Query psy17364
Match_columns 312
No_of_seqs 186 out of 1698
Neff 6.6
Searched_HMMs 46136
Date Fri Aug 16 20:30:07 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17364.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17364hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0264 Tsf Translation elonga 100.0 6.3E-82 1.4E-86 581.5 24.9 255 20-308 2-289 (296)
2 TIGR00116 tsf translation elon 100.0 6.2E-80 1.3E-84 576.0 28.0 253 20-308 1-284 (290)
3 PRK09377 tsf elongation factor 100.0 5.8E-79 1.3E-83 569.5 28.0 252 20-308 2-284 (290)
4 KOG1071|consensus 100.0 1.6E-67 3.5E-72 486.4 19.3 275 22-300 45-335 (340)
5 PF00889 EF_TS: Elongation fac 100.0 3.2E-53 7E-58 384.3 15.6 188 79-296 1-221 (221)
6 PRK12332 tsf elongation factor 100.0 7.5E-52 1.6E-56 368.4 18.7 162 20-185 1-198 (198)
7 CHL00098 tsf elongation factor 100.0 2.6E-49 5.5E-54 352.2 17.8 159 23-185 1-196 (200)
8 CHL00098 tsf elongation factor 99.9 1.2E-24 2.6E-29 194.0 7.3 106 185-300 55-199 (200)
9 PRK12332 tsf elongation factor 99.9 1.2E-21 2.7E-26 174.7 8.8 103 185-297 58-198 (198)
10 COG0264 Tsf Translation elonga 99.7 2.6E-16 5.7E-21 146.2 10.5 116 57-185 126-278 (296)
11 TIGR00116 tsf translation elon 99.7 2.2E-16 4.7E-21 148.3 9.0 115 57-185 122-273 (290)
12 PF00889 EF_TS: Elongation fac 99.6 1.5E-16 3.2E-21 144.7 6.4 121 54-184 64-221 (221)
13 PRK09377 tsf elongation factor 99.6 1.5E-15 3.2E-20 142.8 11.1 115 56-185 122-273 (290)
14 PF00627 UBA: UBA/TS-N domain; 98.5 1.8E-07 4E-12 61.4 4.9 37 22-59 1-37 (37)
15 PRK06369 nac nascent polypepti 97.7 5.6E-05 1.2E-09 61.9 5.4 42 20-61 73-114 (115)
16 TIGR00264 alpha-NAC-related pr 97.7 7E-05 1.5E-09 61.3 5.0 40 21-60 76-115 (116)
17 smart00165 UBA Ubiquitin assoc 97.3 0.00059 1.3E-08 44.3 5.0 35 24-59 2-36 (37)
18 cd00194 UBA Ubiquitin Associat 97.2 0.00084 1.8E-08 43.8 5.2 36 24-60 2-37 (38)
19 KOG1071|consensus 97.1 0.002 4.4E-08 61.1 7.8 109 184-305 104-229 (340)
20 COG1308 EGD2 Transcription fac 95.3 0.041 8.9E-07 45.5 5.4 40 21-60 82-121 (122)
21 PF14555 UBA_4: UBA-like domai 95.2 0.049 1.1E-06 36.7 4.9 37 25-61 2-38 (43)
22 PF03943 TAP_C: TAP C-terminal 94.1 0.044 9.5E-07 38.6 2.6 37 25-61 2-38 (51)
23 smart00804 TAP_C C-terminal do 93.0 0.3 6.5E-06 35.9 5.5 41 22-62 11-51 (63)
24 PF00542 Ribosomal_L12: Riboso 91.0 0.34 7.4E-06 36.1 3.8 36 23-58 13-54 (68)
25 PF02845 CUE: CUE domain; Int 89.4 1.4 3E-05 29.3 5.4 38 24-61 2-40 (42)
26 PRK06771 hypothetical protein; 86.5 0.76 1.6E-05 36.4 3.1 25 22-46 67-91 (93)
27 smart00546 CUE Domain that may 85.7 2.8 6.2E-05 27.8 5.3 39 23-61 2-41 (43)
28 PF06972 DUF1296: Protein of u 82.3 3.9 8.5E-05 29.7 5.0 39 23-61 5-44 (60)
29 TIGR00855 L12 ribosomal protei 77.8 3.7 8.1E-05 34.3 4.3 28 23-50 71-98 (126)
30 PRK00157 rplL 50S ribosomal pr 74.1 5.6 0.00012 33.1 4.4 27 23-49 68-94 (123)
31 cd00387 Ribosomal_L7_L12 Ribos 71.1 11 0.00023 31.6 5.5 27 23-49 73-99 (127)
32 CHL00083 rpl12 ribosomal prote 68.8 13 0.00028 31.3 5.4 27 23-49 76-102 (131)
33 COG0222 RplL Ribosomal protein 67.8 7.5 0.00016 32.3 3.7 27 23-49 69-95 (124)
34 PF08938 HBS1_N: HBS1 N-termin 57.9 3.5 7.7E-05 31.4 0.1 36 27-62 32-70 (79)
35 COG4008 Predicted metal-bindin 57.0 32 0.0007 28.9 5.6 37 24-62 115-151 (153)
36 KOG0944|consensus 54.5 12 0.00026 39.4 3.4 28 35-62 646-673 (763)
37 PRK05441 murQ N-acetylmuramic 54.1 17 0.00036 34.6 4.1 32 30-61 242-273 (299)
38 cd04772 HTH_TioE_rpt1 First He 51.7 68 0.0015 25.2 6.6 38 24-63 47-85 (99)
39 PF11626 Rap1_C: TRF2-interact 50.3 32 0.00069 26.5 4.4 34 27-61 1-34 (87)
40 TIGR00274 N-acetylmuramic acid 48.8 25 0.00053 33.4 4.3 32 30-61 237-268 (291)
41 cd04773 HTH_TioE_rpt2 Second H 41.8 1.2E+02 0.0025 24.2 6.6 42 24-66 47-90 (108)
42 PF03474 DMA: DMRTA motif; In 38.6 29 0.00064 23.1 2.1 18 42-59 21-38 (39)
43 PRK12570 N-acetylmuramic acid- 38.2 40 0.00087 32.1 3.9 32 30-61 238-269 (296)
44 cd00215 PTS_IIA_lac PTS_IIA, P 38.2 42 0.00092 26.6 3.5 29 33-61 11-40 (97)
45 PRK09591 celC cellobiose phosp 37.0 45 0.00097 26.9 3.5 29 33-61 16-45 (104)
46 TIGR00823 EIIA-LAC phosphotran 36.8 46 0.00099 26.6 3.5 29 33-61 13-42 (99)
47 cd04788 HTH_NolA-AlbR Helix-Tu 35.5 1.2E+02 0.0027 23.5 5.7 40 24-67 47-86 (96)
48 KOG2561|consensus 34.0 57 0.0012 33.1 4.3 36 35-74 314-349 (568)
49 PRK08248 O-acetylhomoserine am 33.4 83 0.0018 31.4 5.5 48 261-310 377-426 (431)
50 PF02954 HTH_8: Bacterial regu 33.4 48 0.001 21.7 2.6 19 42-60 11-29 (42)
51 PF14117 DUF4287: Domain of un 32.4 1.1E+02 0.0023 22.4 4.5 39 24-62 3-43 (61)
52 PRK10454 PTS system N,N'-diace 31.5 60 0.0013 26.7 3.4 34 28-61 22-56 (115)
53 PF08285 DPM3: Dolichol-phosph 30.0 21 0.00046 28.1 0.5 25 38-62 63-87 (91)
54 COG2103 Predicted sugar phosph 29.7 1.1E+02 0.0023 29.1 5.1 32 30-61 240-271 (298)
55 cd01106 HTH_TipAL-Mta Helix-Tu 29.3 1.9E+02 0.0041 22.6 5.9 34 25-62 48-81 (103)
56 cd01107 HTH_BmrR Helix-Turn-He 29.2 1.8E+02 0.0039 23.0 5.8 36 24-62 48-83 (108)
57 COG0789 SoxR Predicted transcr 27.9 2E+02 0.0043 22.8 6.0 26 24-50 47-72 (124)
58 TIGR03595 Obg_CgtA_exten Obg f 27.5 97 0.0021 22.9 3.7 36 43-78 20-55 (69)
59 cd00591 HU_IHF Integration hos 26.9 92 0.002 23.3 3.6 26 24-49 3-28 (87)
60 PF00216 Bac_DNA_binding: Bact 26.8 91 0.002 23.4 3.6 26 24-49 4-29 (90)
61 PF02255 PTS_IIA: PTS system, 26.7 86 0.0019 24.8 3.5 27 35-61 12-39 (96)
62 smart00422 HTH_MERR helix_turn 25.8 90 0.002 22.0 3.2 22 24-46 47-68 (70)
63 smart00668 CTLH C-terminal to 25.7 54 0.0012 22.3 1.9 14 49-62 14-27 (58)
64 TIGR03884 sel_bind_Methan sele 25.2 59 0.0013 24.7 2.1 21 48-68 23-43 (74)
65 PRK10564 maltose regulon perip 25.0 77 0.0017 30.4 3.4 32 39-73 262-293 (303)
66 KOG1715|consensus 24.9 1.6E+02 0.0035 26.3 5.1 27 22-48 131-157 (187)
67 cd04780 HTH_MerR-like_sg5 Heli 24.9 2.7E+02 0.0058 21.7 6.0 39 23-61 46-85 (95)
68 cd00592 HTH_MerR-like Helix-Tu 24.4 2.9E+02 0.0062 21.1 6.1 38 24-62 46-85 (100)
69 PF10607 CLTH: CTLH/CRA C-term 24.4 86 0.0019 25.7 3.3 21 40-62 7-27 (145)
70 KOG1364|consensus 24.0 1.4E+02 0.0031 29.2 5.0 40 23-62 6-46 (356)
71 cd04785 HTH_CadR-PbrR-like Hel 23.3 3.3E+02 0.0072 22.1 6.6 43 24-67 47-92 (126)
72 PRK08133 O-succinylhomoserine 23.0 73 0.0016 31.2 2.9 49 261-311 340-390 (390)
73 PRK06702 O-acetylhomoserine am 22.8 76 0.0016 31.9 3.1 51 261-312 374-425 (432)
74 PF13411 MerR_1: MerR HTH fami 22.5 87 0.0019 22.2 2.6 23 24-47 46-68 (69)
75 smart00411 BHL bacterial (prok 22.2 1.3E+02 0.0028 22.6 3.7 26 24-49 4-29 (90)
76 CHL00102 rps20 ribosomal prote 22.1 1.4E+02 0.003 23.6 3.8 24 38-61 32-60 (93)
77 COG5207 UBP14 Isopeptidase T [ 22.1 31 0.00067 35.6 0.1 33 29-61 624-658 (749)
78 cd04776 HTH_GnyR Helix-Turn-He 21.5 4.2E+02 0.009 21.4 6.7 45 24-69 45-95 (118)
79 cd04787 HTH_HMRTR_unk Helix-Tu 20.8 4E+02 0.0086 21.9 6.6 47 23-70 46-95 (133)
80 smart00685 DM14 Repeats in fly 20.7 2E+02 0.0042 20.9 4.0 23 48-73 20-42 (59)
81 PF03765 CRAL_TRIO_N: CRAL/TRI 20.7 99 0.0021 21.2 2.5 21 41-61 34-54 (55)
82 cd04765 HTH_MlrA-like_sg2 Heli 20.5 3.9E+02 0.0084 20.9 6.2 36 27-62 50-88 (99)
No 1
>COG0264 Tsf Translation elongation factor Ts [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=6.3e-82 Score=581.50 Aligned_cols=255 Identities=37% Similarity=0.606 Sum_probs=238.4
Q ss_pred cccCHHHHHHHHHHhCCCHHHHHHHHHHhcCCHHHHHHHHHHHHHhhcHHHHHhhhhhccCCceEEEEe--CCcEEEEEE
Q psy17364 20 LTTNKSLLGKLRKKTGYSFTNCKKALDLNEQDLGKAEKWLQEQAKELGWAKASKLAGRKTSQGLISIAV--EGKHATMVE 97 (312)
Q Consensus 20 ~~~~~~lik~LR~~Tga~~~dCKkAL~e~~gD~ekA~e~Lr~~~~k~G~~~A~Kr~~R~t~eG~V~~~~--~~~~gvlvE 97 (312)
+.+++++||+||++||+|||||||||+|++||+|+|++|||+ +|.++|.||++|.++||+|.+++ +++.|+|||
T Consensus 2 ~~ita~~VKeLRe~TgAGMmdCKkAL~E~~Gd~EkAie~LR~----kG~akA~KKa~R~AaEGli~~~~~~~~~~av~vE 77 (296)
T COG0264 2 AEITAALVKELREKTGAGMMDCKKALEEANGDIEKAIEWLRE----KGIAKAAKKAGRIAAEGLIAAKVDGDGKKAVLVE 77 (296)
T ss_pred CcccHHHHHHHHHHhCCcHHHHHHHHHHcCCCHHHHHHHHHH----hchHhhhhhcCcchhcceEEEEEcCCCcEEEEEE
Confidence 468999999999999999999999999999999999999999 59999999999999999999998 556999999
Q ss_pred EeccchhhhhhhHHHHHHHHHHHHHHhcCCCCCCCCcchhhhhcCHHHHhcccCCCCCCHHHHHHHHHHhhCCceEEEEE
Q psy17364 98 FNCETDFVARNKQFQGMAELISLACLNYTKTQVQPQEPFAKVFLDTAQLQSLAGPENKSLADHVAILISSVGENLVLRRA 177 (312)
Q Consensus 98 lncETDFVArne~F~~la~~ia~~i~a~~p~~~~~~g~i~k~~~~~~~l~q~~~~~~~TV~d~i~~~i~~iGEnI~l~rf 177 (312)
|||||||||||+.|+.|+++|+.++++..|. +++.|...+.++++||.+.+..+++++||||.||||
T Consensus 78 vN~ETDFVAkN~~F~~l~~~ia~~~l~~~~~-------------~ve~l~~~~~~~~~tv~e~~~~~~AkIGENi~lRR~ 144 (296)
T COG0264 78 VNCETDFVAKNAEFQELANKIAKAALEKKPA-------------DVEELKAAFEPGGKTVEEEIAALIAKIGENISLRRF 144 (296)
T ss_pred EeccccceeCChhHHHHHHHHHHHHHHhCcc-------------cHHHHHhhhcccCccHHHHHHHHHHHhccceeEEEE
Confidence 9999999999999999999999999999987 567777777777999999999999999999999999
Q ss_pred EEEEeCCceeEEEeecCCCCCCCCCCCCccEEEEEEEeecCCCccccchHHHHHHHHHHHhhcCCcccCCCC--------
Q psy17364 178 ACVTVNEDHDVAGFTHPSPGLEHTGPILGKFGSLMVYQDLKTGDKQQNVQNVARQLCQHVIGMNPKSIGSEE-------- 249 (312)
Q Consensus 178 ~~~~~geg~~~~~Y~H~~~~~~~~~~~~Gkig~lV~~~~~~~~~~~~~~~~~ak~iAmhi~a~~P~~l~~~~-------- 249 (312)
..++.++ +.+++|+|++ |||||||.+++.. . ...++|+|||||||++|.||+.+|
T Consensus 145 ~~~~~~~-~~v~~Y~H~~----------griGVlv~~~~~~--~----~~~~ak~iAMHiAA~~P~~ls~~dV~~e~v~~ 207 (296)
T COG0264 145 AVLEAGD-GVVGSYLHGN----------GRIGVLVALKGGA--A----DEELAKDIAMHIAAMNPQYLSREDVPAEVVEK 207 (296)
T ss_pred EEeecCc-ccEEEEEeCC----------CcEEEEEEEeccc--h----HHHHHHHHHHHHHhcCCccCChhhCCHHHHHH
Confidence 9998766 5799999997 8999999999851 2 578999999999999999999986
Q ss_pred ------------CCCCCC-----------CcccccccccccccCCCCcHHHHHHHcCCceeeEEEEEecCccccccchHh
Q psy17364 250 ------------DTPNED-----------PEEETIMYHQEFLLDPTQYVGEVIVAAGIKPVEFLRFECGEGCEESEETQT 306 (312)
Q Consensus 250 ------------~kp~~~-----------~~~e~~Ll~Q~fi~d~~~tV~~~l~~~~~~v~~F~r~~vGe~ie~~~~~~~ 306 (312)
|||+++ |+.|+|||+|+|++||++||+++|++.+++|.+|+||++|||||++++||+
T Consensus 208 Er~i~~~~~~~~gKP~~i~eKiVeGr~~Kf~~E~~Ll~Q~fV~d~~~TV~~~lke~~~~v~~FvR~evGegieK~~~dFa 287 (296)
T COG0264 208 EREIFLAQLKAEGKPENIVEKIVEGRMNKFLAEVCLLEQPFVKDPKKTVEQLLKEANAKVTEFVRFEVGEGIEKKEEDFA 287 (296)
T ss_pred HHHHHHHHHHhcCChHHHHHHHHhHHHHHHHHHHhhccCceecCcchhHHHHHHhcCceeeeeeeeeccCCceeccccHH
Confidence 899864 689999999999999999999999999999999999999999999999999
Q ss_pred Hh
Q psy17364 307 QA 308 (312)
Q Consensus 307 ~~ 308 (312)
+=
T Consensus 288 ~E 289 (296)
T COG0264 288 AE 289 (296)
T ss_pred HH
Confidence 74
No 2
>TIGR00116 tsf translation elongation factor Ts. This protein is found in Bacteria, mitochondria, and chloroplasts.
