Query 008078
Match_columns 578
No_of_seqs 261 out of 593
Neff 4.6
Searched_HMMs 46136
Date Thu Mar 28 19:11:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008078.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008078hhsearch_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 4E-35 8.7E-40 250.7 8.6 83 251-334 1-83 (83)
2 PF02362 B3: B3 DNA binding do 99.7 2.4E-17 5.3E-22 141.5 10.8 97 122-223 1-99 (100)
3 KOG0644 Uncharacterized conser 99.4 1.3E-13 2.8E-18 154.8 4.9 150 200-359 874-1044(1113)
4 PF09217 EcoRII-N: Restriction 98.1 1.6E-05 3.5E-10 75.6 8.8 90 118-209 6-110 (156)
5 PF03754 DUF313: Domain of unk 97.7 8.2E-05 1.8E-09 68.0 6.0 81 116-197 18-114 (114)
6 PF02309 AUX_IAA: AUX/IAA fami 94.5 0.012 2.5E-07 58.8 0.4 57 499-563 87-145 (215)
7 smart00743 Agenet Tudor-like d 60.9 13 0.00028 29.6 3.8 27 288-318 2-28 (61)
8 KOG0644 Uncharacterized conser 58.6 5.7 0.00012 47.4 1.9 60 28-87 871-939 (1113)
9 PF11515 Cul7: Mouse developme 57.3 8.5 0.00018 33.5 2.3 71 277-358 6-76 (78)
10 PF04014 Antitoxin-MazE: Antid 51.5 18 0.0004 27.6 3.2 27 193-219 14-40 (47)
11 PF10844 DUF2577: Protein of u 43.8 33 0.00073 30.5 4.1 27 194-220 71-97 (100)
12 PF05641 Agenet: Agenet domain 41.7 48 0.001 27.3 4.4 42 289-341 1-42 (68)
13 TIGR01439 lp_hng_hel_AbrB loop 41.4 38 0.00083 24.7 3.4 27 192-218 13-39 (43)
14 smart00333 TUDOR Tudor domain. 37.3 51 0.0011 25.4 3.7 52 288-357 2-53 (57)
15 PRK03760 hypothetical protein; 33.1 1E+02 0.0022 28.5 5.5 49 160-211 61-117 (117)
16 PF02513 Spin-Ssty: Spin/Ssty 30.3 94 0.002 25.1 4.1 31 291-322 1-31 (50)
17 PF03120 DNA_ligase_OB: NAD-de 27.5 74 0.0016 27.9 3.4 34 192-225 42-76 (82)
18 PF01878 EVE: EVE domain; Int 27.2 62 0.0013 29.9 3.1 26 198-223 38-64 (143)
19 cd04451 S1_IF1 S1_IF1: Transla 25.4 3E+02 0.0065 22.2 6.5 38 161-211 15-52 (64)
20 KOG3207 Beta-tubulin folding c 25.2 65 0.0014 36.5 3.3 41 289-344 3-43 (505)
21 PF02643 DUF192: Uncharacteriz 20.1 2.1E+02 0.0045 25.8 5.0 46 160-208 50-106 (108)
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=4e-35 Score=250.65 Aligned_cols=83 Identities=48% Similarity=0.731 Sum_probs=80.7
Q ss_pred HHHHHHcCCCEEEEEecCCCCCceEEeHHHHHhhhccCcccccEEEEeeeccCCCceeeEEEEEEecCCCCCCCCCCCCC
Q 008078 251 AVERAVLGLPFEVVYYPRAGWADFIVRAEVVDSAMRVFWTAGMRVKMVVETEDSSRMTWIQGTVTAASMPDRGPWCGSPW 330 (578)
Q Consensus 251 A~~~aa~g~~F~V~Y~Pra~~~EFvV~~~~y~~a~~~~w~~GmRFkM~fE~EDssr~~w~~GTI~~v~~~dp~rWp~S~W 330 (578)
|+|+|+++++|+|+||||++++||||++++|++||+++|++||||||+||+||+++++ |+|||++|++.||.+||+|+|
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 AAHAAATGSPFEVFYYPRASPSEFVVPASKYDKALNHPWSVGMRFKMRFETEDSSERR-WQGTIVGVSDLDPIRWPGSKW 79 (83)
T ss_pred ChhHhhcCCeEEEEECCCCCCcceEEEHHHHHHHhcCCCCCCcEEEEEeccCCCccce-eeeEEeEeeccCCCCCCCCCc
Confidence 6899999999999999999999999999999999999999999999999999999887 499999999999999999999
Q ss_pred Ccee
Q 008078 331 GMLE 334 (578)
Q Consensus 331 R~L~ 334 (578)
||||
T Consensus 80 R~Lq 83 (83)
