Query psy8363
Match_columns 536
No_of_seqs 316 out of 1128
Neff 4.0
Searched_HMMs 46136
Date Fri Aug 16 16:46:06 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8363.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8363hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF09606 Med15: ARC105 or Med1 100.0 4E-106 8E-111 891.6 0.0 303 1-305 482-793 (799)
2 KOG4274|consensus 100.0 1.8E-80 4E-85 655.6 16.5 293 2-305 434-736 (742)
3 KOG3436|consensus 100.0 5.4E-41 1.2E-45 297.7 9.8 122 306-429 1-122 (123)
4 PF09606 Med15: ARC105 or Med1 100.0 2E-35 4.4E-40 328.8 0.0 115 422-536 649-765 (799)
5 KOG4274|consensus 99.9 2E-26 4.4E-31 245.8 8.1 111 420-536 595-708 (742)
6 PRK14549 50S ribosomal protein 99.8 1.3E-19 2.9E-24 149.0 7.8 68 306-373 1-68 (69)
7 CHL00154 rpl29 ribosomal prote 99.8 5.6E-19 1.2E-23 144.8 7.6 65 306-371 1-65 (67)
8 COG0255 RpmC Ribosomal protein 99.8 8.5E-19 1.8E-23 144.6 7.7 62 312-374 6-67 (69)
9 PRK00306 50S ribosomal protein 99.7 1.6E-17 3.5E-22 135.1 7.8 64 309-373 1-64 (66)
10 PF00831 Ribosomal_L29: Riboso 99.7 4.4E-17 9.5E-22 129.7 7.1 58 311-369 1-58 (58)
11 PRK00461 rpmC 50S ribosomal pr 99.7 5.4E-17 1.2E-21 139.2 8.2 65 310-375 1-65 (87)
12 cd00427 Ribosomal_L29_HIP Ribo 99.6 3.1E-16 6.7E-21 124.3 6.5 57 312-369 1-57 (57)
13 TIGR00012 L29 ribosomal protei 99.6 3.8E-16 8.2E-21 123.2 6.5 55 313-368 1-55 (55)
14 PF06984 MRP-L47: Mitochondria 95.5 0.043 9.3E-07 47.9 6.4 60 309-369 23-87 (87)
15 PF05773 RWD: RWD domain; Int 90.4 0.86 1.9E-05 38.7 6.3 92 187-280 5-104 (113)
16 KOG3331|consensus 89.8 1.2 2.6E-05 44.4 7.4 64 309-373 66-134 (213)
17 PF05773 RWD: RWD domain; Int 86.9 0.99 2.2E-05 38.3 4.4 86 445-532 4-96 (113)
18 KOG2391|consensus 77.5 30 0.00064 37.5 11.7 68 56-123 214-288 (365)
19 PF10666 Phage_Gp14: Phage pro 72.7 19 0.00042 34.0 7.8 70 312-383 57-136 (140)
20 smart00591 RWD domain in RING 66.6 18 0.0004 30.4 6.1 43 232-274 46-89 (107)
21 smart00591 RWD domain in RING 49.8 29 0.00063 29.2 4.5 39 490-528 45-84 (107)
22 PF12887 SICA_alpha: SICA extr 45.0 60 0.0013 31.7 6.3 80 279-368 2-91 (184)
23 PF09045 L27_2: L27_2; InterP 44.2 4.9 0.00011 33.1 -1.0 37 113-149 7-44 (58)
24 PF05743 UEV: UEV domain; Int 38.3 16 0.00034 33.4 1.2 20 230-249 51-70 (121)
25 PF00179 UQ_con: Ubiquitin-con 36.7 36 0.00077 30.9 3.2 19 231-249 49-67 (140)
26 PF06698 DUF1192: Protein of u 34.1 64 0.0014 26.7 3.9 30 312-341 16-45 (59)
27 smart00212 UBCc Ubiquitin-conj 33.8 37 0.00081 31.0 2.8 20 486-505 46-65 (145)
28 PHA03162 hypothetical protein; 33.7 1.6E+02 0.0034 28.2 6.8 53 315-378 11-63 (135)
29 PF04136 Sec34: Sec34-like fam 33.0 92 0.002 29.7 5.4 98 57-160 2-104 (157)
30 KOG4445|consensus 32.1 58 0.0013 35.0 4.2 97 187-284 3-103 (368)
31 smart00212 UBCc Ubiquitin-conj 31.2 55 0.0012 29.9 3.5 23 227-249 46-68 (145)
32 PRK11020 hypothetical protein; 29.9 1.6E+02 0.0034 27.6 6.0 52 348-408 29-80 (118)
33 COG5493 Uncharacterized conser 29.7 59 0.0013 33.0 3.6 52 318-369 47-107 (231)
34 PRK11546 zraP zinc resistance 28.9 2.5E+02 0.0055 27.0 7.5 55 319-379 63-117 (143)
35 PRK09413 IS2 repressor TnpA; R 24.7 1.9E+02 0.0041 26.0 5.7 39 319-360 73-111 (121)
36 PF07795 DUF1635: Protein of u 24.6 3.8E+02 0.0082 27.5 8.2 55 317-379 1-57 (214)
37 PF14712 Snapin_Pallidin: Snap 24.4 2.5E+02 0.0054 23.8 6.1 60 309-369 21-83 (92)
38 PF05743 UEV: UEV domain; Int 24.3 32 0.0007 31.4 0.7 47 457-505 14-67 (121)
39 KOG2525|consensus 24.0 52 0.0011 37.1 2.3 46 52-100 22-67 (496)
40 KOG0421|consensus 23.6 5.4E+02 0.012 25.2 8.6 132 180-333 26-172 (175)
41 PHA03155 hypothetical protein; 23.4 3E+02 0.0065 25.8 6.6 29 316-344 7-35 (115)
42 KOG4445|consensus 21.0 1E+02 0.0022 33.3 3.5 82 448-530 5-90 (368)
43 PRK06856 DNA polymerase III su 20.1 75 0.0016 29.6 2.2 13 513-525 49-61 (128)
44 COG5078 Ubiquitin-protein liga 20.0 5.3E+02 0.012 24.9 7.9 87 231-333 57-150 (153)
No 1
>PF09606 Med15: ARC105 or Med15 subunit of Mediator complex non-fungal; InterPro: IPR019087 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. The proteins in this entry represent subunit Med15 of the Mediator complex. They contain a single copy of the approximately 70 residue ARC105 domain. The ARC105 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, ARC105 is a critical transducer of gene activation signals that control early metazoan development []. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex; PDB: 2GUT_A.
Probab=100.00 E-value=3.6e-106 Score=891.58 Aligned_cols=303 Identities=52% Similarity=0.845 Sum_probs=0.0
Q ss_pred CCCCCC-CccCCCCCCCCCCCC--CCCcccccCCCCCCCCCCCCCCCCCCCCCCcccHHHHHHHHHHhhhchHHHHHHHH
Q psy8363 1 MVASPA-LVPSPSAPLSQSMPG--QMRSVGMAPSPSGSLNTPGQAQPTSSPCPTQEDQVYRDKIRQLSKYIEPLRRMIAR 77 (536)
Q Consensus 1 ~~~sp~-~~~sps~~~~~~~~~--~~~~~~~~pSPg~~lntP~~~~~sp~~~~~~eeq~Y~eKlrqLskYIePL~RMI~k 77 (536)
|+|||+ ++|||||++++++++ +++++ ++ |||++|||||+|++.+||+|+.||++|+||||||+||||||||||+|
T Consensus 482 ~~psP~~~~p~~spq~~q~~~~~r~~~~~-~v-spg~~~ntpg~~~~~~sP~~~~e~~~y~eK~~qLskYiePL~rmi~k 559 (799)
T PF09606_consen 482 MAPSPQSHVPSPSPQPSQSPQQQRTPGQF-SV-SPGGPLNTPGNPGSVMSPANPSEEQAYLEKLRQLSKYIEPLRRMINK 559 (799)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred CCCCchhhCCCCCCCcccCCCCCCCCCCC-CC-CCCCcCCCCCCcccCCCCCCchHHHHHHHHHHHhcccccHHHHHHHh
Confidence 689994 999999998865433 34455 57 99999999999988888889999999999999999999999999999
Q ss_pred hhcC--ChhhHHhHHHHHHHhcCCCCCcchhhHHhHHHHHhhhhccccccc--cccchHHHHHHHhhcCCCccccccccc
Q psy8363 78 AAND--DIEKTTKMKKLLEILQSPNKRMPLETLLKCEHVLEKLDFKHSSLL--RDHHPLLEAVSGALQSSNANHTLQRTF 153 (536)
Q Consensus 78 ~~~~--~~~~lsKmk~LldIL~np~kr~pL~TL~KCE~~LeKl~~~~~~~~--~~~~PLLdaV~ani~SP~~NHTL~RTF 153 (536)
|+|| +++||+|||+|||||+||+|||||+||+|||+|||||++++++.. ..|+||||||++||+||+|||||+|||
T Consensus 560 ~~~~~~~~~~l~kmk~ll~iL~~p~~r~pl~tL~kce~~l~kl~~~~~~~~~~p~~~pll~~v~~~l~sp~~nhtL~rtf 639 (799)
T PF09606_consen 560 MDKDEGRKKDLSKMKSLLDILSNPSKRCPLETLQKCEIVLEKLKNDMGVPTPPPMCQPLLDAVMSNLQSPVFNHTLQRTF 639 (799)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred cccCCCchhHHHhHHHHHHHhcCCccCCchHHHHHHHHHHHHhhcccCCCCCCCCCchHHHHHHhhcCCcccchhHHHHH
Confidence 9977 689999999999999999999999999999999999999998643 489999999999999999999999999
Q ss_pred cchhhhhcCCCCCCCCCCccccCCCCCC-CCchhhhhHHHhhccCCcccccCCCCCCCCCcEEEEEEecCCCCCCCCCeE
Q psy8363 154 GPCLEILSGPLIKDLPLPVNRKRVEEPA-DDVPEVLQGEIARLDQRFKVSLDPTQQSGSKAIQLVCWLDDRHLPCVPPIQ 232 (536)
Q Consensus 154 ~Pam~al~Gp~i~~~~~P~kr~~~ee~~-~~ip~vlQgEiarLd~kF~V~lDp~~~~~~~~i~LiC~LdDk~LP~VPPl~ 232 (536)
+|||++||||+|+++++|.||+|+||++ ++||+||||||||||+||+|+|||++++++|+||||||||||+|||||||+
T Consensus 640 ~p~~~~~~g~~~~~~~~~~k~~~~~~~~~~~ip~~lqgEva~Ld~kF~v~ldp~~~~~~~~v~Lic~Ldd~~LP~VPPl~ 719 (799)
T PF09606_consen 640 GPAMTALHGPPIKAPPPPPKKRRLEEDERQSIPNVLQGEVARLDPKFKVNLDPSHCSGNGSVHLICKLDDKNLPSVPPLR 719 (799)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred HHHHhhccCCCCCCCCCcchhcccchhhhhhhHHHHHHHHHHhcccceeecChhccCCCCeEEEEEEeCCCCCCCCCCee
Confidence 9999999999999988899998886654 999999999999999999999999999999999999999999999999999
Q ss_pred eecCCCCCCCCCccccC-CcCCCCchHHHHHHHHHHHHhhCCCcccHHHHHHHHHHHHHHHhcCCCCCCCCCCc
Q psy8363 233 VSIPEDYPSHPPRCTMG-HEHNTTPFLTSVKNALESRIKKLPLKYSVSQLLDTWEMSVRQACAPTRNPTSSPSI 305 (536)
Q Consensus 233 v~vP~dYP~~sP~~~~~-~~y~~t~FL~~v~~~~~sRL~~lP~~~SvT~lL~tWe~SvrQac~~~~~~~ap~t~ 305 (536)
|+||+|||++||.|.++ |+|++++||.+|+++|++||++||++||||+|||||||||||||++..+..++++.
