Query 002390
Match_columns 928
No_of_seqs 372 out of 839
Neff 3.8
Searched_HMMs 46136
Date Thu Mar 28 22:57:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002390.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002390hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF06507 Auxin_resp: Auxin res 100.0 4.5E-35 9.8E-40 262.6 8.1 83 284-367 1-83 (83)
2 PF02309 AUX_IAA: AUX/IAA fami 100.0 1.7E-34 3.7E-39 295.9 0.0 94 793-886 107-214 (215)
3 PF02362 B3: B3 DNA binding do 99.7 4.5E-17 9.8E-22 145.9 11.5 97 158-259 1-99 (100)
4 KOG0644 Uncharacterized conser 99.2 2.5E-11 5.3E-16 142.5 6.9 148 236-392 874-1044(1113)
5 PF09217 EcoRII-N: Restriction 98.2 9E-06 1.9E-10 81.4 9.6 90 155-245 7-110 (156)
6 PF03754 DUF313: Domain of unk 97.8 4.1E-05 8.9E-10 73.6 6.4 81 152-233 18-114 (114)
7 PF00564 PB1: PB1 domain; Int 97.0 0.0018 3.8E-08 57.0 6.5 66 798-870 4-70 (84)
8 smart00666 PB1 PB1 domain. Pho 96.0 0.024 5.2E-07 49.9 7.1 65 798-870 4-69 (81)
9 cd05992 PB1 The PB1 domain is 96.0 0.028 6.1E-07 49.2 7.4 65 798-870 3-69 (81)
10 cd06407 PB1_NLP A PB1 domain i 95.4 0.052 1.1E-06 49.7 7.2 53 798-857 3-55 (82)
11 cd06396 PB1_NBR1 The PB1 domai 95.4 0.047 1E-06 50.3 6.7 51 798-857 3-54 (81)
12 cd06398 PB1_Joka2 The PB1 doma 94.7 0.11 2.3E-06 48.6 7.2 66 798-871 3-72 (91)
13 cd06409 PB1_MUG70 The MUG70 pr 94.6 0.065 1.4E-06 49.8 5.5 49 806-858 9-59 (86)
14 cd06403 PB1_Par6 The PB1 domai 92.6 0.33 7.2E-06 44.7 6.2 66 798-870 3-70 (80)
15 cd06404 PB1_aPKC PB1 domain is 91.3 0.57 1.2E-05 43.6 6.3 53 798-858 3-56 (83)
16 cd06401 PB1_TFG The PB1 domain 90.6 0.93 2E-05 42.0 6.9 58 798-860 3-61 (81)
17 cd06402 PB1_p62 The PB1 domain 90.2 1.1 2.3E-05 42.0 7.1 57 796-858 1-63 (87)
18 cd06397 PB1_UP1 Uncharacterize 87.3 1.6 3.5E-05 40.5 6.1 63 799-869 4-67 (82)
19 cd06408 PB1_NoxR The PB1 domai 81.4 4.8 0.00011 37.8 6.6 55 796-860 3-57 (86)
20 KOG3598 Thyroid hormone recept 79.3 1.6 3.4E-05 56.7 3.4 10 269-278 1850-1859(2220)
21 cd06399 PB1_P40 The PB1 domain 73.5 5.3 0.00011 37.9 4.4 50 811-886 23-72 (92)
22 KOG0644 Uncharacterized conser 49.5 12 0.00026 47.1 2.7 65 64-130 872-938 (1113)
23 PRK10737 FKBP-type peptidyl-pr 47.6 40 0.00088 35.9 6.0 104 235-352 2-114 (196)
24 smart00743 Agenet Tudor-like d 44.7 32 0.0007 29.0 3.9 38 322-372 2-39 (61)
25 PF04014 Antitoxin-MazE: Antid 43.4 37 0.00081 27.7 3.9 29 229-257 14-42 (47)
26 KOG3207 Beta-tubulin folding c 43.0 24 0.00052 42.0 3.8 43 323-379 3-45 (505)
27 PF00788 RA: Ras association ( 41.9 71 0.0015 28.2 5.8 66 796-866 3-75 (93)
28 PF10844 DUF2577: Protein of u 40.6 36 0.00078 32.2 3.9 29 230-258 71-99 (100)
29 TIGR01439 lp_hng_hel_AbrB loop 33.8 61 0.0013 25.2 3.7 26 229-254 14-39 (43)
30 smart00333 TUDOR Tudor domain. 30.5 78 0.0017 26.0 3.9 52 322-390 2-53 (57)
31 COG1047 SlpA FKBP-type peptidy 29.1 2.3E+02 0.0049 30.1 7.8 105 235-352 2-115 (174)
32 PRK03760 hypothetical protein; 27.5 1.4E+02 0.003 29.4 5.7 48 196-246 61-116 (117)
33 KOG3598 Thyroid hormone recept 27.3 48 0.001 44.3 3.1 18 63-80 1675-1693(2220)
34 PF05641 Agenet: Agenet domain 27.3 1.5E+02 0.0032 26.1 5.3 42 323-374 1-42 (68)
35 cd06406 PB1_P67 A PB1 domain i 27.1 2.2E+02 0.0047 26.8 6.5 65 797-870 4-69 (80)
36 PF11515 Cul7: Mouse developme 23.7 1.2E+02 0.0027 28.4 4.2 55 312-374 8-62 (78)
37 PF01878 EVE: EVE domain; Int 22.2 83 0.0018 30.9 3.1 27 234-260 38-65 (143)
38 PF14847 Ras_bdg_2: Ras-bindin 21.4 3E+02 0.0065 26.8 6.6 59 797-860 2-64 (105)
39 PF02513 Spin-Ssty: Spin/Ssty 20.5 1.6E+02 0.0035 25.5 4.0 31 325-355 1-31 (50)
40 PF10411 DsbC_N: Disulfide bon 20.3 72 0.0016 27.4 1.9 17 844-860 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=4.5e-35 Score=262.59 Aligned_cols=83 Identities=66% Similarity=1.100 Sum_probs=81.1
Q ss_pred HHHHHHcCCcEEEEEcCCCCCCccccchHHHHHHHhcCCCccccEEEEeeeccccccceeeeEEEEeecCCCCCCCCCCc
Q 002390 284 AAHAAATNSRFTIFYNPRASPSEFVIPLAKYVKAVYHTRVSVGMRFRMLFETEESSVRRYMGTITGISDLDPVRWPNSHW 363 (928)
Q Consensus 284 Aa~aaat~~~F~V~Y~PRas~sEFVVp~~kyvkA~~~~~ws~GMRFrM~fEtEdss~rry~GTI~gvsd~DP~rWP~S~W 363 (928)
|+|||+++++|+|+||||++++|||||++||++|+. ++|++||||||.||+||+++++|+|||+||+++||+|||+|+|
T Consensus 1 A~~aa~~~~~F~V~Y~PRa~~sEFVV~~~k~~~al~-~~~~~GmRfkM~fE~eds~~~~~~GtI~~v~~~dp~~w~~S~W 79 (83)
T PF06507_consen 1 AAHAAATGSPFEVFYYPRASPSEFVVPASKYDKALN-HPWSVGMRFKMRFETEDSSERRWQGTIVGVSDLDPIRWPGSKW 79 (83)
T ss_pred ChhHhhcCCeEEEEECCCCCCcceEEEHHHHHHHhc-CCCCCCcEEEEEeccCCCccceeeeEEeEeeccCCCCCCCCCc
Confidence 689999999999999999999999999999999997 7999999999999999999999999999999999999999999
Q ss_pred eeeE
Q 002390 364 RSVK 367 (928)
Q Consensus 364 R~Lq 367 (928)
||||
T Consensus 80 R~Lq 83 (83)
T PF06507_consen 80 RMLQ 83 (83)
T ss_pred ccCc
Confidence 9997
No 2
>PF02309 AUX_IAA: AUX/IAA family; InterPro: IPR003311 The Aux/IAA family of genes are key regulators of auxin-modified gene expression []. The plant hormone auxin (indole-3-acetic acid, IAA) regulates diverse cellular and developmental responses in plants, including cell division, expansion, differentiation and patterning of embryo responses []. Auxin can regulate the gene expression of several families, including GH3 and SAUR, as well as Aux/IAA itself. The Aux/IAA proteins act as repressors of auxin-induced gene expression, possibly through modulating the activity of DNA-binding auxin response factors (ARFs) (IPR010525 from INTERPRO). Aux/IAA and ARF are thought to interact through C-terminal protein-protein interaction domains found in both Aux/IAA and ARF. Recent evidence suggests that Aux/IAA proteins can also mediate light responses []. Some members of the AUX/IAA family are longer and contain an N-terminal DNA binding domain [] and may have an early function in the establishment of vascular and body patterns in embryonic and post-embryonic development in some plants.; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2P1N_F 2P1Q_C 2P1O_C.