T PF06507_consen 80 RMLQ 83 (83)
T ss_pred ccCc
Confidence 9997
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=99.73 E-value=2.4e-17 Score=141.51 Aligned_cols=97 Identities=29% Similarity=0.448 Sum_probs=74.6
Q ss_pred EEEecccccCCCCCceeEccccccccCCCCCCCCCCCceEEEEEeCCCCeEEEEEEEcCCCcceEeccchhhhhhccCCc
Q 008078 122 FAKILTPSDANNGGGFSVPRFCADSIFPPLNYQVDPPVQNISVTDIHGAVWEFRHIYRGTPRRHLLTTGWSKFVNRKKLI 201 (578)
Q Consensus 122 F~K~LT~SDv~~~grfsVPk~~Ae~~FP~Ld~~~~~p~q~L~~~D~~G~~W~Fr~~yrg~prr~lLTtGWs~FV~~K~L~ 201 (578)
|.|+|+++|+.+.++|.||+++++.+. ++ ...++++.++|..|+.|.+++.+++.+++++|++||..||++++|+
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 899999999999999999999999971 11 1135789999999999999999998888899999999999999999
Q ss_pred CCCEEEEEEcC--CCcEEEEEEEc
Q 008078 202 AGDSVVFMRDS--RGKMYIGLRRS 223 (578)
Q Consensus 202 aGD~VvF~R~~--~G~l~VgIRRa 223 (578)
+||.|+|+... ..++.|.|.|+
T Consensus 76 ~GD~~~F~~~~~~~~~~~v~i~~~ 99 (100)
T PF02362_consen 76 EGDVCVFELIGNSNFTLKVHIFRK 99 (100)
T ss_dssp TT-EEEEEE-SSSCE-EEEEEE--
T ss_pred CCCEEEEEEecCCCceEEEEEEEC
Confidence 99999999865 34679999986
No 3
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=99.41 E-value=1.3e-13 Score=154.81 Aligned_cols=150 Identities=21% Similarity=0.385 Sum_probs=114.0
Q ss_pred CcCCCEEEEEEcCCCcEEEEEEEccCCCCCC---------------------CCCCcccccCccCCHHHHHHHHHHHHcC
Q 008078 200 LIAGDSVVFMRDSRGKMYIGLRRSVRYGNNG---------------------DSAGARWREQTGMKAEAVAVAVERAVLG 258 (578)
Q Consensus 200 L~aGD~VvF~R~~~G~l~VgIRRa~r~~~~~---------------------~~~~~~~~~~~~~~~~~v~~A~~~aa~g 258 (578)
.+.||.|+++|.+..++.=.+|+....-++. +.++. +..+|.+.++-.|. -...
T Consensus 874 pQmgDEViyfrQghqeyl~~~~~n~~~~~~~~p~~~~~v~~~kv~kl~~~~y~~~~~---s~c~m~l~~idp~s--~~~~ 948 (1113)
T KOG0644|consen 874 PQMGDEVIYFRQGHQEYLEAVRLNNIELNNKEPWNKMAVEICKVEKLVYITYPGSGD---SCCKMKLAVIDPAS--KLMD 948 (1113)
T ss_pred ccccceeehhhhhhHHHHhhhhhccccccccCcccccchhhheeeeeeeeeccCCCc---chheeeeeeecchh--hhhh
Confidence 4689999999976555544444444321110 11111 12578886555555 3455
Q ss_pred CCEEEEEecCCCCCceEEeHHHHHhhhccCcccccEEEEeeeccCCCceeeEEEEEEecCCCCCCCCCCCCCCceeeccC
Q 008078 259 LPFEVVYYPRAGWADFIVRAEVVDSAMRVFWTAGMRVKMVVETEDSSRMTWIQGTVTAASMPDRGPWCGSPWGMLEVTWD 338 (578)
Q Consensus 259 ~~F~V~Y~Pra~~~EFvV~~~~y~~a~~~~w~~GmRFkM~fE~EDssr~~w~~GTI~~v~~~dp~rWp~S~WR~L~V~WD 338 (578)
..|.+.|......+||+|.++.|++|++++|..+++||.-|..+-....+||.|+|.+++ +.+..+|+|+|+|..|+||
T Consensus 949 k~F~ltlpdlv~fpDFlV~rsrYd~AiQrnW~~~d~crvwwrda~~e~g~WWeG~ils~~-pksp~fpdSpwery~v~~~ 1027 (1113)
T KOG0644|consen 949 KSFKLTLPDLVTFPDFLVERSRYDAAIQRNWTCRDKCRVWWRDAGEEDGAWWEGRILSVK-PKSPDFPDSPWERYIVRYD 1027 (1113)
T ss_pred ccceeecccccCcchhhhhhhhHHHHHhhccccccceeEEEccCCCcCCceeeeeeeecc-CCCCCCCCCcceeEEEEec
Confidence 679999999999999999999999999999999999999997432223469999999999 5456999999999999999
Q ss_pred ccccccCCCCcCCcceeecCC
Q 008078 339 EPEILQNAKRVSPWQIEFVSP 359 (578)
Q Consensus 339 e~~~~~~~~RVSPWeIEpv~~ 359 (578)
..+. +--||||.|++..
