Query 026005
Match_columns 245
No_of_seqs 208 out of 589
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 02:35:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026005.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026005hhsearch_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 7.2E-70 1.6E-74 476.3 0.4 212 2-237 1-215 (215)
2 PF00564 PB1: PB1 domain; Int 97.5 0.00017 3.8E-09 53.3 5.3 67 129-220 3-70 (84)
3 cd06398 PB1_Joka2 The PB1 doma 97.2 0.0011 2.4E-08 51.9 6.6 68 129-221 2-72 (91)
4 smart00666 PB1 PB1 domain. Pho 97.2 0.0019 4E-08 47.8 7.1 65 130-220 4-69 (81)
5 cd06407 PB1_NLP A PB1 domain i 97.0 0.0024 5.1E-08 49.1 6.7 56 129-209 2-57 (82)
6 cd05992 PB1 The PB1 domain is 97.0 0.0037 8E-08 45.9 7.2 66 129-220 2-69 (81)
7 cd06396 PB1_NBR1 The PB1 domai 96.8 0.0044 9.6E-08 48.0 6.1 53 130-208 3-55 (81)
8 cd06401 PB1_TFG The PB1 domain 96.2 0.021 4.5E-07 44.3 6.8 73 130-225 3-79 (81)
9 cd06403 PB1_Par6 The PB1 domai 96.2 0.012 2.7E-07 45.5 5.4 72 130-225 3-76 (80)
10 cd06409 PB1_MUG70 The MUG70 pr 95.6 0.027 5.8E-07 44.0 5.2 51 137-208 7-59 (86)
11 cd06402 PB1_p62 The PB1 domain 95.6 0.059 1.3E-06 42.2 7.0 59 129-210 2-65 (87)
12 cd06404 PB1_aPKC PB1 domain is 95.4 0.043 9.3E-07 42.8 5.7 55 130-209 3-57 (83)
13 cd06397 PB1_UP1 Uncharacterize 94.5 0.13 2.9E-06 40.0 6.1 65 130-220 3-68 (82)
14 cd06408 PB1_NoxR The PB1 domai 92.1 0.55 1.2E-05 36.8 6.1 65 128-220 3-68 (86)
15 cd06399 PB1_P40 The PB1 domain 67.2 8.9 0.00019 30.5 3.9 38 144-207 23-60 (92)
16 cd06395 PB1_Map2k5 PB1 domain 56.1 22 0.00047 28.1 4.2 49 136-209 10-58 (91)
17 PF10411 DsbC_N: Disulfide bon 52.8 11 0.00023 26.8 1.9 17 194-210 34-50 (57)
18 cd06406 PB1_P67 A PB1 domain i 46.9 86 0.0019 24.3 6.2 66 128-220 3-69 (80)
19 KOG3606 Cell polarity protein 33.8 70 0.0015 30.7 4.6 79 127-231 18-102 (358)
20 PF09840 DUF2067: Uncharacteri 33.3 18 0.00039 32.0 0.6 36 183-222 90-125 (190)
21 KOG3938 RGS-GAIP interacting p 33.1 75 0.0016 30.3 4.7 75 135-235 62-143 (334)
22 PF11576 DUF3236: Protein of u 32.9 16 0.00034 31.6 0.2 10 9-18 100-109 (154)
23 COG0219 CspR Predicted rRNA me 31.6 22 0.00048 30.8 0.9 73 135-229 48-128 (155)
24 cd00771 ThrRS_core Threonyl-tR 25.1 23 0.00049 32.6 -0.2 54 127-203 209-262 (298)
25 PF09676 TraV: Type IV conjuga 24.5 49 0.0011 26.1 1.7 19 192-210 92-110 (119)
26 PRK13361 molybdenum cofactor b 22.7 2.6E+02 0.0055 26.0 6.3 76 133-227 188-266 (329)
27 KOG3957 Predicted L-carnitine 21.3 1.2E+02 0.0025 29.9 3.7 77 139-229 177-254 (387)
28 PF07929 PRiA4_ORF3: Plasmid p 20.7 1.1E+02 0.0024 25.8 3.2 37 127-163 4-42 (179)
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=7.2e-70 Score=476.34 Aligned_cols=212 Identities=56% Similarity=0.914 Sum_probs=6.0
Q ss_pred CCCcccccccCCCCCCCCCCCCCCCCCCCCCcccCccCCCCCCCchhhhhhhcccCCCCCCCc-cccccccCCcCCC-C-
Q 026005 2 INFEATELRLGLPGGNGGSSEGGGGGGGGEKAKNNNINGMKRGFADTVVDLKLNLSTKESGGI-DVIEKTKGKSASA-T- 78 (245)
Q Consensus 2 lnlk~TELRLGLPG~~~~~~~~~~~~~~~~~~~~~~~~~~KRgfsdt~idl~~~~~~~~~~~~-~~~~~~~~~~~~~-~- 78 (245)
||||+|||||||||+.+++. ..........+++||+|+++ |+............. ............. .