Probab=100.00 E-value=6.2e-80 Score=576.02 Aligned_cols=253 Identities=32% Similarity=0.495 Sum_probs=233.7
Q ss_pred cccCHHHHHHHHHHhCCCHHHHHHHHHHhcCCHHHHHHHHHHHHHhhcHHHHHhhhhhccCCceEEEEeCCcEEEEEEEe
Q psy17364 20 LTTNKSLLGKLRKKTGYSFTNCKKALDLNEQDLGKAEKWLQEQAKELGWAKASKLAGRKTSQGLISIAVEGKHATMVEFN 99 (312)
Q Consensus 20 ~~~~~~lik~LR~~Tga~~~dCKkAL~e~~gD~ekA~e~Lr~~~~k~G~~~A~Kr~~R~t~eG~V~~~~~~~~gvlvEln 99 (312)
|++|+++||+||++||+|||||||||+++|||+|+|++|||+ +|+++|.||++|.|+||+|+++++++.|+|||||
T Consensus 1 m~isa~~IK~LRe~Tgagm~dCKkAL~e~~gDiekAi~~LRk----kG~akA~Kk~~R~a~EG~V~~~~~~~~~~ivEln 76 (290)
T TIGR00116 1 MAITAQLVKELRERTGAGMMDCKKALTEANGDFEKAIKNLRE----SGIAKAAKKADRVAAEGVIVLKSDGNKAVIVEVN 76 (290)
T ss_pred CCCCHHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHH----hchhHHHHhcccccCCcEEEEEEcCCEEEEEEEe
Confidence 568999999999999999999999999999999999999999 5999999999999999999999999999999999
Q ss_pred ccchhhhhhhHHHHHHHHHHHHHHhcCCCCCCCCcchhhhhcCHHHHhcccCCCCCCHHHHHHHHHHhhCCceEEEEEEE
Q psy17364 100 CETDFVARNKQFQGMAELISLACLNYTKTQVQPQEPFAKVFLDTAQLQSLAGPENKSLADHVAILISSVGENLVLRRAAC 179 (312)
Q Consensus 100 cETDFVArne~F~~la~~ia~~i~a~~p~~~~~~g~i~k~~~~~~~l~q~~~~~~~TV~d~i~~~i~~iGEnI~l~rf~~ 179 (312)
|||||||||+.|+.|+++|++++++..+. +.+.+.+.+.+++.|| |.+.++++++||||+|+||.+
T Consensus 77 cETDFVArne~F~~l~~~ia~~~~~~~~~-------------~~e~l~~~~~~~~~tv-d~i~~~~a~iGEnI~lrR~~~ 142 (290)
T TIGR00116 77 SETDFVAKNAGFKEFANKLLDELKANKIT-------------TLEELQAQELENREKV-EYLAALAAKIGENINLRRVAV 142 (290)
T ss_pred cCCccccCChHHHHHHHHHHHHHHhcCCC-------------CHHHHhhccccCCCcH-HHHHHHHHHhccceEEEEEEE
Confidence 99999999999999999999999987766 4566766665667899 999999999999999999999
Q ss_pred EEeCCceeEEEeecCCCCCCCCCCCCccEEEEEEEeecCCCccccchHHHHHHHHHHHhhcCCcccCCCC----------
Q psy17364 180 VTVNEDHDVAGFTHPSPGLEHTGPILGKFGSLMVYQDLKTGDKQQNVQNVARQLCQHVIGMNPKSIGSEE---------- 249 (312)
Q Consensus 180 ~~~geg~~~~~Y~H~~~~~~~~~~~~Gkig~lV~~~~~~~~~~~~~~~~~ak~iAmhi~a~~P~~l~~~~---------- 249 (312)
+..++ +++++|+|++ ||||+||.+++.. ..+++|+||||||||+|.||++++
T Consensus 143 ~~~~~-~~v~~Y~H~~----------gkigvlv~~~~~~-------~~~~ak~iAmhIaA~~P~~l~~~~vp~~vie~Er 204 (290)
T TIGR00116 143 LEGDS-NVIGSYLHAG----------ARIGVLVALKGKA-------DEELAKHIAMHVAASKPQFIDPDDVSAEVVKKER 204 (290)
T ss_pred EecCC-CcEEEEEcCC----------CcEEEEEEEecCc-------hHHHHHHHHHHHHhcCCccCchhhCCHHHHHHHH
Confidence 98643 5899999985 8999999998742 246899999999999999999875
Q ss_pred ----------CCCCCC-----------CcccccccccccccCCCCcHHHHHHHcCCceeeEEEEEecCccccccchHhHh
Q psy17364 250 ----------DTPNED-----------PEEETIMYHQEFLLDPTQYVGEVIVAAGIKPVEFLRFECGEGCEESEETQTQA 308 (312)
Q Consensus 250 ----------~kp~~~-----------~~~e~~Ll~Q~fi~d~~~tV~~~l~~~~~~v~~F~r~~vGe~ie~~~~~~~~~ 308 (312)
|||+++ ||+|+|||+|+|++||++||+|||++.+++|++|+||+|||++|++++||++-
T Consensus 205 ei~~~~~~~~gKP~~i~eKIv~Grl~Kf~~E~~Ll~Q~fv~D~~~tV~~~l~~~~~~v~~F~R~~vGegiek~~~~fa~e 284 (290)
T TIGR00116 205 QIQTDQAELSGKPKEIAEKMVEGRMKKFLAEISLLGQKFVMDPSKTVGQFLKEKNAKVTEFIRFEVGEGIEKKEEDFAAE 284 (290)
T ss_pred HHHHHHHHhcCCcHHHHHHHhhhHHHHHhhhceeeecccccCCccCHHHHHHHcCCEEEEEEEEEecCCceeccccHHHH
Confidence 788753 68999999999999999999999999999999999999999999999999874
No 3
>PRK09377 tsf elongation factor Ts; Provisional
Probab=100.00 E-value=5.8e-79 Score=569.47 Aligned_cols=252 Identities=35% Similarity=0.583 Sum_probs=234.2
Q ss_pred cccCHHHHHHHHHHhCCCHHHHHHHHHHhcCCHHHHHHHHHHHHHhhcHHHHHhhhhhccCCceEEEEeCCcEEEEEEEe
Q psy17364 20 LTTNKSLLGKLRKKTGYSFTNCKKALDLNEQDLGKAEKWLQEQAKELGWAKASKLAGRKTSQGLISIAVEGKHATMVEFN 99 (312)
Q Consensus 20 ~~~~~~lik~LR~~Tga~~~dCKkAL~e~~gD~ekA~e~Lr~~~~k~G~~~A~Kr~~R~t~eG~V~~~~~~~~gvlvEln 99 (312)
|.+|+++||+||++||+|||||||||+++|||+|+|++|||+ +|+++|.||++|.|+||+|+++++++.|+|||||
T Consensus 2 ~~is~~~IK~LR~~Tgagm~dCKkAL~e~~gD~ekAi~~Lrk----~G~akA~Kk~~R~a~EG~I~~~~~~~~~~~vEln 77 (290)
T PRK09377 2 AAITAALVKELRERTGAGMMDCKKALTEADGDIEKAIEWLRK----KGLAKAAKKAGRVAAEGLVAAKVDGNKGVLVEVN 77 (290)
T ss_pred CccCHHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHH----hchhhHHHhcCccccceEEEEEeCCCEEEEEEEe
Confidence 679999999999999999999999999999999999999998 5999999999999999999999999999999999
Q ss_pred ccchhhhhhhHHHHHHHHHHHHHHhcCCCCCCCCcchhhhhcCHHHHhcccCCCCCCHHHHHHHHHHhhCCceEEEEEEE
Q psy17364 100 CETDFVARNKQFQGMAELISLACLNYTKTQVQPQEPFAKVFLDTAQLQSLAGPENKSLADHVAILISSVGENLVLRRAAC 179 (312)
Q Consensus 100 cETDFVArne~F~~la~~ia~~i~a~~p~~~~~~g~i~k~~~~~~~l~q~~~~~~~TV~d~i~~~i~~iGEnI~l~rf~~ 179 (312)
|||||||||+.|+.|+++|+.++++..+. +.+.+.+.+. ++.||+|.+.++++++||||.|+||.+
T Consensus 78 cETDFVArne~F~~l~~~i~~~~l~~~~~-------------~~e~ll~~~~-~g~tv~d~i~~~~~~iGEnI~l~R~~~ 143 (290)
T PRK09377 78 SETDFVAKNEDFQALANEVAEAALAAKPA-------------DVEALLALKL-DGGTVEEARTELIAKIGENISLRRFAR 143 (290)
T ss_pred cCCccccCChHHHHHHHHHHHHHHhcCCC-------------CHHHHHhccc-cCCcHHHHHHHHHHHhcCceEEEEEEE
Confidence 99999999999999999999999998776 4456665554 578999999999999999999999999
Q ss_pred EEeCCceeEEEeecCCCCCCCCCCCCccEEEEEEEeecCCCccccchHHHHHHHHHHHhhcCCcccCCCC----------
Q psy17364 180 VTVNEDHDVAGFTHPSPGLEHTGPILGKFGSLMVYQDLKTGDKQQNVQNVARQLCQHVIGMNPKSIGSEE---------- 249 (312)
Q Consensus 180 ~~~geg~~~~~Y~H~~~~~~~~~~~~Gkig~lV~~~~~~~~~~~~~~~~~ak~iAmhi~a~~P~~l~~~~---------- 249 (312)
++. +|+.+++|+|++ ||||+||.+++. .++++|+||||||||+|.||++++
T Consensus 144 ~~~-~~~~i~~Y~H~~----------gkigvlV~~~~~--------~~~~ak~iAMhIaA~~P~~l~~~~vp~~~i~~E~ 204 (290)
T PRK09377 144 LEK-DGGVVGSYLHGG----------GRIGVLVALEGG--------DEELAKDIAMHIAAMNPEYLSREDVPAEVVEKER 204 (290)
T ss_pred Eee-cCCEEEEEEcCC----------CcEEEEEEEccC--------cHHHHHHHHHHHHhcCCccCChhhCCHHHHHHHH
Confidence 977 577999999975 899999999975 257999999999999999999875
Q ss_pred ----------CCCCCC-----------CcccccccccccccCCCCcHHHHHHHcCCceeeEEEEEecCccccccchHhHh
Q psy17364 250 ----------DTPNED-----------PEEETIMYHQEFLLDPTQYVGEVIVAAGIKPVEFLRFECGEGCEESEETQTQA 308 (312)
Q Consensus 250 ----------~kp~~~-----------~~~e~~Ll~Q~fi~d~~~tV~~~l~~~~~~v~~F~r~~vGe~ie~~~~~~~~~ 308 (312)
|||+++ ||+|+|||+|+|++||++||+|||++.+++|++|+||+|||+++++++||+.-
T Consensus 205 ~i~~~~~~~~gKP~~i~eKIv~Grl~Kf~~e~~Ll~Q~fi~D~~~tV~~~l~~~~i~v~~F~R~evGe~~e~~~~~fa~e 284 (290)
T PRK09377 205 EIAKEQAKEEGKPEEIVEKIVEGRLNKFLKEVVLLEQPFVKDPKKTVGQLLKEAGAKVVGFVRFEVGEGIEKKEEDFAAE 284 (290)
T ss_pred HHHHHHHHhcCChHHHHHHHHhHHHHHHhhhceeccCcccCCCCcCHHHHHHHcCCEEEEEEEEEecCcceecccchHHH
Confidence 788753 78999999999999999999999999999999999999999999999999874
No 4
>KOG1071|consensus
Probab=100.00 E-value=1.6e-67 Score=486.45 Aligned_cols=275 Identities=40% Similarity=0.647 Sum_probs=238.5
Q ss_pred cCHHHHHHHHHHhCCCHHHHHHHHHHhcCCHHHHHHHHHHHHHhhcHHHHHhhhhhccCCceEEEEeCCcEEEEEEEecc
Q psy17364 22 TNKSLLGKLRKKTGYSFTNCKKALDLNEQDLGKAEKWLQEQAKELGWAKASKLAGRKTSQGLISIAVEGKHATMVEFNCE 101 (312)
Q Consensus 22 ~~~~lik~LR~~Tga~~~dCKkAL~e~~gD~ekA~e~Lr~~~~k~G~~~A~Kr~~R~t~eG~V~~~~~~~~gvlvElncE 101 (312)
+++++||+||++|||||++|||||+++|||++.|.+||++++++.||.+|.|+++|.|+||+|+++.+++++||||||||
T Consensus 45 ~~~allk~LR~kTgas~~ncKkALee~~gDl~~A~~~L~k~aqk~g~~~A~K~~sR~t~eGlIgv~~~~~r~vlvElNCE 124 (340)
T KOG1071|consen 45 SSKALLKKLREKTGASMVNCKKALEECGGDLVLAEEWLHKKAQKEGWSKAAKKASRTTKEGLIGVLQEDGRTVLVELNCE 124 (340)
T ss_pred ccHHHHHHHHHHcCCcHHHHHHHHHHhCCcHHHHHHHHHHHHHHhhhhHHhhhcccccccceeEEEEeCCeEEEEEeecc
Confidence 46999999999999999999999999999999999999999999999999999999999999999998888899999999
Q ss_pred chhhhhhhHHHHHHHHHHHHHHhcCCC------CC------CCCcchhhhhcCHHHHhcccCCCCC-CHHHHHHHHHHhh
Q psy17364 102 TDFVARNKQFQGMAELISLACLNYTKT------QV------QPQEPFAKVFLDTAQLQSLAGPENK-SLADHVAILISSV 168 (312)
Q Consensus 102 TDFVArne~F~~la~~ia~~i~a~~p~------~~------~~~g~i~k~~~~~~~l~q~~~~~~~-TV~d~i~~~i~~i 168 (312)
|||||||+.|+.|+.+||++++++... .. ...+...+.+.+..++.+++..+|+ ||+|.+...|+++
T Consensus 125 TDFVARn~~Fq~Lv~~iA~~~l~~~~~~~~~~s~~s~e~~l~~~~~g~kl~~~~~~l~~~~d~~gkvsl~d~l~~~i~~~ 204 (340)
T KOG1071|consen 125 TDFVARNDIFQDLVDQIALSVLAHCQTLKTKHSSYSKEKELEMDGRGFKLSESLSLLPNLPDVEGKVSLKDQLALAIGKL 204 (340)
T ss_pred cchhhccchHHHHHHHHHHHHHHhhhhcccChhhhhhhhhccccchHHHhhHHHhhccCCCCcccceeHHHHHHHHHHHh
Confidence 999999999999999999999883311 11 1145666666666777777755555 9999999999999
Q ss_pred CCceEEEEEEEEEeCCceeEEEeecCCCCCC--CCCCCCccEEEEEEEeecCCCccccchHHHHHHHHHHHhhcCCcccC
Q psy17364 169 GENLVLRRAACVTVNEDHDVAGFTHPSPGLE--HTGPILGKFGSLMVYQDLKTGDKQQNVQNVARQLCQHVIGMNPKSIG 246 (312)
Q Consensus 169 GEnI~l~rf~~~~~geg~~~~~Y~H~~~~~~--~~~~~~Gkig~lV~~~~~~~~~~~~~~~~~ak~iAmhi~a~~P~~l~ 246 (312)
|||++++|+.+|++++|..+++|.|+.+.+. ..- .+|++|+||+++...+. ......++++||+||++|.|..+.
T Consensus 205 GENvkvrR~~~~ka~~g~~l~~y~H~A~q~agt~~l-~~g~~~alvAi~~~~s~--~~~~~~~~~~i~q~ivgm~p~s~~ 281 (340)
T KOG1071|consen 205 GENVKVRRAACMKAPSGTYLGSYSHGAPQSAGTHKL-PLGEYGALVAINSVSSQ--LTSLEDVAKQICQHIVGMSPESVG 281 (340)
T ss_pred ccceEEeEEEEEecCCCceEEeeecCCCCCcccccc-ccccchhhhhhhhccch--hhhHHHHHHHHHHHhhccChhhhc
Confidence 9999999999999999999999999887654 111 27999999999875431 112456899999999999999998
Q ss_pred C-CCCCCCCCCcccccccccccccCCCCcHHHHHHHcCCceeeEEEEEecCcccc
Q psy17364 247 S-EEDTPNEDPEEETIMYHQEFLLDPTQYVGEVIVAAGIKPVEFLRFECGEGCEE 300 (312)
Q Consensus 247 ~-~~~kp~~~~~~e~~Ll~Q~fi~d~~~tV~~~l~~~~~~v~~F~r~~vGe~ie~ 300 (312)
+ .+++|....+.|++||+|+|++|+++||++||+.++.+|++|+|||||| .|.
T Consensus 282 e~~k~e~~~~~e~et~ll~q~~lld~~itv~~~l~~~~~~V~DfvR~E~Ge-~e~ 335 (340)
T KOG1071|consen 282 ESLKDEPGQGAEAETALLSQPSLLDPSITVKEYLDPHNVSVVDFVRFEVGE-GER 335 (340)
T ss_pred ccccccccccccchhhheecHhhcCchhhHHHHhccCCcchHHHHHHHhcc-chh
Confidence 3 2367776678999999999999999999999999999999999999999 543
No 5
>PF00889 EF_TS: Elongation factor TS; InterPro: IPR014039 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. Elongation factor EF1B (also known as EF-Ts or EF-1beta/gamma/delta) is a nucleotide exchange factor that is required to regenerate EF1A from its inactive form (EF1A-GDP) to its active form (EF1A-GTP). EF1A is then ready to interact with a new aminoacyl-tRNA to begin the cycle again. EF1B is more complex in eukaryotes than in bacteria, and can consist of three subunits: EF1B-alpha (or EF-1beta), EF1B-gamma (or EF-1gamma) and EF1B-beta (or EF-1delta) []. This entry represents the C-terminal dimerisation domain found primarily in EF-Tu (EF1A) proteins from bacteria, mitochondria and chloroplasts. More information about these proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0003746 translation elongation factor activity, 0006414 translational elongation, 0005622 intracellular; PDB: 1XB2_B 3AVU_A 3AVW_A 3AGQ_A 3AGP_A 3AVT_A 3AVY_A 3AVX_A 3AVV_A 1TFE_A ....
