Query 029985
Match_columns 184
No_of_seqs 133 out of 273
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 06:43:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029985.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029985hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00302 GED Dynamin GTPase 100.0 3.7E-29 8.1E-34 185.8 10.6 83 1-85 9-91 (92)
2 PF02212 GED: Dynamin GTPase e 99.9 1.6E-24 3.5E-29 159.9 8.4 83 2-86 10-92 (92)
3 KOG0446 Vacuolar sorting prote 99.8 4.8E-18 1E-22 162.9 11.3 83 1-84 569-651 (657)
4 COG0699 Predicted GTPases (dyn 94.5 0.45 9.7E-06 42.9 10.5 76 3-81 467-542 (546)
5 COG3579 PepC Aminopeptidase C 68.6 5.1 0.00011 37.9 3.2 53 18-70 152-207 (444)
6 PF15369 KIAA1328: Uncharacter 62.6 58 0.0013 30.3 8.7 49 29-78 20-75 (328)
7 KOG3742 Glycogen synthase [Car 52.9 29 0.00063 34.4 5.4 49 10-67 384-432 (692)
8 cd07620 BAR_SH3BP1 The Bin/Amp 52.3 1.8E+02 0.0039 26.2 11.4 32 52-83 112-144 (257)
9 PF10863 DUF2702: Protein of u 52.0 42 0.00092 27.8 5.5 61 64-130 2-62 (143)
10 PF07560 DUF1539: Domain of Un 50.9 9.9 0.00022 30.7 1.6 62 6-68 20-87 (126)
11 PF12209 SAC3: Leucine permeas 43.8 1.2E+02 0.0026 22.3 6.4 15 11-25 13-27 (79)
12 PF02344 Myc-LZ: Myc leucine z 43.3 26 0.00057 22.3 2.4 26 53-78 4-29 (32)
13 PF05983 Med7: MED7 protein; 42.8 1.3E+02 0.0027 24.8 7.0 30 52-83 132-161 (162)
14 COG1510 Predicted transcriptio 41.2 83 0.0018 27.0 5.8 42 20-66 86-127 (177)
15 PF08544 GHMP_kinases_C: GHMP 39.6 46 0.001 22.6 3.4 47 42-89 3-49 (85)
16 PF09738 DUF2051: Double stran 39.4 2.7E+02 0.0059 25.3 9.2 105 21-130 106-218 (302)
17 PLN03184 chloroplast Hsp70; Pr 38.5 2.8E+02 0.006 27.5 9.7 7 53-59 605-611 (673)
18 KOG4552 Vitamin-D-receptor int 38.2 3E+02 0.0065 24.8 9.1 18 20-37 23-40 (272)
19 PF11594 Med28: Mediator compl 38.2 2E+02 0.0044 22.7 9.3 78 5-97 2-79 (106)
20 KOG0562 Predicted hydrolase (H 37.5 4.3 9.3E-05 34.7 -2.4 16 16-31 28-43 (184)
21 PF05746 DALR_1: DALR anticodo 37.3 1.6E+02 0.0034 21.4 6.2 65 4-84 41-105 (119)
22 PRK10353 3-methyl-adenine DNA 36.4 85 0.0018 26.8 5.1 43 42-88 66-108 (187)
23 PF09440 eIF3_N: eIF3 subunit 36.2 2E+02 0.0043 23.1 7.0 26 58-83 63-88 (133)
24 KOG1899 LAR transmembrane tyro 30.6 4.6E+02 0.01 27.2 9.8 34 52-85 283-316 (861)
25 smart00751 BSD domain in trans 30.6 58 0.0012 21.5 2.6 20 50-69 10-29 (51)
26 PF10397 ADSL_C: Adenylosuccin 30.4 1.6E+02 0.0035 20.9 5.1 40 23-63 8-52 (81)
27 KOG2470 Similar to IMP-GMP spe 30.3 63 0.0014 31.2 3.7 22 108-129 273-297 (510)
28 PF11221 Med21: Subunit 21 of 30.1 2.8E+02 0.0061 22.0 8.2 63 20-84 70-139 (144)
29 PF10987 DUF2806: Protein of u 28.4 1.4E+02 0.003 25.5 5.2 16 110-125 36-51 (219)
30 PRK03926 mevalonate kinase; Pr 27.5 2.1E+02 0.0045 24.5 6.2 56 40-98 204-259 (302)
31 cd01068 sensor_globin Globin d 26.7 2.8E+02 0.0061 20.9 6.5 45 27-73 25-69 (147)
32 PLN02451 homoserine kinase 26.7 1.6E+02 0.0034 27.0 5.6 58 38-98 262-319 (370)
33 PRK09498 sifA secreted effecto 26.6 1.1E+02 0.0024 28.5 4.4 42 20-64 268-311 (336)
34 KOG1923 Rac1 GTPase effector F 26.3 7.8E+02 0.017 25.9 13.4 74 5-78 141-224 (830)
35 PF15030 DUF4527: Protein of u 25.9 1.1E+02 0.0023 27.9 4.2 36 21-58 77-114 (277)
36 PRK12772 bifunctional flagella 25.0 6.6E+02 0.014 24.9 9.8 66 9-74 439-508 (609)
37 PF07303 Occludin_ELL: Occludi 24.7 2.7E+02 0.0058 21.3 5.7 35 53-87 66-100 (101)
38 PF06156 DUF972: Protein of un 24.7 1.6E+02 0.0035 22.8 4.6 41 37-78 17-57 (107)
39 PF12787 EcsC: EcsC protein fa 24.1 4.4E+02 0.0096 22.3 8.5 30 5-34 22-51 (249)
40 KOG1924 RhoA GTPase effector D 23.9 9.2E+02 0.02 25.9 12.7 12 7-18 423-434 (1102)
41 KOG2391 Vacuolar sorting prote 23.8 6.2E+02 0.013 24.1 8.8 37 53-89 242-278 (365)
42 PRK04964 hypothetical protein; 23.7 3E+02 0.0065 20.2 5.6 23 6-28 2-31 (66)
43 TIGR00624 tag DNA-3-methyladen 23.7 1.5E+02 0.0032 25.1 4.4 43 42-88 65-107 (179)
44 KOG3119 Basic region leucine z 22.7 2.8E+02 0.0062 24.4 6.2 33 51-83 223-255 (269)
45 PF05600 DUF773: Protein of un 22.5 6.1E+02 0.013 24.6 8.9 78 5-84 402-487 (507)
46 COG5016 Pyruvate/oxaloacetate 22.4 52 0.0011 31.9 1.7 62 3-64 266-332 (472)
47 PF02341 RcbX: RbcX protein; 22.3 4E+02 0.0086 21.1 6.7 56 14-69 4-74 (111)
48 PF00714 IFN-gamma: Interferon 22.3 49 0.0011 27.2 1.3 73 1-79 55-129 (138)
49 cd00632 Prefoldin_beta Prefold 21.7 3.4E+02 0.0073 20.1 5.7 35 10-44 33-72 (105)
50 PF03114 BAR: BAR domain; Int 21.6 3.9E+02 0.0085 20.8 7.4 37 51-87 122-158 (229)
51 PF08360 TetR_C_5: QacR-like p 21.6 74 0.0016 25.0 2.2 38 5-42 23-61 (131)
52 PF09278 MerR-DNA-bind: MerR, 21.0 2.6E+02 0.0056 18.4 7.6 25 60-84 39-63 (65)
53 KOG2509 Seryl-tRNA synthetase 20.6 8.1E+02 0.018 24.0 10.3 45 28-74 52-99 (455)
54 PF06786 UPF0253: Uncharacteri 20.5 3.5E+02 0.0077 19.8 5.8 23 6-28 2-31 (66)
55 PF13972 TetR: Bacterial trans 20.5 3.1E+02 0.0067 21.0 5.4 41 41-85 38-79 (146)
56 PRK13920 putative anti-sigmaE 20.5 1E+02 0.0023 25.4 2.9 38 41-78 6-43 (206)
57 PRK15366 type III secretion sy 20.4 1.9E+02 0.0042 21.9 4.0 12 52-63 7-18 (80)
58 PF11593 Med3: Mediator comple 20.0 5E+02 0.011 24.8 7.5 57 18-83 21-85 (379)
No 1
>smart00302 GED Dynamin GTPase effector domain.
Probab=99.96 E-value=3.7e-29 Score=185.83 Aligned_cols=83 Identities=30% Similarity=0.490 Sum_probs=79.4
Q ss_pred CchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcchHhHHHHhhcCHHHHHHHHHHHHHHHHHHHHH
Q 029985 1 MSQEVRGYFEAVLNSLATNVSKAIVLCQVEKAKEDMLNQLYSSVGAQSTARIEELLQEDQNVKRRRDRYQKQSELLSKLT 80 (184)
Q Consensus 1 ~~~~V~SYF~IVrk~I~D~VPKAIMh~LVn~sKe~Lq~~L~s~LY~~~~~~l~eLL~Edp~I~~RRe~c~k~L~~LkkA~ 80 (184)
|.++|.+||+||+++|+|+||||||||||+++++.||++||..||+.+ .+++||+|||+|++||++|++++++|++|.
T Consensus 9 i~~lv~sYf~iv~k~i~D~VPKaI~~~lv~~~~~~lq~~L~~~L~~~~--~~~~LL~E~~~i~~kR~~~~~~l~~L~~A~ 86 (92)
T smart00302 9 IKSLVKSYFTIVSKTLADQVPKAIMYLLVNESKDSLQNELLALLYKEE--LLDELLEEDPEIASKRKELKKRLELLKKAR 86 (92)
T ss_pred HHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhCcc--cHHHHHcCCHHHHHHHHHHHHHHHHHHHHH
Confidence 457899999999999999999999999999999999999999999975 799999999999999999999999999999
Q ss_pred HHHhh
Q 029985 81 RQLSI 85 (184)
Q Consensus 81 ~~Lsi 85 (184)
+.|+.
T Consensus 87 ~~l~~ 91 (92)
T smart00302 87 QIIAA 91 (92)
T ss_pred HHHhc
Confidence 99965
No 2
>PF02212 GED: Dynamin GTPase effector domain; InterPro: IPR003130 Dynamin GTPase effector domain found in proteins related to dynamin. Dynamin is a GTP-hydrolysing protein that is an essential participant in clathrin-mediated endocytosis by cells. It self-assembles into 'collars' in vivo at the necks of invaginated coated pits; the self-assembly of dynamin being coordinated by the GTPase domain. Mutation studies indicate that dynamin functions as a molecular regulator of receptor-mediated endocytosis [].; GO: 0003924 GTPase activity, 0005525 GTP binding; PDB: 3ZYS_B 3SZR_A 3LJB_B 3T35_C 3T34_A 2X2F_D 2X2E_D 3SNH_A 3ZYC_D 3ZVR_A.
