Query 002650
Match_columns 896
No_of_seqs 367 out of 800
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 04:18:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002650.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002650hhsearch_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 3.7E-35 8E-40 262.4 8.3 83 253-336 1-83 (83)
2 PF02309 AUX_IAA: AUX/IAA fami 100.0 8.9E-35 1.9E-39 297.4 0.0 95 761-855 107-215 (215)
3 PF02362 B3: B3 DNA binding do 99.7 2.2E-16 4.7E-21 141.3 11.0 97 127-228 1-99 (100)
4 KOG0644 Uncharacterized conser 99.4 4.9E-13 1.1E-17 156.0 6.8 148 205-361 874-1044(1113)
5 PF09217 EcoRII-N: Restriction 98.4 2.4E-06 5.1E-11 85.1 10.2 90 124-214 7-110 (156)
6 PF03754 DUF313: Domain of unk 97.7 9.6E-05 2.1E-09 70.9 6.6 81 121-202 18-114 (114)
7 PF00564 PB1: PB1 domain; Int 96.9 0.0016 3.5E-08 57.2 5.4 66 766-838 4-70 (84)
8 smart00666 PB1 PB1 domain. Pho 96.0 0.022 4.9E-07 49.9 7.0 65 766-838 4-69 (81)
9 cd05992 PB1 The PB1 domain is 95.8 0.029 6.3E-07 48.9 6.6 65 766-838 3-69 (81)
10 cd06396 PB1_NBR1 The PB1 domai 95.6 0.037 8E-07 50.7 6.8 51 766-825 3-54 (81)
11 cd06407 PB1_NLP A PB1 domain i 95.4 0.052 1.1E-06 49.5 7.1 53 766-825 3-55 (82)
12 cd06409 PB1_MUG70 The MUG70 pr 95.0 0.046 1E-06 50.6 5.6 45 778-826 15-59 (86)
13 cd06398 PB1_Joka2 The PB1 doma 94.8 0.1 2.2E-06 48.6 7.1 66 766-839 3-72 (91)
14 cd06403 PB1_Par6 The PB1 domai 92.9 0.28 6.1E-06 45.0 6.1 66 766-838 3-70 (80)
15 cd06404 PB1_aPKC PB1 domain is 91.3 0.54 1.2E-05 43.5 6.2 52 766-825 3-55 (83)
16 cd06401 PB1_TFG The PB1 domain 90.8 0.76 1.7E-05 42.4 6.5 58 766-828 3-61 (81)
17 cd06402 PB1_p62 The PB1 domain 90.5 0.94 2E-05 42.2 7.0 57 764-826 1-63 (87)
18 cd06397 PB1_UP1 Uncharacterize 87.5 1.6 3.4E-05 40.5 6.1 61 767-835 4-65 (82)
19 cd06408 PB1_NoxR The PB1 domai 81.4 4.8 0.0001 37.6 6.5 55 764-828 3-57 (86)
20 cd06399 PB1_P40 The PB1 domain 76.6 4.1 8.9E-05 38.4 4.5 53 779-857 23-75 (92)
21 PRK10737 FKBP-type peptidyl-pr 61.3 20 0.00043 38.0 6.3 104 204-321 2-114 (196)
22 KOG0644 Uncharacterized conser 54.1 9.4 0.0002 47.8 2.8 67 34-102 872-940 (1113)
23 smart00743 Agenet Tudor-like d 49.2 26 0.00056 29.4 4.0 28 291-321 2-29 (61)
24 PF00788 RA: Ras association ( 42.3 67 0.0015 28.3 5.7 65 764-833 3-74 (93)
25 PF04014 Antitoxin-MazE: Antid 39.9 39 0.00084 27.5 3.5 29 198-226 14-42 (47)
26 KOG3598 Thyroid hormone recept 38.5 6.1 0.00013 51.7 -2.0 9 239-247 1851-1859(2220)
27 KOG3207 Beta-tubulin folding c 37.6 27 0.00058 41.4 3.1 43 292-348 3-45 (505)
28 COG1047 SlpA FKBP-type peptidy 31.6 2.1E+02 0.0045 30.3 8.0 105 204-321 2-115 (174)
29 smart00333 TUDOR Tudor domain. 31.4 76 0.0017 25.9 4.0 52 291-359 2-53 (57)
30 TIGR01439 lp_hng_hel_AbrB loop 31.0 56 0.0012 25.3 3.0 26 198-223 14-39 (43)
31 cd06406 PB1_P67 A PB1 domain i 31.0 1.5E+02 0.0033 27.7 6.1 65 765-838 4-69 (80)
32 PF01878 EVE: EVE domain; Int 30.0 49 0.0011 32.4 3.1 26 203-228 38-64 (143)
33 PF10844 DUF2577: Protein of u 29.9 62 0.0014 30.6 3.7 27 199-225 71-97 (100)
34 PF05641 Agenet: Agenet domain 23.3 1.4E+02 0.0031 26.1 4.4 42 292-343 1-42 (68)
35 PF02513 Spin-Ssty: Spin/Ssty 22.7 1.4E+02 0.0031 25.7 4.1 31 294-324 1-31 (50)
36 cd05792 S1_eIF1AD_like S1_eIF1 22.2 65 0.0014 29.8 2.2 35 818-855 40-76 (78)
37 PF10411 DsbC_N: Disulfide bon 21.2 65 0.0014 27.5 1.9 17 812-828 34-50 (57)
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=3.7e-35 Score=262.40 Aligned_cols=83 Identities=65% Similarity=1.088 Sum_probs=81.1
Q ss_pred HHHHHHcCCcEEEEEcCCCCCCccccchHHHHHHHhcCCCccCCEEEEeeeccCcccceeeEEEEEeccCCCCCCCCCCc
Q 002650 253 AAHAAATNSRFTIFYNPRASPSEFVIPLAKYIKAVYHTRVSVGMRFRMLFETEESSVRRYMGTITGISDLDPVKWPNSHW 332 (896)
Q Consensus 253 Aa~aaat~~~F~V~Y~PRas~sEFVVp~~kyvka~~~~~ws~GMRFKM~fEtEdss~rr~~GTI~gv~d~Dp~rWP~S~W 332 (896)
|+|||+++++|+|+||||++++|||||++||++|+. ++|++||||||+||+||+++++|+|||+||+++||+|||+|+|
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 7999999999999999999999999999999999999999999
Q ss_pred ccee
Q 002650 333 RSVK 336 (896)
Q Consensus 333 R~Lq 336 (896)
||||
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=8.9e-35 Score=297.41 Aligned_cols=95 Identities=41% Similarity=0.734 Sum_probs=0.0
Q ss_pred CCcceEEEeecC-cceeeeccCCCCCHHHHHHHHHHHh---ccc----------CccCCCCCCccEEEEEcCCCCeEecc
Q 002650 761 PNRTFVKVYKSG-SFGRSLDITKFSSYHELRSELARMF---GLE----------GHLEDPLRSGWQLVFVDRENDVLLLG 826 (896)
Q Consensus 761 ~~~~~VKV~m~G-~igRkIDL~~~~sY~eL~~~L~~MF---~~~----------g~l~d~~~s~~~lvYeD~EGD~mLvG 826 (896)
..++||||+||| +|||||||++|+||++|+.+|++|| ++. +.++...+++|+|||+|+||||||||
T Consensus 107 ~~~~~vKV~mdG~~igRkVDL~~~~sY~~L~~~L~~MF~~~~i~~~~~~~~~~~~~~~~~~~~~~~l~Y~D~egd~mlvG 186 (215)
