Query 021082
Match_columns 317
No_of_seqs 147 out of 1194
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 07:27:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021082.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021082hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK10353 3-methyl-adenine DNA 100.0 3E-87 6.5E-92 599.9 19.1 183 120-304 1-183 (187)
2 TIGR00624 tag DNA-3-methyladen 100.0 3.2E-85 7E-90 583.3 18.8 179 121-303 1-179 (179)
3 PF03352 Adenine_glyco: Methyl 100.0 1.5E-83 3.3E-88 572.6 15.8 179 125-305 1-179 (179)
4 COG2818 Tag 3-methyladenine DN 100.0 2.8E-83 6.1E-88 572.6 16.6 186 120-306 1-186 (188)
5 TIGR03252 uncharacterized HhH- 95.7 0.23 5E-06 45.3 12.2 117 152-291 18-136 (177)
6 cd00056 ENDO3c endonuclease II 95.7 0.099 2.1E-06 44.5 9.4 104 153-291 1-104 (158)
7 PRK13913 3-methyladenine DNA g 95.0 0.35 7.6E-06 45.1 11.4 104 153-288 31-139 (218)
8 TIGR01083 nth endonuclease III 94.7 0.43 9.4E-06 42.7 10.9 101 152-290 26-126 (191)
9 smart00478 ENDO3c endonuclease 94.4 0.43 9.3E-06 40.3 9.6 88 165-290 5-92 (149)
10 PRK10702 endonuclease III; Pro 92.9 1.1 2.5E-05 41.3 10.3 69 152-224 29-97 (211)
11 PRK10880 adenine DNA glycosyla 89.0 4.4 9.4E-05 40.4 10.9 68 152-224 30-97 (350)
12 TIGR01084 mutY A/G-specific ad 88.8 4 8.7E-05 39.2 10.2 68 152-224 26-93 (275)
13 COG0177 Nth Predicted EndoIII- 87.6 4.3 9.3E-05 38.1 9.3 102 151-291 28-130 (211)
14 PF00730 HhH-GPD: HhH-GPD supe 84.6 6.5 0.00014 31.3 7.8 63 160-224 4-66 (108)
15 PF10023 DUF2265: Predicted am 76.4 9.1 0.0002 38.3 7.2 100 195-305 33-161 (337)
16 COG0122 AlkA 3-methyladenine D 72.4 54 0.0012 31.8 11.2 109 150-291 103-220 (285)
17 PF02142 MGS: MGS-like domain 69.5 4.7 0.0001 32.0 2.8 30 264-293 3-32 (95)
18 PRK01229 N-glycosylase/DNA lya 64.5 46 0.00099 31.1 8.6 107 148-292 33-141 (208)
19 COG1393 ArsC Arsenate reductas 61.4 8.1 0.00018 32.7 2.9 61 142-209 33-93 (117)
20 cd00166 SAM Sterile alpha moti 57.8 28 0.00062 24.3 4.8 43 175-219 17-61 (63)
21 PF00536 SAM_1: SAM domain (St 48.9 34 0.00074 24.8 4.1 43 175-219 18-62 (64)
22 PF13276 HTH_21: HTH-like doma 48.7 22 0.00048 25.8 3.1 31 263-293 23-53 (60)
23 PRK10308 3-methyl-adenine DNA 47.5 1.8E+02 0.0038 28.1 9.9 119 141-294 102-232 (283)
24 COG2231 Uncharacterized protei 46.7 1.7E+02 0.0036 27.9 9.2 83 132-219 14-97 (215)
25 cd00532 MGS-like MGS-like doma 45.1 25 0.00055 28.7 3.2 32 261-292 12-43 (112)
26 smart00851 MGS MGS-like domain 44.9 23 0.00051 27.6 2.9 29 264-292 3-31 (90)
27 PF10911 DUF2717: Protein of u 41.9 14 0.00031 29.9 1.2 42 244-296 3-44 (77)
28 cd01424 MGS_CPS_II Methylglyox 39.3 37 0.0008 27.3 3.3 32 261-292 13-44 (110)
29 PHA02517 putative transposase 39.3 34 0.00073 31.6 3.5 31 263-294 48-78 (277)
30 cd04883 ACT_AcuB C-terminal AC 37.5 21 0.00045 25.9 1.5 19 262-280 53-71 (72)
31 PF12401 DUF3662: Protein of u 37.4 18 0.00039 30.5 1.2 25 260-284 76-100 (116)
32 PF00289 CPSase_L_chain: Carba 37.2 41 0.00089 28.0 3.4 21 262-282 87-107 (110)
33 PF11970 Git3_C: G protein-cou 37.1 18 0.00038 28.7 1.1 36 277-316 41-76 (76)
34 TIGR01529 argR_whole arginine 36.5 41 0.00089 29.4 3.4 31 263-294 19-49 (146)
35 cd01422 MGS Methylglyoxal synt 33.6 46 0.00099 27.7 3.1 32 261-292 12-46 (115)
36 cd07153 Fur_like Ferric uptake 29.8 65 0.0014 25.8 3.3 32 262-294 18-52 (116)
37 cd03036 ArsC_like Arsenate Red 28.3 52 0.0011 26.9 2.5 54 153-209 38-93 (111)
38 cd01423 MGS_CPS_I_III Methylgl 27.9 66 0.0014 26.2 3.1 32 261-292 13-44 (116)
39 cd00956 Transaldolase_FSA Tran 27.4 30 0.00064 31.9 1.1 34 255-290 83-116 (211)
40 PF02173 pKID: pKID domain; I 27.3 25 0.00055 25.3 0.5 17 168-184 13-29 (41)
41 PF13495 Phage_int_SAM_4: Phag 25.8 2.8E+02 0.0061 20.5 6.7 72 152-225 1-72 (85)
42 PF05075 DUF684: Protein of un 25.6 1.2E+02 0.0025 30.1 4.9 40 149-188 115-161 (345)
43 cd01421 IMPCH Inosine monophos 25.2 65 0.0014 29.9 2.8 31 262-292 12-42 (187)
44 COG4081 Uncharacterized protei 23.9 58 0.0013 29.1 2.2 25 254-278 12-36 (148)
45 PF07647 SAM_2: SAM domain (St 23.6 1.3E+02 0.0029 21.7 3.7 43 175-219 19-64 (66)
46 KOG0898 40S ribosomal protein 23.1 1E+02 0.0022 27.7 3.5 32 171-202 13-45 (152)
47 cd00052 EH Eps15 homology doma 22.8 39 0.00083 23.8 0.7 30 177-206 1-30 (67)
48 PF01475 FUR: Ferric uptake re 22.7 1.1E+02 0.0024 24.8 3.5 33 262-295 25-60 (120)
49 PF09399 SARS_lipid_bind: SARS 22.6 31 0.00067 28.4 0.2 19 34-53 39-57 (97)
50 PRK09462 fur ferric uptake reg 22.4 1E+02 0.0022 26.3 3.4 31 263-294 36-69 (148)
51 smart00454 SAM Sterile alpha m 20.7 3E+02 0.0066 19.1 5.2 43 176-220 20-65 (68)
52 PF12415 rpo132: Poxvirus DNA 20.6 91 0.002 21.5 2.1 14 212-225 18-31 (33)
53 KOG1921 Endonuclease III [Repl 20.5 4.2E+02 0.0092 26.2 7.4 88 183-306 108-196 (286)
No 1
>PRK10353 3-methyl-adenine DNA glycosylase I; Provisional
Probab=100.00 E-value=3e-87 Score=599.85 Aligned_cols=183 Identities=36% Similarity=0.781 Sum_probs=179.7
Q ss_pred CccccCccCCCChhHhhhhhhCCCccccChHHHHHHHHHHHhhccccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHH
Q 021082 120 LKRCNWITKNSDKVYVAFHDECWGVPVYDDNQLFELLALSGMLMDYNWTEILKRKELFREAFGGFDPKSVAKMGEKEILE 199 (317)
Q Consensus 120 ~~RC~Wa~~~~dply~~YHD~EWG~Pv~DDr~LFE~L~LE~fQAGLSW~tILkKR~~fr~AF~~FD~~~VA~~~eedie~ 199 (317)
+.||.|++ +||+|++|||+|||+|+|||+.|||+||||+|||||||.|||+||++||+||+||||++||+|+|++|++
T Consensus 1 m~rC~W~~--~~~l~~~YHD~eWG~P~~dd~~LFE~L~Le~~QAGLSW~tIL~Kre~fr~aF~~Fd~~~VA~~~e~die~ 78 (187)
T PRK10353 1 MERCGWVS--QDPLYIAYHDNEWGVPETDSKKLFEMICLEGQQAGLSWITVLKKRENYRACFHQFDPVKVAAMQEEDVER 78 (187)
T ss_pred CCCCCCCC--CChHHHHhhhccCCCcCCCcHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHcCCCHHHHhCCCHHHHHH
Confidence 36999996 5899999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhCCCcchhchhhHHHHHHhHHHHHHHHHhcCCHHHhccccCCCccccCCCCCCCCCCCCCHHHHHHHHHHHHcCCcccC
Q 021082 200 ISSNTAIMLAECRVRCIVDNAKCIVKILNEFGSFSSFMWGYVNFKPMINKFRYPRNVPLRSPKAEAISRDLLKRGFRLVG 279 (317)
Q Consensus 200 L~~d~~IIRnr~KI~AVi~NAr~il~i~~E~GSF~~ylWsfv~~kpi~n~~~~~~~vP~~t~lS~~lsKdLKkrGFkFVG 279 (317)
||+|++|||||+||+|||+||+++++|++|+|||++|||+||+++||+|++.+..++|++|++|++|||+||||||+|||
T Consensus 79 Ll~d~~IIRnr~KI~Avi~NA~~~l~i~~e~gSf~~ylW~fv~~~p~~~~~~~~~~~P~~t~~S~~lskdLKkrGFkFvG 158 (187)
T PRK10353 79 LVQDAGIIRHRGKIQAIIGNARAYLQMEQNGEPFADFVWSFVNHQPQVTQATTLSEIPTSTPASDALSKALKKRGFKFVG 158 (187)
T ss_pred HhcCchhHHhHHHHHHHHHHHHHHHHHHHhcCCHHHHHhhccCCCcccCCccchhcCCCCCHHHHHHHHHHHHcCCcccC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhHHHHHHHhccccccccccccch
Q 021082 280 PVIVYSFMQAAGLTIDHLVDCFRYS 304 (317)
Q Consensus 280 PttvysFMQAvG~vnDHl~~C~r~~ 304 (317)
||||||||||+||||||+++|+++.
T Consensus 159 pt~~ysfmqA~G~vndH~~~C~~~~ 183 (187)
T PRK10353 159 TTICYSFMQACGLVNDHVVGCCCHP 183 (187)
T ss_pred cHHHHHHHHHHCCccccccCccccC
Confidence 9999999999999999999999884
No 2
>TIGR00624 tag DNA-3-methyladenine glycosylase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=100.00 E-value=3.2e-85 Score=583.34 Aligned_cols=179 Identities=34% Similarity=0.767 Sum_probs=175.6
Q ss_pred ccccCccCCCChhHhhhhhhCCCccccChHHHHHHHHHHHhhccccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHh
Q 021082 121 KRCNWITKNSDKVYVAFHDECWGVPVYDDNQLFELLALSGMLMDYNWTEILKRKELFREAFGGFDPKSVAKMGEKEILEI 200 (317)
Q Consensus 121 ~RC~Wa~~~~dply~~YHD~EWG~Pv~DDr~LFE~L~LE~fQAGLSW~tILkKR~~fr~AF~~FD~~~VA~~~eedie~L 200 (317)
.||.|++ +||+|++|||+|||+|+|||+.|||+||||+|||||||.|||+||++||+||+||||++||+|+|++|++|
T Consensus 1 ~rC~W~~--~~~l~~~YHD~eWG~p~~dd~~LFE~L~Le~fQAGLSW~tIL~Kr~~fr~aF~~Fd~~~VA~~~e~~ie~L 78 (179)
T TIGR00624 1 VRCGWAS--VDPLYRAYHDNEWGVPLRDSVALFERMSLEGFQAGLSWITVLRKRENYRRAFSGFDIVKVARMTDADVERL 78 (179)
T ss_pred CCCCCcC--CChHHHHhhhccCCCcCcCCHHHHHHHHHHHHhCcCCHHHHHHhHHHHHHHHcCCCHHHHhCCCHHHHHHH
Confidence 4899996 48999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hCCCcchhchhhHHHHHHhHHHHHHHHHhcCCHHHhccccCCCccccCCCCCCCCCCCCCHHHHHHHHHHHHcCCcccCh
Q 021082 201 SSNTAIMLAECRVRCIVDNAKCIVKILNEFGSFSSFMWGYVNFKPMINKFRYPRNVPLRSPKAEAISRDLLKRGFRLVGP 280 (317)
Q Consensus 201 ~~d~~IIRnr~KI~AVi~NAr~il~i~~E~GSF~~ylWsfv~~kpi~n~~~~~~~vP~~t~lS~~lsKdLKkrGFkFVGP 280 (317)
|+|++|||||+||+|||+||+++++|++| ||++|||+||+++||+|++....++|++|++|++|||+||||||+||||
T Consensus 79 ~~d~~IIRnr~KI~Avi~NA~~~l~i~~e--sf~~ylW~fv~~~Pi~~~~~~~~~~p~~t~~S~~lskdLKkrGfkFvGp 156 (179)
T TIGR00624 79 LQDDGIIRNRGKIEATIANARAALQLEQN--DLVEFLWSFVNHQPQPRQRPTDSEIPSSTPESKAMSKELKKRGFRFVGP 156 (179)
T ss_pred hcCccchhhHHHHHHHHHHHHHHHHHHHc--cHHHHHHhccCCCCccCCccccccCCCCCHHHHHHHHHHHHcCCeecCh
Confidence 99999999999999999999999999887 9999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHHhccccccccccccc
Q 021082 281 VIVYSFMQAAGLTIDHLVDCFRY 303 (317)
Q Consensus 281 ttvysFMQAvG~vnDHl~~C~r~ 303 (317)
|||||||||+||||||+++|+++
T Consensus 157 t~~ysfmqA~G~vndH~~~C~~~ 179 (179)
T TIGR00624 157 TICYALMQATGMVDDHIQGCWVY 179 (179)
T ss_pred HHHHHHHHHHCCccccccCCcCC
Confidence 99999999999999999999975
No 3
>PF03352 Adenine_glyco: Methyladenine glycosylase; InterPro: IPR005019 This family of methyladenine glycosylases includes DNA-3-methyladenine glycosylase I (3.2.2.20 from EC) which acts as a base excision repair enzyme by severing the glycosylic bond of numerous damaged bases. The enzyme is constitutively expressed and is specific for the alkylated 3-methyladenine DNA.; GO: 0008725 DNA-3-methyladenine glycosylase I activity, 0006284 base-excision repair; PDB: 2OFI_A 2OFK_A 2JG6_A 4AIA_E 4AI5_C 4AI4_A 1LMZ_A 1P7M_A 1NKU_A.
