Query 029511
Match_columns 192
No_of_seqs 167 out of 545
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 14:05:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029511.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029511hhsearch_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 1.5E-56 3.2E-61 377.5 0.6 173 18-192 1-191 (215)
2 PF00564 PB1: PB1 domain; Int 97.3 0.0011 2.4E-08 47.1 6.5 55 114-187 3-57 (84)
3 cd06398 PB1_Joka2 The PB1 doma 97.1 0.0017 3.6E-08 49.1 6.6 57 114-187 2-61 (91)
4 cd06407 PB1_NLP A PB1 domain i 97.1 0.0023 4.9E-08 47.5 6.9 54 114-186 2-55 (82)
5 smart00666 PB1 PB1 domain. Pho 96.8 0.0063 1.4E-07 43.2 7.0 54 115-188 4-57 (81)
6 cd06396 PB1_NBR1 The PB1 domai 96.5 0.0093 2E-07 44.6 6.2 52 115-186 3-54 (81)
7 cd05992 PB1 The PB1 domain is 96.3 0.023 5.1E-07 40.0 7.1 55 114-188 2-57 (81)
8 cd06404 PB1_aPKC PB1 domain is 96.1 0.019 4.1E-07 43.3 5.8 52 115-185 3-54 (83)
9 cd06409 PB1_MUG70 The MUG70 pr 95.7 0.028 6.1E-07 42.4 5.5 50 122-186 7-58 (86)
10 cd06402 PB1_p62 The PB1 domain 95.7 0.055 1.2E-06 40.9 7.0 57 113-186 1-62 (87)
11 cd06403 PB1_Par6 The PB1 domai 95.6 0.034 7.3E-07 41.7 5.4 54 115-186 3-56 (80)
12 cd06401 PB1_TFG The PB1 domain 95.4 0.087 1.9E-06 39.6 7.0 57 115-188 3-60 (81)
13 cd06397 PB1_UP1 Uncharacterize 94.9 0.1 2.2E-06 39.4 6.1 52 115-186 3-54 (82)
14 cd06408 PB1_NoxR The PB1 domai 91.3 0.89 1.9E-05 34.4 6.3 54 113-188 3-56 (86)
15 cd06399 PB1_P40 The PB1 domain 72.7 6.2 0.00013 30.4 3.9 39 128-186 22-60 (92)
16 PF12426 DUF3674: RNA dependen 61.4 4.3 9.4E-05 27.0 1.0 30 139-179 6-36 (41)
17 PF10411 DsbC_N: Disulfide bon 61.2 6.9 0.00015 26.7 2.0 17 173-189 34-50 (57)
18 cd06395 PB1_Map2k5 PB1 domain 45.8 43 0.00092 25.6 4.2 48 121-187 10-57 (91)
19 COG3816 Uncharacterized protei 33.4 39 0.00084 29.0 2.6 39 95-149 29-73 (205)
20 COG0219 CspR Predicted rRNA me 28.3 25 0.00054 29.4 0.6 54 120-189 48-104 (155)
21 PF00788 RA: Ras association ( 23.6 2.6E+02 0.0055 19.3 5.4 36 113-148 3-41 (93)
22 PF07929 PRiA4_ORF3: Plasmid p 23.4 99 0.0021 25.1 3.3 35 114-148 6-42 (179)
23 PF11576 DUF3236: Protein of u 22.9 35 0.00076 28.5 0.6 15 19-33 94-108 (154)
24 PF09676 TraV: Type IV conjuga 20.4 66 0.0014 24.4 1.6 19 171-189 92-110 (119)
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=1.5e-56 Score=377.55 Aligned_cols=173 Identities=47% Similarity=0.756 Sum_probs=6.0
Q ss_pred CCccccccccCCCCCCCCCCCCccccccccccCCCCCCcchhhcccCCCCCCCCCC------CCC-----CCCCCCCCCC
Q 029511 18 LMSFDTELTLGLPGESRSPARAPAFAQGHKKNCTKRGFMETVIDLNLGTSHISMPR------GQN-----SESRVSGTGK 86 (192)
Q Consensus 18 l~~~~TELRLGLPG~~~~~~~~~~~~~~~~~~~~KR~fset~~d~~~~~~~~~~~~------~~~-----~~~~~~~~~~ 86 (192)
|||++|||||||||+.... ............++||+|++++ +............ ... ..........