T PF02309_consen 107 SSRSYVKVNMDGVPIGRKVDLSAYSSYEELSSALEKMFSCFSIEQCGSHGLNESGLLDLLNGSEYVLVYEDKEGDWMLVG 186 (215)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred cCCceeEEEecCcccceecCHHHhhCHHHHHHHHHHhcCCCCccccccccccchhhccccCCcceeEEEECCCCCEEEec
Confidence 357999999999 9999999999999999999999999 444 33444567899999999999999999
Q ss_pred CCCchhhhcceeEEEEeChhhhhcccccc
Q 002650 827 DGPWPEFVNSVWCIKILSPPEVQQMGKRG 855 (896)
Q Consensus 827 DvPWe~Fv~svkri~Il~~~e~~~m~~~~ 855 (896)
||||+|||++||||+||+.+|+++|++++
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=99.68 E-value=2.2e-16 Score=141.28 Aligned_cols=97 Identities=28% Similarity=0.417 Sum_probs=75.0
Q ss_pred EEEeecccCCCCCCceeechhhhhhcCCCCCCCCCCCceEEEEEecCCCeEEEEEEEeCCCcceeecccchhhhcccCCc
Q 002650 127 FCKTLTASDTSTHGGFSVPRRAAEKVFPPLDFSQQPPAQELIARDLHDNEWKFRHIFRGQPKRHLLTTGWSVFVSAKRLV 206 (896)
Q Consensus 127 F~K~LT~SDv~~~GrfsVPk~~AE~~FPpLd~~~~~p~q~L~~~D~~G~~W~FR~iyrg~prrhlLTtGWs~FV~~KkL~ 206 (896)
|.|+|+++|+...+++.||++.++.+. +. ...++++.++|..|+.|.+++.|++.+++++|++||..||++++|+
T Consensus 1 F~K~l~~s~~~~~~~l~iP~~f~~~~~--~~---~~~~~~v~l~~~~g~~W~v~~~~~~~~~~~~l~~GW~~Fv~~n~L~ 75 (100)
T PF02362_consen 1 FFKVLKPSDVSSSCRLIIPKEFAKKHG--GN---KRKSREVTLKDPDGRSWPVKLKYRKNSGRYYLTGGWKKFVRDNGLK 75 (100)
T ss_dssp EEEE--TTCCCCTT-EEE-HHHHTTTS-------SS--CEEEEEETTTEEEEEEEEEECCTTEEEEETTHHHHHHHCT--
T ss_pred CEEEEEccCcCCCCEEEeCHHHHHHhC--CC---cCCCeEEEEEeCCCCEEEEEEEEEccCCeEEECCCHHHHHHHcCCC
Confidence 899999999999999999999999882 11 1236789999999999999999999888899999999999999999
Q ss_pred CCCEEEEEEcC--CCcEEEEEEcc
Q 002650 207 AGDSVLFIWND--KNQLLLGIRRA 228 (896)
Q Consensus 207 aGDsVvF~R~~--~G~L~VGIRRa 228 (896)
+||.|+|...+ ..++.|.|.|+
T Consensus 76 ~GD~~~F~~~~~~~~~~~v~i~~~ 99 (100)
T PF02362_consen 76 EGDVCVFELIGNSNFTLKVHIFRK 99 (100)
T ss_dssp TT-EEEEEE-SSSCE-EEEEEE--
T ss_pred CCCEEEEEEecCCCceEEEEEEEC
Confidence 99999999865 45569999886
No 4
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=99.37 E-value=4.9e-13 Score=155.95 Aligned_cols=148 Identities=22% Similarity=0.379 Sum_probs=120.8
Q ss_pred CcCCCEEEEEEcCCCcEEEEEEccCCCCCC---------------------CCCCcccCCccccchHHHHHHHHHcCCcE
Q 002650 205 LVAGDSVLFIWNDKNQLLLGIRRANRPPTV---------------------MPSSVLSSDSMHLGLLAAAAHAAATNSRF 263 (896)
Q Consensus 205 L~aGDsVvF~R~~~G~L~VGIRRa~r~~~~---------------------~pssv~s~~sm~~gvla~Aa~aaat~~~F 263 (896)
.+.||.|+++|.+..+++-.+|+.++.-++ .|.+.-+--.|.+.++.-|.++ -+..|
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 358999999999877777667766553221 1223333346888999887755 56799
Q ss_pred EEEEcCCCCCCccccchHHHHHHHhcCCCccCCEEEEee--eccCcccceeeEEEEEeccCCCCCCCCCCccceeeccCC
Q 002650 264 TIFYNPRASPSEFVIPLAKYIKAVYHTRVSVGMRFRMLF--ETEESSVRRYMGTITGISDLDPVKWPNSHWRSVKVGWDE 341 (896)
Q Consensus 264 ~V~Y~PRas~sEFVVp~~kyvka~~~~~ws~GMRFKM~f--EtEdss~rr~~GTI~gv~d~Dp~rWP~S~WR~LqV~WDe 341 (896)
.+.|......++|+|.+..|..|+. ++|..++|||..+ ++||. -+||.|+|.++.+..| .+|+|+|+|+.|+||.
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 7999999999988 33332 3899999999999887 8999999999999999
Q ss_pred CCCCCCCCCccccccccCCC
Q 002650 342 STAGERQPRVSLWEIEPLTT 361 (896)
Q Consensus 342 ~~~~~~~~RVSPWeIEpv~~ 361 (896)
.+ .+.-||||.|++..
T Consensus 1029 ~e----~~~~spwe~~~i~d 1044 (1113)
T KOG0644|consen 1029 TE----TELHSPWEMEPIPD 1044 (1113)
T ss_pred Cc----ccccCccccCCCcc
Confidence 87 57789999999977
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=98.35 E-value=2.4e-06 Score=85.15 Aligned_cols=90 Identities=24% Similarity=0.399 Sum_probs=59.9
Q ss_pred ceeEEEeecccCCCCCC----ceeechhhhhhcCCCCCC-CCCCCceEEEEEecCC--CeEEEEEEEeCC------Ccce
Q 002650 124 TNYFCKTLTASDTSTHG----GFSVPRRAAEKVFPPLDF-SQQPPAQELIARDLHD--NEWKFRHIFRGQ------PKRH 190 (896)
Q Consensus 124 ~~~F~K~LT~SDv~~~G----rfsVPk~~AE~~FPpLd~-~~~~p~q~L~~~D~~G--~~W~FR~iyrg~------prrh 190 (896)
...|+|.|++.|++..| |+-|||..++.+||.|.. +..+|...|.+++..| ..|+||+||.|+ +..|
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 599999999999998776 6678999999999988 669999999977 6778
Q ss_pred eecccchhhhccc-CCcCCCEEEEE
Q 002650 191 LLTTGWSVFVSAK-RLVAGDSVLFI 214 (896)
Q Consensus 191 lLTtGWs~FV~~K-kL~aGDsVvF~ 214 (896)
.|| .|...-+-- -=..||.+||-
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 343322211 12478888775
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=97.65 E-value=9.6e-05 Score=70.91 Aligned_cols=81 Identities=22% Similarity=0.290 Sum_probs=63.0
Q ss_pred CCCceeEEEeecccCCCCC-CceeechhhhhhcCCCCCCC------------CCCCceEEEEEecCCCeEEEEEEEeCC-
Q 002650 121 KQPTNYFCKTLTASDTSTH-GGFSVPRRAAEKVFPPLDFS------------QQPPAQELIARDLHDNEWKFRHIFRGQ- 186 (896)
Q Consensus 121 ~~~~~~F~K~LT~SDv~~~-GrfsVPk~~AE~~FPpLd~~------------~~~p~q~L~~~D~~G~~W~FR~iyrg~- 186 (896)
..+...++|+|++||++.+ .||+||-..... ...|... ...-++.+.+.|..++.|..++..|..
