Query 005675
Match_columns 684
No_of_seqs 344 out of 846
Neff 4.6
Searched_HMMs 46136
Date Thu Mar 28 12:02:50 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/005675.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/005675hhsearch_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 2.7E-37 5.9E-42 310.1 0.4 94 576-669 107-215 (215)
2 PF06507 Auxin_resp: Auxin res 100.0 3.3E-34 7.1E-39 249.6 8.3 80 249-328 1-83 (83)
3 PF02362 B3: B3 DNA binding do 99.7 1.2E-16 2.6E-21 140.2 10.7 97 123-224 1-99 (100)
4 KOG0644 Uncharacterized conser 99.5 9.1E-15 2E-19 166.5 6.9 147 202-354 875-1045(1113)
5 PF09217 EcoRII-N: Restriction 98.1 1.2E-05 2.7E-10 77.8 9.5 90 119-210 6-110 (156)
6 PF03754 DUF313: Domain of unk 97.5 0.00015 3.2E-09 67.6 5.5 78 120-198 21-114 (114)
7 PF00564 PB1: PB1 domain; Int 96.9 0.0027 5.8E-08 54.4 6.2 67 580-652 3-70 (84)
8 smart00666 PB1 PB1 domain. Pho 96.4 0.015 3.2E-07 49.7 7.5 65 581-652 4-69 (81)
9 cd06407 PB1_NLP A PB1 domain i 96.3 0.014 3.1E-07 51.4 7.1 57 580-642 2-58 (82)
10 cd05992 PB1 The PB1 domain is 96.2 0.024 5.1E-07 48.2 7.9 65 581-652 3-69 (81)
11 cd06398 PB1_Joka2 The PB1 doma 96.2 0.013 2.9E-07 52.7 6.6 67 581-653 3-72 (91)
12 cd06396 PB1_NBR1 The PB1 domai 95.8 0.033 7.1E-07 49.4 7.1 65 580-651 2-67 (81)
13 cd06403 PB1_Par6 The PB1 domai 95.7 0.058 1.2E-06 47.6 7.9 72 581-657 3-78 (80)
14 cd06401 PB1_TFG The PB1 domain 94.4 0.25 5.4E-06 43.9 8.3 71 581-657 3-79 (81)
15 cd06409 PB1_MUG70 The MUG70 pr 93.8 0.099 2.2E-06 46.8 4.7 53 588-642 7-61 (86)
16 cd06404 PB1_aPKC PB1 domain is 93.2 0.29 6.3E-06 43.7 6.5 57 580-642 2-58 (83)
17 cd06408 PB1_NoxR The PB1 domai 92.1 0.4 8.7E-06 43.1 6.1 55 579-642 3-57 (86)
18 cd06402 PB1_p62 The PB1 domain 91.9 0.62 1.4E-05 41.9 7.1 62 580-647 2-68 (87)
19 cd06397 PB1_UP1 Uncharacterize 89.5 1 2.3E-05 40.1 6.1 66 581-653 3-69 (82)
20 PRK10737 FKBP-type peptidyl-pr 65.6 22 0.00047 36.5 7.4 102 200-314 2-114 (196)
21 KOG0644 Uncharacterized conser 62.1 6.3 0.00014 47.9 3.1 67 32-99 872-940 (1113)
22 cd06406 PB1_P67 A PB1 domain i 53.5 56 0.0012 29.3 6.9 68 581-656 5-75 (80)
23 smart00743 Agenet Tudor-like d 51.7 23 0.00049 28.8 4.0 38 284-333 2-39 (61)
24 cd06399 PB1_P40 The PB1 domain 47.4 33 0.00072 31.3 4.5 41 595-642 23-63 (92)
25 PF04014 Antitoxin-MazE: Antid 44.5 26 0.00057 27.4 3.1 27 194-220 14-40 (47)
26 KOG3207 Beta-tubulin folding c 37.3 27 0.00058 40.3 2.9 42 285-339 3-44 (505)
27 PF05641 Agenet: Agenet domain 34.5 1E+02 0.0022 26.0 5.3 42 285-335 1-42 (68)
28 smart00333 TUDOR Tudor domain. 33.5 69 0.0015 25.2 4.0 52 284-351 2-53 (57)
29 PF10844 DUF2577: Protein of u 33.1 55 0.0012 29.9 3.8 28 195-222 71-98 (100)
30 TIGR01439 lp_hng_hel_AbrB loop 31.4 58 0.0013 24.3 3.1 26 194-219 14-39 (43)
31 PF02513 Spin-Ssty: Spin/Ssty 31.3 66 0.0014 26.5 3.5 32 287-318 1-32 (50)
32 PF00788 RA: Ras association ( 30.5 1.2E+02 0.0026 25.9 5.3 70 578-650 2-77 (93)
33 KOG3938 RGS-GAIP interacting p 29.1 74 0.0016 34.6 4.4 73 586-666 62-142 (334)
34 PF01878 EVE: EVE domain; Int 25.5 67 0.0015 30.4 3.1 26 199-224 38-64 (143)
35 COG1047 SlpA FKBP-type peptidy 24.1 3.8E+02 0.0083 27.3 8.2 103 200-314 2-115 (174)
36 PRK14129 heat shock protein Hs 21.3 1.1E+02 0.0024 28.8 3.5 49 282-347 3-52 (105)
37 KOG3606 Cell polarity protein 21.0 95 0.0021 33.9 3.4 80 579-663 19-102 (358)
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=2.7e-37 Score=310.07 Aligned_cols=94 Identities=46% Similarity=0.802 Sum_probs=0.0
Q ss_pred CCcceeEEEecCceeeeeecCCCCCChHHHHHHHHHHh---hcc----------cc--cCCCCceeEEEecCCCCeEEcc
Q 005675 576 SNRSRTKVQMQGVAVGRALDLTTLVGYDHLIDELEEMF---DIK----------GQ--LHTRTKWEIVYTDDEGDMMLVG 640 (684)
Q Consensus 576 s~~~~vKV~m~G~~vGR~vDL~~~~sY~eL~~~L~~MF---~~~----------g~--l~~~~~~~v~Y~D~eGD~mlvG 640 (684)
..++||||+|||++|||||||++|+||++|+.+|++|| +|. +. +..+++|+|||+|+||||||||
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 666 22 3356799999999999999999
Q ss_pred CCChHHHHhcceeEEEeeccccccCCCCC
Q 005675 641 DDPWHEFCNMVKRIFICSSQDVKKMSPGS 669 (684)
Q Consensus 641 D~PW~~F~~~vkri~I~~~~e~~~~~~~~ 669 (684)
||||+|||++||||+||+.+|+++|+|++
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=3.3e-34 Score=249.60 Aligned_cols=80 Identities=55% Similarity=1.010 Sum_probs=78.1
Q ss_pred HHHHHHcCCeeEEEEecCCC--cceeeHHHHHHHHcCCCccCCEEEEEEecCCCCCceeeeEEeeeecCCC-CCCCCCcc
Q 005675 249 ASHAVATQTMFVVYYKPRTS--QFIISLNKYLEAVNNKFAVGMRYKMRFEGEDSPERRFSGTVVGVEDFSP-HWKDSKWR 325 (684)
Q Consensus 249 A~~a~~~~~~F~V~Y~Pr~s--eFvV~~~~y~~A~~~~w~~GmRFkM~fE~eds~~~~~~GTI~~v~~~dp-~wp~S~WR 325 (684)
