Query 005060
Match_columns 716
No_of_seqs 352 out of 861
Neff 4.6
Searched_HMMs 46136
Date Thu Mar 28 17:24:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/005060.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/005060hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02309 AUX_IAA: AUX/IAA fami 100.0 2.1E-36 4.7E-41 304.9 0.4 96 614-709 106-215 (215)
2 PF06507 Auxin_resp: Auxin res 100.0 1.1E-34 2.3E-39 253.9 9.0 83 275-357 1-83 (83)
3 PF02362 B3: B3 DNA binding do 99.7 1.1E-16 2.4E-21 141.1 9.7 97 149-250 1-99 (100)
4 KOG0644 Uncharacterized conser 99.6 9.9E-16 2.1E-20 174.9 6.2 156 227-390 874-1051(1113)
5 PF09217 EcoRII-N: Restriction 98.0 2.3E-05 5E-10 76.4 8.6 90 145-236 6-110 (156)
6 PF03754 DUF313: Domain of unk 97.5 0.00012 2.7E-09 68.5 5.4 78 146-224 21-114 (114)
7 PF00564 PB1: PB1 domain; Int 96.8 0.0031 6.8E-08 54.2 6.6 66 620-692 4-70 (84)
8 smart00666 PB1 PB1 domain. Pho 96.4 0.013 2.8E-07 50.4 7.2 65 620-692 4-69 (81)
9 cd05992 PB1 The PB1 domain is 96.2 0.022 4.8E-07 48.6 7.8 65 620-692 3-69 (81)
10 cd06398 PB1_Joka2 The PB1 doma 96.2 0.015 3.3E-07 52.6 6.9 65 620-693 3-72 (91)
11 cd06407 PB1_NLP A PB1 domain i 96.0 0.023 4.9E-07 50.5 7.1 56 620-682 3-58 (82)
12 cd06396 PB1_NBR1 The PB1 domai 95.9 0.031 6.6E-07 49.8 7.2 64 620-691 3-67 (81)
13 cd06403 PB1_Par6 The PB1 domai 95.7 0.049 1.1E-06 48.3 7.8 67 620-692 3-70 (80)
14 cd06409 PB1_MUG70 The MUG70 pr 94.2 0.07 1.5E-06 48.1 4.6 53 627-682 7-61 (86)
15 cd06404 PB1_aPKC PB1 domain is 93.1 0.27 5.9E-06 44.1 6.3 63 620-691 3-65 (83)
16 cd06408 PB1_NoxR The PB1 domai 92.4 0.35 7.6E-06 43.7 6.2 65 618-692 3-68 (86)
17 cd06401 PB1_TFG The PB1 domain 91.9 1.1 2.3E-05 40.3 8.4 73 620-697 3-79 (81)
18 cd06397 PB1_UP1 Uncharacterize 90.8 0.69 1.5E-05 41.4 6.1 65 621-693 4-69 (82)
19 cd06402 PB1_p62 The PB1 domain 90.7 0.91 2E-05 41.1 6.9 59 619-682 2-65 (87)
20 KOG0644 Uncharacterized conser 69.5 3.6 7.9E-05 50.0 3.1 67 57-124 872-940 (1113)
21 cd06406 PB1_P67 A PB1 domain i 67.0 23 0.0005 31.9 6.8 68 620-696 5-75 (80)
22 PRK10737 FKBP-type peptidyl-pr 60.8 34 0.00074 35.4 7.8 104 226-342 2-114 (196)
23 cd06399 PB1_P40 The PB1 domain 46.2 25 0.00055 32.3 3.6 41 634-682 23-63 (92)
24 PF04014 Antitoxin-MazE: Antid 40.2 27 0.00059 27.5 2.6 27 220-246 14-40 (47)
25 PF10844 DUF2577: Protein of u 36.4 53 0.0011 30.2 4.2 27 221-247 71-97 (100)
26 PF02513 Spin-Ssty: Spin/Ssty 35.0 66 0.0014 26.7 4.1 31 315-345 1-31 (50)
27 smart00743 Agenet Tudor-like d 33.7 62 0.0014 26.4 3.9 28 312-342 2-29 (61)
28 PF00788 RA: Ras association ( 32.7 92 0.002 26.7 5.0 69 618-690 3-77 (93)
29 PF05641 Agenet: Agenet domain 31.9 86 0.0019 26.6 4.5 41 313-363 1-41 (68)
30 TIGR01439 lp_hng_hel_AbrB loop 28.0 58 0.0013 24.4 2.6 26 220-245 14-39 (43)
31 COG1047 SlpA FKBP-type peptidy 27.4 3.7E+02 0.0081 27.6 8.8 105 226-342 2-115 (174)
32 PF11515 Cul7: Mouse developme 24.5 87 0.0019 28.2 3.3 56 301-363 6-61 (78)
33 KOG3938 RGS-GAIP interacting p 24.1 98 0.0021 33.9 4.2 73 624-707 61-143 (334)
34 PF01878 EVE: EVE domain; Int 23.6 74 0.0016 30.3 3.0 26 225-250 38-64 (143)
35 PRK14129 heat shock protein Hs 22.4 1.2E+02 0.0026 28.8 3.9 54 310-381 3-56 (105)
36 cd06410 PB1_UP2 Uncharacterize 22.1 1E+02 0.0022 28.5 3.5 58 623-691 19-79 (97)
37 KOG3606 Cell polarity protein 21.8 1E+02 0.0022 33.8 3.9 66 632-703 33-102 (358)
38 KOG3207 Beta-tubulin folding c 21.5 94 0.002 36.2 3.7 37 313-363 3-39 (505)
39 smart00333 TUDOR Tudor domain. 20.0 1.6E+02 0.0034 23.3 3.8 53 312-382 2-54 (57)
No 1
>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=2.1e-36 Score=304.95 Aligned_cols=96 Identities=41% Similarity=0.694 Sum_probs=0.0
Q ss_pred CCCcceEEEEEcCceeeeeecCCCCCChHHHHHHHHhhh---ccC----------CCcC-CCCCCcEEEEecCCCCeEEc
Q 005060 614 YVSRSCTKVIKFGTALGRSVDLTRFHGYDELISELDQMF---DFN----------GSLI-DGNSGFHIAYMDDEGDMMLV 679 (716)
Q Consensus 614 ~~~~~~vKV~meG~~vGR~vDLs~~~sY~eL~~~L~~MF---~~~----------g~l~-~~~~~~~v~Y~D~eGD~mlv 679 (716)
+..+.||||+|||++|||||||++|+||++|+.+|++|| +|. +.+. ..+++|+|||+|+|||||||
T Consensus 106 ~~~~~~vKV~mdG~~igRkVDL~~~~sY~~L~~~L~~MF~~~~i~~~~~~~~~~~~~~~~~~~~~~~l~Y~D~egd~mlv 185 (215)
T PF02309_consen 106 SSSRSYVKVNMDGVPIGRKVDLSAYSSYEELSSALEKMFSCFSIEQCGSHGLNESGLLDLLNGSEYVLVYEDKEGDWMLV 185 (215)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred ccCCceeEEEecCcccceecCHHHhhCHHHHHHHHHHhcCCCCccccccccccchhhccccCCcceeEEEECCCCCEEEe
Confidence 346899999999999999999999999999999999999 665 2221 14679999999999999999
Q ss_pred cCCChHHHHhcceeeEEecCCccCCcCCCC
Q 005060 680 GDNPWQDFQCAVRRMFICPKEDIDGVIPSS 709 (716)
Q Consensus 680 GD~PW~~F~~~vkri~I~~~~e~~~m~~~~ 709 (716)
|||||++||++||||+||+.+|+++|+|++
T Consensus 186 GD~PW~~F~~~vkRl~I~~~~e~~~~~~r~ 215 (215)
T PF02309_consen 186 GDVPWEEFVKSVKRLRIMKSSEAKGLAPRA 215 (215)
T ss_dssp ------------------------------
T ss_pred cCCCHHHHHHHhhccEEecHHHhcccCCCC
Confidence 999999999999999999999999999874
No 2
>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=1.1e-34 Score=253.86 Aligned_cols=83 Identities=48% Similarity=0.930 Sum_probs=81.5
Q ss_pred HHHHHhcCCeEEEEEecCCCCCceEEehhhHHhhhccCCccccEEEEEecCCcccccceeEEEEeeecCCCCCCCCCccc
Q 005060 275 AFHAISTGTRFTVYYHPWTRPAEFLVPFSQYMKSAEIDYSIGTRFRMVFEGEECADQRIAGTVVGTEDVDHIRWPASEWR 354 (716)
Q Consensus 275 a~~a~~tg~~F~V~Y~Pr~s~~EFvV~~~ky~~A~~~~w~~GmRFkM~fE~ed~~~~~~~GtI~gv~~~dp~~Wp~S~WR 354 (716)
