Query 040477
Match_columns 179
No_of_seqs 198 out of 487
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 08:50:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040477.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040477hhsearch_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 6.2E-49 1.3E-53 327.5 0.5 113 52-179 81-205 (215)
2 PF00564 PB1: PB1 domain; Int 97.7 0.0001 2.2E-09 51.9 6.3 67 97-172 3-70 (84)
3 smart00666 PB1 PB1 domain. Pho 97.4 0.00079 1.7E-08 47.4 7.2 65 98-172 4-69 (81)
4 cd06398 PB1_Joka2 The PB1 doma 97.4 0.00084 1.8E-08 50.2 7.3 68 97-173 2-72 (91)
5 cd06407 PB1_NLP A PB1 domain i 97.4 0.00097 2.1E-08 48.9 7.2 55 98-161 3-57 (82)
6 cd05992 PB1 The PB1 domain is 97.4 0.0011 2.4E-08 46.2 7.2 65 98-172 3-69 (81)
7 cd06396 PB1_NBR1 The PB1 domai 96.9 0.0052 1.1E-07 45.5 7.0 62 98-169 3-65 (81)
8 cd06403 PB1_Par6 The PB1 domai 96.7 0.011 2.4E-07 43.9 7.6 73 98-178 3-79 (80)
9 cd06401 PB1_TFG The PB1 domain 96.5 0.025 5.3E-07 42.1 8.1 73 98-177 3-79 (81)
10 cd06409 PB1_MUG70 The MUG70 pr 96.3 0.011 2.4E-07 44.1 5.4 51 105-160 7-59 (86)
11 cd06404 PB1_aPKC PB1 domain is 96.1 0.025 5.4E-07 42.2 6.4 56 98-162 3-58 (83)
12 cd06397 PB1_UP1 Uncharacterize 95.7 0.04 8.7E-07 41.1 6.2 63 98-170 3-66 (82)
13 cd06402 PB1_p62 The PB1 domain 95.3 0.11 2.4E-06 38.8 7.4 59 97-162 2-65 (87)
14 cd06408 PB1_NoxR The PB1 domai 93.8 0.27 6E-06 36.8 6.5 55 96-162 3-57 (86)
15 cd06399 PB1_P40 The PB1 domain 79.2 3.4 7.4E-05 31.4 4.0 40 112-161 23-62 (92)
16 cd06406 PB1_P67 A PB1 domain i 68.1 33 0.00072 25.4 6.8 68 97-175 4-74 (80)
17 PF10411 DsbC_N: Disulfide bon 51.6 13 0.00028 25.0 2.1 17 146-162 34-50 (57)
18 PF00788 RA: Ras association ( 44.3 98 0.0021 21.3 5.8 69 96-170 3-77 (93)
19 cd06395 PB1_Map2k5 PB1 domain 44.1 45 0.00097 25.3 4.1 50 103-161 9-58 (91)
20 PF06463 Mob_synth_C: Molybden 41.8 58 0.0013 25.2 4.7 64 111-177 17-81 (128)
21 PRK13361 molybdenum cofactor b 38.0 90 0.002 27.4 5.8 73 101-177 188-264 (329)
22 cd06410 PB1_UP2 Uncharacterize 34.8 1.2E+02 0.0025 22.9 5.2 69 101-177 19-95 (97)
23 PF04809 HupH_C: HupH hydrogen 28.5 42 0.00092 26.2 1.9 33 143-175 71-113 (120)
24 PF14688 DUF4461: Domain of un 28.1 40 0.00086 30.3 2.0 29 144-172 81-117 (313)
25 PF09840 DUF2067: Uncharacteri 25.4 40 0.00088 28.3 1.4 29 142-174 97-125 (190)
26 PF12108 SF3a60_bindingd: Spli 25.1 11 0.00024 22.8 -1.5 17 159-175 4-20 (28)
27 PF02013 CBM_10: Cellulose or 21.2 29 0.00063 22.0 -0.2 12 146-157 16-27 (36)
28 COG3816 Uncharacterized protei 20.3 61 0.0013 27.6 1.5 17 102-132 57-73 (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=6.2e-49 Score=327.51 Aligned_cols=113 Identities=44% Similarity=0.705 Sum_probs=6.0
Q ss_pred CCCCCcccCCccccccccccccccccccccchhhhhhhcCCCCcceeEEEecCceeeeeeecCCCCChHHHHHHHHHHhc
Q 040477 52 GYGDDLIEWPETNLQLKNSNRRFQGLVEEDVDEEAEGIQSKERWAYVKVNMDGVMVGRKICILDHCGYSSLACQLEDMFV 131 (179)
Q Consensus 52 ~~~~~vVGWPPirs~rkn~~~~~~~~~~~~~~~~~~~~qs~~~~~~VKV~MdG~piGRKVDL~~~~sY~eL~~~Le~MF~ 131 (179)
..++++||||||+++|||.... .++...++||||+|||+||||||||++|+||++|+.+|++||+
T Consensus 81 ~~~~~~vgwpp~~s~r~n~~~~---------------~~~~~~~~~vKV~mdG~~igRkVDL~~~~sY~~L~~~L~~MF~ 145 (215)
T PF02309_consen 81 ASKAQVVGWPPVRSFRKNSLSE---------------KQSSSSRSYVKVNMDGVPIGRKVDLSAYSSYEELSSALEKMFS 145 (215)
T ss_dssp -----BTTBS----S-----------------------------------------------------------------
T ss_pred cccccccCCCcccccccccccc---------------cccccCCceeEEEecCcccceecCHHHhhCHHHHHHHHHHhcC
Confidence 3568999999999999987631 1223358999999999999999999999999999999999994
Q ss_pred c---c---------ccccccccCCccEEEEEeCCCCeEEcCCCChHHHHhccceeEEccC
Q 040477 132 P---R---------LGLRLFQARSEFSLLYKDGEENWRTVGDVPWTEFVESVKRLRIARN 179 (179)
Q Consensus 132 ~---~---------~~l~~~~~~~~~~l~YeD~eGD~mLVGDvPW~~Fv~svkRLrI~r~ 179 (179)
+ . .++.++..+++|+|||||+||||||||||||+|||++|||||||++
T Consensus 146 ~~~i~~~~~~~~~~~~~~~~~~~~~~~l~Y~D~egd~mlvGD~PW~~F~~~vkRl~I~~~ 205 (215)
