Query 022632
Match_columns 294
No_of_seqs 243 out of 574
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 05:00:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022632.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022632hhsearch_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-63 2E-67 441.6 0.3 207 29-282 1-215 (215)
2 PF00564 PB1: PB1 domain; Int 97.3 0.00067 1.5E-08 51.5 5.7 67 175-265 3-70 (84)
3 cd06398 PB1_Joka2 The PB1 doma 97.0 0.003 6.4E-08 50.9 7.0 68 175-266 2-72 (91)
4 smart00666 PB1 PB1 domain. Pho 96.9 0.0061 1.3E-07 46.2 7.7 66 175-265 3-69 (81)
5 cd06407 PB1_NLP A PB1 domain i 96.8 0.0053 1.2E-07 48.5 7.0 56 175-254 2-57 (82)
6 cd05992 PB1 The PB1 domain is 96.8 0.0083 1.8E-07 45.2 7.7 66 175-265 2-69 (81)
7 cd06396 PB1_NBR1 The PB1 domai 96.4 0.012 2.7E-07 46.9 6.5 62 176-262 3-65 (81)
8 cd06403 PB1_Par6 The PB1 domai 95.7 0.053 1.1E-06 43.3 7.3 68 176-266 3-71 (80)
9 cd06401 PB1_TFG The PB1 domain 95.4 0.078 1.7E-06 42.4 7.3 72 176-269 3-78 (81)
10 cd06404 PB1_aPKC PB1 domain is 94.9 0.085 1.8E-06 42.4 6.0 57 175-255 2-58 (83)
11 cd06409 PB1_MUG70 The MUG70 pr 94.8 0.06 1.3E-06 43.3 5.0 51 183-253 7-59 (86)
12 cd06402 PB1_p62 The PB1 domain 94.3 0.2 4.3E-06 40.4 7.0 59 175-255 2-65 (87)
13 cd06397 PB1_UP1 Uncharacterize 92.6 0.44 9.5E-06 38.3 6.2 66 176-266 3-69 (82)
14 cd06408 PB1_NoxR The PB1 domai 90.4 1 2.2E-05 36.4 6.3 65 174-265 3-68 (86)
15 cd06399 PB1_P40 The PB1 domain 56.2 20 0.00042 29.5 4.1 42 187-253 20-61 (92)
16 cd06395 PB1_Map2k5 PB1 domain 54.4 23 0.0005 28.9 4.2 49 182-254 10-58 (91)
17 PF10411 DsbC_N: Disulfide bon 51.4 12 0.00025 27.4 2.0 17 239-255 34-50 (57)
18 cd06406 PB1_P67 A PB1 domain i 39.1 1.5E+02 0.0032 23.8 6.5 70 174-269 3-75 (80)
19 PF00788 RA: Ras association ( 26.1 2.8E+02 0.006 20.6 7.3 69 174-263 3-77 (93)
20 COG0219 CspR Predicted rRNA me 25.3 26 0.00057 31.3 0.3 68 182-271 49-126 (155)
21 PF04809 HupH_C: HupH hydrogen 23.6 53 0.0011 27.8 1.8 33 236-268 71-113 (120)
22 KOG3957 Predicted L-carnitine 22.2 1.1E+02 0.0024 30.9 3.9 78 185-274 177-254 (387)
23 COG3816 Uncharacterized protei 21.3 62 0.0013 29.7 1.8 17 179-209 56-72 (205)
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-63 Score=441.58 Aligned_cols=207 Identities=44% Similarity=0.661 Sum_probs=6.0
Q ss_pred cCCccceecccccCcCCCC------CCCCCCccccCcccccccccCCCCCCCCCCCCCCCCCCCCcccccccccCCCCCC
Q 022632 29 VESDDDELELGLGLSLGGV------GGGGKGKVVSSWGECGRILTAKDFPSAGRRPSNASSSSPPVAVSGTKRAANSVPR 102 (294)
Q Consensus 29 ~~~~eTEL~LGLpgs~gg~------~~~~k~~~krgfset~dlL~~k~~~~~~~~~~~~sss~~~~~~~~~k~~~~~~~~ 102 (294)
|+|++|||||||||+.... ........||+|+++++.-.......... .... .... ... .........
T Consensus 1 ln~~~TELrLGLPG~~~~~~~~~~~~~~~~~~~kR~F~~aid~~~~~~~~~~~~-~~~~-~~~~---~~~-~~~~~~~~~ 74 (215)
T PF02309_consen 1 LNLKATELRLGLPGSESPDASSSSSSKKSSSGNKRGFSEAIDSSSSNSQSSSSS-SSDS-SSSS---SSS-STSSSSSDS 74 (215)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred CCchhhhhcccCCCCCCCCcccccccccccCcccccchhhhhhccccccccccc-cccc-Cccc---ccc-ccccccccc
Confidence 6899999999999963211 00224456999999888743221111000 0000 0000 000 000111112
Q ss_pred CCCCCCCCCCCcccCCCchhhhhhhcccccCCCCchhhhhhhcccccchhhhhhhcCCCCCccccccccccceeEEEecC
Q 022632 103 EGESSPPSASQVVGWPPIGAYRMNSLVNQAKAPISEEEKVADEKDKSKDASKKKICNGNKTNNIFSEKAHLGFVKVNMDG 182 (294)
Q Consensus 103 ~~~~p~a~~aqVVGWPPVRS~RkN~~~~q~k~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~fVKV~MdG 182 (294)
+...+|+.++|||||||||+||+|++...+.. ..++||||+|||
T Consensus 75 ~~~~~p~~~~~~vgwpp~~s~r~n~~~~~~~~------------------------------------~~~~~vKV~mdG 118 (215)
T PF02309_consen 75 SSSSPPASKAQVVGWPPVRSFRKNSLSEKQSS------------------------------------SSRSYVKVNMDG 118 (215)
T ss_dssp -----------BTTBS----S-----------------------------------------------------------
