Query 004106
Match_columns 773
No_of_seqs 283 out of 617
Neff 4.0
Searched_HMMs 46136
Date Thu Mar 28 17:39:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004106.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/004106hhsearch_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 3.6E-34 7.9E-39 252.3 7.9 83 287-393 1-83 (83)
2 PF02362 B3: B3 DNA binding do 99.7 6.8E-17 1.5E-21 142.4 11.9 97 161-262 1-99 (100)
3 KOG0644 Uncharacterized conser 99.3 6.3E-13 1.4E-17 153.2 5.7 151 239-418 874-1045(1113)
4 PF09217 EcoRII-N: Restriction 98.0 4.4E-05 9.4E-10 75.2 9.7 89 158-248 7-110 (156)
5 PF03754 DUF313: Domain of unk 97.7 8.7E-05 1.9E-09 70.1 6.2 77 159-236 22-114 (114)
6 PF02309 AUX_IAA: AUX/IAA fami 94.5 0.01 2.2E-07 61.0 0.0 22 752-773 108-129 (215)
7 KOG0644 Uncharacterized conser 54.3 7 0.00015 48.2 1.8 63 66-128 872-939 (1113)
8 PF04014 Antitoxin-MazE: Antid 45.0 30 0.00064 27.6 3.5 26 232-257 14-39 (47)
9 PRK10737 FKBP-type peptidyl-pr 41.6 77 0.0017 33.1 6.8 89 238-334 2-99 (196)
10 KOG3207 Beta-tubulin folding c 40.3 38 0.00082 39.7 4.7 29 371-404 16-44 (505)
11 PF10844 DUF2577: Protein of u 36.9 48 0.001 30.7 4.0 28 233-260 71-98 (100)
12 TIGR01439 lp_hng_hel_AbrB loop 33.1 61 0.0013 24.6 3.5 26 232-257 14-39 (43)
13 smart00743 Agenet Tudor-like d 32.9 58 0.0013 26.8 3.6 38 324-398 2-39 (61)
14 PRK03760 hypothetical protein; 28.3 1.3E+02 0.0028 28.9 5.5 48 200-250 62-117 (117)
15 PF11302 DUF3104: Protein of u 24.8 1.3E+02 0.0028 27.4 4.5 45 325-395 6-52 (75)
16 PF08940 DUF1918: Domain of un 22.7 75 0.0016 27.6 2.5 41 326-399 4-44 (58)
17 PF01878 EVE: EVE domain; Int 22.2 86 0.0019 30.1 3.2 26 237-262 38-64 (143)
18 PF05641 Agenet: Agenet domain 21.4 2.1E+02 0.0046 24.5 5.1 40 325-398 1-40 (68)
19 COG1047 SlpA FKBP-type peptidy 21.2 3.5E+02 0.0077 28.1 7.4 94 237-339 1-103 (174)
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=3.6e-34 Score=252.32 Aligned_cols=83 Identities=57% Similarity=1.081 Sum_probs=81.4
Q ss_pred HHHHHHhCCeEEEEEecCCCCCceeeehhHHHhhccCCcccCcEEEEEEecchhhhhhhhhhHHHhhcccccccccccCC
Q 004106 287 VVDAIARKRAFSISYNPRASASEFIIPVNKFLKSLDHSFAVGMRFKMRFETDDAAERRFNIFELVALNSKHYIESYSSLN 366 (773)
Q Consensus 287 a~~a~~~~~~F~V~Y~Pra~~seFIV~~~ky~~a~~~~w~~GmRfkM~fe~eds~e~r~~~~e~~~~~~~~~~~~~~~~~ 366 (773)
|+|||+++++|+|+||||++++|||||++||++||+++|++||||||+||+||++|+|
T Consensus 1 A~~aa~~~~~F~V~Y~PRa~~sEFVV~~~k~~~al~~~~~~GmRfkM~fE~eds~~~~---------------------- 58 (83)
T PF06507_consen 1 AAHAAATGSPFEVFYYPRASPSEFVVPASKYDKALNHPWSVGMRFKMRFETEDSSERR---------------------- 58 (83)
T ss_pred ChhHhhcCCeEEEEECCCCCCcceEEEHHHHHHHhcCCCCCCcEEEEEeccCCCccce----------------------
