Query 028141
Match_columns 213
No_of_seqs 217 out of 575
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 06:52:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028141.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028141hhsearch_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 5E-58 1.1E-62 392.9 0.4 188 2-213 1-191 (215)
2 PF00564 PB1: PB1 domain; Int 97.3 0.00069 1.5E-08 49.0 6.2 55 129-208 3-57 (84)
3 cd06398 PB1_Joka2 The PB1 doma 97.3 0.00087 1.9E-08 51.5 6.5 57 129-208 2-61 (91)
4 cd06407 PB1_NLP A PB1 domain i 97.2 0.0015 3.2E-08 49.2 6.6 54 129-207 2-55 (82)
5 cd06396 PB1_NBR1 The PB1 domai 97.0 0.0023 5.1E-08 48.5 6.1 52 130-207 3-54 (81)
6 smart00666 PB1 PB1 domain. Pho 96.9 0.0046 1E-07 44.6 6.8 54 130-209 4-57 (81)
7 cd05992 PB1 The PB1 domain is 96.5 0.013 2.9E-07 41.9 6.8 55 129-209 2-57 (81)
8 cd06403 PB1_Par6 The PB1 domai 96.3 0.0095 2.1E-07 45.3 5.4 53 130-206 3-55 (80)
9 cd06409 PB1_MUG70 The MUG70 pr 96.2 0.011 2.3E-07 45.4 5.3 50 137-207 7-58 (86)
10 cd06402 PB1_p62 The PB1 domain 95.8 0.045 9.7E-07 42.0 6.8 56 129-207 2-62 (87)
11 cd06404 PB1_aPKC PB1 domain is 95.7 0.03 6.5E-07 42.8 5.6 53 130-207 3-55 (83)
12 cd06397 PB1_UP1 Uncharacterize 95.2 0.066 1.4E-06 40.9 6.0 52 130-207 3-54 (82)
13 cd06401 PB1_TFG The PB1 domain 95.1 0.1 2.2E-06 39.8 6.8 57 130-209 3-60 (81)
14 cd06408 PB1_NoxR The PB1 domai 92.0 0.58 1.3E-05 35.9 6.1 54 128-209 3-56 (86)
15 cd06399 PB1_P40 The PB1 domain 68.2 8.3 0.00018 30.1 3.8 38 144-207 23-60 (92)
16 PF10411 DsbC_N: Disulfide bon 57.9 8.2 0.00018 26.8 2.0 17 194-210 34-50 (57)
17 cd06395 PB1_Map2k5 PB1 domain 47.0 37 0.00081 26.3 4.2 47 136-207 10-56 (91)
18 COG0219 CspR Predicted rRNA me 31.6 21 0.00046 30.3 0.8 30 135-164 48-80 (155)
19 PF07929 PRiA4_ORF3: Plasmid p 25.9 79 0.0017 26.1 3.3 37 127-163 4-42 (179)
20 PF09676 TraV: Type IV conjuga 25.4 45 0.00097 25.8 1.6 19 192-210 92-110 (119)
21 PF12426 DUF3674: RNA dependen 24.1 45 0.00099 22.5 1.2 14 155-168 7-21 (41)
22 PF02013 CBM_10: Cellulose or 24.0 27 0.00058 22.8 0.1 11 194-204 16-26 (36)
23 PF11576 DUF3236: Protein of u 23.6 29 0.00063 29.4 0.2 9 9-17 100-108 (154)
24 cd00771 ThrRS_core Threonyl-tR 22.1 28 0.0006 31.3 -0.2 54 127-203 209-262 (298)
25 cd06406 PB1_P67 A PB1 domain i 21.9 2.7E+02 0.0059 21.1 5.2 33 129-164 4-36 (80)
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=5e-58 Score=392.89 Aligned_cols=188 Identities=53% Similarity=0.907 Sum_probs=6.0
Q ss_pred CCccccccccCCCCCCCCCCCCCCCCCCCCccccCccCCCCCCCchhhhhhhccCCcCCCCC-ccccccccCCcCCC-CC
Q 028141 2 INFEATELRLGLPGGNGGSSEGGGGGGGGEKAKNNNINGMKRGFADTVVDLKLNLSTKESGG-IDVIEKTKGKSASA-TG 79 (213)
Q Consensus 2 lnl~~TELrLGLPG~~~~~~~~~~~~~~~~~~~~~~~~~~KR~fset~vdl~~~l~~~~~~~-~~~~~~~~~~~~~~-~~ 79 (213)
||||+|||||||||+.+ ++ ...........+++||+|+++ |+............ .............. ..
