Query 030018
Match_columns 184
No_of_seqs 131 out of 272
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 07:14:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030018.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030018hhsearch_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 4.4E-29 9.6E-34 185.4 10.6 83 1-85 9-91 (92)
2 PF02212 GED: Dynamin GTPase e 99.9 1.7E-24 3.7E-29 159.7 8.3 83 2-86 10-92 (92)
3 KOG0446 Vacuolar sorting prote 99.7 5.3E-18 1.1E-22 162.7 11.3 83 1-84 569-651 (657)
4 COG0699 Predicted GTPases (dyn 94.2 0.58 1.3E-05 42.2 10.5 76 3-81 467-542 (546)
5 COG3579 PepC Aminopeptidase C 70.0 4.6 0.0001 38.2 3.3 53 18-70 152-207 (444)
6 PF15369 KIAA1328: Uncharacter 62.8 57 0.0012 30.3 8.7 49 29-78 20-75 (328)
7 KOG3742 Glycogen synthase [Car 53.9 27 0.00059 34.6 5.4 49 10-67 384-432 (692)
8 PF10863 DUF2702: Protein of u 53.3 30 0.00065 28.6 4.8 61 64-130 2-62 (143)
9 PF07560 DUF1539: Domain of Un 48.4 11 0.00025 30.4 1.6 62 6-68 20-87 (126)
10 PF11594 Med28: Mediator compl 47.5 1.4E+02 0.003 23.6 9.3 79 5-98 2-80 (106)
11 PF09738 DUF2051: Double stran 47.5 1.7E+02 0.0038 26.6 9.2 104 21-130 106-218 (302)
12 PF02344 Myc-LZ: Myc leucine z 47.0 22 0.00047 22.7 2.4 26 53-78 4-29 (32)
13 cd07620 BAR_SH3BP1 The Bin/Amp 43.1 2.5E+02 0.0055 25.3 11.4 32 52-83 112-144 (257)
14 PF12209 SAC3: Leucine permeas 42.9 1.3E+02 0.0028 22.2 6.4 15 11-25 13-27 (79)
15 COG1510 Predicted transcriptio 41.3 83 0.0018 26.9 5.8 62 20-86 86-147 (177)
16 PF05983 Med7: MED7 protein; 40.9 1.4E+02 0.0031 24.5 7.0 30 52-83 132-161 (162)
17 KOG0562 Predicted hydrolase (H 39.6 3.9 8.5E-05 35.0 -2.4 16 16-31 28-43 (184)
18 KOG4552 Vitamin-D-receptor int 38.9 2.9E+02 0.0063 24.8 9.1 18 20-37 23-40 (272)
19 PF08544 GHMP_kinases_C: GHMP 38.7 49 0.0011 22.5 3.5 45 42-87 3-47 (85)
20 PF05746 DALR_1: DALR anticodo 38.3 1.5E+02 0.0033 21.5 6.2 66 4-85 41-106 (119)
21 PLN03184 chloroplast Hsp70; Pr 36.2 3.2E+02 0.0069 27.1 9.8 7 53-59 605-611 (673)
22 PF09440 eIF3_N: eIF3 subunit 34.5 2.2E+02 0.0047 22.8 7.0 26 58-83 63-88 (133)
23 PRK10353 3-methyl-adenine DNA 32.5 1.1E+02 0.0023 26.1 5.2 43 42-88 66-108 (187)
24 PF10987 DUF2806: Protein of u 32.1 1.1E+02 0.0024 26.2 5.2 15 111-125 37-51 (219)
25 PF15030 DUF4527: Protein of u 32.0 72 0.0016 29.0 4.2 36 21-58 77-114 (277)
26 smart00751 BSD domain in trans 31.3 55 0.0012 21.6 2.6 20 50-69 10-29 (51)
27 KOG2470 Similar to IMP-GMP spe 28.2 73 0.0016 30.8 3.7 22 108-129 273-297 (510)
28 cd01068 sensor_globin Globin d 27.9 2.7E+02 0.0058 21.0 6.5 45 27-73 25-69 (147)
29 PF11221 Med21: Subunit 21 of 27.4 3.2E+02 0.0069 21.7 8.2 63 20-84 70-139 (144)
30 PF10397 ADSL_C: Adenylosuccin 27.3 1.6E+02 0.0035 20.9 4.7 13 51-63 40-52 (81)
31 KOG1899 LAR transmembrane tyro 26.4 6.1E+02 0.013 26.4 9.8 31 53-83 284-314 (861)
32 PRK12772 bifunctional flagella 26.4 6E+02 0.013 25.2 9.8 66 9-74 439-508 (609)
33 PF05600 DUF773: Protein of un 26.2 4.7E+02 0.01 25.3 8.9 78 5-84 402-487 (507)
34 PRK03926 mevalonate kinase; Pr 25.2 2.5E+02 0.0053 24.1 6.2 56 40-98 204-259 (302)
35 PF12787 EcsC: EcsC protein fa 24.3 4.4E+02 0.0095 22.3 8.5 30 5-34 22-51 (249)
36 PLN02451 homoserine kinase 24.3 1.9E+02 0.004 26.6 5.6 58 38-98 262-319 (370)
37 PF06156 DUF972: Protein of un 24.0 1.7E+02 0.0037 22.7 4.6 40 38-78 18-57 (107)
38 COG4997 Uncharacterized conser 23.2 3.6E+02 0.0078 21.0 7.9 67 11-77 3-82 (95)
39 PF08360 TetR_C_5: QacR-like p 23.2 68 0.0015 25.2 2.2 38 5-42 23-61 (131)
40 PRK13920 putative anti-sigmaE 22.8 88 0.0019 25.9 2.9 39 40-78 5-43 (206)
41 PF07303 Occludin_ELL: Occludi 22.8 3.1E+02 0.0067 20.9 5.7 35 53-87 66-100 (101)
42 KOG3119 Basic region leucine z 22.5 2.9E+02 0.0063 24.3 6.3 33 51-83 223-255 (269)
43 COG4575 ElaB Uncharacterized c 22.4 3.9E+02 0.0085 21.1 6.3 37 50-89 22-63 (104)
44 PF03114 BAR: BAR domain; Int 22.1 3.8E+02 0.0083 20.8 7.4 37 51-87 122-158 (229)
45 PF06632 XRCC4: DNA double-str 21.9 2.6E+02 0.0057 25.8 6.0 8 54-61 162-169 (342)
46 cd00632 Prefoldin_beta Prefold 21.5 3.5E+02 0.0075 20.1 5.7 35 10-44 33-72 (105)
47 COG1245 Predicted ATPase, RNas 21.2 1.7E+02 0.0036 29.3 4.8 43 2-44 146-201 (591)
48 PRK12468 flhB flagellar biosyn 21.1 6.9E+02 0.015 23.4 9.7 66 8-73 182-251 (386)
49 PRK09108 type III secretion sy 21.1 6.6E+02 0.014 23.2 9.7 67 8-74 177-247 (353)
50 PF09278 MerR-DNA-bind: MerR, 21.0 2.6E+02 0.0056 18.4 7.6 25 60-84 39-63 (65)
51 KOG1923 Rac1 GTPase effector F 21.0 9.9E+02 0.021 25.2 13.5 73 5-77 141-223 (830)
52 KOG2509 Seryl-tRNA synthetase 20.8 8E+02 0.017 24.0 10.3 47 27-75 51-100 (455)
53 TIGR00624 tag DNA-3-methyladen 20.8 1.8E+02 0.004 24.6 4.4 43 42-88 65-107 (179)
54 PF02341 RcbX: RbcX protein; 20.7 4.3E+02 0.0094 20.9 6.7 56 14-69 4-74 (111)
55 PF08681 DUF1778: Protein of u 20.4 2.9E+02 0.0063 19.8 4.9 40 26-65 31-70 (80)
56 COG5016 Pyruvate/oxaloacetate 20.3 63 0.0014 31.3 1.8 62 3-64 266-332 (472)
57 PF12057 DUF3538: Domain of un 20.2 3.1E+02 0.0067 22.1 5.4 26 51-76 21-51 (120)
58 KOG2391 Vacuolar sorting prote 20.1 7.6E+02 0.017 23.5 8.8 36 54-89 243-278 (365)
No 1
>smart00302 GED Dynamin GTPase effector domain.
