Query 005482
Match_columns 694
No_of_seqs 353 out of 838
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 00:09:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/005482.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/005482hhsearch_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 2E-35 4.3E-40 257.6 8.9 83 289-372 1-83 (83)
2 PF02309 AUX_IAA: AUX/IAA fami 100.0 1.4E-32 3E-37 276.5 0.4 88 606-693 107-212 (215)
3 PF02362 B3: B3 DNA binding do 99.7 5.3E-17 1.2E-21 142.7 10.7 97 127-228 1-99 (100)
4 KOG0644 Uncharacterized conser 99.6 6.2E-16 1.3E-20 176.1 4.5 166 205-397 874-1044(1113)
5 PF09217 EcoRII-N: Restriction 98.1 1.6E-05 3.5E-10 77.2 9.1 91 123-214 6-110 (156)
6 PF03754 DUF313: Domain of unk 97.4 0.0002 4.4E-09 66.9 5.4 79 123-202 20-114 (114)
7 PF00564 PB1: PB1 domain; Int 96.2 0.016 3.5E-07 49.7 7.1 67 610-679 3-70 (84)
8 cd06407 PB1_NLP A PB1 domain i 95.6 0.04 8.6E-07 48.8 6.9 57 610-669 2-58 (82)
9 cd05992 PB1 The PB1 domain is 95.5 0.056 1.2E-06 46.0 7.4 65 611-679 3-69 (81)
10 cd06398 PB1_Joka2 The PB1 doma 95.5 0.046 1E-06 49.3 7.0 68 610-680 2-72 (91)
11 cd06396 PB1_NBR1 The PB1 domai 95.5 0.044 9.5E-07 48.7 6.6 64 610-677 2-66 (81)
12 smart00666 PB1 PB1 domain. Pho 95.1 0.094 2E-06 44.9 7.4 66 610-679 3-69 (81)
13 cd06403 PB1_Par6 The PB1 domai 94.2 0.14 3.1E-06 45.3 6.5 67 611-679 3-70 (80)
14 cd06409 PB1_MUG70 The MUG70 pr 92.8 0.17 3.8E-06 45.4 4.7 51 619-669 8-61 (86)
15 cd06401 PB1_TFG The PB1 domain 92.1 0.7 1.5E-05 41.2 7.5 72 611-684 3-79 (81)
16 cd06404 PB1_aPKC PB1 domain is 91.3 0.6 1.3E-05 41.8 6.2 57 610-669 2-58 (83)
17 cd06402 PB1_p62 The PB1 domain 88.1 1.8 3.8E-05 39.2 6.7 58 610-669 2-65 (87)
18 cd06408 PB1_NoxR The PB1 domai 87.2 1.5 3.2E-05 39.6 5.7 55 609-669 3-57 (86)
19 cd06397 PB1_UP1 Uncharacterize 86.5 1.7 3.7E-05 38.8 5.6 66 611-680 3-69 (82)
20 cd06406 PB1_P67 A PB1 domain i 68.7 18 0.00039 32.4 6.5 69 611-684 5-76 (80)
21 KOG0644 Uncharacterized conser 66.5 4.3 9.3E-05 49.3 2.9 62 36-97 872-940 (1113)
22 smart00743 Agenet Tudor-like d 61.8 12 0.00026 30.5 3.9 28 326-357 2-29 (61)
23 cd06399 PB1_P40 The PB1 domain 46.8 34 0.00074 31.3 4.5 41 625-669 23-63 (92)
24 PF04014 Antitoxin-MazE: Antid 46.6 24 0.00052 27.7 3.2 27 197-223 13-39 (47)
25 smart00333 TUDOR Tudor domain. 36.0 54 0.0012 25.9 3.8 50 326-393 2-51 (57)
26 PF10844 DUF2577: Protein of u 34.9 50 0.0011 30.2 3.8 27 199-225 71-97 (100)
27 TIGR01439 lp_hng_hel_AbrB loop 34.6 49 0.0011 24.7 3.2 27 197-223 13-39 (43)
28 PF02513 Spin-Ssty: Spin/Ssty 30.1 92 0.002 25.7 4.1 31 329-360 1-31 (50)
29 PF00788 RA: Ras association ( 29.8 1.7E+02 0.0036 25.0 6.1 69 609-677 3-77 (93)
30 KOG3207 Beta-tubulin folding c 27.2 73 0.0016 36.9 4.2 42 327-383 3-44 (505)
31 cd01789 Alp11_N Ubiquitin-like 26.4 2.1E+02 0.0045 25.2 6.1 34 626-661 19-52 (84)
32 PF11515 Cul7: Mouse developme 25.4 87 0.0019 28.1 3.5 57 315-379 6-62 (78)
33 PF05641 Agenet: Agenet domain 24.7 1E+02 0.0023 26.0 3.8 42 327-379 1-42 (68)
34 PF01878 EVE: EVE domain; Int 22.3 81 0.0018 29.9 3.0 27 203-229 38-65 (143)
35 PF03120 DNA_ligase_OB: NAD-de 20.2 74 0.0016 28.6 2.1 33 197-229 42-75 (82)
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=2e-35 Score=257.62 Aligned_cols=83 Identities=61% Similarity=0.989 Sum_probs=80.6
Q ss_pred HHHHHHcCCcEEEEEecCCCCCceEEehHHHHHHHhcCcccccEEEEEeecCCCCceeeeeeEEEEeecCCCCCCCCCCc
Q 005482 289 AAALAANGQPFEVVYYPRASTPEFVVKASAVRAAMQIQWCSGMRFKMAFETEDSSRISWFMGTISSVQVADPIRWPNSPW 368 (694)
Q Consensus 289 Aa~~aa~g~~F~V~YyPR~~~~eFvV~~~~y~~A~~~~w~~GmRFkM~fE~eDss~~~w~~GTI~~v~~~dp~~wp~S~W 368 (694)
||++|++|++|+|+||||++++||||++++|++||+++|++||||||+||+||+++++ |+|||+||++.||++||+|+|
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 6899999999999999999999999999999999999999999999999999999965 599999999999999999999
Q ss_pred ccee
Q 005482 369 RLLQ 372 (694)
Q Consensus 369 R~L~ 372 (694)
||||
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=99.97 E-value=1.4e-32 Score=276.54 Aligned_cols=88 Identities=35% Similarity=0.570 Sum_probs=0.0
Q ss_pred CceeeEEEEEccceeeccccCCCcCCHHHHHHHHHhhh---CCC----------CC-CC----ceeEEEEeCCCCeEEcC
Q 005482 606 LEMGHCKVFMESEDVGRTLDLSVLGSYEELYGKLANMF---GIE----------SA-EM----FSNVLYRDAAGSVKHTG 667 (694)
