Query 005075
Match_columns 715
No_of_seqs 340 out of 814
Neff 4.5
Searched_HMMs 46136
Date Thu Mar 28 17:38:50 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/005075.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/005075hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF06507 Auxin_resp: Auxin res 100.0 7.2E-35 1.6E-39 254.9 8.9 83 292-375 1-83 (83)
2 PF02309 AUX_IAA: AUX/IAA fami 100.0 1.5E-30 3.2E-35 262.5 0.3 87 615-704 107-213 (215)
3 PF02362 B3: B3 DNA binding do 99.7 1.2E-16 2.5E-21 140.9 10.3 97 122-223 1-99 (100)
4 KOG0644 Uncharacterized conser 99.6 7E-16 1.5E-20 176.1 4.5 168 200-399 874-1043(1113)
5 PF09217 EcoRII-N: Restriction 98.0 1.7E-05 3.6E-10 77.3 8.7 89 118-209 6-110 (156)
6 PF03754 DUF313: Domain of unk 97.5 0.00018 4E-09 67.4 5.5 79 118-197 20-114 (114)
7 PF00564 PB1: PB1 domain; Int 95.5 0.041 9E-07 47.3 6.7 64 619-685 3-67 (84)
8 cd06407 PB1_NLP A PB1 domain i 94.8 0.092 2E-06 46.7 6.8 57 619-678 2-58 (82)
9 cd06396 PB1_NBR1 The PB1 domai 94.6 0.11 2.5E-06 46.3 6.8 54 619-676 2-55 (81)
10 cd06398 PB1_Joka2 The PB1 doma 94.2 0.17 3.7E-06 45.9 7.2 62 619-685 2-68 (91)
11 cd05992 PB1 The PB1 domain is 94.2 0.18 3.9E-06 43.0 7.0 62 619-684 2-65 (81)
12 smart00666 PB1 PB1 domain. Pho 93.9 0.19 4.1E-06 43.1 6.7 62 619-684 3-65 (81)
13 cd06403 PB1_Par6 The PB1 domai 93.8 0.25 5.3E-06 44.0 7.1 62 620-685 3-64 (80)
14 cd06409 PB1_MUG70 The MUG70 pr 91.8 0.26 5.7E-06 44.4 4.6 52 627-678 7-61 (86)
15 cd06404 PB1_aPKC PB1 domain is 91.0 0.69 1.5E-05 41.6 6.4 57 619-678 2-58 (83)
16 cd06402 PB1_p62 The PB1 domain 88.1 1.9 4.1E-05 39.1 7.0 59 619-678 2-65 (87)
17 cd06401 PB1_TFG The PB1 domain 88.0 2.3 5E-05 38.2 7.3 69 620-690 3-78 (81)
18 cd06408 PB1_NoxR The PB1 domai 88.0 1.5 3.2E-05 39.7 6.2 55 618-678 3-57 (86)
19 cd06397 PB1_UP1 Uncharacterize 87.5 1.7 3.6E-05 39.0 6.1 62 620-685 3-65 (82)
20 smart00743 Agenet Tudor-like d 59.3 14 0.0003 30.2 3.9 28 329-360 2-29 (61)
21 KOG0644 Uncharacterized conser 56.6 7.6 0.00016 47.5 2.6 62 31-92 871-938 (1113)
22 cd06406 PB1_P67 A PB1 domain i 56.5 35 0.00076 30.8 6.1 66 620-690 5-75 (80)
23 cd06399 PB1_P40 The PB1 domain 55.7 20 0.00044 32.9 4.5 41 634-678 23-63 (92)
24 PF04014 Antitoxin-MazE: Antid 40.0 36 0.00079 26.8 3.3 26 193-218 14-39 (47)
25 PF05641 Agenet: Agenet domain 38.0 59 0.0013 27.6 4.5 42 330-382 1-42 (68)
26 smart00333 TUDOR Tudor domain. 34.7 58 0.0012 25.9 3.8 39 329-382 2-40 (57)
27 PF10844 DUF2577: Protein of u 33.3 57 0.0012 29.9 4.0 28 194-221 71-98 (100)
28 KOG3938 RGS-GAIP interacting p 33.3 55 0.0012 35.7 4.3 72 624-701 61-140 (334)
29 TIGR01439 lp_hng_hel_AbrB loop 30.1 66 0.0014 24.1 3.2 27 192-218 13-39 (43)
30 PF00788 RA: Ras association ( 29.2 1.3E+02 0.0029 25.7 5.4 68 618-685 3-76 (93)
31 cd01789 Alp11_N Ubiquitin-like 27.7 2E+02 0.0044 25.4 6.3 40 628-671 14-53 (84)
32 PF14847 Ras_bdg_2: Ras-bindin 26.4 2.2E+02 0.0047 26.8 6.5 67 619-685 1-71 (105)
33 PF02513 Spin-Ssty: Spin/Ssty 24.1 1.3E+02 0.0028 25.0 4.0 31 332-363 1-31 (50)
34 PRK03760 hypothetical protein; 21.3 1.7E+02 0.0037 27.8 4.9 49 160-211 61-117 (117)
35 KOG3207 Beta-tubulin folding c 21.3 1E+02 0.0023 35.9 4.0 42 330-386 3-44 (505)
36 PF01878 EVE: EVE domain; Int 20.3 91 0.002 29.7 2.9 26 198-223 38-64 (143)
No 1
>PF06507 Auxin_resp: Auxin response factor; InterPro: IPR010525 This pattern represents a conserved region of auxin-responsive transcription factors. The plant hormone auxin (indole-3-acetic acid) can regulate the gene expression of several families, including Aux/IAA, GH3 and SAUR families. Two related families of proteins, Aux/IAA proteins (IPR003311 from INTERPRO) and the auxin response factors (ARF), are key regulators of auxin-modulated gene expression []. There are multiple ARF proteins, some of which activate, while others repress transcription. ARF proteins bind to auxin-responsive cis-acting promoter elements (AuxREs) using an N-terminal DNA-binding domain. It is thought that Aux/IAA proteins activate transcription by modifying ARF activity through the C-terminal protein-protein interaction domains (IPR011525 from INTERPRO) found in both Aux/IAA and ARF proteins. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0009725 response to hormone stimulus, 0005634 nucleus
Probab=100.00 E-value=7.2e-35 Score=254.93 Aligned_cols=83 Identities=58% Similarity=0.913 Sum_probs=80.6
Q ss_pred HHHHHHcCCcEEEEEecCCCCCceEEehHHHHHHhhcCcccccEEEEEeeeCCCCceeeeeeEEEEeecCCCCCCCCCCc
Q 005075 292 AATLAANRQPFEVVYYPRASTPEFCVKASMVKAALQIRWCSGMRFKMAFETEDSSRISWFMGTISSVQVSDPLYWPDSPW 371 (715)
Q Consensus 292 Aa~~aa~g~~F~V~Y~Pr~~~~EFvV~~~~~~~a~~~~w~~GmRFkM~fE~EDss~~~wf~GTI~~v~~~Dp~~wP~S~W 371 (715)
||++|++|++|+|+||||++++||||++++|++||+++|++||||||+||+||+++++ |+|||++|++.||++||+|+|
T Consensus 1 A~~aa~~~~~F~V~Y~PRa~~sEFVV~~~k~~~al~~~~~~GmRfkM~fE~eds~~~~-~~GtI~~v~~~dp~~w~~S~W 79 (83)
T PF06507_consen 1 AAHAAATGSPFEVFYYPRASPSEFVVPASKYDKALNHPWSVGMRFKMRFETEDSSERR-WQGTIVGVSDLDPIRWPGSKW 79 (83)
T ss_pred ChhHhhcCCeEEEEECCCCCCcceEEEHHHHHHHhcCCCCCCcEEEEEeccCCCccce-eeeEEeEeeccCCCCCCCCCc
Confidence 6899999999999999999999999999999999999999999999999999999976 599999999999999999999
Q ss_pred ccee
Q 005075 372 RLLQ 375 (715)
Q Consensus 372 R~Lq 375 (715)
||||
T Consensus 80 R~Lq 83 (83)
T PF06507_consen 80 RMLQ 83 (83)
T ss_pred ccCc
Confidence 9997
No 2
>PF02309 AUX_IAA: AUX/IAA family; InterPro: IPR003311 The Aux/IAA family of genes are key regulators of auxin-modified gene expression []. The plant hormone auxin (indole-3-acetic acid, IAA) regulates diverse cellular and developmental responses in plants, including cell division, expansion, differentiation and patterning of embryo responses []. Auxin can regulate the gene expression of several families, including GH3 and SAUR, as well as Aux/IAA itself. The Aux/IAA proteins act as repressors of auxin-induced gene expression, possibly through modulating the activity of DNA-binding auxin response factors (ARFs) (IPR010525 from INTERPRO). Aux/IAA and ARF are thought to interact through C-terminal protein-protein interaction domains found in both Aux/IAA and ARF. Recent evidence suggests that Aux/IAA proteins can also mediate light responses []. Some members of the AUX/IAA family are longer and contain an N-terminal DNA binding domain [] and may have an early function in the establishment of vascular and body patterns in embryonic and post-embryonic development in some plants.; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2P1N_F 2P1Q_C 2P1O_C.
