Query 003505
Match_columns 815
No_of_seqs 353 out of 827
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 00:43:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003505.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003505hhsearch_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 9.4E-35 2E-39 257.4 8.3 83 171-254 1-83 (83)
2 PF02309 AUX_IAA: AUX/IAA fami 100.0 6E-35 1.3E-39 296.0 0.0 94 680-773 107-214 (215)
3 PF02362 B3: B3 DNA binding do 99.7 3.2E-17 6.9E-22 145.2 10.8 97 45-146 1-99 (100)
4 KOG0644 Uncharacterized conser 99.4 1.9E-13 4.2E-18 158.1 6.8 147 124-279 875-1044(1113)
5 PF09217 EcoRII-N: Restriction 98.2 8.6E-06 1.9E-10 80.5 10.0 89 42-132 7-110 (156)
6 PF03754 DUF313: Domain of unk 97.8 4.8E-05 1.1E-09 72.2 6.2 81 39-120 18-114 (114)
7 PF00564 PB1: PB1 domain; Int 97.1 0.0013 2.7E-08 57.2 6.4 66 685-757 4-70 (84)
8 smart00666 PB1 PB1 domain. Pho 96.1 0.018 4E-07 49.9 7.0 65 685-757 4-69 (81)
9 cd05992 PB1 The PB1 domain is 96.1 0.022 4.7E-07 49.2 7.3 65 685-757 3-69 (81)
10 cd06407 PB1_NLP A PB1 domain i 95.8 0.033 7.2E-07 50.2 7.0 53 685-744 3-55 (82)
11 cd06396 PB1_NBR1 The PB1 domai 95.7 0.031 6.8E-07 50.6 6.6 51 685-744 3-54 (81)
12 cd06409 PB1_MUG70 The MUG70 pr 95.3 0.036 7.9E-07 50.7 5.5 49 693-745 9-59 (86)
13 cd06398 PB1_Joka2 The PB1 doma 94.9 0.088 1.9E-06 48.4 7.1 66 685-758 3-72 (91)
14 cd06403 PB1_Par6 The PB1 domai 92.5 0.34 7.3E-06 44.0 6.1 66 685-757 3-70 (80)
15 cd06404 PB1_aPKC PB1 domain is 91.7 0.46 1E-05 43.5 6.0 50 685-742 3-53 (83)
16 cd06401 PB1_TFG The PB1 domain 90.5 0.83 1.8E-05 41.7 6.5 58 685-747 3-61 (81)
17 cd06402 PB1_p62 The PB1 domain 90.3 1 2.2E-05 41.5 7.0 55 683-743 1-61 (87)
18 cd06397 PB1_UP1 Uncharacterize 88.2 1.3 2.8E-05 40.5 5.9 61 686-754 4-65 (82)
19 cd06399 PB1_P40 The PB1 domain 83.8 1.6 3.6E-05 40.5 4.4 51 697-773 22-72 (92)
20 cd06408 PB1_NoxR The PB1 domai 83.0 3.8 8.1E-05 37.9 6.4 54 683-746 3-56 (86)
21 KOG3598 Thyroid hormone recept 77.9 1.9 4.2E-05 55.4 3.6 70 59-131 1663-1741(2220)
22 PRK10737 FKBP-type peptidyl-pr 56.8 26 0.00057 36.7 6.2 104 122-239 2-114 (196)
23 smart00743 Agenet Tudor-like d 48.2 26 0.00057 29.1 3.8 38 209-259 2-39 (61)
24 PF00788 RA: Ras association ( 43.1 64 0.0014 28.1 5.7 66 683-753 3-75 (93)
25 PF04014 Antitoxin-MazE: Antid 41.8 32 0.0007 27.6 3.3 28 116-143 14-41 (47)
26 PF10844 DUF2577: Protein of u 40.9 34 0.00074 31.9 3.8 29 117-145 71-99 (100)
27 KOG3207 Beta-tubulin folding c 36.0 51 0.0011 38.9 4.9 43 210-266 3-45 (505)
28 PF11515 Cul7: Mouse developme 33.1 63 0.0014 29.7 4.0 55 199-261 8-62 (78)
29 cd06406 PB1_P67 A PB1 domain i 32.6 1.5E+02 0.0032 27.4 6.3 65 684-757 4-69 (80)
30 smart00333 TUDOR Tudor domain. 32.4 70 0.0015 25.8 3.9 52 209-277 2-53 (57)
31 PF05641 Agenet: Agenet domain 30.7 1.2E+02 0.0027 26.1 5.3 42 210-261 1-42 (68)
32 TIGR01439 lp_hng_hel_AbrB loop 30.1 65 0.0014 24.6 3.2 26 116-141 14-39 (43)
33 PRK03760 hypothetical protein; 28.8 1.2E+02 0.0027 29.2 5.5 27 104-133 88-116 (117)
34 PF01878 EVE: EVE domain; Int 26.8 70 0.0015 30.9 3.5 26 121-146 38-64 (143)
35 PF02513 Spin-Ssty: Spin/Ssty 25.6 1.1E+02 0.0025 26.0 4.0 31 212-242 1-31 (50)
36 PF10411 DsbC_N: Disulfide bon 24.6 54 0.0012 27.6 2.0 17 731-747 34-50 (57)
37 KOG3598 Thyroid hormone recept 24.0 62 0.0013 42.8 3.2 9 157-165 1851-1859(2220)
38 COG1047 SlpA FKBP-type peptidy 23.2 3.5E+02 0.0077 28.3 7.9 105 122-239 2-115 (174)
39 cd04451 S1_IF1 S1_IF1: Transla 21.7 3.7E+02 0.0079 22.8 6.5 38 84-134 15-52 (64)
40 COG0219 CspR Predicted rRNA me 21.1 29 0.00062 35.4 -0.3 57 687-748 45-105 (155)
41 PF14847 Ras_bdg_2: Ras-bindin 20.9 3.1E+02 0.0066 26.4 6.4 49 684-737 2-50 (105)
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=9.4e-35 Score=257.38 Aligned_cols=83 Identities=66% Similarity=1.100 Sum_probs=81.2
Q ss_pred HHHHHHhCCcEEEEEecCCCCCcceechHHHHHHHhcCCCcccCEEEEeeeccccccceeeeEEEEeecCCCCCCCCCCc
Q 003505 171 AAHAAATNSRFTIFYNPRASPSEFVIPLAKYVKAVYHTRVSVGMRFRMLFETEESSVRRYMGTITGISDLDPVRWPNSHW 250 (815)
Q Consensus 171 Aa~aaa~~~~FtV~Y~PRas~sEFVVp~~ky~kAv~~~~ws~GmRFrM~fEtEdss~rr~~GTI~gi~~~Dp~rWP~S~W 250 (815)
|+|||+++++|+|+||||++++|||||++||++|+. ++|++||||||.||+||+++++|+|||+||+++||.+||+|+|
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 eeeE
Q 003505 251 RSVK 254 (815)
Q Consensus 251 R~Lq 254 (815)
||||
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=6e-35 Score=295.97 Aligned_cols=94 Identities=40% Similarity=0.762 Sum_probs=0.0
Q ss_pred CCcceEEEeccC-cceeeeccCCCCCHHHHHHHHHHHh---cCC----------CCcCCCCCCccEEEEEcCCCceEecC
Q 003505 680 PTRTFVKVHKSG-SFGRSLDISKFSSYDELRSELARMF---GLE----------GQLEDPQRSGWQLVFVDRENDVLLLG 745 (815)
