 (61)
T smart00743 2 DFKKGDRVEVFSKEED---SWWEAVVTKVLG 29 (61)
T ss_pred CcCCCCEEEEEECCCC---EEEEEEEEEECC
Confidence 5889999999996543 899999999964
No 11
>PF09606 Med15: ARC105 or Med15 subunit of Mediator complex non-fungal; InterPro: IPR019087 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. The proteins in this entry represent subunit Med15 of the Mediator complex. They contain a single copy of the approximately 70 residue ARC105 domain. The ARC105 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, ARC105 is a critical transducer of gene activation signals that control early metazoan development []. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex; PDB: 2GUT_A.
Probab=49.50 E-value=5.5 Score=50.14 Aligned_cols=7 Identities=14% Similarity=0.591 Sum_probs=2.7
Q ss_pred eeEEEEE
Q 001969 317 YMGTITG 323 (989)
Q Consensus 317 y~GTItg 323 (989)
|.++|..
T Consensus 39 Yl~~var 45 (799)
T PF09606_consen 39 YLSLVAR 45 (799)
T ss_dssp HHHHHHH
T ss_pred HHHHHHH
Confidence 3444333
No 12
>PF04014 Antitoxin-MazE: Antidote-toxin recognition MazE; InterPro: IPR007159 This domain is found in AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation []. AbrB is thought to interact directly with the transcription initiation regions of genes under its control []. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins []. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator []. DNA-binding activity in this AbrB homologue requires hexamerisation []. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins [].; PDB: 2L66_A 2GLW_A 3TND_D 2W1T_B 2RO5_B 2FY9_A 2RO3_B 1UB4_C 3ZVK_G 1YFB_B ....
Probab=48.99 E-value=19 Score=29.57 Aligned_cols=28 Identities=14% Similarity=0.101 Sum_probs=23.1
Q ss_pred hhhccCCCCCCCeEEEEEccCccEEEEE
Q 001969 203 LFVSGKRLFAGDSVLFIRDEKQQLLLGI 230 (989)
Q Consensus 203 ~FVr~KkL~aGDsVVF~R~e~GeL~VGI 230 (989)
+|.+..+|.+||.|.|.-+++|++.|--
T Consensus 14 ~~~~~l~l~~Gd~v~i~~~~~g~i~i~p 41 (47)
T PF04014_consen 14 EIREKLGLKPGDEVEIEVEGDGKIVIRP 41 (47)
T ss_dssp HHHHHTTSSTTTEEEEEEETTSEEEEEE
T ss_pred HHHHHcCCCCCCEEEEEEeCCCEEEEEE
Confidence 5678889999999999998888666543
No 13
>PF13163 DUF3999: Protein of unknown function (DUF3999)
Probab=40.98 E-value=1.9e+02 Score=34.34 Aligned_cols=164 Identities=16% Similarity=0.228 Sum_probs=96.5
Q ss_pred EeccccCCCCCceeeecc-hhhhcCCCCCCCCCCCceEEEEEecCCCeEEEEEEEeCC-----CCceeecccchh-hhcc
Q 001969 135 TLTASDTSTHGGFSVPRR-AAEKIFPPLDFSMQPPAQELMARDLHDNIWTFRHIYRGQ-----PKRHLLTTGWSL-FVSG 207 (989)
Q Consensus 135 tLT~SDVs~~GrfsVPkr-~AE~~FPpLd~s~~~psq~Lvv~Dl~Gk~W~FR~iyrg~-----prRhlLTTGWs~-FVr~ 207 (989)
.|+.+.-+--.++.+|.. .....-|-| .+|.|.|-.|..-.|....... +.++-| -|.. .+..
T Consensus 9 ~L~~~~~~~~y~l~Lp~~vy~~~~~~dL--------~DvrVfn~~G~~vP~al~~~~~~~~~~~~~~~~--~~fpl~~~~ 78 (429)
T PF13163_consen 9 PLQLSGSAPWYRLTLPLAVYAASRRPDL--------GDVRVFNAAGEPVPYALLPPRAPAAQAPTRQPV--PWFPLPASA 78 (429)
T ss_pred eeecCCCCceEEEECCHHHHHhhccccc--------cceEEECCCCCCCceeecccccccCCCCceeee--eeeecCCcc
Confidence 344444444568888875 233333333 3799999999988887775521 222222 1222 3455
Q ss_pred CCCCCCCe-EEEEEccCccEEEEEEecCCCCCCCCCCcCCCCccccchHHHHHHHHhcCCcEEEEEcCCCCCCcceeehH
Q 001969 208 KRLFAGDS-VLFIRDEKQQLLLGIRRANRQPANLSSSVLSSDSMHIGILAAAAHAAANNSPFTVFYNPRASPSEFVVPLA 286 (989)
Q Consensus 208 KkL~aGDs-VVF~R~e~GeL~VGIRRA~r~~~~~~ssv~ss~sm~~gvlaaAa~aaatgs~FtV~Y~PRas~sEFVVp~~ 286 (989)
.. ..||. +.+.|+.+|.+ |-|+++......... ...|+|...