T Consensus 1028 ~~e~----~~~spwe~~~i~d 1044 (1113)
T KOG0644|consen 1028 NTET----ELHSPWEMEPIPD 1044 (1113)
T ss_pred CCcc----cccCccccCCCcc
Confidence 9984 8899999999854
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=98.07 E-value=1.6e-05 Score=75.64 Aligned_cols=90 Identities=20% Similarity=0.277 Sum_probs=59.9
Q ss_pred ceeEEEEecccccCCCCC----ceeEccccccccCCCCCC-CCCCCceEEEEEeCCC--CeEEEEEEEcCC------Ccc
Q 008078 118 NVVAFAKILTPSDANNGG----GFSVPRFCADSIFPPLNY-QVDPPVQNISVTDIHG--AVWEFRHIYRGT------PRR 184 (578)
Q Consensus 118 ~~~~F~K~LT~SDv~~~g----rfsVPk~~Ae~~FP~Ld~-~~~~p~q~L~~~D~~G--~~W~Fr~~yrg~------prr 184 (578)
....|+|.|++.|++.+| |+.|||..++..||.+.. ....|...|.+++..| ..|+||++|.|+ ...
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 567899999999998654 599999999999998766 5567899999999887 668899999975 667
Q ss_pred eEec--cchhhhhhccCCcCCCEEEEE
Q 008078 185 HLLT--TGWSKFVNRKKLIAGDSVVFM 209 (578)
Q Consensus 185 ~lLT--tGWs~FV~~K~L~aGD~VvF~ 209 (578)
+.|| ++-..|.+.. ..||-+||.
T Consensus 86 ~RIT~~G~~~~~~~~~--~tGaL~vla 110 (156)
T PF09217_consen 86 YRITRFGRGFPLQNPE--NTGALLVLA 110 (156)
T ss_dssp EEEE---TTSGGG-GG--GTT-EEEEE
T ss_pred eEEeeecCCCccCCcc--ccccEEEEE
Confidence 8886 3333344332 467777776
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=97.66 E-value=8.2e-05 Score=67.97 Aligned_cols=81 Identities=19% Similarity=0.211 Sum_probs=62.4
Q ss_pred CcceeEEEEecccccCC-CCCceeEccccccccCCCCCC------------CCCCCceEEEEEeCCCCeEEEEEEEcCC-
Q 008078 116 ENNVVAFAKILTPSDAN-NGGGFSVPRFCADSIFPPLNY------------QVDPPVQNISVTDIHGAVWEFRHIYRGT- 181 (578)
Q Consensus 116 ~~~~~~F~K~LT~SDv~-~~grfsVPk~~Ae~~FP~Ld~------------~~~~p~q~L~~~D~~G~~W~Fr~~yrg~- 181 (578)
.+....+.|+|++||+. .+.||+||-..... ...|.. ....-++.+.+.|..++.|..++..|..
