Query 003592
Match_columns 808
No_of_seqs 374 out of 836
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 02:21:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003592.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003592hhsearch_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 9.9E-36 2.2E-40 263.6 8.5 83 298-380 1-83 (83)
2 PF02309 AUX_IAA: AUX/IAA fami 100.0 3.5E-35 7.6E-40 299.1 0.0 96 676-771 106-215 (215)
3 PF02362 B3: B3 DNA binding do 99.6 8.1E-16 1.8E-20 137.1 11.1 97 172-273 1-99 (100)
4 KOG0644 Uncharacterized conser 99.4 2.6E-13 5.6E-18 157.2 5.4 148 250-405 874-1044(1113)
5 PF09217 EcoRII-N: Restriction 98.2 7.7E-06 1.7E-10 80.7 9.6 90 168-259 6-110 (156)
6 PF03754 DUF313: Domain of unk 97.5 0.00021 4.6E-09 67.9 6.0 78 169-247 21-114 (114)
7 PF00564 PB1: PB1 domain; Int 96.8 0.003 6.4E-08 55.1 6.4 67 681-754 3-70 (84)
8 smart00666 PB1 PB1 domain. Pho 96.0 0.024 5.3E-07 49.3 7.1 65 682-754 4-69 (81)
9 cd05992 PB1 The PB1 domain is 95.6 0.043 9.3E-07 47.5 7.0 65 682-754 3-69 (81)
10 cd06407 PB1_NLP A PB1 domain i 95.4 0.046 1E-06 49.3 6.5 54 681-741 2-55 (82)
11 cd06396 PB1_NBR1 The PB1 domai 95.3 0.049 1.1E-06 49.3 6.4 52 682-741 3-54 (81)
12 cd06398 PB1_Joka2 The PB1 doma 95.2 0.057 1.2E-06 49.6 6.8 58 682-744 3-63 (91)
13 cd06409 PB1_MUG70 The MUG70 pr 94.6 0.058 1.3E-06 49.3 5.0 50 690-742 8-59 (86)
14 cd06402 PB1_p62 The PB1 domain 93.4 0.31 6.6E-06 44.8 7.3 64 681-766 2-70 (87)
15 cd06403 PB1_Par6 The PB1 domai 93.1 0.2 4.4E-06 45.3 5.4 66 682-754 3-70 (80)
16 cd06404 PB1_aPKC PB1 domain is 92.2 0.55 1.2E-05 42.9 7.1 60 682-765 3-62 (83)
17 cd06397 PB1_UP1 Uncharacterize 90.9 0.65 1.4E-05 42.2 6.2 49 683-739 4-52 (82)
18 cd06401 PB1_TFG The PB1 domain 90.4 1.3 2.8E-05 40.4 7.6 58 682-744 3-61 (81)
19 cd06408 PB1_NoxR The PB1 domai 85.7 1.5 3.1E-05 40.4 4.9 55 679-743 2-56 (86)
20 cd06399 PB1_P40 The PB1 domain 83.8 1.6 3.6E-05 40.3 4.4 49 696-769 23-71 (92)
21 PRK10737 FKBP-type peptidyl-pr 66.7 24 0.00053 37.0 8.1 103 249-365 2-114 (196)
22 KOG0644 Uncharacterized conser 54.2 9.3 0.0002 47.4 2.8 66 71-137 872-940 (1113)
23 KOG3207 Beta-tubulin folding c 45.0 27 0.00058 41.0 4.5 43 336-392 3-45 (505)
24 PF04014 Antitoxin-MazE: Antid 40.0 32 0.0007 27.6 3.0 27 243-269 14-40 (47)
25 smart00743 Agenet Tudor-like d 34.8 54 0.0012 27.2 3.7 38 335-385 2-39 (61)
26 PF10844 DUF2577: Protein of u 33.2 55 0.0012 30.5 3.9 27 244-270 71-97 (100)
27 cd06395 PB1_Map2k5 PB1 domain 32.4 83 0.0018 29.2 4.6 58 687-768 9-66 (91)
28 COG1047 SlpA FKBP-type peptidy 30.3 3E+02 0.0065 28.7 8.8 106 248-365 1-115 (174)
29 TIGR01439 lp_hng_hel_AbrB loop 30.3 61 0.0013 24.8 3.1 26 243-268 14-39 (43)
30 PF10411 DsbC_N: Disulfide bon 25.3 58 0.0012 27.4 2.3 17 728-744 34-50 (57)
31 PF00788 RA: Ras association ( 23.3 2.1E+02 0.0045 24.9 5.6 69 680-752 3-77 (93)
32 PF02513 Spin-Ssty: Spin/Ssty 23.2 1.2E+02 0.0026 25.7 3.7 31 338-368 1-31 (50)
33 PF03120 DNA_ligase_OB: NAD-de 22.6 91 0.002 28.7 3.2 36 242-277 42-78 (82)
34 PF01878 EVE: EVE domain; Int 21.6 87 0.0019 30.3 3.1 26 248-273 38-64 (143)
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=9.9e-36 Score=263.64 Aligned_cols=83 Identities=54% Similarity=0.997 Sum_probs=81.5
Q ss_pred HHHHhhcCCeEEEEEcCCCCCCceeeehhHHHHhhccCcccccEEEEEeecCCCCcceeeeEEeeeccCCCCCCCCCCce
Q 003592 298 VANAVSTKSMFHVFYSPRATHADFVIPYQKYVKIIMNPICIGTRFKMRFEMDDSPERRCNGVVTGITDLDPYRWPNSKWR 377 (808)
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 (808)
|+|||+++++|+|+||||++++|||||++||++||+++|++||||||+||+||+++++|+|||+||++.||++||+|+||
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 003592 378 CLM 380 (808)
Q Consensus 378 ~L~ 380 (808)
|||
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=3.5e-35 Score=299.11 Aligned_cols=96 Identities=35% Similarity=0.646 Sum_probs=0.0
Q ss_pred CCCCceeEEeeccceecccccccCCCChHHHHHHHHHHh---hcc----------ccccC-CCCCcEEEEEeCCCCeEEe