Probab=100.00 E-value=1.5e-83 Score=572.58 Aligned_cols=179 Identities=52% Similarity=0.997 Sum_probs=154.1
Q ss_pred CccCCCChhHhhhhhhCCCccccChHHHHHHHHHHHhhccccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhhCCC
Q 021082 125 WITKNSDKVYVAFHDECWGVPVYDDNQLFELLALSGMLMDYNWTEILKRKELFREAFGGFDPKSVAKMGEKEILEISSNT 204 (317)
Q Consensus 125 Wa~~~~dply~~YHD~EWG~Pv~DDr~LFE~L~LE~fQAGLSW~tILkKR~~fr~AF~~FD~~~VA~~~eedie~L~~d~ 204 (317)
|+. ++|+|++|||+|||+|+|||++|||+||||+|||||||.|||+||++||+||+||||++||+|+|++|++||+|+
T Consensus 1 W~~--~~~~~~~YHD~eWG~P~~dD~~LFe~L~Le~fQaGLsW~~Il~Kr~~~r~aF~~Fd~~~vA~~~e~~ie~l~~d~ 78 (179)
T PF03352_consen 1 WAN--SDPLYRAYHDEEWGRPVHDDRKLFEMLTLEGFQAGLSWSTILKKREAFREAFAGFDPEKVAKMDEEDIERLMQDP 78 (179)
T ss_dssp TTT--SSHHHHHHHHHTTTSS---HHHHHHHHHHHHHTTTS-HHHHHHTHHHHHHHTGGGHHHHHHT--HHHHHHHTTST
T ss_pred CCC--CChHHHHHhcccCCCcccCHHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHCCCHHHHHcCCHHHHHHHhcCc
Confidence 885 489999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cchhchhhHHHHHHhHHHHHHHHHhcCCHHHhccccCCCccccCCCCCCCCCCCCCHHHHHHHHHHHHcCCcccChhhHH
Q 021082 205 AIMLAECRVRCIVDNAKCIVKILNEFGSFSSFMWGYVNFKPMINKFRYPRNVPLRSPKAEAISRDLLKRGFRLVGPVIVY 284 (317)
Q Consensus 205 ~IIRnr~KI~AVi~NAr~il~i~~E~GSF~~ylWsfv~~kpi~n~~~~~~~vP~~t~lS~~lsKdLKkrGFkFVGPttvy 284 (317)
+|||||+||+|||+||+++++|++|||||++|||+||+++||+|.+....++|++|++|++|||+|||+||+||||||||
T Consensus 79 ~iIRnr~KI~Avi~NA~~~l~i~~e~gsF~~ylw~f~~~~~i~~~~~~~~~~p~~t~~s~~isk~lkk~GF~FvGpt~vy 158 (179)
T PF03352_consen 79 GIIRNRRKIRAVINNARAILKIQEEFGSFSDYLWSFVNGKPIVNHWRSPEDVPASTPLSEAISKDLKKRGFKFVGPTTVY 158 (179)
T ss_dssp TSS--HHHHHHHHHHHHHHHHHHHTTS-HHHHHHHCTTTS-EE---SSGGGS-S--HHHHHHHHHHHHTT--S--HHHHH
T ss_pred chhhhHHHHHHHHHHHHHHHHHHHhcCCHHHHHHhcCCCcCccccccccccCcCccHHHHHHHHHHHhCcceeECHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhccccccccccccchh
Q 021082 285 SFMQAAGLTIDHLVDCFRYSE 305 (317)
Q Consensus 285 sFMQAvG~vnDHl~~C~r~~~ 305 (317)
|||||+||||||+++|++|.+
T Consensus 159 sflqA~G~vndH~~~C~~~~~ 179 (179)
T PF03352_consen 159 SFLQAIGMVNDHLVDCFRHQE 179 (179)
T ss_dssp HHHHHTTSEE-SSTTSTTS--
T ss_pred HHHHHhCCccccccCccccCC
Confidence 999999999999999999864
No 4
>COG2818 Tag 3-methyladenine DNA glycosylase [DNA replication, recombination, and repair]
Probab=100.00 E-value=2.8e-83 Score=572.56 Aligned_cols=186 Identities=41% Similarity=0.819 Sum_probs=181.4
Q ss_pred CccccCccCCCChhHhhhhhhCCCccccChHHHHHHHHHHHhhccccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHH
Q 021082 120 LKRCNWITKNSDKVYVAFHDECWGVPVYDDNQLFELLALSGMLMDYNWTEILKRKELFREAFGGFDPKSVAKMGEKEILE 199 (317)
Q Consensus 120 ~~RC~Wa~~~~dply~~YHD~EWG~Pv~DDr~LFE~L~LE~fQAGLSW~tILkKR~~fr~AF~~FD~~~VA~~~eedie~ 199 (317)
+.||.|+.. .||+|.+|||+|||+|++||+.|||+||||+|||||||.|||+||++||+||++|||++||.|+|+||++
T Consensus 1 ~~rC~w~~~-~~ply~~YHD~eWG~p~~Dd~~LFE~l~Le~fQAGLSW~tVL~KRe~freaF~~Fd~~kVA~~~~~dver 79 (188)
T COG2818 1 MNRCAWAGG-LDPLYLAYHDTEWGVPLHDDQRLFELLCLEGFQAGLSWLTVLKKREAFREAFHGFDPEKVAAMTEEDVER 79 (188)
T ss_pred CCcccccCC-CCchhhcccccccCCCCCChHHHHHHHHHHHHhccchHHHHHHhHHHHHHHHhcCCHHHHHcCCHHHHHH
Confidence 469999974 4899999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhCCCcchhchhhHHHHHHhHHHHHHHHHhcCCHHHhccccCCCccccCCCCCCCCCCCCCHHHHHHHHHHHHcCCcccC
Q 021082 200 ISSNTAIMLAECRVRCIVDNAKCIVKILNEFGSFSSFMWGYVNFKPMINKFRYPRNVPLRSPKAEAISRDLLKRGFRLVG 279 (317)
Q Consensus 200 L~~d~~IIRnr~KI~AVi~NAr~il~i~~E~GSF~~ylWsfv~~kpi~n~~~~~~~vP~~t~lS~~lsKdLKkrGFkFVG 279 (317)
||+|++|||||+||+|||+|||++++|++|||||++|||+||+++|+++++.+..++|+.|++|++|||+||||||+|||
T Consensus 80 Ll~d~gIIR~r~KI~A~i~NA~~~l~l~~e~Gsf~~flWsf~~~~~~~~~~~~~~~~pa~t~~S~~mskaLKkrGf~fvG 159 (188)
T COG2818 80 LLADAGIIRNRGKIKATINNARAVLELQKEFGSFSEFLWSFVGGKPSRNQVNDGSEVPASTELSDAMSKALKKRGFKFVG 159 (188)
T ss_pred HHhCcchhhhHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHhcCCCcccccccchhhccccchhHHHHHHHHHHccCeecC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhHHHHHHHhccccccccccccchhh
Q 021082 280 PVIVYSFMQAAGLTIDHLVDCFRYSEC 306 (317)
Q Consensus 280 PttvysFMQAvG~vnDHl~~C~r~~~~ 306 (317)
|||||+||||+|+||||+.+|+++...
T Consensus 160 pTt~yafmqA~G~vndH~~~C~~~~~~ 186 (188)
T COG2818 160 PTTVYAFMQATGLVNDHAEGCPCRREI 186 (188)
T ss_pred cHHHHHHHHHHcchHHHHhcCCCcccc
Confidence 999999999999999999999988653
No 5
>TIGR03252 uncharacterized HhH-GPD family protein. This model describes a small, well-conserved bacterial protein family. Its sequence largely consists of a domain, HhH-GPD, found in a variety of related base excision DNA repair enzymes (see pfam00730).
Probab=95.68 E-value=0.23 Score=45.30 Aligned_cols=117 Identities=15% Similarity=0.211 Sum_probs=80.5
Q ss_pred HHHHHHHHHhhccccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhhCC-Ccchh-chhhHHHHHHhHHHHHHHHHh
Q 021082 152 LFELLALSGMLMDYNWTEILKRKELFREAFGGFDPKSVAKMGEKEILEISSN-TAIML-AECRVRCIVDNAKCIVKILNE 229 (317)
Q Consensus 152 LFE~L~LE~fQAGLSW~tILkKR~~fr~AF~~FD~~~VA~~~eedie~L~~d-~~IIR-nr~KI~AVi~NAr~il~i~~E 229 (317)
-||+|+-.+.-+--+|..|.+=-....+.+...||+.++.++.++|++++.. |++.+ .+.|=+-+.+=|+.++ ++
T Consensus 18 pFelLVa~ILSQqTtd~nv~kA~~~L~~~~g~~tp~~La~a~~eeL~~lI~~~pal~Gfy~~KAk~Lk~~a~~ii---e~ 94 (177)
T TIGR03252 18 PFALLTGMLLDQQVPMERAFAGPHKIARRMGSLDAEDIAKYDPQAFVALFSERPAVHRFPGSMAKRVQALAQYVV---DT 94 (177)
T ss_pred hHHHHHHHHHhccCcHHHHHHHHHHHHHHhCCCCHHHHHcCCHHHHHHHHhcCccccCchHHHHHHHHHHHHHHH---HH
Confidence 3899999999999999999877777754444489999999999999999975 45443 2345555555555553 45
Q ss_pred cCCHHHhccccCCCccccCCCCCCCCCCCCCHHHHHHHHHHHHcCCcccChhhHHHHHHHhc
Q 021082 230 FGSFSSFMWGYVNFKPMINKFRYPRNVPLRSPKAEAISRDLLKRGFRLVGPVIVYSFMQAAG 291 (317)
Q Consensus 230 ~GSF~~ylWsfv~~kpi~n~~~~~~~vP~~t~lS~~lsKdLKkrGFkFVGPttvysFMQAvG 291 (317)
||+=-+-||... +| ....+-++|.+ ++-|||.|+--||.-+|
T Consensus 95 y~G~v~~L~~~~--------------~p----~t~~lre~Ll~--LpGVG~KTAnvVL~~l~ 136 (177)
T TIGR03252 95 YDGDATAVWTEG--------------DP----DGKELLRRLKA--LPGFGKQKAKIFLALLG 136 (177)
T ss_pred hCCChhhhhccc--------------CC----CcHHHHHHHHc--CCCCCHHHHHHHHHHHH
Confidence 554323344320 11 12233456665 79999999999988776
No 6
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=95.68 E-value=0.099 Score=44.51 Aligned_cols=104 Identities=21% Similarity=0.248 Sum_probs=80.1
Q ss_pred HHHHHHHHhhccccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhhCCCcchhchhhHHHHHHhHHHHHHHHHhcCC
Q 021082 153 FELLALSGMLMDYNWTEILKRKELFREAFGGFDPKSVAKMGEKEILEISSNTAIMLAECRVRCIVDNAKCIVKILNEFGS 232 (317)
Q Consensus 153 FE~L~LE~fQAGLSW~tILkKR~~fr~AF~~FD~~~VA~~~eedie~L~~d~~IIRnr~KI~AVi~NAr~il~i~~E~GS 232 (317)
||.|+-.++..-.+|..+.+-...|.+.|. .+|+.|+..+++++.++...-+ .+.|.+.++.=|+.+.+ .+++
T Consensus 1 ~e~Li~~il~q~~s~~~a~~~~~~l~~~~g-pt~~~l~~~~~~~l~~~~~~~G---~~~kA~~i~~~a~~~~~---~~~~ 73 (158)
T cd00056 1 FEVLVSEILSQQTTDKAVNKAYERLFERYG-PTPEALAAADEEELRELIRSLG---YRRKAKYLKELARAIVE---GFGG 73 (158)
T ss_pred CHHHHHHHHHhcccHHHHHHHHHHHHHHhC-CCHHHHHCCCHHHHHHHHHhcC---hHHHHHHHHHHHHHHHH---HcCC
Confidence 688888888888999999999999998885 7999999999999999877766 46799999888888753 4443
Q ss_pred HHHhccccCCCccccCCCCCCCCCCCCCHHHHHHHHHHHHcCCcccChhhHHHHHHHhc
Q 021082 233 FSSFMWGYVNFKPMINKFRYPRNVPLRSPKAEAISRDLLKRGFRLVGPVIVYSFMQAAG 291 (317)
Q Consensus 233 F~~ylWsfv~~kpi~n~~~~~~~vP~~t~lS~~lsKdLKkrGFkFVGPttvysFMQAvG 291 (317)
+.. + . +.+-+.|. .++-|||-|+-.+|.-+.
