Query 002516
Match_columns 913
No_of_seqs 360 out of 852
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 01:33:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002516.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002516hhsearch_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 4.4E-34 9.5E-39 256.0 7.9 83 240-323 1-83 (83)
2 PF02309 AUX_IAA: AUX/IAA fami 100.0 1.1E-34 2.4E-39 297.3 0.5 105 787-891 85-215 (215)
3 PF02362 B3: B3 DNA binding do 99.7 7.7E-17 1.7E-21 144.5 11.7 97 114-215 1-99 (100)
4 KOG0644 Uncharacterized conser 99.0 2.9E-10 6.3E-15 133.6 6.0 149 192-349 874-1045(1113)
5 PF09217 EcoRII-N: Restriction 98.0 3.6E-05 7.7E-10 77.1 10.2 90 111-201 7-110 (156)
6 PF03754 DUF313: Domain of unk 97.8 5.2E-05 1.1E-09 72.9 6.7 81 108-189 18-114 (114)
7 PF00564 PB1: PB1 domain; Int 96.6 0.0062 1.3E-07 53.6 6.5 66 802-874 4-70 (84)
8 smart00666 PB1 PB1 domain. Pho 95.7 0.035 7.7E-07 48.8 7.0 65 802-874 4-69 (81)
9 cd05992 PB1 The PB1 domain is 95.5 0.044 9.4E-07 47.9 6.6 65 802-874 3-69 (81)
10 cd06407 PB1_NLP A PB1 domain i 95.3 0.057 1.2E-06 49.3 7.0 53 802-861 3-55 (82)
11 cd06396 PB1_NBR1 The PB1 domai 94.8 0.087 1.9E-06 48.4 6.7 51 802-861 3-54 (81)
12 cd06409 PB1_MUG70 The MUG70 pr 94.4 0.073 1.6E-06 49.4 5.4 45 814-862 15-59 (86)
13 cd06398 PB1_Joka2 The PB1 doma 94.4 0.14 3E-06 47.8 7.2 56 802-863 3-62 (91)
14 cd06403 PB1_Par6 The PB1 domai 93.0 0.27 5.8E-06 45.3 6.2 66 802-874 3-70 (80)
15 cd06404 PB1_aPKC PB1 domain is 91.7 0.47 1E-05 44.0 6.1 50 802-859 3-53 (83)
16 cd06399 PB1_P40 The PB1 domain 91.5 0.41 8.8E-06 44.9 5.6 54 814-893 22-75 (92)
17 cd06402 PB1_p62 The PB1 domain 91.2 0.76 1.6E-05 42.9 7.0 54 801-860 2-61 (87)
18 cd06401 PB1_TFG The PB1 domain 89.0 1.3 2.8E-05 41.0 6.6 58 802-864 3-61 (81)
19 cd06397 PB1_UP1 Uncharacterize 85.7 2.3 4.9E-05 39.5 6.1 52 802-861 3-54 (82)
20 cd06408 PB1_NoxR The PB1 domai 77.2 6.7 0.00015 36.8 6.1 53 801-863 4-56 (86)
21 PRK10737 FKBP-type peptidyl-pr 51.4 59 0.0013 34.6 7.9 104 191-308 2-114 (196)
22 PF04014 Antitoxin-MazE: Antid 44.6 27 0.0006 28.4 3.3 29 185-213 14-42 (47)
23 KOG3207 Beta-tubulin folding c 36.2 32 0.00069 40.9 3.4 46 279-338 3-48 (505)
24 PF10844 DUF2577: Protein of u 35.0 44 0.00096 31.6 3.6 29 186-214 71-99 (100)
25 PF00788 RA: Ras association ( 35.0 1.2E+02 0.0025 26.8 6.1 67 799-870 2-75 (93)
26 TIGR01439 lp_hng_hel_AbrB loop 32.2 58 0.0013 25.3 3.3 26 185-210 14-39 (43)
27 cd06406 PB1_P67 A PB1 domain i 30.3 1.2E+02 0.0027 28.3 5.5 65 801-874 4-69 (80)
28 smart00743 Agenet Tudor-like d 29.6 76 0.0016 26.7 3.8 28 278-308 2-29 (61)
29 KOG3938 RGS-GAIP interacting p 26.1 2.9E+02 0.0063 31.4 8.3 69 806-887 61-141 (334)
30 KOG3598 Thyroid hormone recept 25.3 27 0.00058 46.3 0.4 9 226-234 1851-1859(2220)
31 KOG0644 Uncharacterized conser 24.8 26 0.00057 44.2 0.3 19 55-73 872-890 (1113)
32 PF01878 EVE: EVE domain; Int 24.0 85 0.0018 30.8 3.6 26 190-215 38-64 (143)
33 COG1047 SlpA FKBP-type peptidy 23.8 4.6E+02 0.0099 27.9 8.9 104 191-307 2-114 (174)
34 PRK03760 hypothetical protein; 23.1 1.8E+02 0.004 28.5 5.6 27 173-202 88-116 (117)
35 PF11515 Cul7: Mouse developme 22.4 1.3E+02 0.0028 28.2 4.1 68 269-347 9-76 (78)
36 smart00333 TUDOR Tudor domain. 21.2 1.4E+02 0.0031 24.4 3.9 52 278-346 2-53 (57)
37 COG3542 Uncharacterized conser 21.2 36 0.00079 35.2 0.4 56 4-73 30-88 (162)
38 PF10411 DsbC_N: Disulfide bon 21.0 75 0.0016 27.2 2.2 17 848-864 34-50 (57)
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=4.4e-34 Score=255.98 Aligned_cols=83 Identities=65% Similarity=1.136 Sum_probs=81.2
Q ss_pred HHHHHhcCCeeEEEecCCCCCCCcccchhhHhhhhccCCcccCCEEEEeeeccccCcceeeeEEEeeccCCCCCCCCCCc
Q 002516 240 AAHAASNRSQFTIFYNPRACPSDFVIPLAKYRKSVYGTQMSVGMRFGMMFETEESGKRRYMGTIVGISDLDPLRWPGSKW 319 (913)
Q Consensus 240 Aa~aaa~~~~F~V~Y~PRas~sEFVVp~~Ky~kAv~~~~ws~GMRFrM~fEtedss~rry~GTI~gvsd~DP~rWP~S~W 319 (913)
|+|||+++++|+|+||||++++|||||++||+||+. ++|++||||||.||+||+++++|+|||+||++.||+|||+|+|
T Consensus 1 A~~aa~~~~~F~V~Y~PRa~~sEFVV~~~k~~~al~-~~~~~GmRfkM~fE~eds~~~~~~GtI~~v~~~dp~~w~~S~W 79 (83)
T PF06507_consen 1 AAHAAATGSPFEVFYYPRASPSEFVVPASKYDKALN-HPWSVGMRFKMRFETEDSSERRWQGTIVGVSDLDPIRWPGSKW 79 (83)
T ss_pred ChhHhhcCCeEEEEECCCCCCcceEEEHHHHHHHhc-CCCCCCcEEEEEeccCCCccceeeeEEeEeeccCCCCCCCCCc
Confidence 689999999999999999999999999999999997 8999999999999999999999999999999999999999999
Q ss_pred ccce
Q 002516 320 RNLQ 323 (913)
Q Consensus 320 R~Lk 323 (913)
||||
T Consensus 80 R~Lq 83 (83)
T PF06507_consen 80 RMLQ 83 (83)
T ss_pred ccCc
Confidence 9997
No 2
>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=100.00 E-value=1.1e-34 Score=297.25 Aligned_cols=105 Identities=44% Similarity=0.820 Sum_probs=3.6
Q ss_pred cCCCCCCcCCC------------CcceEEEeccC-ceeeeecCCCCCCHHHHHHHHHHHh---ccc----------cccc
Q 002516 787 QNTSWQPVVPP------------MRTYTKVQKTG-SVGRSIDVTNFKNYDELCSAIERMF---GLE----------GLLN 840 (913)
Q Consensus 787 ~~~g~~~~~~~------------~~~fVKV~m~G-~igRkIDL~~~~sY~eL~~~L~~MF---~~~----------g~l~ 840 (913)
+-+||++++.. .++||||+|+| +|||||||++|+||++|+.+|++|| ++. +.++
T Consensus 85 ~~vgwpp~~s~r~n~~~~~~~~~~~~~vKV~mdG~~igRkVDL~~~~sY~~L~~~L~~MF~~~~i~~~~~~~~~~~~~~~ 164 (215)
T PF02309_consen 85 QVVGWPPVRSFRKNSLSEKQSSSSRSYVKVNMDGVPIGRKVDLSAYSSYEELSSALEKMFSCFSIEQCGSHGLNESGLLD 164 (215)
T ss_dssp -BTTBS----S---------------------------------------------------------------------
T ss_pred cccCCCcccccccccccccccccCCceeEEEecCcccceecCHHHhhCHHHHHHHHHHhcCCCCccccccccccchhhcc
Confidence 44588777541 46999999999 7999999999999999999999999 554 3344
Q ss_pred CCCCCceEEEEEecCCCEEEccCCchhhcccceeEEEEeChhhhhhhhHhh
Q 002516 841 DPRGTEWKLVYVDYENDVLLVGDDPWEEFVGCVRCIRILSPQEVEQMSEEG 891 (913)
Q Consensus 841 d~~~s~~~lvYeD~EGD~mLVGDvPW~~Fv~svkrirIl~~se~~~m~~~~ 891 (913)
...+++|+|||+|+||||||||||||+|||++|||||||+.+|+++|+++.
