Query 004792
Match_columns 730
No_of_seqs 292 out of 596
Neff 4.0
Searched_HMMs 46136
Date Thu Mar 28 12:59:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004792.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/004792hhsearch_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 1.4E-35 3E-40 259.7 9.0 83 277-359 1-83 (83)
2 PF02362 B3: B3 DNA binding do 99.7 6E-17 1.3E-21 141.5 10.6 97 151-252 1-99 (100)
3 KOG0644 Uncharacterized conser 99.5 5.3E-15 1.2E-19 169.0 6.4 150 229-385 874-1045(1113)
4 PF09217 EcoRII-N: Restriction 98.2 7.3E-06 1.6E-10 80.0 9.3 90 147-238 6-110 (156)
5 PF03754 DUF313: Domain of unk 97.6 0.00011 2.3E-09 69.0 5.7 78 148-226 21-114 (114)
6 PRK10737 FKBP-type peptidyl-pr 64.9 24 0.00053 36.4 7.6 104 228-344 2-114 (196)
7 KOG0644 Uncharacterized conser 57.7 8.7 0.00019 47.1 3.3 64 59-126 872-940 (1113)
8 KOG3207 Beta-tubulin folding c 47.6 21 0.00047 41.3 4.2 42 315-370 3-44 (505)
9 smart00743 Agenet Tudor-like d 46.5 32 0.0007 28.1 4.1 38 314-364 2-39 (61)
10 PF04014 Antitoxin-MazE: Antid 45.0 24 0.00052 27.9 3.0 27 222-248 14-40 (47)
11 PF10844 DUF2577: Protein of u 37.5 45 0.00099 30.6 4.0 27 223-249 71-97 (100)
12 PF02513 Spin-Ssty: Spin/Ssty 34.9 62 0.0013 27.1 3.9 32 317-348 1-32 (50)
13 TIGR01439 lp_hng_hel_AbrB loop 34.2 47 0.001 25.0 3.0 26 222-247 14-39 (43)
14 PF02309 AUX_IAA: AUX/IAA fami 30.6 19 0.00041 37.0 0.4 16 714-729 102-117 (215)
15 PF05641 Agenet: Agenet domain 30.5 1.1E+02 0.0025 25.9 5.1 42 315-366 1-42 (68)
16 smart00333 TUDOR Tudor domain. 29.0 94 0.002 24.7 4.1 52 314-382 2-53 (57)
17 COG1047 SlpA FKBP-type peptidy 27.7 3.3E+02 0.0072 28.1 8.5 105 228-344 2-115 (174)
18 PF01878 EVE: EVE domain; Int 24.8 72 0.0016 30.3 3.2 27 227-253 38-65 (143)
19 cd04451 S1_IF1 S1_IF1: Transla 21.3 4E+02 0.0087 22.2 6.6 38 190-240 15-52 (64)
20 PRK03760 hypothetical protein; 21.0 1.9E+02 0.0041 27.6 5.1 49 189-240 61-117 (117)
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=1.4e-35 Score=259.70 Aligned_cols=83 Identities=55% Similarity=1.044 Sum_probs=81.7
Q ss_pred HHHHHHcCCeEEEEEecCCCCCceeEehhHHHHhhccCcccccEEEEEeeCCCCCCceeeEEEEEeecCCCCCCCCCCcc
Q 004792 277 AWHAVSTGTMFTVYYKPRTSPSEFIVPYDQYMESIKNNYSIGMRFKMRFEGEEAPEQRFTGTIVGIEDADPQRWRDSKWR 356 (730)
Q Consensus 277 A~~aa~tg~~F~V~Y~PRas~sEFVVp~~ky~~Al~~~ws~GmRFKM~fEteDss~~r~~GTI~gv~d~DP~rWP~S~WR 356 (730)
|+|||++|++|+|+||||++++|||||++||++||+++|++||||||+||+||+++++|+|||+||+++||.|||+|+||
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 004792 357 CLK 359 (730)
Q Consensus 357 ~L~ 359 (730)
|||
T Consensus 81 ~Lq 83 (83)
T PF06507_consen 81 MLQ 83 (83)
T ss_pred cCc
Confidence 997
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=6e-17 Score=141.48 Aligned_cols=97 Identities=28% Similarity=0.427 Sum_probs=74.7
