Query 003580
Match_columns 809
No_of_seqs 366 out of 846
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 02:07:46 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003580.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003580hhsearch_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 8.8E-36 1.9E-40 264.0 8.5 83 298-380 1-83 (83)
2 PF02309 AUX_IAA: AUX/IAA fami 100.0 7.2E-35 1.6E-39 296.8 0.0 96 676-772 106-215 (215)
3 PF02362 B3: B3 DNA binding do 99.6 9.9E-16 2.1E-20 136.5 11.1 97 172-273 1-99 (100)
4 KOG0644 Uncharacterized conser 99.5 4.3E-14 9.3E-19 163.5 5.7 148 250-405 874-1044(1113)
5 PF09217 EcoRII-N: Restriction 98.1 1.6E-05 3.5E-10 78.5 9.6 89 169-259 7-110 (156)
6 PF03754 DUF313: Domain of unk 97.4 0.00029 6.2E-09 67.0 6.2 78 169-247 21-114 (114)
7 PF00564 PB1: PB1 domain; Int 96.4 0.0075 1.6E-07 52.6 5.8 67 681-755 3-70 (84)
8 cd06396 PB1_NBR1 The PB1 domai 95.4 0.046 1E-06 49.5 6.6 53 682-742 3-55 (81)
9 smart00666 PB1 PB1 domain. Pho 95.4 0.044 9.5E-07 47.7 6.2 65 682-755 4-69 (81)
10 cd06398 PB1_Joka2 The PB1 doma 95.3 0.053 1.2E-06 49.9 6.8 67 682-756 3-72 (91)
11 cd06407 PB1_NLP A PB1 domain i 95.3 0.049 1.1E-06 49.1 6.4 55 681-742 2-56 (82)
12 cd06409 PB1_MUG70 The MUG70 pr 95.2 0.036 7.8E-07 50.7 5.5 52 690-744 8-61 (86)
13 cd05992 PB1 The PB1 domain is 95.0 0.062 1.4E-06 46.5 6.1 65 682-755 3-69 (81)
14 cd06403 PB1_Par6 The PB1 domai 93.0 0.22 4.7E-06 45.1 5.6 56 682-744 3-59 (80)
15 cd06402 PB1_p62 The PB1 domain 90.9 0.72 1.6E-05 42.4 6.6 54 681-739 2-60 (87)
16 cd06404 PB1_aPKC PB1 domain is 90.6 0.68 1.5E-05 42.3 6.0 52 682-740 3-54 (83)
17 cd06397 PB1_UP1 Uncharacterize 89.0 0.95 2.1E-05 41.2 5.6 52 683-742 4-55 (82)
18 cd06401 PB1_TFG The PB1 domain 87.5 1.9 4E-05 39.4 6.5 58 682-744 3-61 (81)
19 cd06408 PB1_NoxR The PB1 domai 85.8 1.5 3.2E-05 40.4 5.0 56 679-744 2-57 (86)
20 cd06399 PB1_P40 The PB1 domain 78.0 3.7 8.1E-05 38.1 4.6 49 696-770 23-71 (92)
21 PRK10737 FKBP-type peptidyl-pr 65.0 28 0.00061 36.5 8.2 103 249-365 2-114 (196)
22 KOG0644 Uncharacterized conser 56.7 8 0.00017 47.9 2.8 66 71-137 872-940 (1113)
23 KOG3207 Beta-tubulin folding c 44.2 28 0.00061 40.9 4.5 43 336-392 3-45 (505)
24 PF04014 Antitoxin-MazE: Antid 38.4 34 0.00074 27.4 3.0 27 243-269 14-40 (47)
25 smart00743 Agenet Tudor-like d 35.1 53 0.0011 27.2 3.7 38 335-385 2-39 (61)
26 COG0219 CspR Predicted rRNA me 31.8 20 0.00043 36.5 0.8 81 685-769 46-133 (155)
27 TIGR01439 lp_hng_hel_AbrB loop 29.3 62 0.0014 24.7 3.0 26 243-268 14-39 (43)
28 PF10844 DUF2577: Protein of u 29.2 67 0.0014 30.0 3.7 27 244-270 71-97 (100)
29 COG1047 SlpA FKBP-type peptidy 28.6 3.4E+02 0.0074 28.3 8.9 106 248-365 1-115 (174)
30 PF10411 DsbC_N: Disulfide bon 25.2 59 0.0013 27.3 2.4 16 728-743 34-49 (57)
31 cd05792 S1_eIF1AD_like S1_eIF1 24.1 60 0.0013 29.5 2.3 32 734-769 40-73 (78)
32 PF02513 Spin-Ssty: Spin/Ssty 23.9 1.1E+02 0.0025 25.9 3.7 31 338-368 1-31 (50)
33 PF03120 DNA_ligase_OB: NAD-de 22.8 87 0.0019 28.8 3.1 36 242-277 42-78 (82)
34 PF11515 Cul7: Mouse developme 22.4 1.2E+02 0.0025 28.0 3.8 55 324-387 6-62 (78)
35 PF01878 EVE: EVE domain; Int 21.5 86 0.0019 30.3 3.1 26 248-273 38-64 (143)
36 PF00788 RA: Ras association ( 21.1 2.5E+02 0.0054 24.4 5.6 58 680-741 3-65 (93)
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=8.8e-36 Score=264.01 Aligned_cols=83 Identities=54% Similarity=0.997 Sum_probs=81.5
Q ss_pred HHHHhhcCCeEEEEEcCCCCCCceeeehhHHHHhhccCcccccEEEEEeecCCCCcceeeeEEeeeccCCCCCCCCCCce
Q 003580 298 VANAVSTKSMFHVFYSPRATHADFVIPYQKYVKIIMNPICIGTRFKMRFEMDDSPERRCNGVVTGITDLDPYRWPNSKWR 377 (809)
Q Consensus 298 a~~a~~t~~~F~V~Y~PRas~sEFVVp~~ky~~A~~~~ws~GmRFKM~fE~EDs~~~r~~GTI~gi~d~Dp~rWP~S~WR 377 (809)
|+|||+++++|+|+||||++++|||||++||++||+++|++||||||+||+||+++++|+|||+||+++||++||+|+||
T Consensus 1 A~~aa~~~~~F~V~Y~PRa~~sEFVV~~~k~~~al~~~~~~GmRfkM~fE~eds~~~~~~GtI~~v~~~dp~~w~~S~WR 80 (83)
T PF06507_consen 1 AAHAAATGSPFEVFYYPRASPSEFVVPASKYDKALNHPWSVGMRFKMRFETEDSSERRWQGTIVGVSDLDPIRWPGSKWR 80 (83)
T ss_pred ChhHhhcCCeEEEEECCCCCCcceEEEHHHHHHHhcCCCCCCcEEEEEeccCCCccceeeeEEeEeeccCCCCCCCCCcc
Confidence 57999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eEE
Q 003580 378 CLM 380 (809)
Q Consensus 378 ~L~ 380 (809)
|||
T Consensus 81 ~Lq 83 (83)
T PF06507_consen 81 MLQ 83 (83)
T ss_pred cCc
Confidence 997
No 2
>PF02309 AUX_IAA: AUX/IAA family; InterPro: IPR003311 The Aux/IAA family of genes are key regulators of auxin-modified gene expression []. The plant hormone auxin (indole-3-acetic acid, IAA) regulates diverse cellular and developmental responses in plants, including cell division, expansion, differentiation and patterning of embryo responses []. Auxin can regulate the gene expression of several families, including GH3 and SAUR, as well as Aux/IAA itself. The Aux/IAA proteins act as repressors of auxin-induced gene expression, possibly through modulating the activity of DNA-binding auxin response factors (ARFs) (IPR010525 from INTERPRO). Aux/IAA and ARF are thought to interact through C-terminal protein-protein interaction domains found in both Aux/IAA and ARF. Recent evidence suggests that Aux/IAA proteins can also mediate light responses []. Some members of the AUX/IAA family are longer and contain an N-terminal DNA binding domain [] and may have an early function in the establishment of vascular and body patterns in embryonic and post-embryonic development in some plants.; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2P1N_F 2P1Q_C 2P1O_C.
