Query 023966
Match_columns 274
No_of_seqs 179 out of 549
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 07:56:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023966.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023966hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02309 AUX_IAA: AUX/IAA fami 100.0 2.3E-62 5E-67 434.9 0.5 212 14-266 3-215 (215)
2 PF00564 PB1: PB1 domain; Int 97.3 0.00065 1.4E-08 51.0 5.8 67 154-249 3-70 (84)
3 cd06398 PB1_Joka2 The PB1 doma 97.1 0.0019 4.2E-08 51.5 7.0 68 154-250 2-72 (91)
4 cd06407 PB1_NLP A PB1 domain i 97.0 0.0023 4.9E-08 50.1 6.7 55 154-237 2-56 (82)
5 smart00666 PB1 PB1 domain. Pho 96.9 0.0059 1.3E-07 45.8 7.6 65 155-249 4-69 (81)
6 cd05992 PB1 The PB1 domain is 96.8 0.0075 1.6E-07 44.9 7.6 66 154-249 2-69 (81)
7 cd06396 PB1_NBR1 The PB1 domai 96.7 0.0064 1.4E-07 48.0 6.6 52 155-236 3-54 (81)
8 cd06401 PB1_TFG The PB1 domain 96.6 0.013 2.9E-07 46.3 7.7 73 155-254 3-79 (81)
9 cd06402 PB1_p62 The PB1 domain 95.5 0.06 1.3E-06 43.0 6.8 59 153-238 1-64 (87)
10 cd06404 PB1_aPKC PB1 domain is 95.4 0.053 1.2E-06 43.1 6.1 55 155-238 3-57 (83)
11 cd06403 PB1_Par6 The PB1 domai 95.3 0.053 1.1E-06 42.9 5.9 68 155-250 3-71 (80)
12 cd06409 PB1_MUG70 The MUG70 pr 95.0 0.05 1.1E-06 43.3 5.0 51 162-237 7-59 (86)
13 cd06397 PB1_UP1 Uncharacterize 94.1 0.17 3.8E-06 40.2 6.2 66 155-250 3-69 (82)
14 cd06408 PB1_NoxR The PB1 domai 86.0 3 6.5E-05 33.4 6.3 65 153-249 3-68 (86)
15 cd06399 PB1_P40 The PB1 domain 63.4 13 0.00028 30.2 4.2 38 167-234 21-58 (92)
16 cd06395 PB1_Map2k5 PB1 domain 48.1 34 0.00073 27.7 4.2 48 160-236 9-56 (91)
17 PF10411 DsbC_N: Disulfide bon 46.2 16 0.00035 26.3 2.0 17 223-239 34-50 (57)
18 PF07929 PRiA4_ORF3: Plasmid p 40.3 62 0.0013 27.9 5.1 35 154-188 6-42 (179)
19 cd06406 PB1_P67 A PB1 domain i 29.7 2.7E+02 0.0057 22.1 6.6 69 154-253 4-75 (80)
20 PF14688 DUF4461: Domain of un 21.0 62 0.0013 31.2 1.9 23 227-249 92-117 (313)
21 KOG3957 Predicted L-carnitine 20.9 1.3E+02 0.0028 30.1 4.1 80 164-260 177-256 (387)
No 1
>PF02309 AUX_IAA: AUX/IAA family; InterPro: IPR003311 The Aux/IAA family of genes are key regulators of auxin-modified gene expression []. The plant hormone auxin (indole-3-acetic acid, IAA) regulates diverse cellular and developmental responses in plants, including cell division, expansion, differentiation and patterning of embryo responses []. Auxin can regulate the gene expression of several families, including GH3 and SAUR, as well as Aux/IAA itself. The Aux/IAA proteins act as repressors of auxin-induced gene expression, possibly through modulating the activity of DNA-binding auxin response factors (ARFs) (IPR010525 from INTERPRO). Aux/IAA and ARF are thought to interact through C-terminal protein-protein interaction domains found in both Aux/IAA and ARF. Recent evidence suggests that Aux/IAA proteins can also mediate light responses []. Some members of the AUX/IAA family are longer and contain an N-terminal DNA binding domain [] and may have an early function in the establishment of vascular and body patterns in embryonic and post-embryonic development in some plants.; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2P1N_F 2P1Q_C 2P1O_C.
Probab=100.00 E-value=2.3e-62 Score=434.88 Aligned_cols=212 Identities=38% Similarity=0.564 Sum_probs=6.0
Q ss_pred cccceeecCCCCCCCCCccccccccccCCCccccccccchhhhccccc-ccccCcccCcchhhhhhccCCCCCccccccc
Q 023966 14 DKKLELRLAPPSPEQDKFPIFLGHSTRNNGFHGAKRAFEDTLRSQGVA-GKQEGFLKSSSSVVAEILYPDKNAFSVAANT 92 (274)
Q Consensus 14 ~kklELrLGpPG~~~~~~~~~~~~~~~~~~~~~akr~~s~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 92 (274)
-|+|||||||||.+++. ....-......++.||+|+++|..+... +.............. . ... ....