T Consensus 1 ln~~~TELrLGLPG~~~~~-~~~~~~~~~~~~~~kR~F~~ai-d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 78 (215)
T PF02309_consen 1 LNLKATELRLGLPGSESPD-ASSSSSSKKSSSGNKRGFSEAI-DSSSSNSQSSSSSSSDSSSSSSSSSTSSSSSDSSSSS 78 (215)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred CCchhhhhcccCCCCCCCC-cccccccccccCcccccchhhh-hhcccccccccccccccCcccccccccccccccccCC
Confidence 7999999999999985321 0001122345778899999987 5443100000000 000 0000112233
Q ss_pred CCCcCCcccccCCCCccccccccC-----CCceEEEEEcCCcccceeecCCCCCHHHHHHHHHHhhcccccCCCcc--hh
Q 029511 87 YPAAKAQVTGWPPVRSFRKKTLEG-----SSKLVKVAVDGAPYLRKVDLQIYSSYQDLFRALEEMFTCFTTRGDYN--ME 159 (192)
Q Consensus 87 ~p~~k~qvVGWPPvrs~rkn~~~~-----~~~~VKV~MdG~pigRKVDL~~~~sY~eL~~aLe~MF~~~~i~~~~~--~~ 159 (192)
.|++++|+||||||++||||.+.. .++||||+|||+||||||||++|+||++|+.+|++||.+|.|..|.+ .+
T Consensus 79 ~p~~~~~~vgwpp~~s~r~n~~~~~~~~~~~~~vKV~mdG~~igRkVDL~~~~sY~~L~~~L~~MF~~~~i~~~~~~~~~ 158 (215)
T PF02309_consen 79 PPASKAQVVGWPPVRSFRKNSLSEKQSSSSRSYVKVNMDGVPIGRKVDLSAYSSYEELSSALEKMFSCFSIEQCGSHGLN 158 (215)
T ss_dssp -------BTTBS----S---------------------------------------------------------------
T ss_pred CCcccccccCCCcccccccccccccccccCCceeEEEecCcccceecCHHHhhCHHHHHHHHHHhcCCCCcccccccccc
Confidence 466789999999999999998762 57999999999999999999999999999999999999988875533 33
Q ss_pred hhhhhCCCCCCCeEEEEEeCCCCeeeccCCCCC
Q 029511 160 ERKLTGALNGREYVPTYEDKDDDWMLLGDVPWK 192 (192)
Q Consensus 160 e~~l~d~~~~~~~~ltYeDkeGDwMLVGDvPWe 192 (192)
|..+.++.++++|+|||||+||||||||||||+
T Consensus 159 ~~~~~~~~~~~~~~l~Y~D~egd~mlvGD~PW~ 191 (215)
T PF02309_consen 159 ESGLLDLLNGSEYVLVYEDKEGDWMLVGDVPWE 191 (215)
T ss_dssp ---------------------------------
T ss_pred chhhccccCCcceeEEEECCCCCEEEecCCCHH
Confidence 445666777889999999999999999999996
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=97.27 E-value=0.0011 Score=47.08 Aligned_cols=55 Identities=27% Similarity=0.404 Sum_probs=45.9
Q ss_pred eEEEEEcCCcccceeecCCCCCHHHHHHHHHHhhcccccCCCcchhhhhhhCCCCCCCeEEEEEeCCCCeeecc
Q 029511 114 LVKVAVDGAPYLRKVDLQIYSSYQDLFRALEEMFTCFTTRGDYNMEERKLTGALNGREYVPTYEDKDDDWMLLG 187 (192)
Q Consensus 114 ~VKV~MdG~pigRKVDL~~~~sY~eL~~aLe~MF~~~~i~~~~~~~e~~l~d~~~~~~~~ltYeDkeGDwMLVG 187 (192)
-|||.-.|. +-|.+.+..--+|.+|...++..|+. . ...+.+.|.|.||||..+-
T Consensus 3 ~vK~~~~~~-~~~~~~~~~~~s~~~L~~~i~~~~~~---~---------------~~~~~l~Y~D~dgD~V~i~ 57 (84)
T PF00564_consen 3 RVKVRYGGD-IRRIISLPSDVSFDDLRSKIREKFGL---L---------------DEDFQLKYKDEDGDLVTIS 57 (84)
T ss_dssp EEEEEETTE-EEEEEEECSTSHHHHHHHHHHHHHTT---S---------------TSSEEEEEEETTSSEEEES
T ss_pred EEEEEECCe-eEEEEEcCCCCCHHHHHHHHHHHhCC---C---------------CccEEEEeeCCCCCEEEeC
Confidence 489999997 44468888888999999999999993 1 3478999999999998875