Probab=99.91 E-value=1.6e-24 Score=159.86 Aligned_cols=83 Identities=33% Similarity=0.456 Sum_probs=76.6
Q ss_pred chhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcchHhHHHHhhcCHHHHHHHHHHHHHHHHHHHHHH
Q 029985 2 SQEVRGYFEAVLNSLATNVSKAIVLCQVEKAKEDMLNQLYSSVGAQSTARIEELLQEDQNVKRRRDRYQKQSELLSKLTR 81 (184)
Q Consensus 2 ~~~V~SYF~IVrk~I~D~VPKAIMh~LVn~sKe~Lq~~L~s~LY~~~~~~l~eLL~Edp~I~~RRe~c~k~L~~LkkA~~ 81 (184)
..+|.+||+||+++|.|+|||+|+||||+++++.|+.+|+.+||..+ .+++||.|||+|+++|++|+++++.|++|.+
T Consensus 10 ~~~l~aY~~ia~kr~~D~Vpk~I~~~lv~~~~~~L~~~l~~~l~~~~--~~~~Ll~Ed~~i~~kR~~l~~~~~~L~~A~~ 87 (92)
T PF02212_consen 10 KALLRAYFEIARKRFIDSVPKAIMHFLVNKSKEQLQSELLNELYDEE--DLEELLQEDPEIAEKREELKKKLERLKKAQQ 87 (92)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCG--GCCCCT--GHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHhHHHHHHHHhccchH--HHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 46899999999999999999999999999999999999999999996 4899999999999999999999999999999
Q ss_pred HHhhh
Q 029985 82 QLSIH 86 (184)
Q Consensus 82 ~Lsi~ 86 (184)
.|+.+
T Consensus 88 ~L~~~ 92 (92)
T PF02212_consen 88 ILSEV 92 (92)
T ss_dssp HHHC-
T ss_pred HHHcC
Confidence 99753
No 3
>KOG0446 consensus Vacuolar sorting protein VPS1, dynamin, and related proteins [Intracellular trafficking, secretion, and vesicular transport; General function prediction only]
Probab=99.75 E-value=4.8e-18 Score=162.94 Aligned_cols=83 Identities=31% Similarity=0.390 Sum_probs=76.8
Q ss_pred CchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcchHhHHHHhhcCHHHHHHHHHHHHHHHHHHHHH
Q 029985 1 MSQEVRGYFEAVLNSLATNVSKAIVLCQVEKAKEDMLNQLYSSVGAQSTARIEELLQEDQNVKRRRDRYQKQSELLSKLT 80 (184)
Q Consensus 1 ~~~~V~SYF~IVrk~I~D~VPKAIMh~LVn~sKe~Lq~~L~s~LY~~~~~~l~eLL~Edp~I~~RRe~c~k~L~~LkkA~ 80 (184)
|.+++.+||+||+++|+|+|||+|||||||.+|+.||++|+..||+ ..++++.||+|+|.|++||++|++|+.+|++|.
T Consensus 569 i~~~~~sY~~iv~~~i~d~vpk~i~~~lv~~~k~~l~~~l~~~L~~-~~~~~~~ll~E~~~i~~~R~~~~~~l~~L~~a~ 647 (657)
T KOG0446|consen 569 ISSCPESYLNIVSDKLVDTVPKALNHELLNEFKDDLPNELDQRLYA-GDEQLESLLKEDPRIKRRRELQQKRLLALQKAL 647 (657)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-chhHHHHHHccCHHHHHHHHHHHHHHHHHHHHH
Confidence 4678999999999999999999999999999999999999999999 245899999999999999999999988888887
Q ss_pred HHHh
Q 029985 81 RQLS 84 (184)
Q Consensus 81 ~~Ls 84 (184)
..+.
T Consensus 648 ~ii~ 651 (657)
T KOG0446|consen 648 SILA 651 (657)
T ss_pred HHHH
Confidence 7764
No 4
>COG0699 Predicted GTPases (dynamin-related) [General function prediction only]
Probab=94.51 E-value=0.45 Score=42.88 Aligned_cols=76 Identities=18% Similarity=0.101 Sum_probs=65.6
Q ss_pred hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcchHhHHHHhhcCHHHHHHHHHHHHHHHHHHHHHH
Q 029985 3 QEVRGYFEAVLNSLATNVSKAIVLCQVEKAKEDMLNQLYSSVGAQSTARIEELLQEDQNVKRRRDRYQKQSELLSKLTR 81 (184)
Q Consensus 3 ~~V~SYF~IVrk~I~D~VPKAIMh~LVn~sKe~Lq~~L~s~LY~~~~~~l~eLL~Edp~I~~RRe~c~k~L~~LkkA~~ 81 (184)
+++.+| .++...+.+.|++++++.+.+..+..........++... ..++|..+.+.+.+.+..|.+.++.+..+..
T Consensus 467 ~l~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~ 542 (546)
T COG0699 467 SLLESL-LILAQKIRDSVLKAIFELLKNKRKRLAQKQRLKRLYLEQ--LEDELLRTAEEILELRLLLEQFLEALKLAAR 542 (546)
T ss_pred HHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHhhHHHHHHHHHHHHHHHHHHHHHH
Confidence 678999 999999999999999999988888877777766766664 5788999999999999999999988888765
No 5
>COG3579 PepC Aminopeptidase C [Amino acid transport and metabolism]
Probab=68.61 E-value=5.1 Score=37.93 Aligned_cols=53 Identities=17% Similarity=0.218 Sum_probs=44.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhcchHhHHHHhhcCHH---HHHHHHHHH
Q 029985 18 TNVSKAIVLCQVEKAKEDMLNQLYSSVGAQSTARIEELLQEDQN---VKRRRDRYQ 70 (184)
Q Consensus 18 D~VPKAIMh~LVn~sKe~Lq~~L~s~LY~~~~~~l~eLL~Edp~---I~~RRe~c~ 70 (184)
-.|||.+|--.+.-+...-+++|+.++.++....+..+++|--. |..+|+++.
T Consensus 152 GvVpK~~ypes~sSS~Sr~ln~~Ln~~LR~dAqiLR~a~~eg~~~~~v~~~kEe~l 207 (444)
T COG3579 152 GVVPKSVYPESFSSSNSRELNALLNKLLRQDAQILRDALKEGADDDTVEALKEELL 207 (444)
T ss_pred CCCchhhcccccccccHHHHHHHHHHHHHHHHHHHHHHHHhccchhHHHHHHHHHH
Confidence 36999999999998998889999999999887788899988666 777777663
No 6
>PF15369 KIAA1328: Uncharacterised protein KIAA1328
Probab=62.63 E-value=58 Score=30.32 Aligned_cols=49 Identities=20% Similarity=0.277 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHHHHHhhcchHhHHHHhhcCHHHHHHHH-------HHHHHHHHHHH
Q 029985 29 VEKAKEDMLNQLYSSVGAQSTARIEELLQEDQNVKRRRD-------RYQKQSELLSK 78 (184)
Q Consensus 29 Vn~sKe~Lq~~L~s~LY~~~~~~l~eLL~Edp~I~~RRe-------~c~k~L~~Lkk 78 (184)
|+.-|+.+-.+|-.+--.-+ .+|..|.+++.-|++.|+ +|++.|.+|++
T Consensus 20 ~~~~~e~~~~~~~~~~~~~e-~~~~~l~~~~~~~~~~~~~~~~qyrecqell~lyq~ 75 (328)
T PF15369_consen 20 VSEEKEVTEERLKAEQESFE-KKIRQLEEQNELIIKEREDLQQQYRECQELLSLYQK 75 (328)
T ss_pred hhhHHHHHHHHHHHHHHHHH-HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45555555555544332222 257777778888888776 45666666654
No 7
>KOG3742 consensus Glycogen synthase [Carbohydrate transport and metabolism]
Probab=52.86 E-value=29 Score=34.40 Aligned_cols=49 Identities=24% Similarity=0.313 Sum_probs=39.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcchHhHHHHhhcCHHHHHHHH
Q 029985 10 EAVLNSLATNVSKAIVLCQVEKAKEDMLNQLYSSVGAQSTARIEELLQEDQNVKRRRD 67 (184)
Q Consensus 10 ~IVrk~I~D~VPKAIMh~LVn~sKe~Lq~~L~s~LY~~~~~~l~eLL~Edp~I~~RRe 67 (184)
..|+|++.|. |+.+|+.+-..+|..+.+-+..++++||+-++.++-+|.
T Consensus 384 qAv~kqL~dt---------v~~Vk~~~Gkrifd~~l~g~lPd~~ell~~~d~v~lKr~ 432 (692)
T KOG3742|consen 384 QAVRKQLWDT---------VNEVKEKVGKRIFDHCLRGELPDLDELLDKDDLVLLKRC 432 (692)
T ss_pred HHHHHHHHHH---------HHHHHHHHHHHHHHHHhcccCCChHHhhChhHHHHHHHH
Confidence 3577777776 688899999999998888776789999999988876654
No 8
>cd07620 BAR_SH3BP1 The Bin/Amphiphysin/Rvs (BAR) domain of SH3-domain Binding Protein 1. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. SH3-domain binding protein 1 (SH3BP1 or 3BP-1) is a Rac GTPase activating protein that inhibits Rac-mediated platelet-derived growth factor (PDGF)-induced membrane ruffling. SH3BP1 contains an N-terminal BAR domain followed by a GAP domain for Rho and Rac GTPases and a C-terminal proline-rich domain. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=52.25 E-value=1.8e+02 Score=26.21 Aligned_cols=32 Identities=13% Similarity=0.299 Sum_probs=25.5
Q ss_pred HHHHhhcC-HHHHHHHHHHHHHHHHHHHHHHHH
Q 029985 52 IEELLQED-QNVKRRRDRYQKQSELLSKLTRQL 83 (184)
Q Consensus 52 l~eLL~Ed-p~I~~RRe~c~k~L~~LkkA~~~L 83 (184)
|..|.++| |+|...|+++.++.--|..++..+
T Consensus 112 L~~L~e~dL~~I~k~rKkL~k~~LD~D~~K~R~ 144 (257)
T cd07620 112 LNKLSEEDLPEILKNKKQFAKLTTDWNSAKSRS 144 (257)
T ss_pred HHHhHHhhHHHHHHHHHHHHhHHhhHHHHHHHH
Confidence 44555555 799999999999988888888776
No 9
>PF10863 DUF2702: Protein of unknown function (DUF2702); InterPro: IPR022592 This entry represents fungal proteins with unknown function.
Probab=51.99 E-value=42 Score=27.76 Aligned_cols=61 Identities=25% Similarity=0.320 Sum_probs=38.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhhhhhhhhccccCCCCCCCcCCCCCCCCCcchHHHHHHHhCCCCC
Q 029985 64 RRRDRYQKQSELLSKLTRQLSIHDNRAAAASNWSDGGGGAESSPRTSAASGDDWRSAFDAAANGPVS 130 (184)
Q Consensus 64 ~RRe~c~k~L~~LkkA~~~Lsi~~~~~~~~~~~~~~~~~~~~s~~~~~~~~d~w~~af~~~~~~~~~ 130 (184)
.||+++++.+++--+.+-+++..... |-+|-..+.+++.+.....-.-++=+.+|- +.|+-
T Consensus 2 sRrkEIkeK~~LQAk~Q~afS~nn~k---vl~WL~~~~~~~~~~~~~~~~~~~s~~~F~---~LPVI 62 (143)
T PF10863_consen 2 SRRKEIKEKLALQAKFQLAFSNNNSK---VLSWLKPSKSKTSSNSTSKTELNDSKDSFF---NLPVI 62 (143)
T ss_pred chHHHHHHHHHHHHHHHHHHhhhHHH---HHHhcCcCccCCCCCccccccCCccHHHhh---cCCcc
Confidence 58999999998877777777655444 567988776554443322223445555653 45553
No 10
>PF07560 DUF1539: Domain of Unknown Function (DUF1539); InterPro: IPR011436 This domain is found in a small number of Chlamydia proteins of unknown function. It occurs together with IPR013044 from INTERPRO.
