Query 048172
Match_columns 158
No_of_seqs 213 out of 588
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 07:01:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/048172.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/048172hhsearch_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 8.1E-55 1.8E-59 355.6 0.4 156 1-158 1-191 (215)
2 PF00564 PB1: PB1 domain; Int 97.5 0.00042 9.1E-09 47.7 6.4 56 88-154 3-58 (84)
3 cd06407 PB1_NLP A PB1 domain i 97.4 0.0007 1.5E-08 48.7 6.5 54 88-152 2-55 (82)
4 cd06398 PB1_Joka2 The PB1 doma 97.3 0.00098 2.1E-08 48.9 6.8 57 88-153 2-61 (91)
5 cd06396 PB1_NBR1 The PB1 domai 97.1 0.0025 5.3E-08 46.3 6.6 52 89-152 3-54 (81)
6 smart00666 PB1 PB1 domain. Pho 97.1 0.0033 7.2E-08 43.2 7.0 54 89-154 4-57 (81)
7 cd05992 PB1 The PB1 domain is 96.7 0.011 2.4E-07 40.3 7.0 55 88-154 2-57 (81)
8 cd06409 PB1_MUG70 The MUG70 pr 96.4 0.0088 1.9E-07 43.8 5.2 50 96-152 7-58 (86)
9 cd06403 PB1_Par6 The PB1 domai 96.3 0.011 2.5E-07 42.9 5.7 54 89-152 3-56 (80)
10 cd06401 PB1_TFG The PB1 domain 96.1 0.023 5.1E-07 41.3 6.0 57 89-154 3-60 (81)
11 cd06404 PB1_aPKC PB1 domain is 96.0 0.022 4.7E-07 41.7 5.8 53 89-152 3-55 (83)
12 cd06397 PB1_UP1 Uncharacterize 95.7 0.047 1E-06 39.9 6.3 53 89-153 3-55 (82)
13 cd06402 PB1_p62 The PB1 domain 94.9 0.15 3.2E-06 37.4 6.8 56 88-152 2-62 (87)
14 cd06408 PB1_NoxR The PB1 domai 94.6 0.14 3.1E-06 37.5 6.2 54 87-154 3-56 (86)
15 cd06399 PB1_P40 The PB1 domain 79.4 3.4 7.4E-05 30.8 4.0 39 102-152 22-60 (92)
16 PF10411 DsbC_N: Disulfide bon 60.7 7.2 0.00016 25.8 2.0 17 139-155 34-50 (57)
17 cd06395 PB1_Map2k5 PB1 domain 44.6 45 0.00097 24.8 4.1 49 94-153 9-57 (91)
18 cd06406 PB1_P67 A PB1 domain i 42.3 95 0.0021 22.5 5.5 47 88-147 4-50 (80)
19 PF11576 DUF3236: Protein of u 34.9 14 0.00031 29.9 0.3 10 8-17 100-109 (154)
20 PF02013 CBM_10: Cellulose or 28.8 19 0.00042 22.4 0.1 13 138-150 15-27 (36)
21 PF00788 RA: Ras association ( 28.6 1.8E+02 0.004 19.4 5.5 57 87-151 3-64 (93)
22 COG3816 Uncharacterized protei 27.5 43 0.00093 27.9 1.9 18 92-123 56-73 (205)
23 PF14468 DUF4427: Protein of u 25.8 66 0.0014 25.5 2.6 38 86-124 56-101 (132)
24 PF07929 PRiA4_ORF3: Plasmid p 22.8 1.1E+02 0.0025 23.9 3.5 37 88-124 6-44 (179)
25 PF13665 DUF4150: Domain of un 22.8 52 0.0011 24.8 1.5 25 87-111 82-106 (110)
26 cd06394 PBP1_iGluR_Kainate_KA1 21.5 78 0.0017 27.6 2.5 41 98-147 106-146 (333)
27 COG0219 CspR Predicted rRNA me 20.3 41 0.00088 27.3 0.4 54 94-155 48-104 (155)
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=8.1e-55 Score=355.55 Aligned_cols=156 Identities=46% Similarity=0.815 Sum_probs=6.0
Q ss_pred CCCcccccccCCCCCCCCCCCCCCCCCCccccccccccccccccc-----------------c-c-------cCCCCCCC
Q 048172 1 MELEITELRLGLPGRDGCDSGLNSSSNNNKNEKKRAFSDICDEAN-----------------Y-E-------TNGERKIN 55 (158)
Q Consensus 1 l~l~~tELrLGLPG~~~~~~~~~~~~~~~~~~~Kr~~~~~~~~~~-----------------~-~-------~~~~~~~p 55 (158)
|||++|||||||||+.+++............++||+|+++.+... . . .......|
T Consensus 1 ln~~~TELrLGLPG~~~~~~~~~~~~~~~~~~~kR~F~~aid~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p 80 (215)
T PF02309_consen 1 LNLKATELRLGLPGSESPDASSSSSSKKSSSGNKRGFSEAIDSSSSNSQSSSSSSSDSSSSSSSSSTSSSSSDSSSSSPP 80 (215)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred CCchhhhhcccCCCCCCCCcccccccccccCcccccchhhhhhcccccccccccccccCcccccccccccccccccCCCC