|+|||+++++|+|+||||++ ||||++++|++||+++|++||||||+||+||+++++|+|||+||++.|| +||+|+||
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 005675 326 SLK 328 (684)
Q Consensus 326 ~L~ 328 (684)
|||
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=99.69 E-value=1.2e-16 Score=140.22 Aligned_cols=97 Identities=31% Similarity=0.397 Sum_probs=74.7
Q ss_pred EEEecccccCCCCCceeEecccccccCCCCCCCCCCCceEEEEEeCCCCeEEEEEEEeCCCcceeecccchhhhcccCCC
Q 005675 123 FSKVLTASDTSTHGGFSVLRKHATECLPPLDMNQSTPTQELVAKDLHGYEWRFKHIFRGQPRRHLLTTGWSTFVTSKRLV 202 (684)
Q Consensus 123 F~K~LT~SDv~~~grfsVPk~~Ae~~FP~Ld~~~~~p~q~L~~~D~~G~~W~Fr~~~rg~prr~lLTtGWs~FV~~K~L~ 202 (684)
|.|+|+++|+...++|.||+++++.+. ++ ....+++.++|..|+.|.+++.+++.++++.|++||..||++++|+
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 899999999999999999999999872 11 1235789999999999999999998888899999999999999999
Q ss_pred CCCEEEEEecC--CCcEEEEEEEc
Q 005675 203 AGDTFVFLRGE--NGELHVGVRCL 224 (684)
Q Consensus 203 aGD~VvF~R~~--~G~l~VgIRRa 224 (684)
+||.|+|+... ..++.|.|.|+
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 45569999986
No 4
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=99.52 E-value=9.1e-15 Score=166.53 Aligned_cols=147 Identities=22% Similarity=0.424 Sum_probs=120.7
Q ss_pred CCCCEEEEEecCCCcEEEEEEEccccCC---------------------CCCCccccCCcccchhHHHHHHHHHcCCeeE
Q 005675 202 VAGDTFVFLRGENGELHVGVRCLARQQS---------------------SMPSSVISSQSMHLGVLATASHAVATQTMFV 260 (684)
Q Consensus 202 ~aGD~VvF~R~~~G~l~VgIRRa~~~~~---------------------~~p~sv~~~~sm~~gvla~A~~a~~~~~~F~ 260 (684)
..||.|+++|.+..++.-.+|+.....+ ..|-+..+.+.|.|.||.-|.++. ...|.
T Consensus 875 QmgDEViyfrQghqeyl~~~~~n~~~~~~~~p~~~~~v~~~kv~kl~~~~y~~~~~s~c~m~l~~idp~s~~~--~k~F~ 952 (1113)
T KOG0644|consen 875 QMGDEVIYFRQGHQEYLEAVRLNNIELNNKEPWNKMAVEICKVEKLVYITYPGSGDSCCKMKLAVIDPASKLM--DKSFK 952 (1113)
T ss_pred cccceeehhhhhhHHHHhhhhhccccccccCcccccchhhheeeeeeeeeccCCCcchheeeeeeecchhhhh--hccce
Confidence 4899999999887777666666543322 124555667999999999999753 56799
Q ss_pred EEEecCCC--cceeeHHHHHHHHcCCCccCCEEEEEEecCCC-CCceeeeEEeeeecCCCCCCCCCcceEEEeecCCCCC
Q 005675 261 VYYKPRTS--QFIISLNKYLEAVNNKFAVGMRYKMRFEGEDS-PERRFSGTVVGVEDFSPHWKDSKWRSLKVQWDEPASI 337 (684)
Q Consensus 261 V~Y~Pr~s--eFvV~~~~y~~A~~~~w~~GmRFkM~fE~eds-~~~~~~GTI~~v~~~dp~wp~S~WR~L~V~WDe~~~~ 337 (684)
+.|..-.. ||+|.++.|++|++++|..+++||.-+..+-- --+||.|+|.++.+.+|++|+|+|.|+.|+||..+
T Consensus 953 ltlpdlv~fpDFlV~rsrYd~AiQrnW~~~d~crvwwrda~~e~g~WWeG~ils~~pksp~fpdSpwery~v~~~~~e-- 1030 (1113)
T KOG0644|consen 953 LTLPDLVTFPDFLVERSRYDAAIQRNWTCRDKCRVWWRDAGEEDGAWWEGRILSVKPKSPDFPDSPWERYIVRYDNTE-- 1030 (1113)
T ss_pred eecccccCcchhhhhhhhHHHHHhhccccccceeEEEccCCCcCCceeeeeeeeccCCCCCCCCCcceeEEEEecCCc--
Confidence 99987665 99999999999999999999999999852210 12899999999999999999999999999999998
Q ss_pred CCCCccccCccccccCC
Q 005675 338 TRPDRVSPWEIEPFVAS 354 (684)
Q Consensus 338 ~~~~RVSPWeIEp~~~~ 354 (684)
.+.-||||.|++...
T Consensus 1031 --~~~~spwe~~~i~de 1045 (1113)
T KOG0644|consen 1031 --TELHSPWEMEPIPDE 1045 (1113)
T ss_pred --ccccCccccCCCccc
Confidence 466799999998765
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=98.13 E-value=1.2e-05 Score=77.83 Aligned_cols=90 Identities=18% Similarity=0.219 Sum_probs=61.0
Q ss_pred cceEEEEecccccCCCCC----ceeEecccccccCCCCCC-CCCCCceEEEEEeCCC--CeEEEEEEEeCC------Ccc
Q 005675 119 KVHSFSKVLTASDTSTHG----GFSVLRKHATECLPPLDM-NQSTPTQELVAKDLHG--YEWRFKHIFRGQ------PRR 185 (684)
Q Consensus 119 ~~~~F~K~LT~SDv~~~g----rfsVPk~~Ae~~FP~Ld~-~~~~p~q~L~~~D~~G--~~W~Fr~~~rg~------prr 185 (684)
....|+|.|++.|++..| |+.||+..++.+||.+.. ....|...|.+++..| ..|+||++|.|+ .+.
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 456899999999999875 799999999999998776 5667889999999877 568899999976 557
Q ss_pred eeec--ccchhhhcccCCCCCCEEEEE
Q 005675 186 HLLT--TGWSTFVTSKRLVAGDTFVFL 210 (684)
Q Consensus 186 ~lLT--tGWs~FV~~K~L~aGD~VvF~ 210 (684)
+.|| ++=..|.+. =..||.+||.
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 333334432 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=97.51 E-value=0.00015 Score=67.64 Aligned_cols=78 Identities=18% Similarity=0.239 Sum_probs=61.1
Q ss_pred ceEEEEecccccCCCC-CceeEecccccccCCCCCC------------CCCCCceEEEEEeCCCCeEEEEEEEeCC---C
Q 005675 120 VHSFSKVLTASDTSTH-GGFSVLRKHATECLPPLDM------------NQSTPTQELVAKDLHGYEWRFKHIFRGQ---P 183 (684)
Q Consensus 120 ~~~F~K~LT~SDv~~~-grfsVPk~~Ae~~FP~Ld~------------~~~~p~q~L~~~D~~G~~W~Fr~~~rg~---p 183 (684)
...|+|+|++||+..+ .||+||-..... ...|.. ....-++.+.+.|..++.|..++..|.. .