Q Consensus 680 ~~~~fVKV~m~G-~iGRkiDL~~~~sY~eL~~~L~~MF---~~e----------g~l~d~~~s~~~lvYeD~EGD~mLvG 745 (815)
..++||||+||| +|||||||++|+||++|+.+|++|| +++ +.++...+++|+|||+|+||||||||
T Consensus 107 ~~~~~vKV~mdG~~igRkVDL~~~~sY~~L~~~L~~MF~~~~i~~~~~~~~~~~~~~~~~~~~~~~l~Y~D~egd~mlvG 186 (215)
T PF02309_consen 107 SSRSYVKVNMDGVPIGRKVDLSAYSSYEELSSALEKMFSCFSIEQCGSHGLNESGLLDLLNGSEYVLVYEDKEGDWMLVG 186 (215)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred cCCceeEEEecCcccceecCHHHhhCHHHHHHHHHHhcCCCCccccccccccchhhccccCCcceeEEEECCCCCEEEec
Confidence 358999999999 9999999999999999999999999 554 33444567899999999999999999
Q ss_pred CcchhhhhcceeEEEEeChHhhhhcccC
Q 003505 746 DDPWQEFVNNVGYIKILSPLEVQQMGKG 773 (815)
Q Consensus 746 DvPWe~Fv~svkrirIl~~~e~~~m~~~ 773 (815)
||||+|||++||||+||+.+|+++|+++
T Consensus 187 D~PW~~F~~~vkRl~I~~~~e~~~~~~r 214 (215)
T PF02309_consen 187 DVPWEEFVKSVKRLRIMKSSEAKGLAPR 214 (215)
T ss_dssp ----------------------------
T ss_pred CCCHHHHHHHhhccEEecHHHhcccCCC
Confidence 9999999999999999999999999875
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=99.72 E-value=3.2e-17 Score=145.25 Aligned_cols=97 Identities=28% Similarity=0.409 Sum_probs=74.9
Q ss_pred EEEecCcccCCCCCceeeecchhhhhCCCCCCCCCCCceEEEEEeCCCCeEEEEEEEeCCCcceeecccchhhhcccCCC
Q 003505 45 FCKTLTASDTSTHGGFSVPRRAAEKVFPPLDYSQTPPAQELIARDLHDNEWKFRHIFRGQPKRHLLTTGWSVFVSAKRLV 124 (815)
Q Consensus 45 F~KtLT~SDv~~~GrfsIPk~~Ae~~FPpLd~s~~~p~q~L~~~Dl~G~~W~FR~iyrg~prrhlLTtGWs~FVk~KkL~ 124 (815)
|.|+|+++|+...++|.||+++++++. ++ ....+++.++|..|+.|.+++.+++.+++++|++||..||++++|+
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 1136799999999999999999998888899999999999999999
Q ss_pred CCCEEEEEEcc--CCcEEEEEEec
Q 003505 125 AGDSVLFIWNE--KNQLLLGIRRA 146 (815)
Q Consensus 125 aGDsVvF~R~e--~G~L~VGIRRa 146 (815)
+||.|+|+... ..++.|+|+|+
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 99999999875 44569999986
No 4
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=99.41 E-value=1.9e-13 Score=158.07 Aligned_cols=147 Identities=20% Similarity=0.377 Sum_probs=120.9
Q ss_pred CCCCEEEEEEccCCcEEEEEEecCCCCCC---------------------CCCCccCCCccchhHHHHHHHHHHhCCcEE
Q 003505 124 VAGDSVLFIWNEKNQLLLGIRRATRPQTV---------------------MPSSVLSSDSMHIGLLAAAAHAAATNSRFT 182 (815)
Q Consensus 124 ~aGDsVvF~R~e~G~L~VGIRRa~r~~~~---------------------~pssv~s~dsm~~g~la~Aa~aaa~~~~Ft 182 (815)
..||.|+.+|....++.-.+|+.+...++ .|-+..+.=.|.+.++.-|.|+ -+..|.
T Consensus 875 QmgDEViyfrQghqeyl~~~~~n~~~~~~~~p~~~~~v~~~kv~kl~~~~y~~~~~s~c~m~l~~idp~s~~--~~k~F~ 952 (1113)
T KOG0644|consen 875 QMGDEVIYFRQGHQEYLEAVRLNNIELNNKEPWNKMAVEICKVEKLVYITYPGSGDSCCKMKLAVIDPASKL--MDKSFK 952 (1113)
T ss_pred cccceeehhhhhhHHHHhhhhhccccccccCcccccchhhheeeeeeeeeccCCCcchheeeeeeecchhhh--hhccce
Confidence 47999999998777766666665543221 2334444457899999888865 568999
Q ss_pred EEEecCCCCCcceechHHHHHHHhcCCCcccCEEEEeee--ccccccceeeeEEEEeecCCCCCCCCCCceeeEEeeCCC
Q 003505 183 IFYNPRASPSEFVIPLAKYVKAVYHTRVSVGMRFRMLFE--TEESSVRRYMGTITGISDLDPVRWPNSHWRSVKVGWDES 260 (815)
Q Consensus 183 V~Y~PRas~sEFVVp~~ky~kAv~~~~ws~GmRFrM~fE--tEdss~rr~~GTI~gi~~~Dp~rWP~S~WR~LqV~WDe~ 260 (815)
+.|......++|+|.+..|+.|+. ++|..+++||..+. +||. .+||.|+|.++.+..| .+|+|+|+|+.|+||..
T Consensus 953 ltlpdlv~fpDFlV~rsrYd~AiQ-rnW~~~d~crvwwrda~~e~-g~WWeG~ils~~pksp-~fpdSpwery~v~~~~~ 1029 (1113)
T KOG0644|consen 953 LTLPDLVTFPDFLVERSRYDAAIQ-RNWTCRDKCRVWWRDAGEED-GAWWEGRILSVKPKSP-DFPDSPWERYIVRYDNT 1029 (1113)
T ss_pred eecccccCcchhhhhhhhHHHHHh-hccccccceeEEEccCCCcC-CceeeeeeeeccCCCC-CCCCCcceeEEEEecCC
Confidence 999999999999999999999986 89999999999983 3342 4899999999999887 89999999999999998
Q ss_pred CCCCCCCCccccccccCCC
Q 003505 261 TAGERQPRVSLWEIEPLTT 279 (815)
Q Consensus 261 ~~~~~~~RVSPWeIEpv~~ 279 (815)
+ .+.-||||.|++..
T Consensus 1030 e----~~~~spwe~~~i~d 1044 (1113)
T KOG0644|consen 1030 E----TELHSPWEMEPIPD 1044 (1113)
T ss_pred c----ccccCccccCCCcc
Confidence 7 47789999999976
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=98.19 E-value=8.6e-06 Score=80.48 Aligned_cols=89 Identities=25% Similarity=0.371 Sum_probs=60.6
Q ss_pred ceeEEEecCcccCCCCC----ceeeecchhhhhCCCCCC-CCCCCceEEEEEeCCC--CeEEEEEEEeCC------Ccce
Q 003505 42 TNYFCKTLTASDTSTHG----GFSVPRRAAEKVFPPLDY-SQTPPAQELIARDLHD--NEWKFRHIFRGQ------PKRH 108 (815)
Q Consensus 42 ~~~F~KtLT~SDv~~~G----rfsIPk~~Ae~~FPpLd~-s~~~p~q~L~~~Dl~G--~~W~FR~iyrg~------prrh 108 (815)
...|+|.|++.|++..| |+.|||..++.+||.+.. +..+|...|.+++..| ..|+||+||.|+ ++.+
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 56799999999999875 799999999999998655 5567899999999888 459999999976 6778
Q ss_pred eec--ccchhhhcccCCCCCCEEEEE
Q 003505 109 LLT--TGWSVFVSAKRLVAGDSVLFI 132 (815)
Q Consensus 109 lLT--tGWs~FVk~KkL~aGDsVvF~ 132 (815)
.|| ++=..|.+. =.+||.+||.