Probab=99.96 E-value=4.4e-29 Score=185.44 Aligned_cols=83 Identities=29% Similarity=0.486 Sum_probs=79.4
Q ss_pred CchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcchHhHHHHhhcCHHHHHHHHHHHHHHHHHHHHH
Q 030018 1 MSQEVRGYFEAVLNSLATNVSKAVVLCQVEKAKEDMLNQLYSSVGAQSTARIEELLQEDQNVKRRRDRYQKQSELLSKLT 80 (184)
Q Consensus 1 ~~~~V~SYf~IVrk~I~D~VPKAIMh~LVn~sKe~Lq~~L~s~LY~~e~~~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 699999999999999999999999999999
Q ss_pred HHHhh
Q 030018 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=1.7e-24 Score=159.70 Aligned_cols=83 Identities=31% Similarity=0.452 Sum_probs=76.5
Q ss_pred chhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcchHhHHHHhhcCHHHHHHHHHHHHHHHHHHHHHH
Q 030018 2 SQEVRGYFEAVLNSLATNVSKAVVLCQVEKAKEDMLNQLYSSVGAQSTARIEELLQEDQNVKRRRDRYQKQSELLSKLTR 81 (184)
Q Consensus 2 ~~~V~SYf~IVrk~I~D~VPKAIMh~LVn~sKe~Lq~~L~s~LY~~e~~~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 46899999999999999999999999999999999999999999986 4899999999999999999999999999999
Q ss_pred HHhhh
Q 030018 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=5.3e-18 Score=162.68 Aligned_cols=83 Identities=31% Similarity=0.381 Sum_probs=76.9
Q ss_pred CchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcchHhHHHHhhcCHHHHHHHHHHHHHHHHHHHHH
Q 030018 1 MSQEVRGYFEAVLNSLATNVSKAVVLCQVEKAKEDMLNQLYSSVGAQSTARIEELLQEDQNVKRRRDRYQKQSELLSKLT 80 (184)
Q Consensus 1 ~~~~V~SYf~IVrk~I~D~VPKAIMh~LVn~sKe~Lq~~L~s~LY~~e~~~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 ISSCPESYLNIVSDKLVDTVPKALNHELLNEFKDDLPNELDQRLYAG-DEQLESLLKEDPRIKRRRELQQKRLLALQKAL 647 (657)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-hhHHHHHHccCHHHHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999999999999999999999999999999992 45899999999999999999999988888887
Q ss_pred HHHh
Q 030018 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=94.19 E-value=0.58 Score=42.17 Aligned_cols=76 Identities=17% Similarity=0.097 Sum_probs=65.3
Q ss_pred hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcchHhHHHHhhcCHHHHHHHHHHHHHHHHHHHHHH
Q 030018 3 QEVRGYFEAVLNSLATNVSKAVVLCQVEKAKEDMLNQLYSSVGAQSTARIEELLQEDQNVKRRRDRYQKQSELLSKLTR 81 (184)
Q Consensus 3 ~~V~SYf~IVrk~I~D~VPKAIMh~LVn~sKe~Lq~~L~s~LY~~e~~~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 578899 999999999999999999988888877777766666664 5788899999999999999999988888765
No 5
>COG3579 PepC Aminopeptidase C [Amino acid transport and metabolism]
Probab=70.00 E-value=4.6 Score=38.22 Aligned_cols=53 Identities=19% Similarity=0.220 Sum_probs=44.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhcchHhHHHHhhcCHH---HHHHHHHHH
Q 030018 18 TNVSKAVVLCQVEKAKEDMLNQLYSSVGAQSTARIEELLQEDQN---VKRRRDRYQ 70 (184)
Q Consensus 18 D~VPKAIMh~LVn~sKe~Lq~~L~s~LY~~e~~~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 36999999999999998889999999989887788999998666 777777763
No 6
>PF15369 KIAA1328: Uncharacterised protein KIAA1328
Probab=62.81 E-value=57 Score=30.35 Aligned_cols=49 Identities=20% Similarity=0.272 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHHHHHHhhcchHhHHHHhhcCHHHHHHHHH-------HHHHHHHHHH
Q 030018 29 VEKAKEDMLNQLYSSVGAQSTARIEELLQEDQNVKRRRDR-------YQKQSELLSK 78 (184)
Q Consensus 29 Vn~sKe~Lq~~L~s~LY~~e~~~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 45555555555544433322 2577787888888887764 5555666543
No 7
>KOG3742 consensus Glycogen synthase [Carbohydrate transport and metabolism]
Probab=53.88 E-value=27 Score=34.58 Aligned_cols=49 Identities=24% Similarity=0.313 Sum_probs=39.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcchHhHHHHhhcCHHHHHHHH
Q 030018 10 EAVLNSLATNVSKAVVLCQVEKAKEDMLNQLYSSVGAQSTARIEELLQEDQNVKRRRD 67 (184)
Q Consensus 10 ~IVrk~I~D~VPKAIMh~LVn~sKe~Lq~~L~s~LY~~e~~~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 688899999999999888776789999999988876654
No 8
>PF10863 DUF2702: Protein of unknown function (DUF2702); InterPro: IPR022592 This entry represents fungal proteins with unknown function.
