Query 004105
Match_columns 773
No_of_seqs 359 out of 815
Neff 4.0
Searched_HMMs 46136
Date Thu Mar 28 17:38:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004105.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/004105hhsearch_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 1.1E-35 2.4E-40 261.9 8.4 83 253-336 1-83 (83)
2 PF02309 AUX_IAA: AUX/IAA fami 99.9 1.2E-27 2.6E-32 241.5 0.0 77 689-765 107-197 (215)
3 PF02362 B3: B3 DNA binding do 99.7 1.2E-16 2.6E-21 140.7 11.2 97 127-228 1-99 (100)
4 KOG0644 Uncharacterized conser 99.4 5.9E-13 1.3E-17 153.5 5.9 148 205-361 874-1044(1113)
5 PF09217 EcoRII-N: Restriction 98.4 1.7E-06 3.8E-11 84.8 10.1 89 124-214 7-110 (156)
6 PF03754 DUF313: Domain of unk 97.7 6.9E-05 1.5E-09 70.8 6.6 81 121-202 18-114 (114)
7 PF00564 PB1: PB1 domain; Int 96.7 0.004 8.8E-08 53.7 6.0 56 694-756 4-59 (84)
8 smart00666 PB1 PB1 domain. Pho 95.9 0.025 5.3E-07 48.8 6.5 54 694-755 4-57 (81)
9 cd06407 PB1_NLP A PB1 domain i 95.5 0.039 8.4E-07 49.4 6.5 54 694-754 3-56 (82)
10 cd06396 PB1_NBR1 The PB1 domai 95.4 0.043 9.2E-07 49.5 6.4 52 694-754 3-55 (81)
11 cd06409 PB1_MUG70 The MUG70 pr 95.3 0.031 6.7E-07 50.8 5.3 49 702-754 9-59 (86)
12 cd05992 PB1 The PB1 domain is 95.2 0.063 1.4E-06 46.0 6.6 54 694-755 3-57 (81)
13 cd06398 PB1_Joka2 The PB1 doma 94.8 0.086 1.9E-06 48.2 6.8 56 694-755 3-62 (91)
14 cd06403 PB1_Par6 The PB1 domai 91.0 0.57 1.2E-05 42.4 5.8 54 694-754 3-57 (80)
15 cd06404 PB1_aPKC PB1 domain is 90.2 0.7 1.5E-05 42.1 5.8 53 694-754 3-56 (83)
16 cd06401 PB1_TFG The PB1 domain 88.8 1.3 2.8E-05 40.2 6.4 57 694-755 3-60 (81)
17 cd06402 PB1_p62 The PB1 domain 88.2 1.6 3.5E-05 40.0 6.7 56 693-754 2-63 (87)
18 cd06397 PB1_UP1 Uncharacterize 87.1 1.4 3.1E-05 40.1 5.5 53 695-755 4-56 (82)
19 cd06408 PB1_NoxR The PB1 domai 81.4 3.6 7.8E-05 37.8 5.6 53 693-755 4-56 (86)
20 PRK10737 FKBP-type peptidyl-pr 69.1 15 0.00031 38.3 7.0 103 205-321 3-114 (196)
21 KOG0644 Uncharacterized conser 55.2 9.2 0.0002 47.2 2.9 67 34-102 872-940 (1113)
22 smart00743 Agenet Tudor-like d 52.3 21 0.00046 29.4 3.9 28 291-321 2-29 (61)
23 PF04014 Antitoxin-MazE: Antid 44.1 27 0.00057 27.9 3.1 38 185-225 4-41 (47)
24 PF00788 RA: Ras association ( 41.1 77 0.0017 27.4 5.8 56 692-752 3-63 (93)
25 COG1047 SlpA FKBP-type peptidy 35.2 1.9E+02 0.0041 30.0 8.3 105 204-321 2-115 (174)
26 smart00333 TUDOR Tudor domain. 34.7 62 0.0013 25.9 3.9 52 291-359 2-53 (57)
27 PF10844 DUF2577: Protein of u 31.4 61 0.0013 30.0 3.8 27 199-225 71-97 (100)
28 TIGR01439 lp_hng_hel_AbrB loop 31.2 58 0.0013 24.7 3.1 26 198-223 14-39 (43)
29 KOG3207 Beta-tubulin folding c 30.0 61 0.0013 38.1 4.2 43 292-348 3-45 (505)
30 PF01878 EVE: EVE domain; Int 29.0 54 0.0012 31.5 3.1 26 203-228 38-64 (143)
31 cd06399 PB1_P40 The PB1 domain 29.0 97 0.0021 29.1 4.5 38 707-753 23-60 (92)
32 PF05641 Agenet: Agenet domain 25.0 1.2E+02 0.0027 25.9 4.3 42 292-343 1-42 (68)
33 PF02513 Spin-Ssty: Spin/Ssty 24.8 1.2E+02 0.0026 25.6 4.0 31 294-324 1-31 (50)
34 PF10411 DsbC_N: Disulfide bon 24.7 68 0.0015 26.9 2.6 17 740-756 34-50 (57)
35 PRK03760 hypothetical protein; 22.3 1.7E+02 0.0037 28.1 5.1 49 165-216 61-117 (117)
36 PF06003 SMN: Survival motor n 20.8 96 0.0021 33.6 3.5 57 290-361 67-123 (264)
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=1.1e-35 Score=261.87 Aligned_cols=83 Identities=65% Similarity=1.048 Sum_probs=81.2
Q ss_pred HHHHHhcCCcEEEEEecCCCCCcceeehhHHHHhhhcCCCccccEEEEeeeccccccceeeEEEEEeccCCCCCCCCCCc
Q 004105 253 AAHAAATNSCFTVFFNPRASPSEFVIPLTKYVKAVFHTRVSVGMRFRMLFETEESSVRRYMGTITGISDLDPVRWSNSHW 332 (773)
Q Consensus 253 Aa~aaa~~~~F~V~Y~PRas~sEFVVp~~kyvkA~~~~~ws~GMRFrM~fEtEDss~rr~~GTI~gvsd~Dp~rWp~S~W 332 (773)
|+|||+++++|+|+||||++++|||||++||++|+. ++|++||||||+||+||+++++|+|||+||+++||+|||+|+|
T Consensus 1 A~~aa~~~~~F~V~Y~PRa~~sEFVV~~~k~~~al~-~~~~~GmRfkM~fE~eds~~~~~~GtI~~v~~~dp~~w~~S~W 79 (83)
T PF06507_consen 1 AAHAAATGSPFEVFYYPRASPSEFVVPASKYDKALN-HPWSVGMRFKMRFETEDSSERRWQGTIVGVSDLDPIRWPGSKW 79 (83)
T ss_pred ChhHhhcCCeEEEEECCCCCCcceEEEHHHHHHHhc-CCCCCCcEEEEEeccCCCccceeeeEEeEeeccCCCCCCCCCc
Confidence 689999999999999999999999999999999997 7999999999999999999999999999999999999999999
Q ss_pred ccee
Q 004105 333 RSVK 336 (773)
Q Consensus 333 R~Lq 336 (773)
||||
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=99.93 E-value=1.2e-27 Score=241.46 Aligned_cols=77 Identities=42% Similarity=0.704 Sum_probs=0.0
Q ss_pred CcccEEEEeccc-cceeecccCCCCCHHHHHHHHHhhh---CCC----------CccCCCCCCccEEEEEeCCCCEEEec
Q 004105 689 PTRTFVKVYKSG-SVGRSLDISRFSSYNELREELGQMF---GIE----------GKFEDPLRSGWQLVFVDRENDVLLLG 754 (773)
Q Consensus 689 ~~~~fVKV~m~G-~iGRkiDL~~f~sY~eL~~~L~~MF---g~~----------g~l~d~~~s~~~lvYeD~EGD~mLVG 754 (773)
..++||||+||| +|||||||++|+||++|+.+|++|| ++. +.++...+++|+|||+|+||||||||
T Consensus 107 ~~~~~vKV~mdG~~igRkVDL~~~~sY~~L~~~L~~MF~~~~i~~~~~~~~~~~~~~~~~~~~~~~l~Y~D~egd~mlvG 186 (215)
T PF02309_consen 107 SSRSYVKVNMDGVPIGRKVDLSAYSSYEELSSALEKMFSCFSIEQCGSHGLNESGLLDLLNGSEYVLVYEDKEGDWMLVG 186 (215)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred cCCceeEEEecCcccceecCHHHhhCHHHHHHHHHHhcCCCCccccccccccchhhccccCCcceeEEEECCCCCEEEec
Confidence 357999999999 9999999999999999999999999 655 33444567899999999999999999
Q ss_pred ccCcCccccCC
Q 004105 755 DDPWEFRSSRP 765 (773)
Q Consensus 755 DvPWe~Fv~~~ 765 (773)
||||+||+++-
T Consensus 187 D~PW~~F~~~v 197 (215)
T PF02309_consen 187 DVPWEEFVKSV 197 (215)
T ss_dssp -----------
T ss_pred CCCHHHHHHHh
Confidence 99999999874
No 3
>PF02362 B3: B3 DNA binding domain; InterPro: IPR003340 Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana contain two distinct amino acid sequence domains found only in higher plant species. The N-terminal regions of RAV1 and RAV2 are homologous to the AP2 DNA-binding domain (see IPR001471 from INTERPRO) present in a family of transcription factors, while the C-terminal region exhibits homology to the highly conserved C-terminal domain, designated B3, of VP1/ABI3 transcription factors []. The AP2 and B3-like domains of RAV1 bind autonomously to the CAACA and CACCTG motifs, respectively, and together achieve a high affinity and specificity of binding. It has been suggested that the AP2 and B3-like domains of RAV1 are connected by a highly flexible structure enabling the two domains to bind to the CAACA and CACCTG motifs in various spacings and orientations [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1WID_A 1YEL_A.
