Query 003298
Match_columns 833
No_of_seqs 366 out of 835
Neff 4.0
Searched_HMMs 46136
Date Thu Mar 28 20:51:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003298.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003298hhsearch_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 2.7E-35 5.9E-40 261.3 8.3 83 254-337 1-83 (83)
2 PF02309 AUX_IAA: AUX/IAA fami 99.9 4.1E-25 8.9E-30 224.7 0.0 71 763-833 107-191 (215)
3 PF02362 B3: B3 DNA binding do 99.7 4.5E-17 9.8E-22 144.5 11.0 97 128-229 1-99 (100)
4 KOG0644 Uncharacterized conser 99.3 1.9E-12 4.1E-17 150.3 7.2 148 206-362 874-1044(1113)
5 PF09217 EcoRII-N: Restriction 98.2 7.4E-06 1.6E-10 81.1 9.9 89 125-215 7-110 (156)
6 PF03754 DUF313: Domain of unk 97.8 4.3E-05 9.4E-10 72.7 6.3 81 122-203 18-114 (114)
7 PF00564 PB1: PB1 domain; Int 96.7 0.0046 1E-07 53.8 6.4 55 768-829 4-58 (84)
8 smart00666 PB1 PB1 domain. Pho 95.8 0.029 6.4E-07 48.8 6.8 54 768-829 4-57 (81)
9 cd06407 PB1_NLP A PB1 domain i 95.5 0.045 9.8E-07 49.5 7.0 54 768-828 3-56 (82)
10 cd06409 PB1_MUG70 The MUG70 pr 95.3 0.032 7E-07 51.1 5.5 49 776-828 9-59 (86)
11 cd06396 PB1_NBR1 The PB1 domai 95.3 0.052 1.1E-06 49.4 6.6 51 768-827 3-54 (81)
12 cd05992 PB1 The PB1 domain is 95.2 0.071 1.5E-06 46.1 6.9 54 768-829 3-57 (81)
13 cd06398 PB1_Joka2 The PB1 doma 94.9 0.088 1.9E-06 48.6 7.0 56 768-829 3-62 (91)
14 cd06403 PB1_Par6 The PB1 domai 92.0 0.41 8.9E-06 43.6 6.1 53 768-827 3-56 (80)
15 cd06404 PB1_aPKC PB1 domain is 90.9 0.59 1.3E-05 42.9 5.9 53 768-828 3-56 (83)
16 cd06401 PB1_TFG The PB1 domain 90.0 0.96 2.1E-05 41.4 6.4 57 768-829 3-60 (81)
17 cd06402 PB1_p62 The PB1 domain 89.4 1.3 2.8E-05 41.0 6.9 56 767-828 2-63 (87)
18 cd06397 PB1_UP1 Uncharacterize 88.0 1.3 2.8E-05 40.6 5.8 53 769-829 4-56 (82)
19 cd06408 PB1_NoxR The PB1 domai 79.0 5.7 0.00012 36.8 6.1 53 767-829 4-56 (86)
20 KOG0644 Uncharacterized conser 60.1 6.3 0.00014 48.8 2.7 67 34-102 872-940 (1113)
21 KOG3598 Thyroid hormone recept 59.0 10 0.00022 49.5 4.2 11 197-207 1724-1734(2220)
22 PRK10737 FKBP-type peptidyl-pr 55.6 30 0.00066 36.4 6.5 103 206-322 3-114 (196)
23 smart00743 Agenet Tudor-like d 51.2 23 0.0005 29.5 4.0 38 292-342 2-39 (61)
24 PF10844 DUF2577: Protein of u 44.9 25 0.00055 32.8 3.6 29 200-228 71-99 (100)
25 PF00788 RA: Ras association ( 44.2 70 0.0015 27.9 6.1 53 766-823 3-60 (93)
26 PF04014 Antitoxin-MazE: Antid 43.7 32 0.00069 27.7 3.5 28 199-226 14-41 (47)
27 KOG3207 Beta-tubulin folding c 42.7 24 0.00052 41.5 3.7 43 293-349 3-45 (505)
28 smart00333 TUDOR Tudor domain. 35.1 61 0.0013 26.2 4.0 52 292-360 2-53 (57)
29 TIGR01439 lp_hng_hel_AbrB loop 34.5 51 0.0011 25.3 3.3 26 199-224 14-39 (43)
30 PF05641 Agenet: Agenet domain 30.0 1.2E+02 0.0027 26.2 5.3 42 293-344 1-42 (68)
31 PF11515 Cul7: Mouse developme 29.0 87 0.0019 28.9 4.2 55 282-344 8-62 (78)
32 PRK03760 hypothetical protein; 27.7 1.3E+02 0.0028 29.2 5.5 47 167-216 62-116 (117)
33 cd06399 PB1_P40 The PB1 domain 27.6 1E+02 0.0023 29.1 4.5 39 780-827 22-60 (92)
34 PF01878 EVE: EVE domain; Int 26.9 60 0.0013 31.4 3.1 26 204-229 38-64 (143)
35 COG1047 SlpA FKBP-type peptidy 26.0 3.1E+02 0.0068 28.7 8.1 105 205-322 2-115 (174)
36 PF02513 Spin-Ssty: Spin/Ssty 25.2 1.2E+02 0.0026 25.9 4.0 31 295-325 1-31 (50)
37 cd04451 S1_IF1 S1_IF1: Transla 24.0 3E+02 0.0066 23.4 6.5 38 167-217 15-52 (64)
38 PF10411 DsbC_N: Disulfide bon 23.5 69 0.0015 27.1 2.5 17 814-830 34-50 (57)
39 PF06003 SMN: Survival motor n 21.3 93 0.002 34.0 3.5 56 291-361 67-122 (264)
40 cd04491 SoSSB_OBF SoSSB_OBF: A 20.6 5E+02 0.011 22.7 7.4 49 164-228 23-75 (82)
No 1
>PF06507 Auxin_resp: Auxin response factor; InterPro: IPR010525 This pattern represents a conserved region of auxin-responsive transcription factors. The plant hormone auxin (indole-3-acetic acid) can regulate the gene expression of several families, including Aux/IAA, GH3 and SAUR families. Two related families of proteins, Aux/IAA proteins (IPR003311 from INTERPRO) and the auxin response factors (ARF), are key regulators of auxin-modulated gene expression []. There are multiple ARF proteins, some of which activate, while others repress transcription. ARF proteins bind to auxin-responsive cis-acting promoter elements (AuxREs) using an N-terminal DNA-binding domain. It is thought that Aux/IAA proteins activate transcription by modifying ARF activity through the C-terminal protein-protein interaction domains (IPR011525 from INTERPRO) found in both Aux/IAA and ARF proteins. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0009725 response to hormone stimulus, 0005634 nucleus
Probab=100.00 E-value=2.7e-35 Score=261.35 Aligned_cols=83 Identities=66% Similarity=1.100 Sum_probs=81.2
Q ss_pred HHHHHHcCCcEEEEEcCCCCCCcceechHHHHHHHhcCCCcccCEEEEeeeccCcccceeeEEEEEeccCCCCCCCCCCc