T PF02309_consen 146 CFSIEQCGSHGLNESGLLDLLNGSEYVLVYEDKEGDWMLVGDVPWEEFVKSVKRLRIMKS 205 (215)
T ss_dssp ------------------------------------------------------------
T ss_pred CCCccccccccccchhhccccCCcceeEEEECCCCCEEEecCCCHHHHHHHhhccEEecH
Confidence 3 3 1233334677999999999999999999999999999999999984
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=97.75 E-value=0.0001 Score=51.88 Aligned_cols=67 Identities=25% Similarity=0.400 Sum_probs=55.0
Q ss_pred eeEEEecCceeeeeeecCCCCChHHHHHHHHHHhcccccccccccCCccEEEEEeCCCCeEEcCC-CChHHHHhccc
Q 040477 97 YVKVNMDGVMVGRKICILDHCGYSSLACQLEDMFVPRLGLRLFQARSEFSLLYKDGEENWRTVGD-VPWTEFVESVK 172 (179)
Q Consensus 97 ~VKV~MdG~piGRKVDL~~~~sY~eL~~~Le~MF~~~~~l~~~~~~~~~~l~YeD~eGD~mLVGD-vPW~~Fv~svk 172 (179)
-||+...|. +=|.+.+..--+|.+|...++..|+.. ...+.|.|.|.||||..+-+ .=|++.++.++
T Consensus 3 ~vK~~~~~~-~~~~~~~~~~~s~~~L~~~i~~~~~~~--------~~~~~l~Y~D~dgD~V~i~sd~Dl~~a~~~~~ 70 (84)
T PF00564_consen 3 RVKVRYGGD-IRRIISLPSDVSFDDLRSKIREKFGLL--------DEDFQLKYKDEDGDLVTISSDEDLQEAIEQAK 70 (84)
T ss_dssp EEEEEETTE-EEEEEEECSTSHHHHHHHHHHHHHTTS--------TSSEEEEEEETTSSEEEESSHHHHHHHHHHHH
T ss_pred EEEEEECCe-eEEEEEcCCCCCHHHHHHHHHHHhCCC--------CccEEEEeeCCCCCEEEeCCHHHHHHHHHHHH
Confidence 479999997 334588888889999999999999975 34589999999999998884 45777777764
No 3
>smart00666 PB1 PB1 domain. Phox and Bem1p domain, present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.
Probab=97.43 E-value=0.00079 Score=47.35 Aligned_cols=65 Identities=18% Similarity=0.332 Sum_probs=52.4
Q ss_pred eEEEecCceeeeeeecCCCCChHHHHHHHHHHhcccccccccccCCccEEEEEeCCCCeEEcCC-CChHHHHhccc
Q 040477 98 VKVNMDGVMVGRKICILDHCGYSSLACQLEDMFVPRLGLRLFQARSEFSLLYKDGEENWRTVGD-VPWTEFVESVK 172 (179)
Q Consensus 98 VKV~MdG~piGRKVDL~~~~sY~eL~~~Le~MF~~~~~l~~~~~~~~~~l~YeD~eGD~mLVGD-vPW~~Fv~svk 172 (179)
|||.-.|. -|.+-+..--+|.+|.+.+.+.|+... ..+.|.|+|.||||..+.+ .=|++.++.++
T Consensus 4 vK~~~~~~--~~~~~~~~~~s~~dL~~~i~~~~~~~~--------~~~~l~Y~Dedgd~v~l~sd~Dl~~a~~~~~ 69 (81)
T smart00666 4 VKLRYGGE--TRRLSVPRDISFEDLRSKVAKRFGLDN--------QSFTLKYQDEDGDLVSLTSDEDLEEAIEEYD 69 (81)
T ss_pred EEEEECCE--EEEEEECCCCCHHHHHHHHHHHhCCCC--------CCeEEEEECCCCCEEEecCHHHHHHHHHHHH
Confidence 67877554 778888889999999999999998532 4589999999999997764 56777776655
No 4
>cd06398 PB1_Joka2 The PB1 domain is present in the Nicotiana plumbaginifolia Joka2 protein which interacts with sulfur stress inducible UP9 protein. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module
Probab=97.40 E-value=0.00084 Score=50.23 Aligned_cols=68 Identities=19% Similarity=0.303 Sum_probs=52.8
Q ss_pred eeEEEecCceeeeeeecC---CCCChHHHHHHHHHHhcccccccccccCCccEEEEEeCCCCeEEcCCCChHHHHhccce
Q 040477 97 YVKVNMDGVMVGRKICIL---DHCGYSSLACQLEDMFVPRLGLRLFQARSEFSLLYKDGEENWRTVGDVPWTEFVESVKR 173 (179)
Q Consensus 97 ~VKV~MdG~piGRKVDL~---~~~sY~eL~~~Le~MF~~~~~l~~~~~~~~~~l~YeD~eGD~mLVGDvPW~~Fv~svkR 173 (179)
-|||.-+|.-+=-++++. .--+|++|...+.+.|.+. ...+++|.|.|.||||..+-.. +++..++.+
T Consensus 2 ~vKv~y~~~~rRf~l~~~~~~~d~~~~~L~~kI~~~f~l~-------~~~~~~l~Y~Dedgd~V~l~~D--~DL~~a~~~ 72 (91)
T cd06398 2 VVKVKYGGTLRRFTFPVAENQLDLNMDGLREKVEELFSLS-------PDADLSLTYTDEDGDVVTLVDD--NDLTDAIQY 72 (91)
T ss_pred EEEEEeCCEEEEEEeccccccCCCCHHHHHHHHHHHhCCC-------CCCcEEEEEECCCCCEEEEccH--HHHHHHHHH
Confidence 489999998444444443 4579999999999999864 3467999999999999999876 666666554
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=97.36 E-value=0.00097 Score=48.90 Aligned_cols=55 Identities=22% Similarity=0.349 Sum_probs=45.3
Q ss_pred eEEEecCceeeeeeecCCCCChHHHHHHHHHHhcccccccccccCCccEEEEEeCCCCeEEcCC
Q 040477 98 VKVNMDGVMVGRKICILDHCGYSSLACQLEDMFVPRLGLRLFQARSEFSLLYKDGEENWRTVGD 161 (179)
Q Consensus 98 VKV~MdG~piGRKVDL~~~~sY~eL~~~Le~MF~~~~~l~~~~~~~~~~l~YeD~eGD~mLVGD 161 (179)
|||...|. -+.+-|..--+|++|.+++.++|+.. ....+.|-|.|.||||..+--
T Consensus 3 vK~~~~~d--~~r~~l~~~~~~~~L~~~i~~r~~~~-------~~~~f~LkY~Ddegd~v~lts 57 (82)
T cd06407 3 VKATYGEE--KIRFRLPPSWGFTELKQEIAKRFKLD-------DMSAFDLKYLDDDEEWVLLTC 57 (82)