Probab=99.96 E-value=1.5e-30 Score=262.50 Aligned_cols=87 Identities=32% Similarity=0.434 Sum_probs=0.0
Q ss_pred CccceEEEEecccceeeecccCCcCCHHHHHHHHHHhh---CCC----------c-ccc----ceeEEEeeCCCCeEecC
Q 005075 615 LETGHCKVFMESEDVGRTLDLSLLGSYDELYKKLAEMF---GIE----------N-AET----LSHLLYRDVTGAVKHIG 676 (715)
Q Consensus 615 ~~~~~vKV~meG~~vgR~vDLs~~~sY~eL~~~L~~MF---~~~----------~-~~l----~~~v~Y~D~eGd~mlvG 676 (715)
..++||||+|||++|||||||++|+||++|+.+|++|| +|. + .++ .|+|||+|+||||||||
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 35799999999999999999999999999999999999 665 1 111 36899999999999999
Q ss_pred Ccchhhhcc--ceEEEcccCccccccCcce
Q 005075 677 DEPFRFQLF--RLLAIFSLYTIISLKGFNL 704 (715)
Q Consensus 677 D~Pw~~F~~--krl~I~~~~~~~~~~~~~~ 704 (715)
||||++||+ |||+| ++.+|+++|.+
T Consensus 187 D~PW~~F~~~vkRl~I---~~~~e~~~~~~ 213 (215)
T PF02309_consen 187 DVPWEEFVKSVKRLRI---MKSSEAKGLAP 213 (215)
T ss_dssp ------------------------------
T ss_pred CCCHHHHHHHhhccEE---ecHHHhcccCC
Confidence 999999999 99999 66799988853
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=140.95 Aligned_cols=97 Identities=31% Similarity=0.414 Sum_probs=74.7
Q ss_pred EEEecccccCCCCCceeeccccccccCCCCCCCCCCCceEEEEEeCCCCeEEEEEEEeCCCCceeeccCchhhhcccCCC
Q 005075 122 FAKTLTQSDANNGGGFSVPRYCAETIFPRLDYSADPPVQTILAKDVHGETWKFRHIYRGTPRRHLLTTGWSTFVNHKKLV 201 (715)
Q Consensus 122 F~K~LT~SDv~~~grfsVPk~~Ae~~FP~Ld~~~~~p~q~L~~~D~~G~~W~Fr~~yr~~~rr~lLTtGWs~FV~~K~L~ 201 (715)
|.|+|+++|+.+.++|.||+++++.+. ++. ...+++.++|..|+.|.+++.+++.+.+++|++||..||++++|+
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--GNK---RKSREVTLKDPDGRSWPVKLKYRKNSGRYYLTGGWKKFVRDNGLK 75 (100)
T ss_dssp EEEE--TTCCCCTT-EEE-HHHHTTTS----S---S--CEEEEEETTTEEEEEEEEEECCTTEEEEETTHHHHHHHCT--
T ss_pred CEEEEEccCcCCCCEEEeCHHHHHHhC--CCc---CCCeEEEEEeCCCCEEEEEEEEEccCCeEEECCCHHHHHHHcCCC
Confidence 899999999999899999999999972 111 124789999999999999999999888999999999999999999
Q ss_pred CCCEEEEEEecC--CcEEEEEEEe
Q 005075 202 AGDSIVFLRAEN--GDLCVGIRRA 223 (715)
Q Consensus 202 aGD~VvF~R~~n--G~l~VGIRRa 223 (715)
+||.|+|+...+ .++.|.|.|+
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 999999998764 4569999986
No 4
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=99.58 E-value=7e-16 Score=176.10 Aligned_cols=168 Identities=23% Similarity=0.408 Sum_probs=130.4
Q ss_pred CCCCCEEEEEEecCCcEEEEEEEeccCcCCCCCCCCCCCCCCCCCCCCcccccccccchhhccCcCCCCCCCCCCCCccc
Q 005075 200 LVAGDSIVFLRAENGDLCVGIRRAKRGIGGGPEVTSGWNGNCVTPYGGFSAFLREDDNKLMRNGIGNVNGPSSNNGNNLM 279 (715)
Q Consensus 200 L~aGD~VvF~R~~nG~l~VGIRRa~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 279 (715)
.+.||.|+++|..+.++.-.+|+...-..+ ..+||.. .++..+-.+ +.++.++++ ...+++|
T Consensus 874 pQmgDEViyfrQghqeyl~~~~~n~~~~~~----~~p~~~~----------~v~~~kv~k-l~~~~y~~~---~~s~c~m 935 (1113)
T KOG0644|consen 874 PQMGDEVIYFRQGHQEYLEAVRLNNIELNN----KEPWNKM----------AVEICKVEK-LVYITYPGS---GDSCCKM 935 (1113)
T ss_pred ccccceeehhhhhhHHHHhhhhhccccccc----cCccccc----------chhhheeee-eeeeeccCC---Ccchhee
Confidence 348999999999988887777776663222 2467763 233222222 234444332 3455666
Q ss_pred cCCCCChHHHHHHHHHHHcCCcEEEEEecCCCCCceEEehHHHHHHhhcCcccccEEEEEe--eeCCCCceeeeeeEEEE
Q 005075 280 AKGKVRPESVIEAATLAANRQPFEVVYYPRASTPEFCVKASMVKAALQIRWCSGMRFKMAF--ETEDSSRISWFMGTISS 357 (715)
Q Consensus 280 ~~g~v~~~~V~~Aa~~aa~g~~F~V~Y~Pr~~~~EFvV~~~~~~~a~~~~w~~GmRFkM~f--E~EDss~~~wf~GTI~~ 357 (715)
.+. |++-+. -+-.+.|.++|....+.+||+|.++.|++|++++|.++++||.-+ ++|+-- +||.|+|-+
T Consensus 936 ~l~------~idp~s-~~~~k~F~ltlpdlv~fpDFlV~rsrYd~AiQrnW~~~d~crvwwrda~~e~g--~WWeG~ils 1006 (1113)
T KOG0644|consen 936 KLA------VIDPAS-KLMDKSFKLTLPDLVTFPDFLVERSRYDAAIQRNWTCRDKCRVWWRDAGEEDG--AWWEGRILS 1006 (1113)
T ss_pred eee------eecchh-hhhhccceeecccccCcchhhhhhhhHHHHHhhccccccceeEEEccCCCcCC--ceeeeeeee
Confidence 666 888666 455678999999999999999999999999999999999999998 333322 699999999
Q ss_pred eecCCCCCCCCCCccceecccCcccccCCCCccccceeeecc
Q 005075 358 VQVSDPLYWPDSPWRLLQVTWDEPDLLQNVKRVSPWLVELVS 399 (715)
Q Consensus 358 v~~~Dp~~wP~S~WR~LqV~WDe~~~~~~~~RVSPWeIE~v~ 399 (715)
+++..| .+|+|+|+++.|+||..+ .+--||||.|++.