Confidence 799999999999998754311122233456788999999533110 0 0 00112235
Q ss_pred CCCCcccCCCCCccccccccccccccccCCcceeEEEecCcccceeeeCCCCCChHHHHHHHHHHhccc--Ccc------
Q 048172 56 PTKSQVVGWPPVCSYRRKNSFNEKDRVESSKMYVKVSMDGAPFLRKIDLGMHQGYPDLAMALEKLFGCF--GLS------ 127 (158)
Q Consensus 56 ~~k~qvVGWPPVrs~Rkn~~~~~~~~~~~~~~~VKV~mdG~pigRkVDL~~~~~Y~eL~~~L~~MF~~~--g~~------ 127 (158)
.+++|+||||||++||+|.+... .....++||||+|||+||||||||++|+||++|+.+|++||.++ +++
T Consensus 81 ~~~~~~vgwpp~~s~r~n~~~~~--~~~~~~~~vKV~mdG~~igRkVDL~~~~sY~~L~~~L~~MF~~~~i~~~~~~~~~ 158 (215)
T PF02309_consen 81 ASKAQVVGWPPVRSFRKNSLSEK--QSSSSRSYVKVNMDGVPIGRKVDLSAYSSYEELSSALEKMFSCFSIEQCGSHGLN 158 (215)
T ss_dssp -----BTTBS----S-----------------------------------------------------------------
T ss_pred cccccccCCCccccccccccccc--ccccCCceeEEEecCcccceecCHHHhhCHHHHHHHHHHhcCCCCcccccccccc
Confidence 57899999999999999987622 11234799999999999999999999999999999999999544 211
Q ss_pred --ccccCCCCCCcEEEEEeCCCCEEecccCCCC
Q 048172 128 --EALKDADSSEFVPIYEDKDGDWMLAGDVPWE 158 (158)
Q Consensus 128 --~~~~~~~~~~~~ltYeD~eGD~mLVGDvPW~ 158 (158)
...+..++++|+|||||+||||||||||||+
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 0111245679999999999999999999996
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=97.50 E-value=0.00042 Score=47.74 Aligned_cols=56 Identities=30% Similarity=0.490 Sum_probs=46.6
Q ss_pred eeEEEecCcccceeeeCCCCCChHHHHHHHHHHhcccCccccccCCCCCCcEEEEEeCCCCEEeccc
Q 048172 88 YVKVSMDGAPFLRKIDLGMHQGYPDLAMALEKLFGCFGLSEALKDADSSEFVPIYEDKDGDWMLAGD 154 (158)
Q Consensus 88 ~VKV~mdG~pigRkVDL~~~~~Y~eL~~~L~~MF~~~g~~~~~~~~~~~~~~ltYeD~eGD~mLVGD 154 (158)
-|||+..|. +=|.+.+..--+|.+|...++..|++.+ ..+.+.|.|.||||..+-+
T Consensus 3 ~vK~~~~~~-~~~~~~~~~~~s~~~L~~~i~~~~~~~~----------~~~~l~Y~D~dgD~V~i~s 58 (84)
T PF00564_consen 3 RVKVRYGGD-IRRIISLPSDVSFDDLRSKIREKFGLLD----------EDFQLKYKDEDGDLVTISS 58 (84)
T ss_dssp EEEEEETTE-EEEEEEECSTSHHHHHHHHHHHHHTTST----------SSEEEEEEETTSSEEEESS
T ss_pred EEEEEECCe-eEEEEEcCCCCCHHHHHHHHHHHhCCCC----------ccEEEEeeCCCCCEEEeCC
Confidence 479999997 4446888888899999999999999751 3699999999999988753
No 3
>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=97.38 E-value=0.0007 Score=48.68 Aligned_cols=54 Identities=26% Similarity=0.361 Sum_probs=43.6
Q ss_pred eeEEEecCcccceeeeCCCCCChHHHHHHHHHHhcccCccccccCCCCCCcEEEEEeCCCCEEec
Q 048172 88 YVKVSMDGAPFLRKIDLGMHQGYPDLAMALEKLFGCFGLSEALKDADSSEFVPIYEDKDGDWMLA 152 (158)
Q Consensus 88 ~VKV~mdG~pigRkVDL~~~~~Y~eL~~~L~~MF~~~g~~~~~~~~~~~~~~ltYeD~eGD~mLV 152 (158)
=|||...|. -+.+-|..--+|++|...+.++|.+.. .+.|.|-|.|.||||.++
T Consensus 2 ~vK~~~~~d--~~r~~l~~~~~~~~L~~~i~~r~~~~~---------~~~f~LkY~Ddegd~v~l 55 (82)
T cd06407 2 RVKATYGEE--KIRFRLPPSWGFTELKQEIAKRFKLDD---------MSAFDLKYLDDDEEWVLL 55 (82)
T ss_pred EEEEEeCCe--EEEEEcCCCCCHHHHHHHHHHHhCCCC---------CCeeEEEEECCCCCeEEe
Confidence 389999887 445555556699999999999999641 147999999999999875
No 4
>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=97.32 E-value=0.00098 Score=48.87 Aligned_cols=57 Identities=23% Similarity=0.279 Sum_probs=45.2
Q ss_pred eeEEEecCcccceeeeCC---CCCChHHHHHHHHHHhcccCccccccCCCCCCcEEEEEeCCCCEEecc
Q 048172 88 YVKVSMDGAPFLRKIDLG---MHQGYPDLAMALEKLFGCFGLSEALKDADSSEFVPIYEDKDGDWMLAG 153 (158)
