Query psy14089
Match_columns 333
No_of_seqs 70 out of 72
Neff 2.8
Searched_HMMs 46136
Date Fri Aug 16 19:15:19 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy14089.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/14089hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4552|consensus 100.0 6.7E-71 1.5E-75 504.9 20.2 226 103-333 2-272 (272)
2 PF10018 Med4: Vitamin-D-recep 99.9 1.5E-26 3.3E-31 202.6 10.2 129 137-266 2-148 (188)
3 PF10417 1-cysPrx_C: C-termina 86.9 0.38 8.1E-06 34.0 1.5 30 222-251 3-34 (40)
4 PF13805 Pil1: Eisosome compon 85.5 17 0.00037 35.5 12.3 40 204-251 209-249 (271)
5 CHL00118 atpG ATP synthase CF0 81.8 11 0.00023 32.6 8.5 86 136-224 45-150 (156)
6 PF11221 Med21: Subunit 21 of 81.3 35 0.00076 29.5 11.4 33 174-206 104-137 (144)
7 TIGR01069 mutS2 MutS2 family p 76.5 51 0.0011 35.9 13.2 103 118-225 494-607 (771)
8 PRK06231 F0F1 ATP synthase sub 73.8 28 0.0006 31.9 9.1 86 137-225 72-177 (205)
9 PF00430 ATP-synt_B: ATP synth 73.6 31 0.00067 27.8 8.4 71 135-207 21-111 (132)
10 PRK07353 F0F1 ATP synthase sub 72.8 38 0.00083 28.1 9.0 22 137-158 29-50 (140)
11 PRK13460 F0F1 ATP synthase sub 71.2 38 0.00082 29.7 9.0 87 136-225 39-145 (173)
12 PF10146 zf-C4H2: Zinc finger- 70.1 72 0.0016 30.2 11.2 31 189-219 90-121 (230)
13 cd03016 PRX_1cys Peroxiredoxin 68.4 7.5 0.00016 34.6 4.1 39 212-250 142-184 (203)
14 PRK05759 F0F1 ATP synthase sub 67.8 47 0.001 28.0 8.6 22 136-157 27-48 (156)
15 PRK07352 F0F1 ATP synthase sub 66.7 47 0.001 29.1 8.6 21 137-157 43-63 (174)
16 PRK14473 F0F1 ATP synthase sub 66.4 30 0.00065 29.8 7.3 24 135-158 30-53 (164)
17 PRK13461 F0F1 ATP synthase sub 65.5 33 0.00071 29.5 7.3 22 136-157 28-49 (159)
18 PRK13453 F0F1 ATP synthase sub 65.4 33 0.00071 30.2 7.5 24 135-158 40-63 (173)
19 PRK13454 F0F1 ATP synthase sub 65.3 1E+02 0.0022 27.6 10.6 22 136-157 54-75 (181)
20 PRK06569 F0F1 ATP synthase sub 64.9 67 0.0015 29.0 9.4 42 182-224 97-138 (155)
21 PRK14472 F0F1 ATP synthase sub 60.9 45 0.00098 29.2 7.5 23 135-157 40-62 (175)
22 PF01923 Cob_adeno_trans: Coba 59.8 1.2E+02 0.0026 26.6 12.8 115 108-225 21-153 (163)
23 CHL00019 atpF ATP synthase CF0 59.5 45 0.00098 29.5 7.3 22 136-157 47-68 (184)
24 PRK08475 F0F1 ATP synthase sub 59.3 50 0.0011 29.1 7.5 23 135-157 44-66 (167)
25 PRK14471 F0F1 ATP synthase sub 59.0 49 0.0011 28.5 7.3 23 135-157 30-52 (164)
26 TIGR03321 alt_F1F0_F0_B altern 58.3 44 0.00096 30.9 7.3 23 136-158 28-50 (246)
27 COG5074 t-SNARE complex subuni 55.2 67 0.0015 31.7 8.2 122 84-211 78-251 (280)
28 PRK00409 recombination and DNA 54.5 1.9E+02 0.004 31.8 12.2 142 117-266 498-653 (782)
29 KOG0963|consensus 54.1 94 0.002 33.9 9.7 87 120-208 87-213 (629)
30 COG2003 RadC DNA repair protei 52.6 85 0.0018 30.1 8.3 140 109-250 10-189 (224)
31 PF15134 DUF4570: Domain of un 52.6 1E+02 0.0022 26.8 8.0 39 208-246 70-108 (109)
32 PRK14474 F0F1 ATP synthase sub 52.4 65 0.0014 30.4 7.5 22 136-157 28-49 (250)
33 PRK13455 F0F1 ATP synthase sub 51.6 77 0.0017 28.0 7.4 22 137-158 51-72 (184)
34 KOG4552|consensus 51.1 89 0.0019 30.5 8.2 45 137-181 26-81 (272)
35 TIGR01144 ATP_synt_b ATP synth 49.9 90 0.002 26.2 7.3 22 136-157 18-39 (147)
36 PRK13428 F0F1 ATP synthase sub 49.5 65 0.0014 32.8 7.5 21 137-157 25-45 (445)
37 PRK08476 F0F1 ATP synthase sub 48.2 1.8E+02 0.0039 25.0 9.0 23 135-157 29-51 (141)
38 KOG0971|consensus 47.5 1.8E+02 0.0039 33.7 10.8 104 110-215 336-448 (1243)
39 PRK09174 F0F1 ATP synthase sub 45.6 2.5E+02 0.0054 25.9 10.3 21 137-157 77-97 (204)
40 PF12329 TMF_DNA_bd: TATA elem 44.9 1.5E+02 0.0033 23.3 7.8 21 137-157 2-22 (74)
41 PRK14475 F0F1 ATP synthase sub 44.7 1.1E+02 0.0024 26.7 7.3 22 136-157 33-54 (167)
42 PRK09173 F0F1 ATP synthase sub 43.5 1.3E+02 0.0028 25.9 7.4 23 135-157 24-46 (159)
43 TIGR03185 DNA_S_dndD DNA sulfu 42.5 3.1E+02 0.0068 28.9 11.3 7 317-323 607-613 (650)
44 KOG0980|consensus 40.5 91 0.002 35.5 7.4 89 109-197 497-609 (980)
45 COG0711 AtpF F0F1-type ATP syn 39.6 2.4E+02 0.0051 24.8 8.6 23 135-157 28-50 (161)
46 PRK06568 F0F1 ATP synthase sub 39.4 2.8E+02 0.0061 24.9 9.1 23 135-157 26-48 (154)
47 KOG0995|consensus 39.4 3.1E+02 0.0067 29.9 10.7 95 110-204 418-523 (581)
48 PLN02320 seryl-tRNA synthetase 38.1 2.6E+02 0.0057 29.6 9.9 37 120-157 74-110 (502)
49 COG5185 HEC1 Protein involved 37.4 2.6E+02 0.0056 30.3 9.7 32 95-129 447-478 (622)
50 PF05400 FliT: Flagellar prote 36.0 1.3E+02 0.0028 22.3 5.5 45 113-157 11-64 (84)
51 cd00088 HPT Histidine Phosphot 36.0 50 0.0011 25.1 3.4 41 187-227 3-46 (94)
52 PF04652 DUF605: Vta1 like; I 35.9 1.2E+02 0.0026 29.2 6.7 95 108-212 39-147 (380)
53 PRK03963 V-type ATP synthase s 35.1 3.1E+02 0.0068 24.1 10.8 24 182-205 76-99 (198)
54 PRK13599 putative peroxiredoxi 34.6 56 0.0012 29.9 4.1 37 212-248 144-189 (215)
55 PLN02678 seryl-tRNA synthetase 34.5 3.1E+02 0.0066 28.5 9.6 37 121-157 14-50 (448)
56 KOG3433|consensus 33.9 4.1E+02 0.009 25.4 9.6 24 109-132 42-65 (203)
57 PF05278 PEARLI-4: Arabidopsis 33.8 2E+02 0.0044 28.3 7.9 44 88-132 102-149 (269)
58 PF06133 DUF964: Protein of un 33.5 2.4E+02 0.0053 22.3 9.9 83 119-201 3-102 (108)
59 cd07686 F-BAR_Fer The F-BAR (F 32.2 3.9E+02 0.0085 25.5 9.3 84 112-203 64-153 (234)
60 TIGR00636 PduO_Nterm ATP:cob(I 32.2 1.9E+02 0.0042 26.3 7.0 54 169-225 82-150 (171)
61 PRK00286 xseA exodeoxyribonucl 31.7 5.3E+02 0.012 25.7 11.6 39 118-156 204-272 (438)
62 TIGR00634 recN DNA repair prot 31.6 2.9E+02 0.0064 28.6 9.0 11 313-323 418-428 (563)
63 PRK10869 recombination and rep 30.9 4.7E+02 0.01 27.5 10.4 50 118-168 113-174 (553)
64 PF05983 Med7: MED7 protein; 30.2 4E+02 0.0087 23.8 8.8 44 137-181 104-149 (162)
65 KOG4603|consensus 30.0 4.4E+02 0.0096 25.1 9.0 47 169-216 102-154 (201)
66 COG1570 XseA Exonuclease VII, 29.4 4.2E+02 0.0092 27.9 9.7 40 118-157 205-274 (440)
67 PF10146 zf-C4H2: Zinc finger- 29.2 5.1E+02 0.011 24.7 10.1 13 119-131 10-22 (230)
68 PF10267 Tmemb_cc2: Predicted 29.1 4.5E+02 0.0097 27.2 9.7 49 155-205 248-305 (395)
69 PF13514 AAA_27: AAA domain 29.1 8.3E+02 0.018 27.6 12.5 38 187-224 252-289 (1111)
70 PF11471 Sugarporin_N: Maltopo 28.8 1E+02 0.0022 23.8 4.0 27 171-197 29-56 (60)
71 PF10168 Nup88: Nuclear pore c 28.7 5.1E+02 0.011 28.5 10.5 13 120-132 503-515 (717)
72 PRK05892 nucleoside diphosphat 28.2 1.4E+02 0.0031 26.5 5.4 26 160-187 49-75 (158)
73 PRK13190 putative peroxiredoxi 27.8 83 0.0018 28.1 3.9 32 210-241 140-173 (202)
74 COG0497 RecN ATPase involved i 26.9 5.6E+02 0.012 27.7 10.2 50 119-168 113-174 (557)
75 PF05546 She9_MDM33: She9 / Md 26.9 3.9E+02 0.0086 25.5 8.3 28 182-209 97-124 (207)
76 COG0497 RecN ATPase involved i 26.8 4.8E+02 0.01 28.2 9.8 22 144-165 259-280 (557)
77 PRK09174 F0F1 ATP synthase sub 26.7 5.1E+02 0.011 23.9 10.3 19 182-200 151-169 (204)
78 PF07083 DUF1351: Protein of u 26.6 3.2E+02 0.007 25.2 7.6 26 107-132 61-86 (215)
79 KOG4657|consensus 26.4 5.1E+02 0.011 25.5 9.0 58 135-198 60-128 (246)
80 PRK13189 peroxiredoxin; Provis 26.0 96 0.0021 28.4 4.0 28 212-239 151-180 (222)
81 KOG0979|consensus 25.9 6.4E+02 0.014 29.5 10.9 124 112-255 224-376 (1072)
82 PRK15000 peroxidase; Provision 25.8 65 0.0014 28.9 2.9 30 212-241 150-181 (200)
83 TIGR01461 greB transcription e 25.6 1.6E+02 0.0035 26.0 5.2 18 168-185 53-71 (156)
84 KOG0976|consensus 25.4 2.8E+02 0.006 32.0 7.9 71 58-132 200-271 (1265)
85 PF10168 Nup88: Nuclear pore c 25.4 6.3E+02 0.014 27.8 10.5 37 168-204 608-652 (717)
86 PRK05724 acetyl-CoA carboxylas 24.9 1.4E+02 0.003 29.8 5.1 46 168-213 11-57 (319)
87 PRK00024 hypothetical protein; 24.9 3.6E+02 0.0077 25.1 7.6 54 103-157 5-65 (224)
88 KOG0971|consensus 24.7 5.5E+02 0.012 30.1 10.0 89 109-197 416-517 (1243)
89 PHA00692 hypothetical protein 24.7 33 0.00072 27.5 0.7 20 86-105 28-47 (74)
90 PF10112 Halogen_Hydrol: 5-bro 24.4 4.8E+02 0.01 23.2 8.0 49 114-165 98-150 (199)
91 PF05667 DUF812: Protein of un 24.0 5.4E+02 0.012 27.8 9.6 72 135-206 456-552 (594)
92 KOG3850|consensus 23.9 6E+02 0.013 26.9 9.5 56 149-206 290-354 (455)
93 PRK01885 greB transcription el 23.8 1.5E+02 0.0033 26.2 4.8 18 168-185 55-73 (157)
94 PF11020 DUF2610: Domain of un 23.6 1.5E+02 0.0033 24.8 4.3 29 196-226 53-81 (82)
95 PRK02292 V-type ATP synthase s 23.6 5E+02 0.011 22.7 9.7 25 182-206 75-99 (188)
96 KOG0810|consensus 23.6 5.7E+02 0.012 25.3 9.0 17 110-126 127-143 (297)
97 cd07654 F-BAR_FCHSD The F-BAR 23.2 6.8E+02 0.015 24.1 10.1 37 168-204 122-158 (264)
98 PF08549 SWI-SNF_Ssr4: Fungal 23.1 88 0.0019 34.3 3.7 26 169-194 384-412 (669)
99 PF07845 DUF1636: Protein of u 23.1 1.1E+02 0.0023 26.4 3.5 38 211-258 77-114 (116)
100 cd07657 F-BAR_Fes_Fer The F-BA 23.1 6.4E+02 0.014 23.7 9.9 84 115-203 67-152 (237)
101 smart00806 AIP3 Actin interact 22.8 9.2E+02 0.02 25.5 11.0 32 98-129 204-236 (426)
102 PF12998 ING: Inhibitor of gro 22.5 3.8E+02 0.0082 20.9 7.9 72 134-206 16-87 (105)
103 COG3679 Regulatory protein inv 22.2 5.4E+02 0.012 22.6 9.4 20 182-201 86-105 (118)
104 PF05529 Bap31: B-cell recepto 22.2 3.9E+02 0.0085 23.6 7.0 33 169-201 156-189 (192)
105 COG5612 Predicted integral mem 22.2 6.1E+02 0.013 23.2 9.6 76 147-232 53-141 (148)
106 PRK05932 RNA polymerase factor 22.1 6.8E+02 0.015 25.9 9.6 116 100-225 92-234 (455)
107 TIGR00414 serS seryl-tRNA synt 22.0 8.4E+02 0.018 24.7 10.6 37 121-157 10-47 (418)
108 PF08654 DASH_Dad2: DASH compl 21.9 4.9E+02 0.011 22.0 9.8 57 140-206 4-64 (103)
109 PRK01194 V-type ATP synthase s 21.7 6E+02 0.013 22.9 10.4 24 182-205 75-98 (185)
110 cd07656 F-BAR_srGAP The F-BAR 21.6 6.9E+02 0.015 23.6 10.2 90 113-207 70-161 (241)
111 PF06098 Radial_spoke_3: Radia 21.4 5E+02 0.011 25.7 8.1 59 127-189 121-186 (291)
112 PRK11820 hypothetical protein; 21.1 7.5E+02 0.016 24.2 9.2 75 147-224 129-214 (288)
113 COG1579 Zn-ribbon protein, pos 21.1 7.6E+02 0.017 23.9 9.9 53 182-234 140-196 (239)
114 PF01627 Hpt: Hpt domain; Int 20.9 1.3E+02 0.0028 21.8 3.2 39 188-226 2-42 (90)
115 PHA02604 rI.-1 hypothetical pr 20.8 3.8E+02 0.0083 24.0 6.5 43 144-201 82-124 (126)
116 PRK00488 pheS phenylalanyl-tRN 20.8 5.4E+02 0.012 26.0 8.4 58 137-205 27-84 (339)
117 smart00073 HPT Histidine Phosp 20.8 1.7E+02 0.0036 21.6 3.8 38 188-226 3-40 (87)
118 PRK13676 hypothetical protein; 20.6 4.8E+02 0.01 21.4 9.7 84 117-200 4-104 (114)
119 PF12005 DUF3499: Protein of u 20.3 59 0.0013 28.8 1.5 22 229-250 51-76 (123)
No 1
>KOG4552|consensus
Probab=100.00 E-value=6.7e-71 Score=504.95 Aligned_cols=226 Identities=42% Similarity=0.569 Sum_probs=197.2
Q ss_pred ccccCccchHHHhhhhhHHHHHHHHHHHhc------------cCchhhHHHHHhcCHHHHHHHHHHHHHHhhhhhhhh--
Q psy14089 103 NMSSKNISTGEKLLSLIDDIELVAKKKQEA------------HNHLQKTVVYFNKNEVVKQSFRIEIEEFTKKSKNAS-- 168 (333)
Q Consensus 103 ~Mas~~~S~re~LL~~lDDlE~lsKeLie~------------~~~~qliElLl~KD~eLk~~Lk~A~qahQe~~k~i~-- 168 (333)
+|+. ++||||+||.++||||.|+|+|||+ ++.-++++||+.||.+|+++|++|+ +++|++..++
T Consensus 2 ~~t~-~~StrerLL~~~dDlE~i~kelie~l~~~~~qk~l~~gE~v~il~Ll~~kd~ef~~llkla~-eq~k~e~~m~~L 79 (272)
T KOG4552|consen 2 AETD-ERSTRERLLESADDLEHIVKELIETLINRDKQKMLKNGETVNILKLLDSKDDEFKTLLKLAP-EQQKREQLMRTL 79 (272)
T ss_pred Cccc-cccHHHHHHHHhhHHHHHHHHHHHHHHhhhHHHHHhcchHHHHHHHHHhccHHHHHHHHHhH-hHHHHHHHHHHH
Confidence 4555 9999999999999999999999997 4666999999999999999999999 7777776655
Q ss_pred hHHHHHH---HHHHHH-hhhhhHHHHHHHHHHHHhHHHHHHhcCCCCChHHHHHHHHHhhccccccCCCCCCCCCCCCCC
Q psy14089 169 TAGFEDA---HGVWES-ASGSNKNEATAIFQAKQKLQSINKANKRPVSSEELIKYAHRISSSNAVCAPLTWQPGDPRRPY 244 (333)
Q Consensus 169 Q~eIEqk---I~~Le~-LKeAE~~L~taI~QAkqKLkSI~kAek~pVssEeLIkYAHrISasnaVsAPl~WqpGdPrRPy 244 (333)
.+++|++ ||+|++ ||+||++|+++||||++||++|++|+||||++|+|||||||||++|+||||++|++|||||||
T Consensus 80 ea~VEkrD~~IQqLqk~LK~aE~iLtta~fqA~qKLksi~~A~krpvsSEelIKyAHrIS~~NaVsAPLTW~~GDprRPy 159 (272)
T KOG4552|consen 80 EAHVEKRDEVIQQLQKNLKSAEVILTTACFQANQKLKSIKEAEKRPVSSEELIKYAHRISKHNAVSAPLTWQMGDPRRPY 159 (272)
T ss_pred HHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhhhcccccCccccccCCCCCCC
Confidence 4456665 888876 999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CchHHhhhhccc----ccCCC---CCCCCCCCCCC---------ccccccCCCc--ccccCccccccCCccc--------
Q psy14089 245 PTDIEMRVGFLG----RLNDS---PLNGHLLPQQS---------LGDLHRTPSE--LSQQNQFSWHSGDMHI-------- 298 (333)
Q Consensus 245 PtE~eMR~G~Lg----~l~~~---~iNGh~~p~~~---------~~d~~r~g~~--~~~~~qf~W~s~~~~m-------- 298 (333)
|||+|||+|+|| .+++. ..||| +|--+ .+|+--+||+ .+.++||.|+++++||
T Consensus 160 Ptd~EmR~GLlGk~~~~in~ps~s~~Ngg-~P~~~~~tl~gsA~tg~~sgagg~~P~~~q~Q~~Wq~~~~~m~m~~p~~s 238 (272)
T KOG4552|consen 160 PTDHEMRAGLLGKQRPLINSPSASSSNGG-APIRTVGTLIGSAPTGDFSGAGGDEPPPIQQQVLWQNSPYNMVMQSPSSS 238 (272)
T ss_pred CchhHHhccCccccccccCCCCcCCCCCC-CCchhhccccccCCCCCccccCCCCCchhhhhccccCCcchhhccCCCCC
Confidence 999999999999 66655 56777 66111 1333333444 8999999999999999
Q ss_pred cCccCCccccCCCC-CCccceeeecCCCCCCCCCCC
Q psy14089 299 GNVPLDRQQQNSNR-ESEDVEVMSTDSSSSSSSDSQ 333 (333)
Q Consensus 299 ~~~~l~~~~~~~~~-~~eDVEvMStDSsSssSSDSq 333 (333)
.+|.|++.| +++ ++||||+||||||||||||++
T Consensus 239 ~~v~Le~~g--~~~~~qDDVE~MStDSSsSSSsdd~ 272 (272)
T KOG4552|consen 239 PNVKLEITG--GIDQVQDDVEQMSTDSSSSSSSDDE 272 (272)
T ss_pred CCeeeecCC--CcccchhhHHHhccCCCCcccccCC
Confidence 458899988 666 999999999999999999975
No 2
>PF10018 Med4: Vitamin-D-receptor interacting Mediator subunit 4; InterPro: IPR019258 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Members of this family represent the Med4 subunit of the Mediator (Med) complex [, ]. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=99.94 E-value=1.5e-26 Score=202.64 Aligned_cols=129 Identities=30% Similarity=0.407 Sum_probs=111.6
Q ss_pred hhHHHHHhcCHHHHHHHHHHHHHHhhhhhhhhhH-----HHHHHHHHH-HHhhhhhHHHHHHHHHHHHhHHHHHHhcCCC
Q psy14089 137 QKTVVYFNKNEVVKQSFRIEIEEFTKKSKNASTA-----GFEDAHGVW-ESASGSNKNEATAIFQAKQKLQSINKANKRP 210 (333)
Q Consensus 137 qliElLl~KD~eLk~~Lk~A~qahQe~~k~i~Q~-----eIEqkI~~L-e~LKeAE~~L~taI~QAkqKLkSI~kAek~p 210 (333)
++++.|+.+|.+|+++|+.+. .||++.++|.+- .++.+|..+ ..|++|+..|.+++++++.|++++.++++++
T Consensus 2 ~~~~~L~~~d~~L~~~L~~l~-~hq~~~~~I~~L~~e~~~ld~~i~~~~~~L~~~~~~L~~~~~~~~~~~~~~~~~~~~~ 80 (188)
T PF10018_consen 2 ELAEDLIEADDELSSALEELQ-EHQENQARIQQLRAEIEELDEQIRDILKQLKEARKELRTLPDQADEKLKSIPKAEKRP 80 (188)
T ss_pred HHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccCC
Confidence 578999999999999999998 899977755522 222234444 2399999999999999999999999999999
Q ss_pred CChHHHHHHHHHhhccccc--------cCCCCCC----CCCCCCCCCchHHhhhhcccccCCCCCCCC
Q psy14089 211 VSSEELIKYAHRISSSNAV--------CAPLTWQ----PGDPRRPYPTDIEMRVGFLGRLNDSPLNGH 266 (333)
Q Consensus 211 VssEeLIkYAHrISasnaV--------sAPl~Wq----pGdPrRPyPtE~eMR~G~Lg~l~~~~iNGh 266 (333)
|++++||+||||||+++++ ++|.+|+ .|++.+|||+|++||+|.|+++......|-
T Consensus 81 v~~~eLL~YA~rISk~t~~p~~~~~~~~~P~~~~~~~~~~~~~~PwP~Ed~mR~G~L~~~~~~~~~~~ 148 (188)
T PF10018_consen 81 VDYEELLSYAHRISKFTSAPPTFPSGSIAPNNWQPGPPSGDFFRPWPQEDQMRRGMLAQLQLLAEEGI 148 (188)
T ss_pred CCHHHHHHHHHHHHHhcCCCCCCCCCCcCCcccccccccccccCCCCCHHHHHHhHHHhhhhhhhcCC
Confidence 9999999999999999888 8899999 677779999999999999999988766554
No 3
>PF10417 1-cysPrx_C: C-terminal domain of 1-Cys peroxiredoxin; InterPro: IPR019479 This entry represents the C-terminal domain of 1-Cys peroxiredoxin, a member of the peroxiredoxin superfamily which protect cells against membrane oxidation through glutathione (GSH)-dependent reduction of phospholipid hydroperoxides to corresponding alcohols []. The C-terminal domain is crucial for providing the extra cysteine necessary for dimerisation of the whole molecule. Loss of the enzyme's peroxidase activity is associated with oxidation of the catalytic cysteine found upstream of this domain. Glutathionylation, presumably through its disruption of protein structure, facilitates access for GSH, resulting in spontaneous reduction of the mixed disulphide to the sulphydryl and consequent activation of the enzyme []. The domain is associated with IPR000866 from INTERPRO, which carries the catalytic cysteine. ; GO: 0051920 peroxiredoxin activity, 0055114 oxidation-reduction process; PDB: 1ZOF_E 2H01_A 3EMP_D 1YF1_G 1YF0_D 1N8J_C 1YEP_D 1YEX_D 2V41_H 2V32_C ....
