Query 003731
Match_columns 799
No_of_seqs 349 out of 820
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 04:56:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003731.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003731hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF06507 Auxin_resp: Auxin res 100.0 2.2E-35 4.9E-40 261.1 8.5 83 241-324 1-83 (83)
2 PF02309 AUX_IAA: AUX/IAA fami 100.0 4.6E-35 9.9E-40 297.8 0.0 95 677-771 107-215 (215)
3 PF02362 B3: B3 DNA binding do 99.7 1.6E-16 3.5E-21 141.3 11.3 97 115-216 1-99 (100)
4 KOG0644 Uncharacterized conser 99.3 3.2E-12 6.9E-17 148.1 6.2 148 193-349 874-1044(1113)
5 PF09217 EcoRII-N: Restriction 98.4 1.1E-06 2.4E-11 86.5 10.1 90 112-202 7-110 (156)
6 PF03754 DUF313: Domain of unk 97.7 7.1E-05 1.5E-09 71.0 6.7 81 109-190 18-114 (114)
7 PF00564 PB1: PB1 domain; Int 96.9 0.0026 5.5E-08 55.4 6.6 67 681-754 3-70 (84)
8 smart00666 PB1 PB1 domain. Pho 96.1 0.025 5.3E-07 49.2 7.5 65 682-754 4-69 (81)
9 cd05992 PB1 The PB1 domain is 95.7 0.041 8.9E-07 47.5 7.3 65 682-754 3-69 (81)
10 cd06407 PB1_NLP A PB1 domain i 95.3 0.05 1.1E-06 49.0 6.7 61 681-748 2-63 (82)
11 cd06396 PB1_NBR1 The PB1 domai 95.0 0.069 1.5E-06 48.3 6.4 52 682-742 3-55 (81)
12 cd06409 PB1_MUG70 The MUG70 pr 94.8 0.053 1.1E-06 49.5 5.3 49 690-742 9-59 (86)
13 cd06398 PB1_Joka2 The PB1 doma 94.7 0.098 2.1E-06 48.0 6.8 57 682-744 3-63 (91)
14 cd06404 PB1_aPKC PB1 domain is 90.8 0.58 1.2E-05 42.7 5.8 54 681-742 2-56 (83)
15 cd06403 PB1_Par6 The PB1 domai 88.6 1.2 2.5E-05 40.5 5.9 67 682-755 3-71 (80)
16 cd06397 PB1_UP1 Uncharacterize 87.6 1.4 3.1E-05 40.1 5.8 65 683-755 4-69 (82)
17 cd06401 PB1_TFG The PB1 domain 87.5 1.7 3.6E-05 39.7 6.2 58 682-744 3-61 (81)
18 cd06408 PB1_NoxR The PB1 domai 84.3 3 6.6E-05 38.3 6.3 56 679-744 2-57 (86)
19 cd06402 PB1_p62 The PB1 domain 83.8 3.7 8E-05 37.8 6.7 57 681-743 2-64 (87)
20 cd06399 PB1_P40 The PB1 domain 73.7 4.7 0.0001 37.4 4.1 53 695-773 23-75 (92)
21 PRK10737 FKBP-type peptidyl-pr 61.0 25 0.00053 36.9 6.9 104 192-309 2-114 (196)
22 KOG0644 Uncharacterized conser 60.1 7 0.00015 48.3 3.1 67 22-90 872-940 (1113)
23 smart00743 Agenet Tudor-like d 46.3 30 0.00064 28.7 3.9 28 279-309 2-29 (61)
24 PF04014 Antitoxin-MazE: Antid 42.9 28 0.00061 27.9 3.1 38 173-213 4-41 (47)
25 PF00788 RA: Ras association ( 41.6 85 0.0018 27.3 6.3 69 679-752 2-77 (93)
26 KOG3207 Beta-tubulin folding c 37.1 41 0.00089 39.5 4.4 43 280-336 3-45 (505)
27 TIGR01439 lp_hng_hel_AbrB loop 31.3 56 0.0012 24.9 3.0 26 186-211 14-39 (43)
28 PF01878 EVE: EVE domain; Int 29.7 51 0.0011 31.9 3.1 26 191-216 38-64 (143)
29 PF10844 DUF2577: Protein of u 29.0 70 0.0015 29.8 3.8 27 187-213 71-97 (100)
30 smart00333 TUDOR Tudor domain. 27.0 99 0.0021 24.9 3.9 52 279-347 2-53 (57)
31 PF05641 Agenet: Agenet domain 25.1 1.3E+02 0.0028 25.9 4.5 42 280-331 1-42 (68)
32 PF10411 DsbC_N: Disulfide bon 25.0 58 0.0013 27.4 2.3 17 728-744 34-50 (57)
33 PF02513 Spin-Ssty: Spin/Ssty 23.5 1.3E+02 0.0028 25.4 4.0 31 282-312 1-31 (50)
34 COG1047 SlpA FKBP-type peptidy 21.5 4.8E+02 0.01 27.2 8.4 105 192-309 2-115 (174)
35 cd06406 PB1_P67 A PB1 domain i 21.3 2.5E+02 0.0055 25.8 5.7 66 681-755 4-70 (80)
No 1
>PF06507 Auxin_resp: Auxin response factor; InterPro: IPR010525 This pattern represents a conserved region of auxin-responsive transcription factors. The plant hormone auxin (indole-3-acetic acid) can regulate the gene expression of several families, including Aux/IAA, GH3 and SAUR families. Two related families of proteins, Aux/IAA proteins (IPR003311 from INTERPRO) and the auxin response factors (ARF), are key regulators of auxin-modulated gene expression []. There are multiple ARF proteins, some of which activate, while others repress transcription. ARF proteins bind to auxin-responsive cis-acting promoter elements (AuxREs) using an N-terminal DNA-binding domain. It is thought that Aux/IAA proteins activate transcription by modifying ARF activity through the C-terminal protein-protein interaction domains (IPR011525 from INTERPRO) found in both Aux/IAA and ARF proteins. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0009725 response to hormone stimulus, 0005634 nucleus
Probab=100.00 E-value=2.2e-35 Score=261.09 Aligned_cols=83 Identities=65% Similarity=1.048 Sum_probs=81.2
Q ss_pred HHHHHhcCCeEEEEEecCCCCCcceechhHHHHhhhcCCCccccEEEEeeeccCcccceeeEEEEEeecCCCCCCCCCCc
Q 003731 241 AAHAAATNSCFTVFFNPRASPSEFVIPLTKYVKAVFHTRVSVGMRFRMLFETEESSVRRYMGTITGISDLDPVRWSNSHW 320 (799)
Q Consensus 241 A~~aa~~~~~F~V~Y~Pras~sEFvVp~~ky~~a~~~~~w~~GmRFkM~fe~Eds~~~~~~GTI~gv~d~Dp~rWp~S~W 320 (799)
