Query 004532
Match_columns 746
No_of_seqs 284 out of 528
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 00:59:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004532.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/004532hhsearch_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 7E-35 1.5E-39 256.2 8.5 83 287-369 1-83 (83)
2 PF02362 B3: B3 DNA binding do 99.7 9.2E-17 2E-21 142.4 11.2 97 161-262 1-99 (100)
3 KOG0644 Uncharacterized conser 99.5 3.4E-14 7.3E-19 163.3 5.6 149 239-393 874-1044(1113)
4 PF09217 EcoRII-N: Restriction 97.9 5.5E-05 1.2E-09 74.1 9.0 89 158-248 7-110 (156)
5 PF03754 DUF313: Domain of unk 97.6 8.8E-05 1.9E-09 69.9 5.7 77 159-236 22-114 (114)
6 PRK10737 FKBP-type peptidyl-pr 64.4 29 0.00063 36.1 8.1 104 238-354 2-114 (196)
7 KOG0644 Uncharacterized conser 61.9 4.5 9.8E-05 49.5 1.9 63 66-128 872-939 (1113)
8 smart00743 Agenet Tudor-like d 52.8 20 0.00044 29.4 3.9 28 324-354 2-29 (61)
9 KOG3207 Beta-tubulin folding c 51.9 19 0.00042 41.7 4.7 42 325-380 3-44 (505)
10 PF04014 Antitoxin-MazE: Antid 47.9 23 0.0005 28.1 3.3 26 232-257 14-39 (47)
11 PF10844 DUF2577: Protein of u 38.0 45 0.00098 30.8 4.1 27 233-259 71-97 (100)
12 PRK03760 hypothetical protein; 35.9 83 0.0018 30.0 5.6 49 199-250 61-117 (117)
13 TIGR01439 lp_hng_hel_AbrB loop 34.1 53 0.0011 24.8 3.3 26 232-257 14-39 (43)
14 PF02513 Spin-Ssty: Spin/Ssty 28.2 85 0.0018 26.2 3.7 31 327-357 1-31 (50)
15 smart00333 TUDOR Tudor domain. 25.6 1.1E+02 0.0024 24.4 3.9 52 324-392 2-54 (57)
16 PF01878 EVE: EVE domain; Int 25.3 69 0.0015 30.7 3.2 25 237-261 38-63 (143)
17 COG1047 SlpA FKBP-type peptidy 23.8 5E+02 0.011 26.8 9.0 106 237-354 1-115 (174)
18 PF02643 DUF192: Uncharacteriz 23.3 1.5E+02 0.0032 27.6 4.9 46 199-247 50-106 (108)
19 cd04451 S1_IF1 S1_IF1: Transla 23.3 3.2E+02 0.007 22.8 6.5 38 200-250 15-52 (64)
20 PF05641 Agenet: Agenet domain 22.7 2E+02 0.0044 24.5 5.2 40 325-374 1-40 (68)
21 PF03120 DNA_ligase_OB: NAD-de 20.7 70 0.0015 29.0 2.1 32 231-262 42-74 (82)
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=7e-35 Score=256.15 Aligned_cols=83 Identities=57% Similarity=1.081 Sum_probs=81.8
Q ss_pred HHHHhhcCCeEEEEEecCCCCCceeeehhhHhhhccCCCccCCeEEEeeecCccccceeeeEEEeeecCCCCCCCCCCce
Q 004532 287 VVDAIARKRAFSISYNPRASASEFIIPVNKFLKSLDHSFAVGMRFKMRFETDDAAERRYTGVIMGVGDVDPVRWPGSKWR 366 (746)
Q Consensus 287 a~~a~~t~~~F~V~Y~Pr~~~sEFIVp~~ky~~s~~~~w~~GmRFkM~fe~EDs~e~r~~GtI~gv~~~dp~rwp~S~WR 366 (746)
|+|||+++++|+|+||||++++||||+++||++||+++|++||||||+||+||+++++|+|||+||++.||++||+|+||
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 004532 367 CLL 369 (746)