T ss_pred EEEEeCCe--EEEEEcCCCCCHHHHHHHHHHHhCCC-------CCCeeEEEEECCCCCeEEeec
Confidence 89999997 55566666669999999999999964 235799999999999998753
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=97.35 E-value=0.0011 Score=46.24 Aligned_cols=65 Identities=22% Similarity=0.374 Sum_probs=52.1
Q ss_pred eEEEecCceeeeeeecC-CCCChHHHHHHHHHHhcccccccccccCCccEEEEEeCCCCeEEcCC-CChHHHHhccc
Q 040477 98 VKVNMDGVMVGRKICIL-DHCGYSSLACQLEDMFVPRLGLRLFQARSEFSLLYKDGEENWRTVGD-VPWTEFVESVK 172 (179)
Q Consensus 98 VKV~MdG~piGRKVDL~-~~~sY~eL~~~Le~MF~~~~~l~~~~~~~~~~l~YeD~eGD~mLVGD-vPW~~Fv~svk 172 (179)
|||+-.|. -|.+-+. .--+|++|...|.+.|+... ..+.+.|.|.||||..+.+ .=|++-++.++
T Consensus 3 vK~~~~~~--~~~~~~~~~~~s~~~L~~~i~~~~~~~~--------~~~~l~y~D~e~d~v~l~sd~Dl~~a~~~~~ 69 (81)
T cd05992 3 VKVKYGGE--IRRFVVVSRSISFEDLRSKIAEKFGLDA--------VSFKLKYPDEDGDLVTISSDEDLEEAIEEAR 69 (81)
T ss_pred EEEEecCC--CEEEEEecCCCCHHHHHHHHHHHhCCCC--------CcEEEEeeCCCCCEEEeCCHHHHHHHHHHHh
Confidence 78888876 4555555 88999999999999998652 4589999999999999987 56676666655
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=96.88 E-value=0.0052 Score=45.50 Aligned_cols=62 Identities=16% Similarity=0.222 Sum_probs=49.8
Q ss_pred eEEEecCceeeeeeecCCCCChHHHHHHHHHHhcccccccccccCCccEEEEEeCCCCeEEcC-CCChHHHHh
Q 040477 98 VKVNMDGVMVGRKICILDHCGYSSLACQLEDMFVPRLGLRLFQARSEFSLLYKDGEENWRTVG-DVPWTEFVE 169 (179)
Q Consensus 98 VKV~MdG~piGRKVDL~~~~sY~eL~~~Le~MF~~~~~l~~~~~~~~~~l~YeD~eGD~mLVG-DvPW~~Fv~ 169 (179)
|||.-.|.-+--+++-+..-+|.+|.+++.++|+.. .+.|.|-|.||||.++- |.=-++.+.
T Consensus 3 vKaty~~d~~rf~~~~~~~~~~~~L~~ev~~rf~l~----------~f~lKYlDde~e~v~lssd~eLeE~~r 65 (81)
T cd06396 3 LKVTYNGESQSFLVSDSENTTWASVEAMVKVSFGLN----------DIQIKYVDEENEEVSVNSQGEYEEALK 65 (81)
T ss_pred EEEEECCeEEEEEecCCCCCCHHHHHHHHHHHhCCC----------cceeEEEcCCCCEEEEEchhhHHHHHH
Confidence 789999987777777777889999999999999976 38999999999998874 333344433
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=96.71 E-value=0.011 Score=43.86 Aligned_cols=73 Identities=18% Similarity=0.181 Sum_probs=52.4
Q ss_pred eEEEecCceeeeeeecCCCCChHHHHHHHHHHhcccccccccccCCccEEEEEeCCCCeEEcC-CCChHHHHhccc---e
Q 040477 98 VKVNMDGVMVGRKICILDHCGYSSLACQLEDMFVPRLGLRLFQARSEFSLLYKDGEENWRTVG-DVPWTEFVESVK---R 173 (179)
Q Consensus 98 VKV~MdG~piGRKVDL~~~~sY~eL~~~Le~MF~~~~~l~~~~~~~~~~l~YeD~eGD~mLVG-DvPW~~Fv~svk---R 173 (179)
||..-|..--=-.+|.....+|+++++-|++||.+.. ..+.|-|.|.+||.+-+- |+-+..=+++++ |
T Consensus 3 VKSkfdaEfRRFsl~r~~~~~f~ef~~ll~~lH~l~~--------~~f~i~Y~D~~gDLLPInNDdNf~kAlssa~plLR 74 (80)
T cd06403 3 VKSKFDAEFRRFSLDRNKPGKFEDFYKLLEHLHHIPN--------VDFLIGYTDPHGDLLPINNDDNFLKALSSANPLLR 74 (80)
T ss_pred eecccCCeEEEEEeccccCcCHHHHHHHHHHHhCCCC--------CcEEEEEeCCCCCEecccCcHHHHHHHHcCCCceE
Confidence 6666666622224555566999999999999998753 459999999999999887 445555455666 5
Q ss_pred eEEcc
Q 040477 174 LRIAR 178 (179)
Q Consensus 174 LrI~r 178 (179)
|.|-|
T Consensus 75 l~iqr 79 (80)
T cd06403 75 IFIQR 79 (80)
T ss_pred EEEEc
Confidence 55544
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=96.45 E-value=0.025 Score=42.06 Aligned_cols=73 Identities=19% Similarity=0.303 Sum_probs=52.2
Q ss_pred eEEEecCceeeeeeecCCC-CChHHHHHHHHHHhcccccccccccCCccEEEEEeCCCCeEEcCCC---ChHHHHhccce
Q 040477 98 VKVNMDGVMVGRKICILDH-CGYSSLACQLEDMFVPRLGLRLFQARSEFSLLYKDGEENWRTVGDV---PWTEFVESVKR 173 (179)
Q Consensus 98 VKV~MdG~piGRKVDL~~~-~sY~eL~~~Le~MF~~~~~l~~~~~~~~~~l~YeD~eGD~mLVGDv---PW~~Fv~svkR 173 (179)
+|+.-.|. =|++=+..- -+|.+|...+.+.|...- .....+.+.|.|.|||+.-+.+. -|..=+...+|
T Consensus 3 iK~~~g~D--iR~~~~~~~~~t~~~L~~~v~~~F~~~~-----~~~~~flIKYkD~dGDlVTIts~~dL~~A~~~~~~~~ 75 (81)
T cd06401 3 LKAQLGDD--IRRIPIHNEDITYDELLLMMQRVFRGKL-----GSSDDVLIKYKDEDGDLITIFDSSDLSFAIQCSRILK 75 (81)
T ss_pred EEEEeCCe--EEEEeccCccccHHHHHHHHHHHhcccc-----CCcccEEEEEECCCCCEEEeccHHHHHHHHhcCcceE
Confidence 67777665 456555543 399999999999999531 23457999999999999999875 44433444556
Q ss_pred eEEc
Q 040477 174 LRIA 177 (179)
Q Consensus 174 LrI~ 177 (179)
|+|.