T Consensus 18 ~d~kli~~K~L~~tDv~~~qsRLsmP~~qi~~-~dFLt~eE~~~i~~~~~~~~~~~Gv~V~lvdp~~~~~~m~lkkW~mg 96 (114)
T PF03754_consen 18 EDPKLIIEKTLFKTDVDPHQSRLSMPFNQIID-NDFLTEEEKRIIKEEKKNNDKKKGVEVILVDPSLRKWTMRLKKWNMG 96 (114)
T ss_pred CCCeEEEeeeecccCCCCCCceeeccHHHhcc-cccCCHHHHHHHHHhhccCcccCCceEEEECCcCcEEEEEEEEeccc
Confidence 34578999999999998 45899999775533 222321 1234578899999999999999999965
Q ss_pred --CcceEeccchhhhhhc
Q 008078 182 --PRRHLLTTGWSKFVNR 197 (578)
Q Consensus 182 --prr~lLTtGWs~FV~~ 197 (578)
.-.|+|++||..+|++
T Consensus 97 ~~~~~YvL~~gWn~VV~~ 114 (114)
T PF03754_consen 97 NGTSNYVLNSGWNKVVED 114 (114)
T ss_pred CCceEEEEEcChHhhccC
Confidence 5579999999999864
No 6
>PF02309 AUX_IAA: AUX/IAA family; InterPro: IPR003311 The Aux/IAA family of genes are key regulators of auxin-modified gene expression []. The plant hormone auxin (indole-3-acetic acid, IAA) regulates diverse cellular and developmental responses in plants, including cell division, expansion, differentiation and patterning of embryo responses []. Auxin can regulate the gene expression of several families, including GH3 and SAUR, as well as Aux/IAA itself. The Aux/IAA proteins act as repressors of auxin-induced gene expression, possibly through modulating the activity of DNA-binding auxin response factors (ARFs) (IPR010525 from INTERPRO). Aux/IAA and ARF are thought to interact through C-terminal protein-protein interaction domains found in both Aux/IAA and ARF. Recent evidence suggests that Aux/IAA proteins can also mediate light responses []. Some members of the AUX/IAA family are longer and contain an N-terminal DNA binding domain [] and may have an early function in the establishment of vascular and body patterns in embryonic and post-embryonic development in some plants.; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2P1N_F 2P1Q_C 2P1O_C.
Probab=94.51 E-value=0.012 Score=58.76 Aligned_cols=57 Identities=19% Similarity=0.117 Sum_probs=2.5
Q ss_pred cCcccEEEeCeeeccccccccCCCCCcCCCCCCCCcccccCCCCccccc--hhhHHHHHHhhccccc
Q 008078 499 VGVRSIQLFGKIIHMKQPVESGFGDVVCPDDDGSKGFSEREDVNLPLDL--SLTYTELLNRFGIQGR 563 (578)
Q Consensus 499 ~~~~s~~LFGk~I~teqq~~~g~~~~~~~~~~~~k~~~e~e~v~~~~~l--~~sy~~l~~~~~~~~~ 563 (578)
++-+.+.-|-+..+.+.+... ...+|||+|||..|+|.+|| ..+|.+|+..|+-+|+
T Consensus 87 vgwpp~~s~r~n~~~~~~~~~--------~~~~vKV~mdG~~igRkVDL~~~~sY~~L~~~L~~MF~ 145 (215)
T PF02309_consen 87 VGWPPVRSFRKNSLSEKQSSS--------SRSYVKVNMDGVPIGRKVDLSAYSSYEELSSALEKMFS 145 (215)
T ss_dssp TTBS----S----------------------------------------------------------
T ss_pred cCCCccccccccccccccccc--------CCceeEEEecCcccceecCHHHhhCHHHHHHHHHHhcC
Confidence 444556666665544322211 25889999999999999999 8999999988888884
No 7
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=60.94 E-value=13 Score=29.55 Aligned_cols=27 Identities=30% Similarity=0.512 Sum_probs=23.0
Q ss_pred CcccccEEEEeeeccCCCceeeEEEEEEecC
Q 008078 288 FWTAGMRVKMVVETEDSSRMTWIQGTVTAAS 318 (578)
Q Consensus 288 ~w~~GmRFkM~fE~EDssr~~w~~GTI~~v~ 318 (578)
.|.+|++|...++.++ .||.|+|+.+.
