Query 004820
Match_columns 728
No_of_seqs 332 out of 812
Neff 4.3
Searched_HMMs 46136
Date Thu Mar 28 13:28:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004820.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/004820hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF06507 Auxin_resp: Auxin res 100.0 2.7E-35 6E-40 258.0 8.2 83 170-253 1-83 (83)
2 PF02309 AUX_IAA: AUX/IAA fami 100.0 9.9E-36 2.1E-40 299.8 0.0 95 606-700 107-215 (215)
3 PF02362 B3: B3 DNA binding do 99.7 9.6E-17 2.1E-21 141.3 11.6 97 44-145 1-99 (100)
4 KOG0644 Uncharacterized conser 99.2 2E-11 4.2E-16 140.6 5.7 148 122-278 874-1044(1113)
5 PF09217 EcoRII-N: Restriction 98.5 5.1E-07 1.1E-11 87.9 9.7 90 41-131 7-110 (156)
6 PF03754 DUF313: Domain of unk 97.7 6.2E-05 1.3E-09 70.6 6.6 80 38-118 18-113 (114)
7 PF00564 PB1: PB1 domain; Int 97.1 0.0013 2.9E-08 56.5 6.6 67 610-683 3-70 (84)
8 smart00666 PB1 PB1 domain. Pho 96.4 0.014 3E-07 50.2 7.6 65 611-683 4-69 (81)
9 cd05992 PB1 The PB1 domain is 96.1 0.024 5.3E-07 48.4 7.5 65 611-683 3-69 (81)
10 cd06407 PB1_NLP A PB1 domain i 95.6 0.036 7.8E-07 49.3 6.7 61 610-677 2-63 (82)
11 cd06396 PB1_NBR1 The PB1 domai 95.5 0.038 8.3E-07 49.4 6.4 52 611-671 3-55 (81)
12 cd06409 PB1_MUG70 The MUG70 pr 95.3 0.034 7.4E-07 50.2 5.3 45 623-671 15-59 (86)
13 cd06398 PB1_Joka2 The PB1 doma 95.0 0.077 1.7E-06 48.2 6.9 65 611-683 3-71 (91)
14 cd06403 PB1_Par6 The PB1 domai 92.2 0.36 7.7E-06 43.2 5.8 66 611-683 3-70 (80)
15 cd06404 PB1_aPKC PB1 domain is 91.9 0.4 8.7E-06 43.2 5.8 53 611-671 3-56 (83)
16 cd06401 PB1_TFG The PB1 domain 89.5 1.1 2.3E-05 40.4 6.3 58 611-673 3-61 (81)
17 cd06397 PB1_UP1 Uncharacterize 89.0 0.99 2.1E-05 40.6 5.6 65 612-684 4-69 (82)
18 cd06402 PB1_p62 The PB1 domain 87.0 2.3 4.9E-05 38.7 6.9 57 610-672 2-64 (87)
19 cd06408 PB1_NoxR The PB1 domai 84.9 2.4 5.3E-05 38.5 5.9 55 608-672 2-56 (86)
20 cd06399 PB1_P40 The PB1 domain 77.3 3.7 7.9E-05 37.7 4.3 53 624-702 23-75 (92)
21 PRK10737 FKBP-type peptidyl-pr 71.7 14 0.00031 38.1 7.6 104 121-238 2-114 (196)
22 PF04014 Antitoxin-MazE: Antid 50.5 21 0.00046 28.2 3.4 38 102-142 4-41 (47)
23 smart00743 Agenet Tudor-like d 46.7 30 0.00065 28.3 3.9 28 208-238 2-29 (61)
24 PF00788 RA: Ras association ( 41.8 78 0.0017 27.2 6.0 68 609-681 3-77 (93)
25 PF10844 DUF2577: Protein of u 37.1 44 0.00096 30.7 3.9 28 116-143 71-98 (100)
26 TIGR01439 lp_hng_hel_AbrB loop 36.0 49 0.0011 24.9 3.3 26 115-140 14-39 (43)
27 smart00333 TUDOR Tudor domain. 31.8 73 0.0016 25.3 3.9 52 208-276 2-53 (57)
28 PF01878 EVE: EVE domain; Int 30.9 46 0.001 31.7 3.1 26 120-145 38-64 (143)
29 cd06919 Asp_decarbox Aspartate 30.3 2.5E+02 0.0055 27.0 7.6 72 46-132 12-88 (111)
30 COG1047 SlpA FKBP-type peptidy 30.0 2.9E+02 0.0064 28.4 8.6 105 121-238 2-115 (174)
31 TIGR00223 panD L-aspartate-alp 28.7 2.7E+02 0.0058 27.4 7.7 71 46-131 13-88 (126)
32 KOG3207 Beta-tubulin folding c 28.2 62 0.0013 37.7 3.9 43 209-265 3-45 (505)
33 PF11515 Cul7: Mouse developme 26.4 1E+02 0.0022 27.9 4.1 55 198-260 8-62 (78)
34 PF10411 DsbC_N: Disulfide bon 25.8 52 0.0011 27.3 2.1 17 657-673 34-50 (57)
35 PRK03760 hypothetical protein; 25.4 1.3E+02 0.0028 28.6 5.0 48 82-132 61-116 (117)
36 PF02261 Asp_decarbox: Asparta 23.9 4.1E+02 0.0089 25.8 7.9 71 46-131 13-88 (116)
37 PF02513 Spin-Ssty: Spin/Ssty 23.7 1.3E+02 0.0029 25.1 4.0 31 211-241 1-31 (50)
38 PRK05449 aspartate alpha-decar 23.6 3.7E+02 0.0081 26.4 7.6 71 46-131 13-88 (126)
39 cd05792 S1_eIF1AD_like S1_eIF1 22.6 62 0.0013 29.1 2.1 34 663-699 40-75 (78)
40 PF04225 OapA: Opacity-associa 21.5 74 0.0016 28.6 2.4 19 120-138 41-59 (85)
No 1
>PF06507 Auxin_resp: Auxin response factor; InterPro: IPR010525 This pattern represents a conserved region of auxin-responsive transcription factors. The plant hormone auxin (indole-3-acetic acid) can regulate the gene expression of several families, including Aux/IAA, GH3 and SAUR families. Two related families of proteins, Aux/IAA proteins (IPR003311 from INTERPRO) and the auxin response factors (ARF), are key regulators of auxin-modulated gene expression []. There are multiple ARF proteins, some of which activate, while others repress transcription. ARF proteins bind to auxin-responsive cis-acting promoter elements (AuxREs) using an N-terminal DNA-binding domain. It is thought that Aux/IAA proteins activate transcription by modifying ARF activity through the C-terminal protein-protein interaction domains (IPR011525 from INTERPRO) found in both Aux/IAA and ARF proteins. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0009725 response to hormone stimulus, 0005634 nucleus
Probab=100.00 E-value=2.7e-35 Score=258.03 Aligned_cols=83 Identities=65% Similarity=1.048 Sum_probs=80.9
Q ss_pred HHHHhhcCCeEEEEEeCCCCCCccccchhhHHHhhhcCCccccCEEeEeecccccccceeeEEEEEeecCCCCCCCCCCc
Q 004820 170 AAHAAATNSCFTVFFNPRASPSEFVIPLTKYVKAVFHTRVSVGMRFRMLFETEESSVRRYMGTITGISDLDPVRWSNSHW 249 (728)
Q Consensus 170 A~haa~t~~~F~V~Y~PR~s~sEFVVp~~ky~~a~~~~~ws~GmRFrM~fe~Eds~~~r~~GTI~gi~d~dp~rWp~S~W 249 (728)
|+|||+++++|+|+||||++++|||||++||++|+. ++|++||||||+||+||+++++|+|||+||+++||.|||+|+|
