Query 004898
Match_columns 724
No_of_seqs 373 out of 826
Neff 4.4
Searched_HMMs 46136
Date Thu Mar 28 14:43:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004898.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/004898hhsearch_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 2.5E-35 5.5E-40 258.1 8.9 83 291-374 1-83 (83)
2 PF02309 AUX_IAA: AUX/IAA fami 100.0 2.8E-33 6E-38 282.1 0.5 88 610-697 107-212 (215)
3 PF02362 B3: B3 DNA binding do 99.7 6.2E-17 1.4E-21 142.5 11.3 97 113-214 1-99 (100)
4 KOG0644 Uncharacterized conser 99.4 2.7E-13 5.7E-18 155.6 4.0 168 191-398 874-1043(1113)
5 PF09217 EcoRII-N: Restriction 98.1 1.2E-05 2.7E-10 78.3 8.1 91 109-200 6-110 (156)
6 PF03754 DUF313: Domain of unk 97.5 0.00017 3.7E-09 67.7 5.5 78 110-188 21-114 (114)
7 PF00564 PB1: PB1 domain; Int 96.4 0.01 2.2E-07 51.1 6.6 67 614-683 3-70 (84)
8 cd05992 PB1 The PB1 domain is 95.7 0.052 1.1E-06 46.4 7.6 66 614-683 2-69 (81)
9 cd06407 PB1_NLP A PB1 domain i 95.7 0.043 9.3E-07 48.8 7.3 62 614-680 2-63 (82)
10 cd06398 PB1_Joka2 The PB1 doma 95.6 0.042 9.1E-07 49.8 7.1 68 614-684 2-72 (91)
11 cd06396 PB1_NBR1 The PB1 domai 95.2 0.069 1.5E-06 47.8 7.0 64 614-681 2-66 (81)
12 smart00666 PB1 PB1 domain. Pho 95.1 0.093 2E-06 45.1 7.5 66 614-683 3-69 (81)
13 cd06403 PB1_Par6 The PB1 domai 94.4 0.14 3.1E-06 45.7 6.7 63 615-681 3-65 (80)
14 cd06401 PB1_TFG The PB1 domain 92.8 0.57 1.2E-05 42.0 7.8 72 615-688 3-79 (81)
15 cd06409 PB1_MUG70 The MUG70 pr 92.1 0.21 4.6E-06 45.1 4.4 51 623-673 8-61 (86)
16 cd06404 PB1_aPKC PB1 domain is 91.9 0.56 1.2E-05 42.3 6.7 65 614-683 2-66 (83)
17 cd06408 PB1_NoxR The PB1 domai 89.1 1.2 2.6E-05 40.5 6.3 55 613-673 3-57 (86)
18 cd06402 PB1_p62 The PB1 domain 88.9 1.6 3.4E-05 39.7 7.0 62 614-678 2-68 (87)
19 cd06397 PB1_UP1 Uncharacterize 86.9 1.8 4E-05 38.9 6.0 66 615-684 3-69 (82)
20 cd06406 PB1_P67 A PB1 domain i 72.1 15 0.00032 33.2 6.7 69 615-688 5-76 (80)
21 smart00743 Agenet Tudor-like d 59.1 14 0.0003 30.2 3.9 28 328-359 2-29 (61)
22 KOG0644 Uncharacterized conser 55.7 8 0.00017 47.4 2.6 62 21-82 871-938 (1113)
23 cd06399 PB1_P40 The PB1 domain 54.9 21 0.00045 32.9 4.5 41 629-673 23-63 (92)
24 PF04014 Antitoxin-MazE: Antid 46.9 30 0.00065 27.3 3.8 26 184-209 14-39 (47)
25 TIGR01439 lp_hng_hel_AbrB loop 36.2 55 0.0012 24.6 3.7 27 183-209 13-39 (43)
26 KOG3938 RGS-GAIP interacting p 35.7 60 0.0013 35.5 5.1 74 620-696 62-141 (334)
27 PF10844 DUF2577: Protein of u 34.9 56 0.0012 30.0 4.2 28 185-212 71-98 (100)
28 smart00333 TUDOR Tudor domain. 34.0 60 0.0013 25.8 3.8 39 328-381 2-40 (57)
29 PRK03760 hypothetical protein; 29.3 1E+02 0.0023 29.3 5.1 27 173-202 89-117 (117)
30 cd01789 Alp11_N Ubiquitin-like 28.8 1.8E+02 0.0038 25.8 6.2 39 623-665 14-52 (84)
31 PF05641 Agenet: Agenet domain 28.7 81 0.0018 26.8 3.8 41 329-380 1-41 (68)
32 PF02513 Spin-Ssty: Spin/Ssty 27.4 98 0.0021 25.8 3.9 31 331-362 1-31 (50)
33 PF11515 Cul7: Mouse developme 24.9 87 0.0019 28.3 3.4 57 317-381 6-62 (78)
34 PF00788 RA: Ras association ( 24.3 2.5E+02 0.0053 24.1 6.2 69 613-681 3-77 (93)
35 cd06410 PB1_UP2 Uncharacterize 23.7 82 0.0018 29.2 3.2 55 625-682 24-79 (97)
36 PF01878 EVE: EVE domain; Int 23.3 74 0.0016 30.4 2.9 27 189-215 38-65 (143)
37 KOG3606 Cell polarity protein 20.8 89 0.0019 34.4 3.2 81 613-695 19-103 (358)
38 KOG3207 Beta-tubulin folding c 20.7 93 0.002 36.3 3.5 41 329-384 3-43 (505)
39 PF03120 DNA_ligase_OB: NAD-de 20.5 86 0.0019 28.4 2.6 34 183-216 42-76 (82)
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=2.5e-35 Score=258.11 Aligned_cols=83 Identities=58% Similarity=0.944 Sum_probs=80.7
Q ss_pred HHHHHHcCCCEEEEEecCCCCCceEEehHHHHHHHhcccccccEEEEEeecCCCCceeeeeeEEEEeecCCCCCCCCCCc
Q 004898 291 AVALAASGKPFEVVYYPRASTPEFCVKASAVKAAMRVHWLCGMRFKMAFETEDSSRISWFMGTISSVQVADPISWPNSPW 370 (724)
Q Consensus 291 Aa~~aa~g~~F~V~Y~Pr~s~~EFvV~~~~y~~A~~~~w~~GmRFkM~fE~EDss~i~wf~GTI~gv~~~dp~~wp~S~W 370 (724)
||++|++|++|+|+||||++++||||++++|++||+++|++||||||+||+||+++++ |+|||++|++.||++||+|+|
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 AAHAAATGSPFEVFYYPRASPSEFVVPASKYDKALNHPWSVGMRFKMRFETEDSSERR-WQGTIVGVSDLDPIRWPGSKW 79 (83)
T ss_pred ChhHhhcCCeEEEEECCCCCCcceEEEHHHHHHHhcCCCCCCcEEEEEeccCCCccce-eeeEEeEeeccCCCCCCCCCc
Confidence 7899999999999999999999999999999999999999999999999999999965 599999999999999999999
Q ss_pred cccc
Q 004898 371 RLLQ 374 (724)
Q Consensus 371 R~L~ 374 (724)
||||
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=99.97 E-value=2.8e-33 Score=282.11 Aligned_cols=88 Identities=38% Similarity=0.567 Sum_probs=0.0
Q ss_pred CccceEEEEecCceeeeeccCCCCCCHHHHHHHHHHhh---CCC----------c-cCC----ceeEEEEeCCCCeeecC
Q 004898 610 LDTGHCKVFLESEDVGRTLDLSVLSSYEELYRRLAIMF---GIE----------R-SDM----LSHVLYQDASGAIKRTG 671 (724)
Q Consensus 610 ~~~~~vKV~meG~~vGR~vDLs~~~sY~eL~~~L~~MF---~i~----------~-~~l----~~~v~Y~D~eGD~mlvG 671 (724)
..+.||||+|||++|||||||++|+||++|+.+|++|| +|+ + .++ .|+|||+|+||||||||
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 35799999999999999999999999999999999999 666 1 122 37999999999999999