Q Consensus 88 ~VKV~mdG~pigRkVDL~---~~~~Y~eL~~~L~~MF~~~g~~~~~~~~~~~~~~ltYeD~eGD~mLVG 153 (158)
-|||.-+|.-+=-++++. .--+|++|...+.+.|.+.. ..+|++.|.|.||||..+-
T Consensus 2 ~vKv~y~~~~rRf~l~~~~~~~d~~~~~L~~kI~~~f~l~~---------~~~~~l~Y~Dedgd~V~l~ 61 (91)
T cd06398 2 VVKVKYGGTLRRFTFPVAENQLDLNMDGLREKVEELFSLSP---------DADLSLTYTDEDGDVVTLV 61 (91)
T ss_pred EEEEEeCCEEEEEEeccccccCCCCHHHHHHHHHHHhCCCC---------CCcEEEEEECCCCCEEEEc
Confidence 389999998444455553 46799999999999998642 2479999999999998764
No 5
>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=97.08 E-value=0.0025 Score=46.30 Aligned_cols=52 Identities=13% Similarity=0.200 Sum_probs=46.2
Q ss_pred eEEEecCcccceeeeCCCCCChHHHHHHHHHHhcccCccccccCCCCCCcEEEEEeCCCCEEec
Q 048172 89 VKVSMDGAPFLRKIDLGMHQGYPDLAMALEKLFGCFGLSEALKDADSSEFVPIYEDKDGDWMLA 152 (158)
Q Consensus 89 VKV~mdG~pigRkVDL~~~~~Y~eL~~~L~~MF~~~g~~~~~~~~~~~~~~ltYeD~eGD~mLV 152 (158)
|||.-.|.-+--+++-+..-+|.+|...+.++|++. .+.|.|-|.||||.++
T Consensus 3 vKaty~~d~~rf~~~~~~~~~~~~L~~ev~~rf~l~------------~f~lKYlDde~e~v~l 54 (81)
T cd06396 3 LKVTYNGESQSFLVSDSENTTWASVEAMVKVSFGLN------------DIQIKYVDEENEEVSV 54 (81)
T ss_pred EEEEECCeEEEEEecCCCCCCHHHHHHHHHHHhCCC------------cceeEEEcCCCCEEEE
Confidence 799999997777787777889999999999999975 3899999999999986
No 6
>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=97.06 E-value=0.0033 Score=43.24 Aligned_cols=54 Identities=28% Similarity=0.437 Sum_probs=44.4
Q ss_pred eEEEecCcccceeeeCCCCCChHHHHHHHHHHhcccCccccccCCCCCCcEEEEEeCCCCEEeccc
Q 048172 89 VKVSMDGAPFLRKIDLGMHQGYPDLAMALEKLFGCFGLSEALKDADSSEFVPIYEDKDGDWMLAGD 154 (158)
Q Consensus 89 VKV~mdG~pigRkVDL~~~~~Y~eL~~~L~~MF~~~g~~~~~~~~~~~~~~ltYeD~eGD~mLVGD 154 (158)
|||.-.| --|.+-+..--+|.+|...+.+.|.+.. ..+.|.|+|.||||..+.+
T Consensus 4 vK~~~~~--~~~~~~~~~~~s~~dL~~~i~~~~~~~~----------~~~~l~Y~Dedgd~v~l~s 57 (81)
T smart00666 4 VKLRYGG--ETRRLSVPRDISFEDLRSKVAKRFGLDN----------QSFTLKYQDEDGDLVSLTS 57 (81)
T ss_pred EEEEECC--EEEEEEECCCCCHHHHHHHHHHHhCCCC----------CCeEEEEECCCCCEEEecC
Confidence 6887754 3677888889999999999999999642 3589999999999987653
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=96.67 E-value=0.011 Score=40.31 Aligned_cols=55 Identities=27% Similarity=0.414 Sum_probs=43.8
Q ss_pred eeEEEecCcccceeeeCC-CCCChHHHHHHHHHHhcccCccccccCCCCCCcEEEEEeCCCCEEeccc
Q 048172 88 YVKVSMDGAPFLRKIDLG-MHQGYPDLAMALEKLFGCFGLSEALKDADSSEFVPIYEDKDGDWMLAGD 154 (158)
Q Consensus 88 ~VKV~mdG~pigRkVDL~-~~~~Y~eL~~~L~~MF~~~g~~~~~~~~~~~~~~ltYeD~eGD~mLVGD 154 (158)
-|||+-.|. -|.+=+. .--+|++|...|.+.|.+.. ..+.+.|.|.||||..+.+
T Consensus 2 ~vK~~~~~~--~~~~~~~~~~~s~~~L~~~i~~~~~~~~----------~~~~l~y~D~e~d~v~l~s 57 (81)
T cd05992 2 RVKVKYGGE--IRRFVVVSRSISFEDLRSKIAEKFGLDA----------VSFKLKYPDEDGDLVTISS 57 (81)
T ss_pred cEEEEecCC--CEEEEEecCCCCHHHHHHHHHHHhCCCC----------CcEEEEeeCCCCCEEEeCC
Confidence 378888765 3445555 88899999999999999642 2589999999999988754
No 8
>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=96.35 E-value=0.0088 Score=43.77 Aligned_cols=50 Identities=18% Similarity=0.252 Sum_probs=39.2
Q ss_pred cccceeeeCC--CCCChHHHHHHHHHHhcccCccccccCCCCCCcEEEEEeCCCCEEec
Q 048172 96 APFLRKIDLG--MHQGYPDLAMALEKLFGCFGLSEALKDADSSEFVPIYEDKDGDWMLA 152 (158)
Q Consensus 96 ~pigRkVDL~--~~~~Y~eL~~~L~~MF~~~g~~~~~~~~~~~~~~ltYeD~eGD~mLV 152 (158)
+|-||.+=++ ...|+.+|..++.+-|+..... ...|.|.|.|.||||.+.
