Query 002624
Match_columns 899
No_of_seqs 361 out of 810
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 03:48:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002624.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002624hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF06507 Auxin_resp: Auxin res 100.0 4.3E-35 9.3E-40 262.0 8.1 83 253-336 1-83 (83)
2 PF02309 AUX_IAA: AUX/IAA fami 100.0 6.7E-35 1.5E-39 298.3 0.0 95 764-858 107-215 (215)
3 PF02362 B3: B3 DNA binding do 99.7 2.1E-16 4.6E-21 141.3 10.3 97 127-228 1-99 (100)
4 KOG0644 Uncharacterized conser 99.4 4.5E-13 9.7E-18 156.3 7.5 148 205-361 874-1044(1113)
5 PF09217 EcoRII-N: Restriction 98.4 1.5E-06 3.2E-11 86.6 9.9 90 124-214 7-110 (156)
6 PF03754 DUF313: Domain of unk 97.7 5.3E-05 1.2E-09 72.7 6.3 81 121-202 18-114 (114)
7 PF00564 PB1: PB1 domain; Int 96.9 0.0016 3.4E-08 57.2 5.3 66 769-841 4-70 (84)
8 smart00666 PB1 PB1 domain. Pho 96.0 0.022 4.8E-07 49.9 6.9 65 769-841 4-69 (81)
9 cd05992 PB1 The PB1 domain is 95.7 0.031 6.6E-07 48.8 6.5 65 769-841 3-69 (81)
10 cd06396 PB1_NBR1 The PB1 domai 95.5 0.038 8.2E-07 50.7 6.6 51 769-828 3-54 (81)
11 cd06407 PB1_NLP A PB1 domain i 95.4 0.054 1.2E-06 49.4 7.0 53 769-828 3-55 (82)
12 cd06409 PB1_MUG70 The MUG70 pr 94.9 0.049 1.1E-06 50.4 5.5 49 777-829 9-59 (86)
13 cd06398 PB1_Joka2 The PB1 doma 94.8 0.092 2E-06 48.8 7.0 66 769-842 3-72 (91)
14 cd06403 PB1_Par6 The PB1 domai 92.6 0.3 6.6E-06 44.8 6.0 66 769-841 3-70 (80)
15 cd06404 PB1_aPKC PB1 domain is 91.3 0.54 1.2E-05 43.6 6.1 52 769-828 3-55 (83)
16 cd06401 PB1_TFG The PB1 domain 90.6 0.76 1.7E-05 42.4 6.4 58 769-831 3-61 (81)
17 cd06402 PB1_p62 The PB1 domain 89.8 1.1 2.4E-05 41.7 6.9 57 767-829 1-63 (87)
18 cd06397 PB1_UP1 Uncharacterize 87.0 1.7 3.6E-05 40.3 5.9 61 770-838 4-65 (82)
19 cd06408 PB1_NoxR The PB1 domai 80.4 5.3 0.00012 37.3 6.4 54 767-830 3-56 (86)
20 cd06399 PB1_P40 The PB1 domain 77.4 3.7 8E-05 38.7 4.5 53 782-860 23-75 (92)
21 KOG0644 Uncharacterized conser 60.9 6.3 0.00014 49.2 2.9 67 34-102 872-940 (1113)
22 PRK10737 FKBP-type peptidyl-pr 56.0 27 0.00058 37.1 6.2 104 204-321 2-114 (196)
23 smart00743 Agenet Tudor-like d 48.4 27 0.00059 29.3 4.0 38 291-341 2-39 (61)
24 KOG3598 Thyroid hormone recept 44.8 4.2 9.1E-05 53.0 -2.0 9 239-247 1851-1859(2220)
25 KOG3207 Beta-tubulin folding c 39.2 28 0.0006 41.3 3.5 43 292-348 3-45 (505)
26 PF04014 Antitoxin-MazE: Antid 38.9 33 0.00071 27.9 3.0 39 185-226 4-42 (47)
27 PF00788 RA: Ras association ( 38.6 77 0.0017 27.9 5.5 65 767-836 3-74 (93)
28 PF10844 DUF2577: Protein of u 31.5 63 0.0014 30.5 4.0 27 199-225 71-97 (100)
29 cd06406 PB1_P67 A PB1 domain i 31.5 1.4E+02 0.003 27.9 6.0 65 768-841 4-69 (80)
30 smart00333 TUDOR Tudor domain. 30.7 80 0.0017 25.8 4.0 52 291-359 2-53 (57)
31 TIGR01439 lp_hng_hel_AbrB loop 27.9 59 0.0013 25.2 2.7 26 198-223 14-39 (43)
32 PF05641 Agenet: Agenet domain 27.4 1.5E+02 0.0032 26.0 5.3 42 292-343 1-42 (68)
33 COG1047 SlpA FKBP-type peptidy 27.3 2.6E+02 0.0056 29.6 7.9 105 204-321 2-115 (174)
34 PF01878 EVE: EVE domain; Int 27.1 59 0.0013 31.8 3.1 26 203-228 38-64 (143)
35 PF10411 DsbC_N: Disulfide bon 22.7 56 0.0012 27.9 1.8 17 815-831 34-50 (57)
36 PF02513 Spin-Ssty: Spin/Ssty 22.3 1.5E+02 0.0032 25.7 4.1 31 294-324 1-31 (50)
37 PF11515 Cul7: Mouse developme 21.5 1.5E+02 0.0032 27.8 4.2 55 281-343 8-62 (78)
38 cd05792 S1_eIF1AD_like S1_eIF1 21.0 70 0.0015 29.6 2.1 35 821-858 40-76 (78)
No 1
>PF06507 Auxin_resp: Auxin response factor; InterPro: IPR010525 This pattern represents a conserved region of auxin-responsive transcription factors. The plant hormone auxin (indole-3-acetic acid) can regulate the gene expression of several families, including Aux/IAA, GH3 and SAUR families. Two related families of proteins, Aux/IAA proteins (IPR003311 from INTERPRO) and the auxin response factors (ARF), are key regulators of auxin-modulated gene expression []. There are multiple ARF proteins, some of which activate, while others repress transcription. ARF proteins bind to auxin-responsive cis-acting promoter elements (AuxREs) using an N-terminal DNA-binding domain. It is thought that Aux/IAA proteins activate transcription by modifying ARF activity through the C-terminal protein-protein interaction domains (IPR011525 from INTERPRO) found in both Aux/IAA and ARF proteins. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0009725 response to hormone stimulus, 0005634 nucleus