T Consensus 87 RIT~~G~~~~~~~~--~~tGaL~vla 110 (156)
T PF09217_consen 87 RITRFGRGFPLQNP--ENTGALLVLA 110 (156)
T ss_dssp EEE---TTSGGG-G--GGTT-EEEEE
T ss_pred EEeeecCCCccCCc--cccccEEEEE
Confidence 886 333334332 2479998887
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=97.76 E-value=4.8e-05 Score=72.20 Aligned_cols=81 Identities=22% Similarity=0.297 Sum_probs=64.2
Q ss_pred CCCceeEEEecCcccCCCC-CceeeecchhhhhCCCCC------------CCCCCCceEEEEEeCCCCeEEEEEEEeCC-
Q 003505 39 KQPTNYFCKTLTASDTSTH-GGFSVPRRAAEKVFPPLD------------YSQTPPAQELIARDLHDNEWKFRHIFRGQ- 104 (815)
Q Consensus 39 ~~~~~~F~KtLT~SDv~~~-GrfsIPk~~Ae~~FPpLd------------~s~~~p~q~L~~~Dl~G~~W~FR~iyrg~- 104 (815)
..+...|+|+|++||+..+ .||+||-..... ...|. .....-++.+.+.|..++.|..++..|..
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 4567899999999999886 899999876633 23231 11234688999999999999999999955
Q ss_pred --Ccceeecccchhhhcc
Q 003505 105 --PKRHLLTTGWSVFVSA 120 (815)
Q Consensus 105 --prrhlLTtGWs~FVk~ 120 (815)
.-.|+|++||..+|++
T Consensus 97 ~~~~~YvL~~gWn~VV~~ 114 (114)
T PF03754_consen 97 NGTSNYVLNSGWNKVVED 114 (114)
T ss_pred CCceEEEEEcChHhhccC
Confidence 5679999999999863
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=97.10 E-value=0.0013 Score=57.21 Aligned_cols=66 Identities=29% Similarity=0.520 Sum_probs=55.0
Q ss_pred EEEeccCcceeeeccCCCCCHHHHHHHHHHHhcCCCCcCCCCCCccEEEEEcCCCceEecCC-cchhhhhccee
Q 003505 685 VKVHKSGSFGRSLDISKFSSYDELRSELARMFGLEGQLEDPQRSGWQLVFVDRENDVLLLGD-DPWQEFVNNVG 757 (815)
Q Consensus 685 VKV~m~G~iGRkiDL~~~~sY~eL~~~L~~MF~~eg~l~d~~~s~~~lvYeD~EGD~mLvGD-vPWe~Fv~svk 757 (815)
|||+-.|.+=|.+.+..--+|++|+..++..|+.. ...++|.|.|.||||..+.+ .=|++.++.++
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 78888887666788888889999999999999986 24699999999999988764 44777777664
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=96.14 E-value=0.018 Score=49.93 Aligned_cols=65 Identities=29% Similarity=0.566 Sum_probs=50.9
Q ss_pred EEEeccCcceeeeccCCCCCHHHHHHHHHHHhcCCCCcCCCCCCccEEEEEcCCCceEec-CCcchhhhhccee
Q 003505 685 VKVHKSGSFGRSLDISKFSSYDELRSELARMFGLEGQLEDPQRSGWQLVFVDRENDVLLL-GDDPWQEFVNNVG 757 (815)
Q Consensus 685 VKV~m~G~iGRkiDL~~~~sY~eL~~~L~~MF~~eg~l~d~~~s~~~lvYeD~EGD~mLv-GDvPWe~Fv~svk 757 (815)
|||.- |.--|.+-+..--+|++|++++.+.|++.. ..+.|-|.|.||||..+ .|.=|++.+..++
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 555678888889999999999999999643 35999999999998755 4556666666554
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=96.12 E-value=0.022 Score=49.18 Aligned_cols=65 Identities=26% Similarity=0.553 Sum_probs=49.7
Q ss_pred EEEeccCcceeeeccC-CCCCHHHHHHHHHHHhcCCCCcCCCCCCccEEEEEcCCCceEecCC-cchhhhhccee
Q 003505 685 VKVHKSGSFGRSLDIS-KFSSYDELRSELARMFGLEGQLEDPQRSGWQLVFVDRENDVLLLGD-DPWQEFVNNVG 757 (815)
Q Consensus 685 VKV~m~G~iGRkiDL~-~~~sY~eL~~~L~~MF~~eg~l~d~~~s~~~lvYeD~EGD~mLvGD-vPWe~Fv~svk 757 (815)
|||+-.|.+ |.+-+. .--+|++|+..|.+.|++.. ..+.+.|.|.||||..+.+ .=|++.++.++
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 688777743 333333 88999999999999999754 3589999999999988776 56666666554
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=95.75 E-value=0.033 Score=50.19 Aligned_cols=53 Identities=25% Similarity=0.439 Sum_probs=41.8
Q ss_pred EEEeccCcceeeeccCCCCCHHHHHHHHHHHhcCCCCcCCCCCCccEEEEEcCCCceEec
Q 003505 685 VKVHKSGSFGRSLDISKFSSYDELRSELARMFGLEGQLEDPQRSGWQLVFVDRENDVLLL 744 (815)
Q Consensus 685 VKV~m~G~iGRkiDL~~~~sY~eL~~~L~~MF~~eg~l~d~~~s~~~lvYeD~EGD~mLv 744 (815)
|||.-.|. -+.+-+..--+|++|+++++++|++.. .+++.|-|.|.||||.++
T Consensus 3 vK~~~~~d-~~r~~l~~~~~~~~L~~~i~~r~~~~~------~~~f~LkY~Ddegd~v~l 55 (82)
T cd06407 3 VKATYGEE-KIRFRLPPSWGFTELKQEIAKRFKLDD------MSAFDLKYLDDDEEWVLL 55 (82)
T ss_pred EEEEeCCe-EEEEEcCCCCCHHHHHHHHHHHhCCCC------CCeeEEEEECCCCCeEEe
Confidence 78888775 334555556699999999999999742 257999999999999765
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=95.70 E-value=0.031 Score=50.62 Aligned_cols=51 Identities=25% Similarity=0.375 Sum_probs=43.5
Q ss_pred EEEeccC-cceeeeccCCCCCHHHHHHHHHHHhcCCCCcCCCCCCccEEEEEcCCCceEec
Q 003505 685 VKVHKSG-SFGRSLDISKFSSYDELRSELARMFGLEGQLEDPQRSGWQLVFVDRENDVLLL 744 (815)
Q Consensus 685 VKV~m~G-~iGRkiDL~~~~sY~eL~~~L~~MF~~eg~l~d~~~s~~~lvYeD~EGD~mLv 744 (815)
|||.-.| .+--+++-+.--+|.+|..+++++|++. .+.|.|.|.||||.++
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 7888888 5555777777889999999999999986 4899999999999765
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=95.25 E-value=0.036 Score=50.68 Aligned_cols=49 Identities=27% Similarity=0.436 Sum_probs=38.3
Q ss_pred ceee--eccCCCCCHHHHHHHHHHHhcCCCCcCCCCCCccEEEEEcCCCceEecC
Q 003505 693 FGRS--LDISKFSSYDELRSELARMFGLEGQLEDPQRSGWQLVFVDRENDVLLLG 745 (815)