T Consensus 7 ~~~GrvhRf~~~~s~~~~~L~~~I~~Rl~~d~~~-------~~~~~L~YlDDEgD~Vll 58 (86)
T cd06409 7 DPKGRVHRFRLRPSESLEELRTLISQRLGDDDFE-------THLYALSYVDDEGDIVLI 58 (86)
T ss_pred CCCCCEEEEEecCCCCHHHHHHHHHHHhCCcccc-------CCcccEEEEcCCCCEEEE
Confidence 4567765554 4789999999999999875321 246999999999999986
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=96.35 E-value=0.011 Score=42.91 Aligned_cols=54 Identities=24% Similarity=0.248 Sum_probs=41.3
Q ss_pred eEEEecCcccceeeeCCCCCChHHHHHHHHHHhcccCccccccCCCCCCcEEEEEeCCCCEEec
Q 048172 89 VKVSMDGAPFLRKIDLGMHQGYPDLAMALEKLFGCFGLSEALKDADSSEFVPIYEDKDGDWMLA 152 (158)
Q Consensus 89 VKV~mdG~pigRkVDL~~~~~Y~eL~~~L~~MF~~~g~~~~~~~~~~~~~~ltYeD~eGD~mLV 152 (158)
||...|..=-=-.+|.....+|++++.-|+.||.+.. ..|+|-|.|.+||.+-+
T Consensus 3 VKSkfdaEfRRFsl~r~~~~~f~ef~~ll~~lH~l~~----------~~f~i~Y~D~~gDLLPI 56 (80)
T cd06403 3 VKSKFDAEFRRFSLDRNKPGKFEDFYKLLEHLHHIPN----------VDFLIGYTDPHGDLLPI 56 (80)
T ss_pred eecccCCeEEEEEeccccCcCHHHHHHHHHHHhCCCC----------CcEEEEEeCCCCCEecc
Confidence 6666666522224555667999999999999999763 36999999999998754
No 10
>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=96.05 E-value=0.023 Score=41.34 Aligned_cols=57 Identities=23% Similarity=0.424 Sum_probs=40.9
Q ss_pred eEEEecCcccceeeeCCCC-CChHHHHHHHHHHhcccCccccccCCCCCCcEEEEEeCCCCEEeccc
Q 048172 89 VKVSMDGAPFLRKIDLGMH-QGYPDLAMALEKLFGCFGLSEALKDADSSEFVPIYEDKDGDWMLAGD 154 (158)
Q Consensus 89 VKV~mdG~pigRkVDL~~~-~~Y~eL~~~L~~MF~~~g~~~~~~~~~~~~~~ltYeD~eGD~mLVGD 154 (158)
+|+...|. | |.+=+..- -+|.+|...+.+.|... . +....+.+.|.|.|||+.-|-+
T Consensus 3 iK~~~g~D-i-R~~~~~~~~~t~~~L~~~v~~~F~~~--~-----~~~~~flIKYkD~dGDlVTIts 60 (81)
T cd06401 3 LKAQLGDD-I-RRIPIHNEDITYDELLLMMQRVFRGK--L-----GSSDDVLIKYKDEDGDLITIFD 60 (81)
T ss_pred EEEEeCCe-E-EEEeccCccccHHHHHHHHHHHhccc--c-----CCcccEEEEEECCCCCEEEecc
Confidence 67776665 4 44444432 39999999999999943 1 1134799999999999986643
No 11
>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=96.02 E-value=0.022 Score=41.69 Aligned_cols=53 Identities=19% Similarity=0.304 Sum_probs=42.8
Q ss_pred eEEEecCcccceeeeCCCCCChHHHHHHHHHHhcccCccccccCCCCCCcEEEEEeCCCCEEec
Q 048172 89 VKVSMDGAPFLRKIDLGMHQGYPDLAMALEKLFGCFGLSEALKDADSSEFVPIYEDKDGDWMLA 152 (158)
Q Consensus 89 VKV~mdG~pigRkVDL~~~~~Y~eL~~~L~~MF~~~g~~~~~~~~~~~~~~ltYeD~eGD~mLV 152 (158)
||++-.|.-+--.+|. .-+|++|.+.+..||.+. ....|++.|.|.|||---+
T Consensus 3 ~K~~y~gdi~it~~d~--~~s~e~L~~~v~~~c~~~---------~~q~ft~kw~DEEGDp~ti 55 (83)
T cd06404 3 VKAAYNGDIMITSIDP--SISLEELCNEVRDMCRFH---------NDQPFTLKWIDEEGDPCTI 55 (83)
T ss_pred EEEEecCcEEEEEcCC--CcCHHHHHHHHHHHhCCC---------CCCcEEEEEECCCCCceee
Confidence 7999999865556665 778999999999999964 1236999999999997543
No 12
>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=95.69 E-value=0.047 Score=39.91 Aligned_cols=53 Identities=26% Similarity=0.279 Sum_probs=44.3
Q ss_pred eEEEecCcccceeeeCCCCCChHHHHHHHHHHhcccCccccccCCCCCCcEEEEEeCCCCEEecc
Q 048172 89 VKVSMDGAPFLRKIDLGMHQGYPDLAMALEKLFGCFGLSEALKDADSSEFVPIYEDKDGDWMLAG 153 (158)
Q Consensus 89 VKV~mdG~pigRkVDL~~~~~Y~eL~~~L~~MF~~~g~~~~~~~~~~~~~~ltYeD~eGD~mLVG 153 (158)
-||+-.|. .|++....-=+|..|...|+.+|.+... .+.|+|.|.|||..-+-
T Consensus 3 fKv~~~g~--~RRf~~~~~pt~~~L~~kl~~Lf~lp~~----------~~~vtYiDeD~D~ITls 55 (82)
T cd06397 3 FKSSFLGD--TRRIVFPDIPTWEALASKLENLYNLPEI----------KVGVTYIDNDNDEITLS 55 (82)
T ss_pred EEEEeCCc--eEEEecCCCccHHHHHHHHHHHhCCChh----------HeEEEEEcCCCCEEEec
Confidence 48888885 7999888889999999999999997621 28999999999987543
No 13