T ss_pred ccCCCCcccccccCCCcccccccccccccccc------------------------------------cCCceeEEEecC
Confidence 33344544499999999999999998721100 114899999999
Q ss_pred cccceeeecCCCCChHHHHHHHHHhhccCCcccccCCCcchhhhhhhhhcC--CCCceEEEEEcCCCCeEEccCCChHHH
Q 022632 183 VPIGRKVDLNAHASYESLAQTLEEMFFASTPAINSIGGEKDLATKAFKLLD--GLSEFVLTYEDKEGDWMLVGDVPWRMF 260 (294)
Q Consensus 183 ~pigRKVDL~~~~sY~eLs~aLe~MF~~~~~~~~~~~g~~~~~~~~~~L~d--~~seyvltYeD~eGDwMLVGDvPWemF 260 (294)
+||||||||++|+||++|+.+|++||.+|.+.+++. +..++.++++ ++++|+|||||+||||||||||||+||
T Consensus 119 ~~igRkVDL~~~~sY~~L~~~L~~MF~~~~i~~~~~-----~~~~~~~~~~~~~~~~~~l~Y~D~egd~mlvGD~PW~~F 193 (215)
T PF02309_consen 119 VPIGRKVDLSAYSSYEELSSALEKMFSCFSIEQCGS-----HGLNESGLLDLLNGSEYVLVYEDKEGDWMLVGDVPWEEF 193 (215)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred cccceecCHHHhhCHHHHHHHHHHhcCCCCcccccc-----ccccchhhccccCCcceeEEEECCCCCEEEecCCCHHHH
Confidence 999999999999999999999999998887665533 2223334444 456999999999999999999999999
Q ss_pred hhccceeEEecCCccCCCCCCC
Q 022632 261 ISSVKRLRIMRTSEANGLGPRF 282 (294)
Q Consensus 261 v~svKRLrImk~sea~gl~~~~ 282 (294)
|++|||||||+.+|+++|+||+
T Consensus 194 ~~~vkRl~I~~~~e~~~~~~r~ 215 (215)
T PF02309_consen 194 VKSVKRLRIMKSSEAKGLAPRA 215 (215)
T ss_dssp ----------------------
T ss_pred HHHhhccEEecHHHhcccCCCC
Confidence 9999999999999999999986
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=97.27 E-value=0.00067 Score=51.48 Aligned_cols=67 Identities=28% Similarity=0.421 Sum_probs=54.4
Q ss_pred eeEEEecCcccceeeecCCCCChHHHHHHHHHhhccCCcccccCCCcchhhhhhhhhcCCCCceEEEEEcCCCCeEEccC
Q 022632 175 FVKVNMDGVPIGRKVDLNAHASYESLAQTLEEMFFASTPAINSIGGEKDLATKAFKLLDGLSEFVLTYEDKEGDWMLVGD 254 (294)
Q Consensus 175 fVKV~MdG~pigRKVDL~~~~sY~eLs~aLe~MF~~~~~~~~~~~g~~~~~~~~~~L~d~~seyvltYeD~eGDwMLVGD 254 (294)
-|||...|. +=|.+.+..--+|++|...|++.|.. . ...+.|.|.|.||||..+-+
T Consensus 3 ~vK~~~~~~-~~~~~~~~~~~s~~~L~~~i~~~~~~-----~------------------~~~~~l~Y~D~dgD~V~i~s 58 (84)
T PF00564_consen 3 RVKVRYGGD-IRRIISLPSDVSFDDLRSKIREKFGL-----L------------------DEDFQLKYKDEDGDLVTISS 58 (84)
T ss_dssp EEEEEETTE-EEEEEEECSTSHHHHHHHHHHHHHTT-----S------------------TSSEEEEEEETTSSEEEESS
T ss_pred EEEEEECCe-eEEEEEcCCCCCHHHHHHHHHHHhCC-----C------------------CccEEEEeeCCCCCEEEeCC
Confidence 489999996 43458888888999999999999961 1 14789999999999998884
Q ss_pred -CChHHHhhccc
Q 022632 255 -VPWRMFISSVK 265 (294)
Q Consensus 255 -vPWemFv~svK 265 (294)
.=|++.++.++
T Consensus 59 d~Dl~~a~~~~~ 70 (84)
T PF00564_consen 59 DEDLQEAIEQAK 70 (84)
T ss_dssp HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHH
Confidence 56888888875
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=96.97 E-value=0.003 Score=50.94 Aligned_cols=68 Identities=22% Similarity=0.347 Sum_probs=51.9
Q ss_pred eeEEEecCcccceeeecC---CCCChHHHHHHHHHhhccCCcccccCCCcchhhhhhhhhcCCCCceEEEEEcCCCCeEE
Q 022632 175 FVKVNMDGVPIGRKVDLN---AHASYESLAQTLEEMFFASTPAINSIGGEKDLATKAFKLLDGLSEFVLTYEDKEGDWML 251 (294)
Q Consensus 175 fVKV~MdG~pigRKVDL~---~~~sY~eLs~aLe~MF~~~~~~~~~~~g~~~~~~~~~~L~d~~seyvltYeD~eGDwML 251 (294)
-|||..+|.-+=-++++. ..-+|++|.+.+.+.|. +. ...+|+|.|.|.||||..
T Consensus 2 ~vKv~y~~~~rRf~l~~~~~~~d~~~~~L~~kI~~~f~-----l~-----------------~~~~~~l~Y~Dedgd~V~ 59 (91)
T cd06398 2 VVKVKYGGTLRRFTFPVAENQLDLNMDGLREKVEELFS-----LS-----------------PDADLSLTYTDEDGDVVT 59 (91)
T ss_pred EEEEEeCCEEEEEEeccccccCCCCHHHHHHHHHHHhC-----CC-----------------CCCcEEEEEECCCCCEEE
Confidence 489999997544455553 46799999999999996 22 125899999999999999
Q ss_pred ccCCChHHHhhccce
Q 022632 252 VGDVPWRMFISSVKR 266 (294)
Q Consensus 252 VGDvPWemFv~svKR 266 (294)
+-+. ++|...+.+
T Consensus 60 l~~D--~DL~~a~~~ 72 (91)
T cd06398 60 LVDD--NDLTDAIQY 72 (91)
T ss_pred EccH--HHHHHHHHH
Confidence 8766 666666554
No 4
>smart00666 PB1 PB1 domain. Phox and Bem1p domain, present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.