T Consensus 1 ln~~~TELrLGLPG~~~--~~-----~~~~~~~~~~~~~~kR~F~~a-id~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 (215)
T PF02309_consen 1 LNLKATELRLGLPGSES--PD-----ASSSSSSKKSSSGNKRGFSEA-IDSSSSNSQSSSSSSSDSSSSSSSSSTSSSSS 72 (215)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred CCchhhhhcccCCCCCC--CC-----cccccccccccCcccccchhh-hhhcccccccccccccccCccccccccccccc
Confidence 89999999999999874 11 000111112347889999998 77654111000000 00000000000000 00
Q ss_pred C-CCCCCCCCCCCCCCCCCccchhhhhhhhcccCcccccccCCCCCCCcceEEEEecCccccceeecCCccCHHHHHHHH
Q 028141 80 A-TDLSKPPAKSQVVGWPPVRSFRKNIMAVQKDNEEGDNKASSSSSSNVAFVKVSMDGAPYLRKVDLKLYKSYQELSDAL 158 (213)
Q Consensus 80 ~-~~~~~p~~k~qvVGWPPVrs~Rkn~~~~~~~~~~~~~~~~~~~~~~~~~VKV~MdG~pigRKVDL~~~~sY~eL~~aL 158 (213)
. .....|.+++|+|||||||+||||++...+ ....++||||+|||+||||||||++|+||++|+.+|
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 0 122235578999999999999999877211 122479999999999999999999999999999999
Q ss_pred HHhhcccccCCcCCCCcccccchhhhhccCCCCCeeEEEeeCCCCeeecccCCCC
Q 028141 159 GKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGDWMLVGDVPWE 213 (213)
Q Consensus 159 e~MF~~~~~g~~~~~g~~~~~~e~~l~d~~~~seyvltYEDkdGDwMLVGDVPWe 213 (213)
++||.+|.|++|++++ .++..+.++.++++|+|||||+||||||||||||+
T Consensus 141 ~~MF~~~~i~~~~~~~----~~~~~~~~~~~~~~~~l~Y~D~egd~mlvGD~PW~ 191 (215)
T PF02309_consen 141 EKMFSCFSIEQCGSHG----LNESGLLDLLNGSEYVLVYEDKEGDWMLVGDVPWE 191 (215)
T ss_dssp -------------------------------------------------------
T ss_pred HHhcCCCCcccccccc----ccchhhccccCCcceeEEEECCCCCEEEecCCCHH
Confidence 9999988888887744 45667778888899999999999999999999996
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=97.34 E-value=0.00069 Score=49.01 Aligned_cols=55 Identities=27% Similarity=0.468 Sum_probs=45.6
Q ss_pred eEEEEecCccccceeecCCccCHHHHHHHHHHhhcccccCCcCCCCcccccchhhhhccCCCCCeeEEEeeCCCCeeecc
Q 028141 129 FVKVSMDGAPYLRKVDLKLYKSYQELSDALGKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGDWMLVG 208 (213)
Q Consensus 129 ~VKV~MdG~pigRKVDL~~~~sY~eL~~aLe~MF~~~~~g~~~~~g~~~~~~e~~l~d~~~~seyvltYEDkdGDwMLVG 208 (213)
-|||+..|. +=|.+.+..--+|.+|...+++.|... ...+.+.|.|.||||..+-
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 489999997 434688888889999999999999861 2468999999999998875
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=97.29 E-value=0.00087 Score=51.48 Aligned_cols=57 Identities=26% Similarity=0.317 Sum_probs=45.3
Q ss_pred eEEEEecCccccceeecC---CccCHHHHHHHHHHhhcccccCCcCCCCcccccchhhhhccCCCCCeeEEEeeCCCCee
Q 028141 129 FVKVSMDGAPYLRKVDLK---LYKSYQELSDALGKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGDWM 205 (213)
Q Consensus 129 ~VKV~MdG~pigRKVDL~---~~~sY~eL~~aLe~MF~~~~~g~~~~~g~~~~~~e~~l~d~~~~seyvltYEDkdGDwM 205 (213)
-|||.-+|.-+=-++++. .--+|++|.+.+.+.|... ...+|+|.|.|.||||.