>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=94.87 E-value=0.15 Score=37.41 Aligned_cols=56 Identities=20% Similarity=0.387 Sum_probs=41.0
Q ss_pred eeEEEecC---cccceeeeC--CCCCChHHHHHHHHHHhcccCccccccCCCCCCcEEEEEeCCCCEEec
Q 048172 88 YVKVSMDG---APFLRKIDL--GMHQGYPDLAMALEKLFGCFGLSEALKDADSSEFVPIYEDKDGDWMLA 152 (158)
Q Consensus 88 ~VKV~mdG---~pigRkVDL--~~~~~Y~eL~~~L~~MF~~~g~~~~~~~~~~~~~~ltYeD~eGD~mLV 152 (158)
.||.+..| .+==|++-| ....+|++|...+.++|..- .+..|++.|.|.|||..-+
T Consensus 2 ~vkayl~~~~~~~EIRRf~l~~~~~~s~~~L~~~V~~~f~~l---------~~~~ftlky~DeeGDlvtI 62 (87)
T cd06402 2 TVKAYLLGKDANAEIRRFAIDEDVSTSYEYLVEKVAAVFPSL---------RGKNFQLFWKDEEGDLVAF 62 (87)
T ss_pred eEEEeecCCCCccceEEEEecCCCCcCHHHHHHHHHHHcccc---------CCCcEEEEEECCCCCEEee
Confidence 57777766 223344444 66679999999999999732 1247999999999998754
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=94.61 E-value=0.14 Score=37.49 Aligned_cols=54 Identities=28% Similarity=0.437 Sum_probs=45.1
Q ss_pred ceeEEEecCcccceeeeCCCCCChHHHHHHHHHHhcccCccccccCCCCCCcEEEEEeCCCCEEeccc
Q 048172 87 MYVKVSMDGAPFLRKIDLGMHQGYPDLAMALEKLFGCFGLSEALKDADSSEFVPIYEDKDGDWMLAGD 154 (158)
Q Consensus 87 ~~VKV~mdG~pigRkVDL~~~~~Y~eL~~~L~~MF~~~g~~~~~~~~~~~~~~ltYeD~eGD~mLVGD 154 (158)
.-|||+-.|. .|-|-+..--+|++|...+.++|++. ..++|-|.|. ||..-+++
T Consensus 3 ikVKv~~~~D--v~~i~v~~~i~f~dL~~kIrdkf~~~-----------~~~~iKykDE-GD~iti~s 56 (86)
T cd06408 3 IRVKVHAQDD--TRYIMIGPDTGFADFEDKIRDKFGFK-----------RRLKIKMKDD-GDMITMGD 56 (86)
T ss_pred EEEEEEecCc--EEEEEcCCCCCHHHHHHHHHHHhCCC-----------CceEEEEEcC-CCCccccC
Confidence 4589999888 66777777778999999999999974 2589999999 99887765
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=79.40 E-value=3.4 Score=30.82 Aligned_cols=39 Identities=23% Similarity=0.227 Sum_probs=32.4
Q ss_pred eeCCCCCChHHHHHHHHHHhcccCccccccCCCCCCcEEEEEeCCCCEEec
Q 048172 102 IDLGMHQGYPDLAMALEKLFGCFGLSEALKDADSSEFVPIYEDKDGDWMLA 152 (158)
Q Consensus 102 VDL~~~~~Y~eL~~~L~~MF~~~g~~~~~~~~~~~~~~ltYeD~eGD~mLV 152 (158)
=||+..-.|.+|..-..+-|.-+ +-.+-|.|.|||..-+
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 36888899999999999988843 4689999999998644
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=60.71 E-value=7.2 Score=25.77 Aligned_cols=17 Identities=29% Similarity=0.755 Sum_probs=14.8
Q ss_pred EEEEEeCCCCEEecccC
Q 048172 139 VPIYEDKDGDWMLAGDV 155 (158)
Q Consensus 139 ~ltYeD~eGD~mLVGDv 155 (158)
.+.|.|.+|+.+++|++
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 69999999999999974
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=44.56 E-value=45 Score=24.77 Aligned_cols=49 Identities=18% Similarity=0.255 Sum_probs=34.8
Q ss_pred cCcccceeeeCCCCCChHHHHHHHHHHhcccCccccccCCCCCCcEEEEEeCCCCEEecc
Q 048172 94 DGAPFLRKIDLGMHQGYPDLAMALEKLFGCFGLSEALKDADSSEFVPIYEDKDGDWMLAG 153 (158)
Q Consensus 94 dG~pigRkVDL~~~~~Y~eL~~~L~~MF~~~g~~~~~~~~~~~~~~ltYeD~eGD~mLVG 153 (158)
+|..+--.||...+=++.+++.++.+..--. .--..-|||.+||.+-|-
T Consensus 9 ~gg~vDw~V~~~~~L~F~DvL~~I~~vlp~a-----------T~tAFeYEDE~gDRITVR 57 (91)
T cd06395 9 NGGAVDWTVQSGPQLLFRDVLDVIGQVLPEA-----------TTTAFEYEDEDGDRITVR 57 (91)
T ss_pred CCCcccccccCcccccHHHHHHHHHHhcccc-----------cccceeeccccCCeeEec
Confidence 3445666777777788999999888765421 123567999999998763
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=42.33 E-value=95 Score=22.49 Aligned_cols=47 Identities=15% Similarity=0.131 Sum_probs=34.2
Q ss_pred eeEEEecCcccceeeeCCCCCChHHHHHHHHHHhcccCccccccCCCCCCcEEEEEeCCC
Q 048172 88 YVKVSMDGAPFLRKIDLGMHQGYPDLAMALEKLFGCFGLSEALKDADSSEFVPIYEDKDG 147 (158)