Probab=100.00 E-value=7.2e-35 Score=296.80 Aligned_cols=96 Identities=35% Similarity=0.646 Sum_probs=0.0
Q ss_pred CCCCceEEEeeccceecccccccCCCChHHHHHHHHHHh---ccc----------ccccC-CCCCcEEEEEcCCCCeEEe
Q 003580 676 PGKRSCTKVHKQGSLVGRAIDLWRLNGYNDLLSELEHLF---NME----------GLLRD-PAKGWRILYTDSENDVMVV 741 (809)
Q Consensus 676 s~~r~~vKV~m~G~~vGRkvDL~~~~~Y~eL~~~L~~MF---~~~----------g~L~~-~~~~w~~vY~D~EGD~mLV 741 (809)
...++||||+|||++|||||||++|+||++|+.+|++|| +|. +.+.. ..++|+|||+|+|||||||
T Consensus 106 ~~~~~~vKV~mdG~~igRkVDL~~~~sY~~L~~~L~~MF~~~~i~~~~~~~~~~~~~~~~~~~~~~~l~Y~D~egd~mlv 185 (215)
T PF02309_consen 106 SSSRSYVKVNMDGVPIGRKVDLSAYSSYEELSSALEKMFSCFSIEQCGSHGLNESGLLDLLNGSEYVLVYEDKEGDWMLV 185 (215)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred ccCCceeEEEecCcccceecCHHHhhCHHHHHHHHHHhcCCCCccccccccccchhhccccCCcceeEEEECCCCCEEEe
Confidence 345999999999999999999999999999999999999 665 23321 3569999999999999999
Q ss_pred cCCCCchhhhccceEEEEecHHhHhccccCC
Q 003580 742 GDDPWHSEFCNEVSKIHIYTQEEVEKMTIGT 772 (809)
Q Consensus 742 GD~PW~~~F~~~vkri~I~~~~e~~~m~~~~ 772 (809)
|||||+ |||++||||+||+.+|+++|+|++
T Consensus 186 GD~PW~-~F~~~vkRl~I~~~~e~~~~~~r~ 215 (215)
T PF02309_consen 186 GDVPWE-EFVKSVKRLRIMKSSEAKGLAPRA 215 (215)
T ss_dssp -------------------------------
T ss_pred cCCCHH-HHHHHhhccEEecHHHhcccCCCC
Confidence 999999 999999999999999999999874
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=99.64 E-value=9.9e-16 Score=136.47 Aligned_cols=97 Identities=32% Similarity=0.476 Sum_probs=74.7
Q ss_pred EEEecCcccCCCCCceeEeccchhhcCCCCCCCCCCCceEEEEeeCCCCeEEEEEEEeCCCCceEeeccchhhhcccCCc
Q 003580 172 FCKTLTASDTSTHGGFSVPRRAAEDCFPPLDYKQQRPSQELVAKDLHGVEWRFRHIYRGQPRRHLLTTGWSIFVSQKNLV 251 (809)
Q Consensus 172 F~K~LT~SDv~~~grfsVPk~~Ae~~FPpLd~~~~~psq~L~~~Dl~G~~W~Fr~iyrg~prrhlLTtGWs~FV~~K~L~ 251 (809)
|.|+|+++|+...++|.||++.++.+.. ....++++.++|..|++|.+++.+++.+.+++|++||..||++++|+
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 FFKVLKPSDVSSSCRLIIPKEFAKKHGG-----NKRKSREVTLKDPDGRSWPVKLKYRKNSGRYYLTGGWKKFVRDNGLK 75 (100)
T ss_dssp EEEE--TTCCCCTT-EEE-HHHHTTTS-------SS--CEEEEEETTTEEEEEEEEEECCTTEEEEETTHHHHHHHCT--
T ss_pred CEEEEEccCcCCCCEEEeCHHHHHHhCC-----CcCCCeEEEEEeCCCCEEEEEEEEEccCCeEEECCCHHHHHHHcCCC
Confidence 8999999999998999999999988721 11235789999999999999999999888999999999999999999
Q ss_pred cCCEEEEEEcCC--CcEEEeEEec
Q 003580 252 SGDAVLFLRGKD--GELRLGIRRS 273 (809)
Q Consensus 252 aGD~VvF~R~~~--Gel~vGVRRa 273 (809)
+||.++|....+ .++.|.|.|+
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 999999998654 4569999986
No 4
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=99.46 E-value=4.3e-14 Score=163.47 Aligned_cols=148 Identities=20% Similarity=0.308 Sum_probs=122.9
Q ss_pred CccCCEEEEEEcCCCcEEEeEEeccCCCCC-CCCC--------------------ccccCCChhhHHHHHHHHhhcCCeE
Q 003580 250 LVSGDAVLFLRGKDGELRLGIRRSVQPRNG-LPDS--------------------ILSKQNSYPNVLSVVANAVSTKSMF 308 (809)
Q Consensus 250 L~aGD~VvF~R~~~Gel~vGVRRa~r~~~~-~p~s--------------------v~s~~~m~~~vlaaa~~a~~t~~~F 308 (809)
.+.||.|+++|...-++.-.+|+..+..++ .|+. --+-.+|.+.||+.|.++. ...|
T Consensus 874 pQmgDEViyfrQghqeyl~~~~~n~~~~~~~~p~~~~~v~~~kv~kl~~~~y~~~~~s~c~m~l~~idp~s~~~--~k~F 951 (1113)
T KOG0644|consen 874 PQMGDEVIYFRQGHQEYLEAVRLNNIELNNKEPWNKMAVEICKVEKLVYITYPGSGDSCCKMKLAVIDPASKLM--DKSF 951 (1113)
T ss_pred ccccceeehhhhhhHHHHhhhhhccccccccCcccccchhhheeeeeeeeeccCCCcchheeeeeeecchhhhh--hccc
Confidence 458999999999887777777776655443 3432 2234679999999998764 6789
Q ss_pred EEEEcCCCCCCceeeehhHHHHhhccCcccccEEEEEee--cCCCCcceeeeEEeeeccCCCCCCCCCCceeEEEEecCC
Q 003580 309 HVFYSPRATHADFVIPYQKYVKIIMNPICIGTRFKMRFE--MDDSPERRCNGVVTGITDLDPYRWPNSKWRCLMVRWDEC 386 (809)
Q Consensus 309 ~V~Y~PRas~sEFVVp~~ky~~A~~~~ws~GmRFKM~fE--~EDs~~~r~~GTI~gi~d~Dp~rWP~S~WR~L~V~WDe~ 386 (809)
.+.|......+||+|.++.|++|++++|..+++||.-+. +|+. -.||.|+|.++.+..| .+|+|+|+|+.|+||..
T Consensus 952 ~ltlpdlv~fpDFlV~rsrYd~AiQrnW~~~d~crvwwrda~~e~-g~WWeG~ils~~pksp-~fpdSpwery~v~~~~~ 1029 (1113)
T KOG0644|consen 952 KLTLPDLVTFPDFLVERSRYDAAIQRNWTCRDKCRVWWRDAGEED-GAWWEGRILSVKPKSP-DFPDSPWERYIVRYDNT 1029 (1113)
T ss_pred eeecccccCcchhhhhhhhHHHHHhhccccccceeEEEccCCCcC-CceeeeeeeeccCCCC-CCCCCcceeEEEEecCC
Confidence 999999999999999999999999999999999999993 2221 2589999999999888 99999999999999999
Q ss_pred CCCCCCCCCCCCcceecCC
Q 003580 387 IGSDHQEQVSPWEIDRSVS 405 (809)
Q Consensus 387 ~~~~~~~RVSPWeIEp~~~ 405 (809)
+. +.-||||.|++..