Q Consensus 606 ~~~~~~KV~meG~~vGR~vDL~~~~sY~eL~~~L~~MF---~i~----------~~-~l----~~~v~Y~D~eGd~mlvG 667 (694)
..+.||||+|||++|||||||++|+||++|+.+|++|| +|. +. ++ .|+|||+|+||||||||
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 666 11 12 47899999999999999
Q ss_pred CCChHHHHhcceeEEEecCCCCCCCC
Q 005482 668 DEPFSEFLKTARRLTILTDSGSDSVG 693 (694)
Q Consensus 668 D~PW~~F~~~vkrl~I~~~~~~~~~~ 693 (694)
||||++||++||||+||+.++..+|+
T Consensus 187 D~PW~~F~~~vkRl~I~~~~e~~~~~ 212 (215)
T PF02309_consen 187 DVPWEEFVKSVKRLRIMKSSEAKGLA 212 (215)
T ss_dssp --------------------------
T ss_pred CCCHHHHHHHhhccEEecHHHhcccC
Confidence 99999999999999999999988875
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=99.71 E-value=5.3e-17 Score=142.72 Aligned_cols=97 Identities=31% Similarity=0.410 Sum_probs=74.7
Q ss_pred EEEecccccCCCCCceEEcccchhhcCCCCCCCCCCCceEEEEEecCCCeEEEEEEEeCCCCceeeccCchhhhcccCCc
Q 005482 127 FAKTLTQSDANNGGGFSVPRYCAETIFPRLDYSAEPPVQTILAKDVHGEVWKFRHIYRGTPRRHLLTTGWSNFVNQKKLV 206 (694)
Q Consensus 127 F~K~LT~SDv~~~grfsVPk~~Ae~~FP~Ld~~~~~p~q~L~~~D~~G~~W~Fr~~yr~~~rr~lLTtGWs~FV~~K~L~ 206 (694)
|.|+|+++|+.+.++|.||+++++.+. ++. ...+.+.++|..|+.|.+++.+++.+.+++|++||..||++++|+
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 899999999999999999999999971 111 124689999999999999999999889999999999999999999
Q ss_pred CCCEEEEEEccC--CcEEEEEEEc
Q 005482 207 AGDSIVFLRAEN--GDLCVGIRRA 228 (694)
Q Consensus 207 aGD~VvF~R~~~--G~l~VGIRR~ 228 (694)
+||.|+|+...+ .++.|.|+|+
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=99.59 E-value=6.2e-16 Score=176.06 Aligned_cols=166 Identities=22% Similarity=0.419 Sum_probs=131.9
Q ss_pred CcCCCEEEEEEccCCcEEEEEEEcccCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccc---ccCCCCCCccCcc
Q 005482 205 LVAGDSIVFLRAENGDLCVGIRRAKKGGIGGGSDYSVGWNSGGGNCGFPFGGYSGYMREDENKS---SRRNSSSDLRGRV 281 (694)
Q Consensus 205 L~aGD~VvF~R~~~G~l~VGIRR~~~~~~~~~p~s~~~w~~~~~~~~~~~~~~s~~lr~~e~~~---~~~~~~~~~~~~v 281 (694)
.+.||.|+.+|....++.-.+|+...--++ -.+||- |-++..+..+ ..|..+....||+
T Consensus 874 pQmgDEViyfrQghqeyl~~~~~n~~~~~~-----~~p~~~-------------~~v~~~kv~kl~~~~y~~~~~s~c~m 935 (1113)
T KOG0644|consen 874 PQMGDEVIYFRQGHQEYLEAVRLNNIELNN-----KEPWNK-------------MAVEICKVEKLVYITYPGSGDSCCKM 935 (1113)
T ss_pred ccccceeehhhhhhHHHHhhhhhccccccc-----cCcccc-------------cchhhheeeeeeeeeccCCCcchhee
Confidence 458999999999888877777766652222 245653 3343333222 2356666678889
Q ss_pred ChHHHHHHHHHHHcCCcEEEEEecCCCCCceEEehHHHHHHHhcCcccccEEEEEee--cCCCCceeeeeeEEEEeecCC
Q 005482 282 RAESVTEAAALAANGQPFEVVYYPRASTPEFVVKASAVRAAMQIQWCSGMRFKMAFE--TEDSSRISWFMGTISSVQVAD 359 (694)
Q Consensus 282 ~~~~V~~Aa~~aa~g~~F~V~YyPR~~~~eFvV~~~~y~~A~~~~w~~GmRFkM~fE--~eDss~~~w~~GTI~~v~~~d 359 (694)
++ +|++.+. -+-.+.|.+.|....+.+||+|.++.|++|++++|.++++||..+. +|+-- +||.|+|.++++.+
T Consensus 936 ~l-~~idp~s-~~~~k~F~ltlpdlv~fpDFlV~rsrYd~AiQrnW~~~d~crvwwrda~~e~g--~WWeG~ils~~pks 1011 (1113)
T KOG0644|consen 936 KL-AVIDPAS-KLMDKSFKLTLPDLVTFPDFLVERSRYDAAIQRNWTCRDKCRVWWRDAGEEDG--AWWEGRILSVKPKS 1011 (1113)
T ss_pred ee-eeecchh-hhhhccceeecccccCcchhhhhhhhHHHHHhhccccccceeEEEccCCCcCC--ceeeeeeeeccCCC
Confidence 88 5889666 5566789999999999999999999999999999999999999995 33322 59999999999999
Q ss_pred CCCCCCCCccceeccccCccccCCCCccccceeeeccC
Q 005482 360 PIRWPNSPWRLLQVAWDEPDLLQNVKRVSPWLVELVSN 397 (694)
Q Consensus 360 p~~wp~S~WR~L~V~WDe~~~~~~~~RVSPWeIE~v~~ 397 (694)
| .+|+|+|.++.|+||..+ .+.-||||+|++..
T Consensus 1012 p-~fpdSpwery~v~~~~~e----~~~~spwe~~~i~d 1044 (1113)
T KOG0644|consen 1012 P-DFPDSPWERYIVRYDNTE----TELHSPWEMEPIPD 1044 (1113)
T ss_pred C-CCCCCcceeEEEEecCCc----ccccCccccCCCcc
Confidence 9 999999999999999998 68889999998863
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=98.07 E-value=1.6e-05 Score=77.19 Aligned_cols=91 Identities=22% Similarity=0.293 Sum_probs=59.2
Q ss_pred cceEEEEecccccCCCCC----ceEEcccchhhcCCCCCC-CCCCCceEEEEEecCC--CeEEEEEEEeCC------CCc
Q 005482 123 KPASFAKTLTQSDANNGG----GFSVPRYCAETIFPRLDY-SAEPPVQTILAKDVHG--EVWKFRHIYRGT------PRR 189 (694)
Q Consensus 123 ~~~~F~K~LT~SDv~~~g----rfsVPk~~Ae~~FP~Ld~-~~~~p~q~L~~~D~~G--~~W~Fr~~yr~~------~rr 189 (694)
....|+|.|++.|++.+| |+-|||..++..||.+.. +..+|...|.+++..| ..|+||++|.|+ ...