Q Consensus 88 ~VKV~mdG~pigRkVDL~~~~~Y~eL~~~L~~MF~~~g~~~~~~~~~~~~~~ltYeD~eG 147 (158)
-|||+..+ .=.|-...=-+|++|...|.+-+.+.++ +-+|.|.|.+.
T Consensus 4 vvKV~f~~---tIaIrvp~~~~y~~L~~ki~~kLkl~~e----------~i~LsYkde~s 50 (80)
T cd06406 4 VVKVHFKY---TVAIQVARGLSYATLLQKISSKLELPAE----------HITLSYKSEAS 50 (80)
T ss_pred EEEEEEEE---EEEEEcCCCCCHHHHHHHHHHHhCCCch----------hcEEEeccCCC
Confidence 57999997 3455566667899999999999997532 34666766653
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=34.94 E-value=14 Score=29.87 Aligned_cols=10 Identities=50% Similarity=0.906 Sum_probs=6.6
Q ss_pred cccCCCCCCC
Q 048172 8 LRLGLPGRDG 17 (158)
Q Consensus 8 LrLGLPG~~~ 17 (158)
=|||.||+++
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 20
>PF02013 CBM_10: Cellulose or protein binding domain; InterPro: IPR002883 This domain is found in two distinct sets of proteins with different functions. Those found in aerobic bacteria bind cellulose (or other carbohydrates); but in anaerobic fungi they are protein binding domains, referred to as dockerin domains or docking domains. They are believed to be responsible for the assembly of a multiprotein cellulase/hemicellulase complex, similar to the cellulosome found in certain anaerobic bacteria. The recycling of photosynthetically fixed carbon in plant cell walls is a key microbial process. Enzyme systems that attack the plant cell wall contain noncatalytic carbohydrate-binding modules that mediate attachment to this composite structure and play a pivotal role in maximizing the hydrolytic process. In anaerobes, the degradation is carried out by a high molecular weight, multifunctional complex termed the cellulosome. This consists of a number of independent enzyme components, each of which contains a conserved 40-residue dockerin domain, which functions to bind the enzyme to a cohesin domain within the scaffoldin protein [, ]. In anaerobic bacteria that degrade plant cell walls, exemplified by Clostridium thermocellum, the dockerin domains of the catalytic polypeptides can bind equally well to any cohesin from the same organism. More recently, anaerobic fungi, typified by Piromyces equi, have been suggested to also synthesise a cellulosome complex, although the dockerin sequences of the bacterial and fungal enzymes are completely different []. For example, the fungal enzymes contain one, two or three copies of the dockerin sequence in tandem within the catalytic polypeptide. In contrast, all the C. thermocellum cellulosome catalytic components contain a single dockerin domain. The anaerobic bacterial dockerins are homologous to EF hands (calcium-binding motifs) and require calcium for activity whereas the fungal dockerin does not require calcium. Finally, the interaction between cohesin and dockerin appears to be species specific in bacteria, there is almost no species specificity of binding within fungal species and no identified sites that distinguish different species. The structure of dockerin from P. equi contains two helical stretches and four short beta-strands which form an antiparallel sheet structure adjacent to an additional short twisted parallel strand. The N- and C-termini are adjacent to each other. Aerobic bacteria contain related regions, however these appear to function as cellulose/carbohydrate binding domains.; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0005975 carbohydrate metabolic process; PDB: 2J4M_A 2J4N_A 1E8R_A 1QLD_A 1E8P_A 1E8Q_A.