T Consensus 79 ~~-~~~~~~~~v~~~~~G~~-ve~~~~~~~~~~~~~-----------------------------------~~~~Lld~s 121 (429)
T PF13163_consen 79 DA-ARGDPQLRVERDADGAL-VEVRPASGAAPADGQ-----------------------------------ARGWLLDLS 121 (429)
T ss_pred cc-ccCCccEEEEECCCCcE-EEecccCCCCccccc-----------------------------------ccEEEEECc
Confidence 55 67774 88889999999 999988764432110 012333333
Q ss_pred HH---HHHHhhCCC-ccCCee--eeeeeccCCCccee----eEEEEEeecCC------CCCCCCCCcceeeecccc
Q 001969 287 KY---YKAVHSNQI-SLGMRF--RMMFETEESGTRRY----MGTITGISDLD------PVRWKNSQWRNLQVGWDE 346 (989)
Q Consensus 287 kY---~kA~~~~~w-s~GMRF--RM~FEtEDss~rry----~GTItgi~d~D------P~rWpnS~WR~LqV~WDE 346 (989)
.. ..++. -.| .....+ |..+|+-|.-+.|+ .|+|..+..-+ .+.-|++..|-|+|.|++
T Consensus 122 ~~~~~l~~L~-L~w~~~~~~~~~~v~VeaSdDl~~W~~l~~~~~l~~L~~~~~~l~~~~I~L~~~~~rYLRl~~~~ 196 (429)
T PF13163_consen 122 ALKEPLDALR-LDWPQSNFNWQARVSVEASDDLQHWRPLAGDAQLMDLSNGGQRLVQDRIELPGSNARYLRLTWND 196 (429)
T ss_pred ccccchhheE-EEeecCCCCceEEEEEEEecCcccceEccCCceEEEeccCCcceeeeeEccCCCCCceEEEEeCC
Confidence 33 23333 456 333344 55566555444554 47777775322 356789999999999965
No 14
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=39.58 E-value=10 Score=49.31 Aligned_cols=36 Identities=33% Similarity=0.409 Sum_probs=24.3
Q ss_pred ccchhhHHhhcCCCc-CCCCCCCeEE---------------EecCCchhhhh
Q 001969 24 TINTELWHACAGPLV-NLPAAGTHVV---------------YFPQGHSEQVA 59 (989)
Q Consensus 24 ~v~~eLW~ACAGPlv-~lP~vGs~V~---------------YFPQGH~Eq~~ 59 (989)
.=|.-||.||||-.. ..|-+-+.|. -|--||.|-|-
T Consensus 1026 kG~T~Lwla~~Gg~lss~~il~~~~ad~d~qdnr~~S~~maafRKgh~~iVk 1077 (2131)
T KOG4369|consen 1026 KGCTVLWLASAGGALSSCPILVSSVADADQQDNRTNSRTMAAFRKGHFAIVK 1077 (2131)
T ss_pred CCCcccchhccCCccccchHHhhcccChhhhhcccccccHHHHHhchhheec
Confidence 346789999999754 5565555443 47778887554
No 15
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=39.16 E-value=43 Score=27.71 Aligned_cols=53 Identities=11% Similarity=0.216 Sum_probs=37.8
Q ss_pred CCccCCeeeeeeeccCCCcceeeEEEEEeecCCCCCCCCCCcceeeeccccCCCCCCCCccccCcccccC
Q 001969 296 QISLGMRFRMMFETEESGTRRYMGTITGISDLDPVRWKNSQWRNLQVGWDESTAGEKRNRVSIWEIEPVT 365 (989)
Q Consensus 296 ~ws~GMRFRM~FEtEDss~rry~GTItgi~d~DP~rWpnS~WR~LqV~WDE~~~~~~~~RVSPWEIEpv~ 365 (989)
.|.+|..+...| .+. .||.|+|+++.. + ..+.|.-++-+. .+-|...+|-++.
