Query 004436
Match_columns 753
No_of_seqs 311 out of 546
Neff 4.7
Searched_HMMs 46136
Date Thu Mar 28 23:24:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004436.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/004436hhsearch_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-34 5E-39 253.1 8.4 83 287-373 1-83 (83)
2 PF02362 B3: B3 DNA binding do 99.7 8.4E-17 1.8E-21 143.0 11.2 97 161-262 1-99 (100)
3 KOG0644 Uncharacterized conser 99.4 1.8E-13 3.9E-18 157.5 5.7 149 239-397 874-1044(1113)
4 PF09217 EcoRII-N: Restriction 97.9 3.8E-05 8.3E-10 75.2 9.0 89 158-248 7-110 (156)
5 PF03754 DUF313: Domain of unk 97.6 8.4E-05 1.8E-09 70.1 5.7 77 159-236 22-114 (114)
6 PF02309 AUX_IAA: AUX/IAA fami 94.3 0.012 2.6E-07 60.7 0.0 22 732-753 108-129 (215)
7 PRK10737 FKBP-type peptidyl-pr 65.9 28 0.0006 36.3 8.3 108 238-358 2-114 (196)
8 KOG3207 Beta-tubulin folding c 64.8 8.5 0.00018 44.5 4.7 42 329-384 3-44 (505)
9 KOG0644 Uncharacterized conser 63.6 4.2 9.1E-05 49.8 2.1 64 66-129 872-940 (1113)
10 smart00743 Agenet Tudor-like d 52.1 22 0.00047 29.2 3.9 28 328-358 2-29 (61)
11 PF04014 Antitoxin-MazE: Antid 49.0 21 0.00046 28.3 3.3 26 232-257 14-39 (47)
12 PF10844 DUF2577: Protein of u 36.8 48 0.001 30.6 4.0 28 233-260 71-98 (100)
13 TIGR01439 lp_hng_hel_AbrB loop 35.3 49 0.0011 25.0 3.3 27 231-257 13-39 (43)
14 PRK03760 hypothetical protein; 29.7 1.1E+02 0.0023 29.4 5.2 48 200-250 62-117 (117)
15 COG1047 SlpA FKBP-type peptidy 29.2 3.4E+02 0.0075 28.0 9.0 106 237-358 1-115 (174)
16 PF02513 Spin-Ssty: Spin/Ssty 27.5 99 0.0021 25.8 3.9 31 331-361 1-31 (50)
17 PF01878 EVE: EVE domain; Int 25.5 65 0.0014 30.9 3.1 26 237-262 38-64 (143)
18 smart00333 TUDOR Tudor domain. 24.6 1.2E+02 0.0026 24.2 4.0 52 328-396 2-54 (57)
19 PF03120 DNA_ligase_OB: NAD-de 20.5 71 0.0015 29.0 2.1 32 231-262 42-74 (82)
20 PF05641 Agenet: Agenet domain 20.5 2.5E+02 0.0055 23.9 5.4 40 329-378 1-40 (68)
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-34 Score=253.12 Aligned_cols=83 Identities=57% Similarity=1.081 Sum_probs=81.7
Q ss_pred HHHHhhcCCeEEEEecCCCCCCCCCcceeeehhhHhhhccCCcccCcEEEEEeecCCccceeeeeEEEeeccCCCCCCCC
Q 004436 287 VVDAIARKRAFSISYNPSPLCRASASEFIIPVNKFLKSLDHSFAVGMRFKMRFETDDAAERRYTGVIMGVGDVDPVRWPG 366 (753)
Q Consensus 287 a~~a~~~~~~F~V~Y~P~~~~r~~~~EFvVp~~~y~~s~~~~w~~GmRfkM~fe~eDs~e~r~~GtI~gv~~~dp~~wp~ 366 (753)