Probab=100.00 E-value=3.2e-53 Score=384.31 Aligned_cols=188 Identities=38% Similarity=0.619 Sum_probs=160.1
Q ss_pred cCCceEEEEeCCcEEEEEEEeccchhhhhhhHHHHHHHHHHHHHHhcCCCCCCCCcchhhhhcCHHHHhcccCCCCCCHH
Q psy17364 79 TSQGLISIAVEGKHATMVEFNCETDFVARNKQFQGMAELISLACLNYTKTQVQPQEPFAKVFLDTAQLQSLAGPENKSLA 158 (312)
Q Consensus 79 t~eG~V~~~~~~~~gvlvElncETDFVArne~F~~la~~ia~~i~a~~p~~~~~~g~i~k~~~~~~~l~q~~~~~~~TV~ 158 (312)
|+||+|+++++++.|+||||||||||||||+.|+.|+++|+.+++...+. +.+.+.+.+.++ .||+
T Consensus 1 a~EG~V~~~v~~~~a~~vElncETDFVArn~~F~~l~~~ia~~~~~~~~~-------------~~~~l~~~~~~~-~tv~ 66 (221)
T PF00889_consen 1 AAEGLVGIAVSGDKAAMVELNCETDFVARNEEFQNLAKEIADAALENKAS-------------DVEELLALPLAS-KTVK 66 (221)
T ss_dssp --EEEEEEEEETTEEEEEEEEESSHHHHTSHHHHHHHHHHHHHHHCTTEE-------------SHHHHHHSB--S-SHHH
T ss_pred CCceEEEEEEeCCcEEEEEEEccccceecCHHHHHHHHHHHHHHHHhCCC-------------CHHHHHhccccc-ccHH
Confidence 57999999999999999999999999999999999999999999965554 556676666544 8999
Q ss_pred HHHHHHHHhhCCceEEEEEEEEEeCCceeEEEeecCCCCCCCCCCCCccEEEEEEEeecCCCccccchHHHHHHHHHHHh
Q psy17364 159 DHVAILISSVGENLVLRRAACVTVNEDHDVAGFTHPSPGLEHTGPILGKFGSLMVYQDLKTGDKQQNVQNVARQLCQHVI 238 (312)
Q Consensus 159 d~i~~~i~~iGEnI~l~rf~~~~~geg~~~~~Y~H~~~~~~~~~~~~Gkig~lV~~~~~~~~~~~~~~~~~ak~iAmhi~ 238 (312)
|.+.++++++||||+|+||.++.. +++++++|+|++ ||+|+||.+++..+. ..++||+||||||
T Consensus 67 d~i~~~i~~igEnI~l~r~~~~~~-~~~~v~~Y~H~~----------gkig~lV~~~~~~~~-----~~~~ak~iAmhIa 130 (221)
T PF00889_consen 67 DAIAELIAKIGENIQLRRAARISA-PNGFVGSYVHNN----------GKIGVLVALEGDNDS-----AKEFAKDIAMHIA 130 (221)
T ss_dssp HHHHHHHHHH-S-EEEEEEEEEE--TTSEEEEEEET-----------TTEEEEEEEET-SHG-----GHHHHHHHHHHHH
T ss_pred HHHHHHHHHhCCCEEEeEEEEEec-cCCEEEEEECCC----------CcEEEEEEEEcCcch-----HHHHHHHHHHHHh
Confidence 999999999999999999999998 678999999997 899999999987432 1589999999999
Q ss_pred hcCCcccCCCC--------------------CCCCCC-----------CcccccccccccccCCCCcHHHHHHHcCC--c
Q psy17364 239 GMNPKSIGSEE--------------------DTPNED-----------PEEETIMYHQEFLLDPTQYVGEVIVAAGI--K 285 (312)
Q Consensus 239 a~~P~~l~~~~--------------------~kp~~~-----------~~~e~~Ll~Q~fi~d~~~tV~~~l~~~~~--~ 285 (312)
||+|.||++++ |||+++ ||+|+|||+|+|++|+++||+|||++.+. +
T Consensus 131 A~~P~~l~~~~vp~~~~~~E~~i~~~~~~~~gKpe~i~ekIv~Gkl~k~~~e~~Ll~Q~fv~D~~~tV~~~l~~~~~~i~ 210 (221)
T PF00889_consen 131 AMNPKYLSEEDVPAEVLEKEKEIAKEQAKAEGKPENIIEKIVEGKLKKFYKENCLLEQPFVKDPKKTVKQYLKEVGKEIK 210 (221)
T ss_dssp HH--SBSSCTGS-CCHHHHHHHHHHHHHHTTTS-HHHHHHHHHHHHHHHHHHCBTCCSBETTETTSBHHHHHHCTTHH-E
T ss_pred hhCccccCcccCCHHHHHHHHHHHHHHhhccCCcHHHHHHHhhhhHhheehheeecCCCccCCCCccHHHHHHhcCCCcE
Confidence 99999999885 788753 68999999999999999999999999876 9
Q ss_pred eeeEEEEEecC
Q psy17364 286 PVEFLRFECGE 296 (312)
Q Consensus 286 v~~F~r~~vGe 296 (312)
|++|+||+|||
T Consensus 211 v~~F~R~~vGE 221 (221)
T PF00889_consen 211 VVGFVRFEVGE 221 (221)
T ss_dssp EEEEEEEETTT
T ss_pred EEEEEEEecCC
Confidence 99999999997
No 6
>PRK12332 tsf elongation factor Ts; Reviewed
Probab=100.00 E-value=7.5e-52 Score=368.38 Aligned_cols=162 Identities=35% Similarity=0.564 Sum_probs=154.1
Q ss_pred cccCHHHHHHHHHHhCCCHHHHHHHHHHhcCCHHHHHHHHHHHHHhhcHHHHHhhhhhccCCceEEEEeC--CcEEEEEE
Q psy17364 20 LTTNKSLLGKLRKKTGYSFTNCKKALDLNEQDLGKAEKWLQEQAKELGWAKASKLAGRKTSQGLISIAVE--GKHATMVE 97 (312)
Q Consensus 20 ~~~~~~lik~LR~~Tga~~~dCKkAL~e~~gD~ekA~e~Lr~~~~k~G~~~A~Kr~~R~t~eG~V~~~~~--~~~gvlvE 97 (312)
|.+++++||+||++||+|||||||||.+++||+|+|++|||+ +|+++|.||++|.|+||+|++|++ ++.|+|||
T Consensus 1 ~~i~a~~ik~LR~~tga~~~~ck~AL~~~~gd~~~A~~~lr~----~g~~~a~kk~~r~~~eG~i~~~i~~~~~~~~lve 76 (198)
T PRK12332 1 MAITAKLVKELREKTGAGMMDCKKALEEANGDMEKAIEWLRE----KGLAKAAKKAGRVAAEGLVGSYIHTGGRIGVLVE 76 (198)
T ss_pred CCCCHHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHH----hhhhHHHHhccccccCceEEEEEecCCCEEEEEE
Confidence 568999999999999999999999999999999999999999 599999999999999999999885 89999999
Q ss_pred EeccchhhhhhhHHHHHHHHHHHHHHhcCCCCCCC---------------------------------CcchhhhhcCHH
Q psy17364 98 FNCETDFVARNKQFQGMAELISLACLNYTKTQVQP---------------------------------QEPFAKVFLDTA 144 (312)
Q Consensus 98 lncETDFVArne~F~~la~~ia~~i~a~~p~~~~~---------------------------------~g~i~k~~~~~~ 144 (312)
|||||||||||+.|+.|+++|||||++++|.+++. +|+++|||.+.|
T Consensus 77 ~n~ETDFVa~n~~F~~lak~iamhIaA~~P~~l~~~~v~~~~i~~E~~i~~~~~~~~gKP~~i~ekiv~Grl~K~~~E~~ 156 (198)
T PRK12332 77 LNCETDFVARTEEFKELAKDIAMQIAAANPEYVSREDVPAEVIEKEKEIYRAQALNEGKPENIVEKIVEGRIEKFYKEVC 156 (198)
T ss_pred EeccCCccccCHHHHHHHHHHHHHHHhhCCccCChhhCCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHhHHHHHHHhhhh
Confidence 99999999999999999999999999999988753 689999999999
Q ss_pred HHhccc-CCCCCCHHHHHHHHHHhhCCceEEEEEEEEEeCCc
Q psy17364 145 QLQSLA-GPENKSLADHVAILISSVGENLVLRRAACVTVNED 185 (312)
Q Consensus 145 ~l~q~~-~~~~~TV~d~i~~~i~~iGEnI~l~rf~~~~~geg 185 (312)
++.|.+ .|++.||+|+|.+.++++||||+|+||.||++|+|
T Consensus 157 Ll~Q~fv~d~~~TV~e~l~e~~a~iGEnI~V~rF~R~evGeg 198 (198)
T PRK12332 157 LLEQPFIKDPSKTVEDLIKEAIAKIGENIVVRRFARFELGEG 198 (198)
T ss_pred hhcCcccCCCCccHHHHHHHHHHHhCCCeEEEEEEEEEcCCC
Confidence 999997 57789999999999999999999999999999875
No 7
>CHL00098 tsf elongation factor Ts
Probab=100.00 E-value=2.6e-49 Score=352.18 Aligned_cols=159 Identities=33% Similarity=0.469 Sum_probs=151.1
Q ss_pred CHHHHHHHHHHhCCCHHHHHHHHHHhcCCHHHHHHHHHHHHHhhcHHHHHhhhhhccCCceEEEEe--CCcEEEEEEEec
Q psy17364 23 NKSLLGKLRKKTGYSFTNCKKALDLNEQDLGKAEKWLQEQAKELGWAKASKLAGRKTSQGLISIAV--EGKHATMVEFNC 100 (312)
Q Consensus 23 ~~~lik~LR~~Tga~~~dCKkAL~e~~gD~ekA~e~Lr~~~~k~G~~~A~Kr~~R~t~eG~V~~~~--~~~~gvlvElnc 100 (312)
++++||+||++||+|||||||||.+++||+|+|++|||+ +|+++|.||++|.|++|+|++|+ +++.|||||+||
T Consensus 1 ~a~~ik~LR~~Tgag~~dck~AL~e~~gd~~~A~~~Lr~----~g~~~a~kk~~r~~~eG~V~~yiH~~gk~gvlVeln~ 76 (200)
T CHL00098 1 SAELVKELRDKTGAGMMDCKKALQEANGDFEKALESLRQ----KGLASANKKSTRITTEGLIESYIHTGGKLGVLVEINC 76 (200)
T ss_pred CHHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHH----hhhhHHHHhhccccccCeEEEEEecCCCEEEEEEEec
Confidence 578999999999999999999999999999999999999 59999999999999999999887 689999999999
Q ss_pred cchhhhhhhHHHHHHHHHHHHHHhc-CCCCCCC---------------------------------CcchhhhhcCHHHH
Q psy17364 101 ETDFVARNKQFQGMAELISLACLNY-TKTQVQP---------------------------------QEPFAKVFLDTAQL 146 (312)
Q Consensus 101 ETDFVArne~F~~la~~ia~~i~a~-~p~~~~~---------------------------------~g~i~k~~~~~~~l 146 (312)
||||||||+.|++|+++|||||+++ +|.+++. +|+++|||.++|++
T Consensus 77 ETDfVArn~~F~~la~~IAmhiaA~p~p~~l~~~~vp~~~i~~E~~i~~~~~~~~gKp~~i~ekiv~Grl~k~~~e~~LL 156 (200)
T CHL00098 77 ETDFVARREEFQKLAKNIAMQIAACPNVKYVSLEDIPEEIINLEKKIESEKDDLQNKPEEIKEKIVEGRIKKRLKELSLL 156 (200)
T ss_pred CcccccccHHHHHHHHHHHHHHHcCCCCeEecHHHCCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHhhHHHHHHHHhhhh
Confidence 9999999999999999999999999 6777653 79999999999999
Q ss_pred hccc-CCCCCCHHHHHHHHHHhhCCceEEEEEEEEEeCCc
Q psy17364 147 QSLA-GPENKSLADHVAILISSVGENLVLRRAACVTVNED 185 (312)
Q Consensus 147 ~q~~-~~~~~TV~d~i~~~i~~iGEnI~l~rf~~~~~geg 185 (312)
+|.+ +|++.||+++|++.++++||||.|+||.||++|+|
T Consensus 157 eQ~fv~D~~~TV~~~l~e~~akiGeni~V~rF~R~~vGeg 196 (200)
T CHL00098 157 DQPFIRDQSITVEELIKQNIAKLGENIQIRRFARFTLGEG 196 (200)
T ss_pred cCcccCCCCccHHHHHHHHHHhcCCCcEEEEEEEEEecCC
Confidence 9997 58899999999999999999999999999999986
No 8
>CHL00098 tsf elongation factor Ts
Probab=99.91 E-value=1.2e-24 Score=194.00 Aligned_cols=106 Identities=25% Similarity=0.388 Sum_probs=90.6
Q ss_pred ceeEEEeecCCCCCCCCCCCCccEEEEEEEeecCCCc-cccchHHHHHHHHHHHhhc-CCcccCCCC-------------
Q psy17364 185 DHDVAGFTHPSPGLEHTGPILGKFGSLMVYQDLKTGD-KQQNVQNVARQLCQHVIGM-NPKSIGSEE------------- 249 (312)
Q Consensus 185 g~~~~~Y~H~~~~~~~~~~~~Gkig~lV~~~~~~~~~-~~~~~~~~ak~iAmhi~a~-~P~~l~~~~------------- 249 (312)
++.+++|+|.+ |++|+||.++++++.. ......++|++|||||||| +|.||++++
T Consensus 55 eG~V~~yiH~~----------gk~gvlVeln~ETDfVArn~~F~~la~~IAmhiaA~p~p~~l~~~~vp~~~i~~E~~i~ 124 (200)
T CHL00098 55 EGLIESYIHTG----------GKLGVLVEINCETDFVARREEFQKLAKNIAMQIAACPNVKYVSLEDIPEEIINLEKKIE 124 (200)
T ss_pred cCeEEEEEecC----------CCEEEEEEEecCcccccccHHHHHHHHHHHHHHHcCCCCeEecHHHCCHHHHHHHHHHH
Confidence 34899999975 8999999999975421 1112367899999999999 799999885
Q ss_pred -------CCCCCC-----------CcccccccccccccCCCCcHHHHHHHc------CCceeeEEEEEecCcccc
Q psy17364 250 -------DTPNED-----------PEEETIMYHQEFLLDPTQYVGEVIVAA------GIKPVEFLRFECGEGCEE 300 (312)
Q Consensus 250 -------~kp~~~-----------~~~e~~Ll~Q~fi~d~~~tV~~~l~~~------~~~v~~F~r~~vGe~ie~ 300 (312)
|||+++ ||+|+|||+|+|++|+++||+++|++. +++|.+|+||+||||+|+
T Consensus 125 ~~~~~~~gKp~~i~ekiv~Grl~k~~~e~~LLeQ~fv~D~~~TV~~~l~e~~akiGeni~V~rF~R~~vGegiek 199 (200)
T CHL00098 125 SEKDDLQNKPEEIKEKIVEGRIKKRLKELSLLDQPFIRDQSITVEELIKQNIAKLGENIQIRRFARFTLGEGEEK 199 (200)
T ss_pred HHHHHhcCCcHHHHHHHHhhHHHHHHHHhhhhcCcccCCCCccHHHHHHHHHHhcCCCcEEEEEEEEEecCCccc
Confidence 888763 799999999999999999999999985 699999999999999986
No 9
>PRK12332 tsf elongation factor Ts; Reviewed
Probab=99.85 E-value=1.2e-21 Score=174.68 Aligned_cols=103 Identities=25% Similarity=0.446 Sum_probs=87.4
Q ss_pred ceeEEEeecCCCCCCCCCCCCccEEEEEEEeecCCCc-cccchHHHHHHHHHHHhhcCCcccCCCC--------------
Q psy17364 185 DHDVAGFTHPSPGLEHTGPILGKFGSLMVYQDLKTGD-KQQNVQNVARQLCQHVIGMNPKSIGSEE-------------- 249 (312)
Q Consensus 185 g~~~~~Y~H~~~~~~~~~~~~Gkig~lV~~~~~~~~~-~~~~~~~~ak~iAmhi~a~~P~~l~~~~-------------- 249 (312)
.+.+++|+|++ |++|+||.+.+.++.. .......++|+||||||||+|.||+.++
T Consensus 58 eG~i~~~i~~~----------~~~~~lve~n~ETDFVa~n~~F~~lak~iamhIaA~~P~~l~~~~v~~~~i~~E~~i~~ 127 (198)
T PRK12332 58 EGLVGSYIHTG----------GRIGVLVELNCETDFVARTEEFKELAKDIAMQIAAANPEYVSREDVPAEVIEKEKEIYR 127 (198)
T ss_pred CceEEEEEecC----------CCEEEEEEEeccCCccccCHHHHHHHHHHHHHHHhhCCccCChhhCCHHHHHHHHHHHH
Confidence 45799999976 7999999999876432 1112356899999999999999999874
Q ss_pred ------CCCCCC-----------CcccccccccccccCCCCcHHHHHHHc------CCceeeEEEEEecCc
Q psy17364 250 ------DTPNED-----------PEEETIMYHQEFLLDPTQYVGEVIVAA------GIKPVEFLRFECGEG 297 (312)
Q Consensus 250 ------~kp~~~-----------~~~e~~Ll~Q~fi~d~~~tV~~~l~~~------~~~v~~F~r~~vGe~ 297 (312)
|||+++ |++|+||++|+|++|++.||.++|++. +++|.+|+||++|||
T Consensus 128 ~~~~~~gKP~~i~ekiv~Grl~K~~~E~~Ll~Q~fv~d~~~TV~e~l~e~~a~iGEnI~V~rF~R~evGeg 198 (198)
T PRK12332 128 AQALNEGKPENIVEKIVEGRIEKFYKEVCLLEQPFIKDPSKTVEDLIKEAIAKIGENIVVRRFARFELGEG 198 (198)
T ss_pred HHHHhcCCcHHHHHHHHhHHHHHHHhhhhhhcCcccCCCCccHHHHHHHHHHHhCCCeEEEEEEEEEcCCC
Confidence 788753 689999999999999999999999974 699999999999986
No 10
>COG0264 Tsf Translation elongation factor Ts [Translation, ribosomal structure and biogenesis]
Probab=99.67 E-value=2.6e-16 Score=146.22 Aligned_cols=116 Identities=10% Similarity=0.110 Sum_probs=101.2
Q ss_pred HHHHHHHHhhcHHHHHhhhhhcc-CCceEEEEe--CCcEEEEEEEeccchhhhhhhHHHHHHHHHHHHHHhcCCCCCCC-
Q psy17364 57 KWLQEQAKELGWAKASKLAGRKT-SQGLISIAV--EGKHATMVEFNCETDFVARNKQFQGMAELISLACLNYTKTQVQP- 132 (312)
Q Consensus 57 e~Lr~~~~k~G~~~A~Kr~~R~t-~eG~V~~~~--~~~~gvlvElncETDFVArne~F~~la~~ia~~i~a~~p~~~~~- 132 (312)
+.+.+.++++|+++..+|+.+.. .+|.|++|+ ++++||||++.+. | ....++++|||||++++|.+++.
