Query 021174
Match_columns 316
No_of_seqs 166 out of 1184
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 08:10:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021174.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021174hhsearch_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 1.1E-88 2.5E-93 608.8 18.8 184 120-304 1-184 (187)
2 TIGR00624 tag DNA-3-methyladen 100.0 1.5E-86 3.3E-91 591.6 18.7 179 121-302 1-179 (179)
3 COG2818 Tag 3-methyladenine DN 100.0 2.8E-85 6.2E-90 585.2 16.5 186 120-305 1-186 (188)
4 PF03352 Adenine_glyco: Methyl 100.0 1.4E-84 2.9E-89 579.1 15.7 179 125-304 1-179 (179)
5 cd00056 ENDO3c endonuclease II 95.6 0.1 2.3E-06 44.3 9.1 104 152-290 1-104 (158)
6 TIGR03252 uncharacterized HhH- 95.4 0.32 6.9E-06 44.4 12.1 117 151-290 18-136 (177)
7 TIGR01083 nth endonuclease III 94.3 0.59 1.3E-05 41.8 10.8 101 151-289 26-126 (191)
8 smart00478 ENDO3c endonuclease 94.1 0.55 1.2E-05 39.6 9.6 88 164-289 5-92 (149)
9 PRK13913 3-methyladenine DNA g 92.8 1.6 3.6E-05 40.7 11.4 77 152-233 31-112 (218)
10 TIGR01084 mutY A/G-specific ad 88.1 4.4 9.5E-05 39.0 9.9 68 151-223 26-93 (275)
11 PRK10702 endonuclease III; Pro 87.3 2.6 5.7E-05 38.9 7.6 69 151-223 29-97 (211)
12 COG0177 Nth Predicted EndoIII- 86.6 4.3 9.4E-05 38.0 8.7 101 150-289 28-129 (211)
13 PF00730 HhH-GPD: HhH-GPD supe 85.7 4.6 9.9E-05 32.1 7.4 63 159-223 4-66 (108)
14 PRK10880 adenine DNA glycosyla 77.4 5.3 0.00011 39.8 5.9 68 151-223 30-97 (350)
15 PF02142 MGS: MGS-like domain 68.3 5.1 0.00011 31.8 2.8 30 263-292 3-32 (95)
16 COG1393 ArsC Arsenate reductas 67.7 5.3 0.00012 33.8 2.9 60 141-207 33-92 (117)
17 cd00166 SAM Sterile alpha moti 64.1 17 0.00038 25.5 4.6 43 174-218 17-61 (63)
18 PRK01229 N-glycosylase/DNA lya 60.6 45 0.00097 31.1 7.9 49 147-203 33-81 (208)
19 PF00536 SAM_1: SAM domain (St 58.6 17 0.00036 26.4 3.8 44 174-219 18-63 (64)
20 COG2231 Uncharacterized protei 56.4 71 0.0015 30.4 8.4 83 131-218 14-97 (215)
21 PRK10308 3-methyl-adenine DNA 52.5 1.5E+02 0.0033 28.5 10.3 118 141-293 103-232 (283)
22 PF13495 Phage_int_SAM_4: Phag 51.0 89 0.0019 23.3 6.9 73 151-225 1-73 (85)
23 PF10023 DUF2265: Predicted am 50.2 13 0.00028 37.3 2.7 103 194-303 33-160 (337)
24 PF13276 HTH_21: HTH-like doma 49.8 20 0.00044 26.0 3.0 31 262-292 23-53 (60)
25 PRK13344 spxA transcriptional 48.7 6.9 0.00015 33.5 0.5 80 120-207 7-91 (132)
26 PF07647 SAM_2: SAM domain (St 46.2 29 0.00063 25.2 3.4 43 174-218 19-64 (66)
27 cd00532 MGS-like MGS-like doma 45.5 25 0.00053 28.8 3.2 32 260-291 12-43 (112)
28 smart00851 MGS MGS-like domain 44.9 23 0.00051 27.6 2.9 29 263-291 3-31 (90)
29 COG0122 AlkA 3-methyladenine D 43.7 1.1E+02 0.0023 29.7 7.8 110 149-291 103-221 (285)
30 cd02977 ArsC_family Arsenate R 42.1 9.3 0.0002 30.6 0.2 46 159-208 45-92 (105)
31 cd01424 MGS_CPS_II Methylglyox 39.3 37 0.00079 27.3 3.3 32 260-291 13-44 (110)
32 PF12401 DUF3662: Protein of u 38.6 17 0.00036 30.7 1.3 25 259-283 76-100 (116)
33 PRK01655 spxA transcriptional 38.0 25 0.00053 29.9 2.2 52 152-207 39-91 (131)
34 cd04883 ACT_AcuB C-terminal AC 37.9 21 0.00045 25.9 1.5 18 262-279 54-71 (72)
35 cd03032 ArsC_Spx Arsenate Redu 37.3 32 0.0007 28.2 2.7 45 160-208 47-92 (115)
36 PHA02517 putative transposase 35.9 40 0.00087 31.1 3.4 31 262-293 48-78 (277)
37 TIGR01529 argR_whole arginine 34.7 45 0.00097 29.2 3.3 31 262-293 19-49 (146)
38 cd01422 MGS Methylglyoxal synt 34.3 45 0.00097 27.8 3.1 33 259-291 11-46 (115)
39 TIGR01617 arsC_related transcr 33.9 20 0.00043 29.5 1.0 54 152-208 38-93 (117)
40 cd00956 Transaldolase_FSA Tran 32.7 22 0.00047 32.7 1.1 34 254-289 83-116 (211)
41 smart00454 SAM Sterile alpha m 32.6 1.3E+02 0.0028 21.0 5.0 43 176-220 21-66 (68)
42 PF00289 CPSase_L_chain: Carba 30.5 33 0.00072 28.5 1.8 21 261-281 87-107 (110)
43 PF05075 DUF684: Protein of un 29.7 91 0.002 30.8 4.9 54 148-201 115-177 (345)
44 PF10911 DUF2717: Protein of u 29.3 30 0.00066 28.0 1.3 42 243-295 3-44 (77)
45 cd01423 MGS_CPS_I_III Methylgl 28.8 62 0.0013 26.3 3.1 32 260-291 13-44 (116)
46 PF13062 DUF3924: Protein of u 28.8 25 0.00055 26.8 0.7 40 4-43 16-56 (62)
47 PRK12559 transcriptional regul 26.2 47 0.001 28.3 2.0 43 161-207 48-91 (131)
48 cd00052 EH Eps15 homology doma 25.8 31 0.00068 24.3 0.7 30 176-205 1-30 (67)
49 cd07153 Fur_like Ferric uptake 25.2 86 0.0019 25.1 3.3 31 262-293 19-52 (116)
50 cd01421 IMPCH Inosine monophos 24.7 67 0.0014 29.8 2.8 32 260-291 11-42 (187)
51 COG4081 Uncharacterized protei 24.4 57 0.0012 29.2 2.2 26 252-277 11-36 (148)
52 cd03036 ArsC_like Arsenate Red 23.5 79 0.0017 25.9 2.8 85 120-208 6-93 (111)
53 PF02173 pKID: pKID domain; I 21.9 41 0.00088 24.3 0.7 17 167-183 13-29 (41)
54 PF08439 Peptidase_M3_N: Oligo 21.3 80 0.0017 23.5 2.2 38 188-225 2-40 (70)
55 PLN02764 glycosyltransferase f 21.0 1.4E+02 0.003 30.9 4.5 83 141-241 359-441 (453)
56 KOG0898 40S ribosomal protein 20.9 1.1E+02 0.0024 27.6 3.2 32 170-201 13-45 (152)
57 COG3200 AroG 3-deoxy-D-arabino 20.8 1.5E+02 0.0033 30.6 4.6 65 208-295 150-222 (445)
58 KOG2198 tRNA cytosine-5-methyl 20.8 1.3E+02 0.0028 30.9 4.1 114 166-292 19-146 (375)
59 PF07592 DDE_Tnp_ISAZ013: Rhod 20.4 1.1E+02 0.0023 30.6 3.4 29 262-291 27-55 (311)
No 1
>PRK10353 3-methyl-adenine DNA glycosylase I; Provisional
Probab=100.00 E-value=1.1e-88 Score=608.78 Aligned_cols=184 Identities=35% Similarity=0.771 Sum_probs=180.2
Q ss_pred CccccCCccCChhhhhhhhcCCCccccChHHHHHHHHHHHhhccccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHh
Q 021174 120 LKRCNWITKNNKVYVAFHDECWGVPVYDDNQLFELLALSGMLMDYNWTEILKRKELFREAFGGFDPKSVAKMGEKEILEI 199 (316)
Q Consensus 120 ~~RC~Wa~~~~~ly~~YHD~EWG~Pv~DDr~LFE~L~LEgfQAGLSW~tILkKRe~fr~AF~~FD~~~VA~~~e~dIerL 199 (316)
|.||.|++ ++|+|++|||+|||+|+|||+.|||+||||+|||||||.|||+||++||+||++|||++||+|+|+|||+|
T Consensus 1 m~rC~W~~-~~~l~~~YHD~eWG~P~~dd~~LFE~L~Le~~QAGLSW~tIL~Kre~fr~aF~~Fd~~~VA~~~e~die~L 79 (187)
T PRK10353 1 MERCGWVS-QDPLYIAYHDNEWGVPETDSKKLFEMICLEGQQAGLSWITVLKKRENYRACFHQFDPVKVAAMQEEDVERL 79 (187)
T ss_pred CCCCCCCC-CChHHHHhhhccCCCcCCCcHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHcCCCHHHHhCCCHHHHHHH
Confidence 46999997 57999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hCCCccccchhhHHHHHHhHHHHHHHHHhcCCHHHhccccCCCccccCCCCCCCCCCCCCHHHHHHHHHHHHcCCcccCh
Q 021174 200 SSNTAIMLAECRVRCIVDNAKCIVKILNEFGSFSSFMWGYVNFKPMINKFRYPRNVPLRSPKAEAISRDLLKRGFRLVGP 279 (316)
Q Consensus 200 m~d~~IIRnr~KI~AvI~NAra~l~i~~e~GSF~~ylWsfv~~kpi~n~~~~~~~vP~~t~~S~~lsKdLKkrGFkFVGP 279 (316)
|+|++|||||+||+|||+|||++++|++|+|||++|||+||+++||+|.+.+..++|++|++|++|||+||||||+||||
T Consensus 80 l~d~~IIRnr~KI~Avi~NA~~~l~i~~e~gSf~~ylW~fv~~~p~~~~~~~~~~~P~~t~~S~~lskdLKkrGFkFvGp 159 (187)
T PRK10353 80 VQDAGIIRHRGKIQAIIGNARAYLQMEQNGEPFADFVWSFVNHQPQVTQATTLSEIPTSTPASDALSKALKKRGFKFVGT 159 (187)
T ss_pred hcCchhHHhHHHHHHHHHHHHHHHHHHHhcCCHHHHHhhccCCCcccCCccchhcCCCCCHHHHHHHHHHHHcCCcccCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHHhccccccccccccchh
Q 021174 280 VIVYSFMQAAGLTIDHLVDCFRYSE 304 (316)
Q Consensus 280 tt~ysfMQAvG~vnDHl~~C~r~~~ 304 (316)
|||||||||+||||||+++|+++..