Probab=50.85 E-value=9.9 Score=30.74 Aligned_cols=62 Identities=15% Similarity=0.113 Sum_probs=42.4
Q ss_pred hHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHhhcchHhHHHHhhcCHHHHHHHHH
Q 029985 6 RGYFEAVLNSLATNVS------KAIVLCQVEKAKEDMLNQLYSSVGAQSTARIEELLQEDQNVKRRRDR 68 (184)
Q Consensus 6 ~SYF~IVrk~I~D~VP------KAIMh~LVn~sKe~Lq~~L~s~LY~~~~~~l~eLL~Edp~I~~RRe~ 68 (184)
..|++-.++.|..+-+ +.|++.++.+...++..+.-.++|..-+..+-.+|+ ||.|-++|+.
T Consensus 20 ~~~~~~L~~~I~~l~~~l~~~W~~IL~~l~~~~~~~~~s~~~~~l~~~~m~~l~~aL~-dp~Is~erK~ 87 (126)
T PF07560_consen 20 TCIHRPLENEIHRLTQNLRRPWFKILDYLSTKSSPEDESHPDQSLFRSTMHQLIKALQ-DPTISKERKR 87 (126)
T ss_pred hHhHHHHHHHHHHHccCCChHHHHHHHHHhccccccccCChhHHHHHHHHHHHHHHhc-CCCCChHHHH
Confidence 4455556777777777 899999999766665555555555544445666665 8888877764
No 11
>PF12209 SAC3: Leucine permease transcriptional regulator helical domain; InterPro: IPR024293 This domain is found in fungal proteins, including the nuclear mRNA export protein SAC3. It has been suggested this domain provides a scaffold within the yeast Sac3:Cdc31:Sus1:Thp1 (TREX-2) complex to integrate interactions between protein complexes to facilitate the coupling of transcription and mRNA export during gene expression [].; PDB: 3FWC_N 3FWB_B.
Probab=43.78 E-value=1.2e+02 Score=22.30 Aligned_cols=15 Identities=13% Similarity=0.166 Sum_probs=7.4
Q ss_pred HHHHHHHHHHHHHHH
Q 029985 11 AVLNSLATNVSKAIV 25 (184)
Q Consensus 11 IVrk~I~D~VPKAIM 25 (184)
+|.+.+...+|+.|-
T Consensus 13 vV~~el~~~l~~~l~ 27 (79)
T PF12209_consen 13 VVHSELSKILKNLLR 27 (79)
T ss_dssp HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHH
Confidence 344555555555433
No 12
>PF02344 Myc-LZ: Myc leucine zipper domain; InterPro: IPR003327 This family consists of the leucine zipper dimerisation domain found in both cellular c-Myc proto-oncogenes and viral v-Myc oncogenes. Dimerisation via the leucine zipper motif with other basic helix-loop-helix-leucine zipper (b/HLH/lz) proteins is required for efficient DNA binding []. The Myc-Max dimer is a transactivating complex activating expression of growth related genes promoting cell proliferation. The dimerisation is facilitated via interdigitating leucine residues every 7th position of the alpha helix. Like charge repulsion of adjacent residues in this region preturbs the formation of homodimers with heterodimers being promoted by opposing charge attractions. It has been demonstrated that in transgenic mice the balance between oncogene-induced proliferation and apoptosis in a given tissue can be a critical determinant in the initiation and maintenance of the tumor [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1NKP_D 1A93_A 2A93_A.
Probab=43.33 E-value=26 Score=22.34 Aligned_cols=26 Identities=27% Similarity=0.607 Sum_probs=19.6
Q ss_pred HHHhhcCHHHHHHHHHHHHHHHHHHH
Q 029985 53 EELLQEDQNVKRRRDRYQKQSELLSK 78 (184)
Q Consensus 53 ~eLL~Edp~I~~RRe~c~k~L~~Lkk 78 (184)
..|+.|-+....+|++++..|+-|+.
T Consensus 4 qkL~sekeqLrrr~eqLK~kLeqlrn 29 (32)
T PF02344_consen 4 QKLISEKEQLRRRREQLKHKLEQLRN 29 (32)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHH--
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 35777788888999999988887764
No 13
>PF05983 Med7: MED7 protein; InterPro: IPR009244 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. This family consists of several eukaryotic proteins, which are homologues of the yeast MED7 protein. Activation of gene transcription in metazoans is a multistep process that is triggered by factors that recognise transcriptional enhancer sites in DNA. These factors work with co-activators such as MED7 to direct transcriptional initiation by the RNA polymerase II apparatus [].; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex; PDB: 3FBI_C 3FBN_A 1YKH_A 1YKE_A.
Probab=42.78 E-value=1.3e+02 Score=24.75 Aligned_cols=30 Identities=13% Similarity=0.336 Sum_probs=20.5
Q ss_pred HHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHH
Q 029985 52 IEELLQEDQNVKRRRDRYQKQSELLSKLTRQL 83 (184)
Q Consensus 52 l~eLL~Edp~I~~RRe~c~k~L~~LkkA~~~L 83 (184)
+..||+| .+.+||+++.++-..+.+|.+.|
T Consensus 132 Li~~me~--Ql~~kr~~i~~i~~~~~~~~~~l 161 (162)
T PF05983_consen 132 LIMMMEE--QLEEKREEIEEIRKVCEKAREVL 161 (162)
T ss_dssp HHHHHHH--HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHH--HHHHHHHHHHHHHHHHHHHHHHh
Confidence 4444543 46678888877777777777766
No 14
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=41.19 E-value=83 Score=26.96 Aligned_cols=42 Identities=14% Similarity=0.085 Sum_probs=19.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhcchHhHHHHhhcCHHHHHHH
Q 029985 20 VSKAIVLCQVEKAKEDMLNQLYSSVGAQSTARIEELLQEDQNVKRRR 66 (184)
Q Consensus 20 VPKAIMh~LVn~sKe~Lq~~L~s~LY~~~~~~l~eLL~Edp~I~~RR 66 (184)
+||.+-.+..+...+..+++.=-.+ +.+.+++.|.++...+|
T Consensus 86 a~~df~~~f~t~f~ek~~ReId~t~-----e~l~k~~~e~~~~~~~~ 127 (177)
T COG1510 86 AEKDFSQIFRTLFEEKWKREIDPTK-----EALKKLLEELNEDLDDR 127 (177)
T ss_pred ccchHHHHHHHHHHHHHHHHhhhHH-----HHHHHHHHHccccccch
Confidence 4555555555555554444432222 23445555544444433
No 15
>PF08544 GHMP_kinases_C: GHMP kinases C terminal ; InterPro: IPR013750 This domain is found in homoserine kinases (2.7.1.39 from EC), galactokinases (2.7.1.6 from EC) and mevalonate kinases (2.7.1.36 from EC). These kinases make up the GHMP kinase superfamily of ATP-dependent enzymes []. These enzymes are involved in the biosynthesis of isoprenes and amino acids as well as in carbohydrate metabolism. The C-terminal domain of homoserine kinase has a central alpha-beta plait fold and an insertion of four helices, which, together with the N-terminal fold, create a novel nucleotide binding fold [].; PDB: 2R3V_C 4EMD_A 4DXL_A 4ED4_A 2GS8_A 1K47_E 3GON_A 3K17_B 1PIE_A 2AJ4_A ....
Probab=39.65 E-value=46 Score=22.63 Aligned_cols=47 Identities=11% Similarity=0.135 Sum_probs=27.8
Q ss_pred HHHhhcchHhHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHHhhhhhh
Q 029985 42 SSVGAQSTARIEELLQEDQNVKRRRDRYQKQSELLSKLTRQLSIHDNR 89 (184)
Q Consensus 42 s~LY~~~~~~l~eLL~Edp~I~~RRe~c~k~L~~LkkA~~~Lsi~~~~ 89 (184)
..|...+.+.+.++|.++... +.+.........+..+.+.+..++..
T Consensus 3 ~al~~~d~~~~~~~~~~~~~~-~~~~~~~~~~~~i~~~~~~~~~~Ga~ 49 (85)
T PF08544_consen 3 KALAEGDLELLGELMNENQEN-EPENYREVLTPEIDELKEAAEENGAL 49 (85)
T ss_dssp HHHHTTCHHHHHHHHHHHHHH-HHHHHTTHHHHHHHHHHHHHHHTTES
T ss_pred HHHHCcCHHHHHHHHHHhhhh-cchHHHHHcCHHHHHHHHHHHHCCCC
Confidence 344445556788888887775 33233333456666777777666633
No 16
>PF09738 DUF2051: Double stranded RNA binding protein (DUF2051); InterPro: IPR019139 This entry represents transcriptional repressors which preferentially bind to the GC-rich consensus sequence (5'-AGCCCCCGGCG-3') and may regulate expression of TNF, EGFR and PDGFA. They may control smooth muscle cell proliferation following artery injury through PDGFA repression and may also bind double-stranded RNA. They interact with the leucine-rich repeat domain of human flightless-I (FliI) protein.
Probab=39.42 E-value=2.7e+02 Score=25.33 Aligned_cols=105 Identities=14% Similarity=0.216 Sum_probs=51.3
Q ss_pred HHHHHHHHHHHHHHHH--HHHHHHHHhhcchHhHHHHhhcCHHHHHHHHHHHHHHHHHH----HHHHHHhhhhhhhhh--
Q 029985 21 SKAIVLCQVEKAKEDM--LNQLYSSVGAQSTARIEELLQEDQNVKRRRDRYQKQSELLS----KLTRQLSIHDNRAAA-- 92 (184)
Q Consensus 21 PKAIMh~LVn~sKe~L--q~~L~s~LY~~~~~~l~eLL~Edp~I~~RRe~c~k~L~~Lk----kA~~~Lsi~~~~~~~-- 92 (184)
=|+-+++.|.-.|+.| +.+.+..+.++ +.+...|-+-.+.....++..+..|+ .--+.|..||.+.-.