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 5899999999999999999999999999999999999999999
Q ss_pred cccc
Q 004820 250 RSVK 253 (728)
Q Consensus 250 R~Lk 253 (728)
||||
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=9.9e-36 Score=299.75 Aligned_cols=95 Identities=38% Similarity=0.712 Sum_probs=0.0
Q ss_pred CCccEEEEeccC-cceeeeccCCCCChHHHHHHHHhhh---cCC----------cccCCCCCCCcEEEEEcCCCCeEecC
Q 004820 606 PTRTFVKVYKSG-SVGRSLDISRFSSYNELREELGQMF---GIE----------GKFEDPLRSGWQLVFVDRENDVLLLG 671 (728)
Q Consensus 606 ~~~~~vKV~m~G-~iGRkvDL~~~~sY~eL~~~L~~MF---~~~----------g~l~d~~~s~~~lvY~D~EgD~mLvG 671 (728)
..++||||+||| +|||||||++|+||++|+.+|++|| +|+ +.+....+++|+|||+|+||||||||
T Consensus 107 ~~~~~vKV~mdG~~igRkVDL~~~~sY~~L~~~L~~MF~~~~i~~~~~~~~~~~~~~~~~~~~~~~l~Y~D~egd~mlvG 186 (215)
T PF02309_consen 107 SSRSYVKVNMDGVPIGRKVDLSAYSSYEELSSALEKMFSCFSIEQCGSHGLNESGLLDLLNGSEYVLVYEDKEGDWMLVG 186 (215)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred cCCceeEEEecCcccceecCHHHhhCHHHHHHHHHHhcCCCCccccccccccchhhccccCCcceeEEEECCCCCEEEec
Confidence 468999999999 9999999999999999999999999 665 33444557899999999999999999
Q ss_pred CcchhHHhhceeEEEEeChhhhhcccccc
Q 004820 672 DDPWEAFVSNVWYIKILSPEDVQKMGEQG 700 (728)
Q Consensus 672 D~PW~~Fv~~v~ri~Il~~~e~~~m~~~~ 700 (728)
||||+|||++||||+||+.+|+++|+|++
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 99999999999999999999999999985
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=99.70 E-value=9.6e-17 Score=141.28 Aligned_cols=97 Identities=28% Similarity=0.406 Sum_probs=74.9
Q ss_pred EEEecCccCCCCCCceeechhhHhhhCCCCCCCCCCCCcEEEEeecCCCeEEeEEEEeCCCCceeeccchhhhhhccCCc
Q 004820 44 FCKTLTASDTSTHGGFSVPRRAAEKVFPSLDFSLQPPAQELIARDLHDVEWKFRHIFRGQPKRHLLTTGWSVFVSAKRLV 123 (728)
Q Consensus 44 F~K~LT~SDv~~~grfsVPk~~Ae~~fP~Ld~~~~~p~q~L~~~D~~G~~W~FR~iyr~~~rrhlLTtGWs~FV~~K~L~ 123 (728)
|.|+|+++|+.+.+++.||+++++.+. +. ...++++.++|..|+.|.+++.|++.+++++|++||..||++++|+
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 1136789999999999999999999888999999999999999999
Q ss_pred CCCEEEEEEcc--CCcEEEEEEec
Q 004820 124 AGDSVLFIWNE--KNQLLLGIRRA 145 (728)
Q Consensus 124 aGD~VvF~R~~--~g~L~vGiRRa 145 (728)
+||.|+|.... ..++.|.|.|+
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=99.17 E-value=2e-11 Score=140.62 Aligned_cols=148 Identities=20% Similarity=0.351 Sum_probs=113.7
Q ss_pred CcCCCEEEEEEccCCcEEEEEEecCCCCC---------------------CCCCccccCcccchhHHHHHHHHhhcCCeE
Q 004820 122 LVAGDSVLFIWNEKNQLLLGIRRAIRPPT---------------------VMPSSVLSSDSMHIGLLAAAAHAAATNSCF 180 (728)
Q Consensus 122 L~aGD~VvF~R~~~g~L~vGiRRa~r~~~---------------------~~pssv~s~~sm~~gvla~A~haa~t~~~F 180 (728)
.+-||.|+.+|-.--++.=.+|+.++.-+ ..|.+--+.=.|.+.|+--|.|+. +..|
T Consensus 874 pQmgDEViyfrQghqeyl~~~~~n~~~~~~~~p~~~~~v~~~kv~kl~~~~y~~~~~s~c~m~l~~idp~s~~~--~k~F 951 (1113)
T KOG0644|consen 874 PQMGDEVIYFRQGHQEYLEAVRLNNIELNNKEPWNKMAVEICKVEKLVYITYPGSGDSCCKMKLAVIDPASKLM--DKSF 951 (1113)
T ss_pred ccccceeehhhhhhHHHHhhhhhccccccccCcccccchhhheeeeeeeeeccCCCcchheeeeeeecchhhhh--hccc
Confidence 46789999998643333333333222111 123333344457888887777654 4679
Q ss_pred EEEEeCCCCCCccccchhhHHHhhhcCCccccCEEeEee--cccccccceeeEEEEEeecCCCCCCCCCCccccccccCC
Q 004820 181 TVFFNPRASPSEFVIPLTKYVKAVFHTRVSVGMRFRMLF--ETEESSVRRYMGTITGISDLDPVRWSNSHWRSVKVGWDE 258 (728)
Q Consensus 181 ~V~Y~PR~s~sEFVVp~~ky~~a~~~~~ws~GmRFrM~f--e~Eds~~~r~~GTI~gi~d~dp~rWp~S~WR~LkV~WDe 258 (728)
.+.|......+||+|-+..|..|+.+ +|+++++||..+ ++||. -.||.|+|.++.+..| .+|+|+|.|..|+||.
T Consensus 952 ~ltlpdlv~fpDFlV~rsrYd~AiQr-nW~~~d~crvwwrda~~e~-g~WWeG~ils~~pksp-~fpdSpwery~v~~~~ 1028 (1113)
T KOG0644|consen 952 KLTLPDLVTFPDFLVERSRYDAAIQR-NWTCRDKCRVWWRDAGEED-GAWWEGRILSVKPKSP-DFPDSPWERYIVRYDN 1028 (1113)
T ss_pred eeecccccCcchhhhhhhhHHHHHhh-ccccccceeEEEccCCCcC-CceeeeeeeeccCCCC-CCCCCcceeEEEEecC
Confidence 99999999999999999999999975 799999999998 44443 4799999999999887 8999999999999999
Q ss_pred CCCCCCCCCcccccceeCCC
Q 004820 259 STAGERQPRVSLWEIEPLTT 278 (728)
Q Consensus 259 ~~~~~~~~RVSPWeIEpv~~ 278 (728)
.+ .+--||||.|++..
T Consensus 1029 ~e----~~~~spwe~~~i~d 1044 (1113)
T KOG0644|consen 1029 TE----TELHSPWEMEPIPD 1044 (1113)
T ss_pred Cc----ccccCccccCCCcc
Confidence 87 47789999999976
No 5
>PF09217 EcoRII-N: Restriction endonuclease EcoRII, N-terminal; InterPro: IPR023372 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry represents the N-terminal effector-binding domain of the type II restriction endonuclease EcoRII, which has a DNA recognition fold, allowing for binding to 5'-CCWGG sequences. It assumes a structure composed of an eight-stranded beta-sheet with the strands in the order of b2, b5, b4, b3, b7, b6, b1 and b8. They are mostly antiparallel to each other except that b3 is parallel to b7. Alternatively, it may also be viewed as consisting of two mini beta-sheets of four antiparallel beta-strands, sheet I from beta-strands b2, b5, b4, b3 and sheet II from strands b7, b6, b1, b8, folded into an open mixed beta-barrel with a novel topology. Sheet I has a simple Greek key motif while sheet II does not []. The domain represented by this entry is only found in bacterial proteins.; PDB: 3HQF_A 1NA6_A.