T Consensus 1 ln~~~TELrLGLPG~~~~~~-------~~~~~~~~~~~~~kR~F~~a-id~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 (215)
T PF02309_consen 1 LNLKATELRLGLPGSESPDA-------SSSSSSKKSSSGNKRGFSEA-IDSSSSNSQSSSSSSSDSSSSSSSSSTSSSSS 72 (215)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred CCchhhhhcccCCCCCCCCc-------ccccccccccCcccccchhh-hhhcccccccccccccccCccccccccccccc
Confidence 89999999999999987631 01112223458999999998 776441000000000 0000000000000 0
Q ss_pred CCCCCCCCCCCCCCCCCCCccchhhhhhhhcccCcccccccCCCCCCCcceEEEEecCccccceeecCCccCHHHHHHHH
Q 026005 79 GATDLSKPPAKSQVVGWPPVRSFRKNIMAVQKDNEEGDNKASSSSSSNVAFVKVSMDGAPYLRKVDLKLYKSYQELSDAL 158 (245)
Q Consensus 79 ~~~~~~~p~akaqvVGWPPVrs~RkN~~~~~~~~~~~~~~~~~~~~~~~~~VKV~MdG~pigRKVDL~~~~sY~~L~~aL 158 (245)
.......|.+++|+||||||++||||.+.... ....++||||+|||+||||||||++|+||++|+.+|
T Consensus 73 ~~~~~~~p~~~~~~vgwpp~~s~r~n~~~~~~------------~~~~~~~vKV~mdG~~igRkVDL~~~~sY~~L~~~L 140 (215)
T PF02309_consen 73 DSSSSSPPASKAQVVGWPPVRSFRKNSLSEKQ------------SSSSRSYVKVNMDGVPIGRKVDLSAYSSYEELSSAL 140 (215)
T ss_dssp -------------BTTBS----S---------------------------------------------------------
T ss_pred ccccCCCCcccccccCCCcccccccccccccc------------cccCCceeEEEecCcccceecCHHHhhCHHHHHHHH
Confidence 01122345578999999999999999876211 122479999999999999999999999999999999
Q ss_pred HhhhcccccCCcCCCCCccccchhhhhhccCCCceeeEEEcCCCCeEeccCCChhhhhhcceeeEEecCCcccCCCchh
Q 026005 159 GKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGDWMLVGDVPWDMFVDSCKRLRIMKGSEAIGLAPRA 237 (245)
Q Consensus 159 e~MF~~~~~~~~~~~g~~~~~~e~~l~d~~~~sey~ltYeDkeGDwMLVGDvPW~mFv~svKRLrImk~sea~gl~~~~ 237 (245)
++||.+|.|++|++++ .++..+.++.++++|+|||||+||||||||||||+|||++|||||||+.+|++||+||+
T Consensus 141 ~~MF~~~~i~~~~~~~----~~~~~~~~~~~~~~~~l~Y~D~egd~mlvGD~PW~~F~~~vkRl~I~~~~e~~~~~~r~ 215 (215)
T PF02309_consen 141 EKMFSCFSIEQCGSHG----LNESGLLDLLNGSEYVLVYEDKEGDWMLVGDVPWEEFVKSVKRLRIMKSSEAKGLAPRA 215 (215)
T ss_dssp -------------------------------------------------------------------------------
T ss_pred HHhcCCCCcccccccc----ccchhhccccCCcceeEEEECCCCCEEEecCCCHHHHHHHhhccEEecHHHhcccCCCC
Confidence 9999988888888754 56677788888899999999999999999999999999999999999999999999996
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=97.55 E-value=0.00017 Score=53.35 Aligned_cols=67 Identities=24% Similarity=0.392 Sum_probs=54.6
Q ss_pred eEEEEecCccccceeecCCccCHHHHHHHHHhhhcccccCCcCCCCCccccchhhhhhccCCCceeeEEEcCCCCeEecc
Q 026005 129 FVKVSMDGAPYLRKVDLKLYKSYQELSDALGKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGDWMLVG 208 (245)
Q Consensus 129 ~VKV~MdG~pigRKVDL~~~~sY~~L~~aLe~MF~~~~~~~~~~~g~~~~~~e~~l~d~~~~sey~ltYeDkeGDwMLVG 208 (245)
-|||...|.. =|.+.+..--+|++|...+++.|... ...+.+.|.|.||||..+-
T Consensus 3 ~vK~~~~~~~-~~~~~~~~~~s~~~L~~~i~~~~~~~------------------------~~~~~l~Y~D~dgD~V~i~ 57 (84)
T PF00564_consen 3 RVKVRYGGDI-RRIISLPSDVSFDDLRSKIREKFGLL------------------------DEDFQLKYKDEDGDLVTIS 57 (84)
T ss_dssp EEEEEETTEE-EEEEEECSTSHHHHHHHHHHHHHTTS------------------------TSSEEEEEEETTSSEEEES
T ss_pred EEEEEECCee-EEEEEcCCCCCHHHHHHHHHHHhCCC------------------------CccEEEEeeCCCCCEEEeC
Confidence 4799999973 33588888889999999999999851 3468999999999999887
Q ss_pred C-CChhhhhhcce
Q 026005 209 D-VPWDMFVDSCK 220 (245)
Q Consensus 209 D-vPW~mFv~svK 220 (245)
+ .=|++.++.++
T Consensus 58 sd~Dl~~a~~~~~ 70 (84)
T PF00564_consen 58 SDEDLQEAIEQAK 70 (84)
T ss_dssp SHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHH
Confidence 5 45888887775
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=97.22 E-value=0.0011 Score=51.93 Aligned_cols=68 Identities=25% Similarity=0.302 Sum_probs=52.8
Q ss_pred eEEEEecCccccceeecC---CccCHHHHHHHHHhhhcccccCCcCCCCCccccchhhhhhccCCCceeeEEEcCCCCeE
Q 026005 129 FVKVSMDGAPYLRKVDLK---LYKSYQELSDALGKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGDWM 205 (245)
Q Consensus 129 ~VKV~MdG~pigRKVDL~---~~~sY~~L~~aLe~MF~~~~~~~~~~~g~~~~~~e~~l~d~~~~sey~ltYeDkeGDwM 205 (245)
-|||..+|.-+=-++++. ..-+|++|...+.+.|... ...+|+|.|.|.||||.
