Query psy3204
Match_columns 264
No_of_seqs 177 out of 458
Neff 3.3
Searched_HMMs 46136
Date Fri Aug 16 18:59:54 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3204.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3204hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3048|consensus 100.0 2.1E-38 4.5E-43 268.9 14.4 124 52-251 3-126 (153)
2 PRK14011 prefoldin subunit alp 99.9 2.3E-26 5.1E-31 193.7 16.0 93 161-256 26-118 (144)
3 PRK01203 prefoldin subunit alp 99.9 2.1E-25 4.5E-30 186.1 13.2 104 157-261 19-122 (130)
4 TIGR00293 prefoldin, archaeal 99.9 4E-24 8.8E-29 171.0 16.4 96 161-257 22-117 (126)
5 COG1730 GIM5 Predicted prefold 99.9 3.3E-23 7.1E-28 175.4 15.6 96 161-256 29-124 (145)
6 cd00584 Prefoldin_alpha Prefol 99.9 5.4E-23 1.2E-27 165.1 16.1 94 161-254 22-115 (129)
7 PF02996 Prefoldin: Prefoldin 99.9 6.5E-23 1.4E-27 161.2 13.2 101 156-256 7-107 (120)
8 PRK03947 prefoldin subunit alp 99.9 2.5E-22 5.4E-27 163.8 16.2 94 161-254 29-122 (140)
9 cd00890 Prefoldin Prefoldin is 99.9 6.3E-21 1.4E-25 150.5 16.6 96 161-256 22-117 (129)
10 KOG3130|consensus 99.1 1E-10 2.3E-15 113.7 5.9 98 156-254 14-111 (514)
11 KOG3047|consensus 98.9 1.4E-08 3E-13 86.8 9.6 90 161-250 39-129 (157)
12 KOG3313|consensus 97.9 0.00012 2.7E-09 65.1 10.6 91 160-250 59-152 (187)
13 cd00890 Prefoldin Prefoldin is 96.8 0.0017 3.7E-08 51.4 4.5 57 186-255 67-123 (129)
14 TIGR02338 gimC_beta prefoldin, 96.4 0.0062 1.3E-07 48.8 5.2 61 171-252 33-93 (110)
15 PF13758 Prefoldin_3: Prefoldi 96.4 0.0015 3.3E-08 53.3 1.6 91 159-251 2-93 (99)
16 PF01920 Prefoldin_2: Prefoldi 96.4 0.06 1.3E-06 41.2 10.3 47 209-256 46-92 (106)
17 TIGR00293 prefoldin, archaeal 96.3 0.0072 1.6E-07 48.6 4.8 87 157-257 11-110 (126)
18 cd00632 Prefoldin_beta Prefold 96.1 0.014 3E-07 46.3 5.5 70 161-254 22-91 (105)
19 PRK03947 prefoldin subunit alp 95.2 0.022 4.8E-07 46.7 3.6 51 206-256 54-117 (140)
20 cd00584 Prefoldin_alpha Prefol 95.0 0.06 1.3E-06 43.4 5.5 58 186-256 67-124 (129)
21 PRK01203 prefoldin subunit alp 91.7 0.28 6E-06 41.8 4.4 48 205-252 46-106 (130)
22 COG1730 GIM5 Predicted prefold 87.2 0.72 1.6E-05 39.8 3.6 43 209-251 57-112 (145)
23 PF02996 Prefoldin: Prefoldin 86.7 1.3 2.9E-05 34.8 4.7 55 186-253 57-111 (120)
24 PRK09343 prefoldin subunit bet 77.5 4.2 9.1E-05 33.5 4.4 40 209-249 55-94 (121)
25 KOG3905|consensus 77.4 6.5 0.00014 39.4 6.4 70 184-264 202-271 (473)
26 COG1382 GimC Prefoldin, chaper 71.6 5.8 0.00013 33.6 3.9 38 209-247 54-91 (119)
27 KOG4098|consensus 66.7 15 0.00034 32.0 5.5 68 161-252 38-105 (140)
28 PRK14011 prefoldin subunit alp 63.4 18 0.0004 31.0 5.4 23 186-208 68-90 (144)
29 PF01330 RuvA_N: RuvA N termin 58.0 27 0.00058 25.1 4.7 30 198-227 3-35 (61)
30 KOG3048|consensus 54.9 5.9 0.00013 34.9 1.0 55 186-253 81-135 (153)
31 PRK05771 V-type ATP synthase s 51.0 63 0.0014 33.0 7.7 37 224-260 213-249 (646)
32 PF05377 FlaC_arch: Flagella a 50.4 51 0.0011 24.7 5.2 33 225-257 13-45 (55)
33 PF09278 MerR-DNA-bind: MerR, 38.1 71 0.0015 22.4 4.3 29 222-250 32-60 (65)
34 PF14962 AIF-MLS: Mitochondria 30.9 16 0.00035 32.9 0.0 30 214-243 57-86 (180)
35 PRK14603 ruvA Holliday junctio 30.2 1E+02 0.0023 27.5 4.9 31 198-228 3-36 (197)
36 PRK14609 4-diphosphocytidyl-2- 28.4 29 0.00062 31.8 1.1 51 21-90 219-269 (269)
37 PRK14605 ruvA Holliday junctio 26.8 1.4E+02 0.0031 26.5 5.1 32 198-229 3-37 (194)
38 PF00384 Molybdopterin: Molybd 24.9 87 0.0019 29.0 3.6 28 215-242 13-40 (432)
39 PRK14604 ruvA Holliday junctio 23.5 1.8E+02 0.004 25.9 5.3 31 198-228 3-36 (195)
40 PRK14606 ruvA Holliday junctio 23.3 1.5E+02 0.0031 26.4 4.6 31 198-228 3-37 (188)
41 PF08800 VirE_N: VirE N-termin 23.2 1E+02 0.0022 25.6 3.4 52 25-76 3-55 (136)
42 PF01486 K-box: K-box region; 23.0 61 0.0013 25.4 1.9 22 58-83 42-63 (100)
43 PF07889 DUF1664: Protein of u 22.9 1.8E+02 0.0038 24.8 4.8 33 223-255 58-90 (126)
44 TIGR03017 EpsF chain length de 22.9 1.7E+02 0.0036 28.0 5.1 33 224-256 169-201 (444)
45 TIGR00084 ruvA Holliday juncti 22.6 1.8E+02 0.0038 25.8 4.9 31 198-228 3-36 (191)
46 PRK13901 ruvA Holliday junctio 22.5 1.7E+02 0.0037 26.5 4.9 30 198-227 3-35 (196)
47 PF10400 Vir_act_alpha_C: Viru 22.2 2.4E+02 0.0051 20.8 4.9 30 222-251 17-46 (90)
48 PF02388 FemAB: FemAB family; 22.0 2E+02 0.0044 27.9 5.6 31 218-248 234-264 (406)
49 TIGR02338 gimC_beta prefoldin, 21.9 2.1E+02 0.0045 22.8 4.8 73 159-252 24-107 (110)
50 cd01109 HTH_YyaN Helix-Turn-He 21.3 2.2E+02 0.0048 22.4 4.8 29 223-251 76-104 (113)
51 TIGR02047 CadR-PbrR Cd(II)/Pb( 21.1 2E+02 0.0043 23.5 4.6 30 222-251 75-104 (127)
52 PLN02318 phosphoribulokinase/u 20.6 1.8E+02 0.0038 31.2 5.1 111 144-255 490-615 (656)
53 PF12841 YvrJ: YvrJ protein fa 20.5 1E+02 0.0022 21.4 2.3 19 231-249 20-38 (38)
54 cd02769 MopB_DMSOR-BSOR-TMAOR 20.3 1.2E+02 0.0025 30.8 3.7 27 215-241 69-95 (609)
55 PF05185 PRMT5: PRMT5 arginine 20.2 1.5E+02 0.0033 29.5 4.5 29 207-236 186-235 (448)
56 cd04772 HTH_TioE_rpt1 First He 20.1 1.4E+02 0.0029 23.5 3.4 26 223-248 73-98 (99)
No 1
>KOG3048|consensus
Probab=100.00 E-value=2.1e-38 Score=268.88 Aligned_cols=124 Identities=46% Similarity=0.771 Sum_probs=120.4
Q ss_pred CCccceecCCCChHHHHHHHHhhhhhhhhhhcchhhccccccccccCCCchhhhhHhhhhchhHHHhhhhcccccccCCc
Q psy3204 52 EGMQQIDLTKLAFPQLTQLKNQLDSVSFQALGLCFKWQGSHLRELFHPTTDFSYLKLLESSNNFILKQFKEGEHCTSAGS 131 (264)
Q Consensus 52 ~~~~~i~l~~l~~~ql~~~k~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~s~~~~~~~~~~~~~~~~~~~ 131 (264)
++.+.||||+|++|||.+||+|+|+ ||+ +|++|
T Consensus 3 ~~s~~idltkLsleQL~~lk~q~dq----El~------------------------~lq~S------------------- 35 (153)
T KOG3048|consen 3 EESKGIDLTKLSLEQLGALKKQFDQ----ELN------------------------FLQDS------------------- 35 (153)
T ss_pred CcccCCChhhCCHHHHHHHHHHHHH----HHH------------------------HHHHH-------------------
Confidence 4668899999999999999999999 999 99999
Q ss_pred cccccccccccCCCCCCCCCCCcccCccchHHHHHHHHHHHHHHHHHHhhCCCCCCCceEEecCCceeEEEEEecCCeEE
Q psy3204 132 EFHNCTAFTKRELPSAVPLCGGTLRRQPNNGALKRAQVKFQDSKESLDKITPSSQGNPIMVPLTDSMYVEGKIADADKVV 211 (264)
Q Consensus 132 ~~~~~~~~~~~~~~~~~~~~~~t~~lqqQLqqLk~Aq~Kf~eskeALe~Lk~~~egkEILVPLGSSLYVpGKL~DteKVL 211 (264)
+++|+.++.||.+|+++|+.++..++|+++|||||+|+||||++.|++++|
T Consensus 36 -----------------------------l~~L~~aq~k~~~~~~aln~~~~~~eGk~~LVPLTsSlYVPGkl~d~~k~l 86 (153)
T KOG3048|consen 36 -----------------------------LNALKGAQTKYEESIAALNDVQAANEGKKLLVPLTSSLYVPGKLSDNSKFL 86 (153)
T ss_pred -----------------------------HHHHHHHHHHHHHHHHHHhhcccCCCCCeEEEecccceeccceecccccee
Confidence 999999999999999999999999999999999999999999999999999
Q ss_pred EEecCcEEEEeChHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy3204 212 IDIGTGFYVEKSIPDAQDYFKRRVAFVTQQMEKLQFIFLL 251 (264)
Q Consensus 212 VDIGTGYYVEKSidEAiefleRRIk~LeeqieKLqkiIq~ 251 (264)
||||||||||||.++|++||+||+++|++++++|++++..
T Consensus 87 VDIGTGYyVEK~~e~akdyfkRKve~l~kq~e~i~~i~~e 126 (153)
T KOG3048|consen 87 VDIGTGYYVEKDAEDAKDYFKRKVEYLTKQIEQIEGILKE 126 (153)
T ss_pred EeccCceEEeechHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999998864
No 2
>PRK14011 prefoldin subunit alpha; Provisional
Probab=99.94 E-value=2.3e-26 Score=193.68 Aligned_cols=93 Identities=19% Similarity=0.369 Sum_probs=87.2
Q ss_pred hHHHHHHHHHHHHHHHHHHhhCCCCCCCceEEecCCceeEEEEEecCCeEEEEecCcEEEEeChHHHHHHHHHHHHHHHH
Q psy3204 161 NGALKRAQVKFQDSKESLDKITPSSQGNPIMVPLTDSMYVEGKIADADKVVIDIGTGFYVEKSIPDAQDYFKRRVAFVTQ 240 (264)
Q Consensus 161 LqqLk~Aq~Kf~eskeALe~Lk~~~egkEILVPLGSSLYVpGKL~DteKVLVDIGTGYYVEKSidEAiefleRRIk~Lee 240 (264)
+++|+.++++|.+|+++|+.++ .+++||||||+|+||||+|.|+++||||||||||||||.++|++||+||+++|++
T Consensus 26 i~~L~~a~~e~~~~ie~L~~l~---~~~eiLVPLg~s~yV~g~i~d~dkVlVdIGtGy~VEk~~~eA~~~~~~ri~~l~~ 102 (144)
T PRK14011 26 LSSIDMMKMELLKSIESMEGLK---TSEEILIPLGPGAFLKAKIVDPDKAILGVGSDIYLEKDVSEVIEDFKKSVEELDK 102 (144)
T ss_pred HHHHHHHHHHHHHHHHHHHccC---CCCeEEEEcCCCcEEeEEecCCCeEEEEccCCeEEEecHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999875 4799999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHH
Q psy3204 241 QMEKLQFIFLLYILIF 256 (264)
Q Consensus 241 qieKLqkiIq~~l~~~ 256 (264)
++++|.+.|+..-.+.