|+|||+++++|+|+||| |++++|||||++||++||+++|++||||||+||+||+++++|+|||+||++.||++||+
T Consensus 1 A~~aa~~~~~F~V~Y~P----Ra~~sEFVV~~~k~~~al~~~~~~GmRfkM~fE~eds~~~~~~GtI~~v~~~dp~~w~~ 76 (83)
T PF06507_consen 1 AAHAAATGSPFEVFYYP----RASPSEFVVPASKYDKALNHPWSVGMRFKMRFETEDSSERRWQGTIVGVSDLDPIRWPG 76 (83)
T ss_pred ChhHhhcCCeEEEEECC----CCCCcceEEEHHHHHHHhcCCCCCCcEEEEEeccCCCccceeeeEEeEeeccCCCCCCC
Confidence 68999999999999999 99999999999999999999999999999999999999999999999999999999999
Q ss_pred CCceeEE
Q 004436 367 SKWRCLL 373 (753)
Q Consensus 367 S~WR~L~ 373 (753)
|+|||||
T Consensus 77 S~WR~Lq 83 (83)
T PF06507_consen 77 SKWRMLQ 83 (83)
T ss_pred CCcccCc
Confidence 9999996
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=99.70 E-value=8.4e-17 Score=143.04 Aligned_cols=97 Identities=32% Similarity=0.471 Sum_probs=74.8
Q ss_pred EEEecccccCCCCCceeeeccchhhcCCCCCCCCCCCceEEEEEeCCCCeEEEEEEEeCCCCceeeccchhhhhhcCCCC
Q 004436 161 FCKTLTASDTSTHGGFSVPRRAAEDCFPPLDYSQQRPSQELVAKDLHGLEWRFRHIYRGQPRRHLLTTGWSAFVNKKKLV 240 (753)
Q Consensus 161 F~K~LT~SDv~~~grfsVPk~~Ae~~FPpLd~~~~~p~q~L~~~D~~G~~W~Fr~~yrg~prrhlLTtGWs~FV~~K~L~ 240 (753)
|.|+|+++|+...++|.||+++++++. ++ ....+++.++|..|+.|.+++.|++.+++++|++||..||++++|+
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 1245789999999999999999998888899999999999999999
Q ss_pred CCCEEEEEEcC--CCcEEEEEEEc
Q 004436 241 SGDAVLFLRGE--DGELRLGIRRA 262 (753)
Q Consensus 241 aGD~VvF~R~~--~G~l~vGIRRa 262 (753)
+||.|+|+... ..++.|.|.|+
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 45569999986
No 3
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=99.40 E-value=1.8e-13 Score=157.52 Aligned_cols=149 Identities=17% Similarity=0.358 Sum_probs=117.8
Q ss_pred CCCCCEEEEEEcCCCcEEEEEEEccCCCCC-------------------C--CCCccccCCCCCcchHHHHHHhhcCCeE
Q 004436 239 LVSGDAVLFLRGEDGELRLGIRRAPHVKSG-------------------A--TFPSFCSQQSSPNSVTEVVDAIARKRAF 297 (753)
Q Consensus 239 L~aGD~VvF~R~~~G~l~vGIRRa~~~~~~-------------------~--~~~~~~~~~~~~~~l~~a~~a~~~~~~F 297 (753)
...||.|+.+|.+..++.-.+|+...-.++ . +-+..+.-+|.+.++.-|.++. ...|
T Consensus 874 pQmgDEViyfrQghqeyl~~~~~n~~~~~~~~p~~~~~v~~~kv~kl~~~~y~~~~~s~c~m~l~~idp~s~~~--~k~F 951 (1113)
T KOG0644|consen 874 PQMGDEVIYFRQGHQEYLEAVRLNNIELNNKEPWNKMAVEICKVEKLVYITYPGSGDSCCKMKLAVIDPASKLM--DKSF 951 (1113)
T ss_pred ccccceeehhhhhhHHHHhhhhhccccccccCcccccchhhheeeeeeeeeccCCCcchheeeeeeecchhhhh--hccc