T Consensus 2 ~~~~G~~~~a~~-~d~---~wyra~I~~~~~-------~---~~~~V~f~D~G~---~~~v~~~~l~~l~ 54 (57)
T smart00333 2 TFKVGDKVAARW-EDG---EWYRARIIKVDG-------E---QLYEVFFIDYGN---EEVVPPSDLRPLP 54 (57)
T ss_pred CCCCCCEEEEEe-CCC---CEEEEEEEEECC-------C---CEEEEEEECCCc---cEEEeHHHeecCC
Confidence 588999999999 433 899999999974 1 456788777442 3556666665554
No 16
>KOG3207 consensus Beta-tubulin folding cofactor E [Posttranslational modification, protein turnover, chaperones]
Probab=38.19 E-value=37 Score=40.72 Aligned_cols=43 Identities=30% Similarity=0.726 Sum_probs=29.8
Q ss_pred CccCCeeeeeeeccCCCcceeeEEEEEeecCCCCCCCCCCcceeeeccccCCCCCCC
Q 001969 297 ISLGMRFRMMFETEESGTRRYMGTITGISDLDPVRWKNSQWRNLQVGWDESTAGEKR 353 (989)
Q Consensus 297 ws~GMRFRM~FEtEDss~rry~GTItgi~d~DP~rWpnS~WR~LqV~WDE~~~~~~~ 353 (989)
..+|.|+|.-+|- +..||.|+|.|. ++ +| +-|.||++.-+.+.
T Consensus 3 ~~IG~RvkI~~~~---~Tvr~iG~V~g~--------~~-~w--~GvEWDd~~RGKH~ 45 (505)
T KOG3207|consen 3 MEIGTRVKIGGEI---ATVRYIGEVEGN--------NS-KW--YGVEWDDPVRGKHD 45 (505)
T ss_pred eeccceEEEcCEE---EEEEEEEEEcCC--------CC-cc--eeeEecCCCccccC
Confidence 4689999987642 336777777654 33 34 78999999876543
No 17
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=37.83 E-value=13 Score=48.56 Aligned_cols=12 Identities=42% Similarity=0.368 Sum_probs=7.1
Q ss_pred cccc-cCCCCCCC
Q 001969 733 QSVI-TDDNPSCS 744 (989)
Q Consensus 733 ~S~i-Tdd~PScS 744 (989)
.++| |..+||.|
T Consensus 1972 ~~~lg~~~~~s~~ 1984 (2131)
T KOG4369|consen 1972 ASVLGQISMPSLS 1984 (2131)
T ss_pred cccccccccchhh
Confidence 4455 46677765
No 18
>TIGR01439 lp_hng_hel_AbrB looped-hinge helix DNA binding domain, AbrB family. This DNA-binding domain family includes AbrB, a transition state regulator in Bacillus subtilis, whose DNA-binding domain structure in solution was determined by NMR. The domain binds DNA as a dimer in what is termed a looped-hinge helix fold. Some members of the family have two copies of the domain in tandem. The domain is found usually at the N-terminus of a small protein. This model excludes members of family TIGR02609.
Probab=35.81 E-value=43 Score=26.27 Aligned_cols=27 Identities=26% Similarity=0.277 Sum_probs=22.7
Q ss_pred hhhccCCCCCCCeEEEEEccCccEEEE
Q 001969 203 LFVSGKRLFAGDSVLFIRDEKQQLLLG 229 (989)
Q Consensus 203 ~FVr~KkL~aGDsVVF~R~e~GeL~VG 229 (989)
.|.+..+++.||.|.+...++|.+.+.
T Consensus 14 ~~r~~l~~~~gd~~~i~~~~~~~l~l~ 40 (43)
T TIGR01439 14 EIREKLGLKEGDRLEVIRVEDGEIILR 40 (43)
T ss_pred HHHHHcCcCCCCEEEEEEeCCCEEEEE
Confidence 688999999999999998777776653
No 19
>PF06003 SMN: Survival motor neuron protein (SMN); InterPro: IPR010304 This family consists of several eukaryotic survival motor neuron (SMN) proteins. The Survival of Motor Neurons (SMN) protein, the product of the spinal muscular atrophy-determining gene, is part of a large macromolecular complex (SMN complex) that functions in the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs). The SMN complex functions as a specificity factor essential for the efficient assembly of Sm proteins on U snRNAs and likely protects cells from illicit, and potentially deleterious, non-specific binding of Sm proteins to RNAs.; GO: 0003723 RNA binding, 0006397 mRNA processing, 0005634 nucleus, 0005737 cytoplasm; PDB: 1MHN_A 4A4G_A 3S6N_M 4A4E_A 1G5V_A 4A4H_A 4A4F_A 2D9T_A.