Q ss_pred CCChhHHHhceeEEEEecCCCCCCcc
Q 004898 672 DEPFSDFMKSAKRLTILMGSGSDSVG 697 (724)
Q Consensus 672 D~PW~~F~~~vkRL~I~~~~~~~~l~ 697 (724)
||||++||++||||+||+.+++.+|+
T Consensus 187 D~PW~~F~~~vkRl~I~~~~e~~~~~ 212 (215)
T PF02309_consen 187 DVPWEEFVKSVKRLRIMKSSEAKGLA 212 (215)
T ss_dssp --------------------------
T ss_pred CCCHHHHHHHhhccEEecHHHhcccC
Confidence 99999999999999999999999987
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=99.71 E-value=6.2e-17 Score=142.54 Aligned_cols=97 Identities=31% Similarity=0.404 Sum_probs=74.7
Q ss_pred EEEecccccCCCCCceEEcccchhhcCCCCCCCCCCCceEEEEEeCCCCeEEEEEEEeCCCCceeeccchhhHhhccCCC
Q 004898 113 FAKTLTQSDANNGGGFSVPRYCAETIFPRLDYTADPPVQTVVAKDVHGEIWKFRHIYRGTPRRHLLTTGWSTFVNQKKLV 192 (724)
Q Consensus 113 F~K~LT~SDv~~~grfsVPk~~Ae~~FP~Ld~~~~~p~q~L~~~D~~G~~W~Fr~~yrg~~rrhlLTtGWs~FV~~KkL~ 192 (724)
|.|+|+++|+...++|.||+++++.+. ++. ...+++.++|..|+.|.+++.+++.+.+++|++||..||++++|+
T Consensus 1 F~K~l~~s~~~~~~~l~iP~~f~~~~~--~~~---~~~~~v~l~~~~g~~W~v~~~~~~~~~~~~l~~GW~~Fv~~n~L~ 75 (100)
T PF02362_consen 1 FFKVLKPSDVSSSCRLIIPKEFAKKHG--GNK---RKSREVTLKDPDGRSWPVKLKYRKNSGRYYLTGGWKKFVRDNGLK 75 (100)
T ss_dssp EEEE--TTCCCCTT-EEE-HHHHTTTS----S---S--CEEEEEETTTEEEEEEEEEECCTTEEEEETTHHHHHHHCT--
T ss_pred CEEEEEccCcCCCCEEEeCHHHHHHhC--CCc---CCCeEEEEEeCCCCEEEEEEEEEccCCeEEECCCHHHHHHHcCCC
Confidence 899999999999899999999999971 111 125689999999999999999999988999999999999999999
Q ss_pred CCCEEEEEEecC--CcEEEEEEEc
Q 004898 193 AGDSIVFLRAQD--GDLCVGIRRA 214 (724)
Q Consensus 193 aGD~VvF~R~~~--GeL~VGIRR~ 214 (724)
+||.|+|+...+ .++.|.|.|+
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 999999998764 4569999986
No 4
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=99.36 E-value=2.7e-13 Score=155.57 Aligned_cols=168 Identities=22% Similarity=0.441 Sum_probs=120.8
Q ss_pred CCCCCEEEEEEecCCcEEEEEEEcccCCCCCCCCCCCCCCCCCCCcccCCCCCCccchhhHHhhhhhhcCCcccCCCCCC
Q 004898 191 LVAGDSIVFLRAQDGDLCVGIRRAKKGIGGGNEYPSSGWNSNNGSCVTGNPFGGFSCFLREEENKMARNGNMNLNSYGSF 270 (724)
Q Consensus 191 L~aGD~VvF~R~~~GeL~VGIRR~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~ 270 (724)
.+-||.|+.+|....++.=.+|+...-..+ .-+||... | +.-+-.+..++.| .+.+
T Consensus 874 pQmgDEViyfrQghqeyl~~~~~n~~~~~~-----~~p~~~~~-----v----------~~~kv~kl~~~~y----~~~~ 929 (1113)
T KOG0644|consen 874 PQMGDEVIYFRQGHQEYLEAVRLNNIELNN-----KEPWNKMA-----V----------EICKVEKLVYITY----PGSG 929 (1113)
T ss_pred ccccceeehhhhhhHHHHhhhhhccccccc-----cCcccccc-----h----------hhheeeeeeeeec----cCCC
Confidence 457999999998776666556555542221 23455431 1 1011011111112 1122
Q ss_pred CCCCCCCCCCCCCChhHHHHHHHHHHcCCCEEEEEecCCCCCceEEehHHHHHHHhcccccccEEEEEee--cCCCCcee
Q 004898 271 NSSGNTRGNGGRVKPEMVLEAVALAASGKPFEVVYYPRASTPEFCVKASAVKAAMRVHWLCGMRFKMAFE--TEDSSRIS 348 (724)
Q Consensus 271 ~~~~~m~g~~~~v~~~~V~~Aa~~aa~g~~F~V~Y~Pr~s~~EFvV~~~~y~~A~~~~w~~GmRFkM~fE--~EDss~i~ 348 (724)
.+...|. + .|++.+. -+-...|.+.|......+||+|.++.|++|++++|.++++||..+. +|+-- +
T Consensus 930 ~s~c~m~-----l---~~idp~s-~~~~k~F~ltlpdlv~fpDFlV~rsrYd~AiQrnW~~~d~crvwwrda~~e~g--~ 998 (1113)
T KOG0644|consen 930 DSCCKMK-----L---AVIDPAS-KLMDKSFKLTLPDLVTFPDFLVERSRYDAAIQRNWTCRDKCRVWWRDAGEEDG--A 998 (1113)
T ss_pred cchheee-----e---eeecchh-hhhhccceeecccccCcchhhhhhhhHHHHHhhccccccceeEEEccCCCcCC--c
Confidence 3444443 2 2888555 3456789999999999999999999999999999999999999993 33322 5
Q ss_pred eeeeEEEEeecCCCCCCCCCCccccccccCCccccCCCCcccceeeeecc
Q 004898 349 WFMGTISSVQVADPISWPNSPWRLLQVTWDEPDLLQNVKRVSPWLVELVS 398 (724)
Q Consensus 349 wf~GTI~gv~~~dp~~wp~S~WR~L~V~WDe~~~~~~~~RVSPWeIE~v~ 398 (724)
||.|+|.++++.+| .+|+|+|.++.|+||..+ .+.-||||+|++.
T Consensus 999 WWeG~ils~~pksp-~fpdSpwery~v~~~~~e----~~~~spwe~~~i~ 1043 (1113)
T KOG0644|consen 999 WWEGRILSVKPKSP-DFPDSPWERYIVRYDNTE----TELHSPWEMEPIP 1043 (1113)
T ss_pred eeeeeeeeccCCCC-CCCCCcceeEEEEecCCc----ccccCccccCCCc
Confidence 99999999999999 999999999999999998 6888999999886
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=98.06 E-value=1.2e-05 Score=78.35 Aligned_cols=91 Identities=21% Similarity=0.283 Sum_probs=59.1
Q ss_pred cceEEEEecccccCCCCC----ceEEcccchhhcCCCCCC-CCCCCceEEEEEeCCC--CeEEEEEEEeCC------CCc
Q 004898 109 KPASFAKTLTQSDANNGG----GFSVPRYCAETIFPRLDY-TADPPVQTVVAKDVHG--EIWKFRHIYRGT------PRR 175 (724)
Q Consensus 109 ~~~~F~K~LT~SDv~~~g----rfsVPk~~Ae~~FP~Ld~-~~~~p~q~L~~~D~~G--~~W~Fr~~yrg~------~rr 175 (724)
.-..|+|.|++.|++.+| |+.||+..++..||.+.. ...+|...|.+++..+ ..|+||++|.|+ +..
T Consensus 6 ~~~~~~K~LSaNDtGaTGgHQaGiyIpk~~~~~lFp~~~~~~~~Np~~~~~~~~~s~~~~~~~~r~iYYnn~~~~gTRNE 85 (156)
T PF09217_consen 6 SWAIYCKRLSANDTGATGGHQAGIYIPKSAAELLFPSINHTKEENPDIWLKARWQSHFVTDSQVRFIYYNNRLFGGTRNE 85 (156)
T ss_dssp SEEEEEEE--CCCCTTTSSS--EEEE-HHHHHHH-GGG-SSSSSS-EEEEEEEETTTT---EEEEEEEE-CCCTTSS--E
T ss_pred ceEEEEEEccCCCCCCcCcccceeEecccHHHHhCCCCCcccccCCceeEEEEECCCCccceeEEEEEEcccccCCCcCc
Confidence 346899999999999654 799999999999998776 5567899999999877 668999999988 577
Q ss_pred eeeccchhhHhhccC-CCCCCEEEEE
Q 004898 176 HLLTTGWSTFVNQKK-LVAGDSIVFL 200 (724)
Q Consensus 176 hlLTtGWs~FV~~Kk-L~aGD~VvF~ 200 (724)
+.|| .|...-.--+ =..||-+||.