T Consensus 720 l~vP~~YP~~sp~~~~~~~~y~~~~Fl~~v~~~~~~Rl~~lP~~~svt~lL~tWe~svrqa~~~~~~~~~~~~~ 793 (799)
T PF09606_consen 720 LTVPADYPRQSPQCSVDRDEYDATPFLQDVQNALTSRLAKLPDKHSVTQLLNTWEMSVRQACAPNQSSVAPSTF 793 (799)
T ss_dssp --------------------------------------------------------------------------
T ss_pred EeCCCCCCccCCcCcccHHHhccChHHHHHHHHHHHHHHhCCCceeHHHHHHHHHHHHHHHHhhhccccccccc
Confidence 99999999999999988 99999999999999999999999999999999999999999999999999999883
No 2
>KOG4274|consensus
Probab=100.00 E-value=1.8e-80 Score=655.62 Aligned_cols=293 Identities=41% Similarity=0.618 Sum_probs=262.3
Q ss_pred CCCCC-CccCCCCCCCCCCCC--CCCcccccCCCCCCCCCCCCCCC--CCCCCCCcccHHHHHHHHHHhhhchHHHHHHH
Q psy8363 2 VASPA-LVPSPSAPLSQSMPG--QMRSVGMAPSPSGSLNTPGQAQP--TSSPCPTQEDQVYRDKIRQLSKYIEPLRRMIA 76 (536)
Q Consensus 2 ~~sp~-~~~sps~~~~~~~~~--~~~~~~~~pSPg~~lntP~~~~~--sp~~~~~~eeq~Y~eKlrqLskYIePL~RMI~ 76 (536)
+|||. |.|||+++|++++.- .+.+--.+|++| ++|||++|+. ++++.++.||++|+||++||+||||||+|||+
T Consensus 434 ~P~P~~~~Psp~~qp~~sP~~mqm~q~p~~~~qq~-p~~~~~~P~~vm~~~g~~~~ee~~Yr~k~kql~kyiepl~rm~a 512 (742)
T KOG4274|consen 434 APSPSSFLPSPSPQPSQSPVTMQMPQNPFSVPQQG-PLNTPVNPSSVMSPAGSSQAEEQQYRDKLKQLSKYIEPLRRMIA 512 (742)
T ss_pred CCCCCCCCCCCCCCccCCCchhccCCCCcccCCCC-cccCCcChhhhcccCCCCchhHHHHHHHhhccccccchhHhhhc
Confidence 56777 778887777655431 222322468888 5899999875 88888999999999999999999999999999
Q ss_pred HhhcC--ChhhHHhHHHHHHHhcCCCCCcchhhHHhHHHHHhhhhccccccccccchHHHHHHHhhcCCCcccccccccc
Q psy8363 77 RAAND--DIEKTTKMKKLLEILQSPNKRMPLETLLKCEHVLEKLDFKHSSLLRDHHPLLEAVSGALQSSNANHTLQRTFG 154 (536)
Q Consensus 77 k~~~~--~~~~lsKmk~LldIL~np~kr~pL~TL~KCE~~LeKl~~~~~~~~~~~~PLLdaV~ani~SP~~NHTL~RTF~ 154 (536)
+|+|+ ++++++||++|||||+||++||||+||+|||+||||+++++++. +-.-||| |.++++||+|||+|||||.
T Consensus 513 ki~n~~~~~~~m~km~~ll~Il~dp~~r~pl~tl~kce~Alek~~~~~~~~-k~~~P~~--i~s~~~spv~nh~lYrtF~ 589 (742)
T KOG4274|consen 513 KIDNNEDRKKDMSKMKSLLDILTDPSKRCPLKTLQKCEIALEKLKNDMPNP-KMGTPLL--IGSMGGSPVLNHLLYRTFL 589 (742)
T ss_pred cCCCcHHHHhhhhhccCccccccCccccCchhhhccccccHhhccCCCCCC-CCCCccc--cccccCCCcccchhhhhcc
Confidence 99988 57999999999999999999999999999999999999999876 3456888 9999999999999999999
Q ss_pred chhhhhcCCCCCCCCCCccccCCCC--CCCCchhhhhHHHhhccCCcccccCCCCCCCCCcEEEEEEecCCCCCCCCCeE
Q psy8363 155 PCLEILSGPLIKDLPLPVNRKRVEE--PADDVPEVLQGEIARLDQRFKVSLDPTQQSGSKAIQLVCWLDDRHLPCVPPIQ 232 (536)
Q Consensus 155 Pam~al~Gp~i~~~~~P~kr~~~ee--~~~~ip~vlQgEiarLd~kF~V~lDp~~~~~~~~i~LiC~LdDk~LP~VPPl~ 232 (536)
|+++.|||++|++ +++.+|.+.+| .+++||++|||||||||.||+|+||..+|.+| +|+|||+||||.|| ||+
T Consensus 590 P~~t~i~g~~iTa-pV~~~~~r~~e~~~rq~lp~vlqgElarLD~kF~v~ld~~~~~nN-~I~liCklddk~lP---Pl~ 664 (742)
T KOG4274|consen 590 PNPTPIDGLQITA-PVGANSMRAGEPVQRQNLPEVLQGELARLDAKFEVDLDHQRHDNN-HIILICKLDDKQLP---PLR 664 (742)
T ss_pred CCCccccCCCccc-ccccccCCCCCchhhhhhhHHHHHHHHhhccceeecCCcccccCC-eeEEEEEecCCCCC---Cee
Confidence 9999999999998 66666655533 56899999999999999999999999999999 99999999999988 699
Q ss_pred eecCCCCCCCCCccccC-CcCCCCchHHHHHHHHHHHHhhCCCcccHHHHHHHHHHHHHHHhcCCCCCCCCCCc
Q psy8363 233 VSIPEDYPSHPPRCTMG-HEHNTTPFLTSVKNALESRIKKLPLKYSVSQLLDTWEMSVRQACAPTRNPTSSPSI 305 (536)
Q Consensus 233 v~vP~dYP~~sP~~~~~-~~y~~t~FL~~v~~~~~sRL~~lP~~~SvT~lL~tWe~SvrQac~~~~~~~ap~t~ 305 (536)
|+||++||+++ .|+++ |.|++++||++|++++.+||.+ |+.||||+||||||++|+|||...+....-|..
T Consensus 665 lsVP~~YPaq~-~~vdr~~~y~a~pflq~vq~s~~~Rlsr-P~~~Sit~lLntWe~~V~Qac~~~sggldVafn 736 (742)
T KOG4274|consen 665 LSVPTTYPAQN-VTVDRAVIYLAAPFLQDVQNSVYERLSR-PGLSSITDLLNTWEEQVNQACNQTSGGLDVAFN 736 (742)
T ss_pred eeccccccccc-hhhhhHHHhhhcHHHHHHHHHHHHHHcc-CCcchHHHHHHHHHHHHHHHhcccccceehhhh
Confidence 99999999999 99999 9999999999999999999999 999999999999999999999999887665543
No 3
>KOG3436|consensus
Probab=100.00 E-value=5.4e-41 Score=297.68 Aligned_cols=122 Identities=61% Similarity=0.825 Sum_probs=119.2
Q ss_pred cccccchhhhcCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCchhHHHHhhhHHHHHHHHhHHHHHHHHHHHHhccCcc
Q psy8363 306 SVKVKCSELRTKDKKELLKQLEELKTELANLRVAKVTGGAASKLSKIRVVRKAILRVYIVMHQKQKENMRNLIRKEHKKY 385 (536)
Q Consensus 306 m~kmKa~ELR~kS~eEL~kqL~eLK~EL~~LR~qkvtG~al~k~skIr~vRK~IARVlTVlnqkqr~~lr~~yk~k~kk~ 385 (536)
|+++|+.|||++++|||.+||+|||.||++|||++++||+.+++++|+++||+|||||||+||++++++|+||+ |+||
T Consensus 1 M~kik~~eLr~~~ke~L~~ql~dLK~ELa~LRv~K~tgg~~~klskik~vrKsiArvLTVine~~k~~lr~~yk--~~k~ 78 (123)
T KOG3436|consen 1 MAKIKARELRGKSKEQLLKQLDDLKVELAQLRVAKVTGGAASKLSKIKVVRKSIARVLTVINEKQKEELREAYK--GKKY 78 (123)
T ss_pred CcchhHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHhhccchhhhHHHHHHHHHHHHHHHHhhhhhHHHHHHHhh--cccc
Confidence 77899999999999999999999999999999999999988999999999999999999999999999999996 9999
Q ss_pred CCCCCCchhhHHHHhhcChhHHhhhhHHHHHHhhcCCCCcccCC
Q psy8363 386 KPLDLRPKKTRALRRRLTKHERKLKTLKEIRRRQAFPPRKDLPL 429 (536)
Q Consensus 386 ~PlDLRpKkTRA~Rr~Ltk~e~~~kt~kq~kk~~~fp~rk~~p~ 429 (536)
+|+|||||+||||||+||+||.+++|.||++|+++||.|+|+..
T Consensus 79 ~p~dLr~KktRa~rr~ltk~~~slkt~kq~~k~~~~p~rk~A~k 122 (123)
T KOG3436|consen 79 LPKDLRPKKTRAIRRRLTKHQLSLKTEKQQAKERLFPLRKYAVK 122 (123)
T ss_pred cchhhhHHHHHHHHHhccccchhHhHHHHHHHHHhchHHHhhcc
Confidence 99999999999999999999999999999999999999999764
No 4
>PF09606 Med15: ARC105 or Med15 subunit of Mediator complex non-fungal; InterPro: IPR019087 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. The proteins in this entry represent subunit Med15 of the Mediator complex. They contain a single copy of the approximately 70 residue ARC105 domain. The ARC105 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, ARC105 is a critical transducer of gene activation signals that control early metazoan development []. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex; PDB: 2GUT_A.