Probab=100.00 E-value=4.3e-35 Score=262.01 Aligned_cols=83 Identities=65% Similarity=1.088 Sum_probs=81.2
Q ss_pred HHHHHHhCCcEEEEEcCCCCCCccccchHHHHHHHhcCCCcccCEEEEeeeccCcccceeeEEEEEeccCCCCCCCCCCc
Q 002624 253 AAHAAATNSRFTIFYNPRASPSEFVIPLAKYIKAVYHTRVSVGMRFRMLFETEESSVRRYMGTITGISDLDPVKWPNSHW 332 (899)
Q Consensus 253 Aa~aaat~~~F~V~Y~PRas~sEFVVp~~ky~ka~~~~~ws~GMRFkM~fEtEdss~rr~~GTI~gv~d~Dp~rWP~S~W 332 (899)
|||||+++++|+|+||||++++|||||++||++|+. ++|++||||||.||+||+++++|+|||+||+++||+|||+|+|
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 002624 333 RSVK 336 (899)
Q Consensus 333 R~Lq 336 (899)
||||
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=6.7e-35 Score=298.26 Aligned_cols=95 Identities=41% Similarity=0.734 Sum_probs=0.0
Q ss_pred CCcceEEEeecC-cceeeeccCCCCCHHHHHHHHHHHh---cCC----------CccCCCCCCccEEEEEcCCCceeecc
Q 002624 764 PNRTFVKVYKSG-SFGRSLDITKFSSYHELRSELARMF---GLE----------GHLEDPLRSGWQLVFVDRENDVLLLG 829 (899)
Q Consensus 764 ~~~~fVKV~m~G-~igRkIDL~~~~sY~eL~~~L~~MF---~~~----------g~l~d~~~s~~~lvYeD~EGD~mLvG 829 (899)
..++||||+||| +|||||||++|+||++|+.+|++|| ++. +.++...+++|+|||+|+||||||||
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 444 23344567899999999999999999
Q ss_pred CCCchhhhcceeEEEEeChhhhhcccccc
Q 002624 830 DGPWPEFVNSVWCIKILSPPEVQQMGKRG 858 (899)
Q Consensus 830 DvPWe~Fv~svkrirIl~~~e~~~m~~~~ 858 (899)
||||+|||++|||||||+.+|+++|++++
T Consensus 187 D~PW~~F~~~vkRl~I~~~~e~~~~~~r~ 215 (215)
T PF02309_consen 187 DVPWEEFVKSVKRLRIMKSSEAKGLAPRA 215 (215)
T ss_dssp -----------------------------
T ss_pred CCCHHHHHHHhhccEEecHHHhcccCCCC
Confidence 99999999999999999999999999874
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=99.67 E-value=2.1e-16 Score=141.30 Aligned_cols=97 Identities=28% Similarity=0.417 Sum_probs=74.9
Q ss_pred EEEeecccCCCCCCceeechhhhhhcCCCCCCCCCCCceEEEEeecCCCeeEEEEEEcCCCCceeecccccccccccCCc
Q 002624 127 FCKTLTASDTSTHGGFSVPRRAAEKVFPPLDFSQQPPAQELIARDLHDNEWKFRHIFRGQPKRHLLTTGWSVFVSAKRLV 206 (899)
Q Consensus 127 F~K~LT~SDv~~~GrfsVPk~~AE~~FPpLd~~~~~p~q~L~v~D~~G~~W~FR~iyrg~prrhlLTtGWs~FV~~KkL~ 206 (899)
|.|+|+++|+...+++.||++.++.+. +. ...++.+.++|..|++|.+++.|++.+++++|++||..||++++|+
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 899999999999999999999999882 11 1236789999999999999999999888899999999999999999
Q ss_pred CCCEEEEEEcC--CCcEEEEEEec
Q 002624 207 AGDSVLFIWND--KNQLLLGIRRA 228 (899)
Q Consensus 207 aGDsVvF~R~~--~g~L~vGIRRa 228 (899)
+||.++|...+ ..++.|.|.|+
T Consensus 76 ~GD~~~F~~~~~~~~~~~v~i~~~ 99 (100)
T PF02362_consen 76 EGDVCVFELIGNSNFTLKVHIFRK 99 (100)
T ss_dssp TT-EEEEEE-SSSCE-EEEEEE--
T ss_pred CCCEEEEEEecCCCceEEEEEEEC
Confidence 99999999865 45569999886
No 4
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=99.38 E-value=4.5e-13 Score=156.30 Aligned_cols=148 Identities=22% Similarity=0.379 Sum_probs=120.7
Q ss_pred CcCCCEEEEEEcCCCcEEEEEEecCCCCCC---------------------CCCCcccCCccccchHHHHHHHHHhCCcE
Q 002624 205 LVAGDSVLFIWNDKNQLLLGIRRANRPPTV---------------------MPSSVLSSDSMHLGLLAAAAHAAATNSRF 263 (899)
Q Consensus 205 L~aGDsVvF~R~~~g~L~vGIRRa~r~~~~---------------------~pssv~ss~sm~~gvla~Aa~aaat~~~F 263 (899)
.+.||.|+++|.+..++.-.+|+.++.-++ .|.+.-+--.|.+.++.-|.++ -+..|
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 358999999998777776666666543221 1223334446889999887755 56899
Q ss_pred EEEEcCCCCCCccccchHHHHHHHhcCCCcccCEEEEee--eccCcccceeeEEEEEeccCCCCCCCCCCceeeEEeeCC
Q 002624 264 TIFYNPRASPSEFVIPLAKYIKAVYHTRVSVGMRFRMLF--ETEESSVRRYMGTITGISDLDPVKWPNSHWRSVKVGWDE 341 (899)
Q Consensus 264 ~V~Y~PRas~sEFVVp~~ky~ka~~~~~ws~GMRFkM~f--EtEdss~rr~~GTI~gv~d~Dp~rWP~S~WR~LqV~WDe 341 (899)
.+.|......++|+|.+..|..|+. ++|..++|||..+ ++||. -+||.|+|.++.+..| .+|+|+|.|+.|+||.