T Consensus 3 ~~~TELrLGLPG~~~~~---~~~~~~~~~~~~~~kR~F~~aid~~~~~~~~~~~~~~~~~~~~~-~----~~~---~~~~ 71 (215)
T PF02309_consen 3 LKATELRLGLPGSESPD---ASSSSSSKKSSSGNKRGFSEAIDSSSSNSQSSSSSSSDSSSSSS-S----SST---SSSS 71 (215)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred chhhhhcccCCCCCCCC---cccccccccccCcccccchhhhhhcccccccccccccccCcccc-c----ccc---cccc
Confidence 47899999999987543 0111123456888899999998866522 111111111100000 0 000 0011
Q ss_pred cccCCCCCCCCCCCccccCCccchhcccccCCCCCCCCCCCCCcchHHHHHhhhcccCCccceEEEecCcccceeeccCC
Q 023966 93 AVTNGSNKRTAPAPVVGWPPIGSFRKNLAAGGSSLSKPDTKPDETTEERIAAKSESLKTNLFVKINMEGVPIGRKINLSA 172 (274)
Q Consensus 93 ~~~~~~~~r~a~~qVVGWPPVrs~RkN~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VKV~MdG~pIGRKVDL~~ 172 (274)
...+....+.+++++|||||||+||+|++... .....++||||+|||+||||||||++
T Consensus 72 ~~~~~~~~p~~~~~~vgwpp~~s~r~n~~~~~----------------------~~~~~~~~vKV~mdG~~igRkVDL~~ 129 (215)
T PF02309_consen 72 SDSSSSSPPASKAQVVGWPPVRSFRKNSLSEK----------------------QSSSSRSYVKVNMDGVPIGRKVDLSA 129 (215)
T ss_dssp --------------BTTBS----S--------------------------------------------------------
T ss_pred cccccCCCCcccccccCCCccccccccccccc----------------------ccccCCceeEEEecCcccceecCHHH
Confidence 11111223446789999999999999988732 01123689999999999999999999
Q ss_pred CCCHHHHHHHHHHHhccccccccchhhhcccccccCCccccCCCCCCCceEEEEecCCCCeEEccCcChhHHhhcceEEE
Q 023966 173 YNSYEELSFAIDELFKGLLPVQQDLFAAGCKNKMEGSKIDTSSVAKSDEYTLLYEDNEGDRMLVGDVPWHMFVSTVKKLL 252 (274)
Q Consensus 173 ~~sY~eL~~aLe~MF~~~~~~q~~~~~~~~~~~~~e~~~~~~ll~gs~eyvltYEDkEGDwMLVGDVPW~mFv~svKRLr 252 (274)
|+||++|+.+|++||.+|.+.++++. ...+....++++++ +|+|||||+||||||||||||+|||++|||||
T Consensus 130 ~~sY~~L~~~L~~MF~~~~i~~~~~~-------~~~~~~~~~~~~~~-~~~l~Y~D~egd~mlvGD~PW~~F~~~vkRl~ 201 (215)
T PF02309_consen 130 YSSYEELSSALEKMFSCFSIEQCGSH-------GLNESGLLDLLNGS-EYVLVYEDKEGDWMLVGDVPWEEFVKSVKRLR 201 (215)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred hhCHHHHHHHHHHhcCCCCccccccc-------cccchhhccccCCc-ceeEEEECCCCCEEEecCCCHHHHHHHhhccE
Confidence 99999999999999988876665541 11122223455565 99999999999999999999999999999999
Q ss_pred EecCcccccccccc
Q 023966 253 VLKSSELSTVQTFG 266 (274)
Q Consensus 253 Imk~sea~~l~~~~ 266 (274)
||+.+|+.+|+|++
T Consensus 202 I~~~~e~~~~~~r~ 215 (215)
T PF02309_consen 202 IMKSSEAKGLAPRA 215 (215)
T ss_dssp --------------
T ss_pred EecHHHhcccCCCC
Confidence 99999999999975
No 2
>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=97.29 E-value=0.00065 Score=51.03 Aligned_cols=67 Identities=27% Similarity=0.429 Sum_probs=54.0
Q ss_pred ceEEEecCcccceeeccCCCCCHHHHHHHHHHHhccccccccchhhhcccccccCCccccCCCCCCCceEEEEecCCCCe
Q 023966 154 FVKINMEGVPIGRKINLSAYNSYEELSFAIDELFKGLLPVQQDLFAAGCKNKMEGSKIDTSSVAKSDEYTLLYEDNEGDR 233 (274)
Q Consensus 154 ~VKV~MdG~pIGRKVDL~~~~sY~eL~~aLe~MF~~~~~~q~~~~~~~~~~~~~e~~~~~~ll~gs~eyvltYEDkEGDw 233 (274)
-|||...|. +=|.+.+..--+|++|...+...|.. . ...+.|.|.|.||||
T Consensus 3 ~vK~~~~~~-~~~~~~~~~~~s~~~L~~~i~~~~~~--------------------------~--~~~~~l~Y~D~dgD~ 53 (84)
T PF00564_consen 3 RVKVRYGGD-IRRIISLPSDVSFDDLRSKIREKFGL--------------------------L--DEDFQLKYKDEDGDL 53 (84)
T ss_dssp EEEEEETTE-EEEEEEECSTSHHHHHHHHHHHHHTT--------------------------S--TSSEEEEEEETTSSE
T ss_pred EEEEEECCe-eEEEEEcCCCCCHHHHHHHHHHHhCC--------------------------C--CccEEEEeeCCCCCE
Confidence 479999996 44468888888999999999999961 0 136999999999999
Q ss_pred EEccC-cChhHHhhcce
Q 023966 234 MLVGD-VPWHMFVSTVK 249 (274)
Q Consensus 234 MLVGD-VPW~mFv~svK 249 (274)
..+-+ .=|.+.+..++
T Consensus 54 V~i~sd~Dl~~a~~~~~ 70 (84)
T PF00564_consen 54 VTISSDEDLQEAIEQAK 70 (84)
T ss_dssp EEESSHHHHHHHHHHHH