T Consensus 160 t~~ysfmqA~G~vndH~~~C~~~~~ 184 (187)
T PRK10353 160 TICYSFMQACGLVNDHVVGCCCHPG 184 (187)
T ss_pred HHHHHHHHHHCCccccccCccccCC
Confidence 9999999999999999999999853
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=1.5e-86 Score=591.63 Aligned_cols=179 Identities=34% Similarity=0.760 Sum_probs=175.7
Q ss_pred ccccCCccCChhhhhhhhcCCCccccChHHHHHHHHHHHhhccccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhh
Q 021174 121 KRCNWITKNNKVYVAFHDECWGVPVYDDNQLFELLALSGMLMDYNWTEILKRKELFREAFGGFDPKSVAKMGEKEILEIS 200 (316)
Q Consensus 121 ~RC~Wa~~~~~ly~~YHD~EWG~Pv~DDr~LFE~L~LEgfQAGLSW~tILkKRe~fr~AF~~FD~~~VA~~~e~dIerLm 200 (316)
.||.|++ ++|+|++|||+|||+|+|||+.|||+||||+|||||||.|||+||++||+||+||||++||+|+|++||+||
T Consensus 1 ~rC~W~~-~~~l~~~YHD~eWG~p~~dd~~LFE~L~Le~fQAGLSW~tIL~Kr~~fr~aF~~Fd~~~VA~~~e~~ie~L~ 79 (179)
T TIGR00624 1 VRCGWAS-VDPLYRAYHDNEWGVPLRDSVALFERMSLEGFQAGLSWITVLRKRENYRRAFSGFDIVKVARMTDADVERLL 79 (179)
T ss_pred CCCCCcC-CChHHHHhhhccCCCcCcCCHHHHHHHHHHHHhCcCCHHHHHHhHHHHHHHHcCCCHHHHhCCCHHHHHHHh
Confidence 4899997 579999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCccccchhhHHHHHHhHHHHHHHHHhcCCHHHhccccCCCccccCCCCCCCCCCCCCHHHHHHHHHHHHcCCcccChh
Q 021174 201 SNTAIMLAECRVRCIVDNAKCIVKILNEFGSFSSFMWGYVNFKPMINKFRYPRNVPLRSPKAEAISRDLLKRGFRLVGPV 280 (316)
Q Consensus 201 ~d~~IIRnr~KI~AvI~NAra~l~i~~e~GSF~~ylWsfv~~kpi~n~~~~~~~vP~~t~~S~~lsKdLKkrGFkFVGPt 280 (316)
+|++|||||+||+|||+|||++++|++| ||++|+|+||+++||+|++....++|++|++|++|||+||||||+|||||
T Consensus 80 ~d~~IIRnr~KI~Avi~NA~~~l~i~~e--sf~~ylW~fv~~~Pi~~~~~~~~~~p~~t~~S~~lskdLKkrGfkFvGpt 157 (179)
T TIGR00624 80 QDDGIIRNRGKIEATIANARAALQLEQN--DLVEFLWSFVNHQPQPRQRPTDSEIPSSTPESKAMSKELKKRGFRFVGPT 157 (179)
T ss_pred cCccchhhHHHHHHHHHHHHHHHHHHHc--cHHHHHHhccCCCCccCCccccccCCCCCHHHHHHHHHHHHcCCeecChH
Confidence 9999999999999999999999999887 99999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHhccccccccccccc
Q 021174 281 IVYSFMQAAGLTIDHLVDCFRY 302 (316)
Q Consensus 281 t~ysfMQAvG~vnDHl~~C~r~ 302 (316)
||||||||+||||||+++|+++
T Consensus 158 ~~ysfmqA~G~vndH~~~C~~~ 179 (179)
T TIGR00624 158 ICYALMQATGMVDDHIQGCWVY 179 (179)
T ss_pred HHHHHHHHHCCccccccCCcCC
Confidence 9999999999999999999985
No 3
>COG2818 Tag 3-methyladenine DNA glycosylase [DNA replication, recombination, and repair]
Probab=100.00 E-value=2.8e-85 Score=585.19 Aligned_cols=186 Identities=41% Similarity=0.812 Sum_probs=181.6
Q ss_pred CccccCCccCChhhhhhhhcCCCccccChHHHHHHHHHHHhhccccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHh
Q 021174 120 LKRCNWITKNNKVYVAFHDECWGVPVYDDNQLFELLALSGMLMDYNWTEILKRKELFREAFGGFDPKSVAKMGEKEILEI 199 (316)
Q Consensus 120 ~~RC~Wa~~~~~ly~~YHD~EWG~Pv~DDr~LFE~L~LEgfQAGLSW~tILkKRe~fr~AF~~FD~~~VA~~~e~dIerL 199 (316)
+.||.|+...+|+|.+|||+|||+|++||+.|||+||||||||||||.|||+|||+||+||++|||++||.|+|+|||+|
T Consensus 1 ~~rC~w~~~~~ply~~YHD~eWG~p~~Dd~~LFE~l~Le~fQAGLSW~tVL~KRe~freaF~~Fd~~kVA~~~~~dverL 80 (188)
T COG2818 1 MNRCAWAGGLDPLYLAYHDTEWGVPLHDDQRLFELLCLEGFQAGLSWLTVLKKREAFREAFHGFDPEKVAAMTEEDVERL 80 (188)
T ss_pred CCcccccCCCCchhhcccccccCCCCCChHHHHHHHHHHHHhccchHHHHHHhHHHHHHHHhcCCHHHHHcCCHHHHHHH
Confidence 46999997547999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hCCCccccchhhHHHHHHhHHHHHHHHHhcCCHHHhccccCCCccccCCCCCCCCCCCCCHHHHHHHHHHHHcCCcccCh
Q 021174 200 SSNTAIMLAECRVRCIVDNAKCIVKILNEFGSFSSFMWGYVNFKPMINKFRYPRNVPLRSPKAEAISRDLLKRGFRLVGP 279 (316)
Q Consensus 200 m~d~~IIRnr~KI~AvI~NAra~l~i~~e~GSF~~ylWsfv~~kpi~n~~~~~~~vP~~t~~S~~lsKdLKkrGFkFVGP 279 (316)
|+|++|||||+||.|||+|||++++|++|+|||++|||+||+++|.++++.+..++|+.|++|++|||+||||||+||||
T Consensus 81 l~d~gIIR~r~KI~A~i~NA~~~l~l~~e~Gsf~~flWsf~~~~~~~~~~~~~~~~pa~t~~S~~mskaLKkrGf~fvGp 160 (188)
T COG2818 81 LADAGIIRNRGKIKATINNARAVLELQKEFGSFSEFLWSFVGGKPSRNQVNDGSEVPASTELSDAMSKALKKRGFKFVGP 160 (188)
T ss_pred HhCcchhhhHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHhcCCCcccccccchhhccccchhHHHHHHHHHHccCeecCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHHhccccccccccccchhh
Q 021174 280 VIVYSFMQAAGLTIDHLVDCFRYSEC 305 (316)
Q Consensus 280 tt~ysfMQAvG~vnDHl~~C~r~~~~ 305 (316)
||||+||||+|+||||+.+|+++..+
T Consensus 161 Tt~yafmqA~G~vndH~~~C~~~~~~ 186 (188)
T COG2818 161 TTVYAFMQATGLVNDHAEGCPCRREI 186 (188)
T ss_pred HHHHHHHHHHcchHHHHhcCCCcccc
Confidence 99999999999999999999998653
No 4
>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=1.4e-84 Score=579.05 Aligned_cols=179 Identities=51% Similarity=0.990 Sum_probs=154.2
Q ss_pred CCccCChhhhhhhhcCCCccccChHHHHHHHHHHHhhccccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhhCCCc
Q 021174 125 WITKNNKVYVAFHDECWGVPVYDDNQLFELLALSGMLMDYNWTEILKRKELFREAFGGFDPKSVAKMGEKEILEISSNTA 204 (316)
Q Consensus 125 Wa~~~~~ly~~YHD~EWG~Pv~DDr~LFE~L~LEgfQAGLSW~tILkKRe~fr~AF~~FD~~~VA~~~e~dIerLm~d~~ 204 (316)
|+. ++|+|++|||+|||+|+|||++|||+||||+|||||||.|||+||++||+||+||||++||+|+|+||++||+|++
T Consensus 1 W~~-~~~~~~~YHD~eWG~P~~dD~~LFe~L~Le~fQaGLsW~~Il~Kr~~~r~aF~~Fd~~~vA~~~e~~ie~l~~d~~ 79 (179)
T PF03352_consen 1 WAN-SDPLYRAYHDEEWGRPVHDDRKLFEMLTLEGFQAGLSWSTILKKREAFREAFAGFDPEKVAKMDEEDIERLMQDPG 79 (179)
T ss_dssp TTT-SSHHHHHHHHHTTTSS---HHHHHHHHHHHHHTTTS-HHHHHHTHHHHHHHTGGGHHHHHHT--HHHHHHHTTSTT
T ss_pred CCC-CChHHHHHhcccCCCcccCHHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHCCCHHHHHcCCHHHHHHHhcCcc
Confidence 886 4699999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccchhhHHHHHHhHHHHHHHHHhcCCHHHhccccCCCccccCCCCCCCCCCCCCHHHHHHHHHHHHcCCcccChhhHHH
Q 021174 205 IMLAECRVRCIVDNAKCIVKILNEFGSFSSFMWGYVNFKPMINKFRYPRNVPLRSPKAEAISRDLLKRGFRLVGPVIVYS 284 (316)
Q Consensus 205 IIRnr~KI~AvI~NAra~l~i~~e~GSF~~ylWsfv~~kpi~n~~~~~~~vP~~t~~S~~lsKdLKkrGFkFVGPtt~ys 284 (316)
|||||+||+|||+||+++++|++++|||++|||+||+++||++.+.+..++|++|++|++|||+|||+||+|||||||||
T Consensus 80 iIRnr~KI~Avi~NA~~~l~i~~e~gsF~~ylw~f~~~~~i~~~~~~~~~~p~~t~~s~~isk~lkk~GF~FvGpt~vys 159 (179)
T PF03352_consen 80 IIRNRRKIRAVINNARAILKIQEEFGSFSDYLWSFVNGKPIVNHWRSPEDVPASTPLSEAISKDLKKRGFKFVGPTTVYS 159 (179)
T ss_dssp SS--HHHHHHHHHHHHHHHHHHHTTS-HHHHHHHCTTTS-EE---SSGGGS-S--HHHHHHHHHHHHTT--S--HHHHHH
T ss_pred hhhhHHHHHHHHHHHHHHHHHHHhcCCHHHHHHhcCCCcCccccccccccCcCccHHHHHHHHHHHhCcceeECHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhccccccccccccchh
Q 021174 285 FMQAAGLTIDHLVDCFRYSE 304 (316)
Q Consensus 285 fMQAvG~vnDHl~~C~r~~~ 304 (316)
||||+||||||+++|++|.+
T Consensus 160 flqA~G~vndH~~~C~~~~~ 179 (179)
T PF03352_consen 160 FLQAIGMVNDHLVDCFRHQE 179 (179)
T ss_dssp HHHHTTSEE-SSTTSTTS--
T ss_pred HHHHhCCccccccCccccCC
Confidence 99999999999999999864
No 5
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=95.55 E-value=0.1 Score=44.34 Aligned_cols=104 Identities=21% Similarity=0.248 Sum_probs=79.8
Q ss_pred HHHHHHHHhhccccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhhCCCccccchhhHHHHHHhHHHHHHHHHhcCC
Q 021174 152 FELLALSGMLMDYNWTEILKRKELFREAFGGFDPKSVAKMGEKEILEISSNTAIMLAECRVRCIVDNAKCIVKILNEFGS 231 (316)
Q Consensus 152 FE~L~LEgfQAGLSW~tILkKRe~fr~AF~~FD~~~VA~~~e~dIerLm~d~~IIRnr~KI~AvI~NAra~l~i~~e~GS 231 (316)
||.|+-.++..-.||..+.+-...|.+.|. .+|+.|+..+++++..+...-| .+.|.+.++.=|+.+.+ .+++
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 678888888888999999999999998886 7999999999999999877766 57899999888888753 4444
Q ss_pred HHHhccccCCCccccCCCCCCCCCCCCCHHHHHHHHHHHHcCCcccChhhHHHHHHHhc
Q 021174 232 FSSFMWGYVNFKPMINKFRYPRNVPLRSPKAEAISRDLLKRGFRLVGPVIVYSFMQAAG 290 (316)
Q Consensus 232 F~~ylWsfv~~kpi~n~~~~~~~vP~~t~~S~~lsKdLKkrGFkFVGPtt~ysfMQAvG 290 (316)
+.. + . +.+-+.|. .++=|||-|+-.+|.-+.
