Query 006471
Match_columns 643
No_of_seqs 339 out of 852
Neff 4.7
Searched_HMMs 46136
Date Thu Mar 28 23:45:20 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/006471.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/006471hhsearch_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 3.8E-37 8.2E-42 307.1 0.4 94 529-622 107-215 (215)
2 PF06507 Auxin_resp: Auxin res 100.0 1.8E-34 3.9E-39 249.5 8.5 80 202-281 1-83 (83)
3 PF02362 B3: B3 DNA binding do 99.7 2.3E-17 4.9E-22 143.9 11.3 97 76-177 1-99 (100)
4 KOG0644 Uncharacterized conser 99.5 5.2E-15 1.1E-19 167.5 6.2 147 154-308 874-1046(1113)
5 PF09217 EcoRII-N: Restriction 98.1 1.8E-05 3.8E-10 76.2 10.4 103 72-176 6-128 (156)
6 PF03754 DUF313: Domain of unk 97.6 0.00013 2.9E-09 67.5 5.9 79 72-151 20-114 (114)
7 PF00564 PB1: PB1 domain; Int 96.9 0.003 6.5E-08 53.7 6.7 67 533-605 3-70 (84)
8 smart00666 PB1 PB1 domain. Pho 96.4 0.012 2.6E-07 49.9 7.3 65 534-605 4-69 (81)
9 cd06407 PB1_NLP A PB1 domain i 96.3 0.013 2.8E-07 51.3 7.0 57 533-595 2-58 (82)
10 cd06398 PB1_Joka2 The PB1 doma 96.3 0.011 2.4E-07 52.7 6.4 65 534-606 3-72 (91)
11 cd05992 PB1 The PB1 domain is 96.2 0.02 4.4E-07 48.2 7.7 65 534-605 3-69 (81)
12 cd06396 PB1_NBR1 The PB1 domai 95.8 0.029 6.2E-07 49.3 6.8 64 534-604 3-67 (81)
13 cd06403 PB1_Par6 The PB1 domai 95.8 0.046 1E-06 47.8 7.6 72 534-610 3-78 (80)
14 cd06401 PB1_TFG The PB1 domain 94.8 0.17 3.8E-06 44.5 8.2 71 534-610 3-79 (81)
15 cd06409 PB1_MUG70 The MUG70 pr 94.2 0.076 1.6E-06 47.2 4.7 53 541-595 7-61 (86)
16 cd06404 PB1_aPKC PB1 domain is 93.2 0.27 5.8E-06 43.5 6.3 57 533-595 2-58 (83)
17 cd06408 PB1_NoxR The PB1 domai 92.5 0.32 7E-06 43.3 5.9 55 532-595 3-57 (86)
18 cd06402 PB1_p62 The PB1 domain 92.0 0.57 1.2E-05 41.8 6.9 62 533-600 2-68 (87)
19 cd06397 PB1_UP1 Uncharacterize 90.3 0.79 1.7E-05 40.5 6.0 66 534-606 3-69 (82)
20 PRK10737 FKBP-type peptidyl-pr 61.8 29 0.00062 35.4 7.4 101 154-267 3-114 (196)
21 cd06406 PB1_P67 A PB1 domain i 56.4 45 0.00098 29.6 6.7 69 533-609 4-75 (80)
22 smart00743 Agenet Tudor-like d 56.1 18 0.00039 29.1 4.0 38 237-286 2-39 (61)
23 cd06399 PB1_P40 The PB1 domain 50.8 28 0.0006 31.6 4.5 41 548-595 23-63 (92)
24 PF04014 Antitoxin-MazE: Antid 45.1 26 0.00057 27.1 3.2 26 147-172 14-39 (47)
25 PF02513 Spin-Ssty: Spin/Ssty 37.0 51 0.0011 26.9 3.7 32 240-271 1-32 (50)
26 PF00788 RA: Ras association ( 36.8 86 0.0019 26.5 5.4 70 531-603 2-77 (93)
27 PF05641 Agenet: Agenet domain 36.5 74 0.0016 26.6 4.8 42 238-288 1-42 (68)
28 smart00333 TUDOR Tudor domain. 35.1 63 0.0014 25.2 4.0 51 237-303 2-52 (57)
29 PF10844 DUF2577: Protein of u 34.5 51 0.0011 29.8 3.8 28 148-175 71-98 (100)
30 TIGR01439 lp_hng_hel_AbrB loop 33.0 55 0.0012 24.2 3.2 26 147-172 14-39 (43)
31 KOG3207 Beta-tubulin folding c 30.8 62 0.0013 37.2 4.4 43 238-293 3-45 (505)
32 KOG3938 RGS-GAIP interacting p 29.7 70 0.0015 34.5 4.3 75 538-620 61-143 (334)
33 PF01878 EVE: EVE domain; Int 25.8 66 0.0014 30.2 3.1 26 152-177 38-64 (143)
34 cd06410 PB1_UP2 Uncharacterize 21.8 1.1E+02 0.0023 28.0 3.5 61 537-604 19-79 (97)
35 PRK14129 heat shock protein Hs 21.6 1.1E+02 0.0024 28.5 3.6 50 235-301 3-53 (105)
36 PF06003 SMN: Survival motor n 21.4 98 0.0021 32.8 3.7 56 235-304 66-121 (264)
37 KOG3606 Cell polarity protein 21.2 92 0.002 33.7 3.4 66 546-616 33-102 (358)
38 cd04451 S1_IF1 S1_IF1: Transla 21.0 3.9E+02 0.0084 21.8 6.4 38 115-165 15-52 (64)
39 COG1047 SlpA FKBP-type peptidy 20.8 4.8E+02 0.01 26.4 8.1 103 153-267 2-115 (174)
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=3.8e-37 Score=307.11 Aligned_cols=94 Identities=46% Similarity=0.802 Sum_probs=0.0
Q ss_pred CCcceeEEEecCceeeeeecCCCCCChHHHHHHHHHHh---hhc----------cc--cCCCCceeEEEecCCCCeEEcc
Q 006471 529 SNRSRTKVQMQGVAVGRALDLTTLVGYDHLIDELEEMF---DIK----------GQ--LHTRTKWEIVYTDDEGDMMLVG 593 (643)
Q Consensus 529 ~~~~~vKV~m~G~~vgR~vDLs~~~~Y~eL~~~L~~MF---~~~----------g~--l~~~~~~~v~Y~D~eGD~mlvG 593 (643)
..++||||+|||++|||||||++|+||++|+.+|++|| +|. +. |...++|+|||+|+||||||||
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 006471 594 DDPWHEFCNMVKRIFICSSQDVKKMSPGS 622 (643)
Q Consensus 594 D~PW~~F~~~vkri~I~~~~e~~~~~~~~ 622 (643)
||||+|||++||||+||+.+|++||+|+.