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 4567899999999999885 999999875422 1222211 234588999999999999999999954
Q ss_pred --Ccceeecccchhhhcc
Q 002650 187 --PKRHLLTTGWSVFVSA 202 (896)
Q Consensus 187 --prrhlLTtGWs~FV~~ 202 (896)
.-.|+|++||..+|+.
T Consensus 97 ~~~~~YvL~~gWn~VV~~ 114 (114)
T PF03754_consen 97 NGTSNYVLNSGWNKVVED 114 (114)
T ss_pred CCceEEEEEcChHhhccC
Confidence 5679999999998863
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=96.92 E-value=0.0016 Score=57.16 Aligned_cols=66 Identities=26% Similarity=0.437 Sum_probs=54.6
Q ss_pred EEEeecCcceeeeccCCCCCHHHHHHHHHHHhcccCccCCCCCCccEEEEEcCCCCeEeccC-CCchhhhccee
Q 002650 766 VKVYKSGSFGRSLDITKFSSYHELRSELARMFGLEGHLEDPLRSGWQLVFVDRENDVLLLGD-GPWPEFVNSVW 838 (896)
Q Consensus 766 VKV~m~G~igRkIDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLvGD-vPWe~Fv~svk 838 (896)
||++-.|.+=|.+.+..--+|++|+..++..|+.. ...++|.|.|.||||..+-+ .=|++.+..++
T Consensus 4 vK~~~~~~~~~~~~~~~~~s~~~L~~~i~~~~~~~-------~~~~~l~Y~D~dgD~V~i~sd~Dl~~a~~~~~ 70 (84)
T PF00564_consen 4 VKVRYGGDIRRIISLPSDVSFDDLRSKIREKFGLL-------DEDFQLKYKDEDGDLVTISSDEDLQEAIEQAK 70 (84)
T ss_dssp EEEEETTEEEEEEEECSTSHHHHHHHHHHHHHTTS-------TSSEEEEEEETTSSEEEESSHHHHHHHHHHHH
T ss_pred EEEEECCeeEEEEEcCCCCCHHHHHHHHHHHhCCC-------CccEEEEeeCCCCCEEEeCCHHHHHHHHHHHH
Confidence 78998887766788888889999999999999986 34699999999999988864 44776666654
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=96.02 E-value=0.022 Score=49.93 Aligned_cols=65 Identities=29% Similarity=0.473 Sum_probs=50.6
Q ss_pred EEEeecCcceeeeccCCCCCHHHHHHHHHHHhcccCccCCCCCCccEEEEEcCCCCeEecc-CCCchhhhccee
Q 002650 766 VKVYKSGSFGRSLDITKFSSYHELRSELARMFGLEGHLEDPLRSGWQLVFVDRENDVLLLG-DGPWPEFVNSVW 838 (896)
Q Consensus 766 VKV~m~G~igRkIDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLvG-DvPWe~Fv~svk 838 (896)
|||.- |.--|.+-+..--+|++|++.+.+.|++.+ ..+.|-|.|.||||..+. |.=|++.+..++
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 555677888889999999999999999653 459999999999998654 455666555544
No 9
>cd05992 PB1 The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as a noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.
Probab=95.78 E-value=0.029 Score=48.93 Aligned_cols=65 Identities=26% Similarity=0.496 Sum_probs=49.2
Q ss_pred EEEeecCcceeeeccC-CCCCHHHHHHHHHHHhcccCccCCCCCCccEEEEEcCCCCeEeccC-CCchhhhccee
Q 002650 766 VKVYKSGSFGRSLDIT-KFSSYHELRSELARMFGLEGHLEDPLRSGWQLVFVDRENDVLLLGD-GPWPEFVNSVW 838 (896)
Q Consensus 766 VKV~m~G~igRkIDL~-~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLvGD-vPWe~Fv~svk 838 (896)
|||+-.|.+ |.+-+. .--+|++|+..|.+.|++.. ..+.+.|.|.||||..+.+ .=|++.++.++
T Consensus 3 vK~~~~~~~-~~~~~~~~~~s~~~L~~~i~~~~~~~~-------~~~~l~y~D~e~d~v~l~sd~Dl~~a~~~~~ 69 (81)
T cd05992 3 VKVKYGGEI-RRFVVVSRSISFEDLRSKIAEKFGLDA-------VSFKLKYPDEDGDLVTISSDEDLEEAIEEAR 69 (81)
T ss_pred EEEEecCCC-EEEEEecCCCCHHHHHHHHHHHhCCCC-------CcEEEEeeCCCCCEEEeCCHHHHHHHHHHHh
Confidence 688777743 333333 88899999999999999753 3589999999999998877 55655555544
No 10
>cd06396 PB1_NBR1 The PB1 domain is an essential part of NBR1 protein, next to BRCA1, a scaffold protein mediating specific protein-protein interaction with both titin protein kinase and with another scaffold protein p62. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The NBR1 protein contains a type I PB1 domain.