Probab=100.00 E-value=2e-35 Score=328.82 Aligned_cols=115 Identities=50% Similarity=0.948 Sum_probs=0.0
Q ss_pred CCCcccCCCCCcccc-CCCCCCchhhhhhhhhhcccccccccCccCCCCCCcEEEEEeecCCCCCCCCCceeecCCCCCC
Q psy8363 422 PPRKDLPLPVNRKRV-EEPADDVPEVLQGEIARLDQRFKVSLDPTQQSGSKAIQLVCWLDDRHLPCVPPIQVSIPEDYPS 500 (536)
Q Consensus 422 p~rk~~p~p~~~~~~-~~~~~~ip~vlqgEiArLd~kF~V~ld~~~~s~~~~v~LiC~LdDk~LP~vPpi~v~vP~dYP~ 500 (536)
|.+++.+.+.||+|. |+++++|||||||||||||+||+|+|||++++++|+||||||||||+|||||||+|+||+|||+
T Consensus 649 ~~~~~~~~~~k~~~~~~~~~~~ip~~lqgEva~Ld~kF~v~ldp~~~~~~~~v~Lic~Ldd~~LP~VPPl~l~vP~~YP~ 728 (799)
T PF09606_consen 649 PPIKAPPPPPKKRRLEEDERQSIPNVLQGEVARLDPKFKVNLDPSHCSGNGSVHLICKLDDKNLPSVPPLRLTVPADYPR 728 (799)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred CCCCCCCCcchhcccchhhhhhhHHHHHHHHHHhcccceeecChhccCCCCeEEEEEEeCCCCCCCCCCeeEeCCCCCCc
Confidence 455565656666665 5566999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCc-cCccCCCCchHHHHHHHHHHHHhhCCCCCC
Q psy8363 501 HPPRCT-MGHEHNTTPFLTSVKNALESRIKKLPLKYS 536 (536)
Q Consensus 501 ~sp~~~-~~~~Y~a~pFl~~v~~~l~srl~~lP~~~s 536 (536)
+||.|. .+++|++|+||.+|+++|++||++|||+||
T Consensus 729 ~sp~~~~~~~~y~~~~Fl~~v~~~~~~Rl~~lP~~~s 765 (799)
T PF09606_consen 729 QSPQCSVDRDEYDATPFLQDVQNALTSRLAKLPDKHS 765 (799)
T ss_dssp -------------------------------------
T ss_pred cCCcCcccHHHhccChHHHHHHHHHHHHHHhCCCcee
Confidence 999998 469999999999999999999999999997
No 5
>KOG4274|consensus
Probab=99.93 E-value=2e-26 Score=245.82 Aligned_cols=111 Identities=37% Similarity=0.632 Sum_probs=102.2
Q ss_pred cCCCCcccCCCCCccccCCC--CCCchhhhhhhhhhcccccccccCccCCCCCCcEEEEEeecCCCCCCCCCceeecCCC
Q psy8363 420 AFPPRKDLPLPVNRKRVEEP--ADDVPEVLQGEIARLDQRFKVSLDPTQQSGSKAIQLVCWLDDRHLPCVPPIQVSIPED 497 (536)
Q Consensus 420 ~fp~rk~~p~p~~~~~~~~~--~~~ip~vlqgEiArLd~kF~V~ld~~~~s~~~~v~LiC~LdDk~LP~vPpi~v~vP~d 497 (536)
.|...-.+|++++|+|.+|. +++||+||||||||||.||+|+||.++|++| +|+|||+||||.|| ||+|+||++
T Consensus 595 i~g~~iTapV~~~~~r~~e~~~rq~lp~vlqgElarLD~kF~v~ld~~~~~nN-~I~liCklddk~lP---Pl~lsVP~~ 670 (742)
T KOG4274|consen 595 IDGLQITAPVGANSMRAGEPVQRQNLPEVLQGELARLDAKFEVDLDHQRHDNN-HIILICKLDDKQLP---PLRLSVPTT 670 (742)
T ss_pred ccCCCcccccccccCCCCCchhhhhhhHHHHHHHHhhccceeecCCcccccCC-eeEEEEEecCCCCC---Ceeeecccc
Confidence 34555567888999998544 7999999999999999999999999999999 99999999999999 599999999
Q ss_pred CCCCCCCCcc-CccCCCCchHHHHHHHHHHHHhhCCCCCC
Q psy8363 498 YPSHPPRCTM-GHEHNTTPFLTSVKNALESRIKKLPLKYS 536 (536)
Q Consensus 498 YP~~sp~~~~-~~~Y~a~pFl~~v~~~l~srl~~lP~~~s 536 (536)
||+++ .|+. .++|.++|||++|++++.+||.+ |++||
T Consensus 671 YPaq~-~~vdr~~~y~a~pflq~vq~s~~~Rlsr-P~~~S 708 (742)
T KOG4274|consen 671 YPAQN-VTVDRAVIYLAAPFLQDVQNSVYERLSR-PGLSS 708 (742)
T ss_pred ccccc-hhhhhHHHhhhcHHHHHHHHHHHHHHcc-CCcch
Confidence 99999 8985 59999999999999999999999 99997
No 6
>PRK14549 50S ribosomal protein L29P; Provisional
Probab=99.80 E-value=1.3e-19 Score=149.02 Aligned_cols=68 Identities=32% Similarity=0.499 Sum_probs=64.7
Q ss_pred cccccchhhhcCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCchhHHHHhhhHHHHHHHHhHHHHHH
Q psy8363 306 SVKVKCSELRTKDKKELLKQLEELKTELANLRVAKVTGGAASKLSKIRVVRKAILRVYIVMHQKQKEN 373 (536)
Q Consensus 306 m~kmKa~ELR~kS~eEL~kqL~eLK~EL~~LR~qkvtG~al~k~skIr~vRK~IARVlTVlnqkqr~~ 373 (536)
|+.||++|||++|.+||.++|.++++|||+|||++++|+.++|+|+|+.+||+||||+||++|++++.
T Consensus 1 M~~mk~~elr~ls~~eL~~~l~elk~eLf~LR~q~~~~~~l~n~~~ir~~Rk~IARi~Tvl~ek~~~~ 68 (69)
T PRK14549 1 MAILRASEIREMSPEEREEKLEELKLELLKERAQAAMGGAPENPGRIREIRRTIARILTIQREKKREA 68 (69)
T ss_pred CCcCcHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHhCcCccccHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 56799999999999999999999999999999999999988999999999999999999999998653
No 7
>CHL00154 rpl29 ribosomal protein L29; Validated
Probab=99.77 E-value=5.6e-19 Score=144.80 Aligned_cols=65 Identities=17% Similarity=0.218 Sum_probs=61.9
Q ss_pred cccccchhhhcCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCchhHHHHhhhHHHHHHHHhHHHH
Q psy8363 306 SVKVKCSELRTKDKKELLKQLEELKTELANLRVAKVTGGAASKLSKIRVVRKAILRVYIVMHQKQK 371 (536)
Q Consensus 306 m~kmKa~ELR~kS~eEL~kqL~eLK~EL~~LR~qkvtG~al~k~skIr~vRK~IARVlTVlnqkqr 371 (536)
|+.||+.|||++|.+||.++|.++++|||+||||+++|+ ++|+|+|+.+||+||||+||++|+.+
T Consensus 1 M~~mk~~elr~ls~~eL~~~l~elk~elf~LRfq~atgq-l~n~~~ir~~RrdIARikTil~ek~~ 65 (67)
T CHL00154 1 MSLPKITDIIDLTDSEISEEIIKTKKELFDLRLKKATRQ-NFKPHLFKHKKHRLAQLLTLLSSRLK 65 (67)
T ss_pred CCCCCHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHhCc-ccChHHHHHHHHHHHHHHHHHHHHhc
Confidence 556999999999999999999999999999999999999 99999999999999999999999753
No 8
>COG0255 RpmC Ribosomal protein L29 [Translation, ribosomal structure and biogenesis]
Probab=99.77 E-value=8.5e-19 Score=144.56 Aligned_cols=62 Identities=42% Similarity=0.557 Sum_probs=59.0
Q ss_pred hhhhcCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCchhHHHHhhhHHHHHHHHhHHHHHHH
Q psy8363 312 SELRTKDKKELLKQLEELKTELANLRVAKVTGGAASKLSKIRVVRKAILRVYIVMHQKQKENM 374 (536)
Q Consensus 312 ~ELR~kS~eEL~kqL~eLK~EL~~LR~qkvtG~al~k~skIr~vRK~IARVlTVlnqkqr~~l 374 (536)
+|||+||.+||.++|.+||+|||+||||+++|+ ++|+|+|+.|||+||||+||++|+++...
T Consensus 6 ~elR~~s~eeL~~~l~eLK~ELf~LR~q~a~g~-l~n~~~ir~vRr~IARi~Tv~~E~~~~~~ 67 (69)
T COG0255 6 KELREKSVEELEEELRELKKELFNLRFQLATGQ-LENPHRIREVRRDIARILTVLREKELEAA 67 (69)
T ss_pred HHHHhCCHHHHHHHHHHHHHHHHHHHHHHHhCC-CCCcHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 499999999999999999999999999999999 79999999999999999999999987543
No 9
>PRK00306 50S ribosomal protein L29; Reviewed
Probab=99.71 E-value=1.6e-17 Score=135.13 Aligned_cols=64 Identities=38% Similarity=0.515 Sum_probs=61.3
Q ss_pred ccchhhhcCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCchhHHHHhhhHHHHHHHHhHHHHHH
Q psy8363 309 VKCSELRTKDKKELLKQLEELKTELANLRVAKVTGGAASKLSKIRVVRKAILRVYIVMHQKQKEN 373 (536)
Q Consensus 309 mKa~ELR~kS~eEL~kqL~eLK~EL~~LR~qkvtG~al~k~skIr~vRK~IARVlTVlnqkqr~~ 373 (536)
||+.|||++|.+||.++|.++++|||+|||++++|+ ++|+|+|+.+||+||||+||++|++.+.
T Consensus 1 Mk~~elr~ls~~eL~~~l~~lkkeL~~lR~~~~~~~-~~n~~~i~~~rk~IARi~Tvl~er~~~~ 64 (66)
T PRK00306 1 MKAKELRELSVEELNEKLLELKKELFNLRFQKATGQ-LENTHRLREVRRDIARIKTVLRERELGA 64 (66)
T ss_pred CCHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHhCC-CcCcHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 789999999999999999999999999999999999 8999999999999999999999998653
No 10
>PF00831 Ribosomal_L29: Ribosomal L29 protein; InterPro: IPR001854 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L29 is one of the proteins from the large ribosomal subunit. L29 belongs to a family of ribosomal proteins of 63 to 138 amino-acid residues which, on the basis of sequence similarities [], groups: Red algal L29. Bacterial L29. Mammalian L35 Caenorhabditis elegans L35 (ZK652.4). Yeast L35. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1VSP_W 3MS1_Y 3MRZ_Y 3F1H_2 3PYT_Y 3PYO_Y 3D5D_2 3D5B_2 3PYR_Y 1VSA_W ....