T Consensus 74 ~~~------~---------------~-----~~~~~~L~--~l~GIG~~tA~~~l~~~~ 104 (158)
T cd00056 74 LVL------D---------------D-----PDAREELL--ALPGVGRKTANVVLLFAL 104 (158)
T ss_pred ccC------C---------------C-----cccHHHHH--cCCCCCHHHHHHHHHHHC
Confidence 332 0 0 12344555 479999999998887553
No 7
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=94.98 E-value=0.35 Score=45.14 Aligned_cols=104 Identities=19% Similarity=0.260 Sum_probs=76.6
Q ss_pred HHHHHHHHhhccccHHHHHHhHHHHHHHhc-----CCCHHHHhcCCHHHHHHhhCCCcchhchhhHHHHHHhHHHHHHHH
Q 021082 153 FELLALSGMLMDYNWTEILKRKELFREAFG-----GFDPKSVAKMGEKEILEISSNTAIMLAECRVRCIVDNAKCIVKIL 227 (317)
Q Consensus 153 FE~L~LE~fQAGLSW~tILkKR~~fr~AF~-----~FD~~~VA~~~eedie~L~~d~~IIRnr~KI~AVi~NAr~il~i~ 227 (317)
||.|+-.+.-.--+|..|.+--+.+++++. .-+|+.|+.+++++|++++.-.|.-| .|.+.+.+=|+.+.
T Consensus 31 fevLV~aILsQqT~~~~v~~a~~~L~~~~~~~~~~~~t~e~L~~a~~eeL~~~Irp~Gf~~--~KA~~Lk~la~~i~--- 105 (218)
T PRK13913 31 FEALLGAVLTQNTKFEAVEKSLENLKNAFILENDDEINLKKIAYIEFSKLAECVRPSGFYN--QKAKRLIDLSENIL--- 105 (218)
T ss_pred HHHHHHHHHHhhhhHHHHHHHHHHHHHhcccccccCCCHHHHHcCCHHHHHHHHHhcCCHH--HHHHHHHHHHHHHH---
Confidence 888888877777889999888777777663 23899999999999999999988766 57777777777774
Q ss_pred HhcCCHHHhccccCCCccccCCCCCCCCCCCCCHHHHHHHHHHHHcCCcccChhhHHHHHH
Q 021082 228 NEFGSFSSFMWGYVNFKPMINKFRYPRNVPLRSPKAEAISRDLLKRGFRLVGPVIVYSFMQ 288 (317)
Q Consensus 228 ~E~GSF~~ylWsfv~~kpi~n~~~~~~~vP~~t~lS~~lsKdLKkrGFkFVGPttvysFMQ 288 (317)
+++|+++.+. . | + .-++|.+ .+-|||-|+-++|-
T Consensus 106 ~~~g~~~~~~----~--------------~---~----~re~Ll~--l~GIG~kTAd~iLl 139 (218)
T PRK13913 106 KDFGSFENFK----Q--------------E---V----TREWLLD--QKGIGKESADAILC 139 (218)
T ss_pred HHcCCchhcc----C--------------c---h----HHHHHHc--CCCccHHHHHHHHH
Confidence 4667765321 0 0 0 1134544 78889988888776
No 8
>TIGR01083 nth endonuclease III. This equivalog model identifes nth members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=94.73 E-value=0.43 Score=42.73 Aligned_cols=101 Identities=21% Similarity=0.308 Sum_probs=76.0
Q ss_pred HHHHHHHHHhhccccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhhCCCcchhchhhHHHHHHhHHHHHHHHHhcC
Q 021082 152 LFELLALSGMLMDYNWTEILKRKELFREAFGGFDPKSVAKMGEKEILEISSNTAIMLAECRVRCIVDNAKCIVKILNEFG 231 (317)
Q Consensus 152 LFE~L~LE~fQAGLSW~tILkKR~~fr~AF~~FD~~~VA~~~eedie~L~~d~~IIRnr~KI~AVi~NAr~il~i~~E~G 231 (317)
-||.|+-++.-.--+|..+.+-...+.+.|- +|+.|+..+++++.+++.--|.-+ .|.+.+.+=|+.+.+ ++|
T Consensus 26 pf~~Li~~ILsqqt~~~~~~~~~~~l~~~~p--t~~~l~~~~~~~L~~~ir~~G~~~--~Ka~~i~~~a~~i~~---~~~ 98 (191)
T TIGR01083 26 PFELLVATILSAQATDKSVNKATKKLFEVYP--TPQALAQAGLEELEEYIKSIGLYR--NKAKNIIALCRILVE---RYG 98 (191)
T ss_pred HHHHHHHHHHHhhCcHHHHHHHHHHHHHHCC--CHHHHHcCCHHHHHHHHHhcCChH--HHHHHHHHHHHHHHH---HcC
Confidence 4899999999889999999988777777664 899999999999999888777665 577778777777653 333
Q ss_pred CHHHhccccCCCccccCCCCCCCCCCCCCHHHHHHHHHHHHcCCcccChhhHHHHHHHh
Q 021082 232 SFSSFMWGYVNFKPMINKFRYPRNVPLRSPKAEAISRDLLKRGFRLVGPVIVYSFMQAA 290 (317)
Q Consensus 232 SF~~ylWsfv~~kpi~n~~~~~~~vP~~t~lS~~lsKdLKkrGFkFVGPttvysFMQAv 290 (317)
+ ++|. .-+.|.+ ++-|||.|+..+|.-+
T Consensus 99 ~----------------------~~~~-------~~~~L~~--l~GIG~ktA~~ill~~ 126 (191)
T TIGR01083 99 G----------------------EVPE-------DREELVK--LPGVGRKTANVVLNVA 126 (191)
T ss_pred C----------------------CCch-------HHHHHHh--CCCCcHHHHHHHHHHH
Confidence 1 0111 1234555 7899999998887543
No 9
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=94.40 E-value=0.43 Score=40.31 Aligned_cols=88 Identities=24% Similarity=0.354 Sum_probs=65.2
Q ss_pred ccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhhCCCcchhchhhHHHHHHhHHHHHHHHHhcCCHHHhccccCCCc
Q 021082 165 YNWTEILKRKELFREAFGGFDPKSVAKMGEKEILEISSNTAIMLAECRVRCIVDNAKCIVKILNEFGSFSSFMWGYVNFK 244 (317)
Q Consensus 165 LSW~tILkKR~~fr~AF~~FD~~~VA~~~eedie~L~~d~~IIRnr~KI~AVi~NAr~il~i~~E~GSF~~ylWsfv~~k 244 (317)
.+|..+.+--..|.+.|- +|+.++..++++|.+++..-+ -.+.|.+.|++.|+.+.+ ++++
T Consensus 5 ~~~~~a~~~~~~l~~~~~--~~~~l~~~~~~eL~~~l~~~g--~~~~ka~~i~~~a~~~~~---~~~~------------ 65 (149)
T smart00478 5 TSDEAVNKATERLFEKFP--TPEDLAAADEEELEELIRPLG--FYRRKAKYLIELARILVE---EYGG------------ 65 (149)
T ss_pred ccHHHHHHHHHHHHHHCC--CHHHHHCCCHHHHHHHHHHcC--ChHHHHHHHHHHHHHHHH---HHCC------------
Confidence 467888888888888887 799999999999998887645 345699999999988754 2221
Q ss_pred cccCCCCCCCCCCCCCHHHHHHHHHHHHcCCcccChhhHHHHHHHh
Q 021082 245 PMINKFRYPRNVPLRSPKAEAISRDLLKRGFRLVGPVIVYSFMQAA 290 (317)
Q Consensus 245 pi~n~~~~~~~vP~~t~lS~~lsKdLKkrGFkFVGPttvysFMQAv 290 (317)
++| ...+.|.+ ++-|||.|+-.||.-+
T Consensus 66 ----------~~~-------~~~~~L~~--l~GIG~~tA~~~l~~~ 92 (149)
T smart00478 66 ----------EVP-------DDREELLK--LPGVGRKTANAVLSFA 92 (149)
T ss_pred ----------Ccc-------HHHHHHHc--CCCCcHHHHHHHHHHH
Confidence 011 12355654 8999999998887765
No 10
>PRK10702 endonuclease III; Provisional
Probab=92.90 E-value=1.1 Score=41.29 Aligned_cols=69 Identities=10% Similarity=0.151 Sum_probs=56.4
Q ss_pred HHHHHHHHHhhccccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhhCCCcchhchhhHHHHHHhHHHHH
Q 021082 152 LFELLALSGMLMDYNWTEILKRKELFREAFGGFDPKSVAKMGEKEILEISSNTAIMLAECRVRCIVDNAKCIV 224 (317)
Q Consensus 152 LFE~L~LE~fQAGLSW~tILkKR~~fr~AF~~FD~~~VA~~~eedie~L~~d~~IIRnr~KI~AVi~NAr~il 224 (317)
-||.|+-++.-+--+|..|.+--+.+.+.| .+|+.++..++++|++++.--|.-+. |-+.+++.|+.+.
T Consensus 29 p~e~lvs~iLsq~t~~~~v~~~~~~L~~~~--pt~e~l~~a~~~~l~~~i~~~G~y~~--kA~~l~~~a~~i~ 97 (211)
T PRK10702 29 PFELLIAVLLSAQATDVSVNKATAKLYPVA--NTPAAMLELGVEGVKTYIKTIGLYNS--KAENVIKTCRILL 97 (211)
T ss_pred hHHHHHHHHHHhhcCHHHHHHHHHHHHHHc--CCHHHHHCCCHHHHHHHHHHcCCHHH--HHHHHHHHHHHHH
Confidence 499999999988899999988888887665 47899999999999999887777665 4556677777764
No 11
>PRK10880 adenine DNA glycosylase; Provisional
Probab=89.03 E-value=4.4 Score=40.44 Aligned_cols=68 Identities=16% Similarity=0.175 Sum_probs=58.0
Q ss_pred HHHHHHHHHhhccccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhhCCCcchhchhhHHHHHHhHHHHH
Q 021082 152 LFELLALSGMLMDYNWTEILKRKELFREAFGGFDPKSVAKMGEKEILEISSNTAIMLAECRVRCIVDNAKCIV 224 (317)
Q Consensus 152 LFE~L~LE~fQAGLSW~tILkKR~~fr~AF~~FD~~~VA~~~eedie~L~~d~~IIRnr~KI~AVi~NAr~il 224 (317)
=|+.|+-|++-.=-+|.+|..--+.|.+.| -+++.+|..++++|.++..--|.-+ |.+-+..-|+.+.
T Consensus 30 py~ilVseILlQQT~v~~v~~~~~rl~~~f--Pt~~~La~a~~eel~~~~~glGyy~---RAr~L~~~A~~i~ 97 (350)
T PRK10880 30 PYKVWLSEVMLQQTQVATVIPYFERFMARF--PTVTDLANAPLDEVLHLWTGLGYYA---RARNLHKAAQQVA 97 (350)
T ss_pred HHHHHHHHHHHhhccHHHHHHHHHHHHHHC--cCHHHHHCcCHHHHHHHHHcCChHH---HHHHHHHHHHHHH
Confidence 478999999999999999999999999987 4799999999999999998888752 6667777777664
No 12
>TIGR01084 mutY A/G-specific adenine glycosylase. This equivalog model identifies mutY members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=88.84 E-value=4 Score=39.25 Aligned_cols=68 Identities=21% Similarity=0.257 Sum_probs=56.9
Q ss_pred HHHHHHHHHhhccccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhhCCCcchhchhhHHHHHHhHHHHH
Q 021082 152 LFELLALSGMLMDYNWTEILKRKELFREAFGGFDPKSVAKMGEKEILEISSNTAIMLAECRVRCIVDNAKCIV 224 (317)
Q Consensus 152 LFE~L~LE~fQAGLSW~tILkKR~~fr~AF~~FD~~~VA~~~eedie~L~~d~~IIRnr~KI~AVi~NAr~il 224 (317)
.|+.|+-+++-.=-+|.+|..-.+.|.+.|- +|+.+|..++++|.++..--|.- + |.+.+.+=|+.+.