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 4789999999999886 899999886632 122311 1234578899999999999999999965 4
Q ss_pred cceeecccchhhhcc
Q 005675 184 RRHLLTTGWSTFVTS 198 (684)
Q Consensus 184 rr~lLTtGWs~FV~~ 198 (684)
-.|+|++||..+|++
T Consensus 100 ~~YvL~~gWn~VV~~ 114 (114)
T PF03754_consen 100 SNYVLNSGWNKVVED 114 (114)
T ss_pred eEEEEEcChHhhccC
Confidence 579999999999863
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=96.85 E-value=0.0027 Score=54.35 Aligned_cols=67 Identities=27% Similarity=0.536 Sum_probs=54.4
Q ss_pred eeEEEecCceeeeeecCCCCCChHHHHHHHHHHhhcccccCCCCceeEEEecCCCCeEEccCC-ChHHHHhcce
Q 005675 580 RTKVQMQGVAVGRALDLTTLVGYDHLIDELEEMFDIKGQLHTRTKWEIVYTDDEGDMMLVGDD-PWHEFCNMVK 652 (684)
Q Consensus 580 ~vKV~m~G~~vGR~vDL~~~~sY~eL~~~L~~MF~~~g~l~~~~~~~v~Y~D~eGD~mlvGD~-PW~~F~~~vk 652 (684)
-+|++..|. +=|.+.+..--+|++|..++++.|++. ...+.+.|.|.||||..+-++ =|++.+..++
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 479999995 444688888889999999999999987 445799999999999988754 4666677664
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=96.36 E-value=0.015 Score=49.74 Aligned_cols=65 Identities=17% Similarity=0.411 Sum_probs=50.9
Q ss_pred eEEEecCceeeeeecCCCCCChHHHHHHHHHHhhcccccCCCCceeEEEecCCCCeEEccC-CChHHHHhcce
Q 005675 581 TKVQMQGVAVGRALDLTTLVGYDHLIDELEEMFDIKGQLHTRTKWEIVYTDDEGDMMLVGD-DPWHEFCNMVK 652 (684)
Q Consensus 581 vKV~m~G~~vGR~vDL~~~~sY~eL~~~L~~MF~~~g~l~~~~~~~v~Y~D~eGD~mlvGD-~PW~~F~~~vk 652 (684)
+||.-.| -=|.+-+..--+|++|..++.+.|++.. ..+.+.|+|.|||+..+.+ +=|.+.+.+++
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 6888755 3678888889999999999999999753 4579999999999986654 45555555554
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=96.29 E-value=0.014 Score=51.42 Aligned_cols=57 Identities=21% Similarity=0.393 Sum_probs=45.9
Q ss_pred eeEEEecCceeeeeecCCCCCChHHHHHHHHHHhhcccccCCCCceeEEEecCCCCeEEccCC
Q 005675 580 RTKVQMQGVAVGRALDLTTLVGYDHLIDELEEMFDIKGQLHTRTKWEIVYTDDEGDMMLVGDD 642 (684)
Q Consensus 580 ~vKV~m~G~~vGR~vDL~~~~sY~eL~~~L~~MF~~~g~l~~~~~~~v~Y~D~eGD~mlvGD~ 642 (684)
-|||...|. -+.+-|..--+|++|..++.++|.+.. ...+.|-|.|+||||..+--+
T Consensus 2 ~vK~~~~~d--~~r~~l~~~~~~~~L~~~i~~r~~~~~----~~~f~LkY~Ddegd~v~ltsd 58 (82)
T cd06407 2 RVKATYGEE--KIRFRLPPSWGFTELKQEIAKRFKLDD----MSAFDLKYLDDDEEWVLLTCD 58 (82)
T ss_pred EEEEEeCCe--EEEEEcCCCCCHHHHHHHHHHHhCCCC----CCeeEEEEECCCCCeEEeecH
Confidence 379999886 445666666699999999999999853 356899999999999987544
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=96.21 E-value=0.024 Score=48.21 Aligned_cols=65 Identities=18% Similarity=0.465 Sum_probs=49.4
Q ss_pred eEEEecCceeeeeecCC-CCCChHHHHHHHHHHhhcccccCCCCceeEEEecCCCCeEEccC-CChHHHHhcce
Q 005675 581 TKVQMQGVAVGRALDLT-TLVGYDHLIDELEEMFDIKGQLHTRTKWEIVYTDDEGDMMLVGD-DPWHEFCNMVK 652 (684)
Q Consensus 581 vKV~m~G~~vGR~vDL~-~~~sY~eL~~~L~~MF~~~g~l~~~~~~~v~Y~D~eGD~mlvGD-~PW~~F~~~vk 652 (684)
+||+-.|.. |.+=+. .--+|++|...|.+.|++.. ..+.+.|.|.|||+..+.+ .=|++.++.++
T Consensus 3 vK~~~~~~~--~~~~~~~~~~s~~~L~~~i~~~~~~~~-----~~~~l~y~D~e~d~v~l~sd~Dl~~a~~~~~ 69 (81)
T cd05992 3 VKVKYGGEI--RRFVVVSRSISFEDLRSKIAEKFGLDA-----VSFKLKYPDEDGDLVTISSDEDLEEAIEEAR 69 (81)
T ss_pred EEEEecCCC--EEEEEecCCCCHHHHHHHHHHHhCCCC-----CcEEEEeeCCCCCEEEeCCHHHHHHHHHHHh
Confidence 688888642 333333 78899999999999999864 4579999999999999887 44555555554
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=96.21 E-value=0.013 Score=52.66 Aligned_cols=67 Identities=22% Similarity=0.453 Sum_probs=51.8
Q ss_pred eEEEecCceeeeeecCC---CCCChHHHHHHHHHHhhcccccCCCCceeEEEecCCCCeEEccCCChHHHHhccee
Q 005675 581 TKVQMQGVAVGRALDLT---TLVGYDHLIDELEEMFDIKGQLHTRTKWEIVYTDDEGDMMLVGDDPWHEFCNMVKR 653 (684)
