Query 029018
Match_columns 200
No_of_seqs 223 out of 553
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 06:10:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029018.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029018hhsearch_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 2.8E-58 6.1E-63 390.6 0.5 184 8-200 1-191 (215)
2 PF00564 PB1: PB1 domain; Int 97.3 0.00082 1.8E-08 48.1 6.2 56 116-196 3-58 (84)
3 cd06398 PB1_Joka2 The PB1 doma 97.2 0.0013 2.9E-08 50.0 6.7 57 116-195 2-61 (91)
4 cd06407 PB1_NLP A PB1 domain i 97.1 0.0024 5.2E-08 47.6 6.9 54 116-194 2-55 (82)
5 smart00666 PB1 PB1 domain. Pho 96.8 0.0059 1.3E-07 43.6 7.0 54 117-196 4-57 (81)
6 cd06396 PB1_NBR1 The PB1 domai 96.8 0.0052 1.1E-07 46.2 6.3 52 117-194 3-54 (81)
7 cd05992 PB1 The PB1 domain is 96.4 0.018 3.9E-07 40.8 7.0 55 116-196 2-57 (81)
8 cd06403 PB1_Par6 The PB1 domai 96.0 0.018 3.9E-07 43.4 5.5 54 117-194 3-56 (80)
9 cd06404 PB1_aPKC PB1 domain is 95.9 0.024 5.3E-07 42.9 5.8 53 117-194 3-55 (83)
10 cd06409 PB1_MUG70 The MUG70 pr 95.8 0.022 4.8E-07 43.2 5.3 50 124-194 7-58 (86)
11 cd06402 PB1_p62 The PB1 domain 95.8 0.051 1.1E-06 41.3 7.1 57 115-194 1-62 (87)
12 cd06401 PB1_TFG The PB1 domain 95.6 0.061 1.3E-06 40.6 6.9 57 117-196 3-60 (81)
13 cd06397 PB1_UP1 Uncharacterize 95.0 0.094 2E-06 39.7 6.1 53 117-195 3-55 (82)
14 cd06408 PB1_NoxR The PB1 domai 93.0 0.39 8.5E-06 36.5 6.2 54 115-196 3-56 (86)
15 cd06399 PB1_P40 The PB1 domain 72.2 6.5 0.00014 30.4 4.0 39 130-194 22-60 (92)
16 PF10411 DsbC_N: Disulfide bon 54.6 10 0.00022 26.0 2.0 17 181-197 34-50 (57)
17 cd06395 PB1_Map2k5 PB1 domain 51.0 30 0.00066 26.5 4.2 48 123-195 10-57 (91)
18 COG0219 CspR Predicted rRNA me 27.3 26 0.00056 29.5 0.6 30 122-151 48-80 (155)
19 PF11576 DUF3236: Protein of u 24.7 27 0.00058 29.3 0.2 12 12-23 97-108 (154)
20 PF03589 Antiterm: Antitermina 24.5 29 0.00064 26.5 0.4 29 8-50 18-46 (95)
21 cd00771 ThrRS_core Threonyl-tR 22.9 22 0.00049 31.6 -0.6 55 113-190 208-262 (298)
22 PF07929 PRiA4_ORF3: Plasmid p 22.4 1E+02 0.0022 25.2 3.2 35 116-150 6-42 (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=2.8e-58 Score=390.64 Aligned_cols=184 Identities=51% Similarity=0.861 Sum_probs=6.0
Q ss_pred CCccccccccCCCCCCCCchhhHhhhhcCCCCCCCCCCCCcchhhhhhhhcccccccccccc-cCCCC-CCCCCCCCCCC
Q 029018 8 MDFKETELCLGLPGGGNNKKDEAAALELTPTPKASNKRGFCETAVIDLKLNLQSKESSVDLN-ENFKN-PPSNNKNHDKD 85 (200)
Q Consensus 8 l~~~~TELRLGLPG~~~~~~~~~~~~~~~~~~~~~~KR~fset~~~dl~l~l~~~~~~~~~~-~~~~~-~~~~~~~~~~d 85 (200)