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 347899999999999764 799999999999998765 6677889999999888 568999999988 577
Q ss_pred eeeccCchhhhcccC-CcCCCEEEEE
Q 005482 190 HLLTTGWSNFVNQKK-LVAGDSIVFL 214 (694)
Q Consensus 190 ~lLTtGWs~FV~~K~-L~aGD~VvF~ 214 (694)
+.|| .|...-.--+ =..||-+||.
T Consensus 86 ~RIT-~~G~~~~~~~~~~tGaL~vla 110 (156)
T PF09217_consen 86 YRIT-RFGRGFPLQNPENTGALLVLA 110 (156)
T ss_dssp EEEE----TTSGGG-GGGTT-EEEEE
T ss_pred eEEe-eecCCCccCCccccccEEEEE
Confidence 8886 4544333111 2467777765
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=97.44 E-value=0.0002 Score=66.90 Aligned_cols=79 Identities=18% Similarity=0.217 Sum_probs=60.5
Q ss_pred cceEEEEecccccCCC-CCceEEcccchhhcCCCCCC------------CCCCCceEEEEEecCCCeEEEEEEEeCC---
Q 005482 123 KPASFAKTLTQSDANN-GGGFSVPRYCAETIFPRLDY------------SAEPPVQTILAKDVHGEVWKFRHIYRGT--- 186 (694)
Q Consensus 123 ~~~~F~K~LT~SDv~~-~grfsVPk~~Ae~~FP~Ld~------------~~~~p~q~L~~~D~~G~~W~Fr~~yr~~--- 186 (694)
....|.|+|++||+.. ..||+||-..... ...|.. ....-+..+.+.|..++.|..++..|..
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 3588999999999985 5899999876533 222221 1122356788999999999999999966
Q ss_pred CCceeeccCchhhhcc
Q 005482 187 PRRHLLTTGWSNFVNQ 202 (694)
Q Consensus 187 ~rr~lLTtGWs~FV~~ 202 (694)
...|+|++||..+|++
T Consensus 99 ~~~YvL~~gWn~VV~~ 114 (114)
T PF03754_consen 99 TSNYVLNSGWNKVVED 114 (114)
T ss_pred ceEEEEEcChHhhccC
Confidence 4789999999999864
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=96.25 E-value=0.016 Score=49.66 Aligned_cols=67 Identities=21% Similarity=0.368 Sum_probs=53.9
Q ss_pred eEEEEEccceeeccccCCCcCCHHHHHHHHHhhhCCCCCCCceeEEEEeCCCCeEEcCCC-ChHHHHhcce
Q 005482 610 HCKVFMESEDVGRTLDLSVLGSYEELYGKLANMFGIESAEMFSNVLYRDAAGSVKHTGDE-PFSEFLKTAR 679 (694)
Q Consensus 610 ~~KV~meG~~vGR~vDL~~~~sY~eL~~~L~~MF~i~~~~l~~~v~Y~D~eGd~mlvGD~-PW~~F~~~vk 679 (694)
.+|+...|. +=|.+.+..--+|++|..++++.|++.+ -...+.|.|.|||+..+-++ =|.+.+..++
T Consensus 3 ~vK~~~~~~-~~~~~~~~~~~s~~~L~~~i~~~~~~~~--~~~~l~Y~D~dgD~V~i~sd~Dl~~a~~~~~ 70 (84)
T PF00564_consen 3 RVKVRYGGD-IRRIISLPSDVSFDDLRSKIREKFGLLD--EDFQLKYKDEDGDLVTISSDEDLQEAIEQAK 70 (84)
T ss_dssp EEEEEETTE-EEEEEEECSTSHHHHHHHHHHHHHTTST--SSEEEEEEETTSSEEEESSHHHHHHHHHHHH
T ss_pred EEEEEECCe-eEEEEEcCCCCCHHHHHHHHHHHhCCCC--ccEEEEeeCCCCCEEEeCCHHHHHHHHHHHH
Confidence 579999885 4446888888899999999999999972 23688999999999988754 5777777765
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=95.62 E-value=0.04 Score=48.78 Aligned_cols=57 Identities=16% Similarity=0.127 Sum_probs=43.6
Q ss_pred eEEEEEccceeeccccCCCcCCHHHHHHHHHhhhCCCCCCCceeEEEEeCCCCeEEcCCC
Q 005482 610 HCKVFMESEDVGRTLDLSVLGSYEELYGKLANMFGIESAEMFSNVLYRDAAGSVKHTGDE 669 (694)
Q Consensus 610 ~~KV~meG~~vGR~vDL~~~~sY~eL~~~L~~MF~i~~~~l~~~v~Y~D~eGd~mlvGD~ 669 (694)
-+||...|.- +.+-|..--+|++|.++++++|++.. .-.+.|-|.|.||||..+--+
T Consensus 2 ~vK~~~~~d~--~r~~l~~~~~~~~L~~~i~~r~~~~~-~~~f~LkY~Ddegd~v~ltsd 58 (82)
T cd06407 2 RVKATYGEEK--IRFRLPPSWGFTELKQEIAKRFKLDD-MSAFDLKYLDDDEEWVLLTCD 58 (82)
T ss_pred EEEEEeCCeE--EEEEcCCCCCHHHHHHHHHHHhCCCC-CCeeEEEEECCCCCeEEeecH
Confidence 4799998863 34445555599999999999999963 234688899999999877543
No 9
>cd05992 PB1 The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as a noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.
