Query 016657
Match_columns 385
No_of_seqs 165 out of 1152
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 08:49:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016657.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016657hhsearch_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 7.9E-86 1.7E-90 603.2 18.8 183 160-344 2-184 (187)
2 TIGR00624 tag DNA-3-methyladen 100.0 7.6E-84 1.6E-88 586.7 18.7 179 160-342 1-179 (179)
3 PF03352 Adenine_glyco: Methyl 100.0 3.9E-82 8.4E-87 575.4 15.4 179 164-344 1-179 (179)
4 COG2818 Tag 3-methyladenine DN 100.0 2.2E-81 4.7E-86 572.7 17.1 186 159-345 1-186 (188)
5 cd00056 ENDO3c endonuclease II 95.6 0.13 2.9E-06 44.7 10.0 104 192-330 1-104 (158)
6 TIGR03252 uncharacterized HhH- 95.0 0.45 9.7E-06 44.6 12.1 117 191-330 18-136 (177)
7 PRK13913 3-methyladenine DNA g 94.6 0.71 1.5E-05 44.2 12.6 118 191-340 30-157 (218)
8 TIGR01083 nth endonuclease III 94.3 0.45 9.7E-06 43.7 10.1 101 191-329 26-126 (191)
9 smart00478 ENDO3c endonuclease 93.6 0.7 1.5E-05 40.0 9.6 88 204-329 5-92 (149)
10 PRK10702 endonuclease III; Pro 91.4 1.1 2.4E-05 42.4 8.5 69 191-263 29-97 (211)
11 PRK10880 adenine DNA glycosyla 91.4 2.2 4.8E-05 43.5 11.3 69 191-264 30-98 (350)
12 TIGR01084 mutY A/G-specific ad 89.5 2.6 5.6E-05 41.5 9.6 68 191-263 26-93 (275)
13 PF00730 HhH-GPD: HhH-GPD supe 88.8 5.7 0.00012 32.4 9.7 63 199-263 4-66 (108)
14 PRK01229 N-glycosylase/DNA lya 83.4 9.6 0.00021 36.5 9.6 108 187-330 33-140 (208)
15 COG0177 Nth Predicted EndoIII- 82.5 15 0.00032 35.4 10.5 101 191-330 29-130 (211)
16 COG0122 AlkA 3-methyladenine D 77.0 38 0.00082 33.7 11.7 109 189-330 103-220 (285)
17 PRK10308 3-methyl-adenine DNA 68.4 56 0.0012 32.4 10.5 118 180-332 102-231 (283)
18 PF02142 MGS: MGS-like domain 66.8 5.4 0.00012 32.5 2.7 29 304-332 4-32 (95)
19 cd00166 SAM Sterile alpha moti 66.6 14 0.00031 26.6 4.7 43 214-258 17-61 (63)
20 COG2231 Uncharacterized protei 62.2 57 0.0012 31.9 9.0 83 171-258 14-97 (215)
21 COG1393 ArsC Arsenate reductas 55.8 12 0.00025 32.6 3.0 67 174-247 26-92 (117)
22 PF00536 SAM_1: SAM domain (St 54.2 26 0.00057 26.1 4.3 43 214-258 18-62 (64)
23 smart00851 MGS MGS-like domain 44.0 22 0.00048 28.5 2.7 29 304-332 4-32 (90)
24 PF07647 SAM_2: SAM domain (St 42.3 41 0.00089 25.1 3.8 43 214-258 19-64 (66)
25 PF13276 HTH_21: HTH-like doma 40.3 34 0.00073 25.6 3.0 30 303-332 24-53 (60)
26 PF13495 Phage_int_SAM_4: Phag 39.3 1.6E+02 0.0034 22.5 6.8 71 191-264 1-72 (85)
27 cd00532 MGS-like MGS-like doma 36.2 42 0.0009 28.2 3.3 33 300-332 12-44 (112)
28 TIGR01529 argR_whole arginine 32.3 47 0.001 29.8 3.1 31 302-333 19-49 (146)
29 PHA02517 putative transposase 31.4 51 0.0011 31.2 3.4 30 303-333 49-78 (277)
30 cd01424 MGS_CPS_II Methylglyox 31.3 57 0.0012 26.9 3.3 32 300-331 13-44 (110)
31 smart00454 SAM Sterile alpha m 30.2 1.4E+02 0.0031 21.4 5.0 43 216-260 21-66 (68)
32 PTZ00411 transaldolase-like pr 28.5 68 0.0015 32.9 3.9 63 251-330 114-176 (333)
33 PF07755 DUF1611: Protein of u 26.6 65 0.0014 32.7 3.3 50 300-351 128-181 (301)
34 cd01422 MGS Methylglyoxal synt 25.5 76 0.0017 27.1 3.1 32 300-331 12-46 (115)
35 COG4081 Uncharacterized protei 25.4 52 0.0011 30.3 2.2 25 293-317 12-36 (148)
36 PRK13910 DNA glycosylase MutY; 25.3 3.4E+02 0.0074 27.3 8.1 47 212-263 14-60 (289)
37 cd01423 MGS_CPS_I_III Methylgl 25.1 80 0.0017 26.4 3.1 32 300-331 13-44 (116)
38 cd04883 ACT_AcuB C-terminal AC 24.2 54 0.0012 24.4 1.8 20 300-319 52-71 (72)
39 PF13068 DUF3932: Protein of u 24.1 20 0.00044 29.5 -0.6 31 261-291 3-34 (81)
40 TIGR00588 ogg 8-oxoguanine DNA 23.6 7.5E+02 0.016 24.8 12.4 129 170-330 99-242 (310)
41 PHA02543 regA translation repr 23.5 29 0.00063 31.2 0.2 58 193-251 55-112 (125)
42 cd07153 Fur_like Ferric uptake 22.9 98 0.0021 25.4 3.3 31 302-333 19-52 (116)
43 cd01421 IMPCH Inosine monophos 22.8 78 0.0017 30.2 2.9 31 301-331 12-42 (187)
44 KOG2198 tRNA cytosine-5-methyl 22.5 1.3E+02 0.0027 31.8 4.6 101 206-319 19-120 (375)
45 PF14493 HTH_40: Helix-turn-he 22.1 2.6E+02 0.0057 22.6 5.5 43 194-238 4-57 (91)
46 PF12401 DUF3662: Protein of u 21.8 46 0.00099 28.8 1.1 25 299-323 76-100 (116)
47 PF12583 TPPII_N: Tripeptidyl 21.5 50 0.0011 30.3 1.3 29 210-238 69-97 (139)
48 cd03036 ArsC_like Arsenate Red 21.2 1E+02 0.0022 26.0 3.0 53 192-247 38-92 (111)
49 cd00052 EH Eps15 homology doma 20.6 49 0.0011 23.9 0.9 29 216-244 1-29 (67)
No 1
>PRK10353 3-methyl-adenine DNA glycosylase I; Provisional
Probab=100.00 E-value=7.9e-86 Score=603.17 Aligned_cols=183 Identities=41% Similarity=0.782 Sum_probs=180.1
Q ss_pred CCCCCCCCCCChhhhhhhhcCCCccccchHHHHHHHHHHHHhcCCcHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHh
Q 016657 160 KRCAWVTPNTDPCYAAFHDEEWGVPVHDDKKLFELLVLSGALSELTWPAILSKRHIFREVFVGFDPIAVSKLNEKKLLAA 239 (385)
Q Consensus 160 ~RC~Wat~~sdply~~YHD~EWG~Pv~DDr~LFE~L~LEgfQAGLSW~tILkKRe~fReAF~~FDp~kVA~~~E~dIe~L 239 (385)
.||.|++ +||+|++|||+|||+|+|||++|||+||||+|||||||.|||+||++||+||++|||++||+|+|+||++|
T Consensus 2 ~rC~W~~--~~~l~~~YHD~eWG~P~~dd~~LFE~L~Le~~QAGLSW~tIL~Kre~fr~aF~~Fd~~~VA~~~e~die~L 79 (187)
T PRK10353 2 ERCGWVS--QDPLYIAYHDNEWGVPETDSKKLFEMICLEGQQAGLSWITVLKKRENYRACFHQFDPVKVAAMQEEDVERL 79 (187)
T ss_pred CCCCCCC--CChHHHHhhhccCCCcCCCcHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHcCCCHHHHhCCCHHHHHHH
Confidence 6999996 89999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccccccchhHHHHHHHHHHHHHHHHHhcCCHHHHHhhhcCCCCccCCCCCCCCCCCCChhHHHHHHHHHHcCCcccch
Q 016657 240 GSAASSLLSELKLRAIIENARQISKVIDEFGSFNNYIWSFVSHKPIVSRFRYPRQVPVKTPKADVISKDLVRRGFRSVGP 319 (385)
Q Consensus 240 m~d~~IIRNr~KI~AVI~NArailkI~~E~GSF~~ylWsFv~~kpiv~~~~~~~~vP~~T~lS~~ISKdLKkrGFkFVGP 319 (385)
|+|++|||||+||+|||+|||++++|++|||||++|||+||+++||+|++.+..++|++|++|++|||+||||||+||||
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 hhHHHHHHHhccccCcccccchhhh
Q 016657 320 TIIYSFMQVAGVTNDHLTSCFRFQE 344 (385)
Q Consensus 320 TtvYSFMQAvGivNDHlv~Cfr~~~ 344 (385)
||||+||||+||||||+++|+++..