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 99999999999999999999999999874
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=1.8e-34 Score=249.54 Aligned_cols=80 Identities=55% Similarity=1.010 Sum_probs=78.2
Q ss_pred HHHHHHcCCeeEEEEecCCC--cceeeHHHHHHHHcCCCccCCEEEEEeecCCCCCceeeeEEeeeecCCC-CCCCCCcc
Q 006471 202 ASHAVATQTMFVVYYKPRTS--QFIISLNKYLEAVNNKFAVGMRYKMRFEGEDSPERRFSGTVVGVEDFSP-HWKDSKWR 278 (643)
Q Consensus 202 A~~a~~t~~~F~V~Y~Pr~s--eFvV~~~~y~~a~~~~w~~GmRFkM~fe~eDs~~~~~~GtI~~v~~~dp-~wp~S~WR 278 (643)
|+|||++|++|+|+||||++ ||||++++|++||+++|++||||||+||+||+++++|+|||+||++.|| +||+|+||
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 006471 279 SLK 281 (643)
Q Consensus 279 ~L~ 281 (643)
|||
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=99.73 E-value=2.3e-17 Score=143.90 Aligned_cols=97 Identities=31% Similarity=0.397 Sum_probs=74.6
Q ss_pred EEEecccccCCCCCceEEecchhhhcCCCCCCCCCCCceEEEEEeCCCCeEEEEEEEeCCCcceeeccchhhhhcccCCC
Q 006471 76 FSKVLTASDTSTHGGFSVLRKHATECLPPLDMNQSTPTQELVAKDLHGYEWRFKHIFRGQPRRHLLTTGWSTFVTSKRLV 155 (643)
Q Consensus 76 F~K~LT~SDv~~~grfsVPk~~Ae~~fP~Ld~~~~~p~q~L~v~D~~G~~W~Fr~~yrg~~rr~lLTtGWs~FV~~K~L~ 155 (643)
|.|+|+++|+...++|.||+++++.|. ++ ....+.+.++|..|++|.+++.+++.+++++|++||..||++++|+
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 899999999999999999999999972 11 1135689999999999999999998888899999999999999999
Q ss_pred CCCEEEEEecC--CCcEEEEEEEc
Q 006471 156 AGDTFVFLRGE--NGELHVGVRCL 177 (643)
Q Consensus 156 aGD~VvF~R~~--~g~l~VgIRRa 177 (643)
+||.|+|+... ..++.|+|+|+
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 99999999864 45569999986
No 4
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=99.54 E-value=5.2e-15 Score=167.51 Aligned_cols=147 Identities=23% Similarity=0.423 Sum_probs=122.1
Q ss_pred CCCCCEEEEEecCCCcEEEEEEEccccCCC---------------------CCCccccCCccchhhHHHHHHHHHcCCee
Q 006471 154 LVAGDTFVFLRGENGELHVGVRCLARQQSS---------------------MPSSVISSQSMHLGVLATASHAVATQTMF 212 (643)
Q Consensus 154 L~aGD~VvF~R~~~g~l~VgIRRa~~~~~~---------------------~p~sv~~~~~~~~~vl~~A~~a~~t~~~F 212 (643)
...||.|+.+|.+..+|.-.+|+.+...++ .|-+..+.|+|.+.||.-|.++ -...|
T Consensus 874 pQmgDEViyfrQghqeyl~~~~~n~~~~~~~~p~~~~~v~~~kv~kl~~~~y~~~~~s~c~m~l~~idp~s~~--~~k~F 951 (1113)
T KOG0644|consen 874 PQMGDEVIYFRQGHQEYLEAVRLNNIELNNKEPWNKMAVEICKVEKLVYITYPGSGDSCCKMKLAVIDPASKL--MDKSF 951 (1113)
T ss_pred ccccceeehhhhhhHHHHhhhhhccccccccCcccccchhhheeeeeeeeeccCCCcchheeeeeeecchhhh--hhccc
Confidence 448999999999887777666665443221 2345567899999999989866 45669
Q ss_pred EEEEecCCC--cceeeHHHHHHHHcCCCccCCEEEEEeecCCCC---CceeeeEEeeeecCCCCCCCCCcceeeeeccCC
Q 006471 213 VVYYKPRTS--QFIISLNKYLEAVNNKFAVGMRYKMRFEGEDSP---ERRFSGTVVGVEDFSPHWKDSKWRSLKVQWDEP 287 (643)
Q Consensus 213 ~V~Y~Pr~s--eFvV~~~~y~~a~~~~w~~GmRFkM~fe~eDs~---~~~~~GtI~~v~~~dp~wp~S~WR~L~V~WDe~ 287 (643)
.+.|..... ||+|.++.|++|++++|..+++||.-.. |+. -+||.|+|.++.+.+|.+|+|+|.|+.|+||..
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 322 279999999999999999999999999999999
Q ss_pred CCCCCCCccccCcceeccCCC
Q 006471 288 ASITRPDRVSPWEIEPFVASA 308 (643)
Q Consensus 288 ~~~~~~~RVSPWeIEp~~~~~ 308 (643)
+ .+.-||||.|++....
T Consensus 1030 e----~~~~spwe~~~i~de~ 1046 (1113)
T KOG0644|consen 1030 E----TELHSPWEMEPIPDEV 1046 (1113)
T ss_pred c----ccccCccccCCCcccc
Confidence 8 5677999999987653
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=1.8e-05 Score=76.23 Aligned_cols=103 Identities=17% Similarity=0.185 Sum_probs=64.7
Q ss_pred ceeeEEEecccccCCCCC----ceEEecchhhhcCCCCCC-CCCCCceEEEEEeCCC--CeEEEEEEEeCC------Ccc
Q 006471 72 KVHSFSKVLTASDTSTHG----GFSVLRKHATECLPPLDM-NQSTPTQELVAKDLHG--YEWRFKHIFRGQ------PRR 138 (643)
Q Consensus 72 ~~~~F~K~LT~SDv~~~g----rfsVPk~~Ae~~fP~Ld~-~~~~p~q~L~v~D~~G--~~W~Fr~~yrg~------~rr 138 (643)
....|+|.|++.|++..| |+-||+..++..||.+.. +...|...|.+++..| ..|+||++|.|+ ...
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 457899999999999874 799999999999998766 5667889999999877 568899999976 445
Q ss_pred eeec--cchhhhhcccCCCCCCEEEEE-----ecCCCcEEEEEEE
Q 006471 139 HLLT--TGWSTFVTSKRLVAGDTFVFL-----RGENGELHVGVRC 176 (643)
Q Consensus 139 ~lLT--tGWs~FV~~K~L~aGD~VvF~-----R~~~g~l~VgIRR 176 (643)
+.|| ++=..|.+. =..||.+||. +.....+.+-|-+
T Consensus 86 ~RIT~~G~~~~~~~~--~~tGaL~vlaf~~~~~~~~~~~~~wVc~ 128 (156)
T PF09217_consen 86 YRITRFGRGFPLQNP--ENTGALLVLAFDPEQKQDCDLYDVWVCE 128 (156)
T ss_dssp EEEE---TTSGGG-G--GGTT-EEEEEEE-TTSS---EEEEEE--
T ss_pred eEEeeecCCCccCCc--cccccEEEEEEccCCCCccceEEEEEEC
Confidence 7786 343344443 2479988887 3334444454444
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=97.56 E-value=0.00013 Score=67.47 Aligned_cols=79 Identities=18% Similarity=0.233 Sum_probs=61.5
Q ss_pred ceeeEEEecccccCCCC-CceEEecchhhhcCCCCCC------------CCCCCceEEEEEeCCCCeEEEEEEEeCC---
Q 006471 72 KVHSFSKVLTASDTSTH-GGFSVLRKHATECLPPLDM------------NQSTPTQELVAKDLHGYEWRFKHIFRGQ--- 135 (643)
Q Consensus 72 ~~~~F~K~LT~SDv~~~-grfsVPk~~Ae~~fP~Ld~------------~~~~p~q~L~v~D~~G~~W~Fr~~yrg~--- 135 (643)
....|.|+|++||+..+ .||+||-..... ...|.. ....-+..+.+.|..++.|..++..|..