T Consensus 103 ~~~~l~~~i~~~~~~~ 118 (144)
T PRK14011 103 TKKEGNKKIEELNKEI 118 (144)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 9999999888765443
No 3
>PRK01203 prefoldin subunit alpha; Provisional
Probab=99.93 E-value=2.1e-25 Score=186.11 Aligned_cols=104 Identities=13% Similarity=0.287 Sum_probs=98.1
Q ss_pred CccchHHHHHHHHHHHHHHHHHHhhCCCCCCCceEEecCCceeEEEEEecCCeEEEEecCcEEEEeChHHHHHHHHHHHH
Q psy3204 157 RQPNNGALKRAQVKFQDSKESLDKITPSSQGNPIMVPLTDSMYVEGKIADADKVVIDIGTGFYVEKSIPDAQDYFKRRVA 236 (264)
Q Consensus 157 lqqQLqqLk~Aq~Kf~eskeALe~Lk~~~egkEILVPLGSSLYVpGKL~DteKVLVDIGTGYYVEKSidEAiefleRRIk 236 (264)
+++++++|+.++++|.+|+++|+.++ ...+++||||||+|+||||+|.|+++|||||||||||||+.++|+++++++++
T Consensus 19 l~~ql~~L~~a~se~~~~ie~L~~~~-~~~~~eiLVPLg~slYV~gki~d~~kVlVdIGTGy~VEK~~e~kie~L~~~ie 97 (130)
T PRK01203 19 VDSQIDSLNKTLSEVQQTISFLSDNE-LDNSKELLISIGSGIFADGNIKKDKDLIVPIGSGVYIAEERERTIERLKENLE 97 (130)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHccc-cCCCCeEEEEccCCceEeEEecCCCeEEEEcCCCeEEEecHHHHHHHHHHHHH
Confidence 78899999999999999999999976 45679999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhhc
Q psy3204 237 FVTQQMEKLQFIFLLYILIFCSLII 261 (264)
Q Consensus 237 ~LeeqieKLqkiIq~~l~~~~~~~~ 261 (264)
.|++.+.+.+..++.+-..|-.|-|
T Consensus 98 ~Le~~i~~K~~~l~~i~~~~~~l~~ 122 (130)
T PRK01203 98 DLKDSIQKLNDQRKTLVDQYNTVYI 122 (130)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999887754
No 4
>TIGR00293 prefoldin, archaeal alpha subunit/eukaryotic subunit 5. This model finds a set of small proteins from the Archaea and from Aquifex aeolicus that may represent two orthologous groups. The proteins are predicted to be mostly coiled coil, and may hit large numbers of proteins that contain coiled coil regions.
Probab=99.92 E-value=4e-24 Score=170.99 Aligned_cols=96 Identities=28% Similarity=0.512 Sum_probs=90.3
Q ss_pred hHHHHHHHHHHHHHHHHHHhhCCCCCCCceEEecCCceeEEEEEecCCeEEEEecCcEEEEeChHHHHHHHHHHHHHHHH
Q psy3204 161 NGALKRAQVKFQDSKESLDKITPSSQGNPIMVPLTDSMYVEGKIADADKVVIDIGTGFYVEKSIPDAQDYFKRRVAFVTQ 240 (264)
Q Consensus 161 LqqLk~Aq~Kf~eskeALe~Lk~~~egkEILVPLGSSLYVpGKL~DteKVLVDIGTGYYVEKSidEAiefleRRIk~Lee 240 (264)
+..|+.++.+|..++++|+.+++. .+.++|||||+++||||+|.++++|+|+||+|||||++.++|++|+++|++.+++
T Consensus 22 i~~l~~~i~e~~~~~~~L~~l~~~-~~~~~lv~lg~~~~v~~~v~~~~~v~v~iG~g~~vE~~~~eA~~~l~~~~~~l~~ 100 (126)
T TIGR00293 22 IAALRALIAELETAIETLEDLKGA-EGKETLVPVGAGSFVKAKVKDTDKVLVSIGSGYYVEKDAEEAIEFLKKRIEELEK 100 (126)
T ss_pred HHHHHHHHHHHHHHHHHHHhcccc-CCCeEEEEcCCCeEEEEEeCCCCEEEEEcCCCEEEEecHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999865 7899999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHh
Q psy3204 241 QMEKLQFIFLLYILIFC 257 (264)
Q Consensus 241 qieKLqkiIq~~l~~~~ 257 (264)
+++++++.+...-..+-
T Consensus 101 ~~~~l~~~l~~l~~~~~ 117 (126)
T TIGR00293 101 AIEKLQEALAELASRAQ 117 (126)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 99999999887655543
No 5
>COG1730 GIM5 Predicted prefoldin, molecular chaperone implicated in de novo protein folding [Posttranslational modification, protein turnover, chaperones]
Probab=99.91 E-value=3.3e-23 Score=175.38 Aligned_cols=96 Identities=30% Similarity=0.567 Sum_probs=89.8
Q ss_pred hHHHHHHHHHHHHHHHHHHhhCCCCCCCceEEecCCceeEEEEEecCCeEEEEecCcEEEEeChHHHHHHHHHHHHHHHH
Q psy3204 161 NGALKRAQVKFQDSKESLDKITPSSQGNPIMVPLTDSMYVEGKIADADKVVIDIGTGFYVEKSIPDAQDYFKRRVAFVTQ 240 (264)
Q Consensus 161 LqqLk~Aq~Kf~eskeALe~Lk~~~egkEILVPLGSSLYVpGKL~DteKVLVDIGTGYYVEKSidEAiefleRRIk~Lee 240 (264)
+..|+.++++++.|+++|+.++...+|+|+|||+|+++||+|++.|.++|||+||+|||||++.++|++|+++|++.|++
T Consensus 29 i~~l~~~~~e~~~~~~tl~~lk~~~~g~E~LVpvGag~fv~~kv~~~~kviV~iGsg~~ae~~~~eAie~l~k~~~~l~~ 108 (145)
T COG1730 29 IAALNAAISELQTAIETLENLKGAGEGKEVLVPVGAGLFVKAKVKDMDKVIVSIGSGYYAEKSADEAIEFLKKRIEELEK 108 (145)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCCceEEEEcCCCceEEEEeccCceEEEEcCCceeeeecHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999986655899999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHH
Q psy3204 241 QMEKLQFIFLLYILIF 256 (264)
Q Consensus 241 qieKLqkiIq~~l~~~ 256 (264)
.++++++.|...-..+
T Consensus 109 ~~~~l~~~l~~l~~~~ 124 (145)
T COG1730 109 AIEKLQQALAELAQRI 124 (145)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 9999998887654443
No 6
>cd00584 Prefoldin_alpha Prefoldin alpha subunit; Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. 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 structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils.
Probab=99.91 E-value=5.4e-23 Score=165.08 Aligned_cols=94 Identities=32% Similarity=0.617 Sum_probs=88.6
Q ss_pred hHHHHHHHHHHHHHHHHHHhhCCCCCCCceEEecCCceeEEEEEecCCeEEEEecCcEEEEeChHHHHHHHHHHHHHHHH
Q psy3204 161 NGALKRAQVKFQDSKESLDKITPSSQGNPIMVPLTDSMYVEGKIADADKVVIDIGTGFYVEKSIPDAQDYFKRRVAFVTQ 240 (264)
Q Consensus 161 LqqLk~Aq~Kf~eskeALe~Lk~~~egkEILVPLGSSLYVpGKL~DteKVLVDIGTGYYVEKSidEAiefleRRIk~Lee 240 (264)
++.|+..+.+|..++++|+.+++...+.++|||||+++||||+|.++++|+|+||+|||||++.++|++|+++|++.|++
T Consensus 22 ~~~l~~~~~e~~~~~~~l~~l~~~~~~~~~lvplg~~~~~~~~i~~~~~v~v~iG~g~~vE~~~~eA~~~l~~r~~~l~~ 101 (129)
T cd00584 22 LARLNEAIAEYEQAKETLETLKKADEGKETLVPLGAGVFVKAKVKDTDKVLVDLGTGYYVEKDLEEAIEFLDKKIEELTK 101 (129)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCeEEeEEeCCCCEEEEEcCCCEEEEecHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999986567899999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHH
Q psy3204 241 QMEKLQFIFLLYIL 254 (264)
Q Consensus 241 qieKLqkiIq~~l~ 254 (264)
.++++++.+..-=.
T Consensus 102 ~~~~l~~~l~~l~~ 115 (129)
T cd00584 102 QIEKLQKELAKLKD 115 (129)
T ss_pred HHHHHHHHHHHHHH
Confidence 99999988765433
No 7
>PF02996 Prefoldin: Prefoldin subunit; InterPro: IPR004127 This entry comprises of several prefoldin subunits. Prefoldin (PFD) is a chaperone that interacts exclusively with type II chaperonins, hetero-oligomers lacking an obligate co-chaperonin that are found only in eukaryotes (chaperonin-containing T-complex polypeptide-1 (CCT)) and archaea. Eukaryotic PFD is a multi-subunit complex containing six polypeptides in the molecular mass range of 14-23 kDa. In archaea, on the other hand, PFD is composed of two types of subunits, two alpha and four beta. The six subunits associate to form two back-to-back up-and-down eight-stranded barrels, from which hang six coiled coils. Each subunit contributes one (beta subunits) or two (alpha subunits) beta hairpin turns to the barrels. The coiled coils are formed by the N and C termini of an individual subunit. Overall, this unique arrangement resembles a jellyfish. The eukaryotic PFD hexamer is composed of six different subunits; however, these can be grouped into two alpha-like (PFD3 and -5) and four beta-like (PFD1, -2, -4, and -6) subunits based on amino acid sequence similarity with their archaeal counterparts. Eukaryotic PFD has a six-legged structure similar to that seen in the archaeal homologue [, ]. This family contains the archaeal alpha subunit, eukaryotic prefoldin subunits 3 and 5 and the UXT (ubiquitously expressed transcript) family. Eukaryotic PFD has been shown to bind both actin and tubulin co-translationally. The chaperone then delivers the target protein to CCT, interacting with the chaperonin through the tips of the coiled coils. No authentic target proteins of any archaeal PFD have been identified, to date.; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0016272 prefoldin complex; PDB: 1FXK_C 2ZDI_C.