Q Consensus 367 ~L~ 369 (746)
|||
T Consensus 81 ~Lq 83 (83)
T PF06507_consen 81 MLQ 83 (83)
T ss_pred cCc
Confidence 996
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=9.2e-17 Score=142.40 Aligned_cols=97 Identities=32% Similarity=0.471 Sum_probs=74.7
Q ss_pred EEEecccccCCCCCceeeeccchhhcCCCCCCCCCCCceEEEEEeCCCCeEEEEEEEeCCCCceeeccchhhhhhccCCC
Q 004532 161 FCKTLTASDTSTHGGFSVPRRAAEDCFPPLDYSQQRPSQELVAKDLHGLEWRFRHIYRGQPRRHLLTTGWSAFVNKKKLV 240 (746)
Q Consensus 161 F~K~LT~SDv~~~grfsVPk~~Ae~~FPpLd~~~~~p~q~L~~~D~~G~~W~Fr~~yrg~prrhlLTtGWs~FV~~K~L~ 240 (746)
|.|+|+++|+...++|.||+++++.+. ++ ....+++.++|..|+.|.+++.|++.+++++|++||..||++++|+
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 1235789999999999999999998888899999999999999999
Q ss_pred CCCEEEEEEcCC--CcEEEEEEEc
Q 004532 241 SGDAVLFLRGED--GELRLGIRRA 262 (746)
Q Consensus 241 aGD~VvF~R~~~--Gel~vGIRRa 262 (746)
+||.|+|+...+ .++.|.|+|+
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 999999998654 5569999986
No 3
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=99.46 E-value=3.4e-14 Score=163.28 Aligned_cols=149 Identities=17% Similarity=0.386 Sum_probs=117.4
Q ss_pred CCCCCEEEEEEcCCCcEEEEEEEcCCCCCC-------------------CCC--CccccCCCCCchHHHHHHHhhcCCeE
Q 004532 239 LVSGDAVLFLRGEDGELRLGIRRAPHVKSG-------------------ATF--PSFCSQQSSPNSVTEVVDAIARKRAF 297 (746)
Q Consensus 239 L~aGD~VvF~R~~~Gel~vGIRRa~~~~~~-------------------~~~--~~~~~~~~~~~~l~~a~~a~~t~~~F 297 (746)
.+-||.|+.+|....++.-.+|+...-.++ ..+ +..+.-+|.+.++.-|.++. ...|
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 567999999998766554444443221100 111 22223368888888888654 5679
Q ss_pred EEEEecCCCCCceeeehhhHhhhccCCCccCCeEEEeeecCccc-cceeeeEEEeeecCCCCCCCCCCceeeEEeecCCC
Q 004532 298 SISYNPRASASEFIIPVNKFLKSLDHSFAVGMRFKMRFETDDAA-ERRYTGVIMGVGDVDPVRWPGSKWRCLLVRWDDVE 376 (746)
Q Consensus 298 ~V~Y~Pr~~~sEFIVp~~ky~~s~~~~w~~GmRFkM~fe~EDs~-e~r~~GtI~gv~~~dp~rwp~S~WR~L~V~WDe~~ 376 (746)
.+.|+.....+||||.++.|++|+.++|.++++||.-+..+-.. -.||.|+|.++++..| .+|+|+|+|+.|+||..|
T Consensus 952 ~ltlpdlv~fpDFlV~rsrYd~AiQrnW~~~d~crvwwrda~~e~g~WWeG~ils~~pksp-~fpdSpwery~v~~~~~e 1030 (1113)
T KOG0644|consen 952 KLTLPDLVTFPDFLVERSRYDAAIQRNWTCRDKCRVWWRDAGEEDGAWWEGRILSVKPKSP-DFPDSPWERYIVRYDNTE 1030 (1113)
T ss_pred eeecccccCcchhhhhhhhHHHHHhhccccccceeEEEccCCCcCCceeeeeeeeccCCCC-CCCCCcceeEEEEecCCc
Confidence 99999999999999999999999999999999999999522111 2399999999999999 999999999999999998
Q ss_pred CCCCCCccccccccCCC
Q 004532 377 SNRHTRVSPWEIEPSGS 393 (746)
Q Consensus 377 ~~~~~RVSPWeIEpv~~ 393 (746)
+ +.-||||.|++..