T Consensus 26 py~vlvseIL~QQT~v~~v~~~~~rl~~~fp--t~~~La~a~~eeL~~~~~~lG~y-~--RAr~L~~~A~~i~ 93 (275)
T TIGR01084 26 PYRVWLSEVMLQQTQVATVIPYFERFLERFP--TVQALANAPQDEVLKLWEGLGYY-A--RARNLHKAAQEVV 93 (275)
T ss_pred HHHHHHHHHHHhhccHHHHHHHHHHHHHhCC--CHHHHHCcCHHHHHHHHHHCCcH-H--HHHHHHHHHHHHH
Confidence 5899999999999999999999999999884 69999999999999998888875 2 4556665566553
No 13
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=87.62 E-value=4.3 Score=38.05 Aligned_cols=102 Identities=21% Similarity=0.273 Sum_probs=68.3
Q ss_pred HHHHHHHHHHhhccccHHHHHHhHHHHHHHhcCC-CHHHHhcCCHHHHHHhhCCCcchhchhhHHHHHHhHHHHHHHHHh
Q 021082 151 QLFELLALSGMLMDYNWTEILKRKELFREAFGGF-DPKSVAKMGEKEILEISSNTAIMLAECRVRCIVDNAKCIVKILNE 229 (317)
Q Consensus 151 ~LFE~L~LE~fQAGLSW~tILkKR~~fr~AF~~F-D~~~VA~~~eedie~L~~d~~IIRnr~KI~AVi~NAr~il~i~~E 229 (317)
--||+|+--+.-|--+=..+.+ +.++.|.-| +|+.++..++++|++++..-|+-|+ |-+.|+.=|+.++ ++
T Consensus 28 ~pf~lLva~iLSaqttD~~vn~---at~~Lf~~~~t~e~l~~a~~~~l~~~I~~iGlyr~--KAk~I~~~~~~l~---e~ 99 (211)
T COG0177 28 DPFELLVAVILSAQTTDEVVNK---ATPALFKRYPTPEDLLNADEEELEELIKSIGLYRN--KAKNIKELARILL---EK 99 (211)
T ss_pred CcHHHHHHHHHhccCchHHHHH---HHHHHHHHcCCHHHHHcCCHHHHHHHHHhcCCcHH--HHHHHHHHHHHHH---HH
Confidence 3478876555544444444444 444445444 4999999999999999999999887 6667777777764 56
Q ss_pred cCCHHHhccccCCCccccCCCCCCCCCCCCCHHHHHHHHHHHHcCCcccChhhHHHHHHHhc
Q 021082 230 FGSFSSFMWGYVNFKPMINKFRYPRNVPLRSPKAEAISRDLLKRGFRLVGPVIVYSFMQAAG 291 (317)
Q Consensus 230 ~GSF~~ylWsfv~~kpi~n~~~~~~~vP~~t~lS~~lsKdLKkrGFkFVGPttvysFMQAvG 291 (317)
||+ ++|..- ++|.+ ---||+.|++=.|.-+.
T Consensus 100 ~~g----------------------~vP~~~-------~eL~~--LPGVGrKTAnvVL~~a~ 130 (211)
T COG0177 100 FGG----------------------EVPDTR-------EELLS--LPGVGRKTANVVLSFAF 130 (211)
T ss_pred cCC----------------------CCCchH-------HHHHh--CCCcchHHHHHHHHhhc
Confidence 665 233211 12333 46799999998887643
No 14
>PF00730 HhH-GPD: HhH-GPD superfamily base excision DNA repair protein This entry corresponds to Endonuclease III This entry corresponds to Alkylbase DNA glycosidase; InterPro: IPR003265 Endonuclease III (4.2.99.18 from EC) is a DNA repair enzyme which removes a number of damaged pyrimidines from DNA via its glycosylase activity and also cleaves the phosphodiester backbone at apurinic / apyrimidinic sites via a beta-elimination mechanism [, ]. The structurally related DNA glycosylase MutY recognises and excises the mutational intermediate 8-oxoguanine-adenine mispair []. The 3-D structures of Escherichia coli endonuclease III [] and catalytic domain of MutY [] have been determined. The structures contain two all-alpha domains: a sequence-continuous, six-helix domain (residues 22-132) and a Greek-key, four-helix domain formed by one N-terminal and three C-terminal helices (residues 1-21 and 133-211) together with the [Fe4S4] cluster. The cluster is bound entirely within the C-terminal loop by four cysteine residues with a ligation pattern Cys-(Xaa)6-Cys-(Xaa)2-Cys-(Xaa)5-Cys which is distinct from all other known Fe4S4 proteins. This structural motif is referred to as a [Fe4S4] cluster loop (FCL) []. Two DNA-binding motifs have been proposed, one at either end of the interdomain groove: the helix-hairpin-helix (HhH) and FCL motifs (see IPR003651 from INTERPRO). The primary role of the iron-sulphur cluster appears to involve positioning conserved basic residues for interaction with the DNA phosphate backbone by forming the loop of the FCL motif [, ]. The HhH-GPD domain gets its name from its hallmark helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate. This domain is found in a diverse range of structurally related DNA repair proteins that include: endonuclease III, 4.2.99.18 from EC and DNA glycosylase MutY, an A/G-specific adenine glycosylase. Both of these enzymes have a C-terminal iron-sulphur cluster loop (FCL). The methyl-CPG binding protein (MBD4) also contain a related domain that is a thymine DNA glycosylase. The family also includes DNA-3-methyladenine glycosylase II 3.2.2.21 from EC, 8-oxoguanine DNA glycosylases and other members of the AlkA family.; GO: 0006284 base-excision repair; PDB: 3F0Z_A 3I0X_A 3F10_A 3I0W_A 3S6I_D 3N5N_Y 1PU7_A 1PU8_B 1PU6_B 1NGN_A ....
Probab=84.65 E-value=6.5 Score=31.25 Aligned_cols=63 Identities=17% Similarity=0.197 Sum_probs=52.8
Q ss_pred HhhccccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhhCCCcchhchhhHHHHHHhHHHHH
Q 021082 160 GMLMDYNWTEILKRKELFREAFGGFDPKSVAKMGEKEILEISSNTAIMLAECRVRCIVDNAKCIV 224 (317)
Q Consensus 160 ~fQAGLSW~tILkKR~~fr~AF~~FD~~~VA~~~eedie~L~~d~~IIRnr~KI~AVi~NAr~il 224 (317)
++..-.+|..+.+-...|.+.|...+|+.|+..++++|.+++..-|+-+ .|-+.+++=|+.++
T Consensus 4 Il~qq~s~~~a~~~~~~l~~~~g~pt~~~l~~~~~~el~~~i~~~G~~~--~ka~~i~~~a~~~~ 66 (108)
T PF00730_consen 4 ILSQQTSIKAARKIYRRLFERYGFPTPEALAEASEEELRELIRPLGFSR--RKAKYIIELARAIL 66 (108)
T ss_dssp HHCTTS-HHHHHHHHHHHHHHHSCSSHHHHHCSHHHHHHHHHTTSTSHH--HHHHHHHHHHHHHH
T ss_pred eecCcCcHHHHHHHHHHHHHHhcCCCHHHHHhCCHHHHHHHhhccCCCH--HHHHHHHHHHHHhh
Confidence 3445568899999999999999999999999999999999999866654 57888888888887
No 15
>PF10023 DUF2265: Predicted aminopeptidase (DUF2265); InterPro: IPR014553 This group represents a predicted aminopeptidase.
Probab=76.38 E-value=9.1 Score=38.32 Aligned_cols=100 Identities=21% Similarity=0.338 Sum_probs=64.6
Q ss_pred HHHHHhhCCCcchhc-hhhHHHHHHhHHHHHHHH----HhcCCHHHhc-----------------------cccCCCccc
Q 021082 195 KEILEISSNTAIMLA-ECRVRCIVDNAKCIVKIL----NEFGSFSSFM-----------------------WGYVNFKPM 246 (317)
Q Consensus 195 edie~L~~d~~IIRn-r~KI~AVi~NAr~il~i~----~E~GSF~~yl-----------------------Wsfv~~kpi 246 (317)
+.|+++++||++=-. |.|+ ..+..+|.+- .. .+.+|+..|. |.| ||
T Consensus 33 ~pv~~vl~dp~~~~~lr~rL-~~~~~iR~FA-~~~L~Lpdn~sY~~YadL~Rp~vvWnV~Aap~~sl~~~~WcF----Pi 106 (337)
T PF10023_consen 33 RPVDDVLADPATPPALRARL-RLAQQIRRFA-SEELGLPDNGSYRSYADLDRPYVVWNVFAAPEFSLEPKTWCF----PI 106 (337)
T ss_pred CcHHHHhhCCCCCHHHHHHH-HHHHHHHHHH-HHhcCCCCCCChhhhhhcCCCcEEEEEEecCcccCCcceeec----cc
Confidence 458888888866432 2232 3344444442 11 2357777775 555 66
Q ss_pred cCCCCCCCCCCCCCHHHHHHHHHHHHcCC-cccChhhHHHHHHHhccccccccccccchh
Q 021082 247 INKFRYPRNVPLRSPKAEAISRDLLKRGF-RLVGPVIVYSFMQAAGLTIDHLVDCFRYSE 305 (317)
Q Consensus 247 ~n~~~~~~~vP~~t~lS~~lsKdLKkrGF-kFVGPttvysFMQAvG~vnDHl~~C~r~~~ 305 (317)
+.-..+-.-- ....+.+.++.|++.|+ .+||+|.+||= .|+.+|=+..-+.+-.
T Consensus 107 ~Gcv~YrGyF--~~~~A~~~a~~L~~~GlDv~v~gV~AYST---LGwF~DPlLSt~l~~~ 161 (337)
T PF10023_consen 107 VGCVPYRGYF--DEADARAEAAELRAQGLDVYVGGVPAYST---LGWFDDPLLSTMLRYP 161 (337)
T ss_pred cccccccCcC--CHHHHHHHHHHHHHcCCceeEeccccccc---ccccCCcccccccCCC
Confidence 5544332222 23568899999999999 69999999997 4888888877765533
No 16
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=72.39 E-value=54 Score=31.77 Aligned_cols=109 Identities=17% Similarity=0.156 Sum_probs=80.6
Q ss_pred HHHHHHHHHHHhhccccHHHHHHhHHHHHHHhcC--------CCHHHHhcCCHHHHHHhhCCCcchhchhhHHHHHHhHH
Q 021082 150 NQLFELLALSGMLMDYNWTEILKRKELFREAFGG--------FDPKSVAKMGEKEILEISSNTAIMLAECRVRCIVDNAK 221 (317)
Q Consensus 150 r~LFE~L~LE~fQAGLSW~tILkKR~~fr~AF~~--------FD~~~VA~~~eedie~L~~d~~IIRnr~KI~AVi~NAr 221 (317)
.-.||.|+--+.+.=+|=..+-+-+..+.++|.+ =.|+.++..+++.+. ++--.+.|.+.|++=|+
T Consensus 103 ~d~fe~lv~aI~~QqvS~~~A~~i~~rl~~~~g~~~~~~~~fptpe~l~~~~~~~l~------~~g~s~~Ka~yi~~~A~ 176 (285)
T COG0122 103 PDPFEALVRAILSQQVSVAAAAKIWARLVSLYGNALEIYHSFPTPEQLAAADEEALR------RCGLSGRKAEYIISLAR 176 (285)
T ss_pred CCHHHHHHHHHHHhHhhHHHHHHHHHHHHHHhCCccccccCCCCHHHHHhcCHHHHH------HhCCcHHHHHHHHHHHH
Confidence 5789999999999999999999999999999994 589999999999988 44556789999999999
Q ss_pred HHHHHHHhcCCHHHhccccCCCccccCCCCCCCCCCCCCHHHHHHHHHHHHcCCcccChhhHHHH-HHHhc
Q 021082 222 CIVKILNEFGSFSSFMWGYVNFKPMINKFRYPRNVPLRSPKAEAISRDLLKRGFRLVGPVIVYSF-MQAAG 291 (317)
Q Consensus 222 ~il~i~~E~GSF~~ylWsfv~~kpi~n~~~~~~~vP~~t~lS~~lsKdLKkrGFkFVGPttvysF-MQAvG 291 (317)
++..=. =++.... . .--+.+-+.|.+ |+-|||-|+--| |.+.|
T Consensus 177 ~~~~g~---~~~~~l~--------------~--------~~~e~a~e~L~~--i~GIG~WTAe~~llf~lg 220 (285)
T COG0122 177 AAAEGE---LDLSELK--------------P--------LSDEEAIEELTA--LKGIGPWTAEMFLLFGLG 220 (285)
T ss_pred HHHcCC---ccHHHhc--------------c--------CCHHHHHHHHHc--CCCcCHHHHHHHHHHcCC
Confidence 885310 0111110 0 012344556666 999999998544 55556
No 17
>PF02142 MGS: MGS-like domain This is a subfamily of this family; InterPro: IPR011607 This domain composes the whole protein of methylglyoxal synthetase and the domain is also found in carbamoyl phosphate synthetase (CPS) where it forms a regulatory domain that binds to the allosteric effector ornithine. The known structures in this domain show a common phosphate binding site []. ; PDB: 4A1O_A 3ZZM_A 1ZCZ_A 1M6V_C 1CS0_C 1C30_E 1C3O_G 1BXR_A 1T36_E 1A9X_A ....