|+|||+++++|+|+||||++++|||||++||++|++ ++|++||||||+||+||+++++|+|||+||+|+||+|||+|+|
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 689999999999999999999999999999999998 6999999999999999999999999999999999999999999
Q ss_pred ccee
Q 003731 321 RSVK 324 (799)
Q Consensus 321 R~Lk 324 (799)
||||
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=4.6e-35 Score=297.84 Aligned_cols=95 Identities=38% Similarity=0.712 Sum_probs=0.0
Q ss_pred CcceeEEEeecc-ccceeeccCCCCChHHHHHHHHHhh---cCC----------CccCCCCCCCceEEEEeCCCceEecC
Q 003731 677 PTRTFVKVYKSG-SVGRSLDISRFSSYNELREELGQMF---GIE----------GKFEDPLRSGWQLVFVDRENDVLLLG 742 (799)
Q Consensus 677 ~~~~~vKV~m~G-~igRkvDL~~~~sY~eL~~~L~~MF---~~~----------g~l~d~~~~~~~lvY~D~EgD~mLvG 742 (799)
..++||||+||| +|||||||++|+||++|+.+|++|| +|+ +.+...++++|+|||+|+||||||||
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 468999999999 8999999999999999999999999 665 33444457799999999999999999
Q ss_pred CcchhhHhcceeEEEEeChhhhhcccccc
Q 003731 743 DDPWEAFVSNVWYIKILSPEDVQKMGEQG 771 (799)
Q Consensus 743 D~PWe~Fv~~vkri~I~~~~e~~~m~~~~ 771 (799)
||||+|||++||||+||+.+|+++|++++
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=99.69 E-value=1.6e-16 Score=141.34 Aligned_cols=97 Identities=28% Similarity=0.406 Sum_probs=75.0
Q ss_pred EEEecCcCCCCCCCceeechhhHhhhCCCCCCCCCCCCcEEEEEecCCCeEEEEEEEeCCCCceeecccchhhhcccCCC
Q 003731 115 FCKTLTASDTSTHGGFSVPRRAAEKVFPSLDFSLQPPAQELIARDLHDVEWKFRHIFRGQPKRHLLTTGWSVFVSAKRLV 194 (799)
Q Consensus 115 F~K~LT~SDv~~~grfsVPk~~Ae~~fP~Ld~~~~~p~q~L~~~D~~G~~W~Fr~~yrg~prrhlLTtGWs~FV~~K~L~ 194 (799)
|.|+|+++|+...+++.||++.++.+. +. ...++++.++|..|++|.+++.|++.+++++|++||..||++++|+
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 899999999999999999999999982 11 1136789999999999999999999888899999999999999999
Q ss_pred CCCEEEEEEcc--CCcEEEEEEec
Q 003731 195 AGDSVLFIWNE--KNQLLLGIRRA 216 (799)
Q Consensus 195 aGD~VvF~R~~--~g~L~vGiRRa 216 (799)
+||.++|...+ ..++.|.|.|+
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 44569999986
No 4
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=99.28 E-value=3.2e-12 Score=148.14 Aligned_cols=148 Identities=20% Similarity=0.346 Sum_probs=118.0
Q ss_pred CCCCCEEEEEEccCCcEEEEEEecCCCCCC---------------------CCCccccCCcccccHHHHHHHHHhcCCeE
Q 003731 193 LVAGDSVLFIWNEKNQLLLGIRRAIRPPTV---------------------MPSSVLSSDSMHIGLLAAAAHAAATNSCF 251 (799)
Q Consensus 193 L~aGD~VvF~R~~~g~L~vGiRRa~r~~~~---------------------~pssv~s~~sm~~gvla~A~~aa~~~~~F 251 (799)
.+.||.|+.+|.+..++.=.+|+..+..++ .|.+.-+.=.|.+.|+--|.++ -+..|
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 458999999998655555455554443221 1333344446888888777755 46789
Q ss_pred EEEEecCCCCCcceechhHHHHhhhcCCCccccEEEEee--eccCcccceeeEEEEEeecCCCCCCCCCCccceeeccCC
Q 003731 252 TVFFNPRASPSEFVIPLTKYVKAVFHTRVSVGMRFRMLF--ETEESSVRRYMGTITGISDLDPVRWSNSHWRSVKVGWDE 329 (799)
Q Consensus 252 ~V~Y~Pras~sEFvVp~~ky~~a~~~~~w~~GmRFkM~f--e~Eds~~~~~~GTI~gv~d~Dp~rWp~S~WR~LkV~WDe 329 (799)
.+.|......++|+|.+..|..|+. .+|.++.+||.-+ ++||. -+||.|+|.++.+..| .+|+|+|.|+.|+||.
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 9999999999999999999999997 5999999999988 33332 3799999999999888 8999999999999999
Q ss_pred CCCCCCCCCcccccceeCCC
Q 003731 330 STAGERQPRVSLWEIEPLTT 349 (799)
Q Consensus 330 ~~~~~~~~RVSPWeIEpv~~ 349 (799)
.+. +.-||||.|++..
T Consensus 1029 ~e~----~~~spwe~~~i~d 1044 (1113)
T KOG0644|consen 1029 TET----ELHSPWEMEPIPD 1044 (1113)
T ss_pred Ccc----cccCccccCCCcc
Confidence 975 7789999999976
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=98.44 E-value=1.1e-06 Score=86.46 Aligned_cols=90 Identities=26% Similarity=0.392 Sum_probs=60.4
Q ss_pred ceeEEEecCcCCCCCCC----ceeechhhHhhhCCCCCC-CCCCCCcEEEEEecCC--CeEEEEEEEeCC------CCce
Q 003731 112 TNYFCKTLTASDTSTHG----GFSVPRRAAEKVFPSLDF-SLQPPAQELIARDLHD--VEWKFRHIFRGQ------PKRH 178 (799)
Q Consensus 112 ~~~F~K~LT~SDv~~~g----rfsVPk~~Ae~~fP~Ld~-~~~~p~q~L~~~D~~G--~~W~Fr~~yrg~------prrh 178 (799)
...|+|.|++.|++..| |+.|||..++..||.|.. +..+|...|.+++..| ..|+||+||.|+ ...|
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 799999999999998766 6778999999999988 479999999987 6779
Q ss_pred eecccchhhhcccC-CCCCCEEEEE
Q 003731 179 LLTTGWSVFVSAKR-LVAGDSVLFI 202 (799)
Q Consensus 179 lLTtGWs~FV~~K~-L~aGD~VvF~ 202 (799)
.|| .|...-.--+ =..||.+||-
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 3443322111 2478888876
No 6
>PF03754 DUF313: Domain of unknown function (DUF313) ; InterPro: IPR005508 This is a family of proteins from Arabidopsis thaliana (Mouse-ear cress) with uncharacterised function.