T Consensus 2 ~vKv~y~~~~rRf~l~~~~~~~d~~~~~L~~kI~~~f~l~-----------------------~~~~~~l~Y~Dedgd~V 58 (91)
T cd06398 2 VVKVKYGGTLRRFTFPVAENQLDLNMDGLREKVEELFSLS-----------------------PDADLSLTYTDEDGDVV 58 (91)
T ss_pred EEEEEeCCEEEEEEeccccccCCCCHHHHHHHHHHHhCCC-----------------------CCCcEEEEEECCCCCEE
Confidence 489999998555555554 4679999999999999851 23579999999999999
Q ss_pred eccCCChhhhhhccee
Q 026005 206 LVGDVPWDMFVDSCKR 221 (245)
Q Consensus 206 LVGDvPW~mFv~svKR 221 (245)
.+-.. +.|...+.+
T Consensus 59 ~l~~D--~DL~~a~~~ 72 (91)
T cd06398 59 TLVDD--NDLTDAIQY 72 (91)
T ss_pred EEccH--HHHHHHHHH
Confidence 98766 666665554
No 4
>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=97.18 E-value=0.0019 Score=47.79 Aligned_cols=65 Identities=20% Similarity=0.415 Sum_probs=51.4
Q ss_pred EEEEecCccccceeecCCccCHHHHHHHHHhhhcccccCCcCCCCCccccchhhhhhccCCCceeeEEEcCCCCeEeccC
Q 026005 130 VKVSMDGAPYLRKVDLKLYKSYQELSDALGKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGDWMLVGD 209 (245)
Q Consensus 130 VKV~MdG~pigRKVDL~~~~sY~~L~~aLe~MF~~~~~~~~~~~g~~~~~~e~~l~d~~~~sey~ltYeDkeGDwMLVGD 209 (245)
|||.-.|. -|.+-+..--+|++|...+.+.|.. ....+.|.|+|.||||..+.+
T Consensus 4 vK~~~~~~--~~~~~~~~~~s~~dL~~~i~~~~~~------------------------~~~~~~l~Y~Dedgd~v~l~s 57 (81)
T smart00666 4 VKLRYGGE--TRRLSVPRDISFEDLRSKVAKRFGL------------------------DNQSFTLKYQDEDGDLVSLTS 57 (81)
T ss_pred EEEEECCE--EEEEEECCCCCHHHHHHHHHHHhCC------------------------CCCCeEEEEECCCCCEEEecC
Confidence 68877543 6777788888999999999999984 123589999999999987765
Q ss_pred -CChhhhhhcce
Q 026005 210 -VPWDMFVDSCK 220 (245)
Q Consensus 210 -vPW~mFv~svK 220 (245)
.=|.+.++.++
T Consensus 58 d~Dl~~a~~~~~ 69 (81)
T smart00666 58 DEDLEEAIEEYD 69 (81)
T ss_pred HHHHHHHHHHHH
Confidence 57777777665
No 5
>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=97.04 E-value=0.0024 Score=49.11 Aligned_cols=56 Identities=23% Similarity=0.338 Sum_probs=44.4
Q ss_pred eEEEEecCccccceeecCCccCHHHHHHHHHhhhcccccCCcCCCCCccccchhhhhhccCCCceeeEEEcCCCCeEecc
Q 026005 129 FVKVSMDGAPYLRKVDLKLYKSYQELSDALGKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGDWMLVG 208 (245)
Q Consensus 129 ~VKV~MdG~pigRKVDL~~~~sY~~L~~aLe~MF~~~~~~~~~~~g~~~~~~e~~l~d~~~~sey~ltYeDkeGDwMLVG 208 (245)
=|||...|. -+.+-|..--+|++|...+.++|.. . +.+.|.|-|.|.||||.++-
T Consensus 2 ~vK~~~~~d--~~r~~l~~~~~~~~L~~~i~~r~~~---~--------------------~~~~f~LkY~Ddegd~v~lt 56 (82)
T cd06407 2 RVKATYGEE--KIRFRLPPSWGFTELKQEIAKRFKL---D--------------------DMSAFDLKYLDDDEEWVLLT 56 (82)
T ss_pred EEEEEeCCe--EEEEEcCCCCCHHHHHHHHHHHhCC---C--------------------CCCeeEEEEECCCCCeEEee
Confidence 389999887 4455556666999999999999985 0 13579999999999999874
Q ss_pred C
Q 026005 209 D 209 (245)
Q Consensus 209 D 209 (245)
-
T Consensus 57 s 57 (82)
T cd06407 57 C 57 (82)
T ss_pred c
Confidence 3
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=96.99 E-value=0.0037 Score=45.88 Aligned_cols=66 Identities=20% Similarity=0.367 Sum_probs=51.3
Q ss_pred eEEEEecCccccceeecC-CccCHHHHHHHHHhhhcccccCCcCCCCCccccchhhhhhccCCCceeeEEEcCCCCeEec
Q 026005 129 FVKVSMDGAPYLRKVDLK-LYKSYQELSDALGKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGDWMLV 207 (245)
Q Consensus 129 ~VKV~MdG~pigRKVDL~-~~~sY~~L~~aLe~MF~~~~~~~~~~~g~~~~~~e~~l~d~~~~sey~ltYeDkeGDwMLV 207 (245)
-|||+-.|. -|.+=+. ..-+|++|...|.+.|... ...+.+.|.|.||||..+
T Consensus 2 ~vK~~~~~~--~~~~~~~~~~~s~~~L~~~i~~~~~~~------------------------~~~~~l~y~D~e~d~v~l 55 (81)
T cd05992 2 RVKVKYGGE--IRRFVVVSRSISFEDLRSKIAEKFGLD------------------------AVSFKLKYPDEDGDLVTI 55 (81)
T ss_pred cEEEEecCC--CEEEEEecCCCCHHHHHHHHHHHhCCC------------------------CCcEEEEeeCCCCCEEEe
Confidence 378888765 3444444 7889999999999999851 135899999999999998
Q ss_pred cC-CChhhhhhcce
Q 026005 208 GD-VPWDMFVDSCK 220 (245)
Q Consensus 208 GD-vPW~mFv~svK 220 (245)
.+ .=|++.++.++
T Consensus 56 ~sd~Dl~~a~~~~~ 69 (81)
T cd05992 56 SSDEDLEEAIEEAR 69 (81)
T ss_pred CCHHHHHHHHHHHh
Confidence 87 56777777665
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=96.76 E-value=0.0044 Score=47.95 Aligned_cols=53 Identities=19% Similarity=0.226 Sum_probs=46.2
Q ss_pred EEEEecCccccceeecCCccCHHHHHHHHHhhhcccccCCcCCCCCccccchhhhhhccCCCceeeEEEcCCCCeEecc
Q 026005 130 VKVSMDGAPYLRKVDLKLYKSYQELSDALGKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGDWMLVG 208 (245)
Q Consensus 130 VKV~MdG~pigRKVDL~~~~sY~~L~~aLe~MF~~~~~~~~~~~g~~~~~~e~~l~d~~~~sey~ltYeDkeGDwMLVG 208 (245)
|||...|.-+--+++-+..-+|++|...+.++|+. + .|.|.|-|.||||.++-
T Consensus 3 vKaty~~d~~rf~~~~~~~~~~~~L~~ev~~rf~l------------------------~--~f~lKYlDde~e~v~ls 55 (81)
T cd06396 3 LKVTYNGESQSFLVSDSENTTWASVEAMVKVSFGL------------------------N--DIQIKYVDEENEEVSVN 55 (81)
T ss_pred EEEEECCeEEEEEecCCCCCCHHHHHHHHHHHhCC------------------------C--cceeEEEcCCCCEEEEE
Confidence 79999998777788887788999999999999985 1 47899999999998874
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=96.22 E-value=0.021 Score=44.34 Aligned_cols=73 Identities=19% Similarity=0.365 Sum_probs=49.2
Q ss_pred EEEEecCccccceeecCCcc-CHHHHHHHHHhhhcccccCCcCCCCCccccchhhhhhccCCCceeeEEEcCCCCeEecc
Q 026005 130 VKVSMDGAPYLRKVDLKLYK-SYQELSDALGKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGDWMLVG 208 (245)
Q Consensus 130 VKV~MdG~pigRKVDL~~~~-sY~~L~~aLe~MF~~~~~~~~~~~g~~~~~~e~~l~d~~~~sey~ltYeDkeGDwMLVG 208 (245)
+|+...|. | |.+=+..-. +|.+|...+.+.|... . .....+.+.|.|.|||+.-+-
T Consensus 3 iK~~~g~D-i-R~~~~~~~~~t~~~L~~~v~~~F~~~----~-----------------~~~~~flIKYkD~dGDlVTIt 59 (81)
T cd06401 3 LKAQLGDD-I-RRIPIHNEDITYDELLLMMQRVFRGK----L-----------------GSSDDVLIKYKDEDGDLITIF 59 (81)
T ss_pred EEEEeCCe-E-EEEeccCccccHHHHHHHHHHHhccc----c-----------------CCcccEEEEEECCCCCEEEec
Confidence 67666554 4 444444322 9999999999999841 1 123479999999999999998
Q ss_pred CC---ChhhhhhcceeeEEe
Q 026005 209 DV---PWDMFVDSCKRLRIM 225 (245)
Q Consensus 209 Dv---PW~mFv~svKRLrIm 225 (245)
+- -|..-+...+||+|.