Probab=69.48 E-value=4.7 Score=32.00 Aligned_cols=30 Identities=17% Similarity=0.380 Sum_probs=26.4
Q ss_pred HHHHHHHHHcCCcccChhhHHHHHHHhccc
Q 021082 264 EAISRDLLKRGFRLVGPVIVYSFMQAAGLT 293 (317)
Q Consensus 264 ~~lsKdLKkrGFkFVGPttvysFMQAvG~v 293 (317)
..++|.|.+.||++++.-..+.||+..|+-
T Consensus 3 ~~~a~~l~~lG~~i~AT~gTa~~L~~~Gi~ 32 (95)
T PF02142_consen 3 VPLAKRLAELGFEIYATEGTAKFLKEHGIE 32 (95)
T ss_dssp HHHHHHHHHTTSEEEEEHHHHHHHHHTT--
T ss_pred HHHHHHHHHCCCEEEEChHHHHHHHHcCCC
Confidence 468999999999999999999999999984
No 18
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=64.47 E-value=46 Score=31.09 Aligned_cols=107 Identities=17% Similarity=0.212 Sum_probs=67.2
Q ss_pred ChHHHHHHHHHHHhhccccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhhCCCc--chhchhhHHHHHHhHHHHHH
Q 021082 148 DDNQLFELLALSGMLMDYNWTEILKRKELFREAFGGFDPKSVAKMGEKEILEISSNTA--IMLAECRVRCIVDNAKCIVK 225 (317)
Q Consensus 148 DDr~LFE~L~LE~fQAGLSW~tILkKR~~fr~AF~~FD~~~VA~~~eedie~L~~d~~--IIRnr~KI~AVi~NAr~il~ 225 (317)
++.-+|+.|+..+.-+.-+|..+.+--+.+. ++.+ .+++++|++++.-.| .-|+ |=+-++.-|+.+
T Consensus 33 ~~~~~f~~Lv~~ILsqnT~~~~v~~a~~~L~-------~~~l-~~~~eeL~~~Ir~~Gygf~~~--KAk~I~~~~~~~-- 100 (208)
T PRK01229 33 DEEDLFSELSFCILTANSSAEGGIKAQKEIG-------DGFL-YLSEEELEEKLKEVGHRFYNK--RAEYIVEARKLY-- 100 (208)
T ss_pred ccCChHHHHHHHHhcCcCcHHHHHHHHHhcC-------HHHc-CCCHHHHHHHHHHhhcccHHH--HHHHHHHHHHHH--
Confidence 7888999999999999999999987666663 4445 789999999986542 4444 333333333332
Q ss_pred HHHhcCCHHHhccccCCCccccCCCCCCCCCCCCCHHHHHHHHHHHHcCCcccChhhHHHHHHHhcc
Q 021082 226 ILNEFGSFSSFMWGYVNFKPMINKFRYPRNVPLRSPKAEAISRDLLKRGFRLVGPVIVYSFMQAAGL 292 (317)
Q Consensus 226 i~~E~GSF~~ylWsfv~~kpi~n~~~~~~~vP~~t~lS~~lsKdLKkrGFkFVGPttvysFMQAvG~ 292 (317)
|.+.+..- . ..++| ..-.+|.+ ..+-|||.|+-.+|..+|.
T Consensus 101 -----~~l~~~~~---~----------~~~~~-------~~R~~Ll~-~lpGIG~KTAd~vL~~~~~ 141 (208)
T PRK01229 101 -----GKLKEIIK---A----------DKDQF-------EAREFLVK-NIKGIGYKEASHFLRNVGY 141 (208)
T ss_pred -----HHHHHHHh---c----------cCCch-------HHHHHHHH-cCCCCcHHHHHHHHHHccC
Confidence 22211110 0 01111 12223332 4788999999999977765
No 19
>COG1393 ArsC Arsenate reductase and related proteins, glutaredoxin family [Inorganic ion transport and metabolism]
Probab=61.40 E-value=8.1 Score=32.73 Aligned_cols=61 Identities=8% Similarity=0.025 Sum_probs=44.2
Q ss_pred CCccccChHHHHHHHHHHHhhccccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhhCCCcchhc
Q 021082 142 WGVPVYDDNQLFELLALSGMLMDYNWTEILKRKELFREAFGGFDPKSVAKMGEKEILEISSNTAIMLA 209 (317)
Q Consensus 142 WG~Pv~DDr~LFE~L~LE~fQAGLSW~tILkKR~~fr~AF~~FD~~~VA~~~eedie~L~~d~~IIRn 209 (317)
...--.+...|=+. .-++|..|..++++|..+-+... .++....+++.++.|+.++.+||-
T Consensus 33 y~~~~~s~~eL~~~----l~~~g~~~~~li~t~~~~~r~L~---~~~~~~~~~~~~~~i~~~~~LikR 93 (117)
T COG1393 33 YLKTPPSREELKKI----LSKLGDGVEELINTRGTTYRELN---LDKEDLSDEELIEALLENPSLIKR 93 (117)
T ss_pred eecCCCCHHHHHHH----HHHcCccHHHHHHhccchHHHcC---CcccccChHHHHHHHHhChhhccC
Confidence 33333444455444 35789999999999998877766 555667788888999999987763
No 20
>cd00166 SAM Sterile alpha motif.; Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerization.
Probab=57.83 E-value=28 Score=24.34 Aligned_cols=43 Identities=12% Similarity=0.222 Sum_probs=31.9
Q ss_pred HHHHHHh--cCCCHHHHhcCCHHHHHHhhCCCcchhchhhHHHHHHh
Q 021082 175 ELFREAF--GGFDPKSVAKMGEKEILEISSNTAIMLAECRVRCIVDN 219 (317)
Q Consensus 175 ~~fr~AF--~~FD~~~VA~~~eedie~L~~d~~IIRnr~KI~AVi~N 219 (317)
+.|.+.| .++|-..+..++++++.++--.. .-+|.||...|..
T Consensus 17 ~~y~~~f~~~~i~g~~L~~l~~~dL~~lgi~~--~g~r~~i~~~i~~ 61 (63)
T cd00166 17 GQYADNFRENGIDGDLLLLLTEEDLKELGITL--PGHRKKILKAIQK 61 (63)
T ss_pred HHHHHHHHHcCCCHHHHhHCCHHHHHHcCCCC--HHHHHHHHHHHHH
Confidence 6677777 57899999999999998554322 5678888766653
No 21
>PF00536 SAM_1: SAM domain (Sterile alpha motif); InterPro: IPR021129 The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [] involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms []. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins [], nevertheless with a low affinity constant []. SAM domains also appear to possess the ability to bind RNA []. Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologs. These results suggest that the SAM domain might have a primary role in RNA binding. Structural analyses show that the SAM domain is arranged in a small five-helix bundle with two large interfaces []. In the case of the SAM domain of EphB2, each of these interfaces is able to form dimers. The presence of these two distinct intermonomers binding surface suggest that SAM could form extended polymeric structures []. This entry represents type 1 SAM domains. ; PDB: 2KIV_A 3HIL_B 3KKA_A 3K1R_B 3SEN_B 3SEI_B 1V85_A 2KE7_A 2EAM_A 1WWV_A ....
Probab=48.89 E-value=34 Score=24.75 Aligned_cols=43 Identities=14% Similarity=0.312 Sum_probs=31.8
Q ss_pred HHHHHHh-cCC-CHHHHhcCCHHHHHHhhCCCcchhchhhHHHHHHh
Q 021082 175 ELFREAF-GGF-DPKSVAKMGEKEILEISSNTAIMLAECRVRCIVDN 219 (317)
Q Consensus 175 ~~fr~AF-~~F-D~~~VA~~~eedie~L~~d~~IIRnr~KI~AVi~N 219 (317)
+.|...| .++ |-..+..++++++.++-- ..+-||.||...|..
T Consensus 18 ~~y~~~F~~~~i~g~~L~~lt~~dL~~lgi--~~~ghr~ki~~~i~~ 62 (64)
T PF00536_consen 18 EQYAENFEKNYIDGEDLLSLTEEDLEELGI--TKLGHRKKILRAIQK 62 (64)
T ss_dssp GGGHHHHHHTTSSHHHHTTSCHHHHHHTT---SSHHHHHHHHHHHHH
T ss_pred HHHHHHHHcCCchHHHHHhcCHHHHHHcCC--CCHHHHHHHHHHHHH
Confidence 6677777 444 999999999999998421 234588898877754
No 22
>PF13276 HTH_21: HTH-like domain
Probab=48.67 E-value=22 Score=25.80 Aligned_cols=31 Identities=26% Similarity=0.215 Sum_probs=26.8
Q ss_pred HHHHHHHHHHcCCcccChhhHHHHHHHhccc
Q 021082 263 AEAISRDLLKRGFRLVGPVIVYSFMQAAGLT 293 (317)
Q Consensus 263 S~~lsKdLKkrGFkFVGPttvysFMQAvG~v 293 (317)
+..|+.+|.+.|---||-.+|+-+|+..|+.
T Consensus 23 ~rri~~~L~~~~~~~v~~krV~RlM~~~gL~ 53 (60)
T PF13276_consen 23 YRRIWAELRREGGIRVSRKRVRRLMREMGLR 53 (60)
T ss_pred hhHHHHHHhccCcccccHHHHHHHHHHcCCc
Confidence 4578999999965579999999999999985
No 23
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=47.54 E-value=1.8e+02 Score=28.13 Aligned_cols=119 Identities=14% Similarity=0.141 Sum_probs=72.7
Q ss_pred CCCccccChHHHHHHHHHHHhhccccHHHHHHhHHHHHHHhc----------CC-CHHHHhcCCHHHHHHhhCCCcchhc
Q 021082 141 CWGVPVYDDNQLFELLALSGMLMDYNWTEILKRKELFREAFG----------GF-DPKSVAKMGEKEILEISSNTAIMLA 209 (317)
Q Consensus 141 EWG~Pv~DDr~LFE~L~LE~fQAGLSW~tILkKR~~fr~AF~----------~F-D~~~VA~~~eedie~L~~d~~IIRn 209 (317)
.=|.-+.-..-.||+|+-.+.-.-.|=..+.+-...+-+.|. -| +|+.|+..+++++..+ ++-
T Consensus 102 ~~GlR~p~~~d~fE~lv~aIigQqisv~~a~~~~~rlv~~~G~~l~~~~~~~~FPtpe~La~~~~~eL~~~----Gl~-- 175 (283)
T PRK10308 102 RPGLRLPGSVDAFEQGVRAILGQLVSVAMAAKLTAKVAQLYGERLDDFPEYVCFPTPERLAAADPQALKAL----GMP-- 175 (283)
T ss_pred CCCCcCCCCCCHHHHHHHHHHHhHHHHHHHHHHHHHHHHHhCccccCCCCccCCCCHHHHHcCCHHHHHHC----CCC--
Confidence 336555555667999887765444443333333333434433 34 7999999999988753 333
Q ss_pred hhhHHHHHHhHHHHHHHHHhcCCHHHhccccCCCccccCCCCCCCCCCCCCHHHHHHHHHHHHcCCcccChhhH-HHHHH
Q 021082 210 ECRVRCIVDNAKCIVKILNEFGSFSSFMWGYVNFKPMINKFRYPRNVPLRSPKAEAISRDLLKRGFRLVGPVIV-YSFMQ 288 (317)
Q Consensus 210 r~KI~AVi~NAr~il~i~~E~GSF~~ylWsfv~~kpi~n~~~~~~~vP~~t~lS~~lsKdLKkrGFkFVGPttv-ysFMQ 288 (317)
+.|.++++.=|+++.+ |.+. ..+ +. + .+.+-+.|.+ ++-|||-|+ |-.|.
T Consensus 176 ~~Ra~~L~~lA~~i~~-----g~l~--------l~~-----------~~--~-~~~~~~~L~~--LpGIGpwTA~~vllr 226 (283)
T PRK10308 176 LKRAEALIHLANAALE-----GTLP--------LTI-----------PG--D-VEQAMKTLQT--FPGIGRWTANYFALR 226 (283)
T ss_pred HHHHHHHHHHHHHHHc-----CCCC--------ccc-----------cC--C-HHHHHHHHhc--CCCcCHHHHHHHHHH
Confidence 4688888888888753 3321 000 00 1 1345566766 899999988 66777
Q ss_pred Hhcccc
Q 021082 289 AAGLTI 294 (317)
Q Consensus 289 AvG~vn 294 (317)
+.|-.+
T Consensus 227 ~lg~~D 232 (283)
T PRK10308 227 GWQAKD 232 (283)
T ss_pred hCCCCC
Confidence 777543
No 24
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=46.75 E-value=1.7e+02 Score=27.95 Aligned_cols=83 Identities=16% Similarity=0.299 Sum_probs=62.4
Q ss_pred hhHhhhhhhCCCccccChHHHHHHHHHHHhhccccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhhCCCcchhchh
Q 021082 132 KVYVAFHDECWGVPVYDDNQLFELLALSGMLMDYNWTEILKRKELFREAFGGFDPKSVAKMGEKEILEISSNTAIMLAEC 211 (317)
Q Consensus 132 ply~~YHD~EWG~Pv~DDr~LFE~L~LE~fQAGLSW~tILkKR~~fr~AF~~FD~~~VA~~~eedie~L~~d~~IIRnr~ 211 (317)
.++.-|+|.-|=--...+ |.++=.+.----+|.-|.+.-++++..+. +++.+|..+++++++++..-.|--+-..