Probab=95.54 E-value=0.056 Score=45.99 Aligned_cols=65 Identities=28% Similarity=0.386 Sum_probs=49.0
Q ss_pred EEEEEccceeeccccCC-CcCCHHHHHHHHHhhhCCCCCCCceeEEEEeCCCCeEEcCC-CChHHHHhcce
Q 005482 611 CKVFMESEDVGRTLDLS-VLGSYEELYGKLANMFGIESAEMFSNVLYRDAAGSVKHTGD-EPFSEFLKTAR 679 (694)
Q Consensus 611 ~KV~meG~~vGR~vDL~-~~~sY~eL~~~L~~MF~i~~~~l~~~v~Y~D~eGd~mlvGD-~PW~~F~~~vk 679 (694)
+||+-.|.. |.+-+. .--+|++|..+|.+.|++.. ....+.|.|.|||+..+.+ +=|++-++.++
T Consensus 3 vK~~~~~~~--~~~~~~~~~~s~~~L~~~i~~~~~~~~--~~~~l~y~D~e~d~v~l~sd~Dl~~a~~~~~ 69 (81)
T cd05992 3 VKVKYGGEI--RRFVVVSRSISFEDLRSKIAEKFGLDA--VSFKLKYPDEDGDLVTISSDEDLEEAIEEAR 69 (81)
T ss_pred EEEEecCCC--EEEEEecCCCCHHHHHHHHHHHhCCCC--CcEEEEeeCCCCCEEEeCCHHHHHHHHHHHh
Confidence 677777642 333333 78899999999999999864 3458889999999999887 45666566554
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=95.49 E-value=0.046 Score=49.32 Aligned_cols=68 Identities=16% Similarity=0.190 Sum_probs=51.9
Q ss_pred eEEEEEccceeeccccCC---CcCCHHHHHHHHHhhhCCCCCCCceeEEEEeCCCCeEEcCCCChHHHHhccee
Q 005482 610 HCKVFMESEDVGRTLDLS---VLGSYEELYGKLANMFGIESAEMFSNVLYRDAAGSVKHTGDEPFSEFLKTARR 680 (694)
Q Consensus 610 ~~KV~meG~~vGR~vDL~---~~~sY~eL~~~L~~MF~i~~~~l~~~v~Y~D~eGd~mlvGD~PW~~F~~~vkr 680 (694)
-+||..+|.-+==++++. .--+|++|..++++.|.+.. ...+.+.|.|.+|||..+-++ .++...+.+
T Consensus 2 ~vKv~y~~~~rRf~l~~~~~~~d~~~~~L~~kI~~~f~l~~-~~~~~l~Y~Dedgd~V~l~~D--~DL~~a~~~ 72 (91)
T cd06398 2 VVKVKYGGTLRRFTFPVAENQLDLNMDGLREKVEELFSLSP-DADLSLTYTDEDGDVVTLVDD--NDLTDAIQY 72 (91)
T ss_pred EEEEEeCCEEEEEEeccccccCCCCHHHHHHHHHHHhCCCC-CCcEEEEEECCCCCEEEEccH--HHHHHHHHH
Confidence 368999886444455543 45799999999999999964 445688999999999998776 666665554
No 11
>cd06396 PB1_NBR1 The PB1 domain is an essential part of NBR1 protein, next to BRCA1, a scaffold protein mediating specific protein-protein interaction with both titin protein kinase and with another scaffold protein p62. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The NBR1 protein contains a type I PB1 domain.
Probab=95.48 E-value=0.044 Score=48.69 Aligned_cols=64 Identities=17% Similarity=0.186 Sum_probs=50.9
Q ss_pred eEEEEEccceeeccccCCCcCCHHHHHHHHHhhhCCCCCCCceeEEEEeCCCCeEEcC-CCChHHHHhc
Q 005482 610 HCKVFMESEDVGRTLDLSVLGSYEELYGKLANMFGIESAEMFSNVLYRDAAGSVKHTG-DEPFSEFLKT 677 (694)
Q Consensus 610 ~~KV~meG~~vGR~vDL~~~~sY~eL~~~L~~MF~i~~~~l~~~v~Y~D~eGd~mlvG-D~PW~~F~~~ 677 (694)
.+||.-.|..+==+++-+.--+|++|..+++++|++. ...|-|.|.||||.++- |.=.++.++.
T Consensus 2 ~vKaty~~d~~rf~~~~~~~~~~~~L~~ev~~rf~l~----~f~lKYlDde~e~v~lssd~eLeE~~rl 66 (81)
T cd06396 2 NLKVTYNGESQSFLVSDSENTTWASVEAMVKVSFGLN----DIQIKYVDEENEEVSVNSQGEYEEALKS 66 (81)
T ss_pred EEEEEECCeEEEEEecCCCCCCHHHHHHHHHHHhCCC----cceeEEEcCCCCEEEEEchhhHHHHHHH
Confidence 3789998887777777777889999999999999998 46888999999998764 3334444443
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=95.07 E-value=0.094 Score=44.86 Aligned_cols=66 Identities=23% Similarity=0.316 Sum_probs=50.0
Q ss_pred eEEEEEccceeeccccCCCcCCHHHHHHHHHhhhCCCCCCCceeEEEEeCCCCeEEcCC-CChHHHHhcce
Q 005482 610 HCKVFMESEDVGRTLDLSVLGSYEELYGKLANMFGIESAEMFSNVLYRDAAGSVKHTGD-EPFSEFLKTAR 679 (694)
Q Consensus 610 ~~KV~meG~~vGR~vDL~~~~sY~eL~~~L~~MF~i~~~~l~~~v~Y~D~eGd~mlvGD-~PW~~F~~~vk 679 (694)
-+||.-.| -=|.+-+..--+|++|+.++.+.|++.. -...+-|+|.|||+..+.+ +=|.+-+.+++
T Consensus 3 ~vK~~~~~--~~~~~~~~~~~s~~dL~~~i~~~~~~~~--~~~~l~Y~Dedgd~v~l~sd~Dl~~a~~~~~ 69 (81)
T smart00666 3 DVKLRYGG--ETRRLSVPRDISFEDLRSKVAKRFGLDN--QSFTLKYQDEDGDLVSLTSDEDLEEAIEEYD 69 (81)
T ss_pred cEEEEECC--EEEEEEECCCCCHHHHHHHHHHHhCCCC--CCeEEEEECCCCCEEEecCHHHHHHHHHHHH
Confidence 36777754 3577778888899999999999999864 2357789999999987665 45666666554
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=94.23 E-value=0.14 Score=45.27 Aligned_cols=67 Identities=22% Similarity=0.305 Sum_probs=49.6
Q ss_pred EEEEEccceeeccccCCCcCCHHHHHHHHHhhhCCCCCCCceeEEEEeCCCCeEEcCCC-ChHHHHhcce
Q 005482 611 CKVFMESEDVGRTLDLSVLGSYEELYGKLANMFGIESAEMFSNVLYRDAAGSVKHTGDE-PFSEFLKTAR 679 (694)