T Consensus 165 ~~~~~~~~l~Y~D~egd~mlvGD~PW~~F~~~vkRl~I~~~~e~~~~~~r~ 215 (215)
T PF02309_consen 165 LLNGSEYVLVYEDKEGDWMLVGDVPWEEFVKSVKRLRIMKSSEAKGLAPRA 215 (215)
T ss_dssp ---------------------------------------------------
T ss_pred ccCCcceeEEEECCCCCEEEecCCCHHHHHHHhhccEEecHHHhcccCCCC
Confidence 456789999999999999999999999999999999999999999999873
No 3
>PF02362 B3: B3 DNA binding domain; InterPro: IPR003340 Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana contain two distinct amino acid sequence domains found only in higher plant species. The N-terminal regions of RAV1 and RAV2 are homologous to the AP2 DNA-binding domain (see IPR001471 from INTERPRO) present in a family of transcription factors, while the C-terminal region exhibits homology to the highly conserved C-terminal domain, designated B3, of VP1/ABI3 transcription factors []. The AP2 and B3-like domains of RAV1 bind autonomously to the CAACA and CACCTG motifs, respectively, and together achieve a high affinity and specificity of binding. It has been suggested that the AP2 and B3-like domains of RAV1 are connected by a highly flexible structure enabling the two domains to bind to the CAACA and CACCTG motifs in various spacings and orientations [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1WID_A 1YEL_A.
Probab=99.71 E-value=7.7e-17 Score=144.50 Aligned_cols=97 Identities=29% Similarity=0.455 Sum_probs=74.9
Q ss_pred EEEEeccccCCCCCceeeehhhhhhcCCCCCCCCCCCceEEEEEecCCCeEEEEEEEeCCCCceEEccchhhhhhccCCc
Q 002516 114 FCKTLTASDTSTHGGFSVPRRAAEKLFPPLDYTMQPPTQELVVRDLHDNTWTFRHIYRGQPKRHLLTTGWSLFVGSKRLR 193 (913)
Q Consensus 114 F~K~LT~SDv~~~GrfsVPkr~Ae~~FPpLd~~~~~p~q~L~~~Dl~Gk~W~FR~~yrg~pkRhlLTtGWs~FVk~KkL~ 193 (913)
|.|+|+++|+...+++.||+++++.|. +. ....+++.++|..|+.|.+++.+++.+++++|++||..||++++|+
T Consensus 1 F~K~l~~s~~~~~~~l~iP~~f~~~~~--~~---~~~~~~v~l~~~~g~~W~v~~~~~~~~~~~~l~~GW~~Fv~~n~L~ 75 (100)
T PF02362_consen 1 FFKVLKPSDVSSSCRLIIPKEFAKKHG--GN---KRKSREVTLKDPDGRSWPVKLKYRKNSGRYYLTGGWKKFVRDNGLK 75 (100)
T ss_dssp EEEE--TTCCCCTT-EEE-HHHHTTTS-------SS--CEEEEEETTTEEEEEEEEEECCTTEEEEETTHHHHHHHCT--
T ss_pred CEEEEEccCcCCCCEEEeCHHHHHHhC--CC---cCCCeEEEEEeCCCCEEEEEEEEEccCCeEEECCCHHHHHHHcCCC
Confidence 899999999999999999999999972 11 1245789999999999999999998888899999999999999999
Q ss_pred cCCEEEEEEcc--CCcEEEEEEec
Q 002516 194 AGDSVLFIRDE--KSQLMVGVRRA 215 (913)
Q Consensus 194 aGDsVvF~R~e--~G~L~VGIRRa 215 (913)
+||.|+|+... ..++.|.|.|+
T Consensus 76 ~GD~~~F~~~~~~~~~~~v~i~~~ 99 (100)
T PF02362_consen 76 EGDVCVFELIGNSNFTLKVHIFRK 99 (100)
T ss_dssp TT-EEEEEE-SSSCE-EEEEEE--
T ss_pred CCCEEEEEEecCCCceEEEEEEEC
Confidence 99999999865 45669999996
No 4
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=99.01 E-value=2.9e-10 Score=133.63 Aligned_cols=149 Identities=21% Similarity=0.393 Sum_probs=113.9
Q ss_pred CccCCEEEEEEccCCcEEEEEEecCcCCCC---------------------CCCcccccCccchhhHHHHHHHHhcCCee
Q 002516 192 LRAGDSVLFIRDEKSQLMVGVRRANRQQTA---------------------LPSSVLSADSMHIGVLAAAAHAASNRSQF 250 (913)
Q Consensus 192 L~aGDsVvF~R~e~G~L~VGIRRa~r~~~~---------------------~pssv~s~dsm~~gvlaaAa~aaa~~~~F 250 (913)
.+-||.|+.+|...-+++=.+|+.+...++ .|-+.-+-=.|...|+.-|.++ .+..|
T Consensus 874 pQmgDEViyfrQghqeyl~~~~~n~~~~~~~~p~~~~~v~~~kv~kl~~~~y~~~~~s~c~m~l~~idp~s~~--~~k~F 951 (1113)
T KOG0644|consen 874 PQMGDEVIYFRQGHQEYLEAVRLNNIELNNKEPWNKMAVEICKVEKLVYITYPGSGDSCCKMKLAVIDPASKL--MDKSF 951 (1113)
T ss_pred ccccceeehhhhhhHHHHhhhhhccccccccCcccccchhhheeeeeeeeeccCCCcchheeeeeeecchhhh--hhccc
Confidence 567999999996444444444443332111 1223333334667777777754 35789
Q ss_pred EEEecCCCCCCCcccchhhHhhhhccCCcccCCEEEEeee--ccccCcceeeeEEEeeccCCCCCCCCCCcccceeeccC
Q 002516 251 TIFYNPRACPSDFVIPLAKYRKSVYGTQMSVGMRFGMMFE--TEESGKRRYMGTIVGISDLDPLRWPGSKWRNLQVEWDE 328 (913)
Q Consensus 251 ~V~Y~PRas~sEFVVp~~Ky~kAv~~~~ws~GMRFrM~fE--tedss~rry~GTI~gvsd~DP~rWP~S~WR~LkV~WDE 328 (913)
.+.|......++|+|-+..|+.|+. ++|..+.|||..+. +|| ...||.|+|.++....| .+|+|+|.++.|+||.
T Consensus 952 ~ltlpdlv~fpDFlV~rsrYd~AiQ-rnW~~~d~crvwwrda~~e-~g~WWeG~ils~~pksp-~fpdSpwery~v~~~~ 1028 (1113)
T KOG0644|consen 952 KLTLPDLVTFPDFLVERSRYDAAIQ-RNWTCRDKCRVWWRDAGEE-DGAWWEGRILSVKPKSP-DFPDSPWERYIVRYDN 1028 (1113)
T ss_pred eeecccccCcchhhhhhhhHHHHHh-hccccccceeEEEccCCCc-CCceeeeeeeeccCCCC-CCCCCcceeEEEEecC
Confidence 9999999999999999999999987 89999999999984 333 35799999999998887 8999999999999999
Q ss_pred CCCCCCCCCcCCcceecCCCC
Q 002516 329 PGCSDKQKRVSPWEIETPESL 349 (913)
Q Consensus 329 ~~~~~r~~RVSPWEIEpv~~~ 349 (913)
.+. +.-||||.|++..-
T Consensus 1029 ~e~----~~~spwe~~~i~de 1045 (1113)
T KOG0644|consen 1029 TET----ELHSPWEMEPIPDE 1045 (1113)
T ss_pred Ccc----cccCccccCCCccc
Confidence 974 77899999999753
No 5
>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=98.00 E-value=3.6e-05 Score=77.09 Aligned_cols=90 Identities=26% Similarity=0.385 Sum_probs=58.5
Q ss_pred ceeEEEEeccccCCCCC----ceeeehhhhhhcCCCCCC-CCCCCceEEEEEecCC--CeEEEEEEEeCC------CCce
Q 002516 111 SEFFCKTLTASDTSTHG----GFSVPRRAAEKLFPPLDY-TMQPPTQELVVRDLHD--NTWTFRHIYRGQ------PKRH 177 (913)
Q Consensus 111 ~~~F~K~LT~SDv~~~G----rfsVPkr~Ae~~FPpLd~-~~~~p~q~L~~~Dl~G--k~W~FR~~yrg~------pkRh 177 (913)
...|+|.|++.|++..| |+-|||..++..||.+.. +...|..+|.+++..| ..|+||++|.|+ ++.+
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 46899999999999764 599999999999998765 4456889999999887 568899999976 6778
Q ss_pred EEccchhhhhhccC-CccCCEEEEE
Q 002516 178 LLTTGWSLFVGSKR-LRAGDSVLFI 201 (913)
Q Consensus 178 lLTtGWs~FVk~Kk-L~aGDsVvF~ 201 (913)
.|| .|...-.--+ =..||.+||.