Confidence 6899999999999999999999999999999999999999999999999999999998
Q ss_pred CceEEEEEeeecCCCCCCCCCCceeeE
Q 004106 367 DRYTGVIMGVGDVDPVRWPGSKWRCLL 393 (773)
Q Consensus 367 ~w~~GtI~gv~~~dp~~wp~S~WR~L~ 393 (773)
|+|||+||+++||++||+|+|||||
T Consensus 59 --~~GtI~~v~~~dp~~w~~S~WR~Lq 83 (83)
T PF06507_consen 59 --WQGTIVGVSDLDPIRWPGSKWRMLQ 83 (83)
T ss_pred --eeeEEeEeeccCCCCCCCCCcccCc
Confidence 7999999999999999999999997
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=99.71 E-value=6.8e-17 Score=142.36 Aligned_cols=97 Identities=32% Similarity=0.481 Sum_probs=74.8
Q ss_pred EEEecccccCCCCCceeeehhhhhhcCCCCCCCCCCCceEEEEEeCCCCeEEEEEEEeCCCcceEeccchhhhhhccCCC
Q 004106 161 FCKTLTASDTSTHGGFSVPRRAAEDCFPPLDYSQQRPSQELVAKDLHGLEWRFRHIYRGQPRRHLLTTGWSAFVNKKKLV 240 (773)
Q Consensus 161 F~K~LT~SDV~~~GrfsVPk~~Ae~~FPpLd~~~~~p~q~L~~kDl~G~~W~FR~~yrg~prrhlLTtGWs~FVr~KkL~ 240 (773)
|.|+|+++|+...++|.||+++++.+.. + ....+++.++|..|+.|.+++.|++.+++++|++||..||++++|+
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 FFKVLKPSDVSSSCRLIIPKEFAKKHGG--N---KRKSREVTLKDPDGRSWPVKLKYRKNSGRYYLTGGWKKFVRDNGLK 75 (100)
T ss_dssp EEEE--TTCCCCTT-EEE-HHHHTTTS-------SS--CEEEEEETTTEEEEEEEEEECCTTEEEEETTHHHHHHHCT--
T ss_pred CEEEEEccCcCCCCEEEeCHHHHHHhCC--C---cCCCeEEEEEeCCCCEEEEEEEEEccCCeEEECCCHHHHHHHcCCC
Confidence 8999999999999999999999999721 1 1235789999999999999999998888899999999999999999
Q ss_pred CCCEEEEEecCC--CcEEEEEEEc
Q 004106 241 SGDAVLFLRGED--GELRLGIRRA 262 (773)
Q Consensus 241 aGDsVvF~R~en--GeL~VGIRRa 262 (773)
+||.|+|+...+ .++.|.|.|+
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 999999998754 5569999986
No 3
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=99.35 E-value=6.3e-13 Score=153.22 Aligned_cols=151 Identities=19% Similarity=0.387 Sum_probs=116.9
Q ss_pred CCCCCEEEEEecCCCcEEEEEEEcCCCCC-------------------CCCCC--cccCCCCCCccHHHHHHHHHhCCeE
Q 004106 239 LVSGDAVLFLRGEDGELRLGIRRAPHVKS-------------------GATFP--SFCSQQSSPNSVTEVVDAIARKRAF 297 (773)
Q Consensus 239 L~aGDsVvF~R~enGeL~VGIRRa~~~~~-------------------~~~~~--~~~~~~~~~~~la~a~~a~~~~~~F 297 (773)
.+-||.|+.+|....++.-.+|+...-.+ ...++ ..+.-+|.+.++.-|.++. ...|
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 56789999999755444333333221110 11122 2222358888998888654 5679
Q ss_pred EEEEecCCCCCceeeehhHHHhhccCCcccCcEEEEEEecchhhhhhhhhhHHHhhcccccccccccCCCceEEEEEeee
Q 004106 298 SISYNPRASASEFIIPVNKFLKSLDHSFAVGMRFKMRFETDDAAERRFNIFELVALNSKHYIESYSSLNDRYTGVIMGVG 377 (773)
Q Consensus 298 ~V~Y~Pra~~seFIV~~~ky~~a~~~~w~~GmRfkM~fe~eds~e~r~~~~e~~~~~~~~~~~~~~~~~~w~~GtI~gv~ 377 (773)
.+.|......+||+|.+..|++|++++|..+++||.-+..+ -|. .|.||.|+|.++.