Probab=99.90 E-value=6.5e-23 Score=161.15 Aligned_cols=101 Identities=30% Similarity=0.561 Sum_probs=90.3
Q ss_pred cCccchHHHHHHHHHHHHHHHHHHhhCCCCCCCceEEecCCceeEEEEEecCCeEEEEecCcEEEEeChHHHHHHHHHHH
Q psy3204 156 RRQPNNGALKRAQVKFQDSKESLDKITPSSQGNPIMVPLTDSMYVEGKIADADKVVIDIGTGFYVEKSIPDAQDYFKRRV 235 (264)
Q Consensus 156 ~lqqQLqqLk~Aq~Kf~eskeALe~Lk~~~egkEILVPLGSSLYVpGKL~DteKVLVDIGTGYYVEKSidEAiefleRRI 235 (264)
.+++++..|+..+.+|..++++|+.+++.+.+.++|||+|+++||||+|.++++|+|+||+|||||+|.++|++|+++|+
T Consensus 7 ~l~~~~~~l~~~~~e~~~~~~~l~~l~~~~~~~~~lvplg~~~~v~g~i~~~~~vlV~lG~~~~vE~s~~eA~~~l~~r~ 86 (120)
T PF02996_consen 7 NLQQQIEQLEEQIEEYEEAKETLEELKKEKKEHEILVPLGSGVFVPGKIPDTDKVLVSLGAGYYVEMSLEEAIEFLKKRI 86 (120)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHTT--TT-EEEEEECTTEEEEEE-SSTTEEEEEEETTEEEEEEHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCceeeecCCCCeEEEEEeCCCCEEEEEeeCCeEEEecHHHHHHHHHHHH
Confidence 35678999999999999999999999865789999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q psy3204 236 AFVTQQMEKLQFIFLLYILIF 256 (264)
Q Consensus 236 k~LeeqieKLqkiIq~~l~~~ 256 (264)
+.++++++++++.+...-..+
T Consensus 87 ~~l~~~~~~l~~~~~~~~~~~ 107 (120)
T PF02996_consen 87 KELEEQLEKLEKELAELQAQI 107 (120)
T ss_dssp HHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999888765443
No 8
>PRK03947 prefoldin subunit alpha; Reviewed
Probab=99.89 E-value=2.5e-22 Score=163.82 Aligned_cols=94 Identities=23% Similarity=0.468 Sum_probs=88.6
Q ss_pred hHHHHHHHHHHHHHHHHHHhhCCCCCCCceEEecCCceeEEEEEecCCeEEEEecCcEEEEeChHHHHHHHHHHHHHHHH
Q psy3204 161 NGALKRAQVKFQDSKESLDKITPSSQGNPIMVPLTDSMYVEGKIADADKVVIDIGTGFYVEKSIPDAQDYFKRRVAFVTQ 240 (264)
Q Consensus 161 LqqLk~Aq~Kf~eskeALe~Lk~~~egkEILVPLGSSLYVpGKL~DteKVLVDIGTGYYVEKSidEAiefleRRIk~Lee 240 (264)
+..|+.++.+|..++++|+.+++...+.+++||||+++||+|+|.++++|+|+||+|||||+++++|++|+++|++.|++
T Consensus 29 ~~~l~~~~~e~~~~~e~l~~l~~~~~~~e~lvplg~~~yv~~~v~~~~kV~v~lG~g~~vE~~~~eA~~~l~~~~~~l~~ 108 (140)
T PRK03947 29 LEELQASINELDTAKETLEELKSKGEGKETLVPIGAGSFVKAKVKDKDKVIVSLGAGYSAEKDLDEAIEILDKRKEELEK 108 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHhhcccCCCCeEEEEcCCCcEEEEEecCCCeEEEEcCCCEEEEecHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999986567899999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHH
Q psy3204 241 QMEKLQFIFLLYIL 254 (264)
Q Consensus 241 qieKLqkiIq~~l~ 254 (264)
+++++++.+...=.
T Consensus 109 ~~~~l~~~l~~~~~ 122 (140)
T PRK03947 109 ALEKLEEALQKLAS 122 (140)
T ss_pred HHHHHHHHHHHHHH
Confidence 99999988876543
No 9
>cd00890 Prefoldin Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. 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 structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils.
Probab=99.87 E-value=6.3e-21 Score=150.53 Aligned_cols=96 Identities=29% Similarity=0.556 Sum_probs=90.2
Q ss_pred hHHHHHHHHHHHHHHHHHHhhCCCCCCCceEEecCCceeEEEEEecCCeEEEEecCcEEEEeChHHHHHHHHHHHHHHHH
Q psy3204 161 NGALKRAQVKFQDSKESLDKITPSSQGNPIMVPLTDSMYVEGKIADADKVVIDIGTGFYVEKSIPDAQDYFKRRVAFVTQ 240 (264)
Q Consensus 161 LqqLk~Aq~Kf~eskeALe~Lk~~~egkEILVPLGSSLYVpGKL~DteKVLVDIGTGYYVEKSidEAiefleRRIk~Lee 240 (264)
+++|+..+.+|..+++.|+.+.....+.+++||+|+++||||+|.++++|+|+||+|||||++.++|++++++|++.+++
T Consensus 22 ~~~l~~~~~e~~~~~~~l~~l~~~~~~~~~l~~~g~~~~~~~~i~~~~~v~v~iG~~~~ve~~~~eA~~~l~~r~~~l~~ 101 (129)
T cd00890 22 LQKLEAQLTEYEKAKETLETLKKAEEEKELLVPLGAGLFVKAEVKDDDKVLVDLGTGVYVEKSLEEAIEFLKKRLETLEK 101 (129)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhccCCCCeEEEecCCceEEEEEECCCCEEEEEecCCEEEEecHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999987778889999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHH
Q psy3204 241 QMEKLQFIFLLYILIF 256 (264)
Q Consensus 241 qieKLqkiIq~~l~~~ 256 (264)
+++++++.+...-..+
T Consensus 102 ~~~~l~~~~~~~~~~~ 117 (129)
T cd00890 102 QIEKLEKQLEKLQDQI 117 (129)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 9999999887654443
No 10
>KOG3130|consensus
Probab=99.09 E-value=1e-10 Score=113.69 Aligned_cols=98 Identities=18% Similarity=0.354 Sum_probs=88.7
Q ss_pred cCccchHHHHHHHHHHHHHHHHHHhhCCCCCCCceEEecCCceeEEEEEecCCeEEEEecCcEEEEeChHHHHHHHHHHH
Q psy3204 156 RRQPNNGALKRAQVKFQDSKESLDKITPSSQGNPIMVPLTDSMYVEGKIADADKVVIDIGTGFYVEKSIPDAQDYFKRRV 235 (264)
Q Consensus 156 ~lqqQLqqLk~Aq~Kf~eskeALe~Lk~~~egkEILVPLGSSLYVpGKL~DteKVLVDIGTGYYVEKSidEAiefleRRI 235 (264)
+++-..+-++.....|...++.+..++ .+-..+||||+|.-.|+||+|+.++.|+|..|.|||.+.|..+|.+++++|+
T Consensus 14 ~~~~ete~~~~v~~dye~~~erl~~~~-kkLs~~Imvpig~~a~mpG~lVhTNevtv~~g~nyf~~CS~h~A~~I~~~R~ 92 (514)
T KOG3130|consen 14 RLEVETECRKKVDNDYEALRERLSTLP-KKLSYNIMVPIGPFAFMPGKLVHTNEVTVLLGDNYFAKCSAHQAVGIVEHRK 92 (514)
T ss_pred HhHHHHHHHHHHhhhHHHHHHHHHHhh-hhcccceeeecccccccccceeeechhhhhhccchHhhhhHHHHHHHHHHHH
Confidence 445556777778888999999999986 4678999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q psy3204 236 AFVTQQMEKLQFIFLLYIL 254 (264)
Q Consensus 236 k~LeeqieKLqkiIq~~l~ 254 (264)
++++++++++.+.|..++-
T Consensus 93 ~~~r~q~~~l~~~~~n~~~ 111 (514)
T KOG3130|consen 93 EHVRKQIDDLKKVMKNFES 111 (514)
T ss_pred HHHHHHHHHHHHHHHhhHH
Confidence 9999999999999988763
No 11
>KOG3047|consensus
Probab=98.87 E-value=1.4e-08 Score=86.85 Aligned_cols=90 Identities=17% Similarity=0.310 Sum_probs=79.3
Q ss_pred hHHHHHHHHHHHHHHHHHHhhC-CCCCCCceEEecCCceeEEEEEecCCeEEEEecCcEEEEeChHHHHHHHHHHHHHHH
Q psy3204 161 NGALKRAQVKFQDSKESLDKIT-PSSQGNPIMVPLTDSMYVEGKIADADKVVIDIGTGFYVEKSIPDAQDYFKRRVAFVT 239 (264)
Q Consensus 161 LqqLk~Aq~Kf~eskeALe~Lk-~~~egkEILVPLGSSLYVpGKL~DteKVLVDIGTGYYVEKSidEAiefleRRIk~Le 239 (264)
+..|+..-++|...+.+++.|. ...+..+.-+.||+++||.-.|.|+.+|+|-+|.|||+|++..+|++|++||...|+
T Consensus 39 ~dKl~eQ~aeY~kLk~t~eRL~eaahkel~~ktdLGcnfFmdi~VpDTk~i~VaL~~~fflElkLadAiKf~DRK~dlLk 118 (157)
T KOG3047|consen 39 FDKLQEQCAEYAKLKFTCERLLEAAHKELEGKTDLGCNFFMDIEVPDTKHIVVALCDDFFLELKLADAIKFCDRKMDLLK 118 (157)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhchhhhhccccccceeeEeeecCCcceEEEEeecceeeeehHHHHHHHHHHhHHHHH
Confidence 6677777788988888888864 234567788999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHH
Q psy3204 240 QQMEKLQFIFL 250 (264)
Q Consensus 240 eqieKLqkiIq 250 (264)
+-+++|++.-.
T Consensus 119 el~ekLqKdsm 129 (157)
T KOG3047|consen 119 ELMEKLQKDSM 129 (157)
T ss_pred HHHHHHHHhHH
Confidence 99999987643
No 12
>KOG3313|consensus
Probab=97.90 E-value=0.00012 Score=65.15 Aligned_cols=91 Identities=15% Similarity=0.277 Sum_probs=77.1
Q ss_pred chHHHHHHHHHHHHHHHHHHhhCCCC---CCCceEEecCCceeEEEEEecCCeEEEEecCcEEEEeChHHHHHHHHHHHH
Q psy3204 160 NNGALKRAQVKFQDSKESLDKITPSS---QGNPIMVPLTDSMYVEGKIADADKVVIDIGTGFYVEKSIPDAQDYFKRRVA 236 (264)
Q Consensus 160 QLqqLk~Aq~Kf~eskeALe~Lk~~~---egkEILVPLGSSLYVpGKL~DteKVLVDIGTGYYVEKSidEAiefleRRIk 236 (264)
+...|+.-+-++..+.+.+..+...+ +..+..+-|..++|.++.|.++++|-+=+|+...+|.+++||.+++++++.
T Consensus 59 ~~~~l~~kIPd~entLeiv~~l~~~~~~~~s~~t~f~lsd~vy~ka~V~~~~kV~LWLGAnVMlEY~leEAeaLLkknl~ 138 (187)
T KOG3313|consen 59 QKRRLKTKIPDIENTLEIVQTLIAKKDEGESFETTFLLSDGVYTKASVPPTDKVYLWLGANVMLEYDLEEAEALLKKNLT 138 (187)
T ss_pred HHHHHHhhchHHHHHHHHHHHHHhCcccCcceeEEEEecccceeeeecCCcCeEEEEecceeEEEecHHHHHHHHHhhHH
Confidence 34556666666777777777775332 236888999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHH
Q psy3204 237 FVTQQMEKLQFIFL 250 (264)
Q Consensus 237 ~LeeqieKLqkiIq 250 (264)
...++++.++..+.
T Consensus 139 sa~k~l~~~~~Dld 152 (187)
T KOG3313|consen 139 SAVKSLDVLEEDLD 152 (187)
T ss_pred HHHHHHHHHHHHHH
Confidence 99999999988764
No 13
>cd00890 Prefoldin Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. 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 structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils.
Probab=96.84 E-value=0.0017 Score=51.35 Aligned_cols=57 Identities=19% Similarity=0.278 Sum_probs=51.3
Q ss_pred CCCceEEecCCceeEEEEEecCCeEEEEecCcEEEEeChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy3204 186 QGNPIMVPLTDSMYVEGKIADADKVVIDIGTGFYVEKSIPDAQDYFKRRVAFVTQQMEKLQFIFLLYILI 255 (264)
Q Consensus 186 egkEILVPLGSSLYVpGKL~DteKVLVDIGTGYYVEKSidEAiefleRRIk~LeeqieKLqkiIq~~l~~ 255 (264)
.+.+|+|+||.+.||.-.+.+. ++.+++.+++++++++.+++++++++..+..+-..