Q 003298 254 AAHAAATNSRFTIFYNPRASPSEFVIPLAKYVKAVYHTRVSVGMRFRMLFETEESSVRRYMGTITGISDLDPVRWPNSHW 333 (833)
Q Consensus 254 Aa~aaat~~~F~V~Y~PRas~sEFVVp~~kyvkA~~~~~ws~GMRFrM~fEtEdss~rry~GTI~gv~d~Dp~rWP~S~W 333 (833)
|+|||+++++|+|+||||++++|||||++||++|+. ++|++||||||.||+||+++++|+|||+||+++||+|||+|+|
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 7999999999999999999999999999999999999999999
Q ss_pred eeeE
Q 003298 334 RSVK 337 (833)
Q Consensus 334 R~Lq 337 (833)
||||
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=99.90 E-value=4.1e-25 Score=224.70 Aligned_cols=71 Identities=45% Similarity=0.855 Sum_probs=0.0
Q ss_pred CCcceEEEeccc-cceeeeccCCCCChHHHHHHHHHhh---CCC----------CCCCCCCCCCeEEEEEeCCCCeEEec
Q 003298 763 PTRTFVKVHKSG-SFGRSLDISKFSSYDELRSELARMF---GLE----------GQLEDPQRSGWQLVFVDRENDVLLLG 828 (833)
Q Consensus 763 ~~~~fVKV~m~G-~iGRkiDL~~~~sY~eL~~~L~~MF---g~~----------g~l~d~~~s~~~lvY~D~EgD~mLvG 828 (833)
..++||||+||| +|||||||++|+||++|+.+|++|| ++. +.++...+++|+|||+|+||||||||
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 357999999999 9999999999999999999999999 555 33444567899999999999999999
Q ss_pred cCCCC
Q 003298 829 DDPWQ 833 (833)
Q Consensus 829 DvPWe 833 (833)
||||+
T Consensus 187 D~PW~ 191 (215)
T PF02309_consen 187 DVPWE 191 (215)
T ss_dssp -----
T ss_pred CCCHH
Confidence 99996
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=4.5e-17 Score=144.49 Aligned_cols=97 Identities=28% Similarity=0.409 Sum_probs=74.9
Q ss_pred EEEeeccccCCCCCceeeecchhhhhCCCCCCCCCCCceEEEEEecCCCeEEEEEEEeCCCCceeecccchhhhhccCCc
Q 003298 128 FCKTLTASDTSTHGGFSVPRRAAEKVFPPLDYSQTPPAQELIARDLHDNEWKFRHIFRGQPKRHLLTTGWSVFVSAKRLV 207 (833)
Q Consensus 128 F~K~LT~SDV~~~GrfsVPk~~Ae~~FP~Ld~~~~~p~q~L~~~Dl~G~~W~FR~iyrg~pkrhlLTtGWs~FVr~K~L~ 207 (833)
|.|+|+++|+...++|.||+++++++. ++ ....+++.++|..|+.|.+++.|++.+++++|++||..||++++|+
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 1236789999999999999999999888899999999999999999
Q ss_pred CCCEEEEEEcc--CCcEEEEEEec
Q 003298 208 AGDSVLFIWNE--KNQLLLGIRRA 229 (833)
Q Consensus 208 aGDsVvF~R~e--~G~L~VGIRRa 229 (833)
+||.|+|.... ..++.|+|.|+
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 45569999986
No 4
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=99.31 E-value=1.9e-12 Score=150.31 Aligned_cols=148 Identities=20% Similarity=0.368 Sum_probs=118.1
Q ss_pred CcCCCEEEEEEccCCcEEEEEEecCCCCCC---------------------CCCCccCCCcccccHHHHHHHHHHcCCcE
Q 003298 206 LVAGDSVLFIWNEKNQLLLGIRRATRPQTV---------------------MPSSVLSSDSMHIGLLAAAAHAAATNSRF 264 (833)
Q Consensus 206 L~aGDsVvF~R~e~G~L~VGIRRa~r~~~~---------------------~pssv~s~~sm~~gvla~Aa~aaat~~~F 264 (833)
...||.|+.+|....+++-.+|+.+..-++ .|.+.-+-=.|.+.|+.-|.++ -+..|
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 468999999998666665555555442221 1223333336888888777744 46799
Q ss_pred EEEEcCCCCCCcceechHHHHHHHhcCCCcccCEEEEee--eccCcccceeeEEEEEeccCCCCCCCCCCceeeEEeeCC
Q 003298 265 TIFYNPRASPSEFVIPLAKYVKAVYHTRVSVGMRFRMLF--ETEESSVRRYMGTITGISDLDPVRWPNSHWRSVKVGWDE 342 (833)
Q Consensus 265 ~V~Y~PRas~sEFVVp~~kyvkA~~~~~ws~GMRFrM~f--EtEdss~rry~GTI~gv~d~Dp~rWP~S~WR~LqV~WDe 342 (833)
.+.|......++|+|.+..|..|+. ++|..+++||..+ ++||. -+||.|+|.++.+..| .+|+|+|+|+.|+||.
T Consensus 952 ~ltlpdlv~fpDFlV~rsrYd~AiQ-rnW~~~d~crvwwrda~~e~-g~WWeG~ils~~pksp-~fpdSpwery~v~~~~ 1028 (1113)
T KOG0644|consen 952 KLTLPDLVTFPDFLVERSRYDAAIQ-RNWTCRDKCRVWWRDAGEED-GAWWEGRILSVKPKSP-DFPDSPWERYIVRYDN 1028 (1113)
T ss_pred eeecccccCcchhhhhhhhHHHHHh-hccccccceeEEEccCCCcC-CceeeeeeeeccCCCC-CCCCCcceeEEEEecC
Confidence 9999999999999999999999986 7999999999988 33342 4899999999999877 8999999999999999
Q ss_pred CCCCCCCCCccccccccCCC
Q 003298 343 STAGERQPRVSLWEIEPLTT 362 (833)
Q Consensus 343 ~~~~~~~~RVSPWEIEpv~~ 362 (833)
.+ .+.-||||.|++..
T Consensus 1029 ~e----~~~~spwe~~~i~d 1044 (1113)
T KOG0644|consen 1029 TE----TELHSPWEMEPIPD 1044 (1113)
T ss_pred Cc----ccccCccccCCCcc
Confidence 97 57789999999987
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=98.21 E-value=7.4e-06 Score=81.11 Aligned_cols=89 Identities=25% Similarity=0.371 Sum_probs=60.2
Q ss_pred ceeEEEeeccccCCCCC----ceeeecchhhhhCCCCCC-CCCCCceEEEEEecCC--CeEEEEEEEeCC------CCce
Q 003298 125 TNYFCKTLTASDTSTHG----GFSVPRRAAEKVFPPLDY-SQTPPAQELIARDLHD--NEWKFRHIFRGQ------PKRH 191 (833)
Q Consensus 125 ~~lF~K~LT~SDV~~~G----rfsVPk~~Ae~~FP~Ld~-~~~~p~q~L~~~Dl~G--~~W~FR~iyrg~------pkrh 191 (833)
...|+|.|++.|++..| |+-|||..++..||.+.. +...|..+|.+++..| ..|+||+||.|+ .+.+
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 56899999999999775 799999999999998665 5566899999999888 459999999976 7778
Q ss_pred eec--ccchhhhhccCCcCCCEEEEE
Q 003298 192 LLT--TGWSVFVSAKRLVAGDSVLFI 215 (833)
Q Consensus 192 lLT--tGWs~FVr~K~L~aGDsVvF~ 215 (833)
.|| ++=..|.+. =..||.+||.