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 12334555 478899999988877543
No 6
>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=95.39 E-value=0.32 Score=44.36 Aligned_cols=117 Identities=15% Similarity=0.204 Sum_probs=81.0
Q ss_pred HHHHHHHHHhhccccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhhCC-Ccccc-chhhHHHHHHhHHHHHHHHHh
Q 021174 151 LFELLALSGMLMDYNWTEILKRKELFREAFGGFDPKSVAKMGEKEILEISSN-TAIML-AECRVRCIVDNAKCIVKILNE 228 (316)
Q Consensus 151 LFE~L~LEgfQAGLSW~tILkKRe~fr~AF~~FD~~~VA~~~e~dIerLm~d-~~IIR-nr~KI~AvI~NAra~l~i~~e 228 (316)
-||.|+--+.-+--+|..|.+=-+.+.+.+...||+.+++++.++|++++.. |++.+ .+.|=+-+.+=|+.+ .++
T Consensus 18 pFelLVa~ILSQqTtd~nv~kA~~~L~~~~g~~tp~~La~a~~eeL~~lI~~~pal~Gfy~~KAk~Lk~~a~~i---ie~ 94 (177)
T TIGR03252 18 PFALLTGMLLDQQVPMERAFAGPHKIARRMGSLDAEDIAKYDPQAFVALFSERPAVHRFPGSMAKRVQALAQYV---VDT 94 (177)
T ss_pred hHHHHHHHHHhccCcHHHHHHHHHHHHHHhCCCCHHHHHcCCHHHHHHHHhcCccccCchHHHHHHHHHHHHHH---HHH
Confidence 3899999999999999999987777755444489999999999999999874 45444 235555555555555 346
Q ss_pred cCCHHHhccccCCCccccCCCCCCCCCCCCCHHHHHHHHHHHHcCCcccChhhHHHHHHHhc
Q 021174 229 FGSFSSFMWGYVNFKPMINKFRYPRNVPLRSPKAEAISRDLLKRGFRLVGPVIVYSFMQAAG 290 (316)
Q Consensus 229 ~GSF~~ylWsfv~~kpi~n~~~~~~~vP~~t~~S~~lsKdLKkrGFkFVGPtt~ysfMQAvG 290 (316)
||+=-+-||.. .+|. ...+-+.|.+ ++=|||.|+--+|.-.|
T Consensus 95 y~G~v~~L~~~--------------~~p~----t~~lre~Ll~--LpGVG~KTAnvVL~~l~ 136 (177)
T TIGR03252 95 YDGDATAVWTE--------------GDPD----GKELLRRLKA--LPGFGKQKAKIFLALLG 136 (177)
T ss_pred hCCChhhhhcc--------------cCCC----cHHHHHHHHc--CCCCCHHHHHHHHHHHH
Confidence 55433334432 0121 2233456665 78999999999888776
No 7
>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=94.29 E-value=0.59 Score=41.83 Aligned_cols=101 Identities=21% Similarity=0.308 Sum_probs=74.5
Q ss_pred HHHHHHHHHhhccccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhhCCCccccchhhHHHHHHhHHHHHHHHHhcC
Q 021174 151 LFELLALSGMLMDYNWTEILKRKELFREAFGGFDPKSVAKMGEKEILEISSNTAIMLAECRVRCIVDNAKCIVKILNEFG 230 (316)
Q Consensus 151 LFE~L~LEgfQAGLSW~tILkKRe~fr~AF~~FD~~~VA~~~e~dIerLm~d~~IIRnr~KI~AvI~NAra~l~i~~e~G 230 (316)
-||.|+-++.-.--+|..+.+--..+.+.|- +|+.|+..+++++++++.--|.-+ .|.+.+++=|+++.+ ++|
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 4899999999899999999988888877664 899999999999999888767654 677777777777643 332
Q ss_pred CHHHhccccCCCccccCCCCCCCCCCCCCHHHHHHHHHHHHcCCcccChhhHHHHHHHh
Q 021174 231 SFSSFMWGYVNFKPMINKFRYPRNVPLRSPKAEAISRDLLKRGFRLVGPVIVYSFMQAA 289 (316)
Q Consensus 231 SF~~ylWsfv~~kpi~n~~~~~~~vP~~t~~S~~lsKdLKkrGFkFVGPtt~ysfMQAv 289 (316)
+ .+|. .-+.|.+ ++-|||.|+..+|.-.
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 1121 1234554 7889999988877433
No 8
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=94.05 E-value=0.55 Score=39.63 Aligned_cols=88 Identities=24% Similarity=0.354 Sum_probs=65.0
Q ss_pred ccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhhCCCccccchhhHHHHHHhHHHHHHHHHhcCCHHHhccccCCCc
Q 021174 164 YNWTEILKRKELFREAFGGFDPKSVAKMGEKEILEISSNTAIMLAECRVRCIVDNAKCIVKILNEFGSFSSFMWGYVNFK 243 (316)
Q Consensus 164 LSW~tILkKRe~fr~AF~~FD~~~VA~~~e~dIerLm~d~~IIRnr~KI~AvI~NAra~l~i~~e~GSF~~ylWsfv~~k 243 (316)
.+|..+.+--..|.+.|- +|+.++..++++|++++..-+ -.+.|.+.+++.|+.+.+ ++++
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 799999999999999887644 346689999999988754 2211
Q ss_pred cccCCCCCCCCCCCCCHHHHHHHHHHHHcCCcccChhhHHHHHHHh
Q 021174 244 PMINKFRYPRNVPLRSPKAEAISRDLLKRGFRLVGPVIVYSFMQAA 289 (316)
Q Consensus 244 pi~n~~~~~~~vP~~t~~S~~lsKdLKkrGFkFVGPtt~ysfMQAv 289 (316)
.+| ...+.|.+ ++-|||-|+-.||.-+
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 012 12355654 8999999998887665
No 9
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=92.84 E-value=1.6 Score=40.71 Aligned_cols=77 Identities=21% Similarity=0.330 Sum_probs=59.8
Q ss_pred HHHHHHHHhhccccHHHHHHhHHHHHHHhc-----CCCHHHHhcCCHHHHHHhhCCCccccchhhHHHHHHhHHHHHHHH
Q 021174 152 FELLALSGMLMDYNWTEILKRKELFREAFG-----GFDPKSVAKMGEKEILEISSNTAIMLAECRVRCIVDNAKCIVKIL 226 (316)
Q Consensus 152 FE~L~LEgfQAGLSW~tILkKRe~fr~AF~-----~FD~~~VA~~~e~dIerLm~d~~IIRnr~KI~AvI~NAra~l~i~ 226 (316)
||.|+-.+.-.--+|..|.+--+++++++. .-+|+.|+.+++++|++++.-.|.- |.|.+.+.+=|+.+.
T Consensus 31 fevLV~aILsQqT~~~~v~~a~~~L~~~~~~~~~~~~t~e~L~~a~~eeL~~~Irp~Gf~--~~KA~~Lk~la~~i~--- 105 (218)
T PRK13913 31 FEALLGAVLTQNTKFEAVEKSLENLKNAFILENDDEINLKKIAYIEFSKLAECVRPSGFY--NQKAKRLIDLSENIL--- 105 (218)
T ss_pred HHHHHHHHHHhhhhHHHHHHHHHHHHHhcccccccCCCHHHHHcCCHHHHHHHHHhcCCH--HHHHHHHHHHHHHHH---
Confidence 788888877777889999888888877763 2389999999999999999888764 556667766677664
Q ss_pred HhcCCHH
Q 021174 227 NEFGSFS 233 (316)
Q Consensus 227 ~e~GSF~ 233 (316)
+++|+++
T Consensus 106 ~~~g~~~ 112 (218)
T PRK13913 106 KDFGSFE 112 (218)
T ss_pred HHcCCch
Confidence 4667765
No 10
>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=88.09 E-value=4.4 Score=38.97 Aligned_cols=68 Identities=21% Similarity=0.257 Sum_probs=56.6
Q ss_pred HHHHHHHHHhhccccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhhCCCccccchhhHHHHHHhHHHHH
Q 021174 151 LFELLALSGMLMDYNWTEILKRKELFREAFGGFDPKSVAKMGEKEILEISSNTAIMLAECRVRCIVDNAKCIV 223 (316)
Q Consensus 151 LFE~L~LEgfQAGLSW~tILkKRe~fr~AF~~FD~~~VA~~~e~dIerLm~d~~IIRnr~KI~AvI~NAra~l 223 (316)
.|+.|+-|++-.=-+|.+|..-.+.|.+.|- +|+.+|..++++|..+..--|.- + |.+.+.+=|+.+.
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 69999999999999998877875 3 4556665556553
No 11
>PRK10702 endonuclease III; Provisional
Probab=87.26 E-value=2.6 Score=38.86 Aligned_cols=69 Identities=10% Similarity=0.146 Sum_probs=55.8
Q ss_pred HHHHHHHHHhhccccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhhCCCccccchhhHHHHHHhHHHHH
Q 021174 151 LFELLALSGMLMDYNWTEILKRKELFREAFGGFDPKSVAKMGEKEILEISSNTAIMLAECRVRCIVDNAKCIV 223 (316)
Q Consensus 151 LFE~L~LEgfQAGLSW~tILkKRe~fr~AF~~FD~~~VA~~~e~dIerLm~d~~IIRnr~KI~AvI~NAra~l 223 (316)
-||.|+-++.-+--+|..|.+--+.+.+.| .+|+.+++.++++|++++.--|.-+.|.| .+++.|+.++
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--NTPAAMLELGVEGVKTYIKTIGLYNSKAE--NVIKTCRILL 97 (211)
T ss_pred hHHHHHHHHHHhhcCHHHHHHHHHHHHHHc--CCHHHHHCCCHHHHHHHHHHcCCHHHHHH--HHHHHHHHHH
Confidence 499999999988899999998888887665 47899999999999999887776555554 5666777764
No 12
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=86.61 E-value=4.3 Score=38.02 Aligned_cols=101 Identities=21% Similarity=0.289 Sum_probs=65.9
Q ss_pred HHHHHHHHHHhhccccHHHHHHhHHHHHHHhcCC-CHHHHhcCCHHHHHHhhCCCccccchhhHHHHHHhHHHHHHHHHh
Q 021174 150 QLFELLALSGMLMDYNWTEILKRKELFREAFGGF-DPKSVAKMGEKEILEISSNTAIMLAECRVRCIVDNAKCIVKILNE 228 (316)
Q Consensus 150 ~LFE~L~LEgfQAGLSW~tILkKRe~fr~AF~~F-D~~~VA~~~e~dIerLm~d~~IIRnr~KI~AvI~NAra~l~i~~e 228 (316)
--||+|+--+.-|-=+=..+-+ +.++.|.-| +|+.++..++++|+.+...-|+-||++| .|+.=|+.++ ++
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---ATPALFKRYPTPEDLLNADEEELEELIKSIGLYRNKAK--NIKELARILL---EK 99 (211)
T ss_pred CcHHHHHHHHHhccCchHHHHH---HHHHHHHHcCCHHHHHcCCHHHHHHHHHhcCCcHHHHH--HHHHHHHHHH---HH
Confidence 3478776555444444444444 444444444 4999999999999999998888776554 6777777764 56
Q ss_pred cCCHHHhccccCCCccccCCCCCCCCCCCCCHHHHHHHHHHHHcCCcccChhhHHHHHHHh
Q 021174 229 FGSFSSFMWGYVNFKPMINKFRYPRNVPLRSPKAEAISRDLLKRGFRLVGPVIVYSFMQAA 289 (316)
Q Consensus 229 ~GSF~~ylWsfv~~kpi~n~~~~~~~vP~~t~~S~~lsKdLKkrGFkFVGPtt~ysfMQAv 289 (316)
||+ +||..- ++|-+ .--||+-|++=.|.-+
T Consensus 100 ~~g----------------------~vP~~~-------~eL~~--LPGVGrKTAnvVL~~a 129 (211)
T COG0177 100 FGG----------------------EVPDTR-------EELLS--LPGVGRKTANVVLSFA 129 (211)
T ss_pred cCC----------------------CCCchH-------HHHHh--CCCcchHHHHHHHHhh
Confidence 666 334311 12332 4569999999888764
No 13
>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=85.70 E-value=4.6 Score=32.11 Aligned_cols=63 Identities=17% Similarity=0.224 Sum_probs=52.2
Q ss_pred HhhccccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhhCCCccccchhhHHHHHHhHHHHH
Q 021174 159 GMLMDYNWTEILKRKELFREAFGGFDPKSVAKMGEKEILEISSNTAIMLAECRVRCIVDNAKCIV 223 (316)
Q Consensus 159 gfQAGLSW~tILkKRe~fr~AF~~FD~~~VA~~~e~dIerLm~d~~IIRnr~KI~AvI~NAra~l 223 (316)
++..-.+|..+.+-...|.+.|...+|+.|+..++++|.++...-|+ ++.|-+.+++=|+.++
T Consensus 4 Il~qq~s~~~a~~~~~~l~~~~g~pt~~~l~~~~~~el~~~i~~~G~--~~~ka~~i~~~a~~~~ 66 (108)
T PF00730_consen 4 ILSQQTSIKAARKIYRRLFERYGFPTPEALAEASEEELRELIRPLGF--SRRKAKYIIELARAIL 66 (108)
T ss_dssp HHCTTS-HHHHHHHHHHHHHHHSCSSHHHHHCSHHHHHHHHHTTSTS--HHHHHHHHHHHHHHHH
T ss_pred eecCcCcHHHHHHHHHHHHHHhcCCCHHHHHhCCHHHHHHHhhccCC--CHHHHHHHHHHHHHhh
Confidence 34445689999999999999999999999999999999999987444 5577778888888886
No 14
>PRK10880 adenine DNA glycosylase; Provisional
Probab=77.43 E-value=5.3 Score=39.83 Aligned_cols=68 Identities=18% Similarity=0.193 Sum_probs=57.8
Q ss_pred HHHHHHHHHhhccccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhhCCCccccchhhHHHHHHhHHHHH
Q 021174 151 LFELLALSGMLMDYNWTEILKRKELFREAFGGFDPKSVAKMGEKEILEISSNTAIMLAECRVRCIVDNAKCIV 223 (316)
Q Consensus 151 LFE~L~LEgfQAGLSW~tILkKRe~fr~AF~~FD~~~VA~~~e~dIerLm~d~~IIRnr~KI~AvI~NAra~l 223 (316)
-|+.|+-|++-.=-+|.+|..--+.|.+.| -+++.+|..++++|.++..--|.= + |.+-+.+-|+.+.
