Query psy8096
Match_columns 118
No_of_seqs 133 out of 1479
Neff 8.8
Searched_HMMs 46136
Date Fri Aug 16 18:20:49 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8096.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8096hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4442|consensus 100.0 1.6E-42 3.5E-47 265.6 10.5 117 1-117 140-257 (729)
2 KOG1080|consensus 100.0 8E-36 1.7E-40 239.1 11.4 117 1-118 886-1003(1005)
3 smart00317 SET SET (Su(var)3-9 99.9 1.2E-26 2.6E-31 145.7 12.7 96 1-96 20-116 (116)
4 KOG1079|consensus 99.9 1E-27 2.3E-32 183.8 7.4 100 1-101 614-713 (739)
5 KOG1082|consensus 99.9 3.5E-27 7.7E-32 175.1 6.2 118 1-118 196-352 (364)
6 KOG1083|consensus 99.9 3.3E-25 7.1E-30 176.1 -0.5 100 1-100 1198-1297(1306)
7 KOG1085|consensus 99.9 5.3E-23 1.2E-27 145.7 8.1 100 1-100 276-380 (392)
8 KOG1141|consensus 99.8 4.4E-20 9.5E-25 144.8 3.7 76 42-117 1178-1259(1262)
9 COG2940 Proteins containing SE 99.8 3.7E-20 8E-25 141.9 1.6 118 1-118 352-478 (480)
10 KOG2589|consensus 99.7 2.8E-17 6.1E-22 119.8 4.7 112 1-118 147-258 (453)
11 PF00856 SET: SET domain; Int 99.7 1.7E-16 3.7E-21 103.6 6.4 56 42-97 107-162 (162)
12 KOG1081|consensus 99.4 1E-13 2.2E-18 105.8 0.9 106 11-117 328-434 (463)
13 KOG2461|consensus 98.3 6.4E-07 1.4E-11 67.6 3.4 89 1-101 50-147 (396)
14 smart00508 PostSET Cysteine-ri 97.2 0.00018 4E-09 33.5 1.0 14 105-118 2-15 (26)
15 KOG2084|consensus 97.2 0.00085 1.8E-08 51.0 5.1 54 56-113 208-272 (482)
16 KOG1337|consensus 96.2 0.0039 8.4E-08 48.3 2.7 42 54-98 237-278 (472)
17 PF08666 SAF: SAF domain; Int 91.1 0.14 3.1E-06 28.2 1.4 16 79-94 3-18 (63)
18 KOG1338|consensus 90.0 0.22 4.8E-06 38.0 2.0 42 52-99 217-261 (466)
19 PF00856 SET: SET domain; Int 83.2 0.83 1.8E-05 28.9 1.7 17 79-95 3-19 (162)
20 TIGR02059 swm_rep_I cyanobacte 81.4 4.7 0.0001 24.9 4.4 25 75-99 74-98 (101)
21 smart00858 SAF This domain fam 80.7 1.2 2.7E-05 24.3 1.6 16 79-94 3-18 (64)
22 KOG2155|consensus 73.0 1.9 4.2E-05 33.6 1.2 46 53-98 204-251 (631)
23 TIGR03569 NeuB_NnaB N-acetylne 58.1 5.7 0.00012 29.7 1.2 19 77-95 277-295 (329)
24 TIGR03170 flgA_cterm flagella 53.6 6.4 0.00014 24.6 0.8 17 79-95 1-17 (122)
25 PF06718 DUF1203: Protein of u 53.4 12 0.00027 23.7 2.0 19 81-99 6-25 (117)
26 smart00561 MBT Present in Dros 53.2 49 0.0011 20.0 5.1 53 59-113 26-78 (96)
27 TIGR03586 PseI pseudaminic aci 46.3 15 0.00032 27.5 1.8 20 76-95 274-293 (327)
28 PF07177 Neuralized: Neuralize 44.7 24 0.00052 20.1 2.2 22 74-95 27-48 (69)
29 COG2089 SpsE Sialic acid synth 41.5 14 0.00031 27.8 1.1 19 77-95 289-307 (347)
30 PF11720 Inhibitor_I78: Peptid 40.4 11 0.00024 20.8 0.3 18 83-100 26-43 (60)
31 PF12947 EGF_3: EGF domain; I 39.7 19 0.00041 17.7 1.1 11 58-68 5-15 (36)
32 cd05468 pVHL von Hippel-Landau 39.7 1E+02 0.0023 20.0 4.9 38 53-95 10-47 (141)
33 TIGR00049 Iron-sulfur cluster 38.2 22 0.00047 21.5 1.4 34 80-113 61-102 (105)
34 PRK12618 flgA flagellar basal 37.7 21 0.00046 23.3 1.4 18 77-94 19-36 (141)
35 PRK06005 flgA flagellar basal 37.7 20 0.00043 23.9 1.3 19 77-95 33-51 (160)
36 PRK13623 iron-sulfur cluster i 37.3 16 0.00034 22.7 0.7 32 82-113 73-112 (115)
37 KOG4078|consensus 36.5 36 0.00079 22.5 2.3 21 88-114 94-114 (173)
38 COG1188 Ribosome-associated he 36.2 24 0.00051 21.9 1.3 29 69-100 35-63 (100)
39 TIGR02011 IscA iron-sulfur clu 34.5 19 0.00041 22.0 0.7 34 80-113 61-102 (105)
40 PF13121 DUF3976: Domain of un 34.2 36 0.00078 17.0 1.5 15 79-93 2-16 (41)
41 PRK09504 sufA iron-sulfur clus 34.2 20 0.00044 22.7 0.8 32 82-113 80-119 (122)
42 PF10246 MRP-S35: Mitochondria 32.8 45 0.00097 20.8 2.1 19 89-113 36-54 (104)
43 TIGR03177 pilus_cpaB Flp pilus 31.4 28 0.00061 24.9 1.3 21 75-95 34-54 (261)
44 COG1465 Predicted alternative 30.2 1.4E+02 0.0031 22.4 4.7 55 41-95 214-290 (376)
45 TIGR03248 galactar-dH20 galact 30.0 35 0.00077 27.2 1.7 18 81-99 42-59 (507)
46 COG3831 Uncharacterized conser 29.3 56 0.0012 19.6 2.1 18 76-97 15-32 (85)
47 COG1261 FlgA Flagellar basal b 27.4 1.3E+02 0.0029 21.2 4.1 18 76-93 94-111 (220)
48 PF00842 Ala_racemase_C: Alani 27.1 29 0.00063 22.2 0.7 23 77-101 5-27 (129)
49 PF01847 VHL: von Hippel-Linda 26.6 1.1E+02 0.0024 20.5 3.3 38 53-95 16-53 (156)
50 PF01835 A2M_N: MG2 domain; I 26.3 84 0.0018 18.4 2.6 15 80-94 4-19 (99)
51 PF14100 PmoA: Methane oxygena 26.2 75 0.0016 23.0 2.7 42 56-98 205-252 (271)
52 COG4118 Phd Antitoxin of toxin 26.2 21 0.00045 21.3 -0.1 13 84-96 19-31 (84)
53 PRK07018 flgA flagellar basal 25.8 40 0.00087 23.8 1.3 18 77-94 110-127 (235)
54 PRK09502 iscA iron-sulfur clus 24.9 33 0.00071 21.0 0.6 33 81-113 64-104 (107)
55 TIGR01997 sufA_proteo FeS asse 24.7 30 0.00065 21.2 0.4 34 80-113 63-104 (107)
56 PF13144 SAF_2: SAF-like 24.0 43 0.00094 22.6 1.1 20 76-95 74-93 (196)
57 COG0787 Alr Alanine racemase [ 23.7 43 0.00094 25.5 1.1 26 76-103 238-263 (360)
58 PRK08515 flgA flagellar basal 23.5 48 0.001 23.3 1.3 17 78-94 101-117 (222)
59 PF04014 Antitoxin-MazE: Antid 23.5 57 0.0012 16.7 1.3 14 85-98 20-33 (47)
60 COG3848 Phosphohistidine swive 23.2 46 0.001 20.8 1.0 17 81-97 83-99 (111)
61 smart00588 NEUZ domain in neur 23.1 86 0.0019 19.9 2.3 21 76-96 30-50 (123)
62 TIGR00286 arginine decarboxyla 22.6 1.3E+02 0.0027 20.1 3.0 15 83-97 52-66 (152)
63 cd03420 SirA_RHOD_Pry_redox Si 22.1 44 0.00095 18.7 0.7 15 82-96 19-33 (69)
64 COG3884 FatA Acyl-ACP thioeste 21.2 1.1E+02 0.0024 22.0 2.7 25 75-99 193-217 (250)
65 PF11910 NdhO: Cyanobacterial 20.7 1.8E+02 0.0039 16.5 3.2 42 1-48 1-42 (67)
66 KOG3422|consensus 20.4 2E+02 0.0043 20.4 3.7 37 1-38 138-174 (221)
67 PF14796 AP3B1_C: Clathrin-ada 20.1 1.2E+02 0.0027 20.0 2.6 52 51-102 88-142 (145)
68 smart00002 PLP Myelin proteoli 20.1 61 0.0013 18.1 1.0 13 41-53 20-32 (60)
No 1
>KOG4442|consensus
Probab=100.00 E-value=1.6e-42 Score=265.58 Aligned_cols=117 Identities=35% Similarity=0.557 Sum_probs=113.5
Q ss_pred CCCCCeeEEeeeEEEChhHHHHHHHHHhhcCC-eeeEEEcCCcEEEecccCCCeeeeeecCCCCCceeEEEEECCccEEE
Q psy8096 1 MEEDCSVSVTLMAVIRASVSDKREKQYMDKGI-GCYMFKIDDRFVIDATMKGNAARFINHSCDPNCYSRVVEIMGKPHII 79 (118)
Q Consensus 1 I~~g~~i~ey~Gevi~~~~~~~~~~~~~~~~~-~~y~~~~~~~~~iDa~~~gn~~RfiNHSC~PN~~~~~~~~~~~~~~~ 79 (118)
|++|+||+||.||||+..++++|...|..... |.|+|.+....+|||+..||++|||||||+|||+++.|.|.+..||+
T Consensus 140 I~~g~FI~EY~GEVI~~~Ef~kR~~~Y~~d~~kh~Yfm~L~~~e~IDAT~KGnlaRFiNHSC~PNa~~~KWtV~~~lRvG 219 (729)
T KOG4442|consen 140 IPKGQFILEYIGEVIEEKEFEKRVKRYAKDGIKHYYFMALQGGEYIDATKKGNLARFINHSCDPNAEVQKWTVPDELRVG 219 (729)
T ss_pred cCCCcEEeeeccccccHHHHHHHHHHHHhcCCceEEEEEecCCceecccccCcHHHhhcCCCCCCceeeeeeeCCeeEEE
Confidence 89999999999999999999999999986665 69999999999999999999999999999999999999999999999
Q ss_pred EEEcCCCCCCCeEEEccCCCCCCCCCeEEEecCCCccC
Q psy8096 80 IFALRKINKGEELTYDYKFPIEDDNKISCHCLAMRCTN 117 (118)
Q Consensus 80 ~~a~rdI~~GeElt~~Yg~~~~~~~~~~C~Cg~~~Cr~ 117 (118)
|||.|+|++||||||||++++.+.....|.||+++|||
T Consensus 220 iFakk~I~~GEEITFDYqf~rYGr~AQ~CyCgeanC~G 257 (729)
T KOG4442|consen 220 IFAKKVIKPGEEITFDYQFDRYGRDAQPCYCGEANCRG 257 (729)
T ss_pred EeEecccCCCceeeEecccccccccccccccCCccccc
Confidence 99999999999999999999999999999999999998
No 2
>KOG1080|consensus
Probab=100.00 E-value=8e-36 Score=239.13 Aligned_cols=117 Identities=50% Similarity=0.901 Sum_probs=112.3
Q ss_pred CCCCCeeEEeeeEEEChhHHHHHHHHHhhcCC-eeeEEEcCCcEEEecccCCCeeeeeecCCCCCceeEEEEECCccEEE
Q psy8096 1 MEEDCSVSVTLMAVIRASVSDKREKQYMDKGI-GCYMFKIDDRFVIDATMKGNAARFINHSCDPNCYSRVVEIMGKPHII 79 (118)
Q Consensus 1 I~~g~~i~ey~Gevi~~~~~~~~~~~~~~~~~-~~y~~~~~~~~~iDa~~~gn~~RfiNHSC~PN~~~~~~~~~~~~~~~ 79 (118)
|.+|++|+||+||++....++.|+..|...+. .+|+|.+++..+|||++.||+||||||||.|||..+.+.+++..+|+
T Consensus 886 i~~~dmViEY~Ge~vR~~iad~RE~~Y~~~gi~~sYlfrid~~~ViDAtk~gniAr~InHsC~PNCyakvi~V~g~~~Iv 965 (1005)
T KOG1080|consen 886 IAAGDMVIEYRGELVRSSIADLREARYERMGIGDSYLFRIDDEVVVDATKKGNIARFINHSCNPNCYAKVITVEGDKRIV 965 (1005)
T ss_pred ccccceEEEeeceehhhhHHHHHHHHHhccCcccceeeecccceEEeccccCchhheeecccCCCceeeEEEecCeeEEE
Confidence 68999999999999999999999999998884 59999999999999999999999999999999999999999999999
Q ss_pred EEEcCCCCCCCeEEEccCCCCCCCCCeEEEecCCCccCC
Q psy8096 80 IFALRKINKGEELTYDYKFPIEDDNKISCHCLAMRCTNN 118 (118)
Q Consensus 80 ~~a~rdI~~GeElt~~Yg~~~~~~~~~~C~Cg~~~Cr~~ 118 (118)
|+|.|+|.+|||||+||.+...+. ...|+||+++|||.