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=97.15 E-value=0.0017 Score=49.14 Aligned_cols=57 Identities=25% Similarity=0.296 Sum_probs=45.0
Q ss_pred eEEEEEcCCcccceeecC---CCCCHHHHHHHHHHhhcccccCCCcchhhhhhhCCCCCCCeEEEEEeCCCCeeecc
Q 029511 114 LVKVAVDGAPYLRKVDLQ---IYSSYQDLFRALEEMFTCFTTRGDYNMEERKLTGALNGREYVPTYEDKDDDWMLLG 187 (192)
Q Consensus 114 ~VKV~MdG~pigRKVDL~---~~~sY~eL~~aLe~MF~~~~i~~~~~~~e~~l~d~~~~~~~~ltYeDkeGDwMLVG 187 (192)
-|||.-+|.-+=-++++. .--+|++|...+.+.|. +. ...+|+|.|-|.||||..+-
T Consensus 2 ~vKv~y~~~~rRf~l~~~~~~~d~~~~~L~~kI~~~f~---l~--------------~~~~~~l~Y~Dedgd~V~l~ 61 (91)
T cd06398 2 VVKVKYGGTLRRFTFPVAENQLDLNMDGLREKVEELFS---LS--------------PDADLSLTYTDEDGDVVTLV 61 (91)
T ss_pred EEEEEeCCEEEEEEeccccccCCCCHHHHHHHHHHHhC---CC--------------CCCcEEEEEECCCCCEEEEc
Confidence 489999998544455553 46799999999999998 32 23589999999999998764
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=97.10 E-value=0.0023 Score=47.45 Aligned_cols=54 Identities=20% Similarity=0.360 Sum_probs=43.2
Q ss_pred eEEEEEcCCcccceeecCCCCCHHHHHHHHHHhhcccccCCCcchhhhhhhCCCCCCCeEEEEEeCCCCeeec
Q 029511 114 LVKVAVDGAPYLRKVDLQIYSSYQDLFRALEEMFTCFTTRGDYNMEERKLTGALNGREYVPTYEDKDDDWMLL 186 (192)
Q Consensus 114 ~VKV~MdG~pigRKVDL~~~~sY~eL~~aLe~MF~~~~i~~~~~~~e~~l~d~~~~~~~~ltYeDkeGDwMLV 186 (192)
=|||...|. .+.+-|..--+|++|...+.++|. +. +...|.|-|.|.||||.++
T Consensus 2 ~vK~~~~~d--~~r~~l~~~~~~~~L~~~i~~r~~---~~--------------~~~~f~LkY~Ddegd~v~l 55 (82)
T cd06407 2 RVKATYGEE--KIRFRLPPSWGFTELKQEIAKRFK---LD--------------DMSAFDLKYLDDDEEWVLL 55 (82)
T ss_pred EEEEEeCCe--EEEEEcCCCCCHHHHHHHHHHHhC---CC--------------CCCeeEEEEECCCCCeEEe
Confidence 389999987 445555556699999999999999 22 1358999999999999875
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=96.83 E-value=0.0063 Score=43.22 Aligned_cols=54 Identities=24% Similarity=0.403 Sum_probs=43.6
Q ss_pred EEEEEcCCcccceeecCCCCCHHHHHHHHHHhhcccccCCCcchhhhhhhCCCCCCCeEEEEEeCCCCeeeccC
Q 029511 115 VKVAVDGAPYLRKVDLQIYSSYQDLFRALEEMFTCFTTRGDYNMEERKLTGALNGREYVPTYEDKDDDWMLLGD 188 (192)
Q Consensus 115 VKV~MdG~pigRKVDL~~~~sY~eL~~aLe~MF~~~~i~~~~~~~e~~l~d~~~~~~~~ltYeDkeGDwMLVGD 188 (192)
|||.-.| --|.+-+..--+|.+|...+.+.|.. . ...+.|.|.|.||||..+.+
T Consensus 4 vK~~~~~--~~~~~~~~~~~s~~dL~~~i~~~~~~---~---------------~~~~~l~Y~Dedgd~v~l~s 57 (81)
T smart00666 4 VKLRYGG--ETRRLSVPRDISFEDLRSKVAKRFGL---D---------------NQSFTLKYQDEDGDLVSLTS 57 (81)
T ss_pred EEEEECC--EEEEEEECCCCCHHHHHHHHHHHhCC---C---------------CCCeEEEEECCCCCEEEecC
Confidence 7887754 36788888899999999999999982 1 24689999999999987653
No 6
>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=96.51 E-value=0.0093 Score=44.60 Aligned_cols=52 Identities=13% Similarity=0.175 Sum_probs=45.1
Q ss_pred EEEEEcCCcccceeecCCCCCHHHHHHHHHHhhcccccCCCcchhhhhhhCCCCCCCeEEEEEeCCCCeeec