Q Consensus 581 vKV~m~G~~vGR~vDL~---~~~sY~eL~~~L~~MF~~~g~l~~~~~~~v~Y~D~eGD~mlvGD~PW~~F~~~vkr 653 (684)
+||.-+|.-+==++++. .--+|++|..++.+.|.+.. ..++.+.|.|.||||..+-++ .++...+.+
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 VKVKYGGTLRRFTFPVAENQLDLNMDGLREKVEELFSLSP----DADLSLTYTDEDGDVVTLVDD--NDLTDAIQY 72 (91)
T ss_pred EEEEeCCEEEEEEeccccccCCCCHHHHHHHHHHHhCCCC----CCcEEEEEECCCCCEEEEccH--HHHHHHHHH
Confidence 79999996333344443 35799999999999998743 467899999999999999777 777655554
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=0.033 Score=49.38 Aligned_cols=65 Identities=15% Similarity=0.222 Sum_probs=50.6
Q ss_pred eeEEEecCceeeeeecCCCCCChHHHHHHHHHHhhcccccCCCCceeEEEecCCCCeEEcc-CCChHHHHhcc
Q 005675 580 RTKVQMQGVAVGRALDLTTLVGYDHLIDELEEMFDIKGQLHTRTKWEIVYTDDEGDMMLVG-DDPWHEFCNMV 651 (684)
Q Consensus 580 ~vKV~m~G~~vGR~vDL~~~~sY~eL~~~L~~MF~~~g~l~~~~~~~v~Y~D~eGD~mlvG-D~PW~~F~~~v 651 (684)
-+||.-.|.-+==+++-+.--+|++|..++.++|++. .+.+.|-|.||||.++- |.=.++.++.+
T Consensus 2 ~vKaty~~d~~rf~~~~~~~~~~~~L~~ev~~rf~l~-------~f~lKYlDde~e~v~lssd~eLeE~~rl~ 67 (81)
T cd06396 2 NLKVTYNGESQSFLVSDSENTTWASVEAMVKVSFGLN-------DIQIKYVDEENEEVSVNSQGEYEEALKSA 67 (81)
T ss_pred EEEEEECCeEEEEEecCCCCCCHHHHHHHHHHHhCCC-------cceeEEEcCCCCEEEEEchhhHHHHHHHH
Confidence 3789999977666777766889999999999999998 46899999999998764 33344444433
No 13
>cd06403 PB1_Par6 The PB1 domain is an essential part of Par6 protein which in complex with Par3 and aPKC proteins is crucial for establishment of apical-basal polarity of animal cells. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. The
Probab=95.65 E-value=0.058 Score=47.65 Aligned_cols=72 Identities=24% Similarity=0.360 Sum_probs=53.4
Q ss_pred eEEEecCceeeeeecCCCCCChHHHHHHHHHHhhcccccCCCCceeEEEecCCCCeEEccCC-ChHHHHhcce---eEEE
Q 005675 581 TKVQMQGVAVGRALDLTTLVGYDHLIDELEEMFDIKGQLHTRTKWEIVYTDDEGDMMLVGDD-PWHEFCNMVK---RIFI 656 (684)
Q Consensus 581 vKV~m~G~~vGR~vDL~~~~sY~eL~~~L~~MF~~~g~l~~~~~~~v~Y~D~eGD~mlvGD~-PW~~F~~~vk---ri~I 656 (684)
||...+++=-==++|.....+|++++..|+.|+.|.+ -.+.|-|+|.+||.+-+-.+ -+..=+.+++ ||.|
T Consensus 3 VKSkfdaEfRRFsl~r~~~~~f~ef~~ll~~lH~l~~-----~~f~i~Y~D~~gDLLPInNDdNf~kAlssa~plLRl~i 77 (80)
T cd06403 3 VKSKFDAEFRRFSLDRNKPGKFEDFYKLLEHLHHIPN-----VDFLIGYTDPHGDLLPINNDDNFLKALSSANPLLRIFI 77 (80)
T ss_pred eecccCCeEEEEEeccccCcCHHHHHHHHHHHhCCCC-----CcEEEEEeCCCCCEecccCcHHHHHHHHcCCCceEEEE
Confidence 5666666533336777778999999999999999976 34789999999999988644 4444456666 5555
Q ss_pred e
Q 005675 657 C 657 (684)
Q Consensus 657 ~ 657 (684)
-
T Consensus 78 q 78 (80)
T cd06403 78 Q 78 (80)
T ss_pred E
Confidence 3
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=94.36 E-value=0.25 Score=43.89 Aligned_cols=71 Identities=23% Similarity=0.483 Sum_probs=49.7
Q ss_pred eEEEecCceeeeeecCCCC-CChHHHHHHHHHHhhcccccCCCCceeEEEecCCCCeEEccCCChHHH-----HhcceeE
Q 005675 581 TKVQMQGVAVGRALDLTTL-VGYDHLIDELEEMFDIKGQLHTRTKWEIVYTDDEGDMMLVGDDPWHEF-----CNMVKRI 654 (684)
Q Consensus 581 vKV~m~G~~vGR~vDL~~~-~sY~eL~~~L~~MF~~~g~l~~~~~~~v~Y~D~eGD~mlvGD~PW~~F-----~~~vkri 654 (684)
+|+..+| +| |.+=+..- -+|.+|...+.+.|... +.+.+.+.|.|.|.|||+.-|.+. +++ +...+||
T Consensus 3 iK~~~g~-Di-R~~~~~~~~~t~~~L~~~v~~~F~~~--~~~~~~flIKYkD~dGDlVTIts~--~dL~~A~~~~~~~~l 76 (81)
T cd06401 3 LKAQLGD-DI-RRIPIHNEDITYDELLLMMQRVFRGK--LGSSDDVLIKYKDEDGDLITIFDS--SDLSFAIQCSRILKL 76 (81)
T ss_pred EEEEeCC-eE-EEEeccCccccHHHHHHHHHHHhccc--cCCcccEEEEEECCCCCEEEeccH--HHHHHHHhcCcceEE
Confidence 5666655 45 44444432 39999999999999843 334566899999999999999886 444 4445566
Q ss_pred EEe
Q 005675 655 FIC 657 (684)
Q Consensus 655 ~I~ 657 (684)
+|.