Probab=53.35 E-value=30 Score=28.62 Aligned_cols=61 Identities=25% Similarity=0.320 Sum_probs=37.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhhhhhhhhccccCCCCCCCcCCCCCCCCCcchHHHHHHHhCCCCC
Q 030018 64 RRRDRYQKQSELLSKLTRQLSIHDNRAAAASNWSDGGGGAESSPRTSAASGDDWRSAFDAAANGPVS 130 (184)
Q Consensus 64 ~RRe~c~k~L~~LkkA~~~Lsi~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~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 58999999998877777666555443 557988776554443322223445555553 45553
No 9
>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=48.37 E-value=11 Score=30.39 Aligned_cols=62 Identities=13% Similarity=0.108 Sum_probs=41.6
Q ss_pred hHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHhhcchHhHHHHhhcCHHHHHHHHH
Q 030018 6 RGYFEAVLNSLATNVS------KAVVLCQVEKAKEDMLNQLYSSVGAQSTARIEELLQEDQNVKRRRDR 68 (184)
Q Consensus 6 ~SYf~IVrk~I~D~VP------KAIMh~LVn~sKe~Lq~~L~s~LY~~e~~~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 899999999766655555555555544444556665 8888877664
No 10
>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=47.53 E-value=1.4e+02 Score=23.61 Aligned_cols=79 Identities=18% Similarity=0.279 Sum_probs=50.0
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcchHhHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHHh
Q 030018 5 VRGYFEAVLNSLATNVSKAVVLCQVEKAKEDMLNQLYSSVGAQSTARIEELLQEDQNVKRRRDRYQKQSELLSKLTRQLS 84 (184)
Q Consensus 5 V~SYf~IVrk~I~D~VPKAIMh~LVn~sKe~Lq~~L~s~LY~~e~~~l~eLL~Edp~I~~RRe~c~k~L~~LkkA~~~Ls 84 (184)
|++|++-....+.|.+=..=-+ .|+.++.-++|+. +..|+|+- -+-+.+|+..=.++++....|.
T Consensus 2 irt~vEq~~~~FlD~aRq~e~~--------FlqKr~~LS~~kp-----e~~lkEEi--~eLK~ElqRKe~Ll~Kh~~kI~ 66 (106)
T PF11594_consen 2 IRTYVEQLIQSFLDVARQMEAF--------FLQKRFELSAYKP-----EQVLKEEI--NELKEELQRKEQLLQKHYEKID 66 (106)
T ss_pred chhHHHHHHHHHHHHHHHHHHH--------HHHHHHHHHhcCH-----HHHHHHHH--HHHHHHHHHHHHHHHHHHHHHH
Confidence 5566665555555543332222 3466666677654 45666653 3444888888888899999999
Q ss_pred hhhhhhhhhccccC
Q 030018 85 IHDNRAAAASNWSD 98 (184)
Q Consensus 85 i~~~~~~~~~~~~~ 98 (184)
.|...+.-+.++..
T Consensus 67 ~w~~lL~d~~~~~k 80 (106)
T PF11594_consen 67 YWEKLLSDAQNQHK 80 (106)
T ss_pred HHHHHHHHHHhhcc
Confidence 99988776664443
No 11
>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=47.48 E-value=1.7e+02 Score=26.58 Aligned_cols=104 Identities=16% Similarity=0.261 Sum_probs=51.2
Q ss_pred HHHHHHHHHHHHHHHH--HHHHHHHHhhcchHhHHHHhhcCHHHHHHHHHHHHHHHHHH----HHHHHHhhhhhhhhhhc
Q 030018 21 SKAVVLCQVEKAKEDM--LNQLYSSVGAQSTARIEELLQEDQNVKRRRDRYQKQSELLS----KLTRQLSIHDNRAAAAS 94 (184)
Q Consensus 21 PKAIMh~LVn~sKe~L--q~~L~s~LY~~e~~~l~eLL~Edp~I~~RRe~c~k~L~~Lk----kA~~~Lsi~~~~~~~~~ 94 (184)
=|+-++..|.-.|+.| +.+.+..+.++ +.+...|-+-.+.....++..+..|+ .-.+.|..||.+.-.-
T Consensus 106 ek~~l~yqvd~Lkd~lee~eE~~~~~~re----~~eK~~elEr~K~~~d~L~~e~~~Lre~L~~rdeli~khGlVlv~~- 180 (302)
T PF09738_consen 106 EKSALMYQVDLLKDKLEELEETLAQLQRE----YREKIRELERQKRAHDSLREELDELREQLKQRDELIEKHGLVLVPD- 180 (302)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCeeeCCC-
Confidence 4777888999888854 34455555554 33333333333333334444444433 4444567788773221
Q ss_pred cccCCCCCCC---cCCCCCCCCCcchHHHHHHHhCCCCC
Q 030018 95 NWSDGGGGAE---SSPRTSAASGDDWRSAFDAAANGPVS 130 (184)
Q Consensus 95 ~~~~~~~~~~---~s~~~~~~~~~~w~~af~~~~~~~~~ 130 (184)
-.++..+.+ +..+.+..|.-+=..+++.+..|+-|
T Consensus 181 -~~ngd~~~~~~~~~~~~~~~vs~e~a~~L~~aG~g~LD 218 (302)
T PF09738_consen 181 -ATNGDTSDEPNNVGHPKRALVSQEAAQLLESAGDGSLD 218 (302)
T ss_pred -CCCCccccCccccCCCcccccchhhhhhhcccCCCCHH
Confidence 111111110 11222223555666667777666653
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=47.00 E-value=22 Score=22.73 Aligned_cols=26 Identities=27% Similarity=0.607 Sum_probs=19.9
Q ss_pred HHHhhcCHHHHHHHHHHHHHHHHHHH
Q 030018 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 35777888888999999988887764
No 13
>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=43.14 E-value=2.5e+02 Score=25.29 Aligned_cols=32 Identities=13% Similarity=0.299 Sum_probs=25.8
Q ss_pred HHHHhhcC-HHHHHHHHHHHHHHHHHHHHHHHH
Q 030018 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 45556666 799999999999988888888876
No 14
>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=42.89 E-value=1.3e+02 Score=22.19 Aligned_cols=15 Identities=13% Similarity=0.144 Sum_probs=7.3
Q ss_pred HHHHHHHHHHHHHHH
Q 030018 11 AVLNSLATNVSKAVV 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 344455555555433
No 15
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=41.25 E-value=83 Score=26.94 Aligned_cols=62 Identities=21% Similarity=0.171 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhcchHhHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 030018 20 VSKAVVLCQVEKAKEDMLNQLYSSVGAQSTARIEELLQEDQNVKRRRDRYQKQSELLSKLTRQLSIH 86 (184)
Q Consensus 20 VPKAIMh~LVn~sKe~Lq~~L~s~LY~~e~~~l~eLL~Edp~I~~RRe~c~k~L~~LkkA~~~Lsi~ 86 (184)
+||.+-.+..+...+..+++.=-.+ +.+.+++.|.++...+|......=+.++++..+|..+
T Consensus 86 a~~df~~~f~t~f~ek~~ReId~t~-----e~l~k~~~e~~~~~~~~~~~~~~ke~~~~l~~~l~~~ 147 (177)
T COG1510 86 AEKDFSQIFRTLFEEKWKREIDPTK-----EALKKLLEELNEDLDDRDLTERIKEIKSKLERLLKWS 147 (177)