Q 029511 115 VKVAVDGAPYLRKVDLQIYSSYQDLFRALEEMFTCFTTRGDYNMEERKLTGALNGREYVPTYEDKDDDWMLL 186 (192)
Q Consensus 115 VKV~MdG~pigRKVDL~~~~sY~eL~~aLe~MF~~~~i~~~~~~~e~~l~d~~~~~~~~ltYeDkeGDwMLV 186 (192)
|||.-.|.-+--+++-+..-+|.+|...+.++|+ +. .+.|.|-|.||||.++
T Consensus 3 vKaty~~d~~rf~~~~~~~~~~~~L~~ev~~rf~---l~-----------------~f~lKYlDde~e~v~l 54 (81)
T cd06396 3 LKVTYNGESQSFLVSDSENTTWASVEAMVKVSFG---LN-----------------DIQIKYVDEENEEVSV 54 (81)
T ss_pred EEEEECCeEEEEEecCCCCCCHHHHHHHHHHHhC---CC-----------------cceeEEEcCCCCEEEE
Confidence 7999999977778888778899999999999999 21 4689999999999886
No 7
>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=96.30 E-value=0.023 Score=39.96 Aligned_cols=55 Identities=25% Similarity=0.386 Sum_probs=43.1
Q ss_pred eEEEEEcCCcccceeecC-CCCCHHHHHHHHHHhhcccccCCCcchhhhhhhCCCCCCCeEEEEEeCCCCeeeccC
Q 029511 114 LVKVAVDGAPYLRKVDLQ-IYSSYQDLFRALEEMFTCFTTRGDYNMEERKLTGALNGREYVPTYEDKDDDWMLLGD 188 (192)
Q Consensus 114 ~VKV~MdG~pigRKVDL~-~~~sY~eL~~aLe~MF~~~~i~~~~~~~e~~l~d~~~~~~~~ltYeDkeGDwMLVGD 188 (192)
-|||+-.|. -|.+=+. .--+|.+|...|.+.|.. . ...+.+.|.|.||||..+.+
T Consensus 2 ~vK~~~~~~--~~~~~~~~~~~s~~~L~~~i~~~~~~---~---------------~~~~~l~y~D~e~d~v~l~s 57 (81)
T cd05992 2 RVKVKYGGE--IRRFVVVSRSISFEDLRSKIAEKFGL---D---------------AVSFKLKYPDEDGDLVTISS 57 (81)
T ss_pred cEEEEecCC--CEEEEEecCCCCHHHHHHHHHHHhCC---C---------------CCcEEEEeeCCCCCEEEeCC
Confidence 378888875 4555555 888999999999999992 1 14679999999999987764
No 8
>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=96.06 E-value=0.019 Score=43.26 Aligned_cols=52 Identities=21% Similarity=0.327 Sum_probs=42.2
Q ss_pred EEEEEcCCcccceeecCCCCCHHHHHHHHHHhhcccccCCCcchhhhhhhCCCCCCCeEEEEEeCCCCeee
Q 029511 115 VKVAVDGAPYLRKVDLQIYSSYQDLFRALEEMFTCFTTRGDYNMEERKLTGALNGREYVPTYEDKDDDWML 185 (192)
Q Consensus 115 VKV~MdG~pigRKVDL~~~~sY~eL~~aLe~MF~~~~i~~~~~~~e~~l~d~~~~~~~~ltYeDkeGDwML 185 (192)
||++-.|.-+--.+|. .-+|++|.+.+..||.. . .+..|++.|.|.|||---
T Consensus 3 ~K~~y~gdi~it~~d~--~~s~e~L~~~v~~~c~~-~----------------~~q~ft~kw~DEEGDp~t 54 (83)
T cd06404 3 VKAAYNGDIMITSIDP--SISLEELCNEVRDMCRF-H----------------NDQPFTLKWIDEEGDPCT 54 (83)
T ss_pred EEEEecCcEEEEEcCC--CcCHHHHHHHHHHHhCC-C----------------CCCcEEEEEECCCCCcee
Confidence 7999999866666666 77899999999999992 1 345799999999999643
No 9
>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=95.71 E-value=0.028 Score=42.39 Aligned_cols=50 Identities=18% Similarity=0.240 Sum_probs=37.8
Q ss_pred CcccceeecC--CCCCHHHHHHHHHHhhcccccCCCcchhhhhhhCCCCCCCeEEEEEeCCCCeeec
Q 029511 122 APYLRKVDLQ--IYSSYQDLFRALEEMFTCFTTRGDYNMEERKLTGALNGREYVPTYEDKDDDWMLL 186 (192)
Q Consensus 122 ~pigRKVDL~--~~~sY~eL~~aLe~MF~~~~i~~~~~~~e~~l~d~~~~~~~~ltYeDkeGDwMLV 186 (192)
+|-||-+=++ ...|+.+|..++.+=|+ +... ....|.|.|.|.||||.|.