T Consensus 67 ~~~~v~v~iG~~~~ve~~~~eA-------------~~~l~~r~~~l~~~~~~l~~~~~~~~~~~~~l~~~ 123 (129)
T cd00890 67 DDDKVLVDLGTGVYVEKSLEEA-------------IEFLKKRLETLEKQIEKLEKQLEKLQDQITELQEE 123 (129)
T ss_pred CCCEEEEEecCCEEEEecHHHH-------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5788999999999999998876 47899999999999999999999999999887654
No 14
>TIGR02338 gimC_beta prefoldin, beta subunit, archaeal. Chaperonins are cytosolic, ATP-dependent molecular chaperones, with a conserved toroidal architecture, that assist in the folding of nascent and/or denatured polypeptide chains. The group I chaperonin system consists of GroEL and GroES, and is found (usually) in bacteria and organelles of bacterial origin. The group II chaperonin system, called the thermosome in Archaea and TRiC or CCT in the Eukaryota, is structurally similar but only distantly related. Prefoldin, also called GimC, is a complex in Archaea and Eukaryota, that works with group II chaperonins. Members of this protein family are the archaeal clade of the beta class of prefoldin subunit. Closely related, but outside the scope of this family are the eukaryotic beta-class prefoldin subunits, Gim-1,3,4 and 6. The alpha class prefoldin subunits are more distantly related.
Probab=96.43 E-value=0.0062 Score=48.78 Aligned_cols=61 Identities=11% Similarity=0.220 Sum_probs=45.6
Q ss_pred HHHHHHHHHhhCCCCCCCceEEecCCceeEEEEEecCCeEEEEecCcEEEEeChHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy3204 171 FQDSKESLDKITPSSQGNPIMVPLTDSMYVEGKIADADKVVIDIGTGFYVEKSIPDAQDYFKRRVAFVTQQMEKLQFIFL 250 (264)
Q Consensus 171 f~eskeALe~Lk~~~egkEILVPLGSSLYVpGKL~DteKVLVDIGTGYYVEKSidEAiefleRRIk~LeeqieKLqkiIq 250 (264)
+.++..++++|...+.+..++.++|. +||+++.++|+..++.|++.++..++.+++.+.
T Consensus 33 ~~E~~~v~~eL~~l~~d~~vyk~VG~---------------------vlv~~~~~e~~~~l~~r~e~ie~~i~~lek~~~ 91 (110)
T TIGR02338 33 LKEAEKALEELERLPDDTPVYKSVGN---------------------LLVKTDKEEAIQELKEKKETLELRVKTLQRQEE 91 (110)
T ss_pred HHHHHHHHHHHHcCCCcchhHHHhch---------------------hhheecHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444445554434456677777776 999999999999999999999999988887765
Q ss_pred HH
Q psy3204 251 LY 252 (264)
Q Consensus 251 ~~ 252 (264)
..
T Consensus 92 ~l 93 (110)
T TIGR02338 92 RL 93 (110)
T ss_pred HH
Confidence 43
No 15
>PF13758 Prefoldin_3: Prefoldin subunit
Probab=96.43 E-value=0.0015 Score=53.30 Aligned_cols=91 Identities=13% Similarity=0.253 Sum_probs=73.0
Q ss_pred cchHHHHHHHHHHHHHHHHHHhhCC-CCCCCceEEecCCceeEEEEEecCCeEEEEecCcEEEEeChHHHHHHHHHHHHH
Q psy3204 159 PNNGALKRAQVKFQDSKESLDKITP-SSQGNPIMVPLTDSMYVEGKIADADKVVIDIGTGFYVEKSIPDAQDYFKRRVAF 237 (264)
Q Consensus 159 qQLqqLk~Aq~Kf~eskeALe~Lk~-~~egkEILVPLGSSLYVpGKL~DteKVLVDIGTGYYVEKSidEAiefleRRIk~ 237 (264)
..|..++.=-++|...++-|..++. .....+=|.-++..+ .|.+.+.+.|=.-+|.|=.+++|.+++++++.||+.+
T Consensus 2 ksL~hWq~w~aEYe~LKEEi~~l~~~~~~~~e~l~~i~r~f--~g~lv~~kEi~~ilG~~~~i~Rt~~Qvv~~l~RRiDY 79 (99)
T PF13758_consen 2 KSLYHWQTWEAEYEGLKEEIEALPEDDDATREDLLRIRRDF--GGSLVTEKEIKEILGEGQGITRTREQVVDVLSRRIDY 79 (99)
T ss_pred chHHHHHHHHHHHHHHHHHHHhccccCCCCHHHHHHHHHhc--CcccccHHHHHHHhCCCCCCCcCHHHHHHHHHHHHHH
Confidence 4578888889999999999999964 222333345555443 3888888877777888888999999999999999999
Q ss_pred HHHHHHHHHHHHHH
Q psy3204 238 VTQQMEKLQFIFLL 251 (264)
Q Consensus 238 LeeqieKLqkiIq~ 251 (264)
+++|++.|++.+..
T Consensus 80 V~~Ni~tleKql~~ 93 (99)
T PF13758_consen 80 VQQNIETLEKQLEA 93 (99)
T ss_pred HHHHHHHHHHHHHH
Confidence 99999999998864
No 16
>PF01920 Prefoldin_2: Prefoldin subunit; InterPro: IPR002777 Prefoldin (PFD) is a chaperone that interacts exclusively with type II chaperonins, hetero-oligomers lacking an obligate co-chaperonin that are found only in eukaryotes (chaperonin-containing T-complex polypeptide-1 (CCT)) and archaea. Eukaryotic PFD is a multi-subunit complex containing six polypeptides in the molecular mass range of 14-23 kDa. In archaea, on the other hand, PFD is composed of two types of subunits, two alpha and four beta. The six subunits associate to form two back-to-back up-and-down eight-stranded barrels, from which hang six coiled coils. Each subunit contributes one (beta subunits) or two (alpha subunits) beta hairpin turns to the barrels. The coiled coils are formed by the N and C termini of an individual subunit. Overall, this unique arrangement resembles a jellyfish. The eukaryotic PFD hexamer is composed of six different subunits; however, these can be grouped into two alpha-like (PFD3 and -5) and four beta-like (PFD1, -2, -4, and -6) subunits based on amino acid sequence similarity with their archaeal counterparts. Eukaryotic PFD has a six-legged structure similar to that seen in the archaeal homologue [, ]. This family contains the archaeal beta subunit, eukaryotic prefoldin subunits 1, 2, 4 and 6. Eukaryotic PFD has been shown to bind both actin and tubulin co-translationally. The chaperone then delivers the target protein to CCT, interacting with the chaperonin through the tips of the coiled coils. No authentic target proteins of any archaeal PFD have been identified, to date.; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0016272 prefoldin complex; PDB: 2ZDI_B 3AEI_B 2ZQM_A 1FXK_A.
Probab=96.40 E-value=0.06 Score=41.19 Aligned_cols=47 Identities=17% Similarity=0.298 Sum_probs=39.4
Q ss_pred eEEEEecCcEEEEeChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy3204 209 KVVIDIGTGFYVEKSIPDAQDYFKRRVAFVTQQMEKLQFIFLLYILIF 256 (264)
Q Consensus 209 KVLVDIGTGYYVEKSidEAiefleRRIk~LeeqieKLqkiIq~~l~~~ 256 (264)
+|...|| +.||+.+.+++++.++.+++.+++.++++++.+...-..+
T Consensus 46 ~~y~~vG-~~fv~~~~~~~~~~L~~~~~~~~~~i~~l~~~~~~l~~~l 92 (106)
T PF01920_consen 46 KVYKSVG-KMFVKQDKEEAIEELEERIEKLEKEIKKLEKQLKYLEKKL 92 (106)
T ss_dssp EEEEEET-TEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hhHHHHh-HHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5555665 5799999999999999999999999999998887665544
No 17
>TIGR00293 prefoldin, archaeal alpha subunit/eukaryotic subunit 5. This model finds a set of small proteins from the Archaea and from Aquifex aeolicus that may represent two orthologous groups. The proteins are predicted to be mostly coiled coil, and may hit large numbers of proteins that contain coiled coil regions.
Probab=96.28 E-value=0.0072 Score=48.57 Aligned_cols=87 Identities=13% Similarity=0.258 Sum_probs=64.5
Q ss_pred CccchHHHHHHHHHHHHHHHHHHhhCCCCCCCceEEecCCceeEEEEEecCCeEEEEecCcEEEEeChHHHH--------
Q psy3204 157 RQPNNGALKRAQVKFQDSKESLDKITPSSQGNPIMVPLTDSMYVEGKIADADKVVIDIGTGFYVEKSIPDAQ-------- 228 (264)
Q Consensus 157 lqqQLqqLk~Aq~Kf~eskeALe~Lk~~~egkEILVPLGSSLYVpGKL~DteKVLVDIGTGYYVEKSidEAi-------- 228 (264)
++++++.|...+..+..+++.++... +++ -+++++ +...++|.+|.|.||+.++++..
T Consensus 11 l~~~i~~l~~~i~~l~~~i~e~~~~~------~~L------~~l~~~--~~~~~lv~lg~~~~v~~~v~~~~~v~v~iG~ 76 (126)
T TIGR00293 11 LQQQVESLQAQIAALRALIAELETAI------ETL------EDLKGA--EGKETLVPVGAGSFVKAKVKDTDKVLVSIGS 76 (126)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH------HHH------Hhcccc--CCCeEEEEcCCCeEEEEEeCCCCEEEEEcCC
Confidence 45566666666666666666665542 333 223444 56889999999999999999887
Q ss_pred -----HHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy3204 229 -----DYFKRRVAFVTQQMEKLQFIFLLYILIFC 257 (264)
Q Consensus 229 -----efleRRIk~LeeqieKLqkiIq~~l~~~~ 257 (264)
.-++.-+++++++++.+++.+..+-..+-
T Consensus 77 g~~vE~~~~eA~~~l~~~~~~l~~~~~~l~~~l~ 110 (126)
T TIGR00293 77 GYYVEKDAEEAIEFLKKRIEELEKAIEKLQEALA 110 (126)
T ss_pred CEEEEecHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 66799999999999999999887765543
No 18
>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=96.10 E-value=0.014 Score=46.25 Aligned_cols=70 Identities=11% Similarity=0.136 Sum_probs=48.8
Q ss_pred hHHHHHHHHHHHHHHHHHHhhCCCCCCCceEEecCCceeEEEEEecCCeEEEEecCcEEEEeChHHHHHHHHHHHHHHHH
Q psy3204 161 NGALKRAQVKFQDSKESLDKITPSSQGNPIMVPLTDSMYVEGKIADADKVVIDIGTGFYVEKSIPDAQDYFKRRVAFVTQ 240 (264)
Q Consensus 161 LqqLk~Aq~Kf~eskeALe~Lk~~~egkEILVPLGSSLYVpGKL~DteKVLVDIGTGYYVEKSidEAiefleRRIk~Lee 240 (264)
++.|.....+...+.+.|+.+ ..+..++.++|. +||+++.++|...++.|++.++.
T Consensus 22 ~~~l~~~~~E~~~v~~EL~~l---~~d~~vy~~VG~---------------------vfv~~~~~ea~~~Le~~~e~le~ 77 (105)
T cd00632 22 RQKVEAQLNENKKALEELEKL---ADDAEVYKLVGN---------------------VLVKQEKEEARTELKERLETIEL 77 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHcC---CCcchHHHHhhh---------------------HHhhccHHHHHHHHHHHHHHHHH
Confidence 344444444444444444443 345566666665 99999999999999999999999
Q ss_pred HHHHHHHHHHHHHH
Q psy3204 241 QMEKLQFIFLLYIL 254 (264)
Q Consensus 241 qieKLqkiIq~~l~ 254 (264)
.++++++.+...-.
T Consensus 78 ~i~~l~~~~~~l~~ 91 (105)
T cd00632 78 RIKRLERQEEDLQE 91 (105)
T ss_pred HHHHHHHHHHHHHH
Confidence 99998887765433
No 19
>PRK03947 prefoldin subunit alpha; Reviewed
Probab=95.17 E-value=0.022 Score=46.73 Aligned_cols=51 Identities=14% Similarity=0.315 Sum_probs=42.9
Q ss_pred cCCeEEEEecCcEEEEeChHHHHH-------------HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy3204 206 DADKVVIDIGTGFYVEKSIPDAQD-------------YFKRRVAFVTQQMEKLQFIFLLYILIF 256 (264)
Q Consensus 206 DteKVLVDIGTGYYVEKSidEAie-------------fleRRIk~LeeqieKLqkiIq~~l~~~ 256 (264)
+..+++|.||.|+||+.++.+..+ -++.-+++++++++.+++.+..+-...