T Consensus 87 RIT-~~G~~~~~~~~~~tGaL~vla 110 (156)
T PF09217_consen 87 RIT-RFGRGFPLQNPENTGALLVLA 110 (156)
T ss_dssp EEE----TTSGGG-GGGTT-EEEEE
T ss_pred EEe-eecCCCccCCccccccEEEEE
Confidence 885 4433332111 2478888876
No 6
>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=97.77 E-value=5.2e-05 Score=72.89 Aligned_cols=81 Identities=22% Similarity=0.296 Sum_probs=64.5
Q ss_pred CCCceeEEEEeccccCCCC-CceeeehhhhhhcCCCCCC------------CCCCCceEEEEEecCCCeEEEEEEEeCC-
Q 002516 108 KHPSEFFCKTLTASDTSTH-GGFSVPRRAAEKLFPPLDY------------TMQPPTQELVVRDLHDNTWTFRHIYRGQ- 173 (913)
Q Consensus 108 ~~~~~~F~K~LT~SDv~~~-GrfsVPkr~Ae~~FPpLd~------------~~~~p~q~L~~~Dl~Gk~W~FR~~yrg~- 173 (913)
..+...|+|+|++||+..+ .||+||-..... ...|.. .....++.+.+.|..++.|..++..|..
T Consensus 18 ~d~kli~~K~L~~tDv~~~qsRLsmP~~qi~~-~dFLt~eE~~~i~~~~~~~~~~~Gv~V~lvdp~~~~~~m~lkkW~mg 96 (114)
T PF03754_consen 18 EDPKLIIEKTLFKTDVDPHQSRLSMPFNQIID-NDFLTEEEKRIIKEEKKNNDKKKGVEVILVDPSLRKWTMRLKKWNMG 96 (114)
T ss_pred CCCeEEEeeeecccCCCCCCceeeccHHHhcc-cccCCHHHHHHHHHhhccCcccCCceEEEECCcCcEEEEEEEEeccc
Confidence 4467899999999999965 999999887743 233321 1245688899999999999999999955
Q ss_pred --CCceEEccchhhhhhc
Q 002516 174 --PKRHLLTTGWSLFVGS 189 (913)
Q Consensus 174 --pkRhlLTtGWs~FVk~ 189 (913)
...|+|++||..+|++
T Consensus 97 ~~~~~YvL~~gWn~VV~~ 114 (114)
T PF03754_consen 97 NGTSNYVLNSGWNKVVED 114 (114)
T ss_pred CCceEEEEEcChHhhccC
Confidence 4679999999999864
No 7
>PF00564 PB1: PB1 domain; InterPro: IPR000270 The Phox and Bem1p domain, is present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.; GO: 0005515 protein binding; PDB: 1IPG_A 1IP9_A 2KFK_A 1WMH_A 1VD2_A 1WI0_A 1OEY_C 1PQS_A 1Q1O_A 1TZ1_A ....
Probab=96.55 E-value=0.0062 Score=53.59 Aligned_cols=66 Identities=26% Similarity=0.469 Sum_probs=53.9
Q ss_pred EEEeccCceeeeecCCCCCCHHHHHHHHHHHhcccccccCCCCCceEEEEEecCCCEEEccC-Cchhhccccee
Q 002516 802 TKVQKTGSVGRSIDVTNFKNYDELCSAIERMFGLEGLLNDPRGTEWKLVYVDYENDVLLVGD-DPWEEFVGCVR 874 (913)
Q Consensus 802 VKV~m~G~igRkIDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLVGD-vPW~~Fv~svk 874 (913)
||+.-.|.+=|.+.+..--+|++|+..++..|++. ...++|.|.|.||||..+-+ .=|++.+..++
T Consensus 4 vK~~~~~~~~~~~~~~~~~s~~~L~~~i~~~~~~~-------~~~~~l~Y~D~dgD~V~i~sd~Dl~~a~~~~~ 70 (84)
T PF00564_consen 4 VKVRYGGDIRRIISLPSDVSFDDLRSKIREKFGLL-------DEDFQLKYKDEDGDLVTISSDEDLQEAIEQAK 70 (84)
T ss_dssp EEEEETTEEEEEEEECSTSHHHHHHHHHHHHHTTS-------TSSEEEEEEETTSSEEEESSHHHHHHHHHHHH
T ss_pred EEEEECCeeEEEEEcCCCCCHHHHHHHHHHHhCCC-------CccEEEEeeCCCCCEEEeCCHHHHHHHHHHHH
Confidence 78888887777788888889999999999999976 34789999999999987764 44666665553
No 8
>smart00666 PB1 PB1 domain. Phox and Bem1p domain, present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.
Probab=95.71 E-value=0.035 Score=48.81 Aligned_cols=65 Identities=23% Similarity=0.423 Sum_probs=50.1
Q ss_pred EEEeccCceeeeecCCCCCCHHHHHHHHHHHhcccccccCCCCCceEEEEEecCCCEEEccC-Cchhhccccee
Q 002516 802 TKVQKTGSVGRSIDVTNFKNYDELCSAIERMFGLEGLLNDPRGTEWKLVYVDYENDVLLVGD-DPWEEFVGCVR 874 (913)
Q Consensus 802 VKV~m~G~igRkIDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLVGD-vPW~~Fv~svk 874 (913)
|||.- |.--|.+-+..--+|.+|+.++.+.|++.+ ..+.|-|.|.||||..+.+ .=|.+.+..++
T Consensus 4 vK~~~-~~~~~~~~~~~~~s~~dL~~~i~~~~~~~~-------~~~~l~Y~Dedgd~v~l~sd~Dl~~a~~~~~ 69 (81)
T smart00666 4 VKLRY-GGETRRLSVPRDISFEDLRSKVAKRFGLDN-------QSFTLKYQDEDGDLVSLTSDEDLEEAIEEYD 69 (81)
T ss_pred EEEEE-CCEEEEEEECCCCCHHHHHHHHHHHhCCCC-------CCeEEEEECCCCCEEEecCHHHHHHHHHHHH
Confidence 67766 555677888889999999999999999653 4689999999999976544 55665555443
No 9
>cd05992 PB1 The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as a noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.