T Consensus 30 py~ilVseILlQQT~v~~v~~~~~rl~~~f--Pt~~~La~a~~eel~~~~~glGyy-~--RAr~L~~~A~~i~ 97 (350)
T PRK10880 30 PYKVWLSEVMLQQTQVATVIPYFERFMARF--PTVTDLANAPLDEVLHLWTGLGYY-A--RARNLHKAAQQVA 97 (350)
T ss_pred HHHHHHHHHHHhhccHHHHHHHHHHHHHHC--cCHHHHHCcCHHHHHHHHHcCChH-H--HHHHHHHHHHHHH
Confidence 478999999999999999999999999987 479999999999999999888874 2 6667777777664
No 15
>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=68.31 E-value=5.1 Score=31.78 Aligned_cols=30 Identities=17% Similarity=0.380 Sum_probs=26.5
Q ss_pred HHHHHHHHHcCCcccChhhHHHHHHHhccc
Q 021174 263 EAISRDLLKRGFRLVGPVIVYSFMQAAGLT 292 (316)
Q Consensus 263 ~~lsKdLKkrGFkFVGPtt~ysfMQAvG~v 292 (316)
..++|.|.+.||++++.-..+.||+..|+-
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 16
>COG1393 ArsC Arsenate reductase and related proteins, glutaredoxin family [Inorganic ion transport and metabolism]
Probab=67.71 E-value=5.3 Score=33.82 Aligned_cols=60 Identities=8% Similarity=0.029 Sum_probs=44.2
Q ss_pred CCccccChHHHHHHHHHHHhhccccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhhCCCcccc
Q 021174 141 WGVPVYDDNQLFELLALSGMLMDYNWTEILKRKELFREAFGGFDPKSVAKMGEKEILEISSNTAIML 207 (316)
Q Consensus 141 WG~Pv~DDr~LFE~L~LEgfQAGLSW~tILkKRe~fr~AF~~FD~~~VA~~~e~dIerLm~d~~IIR 207 (316)
...-..+...|=+. .-++|..|..++++|..+-+... .++..-.+++.++.||.++.+||
T Consensus 33 y~~~~~s~~eL~~~----l~~~g~~~~~li~t~~~~~r~L~---~~~~~~~~~~~~~~i~~~~~Lik 92 (117)
T COG1393 33 YLKTPPSREELKKI----LSKLGDGVEELINTRGTTYRELN---LDKEDLSDEELIEALLENPSLIK 92 (117)
T ss_pred eecCCCCHHHHHHH----HHHcCccHHHHHHhccchHHHcC---CcccccChHHHHHHHHhChhhcc
Confidence 33333444445343 45789999999999998877776 55667778888999999997776
No 17
>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=64.06 E-value=17 Score=25.45 Aligned_cols=43 Identities=12% Similarity=0.222 Sum_probs=32.7
Q ss_pred HHHHHHh--cCCCHHHHhcCCHHHHHHhhCCCccccchhhHHHHHHh
Q 021174 174 ELFREAF--GGFDPKSVAKMGEKEILEISSNTAIMLAECRVRCIVDN 218 (316)
Q Consensus 174 e~fr~AF--~~FD~~~VA~~~e~dIerLm~d~~IIRnr~KI~AvI~N 218 (316)
+.|...| .++|-..+..++++++.++--.. .-+|.||...|..
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 57899999999999999554322 5688888777654
No 18
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=60.64 E-value=45 Score=31.14 Aligned_cols=49 Identities=16% Similarity=0.177 Sum_probs=41.0
Q ss_pred ChHHHHHHHHHHHhhccccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhhCCC
Q 021174 147 DDNQLFELLALSGMLMDYNWTEILKRKELFREAFGGFDPKSVAKMGEKEILEISSNT 203 (316)
Q Consensus 147 DDr~LFE~L~LEgfQAGLSW~tILkKRe~fr~AF~~FD~~~VA~~~e~dIerLm~d~ 203 (316)
++.-+|+.|+..+.-+.-+|..+.+--+.+. ++.+ .+++++|++++.-.
T Consensus 33 ~~~~~f~~Lv~~ILsqnT~~~~v~~a~~~L~-------~~~l-~~~~eeL~~~Ir~~ 81 (208)
T PRK01229 33 DEEDLFSELSFCILTANSSAEGGIKAQKEIG-------DGFL-YLSEEELEEKLKEV 81 (208)
T ss_pred ccCChHHHHHHHHhcCcCcHHHHHHHHHhcC-------HHHc-CCCHHHHHHHHHHh
Confidence 7888999999999999999999988776663 3445 78999999998654
No 19
>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=58.63 E-value=17 Score=26.39 Aligned_cols=44 Identities=14% Similarity=0.296 Sum_probs=32.8
Q ss_pred HHHHHHh-cCC-CHHHHhcCCHHHHHHhhCCCccccchhhHHHHHHhH
Q 021174 174 ELFREAF-GGF-DPKSVAKMGEKEILEISSNTAIMLAECRVRCIVDNA 219 (316)
Q Consensus 174 e~fr~AF-~~F-D~~~VA~~~e~dIerLm~d~~IIRnr~KI~AvI~NA 219 (316)
+.|...| .++ |-..+..++++|+++|-- ..+-||.||...|..-
T Consensus 18 ~~y~~~F~~~~i~g~~L~~lt~~dL~~lgi--~~~ghr~ki~~~i~~L 63 (64)
T PF00536_consen 18 EQYAENFEKNYIDGEDLLSLTEEDLEELGI--TKLGHRKKILRAIQKL 63 (64)
T ss_dssp GGGHHHHHHTTSSHHHHTTSCHHHHHHTT---SSHHHHHHHHHHHHHH
T ss_pred HHHHHHHHcCCchHHHHHhcCHHHHHHcCC--CCHHHHHHHHHHHHHh
Confidence 6677777 444 999999999999999422 2256899998887643
No 20
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=56.35 E-value=71 Score=30.38 Aligned_cols=83 Identities=16% Similarity=0.299 Sum_probs=61.4
Q ss_pred hhhhhhhhcCCCccccChHHHHHHHHHHHhhccccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhhCCCccccchh
Q 021174 131 KVYVAFHDECWGVPVYDDNQLFELLALSGMLMDYNWTEILKRKELFREAFGGFDPKSVAKMGEKEILEISSNTAIMLAEC 210 (316)
Q Consensus 131 ~ly~~YHD~EWG~Pv~DDr~LFE~L~LEgfQAGLSW~tILkKRe~fr~AF~~FD~~~VA~~~e~dIerLm~d~~IIRnr~ 210 (316)
.++.-|+|.-|=--...+ |.++=-+.-=--||.-|.+.-++++..+. +++++|..+++++++++..-.|--+-..
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 467788988885433333 55554455556789999999999998764 6799999999999999999888876554
Q ss_pred h-HHHHHHh
Q 021174 211 R-VRCIVDN 218 (316)
Q Consensus 211 K-I~AvI~N 218 (316)
| +.|.+.|
T Consensus 89 ~rLk~l~k~ 97 (215)
T COG2231 89 KRLKALSKN 97 (215)
T ss_pred HHHHHHHHH
Confidence 4 4444443
No 21
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=52.49 E-value=1.5e+02 Score=28.52 Aligned_cols=118 Identities=14% Similarity=0.145 Sum_probs=72.4
Q ss_pred CCccccChHHHHHHHHHHHhhccccHHHHHHhHHHHHHHhc----------CC-CHHHHhcCCHHHHHHhhCCCccccch
Q 021174 141 WGVPVYDDNQLFELLALSGMLMDYNWTEILKRKELFREAFG----------GF-DPKSVAKMGEKEILEISSNTAIMLAE 209 (316)
Q Consensus 141 WG~Pv~DDr~LFE~L~LEgfQAGLSW~tILkKRe~fr~AF~----------~F-D~~~VA~~~e~dIerLm~d~~IIRnr 209 (316)
=|..+.-..-.||.|+--+.-.-.|=..+.+-...+-+.|. -| +|+.|+..+++++..+ ++ .+
T Consensus 103 ~GlR~p~~~d~fE~lv~aIigQqisv~~a~~~~~rlv~~~G~~l~~~~~~~~FPtpe~La~~~~~eL~~~----Gl--~~ 176 (283)
T PRK10308 103 PGLRLPGSVDAFEQGVRAILGQLVSVAMAAKLTAKVAQLYGERLDDFPEYVCFPTPERLAAADPQALKAL----GM--PL 176 (283)
T ss_pred CCCcCCCCCCHHHHHHHHHHHhHHHHHHHHHHHHHHHHHhCccccCCCCccCCCCHHHHHcCCHHHHHHC----CC--CH
Confidence 36556555667998887764444443333333333444433 34 7999999999988753 33 35
Q ss_pred hhHHHHHHhHHHHHHHHHhcCCHHHhccccCCCccccCCCCCCCCCCCCCHHHHHHHHHHHHcCCcccChhhH-HHHHHH
Q 021174 210 CRVRCIVDNAKCIVKILNEFGSFSSFMWGYVNFKPMINKFRYPRNVPLRSPKAEAISRDLLKRGFRLVGPVIV-YSFMQA 288 (316)
Q Consensus 210 ~KI~AvI~NAra~l~i~~e~GSF~~ylWsfv~~kpi~n~~~~~~~vP~~t~~S~~lsKdLKkrGFkFVGPtt~-ysfMQA 288 (316)
.|.++++.=|+++.+ |.+.- .+ +. + .+++-+.|.+ ++=|||-|+ |-.|.+
T Consensus 177 ~Ra~~L~~lA~~i~~-----g~l~l--------~~-----------~~--~-~~~~~~~L~~--LpGIGpwTA~~vllr~ 227 (283)
T PRK10308 177 KRAEALIHLANAALE-----GTLPL--------TI-----------PG--D-VEQAMKTLQT--FPGIGRWTANYFALRG 227 (283)
T ss_pred HHHHHHHHHHHHHHc-----CCCCc--------cc-----------cC--C-HHHHHHHHhc--CCCcCHHHHHHHHHHh
Confidence 688888888887753 33220 00 10 1 1345566766 899999888 777788
Q ss_pred hcccc
Q 021174 289 AGLTI 293 (316)
Q Consensus 289 vG~vn 293 (316)
.|-.+
T Consensus 228 lg~~D 232 (283)
T PRK10308 228 WQAKD 232 (283)
T ss_pred CCCCC
Confidence 88643
No 22
>PF13495 Phage_int_SAM_4: Phage integrase, N-terminal SAM-like domain; PDB: 2A3V_A.