Probab=99.98 E-value=1.7e-34 Score=295.89 Aligned_cols=94 Identities=40% Similarity=0.762 Sum_probs=0.0
Q ss_pred CCcceEEEeecC-cceeeeccCCCCCHHHHHHHHHHHh---cCC----------CCcCCCCCCceEEEEEcCCCceEecC
Q 002390 793 PTRTFVKVHKSG-SFGRSLDISKFSSYDELRSELARMF---GLE----------GQLEDPQRSGWQLVFVDRENDVLLLG 858 (928)
Q Consensus 793 ~~~~fVKV~m~G-~iGRkIDL~~~~sY~eL~~~L~~MF---~~~----------g~l~d~~~s~~~lvYeD~EGD~mLVG 858 (928)
..++||||+||| +|||||||++|+||++|+.+|++|| +++ +.++..++++|+|||+|+||||||||
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 358999999999 9999999999999999999999999 554 33444567899999999999999999
Q ss_pred CcchhhhhcceeEEEEeChhhhhccccc
Q 002390 859 DDPWQEFVNNVGYIKILSPLEVQQMGKG 886 (928)
Q Consensus 859 DvPWe~Fv~svkrirIl~~~e~~~m~~~ 886 (928)
||||+|||++|||||||+.+|+++|+++
T Consensus 187 D~PW~~F~~~vkRl~I~~~~e~~~~~~r 214 (215)
T PF02309_consen 187 DVPWEEFVKSVKRLRIMKSSEAKGLAPR 214 (215)
T ss_dssp ----------------------------
T ss_pred CCCHHHHHHHhhccEEecHHHhcccCCC
Confidence 9999999999999999999999999975
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=99.72 E-value=4.5e-17 Score=145.95 Aligned_cols=97 Identities=28% Similarity=0.409 Sum_probs=75.0
Q ss_pred EEEeeccccCCCCCceeeecchhhhhCCCCCCCCCCCceEEEEEecCCCeEEEEEEEeCCCCceeEccchhhhhhccCCc
Q 002390 158 FCKTLTASDTSTHGGFSVPRRAAEKVFPPLDYSQTPPAQELIARDLHDNEWKFRHIFRGQPKRHLLTTGWSVFVSAKRLV 237 (928)
Q Consensus 158 F~K~LT~SDV~~~GrfsVPk~~AE~~FP~Ld~s~~~p~q~L~~~Dl~Gk~W~FR~iyrg~pkrhlLTtGWs~FVr~K~L~ 237 (928)
|.|+|+++|+...++|.||+++++++. ++ ....+++.++|..|+.|.+++.|++.+++++|++||..||++++|+
T Consensus 1 F~K~l~~s~~~~~~~l~iP~~f~~~~~--~~---~~~~~~v~l~~~~g~~W~v~~~~~~~~~~~~l~~GW~~Fv~~n~L~ 75 (100)
T PF02362_consen 1 FFKVLKPSDVSSSCRLIIPKEFAKKHG--GN---KRKSREVTLKDPDGRSWPVKLKYRKNSGRYYLTGGWKKFVRDNGLK 75 (100)
T ss_dssp EEEE--TTCCCCTT-EEE-HHHHTTTS-------SS--CEEEEEETTTEEEEEEEEEECCTTEEEEETTHHHHHHHCT--
T ss_pred CEEEEEccCcCCCCEEEeCHHHHHHhC--CC---cCCCeEEEEEeCCCCEEEEEEEEEccCCeEEECCCHHHHHHHcCCC
Confidence 899999999999999999999999972 11 1236789999999999999999999888899999999999999999
Q ss_pred CCCEEEEEEcc--CCeEEEEEEec
Q 002390 238 AGDSVLFIWNE--KNQLLLGIRRA 259 (928)
Q Consensus 238 aGDsVvF~R~e--~GeL~VGIRRa 259 (928)
+||.|+|+... ..++.|+|+|+
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 99999999874 45569999986
No 4
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=99.18 E-value=2.5e-11 Score=142.46 Aligned_cols=148 Identities=20% Similarity=0.373 Sum_probs=115.5
Q ss_pred CcCCCEEEEEEccCCeEEEEEEecCCCCC---------------------CCCCccccCCcccccHHHHHHHHHHcCCcE
Q 002390 236 LVAGDSVLFIWNEKNQLLLGIRRATRPQT---------------------VMPSSVLSSDSMHIGLLAAAAHAAATNSRF 294 (928)
Q Consensus 236 L~aGDsVvF~R~e~GeL~VGIRRa~r~~~---------------------~~pssv~ss~sm~~gvlaaAa~aaat~~~F 294 (928)
..-||.|+.+|...-+++=.+|+.+..-+ ..|.+.-+.-.|.+.|+.-|.++ -+..|
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 46789999998643333333333222111 12445555667888888877755 46789
Q ss_pred EEEEcCCCCCCccccchHHHHHHHhcCCCccccEEEEee--eccccccceeeeEEEEeecCCCCCCCCCCceeeEEeeCC
Q 002390 295 TIFYNPRASPSEFVIPLAKYVKAVYHTRVSVGMRFRMLF--ETEESSVRRYMGTITGISDLDPVRWPNSHWRSVKVGWDE 372 (928)
Q Consensus 295 ~V~Y~PRas~sEFVVp~~kyvkA~~~~~ws~GMRFrM~f--EtEdss~rry~GTI~gvsd~DP~rWP~S~WR~LqV~WDe 372 (928)
.+.|......++|+|.+..|..|+. ++|..+++||..+ ++||. -+||.|+|.++.+..| .+|+|+|+|..|+||.