Confidence 468999999998777766555554331111 0 1122222367888888888554 6789
Q ss_pred EEEecCCCCCCCCCcceeeehhhHhhhccCCcccCcEEEEEeecCCcc-ceeeeeEEEeeccCCCCCCCCCCceeEEEEe
Q 004436 298 SISYNPSPLCRASASEFIIPVNKFLKSLDHSFAVGMRFKMRFETDDAA-ERRYTGVIMGVGDVDPVRWPGSKWRCLLVRW 376 (753)
Q Consensus 298 ~V~Y~P~~~~r~~~~EFvVp~~~y~~s~~~~w~~GmRfkM~fe~eDs~-e~r~~GtI~gv~~~dp~~wp~S~WR~L~V~W 376 (753)
.+.|+. ..+.+||+|.+..|++|+.+||..+++||.-+..+-.. -.||.|+|.++.+..| .+|+|+|+|+.|+|
T Consensus 952 ~ltlpd----lv~fpDFlV~rsrYd~AiQrnW~~~d~crvwwrda~~e~g~WWeG~ils~~pksp-~fpdSpwery~v~~ 1026 (1113)
T KOG0644|consen 952 KLTLPD----LVTFPDFLVERSRYDAAIQRNWTCRDKCRVWWRDAGEEDGAWWEGRILSVKPKSP-DFPDSPWERYIVRY 1026 (1113)
T ss_pred eeeccc----ccCcchhhhhhhhHHHHHhhccccccceeEEEccCCCcCCceeeeeeeeccCCCC-CCCCCcceeEEEEe
Confidence 999999 88999999999999999999999999999999532111 2399999999999999 99999999999999
Q ss_pred cCCCCCCCCcccccccccCCC
Q 004436 377 DDVESNRHTRVSPWEIEPSGS 397 (753)
Q Consensus 377 De~~~~~~~RVSPWeIEpv~~ 397 (753)
|..|+ +.-||||.|++..
T Consensus 1027 ~~~e~---~~~spwe~~~i~d 1044 (1113)
T KOG0644|consen 1027 DNTET---ELHSPWEMEPIPD 1044 (1113)
T ss_pred cCCcc---cccCccccCCCcc
Confidence 99888 6689999999985
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=97.94 E-value=3.8e-05 Score=75.25 Aligned_cols=89 Identities=26% Similarity=0.395 Sum_probs=59.9
Q ss_pred ceeEEEecccccCCCCC----ceeeeccchhhcCCCCCC-CCCCCceEEEEEeCCC--CeEEEEEEEeCC------CCce
Q 004436 158 PHMFCKTLTASDTSTHG----GFSVPRRAAEDCFPPLDY-SQQRPSQELVAKDLHG--LEWRFRHIYRGQ------PRRH 224 (753)
Q Consensus 158 ~~~F~K~LT~SDv~~~g----rfsVPk~~Ae~~FPpLd~-~~~~p~q~L~~~D~~G--~~W~Fr~~yrg~------prrh 224 (753)
-..|+|.|++.|++..| |+.|||..++..||.+.. ....|...|.+++..| ..|+||++|.++ .+.+
T Consensus 7 ~~~~~K~LSaNDtGaTGgHQaGiyIpk~~~~~lFp~~~~~~~~Np~~~~~~~~~s~~~~~~~~r~iYYnn~~~~gTRNE~ 86 (156)
T PF09217_consen 7 WAIYCKRLSANDTGATGGHQAGIYIPKSAAELLFPSINHTKEENPDIWLKARWQSHFVTDSQVRFIYYNNRLFGGTRNEY 86 (156)
T ss_dssp EEEEEEE--CCCCTTTSSS--EEEE-HHHHHHH-GGG-SSSSSS-EEEEEEEETTTT---EEEEEEEE-CCCTTSS--EE
T ss_pred eEEEEEEccCCCCCCcCcccceeEecccHHHHhCCCCCcccccCCceeEEEEECCCCccceeEEEEEEcccccCCCcCce
Confidence 35899999999999764 799999999999998766 5567889999999887 568899999976 5667
Q ss_pred eec--cchhhhhhcCCCCCCCEEEEE
Q 004436 225 LLT--TGWSAFVNKKKLVSGDAVLFL 248 (753)
Q Consensus 225 lLT--tGWs~FV~~K~L~aGD~VvF~ 248 (753)
.|| ++-..|.+.. ..||-+||.