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 996 332333332 2478888886
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=97.78 E-value=4.3e-05 Score=72.69 Aligned_cols=81 Identities=22% Similarity=0.292 Sum_probs=63.9
Q ss_pred CCCceeEEEeeccccCCCC-CceeeecchhhhhCCCCCC------------CCCCCceEEEEEecCCCeEEEEEEEeCC-
Q 003298 122 KQPTNYFCKTLTASDTSTH-GGFSVPRRAAEKVFPPLDY------------SQTPPAQELIARDLHDNEWKFRHIFRGQ- 187 (833)
Q Consensus 122 ~~~~~lF~K~LT~SDV~~~-GrfsVPk~~Ae~~FP~Ld~------------~~~~p~q~L~~~Dl~G~~W~FR~iyrg~- 187 (833)
.++...|+|+|++||+..+ .||+||-..... ...|.. .....++.+.+.|..++.|..++..|..
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 4567899999999999966 899999886633 222311 1234688999999999999999999955
Q ss_pred --CCceeecccchhhhhc
Q 003298 188 --PKRHLLTTGWSVFVSA 203 (833)
Q Consensus 188 --pkrhlLTtGWs~FVr~ 203 (833)
.-.|+|++||..+|++
T Consensus 97 ~~~~~YvL~~gWn~VV~~ 114 (114)
T PF03754_consen 97 NGTSNYVLNSGWNKVVED 114 (114)
T ss_pred CCceEEEEEcChHhhccC
Confidence 5579999999999864
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=96.67 E-value=0.0046 Score=53.78 Aligned_cols=55 Identities=31% Similarity=0.569 Sum_probs=47.7
Q ss_pred EEEeccccceeeeccCCCCChHHHHHHHHHhhCCCCCCCCCCCCCeEEEEEeCCCCeEEecc
Q 003298 768 VKVHKSGSFGRSLDISKFSSYDELRSELARMFGLEGQLEDPQRSGWQLVFVDRENDVLLLGD 829 (833)
Q Consensus 768 VKV~m~G~iGRkiDL~~~~sY~eL~~~L~~MFg~~g~l~d~~~s~~~lvY~D~EgD~mLvGD 829 (833)
||++-.|.+=|.+.+..--+|++|+..++..|++. ...++|.|.|.||||..+.+
T Consensus 4 vK~~~~~~~~~~~~~~~~~s~~~L~~~i~~~~~~~-------~~~~~l~Y~D~dgD~V~i~s 58 (84)
T PF00564_consen 4 VKVRYGGDIRRIISLPSDVSFDDLRSKIREKFGLL-------DEDFQLKYKDEDGDLVTISS 58 (84)
T ss_dssp EEEEETTEEEEEEEECSTSHHHHHHHHHHHHHTTS-------TSSEEEEEEETTSSEEEESS
T ss_pred EEEEECCeeEEEEEcCCCCCHHHHHHHHHHHhCCC-------CccEEEEeeCCCCCEEEeCC
Confidence 78888886666788888889999999999999986 24699999999999998764
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=95.81 E-value=0.029 Score=48.77 Aligned_cols=54 Identities=31% Similarity=0.596 Sum_probs=44.3
Q ss_pred EEEeccccceeeeccCCCCChHHHHHHHHHhhCCCCCCCCCCCCCeEEEEEeCCCCeEEecc
Q 003298 768 VKVHKSGSFGRSLDISKFSSYDELRSELARMFGLEGQLEDPQRSGWQLVFVDRENDVLLLGD 829 (833)
Q Consensus 768 VKV~m~G~iGRkiDL~~~~sY~eL~~~L~~MFg~~g~l~d~~~s~~~lvY~D~EgD~mLvGD 829 (833)
|||+- |.-=|.+-+..--+|++|+.++.+.|++.+ ..++|-|+|.||||..+.+
T Consensus 4 vK~~~-~~~~~~~~~~~~~s~~dL~~~i~~~~~~~~-------~~~~l~Y~Dedgd~v~l~s 57 (81)
T smart00666 4 VKLRY-GGETRRLSVPRDISFEDLRSKVAKRFGLDN-------QSFTLKYQDEDGDLVSLTS 57 (81)
T ss_pred EEEEE-CCEEEEEEECCCCCHHHHHHHHHHHhCCCC-------CCeEEEEECCCCCEEEecC
Confidence 56665 544577778888999999999999999753 4599999999999987754
No 9
>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=95.51 E-value=0.045 Score=49.46 Aligned_cols=54 Identities=24% Similarity=0.411 Sum_probs=41.6
Q ss_pred EEEeccccceeeeccCCCCChHHHHHHHHHhhCCCCCCCCCCCCCeEEEEEeCCCCeEEec
Q 003298 768 VKVHKSGSFGRSLDISKFSSYDELRSELARMFGLEGQLEDPQRSGWQLVFVDRENDVLLLG 828 (833)
Q Consensus 768 VKV~m~G~iGRkiDL~~~~sY~eL~~~L~~MFg~~g~l~d~~~s~~~lvY~D~EgD~mLvG 828 (833)
|||.-.|.+ +.+-+..--+|++|++++.++|++.. .++++|-|.|.||||.++-
T Consensus 3 vK~~~~~d~-~r~~l~~~~~~~~L~~~i~~r~~~~~------~~~f~LkY~Ddegd~v~lt 56 (82)
T cd06407 3 VKATYGEEK-IRFRLPPSWGFTELKQEIAKRFKLDD------MSAFDLKYLDDDEEWVLLT 56 (82)
T ss_pred EEEEeCCeE-EEEEcCCCCCHHHHHHHHHHHhCCCC------CCeeEEEEECCCCCeEEee
Confidence 677776642 33444455599999999999999851 3679999999999998763
No 10
>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=95.35 E-value=0.032 Score=51.14 Aligned_cols=49 Identities=27% Similarity=0.441 Sum_probs=38.5
Q ss_pred ceeee--ccCCCCChHHHHHHHHHhhCCCCCCCCCCCCCeEEEEEeCCCCeEEec
Q 003298 776 FGRSL--DISKFSSYDELRSELARMFGLEGQLEDPQRSGWQLVFVDRENDVLLLG 828 (833)
Q Consensus 776 iGRki--DL~~~~sY~eL~~~L~~MFg~~g~l~d~~~s~~~lvY~D~EgD~mLvG 828 (833)
-||.+ -+....|+.+|++++.+-||++.. ....++|.|.|.||||.|+-
T Consensus 9 ~GrvhRf~~~~s~~~~~L~~~I~~Rl~~d~~----~~~~~~L~YlDDEgD~VllT 59 (86)
T cd06409 9 KGRVHRFRLRPSESLEELRTLISQRLGDDDF----ETHLYALSYVDDEGDIVLIT 59 (86)
T ss_pred CCCEEEEEecCCCCHHHHHHHHHHHhCCccc----cCCcccEEEEcCCCCEEEEe
Confidence 44443 344478999999999999998742 24679999999999999863
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=95.29 E-value=0.052 Score=49.39 Aligned_cols=51 Identities=25% Similarity=0.375 Sum_probs=43.4
Q ss_pred EEEeccc-cceeeeccCCCCChHHHHHHHHHhhCCCCCCCCCCCCCeEEEEEeCCCCeEEe
Q 003298 768 VKVHKSG-SFGRSLDISKFSSYDELRSELARMFGLEGQLEDPQRSGWQLVFVDRENDVLLL 827 (833)