T Consensus 126 e~~~~~~AkIGENi~lRR~~~~~~~~~~v~~Y~H~~griGVlv~~~~~-~------~~~~~ak~iAMHiAA~~P~~ls~~ 198 (296)
T COG0264 126 EEIAALIAKIGENISLRRFAVLEAGDGVVGSYLHGNGRIGVLVALKGG-A------ADEELAKDIAMHIAAMNPQYLSRE 198 (296)
T ss_pred HHHHHHHHHhccceeEEEEEEeecCcccEEEEEeCCCcEEEEEEEecc-c------hHHHHHHHHHHHHHhcCCccCChh
Confidence 56667777899999999998876 357888877 4689999999997 3 45679999999999999998763
Q ss_pred --------------------------------CcchhhhhcCHHHHhccc-CCCCCCHHHHHHHHHHhhCCceEEEEEEE
Q psy17364 133 --------------------------------QEPFAKVFLDTAQLQSLA-GPENKSLADHVAILISSVGENLVLRRAAC 179 (312)
Q Consensus 133 --------------------------------~g~i~k~~~~~~~l~q~~-~~~~~TV~d~i~~~i~~iGEnI~l~rf~~ 179 (312)
+|+|+||+.+.|||+|++ +|+++||+++|++. ++.+.+|+|
T Consensus 199 dV~~e~v~~Er~i~~~~~~~~gKP~~i~eKiVeGr~~Kf~~E~~Ll~Q~fV~d~~~TV~~~lke~------~~~v~~FvR 272 (296)
T COG0264 199 DVPAEVVEKEREIFLAQLKAEGKPENIVEKIVEGRMNKFLAEVCLLEQPFVKDPKKTVEQLLKEA------NAKVTEFVR 272 (296)
T ss_pred hCCHHHHHHHHHHHHHHHHhcCChHHHHHHHHhHHHHHHHHHHhhccCceecCcchhHHHHHHhc------Cceeeeeee
Confidence 799999999999999997 79999999998885 899999999
Q ss_pred EEeCCc
Q psy17364 180 VTVNED 185 (312)
Q Consensus 180 ~~~geg 185 (312)
|++|+|
T Consensus 273 ~evGeg 278 (296)
T COG0264 273 FEVGEG 278 (296)
T ss_pred eeccCC
Confidence 999876
No 11
>TIGR00116 tsf translation elongation factor Ts. This protein is found in Bacteria, mitochondria, and chloroplasts.
Probab=99.66 E-value=2.2e-16 Score=148.35 Aligned_cols=115 Identities=13% Similarity=0.163 Sum_probs=101.6
Q ss_pred HHHHHHHHhhcHHHHHhhhhhccCC-ceEEEEeC--CcEEEEEEEeccchhhhhhhHHHHHHHHHHHHHHhcCCCCCCC-
Q psy17364 57 KWLQEQAKELGWAKASKLAGRKTSQ-GLISIAVE--GKHATMVEFNCETDFVARNKQFQGMAELISLACLNYTKTQVQP- 132 (312)
Q Consensus 57 e~Lr~~~~k~G~~~A~Kr~~R~t~e-G~V~~~~~--~~~gvlvElncETDFVArne~F~~la~~ia~~i~a~~p~~~~~- 132 (312)
++|.+.+++.|+++..+|+.+.... |.|++|++ |++|+||+++|++|. .++++|||||++++|.++++
T Consensus 122 d~i~~~~a~iGEnI~lrR~~~~~~~~~~v~~Y~H~~gkigvlv~~~~~~~~--------~~ak~iAmhIaA~~P~~l~~~ 193 (290)
T TIGR00116 122 EYLAALAAKIGENINLRRVAVLEGDSNVIGSYLHAGARIGVLVALKGKADE--------ELAKHIAMHVAASKPQFIDPD 193 (290)
T ss_pred HHHHHHHHHhccceEEEEEEEEecCCCcEEEEEcCCCcEEEEEEEecCchH--------HHHHHHHHHHHhcCCccCchh
Confidence 7788888889999999999988653 78888875 799999999997662 58999999999999998753
Q ss_pred --------------------------------CcchhhhhcCHHHHhccc-CCCCCCHHHHHHHHHHhhCCceEEEEEEE
Q psy17364 133 --------------------------------QEPFAKVFLDTAQLQSLA-GPENKSLADHVAILISSVGENLVLRRAAC 179 (312)
Q Consensus 133 --------------------------------~g~i~k~~~~~~~l~q~~-~~~~~TV~d~i~~~i~~iGEnI~l~rf~~ 179 (312)
+|+++|||.+.|||+|++ +|+++||.+++++ .+++|.+|.|
T Consensus 194 ~vp~~vie~Erei~~~~~~~~gKP~~i~eKIv~Grl~Kf~~E~~Ll~Q~fv~D~~~tV~~~l~~------~~~~v~~F~R 267 (290)
T TIGR00116 194 DVSAEVVKKERQIQTDQAELSGKPKEIAEKMVEGRMKKFLAEISLLGQKFVMDPSKTVGQFLKE------KNAKVTEFIR 267 (290)
T ss_pred hCCHHHHHHHHHHHHHHHHhcCCcHHHHHHHhhhHHHHHhhhceeeecccccCCccCHHHHHHH------cCCEEEEEEE
Confidence 799999999999999997 6999999998888 4699999999
Q ss_pred EEeCCc
Q psy17364 180 VTVNED 185 (312)
Q Consensus 180 ~~~geg 185 (312)
|++|+|
T Consensus 268 ~~vGeg 273 (290)
T TIGR00116 268 FEVGEG 273 (290)
T ss_pred EEecCC
Confidence 999875
No 12
>PF00889 EF_TS: Elongation factor TS; InterPro: IPR014039 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. Elongation factor EF1B (also known as EF-Ts or EF-1beta/gamma/delta) is a nucleotide exchange factor that is required to regenerate EF1A from its inactive form (EF1A-GDP) to its active form (EF1A-GTP). EF1A is then ready to interact with a new aminoacyl-tRNA to begin the cycle again. EF1B is more complex in eukaryotes than in bacteria, and can consist of three subunits: EF1B-alpha (or EF-1beta), EF1B-gamma (or EF-1gamma) and EF1B-beta (or EF-1delta) []. This entry represents the C-terminal dimerisation domain found primarily in EF-Tu (EF1A) proteins from bacteria, mitochondria and chloroplasts. More information about these proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0003746 translation elongation factor activity, 0006414 translational elongation, 0005622 intracellular; PDB: 1XB2_B 3AVU_A 3AVW_A 3AGQ_A 3AGP_A 3AVT_A 3AVY_A 3AVX_A 3AVV_A 1TFE_A ....
Probab=99.65 E-value=1.5e-16 Score=144.71 Aligned_cols=121 Identities=14% Similarity=0.182 Sum_probs=97.0
Q ss_pred HHHHHHHHHHHhhcHHHHHhhhhhccC-CceEEEEe--CCcEEEEEEEeccchhhhhhhHHHHHHHHHHHHHHhcCCCCC
Q psy17364 54 KAEKWLQEQAKELGWAKASKLAGRKTS-QGLISIAV--EGKHATMVEFNCETDFVARNKQFQGMAELISLACLNYTKTQV 130 (312)
Q Consensus 54 kA~e~Lr~~~~k~G~~~A~Kr~~R~t~-eG~V~~~~--~~~~gvlvElncETDFVArne~F~~la~~ia~~i~a~~p~~~ 130 (312)
.-.+.|.+.+.+.|+++..+|+.+... +|.+++|+ +|++|+||+++++++.. +.++++|||||++++|.++
T Consensus 64 tv~d~i~~~i~~igEnI~l~r~~~~~~~~~~v~~Y~H~~gkig~lV~~~~~~~~~------~~~ak~iAmhIaA~~P~~l 137 (221)
T PF00889_consen 64 TVKDAIAELIAKIGENIQLRRAARISAPNGFVGSYVHNNGKIGVLVALEGDNDSA------KEFAKDIAMHIAAMNPKYL 137 (221)
T ss_dssp HHHHHHHHHHHHH-S-EEEEEEEEEE-TTSEEEEEEET-TTEEEEEEEET-SHGG------HHHHHHHHHHHHHH--SBS
T ss_pred cHHHHHHHHHHHhCCCEEEeEEEEEeccCCEEEEEECCCCcEEEEEEEEcCcchH------HHHHHHHHHHHhhhCcccc
Confidence 344566667777999999999998765 78888876 57999999999998864 7899999999999999987
Q ss_pred CC---------------------------------CcchhhhhcCHHHHhccc-CCCCCCHHHHHHHHHHhhCCceEEEE
Q psy17364 131 QP---------------------------------QEPFAKVFLDTAQLQSLA-GPENKSLADHVAILISSVGENLVLRR 176 (312)
Q Consensus 131 ~~---------------------------------~g~i~k~~~~~~~l~q~~-~~~~~TV~d~i~~~i~~iGEnI~l~r 176 (312)
++ +|+++||+.+.||++|++ +|+++||+|+|++.... |.|.+
T Consensus 138 ~~~~vp~~~~~~E~~i~~~~~~~~gKpe~i~ekIv~Gkl~k~~~e~~Ll~Q~fv~D~~~tV~~~l~~~~~~----i~v~~ 213 (221)
T PF00889_consen 138 SEEDVPAEVLEKEKEIAKEQAKAEGKPENIIEKIVEGKLKKFYKENCLLEQPFVKDPKKTVKQYLKEVGKE----IKVVG 213 (221)
T ss_dssp SCTGS-CCHHHHHHHHHHHHHHTTTS-HHHHHHHHHHHHHHHHHHCBTCCSBETTETTSBHHHHHHCTTHH-----EEEE
T ss_pred CcccCCHHHHHHHHHHHHHHhhccCCcHHHHHHHhhhhHhheehheeecCCCccCCCCccHHHHHHhcCCC----cEEEE
Confidence 64 689999999999999997 68999999988876554 89999
Q ss_pred EEEEEeCC
Q psy17364 177 AACVTVNE 184 (312)
Q Consensus 177 f~~~~~ge 184 (312)
|.||++||
T Consensus 214 F~R~~vGE 221 (221)
T PF00889_consen 214 FVRFEVGE 221 (221)
T ss_dssp EEEEETTT
T ss_pred EEEEecCC
Confidence 99999875
No 13
>PRK09377 tsf elongation factor Ts; Provisional
Probab=99.63 E-value=1.5e-15 Score=142.77 Aligned_cols=115 Identities=12% Similarity=0.133 Sum_probs=98.9
Q ss_pred HHHHHHHHHhhcHHHHHhhhhhcc-CCceEEEEeC--CcEEEEEEEeccchhhhhhhHHHHHHHHHHHHHHhcCCCCCCC
Q psy17364 56 EKWLQEQAKELGWAKASKLAGRKT-SQGLISIAVE--GKHATMVEFNCETDFVARNKQFQGMAELISLACLNYTKTQVQP 132 (312)
Q Consensus 56 ~e~Lr~~~~k~G~~~A~Kr~~R~t-~eG~V~~~~~--~~~gvlvElncETDFVArne~F~~la~~ia~~i~a~~p~~~~~ 132 (312)
.+++.+.+.+.|+++..+|+.+.. ..|.|+.|++ |++|+||.++|+++ +|+++|||||++++|.+++.
T Consensus 122 ~d~i~~~~~~iGEnI~l~R~~~~~~~~~~i~~Y~H~~gkigvlV~~~~~~~---------~~ak~iAMhIaA~~P~~l~~ 192 (290)
T PRK09377 122 EEARTELIAKIGENISLRRFARLEKDGGVVGSYLHGGGRIGVLVALEGGDE---------ELAKDIAMHIAAMNPEYLSR 192 (290)
T ss_pred HHHHHHHHHHhcCceEEEEEEEEeecCCEEEEEEcCCCcEEEEEEEccCcH---------HHHHHHHHHHHhcCCccCCh
Confidence 445566666799999999998886 4678888874 68999999999643 58999999999999998753
Q ss_pred ---------------------------------CcchhhhhcCHHHHhccc-CCCCCCHHHHHHHHHHhhCCceEEEEEE
Q psy17364 133 ---------------------------------QEPFAKVFLDTAQLQSLA-GPENKSLADHVAILISSVGENLVLRRAA 178 (312)
Q Consensus 133 ---------------------------------~g~i~k~~~~~~~l~q~~-~~~~~TV~d~i~~~i~~iGEnI~l~rf~ 178 (312)
+|+++|||.+.|||+|++ +|++.||+++|++ .+++|.+|+
T Consensus 193 ~~vp~~~i~~E~~i~~~~~~~~gKP~~i~eKIv~Grl~Kf~~e~~Ll~Q~fi~D~~~tV~~~l~~------~~i~v~~F~ 266 (290)
T PRK09377 193 EDVPAEVVEKEREIAKEQAKEEGKPEEIVEKIVEGRLNKFLKEVVLLEQPFVKDPKKTVGQLLKE------AGAKVVGFV 266 (290)
T ss_pred hhCCHHHHHHHHHHHHHHHHhcCChHHHHHHHHhHHHHHHhhhceeccCcccCCCCcCHHHHHHH------cCCEEEEEE
Confidence 689999999999999997 6999999998888 479999999
Q ss_pred EEEeCCc
Q psy17364 179 CVTVNED 185 (312)
Q Consensus 179 ~~~~geg 185 (312)
||++|+|
T Consensus 267 R~evGe~ 273 (290)
T PRK09377 267 RFEVGEG 273 (290)
T ss_pred EEEecCc
Confidence 9999875
No 14
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=98.52 E-value=1.8e-07 Score=61.43 Aligned_cols=37 Identities=22% Similarity=0.443 Sum_probs=34.1
Q ss_pred cCHHHHHHHHHHhCCCHHHHHHHHHHhcCCHHHHHHHH
Q psy17364 22 TNKSLLGKLRKKTGYSFTNCKKALDLNEQDLGKAEKWL 59 (312)
Q Consensus 22 ~~~~lik~LR~~Tga~~~dCKkAL~e~~gD~ekA~e~L 59 (312)
++.+.|++|++. |.+--+|++||..++||++.|++||
T Consensus 1 i~~~~v~~L~~m-Gf~~~~~~~AL~~~~~nve~A~~~L 37 (37)
T PF00627_consen 1 IDEEKVQQLMEM-GFSREQAREALRACNGNVERAVDWL 37 (37)
T ss_dssp SHHHHHHHHHHH-TS-HHHHHHHHHHTTTSHHHHHHHH
T ss_pred CCHHHHHHHHHc-CCCHHHHHHHHHHcCCCHHHHHHhC
Confidence 457899999999 9999999999999999999999998
No 15
>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed
Probab=97.73 E-value=5.6e-05 Score=61.92 Aligned_cols=42 Identities=24% Similarity=0.238 Sum_probs=39.5
Q ss_pred cccCHHHHHHHHHHhCCCHHHHHHHHHHhcCCHHHHHHHHHH
Q psy17364 20 LTTNKSLLGKLRKKTGYSFTNCKKALDLNEQDLGKAEKWLQE 61 (312)
Q Consensus 20 ~~~~~~lik~LR~~Tga~~~dCKkAL~e~~gD~ekA~e~Lr~ 61 (312)
..++.+.|+.++++||++..+|++||+++|||+-.|+-+|.+
T Consensus 73 ~~i~~edI~lv~~q~gvs~~~A~~AL~~~~gDl~~AI~~L~~ 114 (115)
T PRK06369 73 VEIPEEDIELVAEQTGVSEEEARKALEEANGDLAEAILKLSS 114 (115)
T ss_pred CCCCHHHHHHHHHHHCcCHHHHHHHHHHcCCcHHHHHHHHhc
Confidence 358999999999999999999999999999999999999974
No 16
>TIGR00264 alpha-NAC-related protein. This hypothetical protein is found so far only in the Archaea. Its C-terminal domain of about 40 amino acids is homologous to the C-termini of the nascent polypeptide-associated complex alpha chain (alpha-NAC) and its yeast ortholog Egd2p and to the huntingtin-interacting protein HYPK. It shows weaker similarity, possibly through shared structural constraints rather than through homology, with the amino-terminal domain of elongation factor Ts. Alpha-NAC plays a role in preventing nascent polypeptides from binding inappropriately to membrane-targeting apparatus during translation, but is also active as a transcription regulator.
Probab=97.67 E-value=7e-05 Score=61.27 Aligned_cols=40 Identities=20% Similarity=0.170 Sum_probs=38.4
Q ss_pred ccCHHHHHHHHHHhCCCHHHHHHHHHHhcCCHHHHHHHHH
Q psy17364 21 TTNKSLLGKLRKKTGYSFTNCKKALDLNEQDLGKAEKWLQ 60 (312)
Q Consensus 21 ~~~~~lik~LR~~Tga~~~dCKkAL~e~~gD~ekA~e~Lr 60 (312)
.++.+.|+.++++||++..+||+||+++|||+-.|+-+|.
T Consensus 76 ~i~~eDI~lV~eq~gvs~e~A~~AL~~~~gDl~~AI~~L~ 115 (116)
T TIGR00264 76 EITEDDIELVMKQCNVSKEEARRALEECGGDLAEAIMKLE 115 (116)
T ss_pred CCCHHHHHHHHHHhCcCHHHHHHHHHHcCCCHHHHHHHhh
Confidence 5899999999999999999999999999999999999885
No 17
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=97.30 E-value=0.00059 Score=44.31 Aligned_cols=35 Identities=23% Similarity=0.387 Sum_probs=31.5
Q ss_pred HHHHHHHHHHhCCCHHHHHHHHHHhcCCHHHHHHHH
Q psy17364 24 KSLLGKLRKKTGYSFTNCKKALDLNEQDLGKAEKWL 59 (312)
Q Consensus 24 ~~lik~LR~~Tga~~~dCKkAL~e~~gD~ekA~e~L 59 (312)
.+.|.+|++. |.+--+|+.||..++||+++|++||
T Consensus 2 ~~~v~~L~~m-Gf~~~~a~~aL~~~~~d~~~A~~~L 36 (37)
T smart00165 2 EEKIDQLLEM-GFSREEALKALRAANGNVERAAEYL 36 (37)
T ss_pred HHHHHHHHHc-CCCHHHHHHHHHHhCCCHHHHHHHH
Confidence 3567788877 8999999999999999999999998
No 18
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=97.24 E-value=0.00084 Score=43.81 Aligned_cols=36 Identities=28% Similarity=0.515 Sum_probs=32.3
Q ss_pred HHHHHHHHHHhCCCHHHHHHHHHHhcCCHHHHHHHHH
Q psy17364 24 KSLLGKLRKKTGYSFTNCKKALDLNEQDLGKAEKWLQ 60 (312)
Q Consensus 24 ~~lik~LR~~Tga~~~dCKkAL~e~~gD~ekA~e~Lr 60 (312)
.+.|.+|++ .|.+--.|..||..++||+++|++||.