Probab=28.84 E-value=19 Score=22.36 Aligned_cols=13 Identities=38% Similarity=0.861 Sum_probs=9.3
Q ss_pred cEEEEEeCCCCEE
Q 048172 138 FVPIYEDKDGDWM 150 (158)
Q Consensus 138 ~~ltYeD~eGD~m 150 (158)
-.+.|.|.+|+|=
T Consensus 15 ~~v~y~d~~g~WG 27 (36)
T PF02013_consen 15 CEVVYTDDDGGWG 27 (36)
T ss_dssp S--SEEETTEEEE
T ss_pred CceEEcCCCCCEe
Confidence 4789999999983
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=28.58 E-value=1.8e+02 Score=19.39 Aligned_cols=57 Identities=14% Similarity=0.144 Sum_probs=41.4
Q ss_pred ceeEEEecCccc---ceeeeCCCCCChHHHHHHHHHHhcccCccccccCCCCCCcEEE-EE-eCCCCEEe
Q 048172 87 MYVKVSMDGAPF---LRKIDLGMHQGYPDLAMALEKLFGCFGLSEALKDADSSEFVPI-YE-DKDGDWML 151 (158)
Q Consensus 87 ~~VKV~mdG~pi---gRkVDL~~~~~Y~eL~~~L~~MF~~~g~~~~~~~~~~~~~~lt-Ye-D~eGD~mL 151 (158)
.++||++...-- -+.|=++....-.+++.++-+.|++.. +..+|.|. +. .......|
T Consensus 3 ~~lrVy~~~~~~~~~~k~i~v~~~tTa~evi~~~l~k~~l~~--------~~~~y~L~~~~~~~~~er~L 64 (93)
T PF00788_consen 3 GVLRVYDGDGSPGSTYKTIKVSSSTTAREVIEMALEKFGLAE--------DPSDYCLVEVEESGGEERPL 64 (93)
T ss_dssp EEEEEEETTSSSCCSEEEEEEETTSBHHHHHHHHHHHTTTSS--------SGGGEEEEEEECTTTEEEEE
T ss_pred eEEEEEcCCCCCCccEEEEEECCCCCHHHHHHHHHHHhCCCC--------CCCCEEEEEEEcCCCEEEEc
Confidence 478999987642 688899999999999999999999832 12468884 33 33444444
No 22
>COG3816 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.48 E-value=43 Score=27.95 Aligned_cols=18 Identities=39% Similarity=0.525 Sum_probs=14.4
Q ss_pred EecCcccceeeeCCCCCChHHHHHHHHHHhcc
Q 048172 92 SMDGAPFLRKIDLGMHQGYPDLAMALEKLFGC 123 (158)
Q Consensus 92 ~mdG~pigRkVDL~~~~~Y~eL~~~L~~MF~~ 123 (158)
+-.|.||||+ .|-++|+.
T Consensus 56 FylGTPIGR~--------------plVrLFSt 73 (205)
T COG3816 56 FYLGTPIGRK--------------PLVRLFST 73 (205)
T ss_pred EEecCccchH--------------HHHHHHHH
Confidence 4568999997 78888983
No 23
>PF14468 DUF4427: Protein of unknown function (DUF4427)
Probab=25.81 E-value=66 Score=25.47 Aligned_cols=38 Identities=29% Similarity=0.266 Sum_probs=25.5
Q ss_pred cceeEEEecCcccceeeeCCCCC----Ch----HHHHHHHHHHhccc
Q 048172 86 KMYVKVSMDGAPFLRKIDLGMHQ----GY----PDLAMALEKLFGCF 124 (158)
Q Consensus 86 ~~~VKV~mdG~pigRkVDL~~~~----~Y----~eL~~~L~~MF~~~ 124 (158)
..-|||+.+|. |+=+||+---+ -= ..|+..|..-|+++
T Consensus 56 ~grV~v~~eGR-YLl~l~~~~s~~plr~kE~~ak~vA~~L~~rF~ve 101 (132)
T PF14468_consen 56 AGRVKVNKEGR-YLLDLDLFDSDWPLRKKEAMAKHVAGWLRHRFGVE 101 (132)
T ss_pred cCceeeccCce-eeeecccccCCCchHHHHHHHHHHHHHHHHHhCcc
Confidence 36899999999 88777764331 12 24556667777765
No 24
>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=22.77 E-value=1.1e+02 Score=23.87 Aligned_cols=37 Identities=30% Similarity=0.506 Sum_probs=29.9
Q ss_pred eeEEEecCc--ccceeeeCCCCCChHHHHHHHHHHhccc
Q 048172 88 YVKVSMDGA--PFLRKIDLGMHQGYPDLAMALEKLFGCF 124 (158)
Q Consensus 88 ~VKV~mdG~--pigRkVDL~~~~~Y~eL~~~L~~MF~~~ 124 (158)
-+||...|. +|=|.|-+..--+..+|-.+|...|+..