Probab=95.45 E-value=0.044 Score=47.94 Aligned_cols=65 Identities=29% Similarity=0.497 Sum_probs=48.4
Q ss_pred EEEeccCceeeeecCC-CCCCHHHHHHHHHHHhcccccccCCCCCceEEEEEecCCCEEEccC-Cchhhccccee
Q 002516 802 TKVQKTGSVGRSIDVT-NFKNYDELCSAIERMFGLEGLLNDPRGTEWKLVYVDYENDVLLVGD-DPWEEFVGCVR 874 (913)
Q Consensus 802 VKV~m~G~igRkIDL~-~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLVGD-vPW~~Fv~svk 874 (913)
|||+-.|.+ |.+-+. .--+|++|+..|.+.|++.. ..+.+.|.|.||||..+.+ .=|++.++.++
T Consensus 3 vK~~~~~~~-~~~~~~~~~~s~~~L~~~i~~~~~~~~-------~~~~l~y~D~e~d~v~l~sd~Dl~~a~~~~~ 69 (81)
T cd05992 3 VKVKYGGEI-RRFVVVSRSISFEDLRSKIAEKFGLDA-------VSFKLKYPDEDGDLVTISSDEDLEEAIEEAR 69 (81)
T ss_pred EEEEecCCC-EEEEEecCCCCHHHHHHHHHHHhCCCC-------CcEEEEeeCCCCCEEEeCCHHHHHHHHHHHh
Confidence 787777753 233333 88899999999999999753 3689999999999988776 55555555443
No 10
>cd06407 PB1_NLP A PB1 domain is present in NIN like proteins (NLP), a key enzyme in a process of establishment of symbiosis betweeen legumes and nitrogen fixing bacteria (Rhizobium). The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes like osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-inte
Probab=95.31 E-value=0.057 Score=49.32 Aligned_cols=53 Identities=19% Similarity=0.292 Sum_probs=41.6
Q ss_pred EEEeccCceeeeecCCCCCCHHHHHHHHHHHhcccccccCCCCCceEEEEEecCCCEEEc
Q 002516 802 TKVQKTGSVGRSIDVTNFKNYDELCSAIERMFGLEGLLNDPRGTEWKLVYVDYENDVLLV 861 (913)
Q Consensus 802 VKV~m~G~igRkIDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLV 861 (913)
|||.-.|. -+.+-|..--+|++|+.+++++|++. ..+++.|-|.|.||||.++
T Consensus 3 vK~~~~~d-~~r~~l~~~~~~~~L~~~i~~r~~~~------~~~~f~LkY~Ddegd~v~l 55 (82)
T cd06407 3 VKATYGEE-KIRFRLPPSWGFTELKQEIAKRFKLD------DMSAFDLKYLDDDEEWVLL 55 (82)
T ss_pred EEEEeCCe-EEEEEcCCCCCHHHHHHHHHHHhCCC------CCCeeEEEEECCCCCeEEe
Confidence 78888775 23344555559999999999999974 1368999999999999765
No 11
>cd06396 PB1_NBR1 The PB1 domain is an essential part of NBR1 protein, next to BRCA1, a scaffold protein mediating specific protein-protein interaction with both titin protein kinase and with another scaffold protein p62. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The NBR1 protein contains a type I PB1 domain.
Probab=94.81 E-value=0.087 Score=48.44 Aligned_cols=51 Identities=24% Similarity=0.363 Sum_probs=43.5
Q ss_pred EEEeccCc-eeeeecCCCCCCHHHHHHHHHHHhcccccccCCCCCceEEEEEecCCCEEEc
Q 002516 802 TKVQKTGS-VGRSIDVTNFKNYDELCSAIERMFGLEGLLNDPRGTEWKLVYVDYENDVLLV 861 (913)
Q Consensus 802 VKV~m~G~-igRkIDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLV 861 (913)
|||.-.|. +--+++-+..-+|.+|..+++++|++. .+.|.|.|.||||.++
T Consensus 3 vKaty~~d~~rf~~~~~~~~~~~~L~~ev~~rf~l~---------~f~lKYlDde~e~v~l 54 (81)
T cd06396 3 LKVTYNGESQSFLVSDSENTTWASVEAMVKVSFGLN---------DIQIKYVDEENEEVSV 54 (81)
T ss_pred EEEEECCeEEEEEecCCCCCCHHHHHHHHHHHhCCC---------cceeEEEcCCCCEEEE
Confidence 78888885 555777777889999999999999977 4799999999999765
No 12
>cd06409 PB1_MUG70 The MUG70 protein is a product of the meiotically up-regulated gene 70 which has a role in meiosis and harbors a PB1 domain. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domains depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic amino acid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is
Probab=94.45 E-value=0.073 Score=49.36 Aligned_cols=45 Identities=24% Similarity=0.408 Sum_probs=36.8
Q ss_pred ecCCCCCCHHHHHHHHHHHhcccccccCCCCCceEEEEEecCCCEEEcc
Q 002516 814 IDVTNFKNYDELCSAIERMFGLEGLLNDPRGTEWKLVYVDYENDVLLVG 862 (913)
Q Consensus 814 IDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLVG 862 (913)
+-+....||.+|.+++++-|+++... ...++|.|.|.||||.|+-
T Consensus 15 f~~~~s~~~~~L~~~I~~Rl~~d~~~----~~~~~L~YlDDEgD~VllT 59 (86)
T cd06409 15 FRLRPSESLEELRTLISQRLGDDDFE----THLYALSYVDDEGDIVLIT 59 (86)
T ss_pred EEecCCCCHHHHHHHHHHHhCCcccc----CCcccEEEEcCCCCEEEEe
Confidence 34445789999999999999977432 4589999999999998764
No 13
>cd06398 PB1_Joka2 The PB1 domain is present in the Nicotiana plumbaginifolia Joka2 protein which interacts with sulfur stress inducible UP9 protein. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module
Probab=94.41 E-value=0.14 Score=47.77 Aligned_cols=56 Identities=29% Similarity=0.379 Sum_probs=44.0
Q ss_pred EEEeccCc-eeeeecCC---CCCCHHHHHHHHHHHhcccccccCCCCCceEEEEEecCCCEEEccC
Q 002516 802 TKVQKTGS-VGRSIDVT---NFKNYDELCSAIERMFGLEGLLNDPRGTEWKLVYVDYENDVLLVGD 863 (913)
Q Consensus 802 VKV~m~G~-igRkIDL~---~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLVGD 863 (913)
|||.-+|. +=-++++. .--+|++|..++++.|.+.. ..+++|.|.|.||||..+-+
T Consensus 3 vKv~y~~~~rRf~l~~~~~~~d~~~~~L~~kI~~~f~l~~------~~~~~l~Y~Dedgd~V~l~~ 62 (91)
T cd06398 3 VKVKYGGTLRRFTFPVAENQLDLNMDGLREKVEELFSLSP------DADLSLTYTDEDGDVVTLVD 62 (91)
T ss_pred EEEEeCCEEEEEEeccccccCCCCHHHHHHHHHHHhCCCC------CCcEEEEEECCCCCEEEEcc
Confidence 89988886 33355543 45799999999999998642 35899999999999987744
No 14
>cd06403 PB1_Par6 The PB1 domain is an essential part of Par6 protein which in complex with Par3 and aPKC proteins is crucial for establishment of apical-basal polarity of animal cells. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. The
Probab=93.00 E-value=0.27 Score=45.26 Aligned_cols=66 Identities=17% Similarity=0.346 Sum_probs=50.5
Q ss_pred EEEeccCceee-eecCCCCCCHHHHHHHHHHHhcccccccCCCCCceEEEEEecCCCEEEcc-CCchhhccccee
Q 002516 802 TKVQKTGSVGR-SIDVTNFKNYDELCSAIERMFGLEGLLNDPRGTEWKLVYVDYENDVLLVG-DDPWEEFVGCVR 874 (913)
Q Consensus 802 VKV~m~G~igR-kIDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLVG-DvPW~~Fv~svk 874 (913)
||.+-++++=| ++|-....+|+|++.-|++|+.+.+ ..+.|-|.|.+||.|-+- |+-+..-+.+++
T Consensus 3 VKSkfdaEfRRFsl~r~~~~~f~ef~~ll~~lH~l~~-------~~f~i~Y~D~~gDLLPInNDdNf~kAlssa~ 70 (80)
T cd06403 3 VKSKFDAEFRRFSLDRNKPGKFEDFYKLLEHLHHIPN-------VDFLIGYTDPHGDLLPINNDDNFLKALSSAN 70 (80)
T ss_pred eecccCCeEEEEEeccccCcCHHHHHHHHHHHhCCCC-------CcEEEEEeCCCCCEecccCcHHHHHHHHcCC
Confidence 66666666443 6777778999999999999999874 368999999999998764 455555555555
No 15
>cd06404 PB1_aPKC PB1 domain is an essential modular domain of the atypical protein kinase C (aPKC) which in complex with Par6 and Par3 proteins is crucial for establishment of apical-basal polarity of animal cells. PB1 domain is a modular domain mediating specific protein-protein interaction which play roles in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi,
Probab=91.66 E-value=0.47 Score=44.03 Aligned_cols=50 Identities=26% Similarity=0.414 Sum_probs=40.4
Q ss_pred EEEeccCc-eeeeecCCCCCCHHHHHHHHHHHhcccccccCCCCCceEEEEEecCCCEE
Q 002516 802 TKVQKTGS-VGRSIDVTNFKNYDELCSAIERMFGLEGLLNDPRGTEWKLVYVDYENDVL 859 (913)
Q Consensus 802 VKV~m~G~-igRkIDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~m 859 (913)
+|+.-.|. .--.+|. .-+|++|.+++++||.+. .+..+++.|.|.|||--
T Consensus 3 ~K~~y~gdi~it~~d~--~~s~e~L~~~v~~~c~~~------~~q~ft~kw~DEEGDp~ 53 (83)
T cd06404 3 VKAAYNGDIMITSIDP--SISLEELCNEVRDMCRFH------NDQPFTLKWIDEEGDPC 53 (83)
T ss_pred EEEEecCcEEEEEcCC--CcCHHHHHHHHHHHhCCC------CCCcEEEEEECCCCCce
Confidence 78888996 4445555 778999999999999963 34579999999999973
No 16
>cd06399 PB1_P40 The PB1 domain is essential part of the p40 adaptor protein which plays an important role in activating phagocyte NADPH oxidase during phagocytosis. The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes , such as osteoclastogenesis, angiogenesis, early cardiovascular development and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The PB1 domain of p40 represents a type I PB1 domain which interacts with the PB1 domain of oxidase activator p67 w
Probab=91.52 E-value=0.41 Score=44.89 Aligned_cols=54 Identities=30% Similarity=0.386 Sum_probs=47.1
Q ss_pred ecCCCCCCHHHHHHHHHHHhcccccccCCCCCceEEEEEecCCCEEEccCCchhhcccceeEEEEeChhhhhhhhHhhhh
Q 002516 814 IDVTNFKNYDELCSAIERMFGLEGLLNDPRGTEWKLVYVDYENDVLLVGDDPWEEFVGCVRCIRILSPQEVEQMSEEGMK 893 (913)
Q Consensus 814 IDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLVGDvPW~~Fv~svkrirIl~~se~~~m~~~~~~ 893 (913)
=||+.--+|.+|..-..+-|..+ +-.|-|.|.|||. ||||+.+|+.-|.+++-.