T Consensus 14 ~L~~~yg~q~WWp~~~~~----EiiigAILtQNT~WknvekAlenLk~~~~-~~l~~I~~~~~~~L~elIrpsGFYnqKa 88 (215)
T COG2231 14 ELLRLYGDQGWWPADNKD----EIIIGAILTQNTSWKNVEKALENLKNEGI-LNLKKILKLDEEELAELIRPSGFYNQKA 88 (215)
T ss_pred HHHHHcCCccCCCCCCch----hHHHHHHHhccccHHHHHHHHHHHHHccc-CCHHHHhcCCHHHHHHHHhccchHHHHH
Confidence 467789998885443333 65555555556789999999999998765 6799999999999999999999887544
Q ss_pred h-HHHHHHh
Q 021082 212 R-VRCIVDN 219 (317)
Q Consensus 212 K-I~AVi~N 219 (317)
| +.|++.|
T Consensus 89 ~rLk~l~k~ 97 (215)
T COG2231 89 KRLKALSKN 97 (215)
T ss_pred HHHHHHHHH
Confidence 3 4444443
No 25
>cd00532 MGS-like MGS-like domain. This domain composes the whole protein of methylglyoxal synthetase, which catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The family also includes the C-terminal domain in carbamoyl phosphate synthetase (CPS) where it catalyzes the last phosphorylation of a coaboxyphosphate intermediate to form the product carbamoyl phosphate and may also play a regulatory role. This family also includes inosine monophosphate cyclohydrolase. The known structures in this family show a common phosphate binding site.
Probab=45.08 E-value=25 Score=28.71 Aligned_cols=32 Identities=19% Similarity=0.235 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHHcCCcccChhhHHHHHHHhcc
Q 021082 261 PKAEAISRDLLKRGFRLVGPVIVYSFMQAAGL 292 (317)
Q Consensus 261 ~lS~~lsKdLKkrGFkFVGPttvysFMQAvG~ 292 (317)
+....+++.|.+.||+.++.-..+.||+..|+
T Consensus 12 ~~~~~~a~~l~~~G~~i~AT~gTa~~L~~~Gi 43 (112)
T cd00532 12 AMLVDLAPKLSSDGFPLFATGGTSRVLADAGI 43 (112)
T ss_pred HHHHHHHHHHHHCCCEEEECcHHHHHHHHcCC
Confidence 45678999999999999999899999999886
No 26
>smart00851 MGS MGS-like domain. This domain composes the whole protein of methylglyoxal synthetase and the domain is also found in Carbamoyl phosphate synthetase (CPS) where it forms a regulatory domain that binds to the allosteric effector ornithine. This family also includes inosicase. The known structures in this family show a common phosphate binding site PUBMED:10526357.
Probab=44.94 E-value=23 Score=27.59 Aligned_cols=29 Identities=31% Similarity=0.490 Sum_probs=25.6
Q ss_pred HHHHHHHHHcCCcccChhhHHHHHHHhcc
Q 021082 264 EAISRDLLKRGFRLVGPVIVYSFMQAAGL 292 (317)
Q Consensus 264 ~~lsKdLKkrGFkFVGPttvysFMQAvG~ 292 (317)
..+++.|.+.||+.+.....+.||+..|+
T Consensus 3 ~~~~~~l~~lG~~i~AT~gTa~~L~~~Gi 31 (90)
T smart00851 3 VELAKRLAELGFELVATGGTAKFLREAGL 31 (90)
T ss_pred HHHHHHHHHCCCEEEEccHHHHHHHHCCC
Confidence 36788999999999988888999999996
No 27
>PF10911 DUF2717: Protein of unknown function (DUF2717); InterPro: IPR020121 The proteins in this entry are uncharacterised.
Probab=41.87 E-value=14 Score=29.86 Aligned_cols=42 Identities=21% Similarity=0.352 Sum_probs=30.5
Q ss_pred ccccCCCCCCCCCCCCCHHHHHHHHHHHHcCCcccChhhHHHHHHHhcccccc
Q 021082 244 KPMINKFRYPRNVPLRSPKAEAISRDLLKRGFRLVGPVIVYSFMQAAGLTIDH 296 (317)
Q Consensus 244 kpi~n~~~~~~~vP~~t~lS~~lsKdLKkrGFkFVGPttvysFMQAvG~vnDH 296 (317)
+||.+...++.|||. .+++.+..|+-| -=++|+.+.|++++-
T Consensus 3 ~~I~h~l~np~DiP~---ipra~aeyLqvr--------fN~~yl~~sG~i~~l 44 (77)
T PF10911_consen 3 KPIQHLLDNPDDIPD---IPRAAAEYLQVR--------FNAAYLMASGIISAL 44 (77)
T ss_pred chHHHHhcCCcccCC---ccHHHHHHHHHH--------hcHHHHHHhhhHHHH
Confidence 577777889999996 666777788876 235677777776653
No 28
>cd01424 MGS_CPS_II Methylglyoxal synthase-like domain from type II glutamine-dependent carbamoyl phosphate synthetase (CSP). CSP, a CarA and CarB heterodimer, catalyzes the production of carbamoyl phosphate which is subsequently employed in the metabolic pathways responsible for the synthesis of pyrimidine nucleotides or arginine. The MGS-like domain is the C-terminal domain of CarB and appears to play a regulatory role in CPS function by binding allosteric effector molecules, including UMP and ornithine.
Probab=39.34 E-value=37 Score=27.33 Aligned_cols=32 Identities=34% Similarity=0.592 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHHcCCcccChhhHHHHHHHhcc
Q 021082 261 PKAEAISRDLLKRGFRLVGPVIVYSFMQAAGL 292 (317)
Q Consensus 261 ~lS~~lsKdLKkrGFkFVGPttvysFMQAvG~ 292 (317)
+....+++.|.+.||+..+.-..+.||+..|+
T Consensus 13 ~~~~~~~~~l~~~G~~l~aT~gT~~~l~~~gi 44 (110)
T cd01424 13 PEAVEIAKRLAELGFKLVATEGTAKYLQEAGI 44 (110)
T ss_pred hHHHHHHHHHHHCCCEEEEchHHHHHHHHcCC
Confidence 45668999999999999999999999999997
No 29
>PHA02517 putative transposase OrfB; Reviewed
Probab=39.33 E-value=34 Score=31.60 Aligned_cols=31 Identities=29% Similarity=0.397 Sum_probs=26.9
Q ss_pred HHHHHHHHHHcCCcccChhhHHHHHHHhcccc
Q 021082 263 AEAISRDLLKRGFRLVGPVIVYSFMQAAGLTI 294 (317)
Q Consensus 263 S~~lsKdLKkrGFkFVGPttvysFMQAvG~vn 294 (317)
..+|+..|+++|+. +|..+|+.+|+..|+.-
T Consensus 48 ~r~I~~~L~~~g~~-vs~~tV~Rim~~~gl~~ 78 (277)
T PHA02517 48 VRKVWRQLNREGIR-VARCTVGRLMKELGLAG 78 (277)
T ss_pred HHHHHHHHHhcCcc-cCHHHHHHHHHHcCCce
Confidence 45788899999986 59999999999999964
No 30
>cd04883 ACT_AcuB C-terminal ACT domain of the Bacillus subtilis acetoin utilization protein, AcuB. This CD includes the C-terminal ACT domain of the Bacillus subtilis acetoin utilization protein, AcuB. AcuB is putatively involved in the anaerobic catabolism of acetoin, and related proteins. Studies report the induction of AcuB by nitrate respiration and also by fermentation. Since acetoin can be secreted and later serve as a source of carbon, it has been proposed that, during anaerobic growth when other carbon sources are exhausted, the induction of the AcuB protein results in acetoin catabolism. AcuB-like proteins have two N-terminal tandem CBS domains and a single C-terminal ACT domain. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=37.48 E-value=21 Score=25.89 Aligned_cols=19 Identities=26% Similarity=0.567 Sum_probs=16.6
Q ss_pred HHHHHHHHHHHcCCcccCh
Q 021082 262 KAEAISRDLLKRGFRLVGP 280 (317)
Q Consensus 262 lS~~lsKdLKkrGFkFVGP 280 (317)
..+.+.+.|++.||+++||
T Consensus 53 ~~~~~~~~L~~~G~~v~~~ 71 (72)
T cd04883 53 NPRPIIEDLRRAGYEVLWP 71 (72)
T ss_pred CHHHHHHHHHHCCCeeeCC
Confidence 3458899999999999998
No 31
>PF12401 DUF3662: Protein of unknown function (DUF2662) ; InterPro: IPR022128 This domain family is found in bacteria, and is approximately 120 amino acids in length. The family is found in association with PF00498 from PFAM. ; PDB: 2LC0_A.
Probab=37.36 E-value=18 Score=30.53 Aligned_cols=25 Identities=28% Similarity=0.517 Sum_probs=16.9
Q ss_pred CHHHHHHHHHHHHcCCcccChhhHH
Q 021082 260 SPKAEAISRDLLKRGFRLVGPVIVY 284 (317)
Q Consensus 260 t~lS~~lsKdLKkrGFkFVGPttvy 284 (317)
.++++.+.+....+||.|+||++|.
T Consensus 76 ~el~~~l~~~a~~qgy~~~G~v~V~ 100 (116)
T PF12401_consen 76 RELADYLAEHAREQGYTFVGPVTVE 100 (116)
T ss_dssp HHHHHHHHHHHHHHT-B-SS--EEE
T ss_pred HHHHHHHHHHHHHCCCeecCCEEEE
Confidence 3677788888889999999998864
No 32
>PF00289 CPSase_L_chain: Carbamoyl-phosphate synthase L chain, N-terminal domain; InterPro: IPR005481 Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates [, ]. CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate []. The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC). Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain []. CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites []. The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain. Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein []. The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP []. There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia []. CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains []. This entry represents the N-terminal domain of the large subunit of carbamoyl phosphate synthase. This domain can also be found in certain other related proteins. ; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 3VA7_A 3OUU_A 3OUZ_B 1W96_B 1W93_A 1ULZ_A 3HB9_C 3HO8_A 3BG5_C 3HBL_A ....
Probab=37.18 E-value=41 Score=27.98 Aligned_cols=21 Identities=14% Similarity=0.313 Sum_probs=16.3
Q ss_pred HHHHHHHHHHHcCCcccChhh
Q 021082 262 KAEAISRDLLKRGFRLVGPVI 282 (317)
Q Consensus 262 lS~~lsKdLKkrGFkFVGPtt 282 (317)
+...+++.+.+.|.+|+||..
T Consensus 87 e~~~fa~~~~~~gi~fiGp~~ 107 (110)
T PF00289_consen 87 ENAEFAEACEDAGIIFIGPSP 107 (110)
T ss_dssp THHHHHHHHHHTT-EESSS-H
T ss_pred HHHHHHHHHHHCCCEEECcCh
Confidence 466888999999999999964
No 33
>PF11970 Git3_C: G protein-coupled glucose receptor regulating Gpa2 C-term; InterPro: IPR022596 This entry contains a functionally uncharacterised region belonging to the Git3 G-protein coupled receptor. Git3 is one of six proteins required for glucose-triggered adenylate cyclase activation, and is a G protein-coupled receptor responsible for the activation of adenylate cyclase through Gpa2 - heterotrimeric G protein alpha subunit, part of the glucose-detection pathway. Git3 contains seven predicted transmembrane domains, a third cytoplasmic loop and a cytoplasmic tail []. This family is the conserved C-terminal domain of the member proteins.
Probab=37.11 E-value=18 Score=28.72 Aligned_cols=36 Identities=33% Similarity=0.623 Sum_probs=22.0
Q ss_pred ccChhhHHHHHHHhccccccccccccchhhhhcccCCCCC
Q 021082 277 LVGPVIVYSFMQAAGLTIDHLVDCFRYSECVSLAERPWRH 316 (317)
Q Consensus 277 FVGPttvysFMQAvG~vnDHl~~C~r~~~~~~~~~~~~~~ 316 (317)
-.||...+..+-++-+.--=.+||-.+ .+.+|||+|
T Consensus 41 ~~~p~~~l~~i~~~~~~~~G~VD~lvf----~~~erpw~~ 76 (76)
T PF11970_consen 41 GHGPSFWLFCIAGFMQPSQGFVDCLVF----TLRERPWRH 76 (76)
T ss_pred CCCCchHHHHHHHHHHHccCHHHhhhe----eeecccCCC
Confidence 456665555555554443344556444 677899997
No 34
>TIGR01529 argR_whole arginine repressor. This model includes most members of the arginine-responsive transcriptional regulator family ArgR. This hexameric protein binds DNA at its amino end to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbor-joining tree, some of these paralogous sequences show long branches and differ significantly in an otherwise well-conserved C-terminal region motif GT[VIL][AC]GDDT. These paralogs are excluded from the seed and score in the gray zone of this model, between trusted and noise cutoffs.
