Query 022668
Match_columns 294
No_of_seqs 141 out of 1345
Neff 7.0
Searched_HMMs 46136
Date Fri Mar 29 05:16:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022668.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022668hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0123 AcuC Deacetylases, inc 100.0 4.2E-71 9.1E-76 520.8 25.4 249 33-293 2-260 (340)
2 PTZ00063 histone deacetylase; 100.0 1.1E-70 2.3E-75 529.1 27.6 254 32-293 3-271 (436)
3 PTZ00346 histone deacetylase; 100.0 1.9E-70 4.2E-75 524.6 27.7 254 32-293 19-289 (429)
4 PF00850 Hist_deacetyl: Histon 100.0 1.1E-68 2.5E-73 501.3 17.5 240 40-293 1-261 (311)
5 KOG1342 Histone deacetylase co 100.0 1.6E-59 3.5E-64 434.5 21.5 257 29-293 3-273 (425)
6 KOG1344 Predicted histone deac 100.0 2.5E-50 5.4E-55 352.9 11.4 268 21-293 2-269 (324)
7 KOG1343 Histone deacetylase co 100.0 2E-41 4.4E-46 344.6 13.1 222 52-292 463-708 (797)
8 KOG1343 Histone deacetylase co 100.0 2.6E-33 5.6E-38 285.4 6.7 257 32-293 28-307 (797)
9 KOG0121 Nuclear cap-binding pr 75.4 2.1 4.6E-05 35.4 2.1 46 163-208 72-122 (153)
10 PRK13236 nitrogenase reductase 66.3 6.5 0.00014 36.5 3.6 34 177-212 22-55 (296)
11 TIGR01969 minD_arch cell divis 64.8 8.3 0.00018 34.1 3.8 22 182-204 22-43 (251)
12 COG0683 LivK ABC-type branched 56.0 46 0.00099 31.6 7.5 36 177-212 135-170 (366)
13 PRK10818 cell division inhibit 52.4 19 0.0004 32.5 4.0 21 186-207 28-48 (270)
14 PHA02518 ParA-like protein; Pr 52.3 21 0.00046 30.5 4.1 23 184-208 24-46 (211)
15 TIGR01287 nifH nitrogenase iro 51.8 20 0.00043 32.6 4.0 22 184-207 23-44 (275)
16 CHL00175 minD septum-site dete 50.4 21 0.00045 32.5 4.0 22 185-207 40-61 (281)
17 PRK13232 nifH nitrogenase redu 50.0 17 0.00036 33.1 3.2 24 185-210 25-48 (273)
18 cd02036 MinD Bacterial cell di 46.8 28 0.00061 28.7 4.0 17 191-207 29-45 (179)
19 cd03111 CpaE_like This protein 45.0 49 0.0011 25.5 4.8 21 191-221 30-50 (106)
20 cd06355 PBP1_FmdD_like Peripla 44.1 64 0.0014 30.1 6.3 35 177-211 120-154 (348)
21 PRK13230 nitrogenase reductase 43.7 26 0.00056 31.9 3.5 25 183-209 23-47 (279)
22 PF09754 PAC2: PAC2 family; I 43.0 23 0.00049 31.0 2.9 26 177-202 12-37 (219)
23 cd02040 NifH NifH gene encodes 42.9 37 0.00081 30.3 4.4 20 187-208 27-46 (270)
24 cd03110 Fer4_NifH_child This p 42.3 17 0.00037 30.5 2.0 16 191-206 25-40 (179)
25 PF11202 PRTase_1: Phosphoribo 40.7 90 0.002 28.7 6.3 14 268-292 178-191 (257)
26 PRK13185 chlL protochlorophyll 39.2 38 0.00082 30.6 3.8 21 187-209 28-48 (270)
27 PRK13234 nifH nitrogenase redu 38.4 36 0.00078 31.6 3.6 24 185-210 28-51 (295)
28 cd02117 NifH_like This family 38.2 37 0.0008 29.5 3.5 19 191-210 29-47 (212)
29 TIGR01968 minD_bact septum sit 38.0 41 0.00089 29.7 3.8 15 191-205 31-45 (261)
30 TIGR02016 BchX chlorophyllide 37.2 41 0.00088 31.3 3.8 19 185-204 24-42 (296)
31 PF02701 zf-Dof: Dof domain, z 37.2 11 0.00024 27.0 0.0 10 169-178 16-25 (63)
32 TIGR01281 DPOR_bchL light-inde 36.7 40 0.00086 30.4 3.6 20 187-208 26-45 (268)
33 PRK13235 nifH nitrogenase redu 34.3 40 0.00086 30.6 3.2 22 182-204 22-43 (274)
34 PRK10037 cell division protein 34.2 43 0.00093 30.0 3.3 21 184-206 25-45 (250)
35 TIGR03371 cellulose_yhjQ cellu 33.4 50 0.0011 29.0 3.6 18 185-204 26-43 (246)
36 cd06334 PBP1_ABC_ligand_bindin 33.1 1.5E+02 0.0033 27.8 7.0 34 178-211 124-161 (351)
37 PF02310 B12-binding: B12 bind 32.7 2.3E+02 0.0049 21.7 7.9 44 177-222 17-60 (121)
38 PF13050 DUF3911: Protein of u 32.1 18 0.0004 26.2 0.4 9 169-177 26-34 (77)
39 PRK13233 nifH nitrogenase redu 31.9 54 0.0012 29.7 3.6 14 191-204 32-45 (275)
40 TIGR01007 eps_fam capsular exo 30.1 65 0.0014 27.6 3.7 13 191-203 47-59 (204)
41 PF12023 DUF3511: Domain of un 30.0 34 0.00073 23.1 1.4 19 9-27 2-20 (47)
42 TIGR03029 EpsG chain length de 29.5 66 0.0014 29.0 3.8 17 187-204 130-146 (274)
43 PRK15404 leucine ABC transport 29.4 1.8E+02 0.004 27.4 7.0 33 179-211 150-182 (369)
44 cd02037 MRP-like MRP (Multiple 29.0 63 0.0014 26.9 3.3 13 191-203 29-41 (169)
45 PF00220 Hormone_4: Neurohypop 28.8 8.6 0.00019 17.1 -1.1 7 172-178 1-7 (9)
46 TIGR03669 urea_ABC_arch urea A 28.3 1.6E+02 0.0035 28.0 6.4 34 177-211 121-154 (374)
47 PF00977 His_biosynth: Histidi 28.0 73 0.0016 28.4 3.7 50 150-206 10-60 (229)
48 TIGR03453 partition_RepA plasm 27.2 76 0.0017 30.5 3.9 19 187-207 131-149 (387)
49 KOG0279 G protein beta subunit 26.7 33 0.00073 32.1 1.2 76 198-284 90-172 (315)
50 PF13458 Peripla_BP_6: Peripla 26.5 1.3E+02 0.0029 27.3 5.3 37 175-211 120-156 (343)
51 TIGR03815 CpaE_hom_Actino heli 26.2 77 0.0017 29.5 3.7 14 191-204 123-136 (322)
52 cd02033 BchX Chlorophyllide re 25.7 72 0.0016 30.4 3.4 20 191-211 60-79 (329)
53 TIGR03018 pepcterm_TyrKin exop 25.5 89 0.0019 27.1 3.7 24 254-281 134-157 (207)
54 CHL00072 chlL photochlorophyll 25.4 75 0.0016 29.4 3.4 23 183-207 22-44 (290)
55 COG1891 Uncharacterized protei 24.8 1.5E+02 0.0032 26.2 4.7 34 248-286 93-127 (235)
56 TIGR03407 urea_ABC_UrtA urea A 24.5 1.6E+02 0.0034 27.6 5.5 35 177-211 121-155 (359)
57 cd02032 Bchl_like This family 24.3 80 0.0017 28.4 3.3 20 186-207 25-44 (267)
58 PF02585 PIG-L: GlcNAc-PI de-N 23.8 1.3E+02 0.0028 23.7 4.1 29 252-284 84-112 (128)
59 PRK11670 antiporter inner memb 22.9 97 0.0021 29.9 3.7 24 185-210 132-155 (369)
60 KOG1530 Rhodanese-related sulf 22.7 1.7E+02 0.0037 24.3 4.6 74 190-280 19-97 (136)
61 COG4671 Predicted glycosyl tra 22.7 2.9E+02 0.0062 27.0 6.7 29 247-279 85-113 (400)
62 TIGR00734 hisAF_rel hisA/hisF 22.2 1.4E+02 0.003 26.6 4.4 36 171-207 32-67 (221)
63 cd04864 LigD_Pol_like_1 LigD_P 22.2 3E+02 0.0066 24.9 6.5 48 225-278 134-181 (228)
64 cd04723 HisA_HisF Phosphoribos 22.1 1.2E+02 0.0026 27.1 4.0 37 168-205 28-64 (233)
65 PF06564 YhjQ: YhjQ protein; 21.2 1E+02 0.0022 28.1 3.3 23 177-200 18-40 (243)
66 COG0489 Mrp ATPases involved i 21.2 1.2E+02 0.0025 27.9 3.7 14 191-204 87-100 (265)
67 PRK13869 plasmid-partitioning 21.1 1.1E+02 0.0024 29.8 3.8 44 59-104 24-70 (405)
68 PRK13231 nitrogenase reductase 20.9 67 0.0015 28.8 2.1 20 185-207 26-45 (264)
69 cd06343 PBP1_ABC_ligand_bindin 20.9 3E+02 0.0065 25.4 6.6 34 178-211 132-165 (362)
70 cd06388 PBP1_iGluR_AMPA_GluR4 20.9 2.8E+02 0.0061 26.4 6.5 43 169-212 101-145 (371)
71 PF01656 CbiA: CobQ/CobB/MinD/ 20.8 1.1E+02 0.0025 25.4 3.4 12 191-202 28-39 (195)
72 PRK13849 putative crown gall t 20.7 1.1E+02 0.0023 27.4 3.3 17 191-208 31-47 (231)
73 cd06331 PBP1_AmiC_like Type I 20.6 3.1E+02 0.0066 25.1 6.5 33 179-212 122-154 (333)
74 cd02514 GT13_GLCNAC-TI GT13_GL 20.6 6.9E+02 0.015 23.9 8.9 45 180-224 88-139 (334)
75 cd06366 PBP1_GABAb_receptor Li 20.5 4.6E+02 0.0099 24.0 7.7 29 184-212 129-157 (350)
76 cd06345 PBP1_ABC_ligand_bindin 20.4 2.8E+02 0.0061 25.4 6.3 25 187-211 141-165 (344)
No 1
>COG0123 AcuC Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]
Probab=100.00 E-value=4.2e-71 Score=520.81 Aligned_cols=249 Identities=27% Similarity=0.392 Sum_probs=228.5
Q ss_pred CceEEEECcccCcccCCCCCCCCCCchHHHHHHHHHHHCCCCCCceeecCCCCCHHHHhccCCHHHHHHHhcCCCccccc
Q 022668 33 FKLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIII 112 (294)
Q Consensus 33 ~~~~iiy~~~~~~h~~~~~~~Hpe~p~R~~~i~~~L~~~gl~~~~~~~~p~~a~~e~L~~vHs~~Yi~~l~~~~~~~~~~ 112 (294)
+.+.++|++.+..|.. +..|||+|.|++.+.++|++.++...+++++|++++.++|++||+++||+.|++.+...+
T Consensus 2 ~~~~~~~~~~~~~~~~--~~~Hpe~p~R~~~~~~~l~~~~~~~~~~~~~p~~~~~~~l~~vH~~~yv~~l~~~~~~~~-- 77 (340)
T COG0123 2 MKTALIYHPEFLEHEP--PPGHPENPDRLRLILELLESSGLPDSLELVEPRPATLEELLLVHSPDYVEFLESLSEEEG-- 77 (340)
T ss_pred CcceEeeCHHHhcCCC--CCCCCCChHHHHHHHHHHHhcCccccccccCCCcCCHHHHHhhCCHHHHHHHHHhccccc--
Confidence 5788999999998875 479999999999999999999988888999999999999999999999999999887521
Q ss_pred cCCCccccCCcccCcccHHHHHHHHhHHHHHHHHHHhc--CcEEecCCCCCCCCCCCCCCccccCcHHHHHHHHHHhCCC
Q 022668 113 EVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLAKER--GWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNI 190 (294)
Q Consensus 113 e~~~~~~~~d~~~~~~~~~~a~~aag~~~~aa~~~~~~--~~a~~~~~GgHHA~~~~~~GFC~fNnvAiAa~~~~~~~~~ 190 (294)
...++.||++++++++++++++|++++|++.+++. ..+++..||||||.+++++|||+|||+||||++|+++ +.
T Consensus 78 ---~~~~d~d~~~s~~~~~~a~~a~G~al~A~~~v~~g~~~~~~~~rppgHHA~~~~a~GFC~fNn~Aiaa~~l~~~-~~ 153 (340)
T COG0123 78 ---YGNLDGDTPVSPGTYEAARLAAGGALTAVDAVLEGEDNAFALVRPPGHHAGRDRASGFCLFNNVAIAAKYLLKK-GV 153 (340)
T ss_pred ---cccccCCCccChHHHHHHHHHhhHHHHHHHHHHcCccceEEECCCCcccccCCCCceeeeecHHHHHHHHHHHc-CC
Confidence 24678999999999999999999999999999875 4555555566999999999999999999999999998 89
Q ss_pred CeEEEEecCCcCChhhhhhhhcCCCEEEEeecCC--CCCCCCCcC------CCceeEeeeCCCCCChHHHHHHHHHHHHH
Q 022668 191 SRVMIIDLDAHQGNGHEKDFSSDSRVYILDMFNP--GIYPRDYEA------RRFIDQKVEVVSGTTTNEYLKKLDEALEV 262 (294)
Q Consensus 191 ~RV~IiD~DvHhGnGtq~if~~d~~Vl~iSiH~~--~~yP~~g~~------~~~~nvNvpl~~g~~d~~yl~~~~~~l~~ 262 (294)
+||+|||||+|||||||+|||+|++|+|+|+|+. .+||+++.. ++++++|||||+|++|++|+.+|++++.+
T Consensus 154 ~RVaIiD~DvHHGnGTqeify~~~~V~~~S~H~~~~~~yPgtg~~~e~g~g~~g~~vNiPLp~g~~d~~y~~a~~~~v~~ 233 (340)
T COG0123 154 KRVAIIDFDVHHGNGTQEIFYDDDDVLTVSLHQDGRPFYPGTGGADEIGEGKEGNNVNIPLPPGTGDDSYLEALEEIVLP 233 (340)
T ss_pred CcEEEEEecCCCChhhHHHHccCCCeEEEeccCCCCCCCCcCCCccccccCcccceEeeecCCCCCcHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999995 799999862 24699999999999999999999999999
Q ss_pred HHhccCCCCCccEEEEeecCCCCCCCCCCCC
Q 022668 263 YMFKTFSVHVFHLLFFPKSFHHYWKEDCGCL 293 (294)
Q Consensus 263 ~~~~~f~P~~~~liv~~~G~D~~~~Dp~G~~ 293 (294)
++++ |+| |+||||||||+|.+||+|+|
T Consensus 234 ~~~~-f~P---dlvivsaG~D~h~~Dpl~~~ 260 (340)
T COG0123 234 LLEE-FKP---DLVIVSAGFDAHRGDPLGRL 260 (340)
T ss_pred HHHh-cCC---CEEEEecCcccCCCCcccee
Confidence 9998 999 99999999999999999987
No 2
>PTZ00063 histone deacetylase; Provisional
Probab=100.00 E-value=1.1e-70 Score=529.10 Aligned_cols=254 Identities=20% Similarity=0.338 Sum_probs=229.8
Q ss_pred CCceEEEECcccCcccCCCCCCCCCCchHHHHHHHHHHHCCCCCCceeecCCCCCHHHHhccCCHHHHHHHhcCCCcccc
Q 022668 32 IFKLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSII 111 (294)
Q Consensus 32 ~~~~~iiy~~~~~~h~~~~~~~Hpe~p~R~~~i~~~L~~~gl~~~~~~~~p~~a~~e~L~~vHs~~Yi~~l~~~~~~~~~ 111 (294)
..+++++|||+|..|.++ .+|||+|.|++.+.++|.++|+...+++++|++|+.++|.+||+++||++|++..+....