T Consensus 952 ~ltlpdlv~fpDFlV~rsrYd~AiQrnW~~~d~crvwwrda--~~e---------------------~g~WWeG~ils~~ 1008 (1113)
T KOG0644|consen 952 KLTLPDLVTFPDFLVERSRYDAAIQRNWTCRDKCRVWWRDA--GEE---------------------DGAWWEGRILSVK 1008 (1113)
T ss_pred eeecccccCcchhhhhhhhHHHHHhhccccccceeEEEccC--CCc---------------------CCceeeeeeeecc
Confidence 99999999999999999999999999999999999998532 111 3679999999999
Q ss_pred cCCCCCCCCCCceeeEEeecCCCCCCCCCccccccccCCCC
Q 004106 378 DVDPVRWPGSKWRCLLVRWDDVESNRHTRVSPWEIEPSGSV 418 (773)
Q Consensus 378 ~~dp~~wp~S~WR~L~V~WDe~~~~~~~RVSPWeIEp~~~~ 418 (773)
...| .+|+|+|+|+.|+||..|+ +.-||||.|++..-
T Consensus 1009 pksp-~fpdSpwery~v~~~~~e~---~~~spwe~~~i~de 1045 (1113)
T KOG0644|consen 1009 PKSP-DFPDSPWERYIVRYDNTET---ELHSPWEMEPIPDE 1045 (1113)
T ss_pred CCCC-CCCCCcceeEEEEecCCcc---cccCccccCCCccc
Confidence 9999 8999999999999999988 47899999999853
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=97.95 E-value=4.4e-05 Score=75.21 Aligned_cols=89 Identities=26% Similarity=0.395 Sum_probs=59.7
Q ss_pred ceeEEEecccccCCCCC----ceeeehhhhhhcCCCCCC-CCCCCceEEEEEeCCC--CeEEEEEEEeCC------Ccce
Q 004106 158 PHMFCKTLTASDTSTHG----GFSVPRRAAEDCFPPLDY-SQQRPSQELVAKDLHG--LEWRFRHIYRGQ------PRRH 224 (773)
Q Consensus 158 ~~~F~K~LT~SDV~~~G----rfsVPk~~Ae~~FPpLd~-~~~~p~q~L~~kDl~G--~~W~FR~~yrg~------prrh 224 (773)
-..|+|.|++.|++..| |+.|||..++..||.+.. ....|...|.+++..| ..|+||++|.|+ .+.+
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 45899999999999875 799999999999998766 4566889999999887 568899999976 6668
Q ss_pred Eec--cchhhhhhccCCCCCCEEEEE
Q 004106 225 LLT--TGWSAFVNKKKLVSGDAVLFL 248 (773)
Q Consensus 225 lLT--tGWs~FVr~KkL~aGDsVvF~ 248 (773)
.|| ++=..|.+.. ..||.+||.