T Consensus 106 ek~~l~yqvd~Lkd~lee~eE~~~~~~re----~~eK~~elEr~K~~~d~L~~e~~~Lre~L~~rdeli~khGlVlv~~~ 181 (302)
T PF09738_consen 106 EKSALMYQVDLLKDKLEELEETLAQLQRE----YREKIRELERQKRAHDSLREELDELREQLKQRDELIEKHGLVLVPDA 181 (302)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCeeeCCCC
Confidence 4777888898888854 34455555554 33334443444444444444444444 344456778877221
Q ss_pred hccccCCCCCCCcCCCCCCCCCcchHHHHHHHhCCCCC
Q 029985 93 ASNWSDGGGGAESSPRTSAASGDDWRSAFDAAANGPVS 130 (184)
Q Consensus 93 ~~~~~~~~~~~~~s~~~~~~~~d~w~~af~~~~~~~~~ 130 (184)
.+|=..+..+. +..+.+..|.-+=..+++.|..|+-|
T Consensus 182 ~ngd~~~~~~~-~~~~~~~~vs~e~a~~L~~aG~g~LD 218 (302)
T PF09738_consen 182 TNGDTSDEPNN-VGHPKRALVSQEAAQLLESAGDGSLD 218 (302)
T ss_pred CCCccccCccc-cCCCcccccchhhhhhhcccCCCCHH
Confidence 11111110000 11222233555666667777666653
No 17
>PLN03184 chloroplast Hsp70; Provisional
Probab=38.47 E-value=2.8e+02 Score=27.45 Aligned_cols=7 Identities=0% Similarity=0.268 Sum_probs=2.8
Q ss_pred HHHhhcC
Q 029985 53 EELLQED 59 (184)
Q Consensus 53 ~eLL~Ed 59 (184)
++.|.++
T Consensus 605 e~wL~~~ 611 (673)
T PLN03184 605 KDAIASG 611 (673)
T ss_pred HHHHhcC
Confidence 3444443
No 18
>KOG4552 consensus Vitamin-D-receptor interacting protein complex component [Transcription]
Probab=38.24 E-value=3e+02 Score=24.77 Aligned_cols=18 Identities=22% Similarity=0.490 Sum_probs=9.5
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 029985 20 VSKAIVLCQVEKAKEDML 37 (184)
Q Consensus 20 VPKAIMh~LVn~sKe~Lq 37 (184)
+-|-|+..|++.-+..|+
T Consensus 23 i~kelie~l~~~~~qk~l 40 (272)
T KOG4552|consen 23 IVKELIETLINRDKQKML 40 (272)
T ss_pred HHHHHHHHHHhhhHHHHH
Confidence 445555556555555443
No 19
>PF11594 Med28: Mediator complex subunit 28; InterPro: IPR021640 Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species [],[]. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function []. Subunit Med28 of the Mediator may function as a scaffolding protein within Mediator by maintaining the stability of a submodule within the head module, and components of this submodule act together in a gene-regulatory programme to suppress smooth muscle cell differentiation. Thus, mammalian Mediator subunit Med28 functions as a repressor of smooth muscle-cell differentiation, which could have implications for disorders associated with abnormalities in smooth muscle cell growth and differentiation, including atherosclerosis, asthma, hypertension, and smooth muscle tumours [].
Probab=38.16 E-value=2e+02 Score=22.74 Aligned_cols=78 Identities=18% Similarity=0.267 Sum_probs=48.5
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcchHhHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHHh
Q 029985 5 VRGYFEAVLNSLATNVSKAIVLCQVEKAKEDMLNQLYSSVGAQSTARIEELLQEDQNVKRRRDRYQKQSELLSKLTRQLS 84 (184)
Q Consensus 5 V~SYF~IVrk~I~D~VPKAIMh~LVn~sKe~Lq~~L~s~LY~~~~~~l~eLL~Edp~I~~RRe~c~k~L~~LkkA~~~Ls 84 (184)
|++|++-....+.|.+=..=-+ .|+..+.-++|+ .+..|+|+- -+-+.+|+..=+++++....|.
T Consensus 2 irt~vEq~~~~FlD~aRq~e~~--------FlqKr~~LS~~k-----pe~~lkEEi--~eLK~ElqRKe~Ll~Kh~~kI~ 66 (106)
T PF11594_consen 2 IRTYVEQLIQSFLDVARQMEAF--------FLQKRFELSAYK-----PEQVLKEEI--NELKEELQRKEQLLQKHYEKID 66 (106)
T ss_pred chhHHHHHHHHHHHHHHHHHHH--------HHHHHHHHHhcC-----HHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHH
Confidence 5566665555555543332222 245565556665 456666653 3344888888888899999998
Q ss_pred hhhhhhhhhcccc
Q 029985 85 IHDNRAAAASNWS 97 (184)
Q Consensus 85 i~~~~~~~~~~~~ 97 (184)
.|.....-+.++.
T Consensus 67 ~w~~lL~d~~~~~ 79 (106)
T PF11594_consen 67 YWEKLLSDAQNQH 79 (106)
T ss_pred HHHHHHHHHHhhc
Confidence 8888866666443
No 20
>KOG0562 consensus Predicted hydrolase (HIT family) [General function prediction only]
Probab=37.51 E-value=4.3 Score=34.73 Aligned_cols=16 Identities=19% Similarity=0.071 Sum_probs=14.2
Q ss_pred HHHHHHHHHHHHHHHH
Q 029985 16 LATNVSKAIVLCQVEK 31 (184)
Q Consensus 16 I~D~VPKAIMh~LVn~ 31 (184)
|+|..|||=||.||--
T Consensus 28 IrD~fPKa~~H~LvLp 43 (184)
T KOG0562|consen 28 IRDKFPKARMHLLVLP 43 (184)
T ss_pred EcccCccceeEEEEec
Confidence 7899999999999854
No 21
>PF05746 DALR_1: DALR anticodon binding domain; InterPro: IPR008909 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This all alpha helical domain is the anticodon binding domain of Arginyl tRNA synthetase. This domain is known as the DALR domain after characteristic conserved amino acids [].; GO: 0004814 arginine-tRNA ligase activity, 0005524 ATP binding, 0006420 arginyl-tRNA aminoacylation; PDB: 2ZUE_A 2ZUF_A 3FNR_A 1F7V_A 1F7U_A 1BS2_A 1IQ0_A.
Probab=37.25 E-value=1.6e+02 Score=21.43 Aligned_cols=65 Identities=14% Similarity=0.207 Sum_probs=40.2
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcchHhHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHH
Q 029985 4 EVRGYFEAVLNSLATNVSKAIVLCQVEKAKEDMLNQLYSSVGAQSTARIEELLQEDQNVKRRRDRYQKQSELLSKLTRQL 83 (184)
Q Consensus 4 ~V~SYF~IVrk~I~D~VPKAIMh~LVn~sKe~Lq~~L~s~LY~~~~~~l~eLL~Edp~I~~RRe~c~k~L~~LkkA~~~L 83 (184)
.+..|-.+|.+.+.+.=|-.++..|.+= ...+.+.|..- -.|.|++.+. ...+|.+++....+|
T Consensus 41 ~l~~~~~~l~~a~~~~~p~~l~~yL~~L------a~~f~~fy~~~-----~I~~~~~~~~-----~~~RL~Ll~~v~~vl 104 (119)
T PF05746_consen 41 QLARFPDVLEKAAKDLEPHKLCDYLYEL------AQAFNSFYDNV-----RILDEDEEIR-----KNNRLALLKAVRQVL 104 (119)
T ss_dssp HHCTHHHHHHHHHHHT-CHHHHHHHHHH------HHHHHHHHHHS------STTSTTCHH------HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhHHHHHHHHHHHHH------HHHHHHHHhhc-----cccccchHHH-----HHHHHHHHHHHHHHH
Confidence 4566777888888888888888888763 44555555432 4677777776 233345555555555
Q ss_pred h
Q 029985 84 S 84 (184)
Q Consensus 84 s 84 (184)
.
T Consensus 105 ~ 105 (119)
T PF05746_consen 105 K 105 (119)
T ss_dssp H
T ss_pred H
Confidence 4
No 22
>PRK10353 3-methyl-adenine DNA glycosylase I; Provisional
Probab=36.36 E-value=85 Score=26.76 Aligned_cols=43 Identities=26% Similarity=0.431 Sum_probs=28.6
Q ss_pred HHHhhcchHhHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 029985 42 SSVGAQSTARIEELLQEDQNVKRRRDRYQKQSELLSKLTRQLSIHDN 88 (184)
Q Consensus 42 s~LY~~~~~~l~eLL~Edp~I~~RRe~c~k~L~~LkkA~~~Lsi~~~ 88 (184)
..+.+-+.++++.||+ |+.|++.|.+++ .+...|+..|.+...
T Consensus 66 ~~VA~~~e~die~Ll~-d~~IIRnr~KI~---Avi~NA~~~l~i~~e 108 (187)
T PRK10353 66 VKVAAMQEEDVERLVQ-DAGIIRHRGKIQ---AIIGNARAYLQMEQN 108 (187)
T ss_pred HHHhCCCHHHHHHHhc-CchhHHhHHHHH---HHHHHHHHHHHHHHh
Confidence 3444444457888887 667777777774 566777777766544
No 23
>PF09440 eIF3_N: eIF3 subunit 6 N terminal domain; InterPro: IPR019010 This entry represents the N-terminal domain of subunit 6 (or e) (eIF3e) of the translation initiation factor eIF3. EIF3 is required in protein synthesis in mammalian cells and, together with other initiation factors, stimulates binding of initiator methionyl-tRNAi and mRNA to the 40S ribosomal subunit to form the 48 S initiation complex []. The eIF3 complex also prevents premature association of the 40 and 60 S ribosomal subunits and interacts with other initiation factors involved in start codon selection. EIF3 has at least 13 protein components (eIF3a-m or 1-13), where subunits h, i, k, and m are likely to be on the periphery of the complex []. Subunit 6 is produced by the int6 gene, one of the frequent integration sites for mouse mammary tumor viruses [].
Probab=36.18 E-value=2e+02 Score=23.07 Aligned_cols=26 Identities=12% Similarity=0.161 Sum_probs=20.3
Q ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHH
Q 029985 58 EDQNVKRRRDRYQKQSELLSKLTRQL 83 (184)
Q Consensus 58 Edp~I~~RRe~c~k~L~~LkkA~~~L 83 (184)
-..+.++||++..++++.|+.....+
T Consensus 63 ~p~e~~~kr~~Vl~~l~~l~~~~~~v 88 (133)
T PF09440_consen 63 VPAELAEKREEVLAELKELEEETEPV 88 (133)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35677899999988888888766554
No 24
>KOG1899 consensus LAR transmembrane tyrosine phosphatase-interacting protein liprin [General function prediction only]
Probab=30.65 E-value=4.6e+02 Score=27.21 Aligned_cols=34 Identities=15% Similarity=0.225 Sum_probs=17.8
Q ss_pred HHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 029985 52 IEELLQEDQNVKRRRDRYQKQSELLSKLTRQLSI 85 (184)
Q Consensus 52 l~eLL~Edp~I~~RRe~c~k~L~~LkkA~~~Lsi 85 (184)
+++||.-+++--.+=+.++..+.-|++-+++..+
T Consensus 283 ~eslm~ane~kdr~ie~lr~~ln~y~k~~~iv~i 316 (861)
T KOG1899|consen 283 LESLMRANEQKDRFIESLRNYLNNYDKNAQIVRI 316 (861)
T ss_pred HHHHHhhchhhhhHHHHHHHHhhhhhhhhhhhhh
Confidence 3455555554444445555555555555555443
No 25
>smart00751 BSD domain in transcription factors and synapse-associated proteins.