T Consensus 1007 ~~pksp-~fpdSpwery~v~~~~~e----~~~~spwe~~~i~ 1043 (1113)
T KOG0644|consen 1007 VKPKSP-DFPDSPWERYIVRYDNTE----TELHSPWEMEPIP 1043 (1113)
T ss_pred ccCCCC-CCCCCcceeEEEEecCCc----ccccCccccCCCc
Confidence 999999 999999999999999998 6888999999886
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=98.05 E-value=1.7e-05 Score=77.32 Aligned_cols=89 Identities=22% Similarity=0.337 Sum_probs=59.1
Q ss_pred cceEEEEecccccCCCCC----ceeeccccccccCCCCCC-CCCCCceEEEEEeCCC--CeEEEEEEEeCC------CCc
Q 005075 118 KPASFAKTLTQSDANNGG----GFSVPRYCAETIFPRLDY-SADPPVQTILAKDVHG--ETWKFRHIYRGT------PRR 184 (715)
Q Consensus 118 ~~~~F~K~LT~SDv~~~g----rfsVPk~~Ae~~FP~Ld~-~~~~p~q~L~~~D~~G--~~W~Fr~~yr~~------~rr 184 (715)
....|+|.|++.|++.+| |+.|||..++..||.+.. +..+|..+|.+++..+ ..|+||++|.|+ .+.
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 456899999999999664 799999999999998776 6677899999999887 668999999987 467
Q ss_pred eeeccCchh---hhcccCCCCCCEEEEE
Q 005075 185 HLLTTGWST---FVNHKKLVAGDSIVFL 209 (715)
Q Consensus 185 ~lLTtGWs~---FV~~K~L~aGD~VvF~ 209 (715)
+.|| +|.. |.+. =..||-+||-
T Consensus 86 ~RIT-~~G~~~~~~~~--~~tGaL~vla 110 (156)
T PF09217_consen 86 YRIT-RFGRGFPLQNP--ENTGALLVLA 110 (156)
T ss_dssp EEEE----TTSGGG-G--GGTT-EEEEE
T ss_pred eEEe-eecCCCccCCc--cccccEEEEE
Confidence 8885 4433 3332 2378887775
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=97.46 E-value=0.00018 Score=67.39 Aligned_cols=79 Identities=18% Similarity=0.225 Sum_probs=60.9
Q ss_pred cceEEEEecccccCC-CCCceeeccccccccCCCCCC------------CCCCCceEEEEEeCCCCeEEEEEEEeCC---
Q 005075 118 KPASFAKTLTQSDAN-NGGGFSVPRYCAETIFPRLDY------------SADPPVQTILAKDVHGETWKFRHIYRGT--- 181 (715)
Q Consensus 118 ~~~~F~K~LT~SDv~-~~grfsVPk~~Ae~~FP~Ld~------------~~~~p~q~L~~~D~~G~~W~Fr~~yr~~--- 181 (715)
.-..|.|+|++||+. ...||+||-..... ...|.. ....-++.+.+.|..++.|..++..|..
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 356999999999998 45899999986633 222311 1123457888999999999999999966
Q ss_pred CCceeeccCchhhhcc
Q 005075 182 PRRHLLTTGWSTFVNH 197 (715)
Q Consensus 182 ~rr~lLTtGWs~FV~~ 197 (715)
...|+|++||..+|++
T Consensus 99 ~~~YvL~~gWn~VV~~ 114 (114)
T PF03754_consen 99 TSNYVLNSGWNKVVED 114 (114)
T ss_pred ceEEEEEcChHhhccC
Confidence 5789999999999864
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=95.54 E-value=0.041 Score=47.27 Aligned_cols=64 Identities=25% Similarity=0.375 Sum_probs=51.0
Q ss_pred eEEEEecccceeeecccCCcCCHHHHHHHHHHhhCCCccccceeEEEeeCCCCeEecCCc-chhhhcc
Q 005075 619 HCKVFMESEDVGRTLDLSLLGSYDELYKKLAEMFGIENAETLSHLLYRDVTGAVKHIGDE-PFRFQLF 685 (715)
Q Consensus 619 ~vKV~meG~~vgR~vDLs~~~sY~eL~~~L~~MF~~~~~~l~~~v~Y~D~eGd~mlvGD~-Pw~~F~~ 685 (715)
.+|+...|+ +=|.+.+..--+|++|..++++.|++.. -...+.|.|.|||+..+-+. =|.+.+.
T Consensus 3 ~vK~~~~~~-~~~~~~~~~~~s~~~L~~~i~~~~~~~~--~~~~l~Y~D~dgD~V~i~sd~Dl~~a~~ 67 (84)
T PF00564_consen 3 RVKVRYGGD-IRRIISLPSDVSFDDLRSKIREKFGLLD--EDFQLKYKDEDGDLVTISSDEDLQEAIE 67 (84)
T ss_dssp EEEEEETTE-EEEEEEECSTSHHHHHHHHHHHHHTTST--SSEEEEEEETTSSEEEESSHHHHHHHHH
T ss_pred EEEEEECCe-eEEEEEcCCCCCHHHHHHHHHHHhCCCC--ccEEEEeeCCCCCEEEeCCHHHHHHHHH
Confidence 579999985 4446888888899999999999999962 23689999999999988865 3555444
No 8
>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=94.83 E-value=0.092 Score=46.65 Aligned_cols=57 Identities=18% Similarity=0.177 Sum_probs=44.5
Q ss_pred eEEEEecccceeeecccCCcCCHHHHHHHHHHhhCCCccccceeEEEeeCCCCeEecCCc
Q 005075 619 HCKVFMESEDVGRTLDLSLLGSYDELYKKLAEMFGIENAETLSHLLYRDVTGAVKHIGDE 678 (715)
Q Consensus 619 ~vKV~meG~~vgR~vDLs~~~sY~eL~~~L~~MF~~~~~~l~~~v~Y~D~eGd~mlvGD~ 678 (715)
.+||...|+ -+.+-|..--+|++|..+++++|++.. .-...|-|.|.||||..+--.