T Consensus 77 ~~~ 79 (81)
T cd06401 77 TLF 79 (81)
T ss_pred EEe
Confidence 654
No 15
>cd06409 PB1_MUG70 The MUG70 protein is a product of the meiotically up-regulated gene 70 which has a role in meiosis and harbors a PB1 domain. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domains depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic amino acid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is
Probab=93.78 E-value=0.099 Score=46.83 Aligned_cols=53 Identities=21% Similarity=0.330 Sum_probs=41.5
Q ss_pred ceeeeeecCC--CCCChHHHHHHHHHHhhcccccCCCCceeEEEecCCCCeEEccCC
Q 005675 588 VAVGRALDLT--TLVGYDHLIDELEEMFDIKGQLHTRTKWEIVYTDDEGDMMLVGDD 642 (684)
Q Consensus 588 ~~vGR~vDL~--~~~sY~eL~~~L~~MF~~~g~l~~~~~~~v~Y~D~eGD~mlvGD~ 642 (684)
.+-||.+=++ ...|+.+|..++.+=|+++... ...+.+.|.|+||||.++--+
T Consensus 7 ~~~GrvhRf~~~~s~~~~~L~~~I~~Rl~~d~~~--~~~~~L~YlDDEgD~VllT~D 61 (86)
T cd06409 7 DPKGRVHRFRLRPSESLEELRTLISQRLGDDDFE--THLYALSYVDDEGDIVLITSD 61 (86)
T ss_pred CCCCCEEEEEecCCCCHHHHHHHHHHHhCCcccc--CCcccEEEEcCCCCEEEEecc
Confidence 3466665554 3689999999999999987643 456899999999999887544
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=93.16 E-value=0.29 Score=43.69 Aligned_cols=57 Identities=19% Similarity=0.396 Sum_probs=46.2
Q ss_pred eeEEEecCceeeeeecCCCCCChHHHHHHHHHHhhcccccCCCCceeEEEecCCCCeEEccCC
Q 005675 580 RTKVQMQGVAVGRALDLTTLVGYDHLIDELEEMFDIKGQLHTRTKWEIVYTDDEGDMMLVGDD 642 (684)
Q Consensus 580 ~vKV~m~G~~vGR~vDL~~~~sY~eL~~~L~~MF~~~g~l~~~~~~~v~Y~D~eGD~mlvGD~ 642 (684)
-+|++-.|.-+==.+|. .-+|++|.+++.+||.+.. ...+++.|.|.|||.--+..+
T Consensus 2 ~~K~~y~gdi~it~~d~--~~s~e~L~~~v~~~c~~~~----~q~ft~kw~DEEGDp~tiSS~ 58 (83)
T cd06404 2 RVKAAYNGDIMITSIDP--SISLEELCNEVRDMCRFHN----DQPFTLKWIDEEGDPCTISSQ 58 (83)
T ss_pred eEEEEecCcEEEEEcCC--CcCHHHHHHHHHHHhCCCC----CCcEEEEEECCCCCceeecCH
Confidence 37899999755555666 6789999999999998743 456899999999999877665
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=92.15 E-value=0.4 Score=43.06 Aligned_cols=55 Identities=31% Similarity=0.523 Sum_probs=46.6
Q ss_pred ceeEEEecCceeeeeecCCCCCChHHHHHHHHHHhhcccccCCCCceeEEEecCCCCeEEccCC
Q 005675 579 SRTKVQMQGVAVGRALDLTTLVGYDHLIDELEEMFDIKGQLHTRTKWEIVYTDDEGDMMLVGDD 642 (684)
Q Consensus 579 ~~vKV~m~G~~vGR~vDL~~~~sY~eL~~~L~~MF~~~g~l~~~~~~~v~Y~D~eGD~mlvGD~ 642 (684)
--|||+-+|. -|.|-+..--+|++|..++.++|++.. ...|-|.|. ||+.-++|.
T Consensus 3 ikVKv~~~~D--v~~i~v~~~i~f~dL~~kIrdkf~~~~------~~~iKykDE-GD~iti~sq 57 (86)
T cd06408 3 IRVKVHAQDD--TRYIMIGPDTGFADFEDKIRDKFGFKR------RLKIKMKDD-GDMITMGDQ 57 (86)
T ss_pred EEEEEEecCc--EEEEEcCCCCCHHHHHHHHHHHhCCCC------ceEEEEEcC-CCCccccCH
Confidence 4689999997 566777777789999999999999953 468999999 999999886
No 18
>cd06402 PB1_p62 The PB1 domain is an essential part of p62 scaffold protein (alias sequestosome 1,SQSTM) involved in cell signaling, receptor internalization, and protein turnover. The PB1 domain is a modular domain mediating specific protein-protein interaction which play roles in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.
Probab=91.92 E-value=0.62 Score=41.90 Aligned_cols=62 Identities=23% Similarity=0.512 Sum_probs=46.1
Q ss_pred eeEEEecC----ceeee-eecCCCCCChHHHHHHHHHHhhcccccCCCCceeEEEecCCCCeEEccCCChHHH
Q 005675 580 RTKVQMQG----VAVGR-ALDLTTLVGYDHLIDELEEMFDIKGQLHTRTKWEIVYTDDEGDMMLVGDDPWHEF 647 (684)
Q Consensus 580 ~vKV~m~G----~~vGR-~vDL~~~~sY~eL~~~L~~MF~~~g~l~~~~~~~v~Y~D~eGD~mlvGD~PW~~F 647 (684)
.||.+..| ..|=| ++|=....+|++|...+.++|..-. ...+.+.|.|.|||..-+..+ +++
T Consensus 2 ~vkayl~~~~~~~EIRRf~l~~~~~~s~~~L~~~V~~~f~~l~----~~~ftlky~DeeGDlvtIssd--eEL 68 (87)
T cd06402 2 TVKAYLLGKDANAEIRRFAIDEDVSTSYEYLVEKVAAVFPSLR----GKNFQLFWKDEEGDLVAFSSD--EEL 68 (87)
T ss_pred eEEEeecCCCCccceEEEEecCCCCcCHHHHHHHHHHHccccC----CCcEEEEEECCCCCEEeecCH--HHH
Confidence 47788877 33333 3444667799999999999995432 356899999999999888776 555
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=89.54 E-value=1 Score=40.06 Aligned_cols=66 Identities=17% Similarity=0.406 Sum_probs=50.5
Q ss_pred eEEEecCceeeeeecCCCCCChHHHHHHHHHHhhcccccCCCCceeEEEecCCCCeEEc-cCCChHHHHhccee
Q 005675 581 TKVQMQGVAVGRALDLTTLVGYDHLIDELEEMFDIKGQLHTRTKWEIVYTDDEGDMMLV-GDDPWHEFCNMVKR 653 (684)
Q Consensus 581 vKV~m~G~~vGR~vDL~~~~sY~eL~~~L~~MF~~~g~l~~~~~~~v~Y~D~eGD~mlv-GD~PW~~F~~~vkr 653 (684)
-||..+| --|++--..-=+|.+|.++|+.+|.+.-. + ..|+|.|.|||..-+ -|+=.++|.+-..+
T Consensus 3 fKv~~~g--~~RRf~~~~~pt~~~L~~kl~~Lf~lp~~----~-~~vtYiDeD~D~ITlssd~eL~d~~~~~~~ 69 (82)
T cd06397 3 FKSSFLG--DTRRIVFPDIPTWEALASKLENLYNLPEI----K-VGVTYIDNDNDEITLSSNKELQDFYRLSHR 69 (82)
T ss_pred EEEEeCC--ceEEEecCCCccHHHHHHHHHHHhCCChh----H-eEEEEEcCCCCEEEecchHHHHHHHHhccc
Confidence 4777777 46888888888999999999999998641 2 689999999998755 45555666665444
No 20
>PRK10737 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=65.55 E-value=22 Score=36.55 Aligned_cols=102 Identities=18% Similarity=0.229 Sum_probs=64.4
Q ss_pred CCCCCCEEEE-E--ecCCCcEEEEEEEccccCCCCCCccccCCcccchhHHHHHHHHHcCCeeEEEEecCC------C--
Q 005675 200 RLVAGDTFVF-L--RGENGELHVGVRCLARQQSSMPSSVISSQSMHLGVLATASHAVATQTMFVVYYKPRT------S-- 268 (684)
Q Consensus 200 ~L~aGD~VvF-~--R~~~G~l~VgIRRa~~~~~~~p~sv~~~~sm~~gvla~A~~a~~~~~~F~V~Y~Pr~------s-- 268 (684)
++..|+.|.+ | |.++|+++---+ ...|...+-....-+--|.+|..-...|..|+|..-|-. .