T Consensus 22 e~l~~~P~~kdLl~lmr~~f~~~---------dIaLNYrD~EGDL-----------------IRllddeDv~LMV~~~r~ 75 (92)
T cd06399 22 EDLSSTPLLKDLLELTRREFQRE---------DIALNYRDAEGDL-----------------IRLLSDEDVALMVRQSRG 75 (92)
T ss_pred cccccCccHHHHHHHHHHHhchh---------heeeeeecCCCCE-----------------EEEcchhhHHHHHHHHhc
Confidence 36788889999999999999855 4588999999998 999999999999988744
No 17
>cd06402 PB1_p62 The PB1 domain is an essential part of p62 scaffold protein (alias sequestosome 1,SQSTM) involved in cell signaling, receptor internalization, and protein turnover. The PB1 domain is a modular domain mediating specific protein-protein interaction which play roles in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.
Probab=91.15 E-value=0.76 Score=42.89 Aligned_cols=54 Identities=26% Similarity=0.360 Sum_probs=41.6
Q ss_pred eEEEeccC----ceeee--ecCCCCCCHHHHHHHHHHHhcccccccCCCCCceEEEEEecCCCEEE
Q 002516 801 YTKVQKTG----SVGRS--IDVTNFKNYDELCSAIERMFGLEGLLNDPRGTEWKLVYVDYENDVLL 860 (913)
Q Consensus 801 fVKV~m~G----~igRk--IDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mL 860 (913)
.||.|..| +=-|+ ||-....+|++|+..+.++|..- .+..++|.|.|.|||..-
T Consensus 2 ~vkayl~~~~~~~EIRRf~l~~~~~~s~~~L~~~V~~~f~~l------~~~~ftlky~DeeGDlvt 61 (87)
T cd06402 2 TVKAYLLGKDANAEIRRFAIDEDVSTSYEYLVEKVAAVFPSL------RGKNFQLFWKDEEGDLVA 61 (87)
T ss_pred eEEEeecCCCCccceEEEEecCCCCcCHHHHHHHHHHHcccc------CCCcEEEEEECCCCCEEe
Confidence 68999987 33344 45567779999999999999632 135799999999999843
No 18
>cd06401 PB1_TFG The PB1 domain found in TFG protein, an oncogenic gene product and fusion partner to nerve growth factor tyrosine kinase receptor TrkA and to the tyrosine kinase ALK. The PB1 domain is a modular domain mediating specific protein-protein interaction in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The PB1 domains of TFG represent a type I/II PB1 domain. The physiological function of TFG remains unknown.
Probab=89.01 E-value=1.3 Score=41.04 Aligned_cols=58 Identities=28% Similarity=0.398 Sum_probs=42.3
Q ss_pred EEEeccCceeeeecCCCCC-CHHHHHHHHHHHhcccccccCCCCCceEEEEEecCCCEEEccCC
Q 002516 802 TKVQKTGSVGRSIDVTNFK-NYDELCSAIERMFGLEGLLNDPRGTEWKLVYVDYENDVLLVGDD 864 (913)
Q Consensus 802 VKV~m~G~igRkIDL~~~~-sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLVGDv 864 (913)
+|+.-.|.|=| +-+..-. +|.+|+..+.+.|... + |...++.+.|.|.|||+.-+.+.
T Consensus 3 iK~~~g~DiR~-~~~~~~~~t~~~L~~~v~~~F~~~--~--~~~~~flIKYkD~dGDlVTIts~ 61 (81)
T cd06401 3 LKAQLGDDIRR-IPIHNEDITYDELLLMMQRVFRGK--L--GSSDDVLIKYKDEDGDLITIFDS 61 (81)
T ss_pred EEEEeCCeEEE-EeccCccccHHHHHHHHHHHhccc--c--CCcccEEEEEECCCCCEEEeccH
Confidence 57666565644 4444423 9999999999999933 2 23457899999999999777764
No 19
>cd06397 PB1_UP1 Uncharacterized protein 1. The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions.
Probab=85.74 E-value=2.3 Score=39.53 Aligned_cols=52 Identities=23% Similarity=0.429 Sum_probs=40.7
Q ss_pred EEEeccCceeeeecCCCCCCHHHHHHHHHHHhcccccccCCCCCceEEEEEecCCCEEEc
Q 002516 802 TKVQKTGSVGRSIDVTNFKNYDELCSAIERMFGLEGLLNDPRGTEWKLVYVDYENDVLLV 861 (913)
Q Consensus 802 VKV~m~G~igRkIDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLV 861 (913)
-||.-.| --|++....-=+|.+|++.|..+|.+... ...|+|.|.|||..-+
T Consensus 3 fKv~~~g-~~RRf~~~~~pt~~~L~~kl~~Lf~lp~~-------~~~vtYiDeD~D~ITl 54 (82)
T cd06397 3 FKSSFLG-DTRRIVFPDIPTWEALASKLENLYNLPEI-------KVGVTYIDNDNDEITL 54 (82)
T ss_pred EEEEeCC-ceEEEecCCCccHHHHHHHHHHHhCCChh-------HeEEEEEcCCCCEEEe
Confidence 3674444 45778888889999999999999997621 2799999999998533
No 20
>cd06408 PB1_NoxR The PB1 domain is present in the Epichloe festucae NoxR protein (NADPH oxidase regulator), a key regulator of NADPH oxidase isoform, NoxA. NoxA is essential for growth control of the fungal endophyte in plant tissue in the process of symbiotic interaction between a fungi and its plant host. The Epichloe festucae p67(phox)-like regulator, NoxR, dispensable in culture but essential in plants for the symbiotic interaction. Plants infected with a noxR deletion mutant show severe stunting and premature senescence, whereas hyphae in the meristematic tissues show increased branching leading to increased fungal colonization of pseudostem and leaf blade tissue. The PB1 domain is a modular domain mediating specific protein-protein interactions which a play role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is
Probab=77.21 E-value=6.7 Score=36.77 Aligned_cols=53 Identities=23% Similarity=0.360 Sum_probs=41.0
Q ss_pred eEEEeccCceeeeecCCCCCCHHHHHHHHHHHhcccccccCCCCCceEEEEEecCCCEEEccC
Q 002516 801 YTKVQKTGSVGRSIDVTNFKNYDELCSAIERMFGLEGLLNDPRGTEWKLVYVDYENDVLLVGD 863 (913)
Q Consensus 801 fVKV~m~G~igRkIDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLVGD 863 (913)
=|||+=.|. -|-|-+..-=+|++|...+..+|++. ..++|-|.|. ||..-++|
T Consensus 4 kVKv~~~~D-v~~i~v~~~i~f~dL~~kIrdkf~~~--------~~~~iKykDE-GD~iti~s 56 (86)
T cd06408 4 RVKVHAQDD-TRYIMIGPDTGFADFEDKIRDKFGFK--------RRLKIKMKDD-GDMITMGD 56 (86)
T ss_pred EEEEEecCc-EEEEEcCCCCCHHHHHHHHHHHhCCC--------CceEEEEEcC-CCCccccC
Confidence 478887775 45555566667999999999999974 2679999999 98865554
No 21
>PRK10737 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=51.43 E-value=59 Score=34.65 Aligned_cols=104 Identities=19% Similarity=0.216 Sum_probs=63.3
Q ss_pred CCccCCEEEE-E--EccCCcEEEEEEecCcCCCCCCCcccccCccchhhHHHHHHHHhcCCeeEEEecCCCCC------C
Q 002516 191 RLRAGDSVLF-I--RDEKSQLMVGVRRANRQQTALPSSVLSADSMHIGVLAAAAHAASNRSQFTIFYNPRACP------S 261 (913)
Q Consensus 191 kL~aGDsVvF-~--R~e~G~L~VGIRRa~r~~~~~pssv~s~dsm~~gvlaaAa~aaa~~~~F~V~Y~PRas~------s 261 (913)
++..|++|.| | |.++|+++=- .+. ..|...+--...-+--|.+|..-...|..|+|..-|-... .