Probab=98.51 E-value=5.1e-07 Score=87.92 Aligned_cols=90 Identities=26% Similarity=0.392 Sum_probs=60.8
Q ss_pred ceeEEEecCccCCCCCC----ceeechhhHhhhCCCCCC-CCCCCCcEEEEeecCC--CeEEeEEEEeCC------CCce
Q 004820 41 TNYFCKTLTASDTSTHG----GFSVPRRAAEKVFPSLDF-SLQPPAQELIARDLHD--VEWKFRHIFRGQ------PKRH 107 (728)
Q Consensus 41 ~~~F~K~LT~SDv~~~g----rfsVPk~~Ae~~fP~Ld~-~~~~p~q~L~~~D~~G--~~W~FR~iyr~~------~rrh 107 (728)
...|+|.|++.|++..| |+.|||..++..||.+.. +..+|...|.+++..| ..|+||+||.|+ +..|
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 799999999999999776 6778999999999988 579999999987 6789
Q ss_pred eeccchhhhhhccC-CcCCCEEEEE
Q 004820 108 LLTTGWSVFVSAKR-LVAGDSVLFI 131 (728)
Q Consensus 108 lLTtGWs~FV~~K~-L~aGD~VvF~ 131 (728)
.|| .|...-.--+ =..||.+||-
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 997 4543332111 2468888876
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=97.74 E-value=6.2e-05 Score=70.65 Aligned_cols=80 Identities=23% Similarity=0.275 Sum_probs=62.8
Q ss_pred CCCceeEEEecCccCCCCC-CceeechhhHhhhCCCCC------------CCCCCCCcEEEEeecCCCeEEeEEEEeCC-
Q 004820 38 KQPTNYFCKTLTASDTSTH-GGFSVPRRAAEKVFPSLD------------FSLQPPAQELIARDLHDVEWKFRHIFRGQ- 103 (728)
Q Consensus 38 ~~~~~~F~K~LT~SDv~~~-grfsVPk~~Ae~~fP~Ld------------~~~~~p~q~L~~~D~~G~~W~FR~iyr~~- 103 (728)
..+...++|+|++|||..+ .||+||-..... ...|. .....-++.+.+.|..++.|..++..|..
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 3457899999999999965 899999875522 12232 12234588999999999999999999965
Q ss_pred --CCceeeccchhhhhh
Q 004820 104 --PKRHLLTTGWSVFVS 118 (728)
Q Consensus 104 --~rrhlLTtGWs~FV~ 118 (728)
.-.|+|++||..+|+
T Consensus 97 ~~~~~YvL~~gWn~VV~ 113 (114)
T PF03754_consen 97 NGTSNYVLNSGWNKVVE 113 (114)
T ss_pred CCceEEEEEcChHhhcc
Confidence 567999999999886
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=97.12 E-value=0.0013 Score=56.55 Aligned_cols=67 Identities=21% Similarity=0.431 Sum_probs=56.5
Q ss_pred EEEEeccCcceeeeccCCCCChHHHHHHHHhhhcCCcccCCCCCCCcEEEEEcCCCCeEecCC-cchhHHhhcee
Q 004820 610 FVKVYKSGSVGRSLDISRFSSYNELREELGQMFGIEGKFEDPLRSGWQLVFVDRENDVLLLGD-DPWEAFVSNVW 683 (728)
Q Consensus 610 ~vKV~m~G~iGRkvDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvY~D~EgD~mLvGD-~PW~~Fv~~v~ 683 (728)
-+|++-.|.+=|.+.+..--+|++|+..+++.|++. ...+.|.|.|.||||..+.+ .=|++.++.++
T Consensus 3 ~vK~~~~~~~~~~~~~~~~~s~~~L~~~i~~~~~~~-------~~~~~l~Y~D~dgD~V~i~sd~Dl~~a~~~~~ 70 (84)
T PF00564_consen 3 RVKVRYGGDIRRIISLPSDVSFDDLRSKIREKFGLL-------DEDFQLKYKDEDGDLVTISSDEDLQEAIEQAK 70 (84)
T ss_dssp EEEEEETTEEEEEEEECSTSHHHHHHHHHHHHHTTS-------TSSEEEEEEETTSSEEEESSHHHHHHHHHHHH
T ss_pred EEEEEECCeeEEEEEcCCCCCHHHHHHHHHHHhCCC-------CccEEEEeeCCCCCEEEeCCHHHHHHHHHHHH
Confidence 378888887666788888889999999999999986 24799999999999998875 45888887765
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=96.40 E-value=0.014 Score=50.20 Aligned_cols=65 Identities=26% Similarity=0.486 Sum_probs=52.0
Q ss_pred EEEeccCcceeeeccCCCCChHHHHHHHHhhhcCCcccCCCCCCCcEEEEEcCCCCeEecC-CcchhHHhhcee
Q 004820 611 VKVYKSGSVGRSLDISRFSSYNELREELGQMFGIEGKFEDPLRSGWQLVFVDRENDVLLLG-DDPWEAFVSNVW 683 (728)
Q Consensus 611 vKV~m~G~iGRkvDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvY~D~EgD~mLvG-D~PW~~Fv~~v~ 683 (728)
+||+- |.--|.+-+..--+|++|++.+.+.|++.. ..+.|-|+|.||||..+. |.=|++.+..++
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 545677788889999999999999999753 468999999999998665 467777777655
No 9
>cd05992 PB1 The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as a noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.
Probab=96.10 E-value=0.024 Score=48.37 Aligned_cols=65 Identities=23% Similarity=0.516 Sum_probs=50.3
Q ss_pred EEEeccCcceeeeccC-CCCChHHHHHHHHhhhcCCcccCCCCCCCcEEEEEcCCCCeEecCC-cchhHHhhcee
Q 004820 611 VKVYKSGSVGRSLDIS-RFSSYNELREELGQMFGIEGKFEDPLRSGWQLVFVDRENDVLLLGD-DPWEAFVSNVW 683 (728)
Q Consensus 611 vKV~m~G~iGRkvDL~-~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvY~D~EgD~mLvGD-~PW~~Fv~~v~ 683 (728)
+||+-.|.+ |.+-+. .--+|++|++.|.+.|++.. ..+.+.|.|.||||..+.+ .=|++.++.++
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 677777643 223333 88899999999999999853 3689999999999998887 66777666655
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=95.64 E-value=0.036 Score=49.34 Aligned_cols=61 Identities=21% Similarity=0.369 Sum_probs=45.2
Q ss_pred EEEEeccCcceeeeccCCCCChHHHHHHHHhhhcCCcccCCCCCCCcEEEEEcCCCCeEecC-CcchhH
Q 004820 610 FVKVYKSGSVGRSLDISRFSSYNELREELGQMFGIEGKFEDPLRSGWQLVFVDRENDVLLLG-DDPWEA 677 (728)
Q Consensus 610 ~vKV~m~G~iGRkvDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvY~D~EgD~mLvG-D~PW~~ 677 (728)
-|||.-.|.+ +.+-|..--+|++|.+++.++|++.. .+++.|-|.|.||||.++- |.=.++
T Consensus 2 ~vK~~~~~d~-~r~~l~~~~~~~~L~~~i~~r~~~~~------~~~f~LkY~Ddegd~v~ltsd~DL~e 63 (82)
T cd06407 2 RVKATYGEEK-IRFRLPPSWGFTELKQEIAKRFKLDD------MSAFDLKYLDDDEEWVLLTCDADLEE 63 (82)
T ss_pred EEEEEeCCeE-EEEEcCCCCCHHHHHHHHHHHhCCCC------CCeeEEEEECCCCCeEEeecHHHHHH
Confidence 3788887742 33555556699999999999999841 3589999999999998763 333443
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=95.50 E-value=0.038 Score=49.40 Aligned_cols=52 Identities=23% Similarity=0.346 Sum_probs=43.7
Q ss_pred EEEeccC-cceeeeccCCCCChHHHHHHHHhhhcCCcccCCCCCCCcEEEEEcCCCCeEecC
Q 004820 611 VKVYKSG-SVGRSLDISRFSSYNELREELGQMFGIEGKFEDPLRSGWQLVFVDRENDVLLLG 671 (728)
Q Consensus 611 vKV~m~G-~iGRkvDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvY~D~EgD~mLvG 671 (728)
|||.--| .+--+++-+.--+|.+|.+++.++|++. .+.|-|.|.||||.++-
T Consensus 3 vKaty~~d~~rf~~~~~~~~~~~~L~~ev~~rf~l~---------~f~lKYlDde~e~v~ls 55 (81)
T cd06396 3 LKVTYNGESQSFLVSDSENTTWASVEAMVKVSFGLN---------DIQIKYVDEENEEVSVN 55 (81)
T ss_pred EEEEECCeEEEEEecCCCCCCHHHHHHHHHHHhCCC---------cceeEEEcCCCCEEEEE
Confidence 7888888 4555666666789999999999999996 48999999999998763
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=95.25 E-value=0.034 Score=50.19 Aligned_cols=45 Identities=27% Similarity=0.388 Sum_probs=36.8
Q ss_pred eccCCCCChHHHHHHHHhhhcCCcccCCCCCCCcEEEEEcCCCCeEecC
Q 004820 623 LDISRFSSYNELREELGQMFGIEGKFEDPLRSGWQLVFVDRENDVLLLG 671 (728)
Q Consensus 623 vDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvY~D~EgD~mLvG 671 (728)
+-+....|+.+|++++.+-|+++... ...++|-|.|.||||.|+-
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 34445789999999999999987532 3589999999999998764
No 13
>cd06398 PB1_Joka2 The PB1 domain is present in the Nicotiana plumbaginifolia Joka2 protein which interacts with sulfur stress inducible UP9 protein. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module
Probab=95.00 E-value=0.077 Score=48.21 Aligned_cols=65 Identities=23% Similarity=0.390 Sum_probs=48.6
Q ss_pred EEEeccCc-ceeeeccC---CCCChHHHHHHHHhhhcCCcccCCCCCCCcEEEEEcCCCCeEecCCcchhHHhhcee
Q 004820 611 VKVYKSGS-VGRSLDIS---RFSSYNELREELGQMFGIEGKFEDPLRSGWQLVFVDRENDVLLLGDDPWEAFVSNVW 683 (728)
Q Consensus 611 vKV~m~G~-iGRkvDL~---~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvY~D~EgD~mLvGD~PW~~Fv~~v~ 683 (728)
|||.-.|. +=-++++. .--+|++|..++++.|.+.. ..+++|.|.|.||||..+-++ +++..++.