T Consensus 1031 ~---~~~spwe~~~i~d 1044 (1113)
T KOG0644|consen 1031 T---ELHSPWEMEPIPD 1044 (1113)
T ss_pred c---cccCccccCCCcc
Confidence 8 6889999999984
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=97.88 E-value=5.5e-05 Score=74.12 Aligned_cols=89 Identities=26% Similarity=0.395 Sum_probs=59.5
Q ss_pred ceeEEEecccccCCCCC----ceeeeccchhhcCCCCCC-CCCCCceEEEEEeCCC--CeEEEEEEEeCC------CCce
Q 004532 158 PHMFCKTLTASDTSTHG----GFSVPRRAAEDCFPPLDY-SQQRPSQELVAKDLHG--LEWRFRHIYRGQ------PRRH 224 (746)
Q Consensus 158 ~~~F~K~LT~SDv~~~g----rfsVPk~~Ae~~FPpLd~-~~~~p~q~L~~~D~~G--~~W~Fr~~yrg~------prrh 224 (746)
-..|+|.|++.|++..| |+.|||..++..||.+.. ....|...|.+++..| ..|+||++|.++ ...+
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 5566889999999888 568899999976 5667
Q ss_pred eec--cchhhhhhccCCCCCCEEEEE
Q 004532 225 LLT--TGWSAFVNKKKLVSGDAVLFL 248 (746)
Q Consensus 225 lLT--tGWs~FV~~K~L~aGD~VvF~ 248 (746)
.|| ++=..|.+.. ..||-+||.
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 3333344432 478888886
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=97.62 E-value=8.8e-05 Score=69.85 Aligned_cols=77 Identities=22% Similarity=0.321 Sum_probs=60.5
Q ss_pred eeEEEecccccCCCC-CceeeeccchhhcCCCCCC------------CCCCCceEEEEEeCCCCeEEEEEEEeCC---CC
Q 004532 159 HMFCKTLTASDTSTH-GGFSVPRRAAEDCFPPLDY------------SQQRPSQELVAKDLHGLEWRFRHIYRGQ---PR 222 (746)
Q Consensus 159 ~~F~K~LT~SDv~~~-grfsVPk~~Ae~~FPpLd~------------~~~~p~q~L~~~D~~G~~W~Fr~~yrg~---pr 222 (746)
..|+|+|++||+..+ .||+||-..... ...|.. .....++.+.+.|..++.|..++..|.. .-
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 004532 223 RHLLTTGWSAFVNK 236 (746)
Q Consensus 223 rhlLTtGWs~FV~~ 236 (746)
.|+|++||..+|++
T Consensus 101 ~YvL~~gWn~VV~~ 114 (114)
T PF03754_consen 101 NYVLNSGWNKVVED 114 (114)
T ss_pred EEEEEcChHhhccC
Confidence 79999999999864
No 6
>PRK10737 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=64.43 E-value=29 Score=36.07 Aligned_cols=104 Identities=21% Similarity=0.231 Sum_probs=64.3
Q ss_pred CCCCCCEEEE-E--EcCCCcEEEEEEEcCCCCCCCCCCccccCCCCCchHHHHHHHhhcCCeEEEEEecCC------CCC
Q 004532 238 KLVSGDAVLF-L--RGEDGELRLGIRRAPHVKSGATFPSFCSQQSSPNSVTEVVDAIARKRAFSISYNPRA------SAS 308 (746)
Q Consensus 238 ~L~aGD~VvF-~--R~~~Gel~vGIRRa~~~~~~~~~~~~~~~~~~~~~l~~a~~a~~t~~~F~V~Y~Pr~------~~s 308 (746)
++..|+.|.+ | |.++|+++---+ ...|...+-....-...|.+|+.-.+.|..|+|..-|-. .-.