Probab=99.69 E-value=1.2e-16 Score=140.67 Aligned_cols=97 Identities=28% Similarity=0.406 Sum_probs=75.1
Q ss_pred EEEeecccCCCCCCceeeehhhhhhhCCCCCCCCCCCceEEEEEecCCCeEEEEEEEcCCCCceeecccchhhhcccCCC
Q 004105 127 FCKTLTASDTSTHGGFSVPRRAAEKVFPSLDFSLQPPAQELIARDLHDVEWKFRHIFRGQPKRHLLTTGWSVFVSAKRLV 206 (773)
Q Consensus 127 F~K~LT~SDv~~~grfsVPk~~AE~~FPpLd~~~~~p~q~L~~~Dl~G~~W~FR~iyrg~prrhlLTtGWs~FV~~KkL~ 206 (773)
|.|+|+++|+...+++.||++.++.+. ++ ...++.+.++|..|+.|.+++.|++.+++++|++||..||++++|+
T Consensus 1 F~K~l~~s~~~~~~~l~iP~~f~~~~~--~~---~~~~~~v~l~~~~g~~W~v~~~~~~~~~~~~l~~GW~~Fv~~n~L~ 75 (100)
T PF02362_consen 1 FFKVLKPSDVSSSCRLIIPKEFAKKHG--GN---KRKSREVTLKDPDGRSWPVKLKYRKNSGRYYLTGGWKKFVRDNGLK 75 (100)
T ss_dssp EEEE--TTCCCCTT-EEE-HHHHTTTS-------SS--CEEEEEETTTEEEEEEEEEECCTTEEEEETTHHHHHHHCT--
T ss_pred CEEEEEccCcCCCCEEEeCHHHHHHhC--CC---cCCCeEEEEEeCCCCEEEEEEEEEccCCeEEECCCHHHHHHHcCCC
Confidence 899999999999999999999999982 11 1236799999999999999999999988999999999999999999
Q ss_pred CCCEEEEEEcc--CCcEEEEEEec
Q 004105 207 AGDSVLFIWNE--KNQLLLGIRRA 228 (773)
Q Consensus 207 aGDsVvF~R~~--~G~L~VGIRRa 228 (773)
+||.|+|...+ ..++.|.|.|+
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 99999999875 45569999886
No 4
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=99.35 E-value=5.9e-13 Score=153.47 Aligned_cols=148 Identities=20% Similarity=0.346 Sum_probs=119.4
Q ss_pred CCCCCEEEEEEccCCcEEEEEEecCCCCCC---------------------CCCCcccCCccchhHHHHHHHHHhcCCcE
Q 004105 205 LVAGDSVLFIWNEKNQLLLGIRRAIRPPTV---------------------MPSSVLSSDSMHIGLLAAAAHAAATNSCF 263 (773)
Q Consensus 205 L~aGDsVvF~R~~~G~L~VGIRRa~r~~~~---------------------~pssv~s~~sm~~gvlaaAa~aaa~~~~F 263 (773)
.+.||.|+.+|.+..++.-.+|+.++.-++ .|.+.-+-=.|.+.|+..|.++ -+..|
T Consensus 874 pQmgDEViyfrQghqeyl~~~~~n~~~~~~~~p~~~~~v~~~kv~kl~~~~y~~~~~s~c~m~l~~idp~s~~--~~k~F 951 (1113)
T KOG0644|consen 874 PQMGDEVIYFRQGHQEYLEAVRLNNIELNNKEPWNKMAVEICKVEKLVYITYPGSGDSCCKMKLAVIDPASKL--MDKSF 951 (1113)
T ss_pred ccccceeehhhhhhHHHHhhhhhccccccccCcccccchhhheeeeeeeeeccCCCcchheeeeeeecchhhh--hhccc
Confidence 458999999998766666666665543221 1222233336888899888755 56799
Q ss_pred EEEEecCCCCCcceeehhHHHHhhhcCCCccccEEEEee--eccccccceeeEEEEEeccCCCCCCCCCCccceeeccCC
Q 004105 264 TVFFNPRASPSEFVIPLTKYVKAVFHTRVSVGMRFRMLF--ETEESSVRRYMGTITGISDLDPVRWSNSHWRSVKVGWDE 341 (773)
Q Consensus 264 ~V~Y~PRas~sEFVVp~~kyvkA~~~~~ws~GMRFrM~f--EtEDss~rr~~GTI~gvsd~Dp~rWp~S~WR~LqV~WDe 341 (773)
.+.|......+||+|.+..|..|+. ++|.++++||..+ ++|| .-+||.|+|.++.+..| .+|+|+|+|..|+||.
T Consensus 952 ~ltlpdlv~fpDFlV~rsrYd~AiQ-rnW~~~d~crvwwrda~~e-~g~WWeG~ils~~pksp-~fpdSpwery~v~~~~ 1028 (1113)
T KOG0644|consen 952 KLTLPDLVTFPDFLVERSRYDAAIQ-RNWTCRDKCRVWWRDAGEE-DGAWWEGRILSVKPKSP-DFPDSPWERYIVRYDN 1028 (1113)
T ss_pred eeecccccCcchhhhhhhhHHHHHh-hccccccceeEEEccCCCc-CCceeeeeeeeccCCCC-CCCCCcceeEEEEecC
Confidence 9999999999999999999999986 8999999999988 3333 24799999999999887 9999999999999999
Q ss_pred CCCCCCCCCcccccceeCCC
Q 004105 342 STAGERQPRVSLWEIEPLTT 361 (773)
Q Consensus 342 ~~~~~~~~RVSPWeIEpv~~ 361 (773)
.+. +.-||||.|++..