T Consensus 966 Iyakr~I~~~EElTYDYkF~~e~~-kipClCgap~Crg~ 1003 (1005)
T KOG1080|consen 966 IYSKRDIAAGEELTYDYKFPTEDD-KIPCLCGAPNCRGF 1003 (1005)
T ss_pred EEEecccccCceeeeecccccccc-ccccccCCCccccc
Confidence 999999999999999999998877 89999999999984
No 3
>smart00317 SET SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain. Putative methyl transferase, based on outlier plant homologues
Probab=99.95 E-value=1.2e-26 Score=145.70 Aligned_cols=96 Identities=45% Similarity=0.762 Sum_probs=85.1
Q ss_pred CCCCCeeEEeeeEEEChhHHHHHHHHHhhcCC-eeeEEEcCCcEEEecccCCCeeeeeecCCCCCceeEEEEECCccEEE
Q psy8096 1 MEEDCSVSVTLMAVIRASVSDKREKQYMDKGI-GCYMFKIDDRFVIDATMKGNAARFINHSCDPNCYSRVVEIMGKPHII 79 (118)
Q Consensus 1 I~~g~~i~ey~Gevi~~~~~~~~~~~~~~~~~-~~y~~~~~~~~~iDa~~~gn~~RfiNHSC~PN~~~~~~~~~~~~~~~ 79 (118)
|++|++|.+|.|.++...+...+...+..... ..|+|......+||++..+|++||+||||.||+.+.....++..++.
T Consensus 20 i~~g~~i~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~id~~~~~~~~~~iNHsc~pN~~~~~~~~~~~~~~~ 99 (116)
T smart00317 20 IPKGEFIGEYVGEIITSEEAEERSKAYDTDGADSFYLFEIDSDLCIDARRKGNIARFINHSCEPNCELLFVEVNGDSRIV 99 (116)
T ss_pred cCCCCEEEEEEeEEECHHHHHHHHHHHHhcCCCCEEEEECCCCEEEeCCccCcHHHeeCCCCCCCEEEEEEEECCCcEEE
Confidence 78999999999999999988887654443333 48888888789999999999999999999999999998887777999
Q ss_pred EEEcCCCCCCCeEEEcc
Q psy8096 80 IFALRKINKGEELTYDY 96 (118)
Q Consensus 80 ~~a~rdI~~GeElt~~Y 96 (118)
++|+|||++|||||++|
T Consensus 100 ~~a~r~I~~GeEi~i~Y 116 (116)
T smart00317 100 IFALRDIKPGEELTIDY 116 (116)
T ss_pred EEECCCcCCCCEEeecC
Confidence 99999999999999998
No 4
>KOG1079|consensus
Probab=99.94 E-value=1e-27 Score=183.77 Aligned_cols=100 Identities=38% Similarity=0.665 Sum_probs=95.0
Q ss_pred CCCCCeeEEeeeEEEChhHHHHHHHHHhhcCCeeeEEEcCCcEEEecccCCCeeeeeecCCCCCceeEEEEECCccEEEE
Q psy8096 1 MEEDCSVSVTLMAVIRASVSDKREKQYMDKGIGCYMFKIDDRFVIDATMKGNAARFINHSCDPNCYSRVVEIMGKPHIII 80 (118)
Q Consensus 1 I~~g~~i~ey~Gevi~~~~~~~~~~~~~~~~~~~y~~~~~~~~~iDa~~~gn~~RfiNHSC~PN~~~~~~~~~~~~~~~~ 80 (118)
+.||+||+||+||+|++.|+++|...|+.... +|+|++..+++|||++.||.+||+|||-.|||..+.+.+.+.+||.|
T Consensus 614 v~KnefisEY~GE~IS~dEADrRGkiYDr~~c-SflFnln~dyviDs~rkGnk~rFANHS~nPNCYAkvm~V~GdhRIGi 692 (739)
T KOG1079|consen 614 VSKNEFISEYTGEIISHDEADRRGKIYDRYMC-SFLFNLNNDYVIDSTRKGNKIRFANHSFNPNCYAKVMMVAGDHRIGI 692 (739)
T ss_pred cCCCceeeeecceeccchhhhhcccccccccc-eeeeeccccceEeeeeecchhhhccCCCCCCcEEEEEEecCCcceee
Confidence 47999999999999999999999999987776 99999999999999999999999999999999999999999999999
Q ss_pred EEcCCCCCCCeEEEccCCCCC
Q psy8096 81 FALRKINKGEELTYDYKFPIE 101 (118)
Q Consensus 81 ~a~rdI~~GeElt~~Yg~~~~ 101 (118)
||.|.|.+|||||+||..+-.
T Consensus 693 fAkRaIeagEELffDYrYs~~ 713 (739)
T KOG1079|consen 693 FAKRAIEAGEELFFDYRYSPE 713 (739)
T ss_pred eehhhcccCceeeeeeccCcc
Confidence 999999999999999986643
No 5
>KOG1082|consensus
Probab=99.94 E-value=3.5e-27 Score=175.09 Aligned_cols=118 Identities=31% Similarity=0.366 Sum_probs=94.0
Q ss_pred CCCCCeeEEeeeEEEChhHHHHHHHHHhhcCC--e-eeEE---------------------EcCCcEEEecccCCCeeee
Q psy8096 1 MEEDCSVSVTLMAVIRASVSDKREKQYMDKGI--G-CYMF---------------------KIDDRFVIDATMKGNAARF 56 (118)
Q Consensus 1 I~~g~~i~ey~Gevi~~~~~~~~~~~~~~~~~--~-~y~~---------------------~~~~~~~iDa~~~gn~~Rf 56 (118)
|++|+||+||+||+++..++..+......... . .+.+ .....+.|||...||++||
T Consensus 196 I~~G~fvcEyaGe~~t~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ida~~~GNv~Rf 275 (364)
T KOG1082|consen 196 IPAGEFVCEYAGEVLTSEEAQRRTHLREYLDDDCDAYSIADREWVDESPVGNTFVAPSLPGGPGRELLIDAKPHGNVARF 275 (364)
T ss_pred ccCCCeeEEEeeEecChHHhhhccccccccccccccchhhhccccccccccccccccccccCCCcceEEchhhccccccc
Confidence 79999999999999999999877422221111 0 1111 1135789999999999999
Q ss_pred eecCCCCCceeEEEEECC----ccEEEEEEcCCCCCCCeEEEccCCCCC-----------CCCCeEEEecCCCccCC
Q psy8096 57 INHSCDPNCYSRVVEIMG----KPHIIIFALRKINKGEELTYDYKFPIE-----------DDNKISCHCLAMRCTNN 118 (118)
Q Consensus 57 iNHSC~PN~~~~~~~~~~----~~~~~~~a~rdI~~GeElt~~Yg~~~~-----------~~~~~~C~Cg~~~Cr~~ 118 (118)
|||||.||+.+..+..+. .++++|||+++|+|++|||+|||..+. ......|.|++..||+.
T Consensus 276 inHSC~PN~~~~~v~~~~~~~~~~~i~ffa~~~I~p~~ELT~dYg~~~~~~~~~~~~~~~~~~~~~c~c~~~~cr~~ 352 (364)
T KOG1082|consen 276 INHSCSPNLLYQAVFQDEFVLLYLRIGFFALRDISPGEELTLDYGKAYKLLVQDGANIYTPVMKKNCNCGLEKCRGL 352 (364)
T ss_pred ccCCCCccceeeeeeecCCccchheeeeeeccccCCCcccchhhcccccccccccccccccccchhhcCCCHHhCcc
Confidence 999999999999988874 478999999999999999999997753 12367899999999973
No 6
>KOG1083|consensus
Probab=99.90 E-value=3.3e-25 Score=176.14 Aligned_cols=100 Identities=36% Similarity=0.556 Sum_probs=91.4
Q ss_pred CCCCCeeEEeeeEEEChhHHHHHHHHHhhcCCeeeEEEcCCcEEEecccCCCeeeeeecCCCCCceeEEEEECCccEEEE
Q psy8096 1 MEEDCSVSVTLMAVIRASVSDKREKQYMDKGIGCYMFKIDDRFVIDATMKGNAARFINHSCDPNCYSRVVEIMGKPHIII 80 (118)
Q Consensus 1 I~~g~~i~ey~Gevi~~~~~~~~~~~~~~~~~~~y~~~~~~~~~iDa~~~gn~~RfiNHSC~PN~~~~~~~~~~~~~~~~ 80 (118)
|++|+||+||+|||++..+.+.+.........+.|...+..+.++|+.+++|.+||+||||+|||+++.|.++|..|++|
T Consensus 1198 ikagtfI~EYvGeVit~ke~e~~mmtl~~~d~~~~cL~I~p~l~id~~R~~n~~RfinhscKPNc~~qkwSVNG~~Rv~L 1277 (1306)
T KOG1083|consen 1198 IKAGTFIMEYVGEVITEKEFEPRMMTLYHNDDDHYCLVIDPGLFIDIPRMGNGARFINHSCKPNCEMQKWSVNGEYRVGL 1277 (1306)
T ss_pred ccccchHHHHHHHHHHHHhhcccccccCCCCCcccccccCccccCChhhccccccccccccCCCCccccccccceeeeee
Confidence 68999999999999999998888554455555699999999999999999999999999999999999999999999999
Q ss_pred EEcCCCCCCCeEEEccCCCC
Q psy8096 81 FALRKINKGEELTYDYKFPI 100 (118)
Q Consensus 81 ~a~rdI~~GeElt~~Yg~~~ 100 (118)
||+|||.+|||||+||+...
T Consensus 1278 ~A~rDi~kGEELtYDYN~ks 1297 (1306)
T KOG1083|consen 1278 FALRDLPKGEELTYDYNFKS 1297 (1306)
T ss_pred eecCCCCCCceEEEeccccc
Confidence 99999999999999998543
No 7
>KOG1085|consensus
Probab=99.89 E-value=5.3e-23 Score=145.73 Aligned_cols=100 Identities=40% Similarity=0.583 Sum_probs=87.6
Q ss_pred CCCCCeeEEeeeEEEChhHHHHHHHHHhhcCC-eeeEE---EcCCcEEEecccCCC-eeeeeecCCCCCceeEEEEECCc
Q psy8096 1 MEEDCSVSVTLMAVIRASVSDKREKQYMDKGI-GCYMF---KIDDRFVIDATMKGN-AARFINHSCDPNCYSRVVEIMGK 75 (118)
Q Consensus 1 I~~g~~i~ey~Gevi~~~~~~~~~~~~~~~~~-~~y~~---~~~~~~~iDa~~~gn-~~RfiNHSC~PN~~~~~~~~~~~ 75 (118)
.++|+||.||.|.+|.-.++..|+..|..... +.|++ +.+..++|||+..-+ ++|+||||-.+|+..+.+.+++.