||||+|||||||||+.+++.. .........+++||+|+++ ++............... ..... ..........+
T Consensus 1 ln~~~TELrLGLPG~~~~~~~---~~~~~~~~~~~~kR~F~~a--id~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 75 (215)
T PF02309_consen 1 LNLKATELRLGLPGSESPDAS---SSSSSKKSSSGNKRGFSEA--IDSSSSNSQSSSSSSSDSSSSSSSSSTSSSSSDSS 75 (215)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred CCchhhhhcccCCCCCCCCcc---cccccccccCcccccchhh--hhhcccccccccccccccCcccccccccccccccc
Confidence 799999999999998654210 0011223567889999998 76543110000000000 00000 00000000112
Q ss_pred CCCCCCccCCccccCCCCccchhhhcc-----CCceeEEEEeCccccceeecCCCCCHHHHHHHHHHhhcccccCCcCCc
Q 029018 86 PAKPSANKAQVVGWPPVRSYRKNAMAE-----TAAFVKVCMDGAPYLRKVDLKTYKSYQELSDALAKMFSSFTMGNYGSQ 160 (200)
Q Consensus 86 ~~~pp~~k~qvVGWPPVrs~Rkn~~~~-----~~~~VKV~MdG~pigRKVDL~~~~sY~eL~~aLe~MF~~~~~~~~~~~ 160 (200)
...+|++++|+|||||||+||||++.. .++||||+|||+||||||||++|+||++|+.+|++||.+|.|.+|+++
T Consensus 76 ~~~~p~~~~~~vgwpp~~s~r~n~~~~~~~~~~~~~vKV~mdG~~igRkVDL~~~~sY~~L~~~L~~MF~~~~i~~~~~~ 155 (215)
T PF02309_consen 76 SSSPPASKAQVVGWPPVRSFRKNSLSEKQSSSSRSYVKVNMDGVPIGRKVDLSAYSSYEELSSALEKMFSCFSIEQCGSH 155 (215)
T ss_dssp ----------BTTBS----S------------------------------------------------------------
T ss_pred cCCCCcccccccCCCcccccccccccccccccCCceeEEEecCcccceecCHHHhhCHHHHHHHHHHhcCCCCccccccc
Confidence 334455789999999999999998773 579999999999999999999999999999999999998888888775
Q ss_pred CccccchhhhhhccCCCCCeEEEEEeCCCCEEecccCCCC
Q 029018 161 GMIDFMNESKLMDLLNSSDYVPTYEDKDGDWMLVGDVPWE 200 (200)
Q Consensus 161 g~~~~~~e~~l~d~~~~seyvltYeDkdGDwMLVGDvPWe 200 (200)
+ .++..+.+++++++|+|||||+||||||||||||+
T Consensus 156 ~----~~~~~~~~~~~~~~~~l~Y~D~egd~mlvGD~PW~ 191 (215)
T PF02309_consen 156 G----LNESGLLDLLNGSEYVLVYEDKEGDWMLVGDVPWE 191 (215)
T ss_dssp ----------------------------------------
T ss_pred c----ccchhhccccCCcceeEEEECCCCCEEEecCCCHH
Confidence 4 55667777788899999999999999999999996
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=97.31 E-value=0.00082 Score=48.12 Aligned_cols=56 Identities=27% Similarity=0.476 Sum_probs=46.3
Q ss_pred eeEEEEeCccccceeecCCCCCHHHHHHHHHHhhcccccCCcCCcCccccchhhhhhccCCCCCeEEEEEeCCCCEEecc
Q 029018 116 FVKVCMDGAPYLRKVDLKTYKSYQELSDALAKMFSSFTMGNYGSQGMIDFMNESKLMDLLNSSDYVPTYEDKDGDWMLVG 195 (200)
Q Consensus 116 ~VKV~MdG~pigRKVDL~~~~sY~eL~~aLe~MF~~~~~~~~~~~g~~~~~~e~~l~d~~~~seyvltYeDkdGDwMLVG 195 (200)
-|||...|. +=|.+.+..--+|.+|...+++.|... ...+.+.|.|.||||..+-
T Consensus 3 ~vK~~~~~~-~~~~~~~~~~~s~~~L~~~i~~~~~~~------------------------~~~~~l~Y~D~dgD~V~i~ 57 (84)