Q Consensus 693 iGRk--iDL~~~~sY~eL~~~L~~MF~~eg~l~d~~~s~~~lvYeD~EGD~mLvG 745 (815)
-||. +-+....|+.+|++++.+-|+.+... ..+++|.|.|.||||.|+-
T Consensus 9 ~GrvhRf~~~~s~~~~~L~~~I~~Rl~~d~~~----~~~~~L~YlDDEgD~VllT 59 (86)
T cd06409 9 KGRVHRFRLRPSESLEELRTLISQRLGDDDFE----THLYALSYVDDEGDIVLIT 59 (86)
T ss_pred CCCEEEEEecCCCCHHHHHHHHHHHhCCcccc----CCcccEEEEcCCCCEEEEe
Confidence 4444 34445789999999999999976532 4579999999999998763
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=94.91 E-value=0.088 Score=48.43 Aligned_cols=66 Identities=26% Similarity=0.462 Sum_probs=47.9
Q ss_pred EEEeccCc-ceeeeccC---CCCCHHHHHHHHHHHhcCCCCcCCCCCCccEEEEEcCCCceEecCCcchhhhhcceeE
Q 003505 685 VKVHKSGS-FGRSLDIS---KFSSYDELRSELARMFGLEGQLEDPQRSGWQLVFVDRENDVLLLGDDPWQEFVNNVGY 758 (815)
Q Consensus 685 VKV~m~G~-iGRkiDL~---~~~sY~eL~~~L~~MF~~eg~l~d~~~s~~~lvYeD~EGD~mLvGDvPWe~Fv~svkr 758 (815)
|||.-+|. +==++++. .--+|++|+.++++.|.+.. ..+++|.|.|.||||..+-++ +++..++.+
T Consensus 3 vKv~y~~~~rRf~l~~~~~~~d~~~~~L~~kI~~~f~l~~------~~~~~l~Y~Dedgd~V~l~~D--~DL~~a~~~ 72 (91)
T cd06398 3 VKVKYGGTLRRFTFPVAENQLDLNMDGLREKVEELFSLSP------DADLSLTYTDEDGDVVTLVDD--NDLTDAIQY 72 (91)
T ss_pred EEEEeCCEEEEEEeccccccCCCCHHHHHHHHHHHhCCCC------CCcEEEEEECCCCCEEEEccH--HHHHHHHHH
Confidence 79988884 33344443 45799999999999998632 357999999999999887544 445544443
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=92.53 E-value=0.34 Score=44.05 Aligned_cols=66 Identities=21% Similarity=0.385 Sum_probs=48.8
Q ss_pred EEEeccCccee-eeccCCCCCHHHHHHHHHHHhcCCCCcCCCCCCccEEEEEcCCCceEec-CCcchhhhhccee
Q 003505 685 VKVHKSGSFGR-SLDISKFSSYDELRSELARMFGLEGQLEDPQRSGWQLVFVDRENDVLLL-GDDPWQEFVNNVG 757 (815)
Q Consensus 685 VKV~m~G~iGR-kiDL~~~~sY~eL~~~L~~MF~~eg~l~d~~~s~~~lvYeD~EGD~mLv-GDvPWe~Fv~svk 757 (815)
||.+-++.+=| ++|-....+|+|++.-|++|+.+.. ..++|-|.|.+||.+=+ -|+-...-+++++
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 56666665433 6777778999999999999999865 25999999999999755 3444554444544
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=0.46 Score=43.49 Aligned_cols=50 Identities=28% Similarity=0.357 Sum_probs=39.6
Q ss_pred EEEeccCcc-eeeeccCCCCCHHHHHHHHHHHhcCCCCcCCCCCCccEEEEEcCCCceE
Q 003505 685 VKVHKSGSF-GRSLDISKFSSYDELRSELARMFGLEGQLEDPQRSGWQLVFVDRENDVL 742 (815)
Q Consensus 685 VKV~m~G~i-GRkiDL~~~~sY~eL~~~L~~MF~~eg~l~d~~~s~~~lvYeD~EGD~m 742 (815)
+|++-.|.| --.+|. ..+|++|.+++++||.+. .+..+++.|.|.|||--
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 788888954 334454 788999999999999972 23469999999999973
No 16
>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=90.47 E-value=0.83 Score=41.70 Aligned_cols=58 Identities=22% Similarity=0.347 Sum_probs=42.2
Q ss_pred EEEeccCcceeeeccCCC-CCHHHHHHHHHHHhcCCCCcCCCCCCccEEEEEcCCCceEecCCc
Q 003505 685 VKVHKSGSFGRSLDISKF-SSYDELRSELARMFGLEGQLEDPQRSGWQLVFVDRENDVLLLGDD 747 (815)
Q Consensus 685 VKV~m~G~iGRkiDL~~~-~sY~eL~~~L~~MF~~eg~l~d~~~s~~~lvYeD~EGD~mLvGDv 747 (815)
+|+.-.|.|=| +-+..- =+|.+|+..+.+.|... + |....+.+.|.|.|||+.-+.+.
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 57666556644 444432 29999999999999942 1 33456999999999999887764
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=90.32 E-value=1 Score=41.51 Aligned_cols=55 Identities=27% Similarity=0.302 Sum_probs=41.6
Q ss_pred ceEEEeccC----cceeee--ccCCCCCHHHHHHHHHHHhcCCCCcCCCCCCccEEEEEcCCCceEe
Q 003505 683 TFVKVHKSG----SFGRSL--DISKFSSYDELRSELARMFGLEGQLEDPQRSGWQLVFVDRENDVLL 743 (815)
Q Consensus 683 ~fVKV~m~G----~iGRki--DL~~~~sY~eL~~~L~~MF~~eg~l~d~~~s~~~lvYeD~EGD~mL 743 (815)
+.||.|..| +=-|++ |-....+|++|+..+.++|..- . +..++|.|.|.|||..-
T Consensus 1 ~~vkayl~~~~~~~EIRRf~l~~~~~~s~~~L~~~V~~~f~~l---~---~~~ftlky~DeeGDlvt 61 (87)
T cd06402 1 LTVKAYLLGKDANAEIRRFAIDEDVSTSYEYLVEKVAAVFPSL---R---GKNFQLFWKDEEGDLVA 61 (87)
T ss_pred CeEEEeecCCCCccceEEEEecCCCCcCHHHHHHHHHHHcccc---C---CCcEEEEEECCCCCEEe
Confidence 368888877 334544 4467779999999999999532 1 24699999999999843
No 18
>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=88.19 E-value=1.3 Score=40.53 Aligned_cols=61 Identities=20% Similarity=0.350 Sum_probs=45.1
Q ss_pred EEeccCcceeeeccCCCCCHHHHHHHHHHHhcCCCCcCCCCCCccEEEEEcCCCceE-ecCCcchhhhhc
Q 003505 686 KVHKSGSFGRSLDISKFSSYDELRSELARMFGLEGQLEDPQRSGWQLVFVDRENDVL-LLGDDPWQEFVN 754 (815)
Q Consensus 686 KV~m~G~iGRkiDL~~~~sY~eL~~~L~~MF~~eg~l~d~~~s~~~lvYeD~EGD~m-LvGDvPWe~Fv~ 754 (815)
||.- |.--|++....-=+|.+|++.|..+|.+.. .+ +.|+|.|.|||.. |+-|+=-++|.+
T Consensus 4 Kv~~-~g~~RRf~~~~~pt~~~L~~kl~~Lf~lp~------~~-~~vtYiDeD~D~ITlssd~eL~d~~~ 65 (82)
T cd06397 4 KSSF-LGDTRRIVFPDIPTWEALASKLENLYNLPE------IK-VGVTYIDNDNDEITLSSNKELQDFYR 65 (82)
T ss_pred EEEe-CCceEEEecCCCccHHHHHHHHHHHhCCCh------hH-eEEEEEcCCCCEEEecchHHHHHHHH