Probab=86.92 E-value=0.38 Score=34.03 Aligned_cols=30 Identities=27% Similarity=0.630 Sum_probs=22.4
Q ss_pred HhhccccccCCCCCCCCCCC--CCCCchHHhh
Q psy14089 222 RISSSNAVCAPLTWQPGDPR--RPYPTDIEMR 251 (333)
Q Consensus 222 rISasnaVsAPl~WqpGdPr--RPyPtE~eMR 251 (333)
+.+..+.+..|-+|+|||+- +|-++.++..
T Consensus 3 Q~~d~~~v~tPanW~pGd~~ivpp~~s~~~a~ 34 (40)
T PF10417_consen 3 QFTDKHGVATPANWKPGDDVIVPPPVSQEEAK 34 (40)
T ss_dssp HHHHHHSSBBCTTTCTTSGEBE-TTSSTTHHH
T ss_pred eehhhhCcccCcCCCCCCCeEcCCCCCHHHHH
Confidence 45566679999999999995 7777776543
No 4
>PF13805 Pil1: Eisosome component PIL1; PDB: 3PLT_B.
Probab=85.54 E-value=17 Score=35.47 Aligned_cols=40 Identities=33% Similarity=0.514 Sum_probs=17.6
Q ss_pred HHhcCCCCChHHHHHHHHHhhccccccCCCCC-CCCCCCCCCCchHHhh
Q psy14089 204 NKANKRPVSSEELIKYAHRISSSNAVCAPLTW-QPGDPRRPYPTDIEMR 251 (333)
Q Consensus 204 ~kAek~pVssEeLIkYAHrISasnaVsAPl~W-qpGdPrRPyPtE~eMR 251 (333)
+.|||..| |-.|+.+|-.- + |.+. +||+++|||.....-|
T Consensus 209 E~aEK~~I----la~~gk~Ll~l--l--dd~pv~PG~~r~~Y~g~~~t~ 249 (271)
T PF13805_consen 209 ERAEKQAI----LAEYGKRLLEL--L--DDTPVVPGDTRPPYDGYEQTR 249 (271)
T ss_dssp HHHHHHHH----HHHHHHHHHTT--S--------TTS-------HHHHH
T ss_pred HHHHHHHH----HHHHHHHHHHh--c--cCCCCCCCCCCCCCCChhHHH
Confidence 44666655 66777777652 2 6666 4999999998766543
No 5
>CHL00118 atpG ATP synthase CF0 B' subunit; Validated
Probab=81.85 E-value=11 Score=32.62 Aligned_cols=86 Identities=13% Similarity=0.160 Sum_probs=50.2
Q ss_pred hhhHHHHHhcCHHHHHHHHHHHHHHhhhhhhhhhHHHHHHHHHHHH--------------------hhhhhHHHHHHHHH
Q psy14089 136 LQKTVVYFNKNEVVKQSFRIEIEEFTKKSKNASTAGFEDAHGVWES--------------------ASGSNKNEATAIFQ 195 (333)
Q Consensus 136 ~qliElLl~KD~eLk~~Lk~A~qahQe~~k~i~Q~eIEqkI~~Le~--------------------LKeAE~~L~taI~Q 195 (333)
.|+...|.++.+.+...+..|++.-++-.. ...+.++++...+. +.+|+..++..+.+
T Consensus 45 ~Pi~~~l~~R~~~I~~~l~~Ae~~~~ea~~--~~~e~e~~L~~A~~ea~~ii~~A~~~a~~~~~~~~~~A~~ea~~~~~~ 122 (156)
T CHL00118 45 KPLLKVLDERKEYIRKNLTKASEILAKANE--LTKQYEQELSKARKEAQLEITQSQKEAKEIVENELKQAQKYIDSLLNE 122 (156)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 347888888888888888888833222222 22222222222211 67777777777777
Q ss_pred HHHhHHHHHHhcCCCCChHHHHHHHHHhh
Q psy14089 196 AKQKLQSINKANKRPVSSEELIKYAHRIS 224 (333)
Q Consensus 196 AkqKLkSI~kAek~pVssEeLIkYAHrIS 224 (333)
|++.++...+.....+. .++...|..|+
T Consensus 123 a~~~i~~ek~~a~~~l~-~~v~~lA~~ia 150 (156)
T CHL00118 123 ATKQLEAQKEKALKSLE-EQVDTLSDQIE 150 (156)
T ss_pred HHHHHHHHHHHHHHHHH-HHHHHHHHHHH
Confidence 77777776665555443 23555555554
No 6
>PF11221 Med21: Subunit 21 of Mediator complex; InterPro: IPR021384 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Med21 has been known as Srb7 in yeasts, hSrb7 in humans and Trap 19 in Drosophila. The heterodimer of the two subunits Med7 and Med21 appears to act as a hinge between the middle and the tail regions of Mediator []. ; PDB: 1YKE_B 1YKH_B.
Probab=81.30 E-value=35 Score=29.51 Aligned_cols=33 Identities=12% Similarity=0.149 Sum_probs=28.5
Q ss_pred HHHHHHHH-hhhhhHHHHHHHHHHHHhHHHHHHh
Q psy14089 174 DAHGVWES-ASGSNKNEATAIFQAKQKLQSINKA 206 (333)
Q Consensus 174 qkI~~Le~-LKeAE~~L~taI~QAkqKLkSI~kA 206 (333)
++|..|+. +++++..|..+|..+++.|+.++.+
T Consensus 104 ~~i~~L~~E~~~~~~el~~~v~e~e~ll~~v~~~ 137 (144)
T PF11221_consen 104 KRIKELEEENEEAEEELQEAVKEAEELLKQVQEL 137 (144)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45778865 9999999999999999999988764
No 7
>TIGR01069 mutS2 MutS2 family protein. Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.
Probab=76.49 E-value=51 Score=35.94 Aligned_cols=103 Identities=11% Similarity=-0.002 Sum_probs=58.4
Q ss_pred hhHHHHHHHHHHHhc--cCchhhHHHHHhcCHHHHHHHHHHHHHHhhhhhhhhhHHHHHHHHHHHH-----hhhhhHHHH
Q psy14089 118 LIDDIELVAKKKQEA--HNHLQKTVVYFNKNEVVKQSFRIEIEEFTKKSKNASTAGFEDAHGVWES-----ASGSNKNEA 190 (333)
Q Consensus 118 ~lDDlE~lsKeLie~--~~~~qliElLl~KD~eLk~~Lk~A~qahQe~~k~i~Q~eIEqkI~~Le~-----LKeAE~~L~ 190 (333)
.=.++-.-|++++.. .+...+++-|-....++.+....+++.-++.++ .+++++++...|++ +.+|+....
T Consensus 494 lp~~ii~~A~~~~~~~~~~~~~li~~L~~~~~~~e~~~~~~~~~~~e~~~--~~~~l~~~~~~l~~~~~~~~~~a~~ea~ 571 (771)
T TIGR01069 494 IPHFIIEQAKTFYGEFKEEINVLIEKLSALEKELEQKNEHLEKLLKEQEK--LKKELEQEMEELKERERNKKLELEKEAQ 571 (771)
T ss_pred cCHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 335555666766655 267777777777777777766666633223233 45555555555543 444444444
Q ss_pred HHHHHHH----HhHHHHHHhcCCCCChHHHHHHHHHhhc
Q psy14089 191 TAIFQAK----QKLQSINKANKRPVSSEELIKYAHRISS 225 (333)
Q Consensus 191 taI~QAk----qKLkSI~kAek~pVssEeLIkYAHrISa 225 (333)
.++.+|+ ..++.+++ +....+++.+..+++..
T Consensus 572 ~~~~~a~~~~~~~i~~lk~---~~~~~~~~~~~~~~~~~ 607 (771)
T TIGR01069 572 EALKALKKEVESIIRELKE---KKIHKAKEIKSIEDLVK 607 (771)
T ss_pred HHHHHHHHHHHHHHHHHHh---ccccHHHHHHHHHHHHH
Confidence 4444444 44444543 44566777776666654
No 8
>PRK06231 F0F1 ATP synthase subunit B; Validated
Probab=73.78 E-value=28 Score=31.88 Aligned_cols=86 Identities=14% Similarity=0.150 Sum_probs=44.9
Q ss_pred hhHHHHHhcCHHHHHHHHHHHHHHhhhhhhhhhHHHHHHHHHHH--------------------HhhhhhHHHHHHHHHH
Q psy14089 137 QKTVVYFNKNEVVKQSFRIEIEEFTKKSKNASTAGFEDAHGVWE--------------------SASGSNKNEATAIFQA 196 (333)
Q Consensus 137 qliElLl~KD~eLk~~Lk~A~qahQe~~k~i~Q~eIEqkI~~Le--------------------~LKeAE~~L~taI~QA 196 (333)
|+...|-.+.+.+++.+..|++.-++-+. .+.+-++++...+ .+++|+...+..+.+|
T Consensus 72 Pi~~~L~~R~~~I~~~L~~Ae~~~~eA~~--~l~e~e~~L~~A~~eA~~Ii~~A~~eAe~~~e~i~~~A~~eae~ii~~A 149 (205)
T PRK06231 72 PTQRFLNKRKELIEAEINQANELKQQAQQ--LLENAKQRHENALAQAKEIIDQANYEALQLKSELEKEANRQANLIIFQA 149 (205)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56677788888888888877722111111 1112222211111 0566666666666666
Q ss_pred HHhHHHHHHhcCCCCChHHHHHHHHHhhc
Q psy14089 197 KQKLQSINKANKRPVSSEELIKYAHRISS 225 (333)
Q Consensus 197 kqKLkSI~kAek~pVssEeLIkYAHrISa 225 (333)
+..++.-.+...+.+ -.++...|-.++.
T Consensus 150 ~~~Ie~Ek~~a~~~L-k~ei~~lAv~iA~ 177 (205)
T PRK06231 150 RQEIEKERRELKEQL-QKESVELAMLAAE 177 (205)
T ss_pred HHHHHHHHHHHHHHH-HHHHHHHHHHHHH
Confidence 666665554443333 3455566655554
No 9
>PF00430 ATP-synt_B: ATP synthase B/B' CF(0); InterPro: IPR002146 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. F-ATPases (also known as F1F0-ATPase, or H(+)-transporting two-sector ATPase) (3.6.3.14 from EC) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), nine in mitochondria (A-G, F6, F8). Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis []. These ATPases can also work in reverse to hydrolyse ATP to create a proton gradient. This entry represents subunits B and B' from the F0 complex in F-ATPases found in chloroplasts and in bacterial plasma membranes. The B subunits are part of the peripheral stalk that links the F1 and F0 complexes together, and which acts as a stator to prevent certain subunits from rotating with the central rotary element. The peripheral stalk differs in subunit composition between mitochondrial, chloroplast and bacterial F-ATPases. In bacterial and chloroplast F-ATPases, the peripheral stalk is composed of one copy of the delta subunit (homologous to OSCP in mitochondria), and two copies of subunit B in bacteria, or one copy each of subunits B and B' in chloroplasts and photosynthetic bacteria []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0015078 hydrogen ion transmembrane transporter activity, 0015986 ATP synthesis coupled proton transport, 0045263 proton-transporting ATP synthase complex, coupling factor F(o); PDB: 1L2P_A 2KHK_A 1B9U_A.
Probab=73.60 E-value=31 Score=27.84 Aligned_cols=71 Identities=10% Similarity=0.048 Sum_probs=36.5
Q ss_pred chhhHHHHHhcCHHHHHHHHHHHHHHhhhhhhhhhHHHHHHHHHHHH--------------------hhhhhHHHHHHHH
Q psy14089 135 HLQKTVVYFNKNEVVKQSFRIEIEEFTKKSKNASTAGFEDAHGVWES--------------------ASGSNKNEATAIF 194 (333)
Q Consensus 135 ~~qliElLl~KD~eLk~~Lk~A~qahQe~~k~i~Q~eIEqkI~~Le~--------------------LKeAE~~L~taI~ 194 (333)
..|+...|..++..++..+..|++.-.+... ...+.++++...+. +.+++..+...+.
T Consensus 21 ~~pi~~~l~~R~~~I~~~~~~a~~~~~ea~~--~~~e~~~~l~~a~~ea~~i~~~a~~~a~~~~~~~~~ea~~~~~~~~~ 98 (132)
T PF00430_consen 21 YKPIKKFLDERKAKIQSELEEAEELKEEAEQ--LLAEYEEKLAEAREEAQEIIEEAKEEAEKEKEEILAEAEKEAERIIE 98 (132)
T ss_dssp HHHHHHHCS--S-HHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHCHHHHHHCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3456667777777777777777722222111 12222222222221 6777777777777
Q ss_pred HHHHhHHHHHHhc
Q psy14089 195 QAKQKLQSINKAN 207 (333)
Q Consensus 195 QAkqKLkSI~kAe 207 (333)
+|+.+++...+.-
T Consensus 99 ~a~~~i~~e~~~a 111 (132)
T PF00430_consen 99 QAEAEIEQEKEKA 111 (132)
T ss_dssp HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHH
Confidence 7777766655543
No 10
>PRK07353 F0F1 ATP synthase subunit B'; Validated
Probab=72.81 E-value=38 Score=28.14 Aligned_cols=22 Identities=9% Similarity=0.025 Sum_probs=18.5
Q ss_pred hhHHHHHhcCHHHHHHHHHHHH
Q psy14089 137 QKTVVYFNKNEVVKQSFRIEIE 158 (333)
Q Consensus 137 qliElLl~KD~eLk~~Lk~A~q 158 (333)
|+...|-++.+.+...+..|++
T Consensus 29 pi~~~l~~R~~~I~~~l~~Ae~ 50 (140)
T PRK07353 29 PVGKVVEEREDYIRTNRAEAKE 50 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 4888888999999999988883
No 11
>PRK13460 F0F1 ATP synthase subunit B; Provisional
Probab=71.22 E-value=38 Score=29.68 Aligned_cols=87 Identities=9% Similarity=0.015 Sum_probs=45.3
Q ss_pred hhhHHHHHhcCHHHHHHHHHHHHHHhhhhhhhhhHHHHHHHHHHHH--------------------hhhhhHHHHHHHHH
Q psy14089 136 LQKTVVYFNKNEVVKQSFRIEIEEFTKKSKNASTAGFEDAHGVWES--------------------ASGSNKNEATAIFQ 195 (333)
Q Consensus 136 ~qliElLl~KD~eLk~~Lk~A~qahQe~~k~i~Q~eIEqkI~~Le~--------------------LKeAE~~L~taI~Q 195 (333)
.|+...|-++.+.+...+..|++.-.+-.. ...+-++++...+. +.+|+...+..+.+
T Consensus 39 kpi~~~l~~R~~~I~~~l~~Ae~~~~eA~~--~~~e~e~~l~~a~~ea~~ii~~A~~ea~~~~~~~~~~A~~ea~~~~~~ 116 (173)
T PRK13460 39 DVILKALDERASGVQNDINKASELRLEAEA--LLKDYEARLNSAKDEANAIVAEAKSDALKLKNKLLEETNNEVKAQKDQ 116 (173)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 457778888888888888887732222111 11111222111110 55666666666666
Q ss_pred HHHhHHHHHHhcCCCCChHHHHHHHHHhhc
Q psy14089 196 AKQKLQSINKANKRPVSSEELIKYAHRISS 225 (333)
Q Consensus 196 AkqKLkSI~kAek~pVssEeLIkYAHrISa 225 (333)
|+..++...+.-...+ -.+++..|..|+.
T Consensus 117 a~~~ie~e~~~a~~el-~~ei~~lA~~~a~ 145 (173)
T PRK13460 117 AVKEIELAKGKALSQL-QNQIVEMTITIAS 145 (173)
T ss_pred HHHHHHHHHHHHHHHH-HHHHHHHHHHHHH
Confidence 6666655554443333 3456666665554
No 12
>PF10146 zf-C4H2: Zinc finger-containing protein ; InterPro: IPR018482 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a family of proteins which appears to have a highly conserved zinc finger domain at the C-terminal end, described as -C-X2-CH-X3-H-X5-C-X2-C-. The structure is predicted to contain a coiled coil. Members of this family are annotated as being tumour-associated antigen HCA127 in humans, but this could not be confirmed.
Probab=70.14 E-value=72 Score=30.21 Aligned_cols=31 Identities=13% Similarity=0.021 Sum_probs=14.0
Q ss_pred HHHHHHHHHHhHHH-HHHhcCCCCChHHHHHH
Q psy14089 189 EATAIFQAKQKLQS-INKANKRPVSSEELIKY 219 (333)
Q Consensus 189 L~taI~QAkqKLkS-I~kAek~pVssEeLIkY 219 (333)
+....++.++.+.+ +.-+.-..+.-|++.+.
T Consensus 90 y~~Lk~~in~~R~e~lgl~~Lp~l~eE~~~~~ 121 (230)
T PF10146_consen 90 YKPLKDEINELRKEYLGLEPLPSLEEEELSKI 121 (230)
T ss_pred HHHHHHHHHHHHHHHcCCCCCCcccccccccc
Confidence 33344444444555 43344445554544443
No 13
>cd03016 PRX_1cys Peroxiredoxin (PRX) family, 1-cys PRX subfamily; composed of PRXs containing only one conserved cysteine, which serves as the peroxidatic cysteine. They are homodimeric thiol-specific antioxidant (TSA) proteins that confer a protective role in cells by reducing and detoxifying hydrogen peroxide, peroxynitrite, and organic hydroperoxides. As with all other PRXs, a cysteine sulfenic acid intermediate is formed upon reaction of 1-cys PRX with its substrates. Having no resolving cysteine, the oxidized enzyme is resolved by an external small-molecule or protein reductant such as thioredoxin or glutaredoxin. Similar to typical 2-cys PRX, 1-cys PRX forms a functional dimeric unit with a B-type interface, as well as a decameric structure which is stabilized in the reduced form of the enzyme. Other oligomeric forms, tetramers and hexamers, have also been reported. Mammalian 1-cys PRX is localized cellularly in the cytosol and is expressed at high levels in brain, eye, testes an
Probab=68.39 E-value=7.5 Score=34.56 Aligned_cols=39 Identities=26% Similarity=0.587 Sum_probs=25.0
Q ss_pred ChHHHHHHHHHhh--ccccccCCCCCCCCCCC--CCCCchHHh
Q psy14089 212 SSEELIKYAHRIS--SSNAVCAPLTWQPGDPR--RPYPTDIEM 250 (333)
Q Consensus 212 ssEeLIkYAHrIS--asnaVsAPl~WqpGdPr--RPyPtE~eM 250 (333)
+.++|++.-..+. ..+.++.|.||++||+- +|--+.+++
T Consensus 142 ~~~ell~~l~~lq~~~~~~~~~p~~w~~g~~~~~~~~~~~~~~ 184 (203)
T cd03016 142 NFDEILRVVDALQLTDKHKVATPANWKPGDDVIVPPSVSDEEA 184 (203)
T ss_pred CHHHHHHHHHHHhhHhhcCcCcCCCCCCCCceecCCCCCHHHH
Confidence 4566666544333 33468889999999984 555555554
No 14
>PRK05759 F0F1 ATP synthase subunit B; Validated
Probab=67.81 E-value=47 Score=28.04 Aligned_cols=22 Identities=0% Similarity=-0.073 Sum_probs=16.6
Q ss_pred hhhHHHHHhcCHHHHHHHHHHH
Q psy14089 136 LQKTVVYFNKNEVVKQSFRIEI 157 (333)
Q Consensus 136 ~qliElLl~KD~eLk~~Lk~A~ 157 (333)
.|+...|-.+...++..+..|.
T Consensus 27 ~pi~~~l~~R~~~I~~~l~~a~ 48 (156)
T PRK05759 27 PPIMKALEERQKKIADGLAAAE 48 (156)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 4567777788888888777777
No 15
>PRK07352 F0F1 ATP synthase subunit B; Validated
Probab=66.66 E-value=47 Score=29.06 Aligned_cols=21 Identities=10% Similarity=0.056 Sum_probs=16.5
Q ss_pred hhHHHHHhcCHHHHHHHHHHH
Q psy14089 137 QKTVVYFNKNEVVKQSFRIEI 157 (333)
Q Consensus 137 qliElLl~KD~eLk~~Lk~A~ 157 (333)
|+...|-.+.+.+...|..|+
T Consensus 43 pI~~~l~~R~~~I~~~l~~A~ 63 (174)
T PRK07352 43 FLGKILEERREAILQALKEAE 63 (174)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 477788888888888888777
No 16
>PRK14473 F0F1 ATP synthase subunit B; Provisional
Probab=66.41 E-value=30 Score=29.82 Aligned_cols=24 Identities=8% Similarity=0.016 Sum_probs=18.8
Q ss_pred chhhHHHHHhcCHHHHHHHHHHHH
Q psy14089 135 HLQKTVVYFNKNEVVKQSFRIEIE 158 (333)
Q Consensus 135 ~~qliElLl~KD~eLk~~Lk~A~q 158 (333)
..|+...|-++...++..+..|++
T Consensus 30 ~kpi~~~l~~R~~~I~~~l~~Ae~ 53 (164)
T PRK14473 30 YRPVLNLLNERTRRIEESLRDAEK 53 (164)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 346777888888888888888883
No 17
>PRK13461 F0F1 ATP synthase subunit B; Provisional
Probab=65.46 E-value=33 Score=29.46 Aligned_cols=22 Identities=5% Similarity=-0.053 Sum_probs=17.7
Q ss_pred hhhHHHHHhcCHHHHHHHHHHH
Q psy14089 136 LQKTVVYFNKNEVVKQSFRIEI 157 (333)
Q Consensus 136 ~qliElLl~KD~eLk~~Lk~A~ 157 (333)
.|+...|-.+.+.+...+..|+
T Consensus 28 kpi~~~l~~R~~~I~~~l~~A~ 49 (159)
T PRK13461 28 DKIKAVIDSRQSEIDNKIEKAD 49 (159)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3677788888888888888877
No 18
>PRK13453 F0F1 ATP synthase subunit B; Provisional
Probab=65.37 E-value=33 Score=30.22 Aligned_cols=24 Identities=4% Similarity=-0.107 Sum_probs=18.8
Q ss_pred chhhHHHHHhcCHHHHHHHHHHHH
Q psy14089 135 HLQKTVVYFNKNEVVKQSFRIEIE 158 (333)
Q Consensus 135 ~~qliElLl~KD~eLk~~Lk~A~q 158 (333)
..|+.+.|-.+.+.+.+.+..|++
T Consensus 40 ~~pi~~~l~~R~~~I~~~l~~Ae~ 63 (173)
T PRK13453 40 WGPLKDVMDKRERDINRDIDDAEQ 63 (173)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 346777888888888888888883
No 19
>PRK13454 F0F1 ATP synthase subunit B'; Provisional
Probab=65.28 E-value=1e+02 Score=27.57 Aligned_cols=22 Identities=5% Similarity=0.048 Sum_probs=16.7
Q ss_pred hhhHHHHHhcCHHHHHHHHHHH
Q psy14089 136 LQKTVVYFNKNEVVKQSFRIEI 157 (333)
Q Consensus 136 ~qliElLl~KD~eLk~~Lk~A~ 157 (333)
.|+...|-++++.+...+..|+
T Consensus 54 ~PI~~~l~~R~~~I~~~l~~Ae 75 (181)
T PRK13454 54 PRIGAVLAERQGTITNDLAAAE 75 (181)
T ss_pred HHHHHHHHHHHHHHHhHHHHHH
Confidence 3677777788888888877777
No 20
>PRK06569 F0F1 ATP synthase subunit B'; Validated
Probab=64.86 E-value=67 Score=28.99 Aligned_cols=42 Identities=21% Similarity=0.200 Sum_probs=33.8
Q ss_pred hhhhhHHHHHHHHHHHHhHHHHHHhcCCCCChHHHHHHHHHhh
Q psy14089 182 ASGSNKNEATAIFQAKQKLQSINKANKRPVSSEELIKYAHRIS 224 (333)
Q Consensus 182 LKeAE~~L~taI~QAkqKLkSI~kAek~pVssEeLIkYAHrIS 224 (333)
-+..|..|.+.+.|.-++...+.+--++. -.++||++|--|.