T Consensus 3 vKv~y~~~~rRf~l~~~~~~~d~~~~~L~~kI~~~f~l~~------~~~~~l~Y~Dedgd~V~l~~D--~DL~~a~~ 71 (91)
T cd06398 3 VKVKYGGTLRRFTFPVAENQLDLNMDGLREKVEELFSLSP------DADLSLTYTDEDGDVVTLVDD--NDLTDAIQ 71 (91)
T ss_pred EEEEeCCEEEEEEeccccccCCCCHHHHHHHHHHHhCCCC------CCcEEEEEECCCCCEEEEccH--HHHHHHHH
Confidence 78888884 33455553 45799999999999998742 358999999999999988665 34444443
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=92.20 E-value=0.36 Score=43.23 Aligned_cols=66 Identities=21% Similarity=0.308 Sum_probs=49.5
Q ss_pred EEEeccCccee-eeccCCCCChHHHHHHHHhhhcCCcccCCCCCCCcEEEEEcCCCCeEecC-CcchhHHhhcee
Q 004820 611 VKVYKSGSVGR-SLDISRFSSYNELREELGQMFGIEGKFEDPLRSGWQLVFVDRENDVLLLG-DDPWEAFVSNVW 683 (728)
Q Consensus 611 vKV~m~G~iGR-kvDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvY~D~EgD~mLvG-D~PW~~Fv~~v~ 683 (728)
||.+-++.+=| ++|-....+|+|++.-|++|+.+.. ..++|-|.|.+||.+-+- |+-...=+.+++
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 55555554333 6777778999999999999999864 369999999999999775 455555555555
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=91.88 E-value=0.4 Score=43.23 Aligned_cols=53 Identities=26% Similarity=0.308 Sum_probs=42.2
Q ss_pred EEEeccCc-ceeeeccCCCCChHHHHHHHHhhhcCCcccCCCCCCCcEEEEEcCCCCeEecC
Q 004820 611 VKVYKSGS-VGRSLDISRFSSYNELREELGQMFGIEGKFEDPLRSGWQLVFVDRENDVLLLG 671 (728)
Q Consensus 611 vKV~m~G~-iGRkvDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvY~D~EgD~mLvG 671 (728)
+|++-.|. +--.+|. .-+|++|.+++.+||.+. .+..+++.|.|.|||---+.
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 78888994 4455555 778999999999999983 24579999999999975543
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=89.54 E-value=1.1 Score=40.44 Aligned_cols=58 Identities=17% Similarity=0.273 Sum_probs=42.7
Q ss_pred EEEeccCcceeeeccCCC-CChHHHHHHHHhhhcCCcccCCCCCCCcEEEEEcCCCCeEecCCc
Q 004820 611 VKVYKSGSVGRSLDISRF-SSYNELREELGQMFGIEGKFEDPLRSGWQLVFVDRENDVLLLGDD 673 (728)
Q Consensus 611 vKV~m~G~iGRkvDL~~~-~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvY~D~EgD~mLvGD~ 673 (728)
+|+.-.|.|=| +-+..- -+|.+|+..+.+.|... + |....+.+-|.|.|||+.-+.+.
T Consensus 3 iK~~~g~DiR~-~~~~~~~~t~~~L~~~v~~~F~~~--~--~~~~~flIKYkD~dGDlVTIts~ 61 (81)
T cd06401 3 LKAQLGDDIRR-IPIHNEDITYDELLLMMQRVFRGK--L--GSSDDVLIKYKDEDGDLITIFDS 61 (81)
T ss_pred EEEEeCCeEEE-EeccCccccHHHHHHHHHHHhccc--c--CCcccEEEEEECCCCCEEEeccH
Confidence 56665555544 444432 39999999999999943 1 23457999999999999998875
No 17
>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=88.98 E-value=0.99 Score=40.62 Aligned_cols=65 Identities=14% Similarity=0.250 Sum_probs=48.2
Q ss_pred EEeccCcceeeeccCCCCChHHHHHHHHhhhcCCcccCCCCCCCcEEEEEcCCCCeEec-CCcchhHHhhceeE
Q 004820 612 KVYKSGSVGRSLDISRFSSYNELREELGQMFGIEGKFEDPLRSGWQLVFVDRENDVLLL-GDDPWEAFVSNVWY 684 (728)
Q Consensus 612 KV~m~G~iGRkvDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvY~D~EgD~mLv-GD~PW~~Fv~~v~r 684 (728)
|| +-|.--|++....-=+|.+|++.|+.+|.+.. . ...|+|.|.+||..-+ -|+=-++|.+-..+
T Consensus 4 Kv-~~~g~~RRf~~~~~pt~~~L~~kl~~Lf~lp~------~-~~~vtYiDeD~D~ITlssd~eL~d~~~~~~~ 69 (82)
T cd06397 4 KS-SFLGDTRRIVFPDIPTWEALASKLENLYNLPE------I-KVGVTYIDNDNDEITLSSNKELQDFYRLSHR 69 (82)
T ss_pred EE-EeCCceEEEecCCCccHHHHHHHHHHHhCCCh------h-HeEEEEEcCCCCEEEecchHHHHHHHHhccc
Confidence 66 33445577778888899999999999999852 2 2899999999998754 44566666654433
No 18
>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=87.04 E-value=2.3 Score=38.71 Aligned_cols=57 Identities=28% Similarity=0.399 Sum_probs=42.6
Q ss_pred EEEEeccC----ccee--eeccCCCCChHHHHHHHHhhhcCCcccCCCCCCCcEEEEEcCCCCeEecCC
Q 004820 610 FVKVYKSG----SVGR--SLDISRFSSYNELREELGQMFGIEGKFEDPLRSGWQLVFVDRENDVLLLGD 672 (728)
Q Consensus 610 ~vKV~m~G----~iGR--kvDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvY~D~EgD~mLvGD 672 (728)
.||.|..| +==| +||-....+|++|++.+.++|... . +..++|.|.|.|||..-+..