Q Consensus 768 VKV~m~G-~iGRkiDL~~~~sY~eL~~~L~~MFg~~g~l~d~~~s~~~lvY~D~EgD~mLv 827 (833)
|||.--| .+--+++-+.--+|.+|..+++++|++. .++|-|.|.||||.++
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 6777777 4555777766789999999999999987 4899999999999986
No 12
>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=95.17 E-value=0.071 Score=46.10 Aligned_cols=54 Identities=30% Similarity=0.613 Sum_probs=42.5
Q ss_pred EEEeccccceeeeccC-CCCChHHHHHHHHHhhCCCCCCCCCCCCCeEEEEEeCCCCeEEecc
Q 003298 768 VKVHKSGSFGRSLDIS-KFSSYDELRSELARMFGLEGQLEDPQRSGWQLVFVDRENDVLLLGD 829 (833)
Q Consensus 768 VKV~m~G~iGRkiDL~-~~~sY~eL~~~L~~MFg~~g~l~d~~~s~~~lvY~D~EgD~mLvGD 829 (833)
|||+-.|.+ |.+-+. .--+|++|+..|.+.|++.. ..+.+.|.|.||||..+.+
T Consensus 3 vK~~~~~~~-~~~~~~~~~~s~~~L~~~i~~~~~~~~-------~~~~l~y~D~e~d~v~l~s 57 (81)
T cd05992 3 VKVKYGGEI-RRFVVVSRSISFEDLRSKIAEKFGLDA-------VSFKLKYPDEDGDLVTISS 57 (81)
T ss_pred EEEEecCCC-EEEEEecCCCCHHHHHHHHHHHhCCCC-------CcEEEEeeCCCCCEEEeCC
Confidence 677766643 233333 88899999999999999863 4589999999999998865
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=48.56 Aligned_cols=56 Identities=27% Similarity=0.414 Sum_probs=43.7
Q ss_pred EEEecccc-ceeeeccC---CCCChHHHHHHHHHhhCCCCCCCCCCCCCeEEEEEeCCCCeEEecc
Q 003298 768 VKVHKSGS-FGRSLDIS---KFSSYDELRSELARMFGLEGQLEDPQRSGWQLVFVDRENDVLLLGD 829 (833)
Q Consensus 768 VKV~m~G~-iGRkiDL~---~~~sY~eL~~~L~~MFg~~g~l~d~~~s~~~lvY~D~EgD~mLvGD 829 (833)
|||.-+|. +==++++. .--+|++|+.++++.|.+.. ..+++|.|.|.||||..+-+
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 78888774 33345543 45799999999999998752 36799999999999998754
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=92.05 E-value=0.41 Score=43.63 Aligned_cols=53 Identities=23% Similarity=0.391 Sum_probs=42.6
Q ss_pred EEEecccccee-eeccCCCCChHHHHHHHHHhhCCCCCCCCCCCCCeEEEEEeCCCCeEEe
Q 003298 768 VKVHKSGSFGR-SLDISKFSSYDELRSELARMFGLEGQLEDPQRSGWQLVFVDRENDVLLL 827 (833)
Q Consensus 768 VKV~m~G~iGR-kiDL~~~~sY~eL~~~L~~MFg~~g~l~d~~~s~~~lvY~D~EgD~mLv 827 (833)
||.+-++.+=| ++|-....+|+|++.-|++|+.+.+ ..+.|-|.|.+||.+-+
T Consensus 3 VKSkfdaEfRRFsl~r~~~~~f~ef~~ll~~lH~l~~-------~~f~i~Y~D~~gDLLPI 56 (80)
T cd06403 3 VKSKFDAEFRRFSLDRNKPGKFEDFYKLLEHLHHIPN-------VDFLIGYTDPHGDLLPI 56 (80)
T ss_pred eecccCCeEEEEEeccccCcCHHHHHHHHHHHhCCCC-------CcEEEEEeCCCCCEecc
Confidence 56665555443 6777778999999999999999874 35999999999998854
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=90.90 E-value=0.59 Score=42.92 Aligned_cols=53 Identities=26% Similarity=0.355 Sum_probs=41.2
Q ss_pred EEEeccccce-eeeccCCCCChHHHHHHHHHhhCCCCCCCCCCCCCeEEEEEeCCCCeEEec
Q 003298 768 VKVHKSGSFG-RSLDISKFSSYDELRSELARMFGLEGQLEDPQRSGWQLVFVDRENDVLLLG 828 (833)
Q Consensus 768 VKV~m~G~iG-RkiDL~~~~sY~eL~~~L~~MFg~~g~l~d~~~s~~~lvY~D~EgD~mLvG 828 (833)
+|++-.|.|- -.+|. .-+|++|.+++..||.+. .+..+++.|.|.|||---+.
T Consensus 3 ~K~~y~gdi~it~~d~--~~s~e~L~~~v~~~c~~~------~~q~ft~kw~DEEGDp~tiS 56 (83)
T cd06404 3 VKAAYNGDIMITSIDP--SISLEELCNEVRDMCRFH------NDQPFTLKWIDEEGDPCTIS 56 (83)
T ss_pred EEEEecCcEEEEEcCC--CcCHHHHHHHHHHHhCCC------CCCcEEEEEECCCCCceeec
Confidence 6888888544 34444 788999999999999874 23569999999999975443
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=89.97 E-value=0.96 Score=41.42 Aligned_cols=57 Identities=21% Similarity=0.315 Sum_probs=40.9
Q ss_pred EEEeccccceeeeccCCCC-ChHHHHHHHHHhhCCCCCCCCCCCCCeEEEEEeCCCCeEEecc
Q 003298 768 VKVHKSGSFGRSLDISKFS-SYDELRSELARMFGLEGQLEDPQRSGWQLVFVDRENDVLLLGD 829 (833)
Q Consensus 768 VKV~m~G~iGRkiDL~~~~-sY~eL~~~L~~MFg~~g~l~d~~~s~~~lvY~D~EgD~mLvGD 829 (833)
+|+.-.|.|=| +-+..-. +|.+|+..+.+.|...- |....+.+-|.|.|||+.-+.+
T Consensus 3 iK~~~g~DiR~-~~~~~~~~t~~~L~~~v~~~F~~~~----~~~~~flIKYkD~dGDlVTIts 60 (81)
T cd06401 3 LKAQLGDDIRR-IPIHNEDITYDELLLMMQRVFRGKL----GSSDDVLIKYKDEDGDLITIFD 60 (81)
T ss_pred EEEEeCCeEEE-EeccCccccHHHHHHHHHHHhcccc----CCcccEEEEEECCCCCEEEecc
Confidence 56665555544 4444322 99999999999998431 3345699999999999987654
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=89.37 E-value=1.3 Score=40.96 Aligned_cols=56 Identities=27% Similarity=0.331 Sum_probs=42.0
Q ss_pred eEEEeccc----ccee--eeccCCCCChHHHHHHHHHhhCCCCCCCCCCCCCeEEEEEeCCCCeEEec
Q 003298 767 FVKVHKSG----SFGR--SLDISKFSSYDELRSELARMFGLEGQLEDPQRSGWQLVFVDRENDVLLLG 828 (833)
Q Consensus 767 fVKV~m~G----~iGR--kiDL~~~~sY~eL~~~L~~MFg~~g~l~d~~~s~~~lvY~D~EgD~mLvG 828 (833)
.||.|..| +==| +||-....+|++|+..+.++|... . +..++|-|.|.|||..-+.