Q 003592 676 PGKRSCTKVHKQGSLVGRAIDLWRLNGYNDLLSELEHLF---NME----------GLLRD-PAKGWRILYTDSENDVMVV 741 (808)
Q Consensus 676 ~~~~~~vKV~m~G~~vGRkVDL~~~~~Y~eL~~~L~~MF---~~~----------g~L~~-~~~~~~lvY~D~EGD~mLV 741 (808)
...++||||+|||++|||||||++|+||++|+.+|++|| +|. +.+.. ..++|+|||+|+|||||||
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 345899999999999999999999999999999999999 665 22321 3569999999999999999
Q ss_pred cCcchhhhhhcceeEEEechHhhhccccCC
Q 003592 742 GDDPWHEFCNEVSKIHIYTQEEVEKMTIGT 771 (808)
Q Consensus 742 GD~PW~~F~~~vkrI~I~~~~ev~~m~~~~ 771 (808)
|||||+|||++||||+||+.+|+++|+|++
T Consensus 186 GD~PW~~F~~~vkRl~I~~~~e~~~~~~r~ 215 (215)
T PF02309_consen 186 GDVPWEEFVKSVKRLRIMKSSEAKGLAPRA 215 (215)
T ss_dssp ------------------------------
T ss_pred cCCCHHHHHHHhhccEEecHHHhcccCCCC
Confidence 999999999999999999999999999874
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=99.65 E-value=8.1e-16 Score=137.06 Aligned_cols=97 Identities=32% Similarity=0.481 Sum_probs=74.7
Q ss_pred EEEecCcccCCCCCceeEeccchhhcCCCCCCCCCCCceEEEEeeCCCCeEEEEEEEeCCCCceeecccchhhhcccCCc
Q 003592 172 FCKTLTASDTSTHGGFSVPRRAAEDCFPPLDYKQQRPSQELVAKDLHGVEWRFRHIYRGQPRRHLLTTGWSIFVSQKNLV 251 (808)
Q Consensus 172 F~K~LT~SDv~~~grfsVPk~~Ae~~FPpLd~~~~~p~q~L~~~Dl~G~~W~Fr~~yrg~prrhlLTtGWs~FV~~K~L~ 251 (808)
|.|+|+++|+...++|.||++.++.+.. + ...++++.++|..|+.|.+++.+++.+.+++|++||..||++++|+
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--N---KRKSREVTLKDPDGRSWPVKLKYRKNSGRYYLTGGWKKFVRDNGLK 75 (100)
T ss_dssp EEEE--TTCCCCTT-EEE-HHHHTTTS-------SS--CEEEEEETTTEEEEEEEEEECCTTEEEEETTHHHHHHHCT--
T ss_pred CEEEEEccCcCCCCEEEeCHHHHHHhCC--C---cCCCeEEEEEeCCCCEEEEEEEEEccCCeEEECCCHHHHHHHcCCC
Confidence 8999999999998999999999988821 1 1235789999999999999999998888999999999999999999
Q ss_pred CCCEEEEEEcCC--CcEEEeEEec
Q 003592 252 SGDAVLFLRGKD--GELRLGIRRS 273 (808)
Q Consensus 252 aGD~VvF~R~~~--Gel~vGIRRa 273 (808)
+||.++|....+ .++.|.|.|+
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 999999998653 4679999986
No 4
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=99.38 E-value=2.6e-13 Score=157.15 Aligned_cols=148 Identities=20% Similarity=0.311 Sum_probs=120.3
Q ss_pred CcCCCEEEEEEcCCCcEEEeEEeccCCCCC-CCC--------------------CccccCCChhhHHHHHHHHhhcCCeE
Q 003592 250 LVSGDAVLFLRGKDGELRLGIRRSVQPRNG-LPD--------------------SILSKQNSYPNVLSVVANAVSTKSMF 308 (808)
Q Consensus 250 L~aGD~VvF~R~~~Gel~vGIRRa~r~~~~-~p~--------------------sv~s~~~m~~~vlaaa~~a~~t~~~F 308 (808)
.+.||.|+.+|...-++.=.+|+..+..++ .|+ +--+-..|.+.||..|.++. ...|
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 468999999998776665555555444333 233 22234579999999998764 6789
Q ss_pred EEEEcCCCCCCceeeehhHHHHhhccCcccccEEEEEee--cCCCCcceeeeEEeeeccCCCCCCCCCCceeEEEEecCC
Q 003592 309 HVFYSPRATHADFVIPYQKYVKIIMNPICIGTRFKMRFE--MDDSPERRCNGVVTGITDLDPYRWPNSKWRCLMVRWDEC 386 (808)
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 (808)
.+.|......+||+|.++.|++|++++|..+++||.-+. +|+. -.||.|+|.++.+..| .+|+|+|+|+.|+||..
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 003592 387 IGSDHQEQVSPWEIDRSVS 405 (808)
Q Consensus 387 ~~~~~~~RVSPWeIEp~~~ 405 (808)
+. +.-||||.|++..
T Consensus 1030 e~----~~~spwe~~~i~d 1044 (1113)
T KOG0644|consen 1030 ET----ELHSPWEMEPIPD 1044 (1113)
T ss_pred cc----cccCccccCCCcc
Confidence 74 5789999999864
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=98.19 E-value=7.7e-06 Score=80.71 Aligned_cols=90 Identities=26% Similarity=0.378 Sum_probs=60.9
Q ss_pred CceeEEEecCcccCCCCC----ceeEeccchhhcCCCCCC-CCCCCceEEEEeeCCC--CeEEEEEEEeCC------CCc
Q 003592 168 TPHMFCKTLTASDTSTHG----GFSVPRRAAEDCFPPLDY-KQQRPSQELVAKDLHG--VEWRFRHIYRGQ------PRR 234 (808)
Q Consensus 168 ~~~~F~K~LT~SDv~~~g----rfsVPk~~Ae~~FPpLd~-~~~~p~q~L~~~Dl~G--~~W~Fr~~yrg~------prr 234 (808)
....|+|.|++.|++..| |+.|||..++..||.+.. ....|...|.+++..| ..|+||+||.|+ ...