T Consensus 2 ~~~~G~~Ve~~~~~~~----~W~~a~V~~~~ 28 (61)
T smart00743 2 DFKKGDRVEVFSKEED----SWWEAVVTKVL 28 (61)
T ss_pred CcCCCCEEEEEECCCC----EEEEEEEEEEC
Confidence 5889999999996533 79999999997
No 8
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=58.55 E-value=5.7 Score=47.41 Aligned_cols=60 Identities=23% Similarity=0.338 Sum_probs=42.1
Q ss_pred ccCCCCCCeEEEecCCcccccCCCC----CCC-----CCCCcceeeeeeEEEeecCCCCceeEEEeeec
Q 008078 28 VQIPSVNSRVYYFPQGHVEQSCPSI----TLS-----VTKPFIPCLITHVEFLADPVTDQVFAKVVLNP 87 (578)
Q Consensus 28 v~lP~~gs~V~YFPqGH~Eq~~~s~----~~~-----~~p~~i~C~V~~V~l~Ad~~TDEVyA~i~L~P 87 (578)
--||+.|..|.||-|||-|-+.+.. ++. ++-..=.|.|..+..--=+..+.--.+|.|.=
T Consensus 871 ryipQmgDEViyfrQghqeyl~~~~~n~~~~~~~~p~~~~~v~~~kv~kl~~~~y~~~~~s~c~m~l~~ 939 (1113)
T KOG0644|consen 871 RYIPQMGDEVIYFRQGHQEYLEAVRLNNIELNNKEPWNKMAVEICKVEKLVYITYPGSGDSCCKMKLAV 939 (1113)
T ss_pred cccccccceeehhhhhhHHHHhhhhhccccccccCcccccchhhheeeeeeeeeccCCCcchheeeeee
Confidence 4689999999999999999987654 111 23345578888776666566666666666643
No 9
>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=57.34 E-value=8.5 Score=33.51 Aligned_cols=71 Identities=17% Similarity=0.138 Sum_probs=38.9
Q ss_pred eHHHHHhhhccCcccccEEEEeeeccCCCceeeEEEEEEecCCCCCCCCCCCCCCceeeccCccccccCCCCcCCcceee
Q 008078 277 RAEVVDSAMRVFWTAGMRVKMVVETEDSSRMTWIQGTVTAASMPDRGPWCGSPWGMLEVTWDEPEILQNAKRVSPWQIEF 356 (578)
Q Consensus 277 ~~~~y~~a~~~~w~~GmRFkM~fE~EDssr~~w~~GTI~~v~~~dp~rWp~S~WR~L~V~WDe~~~~~~~~RVSPWeIEp 356 (578)
+.+.|-..++-+.++||++||.=.-|+-+..- .|+|.-++.. -. +=-.+||.|-.-.. .-.|--=.||+
T Consensus 6 s~d~Ya~YVr~~i~~GM~VRc~~~yeeV~~GD--~G~V~k~~~d-g~-----~~lnvqv~W~~~G~---tyWV~~~~vEi 74 (78)
T PF11515_consen 6 SNDDYAEYVRDNIQPGMRVRCCRDYEEVRAGD--EGEVFKQDRD-GL-----HDLNVQVDWQSKGR---TYWVHWHHVEI 74 (78)
T ss_dssp SSHHHHHHHHHH--TT-EEEESS-BTTB-TT---EEE-EEEE-T-TS-----SE--EEEEETTTTE---EEEEEGGGEEE
T ss_pred chhHHHHHHHHhCCCCcEEEEecccccccccc--cceeEeeccC-CC-----CCcceEEEeeecCc---eEEEEEEEEEE
Confidence 45778888999999999999986666665442 7887766622 21 12358899987653 23343334555
Q ss_pred cC
Q 008078 357 VS 358 (578)
Q Consensus 357 v~ 358 (578)
++
T Consensus 75 ig 76 (78)
T PF11515_consen 75 IG 76 (78)
T ss_dssp --
T ss_pred ec
Confidence 43
No 10
>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=51.51 E-value=18 Score=27.64 Aligned_cols=27 Identities=26% Similarity=0.369 Sum_probs=22.7
Q ss_pred hhhhccCCcCCCEEEEEEcCCCcEEEE
Q 008078 193 KFVNRKKLIAGDSVVFMRDSRGKMYIG 219 (578)
Q Consensus 193 ~FV~~K~L~aGD~VvF~R~~~G~l~Vg 219 (578)
.|.++.+|.+||.|.|.-.++|++.+-
T Consensus 14 ~~~~~l~l~~Gd~v~i~~~~~g~i~i~ 40 (47)
T PF04014_consen 14 EIREKLGLKPGDEVEIEVEGDGKIVIR 40 (47)
T ss_dssp HHHHHTTSSTTTEEEEEEETTSEEEEE
T ss_pred HHHHHcCCCCCCEEEEEEeCCCEEEEE
Confidence 567888999999999999998866554
No 11
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=43.82 E-value=33 Score=30.55 Aligned_cols=27 Identities=33% Similarity=0.503 Sum_probs=22.1