|+|||++|++|+|+||||++++||||++++|++||+++|++||||||+||+||+++++|+|||+||++.||.+||+|+||
T Consensus 1 A~~aa~~~~~F~V~Y~PRa~~sEFVV~~~k~~~al~~~~~~GmRfkM~fE~eds~~~~~~GtI~~v~~~dp~~w~~S~WR 80 (83)
T PF06507_consen 1 AAHAAATGSPFEVFYYPRASPSEFVVPASKYDKALNHPWSVGMRFKMRFETEDSSERRWQGTIVGVSDLDPIRWPGSKWR 80 (83)
T ss_pred ChhHhhcCCeEEEEECCCCCCcceEEEHHHHHHHhcCCCCCCcEEEEEeccCCCccceeeeEEeEeeccCCCCCCCCCcc
Confidence 67999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cee
Q 005060 355 CLK 357 (716)
Q Consensus 355 ~L~ 357 (716)
|||
T Consensus 81 ~Lq 83 (83)
T PF06507_consen 81 MLQ 83 (83)
T ss_pred cCc
Confidence 997
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=99.68 E-value=1.1e-16 Score=141.13 Aligned_cols=97 Identities=35% Similarity=0.532 Sum_probs=74.5
Q ss_pred EEEEeccccCCCCCceeeccccccccCCCCCCCCCCCceEEEEEeCCCCEEEEEEEEeCCCCceeeccccchheecCCCC
Q 005060 149 FSKKLTPSDTSTHGGFSVPKRHADECLPPLDMSKDPPLQELVAKDLHGLEWRFRHIYRGQPKRHLLTSGWSVFVTSKKLV 228 (716)
Q Consensus 149 F~K~LT~SDv~~~grfsVPk~~Ae~~FP~Ld~~~~~p~q~L~~~D~~G~~W~Fr~~yrg~prr~~LTtGWs~FV~~K~L~ 228 (716)
|.|+|+++|+...+++.||+++++.+. ++. ...+++.++|..|++|.+++.+++.+++++|++||..||++++|+
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--GNK---RKSREVTLKDPDGRSWPVKLKYRKNSGRYYLTGGWKKFVRDNGLK 75 (100)
T ss_dssp EEEE--TTCCCCTT-EEE-HHHHTTTS----S---S--CEEEEEETTTEEEEEEEEEECCTTEEEEETTHHHHHHHCT--
T ss_pred CEEEEEccCcCCCCEEEeCHHHHHHhC--CCc---CCCeEEEEEeCCCCEEEEEEEEEccCCeEEECCCHHHHHHHcCCC
Confidence 899999999999999999999999972 111 125789999999999999999998888899999999999999999
Q ss_pred CCCEEEEEEcCC--CcEEEEEEEe
Q 005060 229 AGDVCIFLRGGD--GELRVGVRRA 250 (716)
Q Consensus 229 aGD~VvF~R~~~--G~l~vGIRRa 250 (716)
+||.|+|+...+ .++.|.|.|+
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 999999998754 4569999886
No 4
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=99.59 E-value=9.9e-16 Score=174.94 Aligned_cols=156 Identities=21% Similarity=0.308 Sum_probs=126.3
Q ss_pred CCCCCEEEEEEcCCCcEEEEEEEeccccC---------------------CCCcccccccccccchhHHHHHHHhcCCeE
Q 005060 227 LVAGDVCIFLRGGDGELRVGVRRAMKLQN---------------------NASTSVISSLSMQHGILAGAFHAISTGTRF 285 (716)
Q Consensus 227 L~aGD~VvF~R~~~G~l~vGIRRa~~~~~---------------------~~p~sv~s~~s~~~gvla~a~~a~~tg~~F 285 (716)
.+.||.|+++|....++.-.+|+.....+ ..|.+..+-+.|.+.||+-|.++. ...|
T Consensus 874 pQmgDEViyfrQghqeyl~~~~~n~~~~~~~~p~~~~~v~~~kv~kl~~~~y~~~~~s~c~m~l~~idp~s~~~--~k~F 951 (1113)
T KOG0644|consen 874 PQMGDEVIYFRQGHQEYLEAVRLNNIELNNKEPWNKMAVEICKVEKLVYITYPGSGDSCCKMKLAVIDPASKLM--DKSF 951 (1113)
T ss_pred ccccceeehhhhhhHHHHhhhhhccccccccCcccccchhhheeeeeeeeeccCCCcchheeeeeeecchhhhh--hccc
Confidence 45799999999877666555554433211 124556677899999999999775 4589
Q ss_pred EEEEecCCCCCceEEehhhHHhhhccCCccccEEEEEecCCccc-ccceeEEEEeeecCCCCCCCCCcccceeeecccCC
Q 005060 286 TVYYHPWTRPAEFLVPFSQYMKSAEIDYSIGTRFRMVFEGEECA-DQRIAGTVVGTEDVDHIRWPASEWRCLKVKWDATT 364 (716)
Q Consensus 286 ~V~Y~Pr~s~~EFvV~~~ky~~A~~~~w~~GmRFkM~fE~ed~~-~~~~~GtI~gv~~~dp~~Wp~S~WR~L~V~WDe~~ 364 (716)
.+.|+.....+||+|.++.|++|++++|..+++||.-+..+-.. ..||.|+|.++.+ .+.++|+|+|.|+.|+||..
T Consensus 952 ~ltlpdlv~fpDFlV~rsrYd~AiQrnW~~~d~crvwwrda~~e~g~WWeG~ils~~p-ksp~fpdSpwery~v~~~~~- 1029 (1113)
T KOG0644|consen 952 KLTLPDLVTFPDFLVERSRYDAAIQRNWTCRDKCRVWWRDAGEEDGAWWEGRILSVKP-KSPDFPDSPWERYIVRYDNT- 1029 (1113)
T ss_pred eeecccccCcchhhhhhhhHHHHHhhccccccceeEEEccCCCcCCceeeeeeeeccC-CCCCCCCCcceeEEEEecCC-
Confidence 99999999999999999999999999999999999999765322 2899999999998 56779999999999999999
Q ss_pred CCCCCCCccCCCccccCCCCCCCCCC
Q 005060 365 DSITRPARVSPWNIEPIERTHKRPAS 390 (716)
Q Consensus 365 ~~~~~~~RVSPWeIEpv~~~~~~~~~ 390 (716)
+.+.-||||.|++..---+++|
T Consensus 1030 ----e~~~~spwe~~~i~de~~~~fp 1051 (1113)
T KOG0644|consen 1030 ----ETELHSPWEMEPIPDEVDNRFP 1051 (1113)
T ss_pred ----cccccCccccCCCccccCCCCC
Confidence 5677899999999865433443
No 5
>PF09217 EcoRII-N: Restriction endonuclease EcoRII, N-terminal; InterPro: IPR023372 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry represents the N-terminal effector-binding domain of the type II restriction endonuclease EcoRII, which has a DNA recognition fold, allowing for binding to 5'-CCWGG sequences. It assumes a structure composed of an eight-stranded beta-sheet with the strands in the order of b2, b5, b4, b3, b7, b6, b1 and b8. They are mostly antiparallel to each other except that b3 is parallel to b7. Alternatively, it may also be viewed as consisting of two mini beta-sheets of four antiparallel beta-strands, sheet I from beta-strands b2, b5, b4, b3 and sheet II from strands b7, b6, b1, b8, folded into an open mixed beta-barrel with a novel topology. Sheet I has a simple Greek key motif while sheet II does not []. The domain represented by this entry is only found in bacterial proteins.; PDB: 3HQF_A 1NA6_A.
Probab=98.00 E-value=2.3e-05 Score=76.38 Aligned_cols=90 Identities=20% Similarity=0.301 Sum_probs=60.2
Q ss_pred ceeeEEEEeccccCCCCC----ceeeccccccccCCCCCC-CCCCCceEEEEEeCCC--CEEEEEEEEeCC------CCc
Q 005060 145 NVCSFSKKLTPSDTSTHG----GFSVPKRHADECLPPLDM-SKDPPLQELVAKDLHG--LEWRFRHIYRGQ------PKR 211 (716)
Q Consensus 145 ~~~~F~K~LT~SDv~~~g----rfsVPk~~Ae~~FP~Ld~-~~~~p~q~L~~~D~~G--~~W~Fr~~yrg~------prr 211 (716)
....|+|.|++.|++..| |+-||+..++..||.+.. +..+|...|.+++..| ..|+||++|.|+ ...