T ss_pred ccchHHHHHHHHHHHHHHHHhhhHH-----HHHHHHHHHccccccchhhhHHHHHHHHHHHHHHHHH
Confidence 4555555555555554444432222 2345555555554444433333333333333333333
No 16
>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=40.87 E-value=1.4e+02 Score=24.47 Aligned_cols=30 Identities=13% Similarity=0.336 Sum_probs=20.4
Q ss_pred HHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHH
Q 030018 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 4445543 46677888877777777777766
No 17
>KOG0562 consensus Predicted hydrolase (HIT family) [General function prediction only]
Probab=39.56 E-value=3.9 Score=34.97 Aligned_cols=16 Identities=19% Similarity=0.079 Sum_probs=14.1
Q ss_pred HHHHHHHHHHHHHHHH
Q 030018 16 LATNVSKAVVLCQVEK 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 7899999999999853
No 18
>KOG4552 consensus Vitamin-D-receptor interacting protein complex component [Transcription]
Probab=38.93 E-value=2.9e+02 Score=24.84 Aligned_cols=18 Identities=22% Similarity=0.471 Sum_probs=9.2
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 030018 20 VSKAVVLCQVEKAKEDML 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 445555555555455443
No 19
>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=38.70 E-value=49 Score=22.49 Aligned_cols=45 Identities=11% Similarity=0.160 Sum_probs=27.2
Q ss_pred HHHhhcchHhHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 030018 42 SSVGAQSTARIEELLQEDQNVKRRRDRYQKQSELLSKLTRQLSIHD 87 (184)
Q Consensus 42 s~LY~~e~~~l~eLL~Edp~I~~RRe~c~k~L~~LkkA~~~Lsi~~ 87 (184)
..|...+.+.+.++|.++... +.+.........+..+.+.+..++
T Consensus 3 ~al~~~d~~~~~~~~~~~~~~-~~~~~~~~~~~~i~~~~~~~~~~G 47 (85)
T PF08544_consen 3 KALAEGDLELLGELMNENQEN-EPENYREVLTPEIDELKEAAEENG 47 (85)
T ss_dssp HHHHTTCHHHHHHHHHHHHHH-HHHHHTTHHHHHHHHHHHHHHHTT
T ss_pred HHHHCcCHHHHHHHHHHhhhh-cchHHHHHcCHHHHHHHHHHHHCC
Confidence 334445556788888887775 333333334566677777776666
No 20
>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=38.26 E-value=1.5e+02 Score=21.50 Aligned_cols=66 Identities=15% Similarity=0.198 Sum_probs=41.1
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcchHhHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHH
Q 030018 4 EVRGYFEAVLNSLATNVSKAVVLCQVEKAKEDMLNQLYSSVGAQSTARIEELLQEDQNVKRRRDRYQKQSELLSKLTRQL 83 (184)
Q Consensus 4 ~V~SYf~IVrk~I~D~VPKAIMh~LVn~sKe~Lq~~L~s~LY~~e~~~l~eLL~Edp~I~~RRe~c~k~L~~LkkA~~~L 83 (184)
.+..|-.+|.+.+.+.=|-.++..|.+=+ ..+.+.|..- ..|.|++.+. ...+|.+++....+|
T Consensus 41 ~l~~~~~~l~~a~~~~~p~~l~~yL~~La------~~f~~fy~~~-----~I~~~~~~~~-----~~~RL~Ll~~v~~vl 104 (119)
T PF05746_consen 41 QLARFPDVLEKAAKDLEPHKLCDYLYELA------QAFNSFYDNV-----RILDEDEEIR-----KNNRLALLKAVRQVL 104 (119)
T ss_dssp HHCTHHHHHHHHHHHT-CHHHHHHHHHHH------HHHHHHHHHS------STTSTTCHH------HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhHHHHHHHHHHHHHH------HHHHHHHhhc-----cccccchHHH-----HHHHHHHHHHHHHHH
Confidence 45667778888888888888888887744 4455555432 4677777776 233455556555555
Q ss_pred hh
Q 030018 84 SI 85 (184)
Q Consensus 84 si 85 (184)
..
T Consensus 105 ~~ 106 (119)
T PF05746_consen 105 KN 106 (119)
T ss_dssp HH
T ss_pred HH
Confidence 43
No 21
>PLN03184 chloroplast Hsp70; Provisional
Probab=36.22 E-value=3.2e+02 Score=27.05 Aligned_cols=7 Identities=0% Similarity=0.268 Sum_probs=2.7
Q ss_pred HHHhhcC
Q 030018 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 3334433
No 22
>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=34.51 E-value=2.2e+02 Score=22.83 Aligned_cols=26 Identities=12% Similarity=0.161 Sum_probs=20.1
Q ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHH
Q 030018 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 23
>PRK10353 3-methyl-adenine DNA glycosylase I; Provisional
Probab=32.47 E-value=1.1e+02 Score=26.15 Aligned_cols=43 Identities=26% Similarity=0.431 Sum_probs=28.6
Q ss_pred HHHhhcchHhHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 030018 42 SSVGAQSTARIEELLQEDQNVKRRRDRYQKQSELLSKLTRQLSIHDN 88 (184)
Q Consensus 42 s~LY~~e~~~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 3444444567888887 666777777774 566777777766544
No 24
>PF10987 DUF2806: Protein of unknown function (DUF2806); InterPro: IPR021254 This bacterial family of proteins has no known function.
Probab=32.07 E-value=1.1e+02 Score=26.16 Aligned_cols=15 Identities=27% Similarity=0.375 Sum_probs=11.8
Q ss_pred CCCCcchHHHHHHHh
Q 030018 111 AASGDDWRSAFDAAA 125 (184)
Q Consensus 111 ~~~~~~w~~af~~~~ 125 (184)
-++++||...|-..|
T Consensus 37 ~~vD~DWl~~f~~~A 51 (219)
T PF10987_consen 37 EPVDPDWLYRFFDMA 51 (219)
T ss_pred CCCChHHHHHHHHHH
Confidence 448999999986655
No 25
>PF15030 DUF4527: Protein of unknown function (DUF4527)
Probab=31.97 E-value=72 Score=28.96 Aligned_cols=36 Identities=25% Similarity=0.383 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHHHH--HHHHHHHHHHhhcchHhHHHHhhc
Q 030018 21 SKAVVLCQVEKAKE--DMLNQLYSSVGAQSTARIEELLQE 58 (184)
Q Consensus 21 PKAIMh~LVn~sKe--~Lq~~L~s~LY~~e~~~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 48899999999988 688888888887763 4444444
No 26
>smart00751 BSD domain in transcription factors and synapse-associated proteins.