T Consensus 952 ~ltlpdlv~fpDFlV~rsrYd~AiQ-rnW~~~d~crvwwrda~~e~-g~WWeG~ils~~pksp-~fpdSpwery~v~~~~ 1028 (1113)
T KOG0644|consen 952 KLTLPDLVTFPDFLVERSRYDAAIQ-RNWTCRDKCRVWWRDAGEED-GAWWEGRILSVKPKSP-DFPDSPWERYIVRYDN 1028 (1113)
T ss_pred eeecccccCcchhhhhhhhHHHHHh-hccccccceeEEEccCCCcC-CceeeeeeeeccCCCC-CCCCCcceeEEEEecC
Confidence 9999999999999999999999986 7999999999988 44443 3799999999999887 8999999999999999
Q ss_pred CCCCCCCCCccccccccCCC
Q 002390 373 STAGERQPRVSLWEIEPLTT 392 (928)
Q Consensus 373 ~~~~~~~~RVSPWEIEpv~~ 392 (928)
.+ .+.-||||.|++..
T Consensus 1029 ~e----~~~~spwe~~~i~d 1044 (1113)
T KOG0644|consen 1029 TE----TELHSPWEMEPIPD 1044 (1113)
T ss_pred Cc----ccccCccccCCCcc
Confidence 86 46789999999976
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=98.16 E-value=9e-06 Score=81.40 Aligned_cols=90 Identities=24% Similarity=0.382 Sum_probs=59.6
Q ss_pred ceeEEEeeccccCCCCC----ceeeecchhhhhCCCCCC-CCCCCceEEEEEecCC--CeEEEEEEEeCC------CCce
Q 002390 155 TNYFCKTLTASDTSTHG----GFSVPRRAAEKVFPPLDY-SQTPPAQELIARDLHD--NEWKFRHIFRGQ------PKRH 221 (928)
Q Consensus 155 ~~~F~K~LT~SDV~~~G----rfsVPk~~AE~~FP~Ld~-s~~~p~q~L~~~Dl~G--k~W~FR~iyrg~------pkrh 221 (928)
...|+|.|++.|++..| |+-|||..++..||.+.. +...|..+|.+++..| ..|+||++|.|+ ++.+
T Consensus 7 ~~~~~K~LSaNDtGaTGgHQaGiyIpk~~~~~lFp~~~~~~~~Np~~~~~~~~~s~~~~~~~~r~iYYnn~~~~gTRNE~ 86 (156)
T PF09217_consen 7 WAIYCKRLSANDTGATGGHQAGIYIPKSAAELLFPSINHTKEENPDIWLKARWQSHFVTDSQVRFIYYNNRLFGGTRNEY 86 (156)
T ss_dssp EEEEEEE--CCCCTTTSSS--EEEE-HHHHHHH-GGG-SSSSSS-EEEEEEEETTTT---EEEEEEEE-CCCTTSS--EE
T ss_pred eEEEEEEccCCCCCCcCcccceeEecccHHHHhCCCCCcccccCCceeEEEEECCCCccceeEEEEEEcccccCCCcCce
Confidence 56899999999999775 799999999999988665 5566889999999887 559999999976 7889
Q ss_pred eEccchhhhhhc-cCCcCCCEEEEE
Q 002390 222 LLTTGWSVFVSA-KRLVAGDSVLFI 245 (928)
Q Consensus 222 lLTtGWs~FVr~-K~L~aGDsVvF~ 245 (928)
.|| .|...-.- +-=.+||.++|.
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 34443221 112578888876
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=97.79 E-value=4.1e-05 Score=73.63 Aligned_cols=81 Identities=22% Similarity=0.292 Sum_probs=64.1
Q ss_pred CCCceeEEEeeccccCCCC-CceeeecchhhhhCCCCCC------------CCCCCceEEEEEecCCCeEEEEEEEeCC-
Q 002390 152 KQPTNYFCKTLTASDTSTH-GGFSVPRRAAEKVFPPLDY------------SQTPPAQELIARDLHDNEWKFRHIFRGQ- 217 (928)
Q Consensus 152 ~~~~~~F~K~LT~SDV~~~-GrfsVPk~~AE~~FP~Ld~------------s~~~p~q~L~~~Dl~Gk~W~FR~iyrg~- 217 (928)
.++...|+|+|++|||..+ .||+||-..... ...|.. .....++.+.+.|..++.|..++..|..
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 4568899999999999966 899999886643 233321 1234578999999999999999999955
Q ss_pred --CCceeEccchhhhhhc
Q 002390 218 --PKRHLLTTGWSVFVSA 233 (928)
Q Consensus 218 --pkrhlLTtGWs~FVr~ 233 (928)
.-.|+|++||..+|++
T Consensus 97 ~~~~~YvL~~gWn~VV~~ 114 (114)
T PF03754_consen 97 NGTSNYVLNSGWNKVVED 114 (114)
T ss_pred CCceEEEEEcChHhhccC
Confidence 5679999999999864
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=97.01 E-value=0.0018 Score=57.02 Aligned_cols=66 Identities=29% Similarity=0.520 Sum_probs=55.1
Q ss_pred EEEeecCcceeeeccCCCCCHHHHHHHHHHHhcCCCCcCCCCCCceEEEEEcCCCceEecCC-cchhhhhccee
Q 002390 798 VKVHKSGSFGRSLDISKFSSYDELRSELARMFGLEGQLEDPQRSGWQLVFVDRENDVLLLGD-DPWQEFVNNVG 870 (928)
Q Consensus 798 VKV~m~G~iGRkIDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLVGD-vPWe~Fv~svk 870 (928)
||++-.|.+=|.+.+..--+|++|+..++..|+.. ...+++.|.|.||||..+.+ .=|++.++.++
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 78888887666788888889999999999999976 24599999999999988874 44777777664
No 8
>smart00666 PB1 PB1 domain. Phox and Bem1p domain, present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.