T Consensus 97 ~~~~ea~L~~~~~~~~~~~~~~~~~~~~~-~~~~~i~~~~~i~ 138 (155)
T PRK06569 97 KKNLEQDLKNSINQNIEDINLAAKQFRTN-KSEAIIKLAVNII 138 (155)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHh-HHHHHHHHHHHHH
Confidence 88889999999999988888877733333 4789999998776
No 21
>PRK14472 F0F1 ATP synthase subunit B; Provisional
Probab=60.93 E-value=45 Score=29.20 Aligned_cols=23 Identities=4% Similarity=-0.114 Sum_probs=18.0
Q ss_pred chhhHHHHHhcCHHHHHHHHHHH
Q psy14089 135 HLQKTVVYFNKNEVVKQSFRIEI 157 (333)
Q Consensus 135 ~~qliElLl~KD~eLk~~Lk~A~ 157 (333)
..|+.+.|-++.+.+...+..|+
T Consensus 40 ~kpi~~~l~~R~~~I~~~l~~Ae 62 (175)
T PRK14472 40 WGPILSALEEREKGIQSSIDRAH 62 (175)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 34577788888888888888887
No 22
>PF01923 Cob_adeno_trans: Cobalamin adenosyltransferase; InterPro: IPR002779 ATP:cob(I)alamin (or ATP:corrinoid) adenosyltransferases (2.5.1.17 from EC), catalyse the conversion of cobalamin (vitamin B12) into its coenzyme form, adenosylcobalamin (coenzyme B12) []. Adenosylcobalamin (AdoCbl) is required for the ativity of certain enzymes. AdoCbl contains an adenosyl moiety liganded to the cobalt ion of cobalamin via a covalent Co-C bond, and its synthesis is unique to certain prokaryotes. ATP:cob(I)alamin adenosyltransferases are classed into three groups: CobA-type [], EutT-type [] and PduO-type []. Each of the three enzyme types appears to be specialised for particular AdoCbl-dependent enzymes or for the de novo synthesis AdoCbl. PduO and EutT are distantly related, sharing short conserved motifs, while CobA is evolutionarily unrelated and is an example of convergent evolution. This entry represents EutT- and PduO-type ATP:cob(I)alamin adenosyltransferases. PduO functions to convert cobalamin to AdoCbl for 1,2-propanediol degradation [], while EutT produces AdoCbl for ethanolamine utilisation []. ; GO: 0005524 ATP binding, 0008817 cob(I)yrinic acid a,c-diamide adenosyltransferase activity, 0009236 cobalamin biosynthetic process; PDB: 2ZHY_A 2ZHZ_B 3KE5_C 3KE4_B 2AH6_C 1NOG_A 2IDX_C 3GAH_A 3CI1_A 3CI3_A ....
Probab=59.81 E-value=1.2e+02 Score=26.56 Aligned_cols=115 Identities=8% Similarity=0.070 Sum_probs=68.6
Q ss_pred ccchHHHhhhhhHHHHHHHHHHHhccCchhhHHHHHhcCHHHHHHHHHHHHHHh---hhhhhhhhHHHHHHHHHHHH---
Q psy14089 108 NISTGEKLLSLIDDIELVAKKKQEAHNHLQKTVVYFNKNEVVKQSFRIEIEEFT---KKSKNASTAGFEDAHGVWES--- 181 (333)
Q Consensus 108 ~~S~re~LL~~lDDlE~lsKeLie~~~~~qliElLl~KD~eLk~~Lk~A~qahQ---e~~k~i~Q~eIEqkI~~Le~--- 181 (333)
.-+.|=.+...+|++....=..........+-+.|..-+..|-.+.....-... .....-.-..+|+.|..+.+
T Consensus 21 K~~~rie~~G~lDEl~a~igla~~~~~~~~~~~~L~~iq~~L~~l~~~la~~~~~~~~~i~~~~v~~Le~~i~~~~~~~~ 100 (163)
T PF01923_consen 21 KDDPRIEAYGTLDELNAFIGLARSEIKEEELREILERIQNELFDLGAELATPEEDEEPEITEEDVQELEEEIDEYSEELP 100 (163)
T ss_dssp TTSHHHHHHHHHHHHHHHHHHHHTHCTTHHHHHHHHHHHHHHHHHHHHHHTTTTSSSCS--HHHHHHHHHHHHHHHHHS-
T ss_pred CCCceeeeeeeHHHHHHHHHHHHHHcCchhHHHHHHHHHHHHHHHHHHHcCCCcccccccCHHHHHHHHHHHHHHHhcCC
Confidence 456788889999999887554443333444445555545554444433330000 00000123456667777763
Q ss_pred ------------hhhhhHHHHHHHHHHHHhHHHHHHhcCCCCChHHHHHHHHHhhc
Q psy14089 182 ------------ASGSNKNEATAIFQAKQKLQSINKANKRPVSSEELIKYAHRISS 225 (333)
Q Consensus 182 ------------LKeAE~~L~taI~QAkqKLkSI~kAek~pVssEeLIkYAHrISa 225 (333)
.-.+=..+.+.++.|...+-.+.+... | .+++++|-.|+|.
T Consensus 101 ~~~~Filpgg~~~~a~Lh~aRtv~RraER~~v~l~~~~~--v-~~~il~ylNRLSd 153 (163)
T PF01923_consen 101 PLKGFILPGGSPAAAALHVARTVCRRAERRAVRLFREEE--V-RPDILRYLNRLSD 153 (163)
T ss_dssp SESSCEES-SSHHHHHHHHHHHHHHHHHHHHHHHHHHSS--S--HHHHHHHHHHHH
T ss_pred CCceeEeCCCCHHHHHHHHHHHHHHHHHHHHHHHHHcCC--C-CHHHHHHHHHHHH
Confidence 233334566778888888877776666 6 9999999999996
No 23
>CHL00019 atpF ATP synthase CF0 B subunit
Probab=59.52 E-value=45 Score=29.48 Aligned_cols=22 Identities=9% Similarity=0.010 Sum_probs=17.5
Q ss_pred hhhHHHHHhcCHHHHHHHHHHH
Q psy14089 136 LQKTVVYFNKNEVVKQSFRIEI 157 (333)
Q Consensus 136 ~qliElLl~KD~eLk~~Lk~A~ 157 (333)
-|+...|-++.+.+...+..|+
T Consensus 47 kPI~~~l~~R~~~I~~~l~~Ae 68 (184)
T CHL00019 47 GVLSDLLDNRKQTILNTIRNSE 68 (184)
T ss_pred hHHHHHHHHHHHHHHHHHHHHH
Confidence 4577788888888888888877
No 24
>PRK08475 F0F1 ATP synthase subunit B; Validated
Probab=59.26 E-value=50 Score=29.13 Aligned_cols=23 Identities=4% Similarity=-0.042 Sum_probs=18.6
Q ss_pred chhhHHHHHhcCHHHHHHHHHHH
Q psy14089 135 HLQKTVVYFNKNEVVKQSFRIEI 157 (333)
Q Consensus 135 ~~qliElLl~KD~eLk~~Lk~A~ 157 (333)
..|+...|-++.+.+.+.+..|.
T Consensus 44 ~kPi~~~l~~R~~~I~~~l~~Ae 66 (167)
T PRK08475 44 AKPLKNFYKSRINKISKRLEEIQ 66 (167)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 44677788888888888888888
No 25
>PRK14471 F0F1 ATP synthase subunit B; Provisional
Probab=59.03 E-value=49 Score=28.52 Aligned_cols=23 Identities=4% Similarity=-0.039 Sum_probs=17.3
Q ss_pred chhhHHHHHhcCHHHHHHHHHHH
Q psy14089 135 HLQKTVVYFNKNEVVKQSFRIEI 157 (333)
Q Consensus 135 ~~qliElLl~KD~eLk~~Lk~A~ 157 (333)
..|+...|-.+...++..+..|.
T Consensus 30 ~~pi~~~l~~R~~~I~~~l~~A~ 52 (164)
T PRK14471 30 WKPILGAVKEREDSIKNALASAE 52 (164)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 34577778888888888887777
No 26
>TIGR03321 alt_F1F0_F0_B alternate F1F0 ATPase, F0 subunit B. CC and in principle may run in either direction. This model represents the F0 subunit B of this apparent second ATP synthase.
Probab=58.35 E-value=44 Score=30.94 Aligned_cols=23 Identities=0% Similarity=-0.213 Sum_probs=17.7
Q ss_pred hhhHHHHHhcCHHHHHHHHHHHH
Q psy14089 136 LQKTVVYFNKNEVVKQSFRIEIE 158 (333)
Q Consensus 136 ~qliElLl~KD~eLk~~Lk~A~q 158 (333)
.|+...|-++.+.+...|..|++
T Consensus 28 kPi~~~l~~R~~~I~~~l~~Ae~ 50 (246)
T TIGR03321 28 RPILDAMDAREKKIAGELADADT 50 (246)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 45777888888888888888873
No 27
>COG5074 t-SNARE complex subunit, syntaxin [Intracellular trafficking and secretion]
Probab=55.21 E-value=67 Score=31.67 Aligned_cols=122 Identities=16% Similarity=0.218 Sum_probs=76.8
Q ss_pred CCCcccccccccCCCccccccccCccchHHHhhhhhHHHHHHHHHHHh-------------ccC--------------ch
Q psy14089 84 QKPSRTQIFSRYTPGYHFSNMSSKNISTGEKLLSLIDDIELVAKKKQE-------------AHN--------------HL 136 (333)
Q Consensus 84 ~~~~~~~~~~~~~~~~~~~~Mas~~~S~re~LL~~lDDlE~lsKeLie-------------~~~--------------~~ 136 (333)
|.-+...||+--+-|.|.++--.--+-.|.+++..+.|+-.+-+.-=| .|+ -.
T Consensus 78 q~~~k~di~~~e~~~ihl~~k~aQae~~r~Kf~~~I~~yr~i~~~yree~~e~~rrQy~Ia~P~ATEdeve~aInd~nG~ 157 (280)
T COG5074 78 QRNLKKDIKSAERDGIHLANKQAQAENVRQKFLKLIQDYRIIDSNYREEEKEQARRQYIIAQPEATEDEVEAAINDVNGQ 157 (280)
T ss_pred HHHHHHHHHHHHhcccchhhHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHhhhhcCCccchHHHHHHhcccchH
Confidence 344556788888999999665443456789999999998655322211 131 12
Q ss_pred hhHH-HHH--hcCHHHHHHHHHHHHHHhhhhhhhhhHHHHHHHHHHHH----------------------hhhhhHHHHH
Q psy14089 137 QKTV-VYF--NKNEVVKQSFRIEIEEFTKKSKNASTAGFEDAHGVWES----------------------ASGSNKNEAT 191 (333)
Q Consensus 137 qliE-lLl--~KD~eLk~~Lk~A~qahQe~~k~i~Q~eIEqkI~~Le~----------------------LKeAE~~L~t 191 (333)
|+.. .|+ .+-.+-+.+|+.++.-||++- +||+-|.+|.. +..|+...+.
T Consensus 158 qvfsqalL~anr~geAktaL~Evq~Rh~~ik------kiEkt~ael~qLfndm~~~V~eq~e~Vd~I~~~~~~~~~n~~~ 231 (280)
T COG5074 158 QVFSQALLNANRRGEAKTALAEVQARHQEIK------KIEKTMAELTQLFNDMEELVIEQQENVDVIDKNVEDAQENVEQ 231 (280)
T ss_pred HHHHHHHHhcCccchHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHhhcchHHHHHhhHhhHHhhHHH
Confidence 2222 222 233466777777775555533 34443333321 7778888888
Q ss_pred HHHHHHHhHHHHHHhcCCCC
Q psy14089 192 AIFQAKQKLQSINKANKRPV 211 (333)
Q Consensus 192 aI~QAkqKLkSI~kAek~pV 211 (333)
.+-.-+.-++++++|+|..+
T Consensus 232 g~~h~d~AvksaRaaRkkki 251 (280)
T COG5074 232 GVGHTDKAVKSARAARKKKI 251 (280)
T ss_pred hhhhHHHHHHHHHHHHhcce
Confidence 88888888999999988765
No 28
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=54.48 E-value=1.9e+02 Score=31.78 Aligned_cols=142 Identities=14% Similarity=0.097 Sum_probs=67.4
Q ss_pred hhhHHHHHHHHHHHhc--cCchhhHHHHHhcCHHHHHHHHHHHHHHhhhhhhhhhHHHHHHHHHHHH---------hhhh
Q psy14089 117 SLIDDIELVAKKKQEA--HNHLQKTVVYFNKNEVVKQSFRIEIEEFTKKSKNASTAGFEDAHGVWES---------ASGS 185 (333)
Q Consensus 117 ~~lDDlE~lsKeLie~--~~~~qliElLl~KD~eLk~~Lk~A~qahQe~~k~i~Q~eIEqkI~~Le~---------LKeA 185 (333)
..=.++-.-|++++.. .+...+++-|-+.-.++.+....+++.-++.++ .+++++++...|++ .++|
T Consensus 498 Glp~~ii~~A~~~~~~~~~~~~~li~~l~~~~~~~e~~~~~~~~~~~e~~~--~~~~l~~~~~~l~~~~~~~~~~~~~~a 575 (782)
T PRK00409 498 GLPENIIEEAKKLIGEDKEKLNELIASLEELERELEQKAEEAEALLKEAEK--LKEELEEKKEKLQEEEDKLLEEAEKEA 575 (782)
T ss_pred CcCHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445555556666654 256666766666555555555554422222222 33444444444432 4555
Q ss_pred hHHHHHHHHHHHHhHHHHHHhc---CCCCChHHHHHHHHHhhccccccCCCCCCCCCCCCCCCchHHhhhhcccccCCCC
Q psy14089 186 NKNEATAIFQAKQKLQSINKAN---KRPVSSEELIKYAHRISSSNAVCAPLTWQPGDPRRPYPTDIEMRVGFLGRLNDSP 262 (333)
Q Consensus 186 E~~L~taI~QAkqKLkSI~kAe---k~pVssEeLIkYAHrISasnaVsAPl~WqpGdPrRPyPtE~eMR~G~Lg~l~~~~ 262 (333)
+.+|..+-.++++-++.+++.. ......+++.+..+++......-... ...+.. |. .+++.|---.+..++
T Consensus 576 ~~~l~~a~~~~~~~i~~lk~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~---~~~~~~--~~-~~~~~Gd~V~v~~~~ 649 (782)
T PRK00409 576 QQAIKEAKKEADEIIKELRQLQKGGYASVKAHELIEARKRLNKANEKKEKK---KKKQKE--KQ-EELKVGDEVKYLSLG 649 (782)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhhcccchhhHHHHHHHHHHHHHhhhhhhhc---cccccc--cc-cCCCCCCEEEEccCC
Confidence 5555555555555566665422 12344555555555555422210000 001011 11 446666666666655
Q ss_pred CCCC
Q psy14089 263 LNGH 266 (333)
Q Consensus 263 iNGh 266 (333)
-.|.
T Consensus 650 ~~g~ 653 (782)
T PRK00409 650 QKGE 653 (782)
T ss_pred ceEE
Confidence 5554
No 29
>KOG0963|consensus
Probab=54.09 E-value=94 Score=33.91 Aligned_cols=87 Identities=10% Similarity=0.028 Sum_probs=49.8
Q ss_pred HHHHHHHHHHHhccCchhhHHHHHhcCHHHHH----------HHHHHHHHHhhhhhhhhhHHHHHHHHHHHH--------
Q psy14089 120 DDIELVAKKKQEAHNHLQKTVVYFNKNEVVKQ----------SFRIEIEEFTKKSKNASTAGFEDAHGVWES-------- 181 (333)
Q Consensus 120 DDlE~lsKeLie~~~~~qliElLl~KD~eLk~----------~Lk~A~qahQe~~k~i~Q~eIEqkI~~Le~-------- 181 (333)
.-|-.+.+.|++.|+|.+++......+..+++ .|.....+++-.+. .|..|+..+..+++
T Consensus 87 ~afl~vye~L~eaPDP~pll~sa~~~l~k~~~~~~e~~~lk~~lee~~~el~~~k~--qq~~v~~l~e~l~k~~~~~~~~ 164 (629)
T KOG0963|consen 87 AAFLDVYEKLIEAPDPVPLLASAAELLNKQQKASEENEELKEELEEVNNELADLKT--QQVTVRNLKERLRKLEQLLEIF 164 (629)
T ss_pred HHHHHHHHHHhhCCCCchHHHHHHHHhhhhhhhhhhHHHHHHHHHHHHHHHhhhhh--hHHHHHhHHHHHHHHHHHHHHH
Confidence 34455677888888888877765555444433 33333333333222 22222222111111
Q ss_pred ----------------------hhhhhHHHHHHHHHHHHhHHHHHHhcC
Q psy14089 182 ----------------------ASGSNKNEATAIFQAKQKLQSINKANK 208 (333)
Q Consensus 182 ----------------------LKeAE~~L~taI~QAkqKLkSI~kAek 208 (333)
|++-+..+..-+.+++.|+.++..|-+
T Consensus 165 ie~~a~~~e~~~~q~~~e~e~~L~~~~~~~~~q~~~le~ki~~lq~a~~ 213 (629)
T KOG0963|consen 165 IENAANETEEKLEQEWAEREAGLKDEEQNLQEQLEELEKKISSLQSAIE 213 (629)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 888888888888888888888865543
No 30
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=52.63 E-value=85 Score=30.09 Aligned_cols=140 Identities=19% Similarity=0.213 Sum_probs=72.1
Q ss_pred cchHHHhhh----hhHHHHHHHHHHHhc---cCchhhHHHHHhcCHHHHHHHHHHHHHHhhhhhhhhhHHHHH-HHHHHH
Q psy14089 109 ISTGEKLLS----LIDDIELVAKKKQEA---HNHLQKTVVYFNKNEVVKQSFRIEIEEFTKKSKNASTAGFED-AHGVWE 180 (333)
Q Consensus 109 ~S~re~LL~----~lDDlE~lsKeLie~---~~~~qliElLl~KD~eLk~~Lk~A~qahQe~~k~i~Q~eIEq-kI~~Le 180 (333)
.=.||+|+. .|.|-|.|+--|..- .+.-++...|++.-..|..+++.-.++++...--...+-++- .+.++.
T Consensus 10 ~rPRErll~~G~~~Lsd~ELLailLrtG~~~~~~~~la~~lL~~fg~L~~l~~a~~~el~~v~GiG~aka~~l~a~~El~ 89 (224)
T COG2003 10 ERPRERLLKLGAEALSDAELLAILLRTGTKGESVLDLAKELLQEFGSLAELLKASVEELSSVKGIGLAKAIQIKAAIELG 89 (224)
T ss_pred cchHHHHHHhChhhcchHHHHHHHHhcCCCCCCHHHHHHHHHHHcccHHHHHhCCHHHHhhCCCccHHHHHHHHHHHHHH
Confidence 446888886 488999887644432 166677777777666555555443322222111000000000 011110
Q ss_pred --------------------------HhhhhhHHHHHHHHHHHHhH--H----HHHHhcCCCCChHHHHHHHHHhhcccc
Q psy14089 181 --------------------------SASGSNKNEATAIFQAKQKL--Q----SINKANKRPVSSEELIKYAHRISSSNA 228 (333)
Q Consensus 181 --------------------------~LKeAE~~L~taI~QAkqKL--k----SI~kAek~pVssEeLIkYAHrISasna 228 (333)
+|..=++..-.++|--+|.- + .+=......|-|+|++|+|=+.+++ +
T Consensus 90 ~R~~~~~~~~~~~i~sp~~~~~~l~~~l~~~~~E~f~vL~Ld~qnrlI~~e~lf~GTi~~s~V~PREI~k~Al~~nAa-a 168 (224)
T COG2003 90 KRILAERLREGVVITSPEAVAEYLRAELGGEEREHFVVLYLDSQNRLIATETLFIGTLNVSEVHPREIFKEALKYNAA-A 168 (224)
T ss_pred HHHHHHHhccCCccCCHHHHHHHHHHHhhhhHHHHHHHHHhcCcCceecceeEEeeecccceecHHHHHHHHHHhcch-h
Confidence 03333333333333333220 0 0011356689999999999999986 4
Q ss_pred ccCCCCCCCCCCCCCCCchHHh
Q psy14089 229 VCAPLTWQPGDPRRPYPTDIEM 250 (333)
Q Consensus 229 VsAPl~WqpGdPrRPyPtE~eM 250 (333)
+.-==|-+-|||.| =+.|.+|
T Consensus 169 vIlaHNHPSGd~~P-S~aD~~i 189 (224)
T COG2003 169 VILAHNHPSGDPTP-SRADILI 189 (224)
T ss_pred hheeccCCCCCCCc-CHHHHHH
Confidence 44445566777754 5566655
No 31
>PF15134 DUF4570: Domain of unknown function (DUF4570)
Probab=52.60 E-value=1e+02 Score=26.83 Aligned_cols=39 Identities=28% Similarity=0.296 Sum_probs=33.4
Q ss_pred CCCCChHHHHHHHHHhhccccccCCCCCCCCCCCCCCCc
Q psy14089 208 KRPVSSEELIKYAHRISSSNAVCAPLTWQPGDPRRPYPT 246 (333)
Q Consensus 208 k~pVssEeLIkYAHrISasnaVsAPl~WqpGdPrRPyPt 246 (333)
+++.++++++..=-+--++---++|.-|+=-.++.|||.