T Consensus 1029 ~e~----~~~spwe~~~i~d 1044 (1113)
T KOG0644|consen 1029 TET----ELHSPWEMEPIPD 1044 (1113)
T ss_pred Ccc----cccCccccCCCcc
Confidence 975 7789999999987
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=98.39 E-value=1.7e-06 Score=84.80 Aligned_cols=89 Identities=26% Similarity=0.374 Sum_probs=60.7
Q ss_pred ceeEEEeecccCCCCCC----ceeeehhhhhhhCCCCCC-CCCCCceEEEEEecCC--CeEEEEEEEcCC------CCce
Q 004105 124 TNYFCKTLTASDTSTHG----GFSVPRRAAEKVFPSLDF-SLQPPAQELIARDLHD--VEWKFRHIFRGQ------PKRH 190 (773)
Q Consensus 124 ~~~F~K~LT~SDv~~~g----rfsVPk~~AE~~FPpLd~-~~~~p~q~L~~~Dl~G--~~W~FR~iyrg~------prrh 190 (773)
...|+|.|++.|++..| |+-|||..++.+||.+.. +..+|...|.+++..| ..|+||+||.|+ ...|
T Consensus 7 ~~~~~K~LSaNDtGaTGgHQaGiyIpk~~~~~lFp~~~~~~~~Np~~~~~~~~~s~~~~~~~~r~iYYnn~~~~gTRNE~ 86 (156)
T PF09217_consen 7 WAIYCKRLSANDTGATGGHQAGIYIPKSAAELLFPSINHTKEENPDIWLKARWQSHFVTDSQVRFIYYNNRLFGGTRNEY 86 (156)
T ss_dssp EEEEEEE--CCCCTTTSSS--EEEE-HHHHHHH-GGG-SSSSSS-EEEEEEEETTTT---EEEEEEEE-CCCTTSS--EE
T ss_pred eEEEEEEccCCCCCCcCcccceeEecccHHHHhCCCCCcccccCCceeEEEEECCCCccceeEEEEEEcccccCCCcCce
Confidence 56799999999999875 799999999999998766 6678999999999988 669999999977 6778
Q ss_pred eec--ccchhhhcccCCCCCCEEEEE
Q 004105 191 LLT--TGWSVFVSAKRLVAGDSVLFI 214 (773)
Q Consensus 191 lLT--tGWs~FV~~KkL~aGDsVvF~ 214 (773)
.|| +|=..|.+. =..||.+||-
T Consensus 87 RIT~~G~~~~~~~~--~~tGaL~vla 110 (156)
T PF09217_consen 87 RITRFGRGFPLQNP--ENTGALLVLA 110 (156)
T ss_dssp EEE---TTSGGG-G--GGTT-EEEEE
T ss_pred EEeeecCCCccCCc--cccccEEEEE
Confidence 896 332333332 2478887776
No 6
>PF03754 DUF313: Domain of unknown function (DUF313) ; InterPro: IPR005508 This is a family of proteins from Arabidopsis thaliana (Mouse-ear cress) with uncharacterised function.
Probab=97.72 E-value=6.9e-05 Score=70.75 Aligned_cols=81 Identities=22% Similarity=0.267 Sum_probs=62.7
Q ss_pred CCCceeEEEeecccCCCCC-CceeeehhhhhhhCCCCCC------------CCCCCceEEEEEecCCCeEEEEEEEcCC-
Q 004105 121 KQPTNYFCKTLTASDTSTH-GGFSVPRRAAEKVFPSLDF------------SLQPPAQELIARDLHDVEWKFRHIFRGQ- 186 (773)
Q Consensus 121 ~~~~~~F~K~LT~SDv~~~-grfsVPk~~AE~~FPpLd~------------~~~~p~q~L~~~Dl~G~~W~FR~iyrg~- 186 (773)
..+...++|+|++||++.+ .||+||-..... ...|.. ....-+..+.+.|..++.|..++..|..
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 4457899999999999885 899999875422 122221 1234588999999999999999999954
Q ss_pred --CCceeecccchhhhcc
Q 004105 187 --PKRHLLTTGWSVFVSA 202 (773)
Q Consensus 187 --prrhlLTtGWs~FV~~ 202 (773)
.-.|+|++||..+|+.
T Consensus 97 ~~~~~YvL~~gWn~VV~~ 114 (114)
T PF03754_consen 97 NGTSNYVLNSGWNKVVED 114 (114)
T ss_pred CCceEEEEEcChHhhccC
Confidence 5679999999998863
No 7
>PF00564 PB1: PB1 domain; InterPro: IPR000270 The Phox and Bem1p domain, is present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.; GO: 0005515 protein binding; PDB: 1IPG_A 1IP9_A 2KFK_A 1WMH_A 1VD2_A 1WI0_A 1OEY_C 1PQS_A 1Q1O_A 1TZ1_A ....
Probab=96.68 E-value=0.004 Score=53.69 Aligned_cols=56 Identities=27% Similarity=0.554 Sum_probs=48.2
Q ss_pred EEEeccccceeecccCCCCCHHHHHHHHHhhhCCCCccCCCCCCccEEEEEeCCCCEEEeccc
Q 004105 694 VKVYKSGSVGRSLDISRFSSYNELREELGQMFGIEGKFEDPLRSGWQLVFVDRENDVLLLGDD 756 (773)
Q Consensus 694 VKV~m~G~iGRkiDL~~f~sY~eL~~~L~~MFg~~g~l~d~~~s~~~lvYeD~EGD~mLVGDv 756 (773)
+|++-.|.+=|.+.+..--+|++|+..++..|++. ...+++.|.|.||||..+.++
T Consensus 4 vK~~~~~~~~~~~~~~~~~s~~~L~~~i~~~~~~~-------~~~~~l~Y~D~dgD~V~i~sd 59 (84)
T PF00564_consen 4 VKVRYGGDIRRIISLPSDVSFDDLRSKIREKFGLL-------DEDFQLKYKDEDGDLVTISSD 59 (84)
T ss_dssp EEEEETTEEEEEEEECSTSHHHHHHHHHHHHHTTS-------TSSEEEEEEETTSSEEEESSH
T ss_pred EEEEECCeeEEEEEcCCCCCHHHHHHHHHHHhCCC-------CccEEEEeeCCCCCEEEeCCH
Confidence 78888886666788888889999999999999986 246999999999999988643
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=95.86 E-value=0.025 Score=48.82 Aligned_cols=54 Identities=28% Similarity=0.556 Sum_probs=44.3
Q ss_pred EEEeccccceeecccCCCCCHHHHHHHHHhhhCCCCccCCCCCCccEEEEEeCCCCEEEecc
Q 004105 694 VKVYKSGSVGRSLDISRFSSYNELREELGQMFGIEGKFEDPLRSGWQLVFVDRENDVLLLGD 755 (773)
Q Consensus 694 VKV~m~G~iGRkiDL~~f~sY~eL~~~L~~MFg~~g~l~d~~~s~~~lvYeD~EGD~mLVGD 755 (773)
|||+- |.-=|.+-+..--+|.+|++++.+.|++.. ..++|-|+|.||||..+.+
T Consensus 4 vK~~~-~~~~~~~~~~~~~s~~dL~~~i~~~~~~~~-------~~~~l~Y~Dedgd~v~l~s 57 (81)
T smart00666 4 VKLRY-GGETRRLSVPRDISFEDLRSKVAKRFGLDN-------QSFTLKYQDEDGDLVSLTS 57 (81)
T ss_pred EEEEE-CCEEEEEEECCCCCHHHHHHHHHHHhCCCC-------CCeEEEEECCCCCEEEecC
Confidence 57766 545577778888899999999999999753 4689999999999987764
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=95.52 E-value=0.039 Score=49.44 Aligned_cols=54 Identities=20% Similarity=0.395 Sum_probs=41.6
Q ss_pred EEEeccccceeecccCCCCCHHHHHHHHHhhhCCCCccCCCCCCccEEEEEeCCCCEEEec
Q 004105 694 VKVYKSGSVGRSLDISRFSSYNELREELGQMFGIEGKFEDPLRSGWQLVFVDRENDVLLLG 754 (773)
Q Consensus 694 VKV~m~G~iGRkiDL~~f~sY~eL~~~L~~MFg~~g~l~d~~~s~~~lvYeD~EGD~mLVG 754 (773)
|||.-.|.+ +.+-+..--+|++|++++.++|++.. .++++|-|.|.||||.++-
T Consensus 3 vK~~~~~d~-~r~~l~~~~~~~~L~~~i~~r~~~~~------~~~f~LkY~Ddegd~v~lt 56 (82)
T cd06407 3 VKATYGEEK-IRFRLPPSWGFTELKQEIAKRFKLDD------MSAFDLKYLDDDEEWVLLT 56 (82)
T ss_pred EEEEeCCeE-EEEEcCCCCCHHHHHHHHHHHhCCCC------CCeeEEEEECCCCCeEEee
Confidence 677777742 33444445599999999999999852 3679999999999998763
No 10
>cd06396 PB1_NBR1 The PB1 domain is an essential part of NBR1 protein, next to BRCA1, a scaffold protein mediating specific protein-protein interaction with both titin protein kinase and with another scaffold protein p62. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The NBR1 protein contains a type I PB1 domain.