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 35789999999999886 899999886633 222311 1234477899999999999999999965
Q ss_pred Ccceeeccchhhhhcc
Q 006471 136 PRRHLLTTGWSTFVTS 151 (643)
Q Consensus 136 ~rr~lLTtGWs~FV~~ 151 (643)
.-.|+|++||..+|.+
T Consensus 99 ~~~YvL~~gWn~VV~~ 114 (114)
T PF03754_consen 99 TSNYVLNSGWNKVVED 114 (114)
T ss_pred ceEEEEEcChHhhccC
Confidence 4579999999999863
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=96.88 E-value=0.003 Score=53.66 Aligned_cols=67 Identities=27% Similarity=0.536 Sum_probs=54.3
Q ss_pred eeEEEecCceeeeeecCCCCCChHHHHHHHHHHhhhccccCCCCceeEEEecCCCCeEEccCC-ChHHHHhcce
Q 006471 533 RTKVQMQGVAVGRALDLTTLVGYDHLIDELEEMFDIKGQLHTRTKWEIVYTDDEGDMMLVGDD-PWHEFCNMVK 605 (643)
Q Consensus 533 ~vKV~m~G~~vgR~vDLs~~~~Y~eL~~~L~~MF~~~g~l~~~~~~~v~Y~D~eGD~mlvGD~-PW~~F~~~vk 605 (643)
-+|++..|. +=|.+.+..--+|++|..++++.|++. ...+.+.|.|.||||..+.++ =|.+.++.++
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 479999994 444688888889999999999999987 445799999999999988754 4666666664
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=49.90 Aligned_cols=65 Identities=17% Similarity=0.411 Sum_probs=50.9
Q ss_pred eEEEecCceeeeeecCCCCCChHHHHHHHHHHhhhccccCCCCceeEEEecCCCCeEEccC-CChHHHHhcce
Q 006471 534 TKVQMQGVAVGRALDLTTLVGYDHLIDELEEMFDIKGQLHTRTKWEIVYTDDEGDMMLVGD-DPWHEFCNMVK 605 (643)
Q Consensus 534 vKV~m~G~~vgR~vDLs~~~~Y~eL~~~L~~MF~~~g~l~~~~~~~v~Y~D~eGD~mlvGD-~PW~~F~~~vk 605 (643)
+||.-.| -=|.+-+..--+|++|+.++.+.|++.. ..+.+.|+|.|||+..+.+ +=|.+.+.+++
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 6887755 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=96.32 E-value=0.013 Score=51.32 Aligned_cols=57 Identities=21% Similarity=0.393 Sum_probs=46.2
Q ss_pred eeEEEecCceeeeeecCCCCCChHHHHHHHHHHhhhccccCCCCceeEEEecCCCCeEEccCC
Q 006471 533 RTKVQMQGVAVGRALDLTTLVGYDHLIDELEEMFDIKGQLHTRTKWEIVYTDDEGDMMLVGDD 595 (643)
Q Consensus 533 ~vKV~m~G~~vgR~vDLs~~~~Y~eL~~~L~~MF~~~g~l~~~~~~~v~Y~D~eGD~mlvGD~ 595 (643)
-|||...|. -+.+-|..--+|++|..++.++|++.. ...+.|-|.|.||||..+--+
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 455666666699999999999999853 356899999999999987544
No 10
>cd06398 PB1_Joka2 The PB1 domain is present in the Nicotiana plumbaginifolia Joka2 protein which interacts with sulfur stress inducible UP9 protein. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module
Probab=96.27 E-value=0.011 Score=52.71 Aligned_cols=65 Identities=25% Similarity=0.502 Sum_probs=52.1
Q ss_pred eEEEecCceeeeeecCC-----CCCChHHHHHHHHHHhhhccccCCCCceeEEEecCCCCeEEccCCChHHHHhccee
Q 006471 534 TKVQMQGVAVGRALDLT-----TLVGYDHLIDELEEMFDIKGQLHTRTKWEIVYTDDEGDMMLVGDDPWHEFCNMVKR 606 (643)
Q Consensus 534 vKV~m~G~~vgR~vDLs-----~~~~Y~eL~~~L~~MF~~~g~l~~~~~~~v~Y~D~eGD~mlvGD~PW~~F~~~vkr 606 (643)
+||.-+|. -|++-+. .--+|++|..++++.|.+.. ..++.+.|.|.||||..+-++ .++...+.+
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--LRRFTFPVAENQLDLNMDGLREKVEELFSLSP----DADLSLTYTDEDGDVVTLVDD--NDLTDAIQY 72 (91)
T ss_pred EEEEeCCE--EEEEEeccccccCCCCHHHHHHHHHHHhCCCC----CCcEEEEEECCCCCEEEEccH--HHHHHHHHH
Confidence 79999986 4555544 35799999999999998743 467899999999999999877 777666554
No 11
>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=96.24 E-value=0.02 Score=48.22 Aligned_cols=65 Identities=18% Similarity=0.446 Sum_probs=49.6
Q ss_pred eEEEecCceeeeeecCC-CCCChHHHHHHHHHHhhhccccCCCCceeEEEecCCCCeEEccC-CChHHHHhcce
Q 006471 534 TKVQMQGVAVGRALDLT-TLVGYDHLIDELEEMFDIKGQLHTRTKWEIVYTDDEGDMMLVGD-DPWHEFCNMVK 605 (643)
Q Consensus 534 vKV~m~G~~vgR~vDLs-~~~~Y~eL~~~L~~MF~~~g~l~~~~~~~v~Y~D~eGD~mlvGD-~PW~~F~~~vk 605 (643)
+||+-.|. =|.+=+. .--+|++|...|.+.|++.. ..+.+.|.|.|||+..+.+ .=|++.++.++
T Consensus 3 vK~~~~~~--~~~~~~~~~~~s~~~L~~~i~~~~~~~~-----~~~~l~y~D~e~d~v~l~sd~Dl~~a~~~~~ 69 (81)
T cd05992 3 VKVKYGGE--IRRFVVVSRSISFEDLRSKIAEKFGLDA-----VSFKLKYPDEDGDLVTISSDEDLEEAIEEAR 69 (81)
T ss_pred EEEEecCC--CEEEEEecCCCCHHHHHHHHHHHhCCCC-----CcEEEEeeCCCCCEEEeCCHHHHHHHHHHHh
Confidence 68888874 2444444 88899999999999999864 4579999999999999888 44555555544