T Consensus 70 ~r~~p~P~~~~let~YwasvEe~~P~we~flLgra~~p~ 108 (109)
T PF15134_consen 70 TRPLPPPEVVSLETRYWASVEEYIPKWEQFLLGRAPYPI 108 (109)
T ss_pred cCCCCCchHHHHHHHHHHHHHhhCcccHHHhccCCCCCC
Confidence 348999999999888888766789999998888999995
No 32
>PRK14474 F0F1 ATP synthase subunit B; Provisional
Probab=52.39 E-value=65 Score=30.36 Aligned_cols=22 Identities=5% Similarity=-0.011 Sum_probs=16.2
Q ss_pred hhhHHHHHhcCHHHHHHHHHHH
Q psy14089 136 LQKTVVYFNKNEVVKQSFRIEI 157 (333)
Q Consensus 136 ~qliElLl~KD~eLk~~Lk~A~ 157 (333)
.|++..|-++.+.+...+..|+
T Consensus 28 kPi~~~l~eR~~~I~~~l~~Ae 49 (250)
T PRK14474 28 KPIIQVMKKRQQRIANRWQDAE 49 (250)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3567777777777777777777
No 33
>PRK13455 F0F1 ATP synthase subunit B; Provisional
Probab=51.64 E-value=77 Score=27.99 Aligned_cols=22 Identities=5% Similarity=-0.049 Sum_probs=18.0
Q ss_pred hhHHHHHhcCHHHHHHHHHHHH
Q psy14089 137 QKTVVYFNKNEVVKQSFRIEIE 158 (333)
Q Consensus 137 qliElLl~KD~eLk~~Lk~A~q 158 (333)
++...|-++.+.+...+..|++
T Consensus 51 ~v~~~L~~R~~~I~~~l~~Ae~ 72 (184)
T PRK13455 51 MIGGMLDKRAEGIRSELEEARA 72 (184)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 4677888899999998888883
No 34
>KOG4552|consensus
Probab=51.12 E-value=89 Score=30.52 Aligned_cols=45 Identities=16% Similarity=0.128 Sum_probs=25.7
Q ss_pred hhHHHHHhcCH-------HHHHHHHHHH---HHHhhhhhhhh-hHHHHHHHHHHHH
Q psy14089 137 QKTVVYFNKNE-------VVKQSFRIEI---EEFTKKSKNAS-TAGFEDAHGVWES 181 (333)
Q Consensus 137 qliElLl~KD~-------eLk~~Lk~A~---qahQe~~k~i~-Q~eIEqkI~~Le~ 181 (333)
.+||.|+.+|+ |.-..|++.. .+|+++-+++. |+++|+.|+.|++
T Consensus 26 elie~l~~~~~qk~l~~gE~v~il~Ll~~kd~ef~~llkla~eq~k~e~~m~~Lea 81 (272)
T KOG4552|consen 26 ELIETLINRDKQKMLKNGETVNILKLLDSKDDEFKTLLKLAPEQQKREQLMRTLEA 81 (272)
T ss_pred HHHHHHHhhhHHHHHhcchHHHHHHHHHhccHHHHHHHHHhHhHHHHHHHHHHHHH
Confidence 45666654443 2223444443 56666655544 7777777777765
No 35
>TIGR01144 ATP_synt_b ATP synthase, F0 subunit b. This model describes the F1/F0 ATP synthase b subunit in bacteria only. Scoring just below the trusted cutoff are the N-terminal domains of Mycobacterial b/delta fusion proteins and a subunit from an archaeon, Methanosarcina barkeri, in which the ATP synthase homolog differs in architecture and is not experimentally confirmed. This model helps resolve b from the related b' subunit. Within the family is an example from a sodium-translocating rather than proton-translocating ATP synthase.
Probab=49.94 E-value=90 Score=26.15 Aligned_cols=22 Identities=0% Similarity=-0.087 Sum_probs=16.4
Q ss_pred hhhHHHHHhcCHHHHHHHHHHH
Q psy14089 136 LQKTVVYFNKNEVVKQSFRIEI 157 (333)
Q Consensus 136 ~qliElLl~KD~eLk~~Lk~A~ 157 (333)
.|+...|-.+...+...+..|+
T Consensus 18 ~pi~~~l~~R~~~I~~~l~~A~ 39 (147)
T TIGR01144 18 PPLAKAIETRQKKIADGLASAE 39 (147)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 4566777777888877777777
No 36
>PRK13428 F0F1 ATP synthase subunit delta; Provisional
Probab=49.46 E-value=65 Score=32.75 Aligned_cols=21 Identities=10% Similarity=0.131 Sum_probs=13.0
Q ss_pred hhHHHHHhcCHHHHHHHHHHH
Q psy14089 137 QKTVVYFNKNEVVKQSFRIEI 157 (333)
Q Consensus 137 qliElLl~KD~eLk~~Lk~A~ 157 (333)
|+...|-++.+.+++.|..|+
T Consensus 25 Pi~~~l~~R~~~I~~~L~eAe 45 (445)
T PRK13428 25 PVRRLMAARQDTVRQQLAESA 45 (445)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 355566666666666666665
No 37
>PRK08476 F0F1 ATP synthase subunit B'; Validated
Probab=48.22 E-value=1.8e+02 Score=25.00 Aligned_cols=23 Identities=13% Similarity=-0.013 Sum_probs=17.3
Q ss_pred chhhHHHHHhcCHHHHHHHHHHH
Q psy14089 135 HLQKTVVYFNKNEVVKQSFRIEI 157 (333)
Q Consensus 135 ~~qliElLl~KD~eLk~~Lk~A~ 157 (333)
..|+...|-++.+.+.+.+..|.
T Consensus 29 ~kPi~~~l~~R~~~I~~~l~~A~ 51 (141)
T PRK08476 29 YKPLLKFMDNRNASIKNDLEKVK 51 (141)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 34667777788888888887777
No 38
>KOG0971|consensus
Probab=47.49 E-value=1.8e+02 Score=33.73 Aligned_cols=104 Identities=14% Similarity=0.149 Sum_probs=60.1
Q ss_pred chHHHhhhhhHHHHHHHHHHHhccC---chhhHH--HHHhcCHHHHHHHHHHH----HHHhhhhhhhhhHHHHHHHHHHH
Q psy14089 110 STGEKLLSLIDDIELVAKKKQEAHN---HLQKTV--VYFNKNEVVKQSFRIEI----EEFTKKSKNASTAGFEDAHGVWE 180 (333)
Q Consensus 110 S~re~LL~~lDDlE~lsKeLie~~~---~~qliE--lLl~KD~eLk~~Lk~A~----qahQe~~k~i~Q~eIEqkI~~Le 180 (333)
+++|++-+.--|||.|--++-+.+. ...-.+ -|-.-+..|+++|-..+ ++-|.+++ -+.++|++-.++.
T Consensus 336 ~lkEr~deletdlEILKaEmeekG~~~~~~ss~qfkqlEqqN~rLKdalVrLRDlsA~ek~d~qK--~~kelE~k~sE~~ 413 (1243)
T KOG0971|consen 336 ALKERVDELETDLEILKAEMEEKGSDGQAASSYQFKQLEQQNARLKDALVRLRDLSASEKQDHQK--LQKELEKKNSELE 413 (1243)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCCCcccchHHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHH--HHHHHHHHhhHHH
Confidence 4677777777777777555544432 222222 34455667888887766 22233222 5667777766666
Q ss_pred HhhhhhHHHHHHHHHHHHhHHHHHHhcCCCCChHH
Q psy14089 181 SASGSNKNEATAIFQAKQKLQSINKANKRPVSSEE 215 (333)
Q Consensus 181 ~LKeAE~~L~taI~QAkqKLkSI~kAek~pVssEe 215 (333)
.|+...-.|..-++++.-++..+..-...++-.|+
T Consensus 414 eL~r~kE~Lsr~~d~aEs~iadlkEQVDAAlGAE~ 448 (1243)
T KOG0971|consen 414 ELRRQKERLSRELDQAESTIADLKEQVDAALGAEE 448 (1243)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcHHH
Confidence 66666666777777777766665543333333333
No 39
>PRK09174 F0F1 ATP synthase subunit B'; Validated
Probab=45.58 E-value=2.5e+02 Score=25.91 Aligned_cols=21 Identities=5% Similarity=0.044 Sum_probs=15.8
Q ss_pred hhHHHHHhcCHHHHHHHHHHH
Q psy14089 137 QKTVVYFNKNEVVKQSFRIEI 157 (333)
Q Consensus 137 qliElLl~KD~eLk~~Lk~A~ 157 (333)
++...|-.+...+...|..|+
T Consensus 77 pI~~vLe~R~~~I~~~L~~Ae 97 (204)
T PRK09174 77 RIGGIIETRRDRIAQDLDQAA 97 (204)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 577777777777777777776
No 40
>PF12329 TMF_DNA_bd: TATA element modulatory factor 1 DNA binding; InterPro: IPR022092 This is the middle region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes that contains at its N-terminal section a number of leucine zippers that could potentially form coiled coil structures. The whole proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal [] and plant [] cells.
Probab=44.89 E-value=1.5e+02 Score=23.32 Aligned_cols=21 Identities=14% Similarity=-0.001 Sum_probs=17.6
Q ss_pred hhHHHHHhcCHHHHHHHHHHH
Q psy14089 137 QKTVVYFNKNEVVKQSFRIEI 157 (333)
Q Consensus 137 qliElLl~KD~eLk~~Lk~A~ 157 (333)
.+...|..||..+++++...+
T Consensus 2 sl~~~l~EKDe~Ia~L~eEGe 22 (74)
T PF12329_consen 2 SLEKKLAEKDEQIAQLMEEGE 22 (74)
T ss_pred hHHHHHHhHHHHHHHHHHHHH
Confidence 456788999999999998777
No 41
>PRK14475 F0F1 ATP synthase subunit B; Provisional
Probab=44.66 E-value=1.1e+02 Score=26.71 Aligned_cols=22 Identities=0% Similarity=-0.212 Sum_probs=14.9
Q ss_pred hhhHHHHHhcCHHHHHHHHHHH
Q psy14089 136 LQKTVVYFNKNEVVKQSFRIEI 157 (333)
Q Consensus 136 ~qliElLl~KD~eLk~~Lk~A~ 157 (333)
.|+...|-.+.+.+...|..|+
T Consensus 33 ~pi~~~le~R~~~I~~~l~~Ae 54 (167)
T PRK14475 33 KALAGALDAYAAKIQAELDEAQ 54 (167)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 4566667777777777777666
No 42
>PRK09173 F0F1 ATP synthase subunit B; Validated
Probab=43.55 E-value=1.3e+02 Score=25.88 Aligned_cols=23 Identities=4% Similarity=-0.130 Sum_probs=17.3
Q ss_pred chhhHHHHHhcCHHHHHHHHHHH
Q psy14089 135 HLQKTVVYFNKNEVVKQSFRIEI 157 (333)
Q Consensus 135 ~~qliElLl~KD~eLk~~Lk~A~ 157 (333)
+.++...|-.+.+.+...+..|+
T Consensus 24 ~~pi~~~l~~R~~~I~~~l~~Ae 46 (159)
T PRK09173 24 PGMIARSLDARADRIKNELAEAR 46 (159)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 34577778888888888887777
No 43
>TIGR03185 DNA_S_dndD DNA sulfur modification protein DndD. This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria.
Probab=42.46 E-value=3.1e+02 Score=28.87 Aligned_cols=7 Identities=57% Similarity=0.695 Sum_probs=2.9
Q ss_pred ceeeecC
Q psy14089 317 VEVMSTD 323 (333)
Q Consensus 317 VEvMStD 323 (333)
|=|+|||
T Consensus 607 vIils~d 613 (650)
T TIGR03185 607 VLLLSTD 613 (650)
T ss_pred EEEEech
Confidence 3344444
No 44
>KOG0980|consensus
Probab=40.54 E-value=91 Score=35.47 Aligned_cols=89 Identities=11% Similarity=0.091 Sum_probs=56.0
Q ss_pred cchHHHhhhhhHHHHHHHHHHHhc-----cCchhhHHHHHhcCHHHHHHHHHHHH---HHhhhhhhhhhHHHHHH-----
Q psy14089 109 ISTGEKLLSLIDDIELVAKKKQEA-----HNHLQKTVVYFNKNEVVKQSFRIEIE---EFTKKSKNASTAGFEDA----- 175 (333)
Q Consensus 109 ~S~re~LL~~lDDlE~lsKeLie~-----~~~~qliElLl~KD~eLk~~Lk~A~q---ahQe~~k~i~Q~eIEqk----- 175 (333)
.+||..|.-.+-+|+.+-+.+--. ....++.++|-+||.++..+....++ .-+|.++-|.|.++...
T Consensus 497 e~l~~El~~l~~e~~~lq~~~~~~~qs~~~~~~~l~~~l~~KD~~~~~~~~~~~e~~~~~~e~e~si~ql~l~~~~~~ea 576 (980)
T KOG0980|consen 497 ESLRQELALLLIELEELQRTLSNLAQSHNNQLAQLEDLLKQKDRLAAELVAREEEREALRLEAERSINQLELDSSASTEA 576 (980)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHhhHHHhhcccccchHH
Confidence 468888888888888887764433 24668888999999999888776641 11122222223333311
Q ss_pred -HHHHHH----------hhhhhHHHHHHHHHHH
Q psy14089 176 -HGVWES----------ASGSNKNEATAIFQAK 197 (333)
Q Consensus 176 -I~~Le~----------LKeAE~~L~taI~QAk 197 (333)
+..+.. |..+++.|.+++++-.
T Consensus 577 ~~tQ~~~~~~~~il~~~~~~~~q~lq~al~~ld 609 (980)
T KOG0980|consen 577 GITQLQDDLNDPILDGSLASGIQALQNALYQLD 609 (980)
T ss_pred HHHHHHHHhccHHHHHHHHHHHHHHHHHHHhcC
Confidence 111211 7788888888888744
No 45
>COG0711 AtpF F0F1-type ATP synthase, subunit b [Energy production and conversion]
Probab=39.63 E-value=2.4e+02 Score=24.82 Aligned_cols=23 Identities=0% Similarity=-0.140 Sum_probs=17.5
Q ss_pred chhhHHHHHhcCHHHHHHHHHHH
Q psy14089 135 HLQKTVVYFNKNEVVKQSFRIEI 157 (333)
Q Consensus 135 ~~qliElLl~KD~eLk~~Lk~A~ 157 (333)
..++...|-.+...+++.+..|+
T Consensus 28 ~~pi~~~l~~R~~~I~~~l~~A~ 50 (161)
T COG0711 28 WKPILKALDERQAKIADDLAEAE 50 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 35677778888888888887777
No 46
>PRK06568 F0F1 ATP synthase subunit B; Validated
Probab=39.43 E-value=2.8e+02 Score=24.87 Aligned_cols=23 Identities=9% Similarity=-0.252 Sum_probs=16.5
Q ss_pred chhhHHHHHhcCHHHHHHHHHHH
Q psy14089 135 HLQKTVVYFNKNEVVKQSFRIEI 157 (333)
Q Consensus 135 ~~qliElLl~KD~eLk~~Lk~A~ 157 (333)
.-|++..|-++-+.++..|..|+
T Consensus 26 wkPI~~~LeeR~~~I~~~Ld~Ae 48 (154)
T PRK06568 26 KKAILNSLDAKILEVQEKVLKAE 48 (154)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 45667777777777777777776
No 47
>KOG0995|consensus
Probab=39.38 E-value=3.1e+02 Score=29.90 Aligned_cols=95 Identities=13% Similarity=0.068 Sum_probs=53.7
Q ss_pred chHHHhhhhhHHHHHHHHHHHhc--------cCchhhHHHHHhcCHHHHHHHHHHHHHHhhhhhhhh--hHHHHHHHHHH
Q psy14089 110 STGEKLLSLIDDIELVAKKKQEA--------HNHLQKTVVYFNKNEVVKQSFRIEIEEFTKKSKNAS--TAGFEDAHGVW 179 (333)
Q Consensus 110 S~re~LL~~lDDlE~lsKeLie~--------~~~~qliElLl~KD~eLk~~Lk~A~qahQe~~k~i~--Q~eIEqkI~~L 179 (333)
..+-.|.+.+|.+..-.++.... .+....++.+.+-...+..=|+.|...|+..++..+ +..-..+|..|
T Consensus 418 ~V~~~l~el~~ei~~~~~~~~~~~~tLq~~~~~~~~~i~E~~~~l~~~~~el~~~~~~~~~~k~e~eee~~k~~~E~e~l 497 (581)
T KOG0995|consen 418 YVKPLLKELLDEISEELHEAENELETLQEHFSNKASTIEEKIQILGEIELELKKAESKYELKKEEAEEEWKKCRKEIEKL 497 (581)
T ss_pred HhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 36667777777776655544332 256666666666666666666777656655544322 22222235555
Q ss_pred HH-hhhhhHHHHHHHHHHHHhHHHHH
Q psy14089 180 ES-ASGSNKNEATAIFQAKQKLQSIN 204 (333)
Q Consensus 180 e~-LKeAE~~L~taI~QAkqKLkSI~ 204 (333)
++ |..-+-.+.+.+-+|.+++++++
T Consensus 498 e~~l~~l~l~~~~~m~~a~~~v~s~e 523 (581)
T KOG0995|consen 498 EEELLNLKLVLNTSMKEAEELVKSIE 523 (581)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44 55555555566666666666554
No 48
>PLN02320 seryl-tRNA synthetase
Probab=38.13 E-value=2.6e+02 Score=29.60 Aligned_cols=37 Identities=14% Similarity=0.025 Sum_probs=25.3
Q ss_pred HHHHHHHHHHHhccCchhhHHHHHhcCHHHHHHHHHHH
Q psy14089 120 DDIELVAKKKQEAHNHLQKTVVYFNKNEVVKQSFRIEI 157 (333)
Q Consensus 120 DDlE~lsKeLie~~~~~qliElLl~KD~eLk~~Lk~A~ 157 (333)
++.+.+.+.|-.-.-... ++.+++.|++.+++...++
T Consensus 74 ~n~~~v~~~l~~R~~~~~-vd~l~~ld~~~r~~~~~~~ 110 (502)
T PLN02320 74 DNKEAVAINIRNRNSNAN-LELVLELYENMLALQKEVE 110 (502)
T ss_pred hCHHHHHHHHHhcCCCcC-HHHHHHHHHHHHHHHHHHH
Confidence 466666554443332223 8999999999999888887
No 49
>COG5185 HEC1 Protein involved in chromosome segregation, interacts with SMC proteins [Cell division and chromosome partitioning]
Probab=37.44 E-value=2.6e+02 Score=30.34 Aligned_cols=32 Identities=22% Similarity=0.109 Sum_probs=23.3
Q ss_pred cCCCccccccccCccchHHHhhhhhHHHHHHHHHH
Q psy14089 95 YTPGYHFSNMSSKNISTGEKLLSLIDDIELVAKKK 129 (333)
Q Consensus 95 ~~~~~~~~~Mas~~~S~re~LL~~lDDlE~lsKeL 129 (333)
-.|||-|++|.. +.|.-.++.=+.+....++.
T Consensus 447 E~~~~~~sg~~~---~I~~~i~eln~~i~~~~~~e 478 (622)
T COG5185 447 EQLFPKGSGINE---SIKKSILELNDEIQERIKTE 478 (622)
T ss_pred ccCCccccCchH---hHHHHHHHHhHHHHHHHHHH
Confidence 458999999975 67777777777777666643
No 50
>PF05400 FliT: Flagellar protein FliT; InterPro: IPR008622 This entry represents the bacterial flagellar FliT family of dual-function proteins. Together with FlgN, FliT has been proposed to act as a substrate-specific export chaperone, facilitating the incorporation of the enterobacterial hook-associated axial proteins (HAPs) FlgK/FlgL and FliD into the growing flagellum []. FliT has also been shown to act as a transcriptional regulator in Salmonella typhimurium [].; GO: 0019861 flagellum; PDB: 3A7M_A 3H3M_B 3NKZ_C 2G42_A 2FZT_B.
Probab=36.00 E-value=1.3e+02 Score=22.26 Aligned_cols=45 Identities=13% Similarity=0.145 Sum_probs=25.2
Q ss_pred HHhhhhhHHHHHHHHHHHh--cc-------CchhhHHHHHhcCHHHHHHHHHHH
Q psy14089 113 EKLLSLIDDIELVAKKKQE--AH-------NHLQKTVVYFNKNEVVKQSFRIEI 157 (333)
Q Consensus 113 e~LL~~lDDlE~lsKeLie--~~-------~~~qliElLl~KD~eLk~~Lk~A~ 157 (333)
+.|...+++=+.+...|++ .+ ....++..++..|.++.++++...
T Consensus 11 e~l~~l~~~R~~ll~~l~~~~~~~~~~~~~~~~~~l~~Il~~d~~i~~ll~~~~ 64 (84)
T PF05400_consen 11 EELEELLDERQELLERLFEEQAALSPPEQEELRELLRRILELDQEIRALLQARR 64 (84)
T ss_dssp HHHHHHHHHHHHHHHHHHHCHTTS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHhhccccCChhhHHHHHHHHHHHHHhHHHHHHHHHHHH
Confidence 4555666666666666665 21 233555556666666666655444
No 51
>cd00088 HPT Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is modulated by phosphorylation and dephosphorylation of a conserved aspartic acid residue; two-component proteins are abundant in most eubacteria; In E. coli there are 62 two-component proteins involved in a variety of processes such as chemotaxis, osmoregulation, metabolism and transport 1; also present in both Gram positive and Gram negative pathogenic bacteria where they regulate basic housekeeping functions and control expression of toxins and other proteins important for pathogenesis; in archaea and eukaryotes, two-component pathways constitute a very small number of all signaling systems; in fungi they mediate environmental stress responses and, in pathogenic yeast, hyphal development. In Dictyostelium and in plants, they are i
Probab=35.98 E-value=50 Score=25.13 Aligned_cols=41 Identities=17% Similarity=0.196 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHHhHHHHHHhcC---CCCChHHHHHHHHHhhccc
Q psy14089 187 KNEATAIFQAKQKLQSINKANK---RPVSSEELIKYAHRISSSN 227 (333)
Q Consensus 187 ~~L~taI~QAkqKLkSI~kAek---~pVssEeLIkYAHrISasn 227 (333)
..+...+......++.++++-. .+.+.++|...+|+|-++-
T Consensus 3 ~l~~~f~~~~~~~l~~l~~~~~~~~~~~d~~~l~~~~H~LkGsa 46 (94)
T cd00088 3 ELLELFLEEAEELLEELERALLELEDAEDLNEIFRAAHTLKGSA 46 (94)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhhhHH
Confidence 4556666667777777776665 3678899999999998853
No 52
>PF04652 DUF605: Vta1 like; InterPro: IPR006745 This family contains proteins from the Eukaryota; functionally they are uncharacterised.; PDB: 2RKK_B 2RKL_B 3MHV_A.