Probab=96.00 E-value=0.024 Score=49.88 Aligned_cols=65 Identities=29% Similarity=0.566 Sum_probs=51.0
Q ss_pred EEEeecCcceeeeccCCCCCHHHHHHHHHHHhcCCCCcCCCCCCceEEEEEcCCCceEec-CCcchhhhhccee
Q 002390 798 VKVHKSGSFGRSLDISKFSSYDELRSELARMFGLEGQLEDPQRSGWQLVFVDRENDVLLL-GDDPWQEFVNNVG 870 (928)
Q Consensus 798 VKV~m~G~iGRkIDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLV-GDvPWe~Fv~svk 870 (928)
|||.- |.--|.+-+..--+|++|++++.+.|++.. ..+.|-|+|.||||..+ .|.=|++.+..++
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 545677888889999999999999999643 35999999999999855 4566776666554
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=95.98 E-value=0.028 Score=49.17 Aligned_cols=65 Identities=26% Similarity=0.553 Sum_probs=49.9
Q ss_pred EEEeecCcceeeeccC-CCCCHHHHHHHHHHHhcCCCCcCCCCCCceEEEEEcCCCceEecCC-cchhhhhccee
Q 002390 798 VKVHKSGSFGRSLDIS-KFSSYDELRSELARMFGLEGQLEDPQRSGWQLVFVDRENDVLLLGD-DPWQEFVNNVG 870 (928)
Q Consensus 798 VKV~m~G~iGRkIDL~-~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLVGD-vPWe~Fv~svk 870 (928)
|||+-.|.+ |.+-+. .-.+|++|++.|.+.|++.. ..+.+.|.|.||||..+.+ .=|++.++.++
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 88899999999999999754 3589999999999998877 66666666554
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=95.44 E-value=0.052 Score=49.68 Aligned_cols=53 Identities=25% Similarity=0.439 Sum_probs=41.5
Q ss_pred EEEeecCcceeeeccCCCCCHHHHHHHHHHHhcCCCCcCCCCCCceEEEEEcCCCceEec
Q 002390 798 VKVHKSGSFGRSLDISKFSSYDELRSELARMFGLEGQLEDPQRSGWQLVFVDRENDVLLL 857 (928)
Q Consensus 798 VKV~m~G~iGRkIDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLV 857 (928)
|||.-.|. -+.+-+..--+|++|+++++++|++.. .+++.|-|.|.||||.++
T Consensus 3 vK~~~~~d-~~r~~l~~~~~~~~L~~~i~~r~~~~~------~~~f~LkY~Ddegd~v~l 55 (82)
T cd06407 3 VKATYGEE-KIRFRLPPSWGFTELKQEIAKRFKLDD------MSAFDLKYLDDDEEWVLL 55 (82)
T ss_pred EEEEeCCe-EEEEEcCCCCCHHHHHHHHHHHhCCCC------CCeeEEEEECCCCCeEEe
Confidence 78888774 233445555599999999999999742 357999999999999876
No 11
>cd06396 PB1_NBR1 The PB1 domain is an essential part of NBR1 protein, next to BRCA1, a scaffold protein mediating specific protein-protein interaction with both titin protein kinase and with another scaffold protein p62. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The NBR1 protein contains a type I PB1 domain.
Probab=95.41 E-value=0.047 Score=50.27 Aligned_cols=51 Identities=25% Similarity=0.375 Sum_probs=44.1
Q ss_pred EEEeecC-cceeeeccCCCCCHHHHHHHHHHHhcCCCCcCCCCCCceEEEEEcCCCceEec
Q 002390 798 VKVHKSG-SFGRSLDISKFSSYDELRSELARMFGLEGQLEDPQRSGWQLVFVDRENDVLLL 857 (928)
Q Consensus 798 VKV~m~G-~iGRkIDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLV 857 (928)
|||.-.| .+--+++-+.-.+|.+|..+++++|++. .+.|.|.|.||||.++
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 3899999999999876
No 12
>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=94.75 E-value=0.11 Score=48.59 Aligned_cols=66 Identities=26% Similarity=0.462 Sum_probs=49.2
Q ss_pred EEEeecCc-ceeeeccC---CCCCHHHHHHHHHHHhcCCCCcCCCCCCceEEEEEcCCCceEecCCcchhhhhcceeE
Q 002390 798 VKVHKSGS-FGRSLDIS---KFSSYDELRSELARMFGLEGQLEDPQRSGWQLVFVDRENDVLLLGDDPWQEFVNNVGY 871 (928)
Q Consensus 798 VKV~m~G~-iGRkIDL~---~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLVGDvPWe~Fv~svkr 871 (928)
|||.-+|. +=-++++. .--+|++|++++++.|.+.. ..+++|.|.|.||||..+-++ +++..++.+
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 33345543 45799999999999998632 357999999999999988544 455555554
No 13
>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=94.63 E-value=0.065 Score=49.80 Aligned_cols=49 Identities=27% Similarity=0.436 Sum_probs=38.3
Q ss_pred ceee--eccCCCCCHHHHHHHHHHHhcCCCCcCCCCCCceEEEEEcCCCceEecC
Q 002390 806 FGRS--LDISKFSSYDELRSELARMFGLEGQLEDPQRSGWQLVFVDRENDVLLLG 858 (928)
Q Consensus 806 iGRk--IDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLVG 858 (928)
-||. +-+....|+.+|++++++-|+.+... ...++|.|.|.||||.|+-
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 4444 34444789999999999999976532 4579999999999998763
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=92.56 E-value=0.33 Score=44.74 Aligned_cols=66 Identities=21% Similarity=0.385 Sum_probs=49.6
Q ss_pred EEEeecCccee-eeccCCCCCHHHHHHHHHHHhcCCCCcCCCCCCceEEEEEcCCCceEecC-Ccchhhhhccee
Q 002390 798 VKVHKSGSFGR-SLDISKFSSYDELRSELARMFGLEGQLEDPQRSGWQLVFVDRENDVLLLG-DDPWQEFVNNVG 870 (928)
Q Consensus 798 VKV~m~G~iGR-kIDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLVG-DvPWe~Fv~svk 870 (928)
||.+-++.+=| ++|-....+|+|+++-|++|+.+.. ..+.|-|.|.+||.+-+- |+-...=+.+++
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 56666665533 6777778999999999999999865 259999999999998764 555555455554
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=91.32 E-value=0.57 Score=43.58 Aligned_cols=53 Identities=26% Similarity=0.349 Sum_probs=41.4
Q ss_pred EEEeecCcc-eeeeccCCCCCHHHHHHHHHHHhcCCCCcCCCCCCceEEEEEcCCCceEecC
Q 002390 798 VKVHKSGSF-GRSLDISKFSSYDELRSELARMFGLEGQLEDPQRSGWQLVFVDRENDVLLLG 858 (928)
Q Consensus 798 VKV~m~G~i-GRkIDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLVG 858 (928)
+|++-.|.| --.+|. ..+|++|.+++.+||... .+..+++.|.|.|||---+.
T Consensus 3 ~K~~y~gdi~it~~d~--~~s~e~L~~~v~~~c~~~------~~q~ft~kw~DEEGDp~tiS 56 (83)
T cd06404 3 VKAAYNGDIMITSIDP--SISLEELCNEVRDMCRFH------NDQPFTLKWIDEEGDPCTIS 56 (83)
T ss_pred EEEEecCcEEEEEcCC--CcCHHHHHHHHHHHhCCC------CCCcEEEEEECCCCCceeec
Confidence 788888954 444554 788999999999999972 23469999999999976553
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=90.59 E-value=0.93 Score=42.02 Aligned_cols=58 Identities=21% Similarity=0.299 Sum_probs=42.9
Q ss_pred EEEeecCcceeeeccCCC-CCHHHHHHHHHHHhcCCCCcCCCCCCceEEEEEcCCCceEecCCc
Q 002390 798 VKVHKSGSFGRSLDISKF-SSYDELRSELARMFGLEGQLEDPQRSGWQLVFVDRENDVLLLGDD 860 (928)
Q Consensus 798 VKV~m~G~iGRkIDL~~~-~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLVGDv 860 (928)
+|+.-.|.|=| +-+..- -+|.+|+..+.+.|...- +....+.+.|.|.|||+.-+.+.
