Query 008608
Match_columns 560
No_of_seqs 220 out of 448
Neff 3.8
Searched_HMMs 46136
Date Thu Mar 28 14:18:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008608.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008608hhsearch_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 3.8E-36 8.2E-41 255.7 9.0 83 107-189 1-83 (83)
2 KOG0644 Uncharacterized conser 99.7 7.9E-18 1.7E-22 187.0 6.1 150 59-215 874-1045(1113)
3 PF02362 B3: B3 DNA binding do 99.1 1.2E-10 2.7E-15 98.3 6.2 65 18-82 33-99 (100)
4 PRK10737 FKBP-type peptidyl-pr 72.5 14 0.0003 36.9 7.4 104 58-174 2-114 (196)
5 PF03754 DUF313: Domain of unk 62.4 8.4 0.00018 35.5 3.4 40 17-56 72-114 (114)
6 KOG3207 Beta-tubulin folding c 53.2 16 0.00034 41.1 4.1 42 145-200 3-44 (505)
7 smart00743 Agenet Tudor-like d 53.2 23 0.00049 27.9 4.0 38 144-194 2-39 (61)
8 PF09217 EcoRII-N: Restriction 49.6 34 0.00074 33.4 5.3 63 3-68 36-110 (156)
9 PF05641 Agenet: Agenet domain 44.5 56 0.0012 26.8 5.2 42 145-196 1-42 (68)
10 PF02513 Spin-Ssty: Spin/Ssty 43.4 36 0.00077 27.6 3.7 32 147-178 1-32 (50)
11 PF02309 AUX_IAA: AUX/IAA fami 34.2 15 0.00033 36.4 0.4 16 544-559 102-117 (215)
12 COG1047 SlpA FKBP-type peptidy 33.2 2.4E+02 0.0052 28.1 8.4 106 57-174 1-115 (174)
13 PF10844 DUF2577: Protein of u 32.5 76 0.0016 28.2 4.4 27 53-79 71-97 (100)
14 PF04014 Antitoxin-MazE: Antid 29.9 37 0.0008 25.9 1.8 26 53-78 15-40 (47)
15 smart00333 TUDOR Tudor domain. 29.7 92 0.002 23.8 4.0 51 144-211 2-52 (57)
16 PF11515 Cul7: Mouse developme 28.7 49 0.0011 29.1 2.5 71 133-213 6-76 (78)
17 PF01878 EVE: EVE domain; Int 27.6 58 0.0013 29.8 3.0 38 45-82 20-64 (143)
18 TIGR01439 lp_hng_hel_AbrB loop 25.2 55 0.0012 23.7 1.9 26 52-77 14-39 (43)
19 PF14478 DUF4430: Domain of un 21.1 54 0.0012 26.8 1.3 15 54-68 54-68 (68)
20 PRK15095 FKBP-type peptidyl-pr 20.2 5.1E+02 0.011 24.7 7.9 106 57-174 3-118 (156)
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=3.8e-36 Score=255.73 Aligned_cols=83 Identities=55% Similarity=1.044 Sum_probs=81.5
Q ss_pred HHHHHHcCCeEEEEEecCCCCCceeEehhhHHHHhcCCcccccEEEEEecCCCCCCceeeEEEEEeecCCCCCCCCCCce
Q 008608 107 AWHAVSTGTMFTVYYKPRTSPSEFIVPYDQYMESIKNNYSIGMRFKMRFEGEEAPEQRFTGTIVGIEDADPQRWRDSKWR 186 (560)
Q Consensus 107 A~~aaatgs~F~V~Y~PRas~sEFVVp~~ky~eAl~~~ws~GMRFKM~fE~Edss~~r~~GTI~gi~d~DP~rWP~S~WR 186 (560)
|+|||+++++|+|+||||++++|||||+++|++||+++|++||||||+||+||+++++|+|||+||+++||.|||+|+||