Probab=35.93 E-value=1.2e+02 Score=29.23 Aligned_cols=95 Identities=16% Similarity=0.063 Sum_probs=47.1
Q ss_pred ccchHHHhhhhhHHHHHHHHHHHhcc----------Cchhh-HHHHHhcCHHHHHH---HHHHHHHHhhhhhhhhhHHHH
Q psy14089 108 NISTGEKLLSLIDDIELVAKKKQEAH----------NHLQK-TVVYFNKNEVVKQS---FRIEIEEFTKKSKNASTAGFE 173 (333)
Q Consensus 108 ~~S~re~LL~~lDDlE~lsKeLie~~----------~~~ql-iElLl~KD~eLk~~---Lk~A~qahQe~~k~i~Q~eIE 173 (333)
....+.-|+.+||+||.+=.++-+.. -+.+. +++|..+|++++.- ..+|. .|..- -
T Consensus 39 ~~e~~~~~~~Ll~~lE~~K~~~~~~~~~~~~~~~~~~v~~fa~~~f~~a~~~~~~~~~~~~~~~-~f~~a---------~ 108 (380)
T PF04652_consen 39 SKECRQFLTSLLDKLEKMKAELGDNEAILDDVAAQAYVENFALKLFNRADKEDRAGRATKQTAK-TFYAA---------S 108 (380)
T ss_dssp -HHHHHHHHHHHHHHHHHHHCT---CHHC-HHHHHHHHHHHHHHHHHHHHHHHHSS--SHHHHH-HHHHH---------H
T ss_pred ChhHHHHHHHHHHHHHHhhhccCcHHhhcCHHHHHHHHHHHHHHHHHHHHHHHHcCCcHHHHHH-HHHHH---------H
Confidence 45578899999999998855554320 11111 22333333333210 00000 00000 0
Q ss_pred HHHHHHHHhhhhhHHHHHHHHHHHHhHHHHHHhcCCCCC
Q psy14089 174 DAHGVWESASGSNKNEATAIFQAKQKLQSINKANKRPVS 212 (333)
Q Consensus 174 qkI~~Le~LKeAE~~L~taI~QAkqKLkSI~kAek~pVs 212 (333)
--++.|.-+.+-...+..-+..||-|+..|.||.|....
T Consensus 109 ~~~~~l~~f~~~~~~~~~k~kyak~~a~~i~k~~~~g~~ 147 (380)
T PF04652_consen 109 TFFEVLNIFGELDEEIEEKIKYAKWKAARIAKALKEGED 147 (380)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTS-----
T ss_pred HHHHHHHHhCCCChHHhhceeeeeeeHhhhHHHHHCCCC
Confidence 003333335566777888888899999999998877654
No 53
>PRK03963 V-type ATP synthase subunit E; Provisional
Probab=35.09 E-value=3.1e+02 Score=24.07 Aligned_cols=24 Identities=4% Similarity=0.104 Sum_probs=20.2
Q ss_pred hhhhhHHHHHHHHHHHHhHHHHHH
Q psy14089 182 ASGSNKNEATAIFQAKQKLQSINK 205 (333)
Q Consensus 182 LKeAE~~L~taI~QAkqKLkSI~k 205 (333)
|+.=+..+..++..++++|..+..
T Consensus 76 l~ar~el~~~v~~~a~~~l~~~~~ 99 (198)
T PRK03963 76 LAVQEELISEVLEAVRERLAELPE 99 (198)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhhh
Confidence 777778889999999999998755
No 54
>PRK13599 putative peroxiredoxin; Provisional
Probab=34.59 E-value=56 Score=29.85 Aligned_cols=37 Identities=14% Similarity=0.248 Sum_probs=24.3
Q ss_pred ChHHHHHHHHH--hhccccccCCCCCCC----CCCC---CCCCchH
Q psy14089 212 SSEELIKYAHR--ISSSNAVCAPLTWQP----GDPR---RPYPTDI 248 (333)
Q Consensus 212 ssEeLIkYAHr--ISasnaVsAPl~Wqp----GdPr---RPyPtE~ 248 (333)
+.+||++.-.. ....+.++.|-||+| ||.- ||-+.++
T Consensus 144 ~~~eilr~l~~lq~~~~~~~~~p~~w~~~~~~g~~~~~~~~~~~~~ 189 (215)
T PRK13599 144 NVDEILRALKALQTADQYGVALPEKWPNNYLIKDHVIVPPSTDEAS 189 (215)
T ss_pred CHHHHHHHHHHhhhhhhcCCCcCCCCCCCCCCCCcEEEcCCCCHHH
Confidence 55666655433 344456999999999 8983 5555555
No 55
>PLN02678 seryl-tRNA synthetase
Probab=34.47 E-value=3.1e+02 Score=28.50 Aligned_cols=37 Identities=11% Similarity=-0.008 Sum_probs=24.2
Q ss_pred HHHHHHHHHHhccCchhhHHHHHhcCHHHHHHHHHHH
Q psy14089 121 DIELVAKKKQEAHNHLQKTVVYFNKNEVVKQSFRIEI 157 (333)
Q Consensus 121 DlE~lsKeLie~~~~~qliElLl~KD~eLk~~Lk~A~ 157 (333)
+.+.+.+.|-.-.-...+++.+++.|++.+++...++
T Consensus 14 ~~~~v~~~l~~R~~~~~~id~il~ld~~~r~l~~~~e 50 (448)
T PLN02678 14 DPELIRESQRRRFASVELVDEVIALDKEWRQRQFELD 50 (448)
T ss_pred CHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 4444444333223123468999999999999988888
No 56
>KOG3433|consensus
Probab=33.91 E-value=4.1e+02 Score=25.43 Aligned_cols=24 Identities=25% Similarity=0.281 Sum_probs=20.5
Q ss_pred cchHHHhhhhhHHHHHHHHHHHhc
Q psy14089 109 ISTGEKLLSLIDDIELVAKKKQEA 132 (333)
Q Consensus 109 ~S~re~LL~~lDDlE~lsKeLie~ 132 (333)
.+.++.|.+++||=.+.+..+-++
T Consensus 42 ~tvKdvLQsLvDD~lV~~eKIgtS 65 (203)
T KOG3433|consen 42 QTVKDVLQSLVDDGLVIKEKIGTS 65 (203)
T ss_pred hHHHHHHHHHhccchHHHHHhccc
Confidence 578999999999999888877766
No 57
>PF05278 PEARLI-4: Arabidopsis phospholipase-like protein (PEARLI 4); InterPro: IPR007942 This family contains several phospholipase-like proteins from Arabidopsis thaliana and other members of the Streptophyta which are homologous to PEARLI 4.
Probab=33.79 E-value=2e+02 Score=28.31 Aligned_cols=44 Identities=16% Similarity=0.177 Sum_probs=23.8
Q ss_pred ccccccccC---CCccccccccCccchHHHhhhhhHHHHHH-HHHHHhc
Q psy14089 88 RTQIFSRYT---PGYHFSNMSSKNISTGEKLLSLIDDIELV-AKKKQEA 132 (333)
Q Consensus 88 ~~~~~~~~~---~~~~~~~Mas~~~S~re~LL~~lDDlE~l-sKeLie~ 132 (333)
-.+||..|- -+.++.++.- +...-+.|+.++.+|..- .+.|-+.
T Consensus 102 lq~If~KHGDIAsNc~lkS~~~-RS~yLe~Lc~IIqeLq~t~~~~LS~~ 149 (269)
T PF05278_consen 102 LQKIFEKHGDIASNCKLKSQQF-RSYYLECLCDIIQELQSTPLKELSES 149 (269)
T ss_pred HHHHHHhCccHhhccccCcHHH-HHHHHHHHHHHHHHHhcCcHhhhhHH
Confidence 356787773 3444444443 333456666667777553 3555443
No 58
>PF06133 DUF964: Protein of unknown function (DUF964); InterPro: IPR010368 This entry consists of several relatively short bacterial and archaeal hypothetical sequences. It also includes YlbF and YmcA proteins which are involved in the formation of biofilms []. YlbF regulates sporulation prior to stage II, positively controlling the competence regulator ComK at a post-transcriptional level. It may also modulate the translation, stability or activity of ComS and may work together with YmcA to regulate community development [].; PDB: 2IAZ_C 2OEE_A 2OEQ_D 2PIH_A.
Probab=33.48 E-value=2.4e+02 Score=22.28 Aligned_cols=83 Identities=6% Similarity=-0.009 Sum_probs=45.0
Q ss_pred hHHHHHHHHHHHhccCc--hhhHHHHHhcCHHHHHHHHHHH---HHHhhhhhhhhh--HHHHHHHHHHHH----------
Q psy14089 119 IDDIELVAKKKQEAHNH--LQKTVVYFNKNEVVKQSFRIEI---EEFTKKSKNAST--AGFEDAHGVWES---------- 181 (333)
Q Consensus 119 lDDlE~lsKeLie~~~~--~qliElLl~KD~eLk~~Lk~A~---qahQe~~k~i~Q--~eIEqkI~~Le~---------- 181 (333)
.|....|++.|-+++.. -.-.+.-+..|++++.+++.-. +.++..+..... .+..++++.+.+
T Consensus 3 ~~~a~eL~~~I~~s~ey~~~~~a~~~l~~d~e~~~l~~~f~~~q~~~~~~q~~g~~~~~e~~~~l~~~~~~l~~~p~v~~ 82 (108)
T PF06133_consen 3 YDKANELAEAIKESEEYKRYKAAEEALEADPEAQKLIEEFQKLQQELQNAQMYGKEPPKEEIEELQELQEELMQNPVVKE 82 (108)
T ss_dssp HHHHHHHHHHHHTSHHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHTSHHHHH
T ss_pred HHHHHHHHHHHHcCHHHHHHHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHhhccCCcHHHHHHHHHHHHHHHcCHHHHH
Confidence 45566666666666532 3344466777888887776655 233332221111 122222333332
Q ss_pred hhhhhHHHHHHHHHHHHhHH
Q psy14089 182 ASGSNKNEATAIFQAKQKLQ 201 (333)
Q Consensus 182 LKeAE~~L~taI~QAkqKLk 201 (333)
...|+..|...+.+-.+.+.
T Consensus 83 y~~ae~~~~~ll~~i~~~I~ 102 (108)
T PF06133_consen 83 YLQAEQALQDLLQDINQIIS 102 (108)
T ss_dssp HHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 77788888777777666553
No 59
>cd07686 F-BAR_Fer The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Fer (Fes related) tyrosine kinase. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Fer (Fes related) is a cytoplasmic (or nonreceptor) tyrosine kinase expressed in a wide variety of tissues, and is found to reside in both the cytoplasm and the nucleus. It plays important roles in neuronal polarization and neurite development, cytoskeletal reorganization, cell migration, growth factor signaling, and the regulation of cell-cell interactions mediated by adherens junctions and focal adhesions. Fer kinase also regulates cell cycle progression in malignant cells. It contains an N-terminal F-BAR domain, an SH2 domain, and a C-terminal catalytic kinase domain. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membran
Probab=32.17 E-value=3.9e+02 Score=25.52 Aligned_cols=84 Identities=17% Similarity=0.224 Sum_probs=45.8
Q ss_pred HHHhhhhhHHHHHHHHHHHhcc-----CchhhHHHHHhcCHHHHHHHHHHHHHHhhhhhhhhhHHHHH-HHHHHHHhhhh
Q psy14089 112 GEKLLSLIDDIELVAKKKQEAH-----NHLQKTVVYFNKNEVVKQSFRIEIEEFTKKSKNASTAGFED-AHGVWESASGS 185 (333)
Q Consensus 112 re~LL~~lDDlE~lsKeLie~~-----~~~qliElLl~KD~eLk~~Lk~A~qahQe~~k~i~Q~eIEq-kI~~Le~LKeA 185 (333)
..---..|++.|.|++...... .+..-+..|+.+=..+++.+ .+.|+++ +.+..+ -..+|+++|..
T Consensus 64 ~~sW~~vl~qte~iA~~~~~~aE~l~~~i~~~l~~l~~~~~~~~k~~---~~~~~kl-----~~e~~~~~~~~l~K~K~~ 135 (234)
T cd07686 64 SKSWLHMVQQTEQLSKIMKTHAEELNSGPLHRLTMMIKDKQQVKKSY---IGVHQQI-----EAEMYKVTKTELEKLKCS 135 (234)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHH---HHHHHHH-----HHHHHHHHHHHHHHHHhh
Confidence 3445567888888888655442 22222223322223333333 2222331 222322 34567777877
Q ss_pred hHHHHHHHHHHHHhHHHH
Q psy14089 186 NKNEATAIFQAKQKLQSI 203 (333)
Q Consensus 186 E~~L~taI~QAkqKLkSI 203 (333)
=..+...+..|++|.+..
T Consensus 136 Y~~~~~~~e~ar~K~~~a 153 (234)
T cd07686 136 YRQLTKEVNSAKEKYKDA 153 (234)
T ss_pred HHHHHHHHHHHHHHHHHh
Confidence 778888888888888654
No 60
>TIGR00636 PduO_Nterm ATP:cob(I)alamin adenosyltransferase. This model represents as ATP:cob(I)alamin adenosyltransferase family corresponding to the N-terminal half of Salmonella PduO, a 1,2-propanediol utilization protein that probably is bifunctional. PduO represents one of at least three families of ATP:corrinoid adenosyltransferase: others are CobA (which partially complements PduO) and EutT. It was not clear originally whether ATP:cob(I)alamin adenosyltransferase activity resides in the N-terminal region of PduO, modeled here, but this has now become clear from the characterization of MeaD from Methylobacterium extorquens.
Probab=32.15 E-value=1.9e+02 Score=26.27 Aligned_cols=54 Identities=17% Similarity=0.243 Sum_probs=38.3
Q ss_pred hHHHHHHHHHHHH---------------hhhhhHHHHHHHHHHHHhHHHHHHhcCCCCChHHHHHHHHHhhc
Q psy14089 169 TAGFEDAHGVWES---------------ASGSNKNEATAIFQAKQKLQSINKANKRPVSSEELIKYAHRISS 225 (333)
Q Consensus 169 Q~eIEqkI~~Le~---------------LKeAE~~L~taI~QAkqKLkSI~kAek~pVssEeLIkYAHrISa 225 (333)
-..+|+.|+.+++ .-.+=....++++.|...+-.+.+. ..| .+.+++|..|+|.
T Consensus 82 v~~LE~~id~~~~~l~~l~~FiLPggs~~~A~lh~aRtv~RRAER~~v~l~~~--~~v-~~~~l~ylNRLSD 150 (171)
T TIGR00636 82 VKWLEERIDQYRKELPPLKLFVLPGGTPAAAFLHVARTVARRAERRVVALLKE--EEI-NEVVLVYLNRLSD 150 (171)
T ss_pred HHHHHHHHHHHHhhCCCCCceeeCCCCHHHHHHHHHHHHHHHHHHHHHHHhhc--CCC-CHHHHHHHHHHHH
Confidence 3467777888864 2233345567888899988888663 346 6778899999996
No 61
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=31.65 E-value=5.3e+02 Score=25.68 Aligned_cols=39 Identities=13% Similarity=0.122 Sum_probs=25.0
Q ss_pred hhHHH-----HHHHHHHHhc-------------------------cCchhhHHHHHhcCHHHHHHHHHH
Q psy14089 118 LIDDI-----ELVAKKKQEA-------------------------HNHLQKTVVYFNKNEVVKQSFRIE 156 (333)
Q Consensus 118 ~lDDl-----E~lsKeLie~-------------------------~~~~qliElLl~KD~eLk~~Lk~A 156 (333)
+++|| |.|++.++++ ++|+...|+++..-.++.+.|...
T Consensus 204 S~eDL~~Fn~e~v~~ai~~~~~Pvis~IGHE~D~tl~D~vAd~ra~TPtaaae~~~~~~~e~~q~Ld~l 272 (438)
T PRK00286 204 SLEDLWAFNDEAVARAIAASRIPVISAVGHETDFTIADFVADLRAPTPTAAAELAVPDRAELLQRLQQL 272 (438)
T ss_pred CHHHhhccCcHHHHHHHHcCCCCEEEeccCCCCccHHHHhhhccCCChHHHHHHhCccHHHHHHHHHHH
Confidence 45566 6778888886 467777777666555554444433
No 62
>TIGR00634 recN DNA repair protein RecN. All proteins in this family for which functions are known are ATP binding proteins involved in the initiation of recombination and recombinational repair.
Probab=31.58 E-value=2.9e+02 Score=28.59 Aligned_cols=11 Identities=18% Similarity=0.371 Sum_probs=8.6
Q ss_pred CCccceeeecC
Q psy14089 313 ESEDVEVMSTD 323 (333)
Q Consensus 313 ~~eDVEvMStD 323 (333)
+.|+||++.+.
T Consensus 418 G~d~v~f~~~~ 428 (563)
T TIGR00634 418 GADQVEFLFSA 428 (563)
T ss_pred CceEEEEEEec
Confidence 68899998754
No 63
>PRK10869 recombination and repair protein; Provisional
Probab=30.91 E-value=4.7e+02 Score=27.45 Aligned_cols=50 Identities=8% Similarity=0.131 Sum_probs=27.8
Q ss_pred hhHHHHHHHHHHHhc-----------c-CchhhHHHHHhcCHHHHHHHHHHHHHHhhhhhhhh
Q psy14089 118 LIDDIELVAKKKQEA-----------H-NHLQKTVVYFNKNEVVKQSFRIEIEEFTKKSKNAS 168 (333)
Q Consensus 118 ~lDDlE~lsKeLie~-----------~-~~~qliElLl~KD~eLk~~Lk~A~qahQe~~k~i~ 168 (333)
++.+|..|...|++. | .+..+++.|... ..+.+.++.+.++|++..++.+
T Consensus 113 ~~~~l~~l~~~li~ihgQ~~~~~ll~~~~~~~lLD~~~~~-~~~~~~~~~~y~~~~~~~~~l~ 174 (553)
T PRK10869 113 PLSQLRELGQLLIQIHGQHAHQLLLKPEHQKTLLDAYANE-TSLLQEMRAAYQLWHQSCRDLA 174 (553)
T ss_pred cHHHHHHHHHhhhheeCcChHHHhcCHHHHHHHHHHhccc-HHHHHHHHHHHHHHHHHHHHHH
Confidence 344455555555554 1 444555555543 5666677766666666555443
No 64
>PF05983 Med7: MED7 protein; InterPro: IPR009244 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. This family consists of several eukaryotic proteins, which are homologues of the yeast MED7 protein. Activation of gene transcription in metazoans is a multistep process that is triggered by factors that recognise transcriptional enhancer sites in DNA. These factors work with co-activators such as MED7 to direct transcriptional initiation by the RNA polymerase II apparatus [].; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex; PDB: 3FBI_C 3FBN_A 1YKH_A 1YKE_A.
Probab=30.19 E-value=4e+02 Score=23.80 Aligned_cols=44 Identities=7% Similarity=-0.136 Sum_probs=23.5
Q ss_pred hhHHHHHhcCHHHHHHHHHHHHHHhhhhhhhh--hHHHHHHHHHHHH
Q psy14089 137 QKTVVYFNKNEVVKQSFRIEIEEFTKKSKNAS--TAGFEDAHGVWES 181 (333)
Q Consensus 137 qliElLl~KD~eLk~~Lk~A~qahQe~~k~i~--Q~eIEqkI~~Le~ 181 (333)
.-++-+..---.+--+|..-+ -||.|+..|. +.+++++...+++
T Consensus 104 ~ki~~i~~L~~NmhhllNeyR-PhQARetLi~~me~Ql~~kr~~i~~ 149 (162)
T PF05983_consen 104 RKIEDIRLLFINMHHLLNEYR-PHQARETLIMMMEEQLEEKREEIEE 149 (162)
T ss_dssp HHHHHHHHHHHHHHHHHHHTH-HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHhC-HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444433333345556666666 6777776554 4555555444433
No 65
>KOG4603|consensus
Probab=29.97 E-value=4.4e+02 Score=25.12 Aligned_cols=47 Identities=13% Similarity=0.121 Sum_probs=35.0
Q ss_pred hHHHHHHHHHHHH------hhhhhHHHHHHHHHHHHhHHHHHHhcCCCCChHHH
Q psy14089 169 TAGFEDAHGVWES------ASGSNKNEATAIFQAKQKLQSINKANKRPVSSEEL 216 (333)
Q Consensus 169 Q~eIEqkI~~Le~------LKeAE~~L~taI~QAkqKLkSI~kAek~pVssEeL 216 (333)
.+-+|.+|..|.. +.+--+.|...|..-+++|++|+.+ .+-|.|||-
T Consensus 102 ~s~veaEik~L~s~Lt~eemQe~i~~L~kev~~~~erl~~~k~g-~~~vtpedk 154 (201)
T KOG4603|consen 102 CSYVEAEIKELSSALTTEEMQEEIQELKKEVAGYRERLKNIKAG-TNHVTPEDK 154 (201)
T ss_pred HHHHHHHHHHHHHhcChHHHHHHHHHHHHHHHHHHHHHHHHHHh-cccCCHHHH
Confidence 3455666666654 7777888899999999999999655 567888774
No 66
>COG1570 XseA Exonuclease VII, large subunit [DNA replication, recombination, and repair]
Probab=29.35 E-value=4.2e+02 Score=27.86 Aligned_cols=40 Identities=15% Similarity=0.149 Sum_probs=27.2
Q ss_pred hhHHH-----HHHHHHHHhc-------------------------cCchhhHHHHHhcCHHHHHHHHHHH
Q psy14089 118 LIDDI-----ELVAKKKQEA-------------------------HNHLQKTVVYFNKNEVVKQSFRIEI 157 (333)
Q Consensus 118 ~lDDl-----E~lsKeLie~-------------------------~~~~qliElLl~KD~eLk~~Lk~A~ 157 (333)
+|+|| |.|+|.++++ |+|+...|+..-.-.++.+.+.-..
T Consensus 205 SiEDLW~FNdE~vaRAi~~s~iPvISAVGHEtD~tL~DfVAD~RApTPTaAAE~~vP~~~el~~~l~~~~ 274 (440)
T COG1570 205 SIEDLWAFNDEIVARAIAASRIPVISAVGHETDFTLADFVADLRAPTPTAAAELVVPDSAELLQQLDQLQ 274 (440)
T ss_pred hHHHHhccChHHHHHHHHhCCCCeEeecccCCCccHHHhhhhccCCCchHHHHHhCCCHHHHHHHHHHHH
Confidence 56666 7788999886 5677777777666665665555444
No 67
>PF10146 zf-C4H2: Zinc finger-containing protein ; InterPro: IPR018482 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a family of proteins which appears to have a highly conserved zinc finger domain at the C-terminal end, described as -C-X2-CH-X3-H-X5-C-X2-C-. The structure is predicted to contain a coiled coil. Members of this family are annotated as being tumour-associated antigen HCA127 in humans, but this could not be confirmed.
Probab=29.20 E-value=5.1e+02 Score=24.66 Aligned_cols=13 Identities=8% Similarity=0.100 Sum_probs=5.9
Q ss_pred hHHHHHHHHHHHh
Q psy14089 119 IDDIELVAKKKQE 131 (333)
Q Consensus 119 lDDlE~lsKeLie 131 (333)
+++|+.+.-+|..
T Consensus 10 ~~~lek~k~~i~~ 22 (230)
T PF10146_consen 10 TLELEKLKNEILQ 22 (230)
T ss_pred HHHHHHHHHHHHH
Confidence 3445555444443
No 68
>PF10267 Tmemb_cc2: Predicted transmembrane and coiled-coil 2 protein; InterPro: IPR019394 This family of transmembrane coiled-coil containing proteins is conserved from worms to humans. Its function is unknown.
Probab=29.10 E-value=4.5e+02 Score=27.15 Aligned_cols=49 Identities=10% Similarity=0.127 Sum_probs=30.0
Q ss_pred HHHHHHhhhhhhhhhHHHHHHHHHHHH--------hhhh-hHHHHHHHHHHHHhHHHHHH
Q psy14089 155 IEIEEFTKKSKNASTAGFEDAHGVWES--------ASGS-NKNEATAIFQAKQKLQSINK 205 (333)
Q Consensus 155 ~A~qahQe~~k~i~Q~eIEqkI~~Le~--------LKeA-E~~L~taI~QAkqKLkSI~k 205 (333)
...++.|+.+- ++..+|.+++++-. ||.. ...-+.+-||+.++...|..
