Query 005623
Match_columns 687
No_of_seqs 353 out of 817
Neff 4.5
Searched_HMMs 46136
Date Thu Mar 28 11:13:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/005623.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/005623hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02309 AUX_IAA: AUX/IAA fami 100.0 4.1E-37 8.9E-42 308.2 0.6 94 570-663 107-215 (215)
2 PF06507 Auxin_resp: Auxin res 100.0 7.7E-34 1.7E-38 247.4 8.3 80 254-333 1-83 (83)
3 PF02362 B3: B3 DNA binding do 99.7 4.5E-16 9.6E-21 136.4 11.0 97 128-229 1-99 (100)
4 KOG0644 Uncharacterized conser 99.5 5.6E-15 1.2E-19 168.2 6.6 147 206-360 874-1046(1113)
5 PF09217 EcoRII-N: Restriction 98.4 1.8E-06 3.9E-11 83.6 9.4 90 124-215 6-110 (156)
6 PF03754 DUF313: Domain of unk 97.5 0.00017 3.8E-09 67.2 6.1 78 124-202 20-113 (114)
7 PF00564 PB1: PB1 domain; Int 96.9 0.0026 5.6E-08 54.4 6.9 68 574-647 3-71 (84)
8 smart00666 PB1 PB1 domain. Pho 96.4 0.012 2.7E-07 50.2 7.3 66 574-646 3-69 (81)
9 cd06407 PB1_NLP A PB1 domain i 96.3 0.012 2.6E-07 52.0 6.9 54 574-633 2-55 (82)
10 cd05992 PB1 The PB1 domain is 96.2 0.021 4.5E-07 48.5 7.6 66 574-646 2-69 (81)
11 cd06398 PB1_Joka2 The PB1 doma 95.9 0.028 6E-07 50.7 7.2 65 575-647 3-72 (91)
12 cd06396 PB1_NBR1 The PB1 domai 95.8 0.032 7E-07 49.5 7.0 63 574-643 2-65 (81)
13 cd06409 PB1_MUG70 The MUG70 pr 93.9 0.11 2.4E-06 46.6 5.3 50 583-634 8-59 (86)
14 cd06401 PB1_TFG The PB1 domain 93.4 0.28 6E-06 43.7 6.7 58 575-636 3-61 (81)
15 cd06404 PB1_aPKC PB1 domain is 93.3 0.24 5.2E-06 44.3 6.3 55 574-634 2-56 (83)
16 cd06403 PB1_Par6 The PB1 domai 93.1 0.25 5.5E-06 43.8 6.1 68 575-647 3-71 (80)
17 cd06408 PB1_NoxR The PB1 domai 91.7 0.45 9.8E-06 42.8 6.0 56 572-636 2-57 (86)
18 cd06402 PB1_p62 The PB1 domain 91.5 0.69 1.5E-05 41.7 6.9 57 574-634 2-63 (87)
19 cd06397 PB1_UP1 Uncharacterize 90.4 0.75 1.6E-05 41.0 5.9 66 575-647 3-69 (82)
20 PRK10737 FKBP-type peptidyl-pr 64.2 24 0.00053 36.2 7.4 102 205-319 2-114 (196)
21 KOG0644 Uncharacterized conser 60.0 7.3 0.00016 47.4 3.1 65 37-102 872-938 (1113)
22 cd06399 PB1_P40 The PB1 domain 53.4 23 0.00049 32.5 4.4 51 589-663 23-73 (92)
23 smart00743 Agenet Tudor-like d 50.1 25 0.00054 28.5 4.0 38 289-338 2-39 (61)
24 PF04014 Antitoxin-MazE: Antid 46.9 22 0.00049 27.8 3.1 27 199-225 14-40 (47)
25 KOG3207 Beta-tubulin folding c 38.3 24 0.00051 40.7 2.7 42 290-344 3-44 (505)
26 TIGR01439 lp_hng_hel_AbrB loop 35.2 47 0.001 24.8 3.1 26 199-224 14-39 (43)
27 PF02513 Spin-Ssty: Spin/Ssty 35.0 57 0.0012 27.0 3.7 32 292-323 1-32 (50)
28 PF10844 DUF2577: Protein of u 31.5 64 0.0014 29.5 3.9 27 200-226 71-97 (100)
29 smart00333 TUDOR Tudor domain. 30.5 84 0.0018 24.8 4.0 52 289-356 2-53 (57)
30 PF01878 EVE: EVE domain; Int 30.5 48 0.0011 31.4 3.1 27 204-230 38-65 (143)
31 PF05641 Agenet: Agenet domain 30.3 1.1E+02 0.0023 25.9 4.8 42 290-340 1-42 (68)
32 cd06406 PB1_P67 A PB1 domain i 25.2 2E+02 0.0043 26.0 5.7 66 574-647 4-70 (80)
33 COG1047 SlpA FKBP-type peptidy 25.2 3.8E+02 0.0082 27.4 8.4 103 205-319 2-115 (174)
34 PRK14129 heat shock protein Hs 24.7 90 0.002 29.4 3.6 50 287-353 3-53 (105)
35 PF11515 Cul7: Mouse developme 23.5 96 0.0021 27.8 3.4 57 278-340 6-62 (78)
36 PF10411 DsbC_N: Disulfide bon 20.8 78 0.0017 26.0 2.2 17 620-636 34-50 (57)
37 KOG3938 RGS-GAIP interacting p 20.2 1.2E+02 0.0027 33.0 4.1 75 579-661 61-143 (334)
No 1
>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=4.1e-37 Score=308.25 Aligned_cols=94 Identities=44% Similarity=0.762 Sum_probs=0.0
Q ss_pred CCCCeEEEeecCceeeeeecCCCCCChHHHHHHHHHHH---hhc----------cc--cCCCCCceEEeecCCCCeEEec
Q 005623 570 STRTRTKVQMQGIAVGRAVDLTALKGYDDLFDELEKMF---EIQ----------GQ--LRPRDKWAVVFTDDEGDMMLAG 634 (687)
Q Consensus 570 ~~~~~vKV~m~G~~igRkVDL~~~~~Y~~L~~~L~~MF---~~~----------g~--l~~~~~~~v~Y~D~eGD~mLVG 634 (687)
..++||||+|||++|||||||++|+||++|+.+|++|| +|. +. |..+++|+|||+|+||||||||
T Consensus 107 ~~~~~vKV~mdG~~igRkVDL~~~~sY~~L~~~L~~MF~~~~i~~~~~~~~~~~~~~~~~~~~~~~l~Y~D~egd~mlvG 186 (215)
T PF02309_consen 107 SSRSYVKVNMDGVPIGRKVDLSAYSSYEELSSALEKMFSCFSIEQCGSHGLNESGLLDLLNGSEYVLVYEDKEGDWMLVG 186 (215)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred cCCceeEEEecCcccceecCHHHhhCHHHHHHHHHHhcCCCCccccccccccchhhccccCCcceeEEEECCCCCEEEec
Confidence 46899999999999999999999999999999999999 665 22 3467799999999999999999
Q ss_pred CCChHhHHhccceEEEechhhhccccCCC
Q 005623 635 DDQWPEFCKMVKKIFIYSTEEVKNMATSS 663 (687)
Q Consensus 635 D~PW~~F~~~vkri~I~~~~e~~~~~~~~ 663 (687)
||||+|||++||||+||+.+|+++|+|++
T Consensus 187 D~PW~~F~~~vkRl~I~~~~e~~~~~~r~ 215 (215)
T PF02309_consen 187 DVPWEEFVKSVKRLRIMKSSEAKGLAPRA 215 (215)
T ss_dssp -----------------------------
T ss_pred CCCHHHHHHHhhccEEecHHHhcccCCCC
Confidence 99999999999999999999999999974
No 2
>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=7.7e-34 Score=247.43 Aligned_cols=80 Identities=60% Similarity=1.045 Sum_probs=78.2
Q ss_pred HHHHHhcCCeEEEEEecCCC--cceeeHHHHHHHhccCCccCcEEEEEEecCCCCCceeeeEEEeeccCCC-CCCCCCcc