Probab=96.88 E-value=0.0061 Score=46.20 Aligned_cols=66 Identities=23% Similarity=0.376 Sum_probs=51.6
Q ss_pred eeEEEecCcccceeeecCCCCChHHHHHHHHHhhccCCcccccCCCcchhhhhhhhhcCCCCceEEEEEcCCCCeEEccC
Q 022632 175 FVKVNMDGVPIGRKVDLNAHASYESLAQTLEEMFFASTPAINSIGGEKDLATKAFKLLDGLSEFVLTYEDKEGDWMLVGD 254 (294)
Q Consensus 175 fVKV~MdG~pigRKVDL~~~~sY~eLs~aLe~MF~~~~~~~~~~~g~~~~~~~~~~L~d~~seyvltYeD~eGDwMLVGD 254 (294)
=|||.-.| --|.+-+..--+|++|...|.+.|. .. ...|.|.|+|.||||..+-+
T Consensus 3 ~vK~~~~~--~~~~~~~~~~~s~~dL~~~i~~~~~-----~~------------------~~~~~l~Y~Dedgd~v~l~s 57 (81)
T smart00666 3 DVKLRYGG--ETRRLSVPRDISFEDLRSKVAKRFG-----LD------------------NQSFTLKYQDEDGDLVSLTS 57 (81)
T ss_pred cEEEEECC--EEEEEEECCCCCHHHHHHHHHHHhC-----CC------------------CCCeEEEEECCCCCEEEecC
Confidence 36777754 3577788888999999999999996 21 14689999999999997764
Q ss_pred -CChHHHhhccc
Q 022632 255 -VPWRMFISSVK 265 (294)
Q Consensus 255 -vPWemFv~svK 265 (294)
.=|++.++.++
T Consensus 58 d~Dl~~a~~~~~ 69 (81)
T smart00666 58 DEDLEEAIEEYD 69 (81)
T ss_pred HHHHHHHHHHHH
Confidence 67887777666
No 5
>cd06407 PB1_NLP A PB1 domain is present in NIN like proteins (NLP), a key enzyme in a process of establishment of symbiosis betweeen legumes and nitrogen fixing bacteria (Rhizobium). The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes like osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-inte
Probab=96.80 E-value=0.0053 Score=48.49 Aligned_cols=56 Identities=23% Similarity=0.406 Sum_probs=43.7
Q ss_pred eeEEEecCcccceeeecCCCCChHHHHHHHHHhhccCCcccccCCCcchhhhhhhhhcCCCCceEEEEEcCCCCeEEccC
Q 022632 175 FVKVNMDGVPIGRKVDLNAHASYESLAQTLEEMFFASTPAINSIGGEKDLATKAFKLLDGLSEFVLTYEDKEGDWMLVGD 254 (294)
Q Consensus 175 fVKV~MdG~pigRKVDL~~~~sY~eLs~aLe~MF~~~~~~~~~~~g~~~~~~~~~~L~d~~seyvltYeD~eGDwMLVGD 254 (294)
-|||...|. -+.+-|..--+|++|...+.++|. +. ....|.|.|.|.||||.++--
T Consensus 2 ~vK~~~~~d--~~r~~l~~~~~~~~L~~~i~~r~~-----~~-----------------~~~~f~LkY~Ddegd~v~lts 57 (82)
T cd06407 2 RVKATYGEE--KIRFRLPPSWGFTELKQEIAKRFK-----LD-----------------DMSAFDLKYLDDDEEWVLLTC 57 (82)
T ss_pred EEEEEeCCe--EEEEEcCCCCCHHHHHHHHHHHhC-----CC-----------------CCCeeEEEEECCCCCeEEeec
Confidence 389999886 345556666699999999999996 21 125799999999999998753
No 6
>cd05992 PB1 The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as a noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.
Probab=96.77 E-value=0.0083 Score=45.16 Aligned_cols=66 Identities=26% Similarity=0.382 Sum_probs=51.1
Q ss_pred eeEEEecCcccceeeecC-CCCChHHHHHHHHHhhccCCcccccCCCcchhhhhhhhhcCCCCceEEEEEcCCCCeEEcc
Q 022632 175 FVKVNMDGVPIGRKVDLN-AHASYESLAQTLEEMFFASTPAINSIGGEKDLATKAFKLLDGLSEFVLTYEDKEGDWMLVG 253 (294)
Q Consensus 175 fVKV~MdG~pigRKVDL~-~~~sY~eLs~aLe~MF~~~~~~~~~~~g~~~~~~~~~~L~d~~seyvltYeD~eGDwMLVG 253 (294)
-|||+-.|. =|.+=+. ..-+|++|...|.+.|. .. ...+.+.|.|.||||..+.
T Consensus 2 ~vK~~~~~~--~~~~~~~~~~~s~~~L~~~i~~~~~-----~~------------------~~~~~l~y~D~e~d~v~l~ 56 (81)
T cd05992 2 RVKVKYGGE--IRRFVVVSRSISFEDLRSKIAEKFG-----LD------------------AVSFKLKYPDEDGDLVTIS 56 (81)
T ss_pred cEEEEecCC--CEEEEEecCCCCHHHHHHHHHHHhC-----CC------------------CCcEEEEeeCCCCCEEEeC
Confidence 378888764 2455555 88899999999999996 21 0368999999999999998
Q ss_pred C-CChHHHhhccc
Q 022632 254 D-VPWRMFISSVK 265 (294)
Q Consensus 254 D-vPWemFv~svK 265 (294)
+ .=|++.++.++
T Consensus 57 sd~Dl~~a~~~~~ 69 (81)
T cd05992 57 SDEDLEEAIEEAR 69 (81)
T ss_pred CHHHHHHHHHHHh
Confidence 7 67777777765
No 7
>cd06396 PB1_NBR1 The PB1 domain is an essential part of NBR1 protein, next to BRCA1, a scaffold protein mediating specific protein-protein interaction with both titin protein kinase and with another scaffold protein p62. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The NBR1 protein contains a type I PB1 domain.