Q ss_pred EEEecccccCCCCCceEEcccchhccCCCCCCCCCCCccEEEEEeCCCCeEEEEEEEeCCCCceeeccCchhhccccCCC
Q 004792 151 FCKTLTASDTSTHGGFSVLRRHADECLPPLDMSRQPPTQELAAKDLHGNEWRFRHIFRGQPRRHLLQSGWSVFVSSKRLV 230 (730)
Q Consensus 151 F~K~LT~SDV~~~GrfsVPk~~Ae~~FPpLD~~~~~p~q~L~~kDl~G~~W~FR~iyRg~prrhlLTtGWs~FVr~K~L~ 230 (730)
|.|+|+++|+...++|.||+++++.+. ++ ....+++.++|..|+.|.+++.|++.+++++|++||..||++++|+
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 1125789999999999999999998888899999999999999999
Q ss_pred CCCEEEEEEcCC--CcEEEEEEee
Q 004792 231 AGDAFIFLRGEN--GELRVGVRRA 252 (730)
Q Consensus 231 aGD~VVF~R~en--GeL~VGIRRa 252 (730)
+||.|+|+...+ .++.|.|.|+
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 4569999886
No 3
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=99.54 E-value=5.3e-15 Score=169.02 Aligned_cols=150 Identities=24% Similarity=0.387 Sum_probs=122.4
Q ss_pred CCCCCEEEEEEcCCCcEEEEEEeecccCCCC---------------------CCCccCCCCcchhhHHHHHHHHHcCCeE
Q 004792 229 LVAGDAFIFLRGENGELRVGVRRAMRQQGNV---------------------PSSVISSHSMHLGVLATAWHAVSTGTMF 287 (730)
Q Consensus 229 L~aGD~VVF~R~enGeL~VGIRRa~r~~~~~---------------------p~sv~ss~sm~~gvla~A~~aa~tg~~F 287 (730)
.+.||.|+++|....+|.-.+|+.....++. |.+.-+..+|.+.||..|.++. ...|
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 4589999999987777666666554432221 2233334569999999888764 6889
Q ss_pred EEEEecCCCCCceeEehhHHHHhhccCcccccEEEEEeeCCCC-CCceeeEEEEEeecCCCCCCCCCCcceeeeeecCCC
Q 004792 288 TVYYKPRTSPSEFIVPYDQYMESIKNNYSIGMRFKMRFEGEEA-PEQRFTGTIVGIEDADPQRWRDSKWRCLKVRWDETS 366 (730)
Q Consensus 288 ~V~Y~PRas~sEFVVp~~ky~~Al~~~ws~GmRFKM~fEteDs-s~~r~~GTI~gv~d~DP~rWP~S~WR~L~VrWDe~~ 366 (730)
.+.|......+||+|.++.|++|++++|.++++||.-+.++-. --.||.|+|.++.+..|. +|+|+|+|+.|+||.++
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 9999999999999999999999999999999999999974311 127999999999999998 99999999999999998
Q ss_pred CCCCCCCcccCceeecCCC
Q 004792 367 TIPRPERVSLWKIEPALAP 385 (730)
Q Consensus 367 ~~~~~~RVSPWeIEpv~~~ 385 (730)
.+.-||||.|++..-
T Consensus 1031 ----~~~~spwe~~~i~de 1045 (1113)
T KOG0644|consen 1031 ----TELHSPWEMEPIPDE 1045 (1113)
T ss_pred ----ccccCccccCCCccc
Confidence 467799999998654
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=98.19 E-value=7.3e-06 Score=80.04 Aligned_cols=90 Identities=18% Similarity=0.280 Sum_probs=60.6
Q ss_pred ceeEEEEecccccCCCCC----ceEEcccchhccCCCCCC-CCCCCccEEEEEeCCC--CeEEEEEEEeCC------CCc
Q 004792 147 HVHSFCKTLTASDTSTHG----GFSVLRRHADECLPPLDM-SRQPPTQELAAKDLHG--NEWRFRHIFRGQ------PRR 213 (730)
Q Consensus 147 ~~~~F~K~LT~SDV~~~G----rfsVPk~~Ae~~FPpLD~-~~~~p~q~L~~kDl~G--~~W~FR~iyRg~------prr 213 (730)
....|+|.|++.|++..| |+.|||..++..||.+.. ...+|...|.+++..| ..|+||++|.|+ ...