T Consensus 2 ~~~v~~L~~-mGf~~~~~~~AL~~~~~d~~~A~~~L~ 37 (38)
T cd00194 2 EEKLEQLLE-MGFSREEARKALRATNNNVERAVEWLL 37 (38)
T ss_pred HHHHHHHHH-cCCCHHHHHHHHHHhCCCHHHHHHHHh
Confidence 356888888 499999999999999999999999986
No 19
>KOG1071|consensus
Probab=97.06 E-value=0.002 Score=61.12 Aligned_cols=109 Identities=11% Similarity=0.030 Sum_probs=79.0
Q ss_pred CceeEEEeecCCCCCCCCCCCCccEEEEEEEeecCCCcc-ccchHHHHHHHHHHHhh------cCCcccCCCC-CCCC--
Q psy17364 184 EDHDVAGFTHPSPGLEHTGPILGKFGSLMVYQDLKTGDK-QQNVQNVARQLCQHVIG------MNPKSIGSEE-DTPN-- 253 (312)
Q Consensus 184 eg~~~~~Y~H~~~~~~~~~~~~Gkig~lV~~~~~~~~~~-~~~~~~~ak~iAmhi~a------~~P~~l~~~~-~kp~-- 253 (312)
+| .|+.|+|+ ||+ ++|.++++.+-.. ....+.+.++||+.+.+ .+|..++... -+|.
T Consensus 104 eG-lIgv~~~~-----------~r~-vlvElNCETDFVARn~~Fq~Lv~~iA~~~l~~~~~~~~~~s~~s~e~~l~~~~~ 170 (340)
T KOG1071|consen 104 EG-LIGVLQED-----------GRT-VLVELNCETDFVARNDIFQDLVDQIALSVLAHCQTLKTKHSSYSKEKELEMDGR 170 (340)
T ss_pred cc-eeEEEEeC-----------CeE-EEEEeecccchhhccchHHHHHHHHHHHHHHhhhhcccChhhhhhhhhccccch
Confidence 45 89999997 587 9999999765321 11246789999999888 3444333211 0110
Q ss_pred -CCCcccccccccccccCCCCcHHHHHHHc------CCceeeEEEEEecCccccccchH
Q psy17364 254 -EDPEEETIMYHQEFLLDPTQYVGEVIVAA------GIKPVEFLRFECGEGCEESEETQ 305 (312)
Q Consensus 254 -~~~~~e~~Ll~Q~fi~d~~~tV~~~l~~~------~~~v~~F~r~~vGe~ie~~~~~~ 305 (312)
..-+.+.-|+.|++..|.+.|++|.|... |++|.+|.+|..+++.....-++
T Consensus 171 g~kl~~~~~~l~~~~d~~gkvsl~d~l~~~i~~~GENvkvrR~~~~ka~~g~~l~~y~H 229 (340)
T KOG1071|consen 171 GFKLSESLSLLPNLPDVEGKVSLKDQLALAIGKLGENVKVRRAACMKAPSGTYLGSYSH 229 (340)
T ss_pred HHHhhHHHhhccCCCCcccceeHHHHHHHHHHHhccceEEeEEEEEecCCCceEEeeec
Confidence 01368889999999999999999999863 79999999999999877655444
No 20
>COG1308 EGD2 Transcription factor homologous to NACalpha-BTF3 [Transcription]
Probab=95.28 E-value=0.041 Score=45.49 Aligned_cols=40 Identities=23% Similarity=0.177 Sum_probs=37.4
Q ss_pred ccCHHHHHHHHHHhCCCHHHHHHHHHHhcCCHHHHHHHHH
Q psy17364 21 TTNKSLLGKLRKKTGYSFTNCKKALDLNEQDLGKAEKWLQ 60 (312)
Q Consensus 21 ~~~~~lik~LR~~Tga~~~dCKkAL~e~~gD~ekA~e~Lr 60 (312)
.++.+.|+-.=++||++--+.+|||+++|||+-.|+--|.
T Consensus 82 ~i~eeDIkLV~eQa~VsreeA~kAL~e~~GDlaeAIm~L~ 121 (122)
T COG1308 82 DISEEDIKLVMEQAGVSREEAIKALEEAGGDLAEAIMKLT 121 (122)
T ss_pred CCCHHHHHHHHHHhCCCHHHHHHHHHHcCCcHHHHHHHhc
Confidence 5889999999999999999999999999999999997764
No 21
>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A.
Probab=95.22 E-value=0.049 Score=36.68 Aligned_cols=37 Identities=19% Similarity=0.119 Sum_probs=31.8
Q ss_pred HHHHHHHHHhCCCHHHHHHHHHHhcCCHHHHHHHHHH
Q psy17364 25 SLLGKLRKKTGYSFTNCKKALDLNEQDLGKAEKWLQE 61 (312)
Q Consensus 25 ~lik~LR~~Tga~~~dCKkAL~e~~gD~ekA~e~Lr~ 61 (312)
++|.++...||+.--.|.+-|+.++||++.|+..--.
T Consensus 2 e~i~~F~~iTg~~~~~A~~~L~~~~wdle~Av~~y~~ 38 (43)
T PF14555_consen 2 EKIAQFMSITGADEDVAIQYLEANNWDLEAAVNAYFD 38 (43)
T ss_dssp HHHHHHHHHH-SSHHHHHHHHHHTTT-HHHHHHHHHH
T ss_pred HHHHHHHHHHCcCHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 5799999999999999999999999999999986543
No 22
>PF03943 TAP_C: TAP C-terminal domain; InterPro: IPR005637 This entry contains the NXF family of shuttling transport receptors for nuclear export of mRNA, which include: vertebrate mRNA export factor TAP or nuclear RNA export factor 1 (NXF1). Caenorhabditis elegans nuclear RNA export factor 1 (nxf-1). yeast mRNA export factor MEX67. Members of the NXF family have a modular structure. A nuclear localization sequence and a noncanonical RNA recognition motif (RRM) (see PDOC00030 from PROSITEDOC) followed by four LRR repeats are located in its N-terminal half. The C-terminal half contains a NTF2 domain (see PDOC50177 from PROSITEDOC) followed by a second domain, TAP-C. The TAP-C domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate nuclear shuttling [,]. The Tap-C domain is made of four alpha helices packed against each other. The arrangement of helices 1, 2 and 3 is similar to that seen in a UBA fold. and is joined to the next module by flexible 12-residue Pro-rich linker [, ].; GO: 0051028 mRNA transport, 0005634 nucleus; PDB: 1OAI_A 1GO5_A 2KHH_A 2JP7_A.
Probab=94.14 E-value=0.044 Score=38.55 Aligned_cols=37 Identities=22% Similarity=0.369 Sum_probs=33.3
Q ss_pred HHHHHHHHHhCCCHHHHHHHHHHhcCCHHHHHHHHHH
Q psy17364 25 SLLGKLRKKTGYSFTNCKKALDLNEQDLGKAEKWLQE 61 (312)
Q Consensus 25 ~lik~LR~~Tga~~~dCKkAL~e~~gD~ekA~e~Lr~ 61 (312)
++|.+|..+||.-.-=|.+-|++++||++.|+....+
T Consensus 2 ~mv~~~s~~Tgmn~~~s~~CL~~n~Wd~~~A~~~F~~ 38 (51)
T PF03943_consen 2 EMVQQFSQQTGMNLEWSQKCLEENNWDYERALQNFEE 38 (51)
T ss_dssp HHHHHHHHHCSS-CCHHHHHHHHTTT-CCHHHHHHHH
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 6899999999999999999999999999999999886
No 23
>smart00804 TAP_C C-terminal domain of vertebrate Tap protein. The vertebrate Tap protein is a member of the NXF family of shuttling transport receptors for the nuclear export of mRNA. Its most C-terminal domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate shuttling. This domain forms a compact four-helix fold related to that of a UBA domain.
Probab=93.00 E-value=0.3 Score=35.90 Aligned_cols=41 Identities=20% Similarity=0.242 Sum_probs=37.5
Q ss_pred cCHHHHHHHHHHhCCCHHHHHHHHHHhcCCHHHHHHHHHHH
Q psy17364 22 TNKSLLGKLRKKTGYSFTNCKKALDLNEQDLGKAEKWLQEQ 62 (312)
Q Consensus 22 ~~~~lik~LR~~Tga~~~dCKkAL~e~~gD~ekA~e~Lr~~ 62 (312)
+--.+|.++-.+||.-.-=|.+.|+++|||++.|+....+.
T Consensus 11 ~q~~~v~~~~~~Tgmn~~~s~~cLe~~~Wd~~~Al~~F~~l 51 (63)
T smart00804 11 EQQEMVQAFSAQTGMNAEYSQMCLEDNNWDYERALKNFTEL 51 (63)
T ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 44679999999999999999999999999999999998873
No 24
>PF00542 Ribosomal_L12: Ribosomal protein L7/L12 C-terminal domain; InterPro: IPR013823 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents the C-terminal domain of the large subunit ribosomal proteins, known as the L7/L12 family. L7/L12 is present in each 50S subunit in four copies organised as two dimers. The L8 protein complex consisting of two dimers of L7/L12 and L10 in Escherichia coli ribosomes is assembled on the conserved region of 23 S rRNA termed the GTPase-associated domain []. The L7/L12 dimer probably interacts with EF-Tu. L7 and L12 only differ in a single post translational modification of the addition of an acetyl group to the N terminus of L7.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1DD4_B 1DD3_A 1RQU_B 2GYA_5 2GYC_5 1RQS_A 1RQV_A 1CTF_A 2XUX_L.
Probab=90.96 E-value=0.34 Score=36.12 Aligned_cols=36 Identities=22% Similarity=0.285 Sum_probs=26.0
Q ss_pred CHHHHHHHHHHhCCCHHHHHHHHHHh------cCCHHHHHHH
Q psy17364 23 NKSLLGKLRKKTGYSFTNCKKALDLN------EQDLGKAEKW 58 (312)
Q Consensus 23 ~~~lik~LR~~Tga~~~dCKkAL~e~------~gD~ekA~e~ 58 (312)
-.+.||.+|+.||.|++++|+..+.. +.+-+.|.++
T Consensus 13 ki~vIK~vR~~tgl~L~eAK~~vd~~p~~ik~~v~keeAe~i 54 (68)
T PF00542_consen 13 KIKVIKEVREITGLGLKEAKKLVDSLPKVIKEGVSKEEAEEI 54 (68)
T ss_dssp HHHHHHHHHHHC---HHHHHHHHCTTTEEEEEEE-HHHHHHH
T ss_pred hHHHHHHHHHHhCCcHHHHHHHHHhCCHHHHcCCCHHHHHHH
Confidence 46899999999999999999999887 4456666444
No 25
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=89.39 E-value=1.4 Score=29.31 Aligned_cols=38 Identities=18% Similarity=0.196 Sum_probs=32.5
Q ss_pred HHHHHHHHHH-hCCCHHHHHHHHHHhcCCHHHHHHHHHH
Q psy17364 24 KSLLGKLRKK-TGYSFTNCKKALDLNEQDLGKAEKWLQE 61 (312)
Q Consensus 24 ~~lik~LR~~-Tga~~~dCKkAL~e~~gD~ekA~e~Lr~ 61 (312)
-+.|..|++. .+.+--.-+.+|.+++||+|.|++.|-+
T Consensus 2 ~~~v~~L~~mFP~~~~~~I~~~L~~~~~~ve~ai~~LL~ 40 (42)
T PF02845_consen 2 EEMVQQLQEMFPDLDREVIEAVLQANNGDVEAAIDALLE 40 (42)
T ss_dssp HHHHHHHHHHSSSS-HHHHHHHHHHTTTTHHHHHHHHHH
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHc
Confidence 3578889997 4588999999999999999999999876
No 26
>PRK06771 hypothetical protein; Provisional
Probab=86.52 E-value=0.76 Score=36.35 Aligned_cols=25 Identities=20% Similarity=0.436 Sum_probs=22.3
Q ss_pred cCHHHHHHHHHHhCCCHHHHHHHHH
Q psy17364 22 TNKSLLGKLRKKTGYSFTNCKKALD 46 (312)
Q Consensus 22 ~~~~lik~LR~~Tga~~~dCKkAL~ 46 (312)
-..+.||.+|+.||+|+.+.|++..
T Consensus 67 kki~AIK~~Re~tG~~L~eAK~yVD 91 (93)
T PRK06771 67 QTVTAVKRVREAFGFSLLEAKQYVD 91 (93)
T ss_pred CchHHHHHHHHHcCCCHHHHHHHHh
Confidence 4678999999999999999999864
No 27
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=85.66 E-value=2.8 Score=27.83 Aligned_cols=39 Identities=21% Similarity=0.189 Sum_probs=33.2
Q ss_pred CHHHHHHHHHH-hCCCHHHHHHHHHHhcCCHHHHHHHHHH
Q psy17364 23 NKSLLGKLRKK-TGYSFTNCKKALDLNEQDLGKAEKWLQE 61 (312)
Q Consensus 23 ~~~lik~LR~~-Tga~~~dCKkAL~e~~gD~ekA~e~Lr~ 61 (312)
..+.|..|++. -..+-..-+..|.+++||++.|++.|.+
T Consensus 2 ~~~~v~~L~~mFP~l~~~~I~~~L~~~~g~ve~~i~~LL~ 41 (43)
T smart00546 2 NDEALHDLKDMFPNLDEEVIKAVLEANNGNVEATINNLLE 41 (43)
T ss_pred hHHHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHc
Confidence 35678888887 4578889999999999999999998864
No 28
>PF06972 DUF1296: Protein of unknown function (DUF1296); InterPro: IPR009719 This family represents a conserved region approximately 60 residues long within a number of plant proteins of unknown function.
Probab=82.30 E-value=3.9 Score=29.66 Aligned_cols=39 Identities=15% Similarity=0.136 Sum_probs=35.8
Q ss_pred CHHHHHHHHHHhCC-CHHHHHHHHHHhcCCHHHHHHHHHH
Q psy17364 23 NKSLLGKLRKKTGY-SFTNCKKALDLNEQDLGKAEKWLQE 61 (312)
Q Consensus 23 ~~~lik~LR~~Tga-~~~dCKkAL~e~~gD~ekA~e~Lr~ 61 (312)
+.++|..|++-||. +=-+-...|.++|.|-++|.+-|..
T Consensus 5 ~rk~VQ~iKEiv~~hse~eIya~L~ecnMDpnea~qrLL~ 44 (60)
T PF06972_consen 5 SRKTVQSIKEIVGCHSEEEIYAMLKECNMDPNEAVQRLLS 44 (60)
T ss_pred HHHHHHHHHHHhcCCCHHHHHHHHHHhCCCHHHHHHHHHh
Confidence 56789999999999 9999999999999999999988875
No 29
>TIGR00855 L12 ribosomal protein L7/L12. THis model resembles Pfam model pfam00542 but matches the full length of prokaryotic and organellar proteins rather than just the C-terminus.
Probab=77.80 E-value=3.7 Score=34.33 Aligned_cols=28 Identities=14% Similarity=0.281 Sum_probs=25.0
Q ss_pred CHHHHHHHHHHhCCCHHHHHHHHHHhcC
Q psy17364 23 NKSLLGKLRKKTGYSFTNCKKALDLNEQ 50 (312)
Q Consensus 23 ~~~lik~LR~~Tga~~~dCKkAL~e~~g 50 (312)
-...||.+|..||.|+++.|+..+....
T Consensus 71 Ki~vIK~vR~itgLgLkEAK~lVe~~P~ 98 (126)
T TIGR00855 71 KIAVIKVVREITGLGLKEAKDLVEGAPK 98 (126)
T ss_pred hhHHHHHHHHHcCCcHHHHHHHHHhCcH
Confidence 5689999999999999999999988753
No 30
>PRK00157 rplL 50S ribosomal protein L7/L12; Reviewed
Probab=74.10 E-value=5.6 Score=33.13 Aligned_cols=27 Identities=15% Similarity=0.289 Sum_probs=24.2
Q ss_pred CHHHHHHHHHHhCCCHHHHHHHHHHhc
Q psy17364 23 NKSLLGKLRKKTGYSFTNCKKALDLNE 49 (312)
Q Consensus 23 ~~~lik~LR~~Tga~~~dCKkAL~e~~ 49 (312)
-.+.||.+|+-||.|+++.|+..+...
T Consensus 68 Ki~vIK~vR~itgLgLkEAK~lVe~~P 94 (123)
T PRK00157 68 KIAVIKAVREITGLGLKEAKDLVEGAP 94 (123)
T ss_pred hHHHHHHHHHHhCCCHHHHHHHHHhCC
Confidence 467999999999999999999988763
No 31
>cd00387 Ribosomal_L7_L12 Ribosomal protein L7/L12. Ribosomal protein L7/L12 refers to the large ribosomal subunit proteins L7 and L12, which are identical except that L7 is acetylated at the N terminus. It is a component of the L7/L12 stalk, which is located at the surface of the ribosome. The stalk base consists of a portion of the 23S rRNA and ribosomal proteins L11 and L10. An extended C-terminal helix of L10 provides the binding site for L7/L12. L7/L12 consists of two domains joined by a flexible hinge, with the helical N-terminal domain (NTD) forming pairs of homodimers that bind to the extended helix of L10. It is the only multimeric ribosomal component, with either four or six copies per ribosome that occur as two or three dimers bound to the L10 helix. L7/L12 is the only ribosomal protein that does not interact directly with rRNA, but instead has indirect interactions through L10. The globular C-terminal domains of L7/L12 are highly mobile. They are exposed to the cytoplasm and
Probab=71.14 E-value=11 Score=31.60 Aligned_cols=27 Identities=15% Similarity=0.337 Sum_probs=24.5
Q ss_pred CHHHHHHHHHHhCCCHHHHHHHHHHhc
Q psy17364 23 NKSLLGKLRKKTGYSFTNCKKALDLNE 49 (312)
Q Consensus 23 ~~~lik~LR~~Tga~~~dCKkAL~e~~ 49 (312)
-...||.+|.-||.|+++.|+..+.+.
T Consensus 73 Ki~vIK~VR~it~LgLkEAK~lVe~~P 99 (127)
T cd00387 73 KIAVIKEVREITGLGLKEAKDLVESAP 99 (127)
T ss_pred hHHHHHHHHHHhCCChHHHHHHHHhCc
Confidence 467999999999999999999998874
No 32
>CHL00083 rpl12 ribosomal protein L12
Probab=68.80 E-value=13 Score=31.34 Aligned_cols=27 Identities=19% Similarity=0.272 Sum_probs=24.2
Q ss_pred CHHHHHHHHHHhCCCHHHHHHHHHHhc
Q psy17364 23 NKSLLGKLRKKTGYSFTNCKKALDLNE 49 (312)
Q Consensus 23 ~~~lik~LR~~Tga~~~dCKkAL~e~~ 49 (312)
-...||.+|+-||.|+++.|+..+...