Probab=96.38 E-value=0.012 Score=46.86 Aligned_cols=62 Identities=18% Similarity=0.279 Sum_probs=48.4
Q ss_pred eEEEecCcccceeeecCCCCChHHHHHHHHHhhccCCcccccCCCcchhhhhhhhhcCCCCceEEEEEcCCCCeEEcc-C
Q 022632 176 VKVNMDGVPIGRKVDLNAHASYESLAQTLEEMFFASTPAINSIGGEKDLATKAFKLLDGLSEFVLTYEDKEGDWMLVG-D 254 (294)
Q Consensus 176 VKV~MdG~pigRKVDL~~~~sY~eLs~aLe~MF~~~~~~~~~~~g~~~~~~~~~~L~d~~seyvltYeD~eGDwMLVG-D 254 (294)
|||...|.-+=-+++-+..-+|++|...+.++|. +. .|.|.|-|.||||.++= |
T Consensus 3 vKaty~~d~~rf~~~~~~~~~~~~L~~ev~~rf~-----l~--------------------~f~lKYlDde~e~v~lssd 57 (81)
T cd06396 3 LKVTYNGESQSFLVSDSENTTWASVEAMVKVSFG-----LN--------------------DIQIKYVDEENEEVSVNSQ 57 (81)
T ss_pred EEEEECCeEEEEEecCCCCCCHHHHHHHHHHHhC-----CC--------------------cceeEEEcCCCCEEEEEch
Confidence 7899999877777777778899999999999995 21 57899999999998874 3
Q ss_pred CChHHHhh
Q 022632 255 VPWRMFIS 262 (294)
Q Consensus 255 vPWemFv~ 262 (294)
.=-++.+.
T Consensus 58 ~eLeE~~r 65 (81)
T cd06396 58 GEYEEALK 65 (81)
T ss_pred hhHHHHHH
Confidence 33344433
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=95.74 E-value=0.053 Score=43.30 Aligned_cols=68 Identities=25% Similarity=0.359 Sum_probs=49.1
Q ss_pred eEEEecCcccceeeecCCCCChHHHHHHHHHhhccCCcccccCCCcchhhhhhhhhcCCCCceEEEEEcCCCCeEEcc-C
Q 022632 176 VKVNMDGVPIGRKVDLNAHASYESLAQTLEEMFFASTPAINSIGGEKDLATKAFKLLDGLSEFVLTYEDKEGDWMLVG-D 254 (294)
Q Consensus 176 VKV~MdG~pigRKVDL~~~~sY~eLs~aLe~MF~~~~~~~~~~~g~~~~~~~~~~L~d~~seyvltYeD~eGDwMLVG-D 254 (294)
||...|..=-=-.+|.....+|++++.-|+.||. +. .-.|+|.|.|.+||.+=+- |
T Consensus 3 VKSkfdaEfRRFsl~r~~~~~f~ef~~ll~~lH~-----l~------------------~~~f~i~Y~D~~gDLLPInND 59 (80)
T cd06403 3 VKSKFDAEFRRFSLDRNKPGKFEDFYKLLEHLHH-----IP------------------NVDFLIGYTDPHGDLLPINND 59 (80)
T ss_pred eecccCCeEEEEEeccccCcCHHHHHHHHHHHhC-----CC------------------CCcEEEEEeCCCCCEecccCc
Confidence 5555555422224555567999999999999996 32 1478999999999999775 5
Q ss_pred CChHHHhhccce
Q 022632 255 VPWRMFISSVKR 266 (294)
Q Consensus 255 vPWemFv~svKR 266 (294)
+-+..=++++++
T Consensus 60 dNf~kAlssa~p 71 (80)
T cd06403 60 DNFLKALSSANP 71 (80)
T ss_pred HHHHHHHHcCCC
Confidence 666666667773
No 9
>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=95.43 E-value=0.078 Score=42.42 Aligned_cols=72 Identities=18% Similarity=0.456 Sum_probs=48.6
Q ss_pred eEEEecCcccceeeecCCCC-ChHHHHHHHHHhhccCCcccccCCCcchhhhhhhhhcCCCCceEEEEEcCCCCeEEccC
Q 022632 176 VKVNMDGVPIGRKVDLNAHA-SYESLAQTLEEMFFASTPAINSIGGEKDLATKAFKLLDGLSEFVLTYEDKEGDWMLVGD 254 (294)
Q Consensus 176 VKV~MdG~pigRKVDL~~~~-sY~eLs~aLe~MF~~~~~~~~~~~g~~~~~~~~~~L~d~~seyvltYeD~eGDwMLVGD 254 (294)
+|+...+ .| |++=+..-. +|.+|...+.+.|..- . .....+.+.|.|.|||+.-|-+
T Consensus 3 iK~~~g~-Di-R~~~~~~~~~t~~~L~~~v~~~F~~~----~----------------~~~~~flIKYkD~dGDlVTIts 60 (81)
T cd06401 3 LKAQLGD-DI-RRIPIHNEDITYDELLLMMQRVFRGK----L----------------GSSDDVLIKYKDEDGDLITIFD 60 (81)
T ss_pred EEEEeCC-eE-EEEeccCccccHHHHHHHHHHHhccc----c----------------CCcccEEEEEECCCCCEEEecc
Confidence 6777655 35 444444323 9999999999999620 0 1235789999999999999987
Q ss_pred C---ChHHHhhccceeEE
Q 022632 255 V---PWRMFISSVKRLRI 269 (294)
Q Consensus 255 v---PWemFv~svKRLrI 269 (294)
. -|-.=+...+||+|
T Consensus 61 ~~dL~~A~~~~~~~~l~~ 78 (81)
T cd06401 61 SSDLSFAIQCSRILKLTL 78 (81)
T ss_pred HHHHHHHHhcCcceEEEE
Confidence 4 44433444455555
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=94.87 E-value=0.085 Score=42.39 Aligned_cols=57 Identities=25% Similarity=0.286 Sum_probs=44.4
Q ss_pred eeEEEecCcccceeeecCCCCChHHHHHHHHHhhccCCcccccCCCcchhhhhhhhhcCCCCceEEEEEcCCCCeEEccC
Q 022632 175 FVKVNMDGVPIGRKVDLNAHASYESLAQTLEEMFFASTPAINSIGGEKDLATKAFKLLDGLSEFVLTYEDKEGDWMLVGD 254 (294)
Q Consensus 175 fVKV~MdG~pigRKVDL~~~~sY~eLs~aLe~MF~~~~~~~~~~~g~~~~~~~~~~L~d~~seyvltYeD~eGDwMLVGD 254 (294)
-||++..|.-.--.+|. .-+|++|.+.+.+||.. . ....|++.|.|.|||-.-+..