T Consensus 3 iK~~~g~DiR~-~~~~~~~~t~~~L~~~v~~~F~~~~----~~~~~flIKYkD~dGDlVTIts~ 61 (81)
T cd06401 3 LKAQLGDDIRR-IPIHNEDITYDELLLMMQRVFRGKL----GSSDDVLIKYKDEDGDLITIFDS 61 (81)
T ss_pred EEEEeCCeEEE-EeccCccccHHHHHHHHHHHhcccc----CCcccEEEEEECCCCCEEEeccH
Confidence 57666556644 444432 399999999999999431 23346999999999999999875
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=90.22 E-value=1.1 Score=42.01 Aligned_cols=57 Identities=26% Similarity=0.312 Sum_probs=43.2
Q ss_pred ceEEEeecC----cceeee--ccCCCCCHHHHHHHHHHHhcCCCCcCCCCCCceEEEEEcCCCceEecC
Q 002390 796 TFVKVHKSG----SFGRSL--DISKFSSYDELRSELARMFGLEGQLEDPQRSGWQLVFVDRENDVLLLG 858 (928)
Q Consensus 796 ~fVKV~m~G----~iGRkI--DL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLVG 858 (928)
..||.|..| +=-|++ |-....+|++|+..+.++|..- .+..+++.|.|.|||..-+.
T Consensus 1 ~~vkayl~~~~~~~EIRRf~l~~~~~~s~~~L~~~V~~~f~~l------~~~~ftlky~DeeGDlvtIs 63 (87)
T cd06402 1 LTVKAYLLGKDANAEIRRFAIDEDVSTSYEYLVEKVAAVFPSL------RGKNFQLFWKDEEGDLVAFS 63 (87)
T ss_pred CeEEEeecCCCCccceEEEEecCCCCcCHHHHHHHHHHHcccc------CCCcEEEEEECCCCCEEeec
Confidence 368888877 334544 4467779999999999999532 12469999999999987654
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=87.32 E-value=1.6 Score=40.53 Aligned_cols=63 Identities=19% Similarity=0.318 Sum_probs=47.2
Q ss_pred EEeecCcceeeeccCCCCCHHHHHHHHHHHhcCCCCcCCCCCCceEEEEEcCCCceE-ecCCcchhhhhcce
Q 002390 799 KVHKSGSFGRSLDISKFSSYDELRSELARMFGLEGQLEDPQRSGWQLVFVDRENDVL-LLGDDPWQEFVNNV 869 (928)
Q Consensus 799 KV~m~G~iGRkIDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~m-LVGDvPWe~Fv~sv 869 (928)
||.- |.--|++....-=+|.+|++.|+.+|.+.. .+ +.++|.|.|||.. |+-|+=-++|.+-.
T Consensus 4 Kv~~-~g~~RRf~~~~~pt~~~L~~kl~~Lf~lp~------~~-~~vtYiDeD~D~ITlssd~eL~d~~~~~ 67 (82)
T cd06397 4 KSSF-LGDTRRIVFPDIPTWEALASKLENLYNLPE------IK-VGVTYIDNDNDEITLSSNKELQDFYRLS 67 (82)
T ss_pred EEEe-CCceEEEecCCCccHHHHHHHHHHHhCCCh------hH-eEEEEEcCCCCEEEecchHHHHHHHHhc
Confidence 6744 345678888888899999999999999743 23 8999999999976 44555566665533
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=81.42 E-value=4.8 Score=37.75 Aligned_cols=55 Identities=22% Similarity=0.440 Sum_probs=43.8
Q ss_pred ceEEEeecCcceeeeccCCCCCHHHHHHHHHHHhcCCCCcCCCCCCceEEEEEcCCCceEecCCc
Q 002390 796 TFVKVHKSGSFGRSLDISKFSSYDELRSELARMFGLEGQLEDPQRSGWQLVFVDRENDVLLLGDD 860 (928)
Q Consensus 796 ~fVKV~m~G~iGRkIDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLVGDv 860 (928)
.=|||+-.|. -|-|-+..--+|++|...+.++|++. ..+++-|.|. ||..-++|.
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 45666666778999999999999973 2589999999 998877663
No 20
>KOG3598 consensus Thyroid hormone receptor-associated protein complex, subunit TRAP230 [Transcription]
Probab=79.26 E-value=1.6 Score=56.71 Aligned_cols=10 Identities=30% Similarity=0.275 Sum_probs=6.1
Q ss_pred ccccCCcccc
Q 002390 269 SVLSSDSMHI 278 (928)
Q Consensus 269 sv~ss~sm~~ 278 (928)
.++|++.||+
T Consensus 1850 ~~~s~~~~hh 1859 (2220)
T KOG3598|consen 1850 DVTSEKNEHH 1859 (2220)
T ss_pred CCCChHhhcC
Confidence 3566666665
No 21
>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=73.47 E-value=5.3 Score=37.85 Aligned_cols=50 Identities=30% Similarity=0.357 Sum_probs=43.2
Q ss_pred ccCCCCCHHHHHHHHHHHhcCCCCcCCCCCCceEEEEEcCCCceEecCCcchhhhhcceeEEEEeChhhhhccccc
Q 002390 811 DISKFSSYDELRSELARMFGLEGQLEDPQRSGWQLVFVDRENDVLLLGDDPWQEFVNNVGYIKILSPLEVQQMGKG 886 (928)
Q Consensus 811 DL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EGD~mLVGDvPWe~Fv~svkrirIl~~~e~~~m~~~ 886 (928)
||+.--+|.+|..-..+-|..+ +-.|-|.|.|||. ||||+.+++.=|-++
T Consensus 23 ~l~~~P~~kdLl~lmr~~f~~~---------dIaLNYrD~EGDL-----------------IRllddeDv~LMV~~ 72 (92)
T cd06399 23 DLSSTPLLKDLLELTRREFQRE---------DIALNYRDAEGDL-----------------IRLLSDEDVALMVRQ 72 (92)
T ss_pred ccccCccHHHHHHHHHHHhchh---------heeeeeecCCCCE-----------------EEEcchhhHHHHHHH
Confidence 6778889999999999999853 3689999999996 799999999988776
No 22
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=49.51 E-value=12 Score=47.08 Aligned_cols=65 Identities=26% Similarity=0.448 Sum_probs=43.2
Q ss_pred CCCCCCCEEEEecCcchhhhcccccccccc--cCCCCCCCCCcceeEEeeeeecccCCCcceeeeceee
Q 002390 64 SLPPVGSRVVYFPQGHSEQVAASTNKEVDA--HIPNYPNLPPQLICQLHNLTMHADVETDEVYAQMTLQ 130 (928)
Q Consensus 64 ~lP~vgs~V~YFPQGH~Eq~~as~~~~~~~--~ip~~~~lP~~i~C~V~~V~l~AD~~TDEVyAqitL~ 130 (928)
-||..|..|.||-|||-|-+.+....+.+. ..| -++-..=+|.|..+..--=+-...--.+|+|.
T Consensus 872 yipQmgDEViyfrQghqeyl~~~~~n~~~~~~~~p--~~~~~v~~~kv~kl~~~~y~~~~~s~c~m~l~ 938 (1113)
T KOG0644|consen 872 YIPQMGDEVIYFRQGHQEYLEAVRLNNIELNNKEP--WNKMAVEICKVEKLVYITYPGSGDSCCKMKLA 938 (1113)
T ss_pred ccccccceeehhhhhhHHHHhhhhhccccccccCc--ccccchhhheeeeeeeeeccCCCcchheeeee
Confidence 589999999999999999998864332221 112 14445567888877665555555555555554
No 23
>PRK10737 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=47.65 E-value=40 Score=35.90 Aligned_cols=104 Identities=20% Similarity=0.248 Sum_probs=62.5
Q ss_pred CCcCCCEEEE-E--EccCCeEEEEEEecCCCCCCCCCccccCCcccccHHHHHHHHHHcCCcEEEEEcCCCCCC------
Q 002390 235 RLVAGDSVLF-I--WNEKNQLLLGIRRATRPQTVMPSSVLSSDSMHIGLLAAAAHAAATNSRFTIFYNPRASPS------ 305 (928)
Q Consensus 235 ~L~aGDsVvF-~--R~e~GeL~VGIRRa~r~~~~~pssv~ss~sm~~gvlaaAa~aaat~~~F~V~Y~PRas~s------ 305 (928)
++..|++|.+ | |.++|+++=.-+ . ..|...+--...-+--|.+|..-.+.|..|+|..-|-....