Q Consensus 611 ~KV~meG~~vGR~vDL~~~~sY~eL~~~L~~MF~i~~~~l~~~v~Y~D~eGd~mlvGD~-PW~~F~~~vk 679 (694)
||...+.+--==.+|.....+|++++..|+.|+.|.+ +...|-|.|.+||.+-+-.+ -+..=+.+++
T Consensus 3 VKSkfdaEfRRFsl~r~~~~~f~ef~~ll~~lH~l~~--~~f~i~Y~D~~gDLLPInNDdNf~kAlssa~ 70 (80)
T cd06403 3 VKSKFDAEFRRFSLDRNKPGKFEDFYKLLEHLHHIPN--VDFLIGYTDPHGDLLPINNDDNFLKALSSAN 70 (80)
T ss_pred eecccCCeEEEEEeccccCcCHHHHHHHHHHHhCCCC--CcEEEEEeCCCCCEecccCcHHHHHHHHcCC
Confidence 5555655533336777788999999999999999976 44577899999999988654 4444445555
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=92.80 E-value=0.17 Score=45.39 Aligned_cols=51 Identities=20% Similarity=0.245 Sum_probs=39.6
Q ss_pred eeeccccCC--CcCCHHHHHHHHHhhhCCCCC-CCceeEEEEeCCCCeEEcCCC
Q 005482 619 DVGRTLDLS--VLGSYEELYGKLANMFGIESA-EMFSNVLYRDAAGSVKHTGDE 669 (694)
Q Consensus 619 ~vGR~vDL~--~~~sY~eL~~~L~~MF~i~~~-~l~~~v~Y~D~eGd~mlvGD~ 669 (694)
+-||.+=++ ...|+.+|..++++-|+++.. .-.+++.|.|+||||.++--+
T Consensus 8 ~~GrvhRf~~~~s~~~~~L~~~I~~Rl~~d~~~~~~~~L~YlDDEgD~VllT~D 61 (86)
T cd06409 8 PKGRVHRFRLRPSESLEELRTLISQRLGDDDFETHLYALSYVDDEGDIVLITSD 61 (86)
T ss_pred CCCCEEEEEecCCCCHHHHHHHHHHHhCCccccCCcccEEEEcCCCCEEEEecc
Confidence 456665444 368999999999999999863 245789999999999877533
No 15
>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=92.15 E-value=0.7 Score=41.24 Aligned_cols=72 Identities=19% Similarity=0.250 Sum_probs=48.5
Q ss_pred EEEEEccceeeccccCCCc-CCHHHHHHHHHhhhCCC-CCCCceeEEEEeCCCCeEEcCCC---ChHHHHhcceeEEEe
Q 005482 611 CKVFMESEDVGRTLDLSVL-GSYEELYGKLANMFGIE-SAEMFSNVLYRDAAGSVKHTGDE---PFSEFLKTARRLTIL 684 (694)
Q Consensus 611 ~KV~meG~~vGR~vDL~~~-~sY~eL~~~L~~MF~i~-~~~l~~~v~Y~D~eGd~mlvGD~---PW~~F~~~vkrl~I~ 684 (694)
+|+..+| +|=| +-+..- -+|.+|...+++.|... +..-...|-|.|.|||+.-+-+. -|..=+...+||+|.
T Consensus 3 iK~~~g~-DiR~-~~~~~~~~t~~~L~~~v~~~F~~~~~~~~~flIKYkD~dGDlVTIts~~dL~~A~~~~~~~~l~~~ 79 (81)
T cd06401 3 LKAQLGD-DIRR-IPIHNEDITYDELLLMMQRVFRGKLGSSDDVLIKYKDEDGDLITIFDSSDLSFAIQCSRILKLTLF 79 (81)
T ss_pred EEEEeCC-eEEE-EeccCccccHHHHHHHHHHHhccccCCcccEEEEEECCCCCEEEeccHHHHHHHHhcCcceEEEEe
Confidence 5666644 5655 444332 39999999999999954 21223456699999999999875 344445556677664
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=91.29 E-value=0.6 Score=41.82 Aligned_cols=57 Identities=16% Similarity=0.161 Sum_probs=45.5
Q ss_pred eEEEEEccceeeccccCCCcCCHHHHHHHHHhhhCCCCCCCceeEEEEeCCCCeEEcCCC
Q 005482 610 HCKVFMESEDVGRTLDLSVLGSYEELYGKLANMFGIESAEMFSNVLYRDAAGSVKHTGDE 669 (694)
Q Consensus 610 ~~KV~meG~~vGR~vDL~~~~sY~eL~~~L~~MF~i~~~~l~~~v~Y~D~eGd~mlvGD~ 669 (694)
.+|+.-.|..+-=.+|. .-+|++|.+++.+||.... +-..++-|.|.|||.--+...
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 36888988655555665 6689999999999999854 445789999999999887754
No 17
>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=88.08 E-value=1.8 Score=39.15 Aligned_cols=58 Identities=22% Similarity=0.410 Sum_probs=41.9
Q ss_pred eEEEEEcc----ceeec-cccCCCcCCHHHHHHHHHhhhC-CCCCCCceeEEEEeCCCCeEEcCCC
Q 005482 610 HCKVFMES----EDVGR-TLDLSVLGSYEELYGKLANMFG-IESAEMFSNVLYRDAAGSVKHTGDE 669 (694)
Q Consensus 610 ~~KV~meG----~~vGR-~vDL~~~~sY~eL~~~L~~MF~-i~~~~l~~~v~Y~D~eGd~mlvGD~ 669 (694)
.||.+..| ..|=| +||=....+|++|+..+.++|- +.+ -..++-|.|.|||..-+..+
T Consensus 2 ~vkayl~~~~~~~EIRRf~l~~~~~~s~~~L~~~V~~~f~~l~~--~~ftlky~DeeGDlvtIssd 65 (87)
T cd06402 2 TVKAYLLGKDANAEIRRFAIDEDVSTSYEYLVEKVAAVFPSLRG--KNFQLFWKDEEGDLVAFSSD 65 (87)
T ss_pred eEEEeecCCCCccceEEEEecCCCCcCHHHHHHHHHHHccccCC--CcEEEEEECCCCCEEeecCH
Confidence 46666665 23322 3455667799999999999995 333 34688899999999888765
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=87.19 E-value=1.5 Score=39.55 Aligned_cols=55 Identities=18% Similarity=0.341 Sum_probs=44.6
Q ss_pred eeEEEEEccceeeccccCCCcCCHHHHHHHHHhhhCCCCCCCceeEEEEeCCCCeEEcCCC
Q 005482 609 GHCKVFMESEDVGRTLDLSVLGSYEELYGKLANMFGIESAEMFSNVLYRDAAGSVKHTGDE 669 (694)
Q Consensus 609 ~~~KV~meG~~vGR~vDL~~~~sY~eL~~~L~~MF~i~~~~l~~~v~Y~D~eGd~mlvGD~ 669 (694)
-.|||+-+|. -|.|-+..-=+|++|.+++.++|++.. ...|-|.|. ||+.-+++.