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 489999998555555553 4679999999999999851 23589999999999998
Q ss_pred ecc
Q 028141 206 LVG 208 (213)
Q Consensus 206 LVG 208 (213)
.+-
T Consensus 59 ~l~ 61 (91)
T cd06398 59 TLV 61 (91)
T ss_pred EEc
Confidence 763
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=97.18 E-value=0.0015 Score=49.21 Aligned_cols=54 Identities=24% Similarity=0.348 Sum_probs=43.1
Q ss_pred eEEEEecCccccceeecCCccCHHHHHHHHHHhhcccccCCcCCCCcccccchhhhhccCCCCCeeEEEeeCCCCeeec
Q 028141 129 FVKVSMDGAPYLRKVDLKLYKSYQELSDALGKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGDWMLV 207 (213)
Q Consensus 129 ~VKV~MdG~pigRKVDL~~~~sY~eL~~aLe~MF~~~~~g~~~~~g~~~~~~e~~l~d~~~~seyvltYEDkdGDwMLV 207 (213)
=|||...|. -+.+-|..--+|++|.+.+.++|..- +...|.|-|.|.||||.++
T Consensus 2 ~vK~~~~~d--~~r~~l~~~~~~~~L~~~i~~r~~~~-----------------------~~~~f~LkY~Ddegd~v~l 55 (82)
T cd06407 2 RVKATYGEE--KIRFRLPPSWGFTELKQEIAKRFKLD-----------------------DMSAFDLKYLDDDEEWVLL 55 (82)
T ss_pred EEEEEeCCe--EEEEEcCCCCCHHHHHHHHHHHhCCC-----------------------CCCeeEEEEECCCCCeEEe
Confidence 389999887 44455555669999999999999851 1257999999999999875
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=96.99 E-value=0.0023 Score=48.55 Aligned_cols=52 Identities=19% Similarity=0.228 Sum_probs=45.6
Q ss_pred EEEEecCccccceeecCCccCHHHHHHHHHHhhcccccCCcCCCCcccccchhhhhccCCCCCeeEEEeeCCCCeeec
Q 028141 130 VKVSMDGAPYLRKVDLKLYKSYQELSDALGKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGDWMLV 207 (213)
Q Consensus 130 VKV~MdG~pigRKVDL~~~~sY~eL~~aLe~MF~~~~~g~~~~~g~~~~~~e~~l~d~~~~seyvltYEDkdGDwMLV 207 (213)
|||.-.|.-+--+++-+..-+|++|.+.+.++|+. + .|.|.|-|.||||.++
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 79999999777788887788999999999999986 1 4689999999999986
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=96.88 E-value=0.0046 Score=44.64 Aligned_cols=54 Identities=24% Similarity=0.492 Sum_probs=43.3
Q ss_pred EEEEecCccccceeecCCccCHHHHHHHHHHhhcccccCCcCCCCcccccchhhhhccCCCCCeeEEEeeCCCCeeeccc
Q 028141 130 VKVSMDGAPYLRKVDLKLYKSYQELSDALGKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGDWMLVGD 209 (213)
Q Consensus 130 VKV~MdG~pigRKVDL~~~~sY~eL~~aLe~MF~~~~~g~~~~~g~~~~~~e~~l~d~~~~seyvltYEDkdGDwMLVGD 209 (213)
|||.-.|. -|.+-+..--+|.+|...+.+.|.. ....+.|.|+|.||||..+.+
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 5777788888999999999999985 123689999999999987643
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=96.50 E-value=0.013 Score=41.93 Aligned_cols=55 Identities=24% Similarity=0.414 Sum_probs=42.7
Q ss_pred eEEEEecCccccceeecC-CccCHHHHHHHHHHhhcccccCCcCCCCcccccchhhhhccCCCCCeeEEEeeCCCCeeec