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 885 3323333322 468888886
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=8.7e-05 Score=70.11 Aligned_cols=77 Identities=22% Similarity=0.321 Sum_probs=60.9
Q ss_pred eeEEEecccccCCCC-CceeeehhhhhhcCCCCCC------------CCCCCceEEEEEeCCCCeEEEEEEEeCC---Cc
Q 004106 159 HMFCKTLTASDTSTH-GGFSVPRRAAEDCFPPLDY------------SQQRPSQELVAKDLHGLEWRFRHIYRGQ---PR 222 (773)
Q Consensus 159 ~~F~K~LT~SDV~~~-GrfsVPk~~Ae~~FPpLd~------------~~~~p~q~L~~kDl~G~~W~FR~~yrg~---pr 222 (773)
..|+|+|++||+..+ .||+||-..... ...|.. .....++.+.+.|..++.|..++..|.. .-
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 589999999999986 799999876533 222311 1234578889999999999999999965 56
Q ss_pred ceEeccchhhhhhc
Q 004106 223 RHLLTTGWSAFVNK 236 (773)
Q Consensus 223 rhlLTtGWs~FVr~ 236 (773)
.|+|++||..+|++
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=94.52 E-value=0.01 Score=61.03 Aligned_cols=22 Identities=9% Similarity=0.027 Sum_probs=0.0
Q ss_pred CCceeEeeecccceeeeeeccC
Q 004106 752 GSNCTNVSNHCAVRDMLFDIAL 773 (773)
Q Consensus 752 grScTKV~~Qg~~vgRavDls~ 773 (773)
++.|+||+|||+.|||.|||+.
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
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=54.25 E-value=7 Score=48.16 Aligned_cols=63 Identities=21% Similarity=0.383 Sum_probs=41.4
Q ss_pred CCCCCCCeEEEecCccccccccccccccc-----CCCCCCCceeeEEeeeeccccCCceeeeeeeccc
Q 004106 66 SLPKRGSVVVYFPQGHLEHVSDFSAAASA-----AYDLPPHPFCRVADVKLHAEAASDEVYAQVSLVP 128 (773)
Q Consensus 66 ~lP~~gs~V~YFPqGH~Eq~~~s~~~~~~-----~~~lP~~i~CrV~~V~L~Ad~~TDEVyAqi~L~P 128 (773)
-||..|+.|.||-|||-|-+.+..-.... ..++-..-.|.|..+...-=+....--.+|.|.=
T Consensus 872 yipQmgDEViyfrQghqeyl~~~~~n~~~~~~~~p~~~~~v~~~kv~kl~~~~y~~~~~s~c~m~l~~ 939 (1113)
T KOG0644|consen 872 YIPQMGDEVIYFRQGHQEYLEAVRLNNIELNNKEPWNKMAVEICKVEKLVYITYPGSGDSCCKMKLAV 939 (1113)
T ss_pred ccccccceeehhhhhhHHHHhhhhhccccccccCcccccchhhheeeeeeeeeccCCCcchheeeeee
Confidence 58999999999999999999876421111 1122233358887776655556666666666643
No 8
>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=45.02 E-value=30 Score=27.61 Aligned_cols=26 Identities=27% Similarity=0.325 Sum_probs=22.2
Q ss_pred hhhhccCCCCCCEEEEEecCCCcEEE
Q 004106 232 AFVNKKKLVSGDAVLFLRGEDGELRL 257 (773)
Q Consensus 232 ~FVr~KkL~aGDsVvF~R~enGeL~V 257 (773)
.|.++.+|.+||.|.|.-.++|++.+
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 56788899999999999999886655
No 9
>PRK10737 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=41.58 E-value=77 Score=33.12 Aligned_cols=89 Identities=19% Similarity=0.218 Sum_probs=52.6
Q ss_pred CCCCCCEEEEE---ecCCCcEEEEEEEcCCCCCCCCCCcccCCCCCCccHHHHHHHHHhCCeEEEEEecC------CCCC
Q 004106 238 KLVSGDAVLFL---RGEDGELRLGIRRAPHVKSGATFPSFCSQQSSPNSVTEVVDAIARKRAFSISYNPR------ASAS 308 (773)
Q Consensus 238 kL~aGDsVvF~---R~enGeL~VGIRRa~~~~~~~~~~~~~~~~~~~~~la~a~~a~~~~~~F~V~Y~Pr------a~~s 308 (773)
++..|++|.+. |.++|+++---+ ...|...+-....-...|.+|+.-.+.+..|+|..-|- ....
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 45667777772 456777643211 01222222222333445777777778888999986553 2223
Q ss_pred ceeeehhHHHhhccCCcccCcEEEEE
Q 004106 309 EFIIPVNKFLKSLDHSFAVGMRFKMR 334 (773)
Q Consensus 309 eFIV~~~ky~~a~~~~w~~GmRfkM~ 334 (773)
-..||++.|.... ...+||||.+.