T Consensus 87 RIT~~G~~~~~~~~~--~tGaL~vla 110 (156)
T PF09217_consen 87 RITRFGRGFPLQNPE--NTGALLVLA 110 (156)
T ss_dssp EEE---TTSGGG-GG--GTT-EEEEE
T ss_pred EEeeecCCCccCCcc--ccccEEEEE
Confidence 786 3333444432 479988887
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=97.63 E-value=8.4e-05 Score=70.06 Aligned_cols=77 Identities=22% Similarity=0.321 Sum_probs=60.7
Q ss_pred eeEEEecccccCCCC-CceeeeccchhhcCCCCCC------------CCCCCceEEEEEeCCCCeEEEEEEEeCC---CC
Q 004436 159 HMFCKTLTASDTSTH-GGFSVPRRAAEDCFPPLDY------------SQQRPSQELVAKDLHGLEWRFRHIYRGQ---PR 222 (753)
Q Consensus 159 ~~F~K~LT~SDv~~~-grfsVPk~~Ae~~FPpLd~------------~~~~p~q~L~~~D~~G~~W~Fr~~yrg~---pr 222 (753)
.+|+|+|++||+..+ .||+||-..... ...|.. .....++.+.+.|..++.|..++..|.. .-
T Consensus 22 li~~K~L~~tDv~~~qsRLsmP~~qi~~-~dFLt~eE~~~i~~~~~~~~~~~Gv~V~lvdp~~~~~~m~lkkW~mg~~~~ 100 (114)
T PF03754_consen 22 LIIEKTLFKTDVDPHQSRLSMPFNQIID-NDFLTEEEKRIIKEEKKNNDKKKGVEVILVDPSLRKWTMRLKKWNMGNGTS 100 (114)
T ss_pred EEEeeeecccCCCCCCceeeccHHHhcc-cccCCHHHHHHHHHhhccCcccCCceEEEECCcCcEEEEEEEEecccCCce
Confidence 589999999999965 899999876533 222311 1234578899999999999999999965 56
Q ss_pred ceeeccchhhhhhc
Q 004436 223 RHLLTTGWSAFVNK 236 (753)
Q Consensus 223 rhlLTtGWs~FV~~ 236 (753)
.|+|++||..+|++
T Consensus 101 ~YvL~~gWn~VV~~ 114 (114)
T PF03754_consen 101 NYVLNSGWNKVVED 114 (114)
T ss_pred EEEEEcChHhhccC
Confidence 79999999999864
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=94.29 E-value=0.012 Score=60.70 Aligned_cols=22 Identities=9% Similarity=0.027 Sum_probs=0.0
Q ss_pred CCceeEeeecccceeeeeeccC
Q 004436 732 GSNCTNVSNHCAVRDMLFDIAL 753 (753)
Q Consensus 732 ~~sctKV~~qg~~vgR~vDls~ 753 (753)
++.|+||+|||+.|||.|||+.
T Consensus 108 ~~~~vKV~mdG~~igRkVDL~~ 129 (215)
T PF02309_consen 108 SRSYVKVNMDGVPIGRKVDLSA 129 (215)
T ss_dssp ----------------------
T ss_pred CCceeEEEecCcccceecCHHH
Confidence 4899999999999999999974
No 7
>PRK10737 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=65.92 E-value=28 Score=36.25 Aligned_cols=108 Identities=20% Similarity=0.206 Sum_probs=64.1
Q ss_pred CCCCCCEEEE-E--EcCCCcEEEEEEEccCCCCCCCCCccccCCCCCcchHHHHHHhhcCCeEEEEecCCCC--CCCCCc
Q 004436 238 KLVSGDAVLF-L--RGEDGELRLGIRRAPHVKSGATFPSFCSQQSSPNSVTEVVDAIARKRAFSISYNPSPL--CRASAS 312 (753)
Q Consensus 238 ~L~aGD~VvF-~--R~~~G~l~vGIRRa~~~~~~~~~~~~~~~~~~~~~l~~a~~a~~~~~~F~V~Y~P~~~--~r~~~~ 312 (753)
++..|+.|.+ | |.++|+++---+ ...|...+-....-...|.+|+.-.+.|..|+|..-|.-. .|....