Probab=97.72 E-value=7.1e-05 Score=70.99 Aligned_cols=81 Identities=22% Similarity=0.267 Sum_probs=62.8
Q ss_pred CCCceeEEEecCcCCCCCC-CceeechhhHhhhCCCCCC------------CCCCCCcEEEEEecCCCeEEEEEEEeCC-
Q 003731 109 KQPTNYFCKTLTASDTSTH-GGFSVPRRAAEKVFPSLDF------------SLQPPAQELIARDLHDVEWKFRHIFRGQ- 174 (799)
Q Consensus 109 ~~~~~~F~K~LT~SDv~~~-grfsVPk~~Ae~~fP~Ld~------------~~~~p~q~L~~~D~~G~~W~Fr~~yrg~- 174 (799)
..+...++|+|++||+..+ .||+||-..... ...|.. ....-+..+.+.|..++.|..++..|..
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 4557899999999999965 899999875522 122211 1234578999999999999999999954
Q ss_pred --CCceeecccchhhhcc
Q 003731 175 --PKRHLLTTGWSVFVSA 190 (799)
Q Consensus 175 --prrhlLTtGWs~FV~~ 190 (799)
.-.|+|++||..+|+.
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=0.0026 Score=55.39 Aligned_cols=67 Identities=21% Similarity=0.431 Sum_probs=56.5
Q ss_pred eEEEeeccccceeeccCCCCChHHHHHHHHHhhcCCCccCCCCCCCceEEEEeCCCceEecCC-cchhhHhccee
Q 003731 681 FVKVYKSGSVGRSLDISRFSSYNELREELGQMFGIEGKFEDPLRSGWQLVFVDRENDVLLLGD-DPWEAFVSNVW 754 (799)
Q Consensus 681 ~vKV~m~G~igRkvDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~~~~~lvY~D~EgD~mLvGD-~PWe~Fv~~vk 754 (799)
-+|++-.|.+=|.+.+..--+|++|...+++.|++. ...++|.|.|.||||..+.+ .=|++.++.++
T Consensus 3 ~vK~~~~~~~~~~~~~~~~~s~~~L~~~i~~~~~~~-------~~~~~l~Y~D~dgD~V~i~sd~Dl~~a~~~~~ 70 (84)
T PF00564_consen 3 RVKVRYGGDIRRIISLPSDVSFDDLRSKIREKFGLL-------DEDFQLKYKDEDGDLVTISSDEDLQEAIEQAK 70 (84)
T ss_dssp EEEEEETTEEEEEEEECSTSHHHHHHHHHHHHHTTS-------TSSEEEEEEETTSSEEEESSHHHHHHHHHHHH
T ss_pred EEEEEECCeeEEEEEcCCCCCHHHHHHHHHHHhCCC-------CccEEEEeeCCCCCEEEeCCHHHHHHHHHHHH
Confidence 478998886666788888889999999999999986 24799999999999988875 55888887775
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=96.08 E-value=0.025 Score=49.21 Aligned_cols=65 Identities=26% Similarity=0.486 Sum_probs=51.9
Q ss_pred EEEeeccccceeeccCCCCChHHHHHHHHHhhcCCCccCCCCCCCceEEEEeCCCceEecC-CcchhhHhccee
Q 003731 682 VKVYKSGSVGRSLDISRFSSYNELREELGQMFGIEGKFEDPLRSGWQLVFVDRENDVLLLG-DDPWEAFVSNVW 754 (799)
Q Consensus 682 vKV~m~G~igRkvDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~~~~~lvY~D~EgD~mLvG-D~PWe~Fv~~vk 754 (799)
+||+- |.--|.+-+..--+|++|++++.+.|++.. ..+.|-|+|.||||..+. |+=|++.+.+++
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 445677778888899999999999999743 468999999999998655 567777777665
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=95.72 E-value=0.041 Score=47.53 Aligned_cols=65 Identities=23% Similarity=0.516 Sum_probs=50.4
Q ss_pred EEEeeccccceeeccC-CCCChHHHHHHHHHhhcCCCccCCCCCCCceEEEEeCCCceEecCC-cchhhHhccee
Q 003731 682 VKVYKSGSVGRSLDIS-RFSSYNELREELGQMFGIEGKFEDPLRSGWQLVFVDRENDVLLLGD-DPWEAFVSNVW 754 (799)
Q Consensus 682 vKV~m~G~igRkvDL~-~~~sY~eL~~~L~~MF~~~g~l~d~~~~~~~lvY~D~EgD~mLvGD-~PWe~Fv~~vk 754 (799)
+||+-.|.+ |.+-+. .--+|++|.+.|.+.|++.. ..+.+.|.|.||||..+.+ .=|++.++.++
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 677777632 333333 78899999999999999853 3689999999999998887 66777776665
No 10
>cd06407 PB1_NLP A PB1 domain is present in NIN like proteins (NLP), a key enzyme in a process of establishment of symbiosis betweeen legumes and nitrogen fixing bacteria (Rhizobium). The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes like osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-inte
Probab=95.35 E-value=0.05 Score=48.96 Aligned_cols=61 Identities=21% Similarity=0.372 Sum_probs=44.8
Q ss_pred eEEEeeccccceeeccCCCCChHHHHHHHHHhhcCCCccCCCCCCCceEEEEeCCCceEecC-Ccchhh
Q 003731 681 FVKVYKSGSVGRSLDISRFSSYNELREELGQMFGIEGKFEDPLRSGWQLVFVDRENDVLLLG-DDPWEA 748 (799)
Q Consensus 681 ~vKV~m~G~igRkvDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~~~~~lvY~D~EgD~mLvG-D~PWe~ 748 (799)
-|||.-.|. -+.+-|..--+|++|.+++.++|++.. .+.+.|-|.|.||||.++- |.=.++
T Consensus 2 ~vK~~~~~d-~~r~~l~~~~~~~~L~~~i~~r~~~~~------~~~f~LkY~Ddegd~v~ltsd~DL~e 63 (82)
T cd06407 2 RVKATYGEE-KIRFRLPPSWGFTELKQEIAKRFKLDD------MSAFDLKYLDDDEEWVLLTCDADLEE 63 (82)
T ss_pred EEEEEeCCe-EEEEEcCCCCCHHHHHHHHHHHhCCCC------CCeeEEEEECCCCCeEEeecHHHHHH
Confidence 378888774 233445555599999999999999842 2579999999999998753 333333
No 11
>cd06396 PB1_NBR1 The PB1 domain is an essential part of NBR1 protein, next to BRCA1, a scaffold protein mediating specific protein-protein interaction with both titin protein kinase and with another scaffold protein p62. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The NBR1 protein contains a type I PB1 domain.