T Consensus 2 ~vkayl~~~~~~~EIRRf~l~~~~~~s~~~L~~~V~~~f~~l---~---~~~ftlky~DeeGDlvtIs 63 (87)
T cd06402 2 TVKAYLLGKDANAEIRRFAIDEDVSTSYEYLVEKVAAVFPSL---R---GKNFQLFWKDEEGDLVAFS 63 (87)
T ss_pred eEEEeecCCCCccceEEEEecCCCCcCHHHHHHHHHHHcccc---C---CCcEEEEEECCCCCEEeec
Confidence 68888876 2224 445577779999999999999532 1 2579999999999987654
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=88.03 E-value=1.3 Score=40.63 Aligned_cols=53 Identities=19% Similarity=0.328 Sum_probs=41.8
Q ss_pred EEeccccceeeeccCCCCChHHHHHHHHHhhCCCCCCCCCCCCCeEEEEEeCCCCeEEecc
Q 003298 769 KVHKSGSFGRSLDISKFSSYDELRSELARMFGLEGQLEDPQRSGWQLVFVDRENDVLLLGD 829 (833)
Q Consensus 769 KV~m~G~iGRkiDL~~~~sY~eL~~~L~~MFg~~g~l~d~~~s~~~lvY~D~EgD~mLvGD 829 (833)
||+- |.--|++....-=+|.+|++.|..+|.+.. .+ ..|+|.|.|||..-+-|
T Consensus 4 Kv~~-~g~~RRf~~~~~pt~~~L~~kl~~Lf~lp~------~~-~~vtYiDeD~D~ITlss 56 (82)
T cd06397 4 KSSF-LGDTRRIVFPDIPTWEALASKLENLYNLPE------IK-VGVTYIDNDNDEITLSS 56 (82)
T ss_pred EEEe-CCceEEEecCCCccHHHHHHHHHHHhCCCh------hH-eEEEEEcCCCCEEEecc
Confidence 6633 444577777788899999999999999862 23 89999999999876654
No 19
>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=78.99 E-value=5.7 Score=36.84 Aligned_cols=53 Identities=23% Similarity=0.454 Sum_probs=43.1
Q ss_pred eEEEeccccceeeeccCCCCChHHHHHHHHHhhCCCCCCCCCCCCCeEEEEEeCCCCeEEecc
Q 003298 767 FVKVHKSGSFGRSLDISKFSSYDELRSELARMFGLEGQLEDPQRSGWQLVFVDRENDVLLLGD 829 (833)
Q Consensus 767 fVKV~m~G~iGRkiDL~~~~sY~eL~~~L~~MFg~~g~l~d~~~s~~~lvY~D~EgD~mLvGD 829 (833)
=|||+=.|. -|-|-+..--+|++|..++..+|++. ..++|-|.|. ||..-++|
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 478887675 45666667778999999999999984 2689999999 99987776
No 20
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=60.12 E-value=6.3 Score=48.85 Aligned_cols=67 Identities=25% Similarity=0.444 Sum_probs=45.8
Q ss_pred CCCCCCCEEEEecCcchhhhhcccccccc--ccCCCCCCCCCcceeeEeeeeeccCCCCcceeeeceeeeC
Q 003298 34 SLPPVGSRVVYFPQGHSEQVAASTNKEVD--AHIPNYPNLPPQLICQLHNLTMHADVETDEVYAQMTLQPL 102 (833)
Q Consensus 34 ~lP~vgs~V~YFPQGH~Eq~~as~~~~~~--~~~p~~~~lP~~i~C~V~~V~l~AD~~TDEVyAqi~L~P~ 102 (833)
-||..|..|.||-|||-|-+.+....+.+ -..| -++-..=+|.|..+..--=+-...-..+|+|.=+
T Consensus 872 yipQmgDEViyfrQghqeyl~~~~~n~~~~~~~~p--~~~~~v~~~kv~kl~~~~y~~~~~s~c~m~l~~i 940 (1113)
T KOG0644|consen 872 YIPQMGDEVIYFRQGHQEYLEAVRLNNIELNNKEP--WNKMAVEICKVEKLVYITYPGSGDSCCKMKLAVI 940 (1113)
T ss_pred ccccccceeehhhhhhHHHHhhhhhccccccccCc--ccccchhhheeeeeeeeeccCCCcchheeeeeee
Confidence 58999999999999999999886432222 1122 1444556788888876666666666666666543
No 21
>KOG3598 consensus Thyroid hormone receptor-associated protein complex, subunit TRAP230 [Transcription]
Probab=59.00 E-value=10 Score=49.47 Aligned_cols=11 Identities=36% Similarity=0.924 Sum_probs=4.5
Q ss_pred chhhhhccCCc
Q 003298 197 WSVFVSAKRLV 207 (833)
Q Consensus 197 Ws~FVr~K~L~ 207 (833)
|.-|--.|.+.