Probab=95.41 E-value=0.043 Score=49.49 Aligned_cols=52 Identities=23% Similarity=0.346 Sum_probs=43.9
Q ss_pred EEEeccc-cceeecccCCCCCHHHHHHHHHhhhCCCCccCCCCCCccEEEEEeCCCCEEEec
Q 004105 694 VKVYKSG-SVGRSLDISRFSSYNELREELGQMFGIEGKFEDPLRSGWQLVFVDRENDVLLLG 754 (773)
Q Consensus 694 VKV~m~G-~iGRkiDL~~f~sY~eL~~~L~~MFg~~g~l~d~~~s~~~lvYeD~EGD~mLVG 754 (773)
|||.--| -+--+++-+.--+|.+|..+++++|++. .++|-|.|.||||.++-
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 6888878 4555677766779999999999999997 48999999999998863
No 11
>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=95.32 E-value=0.031 Score=50.82 Aligned_cols=49 Identities=29% Similarity=0.388 Sum_probs=38.6
Q ss_pred ceeec--ccCCCCCHHHHHHHHHhhhCCCCccCCCCCCccEEEEEeCCCCEEEec
Q 004105 702 VGRSL--DISRFSSYNELREELGQMFGIEGKFEDPLRSGWQLVFVDRENDVLLLG 754 (773)
Q Consensus 702 iGRki--DL~~f~sY~eL~~~L~~MFg~~g~l~d~~~s~~~lvYeD~EGD~mLVG 754 (773)
-||.+ -+....|+.+|++++.+-||++... ...++|-|.|.||||.|+-
T Consensus 9 ~GrvhRf~~~~s~~~~~L~~~I~~Rl~~d~~~----~~~~~L~YlDDEgD~VllT 59 (86)
T cd06409 9 KGRVHRFRLRPSESLEELRTLISQRLGDDDFE----THLYALSYVDDEGDIVLIT 59 (86)
T ss_pred CCCEEEEEecCCCCHHHHHHHHHHHhCCcccc----CCcccEEEEcCCCCEEEEe
Confidence 45443 3344789999999999999987531 4679999999999999864
No 12
>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=95.19 E-value=0.063 Score=46.01 Aligned_cols=54 Identities=24% Similarity=0.553 Sum_probs=42.7
Q ss_pred EEEeccccceeecccC-CCCCHHHHHHHHHhhhCCCCccCCCCCCccEEEEEeCCCCEEEecc
Q 004105 694 VKVYKSGSVGRSLDIS-RFSSYNELREELGQMFGIEGKFEDPLRSGWQLVFVDRENDVLLLGD 755 (773)
Q Consensus 694 VKV~m~G~iGRkiDL~-~f~sY~eL~~~L~~MFg~~g~l~d~~~s~~~lvYeD~EGD~mLVGD 755 (773)
|||+-.|.+= .+-+. .--+|.+|++.|.+.|++.. ..+.+.|.|.||||..+.+
T Consensus 3 vK~~~~~~~~-~~~~~~~~~s~~~L~~~i~~~~~~~~-------~~~~l~y~D~e~d~v~l~s 57 (81)
T cd05992 3 VKVKYGGEIR-RFVVVSRSISFEDLRSKIAEKFGLDA-------VSFKLKYPDEDGDLVTISS 57 (81)
T ss_pred EEEEecCCCE-EEEEecCCCCHHHHHHHHHHHhCCCC-------CcEEEEeeCCCCCEEEeCC
Confidence 6777776432 23333 78899999999999999863 4689999999999998876
No 13
>cd06398 PB1_Joka2 The PB1 domain is present in the Nicotiana plumbaginifolia Joka2 protein which interacts with sulfur stress inducible UP9 protein. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module
Probab=94.85 E-value=0.086 Score=48.22 Aligned_cols=56 Identities=25% Similarity=0.405 Sum_probs=43.8
Q ss_pred EEEecccc-ceeecccC---CCCCHHHHHHHHHhhhCCCCccCCCCCCccEEEEEeCCCCEEEecc
Q 004105 694 VKVYKSGS-VGRSLDIS---RFSSYNELREELGQMFGIEGKFEDPLRSGWQLVFVDRENDVLLLGD 755 (773)
Q Consensus 694 VKV~m~G~-iGRkiDL~---~f~sY~eL~~~L~~MFg~~g~l~d~~~s~~~lvYeD~EGD~mLVGD 755 (773)
|||.-+|. +=-++++. .--+|++|++++++.|.+.. ..+++|.|.|.||||..+-+
T Consensus 3 vKv~y~~~~rRf~l~~~~~~~d~~~~~L~~kI~~~f~l~~------~~~~~l~Y~Dedgd~V~l~~ 62 (91)
T cd06398 3 VKVKYGGTLRRFTFPVAENQLDLNMDGLREKVEELFSLSP------DADLSLTYTDEDGDVVTLVD 62 (91)
T ss_pred EEEEeCCEEEEEEeccccccCCCCHHHHHHHHHHHhCCCC------CCcEEEEEECCCCCEEEEcc
Confidence 78888884 33345543 45699999999999998742 36799999999999998754
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=91.02 E-value=0.57 Score=42.38 Aligned_cols=54 Identities=20% Similarity=0.326 Sum_probs=43.5
Q ss_pred EEEecccccee-ecccCCCCCHHHHHHHHHhhhCCCCccCCCCCCccEEEEEeCCCCEEEec
Q 004105 694 VKVYKSGSVGR-SLDISRFSSYNELREELGQMFGIEGKFEDPLRSGWQLVFVDRENDVLLLG 754 (773)
Q Consensus 694 VKV~m~G~iGR-kiDL~~f~sY~eL~~~L~~MFg~~g~l~d~~~s~~~lvYeD~EGD~mLVG 754 (773)
||.+-++.+=| ++|-....+|+|++.-|++|+.+.+ ..+.|-|.|.+||.+-+-
T Consensus 3 VKSkfdaEfRRFsl~r~~~~~f~ef~~ll~~lH~l~~-------~~f~i~Y~D~~gDLLPIn 57 (80)
T cd06403 3 VKSKFDAEFRRFSLDRNKPGKFEDFYKLLEHLHHIPN-------VDFLIGYTDPHGDLLPIN 57 (80)
T ss_pred eecccCCeEEEEEeccccCcCHHHHHHHHHHHhCCCC-------CcEEEEEeCCCCCEeccc
Confidence 56666665443 6777788999999999999999874 469999999999998653
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=90.24 E-value=0.7 Score=42.09 Aligned_cols=53 Identities=26% Similarity=0.323 Sum_probs=41.6
Q ss_pred EEEeccccce-eecccCCCCCHHHHHHHHHhhhCCCCccCCCCCCccEEEEEeCCCCEEEec
Q 004105 694 VKVYKSGSVG-RSLDISRFSSYNELREELGQMFGIEGKFEDPLRSGWQLVFVDRENDVLLLG 754 (773)
Q Consensus 694 VKV~m~G~iG-RkiDL~~f~sY~eL~~~L~~MFg~~g~l~d~~~s~~~lvYeD~EGD~mLVG 754 (773)
+|++-.|.|- -.+|. .-+|++|.+++..||.+. ....+++.|.|.|||-.-+.