T Consensus 54 ~~~e~lvplg~~~yv~~~v~~~~kV~v~lG~g~~vE~~~~eA~~~l~~~~~~l~~~~~~l~~~l 117 (140)
T PRK03947 54 EGKETLVPIGAGSFVKAKVKDKDKVIVSLGAGYSAEKDLDEAIEILDKRKEELEKALEKLEEAL 117 (140)
T ss_pred CCCeEEEEcCCCcEEEEEecCCCeEEEEcCCCEEEEecHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 568999999999999999876655 678999999999999999888765443
No 20
>cd00584 Prefoldin_alpha Prefoldin alpha subunit; Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. 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 structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils.
Probab=94.96 E-value=0.06 Score=43.42 Aligned_cols=58 Identities=14% Similarity=0.222 Sum_probs=52.0
Q ss_pred CCCceEEecCCceeEEEEEecCCeEEEEecCcEEEEeChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy3204 186 QGNPIMVPLTDSMYVEGKIADADKVVIDIGTGFYVEKSIPDAQDYFKRRVAFVTQQMEKLQFIFLLYILIF 256 (264)
Q Consensus 186 egkEILVPLGSSLYVpGKL~DteKVLVDIGTGYYVEKSidEAiefleRRIk~LeeqieKLqkiIq~~l~~~ 256 (264)
...+++||||++.||.-.+.+.. +.++.-++.++++++.+++++.+++..+..+....
T Consensus 67 ~~~~v~v~iG~g~~vE~~~~eA~-------------~~l~~r~~~l~~~~~~l~~~l~~l~~~~~~~~~~l 124 (129)
T cd00584 67 DTDKVLVDLGTGYYVEKDLEEAI-------------EFLDKKIEELTKQIEKLQKELAKLKDQINTLEAEL 124 (129)
T ss_pred CCCEEEEEcCCCEEEEecHHHHH-------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45899999999999999998766 67899999999999999999999999999887653
No 21
>PRK01203 prefoldin subunit alpha; Provisional
Probab=91.71 E-value=0.28 Score=41.79 Aligned_cols=48 Identities=19% Similarity=0.400 Sum_probs=41.5
Q ss_pred ecCCeEEEEecCcEEEEeChHHHHH-------------HHHHHHHHHHHHHHHHHHHHHHH
Q psy3204 205 ADADKVVIDIGTGFYVEKSIPDAQD-------------YFKRRVAFVTQQMEKLQFIFLLY 252 (264)
Q Consensus 205 ~DteKVLVDIGTGYYVEKSidEAie-------------fleRRIk~LeeqieKLqkiIq~~ 252 (264)
.+...|||.+|.|-||.-.+.+..+ -.++|+++|++++++|+++++.=
T Consensus 46 ~~~~eiLVPLg~slYV~gki~d~~kVlVdIGTGy~VEK~~e~kie~L~~~ie~Le~~i~~K 106 (130)
T PRK01203 46 DNSKELLISIGSGIFADGNIKKDKDLIVPIGSGVYIAEERERTIERLKENLEDLKDSIQKL 106 (130)
T ss_pred CCCCeEEEEccCCceEeEEecCCCeEEEEcCCCeEEEecHHHHHHHHHHHHHHHHHHHHHH
Confidence 3568999999999999988887765 36889999999999999998753
No 22
>COG1730 GIM5 Predicted prefoldin, molecular chaperone implicated in de novo protein folding [Posttranslational modification, protein turnover, chaperones]
Probab=87.24 E-value=0.72 Score=39.82 Aligned_cols=43 Identities=21% Similarity=0.505 Sum_probs=28.0
Q ss_pred eEEEEecCcEEEEeChHH-------------HHHHHHHHHHHHHHHHHHHHHHHHH
Q psy3204 209 KVVIDIGTGFYVEKSIPD-------------AQDYFKRRVAFVTQQMEKLQFIFLL 251 (264)
Q Consensus 209 KVLVDIGTGYYVEKSidE-------------AiefleRRIk~LeeqieKLqkiIq~ 251 (264)
.+||.||.|-||.-.+.+ |..-++.=++.|++++++|.+.++.
T Consensus 57 E~LVpvGag~fv~~kv~~~~kviV~iGsg~~ae~~~~eAie~l~k~~~~l~~~~~~ 112 (145)
T COG1730 57 EVLVPVGAGLFVKAKVKDMDKVIVSIGSGYYAEKSADEAIEFLKKRIEELEKAIEK 112 (145)
T ss_pred eEEEEcCCCceEEEEeccCceEEEEcCCceeeeecHHHHHHHHHHHHHHHHHHHHH
Confidence 677777777777666665 4455666667777776666665543
No 23
>PF02996 Prefoldin: Prefoldin subunit; InterPro: IPR004127 This entry comprises of several prefoldin subunits. Prefoldin (PFD) is a chaperone that interacts exclusively with type II chaperonins, hetero-oligomers lacking an obligate co-chaperonin that are found only in eukaryotes (chaperonin-containing T-complex polypeptide-1 (CCT)) and archaea. Eukaryotic PFD is a multi-subunit complex containing six polypeptides in the molecular mass range of 14-23 kDa. In archaea, on the other hand, PFD is composed of two types of subunits, two alpha and four beta. The six subunits associate to form two back-to-back up-and-down eight-stranded barrels, from which hang six coiled coils. Each subunit contributes one (beta subunits) or two (alpha subunits) beta hairpin turns to the barrels. The coiled coils are formed by the N and C termini of an individual subunit. Overall, this unique arrangement resembles a jellyfish. The eukaryotic PFD hexamer is composed of six different subunits; however, these can be grouped into two alpha-like (PFD3 and -5) and four beta-like (PFD1, -2, -4, and -6) subunits based on amino acid sequence similarity with their archaeal counterparts. Eukaryotic PFD has a six-legged structure similar to that seen in the archaeal homologue [, ]. This family contains the archaeal alpha subunit, eukaryotic prefoldin subunits 3 and 5 and the UXT (ubiquitously expressed transcript) family. Eukaryotic PFD has been shown to bind both actin and tubulin co-translationally. The chaperone then delivers the target protein to CCT, interacting with the chaperonin through the tips of the coiled coils. No authentic target proteins of any archaeal PFD have been identified, to date.; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0016272 prefoldin complex; PDB: 1FXK_C 2ZDI_C.
Probab=86.72 E-value=1.3 Score=34.76 Aligned_cols=55 Identities=15% Similarity=0.230 Sum_probs=33.5
Q ss_pred CCCceEEecCCceeEEEEEecCCeEEEEecCcEEEEeChHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy3204 186 QGNPIMVPLTDSMYVEGKIADADKVVIDIGTGFYVEKSIPDAQDYFKRRVAFVTQQMEKLQFIFLLYI 253 (264)
Q Consensus 186 egkEILVPLGSSLYVpGKL~DteKVLVDIGTGYYVEKSidEAiefleRRIk~LeeqieKLqkiIq~~l 253 (264)
...+|+|+||++.||.=.+.+..++ .+.=++.+++.++.+++++.+++..+..+.
T Consensus 57 ~~~~vlV~lG~~~~vE~s~~eA~~~-------------l~~r~~~l~~~~~~l~~~~~~~~~~~~~~~ 111 (120)
T PF02996_consen 57 DTDKVLVSLGAGYYVEMSLEEAIEF-------------LKKRIKELEEQLEKLEKELAELQAQIEQLE 111 (120)
T ss_dssp STTEEEEEEETTEEEEEEHHHHHHH-------------HHHHHHHHHHHHHHHHHHHHHHHHHHHCHH
T ss_pred CCCEEEEEeeCCeEEEecHHHHHHH-------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3566777777777777666654432 455555666666666666666666555443
No 24
>PRK09343 prefoldin subunit beta; Provisional
Probab=77.52 E-value=4.2 Score=33.48 Aligned_cols=40 Identities=13% Similarity=0.144 Sum_probs=25.7
Q ss_pred eEEEEecCcEEEEeChHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy3204 209 KVVIDIGTGFYVEKSIPDAQDYFKRRVAFVTQQMEKLQFIF 249 (264)
Q Consensus 209 KVLVDIGTGYYVEKSidEAiefleRRIk~LeeqieKLqkiI 249 (264)
+|.-.|| ..||..+.++|++-++.|+++++..++.+++..
T Consensus 55 ~VYk~VG-~vlv~qd~~e~~~~l~~r~E~ie~~ik~lekq~ 94 (121)
T PRK09343 55 PIYKIVG-NLLVKVDKTKVEKELKERKELLELRSRTLEKQE 94 (121)
T ss_pred hhHHHhh-HHHhhccHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444 356777888887777777777776666665544
No 25
>KOG3905|consensus
Probab=77.44 E-value=6.5 Score=39.37 Aligned_cols=70 Identities=17% Similarity=0.310 Sum_probs=59.3
Q ss_pred CCCCCceEEecCCceeEEEEEecCCeEEEEecCcEEEEeChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccc
Q psy3204 184 SSQGNPIMVPLTDSMYVEGKIADADKVVIDIGTGFYVEKSIPDAQDYFKRRVAFVTQQMEKLQFIFLLYILIFCSLIIFN 263 (264)
Q Consensus 184 ~~egkEILVPLGSSLYVpGKL~DteKVLVDIGTGYYVEKSidEAiefleRRIk~LeeqieKLqkiIq~~l~~~~~~~~~~ 263 (264)
...+-.+++|||... ..-++|--+.|-.|.-+|...+++--++-.+..+.++.-|+.|-+.|-.-.||.
T Consensus 202 ~~~de~~llPL~~dt-----------Lt~NlGi~vlVV~TK~D~~s~leke~eyrDehfdfiq~~lRkFCLr~GaaLiyT 270 (473)
T KOG3905|consen 202 SSADEHVLLPLGQDT-----------LTHNLGIPVLVVCTKCDAVSVLEKEHEYRDEHFDFIQSHLRKFCLRYGAALIYT 270 (473)
T ss_pred CccccccccccCCcc-----------hhhcCCCcEEEEEeccchhhHhhhcchhhHHHHHHHHHHHHHHHHHcCceeEEe
Confidence 345667899999754 345789999999999999999999999999999999999999988887777765
Q ss_pred C
Q psy3204 264 S 264 (264)
Q Consensus 264 ~ 264 (264)
|
T Consensus 271 S 271 (473)
T KOG3905|consen 271 S 271 (473)
T ss_pred e
Confidence 4
No 26
>COG1382 GimC Prefoldin, chaperonin cofactor [Posttranslational modification, protein turnover, chaperones]
Probab=71.58 E-value=5.8 Score=33.55 Aligned_cols=38 Identities=21% Similarity=0.287 Sum_probs=22.6
Q ss_pred eEEEEecCcEEEEeChHHHHHHHHHHHHHHHHHHHHHHH
Q psy3204 209 KVVIDIGTGFYVEKSIPDAQDYFKRRVAFVTQQMEKLQF 247 (264)
Q Consensus 209 KVLVDIGTGYYVEKSidEAiefleRRIk~LeeqieKLqk 247 (264)
.|-=.|| +.+|..+.++|.+=++.|++.|+..++.|++
T Consensus 54 ~vYk~VG-~llvk~~k~~~~~eL~er~E~Le~ri~tLek 91 (119)
T COG1382 54 PVYKKVG-NLLVKVSKEEAVDELEERKETLELRIKTLEK 91 (119)
T ss_pred HHHHHhh-hHHhhhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3333444 4566777777777666666666655554443
No 27
>KOG4098|consensus
Probab=66.75 E-value=15 Score=31.97 Aligned_cols=68 Identities=15% Similarity=0.199 Sum_probs=49.8
Q ss_pred hHHHHHHHHHHHHHHHHHHhhCCCCCCCceEEecCCceeEEEEEecCCeEEEEecCcEEEEeChHHHHHHHHHHHHHHHH
Q psy3204 161 NGALKRAQVKFQDSKESLDKITPSSQGNPIMVPLTDSMYVEGKIADADKVVIDIGTGFYVEKSIPDAQDYFKRRVAFVTQ 240 (264)
Q Consensus 161 LqqLk~Aq~Kf~eskeALe~Lk~~~egkEILVPLGSSLYVpGKL~DteKVLVDIGTGYYVEKSidEAiefleRRIk~Lee 240 (264)
+..|.+-..++.-.+++|+.+.+.. .. | =-| .|..||+|+.+-.=.+++.++.+++
T Consensus 38 i~~LE~d~~EH~lVi~tlk~~dp~R---KC--------f------------RmI-gGvLVErTVkeVlP~L~~nke~i~~ 93 (140)
T KOG4098|consen 38 ITDLEMDLREHKLVIETLKDLDPTR---KC--------F------------RMI-GGVLVERTVKEVLPILQTNKENIEK 93 (140)
T ss_pred HHHHHHhHHHHHHHHHHHHhcChhh---HH--------H------------HHh-ccchhhhhHHHHhHHHHhhHHHHHH
Confidence 7778888888888888888875322 11 1 011 2678999999999999988888888
Q ss_pred HHHHHHHHHHHH
Q psy3204 241 QMEKLQFIFLLY 252 (264)
Q Consensus 241 qieKLqkiIq~~ 252 (264)
.+.+|.+.+..-
T Consensus 94 ~i~~l~~qL~~k 105 (140)
T KOG4098|consen 94 VIKKLTDQLVQK 105 (140)
T ss_pred HHHHHHHHHHHH
Confidence 888887766543
No 28
>PRK14011 prefoldin subunit alpha; Provisional
Probab=63.35 E-value=18 Score=31.05 Aligned_cols=23 Identities=9% Similarity=0.332 Sum_probs=18.4
Q ss_pred CCCceEEecCCceeEEEEEecCC
Q psy3204 186 QGNPIMVPLTDSMYVEGKIADAD 208 (264)
Q Consensus 186 egkEILVPLGSSLYVpGKL~Dte 208 (264)
...+++|++|++.||.=.+.+.-
T Consensus 68 d~dkVlVdIGtGy~VEk~~~eA~ 90 (144)
T PRK14011 68 DPDKAILGVGSDIYLEKDVSEVI 90 (144)
T ss_pred CCCeEEEEccCCeEEEecHHHHH
Confidence 45789999999999988777643
No 29
>PF01330 RuvA_N: RuvA N terminal domain; InterPro: IPR013849 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. This entry represents domain I of RuvA, which has an OB-fold structure. This domain forms the RuvA tetramer contacts [].; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1HJP_A 1D8L_B 1CUK_A 1C7Y_A 1IXR_B 2ZTC_A 2ZTD_B 2H5X_A 2ZTE_A 1BVS_E ....