Q 028141 129 FVKVSMDGAPYLRKVDLK-LYKSYQELSDALGKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGDWMLV 207 (213)
Q Consensus 129 ~VKV~MdG~pigRKVDL~-~~~sY~eL~~aLe~MF~~~~~g~~~~~g~~~~~~e~~l~d~~~~seyvltYEDkdGDwMLV 207 (213)
-|||+-.|. -|.+=+. .--+|++|...|.+.|... ...+.+.|.|.||||..+
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 136899999999999877
Q ss_pred cc
Q 028141 208 GD 209 (213)
Q Consensus 208 GD 209 (213)
.+
T Consensus 56 ~s 57 (81)
T cd05992 56 SS 57 (81)
T ss_pred CC
Confidence 54
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=96.33 E-value=0.0095 Score=45.26 Aligned_cols=53 Identities=19% Similarity=0.276 Sum_probs=40.0
Q ss_pred EEEEecCccccceeecCCccCHHHHHHHHHHhhcccccCCcCCCCcccccchhhhhccCCCCCeeEEEeeCCCCeee
Q 028141 130 VKVSMDGAPYLRKVDLKLYKSYQELSDALGKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGDWML 206 (213)
Q Consensus 130 VKV~MdG~pigRKVDL~~~~sY~eL~~aLe~MF~~~~~g~~~~~g~~~~~~e~~l~d~~~~seyvltYEDkdGDwML 206 (213)
||...|..=-=-.+|.....+|+++.+-|+.||.+ .+..|+|-|.|.+||.+=
T Consensus 3 VKSkfdaEfRRFsl~r~~~~~f~ef~~ll~~lH~l------------------------~~~~f~i~Y~D~~gDLLP 55 (80)
T cd06403 3 VKSKFDAEFRRFSLDRNKPGKFEDFYKLLEHLHHI------------------------PNVDFLIGYTDPHGDLLP 55 (80)
T ss_pred eecccCCeEEEEEeccccCcCHHHHHHHHHHHhCC------------------------CCCcEEEEEeCCCCCEec
Confidence 56666665222245555669999999999999986 234799999999999874
No 9
>cd06409 PB1_MUG70 The MUG70 protein is a product of the meiotically up-regulated gene 70 which has a role in meiosis and harbors a PB1 domain. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domains depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic amino acid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is
Probab=96.23 E-value=0.011 Score=45.36 Aligned_cols=50 Identities=22% Similarity=0.344 Sum_probs=38.0
Q ss_pred ccccceeecC--CccCHHHHHHHHHHhhcccccCCcCCCCcccccchhhhhccCCCCCeeEEEeeCCCCeeec
Q 028141 137 APYLRKVDLK--LYKSYQELSDALGKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGDWMLV 207 (213)
Q Consensus 137 ~pigRKVDL~--~~~sY~eL~~aLe~MF~~~~~g~~~~~g~~~~~~e~~l~d~~~~seyvltYEDkdGDwMLV 207 (213)
.|-||-+=++ ...|+.+|..++.+-|+.-. .....|.|.|.|.||||.|.
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 4667765544 47899999999999997511 01247899999999999986
No 10
>cd06402 PB1_p62 The PB1 domain is an essential part of p62 scaffold protein (alias sequestosome 1,SQSTM) involved in cell signaling, receptor internalization, and protein turnover. The PB1 domain is a modular domain mediating specific protein-protein interaction which play roles in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.