T ss_pred EEeCCHHHHHHHHHHHH
Confidence 98875 56888888775
No 3
>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=97.12 E-value=0.0019 Score=51.52 Aligned_cols=68 Identities=19% Similarity=0.290 Sum_probs=51.8
Q ss_pred ceEEEecCcccceeeccC---CCCCHHHHHHHHHHHhccccccccchhhhcccccccCCccccCCCCCCCceEEEEecCC
Q 023966 154 FVKINMEGVPIGRKINLS---AYNSYEELSFAIDELFKGLLPVQQDLFAAGCKNKMEGSKIDTSSVAKSDEYTLLYEDNE 230 (274)
Q Consensus 154 ~VKV~MdG~pIGRKVDL~---~~~sY~eL~~aLe~MF~~~~~~q~~~~~~~~~~~~~e~~~~~~ll~gs~eyvltYEDkE 230 (274)
-|||.-+|.-+=-++++. ..-+|+.|...+.+.|.- ....+|+|.|.|.|
T Consensus 2 ~vKv~y~~~~rRf~l~~~~~~~d~~~~~L~~kI~~~f~l---------------------------~~~~~~~l~Y~Ded 54 (91)
T cd06398 2 VVKVKYGGTLRRFTFPVAENQLDLNMDGLREKVEELFSL---------------------------SPDADLSLTYTDED 54 (91)
T ss_pred EEEEEeCCEEEEEEeccccccCCCCHHHHHHHHHHHhCC---------------------------CCCCcEEEEEECCC
Confidence 489999998555566664 567999999999999951 11247999999999
Q ss_pred CCeEEccCcChhHHhhcceE
Q 023966 231 GDRMLVGDVPWHMFVSTVKK 250 (274)
Q Consensus 231 GDwMLVGDVPW~mFv~svKR 250 (274)
|||..+-+. .+|..++.+
T Consensus 55 gd~V~l~~D--~DL~~a~~~ 72 (91)
T cd06398 55 GDVVTLVDD--NDLTDAIQY 72 (91)
T ss_pred CCEEEEccH--HHHHHHHHH
Confidence 999988765 555555554
No 4
>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=97.05 E-value=0.0023 Score=50.10 Aligned_cols=55 Identities=22% Similarity=0.281 Sum_probs=42.1
Q ss_pred ceEEEecCcccceeeccCCCCCHHHHHHHHHHHhccccccccchhhhcccccccCCccccCCCCCCCceEEEEecCCCCe
Q 023966 154 FVKINMEGVPIGRKINLSAYNSYEELSFAIDELFKGLLPVQQDLFAAGCKNKMEGSKIDTSSVAKSDEYTLLYEDNEGDR 233 (274)
Q Consensus 154 ~VKV~MdG~pIGRKVDL~~~~sY~eL~~aLe~MF~~~~~~q~~~~~~~~~~~~~e~~~~~~ll~gs~eyvltYEDkEGDw 233 (274)
=|||...|.- +.+-|..--+|++|...+.++|.- +..+.|.|.|.|.||||
T Consensus 2 ~vK~~~~~d~--~r~~l~~~~~~~~L~~~i~~r~~~---------------------------~~~~~f~LkY~Ddegd~ 52 (82)
T cd06407 2 RVKATYGEEK--IRFRLPPSWGFTELKQEIAKRFKL---------------------------DDMSAFDLKYLDDDEEW 52 (82)
T ss_pred EEEEEeCCeE--EEEEcCCCCCHHHHHHHHHHHhCC---------------------------CCCCeeEEEEECCCCCe
Confidence 3899998863 445555556999999999999961 01136999999999999
Q ss_pred EEcc
Q 023966 234 MLVG 237 (274)
Q Consensus 234 MLVG 237 (274)
.++-
T Consensus 53 v~lt 56 (82)
T cd06407 53 VLLT 56 (82)
T ss_pred EEee
Confidence 8763
No 5
>smart00666 PB1 PB1 domain. Phox and Bem1p domain, present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.
Probab=96.89 E-value=0.0059 Score=45.83 Aligned_cols=65 Identities=22% Similarity=0.362 Sum_probs=50.9
Q ss_pred eEEEecCcccceeeccCCCCCHHHHHHHHHHHhccccccccchhhhcccccccCCccccCCCCCCCceEEEEecCCCCeE
Q 023966 155 VKINMEGVPIGRKINLSAYNSYEELSFAIDELFKGLLPVQQDLFAAGCKNKMEGSKIDTSSVAKSDEYTLLYEDNEGDRM 234 (274)
Q Consensus 155 VKV~MdG~pIGRKVDL~~~~sY~eL~~aLe~MF~~~~~~q~~~~~~~~~~~~~e~~~~~~ll~gs~eyvltYEDkEGDwM 234 (274)
|||.-.| --|.+-+..--+|++|...+.+.|.. . ...+.|.|+|.||||.
T Consensus 4 vK~~~~~--~~~~~~~~~~~s~~dL~~~i~~~~~~---------------------------~-~~~~~l~Y~Dedgd~v 53 (81)
T smart00666 4 VKLRYGG--ETRRLSVPRDISFEDLRSKVAKRFGL---------------------------D-NQSFTLKYQDEDGDLV 53 (81)
T ss_pred EEEEECC--EEEEEEECCCCCHHHHHHHHHHHhCC---------------------------C-CCCeEEEEECCCCCEE
Confidence 6888755 35777788889999999999999961 0 1359999999999998
Q ss_pred EccC-cChhHHhhcce
Q 023966 235 LVGD-VPWHMFVSTVK 249 (274)
Q Consensus 235 LVGD-VPW~mFv~svK 249 (274)
.+.+ .=|.+.++.++
T Consensus 54 ~l~sd~Dl~~a~~~~~ 69 (81)
T smart00666 54 SLTSDEDLEEAIEEYD 69 (81)
T ss_pred EecCHHHHHHHHHHHH
Confidence 7665 57777777665
No 6
>cd05992 PB1 The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as a noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.