Probab=31.33 E-value=55 Score=21.57 Aligned_cols=20 Identities=30% Similarity=0.444 Sum_probs=15.6
Q ss_pred HhHHHHhhcCHHHHHHHHHH
Q 030018 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 27
>KOG2470 consensus Similar to IMP-GMP specific 5'-nucleotidase [Nucleotide transport and metabolism]
Probab=28.15 E-value=73 Score=30.77 Aligned_cols=22 Identities=45% Similarity=0.762 Sum_probs=15.3
Q ss_pred CCCCCCCcchHHHHHH---HhCCCC
Q 030018 108 RTSAASGDDWRSAFDA---AANGPV 129 (184)
Q Consensus 108 ~~~~~~~~~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 3444489999999995 455554
No 28
>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=27.89 E-value=2.7e+02 Score=20.99 Aligned_cols=45 Identities=11% Similarity=0.328 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHHHHHHHHhhcchHhHHHHhhcCHHHHHHHHHHHHHH
Q 030018 27 CQVEKAKEDMLNQLYSSVGAQSTARIEELLQEDQNVKRRRDRYQKQS 73 (184)
Q Consensus 27 ~LVn~sKe~Lq~~L~s~LY~~e~~~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 3466667788999999998875 57888876555555444444333
No 29
>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=27.42 E-value=3.2e+02 Score=21.72 Aligned_cols=63 Identities=24% Similarity=0.297 Sum_probs=37.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhcc------hHhHHHHhhcCHHHHHHHHHHHH-HHHHHHHHHHHHh
Q 030018 20 VSKAVVLCQVEKAKEDMLNQLYSSVGAQS------TARIEELLQEDQNVKRRRDRYQK-QSELLSKLTRQLS 84 (184)
Q Consensus 20 VPKAIMh~LVn~sKe~Lq~~L~s~LY~~e------~~~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 334445556666665 356777664421 34688999999999866665544 4445555555553
No 30
>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=27.34 E-value=1.6e+02 Score=20.93 Aligned_cols=13 Identities=23% Similarity=0.483 Sum_probs=10.7
Q ss_pred hHHHHhhcCHHHH
Q 030018 51 RIEELLQEDQNVK 63 (184)
Q Consensus 51 ~l~eLL~Edp~I~ 63 (184)
.|.+.|.+||.|.
T Consensus 40 ~l~e~l~~d~~i~ 52 (81)
T PF10397_consen 40 DLREVLLADPEIA 52 (81)
T ss_dssp -HHHHHCTTHHHH
T ss_pred CHHHHHHCCHHHH
Confidence 6888999999988
No 31
>KOG1899 consensus LAR transmembrane tyrosine phosphatase-interacting protein liprin [General function prediction only]
Probab=26.43 E-value=6.1e+02 Score=26.40 Aligned_cols=31 Identities=13% Similarity=0.176 Sum_probs=13.5
Q ss_pred HHHhhcCHHHHHHHHHHHHHHHHHHHHHHHH
Q 030018 53 EELLQEDQNVKRRRDRYQKQSELLSKLTRQL 83 (184)
Q Consensus 53 ~eLL~Edp~I~~RRe~c~k~L~~LkkA~~~L 83 (184)
++||.-+++--.+=+.++..+.-|++-+++.
T Consensus 284 eslm~ane~kdr~ie~lr~~ln~y~k~~~iv 314 (861)
T KOG1899|consen 284 ESLMRANEQKDRFIESLRNYLNNYDKNAQIV 314 (861)
T ss_pred HHHHhhchhhhhHHHHHHHHhhhhhhhhhhh
Confidence 3444444443333344444444444444443
No 32
>PRK12772 bifunctional flagellar biosynthesis protein FliR/FlhB; Provisional
Probab=26.41 E-value=6e+02 Score=25.18 Aligned_cols=66 Identities=8% Similarity=0.102 Sum_probs=39.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHhhcchHhHHHHh---hcCHHHHHHHHHHHHHHH
Q 030018 9 FEAVLNSLATNVSKAVVLCQVEKAKE-DMLNQLYSSVGAQSTARIEELL---QEDQNVKRRRDRYQKQSE 74 (184)
Q Consensus 9 f~IVrk~I~D~VPKAIMh~LVn~sKe-~Lq~~L~s~LY~~e~~~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 34444555555555555556666666 4555566655555433343333 448999999999876654
No 33
>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=26.15 E-value=4.7e+02 Score=25.32 Aligned_cols=78 Identities=17% Similarity=0.286 Sum_probs=42.7
Q ss_pred hhHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHhhcchHhHHHHhhcCHHHHHHHHHHHHH-------HHHH
Q 030018 5 VRGYFEAVLNSLATNV-SKAVVLCQVEKAKEDMLNQLYSSVGAQSTARIEELLQEDQNVKRRRDRYQKQ-------SELL 76 (184)
Q Consensus 5 V~SYf~IVrk~I~D~V-PKAIMh~LVn~sKe~Lq~~L~s~LY~~e~~~l~eLL~Edp~I~~RRe~c~k~-------L~~L 76 (184)
|..+...|..-|.-+- |+.--+||+..+. ....+|..+|..+- ...+.|...-..+.+||.+++.. |+.|
T Consensus 402 i~~ml~~V~~ii~~Lt~~~~~~L~~Ik~Sp-rYvdrl~~~L~qk~-~~~~k~~~~~~~l~~kr~e~~~e~~~l~pkL~~l 479 (507)
T PF05600_consen 402 IEEMLSAVEEIISQLTNPRTQHLFMIKSSP-RYVDRLVESLQQKL-KQEEKLRRKREDLEEKRQEAQEEQQELEPKLDAL 479 (507)
T ss_pred HHHHHHHHHHHHHHhcCHHHHHHHHHhcCH-HHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHH
Confidence 4445555554444443 4444445554444 44566666665543 24555666666677777777655 5555
Q ss_pred HHHHHHHh
Q 030018 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 34
>PRK03926 mevalonate kinase; Provisional
Probab=25.20 E-value=2.5e+02 Score=24.10 Aligned_cols=56 Identities=13% Similarity=0.020 Sum_probs=27.8
Q ss_pred HHHHHhhcchHhHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhccccC
Q 030018 40 LYSSVGAQSTARIEELLQEDQNVKRRRDRYQKQSELLSKLTRQLSIHDNRAAAASNWSD 98 (184)
Q Consensus 40 L~s~LY~~e~~~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 33444444555677888777654332211 234444555554444544444554443
No 35
>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=24.31 E-value=4.4e+02 Score=22.30 Aligned_cols=30 Identities=3% Similarity=0.024 Sum_probs=21.2
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 030018 5 VRGYFEAVLNSLATNVSKAVVLCQVEKAKE 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 36
>PLN02451 homoserine kinase
Probab=24.30 E-value=1.9e+02 Score=26.58 Aligned_cols=58 Identities=12% Similarity=0.067 Sum_probs=36.8
Q ss_pred HHHHHHHhhcchHhHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhccccC
Q 030018 38 NQLYSSVGAQSTARIEELLQEDQNVKRRRDRYQKQSELLSKLTRQLSIHDNRAAAASNWSD 98 (184)