T Consensus 160 t~~ysfmqA~G~vndH~~~C~~~~~ 184 (187)
T PRK10353 160 TICYSFMQACGLVNDHVVGCCCHPG 184 (187)
T ss_pred HHHHHHHHHHCCccccccCccccCC
Confidence 9999999999999999999998853
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=7.6e-84 Score=586.71 Aligned_cols=179 Identities=36% Similarity=0.756 Sum_probs=176.0
Q ss_pred CCCCCCCCCCChhhhhhhhcCCCccccchHHHHHHHHHHHHhcCCcHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHh
Q 016657 160 KRCAWVTPNTDPCYAAFHDEEWGVPVHDDKKLFELLVLSGALSELTWPAILSKRHIFREVFVGFDPIAVSKLNEKKLLAA 239 (385)
Q Consensus 160 ~RC~Wat~~sdply~~YHD~EWG~Pv~DDr~LFE~L~LEgfQAGLSW~tILkKRe~fReAF~~FDp~kVA~~~E~dIe~L 239 (385)
.||.|++ +||+|++|||+|||+|+|||++|||+||||+|||||||.|||+||++||+||+||||++||+|+|++|++|
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 79999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccccccchhHHHHHHHHHHHHHHHHHhcCCHHHHHhhhcCCCCccCCCCCCCCCCCCChhHHHHHHHHHHcCCcccch
Q 016657 240 GSAASSLLSELKLRAIIENARQISKVIDEFGSFNNYIWSFVSHKPIVSRFRYPRQVPVKTPKADVISKDLVRRGFRSVGP 319 (385)
Q Consensus 240 m~d~~IIRNr~KI~AVI~NArailkI~~E~GSF~~ylWsFv~~kpiv~~~~~~~~vP~~T~lS~~ISKdLKkrGFkFVGP 319 (385)
|+|++|||||+||+|||+|||++++|++| ||++|||+||+++||+|++.+..+||++|++|++|||+||||||+||||
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 99999999999999999999999999888 9999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHHhccccCcccccchh
Q 016657 320 TIIYSFMQVAGVTNDHLTSCFRF 342 (385)
Q Consensus 320 TtvYSFMQAvGivNDHlv~Cfr~ 342 (385)
||||+||||+||||||+++|+++
T Consensus 157 t~~ysfmqA~G~vndH~~~C~~~ 179 (179)
T TIGR00624 157 TICYALMQATGMVDDHIQGCWVY 179 (179)
T ss_pred HHHHHHHHHHCCccccccCCcCC
Confidence 99999999999999999999875
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=3.9e-82 Score=575.40 Aligned_cols=179 Identities=53% Similarity=0.997 Sum_probs=154.5
Q ss_pred CCCCCCChhhhhhhhcCCCccccchHHHHHHHHHHHHhcCCcHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhcccc
Q 016657 164 WVTPNTDPCYAAFHDEEWGVPVHDDKKLFELLVLSGALSELTWPAILSKRHIFREVFVGFDPIAVSKLNEKKLLAAGSAA 243 (385)
Q Consensus 164 Wat~~sdply~~YHD~EWG~Pv~DDr~LFE~L~LEgfQAGLSW~tILkKRe~fReAF~~FDp~kVA~~~E~dIe~Lm~d~ 243 (385)
|+. ++|+|++|||+|||+|+|||++|||+||||+|||||||.|||+||++||+||+||||++||+|+|++|++||+|+
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 789999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccchhHHHHHHHHHHHHHHHHHhcCCHHHHHhhhcCCCCccCCCCCCCCCCCCChhHHHHHHHHHHcCCcccchhhHH
Q 016657 244 SSLLSELKLRAIIENARQISKVIDEFGSFNNYIWSFVSHKPIVSRFRYPRQVPVKTPKADVISKDLVRRGFRSVGPTIIY 323 (385)
Q Consensus 244 ~IIRNr~KI~AVI~NArailkI~~E~GSF~~ylWsFv~~kpiv~~~~~~~~vP~~T~lS~~ISKdLKkrGFkFVGPTtvY 323 (385)
+|||||+||+|||+||+++++|++|||||++|||+|++++||++.+++..++|++|++|++|||+||+|||+||||||||
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 HHHHHhccccCcccccchhhh
Q 016657 324 SFMQVAGVTNDHLTSCFRFQE 344 (385)
Q Consensus 324 SFMQAvGivNDHlv~Cfr~~~ 344 (385)
|||||+||||||+++|+++++
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=2.2e-81 Score=572.74 Aligned_cols=186 Identities=44% Similarity=0.811 Sum_probs=181.3
Q ss_pred CCCCCCCCCCCChhhhhhhhcCCCccccchHHHHHHHHHHHHhcCCcHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHH
Q 016657 159 KKRCAWVTPNTDPCYAAFHDEEWGVPVHDDKKLFELLVLSGALSELTWPAILSKRHIFREVFVGFDPIAVSKLNEKKLLA 238 (385)
Q Consensus 159 ~~RC~Wat~~sdply~~YHD~EWG~Pv~DDr~LFE~L~LEgfQAGLSW~tILkKRe~fReAF~~FDp~kVA~~~E~dIe~ 238 (385)
+.||.|+. +.||+|.+|||+|||+|++||+.|||+||||+|||||||.|||+||++||+||++|||++||.|+|+||++
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 MNRCAWAG-GLDPLYLAYHDTEWGVPLHDDQRLFELLCLEGFQAGLSWLTVLKKREAFREAFHGFDPEKVAAMTEEDVER 79 (188)
T ss_pred CCcccccC-CCCchhhcccccccCCCCCChHHHHHHHHHHHHhccchHHHHHHhHHHHHHHHhcCCHHHHHcCCHHHHHH
Confidence 36999996 34899999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hccccccccchhHHHHHHHHHHHHHHHHHhcCCHHHHHhhhcCCCCccCCCCCCCCCCCCChhHHHHHHHHHHcCCcccc
Q 016657 239 AGSAASSLLSELKLRAIIENARQISKVIDEFGSFNNYIWSFVSHKPIVSRFRYPRQVPVKTPKADVISKDLVRRGFRSVG 318 (385)
Q Consensus 239 Lm~d~~IIRNr~KI~AVI~NArailkI~~E~GSF~~ylWsFv~~kpiv~~~~~~~~vP~~T~lS~~ISKdLKkrGFkFVG 318 (385)
||+|++|||||+||.|||+|||++++|++|||||++|||+|++++|+++++.+..++|+.|++|++|||+||+|||+|||
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 hhhHHHHHHHhccccCcccccchhhhh
Q 016657 319 PTIIYSFMQVAGVTNDHLTSCFRFQEC 345 (385)
Q Consensus 319 PTtvYSFMQAvGivNDHlv~Cfr~~~~ 345 (385)
|||||+||||+||||||+.+|+++.++
T Consensus 160 pTt~yafmqA~G~vndH~~~C~~~~~~ 186 (188)
T COG2818 160 PTTVYAFMQATGLVNDHAEGCPCRREI 186 (188)
T ss_pred cHHHHHHHHHHcchHHHHhcCCCcccc
Confidence 999999999999999999999988653
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=95.57 E-value=0.13 Score=44.73 Aligned_cols=104 Identities=21% Similarity=0.166 Sum_probs=79.0
Q ss_pred HHHHHHHHHhcCCcHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhccccccccchhHHHHHHHHHHHHHHHHHhcCC
Q 016657 192 FELLVLSGALSELTWPAILSKRHIFREVFVGFDPIAVSKLNEKKLLAAGSAASSLLSELKLRAIIENARQISKVIDEFGS 271 (385)
Q Consensus 192 FE~L~LEgfQAGLSW~tILkKRe~fReAF~~FDp~kVA~~~E~dIe~Lm~d~~IIRNr~KI~AVI~NArailkI~~E~GS 271 (385)
||.|+-.+...-.+|..+.+-...|.+.|. .+|+.|+..++++|..+...-+ .+.|.+.+++=|+.+.+ .++.