Q ss_pred hhhccCCcCCCEEEEEEcCCCcEEEEE
Q 008078 194 FVNRKKLIAGDSVVFMRDSRGKMYIGL 220 (578)
Q Consensus 194 FV~~K~L~aGD~VvF~R~~~G~l~VgI 220 (578)
|.-...|++||.|..+|.++|+.++-+
T Consensus 71 i~~~~~Lk~GD~V~ll~~~~gQ~yiVl 97 (100)
T PF10844_consen 71 ITFTDGLKVGDKVLLLRVQGGQKYIVL 97 (100)
T ss_pred EEEecCCcCCCEEEEEEecCCCEEEEE
Confidence 666778999999999998888766544
No 12
>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=41.69 E-value=48 Score=27.32 Aligned_cols=42 Identities=26% Similarity=0.404 Sum_probs=26.3
Q ss_pred cccccEEEEeeeccCCCceeeEEEEEEecCCCCCCCCCCCCCCceeeccCccc
Q 008078 289 WTAGMRVKMVVETEDSSRMTWIQGTVTAASMPDRGPWCGSPWGMLEVTWDEPE 341 (578)
Q Consensus 289 w~~GmRFkM~fE~EDssr~~w~~GTI~~v~~~dp~rWp~S~WR~L~V~WDe~~ 341 (578)
|..|++|...-+ |+..+..||.|||+.....+ .+.|+.++-.
T Consensus 1 F~~G~~VEV~s~-e~g~~gaWf~a~V~~~~~~~----------~~~V~Y~~~~ 42 (68)
T PF05641_consen 1 FKKGDEVEVSSD-EDGFRGAWFPATVLKENGDD----------KYLVEYDDLP 42 (68)
T ss_dssp --TT-EEEEEE--SBTT--EEEEEEEEEEETT-----------EEEEEETT-S
T ss_pred CCCCCEEEEEEc-CCCCCcEEEEEEEEEeCCCc----------EEEEEECCcc
Confidence 467999988654 45568899999999987222 7788887643
No 13
>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=41.36 E-value=38 Score=24.66 Aligned_cols=27 Identities=19% Similarity=0.375 Sum_probs=22.5
Q ss_pred hhhhhccCCcCCCEEEEEEcCCCcEEE
Q 008078 192 SKFVNRKKLIAGDSVVFMRDSRGKMYI 218 (578)
Q Consensus 192 s~FV~~K~L~aGD~VvF~R~~~G~l~V 218 (578)
..|.++-++..||.|.+....+|.+.+
T Consensus 13 ~~~r~~l~~~~gd~~~i~~~~~~~l~l 39 (43)
T TIGR01439 13 KEIREKLGLKEGDRLEVIRVEDGEIIL 39 (43)
T ss_pred HHHHHHcCcCCCCEEEEEEeCCCEEEE
Confidence 368899999999999999877776554
No 14
>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=37.31 E-value=51 Score=25.39 Aligned_cols=52 Identities=13% Similarity=0.220 Sum_probs=34.8
Q ss_pred CcccccEEEEeeeccCCCceeeEEEEEEecCCCCCCCCCCCCCCceeeccCccccccCCCCcCCcceeec
Q 008078 288 FWTAGMRVKMVVETEDSSRMTWIQGTVTAASMPDRGPWCGSPWGMLEVTWDEPEILQNAKRVSPWQIEFV 357 (578)
Q Consensus 288 ~w~~GmRFkM~fE~EDssr~~w~~GTI~~v~~~dp~rWp~S~WR~L~V~WDe~~~~~~~~RVSPWeIEpv 357 (578)
.|.+|..+...+ .+. .||.|+|+++... ....|.-++-.. .+.|...+|-++
T Consensus 2 ~~~~G~~~~a~~-~d~----~wyra~I~~~~~~----------~~~~V~f~D~G~---~~~v~~~~l~~l 53 (57)
T smart00333 2 TFKVGDKVAARW-EDG----EWYRARIIKVDGE----------QLYEVFFIDYGN---EEVVPPSDLRPL 53 (57)
T ss_pred CCCCCCEEEEEe-CCC----CEEEEEEEEECCC----------CEEEEEEECCCc---cEEEeHHHeecC
Confidence 588999999999 332 6999999999721 446677766432 345555554443
No 15
>PRK03760 hypothetical protein; Provisional
Probab=33.09 E-value=1e+02 Score=28.48 Aligned_cols=49 Identities=22% Similarity=0.449 Sum_probs=31.6
Q ss_pred eEEEEEeCCCCeEEEEE-----EEc-CCCcceEe--ccchhhhhhccCCcCCCEEEEEEc
Q 008078 160 QNISVTDIHGAVWEFRH-----IYR-GTPRRHLL--TTGWSKFVNRKKLIAGDSVVFMRD 211 (578)
Q Consensus 160 q~L~~~D~~G~~W~Fr~-----~yr-g~prr~lL--TtGWs~FV~~K~L~aGD~VvF~R~ 211 (578)
.++.+.|.+|++=.... +|. ..+-+|+| ..|| +.+.++++||.|.|.|+