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 4689998886 456666666679999999999999963 357779999 999998875
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=86.46 E-value=1.7 Score=38.79 Aligned_cols=66 Identities=18% Similarity=0.291 Sum_probs=50.2
Q ss_pred EEEEEccceeeccccCCCcCCHHHHHHHHHhhhCCCCCCCceeEEEEeCCCCeEEc-CCCChHHHHhccee
Q 005482 611 CKVFMESEDVGRTLDLSVLGSYEELYGKLANMFGIESAEMFSNVLYRDAAGSVKHT-GDEPFSEFLKTARR 680 (694)
Q Consensus 611 ~KV~meG~~vGR~vDL~~~~sY~eL~~~L~~MF~i~~~~l~~~v~Y~D~eGd~mlv-GD~PW~~F~~~vkr 680 (694)
-||..+| --|++....-=+|.+|.++|+.+|.|.-. ..-|+|.|.+||..-+ -|+=.++|.+-..|
T Consensus 3 fKv~~~g--~~RRf~~~~~pt~~~L~~kl~~Lf~lp~~--~~~vtYiDeD~D~ITlssd~eL~d~~~~~~~ 69 (82)
T cd06397 3 FKSSFLG--DTRRIVFPDIPTWEALASKLENLYNLPEI--KVGVTYIDNDNDEITLSSNKELQDFYRLSHR 69 (82)
T ss_pred EEEEeCC--ceEEEecCCCccHHHHHHHHHHHhCCChh--HeEEEEEcCCCCEEEecchHHHHHHHHhccc
Confidence 3777766 46777777788999999999999999742 2578899999998755 44566677665555
No 20
>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=68.71 E-value=18 Score=32.39 Aligned_cols=69 Identities=20% Similarity=0.300 Sum_probs=51.6
Q ss_pred EEEEEccceeeccccCCCcCCHHHHHHHHHhhhCCCCCCCceeEEEEeCC-CCeEEcCCCChHHHHhcce--eEEEe
Q 005482 611 CKVFMESEDVGRTLDLSVLGSYEELYGKLANMFGIESAEMFSNVLYRDAA-GSVKHTGDEPFSEFLKTAR--RLTIL 684 (694)
Q Consensus 611 ~KV~meG~~vGR~vDL~~~~sY~eL~~~L~~MF~i~~~~l~~~v~Y~D~e-Gd~mlvGD~PW~~F~~~vk--rl~I~ 684 (694)
+||+.++ -| +|-...=-+|.+|++.|.+-+.+.+++ .+|-|.|.+ |+...++|.=++.=.+.|+ ||+..
T Consensus 5 vKV~f~~-tI--aIrvp~~~~y~~L~~ki~~kLkl~~e~--i~LsYkde~s~~~v~l~d~dle~aws~~~~~~lTLw 76 (80)
T cd06406 5 VKVHFKY-TV--AIQVARGLSYATLLQKISSKLELPAEH--ITLSYKSEASGEDVILSDTNMEDVWSQAKDGCLTLW 76 (80)
T ss_pred EEEEEEE-EE--EEEcCCCCCHHHHHHHHHHHhCCCchh--cEEEeccCCCCCccCcChHHHHHHHHhhcCCeEEEE
Confidence 5999998 23 455556678999999999999997533 367799865 3444559999988888877 67653
No 21
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=66.52 E-value=4.3 Score=49.30 Aligned_cols=62 Identities=24% Similarity=0.522 Sum_probs=47.4
Q ss_pred cCCCCCCeEEEeecchhhcccCC----CCCC---CCCCCCccceEEEEEEeeccccccceeEEEEEeec
Q 005482 36 QMPQINSKVFYFPQGHLEHAKGN----VELP---NFNIPSMIPCRVTAIKFMADAETDEVYARIRLIAL 97 (694)
Q Consensus 36 ~~P~~gs~V~YFPqGH~Eq~~~~----~~~~---~~~~P~~i~CrV~~V~l~Ad~~TDEVyA~i~L~P~ 97 (694)
-||..|..|.||-|||-|-+.+. .++. ..++-..-.|.|..+..-.-|....--.++.|.=+
T Consensus 872 yipQmgDEViyfrQghqeyl~~~~~n~~~~~~~~p~~~~~v~~~kv~kl~~~~y~~~~~s~c~m~l~~i 940 (1113)
T KOG0644|consen 872 YIPQMGDEVIYFRQGHQEYLEAVRLNNIELNNKEPWNKMAVEICKVEKLVYITYPGSGDSCCKMKLAVI 940 (1113)
T ss_pred ccccccceeehhhhhhHHHHhhhhhccccccccCcccccchhhheeeeeeeeeccCCCcchheeeeeee
Confidence 68999999999999999999872 2331 12445567899999888777777777777777644
No 22
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=61.79 E-value=12 Score=30.45 Aligned_cols=28 Identities=25% Similarity=0.465 Sum_probs=23.8
Q ss_pred CcccccEEEEEeecCCCCceeeeeeEEEEeec
Q 005482 326 QWCSGMRFKMAFETEDSSRISWFMGTISSVQV 357 (694)
Q Consensus 326 ~w~~GmRFkM~fE~eDss~~~w~~GTI~~v~~ 357 (694)
.|.+|+++-..++.++ +||.|+|+.+..
T Consensus 2 ~~~~G~~Ve~~~~~~~----~W~~a~V~~~~~ 29 (61)
T smart00743 2 DFKKGDRVEVFSKEED----SWWEAVVTKVLG 29 (61)
T ss_pred CcCCCCEEEEEECCCC----EEEEEEEEEECC
Confidence 5889999999996545 899999999863
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=46.77 E-value=34 Score=31.31 Aligned_cols=41 Identities=27% Similarity=0.288 Sum_probs=33.6
Q ss_pred cCCCcCCHHHHHHHHHhhhCCCCCCCceeEEEEeCCCCeEEcCCC
Q 005482 625 DLSVLGSYEELYGKLANMFGIESAEMFSNVLYRDAAGSVKHTGDE 669 (694)
Q Consensus 625 DL~~~~sY~eL~~~L~~MF~i~~~~l~~~v~Y~D~eGd~mlvGD~ 669 (694)
||+.--+|.+|.....+-|..+. ..+=|+|.|||..-+=|+
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 78899999999999999998875 245599999998765444
No 24
>PF04014 Antitoxin-MazE: Antidote-toxin recognition MazE; InterPro: IPR007159 This domain is found in AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation []. AbrB is thought to interact directly with the transcription initiation regions of genes under its control []. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins []. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator []. DNA-binding activity in this AbrB homologue requires hexamerisation []. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins [].; PDB: 2L66_A 2GLW_A 3TND_D 2W1T_B 2RO5_B 2FY9_A 2RO3_B 1UB4_C 3ZVK_G 1YFB_B ....