Probab=94.97 E-value=0.069 Score=48.33 Aligned_cols=52 Identities=23% Similarity=0.346 Sum_probs=43.4
Q ss_pred EEEeecc-ccceeeccCCCCChHHHHHHHHHhhcCCCccCCCCCCCceEEEEeCCCceEecC
Q 003731 682 VKVYKSG-SVGRSLDISRFSSYNELREELGQMFGIEGKFEDPLRSGWQLVFVDRENDVLLLG 742 (799)
Q Consensus 682 vKV~m~G-~igRkvDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~~~~~lvY~D~EgD~mLvG 742 (799)
+||.--| .+--+++-+.--+|.+|.+++.++|++. .+.|-|.|.||||.++-
T Consensus 3 vKaty~~d~~rf~~~~~~~~~~~~L~~ev~~rf~l~---------~f~lKYlDde~e~v~ls 55 (81)
T cd06396 3 LKVTYNGESQSFLVSDSENTTWASVEAMVKVSFGLN---------DIQIKYVDEENEEVSVN 55 (81)
T ss_pred EEEEECCeEEEEEecCCCCCCHHHHHHHHHHHhCCC---------cceeEEEcCCCCEEEEE
Confidence 7888888 4555666666779999999999999995 47999999999998763
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=94.82 E-value=0.053 Score=49.51 Aligned_cols=49 Identities=29% Similarity=0.388 Sum_probs=38.5
Q ss_pred cceee--ccCCCCChHHHHHHHHHhhcCCCccCCCCCCCceEEEEeCCCceEecC
Q 003731 690 VGRSL--DISRFSSYNELREELGQMFGIEGKFEDPLRSGWQLVFVDRENDVLLLG 742 (799)
Q Consensus 690 igRkv--DL~~~~sY~eL~~~L~~MF~~~g~l~d~~~~~~~lvY~D~EgD~mLvG 742 (799)
-||.+ -+....|+.+|+.+..+-|+++... ...++|-|.|.||||.|+-
T Consensus 9 ~GrvhRf~~~~s~~~~~L~~~I~~Rl~~d~~~----~~~~~L~YlDDEgD~VllT 59 (86)
T cd06409 9 KGRVHRFRLRPSESLEELRTLISQRLGDDDFE----THLYALSYVDDEGDIVLIT 59 (86)
T ss_pred CCCEEEEEecCCCCHHHHHHHHHHHhCCcccc----CCcccEEEEcCCCCEEEEe
Confidence 44443 3444789999999999999987542 3589999999999998764
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=94.70 E-value=0.098 Score=48.05 Aligned_cols=57 Identities=26% Similarity=0.426 Sum_probs=44.6
Q ss_pred EEEeeccc-cceeeccC---CCCChHHHHHHHHHhhcCCCccCCCCCCCceEEEEeCCCceEecCCc
Q 003731 682 VKVYKSGS-VGRSLDIS---RFSSYNELREELGQMFGIEGKFEDPLRSGWQLVFVDRENDVLLLGDD 744 (799)
Q Consensus 682 vKV~m~G~-igRkvDL~---~~~sY~eL~~~L~~MF~~~g~l~d~~~~~~~lvY~D~EgD~mLvGD~ 744 (799)
|||.-+|. +=-++++. .--+|++|.+++++.|.+.. ..+++|.|.|.||||..+-++
T Consensus 3 vKv~y~~~~rRf~l~~~~~~~d~~~~~L~~kI~~~f~l~~------~~~~~l~Y~Dedgd~V~l~~D 63 (91)
T cd06398 3 VKVKYGGTLRRFTFPVAENQLDLNMDGLREKVEELFSLSP------DADLSLTYTDEDGDVVTLVDD 63 (91)
T ss_pred EEEEeCCEEEEEEeccccccCCCCHHHHHHHHHHHhCCCC------CCcEEEEEECCCCCEEEEccH
Confidence 78888884 33344443 45699999999999998832 358999999999999988665
No 14
>cd06404 PB1_aPKC PB1 domain is an essential modular domain of the atypical protein kinase C (aPKC) which in complex with Par6 and Par3 proteins is crucial for establishment of apical-basal polarity of animal cells. PB1 domain is a modular domain mediating specific protein-protein interaction which play roles in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi,
Probab=90.82 E-value=0.58 Score=42.72 Aligned_cols=54 Identities=26% Similarity=0.282 Sum_probs=42.3
Q ss_pred eEEEeeccc-cceeeccCCCCChHHHHHHHHHhhcCCCccCCCCCCCceEEEEeCCCceEecC
Q 003731 681 FVKVYKSGS-VGRSLDISRFSSYNELREELGQMFGIEGKFEDPLRSGWQLVFVDRENDVLLLG 742 (799)
Q Consensus 681 ~vKV~m~G~-igRkvDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~~~~~lvY~D~EgD~mLvG 742 (799)
-+|++-.|. +--.+|. .-+|++|.+++.+||.+. ....+++.|.|.|||---+.
T Consensus 2 ~~K~~y~gdi~it~~d~--~~s~e~L~~~v~~~c~~~------~~q~ft~kw~DEEGDp~tiS 56 (83)
T cd06404 2 RVKAAYNGDIMITSIDP--SISLEELCNEVRDMCRFH------NDQPFTLKWIDEEGDPCTIS 56 (83)
T ss_pred eEEEEecCcEEEEEcCC--CcCHHHHHHHHHHHhCCC------CCCcEEEEEECCCCCceeec
Confidence 378999994 4445565 678999999999999983 23579999999999975443
No 15
>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=88.58 E-value=1.2 Score=40.50 Aligned_cols=67 Identities=21% Similarity=0.288 Sum_probs=50.3
Q ss_pred EEEeeccccce-eeccCCCCChHHHHHHHHHhhcCCCccCCCCCCCceEEEEeCCCceEecC-CcchhhHhcceeE
Q 003731 682 VKVYKSGSVGR-SLDISRFSSYNELREELGQMFGIEGKFEDPLRSGWQLVFVDRENDVLLLG-DDPWEAFVSNVWY 755 (799)
Q Consensus 682 vKV~m~G~igR-kvDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~~~~~lvY~D~EgD~mLvG-D~PWe~Fv~~vkr 755 (799)
||.+-++.+=| ++|-....+|++++.-|++|+.+.+ ..+.|-|+|.+||.+-+- |+-...=+++++.