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 3566777766 3 346777533221 1 22433333223333346777777788899999876654332
Q ss_pred ccccchHHHHHHHhcCCCccccEEEEeeeccccccceeeeEEEEeec
Q 002390 306 EFVIPLAKYVKAVYHTRVSVGMRFRMLFETEESSVRRYMGTITGISD 352 (928)
Q Consensus 306 EFVVp~~kyvkA~~~~~ws~GMRFrM~fEtEdss~rry~GTI~gvsd 352 (928)
-..||++.|. .. ....+||||.+ ++++. ...++|+.|.+
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 3467777652 22 24899999886 45553 35889999975
No 24
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=44.68 E-value=32 Score=28.98 Aligned_cols=38 Identities=13% Similarity=0.131 Sum_probs=29.2
Q ss_pred CCccccEEEEeeeccccccceeeeEEEEeecCCCCCCCCCCceeeEEeeCC
Q 002390 322 RVSVGMRFRMLFETEESSVRRYMGTITGISDLDPVRWPNSHWRSVKVGWDE 372 (928)
Q Consensus 322 ~ws~GMRFrM~fEtEdss~rry~GTI~gvsd~DP~rWP~S~WR~LqV~WDe 372 (928)
.|.+|+++-..++.++ .||.|+|+.+.. -..+.|.-+.
T Consensus 2 ~~~~G~~Ve~~~~~~~---~W~~a~V~~~~~----------~~~~~V~~~~ 39 (61)
T smart00743 2 DFKKGDRVEVFSKEED---SWWEAVVTKVLG----------DGKYLVRYLT 39 (61)
T ss_pred CcCCCCEEEEEECCCC---EEEEEEEEEECC----------CCEEEEEECC
Confidence 5899999999996544 799999999964 1235677665
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=43.38 E-value=37 Score=27.69 Aligned_cols=29 Identities=14% Similarity=0.100 Sum_probs=23.7
Q ss_pred hhhhccCCcCCCEEEEEEccCCeEEEEEE
Q 002390 229 VFVSAKRLVAGDSVLFIWNEKNQLLLGIR 257 (928)
Q Consensus 229 ~FVr~K~L~aGDsVvF~R~e~GeL~VGIR 257 (928)
.|.++.+|++||.|.|.-.++|++.|--.
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 56778899999999999988887766443
No 26
>KOG3207 consensus Beta-tubulin folding cofactor E [Posttranslational modification, protein turnover, chaperones]
Probab=43.02 E-value=24 Score=41.97 Aligned_cols=43 Identities=28% Similarity=0.679 Sum_probs=30.1
Q ss_pred CccccEEEEeeeccccccceeeeEEEEeecCCCCCCCCCCceeeEEeeCCCCCCCCC
Q 002390 323 VSVGMRFRMLFETEESSVRRYMGTITGISDLDPVRWPNSHWRSVKVGWDESTAGERQ 379 (928)
Q Consensus 323 ws~GMRFrM~fEtEdss~rry~GTI~gvsd~DP~rWP~S~WR~LqV~WDe~~~~~~~ 379 (928)
..+|.|+|.-+|- ...||.|+|.|. ++ +| +.|.||++.-+.+.
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 5689999986643 235777776553 44 45 78999999877554
No 27
>PF00788 RA: Ras association (RalGDS/AF-6) domain; InterPro: IPR000159 Proteins with this domain are mostly RasGTP effectors and include guanine-nucleotide releasing factor in mammals []. This factor stimulates the dissociation of GDP from the Ras-related RALA and RALB GTPases, which allows GTP binding and activation of the GTPases. It interacts and acts as an effector molecule for R-ras, K-Ras and Rap []. The domain is also present in a number of other proteins among them the sexual differentiation protein in yeast that is essential for mating and meiosis and yeast adenylate cyclase. These proteins contain repeated leucine-rich (LRR) segments.; GO: 0007165 signal transduction; PDB: 3EC8_A 2C5L_D 2BYF_A 2CS4_A 3KH0_A 2B3A_A 1RAX_A 2RGF_A 1WGR_A 1WXA_A ....
Probab=41.91 E-value=71 Score=28.25 Aligned_cols=66 Identities=20% Similarity=0.205 Sum_probs=48.0
Q ss_pred ceEEEeecC-c---ceeeeccCCCCCHHHHHHHHHHHhcCCCCcCCCCCCceEEE-EE-cCCCceEec-CCcchhhhh
Q 002390 796 TFVKVHKSG-S---FGRSLDISKFSSYDELRSELARMFGLEGQLEDPQRSGWQLV-FV-DRENDVLLL-GDDPWQEFV 866 (928)
Q Consensus 796 ~fVKV~m~G-~---iGRkIDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lv-Ye-D~EGD~mLV-GDvPWe~Fv 866 (928)
.++||+... . .-++|-++...+-.|++.++.+.|++.+ +...|.|+ +. .......|- .+.|+....
T Consensus 3 ~~lrVy~~~~~~~~~~k~i~v~~~tTa~evi~~~l~k~~l~~-----~~~~y~L~~~~~~~~~er~L~~~E~pl~i~~ 75 (93)
T PF00788_consen 3 GVLRVYDGDGSPGSTYKTIKVSSSTTAREVIEMALEKFGLAE-----DPSDYCLVEVEESGGEERPLDDDECPLQIQL 75 (93)
T ss_dssp EEEEEEETTSSSCCSEEEEEEETTSBHHHHHHHHHHHTTTSS-----SGGGEEEEEEECTTTEEEEETTTSBHHHHHH
T ss_pred eEEEEEcCCCCCCccEEEEEECCCCCHHHHHHHHHHHhCCCC-----CCCCEEEEEEEcCCCEEEEcCCCCchHHHHH
Confidence 589999986 3 2899999999999999999999999832 24569995 44 444555554 344555444
No 28
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=40.63 E-value=36 Score=32.24 Aligned_cols=29 Identities=21% Similarity=0.310 Sum_probs=23.4
Q ss_pred hhhccCCcCCCEEEEEEccCCeEEEEEEe
Q 002390 230 FVSAKRLVAGDSVLFIWNEKNQLLLGIRR 258 (928)
Q Consensus 230 FVr~K~L~aGDsVvF~R~e~GeL~VGIRR 258 (928)
|.-...|++||.|..+|.++|+-++=+-|
T Consensus 71 i~~~~~Lk~GD~V~ll~~~~gQ~yiVlDk 99 (100)
T PF10844_consen 71 ITFTDGLKVGDKVLLLRVQGGQKYIVLDK 99 (100)
T ss_pred EEEecCCcCCCEEEEEEecCCCEEEEEEe
Confidence 45567899999999999999987775543
No 29
>TIGR01439 lp_hng_hel_AbrB looped-hinge helix DNA binding domain, AbrB family. This DNA-binding domain family includes AbrB, a transition state regulator in Bacillus subtilis, whose DNA-binding domain structure in solution was determined by NMR. The domain binds DNA as a dimer in what is termed a looped-hinge helix fold. Some members of the family have two copies of the domain in tandem. The domain is found usually at the N-terminus of a small protein. This model excludes members of family TIGR02609.