T Consensus 1030 e~----~~~spwe~~~i~d 1044 (1113)
T KOG0644|consen 1030 ET----ELHSPWEMEPIPD 1044 (1113)
T ss_pred cc----cccCccccCCCcc
Confidence 74 6789999999864
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=98.09 E-value=1.6e-05 Score=78.47 Aligned_cols=89 Identities=26% Similarity=0.376 Sum_probs=60.4
Q ss_pred ceeEEEecCcccCCCCC----ceeEeccchhhcCCCCCC-CCCCCceEEEEeeCCC--CeEEEEEEEeCC------CCce
Q 003580 169 PHMFCKTLTASDTSTHG----GFSVPRRAAEDCFPPLDY-KQQRPSQELVAKDLHG--VEWRFRHIYRGQ------PRRH 235 (809)
Q Consensus 169 ~~~F~K~LT~SDv~~~g----rfsVPk~~Ae~~FPpLd~-~~~~psq~L~~~Dl~G--~~W~Fr~iyrg~------prrh 235 (809)
...|+|.|++.|++..| |+.|||..++..||.+.. ....|+..|.+++..| ..|+||+||.|+ ...+
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 46899999999999875 799999999999998877 5566889999999887 568999999988 3457
Q ss_pred Eee--ccchhhhcccCCccCCEEEEE
Q 003580 236 LLT--TGWSIFVSQKNLVSGDAVLFL 259 (809)
Q Consensus 236 lLT--tGWs~FV~~K~L~aGD~VvF~ 259 (809)
.|| ++=..|.+. =..||-+||-
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 786 443444443 2478888886
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=97.41 E-value=0.00029 Score=67.04 Aligned_cols=78 Identities=22% Similarity=0.306 Sum_probs=60.2
Q ss_pred ceeEEEecCcccCCCC-CceeEeccchhhcCCCCCC------------CCCCCceEEEEeeCCCCeEEEEEEEeCC---C
Q 003580 169 PHMFCKTLTASDTSTH-GGFSVPRRAAEDCFPPLDY------------KQQRPSQELVAKDLHGVEWRFRHIYRGQ---P 232 (809)
Q Consensus 169 ~~~F~K~LT~SDv~~~-grfsVPk~~Ae~~FPpLd~------------~~~~psq~L~~~Dl~G~~W~Fr~iyrg~---p 232 (809)
-..|.|+|++||+..+ +||+||-..... ..-|.. ....-..++.+.|..++.|..++..|.. .
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 4799999999999875 899999875422 122221 1233467889999999999999999955 4
Q ss_pred CceEeeccchhhhcc
Q 003580 233 RRHLLTTGWSIFVSQ 247 (809)
Q Consensus 233 rrhlLTtGWs~FV~~ 247 (809)
-.|+|++||..+|+.
T Consensus 100 ~~YvL~~gWn~VV~~ 114 (114)
T PF03754_consen 100 SNYVLNSGWNKVVED 114 (114)
T ss_pred eEEEEEcChHhhccC
Confidence 689999999999863
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=96.37 E-value=0.0075 Score=52.55 Aligned_cols=67 Identities=22% Similarity=0.404 Sum_probs=53.7
Q ss_pred eEEEeeccceecccccccCCCChHHHHHHHHHHhcccccccCCCCCcEEEEEcCCCCeEEecCC-CCchhhhccce
Q 003580 681 CTKVHKQGSLVGRAIDLWRLNGYNDLLSELEHLFNMEGLLRDPAKGWRILYTDSENDVMVVGDD-PWHSEFCNEVS 755 (809)
Q Consensus 681 ~vKV~m~G~~vGRkvDL~~~~~Y~eL~~~L~~MF~~~g~L~~~~~~w~~vY~D~EGD~mLVGD~-PW~~~F~~~vk 755 (809)
-+|++-.|. +=|.+.+..--+|++|..++++.|++. ...+++.|.|.||||..+-++ =|+ +.++.++
T Consensus 3 ~vK~~~~~~-~~~~~~~~~~~s~~~L~~~i~~~~~~~------~~~~~l~Y~D~dgD~V~i~sd~Dl~-~a~~~~~ 70 (84)
T PF00564_consen 3 RVKVRYGGD-IRRIISLPSDVSFDDLRSKIREKFGLL------DEDFQLKYKDEDGDLVTISSDEDLQ-EAIEQAK 70 (84)
T ss_dssp EEEEEETTE-EEEEEEECSTSHHHHHHHHHHHHHTTS------TSSEEEEEEETTSSEEEESSHHHHH-HHHHHHH
T ss_pred EEEEEECCe-eEEEEEcCCCCCHHHHHHHHHHHhCCC------CccEEEEeeCCCCCEEEeCCHHHHH-HHHHHHH
Confidence 378888886 444688888889999999999999975 467899999999999888754 366 6666554
No 8
>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=95.40 E-value=0.046 Score=49.51 Aligned_cols=53 Identities=19% Similarity=0.224 Sum_probs=43.2
Q ss_pred EEEeeccceecccccccCCCChHHHHHHHHHHhcccccccCCCCCcEEEEEcCCCCeEEec
Q 003580 682 TKVHKQGSLVGRAIDLWRLNGYNDLLSELEHLFNMEGLLRDPAKGWRILYTDSENDVMVVG 742 (809)
Q Consensus 682 vKV~m~G~~vGRkvDL~~~~~Y~eL~~~L~~MF~~~g~L~~~~~~w~~vY~D~EGD~mLVG 742 (809)
+||.-.|.-+-=+++-+.--+|.+|..++.++|++. .+.|-|.|.||||.++-
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 688888874444565555779999999999999986 57799999999998764
No 9
>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=95.36 E-value=0.044 Score=47.73 Aligned_cols=65 Identities=20% Similarity=0.380 Sum_probs=49.1
Q ss_pred EEEeeccceecccccccCCCChHHHHHHHHHHhcccccccCCCCCcEEEEEcCCCCeEEecC-CCCchhhhccce
Q 003580 682 TKVHKQGSLVGRAIDLWRLNGYNDLLSELEHLFNMEGLLRDPAKGWRILYTDSENDVMVVGD-DPWHSEFCNEVS 755 (809)
Q Consensus 682 vKV~m~G~~vGRkvDL~~~~~Y~eL~~~L~~MF~~~g~L~~~~~~w~~vY~D~EGD~mLVGD-~PW~~~F~~~vk 755 (809)
+||+-.| -=|.+-+..--+|++|..++.+.|++.+ ..+.|-|.|.|||+..+.+ .=|. +.+.+++
T Consensus 4 vK~~~~~--~~~~~~~~~~~s~~dL~~~i~~~~~~~~------~~~~l~Y~Dedgd~v~l~sd~Dl~-~a~~~~~ 69 (81)
T smart00666 4 VKLRYGG--ETRRLSVPRDISFEDLRSKVAKRFGLDN------QSFTLKYQDEDGDLVSLTSDEDLE-EAIEEYD 69 (81)
T ss_pred EEEEECC--EEEEEEECCCCCHHHHHHHHHHHhCCCC------CCeEEEEECCCCCEEEecCHHHHH-HHHHHHH
Confidence 6777644 3577888888899999999999999642 6789999999999976654 4455 4444443
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=95.31 E-value=0.053 Score=49.85 Aligned_cols=67 Identities=24% Similarity=0.382 Sum_probs=49.4
Q ss_pred EEEeeccceeccccccc---CCCChHHHHHHHHHHhcccccccCCCCCcEEEEEcCCCCeEEecCCCCchhhhccceE