T Consensus 61 LDiiFld~~g~Vv~i~~~~P~~~~~~~~~a~~VLEl~aG~---~~~~gi~~Gd~v~~~~~ 117 (117)
T PRK03760 61 IDVIFLDSNRRVVDFKTLKPWRIYVPKKPARYIIEGPVGK---IRVLKVEVGDEIEWIDE 117 (117)
T ss_pred eEEEEECCCCeEEEEEeCCCccccCCCccceEEEEeCCCh---HHHcCCCCCCEEEEeeC
Confidence 44566666665443211 122 34456888 6787 78999999999998763
No 16
>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=30.32 E-value=94 Score=25.10 Aligned_cols=31 Identities=26% Similarity=0.428 Sum_probs=22.6
Q ss_pred cccEEEEeeeccCCCceeeEEEEEEecCCCCC
Q 008078 291 AGMRVKMVVETEDSSRMTWIQGTVTAASMPDR 322 (578)
Q Consensus 291 ~GmRFkM~fE~EDssr~~w~~GTI~~v~~~dp 322 (578)
+|-|+.-.||.++.+...| .|+|...-+..|
T Consensus 1 vGk~Veh~~~~g~g~~s~w-~G~Vl~Qvp~~p 31 (50)
T PF02513_consen 1 VGKRVEHTWEDGDGPKSKW-KGMVLHQVPAKP 31 (50)
T ss_dssp TT-EEEEEECTSTS-EEEE-EEEEEEE-TTST
T ss_pred CCceEEEEEccCCCcccEE-EEEEEEEeecCC
Confidence 5889999999998887775 999998765544
No 17
>PF03120 DNA_ligase_OB: NAD-dependent DNA ligase OB-fold domain; InterPro: IPR004150 DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This family is a small domain found after the adenylation domain DNA_ligase_N in NAD+-dependent ligases (IPR001679 from INTERPRO). OB-fold domains generally are involved in nucleic acid binding.; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 2OWO_A 1TAE_A 3UQ8_A 1DGS_A 1V9P_B 3SGI_A.
Probab=27.55 E-value=74 Score=27.93 Aligned_cols=34 Identities=18% Similarity=0.353 Sum_probs=22.4
Q ss_pred hhhhhccCCcCCCEEEEEEcCCCc-EEEEEEEccC
Q 008078 192 SKFVNRKKLIAGDSVVFMRDSRGK-MYIGLRRSVR 225 (578)
Q Consensus 192 s~FV~~K~L~aGD~VvF~R~~~G~-l~VgIRRa~r 225 (578)
-.|+++++|..||.|.++|..+.= ..+++-...|
T Consensus 42 ~~~i~~~~i~~Gd~V~V~raGdVIP~I~~vv~~~r 76 (82)
T PF03120_consen 42 YDYIKELDIRIGDTVLVTRAGDVIPKIVGVVKEKR 76 (82)
T ss_dssp HHHHHHTT-BBT-EEEEEEETTTEEEEEEE-GGG-
T ss_pred HHHHHHcCCCCCCEEEEEECCCccceEeEeehhcC
Confidence 378999999999999999987652 3444444443
No 18
>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=27.17 E-value=62 Score=29.94 Aligned_cols=26 Identities=19% Similarity=0.492 Sum_probs=16.1
Q ss_pred cCCcCCCEEEEEEcC-CCcEEEEEEEc
Q 008078 198 KKLIAGDSVVFMRDS-RGKMYIGLRRS 223 (578)
Q Consensus 198 K~L~aGD~VvF~R~~-~G~l~VgIRRa 223 (578)
++++.||.|+||... .+.-+||+=+-
T Consensus 38 ~~mk~GD~vifY~s~~~~~~ivai~~V 64 (143)
T PF01878_consen 38 KRMKPGDKVIFYHSGCKERGIVAIGEV 64 (143)
T ss_dssp HC--TT-EEEEEETSSSS-EEEEEEEE
T ss_pred hcCCCCCEEEEEEcCCCCCEEEEEEEE
Confidence 489999999999977 45555655443
No 19
>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=25.43 E-value=3e+02 Score=22.18 Aligned_cols=38 Identities=24% Similarity=0.219 Sum_probs=22.9
Q ss_pred EEEEEeCCCCeEEEEEEEcCCCcceEeccchhhhhhccCCcCCCEEEEEEc
Q 008078 161 NISVTDIHGAVWEFRHIYRGTPRRHLLTTGWSKFVNRKKLIAGDSVVFMRD 211 (578)
Q Consensus 161 ~L~~~D~~G~~W~Fr~~yrg~prr~lLTtGWs~FV~~K~L~aGD~VvF~R~ 211 (578)
...+++..|. .++|..||+-|+ +...+.+||.|.|...
