Query 027865
Match_columns 217
No_of_seqs 212 out of 575
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 02:38:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027865.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027865hhsearch_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 9.2E-61 2E-65 411.1 0.4 192 2-217 1-195 (215)
2 PF00564 PB1: PB1 domain; Int 97.3 0.00085 1.8E-08 48.7 6.2 56 129-209 3-58 (84)
3 cd06398 PB1_Joka2 The PB1 doma 97.3 0.0011 2.4E-08 51.1 6.7 57 129-208 2-61 (91)
4 cd06407 PB1_NLP A PB1 domain i 97.1 0.0018 3.9E-08 48.9 6.7 54 129-207 2-55 (82)
5 smart00666 PB1 PB1 domain. Pho 96.9 0.0052 1.1E-07 44.5 7.0 54 130-209 4-57 (81)
6 cd06396 PB1_NBR1 The PB1 domai 96.8 0.0039 8.4E-08 47.5 6.3 52 130-207 3-54 (81)
7 cd05992 PB1 The PB1 domain is 96.5 0.016 3.4E-07 41.7 7.1 55 129-209 2-57 (81)
8 cd06403 PB1_Par6 The PB1 domai 96.3 0.011 2.3E-07 45.1 5.5 54 130-207 3-56 (80)
9 cd06409 PB1_MUG70 The MUG70 pr 96.0 0.017 3.7E-07 44.3 5.2 50 137-207 7-58 (86)
10 cd06404 PB1_aPKC PB1 domain is 95.8 0.028 6E-07 43.1 5.8 53 130-207 3-55 (83)
11 cd06402 PB1_p62 The PB1 domain 95.7 0.048 1E-06 42.0 6.9 56 129-207 2-62 (87)
12 cd06401 PB1_TFG The PB1 domain 95.4 0.08 1.7E-06 40.4 6.9 57 130-209 3-60 (81)
13 cd06397 PB1_UP1 Uncharacterize 95.2 0.073 1.6E-06 40.7 6.1 53 130-208 3-55 (82)
14 cd06408 PB1_NoxR The PB1 domai 92.6 0.47 1E-05 36.5 6.2 54 128-209 3-56 (86)
15 cd06399 PB1_P40 The PB1 domain 73.5 5.6 0.00012 31.1 3.9 39 143-207 22-60 (92)
16 PF10411 DsbC_N: Disulfide bon 56.2 9.3 0.0002 26.6 2.0 17 194-210 34-50 (57)
17 cd06395 PB1_Map2k5 PB1 domain 49.4 32 0.0007 26.7 4.1 48 136-208 10-57 (91)
18 COG0219 CspR Predicted rRNA me 35.2 19 0.00041 30.7 1.0 32 135-166 48-82 (155)
19 PF09676 TraV: Type IV conjuga 25.9 46 0.00099 25.8 1.7 19 192-210 92-110 (119)
20 PF11576 DUF3236: Protein of u 24.6 27 0.00059 29.7 0.2 9 9-17 100-108 (154)
21 PF07929 PRiA4_ORF3: Plasmid p 23.5 96 0.0021 25.7 3.4 36 128-163 5-42 (179)
22 cd00771 ThrRS_core Threonyl-tR 22.7 26 0.00057 31.6 -0.2 54 127-203 209-262 (298)
23 cd06406 PB1_P67 A PB1 domain i 21.0 3E+02 0.0066 20.9 5.3 34 128-164 3-36 (80)
24 PF02013 CBM_10: Cellulose or 20.1 28 0.00062 22.7 -0.4 12 194-205 16-27 (36)
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=9.2e-61 Score=411.08 Aligned_cols=192 Identities=52% Similarity=0.875 Sum_probs=6.0
Q ss_pred CCCcccccccCCCCCCCCCCCCCCCCCCCCcccccccCCCCCCCcchhhhhhcccCCCCCCC-ccccccccCCcCCC-CC
Q 027865 2 INFEATELRLGLPGGNGGSSEGGGGGGGGEKAKNNNINGMKRGFADTVVDLKLNLSTKESGG-IDVIEKTKGKSASA-TG 79 (217)
Q Consensus 2 l~l~~TELRLGLPG~~~~~~~~~~~~~~~~~~~~~~~~~~KR~fset~vdl~l~~~~~~~~~-~~~~~~~~~~~~~~-~~ 79 (217)
||||+|||||||||+.+ ++ ...........+++||+|+++ ++............ ........+..... ..