Probab=57.96 E-value=27 Score=25.15 Aligned_cols=30 Identities=33% Similarity=0.550 Sum_probs=23.3
Q ss_pred eeEEEEEe--cCCeEEEEecC-cEEEEeChHHH
Q psy3204 198 MYVEGKIA--DADKVVIDIGT-GFYVEKSIPDA 227 (264)
Q Consensus 198 LYVpGKL~--DteKVLVDIGT-GYYVEKSidEA 227 (264)
.|++|+|. +++.|+||+|. ||-|-.+....
T Consensus 3 ~~l~G~v~~~~~~~vvi~~~GvGy~v~v~~~~~ 35 (61)
T PF01330_consen 3 AYLKGKVVEKNPDYVVIDVNGVGYEVFVPSNTL 35 (61)
T ss_dssp EEEEEEEEEEESSEEEEEETTEEEEEEE-HHHH
T ss_pred cEEEEEEEEEcCCEEEEEECCEEEEEEeCCchH
Confidence 58999998 58999999986 88887776543
No 30
>KOG3048|consensus
Probab=54.94 E-value=5.9 Score=34.93 Aligned_cols=55 Identities=11% Similarity=0.291 Sum_probs=38.5
Q ss_pred CCCceEEecCCceeEEEEEecCCeEEEEecCcEEEEeChHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy3204 186 QGNPIMVPLTDSMYVEGKIADADKVVIDIGTGFYVEKSIPDAQDYFKRRVAFVTQQMEKLQFIFLLYI 253 (264)
Q Consensus 186 egkEILVPLGSSLYVpGKL~DteKVLVDIGTGYYVEKSidEAiefleRRIk~LeeqieKLqkiIq~~l 253 (264)
.....||.||-+-||.=...+ +..|| +.=++|+.+.++.+++-+.+=......+-
T Consensus 81 d~~k~lVDIGTGYyVEK~~e~--------akdyf-----kRKve~l~kq~e~i~~i~~eK~~~~~~v~ 135 (153)
T KOG3048|consen 81 DNSKFLVDIGTGYYVEKDAED--------AKDYF-----KRKVEYLTKQIEQIEGILKEKTRTRASVM 135 (153)
T ss_pred cccceeEeccCceEEeechHH--------HHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 356889999999999866554 33455 44477888888888877766555544443
No 31
>PRK05771 V-type ATP synthase subunit I; Validated
Probab=50.99 E-value=63 Score=33.05 Aligned_cols=37 Identities=8% Similarity=-0.023 Sum_probs=32.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q psy3204 224 IPDAQDYFKRRVAFVTQQMEKLQFIFLLYILIFCSLI 260 (264)
Q Consensus 224 idEAiefleRRIk~LeeqieKLqkiIq~~l~~~~~~~ 260 (264)
.+++.+-+++|++++++.++++++.++.+...+..++
T Consensus 213 p~~~l~~l~~~l~~l~~~~~~~~~~l~~~~~~~~~~~ 249 (646)
T PRK05771 213 PSELIREIKEELEEIEKERESLLEELKELAKKYLEEL 249 (646)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6788888999999999999999999999988876654
No 32
>PF05377 FlaC_arch: Flagella accessory protein C (FlaC); InterPro: IPR008039 Although archaeal flagella appear superficially similar to those of bacteria, they are quite distinct []. In several archaea, the flagellin genes are followed immediately by the flagellar accessory genes flaCDEFGHIJ. The gene products may have a role in translocation, secretion, or assembly of the flagellum. FlaC is a protein whose exact role is unknown but it has been shown to be membrane-associated (by immuno-blotting fractionated cells) [].
Probab=50.38 E-value=51 Score=24.67 Aligned_cols=33 Identities=9% Similarity=0.124 Sum_probs=28.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy3204 225 PDAQDYFKRRVAFVTQQMEKLQFIFLLYILIFC 257 (264)
Q Consensus 225 dEAiefleRRIk~LeeqieKLqkiIq~~l~~~~ 257 (264)
+-.+.-+++..+.+++.++++++.++-+++.|-
T Consensus 13 ~~~i~tvk~en~~i~~~ve~i~envk~ll~lYE 45 (55)
T PF05377_consen 13 ESSINTVKKENEEISESVEKIEENVKDLLSLYE 45 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445677889999999999999999999999984
No 33
>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=38.10 E-value=71 Score=22.45 Aligned_cols=29 Identities=14% Similarity=0.259 Sum_probs=24.6
Q ss_pred eChHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy3204 222 KSIPDAQDYFKRRVAFVTQQMEKLQFIFL 250 (264)
Q Consensus 222 KSidEAiefleRRIk~LeeqieKLqkiIq 250 (264)
.+.+++...+++|.+.++++++.++....
T Consensus 32 ~~~~~~~~~l~~~~~~i~~~i~~L~~~~~ 60 (65)
T PF09278_consen 32 PPCADRRALLEEKLEEIEEQIAELQALRA 60 (65)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46788889999999999999999986544
No 34
>PF14962 AIF-MLS: Mitochondria Localisation Sequence; PDB: 1M6I_A.
Probab=30.92 E-value=16 Score=32.94 Aligned_cols=30 Identities=20% Similarity=0.506 Sum_probs=0.0
Q ss_pred ecCcEEEEeChHHHHHHHHHHHHHHHHHHH
Q psy3204 214 IGTGFYVEKSIPDAQDYFKRRVAFVTQQME 243 (264)
Q Consensus 214 IGTGYYVEKSidEAiefleRRIk~Leeqie 243 (264)
+|.|||+=||+.+=++-|+.||..|++.-.
T Consensus 57 ~gag~YaYkTv~~dq~Ry~eRi~~l~~r~k 86 (180)
T PF14962_consen 57 SGAGYYAYKTVKSDQARYNERISELKERPK 86 (180)
T ss_dssp ------------------------------
T ss_pred EeeEEEEEEeecchhHHHHHHHHHHhhcCc
Confidence 688999999999999999999999976543
No 35
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=30.21 E-value=1e+02 Score=27.46 Aligned_cols=31 Identities=23% Similarity=0.429 Sum_probs=25.2
Q ss_pred eeEEEEEec--CCeEEEEecC-cEEEEeChHHHH
Q psy3204 198 MYVEGKIAD--ADKVVIDIGT-GFYVEKSIPDAQ 228 (264)
Q Consensus 198 LYVpGKL~D--teKVLVDIGT-GYYVEKSidEAi 228 (264)
.|+.|+|.+ ++.|+||+|. ||.|-.+..-..
T Consensus 3 ~~l~G~i~~~~~~~vvi~~~GvGY~V~vs~~~~~ 36 (197)
T PRK14603 3 AYLSGVVLEKREGSAVLLAGGVGLEVQCPAPTLA 36 (197)
T ss_pred ceEEEEEEEecCCEEEEEECCEEEEEEcCHHHHH
Confidence 489999984 7889999976 999998866443
No 36
>PRK14609 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional
Probab=28.42 E-value=29 Score=31.78 Aligned_cols=51 Identities=33% Similarity=0.667 Sum_probs=27.6
Q ss_pred cchhhhhhhhhhheeeccccccccccccCCCCCccceecCCCChHHHHHHHHhhhhhhhhhhcchhhccc
Q psy3204 21 FPQLTQLKNQLDSVSFQALALSAMSVNQSGGEGMQQIDLTKLAFPQLTQLKNQLDSVSFQALGLCFKWQG 90 (264)
Q Consensus 21 ~~~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~~~i~l~~l~~~ql~~~k~q~~~~~~~~~~~~~~~~~ 90 (264)
+|++.++++.+.. .|+-...||. .|+--+=|.+ -++++|+. ..+.||-|||
T Consensus 219 ~p~l~~i~~~l~~---~ga~~~~mSG-----SG~tvf~l~~--------~~~~~~~~---~~~~~~~~~~ 269 (269)
T PRK14609 219 YPEIAEIKEKLYR---SGALYAAMSG-----SGSSVFGIFK--------KPPNLDEF---AFGICFCWQG 269 (269)
T ss_pred ChHHHHHHHHHHh---CCCCeEEEeC-----ccceeEEEEC--------ChHHcCcc---ccCceEEecC
Confidence 4677777776543 2222233444 2333333322 24466664 5689999998
No 37
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=26.85 E-value=1.4e+02 Score=26.47 Aligned_cols=32 Identities=19% Similarity=0.249 Sum_probs=25.5
Q ss_pred eeEEEEEe--cCCeEEEEecC-cEEEEeChHHHHH
Q psy3204 198 MYVEGKIA--DADKVVIDIGT-GFYVEKSIPDAQD 229 (264)
Q Consensus 198 LYVpGKL~--DteKVLVDIGT-GYYVEKSidEAie 229 (264)
.|+.|+|. .++.|+||+|. ||-|-.+.....+
T Consensus 3 ~~l~G~v~~~~~~~vvi~~~GvGY~v~~s~~~~~~ 37 (194)
T PRK14605 3 SSLNGILEASGKDWAVINVSGVGFRCYMPATSPAL 37 (194)
T ss_pred ceEEEEEEEecCCEEEEEECCEEEEEEeCHHHHHh
Confidence 48899998 47889999976 9999988766543
No 38
>PF00384 Molybdopterin: Molybdopterin oxidoreductase; InterPro: IPR006656 This domain is found in a number of molybdopterin-containing oxidoreductases, tungsten formylmethanofuran dehydrogenase subunit d (FwdD) and molybdenum formylmethanofuran dehydrogenase subunit (FmdD); where a single domain constitutes almost the entire subunit. The formylmethanofuran dehydrogenase catalyses the first step in methane formation from CO2 in methanogenic archaea and has a molybdopterin dinucleotide cofactor []. ; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 1TI2_G 1VLE_M 1VLD_U 1VLF_O 1TI4_I 1TI6_E 3DMR_A 4DMR_A 1H5N_C 1E5V_A ....