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 4566777777 2 456777533211 012222222333345568888888899999999865542 223
Q ss_pred ceeeehhhHhhhccCCCccCCeEEEeeecCccccceeeeEEEeeec
Q 004532 309 EFIIPVNKFLKSLDHSFAVGMRFKMRFETDDAAERRYTGVIMGVGD 354 (746)
Q Consensus 309 EFIVp~~ky~~s~~~~w~~GmRFkM~fe~EDs~e~r~~GtI~gv~~ 354 (746)
-..||++.|.... ...+||||.+. +++. ...++|+.|.+
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 36899998874 4454 35788888865
No 7
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=61.95 E-value=4.5 Score=49.49 Aligned_cols=63 Identities=21% Similarity=0.383 Sum_probs=41.4
Q ss_pred CCCCCCCEEEEeecccccccccchhhccc-----CCCCCCCceeeEEEeeeeccCCCceeEEEeeccc
Q 004532 66 SLPKRGSVVVYFPQGHLEHVSDFSAAASA-----AYDLPPHPFCRVADVKLHAEAASDEVYAQVSLVP 128 (746)
Q Consensus 66 ~lP~~gs~V~YFPqGH~Eq~~~~~~~~~~-----~~~lp~~i~CrV~~V~l~Ad~~TDEVyA~i~L~P 128 (746)
-||..|+.|.||-|||-|-+.+....... ..++-..-.|.|..+...-=+....--.+|.|.=
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 58999999999999999998876421111 1122223358888776665566666666666643
No 8
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=52.82 E-value=20 Score=29.39 Aligned_cols=28 Identities=21% Similarity=0.323 Sum_probs=23.7
Q ss_pred CCccCCeEEEeeecCccccceeeeEEEeeec
Q 004532 324 SFAVGMRFKMRFETDDAAERRYTGVIMGVGD 354 (746)
Q Consensus 324 ~w~~GmRFkM~fe~EDs~e~r~~GtI~gv~~ 354 (746)
.|.+|+++...++.+++ ||.|+|+.+..
T Consensus 2 ~~~~G~~Ve~~~~~~~~---W~~a~V~~~~~ 29 (61)
T smart00743 2 DFKKGDRVEVFSKEEDS---WWEAVVTKVLG 29 (61)
T ss_pred CcCCCCEEEEEECCCCE---EEEEEEEEECC
Confidence 58899999999975444 99999999976
No 9
>KOG3207 consensus Beta-tubulin folding cofactor E [Posttranslational modification, protein turnover, chaperones]
Probab=51.87 E-value=19 Score=41.73 Aligned_cols=42 Identities=31% Similarity=0.590 Sum_probs=27.9
Q ss_pred CccCCeEEEeeecCccccceeeeEEEeeecCCCCCCCCCCceeeEEeecCCCCCCC
Q 004532 325 FAVGMRFKMRFETDDAAERRYTGVIMGVGDVDPVRWPGSKWRCLLVRWDDVESNRH 380 (746)
Q Consensus 325 w~~GmRFkM~fe~EDs~e~r~~GtI~gv~~~dp~rwp~S~WR~L~V~WDe~~~~~~ 380 (746)
+.+|+|+|..++ .+||.=+...+| |++ +| |.|.||++.-..+
T Consensus 3 ~~IG~RvkI~~~---------~~Tvr~iG~V~g--~~~-~w--~GvEWDd~~RGKH 44 (505)
T KOG3207|consen 3 MEIGTRVKIGGE---------IATVRYIGEVEG--NNS-KW--YGVEWDDPVRGKH 44 (505)
T ss_pred eeccceEEEcCE---------EEEEEEEEEEcC--CCC-cc--eeeEecCCCcccc
Confidence 468999999877 344444444444 665 45 7899999665443
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=47.90 E-value=23 Score=28.07 Aligned_cols=26 Identities=27% Similarity=0.325 Sum_probs=21.9
Q ss_pred hhhhccCCCCCCEEEEEEcCCCcEEE
Q 004532 232 AFVNKKKLVSGDAVLFLRGEDGELRL 257 (746)
Q Consensus 232 ~FV~~K~L~aGD~VvF~R~~~Gel~v 257 (746)
+|.++.+|.+||.|.|.-.++|++.+