Confidence 6643 445688888888999999999999999743 23 8999999999975 344444555544
No 19
>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=83.76 E-value=1.6 Score=40.48 Aligned_cols=51 Identities=29% Similarity=0.332 Sum_probs=44.3
Q ss_pred eccCCCCCHHHHHHHHHHHhcCCCCcCCCCCCccEEEEEcCCCceEecCCcchhhhhcceeEEEEeChHhhhhcccC
Q 003505 697 LDISKFSSYDELRSELARMFGLEGQLEDPQRSGWQLVFVDRENDVLLLGDDPWQEFVNNVGYIKILSPLEVQQMGKG 773 (815)
Q Consensus 697 iDL~~~~sY~eL~~~L~~MF~~eg~l~d~~~s~~~lvYeD~EGD~mLvGDvPWe~Fv~svkrirIl~~~e~~~m~~~ 773 (815)
=||+.--+|.+|..-..+-|..+ +-+|-|.|.|||. ||||+.+++.=|-++
T Consensus 22 e~l~~~P~~kdLl~lmr~~f~~~---------dIaLNYrD~EGDL-----------------IRllddeDv~LMV~~ 72 (92)
T cd06399 22 EDLSSTPLLKDLLELTRREFQRE---------DIALNYRDAEGDL-----------------IRLLSDEDVALMVRQ 72 (92)
T ss_pred cccccCccHHHHHHHHHHHhchh---------heeeeeecCCCCE-----------------EEEcchhhHHHHHHH
Confidence 36788889999999999999853 3589999999998 999999999999777
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=82.96 E-value=3.8 Score=37.88 Aligned_cols=54 Identities=22% Similarity=0.442 Sum_probs=43.3
Q ss_pred ceEEEeccCcceeeeccCCCCCHHHHHHHHHHHhcCCCCcCCCCCCccEEEEEcCCCceEecCC
Q 003505 683 TFVKVHKSGSFGRSLDISKFSSYDELRSELARMFGLEGQLEDPQRSGWQLVFVDRENDVLLLGD 746 (815)
Q Consensus 683 ~fVKV~m~G~iGRkiDL~~~~sY~eL~~~L~~MF~~eg~l~d~~~s~~~lvYeD~EGD~mLvGD 746 (815)
.=|||+-.|. -|-|-+..--+|++|...+.++|++. ..++|-|.|. ||..-++|
T Consensus 3 ikVKv~~~~D-v~~i~v~~~i~f~dL~~kIrdkf~~~--------~~~~iKykDE-GD~iti~s 56 (86)
T cd06408 3 IRVKVHAQDD-TRYIMIGPDTGFADFEDKIRDKFGFK--------RRLKIKMKDD-GDMITMGD 56 (86)
T ss_pred EEEEEEecCc-EEEEEcCCCCCHHHHHHHHHHHhCCC--------CceEEEEEcC-CCCccccC
Confidence 3478887775 56677777778999999999999973 2589999999 99866554
No 21
>KOG3598 consensus Thyroid hormone receptor-associated protein complex, subunit TRAP230 [Transcription]
Probab=77.90 E-value=1.9 Score=55.36 Aligned_cols=70 Identities=20% Similarity=0.222 Sum_probs=38.4
Q ss_pred ceeeecchhhhhCCCCCCCCCCCceEE----EEEeCCCC-eEEEEEEEeCCCcceeec----ccchhhhcccCCCCCCEE
Q 003505 59 GFSVPRRAAEKVFPPLDYSQTPPAQEL----IARDLHDN-EWKFRHIFRGQPKRHLLT----TGWSVFVSAKRLVAGDSV 129 (815)
Q Consensus 59 rfsIPk~~Ae~~FPpLd~s~~~p~q~L----~~~Dl~G~-~W~FR~iyrg~prrhlLT----tGWs~FVk~KkL~aGDsV 129 (815)
||+=-.+....++|......+ .+.- ...|..|+ .=.|.-|+.++.. ++.| .-|--|-..|.+..|-.-
T Consensus 1663 r~sds~~kvrqlLPlpKqt~d--vItcep~gslidtkgnkiagFdsi~kK~Gl-qvstkqk~spwdlFEg~k~~aplsW~ 1739 (2220)
T KOG3598|consen 1663 RFSDSTRKVRQLLPLPKQTMD--VITCEPYGSLIDTKGNKIAGFDSIEKKNGL-QVSTKQKKSPWDLFEGTKHLAPLSWK 1739 (2220)
T ss_pred hhhHHHHHHHHhcCCCccccc--eeeecccccccccccceeccchhhhhhcCc-eeccccccCcchhhccCCCCCCccce
Confidence 455445556666775443221 1110 12366664 4677777754433 5554 458888888888776654
Q ss_pred EE
Q 003505 130 LF 131 (815)
Q Consensus 130 vF 131 (815)
-|
T Consensus 1740 wF 1741 (2220)
T KOG3598|consen 1740 WF 1741 (2220)
T ss_pred ee
Confidence 44
No 22
>PRK10737 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=56.80 E-value=26 Score=36.71 Aligned_cols=104 Identities=20% Similarity=0.240 Sum_probs=61.6
Q ss_pred CCCCCCEEEE-E--EccCCcEEEEEEecCCCCCCCCCCccCCCccchhHHHHHHHHHHhCCcEEEEEecCCCC------C
Q 003505 122 RLVAGDSVLF-I--WNEKNQLLLGIRRATRPQTVMPSSVLSSDSMHIGLLAAAAHAAATNSRFTIFYNPRASP------S 192 (815)
Q Consensus 122 kL~aGDsVvF-~--R~e~G~L~VGIRRa~r~~~~~pssv~s~dsm~~g~la~Aa~aaa~~~~FtV~Y~PRas~------s 192 (815)
++..|++|.| | |.++|+++-.-+ . ..|..++--...-+--|.+|..-...|..|+|..-|-..- .
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-V-----SAPLDYLHGHGSLISGLETALEGHEVGDKFDVAVGANDAYGQYDENL 75 (196)
T ss_pred ccCCCCEEEEEEEEEeCCCCEEEecC-C-----CCCeEEEeCCCcchHHHHHHHcCCCCCCEEEEEEChHHhcCCCChHH
Confidence 3566777777 3 346777533221 1 1233333222233334666777777888999987654332 2
Q ss_pred cceechHHHHHHHhcCCCcccCEEEEeeeccccccceeeeEEEEeec
Q 003505 193 EFVIPLAKYVKAVYHTRVSVGMRFRMLFETEESSVRRYMGTITGISD 239 (815)
Q Consensus 193 EFVVp~~ky~kAv~~~~ws~GmRFrM~fEtEdss~rr~~GTI~gi~~ 239 (815)
-..||++.|. .. ....+||||.+ ++++. ...++|+.|.+
T Consensus 76 V~~vpr~~F~-~~--~~l~~G~~~~~--~~~~G---~~~~~V~ev~~ 114 (196)
T PRK10737 76 VQRVPKDVFM-GV--DELQVGMRFLA--ETDQG---PVPVEITAVED 114 (196)
T ss_pred EEEecHHHCC-Cc--cCCCCCCEEEE--eCCCC---cEEEEEEEEcC
Confidence 3567776653 22 24899999886 45552 46889999975
No 23
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=48.25 E-value=26 Score=29.07 Aligned_cols=38 Identities=13% Similarity=0.131 Sum_probs=29.0
Q ss_pred CCcccCEEEEeeeccccccceeeeEEEEeecCCCCCCCCCCceeeEEeeCC
Q 003505 209 RVSVGMRFRMLFETEESSVRRYMGTITGISDLDPVRWPNSHWRSVKVGWDE 259 (815)
Q Consensus 209 ~ws~GmRFrM~fEtEdss~rr~~GTI~gi~~~Dp~rWP~S~WR~LqV~WDe 259 (815)
.|.+|+++...++.++ .||.|+|+.+.. -..+.|.-+.