T Consensus 76 Ki~vIK~vr~it~lgLkeaK~lVe~~P 102 (131)
T CHL00083 76 RIAVLKVVRSLTGLGLKEAKELVESLP 102 (131)
T ss_pred hHHHHHHHHHHcCCCHHHHHHHHHhCC
Confidence 467999999999999999999988764
No 33
>COG0222 RplL Ribosomal protein L7/L12 [Translation, ribosomal structure and biogenesis]
Probab=67.84 E-value=7.5 Score=32.30 Aligned_cols=27 Identities=15% Similarity=0.273 Sum_probs=23.8
Q ss_pred CHHHHHHHHHHhCCCHHHHHHHHHHhc
Q psy17364 23 NKSLLGKLRKKTGYSFTNCKKALDLNE 49 (312)
Q Consensus 23 ~~~lik~LR~~Tga~~~dCKkAL~e~~ 49 (312)
-...||..|+-||.|+++.|+..+.+.
T Consensus 69 KI~VIK~vR~itGLGLKEAKdlVe~aP 95 (124)
T COG0222 69 KIAVIKVVRELTGLGLKEAKDLVEGAP 95 (124)
T ss_pred chhHHHHHHHHhcccHHHHHHHHHhCc
Confidence 567899999999999999999877763
No 34
>PF08938 HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This domain is found in various eukaryotic HBS1-like proteins. ; PDB: 1UFZ_A 3IZQ_1.
Probab=57.90 E-value=3.5 Score=31.37 Aligned_cols=36 Identities=28% Similarity=0.227 Sum_probs=29.2
Q ss_pred HHHHHHHhCCCH---HHHHHHHHHhcCCHHHHHHHHHHH
Q psy17364 27 LGKLRKKTGYSF---TNCKKALDLNEQDLGKAEKWLQEQ 62 (312)
Q Consensus 27 ik~LR~~Tga~~---~dCKkAL~e~~gD~ekA~e~Lr~~ 62 (312)
+-++|+.-|... ..-+.||-.++-|+++|+.||+++
T Consensus 32 l~~vr~~Lg~~~~~e~~i~eal~~~~fDvekAl~~Ll~~ 70 (79)
T PF08938_consen 32 LPQVREVLGDYVPPEEQIKEALWHYYFDVEKALDYLLSK 70 (79)
T ss_dssp CCCHHHHCCCCC--CCHHHHHHHHTTT-CCHHHHHHHHC
T ss_pred HHHHHHHHcccCCCHHHHHHHHHHHcCCHHHHHHHHHHh
Confidence 446778777654 689999999999999999999984
No 35
>COG4008 Predicted metal-binding transcription factor [Transcription]
Probab=57.02 E-value=32 Score=28.86 Aligned_cols=37 Identities=22% Similarity=0.163 Sum_probs=27.9
Q ss_pred HHHHHHHHHHhCCCHHHHHHHHHHhcCCHHHHHHHHHHH
Q psy17364 24 KSLLGKLRKKTGYSFTNCKKALDLNEQDLGKAEKWLQEQ 62 (312)
Q Consensus 24 ~~lik~LR~~Tga~~~dCKkAL~e~~gD~ekA~e~Lr~~ 62 (312)
.+.|+-|-+.- .+--+.++||++++ |+..|.++||.+
T Consensus 115 ~e~v~v~a~a~-v~~eeAr~aleeag-Dl~~A~k~l~~~ 151 (153)
T COG4008 115 VEEVEVLADAF-VTPEEAREALEEAG-DLRTAMKILRMK 151 (153)
T ss_pred HHHHHHHHHhc-CCHHHHHHHHHHcC-CHHHHHHHHHHh
Confidence 34444444433 67778999999999 999999999973
No 36
>KOG0944|consensus
Probab=54.52 E-value=12 Score=39.43 Aligned_cols=28 Identities=25% Similarity=0.525 Sum_probs=24.6
Q ss_pred CCCHHHHHHHHHHhcCCHHHHHHHHHHH
Q psy17364 35 GYSFTNCKKALDLNEQDLGKAEKWLQEQ 62 (312)
Q Consensus 35 ga~~~dCKkAL~e~~gD~ekA~e~Lr~~ 62 (312)
|-+--.|+|||.++|||++.|++|+-..
T Consensus 646 Gf~~~qa~~aL~~~n~nveravDWif~h 673 (763)
T KOG0944|consen 646 GFSRNQAIKALKATNNNVERAVDWIFSH 673 (763)
T ss_pred cCcHHHHHHHHHhcCccHHHHHHHHHhc
Confidence 5555689999999999999999999963
No 37
>PRK05441 murQ N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=54.06 E-value=17 Score=34.64 Aligned_cols=32 Identities=19% Similarity=0.174 Sum_probs=29.1
Q ss_pred HHHHhCCCHHHHHHHHHHhcCCHHHHHHHHHH
Q psy17364 30 LRKKTGYSFTNCKKALDLNEQDLGKAEKWLQE 61 (312)
Q Consensus 30 LR~~Tga~~~dCKkAL~e~~gD~ekA~e~Lr~ 61 (312)
+.+.||.+--+|.++|++++|++..|+-.+..
T Consensus 242 ~~~~~~~~~~~a~~~l~~~~~~vk~a~~~~~~ 273 (299)
T PRK05441 242 VMEATGVSREEAEAALEAADGSVKLAIVMILT 273 (299)
T ss_pred HHHHHCcCHHHHHHHHHHhCCCcHHHHHHHHh
Confidence 55569999999999999999999999998875
No 38
>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=51.65 E-value=68 Score=25.19 Aligned_cols=38 Identities=11% Similarity=0.136 Sum_probs=29.9
Q ss_pred HHHHHHHHHHhCCCHHHHHHHHHHh-cCCHHHHHHHHHHHH
Q psy17364 24 KSLLGKLRKKTGYSFTNCKKALDLN-EQDLGKAEKWLQEQA 63 (312)
Q Consensus 24 ~~lik~LR~~Tga~~~dCKkAL~e~-~gD~ekA~e~Lr~~~ 63 (312)
...|+.|| +|.||...|+-+... +||.+.+.+.|.++.
T Consensus 47 l~~I~~l~--~g~~l~~i~~~~~~~~~~~~~~~~~ll~~~~ 85 (99)
T cd04772 47 LRAYRALL--PGYGYRVAQRIMRAVHAGIVASALALVDAAH 85 (99)
T ss_pred HHHHHHHh--hCCCHHHHHHHHHHHhcCCHHHHHHHHHHHH
Confidence 45566666 699999999877775 589999999998863
No 39
>PF11626 Rap1_C: TRF2-interacting telomeric protein/Rap1 - C terminal domain; InterPro: IPR021661 This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres []. The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C-terminal domain []. ; PDB: 3K6G_C 3CZ6_A 3OWT_A.
Probab=50.27 E-value=32 Score=26.52 Aligned_cols=34 Identities=21% Similarity=0.240 Sum_probs=29.3
Q ss_pred HHHHHHHhCCCHHHHHHHHHHhcCCHHHHHHHHHH
Q psy17364 27 LGKLRKKTGYSFTNCKKALDLNEQDLGKAEKWLQE 61 (312)
Q Consensus 27 ik~LR~~Tga~~~dCKkAL~e~~gD~ekA~e~Lr~ 61 (312)
|+. .+.+|.+.-.+-+||..+.||+..|..++..
T Consensus 1 i~~-~~~~g~~~~~v~~aL~~tSgd~~~a~~~vl~ 34 (87)
T PF11626_consen 1 IKH-YEELGYSREFVTHALYATSGDPELARRFVLN 34 (87)
T ss_dssp -HH-HHHHTB-HHHHHHHHHHTTTBHHHHHHHHHH
T ss_pred Cch-HHHhCCCHHHHHHHHHHhCCCHHHHHHHHHH
Confidence 566 7889999999999999999999999997775
No 40
>TIGR00274 N-acetylmuramic acid 6-phosphate etherase. This protein, MurQ, is involved in recycling components of the bacterial murein sacculus turned over during cell growth. The cell wall metabolite anhydro-N-acetylmuramic acid (anhMurNAc) is converted by a kinase, AnmK, to MurNAc-phosphate, then converted to N-acetylglucosamine-phosphate by this etherase, called MurQ. This family of proteins is similar to the C-terminal half of a number of vertebrate glucokinase regulator proteins and contains a Prosite pattern which is shared by this group of proteins in a region of local similarity.
Probab=48.76 E-value=25 Score=33.44 Aligned_cols=32 Identities=16% Similarity=0.118 Sum_probs=29.0
Q ss_pred HHHHhCCCHHHHHHHHHHhcCCHHHHHHHHHH
Q psy17364 30 LRKKTGYSFTNCKKALDLNEQDLGKAEKWLQE 61 (312)
Q Consensus 30 LR~~Tga~~~dCKkAL~e~~gD~ekA~e~Lr~ 61 (312)
+.+.||++--+|.++|.+++|++..|+-.+..
T Consensus 237 ~~~~~~~~~~~a~~~l~~~~~~vk~Ai~~~~~ 268 (291)
T TIGR00274 237 VRQATDCNKELAEQTLLAADQNVKLAIVMILS 268 (291)
T ss_pred HHHHhCcCHHHHHHHHHHhCCCcHHHHHHHHh
Confidence 55669999999999999999999999998875
No 41
>cd04773 HTH_TioE_rpt2 Second 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 mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=41.78 E-value=1.2e+02 Score=24.21 Aligned_cols=42 Identities=17% Similarity=0.228 Sum_probs=31.1
Q ss_pred HHHHHHHHHHhCCCHHHHHHHHHHh--cCCHHHHHHHHHHHHHhh
Q psy17364 24 KSLLGKLRKKTGYSFTNCKKALDLN--EQDLGKAEKWLQEQAKEL 66 (312)
Q Consensus 24 ~~lik~LR~~Tga~~~dCKkAL~e~--~gD~ekA~e~Lr~~~~k~ 66 (312)
...|+.||+ .|.|+.+.+..|... +++.+...+.|.++.+..
T Consensus 47 l~~I~~lr~-~G~~l~~I~~~l~~~~~~~~~~~~~~~l~~~~~~l 90 (108)
T cd04773 47 ARLIHLLRR-GGYLLEQIATVVEQLRHAGGTEALAAALEQRRVAL 90 (108)
T ss_pred HHHHHHHHH-CCCCHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHH
Confidence 456777765 999999999999875 355677777777764444
No 42
>PF03474 DMA: DMRTA motif; InterPro: IPR005173 This region is found to the C terminus of the DM DNA-binding domain IPR001275 from INTERPRO []. DM-domain proteins with this motif are known as DMRTA proteins. The function of this region is unknown.
Probab=38.59 E-value=29 Score=23.07 Aligned_cols=18 Identities=17% Similarity=0.076 Sum_probs=15.1
Q ss_pred HHHHHHhcCCHHHHHHHH
Q psy17364 42 KKALDLNEQDLGKAEKWL 59 (312)
Q Consensus 42 KkAL~e~~gD~ekA~e~L 59 (312)
--.|.-++||+-+|||.+
T Consensus 21 e~iL~~C~GDvv~AIE~~ 38 (39)
T PF03474_consen 21 ELILQRCNGDVVQAIEQF 38 (39)
T ss_pred HHHHHHcCCcHHHHHHHh
Confidence 346888999999999975
No 43
>PRK12570 N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=38.23 E-value=40 Score=32.08 Aligned_cols=32 Identities=22% Similarity=0.207 Sum_probs=28.7
Q ss_pred HHHHhCCCHHHHHHHHHHhcCCHHHHHHHHHH
Q psy17364 30 LRKKTGYSFTNCKKALDLNEQDLGKAEKWLQE 61 (312)
Q Consensus 30 LR~~Tga~~~dCKkAL~e~~gD~ekA~e~Lr~ 61 (312)
+.+.||.+.-+|.++|++++|++.-|+-.+..
T Consensus 238 ~~~~~~~~~~~a~~~l~~~~~~vk~ai~~~~~ 269 (296)
T PRK12570 238 VMQATGCSEDEAKELLKESDNDVKLAILMILT 269 (296)
T ss_pred HHHHHCcCHHHHHHHHHHhCCccHHHHHHHHh
Confidence 45569999999999999999999999998775
No 44
>cd00215 PTS_IIA_lac PTS_IIA, PTS system, lactose/cellobiose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation. This family of proteins normally function as a homotrimer, stabilized by a centrally located metal ion. Separation into subunits is thought to occur after phosphorylation.
Probab=38.18 E-value=42 Score=26.65 Aligned_cols=29 Identities=31% Similarity=0.443 Sum_probs=24.1
Q ss_pred HhCCCHHHHHHHHHHh-cCCHHHHHHHHHH
Q psy17364 33 KTGYSFTNCKKALDLN-EQDLGKAEKWLQE 61 (312)
Q Consensus 33 ~Tga~~~dCKkAL~e~-~gD~ekA~e~Lr~ 61 (312)
..|-.=..|-+||.++ +||+++|.+.|++
T Consensus 11 ~aG~Ars~~~eAl~~a~~g~fe~A~~~l~e 40 (97)
T cd00215 11 HAGNARSKALEALKAAKEGDFAEAEELLEE 40 (97)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence 3455556889999998 7999999999997
No 45
>PRK09591 celC cellobiose phosphotransferase system IIA component; Reviewed
Probab=36.97 E-value=45 Score=26.88 Aligned_cols=29 Identities=24% Similarity=0.304 Sum_probs=24.2
Q ss_pred HhCCCHHHHHHHHHHh-cCCHHHHHHHHHH
Q psy17364 33 KTGYSFTNCKKALDLN-EQDLGKAEKWLQE 61 (312)
Q Consensus 33 ~Tga~~~dCKkAL~e~-~gD~ekA~e~Lr~ 61 (312)
..|-.=..|.+||..+ +||+++|.+.|.+
T Consensus 16 ~aG~Ars~~~eAl~~ak~gdf~~A~~~l~e 45 (104)
T PRK09591 16 HSGNARTEVHEAFAAMREGNFDLAEQKLNQ 45 (104)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence 3455566899999998 6999999999997
No 46
>TIGR00823 EIIA-LAC phosphotransferase system enzyme II, lactose-specific, factor III. operon. While the Lac permeases consist of two polypeptide chains (IIA and IICB), the Chb permease of E. coli consists of three (IIA, IIB and IIC). In B. subtilis, a PTS permease similar to the Chb permease of E. coli is believed to transport lichenan (a b-1,3;1,4 glucan) degradation products, oligosaccharides of 2-4 glucose units. This model is specific for the IIA subunit of the Lac PTS family.
Probab=36.80 E-value=46 Score=26.55 Aligned_cols=29 Identities=21% Similarity=0.275 Sum_probs=24.1
Q ss_pred HhCCCHHHHHHHHHHh-cCCHHHHHHHHHH
Q psy17364 33 KTGYSFTNCKKALDLN-EQDLGKAEKWLQE 61 (312)
Q Consensus 33 ~Tga~~~dCKkAL~e~-~gD~ekA~e~Lr~ 61 (312)
..|-.=..|-+||.++ +||+++|.+.|.+
T Consensus 13 ~aG~Ars~~~eAl~~a~~gdfe~A~~~l~e 42 (99)
T TIGR00823 13 YAGDARSKALEALKAAKAGDFAKARALVEQ 42 (99)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence 3455566889999998 6999999999997
No 47
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They 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.
Probab=35.52 E-value=1.2e+02 Score=23.47 Aligned_cols=40 Identities=25% Similarity=0.303 Sum_probs=28.8
Q ss_pred HHHHHHHHHHhCCCHHHHHHHHHHhcCCHHHHHHHHHHHHHhhc
Q psy17364 24 KSLLGKLRKKTGYSFTNCKKALDLNEQDLGKAEKWLQEQAKELG 67 (312)
Q Consensus 24 ~~lik~LR~~Tga~~~dCKkAL~e~~gD~ekA~e~Lr~~~~k~G 67 (312)
...|+.||+ +|.++.+.++-|...+. ...++|.++.+..-
T Consensus 47 l~~I~~lr~-~G~~l~eI~~~l~~~~~---~~~~~l~~~~~~l~ 86 (96)
T cd04788 47 LHQIIALRR-LGFSLREIGRALDGPDF---DPLELLRRQLARLE 86 (96)
T ss_pred HHHHHHHHH-cCCCHHHHHHHHhCCCh---hHHHHHHHHHHHHH
Confidence 567888876 79999999999976542 55667777544433
No 48
>KOG2561|consensus
Probab=34.00 E-value=57 Score=33.12 Aligned_cols=36 Identities=22% Similarity=0.270 Sum_probs=29.3
Q ss_pred CCCHHHHHHHHHHhcCCHHHHHHHHHHHHHhhcHHHHHhh
Q psy17364 35 GYSFTNCKKALDLNEQDLGKAEKWLQEQAKELGWAKASKL 74 (312)
Q Consensus 35 ga~~~dCKkAL~e~~gD~ekA~e~Lr~~~~k~G~~~A~Kr 74 (312)
|.-=.|.|-||..++||++.|+++|.+. -+.+|.+|
T Consensus 314 GfeesdaRlaLRsc~g~Vd~AvqfI~er----re~laq~R 349 (568)
T KOG2561|consen 314 GFEESDARLALRSCNGDVDSAVQFIIER----REKLAQKR 349 (568)
T ss_pred CCCchHHHHHHHhccccHHHHHHHHHHH----HHHHHHHH
Confidence 4444699999999999999999999995 55566555
No 49
>PRK08248 O-acetylhomoserine aminocarboxypropyltransferase; Validated
Probab=33.40 E-value=83 Score=31.44 Aligned_cols=48 Identities=19% Similarity=0.192 Sum_probs=34.4
Q ss_pred cccccccccCC-CCcHHHHHHHcCCceeeEEEEEec-CccccccchHhHhhh
Q psy17364 261 IMYHQEFLLDP-TQYVGEVIVAAGIKPVEFLRFECG-EGCEESEETQTQAAT 310 (312)
Q Consensus 261 ~Ll~Q~fi~d~-~~tV~~~l~~~~~~v~~F~r~~vG-e~ie~~~~~~~~~~~ 310 (312)
.|...|..+-- ..+ .+..+..|+. .+++|+.|| |+.++--+|+.||..