T PF00564_consen 3 RVKVRYGGD-IRRIISLPSDVSFDDLRSKIREKFGLL------------------------DEDFQLKYKDEDGDLVTIS 57 (84)
T ss_dssp EEEEEETTE-EEEEEEECSTSHHHHHHHHHHHHHTTS------------------------TSSEEEEEEETTSSEEEES
T ss_pred EEEEEECCe-eEEEEEcCCCCCHHHHHHHHHHHhCCC------------------------CccEEEEeeCCCCCEEEeC
Confidence 489999998 444688888889999999999999751 3468999999999998875
Q ss_pred c
Q 029018 196 D 196 (200)
Q Consensus 196 D 196 (200)
+
T Consensus 58 s 58 (84)
T PF00564_consen 58 S 58 (84)
T ss_dssp S
T ss_pred C
Confidence 3
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=0.0013 Score=49.99 Aligned_cols=57 Identities=25% Similarity=0.276 Sum_probs=45.2
Q ss_pred eeEEEEeCccccceeecC---CCCCHHHHHHHHHHhhcccccCCcCCcCccccchhhhhhccCCCCCeEEEEEeCCCCEE
Q 029018 116 FVKVCMDGAPYLRKVDLK---TYKSYQELSDALAKMFSSFTMGNYGSQGMIDFMNESKLMDLLNSSDYVPTYEDKDGDWM 192 (200)
Q Consensus 116 ~VKV~MdG~pigRKVDL~---~~~sY~eL~~aLe~MF~~~~~~~~~~~g~~~~~~e~~l~d~~~~seyvltYeDkdGDwM 192 (200)
-|||.-+|.-+=-++++. .--+|++|...+.+.|... ...+|+|.|.|.||||.
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 489999999544455553 4679999999999999751 13589999999999998
Q ss_pred ecc
Q 029018 193 LVG 195 (200)
Q Consensus 193 LVG 195 (200)
.+-
T Consensus 59 ~l~ 61 (91)
T cd06398 59 TLV 61 (91)
T ss_pred EEc
Confidence 764
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=97.08 E-value=0.0024 Score=47.60 Aligned_cols=54 Identities=26% Similarity=0.404 Sum_probs=43.3
Q ss_pred eeEEEEeCccccceeecCCCCCHHHHHHHHHHhhcccccCCcCCcCccccchhhhhhccCCCCCeEEEEEeCCCCEEec
Q 029018 116 FVKVCMDGAPYLRKVDLKTYKSYQELSDALAKMFSSFTMGNYGSQGMIDFMNESKLMDLLNSSDYVPTYEDKDGDWMLV 194 (200)
Q Consensus 116 ~VKV~MdG~pigRKVDL~~~~sY~eL~~aLe~MF~~~~~~~~~~~g~~~~~~e~~l~d~~~~seyvltYeDkdGDwMLV 194 (200)
=|||+..|. .+.+-|..--+|++|...+.++|.. . +.+.|.|-|.|.||||.++
T Consensus 2 ~vK~~~~~d--~~r~~l~~~~~~~~L~~~i~~r~~~---~--------------------~~~~f~LkY~Ddegd~v~l 55 (82)
T cd06407 2 RVKATYGEE--KIRFRLPPSWGFTELKQEIAKRFKL---D--------------------DMSAFDLKYLDDDEEWVLL 55 (82)
T ss_pred EEEEEeCCe--EEEEEcCCCCCHHHHHHHHHHHhCC---C--------------------CCCeeEEEEECCCCCeEEe
Confidence 389999887 4455555566999999999999974 0 1357999999999999875
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=96.85 E-value=0.0059 Score=43.63 Aligned_cols=54 Identities=26% Similarity=0.506 Sum_probs=43.7
Q ss_pred eEEEEeCccccceeecCCCCCHHHHHHHHHHhhcccccCCcCCcCccccchhhhhhccCCCCCeEEEEEeCCCCEEeccc
Q 029018 117 VKVCMDGAPYLRKVDLKTYKSYQELSDALAKMFSSFTMGNYGSQGMIDFMNESKLMDLLNSSDYVPTYEDKDGDWMLVGD 196 (200)
Q Consensus 117 VKV~MdG~pigRKVDL~~~~sY~eL~~aLe~MF~~~~~~~~~~~g~~~~~~e~~l~d~~~~seyvltYeDkdGDwMLVGD 196 (200)