Probab=95.60 E-value=0.037 Score=50.73 Aligned_cols=51 Identities=24% Similarity=0.357 Sum_probs=44.4
Q ss_pred EEEeecC-cceeeeccCCCCCHHHHHHHHHHHhcccCccCCCCCCccEEEEEcCCCCeEec
Q 002650 766 VKVYKSG-SFGRSLDITKFSSYHELRSELARMFGLEGHLEDPLRSGWQLVFVDRENDVLLL 825 (896)
Q Consensus 766 VKV~m~G-~igRkIDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLv 825 (896)
|||.-.| .+--+++-+.-.+|.+|..+++++|++. .+.|.|.|.||||.++
T Consensus 3 vKaty~~d~~rf~~~~~~~~~~~~L~~ev~~rf~l~---------~f~lKYlDde~e~v~l 54 (81)
T cd06396 3 LKVTYNGESQSFLVSDSENTTWASVEAMVKVSFGLN---------DIQIKYVDEENEEVSV 54 (81)
T ss_pred EEEEECCeEEEEEecCCCCCCHHHHHHHHHHHhCCC---------cceeEEEcCCCCEEEE
Confidence 7888888 5666777777889999999999999986 4899999999999876
No 11
>cd06407 PB1_NLP A PB1 domain is present in NIN like proteins (NLP), a key enzyme in a process of establishment of symbiosis betweeen legumes and nitrogen fixing bacteria (Rhizobium). The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes like osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-inte
Probab=95.44 E-value=0.052 Score=49.50 Aligned_cols=53 Identities=25% Similarity=0.400 Sum_probs=41.6
Q ss_pred EEEeecCcceeeeccCCCCCHHHHHHHHHHHhcccCccCCCCCCccEEEEEcCCCCeEec
Q 002650 766 VKVYKSGSFGRSLDITKFSSYHELRSELARMFGLEGHLEDPLRSGWQLVFVDRENDVLLL 825 (896)
Q Consensus 766 VKV~m~G~igRkIDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLv 825 (896)
|||.-.|. -+.+-|..--+|++|+++++++|++. ...++.|-|.|.||||.++
T Consensus 3 vK~~~~~d-~~r~~l~~~~~~~~L~~~i~~r~~~~------~~~~f~LkY~Ddegd~v~l 55 (82)
T cd06407 3 VKATYGEE-KIRFRLPPSWGFTELKQEIAKRFKLD------DMSAFDLKYLDDDEEWVLL 55 (82)
T ss_pred EEEEeCCe-EEEEEcCCCCCHHHHHHHHHHHhCCC------CCCeeEEEEECCCCCeEEe
Confidence 78888774 23344444559999999999999974 1357999999999999876
No 12
>cd06409 PB1_MUG70 The MUG70 protein is a product of the meiotically up-regulated gene 70 which has a role in meiosis and harbors a PB1 domain. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domains depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic amino acid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is
Probab=95.03 E-value=0.046 Score=50.56 Aligned_cols=45 Identities=24% Similarity=0.425 Sum_probs=36.7
Q ss_pred eccCCCCCHHHHHHHHHHHhcccCccCCCCCCccEEEEEcCCCCeEecc
Q 002650 778 LDITKFSSYHELRSELARMFGLEGHLEDPLRSGWQLVFVDRENDVLLLG 826 (896)
Q Consensus 778 IDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLvG 826 (896)
+-+....|+.+|.+++.+-|+.+... ...|+|.|.|.||||.|+-
T Consensus 15 f~~~~s~~~~~L~~~I~~Rl~~d~~~----~~~~~L~YlDDEgD~VllT 59 (86)
T cd06409 15 FRLRPSESLEELRTLISQRLGDDDFE----THLYALSYVDDEGDIVLIT 59 (86)
T ss_pred EEecCCCCHHHHHHHHHHHhCCcccc----CCcccEEEEcCCCCEEEEe
Confidence 34445789999999999999986432 4579999999999998863
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=94.77 E-value=0.1 Score=48.58 Aligned_cols=66 Identities=21% Similarity=0.349 Sum_probs=49.0
Q ss_pred EEEeecCc-ceeeeccC---CCCCHHHHHHHHHHHhcccCccCCCCCCccEEEEEcCCCCeEeccCCCchhhhcceeE
Q 002650 766 VKVYKSGS-FGRSLDIT---KFSSYHELRSELARMFGLEGHLEDPLRSGWQLVFVDRENDVLLLGDGPWPEFVNSVWC 839 (896)
Q Consensus 766 VKV~m~G~-igRkIDL~---~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLvGDvPWe~Fv~svkr 839 (896)
|||.-+|. +=-++++. .--+|++|+..+++.|.+.. ..+++|.|.|.||||..+-++ +++..++.+
T Consensus 3 vKv~y~~~~rRf~l~~~~~~~d~~~~~L~~kI~~~f~l~~------~~~~~l~Y~Dedgd~V~l~~D--~DL~~a~~~ 72 (91)
T cd06398 3 VKVKYGGTLRRFTFPVAENQLDLNMDGLREKVEELFSLSP------DADLSLTYTDEDGDVVTLVDD--NDLTDAIQY 72 (91)
T ss_pred EEEEeCCEEEEEEeccccccCCCCHHHHHHHHHHHhCCCC------CCcEEEEEECCCCCEEEEccH--HHHHHHHHH
Confidence 79998884 33355553 45799999999999998742 357999999999999988443 455555544
No 14
>cd06403 PB1_Par6 The PB1 domain is an essential part of Par6 protein which in complex with Par3 and aPKC proteins is crucial for establishment of apical-basal polarity of animal cells. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. The
Probab=92.87 E-value=0.28 Score=45.01 Aligned_cols=66 Identities=21% Similarity=0.317 Sum_probs=50.0
Q ss_pred EEEeecCccee-eeccCCCCCHHHHHHHHHHHhcccCccCCCCCCccEEEEEcCCCCeEecc-CCCchhhhccee
Q 002650 766 VKVYKSGSFGR-SLDITKFSSYHELRSELARMFGLEGHLEDPLRSGWQLVFVDRENDVLLLG-DGPWPEFVNSVW 838 (896)
Q Consensus 766 VKV~m~G~igR-kIDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLvG-DvPWe~Fv~svk 838 (896)
||.+-++.+-| ++|-....+|+|+++-|++|+.+.+ ..+.|-|.|.+||.+-+- |+-+..-+.+++
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 56666665444 6777778999999999999999864 359999999999999764 555555555554
No 15
>cd06404 PB1_aPKC PB1 domain is an essential modular domain of the atypical protein kinase C (aPKC) which in complex with Par6 and Par3 proteins is crucial for establishment of apical-basal polarity of animal cells. PB1 domain is a modular domain mediating specific protein-protein interaction which play roles in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi,
Probab=91.33 E-value=0.54 Score=43.53 Aligned_cols=52 Identities=27% Similarity=0.309 Sum_probs=41.2
Q ss_pred EEEeecCc-ceeeeccCCCCCHHHHHHHHHHHhcccCccCCCCCCccEEEEEcCCCCeEec
Q 002650 766 VKVYKSGS-FGRSLDITKFSSYHELRSELARMFGLEGHLEDPLRSGWQLVFVDRENDVLLL 825 (896)
Q Consensus 766 VKV~m~G~-igRkIDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLv 825 (896)
+|++-.|. .--.+|. --+|++|.+++++||... .+..+++.|.|.|||---+
T Consensus 3 ~K~~y~gdi~it~~d~--~~s~e~L~~~v~~~c~~~------~~q~ft~kw~DEEGDp~ti 55 (83)
T cd06404 3 VKAAYNGDIMITSIDP--SISLEELCNEVRDMCRFH------NDQPFTLKWIDEEGDPCTI 55 (83)
T ss_pred EEEEecCcEEEEEcCC--CcCHHHHHHHHHHHhCCC------CCCcEEEEEECCCCCceee
Confidence 78888894 4444555 788999999999999973 2346999999999997554
No 16
>cd06401 PB1_TFG The PB1 domain found in TFG protein, an oncogenic gene product and fusion partner to nerve growth factor tyrosine kinase receptor TrkA and to the tyrosine kinase ALK. The PB1 domain is a modular domain mediating specific protein-protein interaction in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The PB1 domains of TFG represent a type I/II PB1 domain. The physiological function of TFG remains unknown.
Probab=90.77 E-value=0.76 Score=42.40 Aligned_cols=58 Identities=19% Similarity=0.246 Sum_probs=42.5
Q ss_pred EEEeecCcceeeeccCCC-CCHHHHHHHHHHHhcccCccCCCCCCccEEEEEcCCCCeEeccCC
Q 002650 766 VKVYKSGSFGRSLDITKF-SSYHELRSELARMFGLEGHLEDPLRSGWQLVFVDRENDVLLLGDG 828 (896)
Q Consensus 766 VKV~m~G~igRkIDL~~~-~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLvGDv 828 (896)
+|+.-.|.|=| +-+..- =+|.+|+..+.+.|... -|....+.+.|.|.|||+.-+.+.