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 8999999999988 34443 3899999999999887 8999999999999999
Q ss_pred CCCCCCCCCcccCccccCCC
Q 002624 342 STAGERQPRVSLWEIEPLTT 361 (899)
Q Consensus 342 ~~~~~~~~RVSPWeIEpv~~ 361 (899)
.+ .+.-||||.|++..
T Consensus 1029 ~e----~~~~spwe~~~i~d 1044 (1113)
T KOG0644|consen 1029 TE----TELHSPWEMEPIPD 1044 (1113)
T ss_pred Cc----ccccCccccCCCcc
Confidence 97 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=98.40 E-value=1.5e-06 Score=86.65 Aligned_cols=90 Identities=24% Similarity=0.403 Sum_probs=60.3
Q ss_pred ceeEEEeecccCCCCCC----ceeechhhhhhcCCCCCC-CCCCCceEEEEeecCC--CeeEEEEEEcCC------CCce
Q 002624 124 TNYFCKTLTASDTSTHG----GFSVPRRAAEKVFPPLDF-SQQPPAQELIARDLHD--NEWKFRHIFRGQ------PKRH 190 (899)
Q Consensus 124 ~~lF~K~LT~SDv~~~G----rfsVPk~~AE~~FPpLd~-~~~~p~q~L~v~D~~G--~~W~FR~iyrg~------prrh 190 (899)
...|+|.|++.|++..| |+-|||..++.+||.|.. +..+|...|.+++..| ..|+||+||.|+ +..|
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 799999999999998765 7778999999999988 468999999977 6778
Q ss_pred eecccccccccccC-CcCCCEEEEE
Q 002624 191 LLTTGWSVFVSAKR-LVAGDSVLFI 214 (899)
Q Consensus 191 lLTtGWs~FV~~Kk-L~aGDsVvF~ 214 (899)
.|| .|...-+--+ =..||.+||-
T Consensus 87 RIT-~~G~~~~~~~~~~tGaL~vla 110 (156)
T PF09217_consen 87 RIT-RFGRGFPLQNPENTGALLVLA 110 (156)
T ss_dssp EEE----TTSGGG-GGGTT-EEEEE
T ss_pred EEe-eecCCCccCCccccccEEEEE
Confidence 996 3433222111 2478888875
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=97.75 E-value=5.3e-05 Score=72.68 Aligned_cols=81 Identities=22% Similarity=0.293 Sum_probs=63.6
Q ss_pred CCCceeEEEeecccCCCCC-CceeechhhhhhcCCCCCC------------CCCCCceEEEEeecCCCeeEEEEEEcCC-
Q 002624 121 KQPTNYFCKTLTASDTSTH-GGFSVPRRAAEKVFPPLDF------------SQQPPAQELIARDLHDNEWKFRHIFRGQ- 186 (899)
Q Consensus 121 ~~~~~lF~K~LT~SDv~~~-GrfsVPk~~AE~~FPpLd~------------~~~~p~q~L~v~D~~G~~W~FR~iyrg~- 186 (899)
.++...++|+|++|||..+ .||+||-..... ...|.. ....-+..+.+.|..++.|..++..|..
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 899999875532 223321 1234588999999999999999999954
Q ss_pred --CCceeecccccccccc
Q 002624 187 --PKRHLLTTGWSVFVSA 202 (899)
Q Consensus 187 --prrhlLTtGWs~FV~~ 202 (899)
.-.|+|++||..+|+.
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=96.91 E-value=0.0016 Score=57.18 Aligned_cols=66 Identities=26% Similarity=0.437 Sum_probs=54.6
Q ss_pred EEEeecCcceeeeccCCCCCHHHHHHHHHHHhcCCCccCCCCCCccEEEEEcCCCceeeccC-CCchhhhccee
Q 002624 769 VKVYKSGSFGRSLDITKFSSYHELRSELARMFGLEGHLEDPLRSGWQLVFVDRENDVLLLGD-GPWPEFVNSVW 841 (899)
Q Consensus 769 VKV~m~G~igRkIDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLvGD-vPWe~Fv~svk 841 (899)
||++-.|.+=|.+.+..--+|++|+..+++.|+.. ...+.|.|.|.||||..+-+ .=|++.++.++
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 78988887666788888889999999999999986 34699999999999988864 44777666654
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=96.00 E-value=0.022 Score=49.95 Aligned_cols=65 Identities=29% Similarity=0.473 Sum_probs=50.5
Q ss_pred EEEeecCcceeeeccCCCCCHHHHHHHHHHHhcCCCccCCCCCCccEEEEEcCCCceeecc-CCCchhhhccee
Q 002624 769 VKVYKSGSFGRSLDITKFSSYHELRSELARMFGLEGHLEDPLRSGWQLVFVDRENDVLLLG-DGPWPEFVNSVW 841 (899)
Q Consensus 769 VKV~m~G~igRkIDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLvG-DvPWe~Fv~svk 841 (899)
|||.- |.--|.+-+..--+|++|++.+.+.|+..+ ..+.|-|.|.||||..+. |.=|++.+..++
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 555677888889999999999999999643 469999999999998654 455666555544
No 9
>cd05992 PB1 The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as a noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.