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 3456777776 3 356777643221 123444443333334456778888889999999987643 2
Q ss_pred cceeeHHHHHHHHcCCCccCCEEEEEEecCCCCCceeeeEEeeeec
Q 005675 269 QFIISLNKYLEAVNNKFAVGMRYKMRFEGEDSPERRFSGTVVGVED 314 (684)
Q Consensus 269 eFvV~~~~y~~A~~~~w~~GmRFkM~fE~eds~~~~~~GTI~~v~~ 314 (684)
-..|+++.|... ....+||||.+. +++. .+.++|+.|.+
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 567888777432 236899998864 4553 36889999975
No 21
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=62.10 E-value=6.3 Score=47.87 Aligned_cols=67 Identities=25% Similarity=0.419 Sum_probs=43.1
Q ss_pred cCCCCCCeEEEecCcchhhhhcccchh--hcccCCCCCCCCcceEEEEEeeeeccCCCceeEEEEeeecC
Q 005675 32 DVPKQGQRVYYFPQGHMEQLEASTNQE--LNQRIPLFRLPSKILCRVVNIHLMAEQETDEVYAQITLLPE 99 (684)
Q Consensus 32 ~~P~~gs~V~YFPqGH~Eq~~~s~~~~--~~~~~p~~~lp~~i~C~V~~V~l~Ad~~TDEVyA~i~L~P~ 99 (684)
-||..|+.|.||-|||-|-+.+..-.+ +.... ..++-..=.|.|..+..--=+-...--.+|+|.=.
T Consensus 872 yipQmgDEViyfrQghqeyl~~~~~n~~~~~~~~-p~~~~~v~~~kv~kl~~~~y~~~~~s~c~m~l~~i 940 (1113)
T KOG0644|consen 872 YIPQMGDEVIYFRQGHQEYLEAVRLNNIELNNKE-PWNKMAVEICKVEKLVYITYPGSGDSCCKMKLAVI 940 (1113)
T ss_pred ccccccceeehhhhhhHHHHhhhhhccccccccC-cccccchhhheeeeeeeeeccCCCcchheeeeeee
Confidence 489999999999999999998864211 11111 11233334788888766655555555666665433
No 22
>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=53.54 E-value=56 Score=29.27 Aligned_cols=68 Identities=13% Similarity=0.341 Sum_probs=51.1
Q ss_pred eEEEecCceeeeeecCCCCCChHHHHHHHHHHhhcccccCCCCceeEEEecCCC-CeEEccCCChHHHHhcce--eEEE
Q 005675 581 TKVQMQGVAVGRALDLTTLVGYDHLIDELEEMFDIKGQLHTRTKWEIVYTDDEG-DMMLVGDDPWHEFCNMVK--RIFI 656 (684)
Q Consensus 581 vKV~m~G~~vGR~vDL~~~~sY~eL~~~L~~MF~~~g~l~~~~~~~v~Y~D~eG-D~mlvGD~PW~~F~~~vk--ri~I 656 (684)
||||.++ -| .|-...=-+|.+|+..|.+=+.+-++- -+|-|.|.++ +...++|.=++.-.+.|+ +|+.
T Consensus 5 vKV~f~~-tI--aIrvp~~~~y~~L~~ki~~kLkl~~e~-----i~LsYkde~s~~~v~l~d~dle~aws~~~~~~lTL 75 (80)
T cd06406 5 VKVHFKY-TV--AIQVARGLSYATLLQKISSKLELPAEH-----ITLSYKSEASGEDVILSDTNMEDVWSQAKDGCLTL 75 (80)
T ss_pred EEEEEEE-EE--EEEcCCCCCHHHHHHHHHHHhCCCchh-----cEEEeccCCCCCccCcChHHHHHHHHhhcCCeEEE
Confidence 7999998 33 445556668999999999999885432 3788998653 554559999999888887 6654
No 23
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=51.74 E-value=23 Score=28.76 Aligned_cols=38 Identities=21% Similarity=0.180 Sum_probs=29.7
Q ss_pred CCccCCEEEEEEecCCCCCceeeeEEeeeecCCCCCCCCCcceEEEeecC
Q 005675 284 KFAVGMRYKMRFEGEDSPERRFSGTVVGVEDFSPHWKDSKWRSLKVQWDE 333 (684)
Q Consensus 284 ~w~~GmRFkM~fE~eds~~~~~~GTI~~v~~~dp~wp~S~WR~L~V~WDe 333 (684)
.|++|+++-..++.++ .||.|+|+.+.. -..+.|.-+.
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 899999999963 2346777766
No 24
>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=47.37 E-value=33 Score=31.33 Aligned_cols=41 Identities=24% Similarity=0.387 Sum_probs=32.7
Q ss_pred cCCCCCChHHHHHHHHHHhhcccccCCCCceeEEEecCCCCeEEccCC
Q 005675 595 DLTTLVGYDHLIDELEEMFDIKGQLHTRTKWEIVYTDDEGDMMLVGDD 642 (684)
Q Consensus 595 DL~~~~sY~eL~~~L~~MF~~~g~l~~~~~~~v~Y~D~eGD~mlvGD~ 642 (684)
||+..-+|.+|.....+-|..+. -.+-|+|.|||..-+=|+
T Consensus 23 ~l~~~P~~kdLl~lmr~~f~~~d-------IaLNYrD~EGDLIRlldd 63 (92)
T cd06399 23 DLSSTPLLKDLLELTRREFQRED-------IALNYRDAEGDLIRLLSD 63 (92)
T ss_pred ccccCccHHHHHHHHHHHhchhh-------eeeeeecCCCCEEEEcch
Confidence 78899999999999999998664 366799999997544333
No 25
>PF04014 Antitoxin-MazE: Antidote-toxin recognition MazE; InterPro: IPR007159 This domain is found in AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation []. AbrB is thought to interact directly with the transcription initiation regions of genes under its control []. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins []. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator []. DNA-binding activity in this AbrB homologue requires hexamerisation []. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins [].; PDB: 2L66_A 2GLW_A 3TND_D 2W1T_B 2RO5_B 2FY9_A 2RO3_B 1UB4_C 3ZVK_G 1YFB_B ....
Probab=44.48 E-value=26 Score=27.39 Aligned_cols=27 Identities=15% Similarity=0.191 Sum_probs=22.6
Q ss_pred hhhcccCCCCCCEEEEEecCCCcEEEE
Q 005675 194 TFVTSKRLVAGDTFVFLRGENGELHVG 220 (684)
Q Consensus 194 ~FV~~K~L~aGD~VvF~R~~~G~l~Vg 220 (684)
.|..+.+|.+||.|.|.-.++|++.+-
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 567788999999999999988866653
No 26
>KOG3207 consensus Beta-tubulin folding cofactor E [Posttranslational modification, protein turnover, chaperones]
Probab=37.31 E-value=27 Score=40.25 Aligned_cols=42 Identities=33% Similarity=0.631 Sum_probs=29.9
Q ss_pred CccCCEEEEEEecCCCCCceeeeEEeeeecCCCCCCCCCcceEEEeecCCCCCCC
Q 005675 285 FAVGMRYKMRFEGEDSPERRFSGTVVGVEDFSPHWKDSKWRSLKVQWDEPASITR 339 (684)
Q Consensus 285 w~~GmRFkM~fE~eds~~~~~~GTI~~v~~~dp~wp~S~WR~L~V~WDe~~~~~~ 339 (684)
..+|+|+|..+|- ..-||.|+|.|. ++ +| +.|.||++.-.-+
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 4689999988752 235677777765 33 44 7899999987644
No 27
>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=34.48 E-value=1e+02 Score=26.02 Aligned_cols=42 Identities=19% Similarity=0.295 Sum_probs=27.2
Q ss_pred CccCCEEEEEEecCCCCCceeeeEEeeeecCCCCCCCCCcceEEEeecCCC
Q 005675 285 FAVGMRYKMRFEGEDSPERRFSGTVVGVEDFSPHWKDSKWRSLKVQWDEPA 335 (684)
Q Consensus 285 w~~GmRFkM~fE~eds~~~~~~GTI~~v~~~dp~wp~S~WR~L~V~WDe~~ 335 (684)
|..|+++-..-+.+...-.||.|||+.... ++ .+.|+.+.-.