T Consensus 6 ~~~~~~K~LSaNDtGaTGgHQaGiyIpk~~~~~lFp~~~~~~~~Np~~~~~~~~~s~~~~~~~~r~iYYnn~~~~gTRNE 85 (156)
T PF09217_consen 6 SWAIYCKRLSANDTGATGGHQAGIYIPKSAAELLFPSINHTKEENPDIWLKARWQSHFVTDSQVRFIYYNNRLFGGTRNE 85 (156)
T ss_dssp SEEEEEEE--CCCCTTTSSS--EEEE-HHHHHHH-GGG-SSSSSS-EEEEEEEETTTT---EEEEEEEE-CCCTTSS--E
T ss_pred ceEEEEEEccCCCCCCcCcccceeEecccHHHHhCCCCCcccccCCceeEEEEECCCCccceeEEEEEEcccccCCCcCc
Confidence 346899999999999875 799999999999998877 5567889999999888 569999999988 356
Q ss_pred eeec--ccchhhhcccCCcCCCEEEEE
Q 003592 235 HLLT--TGWSIFVSQKNLVSGDAVLFL 259 (808)
Q Consensus 235 hlLT--tGWs~FV~~K~L~aGD~VvF~ 259 (808)
+.|| ++=..|.+. =..||-+||.
T Consensus 86 ~RIT~~G~~~~~~~~--~~tGaL~vla 110 (156)
T PF09217_consen 86 YRITRFGRGFPLQNP--ENTGALLVLA 110 (156)
T ss_dssp EEEE---TTSGGG-G--GGTT-EEEEE
T ss_pred eEEeeecCCCccCCc--cccccEEEEE
Confidence 7886 333333332 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=97.47 E-value=0.00021 Score=67.93 Aligned_cols=78 Identities=22% Similarity=0.306 Sum_probs=60.5
Q ss_pred ceeEEEecCcccCCCC-CceeEeccchhhcCCCCCC------------CCCCCceEEEEeeCCCCeEEEEEEEeCC---C
Q 003592 169 PHMFCKTLTASDTSTH-GGFSVPRRAAEDCFPPLDY------------KQQRPSQELVAKDLHGVEWRFRHIYRGQ---P 232 (808)
Q Consensus 169 ~~~F~K~LT~SDv~~~-grfsVPk~~Ae~~FPpLd~------------~~~~p~q~L~~~Dl~G~~W~Fr~~yrg~---p 232 (808)
-..|.|+|++||+..+ +||+||-..... ...|.. ....-++...+.|..++.|..++..|.. .
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 122321 1234468899999999999999999955 4
Q ss_pred Cceeecccchhhhcc
Q 003592 233 RRHLLTTGWSIFVSQ 247 (808)
Q Consensus 233 rrhlLTtGWs~FV~~ 247 (808)
-.|+|++||..+|+.
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=96.83 E-value=0.003 Score=55.07 Aligned_cols=67 Identities=22% Similarity=0.405 Sum_probs=55.0
Q ss_pred eeEEeeccceecccccccCCCChHHHHHHHHHHhhccccccCCCCCcEEEEEeCCCCeEEecCcc-hhhhhhcce
Q 003592 681 CTKVHKQGSLVGRAIDLWRLNGYNDLLSELEHLFNMEGLLRDPAKGWRILYTDSENDVMVVGDDP-WHEFCNEVS 754 (808)
Q Consensus 681 ~vKV~m~G~~vGRkVDL~~~~~Y~eL~~~L~~MF~~~g~L~~~~~~~~lvY~D~EGD~mLVGD~P-W~~F~~~vk 754 (808)
-+|++-.|. +=|.+.+..--+|++|...+++.|++. ...+++.|.|.||||..+-++- |++.++.++
T Consensus 3 ~vK~~~~~~-~~~~~~~~~~~s~~~L~~~i~~~~~~~------~~~~~l~Y~D~dgD~V~i~sd~Dl~~a~~~~~ 70 (84)
T PF00564_consen 3 RVKVRYGGD-IRRIISLPSDVSFDDLRSKIREKFGLL------DEDFQLKYKDEDGDLVTISSDEDLQEAIEQAK 70 (84)
T ss_dssp EEEEEETTE-EEEEEEECSTSHHHHHHHHHHHHHTTS------TSSEEEEEEETTSSEEEESSHHHHHHHHHHHH
T ss_pred EEEEEECCe-eEEEEEcCCCCCHHHHHHHHHHHhCCC------CccEEEEeeCCCCCEEEeCCHHHHHHHHHHHH
Confidence 378888886 444688888889999999999999975 4678999999999998887554 777777764
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=95.99 E-value=0.024 Score=49.32 Aligned_cols=65 Identities=20% Similarity=0.380 Sum_probs=50.4
Q ss_pred eEEeeccceecccccccCCCChHHHHHHHHHHhhccccccCCCCCcEEEEEeCCCCeEEecC-cchhhhhhcce
Q 003592 682 TKVHKQGSLVGRAIDLWRLNGYNDLLSELEHLFNMEGLLRDPAKGWRILYTDSENDVMVVGD-DPWHEFCNEVS 754 (808)
Q Consensus 682 vKV~m~G~~vGRkVDL~~~~~Y~eL~~~L~~MF~~~g~L~~~~~~~~lvY~D~EGD~mLVGD-~PW~~F~~~vk 754 (808)
+||+-.| -=|.+-+..--+|++|..++.+.|++.. ..+.|-|+|.||||..+.+ .=|++.+.+++
T Consensus 4 vK~~~~~--~~~~~~~~~~~s~~dL~~~i~~~~~~~~------~~~~l~Y~Dedgd~v~l~sd~Dl~~a~~~~~ 69 (81)
T smart00666 4 VKLRYGG--ETRRLSVPRDISFEDLRSKVAKRFGLDN------QSFTLKYQDEDGDLVSLTSDEDLEEAIEEYD 69 (81)
T ss_pred EEEEECC--EEEEEEECCCCCHHHHHHHHHHHhCCCC------CCeEEEEECCCCCEEEecCHHHHHHHHHHHH
Confidence 6777744 3577778888899999999999999542 5689999999999976654 44666666654
No 9
>cd05992 PB1 The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as a noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.