|||.-.|. -|.+-+..--+|.+|...+.+.|.. ....+.|.|+|.||||..+.+
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 78887544 6777888889999999999999974 124689999999999987653
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=96.75 E-value=0.0052 Score=46.21 Aligned_cols=52 Identities=19% Similarity=0.236 Sum_probs=45.5
Q ss_pred eEEEEeCccccceeecCCCCCHHHHHHHHHHhhcccccCCcCCcCccccchhhhhhccCCCCCeEEEEEeCCCCEEec
Q 029018 117 VKVCMDGAPYLRKVDLKTYKSYQELSDALAKMFSSFTMGNYGSQGMIDFMNESKLMDLLNSSDYVPTYEDKDGDWMLV 194 (200)
Q Consensus 117 VKV~MdG~pigRKVDL~~~~sY~eL~~aLe~MF~~~~~~~~~~~g~~~~~~e~~l~d~~~~seyvltYeDkdGDwMLV 194 (200)
|||.-.|.-+--+++-+..-+|++|...+.++|+. + .|.|.|-|.||||.++
T Consensus 3 vKaty~~d~~rf~~~~~~~~~~~~L~~ev~~rf~l------------------------~--~f~lKYlDde~e~v~l 54 (81)
T cd06396 3 LKVTYNGESQSFLVSDSENTTWASVEAMVKVSFGL------------------------N--DIQIKYVDEENEEVSV 54 (81)
T ss_pred EEEEECCeEEEEEecCCCCCCHHHHHHHHHHHhCC------------------------C--cceeEEEcCCCCEEEE
Confidence 89999999777788887788999999999999975 1 5789999999999986
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=96.42 E-value=0.018 Score=40.83 Aligned_cols=55 Identities=25% Similarity=0.424 Sum_probs=42.9
Q ss_pred eeEEEEeCccccceeecC-CCCCHHHHHHHHHHhhcccccCCcCCcCccccchhhhhhccCCCCCeEEEEEeCCCCEEec
Q 029018 116 FVKVCMDGAPYLRKVDLK-TYKSYQELSDALAKMFSSFTMGNYGSQGMIDFMNESKLMDLLNSSDYVPTYEDKDGDWMLV 194 (200)
Q Consensus 116 ~VKV~MdG~pigRKVDL~-~~~sY~eL~~aLe~MF~~~~~~~~~~~g~~~~~~e~~l~d~~~~seyvltYeDkdGDwMLV 194 (200)
-|||.-.|. -|.+=+. .--+|++|...|.+.|... ...+.+.|.|.||||..+
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 378888865 3444444 8889999999999999751 146799999999999887
Q ss_pred cc
Q 029018 195 GD 196 (200)
Q Consensus 195 GD 196 (200)
.+
T Consensus 56 ~s 57 (81)
T cd05992 56 SS 57 (81)
T ss_pred CC
Confidence 64
No 8
>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=96.04 E-value=0.018 Score=43.37 Aligned_cols=54 Identities=19% Similarity=0.294 Sum_probs=40.8
Q ss_pred eEEEEeCccccceeecCCCCCHHHHHHHHHHhhcccccCCcCCcCccccchhhhhhccCCCCCeEEEEEeCCCCEEec
Q 029018 117 VKVCMDGAPYLRKVDLKTYKSYQELSDALAKMFSSFTMGNYGSQGMIDFMNESKLMDLLNSSDYVPTYEDKDGDWMLV 194 (200)
Q Consensus 117 VKV~MdG~pigRKVDL~~~~sY~eL~~aLe~MF~~~~~~~~~~~g~~~~~~e~~l~d~~~~seyvltYeDkdGDwMLV 194 (200)
||...|..=-=-.+|.....+|+++++-|+.||.. .+..|+|.|.|.+||.+-+
T Consensus 3 VKSkfdaEfRRFsl~r~~~~~f~ef~~ll~~lH~l------------------------~~~~f~i~Y~D~~gDLLPI 56 (80)
T cd06403 3 VKSKFDAEFRRFSLDRNKPGKFEDFYKLLEHLHHI------------------------PNVDFLIGYTDPHGDLLPI 56 (80)