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 3556777776 3 456777533211 0123222222333345688888888999999998655100 022233
Q ss_pred ceeeehhhHhhhccCCcccCcEEEEEeecCCccceeeeeEEEeecc
Q 004436 313 EFIIPVNKFLKSLDHSFAVGMRFKMRFETDDAAERRYTGVIMGVGD 358 (753)
Q Consensus 313 EFvVp~~~y~~s~~~~w~~GmRfkM~fe~eDs~e~r~~GtI~gv~~ 358 (753)
-..||++.|.... ...+||||.+. +++. ...++|+.|.+
T Consensus 76 V~~vpr~~F~~~~--~l~~G~~~~~~--~~~G---~~~~~V~ev~~ 114 (196)
T PRK10737 76 VQRVPKDVFMGVD--ELQVGMRFLAE--TDQG---PVPVEITAVED 114 (196)
T ss_pred EEEecHHHCCCcc--CCCCCCEEEEe--CCCC---cEEEEEEEEcC
Confidence 4678888885322 36899998864 4554 35788888865
No 8
>KOG3207 consensus Beta-tubulin folding cofactor E [Posttranslational modification, protein turnover, chaperones]
Probab=64.79 E-value=8.5 Score=44.51 Aligned_cols=42 Identities=36% Similarity=0.603 Sum_probs=28.4
Q ss_pred cccCcEEEEEeecCCccceeeeeEEEeeccCCCCCCCCCCceeEEEEecCCCCCCC
Q 004436 329 FAVGMRFKMRFETDDAAERRYTGVIMGVGDVDPVRWPGSKWRCLLVRWDDVESNRH 384 (753)
Q Consensus 329 w~~GmRfkM~fe~eDs~e~r~~GtI~gv~~~dp~~wp~S~WR~L~V~WDe~~~~~~ 384 (753)
..+|+|+|..++- +..||.|+|. | |++ +| |.|.||++.-..+
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 4689999988761 1235555554 4 665 56 8899999765544
No 9
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=63.57 E-value=4.2 Score=49.76 Aligned_cols=64 Identities=22% Similarity=0.360 Sum_probs=43.2
Q ss_pred CCCCCCCEEEEeecccccccccchhccccC-CCCC----CCceeeEEEeeeeccCCCceeEEEEeeccc
Q 004436 66 SLPKRGSVVVYFPQGHLEHVSDFSAAASAA-YDLP----PHPFCRVADVKLHAEAASDEVYAQVSLVPD 129 (753)
Q Consensus 66 ~lP~~gs~V~YFPqGH~Eq~~~~~~~~~~~-~~lp----~~i~C~V~~V~l~Ad~~TDEVyA~i~L~P~ 129 (753)
-||..|+.|.||-|||-|-+.+........ --.| ..-.|.|..+..--=+....--.+|.|.-.
T Consensus 872 yipQmgDEViyfrQghqeyl~~~~~n~~~~~~~~p~~~~~v~~~kv~kl~~~~y~~~~~s~c~m~l~~i 940 (1113)
T KOG0644|consen 872 YIPQMGDEVIYFRQGHQEYLEAVRLNNIELNNKEPWNKMAVEICKVEKLVYITYPGSGDSCCKMKLAVI 940 (1113)
T ss_pred ccccccceeehhhhhhHHHHhhhhhccccccccCcccccchhhheeeeeeeeeccCCCcchheeeeeee
Confidence 589999999999999999988764211111 1123 233688888776666666666667666543
No 10
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=52.06 E-value=22 Score=29.25 Aligned_cols=28 Identities=21% Similarity=0.323 Sum_probs=23.7
Q ss_pred CcccCcEEEEEeecCCccceeeeeEEEeecc
Q 004436 328 SFAVGMRFKMRFETDDAAERRYTGVIMGVGD 358 (753)
Q Consensus 328 ~w~~GmRfkM~fe~eDs~e~r~~GtI~gv~~ 358 (753)
.|.+|+++-..++.+++ ||.|+|+.+..