Probab=96.81 E-value=0.0075 Score=44.93 Aligned_cols=66 Identities=23% Similarity=0.302 Sum_probs=50.7
Q ss_pred ceEEEecCcccceeeccC-CCCCHHHHHHHHHHHhccccccccchhhhcccccccCCccccCCCCCCCceEEEEecCCCC
Q 023966 154 FVKINMEGVPIGRKINLS-AYNSYEELSFAIDELFKGLLPVQQDLFAAGCKNKMEGSKIDTSSVAKSDEYTLLYEDNEGD 232 (274)
Q Consensus 154 ~VKV~MdG~pIGRKVDL~-~~~sY~eL~~aLe~MF~~~~~~q~~~~~~~~~~~~~e~~~~~~ll~gs~eyvltYEDkEGD 232 (274)
-|||.-.|. =|.+=+. ..-+|++|...|.+.|.. . ...+.+.|.|.|||
T Consensus 2 ~vK~~~~~~--~~~~~~~~~~~s~~~L~~~i~~~~~~--------------------------~--~~~~~l~y~D~e~d 51 (81)
T cd05992 2 RVKVKYGGE--IRRFVVVSRSISFEDLRSKIAEKFGL--------------------------D--AVSFKLKYPDEDGD 51 (81)
T ss_pred cEEEEecCC--CEEEEEecCCCCHHHHHHHHHHHhCC--------------------------C--CCcEEEEeeCCCCC
Confidence 378888765 3444444 888999999999999961 0 03699999999999
Q ss_pred eEEccC-cChhHHhhcce
Q 023966 233 RMLVGD-VPWHMFVSTVK 249 (274)
Q Consensus 233 wMLVGD-VPW~mFv~svK 249 (274)
|..+.+ .=|++.++.++
T Consensus 52 ~v~l~sd~Dl~~a~~~~~ 69 (81)
T cd05992 52 LVTISSDEDLEEAIEEAR 69 (81)
T ss_pred EEEeCCHHHHHHHHHHHh
Confidence 999887 67777777765
No 7
>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=96.68 E-value=0.0064 Score=47.97 Aligned_cols=52 Identities=15% Similarity=0.289 Sum_probs=45.5
Q ss_pred eEEEecCcccceeeccCCCCCHHHHHHHHHHHhccccccccchhhhcccccccCCccccCCCCCCCceEEEEecCCCCeE
Q 023966 155 VKINMEGVPIGRKINLSAYNSYEELSFAIDELFKGLLPVQQDLFAAGCKNKMEGSKIDTSSVAKSDEYTLLYEDNEGDRM 234 (274)
Q Consensus 155 VKV~MdG~pIGRKVDL~~~~sY~eL~~aLe~MF~~~~~~q~~~~~~~~~~~~~e~~~~~~ll~gs~eyvltYEDkEGDwM 234 (274)
|||.-.|.-+--+++-++.-+|++|...+.++|. ++ .|.|.|-|.||||.
T Consensus 3 vKaty~~d~~rf~~~~~~~~~~~~L~~ev~~rf~---------------------------l~---~f~lKYlDde~e~v 52 (81)
T cd06396 3 LKVTYNGESQSFLVSDSENTTWASVEAMVKVSFG---------------------------LN---DIQIKYVDEENEEV 52 (81)
T ss_pred EEEEECCeEEEEEecCCCCCCHHHHHHHHHHHhC---------------------------CC---cceeEEEcCCCCEE
Confidence 7999999877778888888899999999999995 12 49999999999998
Q ss_pred Ec
Q 023966 235 LV 236 (274)
Q Consensus 235 LV 236 (274)
++
T Consensus 53 ~l 54 (81)
T cd06396 53 SV 54 (81)
T ss_pred EE
Confidence 86
No 8
>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=96.57 E-value=0.013 Score=46.29 Aligned_cols=73 Identities=26% Similarity=0.500 Sum_probs=50.1
Q ss_pred eEEEecCcccceeeccCCC-CCHHHHHHHHHHHhccccccccchhhhcccccccCCccccCCCCCCCceEEEEecCCCCe
Q 023966 155 VKINMEGVPIGRKINLSAY-NSYEELSFAIDELFKGLLPVQQDLFAAGCKNKMEGSKIDTSSVAKSDEYTLLYEDNEGDR 233 (274)
Q Consensus 155 VKV~MdG~pIGRKVDL~~~-~sY~eL~~aLe~MF~~~~~~q~~~~~~~~~~~~~e~~~~~~ll~gs~eyvltYEDkEGDw 233 (274)
+|+...|. | |++=+..- -+|.+|...+.+.|..- +..+..+.+.|.|.|||+
T Consensus 3 iK~~~g~D-i-R~~~~~~~~~t~~~L~~~v~~~F~~~-------------------------~~~~~~flIKYkD~dGDl 55 (81)
T cd06401 3 LKAQLGDD-I-RRIPIHNEDITYDELLLMMQRVFRGK-------------------------LGSSDDVLIKYKDEDGDL 55 (81)
T ss_pred EEEEeCCe-E-EEEeccCccccHHHHHHHHHHHhccc-------------------------cCCcccEEEEEECCCCCE
Confidence 67777653 5 44444432 39999999999999731 122457999999999999
Q ss_pred EEccCc---ChhHHhhcceEEEEe
Q 023966 234 MLVGDV---PWHMFVSTVKKLLVL 254 (274)
Q Consensus 234 MLVGDV---PW~mFv~svKRLrIm 254 (274)
.-|-+- -|..=....+||+|.