Probab=51.03 E-value=89 Score=23.27 Aligned_cols=73 Identities=8% Similarity=-0.005 Sum_probs=46.4
Q ss_pred HHHHHHHHHhhccccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhhCCCccccchhhHHHHHHhHHHHHHH
Q 021174 151 LFELLALSGMLMDYNWTEILKRKELFREAFGGFDPKSVAKMGEKEILEISSNTAIMLAECRVRCIVDNAKCIVKI 225 (316)
Q Consensus 151 LFE~L~LEgfQAGLSW~tILkKRe~fr~AF~~FD~~~VA~~~e~dIerLm~d~~IIRnr~KI~AvI~NAra~l~i 225 (316)
|++.+....-..|+|=.||-.-+-..++-..-|+-..+..++.++|+.-+.. ++..+.==.++|+++...++.
T Consensus 1 Ll~~f~~~l~~~~~s~~Ti~~Y~~~l~~f~~~~~~~~~~~it~~~i~~y~~~--l~~~~~~s~~T~~~~~~~l~~ 73 (85)
T PF13495_consen 1 LLEEFLEYLRLKGLSEKTIKNYRYHLKRFLRFLGNKPPDEITPEDIEQYLNY--LQNERGLSPSTINQYLSALRS 73 (85)
T ss_dssp -HHHHHHHHHHTT--HHHHHHHHHHHHHHHTTSSS--GGG--HHHHHHHHHH--HHTTT---HHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcccCccchhHHHHHHHHHHH--HHHhcCCCHHHHHHHHHHHHH
Confidence 3455555556699999999999999998777777678999999999998874 222232235677777666553
No 23
>PF10023 DUF2265: Predicted aminopeptidase (DUF2265); InterPro: IPR014553 This group represents a predicted aminopeptidase.
Probab=50.22 E-value=13 Score=37.27 Aligned_cols=103 Identities=20% Similarity=0.313 Sum_probs=62.8
Q ss_pred HHHHHhhCCCccccc-hhhHHHHHHhHHHHHHHHH----hcCCHHHhc--------cccCCCc-----------cccCCC
Q 021174 194 KEILEISSNTAIMLA-ECRVRCIVDNAKCIVKILN----EFGSFSSFM--------WGYVNFK-----------PMINKF 249 (316)
Q Consensus 194 ~dIerLm~d~~IIRn-r~KI~AvI~NAra~l~i~~----e~GSF~~yl--------Wsfv~~k-----------pi~n~~ 249 (316)
+-|+++++||++=-. |.|| ..+..+|.+- ..+ +.+|+..|. |..+--. ||+.-.
T Consensus 33 ~pv~~vl~dp~~~~~lr~rL-~~~~~iR~FA-~~~L~Lpdn~sY~~YadL~Rp~vvWnV~Aap~~sl~~~~WcFPi~Gcv 110 (337)
T PF10023_consen 33 RPVDDVLADPATPPALRARL-RLAQQIRRFA-SEELGLPDNGSYRSYADLDRPYVVWNVFAAPEFSLEPKTWCFPIVGCV 110 (337)
T ss_pred CcHHHHhhCCCCCHHHHHHH-HHHHHHHHHH-HHhcCCCCCCChhhhhhcCCCcEEEEEEecCcccCCcceeeccccccc
Confidence 458888888865322 2222 3344444442 111 346666663 3322111 554443
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHcCC-cccChhhHHHHHHHhccccccccccccch
Q 021174 250 RYPRNVPLRSPKAEAISRDLLKRGF-RLVGPVIVYSFMQAAGLTIDHLVDCFRYS 303 (316)
Q Consensus 250 ~~~~~vP~~t~~S~~lsKdLKkrGF-kFVGPtt~ysfMQAvG~vnDHl~~C~r~~ 303 (316)
.+-+-- ....+.+.++.|++.|+ .+||+|.+||= .|+.+|=+..-+.+-
T Consensus 111 ~YrGyF--~~~~A~~~a~~L~~~GlDv~v~gV~AYST---LGwF~DPlLSt~l~~ 160 (337)
T PF10023_consen 111 PYRGYF--DEADARAEAAELRAQGLDVYVGGVPAYST---LGWFDDPLLSTMLRY 160 (337)
T ss_pred cccCcC--CHHHHHHHHHHHHHcCCceeEeccccccc---ccccCCcccccccCC
Confidence 322222 23568899999999999 69999999996 589999888876553
No 24
>PF13276 HTH_21: HTH-like domain
Probab=49.84 E-value=20 Score=26.02 Aligned_cols=31 Identities=26% Similarity=0.215 Sum_probs=26.9
Q ss_pred HHHHHHHHHHcCCcccChhhHHHHHHHhccc
Q 021174 262 AEAISRDLLKRGFRLVGPVIVYSFMQAAGLT 292 (316)
Q Consensus 262 S~~lsKdLKkrGFkFVGPtt~ysfMQAvG~v 292 (316)
+.+|+.+|.+.|---||--+|+-+|+..|+.
T Consensus 23 ~rri~~~L~~~~~~~v~~krV~RlM~~~gL~ 53 (60)
T PF13276_consen 23 YRRIWAELRREGGIRVSRKRVRRLMREMGLR 53 (60)
T ss_pred hhHHHHHHhccCcccccHHHHHHHHHHcCCc
Confidence 4588999999965579999999999999985
No 25
>PRK13344 spxA transcriptional regulator Spx; Reviewed
Probab=48.67 E-value=6.9 Score=33.48 Aligned_cols=80 Identities=15% Similarity=0.277 Sum_probs=46.9
Q ss_pred CccccCCccCChhh----hhhhhcCCCccccChHHHHHHHHHHHhhccccHHHHHHhHHHHHHHhcCCCHHHHhcCCHH-
Q 021174 120 LKRCNWITKNNKVY----VAFHDECWGVPVYDDNQLFELLALSGMLMDYNWTEILKRKELFREAFGGFDPKSVAKMGEK- 194 (316)
Q Consensus 120 ~~RC~Wa~~~~~ly----~~YHD~EWG~Pv~DDr~LFE~L~LEgfQAGLSW~tILkKRe~fr~AF~~FD~~~VA~~~e~- 194 (316)
.++|++|.+.-..+ ++|.-..--.-..+...|-+++ -++|..|..++++|..+.+.-. .+. ..++++
T Consensus 7 ~~~C~~crkA~~~L~~~~i~~~~~d~~~~~~s~~eL~~~l----~~~~~~~~~lin~~~~~~k~L~-~~~---~~ls~~e 78 (132)
T PRK13344 7 ISSCTSCKKAKTWLNAHQLSYKEQNLGKEPLTKEEILAIL----TKTENGIESIVSSKNRYAKALD-CDI---EELSVNE 78 (132)
T ss_pred CCCCHHHHHHHHHHHHcCCCeEEEECCCCCCCHHHHHHHH----HHhCCCHHHhhccCcHHHHhCC-cch---hcCCHHH
Confidence 46787776432222 1222222333333444554444 3468889999999998877543 332 456644
Q ss_pred HHHHhhCCCcccc
Q 021174 195 EILEISSNTAIML 207 (316)
Q Consensus 195 dIerLm~d~~IIR 207 (316)
-++.|++||.+|+
T Consensus 79 ~i~ll~~~P~Lik 91 (132)
T PRK13344 79 VIDLIQENPRILK 91 (132)
T ss_pred HHHHHHhCcccee
Confidence 4577778998887
No 26
>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=46.17 E-value=29 Score=25.17 Aligned_cols=43 Identities=14% Similarity=0.370 Sum_probs=31.7
Q ss_pred HHHHHHhc--CCCH-HHHhcCCHHHHHHhhCCCccccchhhHHHHHHh
Q 021174 174 ELFREAFG--GFDP-KSVAKMGEKEILEISSNTAIMLAECRVRCIVDN 218 (316)
Q Consensus 174 e~fr~AF~--~FD~-~~VA~~~e~dIerLm~d~~IIRnr~KI~AvI~N 218 (316)
+.|..+|. ++|- +.++.++++++.++--.. ..+|.||...|++
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 779999999998774422 5678888877764
No 27
>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=45.50 E-value=25 Score=28.76 Aligned_cols=32 Identities=19% Similarity=0.235 Sum_probs=28.9
Q ss_pred HHHHHHHHHHHHcCCcccChhhHHHHHHHhcc
Q 021174 260 PKAEAISRDLLKRGFRLVGPVIVYSFMQAAGL 291 (316)
Q Consensus 260 ~~S~~lsKdLKkrGFkFVGPtt~ysfMQAvG~ 291 (316)
+....+++.|.+.||+.++.-..+.||+..|+
T Consensus 12 ~~~~~~a~~l~~~G~~i~AT~gTa~~L~~~Gi 43 (112)
T cd00532 12 AMLVDLAPKLSSDGFPLFATGGTSRVLADAGI 43 (112)
T ss_pred HHHHHHHHHHHHCCCEEEECcHHHHHHHHcCC
Confidence 56778999999999999999899999999886
No 28
>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=27.58 Aligned_cols=29 Identities=31% Similarity=0.490 Sum_probs=25.7
Q ss_pred HHHHHHHHHcCCcccChhhHHHHHHHhcc
Q 021174 263 EAISRDLLKRGFRLVGPVIVYSFMQAAGL 291 (316)
Q Consensus 263 ~~lsKdLKkrGFkFVGPtt~ysfMQAvG~ 291 (316)
..+++.|.+.||+.+.....+.||+..|+
T Consensus 3 ~~~~~~l~~lG~~i~AT~gTa~~L~~~Gi 31 (90)
T smart00851 3 VELAKRLAELGFELVATGGTAKFLREAGL 31 (90)
T ss_pred HHHHHHHHHCCCEEEEccHHHHHHHHCCC
Confidence 36789999999999988888999999986
No 29
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=43.74 E-value=1.1e+02 Score=29.74 Aligned_cols=110 Identities=15% Similarity=0.143 Sum_probs=81.2
Q ss_pred HHHHHHHHHHHhhccccHHHHHHhHHHHHHHhcC--------CCHHHHhcCCHHHHHHhhCCCccccchhhHHHHHHhHH
Q 021174 149 NQLFELLALSGMLMDYNWTEILKRKELFREAFGG--------FDPKSVAKMGEKEILEISSNTAIMLAECRVRCIVDNAK 220 (316)
Q Consensus 149 r~LFE~L~LEgfQAGLSW~tILkKRe~fr~AF~~--------FD~~~VA~~~e~dIerLm~d~~IIRnr~KI~AvI~NAr 220 (316)
.-.||.|+--+.+.=+|=..+-+-+..+.++|.+ =.|+.|+..+++++. ++--.+.|.+.|++=|+
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 5689999999999999999999999999999994 589999999999988 44567899999999999
Q ss_pred HHHHHHHhcCCHHHhccccCCCccccCCCCCCCCCCCCCHHHHHHHHHHHHcCCcccChhhH-HHHHHHhcc
Q 021174 221 CIVKILNEFGSFSSFMWGYVNFKPMINKFRYPRNVPLRSPKAEAISRDLLKRGFRLVGPVIV-YSFMQAAGL 291 (316)
Q Consensus 221 a~l~i~~e~GSF~~ylWsfv~~kpi~n~~~~~~~vP~~t~~S~~lsKdLKkrGFkFVGPtt~-ysfMQAvG~ 291 (316)
++.+=. =++.... . .--+.+-+.|.+ |+=|||-|+ +.+|.+.|.