Q 005623 254 AAHAVKTSTLFIVYYKPRTS--QFIIGLNKYLEAVHHCFSVGMRFKMRFEGEDSPERRFTGTIVGVGDFSE-QWPGSKWR 330 (687)
Q Consensus 254 A~~a~~tg~~F~V~Y~PR~s--eFvV~~~ky~~A~~~~w~~GmRFkM~fE~eD~~~~~~~GTIvgv~~~dp-~wp~S~WR 330 (687)
|+|||++|++|+|+||||++ ||||+++||++||+++|++||||||+||+||+++++|+|||+||++.|| +||+|+||
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 68999999999999999995 9999999999999999999999999999999999999999999999999 99999999
Q ss_pred eee
Q 005623 331 SLK 333 (687)
Q Consensus 331 ~L~ 333 (687)
|||
T Consensus 81 ~Lq 83 (83)
T PF06507_consen 81 MLQ 83 (83)
T ss_pred cCc
Confidence 997
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=99.66 E-value=4.5e-16 Score=136.38 Aligned_cols=97 Identities=31% Similarity=0.434 Sum_probs=74.8
Q ss_pred EEEecCccCCCCCCceEEecchhcccCCCCCCCCCCCccEEEEeeCCCCeEEEEEEEcCCCceeeecccchhhhcccCCC
Q 005623 128 FCKILTASDTSTHGGFSVLRKHATECLPPLDMTLATPTQELAAKDLHGYEWRFKHIFRGQPRRHLLTTGWSTFVTSKRLV 207 (687)
Q Consensus 128 F~K~LT~SDv~~~grfsVPk~~Ae~~fP~Ld~~~~~p~q~L~~~D~~G~~W~Fr~~yr~~~rrhlLTtGWs~FV~~K~L~ 207 (687)
|.|+|+++|+...+++.||++.++.+. +. ...++.+.++|..|+.|.+++.|++++++++|++||..||++++|+
T Consensus 1 F~K~l~~s~~~~~~~l~iP~~f~~~~~--~~---~~~~~~v~l~~~~g~~W~v~~~~~~~~~~~~l~~GW~~Fv~~n~L~ 75 (100)
T PF02362_consen 1 FFKVLKPSDVSSSCRLIIPKEFAKKHG--GN---KRKSREVTLKDPDGRSWPVKLKYRKNSGRYYLTGGWKKFVRDNGLK 75 (100)
T ss_dssp EEEE--TTCCCCTT-EEE-HHHHTTTS-------SS--CEEEEEETTTEEEEEEEEEECCTTEEEEETTHHHHHHHCT--
T ss_pred CEEEEEccCcCCCCEEEeCHHHHHHhC--CC---cCCCeEEEEEeCCCCEEEEEEEEEccCCeEEECCCHHHHHHHcCCC
Confidence 899999999999999999999998872 11 1236789999999999999999999888899999999999999999
Q ss_pred CCCEEEEEeCC--CCcEEEEEEec
Q 005623 208 AGDAFVFLRGE--NGELRVGVRRL 229 (687)
Q Consensus 208 aGD~VvF~R~~--~G~L~VGiRRa 229 (687)
+||.++|.... ..++.|.|.|+
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 99999999854 55679999886
No 4
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=99.54 E-value=5.6e-15 Score=168.23 Aligned_cols=147 Identities=23% Similarity=0.416 Sum_probs=120.8
Q ss_pred CCCCCEEEEEeCCCCcEEEEEEeccccCC---------------------CCCCcccccCccccchHHHHHHHHhcCCeE
Q 005623 206 LVAGDAFVFLRGENGELRVGVRRLAHQQS---------------------SMPSSVISSQSMHLGVLATAAHAVKTSTLF 264 (687)
Q Consensus 206 L~aGD~VvF~R~~~G~L~VGiRRa~~~~~---------------------~~p~sv~s~~sm~~gvla~A~~a~~tg~~F 264 (687)
.+.||.|+++|.+..++.-.+|+..+..+ ..|-+..+.|+|.+.||..|.++. ...|
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 45899999999876666555555433221 124455678999999999999774 5569
Q ss_pred EEEEecCCC--cceeeHHHHHHHhccCCccCcEEEEEEecCCCCC---ceeeeEEEeeccCCCCCCCCCcceeeeeccCC
Q 005623 265 IVYYKPRTS--QFIIGLNKYLEAVHHCFSVGMRFKMRFEGEDSPE---RRFTGTIVGVGDFSEQWPGSKWRSLKIQWDEP 339 (687)
Q Consensus 265 ~V~Y~PR~s--eFvV~~~ky~~A~~~~w~~GmRFkM~fE~eD~~~---~~~~GTIvgv~~~dp~wp~S~WR~L~V~WDe~ 339 (687)
.+.|..... ||+|.++.|++|+.+||.++++||.-+. |+.+ +||.|+|.++.+.+|++|+|+|.|+.|+||..
T Consensus 952 ~ltlpdlv~fpDFlV~rsrYd~AiQrnW~~~d~crvwwr--da~~e~g~WWeG~ils~~pksp~fpdSpwery~v~~~~~ 1029 (1113)
T KOG0644|consen 952 KLTLPDLVTFPDFLVERSRYDAAIQRNWTCRDKCRVWWR--DAGEEDGAWWEGRILSVKPKSPDFPDSPWERYIVRYDNT 1029 (1113)
T ss_pred eeecccccCcchhhhhhhhHHHHHhhccccccceeEEEc--cCCCcCCceeeeeeeeccCCCCCCCCCcceeEEEEecCC
Confidence 999987665 9999999999999999999999999885 3322 89999999999999999999999999999999
Q ss_pred CCCCCCCccccCccccccCCC
Q 005623 340 ATVQRPERVSPWEIEPFVASA 360 (687)
Q Consensus 340 ~~~~~~~RVSPWeIEp~~~~~ 360 (687)
+ .+.-||||.||+...-
T Consensus 1030 e----~~~~spwe~~~i~de~ 1046 (1113)
T KOG0644|consen 1030 E----TELHSPWEMEPIPDEV 1046 (1113)
T ss_pred c----ccccCccccCCCcccc
Confidence 8 4677999999997664
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=98.36 E-value=1.8e-06 Score=83.60 Aligned_cols=90 Identities=19% Similarity=0.250 Sum_probs=61.6
Q ss_pred ceeeEEEecCccCCCCCC----ceEEecchhcccCCCCCC-CCCCCccEEEEeeCCC--CeEEEEEEEcCC------Cce
Q 005623 124 TVHSFCKILTASDTSTHG----GFSVLRKHATECLPPLDM-TLATPTQELAAKDLHG--YEWRFKHIFRGQ------PRR 190 (687)
Q Consensus 124 ~~~~F~K~LT~SDv~~~g----rfsVPk~~Ae~~fP~Ld~-~~~~p~q~L~~~D~~G--~~W~Fr~~yr~~------~rr 190 (687)
..+.|+|.|++.|++..| |+.|||..++..||.+.. +..+|...|.+++..+ ..|+||++|.|+ +..
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 457899999999999875 799999999999998776 5677999999999988 578899999987 456
Q ss_pred eeec--ccchhhhcccCCCCCCEEEEE
Q 005623 191 HLLT--TGWSTFVTSKRLVAGDAFVFL 215 (687)
Q Consensus 191 hlLT--tGWs~FV~~K~L~aGD~VvF~ 215 (687)
|.|| ++=..|.+. =..||.+||-
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 8886 333334332 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=97.52 E-value=0.00017 Score=67.24 Aligned_cols=78 Identities=17% Similarity=0.167 Sum_probs=60.8
Q ss_pred ceeeEEEecCccCCCCC-CceEEecchhcccCCCCCC------------CCCCCccEEEEeeCCCCeEEEEEEEcCC---
Q 005623 124 TVHSFCKILTASDTSTH-GGFSVLRKHATECLPPLDM------------TLATPTQELAAKDLHGYEWRFKHIFRGQ--- 187 (687)
Q Consensus 124 ~~~~F~K~LT~SDv~~~-grfsVPk~~Ae~~fP~Ld~------------~~~~p~q~L~~~D~~G~~W~Fr~~yr~~--- 187 (687)
....|+|+|++||++.+ +||+||-..-.. ...|.. ....-++.+.+.|..++.|..++..|..