Probab=30.59 E-value=58 Score=21.49 Aligned_cols=20 Identities=30% Similarity=0.444 Sum_probs=15.5
Q ss_pred HhHHHHhhcCHHHHHHHHHH
Q 029985 50 ARIEELLQEDQNVKRRRDRY 69 (184)
Q Consensus 50 ~~l~eLL~Edp~I~~RRe~c 69 (184)
+.+..||+|+|.+.+-+.++
T Consensus 10 ~~i~~il~~~p~l~~~~~~l 29 (51)
T smart00751 10 EEIESLLKENPLLKKLYNEL 29 (51)
T ss_pred HHHHHHHHHCHHHHHHHHHH
Confidence 46788999999888776664
No 26
>PF10397 ADSL_C: Adenylosuccinate lyase C-terminus; InterPro: IPR019468 Adenylosuccinate lyase catalyses two steps in the synthesis of purine nucleotides: the conversion of succinylaminoimidazole-carboxamide ribotide into aminoimidazole-carboxamide ribotide (the fifth step of de novo IMP biosynthesis); the formation of adenosine monophosphate (AMP) from adenylosuccinate (the final step in the synthesis of AMP from IMP) []. This entry represents the C-terminal, seven alpha-helical, domain of adenylosuccinate lyase [].; PDB: 1YIS_A 1C3U_B 1C3C_A 3C8T_A 2PFM_B 1RE5_D 1Q5N_A 2VD6_D 2J91_B 2X75_A.
Probab=30.43 E-value=1.6e+02 Score=20.89 Aligned_cols=40 Identities=15% Similarity=0.329 Sum_probs=21.2
Q ss_pred HHHHHHHHH--HHH---HHHHHHHHHHhhcchHhHHHHhhcCHHHH
Q 029985 23 AIVLCQVEK--AKE---DMLNQLYSSVGAQSTARIEELLQEDQNVK 63 (184)
Q Consensus 23 AIMh~LVn~--sKe---~Lq~~L~s~LY~~~~~~l~eLL~Edp~I~ 63 (184)
+||..|+.+ .|+ ++..++-..-.... ..|.+.|.+||.|.
T Consensus 8 ~v~~~L~~~G~gR~~Ah~lv~~~a~~a~~~~-~~l~e~l~~d~~i~ 52 (81)
T PF10397_consen 8 RVMLALAEKGLGRQEAHELVQEAAMEAWENG-RDLREVLLADPEIA 52 (81)
T ss_dssp HHHHHHHHTTH-HHHHHHHHHHHHHHHHHTT-S-HHHHHCTTHHHH
T ss_pred HHHHHHHHHccCHHHHHHHHHHHHHHHHHHC-CCHHHHHHCCHHHH
Confidence 456666655 222 22222322233333 26888999999988
No 27
>KOG2470 consensus Similar to IMP-GMP specific 5'-nucleotidase [Nucleotide transport and metabolism]
Probab=30.26 E-value=63 Score=31.15 Aligned_cols=22 Identities=45% Similarity=0.762 Sum_probs=15.4
Q ss_pred CCCCCCCcchHHHHHH---HhCCCC
Q 029985 108 RTSAASGDDWRSAFDA---AANGPV 129 (184)
Q Consensus 108 ~~~~~~~d~w~~af~~---~~~~~~ 129 (184)
++.=-||+|||..||- +|+-|.
T Consensus 273 GM~flvG~~WRdlFDVVIvqA~KP~ 297 (510)
T KOG2470|consen 273 GMRFLVGDDWRDLFDVVIVQANKPE 297 (510)
T ss_pred CceeeeCccHHhhhheeEEecCCCc
Confidence 3444589999999995 455554
No 28
>PF11221 Med21: Subunit 21 of Mediator complex; InterPro: IPR021384 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. Med21 has been known as Srb7 in yeasts, hSrb7 in humans and Trap 19 in Drosophila. The heterodimer of the two subunits Med7 and Med21 appears to act as a hinge between the middle and the tail regions of Mediator []. ; PDB: 1YKE_B 1YKH_B.
Probab=30.15 E-value=2.8e+02 Score=22.01 Aligned_cols=63 Identities=24% Similarity=0.303 Sum_probs=38.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhcc------hHhHHHHhhcCHHHHHHHHHHHH-HHHHHHHHHHHHh
Q 029985 20 VSKAIVLCQVEKAKEDMLNQLYSSVGAQS------TARIEELLQEDQNVKRRRDRYQK-QSELLSKLTRQLS 84 (184)
Q Consensus 20 VPKAIMh~LVn~sKe~Lq~~L~s~LY~~~------~~~l~eLL~Edp~I~~RRe~c~k-~L~~LkkA~~~Ls 84 (184)
-.+-....+|.++|. .+.|+.+|=..+ .+.|.+|-.|..++.++|++..+ .=++|+++...|.
T Consensus 70 ~~~elA~dIi~kakq--Ie~LIdsLPg~~~see~Q~~~i~~L~~E~~~~~~el~~~v~e~e~ll~~v~~~i~ 139 (144)
T PF11221_consen 70 NIKELATDIIRKAKQ--IEYLIDSLPGIEVSEEEQLKRIKELEEENEEAEEELQEAVKEAEELLKQVQELIR 139 (144)
T ss_dssp HHHHHHHHHHHHHHH--HHHHHHHSTTSSS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHH--HHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344445556666665 356677664421 34788999999999866655544 4445555555553
No 29
>PF10987 DUF2806: Protein of unknown function (DUF2806); InterPro: IPR021254 This bacterial family of proteins has no known function.
Probab=28.41 E-value=1.4e+02 Score=25.55 Aligned_cols=16 Identities=25% Similarity=0.360 Sum_probs=12.2
Q ss_pred CCCCCcchHHHHHHHh
Q 029985 110 SAASGDDWRSAFDAAA 125 (184)
Q Consensus 110 ~~~~~d~w~~af~~~~ 125 (184)
.-+++.||+..|-..|
T Consensus 36 ~~~vD~DWl~~f~~~A 51 (219)
T PF10987_consen 36 GEPVDPDWLYRFFDMA 51 (219)
T ss_pred CCCCChHHHHHHHHHH
Confidence 3448999999986655
No 30
>PRK03926 mevalonate kinase; Provisional
Probab=27.52 E-value=2.1e+02 Score=24.52 Aligned_cols=56 Identities=13% Similarity=0.020 Sum_probs=28.3
Q ss_pred HHHHHhhcchHhHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhccccC
Q 029985 40 LYSSVGAQSTARIEELLQEDQNVKRRRDRYQKQSELLSKLTRQLSIHDNRAAAASNWSD 98 (184)
Q Consensus 40 L~s~LY~~~~~~l~eLL~Edp~I~~RRe~c~k~L~~LkkA~~~Lsi~~~~~~~~~~~~~ 98 (184)
++..|...+.+.+.++|.++......+.- ....|..+.+.+...+...+..||...
T Consensus 204 ~~~al~~~d~~~l~~~~~~~~~~~~~~~~---~~p~l~~l~~~~~~~ga~ga~lSGaG~ 259 (302)
T PRK03926 204 GEELILSGDYVSLGELMNINQGLLDALGV---STKELSELIYAARTAGALGAKITGAGG 259 (302)
T ss_pred HHHHHhcCCHHHHHHHHHHHHHHHHhcCC---CCHHHHHHHHHHHhCCCceeeeccCCC
Confidence 34444455555677888777654332211 234444555555445554455554444
No 31
>cd01068 sensor_globin Globin domain present in Globin-Coupled-Sensors (GCS). These domains detect changes in intracellular concentrations of oxygen, carbon monoxyde, or nitrous oxide, which result in aerotaxis and/or gene regulation. One subgroup, the HemATs, are aerotactic heme sensors combining a globin with an MCP signaling domain, others function as gene regulators, by direct combination with DNA-binding domains, with domains modulating 2nd messengers, or with domains interacting with transcription factors or regulators.
Probab=26.71 E-value=2.8e+02 Score=20.86 Aligned_cols=45 Identities=11% Similarity=0.328 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHHHHHHHHhhcchHhHHHHhhcCHHHHHHHHHHHHHH
Q 029985 27 CQVEKAKEDMLNQLYSSVGAQSTARIEELLQEDQNVKRRRDRYQKQS 73 (184)
Q Consensus 27 ~LVn~sKe~Lq~~L~s~LY~~~~~~l~eLL~Edp~I~~RRe~c~k~L 73 (184)
-+|..-.+.+.+.+|..|.+.+ .+..++..+..+.+.+...++-+
T Consensus 25 ~~~~~~~~~i~~~FY~~l~~~p--~~~~~~~~~~~~~~l~~~~~~~~ 69 (147)
T cd01068 25 PVIEANADELVDRFYDHLRRTP--ETAAFLGDESVVERLKSTQRRHW 69 (147)
T ss_pred HHHHHHHHHHHHHHHHHHhcCh--HHHHHhCCchHHHHHHHHHHHHH
Confidence 3456666788999999998885 57888876555555444444333
No 32
>PLN02451 homoserine kinase
Probab=26.65 E-value=1.6e+02 Score=27.03 Aligned_cols=58 Identities=12% Similarity=0.067 Sum_probs=37.2
Q ss_pred HHHHHHHhhcchHhHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhccccC
Q 029985 38 NQLYSSVGAQSTARIEELLQEDQNVKRRRDRYQKQSELLSKLTRQLSIHDNRAAAASNWSD 98 (184)
Q Consensus 38 ~~L~s~LY~~~~~~l~eLL~Edp~I~~RRe~c~k~L~~LkkA~~~Lsi~~~~~~~~~~~~~ 98 (184)
..|+..|...+.+.+.++|.+|......|... ...|.++.+.+...+...+..||+.+
T Consensus 262 ~~l~~al~~~d~~~l~~~m~nD~~~e~~r~~~---~P~l~~l~~~~~~~GA~ga~mSGSGp 319 (370)
T PLN02451 262 AALVAAILQGDAVLLGEALSSDKIVEPTRAPL---IPGMEAVKKAALEAGAYGCTISGAGP 319 (370)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHhHHHHhhh---CccHHHHHHHHHHCCCeEEEEEccch
Confidence 35667776666556777888887777777666 44555666666556665455555444
No 33
>PRK09498 sifA secreted effector protein SifA; Reviewed
Probab=26.57 E-value=1.1e+02 Score=28.53 Aligned_cols=42 Identities=14% Similarity=0.264 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHHHH--HHHHHHHHHHHhhcchHhHHHHhhcCHHHHH
Q 029985 20 VSKAIVLCQVEKAK--EDMLNQLYSSVGAQSTARIEELLQEDQNVKR 64 (184)
Q Consensus 20 VPKAIMh~LVn~sK--e~Lq~~L~s~LY~~~~~~l~eLL~Edp~I~~ 64 (184)
.-|..+.||++.+- ..+|++|..-+.-+ .+..|..|||...+
T Consensus 268 ~~~~~~~~L~~~~~~~q~~l~ei~E~is~~---v~~~lF~~d~q~i~ 311 (336)
T PRK09498 268 ADKTFQAFLVTDPSTSQSMLAEIVEAISDQ---VFHAIFRIDPQAIQ 311 (336)
T ss_pred hhHHHHHHHhcCcchhHHHHHHHHHHHHHH---HHHHHHhcCHHHHH
Confidence 34777888888754 36899999988655 79999999998766
No 34
>KOG1923 consensus Rac1 GTPase effector FRL [Signal transduction mechanisms; Cytoskeleton]
Probab=26.33 E-value=7.8e+02 Score=25.88 Aligned_cols=74 Identities=18% Similarity=0.201 Sum_probs=42.8
Q ss_pred hhHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc-------chHhHHHHhhcCHHHHHHHHHHHHHHH
Q 029985 5 VRGYFEA---VLNSLATNVSKAIVLCQVEKAKEDMLNQLYSSVGAQ-------STARIEELLQEDQNVKRRRDRYQKQSE 74 (184)
Q Consensus 5 V~SYF~I---Vrk~I~D~VPKAIMh~LVn~sKe~Lq~~L~s~LY~~-------~~~~l~eLL~Edp~I~~RRe~c~k~L~ 74 (184)
+.||.+- |+.-+.|.-+|+.++--|....+.+-.+-...+-.+ -....-.|-.|-..+..-|+++...+.