T Consensus 2 kI~~~~vV~l~Y~l~~~dG~v~ds-t~~-----~~Pl~~~~G~g~lipglE~aL~G~~~Gd~~~v~l~peeAyGe~d~~l 75 (196)
T PRK10737 2 KVAKDLVVSLAYQVRTEDGVLVDE-SPV-----SAPLDYLHGHGSLISGLETALEGHEVGDKFDVAVGANDAYGQYDENL 75 (196)
T ss_pred ccCCCCEEEEEEEEEeCCCCEEEe-cCC-----CCCeEEEeCCCcchHHHHHHHcCCCCCCEEEEEEChHHhcCCCChHH
Confidence 3566777776 3 3567776332 111 2243333333333345788888899999999997765322 3
Q ss_pred CcccchhhHhhhhccCCcccCCEEEEeeeccccCcceeeeEEEeecc
Q 002516 262 DFVIPLAKYRKSVYGTQMSVGMRFGMMFETEESGKRRYMGTIVGISD 308 (913)
Q Consensus 262 EFVVp~~Ky~kAv~~~~ws~GMRFrM~fEtedss~rry~GTI~gvsd 308 (913)
-+.||++.|... ....+||||.+ ++++. ...++|+.|.+
T Consensus 76 V~~vpr~~F~~~---~~l~~G~~~~~--~~~~G---~~~~~V~ev~~ 114 (196)
T PRK10737 76 VQRVPKDVFMGV---DELQVGMRFLA--ETDQG---PVPVEITAVED 114 (196)
T ss_pred EEEecHHHCCCc---cCCCCCCEEEE--eCCCC---cEEEEEEEEcC
Confidence 456787766322 24789999876 44442 35888998864
No 22
>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=44.64 E-value=27 Score=28.41 Aligned_cols=29 Identities=14% Similarity=0.172 Sum_probs=23.6
Q ss_pred hhhhccCCccCCEEEEEEccCCcEEEEEE
Q 002516 185 LFVGSKRLRAGDSVLFIRDEKSQLMVGVR 213 (913)
Q Consensus 185 ~FVk~KkL~aGDsVvF~R~e~G~L~VGIR 213 (913)
.|.++.+|.+||.|.|.-.++|++.|--.
T Consensus 14 ~~~~~l~l~~Gd~v~i~~~~~g~i~i~p~ 42 (47)
T PF04014_consen 14 EIREKLGLKPGDEVEIEVEGDGKIVIRPV 42 (47)
T ss_dssp HHHHHTTSSTTTEEEEEEETTSEEEEEES
T ss_pred HHHHHcCCCCCCEEEEEEeCCCEEEEEEC
Confidence 46788899999999999988887766443
No 23
>KOG3207 consensus Beta-tubulin folding cofactor E [Posttranslational modification, protein turnover, chaperones]
Probab=36.21 E-value=32 Score=40.93 Aligned_cols=46 Identities=35% Similarity=0.639 Sum_probs=33.1
Q ss_pred cccCCEEEEeeeccccCcceeeeEEEeeccCCCCCCCCCCcccceeeccCCCCCCCCCCc
Q 002516 279 MSVGMRFGMMFETEESGKRRYMGTIVGISDLDPLRWPGSKWRNLQVEWDEPGCSDKQKRV 338 (913)
Q Consensus 279 ws~GMRFrM~fEtedss~rry~GTI~gvsd~DP~rWP~S~WR~LkV~WDE~~~~~r~~RV 338 (913)
..+|.|+|.-+|- +..||.|+|.|. ++ +| +.|.||++.-+.+.--|
T Consensus 3 ~~IG~RvkI~~~~---~Tvr~iG~V~g~--------~~-~w--~GvEWDd~~RGKH~G~v 48 (505)
T KOG3207|consen 3 MEIGTRVKIGGEI---ATVRYIGEVEGN--------NS-KW--YGVEWDDPVRGKHDGIV 48 (505)
T ss_pred eeccceEEEcCEE---EEEEEEEEEcCC--------CC-cc--eeeEecCCCccccCcee
Confidence 5689999987652 447888888654 33 45 88999999877665444
No 24
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=34.98 E-value=44 Score=31.60 Aligned_cols=29 Identities=24% Similarity=0.397 Sum_probs=24.1
Q ss_pred hhhccCCccCCEEEEEEccCCcEEEEEEe
Q 002516 186 FVGSKRLRAGDSVLFIRDEKSQLMVGVRR 214 (913)
Q Consensus 186 FVk~KkL~aGDsVvF~R~e~G~L~VGIRR 214 (913)
|.-...|++||.|..+|.+.|+.++=+-|
T Consensus 71 i~~~~~Lk~GD~V~ll~~~~gQ~yiVlDk 99 (100)
T PF10844_consen 71 ITFTDGLKVGDKVLLLRVQGGQKYIVLDK 99 (100)
T ss_pred EEEecCCcCCCEEEEEEecCCCEEEEEEe
Confidence 56667899999999999999988876544
No 25
>PF00788 RA: Ras association (RalGDS/AF-6) domain; InterPro: IPR000159 Proteins with this domain are mostly RasGTP effectors and include guanine-nucleotide releasing factor in mammals []. This factor stimulates the dissociation of GDP from the Ras-related RALA and RALB GTPases, which allows GTP binding and activation of the GTPases. It interacts and acts as an effector molecule for R-ras, K-Ras and Rap []. The domain is also present in a number of other proteins among them the sexual differentiation protein in yeast that is essential for mating and meiosis and yeast adenylate cyclase. These proteins contain repeated leucine-rich (LRR) segments.; GO: 0007165 signal transduction; PDB: 3EC8_A 2C5L_D 2BYF_A 2CS4_A 3KH0_A 2B3A_A 1RAX_A 2RGF_A 1WGR_A 1WXA_A ....
Probab=34.96 E-value=1.2e+02 Score=26.85 Aligned_cols=67 Identities=18% Similarity=0.167 Sum_probs=47.8
Q ss_pred cceEEEeccCc----eeeeecCCCCCCHHHHHHHHHHHhcccccccCCCCCceEEE-EE-ecCCCEEEccC-Cchhhcc
Q 002516 799 RTYTKVQKTGS----VGRSIDVTNFKNYDELCSAIERMFGLEGLLNDPRGTEWKLV-YV-DYENDVLLVGD-DPWEEFV 870 (913)
Q Consensus 799 ~~fVKV~m~G~----igRkIDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lv-Ye-D~EGD~mLVGD-vPW~~Fv 870 (913)
..++|||.... .-++|-++...+-.|+...+.+.|++.+ ....|.|+ +. .......|-.| .|+..+.