T Consensus 86 ~RIT-~~G~~~~~~~~~~tGaL~vla 110 (156)
T PF09217_consen 86 YRIT-RFGRGFPLQNPENTGALLVLA 110 (156)
T ss_dssp EEEE----TTSGGG-GGGTT-EEEEE
T ss_pred eEEe-eecCCCccCCccccccEEEEE
Confidence 8886 3433322111 2468877775
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=97.48 E-value=0.00017 Score=67.74 Aligned_cols=78 Identities=19% Similarity=0.224 Sum_probs=60.8
Q ss_pred ceEEEEecccccCC-CCCceEEcccchhhcCCCCCC------------CCCCCceEEEEEeCCCCeEEEEEEEeCC---C
Q 004898 110 PASFAKTLTQSDAN-NGGGFSVPRYCAETIFPRLDY------------TADPPVQTVVAKDVHGEIWKFRHIYRGT---P 173 (724)
Q Consensus 110 ~~~F~K~LT~SDv~-~~grfsVPk~~Ae~~FP~Ld~------------~~~~p~q~L~~~D~~G~~W~Fr~~yrg~---~ 173 (724)
-..|.|+|++||+. ++.||+||-..... ...|.. ....-+..+.+.|..++.|..++..|.. .
T Consensus 21 kli~~K~L~~tDv~~~qsRLsmP~~qi~~-~dFLt~eE~~~i~~~~~~~~~~~Gv~V~lvdp~~~~~~m~lkkW~mg~~~ 99 (114)
T PF03754_consen 21 KLIIEKTLFKTDVDPHQSRLSMPFNQIID-NDFLTEEEKRIIKEEKKNNDKKKGVEVILVDPSLRKWTMRLKKWNMGNGT 99 (114)
T ss_pred eEEEeeeecccCCCCCCceeeccHHHhcc-cccCCHHHHHHHHHhhccCcccCCceEEEECCcCcEEEEEEEEecccCCc
Confidence 47899999999998 45899999876533 122211 1123477889999999999999999976 4
Q ss_pred CceeeccchhhHhhc
Q 004898 174 RRHLLTTGWSTFVNQ 188 (724)
Q Consensus 174 rrhlLTtGWs~FV~~ 188 (724)
..|+|++||..+|++
T Consensus 100 ~~YvL~~gWn~VV~~ 114 (114)
T PF03754_consen 100 SNYVLNSGWNKVVED 114 (114)
T ss_pred eEEEEEcChHhhccC
Confidence 789999999999864
No 7
>PF00564 PB1: PB1 domain; InterPro: IPR000270 The Phox and Bem1p domain, is present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.; GO: 0005515 protein binding; PDB: 1IPG_A 1IP9_A 2KFK_A 1WMH_A 1VD2_A 1WI0_A 1OEY_C 1PQS_A 1Q1O_A 1TZ1_A ....
Probab=96.39 E-value=0.01 Score=51.11 Aligned_cols=67 Identities=19% Similarity=0.356 Sum_probs=53.9
Q ss_pred eEEEEecCceeeeeccCCCCCCHHHHHHHHHHhhCCCccCCceeEEEEeCCCCeeecCCC-ChhHHHhcee
Q 004898 614 HCKVFLESEDVGRTLDLSVLSSYEELYRRLAIMFGIERSDMLSHVLYQDASGAIKRTGDE-PFSDFMKSAK 683 (724)
Q Consensus 614 ~vKV~meG~~vGR~vDLs~~~sY~eL~~~L~~MF~i~~~~l~~~v~Y~D~eGD~mlvGD~-PW~~F~~~vk 683 (724)
.+|+...|. +=|.+.+..--+|++|..++++.|++.. -...+.|+|.|||+..+-++ =|.+.+..++
T Consensus 3 ~vK~~~~~~-~~~~~~~~~~~s~~~L~~~i~~~~~~~~--~~~~l~Y~D~dgD~V~i~sd~Dl~~a~~~~~ 70 (84)
T PF00564_consen 3 RVKVRYGGD-IRRIISLPSDVSFDDLRSKIREKFGLLD--EDFQLKYKDEDGDLVTISSDEDLQEAIEQAK 70 (84)
T ss_dssp EEEEEETTE-EEEEEEECSTSHHHHHHHHHHHHHTTST--SSEEEEEEETTSSEEEESSHHHHHHHHHHHH
T ss_pred EEEEEECCe-eEEEEEcCCCCCHHHHHHHHHHHhCCCC--ccEEEEeeCCCCCEEEeCCHHHHHHHHHHHH
Confidence 579999885 4456888888899999999999999972 23689999999999988755 4666676664
No 8
>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=95.65 E-value=0.052 Score=46.36 Aligned_cols=66 Identities=21% Similarity=0.358 Sum_probs=48.9
Q ss_pred eEEEEecCceeeeeccCC-CCCCHHHHHHHHHHhhCCCccCCceeEEEEeCCCCeeecCCC-ChhHHHhcee
Q 004898 614 HCKVFLESEDVGRTLDLS-VLSSYEELYRRLAIMFGIERSDMLSHVLYQDASGAIKRTGDE-PFSDFMKSAK 683 (724)
Q Consensus 614 ~vKV~meG~~vGR~vDLs-~~~sY~eL~~~L~~MF~i~~~~l~~~v~Y~D~eGD~mlvGD~-PW~~F~~~vk 683 (724)
.+||+-.|.. |.+=+. .--+|++|..+|.+.|++.. -...+.|+|.|||+..+.++ =|.+-++.++
T Consensus 2 ~vK~~~~~~~--~~~~~~~~~~s~~~L~~~i~~~~~~~~--~~~~l~y~D~e~d~v~l~sd~Dl~~a~~~~~ 69 (81)
T cd05992 2 RVKVKYGGEI--RRFVVVSRSISFEDLRSKIAEKFGLDA--VSFKLKYPDEDGDLVTISSDEDLEEAIEEAR 69 (81)
T ss_pred cEEEEecCCC--EEEEEecCCCCHHHHHHHHHHHhCCCC--CcEEEEeeCCCCCEEEeCCHHHHHHHHHHHh
Confidence 3688887652 333333 78899999999999999874 23588999999999999884 4555555544
No 9
>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=95.65 E-value=0.043 Score=48.82 Aligned_cols=62 Identities=16% Similarity=0.140 Sum_probs=46.7
Q ss_pred eEEEEecCceeeeeccCCCCCCHHHHHHHHHHhhCCCccCCceeEEEEeCCCCeeecCCCChhHHHh
Q 004898 614 HCKVFLESEDVGRTLDLSVLSSYEELYRRLAIMFGIERSDMLSHVLYQDASGAIKRTGDEPFSDFMK 680 (724)
Q Consensus 614 ~vKV~meG~~vGR~vDLs~~~sY~eL~~~L~~MF~i~~~~l~~~v~Y~D~eGD~mlvGD~PW~~F~~ 680 (724)
.+||...|. -+.+-|..--+|++|..+++++|++.. .-...|-|.|+||||..+--+ .++-.