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=95.85 E-value=0.029 Score=49.34 Aligned_cols=64 Identities=16% Similarity=0.224 Sum_probs=50.1
Q ss_pred eEEEecCceeeeeecCCCCCChHHHHHHHHHHhhhccccCCCCceeEEEecCCCCeEEcc-CCChHHHHhcc
Q 006471 534 TKVQMQGVAVGRALDLTTLVGYDHLIDELEEMFDIKGQLHTRTKWEIVYTDDEGDMMLVG-DDPWHEFCNMV 604 (643)
Q Consensus 534 vKV~m~G~~vgR~vDLs~~~~Y~eL~~~L~~MF~~~g~l~~~~~~~v~Y~D~eGD~mlvG-D~PW~~F~~~v 604 (643)
+||.-.|.-+==+++-+..-+|++|..++.++|++. .+.|.|-|.||||.++- |.=.++.++.+
T Consensus 3 vKaty~~d~~rf~~~~~~~~~~~~L~~ev~~rf~l~-------~f~lKYlDde~e~v~lssd~eLeE~~rl~ 67 (81)
T cd06396 3 LKVTYNGESQSFLVSDSENTTWASVEAMVKVSFGLN-------DIQIKYVDEENEEVSVNSQGEYEEALKSA 67 (81)
T ss_pred EEEEECCeEEEEEecCCCCCCHHHHHHHHHHHhCCC-------cceeEEEcCCCCEEEEEchhhHHHHHHHH
Confidence 788888876666676666889999999999999998 47899999999998764 33344544443
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=95.76 E-value=0.046 Score=47.85 Aligned_cols=72 Identities=24% Similarity=0.360 Sum_probs=52.4
Q ss_pred eEEEecCceeeeeecCCCCCChHHHHHHHHHHhhhccccCCCCceeEEEecCCCCeEEccCC-ChHHHHhcce---eEEE
Q 006471 534 TKVQMQGVAVGRALDLTTLVGYDHLIDELEEMFDIKGQLHTRTKWEIVYTDDEGDMMLVGDD-PWHEFCNMVK---RIFI 609 (643)
Q Consensus 534 vKV~m~G~~vgR~vDLs~~~~Y~eL~~~L~~MF~~~g~l~~~~~~~v~Y~D~eGD~mlvGD~-PW~~F~~~vk---ri~I 609 (643)
||.+.+++=-==++|.....+|++++..|+.|+.|.+ -.+.|-|+|.+||.+-+-.+ -+..=+.+++ ||.|
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 5666666432335677778999999999999999976 34799999999999988644 4444455666 5555
Q ss_pred e
Q 006471 610 C 610 (643)
Q Consensus 610 ~ 610 (643)
-
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=94.76 E-value=0.17 Score=44.50 Aligned_cols=71 Identities=23% Similarity=0.481 Sum_probs=49.8
Q ss_pred eEEEecCceeeeeecCCCC-CChHHHHHHHHHHhhhccccCCCCceeEEEecCCCCeEEccCCChHHH-----HhcceeE
Q 006471 534 TKVQMQGVAVGRALDLTTL-VGYDHLIDELEEMFDIKGQLHTRTKWEIVYTDDEGDMMLVGDDPWHEF-----CNMVKRI 607 (643)
Q Consensus 534 vKV~m~G~~vgR~vDLs~~-~~Y~eL~~~L~~MF~~~g~l~~~~~~~v~Y~D~eGD~mlvGD~PW~~F-----~~~vkri 607 (643)
+|+..+| .|=| +=+..- -+|.+|...+.+.|... +...+.+.|.|.|.|||+.-+.+. +++ +...++|
T Consensus 3 iK~~~g~-DiR~-~~~~~~~~t~~~L~~~v~~~F~~~--~~~~~~flIKYkD~dGDlVTIts~--~dL~~A~~~~~~~~l 76 (81)
T cd06401 3 LKAQLGD-DIRR-IPIHNEDITYDELLLMMQRVFRGK--LGSSDDVLIKYKDEDGDLITIFDS--SDLSFAIQCSRILKL 76 (81)
T ss_pred EEEEeCC-eEEE-EeccCccccHHHHHHHHHHHhccc--cCCcccEEEEEECCCCCEEEeccH--HHHHHHHhcCcceEE
Confidence 5666655 4544 444332 39999999999999843 334567899999999999999886 444 4455566
Q ss_pred EEe
Q 006471 608 FIC 610 (643)
Q Consensus 608 ~I~ 610 (643)
+|.
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=94.15 E-value=0.076 Score=47.18 Aligned_cols=53 Identities=21% Similarity=0.330 Sum_probs=41.7
Q ss_pred ceeeeeecCC--CCCChHHHHHHHHHHhhhccccCCCCceeEEEecCCCCeEEccCC
Q 006471 541 VAVGRALDLT--TLVGYDHLIDELEEMFDIKGQLHTRTKWEIVYTDDEGDMMLVGDD 595 (643)
Q Consensus 541 ~~vgR~vDLs--~~~~Y~eL~~~L~~MF~~~g~l~~~~~~~v~Y~D~eGD~mlvGD~ 595 (643)
.+-||.+=++ ...|+.+|..+..+=|+++... ...+.|.|.|+||||.++--+
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 3466655544 4689999999999999988643 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=0.27 Score=43.52 Aligned_cols=57 Identities=19% Similarity=0.396 Sum_probs=46.0
Q ss_pred eeEEEecCceeeeeecCCCCCChHHHHHHHHHHhhhccccCCCCceeEEEecCCCCeEEccCC
Q 006471 533 RTKVQMQGVAVGRALDLTTLVGYDHLIDELEEMFDIKGQLHTRTKWEIVYTDDEGDMMLVGDD 595 (643)
Q Consensus 533 ~vKV~m~G~~vgR~vDLs~~~~Y~eL~~~L~~MF~~~g~l~~~~~~~v~Y~D~eGD~mlvGD~ 595 (643)
-+|++-.|.-+==.+|. .-+|++|.+++.+||.+.. ...+++.|.|.|||.--+..+
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 37899999655555665 6689999999999998743 456899999999999877765
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=92.48 E-value=0.32 Score=43.30 Aligned_cols=55 Identities=31% Similarity=0.523 Sum_probs=46.6
Q ss_pred ceeEEEecCceeeeeecCCCCCChHHHHHHHHHHhhhccccCCCCceeEEEecCCCCeEEccCC
Q 006471 532 SRTKVQMQGVAVGRALDLTTLVGYDHLIDELEEMFDIKGQLHTRTKWEIVYTDDEGDMMLVGDD 595 (643)
Q Consensus 532 ~~vKV~m~G~~vgR~vDLs~~~~Y~eL~~~L~~MF~~~g~l~~~~~~~v~Y~D~eGD~mlvGD~ 595 (643)
--|||+-+|. -|.|-+..--+|++|..++.++|++.+ .+.|-|.|. ||+.-++|.