T ss_pred eecccCCeEEEEEeccccCcCHHHHHHHHHHHhCC------------------------CCCcEEEEEeCCCCCEecc
Confidence 66666666222245556679999999999999975 1357899999999998744
No 9
>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=95.91 E-value=0.024 Score=42.91 Aligned_cols=53 Identities=23% Similarity=0.347 Sum_probs=42.8
Q ss_pred eEEEEeCccccceeecCCCCCHHHHHHHHHHhhcccccCCcCCcCccccchhhhhhccCCCCCeEEEEEeCCCCEEec
Q 029018 117 VKVCMDGAPYLRKVDLKTYKSYQELSDALAKMFSSFTMGNYGSQGMIDFMNESKLMDLLNSSDYVPTYEDKDGDWMLV 194 (200)
Q Consensus 117 VKV~MdG~pigRKVDL~~~~sY~eL~~aLe~MF~~~~~~~~~~~g~~~~~~e~~l~d~~~~seyvltYeDkdGDwMLV 194 (200)
||+.-.|.-+--.+|. .-+|++|.+.+.+||.. ..+..|++.|.|.|||---+
T Consensus 3 ~K~~y~gdi~it~~d~--~~s~e~L~~~v~~~c~~-----------------------~~~q~ft~kw~DEEGDp~ti 55 (83)
T cd06404 3 VKAAYNGDIMITSIDP--SISLEELCNEVRDMCRF-----------------------HNDQPFTLKWIDEEGDPCTI 55 (83)
T ss_pred EEEEecCcEEEEEcCC--CcCHHHHHHHHHHHhCC-----------------------CCCCcEEEEEECCCCCceee
Confidence 7999999966666666 67899999999999985 12457999999999996543
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=95.82 E-value=0.022 Score=43.18 Aligned_cols=50 Identities=22% Similarity=0.373 Sum_probs=38.3
Q ss_pred ccccceeecCC--CCCHHHHHHHHHHhhcccccCCcCCcCccccchhhhhhccCCCCCeEEEEEeCCCCEEec
Q 029018 124 APYLRKVDLKT--YKSYQELSDALAKMFSSFTMGNYGSQGMIDFMNESKLMDLLNSSDYVPTYEDKDGDWMLV 194 (200)
Q Consensus 124 ~pigRKVDL~~--~~sY~eL~~aLe~MF~~~~~~~~~~~g~~~~~~e~~l~d~~~~seyvltYeDkdGDwMLV 194 (200)
.|-||.+=++. ..|+.+|..++.+=|+.-. .....|.|.|.|.||||.++
T Consensus 7 ~~~GrvhRf~~~~s~~~~~L~~~I~~Rl~~d~---------------------~~~~~~~L~YlDDEgD~Vll 58 (86)
T cd06409 7 DPKGRVHRFRLRPSESLEELRTLISQRLGDDD---------------------FETHLYALSYVDDEGDIVLI 58 (86)
T ss_pred CCCCCEEEEEecCCCCHHHHHHHHHHHhCCcc---------------------ccCCcccEEEEcCCCCEEEE
Confidence 56777665553 7899999999999997510 01357899999999999986
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=95.78 E-value=0.051 Score=41.29 Aligned_cols=57 Identities=25% Similarity=0.454 Sum_probs=43.0
Q ss_pred ceeEEEEeC---ccccceeec--CCCCCHHHHHHHHHHhhcccccCCcCCcCccccchhhhhhccCCCCCeEEEEEeCCC
Q 029018 115 AFVKVCMDG---APYLRKVDL--KTYKSYQELSDALAKMFSSFTMGNYGSQGMIDFMNESKLMDLLNSSDYVPTYEDKDG 189 (200)
Q Consensus 115 ~~VKV~MdG---~pigRKVDL--~~~~sY~eL~~aLe~MF~~~~~~~~~~~g~~~~~~e~~l~d~~~~seyvltYeDkdG 189 (200)
+.||.+..| .+=-|++-| ....+|++|...+.++|.. +.+..|++.|.|.||
T Consensus 1 ~~vkayl~~~~~~~EIRRf~l~~~~~~s~~~L~~~V~~~f~~-----------------------l~~~~ftlky~DeeG 57 (87)
T cd06402 1 LTVKAYLLGKDANAEIRRFAIDEDVSTSYEYLVEKVAAVFPS-----------------------LRGKNFQLFWKDEEG 57 (87)