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 678888888888999999999999988885 7999999999999998766555 47898888888887754 3433
Q ss_pred HHHHHhhhcCCCCccCCCCCCCCCCCCChhHHHHHHHHHHcCCcccchhhHHHHHHHhc
Q 016657 272 FNNYIWSFVSHKPIVSRFRYPRQVPVKTPKADVISKDLVRRGFRSVGPTIIYSFMQVAG 330 (385)
Q Consensus 272 F~~ylWsFv~~kpiv~~~~~~~~vP~~T~lS~~ISKdLKkrGFkFVGPTtvYSFMQAvG 330 (385)
+.. +. +.+-+.|. .++-|||-|+-.+|.-+.
T Consensus 74 ~~~------~~--------------------~~~~~~L~--~l~GIG~~tA~~~l~~~~ 104 (158)
T cd00056 74 LVL------DD--------------------PDAREELL--ALPGVGRKTANVVLLFAL 104 (158)
T ss_pred ccC------CC--------------------cccHHHHH--cCCCCCHHHHHHHHHHHC
Confidence 322 10 12334555 479999999998887654
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=95.03 E-value=0.45 Score=44.57 Aligned_cols=117 Identities=14% Similarity=0.148 Sum_probs=79.3
Q ss_pred HHHHHHHHHHhcCCcHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhccc-ccccc-chhHHHHHHHHHHHHHHHHHh
Q 016657 191 LFELLVLSGALSELTWPAILSKRHIFREVFVGFDPIAVSKLNEKKLLAAGSA-ASSLL-SELKLRAIIENARQISKVIDE 268 (385)
Q Consensus 191 LFE~L~LEgfQAGLSW~tILkKRe~fReAF~~FDp~kVA~~~E~dIe~Lm~d-~~IIR-Nr~KI~AVI~NArailkI~~E 268 (385)
-||+|+-.+.-+--+|..+.+=-..+.+.+...||+.+++++.++|++++.. +++.+ .+.|=+-+++=|+.++ ++
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 4899999999999999999877666644333389999999999999998763 34333 3466566665556553 45
Q ss_pred cCCHHHHHhhhcCCCCccCCCCCCCCCCCCChhHHHHHHHHHHcCCcccchhhHHHHHHHhc
Q 016657 269 FGSFNNYIWSFVSHKPIVSRFRYPRQVPVKTPKADVISKDLVRRGFRSVGPTIIYSFMQVAG 330 (385)
Q Consensus 269 ~GSF~~ylWsFv~~kpiv~~~~~~~~vP~~T~lS~~ISKdLKkrGFkFVGPTtvYSFMQAvG 330 (385)
||+=-.-||... +|. ...+-++|.+ ++-|||.|+--||.-.|
T Consensus 95 y~G~v~~L~~~~--------------~p~----t~~lre~Ll~--LpGVG~KTAnvVL~~l~ 136 (177)
T TIGR03252 95 YDGDATAVWTEG--------------DPD----GKELLRRLKA--LPGFGKQKAKIFLALLG 136 (177)
T ss_pred hCCChhhhhccc--------------CCC----cHHHHHHHHc--CCCCCHHHHHHHHHHHH
Confidence 554223345321 111 1133345544 79999999999998887
No 7
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=94.61 E-value=0.71 Score=44.21 Aligned_cols=118 Identities=17% Similarity=0.234 Sum_probs=81.8
Q ss_pred HHHHHHHHHHhcCCcHHHHHHhHHHHHHHhc-----CCCHHHHhcCCHHHHHHhccccccccchhHHHHHHHHHHHHHHH
Q 016657 191 LFELLVLSGALSELTWPAILSKRHIFREVFV-----GFDPIAVSKLNEKKLLAAGSAASSLLSELKLRAIIENARQISKV 265 (385)
Q Consensus 191 LFE~L~LEgfQAGLSW~tILkKRe~fReAF~-----~FDp~kVA~~~E~dIe~Lm~d~~IIRNr~KI~AVI~NArailkI 265 (385)
-||.|+-.+.-.--+|..|.+--+.++++|. .-+|+.|+++++++|++++...|. .++|.+.+.+=|+.++
T Consensus 30 ~fevLV~aILsQqT~~~~v~~a~~~L~~~~~~~~~~~~t~e~L~~a~~eeL~~~Irp~Gf--~~~KA~~Lk~la~~i~-- 105 (218)
T PRK13913 30 KFEALLGAVLTQNTKFEAVEKSLENLKNAFILENDDEINLKKIAYIEFSKLAECVRPSGF--YNQKAKRLIDLSENIL-- 105 (218)
T ss_pred HHHHHHHHHHHhhhhHHHHHHHHHHHHHhcccccccCCCHHHHHcCCHHHHHHHHHhcCC--HHHHHHHHHHHHHHHH--
Confidence 3788887777666789998887777777653 238999999999999998776554 5678777877777764
Q ss_pred HHhcCCHHHHHhhhcCCCCccCCCCCCCCCCCCChhHHHHHHHHHHcCCcccchhhHHHHHH-Hhc----cccCcccccc
Q 016657 266 IDEFGSFNNYIWSFVSHKPIVSRFRYPRQVPVKTPKADVISKDLVRRGFRSVGPTIIYSFMQ-VAG----VTNDHLTSCF 340 (385)
Q Consensus 266 ~~E~GSF~~ylWsFv~~kpiv~~~~~~~~vP~~T~lS~~ISKdLKkrGFkFVGPTtvYSFMQ-AvG----ivNDHlv~Cf 340 (385)
++||+++.+. . | ..-++|.+ .+-|||-|+-++|- +.| +|+.|..--+
T Consensus 106 -~~~g~~~~~~----~--------------~-------~~re~Ll~--l~GIG~kTAd~iLlya~~rp~fvVDty~~Rv~ 157 (218)
T PRK13913 106 -KDFGSFENFK----Q--------------E-------VTREWLLD--QKGIGKESADAILCYVCAKEVMVVDKYSYLFL 157 (218)
T ss_pred -HHcCCchhcc----C--------------c-------hHHHHHHc--CCCccHHHHHHHHHHHcCCCccccchhHHHHH
Confidence 4667765321 1 0 11134444 78899999999887 444 4555554333
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=94.26 E-value=0.45 Score=43.67 Aligned_cols=101 Identities=24% Similarity=0.279 Sum_probs=74.5
Q ss_pred HHHHHHHHHHhcCCcHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhccccccccchhHHHHHHHHHHHHHHHHHhcC
Q 016657 191 LFELLVLSGALSELTWPAILSKRHIFREVFVGFDPIAVSKLNEKKLLAAGSAASSLLSELKLRAIIENARQISKVIDEFG 270 (385)
Q Consensus 191 LFE~L~LEgfQAGLSW~tILkKRe~fReAF~~FDp~kVA~~~E~dIe~Lm~d~~IIRNr~KI~AVI~NArailkI~~E~G 270 (385)
-||.|+-.+.-.--+|..+.+-...+.+.|- +|+.|+..++++|.+++.--|. .+.|.+.|++=|+++.+ ++|
T Consensus 26 pf~~Li~~ILsqqt~~~~~~~~~~~l~~~~p--t~~~l~~~~~~~L~~~ir~~G~--~~~Ka~~i~~~a~~i~~---~~~ 98 (191)
T TIGR01083 26 PFELLVATILSAQATDKSVNKATKKLFEVYP--TPQALAQAGLEELEEYIKSIGL--YRNKAKNIIALCRILVE---RYG 98 (191)
T ss_pred HHHHHHHHHHHhhCcHHHHHHHHHHHHHHCC--CHHHHHcCCHHHHHHHHHhcCC--hHHHHHHHHHHHHHHHH---HcC
Confidence 5899999999899999999988777777664 7999999999999887665443 45787888877777654 232
Q ss_pred CHHHHHhhhcCCCCccCCCCCCCCCCCCChhHHHHHHHHHHcCCcccchhhHHHHHHHh
Q 016657 271 SFNNYIWSFVSHKPIVSRFRYPRQVPVKTPKADVISKDLVRRGFRSVGPTIIYSFMQVA 329 (385)
Q Consensus 271 SF~~ylWsFv~~kpiv~~~~~~~~vP~~T~lS~~ISKdLKkrGFkFVGPTtvYSFMQAv 329 (385)
+ .+| ..-+.|.+ ++.|||.|+..+|.-.