Probab=35.51 E-value=35 Score=37.86 Aligned_cols=57 Identities=16% Similarity=0.297 Sum_probs=33.5
Q ss_pred CCCccCCeeeeeeeccCCCcceeeEEEEEeecCCCCCCCCCCcceeeeccccCCCCCCCCccccCcccccCC
Q 001969 295 NQISLGMRFRMMFETEESGTRRYMGTITGISDLDPVRWKNSQWRNLQVGWDESTAGEKRNRVSIWEIEPVTA 366 (989)
Q Consensus 295 ~~ws~GMRFRM~FEtEDss~rry~GTItgi~d~DP~rWpnS~WR~LqV~WDE~~~~~~~~RVSPWEIEpv~~ 366 (989)
..|.+|++.+..|..|. .+|.+||++|..-+- .| .|+.++=+ +.+.|..=+|.+...
T Consensus 67 ~~WkvGd~C~A~~s~Dg---~~Y~A~I~~i~~~~~--------~~-~V~f~gYg---n~e~v~l~dL~~~~~ 123 (264)
T PF06003_consen 67 KKWKVGDKCMAVYSEDG---QYYPATIESIDEEDG--------TC-VVVFTGYG---NEEEVNLSDLKPSEG 123 (264)
T ss_dssp T---TT-EEEEE-TTTS---SEEEEEEEEEETTTT--------EE-EEEETTTT---EEEEEEGGGEEETT-
T ss_pred cCCCCCCEEEEEECCCC---CEEEEEEEEEcCCCC--------EE-EEEEcccC---CeEeeehhhhccccc
Confidence 68999999999995433 799999999974221 23 37776643 235555555555543
No 20
>PF06752 E_Pc_C: Enhancer of Polycomb C-terminus; InterPro: IPR009607 This entry represents the C terminus of eukaryotic enhancer of polycomb proteins, which have roles in heterochromatin formation []. This family contains several conserved motifs.
Probab=35.04 E-value=31 Score=37.90 Aligned_cols=15 Identities=47% Similarity=0.437 Sum_probs=12.0
Q ss_pred ccccHHHHHHHHHHH
Q 001969 589 LQMSDKQIQLHLLQK 603 (989)
Q Consensus 589 ~Q~sd~Q~q~QLLQk 603 (989)
-|+.++|+||.++||
T Consensus 5 EQyQqHQqQL~~MQk 19 (230)
T PF06752_consen 5 EQYQQHQQQLVLMQK 19 (230)
T ss_pred HHHHHHHHHHHHHHH
Confidence 356778899999988
No 21
>COG1047 SlpA FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]
Probab=33.63 E-value=1.5e+02 Score=31.68 Aligned_cols=105 Identities=19% Similarity=0.239 Sum_probs=64.0
Q ss_pred CCCCCCeEEEE---EccCccEEEEEEecCCCCCCCCCCcCCCCccccchHHHHHHHHhcCCcEEEEEcCCCCCCcc----
Q 001969 209 RLFAGDSVLFI---RDEKQQLLLGIRRANRQPANLSSSVLSSDSMHIGILAAAAHAAANNSPFTVFYNPRASPSEF---- 281 (989)
Q Consensus 209 kL~aGDsVVF~---R~e~GeL~VGIRRA~r~~~~~~ssv~ss~sm~~gvlaaAa~aaatgs~FtV~Y~PRas~sEF---- 281 (989)
++..||.|.+. |.++|+++=--+- ...|..++-.+..-+.-|.+|..-..-|..|+|.--|-....||
T Consensus 2 ~i~k~~~V~i~Y~~~~~dg~v~Dtt~e-----~~~P~~~i~G~g~li~glE~al~g~~~Ge~~~V~IpPE~AfGe~~~~l 76 (174)
T COG1047 2 KIEKGDVVSLHYTLKVEDGEVVDTTDE-----NYGPLTFIVGAGQLIPGLEEALLGKEVGEEFTVEIPPEDAFGEYDPDL 76 (174)
T ss_pred cccCCCEEEEEEEEEecCCcEEEcccc-----cCCCeEEEecCCCcchhHHHHHhCCCCCceeEEEeCchHhcCCCChHH
Confidence 46678888773 4455554321111 01122233223333344778888888999999999887655554
Q ss_pred --eeehHHHHHHHhhCCCccCCeeeeeeeccCCCcceeeEEEEEeec
Q 001969 282 --VVPLAKYYKAVHSNQISLGMRFRMMFETEESGTRRYMGTITGISD 326 (989)
Q Consensus 282 --VVp~~kY~kA~~~~~ws~GMRFRM~FEtEDss~rry~GTItgi~d 326 (989)
.||+++|... ....+||+|.. ++++ .-.-|+|+.|..