Probab=95.75 E-value=0.045 Score=42.03 Aligned_cols=56 Identities=23% Similarity=0.485 Sum_probs=41.5
Q ss_pred eEEEEecC---ccccceeec--CCccCHHHHHHHHHHhhcccccCCcCCCCcccccchhhhhccCCCCCeeEEEeeCCCC
Q 028141 129 FVKVSMDG---APYLRKVDL--KLYKSYQELSDALGKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGD 203 (213)
Q Consensus 129 ~VKV~MdG---~pigRKVDL--~~~~sY~eL~~aLe~MF~~~~~g~~~~~g~~~~~~e~~l~d~~~~seyvltYEDkdGD 203 (213)
.||.+..| .+==|++=| ....+|++|...+.++|... .+..|++.|.|.|||
T Consensus 2 ~vkayl~~~~~~~EIRRf~l~~~~~~s~~~L~~~V~~~f~~l-----------------------~~~~ftlky~DeeGD 58 (87)
T cd06402 2 TVKAYLLGKDANAEIRRFAIDEDVSTSYEYLVEKVAAVFPSL-----------------------RGKNFQLFWKDEEGD 58 (87)
T ss_pred eEEEeecCCCCccceEEEEecCCCCcCHHHHHHHHHHHcccc-----------------------CCCcEEEEEECCCCC
Confidence 57777766 233344444 66679999999999999741 235799999999999
Q ss_pred eeec
Q 028141 204 WMLV 207 (213)
Q Consensus 204 wMLV 207 (213)
..-+
T Consensus 59 lvtI 62 (87)
T cd06402 59 LVAF 62 (87)
T ss_pred EEee
Confidence 8654
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=95.70 E-value=0.03 Score=42.83 Aligned_cols=53 Identities=23% Similarity=0.357 Sum_probs=42.0
Q ss_pred EEEEecCccccceeecCCccCHHHHHHHHHHhhcccccCCcCCCCcccccchhhhhccCCCCCeeEEEeeCCCCeeec
Q 028141 130 VKVSMDGAPYLRKVDLKLYKSYQELSDALGKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGDWMLV 207 (213)
Q Consensus 130 VKV~MdG~pigRKVDL~~~~sY~eL~~aLe~MF~~~~~g~~~~~g~~~~~~e~~l~d~~~~seyvltYEDkdGDwMLV 207 (213)
||++-.|.-.--.+|. .-+|++|.+.+.+||... .+..|++.|.|.|||---+
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 7889999855555565 778999999999999851 2347999999999996543
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=95.22 E-value=0.066 Score=40.90 Aligned_cols=52 Identities=21% Similarity=0.280 Sum_probs=42.7
Q ss_pred EEEEecCccccceeecCCccCHHHHHHHHHHhhcccccCCcCCCCcccccchhhhhccCCCCCeeEEEeeCCCCeeec
Q 028141 130 VKVSMDGAPYLRKVDLKLYKSYQELSDALGKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGDWMLV 207 (213)
Q Consensus 130 VKV~MdG~pigRKVDL~~~~sY~eL~~aLe~MF~~~~~g~~~~~g~~~~~~e~~l~d~~~~seyvltYEDkdGDwMLV 207 (213)
-||+-.|. .|++-...-=+|..|.+.|+.+|.+. .-.+.+||.|.|||..-+
T Consensus 3 fKv~~~g~--~RRf~~~~~pt~~~L~~kl~~Lf~lp------------------------~~~~~vtYiDeD~D~ITl 54 (82)
T cd06397 3 FKSSFLGD--TRRIVFPDIPTWEALASKLENLYNLP------------------------EIKVGVTYIDNDNDEITL 54 (82)
T ss_pred EEEEeCCc--eEEEecCCCccHHHHHHHHHHHhCCC------------------------hhHeEEEEEcCCCCEEEe
Confidence 47888886 78888888899999999999999862 112789999999998654
No 13
>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=95.14 E-value=0.1 Score=39.81 Aligned_cols=57 Identities=25% Similarity=0.469 Sum_probs=40.3
Q ss_pred EEEEecCccccceeecCCcc-CHHHHHHHHHHhhcccccCCcCCCCcccccchhhhhccCCCCCeeEEEeeCCCCeeecc
Q 028141 130 VKVSMDGAPYLRKVDLKLYK-SYQELSDALGKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGDWMLVG 208 (213)