T Consensus 3 iK~~~g~DiR~-~~~~~~~~t~~~L~~~v~~~F~~~----~~~~~~flIKYkD~dGDlVTIts~ 61 (81)
T cd06401 3 LKAQLGDDIRR-IPIHNEDITYDELLLMMQRVFRGK----LGSSDDVLIKYKDEDGDLITIFDS 61 (81)
T ss_pred EEEEeCCeEEE-EeccCccccHHHHHHHHHHHhccc----cCCcccEEEEEECCCCCEEEeccH
Confidence 56666555544 444432 29999999999999953 133456999999999999998875
No 17
>cd06402 PB1_p62 The PB1 domain is an essential part of p62 scaffold protein (alias sequestosome 1,SQSTM) involved in cell signaling, receptor internalization, and protein turnover. The PB1 domain is a modular domain mediating specific protein-protein interaction which play roles in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.
Probab=90.50 E-value=0.94 Score=42.20 Aligned_cols=57 Identities=28% Similarity=0.332 Sum_probs=43.1
Q ss_pred ceEEEeecC----cceeee--ccCCCCCHHHHHHHHHHHhcccCccCCCCCCccEEEEEcCCCCeEecc
Q 002650 764 TFVKVYKSG----SFGRSL--DITKFSSYHELRSELARMFGLEGHLEDPLRSGWQLVFVDRENDVLLLG 826 (896)
Q Consensus 764 ~~VKV~m~G----~igRkI--DL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLvG 826 (896)
+.||.|..| +=-|++ |-....+|++|+..+.++|..- .+..+++.|.|.|||..-+.
T Consensus 1 ~~vkayl~~~~~~~EIRRf~l~~~~~~s~~~L~~~V~~~f~~l------~~~~ftlky~DeeGDlvtIs 63 (87)
T cd06402 1 LTVKAYLLGKDANAEIRRFAIDEDVSTSYEYLVEKVAAVFPSL------RGKNFQLFWKDEEGDLVAFS 63 (87)
T ss_pred CeEEEeecCCCCccceEEEEecCCCCcCHHHHHHHHHHHcccc------CCCcEEEEEECCCCCEEeec
Confidence 368888887 344544 4466779999999999999642 12469999999999986553
No 18
>cd06397 PB1_UP1 Uncharacterized protein 1. The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions.
Probab=87.52 E-value=1.6 Score=40.46 Aligned_cols=61 Identities=18% Similarity=0.306 Sum_probs=45.3
Q ss_pred EEeecCcceeeeccCCCCCHHHHHHHHHHHhcccCccCCCCCCccEEEEEcCCCCeEec-cCCCchhhhc
Q 002650 767 KVYKSGSFGRSLDITKFSSYHELRSELARMFGLEGHLEDPLRSGWQLVFVDRENDVLLL-GDGPWPEFVN 835 (896)
Q Consensus 767 KV~m~G~igRkIDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLv-GDvPWe~Fv~ 835 (896)
||.- |--.|++....-=+|.+|++.|+.+|.+.. .+ +.++|.|.|||..-+ -|+=-++|.+
T Consensus 4 Kv~~-~g~~RRf~~~~~pt~~~L~~kl~~Lf~lp~------~~-~~vtYiDeD~D~ITlssd~eL~d~~~ 65 (82)
T cd06397 4 KSSF-LGDTRRIVFPDIPTWEALASKLENLYNLPE------IK-VGVTYIDNDNDEITLSSNKELQDFYR 65 (82)
T ss_pred EEEe-CCceEEEecCCCccHHHHHHHHHHHhCCCh------hH-eEEEEEcCCCCEEEecchHHHHHHHH
Confidence 6744 345677888888899999999999999852 23 899999999998644 3444555544
No 19
>cd06408 PB1_NoxR The PB1 domain is present in the Epichloe festucae NoxR protein (NADPH oxidase regulator), a key regulator of NADPH oxidase isoform, NoxA. NoxA is essential for growth control of the fungal endophyte in plant tissue in the process of symbiotic interaction between a fungi and its plant host. The Epichloe festucae p67(phox)-like regulator, NoxR, dispensable in culture but essential in plants for the symbiotic interaction. Plants infected with a noxR deletion mutant show severe stunting and premature senescence, whereas hyphae in the meristematic tissues show increased branching leading to increased fungal colonization of pseudostem and leaf blade tissue. The PB1 domain is a modular domain mediating specific protein-protein interactions which a play role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is
Probab=81.41 E-value=4.8 Score=37.65 Aligned_cols=55 Identities=20% Similarity=0.367 Sum_probs=43.9
Q ss_pred ceEEEeecCcceeeeccCCCCCHHHHHHHHHHHhcccCccCCCCCCccEEEEEcCCCCeEeccCC
Q 002650 764 TFVKVYKSGSFGRSLDITKFSSYHELRSELARMFGLEGHLEDPLRSGWQLVFVDRENDVLLLGDG 828 (896)
Q Consensus 764 ~~VKV~m~G~igRkIDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLvGDv 828 (896)
.=|||+-.|. .|-|-+..--+|++|...+..+|++. ..+++-|.|. ||..-++|.
T Consensus 3 ikVKv~~~~D-v~~i~v~~~i~f~dL~~kIrdkf~~~--------~~~~iKykDE-GD~iti~sq 57 (86)
T cd06408 3 IRVKVHAQDD-TRYIMIGPDTGFADFEDKIRDKFGFK--------RRLKIKMKDD-GDMITMGDQ 57 (86)
T ss_pred EEEEEEecCc-EEEEEcCCCCCHHHHHHHHHHHhCCC--------CceEEEEEcC-CCCccccCH
Confidence 3478887775 46666667778999999999999983 2689999999 998777653
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=76.63 E-value=4.1 Score=38.37 Aligned_cols=53 Identities=26% Similarity=0.362 Sum_probs=45.4
Q ss_pred ccCCCCCHHHHHHHHHHHhcccCccCCCCCCccEEEEEcCCCCeEeccCCCchhhhcceeEEEEeChhhhhcccccccc
Q 002650 779 DITKFSSYHELRSELARMFGLEGHLEDPLRSGWQLVFVDRENDVLLLGDGPWPEFVNSVWCIKILSPPEVQQMGKRGNE 857 (896)
Q Consensus 779 DL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLvGDvPWe~Fv~svkri~Il~~~e~~~m~~~~~~ 857 (896)
||+.--+|.+|..-..+-|..+ +-.|-|.|.|||. ||||+.+++.=|-+++..
T Consensus 23 ~l~~~P~~kdLl~lmr~~f~~~---------dIaLNYrD~EGDL-----------------IRllddeDv~LMV~~~r~ 75 (92)
T cd06399 23 DLSSTPLLKDLLELTRREFQRE---------DIALNYRDAEGDL-----------------IRLLSDEDVALMVRQSRG 75 (92)
T ss_pred ccccCccHHHHHHHHHHHhchh---------heeeeeecCCCCE-----------------EEEcchhhHHHHHHHHhc
Confidence 6778889999999999999864 3689999999996 799999999999887744
No 21
>PRK10737 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=61.32 E-value=20 Score=38.04 Aligned_cols=104 Identities=18% Similarity=0.236 Sum_probs=62.2
Q ss_pred CCcCCCEEEE-E--EcCCCcEEEEEEccCCCCCCCCCCcccCCccccchHHHHHHHHHcCCcEEEEEcCCCCC------C
Q 002650 204 RLVAGDSVLF-I--WNDKNQLLLGIRRANRPPTVMPSSVLSSDSMHLGLLAAAAHAAATNSRFTIFYNPRASP------S 274 (896)
Q Consensus 204 kL~aGDsVvF-~--R~~~G~L~VGIRRa~r~~~~~pssv~s~~sm~~gvla~Aa~aaat~~~F~V~Y~PRas~------s 274 (896)
++..|+.|.+ | |+++|+++---+ . ..|...+-....-+--|.+|..-.+.|..|+|..-|-... .