T Consensus 2 ~~~~G~~Ve~~~~~~~~---W~~a~V~~~~~ 29 (61)
T smart00743 2 DFKKGDRVEVFSKEEDS---WWEAVVTKVLG 29 (61)
T ss_pred CcCCCCEEEEEECCCCE---EEEEEEEEECC
Confidence 58899999999975454 99999999875
No 11
>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=49.00 E-value=21 Score=28.26 Aligned_cols=26 Identities=27% Similarity=0.325 Sum_probs=22.1
Q ss_pred hhhhcCCCCCCCEEEEEEcCCCcEEE
Q 004436 232 AFVNKKKLVSGDAVLFLRGEDGELRL 257 (753)
Q Consensus 232 ~FV~~K~L~aGD~VvF~R~~~G~l~v 257 (753)
.|.++.+|.+||.|.|.-.++|++.+
T Consensus 14 ~~~~~l~l~~Gd~v~i~~~~~g~i~i 39 (47)
T PF04014_consen 14 EIREKLGLKPGDEVEIEVEGDGKIVI 39 (47)
T ss_dssp HHHHHTTSSTTTEEEEEEETTSEEEE
T ss_pred HHHHHcCCCCCCEEEEEEeCCCEEEE
Confidence 56788899999999999999886554
No 12
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=36.84 E-value=48 Score=30.65 Aligned_cols=28 Identities=29% Similarity=0.389 Sum_probs=22.7
Q ss_pred hhhcCCCCCCCEEEEEEcCCCcEEEEEE
Q 004436 233 FVNKKKLVSGDAVLFLRGEDGELRLGIR 260 (753)
Q Consensus 233 FV~~K~L~aGD~VvF~R~~~G~l~vGIR 260 (753)
|.-...|++||.|..+|..+|+.++=+-
T Consensus 71 i~~~~~Lk~GD~V~ll~~~~gQ~yiVlD 98 (100)
T PF10844_consen 71 ITFTDGLKVGDKVLLLRVQGGQKYIVLD 98 (100)
T ss_pred EEEecCCcCCCEEEEEEecCCCEEEEEE
Confidence 5666789999999999988888666543
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=35.33 E-value=49 Score=25.01 Aligned_cols=27 Identities=37% Similarity=0.487 Sum_probs=22.2
Q ss_pred hhhhhcCCCCCCCEEEEEEcCCCcEEE
Q 004436 231 SAFVNKKKLVSGDAVLFLRGEDGELRL 257 (753)
Q Consensus 231 s~FV~~K~L~aGD~VvF~R~~~G~l~v 257 (753)
..|.++-++..||.|.+....+|.+.+
T Consensus 13 ~~~r~~l~~~~gd~~~i~~~~~~~l~l 39 (43)
T TIGR01439 13 KEIREKLGLKEGDRLEVIRVEDGEIIL 39 (43)
T ss_pred HHHHHHcCcCCCCEEEEEEeCCCEEEE
Confidence 367899999999999999877776544
No 14
>PRK03760 hypothetical protein; Provisional
Probab=29.70 E-value=1.1e+02 Score=29.39 Aligned_cols=48 Identities=21% Similarity=0.387 Sum_probs=30.9
Q ss_pred EEEEEeCCCCeEEEEE-----EEe-CCCCceee--ccchhhhhhcCCCCCCCEEEEEEc
Q 004436 200 ELVAKDLHGLEWRFRH-----IYR-GQPRRHLL--TTGWSAFVNKKKLVSGDAVLFLRG 250 (753)
Q Consensus 200 ~L~~~D~~G~~W~Fr~-----~yr-g~prrhlL--TtGWs~FV~~K~L~aGD~VvF~R~ 250 (753)
++++.|.+|++-.... +|. ..+-+|+| ..|| +.+.++++||.|.|.|+
T Consensus 62 DiiFld~~g~Vv~i~~~~P~~~~~~~~~a~~VLEl~aG~---~~~~gi~~Gd~v~~~~~ 117 (117)
T PRK03760 62 DVIFLDSNRRVVDFKTLKPWRIYVPKKPARYIIEGPVGK---IRVLKVEVGDEIEWIDE 117 (117)
T ss_pred EEEEECCCCeEEEEEeCCCccccCCCccceEEEEeCCCh---HHHcCCCCCCEEEEeeC
Confidence 4566666555433211 122 23556787 6787 78899999999998763
No 15
>COG1047 SlpA FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]
Probab=29.16 E-value=3.4e+02 Score=28.01 Aligned_cols=106 Identities=21% Similarity=0.292 Sum_probs=64.6