T Consensus 177 ~~~~g~---~~~~~l~-----------------~-----~~~e~a~e~L~~--i~GIG~WTAe~~llf~lgr 221 (285)
T COG0122 177 AAAEGE---LDLSELK-----------------P-----LSDEEAIEELTA--LKGIGPWTAEMFLLFGLGR 221 (285)
T ss_pred HHHcCC---ccHHHhc-----------------c-----CCHHHHHHHHHc--CCCcCHHHHHHHHHHcCCC
Confidence 985310 0111110 0 112334456666 999999988 445566663
No 30
>cd02977 ArsC_family Arsenate Reductase (ArsC) family; composed of TRX-fold arsenic reductases and similar proteins including the transcriptional regulator, Spx. ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], using reducing equivalents derived from glutathione (GSH) via glutaredoxin (GRX), through a single catalytic cysteine. This family of predominantly bacterial enzymes is unrelated to two other families of arsenate reductases which show similarity to low-molecular-weight acid phosphatases and phosphotyrosyl phosphatases. Spx is a general regulator that exerts negative and positive control over transcription initiation by binding to the C-terminal domain of the alpha subunit of RNA polymerase.
Probab=42.06 E-value=9.3 Score=30.56 Aligned_cols=46 Identities=4% Similarity=0.096 Sum_probs=31.5
Q ss_pred HhhccccHHHHHHhH-HHHHHHhcCCCHHHHhcCCHHHH-HHhhCCCccccc
Q 021174 159 GMLMDYNWTEILKRK-ELFREAFGGFDPKSVAKMGEKEI-LEISSNTAIMLA 208 (316)
Q Consensus 159 gfQAGLSW~tILkKR-e~fr~AF~~FD~~~VA~~~e~dI-erLm~d~~IIRn 208 (316)
.-+.|..+..++++| ..|++... .....++++++ +.|+++|.+|+.
T Consensus 45 ~~~~~~~~~~li~~~~~~~~~l~~----~~~~~ls~~e~~~~l~~~p~LikR 92 (105)
T cd02977 45 LAKLGLGVEDLFNTRGTPYRKLGL----ADKDELSDEEALELMAEHPKLIKR 92 (105)
T ss_pred HHhcCCCHHHHHhcCCchHHHcCC----ccccCCCHHHHHHHHHhCcCeeeC
Confidence 355678899999998 66665532 22457776665 666788988864
No 31
>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=39.32 E-value=37 Score=27.33 Aligned_cols=32 Identities=34% Similarity=0.592 Sum_probs=28.9
Q ss_pred HHHHHHHHHHHHcCCcccChhhHHHHHHHhcc
Q 021174 260 PKAEAISRDLLKRGFRLVGPVIVYSFMQAAGL 291 (316)
Q Consensus 260 ~~S~~lsKdLKkrGFkFVGPtt~ysfMQAvG~ 291 (316)
+....+++.|.+.||+..+.-..+.||+..|+
T Consensus 13 ~~~~~~~~~l~~~G~~l~aT~gT~~~l~~~gi 44 (110)
T cd01424 13 PEAVEIAKRLAELGFKLVATEGTAKYLQEAGI 44 (110)
T ss_pred hHHHHHHHHHHHCCCEEEEchHHHHHHHHcCC
Confidence 45678999999999999999999999999997
No 32
>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=38.64 E-value=17 Score=30.67 Aligned_cols=25 Identities=28% Similarity=0.517 Sum_probs=16.9
Q ss_pred CHHHHHHHHHHHHcCCcccChhhHH
Q 021174 259 SPKAEAISRDLLKRGFRLVGPVIVY 283 (316)
Q Consensus 259 t~~S~~lsKdLKkrGFkFVGPtt~y 283 (316)
.++++.+.+....+||.|+||++|.
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 3677778888889999999998864
No 33
>PRK01655 spxA transcriptional regulator Spx; Reviewed
Probab=37.98 E-value=25 Score=29.91 Aligned_cols=52 Identities=13% Similarity=0.167 Sum_probs=32.2
Q ss_pred HHHHHHHHhhccccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHH-HHHhhCCCcccc
Q 021174 152 FELLALSGMLMDYNWTEILKRKELFREAFGGFDPKSVAKMGEKE-ILEISSNTAIML 207 (316)
Q Consensus 152 FE~L~LEgfQAGLSW~tILkKRe~fr~AF~~FD~~~VA~~~e~d-IerLm~d~~IIR 207 (316)
.+.|.--..+.|..|..++++|...-+.- +.+. ..+++++ ++-|+++|.+|+
T Consensus 39 ~~eL~~~l~~~~~g~~~lin~~~~~~k~l-~~~~---~~ls~~e~i~ll~~~p~Lik 91 (131)
T PRK01655 39 IDEIKQILRMTEDGTDEIISTRSKVFQKL-NVDV---ESLSLQDLIKLISDNPGLLR 91 (131)
T ss_pred HHHHHHHHHHhcCCHHHHHhcCcHHHHhC-CCCc---ccCCHHHHHHHHHhCcceEe
Confidence 34333333445677999999987654432 3332 3566554 577778999887
No 34
>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=37.94 E-value=21 Score=25.92 Aligned_cols=18 Identities=28% Similarity=0.584 Sum_probs=16.2
Q ss_pred HHHHHHHHHHcCCcccCh
Q 021174 262 AEAISRDLLKRGFRLVGP 279 (316)
Q Consensus 262 S~~lsKdLKkrGFkFVGP 279 (316)
.+.+.+.|++.||+++||
T Consensus 54 ~~~~~~~L~~~G~~v~~~ 71 (72)
T cd04883 54 PRPIIEDLRRAGYEVLWP 71 (72)
T ss_pred HHHHHHHHHHCCCeeeCC
Confidence 458899999999999998
No 35
>cd03032 ArsC_Spx Arsenate Reductase (ArsC) family, Spx subfamily; Spx is a unique RNA polymerase (RNAP)-binding protein present in bacilli and some mollicutes. It inhibits transcription by binding to the C-terminal domain of the alpha subunit of RNAP, disrupting complex formation between RNAP and certain transcriptional activator proteins like ResD and ComA. In response to oxidative stress, Spx can also activate transcription, making it a general regulator that exerts both positive and negative control over transcription initiation. Spx has been shown to exert redox-sensitive transcriptional control over genes like trxA (TRX) and trxB (TRX reductase), genes that function in thiol homeostasis. This redox-sensitive activity is dependent on the presence of a CXXC motif, present in some members of the Spx subfamily, that acts as a thiol/disulfide switch. Spx has also been shown to repress genes in a sulfate-dependent manner independent of the presence of the CXXC motif.
Probab=37.30 E-value=32 Score=28.20 Aligned_cols=45 Identities=16% Similarity=0.207 Sum_probs=30.2
Q ss_pred hhccccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHH-HHHhhCCCccccc
Q 021174 160 MLMDYNWTEILKRKELFREAFGGFDPKSVAKMGEKE-ILEISSNTAIMLA 208 (316)
Q Consensus 160 fQAGLSW~tILkKRe~fr~AF~~FD~~~VA~~~e~d-IerLm~d~~IIRn 208 (316)
-+.|+.|..++++|...-+... .+. ..+++++ ++-|+++|.+|+.
T Consensus 47 ~~~~~~~~~l~n~~~~~~k~l~-~~~---~~ls~~e~i~~l~~~p~LikR 92 (115)
T cd03032 47 SLTENGVEDIISTRSKAFKNLN-IDI---DELSLSELIRLISEHPSLLRR 92 (115)
T ss_pred HHhcCCHHHHHhcCcHHHHHcC-CCc---ccCCHHHHHHHHHhChhheeC
Confidence 3457789999999876655432 222 4567555 5777788988875
No 36
>PHA02517 putative transposase OrfB; Reviewed
Probab=35.94 E-value=40 Score=31.09 Aligned_cols=31 Identities=29% Similarity=0.397 Sum_probs=26.9
Q ss_pred HHHHHHHHHHcCCcccChhhHHHHHHHhcccc
Q 021174 262 AEAISRDLLKRGFRLVGPVIVYSFMQAAGLTI 293 (316)
Q Consensus 262 S~~lsKdLKkrGFkFVGPtt~ysfMQAvG~vn 293 (316)
..+|...|+++|+. ++.-+|+-+|+..|+.-
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 37
>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=34.66 E-value=45 Score=29.15 Aligned_cols=31 Identities=19% Similarity=0.166 Sum_probs=27.5
Q ss_pred HHHHHHHHHHcCCcccChhhHHHHHHHhcccc
Q 021174 262 AEAISRDLLKRGFRLVGPVIVYSFMQAAGLTI 293 (316)
Q Consensus 262 S~~lsKdLKkrGFkFVGPtt~ysfMQAvG~vn 293 (316)
.+.|...|+++||. |.-.|+|-.|...|+|-
T Consensus 19 qeeL~~~L~~~G~~-vsqaTIsRdL~elglvk 49 (146)
T TIGR01529 19 QEELVALLKAEGIE-VTQATVSRDLRELGAVK 49 (146)
T ss_pred HHHHHHHHHHhCCC-cCHHHHHHHHHHcCCEE
Confidence 56788999999999 88889999999999973
No 38
>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=34.26 E-value=45 Score=27.76 Aligned_cols=33 Identities=18% Similarity=0.165 Sum_probs=29.7
Q ss_pred CHHHHHHHHHHHHc--CCcccChhhHHHHHHH-hcc
Q 021174 259 SPKAEAISRDLLKR--GFRLVGPVIVYSFMQA-AGL 291 (316)
Q Consensus 259 t~~S~~lsKdLKkr--GFkFVGPtt~ysfMQA-vG~ 291 (316)
.+....+++.|.+. ||+.+.....+.||+. .|+
T Consensus 11 K~~~~~~a~~~~~ll~Gf~i~AT~gTa~~L~~~~Gi 46 (115)
T cd01422 11 KEDLVEFVKQHQELLSRHRLVATGTTGLLIQEATGL 46 (115)
T ss_pred hHHHHHHHHHHHHHhcCCEEEEechHHHHHHHhhCC
Confidence 36777899999999 9999999999999999 886
No 39
>TIGR01617 arsC_related transcriptional regulator, Spx/MgsR family. This model represents a portion of the proteins within the larger set covered by Pfam model pfam03960. That larger family includes a glutaredoxin-dependent arsenate reductase (TIGR00014). Characterized members of this family include Spx and MgsR from Bacillus subtili. Spx is a global regulator for response to thiol-specific oxidative stress. It interacts with RNA polymerase. MgsR (modulator of the general stress response, also called YqgZ) provides a second level of regulation for more than a third of the proteins in the B. subtilis general stress regulon controlled by Sigma-B.
Probab=33.85 E-value=20 Score=29.45 Aligned_cols=54 Identities=13% Similarity=0.164 Sum_probs=34.9
Q ss_pred HHHHHHHHhhccccHHHHHHhHHHHHHHhcCCCHH-HHhcCCHHHH-HHhhCCCccccc
Q 021174 152 FELLALSGMLMDYNWTEILKRKELFREAFGGFDPK-SVAKMGEKEI-LEISSNTAIMLA 208 (316)
Q Consensus 152 FE~L~LEgfQAGLSW~tILkKRe~fr~AF~~FD~~-~VA~~~e~dI-erLm~d~~IIRn 208 (316)
.+.|.--.-+.|..|..++++|... |...... ++..|+++++ +.|+++|.+|+.
T Consensus 38 ~~el~~l~~~~~~~~~~lin~~~~~---~k~l~~~~~~~~ls~~e~~~~i~~~p~LikR 93 (117)
T TIGR01617 38 REELLDILSLLEDGIDPLLNTRGQS---YRALNTSNTFLDLSDKEALELLAEDPALLRR 93 (117)
T ss_pred HHHHHHHHHHcCCCHHHheeCCCcc---hhhCCchhhcccCCHHHHHHHHHhCcceEec
Confidence 3444444456788899999988755 3333443 3677886655 666688888764
No 40
>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=32.73 E-value=22 Score=32.73 Aligned_cols=34 Identities=18% Similarity=0.341 Sum_probs=28.5
Q ss_pred CCCCCCHHHHHHHHHHHHcCCcccChhhHHHHHHHh
Q 021174 254 NVPLRSPKAEAISRDLLKRGFRLVGPVIVYSFMQAA 289 (316)
Q Consensus 254 ~vP~~t~~S~~lsKdLKkrGFkFVGPtt~ysfMQAv 289 (316)
+||.+. ...+..+.|++.|.+ ||-|+||+..||.