Q Consensus 38 ~~L~s~LY~~e~~~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 35667776666556778888887777777666 45556666666556655455555444
No 37
>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=24.04 E-value=1.7e+02 Score=22.65 Aligned_cols=40 Identities=20% Similarity=0.389 Sum_probs=29.2
Q ss_pred HHHHHHHhhcchHhHHHHhhcCHHHHHHHHHHHHHHHHHHH
Q 030018 38 NQLYSSVGAQSTARIEELLQEDQNVKRRRDRYQKQSELLSK 78 (184)
Q Consensus 38 ~~L~s~LY~~e~~~l~eLL~Edp~I~~RRe~c~k~L~~Lkk 78 (184)
..|+.+|..-. ..+.+|++|+....-.-..++++|.-+.+
T Consensus 18 ~~l~~~~~~LK-~~~~~l~EEN~~L~~EN~~Lr~~l~~~~~ 57 (107)
T PF06156_consen 18 GQLLEELEELK-KQLQELLEENARLRIENEHLRERLEELEQ 57 (107)
T ss_pred HHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 45666665544 36899999999988888888777766555
No 38
>COG4997 Uncharacterized conserved protein [Function unknown]
Probab=23.24 E-value=3.6e+02 Score=20.95 Aligned_cols=67 Identities=10% Similarity=0.118 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHHHHHH----HH---------HHHHHHHHHHHHHHHHhhcchHhHHHHhhcCHHHHHHHHHHHHHHHHHH
Q 030018 11 AVLNSLATNVSKAVVL----CQ---------VEKAKEDMLNQLYSSVGAQSTARIEELLQEDQNVKRRRDRYQKQSELLS 77 (184)
Q Consensus 11 IVrk~I~D~VPKAIMh----~L---------Vn~sKe~Lq~~L~s~LY~~e~~~l~eLL~Edp~I~~RRe~c~k~L~~Lk 77 (184)
|-.|-|+|.+|-.|-. |- -+..++.|+.++-.=+-.+..+.+.+||+==..|+.-|.--++.|..++
T Consensus 3 i~~KliRD~IpEII~nsgr~~~~h~a~d~ey~~~Le~KL~EE~~E~ledk~lEeLadllEvi~~ia~a~gfske~l~~~R 82 (95)
T COG4997 3 IYNKLIRDLIPEIILNSGRIPVTHIAEDEEYKELLENKLLEEVEEFLEDKNLEELADLLEVISRIAEARGFSKENLEALR 82 (95)
T ss_pred cHHHHHHHhhHHHHHhCCCccchhhccHHHHHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHhCCCHHHHHHHH
Confidence 4567889999987752 11 2222333444433333333344455555555555555554444444443
No 39
>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=23.19 E-value=68 Score=25.24 Aligned_cols=38 Identities=26% Similarity=0.340 Sum_probs=23.9
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHH
Q 030018 5 VRGYFEAVLNSLATNVSKAVVLCQVEKAKE-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 445566555777778888888887765443 34444443
No 40
>PRK13920 putative anti-sigmaE protein; Provisional
Probab=22.82 E-value=88 Score=25.89 Aligned_cols=39 Identities=15% Similarity=0.193 Sum_probs=25.8
Q ss_pred HHHHHhhcchHhHHHHhhcCHHHHHHHHHHHHHHHHHHH
Q 030018 40 LYSSVGAQSTARIEELLQEDQNVKRRRDRYQKQSELLSK 78 (184)
Q Consensus 40 L~s~LY~~e~~~l~eLL~Edp~I~~RRe~c~k~L~~Lkk 78 (184)
+...+-.++...|+..|++|++..++=+++++.+..|..
T Consensus 5 vlG~Ls~eE~~~ve~~L~~dp~~~~~v~~~e~~~~~l~~ 43 (206)
T PRK13920 5 ALGALSPEERARVEAALEAYPELWAELRALQEALAALAE 43 (206)
T ss_pred hcCCCCHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHh
Confidence 333444555567888899998888777777666544433
No 41
>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=22.79 E-value=3.1e+02 Score=20.92 Aligned_cols=35 Identities=17% Similarity=0.258 Sum_probs=30.3
Q ss_pred HHHhhcCHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 030018 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 42
>KOG3119 consensus Basic region leucine zipper transcription factor [Transcription]
Probab=22.47 E-value=2.9e+02 Score=24.35 Aligned_cols=33 Identities=27% Similarity=0.457 Sum_probs=29.0
Q ss_pred hHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHH
Q 030018 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 43
>COG4575 ElaB Uncharacterized conserved protein [Function unknown]
Probab=22.38 E-value=3.9e+02 Score=21.09 Aligned_cols=37 Identities=16% Similarity=0.263 Sum_probs=24.8
Q ss_pred HhHHHHhhcCHHHH-----HHHHHHHHHHHHHHHHHHHHhhhhhh
Q 030018 50 ARIEELLQEDQNVK-----RRRDRYQKQSELLSKLTRQLSIHDNR 89 (184)
Q Consensus 50 ~~l~eLL~Edp~I~-----~RRe~c~k~L~~LkkA~~~Lsi~~~~ 89 (184)
+.+++||++.-..+ +-|.+. -.+|++++.+|...++.
T Consensus 22 d~lEevL~ssg~~a~~e~~~lR~r~---~~~Lk~~r~rl~~~~d~ 63 (104)
T COG4575 22 DTLEEVLKSSGSLAGDEAEELRSKA---ESALKEARDRLGDTGDA 63 (104)
T ss_pred HHHHHHHHhcccchhhHHHHHHHHH---HHHHHHHHHHHHhhhhH
Confidence 46889998865443 444444 35778888888877544
No 44
>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=22.09 E-value=3.8e+02 Score=20.82 Aligned_cols=37 Identities=16% Similarity=0.194 Sum_probs=27.6
Q ss_pred hHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 030018 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 4778888888888888777777777777777775433
No 45
>PF06632 XRCC4: DNA double-strand break repair and V(D)J recombination protein XRCC4; InterPro: IPR010585 This entry represents the DNA double-strand break repair and V(D)J recombination protein XRCC4, which is found in certain Metazoans, fungi and plants. XRCC4 binds to DNA, and to DNA ligase IV (LIG4) to form the LIG4-XRCC4 complex []. The LIG4-XRCC4 complex is responsible for the ligation step in the non-homologous end joining (NHEJ) pathway of DNA double-strand break repair. XRCC4 enhances the joining activity of LIG4. It is thought that XRCC4 and LIG4 are essential for alignment-based gap filling, as well as for final ligation of the breaks []. Binding of the LIG4-XRCC4 complex to DNA ends is dependent on the assembly of the DNA-dependent protein kinase complex DNA-PK to these DNA ends. ; GO: 0003677 DNA binding, 0006302 double-strand break repair, 0006310 DNA recombination, 0005634 nucleus; PDB: 3RWR_R 1IK9_B 3SR2_E 3Q4F_H 3II6_B 1FU1_A 3MUD_B.