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 3456777766 3 456777643221 1 1233333222222334677777788899999997664433 2
Q ss_pred ccccchHHHHHHHhcCCCccCCEEEEeeeccCcccceeeEEEEEecc
Q 002650 275 EFVIPLAKYIKAVYHTRVSVGMRFRMLFETEESSVRRYMGTITGISD 321 (896)
Q Consensus 275 EFVVp~~kyvka~~~~~ws~GMRFKM~fEtEdss~rr~~GTI~gv~d 321 (896)
-..||++.|. .. ....+||||.+ ++++. .+.++|+.|.+
T Consensus 76 V~~vpr~~F~-~~--~~l~~G~~~~~--~~~~G---~~~~~V~ev~~ 114 (196)
T PRK10737 76 VQRVPKDVFM-GV--DELQVGMRFLA--ETDQG---PVPVEITAVED 114 (196)
T ss_pred EEEecHHHCC-Cc--cCCCCCCEEEE--eCCCC---cEEEEEEEEcC
Confidence 3567777653 22 24899999886 45553 35889999975
No 22
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=54.09 E-value=9.4 Score=47.78 Aligned_cols=67 Identities=22% Similarity=0.413 Sum_probs=47.9
Q ss_pred CCCCCCCEEEEecCcchhhhccccccccccc--CCCCCCCCCcceeeEeeeeecccCCCcceeeeeeeeeC
Q 002650 34 SLPAVGSRVVYFPQGHSEQVAASTNKEVDAH--IPNYPSLPPQLICQLHNVTMHADIETDEVYAQMTLQPL 102 (896)
Q Consensus 34 ~lP~vgs~V~YFPQGH~Eq~~as~~~~~~~~--~p~~~~lP~~i~C~V~~V~l~AD~~TDEVyAqitL~P~ 102 (896)
-||..|..|.||-|||-|-+.+....+.+.- .| -++-..=+|.|..+..--=+-...-..+|+|.=+
T Consensus 872 yipQmgDEViyfrQghqeyl~~~~~n~~~~~~~~p--~~~~~v~~~kv~kl~~~~y~~~~~s~c~m~l~~i 940 (1113)
T KOG0644|consen 872 YIPQMGDEVIYFRQGHQEYLEAVRLNNIELNNKEP--WNKMAVEICKVEKLVYITYPGSGDSCCKMKLAVI 940 (1113)
T ss_pred ccccccceeehhhhhhHHHHhhhhhccccccccCc--ccccchhhheeeeeeeeeccCCCcchheeeeeee
Confidence 5899999999999999999988643332211 11 0334445899988887777777777777777655
No 23
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=49.22 E-value=26 Score=29.44 Aligned_cols=28 Identities=14% Similarity=0.259 Sum_probs=23.9
Q ss_pred CCccCCEEEEeeeccCcccceeeEEEEEecc
Q 002650 291 RVSVGMRFRMLFETEESSVRRYMGTITGISD 321 (896)
Q Consensus 291 ~ws~GMRFKM~fEtEdss~rr~~GTI~gv~d 321 (896)
.|++|+++-..++.++ .||.|+|+.+..
T Consensus 2 ~~~~G~~Ve~~~~~~~---~W~~a~V~~~~~ 29 (61)
T smart00743 2 DFKKGDRVEVFSKEED---SWWEAVVTKVLG 29 (61)
T ss_pred CcCCCCEEEEEECCCC---EEEEEEEEEECC
Confidence 5899999999996544 799999999974
No 24
>PF00788 RA: Ras association (RalGDS/AF-6) domain; InterPro: IPR000159 Proteins with this domain are mostly RasGTP effectors and include guanine-nucleotide releasing factor in mammals []. This factor stimulates the dissociation of GDP from the Ras-related RALA and RALB GTPases, which allows GTP binding and activation of the GTPases. It interacts and acts as an effector molecule for R-ras, K-Ras and Rap []. The domain is also present in a number of other proteins among them the sexual differentiation protein in yeast that is essential for mating and meiosis and yeast adenylate cyclase. These proteins contain repeated leucine-rich (LRR) segments.; GO: 0007165 signal transduction; PDB: 3EC8_A 2C5L_D 2BYF_A 2CS4_A 3KH0_A 2B3A_A 1RAX_A 2RGF_A 1WGR_A 1WXA_A ....
Probab=42.28 E-value=67 Score=28.31 Aligned_cols=65 Identities=18% Similarity=0.197 Sum_probs=46.4
Q ss_pred ceEEEeecC-c---ceeeeccCCCCCHHHHHHHHHHHhcccCccCCCCCCccEEE--EEcCCCCeEecc-CCCchhh
Q 002650 764 TFVKVYKSG-S---FGRSLDITKFSSYHELRSELARMFGLEGHLEDPLRSGWQLV--FVDRENDVLLLG-DGPWPEF 833 (896)
Q Consensus 764 ~~VKV~m~G-~---igRkIDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lv--YeD~EGD~mLvG-DvPWe~F 833 (896)
.++|||... . .-++|-++...+-.|++..+.+.|++.+ ....|.|+ -........|-. +.|+..+
T Consensus 3 ~~lrVy~~~~~~~~~~k~i~v~~~tTa~evi~~~l~k~~l~~-----~~~~y~L~~~~~~~~~er~L~~~E~pl~i~ 74 (93)
T PF00788_consen 3 GVLRVYDGDGSPGSTYKTIKVSSSTTAREVIEMALEKFGLAE-----DPSDYCLVEVEESGGEERPLDDDECPLQIQ 74 (93)
T ss_dssp EEEEEEETTSSSCCSEEEEEEETTSBHHHHHHHHHHHTTTSS-----SGGGEEEEEEECTTTEEEEETTTSBHHHHH
T ss_pred eEEEEEcCCCCCCccEEEEEECCCCCHHHHHHHHHHHhCCCC-----CCCCEEEEEEEcCCCEEEEcCCCCchHHHH
Confidence 589999986 3 3899999999999999999999999932 24469995 344444444432 3344443
No 25
>PF04014 Antitoxin-MazE: Antidote-toxin recognition MazE; InterPro: IPR007159 This domain is found in AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation []. AbrB is thought to interact directly with the transcription initiation regions of genes under its control []. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins []. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator []. DNA-binding activity in this AbrB homologue requires hexamerisation []. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins [].; PDB: 2L66_A 2GLW_A 3TND_D 2W1T_B 2RO5_B 2FY9_A 2RO3_B 1UB4_C 3ZVK_G 1YFB_B ....