T Consensus 276 F~rgdFVVEY~Gdliei~eAk~rE~~Ya~De~~GcYMYyF~h~sk~yCiDAT~et~~lGRLINHS~~gNl~TKvv~Idg~ 355 (392)
T KOG1085|consen 276 FERGDFVVEYRGDLIEISEAKVREEQYANDEEIGCYMYYFEHNSKKYCIDATKETPWLGRLINHSVRGNLKTKVVEIDGS 355 (392)
T ss_pred cccCceEEEEecceeeechHHHHHHHhccCcccceEEEeeeccCeeeeeecccccccchhhhcccccCcceeeEEEecCC
Confidence 36899999999999999999999998874433 34443 456789999999655 99999999999999999999999
Q ss_pred cEEEEEEcCCCCCCCeEEEccCCCC
Q psy8096 76 PHIIIFALRKINKGEELTYDYKFPI 100 (118)
Q Consensus 76 ~~~~~~a~rdI~~GeElt~~Yg~~~ 100 (118)
+++.++|.|||.+||||++|||+.-
T Consensus 356 pHLiLvA~rdIa~GEELlYDYGDRS 380 (392)
T KOG1085|consen 356 PHLILVARRDIAQGEELLYDYGDRS 380 (392)
T ss_pred ceEEEEeccccccchhhhhhccccc
Confidence 9999999999999999999999753
No 8
>KOG1141|consensus
Probab=99.79 E-value=4.4e-20 Score=144.84 Aligned_cols=76 Identities=38% Similarity=0.757 Sum_probs=67.4
Q ss_pred cEEEecccCCCeeeeeecCCCCCceeEEEEECCc----cEEEEEEcCCCCCCCeEEEccCCCCCCC--CCeEEEecCCCc
Q psy8096 42 RFVIDATMKGNAARFINHSCDPNCYSRVVEIMGK----PHIIIFALRKINKGEELTYDYKFPIEDD--NKISCHCLAMRC 115 (118)
Q Consensus 42 ~~~iDa~~~gn~~RfiNHSC~PN~~~~~~~~~~~----~~~~~~a~rdI~~GeElt~~Yg~~~~~~--~~~~C~Cg~~~C 115 (118)
-++|||...||++||+||||.||+-++.++++.. +-++|||.+-|++|+||||||+..-... ....|.||+.+|
T Consensus 1178 ~yvIDAk~eGNlGRfLNHSC~PNl~VQnVfvdTHdlrfPwVAFFt~kyVkAgtELTWDY~Ye~g~v~~keL~C~CGa~~C 1257 (1262)
T KOG1141|consen 1178 LYVIDAKQEGNLGRFLNHSCDPNLHVQNVFVDTHDLRFPWVAFFTRKYVKAGTELTWDYQYEQGQVATKELTCHCGAENC 1257 (1262)
T ss_pred eEEEecccccchhhhhccCCCccceeeeeeeeccccCCchhhhhhhhhhccCceeeeeccccccccccceEEEecChhhh
Confidence 4789999999999999999999999999999763 5579999999999999999999664432 378999999999
Q ss_pred cC
Q psy8096 116 TN 117 (118)
Q Consensus 116 r~ 117 (118)
||
T Consensus 1258 rg 1259 (1262)
T KOG1141|consen 1258 RG 1259 (1262)
T ss_pred hc
Confidence 98
No 9
>COG2940 Proteins containing SET domain [General function prediction only]
Probab=99.78 E-value=3.7e-20 Score=141.87 Aligned_cols=118 Identities=36% Similarity=0.588 Sum_probs=98.6
Q ss_pred CCCCCeeEEeeeEEEChhHHHHHHHHHhhcCCeeeEEEcCC-cEEEecccCCCeeeeeecCCCCCceeEEEEECCccEEE
Q psy8096 1 MEEDCSVSVTLMAVIRASVSDKREKQYMDKGIGCYMFKIDD-RFVIDATMKGNAARFINHSCDPNCYSRVVEIMGKPHII 79 (118)
Q Consensus 1 I~~g~~i~ey~Gevi~~~~~~~~~~~~~~~~~~~y~~~~~~-~~~iDa~~~gn~~RfiNHSC~PN~~~~~~~~~~~~~~~ 79 (118)
|++|++|.+|.|+++...++..++..+.....+..++.+.. ..++|+...|+.+||+||||.||+........+..++.
T Consensus 352 i~~~e~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~g~~~r~~nHS~~pN~~~~~~~~~g~~~~~ 431 (480)
T COG2940 352 IKKGEFIIEYHGEIIRRKEAREREENYDLLGNEFSFGLLEDKDKVRDSQKAGDVARFINHSCTPNCEASPIEVNGIFKIS 431 (480)
T ss_pred ccchHHHHHhcCcccchHHHHhhhccccccccccchhhccccchhhhhhhcccccceeecCCCCCcceecccccccceee
Confidence 68999999999999999999998876643333333333333 78899999999999999999999988877766667899
Q ss_pred EEEcCCCCCCCeEEEccCCCCCCCC--------CeEEEecCCCccCC
Q psy8096 80 IFALRKINKGEELTYDYKFPIEDDN--------KISCHCLAMRCTNN 118 (118)
Q Consensus 80 ~~a~rdI~~GeElt~~Yg~~~~~~~--------~~~C~Cg~~~Cr~~ 118 (118)
++|+|||.+||||++||+..++... ...|.|+++.|+++
T Consensus 432 ~~~~rDI~~geEl~~dy~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 478 (480)
T COG2940 432 IYAIRDIKAGEELTYDYGPSLEDNRELKKLLEKRWGCACGEDRCSHT 478 (480)
T ss_pred ecccccchhhhhhccccccccccchhhhhhhhhhhccccCCCccCCC
Confidence 9999999999999999998887633 68999999999875
No 10
>KOG2589|consensus
Probab=99.68 E-value=2.8e-17 Score=119.84 Aligned_cols=112 Identities=23% Similarity=0.342 Sum_probs=84.4
Q ss_pred CCCCCeeEEeeeEEEChhHHHHHHHHHhhcCCeeeEEEcCCcEEEecccCCCeeeeeecCCCCCceeEEEEECCccEEEE
Q psy8096 1 MEEDCSVSVTLMAVIRASVSDKREKQYMDKGIGCYMFKIDDRFVIDATMKGNAARFINHSCDPNCYSRVVEIMGKPHIII 80 (118)
Q Consensus 1 I~~g~~i~ey~Gevi~~~~~~~~~~~~~~~~~~~y~~~~~~~~~iDa~~~gn~~RfiNHSC~PN~~~~~~~~~~~~~~~~ 80 (118)
+.+|+-|...+|.|+.-.+.+++.-.....+..+.+++..... |.-.-..|+||||.|.|||++. ..+..++.|
T Consensus 147 w~~ndkIe~LvGcIaeLse~eE~~ll~~g~nDFSvmyStRk~c---aqLwLGPaafINHDCrpnCkFv---s~g~~tacv 220 (453)
T KOG2589|consen 147 WSRNDKIELLVGCIAELSEAEERSLLRGGGNDFSVMYSTRKRC---AQLWLGPAAFINHDCRPNCKFV---STGRDTACV 220 (453)
T ss_pred ccCCccHHHhhhhhhhcChhhhHHHHhccCCceeeeeecccch---hhheeccHHhhcCCCCCCceee---cCCCceeee
Confidence 4688899999999977777766643333333324444433211 3344567889999999999644 457789999
Q ss_pred EEcCCCCCCCeEEEccCCCCCCCCCeEEEecCCCccCC
Q psy8096 81 FALRKINKGEELTYDYKFPIEDDNKISCHCLAMRCTNN 118 (118)
Q Consensus 81 ~a~rdI~~GeElt~~Yg~~~~~~~~~~C~Cg~~~Cr~~ 118 (118)
.++|||+||||||.-||..|++..+..|.|-++.-||+
T Consensus 221 kvlRDIePGeEITcFYgs~fFG~~N~~CeC~TCER~g~ 258 (453)
T KOG2589|consen 221 KVLRDIEPGEEITCFYGSGFFGENNEECECVTCERRGT 258 (453)
T ss_pred ehhhcCCCCceeEEeecccccCCCCceeEEeecccccc
Confidence 99999999999999999999999999999988776653
No 11
>PF00856 SET: SET domain; InterPro: IPR001214 The SET domain appears generally as one part of a larger multidomain protein, and recently there were described three structures of very different proteins with distinct domain compositions: Neurospora crassa DIM-5, a member of the Su(var) family of HKMTs which methylate histone H3 on lysine 9,human SET7 (also called SET9), which methylates H3 on lysine 4 and garden pea Rubisco LSMT, an enzyme that does not modify histones, but instead methylates lysine 14 in the flexible tail of the large subunit of the enzyme Rubisco. The SET domain itself turned out to be an uncommon structure. Although in all three studies, electron density maps revealed the location of the AdoMet or AdoHcy cofactor, the SET domain bears no similarity at all to the canonical/AdoMet-dependent methyltransferase fold. Strictly conserved in the C-terminal motif of the SET domain tyrosine could be involved in abstracting a proton from the protonated amino group of the substrate lysine, promoting its nucleophilic attack on the sulphonium methyl group of the AdoMet cofactor. In contrast to the AdoMet-dependent protein methyltranferases of the classical type, which tend to bind their polypeptide substrates on top of the cofactor, it is noted from the Rubisco LSMT structure that the AdoMet seems to bind in a separate cleft, suggesting how a polypeptide substrate could be subjected to multiple rounds of methylation without having to be released from the enzyme. In contrast, SET7/9 is able to add only a single methyl group to its substrate. It has been demonstrated that association of SET domain and myotubularin-related proteins modulates growth control []. The SET domain-containing Drosophila melanogaster (Fruit fly) protein, enhancer of zeste, has a function in segment determination and the mammalian homologue may be involved in the regulation of gene transcription and chromatin structure. Histone lysine methylation is part of the histone code that regulated chromatin function and epigenetic control of gene function. Histone lysine methyltransferases (HMTase) differ both in their substrate specificity for the various acceptor lysines as well as in their product specificity for the number of methyl groups (one, two, or three) they transfer. With just one exception [], the HMTases belong to SET family that can be classified according to the sequences surrounding the SET domain [, ]. Structural studies on the human SET7/9, a mono-methylase, have revealed the molecular basis for the specificity of the enzyme for the histone-target and the roles of the invariant residues in the SET domain in determining the methylation specificities []. The pre-SET domain, as found in the SUV39 SET family, contains nine invariant cysteine residues that are grouped into two segments separated by a region of variable length. These 9 cysteines coordinate 3 zinc ions to form to form a triangular cluster, where each of the zinc ions is coordinated by 4 four cysteines to give a tetrahedral configuration. The function of this domain is structural, holding together 2 long segments of random coils. The C-terminal region including the post-SET domain is disordered when not interacting with a histone tail and in the absence of zinc. The three conserved cysteines in the post-SET domain form a zinc-binding site when coupled to a fourth conserved cysteine in the knot-like structure close to the SET domain active site []. The structured post-SET region brings in the C-terminal residues that participate in S-adenosylmethine-binding and histone tail interactions. The three conserved cysteine residues are essential for HMTase activity, as replacement with serine abolishes HMTase activity [], []. ; GO: 0005515 protein binding; PDB: 3TG5_A 3S7F_A 3RIB_B 3TG4_A 3S7J_A 3S7D_A 3S7B_A 3H6L_A 3SMT_A 3K5K_A ....
Probab=99.67 E-value=1.7e-16 Score=103.58 Aligned_cols=56 Identities=32% Similarity=0.370 Sum_probs=48.0
Q ss_pred cEEEecccCCCeeeeeecCCCCCceeEEEEECCccEEEEEEcCCCCCCCeEEEccC
Q psy8096 42 RFVIDATMKGNAARFINHSCDPNCYSRVVEIMGKPHIIIFALRKINKGEELTYDYK 97 (118)
Q Consensus 42 ~~~iDa~~~gn~~RfiNHSC~PN~~~~~~~~~~~~~~~~~a~rdI~~GeElt~~Yg 97 (118)
....++....+++.|+||||.|||.+..........+.|+|+|||++|||||++||
T Consensus 107 ~~~~~~~~l~p~~d~~NHsc~pn~~~~~~~~~~~~~~~~~a~r~I~~GeEi~isYG 162 (162)
T PF00856_consen 107 EDDRDGIALYPFADMLNHSCDPNCEVSFDFDGDGGCLVVRATRDIKKGEEIFISYG 162 (162)
T ss_dssp TEEEEEEEEETGGGGSEEESSTSEEEEEEEETTTTEEEEEESS-B-TTSBEEEEST
T ss_pred cccccccccCcHhHheccccccccceeeEeecccceEEEEECCccCCCCEEEEEEC
Confidence 45567777889999999999999988877667789999999999999999999998
No 12
>KOG1081|consensus
Probab=99.37 E-value=1e-13 Score=105.83 Aligned_cols=106 Identities=34% Similarity=0.587 Sum_probs=85.9
Q ss_pred eeEEEChhHHHHHHHHHhhcCCe-eeEEEcCCcEEEecccCCCeeeeeecCCCCCceeEEEEECCccEEEEEEcCCCCCC
Q psy8096 11 LMAVIRASVSDKREKQYMDKGIG-CYMFKIDDRFVIDATMKGNAARFINHSCDPNCYSRVVEIMGKPHIIIFALRKINKG 89 (118)
Q Consensus 11 ~Gevi~~~~~~~~~~~~~~~~~~-~y~~~~~~~~~iDa~~~gn~~RfiNHSC~PN~~~~~~~~~~~~~~~~~a~rdI~~G 89 (118)
+|+++...+...+.......... .|+..+.....||+...+|..||+||||+||++...+.+.+..++.++|.+.|++|
T Consensus 328 vg~~i~~~e~~~~~~~~~~~~~~~~~~~~~e~~~~id~~~~~n~sr~~nh~~~~~v~~~k~~~~~~t~~~~~a~~~i~~g 407 (463)
T KOG1081|consen 328 VGEVIDDKECKARLQRVKESDLVDFYMVFIQKDRIIDAGPKGNYSRFLNHSCQPNVETEKWQVIGDTRVGLFAPRQIEAG 407 (463)
T ss_pred cCcccchhhheeehhhhhccchhhhhhhhhhcccccccccccchhhhhcccCCCceeechhheecccccccccccccccc
Confidence 77888888877766544433332 34333444448999999999999999999999999999999999999999999999
Q ss_pred CeEEEccCCCCCCCCCeEEEecCCCccC
Q psy8096 90 EELTYDYKFPIEDDNKISCHCLAMRCTN 117 (118)
Q Consensus 90 eElt~~Yg~~~~~~~~~~C~Cg~~~Cr~ 117 (118)
+|||++|...-... ...|.|++.+|.+
T Consensus 408 ~e~t~~~n~~~~~~-~~~~~~~~e~~~~ 434 (463)
T KOG1081|consen 408 EELTFNYNGNCEGN-EKRCCCGSENCTE 434 (463)
T ss_pred hhhhheeeccccCC-cceEeeccccccc
Confidence 99999999765544 7789999988865
No 13
>KOG2461|consensus
Probab=98.28 E-value=6.4e-07 Score=67.57 Aligned_cols=89 Identities=24% Similarity=0.206 Sum_probs=61.4
Q ss_pred CCCCCeeEEeeeEEEChhHHHHHHHHHhhcCCeeeEEEc---C-CcEEEeccc--CCCeeeeeecCCCC---CceeEEEE
Q psy8096 1 MEEDCSVSVTLMAVIRASVSDKREKQYMDKGIGCYMFKI---D-DRFVIDATM--KGNAARFINHSCDP---NCYSRVVE 71 (118)
Q Consensus 1 I~~g~~i~ey~Gevi~~~~~~~~~~~~~~~~~~~y~~~~---~-~~~~iDa~~--~gn~~RfiNHSC~P---N~~~~~~~ 71 (118)
|.+|+--+=|.|+++....-+.. ...|+|.+ + .-.+||+.. ..|+.||+|=+++. |. +.