Probab=99.69 E-value=4.4e-17 Score=129.67 Aligned_cols=58 Identities=41% Similarity=0.618 Sum_probs=56.4
Q ss_pred chhhhcCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCchhHHHHhhhHHHHHHHHhHH
Q psy8363 311 CSELRTKDKKELLKQLEELKTELANLRVAKVTGGAASKLSKIRVVRKAILRVYIVMHQK 369 (536)
Q Consensus 311 a~ELR~kS~eEL~kqL~eLK~EL~~LR~qkvtG~al~k~skIr~vRK~IARVlTVlnqk 369 (536)
++|||+||.+||.++|.++++|||+|||++++|+ ++|+++|+.+||+||||+||++|+
T Consensus 1 ~~elr~ls~~eL~~~l~elk~eL~~Lr~q~~~~~-l~n~~~ir~~Rr~IARi~Tvl~er 58 (58)
T PF00831_consen 1 AKELRELSDEELQEKLEELKKELFNLRFQKATGQ-LENPHRIREIRRDIARILTVLRER 58 (58)
T ss_dssp CHHHCHSHHHHHHHHHHHHHHHHHHHHHHHHHSS-SSCCHHHHHHHHHHHHHHHHHHHH
T ss_pred CHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHhcc-cccccHHHHHHHHHHHHHHHHhcC
Confidence 5799999999999999999999999999999999 799999999999999999999986
No 11
>PRK00461 rpmC 50S ribosomal protein L29; Reviewed
Probab=99.69 E-value=5.4e-17 Score=139.23 Aligned_cols=65 Identities=35% Similarity=0.498 Sum_probs=61.4
Q ss_pred cchhhhcCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCchhHHHHhhhHHHHHHHHhHHHHHHHH
Q psy8363 310 KCSELRTKDKKELLKQLEELKTELANLRVAKVTGGAASKLSKIRVVRKAILRVYIVMHQKQKENMR 375 (536)
Q Consensus 310 Ka~ELR~kS~eEL~kqL~eLK~EL~~LR~qkvtG~al~k~skIr~vRK~IARVlTVlnqkqr~~lr 375 (536)
+++|||+||.+||.++|.++++|||+|||++++|+ ++|+|+|+.+||+||||+||++|+++++.-
T Consensus 1 ~~~elR~lS~eEL~e~L~elkkELf~LR~q~atgq-l~n~~~ir~iRR~IARilTvl~Ek~~~~~~ 65 (87)
T PRK00461 1 LFKELRKKSVEELEKLVIELKAELFTLRFKNATGS-LDQTHKIKEIRKDIARILTILNERELEEKE 65 (87)
T ss_pred ChHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHhCc-ccccHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 46899999999999999999999999999999998 899999999999999999999999887653
No 12
>cd00427 Ribosomal_L29_HIP Ribosomal L29 protein/HIP. L29 is a protein of the large ribosomal Subunit. A homolog, called heparin/heparan sulfate interacting protein (HIP), has also been identified in mammals. L29 is located on the surface of the large ribosomal subunit, where it participates in forming a protein ring that surrounds the polypeptide exit channel, providing structural support for the ribosome. L29 is involved in forming the translocon binding site, along with L19, L22, L23, L24, and L31e. In addition, L29 and L23 form the interaction site for trigger factor (TF) on the ribosomal surface, adjacent to the exit tunnel. L29 forms numerous interactions with L23 and with the 23S rRNA. In some eukaryotes, L29 is referred to as L35, which is distinct from L35 found in bacteria and some eukaryotes (primarily plastids and mitochondria). The mammalian homolog, HIP, is found on the surface of many tissues and cell lines. It is believed to play a role in cell adhesion and modulat
Probab=99.64 E-value=3.1e-16 Score=124.33 Aligned_cols=57 Identities=47% Similarity=0.651 Sum_probs=55.1
Q ss_pred hhhhcCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCchhHHHHhhhHHHHHHHHhHH
Q psy8363 312 SELRTKDKKELLKQLEELKTELANLRVAKVTGGAASKLSKIRVVRKAILRVYIVMHQK 369 (536)
Q Consensus 312 ~ELR~kS~eEL~kqL~eLK~EL~~LR~qkvtG~al~k~skIr~vRK~IARVlTVlnqk 369 (536)
.|||++|.+||.++|.++++|||+|||++++|+ ++|+|+|+.+||+||||+||++|+
T Consensus 1 ~eir~ls~~eL~~~l~~l~~elf~Lr~q~~~~~-~~~~~~~~~~Rr~IARi~Til~er 57 (57)
T cd00427 1 KELREKSDEELQEKLDELKKELFNLRFQKATGQ-LENPHRIRKVRKDIARIKTVLNEK 57 (57)
T ss_pred ChHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCC-CcCcHHHHHHHHHHHHHHHHHHcC
Confidence 489999999999999999999999999999999 899999999999999999999984
No 13
>TIGR00012 L29 ribosomal protein L29. called L29 in prokaryotic (50S) large subunits and L35 in eukaryotic (60S) large subunits.
Probab=99.63 E-value=3.8e-16 Score=123.22 Aligned_cols=55 Identities=49% Similarity=0.687 Sum_probs=53.4
Q ss_pred hhhcCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCchhHHHHhhhHHHHHHHHhH
Q psy8363 313 ELRTKDKKELLKQLEELKTELANLRVAKVTGGAASKLSKIRVVRKAILRVYIVMHQ 368 (536)
Q Consensus 313 ELR~kS~eEL~kqL~eLK~EL~~LR~qkvtG~al~k~skIr~vRK~IARVlTVlnq 368 (536)
|||++|.+||.++|.++++|||+|||++++|+ ++|+|+|+.+||+||||+||++|
T Consensus 1 elr~~s~~EL~~~l~~lr~eLf~Lr~~~~~~~-~~~~~~i~~~Rk~IARi~Tvl~e 55 (55)
T TIGR00012 1 ELREKSKEELAKKLDELKKELFELRFQKATGQ-LAKPHRIRQVRRDIARLLTVLRE 55 (55)
T ss_pred CHhhCCHHHHHHHHHHHHHHHHHHHHHHHhCC-cccchHHHHHHHHHHHHHHHHhC
Confidence 69999999999999999999999999999999 79999999999999999999985
No 14
>PF06984 MRP-L47: Mitochondrial 39-S ribosomal protein L47 (MRP-L47); InterPro: IPR010729 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents the N-terminal region (approximately 8 residues) of the eukaryotic mitochondrial 39-S ribosomal protein L47 (MRP-L47). Mitochondrial ribosomal proteins (MRPs) are the counterparts of the cytoplasmic ribosomal proteins, in that they fulfil similar functions in protein biosynthesis. However, they are distinct in number, features and primary structure [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005761 mitochondrial ribosome
Probab=95.46 E-value=0.043 Score=47.91 Aligned_cols=60 Identities=27% Similarity=0.356 Sum_probs=40.9
Q ss_pred ccchhhhcCCHHHHHHH----HHHHHHHHHH-HHHHHHhcCCCCCchhHHHHhhhHHHHHHHHhHH
Q psy8363 309 VKCSELRTKDKKELLKQ----LEELKTELAN-LRVAKVTGGAASKLSKIRVVRKAILRVYIVMHQK 369 (536)
Q Consensus 309 mKa~ELR~kS~eEL~kq----L~eLK~EL~~-LR~qkvtG~al~k~skIr~vRK~IARVlTVlnqk 369 (536)
-.+.|||.||-+||.+. |.| +.-|.. --.....+....++.+++.||++-+||++|++||
T Consensus 23 Wt~~ELR~KS~eDLHkLWyv~lKE-RN~L~T~~~e~~r~~~~~~~~~r~~kV~~sM~~Ik~Vl~ER 87 (87)
T PF06984_consen 23 WTAEELRRKSFEDLHKLWYVCLKE-RNMLLTEEYEARRQGEGMPSPERLEKVRKSMARIKHVLTER 87 (87)
T ss_pred ccHHHHHccCHHHHHHHHHHHHHH-HHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHHHHHhcC
Confidence 56799999999999882 322 222211 1111112222468999999999999999999985
No 15
>PF05773 RWD: RWD domain; InterPro: IPR006575 The RWD eukaryotic domain is found in RING finger (IPR001841 from INTERPRO) and WD repeat (IPR001680 from INTERPRO) containing proteins and DEXDc-like helicase (IPR001410 from INTERPRO) subfamily related to the ubiquitin-conjugating enzymes domain (IPR000608 from INTERPRO). ; GO: 0005515 protein binding; PDB: 2EBM_A 2EBK_A 2DAX_A 2DAW_A 2DAY_A 2DMF_A 1UKX_A 2YZ0_A.
Probab=90.39 E-value=0.86 Score=38.70 Aligned_cols=92 Identities=16% Similarity=0.277 Sum_probs=52.3
Q ss_pred hhhHHHhhccCCcccccCCCCCCCCCcEEEEEEe----cCCCCCCCCCeE--eecCCCCCCCCCccccCCcCCC-CchHH
Q psy8363 187 VLQGEIARLDQRFKVSLDPTQQSGSKAIQLVCWL----DDRHLPCVPPIQ--VSIPEDYPSHPPRCTMGHEHNT-TPFLT 259 (536)
Q Consensus 187 vlQgEiarLd~kF~V~lDp~~~~~~~~i~LiC~L----dDk~LP~VPPl~--v~vP~dYP~~sP~~~~~~~y~~-t~FL~ 259 (536)
..+.||..|..=|.=.. ......+..++.+.| .+.....-+.+. +.+|.+||.++|.+........ .....
T Consensus 5 ~~~~EieaL~sIy~~~~--~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~~p~~YP~~~P~i~l~~~~~~~~~~~~ 82 (113)
T PF05773_consen 5 QQEEEIEALQSIYPDDF--IEIESKSPPSLEVKLDESSSSFESSSFPSVTLHFTLPPGYPESPPKISLESPKNSRNEQIE 82 (113)
T ss_dssp HHHHHHHHHHHHSSSSE--SSSTSSSSEEEEEEE--CEECCTTTTSEEEEEEEEE-SSTTSS--EEEEEEESSSHCHHHH
T ss_pred HHHHHHHHHHHHcCCCc--cccccCCCCceeeeecccccccccccceeEEEEEeCCCcCCCcCCEEEEEcCCCCCHHHHH
Confidence 45567777766554443 222334444445554 233334444544 4589999999999877633333 37778
Q ss_pred HHHHHHHHHHhhCC-CcccHHH
Q psy8363 260 SVKNALESRIKKLP-LKYSVSQ 280 (536)
Q Consensus 260 ~v~~~~~sRL~~lP-~~~SvT~ 280 (536)
.+.+.+...+..+- +..-|-+
T Consensus 83 ~l~~~l~~~~~~~~~G~~~i~~ 104 (113)
T PF05773_consen 83 KLNKELEQIAEENRQGEPCIFQ 104 (113)
T ss_dssp HHHHHHHHHHHHSTTTS-CHHH
T ss_pred HHHHHHHHHHHHhCCCcCHHHH
Confidence 88888888888876 6433333
No 16
>KOG3331|consensus
Probab=89.80 E-value=1.2 Score=44.36 Aligned_cols=64 Identities=23% Similarity=0.304 Sum_probs=47.6
Q ss_pred ccchhhhcCCHHHHHHHHHHH---HHHHHHHHH--HHHhcCCCCCchhHHHHhhhHHHHHHHHhHHHHHH
Q psy8363 309 VKCSELRTKDKKELLKQLEEL---KTELANLRV--AKVTGGAASKLSKIRVVRKAILRVYIVMHQKQKEN 373 (536)
Q Consensus 309 mKa~ELR~kS~eEL~kqL~eL---K~EL~~LR~--qkvtG~al~k~skIr~vRK~IARVlTVlnqkqr~~ 373 (536)
-++.|||=||-.||.+.-=.+ +.-|+..|- +...|. ..|+-+|-.||++.+||.+|++||+++-
T Consensus 66 W~aeELR~KS~nDLH~LWYvcLkErNmL~T~~~~~k~~~~~-~PnpERi~kV~~TM~~I~~Vl~ER~~Ay 134 (213)
T KOG3331|consen 66 WSAEELRLKSFNDLHKLWYVCLKERNMLATMRHELKNIVGS-FPNPERIDKVRTTMWRIEHVLNERNLAY 134 (213)
T ss_pred cchHHHhcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-CCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 568999999999998763322 233443332 233455 6889999999999999999999998753
No 17
>PF05773 RWD: RWD domain; InterPro: IPR006575 The RWD eukaryotic domain is found in RING finger (IPR001841 from INTERPRO) and WD repeat (IPR001680 from INTERPRO) containing proteins and DEXDc-like helicase (IPR001410 from INTERPRO) subfamily related to the ubiquitin-conjugating enzymes domain (IPR000608 from INTERPRO). ; GO: 0005515 protein binding; PDB: 2EBM_A 2EBK_A 2DAX_A 2DAW_A 2DAY_A 2DMF_A 1UKX_A 2YZ0_A.
Probab=86.90 E-value=0.99 Score=38.33 Aligned_cols=86 Identities=17% Similarity=0.322 Sum_probs=50.3
Q ss_pred hhhhhhhhhcccccccccCccCCCCCCcEEEEEee----cCCCCCCCC--CceeecCCCCCCCCCCCccCccCCCC-chH
Q psy8363 445 EVLQGEIARLDQRFKVSLDPTQQSGSKAIQLVCWL----DDRHLPCVP--PIQVSIPEDYPSHPPRCTMGHEHNTT-PFL 517 (536)
Q Consensus 445 ~vlqgEiArLd~kF~V~ld~~~~s~~~~v~LiC~L----dDk~LP~vP--pi~v~vP~dYP~~sp~~~~~~~Y~a~-pFl 517 (536)
+..+-||.-|.+=|--.. ......+..++.+.+ .+.....-+ -|.|.+|.+||.++|.+......+.. ...