T Consensus 76 l~~~ 79 (81)
T cd06401 76 LTLF 79 (81)
T ss_pred EEEe
Confidence 6664
No 10
>cd06409 PB1_MUG70 The MUG70 protein is a product of the meiotically up-regulated gene 70 which has a role in meiosis and harbors a PB1 domain. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domains depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic amino acid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is
Probab=96.28 E-value=0.011 Score=44.13 Aligned_cols=51 Identities=14% Similarity=0.026 Sum_probs=39.8
Q ss_pred ceeeeeeec--CCCCChHHHHHHHHHHhcccccccccccCCccEEEEEeCCCCeEEcC
Q 040477 105 VMVGRKICI--LDHCGYSSLACQLEDMFVPRLGLRLFQARSEFSLLYKDGEENWRTVG 160 (179)
Q Consensus 105 ~piGRKVDL--~~~~sY~eL~~~Le~MF~~~~~l~~~~~~~~~~l~YeD~eGD~mLVG 160 (179)
+|-||.+=+ ....|+.+|.+++.+-|+.... ....+.|.|.|.||||.++-
T Consensus 7 ~~~GrvhRf~~~~s~~~~~L~~~I~~Rl~~d~~-----~~~~~~L~YlDDEgD~VllT 59 (86)
T cd06409 7 DPKGRVHRFRLRPSESLEELRTLISQRLGDDDF-----ETHLYALSYVDDEGDIVLIT 59 (86)
T ss_pred CCCCCEEEEEecCCCCHHHHHHHHHHHhCCccc-----cCCcccEEEEcCCCCEEEEe
Confidence 345665544 4478999999999999987642 13569999999999999875
No 11
>cd06404 PB1_aPKC PB1 domain is an essential modular domain of the atypical protein kinase C (aPKC) which in complex with Par6 and Par3 proteins is crucial for establishment of apical-basal polarity of animal cells. PB1 domain is a modular domain mediating specific protein-protein interaction which play roles in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi,
Probab=96.07 E-value=0.025 Score=42.19 Aligned_cols=56 Identities=21% Similarity=0.223 Sum_probs=45.4
Q ss_pred eEEEecCceeeeeeecCCCCChHHHHHHHHHHhcccccccccccCCccEEEEEeCCCCeEEcCCC
Q 040477 98 VKVNMDGVMVGRKICILDHCGYSSLACQLEDMFVPRLGLRLFQARSEFSLLYKDGEENWRTVGDV 162 (179)
Q Consensus 98 VKV~MdG~piGRKVDL~~~~sY~eL~~~Le~MF~~~~~l~~~~~~~~~~l~YeD~eGD~mLVGDv 162 (179)
+|++-.|...--.+|. .-+|++|.+.+.+||... .+..+++.|.|.|||.--+...
T Consensus 3 ~K~~y~gdi~it~~d~--~~s~e~L~~~v~~~c~~~-------~~q~ft~kw~DEEGDp~tiSS~ 58 (83)
T cd06404 3 VKAAYNGDIMITSIDP--SISLEELCNEVRDMCRFH-------NDQPFTLKWIDEEGDPCTISSQ 58 (83)
T ss_pred EEEEecCcEEEEEcCC--CcCHHHHHHHHHHHhCCC-------CCCcEEEEEECCCCCceeecCH
Confidence 7899999855555665 778999999999999974 2346999999999998777643
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=95.74 E-value=0.04 Score=41.06 Aligned_cols=63 Identities=21% Similarity=0.285 Sum_probs=50.6
Q ss_pred eEEEecCceeeeeeecCCCCChHHHHHHHHHHhcccccccccccCCccEEEEEeCCCCeEEcCC-CChHHHHhc
Q 040477 98 VKVNMDGVMVGRKICILDHCGYSSLACQLEDMFVPRLGLRLFQARSEFSLLYKDGEENWRTVGD-VPWTEFVES 170 (179)
Q Consensus 98 VKV~MdG~piGRKVDL~~~~sY~eL~~~Le~MF~~~~~l~~~~~~~~~~l~YeD~eGD~mLVGD-vPW~~Fv~s 170 (179)
-||.-+|. .|++-...-=+|.+|.+.|+.+|.+.. . .+.|+|.|.|||..-+-| .=-++|.+-
T Consensus 3 fKv~~~g~--~RRf~~~~~pt~~~L~~kl~~Lf~lp~-------~-~~~vtYiDeD~D~ITlssd~eL~d~~~~ 66 (82)
T cd06397 3 FKSSFLGD--TRRIVFPDIPTWEALASKLENLYNLPE-------I-KVGVTYIDNDNDEITLSSNKELQDFYRL 66 (82)
T ss_pred EEEEeCCc--eEEEecCCCccHHHHHHHHHHHhCCCh-------h-HeEEEEEcCCCCEEEecchHHHHHHHHh
Confidence 48888887 899999999999999999999999752 1 279999999999886654 445555443
No 13
>cd06402 PB1_p62 The PB1 domain is an essential part of p62 scaffold protein (alias sequestosome 1,SQSTM) involved in cell signaling, receptor internalization, and protein turnover. The PB1 domain is a modular domain mediating specific protein-protein interaction which play roles in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.