T Consensus 76 V~~vpr~~F~~~~--~l~~G~~~~~~ 99 (196)
T PRK10737 76 VQRVPKDVFMGVD--ELQVGMRFLAE 99 (196)
T ss_pred EEEecHHHCCCcc--CCCCCCEEEEe
Confidence 5678888875322 36899998875
No 10
>KOG3207 consensus Beta-tubulin folding cofactor E [Posttranslational modification, protein turnover, chaperones]
Probab=40.32 E-value=38 Score=39.68 Aligned_cols=29 Identities=31% Similarity=0.648 Sum_probs=18.7
Q ss_pred EEEEeeecCCCCCCCCCCceeeEEeecCCCCCCC
Q 004106 371 GVIMGVGDVDPVRWPGSKWRCLLVRWDDVESNRH 404 (773)
Q Consensus 371 GtI~gv~~~dp~~wp~S~WR~L~V~WDe~~~~~~ 404 (773)
+||.-+..++| |++ +| +.|.||++.-..+
T Consensus 16 ~Tvr~iG~V~g--~~~-~w--~GvEWDd~~RGKH 44 (505)
T KOG3207|consen 16 ATVRYIGEVEG--NNS-KW--YGVEWDDPVRGKH 44 (505)
T ss_pred EEEEEEEEEcC--CCC-cc--eeeEecCCCcccc
Confidence 55555555555 665 55 7899999665443
No 11
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=36.91 E-value=48 Score=30.75 Aligned_cols=28 Identities=29% Similarity=0.389 Sum_probs=22.6
Q ss_pred hhhccCCCCCCEEEEEecCCCcEEEEEE
Q 004106 233 FVNKKKLVSGDAVLFLRGEDGELRLGIR 260 (773)
Q Consensus 233 FVr~KkL~aGDsVvF~R~enGeL~VGIR 260 (773)
|.-...|++||.|..+|.++|+.++=+-
T Consensus 71 i~~~~~Lk~GD~V~ll~~~~gQ~yiVlD 98 (100)
T PF10844_consen 71 ITFTDGLKVGDKVLLLRVQGGQKYIVLD 98 (100)
T ss_pred EEEecCCcCCCEEEEEEecCCCEEEEEE
Confidence 5566789999999999998888766543
No 12
>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=33.06 E-value=61 Score=24.60 Aligned_cols=26 Identities=38% Similarity=0.505 Sum_probs=22.1
Q ss_pred hhhhccCCCCCCEEEEEecCCCcEEE
Q 004106 232 AFVNKKKLVSGDAVLFLRGEDGELRL 257 (773)
Q Consensus 232 ~FVr~KkL~aGDsVvF~R~enGeL~V 257 (773)
.|.+.-++..||.|.+....+|.+.+
T Consensus 14 ~~r~~l~~~~gd~~~i~~~~~~~l~l 39 (43)
T TIGR01439 14 EIREKLGLKEGDRLEVIRVEDGEIIL 39 (43)
T ss_pred HHHHHcCcCCCCEEEEEEeCCCEEEE
Confidence 67899999999999999877776654
No 13
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=32.90 E-value=58 Score=26.82 Aligned_cols=38 Identities=21% Similarity=0.240 Sum_probs=27.8
Q ss_pred CcccCcEEEEEEecchhhhhhhhhhHHHhhcccccccccccCCCceEEEEEeeecCCCCCCCCCCceeeEEeecC
Q 004106 324 SFAVGMRFKMRFETDDAAERRFNIFELVALNSKHYIESYSSLNDRYTGVIMGVGDVDPVRWPGSKWRCLLVRWDD 398 (773)
Q Consensus 324 ~w~~GmRfkM~fe~eds~e~r~~~~e~~~~~~~~~~~~~~~~~~w~~GtI~gv~~~dp~~wp~S~WR~L~V~WDe 398 (773)
.|.+|++|...++.+ +.||.|+|+.+.. -..+.|.-+.