T Consensus 60 s~~dL~~A~~~~~~~~l~~~ 79 (81)
T cd06401 60 DSSDLSFAIQCSRILKLTLF 79 (81)
T ss_pred cHHHHHHHHhcCcceEEEEe
Confidence 74 444334445556553
No 9
>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=96.19 E-value=0.012 Score=45.46 Aligned_cols=72 Identities=21% Similarity=0.294 Sum_probs=52.0
Q ss_pred EEEEecCccccceeecCCccCHHHHHHHHHhhhcccccCCcCCCCCccccchhhhhhccCCCceeeEEEcCCCCeEecc-
Q 026005 130 VKVSMDGAPYLRKVDLKLYKSYQELSDALGKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGDWMLVG- 208 (245)
Q Consensus 130 VKV~MdG~pigRKVDL~~~~sY~~L~~aLe~MF~~~~~~~~~~~g~~~~~~e~~l~d~~~~sey~ltYeDkeGDwMLVG- 208 (245)
||...|..=-=-.+|.....+|+++++-|+.||.. .+..|+|-|.|.+||.+-+-
T Consensus 3 VKSkfdaEfRRFsl~r~~~~~f~ef~~ll~~lH~l------------------------~~~~f~i~Y~D~~gDLLPInN 58 (80)
T cd06403 3 VKSKFDAEFRRFSLDRNKPGKFEDFYKLLEHLHHI------------------------PNVDFLIGYTDPHGDLLPINN 58 (80)
T ss_pred eecccCCeEEEEEeccccCcCHHHHHHHHHHHhCC------------------------CCCcEEEEEeCCCCCEecccC
Confidence 56666665322245555669999999999999985 23479999999999999775
Q ss_pred CCChhhhhhccee-eEEe
Q 026005 209 DVPWDMFVDSCKR-LRIM 225 (245)
Q Consensus 209 DvPW~mFv~svKR-LrIm 225 (245)
|+-+..=++++++ |||+
T Consensus 59 DdNf~kAlssa~plLRl~ 76 (80)
T cd06403 59 DDNFLKALSSANPLLRIF 76 (80)
T ss_pred cHHHHHHHHcCCCceEEE
Confidence 4555555667775 4553
No 10
>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=95.62 E-value=0.027 Score=44.03 Aligned_cols=51 Identities=22% Similarity=0.330 Sum_probs=38.3
Q ss_pred ccccceeecC--CccCHHHHHHHHHhhhcccccCCcCCCCCccccchhhhhhccCCCceeeEEEcCCCCeEecc
Q 026005 137 APYLRKVDLK--LYKSYQELSDALGKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGDWMLVG 208 (245)
Q Consensus 137 ~pigRKVDL~--~~~sY~~L~~aLe~MF~~~~~~~~~~~g~~~~~~e~~l~d~~~~sey~ltYeDkeGDwMLVG 208 (245)
.|-||.+=++ ...||.+|..++.+=|+.-. .-...|.|.|.|.||||.++-
T Consensus 7 ~~~GrvhRf~~~~s~~~~~L~~~I~~Rl~~d~---------------------~~~~~~~L~YlDDEgD~VllT 59 (86)
T cd06409 7 DPKGRVHRFRLRPSESLEELRTLISQRLGDDD---------------------FETHLYALSYVDDEGDIVLIT 59 (86)
T ss_pred CCCCCEEEEEecCCCCHHHHHHHHHHHhCCcc---------------------ccCCcccEEEEcCCCCEEEEe
Confidence 4567765544 47899999999999997510 012468999999999999875
No 11
>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=95.60 E-value=0.059 Score=42.21 Aligned_cols=59 Identities=24% Similarity=0.460 Sum_probs=44.3
Q ss_pred eEEEEecC---ccccceeec--CCccCHHHHHHHHHhhhcccccCCcCCCCCccccchhhhhhccCCCceeeEEEcCCCC
Q 026005 129 FVKVSMDG---APYLRKVDL--KLYKSYQELSDALGKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGD 203 (245)
Q Consensus 129 ~VKV~MdG---~pigRKVDL--~~~~sY~~L~~aLe~MF~~~~~~~~~~~g~~~~~~e~~l~d~~~~sey~ltYeDkeGD 203 (245)
.||.+..| .+=-|++=| ....+|++|...+.++|.. +.+..|.+.|.|.|||
T Consensus 2 ~vkayl~~~~~~~EIRRf~l~~~~~~s~~~L~~~V~~~f~~-----------------------l~~~~ftlky~DeeGD 58 (87)
T cd06402 2 TVKAYLLGKDANAEIRRFAIDEDVSTSYEYLVEKVAAVFPS-----------------------LRGKNFQLFWKDEEGD 58 (87)
T ss_pred eEEEeecCCCCccceEEEEecCCCCcCHHHHHHHHHHHccc-----------------------cCCCcEEEEEECCCCC
Confidence 57777766 333354444 6667999999999999974 1245799999999999
Q ss_pred eEeccCC
Q 026005 204 WMLVGDV 210 (245)
Q Consensus 204 wMLVGDv 210 (245)
..-+...