T Consensus 6 ~~~~~~K~LSaNDtGaTGgHQaGiyIpk~~~~~lFp~~~~~~~~Np~~~~~~~~~s~~~~~~~~r~iYYnn~~~~gTRNE 85 (156)
T PF09217_consen 6 SWAIYCKRLSANDTGATGGHQAGIYIPKSAAELLFPSINHTKEENPDIWLKARWQSHFVTDSQVRFIYYNNRLFGGTRNE 85 (156)
T ss_dssp SEEEEEEE--CCCCTTTSSS--EEEE-HHHHHHH-GGG-SSSSSS-EEEEEEEETTTT---EEEEEEEE-CCCTTSS--E
T ss_pred ceEEEEEEccCCCCCCcCcccceeEecccHHHHhCCCCCcccccCCceeEEEEECCCCccceeEEEEEEcccccCCCcCc
Confidence 456899999999999764 899999999999998766 5667999999999888 568899999976 556
Q ss_pred eeec--cccchheecCCCCCCCEEEEE
Q 005060 212 HLLT--SGWSVFVTSKKLVAGDVCIFL 236 (716)
Q Consensus 212 ~~LT--tGWs~FV~~K~L~aGD~VvF~ 236 (716)
+.|| ++=..|.+.. ..||-+||.
T Consensus 86 ~RIT~~G~~~~~~~~~--~tGaL~vla 110 (156)
T PF09217_consen 86 YRITRFGRGFPLQNPE--NTGALLVLA 110 (156)
T ss_dssp EEEE---TTSGGG-GG--GTT-EEEEE
T ss_pred eEEeeecCCCccCCcc--ccccEEEEE
Confidence 7885 3333344332 368887776
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=97.53 E-value=0.00012 Score=68.52 Aligned_cols=78 Identities=21% Similarity=0.244 Sum_probs=60.1
Q ss_pred eeeEEEEeccccCCCC-CceeeccccccccCCCCC------------CCCCCCceEEEEEeCCCCEEEEEEEEeCC---C
Q 005060 146 VCSFSKKLTPSDTSTH-GGFSVPKRHADECLPPLD------------MSKDPPLQELVAKDLHGLEWRFRHIYRGQ---P 209 (716)
Q Consensus 146 ~~~F~K~LT~SDv~~~-grfsVPk~~Ae~~FP~Ld------------~~~~~p~q~L~~~D~~G~~W~Fr~~yrg~---p 209 (716)
...|.|+|++||+..+ .||+||-..... ..-|. .....-++.+.+.|..++.|..++..|.- .
T Consensus 21 kli~~K~L~~tDv~~~qsRLsmP~~qi~~-~dFLt~eE~~~i~~~~~~~~~~~Gv~V~lvdp~~~~~~m~lkkW~mg~~~ 99 (114)
T PF03754_consen 21 KLIIEKTLFKTDVDPHQSRLSMPFNQIID-NDFLTEEEKRIIKEEKKNNDKKKGVEVILVDPSLRKWTMRLKKWNMGNGT 99 (114)
T ss_pred eEEEeeeecccCCCCCCceeeccHHHhcc-cccCCHHHHHHHHHhhccCcccCCceEEEECCcCcEEEEEEEEecccCCc
Confidence 5789999999999965 899999876532 12221 11223478899999999999999999954 4
Q ss_pred Cceeeccccchheec
Q 005060 210 KRHLLTSGWSVFVTS 224 (716)
Q Consensus 210 rr~~LTtGWs~FV~~ 224 (716)
-.|+|++||..+|++
T Consensus 100 ~~YvL~~gWn~VV~~ 114 (114)
T PF03754_consen 100 SNYVLNSGWNKVVED 114 (114)
T ss_pred eEEEEEcChHhhccC
Confidence 579999999999864
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=96.84 E-value=0.0031 Score=54.24 Aligned_cols=66 Identities=23% Similarity=0.427 Sum_probs=54.2
Q ss_pred EEEEEcCceeeeeecCCCCCChHHHHHHHHhhhccCCCcCCCCCCcEEEEecCCCCeEEccC-CChHHHHhcce
Q 005060 620 TKVIKFGTALGRSVDLTRFHGYDELISELDQMFDFNGSLIDGNSGFHIAYMDDEGDMMLVGD-NPWQDFQCAVR 692 (716)
Q Consensus 620 vKV~meG~~vGR~vDLs~~~sY~eL~~~L~~MF~~~g~l~~~~~~~~v~Y~D~eGD~mlvGD-~PW~~F~~~vk 692 (716)
+|++..|. +=|.+.+..--+|++|..++++.|++. ...+.+.|.|.|||+..+.+ +=|++.++.++
T Consensus 4 vK~~~~~~-~~~~~~~~~~~s~~~L~~~i~~~~~~~------~~~~~l~Y~D~dgD~V~i~sd~Dl~~a~~~~~ 70 (84)
T PF00564_consen 4 VKVRYGGD-IRRIISLPSDVSFDDLRSKIREKFGLL------DEDFQLKYKDEDGDLVTISSDEDLQEAIEQAK 70 (84)
T ss_dssp EEEEETTE-EEEEEEECSTSHHHHHHHHHHHHHTTS------TSSEEEEEEETTSSEEEESSHHHHHHHHHHHH
T ss_pred EEEEECCe-eEEEEEcCCCCCHHHHHHHHHHHhCCC------CccEEEEeeCCCCCEEEeCCHHHHHHHHHHHH
Confidence 69999995 344588888889999999999999986 34579999999999998875 44777777765
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=96.38 E-value=0.013 Score=50.39 Aligned_cols=65 Identities=18% Similarity=0.376 Sum_probs=52.2
Q ss_pred EEEEEcCceeeeeecCCCCCChHHHHHHHHhhhccCCCcCCCCCCcEEEEecCCCCeEEccC-CChHHHHhcce
Q 005060 620 TKVIKFGTALGRSVDLTRFHGYDELISELDQMFDFNGSLIDGNSGFHIAYMDDEGDMMLVGD-NPWQDFQCAVR 692 (716)
Q Consensus 620 vKV~meG~~vGR~vDLs~~~sY~eL~~~L~~MF~~~g~l~~~~~~~~v~Y~D~eGD~mlvGD-~PW~~F~~~vk 692 (716)
+||.-.|. =|.+-+..--+|++|+.++.+.|++.. ..+.+.|+|.|||+..+.+ +=|.+.+.+++
T Consensus 4 vK~~~~~~--~~~~~~~~~~s~~dL~~~i~~~~~~~~------~~~~l~Y~Dedgd~v~l~sd~Dl~~a~~~~~ 69 (81)
T smart00666 4 VKLRYGGE--TRRLSVPRDISFEDLRSKVAKRFGLDN------QSFTLKYQDEDGDLVSLTSDEDLEEAIEEYD 69 (81)
T ss_pred EEEEECCE--EEEEEECCCCCHHHHHHHHHHHhCCCC------CCeEEEEECCCCCEEEecCHHHHHHHHHHHH
Confidence 68888554 688888889999999999999999753 4579999999999987754 56666666655
No 9
>cd05992 PB1 The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as a noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.