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 6888888544 34554 778999999999999874 23569999999999976543
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=88.84 E-value=1.3 Score=40.24 Aligned_cols=57 Identities=18% Similarity=0.251 Sum_probs=41.1
Q ss_pred EEEeccccceeecccCCCC-CHHHHHHHHHhhhCCCCccCCCCCCccEEEEEeCCCCEEEecc
Q 004105 694 VKVYKSGSVGRSLDISRFS-SYNELREELGQMFGIEGKFEDPLRSGWQLVFVDRENDVLLLGD 755 (773)
Q Consensus 694 VKV~m~G~iGRkiDL~~f~-sY~eL~~~L~~MFg~~g~l~d~~~s~~~lvYeD~EGD~mLVGD 755 (773)
+|+.-.|.|=| +-+..-. +|.+|+..+.+.|...- |......+-|.|.|||+.-+.+
T Consensus 3 iK~~~g~DiR~-~~~~~~~~t~~~L~~~v~~~F~~~~----~~~~~flIKYkD~dGDlVTIts 60 (81)
T cd06401 3 LKAQLGDDIRR-IPIHNEDITYDELLLMMQRVFRGKL----GSSDDVLIKYKDEDGDLITIFD 60 (81)
T ss_pred EEEEeCCeEEE-EeccCccccHHHHHHHHHHHhcccc----CCcccEEEEEECCCCCEEEecc
Confidence 56655555544 4444322 99999999999998431 3345799999999999987765
No 17
>cd06402 PB1_p62 The PB1 domain is an essential part of p62 scaffold protein (alias sequestosome 1,SQSTM) involved in cell signaling, receptor internalization, and protein turnover. The PB1 domain is a modular domain mediating specific protein-protein interaction which play roles in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.
Probab=88.23 E-value=1.6 Score=39.98 Aligned_cols=56 Identities=29% Similarity=0.403 Sum_probs=42.2
Q ss_pred EEEEeccc----ccee--ecccCCCCCHHHHHHHHHhhhCCCCccCCCCCCccEEEEEeCCCCEEEec
Q 004105 693 FVKVYKSG----SVGR--SLDISRFSSYNELREELGQMFGIEGKFEDPLRSGWQLVFVDRENDVLLLG 754 (773)
Q Consensus 693 fVKV~m~G----~iGR--kiDL~~f~sY~eL~~~L~~MFg~~g~l~d~~~s~~~lvYeD~EGD~mLVG 754 (773)
.||.|..| +==| +||-....+|++|++.+.++|... . ...+++-|.|.|||..-+.
T Consensus 2 ~vkayl~~~~~~~EIRRf~l~~~~~~s~~~L~~~V~~~f~~l---~---~~~ftlky~DeeGDlvtIs 63 (87)
T cd06402 2 TVKAYLLGKDANAEIRRFAIDEDVSTSYEYLVEKVAAVFPSL---R---GKNFQLFWKDEEGDLVAFS 63 (87)
T ss_pred eEEEeecCCCCccceEEEEecCCCCcCHHHHHHHHHHHcccc---C---CCcEEEEEECCCCCEEeec
Confidence 68888877 2224 455577789999999999999532 1 2579999999999987654
No 18
>cd06397 PB1_UP1 Uncharacterized protein 1. The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions.
Probab=87.13 E-value=1.4 Score=40.05 Aligned_cols=53 Identities=15% Similarity=0.289 Sum_probs=41.3
Q ss_pred EEeccccceeecccCCCCCHHHHHHHHHhhhCCCCccCCCCCCccEEEEEeCCCCEEEecc
Q 004105 695 KVYKSGSVGRSLDISRFSSYNELREELGQMFGIEGKFEDPLRSGWQLVFVDRENDVLLLGD 755 (773)
Q Consensus 695 KV~m~G~iGRkiDL~~f~sY~eL~~~L~~MFg~~g~l~d~~~s~~~lvYeD~EGD~mLVGD 755 (773)
||+- |.--|++....-=+|.+|++.|+.+|.+.. .+ ..++|.|.+||..-+-|
T Consensus 4 Kv~~-~g~~RRf~~~~~pt~~~L~~kl~~Lf~lp~------~~-~~vtYiDeD~D~ITlss 56 (82)
T cd06397 4 KSSF-LGDTRRIVFPDIPTWEALASKLENLYNLPE------IK-VGVTYIDNDNDEITLSS 56 (82)
T ss_pred EEEe-CCceEEEecCCCccHHHHHHHHHHHhCCCh------hH-eEEEEEcCCCCEEEecc
Confidence 6633 334577777778899999999999999863 23 89999999999876544
No 19
>cd06408 PB1_NoxR The PB1 domain is present in the Epichloe festucae NoxR protein (NADPH oxidase regulator), a key regulator of NADPH oxidase isoform, NoxA. NoxA is essential for growth control of the fungal endophyte in plant tissue in the process of symbiotic interaction between a fungi and its plant host. The Epichloe festucae p67(phox)-like regulator, NoxR, dispensable in culture but essential in plants for the symbiotic interaction. Plants infected with a noxR deletion mutant show severe stunting and premature senescence, whereas hyphae in the meristematic tissues show increased branching leading to increased fungal colonization of pseudostem and leaf blade tissue. The PB1 domain is a modular domain mediating specific protein-protein interactions which a play role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is
Probab=81.42 E-value=3.6 Score=37.75 Aligned_cols=53 Identities=21% Similarity=0.414 Sum_probs=43.0
Q ss_pred EEEEeccccceeecccCCCCCHHHHHHHHHhhhCCCCccCCCCCCccEEEEEeCCCCEEEecc
Q 004105 693 FVKVYKSGSVGRSLDISRFSSYNELREELGQMFGIEGKFEDPLRSGWQLVFVDRENDVLLLGD 755 (773)
Q Consensus 693 fVKV~m~G~iGRkiDL~~f~sY~eL~~~L~~MFg~~g~l~d~~~s~~~lvYeD~EGD~mLVGD 755 (773)
=|||+-.|. -|-|-+..--+|++|.+++..+|++. ...++-|.|. ||..-++|
T Consensus 4 kVKv~~~~D-v~~i~v~~~i~f~dL~~kIrdkf~~~--------~~~~iKykDE-GD~iti~s 56 (86)
T cd06408 4 RVKVHAQDD-TRYIMIGPDTGFADFEDKIRDKFGFK--------RRLKIKMKDD-GDMITMGD 56 (86)
T ss_pred EEEEEecCc-EEEEEcCCCCCHHHHHHHHHHHhCCC--------CceEEEEEcC-CCCccccC
Confidence 478887774 45566666677999999999999984 2689999999 99887775
No 20
>PRK10737 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=69.07 E-value=15 Score=38.34 Aligned_cols=103 Identities=21% Similarity=0.223 Sum_probs=63.4
Q ss_pred CCCCCEEEE-E--EccCCcEEEEEEecCCCCCCCCCCcccCCccchhHHHHHHHHHhcCCcEEEEEecCCC------CCc
Q 004105 205 LVAGDSVLF-I--WNEKNQLLLGIRRAIRPPTVMPSSVLSSDSMHIGLLAAAAHAAATNSCFTVFFNPRAS------PSE 275 (773)