T Consensus 56 VTIts~~dL~~A~~~~~~~~l~~~ 79 (81)
T cd06401 56 ITIFDSSDLSFAIQCSRILKLTLF 79 (81)
T ss_pred EEeccHHHHHHHHhcCcceEEEEe
Confidence 999874 455444455566653
No 9
>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=95.47 E-value=0.06 Score=42.96 Aligned_cols=59 Identities=27% Similarity=0.405 Sum_probs=43.0
Q ss_pred cceEEEecC---cccceee--ccCCCCCHHHHHHHHHHHhccccccccchhhhcccccccCCccccCCCCCCCceEEEEe
Q 023966 153 LFVKINMEG---VPIGRKI--NLSAYNSYEELSFAIDELFKGLLPVQQDLFAAGCKNKMEGSKIDTSSVAKSDEYTLLYE 227 (274)
Q Consensus 153 ~~VKV~MdG---~pIGRKV--DL~~~~sY~eL~~aLe~MF~~~~~~q~~~~~~~~~~~~~e~~~~~~ll~gs~eyvltYE 227 (274)
+.||.+..| .+==|++ |=....+|+.|...+.+||... .+ ..|+|.|.
T Consensus 1 ~~vkayl~~~~~~~EIRRf~l~~~~~~s~~~L~~~V~~~f~~l--------------------------~~-~~ftlky~ 53 (87)
T cd06402 1 LTVKAYLLGKDANAEIRRFAIDEDVSTSYEYLVEKVAAVFPSL--------------------------RG-KNFQLFWK 53 (87)
T ss_pred CeEEEeecCCCCccceEEEEecCCCCcCHHHHHHHHHHHcccc--------------------------CC-CcEEEEEE
Confidence 468888877 2233444 4466679999999999999621 11 36999999
Q ss_pred cCCCCeEEccC
Q 023966 228 DNEGDRMLVGD 238 (274)
Q Consensus 228 DkEGDwMLVGD 238 (274)
|.|||..-+..
T Consensus 54 DeeGDlvtIss 64 (87)
T cd06402 54 DEEGDLVAFSS 64 (87)
T ss_pred CCCCCEEeecC
Confidence 99999987654
No 10
>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=95.37 E-value=0.053 Score=43.11 Aligned_cols=55 Identities=25% Similarity=0.309 Sum_probs=42.9
Q ss_pred eEEEecCcccceeeccCCCCCHHHHHHHHHHHhccccccccchhhhcccccccCCccccCCCCCCCceEEEEecCCCCeE
Q 023966 155 VKINMEGVPIGRKINLSAYNSYEELSFAIDELFKGLLPVQQDLFAAGCKNKMEGSKIDTSSVAKSDEYTLLYEDNEGDRM 234 (274)
Q Consensus 155 VKV~MdG~pIGRKVDL~~~~sY~eL~~aLe~MF~~~~~~q~~~~~~~~~~~~~e~~~~~~ll~gs~eyvltYEDkEGDwM 234 (274)
||+.-.|.-.--.+|. .-+|++|.+.+.+||.. .. ...|++.|.|.|||--
T Consensus 3 ~K~~y~gdi~it~~d~--~~s~e~L~~~v~~~c~~--------------------------~~-~q~ft~kw~DEEGDp~ 53 (83)
T cd06404 3 VKAAYNGDIMITSIDP--SISLEELCNEVRDMCRF--------------------------HN-DQPFTLKWIDEEGDPC 53 (83)
T ss_pred EEEEecCcEEEEEcCC--CcCHHHHHHHHHHHhCC--------------------------CC-CCcEEEEEECCCCCce
Confidence 7899999755555665 77899999999999962 01 1359999999999987
Q ss_pred EccC
Q 023966 235 LVGD 238 (274)
Q Consensus 235 LVGD 238 (274)
-+..
T Consensus 54 tiSS 57 (83)
T cd06404 54 TISS 57 (83)
T ss_pred eecC
Confidence 6654
No 11
>cd06403 PB1_Par6 The PB1 domain is an essential part of Par6 protein which in complex with Par3 and aPKC proteins is crucial for establishment of apical-basal polarity of animal cells. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. The
Probab=95.30 E-value=0.053 Score=42.88 Aligned_cols=68 Identities=15% Similarity=0.257 Sum_probs=49.9
Q ss_pred eEEEecCcccceeeccCCCCCHHHHHHHHHHHhccccccccchhhhcccccccCCccccCCCCCCCceEEEEecCCCCeE
Q 023966 155 VKINMEGVPIGRKINLSAYNSYEELSFAIDELFKGLLPVQQDLFAAGCKNKMEGSKIDTSSVAKSDEYTLLYEDNEGDRM 234 (274)
Q Consensus 155 VKV~MdG~pIGRKVDL~~~~sY~eL~~aLe~MF~~~~~~q~~~~~~~~~~~~~e~~~~~~ll~gs~eyvltYEDkEGDwM 234 (274)
||..-|..=-=-.+|.....+|+++++-|+.||. + . .-.|+|.|.|.+||.+
T Consensus 3 VKSkfdaEfRRFsl~r~~~~~f~ef~~ll~~lH~--l-------------------------~-~~~f~i~Y~D~~gDLL 54 (80)
T cd06403 3 VKSKFDAEFRRFSLDRNKPGKFEDFYKLLEHLHH--I-------------------------P-NVDFLIGYTDPHGDLL 54 (80)
T ss_pred eecccCCeEEEEEeccccCcCHHHHHHHHHHHhC--C-------------------------C-CCcEEEEEeCCCCCEe
Confidence 6666776533335566667999999999999996 1 1 1369999999999999
Q ss_pred Ecc-CcChhHHhhcceE
Q 023966 235 LVG-DVPWHMFVSTVKK 250 (274)
Q Consensus 235 LVG-DVPW~mFv~svKR 250 (274)
-+- |+-+..=+++++.