T Consensus 1 A~~aa~~~~~F~V~Y~PRa~~sEFVV~~~k~~~al~~~~~~GmRfkM~fE~eds~~~~~~GtI~~v~~~dp~~w~~S~WR 80 (83)
T PF06507_consen 1 AAHAAATGSPFEVFYYPRASPSEFVVPASKYDKALNHPWSVGMRFKMRFETEDSSERRWQGTIVGVSDLDPIRWPGSKWR 80 (83)
T ss_pred ChhHhhcCCeEEEEECCCCCCcceEEEHHHHHHHhcCCCCCCcEEEEEeccCCCccceeeeEEeEeeccCCCCCCCCCcc
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeE
Q 008608 187 CLK 189 (560)
Q Consensus 187 ~L~ 189 (560)
|||
T Consensus 81 ~Lq 83 (83)
T PF06507_consen 81 MLQ 83 (83)
T ss_pred cCc
Confidence 996
No 2
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=99.70 E-value=7.9e-18 Score=187.01 Aligned_cols=150 Identities=24% Similarity=0.382 Sum_probs=124.9
Q ss_pred CCCCCEEEEEeCCCCcEEEEEEeeccccCCC---------------------CCccccCCCcchhHHHHHHHHHHcCCeE
Q 008608 59 LVAGDAFIFLRGENGELRVGVRRAMRQQGNV---------------------PSSVISSHSMHLGVLATAWHAVSTGTMF 117 (560)
Q Consensus 59 LvaGDsVvF~R~~~geL~VGVRRa~r~~~~~---------------------p~svis~~~m~l~vLa~A~~aaatgs~F 117 (560)
++.||.|+|||+++.++.-.+|+..+..++. |.+.-+.++|.|.||+.|.++ ....|
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 4599999999998777666666554433221 233345678999999999865 46789
Q ss_pred EEEEecCCCCCceeEehhhHHHHhcCCcccccEEEEEecCCCC-CCceeeEEEEEeecCCCCCCCCCCceeeEeeecCCC
Q 008608 118 TVYYKPRTSPSEFIVPYDQYMESIKNNYSIGMRFKMRFEGEEA-PEQRFTGTIVGIEDADPQRWRDSKWRCLKVRWDETS 196 (560)
Q Consensus 118 ~V~Y~PRas~sEFVVp~~ky~eAl~~~ws~GMRFKM~fE~Eds-s~~r~~GTI~gi~d~DP~rWP~S~WR~L~VrWDe~~ 196 (560)
.+.|....+.+||+|.++.|++|+++||.++++||..+.++-- -..||.|+|.++.+..|. +|+|+|+|+.|+||.++
T Consensus 952 ~ltlpdlv~fpDFlV~rsrYd~AiQrnW~~~d~crvwwrda~~e~g~WWeG~ils~~pksp~-fpdSpwery~v~~~~~e 1030 (1113)
T KOG0644|consen 952 KLTLPDLVTFPDFLVERSRYDAAIQRNWTCRDKCRVWWRDAGEEDGAWWEGRILSVKPKSPD-FPDSPWERYIVRYDNTE 1030 (1113)
T ss_pred eeecccccCcchhhhhhhhHHHHHhhccccccceeEEEccCCCcCCceeeeeeeeccCCCCC-CCCCcceeEEEEecCCc
Confidence 9999999999999999999999999999999999999975421 227999999999999997 99999999999999998
Q ss_pred CCCCCCCcccCeeeecCCC
Q 008608 197 TIPRPERVSLWKIEPALAP 215 (560)
Q Consensus 197 ~~~~~eRVSPWeIEpv~s~ 215 (560)
.+--||||+|++..-
T Consensus 1031 ----~~~~spwe~~~i~de 1045 (1113)
T KOG0644|consen 1031 ----TELHSPWEMEPIPDE 1045 (1113)
T ss_pred ----ccccCccccCCCccc
Confidence 567799999998765
No 3
>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=99.11 E-value=1.2e-10 Score=98.29 Aligned_cols=65 Identities=31% Similarity=0.526 Sum_probs=52.9
Q ss_pred CceEEEeeCCCCeeEEeEEecCCCCceeeccccceeeecCCCCCCCEEEEEeCC--CCcEEEEEEee