Probab=33.83 E-value=61 Score=25.19 Aligned_cols=26 Identities=23% Similarity=0.288 Sum_probs=22.3
Q ss_pred hhhhccCCcCCCEEEEEEccCCeEEE
Q 002390 229 VFVSAKRLVAGDSVLFIWNEKNQLLL 254 (928)
Q Consensus 229 ~FVr~K~L~aGDsVvF~R~e~GeL~V 254 (928)
.|.++-+++.||.|.+...++|.+.+
T Consensus 14 ~~r~~l~~~~gd~~~i~~~~~~~l~l 39 (43)
T TIGR01439 14 EIREKLGLKEGDRLEVIRVEDGEIIL 39 (43)
T ss_pred HHHHHcCcCCCCEEEEEEeCCCEEEE
Confidence 78889999999999999877777655
No 30
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=30.46 E-value=78 Score=25.98 Aligned_cols=52 Identities=15% Similarity=0.230 Sum_probs=36.6
Q ss_pred CCccccEEEEeeeccccccceeeeEEEEeecCCCCCCCCCCceeeEEeeCCCCCCCCCCCccccccccC
Q 002390 322 RVSVGMRFRMLFETEESSVRRYMGTITGISDLDPVRWPNSHWRSVKVGWDESTAGERQPRVSLWEIEPL 390 (928)
Q Consensus 322 ~ws~GMRFrM~fEtEdss~rry~GTI~gvsd~DP~rWP~S~WR~LqV~WDe~~~~~~~~RVSPWEIEpv 390 (928)
.|.+|..+...+ .+. .||.|+|+++.. + ....|.-++-+. .+-|...+|-++
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 433 799999999963 2 456788777442 244666655544
No 31
>COG1047 SlpA FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]
Probab=29.08 E-value=2.3e+02 Score=30.10 Aligned_cols=105 Identities=19% Similarity=0.255 Sum_probs=64.9
Q ss_pred CCcCCCEEEEE---EccCCeEEEEEEecCCCCCCCCCccccCCcccccHHHHHHHHHHcCCcEEEEEcCCCCCCcc----
Q 002390 235 RLVAGDSVLFI---WNEKNQLLLGIRRATRPQTVMPSSVLSSDSMHIGLLAAAAHAAATNSRFTIFYNPRASPSEF---- 307 (928)
Q Consensus 235 ~L~aGDsVvF~---R~e~GeL~VGIRRa~r~~~~~pssv~ss~sm~~gvlaaAa~aaat~~~F~V~Y~PRas~sEF---- 307 (928)
++..||.|.+. |.++|+++=--. . ...|..++-.+..-+.-|.+|..-..-|..|+|.--|-..-.|+
T Consensus 2 ~i~k~~~V~i~Y~~~~~dg~v~Dtt~-e----~~~P~~~i~G~g~li~glE~al~g~~~Ge~~~V~IpPE~AfGe~~~~l 76 (174)
T COG1047 2 KIEKGDVVSLHYTLKVEDGEVVDTTD-E----NYGPLTFIVGAGQLIPGLEEALLGKEVGEEFTVEIPPEDAFGEYDPDL 76 (174)
T ss_pred cccCCCEEEEEEEEEecCCcEEEccc-c----cCCCeEEEecCCCcchhHHHHHhCCCCCceeEEEeCchHhcCCCChHH
Confidence 46678888762 335554432111 1 01233333333333344778888889999999998887765554
Q ss_pred --ccchHHHHHHHhcCCCccccEEEEeeeccccccceeeeEEEEeec
Q 002390 308 --VIPLAKYVKAVYHTRVSVGMRFRMLFETEESSVRRYMGTITGISD 352 (928)
Q Consensus 308 --VVp~~kyvkA~~~~~ws~GMRFrM~fEtEdss~rry~GTI~gvsd 352 (928)
.||+++|.+.- ...+||+|.. ++++ .-.-|+|+.|..
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 46666653321 5899999874 5555 456899999974
No 32
>PRK03760 hypothetical protein; Provisional
Probab=27.47 E-value=1.4e+02 Score=29.35 Aligned_cols=48 Identities=21% Similarity=0.338 Sum_probs=30.6
Q ss_pred eEEEEEecCCCeEEEEE-----EEe-CCCCceeE--ccchhhhhhccCCcCCCEEEEEE
Q 002390 196 QELIARDLHDNEWKFRH-----IFR-GQPKRHLL--TTGWSVFVSAKRLVAGDSVLFIW 246 (928)
Q Consensus 196 q~L~~~Dl~Gk~W~FR~-----iyr-g~pkrhlL--TtGWs~FVr~K~L~aGDsVvF~R 246 (928)
.++.+.|.+|++=.... +|. ..+-+|+| ..||.. +.++++||.|.|.|
T Consensus 61 LDiiFld~~g~Vv~i~~~~P~~~~~~~~~a~~VLEl~aG~~~---~~gi~~Gd~v~~~~ 116 (117)
T PRK03760 61 IDVIFLDSNRRVVDFKTLKPWRIYVPKKPARYIIEGPVGKIR---VLKVEVGDEIEWID 116 (117)
T ss_pred eEEEEECCCCeEEEEEeCCCccccCCCccceEEEEeCCChHH---HcCCCCCCEEEEee
Confidence 34666666554333211 122 34556888 577765 99999999999876
No 33
>KOG3598 consensus Thyroid hormone receptor-associated protein complex, subunit TRAP230 [Transcription]
Probab=27.32 E-value=48 Score=44.29 Aligned_cols=18 Identities=22% Similarity=0.335 Sum_probs=9.3
Q ss_pred CCCCCCC-CEEEEecCcch
Q 002390 63 VSLPPVG-SRVVYFPQGHS 80 (928)
Q Consensus 63 v~lP~vg-s~V~YFPQGH~ 80 (928)
.-||+-- +.+-|=|+|-.
T Consensus 1675 LPlpKqt~dvItcep~gsl 1693 (2220)
T KOG3598|consen 1675 LPLPKQTMDVITCEPYGSL 1693 (2220)
T ss_pred cCCCccccceeeecccccc
Confidence 3444432 45566666653
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=27.29 E-value=1.5e+02 Score=26.05 Aligned_cols=42 Identities=12% Similarity=0.082 Sum_probs=27.5
Q ss_pred CccccEEEEeeeccccccceeeeEEEEeecCCCCCCCCCCceeeEEeeCCCC
Q 002390 323 VSVGMRFRMLFETEESSVRRYMGTITGISDLDPVRWPNSHWRSVKVGWDEST 374 (928)
Q Consensus 323 ws~GMRFrM~fEtEdss~rry~GTI~gvsd~DP~rWP~S~WR~LqV~WDe~~ 374 (928)
+..|+++-..-+.+.....||.|||+.....+ .+.|+.++-.