T Consensus 248 ~~~~~LqEEr~--R~erLEeqlNd~~elHq~Ei~~LKqeLa~~EEK~~Yqs~eRaRdi~E 305 (395)
T PF10267_consen 248 FILEALQEERY--RYERLEEQLNDLTELHQNEIYNLKQELASMEEKMAYQSYERARDIWE 305 (395)
T ss_pred HHHHHHHHhHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhHHHH
Confidence 33345555444 77788888887765 4433 22225777888888777743
No 69
>PF13514 AAA_27: AAA domain
Probab=29.06 E-value=8.3e+02 Score=27.63 Aligned_cols=38 Identities=16% Similarity=0.204 Sum_probs=21.4
Q ss_pred HHHHHHHHHHHHhHHHHHHhcCCCCChHHHHHHHHHhh
Q psy14089 187 KNEATAIFQAKQKLQSINKANKRPVSSEELIKYAHRIS 224 (333)
Q Consensus 187 ~~L~taI~QAkqKLkSI~kAek~pVssEeLIkYAHrIS 224 (333)
..+...+.+.+.++...+.....-...+.|+..+..|.
T Consensus 252 ~~~~~~l~~~~~~~~~l~~~~~~l~~~~~ll~~~~~I~ 289 (1111)
T PF13514_consen 252 AEAQAQLERLQEELAQLEEELDALPVDEELLAHAAEIE 289 (1111)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHhhHHHHH
Confidence 34445555566666666665555555555666555554
No 70
>PF11471 Sugarporin_N: Maltoporin periplasmic N-terminal extension; InterPro: IPR021570 This N-terminal domain is found in members of the sugar porin family 1.B.3 from TC, They are related to LamB - the well characterised maltoporin of Escherichia coli for which the three-dimensional structures with and without its substrate have been obtained by X-ray diffraction. The protein consists of an 18 beta-stranded beta-barrel in contrast to proteins of the general bacterial porin family (GBP) and the Rhodobacter PorCa Porin (RPP) family which consist of 16 beta-stranded beta-barrels. Although maltoporin contains a wider beta-barrel than the porins of the GBP and RPP families (1.B.1 from TC and 1.B.7 from TC), it exhibits a narrower channel, showing only 5% of the ionic conductance of the latter porins.
Probab=28.77 E-value=1e+02 Score=23.77 Aligned_cols=27 Identities=19% Similarity=0.172 Sum_probs=19.6
Q ss_pred HHHHHHHHHHH-hhhhhHHHHHHHHHHH
Q psy14089 171 GFEDAHGVWES-ASGSNKNEATAIFQAK 197 (333)
Q Consensus 171 eIEqkI~~Le~-LKeAE~~L~taI~QAk 197 (333)
-||+++..||+ |.++|+.+..+=.+++
T Consensus 29 tiEqRLa~LE~rL~~ae~ra~~ae~~~~ 56 (60)
T PF11471_consen 29 TIEQRLAALEQRLQAAEQRAQAAEARAK 56 (60)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 47888888875 8888888776554444
No 71
>PF10168 Nup88: Nuclear pore component; InterPro: IPR019321 Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein have no obvious structural motifs. It is, however, where it binds to Nup98; one of the components of the nuclear pore. The C-terminal end is a predicted coiled-coil domain []. Nup88 is over expressed in tumour cells [].
Probab=28.72 E-value=5.1e+02 Score=28.48 Aligned_cols=13 Identities=15% Similarity=0.008 Sum_probs=7.7
Q ss_pred HHHHHHHHHHHhc
Q psy14089 120 DDIELVAKKKQEA 132 (333)
Q Consensus 120 DDlE~lsKeLie~ 132 (333)
+-|+...|.|+..
T Consensus 503 ~sF~~~Ik~lL~r 515 (717)
T PF10168_consen 503 PSFEKHIKSLLQR 515 (717)
T ss_pred chHHHHHHHHhcC
Confidence 4466666666654
No 72
>PRK05892 nucleoside diphosphate kinase regulator; Provisional
Probab=28.24 E-value=1.4e+02 Score=26.49 Aligned_cols=26 Identities=8% Similarity=0.095 Sum_probs=17.5
Q ss_pred HhhhhhhhhhHHHHHHHHHHHH-hhhhhH
Q psy14089 160 FTKKSKNASTAGFEDAHGVWES-ASGSNK 187 (333)
Q Consensus 160 hQe~~k~i~Q~eIEqkI~~Le~-LKeAE~ 187 (333)
|...+. +|+.++.+|..|+. |..|+.
T Consensus 49 y~aak~--~q~~~e~RI~~L~~~L~~A~i 75 (158)
T PRK05892 49 AIQRAD--ELARLDDRINELDRRLRTGPT 75 (158)
T ss_pred HHHHHH--HHHHHHHHHHHHHHHHHhCEE
Confidence 444333 68888888888865 666654
No 73
>PRK13190 putative peroxiredoxin; Provisional
Probab=27.78 E-value=83 Score=28.11 Aligned_cols=32 Identities=25% Similarity=0.558 Sum_probs=22.4
Q ss_pred CCChHHHHHHHHHh--hccccccCCCCCCCCCCC
Q psy14089 210 PVSSEELIKYAHRI--SSSNAVCAPLTWQPGDPR 241 (333)
Q Consensus 210 pVssEeLIkYAHrI--SasnaVsAPl~WqpGdPr 241 (333)
..+.+||++.-..+ +..+.+..|-||+||+.-
T Consensus 140 gr~~~ellr~l~~l~~~~~~~~~~p~~w~~g~~~ 173 (202)
T PRK13190 140 GRNIDEIIRITKALQVNWKRKVATPANWQPGQEG 173 (202)
T ss_pred CCCHHHHHHHHHHhhhHHhcCCCcCCCCCcCCce
Confidence 34777777765433 333468889999999983
No 74
>COG0497 RecN ATPase involved in DNA repair [DNA replication, recombination, and repair]
Probab=26.91 E-value=5.6e+02 Score=27.75 Aligned_cols=50 Identities=4% Similarity=0.132 Sum_probs=34.7
Q ss_pred hHHHHHHHHHHHhc-----------c-CchhhHHHHHhcCHHHHHHHHHHHHHHhhhhhhhh
Q psy14089 119 IDDIELVAKKKQEA-----------H-NHLQKTVVYFNKNEVVKQSFRIEIEEFTKKSKNAS 168 (333)
Q Consensus 119 lDDlE~lsKeLie~-----------~-~~~qliElLl~KD~eLk~~Lk~A~qahQe~~k~i~ 168 (333)
+.+|..|.+.||+- | .+.++++.|.......++.++.+.++|+..++..+
T Consensus 113 ~~~L~~l~~~Li~IHGQh~~q~Ll~~~~~r~lLD~f~~~~~~~~~~~~~~y~~w~~~~~~l~ 174 (557)
T COG0497 113 LAQLKELGQLLIDIHGQHEHQSLLKPELQRQLLDAFAGLEELAQEAYQEAYQAWKQARRELE 174 (557)
T ss_pred HHHHHHHHHhhheeeccchHHHhcChHHHHHHHHHhcCchHHHHHHHHHHHHHHHHHHHHHH
Confidence 45566677777775 2 46678888888877777667777777777666443
No 75
>PF05546 She9_MDM33: She9 / Mdm33 family; InterPro: IPR008839 Members of this family are mitochondrial inner membrane proteins with a role in inner mitochondrial membrane organisation and biogenesis []. The yeast Mdm33 protein assembles into an oligomeric complex in the inner membrane where it performs homotypic protein-protein interactions. It has been suggested that Mdm33 plays a distinct role, possibly involved in fission of the mitochondrial inner membrane [].
Probab=26.87 E-value=3.9e+02 Score=25.52 Aligned_cols=28 Identities=14% Similarity=0.145 Sum_probs=24.3
Q ss_pred hhhhhHHHHHHHHHHHHhHHHHHHhcCC
Q psy14089 182 ASGSNKNEATAIFQAKQKLQSINKANKR 209 (333)
Q Consensus 182 LKeAE~~L~taI~QAkqKLkSI~kAek~ 209 (333)
|..-+..+++.+.+|+++|..++..+..
T Consensus 97 Lyr~dH~~e~~e~~ak~~l~~aE~~~e~ 124 (207)
T PF05546_consen 97 LYRNDHENEQAEEEAKEALEEAEEKVEE 124 (207)
T ss_pred HHHhhhhhHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999998876543
No 76
>COG0497 RecN ATPase involved in DNA repair [DNA replication, recombination, and repair]
Probab=26.83 E-value=4.8e+02 Score=28.20 Aligned_cols=22 Identities=5% Similarity=-0.003 Sum_probs=12.4
Q ss_pred hcCHHHHHHHHHHHHHHhhhhh
Q psy14089 144 NKNEVVKQSFRIEIEEFTKKSK 165 (333)
Q Consensus 144 ~KD~eLk~~Lk~A~qahQe~~k 165 (333)
.-|..|.++.....++|...+.
T Consensus 259 ~~d~~l~~~~~~l~ea~~~l~e 280 (557)
T COG0497 259 EYDGKLSELAELLEEALYELEE 280 (557)
T ss_pred ccChhHHHHHHHHHHHHHHHHH
Confidence 3466666666666655554433
No 77
>PRK09174 F0F1 ATP synthase subunit B'; Validated
Probab=26.72 E-value=5.1e+02 Score=23.89 Aligned_cols=19 Identities=11% Similarity=-0.003 Sum_probs=8.6
Q ss_pred hhhhhHHHHHHHHHHHHhH
Q psy14089 182 ASGSNKNEATAIFQAKQKL 200 (333)
Q Consensus 182 LKeAE~~L~taI~QAkqKL 200 (333)
|++|+..++..-.+|...|
T Consensus 151 l~~Ae~~I~~ek~~A~~el 169 (204)
T PRK09174 151 LKEAEARIAAIKAKAMADV 169 (204)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 4444444444444444443
No 78
>PF07083 DUF1351: Protein of unknown function (DUF1351); InterPro: IPR009785 This entry is represented by Lactobacillus prophage Lj928, Orf309. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several bacterial and phage proteins of around 230 residues in length. The function of this family is unknown.
Probab=26.56 E-value=3.2e+02 Score=25.20 Aligned_cols=26 Identities=15% Similarity=0.089 Sum_probs=21.7
Q ss_pred CccchHHHhhhhhHHHHHHHHHHHhc
Q psy14089 107 KNISTGEKLLSLIDDIELVAKKKQEA 132 (333)
Q Consensus 107 ~~~S~re~LL~~lDDlE~lsKeLie~ 132 (333)
.++..+..++.|+++||.-+|+|...
T Consensus 61 ~RK~ikk~~~~P~~~Fe~~~K~l~~~ 86 (215)
T PF07083_consen 61 KRKEIKKEYSKPIKEFEAKIKELIAP 86 (215)
T ss_pred HHHHHHHHHhchHHHHHHHHHHHHHH
Confidence 35668889999999999999998764
No 79
>KOG4657|consensus
Probab=26.44 E-value=5.1e+02 Score=25.49 Aligned_cols=58 Identities=14% Similarity=0.088 Sum_probs=30.7
Q ss_pred chhhHHHHHhcCHHHHHHHHHHHHHHhhhhhhhhhHHHHHHHHHHHH-----------hhhhhHHHHHHHHHHHH
Q psy14089 135 HLQKTVVYFNKNEVVKQSFRIEIEEFTKKSKNASTAGFEDAHGVWES-----------ASGSNKNEATAIFQAKQ 198 (333)
Q Consensus 135 ~~qliElLl~KD~eLk~~Lk~A~qahQe~~k~i~Q~eIEqkI~~Le~-----------LKeAE~~L~taI~QAkq 198 (333)
...+.+.|.+-..++++-.++.. +++.+|..|++.|..++. |++---.+-.+|.+.++
T Consensus 60 ~e~l~~~l~etene~~~~neL~~------ek~~~q~~ieqeik~~q~elEvl~~n~Q~lkeE~dd~keiIs~kr~ 128 (246)
T KOG4657|consen 60 LENLKADLRETENELVKVNELKT------EKEARQMGIEQEIKATQSELEVLRRNLQLLKEEKDDSKEIISQKRQ 128 (246)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHH
Confidence 44455556666666666655554 233356677766544432 33333445556666554
No 80
>PRK13189 peroxiredoxin; Provisional
Probab=25.98 E-value=96 Score=28.38 Aligned_cols=28 Identities=25% Similarity=0.691 Sum_probs=18.2
Q ss_pred ChHHHHHHHH--HhhccccccCCCCCCCCC
Q psy14089 212 SSEELIKYAH--RISSSNAVCAPLTWQPGD 239 (333)
Q Consensus 212 ssEeLIkYAH--rISasnaVsAPl~WqpGd 239 (333)
+.+|+++.-. +....+.+..|-+|+||+
T Consensus 151 ~~~eilr~l~alq~~~~~~~~~p~~w~~g~ 180 (222)
T PRK13189 151 NMDEILRLVKALQTSDEKGVATPANWPPND 180 (222)
T ss_pred CHHHHHHHHHHhhhHhhcCcCcCCCCCCCC
Confidence 3455555543 233444688899999999
No 81
>KOG0979|consensus
Probab=25.95 E-value=6.4e+02 Score=29.48 Aligned_cols=124 Identities=20% Similarity=0.204 Sum_probs=0.0
Q ss_pred HHHhhhhhHHHHHHHHHHHhccCchhhHHHHHhcCHHHHHHHHHHHHHHhhhhhhhhhHHHHHHHHHHHH----------
Q psy14089 112 GEKLLSLIDDIELVAKKKQEAHNHLQKTVVYFNKNEVVKQSFRIEIEEFTKKSKNASTAGFEDAHGVWES---------- 181 (333)
Q Consensus 112 re~LL~~lDDlE~lsKeLie~~~~~qliElLl~KD~eLk~~Lk~A~qahQe~~k~i~Q~eIEqkI~~Le~---------- 181 (333)
|+++++-|+=++.. +.+++--.+.+....+...=+-+++-++...++.+.+.. ...++|.++.++.+
T Consensus 224 r~~~~~~Ie~l~~k-~~~v~y~~~~~ey~~~k~~~~r~k~~~r~l~k~~~pi~~--~~eeLe~~~~et~~~~s~~~~~~~ 300 (1072)
T KOG0979|consen 224 RERKKSKIELLEKK-KKWVEYKKHDREYNAYKQAKDRAKKELRKLEKEIKPIED--KKEELESEKKETRSKISQKQRELN 300 (1072)
T ss_pred HHHHHHHHHHHHHh-ccccchHhhhHHHHHHHHHHHHHHHHHHHHHHhhhhhhh--hhhhHHhHHHhHHHHHHHHHHHHH
Q ss_pred -------------------hhhhhHHHHHHHHHHHHhHHHHHHhcCCCCChHHHHHHHHHhhccccccCCCCCCCCCCCC
Q psy14089 182 -------------------ASGSNKNEATAIFQAKQKLQSINKANKRPVSSEELIKYAHRISSSNAVCAPLTWQPGDPRR 242 (333)
Q Consensus 182 -------------------LKeAE~~L~taI~QAkqKLkSI~kAek~pVssEeLIkYAHrISasnaVsAPl~WqpGdPrR 242 (333)
+.+....|+..-.++++..+.|.+|.| +|..-=-.++. ..+|..
T Consensus 301 e~~~k~~~~~ek~~~~~~~v~~~~~~le~lk~~~~~rq~~i~~~~k------~i~~~q~el~~-----------~~~~e~ 363 (1072)
T KOG0979|consen 301 EALAKVQEKFEKLKEIEDEVEEKKNKLESLKKAAEKRQKRIEKAKK------MILDAQAELQE-----------TEDPEN 363 (1072)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHhhhhh-----------cCCccc
Q ss_pred CCCchHHhhhhcc
Q psy14089 243 PYPTDIEMRVGFL 255 (333)
Q Consensus 243 PyPtE~eMR~G~L 255 (333)
|+|.+.+.+.-++
T Consensus 364 ~~~~~~ei~~~~~ 376 (1072)
T KOG0979|consen 364 PVEEDQEIMKEVL 376 (1072)
T ss_pred cchhHHHHHHHHH
No 82
>PRK15000 peroxidase; Provisional
Probab=25.79 E-value=65 Score=28.93 Aligned_cols=30 Identities=13% Similarity=0.479 Sum_probs=19.6
Q ss_pred ChHHHHHHHHHh--hccccccCCCCCCCCCCC
Q psy14089 212 SSEELIKYAHRI--SSSNAVCAPLTWQPGDPR 241 (333)
Q Consensus 212 ssEeLIkYAHrI--SasnaVsAPl~WqpGdPr 241 (333)
+.+|+++....+ ...+.+..|-+|+||+.-
T Consensus 150 ~~~eilr~l~al~~~~~~~~~~p~~w~~g~~~ 181 (200)
T PRK15000 150 NIDEMLRMVDALQFHEEHGDVCPAQWEKGKEG 181 (200)
T ss_pred CHHHHHHHHHHhhhHHhcCCCcCCCCCCCCce
Confidence 566666654332 223357779999999984
No 83
>TIGR01461 greB transcription elongation factor GreB. The GreA and GreB transcription elongation factors enable to continuation of RNA transcription past template-encoded arresting sites. Among the Proteobacteria, distinct clades of GreA and GreB are found. GreB differs functionally in that it releases larger oligonucleotides. This model describes proteobacterial GreB.
Probab=25.65 E-value=1.6e+02 Score=26.04 Aligned_cols=18 Identities=0% Similarity=-0.115 Sum_probs=12.0
Q ss_pred hhHHHHHHHHHHHH-hhhh
Q psy14089 168 STAGFEDAHGVWES-ASGS 185 (333)
Q Consensus 168 ~Q~eIEqkI~~Le~-LKeA 185 (333)
+|+.++.+|..|+. |+.|
T Consensus 53 ~~~~le~rI~~L~~~L~~A 71 (156)
T TIGR01461 53 RLREIDRRVRFLTKRLENL 71 (156)
T ss_pred HHHHHHHHHHHHHHHHhcC
Confidence 67777777777764 5544
No 84
>KOG0976|consensus
Probab=25.45 E-value=2.8e+02 Score=32.03 Aligned_cols=71 Identities=21% Similarity=0.171 Sum_probs=40.3
Q ss_pred hhhhhccccccccccccceeeeeccCCCCccccccccc-CCCccccccccCccchHHHhhhhhHHHHHHHHHHHhc
Q psy14089 58 EEFTKKSKNASIASTAGSWYLETHSHQKPSRTQIFSRY-TPGYHFSNMSSKNISTGEKLLSLIDDIELVAKKKQEA 132 (333)
Q Consensus 58 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~Mas~~~S~re~LL~~lDDlE~lsKeLie~ 132 (333)
++..+|-++++++----+ ||.|--|--. ..|.+|- --.-||-.|.. -+.+--+|-+..+|+++++++|.|.
T Consensus 200 e~k~~k~~e~~~~nD~~s--le~~~~q~~t-q~vl~ev~QLss~~q~ltp-~rk~~s~i~E~d~~lq~sak~ieE~ 271 (1265)
T KOG0976|consen 200 EEKLEKFKEDLIEKDQKS--LELHKDQENT-QKVLKEVMQLSSQKQTLTP-LRKTCSMIEEQDMDLQASAKEIEEK 271 (1265)
T ss_pred HHHHHHHHHHhhcchHHH--HHHHHHHHHH-HHHHHHHHHHHHhHhhhhh-HhhhhHHHHHHHHHHHHHHHHHHHH
Confidence 455667777777654433 3443332211 1122221 01224555655 4445556778899999999999997
No 85
>PF10168 Nup88: Nuclear pore component; InterPro: IPR019321 Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein have no obvious structural motifs. It is, however, where it binds to Nup98; one of the components of the nuclear pore. The C-terminal end is a predicted coiled-coil domain []. Nup88 is over expressed in tumour cells [].
Probab=25.42 E-value=6.3e+02 Score=27.81 Aligned_cols=37 Identities=11% Similarity=0.070 Sum_probs=25.6
Q ss_pred hhHHHHHHHHHHHH--------hhhhhHHHHHHHHHHHHhHHHHH
Q psy14089 168 STAGFEDAHGVWES--------ASGSNKNEATAIFQAKQKLQSIN 204 (333)
Q Consensus 168 ~Q~eIEqkI~~Le~--------LKeAE~~L~taI~QAkqKLkSI~ 204 (333)
+|..+.++++.+-. |.+||+.....+..-+.+|+.+.
T Consensus 608 ~Qe~L~~R~~~vl~~l~~~~P~LS~AEr~~~~EL~~~~~~l~~l~ 652 (717)
T PF10168_consen 608 KQEKLMKRVDRVLQLLNSQLPVLSEAEREFKKELERMKDQLQDLK 652 (717)
T ss_pred HHHHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 57777777665532 77888887777777777776664
No 86
>PRK05724 acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated
Probab=24.93 E-value=1.4e+02 Score=29.85 Aligned_cols=46 Identities=15% Similarity=0.166 Sum_probs=30.8
Q ss_pred hhHHHHHHHHHHHHhh-hhhHHHHHHHHHHHHhHHHHHHhcCCCCCh
Q psy14089 168 STAGFEDAHGVWESAS-GSNKNEATAIFQAKQKLQSINKANKRPVSS 213 (333)
Q Consensus 168 ~Q~eIEqkI~~Le~LK-eAE~~L~taI~QAkqKLkSI~kAek~pVss 213 (333)
--.++|++|.+|+.+. +....+...|..=++|++...+.--..+++
T Consensus 11 ~i~~l~~~i~~l~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~ 57 (319)
T PRK05724 11 PIAELEAKIEELRAVAEDSDVDLSEEIERLEKKLEELTKKIYSNLTP 57 (319)
T ss_pred HHHHHHHHHHHHHhhhccccccHHHHHHHHHHHHHHHHHHHhcCCCH
Confidence 3467888888888763 345677777887777777775544444443
No 87
>PRK00024 hypothetical protein; Reviewed
Probab=24.85 E-value=3.6e+02 Score=25.14 Aligned_cols=54 Identities=15% Similarity=0.196 Sum_probs=36.4
Q ss_pred ccccCccchHHHhhh----hhHHHHHHHHHHHhc-c--CchhhHHHHHhcCHHHHHHHHHHH
Q psy14089 103 NMSSKNISTGEKLLS----LIDDIELVAKKKQEA-H--NHLQKTVVYFNKNEVVKQSFRIEI 157 (333)
Q Consensus 103 ~Mas~~~S~re~LL~----~lDDlE~lsKeLie~-~--~~~qliElLl~KD~eLk~~Lk~A~ 157 (333)
.|.. +.-+|++|+. .|.|-|+|+--|... + +..++...|+++-..|..++..-.
T Consensus 5 ~~~~-~~rprer~~~~G~~~Lsd~ELLa~lL~~g~~~~~~~~LA~~LL~~fgsL~~l~~as~ 65 (224)
T PRK00024 5 DWPE-EERPRERLLKYGAAALSDAELLAILLRTGTKGKSVLDLARELLQRFGSLRGLLDASL 65 (224)
T ss_pred cCch-hhhHHHHHHhcCcccCCHHHHHHHHHcCCCCCCCHHHHHHHHHHHcCCHHHHHhCCH
Confidence 3444 4558999986 799999997544332 2 566788888887666666665444
No 88
>KOG0971|consensus
Probab=24.75 E-value=5.5e+02 Score=30.09 Aligned_cols=89 Identities=15% Similarity=0.090 Sum_probs=53.1
Q ss_pred cchHHHhhhhhHHHHHHHHHHHhc---c-CchhhHHHHHhcCHHHHHHHHHHHHHHhhhhhhhh--------hHHHHHH-
Q psy14089 109 ISTGEKLLSLIDDIELVAKKKQEA---H-NHLQKTVVYFNKNEVVKQSFRIEIEEFTKKSKNAS--------TAGFEDA- 175 (333)
Q Consensus 109 ~S~re~LL~~lDDlE~lsKeLie~---~-~~~qliElLl~KD~eLk~~Lk~A~qahQe~~k~i~--------Q~eIEqk- 175 (333)
+++||+|-.-+|.+|...-+|-|- + -....++.|..|.-+|.+-+++.+++...++..-+ +++.|..