Probab=96.21 E-value=0.022 Score=48.63 Aligned_cols=65 Identities=22% Similarity=0.419 Sum_probs=50.2
Q ss_pred EEEEEcCceeeeeecCC-CCCChHHHHHHHHhhhccCCCcCCCCCCcEEEEecCCCCeEEccC-CChHHHHhcce
Q 005060 620 TKVIKFGTALGRSVDLT-RFHGYDELISELDQMFDFNGSLIDGNSGFHIAYMDDEGDMMLVGD-NPWQDFQCAVR 692 (716)
Q Consensus 620 vKV~meG~~vGR~vDLs-~~~sY~eL~~~L~~MF~~~g~l~~~~~~~~v~Y~D~eGD~mlvGD-~PW~~F~~~vk 692 (716)
+||+-.|.. |.+=+. .--+|++|...|.+.|++.. ..+.+.|.|.|||+..+.+ +=|++.++.++
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 688888752 344444 88899999999999999864 4579999999999999887 55555555554
No 10
>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=96.19 E-value=0.015 Score=52.56 Aligned_cols=65 Identities=23% Similarity=0.405 Sum_probs=51.8
Q ss_pred EEEEEcCceeeeeecCC-----CCCChHHHHHHHHhhhccCCCcCCCCCCcEEEEecCCCCeEEccCCChHHHHhccee
Q 005060 620 TKVIKFGTALGRSVDLT-----RFHGYDELISELDQMFDFNGSLIDGNSGFHIAYMDDEGDMMLVGDNPWQDFQCAVRR 693 (716)
Q Consensus 620 vKV~meG~~vGR~vDLs-----~~~sY~eL~~~L~~MF~~~g~l~~~~~~~~v~Y~D~eGD~mlvGD~PW~~F~~~vkr 693 (716)
+||.-+|. -|.+-+. .--+|++|..++++.|.+.. ..++.+.|.|.||||..+-++ +++...+.+
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 VKVKYGGT--LRRFTFPVAENQLDLNMDGLREKVEELFSLSP-----DADLSLTYTDEDGDVVTLVDD--NDLTDAIQY 72 (91)
T ss_pred EEEEeCCE--EEEEEeccccccCCCCHHHHHHHHHHHhCCCC-----CCcEEEEEECCCCCEEEEccH--HHHHHHHHH
Confidence 79999997 4555554 35799999999999998743 356899999999999999776 777666654
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=96.02 E-value=0.023 Score=50.48 Aligned_cols=56 Identities=23% Similarity=0.385 Sum_probs=45.9
Q ss_pred EEEEEcCceeeeeecCCCCCChHHHHHHHHhhhccCCCcCCCCCCcEEEEecCCCCeEEccCC
Q 005060 620 TKVIKFGTALGRSVDLTRFHGYDELISELDQMFDFNGSLIDGNSGFHIAYMDDEGDMMLVGDN 682 (716)
Q Consensus 620 vKV~meG~~vGR~vDLs~~~sY~eL~~~L~~MF~~~g~l~~~~~~~~v~Y~D~eGD~mlvGD~ 682 (716)
|||...|. -+.+-|..--+|++|..++.++|++.. ...+.|-|.|+||||..+--+
T Consensus 3 vK~~~~~d--~~r~~l~~~~~~~~L~~~i~~r~~~~~-----~~~f~LkY~Ddegd~v~ltsd 58 (82)
T cd06407 3 VKATYGEE--KIRFRLPPSWGFTELKQEIAKRFKLDD-----MSAFDLKYLDDDEEWVLLTCD 58 (82)
T ss_pred EEEEeCCe--EEEEEcCCCCCHHHHHHHHHHHhCCCC-----CCeeEEEEECCCCCeEEeecH
Confidence 79999986 455666666799999999999999852 256899999999999987443
No 12
>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=95.87 E-value=0.031 Score=49.84 Aligned_cols=64 Identities=17% Similarity=0.246 Sum_probs=50.7
Q ss_pred EEEEEcCceeeeeecCCCCCChHHHHHHHHhhhccCCCcCCCCCCcEEEEecCCCCeEEcc-CCChHHHHhcc
Q 005060 620 TKVIKFGTALGRSVDLTRFHGYDELISELDQMFDFNGSLIDGNSGFHIAYMDDEGDMMLVG-DNPWQDFQCAV 691 (716)
Q Consensus 620 vKV~meG~~vGR~vDLs~~~sY~eL~~~L~~MF~~~g~l~~~~~~~~v~Y~D~eGD~mlvG-D~PW~~F~~~v 691 (716)
+||.-.|.-+==+++-+..-+|++|..++.++|++. .+.|.|-|+||||.++- |.=.+|.++.+
T Consensus 3 vKaty~~d~~rf~~~~~~~~~~~~L~~ev~~rf~l~--------~f~lKYlDde~e~v~lssd~eLeE~~rl~ 67 (81)
T cd06396 3 LKVTYNGESQSFLVSDSENTTWASVEAMVKVSFGLN--------DIQIKYVDEENEEVSVNSQGEYEEALKSA 67 (81)
T ss_pred EEEEECCeEEEEEecCCCCCCHHHHHHHHHHHhCCC--------cceeEEEcCCCCEEEEEchhhHHHHHHHH
Confidence 799999986666666666889999999999999997 36899999999998773 33345555444
No 13
>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=95.74 E-value=0.049 Score=48.33 Aligned_cols=67 Identities=16% Similarity=0.263 Sum_probs=51.4
Q ss_pred EEEEEcCceeeeeecCCCCCChHHHHHHHHhhhccCCCcCCCCCCcEEEEecCCCCeEEcc-CCChHHHHhcce
Q 005060 620 TKVIKFGTALGRSVDLTRFHGYDELISELDQMFDFNGSLIDGNSGFHIAYMDDEGDMMLVG-DNPWQDFQCAVR 692 (716)
Q Consensus 620 vKV~meG~~vGR~vDLs~~~sY~eL~~~L~~MF~~~g~l~~~~~~~~v~Y~D~eGD~mlvG-D~PW~~F~~~vk 692 (716)
||..-+++=-==++|.....+|++++..|++|+.|.+ -.+.|-|+|.+||.+-+- |+-+..=+.+++
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 6766776533336777778999999999999999876 247999999999999885 455555556666
No 14
>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=94.21 E-value=0.07 Score=48.05 Aligned_cols=53 Identities=23% Similarity=0.397 Sum_probs=41.7
Q ss_pred ceeeeeecCC--CCCChHHHHHHHHhhhccCCCcCCCCCCcEEEEecCCCCeEEccCC
Q 005060 627 TALGRSVDLT--RFHGYDELISELDQMFDFNGSLIDGNSGFHIAYMDDEGDMMLVGDN 682 (716)
Q Consensus 627 ~~vGR~vDLs--~~~sY~eL~~~L~~MF~~~g~l~~~~~~~~v~Y~D~eGD~mlvGD~ 682 (716)
.+-||.+=++ ...|+.+|..+..+=|+++.. ....+.|.|.|+||||.++--+
T Consensus 7 ~~~GrvhRf~~~~s~~~~~L~~~I~~Rl~~d~~---~~~~~~L~YlDDEgD~VllT~D 61 (86)
T cd06409 7 DPKGRVHRFRLRPSESLEELRTLISQRLGDDDF---ETHLYALSYVDDEGDIVLITSD 61 (86)
T ss_pred CCCCCEEEEEecCCCCHHHHHHHHHHHhCCccc---cCCcccEEEEcCCCCEEEEecc
Confidence 4467765554 368999999999999998764 2456899999999999887433
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=93.08 E-value=0.27 Score=44.13 Aligned_cols=63 Identities=24% Similarity=0.403 Sum_probs=48.9
Q ss_pred EEEEEcCceeeeeecCCCCCChHHHHHHHHhhhccCCCcCCCCCCcEEEEecCCCCeEEccCCChHHHHhcc
Q 005060 620 TKVIKFGTALGRSVDLTRFHGYDELISELDQMFDFNGSLIDGNSGFHIAYMDDEGDMMLVGDNPWQDFQCAV 691 (716)
Q Consensus 620 vKV~meG~~vGR~vDLs~~~sY~eL~~~L~~MF~~~g~l~~~~~~~~v~Y~D~eGD~mlvGD~PW~~F~~~v 691 (716)
+|++-.|.-+-=.+|. .-+|++|.+++.+||.+.. ...+++.|.|.|||.--+..+ .|.....