T Consensus 377 sl~~~p~~~~h~~~~-~~~~~~~gi~-~~liRlsvGlEd~~dL~~Dl~~Al~ 426 (431)
T PRK08248 377 SLIIHPASTTHQQLS-EEEQLAAGVT-PGLVRLSVGTEAIDDILDDLRQAIR 426 (431)
T ss_pred eeeeCCCcCccccCC-HHHHHhcCCC-CCeEEEEeccCCHHHHHHHHHHHHH
Confidence 66677765543 233 3344456776 679999999 999999999999864
No 50
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=33.37 E-value=48 Score=21.74 Aligned_cols=19 Identities=26% Similarity=0.396 Sum_probs=15.3
Q ss_pred HHHHHHhcCCHHHHHHHHH
Q psy17364 42 KKALDLNEQDLGKAEKWLQ 60 (312)
Q Consensus 42 KkAL~e~~gD~ekA~e~Lr 60 (312)
.+||+.++||+.+|-+.|-
T Consensus 11 ~~aL~~~~gn~~~aA~~Lg 29 (42)
T PF02954_consen 11 RQALERCGGNVSKAARLLG 29 (42)
T ss_dssp HHHHHHTTT-HHHHHHHHT
T ss_pred HHHHHHhCCCHHHHHHHHC
Confidence 5799999999999888764
No 51
>PF14117 DUF4287: Domain of unknown function (DUF4287)
Probab=32.39 E-value=1.1e+02 Score=22.36 Aligned_cols=39 Identities=23% Similarity=0.392 Sum_probs=31.9
Q ss_pred HHHHHHHHHHhCCCHHHHHHHHHHhcC--CHHHHHHHHHHH
Q psy17364 24 KSLLGKLRKKTGYSFTNCKKALDLNEQ--DLGKAEKWLQEQ 62 (312)
Q Consensus 24 ~~lik~LR~~Tga~~~dCKkAL~e~~g--D~ekA~e~Lr~~ 62 (312)
.+++-.++++||-++-+=.+.+.+..+ ...+-+.||+..
T Consensus 3 ~sy~~~Ie~kTGk~~~~W~~~~~~~~~~~k~~e~v~WLK~e 43 (61)
T PF14117_consen 3 QSYLPNIEKKTGKTLDEWLALAREGGPLTKHGEIVAWLKDE 43 (61)
T ss_pred HHHHhHhHHHHCcCHHHHHHHHHHhCCCCcHHHHHHHHHHH
Confidence 467888999999999999999999843 345778888863
No 52
>PRK10454 PTS system N,N'-diacetylchitobiose-specific transporter subunit IIA; Provisional
Probab=31.49 E-value=60 Score=26.68 Aligned_cols=34 Identities=18% Similarity=0.165 Sum_probs=27.5
Q ss_pred HHHHHHhCCCHHHHHHHHHHh-cCCHHHHHHHHHH
Q psy17364 28 GKLRKKTGYSFTNCKKALDLN-EQDLGKAEKWLQE 61 (312)
Q Consensus 28 k~LR~~Tga~~~dCKkAL~e~-~gD~ekA~e~Lr~ 61 (312)
-+|=--.|-.=+.|-+||.++ +||+++|.+.|.+
T Consensus 22 ~~II~~aG~ArS~~~eAl~~Ak~gdfe~A~~~l~e 56 (115)
T PRK10454 22 MGLIINSGQARSLAYAALKQAKQGDFAAAKAMMDQ 56 (115)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHH
Confidence 334445676777899999998 6999999999997
No 53
>PF08285 DPM3: Dolichol-phosphate mannosyltransferase subunit 3 (DPM3); InterPro: IPR013174 This family corresponds to subunit 3 of dolichol-phosphate mannosyltransferase, an enzyme which generates mannosyl donors for glycosylphosphatidylinositols, N-glycan and protein O- and C-mannosylation. DPM3 is an integral membrane protein and plays a role in stabilising the dolichol-phosphate mannosyl transferase complex [].
Probab=29.98 E-value=21 Score=28.08 Aligned_cols=25 Identities=20% Similarity=0.437 Sum_probs=22.5
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHH
Q psy17364 38 FTNCKKALDLNEQDLGKAEKWLQEQ 62 (312)
Q Consensus 38 ~~dCKkAL~e~~gD~ekA~e~Lr~~ 62 (312)
+-||.+|=+|-..++++|.+-||++
T Consensus 63 FnDcpeA~~eL~~eI~eAK~dLr~k 87 (91)
T PF08285_consen 63 FNDCPEAAKELQKEIKEAKADLRKK 87 (91)
T ss_pred cCCCHHHHHHHHHHHHHHHHHHHHc
Confidence 4499999999999999999999983
No 54
>COG2103 Predicted sugar phosphate isomerase [General function prediction only]
Probab=29.67 E-value=1.1e+02 Score=29.13 Aligned_cols=32 Identities=19% Similarity=0.129 Sum_probs=28.8
Q ss_pred HHHHhCCCHHHHHHHHHHhcCCHHHHHHHHHH
Q psy17364 30 LRKKTGYSFTNCKKALDLNEQDLGKAEKWLQE 61 (312)
Q Consensus 30 LR~~Tga~~~dCKkAL~e~~gD~ekA~e~Lr~ 61 (312)
+.+.||++--+...+|.+++++++-|+-.+..
T Consensus 240 v~~aT~~~~~~A~~~L~~~~~~vK~AIvm~~~ 271 (298)
T COG2103 240 VMEATGCSAEEAEALLEEAGGNVKLAIVMLLT 271 (298)
T ss_pred HHHHhCCCHHHHHHHHHHcCCccHhHHHHHHh
Confidence 34459999999999999999999999999886
No 55
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=29.31 E-value=1.9e+02 Score=22.57 Aligned_cols=34 Identities=24% Similarity=0.239 Sum_probs=26.5
Q ss_pred HHHHHHHHHhCCCHHHHHHHHHHhcCCHHHHHHHHHHH
Q psy17364 25 SLLGKLRKKTGYSFTNCKKALDLNEQDLGKAEKWLQEQ 62 (312)
Q Consensus 25 ~lik~LR~~Tga~~~dCKkAL~e~~gD~ekA~e~Lr~~ 62 (312)
..|+.||+ .|.|+.++++.|...+ +...+.|.++
T Consensus 48 ~~i~~lr~-~g~~l~~i~~~~~~~~---~~~~~~l~~~ 81 (103)
T cd01106 48 QQILFLKE-LGFSLKEIKELLKDPS---EDLLEALREQ 81 (103)
T ss_pred HHHHHHHH-cCCCHHHHHHHHHcCc---HHHHHHHHHH
Confidence 45677776 7999999999998765 6666777765
No 56
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares 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.
Probab=29.20 E-value=1.8e+02 Score=23.03 Aligned_cols=36 Identities=25% Similarity=0.433 Sum_probs=27.5
Q ss_pred HHHHHHHHHHhCCCHHHHHHHHHHhcCCHHHHHHHHHHH
Q psy17364 24 KSLLGKLRKKTGYSFTNCKKALDLNEQDLGKAEKWLQEQ 62 (312)
Q Consensus 24 ~~lik~LR~~Tga~~~dCKkAL~e~~gD~ekA~e~Lr~~ 62 (312)
...|+.||+ +|.|+.+.+.-+...+. +.....|..+
T Consensus 48 l~~I~~lr~-~G~sl~~i~~l~~~~~~--~~~~~~l~~~ 83 (108)
T cd01107 48 LNRIKYLRD-LGFPLEEIKEILDADND--DELRKLLREK 83 (108)
T ss_pred HHHHHHHHH-cCCCHHHHHHHHhcCCH--HHHHHHHHHH
Confidence 467888877 99999999998876553 6667777665
No 57
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=27.90 E-value=2e+02 Score=22.82 Aligned_cols=26 Identities=31% Similarity=0.520 Sum_probs=21.7
Q ss_pred HHHHHHHHHHhCCCHHHHHHHHHHhcC
Q psy17364 24 KSLLGKLRKKTGYSFTNCKKALDLNEQ 50 (312)
Q Consensus 24 ~~lik~LR~~Tga~~~dCKkAL~e~~g 50 (312)
...|+.|| .+|.++.+||+.|...+-
T Consensus 47 l~~I~~~r-~~G~~L~~I~~~l~~~~~ 72 (124)
T COG0789 47 LQIIKTLR-ELGFSLAEIKELLDLLSA 72 (124)
T ss_pred HHHHHHHH-HcCCCHHHHHHHHhcccc
Confidence 45677777 899999999999998864
No 58
>TIGR03595 Obg_CgtA_exten Obg family GTPase CgtA, C-terminal extension. CgtA (see model TIGR02729) is a broadly conserved member of the obg family of GTPases associated with ribosome maturation. This model represents a unique C-terminal domain found in some but not all sequences of CgtA. This region is preceded, and may be followed, by a region of low-complexity sequence.
Probab=27.47 E-value=97 Score=22.87 Aligned_cols=36 Identities=19% Similarity=0.208 Sum_probs=30.3
Q ss_pred HHHHHhcCCHHHHHHHHHHHHHhhcHHHHHhhhhhc
Q psy17364 43 KALDLNEQDLGKAEKWLQEQAKELGWAKASKLAGRK 78 (312)
Q Consensus 43 kAL~e~~gD~ekA~e~Lr~~~~k~G~~~A~Kr~~R~ 78 (312)
+-+..+|.|-++|+..+....+++|...++++++-.
T Consensus 20 r~~~~~~~~~~e~~~~f~~~L~~~Gv~~~L~~~G~~ 55 (69)
T TIGR03595 20 RWVAKTPFNNDENLRRFARKLKKLGVEDALRKAGAK 55 (69)
T ss_pred HHHHHcCCCCHHHHHHHHHHHHHCCHHHHHHHcCCC
Confidence 345668889999999999999999999999987643
No 59
>cd00591 HU_IHF Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and higher-order nucleoprotein complex assembly. The dimer subunits associate to form a compact globular core from which two beta ribbon arms (one from each subunit) protrude. The beta arms track and bind the DNA minor groove. Despite sequence and structural similarity, IHF and HU can be distinguished by their different DNA substrate preferences.
Probab=26.90 E-value=92 Score=23.27 Aligned_cols=26 Identities=27% Similarity=0.334 Sum_probs=22.8
Q ss_pred HHHHHHHHHHhCCCHHHHHHHHHHhc
Q psy17364 24 KSLLGKLRKKTGYSFTNCKKALDLNE 49 (312)
Q Consensus 24 ~~lik~LR~~Tga~~~dCKkAL~e~~ 49 (312)
.++++.|-++||.+..|++..|+...
T Consensus 3 ~~l~~~ia~~~~~~~~~v~~vl~~~~ 28 (87)
T cd00591 3 SELIEAIAEKTGLSKKDAEAAVDAFL 28 (87)
T ss_pred HHHHHHHHHHhCcCHHHHHHHHHHHH
Confidence 47899999999999999999987654
No 60
>PF00216 Bac_DNA_binding: Bacterial DNA-binding protein; InterPro: IPR000119 Bacteria synthesise a set of small, usually basic proteins of about 90 residues that bind DNA and are known as histone-like proteins [, ]. Examples include the HU protein in Escherichia coli is a dimer of closely related alpha and beta chains and in other bacteria can be a dimer of identical chains. HU-type proteins have been found in a variety of eubacteria, cyanobacteria and archaebacteria, and are also encoded in the chloroplast genome of some algae []. The integration host factor (IHF), a dimer of closely related chains which seem to function in genetic recombination as well as in translational and transcriptional control [] is found in enterobacteria and viral proteins include the African Swine fever virus protein A104R (or LMW5-AR) []. The exact function of these proteins is not yet clear but they are capable of wrapping DNA and stabilising it from denaturation under extreme environmental conditions. The structure is known for one of these proteins []. The protein exists as a dimer and two "beta-arms" function as the non-specific binding site for bacterial DNA. ; GO: 0003677 DNA binding; PDB: 3C4I_B 2O97_A 1MUL_A 1P78_A 1P51_C 1P71_B 2HT0_A 1OWG_A 2IIF_A 1OUZ_A ....
Probab=26.84 E-value=91 Score=23.40 Aligned_cols=26 Identities=31% Similarity=0.388 Sum_probs=23.2
Q ss_pred HHHHHHHHHHhCCCHHHHHHHHHHhc
Q psy17364 24 KSLLGKLRKKTGYSFTNCKKALDLNE 49 (312)
Q Consensus 24 ~~lik~LR~~Tga~~~dCKkAL~e~~ 49 (312)
.++|+.+.++||.+-.||+..|.+.-
T Consensus 4 ~eli~~ia~~~~~s~~~v~~vl~~~~ 29 (90)
T PF00216_consen 4 KELIKRIAEKTGLSKKDVEAVLDALF 29 (90)
T ss_dssp HHHHHHHHHHHTSSHHHHHHHHHHHH
T ss_pred HHHHHHHHHhcCCCHHHHHHHHHHHH
Confidence 57999999999999999999987764
No 61
>PF02255 PTS_IIA: PTS system, Lactose/Cellobiose specific IIA subunit; InterPro: IPR003188 The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) [, ] is a major carbohydrate transport system in bacteria. The PTS catalyses the phosphorylation of incoming sugar substrates and coupled with translocation across the cell membrane, makes the PTS a link between the uptake and metabolism of sugars. The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred via a signal transduction pathway, to enzyme I (EI) which in turn transfers it to a phosphoryl carrier, the histidine protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease, a membrane-bound complex known as enzyme 2 (EII), which transports the sugar to the cell. EII consists of at least three structurally distinct domains IIA, IIB and IIC []. These can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII). The first domain (IIA or EIIA) carries the first permease-specific phosphorylation site, a histidine which is phosphorylated by phospho-HPr. The second domain (IIB or EIIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the sugar transported. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate concomitantly with the sugar uptake processed by the IIC domain. This third domain (IIC or EIIC) forms the translocation channel and the specific substrate-binding site. An additional transmembrane domain IID, homologous to IIC, can be found in some PTSs, e.g. for mannose [, , , ]. The lactose/cellobiose-specific family are one of four structurally and functionally distinct group IIA PTS system enzymes. This family of proteins normally function as a homotrimer, stabilised by a centrally located metal ion []. Separation into subunits is thought to occur after phosphorylation.; GO: 0005351 sugar:hydrogen symporter activity, 0006810 transport, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system, 0016020 membrane; PDB: 3L8R_D 2E2A_B 1E2A_C 3K1S_C 2LRK_C 2LRL_A 2WY2_A 1WCR_A 2WWV_C.
Probab=26.67 E-value=86 Score=24.76 Aligned_cols=27 Identities=33% Similarity=0.386 Sum_probs=20.7
Q ss_pred CCCHHHHHHHHHHh-cCCHHHHHHHHHH
Q psy17364 35 GYSFTNCKKALDLN-EQDLGKAEKWLQE 61 (312)
Q Consensus 35 ga~~~dCKkAL~e~-~gD~ekA~e~Lr~ 61 (312)
|-.=..|-+||..+ +||+++|.+.|++
T Consensus 12 G~Ars~~~eAl~~a~~~~fe~A~~~l~~ 39 (96)
T PF02255_consen 12 GDARSLAMEALKAAREGDFEEAEELLKE 39 (96)
T ss_dssp HHHHHHHHHHHHHHHTT-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHHHH
Confidence 33345678889887 6999999999997
No 62
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=25.75 E-value=90 Score=22.04 Aligned_cols=22 Identities=23% Similarity=0.549 Sum_probs=18.8
Q ss_pred HHHHHHHHHHhCCCHHHHHHHHH
Q psy17364 24 KSLLGKLRKKTGYSFTNCKKALD 46 (312)
Q Consensus 24 ~~lik~LR~~Tga~~~dCKkAL~ 46 (312)
...|+.||+ .|.++..++++|.
T Consensus 47 l~~i~~lr~-~g~~~~~i~~~l~ 68 (70)
T smart00422 47 LRFIKRLKE-LGFSLEEIKELLE 68 (70)
T ss_pred HHHHHHHHH-cCCCHHHHHHHHh
Confidence 456888887 9999999999885
No 63
>smart00668 CTLH C-terminal to LisH motif. Alpha-helical motif of unknown function.
Probab=25.74 E-value=54 Score=22.33 Aligned_cols=14 Identities=29% Similarity=0.556 Sum_probs=12.8
Q ss_pred cCCHHHHHHHHHHH
Q psy17364 49 EQDLGKAEKWLQEQ 62 (312)
Q Consensus 49 ~gD~ekA~e~Lr~~ 62 (312)
.||+++|++|+.+.
T Consensus 14 ~g~~~~a~~~~~~~ 27 (58)
T smart00668 14 KGDWDEALEWLSSL 27 (58)
T ss_pred cCCHHHHHHHHHHc
Confidence 79999999999974
No 64
>TIGR03884 sel_bind_Methan selenium-binding protein. This model describes a homopentameric selenium-binding protein with a suggested role in selenium transport and delivery to selenophosphate synthase, the SelD protein. This protein family is closely related to pfam01906, but is shorter because of several deleted regions. It is restricted to the archaeal genus Methanococcus.
Probab=25.22 E-value=59 Score=24.68 Aligned_cols=21 Identities=19% Similarity=0.265 Sum_probs=16.4
Q ss_pred hcCCHHHHHHHHHHHHHhhcH
Q psy17364 48 NEQDLGKAEKWLQEQAKELGW 68 (312)
Q Consensus 48 ~~gD~ekA~e~Lr~~~~k~G~ 68 (312)
+..|+|+|++-|.+++++.|.
T Consensus 23 ~~~d~d~Al~eM~e~A~~lGA 43 (74)
T TIGR03884 23 ESDNVDEIVENLREKVKAKGG 43 (74)
T ss_pred ecCCHHHHHHHHHHHHHHcCC
Confidence 345999999999997666663
No 65
>PRK10564 maltose regulon periplasmic protein; Provisional
Probab=25.00 E-value=77 Score=30.45 Aligned_cols=32 Identities=38% Similarity=0.448 Sum_probs=23.2
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHHHHhhcHHHHHh
Q psy17364 39 TNCKKALDLNEQDLGKAEKWLQEQAKELGWAKASK 73 (312)
Q Consensus 39 ~dCKkAL~e~~gD~ekA~e~Lr~~~~k~G~~~A~K 73 (312)
.--|+|++ .||++||+.+|.| +++.|...|..