T Consensus 7 ~~~GrvhRf~~~~s~~~~~L~~~I~~Rl~---~d~~------------~~~~~~L~YlDDEgD~Vll 58 (86)
T cd06409 7 DPKGRVHRFRLRPSESLEELRTLISQRLG---DDDF------------ETHLYALSYVDDEGDIVLI 58 (86)
T ss_pred CCCCCEEEEEecCCCCHHHHHHHHHHHhC---Cccc------------cCCcccEEEEcCCCCEEEE
Confidence 4566655444 47899999999999988 2211 1357899999999999986
No 10
>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=95.69 E-value=0.055 Score=40.89 Aligned_cols=57 Identities=19% Similarity=0.419 Sum_probs=43.1
Q ss_pred ceEEEEEcC---Ccccceeec--CCCCCHHHHHHHHHHhhcccccCCCcchhhhhhhCCCCCCCeEEEEEeCCCCeeec
Q 029511 113 KLVKVAVDG---APYLRKVDL--QIYSSYQDLFRALEEMFTCFTTRGDYNMEERKLTGALNGREYVPTYEDKDDDWMLL 186 (192)
Q Consensus 113 ~~VKV~MdG---~pigRKVDL--~~~~sY~eL~~aLe~MF~~~~i~~~~~~~e~~l~d~~~~~~~~ltYeDkeGDwMLV 186 (192)
+.||.+..| .+=-|++-| ....+|++|...+.++|.. + .+..|.+.|.|.|||..-+
T Consensus 1 ~~vkayl~~~~~~~EIRRf~l~~~~~~s~~~L~~~V~~~f~~--l---------------~~~~ftlky~DeeGDlvtI 62 (87)
T cd06402 1 LTVKAYLLGKDANAEIRRFAIDEDVSTSYEYLVEKVAAVFPS--L---------------RGKNFQLFWKDEEGDLVAF 62 (87)
T ss_pred CeEEEeecCCCCccceEEEEecCCCCcCHHHHHHHHHHHccc--c---------------CCCcEEEEEECCCCCEEee
Confidence 368888877 344455555 6667999999999999972 1 2468999999999998644
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=95.59 E-value=0.034 Score=41.69 Aligned_cols=54 Identities=19% Similarity=0.327 Sum_probs=40.4
Q ss_pred EEEEEcCCcccceeecCCCCCHHHHHHHHHHhhcccccCCCcchhhhhhhCCCCCCCeEEEEEeCCCCeeec
Q 029511 115 VKVAVDGAPYLRKVDLQIYSSYQDLFRALEEMFTCFTTRGDYNMEERKLTGALNGREYVPTYEDKDDDWMLL 186 (192)
Q Consensus 115 VKV~MdG~pigRKVDL~~~~sY~eL~~aLe~MF~~~~i~~~~~~~e~~l~d~~~~~~~~ltYeDkeGDwMLV 186 (192)
||..-|..=-=-.+|.....+|+++..-|+.||. |. +..|+|-|.|.+||.+-+
T Consensus 3 VKSkfdaEfRRFsl~r~~~~~f~ef~~ll~~lH~---l~---------------~~~f~i~Y~D~~gDLLPI 56 (80)
T cd06403 3 VKSKFDAEFRRFSLDRNKPGKFEDFYKLLEHLHH---IP---------------NVDFLIGYTDPHGDLLPI 56 (80)
T ss_pred eecccCCeEEEEEeccccCcCHHHHHHHHHHHhC---CC---------------CCcEEEEEeCCCCCEecc
Confidence 6666666522224555566999999999999998 33 347899999999998754
No 12
>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=95.38 E-value=0.087 Score=39.55 Aligned_cols=57 Identities=18% Similarity=0.425 Sum_probs=41.0
Q ss_pred EEEEEcCCcccceeecCCCC-CHHHHHHHHHHhhcccccCCCcchhhhhhhCCCCCCCeEEEEEeCCCCeeeccC
Q 029511 115 VKVAVDGAPYLRKVDLQIYS-SYQDLFRALEEMFTCFTTRGDYNMEERKLTGALNGREYVPTYEDKDDDWMLLGD 188 (192)
Q Consensus 115 VKV~MdG~pigRKVDL~~~~-sY~eL~~aLe~MF~~~~i~~~~~~~e~~l~d~~~~~~~~ltYeDkeGDwMLVGD 188 (192)
+|+.-.|. -|++=+..-. +|.+|...+++.|.. .+. ....+.+.|.|.|||+.-+-+
T Consensus 3 iK~~~g~D--iR~~~~~~~~~t~~~L~~~v~~~F~~-~~~--------------~~~~flIKYkD~dGDlVTIts 60 (81)
T cd06401 3 LKAQLGDD--IRRIPIHNEDITYDELLLMMQRVFRG-KLG--------------SSDDVLIKYKDEDGDLITIFD 60 (81)
T ss_pred EEEEeCCe--EEEEeccCccccHHHHHHHHHHHhcc-ccC--------------CcccEEEEEECCCCCEEEecc