Probab=95.31 E-value=0.11 Score=38.83 Aligned_cols=59 Identities=20% Similarity=0.198 Sum_probs=43.6
Q ss_pred eeEEEecC---ceeeeee--ecCCCCChHHHHHHHHHHhcccccccccccCCccEEEEEeCCCCeEEcCCC
Q 040477 97 YVKVNMDG---VMVGRKI--CILDHCGYSSLACQLEDMFVPRLGLRLFQARSEFSLLYKDGEENWRTVGDV 162 (179)
Q Consensus 97 ~VKV~MdG---~piGRKV--DL~~~~sY~eL~~~Le~MF~~~~~l~~~~~~~~~~l~YeD~eGD~mLVGDv 162 (179)
.||.+..| .+==|++ |=....+|++|...+.++|... .+..++|.|.|.|||..-+...
T Consensus 2 ~vkayl~~~~~~~EIRRf~l~~~~~~s~~~L~~~V~~~f~~l-------~~~~ftlky~DeeGDlvtIssd 65 (87)
T cd06402 2 TVKAYLLGKDANAEIRRFAIDEDVSTSYEYLVEKVAAVFPSL-------RGKNFQLFWKDEEGDLVAFSSD 65 (87)
T ss_pred eEEEeecCCCCccceEEEEecCCCCcCHHHHHHHHHHHcccc-------CCCcEEEEEECCCCCEEeecCH
Confidence 46666665 2233444 4466679999999999999753 2356999999999999988764
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=93.84 E-value=0.27 Score=36.76 Aligned_cols=55 Identities=25% Similarity=0.334 Sum_probs=46.5
Q ss_pred ceeEEEecCceeeeeeecCCCCChHHHHHHHHHHhcccccccccccCCccEEEEEeCCCCeEEcCCC
Q 040477 96 AYVKVNMDGVMVGRKICILDHCGYSSLACQLEDMFVPRLGLRLFQARSEFSLLYKDGEENWRTVGDV 162 (179)
Q Consensus 96 ~~VKV~MdG~piGRKVDL~~~~sY~eL~~~Le~MF~~~~~l~~~~~~~~~~l~YeD~eGD~mLVGDv 162 (179)
.=|||+-.|. .|-|-+..-=+|++|...+.++|+.. ..++|-|.|. ||..-+++.
T Consensus 3 ikVKv~~~~D--v~~i~v~~~i~f~dL~~kIrdkf~~~---------~~~~iKykDE-GD~iti~sq 57 (86)
T cd06408 3 IRVKVHAQDD--TRYIMIGPDTGFADFEDKIRDKFGFK---------RRLKIKMKDD-GDMITMGDQ 57 (86)
T ss_pred EEEEEEecCc--EEEEEcCCCCCHHHHHHHHHHHhCCC---------CceEEEEEcC-CCCccccCH
Confidence 3589999998 67777777778999999999999974 2589999999 999988874
No 15
>cd06399 PB1_P40 The PB1 domain is essential part of the p40 adaptor protein which plays an important role in activating phagocyte NADPH oxidase during phagocytosis. The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes , such as osteoclastogenesis, angiogenesis, early cardiovascular development and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The PB1 domain of p40 represents a type I PB1 domain which interacts with the PB1 domain of oxidase activator p67 w
Probab=79.21 E-value=3.4 Score=31.44 Aligned_cols=40 Identities=15% Similarity=0.101 Sum_probs=32.9
Q ss_pred ecCCCCChHHHHHHHHHHhcccccccccccCCccEEEEEeCCCCeEEcCC
Q 040477 112 CILDHCGYSSLACQLEDMFVPRLGLRLFQARSEFSLLYKDGEENWRTVGD 161 (179)
Q Consensus 112 DL~~~~sY~eL~~~Le~MF~~~~~l~~~~~~~~~~l~YeD~eGD~mLVGD 161 (179)
||+..-.|.+|..-..+-|..+ +-.|-|.|.|||..-+=|
T Consensus 23 ~l~~~P~~kdLl~lmr~~f~~~----------dIaLNYrD~EGDLIRlld 62 (92)
T cd06399 23 DLSSTPLLKDLLELTRREFQRE----------DIALNYRDAEGDLIRLLS 62 (92)
T ss_pred ccccCccHHHHHHHHHHHhchh----------heeeeeecCCCCEEEEcc
Confidence 6888899999999999999854 358889999999875533
No 16
>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=68.09 E-value=33 Score=25.40 Aligned_cols=68 Identities=18% Similarity=0.173 Sum_probs=51.3
Q ss_pred eeEEEecCceeeeeeecCCCCChHHHHHHHHHHhcccccccccccCCccEEEEEeCCC-CeEEcCCCChHHHHhccc--e
Q 040477 97 YVKVNMDGVMVGRKICILDHCGYSSLACQLEDMFVPRLGLRLFQARSEFSLLYKDGEE-NWRTVGDVPWTEFVESVK--R 173 (179)
Q Consensus 97 ~VKV~MdG~piGRKVDL~~~~sY~eL~~~Le~MF~~~~~l~~~~~~~~~~l~YeD~eG-D~mLVGDvPW~~Fv~svk--R 173 (179)
-|||+-++ .=.|....=-+|.+|...|.+-+..-. .+-+|-|.|.+. +...++|.-++.=.+.|+ |
T Consensus 4 vvKV~f~~---tIaIrvp~~~~y~~L~~ki~~kLkl~~--------e~i~LsYkde~s~~~v~l~d~dle~aws~~~~~~ 72 (80)
T cd06406 4 VVKVHFKY---TVAIQVARGLSYATLLQKISSKLELPA--------EHITLSYKSEASGEDVILSDTNMEDVWSQAKDGC 72 (80)
T ss_pred EEEEEEEE---EEEEEcCCCCCHHHHHHHHHHHhCCCc--------hhcEEEeccCCCCCccCcChHHHHHHHHhhcCCe
Confidence 58999997 345666677789999999999888632 346899998774 444459999998888887 5
Q ss_pred eE
Q 040477 174 LR 175 (179)
Q Consensus 174 Lr 175 (179)
|+
T Consensus 73 lT 74 (80)
T cd06406 73 LT 74 (80)
T ss_pred EE
Confidence 54
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=51.61 E-value=13 Score=25.04 Aligned_cols=17 Identities=24% Similarity=0.560 Sum_probs=14.6
Q ss_pred EEEEEeCCCCeEEcCCC
Q 040477 146 SLLYKDGEENWRTVGDV 162 (179)
Q Consensus 146 ~l~YeD~eGD~mLVGDv 162 (179)
.+.|.|.+|+.+++|+.