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 356899999999999764 799999999999998765 4457899999999888 469999999986 667
Q ss_pred eeec--cCchhhccccCCCCCCEEEEE
Q 004792 214 HLLQ--SGWSVFVSSKRLVAGDAFIFL 238 (730)
Q Consensus 214 hlLT--tGWs~FVr~K~L~aGD~VVF~ 238 (730)
+.|| ++=..|.+. =..||.+||.
T Consensus 86 ~RIT~~G~~~~~~~~--~~tGaL~vla 110 (156)
T PF09217_consen 86 YRITRFGRGFPLQNP--ENTGALLVLA 110 (156)
T ss_dssp EEEE---TTSGGG-G--GGTT-EEEEE
T ss_pred eEEeeecCCCccCCc--cccccEEEEE
Confidence 8886 332333332 2479988886
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=97.59 E-value=0.00011 Score=69.03 Aligned_cols=78 Identities=21% Similarity=0.204 Sum_probs=60.8
Q ss_pred eeEEEEecccccCCCC-CceEEcccchhccCCCCCC------------CCCCCccEEEEEeCCCCeEEEEEEEeCC---C
Q 004792 148 VHSFCKTLTASDTSTH-GGFSVLRRHADECLPPLDM------------SRQPPTQELAAKDLHGNEWRFRHIFRGQ---P 211 (730)
Q Consensus 148 ~~~F~K~LT~SDV~~~-GrfsVPk~~Ae~~FPpLD~------------~~~~p~q~L~~kDl~G~~W~FR~iyRg~---p 211 (730)
...|+|+|+.||+..+ .||+||-..... ...|.. ....-++.+.+.|..++.|..++..|.. .
T Consensus 21 kli~~K~L~~tDv~~~qsRLsmP~~qi~~-~dFLt~eE~~~i~~~~~~~~~~~Gv~V~lvdp~~~~~~m~lkkW~mg~~~ 99 (114)
T PF03754_consen 21 KLIIEKTLFKTDVDPHQSRLSMPFNQIID-NDFLTEEEKRIIKEEKKNNDKKKGVEVILVDPSLRKWTMRLKKWNMGNGT 99 (114)
T ss_pred eEEEeeeecccCCCCCCceeeccHHHhcc-cccCCHHHHHHHHHhhccCcccCCceEEEECCcCcEEEEEEEEecccCCc
Confidence 4689999999999965 899999876533 122211 1223578899999999999999999965 5
Q ss_pred CceeeccCchhhccc
Q 004792 212 RRHLLQSGWSVFVSS 226 (730)
Q Consensus 212 rrhlLTtGWs~FVr~ 226 (730)
-.|+|++||..+|++
T Consensus 100 ~~YvL~~gWn~VV~~ 114 (114)
T PF03754_consen 100 SNYVLNSGWNKVVED 114 (114)
T ss_pred eEEEEEcChHhhccC
Confidence 579999999999864
No 6
>PRK10737 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=64.94 E-value=24 Score=36.44 Aligned_cols=104 Identities=21% Similarity=0.267 Sum_probs=64.3
Q ss_pred CCCCCCEEEE-EE--cCCCcEEEEEEeecccCCCCCCCccCCCCcchhhHHHHHHHHHcCCeEEEEEecCCC------CC
Q 004792 228 RLVAGDAFIF-LR--GENGELRVGVRRAMRQQGNVPSSVISSHSMHLGVLATAWHAVSTGTMFTVYYKPRTS------PS 298 (730)
Q Consensus 228 ~L~aGD~VVF-~R--~enGeL~VGIRRa~r~~~~~p~sv~ss~sm~~gvla~A~~aa~tg~~F~V~Y~PRas------~s 298 (730)
++..|+.|.+ |+ .++|+++-.-+ ...|...+-....-+--|.+|..-...|..|+|..-|-.. -.