Probab=46.61 E-value=24 Score=27.70 Aligned_cols=27 Identities=15% Similarity=0.311 Sum_probs=22.7
Q ss_pred hhhhcccCCcCCCEEEEEEccCCcEEE
Q 005482 197 SNFVNQKKLVAGDSIVFLRAENGDLCV 223 (694)
Q Consensus 197 s~FV~~K~L~aGD~VvF~R~~~G~l~V 223 (694)
.+|.++.+|.+||.|.|.-.++|++.+
T Consensus 13 k~~~~~l~l~~Gd~v~i~~~~~g~i~i 39 (47)
T PF04014_consen 13 KEIREKLGLKPGDEVEIEVEGDGKIVI 39 (47)
T ss_dssp HHHHHHTTSSTTTEEEEEEETTSEEEE
T ss_pred HHHHHHcCCCCCCEEEEEEeCCCEEEE
Confidence 367788899999999999998886554
No 25
>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=36.00 E-value=54 Score=25.93 Aligned_cols=50 Identities=16% Similarity=0.278 Sum_probs=33.8
Q ss_pred CcccccEEEEEeecCCCCceeeeeeEEEEeecCCCCCCCCCCccceeccccCccccCCCCccccceee
Q 005482 326 QWCSGMRFKMAFETEDSSRISWFMGTISSVQVADPIRWPNSPWRLLQVAWDEPDLLQNVKRVSPWLVE 393 (694)
Q Consensus 326 ~w~~GmRFkM~fE~eDss~~~w~~GTI~~v~~~dp~~wp~S~WR~L~V~WDe~~~~~~~~RVSPWeIE 393 (694)
.|.+|..+...+ .+. .||.|+|+++.. + ....|.-++-.. .+-|...+|-
T Consensus 2 ~~~~G~~~~a~~-~d~----~wyra~I~~~~~-------~---~~~~V~f~D~G~---~~~v~~~~l~ 51 (57)
T smart00333 2 TFKVGDKVAARW-EDG----EWYRARIIKVDG-------E---QLYEVFFIDYGN---EEVVPPSDLR 51 (57)
T ss_pred CCCCCCEEEEEe-CCC----CEEEEEEEEECC-------C---CEEEEEEECCCc---cEEEeHHHee
Confidence 688999999998 444 799999999963 2 446677766442 3444444443
No 26
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=34.86 E-value=50 Score=30.18 Aligned_cols=27 Identities=22% Similarity=0.450 Sum_probs=22.1
Q ss_pred hhcccCCcCCCEEEEEEccCCcEEEEE
Q 005482 199 FVNQKKLVAGDSIVFLRAENGDLCVGI 225 (694)
Q Consensus 199 FV~~K~L~aGD~VvF~R~~~G~l~VGI 225 (694)
|.-...|++||.|..+|..+|..++-+
T Consensus 71 i~~~~~Lk~GD~V~ll~~~~gQ~yiVl 97 (100)
T PF10844_consen 71 ITFTDGLKVGDKVLLLRVQGGQKYIVL 97 (100)
T ss_pred EEEecCCcCCCEEEEEEecCCCEEEEE
Confidence 566678999999999999888766544
No 27
>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=34.58 E-value=49 Score=24.72 Aligned_cols=27 Identities=22% Similarity=0.492 Sum_probs=22.4
Q ss_pred hhhhcccCCcCCCEEEEEEccCCcEEE
Q 005482 197 SNFVNQKKLVAGDSIVFLRAENGDLCV 223 (694)
Q Consensus 197 s~FV~~K~L~aGD~VvF~R~~~G~l~V 223 (694)
..|.++-++..||.|.+....+|.+.+
T Consensus 13 ~~~r~~l~~~~gd~~~i~~~~~~~l~l 39 (43)
T TIGR01439 13 KEIREKLGLKEGDRLEVIRVEDGEIIL 39 (43)
T ss_pred HHHHHHcCcCCCCEEEEEEeCCCEEEE
Confidence 478899999999999999877776543
No 28
>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=30.07 E-value=92 Score=25.75 Aligned_cols=31 Identities=23% Similarity=0.400 Sum_probs=22.9
Q ss_pred cccEEEEEeecCCCCceeeeeeEEEEeecCCC
Q 005482 329 SGMRFKMAFETEDSSRISWFMGTISSVQVADP 360 (694)
Q Consensus 329 ~GmRFkM~fE~eDss~~~w~~GTI~~v~~~dp 360 (694)
+|-|+.-.||.++.+... |.|+|...-++.|
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 588999999998888755 5999999876655
No 29
>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=29.76 E-value=1.7e+02 Score=25.02 Aligned_cols=69 Identities=17% Similarity=0.210 Sum_probs=49.1
Q ss_pred eeEEEEEcccee---eccccCCCcCCHHHHHHHHHhhhCCCCCCCceeEE-EEeCCC-CeEEcCCC-ChHHHHhc
Q 005482 609 GHCKVFMESEDV---GRTLDLSVLGSYEELYGKLANMFGIESAEMFSNVL-YRDAAG-SVKHTGDE-PFSEFLKT 677 (694)
Q Consensus 609 ~~~KV~meG~~v---GR~vDL~~~~sY~eL~~~L~~MF~i~~~~l~~~v~-Y~D~eG-d~mlvGD~-PW~~F~~~ 677 (694)
..+||+++...- -++|-++....-.+++..+.+.|++.+..-.|.|+ +.-..| ...|-.|+ |+......
T Consensus 3 ~~lrVy~~~~~~~~~~k~i~v~~~tTa~evi~~~l~k~~l~~~~~~y~L~~~~~~~~~er~L~~~E~pl~i~~~~ 77 (93)
T PF00788_consen 3 GVLRVYDGDGSPGSTYKTIKVSSSTTAREVIEMALEKFGLAEDPSDYCLVEVEESGGEERPLDDDECPLQIQLQW 77 (93)
T ss_dssp EEEEEEETTSSSCCSEEEEEEETTSBHHHHHHHHHHHTTTSSSGGGEEEEEEECTTTEEEEETTTSBHHHHHHTT
T ss_pred eEEEEEcCCCCCCccEEEEEECCCCCHHHHHHHHHHHhCCCCCCCCEEEEEEEcCCCEEEEcCCCCchHHHHHhC
Confidence 578999987653 68899999999999999999999994433456774 444444 44444333 77766655
No 30
>KOG3207 consensus Beta-tubulin folding cofactor E [Posttranslational modification, protein turnover, chaperones]
Probab=27.23 E-value=73 Score=36.95 Aligned_cols=42 Identities=24% Similarity=0.476 Sum_probs=27.7
Q ss_pred cccccEEEEEeecCCCCceeeeeeEEEEeecCCCCCCCCCCccceeccccCccccCC
Q 005482 327 WCSGMRFKMAFETEDSSRISWFMGTISSVQVADPIRWPNSPWRLLQVAWDEPDLLQN 383 (694)
Q Consensus 327 w~~GmRFkM~fE~eDss~~~w~~GTI~~v~~~dp~~wp~S~WR~L~V~WDe~~~~~~ 383 (694)
..+|.|+|..+|- .. -+|.|+|.| |++ +| |.|.||++.-..+
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 4689999987652 22 246776644 444 45 7899999975543
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=26.37 E-value=2.1e+02 Score=25.19 Aligned_cols=34 Identities=24% Similarity=0.169 Sum_probs=24.0
Q ss_pred CCCcCCHHHHHHHHHhhhCCCCCCCceeEEEEeCCC
Q 005482 626 LSVLGSYEELYGKLANMFGIESAEMFSNVLYRDAAG 661 (694)
Q Consensus 626 L~~~~sY~eL~~~L~~MF~i~~~~l~~~v~Y~D~eG 661 (694)
+...-...+|..+|+.+||+.-+.+ ++.|.|.+|
T Consensus 19 ~~~~~Tv~~lK~kl~~~~G~~~~~m--rL~l~~~~~ 52 (84)
T cd01789 19 YSRGLTIAELKKKLELVVGTPASSM--RLQLFDGDD 52 (84)
T ss_pred cCCCCcHHHHHHHHHHHHCCCccce--EEEEEcCCC
Confidence 4455689999999999999976544 444444443
No 32
>PF11515 Cul7: Mouse development and cellular proliferation protein Cullin-7; InterPro: IPR021097 The CPH domain is found in the Cullin-7, PARC and HERC2 proteins, which are all components of known or predicted E3-ubiquitin ligases. The CPH domain is a protein-protein interaction module that binds the teramerisation domain of the tumour suppressor protein p53 []. Structurally it forms a beta-barrel fold similar to the SH3, Tudor and KOW and domains. Unlike the SH3 and Tudor domains, which bind to small peptides, the CPH domain appears to bind to an extended surface on p53.; PDB: 2JUF_A 2JNG_A.