Confidence 67777665 3555444433 999999999999992 111 235789999999999976643
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=94.92 E-value=0.1 Score=39.36 Aligned_cols=52 Identities=23% Similarity=0.309 Sum_probs=42.7
Q ss_pred EEEEEcCCcccceeecCCCCCHHHHHHHHHHhhcccccCCCcchhhhhhhCCCCCCCeEEEEEeCCCCeeec
Q 029511 115 VKVAVDGAPYLRKVDLQIYSSYQDLFRALEEMFTCFTTRGDYNMEERKLTGALNGREYVPTYEDKDDDWMLL 186 (192)
Q Consensus 115 VKV~MdG~pigRKVDL~~~~sY~eL~~aLe~MF~~~~i~~~~~~~e~~l~d~~~~~~~~ltYeDkeGDwMLV 186 (192)
-||+-.|. .|++....-=+|..|.+.|+.+|. |.. . .+.|+|.|.|||..-+
T Consensus 3 fKv~~~g~--~RRf~~~~~pt~~~L~~kl~~Lf~---lp~--------------~-~~~vtYiDeD~D~ITl 54 (82)
T cd06397 3 FKSSFLGD--TRRIVFPDIPTWEALASKLENLYN---LPE--------------I-KVGVTYIDNDNDEITL 54 (82)
T ss_pred EEEEeCCc--eEEEecCCCccHHHHHHHHHHHhC---CCh--------------h-HeEEEEEcCCCCEEEe
Confidence 47888886 789988888999999999999999 321 1 2799999999998654
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=91.27 E-value=0.89 Score=34.39 Aligned_cols=54 Identities=20% Similarity=0.307 Sum_probs=43.9
Q ss_pred ceEEEEEcCCcccceeecCCCCCHHHHHHHHHHhhcccccCCCcchhhhhhhCCCCCCCeEEEEEeCCCCeeeccC
Q 029511 113 KLVKVAVDGAPYLRKVDLQIYSSYQDLFRALEEMFTCFTTRGDYNMEERKLTGALNGREYVPTYEDKDDDWMLLGD 188 (192)
Q Consensus 113 ~~VKV~MdG~pigRKVDL~~~~sY~eL~~aLe~MF~~~~i~~~~~~~e~~l~d~~~~~~~~ltYeDkeGDwMLVGD 188 (192)
.=|||+-.|. .|-|-+..--+|++|...+..+|+ +. ..+.|-|.|. ||..-+++
T Consensus 3 ikVKv~~~~D--v~~i~v~~~i~f~dL~~kIrdkf~---~~----------------~~~~iKykDE-GD~iti~s 56 (86)
T cd06408 3 IRVKVHAQDD--TRYIMIGPDTGFADFEDKIRDKFG---FK----------------RRLKIKMKDD-GDMITMGD 56 (86)
T ss_pred EEEEEEecCc--EEEEEcCCCCCHHHHHHHHHHHhC---CC----------------CceEEEEEcC-CCCccccC
Confidence 4589998888 667777777789999999999998 21 2679999999 99877665
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=72.65 E-value=6.2 Score=30.37 Aligned_cols=39 Identities=23% Similarity=0.303 Sum_probs=30.8
Q ss_pred eecCCCCCHHHHHHHHHHhhcccccCCCcchhhhhhhCCCCCCCeEEEEEeCCCCeeec
Q 029511 128 VDLQIYSSYQDLFRALEEMFTCFTTRGDYNMEERKLTGALNGREYVPTYEDKDDDWMLL 186 (192)
Q Consensus 128 VDL~~~~sY~eL~~aLe~MF~~~~i~~~~~~~e~~l~d~~~~~~~~ltYeDkeGDwMLV 186 (192)
=||+..-.|.+|..-..+-|..+ +-+|-|.|.|||..-+
T Consensus 22 e~l~~~P~~kdLl~lmr~~f~~~--------------------dIaLNYrD~EGDLIRl 60 (92)
T cd06399 22 EDLSSTPLLKDLLELTRREFQRE--------------------DIALNYRDAEGDLIRL 60 (92)
T ss_pred cccccCccHHHHHHHHHHHhchh--------------------heeeeeecCCCCEEEE
Confidence 36888889999999888888831 2367899999998654
No 16
>PF12426 DUF3674: RNA dependent RNA polymerase; InterPro: IPR024378 This domain is found in the RNA-directed RNA polymerase. It is located towards the N terminus and is approximately 40 amino acids in length. There is a conserved MFNLKF sequence motif. There are two completely conserved residues (E and P) that may be functionally important.