Q 003580 682 TKVHKQGSLVGRAIDLW---RLNGYNDLLSELEHLFNMEGLLRDPAKGWRILYTDSENDVMVVGDDPWHSEFCNEVSK 756 (809)
Q Consensus 682 vKV~m~G~~vGRkvDL~---~~~~Y~eL~~~L~~MF~~~g~L~~~~~~w~~vY~D~EGD~mLVGD~PW~~~F~~~vkr 756 (809)
+||.-+|.-.==++++. .--+|++|.+++.+.|.+. +..+++|.|.|.||||..+-++- +|...+.+
T Consensus 3 vKv~y~~~~rRf~l~~~~~~~d~~~~~L~~kI~~~f~l~-----~~~~~~l~Y~Dedgd~V~l~~D~---DL~~a~~~ 72 (91)
T cd06398 3 VKVKYGGTLRRFTFPVAENQLDLNMDGLREKVEELFSLS-----PDADLSLTYTDEDGDVVTLVDDN---DLTDAIQY 72 (91)
T ss_pred EEEEeCCEEEEEEeccccccCCCCHHHHHHHHHHHhCCC-----CCCcEEEEEECCCCCEEEEccHH---HHHHHHHH
Confidence 78988887222244443 3569999999999999863 35789999999999998887663 45444443
No 11
>cd06407 PB1_NLP A PB1 domain is present in NIN like proteins (NLP), a key enzyme in a process of establishment of symbiosis betweeen legumes and nitrogen fixing bacteria (Rhizobium). The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes like osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-inte
Probab=95.29 E-value=0.049 Score=49.12 Aligned_cols=55 Identities=15% Similarity=0.268 Sum_probs=43.2
Q ss_pred eEEEeeccceecccccccCCCChHHHHHHHHHHhcccccccCCCCCcEEEEEcCCCCeEEec
Q 003580 681 CTKVHKQGSLVGRAIDLWRLNGYNDLLSELEHLFNMEGLLRDPAKGWRILYTDSENDVMVVG 742 (809)
Q Consensus 681 ~vKV~m~G~~vGRkvDL~~~~~Y~eL~~~L~~MF~~~g~L~~~~~~w~~vY~D~EGD~mLVG 742 (809)
-+||...|. -+.+-|..--+|.+|.+++.++|.+. ...++.|-|.|+||||.++-
T Consensus 2 ~vK~~~~~d--~~r~~l~~~~~~~~L~~~i~~r~~~~-----~~~~f~LkY~Ddegd~v~lt 56 (82)
T cd06407 2 RVKATYGEE--KIRFRLPPSWGFTELKQEIAKRFKLD-----DMSAFDLKYLDDDEEWVLLT 56 (82)
T ss_pred EEEEEeCCe--EEEEEcCCCCCHHHHHHHHHHHhCCC-----CCCeeEEEEECCCCCeEEee
Confidence 378888886 34455555559999999999999974 23689999999999998764
No 12
>cd06409 PB1_MUG70 The MUG70 protein is a product of the meiotically up-regulated gene 70 which has a role in meiosis and harbors a PB1 domain. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domains depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic amino acid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is
Probab=95.24 E-value=0.036 Score=50.67 Aligned_cols=52 Identities=17% Similarity=0.334 Sum_probs=40.6
Q ss_pred eeccccc--ccCCCChHHHHHHHHHHhcccccccCCCCCcEEEEEcCCCCeEEecCC
Q 003580 690 LVGRAID--LWRLNGYNDLLSELEHLFNMEGLLRDPAKGWRILYTDSENDVMVVGDD 744 (809)
Q Consensus 690 ~vGRkvD--L~~~~~Y~eL~~~L~~MF~~~g~L~~~~~~w~~vY~D~EGD~mLVGD~ 744 (809)
+-||.+= +....|+.+|..+..+-|+++.. ....++|.|.|+||||.|+--|
T Consensus 8 ~~GrvhRf~~~~s~~~~~L~~~I~~Rl~~d~~---~~~~~~L~YlDDEgD~VllT~D 61 (86)
T cd06409 8 PKGRVHRFRLRPSESLEELRTLISQRLGDDDF---ETHLYALSYVDDEGDIVLITSD 61 (86)
T ss_pred CCCCEEEEEecCCCCHHHHHHHHHHHhCCccc---cCCcccEEEEcCCCCEEEEecc
Confidence 4566443 44478999999999999998753 2468999999999999887543
No 13
>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=95.01 E-value=0.062 Score=46.48 Aligned_cols=65 Identities=22% Similarity=0.403 Sum_probs=48.1
Q ss_pred EEEeeccceeccccccc-CCCChHHHHHHHHHHhcccccccCCCCCcEEEEEcCCCCeEEecC-CCCchhhhccce
Q 003580 682 TKVHKQGSLVGRAIDLW-RLNGYNDLLSELEHLFNMEGLLRDPAKGWRILYTDSENDVMVVGD-DPWHSEFCNEVS 755 (809)
Q Consensus 682 vKV~m~G~~vGRkvDL~-~~~~Y~eL~~~L~~MF~~~g~L~~~~~~w~~vY~D~EGD~mLVGD-~PW~~~F~~~vk 755 (809)
+||+-.|. =|.+=+. .--+|++|...|.+.|++.. ..+.+.|.|.||||..+.+ .=|+ +-++.++
T Consensus 3 vK~~~~~~--~~~~~~~~~~~s~~~L~~~i~~~~~~~~------~~~~l~y~D~e~d~v~l~sd~Dl~-~a~~~~~ 69 (81)
T cd05992 3 VKVKYGGE--IRRFVVVSRSISFEDLRSKIAEKFGLDA------VSFKLKYPDEDGDLVTISSDEDLE-EAIEEAR 69 (81)
T ss_pred EEEEecCC--CEEEEEecCCCCHHHHHHHHHHHhCCCC------CcEEEEeeCCCCCEEEeCCHHHHH-HHHHHHh
Confidence 67777764 2444444 78899999999999999753 5688999999999988887 4444 4444443
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=93.01 E-value=0.22 Score=45.12 Aligned_cols=56 Identities=25% Similarity=0.430 Sum_probs=44.8
Q ss_pred EEEeeccceecc-cccccCCCChHHHHHHHHHHhcccccccCCCCCcEEEEEcCCCCeEEecCC
Q 003580 682 TKVHKQGSLVGR-AIDLWRLNGYNDLLSELEHLFNMEGLLRDPAKGWRILYTDSENDVMVVGDD 744 (809)
Q Consensus 682 vKV~m~G~~vGR-kvDL~~~~~Y~eL~~~L~~MF~~~g~L~~~~~~w~~vY~D~EGD~mLVGD~ 744 (809)
||.+-++. +-| ++|.....+|+++..-|++|+.+.+ -.+.|-|+|.+||.+-+-.|
T Consensus 3 VKSkfdaE-fRRFsl~r~~~~~f~ef~~ll~~lH~l~~------~~f~i~Y~D~~gDLLPInND 59 (80)
T cd06403 3 VKSKFDAE-FRRFSLDRNKPGKFEDFYKLLEHLHHIPN------VDFLIGYTDPHGDLLPINND 59 (80)
T ss_pred eecccCCe-EEEEEeccccCcCHHHHHHHHHHHhCCCC------CcEEEEEeCCCCCEecccCc
Confidence 55555554 555 7888888999999999999999753 56999999999999876543
No 15
>cd06402 PB1_p62 The PB1 domain is an essential part of p62 scaffold protein (alias sequestosome 1,SQSTM) involved in cell signaling, receptor internalization, and protein turnover. The PB1 domain is a modular domain mediating specific protein-protein interaction which play roles in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.