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 41
>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=32.64 E-value=1.3e+02 Score=21.02 Aligned_cols=43 Identities=14% Similarity=0.300 Sum_probs=31.6
Q ss_pred HHHHh--cCCCHHHHhcCC-HHHHHHhhCCCccccchhhHHHHHHhHH
Q 021174 176 FREAF--GGFDPKSVAKMG-EKEILEISSNTAIMLAECRVRCIVDNAK 220 (316)
Q Consensus 176 fr~AF--~~FD~~~VA~~~-e~dIerLm~d~~IIRnr~KI~AvI~NAr 220 (316)
|.+.| .+++-..+..++ +++++++--.. +-+|.||...|..-|
T Consensus 21 y~~~f~~~~i~g~~ll~~~~~~~l~~lgi~~--~~~r~~ll~~i~~l~ 66 (68)
T smart00454 21 YADNFRKNGIDGALLLLLTSEEDLKELGITK--LGHRKKILKAIQKLK 66 (68)
T ss_pred HHHHHHHCCCCHHHHHhcChHHHHHHcCCCc--HHHHHHHHHHHHHHH
Confidence 66666 677888899998 88888875422 468889887776643
No 42
>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=30.46 E-value=33 Score=28.53 Aligned_cols=21 Identities=14% Similarity=0.313 Sum_probs=16.5
Q ss_pred HHHHHHHHHHHcCCcccChhh
Q 021174 261 KAEAISRDLLKRGFRLVGPVI 281 (316)
Q Consensus 261 ~S~~lsKdLKkrGFkFVGPtt 281 (316)
+...+++.+.+.|.+|+||..
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 466889999999999999964
No 43
>PF05075 DUF684: Protein of unknown function (DUF684); InterPro: IPR007767 This family contains uncharacterised proteins from Caenorhabditis elegans.
Probab=29.68 E-value=91 Score=30.79 Aligned_cols=54 Identities=13% Similarity=0.156 Sum_probs=38.0
Q ss_pred hHHHHHHHHHHHhhccc-------cHHHHHHhHHHHHHHhcCCCHHHH--hcCCHHHHHHhhC
Q 021174 148 DNQLFELLALSGMLMDY-------NWTEILKRKELFREAFGGFDPKSV--AKMGEKEILEISS 201 (316)
Q Consensus 148 Dr~LFE~L~LEgfQAGL-------SW~tILkKRe~fr~AF~~FD~~~V--A~~~e~dIerLm~ 201 (316)
+..|-.+|.||+|.+|| .+..|+.+-..+.+..+.|+-+.. ..|=++.++.++.
T Consensus 115 ~~vl~q~l~lEafa~Gl~~~~n~~~~~~L~e~~~~~~~~~~~w~~~Y~~~~~yWp~~v~~~v~ 177 (345)
T PF05075_consen 115 DGVLGQLLFLEAFASGLFKDKNMYDPDRLIEKIEEINEKMDKWKEEYKKDESYWPDNVKKFVE 177 (345)
T ss_pred HHHHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhhccccccchHHHHHHHH
Confidence 45688899999999999 677888888777777776665552 2333455555554
No 44
>PF10911 DUF2717: Protein of unknown function (DUF2717); InterPro: IPR020121 The proteins in this entry are uncharacterised.
Probab=29.28 E-value=30 Score=27.99 Aligned_cols=42 Identities=24% Similarity=0.400 Sum_probs=29.8
Q ss_pred ccccCCCCCCCCCCCCCHHHHHHHHHHHHcCCcccChhhHHHHHHHhcccccc
Q 021174 243 KPMINKFRYPRNVPLRSPKAEAISRDLLKRGFRLVGPVIVYSFMQAAGLTIDH 295 (316)
Q Consensus 243 kpi~n~~~~~~~vP~~t~~S~~lsKdLKkrGFkFVGPtt~ysfMQAvG~vnDH 295 (316)
+||.+...++.+||. .+++.+..|+-| | =++|+.+.|++++-
T Consensus 3 ~~I~h~l~np~DiP~---ipra~aeyLqvr-f-------N~~yl~~sG~i~~l 44 (77)
T PF10911_consen 3 KPIQHLLDNPDDIPD---IPRAAAEYLQVR-F-------NAAYLMASGIISAL 44 (77)
T ss_pred chHHHHhcCCcccCC---ccHHHHHHHHHH-h-------cHHHHHHhhhHHHH
Confidence 577777788999996 666777888876 2 25667777776653
No 45
>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=28.85 E-value=62 Score=26.30 Aligned_cols=32 Identities=22% Similarity=0.393 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHcCCcccChhhHHHHHHHhcc
Q 021174 260 PKAEAISRDLLKRGFRLVGPVIVYSFMQAAGL 291 (316)
Q Consensus 260 ~~S~~lsKdLKkrGFkFVGPtt~ysfMQAvG~ 291 (316)
+....+++.|.+.||+..+.-..+.||...|+
T Consensus 13 ~~~~~~a~~l~~~G~~i~aT~gTa~~L~~~gi 44 (116)
T cd01423 13 PELLPTAQKLSKLGYKLYATEGTADFLLENGI 44 (116)
T ss_pred hhHHHHHHHHHHCCCEEEEccHHHHHHHHcCC
Confidence 45668999999999999999999999999997
No 46
>PF13062 DUF3924: Protein of unknown function (DUF3924)
Probab=28.81 E-value=25 Score=26.85 Aligned_cols=40 Identities=23% Similarity=0.388 Sum_probs=33.3
Q ss_pred hhhhHHHHhhcCCCCccCCCCcchhHhhhh-chhccccccc
Q 021174 4 ANVRRHILEKNRSPKEKEPKPTQSLLSKHL-KKVYPIGLHR 43 (316)
Q Consensus 4 ~~~~~~~~ek~~~~~~~~~~~~~~~~~~~~-~~~yp~~~~~ 43 (316)
-..-+++.+|+..-.-++.-+-|.+.||-. +.|-|..||.
T Consensus 16 l~llkqayqkktgatisestlvq~liskefiq~itpfdlqq 56 (62)
T PF13062_consen 16 LDLLKQAYQKKTGATISESTLVQSLISKEFIQAITPFDLQQ 56 (62)
T ss_pred HHHHHHHHHhhcCCccchhHHHHHHHHHHHHHhcCcccHHH
Confidence 345688999999988888888999989876 8999998874
No 47
>PRK12559 transcriptional regulator Spx; Provisional
Probab=26.20 E-value=47 Score=28.34 Aligned_cols=43 Identities=12% Similarity=0.122 Sum_probs=28.9
Q ss_pred hccccHHHHHHhHHHHHHHhcCCCHHHHhcCC-HHHHHHhhCCCcccc
Q 021174 161 LMDYNWTEILKRKELFREAFGGFDPKSVAKMG-EKEILEISSNTAIML 207 (316)
Q Consensus 161 QAGLSW~tILkKRe~fr~AF~~FD~~~VA~~~-e~dIerLm~d~~IIR 207 (316)
++|+.|..++++|..--+.- +.+. ..++ ++-++.|+++|.+|+
T Consensus 48 ~~~~g~~~lin~~~~~~k~l-~~~~---~~ls~~e~i~ll~~~P~Lik 91 (131)
T PRK12559 48 LTEEGATEIISTRSKTFQDL-NINI---EELSLNEFYKLIIEHPLMLR 91 (131)
T ss_pred HcCCCHHHHHhcCcHHHHhC-CCCc---ccCCHHHHHHHHHhCcceEe
Confidence 55777999999887654432 3333 3566 445677778998887
No 48
>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=25.83 E-value=31 Score=24.27 Aligned_cols=30 Identities=13% Similarity=0.339 Sum_probs=24.0
Q ss_pred HHHHhcCCCHHHHhcCCHHHHHHhhCCCcc
Q 021174 176 FREAFGGFDPKSVAKMGEKEILEISSNTAI 205 (316)
Q Consensus 176 fr~AF~~FD~~~VA~~~e~dIerLm~d~~I 205 (316)
|+++|.-||.+.=-.++.+++.+++...++
T Consensus 1 ~~~~F~~~D~~~~G~i~~~el~~~l~~~g~ 30 (67)
T cd00052 1 YDQIFRSLDPDGDGLISGDEARPFLGKSGL 30 (67)
T ss_pred ChHHHHHhCCCCCCcCcHHHHHHHHHHcCC
Confidence 578899999888777888999888865543
No 49
>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=25.15 E-value=86 Score=25.07 Aligned_cols=31 Identities=35% Similarity=0.489 Sum_probs=26.0
Q ss_pred HHHHHHHHHHcCCcccChhhHHH---HHHHhcccc
Q 021174 262 AEAISRDLLKRGFRLVGPVIVYS---FMQAAGLTI 293 (316)
Q Consensus 262 S~~lsKdLKkrGFkFVGPtt~ys---fMQAvG~vn 293 (316)
++.|...|+++|. -+|++|+|- +|...|+|.
T Consensus 19 a~ei~~~l~~~~~-~i~~~TVYR~L~~L~~~Gli~ 52 (116)
T cd07153 19 AEEIYERLRKKGP-SISLATVYRTLELLEEAGLVR 52 (116)
T ss_pred HHHHHHHHHhcCC-CCCHHHHHHHHHHHHhCCCEE
Confidence 6788999999975 699999998 778889874
No 50
>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=24.72 E-value=67 Score=29.79 Aligned_cols=32 Identities=16% Similarity=0.351 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHHcCCcccChhhHHHHHHHhcc
Q 021174 260 PKAEAISRDLLKRGFRLVGPVIVYSFMQAAGL 291 (316)
Q Consensus 260 ~~S~~lsKdLKkrGFkFVGPtt~ysfMQAvG~ 291 (316)
+....+++.|.+.||+.+..-..+.||+..|+
T Consensus 11 ~~l~~lAk~L~~lGf~I~AT~GTAk~L~e~GI 42 (187)
T cd01421 11 TGLVEFAKELVELGVEILSTGGTAKFLKEAGI 42 (187)
T ss_pred ccHHHHHHHHHHCCCEEEEccHHHHHHHHcCC
Confidence 35678999999999999999899999999997
No 51
>COG4081 Uncharacterized protein conserved in archaea [Function unknown]
Probab=24.39 E-value=57 Score=29.22 Aligned_cols=26 Identities=27% Similarity=0.411 Sum_probs=22.3
Q ss_pred CCCCCCCCHHHHHHHHHHHHcCCccc
Q 021174 252 PRNVPLRSPKAEAISRDLLKRGFRLV 277 (316)
Q Consensus 252 ~~~vP~~t~~S~~lsKdLKkrGFkFV 277 (316)
..++|.+.+.+.-++-.|||+||.-.
T Consensus 11 CPeiP~qissaiYls~klkkkgf~v~ 36 (148)
T COG4081 11 CPEIPPQISSAIYLSHKLKKKGFDVT 36 (148)
T ss_pred CCCCCccchHHHHHHHHhhccCccEE
Confidence 34678899999999999999999854
No 52
>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=23.53 E-value=79 Score=25.85 Aligned_cols=85 Identities=15% Similarity=0.209 Sum_probs=45.9
Q ss_pred CccccCCccCChhhhhhhhcCCCc-cccChHHHHHHHHHHHhhccccHHHHHHhHHH-HHHHhcCCCHHHHhcCCHHH-H
Q 021174 120 LKRCNWITKNNKVYVAFHDECWGV-PVYDDNQLFELLALSGMLMDYNWTEILKRKEL-FREAFGGFDPKSVAKMGEKE-I 196 (316)
Q Consensus 120 ~~RC~Wa~~~~~ly~~YHD~EWG~-Pv~DDr~LFE~L~LEgfQAGLSW~tILkKRe~-fr~AF~~FD~~~VA~~~e~d-I 196 (316)
.+.|++|.+. ..+..-|+-++=. .+..+..-.+.|.-=+-+.|..|..+++||.. |++. +.+ +++..+++++ +
T Consensus 6 ~~~C~~c~ka-~~~L~~~~i~~~~idi~~~~~~~~el~~~~~~~~~~~~~l~~~~~~~~~~l--~~~-~~~~~~s~~e~~ 81 (111)
T cd03036 6 YPKCSTCRKA-KKWLDEHGVDYTAIDIVEEPPSKEELKKWLEKSGLPLKKFFNTSGKSYREL--GLK-DKLPSLSEEEAL 81 (111)
T ss_pred CCCCHHHHHH-HHHHHHcCCceEEecccCCcccHHHHHHHHHHcCCCHHHHHhcCCchHHhC--Ccc-cccccCCHHHHH
Confidence 3567777543 2222333222111 11123333344444456678889999999974 4443 222 3456777555 4
Q ss_pred HHhhCCCccccc
Q 021174 197 LEISSNTAIMLA 208 (316)
Q Consensus 197 erLm~d~~IIRn 208 (316)
+.|+++|.+|+-
T Consensus 82 ~~l~~~p~LikR 93 (111)
T cd03036 82 ELLSSDGMLIKR 93 (111)
T ss_pred HHHHhCcCeeeC
Confidence 666788888863
No 53
>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=21.86 E-value=41 Score=24.31 Aligned_cols=17 Identities=29% Similarity=0.608 Sum_probs=14.4
Q ss_pred HHHHHhHHHHHHHhcCC
Q 021174 167 TEILKRKELFREAFGGF 183 (316)
Q Consensus 167 ~tILkKRe~fr~AF~~F 183 (316)
..||.+|+.||..|.+.