T Consensus 2 ~vkayl~~~~~~~EIRRf~l~~~~~~s~~~L~~~V~~~f~~l---~---~~~ftlky~DeeGDlvtIss 64 (87)
T cd06402 2 TVKAYLLGKDANAEIRRFAIDEDVSTSYEYLVEKVAAVFPSL---R---GKNFQLFWKDEEGDLVAFSS 64 (87)
T ss_pred eEEEeecCCCCccceEEEEecCCCCcCHHHHHHHHHHHcccc---C---CCcEEEEEECCCCCEEeecC
Confidence 57888876 2223 455577779999999999999642 1 25799999999999865543
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=84.93 E-value=2.4 Score=38.52 Aligned_cols=55 Identities=20% Similarity=0.411 Sum_probs=44.6
Q ss_pred ccEEEEeccCcceeeeccCCCCChHHHHHHHHhhhcCCcccCCCCCCCcEEEEEcCCCCeEecCC
Q 004820 608 RTFVKVYKSGSVGRSLDISRFSSYNELREELGQMFGIEGKFEDPLRSGWQLVFVDRENDVLLLGD 672 (728)
Q Consensus 608 ~~~vKV~m~G~iGRkvDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvY~D~EgD~mLvGD 672 (728)
+.-|||+-.|. -|-|-+..--+|++|.+.+.++|++. ....|-|.|. ||..-++|
T Consensus 2 ~ikVKv~~~~D-v~~i~v~~~i~f~dL~~kIrdkf~~~--------~~~~iKykDE-GD~iti~s 56 (86)
T cd06408 2 KIRVKVHAQDD-TRYIMIGPDTGFADFEDKIRDKFGFK--------RRLKIKMKDD-GDMITMGD 56 (86)
T ss_pred cEEEEEEecCc-EEEEEcCCCCCHHHHHHHHHHHhCCC--------CceEEEEEcC-CCCccccC
Confidence 34688998785 45566666677999999999999984 2689999999 99888776
No 20
>cd06399 PB1_P40 The PB1 domain is essential part of the p40 adaptor protein which plays an important role in activating phagocyte NADPH oxidase during phagocytosis. The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes , such as osteoclastogenesis, angiogenesis, early cardiovascular development and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The PB1 domain of p40 represents a type I PB1 domain which interacts with the PB1 domain of oxidase activator p67 w
Probab=77.31 E-value=3.7 Score=37.67 Aligned_cols=53 Identities=34% Similarity=0.377 Sum_probs=44.9
Q ss_pred ccCCCCChHHHHHHHHhhhcCCcccCCCCCCCcEEEEEcCCCCeEecCCcchhHHhhceeEEEEeChhhhhcccccccc
Q 004820 624 DISRFSSYNELREELGQMFGIEGKFEDPLRSGWQLVFVDRENDVLLLGDDPWEAFVSNVWYIKILSPEDVQKMGEQGVE 702 (728)
Q Consensus 624 DL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lvY~D~EgD~mLvGD~PW~~Fv~~v~ri~Il~~~e~~~m~~~~~~ 702 (728)
||+.--.|.+|..-..+-|..+ +-.|-|.|.|||. ||||+.+|+.=|-.++..
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 6777889999999999888764 3589999999996 799999999999877644
No 21
>PRK10737 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=71.66 E-value=14 Score=38.12 Aligned_cols=104 Identities=21% Similarity=0.222 Sum_probs=65.1
Q ss_pred CCcCCCEEEE-E--EccCCcEEEEEEecCCCCCCCCCccccCcccchhHHHHHHHHhhcCCeEEEEEeCCCCC------C
Q 004820 121 RLVAGDSVLF-I--WNEKNQLLLGIRRAIRPPTVMPSSVLSSDSMHIGLLAAAAHAAATNSCFTVFFNPRASP------S 191 (728)
Q Consensus 121 ~L~aGD~VvF-~--R~~~g~L~vGiRRa~r~~~~~pssv~s~~sm~~gvla~A~haa~t~~~F~V~Y~PR~s~------s 191 (728)
++..|+.|.+ | |.++|+++=--+ ...|..++-....-+--|-+|....+.|..|+|.--|-... .
T Consensus 2 kI~~~~vV~l~Y~l~~~dG~v~dst~------~~~Pl~~~~G~g~lipglE~aL~G~~~Gd~~~v~l~peeAyGe~d~~l 75 (196)
T PRK10737 2 KVAKDLVVSLAYQVRTEDGVLVDESP------VSAPLDYLHGHGSLISGLETALEGHEVGDKFDVAVGANDAYGQYDENL 75 (196)
T ss_pred ccCCCCEEEEEEEEEeCCCCEEEecC------CCCCeEEEeCCCcchHHHHHHHcCCCCCCEEEEEEChHHhcCCCChHH
Confidence 3556777766 3 356777633221 12355555444445556677888888899999986554332 3
Q ss_pred ccccchhhHHHhhhcCCccccCEEeEeecccccccceeeEEEEEeec
Q 004820 192 EFVIPLTKYVKAVFHTRVSVGMRFRMLFETEESSVRRYMGTITGISD 238 (728)
Q Consensus 192 EFVVp~~ky~~a~~~~~ws~GmRFrM~fe~Eds~~~r~~GTI~gi~d 238 (728)
=..||++.|.. . ....+||||.+ ++++. ...++|+.|.+
T Consensus 76 V~~vpr~~F~~-~--~~l~~G~~~~~--~~~~G---~~~~~V~ev~~ 114 (196)
T PRK10737 76 VQRVPKDVFMG-V--DELQVGMRFLA--ETDQG---PVPVEITAVED 114 (196)
T ss_pred EEEecHHHCCC-c--cCCCCCCEEEE--eCCCC---cEEEEEEEEcC
Confidence 45678776532 2 14789999886 45553 46889999975
No 22
>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=50.46 E-value=21 Score=28.19 Aligned_cols=38 Identities=13% Similarity=0.163 Sum_probs=28.0
Q ss_pred CCCCceeeccchhhhhhccCCcCCCEEEEEEccCCcEEEEE
Q 004820 102 GQPKRHLLTTGWSVFVSAKRLVAGDSVLFIWNEKNQLLLGI 142 (728)
Q Consensus 102 ~~~rrhlLTtGWs~FV~~K~L~aGD~VvF~R~~~g~L~vGi 142 (728)
+++..-.|-. .|.++.+|.+||.|.|.-+++|++.|--
T Consensus 4 g~s~~v~iPk---~~~~~l~l~~Gd~v~i~~~~~g~i~i~p 41 (47)
T PF04014_consen 4 GNSGQVTIPK---EIREKLGLKPGDEVEIEVEGDGKIVIRP 41 (47)
T ss_dssp TTCSEEEE-H---HHHHHTTSSTTTEEEEEEETTSEEEEEE
T ss_pred CCCceEECCH---HHHHHcCCCCCCEEEEEEeCCCEEEEEE
Confidence 4444445544 5678899999999999999998776644
No 23
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=46.71 E-value=30 Score=28.31 Aligned_cols=28 Identities=14% Similarity=0.259 Sum_probs=23.9
Q ss_pred CccccCEEeEeecccccccceeeEEEEEeec
Q 004820 208 RVSVGMRFRMLFETEESSVRRYMGTITGISD 238 (728)
Q Consensus 208 ~ws~GmRFrM~fe~Eds~~~r~~GTI~gi~d 238 (728)
.|.+|+++-..++.++ .||.|+|+.+..
T Consensus 2 ~~~~G~~Ve~~~~~~~---~W~~a~V~~~~~ 29 (61)
T smart00743 2 DFKKGDRVEVFSKEED---SWWEAVVTKVLG 29 (61)
T ss_pred CcCCCCEEEEEECCCC---EEEEEEEEEECC
Confidence 4899999999996544 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=41.80 E-value=78 Score=27.21 Aligned_cols=68 Identities=21% Similarity=0.269 Sum_probs=49.4
Q ss_pred cEEEEeccCc----ceeeeccCCCCChHHHHHHHHhhhcCCcccCCCCCCCcEEE-E-EcCCCCeEecCC-cchhHHhhc
Q 004820 609 TFVKVYKSGS----VGRSLDISRFSSYNELREELGQMFGIEGKFEDPLRSGWQLV-F-VDRENDVLLLGD-DPWEAFVSN 681 (728)
Q Consensus 609 ~~vKV~m~G~----iGRkvDL~~~~sY~eL~~~L~~MF~~~g~l~d~~~s~~~lv-Y-~D~EgD~mLvGD-~PW~~Fv~~ 681 (728)
.++||+.... .-++|-++....-.|++..+.+.|++.. + ..+|.|+ + ........|-.| .|+......