T Consensus 141 ~~sy~dn~~dv~all~ds~~k~~~le~v~~~~~~isher~~~v~~~~~s~~A~l~~~s~sl~~er~~~~~~~~~~~dels 220 (830)
T KOG1923|consen 141 FQSYTDNLTDVRALLRDSFQKTFVLEFVETPADQISHERLQAVEMAQASAPAPLPGASSSLNKEREPQSYQRKALLDELS 220 (830)
T ss_pred HHHHhhhHHHHHHhcccchhhhHHHHhhcchhhhhhHHHHHHHHHHHhcCcccCchhhhhhhhhhhHHHHHHHHhcchhH
Confidence 5677664 578899999999999999888876622222221111 011233445555665655655544444
Q ss_pred HHHH
Q 029985 75 LLSK 78 (184)
Q Consensus 75 ~Lkk 78 (184)
.+++
T Consensus 221 ~m~k 224 (830)
T KOG1923|consen 221 CMQK 224 (830)
T ss_pred HHHH
Confidence 4433
No 35
>PF15030 DUF4527: Protein of unknown function (DUF4527)
Probab=25.88 E-value=1.1e+02 Score=27.91 Aligned_cols=36 Identities=25% Similarity=0.379 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHHHH--HHHHHHHHHHhhcchHhHHHHhhc
Q 029985 21 SKAIVLCQVEKAKE--DMLNQLYSSVGAQSTARIEELLQE 58 (184)
Q Consensus 21 PKAIMh~LVn~sKe--~Lq~~L~s~LY~~~~~~l~eLL~E 58 (184)
=||-+.+||.++++ .|..+|..+|.+-.. .+-||.|
T Consensus 77 LKak~AslV~kc~eRn~Li~~llqel~RHg~--~~~lLse 114 (277)
T PF15030_consen 77 LKAKLASLVQKCRERNRLITHLLQELHRHGP--ANHLLSE 114 (277)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc--hhHHHHH
Confidence 38889999999988 688888888877653 4444443
No 36
>PRK12772 bifunctional flagellar biosynthesis protein FliR/FlhB; Provisional
Probab=25.05 E-value=6.6e+02 Score=24.90 Aligned_cols=66 Identities=8% Similarity=0.099 Sum_probs=39.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHhhcchHhHHHHh---hcCHHHHHHHHHHHHHHH
Q 029985 9 FEAVLNSLATNVSKAIVLCQVEKAKE-DMLNQLYSSVGAQSTARIEELL---QEDQNVKRRRDRYQKQSE 74 (184)
Q Consensus 9 F~IVrk~I~D~VPKAIMh~LVn~sKe-~Lq~~L~s~LY~~~~~~l~eLL---~Edp~I~~RRe~c~k~L~ 74 (184)
...+.+.+...+=..+..++|-.+-| -.|...|.+=-+.+.+++++=. +=||+|+.||++.++.+.
T Consensus 439 ~~~~~~~~~~l~~~~~~~~~via~~D~~~q~~~~~k~lkMskqEvK~E~Ke~EGdP~iK~r~R~~~re~~ 508 (609)
T PRK12772 439 ITELKSLVISIFFRITLIMIIIAVADYVYQKYQYNKDLRMTKQEVKEEYKQDEGDPQIKAKIKQKQREMA 508 (609)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHhccCCHHHHHHHHHHHHHHH
Confidence 44444555555555555566666666 4566666665565533444333 348999999999876654
No 37
>PF07303 Occludin_ELL: Occludin homology domain; InterPro: IPR010844 This represents a conserved region approximately 100 residues long within eukaryotic occludin proteins and the RNA polymerase II elongation factor ELL. Occludin is an integral membrane protein that localises to tight junctions [], while ELL is an elongation factor that can increase the catalytic rate of RNA polymerase II transcription by suppressing transient pausing by polymerase at multiple sites along the DNA []. This shared domain is thought to mediate protein interactions [].; PDB: 1WPA_A 3G7C_A 1XAW_A.
Probab=24.73 E-value=2.7e+02 Score=21.27 Aligned_cols=35 Identities=17% Similarity=0.258 Sum_probs=30.3
Q ss_pred HHHhhcCHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 029985 53 EELLQEDQNVKRRRDRYQKQSELLSKLTRQLSIHD 87 (184)
Q Consensus 53 ~eLL~Edp~I~~RRe~c~k~L~~LkkA~~~Lsi~~ 87 (184)
..+-..||...+++++|.-+-.-|..+++.+..+|
T Consensus 66 ~k~Kk~~p~y~~~K~Rc~yL~~KL~HIK~~I~~yD 100 (101)
T PF07303_consen 66 NKKKKRDPNYQEKKKRCEYLHNKLSHIKQLIQDYD 100 (101)
T ss_dssp HHHHHTSHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHhcCccHHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence 33447799999999999999999999999998886
No 38
>PF06156 DUF972: Protein of unknown function (DUF972); InterPro: IPR010377 FUNCTION: Involved in initiation control of chromosome replication. SUBUNIT: Interacts with both DnaA and DnaN, acting as a bridge between these two proteins. SIMILARITY: Belongs to the YabA family.
Probab=24.68 E-value=1.6e+02 Score=22.78 Aligned_cols=41 Identities=22% Similarity=0.412 Sum_probs=29.8
Q ss_pred HHHHHHHHhhcchHhHHHHhhcCHHHHHHHHHHHHHHHHHHH
Q 029985 37 LNQLYSSVGAQSTARIEELLQEDQNVKRRRDRYQKQSELLSK 78 (184)
Q Consensus 37 q~~L~s~LY~~~~~~l~eLL~Edp~I~~RRe~c~k~L~~Lkk 78 (184)
+..|+.+|..-. ..+.+|++|+......-..++++|.-+.+
T Consensus 17 l~~l~~~~~~LK-~~~~~l~EEN~~L~~EN~~Lr~~l~~~~~ 57 (107)
T PF06156_consen 17 LGQLLEELEELK-KQLQELLEENARLRIENEHLRERLEELEQ 57 (107)
T ss_pred HHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 345666665554 37899999999998888888777766555
No 39
>PF12787 EcsC: EcsC protein family; InterPro: IPR024787 Proteins in this family are related to EcsC from Bacillus subtilis. This protein is found in an operon with EcsA and EcsB which are components of an ABC transport system []. The function of this protein is unknown.
Probab=24.12 E-value=4.4e+02 Score=22.28 Aligned_cols=30 Identities=0% Similarity=0.020 Sum_probs=21.3
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029985 5 VRGYFEAVLNSLATNVSKAIVLCQVEKAKE 34 (184)
Q Consensus 5 V~SYF~IVrk~I~D~VPKAIMh~LVn~sKe 34 (184)
...+++.+.+-|.+.||.-+...+......
T Consensus 22 ~~k~~~~~~~~v~~~iP~~~~~~i~~~~~~ 51 (249)
T PF12787_consen 22 LSKLTKWIQRPVEKKIPEKVQEKITKAIEK 51 (249)
T ss_pred HHHHHHHHHHHHHHHCcHHHHHHHHHHHHH
Confidence 456778888888899998776655544443
No 40
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=23.87 E-value=9.2e+02 Score=25.87 Aligned_cols=12 Identities=8% Similarity=0.476 Sum_probs=6.5
Q ss_pred HHHHHHHHHHHH
Q 029985 7 GYFEAVLNSLAT 18 (184)
Q Consensus 7 SYF~IVrk~I~D 18 (184)
+||.++-.-|.+
T Consensus 423 qYykLIEecISq 434 (1102)
T KOG1924|consen 423 QYYKLIEECISQ 434 (1102)
T ss_pred HHHHHHHHHHHH
Confidence 566665444444
No 41
>KOG2391 consensus Vacuolar sorting protein/ubiquitin receptor VPS23 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=23.80 E-value=6.2e+02 Score=24.06 Aligned_cols=37 Identities=22% Similarity=0.166 Sum_probs=27.7
Q ss_pred HHHhhcCHHHHHHHHHHHHHHHHHHHHHHHHhhhhhh
Q 029985 53 EELLQEDQNVKRRRDRYQKQSELLSKLTRQLSIHDNR 89 (184)
Q Consensus 53 ~eLL~Edp~I~~RRe~c~k~L~~LkkA~~~Lsi~~~~ 89 (184)
++|..-..++...++++++++..|++..++|.-+...
T Consensus 242 EeL~~G~~kL~~~~etLEqq~~~L~~niDIL~~k~~e 278 (365)
T KOG2391|consen 242 EELNIGKQKLVAMKETLEQQLQSLQKNIDILKSKVRE 278 (365)
T ss_pred HHHHhhHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHH
Confidence 3444445667778888888888888888888877766
No 42
>PRK04964 hypothetical protein; Provisional
Probab=23.74 E-value=3e+02 Score=20.17 Aligned_cols=23 Identities=26% Similarity=0.180 Sum_probs=17.4
Q ss_pred hHHHHHHHHHHHH-------HHHHHHHHHH
Q 029985 6 RGYFEAVLNSLAT-------NVSKAIVLCQ 28 (184)
Q Consensus 6 ~SYF~IVrk~I~D-------~VPKAIMh~L 28 (184)
.-|.+.||+.... .|||||-+-+
T Consensus 2 ~~yCelvR~~ya~IgSGd~gYiP~Ai~ca~ 31 (66)
T PRK04964 2 YKYCELVRKRYAEIGSGDLGYVPDALGCVL 31 (66)
T ss_pred hHHHHHHHHHHHHhcCCccccCcHHHHHHH
Confidence 4688888888764 5999997644
No 43
>TIGR00624 tag DNA-3-methyladenine glycosylase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=23.70 E-value=1.5e+02 Score=25.14 Aligned_cols=43 Identities=26% Similarity=0.428 Sum_probs=28.8
Q ss_pred HHHhhcchHhHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 029985 42 SSVGAQSTARIEELLQEDQNVKRRRDRYQKQSELLSKLTRQLSIHDN 88 (184)
Q Consensus 42 s~LY~~~~~~l~eLL~Edp~I~~RRe~c~k~L~~LkkA~~~Lsi~~~ 88 (184)
..+..-+.++++.||+ |+.|++.|.++ ..+...|+-.|.+...