T Consensus 2 ~~~lrVy~~~~~~~~~~k~i~v~~~tTa~evi~~~l~k~~l~~-----~~~~y~L~~~~~~~~~er~L~~~E~pl~i~~ 75 (93)
T PF00788_consen 2 SGVLRVYDGDGSPGSTYKTIKVSSSTTAREVIEMALEKFGLAE-----DPSDYCLVEVEESGGEERPLDDDECPLQIQL 75 (93)
T ss_dssp EEEEEEEETTSSSCCSEEEEEEETTSBHHHHHHHHHHHTTTSS-----SGGGEEEEEEECTTTEEEEETTTSBHHHHHH
T ss_pred CeEEEEEcCCCCCCccEEEEEECCCCCHHHHHHHHHHHhCCCC-----CCCCEEEEEEEcCCCEEEEcCCCCchHHHHH
Confidence 35899999663 3899999999999999999999999832 24579995 44 44444444433 5555443
No 26
>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=32.24 E-value=58 Score=25.29 Aligned_cols=26 Identities=23% Similarity=0.365 Sum_probs=22.3
Q ss_pred hhhhccCCccCCEEEEEEccCCcEEE
Q 002516 185 LFVGSKRLRAGDSVLFIRDEKSQLMV 210 (913)
Q Consensus 185 ~FVk~KkL~aGDsVvF~R~e~G~L~V 210 (913)
.|.++-++..||.|.+...++|.+.|
T Consensus 14 ~~r~~l~~~~gd~~~i~~~~~~~l~l 39 (43)
T TIGR01439 14 EIREKLGLKEGDRLEVIRVEDGEIIL 39 (43)
T ss_pred HHHHHcCcCCCCEEEEEEeCCCEEEE
Confidence 57899999999999999877777665
No 27
>cd06406 PB1_P67 A PB1 domain is present in p67 proteins which forms a signaling complex with p40, a crucial step for activation of NADPH oxidase during phagocytosis. PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes . A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. The p67 proteins contain
Probab=30.29 E-value=1.2e+02 Score=28.29 Aligned_cols=65 Identities=18% Similarity=0.184 Sum_probs=48.0
Q ss_pred eEEEeccCceeeeecCCCCCCHHHHHHHHHHHhcccccccCCCCCceEEEEEecCC-CEEEccCCchhhccccee
Q 002516 801 YTKVQKTGSVGRSIDVTNFKNYDELCSAIERMFGLEGLLNDPRGTEWKLVYVDYEN-DVLLVGDDPWEEFVGCVR 874 (913)
Q Consensus 801 fVKV~m~G~igRkIDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EG-D~mLVGDvPW~~Fv~svk 874 (913)
-|||+=.+ .=-|-+..=-+|.+|+..|.+-+.+.+. +-+|-|.|.+. +...++|.=++.-.+.|+
T Consensus 4 vvKV~f~~--tIaIrvp~~~~y~~L~~ki~~kLkl~~e-------~i~LsYkde~s~~~v~l~d~dle~aws~~~ 69 (80)
T cd06406 4 VVKVHFKY--TVAIQVARGLSYATLLQKISSKLELPAE-------HITLSYKSEASGEDVILSDTNMEDVWSQAK 69 (80)
T ss_pred EEEEEEEE--EEEEEcCCCCCHHHHHHHHHHHhCCCch-------hcEEEeccCCCCCccCcChHHHHHHHHhhc
Confidence 48999887 2334555667899999999999998532 34899998774 333449988888777776
No 28
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=29.60 E-value=76 Score=26.71 Aligned_cols=28 Identities=11% Similarity=0.242 Sum_probs=23.1
Q ss_pred CcccCCEEEEeeeccccCcceeeeEEEeecc
Q 002516 278 QMSVGMRFGMMFETEESGKRRYMGTIVGISD 308 (913)
Q Consensus 278 ~ws~GMRFrM~fEtedss~rry~GTI~gvsd 308 (913)
.|.+|+++-..++.++ .||.|+|+.+..
T Consensus 2 ~~~~G~~Ve~~~~~~~---~W~~a~V~~~~~ 29 (61)
T smart00743 2 DFKKGDRVEVFSKEED---SWWEAVVTKVLG 29 (61)
T ss_pred CcCCCCEEEEEECCCC---EEEEEEEEEECC
Confidence 5789999999996533 799999999953
No 29
>KOG3938 consensus RGS-GAIP interacting protein GIPC, contains PDZ domain [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=26.15 E-value=2.9e+02 Score=31.39 Aligned_cols=69 Identities=25% Similarity=0.436 Sum_probs=50.5
Q ss_pred ccC-ceeeeecCCCCCCHHHHHHHHHHHhccccc------ccCCCCCceEEEEEecCCCEEEccCCchhhcc-----cce
Q 002516 806 KTG-SVGRSIDVTNFKNYDELCSAIERMFGLEGL------LNDPRGTEWKLVYVDYENDVLLVGDDPWEEFV-----GCV 873 (913)
Q Consensus 806 m~G-~igRkIDL~~~~sY~eL~~~L~~MF~~~g~------l~d~~~s~~~lvYeD~EGD~mLVGDvPW~~Fv-----~sv 873 (913)
-.| +.|| +..|++-+||+..++.-|.+.-. |++. --|=+.||-|-.-.++|+ .-.
T Consensus 61 AHGSptg~---Ie~fsnv~ELY~kIAe~F~Is~~dIlfcTlNsh----------KvDM~~llgGqigleDfiFAHvkGq~ 127 (334)
T KOG3938|consen 61 AHGSPTGR---IEGFSNVRELYQKIAEAFDISPDDILFCTLNSH----------KVDMKRLLGGQIGLEDFIFAHVKGQA 127 (334)
T ss_pred ccCCccce---ecccccHHHHHHHHHHHhcCCccceEEEecCCC----------cccHHHHhcCccChhhhhhhhhcCcc
Confidence 367 6887 67899999999999999998531 2211 123345888888888876 456
Q ss_pred eEEEEeChhhhhhh
Q 002516 874 RCIRILSPQEVEQM 887 (913)
Q Consensus 874 krirIl~~se~~~m 887 (913)
|-++|++.+++-++
T Consensus 128 kEv~v~KsedalGl 141 (334)
T KOG3938|consen 128 KEVEVVKSEDALGL 141 (334)
T ss_pred eeEEEEecccccce
Confidence 67888888888765
No 30
>KOG3598 consensus Thyroid hormone receptor-associated protein complex, subunit TRAP230 [Transcription]
Probab=25.25 E-value=27 Score=46.35 Aligned_cols=9 Identities=33% Similarity=0.280 Sum_probs=4.9
Q ss_pred ccccCccch
Q 002516 226 VLSADSMHI 234 (913)
Q Consensus 226 v~s~dsm~~ 234 (913)
++|.+-||+
T Consensus 1851 ~~s~~~~hh 1859 (2220)
T KOG3598|consen 1851 VTSEKNEHH 1859 (2220)
T ss_pred CCChHhhcC
Confidence 455555554
No 31
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=24.78 E-value=26 Score=44.20 Aligned_cols=19 Identities=53% Similarity=1.018 Sum_probs=17.5
Q ss_pred ccCCCCCEEEEecCCcccc
Q 002516 55 FLPQVGSLVYYFPQGHSEQ 73 (913)
Q Consensus 55 ~lP~vgs~V~YFPqGH~Eq 73 (913)
-||..|..|.||-|||-|-
T Consensus 872 yipQmgDEViyfrQghqey 890 (1113)
T KOG0644|consen 872 YIPQMGDEVIYFRQGHQEY 890 (1113)
T ss_pred ccccccceeehhhhhhHHH
Confidence 5899999999999999875
No 32
>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=24.00 E-value=85 Score=30.75 Aligned_cols=26 Identities=31% Similarity=0.608 Sum_probs=18.5
Q ss_pred cCCccCCEEEEEEcc-CCcEEEEEEec
Q 002516 190 KRLRAGDSVLFIRDE-KSQLMVGVRRA 215 (913)
Q Consensus 190 KkL~aGDsVvF~R~e-~G~L~VGIRRa 215 (913)
++++.||.|+||... ++.-+||+=|-
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 599999999999977 67888888774
No 33
>COG1047 SlpA FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]
Probab=23.76 E-value=4.6e+02 Score=27.88 Aligned_cols=104 Identities=17% Similarity=0.269 Sum_probs=62.2
Q ss_pred CCccCCEEEEE---EccCCcEEEEEEecCcCCCCCCCcccccCccchhhHHHHHHHHhcCCeeEEEecCCCCCCCc----
Q 002516 191 RLRAGDSVLFI---RDEKSQLMVGVRRANRQQTALPSSVLSADSMHIGVLAAAAHAASNRSQFTIFYNPRACPSDF---- 263 (913)
Q Consensus 191 kL~aGDsVvF~---R~e~G~L~VGIRRa~r~~~~~pssv~s~dsm~~gvlaaAa~aaa~~~~F~V~Y~PRas~sEF---- 263 (913)
++..||.|.+. |.++|+++=- -+. ..-|-.++--+..-+.-|.+|..-...|..|+|.--|-..-.|+
T Consensus 2 ~i~k~~~V~i~Y~~~~~dg~v~Dt-t~e----~~~P~~~i~G~g~li~glE~al~g~~~Ge~~~V~IpPE~AfGe~~~~l 76 (174)
T COG1047 2 KIEKGDVVSLHYTLKVEDGEVVDT-TDE----NYGPLTFIVGAGQLIPGLEEALLGKEVGEEFTVEIPPEDAFGEYDPDL 76 (174)
T ss_pred cccCCCEEEEEEEEEecCCcEEEc-ccc----cCCCeEEEecCCCcchhHHHHHhCCCCCceeEEEeCchHhcCCCChHH
Confidence 45677887763 3445544311 111 01122233223333334788999999999999998886544443
Q ss_pred --ccchhhHhhhhccCCcccCCEEEEeeeccccCcceeeeEEEeec
Q 002516 264 --VIPLAKYRKSVYGTQMSVGMRFGMMFETEESGKRRYMGTIVGIS 307 (913)
Q Consensus 264 --VVp~~Ky~kAv~~~~ws~GMRFrM~fEtedss~rry~GTI~gvs 307 (913)
.||+.+|...- ...+||+|. +++++ ....|+|+.|.