Q ss_pred CCCCCCCEEEEE---EcCCCcEEEEEEEccCCCCCCCCCccccCCCCCcchHHHHHHhhcCCeEEEEecCCCCCCCCCcc
Q 004436 237 KKLVSGDAVLFL---RGEDGELRLGIRRAPHVKSGATFPSFCSQQSSPNSVTEVVDAIARKRAFSISYNPSPLCRASASE 313 (753)
Q Consensus 237 K~L~aGD~VvF~---R~~~G~l~vGIRRa~~~~~~~~~~~~~~~~~~~~~l~~a~~a~~~~~~F~V~Y~P~~~~r~~~~E 313 (753)
+++..||.|.+. |.++|++.=-=.- ...|...+-.+..-..-|.+|+.-..-|.-|+|.--| -..-.+
T Consensus 1 m~i~k~~~V~i~Y~~~~~dg~v~Dtt~e-----~~~P~~~i~G~g~li~glE~al~g~~~Ge~~~V~IpP----E~AfGe 71 (174)
T COG1047 1 MKIEKGDVVSLHYTLKVEDGEVVDTTDE-----NYGPLTFIVGAGQLIPGLEEALLGKEVGEEFTVEIPP----EDAFGE 71 (174)
T ss_pred CcccCCCEEEEEEEEEecCCcEEEcccc-----cCCCeEEEecCCCcchhHHHHHhCCCCCceeEEEeCc----hHhcCC
Confidence 356678888773 4455654311100 1223333333344456788899989999999999877 222233
Q ss_pred e------eeehhhHhhhccCCcccCcEEEEEeecCCccceeeeeEEEeecc
Q 004436 314 F------IIPVNKFLKSLDHSFAVGMRFKMRFETDDAAERRYTGVIMGVGD 358 (753)
Q Consensus 314 F------vVp~~~y~~s~~~~w~~GmRfkM~fe~eDs~e~r~~GtI~gv~~ 358 (753)
+ .||..+|...- ...+||+|.+ +++| .-.-|+|+.|..
T Consensus 72 ~~~~lvq~vp~~~F~~~~--~~~vGm~~~~--~~~~---~~~~~~V~~V~~ 115 (174)
T COG1047 72 YDPDLVQRVPRDEFQGVG--ELEVGMEVEA--EGGD---GEIPGVVTEVSG 115 (174)
T ss_pred CChHHeEEecHHHhCcCC--CCCCCcEEEE--cCCC---ceeeEEEEEEcC
Confidence 2 57777775433 6889998874 4445 345788988754
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=27.49 E-value=99 Score=25.81 Aligned_cols=31 Identities=23% Similarity=0.530 Sum_probs=24.3
Q ss_pred cCcEEEEEeecCCccceeeeeEEEeeccCCC
Q 004436 331 VGMRFKMRFETDDAAERRYTGVIMGVGDVDP 361 (753)
Q Consensus 331 ~GmRfkM~fe~eDs~e~r~~GtI~gv~~~dp 361 (753)
+|-|+.-.||.++.+...|.|+|...-++.|
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 5889999999888887788999999888776
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=25.47 E-value=65 Score=30.92 Aligned_cols=26 Identities=23% Similarity=0.396 Sum_probs=17.3
Q ss_pred CCCCCCCEEEEEEcC-CCcEEEEEEEc
Q 004436 237 KKLVSGDAVLFLRGE-DGELRLGIRRA 262 (753)
Q Consensus 237 K~L~aGD~VvF~R~~-~G~l~vGIRRa 262 (753)
++++.||.|+||... .+.-+|||=+-
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 489999999999987 56677777554
No 18
>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=24.60 E-value=1.2e+02 Score=24.20 Aligned_cols=52 Identities=25% Similarity=0.369 Sum_probs=36.5
Q ss_pred CcccCcEEEEEeecCCccceeeeeEEEeeccCCCCCCCCCCceeEEEEecC-CCCCCCCcccccccccCC
Q 004436 328 SFAVGMRFKMRFETDDAAERRYTGVIMGVGDVDPVRWPGSKWRCLLVRWDD-VESNRHTRVSPWEIEPSG 396 (753)
Q Consensus 328 ~w~~GmRfkM~fe~eDs~e~r~~GtI~gv~~~dp~~wp~S~WR~L~V~WDe-~~~~~~~RVSPWeIEpv~ 396 (753)
+|.+|..+..+| .+. .||.|+|+++... ....|.-++ ... +-|...+|-++.