T Consensus 50 i~~G~~FGP~~G~~~~~~~~~~~--------n~~y~W~I~~~d~~~~~iDg~d~~~sNWmRYV~~Ar~~eeQNL----~A 117 (396)
T KOG2461|consen 50 ILPGTSFGPFEGEIIASIDSKSA--------NNRYMWEIFSSDNGYEYIDGTDEEHSNWMRYVNSARSEEEQNL----LA 117 (396)
T ss_pred ccCcccccCccCccccccccccc--------cCcceEEEEeCCCceEEeccCChhhcceeeeecccCChhhhhH----HH
Confidence 45677778888887111111111 11555544 2 347899887 77999999988755 63 22
Q ss_pred ECCccEEEEEEcCCCCCCCeEEEccCCCCC
Q psy8096 72 IMGKPHIIIFALRKINKGEELTYDYKFPIE 101 (118)
Q Consensus 72 ~~~~~~~~~~a~rdI~~GeElt~~Yg~~~~ 101 (118)
....-.|.+.|+|+|++||||.+.|+.+|-
T Consensus 118 ~Q~~~~Ifyrt~r~I~p~eELlVWY~~e~~ 147 (396)
T KOG2461|consen 118 FQIGENIFYRTIRDIRPNEELLVWYGSEYA 147 (396)
T ss_pred HhccCceEEEecccCCCCCeEEEEeccchH
Confidence 334568999999999999999999997764
No 14
>smart00508 PostSET Cysteine-rich motif following a subset of SET domains.
Probab=97.17 E-value=0.00018 Score=33.51 Aligned_cols=14 Identities=36% Similarity=0.650 Sum_probs=12.3
Q ss_pred CeEEEecCCCccCC
Q psy8096 105 KISCHCLAMRCTNN 118 (118)
Q Consensus 105 ~~~C~Cg~~~Cr~~ 118 (118)
.+.|.||+++|||.
T Consensus 2 ~~~C~CGs~~CRG~ 15 (26)
T smart00508 2 KQPCLCGAPNCRGF 15 (26)
T ss_pred CeeeeCCCccccce
Confidence 47999999999984
No 15
>KOG2084|consensus
Probab=97.15 E-value=0.00085 Score=51.04 Aligned_cols=54 Identities=35% Similarity=0.603 Sum_probs=39.3
Q ss_pred eeecCCCCCceeEEEEECCccEEEEEEcCCCCCCC-eEEEccCCCCCCCC----------CeEEEecCC
Q psy8096 56 FINHSCDPNCYSRVVEIMGKPHIIIFALRKINKGE-ELTYDYKFPIEDDN----------KISCHCLAM 113 (118)
Q Consensus 56 fiNHSC~PN~~~~~~~~~~~~~~~~~a~rdI~~Ge-Elt~~Yg~~~~~~~----------~~~C~Cg~~ 113 (118)
++||||.||+. . ........+.+.+++.+++ ||++.|-...++.. .|.|.|+.+
T Consensus 208 ~~~hsC~pn~~---~-~~~~~~~~~~~~~~~~~~~~~l~~~y~~~~~~~~~r~~~l~~~~~f~c~c~rc 272 (482)
T KOG2084|consen 208 LFNHSCFPNIS---V-IFDGRGLALLVPAGIDAGEEELTISYTDPLLSTASRQKQLRQSKLFSCQCPRC 272 (482)
T ss_pred hcccCCCCCeE---E-EECCceeEEEeecccCCCCCEEEEeecccccCHHHHHHHHhhccceeeecCCC
Confidence 78999999975 2 2234455667777787776 99999987766542 488888764
No 16
>KOG1337|consensus
Probab=96.19 E-value=0.0039 Score=48.32 Aligned_cols=42 Identities=21% Similarity=0.209 Sum_probs=31.5
Q ss_pred eeeeecCCCCCceeEEEEECCccEEEEEEcCCCCCCCeEEEccCC
Q psy8096 54 ARFINHSCDPNCYSRVVEIMGKPHIIIFALRKINKGEELTYDYKF 98 (118)
Q Consensus 54 ~RfiNHSC~PN~~~~~~~~~~~~~~~~~a~rdI~~GeElt~~Yg~ 98 (118)
.-+.||++++.- .........+.+++.++|.+||||++.||.
T Consensus 237 ~D~~NH~~~~~~---~~~~~~d~~~~l~~~~~v~~geevfi~YG~ 278 (472)
T KOG1337|consen 237 IDLLNHSPEVIK---AGYNQEDEAVELVAERDVSAGEEVFINYGP 278 (472)
T ss_pred HHhhccCchhcc---ccccCCCCcEEEEEeeeecCCCeEEEecCC
Confidence 346899999921 121222348999999999999999999996
No 17
>PF08666 SAF: SAF domain; InterPro: IPR013974 This entry includes a range of different proteins, such as antifreeze proteins, flagellar FlgA proteins, and CpaB pilus proteins. ; PDB: 1C89_A 3NLA_A 3RDN_A 1C8A_A 3FRN_A 1WVO_A 3K3S_H 3G8R_B 1XUU_A 1XUZ_A ....
Probab=91.05 E-value=0.14 Score=28.20 Aligned_cols=16 Identities=31% Similarity=0.482 Sum_probs=12.0
Q ss_pred EEEEcCCCCCCCeEEE
Q psy8096 79 IIFALRKINKGEELTY 94 (118)
Q Consensus 79 ~~~a~rdI~~GeElt~ 94 (118)
+++|.|||++|+.|+-
T Consensus 3 vvVA~~di~~G~~i~~ 18 (63)
T PF08666_consen 3 VVVAARDIPAGTVITA 18 (63)
T ss_dssp EEEESSTB-TT-BECT
T ss_pred EEEEeCccCCCCEEcc
Confidence 5799999999999953
No 18
>KOG1338|consensus
Probab=89.95 E-value=0.22 Score=37.98 Aligned_cols=42 Identities=26% Similarity=0.377 Sum_probs=31.8
Q ss_pred CeeeeeecC---CCCCceeEEEEECCccEEEEEEcCCCCCCCeEEEccCCC
Q psy8096 52 NAARFINHS---CDPNCYSRVVEIMGKPHIIIFALRKINKGEELTYDYKFP 99 (118)
Q Consensus 52 n~~RfiNHS---C~PN~~~~~~~~~~~~~~~~~a~rdI~~GeElt~~Yg~~ 99 (118)
..+-|+||. |..|.. .+...+.++|.|+|++|+|+.-.||..
T Consensus 217 p~ad~lNhd~~k~nanl~------y~~NcL~mva~r~iekgdev~n~dg~~ 261 (466)
T KOG1338|consen 217 PIADFLNHDGLKANANLR------YEDNCLEMVADRNIEKGDEVDNSDGLK 261 (466)
T ss_pred chhhhhccchhhccccee------ccCcceeeeecCCCCCccccccccccC
Confidence 467799995 555532 234566889999999999999999844
No 19
>PF00856 SET: SET domain; InterPro: IPR001214 The SET domain appears generally as one part of a larger multidomain protein, and recently there were described three structures of very different proteins with distinct domain compositions: Neurospora crassa DIM-5, a member of the Su(var) family of HKMTs which methylate histone H3 on lysine 9,human SET7 (also called SET9), which methylates H3 on lysine 4 and garden pea Rubisco LSMT, an enzyme that does not modify histones, but instead methylates lysine 14 in the flexible tail of the large subunit of the enzyme Rubisco. The SET domain itself turned out to be an uncommon structure. Although in all three studies, electron density maps revealed the location of the AdoMet or AdoHcy cofactor, the SET domain bears no similarity at all to the canonical/AdoMet-dependent methyltransferase fold. Strictly conserved in the C-terminal motif of the SET domain tyrosine could be involved in abstracting a proton from the protonated amino group of the substrate lysine, promoting its nucleophilic attack on the sulphonium methyl group of the AdoMet cofactor. In contrast to the AdoMet-dependent protein methyltranferases of the classical type, which tend to bind their polypeptide substrates on top of the cofactor, it is noted from the Rubisco LSMT structure that the AdoMet seems to bind in a separate cleft, suggesting how a polypeptide substrate could be subjected to multiple rounds of methylation without having to be released from the enzyme. In contrast, SET7/9 is able to add only a single methyl group to its substrate. It has been demonstrated that association of SET domain and myotubularin-related proteins modulates growth control []. The SET domain-containing Drosophila melanogaster (Fruit fly) protein, enhancer of zeste, has a function in segment determination and the mammalian homologue may be involved in the regulation of gene transcription and chromatin structure. Histone lysine methylation is part of the histone code that regulated chromatin function and epigenetic control of gene function. Histone lysine methyltransferases (HMTase) differ both in their substrate specificity for the various acceptor lysines as well as in their product specificity for the number of methyl groups (one, two, or three) they transfer. With just one exception [], the HMTases belong to SET family that can be classified according to the sequences surrounding the SET domain [, ]. Structural studies on the human SET7/9, a mono-methylase, have revealed the molecular basis for the specificity of the enzyme for the histone-target and the roles of the invariant residues in the SET domain in determining the methylation specificities []. The pre-SET domain, as found in the SUV39 SET family, contains nine invariant cysteine residues that are grouped into two segments separated by a region of variable length. These 9 cysteines coordinate 3 zinc ions to form to form a triangular cluster, where each of the zinc ions is coordinated by 4 four cysteines to give a tetrahedral configuration. The function of this domain is structural, holding together 2 long segments of random coils. The C-terminal region including the post-SET domain is disordered when not interacting with a histone tail and in the absence of zinc. The three conserved cysteines in the post-SET domain form a zinc-binding site when coupled to a fourth conserved cysteine in the knot-like structure close to the SET domain active site []. The structured post-SET region brings in the C-terminal residues that participate in S-adenosylmethine-binding and histone tail interactions. The three conserved cysteine residues are essential for HMTase activity, as replacement with serine abolishes HMTase activity [], []. ; GO: 0005515 protein binding; PDB: 3TG5_A 3S7F_A 3RIB_B 3TG4_A 3S7J_A 3S7D_A 3S7B_A 3H6L_A 3SMT_A 3K5K_A ....
Probab=83.18 E-value=0.83 Score=28.90 Aligned_cols=17 Identities=35% Similarity=0.479 Sum_probs=12.8
Q ss_pred EEEEcCCCCCCCeEEEc
Q psy8096 79 IIFALRKINKGEELTYD 95 (118)
Q Consensus 79 ~~~a~rdI~~GeElt~~ 95 (118)
.|+|+|||++||-|.+.
T Consensus 3 Gl~At~dI~~Ge~I~~p 19 (162)
T PF00856_consen 3 GLFATRDIKAGEVILIP 19 (162)
T ss_dssp EEEESS-B-TTEEEEEE
T ss_pred EEEECccCCCCCEEEEE
Confidence 68999999999988743
No 20
>TIGR02059 swm_rep_I cyanobacterial long protein repeat. This domain appears in 29 copies in a large (10000 amino protein in Synechococcus sp. WH8102 associated with a novel flagellar system, as one of three different repeats. Similar domains are found in two different large (<3500) proteins of Synechocystis PCC6803.