T Consensus 1724 wdlFEg~k~~a 1734 (2220)
T KOG3598|consen 1724 WDLFEGTKHLA 1734 (2220)
T ss_pred chhhccCCCCC
Confidence 44444444443
No 22
>PRK10737 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=55.56 E-value=30 Score=36.36 Aligned_cols=103 Identities=20% Similarity=0.233 Sum_probs=61.3
Q ss_pred CcCCCEEEE-E--EccCCcEEEEEEecCCCCCCCCCCccCCCcccccHHHHHHHHHHcCCcEEEEEcCCCCC------Cc
Q 003298 206 LVAGDSVLF-I--WNEKNQLLLGIRRATRPQTVMPSSVLSSDSMHIGLLAAAAHAAATNSRFTIFYNPRASP------SE 276 (833)
Q Consensus 206 L~aGDsVvF-~--R~e~G~L~VGIRRa~r~~~~~pssv~s~~sm~~gvla~Aa~aaat~~~F~V~Y~PRas~------sE 276 (833)
+..|+.|.+ | |.++|+++=.-+ . ..|...+--...-+--|.+|..-.+.|..|+|..-|-... .-
T Consensus 3 I~~~~vV~l~Y~l~~~dG~v~dst~-~-----~~Pl~~~~G~g~lipglE~aL~G~~~Gd~~~v~l~peeAyGe~d~~lV 76 (196)
T PRK10737 3 VAKDLVVSLAYQVRTEDGVLVDESP-V-----SAPLDYLHGHGSLISGLETALEGHEVGDKFDVAVGANDAYGQYDENLV 76 (196)
T ss_pred cCCCCEEEEEEEEEeCCCCEEEecC-C-----CCCeEEEeCCCcchHHHHHHHcCCCCCCEEEEEEChHHhcCCCChHHE
Confidence 456777776 3 346777533221 1 1233333222233334667777778889999987655433 23
Q ss_pred ceechHHHHHHHhcCCCcccCEEEEeeeccCcccceeeEEEEEecc
Q 003298 277 FVIPLAKYVKAVYHTRVSVGMRFRMLFETEESSVRRYMGTITGISD 322 (833)
Q Consensus 277 FVVp~~kyvkA~~~~~ws~GMRFrM~fEtEdss~rry~GTI~gv~d 322 (833)
..||++.|. .. ....+||||.+ ++++. ...++|+.|.+
T Consensus 77 ~~vpr~~F~-~~--~~l~~G~~~~~--~~~~G---~~~~~V~ev~~ 114 (196)
T PRK10737 77 QRVPKDVFM-GV--DELQVGMRFLA--ETDQG---PVPVEITAVED 114 (196)
T ss_pred EEecHHHCC-Cc--cCCCCCCEEEE--eCCCC---cEEEEEEEEcC
Confidence 567776552 22 24899999886 45553 46889999975
No 23
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=51.22 E-value=23 Score=29.46 Aligned_cols=38 Identities=13% Similarity=0.131 Sum_probs=29.3
Q ss_pred CCcccCEEEEeeeccCcccceeeEEEEEeccCCCCCCCCCCceeeEEeeCC
Q 003298 292 RVSVGMRFRMLFETEESSVRRYMGTITGISDLDPVRWPNSHWRSVKVGWDE 342 (833)
Q Consensus 292 ~ws~GMRFrM~fEtEdss~rry~GTI~gv~d~Dp~rWP~S~WR~LqV~WDe 342 (833)
.|++|+++-..++.++ .||.|+|+.+.. -..+.|.-+.
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 899999999964 1235677665
No 24
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=44.92 E-value=25 Score=32.82 Aligned_cols=29 Identities=21% Similarity=0.310 Sum_probs=23.9
Q ss_pred hhhccCCcCCCEEEEEEccCCcEEEEEEe
Q 003298 200 FVSAKRLVAGDSVLFIWNEKNQLLLGIRR 228 (833)
Q Consensus 200 FVr~K~L~aGDsVvF~R~e~G~L~VGIRR 228 (833)
|.-...|++||.|..+|.++|+.++-+-|
T Consensus 71 i~~~~~Lk~GD~V~ll~~~~gQ~yiVlDk 99 (100)
T PF10844_consen 71 ITFTDGLKVGDKVLLLRVQGGQKYIVLDK 99 (100)
T ss_pred EEEecCCcCCCEEEEEEecCCCEEEEEEe
Confidence 55677899999999999999987776543
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=44.21 E-value=70 Score=27.93 Aligned_cols=53 Identities=17% Similarity=0.246 Sum_probs=41.3
Q ss_pred ceEEEeccccc----eeeeccCCCCChHHHHHHHHHhhCCCCCCCCCCCCCeEEE-EEeCCCC
Q 003298 766 TFVKVHKSGSF----GRSLDISKFSSYDELRSELARMFGLEGQLEDPQRSGWQLV-FVDREND 823 (833)
Q Consensus 766 ~fVKV~m~G~i----GRkiDL~~~~sY~eL~~~L~~MFg~~g~l~d~~~s~~~lv-Y~D~EgD 823 (833)
.++||+....- -++|-++...+-.|++..+.+.|++.+ ....|.|+ +.-.+|-
T Consensus 3 ~~lrVy~~~~~~~~~~k~i~v~~~tTa~evi~~~l~k~~l~~-----~~~~y~L~~~~~~~~~ 60 (93)
T PF00788_consen 3 GVLRVYDGDGSPGSTYKTIKVSSSTTAREVIEMALEKFGLAE-----DPSDYCLVEVEESGGE 60 (93)
T ss_dssp EEEEEEETTSSSCCSEEEEEEETTSBHHHHHHHHHHHTTTSS-----SGGGEEEEEEECTTTE
T ss_pred eEEEEEcCCCCCCccEEEEEECCCCCHHHHHHHHHHHhCCCC-----CCCCEEEEEEEcCCCE
Confidence 58999998732 799999999999999999999999932 23569996 4444443
No 26
>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=43.73 E-value=32 Score=27.71 Aligned_cols=28 Identities=14% Similarity=0.127 Sum_probs=23.2
Q ss_pred hhhhccCCcCCCEEEEEEccCCcEEEEE
Q 003298 199 VFVSAKRLVAGDSVLFIWNEKNQLLLGI 226 (833)
Q Consensus 199 ~FVr~K~L~aGDsVvF~R~e~G~L~VGI 226 (833)
.|.++.+|++||.|.|.-.++|++.|--
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 5678889999999999998888666543
No 27
>KOG3207 consensus Beta-tubulin folding cofactor E [Posttranslational modification, protein turnover, chaperones]
Probab=42.70 E-value=24 Score=41.50 Aligned_cols=43 Identities=28% Similarity=0.679 Sum_probs=30.5
Q ss_pred CcccCEEEEeeeccCcccceeeEEEEEeccCCCCCCCCCCceeeEEeeCCCCCCCCC
Q 003298 293 VSVGMRFRMLFETEESSVRRYMGTITGISDLDPVRWPNSHWRSVKVGWDESTAGERQ 349 (833)
Q Consensus 293 ws~GMRFrM~fEtEdss~rry~GTI~gv~d~Dp~rWP~S~WR~LqV~WDe~~~~~~~ 349 (833)
..+|.|+|.-+|- ...||.|+|.|. ++ +| +.|.||++.-+.+.
T Consensus 3 ~~IG~RvkI~~~~---~Tvr~iG~V~g~--------~~-~w--~GvEWDd~~RGKH~ 45 (505)
T KOG3207|consen 3 MEIGTRVKIGGEI---ATVRYIGEVEGN--------NS-KW--YGVEWDDPVRGKHD 45 (505)
T ss_pred eeccceEEEcCEE---EEEEEEEEEcCC--------CC-cc--eeeEecCCCccccC
Confidence 5689999987643 236777777654 44 45 78999999877653
No 28
>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=35.09 E-value=61 Score=26.23 Aligned_cols=52 Identities=15% Similarity=0.214 Sum_probs=36.2
Q ss_pred CCcccCEEEEeeeccCcccceeeEEEEEeccCCCCCCCCCCceeeEEeeCCCCCCCCCCCccccccccC
Q 003298 292 RVSVGMRFRMLFETEESSVRRYMGTITGISDLDPVRWPNSHWRSVKVGWDESTAGERQPRVSLWEIEPL 360 (833)
Q Consensus 292 ~ws~GMRFrM~fEtEdss~rry~GTI~gv~d~Dp~rWP~S~WR~LqV~WDe~~~~~~~~RVSPWEIEpv 360 (833)
.|.+|..+...+ .+. .||.|+|+++.. + ..+.|.-++-+.. +-|...+|-++
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 588999999999 443 899999999974 2 4567887774422 34555555443
No 29
>TIGR01439 lp_hng_hel_AbrB looped-hinge helix DNA binding domain, AbrB family. This DNA-binding domain family includes AbrB, a transition state regulator in Bacillus subtilis, whose DNA-binding domain structure in solution was determined by NMR. The domain binds DNA as a dimer in what is termed a looped-hinge helix fold. Some members of the family have two copies of the domain in tandem. The domain is found usually at the N-terminus of a small protein. This model excludes members of family TIGR02609.