Q Consensus 205 L~aGDsVvF-~--R~~~G~L~VGIRRa~r~~~~~pssv~s~~sm~~gvlaaAa~aaa~~~~F~V~Y~PRas------~sE 275 (773)
+..|+.|.+ | |.++|+++---+ . ..|...+--...-+--|.+|....+.|..|+|.--|-.. -.-
T Consensus 3 I~~~~vV~l~Y~l~~~dG~v~dst~-~-----~~Pl~~~~G~g~lipglE~aL~G~~~Gd~~~v~l~peeAyGe~d~~lV 76 (196)
T PRK10737 3 VAKDLVVSLAYQVRTEDGVLVDESP-V-----SAPLDYLHGHGSLISGLETALEGHEVGDKFDVAVGANDAYGQYDENLV 76 (196)
T ss_pred cCCCCEEEEEEEEEeCCCCEEEecC-C-----CCCeEEEeCCCcchHHHHHHHcCCCCCCEEEEEEChHHhcCCCChHHE
Confidence 456777766 3 345777643221 1 234444433333334467788888889999998665432 234
Q ss_pred ceeehhHHHHhhhcCCCccccEEEEeeeccccccceeeEEEEEecc
Q 004105 276 FVIPLTKYVKAVFHTRVSVGMRFRMLFETEESSVRRYMGTITGISD 321 (773)
Q Consensus 276 FVVp~~kyvkA~~~~~ws~GMRFrM~fEtEDss~rr~~GTI~gvsd 321 (773)
..||++.|.. . ....+||||.+ ++++. ...++|+.|.+
T Consensus 77 ~~vpr~~F~~-~--~~l~~G~~~~~--~~~~G---~~~~~V~ev~~ 114 (196)
T PRK10737 77 QRVPKDVFMG-V--DELQVGMRFLA--ETDQG---PVPVEITAVED 114 (196)
T ss_pred EEecHHHCCC-c--cCCCCCCEEEE--eCCCC---cEEEEEEEEcC
Confidence 5788777632 2 24899999886 45553 35889999975
No 21
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=55.15 E-value=9.2 Score=47.20 Aligned_cols=67 Identities=24% Similarity=0.427 Sum_probs=46.8
Q ss_pred CCCCCCCEEEEecCcchhhhcccccccccc--cCCCCCCCCCcceeEEeeeeecccCCCcceeEeeeeeeC
Q 004105 34 SLPTVGTRVVYFPQGHSEQVAATTNKEVDS--HIPNYPNLPPQLICQLHNVTMHADVETDEVYAQMTLQPL 102 (773)
Q Consensus 34 ~lP~vgs~V~YFPQGH~Eq~~as~~~~~~~--~~p~~~~lP~~i~C~V~~V~l~AD~~TDEVyAqi~L~P~ 102 (773)
-||..|..|.||-|||-|-+.+....+.+. ..| -++-..=+|.|..+..--=+-...-..+|+|.=+
T Consensus 872 yipQmgDEViyfrQghqeyl~~~~~n~~~~~~~~p--~~~~~v~~~kv~kl~~~~y~~~~~s~c~m~l~~i 940 (1113)
T KOG0644|consen 872 YIPQMGDEVIYFRQGHQEYLEAVRLNNIELNNKEP--WNKMAVEICKVEKLVYITYPGSGDSCCKMKLAVI 940 (1113)
T ss_pred ccccccceeehhhhhhHHHHhhhhhccccccccCc--ccccchhhheeeeeeeeeccCCCcchheeeeeee
Confidence 589999999999999999998864322221 111 0333445799888877777777777777777654
No 22
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=52.30 E-value=21 Score=29.39 Aligned_cols=28 Identities=14% Similarity=0.259 Sum_probs=24.0
Q ss_pred CCccccEEEEeeeccccccceeeEEEEEecc
Q 004105 291 RVSVGMRFRMLFETEESSVRRYMGTITGISD 321 (773)
Q Consensus 291 ~ws~GMRFrM~fEtEDss~rr~~GTI~gvsd 321 (773)
.|++|+++-..++.++ .||.|+|+.+..
T Consensus 2 ~~~~G~~Ve~~~~~~~---~W~~a~V~~~~~ 29 (61)
T smart00743 2 DFKKGDRVEVFSKEED---SWWEAVVTKVLG 29 (61)
T ss_pred CcCCCCEEEEEECCCC---EEEEEEEEEECC
Confidence 5899999999996544 899999999964
No 23
>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=44.08 E-value=27 Score=27.88 Aligned_cols=38 Identities=13% Similarity=0.163 Sum_probs=27.2
Q ss_pred CCCCceeecccchhhhcccCCCCCCEEEEEEccCCcEEEEE
Q 004105 185 GQPKRHLLTTGWSVFVSAKRLVAGDSVLFIWNEKNQLLLGI 225 (773)
Q Consensus 185 g~prrhlLTtGWs~FV~~KkL~aGDsVvF~R~~~G~L~VGI 225 (773)
|++..-.|-. .|.++.+|.+||.|.|.-+++|++.|--
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 4444444443 5677889999999999999988776643
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=41.10 E-value=77 Score=27.39 Aligned_cols=56 Identities=18% Similarity=0.240 Sum_probs=42.9
Q ss_pred cEEEEeccccc----eeecccCCCCCHHHHHHHHHhhhCCCCccCCCCCCccEEE-EEeCCCCEEE
Q 004105 692 TFVKVYKSGSV----GRSLDISRFSSYNELREELGQMFGIEGKFEDPLRSGWQLV-FVDRENDVLL 752 (773)
Q Consensus 692 ~fVKV~m~G~i----GRkiDL~~f~sY~eL~~~L~~MFg~~g~l~d~~~s~~~lv-YeD~EGD~mL 752 (773)
.++|||....- -+.|-++...+-.|++..+.+.|++.+ ....|.|+ +.-..|--..
T Consensus 3 ~~lrVy~~~~~~~~~~k~i~v~~~tTa~evi~~~l~k~~l~~-----~~~~y~L~~~~~~~~~er~ 63 (93)
T PF00788_consen 3 GVLRVYDGDGSPGSTYKTIKVSSSTTAREVIEMALEKFGLAE-----DPSDYCLVEVEESGGEERP 63 (93)
T ss_dssp EEEEEEETTSSSCCSEEEEEEETTSBHHHHHHHHHHHTTTSS-----SGGGEEEEEEECTTTEEEE
T ss_pred eEEEEEcCCCCCCccEEEEEECCCCCHHHHHHHHHHHhCCCC-----CCCCEEEEEEEcCCCEEEE
Confidence 58999998733 799999999999999999999999932 24579996 5444444333
No 25
>COG1047 SlpA FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]
Probab=35.18 E-value=1.9e+02 Score=30.01 Aligned_cols=105 Identities=20% Similarity=0.269 Sum_probs=65.6
Q ss_pred CCCCCCEEEE---EEccCCcEEEEEEecCCCCCCCCCCcccCCccchhHHHHHHHHHhcCCcEEEEEecCCCCCcc----
Q 004105 204 RLVAGDSVLF---IWNEKNQLLLGIRRAIRPPTVMPSSVLSSDSMHIGLLAAAAHAAATNSCFTVFFNPRASPSEF---- 276 (773)
Q Consensus 204 kL~aGDsVvF---~R~~~G~L~VGIRRa~r~~~~~pssv~s~~sm~~gvlaaAa~aaa~~~~F~V~Y~PRas~sEF---- 276 (773)
++..||.|.+ .|.++|+++=--+- ...|..++-.+..-+.-|.+|.....-|..|+|.--|-..-.|+
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 4567788876 23455655422111 11233444333333445788888889999999998886644444
Q ss_pred --eeehhHHHHhhhcCCCccccEEEEeeeccccccceeeEEEEEecc
Q 004105 277 --VIPLTKYVKAVFHTRVSVGMRFRMLFETEESSVRRYMGTITGISD 321 (773)
Q Consensus 277 --VVp~~kyvkA~~~~~ws~GMRFrM~fEtEDss~rr~~GTI~gvsd 321 (773)
.||+++|.+.- ...+||+|.+ ++++ .-.-|+|+.|..