T Consensus 59 lvtIssd 65 (87)
T cd06402 59 LVAFSSD 65 (87)
T ss_pred EEeecCH
Confidence 9887653
No 12
>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=95.42 E-value=0.043 Score=42.80 Aligned_cols=55 Identities=22% Similarity=0.349 Sum_probs=44.5
Q ss_pred EEEEecCccccceeecCCccCHHHHHHHHHhhhcccccCCcCCCCCccccchhhhhhccCCCceeeEEEcCCCCeEeccC
Q 026005 130 VKVSMDGAPYLRKVDLKLYKSYQELSDALGKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGDWMLVGD 209 (245)
Q Consensus 130 VKV~MdG~pigRKVDL~~~~sY~~L~~aLe~MF~~~~~~~~~~~g~~~~~~e~~l~d~~~~sey~ltYeDkeGDwMLVGD 209 (245)
||++..|.-.--.+|. .-+|++|.+.+.+||... .+..|++.|.|.|||---+..
T Consensus 3 ~K~~y~gdi~it~~d~--~~s~e~L~~~v~~~c~~~-----------------------~~q~ft~kw~DEEGDp~tiSS 57 (83)
T cd06404 3 VKAAYNGDIMITSIDP--SISLEELCNEVRDMCRFH-----------------------NDQPFTLKWIDEEGDPCTISS 57 (83)
T ss_pred EEEEecCcEEEEEcCC--CcCHHHHHHHHHHHhCCC-----------------------CCCcEEEEEECCCCCceeecC
Confidence 7899999865555665 778999999999999851 245699999999999877664
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=94.51 E-value=0.13 Score=40.01 Aligned_cols=65 Identities=18% Similarity=0.215 Sum_probs=48.8
Q ss_pred EEEEecCccccceeecCCccCHHHHHHHHHhhhcccccCCcCCCCCccccchhhhhhccCCCceeeEEEcCCCCeEeccC
Q 026005 130 VKVSMDGAPYLRKVDLKLYKSYQELSDALGKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGDWMLVGD 209 (245)
Q Consensus 130 VKV~MdG~pigRKVDL~~~~sY~~L~~aLe~MF~~~~~~~~~~~g~~~~~~e~~l~d~~~~sey~ltYeDkeGDwMLVGD 209 (245)
-||+..|. .|++-...-=+|..|.+.|+.+|.... . .+.+||-|.|||..-+-|
T Consensus 3 fKv~~~g~--~RRf~~~~~pt~~~L~~kl~~Lf~lp~-----------------------~-~~~vtYiDeD~D~ITlss 56 (82)
T cd06397 3 FKSSFLGD--TRRIVFPDIPTWEALASKLENLYNLPE-----------------------I-KVGVTYIDNDNDEITLSS 56 (82)
T ss_pred EEEEeCCc--eEEEecCCCccHHHHHHHHHHHhCCCh-----------------------h-HeEEEEEcCCCCEEEecc
Confidence 37777775 788888888899999999999999621 1 279999999999886554
Q ss_pred -CChhhhhhcce
Q 026005 210 -VPWDMFVDSCK 220 (245)
Q Consensus 210 -vPW~mFv~svK 220 (245)
.=-+.|..-..
T Consensus 57 d~eL~d~~~~~~ 68 (82)
T cd06397 57 NKELQDFYRLSH 68 (82)
T ss_pred hHHHHHHHHhcc
Confidence 44555554333
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=92.07 E-value=0.55 Score=36.77 Aligned_cols=65 Identities=22% Similarity=0.335 Sum_probs=49.6
Q ss_pred ceEEEEecCccccceeecCCccCHHHHHHHHHhhhcccccCCcCCCCCccccchhhhhhccCCCceeeEEEcCCCCeEec
Q 026005 128 AFVKVSMDGAPYLRKVDLKLYKSYQELSDALGKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGDWMLV 207 (245)
Q Consensus 128 ~~VKV~MdG~pigRKVDL~~~~sY~~L~~aLe~MF~~~~~~~~~~~g~~~~~~e~~l~d~~~~sey~ltYeDkeGDwMLV 207 (245)
.-|||+-.|. .|-|-+..--+|++|...+.++|+. ...+.+-|.|. ||..-+
T Consensus 3 ikVKv~~~~D--v~~i~v~~~i~f~dL~~kIrdkf~~-------------------------~~~~~iKykDE-GD~iti 54 (86)
T cd06408 3 IRVKVHAQDD--TRYIMIGPDTGFADFEDKIRDKFGF-------------------------KRRLKIKMKDD-GDMITM 54 (86)
T ss_pred EEEEEEecCc--EEEEEcCCCCCHHHHHHHHHHHhCC-------------------------CCceEEEEEcC-CCCccc
Confidence 4589998888 5667777777899999999999985 12589999999 999888
Q ss_pred cCC-Chhhhhhcce
Q 026005 208 GDV-PWDMFVDSCK 220 (245)
Q Consensus 208 GDv-PW~mFv~svK 220 (245)
++- =-++-+.++|
T Consensus 55 ~sq~DLd~Ai~~a~ 68 (86)
T cd06408 55 GDQDDLDMAIDTAR 68 (86)
T ss_pred cCHHHHHHHHHHHH
Confidence 873 3344444444
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=67.24 E-value=8.9 Score=30.51 Aligned_cols=38 Identities=24% Similarity=0.364 Sum_probs=30.6
Q ss_pred ecCCccCHHHHHHHHHhhhcccccCCcCCCCCccccchhhhhhccCCCceeeEEEcCCCCeEec
Q 026005 144 DLKLYKSYQELSDALGKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGDWMLV 207 (245)
Q Consensus 144 DL~~~~sY~~L~~aLe~MF~~~~~~~~~~~g~~~~~~e~~l~d~~~~sey~ltYeDkeGDwMLV 207 (245)
||+.--+|.+|..-..+-|... +-+|-|.|.|||..-+
T Consensus 23 ~l~~~P~~kdLl~lmr~~f~~~--------------------------dIaLNYrD~EGDLIRl 60 (92)
T cd06399 23 DLSSTPLLKDLLELTRREFQRE--------------------------DIALNYRDAEGDLIRL 60 (92)
T ss_pred ccccCccHHHHHHHHHHHhchh--------------------------heeeeeecCCCCEEEE
Confidence 6788889999999888888752 2478899999998644
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=56.15 E-value=22 Score=28.10 Aligned_cols=49 Identities=24% Similarity=0.357 Sum_probs=34.8
Q ss_pred CccccceeecCCccCHHHHHHHHHhhhcccccCCcCCCCCccccchhhhhhccCCCceeeEEEcCCCCeEeccC
Q 026005 136 GAPYLRKVDLKLYKSYQELSDALGKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGDWMLVGD 209 (245)
Q Consensus 136 G~pigRKVDL~~~~sY~~L~~aLe~MF~~~~~~~~~~~g~~~~~~e~~l~d~~~~sey~ltYeDkeGDwMLVGD 209 (245)
|..+--.||...+=+|.+++.++.+....-|. -.+-|||.|||..-|--
T Consensus 10 gg~vDw~V~~~~~L~F~DvL~~I~~vlp~aT~-------------------------tAFeYEDE~gDRITVRS 58 (91)
T cd06395 10 GGAVDWTVQSGPQLLFRDVLDVIGQVLPEATT-------------------------TAFEYEDEDGDRITVRS 58 (91)
T ss_pred CCcccccccCcccccHHHHHHHHHHhcccccc-------------------------cceeeccccCCeeEecc
Confidence 44466667777778899998888876653221 14469999999988753
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=52.77 E-value=11 Score=26.75 Aligned_cols=17 Identities=29% Similarity=0.649 Sum_probs=14.4
Q ss_pred eeEEEcCCCCeEeccCC
Q 026005 194 VPTYEDKDGDWMLVGDV 210 (245)
Q Consensus 194 ~ltYeDkeGDwMLVGDv 210 (245)
-+.|.|.||+.+++|+.