Probab=95.71 E-value=0.031 Score=48.78 Aligned_cols=65 Identities=26% Similarity=0.496 Sum_probs=49.1
Q ss_pred EEEeecCcceeeeccC-CCCCHHHHHHHHHHHhcCCCccCCCCCCccEEEEEcCCCceeeccC-CCchhhhccee
Q 002624 769 VKVYKSGSFGRSLDIT-KFSSYHELRSELARMFGLEGHLEDPLRSGWQLVFVDRENDVLLLGD-GPWPEFVNSVW 841 (899)
Q Consensus 769 VKV~m~G~igRkIDL~-~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLvGD-vPWe~Fv~svk 841 (899)
|||+-.|-+ |.+-+. .--+|++|+..|.+.|+... ..+.+.|.|.||||..+.+ .=|++.++.++
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 688777643 333333 88899999999999999753 3589999999999998877 55655555544
No 10
>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=95.55 E-value=0.038 Score=50.66 Aligned_cols=51 Identities=24% Similarity=0.357 Sum_probs=44.4
Q ss_pred EEEeecC-cceeeeccCCCCCHHHHHHHHHHHhcCCCccCCCCCCccEEEEEcCCCceeec
Q 002624 769 VKVYKSG-SFGRSLDITKFSSYHELRSELARMFGLEGHLEDPLRSGWQLVFVDRENDVLLL 828 (899)
Q Consensus 769 VKV~m~G-~igRkIDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLv 828 (899)
|||.-.| -+--+++-+.-.+|.+|..+++++|++. .+.|.|.|.||||.++
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 5666777777889999999999999986 4899999999999876
No 11
>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=95.36 E-value=0.054 Score=49.37 Aligned_cols=53 Identities=25% Similarity=0.400 Sum_probs=41.5
Q ss_pred EEEeecCcceeeeccCCCCCHHHHHHHHHHHhcCCCccCCCCCCccEEEEEcCCCceeec
Q 002624 769 VKVYKSGSFGRSLDITKFSSYHELRSELARMFGLEGHLEDPLRSGWQLVFVDRENDVLLL 828 (899)
Q Consensus 769 VKV~m~G~igRkIDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLv 828 (899)
|||.-.|. -+.+-|..--+|++|++++.++|++. ..++|.|-|.|.||||.++
T Consensus 3 vK~~~~~d-~~r~~l~~~~~~~~L~~~i~~r~~~~------~~~~f~LkY~Ddegd~v~l 55 (82)
T cd06407 3 VKATYGEE-KIRFRLPPSWGFTELKQEIAKRFKLD------DMSAFDLKYLDDDEEWVLL 55 (82)
T ss_pred EEEEeCCe-EEEEEcCCCCCHHHHHHHHHHHhCCC------CCCeeEEEEECCCCCeEEe
Confidence 78888774 23344444559999999999999974 1357999999999999876
No 12
>cd06409 PB1_MUG70 The MUG70 protein is a product of the meiotically up-regulated gene 70 which has a role in meiosis and harbors a PB1 domain. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domains depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic amino acid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is
Probab=94.93 E-value=0.049 Score=50.39 Aligned_cols=49 Identities=27% Similarity=0.411 Sum_probs=38.5
Q ss_pred ceeee--ccCCCCCHHHHHHHHHHHhcCCCccCCCCCCccEEEEEcCCCceeecc
Q 002624 777 FGRSL--DITKFSSYHELRSELARMFGLEGHLEDPLRSGWQLVFVDRENDVLLLG 829 (899)
Q Consensus 777 igRkI--DL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLvG 829 (899)
-||.+ -+....|+.+|.+++.+-|+.+.. ....|+|.|.|.||||.|+-
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 45543 344478999999999999998643 24579999999999998863
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=94.82 E-value=0.092 Score=48.84 Aligned_cols=66 Identities=21% Similarity=0.346 Sum_probs=49.3
Q ss_pred EEEeecCc-ceeeeccC---CCCCHHHHHHHHHHHhcCCCccCCCCCCccEEEEEcCCCceeeccCCCchhhhcceeE
Q 002624 769 VKVYKSGS-FGRSLDIT---KFSSYHELRSELARMFGLEGHLEDPLRSGWQLVFVDRENDVLLLGDGPWPEFVNSVWC 842 (899)
Q Consensus 769 VKV~m~G~-igRkIDL~---~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLvGDvPWe~Fv~svkr 842 (899)
|||.-+|. +=-++++. .--+|++|+.++++.|.+. ...+++|.|.|.||||..+-++ +++..++.+
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 VKVKYGGTLRRFTFPVAENQLDLNMDGLREKVEELFSLS------PDADLSLTYTDEDGDVVTLVDD--NDLTDAIQY 72 (91)
T ss_pred EEEEeCCEEEEEEeccccccCCCCHHHHHHHHHHHhCCC------CCCcEEEEEECCCCCEEEEccH--HHHHHHHHH
Confidence 79998884 44455553 4579999999999999874 2357999999999999988443 455555544
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=92.65 E-value=0.3 Score=44.84 Aligned_cols=66 Identities=21% Similarity=0.317 Sum_probs=49.3
Q ss_pred EEEeecCccee-eeccCCCCCHHHHHHHHHHHhcCCCccCCCCCCccEEEEEcCCCceeecc-CCCchhhhccee
Q 002624 769 VKVYKSGSFGR-SLDITKFSSYHELRSELARMFGLEGHLEDPLRSGWQLVFVDRENDVLLLG-DGPWPEFVNSVW 841 (899)
Q Consensus 769 VKV~m~G~igR-kIDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLvG-DvPWe~Fv~svk 841 (899)
||.+-++.+-| ++|-....+|+|+++-|++|+.+.+ ..++|-|.|.+||.+=+- |+-...-+.+++
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 6777778999999999999999864 359999999999998653 445554445554
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=91.28 E-value=0.54 Score=43.58 Aligned_cols=52 Identities=27% Similarity=0.309 Sum_probs=41.2
Q ss_pred EEEeecCc-ceeeeccCCCCCHHHHHHHHHHHhcCCCccCCCCCCccEEEEEcCCCceeec
Q 002624 769 VKVYKSGS-FGRSLDITKFSSYHELRSELARMFGLEGHLEDPLRSGWQLVFVDRENDVLLL 828 (899)
Q Consensus 769 VKV~m~G~-igRkIDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLv 828 (899)
+|++-.|. .--.+|. ..+|++|.+++.+||... .+..+++.|.|.|||---+
T Consensus 3 ~K~~y~gdi~it~~d~--~~s~e~L~~~v~~~c~~~------~~q~ft~kw~DEEGDp~ti 55 (83)
T cd06404 3 VKAAYNGDIMITSIDP--SISLEELCNEVRDMCRFH------NDQPFTLKWIDEEGDPCTI 55 (83)
T ss_pred EEEEecCcEEEEEcCC--CcCHHHHHHHHHHHhCCC------CCCcEEEEEECCCCCceee
Confidence 78888994 4444555 778999999999999973 2346999999999997544
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=90.64 E-value=0.76 Score=42.42 Aligned_cols=58 Identities=19% Similarity=0.259 Sum_probs=42.7
Q ss_pred EEEeecCcceeeeccCCCC-CHHHHHHHHHHHhcCCCccCCCCCCccEEEEEcCCCceeeccCC
Q 002624 769 VKVYKSGSFGRSLDITKFS-SYHELRSELARMFGLEGHLEDPLRSGWQLVFVDRENDVLLLGDG 831 (899)
Q Consensus 769 VKV~m~G~igRkIDL~~~~-sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLvGDv 831 (899)
+|+.-.|.|=| +-+..-. +|.+|+..+.+.|... -|....+.+.|.|.|||+.-+.+.