Probab=21.86 E-value=2.6e+02 Score=25.85 Aligned_cols=8 Identities=25% Similarity=0.455 Sum_probs=2.9
Q ss_pred HHhhcCHH
Q 030018 54 ELLQEDQN 61 (184)
Q Consensus 54 eLL~Edp~ 61 (184)
.|+.+-+.
T Consensus 162 ~~~~qlE~ 169 (342)
T PF06632_consen 162 KLLKQLEK 169 (342)
T ss_dssp HHHHHHHH
T ss_pred HHHHHHHH
Confidence 33333333
No 46
>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=21.48 E-value=3.5e+02 Score=20.08 Aligned_cols=35 Identities=26% Similarity=0.274 Sum_probs=26.7
Q ss_pred HHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 030018 10 EAVLNSLAT-----NVSKAVVLCQVEKAKEDMLNQLYSSV 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 345566654 58899999999999998888877765
No 47
>COG1245 Predicted ATPase, RNase L inhibitor (RLI) homolog [General function prediction only]
Probab=21.20 E-value=1.7e+02 Score=29.30 Aligned_cols=43 Identities=19% Similarity=0.323 Sum_probs=27.6
Q ss_pred chhhhHHHHHH---------HHHHHHHHHHHH---HHHHHHHHHH-HHHHHHHHHH
Q 030018 2 SQEVRGYFEAV---------LNSLATNVSKAV---VLCQVEKAKE-DMLNQLYSSV 44 (184)
Q Consensus 2 ~~~V~SYf~IV---------rk~I~D~VPKAI---Mh~LVn~sKe-~Lq~~L~s~L 44 (184)
++++..||.-+ +-+..|.+||++ +--|+.+.-+ +...+++..|
T Consensus 146 GtELq~YF~~l~~g~~r~v~K~QYVd~iPk~~KG~v~elLk~~de~g~~devve~l 201 (591)
T COG1245 146 GTELQNYFKKLYEGELRAVHKPQYVDLIPKVVKGKVGELLKKVDERGKFDEVVERL 201 (591)
T ss_pred hhHHHHHHHHHHcCCcceecchHHHHHHHHHhcchHHHHHHhhhhcCcHHHHHHHh
Confidence 46888999866 557889999987 3445555433 3344444443
No 48
>PRK12468 flhB flagellar biosynthesis protein FlhB; Reviewed
Probab=21.11 E-value=6.9e+02 Score=23.42 Aligned_cols=66 Identities=12% Similarity=-0.070 Sum_probs=38.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHhhcchHhHHHH---hhcCHHHHHHHHHHHHHH
Q 030018 8 YFEAVLNSLATNVSKAVVLCQVEKAKE-DMLNQLYSSVGAQSTARIEEL---LQEDQNVKRRRDRYQKQS 73 (184)
Q Consensus 8 Yf~IVrk~I~D~VPKAIMh~LVn~sKe-~Lq~~L~s~LY~~e~~~l~eL---L~Edp~I~~RRe~c~k~L 73 (184)
.+..+.+.+...+=..++.++|-.+-| -.|...|.+=-+.+...+.+= .+=||+|+.||+++++.+
T Consensus 182 ~~~~~~~~~~~l~~~~~~~~~via~~D~~~qr~~~~k~lkMSkqEvKdE~K~~EGdP~iK~r~Rq~~re~ 251 (386)
T PRK12468 182 ALGDALHLIIFCGLVVVLGLSPMVGFDVFYQITSHIKKLRMTKQDIRDEFKNQEGDPHVKGRIRQQQRAM 251 (386)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHhccCCHHHHHHHHHHHHHH
Confidence 344444555555555555556666666 355556655555443333332 345899999999887655
No 49
>PRK09108 type III secretion system protein HrcU; Validated
Probab=21.09 E-value=6.6e+02 Score=23.19 Aligned_cols=67 Identities=13% Similarity=0.158 Sum_probs=38.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHhhcchHhHHHH---hhcCHHHHHHHHHHHHHHH
Q 030018 8 YFEAVLNSLATNVSKAVVLCQVEKAKE-DMLNQLYSSVGAQSTARIEEL---LQEDQNVKRRRDRYQKQSE 74 (184)
Q Consensus 8 Yf~IVrk~I~D~VPKAIMh~LVn~sKe-~Lq~~L~s~LY~~e~~~l~eL---L~Edp~I~~RRe~c~k~L~ 74 (184)
.+..+...+...+=..++.++|-.+-| -.|...|.+=-+.+.+++.+= .+=||+|+.||++.++.+.
T Consensus 177 ~~~~~~~~~~~l~~~~~~~~~via~~D~~~qr~~~~k~lkMSkqEvK~E~K~~EGdP~iK~rrRq~~re~a 247 (353)
T PRK09108 177 LAQILWTVLMKLLAVAAGVFLLVGAADWKIQRWLFIRDNRMSKDEVKREHKESEGDPHIKGERKRLARELA 247 (353)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHhccCCHHHHHHHHHHHHHHH
Confidence 344444555555555555556666656 345555555445443333333 3448999999999876554
No 50
>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=21.03 E-value=2.6e+02 Score=18.42 Aligned_cols=25 Identities=20% Similarity=0.242 Sum_probs=20.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHh
Q 030018 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 5567888888888988888888774
No 51
>KOG1923 consensus Rac1 GTPase effector FRL [Signal transduction mechanisms; Cytoskeleton]
Probab=21.00 E-value=9.9e+02 Score=25.16 Aligned_cols=73 Identities=18% Similarity=0.204 Sum_probs=42.6
Q ss_pred hhHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----hh--cchHhHHHHhhcCHHHHHHHHHHHHHHH
Q 030018 5 VRGYFEA---VLNSLATNVSKAVVLCQVEKAKEDMLNQLYSSV-----GA--QSTARIEELLQEDQNVKRRRDRYQKQSE 74 (184)
Q Consensus 5 V~SYf~I---Vrk~I~D~VPKAIMh~LVn~sKe~Lq~~L~s~L-----Y~--~e~~~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 578899999999999999888876622221111 11 1111233455566666666665544444
Q ss_pred HHH
Q 030018 75 LLS 77 (184)
Q Consensus 75 ~Lk 77 (184)
-+.