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
>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=46.89 E-value=86 Score=24.31 Aligned_cols=66 Identities=14% Similarity=0.146 Sum_probs=47.8
Q ss_pred ceEEEEecCccccceeecCCccCHHHHHHHHHhhhcccccCCcCCCCCccccchhhhhhccCCCceeeEEEcCCC-CeEe
Q 026005 128 AFVKVSMDGAPYLRKVDLKLYKSYQELSDALGKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDG-DWML 206 (245)
Q Consensus 128 ~~VKV~MdG~pigRKVDL~~~~sY~~L~~aLe~MF~~~~~~~~~~~g~~~~~~e~~l~d~~~~sey~ltYeDkeG-DwML 206 (245)
--|||+..+ .=.|-...=-+|++|...|.+=+... +.+-+|.|.|.+. +...
T Consensus 3 ~vvKV~f~~---tIaIrvp~~~~y~~L~~ki~~kLkl~------------------------~e~i~LsYkde~s~~~v~ 55 (80)
T cd06406 3 YVVKVHFKY---TVAIQVARGLSYATLLQKISSKLELP------------------------AEHITLSYKSEASGEDVI 55 (80)
T ss_pred eEEEEEEEE---EEEEEcCCCCCHHHHHHHHHHHhCCC------------------------chhcEEEeccCCCCCccC
Confidence 358999997 33455666678999999999888751 2234788988774 4444
Q ss_pred ccCCChhhhhhcce
Q 026005 207 VGDVPWDMFVDSCK 220 (245)
Q Consensus 207 VGDvPW~mFv~svK 220 (245)
++|-=|+.-.+.|+
T Consensus 56 l~d~dle~aws~~~ 69 (80)
T cd06406 56 LSDTNMEDVWSQAK 69 (80)
T ss_pred cChHHHHHHHHhhc
Confidence 48888888888777
No 19
>KOG3606 consensus Cell polarity protein PAR6 [Signal transduction mechanisms]
Probab=33.82 E-value=70 Score=30.66 Aligned_cols=79 Identities=25% Similarity=0.331 Sum_probs=56.2
Q ss_pred cceEEEEecCccccceeecCC--ccCHHHHHHHHHhhhcccccCCcCCCCCccccchhhhhhccCCCceeeEEEcCCCCe
Q 026005 127 VAFVKVSMDGAPYLRKVDLKL--YKSYQELSDALGKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGDW 204 (245)
Q Consensus 127 ~~~VKV~MdG~pigRKVDL~~--~~sY~~L~~aLe~MF~~~~~~~~~~~g~~~~~~e~~l~d~~~~sey~ltYeDkeGDw 204 (245)
..-||-..|-+ =|..-|.. -.+|++.+.-|+++-.+ .+.++.|-|.|.-||.
T Consensus 18 ~veVKSKFdaE--fRRfsl~r~~~~~f~~F~~Lv~~~H~i------------------------~nvdvllgY~d~hgDL 71 (358)
T KOG3606|consen 18 TVEVKSKFDAE--FRRFSLPRHSASSFDEFYSLVEHLHHI------------------------PNVDVLLGYADTHGDL 71 (358)
T ss_pred eEEeeccccch--hheecccccCcccHHHHHHHHHHHhcC------------------------CCceEEEEEecCCCce
Confidence 45667666654 35555544 46899999999888775 2457899999999999
Q ss_pred Eecc-CCChhhhhhcce---eeEEecCCccc
Q 026005 205 MLVG-DVPWDMFVDSCK---RLRIMKGSEAI 231 (245)
Q Consensus 205 MLVG-DvPW~mFv~svK---RLrImk~sea~ 231 (245)
+-+- |+-+.--+++++ ||.|-|..||.
T Consensus 72 LPinNDDn~~ka~~sa~PlLR~~iQkr~ea~ 102 (358)
T KOG3606|consen 72 LPINNDDNLHKALSSARPLLRLLIQKREEAD 102 (358)
T ss_pred ecccCchhHHHHhhccCchhhhhhhhhhhhh
Confidence 9764 566666667776 66777776665
No 20
>PF09840 DUF2067: Uncharacterized protein conserved in archaea (DUF2067); InterPro: IPR019202 This family of archaeal proteins, have no known function.