T Consensus 3 iK~~~g~DiR~-~~~~~~~~t~~~L~~~v~~~F~~~----~~~~~~flIKYkD~dGDlVTIts~ 61 (81)
T cd06401 3 LKAQLGDDIRR-IPIHNEDITYDELLLMMQRVFRGK----LGSSDDVLIKYKDEDGDLITIFDS 61 (81)
T ss_pred EEEEeCCeEEE-EeccCccccHHHHHHHHHHHhccc----cCCcccEEEEEECCCCCEEEeccH
Confidence 56666555544 4444322 9999999999999953 133456999999999999988775
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=89.83 E-value=1.1 Score=41.74 Aligned_cols=57 Identities=28% Similarity=0.332 Sum_probs=43.1
Q ss_pred ceEEEeecC----cceeee--ccCCCCCHHHHHHHHHHHhcCCCccCCCCCCccEEEEEcCCCceeecc
Q 002624 767 TFVKVYKSG----SFGRSL--DITKFSSYHELRSELARMFGLEGHLEDPLRSGWQLVFVDRENDVLLLG 829 (899)
Q Consensus 767 ~fVKV~m~G----~igRkI--DL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLvG 829 (899)
..||.|..| +=-|++ |-....+|++|+..+.++|..- .+..+++.|.|.|||..-+.
T Consensus 1 ~~vkayl~~~~~~~EIRRf~l~~~~~~s~~~L~~~V~~~f~~l------~~~~ftlky~DeeGDlvtIs 63 (87)
T cd06402 1 LTVKAYLLGKDANAEIRRFAIDEDVSTSYEYLVEKVAAVFPSL------RGKNFQLFWKDEEGDLVAFS 63 (87)
T ss_pred CeEEEeecCCCCccceEEEEecCCCCcCHHHHHHHHHHHcccc------CCCcEEEEEECCCCCEEeec
Confidence 368888877 344544 4467779999999999999542 12469999999999986543
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=87.00 E-value=1.7 Score=40.31 Aligned_cols=61 Identities=20% Similarity=0.353 Sum_probs=45.0
Q ss_pred EEeecCcceeeeccCCCCCHHHHHHHHHHHhcCCCccCCCCCCccEEEEEcCCCceeec-cCCCchhhhc
Q 002624 770 KVYKSGSFGRSLDITKFSSYHELRSELARMFGLEGHLEDPLRSGWQLVFVDRENDVLLL-GDGPWPEFVN 838 (899)
Q Consensus 770 KV~m~G~igRkIDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLv-GDvPWe~Fv~ 838 (899)
||.-.| --|++....-=+|.+|++.|+.+|.+.. .+ +.++|.|.|||..-+ -|+=-++|.+
T Consensus 4 Kv~~~g-~~RRf~~~~~pt~~~L~~kl~~Lf~lp~------~~-~~vtYiDeD~D~ITlssd~eL~d~~~ 65 (82)
T cd06397 4 KSSFLG-DTRRIVFPDIPTWEALASKLENLYNLPE------IK-VGVTYIDNDNDEITLSSNKELQDFYR 65 (82)
T ss_pred EEEeCC-ceEEEecCCCccHHHHHHHHHHHhCCCh------hH-eEEEEEcCCCCEEEecchHHHHHHHH
Confidence 674444 4577778888899999999999999852 22 899999999998644 3444455544
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=80.35 E-value=5.3 Score=37.35 Aligned_cols=54 Identities=20% Similarity=0.380 Sum_probs=43.3
Q ss_pred ceEEEeecCcceeeeccCCCCCHHHHHHHHHHHhcCCCccCCCCCCccEEEEEcCCCceeeccC
Q 002624 767 TFVKVYKSGSFGRSLDITKFSSYHELRSELARMFGLEGHLEDPLRSGWQLVFVDRENDVLLLGD 830 (899)
Q Consensus 767 ~fVKV~m~G~igRkIDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLvGD 830 (899)
.=|||+-.|. .|-|-+..--+|++|...+..+|++. ..+++-|.|. ||..-++|
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 45666667778999999999999983 2689999999 99877765
No 20
>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=77.41 E-value=3.7 Score=38.69 Aligned_cols=53 Identities=26% Similarity=0.362 Sum_probs=45.5
Q ss_pred ccCCCCCHHHHHHHHHHHhcCCCccCCCCCCccEEEEEcCCCceeeccCCCchhhhcceeEEEEeChhhhhcccccccc
Q 002624 782 DITKFSSYHELRSELARMFGLEGHLEDPLRSGWQLVFVDRENDVLLLGDGPWPEFVNSVWCIKILSPPEVQQMGKRGNE 860 (899)
Q Consensus 782 DL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLvGDvPWe~Fv~svkrirIl~~~e~~~m~~~~~~ 860 (899)
||+.--+|.+|..-..+-|..+ +-.|-|.|.|||. ||||+.+++.=|-+++..
T Consensus 23 ~l~~~P~~kdLl~lmr~~f~~~---------dIaLNYrD~EGDL-----------------IRllddeDv~LMV~~~r~ 75 (92)
T cd06399 23 DLSSTPLLKDLLELTRREFQRE---------DIALNYRDAEGDL-----------------IRLLSDEDVALMVRQSRG 75 (92)
T ss_pred ccccCccHHHHHHHHHHHhchh---------heeeeeecCCCCE-----------------EEEcchhhHHHHHHHHhc
Confidence 6778889999999999999864 3689999999996 799999999999887743
No 21
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=60.86 E-value=6.3 Score=49.22 Aligned_cols=67 Identities=22% Similarity=0.410 Sum_probs=48.4
Q ss_pred CCCCCCCEEEEecCcchhhhcccccccccc--cCCCCCCCCCcceeEEeeeeecccCCCcceeeeeeeeeC
Q 002624 34 SLPAVGSRVVYFPQGHSEQVAASTNKEVDA--HIPNYPSLPPQLICQLHNVTMHADIETDEVYAQMTLQPL 102 (899)
Q Consensus 34 ~lP~vgs~V~YFPQGH~Eq~~as~~~~~~~--~~p~~~~lP~~i~C~V~~V~l~AD~eTDEVyAqitL~P~ 102 (899)
-||..|..|.||-|||-|-+.+....+.+. -.| -++-..=+|.|..+..--=+-...-..+|+|.=+
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 589999999999999999998865333321 112 1445556799988877777777777777777655
No 22
>PRK10737 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=56.01 E-value=27 Score=37.08 Aligned_cols=104 Identities=18% Similarity=0.236 Sum_probs=61.7
Q ss_pred CCcCCCEEEE-E--EcCCCcEEEEEEecCCCCCCCCCCcccCCccccchHHHHHHHHHhCCcEEEEEcCCCCC------C
Q 002624 204 RLVAGDSVLF-I--WNDKNQLLLGIRRANRPPTVMPSSVLSSDSMHLGLLAAAAHAAATNSRFTIFYNPRASP------S 274 (899)
Q Consensus 204 kL~aGDsVvF-~--R~~~g~L~vGIRRa~r~~~~~pssv~ss~sm~~gvla~Aa~aaat~~~F~V~Y~PRas~------s 274 (899)
++..|+.|.+ | |.++|+++--- +. ..|...+-....-+--|.+|..-.+.|..|+|..-|-... .