T Consensus 3 ~~~v~~~yd~~~~~h~~g--~~HP~~P~Rl~~~~~ll~~~gl~~~~~~~~p~~At~eeL~~vHs~~YI~~L~~~~~~~~~ 80 (436)
T PTZ00063 3 RKRVSYFYDPDIGSYYYG--PGHPMKPQRIRMAHALILSYDLYKHMEIYRPHKSVEPELVLFHDEEYVDFLSSISPENYR 80 (436)
T ss_pred CceEEEEECccccCcCCc--CcCCcChHHHHHHHHHHHhCCCcccCeEecCCCCCHHHHHHhCCHHHHHHHHHhChhhcc
Confidence 467999999999999754 689999999999999999999999999999999999999999999999999987654211
Q ss_pred ---ccCCCcccc--CCcccCcccHHHHHHHHhHHHHHHHHHHhc--CcEEecCCCCCCCCCCCCCCccccCcHHHHHHHH
Q 022668 112 ---IEVPPVALF--PNCLVQRKVLYPFRKQVGGTILAAKLAKER--GWAINVGGGFHHCSADEGGGFCAYADISLCIHYA 184 (294)
Q Consensus 112 ---~e~~~~~~~--~d~~~~~~~~~~a~~aag~~~~aa~~~~~~--~~a~~~~~GgHHA~~~~~~GFC~fNnvAiAa~~~ 184 (294)
.......++ +||++++++++.+++++||++.||+.++++ ++|++|+||+|||.+++++|||+||||||||++|
T Consensus 81 ~~~~~~~~f~lg~~~D~pv~~gl~~~a~~aaGgsl~Aa~~l~~g~~~iAin~~GG~HHA~~~~A~GFC~~NdiaiAi~~L 160 (436)
T PTZ00063 81 DFTYQLKRFNVGEATDCPVFDGLFEFQQSCAGASIDGAYKLNNHQADICVNWSGGLHHAKRSEASGFCYINDIVLGILEL 160 (436)
T ss_pred cchhhhhhcccCCCCCCCcccHHHHHHHHHHhHHHHHHHHHHcCCCCEEeeCCCCCCCCccCCCCceeeecHHHHHHHHH
Confidence 011111233 599999999999999999999999998753 5899999999999999999999999999999999
Q ss_pred HHhCCCCeEEEEecCCcCChhhhhhhhcCCCEEEEeecCCC-CCCCCCc-------CCCceeEeeeCCCCCChHHHHHHH
Q 022668 185 FVQLNISRVMIIDLDAHQGNGHEKDFSSDSRVYILDMFNPG-IYPRDYE-------ARRFIDQKVEVVSGTTTNEYLKKL 256 (294)
Q Consensus 185 ~~~~~~~RV~IiD~DvHhGnGtq~if~~d~~Vl~iSiH~~~-~yP~~g~-------~~~~~nvNvpl~~g~~d~~yl~~~ 256 (294)
++.+ +||+|||||||||||||+|||.|++|+|+|+|+.+ |||+||. .|+++++||||++|++|++|+.+|
T Consensus 161 ~~~~--~RVliID~DvHHGdGtqe~F~~~~~VltvS~H~~~~ffPgtG~~~e~G~g~G~g~~vNvPL~~G~~D~~Y~~~f 238 (436)
T PTZ00063 161 LKYH--ARVMYIDIDVHHGDGVEEAFYVTHRVMTVSFHKFGDFFPGTGDVTDIGVAQGKYYSVNVPLNDGIDDDSFVDLF 238 (436)
T ss_pred HHhC--CeEEEEeCCCCCCcchHHHhccCCCeEEEEeccCCCcCCCCCCccccCCCCCCceEEEeeCCCCCCHHHHHHHH
Confidence 9874 79999999999999999999999999999999975 9999974 356789999999999999999999
Q ss_pred HHHHHHHHhccCCCCCccEEEEeecCCCCCCCCCCCC
Q 022668 257 DEALEVYMFKTFSVHVFHLLFFPKSFHHYWKEDCGCL 293 (294)
Q Consensus 257 ~~~l~~~~~~~f~P~~~~liv~~~G~D~~~~Dp~G~~ 293 (294)
+++|.+++++ |+| |+||+|||||++.+||+|+|
T Consensus 239 ~~ii~~~i~~-f~P---d~IvvqaG~D~~~~DpLg~l 271 (436)
T PTZ00063 239 KPVISKCVEV-YRP---GAIVLQCGADSLTGDRLGRF 271 (436)
T ss_pred HHHHHHHHHH-hCC---CEEEEECCccccCCCCCCCc
Confidence 9999999998 999 99999999999999999987
No 3
>PTZ00346 histone deacetylase; Provisional
Probab=100.00 E-value=1.9e-70 Score=524.59 Aligned_cols=254 Identities=24% Similarity=0.359 Sum_probs=224.5
Q ss_pred CCceEEE----ECcccCcccCCCCCCCCCCchHHHHHHHHHHHCCCCCCceeecCCCCCHHHHhccCCHHHHHHHhcCCC
Q 022668 32 IFKLPLI----YSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPN 107 (294)
Q Consensus 32 ~~~~~ii----y~~~~~~h~~~~~~~Hpe~p~R~~~i~~~L~~~gl~~~~~~~~p~~a~~e~L~~vHs~~Yi~~l~~~~~ 107 (294)
..++.+| |.+++..+. ++.+|||+|+|++.++++|++.|+.+.++++.|++|+.++|++||+++||++|++...
T Consensus 19 ~~~~~~~~~~~y~~~~~~~~--~~~~HPe~P~Rl~~~~~ll~~~gl~~~~~~~~p~~At~eeL~~vHs~~YI~~l~~~~~ 96 (429)
T PTZ00346 19 RGRVALIDTSGYASDMNISA--FVPQHAMKPYRVLAAMEIVRSLKIDAHCRTVVPPLVKVEELMAYHTDTYLANLGLHSC 96 (429)
T ss_pred cceeEEEecCcccccccccc--CCCcCCCCHHHHHHHHHHHHhcCCcccCeeecCCCCCHHHHHHhCCHHHHHHHHHhcc
Confidence 4567899 555555554 4578999999999999999999999889999999999999999999999999987422
Q ss_pred ccc--cccCCCccccCCcccCcccHHHHHHHHhHHHHHHHHHHhc--CcEEecCCCCCCCCCCCCCCccccCcHHHHHHH
Q 022668 108 VSI--IIEVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLAKER--GWAINVGGGFHHCSADEGGGFCAYADISLCIHY 183 (294)
Q Consensus 108 ~~~--~~e~~~~~~~~d~~~~~~~~~~a~~aag~~~~aa~~~~~~--~~a~~~~~GgHHA~~~~~~GFC~fNnvAiAa~~ 183 (294)
... ..+.....+++||++++++++++++++||++.|++.++++ ++|++++||+|||.+++++|||+|||+||||++
T Consensus 97 ~~~~~~~~~~~~~~d~Dtpv~~~~~~~a~laaGgsl~Aa~~v~~g~~~~Ai~~pGG~HHA~~~~a~GFC~fNdvAIAa~~ 176 (429)
T PTZ00346 97 RSWLWNAETSKVFFSGDCPPVEGLMEHSIATASGTLMGAVLLNSGQVDVAVHWGGGMHHSKCGECSGFCYVNDIVLGILE 176 (429)
T ss_pred cccccccccccccccCCCCCChHHHHHHHHHHHHHHHHHHHHHcCCCCEEEeCCCCcCcCCCCCCCcchHHhHHHHHHHH
Confidence 110 0111223467899999999999999999999999999854 489999998899999999999999999999999
Q ss_pred HHHhCCCCeEEEEecCCcCChhhhhhhhcCCCEEEEeecCCC--CCCCCCc-------CCCceeEeeeCCCCCChHHHHH
Q 022668 184 AFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRVYILDMFNPG--IYPRDYE-------ARRFIDQKVEVVSGTTTNEYLK 254 (294)
Q Consensus 184 ~~~~~~~~RV~IiD~DvHhGnGtq~if~~d~~Vl~iSiH~~~--~yP~~g~-------~~~~~nvNvpl~~g~~d~~yl~ 254 (294)
|++++ +||+|||||||||||||+|||+|++|||+|+|+.+ |||++|. .|.++++|||||+|++|++|+.
T Consensus 177 ll~~~--~RVliID~DVHHGnGTqeiF~~dp~Vl~vSiHq~~~~fyPgtG~~~e~G~g~G~g~~vNVPL~~G~~D~~Yl~ 254 (429)
T PTZ00346 177 LLKCH--DRVLYVDIDMHHGDGVDEAFCTSDRVFTLSLHKFGESFFPGTGHPRDVGYGRGRYYSMNLAVWDGITDFYYLG 254 (429)
T ss_pred HHHcC--CeEEEEeCCCCCCchHHHHHcCCCCeEEEEecCCCCCCCCCCCCccccCCCCCceeEEeeeCCCCcCHHHHHH
Confidence 99874 79999999999999999999999999999999975 9999975 2456899999999999999999
Q ss_pred HHHHHHHHHHhccCCCCCccEEEEeecCCCCCCCCCCCC
Q 022668 255 KLDEALEVYMFKTFSVHVFHLLFFPKSFHHYWKEDCGCL 293 (294)
Q Consensus 255 ~~~~~l~~~~~~~f~P~~~~liv~~~G~D~~~~Dp~G~~ 293 (294)
+|++++.+++++ |+| |+||+|||||++.+||+|.|
T Consensus 255 ~f~~ii~p~l~~-F~P---dlIvvsaG~Da~~~DpLg~l 289 (429)
T PTZ00346 255 LFEHALHSIVRR-YSP---DAIVLQCGADSLAGDRLGLL 289 (429)
T ss_pred HHHHHHHHHHHh-cCC---CEEEEECCccCCCCCCCCCc
Confidence 999999999998 999 99999999999999999986
No 4
>PF00850 Hist_deacetyl: Histone deacetylase domain; InterPro: IPR023801 Regulation of transcription is, in part, modulated by reversible histone acetylation on several lysine. Histone deacetylases (HDA) catalyse the removal of the acetyl group. Histone deacetylases, acetoin utilization proteins and acetylpolyamine amidohydrolases are all members of this ancient protein superfamily []. HDAs function in multi-subunit complexes, reversing the acetylation of histones by histone acetyltransferases [, ], and are also believed to deacetylate general transcription factors such as TFIIF and sequence-specific transcription factors such as p53 []. Thus, HDAs contribute to the regulation of transcription, in particular transcriptional repression []. At N-terminal tails of histones, removal of the acetyl group from the epsilon-amino group of a lysine side chain will restore its positivecharge, which may stabilise the histone-DNA interaction and prevent activating transcription factors binding to promoter elements []. HDAs play important roles in the cell cycle and differentiation, and their deregulation can contribute to the development of cancer [, ]. This entry represents the structural domain found in histone deacetylases. It consists of a 3-layer(alpha-beta-alpha) sandwich.; PDB: 4A69_A 2VQV_A 2VQO_A 2VQJ_A 2VQQ_B 2VQM_A 2VQW_G 3MAX_C 3MEN_D 1T64_B ....
Probab=100.00 E-value=1.1e-68 Score=501.30 Aligned_cols=240 Identities=26% Similarity=0.408 Sum_probs=191.3
Q ss_pred CcccCcccCCCCCCCCCCchHHHHHHHHHHHC-CCCCCceeecCCCCCHHHHhccCCHHHHHHHhcCCCcccccc-CCCc
Q 022668 40 SPDYDISFLGIEKLHPFDSSKWGRICQFLSSE-GFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVSIIIE-VPPV 117 (294)
Q Consensus 40 ~~~~~~h~~~~~~~Hpe~p~R~~~i~~~L~~~-gl~~~~~~~~p~~a~~e~L~~vHs~~Yi~~l~~~~~~~~~~e-~~~~ 117 (294)
||.|. +. ++..|||+|+|++.|.+.|++. ++++. ++|+.++|++|||++||+.|++.+......+ ....
T Consensus 1 ~~~~~-~~--~~~~Hpe~p~R~~~i~~~L~~~~~l~~~------~~a~~~~L~~vH~~~Yv~~l~~~~~~~~~~~~~~~~ 71 (311)
T PF00850_consen 1 HPQYQ-HQ--LGDGHPESPERLESIVEALKESYGLLPR------RPATDEELLRVHDPEYVDFLESASKEAKEEEEAGSP 71 (311)
T ss_dssp ----T-T---CCTTSSSCTHHHHHHHHHHHHTTTGGGG----------HHHHTTTS-HHHHHHHHHHHHHTSGCTHHHHH
T ss_pred CCccc-CC--CCCCcCCCHHHHHHHHHHHHHhcCCCCC------CCCCHHHHHHcCCHHHHHHHHHhccccccccccccc
Confidence 46666 33 5689999999999999999996 77643 8999999999999999999998664432111 0000
Q ss_pred ---c-c-cCCcccCcccHHHHHHHHhHHHHHHHHHHh----cCcEEecCCCCCCCCCCCCCCccccCcHHHHHHHHHHhC
Q 022668 118 ---A-L-FPNCLVQRKVLYPFRKQVGGTILAAKLAKE----RGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQL 188 (294)
Q Consensus 118 ---~-~-~~d~~~~~~~~~~a~~aag~~~~aa~~~~~----~~~a~~~~~GgHHA~~~~~~GFC~fNnvAiAa~~~~~~~ 188 (294)
. . +.||++++++++++++++|+++.|++.+++ +++|+++||| |||.+++++|||+||||||||++|++++
T Consensus 72 ~~~~~~~~~dt~~~~~~~~~a~~a~g~~l~a~~~v~~g~~~~~~a~~rppg-HHA~~~~a~GFC~~Nnvaiaa~~l~~~~ 150 (311)
T PF00850_consen 72 EFPNILDDGDTPISPGSWEAARLAAGGTLEAADAVLSGEIKNAFALVRPPG-HHAERDRAMGFCYFNNVAIAAKYLRKKY 150 (311)
T ss_dssp HHCCBTSSSSSEBCTTHHHHHHHHHHHHHHHHHHHHTTSSSEEEEEESS---TT-BTTBBBTTBSS-HHHHHHHHHHHTT
T ss_pred ccccccCCCCcceehHHHHHHHHHHHHHHHHHHhhhcccccceeeecCccc-cccCcCcCcceeeeccHHHHHHHHhhcc
Confidence 0 1 679999999999999999999999999994 4689996655 9999999999999999999999999988
Q ss_pred CCCeEEEEecCCcCChhhhhhhhcCCCEEEEeecC--CCCCC-CCCcC-------CCceeEeeeCCCCCChHHHHHHHHH
Q 022668 189 NISRVMIIDLDAHQGNGHEKDFSSDSRVYILDMFN--PGIYP-RDYEA-------RRFIDQKVEVVSGTTTNEYLKKLDE 258 (294)
Q Consensus 189 ~~~RV~IiD~DvHhGnGtq~if~~d~~Vl~iSiH~--~~~yP-~~g~~-------~~~~nvNvpl~~g~~d~~yl~~~~~ 258 (294)
|++||+|||||+|||||||+|||+|++|+|+|+|+ .++|| ++|.. +.++|+|||||+|++|++|+.+|++
T Consensus 151 ~~~rV~iiD~DvHhGnGtq~if~~d~~V~~~SiH~~~~~~yP~~tG~~~e~G~~~g~g~~~NipL~~g~~d~~y~~~~~~ 230 (311)
T PF00850_consen 151 GLKRVAIIDFDVHHGNGTQEIFYDDPRVLYISIHQYPGNFYPFGTGFPDEIGEGKGKGYNLNIPLPPGTGDDEYLEAFEE 230 (311)
T ss_dssp TTSSEEEEE-SSS--HHHHHHTTT-SSEEEEEEEE-CTTSTTTSS--TT--ESGGGTTSEEEEEE-TTEBHHHHHHHHHH
T ss_pred ccceEEEEEeCCCCcccchhheeCCCCEEecCccccccccCCCcCCCccccCCCcccceeEecccccccchHHHHHHHhh
Confidence 99999999999999999999999999999999999 68999 77753 4569999999999999999999999
Q ss_pred HHHHHHhccCCCCCccEEEEeecCCCCCCCCCCCC
Q 022668 259 ALEVYMFKTFSVHVFHLLFFPKSFHHYWKEDCGCL 293 (294)
Q Consensus 259 ~l~~~~~~~f~P~~~~liv~~~G~D~~~~Dp~G~~ 293 (294)
++.+++++ |+| |+||+|+|||++++||+|.|
T Consensus 231 ~l~~~~~~-f~P---~~ivvsaG~D~~~~Dplg~~ 261 (311)
T PF00850_consen 231 ILLPALEE-FRP---DLIVVSAGFDAHAGDPLGGL 261 (311)
T ss_dssp HHHHHHHH-HT----SEEEEEE-STTBTTSTT-SE
T ss_pred ccccchhc-ccC---cEEEEccCcccchhccccCc
Confidence 99999998 999 99999999999999999975
No 5
>KOG1342 consensus Histone deacetylase complex, catalytic component RPD3 [Chromatin structure and dynamics]
Probab=100.00 E-value=1.6e-59 Score=434.51 Aligned_cols=257 Identities=23% Similarity=0.373 Sum_probs=234.3
Q ss_pred CCCCCceEEEECcccCcccCCCCCCCCCCchHHHHHHHHHHHCCCCCCceeecCCCCCHHHHhccCCHHHHHHHhcCCCc
Q 022668 29 DIPIFKLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNV 108 (294)
Q Consensus 29 ~~p~~~~~iiy~~~~~~h~~~~~~~Hpe~p~R~~~i~~~L~~~gl~~~~~~~~p~~a~~e~L~~vHs~~Yi~~l~~~~~~ 108 (294)
+....++.+.|+++..... ++.+||+.|.|++.+++++..+||...+++.+|..|+.+|+.++||+|||++|++..+.