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 479999886 344555555699999999999999963 234689999999999987543
No 9
>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=94.64 E-value=0.11 Score=46.28 Aligned_cols=54 Identities=15% Similarity=0.127 Sum_probs=46.4
Q ss_pred eEEEEecccceeeecccCCcCCHHHHHHHHHHhhCCCccccceeEEEeeCCCCeEecC
Q 005075 619 HCKVFMESEDVGRTLDLSLLGSYDELYKKLAEMFGIENAETLSHLLYRDVTGAVKHIG 676 (715)
Q Consensus 619 ~vKV~meG~~vgR~vDLs~~~sY~eL~~~L~~MF~~~~~~l~~~v~Y~D~eGd~mlvG 676 (715)
.+||.-.|+-+==+++.+..-+|++|..+++++|++. ...|-|.|.||||.++-
T Consensus 2 ~vKaty~~d~~rf~~~~~~~~~~~~L~~ev~~rf~l~----~f~lKYlDde~e~v~ls 55 (81)
T cd06396 2 NLKVTYNGESQSFLVSDSENTTWASVEAMVKVSFGLN----DIQIKYVDEENEEVSVN 55 (81)
T ss_pred EEEEEECCeEEEEEecCCCCCCHHHHHHHHHHHhCCC----cceeEEEcCCCCEEEEE
Confidence 4788888886666777777889999999999999998 47899999999998774
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=94.24 E-value=0.17 Score=45.89 Aligned_cols=62 Identities=24% Similarity=0.231 Sum_probs=48.2
Q ss_pred eEEEEecccceeeecccC-----CcCCHHHHHHHHHHhhCCCccccceeEEEeeCCCCeEecCCcchhhhcc
Q 005075 619 HCKVFMESEDVGRTLDLS-----LLGSYDELYKKLAEMFGIENAETLSHLLYRDVTGAVKHIGDEPFRFQLF 685 (715)
Q Consensus 619 ~vKV~meG~~vgR~vDLs-----~~~sY~eL~~~L~~MF~~~~~~l~~~v~Y~D~eGd~mlvGD~Pw~~F~~ 685 (715)
-+||.-+|+ -|.+-+. .--+|++|..++++.|.+.. .....+.|.|.+|||..+-++ .++..
T Consensus 2 ~vKv~y~~~--~rRf~l~~~~~~~d~~~~~L~~kI~~~f~l~~-~~~~~l~Y~Dedgd~V~l~~D--~DL~~ 68 (91)
T cd06398 2 VVKVKYGGT--LRRFTFPVAENQLDLNMDGLREKVEELFSLSP-DADLSLTYTDEDGDVVTLVDD--NDLTD 68 (91)
T ss_pred EEEEEeCCE--EEEEEeccccccCCCCHHHHHHHHHHHhCCCC-CCcEEEEEECCCCCEEEEccH--HHHHH
Confidence 378999886 4544444 35799999999999999964 345689999999999998776 55544
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=94.18 E-value=0.18 Score=43.01 Aligned_cols=62 Identities=26% Similarity=0.348 Sum_probs=46.4
Q ss_pred eEEEEecccceeeecccC-CcCCHHHHHHHHHHhhCCCccccceeEEEeeCCCCeEecCCc-chhhhc
Q 005075 619 HCKVFMESEDVGRTLDLS-LLGSYDELYKKLAEMFGIENAETLSHLLYRDVTGAVKHIGDE-PFRFQL 684 (715)
Q Consensus 619 ~vKV~meG~~vgR~vDLs-~~~sY~eL~~~L~~MF~~~~~~l~~~v~Y~D~eGd~mlvGD~-Pw~~F~ 684 (715)
.+||.-.|.. |.+=+. .--+|++|..+|.+.|++.. ....+.|.|.|||+..+.++ =|.+.+
T Consensus 2 ~vK~~~~~~~--~~~~~~~~~~s~~~L~~~i~~~~~~~~--~~~~l~y~D~e~d~v~l~sd~Dl~~a~ 65 (81)
T cd05992 2 RVKVKYGGEI--RRFVVVSRSISFEDLRSKIAEKFGLDA--VSFKLKYPDEDGDLVTISSDEDLEEAI 65 (81)
T ss_pred cEEEEecCCC--EEEEEecCCCCHHHHHHHHHHHhCCCC--CcEEEEeeCCCCCEEEeCCHHHHHHHH
Confidence 3678777752 333333 78899999999999999864 33689999999999999884 344333
No 12
>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=93.94 E-value=0.19 Score=43.14 Aligned_cols=62 Identities=23% Similarity=0.347 Sum_probs=47.7
Q ss_pred eEEEEecccceeeecccCCcCCHHHHHHHHHHhhCCCccccceeEEEeeCCCCeEecCCc-chhhhc
Q 005075 619 HCKVFMESEDVGRTLDLSLLGSYDELYKKLAEMFGIENAETLSHLLYRDVTGAVKHIGDE-PFRFQL 684 (715)
Q Consensus 619 ~vKV~meG~~vgR~vDLs~~~sY~eL~~~L~~MF~~~~~~l~~~v~Y~D~eGd~mlvGD~-Pw~~F~ 684 (715)
-+||.-.| -=|.+-+..--+|++|..++.+.|++.. -...+-|+|.|||+..+.++ =|.+.+
T Consensus 3 ~vK~~~~~--~~~~~~~~~~~s~~dL~~~i~~~~~~~~--~~~~l~Y~Dedgd~v~l~sd~Dl~~a~ 65 (81)
T smart00666 3 DVKLRYGG--ETRRLSVPRDISFEDLRSKVAKRFGLDN--QSFTLKYQDEDGDLVSLTSDEDLEEAI 65 (81)
T ss_pred cEEEEECC--EEEEEEECCCCCHHHHHHHHHHHhCCCC--CCeEEEEECCCCCEEEecCHHHHHHHH
Confidence 46777755 3677788888999999999999999864 23589999999999987764 344333
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=93.80 E-value=0.25 Score=44.04 Aligned_cols=62 Identities=24% Similarity=0.279 Sum_probs=48.4
Q ss_pred EEEEecccceeeecccCCcCCHHHHHHHHHHhhCCCccccceeEEEeeCCCCeEecCCcchhhhcc
Q 005075 620 CKVFMESEDVGRTLDLSLLGSYDELYKKLAEMFGIENAETLSHLLYRDVTGAVKHIGDEPFRFQLF 685 (715)
Q Consensus 620 vKV~meG~~vgR~vDLs~~~sY~eL~~~L~~MF~~~~~~l~~~v~Y~D~eGd~mlvGD~Pw~~F~~ 685 (715)
||..-+++--==.+|.....+|++++..|+.|+.+.+ +...|-|.|.+||.+-+-.+ ..|.+
T Consensus 3 VKSkfdaEfRRFsl~r~~~~~f~ef~~ll~~lH~l~~--~~f~i~Y~D~~gDLLPInND--dNf~k 64 (80)
T cd06403 3 VKSKFDAEFRRFSLDRNKPGKFEDFYKLLEHLHHIPN--VDFLIGYTDPHGDLLPINND--DNFLK 64 (80)