T Consensus 20 ~kli~~K~L~~tDv~~~qsRLsmP~~qi~~-~dFLt~eE~~~i~~~~~~~~~~~Gv~V~lvdp~~~~~~m~lkkW~mg~~ 98 (114)
T PF03754_consen 20 PKLIIEKTLFKTDVDPHQSRLSMPFNQIID-NDFLTEEEKRIIKEEKKNNDKKKGVEVILVDPSLRKWTMRLKKWNMGNG 98 (114)
T ss_pred CeEEEeeeecccCCCCCCceeeccHHHhcc-cccCCHHHHHHHHHhhccCcccCCceEEEECCcCcEEEEEEEEecccCC
Confidence 35789999999999865 899999875421 122211 1234588999999999999999999965
Q ss_pred Cceeeecccchhhhc
Q 005623 188 PRRHLLTTGWSTFVT 202 (687)
Q Consensus 188 ~rrhlLTtGWs~FV~ 202 (687)
.-.|+|++||..+|+
T Consensus 99 ~~~YvL~~gWn~VV~ 113 (114)
T PF03754_consen 99 TSNYVLNSGWNKVVE 113 (114)
T ss_pred ceEEEEEcChHhhcc
Confidence 458999999999985
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=96.95 E-value=0.0026 Score=54.41 Aligned_cols=68 Identities=24% Similarity=0.488 Sum_probs=56.4
Q ss_pred eEEEeecCceeeeeecCCCCCChHHHHHHHHHHHhhccccCCCCCceEEeecCCCCeEEec-CCChHhHHhccce
Q 005623 574 RTKVQMQGIAVGRAVDLTALKGYDDLFDELEKMFEIQGQLRPRDKWAVVFTDDEGDMMLAG-DDQWPEFCKMVKK 647 (687)
Q Consensus 574 ~vKV~m~G~~igRkVDL~~~~~Y~~L~~~L~~MF~~~g~l~~~~~~~v~Y~D~eGD~mLVG-D~PW~~F~~~vkr 647 (687)
-+|++..|. +=|.+.+..--+|++|...+++.|++. ...+.+.|.|.||||..+. |.=|++.++.+++
T Consensus 3 ~vK~~~~~~-~~~~~~~~~~~s~~~L~~~i~~~~~~~-----~~~~~l~Y~D~dgD~V~i~sd~Dl~~a~~~~~~ 71 (84)
T PF00564_consen 3 RVKVRYGGD-IRRIISLPSDVSFDDLRSKIREKFGLL-----DEDFQLKYKDEDGDLVTISSDEDLQEAIEQAKE 71 (84)
T ss_dssp EEEEEETTE-EEEEEEECSTSHHHHHHHHHHHHHTTS-----TSSEEEEEEETTSSEEEESSHHHHHHHHHHHHH
T ss_pred EEEEEECCe-eEEEEEcCCCCCHHHHHHHHHHHhCCC-----CccEEEEeeCCCCCEEEeCCHHHHHHHHHHHHh
Confidence 479999994 444688888889999999999999986 4678999999999999887 4458888887754
No 8
>smart00666 PB1 PB1 domain. Phox and Bem1p domain, present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.
Probab=96.42 E-value=0.012 Score=50.19 Aligned_cols=66 Identities=18% Similarity=0.397 Sum_probs=53.4
Q ss_pred eEEEeecCceeeeeecCCCCCChHHHHHHHHHHHhhccccCCCCCceEEeecCCCCeEEe-cCCChHhHHhccc
Q 005623 574 RTKVQMQGIAVGRAVDLTALKGYDDLFDELEKMFEIQGQLRPRDKWAVVFTDDEGDMMLA-GDDQWPEFCKMVK 646 (687)
Q Consensus 574 ~vKV~m~G~~igRkVDL~~~~~Y~~L~~~L~~MF~~~g~l~~~~~~~v~Y~D~eGD~mLV-GD~PW~~F~~~vk 646 (687)
-+||+-.| -=|.+-+..--+|++|..++.+.|.+.+ ..+.|.|+|.||||..+ .|.=|++.+++++
T Consensus 3 ~vK~~~~~--~~~~~~~~~~~s~~dL~~~i~~~~~~~~-----~~~~l~Y~Dedgd~v~l~sd~Dl~~a~~~~~ 69 (81)
T smart00666 3 DVKLRYGG--ETRRLSVPRDISFEDLRSKVAKRFGLDN-----QSFTLKYQDEDGDLVSLTSDEDLEEAIEEYD 69 (81)
T ss_pred cEEEEECC--EEEEEEECCCCCHHHHHHHHHHHhCCCC-----CCeEEEEECCCCCEEEecCHHHHHHHHHHHH
Confidence 37888855 4688888889999999999999999653 57899999999999855 4566777777765
No 9
>cd06407 PB1_NLP A PB1 domain is present in NIN like proteins (NLP), a key enzyme in a process of establishment of symbiosis betweeen legumes and nitrogen fixing bacteria (Rhizobium). The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes like osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-inte
Probab=96.35 E-value=0.012 Score=52.00 Aligned_cols=54 Identities=20% Similarity=0.351 Sum_probs=44.9
Q ss_pred eEEEeecCceeeeeecCCCCCChHHHHHHHHHHHhhccccCCCCCceEEeecCCCCeEEe
Q 005623 574 RTKVQMQGIAVGRAVDLTALKGYDDLFDELEKMFEIQGQLRPRDKWAVVFTDDEGDMMLA 633 (687)
Q Consensus 574 ~vKV~m~G~~igRkVDL~~~~~Y~~L~~~L~~MF~~~g~l~~~~~~~v~Y~D~eGD~mLV 633 (687)
-|||...|. -+.+-|..--+|++|..++.++|.+.. ...+.|-|.|+||||.++
T Consensus 2 ~vK~~~~~d--~~r~~l~~~~~~~~L~~~i~~r~~~~~----~~~f~LkY~Ddegd~v~l 55 (82)
T cd06407 2 RVKATYGEE--KIRFRLPPSWGFTELKQEIAKRFKLDD----MSAFDLKYLDDDEEWVLL 55 (82)
T ss_pred EEEEEeCCe--EEEEEcCCCCCHHHHHHHHHHHhCCCC----CCeeEEEEECCCCCeEEe
Confidence 489999886 455666666699999999999999852 468999999999999876
No 10
>cd05992 PB1 The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as a noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.