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 46778899999999999999886554
No 11
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=37.95 E-value=45 Score=30.78 Aligned_cols=27 Identities=30% Similarity=0.407 Sum_probs=22.3
Q ss_pred hhhccCCCCCCEEEEEEcCCCcEEEEE
Q 004532 233 FVNKKKLVSGDAVLFLRGEDGELRLGI 259 (746)
Q Consensus 233 FV~~K~L~aGD~VvF~R~~~Gel~vGI 259 (746)
|.-...|++||.|..+|..+|+.++-+
T Consensus 71 i~~~~~Lk~GD~V~ll~~~~gQ~yiVl 97 (100)
T PF10844_consen 71 ITFTDGLKVGDKVLLLRVQGGQKYIVL 97 (100)
T ss_pred EEEecCCcCCCEEEEEEecCCCEEEEE
Confidence 556678999999999998888866654
No 12
>PRK03760 hypothetical protein; Provisional
Probab=35.87 E-value=83 Score=30.03 Aligned_cols=49 Identities=20% Similarity=0.366 Sum_probs=31.6
Q ss_pred eEEEEEeCCCCeEEEEE-----EEe-CCCCceee--ccchhhhhhccCCCCCCEEEEEEc
Q 004532 199 QELVAKDLHGLEWRFRH-----IYR-GQPRRHLL--TTGWSAFVNKKKLVSGDAVLFLRG 250 (746)
Q Consensus 199 q~L~~~D~~G~~W~Fr~-----~yr-g~prrhlL--TtGWs~FV~~K~L~aGD~VvF~R~ 250 (746)
.++++.|.+|++-.... +|. ..+-+|+| ..|| +.+.++++||.|.|.|+
T Consensus 61 LDiiFld~~g~Vv~i~~~~P~~~~~~~~~a~~VLEl~aG~---~~~~gi~~Gd~v~~~~~ 117 (117)
T PRK03760 61 IDVIFLDSNRRVVDFKTLKPWRIYVPKKPARYIIEGPVGK---IRVLKVEVGDEIEWIDE 117 (117)
T ss_pred eEEEEECCCCeEEEEEeCCCccccCCCccceEEEEeCCCh---HHHcCCCCCCEEEEeeC
Confidence 34566666665433211 122 23556787 6887 78899999999999764
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=34.14 E-value=53 Score=24.80 Aligned_cols=26 Identities=38% Similarity=0.505 Sum_probs=21.8
Q ss_pred hhhhccCCCCCCEEEEEEcCCCcEEE
Q 004532 232 AFVNKKKLVSGDAVLFLRGEDGELRL 257 (746)
Q Consensus 232 ~FV~~K~L~aGD~VvF~R~~~Gel~v 257 (746)
.|.++-++..||.|.+....+|.+.+
T Consensus 14 ~~r~~l~~~~gd~~~i~~~~~~~l~l 39 (43)
T TIGR01439 14 EIREKLGLKEGDRLEVIRVEDGEIIL 39 (43)
T ss_pred HHHHHcCcCCCCEEEEEEeCCCEEEE
Confidence 67899999999999999877776544
No 14
>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=28.21 E-value=85 Score=26.20 Aligned_cols=31 Identities=23% Similarity=0.530 Sum_probs=24.4
Q ss_pred cCCeEEEeeecCccccceeeeEEEeeecCCC
Q 004532 327 VGMRFKMRFETDDAAERRYTGVIMGVGDVDP 357 (746)
Q Consensus 327 ~GmRFkM~fe~EDs~e~r~~GtI~gv~~~dp 357 (746)
+|-|+.-.||.++.+...|.|+|...-+..|
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 5889999999888887788999999888777
No 15
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=25.57 E-value=1.1e+02 Score=24.42 Aligned_cols=52 Identities=25% Similarity=0.369 Sum_probs=37.4
Q ss_pred CCccCCeEEEeeecCccccceeeeEEEeeecCCCCCCCCCCceeeEEeecC-CCCCCCCCccccccccCC
Q 004532 324 SFAVGMRFKMRFETDDAAERRYTGVIMGVGDVDPVRWPGSKWRCLLVRWDD-VESNRHTRVSPWEIEPSG 392 (746)
Q Consensus 324 ~w~~GmRFkM~fe~EDs~e~r~~GtI~gv~~~dp~rwp~S~WR~L~V~WDe-~~~~~~~RVSPWeIEpv~ 392 (746)
+|.+|..+..++ .+. .||.|+|+++... ....|.-++ ... +-|...+|-++.