T Consensus 2 ~~K~~y~gdi~it~~d~--~~s~e~L~~~v~~~c~~-----~-----------------~~q~ft~kw~DEEGDp~tiSS 57 (83)
T cd06404 2 RVKAAYNGDIMITSIDP--SISLEELCNEVRDMCRF-----H-----------------NDQPFTLKWIDEEGDPCTISS 57 (83)
T ss_pred eEEEEecCcEEEEEcCC--CcCHHHHHHHHHHHhCC-----C-----------------CCCcEEEEEECCCCCceeecC
Confidence 37889999755555665 77899999999999962 1 125789999999999887765
Q ss_pred C
Q 022632 255 V 255 (294)
Q Consensus 255 v 255 (294)
.
T Consensus 58 ~ 58 (83)
T cd06404 58 Q 58 (83)
T ss_pred H
Confidence 3
No 11
>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=94.79 E-value=0.06 Score=43.31 Aligned_cols=51 Identities=25% Similarity=0.326 Sum_probs=37.8
Q ss_pred cccceeeecC--CCCChHHHHHHHHHhhccCCcccccCCCcchhhhhhhhhcCCCCceEEEEEcCCCCeEEcc
Q 022632 183 VPIGRKVDLN--AHASYESLAQTLEEMFFASTPAINSIGGEKDLATKAFKLLDGLSEFVLTYEDKEGDWMLVG 253 (294)
Q Consensus 183 ~pigRKVDL~--~~~sY~eLs~aLe~MF~~~~~~~~~~~g~~~~~~~~~~L~d~~seyvltYeD~eGDwMLVG 253 (294)
.|-||.+=++ ...||.+|..++.+=|. +. +. ....|.|.|.|.||||.|+-
T Consensus 7 ~~~GrvhRf~~~~s~~~~~L~~~I~~Rl~-----~d-------~~--------~~~~~~L~YlDDEgD~VllT 59 (86)
T cd06409 7 DPKGRVHRFRLRPSESLEELRTLISQRLG-----DD-------DF--------ETHLYALSYVDDEGDIVLIT 59 (86)
T ss_pred CCCCCEEEEEecCCCCHHHHHHHHHHHhC-----Cc-------cc--------cCCcccEEEEcCCCCEEEEe
Confidence 3566655444 47899999999999995 22 00 12578999999999999875
No 12
>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=94.31 E-value=0.2 Score=40.44 Aligned_cols=59 Identities=25% Similarity=0.380 Sum_probs=42.8
Q ss_pred eeEEEecC---cccceeeec--CCCCChHHHHHHHHHhhccCCcccccCCCcchhhhhhhhhcCCCCceEEEEEcCCCCe
Q 022632 175 FVKVNMDG---VPIGRKVDL--NAHASYESLAQTLEEMFFASTPAINSIGGEKDLATKAFKLLDGLSEFVLTYEDKEGDW 249 (294)
Q Consensus 175 fVKV~MdG---~pigRKVDL--~~~~sY~eLs~aLe~MF~~~~~~~~~~~g~~~~~~~~~~L~d~~seyvltYeD~eGDw 249 (294)
+||.+..| .+==|++=| ...-+|++|...+.++|.. . ....|+|.|.|.|||.
T Consensus 2 ~vkayl~~~~~~~EIRRf~l~~~~~~s~~~L~~~V~~~f~~----l------------------~~~~ftlky~DeeGDl 59 (87)
T cd06402 2 TVKAYLLGKDANAEIRRFAIDEDVSTSYEYLVEKVAAVFPS----L------------------RGKNFQLFWKDEEGDL 59 (87)
T ss_pred eEEEeecCCCCccceEEEEecCCCCcCHHHHHHHHHHHccc----c------------------CCCcEEEEEECCCCCE
Confidence 57777766 222254444 5667999999999999951 1 1157999999999999
Q ss_pred EEccCC
Q 022632 250 MLVGDV 255 (294)
Q Consensus 250 MLVGDv 255 (294)
.-+-..