T Consensus 65 ~~VA~~~e~~ie~L~~-d~~IIRnr~KI---~Avi~NA~~~l~i~~e 107 (179)
T TIGR00624 65 VKVARMTDADVERLLQ-DDGIIRNRGKI---EATIANARAALQLEQN 107 (179)
T ss_pred HHHhCCCHHHHHHHhc-CccchhhHHHH---HHHHHHHHHHHHHHHc
Confidence 4444444457888886 67777777777 4666777777766433
No 44
>KOG3119 consensus Basic region leucine zipper transcription factor [Transcription]
Probab=22.71 E-value=2.8e+02 Score=24.41 Aligned_cols=33 Identities=27% Similarity=0.457 Sum_probs=29.0
Q ss_pred hHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHH
Q 029985 51 RIEELLQEDQNVKRRRDRYQKQSELLSKLTRQL 83 (184)
Q Consensus 51 ~l~eLL~Edp~I~~RRe~c~k~L~~LkkA~~~L 83 (184)
++.+|..|+.....+.+++++.+..|+.+...+
T Consensus 223 r~~~leken~~lr~~v~~l~~el~~~~~~~~~~ 255 (269)
T KOG3119|consen 223 RVAELEKENEALRTQVEQLKKELATLRRLFLQL 255 (269)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 688999999999999999999998888877765
No 45
>PF05600 DUF773: Protein of unknown function (DUF773); InterPro: IPR008491 This family contains several eukaryotic sequences which are thought to be CDK5 activator-binding proteins, however, the function of this family is unknown.
Probab=22.46 E-value=6.1e+02 Score=24.57 Aligned_cols=78 Identities=17% Similarity=0.287 Sum_probs=41.3
Q ss_pred hhHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHhhcchHhHHHHhhcCHHHHHHHHHHHHH-------HHHH
Q 029985 5 VRGYFEAVLNSLATNV-SKAIVLCQVEKAKEDMLNQLYSSVGAQSTARIEELLQEDQNVKRRRDRYQKQ-------SELL 76 (184)
Q Consensus 5 V~SYF~IVrk~I~D~V-PKAIMh~LVn~sKe~Lq~~L~s~LY~~~~~~l~eLL~Edp~I~~RRe~c~k~-------L~~L 76 (184)
|..+...|..-|.-+- |+.--+||+..+.+ -..+|..+|..+- ...+-|+..-..+.+||.++++. |+.|
T Consensus 402 i~~ml~~V~~ii~~Lt~~~~~~L~~Ik~Spr-Yvdrl~~~L~qk~-~~~~k~~~~~~~l~~kr~e~~~e~~~l~pkL~~l 479 (507)
T PF05600_consen 402 IEEMLSAVEEIISQLTNPRTQHLFMIKSSPR-YVDRLVESLQQKL-KQEEKLRRKREDLEEKRQEAQEEQQELEPKLDAL 479 (507)
T ss_pred HHHHHHHHHHHHHHhcCHHHHHHHHHhcCHH-HHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHH
Confidence 4445544544444433 44444555555444 4555555554442 24455555666666777776554 5555
Q ss_pred HHHHHHHh
Q 029985 77 SKLTRQLS 84 (184)
Q Consensus 77 kkA~~~Ls 84 (184)
.+.++.|.
T Consensus 480 ~~~Tr~Lq 487 (507)
T PF05600_consen 480 VERTRELQ 487 (507)
T ss_pred HHHHHHHH
Confidence 55555553
No 46
>COG5016 Pyruvate/oxaloacetate carboxyltransferase [Energy production and conversion]
Probab=22.43 E-value=52 Score=31.89 Aligned_cols=62 Identities=24% Similarity=0.308 Sum_probs=43.3
Q ss_pred hhhhHHHHHHHHHH-HHHHHHHHH---HHHHHHHHHHHHHHHHHHHhhcc-hHhHHHHhhcCHHHHH
Q 029985 3 QEVRGYFEAVLNSL-ATNVSKAIV---LCQVEKAKEDMLNQLYSSVGAQS-TARIEELLQEDQNVKR 64 (184)
Q Consensus 3 ~~V~SYF~IVrk~I-~D~VPKAIM---h~LVn~sKe~Lq~~L~s~LY~~~-~~~l~eLL~Edp~I~~ 64 (184)
.++..||.-|||.- .-.-|.+.+ .-||.+.=-+|+..|.++|-.+. .+++++.|+|=|.|.+
T Consensus 266 ~~~~~yf~~vrkkY~~~~~~~~~~~d~~ili~qvPGGMlSNl~sQLkeqnaldK~~eVLeEvprVre 332 (472)
T COG5016 266 EEIAEYFREVRKKYKGLLEPQAKGVDPRILIYQVPGGMLSNLESQLKEQNALDKLEEVLEEVPRVRE 332 (472)
T ss_pred HHHHHHHHHHHHHHhhccCccccCCCCcceEeeCChHHHHHHHHHHHHcchhhHHHHHHHHhHHHHh
Confidence 36788999999988 444666665 34556666678888888875443 4577888888776643
No 47
>PF02341 RcbX: RbcX protein; InterPro: IPR003435 The RbcX protein has been identified as having a possible chaperonin-like function []. The rbcX gene is juxtaposed to and cotranscribed with rbcL and rbcS encoding RubisCO in Anabaena sp. (strain CA / ATCC 33047). RbcX has been shown to possess a chaperonin-like function assisting correct folding of RubisCO in Escherichia coli expression studies and is needed for RubisCO to reach its maximal activity [].; PDB: 2PEM_B 2PEI_L 2PEK_A 2Z46_E 2Z44_A 2PEJ_F 2PEN_D 2PEQ_B 2Z45_A 3Q20_A ....
Probab=22.33 E-value=4e+02 Score=21.10 Aligned_cols=56 Identities=23% Similarity=0.302 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------Hh--------hcchHhHHHHhhcCHHHHHHHHHH
Q 029985 14 NSLATNVSKAIVLCQVEKAKEDMLNQLYSS-------VG--------AQSTARIEELLQEDQNVKRRRDRY 69 (184)
Q Consensus 14 k~I~D~VPKAIMh~LVn~sKe~Lq~~L~s~-------LY--------~~~~~~l~eLL~Edp~I~~RRe~c 69 (184)
|.|+.-+=|+++.++-=+|-..++.+|++. |+ +.+..=+++||.|+++++.|=-+.
T Consensus 4 ~~~~kdtak~L~~yfTy~Avr~Vl~QL~etnp~~~~wL~~F~~~~~~~DGd~fl~~L~~e~~~LA~RIM~v 74 (111)
T PF02341_consen 4 KQIAKDTAKVLQSYFTYQAVRTVLAQLYETNPPAYIWLYNFLSRNPLQDGDAFLEALMRENQELALRIMEV 74 (111)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHSTCSSHHHHHHHHHCC-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCccHHHHHHHHHHHCHHHHHHHHHH
Confidence 556666666666666666666555554431 11 112234689999999987664333
No 48
>PF00714 IFN-gamma: Interferon gamma This family is a subset of the SCOP family.; InterPro: IPR002069 Interferon gamma (IFN-gamma) is produced by lymphocytes activated by specific antigens or mitogens. IFN-gamma shows antiviral activity and has important immunoregulatory functions. It is a potent activator of microphages and had antiproliferative effects on transformed cells. It can potentiate the antiviral and antitumor effects of the type I interferons. The crystal structures of a number IFN-gamma proteins have been solved, including bovine interferon-gamma at 2.0-A [] and human IFN-gamma at 2.9-A [].; GO: 0005133 interferon-gamma receptor binding, 0006955 immune response, 0005576 extracellular region; PDB: 1FG9_A 1FYH_D 1EKU_B 3BES_L 1RFB_A 1D9G_A 1D9C_B.
Probab=22.27 E-value=49 Score=27.24 Aligned_cols=73 Identities=25% Similarity=0.396 Sum_probs=37.0
Q ss_pred CchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcchHhHHHHhh--cCHHHHHHHHHHHHHHHHHHH
Q 029985 1 MSQEVRGYFEAVLNSLATNVSKAIVLCQVEKAKEDMLNQLYSSVGAQSTARIEELLQ--EDQNVKRRRDRYQKQSELLSK 78 (184)
Q Consensus 1 ~~~~V~SYF~IVrk~I~D~VPKAIMh~LVn~sKe~Lq~~L~s~LY~~~~~~l~eLL~--Edp~I~~RRe~c~k~L~~Lkk 78 (184)
|||-|.=||.|--+ +.|+ .+|- -=+...|++|+..++..-..+ .++|.+|++ ++. ..-.|+++.+....|++
T Consensus 55 ~SqIVs~Y~kiFe~-~k~n--q~ik-~si~~Ike~l~~~ff~~~~~k-l~df~~L~~i~vnD-~~vQrKAi~EL~~V~~~ 128 (138)
T PF00714_consen 55 QSQIVSFYLKIFEN-LKDN--QAIK-ESIKTIKEDLITKFFNSSSAK-LDDFQKLIKIQVND-LQVQRKAINELFKVMQK 128 (138)
T ss_dssp HHHHHHHHHHHHHC-TTTT--CCCH-HHHHHHHHHHHHHHCTTSHHH-HHHHHHHHCS-TTC-HHHHHHHHHCHHHHHHC
T ss_pred HHHHHHHHHHHHHH-cccc--HHHH-HHHHHHHHHHHHHHhcCcHHH-HHHHHHHHcccCcC-HHHHHHHHHHHHHHHHH
Confidence 57888999998643 4444 1211 113445555555544333222 234445543 332 23346777666665554
Q ss_pred H
Q 029985 79 L 79 (184)
Q Consensus 79 A 79 (184)
+
T Consensus 129 L 129 (138)
T PF00714_consen 129 L 129 (138)
T ss_dssp C
T ss_pred h
Confidence 3
No 49
>cd00632 Prefoldin_beta Prefoldin beta; Prefoldin is a hexameric molecular chaperone complex, composed of two evolutionarily related subunits (alpha and beta), which are found in both eukaryotes and archaea. Prefoldin binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The hexameric structure consists of a double beta barrel assembly with six protruding coiled-coils. The alpha prefoldin subunits have two beta hairpin structures while the beta prefoldin subunits (this CD) have only one hairpin that is most similar to the second hairpin of the alpha subunit. The prefoldin hexamer consists of two alpha and four beta subunits and is assembled from the beta hairpins of all six subunits. The alpha subunits initially dimerize providing a structural nucleus for the assembly of the beta subunits. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the st
Probab=21.72 E-value=3.4e+02 Score=20.14 Aligned_cols=35 Identities=23% Similarity=0.271 Sum_probs=26.6
Q ss_pred HHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029985 10 EAVLNSLAT-----NVSKAIVLCQVEKAKEDMLNQLYSSV 44 (184)
Q Consensus 10 ~IVrk~I~D-----~VPKAIMh~LVn~sKe~Lq~~L~s~L 44 (184)
+.|.+.|.. .|++-|-.++|...++.+...|=..+
T Consensus 33 ~~v~~EL~~l~~d~~vy~~VG~vfv~~~~~ea~~~Le~~~ 72 (105)
T cd00632 33 KKALEELEKLADDAEVYKLVGNVLVKQEKEEARTELKERL 72 (105)
T ss_pred HHHHHHHHcCCCcchHHHHhhhHHhhccHHHHHHHHHHHH
Confidence 345555554 58899999999999998888877765
No 50
>PF03114 BAR: BAR domain; InterPro: IPR004148 Endocytosis and intracellular transport involve several mechanistic steps: (1) for the internalisation of cargo molecules, the membrane needs to bend to form a vesicular structure, which requires membrane curvature and a rearrangement of the cytoskeleton; (2) following its formation, the vesicle has to be pinched off the membrane; (3) the cargo has to be subsequently transported through the cell and the vesicle must fuse with the correct cellular compartment. Members of the Amphiphysin protein family are key regulators in the early steps of endocytosis, involved in the formation of clathrin-coated vesicles by promoting the assembly of a protein complex at the plasma membrane and directly assist in the induction of the high curvature of the membrane at the neck of the vesicle. Amphiphysins contain a characteristic domain, known as the BAR (Bin-Amphiphysin-Rvs)-domain, which is required for their in vivo function and their ability to tubulate membranes []. The crystal structure of these proteins suggest the domain forms a crescent-shaped dimer of a three-helix coiled coil with a characteristic set of conserved hydrophobic, aromatic and hydrophilic amino acids. Proteins containing this domain have been shown to homodimerise, heterodimerise or, in a few cases, interact with small GTPases. ; GO: 0005515 protein binding, 0005737 cytoplasm; PDB: 4AVM_A 2D4C_C 1X03_A 1X04_A 2RND_A 2RMY_A 2FIC_A 2C08_A 2Z0V_A 3SOG_A ....