T Consensus 3 ~~~k~~V~y~yd~~vg~~~--Yg~~hpmkP~R~~mth~Lv~~YgL~k~M~i~~p~~a~~~dm~~FHt~eYi~fL~~V~p~ 80 (425)
T KOG1342|consen 3 SLIKRRVSYFYDPDVGNFH--YGQGHPMKPHRIRMTHSLVLNYGLYKKMEIYRPDKASAQDMTRFHTDEYINFLQSVTPE 80 (425)
T ss_pred CcCCceEEEEecCcccccc--ccCCCCCCcceehhhhHHHHhcchhhceeeccCCCCCHHHHHhhchHHHHHHHhhCCcc
Confidence 4457789999999986554 46899999999999999999999999999999999999999999999999999998875
Q ss_pred ccc---ccCCCccccCCcccCcccHHHHHHHHhHHHHHHHHHHh--cCcEEecCCCCCCCCCCCCCCccccCcHHHHHHH
Q 022668 109 SII---IEVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLAKE--RGWAINVGGGFHHCSADEGGGFCAYADISLCIHY 183 (294)
Q Consensus 109 ~~~---~e~~~~~~~~d~~~~~~~~~~a~~aag~~~~aa~~~~~--~~~a~~~~~GgHHA~~~~~~GFC~fNnvAiAa~~ 183 (294)
... .+.....+..||++..++++.+++.+||++.||+.+-. ..+|+||.||.|||.++.++|||++||+++++..
T Consensus 81 n~~~~~~~~~~fNvg~DCPvF~gL~~fC~~~~GgSl~aa~kLn~~~~dIaINW~GGlHHAKK~eASGFCYvNDIVL~ILe 160 (425)
T KOG1342|consen 81 NMETFNKELKQFNVGEDCPVFDGLYDYCQLYTGGSLNAAQKLNRGECDIAINWAGGLHHAKKSEASGFCYVNDIVLGILE 160 (425)
T ss_pred cccccchHHHhcCCCCCCccccCHHHHHHHhcccchHHHHHhCCCCceEEEecCcccccccccccCcceeehHHHHHHHH
Confidence 421 12223567899999999999999999999999988754 3589999999999999999999999999999999
Q ss_pred HHHhCCCCeEEEEecCCcCChhhhhhhhcCCCEEEEeecCC--CCCCCCCc-------CCCceeEeeeCCCCCChHHHHH
Q 022668 184 AFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRVYILDMFNP--GIYPRDYE-------ARRFIDQKVEVVSGTTTNEYLK 254 (294)
Q Consensus 184 ~~~~~~~~RV~IiD~DvHhGnGtq~if~~d~~Vl~iSiH~~--~~yP~~g~-------~~~~~nvNvpl~~g~~d~~yl~ 254 (294)
|++.+ +||++||+|+|||||+|++||..+||+|+|+|.. +|||+||. .|+.|.|||||..|++|+.|..
T Consensus 161 LlK~h--~RVLYIDIDvHHGDGVEeAFy~TDRVmTvSfHKyg~~fFPGTG~l~d~G~~kGkyyavNVPL~dGidD~sy~~ 238 (425)
T KOG1342|consen 161 LLKYH--KRVLYIDIDVHHGDGVEEAFYTTDRVMTVSFHKYGPGFFPGTGDLSDIGAGKGKYYAVNVPLKDGIDDESYES 238 (425)
T ss_pred HHHhC--CceEEEEecccCCccHHHHHhccceeEEEEEEeccCCCCCCCCcceeccCCCCceEEEccchhccCCcHHHHH
Confidence 99985 6999999999999999999999999999999996 49999985 4567899999999999999999
Q ss_pred HHHHHHHHHHhccCCCCCccEEEEeecCCCCCCCCCCCC
Q 022668 255 KLDEALEVYMFKTFSVHVFHLLFFPKSFHHYWKEDCGCL 293 (294)
Q Consensus 255 ~~~~~l~~~~~~~f~P~~~~liv~~~G~D~~~~Dp~G~~ 293 (294)
+|+.++.++++. |+| ++||++||.|+..+|++|||
T Consensus 239 if~pIi~~v~e~-f~P---~AiVLQCGaDSL~gDRlgcF 273 (425)
T KOG1342|consen 239 IFKPIISKVMER-FQP---EAIVLQCGADSLAGDRLGCF 273 (425)
T ss_pred HHHHHHHHHHHH-hCC---ceEEEEcCCccccCCcccee
Confidence 999999999998 999 99999999999999999997
No 6
>KOG1344 consensus Predicted histone deacetylase [Chromatin structure and dynamics]
Probab=100.00 E-value=2.5e-50 Score=352.94 Aligned_cols=268 Identities=54% Similarity=0.919 Sum_probs=254.6
Q ss_pred hhccccccCCCCCceEEEECcccCcccCCCCCCCCCCchHHHHHHHHHHHCCCCCCceeecCCCCCHHHHhccCCHHHHH
Q 022668 21 ILSSKLYFDIPIFKLPLIYSPDYDISFLGIEKLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLK 100 (294)
Q Consensus 21 ~~~~~~~~~~p~~~~~iiy~~~~~~h~~~~~~~Hpe~p~R~~~i~~~L~~~gl~~~~~~~~p~~a~~e~L~~vHs~~Yi~ 100 (294)
+.-++++.+.|..+++|+|++.|...++++++.||++..++..+.+.|.+.++++.-.+++|.++|+|+|++||+.+|++
T Consensus 2 v~~~kly~~vp~~k~pIvyS~~Y~i~FmGlEkLHPFDa~Kwg~v~kfL~~~~~l~d~~lvEp~e~t~e~L~rvHtr~YLk 81 (324)
T KOG1344|consen 2 VVWVKLYDAVPAGKLPIVYSRNYAIRFMGLEKLHPFDAAKWGHVHKFLCAMNLLTDETLVEPNEATKEDLLRVHTRKYLK 81 (324)
T ss_pred ceeeeecccCccccccEEecCccceeecchhhcCcCcccchhHHHHHHHHhccccccccccCcccCHHHHHhHhhHHHHH
Confidence 34567889999999999999999999999999999999999999999999999998889999999999999999999999
Q ss_pred HHhcCCCccccccCCCccccCCcccCcccHHHHHHHHhHHHHHHHHHHhcCcEEecCCCCCCCCCCCCCCccccCcHHHH
Q 022668 101 SLQSSPNVSIIIEVPPVALFPNCLVQRKVLYPFRKQVGGTILAAKLAKERGWAINVGGGFHHCSADEGGGFCAYADISLC 180 (294)
Q Consensus 101 ~l~~~~~~~~~~e~~~~~~~~d~~~~~~~~~~a~~aag~~~~aa~~~~~~~~a~~~~~GgHHA~~~~~~GFC~fNnvAiA 180 (294)
.++..-..+.+.|.+...+.|++++....+.+.++.+||++.|++++++.|+|+|.+||+||+..++++|||.+-|+.+|
T Consensus 82 slr~s~~vA~I~EiP~v~flPn~~iqrk~LrPlR~QagGtilA~kLAle~GWAINvGGGFHHcss~rGGGFC~yADItl~ 161 (324)
T KOG1344|consen 82 SLRWSIKVAQITEIPFVGFLPNCIIQRKLLRPLRLQAGGTILAAKLALERGWAINVGGGFHHCSSSRGGGFCAYADITLA 161 (324)
T ss_pred HhhccceeeEEEeccccccCchhhhhhhhccceeeccCceeehhhhhhhcCeEEeecCccceeccCCCCceeehhhHHHH
Confidence 99988888888999989999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhCCCCeEEEEecCCcCChhhhhhhhcCCCEEEEeecCCCCCCCCCcCCCceeEeeeCCCCCChHHHHHHHHHHH
Q 022668 181 IHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRVYILDMFNPGIYPRDYEARRFIDQKVEVVSGTTTNEYLKKLDEAL 260 (294)
Q Consensus 181 a~~~~~~~~~~RV~IiD~DvHhGnGtq~if~~d~~Vl~iSiH~~~~yP~~g~~~~~~nvNvpl~~g~~d~~yl~~~~~~l 260 (294)
+..+-++..+.|++|||+|+|+|||.+.-|.++ .|.++.++..-+||+...+.+.....|.|..|++|++|++.+++.+
T Consensus 162 I~~lFer~~isr~mivDLDAHQGNghErdf~~~-~vyi~d~ynr~iyp~D~~Ak~~Ir~kVEl~~gTeddeYLrkl~r~l 240 (324)
T KOG1344|consen 162 IFFLFERKAISRAMIVDLDAHQGNGHERDFEDD-AVYIFDMYNRFIYPRDHVAKESIRCKVELRNGTEDDEYLRKLKRCL 240 (324)
T ss_pred HHHHHhhhhhhheEEEecccccCCccccccccc-eeehhhhhhhhccchhHHHHHHhhheeeeecCCCchHHHHHHHHHH
Confidence 999999888999999999999999999999988 8888899888899998777777778899999999999999999999
Q ss_pred HHHHhccCCCCCccEEEEeecCCCCCCCCCCCC
Q 022668 261 EVYMFKTFSVHVFHLLFFPKSFHHYWKEDCGCL 293 (294)
Q Consensus 261 ~~~~~~~f~P~~~~liv~~~G~D~~~~Dp~G~~ 293 (294)
...+++ |+| |+||.-||-|..+|||+|.|
T Consensus 241 ~~sl~e-f~P---d~VvYNAGTDiLeGDpLG~L 269 (324)
T KOG1344|consen 241 MQSLAE-FRP---DMVVYNAGTDILEGDPLGNL 269 (324)
T ss_pred HHHHHh-hCC---cEEEEeCCCccccCCCCCCe
Confidence 999998 999 99999999999999999986
No 7
>KOG1343 consensus Histone deacetylase complex, catalytic component HDA1 [Chromatin structure and dynamics]
Probab=100.00 E-value=2e-41 Score=344.58 Aligned_cols=222 Identities=22% Similarity=0.345 Sum_probs=178.0
Q ss_pred CCCCCCchHHHHHHHHHHHCCCCCCceeecCCCCCHHHHhccCCHHHHHHHhcCCCcc---cc----ccCCCccccCCcc
Q 022668 52 KLHPFDSSKWGRICQFLSSEGFLDKNCIVEPLEASKEDLLVVHSESYLKSLQSSPNVS---II----IEVPPVALFPNCL 124 (294)
Q Consensus 52 ~~Hpe~p~R~~~i~~~L~~~gl~~~~~~~~p~~a~~e~L~~vHs~~Yi~~l~~~~~~~---~~----~e~~~~~~~~d~~ 124 (294)
..||+.|.| ....+. .|++.+|+.+ ||.++|+.||+..|+..+.+..... .. .+...+..++|+
T Consensus 463 ~~~~~~p~r---~~t~~~-~gl~~~c~r~----at~~el~~vHs~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~dt- 533 (797)
T KOG1343|consen 463 SRSPESPAR---FTTGLH-TGLLGKCERI----ATLEELQLVHSEAHVLLYGSRKLLGDLSLKFESRLPCGGIGVDSDT- 533 (797)
T ss_pred cCCcccchh---hhcccc-cccccccccc----cchhhhhhcccchhhcccchhhhcccccchhhhhccccceeecccH-
Confidence 478999999 222232 7888888777 9999999999999999865221111 00 112223344444
Q ss_pred cCcccHHHHHHHHhHHHHHHHHHH------hcCcEEecCCCCCCCCCCCCCCccccCcHHHHHHHHHHhCCCCeEEEEec
Q 022668 125 VQRKVLYPFRKQVGGTILAAKLAK------ERGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDL 198 (294)
Q Consensus 125 ~~~~~~~~a~~aag~~~~aa~~~~------~~~~a~~~~~GgHHA~~~~~~GFC~fNnvAiAa~~~~~~~~~~RV~IiD~ 198 (294)
|.....++|++..++..++ ..|||++|+|| |||.+..++|||+|||+|||+++++..+..+||+|+||
T Consensus 534 -----~~~~~~ssga~~~av~~v~~~~~~~~~g~avvRppG-Hha~~~~a~gfc~fn~vaiaak~l~~~~~~~rilivdw 607 (797)
T KOG1343|consen 534 -----WWNELHSSGAARLAVGCVIELAFKVASGFAVVRPPG-HHAEASTAMGFCFFNSVAIAAKLLQQRSKASRILIVDW 607 (797)
T ss_pred -----HHHHHHHHHHHHHhcchhhhhhhhhhcceeEecCCc-cccccCCcceeeeecchhhhhHHhhhhhhhcceEEEee
Confidence 4444555555555554432 23799999987 99999999999999999999999999888899999999
Q ss_pred CCcCChhhhhhhhcCCCEEEEeecCC---CCCCCCCc-------CCCceeEeeeCCCC-CChHHHHHHHHHHHHHHHhcc
Q 022668 199 DAHQGNGHEKDFSSDSRVYILDMFNP---GIYPRDYE-------ARRFIDQKVEVVSG-TTTNEYLKKLDEALEVYMFKT 267 (294)
Q Consensus 199 DvHhGnGtq~if~~d~~Vl~iSiH~~---~~yP~~g~-------~~~~~nvNvpl~~g-~~d~~yl~~~~~~l~~~~~~~ 267 (294)
|||||||||++||.|++|||+|+|.+ ++||++|. .+.++|+||+++.+ .+|.+|+.++++++.|+.++
T Consensus 608 Dvhhgngtq~~f~~~~~vlyislhr~~~G~~fp~~g~~~e~g~~~g~g~~vNv~~~~~~~~D~ey~~a~~~vv~Pia~~- 686 (797)
T KOG1343|consen 608 DVHHGNGTQQAFYSDPSVLYISLHRHDDGNFFPGSGAPDEVGKGEGVGFNVNVAWTGGLDPDAEYLAAFRTVVMPIAYE- 686 (797)
T ss_pred cccCCcceeeeeccCccccccccchhccCCcCCCCCCchhcccccccceeecccccCCCCCCHHHHHHHHHhhHHHHHH-
Confidence 99999999999999999999999985 58899853 35689999998765 34699999999999999998
Q ss_pred CCCCCccEEEEeecCCCCCCCCCCC
Q 022668 268 FSVHVFHLLFFPKSFHHYWKEDCGC 292 (294)
Q Consensus 268 f~P~~~~liv~~~G~D~~~~Dp~G~ 292 (294)
|.| |+|++|+|||++.+||+|.
T Consensus 687 F~p---d~VlvSagfDaa~~dplg~ 708 (797)
T KOG1343|consen 687 FNP---DLVLVSAGFDAAEGDPLGG 708 (797)
T ss_pred hCC---CeEEEeccccccccCcccc
Confidence 999 9999999999999999995
No 8
>KOG1343 consensus Histone deacetylase complex, catalytic component HDA1 [Chromatin structure and dynamics]
Probab=99.98 E-value=2.6e-33 Score=285.41 Aligned_cols=257 Identities=17% Similarity=0.181 Sum_probs=216.9
Q ss_pred CCceEEEECcccCcccCCCCCCC-CCCchHHHHHHHHHHHCCCCCCceeecC-CCCCHHHHhccCCHHHHHHHhcCCCcc
Q 022668 32 IFKLPLIYSPDYDISFLGIEKLH-PFDSSKWGRICQFLSSEGFLDKNCIVEP-LEASKEDLLVVHSESYLKSLQSSPNVS 109 (294)
Q Consensus 32 ~~~~~iiy~~~~~~h~~~~~~~H-pe~p~R~~~i~~~L~~~gl~~~~~~~~p-~~a~~e~L~~vHs~~Yi~~l~~~~~~~ 109 (294)
..++.++|++.+..|....+..| ++.++|++++.+.+++.++.+.+.+..+ +.+++++++.+|+++|++.+.......
T Consensus 28 ~~~~~l~~~~~~~~h~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~v~~ke~~~~~~~t~~~~ 107 (797)
T KOG1343|consen 28 QIQKQLLFAEFQKQHENQQELLEKEEKLERLRQIEEELERHRLEQPLLILRNKREAKESAVASVHVKEKLQEFLLSKKMT 107 (797)
T ss_pred hhhhhhhhhhhhhhhhcccccccchhhhhHHHHHHHHhhccCCccccccccchhhcccchhcccccHHHHHHHHhhhhhc
Confidence 46789999999999963222334 4999999999999999999888877766 899999999999999999998766322
Q ss_pred ccccCC-CccccCCcccCcccHHHHHHHHhHHHHHHHHHH----hcCcEEecCCCCCCCCCCCCCCccccCcHHHHHHHH
Q 022668 110 IIIEVP-PVALFPNCLVQRKVLYPFRKQVGGTILAAKLAK----ERGWAINVGGGFHHCSADEGGGFCAYADISLCIHYA 184 (294)
Q Consensus 110 ~~~e~~-~~~~~~d~~~~~~~~~~a~~aag~~~~aa~~~~----~~~~a~~~~~GgHHA~~~~~~GFC~fNnvAiAa~~~ 184 (294)
....+. ...-.+..+.++.++..+.++.|+.+...+.++ .++++.++++| ||++++...|||+|||||++++..