Q 008608 18 TQELAAKDLHGNEWRFRHIFRGQPRRHLLQSGWSVFVSSKRLVAGDAFIFLRGE--NGELRVGVRRA 82 (560)
Q Consensus 18 sq~L~~~D~~G~~W~Frhiyrg~prrhlLT~GWs~FV~~KkLvaGDsVvF~R~~--~geL~VGVRRa 82 (560)
.+++.++|..|++|.+++.+++.+.+++|+.||..||++++|+.||.|+|...+ ..++.|.|.|+
T Consensus 33 ~~~v~l~~~~g~~W~v~~~~~~~~~~~~l~~GW~~Fv~~n~L~~GD~~~F~~~~~~~~~~~v~i~~~ 99 (100)
T PF02362_consen 33 SREVTLKDPDGRSWPVKLKYRKNSGRYYLTGGWKKFVRDNGLKEGDVCVFELIGNSNFTLKVHIFRK 99 (100)
T ss_dssp -CEEEEEETTTEEEEEEEEEECCTTEEEEETTHHHHHHHCT--TT-EEEEEE-SSSCE-EEEEEE--
T ss_pred CeEEEEEeCCCCEEEEEEEEEccCCeEEECCCHHHHHHHcCCCCCCEEEEEEecCCCceEEEEEEEC
Confidence 568999999999999999999988889999999999999999999999999854 45569999875
No 4
>PRK10737 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=72.46 E-value=14 Score=36.92 Aligned_cols=104 Identities=22% Similarity=0.275 Sum_probs=65.7
Q ss_pred CCCCCCEEEE---EeCCCCcEEEEEEeeccccCCCCCccccCCCcchhHHHHHHHHHHcCCeEEEEEecCC------CCC
Q 008608 58 RLVAGDAFIF---LRGENGELRVGVRRAMRQQGNVPSSVISSHSMHLGVLATAWHAVSTGTMFTVYYKPRT------SPS 128 (560)
Q Consensus 58 kLvaGDsVvF---~R~~~geL~VGVRRa~r~~~~~p~svis~~~m~l~vLa~A~~aaatgs~F~V~Y~PRa------s~s 128 (560)
++..|+.|.+ +|.++|+++---+ ...|...+-....-+--|++|..-...|..|+|.--|-. .-.
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------VSAPLDYLHGHGSLISGLETALEGHEVGDKFDVAVGANDAYGQYDENL 75 (196)
T ss_pred ccCCCCEEEEEEEEEeCCCCEEEecC------CCCCeEEEeCCCcchHHHHHHHcCCCCCCEEEEEEChHHhcCCCChHH
Confidence 4566777766 3456777644322 123444443344445567788878889999999865542 223
Q ss_pred ceeEehhhHHHHhcCCcccccEEEEEecCCCCCCceeeEEEEEeec
Q 008608 129 EFIVPYDQYMESIKNNYSIGMRFKMRFEGEEAPEQRFTGTIVGIED 174 (560)
Q Consensus 129 EFVVp~~ky~eAl~~~ws~GMRFKM~fE~Edss~~r~~GTI~gi~d 174 (560)
-..||++.|.... ...+||||.+. +++ ....++|+.|.+
T Consensus 76 V~~vpr~~F~~~~--~l~~G~~~~~~--~~~---G~~~~~V~ev~~ 114 (196)
T PRK10737 76 VQRVPKDVFMGVD--ELQVGMRFLAE--TDQ---GPVPVEITAVED 114 (196)
T ss_pred EEEecHHHCCCcc--CCCCCCEEEEe--CCC---CcEEEEEEEEcC
Confidence 4678888885322 36899999874 443 246889999875
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=62.39 E-value=8.4 Score=35.51 Aligned_cols=40 Identities=23% Similarity=0.331 Sum_probs=33.5
Q ss_pred CCceEEEeeCCCCeeEEeEEecCC---CCceeeccccceeeec
Q 008608 17 PTQELAAKDLHGNEWRFRHIFRGQ---PRRHLLQSGWSVFVSS 56 (560)
Q Consensus 17 Psq~L~~~D~~G~~W~Frhiyrg~---prrhlLT~GWs~FV~~ 56 (560)
-..+..+.|..+..|.-+.-.|.. .-.|+|++||..+|+.