T Consensus 3 ~K~~y~gdi~it~~d~--~~s~e~L~~~v~~~c~~~~-----~q~ft~kw~DEEGDp~tiSS~--~EL~EA~ 65 (83)
T cd06404 3 VKAAYNGDIMITSIDP--SISLEELCNEVRDMCRFHN-----DQPFTLKWIDEEGDPCTISSQ--MELEEAF 65 (83)
T ss_pred EEEEecCcEEEEEcCC--CcCHHHHHHHHHHHhCCCC-----CCcEEEEEECCCCCceeecCH--HHHHHHH
Confidence 6999999765555666 6789999999999999732 346899999999999888765 4444333
No 16
>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=92.44 E-value=0.35 Score=43.67 Aligned_cols=65 Identities=23% Similarity=0.331 Sum_probs=50.9
Q ss_pred ceEEEEEcCceeeeeecCCCCCChHHHHHHHHhhhccCCCcCCCCCCcEEEEecCCCCeEEccCC-ChHHHHhcce
Q 005060 618 SCTKVIKFGTALGRSVDLTRFHGYDELISELDQMFDFNGSLIDGNSGFHIAYMDDEGDMMLVGDN-PWQDFQCAVR 692 (716)
Q Consensus 618 ~~vKV~meG~~vGR~vDLs~~~sY~eL~~~L~~MF~~~g~l~~~~~~~~v~Y~D~eGD~mlvGD~-PW~~F~~~vk 692 (716)
.-|||+-+|. -|.+-+..--+|++|..++.++|++.. .+.|-|.|. ||+.-++|. =.++-+.++|
T Consensus 3 ikVKv~~~~D--v~~i~v~~~i~f~dL~~kIrdkf~~~~-------~~~iKykDE-GD~iti~sq~DLd~Ai~~a~ 68 (86)
T cd06408 3 IRVKVHAQDD--TRYIMIGPDTGFADFEDKIRDKFGFKR-------RLKIKMKDD-GDMITMGDQDDLDMAIDTAR 68 (86)
T ss_pred EEEEEEecCc--EEEEEcCCCCCHHHHHHHHHHHhCCCC-------ceEEEEEcC-CCCccccCHHHHHHHHHHHH
Confidence 4589999997 677777777889999999999999853 469999999 999999885 1223344444
No 17
>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=91.94 E-value=1.1 Score=40.29 Aligned_cols=73 Identities=19% Similarity=0.319 Sum_probs=49.6
Q ss_pred EEEEEcCceeeeeecCCCC-CChHHHHHHHHhhhccCCCcCCCCCCcEEEEecCCCCeEEccCC---ChHHHHhcceeeE
Q 005060 620 TKVIKFGTALGRSVDLTRF-HGYDELISELDQMFDFNGSLIDGNSGFHIAYMDDEGDMMLVGDN---PWQDFQCAVRRMF 695 (716)
Q Consensus 620 vKV~meG~~vGR~vDLs~~-~sY~eL~~~L~~MF~~~g~l~~~~~~~~v~Y~D~eGD~mlvGD~---PW~~F~~~vkri~ 695 (716)
+|+...| +| |.+=+..- -+|.+|...+.+.|... + ...+.+.|.|.|.|||+.-+.+. -|-.=+...++|+
T Consensus 3 iK~~~g~-Di-R~~~~~~~~~t~~~L~~~v~~~F~~~--~-~~~~~flIKYkD~dGDlVTIts~~dL~~A~~~~~~~~l~ 77 (81)
T cd06401 3 LKAQLGD-DI-RRIPIHNEDITYDELLLMMQRVFRGK--L-GSSDDVLIKYKDEDGDLITIFDSSDLSFAIQCSRILKLT 77 (81)
T ss_pred EEEEeCC-eE-EEEeccCccccHHHHHHHHHHHhccc--c-CCcccEEEEEECCCCCEEEeccHHHHHHHHhcCcceEEE
Confidence 5777765 45 44444432 39999999999999943 1 23456899999999999999875 1222244455665
Q ss_pred Ee
Q 005060 696 IC 697 (716)
Q Consensus 696 I~ 697 (716)
|.
T Consensus 78 ~~ 79 (81)
T cd06401 78 LF 79 (81)
T ss_pred Ee
Confidence 53
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=90.78 E-value=0.69 Score=41.40 Aligned_cols=65 Identities=20% Similarity=0.424 Sum_probs=51.5
Q ss_pred EEEEcCceeeeeecCCCCCChHHHHHHHHhhhccCCCcCCCCCCcEEEEecCCCCeEEcc-CCChHHHHhccee
Q 005060 621 KVIKFGTALGRSVDLTRFHGYDELISELDQMFDFNGSLIDGNSGFHIAYMDDEGDMMLVG-DNPWQDFQCAVRR 693 (716)
Q Consensus 621 KV~meG~~vGR~vDLs~~~sY~eL~~~L~~MF~~~g~l~~~~~~~~v~Y~D~eGD~mlvG-D~PW~~F~~~vkr 693 (716)
||.-+|. -|++-...-=+|.+|.++|+.+|.+.-. ...|+|.|.|||..-+- |+=.++|.+-..+
T Consensus 4 Kv~~~g~--~RRf~~~~~pt~~~L~~kl~~Lf~lp~~------~~~vtYiDeD~D~ITlssd~eL~d~~~~~~~ 69 (82)
T cd06397 4 KSSFLGD--TRRIVFPDIPTWEALASKLENLYNLPEI------KVGVTYIDNDNDEITLSSNKELQDFYRLSHR 69 (82)
T ss_pred EEEeCCc--eEEEecCCCccHHHHHHHHHHHhCCChh------HeEEEEEcCCCCEEEecchHHHHHHHHhccc
Confidence 8988884 7888888899999999999999998641 26899999999987554 4556666665444
No 19
>cd06402 PB1_p62 The PB1 domain is an essential part of p62 scaffold protein (alias sequestosome 1,SQSTM) involved in cell signaling, receptor internalization, and protein turnover. The PB1 domain is a modular domain mediating specific protein-protein interaction which play roles in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.
Probab=90.72 E-value=0.91 Score=41.12 Aligned_cols=59 Identities=20% Similarity=0.435 Sum_probs=44.4
Q ss_pred eEEEEEcC----ceeee-eecCCCCCChHHHHHHHHhhhccCCCcCCCCCCcEEEEecCCCCeEEccCC
Q 005060 619 CTKVIKFG----TALGR-SVDLTRFHGYDELISELDQMFDFNGSLIDGNSGFHIAYMDDEGDMMLVGDN 682 (716)
Q Consensus 619 ~vKV~meG----~~vGR-~vDLs~~~sY~eL~~~L~~MF~~~g~l~~~~~~~~v~Y~D~eGD~mlvGD~ 682 (716)
.||.+..| ..|=| ++|=....+|++|...+.++|..-. +..+.+.|.|.|||..-+..+
T Consensus 2 ~vkayl~~~~~~~EIRRf~l~~~~~~s~~~L~~~V~~~f~~l~-----~~~ftlky~DeeGDlvtIssd 65 (87)
T cd06402 2 TVKAYLLGKDANAEIRRFAIDEDVSTSYEYLVEKVAAVFPSLR-----GKNFQLFWKDEEGDLVAFSSD 65 (87)
T ss_pred eEEEeecCCCCccceEEEEecCCCCcCHHHHHHHHHHHccccC-----CCcEEEEEECCCCCEEeecCH
Confidence 47888777 33433 3455667799999999999996322 256899999999999888765
No 20
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=69.49 E-value=3.6 Score=50.05 Aligned_cols=67 Identities=28% Similarity=0.455 Sum_probs=45.7
Q ss_pred ccCCCCCEEEEEecchhhhhccccCcc--ccccCCCCCCCCcceEEEEeeEeeccCCCCeeeEEEEeecC
Q 005060 57 YVPRVGDIVYYFLQGHMEQVEAYNSQD--DKAELPIYNLPPKILCEVVYAQLKAEPGTDEVFAQITLLPR 124 (716)
Q Consensus 57 ~lP~~gs~V~YFPqGH~Eq~~~s~~~~--~~~~~p~~~lp~~i~C~V~~V~l~Ad~~TDEVyA~i~L~P~ 124 (716)
.||..|+.|.||-|||-|-+.+..-.. .... -..++-..=.|.|..+..--=+....--.+|+|.=+
T Consensus 872 yipQmgDEViyfrQghqeyl~~~~~n~~~~~~~-~p~~~~~v~~~kv~kl~~~~y~~~~~s~c~m~l~~i 940 (1113)
T KOG0644|consen 872 YIPQMGDEVIYFRQGHQEYLEAVRLNNIELNNK-EPWNKMAVEICKVEKLVYITYPGSGDSCCKMKLAVI 940 (1113)
T ss_pred ccccccceeehhhhhhHHHHhhhhhcccccccc-CcccccchhhheeeeeeeeeccCCCcchheeeeeee
Confidence 589999999999999999999865211 1111 111233334899988877777777777777777544
No 21
>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=67.01 E-value=23 Score=31.87 Aligned_cols=68 Identities=12% Similarity=0.276 Sum_probs=52.1
Q ss_pred EEEEEcCceeeeeecCCCCCChHHHHHHHHhhhccCCCcCCCCCCcEEEEecCCC-CeEEccCCChHHHHhcce--eeEE
Q 005060 620 TKVIKFGTALGRSVDLTRFHGYDELISELDQMFDFNGSLIDGNSGFHIAYMDDEG-DMMLVGDNPWQDFQCAVR--RMFI 696 (716)
Q Consensus 620 vKV~meG~~vGR~vDLs~~~sY~eL~~~L~~MF~~~g~l~~~~~~~~v~Y~D~eG-D~mlvGD~PW~~F~~~vk--ri~I 696 (716)
||||-++ -| .|-...=-+|.+|+..|.+=+.+.++- -+|-|.|.+. +...++|.=++.-.+.|+ +|+.