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 688999999999 332 5999999999752 456788888 444 456666655543
No 16
>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=25.26 E-value=69 Score=30.69 Aligned_cols=25 Identities=24% Similarity=0.410 Sum_probs=15.9
Q ss_pred cCCCCCCEEEEEEcC-CCcEEEEEEE
Q 004532 237 KKLVSGDAVLFLRGE-DGELRLGIRR 261 (746)
Q Consensus 237 K~L~aGD~VvF~R~~-~Gel~vGIRR 261 (746)
++++.||.|+||... .+.-+|||=+
T Consensus 38 ~~mk~GD~vifY~s~~~~~~ivai~~ 63 (143)
T PF01878_consen 38 KRMKPGDKVIFYHSGCKERGIVAIGE 63 (143)
T ss_dssp HC--TT-EEEEEETSSSS-EEEEEEE
T ss_pred hcCCCCCEEEEEEcCCCCCEEEEEEE
Confidence 489999999999987 5566666644
No 17
>COG1047 SlpA FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]
Probab=23.77 E-value=5e+02 Score=26.85 Aligned_cols=106 Identities=20% Similarity=0.281 Sum_probs=66.5
Q ss_pred cCCCCCCEEEEE---EcCCCcEEEEEEEcCCCCCCCCCCccccCCCCCchHHHHHHHhhcCCeEEEEEecCCCCCce---
Q 004532 237 KKLVSGDAVLFL---RGEDGELRLGIRRAPHVKSGATFPSFCSQQSSPNSVTEVVDAIARKRAFSISYNPRASASEF--- 310 (746)
Q Consensus 237 K~L~aGD~VvF~---R~~~Gel~vGIRRa~~~~~~~~~~~~~~~~~~~~~l~~a~~a~~t~~~F~V~Y~Pr~~~sEF--- 310 (746)
+++..||.|.+. |.++|++.=-=.- ...|...+-.+..-..-|.+|+.-..-|.-|+|.--|-..-.++
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 356678888773 4455654311100 11233333334444567889999999999999998886544443
Q ss_pred ---eeehhhHhhhccCCCccCCeEEEeeecCccccceeeeEEEeeec
Q 004532 311 ---IIPVNKFLKSLDHSFAVGMRFKMRFETDDAAERRYTGVIMGVGD 354 (746)
Q Consensus 311 ---IVp~~ky~~s~~~~w~~GmRFkM~fe~EDs~e~r~~GtI~gv~~ 354 (746)
+||..+|...- ...+||+|.+. ++| .-.-|+|+.|..