T Consensus 2 ~vK~~~~~d--~~r~~l~~~~~~~~L~~~i~~r~~~~~-~~~f~LkY~Ddegd~v~ltsd--~DL~e 63 (82)
T cd06407 2 RVKATYGEE--KIRFRLPPSWGFTELKQEIAKRFKLDD-MSAFDLKYLDDDEEWVLLTCD--ADLEE 63 (82)
T ss_pred EEEEEeCCe--EEEEEcCCCCCHHHHHHHHHHHhCCCC-CCeeEEEEECCCCCeEEeecH--HHHHH
Confidence 479999886 344555555699999999999999963 234688899999999987655 44433
No 10
>cd06398 PB1_Joka2 The PB1 domain is present in the Nicotiana plumbaginifolia Joka2 protein which interacts with sulfur stress inducible UP9 protein. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module
Probab=95.59 E-value=0.042 Score=49.83 Aligned_cols=68 Identities=16% Similarity=0.204 Sum_probs=52.5
Q ss_pred eEEEEecCceeeeeccCC---CCCCHHHHHHHHHHhhCCCccCCceeEEEEeCCCCeeecCCCChhHHHhceeE
Q 004898 614 HCKVFLESEDVGRTLDLS---VLSSYEELYRRLAIMFGIERSDMLSHVLYQDASGAIKRTGDEPFSDFMKSAKR 684 (724)
Q Consensus 614 ~vKV~meG~~vGR~vDLs---~~~sY~eL~~~L~~MF~i~~~~l~~~v~Y~D~eGD~mlvGD~PW~~F~~~vkR 684 (724)
-+||.-+|+-+==++++. .--+|++|..++++.|.+.. .....+.|.|.+|||..+-++ .++...+.+
T Consensus 2 ~vKv~y~~~~rRf~l~~~~~~~d~~~~~L~~kI~~~f~l~~-~~~~~l~Y~Dedgd~V~l~~D--~DL~~a~~~ 72 (91)
T cd06398 2 VVKVKYGGTLRRFTFPVAENQLDLNMDGLREKVEELFSLSP-DADLSLTYTDEDGDVVTLVDD--NDLTDAIQY 72 (91)
T ss_pred EEEEEeCCEEEEEEeccccccCCCCHHHHHHHHHHHhCCCC-CCcEEEEEECCCCCEEEEccH--HHHHHHHHH
Confidence 369999886333344443 35799999999999999964 445688999999999999888 777776665
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=95.22 E-value=0.069 Score=47.76 Aligned_cols=64 Identities=16% Similarity=0.217 Sum_probs=50.1
Q ss_pred eEEEEecCceeeeeccCCCCCCHHHHHHHHHHhhCCCccCCceeEEEEeCCCCeeecC-CCChhHHHhc
Q 004898 614 HCKVFLESEDVGRTLDLSVLSSYEELYRRLAIMFGIERSDMLSHVLYQDASGAIKRTG-DEPFSDFMKS 681 (724)
Q Consensus 614 ~vKV~meG~~vGR~vDLs~~~sY~eL~~~L~~MF~i~~~~l~~~v~Y~D~eGD~mlvG-D~PW~~F~~~ 681 (724)
.+||.-.|..+==+++-+..-+|++|..+++++|++. ...|-|.|+||||.++- |.=.++.++.
T Consensus 2 ~vKaty~~d~~rf~~~~~~~~~~~~L~~ev~~rf~l~----~f~lKYlDde~e~v~lssd~eLeE~~rl 66 (81)
T cd06396 2 NLKVTYNGESQSFLVSDSENTTWASVEAMVKVSFGLN----DIQIKYVDEENEEVSVNSQGEYEEALKS 66 (81)
T ss_pred EEEEEECCeEEEEEecCCCCCCHHHHHHHHHHHhCCC----cceeEEEcCCCCEEEEEchhhHHHHHHH
Confidence 4789998886666777777889999999999999999 46888999999998764 3334444443
No 12
>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=95.13 E-value=0.093 Score=45.07 Aligned_cols=66 Identities=20% Similarity=0.313 Sum_probs=50.3
Q ss_pred eEEEEecCceeeeeccCCCCCCHHHHHHHHHHhhCCCccCCceeEEEEeCCCCeeecCCC-ChhHHHhcee
Q 004898 614 HCKVFLESEDVGRTLDLSVLSSYEELYRRLAIMFGIERSDMLSHVLYQDASGAIKRTGDE-PFSDFMKSAK 683 (724)
Q Consensus 614 ~vKV~meG~~vGR~vDLs~~~sY~eL~~~L~~MF~i~~~~l~~~v~Y~D~eGD~mlvGD~-PW~~F~~~vk 683 (724)
-+||.-.| -=|.+-+..--+|++|+.++.+.|++.. -...+-|+|.|||+..+.++ =|.+-+.+++
T Consensus 3 ~vK~~~~~--~~~~~~~~~~~s~~dL~~~i~~~~~~~~--~~~~l~Y~Dedgd~v~l~sd~Dl~~a~~~~~ 69 (81)
T smart00666 3 DVKLRYGG--ETRRLSVPRDISFEDLRSKVAKRFGLDN--QSFTLKYQDEDGDLVSLTSDEDLEEAIEEYD 69 (81)
T ss_pred cEEEEECC--EEEEEEECCCCCHHHHHHHHHHHhCCCC--CCeEEEEECCCCCEEEecCHHHHHHHHHHHH
Confidence 46888755 3677788888999999999999999864 12578899999999877654 5555555544
No 13
>cd06403 PB1_Par6 The PB1 domain is an essential part of Par6 protein which in complex with Par3 and aPKC proteins is crucial for establishment of apical-basal polarity of animal cells. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. The
Probab=94.38 E-value=0.14 Score=45.66 Aligned_cols=63 Identities=21% Similarity=0.337 Sum_probs=48.1
Q ss_pred EEEEecCceeeeeccCCCCCCHHHHHHHHHHhhCCCccCCceeEEEEeCCCCeeecCCCChhHHHhc
Q 004898 615 CKVFLESEDVGRTLDLSVLSSYEELYRRLAIMFGIERSDMLSHVLYQDASGAIKRTGDEPFSDFMKS 681 (724)
Q Consensus 615 vKV~meG~~vGR~vDLs~~~sY~eL~~~L~~MF~i~~~~l~~~v~Y~D~eGD~mlvGD~PW~~F~~~ 681 (724)
||..-+++--==.+|.....+|++++..|+.|+.|.+ +...|-|.|.+||.+-+-.+ ..|.+.
T Consensus 3 VKSkfdaEfRRFsl~r~~~~~f~ef~~ll~~lH~l~~--~~f~i~Y~D~~gDLLPInND--dNf~kA 65 (80)
T cd06403 3 VKSKFDAEFRRFSLDRNKPGKFEDFYKLLEHLHHIPN--VDFLIGYTDPHGDLLPINND--DNFLKA 65 (80)
T ss_pred eecccCCeEEEEEeccccCcCHHHHHHHHHHHhCCCC--CcEEEEEeCCCCCEecccCc--HHHHHH
Confidence 5666666532236777778999999999999999986 44577899999999988766 555543
No 14
>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=92.77 E-value=0.57 Score=42.05 Aligned_cols=72 Identities=21% Similarity=0.263 Sum_probs=48.4
Q ss_pred EEEEecCceeeeeccCCCC-CCHHHHHHHHHHhhCCCccCC-ceeEEEEeCCCCeeecCCC---ChhHHHhceeEEEEe
Q 004898 615 CKVFLESEDVGRTLDLSVL-SSYEELYRRLAIMFGIERSDM-LSHVLYQDASGAIKRTGDE---PFSDFMKSAKRLTIL 688 (724)
Q Consensus 615 vKV~meG~~vGR~vDLs~~-~sY~eL~~~L~~MF~i~~~~l-~~~v~Y~D~eGD~mlvGD~---PW~~F~~~vkRL~I~ 688 (724)
+|+..+| +|=| +=+..- -+|.+|...+++.|...-..+ ...|-|+|.|||+.-+-+. -|..=+...+||+|.