Probab=96.22 E-value=0.021 Score=48.50 Aligned_cols=66 Identities=18% Similarity=0.368 Sum_probs=51.6
Q ss_pred eEEEeecCceeeeeecCC-CCCChHHHHHHHHHHHhhccccCCCCCceEEeecCCCCeEEecC-CChHhHHhccc
Q 005623 574 RTKVQMQGIAVGRAVDLT-ALKGYDDLFDELEKMFEIQGQLRPRDKWAVVFTDDEGDMMLAGD-DQWPEFCKMVK 646 (687)
Q Consensus 574 ~vKV~m~G~~igRkVDL~-~~~~Y~~L~~~L~~MF~~~g~l~~~~~~~v~Y~D~eGD~mLVGD-~PW~~F~~~vk 646 (687)
-+||+-.|. =|.+=+. .--+|++|...|.+.|++.. ..+.+.|.|.||||..+.+ .=|++.++.++
T Consensus 2 ~vK~~~~~~--~~~~~~~~~~~s~~~L~~~i~~~~~~~~-----~~~~l~y~D~e~d~v~l~sd~Dl~~a~~~~~ 69 (81)
T cd05992 2 RVKVKYGGE--IRRFVVVSRSISFEDLRSKIAEKFGLDA-----VSFKLKYPDEDGDLVTISSDEDLEEAIEEAR 69 (81)
T ss_pred cEEEEecCC--CEEEEEecCCCCHHHHHHHHHHHhCCCC-----CcEEEEeeCCCCCEEEeCCHHHHHHHHHHHh
Confidence 378888864 2444444 88899999999999999753 5779999999999998887 66666666665
No 11
>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=95.91 E-value=0.028 Score=50.68 Aligned_cols=65 Identities=23% Similarity=0.452 Sum_probs=50.0
Q ss_pred EEEeecCceeeeeecCC-----CCCChHHHHHHHHHHHhhccccCCCCCceEEeecCCCCeEEecCCChHhHHhccce
Q 005623 575 TKVQMQGIAVGRAVDLT-----ALKGYDDLFDELEKMFEIQGQLRPRDKWAVVFTDDEGDMMLAGDDQWPEFCKMVKK 647 (687)
Q Consensus 575 vKV~m~G~~igRkVDL~-----~~~~Y~~L~~~L~~MF~~~g~l~~~~~~~v~Y~D~eGD~mLVGD~PW~~F~~~vkr 647 (687)
+||..+|. -|++-+. .--+|++|..++.+.|.+. ...++.+.|.|.||||..+-++ .++...+.+
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 VKVKYGGT--LRRFTFPVAENQLDLNMDGLREKVEELFSLS----PDADLSLTYTDEDGDVVTLVDD--NDLTDAIQY 72 (91)
T ss_pred EEEEeCCE--EEEEEeccccccCCCCHHHHHHHHHHHhCCC----CCCcEEEEEECCCCCEEEEccH--HHHHHHHHH
Confidence 79999996 4555554 3579999999999999874 3578999999999999988544 455554443
No 12
>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=95.81 E-value=0.032 Score=49.48 Aligned_cols=63 Identities=14% Similarity=0.208 Sum_probs=49.1
Q ss_pred eEEEeecCceeeeeecCCCCCChHHHHHHHHHHHhhccccCCCCCceEEeecCCCCeEEec-CCChHhHHh
Q 005623 574 RTKVQMQGIAVGRAVDLTALKGYDDLFDELEKMFEIQGQLRPRDKWAVVFTDDEGDMMLAG-DDQWPEFCK 643 (687)
Q Consensus 574 ~vKV~m~G~~igRkVDL~~~~~Y~~L~~~L~~MF~~~g~l~~~~~~~v~Y~D~eGD~mLVG-D~PW~~F~~ 643 (687)
-+||...|.-+==+++-+..-+|++|..++.++|++. .+.|.|-|.||||.++- |.=-++.++
T Consensus 2 ~vKaty~~d~~rf~~~~~~~~~~~~L~~ev~~rf~l~-------~f~lKYlDde~e~v~lssd~eLeE~~r 65 (81)
T cd06396 2 NLKVTYNGESQSFLVSDSENTTWASVEAMVKVSFGLN-------DIQIKYVDEENEEVSVNSQGEYEEALK 65 (81)
T ss_pred EEEEEECCeEEEEEecCCCCCCHHHHHHHHHHHhCCC-------cceeEEEcCCCCEEEEEchhhHHHHHH
Confidence 3799999976655666666789999999999999987 57999999999998763 333444433
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=93.93 E-value=0.11 Score=46.56 Aligned_cols=50 Identities=20% Similarity=0.331 Sum_probs=39.7
Q ss_pred eeeeeecCC--CCCChHHHHHHHHHHHhhccccCCCCCceEEeecCCCCeEEec
Q 005623 583 AVGRAVDLT--ALKGYDDLFDELEKMFEIQGQLRPRDKWAVVFTDDEGDMMLAG 634 (687)
Q Consensus 583 ~igRkVDL~--~~~~Y~~L~~~L~~MF~~~g~l~~~~~~~v~Y~D~eGD~mLVG 634 (687)
+-||.+=++ -..|+.+|..+..+=|+++... ...+.|.|.|+||||.+.-
T Consensus 8 ~~GrvhRf~~~~s~~~~~L~~~I~~Rl~~d~~~--~~~~~L~YlDDEgD~VllT 59 (86)
T cd06409 8 PKGRVHRFRLRPSESLEELRTLISQRLGDDDFE--THLYALSYVDDEGDIVLIT 59 (86)
T ss_pred CCCCEEEEEecCCCCHHHHHHHHHHHhCCcccc--CCcccEEEEcCCCCEEEEe
Confidence 456655444 3689999999999999887542 4678999999999998764
No 14
>cd06401 PB1_TFG The PB1 domain found in TFG protein, an oncogenic gene product and fusion partner to nerve growth factor tyrosine kinase receptor TrkA and to the tyrosine kinase ALK. The PB1 domain is a modular domain mediating specific protein-protein interaction in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The PB1 domains of TFG represent a type I/II PB1 domain. The physiological function of TFG remains unknown.
Probab=93.38 E-value=0.28 Score=43.71 Aligned_cols=58 Identities=22% Similarity=0.440 Sum_probs=44.1
Q ss_pred EEEeecCceeeeeecCCCC-CChHHHHHHHHHHHhhccccCCCCCceEEeecCCCCeEEecCC
Q 005623 575 TKVQMQGIAVGRAVDLTAL-KGYDDLFDELEKMFEIQGQLRPRDKWAVVFTDDEGDMMLAGDD 636 (687)
Q Consensus 575 vKV~m~G~~igRkVDL~~~-~~Y~~L~~~L~~MF~~~g~l~~~~~~~v~Y~D~eGD~mLVGD~ 636 (687)
+|+..+| .| |.+=+..- -+|.+|...+.+.|.. .+.+...+.|.|.|.|||+.-+.+.
T Consensus 3 iK~~~g~-Di-R~~~~~~~~~t~~~L~~~v~~~F~~--~~~~~~~flIKYkD~dGDlVTIts~ 61 (81)
T cd06401 3 LKAQLGD-DI-RRIPIHNEDITYDELLLMMQRVFRG--KLGSSDDVLIKYKDEDGDLITIFDS 61 (81)
T ss_pred EEEEeCC-eE-EEEeccCccccHHHHHHHHHHHhcc--ccCCcccEEEEEECCCCCEEEeccH
Confidence 5777665 34 44544442 3999999999999993 3445678999999999999998875
No 15
>cd06404 PB1_aPKC PB1 domain is an essential modular domain of the atypical protein kinase C (aPKC) which in complex with Par6 and Par3 proteins is crucial for establishment of apical-basal polarity of animal cells. PB1 domain is a modular domain mediating specific protein-protein interaction which play roles in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi,
Probab=93.31 E-value=0.24 Score=44.27 Aligned_cols=55 Identities=20% Similarity=0.354 Sum_probs=45.0
Q ss_pred eEEEeecCceeeeeecCCCCCChHHHHHHHHHHHhhccccCCCCCceEEeecCCCCeEEec
Q 005623 574 RTKVQMQGIAVGRAVDLTALKGYDDLFDELEKMFEIQGQLRPRDKWAVVFTDDEGDMMLAG 634 (687)
Q Consensus 574 ~vKV~m~G~~igRkVDL~~~~~Y~~L~~~L~~MF~~~g~l~~~~~~~v~Y~D~eGD~mLVG 634 (687)
-+|++-.|.-+-=.+|. .-+|++|.+++.+||.+.. ...+++.|.|.|||.--+.
T Consensus 2 ~~K~~y~gdi~it~~d~--~~s~e~L~~~v~~~c~~~~----~q~ft~kw~DEEGDp~tiS 56 (83)
T cd06404 2 RVKAAYNGDIMITSIDP--SISLEELCNEVRDMCRFHN----DQPFTLKWIDEEGDPCTIS 56 (83)
T ss_pred eEEEEecCcEEEEEcCC--CcCHHHHHHHHHHHhCCCC----CCcEEEEEECCCCCceeec
Confidence 47999999766656666 6679999999999999743 5678999999999986554
No 16
>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=93.15 E-value=0.25 Score=43.81 Aligned_cols=68 Identities=18% Similarity=0.311 Sum_probs=51.0
Q ss_pred EEEeecCceeeeeecCCCCCChHHHHHHHHHHHhhccccCCCCCceEEeecCCCCeEEec-CCChHhHHhccce
Q 005623 575 TKVQMQGIAVGRAVDLTALKGYDDLFDELEKMFEIQGQLRPRDKWAVVFTDDEGDMMLAG-DDQWPEFCKMVKK 647 (687)
Q Consensus 575 vKV~m~G~~igRkVDL~~~~~Y~~L~~~L~~MF~~~g~l~~~~~~~v~Y~D~eGD~mLVG-D~PW~~F~~~vkr 647 (687)
||.+.+++=-==++|.....+|++++.-|++||.+.+ -.+.|-|+|.+||.+-+- |+-+..=+++++.