Probab=95.60 E-value=0.043 Score=47.49 Aligned_cols=65 Identities=22% Similarity=0.403 Sum_probs=49.3
Q ss_pred eEEeeccceeccccccc-CCCChHHHHHHHHHHhhccccccCCCCCcEEEEEeCCCCeEEecC-cchhhhhhcce
Q 003592 682 TKVHKQGSLVGRAIDLW-RLNGYNDLLSELEHLFNMEGLLRDPAKGWRILYTDSENDVMVVGD-DPWHEFCNEVS 754 (808)
Q Consensus 682 vKV~m~G~~vGRkVDL~-~~~~Y~eL~~~L~~MF~~~g~L~~~~~~~~lvY~D~EGD~mLVGD-~PW~~F~~~vk 754 (808)
+||+-.|. =|.+=+. .--+|++|...|.+.|++.. ..+.+.|.|.||||..+.+ .=|++.++.++
T Consensus 3 vK~~~~~~--~~~~~~~~~~~s~~~L~~~i~~~~~~~~------~~~~l~y~D~e~d~v~l~sd~Dl~~a~~~~~ 69 (81)
T cd05992 3 VKVKYGGE--IRRFVVVSRSISFEDLRSKIAEKFGLDA------VSFKLKYPDEDGDLVTISSDEDLEEAIEEAR 69 (81)
T ss_pred EEEEecCC--CEEEEEecCCCCHHHHHHHHHHHhCCCC------CcEEEEeeCCCCCEEEeCCHHHHHHHHHHHh
Confidence 67777764 2344444 78899999999999999753 5688999999999988777 44666666654
No 10
>cd06407 PB1_NLP A PB1 domain is present in NIN like proteins (NLP), a key enzyme in a process of establishment of symbiosis betweeen legumes and nitrogen fixing bacteria (Rhizobium). The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes like osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-inte
Probab=95.37 E-value=0.046 Score=49.26 Aligned_cols=54 Identities=15% Similarity=0.279 Sum_probs=42.0
Q ss_pred eeEEeeccceecccccccCCCChHHHHHHHHHHhhccccccCCCCCcEEEEEeCCCCeEEe
Q 003592 681 CTKVHKQGSLVGRAIDLWRLNGYNDLLSELEHLFNMEGLLRDPAKGWRILYTDSENDVMVV 741 (808)
Q Consensus 681 ~vKV~m~G~~vGRkVDL~~~~~Y~eL~~~L~~MF~~~g~L~~~~~~~~lvY~D~EGD~mLV 741 (808)
-|||...|. -+.+-|..--+|++|.+++.++|.+. ....+.|-|.|.||||.++
T Consensus 2 ~vK~~~~~d--~~r~~l~~~~~~~~L~~~i~~r~~~~-----~~~~f~LkY~Ddegd~v~l 55 (82)
T cd06407 2 RVKATYGEE--KIRFRLPPSWGFTELKQEIAKRFKLD-----DMSAFDLKYLDDDEEWVLL 55 (82)
T ss_pred EEEEEeCCe--EEEEEcCCCCCHHHHHHHHHHHhCCC-----CCCeeEEEEECCCCCeEEe
Confidence 378888886 23444445559999999999999974 2367999999999999654
No 11
>cd06396 PB1_NBR1 The PB1 domain is an essential part of NBR1 protein, next to BRCA1, a scaffold protein mediating specific protein-protein interaction with both titin protein kinase and with another scaffold protein p62. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The NBR1 protein contains a type I PB1 domain.
Probab=95.30 E-value=0.049 Score=49.32 Aligned_cols=52 Identities=19% Similarity=0.226 Sum_probs=43.0
Q ss_pred eEEeeccceecccccccCCCChHHHHHHHHHHhhccccccCCCCCcEEEEEeCCCCeEEe
Q 003592 682 TKVHKQGSLVGRAIDLWRLNGYNDLLSELEHLFNMEGLLRDPAKGWRILYTDSENDVMVV 741 (808)
Q Consensus 682 vKV~m~G~~vGRkVDL~~~~~Y~eL~~~L~~MF~~~g~L~~~~~~~~lvY~D~EGD~mLV 741 (808)
+||.-.|.-+-=+++-+.--+|.+|..++.++|++. .+.|-|.|.||||.++
T Consensus 3 vKaty~~d~~rf~~~~~~~~~~~~L~~ev~~rf~l~--------~f~lKYlDde~e~v~l 54 (81)
T cd06396 3 LKVTYNGESQSFLVSDSENTTWASVEAMVKVSFGLN--------DIQIKYVDEENEEVSV 54 (81)
T ss_pred EEEEECCeEEEEEecCCCCCCHHHHHHHHHHHhCCC--------cceeEEEcCCCCEEEE
Confidence 788888875444666666779999999999999986 5789999999999665
No 12
>cd06398 PB1_Joka2 The PB1 domain is present in the Nicotiana plumbaginifolia Joka2 protein which interacts with sulfur stress inducible UP9 protein. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module
Probab=95.24 E-value=0.057 Score=49.63 Aligned_cols=58 Identities=28% Similarity=0.402 Sum_probs=44.7
Q ss_pred eEEeeccceeccccccc---CCCChHHHHHHHHHHhhccccccCCCCCcEEEEEeCCCCeEEecCc
Q 003592 682 TKVHKQGSLVGRAIDLW---RLNGYNDLLSELEHLFNMEGLLRDPAKGWRILYTDSENDVMVVGDD 744 (808)
Q Consensus 682 vKV~m~G~~vGRkVDL~---~~~~Y~eL~~~L~~MF~~~g~L~~~~~~~~lvY~D~EGD~mLVGD~ 744 (808)
+||.-+|.-+==++++. .--+|++|.+++.+.|.+. +..+++|.|.|.||||..+-++
T Consensus 3 vKv~y~~~~rRf~l~~~~~~~d~~~~~L~~kI~~~f~l~-----~~~~~~l~Y~Dedgd~V~l~~D 63 (91)
T cd06398 3 VKVKYGGTLRRFTFPVAENQLDLNMDGLREKVEELFSLS-----PDADLSLTYTDEDGDVVTLVDD 63 (91)
T ss_pred EEEEeCCEEEEEEeccccccCCCCHHHHHHHHHHHhCCC-----CCCcEEEEEECCCCCEEEEccH
Confidence 79998887322255553 4579999999999999863 3478999999999999766544
No 13
>cd06409 PB1_MUG70 The MUG70 protein is a product of the meiotically up-regulated gene 70 which has a role in meiosis and harbors a PB1 domain. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domains depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic amino acid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is
Probab=94.60 E-value=0.058 Score=49.33 Aligned_cols=50 Identities=16% Similarity=0.312 Sum_probs=39.5
Q ss_pred eeccccc--ccCCCChHHHHHHHHHHhhccccccCCCCCcEEEEEeCCCCeEEec
Q 003592 690 LVGRAID--LWRLNGYNDLLSELEHLFNMEGLLRDPAKGWRILYTDSENDVMVVG 742 (808)
Q Consensus 690 ~vGRkVD--L~~~~~Y~eL~~~L~~MF~~~g~L~~~~~~~~lvY~D~EGD~mLVG 742 (808)
+-||.+= +....|+.+|..+..+-|+++.. ....++|.|.|+||||.++-
T Consensus 8 ~~GrvhRf~~~~s~~~~~L~~~I~~Rl~~d~~---~~~~~~L~YlDDEgD~VllT 59 (86)
T cd06409 8 PKGRVHRFRLRPSESLEELRTLISQRLGDDDF---ETHLYALSYVDDEGDIVLIT 59 (86)
T ss_pred CCCCEEEEEecCCCCHHHHHHHHHHHhCCccc---cCCcccEEEEcCCCCEEEEe
Confidence 4566443 34478999999999999998764 24689999999999998764
No 14
>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=93.44 E-value=0.31 Score=44.79 Aligned_cols=64 Identities=23% Similarity=0.358 Sum_probs=49.7
Q ss_pred eeEEeecc----ceecc-cccccCCCChHHHHHHHHHHhhccccccCCCCCcEEEEEeCCCCeEEecCcchhhhhhccee
Q 003592 681 CTKVHKQG----SLVGR-AIDLWRLNGYNDLLSELEHLFNMEGLLRDPAKGWRILYTDSENDVMVVGDDPWHEFCNEVSK 755 (808)
Q Consensus 681 ~vKV~m~G----~~vGR-kVDL~~~~~Y~eL~~~L~~MF~~~g~L~~~~~~~~lvY~D~EGD~mLVGD~PW~~F~~~vkr 755 (808)
.||.+..| ..|=| +||=....+|++|...+.++|..- ....++|-|.|.|||.