Probab=81.36 E-value=4.7 Score=24.90 Aligned_cols=25 Identities=20% Similarity=0.373 Sum_probs=21.4
Q ss_pred ccEEEEEEcCCCCCCCeEEEccCCC
Q psy8096 75 KPHIIIFALRKINKGEELTYDYKFP 99 (118)
Q Consensus 75 ~~~~~~~a~rdI~~GeElt~~Yg~~ 99 (118)
...+.|.-.+.|..||+++++|..+
T Consensus 74 ~ktVTLTL~~~V~~Gq~VTVsYt~p 98 (101)
T TIGR02059 74 NTTITLTLAQVVEDGDEVTLSYTKN 98 (101)
T ss_pred ccEEEEEecccccCCCEEEEEeeCC
Confidence 3578888899999999999999754
No 21
>smart00858 SAF This domain family includes a range of different proteins. Such as antifreeze proteins and flagellar FlgA proteins, and CpaB pilus proteins.
Probab=80.72 E-value=1.2 Score=24.25 Aligned_cols=16 Identities=31% Similarity=0.534 Sum_probs=14.0
Q ss_pred EEEEcCCCCCCCeEEE
Q psy8096 79 IIFALRKINKGEELTY 94 (118)
Q Consensus 79 ~~~a~rdI~~GeElt~ 94 (118)
+++|.++|++|+.|+-
T Consensus 3 v~va~~~i~~G~~i~~ 18 (64)
T smart00858 3 VVVAARDLPAGEVITA 18 (64)
T ss_pred EEEEeCccCCCCCcch
Confidence 5789999999999885
No 22
>KOG2155|consensus
Probab=72.95 E-value=1.9 Score=33.64 Aligned_cols=46 Identities=26% Similarity=0.356 Sum_probs=34.6
Q ss_pred eeeeeecCCCCCceeEEEEECC--ccEEEEEEcCCCCCCCeEEEccCC
Q psy8096 53 AARFINHSCDPNCYSRVVEIMG--KPHIIIFALRKINKGEELTYDYKF 98 (118)
Q Consensus 53 ~~RfiNHSC~PN~~~~~~~~~~--~~~~~~~a~rdI~~GeElt~~Yg~ 98 (118)
.+.-++||-.||..+.....-. ...-.++-+|+...|||+|-|+..
T Consensus 204 fGsrvrHsdePnf~~aPf~fmPq~vaYsimwp~k~~~tgeE~trDfas 251 (631)
T KOG2155|consen 204 FGSRVRHSDEPNFRIAPFMFMPQNVAYSIMWPTKPVNTGEEITRDFAS 251 (631)
T ss_pred hhhhhccCCCCcceeeeheecchhcceeEEeeccCCCCchHHHHHHhh
Confidence 4455899999998776665532 233467889999999999999753
No 23
>TIGR03569 NeuB_NnaB N-acetylneuraminate synthase. This family is a subset of the Pfam model pfam03102 and is believed to include only authentic NeuB N-acetylneuraminate (sialic acid) synthase enzymes. The majority of the genes identified by this model are observed adjacent to both the NeuA and NeuC genes which together effect the biosynthesis of CMP-N-acetylneuraminate from UDP-N-acetylglucosamine.
Probab=58.07 E-value=5.7 Score=29.69 Aligned_cols=19 Identities=37% Similarity=0.457 Sum_probs=17.0
Q ss_pred EEEEEEcCCCCCCCeEEEc
Q psy8096 77 HIIIFALRKINKGEELTYD 95 (118)
Q Consensus 77 ~~~~~a~rdI~~GeElt~~ 95 (118)
|=.|+|.+||++||.||.+
T Consensus 277 rrsl~a~~di~~G~~lt~~ 295 (329)
T TIGR03569 277 RKSLVAAKDIKKGEIFTED 295 (329)
T ss_pred ceEEEEccCcCCCCEecHH
Confidence 5679999999999999976
No 24
>TIGR03170 flgA_cterm flagella basal body P-ring formation protein FlgA. This model describes a conserved C-terminal region of the flagellar basal body P-ring formation protein FlgA. This sequence region contains a SAF domain, now described by Pfam model pfam08666.
Probab=53.55 E-value=6.4 Score=24.58 Aligned_cols=17 Identities=24% Similarity=0.573 Sum_probs=14.0
Q ss_pred EEEEcCCCCCCCeEEEc
Q psy8096 79 IIFALRKINKGEELTYD 95 (118)
Q Consensus 79 ~~~a~rdI~~GeElt~~ 95 (118)
+++|.++|++|+-|+-+
T Consensus 1 V~Va~r~I~~G~~i~~~ 17 (122)
T TIGR03170 1 VVVAKRPLKRGEVISPE 17 (122)
T ss_pred CEEECcccCCCCCcCHH
Confidence 36899999999998753
No 25
>PF06718 DUF1203: Protein of unknown function (DUF1203); InterPro: IPR009593 This family consists of several hypothetical bacterial proteins of around 155 residues in length. Family members are present in Rhizobium, Agrobacterium and Streptomyces species.
Probab=53.38 E-value=12 Score=23.73 Aligned_cols=19 Identities=37% Similarity=0.509 Sum_probs=14.4
Q ss_pred EEcCCCCCCCe-EEEccCCC
Q psy8096 81 FALRKINKGEE-LTYDYKFP 99 (118)
Q Consensus 81 ~a~rdI~~GeE-lt~~Yg~~ 99 (118)
..+||+++||+ |.++|...
T Consensus 6 ~cL~~~~~Ge~~lLlsy~p~ 25 (117)
T PF06718_consen 6 HCLRDAEPGEELLLLSYRPF 25 (117)
T ss_pred EecccCCCCCeEEEEecCCC
Confidence 46899999999 55677543
No 26
>smart00561 MBT Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2. Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2. These proteins are involved in transcriptional regulation.
Probab=53.21 E-value=49 Score=20.03 Aligned_cols=53 Identities=11% Similarity=0.165 Sum_probs=35.1
Q ss_pred cCCCCCceeEEEEECCccEEEEEEcCCCCCCCeEEEccCCCCCCCCCeEEEecCC
Q psy8096 59 HSCDPNCYSRVVEIMGKPHIIIFALRKINKGEELTYDYKFPIEDDNKISCHCLAM 113 (118)
Q Consensus 59 HSC~PN~~~~~~~~~~~~~~~~~a~rdI~~GeElt~~Yg~~~~~~~~~~C~Cg~~ 113 (118)
|.-+++++++.+.-.....+.+.++.+|. |..|.+.|. .+.+...+-|...|+
T Consensus 26 ~~F~vGmkLEavD~~~~~~i~vAtV~~v~-g~~l~v~~d-g~~~~~D~W~~~~S~ 78 (96)
T smart00561 26 NGFKVGMKLEAVDPRNPSLICVATVVEVK-GYRLLLHFD-GWDDKYDFWCDADSP 78 (96)
T ss_pred CcccCCCEEEEECCCCCceEEEEEEEEEE-CCEEEEEEc-cCCCcCCEEEECCCC
Confidence 33466777776655555667777777777 889999986 223334677776664
No 27
>TIGR03586 PseI pseudaminic acid synthase.
Probab=46.28 E-value=15 Score=27.50 Aligned_cols=20 Identities=25% Similarity=0.471 Sum_probs=17.3
Q ss_pred cEEEEEEcCCCCCCCeEEEc
Q psy8096 76 PHIIIFALRKINKGEELTYD 95 (118)
Q Consensus 76 ~~~~~~a~rdI~~GeElt~~ 95 (118)
.|=.|+|.|||++|+-||.+
T Consensus 274 ~rrsl~a~~di~~G~~it~~ 293 (327)
T TIGR03586 274 FRRSLYVVKDIKKGETFTEE 293 (327)
T ss_pred eeEEEEEccCcCCCCEecHH
Confidence 35678999999999999976
No 28
>PF07177 Neuralized: Neuralized; InterPro: IPR006573 NEUZ is a domain of unknown function found in neuralized proteins, i.e. proteins involved in the specification of the neuroblast during cellular differentiation. ; PDB: 2YUE_A 2E63_A.
Probab=44.66 E-value=24 Score=20.06 Aligned_cols=22 Identities=23% Similarity=0.350 Sum_probs=13.8
Q ss_pred CccEEEEEEcCCCCCCCeEEEc
Q psy8096 74 GKPHIIIFALRKINKGEELTYD 95 (118)
Q Consensus 74 ~~~~~~~~a~rdI~~GeElt~~ 95 (118)
+.-+-.+|+-|+|+.||.+.+-
T Consensus 27 sf~~giVFS~rPl~~~E~~~v~ 48 (69)
T PF07177_consen 27 SFNNGIVFSSRPLRIGEKFEVR 48 (69)
T ss_dssp -SSS-EEEESS-B-TT-EEEEE
T ss_pred cCCceEEEecCCccCCCEEEEE
Confidence 3445679999999999998774
No 29
>COG2089 SpsE Sialic acid synthase [Cell envelope biogenesis, outer membrane]
Probab=41.55 E-value=14 Score=27.77 Aligned_cols=19 Identities=37% Similarity=0.468 Sum_probs=16.2
Q ss_pred EEEEEEcCCCCCCCeEEEc
Q psy8096 77 HIIIFALRKINKGEELTYD 95 (118)
Q Consensus 77 ~~~~~a~rdI~~GeElt~~ 95 (118)
+-.+++++||++||-|+-+
T Consensus 289 ~Rsl~~~kdikkGe~ls~~ 307 (347)
T COG2089 289 RRSLVATKDIKKGEILSED 307 (347)
T ss_pred hhheeeecccccCcccccc
Confidence 4569999999999998865
No 30
>PF11720 Inhibitor_I78: Peptidase inhibitor I78 family; InterPro: IPR021719 This family includes Aspergillus elastase inhibitor and belongs to MEROPS peptidase inhibitor family I78.
Probab=40.39 E-value=11 Score=20.79 Aligned_cols=18 Identities=33% Similarity=0.560 Sum_probs=14.6
Q ss_pred cCCCCCCCeEEEccCCCC
Q psy8096 83 LRKINKGEELTYDYKFPI 100 (118)
Q Consensus 83 ~rdI~~GeElt~~Yg~~~ 100 (118)
.|=|.||+.+|.||..+.
T Consensus 26 ~Rvi~Pg~~vTmDyr~dR 43 (60)
T PF11720_consen 26 VRVIRPGDAVTMDYRPDR 43 (60)
T ss_pred eEEeCCCCcCcccCCCCc
Confidence 455889999999998663
No 31
>PF12947 EGF_3: EGF domain; InterPro: IPR024731 This entry represents an EGF domain found in the the C terminus of malarial parasite merozoite surface protein 1 [], as well as other proteins.; PDB: 2NPR_A 1N1I_C 1B9W_A 1YO8_A 2RHP_A.
Probab=39.69 E-value=19 Score=17.72 Aligned_cols=11 Identities=36% Similarity=0.745 Sum_probs=7.5
Q ss_pred ecCCCCCceeE
Q psy8096 58 NHSCDPNCYSR 68 (118)
Q Consensus 58 NHSC~PN~~~~ 68 (118)
||.|+||+.-.
T Consensus 5 ~~~C~~nA~C~ 15 (36)
T PF12947_consen 5 NGGCHPNATCT 15 (36)
T ss_dssp GGGS-TTCEEE
T ss_pred CCCCCCCcEee
Confidence 68899998544
No 32
>cd05468 pVHL von Hippel-Landau (pVHL) tumor suppressor protein. von Hippel-Landau (pVHL) protein, the gene product of VHL, is a critical regulator of the ubiquitous oxygen-sensing pathway. It is conserved throughout evolution, as its homologs are found in organisms ranging from mammals to the Drosophila melanogaster, Anopheles gambiae insects and the Caenorhabditis elegans nematode. pVHL acts as the substrate recognition component of an E3 ubiquitin ligase complex. Several proteins have been identified as pVHL-binding proteins that are subject to ubiquitin-mediated proteolysis; the best characterized putative substrates are the alpha subunits of the hypoxia-inducible factor (HIF1alpha, HIF2alpha, and HIF3alpha). In addition to HIF degradation, pVHL has been implicated to be involved in HIF independent cellular processes. Germline VHL mutations cause renal cell carcinomas, hemangioblastomas and pheochromocytomas in humans. pVHL can bind to and direct the proper deposition of fibronecti
Probab=39.66 E-value=1e+02 Score=19.96 Aligned_cols=38 Identities=18% Similarity=0.329 Sum_probs=21.8
Q ss_pred eeeeeecCCCCCceeEEEEECCccEEEEEEcCCCCCCCeEEEc
Q psy8096 53 AARFINHSCDPNCYSRVVEIMGKPHIIIFALRKINKGEELTYD 95 (118)
Q Consensus 53 ~~RfiNHSC~PN~~~~~~~~~~~~~~~~~a~rdI~~GeElt~~ 95 (118)
..+|+|++..| ++...++.......++ .|+||++.+++
T Consensus 10 ~v~F~N~t~~~---v~~~Wid~~G~~~~Y~--~l~pg~~~~~~ 47 (141)
T cd05468 10 TVRFVNRTDRP---VELYWIDYDGKPVSYG--TLQPGETVRQN 47 (141)
T ss_pred EEEEEeCCCCe---EEEEEECCCCCEEEee--eeCCCCEEeec
Confidence 44578877433 3345555444444444 37777777665
No 33
>TIGR00049 Iron-sulfur cluster assembly accessory protein. Proteins in this subfamily appear to be associated with the process of FeS-cluster assembly. The HesB proteins are associated with the nif gene cluster and the Rhizobium gene IscN has been shown to be required for nitrogen fixation. Nitrogenase includes multiple FeS clusters and many genes for their assembly. The E. coli SufA protein is associated with SufS, a NifS homolog and SufD which are involved in the FeS cluster assembly of the FhnF protein. The Azotobacter protein IscA (homologs of which are also found in E.coli) is associated which IscS, another NifS homolog and IscU, a nifU homolog as well as other factors consistent with a role in FeS cluster chemistry. A homolog from Geobacter contains a selenocysteine in place of an otherwise invariant cysteine, further suggesting a role in redox chemistry.