Probab=90.91 E-value=0.72 Score=42.41 Aligned_cols=54 Identities=24% Similarity=0.375 Sum_probs=41.4
Q ss_pred eEEEeecc----ceecc-cccccCCCChHHHHHHHHHHhcccccccCCCCCcEEEEEcCCCCeE
Q 003580 681 CTKVHKQG----SLVGR-AIDLWRLNGYNDLLSELEHLFNMEGLLRDPAKGWRILYTDSENDVM 739 (809)
Q Consensus 681 ~vKV~m~G----~~vGR-kvDL~~~~~Y~eL~~~L~~MF~~~g~L~~~~~~w~~vY~D~EGD~m 739 (809)
.||.+..| ..|=| +||-...-+|++|.+.+.++|..- ....++|-|.|.|||..
T Consensus 2 ~vkayl~~~~~~~EIRRf~l~~~~~~s~~~L~~~V~~~f~~l-----~~~~ftlky~DeeGDlv 60 (87)
T cd06402 2 TVKAYLLGKDANAEIRRFAIDEDVSTSYEYLVEKVAAVFPSL-----RGKNFQLFWKDEEGDLV 60 (87)
T ss_pred eEEEeecCCCCccceEEEEecCCCCcCHHHHHHHHHHHcccc-----CCCcEEEEEECCCCCEE
Confidence 57888877 33434 556677779999999999999632 23689999999999983
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=90.55 E-value=0.68 Score=42.31 Aligned_cols=52 Identities=17% Similarity=0.294 Sum_probs=42.1
Q ss_pred EEEeeccceecccccccCCCChHHHHHHHHHHhcccccccCCCCCcEEEEEcCCCCeEE
Q 003580 682 TKVHKQGSLVGRAIDLWRLNGYNDLLSELEHLFNMEGLLRDPAKGWRILYTDSENDVMV 740 (809)
Q Consensus 682 vKV~m~G~~vGRkvDL~~~~~Y~eL~~~L~~MF~~~g~L~~~~~~w~~vY~D~EGD~mL 740 (809)
+|++-.|.-+-=.+|. .-+|++|.+++.+||.+. ....+++.|.|.|||.--
T Consensus 3 ~K~~y~gdi~it~~d~--~~s~e~L~~~v~~~c~~~-----~~q~ft~kw~DEEGDp~t 54 (83)
T cd06404 3 VKAAYNGDIMITSIDP--SISLEELCNEVRDMCRFH-----NDQPFTLKWIDEEGDPCT 54 (83)
T ss_pred EEEEecCcEEEEEcCC--CcCHHHHHHHHHHHhCCC-----CCCcEEEEEECCCCCcee
Confidence 7899999755445666 667999999999999973 346899999999999743
No 17
>cd06397 PB1_UP1 Uncharacterized protein 1. The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions.
Probab=88.96 E-value=0.95 Score=41.25 Aligned_cols=52 Identities=27% Similarity=0.397 Sum_probs=41.2
Q ss_pred EEeeccceecccccccCCCChHHHHHHHHHHhcccccccCCCCCcEEEEEcCCCCeEEec
Q 003580 683 KVHKQGSLVGRAIDLWRLNGYNDLLSELEHLFNMEGLLRDPAKGWRILYTDSENDVMVVG 742 (809)
Q Consensus 683 KV~m~G~~vGRkvDL~~~~~Y~eL~~~L~~MF~~~g~L~~~~~~w~~vY~D~EGD~mLVG 742 (809)
||.-.|. -|++.-..-=+|..|.+.|+.+|.+.- -...|+|.|.|||..-+-
T Consensus 4 Kv~~~g~--~RRf~~~~~pt~~~L~~kl~~Lf~lp~------~~~~vtYiDeD~D~ITls 55 (82)
T cd06397 4 KSSFLGD--TRRIVFPDIPTWEALASKLENLYNLPE------IKVGVTYIDNDNDEITLS 55 (82)
T ss_pred EEEeCCc--eEEEecCCCccHHHHHHHHHHHhCCCh------hHeEEEEEcCCCCEEEec
Confidence 7766664 677777778899999999999999752 127799999999985443
No 18
>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=87.47 E-value=1.9 Score=39.41 Aligned_cols=58 Identities=22% Similarity=0.413 Sum_probs=41.8
Q ss_pred EEEeeccceecccccccCCC-ChHHHHHHHHHHhcccccccCCCCCcEEEEEcCCCCeEEecCC
Q 003580 682 TKVHKQGSLVGRAIDLWRLN-GYNDLLSELEHLFNMEGLLRDPAKGWRILYTDSENDVMVVGDD 744 (809)
Q Consensus 682 vKV~m~G~~vGRkvDL~~~~-~Y~eL~~~L~~MF~~~g~L~~~~~~w~~vY~D~EGD~mLVGD~ 744 (809)
+|+.-.|. | |.+=+..-. +|.+|...+.+.|... + ...+...|-|.|.|||+.-+.+.
T Consensus 3 iK~~~g~D-i-R~~~~~~~~~t~~~L~~~v~~~F~~~--~-~~~~~flIKYkD~dGDlVTIts~ 61 (81)
T cd06401 3 LKAQLGDD-I-RRIPIHNEDITYDELLLMMQRVFRGK--L-GSSDDVLIKYKDEDGDLITIFDS 61 (81)
T ss_pred EEEEeCCe-E-EEEeccCccccHHHHHHHHHHHhccc--c-CCcccEEEEEECCCCCEEEeccH
Confidence 56665443 4 444444323 9999999999999943 2 23468999999999999888775
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=85.78 E-value=1.5 Score=40.39 Aligned_cols=56 Identities=25% Similarity=0.438 Sum_probs=45.2
Q ss_pred CceEEEeeccceecccccccCCCChHHHHHHHHHHhcccccccCCCCCcEEEEEcCCCCeEEecCC
Q 003580 679 RSCTKVHKQGSLVGRAIDLWRLNGYNDLLSELEHLFNMEGLLRDPAKGWRILYTDSENDVMVVGDD 744 (809)
Q Consensus 679 r~~vKV~m~G~~vGRkvDL~~~~~Y~eL~~~L~~MF~~~g~L~~~~~~w~~vY~D~EGD~mLVGD~ 744 (809)
+.-||||-+|. -|.|-+..-=+|++|.+++.++|++. ...+|-|.|. ||+.-++|.
T Consensus 2 ~ikVKv~~~~D--v~~i~v~~~i~f~dL~~kIrdkf~~~-------~~~~iKykDE-GD~iti~sq 57 (86)
T cd06408 2 KIRVKVHAQDD--TRYIMIGPDTGFADFEDKIRDKFGFK-------RRLKIKMKDD-GDMITMGDQ 57 (86)
T ss_pred cEEEEEEecCc--EEEEEcCCCCCHHHHHHHHHHHhCCC-------CceEEEEEcC-CCCccccCH
Confidence 34689998886 46666667778999999999999984 3678999999 999766653
No 20
>cd06399 PB1_P40 The PB1 domain is essential part of the p40 adaptor protein which plays an important role in activating phagocyte NADPH oxidase during phagocytosis. The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes , such as osteoclastogenesis, angiogenesis, early cardiovascular development and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The PB1 domain of p40 represents a type I PB1 domain which interacts with the PB1 domain of oxidase activator p67 w
Probab=77.95 E-value=3.7 Score=38.08 Aligned_cols=49 Identities=31% Similarity=0.387 Sum_probs=41.8
Q ss_pred cccCCCChHHHHHHHHHHhcccccccCCCCCcEEEEEcCCCCeEEecCCCCchhhhccceEEEEecHHhHhcccc
Q 003580 696 DLWRLNGYNDLLSELEHLFNMEGLLRDPAKGWRILYTDSENDVMVVGDDPWHSEFCNEVSKIHIYTQEEVEKMTI 770 (809)
Q Consensus 696 DL~~~~~Y~eL~~~L~~MF~~~g~L~~~~~~w~~vY~D~EGD~mLVGD~PW~~~F~~~vkri~I~~~~e~~~m~~ 770 (809)
||+.--.|.+|+.-..+-|..+. =.+-|.|.|||. |+|++.||+.-|-.