T Consensus 99 ~----------------------~~~-------~~~~~L~~--l~GIG~ktA~~ill~~ 126 (191)
T TIGR01083 99 G----------------------EVP-------EDREELVK--LPGVGRKTANVVLNVA 126 (191)
T ss_pred C----------------------CCc-------hHHHHHHh--CCCCcHHHHHHHHHHH
Confidence 1 011 11234554 7999999999887544
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=93.62 E-value=0.7 Score=39.96 Aligned_cols=88 Identities=22% Similarity=0.283 Sum_probs=65.1
Q ss_pred CcHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhccccccccchhHHHHHHHHHHHHHHHHHhcCCHHHHHhhhcCCC
Q 016657 204 LTWPAILSKRHIFREVFVGFDPIAVSKLNEKKLLAAGSAASSLLSELKLRAIIENARQISKVIDEFGSFNNYIWSFVSHK 283 (385)
Q Consensus 204 LSW~tILkKRe~fReAF~~FDp~kVA~~~E~dIe~Lm~d~~IIRNr~KI~AVI~NArailkI~~E~GSF~~ylWsFv~~k 283 (385)
.+|..+.+--..|.+.|- +|+.|+..++++|.+++..-+ -.+.|.+.|++.|+.+.+ ++++
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 478888888888888887 799999999999988766522 457799999999987654 2211
Q ss_pred CccCCCCCCCCCCCCChhHHHHHHHHHHcCCcccchhhHHHHHHHh
Q 016657 284 PIVSRFRYPRQVPVKTPKADVISKDLVRRGFRSVGPTIIYSFMQVA 329 (385)
Q Consensus 284 piv~~~~~~~~vP~~T~lS~~ISKdLKkrGFkFVGPTtvYSFMQAv 329 (385)
.+| ...+.|.+ ++-|||-|+-.||.-+
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 12355653 8999999998888776
No 10
>PRK10702 endonuclease III; Provisional
Probab=91.40 E-value=1.1 Score=42.42 Aligned_cols=69 Identities=17% Similarity=0.099 Sum_probs=54.8
Q ss_pred HHHHHHHHHHhcCCcHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhccccccccchhHHHHHHHHHHHHH
Q 016657 191 LFELLVLSGALSELTWPAILSKRHIFREVFVGFDPIAVSKLNEKKLLAAGSAASSLLSELKLRAIIENARQIS 263 (385)
Q Consensus 191 LFE~L~LEgfQAGLSW~tILkKRe~fReAF~~FDp~kVA~~~E~dIe~Lm~d~~IIRNr~KI~AVI~NArail 263 (385)
-||.|+-++..+--+|..|.+--+.+.+.| .+|+.+++.++++|++++.--|.- +.|=+.+++.|+.++
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--NTPAAMLELGVEGVKTYIKTIGLY--NSKAENVIKTCRILL 97 (211)
T ss_pred hHHHHHHHHHHhhcCHHHHHHHHHHHHHHc--CCHHHHHCCCHHHHHHHHHHcCCH--HHHHHHHHHHHHHHH
Confidence 499999999988899999988888777665 478999999999999887655543 445556777788765
No 11
>PRK10880 adenine DNA glycosylase; Provisional
Probab=91.37 E-value=2.2 Score=43.51 Aligned_cols=69 Identities=10% Similarity=0.121 Sum_probs=56.8
Q ss_pred HHHHHHHHHHhcCCcHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhccccccccchhHHHHHHHHHHHHHH
Q 016657 191 LFELLVLSGALSELTWPAILSKRHIFREVFVGFDPIAVSKLNEKKLLAAGSAASSLLSELKLRAIIENARQISK 264 (385)
Q Consensus 191 LFE~L~LEgfQAGLSW~tILkKRe~fReAF~~FDp~kVA~~~E~dIe~Lm~d~~IIRNr~KI~AVI~NArailk 264 (385)
-|+.|+-|++..=-+|.+|..--+.|.+.| .+++.+|..++++|.++..--|.- + |-+-+..-|+.+.+
T Consensus 30 py~ilVseILlQQT~v~~v~~~~~rl~~~f--Pt~~~La~a~~eel~~~~~glGyy--~-RAr~L~~~A~~i~~ 98 (350)
T PRK10880 30 PYKVWLSEVMLQQTQVATVIPYFERFMARF--PTVTDLANAPLDEVLHLWTGLGYY--A-RARNLHKAAQQVAT 98 (350)
T ss_pred HHHHHHHHHHHhhccHHHHHHHHHHHHHHC--cCHHHHHCcCHHHHHHHHHcCChH--H-HHHHHHHHHHHHHH
Confidence 478899999988899999999999999987 479999999999999987766664 2 66677777776643
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=89.46 E-value=2.6 Score=41.55 Aligned_cols=68 Identities=12% Similarity=0.158 Sum_probs=55.4
Q ss_pred HHHHHHHHHHhcCCcHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhccccccccchhHHHHHHHHHHHHH
Q 016657 191 LFELLVLSGALSELTWPAILSKRHIFREVFVGFDPIAVSKLNEKKLLAAGSAASSLLSELKLRAIIENARQIS 263 (385)
Q Consensus 191 LFE~L~LEgfQAGLSW~tILkKRe~fReAF~~FDp~kVA~~~E~dIe~Lm~d~~IIRNr~KI~AVI~NArail 263 (385)
.|+.|+-+++..=.+|.+|+.-.+.|.+.|- +|+.||+.++++|..+...-|.- + |.+.+.+=|+.+.