Probab=33.28 E-value=18 Score=31.99 Aligned_cols=36 Identities=28% Similarity=0.493 Sum_probs=29.6
Q ss_pred hhhhccCCCceeeEEEcCCCCeEeccCCChhhhhhcceee
Q 026005 183 KLIDLLNGSDYVPTYEDKDGDWMLVGDVPWDMFVDSCKRL 222 (245)
Q Consensus 183 ~l~d~~~~sey~ltYeDkeGDwMLVGDvPW~mFv~svKRL 222 (245)
-|.|.+.-.+|..-|.+. .|..|.||+.+++.++||
T Consensus 90 ~L~~~L~~~G~~ae~~~~----~i~T~a~~eev~~l~~~L 125 (190)
T PF09840_consen 90 LLVDALKLLGYKAEYRED----VIKTDAPLEEVVELAERL 125 (190)
T ss_pred HHHHHHHhCCCeeEEeCC----eEEecCCHHHHHHHHHHH
Confidence 455666667898888655 889999999999999986
No 21
>KOG3938 consensus RGS-GAIP interacting protein GIPC, contains PDZ domain [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=33.15 E-value=75 Score=30.34 Aligned_cols=75 Identities=24% Similarity=0.414 Sum_probs=52.1
Q ss_pred cCccccceeecCCccCHHHHHHHHHhhhcccccC--CcCCCCCccccchhhhhhccCCCceeeEEEcCCCCeEeccCCCh
Q 026005 135 DGAPYLRKVDLKLYKSYQELSDALGKMFSSFTIG--NCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGDWMLVGDVPW 212 (245)
Q Consensus 135 dG~pigRKVDL~~~~sY~~L~~aLe~MF~~~~~~--~~~~~g~~~~~~e~~l~d~~~~sey~ltYeDkeGDwMLVGDvPW 212 (245)
+|.|.|| +.-|++-++|++.+..-|.+.... -|- +| .|. -|=+.||-|-.-.
T Consensus 62 HGSptg~---Ie~fsnv~ELY~kIAe~F~Is~~dIlfcT----------------lN--shK-----vDM~~llgGqigl 115 (334)
T KOG3938|consen 62 HGSPTGR---IEGFSNVRELYQKIAEAFDISPDDILFCT----------------LN--SHK-----VDMKRLLGGQIGL 115 (334)
T ss_pred cCCccce---ecccccHHHHHHHHHHHhcCCccceEEEe----------------cC--CCc-----ccHHHHhcCccCh
Confidence 5667776 457899999999999999862110 011 01 011 2334588888888
Q ss_pred hhhh-----hcceeeEEecCCcccCCCc
Q 026005 213 DMFV-----DSCKRLRIMKGSEAIGLAP 235 (245)
Q Consensus 213 ~mFv-----~svKRLrImk~sea~gl~~ 235 (245)
+.|+ .-.|-++|+|..+|-||+.
T Consensus 116 eDfiFAHvkGq~kEv~v~KsedalGlTI 143 (334)
T KOG3938|consen 116 EDFIFAHVKGQAKEVEVVKSEDALGLTI 143 (334)
T ss_pred hhhhhhhhcCcceeEEEEecccccceEE
Confidence 8887 4567899999999998873
No 22
>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=32.95 E-value=16 Score=31.60 Aligned_cols=10 Identities=50% Similarity=0.936 Sum_probs=6.6
Q ss_pred cccCCCCCCC
Q 026005 9 LRLGLPGGNG 18 (245)
Q Consensus 9 LRLGLPG~~~ 18 (245)
=|||.||+++
T Consensus 100 GRLGvPGSGS 109 (154)
T PF11576_consen 100 GRLGVPGSGS 109 (154)
T ss_dssp EE-SSTTS-E
T ss_pred ccccCCCCcc
Confidence 3999999874
No 23
>COG0219 CspR Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]
Probab=31.56 E-value=22 Score=30.78 Aligned_cols=73 Identities=25% Similarity=0.399 Sum_probs=45.5
Q ss_pred cCccccceeecCCccCHHHHHHHH---HhhhcccccCCcCCCCCccccchhhhhhccCCCceeeEEEcCCCCeEeccCC-
Q 026005 135 DGAPYLRKVDLKLYKSYQELSDAL---GKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGDWMLVGDV- 210 (245)
Q Consensus 135 dG~pigRKVDL~~~~sY~~L~~aL---e~MF~~~~~~~~~~~g~~~~~~e~~l~d~~~~sey~ltYeDkeGDwMLVGDv- 210 (245)
-|-.|.-+++|..|++|++...+. .++|-..+-+. .-|. -+....|||+|-|-.
T Consensus 48 AGlDY~~~~~l~~h~s~e~fl~~~~~~~rl~~~tt~~~---------------------~~~~-~~~f~~~d~llFG~Es 105 (155)
T COG0219 48 AGLDYHEKASLTEHDSLEAFLEAEPIGGRLFALTTKGT---------------------TTYT-DVSFQKGDYLLFGPES 105 (155)
T ss_pred cccchHhhcceEEeCCHHHHHhhccCCceEEEEEeccc---------------------cccc-cccCCCCCEEEECCCC
Confidence 366799999999999999999998 46776433221 0111 144466999999964
Q ss_pred ---Chhhhhh-cceeeEEecCCc
Q 026005 211 ---PWDMFVD-SCKRLRIMKGSE 229 (245)
Q Consensus 211 ---PW~mFv~-svKRLrImk~se 229 (245)
|=+.--. .-++|||=-..+
T Consensus 106 ~GLP~~i~~~~~~~~irIPm~~~ 128 (155)
T COG0219 106 RGLPEEILDAAPDRCIRIPMRPG 128 (155)
T ss_pred CCCCHHHHHhCccceEEeccCCC
Confidence 5222222 223588844333
No 24
>cd00771 ThrRS_core Threonyl-tRNA synthetase (ThrRS) class II core catalytic domain. ThrRS is a homodimer. It is responsible for the attachment of threonine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core domain.
Probab=25.11 E-value=23 Score=32.62 Aligned_cols=54 Identities=26% Similarity=0.421 Sum_probs=33.0
Q ss_pred cceEEEEecCccccceeecCCccCHHHHHHHHHhhhcccccCCcCCCCCccccchhhhhhccCCCceeeEEEcCCCC
Q 026005 127 VAFVKVSMDGAPYLRKVDLKLYKSYQELSDALGKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGD 203 (245)
Q Consensus 127 ~~~VKV~MdG~pigRKVDL~~~~sY~~L~~aLe~MF~~~~~~~~~~~g~~~~~~e~~l~d~~~~sey~ltYeDkeGD 203 (245)
-.|.-.-=||+-||-|||..+.++ |.+-+.+-|+ + .|.....-|-|+|.|.||.