Probab=36.54 E-value=41 Score=29.39 Aligned_cols=31 Identities=19% Similarity=0.166 Sum_probs=27.5
Q ss_pred HHHHHHHHHHcCCcccChhhHHHHHHHhcccc
Q 021082 263 AEAISRDLLKRGFRLVGPVIVYSFMQAAGLTI 294 (317)
Q Consensus 263 S~~lsKdLKkrGFkFVGPttvysFMQAvG~vn 294 (317)
.+.|...|+++||. |.-.|+|-.|...|++-
T Consensus 19 qeeL~~~L~~~G~~-vsqaTIsRdL~elglvk 49 (146)
T TIGR01529 19 QEELVALLKAEGIE-VTQATVSRDLRELGAVK 49 (146)
T ss_pred HHHHHHHHHHhCCC-cCHHHHHHHHHHcCCEE
Confidence 56788999999999 78889999999999973
No 35
>cd01422 MGS Methylglyoxal synthase catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The first part of the catalytic mechanism is believed to be similar to TIM (triosephosphate isomerase) in that both enzymes utilize DHAP to form an ene-diolate phosphate intermediate. In MGS, the second catalytic step is characterized by the elimination of phosphate and collapse of the enediolate to form methylglyoxal instead of reprotonation to form the isomer glyceraldehyde 3-phosphate, as in TIM. This is the first reaction in the methylglyoxal bypass of the Embden-Myerhoff glycolytic pathway and is believed to provide physiological benefits under non-ideal growth conditions in bacteria.
Probab=33.64 E-value=46 Score=27.71 Aligned_cols=32 Identities=19% Similarity=0.169 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHHc--CCcccChhhHHHHHHH-hcc
Q 021082 261 PKAEAISRDLLKR--GFRLVGPVIVYSFMQA-AGL 292 (317)
Q Consensus 261 ~lS~~lsKdLKkr--GFkFVGPttvysFMQA-vG~ 292 (317)
+....+++.+.+. ||+.+.....+.||+. .|+
T Consensus 12 ~~~~~~a~~~~~ll~Gf~i~AT~gTa~~L~~~~Gi 46 (115)
T cd01422 12 EDLVEFVKQHQELLSRHRLVATGTTGLLIQEATGL 46 (115)
T ss_pred HHHHHHHHHHHHHhcCCEEEEechHHHHHHHhhCC
Confidence 5677899999999 9999999999999999 886
No 36
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=29.82 E-value=65 Score=25.81 Aligned_cols=32 Identities=34% Similarity=0.475 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHcCCcccChhhHHH---HHHHhcccc
Q 021082 262 KAEAISRDLLKRGFRLVGPVIVYS---FMQAAGLTI 294 (317)
Q Consensus 262 lS~~lsKdLKkrGFkFVGPttvys---FMQAvG~vn 294 (317)
-++.|...|+++|. -+|++|+|- +|...|+|.
T Consensus 18 sa~ei~~~l~~~~~-~i~~~TVYR~L~~L~~~Gli~ 52 (116)
T cd07153 18 TAEEIYERLRKKGP-SISLATVYRTLELLEEAGLVR 52 (116)
T ss_pred CHHHHHHHHHhcCC-CCCHHHHHHHHHHHHhCCCEE
Confidence 36789999999985 699999998 778889875
No 37
>cd03036 ArsC_like Arsenate Reductase (ArsC) family, unknown subfamily; uncharacterized proteins containing a CXXC motif with similarity to thioredoxin (TRX)-fold arsenic reductases, ArsC. Proteins containing a redox active CXXC motif like TRX and glutaredoxin (GRX) function as protein disulfide oxidoreductases, altering the redox state of target proteins via the reversible oxidation of the active site dithiol. ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], using reducing equivalents derived from glutathione via GRX, through a single catalytic cysteine.
Probab=28.28 E-value=52 Score=26.95 Aligned_cols=54 Identities=17% Similarity=0.184 Sum_probs=34.5
Q ss_pred HHHHHHHHhhccccHHHHHHhHHH-HHHHhcCCCHHHHhcCCHHH-HHHhhCCCcchhc
Q 021082 153 FELLALSGMLMDYNWTEILKRKEL-FREAFGGFDPKSVAKMGEKE-ILEISSNTAIMLA 209 (317)
Q Consensus 153 FE~L~LE~fQAGLSW~tILkKR~~-fr~AF~~FD~~~VA~~~eed-ie~L~~d~~IIRn 209 (317)
.+.|.-=+-+.|..|..+++||.. |++. +.+ +++..+++++ ++.|+++|.+|+-
T Consensus 38 ~~el~~~~~~~~~~~~~l~~~~~~~~~~l--~~~-~~~~~~s~~e~~~~l~~~p~LikR 93 (111)
T cd03036 38 KEELKKWLEKSGLPLKKFFNTSGKSYREL--GLK-DKLPSLSEEEALELLSSDGMLIKR 93 (111)
T ss_pred HHHHHHHHHHcCCCHHHHHhcCCchHHhC--Ccc-cccccCCHHHHHHHHHhCcCeeeC
Confidence 333444445668889999999974 4444 222 3356777555 4677788988873
No 38
>cd01423 MGS_CPS_I_III Methylglyoxal synthase-like domain found in pyr1 and URA1-like carbamoyl phosphate synthetases (CPS), including ammonia-dependent CPS Type I, and glutamine-dependent CPS Type III. These are multidomain proteins, in which MGS is the C-terminal domain.
Probab=27.91 E-value=66 Score=26.16 Aligned_cols=32 Identities=22% Similarity=0.393 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHcCCcccChhhHHHHHHHhcc
Q 021082 261 PKAEAISRDLLKRGFRLVGPVIVYSFMQAAGL 292 (317)
Q Consensus 261 ~lS~~lsKdLKkrGFkFVGPttvysFMQAvG~ 292 (317)
+....+++.|.+.||+..+.-..+.||...|+
T Consensus 13 ~~~~~~a~~l~~~G~~i~aT~gTa~~L~~~gi 44 (116)
T cd01423 13 PELLPTAQKLSKLGYKLYATEGTADFLLENGI 44 (116)
T ss_pred hhHHHHHHHHHHCCCEEEEccHHHHHHHHcCC
Confidence 34568999999999999999999999999897
No 39
>cd00956 Transaldolase_FSA Transaldolase-like fructose-6-phosphate aldolases (FSA) found in bacteria and archaea, which are member of the MipB/TalC subfamily of class I aldolases. FSA catalyze an aldol cleavage of fructose 6-phosphate and do not utilize fructose, fructose 1-phosphate, fructose 1,6-phosphate, or dihydroxyacetone phosphate. The enzymes belong to the transaldolase family that serves in transfer reactions in the pentose phosphate cycle, and are more distantly related to fructose 1,6-bisphosphate aldolase.
Probab=27.45 E-value=30 Score=31.87 Aligned_cols=34 Identities=18% Similarity=0.341 Sum_probs=28.1
Q ss_pred CCCCCCHHHHHHHHHHHHcCCcccChhhHHHHHHHh
Q 021082 255 NVPLRSPKAEAISRDLLKRGFRLVGPVIVYSFMQAA 290 (317)
Q Consensus 255 ~vP~~t~lS~~lsKdLKkrGFkFVGPttvysFMQAv 290 (317)
+||.+. ..-+..+.|++.|.+ ||-|+||+..||.
T Consensus 83 KIP~T~-~gl~ai~~L~~~gi~-v~~T~V~s~~Qa~ 116 (211)
T cd00956 83 KIPVTE-DGLKAIKKLSEEGIK-TNVTAIFSAAQAL 116 (211)
T ss_pred EEcCcH-hHHHHHHHHHHcCCc-eeeEEecCHHHHH
Confidence 567655 677888999999977 8999999999985
No 40
>PF02173 pKID: pKID domain; InterPro: IPR003102 The nuclear factor CREB activates transcription of target genes in part through direct interactions with the KIX domain of the coactivator CBP in a phosphorylation-dependent manner. CBP and P300 bind to the pKID (phosphorylated kinase-inducible-domain) domain of CREB [].; GO: 0005515 protein binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1KDX_B.
Probab=27.27 E-value=25 Score=25.35 Aligned_cols=17 Identities=29% Similarity=0.608 Sum_probs=14.5
Q ss_pred HHHHHhHHHHHHHhcCC
Q 021082 168 TEILKRKELFREAFGGF 184 (317)
Q Consensus 168 ~tILkKR~~fr~AF~~F 184 (317)
..||.+||.||+.|.+.
T Consensus 13 ReiLsRRPSYRKIlndL 29 (41)
T PF02173_consen 13 REILSRRPSYRKILNDL 29 (41)
T ss_dssp HHHHTTSTHHHHHHHHH
T ss_pred HHHHhhCchHHHHHHHh
Confidence 67999999999998654
No 41
>PF13495 Phage_int_SAM_4: Phage integrase, N-terminal SAM-like domain; PDB: 2A3V_A.
Probab=25.79 E-value=2.8e+02 Score=20.54 Aligned_cols=72 Identities=8% Similarity=0.003 Sum_probs=44.0
Q ss_pred HHHHHHHHHhhccccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhhCCCcchhchhhHHHHHHhHHHHHH
Q 021082 152 LFELLALSGMLMDYNWTEILKRKELFREAFGGFDPKSVAKMGEKEILEISSNTAIMLAECRVRCIVDNAKCIVK 225 (317)
Q Consensus 152 LFE~L~LE~fQAGLSW~tILkKR~~fr~AF~~FD~~~VA~~~eedie~L~~d~~IIRnr~KI~AVi~NAr~il~ 225 (317)
|++.+....-..|+|=.||-.-+-..+.-..-|+-..+..++.++|+.-+.. +...+.==.++|+++...++
T Consensus 1 Ll~~f~~~l~~~~~s~~Ti~~Y~~~l~~f~~~~~~~~~~~it~~~i~~y~~~--l~~~~~~s~~T~~~~~~~l~ 72 (85)
T PF13495_consen 1 LLEEFLEYLRLKGLSEKTIKNYRYHLKRFLRFLGNKPPDEITPEDIEQYLNY--LQNERGLSPSTINQYLSALR 72 (85)
T ss_dssp -HHHHHHHHHHTT--HHHHHHHHHHHHHHHTTSSS--GGG--HHHHHHHHHH--HHTTT---HHHHHHHHHHHH
T ss_pred CHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcccCccchhHHHHHHHHHHH--HHHhcCCCHHHHHHHHHHHH
Confidence 3455555556699999999999999998777777678899999999888765 22111112455666655554
No 42
>PF05075 DUF684: Protein of unknown function (DUF684); InterPro: IPR007767 This family contains uncharacterised proteins from Caenorhabditis elegans.
Probab=25.64 E-value=1.2e+02 Score=30.07 Aligned_cols=40 Identities=18% Similarity=0.230 Sum_probs=30.5
Q ss_pred hHHHHHHHHHHHhhccc-------cHHHHHHhHHHHHHHhcCCCHHH
Q 021082 149 DNQLFELLALSGMLMDY-------NWTEILKRKELFREAFGGFDPKS 188 (317)
Q Consensus 149 Dr~LFE~L~LE~fQAGL-------SW~tILkKR~~fr~AF~~FD~~~ 188 (317)
+..|-.+|.||+|.+|| .+..|+.+-..+.+..+.|.-+.
T Consensus 115 ~~vl~q~l~lEafa~Gl~~~~n~~~~~~L~e~~~~~~~~~~~w~~~Y 161 (345)
T PF05075_consen 115 DGVLGQLLFLEAFASGLFKDKNMYDPDRLIEKIEEINEKMDKWKEEY 161 (345)
T ss_pred HHHHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence 45688999999999999 66777777777766666655544
No 43
>cd01421 IMPCH Inosine monophosphate cyclohydrolase domain. This is the N-terminal domain in the purine biosynthesis pathway protein ATIC (purH). The bifunctional ATIC protein contains a C-terminal ATIC formylase domain that formylates 5-aminoimidazole-4-carboxamide-ribonucleotide. The IMPCH domain then converts the formyl-5-aminoimidazole-4-carboxamide-ribonucleotide to inosine monophosphate. This is the final step in de novo purine production.
Probab=25.17 E-value=65 Score=29.88 Aligned_cols=31 Identities=16% Similarity=0.362 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHcCCcccChhhHHHHHHHhcc
Q 021082 262 KAEAISRDLLKRGFRLVGPVIVYSFMQAAGL 292 (317)
Q Consensus 262 lS~~lsKdLKkrGFkFVGPttvysFMQAvG~ 292 (317)
....+++.|.+.||+.+..-..+.||+..|+
T Consensus 12 ~l~~lAk~L~~lGf~I~AT~GTAk~L~e~GI 42 (187)
T cd01421 12 GLVEFAKELVELGVEILSTGGTAKFLKEAGI 42 (187)
T ss_pred cHHHHHHHHHHCCCEEEEccHHHHHHHHcCC
Confidence 4668999999999999999899999999997
No 44
>COG4081 Uncharacterized protein conserved in archaea [Function unknown]
Probab=23.93 E-value=58 Score=29.14 Aligned_cols=25 Identities=28% Similarity=0.469 Sum_probs=21.7
Q ss_pred CCCCCCCHHHHHHHHHHHHcCCccc
Q 021082 254 RNVPLRSPKAEAISRDLLKRGFRLV 278 (317)
Q Consensus 254 ~~vP~~t~lS~~lsKdLKkrGFkFV 278 (317)
.++|.+.+.+.-++-.||++||.-.