T Consensus 23 ~l~~~P~~kdLl~lmr~~f~~~d--------IaLNYrD~EGDL------------------IRllddeDv~LMV~ 71 (92)
T cd06399 23 DLSSTPLLKDLLELTRREFQRED--------IALNYRDAEGDL------------------IRLLSDEDVALMVR 71 (92)
T ss_pred ccccCccHHHHHHHHHHHhchhh--------eeeeeecCCCCE------------------EEEcchhhHHHHHH
Confidence 68888999999999999998653 347899999998 99999999988843
No 21
>PRK10737 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=65.04 E-value=28 Score=36.51 Aligned_cols=103 Identities=16% Similarity=0.200 Sum_probs=62.9
Q ss_pred CCccCCEEEE---EEcCCCcEEEeEEeccCCCCCCCCCc-cccCCChhhHHHHHHHHhhcCCeEEEEEcCCCC------C
Q 003580 249 NLVSGDAVLF---LRGKDGELRLGIRRSVQPRNGLPDSI-LSKQNSYPNVLSVVANAVSTKSMFHVFYSPRAT------H 318 (809)
Q Consensus 249 ~L~aGD~VvF---~R~~~Gel~vGVRRa~r~~~~~p~sv-~s~~~m~~~vlaaa~~a~~t~~~F~V~Y~PRas------~ 318 (809)
++..|+.|.+ +|.++|+++---+ ...|... ++...+-.+ |++|..-...|..|+|..-|-.. -
T Consensus 2 kI~~~~vV~l~Y~l~~~dG~v~dst~------~~~Pl~~~~G~g~lipg-lE~aL~G~~~Gd~~~v~l~peeAyGe~d~~ 74 (196)
T PRK10737 2 KVAKDLVVSLAYQVRTEDGVLVDESP------VSAPLDYLHGHGSLISG-LETALEGHEVGDKFDVAVGANDAYGQYDEN 74 (196)
T ss_pred ccCCCCEEEEEEEEEeCCCCEEEecC------CCCCeEEEeCCCcchHH-HHHHHcCCCCCCEEEEEEChHHhcCCCChH
Confidence 4567777777 2567787643221 1235443 344444344 45565566778899998765422 2
Q ss_pred CceeeehhHHHHhhccCcccccEEEEEeecCCCCcceeeeEEeeecc
Q 003580 319 ADFVIPYQKYVKIIMNPICIGTRFKMRFEMDDSPERRCNGVVTGITD 365 (809)
Q Consensus 319 sEFVVp~~ky~~A~~~~ws~GmRFKM~fE~EDs~~~r~~GTI~gi~d 365 (809)
.-..||++.|... ....+||||.+. +++. ...++|+.|.+
T Consensus 75 lV~~vpr~~F~~~--~~l~~G~~~~~~--~~~G---~~~~~V~ev~~ 114 (196)
T PRK10737 75 LVQRVPKDVFMGV--DELQVGMRFLAE--TDQG---PVPVEITAVED 114 (196)
T ss_pred HEEEecHHHCCCc--cCCCCCCEEEEe--CCCC---cEEEEEEEEcC
Confidence 3456888877432 247899998874 4554 36889999875
No 22
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=56.71 E-value=8 Score=47.90 Aligned_cols=66 Identities=24% Similarity=0.411 Sum_probs=44.9
Q ss_pred CCCCCCCeEEEecCcchhhhccCCCCCCCCCCC---CCCCCcceEEEEEeeeeccccCCceeEeEeeecC
Q 003580 71 SLPKKGNVVVYFPQGHLEQVASSSAFPPIEVPN---FDLQPQIFCKVVDVQLLANKENDEVYTQVALLPQ 137 (809)
Q Consensus 71 ~lP~~gs~V~YFPQGH~Eq~~~s~~~~~~~~p~---~~lp~~i~CrV~~V~L~Ad~~TDEVyAqi~L~P~ 137 (809)
-||..|+.|.||-|||-|-+.+..-- +.+.-. .++-..=.|.|..+..---+....--.+|+|.=.
T Consensus 872 yipQmgDEViyfrQghqeyl~~~~~n-~~~~~~~~p~~~~~v~~~kv~kl~~~~y~~~~~s~c~m~l~~i 940 (1113)
T KOG0644|consen 872 YIPQMGDEVIYFRQGHQEYLEAVRLN-NIELNNKEPWNKMAVEICKVEKLVYITYPGSGDSCCKMKLAVI 940 (1113)
T ss_pred ccccccceeehhhhhhHHHHhhhhhc-cccccccCcccccchhhheeeeeeeeeccCCCcchheeeeeee
Confidence 58999999999999999999886421 111111 1222233699888877777777777777777544
No 23
>KOG3207 consensus Beta-tubulin folding cofactor E [Posttranslational modification, protein turnover, chaperones]
Probab=44.16 E-value=28 Score=40.87 Aligned_cols=43 Identities=37% Similarity=0.618 Sum_probs=29.9
Q ss_pred cccccEEEEEeecCCCCcceeeeEEeeeccCCCCCCCCCCceeEEEEecCCCCCCCC
Q 003580 336 ICIGTRFKMRFEMDDSPERRCNGVVTGITDLDPYRWPNSKWRCLMVRWDECIGSDHQ 392 (809)
Q Consensus 336 ws~GmRFKM~fE~EDs~~~r~~GTI~gi~d~Dp~rWP~S~WR~L~V~WDe~~~~~~~ 392 (809)
..+|+|+|..+|- +..||.|+|.| |++ +| +.|.||++.-..|.
T Consensus 3 ~~IG~RvkI~~~~---~Tvr~iG~V~g--------~~~-~w--~GvEWDd~~RGKH~ 45 (505)
T KOG3207|consen 3 MEIGTRVKIGGEI---ATVRYIGEVEG--------NNS-KW--YGVEWDDPVRGKHD 45 (505)
T ss_pred eeccceEEEcCEE---EEEEEEEEEcC--------CCC-cc--eeeEecCCCccccC
Confidence 4689999998642 33456666654 554 45 78999999877654
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=38.44 E-value=34 Score=27.42 Aligned_cols=27 Identities=22% Similarity=0.252 Sum_probs=22.7
Q ss_pred hhhcccCCccCCEEEEEEcCCCcEEEe
Q 003580 243 IFVSQKNLVSGDAVLFLRGKDGELRLG 269 (809)
Q Consensus 243 ~FV~~K~L~aGD~VvF~R~~~Gel~vG 269 (809)
.|.++-+|.+||.|.|.-.++|++.+-
T Consensus 14 ~~~~~l~l~~Gd~v~i~~~~~g~i~i~ 40 (47)
T PF04014_consen 14 EIREKLGLKPGDEVEIEVEGDGKIVIR 40 (47)
T ss_dssp HHHHHTTSSTTTEEEEEEETTSEEEEE
T ss_pred HHHHHcCCCCCCEEEEEEeCCCEEEEE
Confidence 566788999999999999999876653
No 25
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=35.06 E-value=53 Score=27.24 Aligned_cols=38 Identities=21% Similarity=0.185 Sum_probs=29.3
Q ss_pred CcccccEEEEEeecCCCCcceeeeEEeeeccCCCCCCCCCCceeEEEEecC
Q 003580 335 PICIGTRFKMRFEMDDSPERRCNGVVTGITDLDPYRWPNSKWRCLMVRWDE 385 (809)
Q Consensus 335 ~ws~GmRFKM~fE~EDs~~~r~~GTI~gi~d~Dp~rWP~S~WR~L~V~WDe 385 (809)
.|.+|+++...++.++ .||.|+|+.+.. -..+.|.-+.