Q Consensus 130 VKV~MdG~pigRKVDL~~~~-sY~eL~~aLe~MF~~~~~g~~~~~g~~~~~~e~~l~d~~~~seyvltYEDkdGDwMLVG 208 (213)
+|+...|. | |++=+..-. +|.+|...+.+.|..- .+ ....+.+.|.|.|||+.-|-
T Consensus 3 iK~~~g~D-i-R~~~~~~~~~t~~~L~~~v~~~F~~~----~~-----------------~~~~flIKYkD~dGDlVTIt 59 (81)
T cd06401 3 LKAQLGDD-I-RRIPIHNEDITYDELLLMMQRVFRGK----LG-----------------SSDDVLIKYKDEDGDLITIF 59 (81)
T ss_pred EEEEeCCe-E-EEEeccCccccHHHHHHHHHHHhccc----cC-----------------CcccEEEEEECCCCCEEEec
Confidence 67766655 4 444444323 9999999999999851 11 23478999999999997664
Q ss_pred c
Q 028141 209 D 209 (213)
Q Consensus 209 D 209 (213)
+
T Consensus 60 s 60 (81)
T cd06401 60 D 60 (81)
T ss_pred c
Confidence 3
No 14
>cd06408 PB1_NoxR The PB1 domain is present in the Epichloe festucae NoxR protein (NADPH oxidase regulator), a key regulator of NADPH oxidase isoform, NoxA. NoxA is essential for growth control of the fungal endophyte in plant tissue in the process of symbiotic interaction between a fungi and its plant host. The Epichloe festucae p67(phox)-like regulator, NoxR, dispensable in culture but essential in plants for the symbiotic interaction. Plants infected with a noxR deletion mutant show severe stunting and premature senescence, whereas hyphae in the meristematic tissues show increased branching leading to increased fungal colonization of pseudostem and leaf blade tissue. The PB1 domain is a modular domain mediating specific protein-protein interactions which a play role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is
Probab=91.98 E-value=0.58 Score=35.94 Aligned_cols=54 Identities=20% Similarity=0.302 Sum_probs=44.0
Q ss_pred ceEEEEecCccccceeecCCccCHHHHHHHHHHhhcccccCCcCCCCcccccchhhhhccCCCCCeeEEEeeCCCCeeec
Q 028141 128 AFVKVSMDGAPYLRKVDLKLYKSYQELSDALGKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGDWMLV 207 (213)
Q Consensus 128 ~~VKV~MdG~pigRKVDL~~~~sY~eL~~aLe~MF~~~~~g~~~~~g~~~~~~e~~l~d~~~~seyvltYEDkdGDwMLV 207 (213)
.=|||+-.|. .|-|-+..--+|++|...+.++|+. ...+.+-|.|. ||..-+
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 12678999999 998777
Q ss_pred cc
Q 028141 208 GD 209 (213)
Q Consensus 208 GD 209 (213)
+|
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=68.24 E-value=8.3 Score=30.12 Aligned_cols=38 Identities=24% Similarity=0.364 Sum_probs=30.4
Q ss_pred ecCCccCHHHHHHHHHHhhcccccCCcCCCCcccccchhhhhccCCCCCeeEEEeeCCCCeeec
Q 028141 144 DLKLYKSYQELSDALGKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGDWMLV 207 (213)
Q Consensus 144 DL~~~~sY~eL~~aLe~MF~~~~~g~~~~~g~~~~~~e~~l~d~~~~seyvltYEDkdGDwMLV 207 (213)
||+.--+|.+|..-..+-|..+ +-+|-|.|.|||..-+
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 3468899999998643
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=57.86 E-value=8.2 Score=26.79 Aligned_cols=17 Identities=29% Similarity=0.649 Sum_probs=14.4
Q ss_pred eEEEeeCCCCeeecccC
Q 028141 194 VPTYEDKDGDWMLVGDV 210 (213)
Q Consensus 194 vltYEDkdGDwMLVGDV 210 (213)
-+.|.|.||+.+++|+.