T Consensus 4 e~~~~EieaL~sIy~~~~--~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~~p~~YP~~~P~i~l~~~~~~~~~~~ 81 (113)
T PF05773_consen 4 EQQEEEIEALQSIYPDDF--IEIESKSPPSLEVKLDESSSSFESSSFPSVTLHFTLPPGYPESPPKISLESPKNSRNEQI 81 (113)
T ss_dssp HHHHHHHHHHHHHSSSSE--SSSTSSSSEEEEEEE--CEECCTTTTSEEEEEEEEE-SSTTSS--EEEEEEESSSHCHHH
T ss_pred HHHHHHHHHHHHHcCCCc--cccccCCCCceeeeecccccccccccceeEEEEEeCCCcCCCcCCEEEEEcCCCCCHHHH
Confidence 346678888877776555 222334445555555 222222222 35678899999999998755444443 777
Q ss_pred HHHHHHHHHHHhhCC
Q psy8363 518 TSVKNALESRIKKLP 532 (536)
Q Consensus 518 ~~v~~~l~srl~~lP 532 (536)
..+.+.|...+..+-
T Consensus 82 ~~l~~~l~~~~~~~~ 96 (113)
T PF05773_consen 82 EKLNKELEQIAEENR 96 (113)
T ss_dssp HHHHHHHHHHHHHST
T ss_pred HHHHHHHHHHHHHhC
Confidence 788777777666553
No 18
>KOG2391|consensus
Probab=77.50 E-value=30 Score=37.48 Aligned_cols=68 Identities=19% Similarity=0.238 Sum_probs=31.9
Q ss_pred HHHHHHHH-HhhhchHHHHHHHHhh--cCC-hhhHHhHHHHHHHhcCCCCC--cchhhHH-hHHHHHhhhhcccc
Q psy8363 56 VYRDKIRQ-LSKYIEPLRRMIARAA--NDD-IEKTTKMKKLLEILQSPNKR--MPLETLL-KCEHVLEKLDFKHS 123 (536)
Q Consensus 56 ~Y~eKlrq-LskYIePL~RMI~k~~--~~~-~~~lsKmk~LldIL~np~kr--~pL~TL~-KCE~~LeKl~~~~~ 123 (536)
+|.||+|. ..+=+|=+.-|++-+. .|+ .+...||+...+.|...-.- ...+.|. |-|.+|||+.+...
T Consensus 214 a~~eklR~r~eeeme~~~aeq~slkRt~EeL~~G~~kL~~~~etLEqq~~~L~~niDIL~~k~~eal~~~~n~~~ 288 (365)
T KOG2391|consen 214 AVREKLRRRREEEMERLQAEQESLKRTEEELNIGKQKLVAMKETLEQQLQSLQKNIDILKSKVREALEKAENLEA 288 (365)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHhhHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHhhhccCcC
Confidence 68888764 3344444555544444 111 23445555555555421110 0122221 34557777766444
No 19
>PF10666 Phage_Gp14: Phage protein Gp14; InterPro: IPR018923 This Listeria phage Gp14 protein family is of unknown function but is expressed from within a cluster of tail- and base plate genes [].
Probab=72.67 E-value=19 Score=33.96 Aligned_cols=70 Identities=16% Similarity=0.140 Sum_probs=53.9
Q ss_pred hhhhcCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCchhHHHHhhhHHHHHHHHhHH----------HHHHHHHHHHhc
Q psy8363 312 SELRTKDKKELLKQLEELKTELANLRVAKVTGGAASKLSKIRVVRKAILRVYIVMHQK----------QKENMRNLIRKE 381 (536)
Q Consensus 312 ~ELR~kS~eEL~kqL~eLK~EL~~LR~qkvtG~al~k~skIr~vRK~IARVlTVlnqk----------qr~~lr~~yk~k 381 (536)
.+++++|.+|+.+ |.+-.+|+...-+.--.|. -+-..++-...|+|-|++||.+|- +....|+.|+++
T Consensus 57 d~~~EmS~e~~~a-Le~~~re~L~ea~~~~l~d-e~tfee~Ye~~k~~~~M~~v~~~v~e~~~~~m~v~Q~e~qk~Y~~k 134 (140)
T PF10666_consen 57 DFDREMSSEEYRA-LEEQQREALKEAIEIFLGD-ENTFEECYEKCKDLVNMTKVYMQVSEWLVGKMEVQQNEIQKKYKAK 134 (140)
T ss_pred cchhhcCHHHHHH-HHHHHHHHHHHHHHHHhCc-HhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4458899888766 5666778888888888885 366789999999999999999874 346678888744
Q ss_pred cC
Q psy8363 382 HK 383 (536)
Q Consensus 382 ~k 383 (536)
.+
T Consensus 135 ~~ 136 (140)
T PF10666_consen 135 MT 136 (140)
T ss_pred hh
Confidence 33
No 20
>smart00591 RWD domain in RING finger and WD repeat containing proteins and DEXDc-like helicases subfamily related to the UBCc domain.
Probab=66.60 E-value=18 Score=30.41 Aligned_cols=43 Identities=26% Similarity=0.343 Sum_probs=24.3
Q ss_pred EeecCCCCCCCCCccccC-CcCCCCchHHHHHHHHHHHHhhCCC
Q psy8363 232 QVSIPEDYPSHPPRCTMG-HEHNTTPFLTSVKNALESRIKKLPL 274 (536)
Q Consensus 232 ~v~vP~dYP~~sP~~~~~-~~y~~t~FL~~v~~~~~sRL~~lP~ 274 (536)
.+..|++||..+|.+... ...-.......++..+..-.....+
T Consensus 46 ~~~~p~~YP~~~P~i~~~~~~~l~~~~~~~l~~~l~~~~~e~~g 89 (107)
T smart00591 46 QVKLPENYPDEAPPISLLNSEGLSDEQLAELLKKLEEIAEENLG 89 (107)
T ss_pred EEECCCCCCCCCCCeEEECCCCCCHHHHHHHHHHHHHHHHHhCC
Confidence 345699999999988655 2212333344455555444443333
No 21
>smart00591 RWD domain in RING finger and WD repeat containing proteins and DEXDc-like helicases subfamily related to the UBCc domain.
Probab=49.78 E-value=29 Score=29.20 Aligned_cols=39 Identities=28% Similarity=0.464 Sum_probs=23.4
Q ss_pred ceeecCCCCCCCCCCCccC-ccCCCCchHHHHHHHHHHHH
Q psy8363 490 IQVSIPEDYPSHPPRCTMG-HEHNTTPFLTSVKNALESRI 528 (536)
Q Consensus 490 i~v~vP~dYP~~sp~~~~~-~~Y~a~pFl~~v~~~l~srl 528 (536)
|.|..|++||..+|.+... ...-.......+.+.|..-+
T Consensus 45 l~~~~p~~YP~~~P~i~~~~~~~l~~~~~~~l~~~l~~~~ 84 (107)
T smart00591 45 LQVKLPENYPDEAPPISLLNSEGLSDEQLAELLKKLEEIA 84 (107)
T ss_pred EEEECCCCCCCCCCCeEEECCCCCCHHHHHHHHHHHHHHH
Confidence 4566799999999987643 33333444445555444433
No 22
>PF12887 SICA_alpha: SICA extracellular alpha domain; InterPro: IPR024290 The schizont-infected cell agglutination (SICA) proteins of Plasmodium knowlesi, one of the variant antigen gene families, are associated with parasitic virulence. SICA proteins comprise multiple domains, with the extracellular cysteine-rich domains (CRDs) occurring at different frequencies. They contain a five-cysteine CRD (SICA-alpha) at the N terminus, which occurs once or twice, then between 1 and 10 SICA-beta CRDs with 7-10 cysteine residues, a transmembrane domain, and a conserved C-terminal domain []. This entry represents the extracellular SICA-alpha domain.
Probab=45.02 E-value=60 Score=31.66 Aligned_cols=80 Identities=30% Similarity=0.405 Sum_probs=51.8
Q ss_pred HHHHHHHHHHHHHHhcCCCCCCCCCCccccccchhhhcCCHHHHHHHHHHHHH--------HHHHHHHH--HHhcCCCCC
Q psy8363 279 SQLLDTWEMSVRQACAPTRNPTSSPSISVKVKCSELRTKDKKELLKQLEELKT--------ELANLRVA--KVTGGAASK 348 (536)
Q Consensus 279 T~lL~tWe~SvrQac~~~~~~~ap~t~m~kmKa~ELR~kS~eEL~kqL~eLK~--------EL~~LR~q--kvtG~al~k 348 (536)
+.||..|-....+.-...-+.. +.+|.+.=+++|.+..++|+. |..+|... ...++....
T Consensus 2 ~~L~~~Wl~~~~~~~~~~~~~~----------a~~i~~~Lk~~l~~~~~~L~~~l~~~~s~ei~~lC~~~~~~~~~~~~~ 71 (184)
T PF12887_consen 2 TGLLQEWLQKLLKNGGTTGTGG----------AKEITEKLKKDLEEMFDELKSWLDRQESNEIANLCADGKLVWGGGGGK 71 (184)
T ss_pred cHHHHHHHHHHHhccCCCCCCc----------hhHHHHHHHHHHHHHHHHHHHHHcccCchHHHHHhcCCCCCCCCCCCC
Confidence 5789999988755432211111 455554447788888888887 45566665 222222345
Q ss_pred chhHHHHhhhHHHHHHHHhH
Q psy8363 349 LSKIRVVRKAILRVYIVMHQ 368 (536)
Q Consensus 349 ~skIr~vRK~IARVlTVlnq 368 (536)
....+.+.|.|++|+..++-
T Consensus 72 ~~~~K~lCk~ivei~Yfm~G 91 (184)
T PF12887_consen 72 TDYMKNLCKAIVEIRYFMSG 91 (184)
T ss_pred cchHHHHhHHHHHHHHHHhC
Confidence 66779999999999998874
No 23
>PF09045 L27_2: L27_2; InterPro: IPR015132 The L27_2 domain is a protein-protein interaction domain capable of organising scaffold proteins into supramolecular assemblies by formation of heteromeric L27_2 domain complexes. L27_2 domain-mediated protein assemblies have been shown to play essential roles in cellular processes including asymmetric cell division, establishment and maintenance of cell polarity, and clustering of receptors and ion channels. Members of this family form specific heterotetrameric complexes, in which each domain contains three alpha-helices. The two N-terminal helices of each L27_2 domain pack together to form a tight, four-helix bundle in the heterodimer, whilst the third helix of each L27_2 domain forms another four-helix bundle that assembles the two units of the heterodimer into a tetramer []. ; PDB: 3UIT_A 1VF6_B.