T Consensus 5 vKV~f~~-tI--aIrvp~~~~y~~L~~ki~~kLkl~~e~------i~LsYkde~s~~~v~l~d~dle~aws~~~~~~lTL 75 (80)
T cd06406 5 VKVHFKY-TV--AIQVARGLSYATLLQKISSKLELPAEH------ITLSYKSEASGEDVILSDTNMEDVWSQAKDGCLTL 75 (80)
T ss_pred EEEEEEE-EE--EEEcCCCCCHHHHHHHHHHHhCCCchh------cEEEeccCCCCCccCcChHHHHHHHHhhcCCeEEE
Confidence 6999998 33 455666678999999999999986532 3899998664 554559999999888888 5654
No 22
>PRK10737 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=60.78 E-value=34 Score=35.36 Aligned_cols=104 Identities=19% Similarity=0.188 Sum_probs=63.8
Q ss_pred CCCCCCEEEE-E--EcCCCcEEEEEEEeccccCCCCcccccccccccchhHHHHHHHhcCCeEEEEEecCCC------CC
Q 005060 226 KLVAGDVCIF-L--RGGDGELRVGVRRAMKLQNNASTSVISSLSMQHGILAGAFHAISTGTRFTVYYHPWTR------PA 296 (716)
Q Consensus 226 ~L~aGD~VvF-~--R~~~G~l~vGIRRa~~~~~~~p~sv~s~~s~~~gvla~a~~a~~tg~~F~V~Y~Pr~s------~~ 296 (716)
++..|+.|.+ | |.++|+++---+ ...|-..+-....-+--|++|....+.|..|+|..-|-.. -.
T Consensus 2 kI~~~~vV~l~Y~l~~~dG~v~dst~------~~~Pl~~~~G~g~lipglE~aL~G~~~Gd~~~v~l~peeAyGe~d~~l 75 (196)
T PRK10737 2 KVAKDLVVSLAYQVRTEDGVLVDESP------VSAPLDYLHGHGSLISGLETALEGHEVGDKFDVAVGANDAYGQYDENL 75 (196)
T ss_pred ccCCCCEEEEEEEEEeCCCCEEEecC------CCCCeEEEeCCCcchHHHHHHHcCCCCCCEEEEEEChHHhcCCCChHH
Confidence 3556777777 3 346777633221 1234433333333333477888888899999999766322 12
Q ss_pred ceEEehhhHHhhhccCCccccEEEEEecCCcccccceeEEEEeeec
Q 005060 297 EFLVPFSQYMKSAEIDYSIGTRFRMVFEGEECADQRIAGTVVGTED 342 (716)
Q Consensus 297 EFvV~~~ky~~A~~~~w~~GmRFkM~fE~ed~~~~~~~GtI~gv~~ 342 (716)
=..||++.+.... ...+||||.+.- ++ ..+.++|+.|.+
T Consensus 76 V~~vpr~~F~~~~--~l~~G~~~~~~~--~~---G~~~~~V~ev~~ 114 (196)
T PRK10737 76 VQRVPKDVFMGVD--ELQVGMRFLAET--DQ---GPVPVEITAVED 114 (196)
T ss_pred EEEecHHHCCCcc--CCCCCCEEEEeC--CC---CcEEEEEEEEcC
Confidence 3577887774322 368999998754 33 246889999986
No 23
>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=46.16 E-value=25 Score=32.26 Aligned_cols=41 Identities=22% Similarity=0.364 Sum_probs=33.2
Q ss_pred cCCCCCChHHHHHHHHhhhccCCCcCCCCCCcEEEEecCCCCeEEccCC
Q 005060 634 DLTRFHGYDELISELDQMFDFNGSLIDGNSGFHIAYMDDEGDMMLVGDN 682 (716)
Q Consensus 634 DLs~~~sY~eL~~~L~~MF~~~g~l~~~~~~~~v~Y~D~eGD~mlvGD~ 682 (716)
||+..-+|.+|.....+-|.-+. -.+-|+|.|||..-+=|+
T Consensus 23 ~l~~~P~~kdLl~lmr~~f~~~d--------IaLNYrD~EGDLIRlldd 63 (92)
T cd06399 23 DLSSTPLLKDLLELTRREFQRED--------IALNYRDAEGDLIRLLSD 63 (92)
T ss_pred ccccCccHHHHHHHHHHHhchhh--------eeeeeecCCCCEEEEcch
Confidence 78899999999999999998654 267799999998544333
No 24
>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=40.16 E-value=27 Score=27.48 Aligned_cols=27 Identities=22% Similarity=0.256 Sum_probs=22.4
Q ss_pred hheecCCCCCCCEEEEEEcCCCcEEEE
Q 005060 220 VFVTSKKLVAGDVCIFLRGGDGELRVG 246 (716)
Q Consensus 220 ~FV~~K~L~aGD~VvF~R~~~G~l~vG 246 (716)
.|.++.+|.+||.|.|.-.++|++.+-
T Consensus 14 ~~~~~l~l~~Gd~v~i~~~~~g~i~i~ 40 (47)
T PF04014_consen 14 EIREKLGLKPGDEVEIEVEGDGKIVIR 40 (47)
T ss_dssp HHHHHTTSSTTTEEEEEEETTSEEEEE
T ss_pred HHHHHcCCCCCCEEEEEEeCCCEEEEE
Confidence 566788999999999999998866543
No 25
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=36.38 E-value=53 Score=30.16 Aligned_cols=27 Identities=22% Similarity=0.335 Sum_probs=22.3
Q ss_pred heecCCCCCCCEEEEEEcCCCcEEEEE
Q 005060 221 FVTSKKLVAGDVCIFLRGGDGELRVGV 247 (716)
Q Consensus 221 FV~~K~L~aGD~VvF~R~~~G~l~vGI 247 (716)
|.-...|++||.|..+|.++|..++-+
T Consensus 71 i~~~~~Lk~GD~V~ll~~~~gQ~yiVl 97 (100)
T PF10844_consen 71 ITFTDGLKVGDKVLLLRVQGGQKYIVL 97 (100)
T ss_pred EEEecCCcCCCEEEEEEecCCCEEEEE
Confidence 666778999999999999888766544
No 26
>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=35.05 E-value=66 Score=26.68 Aligned_cols=31 Identities=16% Similarity=0.314 Sum_probs=24.6
Q ss_pred cccEEEEEecCCcccccceeEEEEeeecCCC
Q 005060 315 IGTRFRMVFEGEECADQRIAGTVVGTEDVDH 345 (716)
Q Consensus 315 ~GmRFkM~fE~ed~~~~~~~GtI~gv~~~dp 345 (716)
+|-|+.-.||+++.+...|.|+|....++.|
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 5889999999999888899999999887654
No 27
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=33.66 E-value=62 Score=26.36 Aligned_cols=28 Identities=18% Similarity=0.246 Sum_probs=23.9
Q ss_pred CCccccEEEEEecCCcccccceeEEEEeeec
Q 005060 312 DYSIGTRFRMVFEGEECADQRIAGTVVGTED 342 (716)
Q Consensus 312 ~w~~GmRFkM~fE~ed~~~~~~~GtI~gv~~ 342 (716)
.|++|+++-..++. ...||.|+|+.+..
T Consensus 2 ~~~~G~~Ve~~~~~---~~~W~~a~V~~~~~ 29 (61)
T smart00743 2 DFKKGDRVEVFSKE---EDSWWEAVVTKVLG 29 (61)
T ss_pred CcCCCCEEEEEECC---CCEEEEEEEEEECC
Confidence 58899999999964 25899999999875
No 28
>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=32.70 E-value=92 Score=26.74 Aligned_cols=69 Identities=12% Similarity=0.045 Sum_probs=50.8
Q ss_pred ceEEEEEcCcee---eeeecCCCCCChHHHHHHHHhhhccCCCcCCCCCCcEEE-E-ecCCCCeEEcc-CCChHHHHhc
Q 005060 618 SCTKVIKFGTAL---GRSVDLTRFHGYDELISELDQMFDFNGSLIDGNSGFHIA-Y-MDDEGDMMLVG-DNPWQDFQCA 690 (716)
Q Consensus 618 ~~vKV~meG~~v---GR~vDLs~~~sY~eL~~~L~~MF~~~g~l~~~~~~~~v~-Y-~D~eGD~mlvG-D~PW~~F~~~ 690 (716)
.++||+++...- -++|=++....-.+++..+.+-|++.+ ...+|.|+ + ........|-. +.|+..+...