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 69999999999998887766664 2 4556665556543
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=88.78 E-value=5.7 Score=32.36 Aligned_cols=63 Identities=22% Similarity=0.045 Sum_probs=52.5
Q ss_pred HHhcCCcHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhccccccccchhHHHHHHHHHHHHH
Q 016657 199 GALSELTWPAILSKRHIFREVFVGFDPIAVSKLNEKKLLAAGSAASSLLSELKLRAIIENARQIS 263 (385)
Q Consensus 199 gfQAGLSW~tILkKRe~fReAF~~FDp~kVA~~~E~dIe~Lm~d~~IIRNr~KI~AVI~NArail 263 (385)
++..-.+|..+.+-...|.+.|...+|+.|+..++++|.++... .--++.|-+.+++=|+.++
T Consensus 4 Il~qq~s~~~a~~~~~~l~~~~g~pt~~~l~~~~~~el~~~i~~--~G~~~~ka~~i~~~a~~~~ 66 (108)
T PF00730_consen 4 ILSQQTSIKAARKIYRRLFERYGFPTPEALAEASEEELRELIRP--LGFSRRKAKYIIELARAIL 66 (108)
T ss_dssp HHCTTS-HHHHHHHHHHHHHHHSCSSHHHHHCSHHHHHHHHHTT--STSHHHHHHHHHHHHHHHH
T ss_pred eecCcCcHHHHHHHHHHHHHHhcCCCHHHHHhCCHHHHHHHhhc--cCCCHHHHHHHHHHHHHhh
Confidence 44555789999999999999999899999999999999998765 3346788888999899887
No 14
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=83.45 E-value=9.6 Score=36.48 Aligned_cols=108 Identities=15% Similarity=0.159 Sum_probs=66.8
Q ss_pred chHHHHHHHHHHHHhcCCcHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhccccccccchhHHHHHHHHHHHHHHHH
Q 016657 187 DDKKLFELLVLSGALSELTWPAILSKRHIFREVFVGFDPIAVSKLNEKKLLAAGSAASSLLSELKLRAIIENARQISKVI 266 (385)
Q Consensus 187 DDr~LFE~L~LEgfQAGLSW~tILkKRe~fReAF~~FDp~kVA~~~E~dIe~Lm~d~~IIRNr~KI~AVI~NArailkI~ 266 (385)
|+.-+|+.|+..+.-+.-+|..+.+--+.+. ++.+ .+++++|++++...+-=-.++|=+-|++-|+.+
T Consensus 33 ~~~~~f~~Lv~~ILsqnT~~~~v~~a~~~L~-------~~~l-~~~~eeL~~~Ir~~Gygf~~~KAk~I~~~~~~~---- 100 (208)
T PRK01229 33 DEEDLFSELSFCILTANSSAEGGIKAQKEIG-------DGFL-YLSEEELEEKLKEVGHRFYNKRAEYIVEARKLY---- 100 (208)
T ss_pred ccCChHHHHHHHHhcCcCcHHHHHHHHHhcC-------HHHc-CCCHHHHHHHHHHhhcccHHHHHHHHHHHHHHH----
Confidence 7778999999999999999999987666653 4445 789999998875542112344444444444432
Q ss_pred HhcCCHHHHHhhhcCCCCccCCCCCCCCCCCCChhHHHHHHHHHHcCCcccchhhHHHHHHHhc
Q 016657 267 DEFGSFNNYIWSFVSHKPIVSRFRYPRQVPVKTPKADVISKDLVRRGFRSVGPTIIYSFMQVAG 330 (385)
Q Consensus 267 ~E~GSF~~ylWsFv~~kpiv~~~~~~~~vP~~T~lS~~ISKdLKkrGFkFVGPTtvYSFMQAvG 330 (385)
|.+.+ .+..+. ++| ..-.+|.+ ..+-|||-|+-.||..+|
T Consensus 101 ---~~l~~---~~~~~~----------~~~-------~~R~~Ll~-~lpGIG~KTAd~vL~~~~ 140 (208)
T PRK01229 101 ---GKLKE---IIKADK----------DQF-------EAREFLVK-NIKGIGYKEASHFLRNVG 140 (208)
T ss_pred ---HHHHH---HHhccC----------Cch-------HHHHHHHH-cCCCCcHHHHHHHHHHcc
Confidence 22211 110110 111 22223332 478899999999998777
No 15
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=82.47 E-value=15 Score=35.44 Aligned_cols=101 Identities=23% Similarity=0.245 Sum_probs=64.7
Q ss_pred HHHHHHHHHHhcCCcHHHHHHhHHHHHHHhcCCC-HHHHhcCCHHHHHHhccccccccchhHHHHHHHHHHHHHHHHHhc
Q 016657 191 LFELLVLSGALSELTWPAILSKRHIFREVFVGFD-PIAVSKLNEKKLLAAGSAASSLLSELKLRAIIENARQISKVIDEF 269 (385)
Q Consensus 191 LFE~L~LEgfQAGLSW~tILkKRe~fReAF~~FD-p~kVA~~~E~dIe~Lm~d~~IIRNr~KI~AVI~NArailkI~~E~ 269 (385)
-||+|+--+..|-=+=..+- .++++.|.-|+ |+.+++.++++|+.+...-|+-| .|-..|+.=|+.++ ++|
T Consensus 29 pf~lLva~iLSaqttD~~vn---~at~~Lf~~~~t~e~l~~a~~~~l~~~I~~iGlyr--~KAk~I~~~~~~l~---e~~ 100 (211)
T COG0177 29 PFELLVAVILSAQTTDEVVN---KATPALFKRYPTPEDLLNADEEELEELIKSIGLYR--NKAKNIKELARILL---EKF 100 (211)
T ss_pred cHHHHHHHHHhccCchHHHH---HHHHHHHHHcCCHHHHHcCCHHHHHHHHHhcCCcH--HHHHHHHHHHHHHH---HHc
Confidence 47877654444433333333 34555555555 99999999999999988766555 55557887777764 566
Q ss_pred CCHHHHHhhhcCCCCccCCCCCCCCCCCCChhHHHHHHHHHHcCCcccchhhHHHHHHHhc
Q 016657 270 GSFNNYIWSFVSHKPIVSRFRYPRQVPVKTPKADVISKDLVRRGFRSVGPTIIYSFMQVAG 330 (385)
Q Consensus 270 GSF~~ylWsFv~~kpiv~~~~~~~~vP~~T~lS~~ISKdLKkrGFkFVGPTtvYSFMQAvG 330 (385)
|+ +||..- ++|.+ .--||+-|++-.|.-+.
T Consensus 101 ~g----------------------~vP~~~-------~eL~~--LPGVGrKTAnvVL~~a~ 130 (211)
T COG0177 101 GG----------------------EVPDTR-------EELLS--LPGVGRKTANVVLSFAF 130 (211)
T ss_pred CC----------------------CCCchH-------HHHHh--CCCcchHHHHHHHHhhc
Confidence 55 222111 12322 46799999998887743
No 16
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=77.01 E-value=38 Score=33.67 Aligned_cols=109 Identities=18% Similarity=0.153 Sum_probs=79.8
Q ss_pred HHHHHHHHHHHHhcCCcHHHHHHhHHHHHHHhcC--------CCHHHHhcCCHHHHHHhccccccccchhHHHHHHHHHH
Q 016657 189 KKLFELLVLSGALSELTWPAILSKRHIFREVFVG--------FDPIAVSKLNEKKLLAAGSAASSLLSELKLRAIIENAR 260 (385)
Q Consensus 189 r~LFE~L~LEgfQAGLSW~tILkKRe~fReAF~~--------FDp~kVA~~~E~dIe~Lm~d~~IIRNr~KI~AVI~NAr 260 (385)
.-+||.|+--+.+.=+|=..+-+-+..|.+.|-+ =.|+.|+..+++++.++ -..+.|.+.|++=|+
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 PDPFEALVRAILSQQVSVAAAAKIWARLVSLYGNALEIYHSFPTPEQLAAADEEALRRC------GLSGRKAEYIISLAR 176 (285)
T ss_pred CCHHHHHHHHHHHhHhhHHHHHHHHHHHHHHhCCccccccCCCCHHHHHhcCHHHHHHh------CCcHHHHHHHHHHHH
Confidence 4589999999999999988888888999999984 58999999999999754 357899999999999
Q ss_pred HHHHHHHhcCCHHHHHhhhcCCCCccCCCCCCCCCCCCChhHHHHHHHHHHcCCcccchhhHHH-HHHHhc
Q 016657 261 QISKVIDEFGSFNNYIWSFVSHKPIVSRFRYPRQVPVKTPKADVISKDLVRRGFRSVGPTIIYS-FMQVAG 330 (385)
Q Consensus 261 ailkI~~E~GSF~~ylWsFv~~kpiv~~~~~~~~vP~~T~lS~~ISKdLKkrGFkFVGPTtvYS-FMQAvG 330 (385)
++..-. =++.... + ---+.+-+.|.+ |+-|||-|+-- +|.+.|
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 886410 0111110 0 001244456666 99999988854 455566
No 17
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=68.38 E-value=56 Score=32.36 Aligned_cols=118 Identities=17% Similarity=0.152 Sum_probs=72.7
Q ss_pred CCCccccchHHHHHHHHHHHHhcCCcHHHHHHhHHHHHHHh----------cCC-CHHHHhcCCHHHHHHhccccccccc
Q 016657 180 EWGVPVHDDKKLFELLVLSGALSELTWPAILSKRHIFREVF----------VGF-DPIAVSKLNEKKLLAAGSAASSLLS 248 (385)
Q Consensus 180 EWG~Pv~DDr~LFE~L~LEgfQAGLSW~tILkKRe~fReAF----------~~F-Dp~kVA~~~E~dIe~Lm~d~~IIRN 248 (385)
.=|.-+.-..-+||+|+-.+.-.-.|=..+-+-...+-+.| .-| +|+.|++.++++|..+. -.