T Consensus 77 vq~vp~~~F~~~---~~~~vGm~~~~--~~~~---~~~~~~V~~V~~ 115 (174)
T COG1047 77 VQRVPRDEFQGV---GELEVGMEVEA--EGGD---GEIPGVVTEVSG 115 (174)
T ss_pred eEEecHHHhCcC---CCCCCCcEEEE--cCCC---ceeeEEEEEEcC
Confidence 4666665543 14779999875 4444 446799999974
No 22
>PRK03760 hypothetical protein; Provisional
Probab=31.99 E-value=97 Score=30.65 Aligned_cols=48 Identities=21% Similarity=0.418 Sum_probs=30.2
Q ss_pred EEEEEecCCCeEEEEE-----EEe-CCCCceee--cccchhhhccCCCCCCCeEEEEEc
Q 001969 171 ELMARDLHDNIWTFRH-----IYR-GQPKRHLL--TTGWSLFVSGKRLFAGDSVLFIRD 221 (989)
Q Consensus 171 ~Lvv~Dl~Gk~W~FR~-----iyr-g~prRhlL--TTGWs~FVr~KkL~aGDsVVF~R~ 221 (989)
++++.|.+|++-.... +|. ..+-+|+| ..||. .+.++++||.|.|.|+
T Consensus 62 DiiFld~~g~Vv~i~~~~P~~~~~~~~~a~~VLEl~aG~~---~~~gi~~Gd~v~~~~~ 117 (117)
T PRK03760 62 DVIFLDSNRRVVDFKTLKPWRIYVPKKPARYIIEGPVGKI---RVLKVEVGDEIEWIDE 117 (117)
T ss_pred EEEEECCCCeEEEEEeCCCccccCCCccceEEEEeCCChH---HHcCCCCCCEEEEeeC
Confidence 4566666665433211 122 23456887 57765 7899999999999873
No 23
>PF11515 Cul7: Mouse development and cellular proliferation protein Cullin-7; InterPro: IPR021097 The CPH domain is found in the Cullin-7, PARC and HERC2 proteins, which are all components of known or predicted E3-ubiquitin ligases. The CPH domain is a protein-protein interaction module that binds the teramerisation domain of the tumour suppressor protein p53 []. Structurally it forms a beta-barrel fold similar to the SH3, Tudor and KOW and domains. Unlike the SH3 and Tudor domains, which bind to small peptides, the CPH domain appears to bind to an extended surface on p53.; PDB: 2JUF_A 2JNG_A.
Probab=28.11 E-value=74 Score=30.02 Aligned_cols=70 Identities=23% Similarity=0.226 Sum_probs=33.2
Q ss_pred hHHHHHHHhhCCCccCCeeeeeeeccCCCcceeeEEEEEeecCCCCCCCCCCcceeeeccccCCCCCCCCccccCccccc
Q 001969 285 LAKYYKAVHSNQISLGMRFRMMFETEESGTRRYMGTITGISDLDPVRWKNSQWRNLQVGWDESTAGEKRNRVSIWEIEPV 364 (989)
Q Consensus 285 ~~kY~kA~~~~~ws~GMRFRM~FEtEDss~rry~GTItgi~d~DP~rWpnS~WR~LqV~WDE~~~~~~~~RVSPWEIEpv 364 (989)
.+.|..-+. -++.+||++||.=.-|+-. .-=.|+|.-++.- .-| =-.++|.|-.... .-.|--=.||.+
T Consensus 7 ~d~Ya~YVr-~~i~~GM~VRc~~~yeeV~-~GD~G~V~k~~~d---g~~---~lnvqv~W~~~G~---tyWV~~~~vEii 75 (78)
T PF11515_consen 7 NDDYAEYVR-DNIQPGMRVRCCRDYEEVR-AGDEGEVFKQDRD---GLH---DLNVQVDWQSKGR---TYWVHWHHVEII 75 (78)
T ss_dssp SHHHHHHHH-HH--TT-EEEESS-BTTB--TT-EEE-EEEE-T---TSS---E--EEEEETTTTE---EEEEEGGGEEE-
T ss_pred hhHHHHHHH-HhCCCCcEEEEeccccccc-ccccceeEeeccC---CCC---CcceEEEeeecCc---eEEEEEEEEEEe
Confidence 456777776 6789999999974333321 1236776666531 112 2357888876652 223333355555
Q ss_pred C
Q 001969 365 T 365 (989)
Q Consensus 365 ~ 365 (989)
+
T Consensus 76 g 76 (78)
T PF11515_consen 76 G 76 (78)
T ss_dssp -
T ss_pred c
Confidence 4
No 24
>PF05641 Agenet: Agenet domain; InterPro: IPR008395 This domain is related to the TUDOR domain IPR008191 from INTERPRO []. The function of the agenet domain is unknown. This signature matches one of the two Agenet domains in the FMR proteins [].; GO: 0003723 RNA binding; PDB: 2BKD_N 3O8V_A 3KUF_A 3H8Z_A.