T Consensus 416 ~r~kE~Lsr~~d~aEs~iadlkEQVDAAlGAE~MV~qLtdknlnlEekVklLeetv~dlEalee~~EQL~Esn~ele~DL 495 (1243)
T KOG0971|consen 416 RRQKERLSRELDQAESTIADLKEQVDAALGAEEMVEQLTDKNLNLEEKVKLLEETVGDLEALEEMNEQLQESNRELELDL 495 (1243)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhcHHHHHHHHHhhccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 568999999999999988777775 2 45567777777777777766666633333222111 2222221
Q ss_pred HHHHHHhhhhhHHHHHHHHHHH
Q psy14089 176 HGVWESASGSNKNEATAIFQAK 197 (333)
Q Consensus 176 I~~Le~LKeAE~~L~taI~QAk 197 (333)
+.+|+.|+.+.++|..-+.-|.
T Consensus 496 reEld~~~g~~kel~~r~~aaq 517 (1243)
T KOG0971|consen 496 REELDMAKGARKELQKRVEAAQ 517 (1243)
T ss_pred HHHHHHHhhHHHHHHHHHHHHH
Confidence 4444446666665555544443
No 89
>PHA00692 hypothetical protein
Probab=24.72 E-value=33 Score=27.51 Aligned_cols=20 Identities=35% Similarity=0.810 Sum_probs=17.1
Q ss_pred CcccccccccCCCccccccc
Q psy14089 86 PSRTQIFSRYTPGYHFSNMS 105 (333)
Q Consensus 86 ~~~~~~~~~~~~~~~~~~Ma 105 (333)
..||..|-.|.|||.|.+--
T Consensus 28 edrthyfveyppgfrfggcr 47 (74)
T PHA00692 28 EDRTHYFVEYPPGFRFGGCR 47 (74)
T ss_pred ccceeEeEecCCCcccccee
Confidence 36899999999999998754
No 90
>PF10112 Halogen_Hydrol: 5-bromo-4-chloroindolyl phosphate hydrolysis protein; InterPro: IPR018770 This entry consists of prokaryotic proteins that mediate the hydrolysis of 5-bromo-4-chloroindolyl phosphate bonds.
Probab=24.45 E-value=4.8e+02 Score=23.21 Aligned_cols=49 Identities=8% Similarity=0.222 Sum_probs=28.2
Q ss_pred HhhhhhHHHHHHHHHHHhc----cCchhhHHHHHhcCHHHHHHHHHHHHHHhhhhh
Q psy14089 114 KLLSLIDDIELVAKKKQEA----HNHLQKTVVYFNKNEVVKQSFRIEIEEFTKKSK 165 (333)
Q Consensus 114 ~LL~~lDDlE~lsKeLie~----~~~~qliElLl~KD~eLk~~Lk~A~qahQe~~k 165 (333)
++...+.+++.+++.+|+. |.....++.|+. --|-.++++.+ .|.++..
T Consensus 98 ~~~~~~~~~~~~~~~I~~~v~~~P~~l~~a~~Fl~--~yLp~~~~l~~-kY~~l~~ 150 (199)
T PF10112_consen 98 EMIEKVSRIEKIARRIFKYVEKDPERLTQARKFLY--YYLPTAVKLLE-KYAELES 150 (199)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCHHhHHHHHHHHH--HHhhHHHHHHH-HHHHHHh
Confidence 3455667777777777765 333344444443 34566666666 5665444
No 91
>PF05667 DUF812: Protein of unknown function (DUF812); InterPro: IPR008530 This family consists of several eukaryotic proteins of unknown function.
Probab=24.00 E-value=5.4e+02 Score=27.76 Aligned_cols=72 Identities=14% Similarity=0.075 Sum_probs=42.8
Q ss_pred chhhHHHHHhcCHHHHHHHHHHH--------HHHhhhhhhhh------hHHH----------HHHHHHHH-HhhhhhHHH
Q psy14089 135 HLQKTVVYFNKNEVVKQSFRIEI--------EEFTKKSKNAS------TAGF----------EDAHGVWE-SASGSNKNE 189 (333)
Q Consensus 135 ~~qliElLl~KD~eLk~~Lk~A~--------qahQe~~k~i~------Q~eI----------EqkI~~Le-~LKeAE~~L 189 (333)
.-.+.+.+..|++.++++.+..+ .+|+.++..|. +.+| +++|+.|. +|...-...
T Consensus 456 ~k~~~~e~~~Kee~~~qL~~e~e~~~k~~~Rs~Yt~RIlEIv~NI~KQk~eI~KIl~DTr~lQkeiN~l~gkL~RtF~v~ 535 (594)
T PF05667_consen 456 IKEIEEEIRQKEELYKQLVKELEKLPKDVNRSAYTRRILEIVKNIRKQKEEIEKILSDTRELQKEINSLTGKLDRTFTVT 535 (594)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHH
Confidence 33555677777887777766655 67777665443 2223 33344443 377777777
Q ss_pred HHHHHHHHHhHHHHHHh
Q psy14089 190 ATAIFQAKQKLQSINKA 206 (333)
Q Consensus 190 ~taI~QAkqKLkSI~kA 206 (333)
...||+.-+|=...++|
T Consensus 536 dElifrdAKkDe~~rka 552 (594)
T PF05667_consen 536 DELIFRDAKKDEAARKA 552 (594)
T ss_pred HHHHHHHhhcCHHHHHH
Confidence 77777766654444444
No 92
>KOG3850|consensus
Probab=23.94 E-value=6e+02 Score=26.92 Aligned_cols=56 Identities=13% Similarity=0.214 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHHhhhhhhhhhHHHHHHHHHHHH--------hh-hhhHHHHHHHHHHHHhHHHHHHh
Q psy14089 149 VKQSFRIEIEEFTKKSKNASTAGFEDAHGVWES--------AS-GSNKNEATAIFQAKQKLQSINKA 206 (333)
Q Consensus 149 Lk~~Lk~A~qahQe~~k~i~Q~eIEqkI~~Le~--------LK-eAE~~L~taI~QAkqKLkSI~kA 206 (333)
++.=++..-|.-||.| .++.++|.++++|-. || +--..-+.+-||+-++-..|.+|
T Consensus 290 ~krdy~fi~etLQEER--yR~erLEEqLNdlteLqQnEi~nLKqElasmeervaYQsyERaRdIqEa 354 (455)
T KOG3850|consen 290 IKRDYKFIAETLQEER--YRYERLEEQLNDLTELQQNEIANLKQELASMEERVAYQSYERARDIQEA 354 (455)
T ss_pred HHHHHHHHHHHHHHHH--HHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3333333334555544 488888888777765 44 33333345667777776666554
No 93
>PRK01885 greB transcription elongation factor GreB; Reviewed
Probab=23.77 E-value=1.5e+02 Score=26.17 Aligned_cols=18 Identities=0% Similarity=-0.115 Sum_probs=11.4
Q ss_pred hhHHHHHHHHHHHH-hhhh
Q psy14089 168 STAGFEDAHGVWES-ASGS 185 (333)
Q Consensus 168 ~Q~eIEqkI~~Le~-LKeA 185 (333)
+|+.++.+|..|+. |+.|
T Consensus 55 ~~~~~e~rI~~L~~~L~~A 73 (157)
T PRK01885 55 RLREIDRRVRFLTKRLENL 73 (157)
T ss_pred HHHHHHHHHHHHHHHHccC
Confidence 56777777777754 4444
No 94
>PF11020 DUF2610: Domain of unknown function (DUF2610); InterPro: IPR021277 This family is conserved in Proteobacteria. One member is annotated as being elongation factor P but this could not be confirmed.
Probab=23.61 E-value=1.5e+02 Score=24.78 Aligned_cols=29 Identities=34% Similarity=0.406 Sum_probs=20.9
Q ss_pred HHHhHHHHHHhcCCCCChHHHHHHHHHhhcc
Q psy14089 196 AKQKLQSINKANKRPVSSEELIKYAHRISSS 226 (333)
Q Consensus 196 AkqKLkSI~kAek~pVssEeLIkYAHrISas 226 (333)
|=.||-.+ |.+..|+-|||+.||-..+..
T Consensus 53 sl~kL~~L--a~~N~v~feeLc~YAL~~a~~ 81 (82)
T PF11020_consen 53 SLSKLYKL--AKENNVSFEELCVYALGVAQN 81 (82)
T ss_pred HHHHHHHH--HHHcCCCHHHHHHHHHHHhcc
Confidence 33444333 678999999999999776653
No 95
>PRK02292 V-type ATP synthase subunit E; Provisional
Probab=23.60 E-value=5e+02 Score=22.73 Aligned_cols=25 Identities=8% Similarity=0.084 Sum_probs=22.3
Q ss_pred hhhhhHHHHHHHHHHHHhHHHHHHh
Q psy14089 182 ASGSNKNEATAIFQAKQKLQSINKA 206 (333)
Q Consensus 182 LKeAE~~L~taI~QAkqKLkSI~kA 206 (333)
|..=+..|..++..++.||..+.+.
T Consensus 75 L~~r~~~l~~v~~~a~~kL~~~~~~ 99 (188)
T PRK02292 75 LNARKEVLEDVRNQVEDEIASLDGD 99 (188)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcchh
Confidence 8888899999999999999998653
No 96
>KOG0810|consensus
Probab=23.57 E-value=5.7e+02 Score=25.34 Aligned_cols=17 Identities=18% Similarity=0.347 Sum_probs=12.3
Q ss_pred chHHHhhhhhHHHHHHH
Q psy14089 110 STGEKLLSLIDDIELVA 126 (333)
Q Consensus 110 S~re~LL~~lDDlE~ls 126 (333)
.++.+|.+.++++.-+=
T Consensus 127 ~~~kkf~~~M~~f~~~~ 143 (297)
T KOG0810|consen 127 ALSKKLKELMNEFNRTQ 143 (297)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 36678888888886653
No 97
>cd07654 F-BAR_FCHSD The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of FCH and double SH3 domains proteins (FCHSD). F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. This subfamily is composed of FCH and double SH3 domain (FCHSD) proteins, so named as they contain an N-terminal F-BAR domain and two SH3 domains at the C-terminus. Vertebrates harbor two subfamily members, FCHSD1 and FCHSD2, which have been characterized only in silico. Their biological function is still unknown. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules.
Probab=23.20 E-value=6.8e+02 Score=24.09 Aligned_cols=37 Identities=8% Similarity=0.084 Sum_probs=25.3
Q ss_pred hhHHHHHHHHHHHHhhhhhHHHHHHHHHHHHhHHHHH
Q psy14089 168 STAGFEDAHGVWESASGSNKNEATAIFQAKQKLQSIN 204 (333)
Q Consensus 168 ~Q~eIEqkI~~Le~LKeAE~~L~taI~QAkqKLkSI~ 204 (333)
-|.++++-+.+|++.|..=........+|++|++..+
T Consensus 122 lq~el~~~~~eL~ksKK~Y~~~~~~~~~ar~K~~~a~ 158 (264)
T cd07654 122 AQAEVQQTVRELSKSRKTYFEREQVAHLAREKAADVQ 158 (264)
T ss_pred HHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHH
Confidence 4566666777887766555566667778888877643
No 98
>PF08549 SWI-SNF_Ssr4: Fungal domain of unknown function (DUF1750); InterPro: IPR013859 This is a fungal protein of unknown function.
Probab=23.09 E-value=88 Score=34.32 Aligned_cols=26 Identities=12% Similarity=0.088 Sum_probs=18.5
Q ss_pred hHHHHHHHHHHHH---hhhhhHHHHHHHH
Q psy14089 169 TAGFEDAHGVWES---ASGSNKNEATAIF 194 (333)
Q Consensus 169 Q~eIEqkI~~Le~---LKeAE~~L~taI~ 194 (333)
+++=.++|..+++ ||+||+.|..++.
T Consensus 384 K~~Hak~m~k~k~~s~lk~AE~~LR~a~~ 412 (669)
T PF08549_consen 384 KARHAKRMAKFKRNSLLKDAEKELRDAVE 412 (669)
T ss_pred HHHHHHHHHHHhhccHHHHHHHHHHhccC
Confidence 3333444666655 9999999999887
No 99
>PF07845 DUF1636: Protein of unknown function (DUF1636); InterPro: IPR012863 The sequences featured in this family are derived from a number of hypothetical prokaryotic proteins. The region in question is approximately 130 amino acids long.
Probab=23.08 E-value=1.1e+02 Score=26.35 Aligned_cols=38 Identities=26% Similarity=0.467 Sum_probs=31.6
Q ss_pred CChHHHHHHHHHhhccccccCCCCCCCCCCCCCCCchHHhhhhccccc
Q psy14089 211 VSSEELIKYAHRISSSNAVCAPLTWQPGDPRRPYPTDIEMRVGFLGRL 258 (333)
Q Consensus 211 VssEeLIkYAHrISasnaVsAPl~WqpGdPrRPyPtE~eMR~G~Lg~l 258 (333)
=+.++|+.||..-.+ +|.+|.|-.-|| ..+|.++|.|+
T Consensus 77 ~~a~~il~~a~~Y~~-----s~dG~vp~~~rP-----~~lr~~~~aRi 114 (116)
T PF07845_consen 77 EDAEDILAFAALYAA-----SPDGLVPWRERP-----EGLRKGFLARI 114 (116)
T ss_pred cCHHHHHHHHHHHHh-----CCCCccccccCC-----HHHHhCeeecc
Confidence 456899999998887 488998877777 88999999874
No 100
>cd07657 F-BAR_Fes_Fer The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Fes (feline sarcoma) and Fer (Fes related) tyrosine kinases. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Fes (feline sarcoma), also called Fps (Fujinami poultry sarcoma), and Fer (Fes related) are cytoplasmic (or nonreceptor) tyrosine kinases that play roles in haematopoiesis, inflammation and immunity, growth factor signaling, cytoskeletal regulation, cell migration and adhesion, and the regulation of cell-cell interactions. Although Fes and Fer show redundancy in their biological functions, they show differences in their expression patterns. Fer is ubiquitously expressed while Fes is expressed predominantly in myeloid and endothelial cells. Fes and Fer contain an N-terminal F-BAR domain, an SH2 domain, and a C-terminal catalytic kinase domain. F-BAR domains form banana-shaped dimers with a posit
Probab=23.06 E-value=6.4e+02 Score=23.71 Aligned_cols=84 Identities=10% Similarity=0.008 Sum_probs=39.4
Q ss_pred hhhhhHHHHHHHHHHHhccC--chhhHHHHHhcCHHHHHHHHHHHHHHhhhhhhhhhHHHHHHHHHHHHhhhhhHHHHHH
Q psy14089 115 LLSLIDDIELVAKKKQEAHN--HLQKTVVYFNKNEVVKQSFRIEIEEFTKKSKNASTAGFEDAHGVWESASGSNKNEATA 192 (333)
Q Consensus 115 LL~~lDDlE~lsKeLie~~~--~~qliElLl~KD~eLk~~Lk~A~qahQe~~k~i~Q~eIEqkI~~Le~LKeAE~~L~ta 192 (333)
-...|++++.++++.--.++ ..++++-|..--.+++.+.|.-.+.+++ -+.+++.-+.+|++.|..=..+-..
T Consensus 67 W~~iL~ete~~A~~~~~~ae~l~~~i~~~l~~l~~~~~~~rK~~~~~~~k-----l~~el~~~~~el~k~Kk~Y~~~~~e 141 (237)
T cd07657 67 WKEIMDSTDQLSKLIKQHAEALESGTLDKLTLLIKDKRKAKKAYQEERQQ-----IDEQYKKLTDEVEKLKSEYQKLLED 141 (237)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 55667777777774333211 1122222222222333333333322222 3455555566776655555555555
Q ss_pred HHHHHHhHHHH
Q psy14089 193 IFQAKQKLQSI 203 (333)
Q Consensus 193 I~QAkqKLkSI 203 (333)
...|++|++..
T Consensus 142 ~e~Ar~k~e~a 152 (237)
T cd07657 142 YKAAKSKFEEA 152 (237)
T ss_pred HHHHHHHHHHH
Confidence 55666665444
No 101
>smart00806 AIP3 Actin interacting protein 3. Aip3p/Bud6p is a regulator of cell and cytoskeletal polarity in Saccharomyces cerevisiae that was previously identified as an actin-interacting protein. Actin-interacting protein 3 (Aip3p) localizes at the cell cortex where cytoskeleton assembly must be achieved to execute polarized cell growth, and deletion of AIP3 causes gross defects in cell and cytoskeletal polarity. Aip3p localization is mediated by the secretory pathway, mutations in early- or late-acting components of the secretory apparatus lead to Aip3p mislocalization PUBMED:10679021.
Probab=22.78 E-value=9.2e+02 Score=25.46 Aligned_cols=32 Identities=22% Similarity=0.390 Sum_probs=20.0
Q ss_pred CccccccccCccc-hHHHhhhhhHHHHHHHHHH
Q psy14089 98 GYHFSNMSSKNIS-TGEKLLSLIDDIELVAKKK 129 (333)
Q Consensus 98 ~~~~~~Mas~~~S-~re~LL~~lDDlE~lsKeL 129 (333)
|.-|+.++-+..| --+.||.-+|||+-+.-.|
T Consensus 204 ~R~y~e~~k~kL~~~Sd~lltkVDDLQD~vE~L 236 (426)
T smart00806 204 NRAYVESSKKKLSEDSDSLLTKVDDLQDIIEAL 236 (426)
T ss_pred chHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4445555532322 4688999999998775443
No 102
>PF12998 ING: Inhibitor of growth proteins N-terminal histone-binding; InterPro: IPR024610 Histones undergo numerous post-translational modifications, including acetylation and methylation, at residues which are then probable docking sites for various chromatin remodelling complexes. Inhibitor of growth proteins (INGs) specifically bind to residues that have been thus modified. INGs carry a well-characterised C-terminal PHD-type zinc-finger domain, binding with lysine 4-tri-methylated histone H3 (H3K4me3), as well as this N-terminal domain that binds unmodified H3 tails. Although these two regions can bind histones independently, together they increase the apparent association of the ING for the H3 tail. This entry represents the N-terminal histone binding domain found in inhibitor proteins.; PDB: 4AFL_A.
Probab=22.49 E-value=3.8e+02 Score=20.87 Aligned_cols=72 Identities=10% Similarity=0.018 Sum_probs=37.8
Q ss_pred CchhhHHHHHhcCHHHHHHHHHHHHHHhhhhhhhhhHHHHHHHHHHHHhhhhhHHHHHHHHHHHHhHHHHHHh
Q psy14089 134 NHLQKTVVYFNKNEVVKQSFRIEIEEFTKKSKNASTAGFEDAHGVWESASGSNKNEATAIFQAKQKLQSINKA 206 (333)
Q Consensus 134 ~~~qliElLl~KD~eLk~~Lk~A~qahQe~~k~i~Q~eIEqkI~~Le~LKeAE~~L~taI~QAkqKLkSI~kA 206 (333)
+..-.+.++...|...+..++.+.+.+++--+.+..+.+... .....+++.+..+..++.-+++|+.-+.+|
T Consensus 16 el~r~l~~irelD~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~I~~~~~~~~~l~deKv~lA~~~ 87 (105)
T PF12998_consen 16 ELQRNLTLIRELDAKSQDLLEELDQQIQKFIKNHGSPSLSPE-KRRELLKEIQEEYERALELSDEKVALAQQA 87 (105)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCTTS--S-HH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHhhcccccCChH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444556677777877777777777444443332222111111 222235555566666666666666655443
No 103
>COG3679 Regulatory protein involved in competence development and sporulation [Replication, recombination and repair; Signal transduction mechanisms]
Probab=22.21 E-value=5.4e+02 Score=22.57 Aligned_cols=20 Identities=0% Similarity=-0.016 Sum_probs=16.6
Q ss_pred hhhhhHHHHHHHHHHHHhHH
Q psy14089 182 ASGSNKNEATAIFQAKQKLQ 201 (333)
Q Consensus 182 LKeAE~~L~taI~QAkqKLk 201 (333)
+++||..|...|..-.+++.
T Consensus 86 f~eaE~~L~~~l~el~~iI~ 105 (118)
T COG3679 86 FMEAEQALSSLLDELNKIIA 105 (118)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 99999999999887776653
No 104
>PF05529 Bap31: B-cell receptor-associated protein 31-like ; InterPro: IPR008417 Bap31 is a polytopic integral protein of the endoplasmic reticulum membrane and a substrate of caspase-8. Bap31 is cleaved within its cytosolic domain, generating pro-apoptotic p20 Bap31 [].; GO: 0006886 intracellular protein transport, 0005783 endoplasmic reticulum, 0016021 integral to membrane
Probab=22.21 E-value=3.9e+02 Score=23.62 Aligned_cols=33 Identities=6% Similarity=-0.039 Sum_probs=24.5
Q ss_pred hHHHHHHHHHHHH-hhhhhHHHHHHHHHHHHhHH
Q psy14089 169 TAGFEDAHGVWES-ASGSNKNEATAIFQAKQKLQ 201 (333)
Q Consensus 169 Q~eIEqkI~~Le~-LKeAE~~L~taI~QAkqKLk 201 (333)
..+.+++|..|++ |+.++..+++.-.|++.-.+
T Consensus 156 ~~~~~~ei~~lk~el~~~~~~~~~LkkQ~~~l~~ 189 (192)
T PF05529_consen 156 NKKLSEEIEKLKKELEKKEKEIEALKKQSEGLQK 189 (192)
T ss_pred hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3455666777865 88999999999888876544
No 105
>COG5612 Predicted integral membrane protein [Function unknown]
Probab=22.16 E-value=6.1e+02 Score=23.18 Aligned_cols=76 Identities=20% Similarity=0.145 Sum_probs=48.2
Q ss_pred HHHHHHHHHHHHHHhhhhhhhhhHHHHHH-------------HHHHHHhhhhhHHHHHHHHHHHHhHHHHHHhcCCCCCh
Q psy14089 147 EVVKQSFRIEIEEFTKKSKNASTAGFEDA-------------HGVWESASGSNKNEATAIFQAKQKLQSINKANKRPVSS 213 (333)
Q Consensus 147 ~eLk~~Lk~A~qahQe~~k~i~Q~eIEqk-------------I~~Le~LKeAE~~L~taI~QAkqKLkSI~kAek~pVss 213 (333)
.-|+++|..|.|.--++..+++|+.+|-. -..|++-+++|....+.|.++-. +=.+..|+
T Consensus 53 ~~fRqaLr~arq~~rei~~~arqaRreAa~ll~~p~lDtaals~aLerAR~ae~~vR~~vE~~~~-------~FAatlS~ 125 (148)
T COG5612 53 RGFRQALRAARQKNREITQRARQARREAAALLASPGLDTAALSRALERARDAEIQVRGNVETALA-------TFAATLSP 125 (148)
T ss_pred HHHHHHHHHHHhhhhHhHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhcchHHHHHHHHHHHH-------HHHHhcCH
Confidence 44677788887766666666677777653 23334455556555555544322 22456888
Q ss_pred HHHHHHHHHhhccccccCC
Q psy14089 214 EELIKYAHRISSSNAVCAP 232 (333)
Q Consensus 214 EeLIkYAHrISasnaVsAP 232 (333)
++=-..|.-+|. ..||
T Consensus 126 ~~R~~LAeGLs~---r~aP 141 (148)
T COG5612 126 QERAALAEGLSE---RYAP 141 (148)
T ss_pred HHHHHHHhHHhh---hcCC
Confidence 888888888886 6666
No 106
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=22.09 E-value=6.8e+02 Score=25.90 Aligned_cols=116 Identities=14% Similarity=0.050 Sum_probs=64.8
Q ss_pred cccccccCccchHHHhhhhhHH------HHHHHHHHHhc--------cCchhhHHHHHhcCHHHHHHHHHHHHHHhhhhh
Q psy14089 100 HFSNMSSKNISTGEKLLSLIDD------IELVAKKKQEA--------HNHLQKTVVYFNKNEVVKQSFRIEIEEFTKKSK 165 (333)
Q Consensus 100 ~~~~Mas~~~S~re~LL~~lDD------lE~lsKeLie~--------~~~~qliElLl~KD~eLk~~Lk~A~qahQe~~k 165 (333)
++.++.....|+.+.|+.-|.. ...++..||.+ .+...+.+.|---..++.++|+..+ .