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-CCCCCCCCCCCCCCCCCcccchhhhhhhcccCcccccccCCCCCCCcceEEEEEcCccccceeecCCccCHHHHHHHH
Q 027865 80 A-TDLSKPPAKSQVVGWPPVRSFRKNIMAVQKDNEEGDNKASSSSSSNVAFVKVSMDGAPYLRKVDLKLYKSYQELSDAL 158 (217)
Q Consensus 80 ~-~~~~~p~~k~qvVGWPPVrs~Rkn~~~~~~~~~~~~~~~~~~~~~~~~~VKV~MdG~pigRKVDL~~~~sY~~L~~aL 158 (217)
. .....|.+++|+|||||||+||||.+.... ....++||||+|||+||||||||++|+||++|+.+|
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 122235578999999999999999876211 112479999999999999999999999999999999
Q ss_pred HHhhcccccCCcCCCCcccccchhhhhcccCCCCeeEEEEcCCCCeEecCCcCCCCCCC
Q 027865 159 GKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGDWMLVGDVPWDTKGS 217 (217)
Q Consensus 159 e~MF~~~~~g~~~~~g~~~~~~e~~l~d~~~~seyvltYeDkeGDwMLVGDVPWemF~~ 217 (217)
++||.+|.+++|++++ .++..+.+++++++|+|||||+||||||||||||+|||+
T Consensus 141 ~~MF~~~~i~~~~~~~----~~~~~~~~~~~~~~~~l~Y~D~egd~mlvGD~PW~~F~~ 195 (215)
T PF02309_consen 141 EKMFSCFSIEQCGSHG----LNESGLLDLLNGSEYVLVYEDKEGDWMLVGDVPWEEFVK 195 (215)
T ss_dssp -----------------------------------------------------------
T ss_pred HHhcCCCCcccccccc----ccchhhccccCCcceeEEEECCCCCEEEecCCCHHHHHH
Confidence 9999888888887744 456667777888999999999999999999999999985
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=97.29 E-value=0.00085 Score=48.68 Aligned_cols=56 Identities=27% Similarity=0.462 Sum_probs=46.4
Q ss_pred eEEEEEcCccccceeecCCccCHHHHHHHHHHhhcccccCCcCCCCcccccchhhhhcccCCCCeeEEEEcCCCCeEecC
Q 027865 129 FVKVSMDGAPYLRKVDLKLYKSYQELSDALGKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGDWMLVG 208 (217)
Q Consensus 129 ~VKV~MdG~pigRKVDL~~~~sY~~L~~aLe~MF~~~~~g~~~~~g~~~~~~e~~l~d~~~~seyvltYeDkeGDwMLVG 208 (217)
-|||+..|. +=|.+.+..--+|.+|...+++.|... ...+.|.|.|.||||..+-
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 444688888889999999999999851 2378999999999999875
Q ss_pred C
Q 027865 209 D 209 (217)
Q Consensus 209 D 209 (217)
+
T Consensus 58 s 58 (84)
T PF00564_consen 58 S 58 (84)
T ss_dssp S
T ss_pred C
Confidence 4
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=97.26 E-value=0.0011 Score=51.07 Aligned_cols=57 Identities=26% Similarity=0.317 Sum_probs=45.0
Q ss_pred eEEEEEcCccccceeecC---CccCHHHHHHHHHHhhcccccCCcCCCCcccccchhhhhcccCCCCeeEEEEcCCCCeE
Q 027865 129 FVKVSMDGAPYLRKVDLK---LYKSYQELSDALGKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGDWM 205 (217)
Q Consensus 129 ~VKV~MdG~pigRKVDL~---~~~sY~~L~~aLe~MF~~~~~g~~~~~g~~~~~~e~~l~d~~~~seyvltYeDkeGDwM 205 (217)
-|||.-+|.-+=-++++. ..-+|++|.+.+.+.|... ...+|+|.|-|.||||.