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 KVAKDLVVSLAYQVRTEDGVLVDES-PV-----SAPLDYLHGHGSLISGLETALEGHEVGDKFDVAVGANDAYGQYDENL 75 (196)
T ss_pred ccCCCCEEEEEEEEEeCCCCEEEec-CC-----CCCeEEEeCCCcchHHHHHHHcCCCCCCEEEEEEChHHhcCCCChHH
Confidence 3456777776 3 35677764322 11 1233333222222334667777778889999987665433 2
Q ss_pred ccccchHHHHHHHhcCCCcccCEEEEeeeccCcccceeeEEEEEecc
Q 002624 275 EFVIPLAKYIKAVYHTRVSVGMRFRMLFETEESSVRRYMGTITGISD 321 (899)
Q Consensus 275 EFVVp~~ky~ka~~~~~ws~GMRFkM~fEtEdss~rr~~GTI~gv~d 321 (899)
-..||++.|. .. ....+||||.+ ++++. .+.++|+.|.+
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 3467777552 22 24899999886 45553 36889999975
No 23
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=48.38 E-value=27 Score=29.32 Aligned_cols=38 Identities=13% Similarity=0.131 Sum_probs=29.3
Q ss_pred CCcccCEEEEeeeccCcccceeeEEEEEeccCCCCCCCCCCceeeEEeeCC
Q 002624 291 RVSVGMRFRMLFETEESSVRRYMGTITGISDLDPVKWPNSHWRSVKVGWDE 341 (899)
Q Consensus 291 ~ws~GMRFkM~fEtEdss~rr~~GTI~gv~d~Dp~rWP~S~WR~LqV~WDe 341 (899)
.|++|+++-..++.++ .||.|+|+.+.. -..+.|.-+.
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 2235677665
No 24
>KOG3598 consensus Thyroid hormone receptor-associated protein complex, subunit TRAP230 [Transcription]
Probab=44.75 E-value=4.2 Score=52.99 Aligned_cols=9 Identities=33% Similarity=0.298 Sum_probs=4.8
Q ss_pred cccCCcccc
Q 002624 239 VLSSDSMHL 247 (899)
Q Consensus 239 v~ss~sm~~ 247 (899)
++|++.||+
T Consensus 1851 ~~s~~~~hh 1859 (2220)
T KOG3598|consen 1851 VTSEKNEHH 1859 (2220)
T ss_pred CCChHhhcC
Confidence 455555554
No 25
>KOG3207 consensus Beta-tubulin folding cofactor E [Posttranslational modification, protein turnover, chaperones]
Probab=39.15 E-value=28 Score=41.34 Aligned_cols=43 Identities=28% Similarity=0.679 Sum_probs=30.0
Q ss_pred CcccCEEEEeeeccCcccceeeEEEEEeccCCCCCCCCCCceeeEEeeCCCCCCCCC
Q 002624 292 VSVGMRFRMLFETEESSVRRYMGTITGISDLDPVKWPNSHWRSVKVGWDESTAGERQ 348 (899)
Q Consensus 292 ws~GMRFkM~fEtEdss~rr~~GTI~gv~d~Dp~rWP~S~WR~LqV~WDe~~~~~~~ 348 (899)
..+|.|+|.-+|- ...||.|+|.|. ++ +| +.|.||++.-+.+.
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 235677777554 44 44 78999999877653
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=38.94 E-value=33 Score=27.90 Aligned_cols=39 Identities=13% Similarity=0.149 Sum_probs=27.7
Q ss_pred CCCCceeecccccccccccCCcCCCEEEEEEcCCCcEEEEEE
Q 002624 185 GQPKRHLLTTGWSVFVSAKRLVAGDSVLFIWNDKNQLLLGIR 226 (899)
Q Consensus 185 g~prrhlLTtGWs~FV~~KkL~aGDsVvF~R~~~g~L~vGIR 226 (899)
|++..-.|-. .|.++.+|.+||.|.|.-+++|++.|--.