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 3456777766 33 46777633221 1234444433344444577888888899999998765422 23
Q ss_pred ceeEehhHHHHhhccCcccccEEEEEeeCCCCCCceeeEEEEEeec
Q 004792 299 EFIVPYDQYMESIKNNYSIGMRFKMRFEGEEAPEQRFTGTIVGIED 344 (730)
Q Consensus 299 EFVVp~~ky~~Al~~~ws~GmRFKM~fEteDss~~r~~GTI~gv~d 344 (730)
-..||++.|.... ...+||||.+. +++. .+.++|+.|.+
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 4678888875322 36899999874 4442 46889999875
No 7
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=57.75 E-value=8.7 Score=47.10 Aligned_cols=64 Identities=25% Similarity=0.412 Sum_probs=44.2
Q ss_pred CCCCCCCeEEEeccchhhhhhccccccccccCCCC-CCCC----cceEEEEEeeeeccCCCcceeEEEeeecC
Q 004792 59 TVPREGERVYYFPQGHIEQVEASTNQVADQQMPVY-DLPS----KILCRVINVQLKAEPDTDEVFAQVTLLPE 126 (730)
Q Consensus 59 ~lP~~gs~VyYFPQGH~Eq~~as~~~~~~~~~p~~-~lP~----~ilCrV~~V~L~Ad~~TDEVyAqi~L~P~ 126 (730)
-||..|+.|.||-|||-|-+.+..-.. +++- ..|. .=.|.|..+..--=+....--.+|.|.=+
T Consensus 872 yipQmgDEViyfrQghqeyl~~~~~n~----~~~~~~~p~~~~~v~~~kv~kl~~~~y~~~~~s~c~m~l~~i 940 (1113)
T KOG0644|consen 872 YIPQMGDEVIYFRQGHQEYLEAVRLNN----IELNNKEPWNKMAVEICKVEKLVYITYPGSGDSCCKMKLAVI 940 (1113)
T ss_pred ccccccceeehhhhhhHHHHhhhhhcc----ccccccCcccccchhhheeeeeeeeeccCCCcchheeeeeee
Confidence 589999999999999999998764321 1221 1233 23788888876666666666666666544
No 8
>KOG3207 consensus Beta-tubulin folding cofactor E [Posttranslational modification, protein turnover, chaperones]
Probab=47.58 E-value=21 Score=41.31 Aligned_cols=42 Identities=31% Similarity=0.548 Sum_probs=29.2
Q ss_pred cccccEEEEEeeCCCCCCceeeEEEEEeecCCCCCCCCCCcceeeeeecCCCCCCC
Q 004792 315 YSIGMRFKMRFEGEEAPEQRFTGTIVGIEDADPQRWRDSKWRCLKVRWDETSTIPR 370 (730)
Q Consensus 315 ws~GmRFKM~fEteDss~~r~~GTI~gv~d~DP~rWP~S~WR~L~VrWDe~~~~~~ 370 (730)
+.+|.|+|..++- ...||.|+|.| |++ +| |.|.||++.-.-+
T Consensus 3 ~~IG~RvkI~~~~---~Tvr~iG~V~g--------~~~-~w--~GvEWDd~~RGKH 44 (505)
T KOG3207|consen 3 MEIGTRVKIGGEI---ATVRYIGEVEG--------NNS-KW--YGVEWDDPVRGKH 44 (505)
T ss_pred eeccceEEEcCEE---EEEEEEEEEcC--------CCC-cc--eeeEecCCCcccc
Confidence 4689999987762 22566666654 666 56 8999999975433
No 9
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=46.50 E-value=32 Score=28.09 Aligned_cols=38 Identities=13% Similarity=0.171 Sum_probs=29.3
Q ss_pred CcccccEEEEEeeCCCCCCceeeEEEEEeecCCCCCCCCCCcceeeeeecC
Q 004792 314 NYSIGMRFKMRFEGEEAPEQRFTGTIVGIEDADPQRWRDSKWRCLKVRWDE 364 (730)
Q Consensus 314 ~ws~GmRFKM~fEteDss~~r~~GTI~gv~d~DP~rWP~S~WR~L~VrWDe 364 (730)
.|.+|+++-..++.++ .||.|+|+.+.. -..+.|.-+.