T Consensus 3 VKSkfdaEfRRFsl~r~~~~~f~ef~~ll~~lH~l~~-------~~f~i~Y~D~~gDLLPInNDdNf~kAlssa~p 71 (80)
T cd06403 3 VKSKFDAEFRRFSLDRNKPGKFEDFYKLLEHLHHIPN-------VDFLIGYTDPHGDLLPINNDDNFLKALSSANP 71 (80)
T ss_pred eecccCCeEEEEEeccccCcCHHHHHHHHHHHhCCCC-------CcEEEEEeCCCCCEecccCcHHHHHHHHcCCC
Confidence 45555554332 6777778999999999999999954 369999999999999774 5666666666643
No 16
>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=87.61 E-value=1.4 Score=40.06 Aligned_cols=65 Identities=15% Similarity=0.281 Sum_probs=48.6
Q ss_pred EEeeccccceeeccCCCCChHHHHHHHHHhhcCCCccCCCCCCCceEEEEeCCCceEec-CCcchhhHhcceeE
Q 003731 683 KVYKSGSVGRSLDISRFSSYNELREELGQMFGIEGKFEDPLRSGWQLVFVDRENDVLLL-GDDPWEAFVSNVWY 755 (799)
Q Consensus 683 KV~m~G~igRkvDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~~~~~lvY~D~EgD~mLv-GD~PWe~Fv~~vkr 755 (799)
||+-.| -.|++....-=+|.+|++.|+.+|.+.- . ...|+|.|.|||..-+ -|+=-++|.+-..+
T Consensus 4 Kv~~~g-~~RRf~~~~~pt~~~L~~kl~~Lf~lp~------~-~~~vtYiDeD~D~ITlssd~eL~d~~~~~~~ 69 (82)
T cd06397 4 KSSFLG-DTRRIVFPDIPTWEALASKLENLYNLPE------I-KVGVTYIDNDNDEITLSSNKELQDFYRLSHR 69 (82)
T ss_pred EEEeCC-ceEEEecCCCccHHHHHHHHHHHhCCCh------h-HeEEEEEcCCCCEEEecchHHHHHHHHhccc
Confidence 674444 5677778888899999999999999942 1 3899999999997644 44566666654443
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=87.49 E-value=1.7 Score=39.65 Aligned_cols=58 Identities=17% Similarity=0.287 Sum_probs=42.4
Q ss_pred EEEeeccccceeeccCCCC-ChHHHHHHHHHhhcCCCccCCCCCCCceEEEEeCCCceEecCCc
Q 003731 682 VKVYKSGSVGRSLDISRFS-SYNELREELGQMFGIEGKFEDPLRSGWQLVFVDRENDVLLLGDD 744 (799)
Q Consensus 682 vKV~m~G~igRkvDL~~~~-sY~eL~~~L~~MF~~~g~l~d~~~~~~~lvY~D~EgD~mLvGD~ 744 (799)
+|+.-.|.|=| +-+..-. +|.+|+..+.+.|... + |......+-|.|.|||+.-+.+.
T Consensus 3 iK~~~g~DiR~-~~~~~~~~t~~~L~~~v~~~F~~~--~--~~~~~flIKYkD~dGDlVTIts~ 61 (81)
T cd06401 3 LKAQLGDDIRR-IPIHNEDITYDELLLMMQRVFRGK--L--GSSDDVLIKYKDEDGDLITIFDS 61 (81)
T ss_pred EEEEeCCeEEE-EeccCccccHHHHHHHHHHHhccc--c--CCcccEEEEEECCCCCEEEeccH
Confidence 56666555544 4444323 9999999999999953 1 23347999999999999998875
No 18
>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=84.30 E-value=3 Score=38.34 Aligned_cols=56 Identities=20% Similarity=0.409 Sum_probs=45.1
Q ss_pred ceeEEEeeccccceeeccCCCCChHHHHHHHHHhhcCCCccCCCCCCCceEEEEeCCCceEecCCc
Q 003731 679 RTFVKVYKSGSVGRSLDISRFSSYNELREELGQMFGIEGKFEDPLRSGWQLVFVDRENDVLLLGDD 744 (799)
Q Consensus 679 ~~~vKV~m~G~igRkvDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~~~~~lvY~D~EgD~mLvGD~ 744 (799)
+.-|||+-.|. -|-|-+..--+|++|.+.+.++|++. ...+|-|.|. ||+.-++|.
T Consensus 2 ~ikVKv~~~~D-v~~i~v~~~i~f~dL~~kIrdkf~~~--------~~~~iKykDE-GD~iti~sq 57 (86)
T cd06408 2 KIRVKVHAQDD-TRYIMIGPDTGFADFEDKIRDKFGFK--------RRLKIKMKDD-GDMITMGDQ 57 (86)
T ss_pred cEEEEEEecCc-EEEEEcCCCCCHHHHHHHHHHHhCCC--------CceEEEEEcC-CCCccccCH
Confidence 45689998885 45566666667999999999999984 2689999999 999888763
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=83.80 E-value=3.7 Score=37.81 Aligned_cols=57 Identities=28% Similarity=0.448 Sum_probs=42.0
Q ss_pred eEEEeecc----c-cce-eeccCCCCChHHHHHHHHHhhcCCCccCCCCCCCceEEEEeCCCceEecCC
Q 003731 681 FVKVYKSG----S-VGR-SLDISRFSSYNELREELGQMFGIEGKFEDPLRSGWQLVFVDRENDVLLLGD 743 (799)
Q Consensus 681 ~vKV~m~G----~-igR-kvDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~~~~~lvY~D~EgD~mLvGD 743 (799)
.||.+..| + |=| +||-....+|++|++.+.++|..- . ...++|-|.|.|||..-+..