T Consensus 3 VKSkfdaEfRRFsl~r~~~~~f~ef~~ll~~lH~l~~-----~~f~i~Y~D~~gDLLPInNDdNf~kAlssa~p 71 (80)
T cd06403 3 VKSKFDAEFRRFSLDRNKPGKFEDFYKLLEHLHHIPN-----VDFLIGYTDPHGDLLPINNDDNFLKALSSANP 71 (80)
T ss_pred eecccCCeEEEEEeccccCcCHHHHHHHHHHHhCCCC-----CcEEEEEeCCCCCEecccCcHHHHHHHHcCCC
Confidence 5666666422225667777999999999999999864 578999999999998764 5566655666653
No 17
>cd06408 PB1_NoxR The PB1 domain is present in the Epichloe festucae NoxR protein (NADPH oxidase regulator), a key regulator of NADPH oxidase isoform, NoxA. NoxA is essential for growth control of the fungal endophyte in plant tissue in the process of symbiotic interaction between a fungi and its plant host. The Epichloe festucae p67(phox)-like regulator, NoxR, dispensable in culture but essential in plants for the symbiotic interaction. Plants infected with a noxR deletion mutant show severe stunting and premature senescence, whereas hyphae in the meristematic tissues show increased branching leading to increased fungal colonization of pseudostem and leaf blade tissue. The PB1 domain is a modular domain mediating specific protein-protein interactions which a play role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is
Probab=91.74 E-value=0.45 Score=42.80 Aligned_cols=56 Identities=29% Similarity=0.511 Sum_probs=46.9
Q ss_pred CCeEEEeecCceeeeeecCCCCCChHHHHHHHHHHHhhccccCCCCCceEEeecCCCCeEEecCC
Q 005623 572 RTRTKVQMQGIAVGRAVDLTALKGYDDLFDELEKMFEIQGQLRPRDKWAVVFTDDEGDMMLAGDD 636 (687)
Q Consensus 572 ~~~vKV~m~G~~igRkVDL~~~~~Y~~L~~~L~~MF~~~g~l~~~~~~~v~Y~D~eGD~mLVGD~ 636 (687)
+.-|||+-+|. -|.|-+..--+|++|.+++.++|++. ..+.|-|.|. ||+.-++|.
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 34689999997 56777777778999999999999984 3679999999 999888764
No 18
>cd06402 PB1_p62 The PB1 domain is an essential part of p62 scaffold protein (alias sequestosome 1,SQSTM) involved in cell signaling, receptor internalization, and protein turnover. The PB1 domain is a modular domain mediating specific protein-protein interaction which play roles in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.
Probab=91.50 E-value=0.69 Score=41.69 Aligned_cols=57 Identities=21% Similarity=0.356 Sum_probs=42.2
Q ss_pred eEEEeecC---ceeeeee--cCCCCCChHHHHHHHHHHHhhccccCCCCCceEEeecCCCCeEEec
Q 005623 574 RTKVQMQG---IAVGRAV--DLTALKGYDDLFDELEKMFEIQGQLRPRDKWAVVFTDDEGDMMLAG 634 (687)
Q Consensus 574 ~vKV~m~G---~~igRkV--DL~~~~~Y~~L~~~L~~MF~~~g~l~~~~~~~v~Y~D~eGD~mLVG 634 (687)
.||.+..| .+==|++ |=....+|++|...+.++|..-. +..+++.|.|.|||..-+.
T Consensus 2 ~vkayl~~~~~~~EIRRf~l~~~~~~s~~~L~~~V~~~f~~l~----~~~ftlky~DeeGDlvtIs 63 (87)
T cd06402 2 TVKAYLLGKDANAEIRRFAIDEDVSTSYEYLVEKVAAVFPSLR----GKNFQLFWKDEEGDLVAFS 63 (87)
T ss_pred eEEEeecCCCCccceEEEEecCCCCcCHHHHHHHHHHHccccC----CCcEEEEEECCCCCEEeec
Confidence 57888877 2222444 44666799999999999995322 4689999999999986654
No 19
>cd06397 PB1_UP1 Uncharacterized protein 1. The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions.
Probab=90.35 E-value=0.75 Score=41.03 Aligned_cols=66 Identities=17% Similarity=0.412 Sum_probs=50.6
Q ss_pred EEEeecCceeeeeecCCCCCChHHHHHHHHHHHhhccccCCCCCceEEeecCCCCeEE-ecCCChHhHHhccce
Q 005623 575 TKVQMQGIAVGRAVDLTALKGYDDLFDELEKMFEIQGQLRPRDKWAVVFTDDEGDMML-AGDDQWPEFCKMVKK 647 (687)
Q Consensus 575 vKV~m~G~~igRkVDL~~~~~Y~~L~~~L~~MF~~~g~l~~~~~~~v~Y~D~eGD~mL-VGD~PW~~F~~~vkr 647 (687)
-||..+| --|++.-..-=+|..|.+.|+.+|.+.- . ...|+|.|.|||..- +-|+=-++|.+-..+
T Consensus 3 fKv~~~g--~~RRf~~~~~pt~~~L~~kl~~Lf~lp~----~-~~~vtYiDeD~D~ITlssd~eL~d~~~~~~~ 69 (82)
T cd06397 3 FKSSFLG--DTRRIVFPDIPTWEALASKLENLYNLPE----I-KVGVTYIDNDNDEITLSSNKELQDFYRLSHR 69 (82)
T ss_pred EEEEeCC--ceEEEecCCCccHHHHHHHHHHHhCCCh----h-HeEEEEEcCCCCEEEecchHHHHHHHHhccc
Confidence 3787777 4688888888899999999999999863 2 279999999999764 445556666654444
No 20
>PRK10737 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=64.22 E-value=24 Score=36.24 Aligned_cols=102 Identities=19% Similarity=0.205 Sum_probs=64.0
Q ss_pred CCCCCCEEEE-E--eCCCCcEEEEEEeccccCCCCCCcccccCccccchHHHHHHHHhcCCeEEEEEecCC------C--
Q 005623 205 RLVAGDAFVF-L--RGENGELRVGVRRLAHQQSSMPSSVISSQSMHLGVLATAAHAVKTSTLFIVYYKPRT------S-- 273 (687)
Q Consensus 205 ~L~aGD~VvF-~--R~~~G~L~VGiRRa~~~~~~~p~sv~s~~sm~~gvla~A~~a~~tg~~F~V~Y~PR~------s-- 273 (687)
++..|+.|.+ | |.++|+++---+ ...|...+-....-+--|.+|..-.+.|..|+|..-|-. .