T Consensus 1 F~~G~~VEV~s~e~g~~gaWf~a~V~~~~~------~~---~~~V~Y~~~~ 42 (68)
T PF05641_consen 1 FKKGDEVEVSSDEDGFRGAWFPATVLKENG------DD---KYLVEYDDLP 42 (68)
T ss_dssp --TT-EEEEEE-SBTT--EEEEEEEEEEET------T----EEEEEETT-S
T ss_pred CCCCCEEEEEEcCCCCCcEEEEEEEEEeCC------Cc---EEEEEECCcc
Confidence 568999998877555544999999999974 22 7889996554
No 28
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=33.48 E-value=69 Score=25.24 Aligned_cols=52 Identities=17% Similarity=0.440 Sum_probs=37.6
Q ss_pred CCccCCEEEEEEecCCCCCceeeeEEeeeecCCCCCCCCCcceEEEeecCCCCCCCCCccccCccccc
Q 005675 284 KFAVGMRYKMRFEGEDSPERRFSGTVVGVEDFSPHWKDSKWRSLKVQWDEPASITRPDRVSPWEIEPF 351 (684)
Q Consensus 284 ~w~~GmRFkM~fE~eds~~~~~~GTI~~v~~~dp~wp~S~WR~L~V~WDe~~~~~~~~RVSPWeIEp~ 351 (684)
+|.+|..+..++ .+. .||.|+|+++.. + ....|.-++-.. .+-|...+|-++
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 567888887553 234566555543
No 29
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=33.12 E-value=55 Score=29.87 Aligned_cols=28 Identities=21% Similarity=0.362 Sum_probs=22.0
Q ss_pred hhcccCCCCCCEEEEEecCCCcEEEEEE
Q 005675 195 FVTSKRLVAGDTFVFLRGENGELHVGVR 222 (684)
Q Consensus 195 FV~~K~L~aGD~VvF~R~~~G~l~VgIR 222 (684)
|.-...|++||.|..+|...|..++-+-
T Consensus 71 i~~~~~Lk~GD~V~ll~~~~gQ~yiVlD 98 (100)
T PF10844_consen 71 ITFTDGLKVGDKVLLLRVQGGQKYIVLD 98 (100)
T ss_pred EEEecCCcCCCEEEEEEecCCCEEEEEE
Confidence 5556789999999999988887665443
No 30
>TIGR01439 lp_hng_hel_AbrB looped-hinge helix DNA binding domain, AbrB family. This DNA-binding domain family includes AbrB, a transition state regulator in Bacillus subtilis, whose DNA-binding domain structure in solution was determined by NMR. The domain binds DNA as a dimer in what is termed a looped-hinge helix fold. Some members of the family have two copies of the domain in tandem. The domain is found usually at the N-terminus of a small protein. This model excludes members of family TIGR02609.
Probab=31.44 E-value=58 Score=24.25 Aligned_cols=26 Identities=27% Similarity=0.412 Sum_probs=21.8
Q ss_pred hhhcccCCCCCCEEEEEecCCCcEEE
Q 005675 194 TFVTSKRLVAGDTFVFLRGENGELHV 219 (684)
Q Consensus 194 ~FV~~K~L~aGD~VvF~R~~~G~l~V 219 (684)
.|.++-++..||.|.+....+|.+.+
T Consensus 14 ~~r~~l~~~~gd~~~i~~~~~~~l~l 39 (43)
T TIGR01439 14 EIREKLGLKEGDRLEVIRVEDGEIIL 39 (43)
T ss_pred HHHHHcCcCCCCEEEEEEeCCCEEEE
Confidence 68889999999999999877776554
No 31
>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=31.29 E-value=66 Score=26.50 Aligned_cols=32 Identities=28% Similarity=0.515 Sum_probs=24.6
Q ss_pred cCCEEEEEEecCCCCCceeeeEEeeeecCCCC
Q 005675 287 VGMRYKMRFEGEDSPERRFSGTVVGVEDFSPH 318 (684)
Q Consensus 287 ~GmRFkM~fE~eds~~~~~~GTI~~v~~~dp~ 318 (684)
+|-|+.-.||.++.+...+.|+|...-+..|.
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 58899999998888888889999998876654
No 32
>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=30.50 E-value=1.2e+02 Score=25.90 Aligned_cols=70 Identities=10% Similarity=0.076 Sum_probs=50.4
Q ss_pred cceeEEEecCcee---eeeecCCCCCChHHHHHHHHHHhhcccccCCCCceeEE-Ee-cCCCCeEEc-cCCChHHHHhc
Q 005675 578 RSRTKVQMQGVAV---GRALDLTTLVGYDHLIDELEEMFDIKGQLHTRTKWEIV-YT-DDEGDMMLV-GDDPWHEFCNM 650 (684)
Q Consensus 578 ~~~vKV~m~G~~v---GR~vDL~~~~sY~eL~~~L~~MF~~~g~l~~~~~~~v~-Y~-D~eGD~mlv-GD~PW~~F~~~ 650 (684)
...+||+++...- -++|=++....-.|++..+.+-|++.+ ...+|.|+ +. .......|- .+.|+..+...