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 4689999897 566777777789999999999999953 469999999 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=92.00 E-value=0.57 Score=41.83 Aligned_cols=62 Identities=23% Similarity=0.449 Sum_probs=45.9
Q ss_pred eeEEEecCc---eeeeee--cCCCCCChHHHHHHHHHHhhhccccCCCCceeEEEecCCCCeEEccCCChHHH
Q 006471 533 RTKVQMQGV---AVGRAL--DLTTLVGYDHLIDELEEMFDIKGQLHTRTKWEIVYTDDEGDMMLVGDDPWHEF 600 (643)
Q Consensus 533 ~vKV~m~G~---~vgR~v--DLs~~~~Y~eL~~~L~~MF~~~g~l~~~~~~~v~Y~D~eGD~mlvGD~PW~~F 600 (643)
.||.+..|. +==|++ |=....+|++|...+.++|..-. ...+.+.|.|.|||..-+..+ +++
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 578888772 222444 44666799999999999995432 356899999999999988776 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=90.35 E-value=0.79 Score=40.47 Aligned_cols=66 Identities=17% Similarity=0.406 Sum_probs=50.1
Q ss_pred eEEEecCceeeeeecCCCCCChHHHHHHHHHHhhhccccCCCCceeEEEecCCCCeEEcc-CCChHHHHhccee
Q 006471 534 TKVQMQGVAVGRALDLTTLVGYDHLIDELEEMFDIKGQLHTRTKWEIVYTDDEGDMMLVG-DDPWHEFCNMVKR 606 (643)
Q Consensus 534 vKV~m~G~~vgR~vDLs~~~~Y~eL~~~L~~MF~~~g~l~~~~~~~v~Y~D~eGD~mlvG-D~PW~~F~~~vkr 606 (643)
-||.-+| --|++.-..-=+|.+|..+|+.+|.+... + ..|+|.|.+||..-+- |+=.++|.+-..+
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 3777777 56888888889999999999999998641 2 6899999999987554 4445566554444
No 20
>PRK10737 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=61.82 E-value=29 Score=35.43 Aligned_cols=101 Identities=18% Similarity=0.223 Sum_probs=62.7
Q ss_pred CCCCCEEEE-E--ecCCCcEEEEEEEccccCCCCCCccccCCccchhhHHHHHHHHHcCCeeEEEEecCC------C--c
Q 006471 154 LVAGDTFVF-L--RGENGELHVGVRCLARQQSSMPSSVISSQSMHLGVLATASHAVATQTMFVVYYKPRT------S--Q 222 (643)
Q Consensus 154 L~aGD~VvF-~--R~~~g~l~VgIRRa~~~~~~~p~sv~~~~~~~~~vl~~A~~a~~t~~~F~V~Y~Pr~------s--e 222 (643)
+..|+.|.+ | |.++|++.---+ ...|...+-....-+--|.+|..-...|..|+|..-|-. . -
T Consensus 3 I~~~~vV~l~Y~l~~~dG~v~dst~------~~~Pl~~~~G~g~lipglE~aL~G~~~Gd~~~v~l~peeAyGe~d~~lV 76 (196)
T PRK10737 3 VAKDLVVSLAYQVRTEDGVLVDESP------VSAPLDYLHGHGSLISGLETALEGHEVGDKFDVAVGANDAYGQYDENLV 76 (196)
T ss_pred cCCCCEEEEEEEEEeCCCCEEEecC------CCCCeEEEeCCCcchHHHHHHHcCCCCCCEEEEEEChHHhcCCCChHHE
Confidence 456677766 2 346676533211 123444443333333446778888889999999977643 2 5
Q ss_pred ceeeHHHHHHHHcCCCccCCEEEEEeecCCCCCceeeeEEeeeec
Q 006471 223 FIISLNKYLEAVNNKFAVGMRYKMRFEGEDSPERRFSGTVVGVED 267 (643)
Q Consensus 223 FvV~~~~y~~a~~~~w~~GmRFkM~fe~eDs~~~~~~GtI~~v~~ 267 (643)
..|+++.|... ....+||||.+. +++. .+.++|+.|.+
T Consensus 77 ~~vpr~~F~~~--~~l~~G~~~~~~--~~~G---~~~~~V~ev~~ 114 (196)
T PRK10737 77 QRVPKDVFMGV--DELQVGMRFLAE--TDQG---PVPVEITAVED 114 (196)
T ss_pred EEecHHHCCCc--cCCCCCCEEEEe--CCCC---cEEEEEEEEcC
Confidence 67888776432 236899998864 4552 36889999875
No 21
>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=56.42 E-value=45 Score=29.59 Aligned_cols=69 Identities=14% Similarity=0.356 Sum_probs=51.6
Q ss_pred eeEEEecCceeeeeecCCCCCChHHHHHHHHHHhhhccccCCCCceeEEEecCC-CCeEEccCCChHHHHhcce--eEEE
Q 006471 533 RTKVQMQGVAVGRALDLTTLVGYDHLIDELEEMFDIKGQLHTRTKWEIVYTDDE-GDMMLVGDDPWHEFCNMVK--RIFI 609 (643)
Q Consensus 533 ~vKV~m~G~~vgR~vDLs~~~~Y~eL~~~L~~MF~~~g~l~~~~~~~v~Y~D~e-GD~mlvGD~PW~~F~~~vk--ri~I 609 (643)
-||||-++ -| .|-...=-+|.+|+..|.+=+.+.++- -+|-|.|.+ |+...++|.=++.-.+.|+ +|+.
T Consensus 4 vvKV~f~~-tI--aIrvp~~~~y~~L~~ki~~kLkl~~e~-----i~LsYkde~s~~~v~l~d~dle~aws~~~~~~lTL 75 (80)
T cd06406 4 VVKVHFKY-TV--AIQVARGLSYATLLQKISSKLELPAEH-----ITLSYKSEASGEDVILSDTNMEDVWSQAKDGCLTL 75 (80)
T ss_pred EEEEEEEE-EE--EEEcCCCCCHHHHHHHHHHHhCCCchh-----cEEEeccCCCCCccCcChHHHHHHHHhhcCCeEEE
Confidence 37999998 33 455556668999999999999885432 378899865 4554559999999888888 6654
No 22
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=56.09 E-value=18 Score=29.14 Aligned_cols=38 Identities=21% Similarity=0.180 Sum_probs=29.3
Q ss_pred CCccCCEEEEEeecCCCCCceeeeEEeeeecCCCCCCCCCcceeeeeccC
Q 006471 237 KFAVGMRYKMRFEGEDSPERRFSGTVVGVEDFSPHWKDSKWRSLKVQWDE 286 (643)
Q Consensus 237 ~w~~GmRFkM~fe~eDs~~~~~~GtI~~v~~~dp~wp~S~WR~L~V~WDe 286 (643)
.|.+|+++-..++.++ .||.|+|+.+.. -..+.|.-+.