T ss_pred eecccCCeEEEEEeccccCcCHHHHHHHHHHHhCCCC--CcEEEEEeCCCCCEecccCc--HHHHH
Confidence 5666666532236777788999999999999999976 55689999999999988766 55544
No 14
>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=91.81 E-value=0.26 Score=44.43 Aligned_cols=52 Identities=25% Similarity=0.351 Sum_probs=40.2
Q ss_pred cceeeecccCC--cCCHHHHHHHHHHhhCCCcc-ccceeEEEeeCCCCeEecCCc
Q 005075 627 EDVGRTLDLSL--LGSYDELYKKLAEMFGIENA-ETLSHLLYRDVTGAVKHIGDE 678 (715)
Q Consensus 627 ~~vgR~vDLs~--~~sY~eL~~~L~~MF~~~~~-~l~~~v~Y~D~eGd~mlvGD~ 678 (715)
.+-||.+=++. ..|+++|..++++=|+++.. .-...|.|.|+||||.++--+
T Consensus 7 ~~~GrvhRf~~~~s~~~~~L~~~I~~Rl~~d~~~~~~~~L~YlDDEgD~VllT~D 61 (86)
T cd06409 7 DPKGRVHRFRLRPSESLEELRTLISQRLGDDDFETHLYALSYVDDEGDIVLITSD 61 (86)
T ss_pred CCCCCEEEEEecCCCCHHHHHHHHHHHhCCccccCCcccEEEEcCCCCEEEEecc
Confidence 34666655543 68999999999999999763 234689999999999987543
No 15
>cd06404 PB1_aPKC PB1 domain is an essential modular domain of the atypical protein kinase C (aPKC) which in complex with Par6 and Par3 proteins is crucial for establishment of apical-basal polarity of animal cells. PB1 domain is a modular domain mediating specific protein-protein interaction which play roles in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi,
Probab=91.04 E-value=0.69 Score=41.60 Aligned_cols=57 Identities=19% Similarity=0.211 Sum_probs=46.0
Q ss_pred eEEEEecccceeeecccCCcCCHHHHHHHHHHhhCCCccccceeEEEeeCCCCeEecCCc
Q 005075 619 HCKVFMESEDVGRTLDLSLLGSYDELYKKLAEMFGIENAETLSHLLYRDVTGAVKHIGDE 678 (715)
Q Consensus 619 ~vKV~meG~~vgR~vDLs~~~sY~eL~~~L~~MF~~~~~~l~~~v~Y~D~eGd~mlvGD~ 678 (715)
.+|+.-+|.-+-=.+|. .-+|++|.+++.+||.... +...++-|.|.|||.--+...
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 47899999755555666 6689999999999999854 345799999999999887654
No 16
>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=88.14 E-value=1.9 Score=39.12 Aligned_cols=59 Identities=20% Similarity=0.380 Sum_probs=42.3
Q ss_pred eEEEEecc----cceee-ecccCCcCCHHHHHHHHHHhhCCCccccceeEEEeeCCCCeEecCCc
Q 005075 619 HCKVFMES----EDVGR-TLDLSLLGSYDELYKKLAEMFGIENAETLSHLLYRDVTGAVKHIGDE 678 (715)
Q Consensus 619 ~vKV~meG----~~vgR-~vDLs~~~sY~eL~~~L~~MF~~~~~~l~~~v~Y~D~eGd~mlvGD~ 678 (715)
.||.+..| ..|=| +||=....+|++|+..+.++|..-. +-...+-|.|.|||..-+...
T Consensus 2 ~vkayl~~~~~~~EIRRf~l~~~~~~s~~~L~~~V~~~f~~l~-~~~ftlky~DeeGDlvtIssd 65 (87)
T cd06402 2 TVKAYLLGKDANAEIRRFAIDEDVSTSYEYLVEKVAAVFPSLR-GKNFQLFWKDEEGDLVAFSSD 65 (87)
T ss_pred eEEEeecCCCCccceEEEEecCCCCcCHHHHHHHHHHHccccC-CCcEEEEEECCCCCEEeecCH
Confidence 46666666 33333 3444667799999999999995422 234689999999999888765
No 17
>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=88.00 E-value=2.3 Score=38.18 Aligned_cols=69 Identities=23% Similarity=0.277 Sum_probs=46.5
Q ss_pred EEEEecccceeeecccCCc-CCHHHHHHHHHHhhCCCc-cccceeEEEeeCCCCeEecCCc---chhhhcc--ceEEE
Q 005075 620 CKVFMESEDVGRTLDLSLL-GSYDELYKKLAEMFGIEN-AETLSHLLYRDVTGAVKHIGDE---PFRFQLF--RLLAI 690 (715)
Q Consensus 620 vKV~meG~~vgR~vDLs~~-~sY~eL~~~L~~MF~~~~-~~l~~~v~Y~D~eGd~mlvGD~---Pw~~F~~--krl~I 690 (715)
+|+.-+| +|=| +-+..- -+|.+|...+.+.|...- ..-...|-|+|.|||+.-+-+. -|..-+. +||+|
T Consensus 3 iK~~~g~-DiR~-~~~~~~~~t~~~L~~~v~~~F~~~~~~~~~flIKYkD~dGDlVTIts~~dL~~A~~~~~~~~l~~ 78 (81)
T cd06401 3 LKAQLGD-DIRR-IPIHNEDITYDELLLMMQRVFRGKLGSSDDVLIKYKDEDGDLITIFDSSDLSFAIQCSRILKLTL 78 (81)
T ss_pred EEEEeCC-eEEE-EeccCccccHHHHHHHHHHHhccccCCcccEEEEEECCCCCEEEeccHHHHHHHHhcCcceEEEE
Confidence 4666655 4544 444432 399999999999999642 2233579999999999999875 2332233 66665
No 18
>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=87.99 E-value=1.5 Score=39.75 Aligned_cols=55 Identities=18% Similarity=0.346 Sum_probs=45.9
Q ss_pred ceEEEEecccceeeecccCCcCCHHHHHHHHHHhhCCCccccceeEEEeeCCCCeEecCCc
Q 005075 618 GHCKVFMESEDVGRTLDLSLLGSYDELYKKLAEMFGIENAETLSHLLYRDVTGAVKHIGDE 678 (715)
Q Consensus 618 ~~vKV~meG~~vgR~vDLs~~~sY~eL~~~L~~MF~~~~~~l~~~v~Y~D~eGd~mlvGD~ 678 (715)
-.|||+-+|. -|.|-+..-=+|++|..++.++|++.. ...|-|.|. ||+.-+++.