T Consensus 209 ~~~~~~~g~~afygpkid~~~~d~-------~gr~~q~~t~---------------q-ld~~~~~~f~l~y~~~~~~ 262 (298)
T cd00771 209 LPYEINEGEGAFYGPKIDFHVKDA-------LGREWQCSTI---------------Q-LDFNLPERFDLTYIGEDGE 262 (298)
T ss_pred CCceECCCCcccccceEEEEEEeC-------CCCeeeccee---------------E-eeccChhhcCCEEEccCCC
Confidence 346666667788888888877653 3333333221 1 2222345788999999986
No 25
>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=24.53 E-value=49 Score=26.13 Aligned_cols=19 Identities=37% Similarity=0.548 Sum_probs=16.5
Q ss_pred ceeeEEEcCCCCeEeccCC
Q 026005 192 DYVPTYEDKDGDWMLVGDV 210 (245)
Q Consensus 192 ey~ltYeDkeGDwMLVGDv 210 (245)
=|++-|+|.+||+..-|.|
T Consensus 92 iwiaP~~D~~g~l~~~~~V 110 (119)
T PF09676_consen 92 IWIAPWEDADGDLHDPGYV 110 (119)
T ss_pred EEEeeeECCCCCEeccceE
Confidence 4899999999999888766
No 26
>PRK13361 molybdenum cofactor biosynthesis protein A; Provisional
Probab=22.68 E-value=2.6e+02 Score=25.96 Aligned_cols=76 Identities=14% Similarity=0.190 Sum_probs=42.6
Q ss_pred EecCccccceee--cCCccCHHHHHHHHHhhhcccccCCcCCCCCccccchhhhhhccCC-CceeeEEEcCCCCeEeccC
Q 026005 133 SMDGAPYLRKVD--LKLYKSYQELSDALGKMFSSFTIGNCGSQGMKDFMNESKLIDLLNG-SDYVPTYEDKDGDWMLVGD 209 (245)
Q Consensus 133 ~MdG~pigRKVD--L~~~~sY~~L~~aLe~MF~~~~~~~~~~~g~~~~~~e~~l~d~~~~-sey~ltYeDkeGDwMLVGD 209 (245)
+++-.|+|+--+ -..+=+.+++...|++.|....+.. . .++ ..| ..+.|..|-.=++.-
T Consensus 188 ~ie~mP~g~~~~~~~~~~~~~~e~~~~l~~~~~~~~~~~-~----------------~~~~~~~-~~~~~~~~~ig~I~~ 249 (329)
T PRK13361 188 FIEEMPLGEIDERRRARHCSSDEVRAIIETRYPLTPSNK-R----------------TGGPARY-YTMADSPIHIGFISP 249 (329)
T ss_pred EEecccCCCccchhhccCcCHHHHHHHHHHhCCcccCCC-C----------------CCCCCeE-EEECCCCeEEEEEcC
Confidence 456678887222 3456678888888888876322210 0 011 112 112233344444444
Q ss_pred CChhhhhhcceeeEEecC
Q 026005 210 VPWDMFVDSCKRLRIMKG 227 (245)
Q Consensus 210 vPW~mFv~svKRLrImk~ 227 (245)
+-+. ||.+|-||||-..
T Consensus 250 ~s~~-fC~~Cnr~rlt~~ 266 (329)
T PRK13361 250 HSHN-FCHECNRVRVTAE 266 (329)
T ss_pred CCcc-ccccCCeEEEccC
Confidence 4454 9999999999654
No 27
>KOG3957 consensus Predicted L-carnitine dehydratase/alpha-methylacyl-CoA racemase [Lipid transport and metabolism]
Probab=21.31 E-value=1.2e+02 Score=29.87 Aligned_cols=77 Identities=22% Similarity=0.233 Sum_probs=53.4
Q ss_pred ccceeecCCccCHHHHHHHHHhhhcccccCCcCCCCCccccchhhhhhccCC-CceeeEEEcCCCCeEeccCCChhhhhh
Q 026005 139 YLRKVDLKLYKSYQELSDALGKMFSSFTIGNCGSQGMKDFMNESKLIDLLNG-SDYVPTYEDKDGDWMLVGDVPWDMFVD 217 (245)
Q Consensus 139 igRKVDL~~~~sY~~L~~aLe~MF~~~~~~~~~~~g~~~~~~e~~l~d~~~~-sey~ltYeDkeGDwMLVGDvPW~mFv~ 217 (245)
-|-.||-++..+-.-|+.-|..-+.. +.++..- ..+.+| .-+-=||+-|||-.|.||-.- .-|.+
T Consensus 177 kGqviD~~m~eg~ayl~S~v~~~y~~---s~~ea~R----------~~~~~G~~~~Y~tykTkDG~fmavga~e-pQF~~ 242 (387)
T KOG3957|consen 177 KGQVIDCNMLEGVAYLLSFVQKNYLQ---SLWEADR----------YGTAHGSIPPYQTYKTKDGYFMAVGALE-PQFYE 242 (387)
T ss_pred CceEEEechhHhHHHHHHHHHHHhhh---hhccccc----------cccccCCCccceeeeccCceEEEecccc-HHHHH
Confidence 47789999999888888877766653 3333210 112233 345558999999999999863 36999
Q ss_pred cceeeEEecCCc
Q 026005 218 SCKRLRIMKGSE 229 (245)
Q Consensus 218 svKRLrImk~se 229 (245)
.|+++-..+.-+
T Consensus 243 ~l~~ll~~~~d~ 254 (387)
T KOG3957|consen 243 LLKKLLGLKLDE 254 (387)
T ss_pred HHHHhhCccccc
Confidence 999887776553
No 28
>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=20.75 E-value=1.1e+02 Score=25.84 Aligned_cols=37 Identities=24% Similarity=0.482 Sum_probs=30.9
Q ss_pred cceEEEEecCc--cccceeecCCccCHHHHHHHHHhhhc
Q 026005 127 VAFVKVSMDGA--PYLRKVDLKLYKSYQELSDALGKMFS 163 (245)
Q Consensus 127 ~~~VKV~MdG~--pigRKVDL~~~~sY~~L~~aLe~MF~ 163 (245)
..-+||..+|. +|=|.|-+..--+..+|..+|+..|+
T Consensus 4 ~y~lkV~L~~~~p~iwRri~Vp~~~tl~~Lh~~Iq~afg 42 (179)
T PF07929_consen 4 VYQLKVSLKGSKPPIWRRIEVPADITLADLHEVIQAAFG 42 (179)
T ss_dssp EEEEEEEETT-SS-EEEEEEEETT-BHHHHHHHHHHHTT
T ss_pred EEEEEEEEcCCCCCeEEEEEECCCCCHHHHHHHHHHHhC
Confidence 34579999885 89999999999999999999999997
Done!