Probab=27.61 E-value=1.1e+02 Score=27.16 Aligned_cols=42 Identities=12% Similarity=0.121 Sum_probs=26.5
Q ss_pred CccCCeeeeeeeccCCCcceeeEEEEEeecCCCCCCCCCCcceeeeccccCC
Q 001969 297 ISLGMRFRMMFETEESGTRRYMGTITGISDLDPVRWKNSQWRNLQVGWDEST 348 (989)
Q Consensus 297 ws~GMRFRM~FEtEDss~rry~GTItgi~d~DP~rWpnS~WR~LqV~WDE~~ 348 (989)
++.|+++-..-+.+.....||.|||+.....+ .+.|+.++-.
T Consensus 1 F~~G~~VEV~s~e~g~~gaWf~a~V~~~~~~~----------~~~V~Y~~~~ 42 (68)
T PF05641_consen 1 FKKGDEVEVSSDEDGFRGAWFPATVLKENGDD----------KYLVEYDDLP 42 (68)
T ss_dssp --TT-EEEEEE-SBTT--EEEEEEEEEEETT-----------EEEEEETT-S
T ss_pred CCCCCEEEEEEcCCCCCcEEEEEEEEEeCCCc----------EEEEEECCcc
Confidence 46899999887544444479999999997532 6788886544
No 25
>cd04491 SoSSB_OBF SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB). SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is limiting, and supporting transcription when TBP is absent. SSoSSB selectively melts the duplex DNA of promoter sequences. It also relieves transcriptional repression by the chromatin Alba. In addition, SSoSSB activates reverse gyrase activity, which involves DNA binding, DNA cleavage, strand passage and ligation. SSoSSB stimulates all these steps in the presence of the chromatin protein, Sul7d. SSoSSB antagonizes the inhibitory effect of Sul7d on reverse gyrase supercoiling activity. It also physically and functionally interacts with Mini-chromosome Maintenance (MCM), stimulating
Probab=27.03 E-value=3.2e+02 Score=24.44 Aligned_cols=49 Identities=20% Similarity=0.206 Sum_probs=34.3
Q ss_pred CceEEEEEecCCCeEEEEEEEeCCCCceeecccchhhhccCCCCCCCeEEEEE----ccCccEEEEEEe
Q 001969 168 PAQELMARDLHDNIWTFRHIYRGQPKRHLLTTGWSLFVSGKRLFAGDSVLFIR----DEKQQLLLGIRR 232 (989)
Q Consensus 168 psq~Lvv~Dl~Gk~W~FR~iyrg~prRhlLTTGWs~FVr~KkL~aGDsVVF~R----~e~GeL~VGIRR 232 (989)
....+.+.|..| ..++.+|+..- ...|..||.|.+.. .-+|.+.+.+.+
T Consensus 23 ~~~~~~l~D~TG---~i~~~~W~~~~-------------~~~~~~G~vv~i~~~~v~~~~g~~ql~i~~ 75 (82)
T cd04491 23 KVQSGLVGDETG---TIRFTLWDEKA-------------ADDLEPGDVVRIENAYVREFNGRLELSVGK 75 (82)
T ss_pred EEEEEEEECCCC---EEEEEEECchh-------------cccCCCCCEEEEEeEEEEecCCcEEEEeCC
Confidence 356788999988 57888886421 34588999888872 246677776654
No 26
>cd04451 S1_IF1 S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the formation of the first peptide bond. In Escherichia coli, the initiation mechanism requires, in addition to mRNA, fMet-tRNA, and ribosomal subunits, the presence of three additional proteins (initiation factors IF1, IF2, and IF3) and at least one GTP molecule. The three initiation factors influence both the kinetics and the stability of ternary complex formation. IF1 is the smallest of the three factors. IF1 enhances the rate of 70S ribosome subunit association and dissociation and the interaction of 30S ribosomal subunit with IF2 and IF3. It stimulates 30S complex formation. In addition, by binding to the A-site of the 30S ribosomal subunit, IF1 may contribute to the fidelity of the selection of the initiation site of th
Probab=25.84 E-value=2.6e+02 Score=24.31 Aligned_cols=38 Identities=13% Similarity=0.080 Sum_probs=22.7
Q ss_pred EEEEEecCCCeEEEEEEEeCCCCceeecccchhhhccCCCCCCCeEEEEEc
Q 001969 171 ELMARDLHDNIWTFRHIYRGQPKRHLLTTGWSLFVSGKRLFAGDSVLFIRD 221 (989)
Q Consensus 171 ~Lvv~Dl~Gk~W~FR~iyrg~prRhlLTTGWs~FVr~KkL~aGDsVVF~R~ 221 (989)
...+++..|. .++|..||+-| . +...+.+||.|.|...