T Consensus 3 iK~~~g~-DiR~-~~~~~~~~t~~~L~~~v~~~F~~~~~~~~~flIKYkD~dGDlVTIts~~dL~~A~~~~~~~~l~~~ 79 (81)
T cd06401 3 LKAQLGD-DIRR-IPIHNEDITYDELLLMMQRVFRGKLGSSDDVLIKYKDEDGDLITIFDSSDLSFAIQCSRILKLTLF 79 (81)
T ss_pred EEEEeCC-eEEE-EeccCccccHHHHHHHHHHHhccccCCcccEEEEEECCCCCEEEeccHHHHHHHHhcCcceEEEEe
Confidence 5766654 5655 444332 399999999999999542112 2456699999999999876 344335556677664
No 15
>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=92.11 E-value=0.21 Score=45.14 Aligned_cols=51 Identities=24% Similarity=0.245 Sum_probs=39.6
Q ss_pred eeeeeccCC--CCCCHHHHHHHHHHhhCCCcc-CCceeEEEEeCCCCeeecCCC
Q 004898 623 DVGRTLDLS--VLSSYEELYRRLAIMFGIERS-DMLSHVLYQDASGAIKRTGDE 673 (724)
Q Consensus 623 ~vGR~vDLs--~~~sY~eL~~~L~~MF~i~~~-~l~~~v~Y~D~eGD~mlvGD~ 673 (724)
+-||.+=++ ...|+++|..+.++=|+++.. .-..+|.|.|+||||.++--+
T Consensus 8 ~~GrvhRf~~~~s~~~~~L~~~I~~Rl~~d~~~~~~~~L~YlDDEgD~VllT~D 61 (86)
T cd06409 8 PKGRVHRFRLRPSESLEELRTLISQRLGDDDFETHLYALSYVDDEGDIVLITSD 61 (86)
T ss_pred CCCCEEEEEecCCCCHHHHHHHHHHHhCCccccCCcccEEEEcCCCCEEEEecc
Confidence 456655444 368999999999999999863 235789999999999887654
No 16
>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=91.86 E-value=0.56 Score=42.28 Aligned_cols=65 Identities=15% Similarity=0.148 Sum_probs=49.2
Q ss_pred eEEEEecCceeeeeccCCCCCCHHHHHHHHHHhhCCCccCCceeEEEEeCCCCeeecCCCChhHHHhcee
Q 004898 614 HCKVFLESEDVGRTLDLSVLSSYEELYRRLAIMFGIERSDMLSHVLYQDASGAIKRTGDEPFSDFMKSAK 683 (724)
Q Consensus 614 ~vKV~meG~~vGR~vDLs~~~sY~eL~~~L~~MF~i~~~~l~~~v~Y~D~eGD~mlvGD~PW~~F~~~vk 683 (724)
.+|+.-.|..+-=.+|. .-+|++|.+++.+||.... +-..++-|.|.|||.--+... .+.....|
T Consensus 2 ~~K~~y~gdi~it~~d~--~~s~e~L~~~v~~~c~~~~-~q~ft~kw~DEEGDp~tiSS~--~EL~EA~r 66 (83)
T cd06404 2 RVKAAYNGDIMITSIDP--SISLEELCNEVRDMCRFHN-DQPFTLKWIDEEGDPCTISSQ--MELEEAFR 66 (83)
T ss_pred eEEEEecCcEEEEEcCC--CcCHHHHHHHHHHHhCCCC-CCcEEEEEECCCCCceeecCH--HHHHHHHH
Confidence 47899999755555666 6689999999999999865 445789999999999887765 44444333
No 17
>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=89.05 E-value=1.2 Score=40.45 Aligned_cols=55 Identities=18% Similarity=0.341 Sum_probs=45.3
Q ss_pred ceEEEEecCceeeeeccCCCCCCHHHHHHHHHHhhCCCccCCceeEEEEeCCCCeeecCCC
Q 004898 613 GHCKVFLESEDVGRTLDLSVLSSYEELYRRLAIMFGIERSDMLSHVLYQDASGAIKRTGDE 673 (724)
Q Consensus 613 ~~vKV~meG~~vGR~vDLs~~~sY~eL~~~L~~MF~i~~~~l~~~v~Y~D~eGD~mlvGD~ 673 (724)
..|||+-+|. -|.|-+..-=+|++|..++.++|++.. ...|-|.|. ||+.-+++.
T Consensus 3 ikVKv~~~~D--v~~i~v~~~i~f~dL~~kIrdkf~~~~---~~~iKykDE-GD~iti~sq 57 (86)
T cd06408 3 IRVKVHAQDD--TRYIMIGPDTGFADFEDKIRDKFGFKR---RLKIKMKDD-GDMITMGDQ 57 (86)
T ss_pred EEEEEEecCc--EEEEEcCCCCCHHHHHHHHHHHhCCCC---ceEEEEEcC-CCCccccCH
Confidence 4689999887 466666666679999999999999964 347789999 999999886
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=88.93 E-value=1.6 Score=39.68 Aligned_cols=62 Identities=23% Similarity=0.413 Sum_probs=43.8
Q ss_pred eEEEEecC----ceeee-eccCCCCCCHHHHHHHHHHhhCCCccCCceeEEEEeCCCCeeecCCCChhHH
Q 004898 614 HCKVFLES----EDVGR-TLDLSVLSSYEELYRRLAIMFGIERSDMLSHVLYQDASGAIKRTGDEPFSDF 678 (724)
Q Consensus 614 ~vKV~meG----~~vGR-~vDLs~~~sY~eL~~~L~~MF~i~~~~l~~~v~Y~D~eGD~mlvGD~PW~~F 678 (724)
.||.+..| ..|=| +||=....+|++|+..+.++|..-. +-...+-|.|.|||..-+... +++
T Consensus 2 ~vkayl~~~~~~~EIRRf~l~~~~~~s~~~L~~~V~~~f~~l~-~~~ftlky~DeeGDlvtIssd--eEL 68 (87)
T cd06402 2 TVKAYLLGKDANAEIRRFAIDEDVSTSYEYLVEKVAAVFPSLR-GKNFQLFWKDEEGDLVAFSSD--EEL 68 (87)
T ss_pred eEEEeecCCCCccceEEEEecCCCCcCHHHHHHHHHHHccccC-CCcEEEEEECCCCCEEeecCH--HHH
Confidence 46666666 33333 3455667799999999999995322 233588899999999888766 444
No 19
>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=86.89 E-value=1.8 Score=38.92 Aligned_cols=66 Identities=17% Similarity=0.253 Sum_probs=50.1
Q ss_pred EEEEecCceeeeeccCCCCCCHHHHHHHHHHhhCCCccCCceeEEEEeCCCCeeecCC-CChhHHHhceeE
Q 004898 615 CKVFLESEDVGRTLDLSVLSSYEELYRRLAIMFGIERSDMLSHVLYQDASGAIKRTGD-EPFSDFMKSAKR 684 (724)
Q Consensus 615 vKV~meG~~vGR~vDLs~~~sY~eL~~~L~~MF~i~~~~l~~~v~Y~D~eGD~mlvGD-~PW~~F~~~vkR 684 (724)
-||.-+| --|++-...-=+|..|..+|+.+|.|... ...|+|.|.+||..-+-| +=.++|.+-..|
T Consensus 3 fKv~~~g--~~RRf~~~~~pt~~~L~~kl~~Lf~lp~~--~~~vtYiDeD~D~ITlssd~eL~d~~~~~~~ 69 (82)
T cd06397 3 FKSSFLG--DTRRIVFPDIPTWEALASKLENLYNLPEI--KVGVTYIDNDNDEITLSSNKELQDFYRLSHR 69 (82)
T ss_pred EEEEeCC--ceEEEecCCCccHHHHHHHHHHHhCCChh--HeEEEEEcCCCCEEEecchHHHHHHHHhccc
Confidence 4777777 46777777888999999999999999742 257899999999875554 455666654444
No 20
>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=72.13 E-value=15 Score=33.16 Aligned_cols=69 Identities=20% Similarity=0.292 Sum_probs=52.3
Q ss_pred EEEEecCceeeeeccCCCCCCHHHHHHHHHHhhCCCccCCceeEEEEeCC-CCeeecCCCChhHHHhcee--EEEEe
Q 004898 615 CKVFLESEDVGRTLDLSVLSSYEELYRRLAIMFGIERSDMLSHVLYQDAS-GAIKRTGDEPFSDFMKSAK--RLTIL 688 (724)
Q Consensus 615 vKV~meG~~vGR~vDLs~~~sY~eL~~~L~~MF~i~~~~l~~~v~Y~D~e-GD~mlvGD~PW~~F~~~vk--RL~I~ 688 (724)
+||+-++ -| +|-...=-+|.+|+++|.+=+.+.+++ .+|-|+|.+ |+...++|.=++.=.+.|| ||++.
T Consensus 5 vKV~f~~-tI--aIrvp~~~~y~~L~~ki~~kLkl~~e~--i~LsYkde~s~~~v~l~d~dle~aws~~~~~~lTLw 76 (80)
T cd06406 5 VKVHFKY-TV--AIQVARGLSYATLLQKISSKLELPAEH--ITLSYKSEASGEDVILSDTNMEDVWSQAKDGCLTLW 76 (80)
T ss_pred EEEEEEE-EE--EEEcCCCCCHHHHHHHHHHHhCCCchh--cEEEeccCCCCCccCcChHHHHHHHHhhcCCeEEEE
Confidence 4999998 33 455566678999999999999996534 377899865 4554559999998888887 77653
No 21
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=59.10 E-value=14 Score=30.23 Aligned_cols=28 Identities=25% Similarity=0.433 Sum_probs=23.9
Q ss_pred ccccccEEEEEeecCCCCceeeeeeEEEEeec
Q 004898 328 HWLCGMRFKMAFETEDSSRISWFMGTISSVQV 359 (724)
Q Consensus 328 ~w~~GmRFkM~fE~EDss~i~wf~GTI~gv~~ 359 (724)
.|.+|+++-..++.++ .||.|+|+.+..