Probab=21.65 E-value=3.9e+02 Score=20.76 Aligned_cols=37 Identities=16% Similarity=0.194 Sum_probs=27.7
Q ss_pred hHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 029985 51 RIEELLQEDQNVKRRRDRYQKQSELLSKLTRQLSIHD 87 (184)
Q Consensus 51 ~l~eLL~Edp~I~~RRe~c~k~L~~LkkA~~~Lsi~~ 87 (184)
.+.+++.+-++|...++++.+.+--|..+.+.+.-..
T Consensus 122 pl~~~~~~~~~i~~~~kkr~~~~ldyd~~~~k~~k~~ 158 (229)
T PF03114_consen 122 PLKEFLKEFKEIKKLIKKREKKRLDYDSARSKLEKLR 158 (229)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCH
T ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4778888888888888888777777777777775443
No 51
>PF08360 TetR_C_5: QacR-like protein, C-terminal region; InterPro: IPR013571 This entry represents the C-terminal domain found in the multidrug-binding transcription regulator QacR (P23217 from SWISSPROT) from Staphylococcus aureus, which is a member of the TetR (tetracycline-resistance) transcriptional regulator family of proteins. QacR is able to bind various environmental agents, which include a number of cationic lipophilic compounds, and thus regulate the transcription of QacA (P23215 from SWISSPROT), a multidrug efflux pump []. The C-terminal region of QacR contains a multifaceted, expansive drug-binding pocket, which is composed of several separate, but linked, binding sites []. The C-terminal domains of QacR and TetR share a multi-helical, interlocking structure.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G0E_E 1JUM_A 1RPW_D 1QVT_B 2HQ5_D 1JT0_B 2DTZ_E 1JUP_D 1JT6_D 1JUS_E ....
Probab=21.60 E-value=74 Score=25.04 Aligned_cols=38 Identities=26% Similarity=0.329 Sum_probs=23.3
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHH
Q 029985 5 VRGYFEAVLNSLATNVSKAIVLCQVEKAKE-DMLNQLYS 42 (184)
Q Consensus 5 V~SYF~IVrk~I~D~VPKAIMh~LVn~sKe-~Lq~~L~s 42 (184)
+..|.+-+...|..-+.||+.-|..+..++ .+.++|+.
T Consensus 23 Ly~~a~~~~~~i~~pl~~a~~EF~~~~~~~~ev~~~l~~ 61 (131)
T PF08360_consen 23 LYGMAEHMLDDIQTPLSKAGEEFYSNQSKNPEVLEKLNE 61 (131)
T ss_dssp HHHHHHHHHHSSSGGGHHHHHHHHHHCSSSHHHHHHHHH
T ss_pred HHHHHHHHHHHhccHHHHHHHHHHHcccCCHHHHHHHHH
Confidence 345556555777777888888777765443 34444433
No 52
>PF09278 MerR-DNA-bind: MerR, DNA binding; InterPro: IPR015358 This entry represents a family of DNA-binding domains that are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold []. ; PDB: 3QAO_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q09_A 1Q08_B 1Q0A_B 1Q07_A ....
Probab=20.97 E-value=2.6e+02 Score=18.41 Aligned_cols=25 Identities=20% Similarity=0.242 Sum_probs=20.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHh
Q 029985 60 QNVKRRRDRYQKQSELLSKLTRQLS 84 (184)
Q Consensus 60 p~I~~RRe~c~k~L~~LkkA~~~Ls 84 (184)
.-+.++++++.++++.|.++...|.
T Consensus 39 ~~l~~~~~~i~~~i~~L~~~~~~L~ 63 (65)
T PF09278_consen 39 ALLEEKLEEIEEQIAELQALRAQLE 63 (65)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 5667888889889988888888774
No 53
>KOG2509 consensus Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=20.59 E-value=8.1e+02 Score=23.99 Aligned_cols=45 Identities=11% Similarity=0.195 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHHHH-HHHhhcchHhHHHHhhcCHHHHHH--HHHHHHHHH
Q 029985 28 QVEKAKEDMLNQLY-SSVGAQSTARIEELLQEDQNVKRR--RDRYQKQSE 74 (184)
Q Consensus 28 LVn~sKe~Lq~~L~-s~LY~~~~~~l~eLL~Edp~I~~R--Re~c~k~L~ 74 (184)
-.|+-++.|.+++- -++.+.+ ...+|+++-+.+.+. |+.+++.+.
T Consensus 52 eln~~~n~l~k~i~~~k~kkke--~~~~l~~~~~~~~~~~~~~~l~e~~~ 99 (455)
T KOG2509|consen 52 ELNKEKNKLNKEIGDLKLKKKE--DIGQLEESKAKNTEGAERKLLKEEAV 99 (455)
T ss_pred HHHHHHHHhhhHhhHHHHhhcc--hhhHHHHhhhHhhhhhhhhhhHHHHH
Confidence 34555666776666 5666543 577888877777764 444444433
No 54
>PF06786 UPF0253: Uncharacterised protein family (UPF0253); InterPro: IPR009624 This is a group of proteins of unknown function.
Probab=20.52 E-value=3.5e+02 Score=19.80 Aligned_cols=23 Identities=22% Similarity=0.187 Sum_probs=17.3
Q ss_pred hHHHHHHHHHHHH-------HHHHHHHHHH
Q 029985 6 RGYFEAVLNSLAT-------NVSKAIVLCQ 28 (184)
Q Consensus 6 ~SYF~IVrk~I~D-------~VPKAIMh~L 28 (184)
.-|.+.||+.... .|||||-+-+
T Consensus 2 ~~YCeliR~~ya~IgSGd~gYiP~Ai~cal 31 (66)
T PF06786_consen 2 QVYCELIRELYAQIGSGDQGYIPDAIGCAL 31 (66)
T ss_pred cHHHHHHHHHHHHhcCCccccCcHHHHHHH
Confidence 4578888888764 5999998654
No 55
>PF13972 TetR: Bacterial transcriptional repressor; PDB: 3RH2_A 3NNR_A.
Probab=20.48 E-value=3.1e+02 Score=20.96 Aligned_cols=41 Identities=27% Similarity=0.398 Sum_probs=25.1
Q ss_pred HHHHhhcchHhHHHHhhcCHHHHHHHHHHHH-HHHHHHHHHHHHhh
Q 029985 41 YSSVGAQSTARIEELLQEDQNVKRRRDRYQK-QSELLSKLTRQLSI 85 (184)
Q Consensus 41 ~s~LY~~~~~~l~eLL~Edp~I~~RRe~c~k-~L~~LkkA~~~Lsi 85 (184)
|+=+|+ ++.+||..+|+++++-.+..+ +.+.+.+..+.|..
T Consensus 38 YRF~~~----dl~~Ll~~~p~L~~~~~~~~~~~~~~~~~l~~~l~~ 79 (146)
T PF13972_consen 38 YRFFYR----DLPDLLRRDPELKKRYRQLQQRRREQLRQLLQSLIE 79 (146)
T ss_dssp THHHHH----SHHHHHHC-HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hhhHHc----cHHHHHHhCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444555 478999999999987666543 34444444444433
No 56
>PRK13920 putative anti-sigmaE protein; Provisional
Probab=20.46 E-value=1e+02 Score=25.44 Aligned_cols=38 Identities=16% Similarity=0.209 Sum_probs=25.0
Q ss_pred HHHHhhcchHhHHHHhhcCHHHHHHHHHHHHHHHHHHH
Q 029985 41 YSSVGAQSTARIEELLQEDQNVKRRRDRYQKQSELLSK 78 (184)
Q Consensus 41 ~s~LY~~~~~~l~eLL~Edp~I~~RRe~c~k~L~~Lkk 78 (184)
...+-.++...|+..|++|++..++=+++++.+..|..
T Consensus 6 lG~Ls~eE~~~ve~~L~~dp~~~~~v~~~e~~~~~l~~ 43 (206)
T PRK13920 6 LGALSPEERARVEAALEAYPELWAELRALQEALAALAE 43 (206)
T ss_pred cCCCCHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHh
Confidence 33444455557888899998888777777666544433
No 57
>PRK15366 type III secretion system chaperone SsaE; Provisional
Probab=20.42 E-value=1.9e+02 Score=21.90 Aligned_cols=12 Identities=25% Similarity=0.459 Sum_probs=6.8
Q ss_pred HHHHhhcCHHHH
Q 029985 52 IEELLQEDQNVK 63 (184)
Q Consensus 52 l~eLL~Edp~I~ 63 (184)
+++.|.+||+-.
T Consensus 7 LEDsLr~~~~~a 18 (80)
T PRK15366 7 LEDLLLHSREEA 18 (80)
T ss_pred HHHHHhcCHHHH
Confidence 555556665555
No 58
>PF11593 Med3: Mediator complex subunit 3 fungal; InterPro: IPR020998 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. This entry represents the subunit Med3, which is a physical target for Cyc8-Tup1, a yeast transcriptional co-repressor []. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=20.02 E-value=5e+02 Score=24.82 Aligned_cols=57 Identities=30% Similarity=0.418 Sum_probs=38.0
Q ss_pred HHHHHHHHHHHHHHHHHHHH------HHHHHHHhhcchHhHHHHhhcCHHHH--HHHHHHHHHHHHHHHHHHHH
Q 029985 18 TNVSKAIVLCQVEKAKEDML------NQLYSSVGAQSTARIEELLQEDQNVK--RRRDRYQKQSELLSKLTRQL 83 (184)
Q Consensus 18 D~VPKAIMh~LVn~sKe~Lq------~~L~s~LY~~~~~~l~eLL~Edp~I~--~RRe~c~k~L~~LkkA~~~L 83 (184)
|. +|-+|.-.|..+++.|| ++|+.-+ ..||++=++++..+ .-|.++ |+++.++++.-
T Consensus 21 d~-~Kd~V~~~I~ea~~sILPlRL~FNeFi~tm-----a~Ie~~~~~s~qeKFl~IR~Kl---leL~~~lQ~lS 85 (379)
T PF11593_consen 21 DN-SKDSVMDKISEAQDSILPLRLQFNEFIQTM-----ANIEEMNNKSPQEKFLLIRSKL---LELYNKLQELS 85 (379)
T ss_pred Cc-hHHHHHHHHHHHHhccccHHHHHHHHHHHH-----HHhhcccccCHHHHHHHHHHHH---HHHHHHHHHHH
Confidence 55 89999999999999654 4555555 34667777776655 567777 55555554433
Done!