T Consensus 2 ~~~~G~~Ve~~~~~~---------------------------~~W~~a~V~~~~~----------~~~~~V~~~~ 39 (61)
T smart00743 2 DFKKGDRVEVFSKEE---------------------------DSWWEAVVTKVLG----------DGKYLVRYLT 39 (61)
T ss_pred CcCCCCEEEEEECCC---------------------------CEEEEEEEEEECC----------CCEEEEEECC
Confidence 588999999988642 3599999999875 1235677665
No 14
>PRK03760 hypothetical protein; Provisional
Probab=28.34 E-value=1.3e+02 Score=28.95 Aligned_cols=48 Identities=21% Similarity=0.387 Sum_probs=31.0
Q ss_pred EEEEEeCCCCeEEEEE-----EEe-CCCcceEe--ccchhhhhhccCCCCCCEEEEEec
Q 004106 200 ELVAKDLHGLEWRFRH-----IYR-GQPRRHLL--TTGWSAFVNKKKLVSGDAVLFLRG 250 (773)
Q Consensus 200 ~L~~kDl~G~~W~FR~-----~yr-g~prrhlL--TtGWs~FVr~KkL~aGDsVvF~R~ 250 (773)
++.+.|.+|++-.... +|. ..+-+|+| ..|| +.+.++++||.|.|.|+
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 4566666665433211 122 23556887 6887 78999999999998763
No 15
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=24.76 E-value=1.3e+02 Score=27.40 Aligned_cols=45 Identities=16% Similarity=0.152 Sum_probs=30.3
Q ss_pred cccCcEEEEEEecchhhhhhhhhhHHHhhcccccccccccCCCceEEEEEeeec--CCCCCCCCCCceeeEEe
Q 004106 325 FAVGMRFKMRFETDDAAERRFNIFELVALNSKHYIESYSSLNDRYTGVIMGVGD--VDPVRWPGSKWRCLLVR 395 (773)
Q Consensus 325 w~~GmRfkM~fe~eds~e~r~~~~e~~~~~~~~~~~~~~~~~~w~~GtI~gv~~--~dp~~wp~S~WR~L~V~ 395 (773)
..+||-+-..=+.+...+ ...+||+|.|+.... -|| ..|..+||-
T Consensus 6 Vk~Gd~ViV~~~~~~~~~---------------------~~~dWWmg~Vi~~~ggaR~P-----~~~tlFQVa 52 (75)
T PF11302_consen 6 VKPGDTVIVQDEQEVGQK---------------------QDKDWWMGQVIHCEGGARDP-----KVPTLFQVA 52 (75)
T ss_pred cCCCCEEEEecCcccccc---------------------CCCCcEEEEEEEEeccccCC-----CCCceEEEE
Confidence 567888876655433221 246899999998754 465 468999873
No 16
>PF08940 DUF1918: Domain of unknown function (DUF1918); InterPro: IPR015035 This domain is found in various hypothetical bacterial proteins, and has no known function. ; PDB: 2A7Y_A.
Probab=22.67 E-value=75 Score=27.59 Aligned_cols=41 Identities=37% Similarity=0.542 Sum_probs=23.0
Q ss_pred ccCcEEEEEEecchhhhhhhhhhHHHhhcccccccccccCCCceEEEEEeeecCCCCCCCCCCceeeEEeecCC
Q 004106 326 AVGMRFKMRFETDDAAERRFNIFELVALNSKHYIESYSSLNDRYTGVIMGVGDVDPVRWPGSKWRCLLVRWDDV 399 (773)
Q Consensus 326 ~~GmRfkM~fe~eds~e~r~~~~e~~~~~~~~~~~~~~~~~~w~~GtI~gv~~~dp~~wp~S~WR~L~V~WDe~ 399 (773)
.+|+|+.+.=.+-+..+| .|.|+.+.-.|- ..| +.|||++.