T Consensus 2 ~~~~G~~Ve~~~~~~~----~W~~a~V~~~~~ 29 (61)
T smart00743 2 DFKKGDRVEVFSKEED----SWWEAVVTKVLG 29 (61)
T ss_pred CcCCCCEEEEEECCCC----EEEEEEEEEECC
Confidence 5889999999996544 899999999964
No 22
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=55.73 E-value=8 Score=47.37 Aligned_cols=62 Identities=24% Similarity=0.412 Sum_probs=45.3
Q ss_pred ccCCCCCCeEEEecccccccccCCC----CCCCC--CCCCCcceeEEEEeEeeccCCccceeEEEEee
Q 004898 21 VQIPPLNSTVFYFPQGHAEHSLGSV----NFPSS--SRIPPLIFCRVSSLKFLADSETDEVYAKIKLV 82 (724)
Q Consensus 21 v~~P~~gs~V~YFPqGH~Eq~~~~~----~~~~~--~~~P~~ilCrV~~V~l~Ad~~TDEVyAki~L~ 82 (724)
-.||..|..|.||-|||-|-+.+.- ++... -++-..-.|.|..+.+---|-...--.|+.|.
T Consensus 871 ryipQmgDEViyfrQghqeyl~~~~~n~~~~~~~~p~~~~~v~~~kv~kl~~~~y~~~~~s~c~m~l~ 938 (1113)
T KOG0644|consen 871 RYIPQMGDEVIYFRQGHQEYLEAVRLNNIELNNKEPWNKMAVEICKVEKLVYITYPGSGDSCCKMKLA 938 (1113)
T ss_pred cccccccceeehhhhhhHHHHhhhhhccccccccCcccccchhhheeeeeeeeeccCCCcchheeeee
Confidence 3689999999999999999998732 22111 13445668999988877767777777777765
No 23
>cd06399 PB1_P40 The PB1 domain is essential part of the p40 adaptor protein which plays an important role in activating phagocyte NADPH oxidase during phagocytosis. The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes , such as osteoclastogenesis, angiogenesis, early cardiovascular development and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The PB1 domain of p40 represents a type I PB1 domain which interacts with the PB1 domain of oxidase activator p67 w
Probab=54.85 E-value=21 Score=32.88 Aligned_cols=41 Identities=27% Similarity=0.291 Sum_probs=33.9
Q ss_pred cCCCCCCHHHHHHHHHHhhCCCccCCceeEEEEeCCCCeeecCCC
Q 004898 629 DLSVLSSYEELYRRLAIMFGIERSDMLSHVLYQDASGAIKRTGDE 673 (724)
Q Consensus 629 DLs~~~sY~eL~~~L~~MF~i~~~~l~~~v~Y~D~eGD~mlvGD~ 673 (724)
||+.--+|.+|.....+-|..+. -.+-|+|.|||..-+=|+
T Consensus 23 ~l~~~P~~kdLl~lmr~~f~~~d----IaLNYrD~EGDLIRlldd 63 (92)
T cd06399 23 DLSSTPLLKDLLELTRREFQRED----IALNYRDAEGDLIRLLSD 63 (92)
T ss_pred ccccCccHHHHHHHHHHHhchhh----eeeeeecCCCCEEEEcch
Confidence 78899999999999999999875 356699999998554444
No 24
>PF04014 Antitoxin-MazE: Antidote-toxin recognition MazE; InterPro: IPR007159 This domain is found in AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation []. AbrB is thought to interact directly with the transcription initiation regions of genes under its control []. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins []. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator []. DNA-binding activity in this AbrB homologue requires hexamerisation []. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins [].; PDB: 2L66_A 2GLW_A 3TND_D 2W1T_B 2RO5_B 2FY9_A 2RO3_B 1UB4_C 3ZVK_G 1YFB_B ....
Probab=46.89 E-value=30 Score=27.32 Aligned_cols=26 Identities=19% Similarity=0.339 Sum_probs=22.1
Q ss_pred hHhhccCCCCCCEEEEEEecCCcEEE
Q 004898 184 TFVNQKKLVAGDSIVFLRAQDGDLCV 209 (724)
Q Consensus 184 ~FV~~KkL~aGD~VvF~R~~~GeL~V 209 (724)
.|.++.+|.+||.|.|.-.++|++.+
T Consensus 14 ~~~~~l~l~~Gd~v~i~~~~~g~i~i 39 (47)
T PF04014_consen 14 EIREKLGLKPGDEVEIEVEGDGKIVI 39 (47)
T ss_dssp HHHHHTTSSTTTEEEEEEETTSEEEE
T ss_pred HHHHHcCCCCCCEEEEEEeCCCEEEE
Confidence 56788899999999999998886554
No 25
>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=36.20 E-value=55 Score=24.62 Aligned_cols=27 Identities=22% Similarity=0.487 Sum_probs=22.3
Q ss_pred hhHhhccCCCCCCEEEEEEecCCcEEE
Q 004898 183 STFVNQKKLVAGDSIVFLRAQDGDLCV 209 (724)
Q Consensus 183 s~FV~~KkL~aGD~VvF~R~~~GeL~V 209 (724)
..|.++-++..||.|.+....+|.+.+
T Consensus 13 ~~~r~~l~~~~gd~~~i~~~~~~~l~l 39 (43)
T TIGR01439 13 KEIREKLGLKEGDRLEVIRVEDGEIIL 39 (43)
T ss_pred HHHHHHcCcCCCCEEEEEEeCCCEEEE
Confidence 368899999999999999877776543
No 26
>KOG3938 consensus RGS-GAIP interacting protein GIPC, contains PDZ domain [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=35.75 E-value=60 Score=35.51 Aligned_cols=74 Identities=23% Similarity=0.354 Sum_probs=53.4
Q ss_pred cCceeeeeccCCCCCCHHHHHHHHHHhhCCCccCCceeEEE-EeCCCCeeecCCCChhHHH-----hceeEEEEecCCCC
Q 004898 620 ESEDVGRTLDLSVLSSYEELYRRLAIMFGIERSDMLSHVLY-QDASGAIKRTGDEPFSDFM-----KSAKRLTILMGSGS 693 (724)
Q Consensus 620 eG~~vGR~vDLs~~~sY~eL~~~L~~MF~i~~~~l~~~v~Y-~D~eGD~mlvGD~PW~~F~-----~~vkRL~I~~~~~~ 693 (724)
+|.|+|| +.-|++-+|||..+++-|+|...++.+.-+- ---|=+-||-|-.-+++|+ .-.|-+.|++.+++
T Consensus 62 HGSptg~---Ie~fsnv~ELY~kIAe~F~Is~~dIlfcTlNshKvDM~~llgGqigleDfiFAHvkGq~kEv~v~Kseda 138 (334)
T KOG3938|consen 62 HGSPTGR---IEGFSNVRELYQKIAEAFDISPDDILFCTLNSHKVDMKRLLGGQIGLEDFIFAHVKGQAKEVEVVKSEDA 138 (334)
T ss_pred cCCccce---ecccccHHHHHHHHHHHhcCCccceEEEecCCCcccHHHHhcCccChhhhhhhhhcCcceeEEEEecccc
Confidence 6889998 4578999999999999999987665332110 0123345888989999986 34678999988776
Q ss_pred CCc
Q 004898 694 DSV 696 (724)
Q Consensus 694 ~~l 696 (724)
-++
T Consensus 139 lGl 141 (334)
T KOG3938|consen 139 LGL 141 (334)
T ss_pred cce
Confidence 433
No 27
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=34.95 E-value=56 Score=30.04 Aligned_cols=28 Identities=25% Similarity=0.439 Sum_probs=22.4
Q ss_pred HhhccCCCCCCEEEEEEecCCcEEEEEE
Q 004898 185 FVNQKKLVAGDSIVFLRAQDGDLCVGIR 212 (724)
Q Consensus 185 FV~~KkL~aGD~VvF~R~~~GeL~VGIR 212 (724)
|.-...|++||.|..+|.++|..++=+-
T Consensus 71 i~~~~~Lk~GD~V~ll~~~~gQ~yiVlD 98 (100)
T PF10844_consen 71 ITFTDGLKVGDKVLLLRVQGGQKYIVLD 98 (100)
T ss_pred EEEecCCcCCCEEEEEEecCCCEEEEEE
Confidence 5566789999999999998887666443
No 28
>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=34.05 E-value=60 Score=25.82 Aligned_cols=39 Identities=15% Similarity=0.364 Sum_probs=29.3
Q ss_pred ccccccEEEEEeecCCCCceeeeeeEEEEeecCCCCCCCCCCccccccccCCcc
Q 004898 328 HWLCGMRFKMAFETEDSSRISWFMGTISSVQVADPISWPNSPWRLLQVTWDEPD 381 (724)
Q Consensus 328 ~w~~GmRFkM~fE~EDss~i~wf~GTI~gv~~~dp~~wp~S~WR~L~V~WDe~~ 381 (724)
.|.+|..+...+ .+. .||.|+|+++.. + ....|.-+.-.