T Consensus 72 ~Gv~V~lvdp~~~~~~m~lkkW~mg~~~~~YvL~~gWn~VV~~ 114 (114)
T PF03754_consen 72 KGVEVILVDPSLRKWTMRLKKWNMGNGTSNYVLNSGWNKVVED 114 (114)
T ss_pred CCceEEEECCcCcEEEEEEEEecccCCceEEEEEcChHhhccC
Confidence 355688999999999999999965 4579999999998863
No 6
>KOG3207 consensus Beta-tubulin folding cofactor E [Posttranslational modification, protein turnover, chaperones]
Probab=53.24 E-value=16 Score=41.12 Aligned_cols=42 Identities=29% Similarity=0.483 Sum_probs=28.2
Q ss_pred cccccEEEEEecCCCCCCceeeEEEEEeecCCCCCCCCCCceeeEeeecCCCCCCC
Q 008608 145 YSIGMRFKMRFEGEEAPEQRFTGTIVGIEDADPQRWRDSKWRCLKVRWDETSTIPR 200 (560)
Q Consensus 145 ws~GMRFKM~fE~Edss~~r~~GTI~gi~d~DP~rWP~S~WR~L~VrWDe~~~~~~ 200 (560)
+.+|+|+|...+- +..||.|+|. + |++ +| |.|.||++.-.-+
T Consensus 3 ~~IG~RvkI~~~~---~Tvr~iG~V~------g--~~~-~w--~GvEWDd~~RGKH 44 (505)
T KOG3207|consen 3 MEIGTRVKIGGEI---ATVRYIGEVE------G--NNS-KW--YGVEWDDPVRGKH 44 (505)
T ss_pred eeccceEEEcCEE---EEEEEEEEEc------C--CCC-cc--eeeEecCCCcccc
Confidence 5689999986653 1245555554 3 555 44 8999999986544
No 7
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=53.22 E-value=23 Score=27.93 Aligned_cols=38 Identities=13% Similarity=0.171 Sum_probs=29.3
Q ss_pred CcccccEEEEEecCCCCCCceeeEEEEEeecCCCCCCCCCCceeeEeeecC
Q 008608 144 NYSIGMRFKMRFEGEEAPEQRFTGTIVGIEDADPQRWRDSKWRCLKVRWDE 194 (560)
Q Consensus 144 ~ws~GMRFKM~fE~Edss~~r~~GTI~gi~d~DP~rWP~S~WR~L~VrWDe 194 (560)
.|.+|+++...++.++ .||.|+|+.+.. -..+.|.-+.
T Consensus 2 ~~~~G~~Ve~~~~~~~---~W~~a~V~~~~~----------~~~~~V~~~~ 39 (61)
T smart00743 2 DFKKGDRVEVFSKEED---SWWEAVVTKVLG----------DGKYLVRYLT 39 (61)
T ss_pred CcCCCCEEEEEECCCC---EEEEEEEEEECC----------CCEEEEEECC
Confidence 5889999999996533 799999999975 1236777766
No 8
>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=49.56 E-value=34 Score=33.44 Aligned_cols=63 Identities=13% Similarity=0.243 Sum_probs=35.6
Q ss_pred ccccCCCCCC-CCCCCCceEEEeeCCC--CeeEEeEEecCC-----CC-ceeeccccce---eeecCCCCCCCEEEEE
Q 008608 3 MSVFHPWLDM-SRQPPTQELAAKDLHG--NEWRFRHIFRGQ-----PR-RHLLQSGWSV---FVSSKRLVAGDAFIFL 68 (560)
Q Consensus 3 Ae~~FPpLD~-s~~~Psq~L~~~D~~G--~~W~Frhiyrg~-----pr-rhlLT~GWs~---FV~~KkLvaGDsVvF~ 68 (560)
++.+||.|.. ...-|...|.+++..+ ..|+||.||-++ -| -+-|| .|-. |.+.. ..||-+||-
T Consensus 36 ~~~lFp~~~~~~~~Np~~~~~~~~~s~~~~~~~~r~iYYnn~~~~gTRNE~RIT-~~G~~~~~~~~~--~tGaL~vla 110 (156)
T PF09217_consen 36 AELLFPSINHTKEENPDIWLKARWQSHFVTDSQVRFIYYNNRLFGGTRNEYRIT-RFGRGFPLQNPE--NTGALLVLA 110 (156)
T ss_dssp HHHH-GGG-SSSSSS-EEEEEEEETTTT---EEEEEEEE-CCCTTSS--EEEEE----TTSGGG-GG--GTT-EEEEE
T ss_pred HHHhCCCCCcccccCCceeEEEEECCCCccceeEEEEEEcccccCCCcCceEEe-eecCCCccCCcc--ccccEEEEE
Confidence 4678999876 4445889999999988 669999999986 23 23444 3333 43322 367777765
No 9