T Consensus 221 ~m~ 223 (830)
T KOG1923|consen 221 CMQ 223 (830)
T ss_pred HHH
Confidence 443
No 52
>KOG2509 consensus Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=20.82 E-value=8e+02 Score=24.03 Aligned_cols=47 Identities=11% Similarity=0.144 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHHHH-HHHhhcchHhHHHHhhcCHHHHHH--HHHHHHHHHH
Q 030018 27 CQVEKAKEDMLNQLY-SSVGAQSTARIEELLQEDQNVKRR--RDRYQKQSEL 75 (184)
Q Consensus 27 ~LVn~sKe~Lq~~L~-s~LY~~e~~~l~eLL~Edp~I~~R--Re~c~k~L~~ 75 (184)
--.|+-++.|.+.+- -++.+.+ ...+|++|-+.+.+. |+.+++.+.-
T Consensus 51 deln~~~n~l~k~i~~~k~kkke--~~~~l~~~~~~~~~~~~~~~l~e~~~~ 100 (455)
T KOG2509|consen 51 DELNKEKNKLNKEIGDLKLKKKE--DIGQLEESKAKNTEGAERKLLKEEAVE 100 (455)
T ss_pred HHHHHHHHHhhhHhhHHHHhhcc--hhhHHHHhhhHhhhhhhhhhhHHHHHh
Confidence 335555666777766 5666544 577888887777764 4444444433
No 53
>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=20.77 E-value=1.8e+02 Score=24.56 Aligned_cols=43 Identities=26% Similarity=0.440 Sum_probs=28.6
Q ss_pred HHHhhcchHhHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 030018 42 SSVGAQSTARIEELLQEDQNVKRRRDRYQKQSELLSKLTRQLSIHDN 88 (184)
Q Consensus 42 s~LY~~e~~~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-DDGIIRNRGKIE---ATIANARAALQLEQN 107 (179)
T ss_pred HHHhCCCHHHHHHHhc-CccchhhHHHHH---HHHHHHHHHHHHHHc
Confidence 4444444567888886 677777777773 566777777766443
No 54
>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=20.70 E-value=4.3e+02 Score=20.89 Aligned_cols=56 Identities=23% Similarity=0.296 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------Hh--------hcchHhHHHHhhcCHHHHHHHHHH
Q 030018 14 NSLATNVSKAVVLCQVEKAKEDMLNQLYSS-------VG--------AQSTARIEELLQEDQNVKRRRDRY 69 (184)
Q Consensus 14 k~I~D~VPKAIMh~LVn~sKe~Lq~~L~s~-------LY--------~~e~~~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 556666666666666666555555554321 11 112234789999999987664333
No 55
>PF08681 DUF1778: Protein of unknown function (DUF1778); InterPro: IPR014795 This entry is represented by Vibrio phage ICP1, Orf50. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a family of uncharacterised proteins. The structure of one of the hypothetical proteins in this family has been solved and it forms a helix structure which may form interactions with DNA. ; PDB: 1Y9B_A.
Probab=20.37 E-value=2.9e+02 Score=19.81 Aligned_cols=40 Identities=15% Similarity=0.121 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHHHHHHHHhhcchHhHHHHhhcCHHHHHH
Q 030018 26 LCQVEKAKEDMLNQLYSSVGAQSTARIEELLQEDQNVKRR 65 (184)
Q Consensus 26 h~LVn~sKe~Lq~~L~s~LY~~e~~~l~eLL~Edp~I~~R 65 (184)
...+.++++.|.++=+-.|..++-+.|-++|.+.|.-..+
T Consensus 31 ~aa~~~A~~~i~~~~~~~Ls~~~~~~f~~aLd~p~~p~~~ 70 (80)
T PF08681_consen 31 SAALEAAEEVIEEHERIRLSAEDFEAFMAALDNPPQPNER 70 (80)
T ss_dssp HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH-HHHHHHH
T ss_pred HHHHHHHHHHHhhcceeEcCHHHHHHHHHHHhCCCCCCHH
Confidence 3345677778888877788777767788888887666543
No 56
>COG5016 Pyruvate/oxaloacetate carboxyltransferase [Energy production and conversion]
Probab=20.26 E-value=63 Score=31.35 Aligned_cols=62 Identities=24% Similarity=0.311 Sum_probs=43.0
Q ss_pred hhhhHHHHHHHHHH-HHHHHHHHH---HHHHHHHHHHHHHHHHHHHhhcc-hHhHHHHhhcCHHHHH
Q 030018 3 QEVRGYFEAVLNSL-ATNVSKAVV---LCQVEKAKEDMLNQLYSSVGAQS-TARIEELLQEDQNVKR 64 (184)
Q Consensus 3 ~~V~SYf~IVrk~I-~D~VPKAIM---h~LVn~sKe~Lq~~L~s~LY~~e-~~~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 35788999999988 444666665 44566666678888888775443 4567888887776643
No 57
>PF12057 DUF3538: Domain of unknown function (DUF3538); InterPro: IPR021925 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 120 amino acids in length. This domain is found associated with PF00240 from PFAM. This domain has a conserved SDL sequence motif.
Probab=20.16 E-value=3.1e+02 Score=22.09 Aligned_cols=26 Identities=35% Similarity=0.563 Sum_probs=16.4
Q ss_pred hHHHHhhcCHHHH-----HHHHHHHHHHHHH
Q 030018 51 RIEELLQEDQNVK-----RRRDRYQKQSELL 76 (184)
Q Consensus 51 ~l~eLL~Edp~I~-----~RRe~c~k~L~~L 76 (184)
..-++|+||+..- +.|++++..++.-
T Consensus 21 ry~~iL~~~~~~e~~~~~~~re~~QRi~d~V 51 (120)
T PF12057_consen 21 RYHEILQEDPSFEYENNTQEREEDQRIFDLV 51 (120)
T ss_pred HHHHHHhcCCCCCCCCCccchhhHhHHHHHH
Confidence 3456777777555 6677777665443
No 58
>KOG2391 consensus Vacuolar sorting protein/ubiquitin receptor VPS23 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=20.06 E-value=7.6e+02 Score=23.49 Aligned_cols=36 Identities=19% Similarity=0.137 Sum_probs=26.7
Q ss_pred HHhhcCHHHHHHHHHHHHHHHHHHHHHHHHhhhhhh
Q 030018 54 ELLQEDQNVKRRRDRYQKQSELLSKLTRQLSIHDNR 89 (184)
Q Consensus 54 eLL~Edp~I~~RRe~c~k~L~~LkkA~~~Lsi~~~~ 89 (184)
+|..-..++.+.++++++++..|++..++|.-+...
T Consensus 243 eL~~G~~kL~~~~etLEqq~~~L~~niDIL~~k~~e 278 (365)
T KOG2391|consen 243 ELNIGKQKLVAMKETLEQQLQSLQKNIDILKSKVRE 278 (365)
T ss_pred HHHhhHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHH
Confidence 444445566777888888888888888888777766
Done!