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 2235677665
No 23
>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=50.75 E-value=28 Score=31.56 Aligned_cols=41 Identities=24% Similarity=0.387 Sum_probs=32.8
Q ss_pred cCCCCCChHHHHHHHHHHhhhccccCCCCceeEEEecCCCCeEEccCC
Q 006471 548 DLTTLVGYDHLIDELEEMFDIKGQLHTRTKWEIVYTDDEGDMMLVGDD 595 (643)
Q Consensus 548 DLs~~~~Y~eL~~~L~~MF~~~g~l~~~~~~~v~Y~D~eGD~mlvGD~ 595 (643)
||+..-.|.+|.....+-|..+. -.+-|+|.|||..-+=|+
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 78899999999999999888664 367799999998544333
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=45.10 E-value=26 Score=27.13 Aligned_cols=26 Identities=15% Similarity=0.211 Sum_probs=21.7
Q ss_pred hhhcccCCCCCCEEEEEecCCCcEEE
Q 006471 147 TFVTSKRLVAGDTFVFLRGENGELHV 172 (643)
Q Consensus 147 ~FV~~K~L~aGD~VvF~R~~~g~l~V 172 (643)
.|....+|.+||.|.|.-.++|++.+
T Consensus 14 ~~~~~l~l~~Gd~v~i~~~~~g~i~i 39 (47)
T PF04014_consen 14 EIREKLGLKPGDEVEIEVEGDGKIVI 39 (47)
T ss_dssp HHHHHTTSSTTTEEEEEEETTSEEEE
T ss_pred HHHHHcCCCCCCEEEEEEeCCCEEEE
Confidence 56677799999999999998886654
No 25
>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=36.95 E-value=51 Score=26.89 Aligned_cols=32 Identities=28% Similarity=0.515 Sum_probs=24.6
Q ss_pred cCCEEEEEeecCCCCCceeeeEEeeeecCCCC
Q 006471 240 VGMRYKMRFEGEDSPERRFSGTVVGVEDFSPH 271 (643)
Q Consensus 240 ~GmRFkM~fe~eDs~~~~~~GtI~~v~~~dp~ 271 (643)
+|-|+.-.||.++.+...|.|+|...-++.|.
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 58899999998888888889999998776664
No 26
>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=36.78 E-value=86 Score=26.52 Aligned_cols=70 Identities=10% Similarity=0.068 Sum_probs=50.9
Q ss_pred cceeEEEecCcee---eeeecCCCCCChHHHHHHHHHHhhhccccCCCCceeEE--EecCCCCeEEc-cCCChHHHHhc
Q 006471 531 RSRTKVQMQGVAV---GRALDLTTLVGYDHLIDELEEMFDIKGQLHTRTKWEIV--YTDDEGDMMLV-GDDPWHEFCNM 603 (643)
Q Consensus 531 ~~~vKV~m~G~~v---gR~vDLs~~~~Y~eL~~~L~~MF~~~g~l~~~~~~~v~--Y~D~eGD~mlv-GD~PW~~F~~~ 603 (643)
..++||+++...- -++|-++....-.+++..+.+-|++.+ ...+|.|. -........|- .+.|+..+...
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 3689999988654 689999999999999999999999932 34568884 44555555554 34466655544
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=36.51 E-value=74 Score=26.59 Aligned_cols=42 Identities=19% Similarity=0.295 Sum_probs=27.1
Q ss_pred CccCCEEEEEeecCCCCCceeeeEEeeeecCCCCCCCCCcceeeeeccCCC
Q 006471 238 FAVGMRYKMRFEGEDSPERRFSGTVVGVEDFSPHWKDSKWRSLKVQWDEPA 288 (643)
Q Consensus 238 w~~GmRFkM~fe~eDs~~~~~~GtI~~v~~~dp~wp~S~WR~L~V~WDe~~ 288 (643)
|..|+++-..-+.+...-.||.|||+.... ++ .+.|+.++-.
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 568999998887555544999999999974 22 7888886554
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=35.08 E-value=63 Score=25.24 Aligned_cols=51 Identities=18% Similarity=0.436 Sum_probs=36.7
Q ss_pred CCccCCEEEEEeecCCCCCceeeeEEeeeecCCCCCCCCCcceeeeeccCCCCCCCCCccccCccee
Q 006471 237 KFAVGMRYKMRFEGEDSPERRFSGTVVGVEDFSPHWKDSKWRSLKVQWDEPASITRPDRVSPWEIEP 303 (643)
Q Consensus 237 ~w~~GmRFkM~fe~eDs~~~~~~GtI~~v~~~dp~wp~S~WR~L~V~WDe~~~~~~~~RVSPWeIEp 303 (643)
.|.+|..+..++ .+. .||.|+|+++.. + ....|.-++-.. .+-|...+|-+
T Consensus 2 ~~~~G~~~~a~~-~d~---~wyra~I~~~~~------~---~~~~V~f~D~G~---~~~v~~~~l~~ 52 (57)
T smart00333 2 TFKVGDKVAARW-EDG---EWYRARIIKVDG------E---QLYEVFFIDYGN---EEVVPPSDLRP 52 (57)
T ss_pred CCCCCCEEEEEe-CCC---CEEEEEEEEECC------C---CEEEEEEECCCc---cEEEeHHHeec
Confidence 688999999999 444 899999999963 2 567788877543 34455555554
No 29
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=34.53 E-value=51 Score=29.82 Aligned_cols=28 Identities=21% Similarity=0.362 Sum_probs=22.4
Q ss_pred hhcccCCCCCCEEEEEecCCCcEEEEEE
Q 006471 148 FVTSKRLVAGDTFVFLRGENGELHVGVR 175 (643)
Q Consensus 148 FV~~K~L~aGD~VvF~R~~~g~l~VgIR 175 (643)
|.-...|++||.|..+|...|..++-+-
T Consensus 71 i~~~~~Lk~GD~V~ll~~~~gQ~yiVlD 98 (100)
T PF10844_consen 71 ITFTDGLKVGDKVLLLRVQGGQKYIVLD 98 (100)
T ss_pred EEEecCCcCCCEEEEEEecCCCEEEEEE
Confidence 5566789999999999988887665443
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=33.00 E-value=55 Score=24.16 Aligned_cols=26 Identities=27% Similarity=0.412 Sum_probs=21.9
Q ss_pred hhhcccCCCCCCEEEEEecCCCcEEE
Q 006471 147 TFVTSKRLVAGDTFVFLRGENGELHV 172 (643)
Q Consensus 147 ~FV~~K~L~aGD~VvF~R~~~g~l~V 172 (643)
.|.+.-++..||.|.+....+|.+.+
T Consensus 14 ~~r~~l~~~~gd~~~i~~~~~~~l~l 39 (43)
T TIGR01439 14 EIREKLGLKEGDRLEVIRVEDGEIIL 39 (43)
T ss_pred HHHHHcCcCCCCEEEEEEeCCCEEEE
Confidence 67888899999999999877776655
No 31
>KOG3207 consensus Beta-tubulin folding cofactor E [Posttranslational modification, protein turnover, chaperones]
Probab=30.76 E-value=62 Score=37.17 Aligned_cols=43 Identities=33% Similarity=0.632 Sum_probs=30.2
Q ss_pred CccCCEEEEEeecCCCCCceeeeEEeeeecCCCCCCCCCcceeeeeccCCCCCCCC
Q 006471 238 FAVGMRYKMRFEGEDSPERRFSGTVVGVEDFSPHWKDSKWRSLKVQWDEPASITRP 293 (643)
Q Consensus 238 w~~GmRFkM~fe~eDs~~~~~~GtI~~v~~~dp~wp~S~WR~L~V~WDe~~~~~~~ 293 (643)
..+|+|+|..+| -..-||.|+|.|. ++ +| +.|.||++.-.-+.