T Consensus 108 ~e~~l~~~~~~~~~~~~~~~s~~~a~~a~~~~~~~~~~~~~~~~~n~~a~v~p~~-hhsep~~~~~~cl~n~Va~~~~~~ 186 (797)
T KOG1343|consen 108 AEEGLNHSSSRYPSLYYTSASHSSADQASGSLSGSYKAVLAGKASNGKADFRPPG-HHSEPNLKVGFCLFNNVAERRSSP 186 (797)
T ss_pred chhhhhcccCCCCcceecCCchhhhcccCcccccccccccCCcccCccCcCCCCC-CccccchhcchhHHHHHHHHhhcc
Confidence 111111 122356778888899999999999888666543 45789988887 999999999999999999999999
Q ss_pred HHhCCCCeEEEEecCCcCChhhhhhhhc--CCCEEEEeecCC---CCCCCCC---------cCCCceeEeeeC-CCCCCh
Q 022668 185 FVQLNISRVMIIDLDAHQGNGHEKDFSS--DSRVYILDMFNP---GIYPRDY---------EARRFIDQKVEV-VSGTTT 249 (294)
Q Consensus 185 ~~~~~~~RV~IiD~DvHhGnGtq~if~~--d~~Vl~iSiH~~---~~yP~~g---------~~~~~~nvNvpl-~~g~~d 249 (294)
..++..+||+|+|||+|||+|||..|+. |++|+++|+|+. .|||... +.+.|+++|+|+ +-|++|
T Consensus 187 ~~~~~~rri~i~d~dvh~g~Gtq~~~~~~~d~~vl~~s~~r~e~~~f~P~~~~g~~~~~~~g~~~g~~~nl~~~~~g~~~ 266 (797)
T KOG1343|consen 187 LLRRKKRRILIVDWDVHHGPGTQPSSPNNGDQRVLYFSLHRLETGPFLPNITLGLATLRGGGPGLGQTGNLPWNQVGMTD 266 (797)
T ss_pred ccccccceeEeecccccCCCCCCCccCCCcccccccccchhcccCCcCCCCccchHHHhCcCCCcceeeccchhhcCCcc
Confidence 8887789999999999999999999999 999999999984 6999954 245679999998 668999
Q ss_pred HHHHHHHHHHHHHHHhccCCCCCccEEEEeecCCCCCCCC-CCCC
Q 022668 250 NEYLKKLDEALEVYMFKTFSVHVFHLLFFPKSFHHYWKED-CGCL 293 (294)
Q Consensus 250 ~~yl~~~~~~l~~~~~~~f~P~~~~liv~~~G~D~~~~Dp-~G~~ 293 (294)
.+|..+|..++.+...+ |+| |||++++|||+.-+|| +|.|
T Consensus 267 ~dy~~~~~~~~~~~~~e-fqp---~Lv~~sag~dA~lg~~~~~~m 307 (797)
T KOG1343|consen 267 ADYEAAFLHVLLPHASE-FQP---DLLLVSAGFDALLGDGPVGLM 307 (797)
T ss_pred hhhhhhhhccCccchhh-cCc---ceEEeeccccccccCcccCcc
Confidence 99999999999999998 999 9999999999999997 5766
No 9
>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]
Probab=75.37 E-value=2.1 Score=35.40 Aligned_cols=46 Identities=24% Similarity=0.203 Sum_probs=34.2
Q ss_pred CCCCCCCCcccc-----CcHHHHHHHHHHhCCCCeEEEEecCCcCChhhhh
Q 022668 163 CSADEGGGFCAY-----ADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEK 208 (294)
Q Consensus 163 A~~~~~~GFC~f-----NnvAiAa~~~~~~~~~~RV~IiD~DvHhGnGtq~ 208 (294)
-..-.++|||++ .++-.|++|+-...--+|++-+|||.-.=+|-|.
T Consensus 72 r~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D~GF~eGRQy 122 (153)
T KOG0121|consen 72 RFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWDAGFVEGRQY 122 (153)
T ss_pred cCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeeccccchhhhhh
Confidence 344567999987 4566777777554335799999999988888884
No 10
>PRK13236 nitrogenase reductase; Reviewed
Probab=66.26 E-value=6.5 Score=36.54 Aligned_cols=34 Identities=18% Similarity=0.241 Sum_probs=23.6
Q ss_pred HHHHHHHHHHhCCCCeEEEEecCCcCChhhhhhhhc
Q 022668 177 ISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSS 212 (294)
Q Consensus 177 vAiAa~~~~~~~~~~RV~IiD~DvHhGnGtq~if~~ 212 (294)
+|+-+.+++.+.| +||++||+|.+.+| |.-+|..
T Consensus 22 ~a~NLA~~La~~G-~rVLliD~D~q~~~-~~~l~~~ 55 (296)
T PRK13236 22 TSQNTLAAMAEMG-QRILIVGCDPKADS-TRLMLHS 55 (296)
T ss_pred HHHHHHHHHHHCC-CcEEEEEccCCCCc-cchhccC
Confidence 3444445555555 79999999999888 6555543
No 11
>TIGR01969 minD_arch cell division ATPase MinD, archaeal. This model represents the archaeal branch of the MinD family. MinD, a weak ATPase, works in bacteria with MinC as a generalized cell division inhibitor and, through interaction with MinE, prevents septum placement inappropriate sites. Often several members of this family are found in archaeal genomes, and the function is uncharacterized. More distantly related proteins include flagellar biosynthesis proteins and ParA chromosome partitioning proteins. The exact roles of the various archaeal MinD homologs are unknown.
Probab=64.75 E-value=8.3 Score=34.09 Aligned_cols=22 Identities=27% Similarity=0.445 Sum_probs=16.3
Q ss_pred HHHHHhCCCCeEEEEecCCcCCh
Q 022668 182 HYAFVQLNISRVMIIDLDAHQGN 204 (294)
Q Consensus 182 ~~~~~~~~~~RV~IiD~DvHhGn 204 (294)
-++..+.| +||++||+|..+||
T Consensus 22 A~~la~~g-~~VlliD~D~~~~~ 43 (251)
T TIGR01969 22 GVALAKLG-KKVLALDADITMAN 43 (251)
T ss_pred HHHHHHCC-CeEEEEeCCCCCcc
Confidence 33344445 79999999998887
No 12
>COG0683 LivK ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]
Probab=56.03 E-value=46 Score=31.60 Aligned_cols=36 Identities=25% Similarity=0.296 Sum_probs=30.9
Q ss_pred HHHHHHHHHHhCCCCeEEEEecCCcCChhhhhhhhc
Q 022668 177 ISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSS 212 (294)
Q Consensus 177 vAiAa~~~~~~~~~~RV~IiD~DvHhGnGtq~if~~ 212 (294)
.+.++.++.++.+.+||+||+-|.=.|.|..+.|..
T Consensus 135 ~~~~~~~l~~~~~~k~v~ii~~~~~yg~~~~~~~~~ 170 (366)
T COG0683 135 AAAAADYLVKKGGKKRVAIIGDDYAYGEGLADAFKA 170 (366)
T ss_pred HHHHHHHHHHhcCCcEEEEEeCCCCcchhHHHHHHH
Confidence 455778888887767999999999999999999874
No 13
>PRK10818 cell division inhibitor MinD; Provisional
Probab=52.45 E-value=19 Score=32.55 Aligned_cols=21 Identities=24% Similarity=0.259 Sum_probs=16.1
Q ss_pred HhCCCCeEEEEecCCcCChhhh
Q 022668 186 VQLNISRVMIIDLDAHQGNGHE 207 (294)
Q Consensus 186 ~~~~~~RV~IiD~DvHhGnGtq 207 (294)
.+.| +||++||+|.+.||-+.
T Consensus 28 a~~g-~~vllvD~D~~~~~~~~ 48 (270)
T PRK10818 28 AQKG-KKTVVIDFDIGLRNLDL 48 (270)
T ss_pred HHCC-CeEEEEECCCCCCChhh
Confidence 3445 79999999998887543
No 14
>PHA02518 ParA-like protein; Provisional
Probab=52.34 E-value=21 Score=30.52 Aligned_cols=23 Identities=26% Similarity=0.442 Sum_probs=15.8
Q ss_pred HHHhCCCCeEEEEecCCcCChhhhh
Q 022668 184 AFVQLNISRVMIIDLDAHQGNGHEK 208 (294)
Q Consensus 184 ~~~~~~~~RV~IiD~DvHhGnGtq~ 208 (294)
+..+.| +||++||+|- +++-+..
T Consensus 24 ~la~~g-~~vlliD~D~-q~~~~~~ 46 (211)
T PHA02518 24 WLHADG-HKVLLVDLDP-QGSSTDW 46 (211)
T ss_pred HHHhCC-CeEEEEeCCC-CCChHHH
Confidence 334444 7999999996 5666654
No 15
>TIGR01287 nifH nitrogenase iron protein. This model describes nitrogenase (EC 1.18.6.1) iron protein, also called nitrogenase reductase or nitrogenase component II. This model includes molybdenum-iron nitrogenase reductase (nifH), vanadium-iron nitrogenase reductase (vnfH), and iron-iron nitrogenase reductase (anfH). The model excludes the homologous protein from the light-independent protochlorophyllide reductase.
Probab=51.85 E-value=20 Score=32.56 Aligned_cols=22 Identities=23% Similarity=0.522 Sum_probs=15.2
Q ss_pred HHHhCCCCeEEEEecCCcCChhhh
Q 022668 184 AFVQLNISRVMIIDLDAHQGNGHE 207 (294)
Q Consensus 184 ~~~~~~~~RV~IiD~DvHhGnGtq 207 (294)
++.+.| +||++||+|.. ||.|.
T Consensus 23 ~La~~G-~~VlliD~D~q-~~~~~ 44 (275)
T TIGR01287 23 ALAEMG-KKVMIVGCDPK-ADSTR 44 (275)
T ss_pred HHHHCC-CeEEEEeCCCC-CCccc
Confidence 334445 79999999987 44444
No 16
>CHL00175 minD septum-site determining protein; Validated
Probab=50.37 E-value=21 Score=32.51 Aligned_cols=22 Identities=32% Similarity=0.300 Sum_probs=17.2
Q ss_pred HHhCCCCeEEEEecCCcCChhhh
Q 022668 185 FVQLNISRVMIIDLDAHQGNGHE 207 (294)
Q Consensus 185 ~~~~~~~RV~IiD~DvHhGnGtq 207 (294)
..+.| +||++||.|...||-+.
T Consensus 40 La~~g-~~vlliD~D~~~~~l~~ 61 (281)
T CHL00175 40 IARLG-YRVALIDADIGLRNLDL 61 (281)
T ss_pred HHhCC-CeEEEEeCCCCCCChhh
Confidence 33445 79999999999998664
No 17
>PRK13232 nifH nitrogenase reductase; Reviewed
Probab=50.00 E-value=17 Score=33.11 Aligned_cols=24 Identities=4% Similarity=0.297 Sum_probs=16.7
Q ss_pred HHhCCCCeEEEEecCCcCChhhhhhh
Q 022668 185 FVQLNISRVMIIDLDAHQGNGHEKDF 210 (294)
Q Consensus 185 ~~~~~~~RV~IiD~DvHhGnGtq~if 210 (294)
+.+.| +||++||+|.+..+ |..++
T Consensus 25 La~~G-~rVllvD~Dpq~~~-~~~l~ 48 (273)
T PRK13232 25 LSTMG-NKILLVGCDPKADS-TRMLL 48 (273)
T ss_pred HHhhC-CCeEEEeccccccc-chhhc
Confidence 33445 79999999998665 44443
No 18
>cd02036 MinD Bacterial cell division requires the formation of a septum at mid-cell. The site is determined by the min operon products MinC, MinD and MinE. MinC is a nonspecific inhibitor of the septum protein FtsZ. MinE is the supressor of MinC. MinD plays a pivotal role, selecting the mid-cell over other sites through the activation and regulation of MinC and MinE. MinD is a membrane-associated ATPase, related to nitrogenase iron protein. More distantly related proteins include flagellar biosynthesis proteins and ParA chromosome partitioning proteins. MinD is a monomer.
Probab=46.76 E-value=28 Score=28.73 Aligned_cols=17 Identities=29% Similarity=0.249 Sum_probs=14.7
Q ss_pred CeEEEEecCCcCChhhh
Q 022668 191 SRVMIIDLDAHQGNGHE 207 (294)
Q Consensus 191 ~RV~IiD~DvHhGnGtq 207 (294)
+||++||.|...||-+.
T Consensus 29 ~~vllvD~D~~~~~~~~ 45 (179)
T cd02036 29 YKVVLIDADLGLRNLDL 45 (179)
T ss_pred CeEEEEeCCCCCCCchh
Confidence 79999999999887655
No 19
>cd03111 CpaE_like This protein family consists of proteins similar to the cpaE protein of the Caulobacter pilus assembly and the orf4 protein of Actinobacillus pilus formation gene cluster. The function of these proteins are unkown. The Caulobacter pilus assembly contains 7 genes: pilA, cpaA, cpaB, cpaC, cpaD, cpaE and cpaF. These genes are clustered together on chromosome.
Probab=45.01 E-value=49 Score=25.54 Aligned_cols=21 Identities=33% Similarity=0.732 Sum_probs=17.7
Q ss_pred CeEEEEecCCcCChhhhhhhhcCCCEEEEee
Q 022668 191 SRVMIIDLDAHQGNGHEKDFSSDSRVYILDM 221 (294)
Q Consensus 191 ~RV~IiD~DvHhGnGtq~if~~d~~Vl~iSi 221 (294)
++|+++|.|.++++ ++.+++.
T Consensus 30 ~~~~l~d~d~~~~~----------D~IIiDt 50 (106)
T cd03111 30 RRVLLVDLDLQFGD----------DYVVVDL 50 (106)
T ss_pred CcEEEEECCCCCCC----------CEEEEeC
Confidence 79999999999987 5666665
No 20
>cd06355 PBP1_FmdD_like Periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF). This group includes the periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF), found in Methylophilus methylotrophus, and its homologs from other bacteria. FmdD, a type I periplasmic binding protein, is induced by short-chain amides and urea and repressed by excess ammonia, while FmdE and FmdF are hydrophobic transmembrane proteins. FmdDEF is predicted to be an ATP-dependent transporter and closely resembles the periplasmic binding protein and the two transmembrane proteins present in various hydrophobic amino acid-binding transport systems.
Probab=44.05 E-value=64 Score=30.09 Aligned_cols=35 Identities=11% Similarity=0.083 Sum_probs=27.7
Q ss_pred HHHHHHHHHHhCCCCeEEEEecCCcCChhhhhhhh
Q 022668 177 ISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFS 211 (294)
Q Consensus 177 vAiAa~~~~~~~~~~RV~IiD~DvHhGnGtq~if~ 211 (294)
+..+++|+.++.+.+||++|--|.=.|.+..+.|.
T Consensus 120 ~~~~~~~~~~~~g~k~vaii~~d~~~g~~~~~~~~ 154 (348)
T cd06355 120 IIPAVDWLMSNKGGKRFYLVGSDYVYPRTANKILK 154 (348)
T ss_pred HHHHHHHHHhccCCCeEEEECCcchHHHHHHHHHH
Confidence 35677888887789999999888778888877664
No 21
>PRK13230 nitrogenase reductase-like protein; Reviewed
Probab=43.70 E-value=26 Score=31.94 Aligned_cols=25 Identities=12% Similarity=0.259 Sum_probs=17.3
Q ss_pred HHHHhCCCCeEEEEecCCcCChhhhhh
Q 022668 183 YAFVQLNISRVMIIDLDAHQGNGHEKD 209 (294)
Q Consensus 183 ~~~~~~~~~RV~IiD~DvHhGnGtq~i 209 (294)
+++.+.| +||++||+|.. ||=|+.+
T Consensus 23 ~~La~~G-~rVLliD~Dpq-~n~t~~l 47 (279)
T PRK13230 23 AALAESG-KKVLVVGCDPK-ADCTRNL 47 (279)
T ss_pred HHHHhCC-CEEEEEeeCCc-ccccccc
Confidence 3344445 69999999994 6666654
No 22
>PF09754 PAC2: PAC2 family; InterPro: IPR019151 This PAC2 (Proteasome assembly chaperone) family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 247 and 307 amino acids in length. These proteins function as a chaperone for the 26S proteasome, which is about 2000 kilodaltons (kDa) in molecular mass and contains one 20S core particle structure and two 19S regulatory caps. The 26S proteasome mediates ubiquitin-dependent proteolysis in eukaryotic cells. A number of studies including very recent ones have revealed that assembly of its 20S catalytic core particle is an ordered process that involves several conserved proteasome assembly chaperones (PACs). Two heterodimeric chaperones, PAC1-PAC2 and PAC3-PAC4, promote the assembly of rings composed of seven alpha subunits [, , , ].; PDB: 3MNF_A 2P90_B 3E35_A 3GAA_D 2WAM_C.
Probab=43.05 E-value=23 Score=31.01 Aligned_cols=26 Identities=27% Similarity=0.250 Sum_probs=20.6
Q ss_pred HHHHHHHHHHhCCCCeEEEEecCCcC
Q 022668 177 ISLCIHYAFVQLNISRVMIIDLDAHQ 202 (294)
Q Consensus 177 vAiAa~~~~~~~~~~RV~IiD~DvHh 202 (294)
.-+|+.++.++.+.++|..||-|.+.