T Consensus 2 ~~~~G~~~~a~~-~d~---~wyra~I~~~~~~----------~~~~V~f~D~G~~---~~v~~~~l~~l~ 54 (57)
T smart00333 2 TFKVGDKVAARW-EDG---EWYRARIIKVDGE----------QLYEVFFIDYGNE---EVVPPSDLRPLP 54 (57)
T ss_pred CCCCCCEEEEEe-CCC---CEEEEEEEEECCC----------CEEEEEEECCCcc---EEEeHHHeecCC
Confidence 588999999999 433 4999999999752 446787777 443 346666655443
No 19
>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=20.52 E-value=71 Score=28.99 Aligned_cols=32 Identities=22% Similarity=0.359 Sum_probs=21.5
Q ss_pred hhhhhcCCCCCCCEEEEEEcCCCc-EEEEEEEc
Q 004436 231 SAFVNKKKLVSGDAVLFLRGEDGE-LRLGIRRA 262 (753)
Q Consensus 231 s~FV~~K~L~aGD~VvF~R~~~G~-l~vGIRRa 262 (753)
..|+++++|..||.|.++|..+.= ..+++-..
T Consensus 42 ~~~i~~~~i~~Gd~V~V~raGdVIP~I~~vv~~ 74 (82)
T PF03120_consen 42 YDYIKELDIRIGDTVLVTRAGDVIPKIVGVVKE 74 (82)
T ss_dssp HHHHHHTT-BBT-EEEEEEETTTEEEEEEE-GG
T ss_pred HHHHHHcCCCCCCEEEEEECCCccceEeEeehh
Confidence 378999999999999999976643 34444433
No 20
>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=20.47 E-value=2.5e+02 Score=23.90 Aligned_cols=40 Identities=20% Similarity=0.332 Sum_probs=26.4
Q ss_pred cccCcEEEEEeecCCccceeeeeEEEeeccCCCCCCCCCCceeEEEEecC
Q 004436 329 FAVGMRFKMRFETDDAAERRYTGVIMGVGDVDPVRWPGSKWRCLLVRWDD 378 (753)
Q Consensus 329 w~~GmRfkM~fe~eDs~e~r~~GtI~gv~~~dp~~wp~S~WR~L~V~WDe 378 (753)
|.+|+++-..-+.+...--||.|+|+.....+ .+.|+.++
T Consensus 1 F~~G~~VEV~s~e~g~~gaWf~a~V~~~~~~~----------~~~V~Y~~ 40 (68)
T PF05641_consen 1 FKKGDEVEVSSDEDGFRGAWFPATVLKENGDD----------KYLVEYDD 40 (68)
T ss_dssp --TT-EEEEEE-SBTT--EEEEEEEEEEETT-----------EEEEEETT
T ss_pred CCCCCEEEEEEcCCCCCcEEEEEEEEEeCCCc----------EEEEEECC
Confidence 56899999887644333349999999987643 78899988
Done!