T Consensus 2 kI~~~~vV~l~Y~l~~~dG~v~dst~------~~~Pl~~~~G~g~lipglE~aL~G~~~Gd~~~v~l~peeAyGe~d~~l 75 (196)
T PRK10737 2 KVAKDLVVSLAYQVRTEDGVLVDESP------VSAPLDYLHGHGSLISGLETALEGHEVGDKFDVAVGANDAYGQYDENL 75 (196)
T ss_pred ccCCCCEEEEEEEEEeCCCCEEEecC------CCCCeEEEeCCCcchHHHHHHHcCCCCCCEEEEEEChHHhcCCCChHH
Confidence 3556777766 3 356787643221 123444433333333456778888889999999987643 2
Q ss_pred cceeeHHHHHHHhccCCccCcEEEEEEecCCCCCceeeeEEEeecc
Q 005623 274 QFIIGLNKYLEAVHHCFSVGMRFKMRFEGEDSPERRFTGTIVGVGD 319 (687)
Q Consensus 274 eFvV~~~ky~~A~~~~w~~GmRFkM~fE~eD~~~~~~~GTIvgv~~ 319 (687)
-..||++.|... ....+||||.+. +++. .+.++|+.|.+
T Consensus 76 V~~vpr~~F~~~--~~l~~G~~~~~~--~~~G---~~~~~V~ev~~ 114 (196)
T PRK10737 76 VQRVPKDVFMGV--DELQVGMRFLAE--TDQG---PVPVEITAVED 114 (196)
T ss_pred EEEecHHHCCCc--cCCCCCCEEEEe--CCCC---cEEEEEEEEcC
Confidence 567888777422 247899999864 4542 36889999875
No 21
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=60.01 E-value=7.3 Score=47.44 Aligned_cols=65 Identities=28% Similarity=0.529 Sum_probs=39.3
Q ss_pred ccCCCCCeEEEecCcchhhhhcccccc--cccCCCCCCCCCcceEEEEEeeeecccCCceeEEEEeee
Q 005623 37 EVPRNGERVYYFPQGHIEQLEASTNQE--LTHQEPLFDLPSKILCRVVHIELLAEQETDEVYAQITLH 102 (687)
Q Consensus 37 ~~P~~g~~V~YFPqGH~Eq~~~s~~~~--~~~~~p~~~lp~~i~C~V~~V~L~Ad~~TDEVyAqi~L~ 102 (687)
-||..|+.|.||-|||-|-+.+..-.. +....| -++-..=.|+|..+..---+-...--.+|+|.
T Consensus 872 yipQmgDEViyfrQghqeyl~~~~~n~~~~~~~~p-~~~~~v~~~kv~kl~~~~y~~~~~s~c~m~l~ 938 (1113)
T KOG0644|consen 872 YIPQMGDEVIYFRQGHQEYLEAVRLNNIELNNKEP-WNKMAVEICKVEKLVYITYPGSGDSCCKMKLA 938 (1113)
T ss_pred ccccccceeehhhhhhHHHHhhhhhccccccccCc-ccccchhhheeeeeeeeeccCCCcchheeeee
Confidence 489999999999999999998864321 111111 12222336888776554444444444444443
No 22
>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=53.40 E-value=23 Score=32.45 Aligned_cols=51 Identities=31% Similarity=0.458 Sum_probs=40.4
Q ss_pred cCCCCCChHHHHHHHHHHHhhccccCCCCCceEEeecCCCCeEEecCCChHhHHhccceEEEechhhhccccCCC
Q 005623 589 DLTALKGYDDLFDELEKMFEIQGQLRPRDKWAVVFTDDEGDMMLAGDDQWPEFCKMVKKIFIYSTEEVKNMATSS 663 (687)
Q Consensus 589 DL~~~~~Y~~L~~~L~~MF~~~g~l~~~~~~~v~Y~D~eGD~mLVGD~PW~~F~~~vkri~I~~~~e~~~~~~~~ 663 (687)
||+..-.|.+|..-..+-|..+. -.+-|+|.|||. |+|+..+++.=|-..+
T Consensus 23 ~l~~~P~~kdLl~lmr~~f~~~d-------IaLNYrD~EGDL-----------------IRllddeDv~LMV~~~ 73 (92)
T cd06399 23 DLSSTPLLKDLLELTRREFQRED-------IALNYRDAEGDL-----------------IRLLSDEDVALMVRQS 73 (92)
T ss_pred ccccCccHHHHHHHHHHHhchhh-------eeeeeecCCCCE-----------------EEEcchhhHHHHHHHH
Confidence 78899999999999999998553 388999999997 5677777776555433
No 23
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=50.13 E-value=25 Score=28.53 Aligned_cols=38 Identities=16% Similarity=0.141 Sum_probs=29.3
Q ss_pred CCccCcEEEEEEecCCCCCceeeeEEEeeccCCCCCCCCCcceeeeeccC
Q 005623 289 CFSVGMRFKMRFEGEDSPERRFTGTIVGVGDFSEQWPGSKWRSLKIQWDE 338 (687)
Q Consensus 289 ~w~~GmRFkM~fE~eD~~~~~~~GTIvgv~~~dp~wp~S~WR~L~V~WDe 338 (687)
.|.+|+++-..++.++ .||.|+|+.+.. -..+.|.-+.
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 5899999999997544 899999999964 2235676665
No 24
>PF04014 Antitoxin-MazE: Antidote-toxin recognition MazE; InterPro: IPR007159 This domain is found in AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation []. AbrB is thought to interact directly with the transcription initiation regions of genes under its control []. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins []. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator []. DNA-binding activity in this AbrB homologue requires hexamerisation []. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins [].; PDB: 2L66_A 2GLW_A 3TND_D 2W1T_B 2RO5_B 2FY9_A 2RO3_B 1UB4_C 3ZVK_G 1YFB_B ....
Probab=46.88 E-value=22 Score=27.82 Aligned_cols=27 Identities=15% Similarity=0.192 Sum_probs=22.6
Q ss_pred hhhcccCCCCCCEEEEEeCCCCcEEEE
Q 005623 199 TFVTSKRLVAGDAFVFLRGENGELRVG 225 (687)
Q Consensus 199 ~FV~~K~L~aGD~VvF~R~~~G~L~VG 225 (687)
.|.++-+|.+||.|.|.-.++|++.+-
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 566777999999999999998876654
No 25
>KOG3207 consensus Beta-tubulin folding cofactor E [Posttranslational modification, protein turnover, chaperones]
Probab=38.26 E-value=24 Score=40.67 Aligned_cols=42 Identities=29% Similarity=0.654 Sum_probs=29.9
Q ss_pred CccCcEEEEEEecCCCCCceeeeEEEeeccCCCCCCCCCcceeeeeccCCCCCCC
Q 005623 290 FSVGMRFKMRFEGEDSPERRFTGTIVGVGDFSEQWPGSKWRSLKIQWDEPATVQR 344 (687)
Q Consensus 290 w~~GmRFkM~fE~eD~~~~~~~GTIvgv~~~dp~wp~S~WR~L~V~WDe~~~~~~ 344 (687)
+.+|+|+|..+|- ...||.|+|.|. ++ +| +.|.||++.-.-+
T Consensus 3 ~~IG~RvkI~~~~---~Tvr~iG~V~g~-------~~-~w--~GvEWDd~~RGKH 44 (505)
T KOG3207|consen 3 MEIGTRVKIGGEI---ATVRYIGEVEGN-------NS-KW--YGVEWDDPVRGKH 44 (505)
T ss_pred eeccceEEEcCEE---EEEEEEEEEcCC-------CC-cc--eeeEecCCCcccc
Confidence 5689999988752 336778877765 33 34 7899999986443
No 26
>TIGR01439 lp_hng_hel_AbrB looped-hinge helix DNA binding domain, AbrB family. This DNA-binding domain family includes AbrB, a transition state regulator in Bacillus subtilis, whose DNA-binding domain structure in solution was determined by NMR. The domain binds DNA as a dimer in what is termed a looped-hinge helix fold. Some members of the family have two copies of the domain in tandem. The domain is found usually at the N-terminus of a small protein. This model excludes members of family TIGR02609.
Probab=35.15 E-value=47 Score=24.80 Aligned_cols=26 Identities=27% Similarity=0.404 Sum_probs=22.1
Q ss_pred hhhcccCCCCCCEEEEEeCCCCcEEE
Q 005623 199 TFVTSKRLVAGDAFVFLRGENGELRV 224 (687)
Q Consensus 199 ~FV~~K~L~aGD~VvF~R~~~G~L~V 224 (687)
.|.++-++..||.|.+....+|.+.+
T Consensus 14 ~~r~~l~~~~gd~~~i~~~~~~~l~l 39 (43)
T TIGR01439 14 EIREKLGLKEGDRLEVIRVEDGEIIL 39 (43)
T ss_pred HHHHHcCcCCCCEEEEEEeCCCEEEE
Confidence 67888899999999999877777654
No 27
>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=35.01 E-value=57 Score=26.96 Aligned_cols=32 Identities=22% Similarity=0.430 Sum_probs=24.5
Q ss_pred cCcEEEEEEecCCCCCceeeeEEEeeccCCCC
Q 005623 292 VGMRFKMRFEGEDSPERRFTGTIVGVGDFSEQ 323 (687)
Q Consensus 292 ~GmRFkM~fE~eD~~~~~~~GTIvgv~~~dp~ 323 (687)
+|-|+.-.||+++.+...+.|+|...-+..|.