T Consensus 2 ~vkayl~~~~~~~EIRRf~l~~~~~~s~~~L~~~V~~~f~~l---~---~~~ftlky~DeeGDlvtIss 64 (87)
T cd06402 2 TVKAYLLGKDANAEIRRFAIDEDVSTSYEYLVEKVAAVFPSL---R---GKNFQLFWKDEEGDLVAFSS 64 (87)
T ss_pred eEEEeecCCCCccceEEEEecCCCCcCHHHHHHHHHHHcccc---C---CCcEEEEEECCCCCEEeecC
Confidence 57888776 2 322 455567779999999999999642 1 24799999999999865543
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=73.70 E-value=4.7 Score=37.41 Aligned_cols=53 Identities=34% Similarity=0.377 Sum_probs=44.5
Q ss_pred ccCCCCChHHHHHHHHHhhcCCCccCCCCCCCceEEEEeCCCceEecCCcchhhHhcceeEEEEeChhhhhcccccccc
Q 003731 695 DISRFSSYNELREELGQMFGIEGKFEDPLRSGWQLVFVDRENDVLLLGDDPWEAFVSNVWYIKILSPEDVQKMGEQGVE 773 (799)
Q Consensus 695 DL~~~~sY~eL~~~L~~MF~~~g~l~d~~~~~~~lvY~D~EgD~mLvGD~PWe~Fv~~vkri~I~~~~e~~~m~~~~~~ 773 (799)
||+.--.|.+|..-..+-|..+ +=.|-|.|.|||. |+||+.+|+.-|-.++..
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 6778889999999999888864 3489999999996 799999999999776643
No 21
>PRK10737 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=61.00 E-value=25 Score=36.88 Aligned_cols=104 Identities=21% Similarity=0.220 Sum_probs=63.2
Q ss_pred CCCCCCEEEE-E--EccCCcEEEEEEecCCCCCCCCCccccCCcccccHHHHHHHHHhcCCeEEEEEecCCC------CC
Q 003731 192 RLVAGDSVLF-I--WNEKNQLLLGIRRAIRPPTVMPSSVLSSDSMHIGLLAAAAHAAATNSCFTVFFNPRAS------PS 262 (799)
Q Consensus 192 ~L~aGD~VvF-~--R~~~g~L~vGiRRa~r~~~~~pssv~s~~sm~~gvla~A~~aa~~~~~F~V~Y~Pras------~s 262 (799)
++..|+.|.+ | |.++|+++---+ . ..|...+-....-+--|-+|..-.+.|..|+|..-|-.. -.
T Consensus 2 kI~~~~vV~l~Y~l~~~dG~v~dst~-~-----~~Pl~~~~G~g~lipglE~aL~G~~~Gd~~~v~l~peeAyGe~d~~l 75 (196)
T PRK10737 2 KVAKDLVVSLAYQVRTEDGVLVDESP-V-----SAPLDYLHGHGSLISGLETALEGHEVGDKFDVAVGANDAYGQYDENL 75 (196)
T ss_pred ccCCCCEEEEEEEEEeCCCCEEEecC-C-----CCCeEEEeCCCcchHHHHHHHcCCCCCCEEEEEEChHHhcCCCChHH
Confidence 3456777776 3 356777643221 1 235444433333333466777788888899998655432 23
Q ss_pred cceechhHHHHhhhcCCCccccEEEEeeeccCcccceeeEEEEEeec
Q 003731 263 EFVIPLTKYVKAVFHTRVSVGMRFRMLFETEESSVRRYMGTITGISD 309 (799)
Q Consensus 263 EFvVp~~ky~~a~~~~~w~~GmRFkM~fe~Eds~~~~~~GTI~gv~d 309 (799)
-..||++.|. ... ...+||||.+ ++++. .+.++|+.|.+
T Consensus 76 V~~vpr~~F~-~~~--~l~~G~~~~~--~~~~G---~~~~~V~ev~~ 114 (196)
T PRK10737 76 VQRVPKDVFM-GVD--ELQVGMRFLA--ETDQG---PVPVEITAVED 114 (196)
T ss_pred EEEecHHHCC-Ccc--CCCCCCEEEE--eCCCC---cEEEEEEEEcC
Confidence 4578877653 222 4889999886 45553 46889999975
No 22
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=60.12 E-value=7 Score=48.31 Aligned_cols=67 Identities=24% Similarity=0.449 Sum_probs=43.1
Q ss_pred CCCCCCCEEEEecCchhhhhhcccccccc--ccCCCCCCCCCcceeEEEEeeecccCCCcceeeeeeeeeC
Q 003731 22 SLPTVGTRVVYFPQGHSEQVAATTNKEVD--SHIPNYPNLPPQLICQLHNVTMHADVETDEVYAQMTLQPL 90 (799)
Q Consensus 22 ~lP~~gs~V~YFPqGH~Eq~~~s~~~~~~--~~~p~~~~lP~~i~C~V~~V~l~Ad~~TDEVyAqi~L~P~ 90 (799)
-||..|+.|.||-|||-|-+.+..--+.+ ...|- ++-..=.|.|..+..---+-...--.+|+|.=.
T Consensus 872 yipQmgDEViyfrQghqeyl~~~~~n~~~~~~~~p~--~~~~v~~~kv~kl~~~~y~~~~~s~c~m~l~~i 940 (1113)
T KOG0644|consen 872 YIPQMGDEVIYFRQGHQEYLEAVRLNNIELNNKEPW--NKMAVEICKVEKLVYITYPGSGDSCCKMKLAVI 940 (1113)
T ss_pred ccccccceeehhhhhhHHHHhhhhhccccccccCcc--cccchhhheeeeeeeeeccCCCcchheeeeeee
Confidence 58999999999999999999886422222 11121 333345788887765555555555555555443
No 23
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=46.34 E-value=30 Score=28.70 Aligned_cols=28 Identities=14% Similarity=0.259 Sum_probs=23.8
Q ss_pred CCccccEEEEeeeccCcccceeeEEEEEeec
Q 003731 279 RVSVGMRFRMLFETEESSVRRYMGTITGISD 309 (799)
Q Consensus 279 ~w~~GmRFkM~fe~Eds~~~~~~GTI~gv~d 309 (799)
.|.+|+++-..++.++ .||.|+|+.+..