>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=44.54 E-value=56 Score=26.79 Aligned_cols=42 Identities=14% Similarity=0.249 Sum_probs=28.1
Q ss_pred cccccEEEEEecCCCCCCceeeEEEEEeecCCCCCCCCCCceeeEeeecCCC
Q 008608 145 YSIGMRFKMRFEGEEAPEQRFTGTIVGIEDADPQRWRDSKWRCLKVRWDETS 196 (560)
Q Consensus 145 ws~GMRFKM~fE~Edss~~r~~GTI~gi~d~DP~rWP~S~WR~L~VrWDe~~ 196 (560)
|..|+++...-+.+...-.||.|+|+.....+ .+.|+.++-.
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 56899999988776665599999999998532 7888886554
No 10
>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=43.41 E-value=36 Score=27.58 Aligned_cols=32 Identities=22% Similarity=0.559 Sum_probs=25.7
Q ss_pred cccEEEEEecCCCCCCceeeEEEEEeecCCCC
Q 008608 147 IGMRFKMRFEGEEAPEQRFTGTIVGIEDADPQ 178 (560)
Q Consensus 147 ~GMRFKM~fE~Edss~~r~~GTI~gi~d~DP~ 178 (560)
+|-|+.-.||+++.+...|.|+|....++-|.
T Consensus 1 vGk~Veh~~~~g~g~~s~w~G~Vl~Qvp~~ps 32 (50)
T PF02513_consen 1 VGKRVEHTWEDGDGPKSKWKGMVLHQVPAKPS 32 (50)
T ss_dssp TT-EEEEEECTSTS-EEEEEEEEEEE-TTSTT
T ss_pred CCceEEEEEccCCCcccEEEEEEEEEeecCCc
Confidence 58899999999988888889999999988775
No 11
>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=34.19 E-value=15 Score=36.38 Aligned_cols=16 Identities=38% Similarity=0.468 Sum_probs=0.0
Q ss_pred cCCCCCCcceeeccCC
Q 008608 544 KTQCGSTRSCTKVPLP 559 (560)
Q Consensus 544 k~q~~StRsctKVhKq 559 (560)
..+.++.|+|+|||++
T Consensus 102 ~~~~~~~~~~vKV~md 117 (215)
T PF02309_consen 102 EKQSSSSRSYVKVNMD 117 (215)
T ss_dssp ----------------
T ss_pred ccccccCCceeEEEec
Confidence 4556667999999985
No 12
>COG1047 SlpA FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]
Probab=33.23 E-value=2.4e+02 Score=28.09 Aligned_cols=106 Identities=23% Similarity=0.354 Sum_probs=68.2
Q ss_pred CCCCCCCEEEE---EeCCCCcEEEEEEeeccccCCCCCccccCCCcchhHHHHHHHHHHcCCeEEEEEecCCCCCce---
Q 008608 57 KRLVAGDAFIF---LRGENGELRVGVRRAMRQQGNVPSSVISSHSMHLGVLATAWHAVSTGTMFTVYYKPRTSPSEF--- 130 (560)
Q Consensus 57 KkLvaGDsVvF---~R~~~geL~VGVRRa~r~~~~~p~svis~~~m~l~vLa~A~~aaatgs~F~V~Y~PRas~sEF--- 130 (560)
+++..||.|.. +|.++|+++---.- ...|-.++-.+..-+.-|++|......|.-|+|.--|-..-.++
T Consensus 1 m~i~k~~~V~i~Y~~~~~dg~v~Dtt~e-----~~~P~~~i~G~g~li~glE~al~g~~~Ge~~~V~IpPE~AfGe~~~~ 75 (174)
T COG1047 1 MKIEKGDVVSLHYTLKVEDGEVVDTTDE-----NYGPLTFIVGAGQLIPGLEEALLGKEVGEEFTVEIPPEDAFGEYDPD 75 (174)
T ss_pred CcccCCCEEEEEEEEEecCCcEEEcccc-----cCCCeEEEecCCCcchhHHHHHhCCCCCceeEEEeCchHhcCCCChH
Confidence 35667887776 24455665432221 12244444445555566788888889999999998886544443
Q ss_pred ---eEehhhHHHHhcCCcccccEEEEEecCCCCCCceeeEEEEEeec
Q 008608 131 ---IVPYDQYMESIKNNYSIGMRFKMRFEGEEAPEQRFTGTIVGIED 174 (560)
Q Consensus 131 ---VVp~~ky~eAl~~~ws~GMRFKM~fE~Edss~~r~~GTI~gi~d 174 (560)
+||+.+|...= ...+||+|.+ ++++ .-.-|+|+.|..