T Consensus 3 ~~lrVy~~~~~~~~~~k~i~v~~~tTa~evi~~~l~k~~l~~----~~~~y~L~~~~~~~~~er~L~~~E~pl~i~~~~ 77 (93)
T PF00788_consen 3 GVLRVYDGDGSPGSTYKTIKVSSSTTAREVIEMALEKFGLAE----DPSDYCLVEVEESGGEERPLDDDECPLQIQLQW 77 (93)
T ss_dssp EEEEEEETTSSSCCSEEEEEEETTSBHHHHHHHHHHHTTTSS----SGGGEEEEEEECTTTEEEEETTTSBHHHHHHTT
T ss_pred eEEEEEcCCCCCCccEEEEEECCCCCHHHHHHHHHHHhCCCC----CCCCEEEEEEEcCCCEEEEcCCCCchHHHHHhC
Confidence 578999988653 689999999999999999999999933 45679994 4 44555555543 3566666554
No 29
>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=31.95 E-value=86 Score=26.60 Aligned_cols=41 Identities=12% Similarity=0.188 Sum_probs=28.0
Q ss_pred CccccEEEEEecCCcccccceeEEEEeeecCCCCCCCCCcccceeeecccC
Q 005060 313 YSIGTRFRMVFEGEECADQRIAGTVVGTEDVDHIRWPASEWRCLKVKWDAT 363 (716)
Q Consensus 313 w~~GmRFkM~fE~ed~~~~~~~GtI~gv~~~dp~~Wp~S~WR~L~V~WDe~ 363 (716)
|.+|+++-..-+.+.....||.|+|+..... + .+.|+.++-
T Consensus 1 F~~G~~VEV~s~e~g~~gaWf~a~V~~~~~~-------~---~~~V~Y~~~ 41 (68)
T PF05641_consen 1 FKKGDEVEVSSDEDGFRGAWFPATVLKENGD-------D---KYLVEYDDL 41 (68)
T ss_dssp --TT-EEEEEE-SBTT--EEEEEEEEEEETT-----------EEEEEETT-
T ss_pred CCCCCEEEEEEcCCCCCcEEEEEEEEEeCCC-------c---EEEEEECCc
Confidence 5689999998877666669999999999872 2 778888765
No 30
>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=27.99 E-value=58 Score=24.42 Aligned_cols=26 Identities=27% Similarity=0.282 Sum_probs=21.7
Q ss_pred hheecCCCCCCCEEEEEEcCCCcEEE
Q 005060 220 VFVTSKKLVAGDVCIFLRGGDGELRV 245 (716)
Q Consensus 220 ~FV~~K~L~aGD~VvF~R~~~G~l~v 245 (716)
.|.++.++..||.|.+....+|.+.+
T Consensus 14 ~~r~~l~~~~gd~~~i~~~~~~~l~l 39 (43)
T TIGR01439 14 EIREKLGLKEGDRLEVIRVEDGEIIL 39 (43)
T ss_pred HHHHHcCcCCCCEEEEEEeCCCEEEE
Confidence 67789999999999999877776544
No 31
>COG1047 SlpA FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]
Probab=27.39 E-value=3.7e+02 Score=27.61 Aligned_cols=105 Identities=24% Similarity=0.309 Sum_probs=64.9
Q ss_pred CCCCCCEEEEE---EcCCCcEEEEEEEeccccCCCCcccccccccccchhHHHHHHHhcCCeEEEEEecCCCCCce----
Q 005060 226 KLVAGDVCIFL---RGGDGELRVGVRRAMKLQNNASTSVISSLSMQHGILAGAFHAISTGTRFTVYYHPWTRPAEF---- 298 (716)
Q Consensus 226 ~L~aGD~VvF~---R~~~G~l~vGIRRa~~~~~~~p~sv~s~~s~~~gvla~a~~a~~tg~~F~V~Y~Pr~s~~EF---- 298 (716)
++..||.|.+. |.++|+++=--.- ...|-.++-++..-+.-|++|.....-|.-|+|.--|-..-.++
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 45678888773 3455654321110 12344444344333345788888889999999998885433333
Q ss_pred --EEehhhHHhhhccCCccccEEEEEecCCcccccceeEEEEeeec
Q 005060 299 --LVPFSQYMKSAEIDYSIGTRFRMVFEGEECADQRIAGTVVGTED 342 (716)
Q Consensus 299 --vV~~~ky~~A~~~~w~~GmRFkM~fE~ed~~~~~~~GtI~gv~~ 342 (716)
.|+++++...= ...+||+|.. ++++ .-.-|+|+.|..
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 46666665542 6789999874 4444 457899998875
No 32
>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=24.48 E-value=87 Score=28.21 Aligned_cols=56 Identities=20% Similarity=0.267 Sum_probs=31.4
Q ss_pred ehhhHHhhhccCCccccEEEEEecCCcccccceeEEEEeeecCCCCCCCCCcccceeeecccC
Q 005060 301 PFSQYMKSAEIDYSIGTRFRMVFEGEECADQRIAGTVVGTEDVDHIRWPASEWRCLKVKWDAT 363 (716)
Q Consensus 301 ~~~ky~~A~~~~w~~GmRFkM~fE~ed~~~~~~~GtI~gv~~~dp~~Wp~S~WR~L~V~WDe~ 363 (716)
+.+.|..=++-+.++||++||.=.=|+-. .-=.|+|.-++. |- -|+ -.+||.|...
T Consensus 6 s~d~Ya~YVr~~i~~GM~VRc~~~yeeV~-~GD~G~V~k~~~-dg--~~~---lnvqv~W~~~ 61 (78)
T PF11515_consen 6 SNDDYAEYVRDNIQPGMRVRCCRDYEEVR-AGDEGEVFKQDR-DG--LHD---LNVQVDWQSK 61 (78)
T ss_dssp SSHHHHHHHHHH--TT-EEEESS-BTTB--TT-EEE-EEEE--TT--SSE-----EEEEETTT
T ss_pred chhHHHHHHHHhCCCCcEEEEeccccccc-ccccceeEeecc-CC--CCC---cceEEEeeec
Confidence 35678888888999999999986665543 234677666664 21 122 3578888765
No 33
>KOG3938 consensus RGS-GAIP interacting protein GIPC, contains PDZ domain [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=24.07 E-value=98 Score=33.90 Aligned_cols=73 Identities=22% Similarity=0.367 Sum_probs=55.0
Q ss_pred EcCceeeeeecCCCCCChHHHHHHHHhhhccCCCcCCCCCCcEEEEe---c--CCCCeEEccCCChHHHH-----hccee
Q 005060 624 KFGTALGRSVDLTRFHGYDELISELDQMFDFNGSLIDGNSGFHIAYM---D--DEGDMMLVGDNPWQDFQ-----CAVRR 693 (716)
Q Consensus 624 meG~~vGR~vDLs~~~sY~eL~~~L~~MF~~~g~l~~~~~~~~v~Y~---D--~eGD~mlvGD~PW~~F~-----~~vkr 693 (716)
-+|.|+|| +..|++-+|||..+++-|+|.-. .|.|- + .|=+-||-|-.-+++|+ .-.|.
T Consensus 61 AHGSptg~---Ie~fsnv~ELY~kIAe~F~Is~~--------dIlfcTlNshKvDM~~llgGqigleDfiFAHvkGq~kE 129 (334)
T KOG3938|consen 61 AHGSPTGR---IEGFSNVRELYQKIAEAFDISPD--------DILFCTLNSHKVDMKRLLGGQIGLEDFIFAHVKGQAKE 129 (334)
T ss_pred ccCCccce---ecccccHHHHHHHHHHHhcCCcc--------ceEEEecCCCcccHHHHhcCccChhhhhhhhhcCccee
Confidence 36889998 46789999999999999999652 12222 2 34445888999999985 45678
Q ss_pred eEEecCCccCCcCC
Q 005060 694 MFICPKEDIDGVIP 707 (716)
Q Consensus 694 i~I~~~~e~~~m~~ 707 (716)
+.|++.+++-+++.