T ss_pred CeEEEeecCCCCccceEEEEecCCCCcCHHHHHHHHHHHccc-----------------------cCCCcEEEEEECCCC
Confidence 368888877 333455444 6667999999999999964 124689999999999
Q ss_pred CEEec
Q 029018 190 DWMLV 194 (200)
Q Consensus 190 DwMLV 194 (200)
|..-+
T Consensus 58 DlvtI 62 (87)
T cd06402 58 DLVAF 62 (87)
T ss_pred CEEee
Confidence 98654
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=95.61 E-value=0.061 Score=40.57 Aligned_cols=57 Identities=25% Similarity=0.412 Sum_probs=40.8
Q ss_pred eEEEEeCccccceeecCCC-CCHHHHHHHHHHhhcccccCCcCCcCccccchhhhhhccCCCCCeEEEEEeCCCCEEecc
Q 029018 117 VKVCMDGAPYLRKVDLKTY-KSYQELSDALAKMFSSFTMGNYGSQGMIDFMNESKLMDLLNSSDYVPTYEDKDGDWMLVG 195 (200)
Q Consensus 117 VKV~MdG~pigRKVDL~~~-~sY~eL~~aLe~MF~~~~~~~~~~~g~~~~~~e~~l~d~~~~seyvltYeDkdGDwMLVG 195 (200)
+|+.-.|. | |++=+..- -+|.+|...+++.|.... -....+.+.|.|.|||+.-|-
T Consensus 3 iK~~~g~D-i-R~~~~~~~~~t~~~L~~~v~~~F~~~~---------------------~~~~~flIKYkD~dGDlVTIt 59 (81)
T cd06401 3 LKAQLGDD-I-RRIPIHNEDITYDELLLMMQRVFRGKL---------------------GSSDDVLIKYKDEDGDLITIF 59 (81)
T ss_pred EEEEeCCe-E-EEEeccCccccHHHHHHHHHHHhcccc---------------------CCcccEEEEEECCCCCEEEec
Confidence 67777665 4 55544442 399999999999998410 013478999999999998664
Q ss_pred c
Q 029018 196 D 196 (200)
Q Consensus 196 D 196 (200)
+
T Consensus 60 s 60 (81)
T cd06401 60 D 60 (81)
T ss_pred c
Confidence 3
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=94.96 E-value=0.094 Score=39.67 Aligned_cols=53 Identities=19% Similarity=0.299 Sum_probs=43.4
Q ss_pred eEEEEeCccccceeecCCCCCHHHHHHHHHHhhcccccCCcCCcCccccchhhhhhccCCCCCeEEEEEeCCCCEEecc
Q 029018 117 VKVCMDGAPYLRKVDLKTYKSYQELSDALAKMFSSFTMGNYGSQGMIDFMNESKLMDLLNSSDYVPTYEDKDGDWMLVG 195 (200)
Q Consensus 117 VKV~MdG~pigRKVDL~~~~sY~eL~~aLe~MF~~~~~~~~~~~g~~~~~~e~~l~d~~~~seyvltYeDkdGDwMLVG 195 (200)
-||+-.|. .|++-...-=+|..|...|+.+|.... . .+.+||.|.|||..-+-
T Consensus 3 fKv~~~g~--~RRf~~~~~pt~~~L~~kl~~Lf~lp~-----------------------~-~~~vtYiDeD~D~ITls 55 (82)
T cd06397 3 FKSSFLGD--TRRIVFPDIPTWEALASKLENLYNLPE-----------------------I-KVGVTYIDNDNDEITLS 55 (82)
T ss_pred EEEEeCCc--eEEEecCCCccHHHHHHHHHHHhCCCh-----------------------h-HeEEEEEcCCCCEEEec
Confidence 47888886 788888888999999999999998621 1 27999999999987543
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=92.97 E-value=0.39 Score=36.51 Aligned_cols=54 Identities=20% Similarity=0.320 Sum_probs=44.0
Q ss_pred ceeEEEEeCccccceeecCCCCCHHHHHHHHHHhhcccccCCcCCcCccccchhhhhhccCCCCCeEEEEEeCCCCEEec
Q 029018 115 AFVKVCMDGAPYLRKVDLKTYKSYQELSDALAKMFSSFTMGNYGSQGMIDFMNESKLMDLLNSSDYVPTYEDKDGDWMLV 194 (200)