T Consensus 76 lvq~vp~~~F~~~~--~~~vGm~~~~--~~~~---~~~~~~V~~V~~ 115 (174)
T COG1047 76 LVQRVPRDEFQGVG--ELEVGMEVEA--EGGD---GEIPGVVTEVSG 115 (174)
T ss_pred HeEEecHHHhCcCC--CCCCCcEEEE--cCCC---ceeeEEEEEEcC
Confidence 56777766543 6889999874 4444 356899999874
No 13
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=32.50 E-value=76 Score=28.17 Aligned_cols=27 Identities=22% Similarity=0.383 Sum_probs=23.0
Q ss_pred eeecCCCCCCCEEEEEeCCCCcEEEEE
Q 008608 53 FVSSKRLVAGDAFIFLRGENGELRVGV 79 (560)
Q Consensus 53 FV~~KkLvaGDsVvF~R~~~geL~VGV 79 (560)
|.-...|++||.|+-+|..+|+.|+=+
T Consensus 71 i~~~~~Lk~GD~V~ll~~~~gQ~yiVl 97 (100)
T PF10844_consen 71 ITFTDGLKVGDKVLLLRVQGGQKYIVL 97 (100)
T ss_pred EEEecCCcCCCEEEEEEecCCCEEEEE
Confidence 666778999999999998888877654
No 14
>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=29.92 E-value=37 Score=25.89 Aligned_cols=26 Identities=15% Similarity=0.194 Sum_probs=20.6
Q ss_pred eeecCCCCCCCEEEEEeCCCCcEEEE
Q 008608 53 FVSSKRLVAGDAFIFLRGENGELRVG 78 (560)
Q Consensus 53 FV~~KkLvaGDsVvF~R~~~geL~VG 78 (560)
|..+-+|.+||.|.+.-.++|+|.+-
T Consensus 15 ~~~~l~l~~Gd~v~i~~~~~g~i~i~ 40 (47)
T PF04014_consen 15 IREKLGLKPGDEVEIEVEGDGKIVIR 40 (47)
T ss_dssp HHHHTTSSTTTEEEEEEETTSEEEEE
T ss_pred HHHHcCCCCCCEEEEEEeCCCEEEEE
Confidence 44566899999999999988866553
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=29.75 E-value=92 Score=23.80 Aligned_cols=51 Identities=14% Similarity=0.356 Sum_probs=36.1
Q ss_pred CcccccEEEEEecCCCCCCceeeEEEEEeecCCCCCCCCCCceeeEeeecCCCCCCCCCCcccCeeee
Q 008608 144 NYSIGMRFKMRFEGEEAPEQRFTGTIVGIEDADPQRWRDSKWRCLKVRWDETSTIPRPERVSLWKIEP 211 (560)
Q Consensus 144 ~ws~GMRFKM~fE~Edss~~r~~GTI~gi~d~DP~rWP~S~WR~L~VrWDe~~~~~~~eRVSPWeIEp 211 (560)
.|.+|..+..++ .+ ..||.|+|+++... ..+.|.-++-.. .+-|...+|-+
T Consensus 2 ~~~~G~~~~a~~-~d---~~wyra~I~~~~~~----------~~~~V~f~D~G~---~~~v~~~~l~~ 52 (57)
T smart00333 2 TFKVGDKVAARW-ED---GEWYRARIIKVDGE----------QLYEVFFIDYGN---EEVVPPSDLRP 52 (57)
T ss_pred CCCCCCEEEEEe-CC---CCEEEEEEEEECCC----------CEEEEEEECCCc---cEEEeHHHeec
Confidence 588999999999 43 27999999999741 457788877443 34555555543
No 16
>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=28.70 E-value=49 Score=29.07 Aligned_cols=71 Identities=21% Similarity=0.294 Sum_probs=35.8