T Consensus 3 ~~IG~RvkI~~~---~~Tvr~iG~V~g~-------~~-~w--~GvEWDd~~RGKH~ 45 (505)
T KOG3207|consen 3 MEIGTRVKIGGE---IATVRYIGEVEGN-------NS-KW--YGVEWDDPVRGKHD 45 (505)
T ss_pred eeccceEEEcCE---EEEEEEEEEEcCC-------CC-cc--eeeEecCCCccccC
Confidence 468999998875 2235677777654 33 44 78999999876543
No 32
>KOG3938 consensus RGS-GAIP interacting protein GIPC, contains PDZ domain [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=29.69 E-value=70 Score=34.47 Aligned_cols=75 Identities=21% Similarity=0.346 Sum_probs=55.8
Q ss_pred ecCceeeeeecCCCCCChHHHHHHHHHHhhhccc--c-CCCCceeEEEecCCCCeEEccCCChHHHH-----hcceeEEE
Q 006471 538 MQGVAVGRALDLTTLVGYDHLIDELEEMFDIKGQ--L-HTRTKWEIVYTDDEGDMMLVGDDPWHEFC-----NMVKRIFI 609 (643)
Q Consensus 538 m~G~~vgR~vDLs~~~~Y~eL~~~L~~MF~~~g~--l-~~~~~~~v~Y~D~eGD~mlvGD~PW~~F~-----~~vkri~I 609 (643)
-+|.|+|| +..|++-+|||..+++-|+|.-. | ..-+.+.+ |=+-||-|-.-+++|+ .-.|.+.|
T Consensus 61 AHGSptg~---Ie~fsnv~ELY~kIAe~F~Is~~dIlfcTlNshKv-----DM~~llgGqigleDfiFAHvkGq~kEv~v 132 (334)
T KOG3938|consen 61 AHGSPTGR---IEGFSNVRELYQKIAEAFDISPDDILFCTLNSHKV-----DMKRLLGGQIGLEDFIFAHVKGQAKEVEV 132 (334)
T ss_pred ccCCccce---ecccccHHHHHHHHHHHhcCCccceEEEecCCCcc-----cHHHHhcCccChhhhhhhhhcCcceeEEE
Confidence 36888888 46789999999999999999753 1 11111222 3345899999999996 56678999
Q ss_pred eeccccccCCC
Q 006471 610 CSSQDVKKMSP 620 (643)
Q Consensus 610 ~~~~e~~~~~~ 620 (643)
++.+++-+++.
T Consensus 133 ~KsedalGlTI 143 (334)
T KOG3938|consen 133 VKSEDALGLTI 143 (334)
T ss_pred EecccccceEE
Confidence 99999987764
No 33
>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=25.79 E-value=66 Score=30.23 Aligned_cols=26 Identities=23% Similarity=0.382 Sum_probs=17.4
Q ss_pred cCCCCCCEEEEEecC-CCcEEEEEEEc
Q 006471 152 KRLVAGDTFVFLRGE-NGELHVGVRCL 177 (643)
Q Consensus 152 K~L~aGD~VvF~R~~-~g~l~VgIRRa 177 (643)
++++.||.|+||... .+.-+||+=+-
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 56677777664
No 34
>cd06410 PB1_UP2 Uncharacterized protein 2. 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 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.
Probab=21.79 E-value=1.1e+02 Score=27.95 Aligned_cols=61 Identities=20% Similarity=0.405 Sum_probs=37.0
Q ss_pred EecCceeeeeecCCCCCChHHHHHHHHHHhhhccccCCCCceeEEEecCCCCeEEccCCChHHHHhcc
Q 006471 537 QMQGVAVGRALDLTTLVGYDHLIDELEEMFDIKGQLHTRTKWEIVYTDDEGDMMLVGDDPWHEFCNMV 604 (643)
Q Consensus 537 ~m~G~~vgR~vDLs~~~~Y~eL~~~L~~MF~~~g~l~~~~~~~v~Y~D~eGD~mlvGD~PW~~F~~~v 604 (643)
++.|+ -|-|.+.+--+|.||..+|.++|++.... .=+|++-++|.+ -..-|-++ ++..+|+
T Consensus 19 Y~GG~--tr~i~V~r~~s~~el~~kl~~~~~~~~~~--~lky~Lp~edld-~Lisv~~D--eDl~~M~ 79 (97)
T cd06410 19 YVGGE--TRIVSVDRSISFKELVSKLSELFGAGVVV--TLKYQLPDEDLD-ALISVSND--EDLKNMM 79 (97)
T ss_pred EcCCc--eEEEEEcCCCCHHHHHHHHHHHhCCCCce--EEEEEcCCCCcc-eeEEecCc--HHHHHHH
Confidence 44553 45566666679999999999999987531 113444444443 25555555 4444444
No 35
>PRK14129 heat shock protein HspQ; Provisional
Probab=21.60 E-value=1.1e+02 Score=28.48 Aligned_cols=50 Identities=26% Similarity=0.418 Sum_probs=34.3
Q ss_pred cCCCccCCEEEEEeecCCCCCceeeeEEeeeecCCCCCCCC-CcceeeeeccCCCCCCCCCccccCcc
Q 006471 235 NNKFAVGMRYKMRFEGEDSPERRFSGTVVGVEDFSPHWKDS-KWRSLKVQWDEPASITRPDRVSPWEI 301 (643)
Q Consensus 235 ~~~w~~GmRFkM~fe~eDs~~~~~~GtI~~v~~~dp~wp~S-~WR~L~V~WDe~~~~~~~~RVSPWeI 301 (643)
..+|.+|.-+|-+. -.|-|.|+.| ||.+.++ +| |++-... ++.|=.||==
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 46789999999887 3589999977 5655432 44 5555543 6667778753
No 36
>PF06003 SMN: Survival motor neuron protein (SMN); InterPro: IPR010304 This family consists of several eukaryotic survival motor neuron (SMN) proteins. The Survival of Motor Neurons (SMN) protein, the product of the spinal muscular atrophy-determining gene, is part of a large macromolecular complex (SMN complex) that functions in the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs). The SMN complex functions as a specificity factor essential for the efficient assembly of Sm proteins on U snRNAs and likely protects cells from illicit, and potentially deleterious, non-specific binding of Sm proteins to RNAs.; GO: 0003723 RNA binding, 0006397 mRNA processing, 0005634 nucleus, 0005737 cytoplasm; PDB: 1MHN_A 4A4G_A 3S6N_M 4A4E_A 1G5V_A 4A4H_A 4A4F_A 2D9T_A.