T Consensus 4 g~s~~v~iPk---~~~~~l~l~~Gd~v~i~~~~~g~i~i~p~ 42 (47)
T PF04014_consen 4 GNSGQVTIPK---EIREKLGLKPGDEVEIEVEGDGKIVIRPV 42 (47)
T ss_dssp TTCSEEEE-H---HHHHHTTSSTTTEEEEEEETTSEEEEEES
T ss_pred CCCceEECCH---HHHHHcCCCCCCEEEEEEeCCCEEEEEEC
Confidence 4444444433 56778899999999999999887766443
No 27
>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=38.57 E-value=77 Score=27.93 Aligned_cols=65 Identities=18% Similarity=0.217 Sum_probs=46.1
Q ss_pred ceEEEeecC-c---ceeeeccCCCCCHHHHHHHHHHHhcCCCccCCCCCCccEEE-EE-cCCCceeec-cCCCchhh
Q 002624 767 TFVKVYKSG-S---FGRSLDITKFSSYHELRSELARMFGLEGHLEDPLRSGWQLV-FV-DRENDVLLL-GDGPWPEF 836 (899)
Q Consensus 767 ~fVKV~m~G-~---igRkIDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lv-Ye-D~EGD~mLv-GDvPWe~F 836 (899)
.++|||... . .-+.|-++....-.|++..+.+.|++.+ ....|.|+ +. .......|- .+.|+..+
T Consensus 3 ~~lrVy~~~~~~~~~~k~i~v~~~tTa~evi~~~l~k~~l~~-----~~~~y~L~~~~~~~~~er~L~~~E~pl~i~ 74 (93)
T PF00788_consen 3 GVLRVYDGDGSPGSTYKTIKVSSSTTAREVIEMALEKFGLAE-----DPSDYCLVEVEESGGEERPLDDDECPLQIQ 74 (93)
T ss_dssp EEEEEEETTSSSCCSEEEEEEETTSBHHHHHHHHHHHTTTSS-----SGGGEEEEEEECTTTEEEEETTTSBHHHHH
T ss_pred eEEEEEcCCCCCCccEEEEEECCCCCHHHHHHHHHHHhCCCC-----CCCCEEEEEEEcCCCEEEEcCCCCchHHHH
Confidence 589999966 3 3899999999999999999999999932 24469995 43 444444443 23344443
No 28
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=31.49 E-value=63 Score=30.54 Aligned_cols=27 Identities=22% Similarity=0.293 Sum_probs=22.2
Q ss_pred cccccCCcCCCEEEEEEcCCCcEEEEE
Q 002624 199 FVSAKRLVAGDSVLFIWNDKNQLLLGI 225 (899)
Q Consensus 199 FV~~KkL~aGDsVvF~R~~~g~L~vGI 225 (899)
|.-...|++||.|..+|.+.|+-++=+
T Consensus 71 i~~~~~Lk~GD~V~ll~~~~gQ~yiVl 97 (100)
T PF10844_consen 71 ITFTDGLKVGDKVLLLRVQGGQKYIVL 97 (100)
T ss_pred EEEecCCcCCCEEEEEEecCCCEEEEE
Confidence 555678999999999999888877644
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=31.46 E-value=1.4e+02 Score=27.91 Aligned_cols=65 Identities=15% Similarity=0.179 Sum_probs=48.9
Q ss_pred eEEEeecCcceeeeccCCCCCHHHHHHHHHHHhcCCCccCCCCCCccEEEEEcCCC-ceeeccCCCchhhhccee
Q 002624 768 FVKVYKSGSFGRSLDITKFSSYHELRSELARMFGLEGHLEDPLRSGWQLVFVDREN-DVLLLGDGPWPEFVNSVW 841 (899)
Q Consensus 768 fVKV~m~G~igRkIDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EG-D~mLvGDvPWe~Fv~svk 841 (899)
-|||+-.+ .=-|-+..=-+|.+|+..|.+-+.+.+. +=+|-|.|.+. +..-++|.=+|.-.+.|+
T Consensus 4 vvKV~f~~--tIaIrvp~~~~y~~L~~ki~~kLkl~~e-------~i~LsYkde~s~~~v~l~d~dle~aws~~~ 69 (80)
T cd06406 4 VVKVHFKY--TVAIQVARGLSYATLLQKISSKLELPAE-------HITLSYKSEASGEDVILSDTNMEDVWSQAK 69 (80)
T ss_pred EEEEEEEE--EEEEEcCCCCCHHHHHHHHHHHhCCCch-------hcEEEeccCCCCCccCcChHHHHHHHHhhc
Confidence 58999888 2234455666899999999999988531 35889998874 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=30.72 E-value=80 Score=25.82 Aligned_cols=52 Identities=15% Similarity=0.230 Sum_probs=36.2
Q ss_pred CCcccCEEEEeeeccCcccceeeEEEEEeccCCCCCCCCCCceeeEEeeCCCCCCCCCCCcccCccccC
Q 002624 291 RVSVGMRFRMLFETEESSVRRYMGTITGISDLDPVKWPNSHWRSVKVGWDESTAGERQPRVSLWEIEPL 359 (899)
Q Consensus 291 ~ws~GMRFkM~fEtEdss~rr~~GTI~gv~d~Dp~rWP~S~WR~LqV~WDe~~~~~~~~RVSPWeIEpv 359 (899)
.|.+|..+...+ .+. .||.|+|+++.. + ..+.|.-++-.. .+-|...+|-++
T Consensus 2 ~~~~G~~~~a~~-~d~---~wyra~I~~~~~-------~---~~~~V~f~D~G~---~~~v~~~~l~~l 53 (57)
T smart00333 2 TFKVGDKVAARW-EDG---EWYRARIIKVDG-------E---QLYEVFFIDYGN---EEVVPPSDLRPL 53 (57)
T ss_pred CCCCCCEEEEEe-CCC---CEEEEEEEEECC-------C---CEEEEEEECCCc---cEEEeHHHeecC
Confidence 588999999999 443 899999999974 2 556787776442 244555555443
No 31
>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=27.91 E-value=59 Score=25.18 Aligned_cols=26 Identities=19% Similarity=0.276 Sum_probs=22.3
Q ss_pred ccccccCCcCCCEEEEEEcCCCcEEE
Q 002624 198 VFVSAKRLVAGDSVLFIWNDKNQLLL 223 (899)
Q Consensus 198 ~FV~~KkL~aGDsVvF~R~~~g~L~v 223 (899)
.|.++-++..||.|.+...++|.|.|
T Consensus 14 ~~r~~l~~~~gd~~~i~~~~~~~l~l 39 (43)
T TIGR01439 14 EIREKLGLKEGDRLEVIRVEDGEIIL 39 (43)
T ss_pred HHHHHcCcCCCCEEEEEEeCCCEEEE
Confidence 67889999999999999887777665
No 32
>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=27.42 E-value=1.5e+02 Score=26.02 Aligned_cols=42 Identities=12% Similarity=0.082 Sum_probs=27.6
Q ss_pred CcccCEEEEeeeccCcccceeeEEEEEeccCCCCCCCCCCceeeEEeeCCCC
Q 002624 292 VSVGMRFRMLFETEESSVRRYMGTITGISDLDPVKWPNSHWRSVKVGWDEST 343 (899)
Q Consensus 292 ws~GMRFkM~fEtEdss~rr~~GTI~gv~d~Dp~rWP~S~WR~LqV~WDe~~ 343 (899)
+..|+++-..-+.+...-.||.|||+.....+ .+.|+.++-.