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 48899999999999974
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=47.00 E-value=37 Score=26.34 Aligned_cols=47 Identities=26% Similarity=0.376 Sum_probs=33.4
Q ss_pred CccccceeecCCccCHHHHHHHHHHhhcccccCCcCCCCcccccchhhhhccCCCCCeeEEEeeCCCCeeec
Q 028141 136 GAPYLRKVDLKLYKSYQELSDALGKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGDWMLV 207 (213)
Q Consensus 136 G~pigRKVDL~~~~sY~eL~~aLe~MF~~~~~g~~~~~g~~~~~~e~~l~d~~~~seyvltYEDkdGDwMLV 207 (213)
|..+--.||...+=+|.+++.++.+....-|. -..-|||.|||..-|
T Consensus 10 gg~vDw~V~~~~~L~F~DvL~~I~~vlp~aT~-------------------------tAFeYEDE~gDRITV 56 (91)
T cd06395 10 GGAVDWTVQSGPQLLFRDVLDVIGQVLPEATT-------------------------TAFEYEDEDGDRITV 56 (91)
T ss_pred CCcccccccCcccccHHHHHHHHHHhcccccc-------------------------cceeeccccCCeeEe
Confidence 34456667777777899999888876653221 136699999999876
No 18
>COG0219 CspR Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]
Probab=31.62 E-value=21 Score=30.30 Aligned_cols=30 Identities=27% Similarity=0.427 Sum_probs=25.8
Q ss_pred cCccccceeecCCccCHHHHHHHH---HHhhcc
Q 028141 135 DGAPYLRKVDLKLYKSYQELSDAL---GKMFSS 164 (213)
Q Consensus 135 dG~pigRKVDL~~~~sY~eL~~aL---e~MF~~ 164 (213)
-|--|.-+++|..|++|++...+. .++|-.
T Consensus 48 AGlDY~~~~~l~~h~s~e~fl~~~~~~~rl~~~ 80 (155)
T COG0219 48 AGLDYHEKASLTEHDSLEAFLEAEPIGGRLFAL 80 (155)
T ss_pred cccchHhhcceEEeCCHHHHHhhccCCceEEEE
Confidence 477799999999999999999998 467765
No 19
>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=25.94 E-value=79 Score=26.11 Aligned_cols=37 Identities=24% Similarity=0.482 Sum_probs=30.9
Q ss_pred cceEEEEecCc--cccceeecCCccCHHHHHHHHHHhhc
Q 028141 127 VAFVKVSMDGA--PYLRKVDLKLYKSYQELSDALGKMFS 163 (213)
Q Consensus 127 ~~~VKV~MdG~--pigRKVDL~~~~sY~eL~~aLe~MF~ 163 (213)
..-+||...|. +|=|.|-+..--+..+|..+|+..|+
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
No 20
>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=25.37 E-value=45 Score=25.78 Aligned_cols=19 Identities=37% Similarity=0.548 Sum_probs=15.8
Q ss_pred CeeEEEeeCCCCeeecccC
Q 028141 192 DYVPTYEDKDGDWMLVGDV 210 (213)
Q Consensus 192 eyvltYEDkdGDwMLVGDV 210 (213)
=|+.-|+|.+||+..-|.|
T Consensus 92 iwiaP~~D~~g~l~~~~~V 110 (119)
T PF09676_consen 92 IWIAPWEDADGDLHDPGYV 110 (119)
T ss_pred EEEeeeECCCCCEeccceE
Confidence 5889999999999876654
No 21
>PF12426 DUF3674: RNA dependent RNA polymerase; InterPro: IPR024378 This domain is found in the RNA-directed RNA polymerase. It is located towards the N terminus and is approximately 40 amino acids in length. There is a conserved MFNLKF sequence motif. There are two completely conserved residues (E and P) that may be functionally important.