Probab=21.40 E-value=98 Score=32.83 Aligned_cols=56 Identities=14% Similarity=0.304 Sum_probs=32.8
Q ss_pred cCCCccCCEEEEEeecCCCCCceeeeEEeeeecCCCCCCCCCcceeeeeccCCCCCCCCCccccCcceec
Q 006471 235 NNKFAVGMRYKMRFEGEDSPERRFSGTVVGVEDFSPHWKDSKWRSLKVQWDEPASITRPDRVSPWEIEPF 304 (643)
Q Consensus 235 ~~~w~~GmRFkM~fe~eDs~~~~~~GtI~~v~~~dp~wp~S~WR~L~V~WDe~~~~~~~~RVSPWeIEp~ 304 (643)
...|.+|++++-.+..|. .+|.+||.+|..-+ ....|+-++=. +.+.|+.=+|.+.
T Consensus 66 ~~~WkvGd~C~A~~s~Dg---~~Y~A~I~~i~~~~--------~~~~V~f~gYg---n~e~v~l~dL~~~ 121 (264)
T PF06003_consen 66 NKKWKVGDKCMAVYSEDG---QYYPATIESIDEED--------GTCVVVFTGYG---NEEEVNLSDLKPS 121 (264)
T ss_dssp TT---TT-EEEEE-TTTS---SEEEEEEEEEETTT--------TEEEEEETTTT---EEEEEEGGGEEET
T ss_pred ccCCCCCCEEEEEECCCC---CEEEEEEEEEcCCC--------CEEEEEEcccC---CeEeeehhhhccc
Confidence 579999999999886444 79999999997422 12337777654 3344554444443
No 37
>KOG3606 consensus Cell polarity protein PAR6 [Signal transduction mechanisms]
Probab=21.24 E-value=92 Score=33.70 Aligned_cols=66 Identities=20% Similarity=0.401 Sum_probs=49.3
Q ss_pred eecCCCCCChHHHHHHHHHHhhhccccCCCCceeEEEecCCCCeEEcc-CCChHHHHhcce---eEEEeeccccc
Q 006471 546 ALDLTTLVGYDHLIDELEEMFDIKGQLHTRTKWEIVYTDDEGDMMLVG-DDPWHEFCNMVK---RIFICSSQDVK 616 (643)
Q Consensus 546 ~vDLs~~~~Y~eL~~~L~~MF~~~g~l~~~~~~~v~Y~D~eGD~mlvG-D~PW~~F~~~vk---ri~I~~~~e~~ 616 (643)
.++-..-.+|++.+.-|+..-.|.+ -++.|-|.|.-||.+-+- |+-+..-+++++ ||.|-+++|+.
T Consensus 33 sl~r~~~~~f~~F~~Lv~~~H~i~n-----vdvllgY~d~hgDLLPinNDDn~~ka~~sa~PlLR~~iQkr~ea~ 102 (358)
T KOG3606|consen 33 SLPRHSASSFDEFYSLVEHLHHIPN-----VDVLLGYADTHGDLLPINNDDNLHKALSSARPLLRLLIQKREEAD 102 (358)
T ss_pred cccccCcccHHHHHHHHHHHhcCCC-----ceEEEEEecCCCceecccCchhHHHHhhccCchhhhhhhhhhhhh
Confidence 3444555799999999988877765 346888999999999775 555555555665 88999998875
No 38
>cd04451 S1_IF1 S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the formation of the first peptide bond. In Escherichia coli, the initiation mechanism requires, in addition to mRNA, fMet-tRNA, and ribosomal subunits, the presence of three additional proteins (initiation factors IF1, IF2, and IF3) and at least one GTP molecule. The three initiation factors influence both the kinetics and the stability of ternary complex formation. IF1 is the smallest of the three factors. IF1 enhances the rate of 70S ribosome subunit association and dissociation and the interaction of 30S ribosomal subunit with IF2 and IF3. It stimulates 30S complex formation. In addition, by binding to the A-site of the 30S ribosomal subunit, IF1 may contribute to the fidelity of the selection of the initiation site of th
Probab=20.98 E-value=3.9e+02 Score=21.84 Aligned_cols=38 Identities=16% Similarity=0.126 Sum_probs=22.6
Q ss_pred EEEEEeCCCCeEEEEEEEeCCCcceeeccchhhhhcccCCCCCCEEEEEec
Q 006471 115 ELVAKDLHGYEWRFKHIFRGQPRRHLLTTGWSTFVTSKRLVAGDTFVFLRG 165 (643)
Q Consensus 115 ~L~v~D~~G~~W~Fr~~yrg~~rr~lLTtGWs~FV~~K~L~aGD~VvF~R~ 165 (643)
...+++..|. .++|..||+-|+ +...+.+||.|.|...
T Consensus 15 ~~~V~~~~g~--~~~c~~rGklr~-----------~~~~~~vGD~V~~~~~ 52 (64)
T cd04451 15 MFRVELENGH--EVLAHISGKMRM-----------NYIRILPGDRVKVELS 52 (64)
T ss_pred EEEEEeCCCC--EEEEEECceeec-----------CCcccCCCCEEEEEEe
Confidence 3455666776 444445542221 2334889999999854
No 39
>COG1047 SlpA FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]
Probab=20.85 E-value=4.8e+02 Score=26.42 Aligned_cols=103 Identities=20% Similarity=0.275 Sum_probs=62.6
Q ss_pred CCCCCCEEEEE---ecCCCcEEEEEEEccccCCCCCCccccCCccchhhHHHHHHHHHcCCeeEEEEecCCC------cc
Q 006471 153 RLVAGDTFVFL---RGENGELHVGVRCLARQQSSMPSSVISSQSMHLGVLATASHAVATQTMFVVYYKPRTS------QF 223 (643)
Q Consensus 153 ~L~aGD~VvF~---R~~~g~l~VgIRRa~~~~~~~p~sv~~~~~~~~~vl~~A~~a~~t~~~F~V~Y~Pr~s------eF 223 (643)
++..||.|.+. |.++|++.=--.- ...|..++-++..-+.-|.+|..-..-|.-|+|.--|-.. +.
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 3344544311100 1124444444444444568888888999999999888542 22
Q ss_pred --eeeHHHHHHHHcCCCccCCEEEEEeecCCCCCceeeeEEeeeec
Q 006471 224 --IISLNKYLEAVNNKFAVGMRYKMRFEGEDSPERRFSGTVVGVED 267 (643)
Q Consensus 224 --vV~~~~y~~a~~~~w~~GmRFkM~fe~eDs~~~~~~GtI~~v~~ 267 (643)
.|++++|...= ...+||+|. ++++| .-.-|+|+.|..
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 689999987 44455 446899999864
Done!