T Consensus 102 ~~GlR~p~~~d~fE~lv~aIigQqisv~~a~~~~~rlv~~~G~~l~~~~~~~~FPtpe~La~~~~~eL~~~G------l~ 175 (283)
T PRK10308 102 RPGLRLPGSVDAFEQGVRAILGQLVSVAMAAKLTAKVAQLYGERLDDFPEYVCFPTPERLAAADPQALKALG------MP 175 (283)
T ss_pred CCCCcCCCCCCHHHHHHHHHHHhHHHHHHHHHHHHHHHHHhCccccCCCCccCCCCHHHHHcCCHHHHHHCC------CC
Confidence 34555544455799988776544444333333333333333 334 79999999999987542 35
Q ss_pred hhHHHHHHHHHHHHHHHHHhcCCHHHHHhhhcCCCCccCCCCCCCCCCCCChhHHHHHHHHHHcCCcccchhhH-HHHHH
Q 016657 249 ELKLRAIIENARQISKVIDEFGSFNNYIWSFVSHKPIVSRFRYPRQVPVKTPKADVISKDLVRRGFRSVGPTII-YSFMQ 327 (385)
Q Consensus 249 r~KI~AVI~NArailkI~~E~GSF~~ylWsFv~~kpiv~~~~~~~~vP~~T~lS~~ISKdLKkrGFkFVGPTtv-YSFMQ 327 (385)
+.|.++|+.=|+++.+ |.++- .. +. + .+.+-+.|.+ ++-|||-|+ |-.|.
T Consensus 176 ~~Ra~~L~~lA~~i~~-----g~l~l--------~~-----------~~--~-~~~~~~~L~~--LpGIGpwTA~~vllr 226 (283)
T PRK10308 176 LKRAEALIHLANAALE-----GTLPL--------TI-----------PG--D-VEQAMKTLQT--FPGIGRWTANYFALR 226 (283)
T ss_pred HHHHHHHHHHHHHHHc-----CCCCc--------cc-----------cC--C-HHHHHHHHhc--CCCcCHHHHHHHHHH
Confidence 6788899988888764 32210 00 00 1 1345566666 899999888 77778
Q ss_pred Hhccc
Q 016657 328 VAGVT 332 (385)
Q Consensus 328 AvGiv 332 (385)
+.|-.
T Consensus 227 ~lg~~ 231 (283)
T PRK10308 227 GWQAK 231 (283)
T ss_pred hCCCC
Confidence 88843
No 18
>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=66.76 E-value=5.4 Score=32.49 Aligned_cols=29 Identities=21% Similarity=0.345 Sum_probs=25.9
Q ss_pred HHHHHHHHcCCcccchhhHHHHHHHhccc
Q 016657 304 VISKDLVRRGFRSVGPTIIYSFMQVAGVT 332 (385)
Q Consensus 304 ~ISKdLKkrGFkFVGPTtvYSFMQAvGiv 332 (385)
.++|.|.+.||++++.-..+.||+..|+-
T Consensus 4 ~~a~~l~~lG~~i~AT~gTa~~L~~~Gi~ 32 (95)
T PF02142_consen 4 PLAKRLAELGFEIYATEGTAKFLKEHGIE 32 (95)
T ss_dssp HHHHHHHHTTSEEEEEHHHHHHHHHTT--
T ss_pred HHHHHHHHCCCEEEEChHHHHHHHHcCCC
Confidence 68899999999999999999999999985
No 19
>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=66.62 E-value=14 Score=26.62 Aligned_cols=43 Identities=21% Similarity=0.196 Sum_probs=32.9
Q ss_pred HHHHHHh--cCCCHHHHhcCCHHHHHHhccccccccchhHHHHHHHH
Q 016657 214 HIFREVF--VGFDPIAVSKLNEKKLLAAGSAASSLLSELKLRAIIEN 258 (385)
Q Consensus 214 e~fReAF--~~FDp~kVA~~~E~dIe~Lm~d~~IIRNr~KI~AVI~N 258 (385)
+.|.+.| .++|-..+..++++++..+.... .-+|.||...|.+
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 57899999999999999765532 4688888776654
No 20
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=62.16 E-value=57 Score=31.88 Aligned_cols=83 Identities=16% Similarity=0.237 Sum_probs=58.6
Q ss_pred hhhhhhhhcCCCccccchHHHHHHHHHHHHhcCCcHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhccccccccchh
Q 016657 171 PCYAAFHDEEWGVPVHDDKKLFELLVLSGALSELTWPAILSKRHIFREVFVGFDPIAVSKLNEKKLLAAGSAASSLLSEL 250 (385)
Q Consensus 171 ply~~YHD~EWG~Pv~DDr~LFE~L~LEgfQAGLSW~tILkKRe~fReAF~~FDp~kVA~~~E~dIe~Lm~d~~IIRNr~ 250 (385)
.|+..|+|.-|=--...+ |.++=-+.----+|..|.+.-++++..+. +++.+|..+++++++.+..-.|--+-..
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 466788888885444333 54443344445679999999999998865 6799999999999999988777655432
Q ss_pred H-HHHHHHH
Q 016657 251 K-LRAIIEN 258 (385)
Q Consensus 251 K-I~AVI~N 258 (385)
| |.|++.|
T Consensus 89 ~rLk~l~k~ 97 (215)
T COG2231 89 KRLKALSKN 97 (215)
T ss_pred HHHHHHHHH
Confidence 2 3344443
No 21
>COG1393 ArsC Arsenate reductase and related proteins, glutaredoxin family [Inorganic ion transport and metabolism]
Probab=55.79 E-value=12 Score=32.64 Aligned_cols=67 Identities=7% Similarity=-0.098 Sum_probs=45.0
Q ss_pred hhhhhcCCCccccchHHHHHHHHHHHHhcCCcHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhcccccccc
Q 016657 174 AAFHDEEWGVPVHDDKKLFELLVLSGALSELTWPAILSKRHIFREVFVGFDPIAVSKLNEKKLLAAGSAASSLL 247 (385)
Q Consensus 174 ~~YHD~EWG~Pv~DDr~LFE~L~LEgfQAGLSW~tILkKRe~fReAF~~FDp~kVA~~~E~dIe~Lm~d~~IIR 247 (385)
+.|+-.....---+...|-++ ..+.|..|..++++|..+-+... .++..-.+++.++.++.++.+||
T Consensus 26 i~~~~~~y~~~~~s~~eL~~~----l~~~g~~~~~li~t~~~~~r~L~---~~~~~~~~~~~~~~i~~~~~Lik 92 (117)
T COG1393 26 IEYTFIDYLKTPPSREELKKI----LSKLGDGVEELINTRGTTYRELN---LDKEDLSDEELIEALLENPSLIK 92 (117)
T ss_pred CCcEEEEeecCCCCHHHHHHH----HHHcCccHHHHHHhccchHHHcC---CcccccChHHHHHHHHhChhhcc
Confidence 344433344333444445443 46789999999999988777766 45556677778888888886655
No 22
>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=54.17 E-value=26 Score=26.05 Aligned_cols=43 Identities=23% Similarity=0.257 Sum_probs=32.3
Q ss_pred HHHHHHh-cC-CCHHHHhcCCHHHHHHhccccccccchhHHHHHHHH
Q 016657 214 HIFREVF-VG-FDPIAVSKLNEKKLLAAGSAASSLLSELKLRAIIEN 258 (385)
Q Consensus 214 e~fReAF-~~-FDp~kVA~~~E~dIe~Lm~d~~IIRNr~KI~AVI~N 258 (385)
+.|.+.| .+ -|-..+..++++++.++... .+-||.||...|..