Probab=61.44 E-value=4.3 Score=26.96 Aligned_cols=30 Identities=33% Similarity=0.471 Sum_probs=19.3
Q ss_pred HHHHHHHhhc-ccccCCCcchhhhhhhCCCCCCCeEEEEEeC
Q 029511 139 LFRALEEMFT-CFTTRGDYNMEERKLTGALNGREYVPTYEDK 179 (192)
Q Consensus 139 L~~aLe~MF~-~~~i~~~~~~~e~~l~d~~~~~~~~ltYeDk 179 (192)
=..+||.||+ .|.|++.. ...-|++.|.+.
T Consensus 6 ER~aLEAMFNLKFhi~~~k-----------~~~y~IP~Y~~~ 36 (41)
T PF12426_consen 6 ERSALEAMFNLKFHIGGPK-----------TQPYYIPDYRGI 36 (41)
T ss_pred HHHHHHHHhceeeeeCCcc-----------cccccCCCCCCc
Confidence 3789999999 46665431 233566667654
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=61.21 E-value=6.9 Score=26.73 Aligned_cols=17 Identities=24% Similarity=0.520 Sum_probs=14.3
Q ss_pred EEEEEeCCCCeeeccCC
Q 029511 173 VPTYEDKDDDWMLLGDV 189 (192)
Q Consensus 173 ~ltYeDkeGDwMLVGDv 189 (192)
-+.|.|.||+.+++|+.
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 47899999999999974
No 18
>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=45.81 E-value=43 Score=25.64 Aligned_cols=48 Identities=19% Similarity=0.241 Sum_probs=34.2
Q ss_pred CCcccceeecCCCCCHHHHHHHHHHhhcccccCCCcchhhhhhhCCCCCCCeEEEEEeCCCCeeecc
Q 029511 121 GAPYLRKVDLQIYSSYQDLFRALEEMFTCFTTRGDYNMEERKLTGALNGREYVPTYEDKDDDWMLLG 187 (192)
Q Consensus 121 G~pigRKVDL~~~~sY~eL~~aLe~MF~~~~i~~~~~~~e~~l~d~~~~~~~~ltYeDkeGDwMLVG 187 (192)
|-.+--.||....=+|.+++.++.+..-.-| --..-|||.|||..-|-
T Consensus 10 gg~vDw~V~~~~~L~F~DvL~~I~~vlp~aT-------------------~tAFeYEDE~gDRITVR 57 (91)
T cd06395 10 GGAVDWTVQSGPQLLFRDVLDVIGQVLPEAT-------------------TTAFEYEDEDGDRITVR 57 (91)
T ss_pred CCcccccccCcccccHHHHHHHHHHhccccc-------------------ccceeeccccCCeeEec
Confidence 3446667777777889999999888655211 11456999999998763
No 19
>COG3816 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.36 E-value=39 Score=29.04 Aligned_cols=39 Identities=26% Similarity=0.350 Sum_probs=22.7
Q ss_pred cccCCCCccccccccCCCceEE------EEEcCCcccceeecCCCCCHHHHHHHHHHhhcc
Q 029511 95 TGWPPVRSFRKKTLEGSSKLVK------VAVDGAPYLRKVDLQIYSSYQDLFRALEEMFTC 149 (192)
Q Consensus 95 VGWPPvrs~rkn~~~~~~~~VK------V~MdG~pigRKVDL~~~~sY~eL~~aLe~MF~~ 149 (192)
-|-|||..|..-- + +-.=.. -+-.|.||||| .|-++|+.
T Consensus 29 rGlpPV~rWNPpf-C-GdiDmeIr~DGtWFylGTPIGR~--------------plVrLFSt 73 (205)
T COG3816 29 RGLPPVERWNPPF-C-GDIDMEIRADGTWFYLGTPIGRK--------------PLVRLFST 73 (205)
T ss_pred cCCCchhhcCCCC-c-cceeeEEecCceEEEecCccchH--------------HHHHHHHH
Confidence 4778888775321 1 111111 23358899986 67888884
No 20
>COG0219 CspR Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]
Probab=28.29 E-value=25 Score=29.42 Aligned_cols=54 Identities=26% Similarity=0.442 Sum_probs=37.2
Q ss_pred cCCcccceeecCCCCCHHHHHHHH---HHhhcccccCCCcchhhhhhhCCCCCCCeEEEEEeCCCCeeeccCC
Q 029511 120 DGAPYLRKVDLQIYSSYQDLFRAL---EEMFTCFTTRGDYNMEERKLTGALNGREYVPTYEDKDDDWMLLGDV 189 (192)
Q Consensus 120 dG~pigRKVDL~~~~sY~eL~~aL---e~MF~~~~i~~~~~~~e~~l~d~~~~~~~~ltYeDkeGDwMLVGDv 189 (192)
-|--|.-+|+|..|++|+++..+. .++|- |+..+.. -|.- +....|||+|-|-.