T Consensus 15 ~~~V~~~~g~--~~~c~~rGklr-----~------~~~~~~vGD~V~~~~~ 52 (64)
T cd04451 15 MFRVELENGH--EVLAHISGKMR-----M------NYIRILPGDRVKVELS 52 (64)
T ss_pred EEEEEeCCCC--EEEEEECceee-----c------CCcccCCCCEEEEEEe
Confidence 3445666665 45555555321 0 2334899999999854
No 27
>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=25.24 E-value=74 Score=31.42 Aligned_cols=27 Identities=30% Similarity=0.498 Sum_probs=18.3
Q ss_pred CCCCCCCeEEEEEcc-CccEEEEEEecC
Q 001969 208 KRLFAGDSVLFIRDE-KQQLLLGIRRAN 234 (989)
Q Consensus 208 KkL~aGDsVVF~R~e-~GeL~VGIRRA~ 234 (989)
++++.||.|+||... ++.-++||=|..
T Consensus 38 ~~mk~GD~vifY~s~~~~~~ivai~~V~ 65 (143)
T PF01878_consen 38 KRMKPGDKVIFYHSGCKERGIVAIGEVV 65 (143)
T ss_dssp HC--TT-EEEEEETSSSS-EEEEEEEEE
T ss_pred hcCCCCCEEEEEEcCCCCCEEEEEEEEe
Confidence 489999999999987 677777776654
No 28
>PF02513 Spin-Ssty: Spin/Ssty Family; InterPro: IPR003671 Spindlin (Spin) and Ssty were first identified for their involvement in gametogenesis. Spindlin was identified as a maternal transcript present in the unfertilised egg and early embryo, and was subsequently shown to interact with the spindle apparatus during oogenesis, and may therefore be important for mitosis []. In addition, spindlin appears to be a target for cell cycle-dependent phosphorylation, and as such may play a role in cell cycle regulation during the transition from gamete to embryo []. Ssty is a multi-copy, Y-linked spermatogenesis-specific transcript that appears to be required for normal spermatogenesis []. Ssty may play an analogous role to spindlin in sperm cells, namely during the transition from sperm cells to early embryo, and in mitosis.; GO: 0007276 gamete generation; PDB: 2NS2_A.
Probab=23.02 E-value=1.2e+02 Score=26.45 Aligned_cols=31 Identities=16% Similarity=0.358 Sum_probs=24.0
Q ss_pred cCCeeeeeeeccCCCcceeeEEEEEeecCCC
Q 001969 299 LGMRFRMMFETEESGTRRYMGTITGISDLDP 329 (989)
Q Consensus 299 ~GMRFRM~FEtEDss~rry~GTItgi~d~DP 329 (989)
+|-|+.-.||.++.+...|.|+|..--+..|
T Consensus 1 vGk~Veh~~~~g~g~~s~w~G~Vl~Qvp~~p 31 (50)
T PF02513_consen 1 VGKRVEHTWEDGDGPKSKWKGMVLHQVPAKP 31 (50)
T ss_dssp TT-EEEEEECTSTS-EEEEEEEEEEE-TTST
T ss_pred CCceEEEEEccCCCcccEEEEEEEEEeecCC
Confidence 5889999999988888888999999877654
No 29
>smart00536 AXH domain in Ataxins and HMG containing proteins. unknown function
Probab=22.55 E-value=2e+02 Score=29.03 Aligned_cols=28 Identities=29% Similarity=0.417 Sum_probs=21.5
Q ss_pred CCCceeecccchhhhc----------cCCCCCCCeEEEE
Q 001969 191 QPKRHLLTTGWSLFVS----------GKRLFAGDSVLFI 219 (989)
Q Consensus 191 ~prRhlLTTGWs~FVr----------~KkL~aGDsVVF~ 219 (989)
+|- +|..+||+.|-- -+.|.+||+|+..
T Consensus 76 HPf-FV~gqGWsSc~P~lT~~~ygL~C~~L~vGDVCl~l 113 (116)
T smart00536 76 HPF-FVKGKGWSSCYPSLTVQLYGLPCCELQVGDVCLSL 113 (116)
T ss_pred CCe-EEcCccccccChhhhhhhcCCcceecccCCEEecc
Confidence 454 777899999864 4678999999854
No 30
>PF08922 DUF1905: Domain of unknown function (DUF1905); InterPro: IPR015018 This family consist of hypothetical bacterial proteins. ; PDB: 2D9R_A.