T Consensus 3 ~~lrVy~~~~~~~~~~k~i~v~~~tTa~evi~~~l~k~~l~~---~--~~~y~L~~~~~~~~~er~L~~~E~pl~i~~~~ 77 (93)
T PF00788_consen 3 GVLRVYDGDGSPGSTYKTIKVSSSTTAREVIEMALEKFGLAE---D--PSDYCLVEVEESGGEERPLDDDECPLQIQLQW 77 (93)
T ss_dssp EEEEEEETTSSSCCSEEEEEEETTSBHHHHHHHHHHHTTTSS---S--GGGEEEEEEECTTTEEEEETTTSBHHHHHHTT
T ss_pred eEEEEEcCCCCCCccEEEEEECCCCCHHHHHHHHHHHhCCCC---C--CCCEEEEEEEcCCCEEEEcCCCCchHHHHHhC
Confidence 5899999763 2799999999999999999999999932 2 3579995 4 444445555433 566665543
No 25
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=37.08 E-value=44 Score=30.72 Aligned_cols=28 Identities=21% Similarity=0.289 Sum_probs=22.9
Q ss_pred hhhccCCcCCCEEEEEEccCCcEEEEEE
Q 004820 116 FVSAKRLVAGDSVLFIWNEKNQLLLGIR 143 (728)
Q Consensus 116 FV~~K~L~aGD~VvF~R~~~g~L~vGiR 143 (728)
|.-...|++||.|..+|.+.|+-++=+-
T Consensus 71 i~~~~~Lk~GD~V~ll~~~~gQ~yiVlD 98 (100)
T PF10844_consen 71 ITFTDGLKVGDKVLLLRVQGGQKYIVLD 98 (100)
T ss_pred EEEecCCcCCCEEEEEEecCCCEEEEEE
Confidence 5556789999999999999998776543
No 26
>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=35.99 E-value=49 Score=24.93 Aligned_cols=26 Identities=23% Similarity=0.288 Sum_probs=22.6
Q ss_pred hhhhccCCcCCCEEEEEEccCCcEEE
Q 004820 115 VFVSAKRLVAGDSVLFIWNEKNQLLL 140 (728)
Q Consensus 115 ~FV~~K~L~aGD~VvF~R~~~g~L~v 140 (728)
.|.+.-++..||.|.+...++|.|.|
T Consensus 14 ~~r~~l~~~~gd~~~i~~~~~~~l~l 39 (43)
T TIGR01439 14 EIREKLGLKEGDRLEVIRVEDGEIIL 39 (43)
T ss_pred HHHHHcCcCCCCEEEEEEeCCCEEEE
Confidence 68899999999999999887887665
No 27
>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=31.80 E-value=73 Score=25.34 Aligned_cols=52 Identities=15% Similarity=0.214 Sum_probs=35.9
Q ss_pred CccccCEEeEeecccccccceeeEEEEEeecCCCCCCCCCCccccccccCCCCCCCCCCCcccccceeC
Q 004820 208 RVSVGMRFRMLFETEESSVRRYMGTITGISDLDPVRWSNSHWRSVKVGWDESTAGERQPRVSLWEIEPL 276 (728)
Q Consensus 208 ~ws~GmRFrM~fe~Eds~~~r~~GTI~gi~d~dp~rWp~S~WR~LkV~WDe~~~~~~~~RVSPWeIEpv 276 (728)
.|.+|..+...+ .+. .||.|+|+++.. + ..+.|.-++-+.. +-|...+|-++
T Consensus 2 ~~~~G~~~~a~~-~d~---~wyra~I~~~~~-------~---~~~~V~f~D~G~~---~~v~~~~l~~l 53 (57)
T smart00333 2 TFKVGDKVAARW-EDG---EWYRARIIKVDG-------E---QLYEVFFIDYGNE---EVVPPSDLRPL 53 (57)
T ss_pred CCCCCCEEEEEe-CCC---CEEEEEEEEECC-------C---CEEEEEEECCCcc---EEEeHHHeecC
Confidence 488999999999 444 799999999974 2 4467777764432 34555555444
No 28
>PF01878 EVE: EVE domain; InterPro: IPR002740 The EVE domain is part of the wider PUA domain superfamily. The function of this domain is not known but, given the structural similarities to PUA, is likely to involve RNA binding []. ; PDB: 2G2X_B 2AR1_A 3EOP_A 2EVE_A 2HD9_A 2ZBN_A 1WMM_A 2P5D_A 2GBS_A 1ZCE_A.
Probab=30.91 E-value=46 Score=31.73 Aligned_cols=26 Identities=31% Similarity=0.543 Sum_probs=17.9
Q ss_pred cCCcCCCEEEEEEcc-CCcEEEEEEec
Q 004820 120 KRLVAGDSVLFIWNE-KNQLLLGIRRA 145 (728)
Q Consensus 120 K~L~aGD~VvF~R~~-~g~L~vGiRRa 145 (728)
++++.||.|+||... .++-+||+=+-
T Consensus 38 ~~mk~GD~vifY~s~~~~~~ivai~~V 64 (143)
T PF01878_consen 38 KRMKPGDKVIFYHSGCKERGIVAIGEV 64 (143)
T ss_dssp HC--TT-EEEEEETSSSS-EEEEEEEE
T ss_pred hcCCCCCEEEEEEcCCCCCEEEEEEEE
Confidence 599999999999987 67778887554
No 29
>cd06919 Asp_decarbox Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production. Decarboxylation of aspartate is the major route of beta-alanine production in bacteria, and is catalyzed by the enzyme L-aspartate decarboxylase (ADC), EC:4.1.1.11 which requires a pyruvoyl group for its activity. The pyruvoyl cofactor is covalently bound to the enzyme. The protein is synthesized as a proenzyme and cleaved via self-processing at Gly23-Ser24 to yield an alpha chain (C-terminal fragment) and beta chain (N-terminal fragment), and the pyruvoyl group. Beta-alanine is required for the biosynthesis of pantothenate, in which the enzyme plays a critical regulatory role. The active site of the tetrameric enzyme is located at the interface of two subunits, with a Lysine and a Histidine from the beta chain of one subunit forming the active site with residues from the alpha chain of the adjacent subunit. This alignment
Probab=30.27 E-value=2.5e+02 Score=27.03 Aligned_cols=72 Identities=17% Similarity=0.335 Sum_probs=53.0
Q ss_pred EecCccCCCCCCceeechhhHhh--hCCCCCCCCCCCCcEEEEeecC-CCeEEeEEEEeCC--CCceeeccchhhhhhcc
Q 004820 46 KTLTASDTSTHGGFSVPRRAAEK--VFPSLDFSLQPPAQELIARDLH-DVEWKFRHIFRGQ--PKRHLLTTGWSVFVSAK 120 (728)
Q Consensus 46 K~LT~SDv~~~grfsVPk~~Ae~--~fP~Ld~~~~~p~q~L~~~D~~-G~~W~FR~iyr~~--~rrhlLTtGWs~FV~~K 120 (728)
-+.|..|..-.|.+.|.....+. ++| ...+.+.|.. |.+|. .|...|. ++.-.|... -+.
T Consensus 12 atVT~a~L~YeGSitID~~Ll~aagi~~---------~E~V~I~Nv~NG~Rf~-TYvI~g~~gSg~I~lNGA-----AAr 76 (111)
T cd06919 12 ATVTEADLNYEGSITIDEDLLEAAGILP---------YEKVLVVNVNNGARFE-TYVIPGERGSGVICLNGA-----AAR 76 (111)
T ss_pred eEEeccccccceeEEECHHHHHhcCCCC---------CCEEEEEECCCCcEEE-EEEEEcCCCCCEEEeCCH-----HHh
Confidence 46888999889999999875443 444 4668888875 88776 4677776 466666533 677
Q ss_pred CCcCCCEEEEEE
Q 004820 121 RLVAGDSVLFIW 132 (728)
Q Consensus 121 ~L~aGD~VvF~R 132 (728)
....||.||++-
T Consensus 77 ~~~~GD~vII~s 88 (111)
T cd06919 77 LGQPGDRVIIMA 88 (111)
T ss_pred cCCCCCEEEEEE
Confidence 788999999873
No 30
>COG1047 SlpA FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]
Probab=29.96 E-value=2.9e+02 Score=28.42 Aligned_cols=105 Identities=20% Similarity=0.269 Sum_probs=66.4
Q ss_pred CCcCCCEEEE---EEccCCcEEEEEEecCCCCCCCCCccccCcccchhHHHHHHHHhhcCCeEEEEEeCCCCCCcc----
Q 004820 121 RLVAGDSVLF---IWNEKNQLLLGIRRAIRPPTVMPSSVLSSDSMHIGLLAAAAHAAATNSCFTVFFNPRASPSEF---- 193 (728)
Q Consensus 121 ~L~aGD~VvF---~R~~~g~L~vGiRRa~r~~~~~pssv~s~~sm~~gvla~A~haa~t~~~F~V~Y~PR~s~sEF---- 193 (728)
++..||.|.+ .|.++|+++=--+- ..-|..++-.+..-+.-|-+|.....-|..|+|.--|-....|+
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 4566777776 23455654321111 12244444444444556778888888999999998887665554
Q ss_pred --ccchhhHHHhhhcCCccccCEEeEeecccccccceeeEEEEEeec
Q 004820 194 --VIPLTKYVKAVFHTRVSVGMRFRMLFETEESSVRRYMGTITGISD 238 (728)
Q Consensus 194 --VVp~~ky~~a~~~~~ws~GmRFrM~fe~Eds~~~r~~GTI~gi~d 238 (728)
.||+++|.+.- ...+||+|.. ++++ .-.-|+|+.|..