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 5889999999997544 799999999864 2236777766
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=45.02 E-value=24 Score=27.89 Aligned_cols=27 Identities=15% Similarity=0.164 Sum_probs=22.3
Q ss_pred hhccccCCCCCCEEEEEEcCCCcEEEE
Q 004792 222 VFVSSKRLVAGDAFIFLRGENGELRVG 248 (730)
Q Consensus 222 ~FVr~K~L~aGD~VVF~R~enGeL~VG 248 (730)
.|.++.+|.+||.|.|.-.++|++.+-
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 566788999999999999988866553
No 11
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=37.52 E-value=45 Score=30.64 Aligned_cols=27 Identities=22% Similarity=0.383 Sum_probs=22.1
Q ss_pred hccccCCCCCCEEEEEEcCCCcEEEEE
Q 004792 223 FVSSKRLVAGDAFIFLRGENGELRVGV 249 (730)
Q Consensus 223 FVr~K~L~aGD~VVF~R~enGeL~VGI 249 (730)
|.-...|++||.|+.+|.++|+.++=+
T Consensus 71 i~~~~~Lk~GD~V~ll~~~~gQ~yiVl 97 (100)
T PF10844_consen 71 ITFTDGLKVGDKVLLLRVQGGQKYIVL 97 (100)
T ss_pred EEEecCCcCCCEEEEEEecCCCEEEEE
Confidence 566778999999999999888766544
No 12
>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=34.87 E-value=62 Score=27.13 Aligned_cols=32 Identities=22% Similarity=0.559 Sum_probs=25.2
Q ss_pred cccEEEEEeeCCCCCCceeeEEEEEeecCCCC
Q 004792 317 IGMRFKMRFEGEEAPEQRFTGTIVGIEDADPQ 348 (730)
Q Consensus 317 ~GmRFKM~fEteDss~~r~~GTI~gv~d~DP~ 348 (730)
+|-|+.-.||+++.+...|.|+|....++-|.
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 58899999999988888889999999887664
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=34.21 E-value=47 Score=25.03 Aligned_cols=26 Identities=27% Similarity=0.374 Sum_probs=21.8
Q ss_pred hhccccCCCCCCEEEEEEcCCCcEEE
Q 004792 222 VFVSSKRLVAGDAFIFLRGENGELRV 247 (730)
Q Consensus 222 ~FVr~K~L~aGD~VVF~R~enGeL~V 247 (730)
.|.++-++..||.|.+....+|.|.+
T Consensus 14 ~~r~~l~~~~gd~~~i~~~~~~~l~l 39 (43)
T TIGR01439 14 EIREKLGLKEGDRLEVIRVEDGEIIL 39 (43)
T ss_pred HHHHHcCcCCCCEEEEEEeCCCEEEE
Confidence 67889999999999999877776544
No 14
>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=30.60 E-value=19 Score=37.04 Aligned_cols=16 Identities=38% Similarity=0.468 Sum_probs=0.0
Q ss_pred cCCCCCCcceeeccCC
Q 004792 714 KTQCGSTRSCTKVPLP 729 (730)
Q Consensus 714 k~q~~stRsctKVhKQ 729 (730)
..+.++.|+|+|||++
T Consensus 102 ~~~~~~~~~~vKV~md 117 (215)
T PF02309_consen 102 EKQSSSSRSYVKVNMD 117 (215)
T ss_dssp ----------------
T ss_pred ccccccCCceeEEEec
Confidence 4556667999999986
No 15
>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=30.49 E-value=1.1e+02 Score=25.92 Aligned_cols=42 Identities=14% Similarity=0.249 Sum_probs=27.6
Q ss_pred cccccEEEEEeeCCCCCCceeeEEEEEeecCCCCCCCCCCcceeeeeecCCC
Q 004792 315 YSIGMRFKMRFEGEEAPEQRFTGTIVGIEDADPQRWRDSKWRCLKVRWDETS 366 (730)
Q Consensus 315 ws~GmRFKM~fEteDss~~r~~GTI~gv~d~DP~rWP~S~WR~L~VrWDe~~ 366 (730)
|..|+++-..-+.+...-.||.|+|+.....+ .+.|+.++-.