Q Consensus 115 ~~VKV~MdG~pigRKVDL~~~~sY~eL~~aLe~MF~~~~~~~~~~~g~~~~~~e~~l~d~~~~seyvltYeDkdGDwMLV 194 (200)
.-|||+-.|. .|-|-+..-=+|++|...+.++|+. ...+.+-|.|. ||..-+
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 3589998888 6667777777899999999999984 13579999999 998777
Q ss_pred cc
Q 029018 195 GD 196 (200)
Q Consensus 195 GD 196 (200)
++
T Consensus 55 ~s 56 (86)
T cd06408 55 GD 56 (86)
T ss_pred cC
Confidence 65
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=72.21 E-value=6.5 Score=30.38 Aligned_cols=39 Identities=23% Similarity=0.373 Sum_probs=30.8
Q ss_pred eecCCCCCHHHHHHHHHHhhcccccCCcCCcCccccchhhhhhccCCCCCeEEEEEeCCCCEEec
Q 029018 130 VDLKTYKSYQELSDALAKMFSSFTMGNYGSQGMIDFMNESKLMDLLNSSDYVPTYEDKDGDWMLV 194 (200)
Q Consensus 130 VDL~~~~sY~eL~~aLe~MF~~~~~~~~~~~g~~~~~~e~~l~d~~~~seyvltYeDkdGDwMLV 194 (200)
=||+.--+|.+|..-..+-|... +-+|-|.|.|||..-+
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 36888889999999888888742 2367799999998644
No 16
>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=54.62 E-value=10 Score=26.01 Aligned_cols=17 Identities=29% Similarity=0.649 Sum_probs=14.4
Q ss_pred EEEEEeCCCCEEecccC
Q 029018 181 VPTYEDKDGDWMLVGDV 197 (200)
Q Consensus 181 vltYeDkdGDwMLVGDv 197 (200)
-+.|.|.||+.+++|++
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 17
>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=50.99 E-value=30 Score=26.55 Aligned_cols=48 Identities=23% Similarity=0.336 Sum_probs=33.5
Q ss_pred CccccceeecCCCCCHHHHHHHHHHhhcccccCCcCCcCccccchhhhhhccCCCCCeEEEEEeCCCCEEecc
Q 029018 123 GAPYLRKVDLKTYKSYQELSDALAKMFSSFTMGNYGSQGMIDFMNESKLMDLLNSSDYVPTYEDKDGDWMLVG 195 (200)
Q Consensus 123 G~pigRKVDL~~~~sY~eL~~aLe~MF~~~~~~~~~~~g~~~~~~e~~l~d~~~~seyvltYeDkdGDwMLVG 195 (200)
|..+--.||....=++.+++.++.+....-|. -..-|||.|||..-|-
T Consensus 10 gg~vDw~V~~~~~L~F~DvL~~I~~vlp~aT~-------------------------tAFeYEDE~gDRITVR 57 (91)
T cd06395 10 GGAVDWTVQSGPQLLFRDVLDVIGQVLPEATT-------------------------TAFEYEDEDGDRITVR 57 (91)
T ss_pred CCcccccccCcccccHHHHHHHHHHhcccccc-------------------------cceeeccccCCeeEec
Confidence 34466667777777899999888876653211 1455999999998763
No 18
>COG0219 CspR Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]
Probab=27.35 E-value=26 Score=29.47 Aligned_cols=30 Identities=23% Similarity=0.389 Sum_probs=25.6
Q ss_pred eCccccceeecCCCCCHHHHHHHH---HHhhcc
Q 029018 122 DGAPYLRKVDLKTYKSYQELSDAL---AKMFSS 151 (200)
Q Consensus 122 dG~pigRKVDL~~~~sY~eL~~aL---e~MF~~ 151 (200)
-|-.|.-+++|..|+||++...+. .++|-.