T Consensus 60 vtIssd 65 (87)
T cd06402 60 VAFSSD 65 (87)
T ss_pred EeecCH
Confidence 887753
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=92.59 E-value=0.44 Score=38.29 Aligned_cols=66 Identities=23% Similarity=0.341 Sum_probs=49.4
Q ss_pred eEEEecCcccceeeecCCCCChHHHHHHHHHhhccCCcccccCCCcchhhhhhhhhcCCCCceEEEEEcCCCCeEEccC-
Q 022632 176 VKVNMDGVPIGRKVDLNAHASYESLAQTLEEMFFASTPAINSIGGEKDLATKAFKLLDGLSEFVLTYEDKEGDWMLVGD- 254 (294)
Q Consensus 176 VKV~MdG~pigRKVDL~~~~sY~eLs~aLe~MF~~~~~~~~~~~g~~~~~~~~~~L~d~~seyvltYeD~eGDwMLVGD- 254 (294)
-||+.+| -.|++....-=+|..|...|+.+|. +. . -.+.|+|.|.|||..-+-|
T Consensus 3 fKv~~~g--~~RRf~~~~~pt~~~L~~kl~~Lf~-----lp----~--------------~~~~vtYiDeD~D~ITlssd 57 (82)
T cd06397 3 FKSSFLG--DTRRIVFPDIPTWEALASKLENLYN-----LP----E--------------IKVGVTYIDNDNDEITLSSN 57 (82)
T ss_pred EEEEeCC--ceEEEecCCCccHHHHHHHHHHHhC-----CC----h--------------hHeEEEEEcCCCCEEEecch
Confidence 3777777 3688888888899999999999997 32 0 1279999999999886554
Q ss_pred CChHHHhhccce
Q 022632 255 VPWRMFISSVKR 266 (294)
Q Consensus 255 vPWemFv~svKR 266 (294)
.=-++|.+-..|
T Consensus 58 ~eL~d~~~~~~~ 69 (82)
T cd06397 58 KELQDFYRLSHR 69 (82)
T ss_pred HHHHHHHHhccc
Confidence 556666664444
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=90.39 E-value=1 Score=36.41 Aligned_cols=65 Identities=18% Similarity=0.338 Sum_probs=49.0
Q ss_pred ceeEEEecCcccceeeecCCCCChHHHHHHHHHhhccCCcccccCCCcchhhhhhhhhcCCCCceEEEEEcCCCCeEEcc
Q 022632 174 GFVKVNMDGVPIGRKVDLNAHASYESLAQTLEEMFFASTPAINSIGGEKDLATKAFKLLDGLSEFVLTYEDKEGDWMLVG 253 (294)
Q Consensus 174 ~fVKV~MdG~pigRKVDL~~~~sY~eLs~aLe~MF~~~~~~~~~~~g~~~~~~~~~~L~d~~seyvltYeD~eGDwMLVG 253 (294)
.-|||+-.|. .|-|-+..-=+|++|...+.++|. +. ..++|-|.|. ||..-++
T Consensus 3 ikVKv~~~~D--v~~i~v~~~i~f~dL~~kIrdkf~-----~~-------------------~~~~iKykDE-GD~iti~ 55 (86)
T cd06408 3 IRVKVHAQDD--TRYIMIGPDTGFADFEDKIRDKFG-----FK-------------------RRLKIKMKDD-GDMITMG 55 (86)
T ss_pred EEEEEEecCc--EEEEEcCCCCCHHHHHHHHHHHhC-----CC-------------------CceEEEEEcC-CCCcccc
Confidence 4689998887 466666666779999999999995 21 3679999999 9999888
Q ss_pred CC-ChHHHhhccc
Q 022632 254 DV-PWRMFISSVK 265 (294)
Q Consensus 254 Dv-PWemFv~svK 265 (294)
|. =-++-+.++|
T Consensus 56 sq~DLd~Ai~~a~ 68 (86)
T cd06408 56 DQDDLDMAIDTAR 68 (86)
T ss_pred CHHHHHHHHHHHH
Confidence 73 3344455544
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=56.23 E-value=20 Score=29.54 Aligned_cols=42 Identities=24% Similarity=0.359 Sum_probs=32.3
Q ss_pred eeeecCCCCChHHHHHHHHHhhccCCcccccCCCcchhhhhhhhhcCCCCceEEEEEcCCCCeEEcc
Q 022632 187 RKVDLNAHASYESLAQTLEEMFFASTPAINSIGGEKDLATKAFKLLDGLSEFVLTYEDKEGDWMLVG 253 (294)
Q Consensus 187 RKVDL~~~~sY~eLs~aLe~MF~~~~~~~~~~~g~~~~~~~~~~L~d~~seyvltYeD~eGDwMLVG 253 (294)
=-=||+..-+|.+|..-..+-|.. .+-.|-|.|.|||..-+=
T Consensus 20 vee~l~~~P~~kdLl~lmr~~f~~-------------------------~dIaLNYrD~EGDLIRll 61 (92)
T cd06399 20 VEEDLSSTPLLKDLLELTRREFQR-------------------------EDIALNYRDAEGDLIRLL 61 (92)
T ss_pred eecccccCccHHHHHHHHHHHhch-------------------------hheeeeeecCCCCEEEEc
Confidence 334788889999999999988951 134788999999986443
No 16
>cd06395 PB1_Map2k5 PB1 domain is essential part of the mitogen-activated protein kinase kinase 5 (Map2k5, alias MEK5) one of the key member of the signaling kinases cascade which involved in angiogenesis and early cardiovascular development. The PB1 domain of Map2k5 interacts with the PB1 domain of another members of kinase cascade MEKK2 (or MEKK3). A canonical PB1-PB1 interaction, involving heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The Map2k5 protein contains a type I PB1 domain.
Probab=54.38 E-value=23 Score=28.87 Aligned_cols=49 Identities=18% Similarity=0.371 Sum_probs=35.8
Q ss_pred CcccceeeecCCCCChHHHHHHHHHhhccCCcccccCCCcchhhhhhhhhcCCCCceEEEEEcCCCCeEEccC
Q 022632 182 GVPIGRKVDLNAHASYESLAQTLEEMFFASTPAINSIGGEKDLATKAFKLLDGLSEFVLTYEDKEGDWMLVGD 254 (294)
Q Consensus 182 G~pigRKVDL~~~~sY~eLs~aLe~MF~~~~~~~~~~~g~~~~~~~~~~L~d~~seyvltYeD~eGDwMLVGD 254 (294)
|..+--.||...+=+|.+|..++.+..-.-|. -.+-|||.|||++-|--
T Consensus 10 gg~vDw~V~~~~~L~F~DvL~~I~~vlp~aT~------------------------tAFeYEDE~gDRITVRS 58 (91)
T cd06395 10 GGAVDWTVQSGPQLLFRDVLDVIGQVLPEATT------------------------TAFEYEDEDGDRITVRS 58 (91)
T ss_pred CCcccccccCcccccHHHHHHHHHHhcccccc------------------------cceeeccccCCeeEecc
Confidence 44566778887778899999998888742111 13459999999998864
No 17
>PF10411 DsbC_N: Disulfide bond isomerase protein N-terminus; InterPro: IPR018950 This is the N-terminal domain of the disulphide bond isomerase DsbC. The whole molecule is V-shaped, where each arm is a DsbC monomer of two domains linked by a hinge; and the N-termini of each monomer join to form the dimer interface at the base of the V, so are vital for dimerisation []. DsbC is required for disulphide bond formation and functions as a disulphide bond isomerase during oxidative protein-folding in bacterial periplasm. It also has chaperone activity []. ; PDB: 1EEJ_B 2IYJ_A 1TJD_A 1JZD_B 1JZO_A 1G0T_B 1T3B_A.