T Consensus 2 ~~~~G~~Ve~~~~~~~---~W~~a~V~~~~~----------~~~~~V~~~~ 39 (61)
T smart00743 2 DFKKGDRVEVFSKEED---SWWEAVVTKVLG----------DGKYLVRYLT 39 (61)
T ss_pred CcCCCCEEEEEECCCC---EEEEEEEEEECC----------CCEEEEEECC
Confidence 5899999999996544 799999999964 1235677665
No 24
>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=43.06 E-value=64 Score=28.11 Aligned_cols=66 Identities=18% Similarity=0.193 Sum_probs=47.7
Q ss_pred ceEEEeccCcc----eeeeccCCCCCHHHHHHHHHHHhcCCCCcCCCCCCccEEE-EE-cCCCceEec-CCcchhhhh
Q 003505 683 TFVKVHKSGSF----GRSLDISKFSSYDELRSELARMFGLEGQLEDPQRSGWQLV-FV-DRENDVLLL-GDDPWQEFV 753 (815)
Q Consensus 683 ~fVKV~m~G~i----GRkiDL~~~~sY~eL~~~L~~MF~~eg~l~d~~~s~~~lv-Ye-D~EGD~mLv-GDvPWe~Fv 753 (815)
.++|||....- -++|-++....-.|+...+.+.|++.. ....|.|+ +. .......|- .+.|+..+.
T Consensus 3 ~~lrVy~~~~~~~~~~k~i~v~~~tTa~evi~~~l~k~~l~~-----~~~~y~L~~~~~~~~~er~L~~~E~pl~i~~ 75 (93)
T PF00788_consen 3 GVLRVYDGDGSPGSTYKTIKVSSSTTAREVIEMALEKFGLAE-----DPSDYCLVEVEESGGEERPLDDDECPLQIQL 75 (93)
T ss_dssp EEEEEEETTSSSCCSEEEEEEETTSBHHHHHHHHHHHTTTSS-----SGGGEEEEEEECTTTEEEEETTTSBHHHHHH
T ss_pred eEEEEEcCCCCCCccEEEEEECCCCCHHHHHHHHHHHhCCCC-----CCCCEEEEEEEcCCCEEEEcCCCCchHHHHH
Confidence 58999998632 899999999999999999999999822 23469995 44 444455554 344555443
No 25
>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=41.81 E-value=32 Score=27.60 Aligned_cols=28 Identities=14% Similarity=0.127 Sum_probs=23.0
Q ss_pred hhhcccCCCCCCEEEEEEccCCcEEEEE
Q 003505 116 VFVSAKRLVAGDSVLFIWNEKNQLLLGI 143 (815)
Q Consensus 116 ~FVk~KkL~aGDsVvF~R~e~G~L~VGI 143 (815)
.|..+.+|.+||.|.|.-.++|++.+--
T Consensus 14 ~~~~~l~l~~Gd~v~i~~~~~g~i~i~p 41 (47)
T PF04014_consen 14 EIREKLGLKPGDEVEIEVEGDGKIVIRP 41 (47)
T ss_dssp HHHHHTTSSTTTEEEEEEETTSEEEEEE
T ss_pred HHHHHcCCCCCCEEEEEEeCCCEEEEEE
Confidence 5677889999999999998888666543
No 26
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=40.86 E-value=34 Score=31.89 Aligned_cols=29 Identities=21% Similarity=0.310 Sum_probs=23.8
Q ss_pred hhcccCCCCCCEEEEEEccCCcEEEEEEe
Q 003505 117 FVSAKRLVAGDSVLFIWNEKNQLLLGIRR 145 (815)
Q Consensus 117 FVk~KkL~aGDsVvF~R~e~G~L~VGIRR 145 (815)
|.-...|++||.|..+|.+.|+.++=+-|
T Consensus 71 i~~~~~Lk~GD~V~ll~~~~gQ~yiVlDk 99 (100)
T PF10844_consen 71 ITFTDGLKVGDKVLLLRVQGGQKYIVLDK 99 (100)
T ss_pred EEEecCCcCCCEEEEEEecCCCEEEEEEe
Confidence 55578899999999999999987776543
No 27
>KOG3207 consensus Beta-tubulin folding cofactor E [Posttranslational modification, protein turnover, chaperones]
Probab=35.97 E-value=51 Score=38.88 Aligned_cols=43 Identities=28% Similarity=0.673 Sum_probs=30.2
Q ss_pred CcccCEEEEeeeccccccceeeeEEEEeecCCCCCCCCCCceeeEEeeCCCCCCCCC
Q 003505 210 VSVGMRFRMLFETEESSVRRYMGTITGISDLDPVRWPNSHWRSVKVGWDESTAGERQ 266 (815)
Q Consensus 210 ws~GmRFrM~fEtEdss~rr~~GTI~gi~~~Dp~rWP~S~WR~LqV~WDe~~~~~~~ 266 (815)
..+|.|+|.-+|- ...||.|+|.| |++ +| +.|.||++.-+.+.