T Consensus 2 ~~~~G~~Ve~~~~~~~---~W~~a~V~~~~~ 29 (61)
T smart00743 2 DFKKGDRVEVFSKEED---SWWEAVVTKVLG 29 (61)
T ss_pred CcCCCCEEEEEECCCC---EEEEEEEEEECC
Confidence 5899999999996544 799999999964
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=42.88 E-value=28 Score=27.86 Aligned_cols=38 Identities=13% Similarity=0.163 Sum_probs=27.5
Q ss_pred CCCCceeecccchhhhcccCCCCCCEEEEEEccCCcEEEEE
Q 003731 173 GQPKRHLLTTGWSVFVSAKRLVAGDSVLFIWNEKNQLLLGI 213 (799)
Q Consensus 173 g~prrhlLTtGWs~FV~~K~L~aGD~VvF~R~~~g~L~vGi 213 (799)
|++..-.|-. .|.++.+|.+||.|.|.-.++|++.|--
T Consensus 4 g~s~~v~iPk---~~~~~l~l~~Gd~v~i~~~~~g~i~i~p 41 (47)
T PF04014_consen 4 GNSGQVTIPK---EIREKLGLKPGDEVEIEVEGDGKIVIRP 41 (47)
T ss_dssp TTCSEEEE-H---HHHHHTTSSTTTEEEEEEETTSEEEEEE
T ss_pred CCCceEECCH---HHHHHcCCCCCCEEEEEEeCCCEEEEEE
Confidence 4444444543 5677889999999999999988766643
No 25
>PF00788 RA: Ras association (RalGDS/AF-6) domain; InterPro: IPR000159 Proteins with this domain are mostly RasGTP effectors and include guanine-nucleotide releasing factor in mammals []. This factor stimulates the dissociation of GDP from the Ras-related RALA and RALB GTPases, which allows GTP binding and activation of the GTPases. It interacts and acts as an effector molecule for R-ras, K-Ras and Rap []. The domain is also present in a number of other proteins among them the sexual differentiation protein in yeast that is essential for mating and meiosis and yeast adenylate cyclase. These proteins contain repeated leucine-rich (LRR) segments.; GO: 0007165 signal transduction; PDB: 3EC8_A 2C5L_D 2BYF_A 2CS4_A 3KH0_A 2B3A_A 1RAX_A 2RGF_A 1WGR_A 1WXA_A ....
Probab=41.59 E-value=85 Score=27.32 Aligned_cols=69 Identities=17% Similarity=0.222 Sum_probs=49.5
Q ss_pred ceeEEEeecccc----ceeeccCCCCChHHHHHHHHHhhcCCCccCCCCCCCceEE-EEeC-CCceEecC-CcchhhHhc
Q 003731 679 RTFVKVYKSGSV----GRSLDISRFSSYNELREELGQMFGIEGKFEDPLRSGWQLV-FVDR-ENDVLLLG-DDPWEAFVS 751 (799)
Q Consensus 679 ~~~vKV~m~G~i----gRkvDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~~~~~lv-Y~D~-EgD~mLvG-D~PWe~Fv~ 751 (799)
..++||+....- -++|-++....-.|++..+.+.|++.+ +..+|.|+ +.-. .....|-. +.|+..+..
T Consensus 2 ~~~lrVy~~~~~~~~~~k~i~v~~~tTa~evi~~~l~k~~l~~-----~~~~y~L~~~~~~~~~er~L~~~E~pl~i~~~ 76 (93)
T PF00788_consen 2 SGVLRVYDGDGSPGSTYKTIKVSSSTTAREVIEMALEKFGLAE-----DPSDYCLVEVEESGGEERPLDDDECPLQIQLQ 76 (93)
T ss_dssp EEEEEEEETTSSSCCSEEEEEEETTSBHHHHHHHHHHHTTTSS-----SGGGEEEEEEECTTTEEEEETTTSBHHHHHHT
T ss_pred CeEEEEEcCCCCCCccEEEEEECCCCCHHHHHHHHHHHhCCCC-----CCCCEEEEEEEcCCCEEEEcCCCCchHHHHHh
Confidence 358999997632 799999999999999999999999932 23579995 4444 44444443 356666554
Q ss_pred c
Q 003731 752 N 752 (799)
Q Consensus 752 ~ 752 (799)
.
T Consensus 77 ~ 77 (93)
T PF00788_consen 77 W 77 (93)
T ss_dssp T
T ss_pred C
Confidence 3
No 26
>KOG3207 consensus Beta-tubulin folding cofactor E [Posttranslational modification, protein turnover, chaperones]
Probab=37.15 E-value=41 Score=39.53 Aligned_cols=43 Identities=28% Similarity=0.687 Sum_probs=29.5
Q ss_pred CccccEEEEeeeccCcccceeeEEEEEeecCCCCCCCCCCccceeeccCCCCCCCCC
Q 003731 280 VSVGMRFRMLFETEESSVRRYMGTITGISDLDPVRWSNSHWRSVKVGWDESTAGERQ 336 (799)
Q Consensus 280 w~~GmRFkM~fe~Eds~~~~~~GTI~gv~d~Dp~rWp~S~WR~LkV~WDe~~~~~~~ 336 (799)
..+|.|+|..+|- ..-||.|+|.| |++ +| +.|.||++.-+.+.
T Consensus 3 ~~IG~RvkI~~~~---~Tvr~iG~V~g--------~~~-~w--~GvEWDd~~RGKH~ 45 (505)
T KOG3207|consen 3 MEIGTRVKIGGEI---ATVRYIGEVEG--------NNS-KW--YGVEWDDPVRGKHD 45 (505)
T ss_pred eeccceEEEcCEE---EEEEEEEEEcC--------CCC-cc--eeeEecCCCccccC
Confidence 5789999987642 22466666654 444 34 88999999876653
No 27
>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=31.29 E-value=56 Score=24.90 Aligned_cols=26 Identities=23% Similarity=0.288 Sum_probs=22.4
Q ss_pred hhhcccCCCCCCEEEEEEccCCcEEE
Q 003731 186 VFVSAKRLVAGDSVLFIWNEKNQLLL 211 (799)
Q Consensus 186 ~FV~~K~L~aGD~VvF~R~~~g~L~v 211 (799)
.|.+.-++..||.|.+...++|.|.+
T Consensus 14 ~~r~~l~~~~gd~~~i~~~~~~~l~l 39 (43)
T TIGR01439 14 EIREKLGLKEGDRLEVIRVEDGEIIL 39 (43)
T ss_pred HHHHHcCcCCCCEEEEEEeCCCEEEE
Confidence 68889999999999999887777665
No 28
>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=29.67 E-value=51 Score=31.85 Aligned_cols=26 Identities=31% Similarity=0.543 Sum_probs=17.9
Q ss_pred cCCCCCCEEEEEEcc-CCcEEEEEEec
Q 003731 191 KRLVAGDSVLFIWNE-KNQLLLGIRRA 216 (799)
Q Consensus 191 K~L~aGD~VvF~R~~-~g~L~vGiRRa 216 (799)
++++.||.|+||... .++-++|+=+-
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 599999999999987 67778877654
No 29
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=28.96 E-value=70 Score=29.80 Aligned_cols=27 Identities=22% Similarity=0.303 Sum_probs=21.9
Q ss_pred hhcccCCCCCCEEEEEEccCCcEEEEE
Q 003731 187 FVSAKRLVAGDSVLFIWNEKNQLLLGI 213 (799)
Q Consensus 187 FV~~K~L~aGD~VvF~R~~~g~L~vGi 213 (799)
|.-...|++||.|+.+|.+.|+-++=+
T Consensus 71 i~~~~~Lk~GD~V~ll~~~~gQ~yiVl 97 (100)
T PF10844_consen 71 ITFTDGLKVGDKVLLLRVQGGQKYIVL 97 (100)
T ss_pred EEEecCCcCCCEEEEEEecCCCEEEEE
Confidence 445678999999999999988876644
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=27.04 E-value=99 Score=24.90 Aligned_cols=52 Identities=15% Similarity=0.230 Sum_probs=36.1
Q ss_pred CCccccEEEEeeeccCcccceeeEEEEEeecCCCCCCCCCCccceeeccCCCCCCCCCCCcccccceeC
Q 003731 279 RVSVGMRFRMLFETEESSVRRYMGTITGISDLDPVRWSNSHWRSVKVGWDESTAGERQPRVSLWEIEPL 347 (799)
Q Consensus 279 ~w~~GmRFkM~fe~Eds~~~~~~GTI~gv~d~Dp~rWp~S~WR~LkV~WDe~~~~~~~~RVSPWeIEpv 347 (799)
.|.+|..+...+ .+. .||.|+|+++.. + ....|.-++-+. .+-|...+|-++
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 588999999998 443 799999999974 2 456777776443 244555555443
No 31
>PF05641 Agenet: Agenet domain; InterPro: IPR008395 This domain is related to the TUDOR domain IPR008191 from INTERPRO []. The function of the agenet domain is unknown. This signature matches one of the two Agenet domains in the FMR proteins [].; GO: 0003723 RNA binding; PDB: 2BKD_N 3O8V_A 3KUF_A 3H8Z_A.