Probab=25.36 E-value=87 Score=28.11 Aligned_cols=57 Identities=16% Similarity=0.160 Sum_probs=29.5
Q ss_pred ehHHHHHHHhcCcccccEEEEEeecCCCCceeeeeeEEEEeecCCCCCCCCCCccceeccccCcc
Q 005482 315 KASAVRAAMQIQWCSGMRFKMAFETEDSSRISWFMGTISSVQVADPIRWPNSPWRLLQVAWDEPD 379 (694)
Q Consensus 315 ~~~~y~~A~~~~w~~GmRFkM~fE~eDss~~~w~~GTI~~v~~~dp~~wp~S~WR~L~V~WDe~~ 379 (694)
+.+.|-.=++-+.++||++||.=.-|+-+.- =.|+|.-++. | .-|+ -.+||.|-.-.
T Consensus 6 s~d~Ya~YVr~~i~~GM~VRc~~~yeeV~~G--D~G~V~k~~~-d--g~~~---lnvqv~W~~~G 62 (78)
T PF11515_consen 6 SNDDYAEYVRDNIQPGMRVRCCRDYEEVRAG--DEGEVFKQDR-D--GLHD---LNVQVDWQSKG 62 (78)
T ss_dssp SSHHHHHHHHHH--TT-EEEESS-BTTB-TT---EEE-EEEE--T--TSSE-----EEEEETTTT
T ss_pred chhHHHHHHHHhCCCCcEEEEeccccccccc--ccceeEeecc-C--CCCC---cceEEEeeecC
Confidence 3567777788889999999997544443321 2455444442 1 1222 35788887655
No 33
>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=24.72 E-value=1e+02 Score=25.97 Aligned_cols=42 Identities=19% Similarity=0.312 Sum_probs=26.2
Q ss_pred cccccEEEEEeecCCCCceeeeeeEEEEeecCCCCCCCCCCccceeccccCcc
Q 005482 327 WCSGMRFKMAFETEDSSRISWFMGTISSVQVADPIRWPNSPWRLLQVAWDEPD 379 (694)
Q Consensus 327 w~~GmRFkM~fE~eDss~~~w~~GTI~~v~~~dp~~wp~S~WR~L~V~WDe~~ 379 (694)
|..|+++-..-+. +..+-+||.|||+..... + .+.|+.+.-.
T Consensus 1 F~~G~~VEV~s~e-~g~~gaWf~a~V~~~~~~-------~---~~~V~Y~~~~ 42 (68)
T PF05641_consen 1 FKKGDEVEVSSDE-DGFRGAWFPATVLKENGD-------D---KYLVEYDDLP 42 (68)
T ss_dssp --TT-EEEEEE-S-BTT--EEEEEEEEEEETT-----------EEEEEETT-S
T ss_pred CCCCCEEEEEEcC-CCCCcEEEEEEEEEeCCC-------c---EEEEEECCcc
Confidence 5689999887653 555779999999998742 1 7778886543
No 34
>PF01878 EVE: EVE domain; InterPro: IPR002740 The EVE domain is part of the wider PUA domain superfamily. The function of this domain is not known but, given the structural similarities to PUA, is likely to involve RNA binding []. ; PDB: 2G2X_B 2AR1_A 3EOP_A 2EVE_A 2HD9_A 2ZBN_A 1WMM_A 2P5D_A 2GBS_A 1ZCE_A.
Probab=22.30 E-value=81 Score=29.93 Aligned_cols=27 Identities=22% Similarity=0.405 Sum_probs=17.7
Q ss_pred cCCcCCCEEEEEEcc-CCcEEEEEEEcc
Q 005482 203 KKLVAGDSIVFLRAE-NGDLCVGIRRAK 229 (694)
Q Consensus 203 K~L~aGD~VvF~R~~-~G~l~VGIRR~~ 229 (694)
++++.||.|+||... .+.-+|||=+-.
T Consensus 38 ~~mk~GD~vifY~s~~~~~~ivai~~V~ 65 (143)
T PF01878_consen 38 KRMKPGDKVIFYHSGCKERGIVAIGEVV 65 (143)
T ss_dssp HC--TT-EEEEEETSSSS-EEEEEEEEE
T ss_pred hcCCCCCEEEEEEcCCCCCEEEEEEEEe
Confidence 489999999999988 566677765554
No 35
>PF03120 DNA_ligase_OB: NAD-dependent DNA ligase OB-fold domain; InterPro: IPR004150 DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This family is a small domain found after the adenylation domain DNA_ligase_N in NAD+-dependent ligases (IPR001679 from INTERPRO). OB-fold domains generally are involved in nucleic acid binding.; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 2OWO_A 1TAE_A 3UQ8_A 1DGS_A 1V9P_B 3SGI_A.
Probab=20.18 E-value=74 Score=28.59 Aligned_cols=33 Identities=21% Similarity=0.416 Sum_probs=22.0
Q ss_pred hhhhcccCCcCCCEEEEEEccCCc-EEEEEEEcc
Q 005482 197 SNFVNQKKLVAGDSIVFLRAENGD-LCVGIRRAK 229 (694)
Q Consensus 197 s~FV~~K~L~aGD~VvF~R~~~G~-l~VGIRR~~ 229 (694)
..|+++++|..||.|.++|..+.= ..+++-..+
T Consensus 42 ~~~i~~~~i~~Gd~V~V~raGdVIP~I~~vv~~~ 75 (82)
T PF03120_consen 42 YDYIKELDIRIGDTVLVTRAGDVIPKIVGVVKEK 75 (82)
T ss_dssp HHHHHHTT-BBT-EEEEEEETTTEEEEEEE-GGG
T ss_pred HHHHHHcCCCCCCEEEEEECCCccceEeEeehhc
Confidence 489999999999999999987653 233444333
Done!