T Consensus 77 vq~vp~~~F~~~~---~~~vGm~~~--~~~~~---~~~~~~V~~V~ 114 (174)
T COG1047 77 VQRVPRDEFQGVG---ELEVGMEVE--AEGGD---GEIPGVVTEVS 114 (174)
T ss_pred eEEecHHHhCcCC---CCCCCcEEE--EcCCC---ceeeEEEEEEc
Confidence 46666655431 578999875 44444 45689999885
No 34
>PRK03760 hypothetical protein; Provisional
Probab=23.06 E-value=1.8e+02 Score=28.50 Aligned_cols=27 Identities=22% Similarity=0.533 Sum_probs=22.6
Q ss_pred CCCceEE--ccchhhhhhccCCccCCEEEEEE
Q 002516 173 QPKRHLL--TTGWSLFVGSKRLRAGDSVLFIR 202 (913)
Q Consensus 173 ~pkRhlL--TtGWs~FVk~KkL~aGDsVvF~R 202 (913)
.+-+|+| ..|| +.+.++++||.|.|.|
T Consensus 88 ~~a~~VLEl~aG~---~~~~gi~~Gd~v~~~~ 116 (117)
T PRK03760 88 KPARYIIEGPVGK---IRVLKVEVGDEIEWID 116 (117)
T ss_pred ccceEEEEeCCCh---HHHcCCCCCCEEEEee
Confidence 4566888 6887 8899999999999876
No 35
>PF11515 Cul7: Mouse development and cellular proliferation protein Cullin-7; InterPro: IPR021097 The CPH domain is found in the Cullin-7, PARC and HERC2 proteins, which are all components of known or predicted E3-ubiquitin ligases. The CPH domain is a protein-protein interaction module that binds the teramerisation domain of the tumour suppressor protein p53 []. Structurally it forms a beta-barrel fold similar to the SH3, Tudor and KOW and domains. Unlike the SH3 and Tudor domains, which bind to small peptides, the CPH domain appears to bind to an extended surface on p53.; PDB: 2JUF_A 2JNG_A.
Probab=22.43 E-value=1.3e+02 Score=28.18 Aligned_cols=68 Identities=25% Similarity=0.315 Sum_probs=32.3
Q ss_pred hHhhhhccCCcccCCEEEEeeeccccCcceeeeEEEeeccCCCCCCCCCCcccceeeccCCCCCCCCCCcCCcceecCC
Q 002516 269 KYRKSVYGTQMSVGMRFGMMFETEESGKRRYMGTIVGISDLDPLRWPGSKWRNLQVEWDEPGCSDKQKRVSPWEIETPE 347 (913)
Q Consensus 269 Ky~kAv~~~~ws~GMRFrM~fEtedss~rry~GTI~gvsd~DP~rWP~S~WR~LkV~WDE~~~~~r~~RVSPWEIEpv~ 347 (913)
.|..-+. -++.+||++||.=.-|+-. .-=.|+|.-++. | +-+=-.++|.|..-. +.-.|--..||.+.
T Consensus 9 ~Ya~YVr-~~i~~GM~VRc~~~yeeV~-~GD~G~V~k~~~-d-----g~~~lnvqv~W~~~G---~tyWV~~~~vEiig 76 (78)
T PF11515_consen 9 DYAEYVR-DNIQPGMRVRCCRDYEEVR-AGDEGEVFKQDR-D-----GLHDLNVQVDWQSKG---RTYWVHWHHVEIIG 76 (78)
T ss_dssp HHHHHHH-HH--TT-EEEESS-BTTB--TT-EEE-EEEE--T-----TSSE--EEEEETTTT---EEEEEEGGGEEE--
T ss_pred HHHHHHH-HhCCCCcEEEEeccccccc-ccccceeEeecc-C-----CCCCcceEEEeeecC---ceEEEEEEEEEEec
Confidence 3443333 3579999999974433321 123677655543 2 222356899997664 23446666777664
No 36
>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=21.21 E-value=1.4e+02 Score=24.38 Aligned_cols=52 Identities=15% Similarity=0.293 Sum_probs=35.9
Q ss_pred CcccCCEEEEeeeccccCcceeeeEEEeeccCCCCCCCCCCcccceeeccCCCCCCCCCCcCCcceecC
Q 002516 278 QMSVGMRFGMMFETEESGKRRYMGTIVGISDLDPLRWPGSKWRNLQVEWDEPGCSDKQKRVSPWEIETP 346 (913)
Q Consensus 278 ~ws~GMRFrM~fEtedss~rry~GTI~gvsd~DP~rWP~S~WR~LkV~WDE~~~~~r~~RVSPWEIEpv 346 (913)
.|.+|..+...+ .+ ..||.|+|+++.. + ....|.-++-+. .+-|...+|-++
T Consensus 2 ~~~~G~~~~a~~-~d---~~wyra~I~~~~~-------~---~~~~V~f~D~G~---~~~v~~~~l~~l 53 (57)
T smart00333 2 TFKVGDKVAARW-ED---GEWYRARIIKVDG-------E---QLYEVFFIDYGN---EEVVPPSDLRPL 53 (57)
T ss_pred CCCCCCEEEEEe-CC---CCEEEEEEEEECC-------C---CEEEEEEECCCc---cEEEeHHHeecC
Confidence 578899998888 43 3899999999953 1 557788777543 244555555544
No 37
>COG3542 Uncharacterized conserved protein [Function unknown]
Probab=21.19 E-value=36 Score=35.18 Aligned_cols=56 Identities=34% Similarity=0.420 Sum_probs=34.9
Q ss_pred chhhhccCccchhhhHh---HHHHHHhhccccCCCcCccccChhhhhhhcCCccccCCCCCEEEEecCCcccc
Q 002516 4 VEEKIKAGGLVIRAQTT---LLEEMKLLKEMQDQSGARKAINSELWHACAGPLVFLPQVGSLVYYFPQGHSEQ 73 (913)
Q Consensus 4 ~~~~~~~~~~~~~~~~~---~~~~m~l~~~~~~~~~~~~~v~~elW~aCAGplv~lP~vgs~V~YFPqGH~Eq 73 (913)
++||..+||-+|++-|. ||+|=..|. =.|.--.|+||.-||.-. .||.+.+||.|.
T Consensus 30 s~e~~~~G~~~R~~sT~IYyLLe~~~~s~-------~HRv~a~eiwHf~ag~pl-------~~~l~~dG~~~s 88 (162)
T COG3542 30 SEEKDAAGGDVRNHSTAIYYLLEEDNISA-------WHRVTADEIWHFYAGAPL-------ELHLSEDGGAES 88 (162)
T ss_pred cccccCCCccccceeEEEEEEecCCccch-------heecchhheEEEecCCce-------EEEEEeCCCeEE
Confidence 36899999866554442 455444331 122225699999999533 356666999874
No 38
>PF10411 DsbC_N: Disulfide bond isomerase protein N-terminus; InterPro: IPR018950 This is the N-terminal domain of the disulphide bond isomerase DsbC. The whole molecule is V-shaped, where each arm is a DsbC monomer of two domains linked by a hinge; and the N-termini of each monomer join to form the dimer interface at the base of the V, so are vital for dimerisation []. DsbC is required for disulphide bond formation and functions as a disulphide bond isomerase during oxidative protein-folding in bacterial periplasm. It also has chaperone activity []. ; PDB: 1EEJ_B 2IYJ_A 1TJD_A 1JZD_B 1JZO_A 1G0T_B 1T3B_A.
Probab=21.00 E-value=75 Score=27.20 Aligned_cols=17 Identities=29% Similarity=0.534 Sum_probs=14.7
Q ss_pred EEEEEecCCCEEEccCC
Q 002516 848 KLVYVDYENDVLLVGDD 864 (913)
Q Consensus 848 ~lvYeD~EGD~mLVGDv 864 (913)
.++|.|.+|+.+++|+.
T Consensus 34 ~i~Y~~~dg~yli~G~l 50 (57)
T PF10411_consen 34 GILYVDEDGRYLIQGQL 50 (57)
T ss_dssp EEEEEETTSSEEEES-E
T ss_pred eEEEEcCCCCEEEEeEE
Confidence 68999999999999974
Done!