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 46799999877665555799999999997522 7889997554
No 33
>COG1047 SlpA FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]
Probab=27.34 E-value=2.6e+02 Score=29.59 Aligned_cols=105 Identities=17% Similarity=0.271 Sum_probs=63.8
Q ss_pred CCcCCCEEEE---EEcCCCcEEEEEEecCCCCCCCCCCcccCCccccchHHHHHHHHHhCCcEEEEEcCCCCCCcc----
Q 002624 204 RLVAGDSVLF---IWNDKNQLLLGIRRANRPPTVMPSSVLSSDSMHLGLLAAAAHAAATNSRFTIFYNPRASPSEF---- 276 (899)
Q Consensus 204 kL~aGDsVvF---~R~~~g~L~vGIRRa~r~~~~~pssv~ss~sm~~gvla~Aa~aaat~~~F~V~Y~PRas~sEF---- 276 (899)
++..||.|.+ .|.++|+++=--+- ...|..++-.+..-+.-|.+|.....-|..|+|.--|-....|+
T Consensus 2 ~i~k~~~V~i~Y~~~~~dg~v~Dtt~e-----~~~P~~~i~G~g~li~glE~al~g~~~Ge~~~V~IpPE~AfGe~~~~l 76 (174)
T COG1047 2 KIEKGDVVSLHYTLKVEDGEVVDTTDE-----NYGPLTFIVGAGQLIPGLEEALLGKEVGEEFTVEIPPEDAFGEYDPDL 76 (174)
T ss_pred cccCCCEEEEEEEEEecCCcEEEcccc-----cCCCeEEEecCCCcchhHHHHHhCCCCCceeEEEeCchHhcCCCChHH
Confidence 4567788776 23455655422111 01133333222222334678888889999999998887655444
Q ss_pred --ccchHHHHHHHhcCCCcccCEEEEeeeccCcccceeeEEEEEecc
Q 002624 277 --VIPLAKYIKAVYHTRVSVGMRFRMLFETEESSVRRYMGTITGISD 321 (899)
Q Consensus 277 --VVp~~ky~ka~~~~~ws~GMRFkM~fEtEdss~rr~~GTI~gv~d 321 (899)
.||+.+|.+. ....+||+|.+ ++++ .-.-|+|+.|..
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 15899999874 5555 456899999974
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=27.10 E-value=59 Score=31.79 Aligned_cols=26 Identities=31% Similarity=0.555 Sum_probs=17.9
Q ss_pred cCCcCCCEEEEEEcC-CCcEEEEEEec
Q 002624 203 KRLVAGDSVLFIWND-KNQLLLGIRRA 228 (899)
Q Consensus 203 KkL~aGDsVvF~R~~-~g~L~vGIRRa 228 (899)
++++.||.|+||... .++-++|+=+-
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 589999999999987 67777877654
No 35
>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=22.74 E-value=56 Score=27.89 Aligned_cols=17 Identities=24% Similarity=0.534 Sum_probs=14.7
Q ss_pred EEEEEcCCCceeeccCC
Q 002624 815 QLVFVDRENDVLLLGDG 831 (899)
Q Consensus 815 ~lvYeD~EGD~mLvGDv 831 (899)
.++|.|.+|+.+++|+.
T Consensus 34 ~i~Y~~~dg~yli~G~l 50 (57)
T PF10411_consen 34 GILYVDEDGRYLIQGQL 50 (57)
T ss_dssp EEEEEETTSSEEEES-E
T ss_pred eEEEEcCCCCEEEEeEE
Confidence 68999999999999974
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=22.29 E-value=1.5e+02 Score=25.66 Aligned_cols=31 Identities=19% Similarity=0.370 Sum_probs=24.3
Q ss_pred ccCEEEEeeeccCcccceeeEEEEEeccCCC
Q 002624 294 VGMRFRMLFETEESSVRRYMGTITGISDLDP 324 (899)
Q Consensus 294 ~GMRFkM~fEtEdss~rr~~GTI~gv~d~Dp 324 (899)
+|-|+.-.||.++.++..|.|+|...-+..|
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 5889999999998888889999999887655
No 37
>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=21.55 E-value=1.5e+02 Score=27.81 Aligned_cols=55 Identities=24% Similarity=0.289 Sum_probs=25.9
Q ss_pred HHHHHHHhcCCCcccCEEEEeeeccCcccceeeEEEEEeccCCCCCCCCCCceeeEEeeCCCC
Q 002624 281 AKYIKAVYHTRVSVGMRFRMLFETEESSVRRYMGTITGISDLDPVKWPNSHWRSVKVGWDEST 343 (899)
Q Consensus 281 ~ky~ka~~~~~ws~GMRFkM~fEtEdss~rr~~GTI~gv~d~Dp~rWP~S~WR~LqV~WDe~~ 343 (899)
+.|..-+. -++++||++||.=.-|+-. .-=.|+|.-++. | .-| =-.+||.|-.-.
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 3589999999963333322 112677666654 2 112 235889997654
No 38
>cd05792 S1_eIF1AD_like S1_eIF1AD_like: eukaryotic translation initiation factor 1A domain containing protein (eIF1AD)-like, S1-like RNA-binding domain. eIF1AD is also known as MGC11102 protein. Little is known about the function of eIF1AD. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins, including translation initiation factor IF1A (also referred to as eIF1A in eukaryotes). eIF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors.
Probab=20.98 E-value=70 Score=29.56 Aligned_cols=35 Identities=26% Similarity=0.414 Sum_probs=27.4
Q ss_pred CCCceeeccCCCchhhhcceeE--EEEeChhhhhcccccc
Q 002624 821 RENDVLLLGDGPWPEFVNSVWC--IKILSPPEVQQMGKRG 858 (899)
Q Consensus 821 ~EGD~mLvGDvPWe~Fv~svkr--irIl~~~e~~~m~~~~ 858 (899)
|+||..|| +||+ |-+-+|. +.|+..+++..+-+.+
T Consensus 40 krGd~VlV--~p~~-~~~kvkgeIv~i~~~~qvk~L~k~g 76 (78)
T cd05792 40 KRGDFVLV--EPIE-EGDKVKAEIVKILTRDHVKYIKEEG 76 (78)
T ss_pred EeCCEEEE--Eecc-cCCceEEEEEEEECHHHHHHHHHcC
Confidence 78999999 7998 5555664 8899999888776654
Done!