T Consensus 55 PInNDdNf~kAlssa~p 71 (80)
T cd06403 55 PINNDDNFLKALSSANP 71 (80)
T ss_pred cccCcHHHHHHHHcCCC
Confidence 775 5566666667763
No 12
>cd06409 PB1_MUG70 The MUG70 protein is a product of the meiotically up-regulated gene 70 which has a role in meiosis and harbors a PB1 domain. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domains depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic amino acid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is
Probab=94.99 E-value=0.05 Score=43.31 Aligned_cols=51 Identities=31% Similarity=0.448 Sum_probs=37.3
Q ss_pred cccceeeccC--CCCCHHHHHHHHHHHhccccccccchhhhcccccccCCccccCCCCCCCceEEEEecCCCCeEEcc
Q 023966 162 VPIGRKINLS--AYNSYEELSFAIDELFKGLLPVQQDLFAAGCKNKMEGSKIDTSSVAKSDEYTLLYEDNEGDRMLVG 237 (274)
Q Consensus 162 ~pIGRKVDL~--~~~sY~eL~~aLe~MF~~~~~~q~~~~~~~~~~~~~e~~~~~~ll~gs~eyvltYEDkEGDwMLVG 237 (274)
.|-||.+=++ ...||.+|..++.+=|+. . + .....|.|.|.|.||||.|.-
T Consensus 7 ~~~GrvhRf~~~~s~~~~~L~~~I~~Rl~~-------------d----------~--~~~~~~~L~YlDDEgD~VllT 59 (86)
T cd06409 7 DPKGRVHRFRLRPSESLEELRTLISQRLGD-------------D----------D--FETHLYALSYVDDEGDIVLIT 59 (86)
T ss_pred CCCCCEEEEEecCCCCHHHHHHHHHHHhCC-------------c----------c--ccCCcccEEEEcCCCCEEEEe
Confidence 4567765544 478999999999999961 0 0 002369999999999999863
No 13
>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=94.15 E-value=0.17 Score=40.15 Aligned_cols=66 Identities=18% Similarity=0.322 Sum_probs=49.4
Q ss_pred eEEEecCcccceeeccCCCCCHHHHHHHHHHHhccccccccchhhhcccccccCCccccCCCCCCCceEEEEecCCCCeE
Q 023966 155 VKINMEGVPIGRKINLSAYNSYEELSFAIDELFKGLLPVQQDLFAAGCKNKMEGSKIDTSSVAKSDEYTLLYEDNEGDRM 234 (274)
Q Consensus 155 VKV~MdG~pIGRKVDL~~~~sY~eL~~aLe~MF~~~~~~q~~~~~~~~~~~~~e~~~~~~ll~gs~eyvltYEDkEGDwM 234 (274)
-||+-+|. .|++....-=+|..|.+.|+.+|.- ... .+.|+|.|.|||..
T Consensus 3 fKv~~~g~--~RRf~~~~~pt~~~L~~kl~~Lf~l---------------------------p~~-~~~vtYiDeD~D~I 52 (82)
T cd06397 3 FKSSFLGD--TRRIVFPDIPTWEALASKLENLYNL---------------------------PEI-KVGVTYIDNDNDEI 52 (82)
T ss_pred EEEEeCCc--eEEEecCCCccHHHHHHHHHHHhCC---------------------------Chh-HeEEEEEcCCCCEE
Confidence 48888884 7888888889999999999999961 111 38999999999987
Q ss_pred EccC-cChhHHhhcceE
Q 023966 235 LVGD-VPWHMFVSTVKK 250 (274)
Q Consensus 235 LVGD-VPW~mFv~svKR 250 (274)
-+-| .=-++|.+-..|
T Consensus 53 Tlssd~eL~d~~~~~~~ 69 (82)
T cd06397 53 TLSSNKELQDFYRLSHR 69 (82)
T ss_pred EecchHHHHHHHHhccc
Confidence 5544 455566554444
No 14
>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=85.96 E-value=3 Score=33.36 Aligned_cols=65 Identities=20% Similarity=0.331 Sum_probs=47.5
Q ss_pred cceEEEecCcccceeeccCCCCCHHHHHHHHHHHhccccccccchhhhcccccccCCccccCCCCCCCceEEEEecCCCC
Q 023966 153 LFVKINMEGVPIGRKINLSAYNSYEELSFAIDELFKGLLPVQQDLFAAGCKNKMEGSKIDTSSVAKSDEYTLLYEDNEGD 232 (274)
Q Consensus 153 ~~VKV~MdG~pIGRKVDL~~~~sY~eL~~aLe~MF~~~~~~q~~~~~~~~~~~~~e~~~~~~ll~gs~eyvltYEDkEGD 232 (274)
+=|||+-.|. -|-|-+..-=+|++|...+.++|.- . ..++|-|.|. ||
T Consensus 3 ikVKv~~~~D--v~~i~v~~~i~f~dL~~kIrdkf~~---------------------------~--~~~~iKykDE-GD 50 (86)
T cd06408 3 IRVKVHAQDD--TRYIMIGPDTGFADFEDKIRDKFGF---------------------------K--RRLKIKMKDD-GD 50 (86)
T ss_pred EEEEEEecCc--EEEEEcCCCCCHHHHHHHHHHHhCC---------------------------C--CceEEEEEcC-CC
Confidence 4589998887 4566666666799999999999961 1 2699999999 99
Q ss_pred eEEccCc-ChhHHhhcce
Q 023966 233 RMLVGDV-PWHMFVSTVK 249 (274)
Q Consensus 233 wMLVGDV-PW~mFv~svK 249 (274)
..-++|- =-++-+.++|
T Consensus 51 ~iti~sq~DLd~Ai~~a~ 68 (86)
T cd06408 51 MITMGDQDDLDMAIDTAR 68 (86)
T ss_pred CccccCHHHHHHHHHHHH
Confidence 9888773 2334444443
No 15
>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=63.45 E-value=13 Score=30.24 Aligned_cols=38 Identities=26% Similarity=0.371 Sum_probs=30.6
Q ss_pred eeccCCCCCHHHHHHHHHHHhccccccccchhhhcccccccCCccccCCCCCCCceEEEEecCCCCeE
Q 023966 167 KINLSAYNSYEELSFAIDELFKGLLPVQQDLFAAGCKNKMEGSKIDTSSVAKSDEYTLLYEDNEGDRM 234 (274)
Q Consensus 167 KVDL~~~~sY~eL~~aLe~MF~~~~~~q~~~~~~~~~~~~~e~~~~~~ll~gs~eyvltYEDkEGDwM 234 (274)
-=||+..-+|.+|..-..+-|.. .+-+|-|.|.|||..