T Consensus 3 ~~IG~RvkI~~~~---~Tvr~iG~V~g--------~~~-~w--~GvEWDd~~RGKH~ 45 (505)
T KOG3207|consen 3 MEIGTRVKIGGEI---ATVRYIGEVEG--------NNS-KW--YGVEWDDPVRGKHD 45 (505)
T ss_pred eeccceEEEcCEE---EEEEEEEEEcC--------CCC-cc--eeeEecCCCccccC
Confidence 5789999986642 23567776654 444 55 78999999977654
No 28
>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=33.12 E-value=63 Score=29.71 Aligned_cols=55 Identities=22% Similarity=0.287 Sum_probs=26.4
Q ss_pred HHHHHHHhcCCCcccCEEEEeeeccccccceeeeEEEEeecCCCCCCCCCCceeeEEeeCCCC
Q 003505 199 AKYVKAVYHTRVSVGMRFRMLFETEESSVRRYMGTITGISDLDPVRWPNSHWRSVKVGWDEST 261 (815)
Q Consensus 199 ~ky~kAv~~~~ws~GmRFrM~fEtEdss~rr~~GTI~gi~~~Dp~rWP~S~WR~LqV~WDe~~ 261 (815)
+.|..-+. -++.+||++||.=.-||-. .-=.|+|.-++.- .-|+ -.++|.|-.-+
T Consensus 8 d~Ya~YVr-~~i~~GM~VRc~~~yeeV~-~GD~G~V~k~~~d---g~~~---lnvqv~W~~~G 62 (78)
T PF11515_consen 8 DDYAEYVR-DNIQPGMRVRCCRDYEEVR-AGDEGEVFKQDRD---GLHD---LNVQVDWQSKG 62 (78)
T ss_dssp HHHHHHHH-HH--TT-EEEESS-BTTB--TT-EEE-EEEE-T---TSSE-----EEEEETTTT
T ss_pred hHHHHHHH-HhCCCCcEEEEeccccccc-ccccceeEeeccC---CCCC---cceEEEeeecC
Confidence 44544454 3689999999964334422 1236776666531 2222 35889997654
No 29
>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=32.59 E-value=1.5e+02 Score=27.43 Aligned_cols=65 Identities=17% Similarity=0.257 Sum_probs=48.9
Q ss_pred eEEEeccCcceeeeccCCCCCHHHHHHHHHHHhcCCCCcCCCCCCccEEEEEcCCC-ceEecCCcchhhhhccee
Q 003505 684 FVKVHKSGSFGRSLDISKFSSYDELRSELARMFGLEGQLEDPQRSGWQLVFVDREN-DVLLLGDDPWQEFVNNVG 757 (815)
Q Consensus 684 fVKV~m~G~iGRkiDL~~~~sY~eL~~~L~~MF~~eg~l~d~~~s~~~lvYeD~EG-D~mLvGDvPWe~Fv~svk 757 (815)
-|||+-.+ -=-|-+..=-+|.+|+..|.+-+.+-+ .+=+|-|.|.+. +...++|.=++.-.+.|+
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--TVAIQVARGLSYATLLQKISSKLELPA-------EHITLSYKSEASGEDVILSDTNMEDVWSQAK 69 (80)
T ss_pred EEEEEEEE--EEEEEcCCCCCHHHHHHHHHHHhCCCc-------hhcEEEeccCCCCCccCcChHHHHHHHHhhc
Confidence 58999887 233555666789999999999998753 135899998874 333449999998888887
No 30
>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=32.36 E-value=70 Score=25.83 Aligned_cols=52 Identities=15% Similarity=0.214 Sum_probs=36.4
Q ss_pred CCcccCEEEEeeeccccccceeeeEEEEeecCCCCCCCCCCceeeEEeeCCCCCCCCCCCccccccccC
Q 003505 209 RVSVGMRFRMLFETEESSVRRYMGTITGISDLDPVRWPNSHWRSVKVGWDESTAGERQPRVSLWEIEPL 277 (815)
Q Consensus 209 ~ws~GmRFrM~fEtEdss~rr~~GTI~gi~~~Dp~rWP~S~WR~LqV~WDe~~~~~~~~RVSPWeIEpv 277 (815)
.|.+|..+...+ .+. .||.|+|+++.. + ..+.|.-++-+.. +-|...+|-++
T Consensus 2 ~~~~G~~~~a~~-~d~---~wyra~I~~~~~-------~---~~~~V~f~D~G~~---~~v~~~~l~~l 53 (57)
T smart00333 2 TFKVGDKVAARW-EDG---EWYRARIIKVDG-------E---QLYEVFFIDYGNE---EVVPPSDLRPL 53 (57)
T ss_pred CCCCCCEEEEEe-CCC---CEEEEEEEEECC-------C---CEEEEEEECCCcc---EEEeHHHeecC
Confidence 588999999998 443 799999999973 2 4567887764432 34555555544
No 31
>PF05641 Agenet: Agenet domain; InterPro: IPR008395 This domain is related to the TUDOR domain IPR008191 from INTERPRO []. The function of the agenet domain is unknown. This signature matches one of the two Agenet domains in the FMR proteins [].; GO: 0003723 RNA binding; PDB: 2BKD_N 3O8V_A 3KUF_A 3H8Z_A.
Probab=30.68 E-value=1.2e+02 Score=26.14 Aligned_cols=42 Identities=12% Similarity=0.082 Sum_probs=27.1
Q ss_pred CcccCEEEEeeeccccccceeeeEEEEeecCCCCCCCCCCceeeEEeeCCCC
Q 003505 210 VSVGMRFRMLFETEESSVRRYMGTITGISDLDPVRWPNSHWRSVKVGWDEST 261 (815)
Q Consensus 210 ws~GmRFrM~fEtEdss~rr~~GTI~gi~~~Dp~rWP~S~WR~LqV~WDe~~ 261 (815)
+..|+++-..-+.+.....||.|||+.....+ .+.|+.+.-.
T Consensus 1 F~~G~~VEV~s~e~g~~gaWf~a~V~~~~~~~----------~~~V~Y~~~~ 42 (68)
T PF05641_consen 1 FKKGDEVEVSSDEDGFRGAWFPATVLKENGDD----------KYLVEYDDLP 42 (68)
T ss_dssp --TT-EEEEEE-SBTT--EEEEEEEEEEETT-----------EEEEEETT-S
T ss_pred CCCCCEEEEEEcCCCCCcEEEEEEEEEeCCCc----------EEEEEECCcc
Confidence 46799999877655555689999999997532 7889987544
No 32
>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=30.07 E-value=65 Score=24.61 Aligned_cols=26 Identities=23% Similarity=0.288 Sum_probs=22.0
Q ss_pred hhhcccCCCCCCEEEEEEccCCcEEE
Q 003505 116 VFVSAKRLVAGDSVLFIWNEKNQLLL 141 (815)
Q Consensus 116 ~FVk~KkL~aGDsVvF~R~e~G~L~V 141 (815)
.|.++-++..||.|.+...++|.+.+
T Consensus 14 ~~r~~l~~~~gd~~~i~~~~~~~l~l 39 (43)
T TIGR01439 14 EIREKLGLKEGDRLEVIRVEDGEIIL 39 (43)
T ss_pred HHHHHcCcCCCCEEEEEEeCCCEEEE
Confidence 68889999999999999877776654
No 33
>PRK03760 hypothetical protein; Provisional
Probab=28.83 E-value=1.2e+02 Score=29.24 Aligned_cols=27 Identities=22% Similarity=0.385 Sum_probs=21.9
Q ss_pred CCcceee--cccchhhhcccCCCCCCEEEEEE
Q 003505 104 QPKRHLL--TTGWSVFVSAKRLVAGDSVLFIW 133 (815)
Q Consensus 104 ~prrhlL--TtGWs~FVk~KkL~aGDsVvF~R 133 (815)
.+-+|+| ..||.. +.++++||.|.|.|
T Consensus 88 ~~a~~VLEl~aG~~~---~~gi~~Gd~v~~~~ 116 (117)
T PRK03760 88 KPARYIIEGPVGKIR---VLKVEVGDEIEWID 116 (117)
T ss_pred ccceEEEEeCCChHH---HcCCCCCCEEEEee
Confidence 4556888 688765 89999999999876
No 34
>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=26.79 E-value=70 Score=30.89 Aligned_cols=26 Identities=31% Similarity=0.543 Sum_probs=18.1
Q ss_pred cCCCCCCEEEEEEcc-CCcEEEEEEec
Q 003505 121 KRLVAGDSVLFIWNE-KNQLLLGIRRA 146 (815)
Q Consensus 121 KkL~aGDsVvF~R~e-~G~L~VGIRRa 146 (815)
++++.||.|+||... .+.-+|||=+-
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 589999999999986 67788888664
No 35
>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=25.57 E-value=1.1e+02 Score=25.95 Aligned_cols=31 Identities=19% Similarity=0.370 Sum_probs=23.9
Q ss_pred ccCEEEEeeeccccccceeeeEEEEeecCCC
Q 003505 212 VGMRFRMLFETEESSVRRYMGTITGISDLDP 242 (815)
Q Consensus 212 ~GmRFrM~fEtEdss~rr~~GTI~gi~~~Dp 242 (815)
+|-|+.-.||.++.++..|.|+|..--+..|
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 5889999999888888889999999877644
No 36
>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=24.60 E-value=54 Score=27.63 Aligned_cols=17 Identities=24% Similarity=0.542 Sum_probs=14.8
Q ss_pred EEEEEcCCCceEecCCc
Q 003505 731 QLVFVDRENDVLLLGDD 747 (815)
Q Consensus 731 ~lvYeD~EGD~mLvGDv 747 (815)
.++|.|.+|+.+++|+.