T Consensus 1 vGk~Veh~~~~g~g~~s~w~G~Vl~Qvp~~ps 32 (50)
T PF02513_consen 1 VGKRVEHTWEDGDGPKSKWKGMVLHQVPAKPS 32 (50)
T ss_dssp TT-EEEEEECTSTS-EEEEEEEEEEE-TTSTT
T ss_pred CCceEEEEEccCCCcccEEEEEEEEEeecCCc
Confidence 58899999998888888899999998776653
No 28
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=31.50 E-value=64 Score=29.47 Aligned_cols=27 Identities=22% Similarity=0.378 Sum_probs=21.2
Q ss_pred hhcccCCCCCCEEEEEeCCCCcEEEEE
Q 005623 200 FVTSKRLVAGDAFVFLRGENGELRVGV 226 (687)
Q Consensus 200 FV~~K~L~aGD~VvF~R~~~G~L~VGi 226 (687)
|.-...|++||.|..+|...|+.++=+
T Consensus 71 i~~~~~Lk~GD~V~ll~~~~gQ~yiVl 97 (100)
T PF10844_consen 71 ITFTDGLKVGDKVLLLRVQGGQKYIVL 97 (100)
T ss_pred EEEecCCcCCCEEEEEEecCCCEEEEE
Confidence 445568999999999998888766543
No 29
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=30.51 E-value=84 Score=24.78 Aligned_cols=52 Identities=19% Similarity=0.415 Sum_probs=36.9
Q ss_pred CCccCcEEEEEEecCCCCCceeeeEEEeeccCCCCCCCCCcceeeeeccCCCCCCCCCccccCccccc
Q 005623 289 CFSVGMRFKMRFEGEDSPERRFTGTIVGVGDFSEQWPGSKWRSLKIQWDEPATVQRPERVSPWEIEPF 356 (687)
Q Consensus 289 ~w~~GmRFkM~fE~eD~~~~~~~GTIvgv~~~dp~wp~S~WR~L~V~WDe~~~~~~~~RVSPWeIEp~ 356 (687)
+|.+|..+..++ .+. .||.|+|+++.. + ....|.-++-.. .+-|...+|-++
T Consensus 2 ~~~~G~~~~a~~-~d~---~wyra~I~~~~~------~---~~~~V~f~D~G~---~~~v~~~~l~~l 53 (57)
T smart00333 2 TFKVGDKVAARW-EDG---EWYRARIIKVDG------E---QLYEVFFIDYGN---EEVVPPSDLRPL 53 (57)
T ss_pred CCCCCCEEEEEe-CCC---CEEEEEEEEECC------C---CEEEEEEECCCc---cEEEeHHHeecC
Confidence 688999999999 444 899999999963 2 567788777443 234555555543
No 30
>PF01878 EVE: EVE domain; InterPro: IPR002740 The EVE domain is part of the wider PUA domain superfamily. The function of this domain is not known but, given the structural similarities to PUA, is likely to involve RNA binding []. ; PDB: 2G2X_B 2AR1_A 3EOP_A 2EVE_A 2HD9_A 2ZBN_A 1WMM_A 2P5D_A 2GBS_A 1ZCE_A.
Probab=30.46 E-value=48 Score=31.38 Aligned_cols=27 Identities=22% Similarity=0.402 Sum_probs=18.2
Q ss_pred cCCCCCCEEEEEeCC-CCcEEEEEEecc
Q 005623 204 KRLVAGDAFVFLRGE-NGELRVGVRRLA 230 (687)
Q Consensus 204 K~L~aGD~VvF~R~~-~G~L~VGiRRa~ 230 (687)
++++.||.|+||... .+.-+||+=+-.
T Consensus 38 ~~mk~GD~vifY~s~~~~~~ivai~~V~ 65 (143)
T PF01878_consen 38 KRMKPGDKVIFYHSGCKERGIVAIGEVV 65 (143)
T ss_dssp HC--TT-EEEEEETSSSS-EEEEEEEEE
T ss_pred hcCCCCCEEEEEEcCCCCCEEEEEEEEe
Confidence 489999999999987 567778776653
No 31
>PF05641 Agenet: Agenet domain; InterPro: IPR008395 This domain is related to the TUDOR domain IPR008191 from INTERPRO []. The function of the agenet domain is unknown. This signature matches one of the two Agenet domains in the FMR proteins [].; GO: 0003723 RNA binding; PDB: 2BKD_N 3O8V_A 3KUF_A 3H8Z_A.
Probab=30.25 E-value=1.1e+02 Score=25.91 Aligned_cols=42 Identities=12% Similarity=0.225 Sum_probs=26.9
Q ss_pred CccCcEEEEEEecCCCCCceeeeEEEeeccCCCCCCCCCcceeeeeccCCC
Q 005623 290 FSVGMRFKMRFEGEDSPERRFTGTIVGVGDFSEQWPGSKWRSLKIQWDEPA 340 (687)
Q Consensus 290 w~~GmRFkM~fE~eD~~~~~~~GTIvgv~~~dp~wp~S~WR~L~V~WDe~~ 340 (687)
|..|+++-..-+.+...-.||.|||+..... + .+.|+.+.-.
T Consensus 1 F~~G~~VEV~s~e~g~~gaWf~a~V~~~~~~------~---~~~V~Y~~~~ 42 (68)
T PF05641_consen 1 FKKGDEVEVSSDEDGFRGAWFPATVLKENGD------D---KYLVEYDDLP 42 (68)
T ss_dssp --TT-EEEEEE-SBTT--EEEEEEEEEEETT----------EEEEEETT-S
T ss_pred CCCCCEEEEEEcCCCCCcEEEEEEEEEeCCC------c---EEEEEECCcc
Confidence 5789999988875555458999999999742 2 7888886544
No 32
>cd06406 PB1_P67 A PB1 domain is present in p67 proteins which forms a signaling complex with p40, a crucial step for activation of NADPH oxidase during phagocytosis. PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes . A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. The p67 proteins contain
Probab=25.23 E-value=2e+02 Score=25.96 Aligned_cols=66 Identities=14% Similarity=0.303 Sum_probs=48.9
Q ss_pred eEEEeecCceeeeeecCCCCCChHHHHHHHHHHHhhccccCCCCCceEEeecCCC-CeEEecCCChHhHHhccce
Q 005623 574 RTKVQMQGIAVGRAVDLTALKGYDDLFDELEKMFEIQGQLRPRDKWAVVFTDDEG-DMMLAGDDQWPEFCKMVKK 647 (687)
Q Consensus 574 ~vKV~m~G~~igRkVDL~~~~~Y~~L~~~L~~MF~~~g~l~~~~~~~v~Y~D~eG-D~mLVGD~PW~~F~~~vkr 647 (687)
-||||.++ -| .|-...=-+|.+|.+.|.+=+.+.++ .=+|-|.|.+. +...++|.=++.-.+.|+-
T Consensus 4 vvKV~f~~-tI--aIrvp~~~~y~~L~~ki~~kLkl~~e-----~i~LsYkde~s~~~v~l~d~dle~aws~~~~ 70 (80)
T cd06406 4 VVKVHFKY-TV--AIQVARGLSYATLLQKISSKLELPAE-----HITLSYKSEASGEDVILSDTNMEDVWSQAKD 70 (80)
T ss_pred EEEEEEEE-EE--EEEcCCCCCHHHHHHHHHHHhCCCch-----hcEEEeccCCCCCccCcChHHHHHHHHhhcC
Confidence 37999998 33 45555666899999999998888542 34889998774 4444599999888887753
No 33
>COG1047 SlpA FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]
Probab=25.18 E-value=3.8e+02 Score=27.41 Aligned_cols=103 Identities=19% Similarity=0.283 Sum_probs=64.6
Q ss_pred CCCCCCEEEE-E--eCCCCcEEEEEEeccccCCCCCCcccccCccccchHHHHHHHHhcCCeEEEEEecCCC------cc
Q 005623 205 RLVAGDAFVF-L--RGENGELRVGVRRLAHQQSSMPSSVISSQSMHLGVLATAAHAVKTSTLFIVYYKPRTS------QF 275 (687)
Q Consensus 205 ~L~aGD~VvF-~--R~~~G~L~VGiRRa~~~~~~~p~sv~s~~sm~~gvla~A~~a~~tg~~F~V~Y~PR~s------eF 275 (687)
++..||.|.+ | |.++|+++=--.- ..-|..++-.+..-+.-|.+|..-..-|.-|+|.--|-.. +.