T Consensus 21 ee~l~~~P~~kdLl~lmr~~f~~------------------------------~dIaLNYrD~EGDLI 58 (92)
T cd06399 21 EEDLSSTPLLKDLLELTRREFQR------------------------------EDIALNYRDAEGDLI 58 (92)
T ss_pred ecccccCccHHHHHHHHHHHhch------------------------------hheeeeeecCCCCEE
Confidence 34788889999999988888852 146788999999974
No 16
>cd06395 PB1_Map2k5 PB1 domain is essential part of the mitogen-activated protein kinase kinase 5 (Map2k5, alias MEK5) one of the key member of the signaling kinases cascade which involved in angiogenesis and early cardiovascular development. The PB1 domain of Map2k5 interacts with the PB1 domain of another members of kinase cascade MEKK2 (or MEKK3). A canonical PB1-PB1 interaction, involving 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 Map2k5 protein contains a type I PB1 domain.
Probab=48.06 E-value=34 Score=27.66 Aligned_cols=48 Identities=19% Similarity=0.342 Sum_probs=33.4
Q ss_pred cCcccceeeccCCCCCHHHHHHHHHHHhccccccccchhhhcccccccCCccccCCCCCCCceEEEEecCCCCeEEc
Q 023966 160 EGVPIGRKINLSAYNSYEELSFAIDELFKGLLPVQQDLFAAGCKNKMEGSKIDTSSVAKSDEYTLLYEDNEGDRMLV 236 (274)
Q Consensus 160 dG~pIGRKVDL~~~~sY~eL~~aLe~MF~~~~~~q~~~~~~~~~~~~~e~~~~~~ll~gs~eyvltYEDkEGDwMLV 236 (274)
+|.++--.||...+=+|.+|..++.+..-.-+ --.+-|||.|||++-|
T Consensus 9 ~gg~vDw~V~~~~~L~F~DvL~~I~~vlp~aT-----------------------------~tAFeYEDE~gDRITV 56 (91)
T cd06395 9 NGGAVDWTVQSGPQLLFRDVLDVIGQVLPEAT-----------------------------TTAFEYEDEDGDRITV 56 (91)
T ss_pred CCCcccccccCcccccHHHHHHHHHHhccccc-----------------------------ccceeeccccCCeeEe
Confidence 34556667777777788888888877764111 1245699999997766
No 17
>PF10411 DsbC_N: Disulfide bond isomerase protein N-terminus; InterPro: IPR018950 This is the N-terminal domain of the disulphide bond isomerase DsbC. The whole molecule is V-shaped, where each arm is a DsbC monomer of two domains linked by a hinge; and the N-termini of each monomer join to form the dimer interface at the base of the V, so are vital for dimerisation []. DsbC is required for disulphide bond formation and functions as a disulphide bond isomerase during oxidative protein-folding in bacterial periplasm. It also has chaperone activity []. ; PDB: 1EEJ_B 2IYJ_A 1TJD_A 1JZD_B 1JZO_A 1G0T_B 1T3B_A.
Probab=46.20 E-value=16 Score=26.35 Aligned_cols=17 Identities=29% Similarity=0.741 Sum_probs=14.5
Q ss_pred EEEEecCCCCeEEccCc
Q 023966 223 TLLYEDNEGDRMLVGDV 239 (274)
Q Consensus 223 vltYEDkEGDwMLVGDV 239 (274)
-+.|.|.||+.+++|++
T Consensus 34 ~i~Y~~~dg~yli~G~l 50 (57)
T PF10411_consen 34 GILYVDEDGRYLIQGQL 50 (57)
T ss_dssp EEEEEETTSSEEEES-E
T ss_pred eEEEEcCCCCEEEEeEE
Confidence 47899999999999985
No 18
>PF07929 PRiA4_ORF3: Plasmid pRiA4b ORF-3-like protein; InterPro: IPR012912 Members of this family are similar to the protein product of ORF-3 (Q44206 from SWISSPROT) found on plasmid pRiA4 in the bacterium Agrobacterium rhizogenes. This plasmid is responsible for tumourigenesis at wound sites of plants infected by this bacterium, but the ORF-3 product does not seem to be involved in the pathogenetic process []. Other proteins found in this family are annotated as being putative TnpR resolvases (Q9LCU7 from SWISSPROT, Q50439 from SWISSPROT), but no further evidence was found to back this. Moreover, another member of this family is described as a probable lexA repressor (Q7UEI4 from SWISSPROT) and in fact carries a LexA DNA binding domain (IPR006199 from INTERPRO), but no references were found to expand on this. ; PDB: 2I1S_A.