Probab=24.92 E-value=87 Score=29.03 Aligned_cols=28 Identities=21% Similarity=0.332 Sum_probs=23.1
Q ss_pred cCcEEEEeChHHHHHHHHHHHHHHHHHH
Q psy3204 215 GTGFYVEKSIPDAQDYFKRRVAFVTQQM 242 (264)
Q Consensus 215 GTGYYVEKSidEAiefleRRIk~Leeqi 242 (264)
|.|=|++.|.|||.+.+.+|++.+.++-
T Consensus 13 g~~~~~~isWdeAl~~ia~~l~~~~~~~ 40 (432)
T PF00384_consen 13 GDGKFVRISWDEALDEIAEKLKEIIDKY 40 (432)
T ss_dssp TSSSEEE--HHHHHHHHHHHHHHHHHHC
T ss_pred CCCCEEEccHHHHHHHhhhhcccccccc
Confidence 7788999999999999999999987653
No 39
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=23.49 E-value=1.8e+02 Score=25.91 Aligned_cols=31 Identities=16% Similarity=0.352 Sum_probs=24.6
Q ss_pred eeEEEEEe--cCCeEEEEecC-cEEEEeChHHHH
Q psy3204 198 MYVEGKIA--DADKVVIDIGT-GFYVEKSIPDAQ 228 (264)
Q Consensus 198 LYVpGKL~--DteKVLVDIGT-GYYVEKSidEAi 228 (264)
.|+.|+|. .++.|+||+|. ||-|-.+.....
T Consensus 3 ~~i~G~i~~~~~~~viie~~GvGY~v~vs~~~~~ 36 (195)
T PRK14604 3 ASIRGIIQSIGNDHLIVETGGVGLLIYAPRSVLA 36 (195)
T ss_pred ceEEEEEEEEcCCEEEEEECCEEEEEEeCHHHHH
Confidence 48899998 47889999977 999988855443
No 40
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=23.35 E-value=1.5e+02 Score=26.42 Aligned_cols=31 Identities=10% Similarity=0.333 Sum_probs=24.2
Q ss_pred eeEEEEEe--cCCeEEEE-e-cCcEEEEeChHHHH
Q psy3204 198 MYVEGKIA--DADKVVID-I-GTGFYVEKSIPDAQ 228 (264)
Q Consensus 198 LYVpGKL~--DteKVLVD-I-GTGYYVEKSidEAi 228 (264)
.|+.|+|. +++.|+|| + |-||-|-.+..-..
T Consensus 3 ~~l~G~v~~~~~~~vvie~~~GvGY~v~~~~~~~~ 37 (188)
T PRK14606 3 AGISGRVLKKSGNVLLVETKSGVVFEIVCDVQTSE 37 (188)
T ss_pred ceEEEEEEEecCCEEEEEeCCcEEEEEEeCHHHHH
Confidence 48999998 47899999 4 88998888755443
No 41
>PF08800 VirE_N: VirE N-terminal domain; InterPro: IPR014907 This domain is associated with the N terminus of Virulence E proteins. The function of the domain is unknown.
Probab=23.25 E-value=1e+02 Score=25.63 Aligned_cols=52 Identities=17% Similarity=0.213 Sum_probs=35.3
Q ss_pred hhhhhhhhheeecccccccccccc-CCCCCccceecCCCChHHHHHHHHhhhh
Q psy3204 25 TQLKNQLDSVSFQALALSAMSVNQ-SGGEGMQQIDLTKLAFPQLTQLKNQLDS 76 (264)
Q Consensus 25 ~~~~~~~~~~~~~~~~~~~m~~~~-~~~~~~~~i~l~~l~~~ql~~~k~q~~~ 76 (264)
.++|++|.-|++.|.--..-...+ ..-.|--.||++.|+.+++.++|+++-.
T Consensus 3 ~~~K~~LP~vt~~g~F~~~r~~~~l~~~sglv~lDiD~l~~ee~~~~r~~l~~ 55 (136)
T PF08800_consen 3 KELKKKLPYVTPSGTFSGGRNADNLKAYSGLVVLDIDHLDPEEAEELRQLLFE 55 (136)
T ss_pred hHHHhcCCEEEEEEEECCCcchhhhhhCCCcEEEEeCCCCHHHHHHHHHHHhc
Confidence 467888888877664433111111 1233555699999999999999999876
No 42
>PF01486 K-box: K-box region; InterPro: IPR002487 MADS genes in plants encode key developmental regulators of vegetative and reproductive development. The majority of the plant MADS proteins share a stereotypical MIKC structure. It comprises (from N- to C-terminal) an N-terminal domain, which is, however, present only in a minority of proteins; a MADS domain (see PDOC00302 from PROSITEDOC, IPR002100 from INTERPRO), which is the major determinant of DNA-binding but which also performs dimerisation and accessory factor binding functions; a weakly conserved intervening (I) domain, which constitutes a key molecular determinant for the selective formation of DNA-binding dimers; a keratin-like (K-box) domain, which promotes protein dimerisation; and a C-terminal (C) domain, which is involved in transcriptional activation or in the formation of ternary or quaternary protein complexes. The 80-amino acid K-box domain was originally identified as a region with low but significant similarity to a region of keratin, which is part of the coiled-coil sequence constituting the central rod-shaped domain of keratin [, , ]. The K-box protein-protein interaction domain which mediates heterodimerization of MIKC-type MADS proteins contains several heptad repeats in which the first and the fourth positions are occupied by hydrophobic amino acids suggesting that the K-box domain forms three amphipathic alpha-helices referred to as K1, K2, and K3 [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=23.02 E-value=61 Score=25.36 Aligned_cols=22 Identities=50% Similarity=0.703 Sum_probs=20.1
Q ss_pred ecCCCChHHHHHHHHhhhhhhhhhhc
Q psy3204 58 DLTKLAFPQLTQLKNQLDSVSFQALG 83 (264)
Q Consensus 58 ~l~~l~~~ql~~~k~q~~~~~~~~~~ 83 (264)
||..|++++|.+|.+||+. .|.
T Consensus 42 dL~~Ls~~eL~~LE~~Le~----aL~ 63 (100)
T PF01486_consen 42 DLESLSLKELQQLEQQLES----ALK 63 (100)
T ss_pred cccccchHHHHHHHHhhhh----hHH
Confidence 7999999999999999998 665
No 43
>PF07889 DUF1664: Protein of unknown function (DUF1664); InterPro: IPR012458 The members of this family are hypothetical plant proteins of unknown function. The region featured in this family is approximately 100 amino acids long.
Probab=22.86 E-value=1.8e+02 Score=24.79 Aligned_cols=33 Identities=12% Similarity=0.110 Sum_probs=26.6
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy3204 223 SIPDAQDYFKRRVAFVTQQMEKLQFIFLLYILI 255 (264)
Q Consensus 223 SidEAiefleRRIk~LeeqieKLqkiIq~~l~~ 255 (264)
++..|++++..||+.|..++++..++.+..-.+
T Consensus 58 ~l~~tKkhLsqRId~vd~klDe~~ei~~~i~~e 90 (126)
T PF07889_consen 58 SLSSTKKHLSQRIDRVDDKLDEQKEISKQIKDE 90 (126)
T ss_pred HHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHH
Confidence 467889999999999999999888877765544
No 44
>TIGR03017 EpsF chain length determinant protein EpsF. Sequences in this family of proteins are members of the chain length determinant family (pfam02706) which includes the wzc protein from E.coli. This family of proteins are homologous to the EpsF protein of the methanolan biosynthesis operon of Methylobacillus species strain 12S. The distribution of this protein appears to be restricted to a subset of exopolysaccharide operons containing a syntenic grouping of genes including a variant of the EpsH exosortase protein. Exosortase has been proposed to be involved in the targetting and processing of proteins containing the PEP-CTERM domain to the exopolysaccharide layer.
Probab=22.86 E-value=1.7e+02 Score=27.96 Aligned_cols=33 Identities=15% Similarity=0.170 Sum_probs=29.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy3204 224 IPDAQDYFKRRVAFVTQQMEKLQFIFLLYILIF 256 (264)
Q Consensus 224 idEAiefleRRIk~LeeqieKLqkiIq~~l~~~ 256 (264)
...|.+|++++++.+++++++.+..++.|-.+.
T Consensus 169 ~~~~~~fl~~ql~~~~~~l~~ae~~l~~fr~~~ 201 (444)
T TIGR03017 169 AQKAALWFVQQIAALREDLARAQSKLSAYQQEK 201 (444)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 346789999999999999999999999998875
No 45
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=22.63 E-value=1.8e+02 Score=25.82 Aligned_cols=31 Identities=19% Similarity=0.440 Sum_probs=24.9
Q ss_pred eeEEEEEe--cCCeEEEEecC-cEEEEeChHHHH
Q psy3204 198 MYVEGKIA--DADKVVIDIGT-GFYVEKSIPDAQ 228 (264)
Q Consensus 198 LYVpGKL~--DteKVLVDIGT-GYYVEKSidEAi 228 (264)
.|+.|+|. .++.|+||+|. ||-|-.+.....
T Consensus 3 ~~l~G~v~~~~~~~vvi~v~GvGY~v~v~~~~~~ 36 (191)
T TIGR00084 3 GFLFGKVIEVSKPKIIIEVNGVGYELQVPMTCAY 36 (191)
T ss_pred ceEEEEEEEEcCCEEEEEECCEEEEEEecHHHHH
Confidence 48899998 47889999976 998888866554
No 46
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=22.54 E-value=1.7e+02 Score=26.47 Aligned_cols=30 Identities=23% Similarity=0.101 Sum_probs=24.2
Q ss_pred eeEEEEEe--cCCeEEEEecC-cEEEEeChHHH
Q psy3204 198 MYVEGKIA--DADKVVIDIGT-GFYVEKSIPDA 227 (264)
Q Consensus 198 LYVpGKL~--DteKVLVDIGT-GYYVEKSidEA 227 (264)
.|++|+|. .++.|+||+|. ||-|-.+..-.
T Consensus 3 ~~l~G~v~~~~~~~vvidv~GVGY~v~vs~~~~ 35 (196)
T PRK13901 3 NKIYGKIIEKKESSIVIMATPFEFELLVSSFCL 35 (196)
T ss_pred cEEEEEEEEEeCCEEEEEeCCEEEEEEecHHHH
Confidence 48999998 47889999976 99988886544
No 47
>PF10400 Vir_act_alpha_C: Virulence activator alpha C-term; InterPro: IPR018309 Phenolic acids, also called substituted hydroxycinnamic acids, are abundant in the plant kingdom because they are involved in the structure of plant cell walls and are present in some vacuoles. In plant-soil ecosystems they are released as free acids by hemicellulases produced by several fungi and bacteria. Of these weak acids, the most abundant are p-coumaric, ferulic, and caffeic acids, considered to be natural toxins that inhibit the growth of microorganisms, especially at low pHs. In spite of this chemical stress, some bacteria can use phenolic acids as a sole source of carbon. For other microorganisms, these compounds induce a specific response by which the organism adapts to its environment. The ubiquitous lactic acid bacterium Lactobacillus plantarum exhibits an inducible phenolic acid decarboxylase (PAD) activity which converts these substrates into less-toxic vinyl phenol derivatives. PadR acts as a repressor of padA gene expression in the phenolic acid stress response []. This entry represents the C-terminal domain.; PDB: 1YG2_A.
Probab=22.23 E-value=2.4e+02 Score=20.79 Aligned_cols=30 Identities=10% Similarity=0.041 Sum_probs=25.5
Q ss_pred eChHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy3204 222 KSIPDAQDYFKRRVAFVTQQMEKLQFIFLL 251 (264)
Q Consensus 222 KSidEAiefleRRIk~LeeqieKLqkiIq~ 251 (264)
.+.+++++.++++++..++.++.++.+.+.