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 46899999988766655599999999987532 7888886554
No 16
>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=29.00 E-value=94 Score=24.68 Aligned_cols=52 Identities=13% Similarity=0.358 Sum_probs=36.9
Q ss_pred CcccccEEEEEeeCCCCCCceeeEEEEEeecCCCCCCCCCCcceeeeeecCCCCCCCCCCcccCceeec
Q 004792 314 NYSIGMRFKMRFEGEEAPEQRFTGTIVGIEDADPQRWRDSKWRCLKVRWDETSTIPRPERVSLWKIEPA 382 (730)
Q Consensus 314 ~ws~GmRFKM~fEteDss~~r~~GTI~gv~d~DP~rWP~S~WR~L~VrWDe~~~~~~~~RVSPWeIEpv 382 (730)
.|.+|..+..++ .+. .||.|+|+++.. + ..+.|.-++-.. .+-|...+|-++
T Consensus 2 ~~~~G~~~~a~~-~d~---~wyra~I~~~~~-------~---~~~~V~f~D~G~---~~~v~~~~l~~l 53 (57)
T smart00333 2 TFKVGDKVAARW-EDG---EWYRARIIKVDG-------E---QLYEVFFIDYGN---EEVVPPSDLRPL 53 (57)
T ss_pred CCCCCCEEEEEe-CCC---CEEEEEEEEECC-------C---CEEEEEEECCCc---cEEEeHHHeecC
Confidence 588999999999 433 799999999974 1 557788887543 345555555443
No 17
>COG1047 SlpA FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]
Probab=27.75 E-value=3.3e+02 Score=28.09 Aligned_cols=105 Identities=22% Similarity=0.343 Sum_probs=65.9
Q ss_pred CCCCCCEEEEE---EcCCCcEEEEEEeecccCCCCCCCccCCCCcchhhHHHHHHHHHcCCeEEEEEecCCCCCce----
Q 004792 228 RLVAGDAFIFL---RGENGELRVGVRRAMRQQGNVPSSVISSHSMHLGVLATAWHAVSTGTMFTVYYKPRTSPSEF---- 300 (730)
Q Consensus 228 ~L~aGD~VVF~---R~enGeL~VGIRRa~r~~~~~p~sv~ss~sm~~gvla~A~~aa~tg~~F~V~Y~PRas~sEF---- 300 (730)
.+..||.|.+. |.++|+++=--.- ...|-.++-.+..-+--|.+|..-...|.-|+|.--|-..-.++
T Consensus 2 ~i~k~~~V~i~Y~~~~~dg~v~Dtt~e-----~~~P~~~i~G~g~li~glE~al~g~~~Ge~~~V~IpPE~AfGe~~~~l 76 (174)
T COG1047 2 KIEKGDVVSLHYTLKVEDGEVVDTTDE-----NYGPLTFIVGAGQLIPGLEEALLGKEVGEEFTVEIPPEDAFGEYDPDL 76 (174)
T ss_pred cccCCCEEEEEEEEEecCCcEEEcccc-----cCCCeEEEecCCCcchhHHHHHhCCCCCceeEEEeCchHhcCCCChHH
Confidence 46678888763 3355655321110 11233344344444456788888899999999998886544443
Q ss_pred --eEehhHHHHhhccCcccccEEEEEeeCCCCCCceeeEEEEEeec
Q 004792 301 --IVPYDQYMESIKNNYSIGMRFKMRFEGEEAPEQRFTGTIVGIED 344 (730)
Q Consensus 301 --VVp~~ky~~Al~~~ws~GmRFKM~fEteDss~~r~~GTI~gv~d 344 (730)
+||+++|...= ...+||+|.. +++| .-.-|+|+.|..