T Consensus 4 ~vGD~lvv~g~~vg~~~r--------------------------~GeIveV~g~dG----~PP---Y~VRw~D~ 44 (58)
T PF08940_consen 4 SVGDRLVVHGRTVGQPDR--------------------------HGEIVEVRGPDG----SPP---YLVRWDDT 44 (58)
T ss_dssp -TTEEEEES-TTTS--EE--------------------------EEEEEE-S-SSS-----S----EEEEETTT
T ss_pred CCCCEEEEcCCcCCCCCc--------------------------EeEEEEEECCCC----CCC---EEEEecCC
Confidence 478888877655555544 499999865432 113 45999983
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=22.19 E-value=86 Score=30.06 Aligned_cols=26 Identities=23% Similarity=0.396 Sum_probs=16.7
Q ss_pred cCCCCCCEEEEEecC-CCcEEEEEEEc
Q 004106 237 KKLVSGDAVLFLRGE-DGELRLGIRRA 262 (773)
Q Consensus 237 KkL~aGDsVvF~R~e-nGeL~VGIRRa 262 (773)
++++.||.|+||... .+.-++||=+-
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 499999999999987 56666666443
No 18
>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=21.36 E-value=2.1e+02 Score=24.50 Aligned_cols=40 Identities=20% Similarity=0.331 Sum_probs=25.7
Q ss_pred cccCcEEEEEEecchhhhhhhhhhHHHhhcccccccccccCCCceEEEEEeeecCCCCCCCCCCceeeEEeecC
Q 004106 325 FAVGMRFKMRFETDDAAERRFNIFELVALNSKHYIESYSSLNDRYTGVIMGVGDVDPVRWPGSKWRCLLVRWDD 398 (773)
Q Consensus 325 w~~GmRfkM~fe~eds~e~r~~~~e~~~~~~~~~~~~~~~~~~w~~GtI~gv~~~dp~~wp~S~WR~L~V~WDe 398 (773)
|..|++|...-+.+.. .+.||.++|+.....+ .+.|+.++
T Consensus 1 F~~G~~VEV~s~e~g~------------------------~gaWf~a~V~~~~~~~----------~~~V~Y~~ 40 (68)
T PF05641_consen 1 FKKGDEVEVSSDEDGF------------------------RGAWFPATVLKENGDD----------KYLVEYDD 40 (68)
T ss_dssp --TT-EEEEEE-SBTT--------------------------EEEEEEEEEEETT-----------EEEEEETT
T ss_pred CCCCCEEEEEEcCCCC------------------------CcEEEEEEEEEeCCCc----------EEEEEECC
Confidence 5678888887543221 3679999999987533 78899988
No 19
>COG1047 SlpA FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]
Probab=21.20 E-value=3.5e+02 Score=28.09 Aligned_cols=94 Identities=19% Similarity=0.266 Sum_probs=57.3
Q ss_pred cCCCCCCEEEEE---ecCCCcEEEEEEEcCCCCCCCCCCcccCCCCCCccHHHHHHHHHhCCeEEEEEecCCCCCce---
Q 004106 237 KKLVSGDAVLFL---RGEDGELRLGIRRAPHVKSGATFPSFCSQQSSPNSVTEVVDAIARKRAFSISYNPRASASEF--- 310 (773)
Q Consensus 237 KkL~aGDsVvF~---R~enGeL~VGIRRa~~~~~~~~~~~~~~~~~~~~~la~a~~a~~~~~~F~V~Y~Pra~~seF--- 310 (773)
+++..||.|.+. |.++|++.=--.- ...|...+-.+..-..-|.+|..-..-|.-|+|.--|-..-.++
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 356778888773 4456654421110 11233333333333456788888888899999998886543333
Q ss_pred ---eeehhHHHhhccCCcccCcEEEEEEecch
Q 004106 311 ---IIPVNKFLKSLDHSFAVGMRFKMRFETDD 339 (773)
Q Consensus 311 ---IV~~~ky~~a~~~~w~~GmRfkM~fe~ed 339 (773)
+||..+|...- ...+||+|.+. +.|
T Consensus 76 lvq~vp~~~F~~~~--~~~vGm~~~~~--~~~ 103 (174)
T COG1047 76 LVQRVPRDEFQGVG--ELEVGMEVEAE--GGD 103 (174)
T ss_pred HeEEecHHHhCcCC--CCCCCcEEEEc--CCC
Confidence 57777776543 78999998854 544
Done!