Probab=20.42 E-value=3.2e+02 Score=25.19 Aligned_cols=79 Identities=18% Similarity=0.095 Sum_probs=38.0
Q ss_pred EEEEeccccCCCCCceeeecchhhhcCCCCCCCCCCCceEEEEEecCCCeEEEEEEEeCCCCceeecccchhhhccCCCC
Q 001969 132 FCKTLTASDTSTHGGFSVPRRAAEKIFPPLDFSMQPPAQELMARDLHDNIWTFRHIYRGQPKRHLLTTGWSLFVSGKRLF 211 (989)
Q Consensus 132 F~KtLT~SDVs~~GrfsVPkr~AE~~FPpLd~s~~~psq~Lvv~Dl~Gk~W~FR~iyrg~prRhlLTTGWs~FVr~KkL~ 211 (989)
|.-+|-+.+.+. ..+.||.+.++.+... +.....+.++ ..|.+|+-+..-.+ ...|+|-=- .+.-+.-++.
T Consensus 1 F~a~l~~~~~~~-~fv~vP~~v~~~l~~~-----~~g~v~V~~t-I~g~~~~~sl~p~g-~G~~~Lpv~-~~vRk~~g~~ 71 (80)
T PF08922_consen 1 FTATLWKGEGGW-TFVEVPFDVAEELGEG-----GWGRVPVRGT-IDGHPWRTSLFPMG-NGGYILPVK-AAVRKAIGKE 71 (80)
T ss_dssp EEEE-EE-TTS--EEEE--S-HHHHH--S-------S-EEEEEE-ETTEEEEEEEEESS-TT-EEEEE--HHHHHHHT--
T ss_pred CeEEEEecCCce-EEEEeCHHHHHHhccc-----cCCceEEEEE-ECCEEEEEEEEECC-CCCEEEEEc-HHHHHHcCCC
Confidence 444555544433 2477999999885443 1123344443 57788887555433 245766100 2456678899
Q ss_pred CCCeEEEE
Q 001969 212 AGDSVLFI 219 (989)
Q Consensus 212 aGDsVVF~ 219 (989)
+||.|.+.
T Consensus 72 ~Gd~V~v~ 79 (80)
T PF08922_consen 72 AGDTVEVT 79 (80)
T ss_dssp TTSEEEEE
T ss_pred CCCEEEEE
Confidence 99999874
No 31
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=20.01 E-value=4.4e+02 Score=26.28 Aligned_cols=79 Identities=20% Similarity=0.309 Sum_probs=53.4
Q ss_pred CCeEEEEEccCccEEEEEEecCCCCCCCCCCcCCCCccccchHHHHHHHHhcCCcEEEEEc-CCC--CCCcceeehHHHH
Q 001969 213 GDSVLFIRDEKQQLLLGIRRANRQPANLSSSVLSSDSMHIGILAAAAHAAANNSPFTVFYN-PRA--SPSEFVVPLAKYY 289 (989)
Q Consensus 213 GDsVVF~R~e~GeL~VGIRRA~r~~~~~~ssv~ss~sm~~gvlaaAa~aaatgs~FtV~Y~-PRa--s~sEFVVp~~kY~ 289 (989)
|..|+=-+++||-++.|.-++.- ++..|.|.|+ .+. -..+|||...
T Consensus 1 g~~VlAR~~~DG~YY~GtV~~~~----------------------------~~~~~lV~f~~~~~~~v~~~~iI~~~--- 49 (124)
T PF15057_consen 1 GQKVLARREEDGFYYPGTVKKCV----------------------------SSGQFLVEFDDGDTQEVPISDIIALS--- 49 (124)
T ss_pred CCeEEEeeCCCCcEEeEEEEEcc----------------------------CCCEEEEEECCCCEEEeChHHeEEcc---
Confidence 45566666788888888653322 3455777773 222 1478888875
Q ss_pred HHHhhCCCccCCeeeeeeeccCCCcceeeEEEEEee
Q 001969 290 KAVHSNQISLGMRFRMMFETEESGTRRYMGTITGIS 325 (989)
Q Consensus 290 kA~~~~~ws~GMRFRM~FEtEDss~rry~GTItgi~ 325 (989)
.++. +...+|+.+-+..|..+ .++.=|||.+.-
T Consensus 50 ~~~~-~~L~~GD~VLA~~~~~~--~~Y~Pg~V~~~~ 82 (124)
T PF15057_consen 50 DAMR-HSLQVGDKVLAPWEPDD--CRYGPGTVIAGP 82 (124)
T ss_pred Cccc-CcCCCCCEEEEecCcCC--CEEeCEEEEECc
Confidence 4665 89999999999975544 346669999753
Done!