T Consensus 77 vq~vp~~~F~~~~--~~~vGm~~~~--~~~~---~~~~~~V~~V~~ 115 (174)
T COG1047 77 VQRVPRDEFQGVG--ELEVGMEVEA--EGGD---GEIPGVVTEVSG 115 (174)
T ss_pred eEEecHHHhCcCC--CCCCCcEEEE--cCCC---ceeeEEEEEEcC
Confidence 56777665543 6789999874 4444 356899998864
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=24.76 E-value=72 Score=30.33 Aligned_cols=27 Identities=26% Similarity=0.411 Sum_probs=17.8
Q ss_pred cCCCCCCEEEEEEcC-CCcEEEEEEeec
Q 004792 227 KRLVAGDAFIFLRGE-NGELRVGVRRAM 253 (730)
Q Consensus 227 K~L~aGD~VVF~R~e-nGeL~VGIRRa~ 253 (730)
++++.||.|+||... .+.-+|||=+-.
T Consensus 38 ~~mk~GD~vifY~s~~~~~~ivai~~V~ 65 (143)
T PF01878_consen 38 KRMKPGDKVIFYHSGCKERGIVAIGEVV 65 (143)
T ss_dssp HC--TT-EEEEEETSSSS-EEEEEEEEE
T ss_pred hcCCCCCEEEEEEcCCCCCEEEEEEEEe
Confidence 589999999999987 567777775543
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=21.34 E-value=4e+02 Score=22.21 Aligned_cols=38 Identities=16% Similarity=0.163 Sum_probs=23.1
Q ss_pred EEEEEeCCCCeEEEEEEEeCCCCceeeccCchhhccccCCCCCCEEEEEEc
Q 004792 190 ELAAKDLHGNEWRFRHIFRGQPRRHLLQSGWSVFVSSKRLVAGDAFIFLRG 240 (730)
Q Consensus 190 ~L~~kDl~G~~W~FR~iyRg~prrhlLTtGWs~FVr~K~L~aGD~VVF~R~ 240 (730)
...+++..|. .++|..||+-|. +...+.+||.|.|...
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 3455666676 455555553221 2334899999999854
No 20
>PRK03760 hypothetical protein; Provisional
Probab=21.03 E-value=1.9e+02 Score=27.57 Aligned_cols=49 Identities=16% Similarity=0.276 Sum_probs=30.5
Q ss_pred cEEEEEeCCCCeEEEEE-----EEe-CCCCceee--ccCchhhccccCCCCCCEEEEEEc
Q 004792 189 QELAAKDLHGNEWRFRH-----IFR-GQPRRHLL--QSGWSVFVSSKRLVAGDAFIFLRG 240 (730)
Q Consensus 189 q~L~~kDl~G~~W~FR~-----iyR-g~prrhlL--TtGWs~FVr~K~L~aGD~VVF~R~ 240 (730)
.++.+.|.+|++-.... +|. ..+=+|+| ..||.. +.++++||.|.|.|+
T Consensus 61 LDiiFld~~g~Vv~i~~~~P~~~~~~~~~a~~VLEl~aG~~~---~~gi~~Gd~v~~~~~ 117 (117)
T PRK03760 61 IDVIFLDSNRRVVDFKTLKPWRIYVPKKPARYIIEGPVGKIR---VLKVEVGDEIEWIDE 117 (117)
T ss_pred eEEEEECCCCeEEEEEeCCCccccCCCccceEEEEeCCChHH---HcCCCCCCEEEEeeC
Confidence 44666666665333211 122 22445888 777664 889999999998763
Done!