T Consensus 92 ~~~~~~~~~~sL~e~L~~Ql~~~~l~~~~~~ia~~iI~~LD~~GyL~~~~~eia~~l~~~~~~v~~~l~~lQ----~--- 164 (455)
T PRK05932 92 LPVYQGETTESLQDHLLEQIELTPFSETDRAIATYIIDALDDEGYLTEDLEEIAESLGVELDEVEAVLKRIQ----S--- 164 (455)
T ss_pred chhhhccCCCCHHHHHHHHHcccCCCHHHHHHHHHHHHhCCCCCCCCCCHHHHHHHcCCCHHHHHHHHHHHh----c---
Confidence 3333444378999999887754 36778888887 2556666665333455555555544 0
Q ss_pred hhhhH-----HHHH-HHHHHHH------hhhhhHHHHHHH-HHHHHhHHHHHHhcCCCCChHHHHHHHHHhhc
Q psy14089 166 NASTA-----GFED-AHGVWES------ASGSNKNEATAI-FQAKQKLQSINKANKRPVSSEELIKYAHRISS 225 (333)
Q Consensus 166 ~i~Q~-----eIEq-kI~~Le~------LKeAE~~L~taI-~QAkqKLkSI~kAek~pVssEeLIkYAHrISa 225 (333)
.+=. -+.. .+-+|++ +..+..+|..-+ .-|+.+++.|. ++-.|+.++|.++...|..
T Consensus 165 -leP~GigAr~L~ECLllQl~~~~~~~~~~~~~~il~~~le~la~~~~~~ia--~~l~is~~~v~~~~~~Ir~ 234 (455)
T PRK05932 165 -FDPAGVGARDLQECLLLQLEQLDDTPRLDEAMEIISDHLDLLARRDFRTLA--KKLGVKEEDLQEALDLIRS 234 (455)
T ss_pred -CCCCccCcCCHHHHHHHHHhccCCCchHHHHHHHHHHHHHHHHcCCHHHHH--HHHCcCHHHHHHHHHHHhC
Confidence 1111 1111 1222322 122333333322 22556666664 4557899999999998886
No 107
>TIGR00414 serS seryl-tRNA synthetase. This model represents the seryl-tRNA synthetase found in most organisms. This protein is a class II tRNA synthetase, and is recognized by the pfam model tRNA-synt_2b. The seryl-tRNA synthetases of two archaeal species, Methanococcus jannaschii and Methanobacterium thermoautotrophicum, differ considerably and are included in a different model.
Probab=22.04 E-value=8.4e+02 Score=24.73 Aligned_cols=37 Identities=8% Similarity=-0.065 Sum_probs=24.0
Q ss_pred HHHHHHHHHHhcc-CchhhHHHHHhcCHHHHHHHHHHH
Q psy14089 121 DIELVAKKKQEAH-NHLQKTVVYFNKNEVVKQSFRIEI 157 (333)
Q Consensus 121 DlE~lsKeLie~~-~~~qliElLl~KD~eLk~~Lk~A~ 157 (333)
+.+.+.+.|-.-. +....++.++..|++.+++...++
T Consensus 10 n~~~v~~~l~~R~~~~~~~vd~i~~ld~~~r~~~~~~~ 47 (418)
T TIGR00414 10 NPDLVKESLKARGLSVDIDLEKLIALDDERKKLLSEIE 47 (418)
T ss_pred CHHHHHHHHHhcCCChhhhHHHHHHHHHHHHHHHHHHH
Confidence 4444444333333 222258999999999999988887
No 108
>PF08654 DASH_Dad2: DASH complex subunit Dad2; InterPro: IPR013963 The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis []. In Saccharomyces cerevisiae (Baker's yeast) DASH forms both rings and spiral structures on microtubules in vitro [, ].
Probab=21.93 E-value=4.9e+02 Score=22.00 Aligned_cols=57 Identities=11% Similarity=0.088 Sum_probs=35.4
Q ss_pred HHHHhcCHHHHHHHHHHHHHHhhhhhhhhhHHHHHHHHHH----HHhhhhhHHHHHHHHHHHHhHHHHHHh
Q psy14089 140 VVYFNKNEVVKQSFRIEIEEFTKKSKNASTAGFEDAHGVW----ESASGSNKNEATAIFQAKQKLQSINKA 206 (333)
Q Consensus 140 ElLl~KD~eLk~~Lk~A~qahQe~~k~i~Q~eIEqkI~~L----e~LKeAE~~L~taI~QAkqKLkSI~kA 206 (333)
..+.+|..||..+-++-. --..+-.+++.| +.|.++-...+.++..=.--+.+|..|
T Consensus 4 ~ri~eKk~ELe~L~~l~~----------lS~~L~~qle~L~~kl~~m~dg~e~Va~Vl~NW~nV~r~Is~A 64 (103)
T PF08654_consen 4 ARIAEKKAELEALKQLRD----------LSADLASQLEALSEKLETMADGAEAVASVLANWQNVFRAISMA 64 (103)
T ss_pred HHHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHHHhccHHHHHHHHhHHHHHHHHHHH
Confidence 456667777766555544 223333333333 347777778888887777777777777
No 109
>PRK01194 V-type ATP synthase subunit E; Provisional
Probab=21.74 E-value=6e+02 Score=22.90 Aligned_cols=24 Identities=17% Similarity=0.033 Sum_probs=21.0
Q ss_pred hhhhhHHHHHHHHHHHHhHHHHHH
Q psy14089 182 ASGSNKNEATAIFQAKQKLQSINK 205 (333)
Q Consensus 182 LKeAE~~L~taI~QAkqKLkSI~k 205 (333)
|..=+..|..++.+|.++|..+.+
T Consensus 75 L~aree~I~~v~~~a~e~L~~l~~ 98 (185)
T PRK01194 75 REKRREILKDYLDIAYEHLMNITK 98 (185)
T ss_pred HHHHHHHHHHHHHHHHHHHHcccC
Confidence 777789999999999999999843
No 110
>cd07656 F-BAR_srGAP The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Slit-Robo GTPase Activating Proteins. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Slit-Robo GTPase Activating Proteins (srGAPs) are Rho GAPs that interact with Robo1, the transmembrane receptor of Slit proteins. Slit proteins are secreted proteins that control axon guidance and the migration of neurons and leukocytes. Vertebrates contain three isoforms of srGAPs, all of which are expressed during embryonic and early development in the nervous system but with different localization and timing. srGAPs contain an N-terminal F-BAR domain, a Rho GAP domain, and a C-terminal SH3 domain. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules.
Probab=21.61 E-value=6.9e+02 Score=23.59 Aligned_cols=90 Identities=9% Similarity=-0.030 Sum_probs=43.1
Q ss_pred HHhhhhhHHHHHHHHHHHhccC--chhhHHHHHhcCHHHHHHHHHHHHHHhhhhhhhhhHHHHHHHHHHHHhhhhhHHHH
Q psy14089 113 EKLLSLIDDIELVAKKKQEAHN--HLQKTVVYFNKNEVVKQSFRIEIEEFTKKSKNASTAGFEDAHGVWESASGSNKNEA 190 (333)
Q Consensus 113 e~LL~~lDDlE~lsKeLie~~~--~~qliElLl~KD~eLk~~Lk~A~qahQe~~k~i~Q~eIEqkI~~Le~LKeAE~~L~ 190 (333)
..--..|++.+.+++.--...+ ..+++.-|...-..++.+.+.-.+..++ -|.++..-+++|++.|..=..+.
T Consensus 70 ~~W~~lL~qt~~~a~~h~~lse~l~~~i~~~l~~l~~d~~~~~Kk~~e~~~~-----lq~el~~~~~eL~k~kK~Y~~~~ 144 (241)
T cd07656 70 NCWNTLLVQTKQESRDHSTLSDIYSNNLVQRLGQMSEDLQRISKKCREIGSQ-----LHDELLRVLNELQTAMKTYHTYH 144 (241)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344566666666665444321 1123333333333344444444422222 34455555666666444444455
Q ss_pred HHHHHHHHhHHHHHHhc
Q psy14089 191 TAIFQAKQKLQSINKAN 207 (333)
Q Consensus 191 taI~QAkqKLkSI~kAe 207 (333)
..-.+|+.|++.++...
T Consensus 145 ~ea~~A~~K~~~ae~~~ 161 (241)
T cd07656 145 AESKSAERKLKEAEKQE 161 (241)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 55555666666665553
No 111
>PF06098 Radial_spoke_3: Radial spoke protein 3; InterPro: IPR009290 This family consists of several radial spoke protein 3 (RSP3) sequences. Eukaryotic cilia and flagella present in diverse types of cells perform motile, sensory, and developmental functions in organisms from protists to humans. They are centred by precisely organised, microtubule-based structures, the axonemes. The axoneme consists of two central singlet microtubules, called the central pair, and nine outer doublet microtubules. These structures are well conserved during evolution. The outer doublet microtubules, each composed of A and B sub-fibres, are connected to each other by nexin links, while the central pair is held at the centre of the axoneme by radial spokes. The radial spokes are T-shaped structures extending from the A-tubule of each outer doublet microtubule to the centre of the axoneme. Radial spoke protein 3 (RSP3), is present at the proximal end of the spoke stalk and helps in anchoring the radial spoke to the outer doublet. It is thought that radial spokes regulate the activity of inner arm dynein through protein phosphorylation and dephosphorylation [].
Probab=21.35 E-value=5e+02 Score=25.71 Aligned_cols=59 Identities=14% Similarity=0.119 Sum_probs=29.7
Q ss_pred HHHHhc-cCchhhHHHHHhcCHHHHHHHHHHH--HHHhhhhhhhhhHHHHHH----HHHHHHhhhhhHHH
Q psy14089 127 KKKQEA-HNHLQKTVVYFNKNEVVKQSFRIEI--EEFTKKSKNASTAGFEDA----HGVWESASGSNKNE 189 (333)
Q Consensus 127 KeLie~-~~~~qliElLl~KD~eLk~~Lk~A~--qahQe~~k~i~Q~eIEqk----I~~Le~LKeAE~~L 189 (333)
-+||.+ -++.|+++.|+.| .|-++|..+. ++-..++. .|...++. ...+.+|.++|..+
T Consensus 121 gdLFDFd~EV~PiLeVLVgK--tlEQAl~EV~EEeEL~~lr~--~q~~fe~~R~aEl~e~qrlE~~e~r~ 186 (291)
T PF06098_consen 121 GDLFDFDEEVKPILEVLVGK--TLEQALMEVMEEEELAALRR--QQRAFEELRNAELAEVQRLEEAEKRR 186 (291)
T ss_pred ccccchHhhhhhHHHHHHHH--HHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345655 3777888888764 4444444444 22222222 45555443 33334455555544
No 112
>PRK11820 hypothetical protein; Provisional
Probab=21.10 E-value=7.5e+02 Score=24.20 Aligned_cols=75 Identities=7% Similarity=0.140 Sum_probs=41.0
Q ss_pred HHHHHHHHHHHHHHhhhhhhhh-----hHHHHHHHHHHHH-hhhhhHHHHHHHHHHHHhHH-HHHHhcCCCCCh----HH
Q psy14089 147 EVVKQSFRIEIEEFTKKSKNAS-----TAGFEDAHGVWES-ASGSNKNEATAIFQAKQKLQ-SINKANKRPVSS----EE 215 (333)
Q Consensus 147 ~eLk~~Lk~A~qahQe~~k~i~-----Q~eIEqkI~~Le~-LKeAE~~L~taI~QAkqKLk-SI~kAek~pVss----Ee 215 (333)
..+.+++..|.+.+.++|. + ++.+..++..++. +...+.....++.+.++||. .+++.- ..++. .|
T Consensus 129 ~~l~~al~~AL~~l~~~R~--~EG~~L~~dl~~rl~~i~~~~~~i~~~~p~~~~~~~~rL~~rl~el~-~~~d~~Rl~qE 205 (288)
T PRK11820 129 AALLAALDEALDDLIEMRE--REGAALKADLLQRLDAIEALVAKIEALAPEILEEYRERLRERLEELL-GELDENRLEQE 205 (288)
T ss_pred HHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHhchHHHHHHHHHHHHHHHHHH-hhcCHHHHHHH
Confidence 3455555555555555444 3 3445556666655 66666666666666666654 233332 45666 34
Q ss_pred HHHHHHHhh
Q psy14089 216 LIKYAHRIS 224 (333)
Q Consensus 216 LIkYAHrIS 224 (333)
+.=||.|+-
T Consensus 206 val~adK~D 214 (288)
T PRK11820 206 VALLAQKAD 214 (288)
T ss_pred HHHHHHHcc
Confidence 455665544
No 113
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=21.08 E-value=7.6e+02 Score=23.89 Aligned_cols=53 Identities=13% Similarity=0.179 Sum_probs=33.1
Q ss_pred hhhhhHHHHHHHHHHHHhHHHHHH---hcCCCCChHHHHHHHHHhhcc-ccccCCCC
Q psy14089 182 ASGSNKNEATAIFQAKQKLQSINK---ANKRPVSSEELIKYAHRISSS-NAVCAPLT 234 (333)
Q Consensus 182 LKeAE~~L~taI~QAkqKLkSI~k---Aek~pVssEeLIkYAHrISas-naVsAPl~ 234 (333)
|.+++..++..+...+++...+.. --+..++++-|=.|=+-+... +.+.+|+.
T Consensus 140 ~~e~~~~~e~e~~~i~e~~~~~~~~~~~L~~~l~~ell~~yeri~~~~kg~gvvpl~ 196 (239)
T COG1579 140 LAEAEARLEEEVAEIREEGQELSSKREELKEKLDPELLSEYERIRKNKKGVGVVPLE 196 (239)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHhcCCCceEEeec
Confidence 777888888887777776544433 224456666666666666655 44555553
No 114
>PF01627 Hpt: Hpt domain; InterPro: IPR008207 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms [, ]. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and (with bifunctional enzymes) the phosphotransfer from aspartyl phosphate back to ADP or to water []. The kinase core has a unique fold, distinct from that of the Ser/Thr/Tyr kinase superfamily. HKs can be roughly divided into two classes: orthodox and hybrid kinases [, ]. Most orthodox HKs, typified by the Escherichia coli EnvZ protein, function as periplasmic membrane receptors and have a signal peptide and transmembrane segment(s) that separate the protein into a periplasmic N-terminal sensing domain and a highly conserved cytoplasmic C-terminal kinase core. Members of this family, however, have an integral membrane sensor domain. Not all orthodox kinases are membrane bound, e.g., the nitrogen regulatory kinase NtrB (GlnL) is a soluble cytoplasmic HK []. Hybrid kinases contain multiple phosphodonor and phosphoacceptor sites and use multi-step phospho-relay schemes instead of promoting a single phosphoryl transfer. In addition to the sensor domain and kinase core, they contain a CheY-like receiver domain and a His-containing phosphotransfer (HPt) domain. This entry represents a domain present at the N terminus in proteins which undergo autophosphorylation. The group includes, the gliding motility regulatory protein from Myxococcus xanthus and a number of bacterial chemotaxis proteins.; GO: 0004871 signal transducer activity, 0000160 two-component signal transduction system (phosphorelay); PDB: 3KYJ_A 3KYI_A 3IQT_A 1Y6D_A 2LD6_A 1TQG_A 2R25_A 1OXB_A 1QSP_B 1C03_B ....
Probab=20.91 E-value=1.3e+02 Score=21.78 Aligned_cols=39 Identities=26% Similarity=0.277 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHhHHHHHHhcCC--CCChHHHHHHHHHhhcc
Q psy14089 188 NEATAIFQAKQKLQSINKANKR--PVSSEELIKYAHRISSS 226 (333)
Q Consensus 188 ~L~taI~QAkqKLkSI~kAek~--pVssEeLIkYAHrISas 226 (333)
.|+.-+.+..+.++.++++-.. .-+.++|.+.||+|-++
T Consensus 2 ll~~f~~~~~~~~~~l~~~~~~~~~~d~~~l~~~~H~lkG~ 42 (90)
T PF01627_consen 2 LLDIFLEEAPEDLEQLEQALQALEQEDWEELRRLAHRLKGS 42 (90)
T ss_dssp HHHHHHHHHHHHHHHHHHHHCSSHHCHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhHhhHHHHHHHHHHHhhh
Confidence 4566677777788888777631 56889999999999874
No 115
>PHA02604 rI.-1 hypothetical protein; Provisional
Probab=20.84 E-value=3.8e+02 Score=23.97 Aligned_cols=43 Identities=12% Similarity=0.147 Sum_probs=31.1
Q ss_pred hcCHHHHHHHHHHHHHHhhhhhhhhhHHHHHHHHHHHHhhhhhHHHHHHHHHHHHhHH
Q psy14089 144 NKNEVVKQSFRIEIEEFTKKSKNASTAGFEDAHGVWESASGSNKNEATAIFQAKQKLQ 201 (333)
Q Consensus 144 ~KD~eLk~~Lk~A~qahQe~~k~i~Q~eIEqkI~~Le~LKeAE~~L~taI~QAkqKLk 201 (333)
.+-+=|+.+++.|.+.|.+.. -.|+.+.-.+.+.|+|++-||.
T Consensus 82 d~~~~l~~~l~~a~~i~~~l~---------------s~L~N~~DdI~~~~~qt~YkLt 124 (126)
T PHA02604 82 DTIAFLDELLQEAEEIYKELP---------------SALQSTLDDITGLCYQTKYKLT 124 (126)
T ss_pred CHHHHHHHHHHHHHHHHHHhh---------------HHHHHHHHHHHHHHHHHHHHHh
Confidence 555667778888885444311 2288888889999999999885
No 116
>PRK00488 pheS phenylalanyl-tRNA synthetase subunit alpha; Validated
Probab=20.83 E-value=5.4e+02 Score=25.99 Aligned_cols=58 Identities=10% Similarity=0.041 Sum_probs=34.1
Q ss_pred hhHHHHHhcCHHHHHHHHHHHHHHhhhhhhhhhHHHHHHHHHHHHhhhhhHHHHHHHHHHHHhHHHHHH
Q psy14089 137 QKTVVYFNKNEVVKQSFRIEIEEFTKKSKNASTAGFEDAHGVWESASGSNKNEATAIFQAKQKLQSINK 205 (333)
Q Consensus 137 qliElLl~KD~eLk~~Lk~A~qahQe~~k~i~Q~eIEqkI~~Le~LKeAE~~L~taI~QAkqKLkSI~k 205 (333)
++=-.++-|...|..+++..... ... +...+=+ .+.+++..++.++.+.++.|+..+.
T Consensus 27 ~~r~~~lgkkg~l~~~~~~l~~l-~~e----er~~~G~------~~n~~k~~~~~~~~~~~~~l~~~~~ 84 (339)
T PRK00488 27 ALRVKYLGKKGELTELLKGLGKL-PPE----ERKEAGA------LINELKQAIEAALEERKEELEAAAL 84 (339)
T ss_pred HHHHHHhCCchHHHHHHHHHhcC-CHH----HHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33336778888999888877610 000 1112222 2445566777778877777776654
No 117
>smart00073 HPT Histidine Phosphotransfer domain. Contains an active histidine residue that mediates phosphotransfer reactions. Domain detected only in eubacteria. This alignment is an extension to that shown in the Cell structure paper.
Probab=20.79 E-value=1.7e+02 Score=21.60 Aligned_cols=38 Identities=21% Similarity=0.252 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHhHHHHHHhcCCCCChHHHHHHHHHhhcc
Q psy14089 188 NEATAIFQAKQKLQSINKANKRPVSSEELIKYAHRISSS 226 (333)
Q Consensus 188 ~L~taI~QAkqKLkSI~kAek~pVssEeLIkYAHrISas 226 (333)
.+..-+.+..+.+..++++- ..-+.+++.+.+|+|-++
T Consensus 3 ~~~~f~~~~~~~l~~l~~~~-~~~~~~~l~~~~H~LKG~ 40 (87)
T smart00073 3 ELAEFLQSLEEGLLELEKAL-DAQDVNEIFRAAHTLKGS 40 (87)
T ss_pred HHHHHHHHHHHHHHHHHhCc-CHhHHHHHHHHHHhhhhh
Confidence 34555666666677776665 355677888888888774
No 118
>PRK13676 hypothetical protein; Provisional
Probab=20.58 E-value=4.8e+02 Score=21.36 Aligned_cols=84 Identities=11% Similarity=0.007 Sum_probs=46.6
Q ss_pred hhhHHHHHHHHHHHhccCchhhH--HHHHhcCHHHHHHHHHHH---HHHhhhhhhhh--hHHHHHHHHHHHH--------
Q psy14089 117 SLIDDIELVAKKKQEAHNHLQKT--VVYFNKNEVVKQSFRIEI---EEFTKKSKNAS--TAGFEDAHGVWES-------- 181 (333)
Q Consensus 117 ~~lDDlE~lsKeLie~~~~~qli--ElLl~KD~eLk~~Lk~A~---qahQe~~k~i~--Q~eIEqkI~~Le~-------- 181 (333)
.++|-...|++.|-++++...+. ..-+..|++.+++++.-. +.++..+.... -.+..++++.+.+
T Consensus 4 ni~d~A~eL~~aI~~s~ey~~~~~A~~~l~~d~~a~~li~~F~~~q~~~~~~q~~g~~~~~e~~~~l~~l~~~i~~n~~i 83 (114)
T PRK13676 4 NIYDLANELERALRELPEYKALKEAKEAVKADEEAKKLFDEFRALQLEIQQKQMTGQEITEEEQQKAQELGQKIQQNELL 83 (114)
T ss_pred hHHHHHHHHHHHHHcCHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHhcCHHH
Confidence 35667777788777776444333 355678888777766544 11211111111 0122233444432
Q ss_pred --hhhhhHHHHHHHHHHHHhH
Q psy14089 182 --ASGSNKNEATAIFQAKQKL 200 (333)
Q Consensus 182 --LKeAE~~L~taI~QAkqKL 200 (333)
+..||..|...+.+-.+.+
T Consensus 84 ~~y~~Ae~~l~~ll~~v~~iI 104 (114)
T PRK13676 84 SKLMEAEQRLSVYINDINKII 104 (114)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 8888888888877766554
No 119
>PF12005 DUF3499: Protein of unknown function (DUF3499); InterPro: IPR021888 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 125 to 163 amino acids in length.
Probab=20.31 E-value=59 Score=28.75 Aligned_cols=22 Identities=32% Similarity=0.644 Sum_probs=16.8
Q ss_pred ccCCCCCC----CCCCCCCCCchHHh
Q psy14089 229 VCAPLTWQ----PGDPRRPYPTDIEM 250 (333)
Q Consensus 229 VsAPl~Wq----pGdPrRPyPtE~eM 250 (333)
+.||.+|+ .+...+|.|.+.+|
T Consensus 51 lTaP~GWevvR~~~~~~~~~p~~DDL 76 (123)
T PF12005_consen 51 LTAPRGWEVVRLEGPFAPPPPDDDDL 76 (123)
T ss_pred ccCCCCcEEEeccCCCCCCCCChhHH
Confidence 67899999 55555778888776
Done!