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 58899999999999975
No 18
>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=44.33 E-value=98 Score=21.27 Aligned_cols=69 Identities=13% Similarity=0.052 Sum_probs=50.8
Q ss_pred ceeEEEecCcee---eeeeecCCCCChHHHHHHHHHHhcccccccccccCCccEEE--EEeCCCCeEEcCC-CChHHHHh
Q 040477 96 AYVKVNMDGVMV---GRKICILDHCGYSSLACQLEDMFVPRLGLRLFQARSEFSLL--YKDGEENWRTVGD-VPWTEFVE 169 (179)
Q Consensus 96 ~~VKV~MdG~pi---GRKVDL~~~~sY~eL~~~Le~MF~~~~~l~~~~~~~~~~l~--YeD~eGD~mLVGD-vPW~~Fv~ 169 (179)
.++||++....- -+.|=+.....-.+++.++-+.|++.. ...+|.|+ -........|-.| .|+..+..
T Consensus 3 ~~lrVy~~~~~~~~~~k~i~v~~~tTa~evi~~~l~k~~l~~------~~~~y~L~~~~~~~~~er~L~~~E~pl~i~~~ 76 (93)
T PF00788_consen 3 GVLRVYDGDGSPGSTYKTIKVSSSTTAREVIEMALEKFGLAE------DPSDYCLVEVEESGGEERPLDDDECPLQIQLQ 76 (93)
T ss_dssp EEEEEEETTSSSCCSEEEEEEETTSBHHHHHHHHHHHTTTSS------SGGGEEEEEEECTTTEEEEETTTSBHHHHHHT
T ss_pred eEEEEEcCCCCCCccEEEEEECCCCCHHHHHHHHHHHhCCCC------CCCCEEEEEEEcCCCEEEEcCCCCchHHHHHh
Confidence 478999987642 688899999999999999999999822 34569994 4455555666544 47777665
Q ss_pred c
Q 040477 170 S 170 (179)
Q Consensus 170 s 170 (179)
-
T Consensus 77 ~ 77 (93)
T PF00788_consen 77 W 77 (93)
T ss_dssp T
T ss_pred C
Confidence 4
No 19
>cd06395 PB1_Map2k5 PB1 domain is essential part of the mitogen-activated protein kinase kinase 5 (Map2k5, alias MEK5) one of the key member of the signaling kinases cascade which involved in angiogenesis and early cardiovascular development. The PB1 domain of Map2k5 interacts with the PB1 domain of another members of kinase cascade MEKK2 (or MEKK3). A canonical PB1-PB1 interaction, involving heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The Map2k5 protein contains a type I PB1 domain.
Probab=44.14 E-value=45 Score=25.28 Aligned_cols=50 Identities=12% Similarity=0.127 Sum_probs=36.6
Q ss_pred cCceeeeeeecCCCCChHHHHHHHHHHhcccccccccccCCccEEEEEeCCCCeEEcCC
Q 040477 103 DGVMVGRKICILDHCGYSSLACQLEDMFVPRLGLRLFQARSEFSLLYKDGEENWRTVGD 161 (179)
Q Consensus 103 dG~piGRKVDL~~~~sY~eL~~~Le~MF~~~~~l~~~~~~~~~~l~YeD~eGD~mLVGD 161 (179)
+|..+--.||....=++.+++.++.+..... .--..-|||.+||.+-|--
T Consensus 9 ~gg~vDw~V~~~~~L~F~DvL~~I~~vlp~a---------T~tAFeYEDE~gDRITVRS 58 (91)
T cd06395 9 NGGAVDWTVQSGPQLLFRDVLDVIGQVLPEA---------TTTAFEYEDEDGDRITVRS 58 (91)
T ss_pred CCCcccccccCcccccHHHHHHHHHHhcccc---------cccceeeccccCCeeEecc
Confidence 4445666777777788999999988766532 2235669999999998853
No 20
>PF06463 Mob_synth_C: Molybdenum Cofactor Synthesis C; InterPro: IPR010505 The majority of molybdenum-containing enzymes utilise a molybdenum cofactor (MoCF or Moco) consisting of a Mo atom coordinated via a cis-dithiolene moiety to molybdopterin (MPT). MoCF is ubiquitous in nature, and the pathway for MoCF biosynthesis is conserved in all three domains of life. MoCF-containing enzymes function as oxidoreductases in carbon, nitrogen, and sulphur metabolism [, ]. In Escherichia coli, biosynthesis of MoCF is a three stage process. It begins with the MoaA and MoaC conversion of GTP to the meta-stable pterin intermediate precursor Z. The second stage involves MPT synthase (MoaD and MoaE), which converts precursor Z to MPT; MoeB is involved in the recycling of MPT synthase. The final step in MoCF synthesis is the attachment of mononuclear Mo to MPT, a process that requires MoeA and which is enhanced by MogA in an Mg2 ATP-dependent manner []. MoCF is the active co-factor in eukaryotic and some prokaryotic molybdo-enzymes, but the majority of bacterial enzymes requiring MoCF, need a modification of MTP for it to be active; MobA is involved in the attachment of a nucleotide monophosphate to MPT resulting in the MGD co-factor, the active co-factor for most prokaryotic molybdo-enzymes. Bacterial two-hybrid studies have revealed the close interactions between MoeA, MogA, and MobA in the synthesis of MoCF []. Moreover the close functional association of MoeA and MogA in the synthesis of MoCF is supported by fact that the known eukaryotic homologues to MoeA and MogA exist as fusion proteins: CNX1 (Q39054 from SWISSPROT) of Arabidopsis thaliana (Mouse-ear cress), mammalian Gephryin (e.g. Q9NQX3 from SWISSPROT) and Drosophila melanogaster (Fruit fly) Cinnamon (P39205 from SWISSPROT) []. This entry represents MoaA, which belongs to a family of enzymes involved in the synthesis of metallo-cofactors (IPR000385 from INTERPRO). Each subunit of the MoaA dimer is comprised of an N-terminal SAM domain (IPR007197 from INTERPRO) that contains the [4Fe-4S] cluster typical for this family of enzymes, as well as an additional [4Fe-4S] cluster in the C-terminal domain that is unique to MoaA proteins []. The unique Fe site of the C-terminal [4Fe-4S] cluster is thought to be involved in the binding and activation of 5'-GTP. Mutations in the human MoCF biosynthesis proteins MOCS1, MOCS2 or GEPH cause MoCF Deficiency type A (MOCOD), causing the loss of activity of MoCF-containing enzymes, resulting in neurological abnormalities and death [].; GO: 0051539 4 iron, 4 sulfur cluster binding, 0006777 Mo-molybdopterin cofactor biosynthetic process, 0019008 molybdopterin synthase complex; PDB: 2FB2_A 2FB3_A 1TV8_B 1TV7_A.