T Consensus 2 ~vkayl~~~~~~~EIRRf~l~~~~~~s~~~L~~~V~~~f~~l-----~~~~ftlky~DeeGDl----------------- 59 (87)
T cd06402 2 TVKAYLLGKDANAEIRRFAIDEDVSTSYEYLVEKVAAVFPSL-----RGKNFQLFWKDEEGDL----------------- 59 (87)
T ss_pred eEEEeecCCCCccceEEEEecCCCCcCHHHHHHHHHHHcccc-----CCCcEEEEEECCCCCE-----------------
Confidence 57888877 44444 566677789999999999999531 1367999999999999
Q ss_pred EEEechHhhhc
Q 003592 756 IHIYTQEEVEK 766 (808)
Q Consensus 756 I~I~~~~ev~~ 766 (808)
|.|-+.+|.+.
T Consensus 60 vtIssdeEL~~ 70 (87)
T cd06402 60 VAFSSDEELVM 70 (87)
T ss_pred EeecCHHHHHH
Confidence 77888887764
No 15
>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=93.06 E-value=0.2 Score=45.29 Aligned_cols=66 Identities=23% Similarity=0.379 Sum_probs=50.3
Q ss_pred eEEeeccceecc-cccccCCCChHHHHHHHHHHhhccccccCCCCCcEEEEEeCCCCeEEec-Ccchhhhhhcce
Q 003592 682 TKVHKQGSLVGR-AIDLWRLNGYNDLLSELEHLFNMEGLLRDPAKGWRILYTDSENDVMVVG-DDPWHEFCNEVS 754 (808)
Q Consensus 682 vKV~m~G~~vGR-kVDL~~~~~Y~eL~~~L~~MF~~~g~L~~~~~~~~lvY~D~EGD~mLVG-D~PW~~F~~~vk 754 (808)
||.+-++. +-| ++|.....+|+++..-|++|+.+.+ -.+.|-|+|.+||.+-+- |+-...=+++++
T Consensus 3 VKSkfdaE-fRRFsl~r~~~~~f~ef~~ll~~lH~l~~------~~f~i~Y~D~~gDLLPInNDdNf~kAlssa~ 70 (80)
T cd06403 3 VKSKFDAE-FRRFSLDRNKPGKFEDFYKLLEHLHHIPN------VDFLIGYTDPHGDLLPINNDDNFLKALSSAN 70 (80)
T ss_pred eecccCCe-EEEEEeccccCcCHHHHHHHHHHHhCCCC------CcEEEEEeCCCCCEecccCcHHHHHHHHcCC
Confidence 56655554 555 7888888999999999999999754 469999999999998664 444555555554
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=92.24 E-value=0.55 Score=42.90 Aligned_cols=60 Identities=22% Similarity=0.326 Sum_probs=48.2
Q ss_pred eEEeeccceecccccccCCCChHHHHHHHHHHhhccccccCCCCCcEEEEEeCCCCeEEecCcchhhhhhcceeEEEech
Q 003592 682 TKVHKQGSLVGRAIDLWRLNGYNDLLSELEHLFNMEGLLRDPAKGWRILYTDSENDVMVVGDDPWHEFCNEVSKIHIYTQ 761 (808)
Q Consensus 682 vKV~m~G~~vGRkVDL~~~~~Y~eL~~~L~~MF~~~g~L~~~~~~~~lvY~D~EGD~mLVGD~PW~~F~~~vkrI~I~~~ 761 (808)
+|++-.|..+-=.+|. .-+|++|.+++.+||.+. ....+++.|.|.|||. +.|-+.
T Consensus 3 ~K~~y~gdi~it~~d~--~~s~e~L~~~v~~~c~~~-----~~q~ft~kw~DEEGDp-----------------~tiSS~ 58 (83)
T cd06404 3 VKAAYNGDIMITSIDP--SISLEELCNEVRDMCRFH-----NDQPFTLKWIDEEGDP-----------------CTISSQ 58 (83)
T ss_pred EEEEecCcEEEEEcCC--CcCHHHHHHHHHHHhCCC-----CCCcEEEEEECCCCCc-----------------eeecCH
Confidence 7899999755556666 667999999999999962 3457999999999998 677777
Q ss_pred Hhhh
Q 003592 762 EEVE 765 (808)
Q Consensus 762 ~ev~ 765 (808)
+|++
T Consensus 59 ~EL~ 62 (83)
T cd06404 59 MELE 62 (83)
T ss_pred HHHH
Confidence 6664
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=90.94 E-value=0.65 Score=42.24 Aligned_cols=49 Identities=29% Similarity=0.406 Sum_probs=39.9
Q ss_pred EEeeccceecccccccCCCChHHHHHHHHHHhhccccccCCCCCcEEEEEeCCCCeE
Q 003592 683 KVHKQGSLVGRAIDLWRLNGYNDLLSELEHLFNMEGLLRDPAKGWRILYTDSENDVM 739 (808)
Q Consensus 683 KV~m~G~~vGRkVDL~~~~~Y~eL~~~L~~MF~~~g~L~~~~~~~~lvY~D~EGD~m 739 (808)
||.-.|. -|++.-..-=+|..|.+.|+.+|.+.- ....|+|.|.|||..