Probab=38.19 E-value=22 Score=21.51 Aligned_cols=34 Identities=15% Similarity=0.199 Sum_probs=20.9
Q ss_pred EEEcCCCCCCCeEEEccCCCCCCC--------CCeEEEecCC
Q psy8096 80 IFALRKINKGEELTYDYKFPIEDD--------NKISCHCLAM 113 (118)
Q Consensus 80 ~~a~rdI~~GeElt~~Yg~~~~~~--------~~~~C~Cg~~ 113 (118)
++...++.-=+.++|||.....+. ..-.|.||+.
T Consensus 61 ~id~~~~~~l~~~~IDy~~~~~~~~f~i~nPn~~~~c~cg~s 102 (105)
T TIGR00049 61 VVDPKSLPYLDGSEIDYVEELLGSGFTFTNPNAKGTCGCGKS 102 (105)
T ss_pred EEeHHHHhhhCCCEEEEeecCCcceEEEECCCCCccCCCCcC
Confidence 344445555556999997653322 1567999864
No 34
>PRK12618 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=37.71 E-value=21 Score=23.29 Aligned_cols=18 Identities=17% Similarity=0.041 Sum_probs=14.5
Q ss_pred EEEEEEcCCCCCCCeEEE
Q psy8096 77 HIIIFALRKINKGEELTY 94 (118)
Q Consensus 77 ~~~~~a~rdI~~GeElt~ 94 (118)
.-+++|.|+|.+||-|+-
T Consensus 19 ~~VvVA~r~L~rGevIt~ 36 (141)
T PRK12618 19 AETVVAARTIRALTVIGA 36 (141)
T ss_pred eEEEEEccCcCCCCCcCH
Confidence 346889999999998863
No 35
>PRK06005 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=37.67 E-value=20 Score=23.92 Aligned_cols=19 Identities=16% Similarity=0.237 Sum_probs=15.7
Q ss_pred EEEEEEcCCCCCCCeEEEc
Q psy8096 77 HIIIFALRKINKGEELTYD 95 (118)
Q Consensus 77 ~~~~~a~rdI~~GeElt~~ 95 (118)
.-+++|.|+|.+||-|+-+
T Consensus 33 v~vvVa~r~I~rGevIt~~ 51 (160)
T PRK06005 33 IAFVVPSTTIYPGETISDS 51 (160)
T ss_pred EEEEEEccCcCCCCCcCHH
Confidence 3478999999999998754
No 36
>PRK13623 iron-sulfur cluster insertion protein ErpA; Provisional
Probab=37.26 E-value=16 Score=22.74 Aligned_cols=32 Identities=19% Similarity=0.242 Sum_probs=18.7
Q ss_pred EcCCCCCCCeEEEccCCCCCCCC--------CeEEEecCC
Q psy8096 82 ALRKINKGEELTYDYKFPIEDDN--------KISCHCLAM 113 (118)
Q Consensus 82 a~rdI~~GeElt~~Yg~~~~~~~--------~~~C~Cg~~ 113 (118)
....+.-=+.++|||..+..... .-.|.||+.
T Consensus 73 d~~s~~~l~g~~IDy~~~~~~~~F~f~NPn~~~~CgCg~S 112 (115)
T PRK13623 73 DPMSLQYLVGAEVDYTEGLEGSRFVIKNPNAKTTCGCGSS 112 (115)
T ss_pred cHHHHHHhCCCEEEeecCCCcceEEEECCCCCcCCCCCcC
Confidence 33333333446999976644332 557999863
No 37
>KOG4078|consensus
Probab=36.49 E-value=36 Score=22.48 Aligned_cols=21 Identities=29% Similarity=0.515 Sum_probs=16.4
Q ss_pred CCCeEEEccCCCCCCCCCeEEEecCCC
Q psy8096 88 KGEELTYDYKFPIEDDNKISCHCLAMR 114 (118)
Q Consensus 88 ~GeElt~~Yg~~~~~~~~~~C~Cg~~~ 114 (118)
.++.|.||+| | .|.|.|..|.
T Consensus 94 V~~DlYIDFG---~---KFhcVC~rP~ 114 (173)
T KOG4078|consen 94 VEEDLYIDFG---G---KFHCVCKRPA 114 (173)
T ss_pred eccceEEecC---C---eEEEEEcCcC
Confidence 4788999999 3 6788887664
No 38
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=36.22 E-value=24 Score=21.85 Aligned_cols=29 Identities=17% Similarity=0.221 Sum_probs=21.6
Q ss_pred EEEECCccEEEEEEcCCCCCCCeEEEccCCCC
Q psy8096 69 VVEIMGKPHIIIFALRKINKGEELTYDYKFPI 100 (118)
Q Consensus 69 ~~~~~~~~~~~~~a~rdI~~GeElt~~Yg~~~ 100 (118)
.+.++|. ..-+..+++.|++|+|.|+...
T Consensus 35 rV~vNG~---~aKpS~~VK~GD~l~i~~~~~~ 63 (100)
T COG1188 35 RVKVNGQ---RAKPSKEVKVGDILTIRFGNKE 63 (100)
T ss_pred eEEECCE---EcccccccCCCCEEEEEeCCcE
Confidence 4445443 2388899999999999998653
No 39
>TIGR02011 IscA iron-sulfur cluster assembly protein IscA. This clade is limited to the proteobacteria.
Probab=34.53 E-value=19 Score=22.00 Aligned_cols=34 Identities=12% Similarity=0.174 Sum_probs=20.2
Q ss_pred EEEcCCCCCCCeEEEccCCCCCCCC--------CeEEEecCC
Q psy8096 80 IFALRKINKGEELTYDYKFPIEDDN--------KISCHCLAM 113 (118)
Q Consensus 80 ~~a~rdI~~GeElt~~Yg~~~~~~~--------~~~C~Cg~~ 113 (118)
++....+.-=+..+|||..+..+.. .-.|.||+.
T Consensus 61 ~id~~s~~~l~g~~IDy~~~~~~~~F~~~nPna~~~CgCg~S 102 (105)
T TIGR02011 61 VIDGKSLQYLDGTQLDFVKEGLNEGFKFTNPNVKDECGCGES 102 (105)
T ss_pred EEcHHHhHHhCCCEEEEecCCCcceEEEECCCCCccCCCCCC
Confidence 3444445555566999976543321 457999863
No 40
>PF13121 DUF3976: Domain of unknown function (DUF3976)
Probab=34.24 E-value=36 Score=16.99 Aligned_cols=15 Identities=33% Similarity=0.523 Sum_probs=12.3
Q ss_pred EEEEcCCCCCCCeEE
Q psy8096 79 IIFALRKINKGEELT 93 (118)
Q Consensus 79 ~~~a~rdI~~GeElt 93 (118)
.+|..+||.+|..||
T Consensus 2 y~fvrkdit~~ntlt 16 (41)
T PF13121_consen 2 YFFVRKDITKDNTLT 16 (41)
T ss_pred EEEEEeeccCCCeee
Confidence 477889998888887
No 41
>PRK09504 sufA iron-sulfur cluster assembly scaffold protein; Provisional
Probab=34.17 E-value=20 Score=22.67 Aligned_cols=32 Identities=16% Similarity=0.142 Sum_probs=18.7
Q ss_pred EcCCCCCCCeEEEccCCCCCCCC--------CeEEEecCC
Q psy8096 82 ALRKINKGEELTYDYKFPIEDDN--------KISCHCLAM 113 (118)
Q Consensus 82 a~rdI~~GeElt~~Yg~~~~~~~--------~~~C~Cg~~ 113 (118)
....+.-=+.++|||..+..... .-.|.||+.
T Consensus 80 d~~s~~~L~g~~IDy~~~~~~~gF~f~NPna~~~CgCG~S 119 (122)
T PRK09504 80 PLQAMPFIDGTEVDYVREGLNQIFKFHNPKAQNECGCGES 119 (122)
T ss_pred cHHHHHhhCCcEEEeecCCCcceEEEECCCCCCCcCCCCC
Confidence 33333334458999976533322 567999863
No 42
>PF10246 MRP-S35: Mitochondrial ribosomal protein MRP-S35; InterPro: IPR019375 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This is a family of short mitochondrial ribosomal proteins, less than 200 amino acids long. MRP-S35 was proposed as a more appropriate name to this group of proteins [].
Probab=32.78 E-value=45 Score=20.76 Aligned_cols=19 Identities=26% Similarity=0.609 Sum_probs=14.1
Q ss_pred CCeEEEccCCCCCCCCCeEEEecCC
Q psy8096 89 GEELTYDYKFPIEDDNKISCHCLAM 113 (118)
Q Consensus 89 GeElt~~Yg~~~~~~~~~~C~Cg~~ 113 (118)
++-|.||+| | .|.|.|-.|
T Consensus 36 ~ddLYIDfG---~---KFhcVc~rp 54 (104)
T PF10246_consen 36 DDDLYIDFG---G---KFHCVCKRP 54 (104)
T ss_pred cCceEEEeC---C---ceeEEEecc
Confidence 358999999 3 567887655
No 43
>TIGR03177 pilus_cpaB Flp pilus assembly protein CpaB. Members of this protein family are the CpaB protein of Flp-type pilus assembly. Similar proteins include the FlgA protein of bacterial flagellum biosynthesis.
Probab=31.45 E-value=28 Score=24.87 Aligned_cols=21 Identities=19% Similarity=0.333 Sum_probs=17.1
Q ss_pred ccEEEEEEcCCCCCCCeEEEc
Q psy8096 75 KPHIIIFALRKINKGEELTYD 95 (118)
Q Consensus 75 ~~~~~~~a~rdI~~GeElt~~ 95 (118)
...-+++|.+||++|+.|+=+
T Consensus 34 ~~~~V~VA~~~I~~G~~I~~~ 54 (261)
T TIGR03177 34 PTVPVVVAARDLPAGTPITAE 54 (261)
T ss_pred CceeEEEEcccCCCCCCCCHH
Confidence 445678999999999999844
No 44
>COG1465 Predicted alternative 3-dehydroquinate synthase [Amino acid transport and metabolism]
Probab=30.21 E-value=1.4e+02 Score=22.42 Aligned_cols=55 Identities=27% Similarity=0.459 Sum_probs=36.1
Q ss_pred CcEEEec---------ccCCCeee--eeecCC---CCCceeEEEEECC-ccEEEEEE-------cCCCCCCCeEEEc
Q psy8096 41 DRFVIDA---------TMKGNAAR--FINHSC---DPNCYSRVVEIMG-KPHIIIFA-------LRKINKGEELTYD 95 (118)
Q Consensus 41 ~~~~iDa---------~~~gn~~R--fiNHSC---~PN~~~~~~~~~~-~~~~~~~a-------~rdI~~GeElt~~ 95 (118)
+..|||. +-.||.+| |+=||= .|-+..+.+.++. ..++.+.. +..+++|+|+++-
T Consensus 214 DRVCVDTcsLm~~gEGMLVGs~s~gmFlVhsEs~espYVAaRPFRVNAG~VhaYi~vPg~kTkYLaEL~aGDeV~iV 290 (376)
T COG1465 214 DRVCVDTCSLMTRGEGMLVGSQSRGMFLVHSESEESPYVAARPFRVNAGAVHAYIRVPGGKTKYLAELKAGDEVLIV 290 (376)
T ss_pred ceEEEeeecccccCCceEeecccCcEEEEecccccCcccccCceeecccceeEEEEcCCCceEEhhhhcCCCeEEEE
Confidence 4678884 33666554 567873 6777777777754 44555544 5778999998763
No 45
>TIGR03248 galactar-dH20 galactarate dehydratase. Galactarate dehydratase converts D-galactarate to 5-dehydro-4-deoxyglucarate which is subsequently acted on by GarL, tartronate semialdehyde reductase and glycerate kinase (, GenProp0714).