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 69999999999999974
No 37
>KOG3598 consensus Thyroid hormone receptor-associated protein complex, subunit TRAP230 [Transcription]
Probab=24.02 E-value=62 Score=42.84 Aligned_cols=9 Identities=33% Similarity=0.287 Sum_probs=4.3
Q ss_pred ccCCCccch
Q 003505 157 VLSSDSMHI 165 (815)
Q Consensus 157 v~s~dsm~~ 165 (815)
++|.+-||.
T Consensus 1851 ~~s~~~~hh 1859 (2220)
T KOG3598|consen 1851 VTSEKNEHH 1859 (2220)
T ss_pred CCChHhhcC
Confidence 445555543
No 38
>COG1047 SlpA FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]
Probab=23.16 E-value=3.5e+02 Score=28.27 Aligned_cols=105 Identities=19% Similarity=0.262 Sum_probs=62.3
Q ss_pred CCCCCCEEEEE---EccCCcEEEEEEecCCCCCCCCCCccCCCccchhHHHHHHHHHHhCCcEEEEEecCCCCCcc----
Q 003505 122 RLVAGDSVLFI---WNEKNQLLLGIRRATRPQTVMPSSVLSSDSMHIGLLAAAAHAAATNSRFTIFYNPRASPSEF---- 194 (815)
Q Consensus 122 kL~aGDsVvF~---R~e~G~L~VGIRRa~r~~~~~pssv~s~dsm~~g~la~Aa~aaa~~~~FtV~Y~PRas~sEF---- 194 (815)
++..||.|.+. |.++|+++=--. . ..-|..++-.+..-+.-|.+|..-..-|..|+|.--|-..-.|+
T Consensus 2 ~i~k~~~V~i~Y~~~~~dg~v~Dtt~-e----~~~P~~~i~G~g~li~glE~al~g~~~Ge~~~V~IpPE~AfGe~~~~l 76 (174)
T COG1047 2 KIEKGDVVSLHYTLKVEDGEVVDTTD-E----NYGPLTFIVGAGQLIPGLEEALLGKEVGEEFTVEIPPEDAFGEYDPDL 76 (174)
T ss_pred cccCCCEEEEEEEEEecCCcEEEccc-c----cCCCeEEEecCCCcchhHHHHHhCCCCCceeEEEeCchHhcCCCChHH
Confidence 45677887762 334554432111 0 01122222222233344778888888899999998887655444
Q ss_pred --eechHHHHHHHhcCCCcccCEEEEeeeccccccceeeeEEEEeec
Q 003505 195 --VIPLAKYVKAVYHTRVSVGMRFRMLFETEESSVRRYMGTITGISD 239 (815)
Q Consensus 195 --VVp~~ky~kAv~~~~ws~GmRFrM~fEtEdss~rr~~GTI~gi~~ 239 (815)
.||+.+|... ....+||+|.. ++++ .-.-|+|+.|..
T Consensus 77 vq~vp~~~F~~~---~~~~vGm~~~~--~~~~---~~~~~~V~~V~~ 115 (174)
T COG1047 77 VQRVPRDEFQGV---GELEVGMEVEA--EGGD---GEIPGVVTEVSG 115 (174)
T ss_pred eEEecHHHhCcC---CCCCCCcEEEE--cCCC---ceeeEEEEEEcC
Confidence 4566654322 15899999885 5555 456899999973
No 39
>cd04451 S1_IF1 S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the formation of the first peptide bond. In Escherichia coli, the initiation mechanism requires, in addition to mRNA, fMet-tRNA, and ribosomal subunits, the presence of three additional proteins (initiation factors IF1, IF2, and IF3) and at least one GTP molecule. The three initiation factors influence both the kinetics and the stability of ternary complex formation. IF1 is the smallest of the three factors. IF1 enhances the rate of 70S ribosome subunit association and dissociation and the interaction of 30S ribosomal subunit with IF2 and IF3. It stimulates 30S complex formation. In addition, by binding to the A-site of the 30S ribosomal subunit, IF1 may contribute to the fidelity of the selection of the initiation site of th
Probab=21.70 E-value=3.7e+02 Score=22.79 Aligned_cols=38 Identities=13% Similarity=0.121 Sum_probs=22.8
Q ss_pred EEEEEeCCCCeEEEEEEEeCCCcceeecccchhhhcccCCCCCCEEEEEEc
Q 003505 84 ELIARDLHDNEWKFRHIFRGQPKRHLLTTGWSVFVSAKRLVAGDSVLFIWN 134 (815)
Q Consensus 84 ~L~~~Dl~G~~W~FR~iyrg~prrhlLTtGWs~FVk~KkL~aGDsVvF~R~ 134 (815)
...+++..|. .++|..||+-|+ +...+.+||.|.|...
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 4445666676 445555544321 2334899999999854
No 40
>COG0219 CspR Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]
Probab=21.11 E-value=29 Score=35.44 Aligned_cols=57 Identities=16% Similarity=0.330 Sum_probs=40.9
Q ss_pred EeccC-cceeeeccCCCCCHHHHHHHH---HHHhcCCCCcCCCCCCccEEEEEcCCCceEecCCcc
Q 003505 687 VHKSG-SFGRSLDISKFSSYDELRSEL---ARMFGLEGQLEDPQRSGWQLVFVDRENDVLLLGDDP 748 (815)
Q Consensus 687 V~m~G-~iGRkiDL~~~~sY~eL~~~L---~~MF~~eg~l~d~~~s~~~lvYeD~EGD~mLvGDvP 748 (815)
+.+-| .|--+++|..|+||++...+. .++|.++.+-.... .. +....||++|-|-..
T Consensus 45 lkRAGlDY~~~~~l~~h~s~e~fl~~~~~~~rl~~~tt~~~~~~---~~--~~f~~~d~llFG~Es 105 (155)
T COG0219 45 LKRAGLDYHEKASLTEHDSLEAFLEAEPIGGRLFALTTKGTTTY---TD--VSFQKGDYLLFGPES 105 (155)
T ss_pred hhhcccchHhhcceEEeCCHHHHHhhccCCceEEEEEecccccc---cc--ccCCCCCEEEECCCC
Confidence 34468 899999999999999999988 56777654322111 11 444669999999754
No 41
>PF14847 Ras_bdg_2: Ras-binding domain of Byr2; PDB: 1I35_A 1K8R_B.
Probab=20.92 E-value=3.1e+02 Score=26.37 Aligned_cols=49 Identities=12% Similarity=0.295 Sum_probs=33.2
Q ss_pred eEEEeccCcceeeeccCCCCCHHHHHHHHHHHhcCCCCcCCCCCCccEEEEEcC
Q 003505 684 FVKVHKSGSFGRSLDISKFSSYDELRSELARMFGLEGQLEDPQRSGWQLVFVDR 737 (815)
Q Consensus 684 fVKV~m~G~iGRkiDL~~~~sY~eL~~~L~~MF~~eg~l~d~~~s~~~lvYeD~ 737 (815)
.++|.-++-.-|+||++...+.+|+....-+-||+.+. ...|.....|.
T Consensus 2 vi~~I~~dG~tk~VNV~~c~~a~eI~~rvLKKfg~~~~-----~~~~~~~v~d~ 50 (105)
T PF14847_consen 2 VIRFILEDGSTKTVNVSGCFNAQEIKRRVLKKFGLPEH-----PRNYCFYVLDG 50 (105)
T ss_dssp EEEEEETTTEEEEEE--S--HHHHHHHHHHHHHTSS-------CCCEEEEEE-S
T ss_pred EEEEECCCCcEEEEEECCCCCHHHHHHHHHHHcCCccc-----cccceEEEecc
Confidence 36777777788999999999999999999999998772 23466655555
Done!