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 489999998544455553 4679999999999999851 23589999999999998
Q ss_pred ecC
Q 027865 206 LVG 208 (217)
Q Consensus 206 LVG 208 (217)
.+-
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=97.14 E-value=0.0018 Score=48.89 Aligned_cols=54 Identities=24% Similarity=0.377 Sum_probs=43.4
Q ss_pred eEEEEEcCccccceeecCCccCHHHHHHHHHHhhcccccCCcCCCCcccccchhhhhcccCCCCeeEEEEcCCCCeEec
Q 027865 129 FVKVSMDGAPYLRKVDLKLYKSYQELSDALGKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGDWMLV 207 (217)
Q Consensus 129 ~VKV~MdG~pigRKVDL~~~~sY~~L~~aLe~MF~~~~~g~~~~~g~~~~~~e~~l~d~~~~seyvltYeDkeGDwMLV 207 (217)
=|||...|. -+.+-|..--+|++|.+.+.++|.. . +.+.|.|-|.|.||||.++
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 4455555566999999999999985 1 1258999999999999875
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=96.88 E-value=0.0052 Score=44.52 Aligned_cols=54 Identities=24% Similarity=0.492 Sum_probs=43.7
Q ss_pred EEEEEcCccccceeecCCccCHHHHHHHHHHhhcccccCCcCCCCcccccchhhhhcccCCCCeeEEEEcCCCCeEecCC
Q 027865 130 VKVSMDGAPYLRKVDLKLYKSYQELSDALGKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGDWMLVGD 209 (217)
Q Consensus 130 VKV~MdG~pigRKVDL~~~~sY~~L~~aLe~MF~~~~~g~~~~~g~~~~~~e~~l~d~~~~seyvltYeDkeGDwMLVGD 209 (217)
|||.-.|. -|.+-+..--+|.+|...+.+.|.. ....+.|.|+|.||||..+.+
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 6777788888999999999999985 123689999999999987654
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=96.85 E-value=0.0039 Score=47.46 Aligned_cols=52 Identities=19% Similarity=0.228 Sum_probs=45.6
Q ss_pred EEEEEcCccccceeecCCccCHHHHHHHHHHhhcccccCCcCCCCcccccchhhhhcccCCCCeeEEEEcCCCCeEec
Q 027865 130 VKVSMDGAPYLRKVDLKLYKSYQELSDALGKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGDWMLV 207 (217)
Q Consensus 130 VKV~MdG~pigRKVDL~~~~sY~~L~~aLe~MF~~~~~g~~~~~g~~~~~~e~~l~d~~~~seyvltYeDkeGDwMLV 207 (217)
|||.-.|.-+--+++-+..-+|++|.+.+.++|+. + .|.|.|-|.||||.++
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 79999999777788887788999999999999985 1 5689999999999986
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=96.46 E-value=0.016 Score=41.67 Aligned_cols=55 Identities=24% Similarity=0.414 Sum_probs=43.1
Q ss_pred eEEEEEcCccccceeecC-CccCHHHHHHHHHHhhcccccCCcCCCCcccccchhhhhcccCCCCeeEEEEcCCCCeEec
Q 027865 129 FVKVSMDGAPYLRKVDLK-LYKSYQELSDALGKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGDWMLV 207 (217)
Q Consensus 129 ~VKV~MdG~pigRKVDL~-~~~sY~~L~~aLe~MF~~~~~g~~~~~g~~~~~~e~~l~d~~~~seyvltYeDkeGDwMLV 207 (217)
-|||+-.|. -|.+=+. ..-+|++|...|.+.|... ...+.+.|.|.||||..+
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 8889999999999999851 136899999999999887
Q ss_pred CC
Q 027865 208 GD 209 (217)
Q Consensus 208 GD 209 (217)
.+
T Consensus 56 ~s 57 (81)
T cd05992 56 SS 57 (81)
T ss_pred CC
Confidence 65
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=96.31 E-value=0.011 Score=45.11 Aligned_cols=54 Identities=19% Similarity=0.290 Sum_probs=40.3
Q ss_pred EEEEEcCccccceeecCCccCHHHHHHHHHHhhcccccCCcCCCCcccccchhhhhcccCCCCeeEEEEcCCCCeEec
Q 027865 130 VKVSMDGAPYLRKVDLKLYKSYQELSDALGKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGDWMLV 207 (217)
Q Consensus 130 VKV~MdG~pigRKVDL~~~~sY~~L~~aLe~MF~~~~~g~~~~~g~~~~~~e~~l~d~~~~seyvltYeDkeGDwMLV 207 (217)
||..-|..=-=-.+|.....+|+++++-|+.||.+ .+..|+|-|.|.+||.+-+
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 56666665222245555569999999999999986 1347999999999998754
No 9
>cd06409 PB1_MUG70 The MUG70 protein is a product of the meiotically up-regulated gene 70 which has a role in meiosis and harbors a PB1 domain. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domains depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic amino acid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is
Probab=95.96 E-value=0.017 Score=44.33 Aligned_cols=50 Identities=22% Similarity=0.337 Sum_probs=37.9
Q ss_pred ccccceeecC--CccCHHHHHHHHHHhhcccccCCcCCCCcccccchhhhhcccCCCCeeEEEEcCCCCeEec
Q 027865 137 APYLRKVDLK--LYKSYQELSDALGKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGDWMLV 207 (217)
Q Consensus 137 ~pigRKVDL~--~~~sY~~L~~aLe~MF~~~~~g~~~~~g~~~~~~e~~l~d~~~~seyvltYeDkeGDwMLV 207 (217)
.|-||.+=++ ...|+.+|..++.+-|+.-.. ....|.|.|.|.||||.|.