T Consensus 12 g~la~d~Li~~l~~~~vg~i~~~~~~ 37 (219)
T PF09754_consen 12 GQLAVDHLIESLNLEKVGYIDSDPLF 37 (219)
T ss_dssp HHHHHHHHHHHSCEEEEEEE-HHHHS
T ss_pred HHHHHHHHHHhCCCEEEEEEeccccC
Confidence 34699999999999999999985443
No 23
>cd02040 NifH NifH gene encodes component II (iron protein) of nitrogenase. Nitrogenase is responsible for the biological nitrogen fixation, i.e. reduction of molecular nitrogen to ammonia. NifH consists of two oxygen-sensitive metallosulfur proteins: the mollybdenum-iron (alternatively, vanadium-iron or iron-iron) protein (commonly referred to as component 1), and the iron protein (commonly referred to as component 2). The iron protein is a homodimer, with an Fe4S4 cluster bound between the subunits and two ATP-binding domains. It supplies energy by ATP hydrolysis, and transfers electrons from reduced ferredoxin or flavodoxin to component 1 for the reduction of molecular nitrogen to ammonia.
Probab=42.86 E-value=37 Score=30.34 Aligned_cols=20 Identities=20% Similarity=0.479 Sum_probs=14.6
Q ss_pred hCCCCeEEEEecCCcCChhhhh
Q 022668 187 QLNISRVMIIDLDAHQGNGHEK 208 (294)
Q Consensus 187 ~~~~~RV~IiD~DvHhGnGtq~ 208 (294)
+.| +||++||+|- +||-|..
T Consensus 27 ~~G-~kVlliD~Dp-q~n~~~~ 46 (270)
T cd02040 27 EMG-KKVMIVGCDP-KADSTRL 46 (270)
T ss_pred hCC-CeEEEEEcCC-CCCchhh
Confidence 344 6999999998 4665543
No 24
>cd03110 Fer4_NifH_child This protein family's function is unkown. It contains nucleotide binding site. It uses NTP as energy source to transfer electron or ion.
Probab=42.30 E-value=17 Score=30.49 Aligned_cols=16 Identities=31% Similarity=0.405 Sum_probs=13.6
Q ss_pred CeEEEEecCCcCChhh
Q 022668 191 SRVMIIDLDAHQGNGH 206 (294)
Q Consensus 191 ~RV~IiD~DvHhGnGt 206 (294)
+||++||.|...+|-.
T Consensus 25 ~~vlliD~D~~~~~~~ 40 (179)
T cd03110 25 KNVVLADCDVDAPNLH 40 (179)
T ss_pred hCcEEEECCCCCCchh
Confidence 6999999999987743
No 25
>PF11202 PRTase_1: Phosphoribosyl transferase (PRTase); InterPro: IPR011215 This is a family of uncharacterised bacterial proteins.
Probab=40.65 E-value=90 Score=28.70 Aligned_cols=14 Identities=29% Similarity=0.681 Sum_probs=11.1
Q ss_pred CCCCCccEEEEeecCCCCCCCCCCC
Q 022668 268 FSVHVFHLLFFPKSFHHYWKEDCGC 292 (294)
Q Consensus 268 f~P~~~~liv~~~G~D~~~~Dp~G~ 292 (294)
++| +|.|++ ||.||
T Consensus 178 ~~~---~LaVLa--------Dp~g~ 191 (257)
T PF11202_consen 178 LSP---DLAVLA--------DPAGC 191 (257)
T ss_pred CCC---CeEEEe--------cCccc
Confidence 788 999985 77776
No 26
>PRK13185 chlL protochlorophyllide reductase iron-sulfur ATP-binding protein; Provisional
Probab=39.17 E-value=38 Score=30.56 Aligned_cols=21 Identities=19% Similarity=0.243 Sum_probs=15.2
Q ss_pred hCCCCeEEEEecCCcCChhhhhh
Q 022668 187 QLNISRVMIIDLDAHQGNGHEKD 209 (294)
Q Consensus 187 ~~~~~RV~IiD~DvHhGnGtq~i 209 (294)
+.| +||++||.|- +||=|+.+
T Consensus 28 ~~G-~kVLliD~Dp-q~~~t~~l 48 (270)
T PRK13185 28 KLG-KKVLQIGCDP-KHDSTFTL 48 (270)
T ss_pred HCC-CeEEEEeccC-Ccchhhhh
Confidence 345 6999999997 56666543
No 27
>PRK13234 nifH nitrogenase reductase; Reviewed
Probab=38.43 E-value=36 Score=31.56 Aligned_cols=24 Identities=13% Similarity=0.382 Sum_probs=16.5
Q ss_pred HHhCCCCeEEEEecCCcCChhhhhhh
Q 022668 185 FVQLNISRVMIIDLDAHQGNGHEKDF 210 (294)
Q Consensus 185 ~~~~~~~RV~IiD~DvHhGnGtq~if 210 (294)
+.+.| +||++||+|.+..+ |+-+|
T Consensus 28 la~~g-~kVLliD~D~q~~~-~~~~~ 51 (295)
T PRK13234 28 LVEMG-QKILIVGCDPKADS-TRLIL 51 (295)
T ss_pred HHHCC-CeEEEEeccccccc-ccccc
Confidence 33445 79999999998655 44344
No 28
>cd02117 NifH_like This family contains the NifH (iron protein) of nitrogenase, L subunit (BchL/ChlL) of the protochlorophyllide reductase and the BchX subunit of the Chlorophyllide reductase. Members of this family use energey from ATP hydrolysis and transfer electrons through a Fe4-S4 cluster to other subunit for reduction of substrate.
Probab=38.24 E-value=37 Score=29.55 Aligned_cols=19 Identities=11% Similarity=0.239 Sum_probs=14.0
Q ss_pred CeEEEEecCCcCChhhhhhh
Q 022668 191 SRVMIIDLDAHQGNGHEKDF 210 (294)
Q Consensus 191 ~RV~IiD~DvHhGnGtq~if 210 (294)
+||++||.|.. ||.|...+
T Consensus 29 ~rvLliD~D~q-~~~~~~~~ 47 (212)
T cd02117 29 KKVLQVGCDPK-ADSTRLLL 47 (212)
T ss_pred CcEEEEeCCCC-CCcccccc
Confidence 69999999965 56665443
No 29
>TIGR01968 minD_bact septum site-determining protein MinD. This model describes the bacterial and chloroplast form of MinD, a multifunctional cell division protein that guides correct placement of the septum. The homologous archaeal MinD proteins, with many archaeal genomes having two or more forms, are described by a separate model.
Probab=38.03 E-value=41 Score=29.71 Aligned_cols=15 Identities=33% Similarity=0.388 Sum_probs=12.7
Q ss_pred CeEEEEecCCcCChh
Q 022668 191 SRVMIIDLDAHQGNG 205 (294)
Q Consensus 191 ~RV~IiD~DvHhGnG 205 (294)
+||++||.|...||-
T Consensus 31 ~~vlliD~D~~~~~~ 45 (261)
T TIGR01968 31 KKVVLIDADIGLRNL 45 (261)
T ss_pred CeEEEEECCCCCCCe
Confidence 699999999987663
No 30
>TIGR02016 BchX chlorophyllide reductase iron protein subunit X. This model represents the X subunit of the three-subunit enzyme, (bacterio)chlorophyllide reductase. This enzyme is responsible for the reduction of the chlorin B-ring and is closely related to the protochlorophyllide reductase complex which reduces the D-ring. Both of these complexes in turn are homologous to nitrogenase. This subunit is homologous to the nitrogenase component II, or "iron" protein.
Probab=37.24 E-value=41 Score=31.34 Aligned_cols=19 Identities=16% Similarity=0.438 Sum_probs=13.9
Q ss_pred HHhCCCCeEEEEecCCcCCh
Q 022668 185 FVQLNISRVMIIDLDAHQGN 204 (294)
Q Consensus 185 ~~~~~~~RV~IiD~DvHhGn 204 (294)
+.+.| +||++||+|...++
T Consensus 24 La~~g-~rVLlID~Dpq~~~ 42 (296)
T TIGR02016 24 MAEMG-KRVLQLGCDPKHDS 42 (296)
T ss_pred HHHCC-CeEEEEEecCCCCc
Confidence 33344 69999999998643
No 31
>PF02701 zf-Dof: Dof domain, zinc finger; InterPro: IPR003851 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 consists of proteins containing a Dof domain, which is a zinc finger DNA-binding domain that shows resemblance to the Cys2 zinc finger, although it has a longer putative loop where an extra Cys residue is conserved []. AOBP, a DNA-binding protein in pumpkin (Cucurbita maxima), contains a 52 amino acid Dof domain, which is highly conserved in several DNA-binding proteins of higher plants. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent
Probab=37.18 E-value=11 Score=26.98 Aligned_cols=10 Identities=30% Similarity=0.800 Sum_probs=7.7
Q ss_pred CCccccCcHH
Q 022668 169 GGFCAYADIS 178 (294)
Q Consensus 169 ~GFC~fNnvA 178 (294)
--||||||--
T Consensus 16 TKFcYyNNy~ 25 (63)
T PF02701_consen 16 TKFCYYNNYN 25 (63)
T ss_pred CEEEeecCCC
Confidence 4599999953
No 32
>TIGR01281 DPOR_bchL light-independent protochlorophyllide reductase, iron-sulfur ATP-binding protein. The BchL peptide (ChlL in chloroplast and cyanobacteria) is an ATP-binding iron-sulfur protein of the dark form protochlorophyllide reductase, an enzyme similar to nitrogenase. This subunit resembles the nitrogenase NifH subunit.
Probab=36.75 E-value=40 Score=30.37 Aligned_cols=20 Identities=25% Similarity=0.355 Sum_probs=14.6
Q ss_pred hCCCCeEEEEecCCcCChhhhh
Q 022668 187 QLNISRVMIIDLDAHQGNGHEK 208 (294)
Q Consensus 187 ~~~~~RV~IiD~DvHhGnGtq~ 208 (294)
+.| +||++||+|- +||-|+.
T Consensus 26 ~~g-~rVLliD~D~-q~~~~~~ 45 (268)
T TIGR01281 26 KLG-KRVLQIGCDP-KHDSTFT 45 (268)
T ss_pred hCC-CeEEEEecCc-cccccce
Confidence 334 7999999997 4666653
No 33
>PRK13235 nifH nitrogenase reductase; Reviewed
Probab=34.30 E-value=40 Score=30.60 Aligned_cols=22 Identities=14% Similarity=0.380 Sum_probs=14.9
Q ss_pred HHHHHhCCCCeEEEEecCCcCCh
Q 022668 182 HYAFVQLNISRVMIIDLDAHQGN 204 (294)
Q Consensus 182 ~~~~~~~~~~RV~IiD~DvHhGn 204 (294)
-+++.+.| +||++||+|....+
T Consensus 22 A~~La~~G-~rVLlID~Dpq~~~ 43 (274)
T PRK13235 22 VAGLAEMG-KKVMVVGCDPKADS 43 (274)
T ss_pred HHHHHHCC-CcEEEEecCCcccc
Confidence 33444445 69999999986544
No 34
>PRK10037 cell division protein; Provisional
Probab=34.22 E-value=43 Score=29.97 Aligned_cols=21 Identities=19% Similarity=0.214 Sum_probs=14.6
Q ss_pred HHHhCCCCeEEEEecCCcCChhh
Q 022668 184 AFVQLNISRVMIIDLDAHQGNGH 206 (294)
Q Consensus 184 ~~~~~~~~RV~IiD~DvHhGnGt 206 (294)
++.+.| +||++||+|-. ||-+
T Consensus 25 ~La~~G-~rVLlID~D~q-~~~s 45 (250)
T PRK10037 25 SLQMLG-ENVLVIDACPD-NLLR 45 (250)
T ss_pred HHHhcC-CcEEEEeCChh-hhHH
Confidence 334444 79999999994 5544
No 35
>TIGR03371 cellulose_yhjQ cellulose synthase operon protein YhjQ. Members of this family are the YhjQ protein, found immediately upsteam of bacterial cellulose synthase (bcs) genes in a broad range of bacteria, including both copies of the bcs locus in Klebsiella pneumoniae. In several species it is seen clearly as part of the bcs operon. It is identified as a probable component of the bacterial cellulose metabolic process not only by gene location, but also by partial phylogenetic profiling, or Haft-Selengut algorithm (PubMed:16930487), based on a bacterial cellulose biosynthesis genome property profile. Cellulose plays an important role in biofilm formation and structural integrity in some bacteria. Mutants in yhjQ in Escherichia coli, show altered morphology an growth, but the function of YhjQ has not yet been determined.
Probab=33.44 E-value=50 Score=29.02 Aligned_cols=18 Identities=33% Similarity=0.447 Sum_probs=12.8
Q ss_pred HHhCCCCeEEEEecCCcCCh
Q 022668 185 FVQLNISRVMIIDLDAHQGN 204 (294)
Q Consensus 185 ~~~~~~~RV~IiD~DvHhGn 204 (294)
..+.| +||++||.|.. |+
T Consensus 26 la~~g-~~VlliD~D~q-~~ 43 (246)
T TIGR03371 26 LKLLG-EPVLAIDLDPQ-NL 43 (246)
T ss_pred HHhCC-CcEEEEeCCCc-ch
Confidence 33344 69999999984 44
No 36
>cd06334 PBP1_ABC_ligand_binding_like_1 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters, such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=33.07 E-value=1.5e+02 Score=27.80 Aligned_cols=34 Identities=12% Similarity=0.146 Sum_probs=26.9
Q ss_pred HHHHHHHHHhC----CCCeEEEEecCCcCChhhhhhhh
Q 022668 178 SLCIHYAFVQL----NISRVMIIDLDAHQGNGHEKDFS 211 (294)
Q Consensus 178 AiAa~~~~~~~----~~~RV~IiD~DvHhGnGtq~if~ 211 (294)
...++|+.++. +.+||+||=-|.-.|.+..+.|.
T Consensus 124 ~~l~~~~~~~~~~~~~~~kvaiv~~~~~~g~~~~~~~~ 161 (351)
T cd06334 124 RALVQYIAEQEGGKLKGKKIALVYHDSPFGKEPIEALK 161 (351)
T ss_pred HHHHHHHHHhcccCCCCCeEEEEeCCCccchhhHHHHH
Confidence 44567777766 58999999889889988887775
No 37
>PF02310 B12-binding: B12 binding domain; InterPro: IPR006158 The cobalamin (vitamin B12) binding domain can bind two different forms of the cobalamin cofactor, with cobalt bonded either to a methyl group (methylcobalamin) or to 5'-deoxyadenosine (adenosylcobalamin). Cobalamin-binding domains are mainly found in two families of enzymes present in animals and prokaryotes, which perform distinct kinds of reactions at the cobalt-carbon bond. Enzymes that require methylcobalamin carry out methyl transfer reactions. Enzymes that require adenosylcobalamin catalyse reactions in which the first step is the cleavage of adenosylcobalamin to form cob(II)alamin and the 5'-deoxyadenosyl radical, and thus act as radical generators. In both types of enzymes the B12-binding domain uses a histidine to bind the cobalt atom of cobalamin cofactors. This histidine is embedded in a DXHXXG sequence, the most conserved primary sequence motif of the domain [, , ]. Proteins containing the cobalamin-binding domain include: Animal and prokaryotic methionine synthase (2.1.1.13 from EC), which catalyse the transfer of a methyl group from methyl-cobalamin to homocysteine, yielding enzyme-bound cob(I)alamin and methionine. Animal and prokaryotic methylmalonyl-CoA mutase (5.4.99.2 from EC), which are involved in the degradation of several amino acids, odd-chain fatty acids and cholesterol via propionyl-CoA to the tricarboxylic acid cycle. Prokaryotic lysine 5,6-aminomutase (5.4.3.4 from EC). Prokaryotic glutamate mutase (5.4.99.1 from EC) []. Prokaryotic methyleneglutarate mutase (5.4.99.4 from EC). Prokaryotic isobutyryl-CoA mutase (5.4.99.13 from EC). The core structure of the cobalamin-binding domain is characterised by a five-stranded alpha/beta (Rossmann) fold, which consists of 5 parallel beta-sheets surrounded by 4-5 alpha helices in three layers (alpha/beta/alpha) []. Upon binding cobalamin, important elements of the binding site appear to become structured, including an alpha-helix that forms on one side of the cleft accommodating the nucleotide 'tail' of the cofactor. In cobalamin, the cobalt atom can be either free (dmb-off) or bound to dimethylbenzimidazole (dmb-on) according to the pH. When bound to the cobalamin-binding domain, the dimethylbenzimidazole ligand is replaced by the active histidine (His-on) of the DXHXXG motif. The replacement of dimethylbenzimidazole by histidine allows switching between the catalytic and activation cycles []. In methionine synthase the cobalamin cofactor is sandwiched between the cobalamin-binding domain and an approximately 90 residues N-terminal domain forming a helical bundle comprising two pairs of antiparallel helices []. In methionine synthase, there is a second, adjacent domain involved in cobalamin binding that forms a 4-helical bundle cap (IPR003759 from INTERPRO); in the conversion to the active conformation of this enzyme, the 4-helical cap rotates to allow the cobalamin cofactor to bind the activation domain (IPR004223 from INTERPRO) [].; GO: 0031419 cobalamin binding, 0046872 metal ion binding; PDB: 1Y80_A 3BUL_A 1K7Y_A 1BMT_A 3IV9_A 1K98_A 3IVA_A 3KP1_A 3KOW_A 3KOZ_A ....