T Consensus 77 vq~vp~~~F~~~~---~~~vGm~~~~--~~~~---~~~~~~V~~V~~ 115 (174)
T COG1047 77 VQRVPRDEFQGVG---ELEVGMEVEA--EGGD---GEIPGVVTEVSG 115 (174)
T ss_pred eEEecHHHhCcCC---CCCCCcEEEE--cCCC---ceeeEEEEEEcC
Confidence 56766653321 5899999885 5555 556799999974
No 26
>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=34.69 E-value=62 Score=25.93 Aligned_cols=52 Identities=15% Similarity=0.230 Sum_probs=36.7
Q ss_pred CCccccEEEEeeeccccccceeeEEEEEeccCCCCCCCCCCccceeeccCCCCCCCCCCCcccccceeC
Q 004105 291 RVSVGMRFRMLFETEESSVRRYMGTITGISDLDPVRWSNSHWRSVKVGWDESTAGERQPRVSLWEIEPL 359 (773)
Q Consensus 291 ~ws~GMRFrM~fEtEDss~rr~~GTI~gvsd~Dp~rWp~S~WR~LqV~WDe~~~~~~~~RVSPWeIEpv 359 (773)
.|.+|..+...+ .+. .||.|+|+++.. + ..+.|.-++-+. .+-|...+|-++
T Consensus 2 ~~~~G~~~~a~~-~d~---~wyra~I~~~~~-------~---~~~~V~f~D~G~---~~~v~~~~l~~l 53 (57)
T smart00333 2 TFKVGDKVAARW-EDG---EWYRARIIKVDG-------E---QLYEVFFIDYGN---EEVVPPSDLRPL 53 (57)
T ss_pred CCCCCCEEEEEe-CCC---CEEEEEEEEECC-------C---CEEEEEEECCCc---cEEEeHHHeecC
Confidence 588999999999 444 899999999974 2 456777776443 244666665554
No 27
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=31.38 E-value=61 Score=30.04 Aligned_cols=27 Identities=22% Similarity=0.303 Sum_probs=21.8
Q ss_pred hhcccCCCCCCEEEEEEccCCcEEEEE
Q 004105 199 FVSAKRLVAGDSVLFIWNEKNQLLLGI 225 (773)
Q Consensus 199 FV~~KkL~aGDsVvF~R~~~G~L~VGI 225 (773)
|.-...|++||.|+.+|.+.|+-++=+
T Consensus 71 i~~~~~Lk~GD~V~ll~~~~gQ~yiVl 97 (100)
T PF10844_consen 71 ITFTDGLKVGDKVLLLRVQGGQKYIVL 97 (100)
T ss_pred EEEecCCcCCCEEEEEEecCCCEEEEE
Confidence 445678999999999999888866544
No 28
>TIGR01439 lp_hng_hel_AbrB looped-hinge helix DNA binding domain, AbrB family. This DNA-binding domain family includes AbrB, a transition state regulator in Bacillus subtilis, whose DNA-binding domain structure in solution was determined by NMR. The domain binds DNA as a dimer in what is termed a looped-hinge helix fold. Some members of the family have two copies of the domain in tandem. The domain is found usually at the N-terminus of a small protein. This model excludes members of family TIGR02609.
Probab=31.24 E-value=58 Score=24.72 Aligned_cols=26 Identities=23% Similarity=0.288 Sum_probs=22.3
Q ss_pred hhhcccCCCCCCEEEEEEccCCcEEE
Q 004105 198 VFVSAKRLVAGDSVLFIWNEKNQLLL 223 (773)
Q Consensus 198 ~FV~~KkL~aGDsVvF~R~~~G~L~V 223 (773)
.|.++-++..||.|.+....+|.|.|
T Consensus 14 ~~r~~l~~~~gd~~~i~~~~~~~l~l 39 (43)
T TIGR01439 14 EIREKLGLKEGDRLEVIRVEDGEIIL 39 (43)
T ss_pred HHHHHcCcCCCCEEEEEEeCCCEEEE
Confidence 68889999999999999887777665
No 29
>KOG3207 consensus Beta-tubulin folding cofactor E [Posttranslational modification, protein turnover, chaperones]
Probab=29.99 E-value=61 Score=38.08 Aligned_cols=43 Identities=28% Similarity=0.693 Sum_probs=30.2
Q ss_pred CccccEEEEeeeccccccceeeEEEEEeccCCCCCCCCCCccceeeccCCCCCCCCC
Q 004105 292 VSVGMRFRMLFETEESSVRRYMGTITGISDLDPVRWSNSHWRSVKVGWDESTAGERQ 348 (773)
Q Consensus 292 ws~GMRFrM~fEtEDss~rr~~GTI~gvsd~Dp~rWp~S~WR~LqV~WDe~~~~~~~ 348 (773)
..+|.|+|.-+|- ...||.|+|.|. ++ +| +.|.||++.-+.+.
T Consensus 3 ~~IG~RvkI~~~~---~Tvr~iG~V~g~--------~~-~w--~GvEWDd~~RGKH~ 45 (505)
T KOG3207|consen 3 MEIGTRVKIGGEI---ATVRYIGEVEGN--------NS-KW--YGVEWDDPVRGKHD 45 (505)
T ss_pred eeccceEEEcCEE---EEEEEEEEEcCC--------CC-cc--eeeEecCCCccccC
Confidence 5689999987653 236777776654 34 45 78999999876553
No 30
>PF01878 EVE: EVE domain; InterPro: IPR002740 The EVE domain is part of the wider PUA domain superfamily. The function of this domain is not known but, given the structural similarities to PUA, is likely to involve RNA binding []. ; PDB: 2G2X_B 2AR1_A 3EOP_A 2EVE_A 2HD9_A 2ZBN_A 1WMM_A 2P5D_A 2GBS_A 1ZCE_A.
Probab=29.00 E-value=54 Score=31.46 Aligned_cols=26 Identities=31% Similarity=0.543 Sum_probs=17.5
Q ss_pred cCCCCCCEEEEEEcc-CCcEEEEEEec
Q 004105 203 KRLVAGDSVLFIWNE-KNQLLLGIRRA 228 (773)
Q Consensus 203 KkL~aGDsVvF~R~~-~G~L~VGIRRa 228 (773)
++++.||.|+||... .++-++|+=+-
T Consensus 38 ~~mk~GD~vifY~s~~~~~~ivai~~V 64 (143)
T PF01878_consen 38 KRMKPGDKVIFYHSGCKERGIVAIGEV 64 (143)
T ss_dssp HC--TT-EEEEEETSSSS-EEEEEEEE
T ss_pred hcCCCCCEEEEEEcCCCCCEEEEEEEE
Confidence 589999999999987 66777776553
No 31
>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=28.99 E-value=97 Score=29.09 Aligned_cols=38 Identities=29% Similarity=0.337 Sum_probs=32.0
Q ss_pred ccCCCCCHHHHHHHHHhhhCCCCccCCCCCCccEEEEEeCCCCEEEe
Q 004105 707 DISRFSSYNELREELGQMFGIEGKFEDPLRSGWQLVFVDRENDVLLL 753 (773)
Q Consensus 707 DL~~f~sY~eL~~~L~~MFg~~g~l~d~~~s~~~lvYeD~EGD~mLV 753 (773)
||+.--+|.+|..-..+-|+.+ +-.|-|.|.|||..-+
T Consensus 23 ~l~~~P~~kdLl~lmr~~f~~~---------dIaLNYrD~EGDLIRl 60 (92)
T cd06399 23 DLSSTPLLKDLLELTRREFQRE---------DIALNYRDAEGDLIRL 60 (92)
T ss_pred ccccCccHHHHHHHHHHHhchh---------heeeeeecCCCCEEEE
Confidence 6778889999999999999865 3589999999998654
No 32
>PF05641 Agenet: Agenet domain; InterPro: IPR008395 This domain is related to the TUDOR domain IPR008191 from INTERPRO []. The function of the agenet domain is unknown. This signature matches one of the two Agenet domains in the FMR proteins [].; GO: 0003723 RNA binding; PDB: 2BKD_N 3O8V_A 3KUF_A 3H8Z_A.