T Consensus 7 ~~~GrvhRf~~~~s~~~~~L~~~I~~Rl~~d~~---------------------~~~~~~L~YlDDEgD~Vll 58 (86)
T cd06409 7 DPKGRVHRFRLRPSESLEELRTLISQRLGDDDF---------------------ETHLYALSYVDDEGDIVLI 58 (86)
T ss_pred CCCCCEEEEEecCCCCHHHHHHHHHHHhCCccc---------------------cCCcccEEEEcCCCCEEEE
Confidence 4567765544 478999999999999975110 1347899999999999986
No 10
>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=95.81 E-value=0.028 Score=43.12 Aligned_cols=53 Identities=23% Similarity=0.355 Sum_probs=42.4
Q ss_pred EEEEEcCccccceeecCCccCHHHHHHHHHHhhcccccCCcCCCCcccccchhhhhcccCCCCeeEEEEcCCCCeEec
Q 027865 130 VKVSMDGAPYLRKVDLKLYKSYQELSDALGKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGDWMLV 207 (217)
Q Consensus 130 VKV~MdG~pigRKVDL~~~~sY~~L~~aLe~MF~~~~~g~~~~~g~~~~~~e~~l~d~~~~seyvltYeDkeGDwMLV 207 (217)
||++-.|.-.--.+|. .-+|++|.+.+.+||.. . .+..|++.|.|.|||---+
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-H----------------------NDQPFTLKWIDEEGDPCTI 55 (83)
T ss_pred EEEEecCcEEEEEcCC--CcCHHHHHHHHHHHhCC-C----------------------CCCcEEEEEECCCCCceee
Confidence 7999999865555666 67899999999999985 1 2447999999999996543
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=95.73 E-value=0.048 Score=41.96 Aligned_cols=56 Identities=25% Similarity=0.497 Sum_probs=41.7
Q ss_pred eEEEEEcC---ccccceeec--CCccCHHHHHHHHHHhhcccccCCcCCCCcccccchhhhhcccCCCCeeEEEEcCCCC
Q 027865 129 FVKVSMDG---APYLRKVDL--KLYKSYQELSDALGKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGD 203 (217)
Q Consensus 129 ~VKV~MdG---~pigRKVDL--~~~~sY~~L~~aLe~MF~~~~~g~~~~~g~~~~~~e~~l~d~~~~seyvltYeDkeGD 203 (217)
.||.+..| .+==|++-| ....+|++|...+.++|.. +.+..|+|.|.|.|||
T Consensus 2 ~vkayl~~~~~~~EIRRf~l~~~~~~s~~~L~~~V~~~f~~-----------------------l~~~~ftlky~DeeGD 58 (87)
T cd06402 2 TVKAYLLGKDANAEIRRFAIDEDVSTSYEYLVEKVAAVFPS-----------------------LRGKNFQLFWKDEEGD 58 (87)
T ss_pred eEEEeecCCCCccceEEEEecCCCCcCHHHHHHHHHHHccc-----------------------cCCCcEEEEEECCCCC
Confidence 57777766 333355444 5667999999999999974 1235899999999999
Q ss_pred eEec
Q 027865 204 WMLV 207 (217)
Q Consensus 204 wMLV 207 (217)
..-+
T Consensus 59 lvtI 62 (87)
T cd06402 59 LVAF 62 (87)
T ss_pred EEee
Confidence 8654
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=95.37 E-value=0.08 Score=40.42 Aligned_cols=57 Identities=23% Similarity=0.429 Sum_probs=41.1
Q ss_pred EEEEEcCccccceeecCCcc-CHHHHHHHHHHhhcccccCCcCCCCcccccchhhhhcccCCCCeeEEEEcCCCCeEecC
Q 027865 130 VKVSMDGAPYLRKVDLKLYK-SYQELSDALGKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGDWMLVG 208 (217)