Q ss_pred ehhhHHHHhcCCcccccEEEEEecCCCCCCceeeEEEEEeecCCCCCCCCCCceeeEeeecCCCCCCCCCCcccCeeeec
Q 008608 133 PYDQYMESIKNNYSIGMRFKMRFEGEEAPEQRFTGTIVGIEDADPQRWRDSKWRCLKVRWDETSTIPRPERVSLWKIEPA 212 (560)
Q Consensus 133 p~~ky~eAl~~~ws~GMRFKM~fE~Edss~~r~~GTI~gi~d~DP~rWP~S~WR~L~VrWDe~~~~~~~eRVSPWeIEpv 212 (560)
..+.|.+=++-+.++||++||.=.=|+-.+ -=.|.|.-++.-. -|+ -.++|.|-.... .-.|--=.||++
T Consensus 6 s~d~Ya~YVr~~i~~GM~VRc~~~yeeV~~-GD~G~V~k~~~dg---~~~---lnvqv~W~~~G~---tyWV~~~~vEii 75 (78)
T PF11515_consen 6 SNDDYAEYVRDNIQPGMRVRCCRDYEEVRA-GDEGEVFKQDRDG---LHD---LNVQVDWQSKGR---TYWVHWHHVEII 75 (78)
T ss_dssp SSHHHHHHHHHH--TT-EEEESS-BTTB-T-T-EEE-EEEE-TT---SSE-----EEEEETTTTE---EEEEEGGGEEE-
T ss_pred chhHHHHHHHHhCCCCcEEEEecccccccc-cccceeEeeccCC---CCC---cceEEEeeecCc---eEEEEEEEEEEe
Confidence 346678888889999999999665554332 2367766665421 122 258888887652 223333345555
Q ss_pred C
Q 008608 213 L 213 (560)
Q Consensus 213 ~ 213 (560)
+
T Consensus 76 g 76 (78)
T PF11515_consen 76 G 76 (78)
T ss_dssp -
T ss_pred c
Confidence 4
No 17
>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=27.55 E-value=58 Score=29.82 Aligned_cols=38 Identities=21% Similarity=0.278 Sum_probs=23.9
Q ss_pred eeccccceeee------cCCCCCCCEEEEEeCC-CCcEEEEEEee
Q 008608 45 LLQSGWSVFVS------SKRLVAGDAFIFLRGE-NGELRVGVRRA 82 (560)
Q Consensus 45 lLT~GWs~FV~------~KkLvaGDsVvF~R~~-~geL~VGVRRa 82 (560)
.-..-|..+.+ -|+++.||.|+||..+ .+.-+||+=+.
T Consensus 20 ~~~~~~~gv~~~~~~~~l~~mk~GD~vifY~s~~~~~~ivai~~V 64 (143)
T PF01878_consen 20 WGVTVWDGVRNYQARKNLKRMKPGDKVIFYHSGCKERGIVAIGEV 64 (143)
T ss_dssp HSEEECHTEEEHHHHHHHHC--TT-EEEEEETSSSS-EEEEEEEE
T ss_pred cceEEEcCEeehhhhhhhhcCCCCCEEEEEEcCCCCCEEEEEEEE
Confidence 34555666665 2589999999999987 56778887444
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=25.23 E-value=55 Score=23.71 Aligned_cols=26 Identities=27% Similarity=0.374 Sum_probs=20.7
Q ss_pred eeeecCCCCCCCEEEEEeCCCCcEEE
Q 008608 52 VFVSSKRLVAGDAFIFLRGENGELRV 77 (560)
Q Consensus 52 ~FV~~KkLvaGDsVvF~R~~~geL~V 77 (560)
.|.+.-++..||.|.+....+|.|.+
T Consensus 14 ~~r~~l~~~~gd~~~i~~~~~~~l~l 39 (43)
T TIGR01439 14 EIREKLGLKEGDRLEVIRVEDGEIIL 39 (43)
T ss_pred HHHHHcCcCCCCEEEEEEeCCCEEEE
Confidence 46677889999999999877776654
No 19
>PF14478 DUF4430: Domain of unknown function (DUF4430); PDB: 3U7Z_B 2BB5_A.