Probab=41.77 E-value=58 Score=25.25 Aligned_cols=64 Identities=13% Similarity=0.148 Sum_probs=29.2
Q ss_pred eecCCCCChHHHHHHHHHHhccccccc-ccccCCccEEEEEeCCCCeEEcCCCChHHHHhccceeEEc
Q 040477 111 ICILDHCGYSSLACQLEDMFVPRLGLR-LFQARSEFSLLYKDGEENWRTVGDVPWTEFVESVKRLRIA 177 (179)
Q Consensus 111 VDL~~~~sY~eL~~~Le~MF~~~~~l~-~~~~~~~~~l~YeD~eGD~mLVGDvPW~~Fv~svkRLrI~ 177 (179)
+--..|-+++++...|++.|....... ...+..-|.+ .+..|.+=++.-+- +.||.+|.||||.
T Consensus 17 ~~~~~~~~~~ei~~~l~~~~~~~~~~~~~~~pa~~y~~--~g~~g~vG~I~~~s-~~FC~~CNRiRlT 81 (128)
T PF06463_consen 17 WFEEEFVPAQEILERLEERYELLPSEKRPNGPARYYRI--PGGKGRVGFISPVS-NPFCSSCNRIRLT 81 (128)
T ss_dssp B-TTTB--HHHHHHHHHHHS-EEEE--SST-SSEEEEE--TTT--EEEEE-TTT-S--GGG--EEEE-
T ss_pred chhhcCcCHHHHHHHHHHhCCccccccccCCcceEEEE--CCCCcEEEEEeCCC-CCCCCcCCEEEEc
Confidence 344678889999999999998743221 1111112222 23333343443332 2499999999985
No 21
>PRK13361 molybdenum cofactor biosynthesis protein A; Provisional
Probab=37.98 E-value=90 Score=27.45 Aligned_cols=73 Identities=12% Similarity=0.180 Sum_probs=44.1
Q ss_pred EecCceeeeeee--cCCCCChHHHHHHHHHHhcccccccccccCCccEEEEE--eCCCCeEEcCCCChHHHHhccceeEE
Q 040477 101 NMDGVMVGRKIC--ILDHCGYSSLACQLEDMFVPRLGLRLFQARSEFSLLYK--DGEENWRTVGDVPWTEFVESVKRLRI 176 (179)
Q Consensus 101 ~MdG~piGRKVD--L~~~~sY~eL~~~Le~MF~~~~~l~~~~~~~~~~l~Ye--D~eGD~mLVGDvPW~~Fv~svkRLrI 176 (179)
+.+-.|+|+--+ -..+=+.+++...|+..|........ .. +-.-.|. |..|-+=++.-+-.. ||.+|.||||
T Consensus 188 ~ie~mP~g~~~~~~~~~~~~~~e~~~~l~~~~~~~~~~~~-~~--~~~~~~~~~~~~~~ig~I~~~s~~-fC~~Cnr~rl 263 (329)
T PRK13361 188 FIEEMPLGEIDERRRARHCSSDEVRAIIETRYPLTPSNKR-TG--GPARYYTMADSPIHIGFISPHSHN-FCHECNRVRV 263 (329)
T ss_pred EEecccCCCccchhhccCcCHHHHHHHHHHhCCcccCCCC-CC--CCCeEEEECCCCeEEEEEcCCCcc-ccccCCeEEE
Confidence 566778887322 34566889999999998764321111 11 1112343 444555555544454 9999999998
Q ss_pred c
Q 040477 177 A 177 (179)
Q Consensus 177 ~ 177 (179)
.
T Consensus 264 t 264 (329)
T PRK13361 264 T 264 (329)
T ss_pred c
Confidence 5
No 22
>cd06410 PB1_UP2 Uncharacterized protein 2. 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 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.