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 4689998887 566666666789999999999999963 358999999 999999886
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=87.51 E-value=1.7 Score=39.05 Aligned_cols=62 Identities=11% Similarity=0.130 Sum_probs=48.4
Q ss_pred EEEEecccceeeecccCCcCCHHHHHHHHHHhhCCCccccceeEEEeeCCCCeEecCCc-chhhhcc
Q 005075 620 CKVFMESEDVGRTLDLSLLGSYDELYKKLAEMFGIENAETLSHLLYRDVTGAVKHIGDE-PFRFQLF 685 (715)
Q Consensus 620 vKV~meG~~vgR~vDLs~~~sY~eL~~~L~~MF~~~~~~l~~~v~Y~D~eGd~mlvGD~-Pw~~F~~ 685 (715)
-||.-+| --|++.-..-=+|.+|..+|+.+|.+... ..-|+|.|.+||..-+-|+ =.++|.+
T Consensus 3 fKv~~~g--~~RRf~~~~~pt~~~L~~kl~~Lf~lp~~--~~~vtYiDeD~D~ITlssd~eL~d~~~ 65 (82)
T cd06397 3 FKSSFLG--DTRRIVFPDIPTWEALASKLENLYNLPEI--KVGVTYIDNDNDEITLSSNKELQDFYR 65 (82)
T ss_pred EEEEeCC--ceEEEecCCCccHHHHHHHHHHHhCCChh--HeEEEEEcCCCCEEEecchHHHHHHHH
Confidence 4777777 46788788888999999999999999753 2689999999998876664 4445544
No 20
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=59.33 E-value=14 Score=30.22 Aligned_cols=28 Identities=25% Similarity=0.451 Sum_probs=23.8
Q ss_pred CcccccEEEEEeeeCCCCceeeeeeEEEEeec
Q 005075 329 RWCSGMRFKMAFETEDSSRISWFMGTISSVQV 360 (715)
Q Consensus 329 ~w~~GmRFkM~fE~EDss~~~wf~GTI~~v~~ 360 (715)
.|++|+++-..++.++ +||.|+|+.+..
T Consensus 2 ~~~~G~~Ve~~~~~~~----~W~~a~V~~~~~ 29 (61)
T smart00743 2 DFKKGDRVEVFSKEED----SWWEAVVTKVLG 29 (61)
T ss_pred CcCCCCEEEEEECCCC----EEEEEEEEEECC
Confidence 5889999999996554 799999999964
No 21
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=56.62 E-value=7.6 Score=47.47 Aligned_cols=62 Identities=23% Similarity=0.457 Sum_probs=44.5
Q ss_pred ccCCCCCCeEEEeccCccccccCC----CCCCCC--CCCCCcceeeEeeeEeeeCCCccceeEEEEee
Q 005075 31 VQMPPVNSRVFYFPQGHAEHACGP----VDFRSC--RRIPPYILCRVSPIKFMADPETDEVYAKIKLV 92 (715)
Q Consensus 31 v~~P~vgs~V~YFPqGH~Eq~~~~----~~~~~~--~~~P~~i~CrV~~V~l~Ad~~TDEVyAki~L~ 92 (715)
-.||..|..|.||-|||-|-+.+. .++... .++-..=.|.|..+.+---|-...--.+|.|.
T Consensus 871 ryipQmgDEViyfrQghqeyl~~~~~n~~~~~~~~p~~~~~v~~~kv~kl~~~~y~~~~~s~c~m~l~ 938 (1113)
T KOG0644|consen 871 RYIPQMGDEVIYFRQGHQEYLEAVRLNNIELNNKEPWNKMAVEICKVEKLVYITYPGSGDSCCKMKLA 938 (1113)
T ss_pred cccccccceeehhhhhhHHHHhhhhhccccccccCcccccchhhheeeeeeeeeccCCCcchheeeee
Confidence 368999999999999999998873 222221 11334667999888877666666667777665
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=56.54 E-value=35 Score=30.75 Aligned_cols=66 Identities=18% Similarity=0.230 Sum_probs=48.6
Q ss_pred EEEEecccceeeecccCCcCCHHHHHHHHHHhhCCCccccceeEEEeeCC-CCeEecCCcchhhhcc----ceEEE
Q 005075 620 CKVFMESEDVGRTLDLSLLGSYDELYKKLAEMFGIENAETLSHLLYRDVT-GAVKHIGDEPFRFQLF----RLLAI 690 (715)
Q Consensus 620 vKV~meG~~vgR~vDLs~~~sY~eL~~~L~~MF~~~~~~l~~~v~Y~D~e-Gd~mlvGD~Pw~~F~~----krl~I 690 (715)
+||+-++ -| .|-...=-+|.+|+++|.+=+.+.+++ .+|-|+|.+ |+...++|.=++.-.+ .||+.
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 6999998 23 444555668999999999999996433 478999855 4554559887776665 77776
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=55.71 E-value=20 Score=32.88 Aligned_cols=41 Identities=27% Similarity=0.325 Sum_probs=34.7
Q ss_pred ccCCcCCHHHHHHHHHHhhCCCccccceeEEEeeCCCCeEecCCc
Q 005075 634 DLSLLGSYDELYKKLAEMFGIENAETLSHLLYRDVTGAVKHIGDE 678 (715)
Q Consensus 634 DLs~~~sY~eL~~~L~~MF~~~~~~l~~~v~Y~D~eGd~mlvGD~ 678 (715)
||+.--+|.+|.....+-|..+. -.+=|+|.|||..-+=|+
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 78999999999999999999876 367799999998755443
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=39.97 E-value=36 Score=26.78 Aligned_cols=26 Identities=15% Similarity=0.298 Sum_probs=21.8
Q ss_pred hhhcccCCCCCCEEEEEEecCCcEEE
Q 005075 193 TFVNHKKLVAGDSIVFLRAENGDLCV 218 (715)
Q Consensus 193 ~FV~~K~L~aGD~VvF~R~~nG~l~V 218 (715)
.|.++.+|.+||.|.|.-.++|++.+
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 56778899999999999999886554
No 25
>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=38.03 E-value=59 Score=27.61 Aligned_cols=42 Identities=24% Similarity=0.380 Sum_probs=26.6
Q ss_pred cccccEEEEEeeeCCCCceeeeeeEEEEeecCCCCCCCCCCccceecccCccc
Q 005075 330 WCSGMRFKMAFETEDSSRISWFMGTISSVQVSDPLYWPDSPWRLLQVTWDEPD 382 (715)
Q Consensus 330 w~~GmRFkM~fE~EDss~~~wf~GTI~~v~~~Dp~~wP~S~WR~LqV~WDe~~ 382 (715)
|..|+++-..-+ |+..+-+||.|||......+ .+.|+.++-.
T Consensus 1 F~~G~~VEV~s~-e~g~~gaWf~a~V~~~~~~~----------~~~V~Y~~~~ 42 (68)
T PF05641_consen 1 FKKGDEVEVSSD-EDGFRGAWFPATVLKENGDD----------KYLVEYDDLP 42 (68)
T ss_dssp --TT-EEEEEE--SBTT--EEEEEEEEEEETT-----------EEEEEETT-S
T ss_pred CCCCCEEEEEEc-CCCCCcEEEEEEEEEeCCCc----------EEEEEECCcc
Confidence 467999998765 45557799999999987421 6778886553
No 26
>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=34.66 E-value=58 Score=25.87 Aligned_cols=39 Identities=15% Similarity=0.365 Sum_probs=28.9
Q ss_pred CcccccEEEEEeeeCCCCceeeeeeEEEEeecCCCCCCCCCCccceecccCccc
Q 005075 329 RWCSGMRFKMAFETEDSSRISWFMGTISSVQVSDPLYWPDSPWRLLQVTWDEPD 382 (715)
Q Consensus 329 ~w~~GmRFkM~fE~EDss~~~wf~GTI~~v~~~Dp~~wP~S~WR~LqV~WDe~~ 382 (715)
.|.+|..+...+ .+. .||.|+|.++.. + ....|.-++-.