T Consensus 2 ~~~~G~~~~a~~-~d~----~wyra~I~~~~~-------~---~~~~V~f~D~G 40 (57)
T smart00333 2 TFKVGDKVAARW-EDG----EWYRARIIKVDG-------E---QLYEVFFIDYG 40 (57)
T ss_pred CCCCCCEEEEEe-CCC----CEEEEEEEEECC-------C---CEEEEEEECCC
Confidence 588999999999 444 799999999973 2 44667776643
No 29
>PRK03760 hypothetical protein; Provisional
Probab=29.28 E-value=1e+02 Score=29.27 Aligned_cols=27 Identities=26% Similarity=0.507 Sum_probs=22.1
Q ss_pred CCceee--ccchhhHhhccCCCCCCEEEEEEe
Q 004898 173 PRRHLL--TTGWSTFVNQKKLVAGDSIVFLRA 202 (724)
Q Consensus 173 ~rrhlL--TtGWs~FV~~KkL~aGD~VvF~R~ 202 (724)
+-+|+| ..|| +.+.++++||.|.|.|+
T Consensus 89 ~a~~VLEl~aG~---~~~~gi~~Gd~v~~~~~ 117 (117)
T PRK03760 89 PARYIIEGPVGK---IRVLKVEVGDEIEWIDE 117 (117)
T ss_pred cceEEEEeCCCh---HHHcCCCCCCEEEEeeC
Confidence 466787 6787 78999999999998763
No 30
>cd01789 Alp11_N Ubiquitin-like domain of Alp11 tubulin-folding cofactor B. Alp11, also known as tubulin-folding cofactor B, is one of at least three proteins required for the proper folding of tubulins prior to their incorporation into microtubules. These cofactors are necessary for the biogenesis of microtubules and for cell viability. Alp11 has three domains including an N-terminal ubiquitin-like domain (represented by this CD) which executes the essential function, a central coiled-coil domain necessary for maintenance of cellular alpha-tubulin levels, and a C-terminal CLIP-170 domain is required for efficient binding to alpha-tubulin.
Probab=28.82 E-value=1.8e+02 Score=25.77 Aligned_cols=39 Identities=18% Similarity=0.264 Sum_probs=27.0
Q ss_pred eeeeeccCCCCCCHHHHHHHHHHhhCCCccCCceeEEEEeCCC
Q 004898 623 DVGRTLDLSVLSSYEELYRRLAIMFGIERSDMLSHVLYQDASG 665 (724)
Q Consensus 623 ~vGR~vDLs~~~sY~eL~~~L~~MF~i~~~~l~~~v~Y~D~eG 665 (724)
..-|+++ ..-+..+|..+|+.+||+.-+.+ ++.|.|.+|
T Consensus 14 ~~ekr~~--~~~Tv~~lK~kl~~~~G~~~~~m--rL~l~~~~~ 52 (84)
T cd01789 14 SFEKKYS--RGLTIAELKKKLELVVGTPASSM--RLQLFDGDD 52 (84)
T ss_pred eeeEecC--CCCcHHHHHHHHHHHHCCCccce--EEEEEcCCC
Confidence 3445555 45689999999999999976443 555445544
No 31
>PF05641 Agenet: Agenet domain; InterPro: IPR008395 This domain is related to the TUDOR domain IPR008191 from INTERPRO []. The function of the agenet domain is unknown. This signature matches one of the two Agenet domains in the FMR proteins [].; GO: 0003723 RNA binding; PDB: 2BKD_N 3O8V_A 3KUF_A 3H8Z_A.
Probab=28.67 E-value=81 Score=26.81 Aligned_cols=41 Identities=22% Similarity=0.336 Sum_probs=26.4
Q ss_pred cccccEEEEEeecCCCCceeeeeeEEEEeecCCCCCCCCCCccccccccCCc
Q 004898 329 WLCGMRFKMAFETEDSSRISWFMGTISSVQVADPISWPNSPWRLLQVTWDEP 380 (724)
Q Consensus 329 w~~GmRFkM~fE~EDss~i~wf~GTI~gv~~~dp~~wp~S~WR~L~V~WDe~ 380 (724)
|..|+++-..-+ |+..+-+||.|||+..... + .+.|+.+.-
T Consensus 1 F~~G~~VEV~s~-e~g~~gaWf~a~V~~~~~~-------~---~~~V~Y~~~ 41 (68)
T PF05641_consen 1 FKKGDEVEVSSD-EDGFRGAWFPATVLKENGD-------D---KYLVEYDDL 41 (68)
T ss_dssp --TT-EEEEEE--SBTT--EEEEEEEEEEETT-----------EEEEEETT-
T ss_pred CCCCCEEEEEEc-CCCCCcEEEEEEEEEeCCC-------c---EEEEEECCc
Confidence 467999998875 4556779999999998742 2 777888654
No 32
>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=27.42 E-value=98 Score=25.80 Aligned_cols=31 Identities=23% Similarity=0.411 Sum_probs=22.8
Q ss_pred cccEEEEEeecCCCCceeeeeeEEEEeecCCC
Q 004898 331 CGMRFKMAFETEDSSRISWFMGTISSVQVADP 362 (724)
Q Consensus 331 ~GmRFkM~fE~EDss~i~wf~GTI~gv~~~dp 362 (724)
+|-|+.-.||.++.+... |.|+|...-++.|
T Consensus 1 vGk~Veh~~~~g~g~~s~-w~G~Vl~Qvp~~p 31 (50)
T PF02513_consen 1 VGKRVEHTWEDGDGPKSK-WKGMVLHQVPAKP 31 (50)
T ss_dssp TT-EEEEEECTSTS-EEE-EEEEEEEE-TTST
T ss_pred CCceEEEEEccCCCcccE-EEEEEEEEeecCC
Confidence 588999999988888755 5999999877655
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=24.88 E-value=87 Score=28.33 Aligned_cols=57 Identities=18% Similarity=0.182 Sum_probs=30.2
Q ss_pred ehHHHHHHHhcccccccEEEEEeecCCCCceeeeeeEEEEeecCCCCCCCCCCccccccccCCcc
Q 004898 317 KASAVKAAMRVHWLCGMRFKMAFETEDSSRISWFMGTISSVQVADPISWPNSPWRLLQVTWDEPD 381 (724)
Q Consensus 317 ~~~~y~~A~~~~w~~GmRFkM~fE~EDss~i~wf~GTI~gv~~~dp~~wp~S~WR~L~V~WDe~~ 381 (724)
+.+.|-+=++-+.++||++||.=.-|+-+.- =.|+|..++. | .-|+ -.+||.|..-.
T Consensus 6 s~d~Ya~YVr~~i~~GM~VRc~~~yeeV~~G--D~G~V~k~~~-d--g~~~---lnvqv~W~~~G 62 (78)
T PF11515_consen 6 SNDDYAEYVRDNIQPGMRVRCCRDYEEVRAG--DEGEVFKQDR-D--GLHD---LNVQVDWQSKG 62 (78)
T ss_dssp SSHHHHHHHHHH--TT-EEEESS-BTTB-TT---EEE-EEEE--T--TSSE-----EEEEETTTT
T ss_pred chhHHHHHHHHhCCCCcEEEEeccccccccc--ccceeEeecc-C--CCCC---cceEEEeeecC
Confidence 4567777788899999999998655553321 2455555543 1 2222 24788887654
No 34
>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=24.27 E-value=2.5e+02 Score=24.09 Aligned_cols=69 Identities=16% Similarity=0.205 Sum_probs=48.6
Q ss_pred ceEEEEecCcee---eeeccCCCCCCHHHHHHHHHHhhCCCccCCceeEE-EEeCCC-CeeecCCC-ChhHHHhc
Q 004898 613 GHCKVFLESEDV---GRTLDLSVLSSYEELYRRLAIMFGIERSDMLSHVL-YQDASG-AIKRTGDE-PFSDFMKS 681 (724)
Q Consensus 613 ~~vKV~meG~~v---GR~vDLs~~~sY~eL~~~L~~MF~i~~~~l~~~v~-Y~D~eG-D~mlvGD~-PW~~F~~~ 681 (724)
..+||+++...- -++|-++...+-.|++..+.+-|++....-.|.|+ +.-..| ...|-.|+ |+......