Probab=39.90 E-value=39 Score=27.49 Aligned_cols=29 Identities=14% Similarity=0.110 Sum_probs=24.0
Q ss_pred hhhcccCCcCCCEEEEEEcCCCcEEEEEE
Q 002650 198 VFVSAKRLVAGDSVLFIWNDKNQLLLGIR 226 (896)
Q Consensus 198 ~FV~~KkL~aGDsVvF~R~~~G~L~VGIR 226 (896)
.|.++.+|.+||.|.|.-+++|++.|--.
T Consensus 14 ~~~~~l~l~~Gd~v~i~~~~~g~i~i~p~ 42 (47)
T PF04014_consen 14 EIREKLGLKPGDEVEIEVEGDGKIVIRPV 42 (47)
T ss_dssp HHHHHTTSSTTTEEEEEEETTSEEEEEES
T ss_pred HHHHHcCCCCCCEEEEEEeCCCEEEEEEC
Confidence 56778899999999999999987776443
No 26
>KOG3598 consensus Thyroid hormone receptor-associated protein complex, subunit TRAP230 [Transcription]
Probab=38.46 E-value=6.1 Score=51.66 Aligned_cols=9 Identities=33% Similarity=0.298 Sum_probs=4.8
Q ss_pred cccCCcccc
Q 002650 239 VLSSDSMHL 247 (896)
Q Consensus 239 v~s~~sm~~ 247 (896)
+++++.||+
T Consensus 1851 ~~s~~~~hh 1859 (2220)
T KOG3598|consen 1851 VTSEKNEHH 1859 (2220)
T ss_pred CCChHhhcC
Confidence 455555554
No 27
>KOG3207 consensus Beta-tubulin folding cofactor E [Posttranslational modification, protein turnover, chaperones]
Probab=37.60 E-value=27 Score=41.44 Aligned_cols=43 Identities=28% Similarity=0.679 Sum_probs=30.6
Q ss_pred CccCCEEEEeeeccCcccceeeEEEEEeccCCCCCCCCCCccceeeccCCCCCCCCC
Q 002650 292 VSVGMRFRMLFETEESSVRRYMGTITGISDLDPVKWPNSHWRSVKVGWDESTAGERQ 348 (896)
Q Consensus 292 ws~GMRFKM~fEtEdss~rr~~GTI~gv~d~Dp~rWP~S~WR~LqV~WDe~~~~~~~ 348 (896)
..+|.|+|.-+|- ...||.|+|.|. ++ +| +.|.||++.-+.+.
T Consensus 3 ~~IG~RvkI~~~~---~Tvr~iG~V~g~--------~~-~w--~GvEWDd~~RGKH~ 45 (505)
T KOG3207|consen 3 MEIGTRVKIGGEI---ATVRYIGEVEGN--------NS-KW--YGVEWDDPVRGKHD 45 (505)
T ss_pred eeccceEEEcCEE---EEEEEEEEEcCC--------CC-cc--eeeEecCCCccccC
Confidence 5689999987653 236777777654 44 45 78999999876654
No 28
>COG1047 SlpA FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]
Probab=31.57 E-value=2.1e+02 Score=30.29 Aligned_cols=105 Identities=17% Similarity=0.271 Sum_probs=63.9
Q ss_pred CCcCCCEEEE---EEcCCCcEEEEEEccCCCCCCCCCCcccCCccccchHHHHHHHHHcCCcEEEEEcCCCCCCcc----
Q 002650 204 RLVAGDSVLF---IWNDKNQLLLGIRRANRPPTVMPSSVLSSDSMHLGLLAAAAHAAATNSRFTIFYNPRASPSEF---- 276 (896)
Q Consensus 204 kL~aGDsVvF---~R~~~G~L~VGIRRa~r~~~~~pssv~s~~sm~~gvla~Aa~aaat~~~F~V~Y~PRas~sEF---- 276 (896)
++..||.|.+ .|.++|+++=--.- ...|..++-.+..-+.-|.+|.....-|..|+|.--|-....|+
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 4567777776 34455655421111 01133333223333334788888889999999998887655444
Q ss_pred --ccchHHHHHHHhcCCCccCCEEEEeeeccCcccceeeEEEEEecc
Q 002650 277 --VIPLAKYIKAVYHTRVSVGMRFRMLFETEESSVRRYMGTITGISD 321 (896)
Q Consensus 277 --VVp~~kyvka~~~~~ws~GMRFKM~fEtEdss~rr~~GTI~gv~d 321 (896)
.||+++|.+. ....+||+|.+ ++++ .-.-|+|+.|..
T Consensus 77 vq~vp~~~F~~~---~~~~vGm~~~~--~~~~---~~~~~~V~~V~~ 115 (174)
T COG1047 77 VQRVPRDEFQGV---GELEVGMEVEA--EGGD---GEIPGVVTEVSG 115 (174)
T ss_pred eEEecHHHhCcC---CCCCCCcEEEE--cCCC---ceeeEEEEEEcC
Confidence 4566665322 15899999874 5555 456899999964
No 29
>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=31.40 E-value=76 Score=25.92 Aligned_cols=52 Identities=15% Similarity=0.230 Sum_probs=35.8
Q ss_pred CCccCCEEEEeeeccCcccceeeEEEEEeccCCCCCCCCCCccceeeccCCCCCCCCCCCccccccccC
Q 002650 291 RVSVGMRFRMLFETEESSVRRYMGTITGISDLDPVKWPNSHWRSVKVGWDESTAGERQPRVSLWEIEPL 359 (896)
Q Consensus 291 ~ws~GMRFKM~fEtEdss~rr~~GTI~gv~d~Dp~rWP~S~WR~LqV~WDe~~~~~~~~RVSPWeIEpv 359 (896)
.|.+|..+...+ .+. .||.|+|+++.. + ..+.|.-++-+. .+-|...+|-++
T Consensus 2 ~~~~G~~~~a~~-~d~---~wyra~I~~~~~-------~---~~~~V~f~D~G~---~~~v~~~~l~~l 53 (57)
T smart00333 2 TFKVGDKVAARW-EDG---EWYRARIIKVDG-------E---QLYEVFFIDYGN---EEVVPPSDLRPL 53 (57)
T ss_pred CCCCCCEEEEEe-CCC---CEEEEEEEEECC-------C---CEEEEEEECCCc---cEEEeHHHeecC
Confidence 588999999999 443 899999999974 2 456777766432 244555555443
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=31.03 E-value=56 Score=25.30 Aligned_cols=26 Identities=19% Similarity=0.276 Sum_probs=22.5
Q ss_pred hhhcccCCcCCCEEEEEEcCCCcEEE
Q 002650 198 VFVSAKRLVAGDSVLFIWNDKNQLLL 223 (896)
Q Consensus 198 ~FV~~KkL~aGDsVvF~R~~~G~L~V 223 (896)
.|.++-++..||.|.+...++|.|.|
T Consensus 14 ~~r~~l~~~~gd~~~i~~~~~~~l~l 39 (43)
T TIGR01439 14 EIREKLGLKEGDRLEVIRVEDGEIIL 39 (43)
T ss_pred HHHHHcCcCCCCEEEEEEeCCCEEEE
Confidence 68889999999999999887787765
No 31
>cd06406 PB1_P67 A PB1 domain is present in p67 proteins which forms a signaling complex with p40, a crucial step for activation of NADPH oxidase during phagocytosis. PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes . A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. The p67 proteins contain
Probab=31.00 E-value=1.5e+02 Score=27.71 Aligned_cols=65 Identities=15% Similarity=0.179 Sum_probs=49.2
Q ss_pred eEEEeecCcceeeeccCCCCCHHHHHHHHHHHhcccCccCCCCCCccEEEEEcCCC-CeEeccCCCchhhhccee
Q 002650 765 FVKVYKSGSFGRSLDITKFSSYHELRSELARMFGLEGHLEDPLRSGWQLVFVDREN-DVLLLGDGPWPEFVNSVW 838 (896)