Probab=44.17 E-value=4.9 Score=33.07 Aligned_cols=37 Identities=30% Similarity=0.277 Sum_probs=22.5
Q ss_pred HHHhhhhcccccccc-ccchHHHHHHHhhcCCCccccc
Q psy8363 113 HVLEKLDFKHSSLLR-DHHPLLEAVSGALQSSNANHTL 149 (536)
Q Consensus 113 ~~LeKl~~~~~~~~~-~~~PLLdaV~ani~SP~~NHTL 149 (536)
.|||+|..+-...-. .++-=|.++.+.++||+|||-|
T Consensus 7 ~~lerlq~KL~~rGd~s~~e~L~~l~~~LqSPLF~~iL 44 (58)
T PF09045_consen 7 QALERLQAKLKERGDTSHSEKLSLLKDTLQSPLFNQIL 44 (58)
T ss_dssp HHHHHHHHHHHHCT--TTHHHHHHHHHHHH-HHHHHHH
T ss_pred HHHHHHHHHHHHccCcccHHHHHHHHHHHhChHHHHHH
Confidence 356766655432111 2234588899999999999943
No 24
>PF05743 UEV: UEV domain; InterPro: IPR008883 The N-terminal ubiquitin E2 variant (UEV) domain is ~145 amino acid residues in length and shows significant sequence similarity to E2 ubiquitin ligases but is unable to catalyze ubiquitin transfer as it lacks the active site cysteine that forms the transient thioester bond with the C terminus of ubiquitin (Ub). Nevertheless, at least some UEVs have retained the ability to bind Ub, and appear to act either as cofactors in ubiquitylation reactions, or as ubiquitin sensors. UEV domains also frequently contain other protein recognition motifs, and may generally serve to couple protein and Ub binding functions to facilitate the formation of multiprotein complexes [, , , ]. The UEV domain consists of a twisted four-stranded antiparallel beta-sheet having a meander topology, with four alpha-helices packed against one face of the sheet. The UEV fold is generally similar to canonical E2 ligases in the hydrophobic core and 'active site' regions, but differs significantly at both its N- and C-termini [, ]. The UEV domain is found in the eukaryotic tumour susceptibility gene 101 protein (TSG101). Altered transcripts of this gene have been detected in sporadic breast cancers and many other Homo sapiens malignancies. However, the involvement of this gene in neoplastic transformation and tumourigenesis is still elusive. TSG101 is required for normal cell function of embryonic and adult tissues but this gene is not a tumour suppressor for sporadic forms of breast cancer [].; GO: 0006464 protein modification process, 0015031 protein transport; PDB: 3R3Q_A 3R42_A 1UZX_A 3OBX_A 3OBS_A 3P9H_A 2F0R_A 3P9G_A 3OBQ_A 3OBU_A ....
Probab=38.35 E-value=16 Score=33.37 Aligned_cols=20 Identities=40% Similarity=0.833 Sum_probs=16.4
Q ss_pred CeEeecCCCCCCCCCccccC
Q psy8363 230 PIQVSIPEDYPSHPPRCTMG 249 (536)
Q Consensus 230 Pl~v~vP~dYP~~sP~~~~~ 249 (536)
||.|.||.+||..+|.|-..
T Consensus 51 Pi~Iwlp~~yP~~pP~v~v~ 70 (121)
T PF05743_consen 51 PICIWLPENYPYSPPIVYVR 70 (121)
T ss_dssp EEEEEE-TTTTTSSSEEEE-
T ss_pred eEEEEEcccCCCCCCEEEEe
Confidence 89999999999999999544
No 25
>PF00179 UQ_con: Ubiquitin-conjugating enzyme; InterPro: IPR000608 The post-translational attachment of ubiquitin (IPR000626 from INTERPRO) to proteins (ubiquitinylation) alters the function, location or trafficking of a protein, or targets it to the 26S proteasome for degradation [, , ]. Ubiquitinylation is an ATP-dependent process that involves the action of at least three enzymes: a ubiquitin-activating enzyme (E1, IPR000011 from INTERPRO), a ubiquitin-conjugating enzyme (E2), and a ubiquitin ligase (E3, IPR000569 from INTERPRO, IPR003613 from INTERPRO), which work sequentially in a cascade []. The E1 enzyme mediates an ATP-dependent transfer of a thioester-linked ubiquitin molecule to a cysteine residue on the E2 enzyme. The E2 enzyme (6.3.2.19 from EC) then either transfers the ubiquitin moiety directly to a substrate, or to an E3 ligase, which can also ubiquitinylate a substrate. There are several different E2 enzymes (over 30 in humans), which are broadly grouped into four classes, all of which have a core catalytic domain (containing the active site cysteine), and some of which have short N- and C-terminal amino acid extensions: class I enzymes consist of just the catalytic core domain (UBC), class II possess a UBC and a C-terminal extension, class III possess a UBC and an N-terminal extension, and class IV possess a UBC and both N- and C-terminal extensions. These extensions appear to be important for some subfamily function, including E2 localisation and protein-protein interactions []. In addition, there are proteins with an E2-like fold that are devoid of catalytic activity, but which appear to assist in poly-ubiquitin chain formation.; GO: 0016881 acid-amino acid ligase activity; PDB: 2AAK_A 3SY2_C 1FBV_C 3SQV_C 1C4Z_D 1JAT_B 2GMI_B 2H2Y_D 2R0J_A 3E95_B ....
Probab=36.70 E-value=36 Score=30.90 Aligned_cols=19 Identities=37% Similarity=0.840 Sum_probs=12.3
Q ss_pred eEeecCCCCCCCCCccccC
Q psy8363 231 IQVSIPEDYPSHPPRCTMG 249 (536)
Q Consensus 231 l~v~vP~dYP~~sP~~~~~ 249 (536)
+.|.+|.|||.++|.....
T Consensus 49 ~~i~~p~~YP~~pP~v~f~ 67 (140)
T PF00179_consen 49 FRISFPPDYPFSPPKVRFL 67 (140)
T ss_dssp EEEEETTTTTTS--EEEES
T ss_pred ccccccccccccccccccc
Confidence 4566689999998876544
No 26
>PF06698 DUF1192: Protein of unknown function (DUF1192); InterPro: IPR009579 This family consists of several short, hypothetical, bacterial proteins of around 60 residues in length. The function of this family is unknown.
Probab=34.14 E-value=64 Score=26.68 Aligned_cols=30 Identities=27% Similarity=0.341 Sum_probs=25.7
Q ss_pred hhhhcCCHHHHHHHHHHHHHHHHHHHHHHH
Q psy8363 312 SELRTKDKKELLKQLEELKTELANLRVAKV 341 (536)
Q Consensus 312 ~ELR~kS~eEL~kqL~eLK~EL~~LR~qkv 341 (536)
.+|-.+|.+||.+.+.-|+.|...++-...
T Consensus 16 ~dLs~lSv~EL~~RIa~L~aEI~R~~~~~~ 45 (59)
T PF06698_consen 16 EDLSLLSVEELEERIALLEAEIARLEAAIA 45 (59)
T ss_pred CCchhcCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 578899999999999999999887776554
No 27
>smart00212 UBCc Ubiquitin-conjugating enzyme E2, catalytic domain homologues. Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. This pathway functions in regulating many fundamental processes required for cell viability.TSG101 is one of several UBC homologues that lacks this active site cysteine.
Probab=33.84 E-value=37 Score=31.03 Aligned_cols=20 Identities=30% Similarity=0.778 Sum_probs=16.0
Q ss_pred CCCCceeecCCCCCCCCCCC
Q psy8363 486 CVPPIQVSIPEDYPSHPPRC 505 (536)
Q Consensus 486 ~vPpi~v~vP~dYP~~sp~~ 505 (536)
..=.+.|.+|++||..+|..
T Consensus 46 ~~f~~~l~~p~~yP~~pP~v 65 (145)
T smart00212 46 GIFKLTIEFPPDYPFKPPKV 65 (145)
T ss_pred cEEEEEEECCcccCCCCCEE
Confidence 34467888999999999874
No 28
>PHA03162 hypothetical protein; Provisional
Probab=33.68 E-value=1.6e+02 Score=28.22 Aligned_cols=53 Identities=17% Similarity=0.186 Sum_probs=36.5
Q ss_pred hcCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCchhHHHHhhhHHHHHHHHhHHHHHHHHHHH
Q psy8363 315 RTKDKKELLKQLEELKTELANLRVAKVTGGAASKLSKIRVVRKAILRVYIVMHQKQKENMRNLI 378 (536)
Q Consensus 315 R~kS~eEL~kqL~eLK~EL~~LR~qkvtG~al~k~skIr~vRK~IARVlTVlnqkqr~~lr~~y 378 (536)
.+++.|||.++|..|+-|=..|+=+-..|+..+-...= + +|+..|++.+-..|
T Consensus 11 ~~~tmEeLaaeL~kLqmENK~LKkkl~~~~~~~~~p~d--------~---~LTp~qKea~I~s~ 63 (135)
T PHA03162 11 AQPTMEDLAAEIAKLQLENKALKKKIKEGTDDDPLPGD--------P---ILTPAAKEAMIGAA 63 (135)
T ss_pred cCCCHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCCC--------c---cCCHHHHHHHHHHH
Confidence 46899999999999999999999877555432210000 0 36677777776655
No 29
>PF04136 Sec34: Sec34-like family ; InterPro: IPR007265 Sec34 and Sec35 form a sub-complex in a seven-protein complex that includes Dor1. This complex is thought to be important for tethering vesicles to the Golgi [].; GO: 0006886 intracellular protein transport, 0005801 cis-Golgi network, 0016020 membrane
Probab=33.00 E-value=92 Score=29.69 Aligned_cols=98 Identities=16% Similarity=0.321 Sum_probs=60.5
Q ss_pred HHHHHHHHhhhchHHHHHHHHhhcCChhhHHhHHHHHHHhcCCCCCcchhhHHhHHHHHhhhhc--cccccc--ccc-ch
Q psy8363 57 YRDKIRQLSKYIEPLRRMIARAANDDIEKTTKMKKLLEILQSPNKRMPLETLLKCEHVLEKLDF--KHSSLL--RDH-HP 131 (536)
Q Consensus 57 Y~eKlrqLskYIePL~RMI~k~~~~~~~~lsKmk~LldIL~np~kr~pL~TL~KCE~~LeKl~~--~~~~~~--~~~-~P 131 (536)
|.+-+.+|+.|.+-..-+++.+++- .+.|..|..-.+..++-+. .-=..||..|+.-.. ..+..+ ... +-
T Consensus 2 y~~y~~~L~~~~~~~~~ll~~~~~~-~~~l~~l~~~~~~Vs~kT~----~l~~~ce~Ll~eq~~L~~~ae~I~~~L~yF~ 76 (157)
T PF04136_consen 2 YRQYLDYLQQYREECDQLLDQTDEI-LDQLDELQEQYNSVSEKTN----SLHEACEQLLEEQTRLEELAEEISEKLQYFE 76 (157)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHhHH----HHHHHHHHHHHHHHHHHHHHHHHHHHhHHHh
Confidence 3444444555555555666665533 4567777777777777665 222459999886321 111122 111 25
Q ss_pred HHHHHHHhhcCCCccccccccccchhhhh
Q psy8363 132 LLEAVSGALQSSNANHTLQRTFGPCLEIL 160 (536)
Q Consensus 132 LLdaV~ani~SP~~NHTL~RTF~Pam~al 160 (536)
-||.|...+.+|.++.+ .-.|.+.|..|
T Consensus 77 ~Ld~itr~Ln~p~~sV~-~~~F~~~L~~L 104 (157)
T PF04136_consen 77 ELDPITRRLNSPGSSVN-SDSFKPMLSRL 104 (157)
T ss_pred hHHHHHHHHcCCCCccc-chHHHHHHHHH
Confidence 58999999999988877 77899866554
No 30
>KOG4445|consensus
Probab=32.10 E-value=58 Score=35.00 Aligned_cols=97 Identities=15% Similarity=0.228 Sum_probs=57.5
Q ss_pred hhhHHHhhccCCcccccCCCCCC--CCCcEEEEEEecCCCCCCCCCeEeecCCCCCCCCCccccC--CcCCCCchHHHHH
Q psy8363 187 VLQGEIARLDQRFKVSLDPTQQS--GSKAIQLVCWLDDRHLPCVPPIQVSIPEDYPSHPPRCTMG--HEHNTTPFLTSVK 262 (536)
Q Consensus 187 vlQgEiarLd~kF~V~lDp~~~~--~~~~i~LiC~LdDk~LP~VPPl~v~vP~dYP~~sP~~~~~--~~y~~t~FL~~v~ 262 (536)
+..|||-.||+=....-.++... .--++|=+-.++|.+-=.-==|+|.|++.||.-||..... --.+..- |..|+
T Consensus 3 ~~~~e~~~ld~i~~~~~~~s~~~~~i~~t~hpit~eedesqyvcvtl~m~vs~gYP~esPtvtl~nPRGl~d~~-~~~i~ 81 (368)
T KOG4445|consen 3 SADGEIEALDSIWDGVHVESKLEASIRYTKHPITSEEDESQYVCVTLEMTVSEGYPAESPTVTLSNPRGLGDPE-FREIQ 81 (368)
T ss_pred ccchhhHhhhhHhhccCCCCCChhhheeeecccccccccceeEEEEEEEecCCCCCCcCCceEecCCCCCCcHH-HHHHH
Confidence 34577777877544433333221 2223332323333221111126789999999999998766 3344444 59999
Q ss_pred HHHHHHHhhCCCcccHHHHHHH
Q psy8363 263 NALESRIKKLPLKYSVSQLLDT 284 (536)
Q Consensus 263 ~~~~sRL~~lP~~~SvT~lL~t 284 (536)
+++..-+.+--+.--|-+|++-
T Consensus 82 ~~~~~iikq~~g~pii~~lie~ 103 (368)
T KOG4445|consen 82 RQIQEIIKQNSGMPIICQLIEH 103 (368)
T ss_pred HHHHHHHHhcCCCchhHHHHHH
Confidence 9999988887775556666654
No 31
>smart00212 UBCc Ubiquitin-conjugating enzyme E2, catalytic domain homologues. Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. This pathway functions in regulating many fundamental processes required for cell viability.TSG101 is one of several UBC homologues that lacks this active site cysteine.