T Consensus 48 AGlDY~~~~~l~~h~s~e~fl~~~~~~~rl~~-~tt~~~~--------------~~~~-~~f~~~d~llFG~E 104 (155)
T COG0219 48 AGLDYHEKASLTEHDSLEAFLEAEPIGGRLFA-LTTKGTT--------------TYTD-VSFQKGDYLLFGPE 104 (155)
T ss_pred cccchHhhcceEEeCCHHHHHhhccCCceEEE-EEecccc--------------cccc-ccCCCCCEEEECCC
Confidence 467799999999999999999999 46766 3332211 1111 33456899998854
No 21
>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=23.64 E-value=2.6e+02 Score=19.34 Aligned_cols=36 Identities=8% Similarity=0.167 Sum_probs=31.3
Q ss_pred ceEEEEEcCCcc---cceeecCCCCCHHHHHHHHHHhhc
Q 029511 113 KLVKVAVDGAPY---LRKVDLQIYSSYQDLFRALEEMFT 148 (192)
Q Consensus 113 ~~VKV~MdG~pi---gRKVDL~~~~sY~eL~~aLe~MF~ 148 (192)
.++||+++...- -+.|=+.....-.+++.++-+.|+
T Consensus 3 ~~lrVy~~~~~~~~~~k~i~v~~~tTa~evi~~~l~k~~ 41 (93)
T PF00788_consen 3 GVLRVYDGDGSPGSTYKTIKVSSSTTAREVIEMALEKFG 41 (93)
T ss_dssp EEEEEEETTSSSCCSEEEEEEETTSBHHHHHHHHHHHTT
T ss_pred eEEEEEcCCCCCCccEEEEEECCCCCHHHHHHHHHHHhC
Confidence 579999987753 678889999999999999999998
No 22
>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=23.42 E-value=99 Score=25.06 Aligned_cols=35 Identities=23% Similarity=0.511 Sum_probs=29.9
Q ss_pred eEEEEEcCC--cccceeecCCCCCHHHHHHHHHHhhc
Q 029511 114 LVKVAVDGA--PYLRKVDLQIYSSYQDLFRALEEMFT 148 (192)
Q Consensus 114 ~VKV~MdG~--pigRKVDL~~~~sY~eL~~aLe~MF~ 148 (192)
-+||...|. +|=|.|-+..-.+..+|-.+|+..|+
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 478998884 89999999999999999999999997
No 23
>PF11576 DUF3236: Protein of unknown function (DUF3236); InterPro: IPR012019 This family of proteins with unknown function appears to be restricted to Methanobacteria. ; PDB: 3BRC_B.
Probab=22.87 E-value=35 Score=28.51 Aligned_cols=15 Identities=27% Similarity=0.330 Sum_probs=9.0
Q ss_pred CccccccccCCCCCC
Q 029511 19 MSFDTELTLGLPGES 33 (192)
Q Consensus 19 ~~~~TELRLGLPG~~ 33 (192)
||=..-=|||.||++
T Consensus 94 DlvIARGRLGvPGSG 108 (154)
T PF11576_consen 94 DLVIARGRLGVPGSG 108 (154)
T ss_dssp SEEEEEEE-SSTTS-
T ss_pred cEEEEcccccCCCCc
Confidence 344445599999985
No 24
>PF09676 TraV: Type IV conjugative transfer system lipoprotein (TraV); InterPro: IPR014118 This entry represents TraV, a component of a conjugative type IV secretion system. TraV is an outer membrane lipoprotein that is believed to interact with the secretin TraK [, , ]. This protein contains three conserved cysteines in the N-terminal half.
Probab=20.40 E-value=66 Score=24.39 Aligned_cols=19 Identities=32% Similarity=0.445 Sum_probs=15.3
Q ss_pred CeEEEEEeCCCCeeeccCC
Q 029511 171 EYVPTYEDKDDDWMLLGDV 189 (192)
Q Consensus 171 ~~~ltYeDkeGDwMLVGDv 189 (192)
=|+.=|+|.+||+..-|.|
T Consensus 92 iwiaP~~D~~g~l~~~~~V 110 (119)
T PF09676_consen 92 IWIAPWEDADGDLHDPGYV 110 (119)
T ss_pred EEEeeeECCCCCEeccceE
Confidence 5788899999998876654
Done!