Probab=21.08 E-value=54 Score=26.78 Aligned_cols=15 Identities=27% Similarity=0.450 Sum_probs=9.2
Q ss_pred eecCCCCCCCEEEEE
Q 008608 54 VSSKRLVAGDAFIFL 68 (560)
Q Consensus 54 V~~KkLvaGDsVvF~ 68 (560)
+...+|.+||.|+|.
T Consensus 54 a~~~~l~~GD~i~~~ 68 (68)
T PF14478_consen 54 AGSYKLKDGDKITWY 68 (68)
T ss_dssp CCC-B--TTEEEEE-
T ss_pred cceeEeCCCCEEEeC
Confidence 447789999999984
No 20
>PRK15095 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=20.21 E-value=5.1e+02 Score=24.73 Aligned_cols=106 Identities=15% Similarity=0.236 Sum_probs=63.4
Q ss_pred CCCCCCCEEEE---EeCCCCcEEEEEEeeccccCCCCCcc-ccCCCcchhHHHHHHHHHHcCCeEEEEEecC------CC
Q 008608 57 KRLVAGDAFIF---LRGENGELRVGVRRAMRQQGNVPSSV-ISSHSMHLGVLATAWHAVSTGTMFTVYYKPR------TS 126 (560)
Q Consensus 57 KkLvaGDsVvF---~R~~~geL~VGVRRa~r~~~~~p~sv-is~~~m~l~vLa~A~~aaatgs~F~V~Y~PR------as 126 (560)
+....||.|.+ .+..+|+++-.-+. .+.|... +....+ +--|.+|......|..++|.--|- ..
T Consensus 3 m~i~~~~~V~v~Y~~~~~dG~v~dst~~-----~~~P~~f~~G~g~v-i~gle~aL~gm~~Ge~~~v~ipp~~ayG~~d~ 76 (156)
T PRK15095 3 ESVQSNSAVLVHFTLKLDDGSTAESTRN-----NGKPALFRLGDGSL-SEGLEQQLLGLKVGDKKTFSLEPEAAFGVPSP 76 (156)
T ss_pred cccCCCCEEEEEEEEEeCCCCEEEECCC-----CCCCEEEEeCCCCc-cHHHHHHHcCCCCCCEEEEEEChHHhcCCCCh
Confidence 45678998887 33467886554331 1234333 222223 233456666677888888875543 22
Q ss_pred CCceeEehhhHHHHhcCCcccccEEEEEecCCCCCCceeeEEEEEeec
Q 008608 127 PSEFIVPYDQYMESIKNNYSIGMRFKMRFEGEEAPEQRFTGTIVGIED 174 (560)
Q Consensus 127 ~sEFVVp~~ky~eAl~~~ws~GMRFKM~fE~Edss~~r~~GTI~gi~d 174 (560)
-.-+.||+..|.+. ....+||.+.+ ++++ ...+.++|+.|.+
T Consensus 77 ~~v~~vp~~~f~~~--~~~~~G~~~~~--~~~~--G~~~~~~V~~i~~ 118 (156)
T PRK15095 77 DLIQYFSRRDFMDA--GEPEIGAIMLF--TAMD--GSEMPGVIREING 118 (156)
T ss_pred HHEEEecHHHCCcc--cCCCCCCEEEE--ECCC--CCEEEEEEEEEcC
Confidence 23466788887554 34789999665 4432 2467899999875
Done!