Probab=25.14 E-value=1.3e+02 Score=25.94 Aligned_cols=42 Identities=12% Similarity=0.082 Sum_probs=26.7
Q ss_pred CccccEEEEeeeccCcccceeeEEEEEeecCCCCCCCCCCccceeeccCCCC
Q 003731 280 VSVGMRFRMLFETEESSVRRYMGTITGISDLDPVRWSNSHWRSVKVGWDEST 331 (799)
Q Consensus 280 w~~GmRFkM~fe~Eds~~~~~~GTI~gv~d~Dp~rWp~S~WR~LkV~WDe~~ 331 (799)
|..|+++-..-+.+...-.||.|||+.....+ .+.|+.++-.
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 46799999877555555679999999997522 7788886544
No 32
>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=25.03 E-value=58 Score=27.37 Aligned_cols=17 Identities=24% Similarity=0.542 Sum_probs=14.8
Q ss_pred eEEEEeCCCceEecCCc
Q 003731 728 QLVFVDRENDVLLLGDD 744 (799)
Q Consensus 728 ~lvY~D~EgD~mLvGD~ 744 (799)
.++|.|.+|+.+++|+.
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 69999999999999973
No 33
>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=23.45 E-value=1.3e+02 Score=25.45 Aligned_cols=31 Identities=19% Similarity=0.370 Sum_probs=24.0
Q ss_pred cccEEEEeeeccCcccceeeEEEEEeecCCC
Q 003731 282 VGMRFRMLFETEESSVRRYMGTITGISDLDP 312 (799)
Q Consensus 282 ~GmRFkM~fe~Eds~~~~~~GTI~gv~d~Dp 312 (799)
+|-|+.-.||.++.++..+.|+|..--+..|
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 5889999999998888888999999877654
No 34
>COG1047 SlpA FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]
Probab=21.48 E-value=4.8e+02 Score=27.23 Aligned_cols=105 Identities=20% Similarity=0.269 Sum_probs=65.0
Q ss_pred CCCCCCEEEE---EEccCCcEEEEEEecCCCCCCCCCccccCCcccccHHHHHHHHHhcCCeEEEEEecCCCCCcc----
Q 003731 192 RLVAGDSVLF---IWNEKNQLLLGIRRAIRPPTVMPSSVLSSDSMHIGLLAAAAHAAATNSCFTVFFNPRASPSEF---- 264 (799)
Q Consensus 192 ~L~aGD~VvF---~R~~~g~L~vGiRRa~r~~~~~pssv~s~~sm~~gvla~A~~aa~~~~~F~V~Y~Pras~sEF---- 264 (799)
++..||.|.+ .|.++|+++=--.- ..-|..++-.+..-+.-|-+|..-..-|..|+|.--|-..--++
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 4567788777 24455655421111 11244444444333444678888888999999998877644443
Q ss_pred --eechhHHHHhhhcCCCccccEEEEeeeccCcccceeeEEEEEeec
Q 003731 265 --VIPLTKYVKAVFHTRVSVGMRFRMLFETEESSVRRYMGTITGISD 309 (799)
Q Consensus 265 --vVp~~ky~~a~~~~~w~~GmRFkM~fe~Eds~~~~~~GTI~gv~d 309 (799)
.||+++|.+.- ...+||+|.. ++++ .-.-|+|+.|..
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 56766653321 5899999874 5555 456799999874
No 35
>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=21.28 E-value=2.5e+02 Score=25.84 Aligned_cols=66 Identities=18% Similarity=0.202 Sum_probs=49.2
Q ss_pred eEEEeeccccceeeccCCCCChHHHHHHHHHhhcCCCccCCCCCCCceEEEEeCCC-ceEecCCcchhhHhcceeE
Q 003731 681 FVKVYKSGSVGRSLDISRFSSYNELREELGQMFGIEGKFEDPLRSGWQLVFVDREN-DVLLLGDDPWEAFVSNVWY 755 (799)
Q Consensus 681 ~vKV~m~G~igRkvDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~~~~~lvY~D~Eg-D~mLvGD~PWe~Fv~~vkr 755 (799)
-|||+-++ .=.|-...=-+|.+|++.|.+-+.+.++ .=+|-|.|.+. +...++|.=++.-.+.|+-
T Consensus 4 vvKV~f~~--tIaIrvp~~~~y~~L~~ki~~kLkl~~e-------~i~LsYkde~s~~~v~l~d~dle~aws~~~~ 70 (80)
T cd06406 4 VVKVHFKY--TVAIQVARGLSYATLLQKISSKLELPAE-------HITLSYKSEASGEDVILSDTNMEDVWSQAKD 70 (80)
T ss_pred EEEEEEEE--EEEEEcCCCCCHHHHHHHHHHHhCCCch-------hcEEEeccCCCCCccCcChHHHHHHHHhhcC
Confidence 57999998 3334455566899999999999998532 34899999663 5545599999988888753
Done!