Probab=25.02 E-value=1.2e+02 Score=25.92 Aligned_cols=42 Identities=10% Similarity=0.049 Sum_probs=26.8
Q ss_pred CccccEEEEeeeccccccceeeEEEEEeccCCCCCCCCCCccceeeccCCCC
Q 004105 292 VSVGMRFRMLFETEESSVRRYMGTITGISDLDPVRWSNSHWRSVKVGWDEST 343 (773)
Q Consensus 292 ws~GMRFrM~fEtEDss~rr~~GTI~gvsd~Dp~rWp~S~WR~LqV~WDe~~ 343 (773)
|..|+++-..-+.+.....||.|||+..... + .+.|+.+.-.
T Consensus 1 F~~G~~VEV~s~e~g~~gaWf~a~V~~~~~~-------~---~~~V~Y~~~~ 42 (68)
T PF05641_consen 1 FKKGDEVEVSSDEDGFRGAWFPATVLKENGD-------D---KYLVEYDDLP 42 (68)
T ss_dssp --TT-EEEEEE-SBTT--EEEEEEEEEEETT-----------EEEEEETT-S
T ss_pred CCCCCEEEEEEcCCCCCcEEEEEEEEEeCCC-------c---EEEEEECCcc
Confidence 4689999988765555568999999999752 1 6788886544
No 33
>PF02513 Spin-Ssty: Spin/Ssty Family; InterPro: IPR003671 Spindlin (Spin) and Ssty were first identified for their involvement in gametogenesis. Spindlin was identified as a maternal transcript present in the unfertilised egg and early embryo, and was subsequently shown to interact with the spindle apparatus during oogenesis, and may therefore be important for mitosis []. In addition, spindlin appears to be a target for cell cycle-dependent phosphorylation, and as such may play a role in cell cycle regulation during the transition from gamete to embryo []. Ssty is a multi-copy, Y-linked spermatogenesis-specific transcript that appears to be required for normal spermatogenesis []. Ssty may play an analogous role to spindlin in sperm cells, namely during the transition from sperm cells to early embryo, and in mitosis.; GO: 0007276 gamete generation; PDB: 2NS2_A.
Probab=24.77 E-value=1.2e+02 Score=25.65 Aligned_cols=31 Identities=19% Similarity=0.370 Sum_probs=24.0
Q ss_pred cccEEEEeeeccccccceeeEEEEEeccCCC
Q 004105 294 VGMRFRMLFETEESSVRRYMGTITGISDLDP 324 (773)
Q Consensus 294 ~GMRFrM~fEtEDss~rr~~GTI~gvsd~Dp 324 (773)
+|-|+.-.||.++.++..|.|+|...-+..|
T Consensus 1 vGk~Veh~~~~g~g~~s~w~G~Vl~Qvp~~p 31 (50)
T PF02513_consen 1 VGKRVEHTWEDGDGPKSKWKGMVLHQVPAKP 31 (50)
T ss_dssp TT-EEEEEECTSTS-EEEEEEEEEEE-TTST
T ss_pred CCceEEEEEccCCCcccEEEEEEEEEeecCC
Confidence 5889999999998888888999999877654
No 34
>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=24.70 E-value=68 Score=26.86 Aligned_cols=17 Identities=24% Similarity=0.542 Sum_probs=14.9
Q ss_pred EEEEEeCCCCEEEeccc
Q 004105 740 QLVFVDRENDVLLLGDD 756 (773)
Q Consensus 740 ~lvYeD~EGD~mLVGDv 756 (773)
.++|.|.+|+.+++|+.
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=22.30 E-value=1.7e+02 Score=28.10 Aligned_cols=49 Identities=20% Similarity=0.321 Sum_probs=31.3
Q ss_pred eEEEEEecCCCeEEEEE-----EEc-CCCCceee--cccchhhhcccCCCCCCEEEEEEc
Q 004105 165 QELIARDLHDVEWKFRH-----IFR-GQPKRHLL--TTGWSVFVSAKRLVAGDSVLFIWN 216 (773)
Q Consensus 165 q~L~~~Dl~G~~W~FR~-----iyr-g~prrhlL--TtGWs~FV~~KkL~aGDsVvF~R~ 216 (773)
.++.+.|.+|++=.... +|. ..+=+|+| ..||.. +.++++||.|.|-|+
T Consensus 61 LDiiFld~~g~Vv~i~~~~P~~~~~~~~~a~~VLEl~aG~~~---~~gi~~Gd~v~~~~~ 117 (117)
T PRK03760 61 IDVIFLDSNRRVVDFKTLKPWRIYVPKKPARYIIEGPVGKIR---VLKVEVGDEIEWIDE 117 (117)
T ss_pred eEEEEECCCCeEEEEEeCCCccccCCCccceEEEEeCCChHH---HcCCCCCCEEEEeeC
Confidence 44666666664433211 122 33556888 677755 899999999998763
No 36
>PF06003 SMN: Survival motor neuron protein (SMN); InterPro: IPR010304 This family consists of several eukaryotic survival motor neuron (SMN) proteins. The Survival of Motor Neurons (SMN) protein, the product of the spinal muscular atrophy-determining gene, is part of a large macromolecular complex (SMN complex) that functions in the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs). The SMN complex functions as a specificity factor essential for the efficient assembly of Sm proteins on U snRNAs and likely protects cells from illicit, and potentially deleterious, non-specific binding of Sm proteins to RNAs.; GO: 0003723 RNA binding, 0006397 mRNA processing, 0005634 nucleus, 0005737 cytoplasm; PDB: 1MHN_A 4A4G_A 3S6N_M 4A4E_A 1G5V_A 4A4H_A 4A4F_A 2D9T_A.
Probab=20.82 E-value=96 Score=33.59 Aligned_cols=57 Identities=19% Similarity=0.316 Sum_probs=33.2
Q ss_pred CCCccccEEEEeeeccccccceeeEEEEEeccCCCCCCCCCCccceeeccCCCCCCCCCCCcccccceeCCC
Q 004105 290 TRVSVGMRFRMLFETEESSVRRYMGTITGISDLDPVRWSNSHWRSVKVGWDESTAGERQPRVSLWEIEPLTT 361 (773)
Q Consensus 290 ~~ws~GMRFrM~fEtEDss~rr~~GTI~gvsd~Dp~rWp~S~WR~LqV~WDe~~~~~~~~RVSPWeIEpv~~ 361 (773)
..|.||++.+..+..|. .+|-+||++|..-+ ....|+-++=+ +.+.|+.=+|.+...
T Consensus 67 ~~WkvGd~C~A~~s~Dg---~~Y~A~I~~i~~~~---------~~~~V~f~gYg---n~e~v~l~dL~~~~~ 123 (264)
T PF06003_consen 67 KKWKVGDKCMAVYSEDG---QYYPATIESIDEED---------GTCVVVFTGYG---NEEEVNLSDLKPSEG 123 (264)
T ss_dssp T---TT-EEEEE-TTTS---SEEEEEEEEEETTT---------TEEEEEETTTT---EEEEEEGGGEEETT-
T ss_pred cCCCCCCEEEEEECCCC---CEEEEEEEEEcCCC---------CEEEEEEcccC---CeEeeehhhhccccc
Confidence 57999999999995444 79999999997422 12347776543 234455555555543
Done!