Q Consensus 765 ~VKV~m~G~igRkIDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EG-D~mLvGDvPWe~Fv~svk 838 (896)
-|||+-.+ .=-|-+..=-+|.+|+..|.+-+.+.+. +-+|-|.|.+. +...++|.=+|.-.+.|+
T Consensus 4 vvKV~f~~--tIaIrvp~~~~y~~L~~ki~~kLkl~~e-------~i~LsYkde~s~~~v~l~d~dle~aws~~~ 69 (80)
T cd06406 4 VVKVHFKY--TVAIQVARGLSYATLLQKISSKLELPAE-------HITLSYKSEASGEDVILSDTNMEDVWSQAK 69 (80)
T ss_pred EEEEEEEE--EEEEEcCCCCCHHHHHHHHHHHhCCCch-------hcEEEeccCCCCCccCcChHHHHHHHHhhc
Confidence 58999888 2234455566899999999999998531 35899999874 443449999999888887
No 32
>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=30.04 E-value=49 Score=32.35 Aligned_cols=26 Identities=31% Similarity=0.555 Sum_probs=18.1
Q ss_pred cCCcCCCEEEEEEcC-CCcEEEEEEcc
Q 002650 203 KRLVAGDSVLFIWND-KNQLLLGIRRA 228 (896)
Q Consensus 203 KkL~aGDsVvF~R~~-~G~L~VGIRRa 228 (896)
++++.||.|+||... .++-++|+=+-
T Consensus 38 ~~mk~GD~vifY~s~~~~~~ivai~~V 64 (143)
T PF01878_consen 38 KRMKPGDKVIFYHSGCKERGIVAIGEV 64 (143)
T ss_dssp HC--TT-EEEEEETSSSS-EEEEEEEE
T ss_pred hcCCCCCEEEEEEcCCCCCEEEEEEEE
Confidence 589999999999987 67778887664
No 33
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=29.93 E-value=62 Score=30.55 Aligned_cols=27 Identities=22% Similarity=0.293 Sum_probs=22.1
Q ss_pred hhcccCCcCCCEEEEEEcCCCcEEEEE
Q 002650 199 FVSAKRLVAGDSVLFIWNDKNQLLLGI 225 (896)
Q Consensus 199 FV~~KkL~aGDsVvF~R~~~G~L~VGI 225 (896)
|.-...|++||.|+.+|.+.|+-++=+
T Consensus 71 i~~~~~Lk~GD~V~ll~~~~gQ~yiVl 97 (100)
T PF10844_consen 71 ITFTDGLKVGDKVLLLRVQGGQKYIVL 97 (100)
T ss_pred EEEecCCcCCCEEEEEEecCCCEEEEE
Confidence 455678999999999999988876644
No 34
>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=23.34 E-value=1.4e+02 Score=26.08 Aligned_cols=42 Identities=12% Similarity=0.082 Sum_probs=27.1
Q ss_pred CccCCEEEEeeeccCcccceeeEEEEEeccCCCCCCCCCCccceeeccCCCC
Q 002650 292 VSVGMRFRMLFETEESSVRRYMGTITGISDLDPVKWPNSHWRSVKVGWDEST 343 (896)
Q Consensus 292 ws~GMRFKM~fEtEdss~rr~~GTI~gv~d~Dp~rWP~S~WR~LqV~WDe~~ 343 (896)
|..|+++-..-+.+...-.||.|||+.....+ .+.|+.+.-.
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 46799999887665555689999999997522 7788886543
No 35
>PF02513 Spin-Ssty: Spin/Ssty Family; InterPro: IPR003671 Spindlin (Spin) and Ssty were first identified for their involvement in gametogenesis. Spindlin was identified as a maternal transcript present in the unfertilised egg and early embryo, and was subsequently shown to interact with the spindle apparatus during oogenesis, and may therefore be important for mitosis []. In addition, spindlin appears to be a target for cell cycle-dependent phosphorylation, and as such may play a role in cell cycle regulation during the transition from gamete to embryo []. Ssty is a multi-copy, Y-linked spermatogenesis-specific transcript that appears to be required for normal spermatogenesis []. Ssty may play an analogous role to spindlin in sperm cells, namely during the transition from sperm cells to early embryo, and in mitosis.; GO: 0007276 gamete generation; PDB: 2NS2_A.
Probab=22.73 E-value=1.4e+02 Score=25.71 Aligned_cols=31 Identities=19% Similarity=0.370 Sum_probs=24.0
Q ss_pred cCCEEEEeeeccCcccceeeEEEEEeccCCC
Q 002650 294 VGMRFRMLFETEESSVRRYMGTITGISDLDP 324 (896)
Q Consensus 294 ~GMRFKM~fEtEdss~rr~~GTI~gv~d~Dp 324 (896)
+|-|+.-.||.++.++..|.|+|...-+..|
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 5889999999998888889999999876654
No 36
>cd05792 S1_eIF1AD_like S1_eIF1AD_like: eukaryotic translation initiation factor 1A domain containing protein (eIF1AD)-like, S1-like RNA-binding domain. eIF1AD is also known as MGC11102 protein. Little is known about the function of eIF1AD. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins, including translation initiation factor IF1A (also referred to as eIF1A in eukaryotes). eIF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors.
Probab=22.20 E-value=65 Score=29.75 Aligned_cols=35 Identities=26% Similarity=0.414 Sum_probs=27.5
Q ss_pred CCCCeEeccCCCchhhhcceeE--EEEeChhhhhcccccc
Q 002650 818 RENDVLLLGDGPWPEFVNSVWC--IKILSPPEVQQMGKRG 855 (896)
Q Consensus 818 ~EGD~mLvGDvPWe~Fv~svkr--i~Il~~~e~~~m~~~~ 855 (896)
++||..|| +||+ |-+-+|. +.|+..+++..|-+.+
T Consensus 40 krGd~VlV--~p~~-~~~kvkgeIv~i~~~~qvk~L~k~g 76 (78)
T cd05792 40 KRGDFVLV--EPIE-EGDKVKAEIVKILTRDHVKYIKEEG 76 (78)
T ss_pred EeCCEEEE--Eecc-cCCceEEEEEEEECHHHHHHHHHcC
Confidence 78999999 7998 5555664 8899999988776654
No 37
>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=21.20 E-value=65 Score=27.50 Aligned_cols=17 Identities=24% Similarity=0.534 Sum_probs=14.7
Q ss_pred EEEEEcCCCCeEeccCC
Q 002650 812 QLVFVDRENDVLLLGDG 828 (896)
Q Consensus 812 ~lvYeD~EGD~mLvGDv 828 (896)
.++|.|.+|+.+++|+.
T Consensus 34 ~i~Y~~~dg~yli~G~l 50 (57)
T PF10411_consen 34 GILYVDEDGRYLIQGQL 50 (57)
T ss_dssp EEEEEETTSSEEEES-E
T ss_pred eEEEEcCCCCEEEEeEE
Confidence 69999999999999974
Done!