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 46799999887666555799999999997532 7889997554
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=27.14 E-value=2.2e+02 Score=26.81 Aligned_cols=65 Identities=17% Similarity=0.270 Sum_probs=48.6
Q ss_pred eEEEeecCcceeeeccCCCCCHHHHHHHHHHHhcCCCCcCCCCCCceEEEEEcCCC-ceEecCCcchhhhhccee
Q 002390 797 FVKVHKSGSFGRSLDISKFSSYDELRSELARMFGLEGQLEDPQRSGWQLVFVDREN-DVLLLGDDPWQEFVNNVG 870 (928)
Q Consensus 797 fVKV~m~G~iGRkIDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~EG-D~mLVGDvPWe~Fv~svk 870 (928)
-|||+-.+- =-|-...=-+|.+|+..|.+-+.+.+ .+-+|-|.|.+. +...++|.=+|.-.+.|+
T Consensus 4 vvKV~f~~t--IaIrvp~~~~y~~L~~ki~~kLkl~~-------e~i~LsYkde~s~~~v~l~d~dle~aws~~~ 69 (80)
T cd06406 4 VVKVHFKYT--VAIQVARGLSYATLLQKISSKLELPA-------EHITLSYKSEASGEDVILSDTNMEDVWSQAK 69 (80)
T ss_pred EEEEEEEEE--EEEEcCCCCCHHHHHHHHHHHhCCCc-------hhcEEEeccCCCCCccCcChHHHHHHHHhhc
Confidence 489998882 23445555689999999999998753 235899998874 443449999998888887
No 36
>PF11515 Cul7: Mouse development and cellular proliferation protein Cullin-7; InterPro: IPR021097 The CPH domain is found in the Cullin-7, PARC and HERC2 proteins, which are all components of known or predicted E3-ubiquitin ligases. The CPH domain is a protein-protein interaction module that binds the teramerisation domain of the tumour suppressor protein p53 []. Structurally it forms a beta-barrel fold similar to the SH3, Tudor and KOW and domains. Unlike the SH3 and Tudor domains, which bind to small peptides, the CPH domain appears to bind to an extended surface on p53.; PDB: 2JUF_A 2JNG_A.
Probab=23.69 E-value=1.2e+02 Score=28.37 Aligned_cols=55 Identities=22% Similarity=0.247 Sum_probs=25.7
Q ss_pred HHHHHHHhcCCCccccEEEEeeeccccccceeeeEEEEeecCCCCCCCCCCceeeEEeeCCCC
Q 002390 312 AKYVKAVYHTRVSVGMRFRMLFETEESSVRRYMGTITGISDLDPVRWPNSHWRSVKVGWDEST 374 (928)
Q Consensus 312 ~kyvkA~~~~~ws~GMRFrM~fEtEdss~rry~GTI~gvsd~DP~rWP~S~WR~LqV~WDe~~ 374 (928)
+.|..=+. .++.+||++||.=.-|+-.. -=.|+|.-++.- .-| =-.+||.|-.-+
T Consensus 8 d~Ya~YVr-~~i~~GM~VRc~~~yeeV~~-GD~G~V~k~~~d---g~~---~lnvqv~W~~~G 62 (78)
T PF11515_consen 8 DDYAEYVR-DNIQPGMRVRCCRDYEEVRA-GDEGEVFKQDRD---GLH---DLNVQVDWQSKG 62 (78)
T ss_dssp HHHHHHHH-HH--TT-EEEESS-BTTB-T-T-EEE-EEEE-T---TSS---E--EEEEETTTT
T ss_pred hHHHHHHH-HhCCCCcEEEEecccccccc-cccceeEeeccC---CCC---CcceEEEeeecC
Confidence 33444443 35899999999643343221 126776666541 122 235889998654
No 37
>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=22.25 E-value=83 Score=30.87 Aligned_cols=27 Identities=30% Similarity=0.523 Sum_probs=18.3
Q ss_pred cCCcCCCEEEEEEcc-CCeEEEEEEecC
Q 002390 234 KRLVAGDSVLFIWNE-KNQLLLGIRRAT 260 (928)
Q Consensus 234 K~L~aGDsVvF~R~e-~GeL~VGIRRa~ 260 (928)
++++.||.|+||... ++.-+|||=+-.
T Consensus 38 ~~mk~GD~vifY~s~~~~~~ivai~~V~ 65 (143)
T PF01878_consen 38 KRMKPGDKVIFYHSGCKERGIVAIGEVV 65 (143)
T ss_dssp HC--TT-EEEEEETSSSS-EEEEEEEEE
T ss_pred hcCCCCCEEEEEEcCCCCCEEEEEEEEe
Confidence 599999999999986 677888876643
No 38
>PF14847 Ras_bdg_2: Ras-binding domain of Byr2; PDB: 1I35_A 1K8R_B.
Probab=21.40 E-value=3e+02 Score=26.85 Aligned_cols=59 Identities=14% Similarity=0.269 Sum_probs=37.5
Q ss_pred eEEEeecCcceeeeccCCCCCHHHHHHHHHHHhcCCCCcCCCCCCceEEEEEcC----CCceEecCCc
Q 002390 797 FVKVHKSGSFGRSLDISKFSSYDELRSELARMFGLEGQLEDPQRSGWQLVFVDR----ENDVLLLGDD 860 (928)
Q Consensus 797 fVKV~m~G~iGRkIDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvYeD~----EGD~mLVGDv 860 (928)
.++|.-++..-|+||++...+.+|+....-+-||+.+. ...|.....|. ++..-++.|+
T Consensus 2 vi~~I~~dG~tk~VNV~~c~~a~eI~~rvLKKfg~~~~-----~~~~~~~v~d~~~~~~~~~~~LsD~ 64 (105)
T PF14847_consen 2 VIRFILEDGSTKTVNVSGCFNAQEIKRRVLKKFGLPEH-----PRNYCFYVLDGESPDPSNCRPLSDV 64 (105)
T ss_dssp EEEEEETTTEEEEEE--S--HHHHHHHHHHHHHTSS-------CCCEEEEEE-S-----SSEEEE-SS
T ss_pred EEEEECCCCcEEEEEECCCCCHHHHHHHHHHHcCCccc-----cccceEEEecccccccccceECcHH
Confidence 36777777788999999999999999999999998772 33466666666 3444444443
No 39
>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=20.48 E-value=1.6e+02 Score=25.49 Aligned_cols=31 Identities=19% Similarity=0.370 Sum_probs=23.9
Q ss_pred cccEEEEeeeccccccceeeeEEEEeecCCC
Q 002390 325 VGMRFRMLFETEESSVRRYMGTITGISDLDP 355 (928)
Q Consensus 325 ~GMRFrM~fEtEdss~rry~GTI~gvsd~DP 355 (928)
+|-|+.-.||.++.++..+.|+|..--+..|
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 5889999999998888889999999876544
No 40
>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=20.28 E-value=72 Score=27.37 Aligned_cols=17 Identities=24% Similarity=0.542 Sum_probs=14.8
Q ss_pred EEEEEcCCCceEecCCc
Q 002390 844 QLVFVDRENDVLLLGDD 860 (928)
Q Consensus 844 ~lvYeD~EGD~mLVGDv 860 (928)
.++|.|.+|+.+++|+.
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!