Probab=32.66 E-value=2.3e+02 Score=21.72 Aligned_cols=44 Identities=14% Similarity=0.003 Sum_probs=34.2
Q ss_pred HHHHHHHHHHhCCCCeEEEEecCCcCChhhhhhhhcCCCEEEEeec
Q 022668 177 ISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSSDSRVYILDMF 222 (294)
Q Consensus 177 vAiAa~~~~~~~~~~RV~IiD~DvHhGnGtq~if~~d~~Vl~iSiH 222 (294)
+.+.+.+++++ |. .|-++|.+++..+-.+.+-..++++.-+|.+
T Consensus 17 l~~la~~l~~~-G~-~v~~~d~~~~~~~l~~~~~~~~pd~V~iS~~ 60 (121)
T PF02310_consen 17 LLYLAAYLRKA-GH-EVDILDANVPPEELVEALRAERPDVVGISVS 60 (121)
T ss_dssp HHHHHHHHHHT-TB-EEEEEESSB-HHHHHHHHHHTTCSEEEEEES
T ss_pred HHHHHHHHHHC-CC-eEEEECCCCCHHHHHHHHhcCCCcEEEEEcc
Confidence 44555556554 54 8999999999988888888899999999985
No 38
>PF13050 DUF3911: Protein of unknown function (DUF3911)
Probab=32.11 E-value=18 Score=26.17 Aligned_cols=9 Identities=33% Similarity=1.106 Sum_probs=7.9
Q ss_pred CCccccCcH
Q 022668 169 GGFCAYADI 177 (294)
Q Consensus 169 ~GFC~fNnv 177 (294)
.|||-|||-
T Consensus 26 kgfckf~ny 34 (77)
T PF13050_consen 26 KGFCKFNNY 34 (77)
T ss_pred ccccccCCE
Confidence 699999985
No 39
>PRK13233 nifH nitrogenase reductase; Reviewed
Probab=31.89 E-value=54 Score=29.67 Aligned_cols=14 Identities=21% Similarity=0.349 Sum_probs=11.9
Q ss_pred CeEEEEecCCcCCh
Q 022668 191 SRVMIIDLDAHQGN 204 (294)
Q Consensus 191 ~RV~IiD~DvHhGn 204 (294)
+||++||+|.+..+
T Consensus 32 ~rvLliD~Dpq~~~ 45 (275)
T PRK13233 32 KKVFIHGCDPKADS 45 (275)
T ss_pred CeEEEeccCcCcCh
Confidence 69999999998644
No 40
>TIGR01007 eps_fam capsular exopolysaccharide family. This model describes the capsular exopolysaccharide proteins in bacteria. The exopolysaccharide gene cluster consists of several genes which encode a number of proteins which regulate the exoploysaccharide biosynthesis(EPS). Atleast 13 genes espA to espM in streptococcus species seem to direct the EPS proteins and all of which share high homology. Functional roles were characterized by gene disruption experiments which resulted in exopolysaccharide-deficient phenotypes.
Probab=30.06 E-value=65 Score=27.62 Aligned_cols=13 Identities=23% Similarity=0.422 Sum_probs=11.2
Q ss_pred CeEEEEecCCcCC
Q 022668 191 SRVMIIDLDAHQG 203 (294)
Q Consensus 191 ~RV~IiD~DvHhG 203 (294)
+||++||+|...+
T Consensus 47 ~rVllID~D~~~~ 59 (204)
T TIGR01007 47 YKTLLIDGDMRNS 59 (204)
T ss_pred CeEEEEeCCCCCh
Confidence 6999999998754
No 41
>PF12023 DUF3511: Domain of unknown function (DUF3511); InterPro: IPR021899 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 50 amino acids in length. This domain has two completely conserved residues (Y and K) that may be functionally important.
Probab=29.98 E-value=34 Score=23.15 Aligned_cols=19 Identities=32% Similarity=0.471 Sum_probs=14.4
Q ss_pred CCCcHHHHhhhhhhccccc
Q 022668 9 VTTDAETLKRNRILSSKLY 27 (294)
Q Consensus 9 ~~~~~~~~~~~~~~~~~~~ 27 (294)
+.++||.+||.|+-+-..+
T Consensus 2 ~~~dpE~kRkkRVA~Yk~y 20 (47)
T PF12023_consen 2 GFNDPEMKRKKRVASYKVY 20 (47)
T ss_pred CCCCHHHHHHHHHHhhhee
Confidence 3579999999999654443
No 42
>TIGR03029 EpsG chain length determinant protein tyrosine kinase EpsG. The proteins in this family are homologs of the EpsG protein found in Methylobacillus strain 12S and are generally found in operons with other Eps homologs. The protein is believed to function as the protein tyrosine kinase component of the chain length regulator (along with the transmembrane component EpsF).
Probab=29.54 E-value=66 Score=29.04 Aligned_cols=17 Identities=24% Similarity=0.429 Sum_probs=13.6
Q ss_pred hCCCCeEEEEecCCcCCh
Q 022668 187 QLNISRVMIIDLDAHQGN 204 (294)
Q Consensus 187 ~~~~~RV~IiD~DvHhGn 204 (294)
+.| +||++||+|.+..+
T Consensus 130 ~~g-~~VllID~D~~~~~ 146 (274)
T TIGR03029 130 QLG-EKTLLIDANLRDPV 146 (274)
T ss_pred hcC-CeEEEEeCCCCCcc
Confidence 334 79999999998765
No 43
>PRK15404 leucine ABC transporter subunit substrate-binding protein LivK; Provisional
Probab=29.37 E-value=1.8e+02 Score=27.44 Aligned_cols=33 Identities=12% Similarity=0.330 Sum_probs=24.9
Q ss_pred HHHHHHHHhCCCCeEEEEecCCcCChhhhhhhh
Q 022668 179 LCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFS 211 (294)
Q Consensus 179 iAa~~~~~~~~~~RV~IiD~DvHhGnGtq~if~ 211 (294)
..++|+.++.+.+||++|--|.-.|+...+.|.
T Consensus 150 ~~~~~~~~~~~~k~va~i~~d~~~g~~~~~~~~ 182 (369)
T PRK15404 150 TAAKYILEKVKPKRIAVLHDKQQYGEGLARSVK 182 (369)
T ss_pred HHHHHHHHhcCCCEEEEEeCCCchhHHHHHHHH
Confidence 456888777788999999888777877666553
No 44
>cd02037 MRP-like MRP (Multiple Resistance and pH adaptation) is a homologue of the Fer4_NifH superfamily. Like the other members of the superfamily, MRP contains a ATP-binding domain at the N-termini. It is found in bacteria as a membrane-spanning protein and functions as a Na+/H+ antiporter.
Probab=29.02 E-value=63 Score=26.87 Aligned_cols=13 Identities=23% Similarity=0.230 Sum_probs=10.9
Q ss_pred CeEEEEecCCcCC
Q 022668 191 SRVMIIDLDAHQG 203 (294)
Q Consensus 191 ~RV~IiD~DvHhG 203 (294)
+||++||.|.-..
T Consensus 29 ~~vllvD~D~q~~ 41 (169)
T cd02037 29 YKVGLLDADIYGP 41 (169)
T ss_pred CcEEEEeCCCCCC
Confidence 7999999998543
No 45
>PF00220 Hormone_4: Neurohypophysial hormones, N-terminal Domain; InterPro: IPR022423 Oxytocin (or ocytocin) and vasopressin [] are small (nine amino acid residues), structurally and functionally related neurohypophysial peptide hormones. Oxytocin causes contraction of the smooth muscle of the uterus and of the mammary gland while vasopressin has a direct antidiuretic action on the kidney and also causes vasoconstriction of the peripheral vessels. Like the majority of active peptides, both hormones are synthesized as larger protein precursors that are enzymatically converted to their mature forms. Peptides belonging to this family are also found in birds, fish, reptiles and amphibians (mesotocin, isotocin, valitocin, glumitocin, aspargtocin, vasotocin, seritocin, asvatocin, phasvatocin), in worms (annetocin), octopi (cephalotocin), locust (locupressin or neuropeptide F1/F2) and in molluscs (conopressins G and S) []. The pattern developed to detect this category of peptides spans their entire sequence and includes four invariant amino acid residues. .; GO: 0005185 neurohypophyseal hormone activity, 0005576 extracellular region
Probab=28.85 E-value=8.6 Score=17.13 Aligned_cols=7 Identities=14% Similarity=0.453 Sum_probs=4.7
Q ss_pred cccCcHH
Q 022668 172 CAYADIS 178 (294)
Q Consensus 172 C~fNnvA 178 (294)
|+++|+-
T Consensus 1 C~i~nCP 7 (9)
T PF00220_consen 1 CYIRNCP 7 (9)
T ss_pred CccccCC
Confidence 7777753
No 46
>TIGR03669 urea_ABC_arch urea ABC transporter, substrate-binding protein, archaeal type. Members of this protein family are identified as the substrate-binding protein of a urea ABC transport system by similarity to a known urea transporter from Corynebacterium glutamicum, operon structure, proximity of its operons to urease (urea-utilization protein) operons, and by Partial Phylogenetic Profiling vs. urea utilization.
Probab=28.34 E-value=1.6e+02 Score=28.04 Aligned_cols=34 Identities=12% Similarity=0.178 Sum_probs=26.4
Q ss_pred HHHHHHHHHHhCCCCeEEEEecCCcCChhhhhhhh
Q 022668 177 ISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFS 211 (294)
Q Consensus 177 vAiAa~~~~~~~~~~RV~IiD~DvHhGnGtq~if~ 211 (294)
++.+++|+.++.+ +||++|--|.=.|.+..+.|.
T Consensus 121 ~~~~~~~~~~~~g-~~va~l~~d~~~g~~~~~~~~ 154 (374)
T TIGR03669 121 LGTVVPYMVEEYG-KKIYTIAADYNFGQLSADWVR 154 (374)
T ss_pred HHHHHHHHHHcCC-CeEEEEcCCcHHHHHHHHHHH
Confidence 4566788887766 799999999888887766654
No 47
>PF00977 His_biosynth: Histidine biosynthesis protein; InterPro: IPR006062 Histidine is formed by several complex and distinct biochemical reactions catalysed by eight enzymes. Proteins involved in steps 4 and 6 of the histidine biosynthesis pathway are contained in one family. These enzymes are called His6 and His7 in eukaryotes and HisA and HisF in prokaryotes. HisA is a phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (5.3.1.16 from EC), involved in the fourth step of histidine biosynthesis. The bacterial HisF protein is a cyclase which catalyzes the cyclization reaction that produces D-erythro-imidazole glycerol phosphate during the sixth step of histidine biosynthesis. The yeast His7 protein is a bifunctional protein which catalyzes an amido-transferase reaction that generates imidazole-glycerol phosphate and 5-aminoimidazol-4-carboxamide. The latter is the ribonucleotide used for purine biosynthesis. The enzyme also catalyzes the cyclization reaction that produces D-erythro-imidazole glycerol phosphate, and is involved in the fifth and sixth steps in histidine biosynthesis.; GO: 0000105 histidine biosynthetic process; PDB: 2VEP_A 2X30_A 1VZW_A 2WJZ_A 2LLE_A 2A0N_A 1THF_D 1GPW_E 1VH7_A 1KA9_F ....
Probab=28.00 E-value=73 Score=28.39 Aligned_cols=50 Identities=22% Similarity=0.242 Sum_probs=35.4
Q ss_pred cCcEEecCCCCCCCCCCCCCCccccCcHHHHHHHHHHhCCCCeEEEEecCCc-CChhh
Q 022668 150 RGWAINVGGGFHHCSADEGGGFCAYADISLCIHYAFVQLNISRVMIIDLDAH-QGNGH 206 (294)
Q Consensus 150 ~~~a~~~~~GgHHA~~~~~~GFC~fNnvAiAa~~~~~~~~~~RV~IiD~DvH-hGnGt 206 (294)
+|.++..-.| ++....|+..|..=.|+.+ +..|++++.|+|+|.= .|.+.
T Consensus 10 ~G~~Vr~~~G------~~~~~~~~~~dP~~~a~~~-~~~g~~~l~ivDLdaa~~g~~~ 60 (229)
T PF00977_consen 10 NGRVVRLVKG------DRFSETVYSGDPVEVAKAF-NEQGADELHIVDLDAAKEGRGS 60 (229)
T ss_dssp TTEEEEESTT------CCSCEECECCCHHHHHHHH-HHTT-SEEEEEEHHHHCCTHHH
T ss_pred CCEEEECCCe------ecceeeEECcCHHHHHHHH-HHcCCCEEEEEEccCcccCchh
Confidence 4566655555 3456788888888888877 5568999999999965 46663
No 48
>TIGR03453 partition_RepA plasmid partitioning protein RepA. Members of this family are the RepA (or ParA) protein involved in replicon partitioning. All known examples occur in bacterial species with two or more replicons, on a plasmid or the smaller chromosome. Note that an apparent exception may be seen as a pseudomolecule from assembly of an incompletely sequenced genome. Members of this family belong to a larger family that also includes the enzyme cobyrinic acid a,c-diamide synthase, but assignment of that name to members of this family would be in error.
Probab=27.24 E-value=76 Score=30.54 Aligned_cols=19 Identities=37% Similarity=0.387 Sum_probs=14.6
Q ss_pred hCCCCeEEEEecCCcCChhhh
Q 022668 187 QLNISRVMIIDLDAHQGNGHE 207 (294)
Q Consensus 187 ~~~~~RV~IiD~DvHhGnGtq 207 (294)
+.| +||++||+|. +||-|+
T Consensus 131 ~~G-~rVLlID~Dp-Q~~ls~ 149 (387)
T TIGR03453 131 LRG-YRVLAIDLDP-QASLSA 149 (387)
T ss_pred hcC-CCEEEEecCC-CCCHHH
Confidence 345 6999999997 677555
No 49
>KOG0279 consensus G protein beta subunit-like protein [Signal transduction mechanisms]
Probab=26.66 E-value=33 Score=32.06 Aligned_cols=76 Identities=11% Similarity=0.108 Sum_probs=47.5
Q ss_pred cCCcCChhhhhhhhcCCCEEEEeecCCCCCCCCCcCCCcee-Ee------eeCCCCCChHHHHHHHHHHHHHHHhccCCC
Q 022668 198 LDAHQGNGHEKDFSSDSRVYILDMFNPGIYPRDYEARRFID-QK------VEVVSGTTTNEYLKKLDEALEVYMFKTFSV 270 (294)
Q Consensus 198 ~DvHhGnGtq~if~~d~~Vl~iSiH~~~~yP~~g~~~~~~n-vN------vpl~~g~~d~~yl~~~~~~l~~~~~~~f~P 270 (294)
||.|-|.-||.+.....+||-+++--.+-=-.+|.-.++.+ .| +-+..+++ .++..-+ .|.|
T Consensus 90 WDl~~g~~t~~f~GH~~dVlsva~s~dn~qivSGSrDkTiklwnt~g~ck~t~~~~~~-~~WVscv----------rfsP 158 (315)
T KOG0279|consen 90 WDLATGESTRRFVGHTKDVLSVAFSTDNRQIVSGSRDKTIKLWNTLGVCKYTIHEDSH-REWVSCV----------RFSP 158 (315)
T ss_pred EEecCCcEEEEEEecCCceEEEEecCCCceeecCCCcceeeeeeecccEEEEEecCCC-cCcEEEE----------EEcC
Confidence 78999999999989999999999865321111222222221 12 22223322 3444333 4999
Q ss_pred CCccEEEEeecCCC
Q 022668 271 HVFHLLFFPKSFHH 284 (294)
Q Consensus 271 ~~~~liv~~~G~D~ 284 (294)
..-+.+++|+|+|-
T Consensus 159 ~~~~p~Ivs~s~Dk 172 (315)
T KOG0279|consen 159 NESNPIIVSASWDK 172 (315)
T ss_pred CCCCcEEEEccCCc
Confidence 77789999999984
No 50
>PF13458 Peripla_BP_6: Periplasmic binding protein; PDB: 4EVS_A 4EY3_A 4EYG_B 4EYK_A 3H5L_B 3TD9_A 3EAF_A 1Z18_A 1Z17_A 2LIV_A ....
Probab=26.50 E-value=1.3e+02 Score=27.27 Aligned_cols=37 Identities=19% Similarity=0.252 Sum_probs=26.0
Q ss_pred CcHHHHHHHHHHhCCCCeEEEEecCCcCChhhhhhhh
Q 022668 175 ADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFS 211 (294)
Q Consensus 175 NnvAiAa~~~~~~~~~~RV~IiD~DvHhGnGtq~if~ 211 (294)
..+...++|++++.|.+||+||--|.=.|+...+.|.