T Consensus 76 lvq~vp~~~F~~~~--~~~vGm~~~~~--~~~---~~~~~~V~~V~~ 115 (174)
T COG1047 76 LVQRVPRDEFQGVG--ELEVGMEVEAE--GGD---GEIPGVVTEVSG 115 (174)
T ss_pred HeEEecHHHhCcCC--CCCCCcEEEEc--CCC---ceeeEEEEEEcC
Confidence 57777775433 67899988754 444 345788988753
No 18
>PF02643 DUF192: Uncharacterized ACR, COG1430; InterPro: IPR003795 This entry describes proteins of unknown function.; PDB: 3M7A_B 3PJY_B.
Probab=23.28 E-value=1.5e+02 Score=27.64 Aligned_cols=46 Identities=24% Similarity=0.407 Sum_probs=28.5
Q ss_pred eEEEEEeCCCCeEEEEEEEe---------CCCCceee--ccchhhhhhccCCCCCCEEEE
Q 004532 199 QELVAKDLHGLEWRFRHIYR---------GQPRRHLL--TTGWSAFVNKKKLVSGDAVLF 247 (746)
Q Consensus 199 q~L~~~D~~G~~W~Fr~~yr---------g~prrhlL--TtGWs~FV~~K~L~aGD~VvF 247 (746)
.++.+.|..|++-....... ..+-+|+| ..|| +.+.+|++||.|.|
T Consensus 50 LDi~fld~~g~Vv~i~~~~~P~~~~~~~~~~~a~~vLE~~aG~---~~~~~i~~Gd~v~~ 106 (108)
T PF02643_consen 50 LDIAFLDSDGRVVKIERMVPPWRTYPCPSYKPARYVLELPAGW---FEKLGIKVGDRVRI 106 (108)
T ss_dssp EEEEEE-TTSBEEEEEEEE-TT--S-EEECCEECEEEEEETTH---HHHHT--TT-EEE-
T ss_pred EEEEEECCCCeEEEEEccCCCCccCCCCCCCccCEEEEcCCCc---hhhcCCCCCCEEEe
Confidence 56888888888665554441 13346887 5665 78999999999987
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=23.28 E-value=3.2e+02 Score=22.80 Aligned_cols=38 Identities=18% Similarity=0.145 Sum_probs=23.3
Q ss_pred EEEEEeCCCCeEEEEEEEeCCCCceeeccchhhhhhccCCCCCCEEEEEEc
Q 004532 200 ELVAKDLHGLEWRFRHIYRGQPRRHLLTTGWSAFVNKKKLVSGDAVLFLRG 250 (746)
Q Consensus 200 ~L~~~D~~G~~W~Fr~~yrg~prrhlLTtGWs~FV~~K~L~aGD~VvF~R~ 250 (746)
.+.+++..|. .++|..||+-|+ +...+.+||.|.|...
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 3455666776 445556653221 2334899999999854
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=22.72 E-value=2e+02 Score=24.47 Aligned_cols=40 Identities=20% Similarity=0.332 Sum_probs=26.9
Q ss_pred CccCCeEEEeeecCccccceeeeEEEeeecCCCCCCCCCCceeeEEeecC
Q 004532 325 FAVGMRFKMRFETDDAAERRYTGVIMGVGDVDPVRWPGSKWRCLLVRWDD 374 (746)
Q Consensus 325 w~~GmRFkM~fe~EDs~e~r~~GtI~gv~~~dp~rwp~S~WR~L~V~WDe 374 (746)
|.+|+++-..-+.+...--||.++|+.....+ .+.|+.++
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 46899999887644433349999999998643 78899988
No 21
>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=20.71 E-value=70 Score=29.03 Aligned_cols=32 Identities=22% Similarity=0.359 Sum_probs=21.6
Q ss_pred hhhhhccCCCCCCEEEEEEcCCCc-EEEEEEEc
Q 004532 231 SAFVNKKKLVSGDAVLFLRGEDGE-LRLGIRRA 262 (746)
Q Consensus 231 s~FV~~K~L~aGD~VvF~R~~~Ge-l~vGIRRa 262 (746)
..|+++++|..||.|.++|..+.= ..+++-..
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 378999999999999999986643 33444433
Done!