Probab=31.23 E-value=55 Score=29.95 Aligned_cols=23 Identities=26% Similarity=0.637 Sum_probs=18.2
Q ss_pred CCCCeEeecCCCCCCCCCccccC
Q psy8363 227 CVPPIQVSIPEDYPSHPPRCTMG 249 (536)
Q Consensus 227 ~VPPl~v~vP~dYP~~sP~~~~~ 249 (536)
..=.+.|.+|.+||..+|.+...
T Consensus 46 ~~f~~~l~~p~~yP~~pP~v~f~ 68 (145)
T smart00212 46 GIFKLTIEFPPDYPFKPPKVKFI 68 (145)
T ss_pred cEEEEEEECCcccCCCCCEEEEe
Confidence 44578888999999999988553
No 32
>PRK11020 hypothetical protein; Provisional
Probab=29.93 E-value=1.6e+02 Score=27.61 Aligned_cols=52 Identities=17% Similarity=0.183 Sum_probs=24.9
Q ss_pred CchhHHHHhhhHHHHHHHHhHHHHHHHHHHHHhccCccCCCCCCchhhHHHHhhcChhHHh
Q psy8363 348 KLSKIRVVRKAILRVYIVMHQKQKENMRNLIRKEHKKYKPLDLRPKKTRALRRRLTKHERK 408 (536)
Q Consensus 348 k~skIr~vRK~IARVlTVlnqkqr~~lr~~yk~k~kk~~PlDLRpKkTRA~Rr~Ltk~e~~ 408 (536)
+...|....+.|+-+-.-|+.-.-.+-++.-+ ++++..= =...|++||.|..
T Consensus 29 d~~~i~qf~~E~~~l~k~I~~lk~~~~~~lsk-e~~~l~~--------lpF~R~iTK~EQA 80 (118)
T PRK11020 29 DAEKYAQFEKEKATLEAEIARLKEVQSQKLSK-EAQKLMK--------LPFSRAITKKEQA 80 (118)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHc--------CCcchhccHHHHH
Confidence 44555555555555544444332222233322 2333211 1357899988754
No 33
>COG5493 Uncharacterized conserved protein containing a coiled-coil domain [Function unknown]
Probab=29.69 E-value=59 Score=33.04 Aligned_cols=52 Identities=27% Similarity=0.348 Sum_probs=35.1
Q ss_pred CHHHHHHHHHHHHHHHHH----HHHHHHhcCCCC-----CchhHHHHhhhHHHHHHHHhHH
Q psy8363 318 DKKELLKQLEELKTELAN----LRVAKVTGGAAS-----KLSKIRVVRKAILRVYIVMHQK 369 (536)
Q Consensus 318 S~eEL~kqL~eLK~EL~~----LR~qkvtG~al~-----k~skIr~vRK~IARVlTVlnqk 369 (536)
+.+||.++++..+++|.. -|++++|...+. ...+++.++++|-|+-|+|+--
T Consensus 47 dve~l~~e~E~~~k~l~de~~E~r~~~~tke~lk~l~~~~~~~f~a~~edi~rlE~~i~~l 107 (231)
T COG5493 47 DVEELRKETEQRQKELADEKLEVRKQKATKEDLKLLQRFQEEEFRATKEDIKRLETIITGL 107 (231)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456666666666666664 677777655211 1335888999999999988763
No 34
>PRK11546 zraP zinc resistance protein; Provisional
Probab=28.93 E-value=2.5e+02 Score=26.97 Aligned_cols=55 Identities=20% Similarity=0.187 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCCCCCchhHHHHhhhHHHHHHHHhHHHHHHHHHHHH
Q psy8363 319 KKELLKQLEELKTELANLRVAKVTGGAASKLSKIRVVRKAILRVYIVMHQKQKENMRNLIR 379 (536)
Q Consensus 319 ~eEL~kqL~eLK~EL~~LR~qkvtG~al~k~skIr~vRK~IARVlTVlnqkqr~~lr~~yk 379 (536)
.++|.++|-.-+.||-.| ..+. .....+|+.+.+.|+.+.+-|-++. .+++..+.
T Consensus 63 t~~LRqqL~aKr~ELnAL----l~~~-~pD~~kI~aL~kEI~~Lr~kL~e~r-~~~~~~~~ 117 (143)
T PRK11546 63 TSALRQQLVSKRYEYNAL----LTAN-PPDSSKINAVAKEMENLRQSLDELR-VKRDIAMA 117 (143)
T ss_pred HHHHHHHHHHHHHHHHHH----HcCC-CCCHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHH
Confidence 444555555555554444 2233 4678999999999999999777653 34444443
No 35
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=24.74 E-value=1.9e+02 Score=26.00 Aligned_cols=39 Identities=18% Similarity=0.155 Sum_probs=24.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCCCCCchhHHHHhhhHH
Q psy8363 319 KKELLKQLEELKTELANLRVAKVTGGAASKLSKIRVVRKAIL 360 (536)
Q Consensus 319 ~eEL~kqL~eLK~EL~~LR~qkvtG~al~k~skIr~vRK~IA 360 (536)
.+++.+++.+|++|+.+|++.... +.+...|..-|+-||
T Consensus 73 ~~~~~~ei~~L~~el~~L~~E~di---LKKa~~~~~~~~~~~ 111 (121)
T PRK09413 73 LAAAMKQIKELQRLLGKKTMENEL---LKEAVEYGRAKKWIA 111 (121)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHhchhhhhh
Confidence 346777788888888888887764 334444444444443
No 36
>PF07795 DUF1635: Protein of unknown function (DUF1635); InterPro: IPR012862 The members of this family include sequences that are parts of hypothetical proteins expressed by plant species. The region in question is about 170 amino acids long.
Probab=24.58 E-value=3.8e+02 Score=27.46 Aligned_cols=55 Identities=15% Similarity=0.264 Sum_probs=44.5
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCchhHHHHhhhHHHHHHHHhH--HHHHHHHHHHH
Q psy8363 317 KDKKELLKQLEELKTELANLRVAKVTGGAASKLSKIRVVRKAILRVYIVMHQ--KQKENMRNLIR 379 (536)
Q Consensus 317 kS~eEL~kqL~eLK~EL~~LR~qkvtG~al~k~skIr~vRK~IARVlTVlnq--kqr~~lr~~yk 379 (536)
+|.|||...|.-..-||-.+|+... .+||.-+-.|++++-.++. ++|.++|..+.
T Consensus 1 ~s~EELRq~Ll~TTlELE~~k~~A~--------EElRk~eeqi~~L~~Ll~~a~~ERDEAr~qlq 57 (214)
T PF07795_consen 1 ESMEELRQKLLYTTLELEATKMEAN--------EELRKREEQIAHLKDLLKKAYQERDEAREQLQ 57 (214)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4678999999999999999888654 5788888889999888775 67788888774
No 37
>PF14712 Snapin_Pallidin: Snapin/Pallidin
Probab=24.40 E-value=2.5e+02 Score=23.80 Aligned_cols=60 Identities=20% Similarity=0.305 Sum_probs=43.2
Q ss_pred ccchhhhcCCHHHHHHHHHHHHHHHHHHHHHHHhc-C--CCCCchhHHHHhhhHHHHHHHHhHH
Q psy8363 309 VKCSELRTKDKKELLKQLEELKTELANLRVAKVTG-G--AASKLSKIRVVRKAILRVYIVMHQK 369 (536)
Q Consensus 309 mKa~ELR~kS~eEL~kqL~eLK~EL~~LR~qkvtG-~--al~k~skIr~vRK~IARVlTVlnqk 369 (536)
-++.|++. |-++|..+++.+..+|..+.-..... . -..-..++..+||.+..+...+..-
T Consensus 21 ~~l~el~~-sQ~~L~~~i~~~~~~L~~~~~~~~~~~~~~~~~y~~KL~~ikkrm~~l~~~l~~l 83 (92)
T PF14712_consen 21 QQLQELRQ-SQEELLQQIDRLNEKLKELNEVEQINEPFDLDPYVKKLVNIKKRMSNLHERLQKL 83 (92)
T ss_pred HHHHHHHH-HHHHHHHHHHHHHHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45678886 79999999999999998887722222 1 0124677888888888888776653
No 38
>PF05743 UEV: UEV domain; InterPro: IPR008883 The N-terminal ubiquitin E2 variant (UEV) domain is ~145 amino acid residues in length and shows significant sequence similarity to E2 ubiquitin ligases but is unable to catalyze ubiquitin transfer as it lacks the active site cysteine that forms the transient thioester bond with the C terminus of ubiquitin (Ub). Nevertheless, at least some UEVs have retained the ability to bind Ub, and appear to act either as cofactors in ubiquitylation reactions, or as ubiquitin sensors. UEV domains also frequently contain other protein recognition motifs, and may generally serve to couple protein and Ub binding functions to facilitate the formation of multiprotein complexes [, , , ]. The UEV domain consists of a twisted four-stranded antiparallel beta-sheet having a meander topology, with four alpha-helices packed against one face of the sheet. The UEV fold is generally similar to canonical E2 ligases in the hydrophobic core and 'active site' regions, but differs significantly at both its N- and C-termini [, ]. The UEV domain is found in the eukaryotic tumour susceptibility gene 101 protein (TSG101). Altered transcripts of this gene have been detected in sporadic breast cancers and many other Homo sapiens malignancies. However, the involvement of this gene in neoplastic transformation and tumourigenesis is still elusive. TSG101 is required for normal cell function of embryonic and adult tissues but this gene is not a tumour suppressor for sporadic forms of breast cancer [].; GO: 0006464 protein modification process, 0015031 protein transport; PDB: 3R3Q_A 3R42_A 1UZX_A 3OBX_A 3OBS_A 3P9H_A 2F0R_A 3P9G_A 3OBQ_A 3OBU_A ....