T Consensus 12 PeiP~qissaiYls~klkkkgf~v~ 36 (148)
T COG4081 12 PEIPPQISSAIYLSHKLKKKGFDVT 36 (148)
T ss_pred CCCCccchHHHHHHHHhhccCccEE
Confidence 3678888999999999999999854
No 45
>PF07647 SAM_2: SAM domain (Sterile alpha motif); InterPro: IPR011510 The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [] involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms []. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins [], nevertheless with a low affinity constant []. SAM domains also appear to possess the ability to bind RNA []. Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologs. These results suggest that the SAM domain might have a primary role in RNA binding. Structural analyses show that the SAM domain is arranged in a small five-helix bundle with two large interfaces []. In the case of the SAM domain of EphB2, each of these interfaces is able to form dimers. The presence of these two distinct intermonomers binding surface suggest that SAM could form extended polymeric structures []. This entry represents a second domain related to the SAM domain. ; GO: 0005515 protein binding; PDB: 1B0X_A 1X9X_B 1OW5_A 1V38_A 3BS7_A 3BS5_A 3TAD_A 3TAC_B 2K60_A 2DL0_A ....
Probab=23.62 E-value=1.3e+02 Score=21.66 Aligned_cols=43 Identities=14% Similarity=0.370 Sum_probs=29.8
Q ss_pred HHHHHHhc--CCCH-HHHhcCCHHHHHHhhCCCcchhchhhHHHHHHh
Q 021082 175 ELFREAFG--GFDP-KSVAKMGEKEILEISSNTAIMLAECRVRCIVDN 219 (317)
Q Consensus 175 ~~fr~AF~--~FD~-~~VA~~~eedie~L~~d~~IIRnr~KI~AVi~N 219 (317)
+.|..+|. ++|- +.++.++++++.++--.. ..+|.||...|..
T Consensus 19 ~~y~~~f~~~~i~g~~~L~~l~~~~L~~lGI~~--~~~r~kll~~i~~ 64 (66)
T PF07647_consen 19 EQYADNFRENGIDGLEDLLQLTEEDLKELGITN--LGHRRKLLSAIQE 64 (66)
T ss_dssp GGGHHHHHHTTCSHHHHHTTSCHHHHHHTTTTH--HHHHHHHHHHHHH
T ss_pred HHHHHHHHHcCCcHHHHHhhCCHHHHHHcCCCC--HHHHHHHHHHHHH
Confidence 56777776 6666 779999999998664322 3466777666554
No 46
>KOG0898 consensus 40S ribosomal protein S15 [Translation, ribosomal structure and biogenesis]
Probab=23.09 E-value=1e+02 Score=27.72 Aligned_cols=32 Identities=25% Similarity=0.567 Sum_probs=28.3
Q ss_pred HHhHHHHHH-HhcCCCHHHHhcCCHHHHHHhhC
Q 021082 171 LKRKELFRE-AFGGFDPKSVAKMGEKEILEISS 202 (317)
Q Consensus 171 LkKR~~fr~-AF~~FD~~~VA~~~eedie~L~~ 202 (317)
++|...|++ .|-|+|++.+..|+-+|+..|+.
T Consensus 13 ~kKKRTFrkftyrGVdld~Lldms~~~~~~l~~ 45 (152)
T KOG0898|consen 13 LKKKRTFRKFTYRGVDLDQLLDMSTEQLVKLFP 45 (152)
T ss_pred HhhhhhhhhccccCCCHHHHhcCCHHHHHHHHH
Confidence 677777776 69999999999999999999887
No 47
>cd00052 EH Eps15 homology domain; found in proteins implicated in endocytosis, vesicle transport, and signal transduction. The alignment contains a pair of EF-hand motifs, typically one of them is canonical and binds to Ca2+, while the other may not bind to Ca2+. A hydrophobic binding pocket is formed by residues from both EF-hand motifs. The EH domain binds to proteins containing NPF (class I), [WF]W or SWG (class II), or H[TS]F (class III) sequence motifs.
Probab=22.82 E-value=39 Score=23.80 Aligned_cols=30 Identities=13% Similarity=0.339 Sum_probs=23.7
Q ss_pred HHHHhcCCCHHHHhcCCHHHHHHhhCCCcc
Q 021082 177 FREAFGGFDPKSVAKMGEKEILEISSNTAI 206 (317)
Q Consensus 177 fr~AF~~FD~~~VA~~~eedie~L~~d~~I 206 (317)
|+++|.-||...=-.++.+++..++...++
T Consensus 1 ~~~~F~~~D~~~~G~i~~~el~~~l~~~g~ 30 (67)
T cd00052 1 YDQIFRSLDPDGDGLISGDEARPFLGKSGL 30 (67)
T ss_pred ChHHHHHhCCCCCCcCcHHHHHHHHHHcCC
Confidence 578899999887777888899888865543
No 48
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=22.66 E-value=1.1e+02 Score=24.82 Aligned_cols=33 Identities=36% Similarity=0.526 Sum_probs=25.4
Q ss_pred HHHHHHHHHHHcCCcccChhhHHH---HHHHhccccc
Q 021082 262 KAEAISRDLLKRGFRLVGPVIVYS---FMQAAGLTID 295 (317)
Q Consensus 262 lS~~lsKdLKkrGFkFVGPttvys---FMQAvG~vnD 295 (317)
-++.|.+.|++.|.+. |.+|||- +|...|+|.-
T Consensus 25 ta~ei~~~l~~~~~~i-s~~TVYR~L~~L~e~Gli~~ 60 (120)
T PF01475_consen 25 TAEEIYDKLRKKGPRI-SLATVYRTLDLLEEAGLIRK 60 (120)
T ss_dssp EHHHHHHHHHHTTTT---HHHHHHHHHHHHHTTSEEE
T ss_pred CHHHHHHHhhhccCCc-CHHHHHHHHHHHHHCCeEEE
Confidence 4678999999988765 9999995 6788999853
No 49
>PF09399 SARS_lipid_bind: SARS lipid binding protein; InterPro: IPR018542 This is a family of proteins found in SARS coronavirus (SARS-CoV) (Severe acute respiratory syndrome coronavirus). The protein has a novel fold which forms a dimeric tent-like beta structure with an amphipathic surface, and a central hydrophobic cavity that binds lipid molecules []. This cavity is likely to be involved in membrane attachment []. ; PDB: 2CME_C.
Probab=22.56 E-value=31 Score=28.37 Aligned_cols=19 Identities=63% Similarity=0.756 Sum_probs=11.9
Q ss_pred ccccccceecccCccccccc
Q 021082 34 KKVYPIGLHRSSSSLSLSSL 53 (317)
Q Consensus 34 ~~~yp~~~~~s~s~~slss~ 53 (317)
-|||||-| |=.|.||||-+
T Consensus 39 pkvypiil-rlgsqlslsm~ 57 (97)
T PF09399_consen 39 PKVYPIIL-RLGSQLSLSMV 57 (97)
T ss_dssp BEEEEEEE---SS-EEEEEE
T ss_pred Cceeeeee-eecchhhhHHH
Confidence 47999965 66777777654
No 50
>PRK09462 fur ferric uptake regulator; Provisional
Probab=22.40 E-value=1e+02 Score=26.30 Aligned_cols=31 Identities=29% Similarity=0.466 Sum_probs=25.6
Q ss_pred HHHHHHHHHHcCCcccChhhHHH---HHHHhcccc
Q 021082 263 AEAISRDLLKRGFRLVGPVIVYS---FMQAAGLTI 294 (317)
Q Consensus 263 S~~lsKdLKkrGFkFVGPttvys---FMQAvG~vn 294 (317)
++.|...|++.|. -+|++|||- +|...|+|.
T Consensus 36 a~eI~~~l~~~~~-~i~~aTVYR~L~~L~e~Gli~ 69 (148)
T PRK09462 36 AEDLYKRLIDMGE-EIGLATVYRVLNQFDDAGIVT 69 (148)
T ss_pred HHHHHHHHHhhCC-CCCHHHHHHHHHHHHHCCCEE
Confidence 6789999999995 599999995 567788874
No 51
>smart00454 SAM Sterile alpha motif. Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerisation.
Probab=20.67 E-value=3e+02 Score=19.08 Aligned_cols=43 Identities=12% Similarity=0.263 Sum_probs=30.2
Q ss_pred HHHHHh--cCCCHHHHhcCC-HHHHHHhhCCCcchhchhhHHHHHHhH
Q 021082 176 LFREAF--GGFDPKSVAKMG-EKEILEISSNTAIMLAECRVRCIVDNA 220 (317)
Q Consensus 176 ~fr~AF--~~FD~~~VA~~~-eedie~L~~d~~IIRnr~KI~AVi~NA 220 (317)
.|.+.| .++|-..+..++ +++++++--.. +-+|.||...|..-
T Consensus 20 ~y~~~f~~~~i~g~~ll~~~~~~~l~~lgi~~--~~~r~~ll~~i~~l 65 (68)
T smart00454 20 QYADNFRKNGIDGALLLLLTSEEDLKELGITK--LGHRKKILKAIQKL 65 (68)
T ss_pred HHHHHHHHCCCCHHHHHhcChHHHHHHcCCCc--HHHHHHHHHHHHHH
Confidence 366666 677888888998 88888875422 35778887766654
No 52
>PF12415 rpo132: Poxvirus DNA dependent RNA polymerase; InterPro: IPR024390 All three classes of poxvirus genes - early, intermediate and late - are transcribed by the viral RNA polymerase compex []. This complex is composed of nine distinct subunits which total more than 500kDa in mass. The two largest subunits (147 and 136kDa) are homologous to the largest subunits of eukaryotic and prokaryotic RNA polymerases and, like them, are thought to form a claw-shaped structure whose cleft is the site of template interaction and phosphodiester bond formation. While the smaller subunits of poxvirus RNA polymerase show much less similarity, if any, to the smaller subunits of the eukaryotic and prokaryotic enzymes, it is thought that they may play a similar role in interacting with transcription factors. The 132kDa subunit is the second largest subunit of the poxvirus DNA dependent RNA polymerase and shows structural similarity to the second-largest RNA polymerase subunits of eubacteria, archaebacteria, and eukaryotes.
Probab=20.57 E-value=91 Score=21.54 Aligned_cols=14 Identities=21% Similarity=0.441 Sum_probs=12.5
Q ss_pred hHHHHHHhHHHHHH
Q 021082 212 RVRCIVDNAKCIVK 225 (317)
Q Consensus 212 KI~AVi~NAr~il~ 225 (317)
+|.|+|+|++.+++
T Consensus 18 lvnalIestk~i~~ 31 (33)
T PF12415_consen 18 LVNALIESTKRILA 31 (33)
T ss_pred HHHHHHHHHHHHHh
Confidence 89999999999864
No 53
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=20.51 E-value=4.2e+02 Score=26.20 Aligned_cols=88 Identities=24% Similarity=0.320 Sum_probs=56.5
Q ss_pred CCCHHHHhcCCHHHHHHhhCCCcchhchhhHHHHHHhHHHHHHHHHhcCCHHHhccccCCCccccCCCCCCCCCCCCCHH
Q 021082 183 GFDPKSVAKMGEKEILEISSNTAIMLAECRVRCIVDNAKCIVKILNEFGSFSSFMWGYVNFKPMINKFRYPRNVPLRSPK 262 (317)
Q Consensus 183 ~FD~~~VA~~~eedie~L~~d~~IIRnr~KI~AVi~NAr~il~i~~E~GSF~~ylWsfv~~kpi~n~~~~~~~vP~~t~l 262 (317)
|.-+++|.+++|..|++|+---+--. +|-.=+-.-|+.++ .+| ..|||.+ +
T Consensus 108 gLT~e~v~~~de~~l~~LI~~VgFy~--rKA~ylkkta~IL~---d~f----------------------~gDIP~~--v 158 (286)
T KOG1921|consen 108 GLTLEAVLKIDEPTLNELIYPVGFYT--RKAKYLKKTAKILQ---DKF----------------------DGDIPDT--V 158 (286)
T ss_pred CCCHHHHhccChHhHHhhhhhccchH--HHHHHHHHHHHHHH---HHh----------------------CCCCchh--H
Confidence 89999999999999999998766644 45554544555443 232 2356642 2
Q ss_pred HHHHHHHHHHcCCcccChhhHHHHHH-Hhccccccccccccchhh
Q 021082 263 AEAISRDLLKRGFRLVGPVIVYSFMQ-AAGLTIDHLVDCFRYSEC 306 (317)
Q Consensus 263 S~~lsKdLKkrGFkFVGPttvysFMQ-AvG~vnDHl~~C~r~~~~ 306 (317)
- +|- +.--|||..+|-.|| |.|-|-.-.++-+.|.-|
T Consensus 159 ~-----dLl--sLPGVGPKMa~L~m~~AWn~i~GI~VDtHVHRi~ 196 (286)
T KOG1921|consen 159 E-----DLL--SLPGVGPKMAHLTMQVAWNKIVGICVDTHVHRIC 196 (286)
T ss_pred H-----HHh--cCCCCchHHHHHHHHHHhccceeEEeehHHHHHH
Confidence 2 222 577899999999998 455544444444444433
Done!