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 GVLRVYDGDGSPGSTYKTIKVSSSTTAREVIEMALEKFGLAEDPSDYCLVEVEESGGEERPLDDDECPLQIQLQW 77 (93)
T ss_dssp EEEEEEETTSSSCCSEEEEEEETTSBHHHHHHHHHHHTTTSSSGGGEEEEEEECTTTEEEEETTTSBHHHHHHTT
T ss_pred eEEEEEcCCCCCCccEEEEEECCCCCHHHHHHHHHHHhCCCCCCCCEEEEEEEcCCCEEEEcCCCCchHHHHHhC
Confidence 578999987653 68899999999999999999999994423346774 444444 44443333 77666554
No 35
>cd06410 PB1_UP2 Uncharacterized protein 2. The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions.
Probab=23.70 E-value=82 Score=29.17 Aligned_cols=55 Identities=18% Similarity=0.294 Sum_probs=34.3
Q ss_pred eeeccCCCCCCHHHHHHHHHHhhCCCcc-CCceeEEEEeCCCCeeecCCCChhHHHhce
Q 004898 625 GRTLDLSVLSSYEELYRRLAIMFGIERS-DMLSHVLYQDASGAIKRTGDEPFSDFMKSA 682 (724)
Q Consensus 625 GR~vDLs~~~sY~eL~~~L~~MF~i~~~-~l~~~v~Y~D~eGD~mlvGD~PW~~F~~~v 682 (724)
-|.|.+..--||.||..+|.++|++... .+.|++-.+|.+ -..-|-++ ++..+|+
T Consensus 24 tr~i~V~r~~s~~el~~kl~~~~~~~~~~~lky~Lp~edld-~Lisv~~D--eDl~~M~ 79 (97)
T cd06410 24 TRIVSVDRSISFKELVSKLSELFGAGVVVTLKYQLPDEDLD-ALISVSND--EDLKNMM 79 (97)
T ss_pred eEEEEEcCCCCHHHHHHHHHHHhCCCCceEEEEEcCCCCcc-eeEEecCc--HHHHHHH
Confidence 3455555556999999999999998763 334555554444 25555555 3444443
No 36
>PF01878 EVE: EVE domain; InterPro: IPR002740 The EVE domain is part of the wider PUA domain superfamily. The function of this domain is not known but, given the structural similarities to PUA, is likely to involve RNA binding []. ; PDB: 2G2X_B 2AR1_A 3EOP_A 2EVE_A 2HD9_A 2ZBN_A 1WMM_A 2P5D_A 2GBS_A 1ZCE_A.
Probab=23.28 E-value=74 Score=30.36 Aligned_cols=27 Identities=22% Similarity=0.399 Sum_probs=17.7
Q ss_pred cCCCCCCEEEEEEec-CCcEEEEEEEcc
Q 004898 189 KKLVAGDSIVFLRAQ-DGDLCVGIRRAK 215 (724)
Q Consensus 189 KkL~aGD~VvF~R~~-~GeL~VGIRR~~ 215 (724)
++++.||.|+||... .+.-+|||=+-.
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 499999999999987 566777765543
No 37
>KOG3606 consensus Cell polarity protein PAR6 [Signal transduction mechanisms]
Probab=20.76 E-value=89 Score=34.36 Aligned_cols=81 Identities=22% Similarity=0.276 Sum_probs=53.6
Q ss_pred ceEEEEecCceeeeeccCCCCCCHHHHHHHHHHhhCCCccCCceeEEEEeCCCCeeecCCC-ChhHHHhcee---EEEEe
Q 004898 613 GHCKVFLESEDVGRTLDLSVLSSYEELYRRLAIMFGIERSDMLSHVLYQDASGAIKRTGDE-PFSDFMKSAK---RLTIL 688 (724)
Q Consensus 613 ~~vKV~meG~~vGR~vDLs~~~sY~eL~~~L~~MF~i~~~~l~~~v~Y~D~eGD~mlvGD~-PW~~F~~~vk---RL~I~ 688 (724)
.-||-..+-+=--=.++-..-++|++.+.-|+.+-.|.+.+ ..|-|.|.-||.+-+-.+ -+..=+++++ ||.|-
T Consensus 19 veVKSKFdaEfRRfsl~r~~~~~f~~F~~Lv~~~H~i~nvd--vllgY~d~hgDLLPinNDDn~~ka~~sa~PlLR~~iQ 96 (358)
T KOG3606|consen 19 VEVKSKFDAEFRRFSLPRHSASSFDEFYSLVEHLHHIPNVD--VLLGYADTHGDLLPINNDDNLHKALSSARPLLRLLIQ 96 (358)
T ss_pred EEeeccccchhheecccccCcccHHHHHHHHHHHhcCCCce--EEEEEecCCCceecccCchhHHHHhhccCchhhhhhh
Confidence 44555554432112455556679999999999998887622 356799999999988655 3433344454 88888
Q ss_pred cCCCCCC
Q 004898 689 MGSGSDS 695 (724)
Q Consensus 689 ~~~~~~~ 695 (724)
+.+|+.+
T Consensus 97 kr~ea~~ 103 (358)
T KOG3606|consen 97 KREEADE 103 (358)
T ss_pred hhhhhhh
Confidence 8866653
No 38
>KOG3207 consensus Beta-tubulin folding cofactor E [Posttranslational modification, protein turnover, chaperones]
Probab=20.74 E-value=93 Score=36.34 Aligned_cols=41 Identities=24% Similarity=0.485 Sum_probs=27.5
Q ss_pred cccccEEEEEeecCCCCceeeeeeEEEEeecCCCCCCCCCCccccccccCCccccC
Q 004898 329 WLCGMRFKMAFETEDSSRISWFMGTISSVQVADPISWPNSPWRLLQVTWDEPDLLQ 384 (724)
Q Consensus 329 w~~GmRFkM~fE~EDss~i~wf~GTI~gv~~~dp~~wp~S~WR~L~V~WDe~~~~~ 384 (724)
..+|.|+|..+|- .. .+|.|+|.| |++ +| +.|.||.+.-..
T Consensus 3 ~~IG~RvkI~~~~---~T-vr~iG~V~g--------~~~-~w--~GvEWDd~~RGK 43 (505)
T KOG3207|consen 3 MEIGTRVKIGGEI---AT-VRYIGEVEG--------NNS-KW--YGVEWDDPVRGK 43 (505)
T ss_pred eeccceEEEcCEE---EE-EEEEEEEcC--------CCC-cc--eeeEecCCCccc
Confidence 4689999987752 22 357777744 444 45 789999997543
No 39
>PF03120 DNA_ligase_OB: NAD-dependent DNA ligase OB-fold domain; InterPro: IPR004150 DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This family is a small domain found after the adenylation domain DNA_ligase_N in NAD+-dependent ligases (IPR001679 from INTERPRO). OB-fold domains generally are involved in nucleic acid binding.; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 2OWO_A 1TAE_A 3UQ8_A 1DGS_A 1V9P_B 3SGI_A.
Probab=20.46 E-value=86 Score=28.40 Aligned_cols=34 Identities=24% Similarity=0.432 Sum_probs=22.0
Q ss_pred hhHhhccCCCCCCEEEEEEecCCc-EEEEEEEccc
Q 004898 183 STFVNQKKLVAGDSIVFLRAQDGD-LCVGIRRAKK 216 (724)
Q Consensus 183 s~FV~~KkL~aGD~VvF~R~~~Ge-L~VGIRR~~~ 216 (724)
..|+++++|..||.|.++|..+.= ..+++-..+|
T Consensus 42 ~~~i~~~~i~~Gd~V~V~raGdVIP~I~~vv~~~r 76 (82)
T PF03120_consen 42 YDYIKELDIRIGDTVLVTRAGDVIPKIVGVVKEKR 76 (82)
T ss_dssp HHHHHHTT-BBT-EEEEEEETTTEEEEEEE-GGG-
T ss_pred HHHHHHcCCCCCCEEEEEECCCccceEeEeehhcC
Confidence 378999999999999999987653 3334444333
Done!