Probab=24.29 E-value=32 Score=31.38 Aligned_cols=47 Identities=26% Similarity=0.518 Sum_probs=28.2
Q ss_pred ccccccCccCCCCCCcEEEEEeecCCCCC-------CCCCceeecCCCCCCCCCCC
Q psy8363 457 RFKVSLDPTQQSGSKAIQLVCWLDDRHLP-------CVPPIQVSIPEDYPSHPPRC 505 (536)
Q Consensus 457 kF~V~ld~~~~s~~~~v~LiC~LdDk~LP-------~vPpi~v~vP~dYP~~sp~~ 505 (536)
.|+...|.--.+++.+..|+|--- .+| --=||.|-||++||..+|.|
T Consensus 14 ~L~p~~~~ft~~~G~~~~LL~L~G--tipi~y~g~~y~iPi~Iwlp~~yP~~pP~v 67 (121)
T PF05743_consen 14 SLRPRTDTFTFNDGSSKLLLCLYG--TIPITYKGSTYNIPICIWLPENYPYSPPIV 67 (121)
T ss_dssp TEEEEEEEEESTTSTEEEEEEEEE--EEEECCTTCCEEEEEEEEE-TTTTTSSSEE
T ss_pred CCcEeeeeeEcCCCChheEEEEec--CcccccCCcccceeEEEEEcccCCCCCCEE
Confidence 444445433334444567777431 222 11269999999999999987
No 39
>KOG2525|consensus
Probab=24.01 E-value=52 Score=37.15 Aligned_cols=46 Identities=30% Similarity=0.408 Sum_probs=38.0
Q ss_pred cccHHHHHHHHHHhhhchHHHHHHHHhhcCChhhHHhHHHHHHHhcCCC
Q psy8363 52 QEDQVYRDKIRQLSKYIEPLRRMIARAANDDIEKTTKMKKLLEILQSPN 100 (536)
Q Consensus 52 ~eeq~Y~eKlrqLskYIePL~RMI~k~~~~~~~~lsKmk~LldIL~np~ 100 (536)
++---|++-|+-+.++|++++|+=+ +.+...|.-|..+|+-|+||.
T Consensus 22 ~~~v~~lnsLqsn~~~i~~~~~~~~---~~~~~~l~~m~~~L~~lg~p~ 67 (496)
T KOG2525|consen 22 EDAVRYLNSLQSNAALIEKLRRQDD---NPQGLTLPRMRKLLERLGNPE 67 (496)
T ss_pred HHHHHHHHHHHhHHHhhhhhhhccC---CccccCHHHHHHHHHHhCChh
Confidence 4555899999999999999998732 345568999999999999983
No 40
>KOG0421|consensus
Probab=23.60 E-value=5.4e+02 Score=25.21 Aligned_cols=132 Identities=26% Similarity=0.364 Sum_probs=79.1
Q ss_pred CCCCchhhhhHHHhhccCCcccccCCC-CCCCCCcEEEEEEecCCCCCCCCC-------eEeecCCCCCCCCCc------
Q psy8363 180 PADDVPEVLQGEIARLDQRFKVSLDPT-QQSGSKAIQLVCWLDDRHLPCVPP-------IQVSIPEDYPSHPPR------ 245 (536)
Q Consensus 180 ~~~~ip~vlQgEiarLd~kF~V~lDp~-~~~~~~~i~LiC~LdDk~LP~VPP-------l~v~vP~dYP~~sP~------ 245 (536)
+.+.+-.-||.|+..|=- +=++. +..-.++ -|+||..-..=|.--+ |.+..|.+||..+|.
T Consensus 26 ~~~~V~KRLq~ELm~Lmm----s~~~gISAFP~~d-nlf~WvGtItGp~dTvyegl~yklSl~Fp~~YPy~pP~vkFltp 100 (175)
T KOG0421|consen 26 DGHSVTKRLQSELMGLMM----SNTPGISAFPESD-NLFKWVGTITGPKDTVYEGLKYKLSLSFPNNYPYKPPTVKFLTP 100 (175)
T ss_pred cCchHHHHHHHHHHHHHh----cCCCCcccCcCcC-ceeEEeeEeeCCCCccccCcEEEEEEecCCCCCCCCCeeEeecc
Confidence 356778889999877632 11111 0111222 5777776655444333 568899999999875
Q ss_pred -cccCCcCCCCchHHHHHHHHHHHHhhCCCcccHHHHHHHHHHHHHHHhcCCCCCCCCCCccccccchhhhcCCHHHHHH
Q psy8363 246 -CTMGHEHNTTPFLTSVKNALESRIKKLPLKYSVSQLLDTWEMSVRQACAPTRNPTSSPSISVKVKCSELRTKDKKELLK 324 (536)
Q Consensus 246 -~~~~~~y~~t~FL~~v~~~~~sRL~~lP~~~SvT~lL~tWe~SvrQac~~~~~~~ap~t~m~kmKa~ELR~kS~eEL~k 324 (536)
|+...+-.++.-|+-++.--++ .|-|-.|| .|+ |..++-+.-.+|.. -.+.||++ +.+|-.+
T Consensus 101 c~HPNVD~~GnIcLDILkdKWSa-------~YdVrTIL----LSi-QSLLGEPNn~SPLN----aqAAelW~-d~~eykk 163 (175)
T KOG0421|consen 101 CFHPNVDLSGNICLDILKDKWSA-------VYDVRTIL----LSI-QSLLGEPNNSSPLN----AQAAELWS-DQEEYKK 163 (175)
T ss_pred ccCCCccccccchHHHHHHHHHH-------HHhHHHHH----HHH-HHHhCCCCCCCcch----hHHHHHhc-CHHHHHH
Confidence 4444444455555544433222 23343333 232 66777777777765 45789998 8999998
Q ss_pred HHHHHHHHH
Q psy8363 325 QLEELKTEL 333 (536)
Q Consensus 325 qL~eLK~EL 333 (536)
.|+++-+|.
T Consensus 164 ~l~~~Y~~~ 172 (175)
T KOG0421|consen 164 YLEALYKEI 172 (175)
T ss_pred HHHHHhhcc
Confidence 888876654
No 41
>PHA03155 hypothetical protein; Provisional
Probab=23.40 E-value=3e+02 Score=25.76 Aligned_cols=29 Identities=34% Similarity=0.414 Sum_probs=26.1
Q ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHHhcC
Q psy8363 316 TKDKKELLKQLEELKTELANLRVAKVTGG 344 (536)
Q Consensus 316 ~kS~eEL~kqL~eLK~EL~~LR~qkvtG~ 344 (536)
+++.|||.++|..|+-|=..|+=+-..|+
T Consensus 7 ~~tvEeLaaeL~kL~~ENK~LKkkl~~~~ 35 (115)
T PHA03155 7 CADVEELEKELQKLKIENKALKKKLLQHG 35 (115)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHccC
Confidence 78999999999999999999998876665
No 42
>KOG4445|consensus
Probab=20.98 E-value=1e+02 Score=33.30 Aligned_cols=82 Identities=21% Similarity=0.357 Sum_probs=51.6
Q ss_pred hhhhhhcccccccccCccCC--CCCCcEEEEEeecCCC-CCCCCCceeecCCCCCCCCCCCccC-ccCCCCchHHHHHHH
Q psy8363 448 QGEIARLDQRFKVSLDPTQQ--SGSKAIQLVCWLDDRH-LPCVPPIQVSIPEDYPSHPPRCTMG-HEHNTTPFLTSVKNA 523 (536)
Q Consensus 448 qgEiArLd~kF~V~ld~~~~--s~~~~v~LiC~LdDk~-LP~vPpi~v~vP~dYP~~sp~~~~~-~~Y~a~pFl~~v~~~ 523 (536)
-|||.-||+-+-..=.+|.. +.--++|=|=.++|-. -=||. |++.|+++||.-||+..+. ..=-..+=|..|+++
T Consensus 5 ~~e~~~ld~i~~~~~~~s~~~~~i~~t~hpit~eedesqyvcvt-l~m~vs~gYP~esPtvtl~nPRGl~d~~~~~i~~~ 83 (368)
T KOG4445|consen 5 DGEIEALDSIWDGVHVESKLEASIRYTKHPITSEEDESQYVCVT-LEMTVSEGYPAESPTVTLSNPRGLGDPEFREIQRQ 83 (368)
T ss_pred chhhHhhhhHhhccCCCCCChhhheeeecccccccccceeEEEE-EEEecCCCCCCcCCceEecCCCCCCcHHHHHHHHH
Confidence 47777777766555444432 2233444444444332 23333 8999999999999998754 333345677888888
Q ss_pred HHHHHhh
Q psy8363 524 LESRIKK 530 (536)
Q Consensus 524 l~srl~~ 530 (536)
+...+.+
T Consensus 84 ~~~iikq 90 (368)
T KOG4445|consen 84 IQEIIKQ 90 (368)
T ss_pred HHHHHHh
Confidence 8776654
No 43
>PRK06856 DNA polymerase III subunit psi; Validated
Probab=20.07 E-value=75 Score=29.62 Aligned_cols=13 Identities=38% Similarity=0.595 Sum_probs=9.6
Q ss_pred CCchHHHHHHHHH
Q psy8363 513 TTPFLTSVKNALE 525 (536)
Q Consensus 513 a~pFl~~v~~~l~ 525 (536)
.+||+..|.++|.
T Consensus 49 ~~~L~~dVLrsl~ 61 (128)
T PRK06856 49 TDPLLQDVLRSLT 61 (128)
T ss_pred cChHHHHHHHHcC
Confidence 4678888888774
No 44
>COG5078 Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=20.04 E-value=5.3e+02 Score=24.95 Aligned_cols=87 Identities=24% Similarity=0.416 Sum_probs=50.6
Q ss_pred eEeecCCCCCCCCCccccC-CcCC------CCchHHHHHHHHHHHHhhCCCcccHHHHHHHHHHHHHHHhcCCCCCCCCC
Q psy8363 231 IQVSIPEDYPSHPPRCTMG-HEHN------TTPFLTSVKNALESRIKKLPLKYSVSQLLDTWEMSVRQACAPTRNPTSSP 303 (536)
Q Consensus 231 l~v~vP~dYP~~sP~~~~~-~~y~------~t~FL~~v~~~~~sRL~~lP~~~SvT~lL~tWe~SvrQac~~~~~~~ap~ 303 (536)
+.|.+|.|||..+|...+. .-|- |+-=|.-++ .+=---+||..+|. +|.. .+..+....|-
T Consensus 57 ~~l~fP~~YP~~PPkv~F~t~i~HPNV~~~G~vCLdIL~-------~~WsP~~~l~sILl----sl~s-lL~~PN~~~Pl 124 (153)
T COG5078 57 LTLEFPEDYPFKPPKVRFTTKIFHPNVDPSGNVCLDILK-------DRWSPVYTLETILL----SLQS-LLLSPNPDSPL 124 (153)
T ss_pred EEEECCCCCCCCCCeeeeccCCcCCCcCCCCCChhHHHh-------CCCCccccHHHHHH----HHHH-HHcCCCCCCCC
Confidence 4566799999999987654 2222 222222222 11112367766664 3433 33335555554
Q ss_pred CccccccchhhhcCCHHHHHHHHHHHHHHH
Q psy8363 304 SISVKVKCSELRTKDKKELLKQLEELKTEL 333 (536)
Q Consensus 304 t~m~kmKa~ELR~kS~eEL~kqL~eLK~EL 333 (536)
. ..+.++...+.+|-.+...+.-++.
T Consensus 125 n----~daa~~~~~d~~~y~~~vr~~~~~~ 150 (153)
T COG5078 125 N----TEAATLYREDKEEYEKKVREWVKKY 150 (153)
T ss_pred C----hHHHHHHHhCHHHHHHHHHHHHHHh
Confidence 4 5667777678888888877765544
Done!