Probab=24.10 E-value=45 Score=22.51 Aligned_cols=14 Identities=50% Similarity=0.783 Sum_probs=10.7
Q ss_pred HHHHHHhhcc-cccC
Q 028141 155 SDALGKMFSS-FTIG 168 (213)
Q Consensus 155 ~~aLe~MF~~-~~~g 168 (213)
..+||.||.. |.++
T Consensus 7 R~aLEAMFNLKFhi~ 21 (41)
T PF12426_consen 7 RSALEAMFNLKFHIG 21 (41)
T ss_pred HHHHHHHhceeeeeC
Confidence 6899999996 5443
No 22
>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=23.96 E-value=27 Score=22.78 Aligned_cols=11 Identities=45% Similarity=1.054 Sum_probs=8.5
Q ss_pred eEEEeeCCCCe
Q 028141 194 VPTYEDKDGDW 204 (213)
Q Consensus 194 vltYEDkdGDw 204 (213)
.+.|.|.+|+|
T Consensus 16 ~v~y~d~~g~W 26 (36)
T PF02013_consen 16 EVVYTDDDGGW 26 (36)
T ss_dssp --SEEETTEEE
T ss_pred ceEEcCCCCCE
Confidence 57899999998
No 23
>PF11576 DUF3236: Protein of unknown function (DUF3236); InterPro: IPR012019 This family of proteins with unknown function appears to be restricted to Methanobacteria. ; PDB: 3BRC_B.
Probab=23.63 E-value=29 Score=29.43 Aligned_cols=9 Identities=56% Similarity=1.025 Sum_probs=6.1
Q ss_pred cccCCCCCC
Q 028141 9 LRLGLPGGN 17 (213)
Q Consensus 9 LrLGLPG~~ 17 (213)
=|||.||+.
T Consensus 100 GRLGvPGSG 108 (154)
T PF11576_consen 100 GRLGVPGSG 108 (154)
T ss_dssp EE-SSTTS-
T ss_pred ccccCCCCc
Confidence 499999985
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=22.13 E-value=28 Score=31.31 Aligned_cols=54 Identities=26% Similarity=0.421 Sum_probs=32.1
Q ss_pred cceEEEEecCccccceeecCCccCHHHHHHHHHHhhcccccCCcCCCCcccccchhhhhccCCCCCeeEEEeeCCCC
Q 028141 127 VAFVKVSMDGAPYLRKVDLKLYKSYQELSDALGKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGD 203 (213)
Q Consensus 127 ~~~VKV~MdG~pigRKVDL~~~~sY~eL~~aLe~MF~~~~~g~~~~~g~~~~~~e~~l~d~~~~seyvltYEDkdGD 203 (213)
-.|.-.-=||+-||-|||..+.++ |.+.+.+-|+ + .|......|-|+|.|+||.
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 346666667778888888877643 3333333221 1 1222234678999999985
No 25
>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=21.90 E-value=2.7e+02 Score=21.12 Aligned_cols=33 Identities=18% Similarity=0.159 Sum_probs=26.6
Q ss_pred eEEEEecCccccceeecCCccCHHHHHHHHHHhhcc
Q 028141 129 FVKVSMDGAPYLRKVDLKLYKSYQELSDALGKMFSS 164 (213)
Q Consensus 129 ~VKV~MdG~pigRKVDL~~~~sY~eL~~aLe~MF~~ 164 (213)
-|||+..+ .=.|-...=-+|++|...|.+-+..
T Consensus 4 vvKV~f~~---tIaIrvp~~~~y~~L~~ki~~kLkl 36 (80)
T cd06406 4 VVKVHFKY---TVAIQVARGLSYATLLQKISSKLEL 36 (80)
T ss_pred EEEEEEEE---EEEEEcCCCCCHHHHHHHHHHHhCC
Confidence 58999997 3456666677999999999998886
Done!