Probab=34.75 E-value=1.2e+02 Score=22.88 Aligned_cols=69 Identities=17% Similarity=0.222 Sum_probs=40.9
Q ss_pred EecCceeeeeeecCCCCChHHHHHHHHHHhcccccccccccCCccEEEEEeCCCCeEEcCCC--ChHHHHhcc------c
Q 040477 101 NMDGVMVGRKICILDHCGYSSLACQLEDMFVPRLGLRLFQARSEFSLLYKDGEENWRTVGDV--PWTEFVESV------K 172 (179)
Q Consensus 101 ~MdG~piGRKVDL~~~~sY~eL~~~Le~MF~~~~~l~~~~~~~~~~l~YeD~eGD~mLVGDv--PW~~Fv~sv------k 172 (179)
++-|. -|-|.+..--+|.||...|.++|++..... -.|+|-.+|.++ ..-|-++ =|.|+-+.- -
T Consensus 19 Y~GG~--tr~i~V~r~~s~~el~~kl~~~~~~~~~~~-----lky~Lp~edld~-Lisv~~DeDl~~M~~e~~~~~~~~~ 90 (97)
T cd06410 19 YVGGE--TRIVSVDRSISFKELVSKLSELFGAGVVVT-----LKYQLPDEDLDA-LISVSNDEDLKNMMEEYDRLSGGSA 90 (97)
T ss_pred EcCCc--eEEEEEcCCCCHHHHHHHHHHHhCCCCceE-----EEEEcCCCCcce-eEEecCcHHHHHHHHhhccccCCCc
Confidence 44565 666777777799999999999998764211 135555544441 4444432 455543333 3
Q ss_pred eeEEc
Q 040477 173 RLRIA 177 (179)
Q Consensus 173 RLrI~ 177 (179)
||||.
T Consensus 91 rirvf 95 (97)
T cd06410 91 RLRVF 95 (97)
T ss_pred eEEEE
Confidence 66653
No 23
>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=28.50 E-value=42 Score=26.18 Aligned_cols=33 Identities=30% Similarity=0.514 Sum_probs=23.2
Q ss_pred CccEEEEEeCCC----CeEEcCCCCh------HHHHhccceeE
Q 040477 143 SEFSLLYKDGEE----NWRTVGDVPW------TEFVESVKRLR 175 (179)
Q Consensus 143 ~~~~l~YeD~eG----D~mLVGDvPW------~~Fv~svkRLr 175 (179)
.=|.+.|.|.+| |.+-||++|= ++|..++.||+
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 459999999997 5677999995 46777777664
No 24
>PF14688 DUF4461: Domain of unknown function (DUF4461)
Probab=28.09 E-value=40 Score=30.32 Aligned_cols=29 Identities=28% Similarity=0.583 Sum_probs=20.7
Q ss_pred ccEEEE-----EeCCCCeEE-cCCCC--hHHHHhccc
Q 040477 144 EFSLLY-----KDGEENWRT-VGDVP--WTEFVESVK 172 (179)
Q Consensus 144 ~~~l~Y-----eD~eGD~mL-VGDvP--W~~Fv~svk 172 (179)
+.+|++ .|.+|++|| +|||| |..|++.+.
T Consensus 81 G~tvvF~~~sGv~~~G~v~L~~~Dv~~~W~~~l~~l~ 117 (313)
T PF14688_consen 81 GRTVVFGDFSGVSLDGHVMLGTGDVPHQWTSFLERLP 117 (313)
T ss_pred CCEEEecCCCccCCCCCEEecCCCcHHHHHHHHHhCC
Confidence 456655 367888887 67886 888887654
No 25
>PF09840 DUF2067: Uncharacterized protein conserved in archaea (DUF2067); InterPro: IPR019202 This family of archaeal proteins, have no known function.
Probab=25.39 E-value=40 Score=28.34 Aligned_cols=29 Identities=28% Similarity=0.394 Sum_probs=24.3
Q ss_pred CCccEEEEEeCCCCeEEcCCCChHHHHhcccee
Q 040477 142 RSEFSLLYKDGEENWRTVGDVPWTEFVESVKRL 174 (179)
Q Consensus 142 ~~~~~l~YeD~eGD~mLVGDvPW~~Fv~svkRL 174 (179)
-.+|..-|.+. .+..|.||+++++.+++|
T Consensus 97 ~~G~~ae~~~~----~i~T~a~~eev~~l~~~L 125 (190)
T PF09840_consen 97 LLGYKAEYRED----VIKTDAPLEEVVELAERL 125 (190)
T ss_pred hCCCeeEEeCC----eEEecCCHHHHHHHHHHH
Confidence 45788888554 888999999999999886
No 26
>PF12108 SF3a60_bindingd: Splicing factor SF3a60 binding domain; InterPro: IPR021966 This domain is found in eukaryotes. This domain is about 30 amino acids in length. This domain has a single completely conserved residue Y that may be functionally important. SF3a60 makes up the SF3a complex with SF3a66 and SF3a120. This domain is the binding site of SF3a60 for SF3a120. The SF3a complex is part of the spliceosome, a protein complex involved in splicing mRNA after transcription. ; PDB: 2DT7_A.
Probab=25.11 E-value=11 Score=22.80 Aligned_cols=17 Identities=35% Similarity=0.770 Sum_probs=11.5
Q ss_pred cCCCChHHHHhccceeE
Q 040477 159 VGDVPWTEFVESVKRLR 175 (179)
Q Consensus 159 VGDvPW~~Fv~svkRLr 175 (179)
-|..||++|-+-.|.||
T Consensus 4 s~~d~f~eFY~rlk~Ik 20 (28)
T PF12108_consen 4 SGGDPFSEFYERLKEIK 20 (28)
T ss_dssp -S--HHHHHHHHHHHHH
T ss_pred CCCChHHHHHHHHHHHH
Confidence 47889999988877664
No 27
>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=21.23 E-value=29 Score=22.02 Aligned_cols=12 Identities=25% Similarity=0.889 Sum_probs=8.8
Q ss_pred EEEEEeCCCCeE
Q 040477 146 SLLYKDGEENWR 157 (179)
Q Consensus 146 ~l~YeD~eGD~m 157 (179)
.++|.|.+|+|=
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 678999999983
No 28
>COG3816 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.30 E-value=61 Score=27.59 Aligned_cols=17 Identities=35% Similarity=0.552 Sum_probs=14.1
Q ss_pred ecCceeeeeeecCCCCChHHHHHHHHHHhcc
Q 040477 102 MDGVMVGRKICILDHCGYSSLACQLEDMFVP 132 (179)
Q Consensus 102 MdG~piGRKVDL~~~~sY~eL~~~Le~MF~~ 132 (179)
-.|.||||+ .|-++|+.
T Consensus 57 ylGTPIGR~--------------plVrLFSt 73 (205)
T COG3816 57 YLGTPIGRK--------------PLVRLFST 73 (205)
T ss_pred EecCccchH--------------HHHHHHHH
Confidence 369999997 78888986
Done!