T Consensus 262 ~aI~~AVk--~gDi~KAL~LldE-Ae~LG~~~Ar~ 293 (303)
T PRK10564 262 QAIKQAVK--KGDVDKALKLLDE-AERLGSTSARS 293 (303)
T ss_pred HHHHHHHH--cCCHHHHHHHHHH-HHHhCCchHHH
Confidence 34455554 6999999999997 66777666643
No 66
>KOG1715|consensus
Probab=24.90 E-value=1.6e+02 Score=26.28 Aligned_cols=27 Identities=19% Similarity=0.363 Sum_probs=23.3
Q ss_pred cCHHHHHHHHHHhCCCHHHHHHHHHHh
Q psy17364 22 TNKSLLGKLRKKTGYSFTNCKKALDLN 48 (312)
Q Consensus 22 ~~~~lik~LR~~Tga~~~dCKkAL~e~ 48 (312)
.-++.||++|--||.|+.+.||=.+.+
T Consensus 131 ~KIkVIKEVR~~tgL~LkeAKklVE~a 157 (187)
T KOG1715|consen 131 SKIKVIKEVRALTGLGLKEAKKLVEKA 157 (187)
T ss_pred chhHHHHHHHHhccccHHHHHHHHHhc
Confidence 346899999999999999999877665
No 67
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), 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 two 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=24.86 E-value=2.7e+02 Score=21.67 Aligned_cols=39 Identities=21% Similarity=0.265 Sum_probs=28.2
Q ss_pred CHHHHHHHHHHhCCCHHHHHHHHHH-hcCCHHHHHHHHHH
Q psy17364 23 NKSLLGKLRKKTGYSFTNCKKALDL-NEQDLGKAEKWLQE 61 (312)
Q Consensus 23 ~~~lik~LR~~Tga~~~dCKkAL~e-~~gD~ekA~e~Lr~ 61 (312)
....|+.||+..|.++.++|+.|.. -+..+..=.+.|.+
T Consensus 46 ~l~~I~~L~~~~G~~l~~I~~~l~~~~~~~~~~~~~~~~~ 85 (95)
T cd04780 46 RLRLIRALQQEGGLPISQIKEVLDAIADASLPSTLLALAV 85 (95)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHhcCcccHHHHHHHHHH
Confidence 3567888888899999999999987 22344455555554
No 68
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two 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=24.44 E-value=2.9e+02 Score=21.14 Aligned_cols=38 Identities=26% Similarity=0.458 Sum_probs=28.7
Q ss_pred HHHHHHHHHHhCCCHHHHHHHHHHhcCC--HHHHHHHHHHH
Q psy17364 24 KSLLGKLRKKTGYSFTNCKKALDLNEQD--LGKAEKWLQEQ 62 (312)
Q Consensus 24 ~~lik~LR~~Tga~~~dCKkAL~e~~gD--~ekA~e~Lr~~ 62 (312)
...|+.||. .|.++.+.++.|...+.+ .+...+.|..+
T Consensus 46 l~~i~~l~~-~g~~~~~i~~~l~~~~~~~~~~~~~~~~~~~ 85 (100)
T cd00592 46 LRLIRRLRE-LGLSLKEIRELLDARDEELSLAALLALLDEK 85 (100)
T ss_pred HHHHHHHHH-cCCCHHHHHHHHhcccccchHHHHHHHHHHH
Confidence 467888988 999999999999877544 44555555553
No 69
>PF10607 CLTH: CTLH/CRA C-terminal to LisH motif domain; InterPro: IPR019589 This entry represents the CRA (or CT11-RanBPM) domain, which is a protein-protein interaction domain present in crown eukaryotes (plants, animals, fungi) and which is found in Ran-binding proteins such as Ran-binding protein 9 (RanBP9 or RanBPM) and RanBP10. RanBPM is a scaffolding protein important in regulating cellular function in both the immune system and the nervous system, and may act as an adapter protein to couple membrane receptors to intracellular signaling pathways. This domain is at the C terminus of the proteins and is the binding domain for the CRA motif, which is comprised of approximately 100 amino acids at the C-terminal of RanBPM. It was found to be important for the interaction of RanBPM with fragile X mental retardation protein (FMRP), but its functional significance has yet to be determined [].
Probab=24.41 E-value=86 Score=25.75 Aligned_cols=21 Identities=29% Similarity=0.590 Sum_probs=17.0
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHH
Q psy17364 40 NCKKALDLNEQDLGKAEKWLQEQ 62 (312)
Q Consensus 40 dCKkAL~e~~gD~ekA~e~Lr~~ 62 (312)
..++++ -+||++.|++|+.+.
T Consensus 7 ~I~~~I--~~g~i~~Ai~w~~~~ 27 (145)
T PF10607_consen 7 KIRQAI--LNGDIDPAIEWLNEN 27 (145)
T ss_pred HHHHHH--HcCCHHHHHHHHHHc
Confidence 455666 689999999999974
No 70
>KOG1364|consensus
Probab=23.96 E-value=1.4e+02 Score=29.24 Aligned_cols=40 Identities=20% Similarity=0.184 Sum_probs=36.4
Q ss_pred CHHHHHHHHHHhC-CCHHHHHHHHHHhcCCHHHHHHHHHHH
Q psy17364 23 NKSLLGKLRKKTG-YSFTNCKKALDLNEQDLGKAEKWLQEQ 62 (312)
Q Consensus 23 ~~~lik~LR~~Tg-a~~~dCKkAL~e~~gD~ekA~e~Lr~~ 62 (312)
-.+||++.+.-|+ -.+-..++=|..++||++.|+.++++.
T Consensus 6 ~~~lv~~fl~It~~~t~e~A~q~L~~~~~~le~ai~Lffe~ 46 (356)
T KOG1364|consen 6 QRALVSKFLAITVQQTVEIATQYLSAADWDLEAAINLFFEH 46 (356)
T ss_pred HHHHHHHHHHHhccccHHHHHHHHHhcCCcHHHHHHHHHHh
Confidence 3579999999999 777789999999999999999999995
No 71
>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators. Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. 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.
Probab=23.35 E-value=3.3e+02 Score=22.09 Aligned_cols=43 Identities=14% Similarity=0.338 Sum_probs=29.8
Q ss_pred HHHHHHHHHHhCCCHHHHHHHHHHhc---CCHHHHHHHHHHHHHhhc
Q psy17364 24 KSLLGKLRKKTGYSFTNCKKALDLNE---QDLGKAEKWLQEQAKELG 67 (312)
Q Consensus 24 ~~lik~LR~~Tga~~~dCKkAL~e~~---gD~ekA~e~Lr~~~~k~G 67 (312)
...|+.|| .+|.++.+.|+-|.... .+..+....|.++.+..-
T Consensus 47 l~~I~~lr-~~G~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~ 92 (126)
T cd04785 47 LRFIRRAR-DLGFSLEEIRALLALSDRPDRSCAEADAIARAHLADVR 92 (126)
T ss_pred HHHHHHHH-HCCCCHHHHHHHHhhhhcCCCCHHHHHHHHHHHHHHHH
Confidence 55677776 79999999999887543 255666666666543333
No 72
>PRK08133 O-succinylhomoserine sulfhydrylase; Validated
Probab=22.95 E-value=73 Score=31.18 Aligned_cols=49 Identities=18% Similarity=0.180 Sum_probs=33.1
Q ss_pred cccccccccCC-CCcHHHHHHHcCCceeeEEEEEec-CccccccchHhHhhhc
Q psy17364 261 IMYHQEFLLDP-TQYVGEVIVAAGIKPVEFLRFECG-EGCEESEETQTQAATA 311 (312)
Q Consensus 261 ~Ll~Q~fi~d~-~~tV~~~l~~~~~~v~~F~r~~vG-e~ie~~~~~~~~~~~~ 311 (312)
.|+.+|+.+-- ..+ .+..+..|+. .+++|+.|| |+.|+--+|+.||..|
T Consensus 340 sl~~~p~~~~~~~~~-~~~~~~~gi~-~~liR~svGlE~~~dl~~dl~~al~~ 390 (390)
T PRK08133 340 TTITHPATTTHGRLS-PEARAAAGIT-EGLIRVAVGLEDVADIKADLARGLAA 390 (390)
T ss_pred eeeecCCCCCcccCC-HHHHHhcCCC-CCeEEEEeCcCCHHHHHHHHHHHhhC
Confidence 45556665532 222 3444455553 479999999 8999999999998754
No 73
>PRK06702 O-acetylhomoserine aminocarboxypropyltransferase; Validated
Probab=22.84 E-value=76 Score=31.88 Aligned_cols=51 Identities=18% Similarity=0.181 Sum_probs=33.5
Q ss_pred cccccccccCCCCcHHHHHHHcCCceeeEEEEEec-CccccccchHhHhhhcC
Q psy17364 261 IMYHQEFLLDPTQYVGEVIVAAGIKPVEFLRFECG-EGCEESEETQTQAATAG 312 (312)
Q Consensus 261 ~Ll~Q~fi~d~~~tV~~~l~~~~~~v~~F~r~~vG-e~ie~~~~~~~~~~~~~ 312 (312)
.|..+|..+--..--.+..+..|+. -+++|+.|| |+.|+--+|+.||...|
T Consensus 374 Slv~~p~~~th~~~~~~~~~~~Gi~-~~liRlSvGlEd~eDLi~Dl~~Al~~~ 425 (432)
T PRK06702 374 TCVIHPASTTHRQLSAEDQRLAGVT-SDLIRLSVGIEDVSDIIADLEAALVGG 425 (432)
T ss_pred cceECCCCCCcccCCHHHHHhcCCC-CCeEEEEeccCCHHHHHHHHHHHHhcC
Confidence 4555555443222113444445654 469999999 99999999999997654
No 74
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=22.52 E-value=87 Score=22.15 Aligned_cols=23 Identities=35% Similarity=0.408 Sum_probs=18.1
Q ss_pred HHHHHHHHHHhCCCHHHHHHHHHH
Q psy17364 24 KSLLGKLRKKTGYSFTNCKKALDL 47 (312)
Q Consensus 24 ~~lik~LR~~Tga~~~dCKkAL~e 47 (312)
...|+.||+ .|.++.+.++.|.+
T Consensus 46 l~~i~~l~~-~G~sl~~I~~~l~~ 68 (69)
T PF13411_consen 46 LREIKELRK-QGMSLEEIKKLLKQ 68 (69)
T ss_dssp HHHHHHHHH-TTTHHHHHHHHH--
T ss_pred HHHHHHHHH-CcCCHHHHHHHHcc
Confidence 467888888 99999999998864
No 75
>smart00411 BHL bacterial (prokaryotic) histone like domain.
Probab=22.25 E-value=1.3e+02 Score=22.60 Aligned_cols=26 Identities=27% Similarity=0.346 Sum_probs=22.6
Q ss_pred HHHHHHHHHHhCCCHHHHHHHHHHhc
Q psy17364 24 KSLLGKLRKKTGYSFTNCKKALDLNE 49 (312)
Q Consensus 24 ~~lik~LR~~Tga~~~dCKkAL~e~~ 49 (312)
.+++++|.++||.+-.++++.|+..-
T Consensus 4 ~eli~~ia~~~~~~~~~v~~vl~~l~ 29 (90)
T smart00411 4 SELIDAIAEKAGLSKKDAKAAVDAFL 29 (90)
T ss_pred HHHHHHHHHHhCCCHHHHHHHHHHHH
Confidence 57899999999999999999887653
No 76
>CHL00102 rps20 ribosomal protein S20
Probab=22.05 E-value=1.4e+02 Score=23.63 Aligned_cols=24 Identities=21% Similarity=0.220 Sum_probs=18.0
Q ss_pred HHHHHHHHHH-----hcCCHHHHHHHHHH
Q psy17364 38 FTNCKKALDL-----NEQDLGKAEKWLQE 61 (312)
Q Consensus 38 ~~dCKkAL~e-----~~gD~ekA~e~Lr~ 61 (312)
|-.|..|+++ ..||.++|.++|.+
T Consensus 32 iKk~~~ai~~~~~~~~~~d~~~a~~~l~~ 60 (93)
T CHL00102 32 IKKYLKNLEDYKTSPNSNNKKKVQETLSS 60 (93)
T ss_pred HHHHHHHHHhhcccCCcccHHHHHHHHHH
Confidence 4456677766 24899999999986
No 77
>COG5207 UBP14 Isopeptidase T [Posttranslational modification, protein turnover, chaperones]
Probab=22.05 E-value=31 Score=35.58 Aligned_cols=33 Identities=27% Similarity=0.341 Sum_probs=27.0
Q ss_pred HHHHH--hCCCHHHHHHHHHHhcCCHHHHHHHHHH
Q psy17364 29 KLRKK--TGYSFTNCKKALDLNEQDLGKAEKWLQE 61 (312)
Q Consensus 29 ~LR~~--Tga~~~dCKkAL~e~~gD~ekA~e~Lr~ 61 (312)
++|.. -|.....|+|||.+.|+|++.+++|...
T Consensus 624 ~~~Slle~Gln~n~~Rkal~~~n~d~~r~V~w~~N 658 (749)
T COG5207 624 KARSLLENGLNPNLCRKALMDMNTDSKRRVVWCIN 658 (749)
T ss_pred HHHHHHHcCCCHHHHHHHHHHccCCchheEEEEEe
Confidence 45553 5777789999999999999999999764
No 78
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. 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. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=21.52 E-value=4.2e+02 Score=21.38 Aligned_cols=45 Identities=22% Similarity=0.340 Sum_probs=29.8
Q ss_pred HHHHHHHHHHhCCCHHHHHHHHHHhc-CC-----HHHHHHHHHHHHHhhcHH
Q psy17364 24 KSLLGKLRKKTGYSFTNCKKALDLNE-QD-----LGKAEKWLQEQAKELGWA 69 (312)
Q Consensus 24 ~~lik~LR~~Tga~~~dCKkAL~e~~-gD-----~ekA~e~Lr~~~~k~G~~ 69 (312)
...|+.||+ +|.|+.+.|+-|.... |+ +++..+.|.++.+..-..
T Consensus 45 l~~I~~lr~-~G~~L~~I~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~ 95 (118)
T cd04776 45 LKLILRGKR-LGFSLEEIRELLDLYDPPGGNRKQLEKMLEKIEKRRAELEQQ 95 (118)
T ss_pred HHHHHHHHH-CCCCHHHHHHHHHhhccCCchHHHHHHHHHHHHHHHHHHHHH
Confidence 456777776 8999999999998753 22 345556666654444333
No 79
>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators. Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal 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 two 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. This subgroup lacks one of the c
Probab=20.84 E-value=4e+02 Score=21.87 Aligned_cols=47 Identities=13% Similarity=0.221 Sum_probs=31.7
Q ss_pred CHHHHHHHHHHhCCCHHHHHHHHHHhc-CC--HHHHHHHHHHHHHhhcHHH
Q psy17364 23 NKSLLGKLRKKTGYSFTNCKKALDLNE-QD--LGKAEKWLQEQAKELGWAK 70 (312)
Q Consensus 23 ~~~lik~LR~~Tga~~~dCKkAL~e~~-gD--~ekA~e~Lr~~~~k~G~~~ 70 (312)
....|+.|| .+|.++.+.|+-|...+ ++ .....++|+++.+..-..+
T Consensus 46 ~l~~I~~lr-~~G~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i 95 (133)
T cd04787 46 RLRFILSAR-QLGFSLKDIKEILSHADQGESPCPMVRRLIEQRLAETERRI 95 (133)
T ss_pred HHHHHHHHH-HcCCCHHHHHHHHhhhccCCCcHHHHHHHHHHHHHHHHHHH
Confidence 356788887 59999999999998654 22 3455667776544444333
No 80
>smart00685 DM14 Repeats in fly CG4713, worm Y37H9A.3 and human FLJ20241.
Probab=20.70 E-value=2e+02 Score=20.88 Aligned_cols=23 Identities=26% Similarity=0.225 Sum_probs=17.3
Q ss_pred hcCCHHHHHHHHHHHHHhhcHHHHHh
Q psy17364 48 NEQDLGKAEKWLQEQAKELGWAKASK 73 (312)
Q Consensus 48 ~~gD~ekA~e~Lr~~~~k~G~~~A~K 73 (312)
..||.++|..++|-. +|...+.+
T Consensus 20 ~~gd~~kAr~~~R~~---K~~~~~I~ 42 (59)
T smart00685 20 RAGDEEKARRHLRIA---KQFDDAIK 42 (59)
T ss_pred HcCCHHHHHHHHHHH---hhHHHHHH
Confidence 479999999999974 55555443
No 81
>PF03765 CRAL_TRIO_N: CRAL/TRIO, N-terminal domain; InterPro: IPR008273 This entry defines the N-terminal of various retinaldehyde/retinal-binding proteins that may be functional components of the visual cycle. Cellular retinaldehyde-binding protein (CRALBP) carries 11-cis-retinol or 11-cis-retinaldehyde as endogenous ligands and may function as a substrate carrier protein that modulates interaction of these retinoids with visual cycle enzymes []. The multidomain protein Trio binds the LAR transmembrane tyrosine phosphatase, contains a protein kinase domain, and has separate rac-specific and rho-specific guanine nucleotide exchange factor domains []. Trio is a multifunctional protein that integrates and amplifies signals involved in coordinating actin remodeling, which is necessary for cell migration and growth. Other members of the family are transfer proteins that include, guanine nucleotide exchange factor that may function as an effector of RAC1, phosphatidylinositol/phosphatidylcholine transfer protein that is required for the transport of secretory proteins from the golgi complex and alpha-tocopherol transfer protein that enhances the transfer of the ligand between separate membranes.; PDB: 1OIZ_A 1R5L_A 1OIP_A 3HX3_A 3HY5_A 1AUA_A 3Q8G_A 3B7Q_B 3B7Z_A 3B7N_A ....
Probab=20.69 E-value=99 Score=21.21 Aligned_cols=21 Identities=29% Similarity=0.232 Sum_probs=15.2
Q ss_pred HHHHHHHhcCCHHHHHHHHHH
Q psy17364 41 CKKALDLNEQDLGKAEKWLQE 61 (312)
Q Consensus 41 CKkAL~e~~gD~ekA~e~Lr~ 61 (312)
+-+=|.+.++|+++|.+.|++
T Consensus 34 llRFLRARkf~v~~A~~mL~~ 54 (55)
T PF03765_consen 34 LLRFLRARKFDVEKAFKMLKK 54 (55)
T ss_dssp HHHHHHHTTT-HHHHHHHHHH
T ss_pred HHHHHHHccCCHHHHHHHHHh
Confidence 334466779999999999875
No 82
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=20.49 E-value=3.9e+02 Score=20.90 Aligned_cols=36 Identities=25% Similarity=0.335 Sum_probs=26.4
Q ss_pred HHHHHHHhCCCHHHHHHHHHHhcC---CHHHHHHHHHHH
Q psy17364 27 LGKLRKKTGYSFTNCKKALDLNEQ---DLGKAEKWLQEQ 62 (312)
Q Consensus 27 ik~LR~~Tga~~~dCKkAL~e~~g---D~ekA~e~Lr~~ 62 (312)
|+.|-+..|.++.++++-|...++ +-+.+...|++.
T Consensus 50 I~~llr~~G~~l~~i~~~l~~~~~~~~~~~~~~~~~~~~ 88 (99)
T cd04765 50 IKHLLYEKGYTIEGAKQALKEDGAAAIREEEAEERLPSI 88 (99)
T ss_pred HHHHHHHCCCCHHHHHHHHHhccccccchhhHHHHHHHH
Confidence 333335689999999999998764 466777777765
Done!