T Consensus 2 ~~~~G~~~~a~~-~d~----~wyra~I~~~~~-------~---~~~~V~f~D~G 40 (57)
T smart00333 2 TFKVGDKVAARW-EDG----EWYRARIIKVDG-------E---QLYEVFFIDYG 40 (57)
T ss_pred CCCCCCEEEEEe-CCC----CEEEEEEEEECC-------C---CEEEEEEECCC
Confidence 588999999999 444 699999999963 2 44567766643
No 27
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=33.35 E-value=57 Score=29.92 Aligned_cols=28 Identities=21% Similarity=0.427 Sum_probs=22.4
Q ss_pred hhcccCCCCCCEEEEEEecCCcEEEEEE
Q 005075 194 FVNHKKLVAGDSIVFLRAENGDLCVGIR 221 (715)
Q Consensus 194 FV~~K~L~aGD~VvF~R~~nG~l~VGIR 221 (715)
|.-...|++||.|..+|.++|..++-+-
T Consensus 71 i~~~~~Lk~GD~V~ll~~~~gQ~yiVlD 98 (100)
T PF10844_consen 71 ITFTDGLKVGDKVLLLRVQGGQKYIVLD 98 (100)
T ss_pred EEEecCCcCCCEEEEEEecCCCEEEEEE
Confidence 5667789999999999998887665443
No 28
>KOG3938 consensus RGS-GAIP interacting protein GIPC, contains PDZ domain [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=33.25 E-value=55 Score=35.72 Aligned_cols=72 Identities=22% Similarity=0.250 Sum_probs=51.1
Q ss_pred ecccceeeecccCCcCCHHHHHHHHHHhhCCCccccceeEEEe-eCCCCeEecCCcchhhhcc-------ceEEEcccCc
Q 005075 624 MESEDVGRTLDLSLLGSYDELYKKLAEMFGIENAETLSHLLYR-DVTGAVKHIGDEPFRFQLF-------RLLAIFSLYT 695 (715)
Q Consensus 624 meG~~vgR~vDLs~~~sY~eL~~~L~~MF~~~~~~l~~~v~Y~-D~eGd~mlvGD~Pw~~F~~-------krl~I~~~~~ 695 (715)
-+|.|+|| +..|++-+|||..+++-|.|...++.+.-+-. --|=+.||-|-.-+++|+- |.+.| ++
T Consensus 61 AHGSptg~---Ie~fsnv~ELY~kIAe~F~Is~~dIlfcTlNshKvDM~~llgGqigleDfiFAHvkGq~kEv~v---~K 134 (334)
T KOG3938|consen 61 AHGSPTGR---IEGFSNVRELYQKIAEAFDISPDDILFCTLNSHKVDMKRLLGGQIGLEDFIFAHVKGQAKEVEV---VK 134 (334)
T ss_pred ccCCccce---ecccccHHHHHHHHHHHhcCCccceEEEecCCCcccHHHHhcCccChhhhhhhhhcCcceeEEE---Ee
Confidence 36888998 46789999999999999999876654321110 1233458889999999975 77888 55
Q ss_pred cccccC
Q 005075 696 IISLKG 701 (715)
Q Consensus 696 ~~~~~~ 701 (715)
.++.-+
T Consensus 135 sedalG 140 (334)
T KOG3938|consen 135 SEDALG 140 (334)
T ss_pred cccccc
Confidence 555433
No 29
>TIGR01439 lp_hng_hel_AbrB looped-hinge helix DNA binding domain, AbrB family. This DNA-binding domain family includes AbrB, a transition state regulator in Bacillus subtilis, whose DNA-binding domain structure in solution was determined by NMR. The domain binds DNA as a dimer in what is termed a looped-hinge helix fold. Some members of the family have two copies of the domain in tandem. The domain is found usually at the N-terminus of a small protein. This model excludes members of family TIGR02609.
Probab=30.12 E-value=66 Score=24.13 Aligned_cols=27 Identities=22% Similarity=0.469 Sum_probs=22.2
Q ss_pred hhhhcccCCCCCCEEEEEEecCCcEEE
Q 005075 192 STFVNHKKLVAGDSIVFLRAENGDLCV 218 (715)
Q Consensus 192 s~FV~~K~L~aGD~VvF~R~~nG~l~V 218 (715)
..|.++-++..||.|.+....+|.+.+
T Consensus 13 ~~~r~~l~~~~gd~~~i~~~~~~~l~l 39 (43)
T TIGR01439 13 KEIREKLGLKEGDRLEVIRVEDGEIIL 39 (43)
T ss_pred HHHHHHcCcCCCCEEEEEEeCCCEEEE
Confidence 467889999999999999877776543
No 30
>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=29.21 E-value=1.3e+02 Score=25.72 Aligned_cols=68 Identities=19% Similarity=0.191 Sum_probs=48.7
Q ss_pred ceEEEEecccce---eeecccCCcCCHHHHHHHHHHhhCCCccccceeEE-Eee-CCCCeEecCC-cchhhhcc
Q 005075 618 GHCKVFMESEDV---GRTLDLSLLGSYDELYKKLAEMFGIENAETLSHLL-YRD-VTGAVKHIGD-EPFRFQLF 685 (715)
Q Consensus 618 ~~vKV~meG~~v---gR~vDLs~~~sY~eL~~~L~~MF~~~~~~l~~~v~-Y~D-~eGd~mlvGD-~Pw~~F~~ 685 (715)
+.+||+++...- -++|-++...+-.|++..+.+.|++....-.+.|+ +.- ......|-.| .|+.....
T Consensus 3 ~~lrVy~~~~~~~~~~k~i~v~~~tTa~evi~~~l~k~~l~~~~~~y~L~~~~~~~~~er~L~~~E~pl~i~~~ 76 (93)
T PF00788_consen 3 GVLRVYDGDGSPGSTYKTIKVSSSTTAREVIEMALEKFGLAEDPSDYCLVEVEESGGEERPLDDDECPLQIQLQ 76 (93)
T ss_dssp EEEEEEETTSSSCCSEEEEEEETTSBHHHHHHHHHHHTTTSSSGGGEEEEEEECTTTEEEEETTTSBHHHHHHT
T ss_pred eEEEEEcCCCCCCccEEEEEECCCCCHHHHHHHHHHHhCCCCCCCCEEEEEEEcCCCEEEEcCCCCchHHHHHh
Confidence 578999988653 68899999999999999999999994434457774 444 4444444444 36666554
No 31
>cd01789 Alp11_N Ubiquitin-like domain of Alp11 tubulin-folding cofactor B. Alp11, also known as tubulin-folding cofactor B, is one of at least three proteins required for the proper folding of tubulins prior to their incorporation into microtubules. These cofactors are necessary for the biogenesis of microtubules and for cell viability. Alp11 has three domains including an N-terminal ubiquitin-like domain (represented by this CD) which executes the essential function, a central coiled-coil domain necessary for maintenance of cellular alpha-tubulin levels, and a C-terminal CLIP-170 domain is required for efficient binding to alpha-tubulin.