T Consensus 130 v~v~KsedalGlTI 143 (334)
T KOG3938|consen 130 VEVVKSEDALGLTI 143 (334)
T ss_pred EEEEecccccceEE
Confidence 99999999877754
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=23.59 E-value=74 Score=30.31 Aligned_cols=26 Identities=27% Similarity=0.454 Sum_probs=17.2
Q ss_pred CCCCCCCEEEEEEcC-CCcEEEEEEEe
Q 005060 225 KKLVAGDVCIFLRGG-DGELRVGVRRA 250 (716)
Q Consensus 225 K~L~aGD~VvF~R~~-~G~l~vGIRRa 250 (716)
++++.||.|+||... .+.-+||+=+-
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 489999999999987 56677776554
No 35
>PRK14129 heat shock protein HspQ; Provisional
Probab=22.44 E-value=1.2e+02 Score=28.80 Aligned_cols=54 Identities=19% Similarity=0.246 Sum_probs=37.7
Q ss_pred ccCCccccEEEEEecCCcccccceeEEEEeeecCCCCCCCCCcccceeeecccCCCCCCCCCccCCCccccC
Q 005060 310 EIDYSIGTRFRMVFEGEECADQRIAGTVVGTEDVDHIRWPASEWRCLKVKWDATTDSITRPARVSPWNIEPI 381 (716)
Q Consensus 310 ~~~w~~GmRFkM~fE~ed~~~~~~~GtI~gv~~~dp~~Wp~S~WR~L~V~WDe~~~~~~~~~RVSPWeIEpv 381 (716)
..+|.+|.-+|-+.- .|-|.|+.|.+..+. ..+| |++- ... ++.|=.||==-++
T Consensus 3 ~akF~IGQ~VrHrl~-------~yrGVV~DVDP~fs~---~e~w------~~~i-a~~-~p~kdqPwYHvl~ 56 (105)
T PRK14129 3 ASKFGIGQQVRHSLL-------GYLGVVVDIDPEYSL---EEPS------PDEL-AVN-DELRAAPWYHVVM 56 (105)
T ss_pred cccccCCcEEEEeec-------CCCeEEEeeCCCcCC---Cchh------HHhh-ccC-CCccCCCceEEEE
Confidence 468899999998876 499999999875442 3455 6665 332 6677788854444
No 36
>cd06410 PB1_UP2 Uncharacterized protein 2. 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 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.
Probab=22.15 E-value=1e+02 Score=28.49 Aligned_cols=58 Identities=24% Similarity=0.437 Sum_probs=36.5
Q ss_pred EEcCceeeeeecCCCCCChHHHHHHHHhhhccCCCcCCCCCCcEEEEe--cCCCC-eEEccCCChHHHHhcc
Q 005060 623 IKFGTALGRSVDLTRFHGYDELISELDQMFDFNGSLIDGNSGFHIAYM--DDEGD-MMLVGDNPWQDFQCAV 691 (716)
Q Consensus 623 ~meG~~vGR~vDLs~~~sY~eL~~~L~~MF~~~g~l~~~~~~~~v~Y~--D~eGD-~mlvGD~PW~~F~~~v 691 (716)
++.|+ -|-|.+.+--+|.||..+|.++|++... +.+-|+ +++-| ..-|-++ ++..+|+
T Consensus 19 Y~GG~--tr~i~V~r~~s~~el~~kl~~~~~~~~~-------~~lky~Lp~edld~Lisv~~D--eDl~~M~ 79 (97)
T cd06410 19 YVGGE--TRIVSVDRSISFKELVSKLSELFGAGVV-------VTLKYQLPDEDLDALISVSND--EDLKNMM 79 (97)
T ss_pred EcCCc--eEEEEEcCCCCHHHHHHHHHHHhCCCCc-------eEEEEEcCCCCcceeEEecCc--HHHHHHH
Confidence 45554 4666666667999999999999998652 344444 34444 4555554 4444444
No 37
>KOG3606 consensus Cell polarity protein PAR6 [Signal transduction mechanisms]
Probab=21.77 E-value=1e+02 Score=33.84 Aligned_cols=66 Identities=21% Similarity=0.432 Sum_probs=50.0
Q ss_pred eecCCCCCChHHHHHHHHhhhccCCCcCCCCCCcEEEEecCCCCeEEcc-CCChHHHHhcce---eeEEecCCccC
Q 005060 632 SVDLTRFHGYDELISELDQMFDFNGSLIDGNSGFHIAYMDDEGDMMLVG-DNPWQDFQCAVR---RMFICPKEDID 703 (716)
Q Consensus 632 ~vDLs~~~sY~eL~~~L~~MF~~~g~l~~~~~~~~v~Y~D~eGD~mlvG-D~PW~~F~~~vk---ri~I~~~~e~~ 703 (716)
+++-..-.+|++.+.-|+.+-.|.+ .++.|-|.|.-||.+-+- |+-+..-+++++ ||.|-+++|+.
T Consensus 33 sl~r~~~~~f~~F~~Lv~~~H~i~n------vdvllgY~d~hgDLLPinNDDn~~ka~~sa~PlLR~~iQkr~ea~ 102 (358)
T KOG3606|consen 33 SLPRHSASSFDEFYSLVEHLHHIPN------VDVLLGYADTHGDLLPINNDDNLHKALSSARPLLRLLIQKREEAD 102 (358)
T ss_pred cccccCcccHHHHHHHHHHHhcCCC------ceEEEEEecCCCceecccCchhHHHHhhccCchhhhhhhhhhhhh
Confidence 3445556799999999999888765 346889999999999875 555555555666 88899987774
No 38
>KOG3207 consensus Beta-tubulin folding cofactor E [Posttranslational modification, protein turnover, chaperones]
Probab=21.47 E-value=94 Score=36.25 Aligned_cols=37 Identities=38% Similarity=0.631 Sum_probs=25.1
Q ss_pred CccccEEEEEecCCcccccceeEEEEeeecCCCCCCCCCcccceeeecccC
Q 005060 313 YSIGTRFRMVFEGEECADQRIAGTVVGTEDVDHIRWPASEWRCLKVKWDAT 363 (716)
Q Consensus 313 w~~GmRFkM~fE~ed~~~~~~~GtI~gv~~~dp~~Wp~S~WR~L~V~WDe~ 363 (716)
+.+|.|+|..++ -+..||.|+|.| |++ +| |.|.||++
T Consensus 3 ~~IG~RvkI~~~---~~Tvr~iG~V~g--------~~~-~w--~GvEWDd~ 39 (505)
T KOG3207|consen 3 MEIGTRVKIGGE---IATVRYIGEVEG--------NNS-KW--YGVEWDDP 39 (505)
T ss_pred eeccceEEEcCE---EEEEEEEEEEcC--------CCC-cc--eeeEecCC
Confidence 458999998776 223556666544 444 44 78999999
No 39
>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=20.05 E-value=1.6e+02 Score=23.33 Aligned_cols=53 Identities=9% Similarity=0.298 Sum_probs=37.4
Q ss_pred CCccccEEEEEecCCcccccceeEEEEeeecCCCCCCCCCcccceeeecccCCCCCCCCCccCCCccccCC
Q 005060 312 DYSIGTRFRMVFEGEECADQRIAGTVVGTEDVDHIRWPASEWRCLKVKWDATTDSITRPARVSPWNIEPIE 382 (716)
Q Consensus 312 ~w~~GmRFkM~fE~ed~~~~~~~GtI~gv~~~dp~~Wp~S~WR~L~V~WDe~~~~~~~~~RVSPWeIEpv~ 382 (716)
.|.+|..+...+ . | ..||.|+|+++.. + ..+.|.-++- + +.+-|...+|-++.
T Consensus 2 ~~~~G~~~~a~~-~-d--~~wyra~I~~~~~-------~---~~~~V~f~D~-G---~~~~v~~~~l~~l~ 54 (57)
T smart00333 2 TFKVGDKVAARW-E-D--GEWYRARIIKVDG-------E---QLYEVFFIDY-G---NEEVVPPSDLRPLP 54 (57)
T ss_pred CCCCCCEEEEEe-C-C--CCEEEEEEEEECC-------C---CEEEEEEECC-C---ccEEEeHHHeecCC
Confidence 588999999999 3 2 5899999999986 1 4567888774 2 23455655555443
Done!