T Consensus 120 ~~~~~~~~~~~~~~g~~~v~iv~~~~~~g~~~~~~~~ 156 (343)
T PF13458_consen 120 QQAAALAEYLAKKLGAKKVAIVYPDDPYGRSLAEAFR 156 (343)
T ss_dssp HHHHHHHHHHHHTTTTSEEEEEEESSHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcCCcEEEEEecCchhhhHHHHHHH
Confidence 3456677888887789999999777555555555553
No 51
>TIGR03815 CpaE_hom_Actino helicase/secretion neighborhood CpaE-like protein. Members of this protein family belong to the MinD/ParA family of P-loop NTPases, and in particular show homology to the CpaE family of pilus assembly proteins (see PubMed:12370432). Nearly all members are found, not only in a gene context consistent with pilus biogenesis or a pilus-like secretion apparatus, but also near a DEAD/DEAH-box helicase, suggesting an involvement in DNA transfer activity. The model describes a clade restricted to the Actinobacteria.
Probab=26.21 E-value=77 Score=29.54 Aligned_cols=14 Identities=29% Similarity=0.596 Sum_probs=11.7
Q ss_pred CeEEEEecCCcCCh
Q 022668 191 SRVMIIDLDAHQGN 204 (294)
Q Consensus 191 ~RV~IiD~DvHhGn 204 (294)
+||++||.|...|+
T Consensus 123 ~~VlLvD~D~~~~~ 136 (322)
T TIGR03815 123 LRTLLVDADPWGGG 136 (322)
T ss_pred CCEEEEecCCCCCC
Confidence 79999999977654
No 52
>cd02033 BchX Chlorophyllide reductase converts chlorophylls into bacteriochlorophylls by reducing the chlorin B-ring. This family contains the X subunit of this three-subunit enzyme. Sequence and structure similarity between bchX, protochlorophyllide reductase L subunit (bchL and chlL) and nitrogenase Fe protein (nifH gene) suggest their functional similarity. Members of the BchX family serve as the unique electron donors to their respective catalytic subunits (bchN-bchB, bchY-bchZ and nitrogenase component 1). Mechanistically, they hydrolyze ATP and transfer electrons through a Fe4-S4 cluster.
Probab=25.74 E-value=72 Score=30.39 Aligned_cols=20 Identities=25% Similarity=0.401 Sum_probs=16.0
Q ss_pred CeEEEEecCCcCChhhhhhhh
Q 022668 191 SRVMIIDLDAHQGNGHEKDFS 211 (294)
Q Consensus 191 ~RV~IiD~DvHhGnGtq~if~ 211 (294)
+||++||.|.++++ +..+|.
T Consensus 60 ~rVllid~D~~~~~-~~~~~g 79 (329)
T cd02033 60 KRVLLIGCDPKSDT-TSLLFG 79 (329)
T ss_pred CcEEEEEeeecccc-cchhcc
Confidence 79999999999865 555654
No 53
>TIGR03018 pepcterm_TyrKin exopolysaccharide/PEPCTERM locus tyrosine autokinase. Members of this protein family are related to a known protein-tyrosine autokinase and to numerous homologs from exopolysaccharide biosynthesis region proteins, many of which are designated as chain length determinants. Most members of this family contain a short region, immediately C-terminal to the region modeled here, with an abundance of Tyr residues. These C-terminal tyrosine residues are likely to be autophosphorylation sites. Some members of this family are fusion proteins.
Probab=25.54 E-value=89 Score=27.06 Aligned_cols=24 Identities=4% Similarity=0.246 Sum_probs=17.8
Q ss_pred HHHHHHHHHHHhccCCCCCccEEEEeec
Q 022668 254 KKLDEALEVYMFKTFSVHVFHLLFFPKS 281 (294)
Q Consensus 254 ~~~~~~l~~~~~~~f~P~~~~liv~~~G 281 (294)
..+.+.+..+.++ |.+ |+||+=++
T Consensus 134 ~~l~~~l~~l~~~-y~~---D~IiiD~p 157 (207)
T TIGR03018 134 QRMRSLLHELARR-YPD---RIIIIDTP 157 (207)
T ss_pred HHHHHHHHHHHhh-CCC---CEEEEECC
Confidence 3567777777777 877 89998654
No 54
>CHL00072 chlL photochlorophyllide reductase subunit L
Probab=25.36 E-value=75 Score=29.41 Aligned_cols=23 Identities=17% Similarity=0.231 Sum_probs=15.6
Q ss_pred HHHHhCCCCeEEEEecCCcCChhhh
Q 022668 183 YAFVQLNISRVMIIDLDAHQGNGHE 207 (294)
Q Consensus 183 ~~~~~~~~~RV~IiD~DvHhGnGtq 207 (294)
+++.+.| +||++||+|-. ||-|.
T Consensus 22 ~~La~~G-~rVLlID~DpQ-~n~t~ 44 (290)
T CHL00072 22 IALARRG-KKVLQIGCDPK-HDSTF 44 (290)
T ss_pred HHHHHCC-CeEEEEeccCC-Ccccc
Confidence 3344445 69999999986 55444
No 55
>COG1891 Uncharacterized protein conserved in archaea [Function unknown]
Probab=24.83 E-value=1.5e+02 Score=26.15 Aligned_cols=34 Identities=9% Similarity=0.130 Sum_probs=25.1
Q ss_pred ChHHHHHHHHHHHHHHHhccCCCCCccEEEEeecC-CCCC
Q 022668 248 TTNEYLKKLDEALEVYMFKTFSVHVFHLLFFPKSF-HHYW 286 (294)
Q Consensus 248 ~d~~yl~~~~~~l~~~~~~~f~P~~~~liv~~~G~-D~~~ 286 (294)
+.++-+..+..++..+. +|+| +-+|+.+|+ |+|.
T Consensus 93 n~~eA~e~m~~vvrAVk--d~d~---~k~VVAaGYaDa~R 127 (235)
T COG1891 93 NEEEALEVMKNVVRAVK--DFDP---SKKVVAAGYADAHR 127 (235)
T ss_pred cHHHHHHHHHHHHHHHh--ccCC---CceEEeccccchhh
Confidence 34556667766666555 5999 999999999 7764
No 56
>TIGR03407 urea_ABC_UrtA urea ABC transporter, urea binding protein. Members of this protein family are ABC transporter substrate-binding proteins associated with urea transport and metabolism. This protein is found in a conserved five-gene transport operon typically found adjacent to urease genes. It was shown in Cyanobacteria that disruption leads to the loss of high-affinity urea transport activity. Members of this protein family tend to have the twin-arginine signal for Sec-independent transport across the plasma membrane.
Probab=24.54 E-value=1.6e+02 Score=27.63 Aligned_cols=35 Identities=14% Similarity=0.161 Sum_probs=25.9
Q ss_pred HHHHHHHHHHhCCCCeEEEEecCCcCChhhhhhhh
Q 022668 177 ISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFS 211 (294)
Q Consensus 177 vAiAa~~~~~~~~~~RV~IiD~DvHhGnGtq~if~ 211 (294)
++.+++|+.++.|.+||++|--|.=.|.+..+.|.
T Consensus 121 ~~~~~~~~~~~~g~k~v~~l~~d~~~g~~~~~~~~ 155 (359)
T TIGR03407 121 IIPAVDYLLSKKGAKRFFLLGSDYVFPRTANKIIK 155 (359)
T ss_pred HHHHHHHHHhccCCceEEEecCccHHHHHHHHHHH
Confidence 45566888877688999999877666777666553
No 57
>cd02032 Bchl_like This family of proteins contains bchL and chlL. Protochlorophyllide reductase catalyzes the reductive formation of chlorophyllide from protochlorophyllide during biosynthesis of chlorophylls and bacteriochlorophylls. Three genes, bchL, bchN and bchB, are involved in light-independent protochlorophyllide reduction in bacteriochlorophyll biosynthesis. In cyanobacteria, algae, and gymnosperms, three similar genes, chlL, chlN and chlB are involved in protochlorophyllide reduction during chlorophylls biosynthesis. BchL/chlL, bchN/chlN and bchB/chlB exhibit significant sequence similarity to the nifH, nifD and nifK subunits of nitrogenase, respectively. Nitrogenase catalyzes the reductive formation of ammonia from dinitrogen.
Probab=24.33 E-value=80 Score=28.39 Aligned_cols=20 Identities=15% Similarity=0.218 Sum_probs=13.8
Q ss_pred HhCCCCeEEEEecCCcCChhhh
Q 022668 186 VQLNISRVMIIDLDAHQGNGHE 207 (294)
Q Consensus 186 ~~~~~~RV~IiD~DvHhGnGtq 207 (294)
.+.| +||++||.|- +||-++
T Consensus 25 a~~G-~rvlliD~Dp-q~~~~~ 44 (267)
T cd02032 25 AKRG-KKVLQIGCDP-KHDSTF 44 (267)
T ss_pred HHCC-CcEEEEecCC-CCCcce
Confidence 3444 7999999996 455443
No 58
>PF02585 PIG-L: GlcNAc-PI de-N-acetylase; InterPro: IPR003737 A number of the members of this family have been characterised as a probable N-acetylglucosaminyl-phosphatidylinositol de-N-acetylase, (3.5.1.89 from EC) that catalyses the second step in glycosylphosphatidylinositol (GPI) biosynthesis [, ]. The family also includes a number of thiol biosynthesis proteins. ; PDB: 2XAD_C 2X9L_A 3DFK_A 3DFM_A 3DFF_A 2IXD_A 1UAN_A 1Q74_B 1Q7T_B 3DFI_A.
Probab=23.82 E-value=1.3e+02 Score=23.65 Aligned_cols=29 Identities=21% Similarity=0.266 Sum_probs=20.2
Q ss_pred HHHHHHHHHHHHHhccCCCCCccEEEEeecCCC
Q 022668 252 YLKKLDEALEVYMFKTFSVHVFHLLFFPKSFHH 284 (294)
Q Consensus 252 yl~~~~~~l~~~~~~~f~P~~~~liv~~~G~D~ 284 (294)
....+.+.|..++++ ++| ++|+.....|.
T Consensus 84 ~~~~~~~~l~~~i~~-~~p---~~V~t~~~~~~ 112 (128)
T PF02585_consen 84 SWEELVRDLEDLIRE-FRP---DVVFTPDPDDG 112 (128)
T ss_dssp HHHHHHHHHHHHHHH-H-E---SEEEEE-STTS
T ss_pred cHHHHHHHHHHHHHH-cCC---CEEEECCCCCC
Confidence 344455667777777 999 99999988887
No 59
>PRK11670 antiporter inner membrane protein; Provisional
Probab=22.89 E-value=97 Score=29.87 Aligned_cols=24 Identities=17% Similarity=0.140 Sum_probs=15.9
Q ss_pred HHhCCCCeEEEEecCCcCChhhhhhh
Q 022668 185 FVQLNISRVMIIDLDAHQGNGHEKDF 210 (294)
Q Consensus 185 ~~~~~~~RV~IiD~DvHhGnGtq~if 210 (294)
+.+.| +||++||.|....+ +..+|
T Consensus 132 LA~~G-~rVlLID~D~qgps-~~~~l 155 (369)
T PRK11670 132 LAAEG-AKVGILDADIYGPS-IPTML 155 (369)
T ss_pred HHHCC-CcEEEEeCCCCCCC-cchhc
Confidence 33444 69999999996654 33344
No 60
>KOG1530 consensus Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]
Probab=22.73 E-value=1.7e+02 Score=24.30 Aligned_cols=74 Identities=14% Similarity=0.172 Sum_probs=43.7
Q ss_pred CCeEEEEecCCcCChhhhhhhhcCCCEEEEeecCCCCCCCCCcCCCceeEeeeC----CC-CCChHHHHHHHHHHHHHHH
Q 022668 190 ISRVMIIDLDAHQGNGHEKDFSSDSRVYILDMFNPGIYPRDYEARRFIDQKVEV----VS-GTTTNEYLKKLDEALEVYM 264 (294)
Q Consensus 190 ~~RV~IiD~DvHhGnGtq~if~~d~~Vl~iSiH~~~~yP~~g~~~~~~nvNvpl----~~-g~~d~~yl~~~~~~l~~~~ 264 (294)
.+.+.++|+|+ ..+ .-+.++++++++-...-|--++ -...+|||+ +. ...+.+|+..+..
T Consensus 19 ~~~~~sv~~~q-----vk~-L~~~~~~~llDVRepeEfk~gh---~~~siNiPy~~~~~~~~l~~~eF~kqvg~------ 83 (136)
T KOG1530|consen 19 ASNPQSVSVEQ-----VKN-LLQHPDVVLLDVREPEEFKQGH---IPASINIPYMSRPGAGALKNPEFLKQVGS------ 83 (136)
T ss_pred cCCcEEEEHHH-----HHH-HhcCCCEEEEeecCHHHhhccC---CcceEeccccccccccccCCHHHHHHhcc------
Confidence 56778888775 222 3345668888885532222111 124689998 22 2456777776643
Q ss_pred hccCCCCCccEEEEee
Q 022668 265 FKTFSVHVFHLLFFPK 280 (294)
Q Consensus 265 ~~~f~P~~~~liv~~~ 280 (294)
.+.|+++++||.+.
T Consensus 84 --~kp~~d~eiIf~C~ 97 (136)
T KOG1530|consen 84 --SKPPHDKEIIFGCA 97 (136)
T ss_pred --cCCCCCCcEEEEec
Confidence 35666668888753
No 61
>COG4671 Predicted glycosyl transferase [General function prediction only]
Probab=22.68 E-value=2.9e+02 Score=27.02 Aligned_cols=29 Identities=10% Similarity=0.020 Sum_probs=24.4
Q ss_pred CChHHHHHHHHHHHHHHHhccCCCCCccEEEEe
Q 022668 247 TTTNEYLKKLDEALEVYMFKTFSVHVFHLLFFP 279 (294)
Q Consensus 247 ~~d~~yl~~~~~~l~~~~~~~f~P~~~~liv~~ 279 (294)
.+.+++.+.=++++....++ |+| |+++|=
T Consensus 85 ~~l~e~~~~Rs~lil~t~~~-fkP---Di~IVd 113 (400)
T COG4671 85 GDLEETKKLRSQLILSTAET-FKP---DIFIVD 113 (400)
T ss_pred CCHHHHHHHHHHHHHHHHHh-cCC---CEEEEe
Confidence 45788888888888889988 999 999873
No 62
>TIGR00734 hisAF_rel hisA/hisF family protein. This alignment models a family of proteins found so far in three archaeal species: Methanobacterium thermoautotrophicum, Methanococcus jannaschii, and Archaeoglobus fulgidus. This protein is homologous to phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (HisA) and, with lower similarity, to the cyclase HisF, both of which are enzymes of histidine biosynthesis. Each species with this protein also encodes HisA. The function of this protein is unknown.
Probab=22.24 E-value=1.4e+02 Score=26.55 Aligned_cols=36 Identities=17% Similarity=0.055 Sum_probs=28.1
Q ss_pred ccccCcHHHHHHHHHHhCCCCeEEEEecCCcCChhhh
Q 022668 171 FCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHE 207 (294)
Q Consensus 171 FC~fNnvAiAa~~~~~~~~~~RV~IiD~DvHhGnGtq 207 (294)
.|+..|..-.|+++.+ .|++.+-|+|+|..-|.+.+
T Consensus 32 ~~~~~dP~~~a~~~~~-~g~~~l~ivDLd~~~~~~~n 67 (221)
T TIGR00734 32 SRLSSSPDDAAKVIEE-IGARFIYIADLDRIVGLGDN 67 (221)
T ss_pred eecCCCHHHHHHHHHH-cCCCEEEEEEcccccCCcch
Confidence 5888887777776664 58999999999998766543
No 63
>cd04864 LigD_Pol_like_1 LigD_Pol_like_1: Polymerase (Pol) domain of mostly bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD, subgroup 1. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The Pol domains of PaeLigD and Mycobacterium tuberculosis (Mt)LigD are stimulated by manganese, are error-prone, and prefer adding rNTPs to dNTPs in vitro; however PaeLigD and MtLigD belong to other subgroups, proteins in this subgroup await functional characterization.
Probab=22.22 E-value=3e+02 Score=24.90 Aligned_cols=48 Identities=10% Similarity=-0.065 Sum_probs=30.0
Q ss_pred CCCCCCCcCCCceeEeeeCCCCCChHHHHHHHHHHHHHHHhccCCCCCccEEEE
Q 022668 225 GIYPRDYEARRFIDQKVEVVSGTTTNEYLKKLDEALEVYMFKTFSVHVFHLLFF 278 (294)
Q Consensus 225 ~~yP~~g~~~~~~nvNvpl~~g~~d~~yl~~~~~~l~~~~~~~f~P~~~~liv~ 278 (294)
..||-|. +++|..|-|||.++.+.++-...- +.+...+++ =.| |++..