T Consensus 17 ~~~~~~~~~l~~~~~~~~~~l~~~~~~~~~ 46 (90)
T PF10400_consen 17 LDPEEAIELLEERREQHEERLAEYEEIEQE 46 (90)
T ss_dssp S-HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 468899999999999999999999887655
No 48
>PF02388 FemAB: FemAB family; InterPro: IPR003447 The femAB operon codes for two nearly identical approximately 50kDa proteins involved in the formation of the Staphylococcal pentaglycine interpeptide bridge in peptidoglycan []. These proteins are also considered as a factor influencing the level of methicillin resistance [].; GO: 0016755 transferase activity, transferring amino-acyl groups; PDB: 1XE4_A 1NE9_A 3GKR_A 1XIX_A 1P4N_A 1XF8_A 1LRZ_A.
Probab=22.01 E-value=2e+02 Score=27.90 Aligned_cols=31 Identities=16% Similarity=0.250 Sum_probs=25.8
Q ss_pred EEEEeChHHHHHHHHHHHHHHHHHHHHHHHH
Q psy3204 218 FYVEKSIPDAQDYFKRRVAFVTQQMEKLQFI 248 (264)
Q Consensus 218 YYVEKSidEAiefleRRIk~LeeqieKLqki 248 (264)
+.++.+.+++++.++.+++.+++.+++++..
T Consensus 234 ~~A~l~~~~~~~~l~~~~~~~~~~i~~l~~~ 264 (406)
T PF02388_consen 234 FLAELNGKEYLESLQEKLEKLEKEIEKLEEK 264 (406)
T ss_dssp EEEEECCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred EEEEEcHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4588899999999999888888887777765
No 49
>TIGR02338 gimC_beta prefoldin, beta subunit, archaeal. Chaperonins are cytosolic, ATP-dependent molecular chaperones, with a conserved toroidal architecture, that assist in the folding of nascent and/or denatured polypeptide chains. The group I chaperonin system consists of GroEL and GroES, and is found (usually) in bacteria and organelles of bacterial origin. The group II chaperonin system, called the thermosome in Archaea and TRiC or CCT in the Eukaryota, is structurally similar but only distantly related. Prefoldin, also called GimC, is a complex in Archaea and Eukaryota, that works with group II chaperonins. Members of this protein family are the archaeal clade of the beta class of prefoldin subunit. Closely related, but outside the scope of this family are the eukaryotic beta-class prefoldin subunits, Gim-1,3,4 and 6. The alpha class prefoldin subunits are more distantly related.
Probab=21.86 E-value=2.1e+02 Score=22.82 Aligned_cols=73 Identities=10% Similarity=0.135 Sum_probs=45.0
Q ss_pred cchHHHHHHHHHHHHHHHHHHhhCCCCC----CCceEEecCCceeEEEEEecCCeEEEEecCcEEEEeCh-------HHH
Q psy3204 159 PNNGALKRAQVKFQDSKESLDKITPSSQ----GNPIMVPLTDSMYVEGKIADADKVVIDIGTGFYVEKSI-------PDA 227 (264)
Q Consensus 159 qQLqqLk~Aq~Kf~eskeALe~Lk~~~e----gkEILVPLGSSLYVpGKL~DteKVLVDIGTGYYVEKSi-------dEA 227 (264)
.++++|....++...+.+.|+.++++.. =-.|||.-+- +. +..+. +.+
T Consensus 24 ~q~~~le~~~~E~~~v~~eL~~l~~d~~vyk~VG~vlv~~~~-----------~e----------~~~~l~~r~e~ie~~ 82 (110)
T TIGR02338 24 TQKQQVEAQLKEAEKALEELERLPDDTPVYKSVGNLLVKTDK-----------EE----------AIQELKEKKETLELR 82 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCCcchhHHHhchhhheecH-----------HH----------HHHHHHHHHHHHHHH
Confidence 3488999999999999999999986532 1236665331 11 11223 555
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q psy3204 228 QDYFKRRVAFVTQQMEKLQFIFLLY 252 (264)
Q Consensus 228 iefleRRIk~LeeqieKLqkiIq~~ 252 (264)
++-++++++.+++++.++++.++.-
T Consensus 83 i~~lek~~~~l~~~l~e~q~~l~~~ 107 (110)
T TIGR02338 83 VKTLQRQEERLREQLKELQEKIQEA 107 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5556666666666666666655543
No 50
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=21.26 E-value=2.2e+02 Score=22.43 Aligned_cols=29 Identities=17% Similarity=0.316 Sum_probs=24.8
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy3204 223 SIPDAQDYFKRRVAFVTQQMEKLQFIFLL 251 (264)
Q Consensus 223 SidEAiefleRRIk~LeeqieKLqkiIq~ 251 (264)
+.++..+.++++++.|+++++.|+..+..
T Consensus 76 ~~~~~~~~l~~~~~~l~~~i~~l~~~~~~ 104 (113)
T cd01109 76 TIPERLELLEEHREELEEQIAELQETLAY 104 (113)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46788999999999999999999877743
No 51
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator. This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=21.07 E-value=2e+02 Score=23.48 Aligned_cols=30 Identities=23% Similarity=0.321 Sum_probs=24.6
Q ss_pred eChHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy3204 222 KSIPDAQDYFKRRVAFVTQQMEKLQFIFLL 251 (264)
Q Consensus 222 KSidEAiefleRRIk~LeeqieKLqkiIq~ 251 (264)
.+.++..++++++++.|+.++++|+.....
T Consensus 75 ~~~~~~~~~l~~~~~~l~~~i~~L~~~~~~ 104 (127)
T TIGR02047 75 KSCSDVNALLDEHISHVRARIIKLQALIEQ 104 (127)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 466788999999999999999998766544
No 52
>PLN02318 phosphoribulokinase/uridine kinase
Probab=20.57 E-value=1.8e+02 Score=31.20 Aligned_cols=111 Identities=15% Similarity=0.110 Sum_probs=68.5
Q ss_pred CCCCCCCCCCcccCccchHHHHHHHHHHHHHHHHHHh-hCCCC----CCCceEEec------CCceeEEEEEe----cCC
Q psy3204 144 LPSAVPLCGGTLRRQPNNGALKRAQVKFQDSKESLDK-ITPSS----QGNPIMVPL------TDSMYVEGKIA----DAD 208 (264)
Q Consensus 144 ~~~~~~~~~~t~~lqqQLqqLk~Aq~Kf~eskeALe~-Lk~~~----egkEILVPL------GSSLYVpGKL~----Dte 208 (264)
.|.++ -+|...++++|+..|+.-..+|..+++-|+. +...+ ...-.+-+- ..+.|+.|--. .+-
T Consensus 490 ~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 568 (656)
T PLN02318 490 SPAAL-NQGAITQLSEQISSLNERMDEFTSRIEELNSKLSIKKNSPSQQNLALQAEACNGSAPTSYFVSGLGNGSLTGSI 568 (656)
T ss_pred Cchhh-ccchHHHHHHhhcchhhhhHHHHHHHHHHhhccccccCChhhhhhhccccccCCCCcchhhhccCCCccccccc
Confidence 34444 6899999999999999999999888888776 32110 000001110 11233332111 000
Q ss_pred eEEEEecCcEEEEeChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy3204 209 KVVIDIGTGFYVEKSIPDAQDYFKRRVAFVTQQMEKLQFIFLLYILI 255 (264)
Q Consensus 209 KVLVDIGTGYYVEKSidEAiefleRRIk~LeeqieKLqkiIq~~l~~ 255 (264)
--.-..-.+.+-|-.+-|-+..+.|--..+-.+++.|...+..++-+
T Consensus 569 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 615 (656)
T PLN02318 569 LPLSSSSSQLAKESPLMEEILGIARGQRQVMHQLDNLSNLLHESLGE 615 (656)
T ss_pred ccccccccccCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 01112233455578888888999998899999999998888877744
No 53
>PF12841 YvrJ: YvrJ protein family; InterPro: IPR024419 This entry is represents a family of uncharacterised protein. The function of the Bacillus subtilis YvrJ protein is not known, but its expression is regulated by the cell envelope stress-inducible sigma factor YvrI [].
Probab=20.48 E-value=1e+02 Score=21.36 Aligned_cols=19 Identities=11% Similarity=0.291 Sum_probs=15.3
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q psy3204 231 FKRRVAFVTQQMEKLQFIF 249 (264)
Q Consensus 231 leRRIk~LeeqieKLqkiI 249 (264)
+++|++.|.+.+.+|.+.|
T Consensus 20 ~E~kld~L~~~i~~L~~~I 38 (38)
T PF12841_consen 20 IEKKLDELTESINELSEAI 38 (38)
T ss_pred HHHHHHHHHHHHHHHHhhC
Confidence 5788899999888887653
No 54
>cd02769 MopB_DMSOR-BSOR-TMAOR The MopB_DMSOR-BSOR-TMAOR CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its cellular location and oligomerization state are organism-dependent. For example, in Rhodobacter sphaeriodes and Rhodobacter capsulatus, it is an 82-kDa monomeric soluble protein found in the periplasmic space; in E. coli, it is membrane-bound and exists as a heterotrimer. BSOR catalyzes the reduction of biotin sulfixode to biotin, and is unique among Mo enzymes because no additional auxiliary proteins or cofactors are required. TMAOR is similar to DMSOR, but its only natural substrate is TMAO. Members of this CD belong to the molybdopterin_binding (MopB) superfamily of proteins.
Probab=20.30 E-value=1.2e+02 Score=30.83 Aligned_cols=27 Identities=22% Similarity=0.242 Sum_probs=24.9
Q ss_pred cCcEEEEeChHHHHHHHHHHHHHHHHH
Q psy3204 215 GTGFYVEKSIPDAQDYFKRRVAFVTQQ 241 (264)
Q Consensus 215 GTGYYVEKSidEAiefleRRIk~Leeq 241 (264)
|.|=|++-|.|||.+.+.+|++.+.++
T Consensus 69 G~g~~~~ISWdEAld~IA~kl~~i~~~ 95 (609)
T cd02769 69 GKEEFVRVSWDEALDLVAAELKRVRKT 95 (609)
T ss_pred CCCCeEEecHHHHHHHHHHHHHHHHHh
Confidence 678999999999999999999999764
No 55
>PF05185 PRMT5: PRMT5 arginine-N-methyltransferase; InterPro: IPR007857 The human homologue of Saccharomyces cerevisiae Skb1 (Shk1 kinase-binding protein 1) is a protein methyltransferase []. These proteins seem to play a role in Jak signalling.; GO: 0008168 methyltransferase activity, 0005737 cytoplasm; PDB: 2Y1W_C 2Y1X_D 2V7E_B 2V74_H 3R0Q_G 3B3F_B 3B3J_A 3B3G_A 3UA3_A 3UA4_B ....
Probab=20.22 E-value=1.5e+02 Score=29.55 Aligned_cols=29 Identities=48% Similarity=0.834 Sum_probs=21.1
Q ss_pred CCeEEEEecCc---------------------EEEEeChHHHHHHHHHHHH
Q psy3204 207 ADKVVIDIGTG---------------------FYVEKSIPDAQDYFKRRVA 236 (264)
Q Consensus 207 teKVLVDIGTG---------------------YYVEKSidEAiefleRRIk 236 (264)
.++|++|||+| |-|||+ +.|...++++++
T Consensus 186 ~~~vVldVGAGrGpL~~~al~A~~~~~~a~~VyAVEkn-~~A~~~l~~~v~ 235 (448)
T PF05185_consen 186 KDKVVLDVGAGRGPLSMFALQAGARAGGAVKVYAVEKN-PNAVVTLQKRVN 235 (448)
T ss_dssp TT-EEEEES-TTSHHHHHHHHTTHHHCCESEEEEEESS-THHHHHHHHHHH
T ss_pred cceEEEEeCCCccHHHHHHHHHHHHhCCCeEEEEEcCC-HhHHHHHHHHHH
Confidence 78899999987 889998 567777776654
No 56
>cd04772 HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.
Probab=20.09 E-value=1.4e+02 Score=23.46 Aligned_cols=26 Identities=12% Similarity=0.093 Sum_probs=22.5
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHH
Q psy3204 223 SIPDAQDYFKRRVAFVTQQMEKLQFI 248 (264)
Q Consensus 223 SidEAiefleRRIk~LeeqieKLqki 248 (264)
+.+++.+.++++.+.++++++.|++.
T Consensus 73 ~~~~~~~ll~~~~~~l~~~i~~L~~~ 98 (99)
T cd04772 73 IVASALALVDAAHALLQRYRQQLDQE 98 (99)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 35689999999999999999999764
Done!