T Consensus 4 Kv~~~g~--~RRf~~~~~pt~~~L~~kl~~Lf~lp~------~~~~vtYiDeD~D~I 52 (82)
T cd06397 4 KSSFLGD--TRRIVFPDIPTWEALASKLENLYNLPE------IKVGVTYIDNDNDEI 52 (82)
T ss_pred EEEeCCc--eEEEecCCCccHHHHHHHHHHHhCCCh------hHeEEEEEcCCCCEE
Confidence 7766664 577777778899999999999999753 127799999999984
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=90.40 E-value=1.3 Score=40.37 Aligned_cols=58 Identities=22% Similarity=0.384 Sum_probs=40.9
Q ss_pred eEEeeccceecccccccCC-CChHHHHHHHHHHhhccccccCCCCCcEEEEEeCCCCeEEecCc
Q 003592 682 TKVHKQGSLVGRAIDLWRL-NGYNDLLSELEHLFNMEGLLRDPAKGWRILYTDSENDVMVVGDD 744 (808)
Q Consensus 682 vKV~m~G~~vGRkVDL~~~-~~Y~eL~~~L~~MF~~~g~L~~~~~~~~lvY~D~EGD~mLVGD~ 744 (808)
+|+.-.|. | |.+=+..- -+|.+|...+.+.|... + ...+.+.|-|.|.|||+.-+.+.
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 56665553 4 44444332 39999999999999843 2 23468999999999999766654
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=85.68 E-value=1.5 Score=40.44 Aligned_cols=55 Identities=25% Similarity=0.440 Sum_probs=43.8
Q ss_pred CceeEEeeccceecccccccCCCChHHHHHHHHHHhhccccccCCCCCcEEEEEeCCCCeEEecC
Q 003592 679 RSCTKVHKQGSLVGRAIDLWRLNGYNDLLSELEHLFNMEGLLRDPAKGWRILYTDSENDVMVVGD 743 (808)
Q Consensus 679 ~~~vKV~m~G~~vGRkVDL~~~~~Y~eL~~~L~~MF~~~g~L~~~~~~~~lvY~D~EGD~mLVGD 743 (808)
+.-||||-+|. -|.|-+..-=+|++|.+++..+|++. ...+|-|.|. ||+.-++|
T Consensus 2 ~ikVKv~~~~D--v~~i~v~~~i~f~dL~~kIrdkf~~~-------~~~~iKykDE-GD~iti~s 56 (86)
T cd06408 2 KIRVKVHAQDD--TRYIMIGPDTGFADFEDKIRDKFGFK-------RRLKIKMKDD-GDMITMGD 56 (86)
T ss_pred cEEEEEEecCc--EEEEEcCCCCCHHHHHHHHHHHhCCC-------CceEEEEEcC-CCCccccC
Confidence 34689998887 46666666777999999999999984 3678999999 99955544
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=83.84 E-value=1.6 Score=40.32 Aligned_cols=49 Identities=31% Similarity=0.387 Sum_probs=42.1
Q ss_pred cccCCCChHHHHHHHHHHhhccccccCCCCCcEEEEEeCCCCeEEecCcchhhhhhcceeEEEechHhhhcccc
Q 003592 696 DLWRLNGYNDLLSELEHLFNMEGLLRDPAKGWRILYTDSENDVMVVGDDPWHEFCNEVSKIHIYTQEEVEKMTI 769 (808)
Q Consensus 696 DL~~~~~Y~eL~~~L~~MF~~~g~L~~~~~~~~lvY~D~EGD~mLVGD~PW~~F~~~vkrI~I~~~~ev~~m~~ 769 (808)
||+.--.|.+|..-..+-|..+. =.+-|.|.|||. |+|++.++|.-|-.
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 68888899999999999998553 347899999999 99999999998843
No 21
>PRK10737 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=66.75 E-value=24 Score=36.97 Aligned_cols=103 Identities=16% Similarity=0.194 Sum_probs=63.1
Q ss_pred CCcCCCEEEE-E--EcCCCcEEEeEEeccCCCCCCCCCc-cccCCChhhHHHHHHHHhhcCCeEEEEEcCCCC------C
Q 003592 249 NLVSGDAVLF-L--RGKDGELRLGIRRSVQPRNGLPDSI-LSKQNSYPNVLSVVANAVSTKSMFHVFYSPRAT------H 318 (808)
Q Consensus 249 ~L~aGD~VvF-~--R~~~Gel~vGIRRa~r~~~~~p~sv-~s~~~m~~~vlaaa~~a~~t~~~F~V~Y~PRas------~ 318 (808)
++..|+.|.+ | |.++|+++-.-+ ...|... ++...+-.+ |++|..-...|..|+|..-|-.. -
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 2 567787643221 1234443 344444344 45555566788999998765422 2
Q ss_pred CceeeehhHHHHhhccCcccccEEEEEeecCCCCcceeeeEEeeecc
Q 003592 319 ADFVIPYQKYVKIIMNPICIGTRFKMRFEMDDSPERRCNGVVTGITD 365 (808)
Q Consensus 319 sEFVVp~~ky~~A~~~~ws~GmRFKM~fE~EDs~~~r~~GTI~gi~d 365 (808)
.-..||++.|... ....+||||.+. +++. ...++|+.|.+
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 237899998864 5554 36889999975
No 22
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=54.15 E-value=9.3 Score=47.35 Aligned_cols=66 Identities=24% Similarity=0.411 Sum_probs=43.9
Q ss_pred CCCCCCCeEEEecCcchhhhccCCCCCCCCCCC---CCCCCcceEEEEEeeeeccccCCceeEeEeeecC
Q 003592 71 SLPKKGNVVVYFPQGHLEQVASSSAFPPIEVPN---FDLQPQIFCKVVDVQLLANKENDEVYTQVALLPQ 137 (808)
Q Consensus 71 ~lP~~gs~V~YFPqGH~Eq~~~s~~~~~~~~p~---~~lp~~i~CrV~~V~L~Ad~~TDEVyAqi~L~P~ 137 (808)
-||..|+.|.||-|||-|-+.+..-- +.+.-. .++-..=.|.|..+..---+....--.+|+|.=.