Q Consensus 130 VKV~MdG~pigRKVDL~~~~-sY~~L~~aLe~MF~~~~~g~~~~~g~~~~~~e~~l~d~~~~seyvltYeDkeGDwMLVG 208 (217)
+|+.-.|. | |++=+..-. +|.+|...+++.|.. .. .....+.+.|.|.|||+.-+-
T Consensus 3 iK~~~g~D-i-R~~~~~~~~~t~~~L~~~v~~~F~~----~~-----------------~~~~~flIKYkD~dGDlVTIt 59 (81)
T cd06401 3 LKAQLGDD-I-RRIPIHNEDITYDELLLMMQRVFRG----KL-----------------GSSDDVLIKYKDEDGDLITIF 59 (81)
T ss_pred EEEEeCCe-E-EEEeccCccccHHHHHHHHHHHhcc----cc-----------------CCcccEEEEEECCCCCEEEec
Confidence 67777665 4 555444433 999999999999985 11 123489999999999998765
Q ss_pred C
Q 027865 209 D 209 (217)
Q Consensus 209 D 209 (217)
+
T Consensus 60 s 60 (81)
T cd06401 60 D 60 (81)
T ss_pred c
Confidence 4
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=95.15 E-value=0.073 Score=40.73 Aligned_cols=53 Identities=21% Similarity=0.265 Sum_probs=43.2
Q ss_pred EEEEEcCccccceeecCCccCHHHHHHHHHHhhcccccCCcCCCCcccccchhhhhcccCCCCeeEEEEcCCCCeEecC
Q 027865 130 VKVSMDGAPYLRKVDLKLYKSYQELSDALGKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGDWMLVG 208 (217)
Q Consensus 130 VKV~MdG~pigRKVDL~~~~sY~~L~~aLe~MF~~~~~g~~~~~g~~~~~~e~~l~d~~~~seyvltYeDkeGDwMLVG 208 (217)
-||+-.|. .|++....-=+|..|...|+.+|.+.. . .+.|+|.|.|||..-+-
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 37899999999986543
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=92.56 E-value=0.47 Score=36.53 Aligned_cols=54 Identities=20% Similarity=0.302 Sum_probs=44.0
Q ss_pred ceEEEEEcCccccceeecCCccCHHHHHHHHHHhhcccccCCcCCCCcccccchhhhhcccCCCCeeEEEEcCCCCeEec
Q 027865 128 AFVKVSMDGAPYLRKVDLKLYKSYQELSDALGKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGDWMLV 207 (217)
Q Consensus 128 ~~VKV~MdG~pigRKVDL~~~~sY~~L~~aLe~MF~~~~~g~~~~~g~~~~~~e~~l~d~~~~seyvltYeDkeGDwMLV 207 (217)
.-|||+-.|. .|-|-+..-=+|++|...+.++|+. ...+.|-|.|. ||..-+
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 4589999888 5667777777899999999999985 12678999999 998777
Q ss_pred CC
Q 027865 208 GD 209 (217)
Q Consensus 208 GD 209 (217)
+|
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=73.47 E-value=5.6 Score=31.12 Aligned_cols=39 Identities=23% Similarity=0.339 Sum_probs=31.3
Q ss_pred eecCCccCHHHHHHHHHHhhcccccCCcCCCCcccccchhhhhcccCCCCeeEEEEcCCCCeEec
Q 027865 143 VDLKLYKSYQELSDALGKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGDWMLV 207 (217)
Q Consensus 143 VDL~~~~sY~~L~~aLe~MF~~~~~g~~~~~g~~~~~~e~~l~d~~~~seyvltYeDkeGDwMLV 207 (217)
=||+.--+|.+|..-..+-|... +-+|-|.|.|||..-+