Probab=34.50 E-value=51 Score=25.26 Aligned_cols=26 Identities=23% Similarity=0.288 Sum_probs=22.3
Q ss_pred hhhhccCCcCCCEEEEEEccCCcEEE
Q 003298 199 VFVSAKRLVAGDSVLFIWNEKNQLLL 224 (833)
Q Consensus 199 ~FVr~K~L~aGDsVvF~R~e~G~L~V 224 (833)
.|.++-+++.||.|.+...++|.+.+
T Consensus 14 ~~r~~l~~~~gd~~~i~~~~~~~l~l 39 (43)
T TIGR01439 14 EIREKLGLKEGDRLEVIRVEDGEIIL 39 (43)
T ss_pred HHHHHcCcCCCCEEEEEEeCCCEEEE
Confidence 68899999999999999877776655
No 30
>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=30.04 E-value=1.2e+02 Score=26.18 Aligned_cols=42 Identities=12% Similarity=0.082 Sum_probs=27.4
Q ss_pred CcccCEEEEeeeccCcccceeeEEEEEeccCCCCCCCCCCceeeEEeeCCCC
Q 003298 293 VSVGMRFRMLFETEESSVRRYMGTITGISDLDPVRWPNSHWRSVKVGWDEST 344 (833)
Q Consensus 293 ws~GMRFrM~fEtEdss~rry~GTI~gv~d~Dp~rWP~S~WR~LqV~WDe~~ 344 (833)
+..|+++-..-+.+.....||.|||+.....+ .+.|+.++-.
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 46799999887666556799999999997521 7889986544
No 31
>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=28.99 E-value=87 Score=28.94 Aligned_cols=55 Identities=24% Similarity=0.295 Sum_probs=26.1
Q ss_pred HHHHHHHhcCCCcccCEEEEeeeccCcccceeeEEEEEeccCCCCCCCCCCceeeEEeeCCCC
Q 003298 282 AKYVKAVYHTRVSVGMRFRMLFETEESSVRRYMGTITGISDLDPVRWPNSHWRSVKVGWDEST 344 (833)
Q Consensus 282 ~kyvkA~~~~~ws~GMRFrM~fEtEdss~rry~GTI~gv~d~Dp~rWP~S~WR~LqV~WDe~~ 344 (833)
+.|..=+. .++++||++||.=.-|+-. .-=.|+|.-++. | .-| =-.+||.|-.-+
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-AGDEGEVFKQDR-D--GLH---DLNVQVDWQSKG 62 (78)
T ss_dssp HHHHHHHH-HH--TT-EEEESS-BTTB--TT-EEE-EEEE--T--TSS---E--EEEEETTTT
T ss_pred hHHHHHHH-HhCCCCcEEEEeccccccc-ccccceeEeecc-C--CCC---CcceEEEeeecC
Confidence 34444443 3689999999964334322 122677766654 1 112 235889997654
No 32
>PRK03760 hypothetical protein; Provisional
Probab=27.70 E-value=1.3e+02 Score=29.15 Aligned_cols=47 Identities=21% Similarity=0.371 Sum_probs=30.2
Q ss_pred EEEEEecCCCeEEEEE-----EEe-CCCCceee--cccchhhhhccCCcCCCEEEEEE
Q 003298 167 ELIARDLHDNEWKFRH-----IFR-GQPKRHLL--TTGWSVFVSAKRLVAGDSVLFIW 216 (833)
Q Consensus 167 ~L~~~Dl~G~~W~FR~-----iyr-g~pkrhlL--TtGWs~FVr~K~L~aGDsVvF~R 216 (833)
++.+.|.+|++=.... +|. ..+-+|+| ..||. .+.++++||.|.|.|
T Consensus 62 DiiFld~~g~Vv~i~~~~P~~~~~~~~~a~~VLEl~aG~~---~~~gi~~Gd~v~~~~ 116 (117)
T PRK03760 62 DVIFLDSNRRVVDFKTLKPWRIYVPKKPARYIIEGPVGKI---RVLKVEVGDEIEWID 116 (117)
T ss_pred EEEEECCCCeEEEEEeCCCccccCCCccceEEEEeCCChH---HHcCCCCCCEEEEee
Confidence 4666665554333211 122 34556888 67765 889999999999876
No 33
>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=27.58 E-value=1e+02 Score=29.13 Aligned_cols=39 Identities=28% Similarity=0.308 Sum_probs=32.6
Q ss_pred eccCCCCChHHHHHHHHHhhCCCCCCCCCCCCCeEEEEEeCCCCeEEe
Q 003298 780 LDISKFSSYDELRSELARMFGLEGQLEDPQRSGWQLVFVDRENDVLLL 827 (833)
Q Consensus 780 iDL~~~~sY~eL~~~L~~MFg~~g~l~d~~~s~~~lvY~D~EgD~mLv 827 (833)
=||+.--+|.+|..-..+-|+.+ +-.|-|.|.|||..-+
T Consensus 22 e~l~~~P~~kdLl~lmr~~f~~~---------dIaLNYrD~EGDLIRl 60 (92)
T cd06399 22 EDLSSTPLLKDLLELTRREFQRE---------DIALNYRDAEGDLIRL 60 (92)
T ss_pred cccccCccHHHHHHHHHHHhchh---------heeeeeecCCCCEEEE
Confidence 37788889999999999999865 2689999999997644
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=26.89 E-value=60 Score=31.45 Aligned_cols=26 Identities=31% Similarity=0.543 Sum_probs=17.8
Q ss_pred cCCcCCCEEEEEEcc-CCcEEEEEEec
Q 003298 204 KRLVAGDSVLFIWNE-KNQLLLGIRRA 229 (833)
Q Consensus 204 K~L~aGDsVvF~R~e-~G~L~VGIRRa 229 (833)
++++.||.|+||... ++.-+|||=+-
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 67778877654
No 35
>COG1047 SlpA FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]
Probab=25.96 E-value=3.1e+02 Score=28.72 Aligned_cols=105 Identities=19% Similarity=0.255 Sum_probs=63.4
Q ss_pred CCcCCCEEEEE---EccCCcEEEEEEecCCCCCCCCCCccCCCcccccHHHHHHHHHHcCCcEEEEEcCCCCCCcc----
Q 003298 205 RLVAGDSVLFI---WNEKNQLLLGIRRATRPQTVMPSSVLSSDSMHIGLLAAAAHAAATNSRFTIFYNPRASPSEF---- 277 (833)
Q Consensus 205 ~L~aGDsVvF~---R~e~G~L~VGIRRa~r~~~~~pssv~s~~sm~~gvla~Aa~aaat~~~F~V~Y~PRas~sEF---- 277 (833)
++..||.|.+. |.++|+++=--. . ..-|..++-.+..-+.-|.+|.....-|..|+|.--|-..-.|+
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 45677887763 334554432111 1 01122233223333344778888888999999998887655454
Q ss_pred --eechHHHHHHHhcCCCcccCEEEEeeeccCcccceeeEEEEEecc
Q 003298 278 --VIPLAKYVKAVYHTRVSVGMRFRMLFETEESSVRRYMGTITGISD 322 (833)
Q Consensus 278 --VVp~~kyvkA~~~~~ws~GMRFrM~fEtEdss~rry~GTI~gv~d 322 (833)
.||+++|.+.- ...+||+|.+ ++++ .-.-|+|+.|..