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 58999999999999999999885421 111111 1222223688888777666666666777776544
No 23
>KOG3207 consensus Beta-tubulin folding cofactor E [Posttranslational modification, protein turnover, chaperones]
Probab=44.96 E-value=27 Score=41.01 Aligned_cols=43 Identities=37% Similarity=0.618 Sum_probs=29.8
Q ss_pred cccccEEEEEeecCCCCcceeeeEEeeeccCCCCCCCCCCceeEEEEecCCCCCCCC
Q 003592 336 ICIGTRFKMRFEMDDSPERRCNGVVTGITDLDPYRWPNSKWRCLMVRWDECIGSDHQ 392 (808)
Q Consensus 336 ws~GmRFKM~fE~EDs~~~r~~GTI~gi~d~Dp~rWP~S~WR~L~V~WDe~~~~~~~ 392 (808)
..+|+|+|..+|- ...||.|+|.| |++ +| +.|.||++.-..|.
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 44 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=40.01 E-value=32 Score=27.56 Aligned_cols=27 Identities=22% Similarity=0.252 Sum_probs=22.8
Q ss_pred hhhcccCCcCCCEEEEEEcCCCcEEEe
Q 003592 243 IFVSQKNLVSGDAVLFLRGKDGELRLG 269 (808)
Q Consensus 243 ~FV~~K~L~aGD~VvF~R~~~Gel~vG 269 (808)
.|.++.+|.+||.|.|.-.++|++.+-
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 567888999999999999999866653
No 25
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=34.79 E-value=54 Score=27.20 Aligned_cols=38 Identities=21% Similarity=0.185 Sum_probs=29.2
Q ss_pred CcccccEEEEEeecCCCCcceeeeEEeeeccCCCCCCCCCCceeEEEEecC
Q 003592 335 PICIGTRFKMRFEMDDSPERRCNGVVTGITDLDPYRWPNSKWRCLMVRWDE 385 (808)
Q Consensus 335 ~ws~GmRFKM~fE~EDs~~~r~~GTI~gi~d~Dp~rWP~S~WR~L~V~WDe 385 (808)
.|.+|+++...++.++ .||.|+|+.+.. -..+.|.-+.
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 1236777776
No 26
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=33.17 E-value=55 Score=30.54 Aligned_cols=27 Identities=30% Similarity=0.426 Sum_probs=21.7
Q ss_pred hhcccCCcCCCEEEEEEcCCCcEEEeE
Q 003592 244 FVSQKNLVSGDAVLFLRGKDGELRLGI 270 (808)
Q Consensus 244 FV~~K~L~aGD~VvF~R~~~Gel~vGI 270 (808)
|.-...|++||.|+.+|.++|+.++=+
T Consensus 71 i~~~~~Lk~GD~V~ll~~~~gQ~yiVl 97 (100)
T PF10844_consen 71 ITFTDGLKVGDKVLLLRVQGGQKYIVL 97 (100)
T ss_pred EEEecCCcCCCEEEEEEecCCCEEEEE
Confidence 555668999999999999988766543
No 27
>cd06395 PB1_Map2k5 PB1 domain is essential part of the mitogen-activated protein kinase kinase 5 (Map2k5, alias MEK5) one of the key member of the signaling kinases cascade which involved in angiogenesis and early cardiovascular development. The PB1 domain of Map2k5 interacts with the PB1 domain of another members of kinase cascade MEKK2 (or MEKK3). A canonical PB1-PB1 interaction, involving 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 Map2k5 protein contains a type I PB1 domain.
Probab=32.42 E-value=83 Score=29.22 Aligned_cols=58 Identities=21% Similarity=0.286 Sum_probs=42.9
Q ss_pred ccceecccccccCCCChHHHHHHHHHHhhccccccCCCCCcEEEEEeCCCCeEEecCcchhhhhhcceeEEEechHhhhc
Q 003592 687 QGSLVGRAIDLWRLNGYNDLLSELEHLFNMEGLLRDPAKGWRILYTDSENDVMVVGDDPWHEFCNEVSKIHIYTQEEVEK 766 (808)
Q Consensus 687 ~G~~vGRkVDL~~~~~Y~eL~~~L~~MF~~~g~L~~~~~~~~lvY~D~EGD~mLVGD~PW~~F~~~vkrI~I~~~~ev~~ 766 (808)
+|.++--+||....=++.+++..+.+..-- ..-=.+-|+|.+||. |.+-+.+|.+.
T Consensus 9 ~gg~vDw~V~~~~~L~F~DvL~~I~~vlp~-------aT~tAFeYEDE~gDR-----------------ITVRSDeEm~A 64 (91)
T cd06395 9 NGGAVDWTVQSGPQLLFRDVLDVIGQVLPE-------ATTTAFEYEDEDGDR-----------------ITVRSDEEMKA 64 (91)
T ss_pred CCCcccccccCcccccHHHHHHHHHHhccc-------ccccceeeccccCCe-----------------eEecchHHHHH
Confidence 556678888888888899999988876531 122336799999997 77777888877
Q ss_pred cc
Q 003592 767 MT 768 (808)
Q Consensus 767 m~ 768 (808)
|-
T Consensus 65 Ml 66 (91)
T cd06395 65 ML 66 (91)
T ss_pred HH
Confidence 63
No 28
>COG1047 SlpA FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]
Probab=30.30 E-value=3e+02 Score=28.75 Aligned_cols=106 Identities=19% Similarity=0.244 Sum_probs=64.9
Q ss_pred cCCcCCCEEEEE---EcCCCcEEEeEEeccCCCCCCCCCccccCCChhhHHHHHHHHhhcCCeEEEEEcCCCCCCce---
Q 003592 248 KNLVSGDAVLFL---RGKDGELRLGIRRSVQPRNGLPDSILSKQNSYPNVLSVVANAVSTKSMFHVFYSPRATHADF--- 321 (808)
Q Consensus 248 K~L~aGD~VvF~---R~~~Gel~vGIRRa~r~~~~~p~sv~s~~~m~~~vlaaa~~a~~t~~~F~V~Y~PRas~sEF--- 321 (808)
+++..||.|.+. |.++|+++=--.- ...|..++--+..-+.-|+.|..-..-|.-|+|.--|-..-.++
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 5566765421111 12344443333333444566766677899999998886433333
Q ss_pred ---eeehhHHHHhhccCcccccEEEEEeecCCCCcceeeeEEeeecc
Q 003592 322 ---VIPYQKYVKIIMNPICIGTRFKMRFEMDDSPERRCNGVVTGITD 365 (808)
Q Consensus 322 ---VVp~~ky~~A~~~~ws~GmRFKM~fE~EDs~~~r~~GTI~gi~d 365 (808)
+||..+|...= ...+||+|.+ +++| ...-|+|+.|..