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 36788889999999999888752 3468899999998654
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=56.15 E-value=9.3 Score=26.57 Aligned_cols=17 Identities=29% Similarity=0.649 Sum_probs=14.4
Q ss_pred eEEEEcCCCCeEecCCc
Q 027865 194 VPTYEDKDGDWMLVGDV 210 (217)
Q Consensus 194 vltYeDkeGDwMLVGDV 210 (217)
-+.|.|.||+.+++|++
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=49.41 E-value=32 Score=26.71 Aligned_cols=48 Identities=25% Similarity=0.365 Sum_probs=34.0
Q ss_pred CccccceeecCCccCHHHHHHHHHHhhcccccCCcCCCCcccccchhhhhcccCCCCeeEEEEcCCCCeEecC
Q 027865 136 GAPYLRKVDLKLYKSYQELSDALGKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGDWMLVG 208 (217)
Q Consensus 136 G~pigRKVDL~~~~sY~~L~~aLe~MF~~~~~g~~~~~g~~~~~~e~~l~d~~~~seyvltYeDkeGDwMLVG 208 (217)
|..+--.||...+=+|.+++.++.+....-| --.+-|||.|||+.-|-
T Consensus 10 gg~vDw~V~~~~~L~F~DvL~~I~~vlp~aT-------------------------~tAFeYEDE~gDRITVR 57 (91)
T cd06395 10 GGAVDWTVQSGPQLLFRDVLDVIGQVLPEAT-------------------------TTAFEYEDEDGDRITVR 57 (91)
T ss_pred CCcccccccCcccccHHHHHHHHHHhccccc-------------------------ccceeeccccCCeeEec
Confidence 3446666777777789999988887665322 11366999999998763
No 18
>COG0219 CspR Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]
Probab=35.18 E-value=19 Score=30.68 Aligned_cols=32 Identities=28% Similarity=0.403 Sum_probs=26.6
Q ss_pred cCccccceeecCCccCHHHHHHHH---HHhhcccc
Q 027865 135 DGAPYLRKVDLKLYKSYQELSDAL---GKMFSSFT 166 (217)
Q Consensus 135 dG~pigRKVDL~~~~sY~~L~~aL---e~MF~~~~ 166 (217)
-|-.|.-+++|..|++|++...+. .++|-..+
T Consensus 48 AGlDY~~~~~l~~h~s~e~fl~~~~~~~rl~~~tt 82 (155)
T COG0219 48 AGLDYHEKASLTEHDSLEAFLEAEPIGGRLFALTT 82 (155)
T ss_pred cccchHhhcceEEeCCHHHHHhhccCCceEEEEEe
Confidence 477799999999999999999998 46776533
No 19
>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=25.93 E-value=46 Score=25.80 Aligned_cols=19 Identities=37% Similarity=0.548 Sum_probs=16.2
Q ss_pred CeeEEEEcCCCCeEecCCc
Q 027865 192 DYVPTYEDKDGDWMLVGDV 210 (217)
Q Consensus 192 eyvltYeDkeGDwMLVGDV 210 (217)
=|+.-|+|.+||+..-|.|
T Consensus 92 iwiaP~~D~~g~l~~~~~V 110 (119)
T PF09676_consen 92 IWIAPWEDADGDLHDPGYV 110 (119)
T ss_pred EEEeeeECCCCCEeccceE
Confidence 5889999999999877765
No 20
>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=24.60 E-value=27 Score=29.66 Aligned_cols=9 Identities=56% Similarity=1.025 Sum_probs=6.1
Q ss_pred cccCCCCCC
Q 027865 9 LRLGLPGGN 17 (217)
Q Consensus 9 LRLGLPG~~ 17 (217)
=|||.||+.