T Consensus 2 ~~~lrVy~~~~~~~~~~k~i~v~~~tTa~evi~~~l~k~~l~~---~~~~y~L~~~~~~~~~er~L~~~E~pl~i~~~~ 77 (93)
T PF00788_consen 2 SGVLRVYDGDGSPGSTYKTIKVSSSTTAREVIEMALEKFGLAE---DPSDYCLVEVEESGGEERPLDDDECPLQIQLQW 77 (93)
T ss_dssp EEEEEEEETTSSSCCSEEEEEEETTSBHHHHHHHHHHHTTTSS---SGGGEEEEEEECTTTEEEEETTTSBHHHHHHTT
T ss_pred CeEEEEEcCCCCCCccEEEEEECCCCCHHHHHHHHHHHhCCCC---CCCCEEEEEEEcCCCEEEEcCCCCchHHHHHhC
Confidence 3578999988653 689999999999999999999999933 34568884 44 445555554 34466665544
No 33
>KOG3938 consensus RGS-GAIP interacting protein GIPC, contains PDZ domain [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=29.09 E-value=74 Score=34.57 Aligned_cols=73 Identities=22% Similarity=0.343 Sum_probs=54.4
Q ss_pred cCceeeeeecCCCCCChHHHHHHHHHHhhcccc--c-CCCCceeEEEecCCCCeEEccCCChHHHH-----hcceeEEEe
Q 005675 586 QGVAVGRALDLTTLVGYDHLIDELEEMFDIKGQ--L-HTRTKWEIVYTDDEGDMMLVGDDPWHEFC-----NMVKRIFIC 657 (684)
Q Consensus 586 ~G~~vGR~vDL~~~~sY~eL~~~L~~MF~~~g~--l-~~~~~~~v~Y~D~eGD~mlvGD~PW~~F~-----~~vkri~I~ 657 (684)
.|.|+|| +..|++-+|||..+++-|+|.-. | ..-+.+. -|=+-||-|-.-+++|+ .-.|.++|+
T Consensus 62 HGSptg~---Ie~fsnv~ELY~kIAe~F~Is~~dIlfcTlNshK-----vDM~~llgGqigleDfiFAHvkGq~kEv~v~ 133 (334)
T KOG3938|consen 62 HGSPTGR---IEGFSNVRELYQKIAEAFDISPDDILFCTLNSHK-----VDMKRLLGGQIGLEDFIFAHVKGQAKEVEVV 133 (334)
T ss_pred cCCccce---ecccccHHHHHHHHHHHhcCCccceEEEecCCCc-----ccHHHHhcCccChhhhhhhhhcCcceeEEEE
Confidence 5778887 45789999999999999999642 1 1111111 23345899999999996 567789999
Q ss_pred eccccccCC
Q 005675 658 SSQDVKKMS 666 (684)
Q Consensus 658 ~~~e~~~~~ 666 (684)
+.+++-+++
T Consensus 134 KsedalGlT 142 (334)
T KOG3938|consen 134 KSEDALGLT 142 (334)
T ss_pred ecccccceE
Confidence 999998765
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=25.49 E-value=67 Score=30.42 Aligned_cols=26 Identities=23% Similarity=0.382 Sum_probs=17.3
Q ss_pred cCCCCCCEEEEEecC-CCcEEEEEEEc
Q 005675 199 KRLVAGDTFVFLRGE-NGELHVGVRCL 224 (684)
Q Consensus 199 K~L~aGD~VvF~R~~-~G~l~VgIRRa 224 (684)
++++.||.|+||... .+.-+||+=+-
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 489999999999977 56677776664
No 35
>COG1047 SlpA FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]
Probab=24.06 E-value=3.8e+02 Score=27.34 Aligned_cols=103 Identities=20% Similarity=0.275 Sum_probs=63.8
Q ss_pred CCCCCCEEEEE---ecCCCcEEEEEEEccccCCCCCCccccCCcccchhHHHHHHHHHcCCeeEEEEecCCC------cc
Q 005675 200 RLVAGDTFVFL---RGENGELHVGVRCLARQQSSMPSSVISSQSMHLGVLATASHAVATQTMFVVYYKPRTS------QF 270 (684)
Q Consensus 200 ~L~aGD~VvF~---R~~~G~l~VgIRRa~~~~~~~p~sv~~~~sm~~gvla~A~~a~~~~~~F~V~Y~Pr~s------eF 270 (684)
++..||.|.+. |.++|+++=--.- ...|..++-++..-+.-|.+|..-..-|.-|+|.--|-.. +.
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 45667777762 3455554321111 1124444444444444578888888999999999988542 22
Q ss_pred --eeeHHHHHHHHcCCCccCCEEEEEEecCCCCCceeeeEEeeeec
Q 005675 271 --IISLNKYLEAVNNKFAVGMRYKMRFEGEDSPERRFSGTVVGVED 314 (684)
Q Consensus 271 --vV~~~~y~~A~~~~w~~GmRFkM~fE~eds~~~~~~GTI~~v~~ 314 (684)
.|++++|...= ...+||+|. ++++| ...-|+|+.|..
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 46666655432 679999987 45555 457899999974
No 36
>PRK14129 heat shock protein HspQ; Provisional
Probab=21.29 E-value=1.1e+02 Score=28.82 Aligned_cols=49 Identities=27% Similarity=0.442 Sum_probs=33.7
Q ss_pred cCCCccCCEEEEEEecCCCCCceeeeEEeeeecCCCCCCCC-CcceEEEeecCCCCCCCCCccccCc
Q 005675 282 NNKFAVGMRYKMRFEGEDSPERRFSGTVVGVEDFSPHWKDS-KWRSLKVQWDEPASITRPDRVSPWE 347 (684)
Q Consensus 282 ~~~w~~GmRFkM~fE~eds~~~~~~GTI~~v~~~dp~wp~S-~WR~L~V~WDe~~~~~~~~RVSPWe 347 (684)
..+|.+|.-+|-+. -.|-|.|+.| ||.+.++ +| |++-... ++.|=.||=
T Consensus 3 ~akF~IGQ~VrHrl-------~~yrGVV~DV---DP~fs~~e~w------~~~ia~~-~p~kdqPwY 52 (105)
T PRK14129 3 ASKFGIGQQVRHSL-------LGYLGVVVDI---DPEYSLEEPS------PDELAVN-DELRAAPWY 52 (105)
T ss_pred cccccCCcEEEEee-------cCCCeEEEee---CCCcCCCchh------HHhhccC-CCccCCCce
Confidence 45889999999887 3599999987 5554432 44 5554443 666777774
No 37
>KOG3606 consensus Cell polarity protein PAR6 [Signal transduction mechanisms]
Probab=20.98 E-value=95 Score=33.87 Aligned_cols=80 Identities=18% Similarity=0.314 Sum_probs=55.2
Q ss_pred ceeEEEecCceeeeeecCCCCCChHHHHHHHHHHhhcccccCCCCceeEEEecCCCCeEEcc-CCChHHHHhcce---eE
Q 005675 579 SRTKVQMQGVAVGRALDLTTLVGYDHLIDELEEMFDIKGQLHTRTKWEIVYTDDEGDMMLVG-DDPWHEFCNMVK---RI 654 (684)
Q Consensus 579 ~~vKV~m~G~~vGR~vDL~~~~sY~eL~~~L~~MF~~~g~l~~~~~~~v~Y~D~eGD~mlvG-D~PW~~F~~~vk---ri 654 (684)
.-||-..+-+=--=+++-..-.+|++.+.-|+..-.|.+ .++.+-|.|.-||.+-+- |+-+..-+++++ ||
T Consensus 19 veVKSKFdaEfRRfsl~r~~~~~f~~F~~Lv~~~H~i~n-----vdvllgY~d~hgDLLPinNDDn~~ka~~sa~PlLR~ 93 (358)
T KOG3606|consen 19 VEVKSKFDAEFRRFSLPRHSASSFDEFYSLVEHLHHIPN-----VDVLLGYADTHGDLLPINNDDNLHKALSSARPLLRL 93 (358)
T ss_pred EEeeccccchhheecccccCcccHHHHHHHHHHHhcCCC-----ceEEEEEecCCCceecccCchhHHHHhhccCchhhh
Confidence 345544444322224455556799999999998887765 346788999999999775 444544455665 88
Q ss_pred EEeeccccc
Q 005675 655 FICSSQDVK 663 (684)
Q Consensus 655 ~I~~~~e~~ 663 (684)
.|-+++|+.
T Consensus 94 ~iQkr~ea~ 102 (358)
T KOG3606|consen 94 LIQKREEAD 102 (358)
T ss_pred hhhhhhhhh
Confidence 999998875
Done!