T Consensus 2 ~~~~G~~Ve~~~~~~~---~W~~a~V~~~~~----------~~~~~V~~~~ 39 (61)
T smart00743 2 DFKKGDRVEVFSKEED---SWWEAVVTKVLG----------DGKYLVRYLT 39 (61)
T ss_pred CcCCCCEEEEEECCCC---EEEEEEEEEECC----------CCEEEEEECC
Confidence 5889999999996544 489999999964 1246777776
No 26
>COG0219 CspR Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]
Probab=31.83 E-value=20 Score=36.50 Aligned_cols=81 Identities=14% Similarity=0.144 Sum_probs=52.5
Q ss_pred eeccceecccccccCCCChHHHHHHH---HHHhcccccccCCCCCcEEEEEcCCCCeEEecCCCCch--hhhccc--eEE
Q 003580 685 HKQGSLVGRAIDLWRLNGYNDLLSEL---EHLFNMEGLLRDPAKGWRILYTDSENDVMVVGDDPWHS--EFCNEV--SKI 757 (809)
Q Consensus 685 ~m~G~~vGRkvDL~~~~~Y~eL~~~L---~~MF~~~g~L~~~~~~w~~vY~D~EGD~mLVGD~PW~~--~F~~~v--kri 757 (809)
..-|-.+--+++|..|++|++.+++. .++|-+.-.-.....+ +....||++|-|-..=.+ ++.+.. ++|
T Consensus 46 kRAGlDY~~~~~l~~h~s~e~fl~~~~~~~rl~~~tt~~~~~~~~----~~f~~~d~llFG~Es~GLP~~i~~~~~~~~i 121 (155)
T COG0219 46 KRAGLDYHEKASLTEHDSLEAFLEAEPIGGRLFALTTKGTTTYTD----VSFQKGDYLLFGPESRGLPEEILDAAPDRCI 121 (155)
T ss_pred hhcccchHhhcceEEeCCHHHHHhhccCCceEEEEEecccccccc----ccCCCCCEEEECCCCCCCCHHHHHhCccceE
Confidence 34688889999999999999999998 5677765321111111 445669999999876553 233222 257
Q ss_pred EEecHHhHhccc
Q 003580 758 HIYTQEEVEKMT 769 (809)
Q Consensus 758 ~I~~~~e~~~m~ 769 (809)
+|=..+++..|+
T Consensus 122 rIPm~~~~RSLN 133 (155)
T COG0219 122 RIPMRPGVRSLN 133 (155)
T ss_pred EeccCCCCccch
Confidence 776555555543
No 27
>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=29.33 E-value=62 Score=24.70 Aligned_cols=26 Identities=31% Similarity=0.428 Sum_probs=22.2
Q ss_pred hhhcccCCccCCEEEEEEcCCCcEEE
Q 003580 243 IFVSQKNLVSGDAVLFLRGKDGELRL 268 (809)
Q Consensus 243 ~FV~~K~L~aGD~VvF~R~~~Gel~v 268 (809)
.|.++-++..||.|.+...++|.|.+
T Consensus 14 ~~r~~l~~~~gd~~~i~~~~~~~l~l 39 (43)
T TIGR01439 14 EIREKLGLKEGDRLEVIRVEDGEIIL 39 (43)
T ss_pred HHHHHcCcCCCCEEEEEEeCCCEEEE
Confidence 67889999999999999887777654
No 28
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=29.20 E-value=67 Score=29.98 Aligned_cols=27 Identities=30% Similarity=0.426 Sum_probs=21.9
Q ss_pred hhcccCCccCCEEEEEEcCCCcEEEeE
Q 003580 244 FVSQKNLVSGDAVLFLRGKDGELRLGI 270 (809)
Q Consensus 244 FV~~K~L~aGD~VvF~R~~~Gel~vGV 270 (809)
|.-...|++||.|+.+|..+|+.++=+
T Consensus 71 i~~~~~Lk~GD~V~ll~~~~gQ~yiVl 97 (100)
T PF10844_consen 71 ITFTDGLKVGDKVLLLRVQGGQKYIVL 97 (100)
T ss_pred EEEecCCcCCCEEEEEEecCCCEEEEE
Confidence 555678999999999999988766544
No 29
>COG1047 SlpA FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]
Probab=28.62 E-value=3.4e+02 Score=28.34 Aligned_cols=106 Identities=19% Similarity=0.244 Sum_probs=64.7
Q ss_pred cCCccCCEEEEE---EcCCCcEEEeEEeccCCCCCCCCCccccCCChhhHHHHHHHHhhcCCeEEEEEcCCCCCCce---
Q 003580 248 KNLVSGDAVLFL---RGKDGELRLGIRRSVQPRNGLPDSILSKQNSYPNVLSVVANAVSTKSMFHVFYSPRATHADF--- 321 (809)
Q Consensus 248 K~L~aGD~VvF~---R~~~Gel~vGVRRa~r~~~~~p~sv~s~~~m~~~vlaaa~~a~~t~~~F~V~Y~PRas~sEF--- 321 (809)
+++..||.|.+. |.++|++.=--.- ...|-.++-.+..-+.-|+.|..-..-|.-|+|.--|-..-.++
T Consensus 1 m~i~k~~~V~i~Y~~~~~dg~v~Dtt~e-----~~~P~~~i~G~g~li~glE~al~g~~~Ge~~~V~IpPE~AfGe~~~~ 75 (174)
T COG1047 1 MKIEKGDVVSLHYTLKVEDGEVVDTTDE-----NYGPLTFIVGAGQLIPGLEEALLGKEVGEEFTVEIPPEDAFGEYDPD 75 (174)
T ss_pred CcccCCCEEEEEEEEEecCCcEEEcccc-----cCCCeEEEecCCCcchhHHHHHhCCCCCceeEEEeCchHhcCCCChH
Confidence 356678888773 5566665421111 12344443233333444566766677899999998886433333
Q ss_pred ---eeehhHHHHhhccCcccccEEEEEeecCCCCcceeeeEEeeecc
Q 003580 322 ---VIPYQKYVKIIMNPICIGTRFKMRFEMDDSPERRCNGVVTGITD 365 (809)
Q Consensus 322 ---VVp~~ky~~A~~~~ws~GmRFKM~fE~EDs~~~r~~GTI~gi~d 365 (809)
.||..+|...= ...+||+|.+ +++| ...-|+|+.|..
T Consensus 76 lvq~vp~~~F~~~~--~~~vGm~~~~--~~~~---~~~~~~V~~V~~ 115 (174)
T COG1047 76 LVQRVPRDEFQGVG--ELEVGMEVEA--EGGD---GEIPGVVTEVSG 115 (174)
T ss_pred HeEEecHHHhCcCC--CCCCCcEEEE--cCCC---ceeeEEEEEEcC
Confidence 37777766532 7899999875 4444 346899999974
No 30
>PF10411 DsbC_N: Disulfide bond isomerase protein N-terminus; InterPro: IPR018950 This is the N-terminal domain of the disulphide bond isomerase DsbC. The whole molecule is V-shaped, where each arm is a DsbC monomer of two domains linked by a hinge; and the N-termini of each monomer join to form the dimer interface at the base of the V, so are vital for dimerisation []. DsbC is required for disulphide bond formation and functions as a disulphide bond isomerase during oxidative protein-folding in bacterial periplasm. It also has chaperone activity []. ; PDB: 1EEJ_B 2IYJ_A 1TJD_A 1JZD_B 1JZO_A 1G0T_B 1T3B_A.