Probab=27.75 E-value=2e+02 Score=25.38 Aligned_cols=40 Identities=20% Similarity=0.120 Sum_probs=27.7
Q ss_pred ceeeecccCCcCCHHHHHHHHHHhhCCCccccceeEEEeeCCCC
Q 005075 628 DVGRTLDLSLLGSYDELYKKLAEMFGIENAETLSHLLYRDVTGA 671 (715)
Q Consensus 628 ~vgR~vDLs~~~sY~eL~~~L~~MF~~~~~~l~~~v~Y~D~eGd 671 (715)
..-|+++ ..-+..+|..+|+.+||+.-+.+ +|.|.|.+|.
T Consensus 14 ~~ekr~~--~~~Tv~~lK~kl~~~~G~~~~~m--rL~l~~~~~~ 53 (84)
T cd01789 14 SFEKKYS--RGLTIAELKKKLELVVGTPASSM--RLQLFDGDDK 53 (84)
T ss_pred eeeEecC--CCCcHHHHHHHHHHHHCCCccce--EEEEEcCCCC
Confidence 3445555 45689999999999999976443 5655555543
No 32
>PF14847 Ras_bdg_2: Ras-binding domain of Byr2; PDB: 1I35_A 1K8R_B.
Probab=26.41 E-value=2.2e+02 Score=26.83 Aligned_cols=67 Identities=13% Similarity=0.162 Sum_probs=42.0
Q ss_pred eEEEEecccceeeecccCCcCCHHHHHHHHHHhhCCCccccceeEEEeeC----CCCeEecCCcchhhhcc
Q 005075 619 HCKVFMESEDVGRTLDLSLLGSYDELYKKLAEMFGIENAETLSHLLYRDV----TGAVKHIGDEPFRFQLF 685 (715)
Q Consensus 619 ~vKV~meG~~vgR~vDLs~~~sY~eL~~~L~~MF~~~~~~l~~~v~Y~D~----eGd~mlvGD~Pw~~F~~ 685 (715)
||+.+......-|+||.+-..+.+++..+.-+=||+.+..-.|.+...|. +....++.|+=.-..|.
T Consensus 1 hvi~~I~~dG~tk~VNV~~c~~a~eI~~rvLKKfg~~~~~~~~~~~v~d~~~~~~~~~~~LsD~EL~~IC~ 71 (105)
T PF14847_consen 1 HVIRFILEDGSTKTVNVSGCFNAQEIKRRVLKKFGLPEHPRNYCFYVLDGESPDPSNCRPLSDVELVTICH 71 (105)
T ss_dssp -EEEEEETTTEEEEEE--S--HHHHHHHHHHHHHTSS--CCCEEEEEE-S-----SSEEEE-SSHHHHHHH
T ss_pred CEEEEECCCCcEEEEEECCCCCHHHHHHHHHHHcCCccccccceEEEecccccccccceECcHHHHHHHHc
Confidence 35555554568899999999999999999999999987433454434444 67888999985555565
No 33
>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=24.14 E-value=1.3e+02 Score=25.01 Aligned_cols=31 Identities=19% Similarity=0.386 Sum_probs=22.6
Q ss_pred cccEEEEEeeeCCCCceeeeeeEEEEeecCCC
Q 005075 332 SGMRFKMAFETEDSSRISWFMGTISSVQVSDP 363 (715)
Q Consensus 332 ~GmRFkM~fE~EDss~~~wf~GTI~~v~~~Dp 363 (715)
+|-|+.-.||.++.+... |.|+|...-+..|
T Consensus 1 vGk~Veh~~~~g~g~~s~-w~G~Vl~Qvp~~p 31 (50)
T PF02513_consen 1 VGKRVEHTWEDGDGPKSK-WKGMVLHQVPAKP 31 (50)
T ss_dssp TT-EEEEEECTSTS-EEE-EEEEEEEE-TTST
T ss_pred CCceEEEEEccCCCcccE-EEEEEEEEeecCC
Confidence 578999999988888755 5999999876655
No 34
>PRK03760 hypothetical protein; Provisional
Probab=21.35 E-value=1.7e+02 Score=27.81 Aligned_cols=49 Identities=22% Similarity=0.413 Sum_probs=30.8
Q ss_pred eEEEEEeCCCCeEEEEE-----EEe-CCCCceee--ccCchhhhcccCCCCCCEEEEEEe
Q 005075 160 QTILAKDVHGETWKFRH-----IYR-GTPRRHLL--TTGWSTFVNHKKLVAGDSIVFLRA 211 (715)
Q Consensus 160 q~L~~~D~~G~~W~Fr~-----~yr-~~~rr~lL--TtGWs~FV~~K~L~aGD~VvF~R~ 211 (715)
.++.+.|.+|++-.... +|. ..+-+|+| ..|| +.+.++++||.|.|.|+
T Consensus 61 LDiiFld~~g~Vv~i~~~~P~~~~~~~~~a~~VLEl~aG~---~~~~gi~~Gd~v~~~~~ 117 (117)
T PRK03760 61 IDVIFLDSNRRVVDFKTLKPWRIYVPKKPARYIIEGPVGK---IRVLKVEVGDEIEWIDE 117 (117)
T ss_pred eEEEEECCCCeEEEEEeCCCccccCCCccceEEEEeCCCh---HHHcCCCCCCEEEEeeC
Confidence 34555665555443311 122 23456776 5776 78899999999998763
No 35
>KOG3207 consensus Beta-tubulin folding cofactor E [Posttranslational modification, protein turnover, chaperones]
Probab=21.33 E-value=1e+02 Score=35.87 Aligned_cols=42 Identities=24% Similarity=0.472 Sum_probs=27.8
Q ss_pred cccccEEEEEeeeCCCCceeeeeeEEEEeecCCCCCCCCCCccceecccCcccccCC
Q 005075 330 WCSGMRFKMAFETEDSSRISWFMGTISSVQVSDPLYWPDSPWRLLQVTWDEPDLLQN 386 (715)
Q Consensus 330 w~~GmRFkM~fE~EDss~~~wf~GTI~~v~~~Dp~~wP~S~WR~LqV~WDe~~~~~~ 386 (715)
..+|.|+|..+|- .. -+|.|+|.+ |++ +| |.|.||++.-..+
T Consensus 3 ~~IG~RvkI~~~~---~T-vr~iG~V~g--------~~~-~w--~GvEWDd~~RGKH 44 (505)
T KOG3207|consen 3 MEIGTRVKIGGEI---AT-VRYIGEVEG--------NNS-KW--YGVEWDDPVRGKH 44 (505)
T ss_pred eeccceEEEcCEE---EE-EEEEEEEcC--------CCC-cc--eeeEecCCCcccc
Confidence 4689999987742 11 246676643 444 45 8899999976543
No 36
>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=20.30 E-value=91 Score=29.69 Aligned_cols=26 Identities=23% Similarity=0.442 Sum_probs=17.0
Q ss_pred cCCCCCCEEEEEEec-CCcEEEEEEEe
Q 005075 198 KKLVAGDSIVFLRAE-NGDLCVGIRRA 223 (715)
Q Consensus 198 K~L~aGD~VvF~R~~-nG~l~VGIRRa 223 (715)
++++.||.|+||... .+.-+||+=+-
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 489999999999988 56666666544
Done!