T Consensus 15 ~~~V~~~~g~--~~~c~~rGklr~-----------~~~~~~vGD~V~~~~~ 52 (64)
T cd04451 15 MFRVELENGH--EVLAHISGKMRM-----------NYIRILPGDRVKVELS 52 (64)
T ss_pred EEEEEeCCCC--EEEEEECceeec-----------CCcccCCCCEEEEEEe
Confidence 3445666676 445555543221 2334899999999864
No 20
>KOG3207 consensus Beta-tubulin folding cofactor E [Posttranslational modification, protein turnover, chaperones]
Probab=25.21 E-value=65 Score=36.53 Aligned_cols=41 Identities=29% Similarity=0.470 Sum_probs=28.2
Q ss_pred cccccEEEEeeeccCCCceeeEEEEEEecCCCCCCCCCCCCCCceeeccCcccccc
Q 008078 289 WTAGMRVKMVVETEDSSRMTWIQGTVTAASMPDRGPWCGSPWGMLEVTWDEPEILQ 344 (578)
Q Consensus 289 w~~GmRFkM~fE~EDssr~~w~~GTI~~v~~~dp~rWp~S~WR~L~V~WDe~~~~~ 344 (578)
..+|.|+|...|- +- ..|.|+|.+. ++ +| +.|.||++.-+.
T Consensus 3 ~~IG~RvkI~~~~---~T-vr~iG~V~g~--------~~-~w--~GvEWDd~~RGK 43 (505)
T KOG3207|consen 3 MEIGTRVKIGGEI---AT-VRYIGEVEGN--------NS-KW--YGVEWDDPVRGK 43 (505)
T ss_pred eeccceEEEcCEE---EE-EEEEEEEcCC--------CC-cc--eeeEecCCCccc
Confidence 4689999987663 11 2377877754 33 45 899999987653
No 21
>PF02643 DUF192: Uncharacterized ACR, COG1430; InterPro: IPR003795 This entry describes proteins of unknown function.; PDB: 3M7A_B 3PJY_B.
Probab=20.07 E-value=2.1e+02 Score=25.76 Aligned_cols=46 Identities=26% Similarity=0.479 Sum_probs=28.7
Q ss_pred eEEEEEeCCCCeEEEEEEEc---------CCCcceEe--ccchhhhhhccCCcCCCEEEE
Q 008078 160 QNISVTDIHGAVWEFRHIYR---------GTPRRHLL--TTGWSKFVNRKKLIAGDSVVF 208 (578)
Q Consensus 160 q~L~~~D~~G~~W~Fr~~yr---------g~prr~lL--TtGWs~FV~~K~L~aGD~VvF 208 (578)
.++.+.|..|++=....... ..+-+|+| ..|| +.+.+|++||.|.|
T Consensus 50 LDi~fld~~g~Vv~i~~~~~P~~~~~~~~~~~a~~vLE~~aG~---~~~~~i~~Gd~v~~ 106 (108)
T PF02643_consen 50 LDIAFLDSDGRVVKIERMVPPWRTYPCPSYKPARYVLELPAGW---FEKLGIKVGDRVRI 106 (108)
T ss_dssp EEEEEE-TTSBEEEEEEEE-TT--S-EEECCEECEEEEEETTH---HHHHT--TT-EEE-
T ss_pred EEEEEECCCCeEEEEEccCCCCccCCCCCCCccCEEEEcCCCc---hhhcCCCCCCEEEe
Confidence 66888888887766555441 13347888 5665 88999999999986
Done!