T Consensus 134 ~~f~KTS-G~kGlHv~vPl~~~~~~~~~r~fa-~~lA~~l~~-~~P---~~~t~ 181 (228)
T cd04864 134 PSFVKTT-GSRGFHVVVPLDGRGDFDDVRAFA-AEAADALAK-RDP---DLLTT 181 (228)
T ss_pred ccceEcc-CCCeEEEEEEcCCCCCHHHHHHHH-HHHHHHHHH-HCc---hhhhH
Confidence 3577664 357889999999887766554444 444444443 377 66543
No 64
>cd04723 HisA_HisF Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase (HisA) and the cyclase subunit of imidazoleglycerol phosphate synthase (HisF). The ProFAR isomerase catalyzes the fourth step in histidine biosynthesis, an isomerisation of the aminoaldose moiety of ProFAR to the aminoketose of PRFAR (N-(5'-phospho-D-1'-ribulosylformimino)-5-amino-1-(5''-phospho-ribosyl)-4-imidazolecarboxamide). In bacteria and archaea, ProFAR isomerase is encoded by the HisA gene. The Imidazole glycerol phosphate synthase (IGPS) catalyzes the fifth step of histidine biosynthesis, the formation of the imidazole ring. IGPS converts N1-(5'-phosphoribulosyl)-formimino-5-aminoimidazole-4-carboxamide ribonucleotide (PRFAR) to imidazole glycerol phosphate (ImGP) and 5'-(5-aminoimidazole-4-carboxamide) ribonucleotide (AICAR). This conversion involves two tightly coupled reactions in distinct active sites of IGPS. The two catalytic domains can be fused, like in fungi and pl
Probab=22.09 E-value=1.2e+02 Score=27.07 Aligned_cols=37 Identities=24% Similarity=0.265 Sum_probs=29.4
Q ss_pred CCCccccCcHHHHHHHHHHhCCCCeEEEEecCCcCChh
Q 022668 168 GGGFCAYADISLCIHYAFVQLNISRVMIIDLDAHQGNG 205 (294)
Q Consensus 168 ~~GFC~fNnvAiAa~~~~~~~~~~RV~IiD~DvHhGnG 205 (294)
.+.||+..|..=.|+.+.++ |++++.|+|+|.--|.+
T Consensus 28 ~~~~~~~~dp~~~a~~~~~~-g~~~l~i~DLd~~~~~~ 64 (233)
T cd04723 28 TSNLCSTSDPLDVARAYKEL-GFRGLYIADLDAIMGRG 64 (233)
T ss_pred ccCcccCCCHHHHHHHHHHC-CCCEEEEEeCccccCCC
Confidence 36789888877777777766 89999999999865544
No 65
>PF06564 YhjQ: YhjQ protein; InterPro: IPR017746 The YhjQ protein is encoded immediately upstream of bacterial cellulose synthase (bcs) genes in a broad range of bacteria, including both copies of the bcs locus in Klebsiella pneumoniae, and in several species is clearly part of the bcs operon. It is identified as a probable component of the bacterial cellulose metabolic process not only by gene location, but also by partial phylogenetic profiling, or Haft-Selengut algorithm [], based on a bacterial cellulose biosynthesis genome property profile. Cellulose plays an important role in biofilm formation and structural integrity in some bacteria. Mutants in yhjQ in Escherichia coli, show altered morphology an growth, but the function of YhjQ has not yet been determined.
Probab=21.21 E-value=1e+02 Score=28.12 Aligned_cols=23 Identities=30% Similarity=0.593 Sum_probs=16.9
Q ss_pred HHHHHHHHHHhCCCCeEEEEecCC
Q 022668 177 ISLCIHYAFVQLNISRVMIIDLDA 200 (294)
Q Consensus 177 vAiAa~~~~~~~~~~RV~IiD~Dv 200 (294)
++.+.-+++++.| ++|+.||+|.
T Consensus 18 ltAnLA~aL~~~G-~~VlaID~dp 40 (243)
T PF06564_consen 18 LTANLAWALARLG-ESVLAIDLDP 40 (243)
T ss_pred HHHHHHHHHHHCC-CcEEEEeCCc
Confidence 4555556666666 7999999994
No 66
>COG0489 Mrp ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]
Probab=21.16 E-value=1.2e+02 Score=27.89 Aligned_cols=14 Identities=29% Similarity=0.536 Sum_probs=12.4
Q ss_pred CeEEEEecCCcCCh
Q 022668 191 SRVMIIDLDAHQGN 204 (294)
Q Consensus 191 ~RV~IiD~DvHhGn 204 (294)
+||++||.|.+...
T Consensus 87 ~rVlliDaD~~gps 100 (265)
T COG0489 87 KRVLLLDADLRGPS 100 (265)
T ss_pred CcEEEEeCcCCCCc
Confidence 79999999998764
No 67
>PRK13869 plasmid-partitioning protein RepA; Provisional
Probab=21.08 E-value=1.1e+02 Score=29.80 Aligned_cols=44 Identities=16% Similarity=0.137 Sum_probs=25.4
Q ss_pred hHHHHHHHHHHHCCCCCCceeecCCCCCH---HHHhccCCHHHHHHHhc
Q 022668 59 SKWGRICQFLSSEGFLDKNCIVEPLEASK---EDLLVVHSESYLKSLQS 104 (294)
Q Consensus 59 ~R~~~i~~~L~~~gl~~~~~~~~p~~a~~---e~L~~vHs~~Yi~~l~~ 104 (294)
+|+...++.+++..+.+.-. ..++..+. ++++.| ++.+|+.+..
T Consensus 24 ~~~~~~~~~~~~~~~~p~~~-k~~r~ft~~e~A~~lgv-s~~tlr~~~~ 70 (405)
T PRK13869 24 EQLSSQLQAMSEALFPPTSH-KSLRKFTSGEAARLMKI-SDSTLRKMTL 70 (405)
T ss_pred HHHHHHHHHHHHhcCCCCCC-CCCCCCCHHHHHHHhCc-CHHHHHHHHH
Confidence 46666677777665544322 23344444 345556 7888888765
No 68
>PRK13231 nitrogenase reductase-like protein; Reviewed
Probab=20.89 E-value=67 Score=28.83 Aligned_cols=20 Identities=20% Similarity=0.433 Sum_probs=13.7
Q ss_pred HHhCCCCeEEEEecCCcCChhhh
Q 022668 185 FVQLNISRVMIIDLDAHQGNGHE 207 (294)
Q Consensus 185 ~~~~~~~RV~IiD~DvHhGnGtq 207 (294)
+.+.| ||++||+|.. ||-|+
T Consensus 26 La~~G--rVLliD~Dpq-~~~~~ 45 (264)
T PRK13231 26 YSNDH--RVLVIGCDPK-ADTTR 45 (264)
T ss_pred cCCCC--EEEEEeEccC-cccch
Confidence 33456 8999999986 34343
No 69
>cd06343 PBP1_ABC_ligand_binding_like_8 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); however its ligand specificity has not been determined experimentally.
Probab=20.89 E-value=3e+02 Score=25.44 Aligned_cols=34 Identities=9% Similarity=0.177 Sum_probs=26.6
Q ss_pred HHHHHHHHHhCCCCeEEEEecCCcCChhhhhhhh
Q 022668 178 SLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFS 211 (294)
Q Consensus 178 AiAa~~~~~~~~~~RV~IiD~DvHhGnGtq~if~ 211 (294)
...++++.++.|.+||++|=-|-..|+...+.|.
T Consensus 132 ~~~~~~~~~~~g~~~v~ii~~~~~~g~~~~~~~~ 165 (362)
T cd06343 132 RIYAKYLVEEKPNAKIAVLYQNDDFGKDYLKGLK 165 (362)
T ss_pred HHHHHHHHHhCCCceEEEEEeccHHHHHHHHHHH
Confidence 4567778888788999999888888887766654
No 70
>cd06388 PBP1_iGluR_AMPA_GluR4 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR4 subunit of the AMPA receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR4 subunit of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor. The AMPA receptor is a member of the glutamate-receptor ion channels (iGluRs) which are the major mediators of excitatory synaptic transmission in the central nervous system. AMPA receptors are composed of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important role in mediating the rapid excitatory synaptic current. Furthermore, this N-terminal domain of the iGluRs has homology with LIVBP, a bacterial periplasmic binding protein, as well as with the structurally related glutamate-binding domain of the G-protein-coupled metabotropic receptors (mGluRs).
Probab=20.86 E-value=2.8e+02 Score=26.39 Aligned_cols=43 Identities=9% Similarity=0.117 Sum_probs=31.0
Q ss_pred CCc--cccCcHHHHHHHHHHhCCCCeEEEEecCCcCChhhhhhhhc
Q 022668 169 GGF--CAYADISLCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSS 212 (294)
Q Consensus 169 ~GF--C~fNnvAiAa~~~~~~~~~~RV~IiD~DvHhGnGtq~if~~ 212 (294)
..| |+-.+..-|+.-+.+.++.+||+||- |.-.|-|.-+.|.+
T Consensus 101 ~~f~i~~~p~~~~a~~~~i~~~~wk~vaiiY-d~~~~~~~lq~l~~ 145 (371)
T cd06388 101 SQFVLQLRPSLRGALLSLLDHYEWNRFVFLY-DTDRGYSILQAIME 145 (371)
T ss_pred CceEEEeChhhhhHHHHHHHhcCceEEEEEe-cCCccHHHHHHHHH
Confidence 455 77777766666677888999999997 65566676666654
No 71
>PF01656 CbiA: CobQ/CobB/MinD/ParA nucleotide binding domain; InterPro: IPR002586 This entry consists of various cobyrinic acid a,c-diamide synthases. These include CbiA and CbiP from Salmonella typhimurium []., and CobQ from Rhodobacter capsulatus []. These amidases catalyse amidations to various side chains of hydrogenobyrinic acid or cobyrinic acid a,c-diamide in the biosynthesis of cobalamin (vitamin B12) from uroporphyrinogen III. Vitamin B12 is an important cofactor and an essential nutrient for many plants and animals and is primarily produced by bacteria [].; PDB: 3K9G_A 3K9H_B 3EZ9_B 3EZF_A 3EZ2_B 3EZ6_A 3EZ7_A 1G3Q_A 1G3R_A 1DTS_A ....
Probab=20.83 E-value=1.1e+02 Score=25.35 Aligned_cols=12 Identities=42% Similarity=0.847 Sum_probs=9.5
Q ss_pred CeEEEEecCCcC
Q 022668 191 SRVMIIDLDAHQ 202 (294)
Q Consensus 191 ~RV~IiD~DvHh 202 (294)
+||++||+|.--
T Consensus 28 ~~VlliD~D~~~ 39 (195)
T PF01656_consen 28 KKVLLIDLDPQA 39 (195)
T ss_dssp S-EEEEEESTTS
T ss_pred ccccccccCccc
Confidence 799999999854
No 72
>PRK13849 putative crown gall tumor protein VirC1; Provisional
Probab=20.67 E-value=1.1e+02 Score=27.43 Aligned_cols=17 Identities=18% Similarity=0.169 Sum_probs=13.1
Q ss_pred CeEEEEecCCcCChhhhh
Q 022668 191 SRVMIIDLDAHQGNGHEK 208 (294)
Q Consensus 191 ~RV~IiD~DvHhGnGtq~ 208 (294)
+||++||.|- +|+-+..
T Consensus 31 ~~VlliD~Dp-Q~s~~~w 47 (231)
T PRK13849 31 KRVALFEADE-NRPLTRW 47 (231)
T ss_pred CcEEEEeCCC-CCCHHHH
Confidence 6999999996 6665543
No 73
>cd06331 PBP1_AmiC_like Type I periplasmic components of amide-binding protein (AmiC) and the active transport system for short-chain and urea (FmdDEF). This group includes the type I periplasmic components of amide-binding protein (AmiC) and the active transport system for short-chain and urea (FmdDEF), found in bacteria and Archaea. AmiC controls expression of the amidase operon by a ligand-triggered conformational switch. In the absence of ligand or presence of butyramide (repressor), AmiC (the ligand sensor and negative regulator) adopts an open conformation and inhibits the transcription antitermination function of AmiR by direct protein-protein interaction. In the presence of inducing ligands such as acetamide, AmiC adopts a closed conformation which disrupts a silencing AmiC-AmiR complex and the expression of amidase and other genes of the operon is induced. FmdDEF is predicted to be an ATP-dependent transporter and closely resembles the periplasmic binding protein and the two t
Probab=20.62 E-value=3.1e+02 Score=25.06 Aligned_cols=33 Identities=15% Similarity=0.061 Sum_probs=25.2
Q ss_pred HHHHHHHHhCCCCeEEEEecCCcCChhhhhhhhc
Q 022668 179 LCIHYAFVQLNISRVMIIDLDAHQGNGHEKDFSS 212 (294)
Q Consensus 179 iAa~~~~~~~~~~RV~IiD~DvHhGnGtq~if~~ 212 (294)
.+++++.+++ .+||++|.-|-=.|.+..+.|..
T Consensus 122 ~~~~~~~~~~-~~~v~il~~d~~~g~~~~~~~~~ 154 (333)
T cd06331 122 PLIPYLMEKY-GKRFYLIGSDYVWPRESNRIARA 154 (333)
T ss_pred HHHHHHHHhc-CCeEEEECCCchhHHHHHHHHHH
Confidence 3567777765 79999998888788877777653
No 74
>cd02514 GT13_GLCNAC-TI GT13_GLCNAC-TI is involved in an essential step in the synthesis of complex or hybrid-type N-linked oligosaccharides. Alpha-1,3-mannosyl-glycoprotein beta-1,2-N-acetylglucosaminyltransferase (GLCNAC-T I , GNT-I) transfers N-acetyl-D-glucosamine from UDP to high-mannose glycoprotein N-oligosaccharide, an essential step in the synthesis of complex or hybrid-type N-linked oligosaccharides. The enzyme is an integral membrane protein localized to the Golgi apparatus. The catalytic domain is located at the C-terminus. These proteins are members of the glycosy transferase family 13.
Probab=20.57 E-value=6.9e+02 Score=23.87 Aligned_cols=45 Identities=18% Similarity=0.321 Sum_probs=35.4
Q ss_pred HHHHHHHhCCCCeEEEEe--cCCcCC-----hhhhhhhhcCCCEEEEeecCC
Q 022668 180 CIHYAFVQLNISRVMIID--LDAHQG-----NGHEKDFSSDSRVYILDMFNP 224 (294)
Q Consensus 180 Aa~~~~~~~~~~RV~IiD--~DvHhG-----nGtq~if~~d~~Vl~iSiH~~ 224 (294)
|+.++..+.+.++|.||| ++++.. +.+-+....|++|..||-+..
T Consensus 88 aln~vF~~~~~~~vIILEDDl~~sPdFf~yf~~~l~~y~~D~~v~~ISa~Nd 139 (334)
T cd02514 88 ALTQTFNLFGYSFVIILEDDLDIAPDFFSYFQATLPLLEEDPSLWCISAWND 139 (334)
T ss_pred HHHHHHHhcCCCEEEEECCCCccCHhHHHHHHHHHHHHhcCCCEEEEEeecc
Confidence 666776666678999996 455666 778888899999999998864
No 75
>cd06366 PBP1_GABAb_receptor Ligand-binding domain of GABAb receptors, which are metabotropic transmembrane receptors for gamma-aminobutyric acid (GABA). Ligand-binding domain of GABAb receptors, which are metabotropic transmembrane receptors for gamma-aminobutyric acid (GABA). GABA is the major inhibitory neurotransmitter in the mammalian CNS and, like glutamate and other transmitters, acts via both ligand gated ion channels (GABAa receptors) and G-protein coupled receptors (GABAb). GABAa receptors are members of the ionotropic receptor superfamily which includes alpha-adrenergic and glycine receptors. The GABAb receptor is a member of a receptor superfamily which includes the mGlu receptors. The GABAb receptor is coupled to G alpha_i proteins, and activation causes a decrease in calcium, an increase in potassium membrane conductance, and inhibition of cAMP formation. The response is thus inhibitory and leads to hyperpolarization and decreased neurotransmitter release, for example.
Probab=20.48 E-value=4.6e+02 Score=24.05 Aligned_cols=29 Identities=24% Similarity=0.287 Sum_probs=20.5
Q ss_pred HHHhCCCCeEEEEecCCcCChhhhhhhhc
Q 022668 184 AFVQLNISRVMIIDLDAHQGNGHEKDFSS 212 (294)
Q Consensus 184 ~~~~~~~~RV~IiD~DvHhGnGtq~if~~ 212 (294)
+.++++.+||++|=-|--.|.+..+.|..
T Consensus 129 ~~~~~~~~~v~ii~~~~~~g~~~~~~~~~ 157 (350)
T cd06366 129 LLKKFGWRRVATIYEDDDYGSGGLPDLVD 157 (350)
T ss_pred HHHHCCCcEEEEEEEcCcccchhHHHHHH
Confidence 34567899999886666677777666643
No 76
>cd06345 PBP1_ABC_ligand_binding_like_10 Type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); however its ligand specificity has not been determined experimentally.
Probab=20.40 E-value=2.8e+02 Score=25.44 Aligned_cols=25 Identities=20% Similarity=0.311 Sum_probs=20.5
Q ss_pred hCCCCeEEEEecCCcCChhhhhhhh
Q 022668 187 QLNISRVMIIDLDAHQGNGHEKDFS 211 (294)
Q Consensus 187 ~~~~~RV~IiD~DvHhGnGtq~if~ 211 (294)
+.+.+||++|--|--.|....+.|.
T Consensus 141 ~~~~~~va~l~~~~~~g~~~~~~~~ 165 (344)
T cd06345 141 KHGFKTAAIVAEDAAWGKGIDAGIK 165 (344)
T ss_pred cCCCceEEEEecCchhhhHHHHHHH
Confidence 4688999999888888888877764
Done!