Probab=30.03 E-value=35 Score=27.19 Aligned_cols=18 Identities=28% Similarity=0.409 Sum_probs=13.0
Q ss_pred EEcCCCCCCCeEEEccCCC
Q psy8096 81 FALRKINKGEELTYDYKFP 99 (118)
Q Consensus 81 ~a~rdI~~GeElt~~Yg~~ 99 (118)
+|++||++||+|. -||..
T Consensus 42 iAl~dI~~Ge~Vi-KYG~~ 59 (507)
T TIGR03248 42 VALVDLAKGTAII-RYGET 59 (507)
T ss_pred EEecccCCCCeeE-ECCce
Confidence 6778888888874 66643
No 46
>COG3831 Uncharacterized conserved protein [Function unknown]
Probab=29.30 E-value=56 Score=19.57 Aligned_cols=18 Identities=22% Similarity=0.442 Sum_probs=13.8
Q ss_pred cEEEEEEcCCCCCCCeEEEccC
Q psy8096 76 PHIIIFALRKINKGEELTYDYK 97 (118)
Q Consensus 76 ~~~~~~a~rdI~~GeElt~~Yg 97 (118)
.++..++++ |.||+++||
T Consensus 15 ~kFy~~~i~----g~~L~~~wG 32 (85)
T COG3831 15 AKFYAVEIE----GAELTRNWG 32 (85)
T ss_pred cceEEEEEe----cceeEEeec
Confidence 455556655 999999998
No 47
>COG1261 FlgA Flagellar basal body P-ring biosynthesis protein [Cell motility and secretion / Posttranslational modification, protein turnover, chaperones]
Probab=27.35 E-value=1.3e+02 Score=21.23 Aligned_cols=18 Identities=33% Similarity=0.682 Sum_probs=15.6
Q ss_pred cEEEEEEcCCCCCCCeEE
Q psy8096 76 PHIIIFALRKINKGEELT 93 (118)
Q Consensus 76 ~~~~~~a~rdI~~GeElt 93 (118)
+.-+++|.|+|++||-|.
T Consensus 94 ~~~~~va~r~I~~Ge~i~ 111 (220)
T COG1261 94 PGEVVVAARTIYRGEKIS 111 (220)
T ss_pred cceEEEEecccCCCCccC
Confidence 447899999999999887
No 48
>PF00842 Ala_racemase_C: Alanine racemase, C-terminal domain; InterPro: IPR011079 Alanine racemase (5.1.1.1 from EC) plays a role in providing the D-alanine required for cell wall biosynthesis by isomerising L-alanine to D-alanine. Proteins contains this domain are found in both prokaryotic and eukaryotic proteins [,]. The molecular structure of alanine racemase from Bacillus stearothermophilus (Geobacillus stearothermophilus) was determined by X-ray crystallography to a resolution of 1.9 A []. The alanine racemase monomer is composed of two domains, an eight-stranded alpha/beta barrel at the N terminus, and a C-terminal domain essentially composed of beta-strand. The pyridoxal 5'-phosphate (PLP) cofactor lies in and above the mouth of the alpha/beta barrel and is covalently linked via an aldimine linkage to a lysine residue, which is at the C terminus of the first beta-strand of the alpha/beta barrel.; GO: 0008784 alanine racemase activity, 0006522 alanine metabolic process; PDB: 3HUR_A 4A3Q_B 3S46_A 1RCQ_A 3CO8_A 1VFT_B 1VFH_A 1VFS_B 2DY3_B 4ECL_C ....
Probab=27.05 E-value=29 Score=22.19 Aligned_cols=23 Identities=30% Similarity=0.440 Sum_probs=15.8
Q ss_pred EEEEEEcCCCCCCCeEEEccCCCCC
Q psy8096 77 HIIIFALRKINKGEELTYDYKFPIE 101 (118)
Q Consensus 77 ~~~~~a~rdI~~GeElt~~Yg~~~~ 101 (118)
+..+..+|+|++|| ++.|+..|-
T Consensus 5 ~a~i~~v~~v~~G~--~VgYg~~~~ 27 (129)
T PF00842_consen 5 KARIIQVREVPKGE--TVGYGRTYR 27 (129)
T ss_dssp EEEEEEEEEE-TT---EESGGGSEE
T ss_pred EEEEEEEEEeCCCC--CCcCCCEEE
Confidence 45678899999999 577876654
No 49
>PF01847 VHL: von Hippel-Lindau disease tumour suppressor protein; InterPro: IPR022772 Von Hippel-Lindau disease tumor suppressor (VHL) has two domains: a roughly 100-residue N-terminal domain rich in beta sheet (beta domain) and a smaller alpha-helical domain (alpha domain), held together by two linkers and a polar interface. A large portion of the alpha domain surface, and a small portion of the beta domain, interact with ElonginC. About half of the tumorigenic mutations map to the alpha domain and its residues that contact ElonginC. The remaining mutations map to the beta domain, and significantly, to a beta domain surface patch uninvolved in ElonginC binding. This suggests that two intact macromolecular binding sites may be required for the tumor suppressor effects of VHL []. This entry represents both beta and alpha domains of VHL.; PDB: 3ZRF_L 3ZRC_C 1LM8_V 1LQB_C 1VCB_F.
Probab=26.64 E-value=1.1e+02 Score=20.52 Aligned_cols=38 Identities=16% Similarity=0.155 Sum_probs=15.9
Q ss_pred eeeeeecCCCCCceeEEEEECCccEEEEEEcCCCCCCCeEEEc
Q psy8096 53 AARFINHSCDPNCYSRVVEIMGKPHIIIFALRKINKGEELTYD 95 (118)
Q Consensus 53 ~~RfiNHSC~PN~~~~~~~~~~~~~~~~~a~rdI~~GeElt~~ 95 (118)
..+|+|+|..+= ....++-.+.-..+ ..++||++..++
T Consensus 16 ~V~F~N~s~r~V---~v~Wldy~G~~~~Y--~~L~Pg~~~~~~ 53 (156)
T PF01847_consen 16 FVRFVNRSPRTV---DVYWLDYDGKPVPY--GTLKPGQGRRQN 53 (156)
T ss_dssp EEEEEE-SSS-E---EEEEE-TTS-EEE-----B-TTEEEEEE
T ss_pred EEEEEECCCCEE---EEEEEcCCCcEeec--cccCCCCeEEcc
Confidence 456888875542 23444433333333 336666666554
No 50
>PF01835 A2M_N: MG2 domain; InterPro: IPR002890 The proteinase-binding alpha-macroglobulins (A2M) [] are large glycoproteins found in the plasma of vertebrates, in the hemolymph of some invertebrates and in reptilian and avian egg white. A2M-like proteins are able to inhibit all four classes of proteinases by a 'trapping' mechanism. They have a peptide stretch, called the 'bait region', which contains specific cleavage sites for different proteinases. When a proteinase cleaves the bait region, a conformational change is induced in the protein, thus trapping the proteinase. The entrapped enzyme remains active against low molecular weight substrates, whilst its activity toward larger substrates is greatly reduced, due to steric hindrance. Following cleavage in the bait region, a thiol ester bond, formed between the side chains of a cysteine and a glutamine, is cleaved and mediates the covalent binding of the A2M-like protein to the proteinase. This family includes the N-terminal region of the alpha-2-macroglobulin family. The inhibitor domains belong to MEROPS inhibitor family I39.; GO: 0004866 endopeptidase inhibitor activity; PDB: 2B39_B 3KLS_B 3PRX_C 3KM9_B 3PVM_C 3CU7_A 4E0S_A 4A5W_A 4ACQ_C 2P9R_B ....
Probab=26.26 E-value=84 Score=18.43 Aligned_cols=15 Identities=33% Similarity=0.501 Sum_probs=6.2
Q ss_pred EEEcCCC-CCCCeEEE
Q psy8096 80 IFALRKI-NKGEELTY 94 (118)
Q Consensus 80 ~~a~rdI-~~GeElt~ 94 (118)
|++-|+| +|||.|.+
T Consensus 4 i~TDr~iYrPGetV~~ 19 (99)
T PF01835_consen 4 IQTDRPIYRPGETVHF 19 (99)
T ss_dssp EEESSSEE-TTSEEEE
T ss_pred EECCccCcCCCCEEEE
Confidence 3444444 44444443
No 51
>PF14100 PmoA: Methane oxygenase PmoA
Probab=26.24 E-value=75 Score=22.99 Aligned_cols=42 Identities=21% Similarity=0.289 Sum_probs=27.4
Q ss_pred eeecCCCCCceeEEEEECCccEEEE------EEcCCCCCCCeEEEccCC
Q psy8096 56 FINHSCDPNCYSRVVEIMGKPHIII------FALRKINKGEELTYDYKF 98 (118)
Q Consensus 56 fiNHSC~PN~~~~~~~~~~~~~~~~------~a~rdI~~GeElt~~Yg~ 98 (118)
|++|.-.||-- ..+.+.+...+++ ..--.|++||.|++.|..
T Consensus 205 ~~dhP~N~~~P-~~W~vR~~g~~~~~p~~~~~~~~~l~~G~~l~~rYr~ 252 (271)
T PF14100_consen 205 ILDHPSNPNYP-TPWHVRGYGLFGANPAPAFDGPLTLPPGETLTLRYRV 252 (271)
T ss_pred EEeCCCCCCCC-cceEEeccCcceecccccccCceecCCCCeEEEEEEE
Confidence 77887666532 3555554444433 444678999999999963
No 52
>COG4118 Phd Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]
Probab=26.23 E-value=21 Score=21.28 Aligned_cols=13 Identities=31% Similarity=0.580 Sum_probs=10.1
Q ss_pred CCCCCCCeEEEcc
Q psy8096 84 RKINKGEELTYDY 96 (118)
Q Consensus 84 rdI~~GeElt~~Y 96 (118)
+-+++|||++|.=
T Consensus 19 ~rV~aGEev~IT~ 31 (84)
T COG4118 19 RRVRAGEEVIITK 31 (84)
T ss_pred HHHhCCCEEEEee
Confidence 4568999999864
No 53
>PRK07018 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=25.78 E-value=40 Score=23.78 Aligned_cols=18 Identities=28% Similarity=0.440 Sum_probs=15.1
Q ss_pred EEEEEEcCCCCCCCeEEE
Q psy8096 77 HIIIFALRKINKGEELTY 94 (118)
Q Consensus 77 ~~~~~a~rdI~~GeElt~ 94 (118)
.-+++|.|+|++|+.|+-
T Consensus 110 ~~VvVA~r~I~rG~~I~~ 127 (235)
T PRK07018 110 GPYVVAARPLARGEKLSA 127 (235)
T ss_pred EEEEEEccccCCCCCcCH
Confidence 347889999999999873
No 54
>PRK09502 iscA iron-sulfur cluster assembly protein; Provisional
Probab=24.87 E-value=33 Score=21.05 Aligned_cols=33 Identities=12% Similarity=0.126 Sum_probs=18.7
Q ss_pred EEcCCCCCCCeEEEccCCCCCCCC--------CeEEEecCC
Q psy8096 81 FALRKINKGEELTYDYKFPIEDDN--------KISCHCLAM 113 (118)
Q Consensus 81 ~a~rdI~~GeElt~~Yg~~~~~~~--------~~~C~Cg~~ 113 (118)
+....+.-=+..+|||..+..+.. .-.|.||+.
T Consensus 64 id~~s~~~l~g~~IDy~~~~~~~~F~f~NPna~~~CgCG~S 104 (107)
T PRK09502 64 VDGKSLQFLDGTQLDFVKEGLNEGFKFTNPNVKDECGCGES 104 (107)
T ss_pred EeHHHHhHhCCCEEEEeeCCCCceEEEECCCCCCccCCCCC
Confidence 344444444555888865533221 567999863
No 55
>TIGR01997 sufA_proteo FeS assembly scaffold SufA. This model represents the SufA protein of the SUF system of iron-sulfur cluster biosynthesis. This system performs FeS biosynthesis even during oxidative stress and tends to be absent in obligate anaerobic and microaerophilic bacteria.
Probab=24.69 E-value=30 Score=21.20 Aligned_cols=34 Identities=12% Similarity=0.054 Sum_probs=18.8
Q ss_pred EEEcCCCCCCCeEEEccCCCCCCCC--------CeEEEecCC
Q psy8096 80 IFALRKINKGEELTYDYKFPIEDDN--------KISCHCLAM 113 (118)
Q Consensus 80 ~~a~rdI~~GeElt~~Yg~~~~~~~--------~~~C~Cg~~ 113 (118)
++....+.-=+..+|||..+..... ...|.||+.