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 29
>TIGR01439 lp_hng_hel_AbrB looped-hinge helix DNA binding domain, AbrB family. This DNA-binding domain family includes AbrB, a transition state regulator in Bacillus subtilis, whose DNA-binding domain structure in solution was determined by NMR. The domain binds DNA as a dimer in what is termed a looped-hinge helix fold. Some members of the family have two copies of the domain in tandem. The domain is found usually at the N-terminus of a small protein. This model excludes members of family TIGR02609.
Probab=30.29 E-value=61 Score=24.77 Aligned_cols=26 Identities=31% Similarity=0.428 Sum_probs=22.3
Q ss_pred hhhcccCCcCCCEEEEEEcCCCcEEE
Q 003592 243 IFVSQKNLVSGDAVLFLRGKDGELRL 268 (808)
Q Consensus 243 ~FV~~K~L~aGD~VvF~R~~~Gel~v 268 (808)
.|.++-++..||.|.+....+|.|.+
T Consensus 14 ~~r~~l~~~~gd~~~i~~~~~~~l~l 39 (43)
T TIGR01439 14 EIREKLGLKEGDRLEVIRVEDGEIIL 39 (43)
T ss_pred HHHHHcCcCCCCEEEEEEeCCCEEEE
Confidence 67899999999999999887777654
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=25.33 E-value=58 Score=27.41 Aligned_cols=17 Identities=29% Similarity=0.575 Sum_probs=14.7
Q ss_pred EEEEEeCCCCeEEecCc
Q 003592 728 RILYTDSENDVMVVGDD 744 (808)
Q Consensus 728 ~lvY~D~EGD~mLVGD~ 744 (808)
.++|.|.+|+.+++|+.
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 59999999999999974
No 31
>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=23.33 E-value=2.1e+02 Score=24.94 Aligned_cols=69 Identities=6% Similarity=0.061 Sum_probs=48.8
Q ss_pred ceeEEeecccee---cccccccCCCChHHHHHHHHHHhhccccccCCCCCcEEE-EEe-CCCCeEEe-cCcchhhhhhc
Q 003592 680 SCTKVHKQGSLV---GRAIDLWRLNGYNDLLSELEHLFNMEGLLRDPAKGWRIL-YTD-SENDVMVV-GDDPWHEFCNE 752 (808)
Q Consensus 680 ~~vKV~m~G~~v---GRkVDL~~~~~Y~eL~~~L~~MF~~~g~L~~~~~~~~lv-Y~D-~EGD~mLV-GD~PW~~F~~~ 752 (808)
.++||+.+...- -+.|-++....-.+++..+.+-|++. +...+|.|+ +.- ......|- .+.|+..+...
T Consensus 3 ~~lrVy~~~~~~~~~~k~i~v~~~tTa~evi~~~l~k~~l~----~~~~~y~L~~~~~~~~~er~L~~~E~pl~i~~~~ 77 (93)
T PF00788_consen 3 GVLRVYDGDGSPGSTYKTIKVSSSTTAREVIEMALEKFGLA----EDPSDYCLVEVEESGGEERPLDDDECPLQIQLQW 77 (93)
T ss_dssp EEEEEEETTSSSCCSEEEEEEETTSBHHHHHHHHHHHTTTS----SSGGGEEEEEEECTTTEEEEETTTSBHHHHHHTT
T ss_pred eEEEEEcCCCCCCccEEEEEECCCCCHHHHHHHHHHHhCCC----CCCCCEEEEEEEcCCCEEEEcCCCCchHHHHHhC
Confidence 578999877643 57899999999999999999999982 345679995 444 44444443 33456655444
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=23.21 E-value=1.2e+02 Score=25.69 Aligned_cols=31 Identities=26% Similarity=0.517 Sum_probs=24.1
Q ss_pred cccEEEEEeecCCCCcceeeeEEeeeccCCC
Q 003592 338 IGTRFKMRFEMDDSPERRCNGVVTGITDLDP 368 (808)
Q Consensus 338 ~GmRFKM~fE~EDs~~~r~~GTI~gi~d~Dp 368 (808)
+|-|+.-.||.++.+...|.|+|..--+..|
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 5889999999888888789999999877655
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=22.58 E-value=91 Score=28.66 Aligned_cols=36 Identities=19% Similarity=0.290 Sum_probs=23.8
Q ss_pred hhhhcccCCcCCCEEEEEEcCCCc-EEEeEEeccCCC
Q 003592 242 SIFVSQKNLVSGDAVLFLRGKDGE-LRLGIRRSVQPR 277 (808)
Q Consensus 242 s~FV~~K~L~aGD~VvF~R~~~Ge-l~vGIRRa~r~~ 277 (808)
..|+++++|..||.|.++|..+.= ..+++-...|..
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 378999999999999999987763 345665555544
No 34
>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=21.64 E-value=87 Score=30.31 Aligned_cols=26 Identities=23% Similarity=0.348 Sum_probs=16.2
Q ss_pred cCCcCCCEEEEEEcC-CCcEEEeEEec
Q 003592 248 KNLVSGDAVLFLRGK-DGELRLGIRRS 273 (808)
Q Consensus 248 K~L~aGD~VvF~R~~-~Gel~vGIRRa 273 (808)
++++.||.|+||... .+.-++|+=+-
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 45556665543
Done!