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 56776654331 4899999874 5555 456899999974
No 31
>TIGR00223 panD L-aspartate-alpha-decarboxylase. Members of this family are aspartate 1-decarboxylase, the enzyme that makes beta-alanine and C02 from aspartate. Beta-alanine is then used to make the vitamin pantothenate, from which coenzyme A is made. Aspartate 1-decarboxylase is synthesized as a proenzyme, then cleaved to an alpha (C-terminal) and beta (N-terminal) subunit with a pyruvoyl group.
Probab=28.68 E-value=2.7e+02 Score=27.41 Aligned_cols=71 Identities=11% Similarity=0.248 Sum_probs=52.3
Q ss_pred EecCccCCCCCCceeechhhHhh--hCCCCCCCCCCCCcEEEEeecC-CCeEEeEEEEeCCC--Cceeeccchhhhhhcc
Q 004820 46 KTLTASDTSTHGGFSVPRRAAEK--VFPSLDFSLQPPAQELIARDLH-DVEWKFRHIFRGQP--KRHLLTTGWSVFVSAK 120 (728)
Q Consensus 46 K~LT~SDv~~~grfsVPk~~Ae~--~fP~Ld~~~~~p~q~L~~~D~~-G~~W~FR~iyr~~~--rrhlLTtGWs~FV~~K 120 (728)
-+.|..|..-.|.+.|-..-.+. ++| ...+.+.|.. |.+|. .|...|.+ +.-.|... -+.
T Consensus 13 atVT~a~L~Y~GSItID~~Lm~aagi~p---------~E~V~V~Nv~NG~Rf~-TYvI~G~~GSg~I~lNGA-----AAr 77 (126)
T TIGR00223 13 ATVTHANLNYEGSITIDEDLLDAAGILE---------NEKVDIVNVNNGKRFS-TYAIAGKRGSRIICVNGA-----AAR 77 (126)
T ss_pred eEEeccccccceeEEECHHHHHhcCCCC---------CCEEEEEECCCCcEEE-EEEEEcCCCCCEEEeCCH-----HHh
Confidence 46888899888999999875443 554 4568888875 88776 46777764 55666533 677
Q ss_pred CCcCCCEEEEE
Q 004820 121 RLVAGDSVLFI 131 (728)
Q Consensus 121 ~L~aGD~VvF~ 131 (728)
....||.||++
T Consensus 78 l~~~GD~VII~ 88 (126)
T TIGR00223 78 CVSVGDIVIIA 88 (126)
T ss_pred cCCCCCEEEEE
Confidence 78899999987
No 32
>KOG3207 consensus Beta-tubulin folding cofactor E [Posttranslational modification, protein turnover, chaperones]
Probab=28.20 E-value=62 Score=37.75 Aligned_cols=43 Identities=28% Similarity=0.687 Sum_probs=29.9
Q ss_pred ccccCEEeEeecccccccceeeEEEEEeecCCCCCCCCCCccccccccCCCCCCCCC
Q 004820 209 VSVGMRFRMLFETEESSVRRYMGTITGISDLDPVRWSNSHWRSVKVGWDESTAGERQ 265 (728)
Q Consensus 209 ws~GmRFrM~fe~Eds~~~r~~GTI~gi~d~dp~rWp~S~WR~LkV~WDe~~~~~~~ 265 (728)
+.+|.|+|..+|- ...||.|+|.| |++ +| +.|.||.+.-+.+.
T Consensus 3 ~~IG~RvkI~~~~---~Tvr~iG~V~g--------~~~-~w--~GvEWDd~~RGKH~ 45 (505)
T KOG3207|consen 3 MEIGTRVKIGGEI---ATVRYIGEVEG--------NNS-KW--YGVEWDDPVRGKHD 45 (505)
T ss_pred eeccceEEEcCEE---EEEEEEEEEcC--------CCC-cc--eeeEecCCCccccC
Confidence 5789999987642 23567776655 444 45 78999999876553
No 33
>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=26.36 E-value=1e+02 Score=27.89 Aligned_cols=55 Identities=24% Similarity=0.296 Sum_probs=26.6
Q ss_pred hhHHHhhhcCCccccCEEeEeecccccccceeeEEEEEeecCCCCCCCCCCccccccccCCCC
Q 004820 198 TKYVKAVFHTRVSVGMRFRMLFETEESSVRRYMGTITGISDLDPVRWSNSHWRSVKVGWDEST 260 (728)
Q Consensus 198 ~ky~~a~~~~~ws~GmRFrM~fe~Eds~~~r~~GTI~gi~d~dp~rWp~S~WR~LkV~WDe~~ 260 (728)
+.|..-+.. ++++||++||.=.-|+-. .-=.|+|.-++. | .-| =-.++|.|-...
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 DDYAEYVRD-NIQPGMRVRCCRDYEEVR-AGDEGEVFKQDR-D--GLH---DLNVQVDWQSKG 62 (78)
T ss_dssp HHHHHHHHH-H--TT-EEEESS-BTTB--TT-EEE-EEEE--T--TSS---E--EEEEETTTT
T ss_pred hHHHHHHHH-hCCCCcEEEEeccccccc-ccccceeEeecc-C--CCC---CcceEEEeeecC
Confidence 445555543 589999999974444422 223677777664 1 112 234788887554
No 34
>PF10411 DsbC_N: Disulfide bond isomerase protein N-terminus; InterPro: IPR018950 This is the N-terminal domain of the disulphide bond isomerase DsbC. The whole molecule is V-shaped, where each arm is a DsbC monomer of two domains linked by a hinge; and the N-termini of each monomer join to form the dimer interface at the base of the V, so are vital for dimerisation []. DsbC is required for disulphide bond formation and functions as a disulphide bond isomerase during oxidative protein-folding in bacterial periplasm. It also has chaperone activity []. ; PDB: 1EEJ_B 2IYJ_A 1TJD_A 1JZD_B 1JZO_A 1G0T_B 1T3B_A.
Probab=25.81 E-value=52 Score=27.29 Aligned_cols=17 Identities=24% Similarity=0.542 Sum_probs=14.8
Q ss_pred EEEEEcCCCCeEecCCc
Q 004820 657 QLVFVDRENDVLLLGDD 673 (728)
Q Consensus 657 ~lvY~D~EgD~mLvGD~ 673 (728)
.++|.|.+|+.+++|+.
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
No 35
>PRK03760 hypothetical protein; Provisional
Probab=25.41 E-value=1.3e+02 Score=28.63 Aligned_cols=48 Identities=21% Similarity=0.334 Sum_probs=31.3
Q ss_pred cEEEEeecCCCeEEeEE-----EEe-CCCCceee--ccchhhhhhccCCcCCCEEEEEE
Q 004820 82 QELIARDLHDVEWKFRH-----IFR-GQPKRHLL--TTGWSVFVSAKRLVAGDSVLFIW 132 (728)
Q Consensus 82 q~L~~~D~~G~~W~FR~-----iyr-~~~rrhlL--TtGWs~FV~~K~L~aGD~VvF~R 132 (728)
.++++.|.+|++=.... +|. ..+-+|+| ..||. .+.++++||.|.|-|
T Consensus 61 LDiiFld~~g~Vv~i~~~~P~~~~~~~~~a~~VLEl~aG~~---~~~gi~~Gd~v~~~~ 116 (117)
T PRK03760 61 IDVIFLDSNRRVVDFKTLKPWRIYVPKKPARYIIEGPVGKI---RVLKVEVGDEIEWID 116 (117)
T ss_pred eEEEEECCCCeEEEEEeCCCccccCCCccceEEEEeCCChH---HHcCCCCCCEEEEee
Confidence 44666666665433211 122 34566898 57766 899999999999876
No 36
>PF02261 Asp_decarbox: Aspartate decarboxylase; InterPro: IPR003190 Decarboxylation of aspartate is the major route of alanine production in bacteria, and is catalysed by the enzyme aspartate decarboxylase. The enzyme is translated as an inactive proenzyme of two chains, A and B. This family contains both chains of aspartate decarboxylase.; GO: 0004068 aspartate 1-decarboxylase activity, 0006523 alanine biosynthetic process; PDB: 1PYU_C 1AW8_A 1PYQ_B 3TM7_C 1PT1_A 1PQH_A 1PPY_B 1PT0_B 1PQF_A 1PQE_A ....