T Consensus 6 ~lkV~L~~~~p~iwRri~Vp~~~tl~~Lh~~Iq~afgw~ 44 (179)
T PF07929_consen 6 QLKVSLKGSKPPIWRRIEVPADITLADLHEVIQAAFGWD 44 (179)
T ss_dssp EEEEEETT-SS-EEEEEEEETT-BHHHHHHHHHHHTT--
T ss_pred EEEEEEcCCCCCeEEEEEECCCCCHHHHHHHHHHHhCcC
Confidence 468888874 8999999999999999999999999854
No 25
>PF13665 DUF4150: Domain of unknown function (DUF4150)
Probab=22.76 E-value=52 Score=24.79 Aligned_cols=25 Identities=24% Similarity=0.256 Sum_probs=21.3
Q ss_pred ceeEEEecCcccceeeeCCCCCChH
Q 048172 87 MYVKVSMDGAPFLRKIDLGMHQGYP 111 (158)
Q Consensus 87 ~~VKV~mdG~pigRkVDL~~~~~Y~ 111 (158)
.-.+|.++|.|+.|--|+...+++.
T Consensus 82 ~S~~V~ieG~p~~R~~d~~~~N~~N 106 (110)
T PF13665_consen 82 GSFTVKIEGKPATRLTDLTWMNNKN 106 (110)
T ss_pred cCCeEEECCEEEEEcCCCccccCCC
Confidence 3468999999999999999988653
No 26
>cd06394 PBP1_iGluR_Kainate_KA1_2 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the KA1 and KA2 subunits of Kainate receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the KA1 and KA2 subunits of Kainate receptor. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. There are five types of kainate receptors, GluR5, GluR6, GluR7, KA1, and KA2, which are structurally similar to AMPA and NMDA subunits of ionotropic glutamate receptors. KA1 and KA2 subunits can only form functional receptors with one of the GluR5-7 subunits. Moreover, GluR5-7 can also form functional homomeric receptor channels act
Probab=21.50 E-value=78 Score=27.55 Aligned_cols=41 Identities=17% Similarity=0.363 Sum_probs=32.4
Q ss_pred cceeeeCCCCCChHHHHHHHHHHhcccCccccccCCCCCCcEEEEEeCCC
Q 048172 98 FLRKIDLGMHQGYPDLAMALEKLFGCFGLSEALKDADSSEFVPIYEDKDG 147 (158)
Q Consensus 98 igRkVDL~~~~~Y~eL~~~L~~MF~~~g~~~~~~~~~~~~~~ltYeD~eG 147 (158)
+.+-.-+.+|-++..+..++..+....+.. .++++|+|.||
T Consensus 106 ~~~~~~i~l~P~~~~~~~Ai~dli~~~~W~---------~v~~iYe~d~~ 146 (333)
T cd06394 106 YLRFASVNLHPSNEDISVAVAGILNSFNYP---------TASLICAKAEC 146 (333)
T ss_pred cccceEEEecCCHHHHHHHHHHHHHhcCCC---------EEEEEEeCcHH
Confidence 344434778889999999999999877653 68999999987
No 27
>COG0219 CspR Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]
Probab=20.29 E-value=41 Score=27.30 Aligned_cols=54 Identities=20% Similarity=0.309 Sum_probs=37.1
Q ss_pred cCcccceeeeCCCCCChHHHHHHH---HHHhcccCccccccCCCCCCcEEEEEeCCCCEEecccC
Q 048172 94 DGAPFLRKIDLGMHQGYPDLAMAL---EKLFGCFGLSEALKDADSSEFVPIYEDKDGDWMLAGDV 155 (158)
Q Consensus 94 dG~pigRkVDL~~~~~Y~eL~~~L---~~MF~~~g~~~~~~~~~~~~~~ltYeD~eGD~mLVGDv 155 (158)
-|-.|--+++|..|+++++...+. .++|-+.-.-. .-|.- +....||++|-|-.
T Consensus 48 AGlDY~~~~~l~~h~s~e~fl~~~~~~~rl~~~tt~~~-------~~~~~-~~f~~~d~llFG~E 104 (155)
T COG0219 48 AGLDYHEKASLTEHDSLEAFLEAEPIGGRLFALTTKGT-------TTYTD-VSFQKGDYLLFGPE 104 (155)
T ss_pred cccchHhhcceEEeCCHHHHHhhccCCceEEEEEeccc-------ccccc-ccCCCCCEEEECCC
Confidence 477788999999999999999998 46776541110 01111 34455889998864
Done!