Probab=51.41 E-value=12 Score=27.40 Aligned_cols=17 Identities=24% Similarity=0.716 Sum_probs=14.6
Q ss_pred EEEEEcCCCCeEEccCC
Q 022632 239 VLTYEDKEGDWMLVGDV 255 (294)
Q Consensus 239 vltYeD~eGDwMLVGDv 255 (294)
.+.|.|.||+++++|+.
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 58899999999999974
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=39.06 E-value=1.5e+02 Score=23.85 Aligned_cols=70 Identities=19% Similarity=0.261 Sum_probs=50.5
Q ss_pred ceeEEEecCcccceeeecCCCCChHHHHHHHHHhhccCCcccccCCCcchhhhhhhhhcCCCCceEEEEEcCCC-CeEEc
Q 022632 174 GFVKVNMDGVPIGRKVDLNAHASYESLAQTLEEMFFASTPAINSIGGEKDLATKAFKLLDGLSEFVLTYEDKEG-DWMLV 252 (294)
Q Consensus 174 ~fVKV~MdG~pigRKVDL~~~~sY~eLs~aLe~MF~~~~~~~~~~~g~~~~~~~~~~L~d~~seyvltYeD~eG-DwMLV 252 (294)
.-|||+..+ .=.|-...=-+|.+|...|.+=+. +. + .+-+|.|.|.+. +...+
T Consensus 3 ~vvKV~f~~---tIaIrvp~~~~y~~L~~ki~~kLk-----l~---~---------------e~i~LsYkde~s~~~v~l 56 (80)
T cd06406 3 YVVKVHFKY---TVAIQVARGLSYATLLQKISSKLE-----LP---A---------------EHITLSYKSEASGEDVIL 56 (80)
T ss_pred eEEEEEEEE---EEEEEcCCCCCHHHHHHHHHHHhC-----CC---c---------------hhcEEEeccCCCCCccCc
Confidence 468999997 345666666789999999998885 21 1 234788998774 44445
Q ss_pred cCCChHHHhhccc--eeEE
Q 022632 253 GDVPWRMFISSVK--RLRI 269 (294)
Q Consensus 253 GDvPWemFv~svK--RLrI 269 (294)
+|.=|+.-.+.|+ ||+.
T Consensus 57 ~d~dle~aws~~~~~~lTL 75 (80)
T cd06406 57 SDTNMEDVWSQAKDGCLTL 75 (80)
T ss_pred ChHHHHHHHHhhcCCeEEE
Confidence 9999998888887 5554
No 19
>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=26.11 E-value=2.8e+02 Score=20.62 Aligned_cols=69 Identities=14% Similarity=0.204 Sum_probs=50.6
Q ss_pred ceeEEEecCccc---ceeeecCCCCChHHHHHHHHHhhccCCcccccCCCcchhhhhhhhhcCCCCceEE--EEEcCCCC
Q 022632 174 GFVKVNMDGVPI---GRKVDLNAHASYESLAQTLEEMFFASTPAINSIGGEKDLATKAFKLLDGLSEFVL--TYEDKEGD 248 (294)
Q Consensus 174 ~fVKV~MdG~pi---gRKVDL~~~~sY~eLs~aLe~MF~~~~~~~~~~~g~~~~~~~~~~L~d~~seyvl--tYeD~eGD 248 (294)
.++||+++...- -+.|=+.....-.+++.++-+-|. +. +...+|.| .-......
T Consensus 3 ~~lrVy~~~~~~~~~~k~i~v~~~tTa~evi~~~l~k~~-----l~----------------~~~~~y~L~~~~~~~~~e 61 (93)
T PF00788_consen 3 GVLRVYDGDGSPGSTYKTIKVSSSTTAREVIEMALEKFG-----LA----------------EDPSDYCLVEVEESGGEE 61 (93)
T ss_dssp EEEEEEETTSSSCCSEEEEEEETTSBHHHHHHHHHHHTT-----TS----------------SSGGGEEEEEEECTTTEE
T ss_pred eEEEEEcCCCCCCccEEEEEECCCCCHHHHHHHHHHHhC-----CC----------------CCCCCEEEEEEEcCCCEE
Confidence 489999987652 678889999999999999999996 21 12368999 45566666
Q ss_pred eEEccC-CChHHHhhc
Q 022632 249 WMLVGD-VPWRMFISS 263 (294)
Q Consensus 249 wMLVGD-vPWemFv~s 263 (294)
+.|--| .|+..+..-
T Consensus 62 r~L~~~E~pl~i~~~~ 77 (93)
T PF00788_consen 62 RPLDDDECPLQIQLQW 77 (93)
T ss_dssp EEETTTSBHHHHHHTT
T ss_pred EEcCCCCchHHHHHhC
Confidence 666544 588777654
No 20
>COG0219 CspR Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]
Probab=25.31 E-value=26 Score=31.29 Aligned_cols=68 Identities=25% Similarity=0.424 Sum_probs=45.6
Q ss_pred CcccceeeecCCCCChHHHHHHH---HHhhccCCcccccCCCcchhhhhhhhhcCCCCceEEEEEcCCCCeEEccCC---
Q 022632 182 GVPIGRKVDLNAHASYESLAQTL---EEMFFASTPAINSIGGEKDLATKAFKLLDGLSEFVLTYEDKEGDWMLVGDV--- 255 (294)
Q Consensus 182 G~pigRKVDL~~~~sY~eLs~aL---e~MF~~~~~~~~~~~g~~~~~~~~~~L~d~~seyvltYeD~eGDwMLVGDv--- 255 (294)
|-.|--+|+|..|++|++...+. .++|...+.+.. -|.- +....|||+|-|-.