Probab=25.21 E-value=59 Score=27.34 Aligned_cols=16 Identities=31% Similarity=0.694 Sum_probs=14.3
Q ss_pred EEEEEcCCCCeEEecC
Q 003580 728 RILYTDSENDVMVVGD 743 (809)
Q Consensus 728 ~~vY~D~EGD~mLVGD 743 (809)
.++|.|.+|+.+++|+
T Consensus 34 ~i~Y~~~dg~yli~G~ 49 (57)
T PF10411_consen 34 GILYVDEDGRYLIQGQ 49 (57)
T ss_dssp EEEEEETTSSEEEES-
T ss_pred eEEEEcCCCCEEEEeE
Confidence 5999999999999997
No 31
>cd05792 S1_eIF1AD_like S1_eIF1AD_like: eukaryotic translation initiation factor 1A domain containing protein (eIF1AD)-like, S1-like RNA-binding domain. eIF1AD is also known as MGC11102 protein. Little is known about the function of eIF1AD. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins, including translation initiation factor IF1A (also referred to as eIF1A in eukaryotes). eIF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors.
Probab=24.11 E-value=60 Score=29.55 Aligned_cols=32 Identities=22% Similarity=0.421 Sum_probs=25.3
Q ss_pred CCCCeEEecCCCCchhhhccc--eEEEEecHHhHhccc
Q 003580 734 SENDVMVVGDDPWHSEFCNEV--SKIHIYTQEEVEKMT 769 (809)
Q Consensus 734 ~EGD~mLVGD~PW~~~F~~~v--kri~I~~~~e~~~m~ 769 (809)
++||..|| +||+ |-+-+ -=++||++++++.|.
T Consensus 40 krGd~VlV--~p~~--~~~kvkgeIv~i~~~~qvk~L~ 73 (78)
T cd05792 40 KRGDFVLV--EPIE--EGDKVKAEIVKILTRDHVKYIK 73 (78)
T ss_pred EeCCEEEE--Eecc--cCCceEEEEEEEECHHHHHHHH
Confidence 78999999 6999 76533 348999999998773
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=23.90 E-value=1.1e+02 Score=25.85 Aligned_cols=31 Identities=26% Similarity=0.517 Sum_probs=24.1
Q ss_pred cccEEEEEeecCCCCcceeeeEEeeeccCCC
Q 003580 338 IGTRFKMRFEMDDSPERRCNGVVTGITDLDP 368 (809)
Q Consensus 338 ~GmRFKM~fE~EDs~~~r~~GTI~gi~d~Dp 368 (809)
+|-|+.-.||.++.+...|.|+|...-+..|
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 5889999999888888789999999877665
No 33
>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=22.78 E-value=87 Score=28.78 Aligned_cols=36 Identities=19% Similarity=0.290 Sum_probs=23.7
Q ss_pred hhhhcccCCccCCEEEEEEcCCCc-EEEeEEeccCCC
Q 003580 242 SIFVSQKNLVSGDAVLFLRGKDGE-LRLGIRRSVQPR 277 (809)
Q Consensus 242 s~FV~~K~L~aGD~VvF~R~~~Ge-l~vGVRRa~r~~ 277 (809)
..|+++++|..||.|.++|..+.= ..+++-...|..
T Consensus 42 ~~~i~~~~i~~Gd~V~V~raGdVIP~I~~vv~~~r~~ 78 (82)
T PF03120_consen 42 YDYIKELDIRIGDTVLVTRAGDVIPKIVGVVKEKRTG 78 (82)
T ss_dssp HHHHHHTT-BBT-EEEEEEETTTEEEEEEE-GGG--S
T ss_pred HHHHHHcCCCCCCEEEEEECCCccceEeEeehhcCCC
Confidence 478999999999999999987763 344555555544
No 34
>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=22.39 E-value=1.2e+02 Score=27.95 Aligned_cols=55 Identities=20% Similarity=0.253 Sum_probs=29.5
Q ss_pred ehhHHHHhhccCcccccEEEEEeecCCCCcce--eeeEEeeeccCCCCCCCCCCceeEEEEecCCC
Q 003580 324 PYQKYVKIIMNPICIGTRFKMRFEMDDSPERR--CNGVVTGITDLDPYRWPNSKWRCLMVRWDECI 387 (809)
Q Consensus 324 p~~ky~~A~~~~ws~GmRFKM~fE~EDs~~~r--~~GTI~gi~d~Dp~rWP~S~WR~L~V~WDe~~ 387 (809)
..+.|..=++-+..+||++||.=.-| +++ =.|+|.-++. | .-|+ -.++|.|-...
T Consensus 6 s~d~Ya~YVr~~i~~GM~VRc~~~ye---eV~~GD~G~V~k~~~-d--g~~~---lnvqv~W~~~G 62 (78)
T PF11515_consen 6 SNDDYAEYVRDNIQPGMRVRCCRDYE---EVRAGDEGEVFKQDR-D--GLHD---LNVQVDWQSKG 62 (78)
T ss_dssp SSHHHHHHHHHH--TT-EEEESS-BT---TB-TT-EEE-EEEE--T--TSSE-----EEEEETTTT
T ss_pred chhHHHHHHHHhCCCCcEEEEecccc---cccccccceeEeecc-C--CCCC---cceEEEeeecC
Confidence 34567777888999999999973333 333 3777666654 2 1121 25888887654
No 35
>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=21.54 E-value=86 Score=30.33 Aligned_cols=26 Identities=23% Similarity=0.348 Sum_probs=16.5
Q ss_pred cCCccCCEEEEEEcC-CCcEEEeEEec
Q 003580 248 KNLVSGDAVLFLRGK-DGELRLGIRRS 273 (809)
Q Consensus 248 K~L~aGD~VvF~R~~-~Gel~vGVRRa 273 (809)
|+++.||.|+||... .+.-++|+=+-
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 45556665553
No 36
>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=21.11 E-value=2.5e+02 Score=24.43 Aligned_cols=58 Identities=7% Similarity=0.095 Sum_probs=43.3
Q ss_pred ceEEEeecccee---cccccccCCCChHHHHHHHHHHhcccccccCCCCCcEEE-EEcCCC-CeEEe
Q 003580 680 SCTKVHKQGSLV---GRAIDLWRLNGYNDLLSELEHLFNMEGLLRDPAKGWRIL-YTDSEN-DVMVV 741 (809)
Q Consensus 680 ~~vKV~m~G~~v---GRkvDL~~~~~Y~eL~~~L~~MF~~~g~L~~~~~~w~~v-Y~D~EG-D~mLV 741 (809)
.++||+.+...- -+.|-++.-..-.+++..+-+-|++. +...+|.|+ +.-..| ...|-
T Consensus 3 ~~lrVy~~~~~~~~~~k~i~v~~~tTa~evi~~~l~k~~l~----~~~~~y~L~~~~~~~~~er~L~ 65 (93)
T PF00788_consen 3 GVLRVYDGDGSPGSTYKTIKVSSSTTAREVIEMALEKFGLA----EDPSDYCLVEVEESGGEERPLD 65 (93)
T ss_dssp EEEEEEETTSSSCCSEEEEEEETTSBHHHHHHHHHHHTTTS----SSGGGEEEEEEECTTTEEEEET
T ss_pred eEEEEEcCCCCCCccEEEEEECCCCCHHHHHHHHHHHhCCC----CCCCCEEEEEEEcCCCEEEEcC
Confidence 478999877643 57899999999999999999999982 345689995 444444 44443
Done!