Probab=23.88 E-value=4.1e+02 Score=25.83 Aligned_cols=71 Identities=15% Similarity=0.342 Sum_probs=45.1
Q ss_pred EecCccCCCCCCceeechhhHh--hhCCCCCCCCCCCCcEEEEeecC-CCeEEeEEEEeCCC--Cceeeccchhhhhhcc
Q 004820 46 KTLTASDTSTHGGFSVPRRAAE--KVFPSLDFSLQPPAQELIARDLH-DVEWKFRHIFRGQP--KRHLLTTGWSVFVSAK 120 (728)
Q Consensus 46 K~LT~SDv~~~grfsVPk~~Ae--~~fP~Ld~~~~~p~q~L~~~D~~-G~~W~FR~iyr~~~--rrhlLTtGWs~FV~~K 120 (728)
-++|..|..-.|.++|...-.+ .++| ...+.+.+.. |.+|. .|...|.+ +.-.|... -++
T Consensus 13 atVT~a~L~Y~GSitID~~Ll~aagi~p---------~E~V~V~Nv~nG~Rf~-TYvI~g~~GSg~I~lNGa-----AAr 77 (116)
T PF02261_consen 13 ATVTEADLNYEGSITIDEDLLDAAGILP---------YEQVQVVNVNNGERFE-TYVIPGERGSGVICLNGA-----AAR 77 (116)
T ss_dssp EE--EEETTSTSCEEEEHHHHHHCT--T---------TBEEEEEETTT--EEE-EEEEEESTTTT-EEEEGG-----GGG
T ss_pred eEEeccccccceeeEECHHHHHHcCCCc---------CCEEEEEECCCCcEEE-EEEEEccCCCcEEEECCH-----HHh
Confidence 3689999999999999998533 3555 4568888875 88776 46666654 55566533 677
Q ss_pred CCcCCCEEEEE
Q 004820 121 RLVAGDSVLFI 131 (728)
Q Consensus 121 ~L~aGD~VvF~ 131 (728)
.-..||.||++
T Consensus 78 l~~~GD~vII~ 88 (116)
T PF02261_consen 78 LVQVGDRVIIM 88 (116)
T ss_dssp CS-TT-EEEEE
T ss_pred ccCCCCEEEEE
Confidence 78999999986
No 37
>PF02513 Spin-Ssty: Spin/Ssty Family; InterPro: IPR003671 Spindlin (Spin) and Ssty were first identified for their involvement in gametogenesis. Spindlin was identified as a maternal transcript present in the unfertilised egg and early embryo, and was subsequently shown to interact with the spindle apparatus during oogenesis, and may therefore be important for mitosis []. In addition, spindlin appears to be a target for cell cycle-dependent phosphorylation, and as such may play a role in cell cycle regulation during the transition from gamete to embryo []. Ssty is a multi-copy, Y-linked spermatogenesis-specific transcript that appears to be required for normal spermatogenesis []. Ssty may play an analogous role to spindlin in sperm cells, namely during the transition from sperm cells to early embryo, and in mitosis.; GO: 0007276 gamete generation; PDB: 2NS2_A.
Probab=23.71 E-value=1.3e+02 Score=25.07 Aligned_cols=31 Identities=19% Similarity=0.370 Sum_probs=23.7
Q ss_pred ccCEEeEeecccccccceeeEEEEEeecCCC
Q 004820 211 VGMRFRMLFETEESSVRRYMGTITGISDLDP 241 (728)
Q Consensus 211 ~GmRFrM~fe~Eds~~~r~~GTI~gi~d~dp 241 (728)
+|-|+.-.||.++.++..+.|+|..--+.-|
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 5889999999998888888999999876544
No 38
>PRK05449 aspartate alpha-decarboxylase; Provisional
Probab=23.58 E-value=3.7e+02 Score=26.44 Aligned_cols=71 Identities=14% Similarity=0.296 Sum_probs=52.2
Q ss_pred EecCccCCCCCCceeechhhHhh--hCCCCCCCCCCCCcEEEEeecC-CCeEEeEEEEeCCC--Cceeeccchhhhhhcc
Q 004820 46 KTLTASDTSTHGGFSVPRRAAEK--VFPSLDFSLQPPAQELIARDLH-DVEWKFRHIFRGQP--KRHLLTTGWSVFVSAK 120 (728)
Q Consensus 46 K~LT~SDv~~~grfsVPk~~Ae~--~fP~Ld~~~~~p~q~L~~~D~~-G~~W~FR~iyr~~~--rrhlLTtGWs~FV~~K 120 (728)
-+.|..|..-.|.++|-....+. ++| ...+.+.|.. |.+|. .|...|.+ +.-.|... -+.
T Consensus 13 atVT~a~L~Y~GSitID~~Ll~aagi~p---------~E~V~V~Nv~NG~Rf~-TYvI~g~~GSg~I~lNGA-----AAr 77 (126)
T PRK05449 13 ATVTEADLNYEGSITIDEDLLDAAGILE---------NEKVQIVNVNNGARFE-TYVIAGERGSGVICLNGA-----AAR 77 (126)
T ss_pred eEEeccccccceeEEECHHHHHhcCCCC---------CCEEEEEECCCCcEEE-EEEEEcCCCCCEEEeCCH-----HHh
Confidence 46888999888999999885443 554 4568888875 88776 46677764 55666533 677
Q ss_pred CCcCCCEEEEE
Q 004820 121 RLVAGDSVLFI 131 (728)
Q Consensus 121 ~L~aGD~VvF~ 131 (728)
....||.||++
T Consensus 78 ~~~~GD~vII~ 88 (126)
T PRK05449 78 LVQVGDLVIIA 88 (126)
T ss_pred cCCCCCEEEEE
Confidence 78899999987
No 39
>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=22.57 E-value=62 Score=29.07 Aligned_cols=34 Identities=29% Similarity=0.465 Sum_probs=26.3
Q ss_pred CCCCeEecCCcchhHHhhceeE--EEEeChhhhhccccc
Q 004820 663 RENDVLLLGDDPWEAFVSNVWY--IKILSPEDVQKMGEQ 699 (728)
Q Consensus 663 ~EgD~mLvGD~PW~~Fv~~v~r--i~Il~~~e~~~m~~~ 699 (728)
++||..|| +||+ |=+-++. +.||..+++..|-..
T Consensus 40 krGd~VlV--~p~~-~~~kvkgeIv~i~~~~qvk~L~k~ 75 (78)
T cd05792 40 KRGDFVLV--EPIE-EGDKVKAEIVKILTRDHVKYIKEE 75 (78)
T ss_pred EeCCEEEE--Eecc-cCCceEEEEEEEECHHHHHHHHHc
Confidence 78999999 6999 4444564 889999998877554
No 40
>PF04225 OapA: Opacity-associated protein A LysM-like domain; InterPro: IPR007340 This entry includes the Haemophilus influenzae opacity-associated protein. This protein is required for efficient nasopharyngeal mucosal colonization, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation [].; PDB: 2GU1_A.
Probab=21.46 E-value=74 Score=28.58 Aligned_cols=19 Identities=37% Similarity=0.583 Sum_probs=12.6
Q ss_pred cCCcCCCEEEEEEccCCcE
Q 004820 120 KRLVAGDSVLFIWNEKNQL 138 (728)
Q Consensus 120 K~L~aGD~VvF~R~~~g~L 138 (728)
.+|++||.|.|..+++|+|
T Consensus 41 ~~L~pGq~l~f~~d~~g~L 59 (85)
T PF04225_consen 41 TRLKPGQTLEFQLDEDGQL 59 (85)
T ss_dssp GG--TT-EEEEEE-TTS-E
T ss_pred hhCCCCCEEEEEECCCCCE
Confidence 4689999999999999997
Done!