T Consensus 77 vq~vp~~~F~~~~---~~~vGm~~~~--~~~~---~~~~~~V~~V~~ 115 (174)
T COG1047 77 VQRVPRDEFQGVG---ELEVGMEVEA--EGGD---GEIPGVVTEVSG 115 (174)
T ss_pred eEEecHHHhCcCC---CCCCCcEEEE--cCCC---ceeeEEEEEEcC
Confidence 46666543321 5899999874 5555 456899999974
No 36
>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=25.19 E-value=1.2e+02 Score=25.94 Aligned_cols=31 Identities=19% Similarity=0.370 Sum_probs=24.2
Q ss_pred ccCEEEEeeeccCcccceeeEEEEEeccCCC
Q 003298 295 VGMRFRMLFETEESSVRRYMGTITGISDLDP 325 (833)
Q Consensus 295 ~GMRFrM~fEtEdss~rry~GTI~gv~d~Dp 325 (833)
+|-|+.-.||.++.++..|.|+|...-+..|
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 5889999999998888889999999887654
No 37
>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=24.04 E-value=3e+02 Score=23.35 Aligned_cols=38 Identities=13% Similarity=0.121 Sum_probs=22.9
Q ss_pred EEEEEecCCCeEEEEEEEeCCCCceeecccchhhhhccCCcCCCEEEEEEc
Q 003298 167 ELIARDLHDNEWKFRHIFRGQPKRHLLTTGWSVFVSAKRLVAGDSVLFIWN 217 (833)
Q Consensus 167 ~L~~~Dl~G~~W~FR~iyrg~pkrhlLTtGWs~FVr~K~L~aGDsVvF~R~ 217 (833)
...+++..|. .++|..||+-|+ +...+.+||.|.|...
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 3445666676 445555544221 2334899999999854
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=23.54 E-value=69 Score=27.08 Aligned_cols=17 Identities=24% Similarity=0.542 Sum_probs=14.8
Q ss_pred EEEEEeCCCCeEEeccC
Q 003298 814 QLVFVDRENDVLLLGDD 830 (833)
Q Consensus 814 ~lvY~D~EgD~mLvGDv 830 (833)
.++|.|.+|+.+++|+.
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 39
>PF06003 SMN: Survival motor neuron protein (SMN); InterPro: IPR010304 This family consists of several eukaryotic survival motor neuron (SMN) proteins. The Survival of Motor Neurons (SMN) protein, the product of the spinal muscular atrophy-determining gene, is part of a large macromolecular complex (SMN complex) that functions in the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs). The SMN complex functions as a specificity factor essential for the efficient assembly of Sm proteins on U snRNAs and likely protects cells from illicit, and potentially deleterious, non-specific binding of Sm proteins to RNAs.; GO: 0003723 RNA binding, 0006397 mRNA processing, 0005634 nucleus, 0005737 cytoplasm; PDB: 1MHN_A 4A4G_A 3S6N_M 4A4E_A 1G5V_A 4A4H_A 4A4F_A 2D9T_A.
Probab=21.29 E-value=93 Score=33.98 Aligned_cols=56 Identities=20% Similarity=0.328 Sum_probs=32.9
Q ss_pred CCCcccCEEEEeeeccCcccceeeEEEEEeccCCCCCCCCCCceeeEEeeCCCCCCCCCCCccccccccCC
Q 003298 291 TRVSVGMRFRMLFETEESSVRRYMGTITGISDLDPVRWPNSHWRSVKVGWDESTAGERQPRVSLWEIEPLT 361 (833)
Q Consensus 291 ~~ws~GMRFrM~fEtEdss~rry~GTI~gv~d~Dp~rWP~S~WR~LqV~WDe~~~~~~~~RVSPWEIEpv~ 361 (833)
..|.+|++.+..+..|. .+|-+||++|..-+ ....|+-++=+ +.+.|+.=+|.+..
T Consensus 67 ~~WkvGd~C~A~~s~Dg---~~Y~A~I~~i~~~~---------~~~~V~f~gYg---n~e~v~l~dL~~~~ 122 (264)
T PF06003_consen 67 KKWKVGDKCMAVYSEDG---QYYPATIESIDEED---------GTCVVVFTGYG---NEEEVNLSDLKPSE 122 (264)
T ss_dssp T---TT-EEEEE-TTTS---SEEEEEEEEEETTT---------TEEEEEETTTT---EEEEEEGGGEEETT
T ss_pred cCCCCCCEEEEEECCCC---CEEEEEEEEEcCCC---------CEEEEEEcccC---CeEeeehhhhcccc
Confidence 58999999999995444 68999999997522 13348877654 23445554544443
No 40
>cd04491 SoSSB_OBF SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB). SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is limiting, and supporting transcription when TBP is absent. SSoSSB selectively melts the duplex DNA of promoter sequences. It also relieves transcriptional repression by the chromatin Alba. In addition, SSoSSB activates reverse gyrase activity, which involves DNA binding, DNA cleavage, strand passage and ligation. SSoSSB stimulates all these steps in the presence of the chromatin protein, Sul7d. SSoSSB antagonizes the inhibitory effect of Sul7d on reverse gyrase supercoiling activity. It also physically and functionally interacts with Mini-chromosome Maintenance (MCM), stimulating
Probab=20.61 E-value=5e+02 Score=22.70 Aligned_cols=49 Identities=20% Similarity=0.201 Sum_probs=34.7
Q ss_pred CceEEEEEecCCCeEEEEEEEeCCCCceeecccchhhhhccCCcCCCEEEEEE----ccCCcEEEEEEe
Q 003298 164 PAQELIARDLHDNEWKFRHIFRGQPKRHLLTTGWSVFVSAKRLVAGDSVLFIW----NEKNQLLLGIRR 228 (833)
Q Consensus 164 p~q~L~~~Dl~G~~W~FR~iyrg~pkrhlLTtGWs~FVr~K~L~aGDsVvF~R----~e~G~L~VGIRR 228 (833)
....+.+.|.+| ..++++|+..- ...|..||.|.+.. .-+|.+.+.+.+
T Consensus 23 ~~~~~~l~D~TG---~i~~~~W~~~~-------------~~~~~~G~vv~i~~~~v~~~~g~~ql~i~~ 75 (82)
T cd04491 23 KVQSGLVGDETG---TIRFTLWDEKA-------------ADDLEPGDVVRIENAYVREFNGRLELSVGK 75 (82)
T ss_pred EEEEEEEECCCC---EEEEEEECchh-------------cccCCCCCEEEEEeEEEEecCCcEEEEeCC
Confidence 467889999998 57778886431 34588999888762 246777776664
Done!