T Consensus 13 ReiLsRRPSYRKIlndL 29 (41)
T PF02173_consen 13 REILSRRPSYRKILNDL 29 (41)
T ss_dssp HHHHTTSTHHHHHHHHH
T ss_pred HHHHhhCchHHHHHHHh
Confidence 67999999999988654
No 54
>PF08439 Peptidase_M3_N: Oligopeptidase F; InterPro: IPR013647 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This domain is found towards the N terminus of metallopeptidases belonging to MEROPS peptidase subfamily M3B (oligopeptidase F, clan MA). An example protein is Lactococcus lactisPepF []. The function of this N-terminal domain is unknown.; GO: 0008237 metallopeptidase activity, 0008270 zinc ion binding; PDB: 2QR4_B 3CE2_A.
Probab=21.31 E-value=80 Score=23.55 Aligned_cols=38 Identities=8% Similarity=0.050 Sum_probs=28.6
Q ss_pred HhcCCHHHHHHhh-CCCccccchhhHHHHHHhHHHHHHH
Q 021174 188 VAKMGEKEILEIS-SNTAIMLAECRVRCIVDNAKCIVKI 225 (316)
Q Consensus 188 VA~~~e~dIerLm-~d~~IIRnr~KI~AvI~NAra~l~i 225 (316)
+..++++.|++++ +||.+-..+.-|+-++.+++-+|.=
T Consensus 2 l~~l~e~~l~~~~~~~~~l~~y~~~l~~i~r~k~H~Ls~ 40 (70)
T PF08439_consen 2 LLSLPEEKLESLIKEDPELKEYRFYLEEIRRYKKHTLSE 40 (70)
T ss_dssp HCTS-HHHHHHHHHH-CCCGGGHHHHHHHHGGGGG---H
T ss_pred hhhCCHHHHHHHHhcCccHHHHHHHHHHHHHhCCcCCCH
Confidence 5688999999999 5999999999999888888776643
No 55
>PLN02764 glycosyltransferase family protein
Probab=20.95 E-value=1.4e+02 Score=30.88 Aligned_cols=83 Identities=17% Similarity=0.163 Sum_probs=55.6
Q ss_pred CCccccChHHHHHHHHHHHhhccccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhhCCCccccchhhHHHHHHhHH
Q 021174 141 WGVPVYDDNQLFELLALSGMLMDYNWTEILKRKELFREAFGGFDPKSVAKMGEKEILEISSNTAIMLAECRVRCIVDNAK 220 (316)
Q Consensus 141 WG~Pv~DDr~LFE~L~LEgfQAGLSW~tILkKRe~fr~AF~~FD~~~VA~~~e~dIerLm~d~~IIRnr~KI~AvI~NAr 220 (316)
-+.|..-|+.+...+.-++.-+|+.= ++.+ ...++.+.|+ +-|.++|.|++ .+=+.+..||+
T Consensus 359 l~~P~~~DQ~~na~~l~~~~g~gv~~----~~~~-----~~~~~~e~i~----~av~~vm~~~~-----~~g~~~r~~a~ 420 (453)
T PLN02764 359 VLVPQLGDQVLNTRLLSDELKVSVEV----AREE-----TGWFSKESLR----DAINSVMKRDS-----EIGNLVKKNHT 420 (453)
T ss_pred EeCCcccchHHHHHHHHHHhceEEEe----cccc-----CCccCHHHHH----HHHHHHhcCCc-----hhHHHHHHHHH
Confidence 34578899999998877888888751 1110 0124555554 34777887653 22335778888
Q ss_pred HHHHHHHhcCCHHHhccccCC
Q 021174 221 CIVKILNEFGSFSSFMWGYVN 241 (316)
Q Consensus 221 a~l~i~~e~GSF~~ylWsfv~ 241 (316)
.+.+..+++||-..+|=.|++
T Consensus 421 ~~~~~~~~~GSS~~~l~~lv~ 441 (453)
T PLN02764 421 KWRETLASPGLLTGYVDNFIE 441 (453)
T ss_pred HHHHHHHhcCCHHHHHHHHHH
Confidence 888888999998888876654
No 56
>KOG0898 consensus 40S ribosomal protein S15 [Translation, ribosomal structure and biogenesis]
Probab=20.85 E-value=1.1e+02 Score=27.58 Aligned_cols=32 Identities=25% Similarity=0.567 Sum_probs=28.3
Q ss_pred HHhHHHHHH-HhcCCCHHHHhcCCHHHHHHhhC
Q 021174 170 LKRKELFRE-AFGGFDPKSVAKMGEKEILEISS 201 (316)
Q Consensus 170 LkKRe~fr~-AF~~FD~~~VA~~~e~dIerLm~ 201 (316)
++|...||. .|.|+|++.+..|+-+++..|+.
T Consensus 13 ~kKKRTFrkftyrGVdld~Lldms~~~~~~l~~ 45 (152)
T KOG0898|consen 13 LKKKRTFRKFTYRGVDLDQLLDMSTEQLVKLFP 45 (152)
T ss_pred HhhhhhhhhccccCCCHHHHhcCCHHHHHHHHH
Confidence 677777776 69999999999999999999887
No 57
>COG3200 AroG 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase [Amino acid transport and metabolism]
Probab=20.85 E-value=1.5e+02 Score=30.62 Aligned_cols=65 Identities=23% Similarity=0.407 Sum_probs=43.4
Q ss_pred chhhHHHHHHhHHHHHHHHHhcC--CHHH------hccccCCCccccCCCCCCCCCCCCCHHHHHHHHHHHHcCCcccCh
Q 021174 208 AECRVRCIVDNAKCIVKILNEFG--SFSS------FMWGYVNFKPMINKFRYPRNVPLRSPKAEAISRDLLKRGFRLVGP 279 (316)
Q Consensus 208 nr~KI~AvI~NAra~l~i~~e~G--SF~~------ylWsfv~~kpi~n~~~~~~~vP~~t~~S~~lsKdLKkrGFkFVGP 279 (316)
+..++.-...||-+.+.|.+.++ ++++ |--.||..-|.-.+| ..++++|+..
T Consensus 150 dP~R~l~aY~qsaAtlNLlRafa~gG~A~L~~vh~W~l~Fv~~sp~~~rY---------~~la~~I~~~----------- 209 (445)
T COG3200 150 DPERLLKAYAQSAATLNLLRAFASGGLADLENVHRWNLGFVKNSPQGARY---------EALADRISET----------- 209 (445)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHhccccchHHHHHHHHHhhhcCCchHHHH---------HHHHHHHHHH-----------
Confidence 34556667888889989888754 4444 555687766554332 3466666654
Q ss_pred hhHHHHHHHhcccccc
Q 021174 280 VIVYSFMQAAGLTIDH 295 (316)
Q Consensus 280 tt~ysfMQAvG~vnDH 295 (316)
..||+|||+..|+
T Consensus 210 ---l~FM~A~Gv~~~~ 222 (445)
T COG3200 210 ---LAFMRACGVTNDP 222 (445)
T ss_pred ---HHHHHHhCCCCCc
Confidence 4699999997655
No 58
>KOG2198 consensus tRNA cytosine-5-methylases and related enzymes of the NOL1/NOP2/sun superfamily [Translation, ribosomal structure and biogenesis]
Probab=20.82 E-value=1.3e+02 Score=30.89 Aligned_cols=114 Identities=21% Similarity=0.214 Sum_probs=75.3
Q ss_pred HHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhhCCC-ccccchhhHHHHHHhHHHHHHHHHhcCCHHHhccccCCCcc
Q 021174 166 WTEILKRKELFREAFGGFDPKSVAKMGEKEILEISSNT-AIMLAECRVRCIVDNAKCIVKILNEFGSFSSFMWGYVNFKP 244 (316)
Q Consensus 166 W~tILkKRe~fr~AF~~FD~~~VA~~~e~dIerLm~d~-~IIRnr~KI~AvI~NAra~l~i~~e~GSF~~ylWsfv~~kp 244 (316)
|..--.+.+.|.++..+||. +++.+.++..- ...-..-++.|.++||.+++.+.+++-.-..|--. ..+
T Consensus 19 ~~~~~~~~~~~~~~l~~f~~-------~~e~~~~~~~ir~~Lps~fr~~~~~~~~~~~~~~~~~~~~~~~~~~~-~E~-- 88 (375)
T KOG2198|consen 19 IAKTNPKFEKYYKALDHFDK-------EDEFGDFWETIRKPLPSTFRYTALVNNADALLSIFEEYEFESLKDRV-IEG-- 88 (375)
T ss_pred hhccchhhHHHHHHHhcCcc-------hHHHHHHHHHHHhccchhhhHHHhccchHHHHHHHhhccchhhhhhh-ccc--
Confidence 45555678899999999986 66666665431 12345678999999999999887664333322222 222
Q ss_pred ccCCCCCCCCCCCCCHHHHHHHHHHHHcCCcccCh-------------hhHHHHHHHhccc
Q 021174 245 MINKFRYPRNVPLRSPKAEAISRDLLKRGFRLVGP-------------VIVYSFMQAAGLT 292 (316)
Q Consensus 245 i~n~~~~~~~vP~~t~~S~~lsKdLKkrGFkFVGP-------------tt~ysfMQAvG~v 292 (316)
..++.+...|- .|..-+.-++.++-+|+-.+| +..|..|.|+-|+
T Consensus 89 --~~~e~~~~~p~-~p~~~a~~~~~~~~~~r~~~~l~rf~~fl~~e~~vg~i~rqeavSml 146 (375)
T KOG2198|consen 89 --LKFEAPFELPW-YPDNLAFEKDVKLDEIRKSPPLSRFHGFLKLETGVGNIYRQEAVSML 146 (375)
T ss_pred --cccCccccCCC-CcccchhhhcCcccccccCCchhhcchHhhhhcccccchhhhhhhcc
Confidence 22444444553 367778889999999988775 4456667777776
No 59
>PF07592 DDE_Tnp_ISAZ013: Rhodopirellula transposase DDE domain; InterPro: IPR011518 These transposases are found in the planctomycete Rhodopirellula baltica, the cyanobacterium Nostoc, and the Gram-positive bacterium Streptomyces. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=20.40 E-value=1.1e+02 Score=30.63 Aligned_cols=29 Identities=17% Similarity=0.369 Sum_probs=26.9
Q ss_pred HHHHHHHHHHcCCcccChhhHHHHHHHhcc
Q 021174 262 AEAISRDLLKRGFRLVGPVIVYSFMQAAGL 291 (316)
Q Consensus 262 S~~lsKdLKkrGFkFVGPtt~ysfMQAvG~ 291 (316)
..+|+++|.++||. |...||.-+|...|.
T Consensus 27 ~~~la~~L~~~G~~-vS~~tV~~lL~~lGY 55 (311)
T PF07592_consen 27 TRKLAEELRRQGHP-VSARTVARLLNRLGY 55 (311)
T ss_pred HHHHHHHHHHcCCC-ccHHHHHHHHHHcCc
Confidence 56899999999999 999999999999996
Done!