T Consensus 48 AGlDY~~~~~l~~h~s~e~fl~~~~~~~rl~~~ 80 (155)
T COG0219 48 AGLDYHEKASLTEHDSLEAFLEAEPIGGRLFAL 80 (155)
T ss_pred cccchHhhcceEEeCCHHHHHhhccCCceEEEE
Confidence 377799999999999999999998 467764
No 19
>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=24.66 E-value=27 Score=29.32 Aligned_cols=12 Identities=42% Similarity=0.703 Sum_probs=7.6
Q ss_pred ccccccCCCCCC
Q 029018 12 ETELCLGLPGGG 23 (200)
Q Consensus 12 ~TELRLGLPG~~ 23 (200)
..-=|||.||++
T Consensus 97 IARGRLGvPGSG 108 (154)
T PF11576_consen 97 IARGRLGVPGSG 108 (154)
T ss_dssp EEEEE-SSTTS-
T ss_pred EEcccccCCCCc
Confidence 344599999984
No 20
>PF03589 Antiterm: Antitermination protein; InterPro: IPR003222 This entry consists of antitermination proteins found in bacteriophages, such as protein Q from phage lambda, and some bacterial homologues. Protein Q positively regulates expression of the phage late gene operon by binding to the bacterial host RNA polymerase (RNAP) and modifying it. The modified RNAP transcribes through termination sites that otherwise prevent expression of the regulated genes [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=24.54 E-value=29 Score=26.49 Aligned_cols=29 Identities=21% Similarity=0.417 Sum_probs=22.4
Q ss_pred CCccccccccCCCCCCCCchhhHhhhhcCCCCCCCCCCCCcch
Q 029018 8 MDFKETELCLGLPGGGNNKKDEAAALELTPTPKASNKRGFCET 50 (200)
Q Consensus 8 l~~~~TELRLGLPG~~~~~~~~~~~~~~~~~~~~~~KR~fset 50 (200)
|++++|++++|+|=-.. -..++||||+..
T Consensus 18 l~~~~s~~~~G~pvfk~--------------c~rcgg~G~sr~ 46 (95)
T PF03589_consen 18 LDMKQSKAQFGVPVFKD--------------CERCGGRGYSRL 46 (95)
T ss_pred ccHHHhHhccCCchhhh--------------hhhhcCCCCCCC
Confidence 89999999999997521 245789999953
No 21
>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=22.85 E-value=22 Score=31.55 Aligned_cols=55 Identities=22% Similarity=0.324 Sum_probs=34.4
Q ss_pred CCceeEEEEeCccccceeecCCCCCHHHHHHHHHHhhcccccCCcCCcCccccchhhhhhccCCCCCeEEEEEeCCCC
Q 029018 113 TAAFVKVCMDGAPYLRKVDLKTYKSYQELSDALAKMFSSFTMGNYGSQGMIDFMNESKLMDLLNSSDYVPTYEDKDGD 190 (200)
Q Consensus 113 ~~~~VKV~MdG~pigRKVDL~~~~sY~eL~~aLe~MF~~~~~~~~~~~g~~~~~~e~~l~d~~~~seyvltYeDkdGD 190 (200)
+-.|...-=||+-||-|||..+.++ +.+-+.+-|+ + .|.....-|-|+|.|+||.
T Consensus 208 ~~~~~~~~g~~afygpkid~~~~d~-------~gr~~q~~t~---------------q-ld~~~~~~f~l~y~~~~~~ 262 (298)
T cd00771 208 GLPYEINEGEGAFYGPKIDFHVKDA-------LGREWQCSTI---------------Q-LDFNLPERFDLTYIGEDGE 262 (298)
T ss_pred CCCceECCCCcccccceEEEEEEeC-------CCCeeeccee---------------E-eeccChhhcCCEEEccCCC
Confidence 4456666677888888888887653 3333433221 1 1222245788999999985
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=22.37 E-value=1e+02 Score=25.21 Aligned_cols=35 Identities=20% Similarity=0.503 Sum_probs=29.9
Q ss_pred eeEEEEeCc--cccceeecCCCCCHHHHHHHHHHhhc
Q 029018 116 FVKVCMDGA--PYLRKVDLKTYKSYQELSDALAKMFS 150 (200)
Q Consensus 116 ~VKV~MdG~--pigRKVDL~~~~sY~eL~~aLe~MF~ 150 (200)
-+||..+|. +|=|.|-+..--+..+|-.+|+..|+
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 478998885 89999999999999999999999997
Done!