T Consensus 18 ~~y~~~F~~~~i~g~~L~~lt~~dL~~lgi~--~~ghr~ki~~~i~~ 62 (64)
T PF00536_consen 18 EQYAENFEKNYIDGEDLLSLTEEDLEELGIT--KLGHRKKILRAIQK 62 (64)
T ss_dssp GGGHHHHHHTTSSHHHHTTSCHHHHHHTT-S--SHHHHHHHHHHHHH
T ss_pred HHHHHHHHcCCchHHHHHhcCHHHHHHcCCC--CHHHHHHHHHHHHH
Confidence 5677777 44 49999999999999995432 24689999887764
No 23
>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=43.98 E-value=22 Score=28.47 Aligned_cols=29 Identities=28% Similarity=0.405 Sum_probs=25.9
Q ss_pred HHHHHHHHcCCcccchhhHHHHHHHhccc
Q 016657 304 VISKDLVRRGFRSVGPTIIYSFMQVAGVT 332 (385)
Q Consensus 304 ~ISKdLKkrGFkFVGPTtvYSFMQAvGiv 332 (385)
.+++.|.+.||+.+.....+.||+..|+-
T Consensus 4 ~~~~~l~~lG~~i~AT~gTa~~L~~~Gi~ 32 (90)
T smart00851 4 ELAKRLAELGFELVATGGTAKFLREAGLP 32 (90)
T ss_pred HHHHHHHHCCCEEEEccHHHHHHHHCCCc
Confidence 67889999999999998889999999963
No 24
>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=42.33 E-value=41 Score=25.09 Aligned_cols=43 Identities=26% Similarity=0.331 Sum_probs=31.3
Q ss_pred HHHHHHhc--CCCH-HHHhcCCHHHHHHhccccccccchhHHHHHHHH
Q 016657 214 HIFREVFV--GFDP-IAVSKLNEKKLLAAGSAASSLLSELKLRAIIEN 258 (385)
Q Consensus 214 e~fReAF~--~FDp-~kVA~~~E~dIe~Lm~d~~IIRNr~KI~AVI~N 258 (385)
+.|.++|. ++|- +.++.++++++.++.... .-+|.||-..|.+
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 55667776 6666 779999999999876532 3577887776654
No 25
>PF13276 HTH_21: HTH-like domain
Probab=40.30 E-value=34 Score=25.55 Aligned_cols=30 Identities=23% Similarity=0.243 Sum_probs=26.2
Q ss_pred HHHHHHHHHcCCcccchhhHHHHHHHhccc
Q 016657 303 DVISKDLVRRGFRSVGPTIIYSFMQVAGVT 332 (385)
Q Consensus 303 ~~ISKdLKkrGFkFVGPTtvYSFMQAvGiv 332 (385)
..|+.+|.+.|---||-.+||-+|+..||.
T Consensus 24 rri~~~L~~~~~~~v~~krV~RlM~~~gL~ 53 (60)
T PF13276_consen 24 RRIWAELRREGGIRVSRKRVRRLMREMGLR 53 (60)
T ss_pred hHHHHHHhccCcccccHHHHHHHHHHcCCc
Confidence 389999999965568999999999999985
No 26
>PF13495 Phage_int_SAM_4: Phage integrase, N-terminal SAM-like domain; PDB: 2A3V_A.
Probab=39.28 E-value=1.6e+02 Score=22.52 Aligned_cols=71 Identities=14% Similarity=0.052 Sum_probs=44.5
Q ss_pred HHHHHHHHHHhcCCcHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhccccccccchhHH-HHHHHHHHHHHH
Q 016657 191 LFELLVLSGALSELTWPAILSKRHIFREVFVGFDPIAVSKLNEKKLLAAGSAASSLLSELKL-RAIIENARQISK 264 (385)
Q Consensus 191 LFE~L~LEgfQAGLSW~tILkKRe~fReAF~~FDp~kVA~~~E~dIe~Lm~d~~IIRNr~KI-~AVI~NArailk 264 (385)
|++.+....-..|+|=.||-.-+-.++.-..-|+-..+..++.++|+..+.. +.+.+++ .+.|+++...++
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 4455556666699999999999999998777777678999999999987664 2323332 345666555544
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=36.18 E-value=42 Score=28.18 Aligned_cols=33 Identities=15% Similarity=0.135 Sum_probs=28.6
Q ss_pred hhHHHHHHHHHHcCCcccchhhHHHHHHHhccc
Q 016657 300 PKADVISKDLVRRGFRSVGPTIIYSFMQVAGVT 332 (385)
Q Consensus 300 ~lS~~ISKdLKkrGFkFVGPTtvYSFMQAvGiv 332 (385)
+....+++.|.+.||+.++....+.||+..|+-
T Consensus 12 ~~~~~~a~~l~~~G~~i~AT~gTa~~L~~~Gi~ 44 (112)
T cd00532 12 AMLVDLAPKLSSDGFPLFATGGTSRVLADAGIP 44 (112)
T ss_pred HHHHHHHHHHHHCCCEEEECcHHHHHHHHcCCc
Confidence 445688999999999999999999999998863
No 28
>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=32.35 E-value=47 Score=29.85 Aligned_cols=31 Identities=13% Similarity=0.168 Sum_probs=27.2
Q ss_pred HHHHHHHHHHcCCcccchhhHHHHHHHhcccc
Q 016657 302 ADVISKDLVRRGFRSVGPTIIYSFMQVAGVTN 333 (385)
Q Consensus 302 S~~ISKdLKkrGFkFVGPTtvYSFMQAvGivN 333 (385)
.+.|...|+++||. |.-.|+|-.|...|++-
T Consensus 19 qeeL~~~L~~~G~~-vsqaTIsRdL~elglvk 49 (146)
T TIGR01529 19 QEELVALLKAEGIE-VTQATVSRDLRELGAVK 49 (146)
T ss_pred HHHHHHHHHHhCCC-cCHHHHHHHHHHcCCEE
Confidence 35788899999999 88899999999999863
No 29
>PHA02517 putative transposase OrfB; Reviewed
Probab=31.40 E-value=51 Score=31.16 Aligned_cols=30 Identities=23% Similarity=0.396 Sum_probs=26.3
Q ss_pred HHHHHHHHHcCCcccchhhHHHHHHHhcccc
Q 016657 303 DVISKDLVRRGFRSVGPTIIYSFMQVAGVTN 333 (385)
Q Consensus 303 ~~ISKdLKkrGFkFVGPTtvYSFMQAvGivN 333 (385)
..|...|+++|+. ++..+||-+|+..||..
T Consensus 49 r~I~~~L~~~g~~-vs~~tV~Rim~~~gl~~ 78 (277)
T PHA02517 49 RKVWRQLNREGIR-VARCTVGRLMKELGLAG 78 (277)
T ss_pred HHHHHHHHhcCcc-cCHHHHHHHHHHcCCce
Confidence 3888899999996 59999999999999853
No 30
>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=31.26 E-value=57 Score=26.92 Aligned_cols=32 Identities=34% Similarity=0.505 Sum_probs=28.1
Q ss_pred hhHHHHHHHHHHcCCcccchhhHHHHHHHhcc
Q 016657 300 PKADVISKDLVRRGFRSVGPTIIYSFMQVAGV 331 (385)
Q Consensus 300 ~lS~~ISKdLKkrGFkFVGPTtvYSFMQAvGi 331 (385)
+....+++.|.+.||+..+....+.||+..|+
T Consensus 13 ~~~~~~~~~l~~~G~~l~aT~gT~~~l~~~gi 44 (110)
T cd01424 13 PEAVEIAKRLAELGFKLVATEGTAKYLQEAGI 44 (110)
T ss_pred hHHHHHHHHHHHCCCEEEEchHHHHHHHHcCC
Confidence 34557889999999999999999999999996
No 31
>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=30.23 E-value=1.4e+02 Score=21.36 Aligned_cols=43 Identities=23% Similarity=0.311 Sum_probs=31.7
Q ss_pred HHHHh--cCCCHHHHhcCC-HHHHHHhccccccccchhHHHHHHHHHH
Q 016657 216 FREVF--VGFDPIAVSKLN-EKKLLAAGSAASSLLSELKLRAIIENAR 260 (385)
Q Consensus 216 fReAF--~~FDp~kVA~~~-E~dIe~Lm~d~~IIRNr~KI~AVI~NAr 260 (385)
|.+.| .+++-..+..++ +++++++.... +-+|.||-..|..-+
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 677888999998 88888876522 458888887776643
No 32
>PTZ00411 transaldolase-like protein; Provisional
Probab=28.54 E-value=68 Score=32.91 Aligned_cols=63 Identities=25% Similarity=0.377 Sum_probs=45.8
Q ss_pred HHHHHHHHHHHHHHHHHhcCCHHHHHhhhcCCCCccCCCCCCCCCCCCChhHHHHHHHHHHcCCcccchhhHHHHHHHhc
Q 016657 251 KLRAIIENARQISKVIDEFGSFNNYIWSFVSHKPIVSRFRYPRQVPVKTPKADVISKDLVRRGFRSVGPTIIYSFMQVAG 330 (385)
Q Consensus 251 KI~AVI~NArailkI~~E~GSF~~ylWsFv~~kpiv~~~~~~~~vP~~T~lS~~ISKdLKkrGFkFVGPTtvYSFMQAvG 330 (385)
-.+++|..|+.+.++.++.| ++...+ .=.||++ ...-..++.|.+.|.+.-. |.+|++.||+-
T Consensus 114 d~e~~i~~A~~l~~l~~~~g---------i~~~ri------lIKIPaT-~eGi~Aa~~L~~eGI~~N~-TlvFS~~QA~a 176 (333)
T PTZ00411 114 DKQAMVDKARKIIKMYEEAG---------ISKDRI------LIKLAST-WEGIQAAKALEKEGIHCNL-TLLFSFAQAVA 176 (333)
T ss_pred CHHHHHHHHHHHHHhhhhhc---------CCCCcE------EEEeCCC-HHHHHHHHHHHHCCCceeE-eEecCHHHHHH
Confidence 36788999999988865532 222222 2257765 6667888999999999877 78999999863
No 33
>PF07755 DUF1611: Protein of unknown function (DUF1611); InterPro: IPR011669 This entry contains a number of hypothetical bacterial and archaeal proteins. The region is approximately 350 residues long. A member of this family (Q6M063 from SWISSPROT) is thought to associate with another subunit to form an H+-transporting ATPase, but no evidence has been found to support this.; PDB: 2G0T_A 2OBN_A.