T Consensus 2 ~i~k~~~V~i~Y~~~~~dg~v~Dtt~e-----~~~P~~~i~G~g~li~glE~al~g~~~Ge~~~V~IpPE~AfGe~~~~l 76 (174)
T COG1047 2 KIEKGDVVSLHYTLKVEDGEVVDTTDE-----NYGPLTFIVGAGQLIPGLEEALLGKEVGEEFTVEIPPEDAFGEYDPDL 76 (174)
T ss_pred cccCCCEEEEEEEEEecCCcEEEcccc-----cCCCeEEEecCCCcchhHHHHHhCCCCCceeEEEeCchHhcCCCChHH
Confidence 4667888866 2 3456665421111 1124444433433344568888888999999999988542 22
Q ss_pred --eeeHHHHHHHhccCCccCcEEEEEEecCCCCCceeeeEEEeecc
Q 005623 276 --IIGLNKYLEAVHHCFSVGMRFKMRFEGEDSPERRFTGTIVGVGD 319 (687)
Q Consensus 276 --vV~~~ky~~A~~~~w~~GmRFkM~fE~eD~~~~~~~GTIvgv~~ 319 (687)
.|++++|...= ...+||+|. ++++| ...-|+|+.|..
T Consensus 77 vq~vp~~~F~~~~--~~~vGm~~~--~~~~~---~~~~~~V~~V~~ 115 (174)
T COG1047 77 VQRVPRDEFQGVG--ELEVGMEVE--AEGGD---GEIPGVVTEVSG 115 (174)
T ss_pred eEEecHHHhCcCC--CCCCCcEEE--EcCCC---ceeeEEEEEEcC
Confidence 46777665542 689999987 44454 456899999875
No 34
>PRK14129 heat shock protein HspQ; Provisional
Probab=24.73 E-value=90 Score=29.42 Aligned_cols=50 Identities=20% Similarity=0.351 Sum_probs=35.3
Q ss_pred ccCCccCcEEEEEEecCCCCCceeeeEEEeeccCCCCCCC-CCcceeeeeccCCCCCCCCCccccCcc
Q 005623 287 HHCFSVGMRFKMRFEGEDSPERRFTGTIVGVGDFSEQWPG-SKWRSLKIQWDEPATVQRPERVSPWEI 353 (687)
Q Consensus 287 ~~~w~~GmRFkM~fE~eD~~~~~~~GTIvgv~~~dp~wp~-S~WR~L~V~WDe~~~~~~~~RVSPWeI 353 (687)
..+|.+|.-+|-+. -.|-|.|+.| ||.+.+ .+| |++-... ++.|=.||==
T Consensus 3 ~akF~IGQ~VrHrl-------~~yrGVV~DV---DP~fs~~e~w------~~~ia~~-~p~kdqPwYH 53 (105)
T PRK14129 3 ASKFGIGQQVRHSL-------LGYLGVVVDI---DPEYSLEEPS------PDELAVN-DELRAAPWYH 53 (105)
T ss_pred cccccCCcEEEEee-------cCCCeEEEee---CCCcCCCchh------HHhhccC-CCccCCCceE
Confidence 46899999999887 3489999988 454432 244 5665543 7777888853
No 35
>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=23.48 E-value=96 Score=27.85 Aligned_cols=57 Identities=16% Similarity=0.247 Sum_probs=29.8
Q ss_pred eHHHHHHHhccCCccCcEEEEEEecCCCCCceeeeEEEeeccCCCCCCCCCcceeeeeccCCC
Q 005623 278 GLNKYLEAVHHCFSVGMRFKMRFEGEDSPERRFTGTIVGVGDFSEQWPGSKWRSLKIQWDEPA 340 (687)
Q Consensus 278 ~~~ky~~A~~~~w~~GmRFkM~fE~eD~~~~~~~GTIvgv~~~dp~wp~S~WR~L~V~WDe~~ 340 (687)
+.+.|.+=+.-+..+||++||.=.-|+-.+ -=.|+|.-++... -|+ -.+||.|-.-.
T Consensus 6 s~d~Ya~YVr~~i~~GM~VRc~~~yeeV~~-GD~G~V~k~~~dg--~~~---lnvqv~W~~~G 62 (78)
T PF11515_consen 6 SNDDYAEYVRDNIQPGMRVRCCRDYEEVRA-GDEGEVFKQDRDG--LHD---LNVQVDWQSKG 62 (78)
T ss_dssp SSHHHHHHHHHH--TT-EEEESS-BTTB-T-T-EEE-EEEE-TT--SSE-----EEEEETTTT
T ss_pred chhHHHHHHHHhCCCCcEEEEecccccccc-cccceeEeeccCC--CCC---cceEEEeeecC
Confidence 456688888889999999999754444322 2367766665311 111 24777776654
No 36
>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=20.80 E-value=78 Score=26.04 Aligned_cols=17 Identities=18% Similarity=0.698 Sum_probs=14.7
Q ss_pred eEEeecCCCCeEEecCC
Q 005623 620 AVVFTDDEGDMMLAGDD 636 (687)
Q Consensus 620 ~v~Y~D~eGD~mLVGD~ 636 (687)
.+.|.|.+|+.+++|+.
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 69999999999999973
No 37
>KOG3938 consensus RGS-GAIP interacting protein GIPC, contains PDZ domain [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=20.23 E-value=1.2e+02 Score=33.02 Aligned_cols=75 Identities=16% Similarity=0.346 Sum_probs=56.0
Q ss_pred ecCceeeeeecCCCCCChHHHHHHHHHHHhhccc--c-CCCCCceEEeecCCCCeEEecCCChHhHH-----hccceEEE
Q 005623 579 MQGIAVGRAVDLTALKGYDDLFDELEKMFEIQGQ--L-RPRDKWAVVFTDDEGDMMLAGDDQWPEFC-----KMVKKIFI 650 (687)
Q Consensus 579 m~G~~igRkVDL~~~~~Y~~L~~~L~~MF~~~g~--l-~~~~~~~v~Y~D~eGD~mLVGD~PW~~F~-----~~vkri~I 650 (687)
-+|.|.|| +..|++-+||+..+.+-|+|.-. | ..-+.+. -|=+-||-|-.-.++|+ .-.|.++|
T Consensus 61 AHGSptg~---Ie~fsnv~ELY~kIAe~F~Is~~dIlfcTlNshK-----vDM~~llgGqigleDfiFAHvkGq~kEv~v 132 (334)
T KOG3938|consen 61 AHGSPTGR---IEGFSNVRELYQKIAEAFDISPDDILFCTLNSHK-----VDMKRLLGGQIGLEDFIFAHVKGQAKEVEV 132 (334)
T ss_pred ccCCccce---ecccccHHHHHHHHHHHhcCCccceEEEecCCCc-----ccHHHHhcCccChhhhhhhhhcCcceeEEE
Confidence 46889998 56799999999999999999632 1 1111111 23345899999999996 45688999
Q ss_pred echhhhccccC
Q 005623 651 YSTEEVKNMAT 661 (687)
Q Consensus 651 ~~~~e~~~~~~ 661 (687)
++.+++-+++-
T Consensus 133 ~KsedalGlTI 143 (334)
T KOG3938|consen 133 VKSEDALGLTI 143 (334)
T ss_pred EecccccceEE
Confidence 99999988763
Done!