T Consensus 63 ~id~~s~~~l~g~~IDy~~~~~~~~F~~~NPn~~~~CgCG~S 104 (107)
T TIGR01997 63 FVAPEAVLFILGTQVDFVRTTLRQGFKFNNPNATSACGCGES 104 (107)
T ss_pred EEcHHHHhhhCCCEEEEEEcCCcceEEEECCCCCCccCCCCC
Confidence 3333444444455888865543332 456999864
No 56
>PF13144 SAF_2: SAF-like
Probab=24.03 E-value=43 Score=22.62 Aligned_cols=20 Identities=35% Similarity=0.443 Sum_probs=16.0
Q ss_pred cEEEEEEcCCCCCCCeEEEc
Q psy8096 76 PHIIIFALRKINKGEELTYD 95 (118)
Q Consensus 76 ~~~~~~a~rdI~~GeElt~~ 95 (118)
..-+++|.++|++|+-|+-+
T Consensus 74 ~~~v~va~~~i~~G~~i~~~ 93 (196)
T PF13144_consen 74 YVEVVVAKRPIKRGEVITAD 93 (196)
T ss_pred EEEEEEEeeecCCCCccCHH
Confidence 34578999999999998743
No 57
>COG0787 Alr Alanine racemase [Cell envelope biogenesis, outer membrane]
Probab=23.71 E-value=43 Score=25.47 Aligned_cols=26 Identities=23% Similarity=0.358 Sum_probs=20.6
Q ss_pred cEEEEEEcCCCCCCCeEEEccCCCCCCC
Q psy8096 76 PHIIIFALRKINKGEELTYDYKFPIEDD 103 (118)
Q Consensus 76 ~~~~~~a~rdI~~GeElt~~Yg~~~~~~ 103 (118)
....++.+|.+++|| ++.||..|-..
T Consensus 238 l~a~ii~vr~v~~Ge--~VgYG~t~~a~ 263 (360)
T COG0787 238 LKARIIQVRTVPAGE--TVGYGATFTAE 263 (360)
T ss_pred EEEEEEEEEEeCCCC--cccCCcEEEcc
Confidence 456788999999999 88998766443
No 58
>PRK08515 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=23.50 E-value=48 Score=23.26 Aligned_cols=17 Identities=29% Similarity=0.473 Sum_probs=14.7
Q ss_pred EEEEEcCCCCCCCeEEE
Q psy8096 78 IIIFALRKINKGEELTY 94 (118)
Q Consensus 78 ~~~~a~rdI~~GeElt~ 94 (118)
-+++|.|+|.+|+-|+-
T Consensus 101 ~v~Va~r~i~rG~~I~~ 117 (222)
T PRK08515 101 EVLKSIRAIKKDDNLTA 117 (222)
T ss_pred EEEEEccccCCCCCCCH
Confidence 46899999999999874
No 59
>PF04014 Antitoxin-MazE: Antidote-toxin recognition MazE; InterPro: IPR007159 This domain is found in AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation []. AbrB is thought to interact directly with the transcription initiation regions of genes under its control []. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins []. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator []. DNA-binding activity in this AbrB homologue requires hexamerisation []. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins [].; PDB: 2L66_A 2GLW_A 3TND_D 2W1T_B 2RO5_B 2FY9_A 2RO3_B 1UB4_C 3ZVK_G 1YFB_B ....
Probab=23.50 E-value=57 Score=16.67 Aligned_cols=14 Identities=14% Similarity=0.320 Sum_probs=11.7
Q ss_pred CCCCCCeEEEccCC
Q psy8096 85 KINKGEELTYDYKF 98 (118)
Q Consensus 85 dI~~GeElt~~Yg~ 98 (118)
.|.+|+||.+.+..
T Consensus 20 ~l~~Gd~v~i~~~~ 33 (47)
T PF04014_consen 20 GLKPGDEVEIEVEG 33 (47)
T ss_dssp TSSTTTEEEEEEET
T ss_pred CCCCCCEEEEEEeC
Confidence 68999999998764
No 60
>COG3848 Phosphohistidine swiveling domain [Signal transduction mechanisms]
Probab=23.21 E-value=46 Score=20.81 Aligned_cols=17 Identities=29% Similarity=0.259 Sum_probs=14.7
Q ss_pred EEcCCCCCCCeEEEccC
Q psy8096 81 FALRKINKGEELTYDYK 97 (118)
Q Consensus 81 ~a~rdI~~GeElt~~Yg 97 (118)
.|++.|+.|+.+|+|=.
T Consensus 83 ~at~~i~dG~~vTvD~~ 99 (111)
T COG3848 83 KATQLIRDGAIVTVDAQ 99 (111)
T ss_pred chhhhccCCCEEEEecc
Confidence 48899999999999953
No 61
>smart00588 NEUZ domain in neuralized proteins.
Probab=23.14 E-value=86 Score=19.87 Aligned_cols=21 Identities=14% Similarity=0.271 Sum_probs=17.3
Q ss_pred cEEEEEEcCCCCCCCeEEEcc
Q psy8096 76 PHIIIFALRKINKGEELTYDY 96 (118)
Q Consensus 76 ~~~~~~a~rdI~~GeElt~~Y 96 (118)
-+-.+|+-|+|+.||-+.+--
T Consensus 30 ~~givFS~rPl~~~E~~~v~i 50 (123)
T smart00588 30 CNALVFSARPLRINELFEVKI 50 (123)
T ss_pred CceEEecCCCCcCCCEEEEEE
Confidence 345789999999999988765
No 62
>TIGR00286 arginine decarboxylase, pyruvoyl-dependent. The three copies present in Archeoglobus fulgidus, one of which is only half-length and excluded from the seed alignment, are very closely related and clearly arose by duplication after the separation from well-studied species. The other completed archaeal genomes each contain a single copy. The lone, weak (below trusted cutoff) hit to a non-archaeal sequence is to an uncharacterized protein of Chlamydia, with the greatest similarity in the amino-terminal half of the model.
Probab=22.59 E-value=1.3e+02 Score=20.11 Aligned_cols=15 Identities=20% Similarity=0.208 Sum_probs=8.7
Q ss_pred cCCCCCCCeEEEccC
Q psy8096 83 LRKINKGEELTYDYK 97 (118)
Q Consensus 83 ~rdI~~GeElt~~Yg 97 (118)
+.++++|+-|+.-|+
T Consensus 52 l~~l~~G~iv~~Vma 66 (152)
T TIGR00286 52 LPKLPPGQIVFCVMS 66 (152)
T ss_pred cCCCCCCCEEEEEEE
Confidence 455666666665553
No 63
>cd03420 SirA_RHOD_Pry_redox SirA_RHOD_Pry_redox. SirA-like domain located within a multidomain protein of unknown function. Other domains include RHOD (rhodanese homology domain), and Pry_redox (pyridine nucleotide-disulphide oxidoreductase) as well as a C-terminal domain that corresponds to COG2210. This fold is referred to as a two-layered alpha/beta sandwich, structurally similar to that of translation initiation factor 3.
Probab=22.05 E-value=44 Score=18.67 Aligned_cols=15 Identities=27% Similarity=0.505 Sum_probs=11.2
Q ss_pred EcCCCCCCCeEEEcc
Q psy8096 82 ALRKINKGEELTYDY 96 (118)
Q Consensus 82 a~rdI~~GeElt~~Y 96 (118)
|++++++|++|.+-=
T Consensus 19 al~~l~~G~~l~V~~ 33 (69)
T cd03420 19 EIDKLQDGEQLEVKA 33 (69)
T ss_pred HHHcCCCCCEEEEEE
Confidence 678899999776543
No 64
>COG3884 FatA Acyl-ACP thioesterase [Lipid metabolism]
Probab=21.23 E-value=1.1e+02 Score=22.04 Aligned_cols=25 Identities=16% Similarity=0.343 Sum_probs=21.6
Q ss_pred ccEEEEEEcCCCCCCCeEEEccCCC
Q psy8096 75 KPHIIIFALRKINKGEELTYDYKFP 99 (118)
Q Consensus 75 ~~~~~~~a~rdI~~GeElt~~Yg~~ 99 (118)
..++.+-=.+++++|+.||+.|...
T Consensus 193 p~r~~l~y~keva~G~~iti~~e~~ 217 (250)
T COG3884 193 PLRLTLEYVKEVAPGEKITIVYEVH 217 (250)
T ss_pred cceeEEEEEcccCCCCeEEEEEEEc
Confidence 4678888889999999999999755
No 65
>PF11910 NdhO: Cyanobacterial and plant NDH-1 subunit O; InterPro: IPR020905 NAD(P)H-quinone oxidoreductase (NDH-1) shuttles electrons from an unknown electron donor, via FMN and iron-sulphur (Fe-S) centres, to quinones in the respiratory and/or the photosynthetic chain. The immediate electron acceptor for the enzyme in this species is believed to be plastoquinone. It couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient. Cyanobacterial NDH-1 also plays a role in inorganic carbon-concentration. NDH-1 can be composed of about 15 different subunits, although different subcomplexes with different compositions have been identified which probably have different functions. This entry represents subunit O. ; GO: 0016655 oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor, 0055114 oxidation-reduction process, 0005886 plasma membrane
Probab=20.72 E-value=1.8e+02 Score=16.52 Aligned_cols=42 Identities=19% Similarity=0.233 Sum_probs=21.3
Q ss_pred CCCCCeeEEeeeEEEChhHHHHHHHHHhhcCCeeeEEEcCCcEEEecc
Q psy8096 1 MEEDCSVSVTLMAVIRASVSDKREKQYMDKGIGCYMFKIDDRFVIDAT 48 (118)
Q Consensus 1 I~~g~~i~ey~Gevi~~~~~~~~~~~~~~~~~~~y~~~~~~~~~iDa~ 48 (118)
|+||++|---.... ...-+....+.....|+|.-... ++|..
T Consensus 1 lKKG~lVrv~re~~-----~nSlEa~ASD~~~P~Yife~~GE-vl~ik 42 (67)
T PF11910_consen 1 LKKGSLVRVNREKY-----ENSLEAKASDPRPPSYIFEGPGE-VLDIK 42 (67)
T ss_pred CCcceEEEeehHhh-----cCchhhhhcCCCCCcceecCCCe-EEEec
Confidence 57777764333222 22222233334445899987643 45544
No 66
>KOG3422|consensus
Probab=20.44 E-value=2e+02 Score=20.39 Aligned_cols=37 Identities=11% Similarity=-0.129 Sum_probs=25.5
Q ss_pred CCCCCeeEEeeeEEEChhHHHHHHHHHhhcCCeeeEEE
Q psy8096 1 MEEDCSVSVTLMAVIRASVSDKREKQYMDKGIGCYMFK 38 (118)
Q Consensus 1 I~~g~~i~ey~Gevi~~~~~~~~~~~~~~~~~~~y~~~ 38 (118)
|+.|.+|.|..|. ++..++.+--......-...|-|-
T Consensus 138 V~~GrIl~EmgG~-~~~~~Ar~al~~aa~klp~~~efV 174 (221)
T KOG3422|consen 138 VKAGRILFEMGGD-VEEEEARQALLQAAHKLPFKYEFV 174 (221)
T ss_pred ecCCcEEEEeCCc-ccHHHHHHHHHHHHhcCCccEEEe
Confidence 6789999999999 777777666555444433345443
No 67
>PF14796 AP3B1_C: Clathrin-adaptor complex-3 beta-1 subunit C-terminal
Probab=20.09 E-value=1.2e+02 Score=19.97 Aligned_cols=52 Identities=17% Similarity=0.176 Sum_probs=29.2
Q ss_pred CCeeeeeecCCCCCceeEEEEEC--CccEE-EEEEcCCCCCCCeEEEccCCCCCC
Q psy8096 51 GNAARFINHSCDPNCYSRVVEIM--GKPHI-IIFALRKINKGEELTYDYKFPIED 102 (118)
Q Consensus 51 gn~~RfiNHSC~PN~~~~~~~~~--~~~~~-~~~a~rdI~~GeElt~~Yg~~~~~ 102 (118)
.=.-.|-|||..|=...+...-+ ...++ .+--+..++||+.+|..-|-++.+
T Consensus 88 sIql~ftN~s~~~i~~I~i~~k~l~~g~~i~~F~~I~~L~pg~s~t~~lgIDF~D 142 (145)
T PF14796_consen 88 SIQLTFTNNSDEPIKNIHIGEKKLPAGMRIHEFPEIESLEPGASVTVSLGIDFND 142 (145)
T ss_pred EEEEEEEecCCCeecceEECCCCCCCCcEeeccCcccccCCCCeEEEEEEEeccc
Confidence 33456788888763222211111 12233 344567789999988877766543
No 68
>smart00002 PLP Myelin proteolipid protein (PLP or lipophilin).
Probab=20.09 E-value=61 Score=18.09 Aligned_cols=13 Identities=23% Similarity=0.294 Sum_probs=10.3
Q ss_pred CcEEEecccCCCe
Q psy8096 41 DRFVIDATMKGNA 53 (118)
Q Consensus 41 ~~~~iDa~~~gn~ 53 (118)
+.+++|++.+|=+
T Consensus 20 ~~lC~D~RQyGil 32 (60)
T smart00002 20 GTLCVDARQYGIL 32 (60)
T ss_pred CCEEeechhccee
Confidence 3589999999943
Done!