T Consensus 49 GlDY~~~~~l~~h~s~e~fl~~~~~~~rl~~~tt~~~~--------------------~~~~-~~f~~~d~llFG~Es~G 107 (155)
T COG0219 49 GLDYHEKASLTEHDSLEAFLEAEPIGGRLFALTTKGTT--------------------TYTD-VSFQKGDYLLFGPESRG 107 (155)
T ss_pred ccchHhhcceEEeCCHHHHHhhccCCceEEEEEecccc--------------------cccc-ccCCCCCEEEECCCCCC
Confidence 77899999999999999999998 567753222211 1111 44456999999975
Q ss_pred -ChHHHhhc--cceeEE-ec
Q 022632 256 -PWRMFISS--VKRLRI-MR 271 (294)
Q Consensus 256 -PWemFv~s--vKRLrI-mk 271 (294)
|= .+++. -++||| |.
T Consensus 108 LP~-~i~~~~~~~~irIPm~ 126 (155)
T COG0219 108 LPE-EILDAAPDRCIRIPMR 126 (155)
T ss_pred CCH-HHHHhCccceEEeccC
Confidence 52 33432 236999 66
No 21
>PF04809 HupH_C: HupH hydrogenase expression protein, C-terminal conserved region; InterPro: IPR006894 This entry represents the C-terminal conserved domain found in bacterial hydrogenase expression proteins (HupH), which are necessary for hydrogenase synthesis. The precise function of HupH is unknown [].; PDB: 3SB1_A.
Probab=23.65 E-value=53 Score=27.78 Aligned_cols=33 Identities=36% Similarity=0.545 Sum_probs=23.7
Q ss_pred CceEEEEEcCCC----CeEEccCCCh------HHHhhccceeE
Q 022632 236 SEFVLTYEDKEG----DWMLVGDVPW------RMFISSVKRLR 268 (294)
Q Consensus 236 seyvltYeD~eG----DwMLVGDvPW------emFv~svKRLr 268 (294)
.=|.+.|.|.+| |.+-|||+|= ++|..++.||+
T Consensus 71 gVWrV~~~n~~~~~i~d~iEV~~vP~~v~aa~eD~~ds~~rL~ 113 (120)
T PF04809_consen 71 GVWRVRYFNSDGRLILDTIEVGDVPEVVRAAPEDLADSAARLR 113 (120)
T ss_dssp TEEEEEEE-TTS-EEEEEEEESSS-GGGS--HHHHHHHHHHH-
T ss_pred CEEEEEEECCCCCEeeeeEEEeCCcHHHhccHhhHHHHHHHHh
Confidence 469999999986 6778999995 35777777765
No 22
>KOG3957 consensus Predicted L-carnitine dehydratase/alpha-methylacyl-CoA racemase [Lipid transport and metabolism]
Probab=22.16 E-value=1.1e+02 Score=30.93 Aligned_cols=78 Identities=22% Similarity=0.287 Sum_probs=56.5
Q ss_pred cceeeecCCCCChHHHHHHHHHhhccCCcccccCCCcchhhhhhhhhcCCCCceEEEEEcCCCCeEEccCCChHHHhhcc
Q 022632 185 IGRKVDLNAHASYESLAQTLEEMFFASTPAINSIGGEKDLATKAFKLLDGLSEFVLTYEDKEGDWMLVGDVPWRMFISSV 264 (294)
Q Consensus 185 igRKVDL~~~~sY~eLs~aLe~MF~~~~~~~~~~~g~~~~~~~~~~L~d~~seyvltYeD~eGDwMLVGDvPWemFv~sv 264 (294)
-|..||-+|..+-.-|+.-|..-+.... .. .+- -.+.+++.-+-=||+-+||-.|+||-.- .-|.+.|
T Consensus 177 kGqviD~~m~eg~ayl~S~v~~~y~~s~--~e------a~R---~~~~~G~~~~Y~tykTkDG~fmavga~e-pQF~~~l 244 (387)
T KOG3957|consen 177 KGQVIDCNMLEGVAYLLSFVQKNYLQSL--WE------ADR---YGTAHGSIPPYQTYKTKDGYFMAVGALE-PQFYELL 244 (387)
T ss_pred CceEEEechhHhHHHHHHHHHHHhhhhh--cc------ccc---cccccCCCccceeeeccCceEEEecccc-HHHHHHH
Confidence 5788999999998888888877765211 00 010 1355666667779999999999999863 3699999
Q ss_pred ceeEEecCCc
Q 022632 265 KRLRIMRTSE 274 (294)
Q Consensus 265 KRLrImk~se 274 (294)
+++...+..|
T Consensus 245 ~~ll~~~~d~ 254 (387)
T KOG3957|consen 245 KKLLGLKLDE 254 (387)
T ss_pred HHhhCccccc
Confidence 9888777554
No 23
>COG3816 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.29 E-value=62 Score=29.68 Aligned_cols=17 Identities=47% Similarity=0.686 Sum_probs=13.8
Q ss_pred EecCcccceeeecCCCCChHHHHHHHHHhhc
Q 022632 179 NMDGVPIGRKVDLNAHASYESLAQTLEEMFF 209 (294)
Q Consensus 179 ~MdG~pigRKVDL~~~~sY~eLs~aLe~MF~ 209 (294)
+..|.||||+ .|-++|+
T Consensus 56 FylGTPIGR~--------------plVrLFS 72 (205)
T COG3816 56 FYLGTPIGRK--------------PLVRLFS 72 (205)
T ss_pred EEecCccchH--------------HHHHHHH
Confidence 4569999997 7888996
Done!