T Consensus 100 GRLGvPGSG 108 (154)
T PF11576_consen 100 GRLGVPGSG 108 (154)
T ss_dssp EE-SSTTS-
T ss_pred ccccCCCCc
Confidence 399999985
No 21
>PF07929 PRiA4_ORF3: Plasmid pRiA4b ORF-3-like protein; InterPro: IPR012912 Members of this family are similar to the protein product of ORF-3 (Q44206 from SWISSPROT) found on plasmid pRiA4 in the bacterium Agrobacterium rhizogenes. This plasmid is responsible for tumourigenesis at wound sites of plants infected by this bacterium, but the ORF-3 product does not seem to be involved in the pathogenetic process []. Other proteins found in this family are annotated as being putative TnpR resolvases (Q9LCU7 from SWISSPROT, Q50439 from SWISSPROT), but no further evidence was found to back this. Moreover, another member of this family is described as a probable lexA repressor (Q7UEI4 from SWISSPROT) and in fact carries a LexA DNA binding domain (IPR006199 from INTERPRO), but no references were found to expand on this. ; PDB: 2I1S_A.
Probab=23.55 E-value=96 Score=25.66 Aligned_cols=36 Identities=22% Similarity=0.464 Sum_probs=30.4
Q ss_pred ceEEEEEcCc--cccceeecCCccCHHHHHHHHHHhhc
Q 027865 128 AFVKVSMDGA--PYLRKVDLKLYKSYQELSDALGKMFS 163 (217)
Q Consensus 128 ~~VKV~MdG~--pigRKVDL~~~~sY~~L~~aLe~MF~ 163 (217)
--+||...|. +|=|.|-+..--+..+|-.+|+..|+
T Consensus 5 y~lkV~L~~~~p~iwRri~Vp~~~tl~~Lh~~Iq~afg 42 (179)
T PF07929_consen 5 YQLKVSLKGSKPPIWRRIEVPADITLADLHEVIQAAFG 42 (179)
T ss_dssp EEEEEEETT-SS-EEEEEEEETT-BHHHHHHHHHHHTT
T ss_pred EEEEEEEcCCCCCeEEEEEECCCCCHHHHHHHHHHHhC
Confidence 4579999885 89999999999999999999999997
No 22
>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=22.74 E-value=26 Score=31.56 Aligned_cols=54 Identities=28% Similarity=0.428 Sum_probs=32.3
Q ss_pred cceEEEEEcCccccceeecCCccCHHHHHHHHHHhhcccccCCcCCCCcccccchhhhhcccCCCCeeEEEEcCCCC
Q 027865 127 VAFVKVSMDGAPYLRKVDLKLYKSYQELSDALGKMFSSFTIGNCGSQGMKDFMNESKLIDLLNGSDYVPTYEDKDGD 203 (217)
Q Consensus 127 ~~~VKV~MdG~pigRKVDL~~~~sY~~L~~aLe~MF~~~~~g~~~~~g~~~~~~e~~l~d~~~~seyvltYeDkeGD 203 (217)
-.|...-=||+-||-|||..+.++ |.+.+.+-|+ | .|......|-|+|.|+||.
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 1222234788999999985
No 23
>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=20.98 E-value=3e+02 Score=20.92 Aligned_cols=34 Identities=18% Similarity=0.132 Sum_probs=26.8
Q ss_pred ceEEEEEcCccccceeecCCccCHHHHHHHHHHhhcc
Q 027865 128 AFVKVSMDGAPYLRKVDLKLYKSYQELSDALGKMFSS 164 (217)
Q Consensus 128 ~~VKV~MdG~pigRKVDL~~~~sY~~L~~aLe~MF~~ 164 (217)
--|||+-.+ .=.|-...=-+|++|...|.+-+..
T Consensus 3 ~vvKV~f~~---tIaIrvp~~~~y~~L~~ki~~kLkl 36 (80)
T cd06406 3 YVVKVHFKY---TVAIQVARGLSYATLLQKISSKLEL 36 (80)
T ss_pred eEEEEEEEE---EEEEEcCCCCCHHHHHHHHHHHhCC
Confidence 358999997 3355666667899999999998885
No 24
>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=20.14 E-value=28 Score=22.69 Aligned_cols=12 Identities=42% Similarity=0.869 Sum_probs=8.8
Q ss_pred eEEEEcCCCCeE
Q 027865 194 VPTYEDKDGDWM 205 (217)
Q Consensus 194 vltYeDkeGDwM 205 (217)
.+.|.|.+|+|=
T Consensus 16 ~v~y~d~~g~WG 27 (36)
T PF02013_consen 16 EVVYTDDDGGWG 27 (36)
T ss_dssp --SEEETTEEEE
T ss_pred ceEEcCCCCCEe
Confidence 578999999983
Done!