Probab=40.33 E-value=62 Score=27.85 Aligned_cols=35 Identities=29% Similarity=0.465 Sum_probs=30.0
Q ss_pred ceEEEecCc--ccceeeccCCCCCHHHHHHHHHHHhc
Q 023966 154 FVKINMEGV--PIGRKINLSAYNSYEELSFAIDELFK 188 (274)
Q Consensus 154 ~VKV~MdG~--pIGRKVDL~~~~sY~eL~~aLe~MF~ 188 (274)
-+||..+|. +|=|.|.+..--+..+|..+|...|+
T Consensus 6 ~lkV~L~~~~p~iwRri~Vp~~~tl~~Lh~~Iq~afg 42 (179)
T PF07929_consen 6 QLKVSLKGSKPPIWRRIEVPADITLADLHEVIQAAFG 42 (179)
T ss_dssp EEEEEETT-SS-EEEEEEEETT-BHHHHHHHHHHHTT
T ss_pred EEEEEEcCCCCCeEEEEEECCCCCHHHHHHHHHHHhC
Confidence 489999885 89999999999999999999999995
No 19
>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=29.75 E-value=2.7e+02 Score=22.12 Aligned_cols=69 Identities=20% Similarity=0.253 Sum_probs=48.3
Q ss_pred ceEEEecCcccceeeccCCCCCHHHHHHHHHHHhccccccccchhhhcccccccCCccccCCCCCCCceEEEEecCCC-C
Q 023966 154 FVKINMEGVPIGRKINLSAYNSYEELSFAIDELFKGLLPVQQDLFAAGCKNKMEGSKIDTSSVAKSDEYTLLYEDNEG-D 232 (274)
Q Consensus 154 ~VKV~MdG~pIGRKVDL~~~~sY~eL~~aLe~MF~~~~~~q~~~~~~~~~~~~~e~~~~~~ll~gs~eyvltYEDkEG-D 232 (274)
-|||+-.+ -| .|-...=-+|.+|...|.+=+.- . + .+-+|.|.|.+. +
T Consensus 4 vvKV~f~~-tI--aIrvp~~~~y~~L~~ki~~kLkl--------------------------~-~-e~i~LsYkde~s~~ 52 (80)
T cd06406 4 VVKVHFKY-TV--AIQVARGLSYATLLQKISSKLEL--------------------------P-A-EHITLSYKSEASGE 52 (80)
T ss_pred EEEEEEEE-EE--EEEcCCCCCHHHHHHHHHHHhCC--------------------------C-c-hhcEEEeccCCCCC
Confidence 48999997 23 45555666899999999888851 1 1 246788988774 4
Q ss_pred eEEccCcChhHHhhcce--EEEE
Q 023966 233 RMLVGDVPWHMFVSTVK--KLLV 253 (274)
Q Consensus 233 wMLVGDVPW~mFv~svK--RLrI 253 (274)
...++|-=|+.-.+.|+ ||++
T Consensus 53 ~v~l~d~dle~aws~~~~~~lTL 75 (80)
T cd06406 53 DVILSDTNMEDVWSQAKDGCLTL 75 (80)
T ss_pred ccCcChHHHHHHHHhhcCCeEEE
Confidence 44449988888888877 5543
No 20
>PF14688 DUF4461: Domain of unknown function (DUF4461)
Probab=21.01 E-value=62 Score=31.19 Aligned_cols=23 Identities=39% Similarity=0.817 Sum_probs=18.2
Q ss_pred ecCCCCeEE-ccCcC--hhHHhhcce
Q 023966 227 EDNEGDRML-VGDVP--WHMFVSTVK 249 (274)
Q Consensus 227 EDkEGDwML-VGDVP--W~mFv~svK 249 (274)
.|-+|+.|| +|||| |..|++.+.
T Consensus 92 v~~~G~v~L~~~Dv~~~W~~~l~~l~ 117 (313)
T PF14688_consen 92 VSLDGHVMLGTGDVPHQWTSFLERLP 117 (313)
T ss_pred cCCCCCEEecCCCcHHHHHHHHHhCC
Confidence 478999888 68887 888887665
No 21
>KOG3957 consensus Predicted L-carnitine dehydratase/alpha-methylacyl-CoA racemase [Lipid transport and metabolism]
Probab=20.91 E-value=1.3e+02 Score=30.10 Aligned_cols=80 Identities=21% Similarity=0.159 Sum_probs=56.5
Q ss_pred cceeeccCCCCCHHHHHHHHHHHhccccccccchhhhcccccccCCccccCCCCCCCceEEEEecCCCCeEEccCcChhH
Q 023966 164 IGRKINLSAYNSYEELSFAIDELFKGLLPVQQDLFAAGCKNKMEGSKIDTSSVAKSDEYTLLYEDNEGDRMLVGDVPWHM 243 (274)
Q Consensus 164 IGRKVDL~~~~sY~eL~~aLe~MF~~~~~~q~~~~~~~~~~~~~e~~~~~~ll~gs~eyvltYEDkEGDwMLVGDVPW~m 243 (274)
-|-.||-++..+-.-|++-|..=+. ..+ -+... .++++|+.-+-=||+-+||-.|.||-+- .-
T Consensus 177 kGqviD~~m~eg~ayl~S~v~~~y~---~s~------------~ea~R-~~~~~G~~~~Y~tykTkDG~fmavga~e-pQ 239 (387)
T KOG3957|consen 177 KGQVIDCNMLEGVAYLLSFVQKNYL---QSL------------WEADR-YGTAHGSIPPYQTYKTKDGYFMAVGALE-PQ 239 (387)
T ss_pred CceEEEechhHhHHHHHHHHHHHhh---hhh------------ccccc-cccccCCCccceeeeccCceEEEecccc-HH
Confidence 4677888888888778777665553 110 01111 3567777666778999999999999874 35
Q ss_pred HhhcceEEEEecCcccc
Q 023966 244 FVSTVKKLLVLKSSELS 260 (274)
Q Consensus 244 Fv~svKRLrImk~sea~ 260 (274)
|...|+++..++..+..
T Consensus 240 F~~~l~~ll~~~~d~~p 256 (387)
T KOG3957|consen 240 FYELLKKLLGLKLDENP 256 (387)
T ss_pred HHHHHHHhhCcccccch
Confidence 99999998887766543
Done!