Probab=26.58 E-value=65 Score=32.68 Aligned_cols=50 Identities=26% Similarity=0.172 Sum_probs=32.1
Q ss_pred hhHHHHHHHHHHcCCc--ccchhhHHHHHHHhc--cccCcccccchhhhhhhhhhh
Q 016657 300 PKADVISKDLVRRGFR--SVGPTIIYSFMQVAG--VTNDHLTSCFRFQECINAAEV 351 (385)
Q Consensus 300 ~lS~~ISKdLKkrGFk--FVGPTtvYSFMQAvG--ivNDHlv~Cfr~~~~~~~~~~ 351 (385)
..+-.|.+.|+++|++ |+| |..-.+|| .| ++-|.++.+|....+....-.
T Consensus 128 tTal~L~~~l~~~G~~a~fva-TGQTGimi-a~~Gv~iDav~~DFvaGavE~~v~~ 181 (301)
T PF07755_consen 128 TTALELRRALRERGINAGFVA-TGQTGIMI-AGYGVPIDAVPSDFVAGAVEALVPE 181 (301)
T ss_dssp HHHHHHHHHHHHTT--EEEEE--SHHHHHC-HSEC--GGGSBGGGHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCCceEEe-cCCceEEE-ecCCeeccchhhhhHHHHHHHHHHh
Confidence 3455899999999875 554 44455667 54 888999999988775544433
No 34
>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=25.47 E-value=76 Score=27.14 Aligned_cols=32 Identities=16% Similarity=0.047 Sum_probs=28.5
Q ss_pred hhHHHHHHHHHHc--CCcccchhhHHHHHHH-hcc
Q 016657 300 PKADVISKDLVRR--GFRSVGPTIIYSFMQV-AGV 331 (385)
Q Consensus 300 ~lS~~ISKdLKkr--GFkFVGPTtvYSFMQA-vGi 331 (385)
+....+++.|... ||+++.....+.||+. .|+
T Consensus 12 ~~~~~~a~~~~~ll~Gf~i~AT~gTa~~L~~~~Gi 46 (115)
T cd01422 12 EDLVEFVKQHQELLSRHRLVATGTTGLLIQEATGL 46 (115)
T ss_pred HHHHHHHHHHHHHhcCCEEEEechHHHHHHHhhCC
Confidence 5566888999999 9999999999999999 887
No 35
>COG4081 Uncharacterized protein conserved in archaea [Function unknown]
Probab=25.40 E-value=52 Score=30.34 Aligned_cols=25 Identities=24% Similarity=0.464 Sum_probs=22.4
Q ss_pred CCCCCCChhHHHHHHHHHHcCCccc
Q 016657 293 RQVPVKTPKADVISKDLVRRGFRSV 317 (385)
Q Consensus 293 ~~vP~~T~lS~~ISKdLKkrGFkFV 317 (385)
-++|.+.+.+--++..||++||.-.
T Consensus 12 PeiP~qissaiYls~klkkkgf~v~ 36 (148)
T COG4081 12 PEIPPQISSAIYLSHKLKKKGFDVT 36 (148)
T ss_pred CCCCccchHHHHHHHHhhccCccEE
Confidence 4689999999999999999999854
No 36
>PRK13910 DNA glycosylase MutY; Provisional
Probab=25.29 E-value=3.4e+02 Score=27.28 Aligned_cols=47 Identities=13% Similarity=0.052 Sum_probs=33.0
Q ss_pred hHHHHHHHhcCCCHHHHhcCCHHHHHHhccccccccchhHHHHHHHHHHHHH
Q 016657 212 KRHIFREVFVGFDPIAVSKLNEKKLLAAGSAASSLLSELKLRAIIENARQIS 263 (385)
Q Consensus 212 KRe~fReAF~~FDp~kVA~~~E~dIe~Lm~d~~IIRNr~KI~AVI~NArail 263 (385)
-.+.|-+.|- +++.+|..++++|+++..--|.- + |-+.+.+=|+.+.
T Consensus 14 yy~rf~~~fP--t~e~La~a~~~el~~~~~glGyy-~--RAr~L~~~A~~i~ 60 (289)
T PRK13910 14 FYSPFLEAFP--TLKDLANAPLEEVLLLWRGLGYY-S--RAKNLKKSAEICV 60 (289)
T ss_pred HHHHHHHHCC--CHHHHHCCCHHHHHHHHHcCCcH-H--HHHHHHHHHHHHH
Confidence 3455556666 68999999999999988777764 3 4555555556553
No 37
>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=25.05 E-value=80 Score=26.38 Aligned_cols=32 Identities=16% Similarity=0.297 Sum_probs=28.4
Q ss_pred hhHHHHHHHHHHcCCcccchhhHHHHHHHhcc
Q 016657 300 PKADVISKDLVRRGFRSVGPTIIYSFMQVAGV 331 (385)
Q Consensus 300 ~lS~~ISKdLKkrGFkFVGPTtvYSFMQAvGi 331 (385)
+....+++.|.+.||+..+.-..+.||...|+
T Consensus 13 ~~~~~~a~~l~~~G~~i~aT~gTa~~L~~~gi 44 (116)
T cd01423 13 PELLPTAQKLSKLGYKLYATEGTADFLLENGI 44 (116)
T ss_pred hhHHHHHHHHHHCCCEEEEccHHHHHHHHcCC
Confidence 34558899999999999999999999999997
No 38
>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=24.17 E-value=54 Score=24.36 Aligned_cols=20 Identities=30% Similarity=0.456 Sum_probs=17.1
Q ss_pred hhHHHHHHHHHHcCCcccch
Q 016657 300 PKADVISKDLVRRGFRSVGP 319 (385)
Q Consensus 300 ~lS~~ISKdLKkrGFkFVGP 319 (385)
...+.+-+.|++.||++.+|
T Consensus 52 ~~~~~~~~~L~~~G~~v~~~ 71 (72)
T cd04883 52 MNPRPIIEDLRRAGYEVLWP 71 (72)
T ss_pred CCHHHHHHHHHHCCCeeeCC
Confidence 34558999999999999998
No 39
>PF13068 DUF3932: Protein of unknown function (DUF3932)
Probab=24.08 E-value=20 Score=29.50 Aligned_cols=31 Identities=26% Similarity=0.551 Sum_probs=23.5
Q ss_pred HHHHHHHhcC-CHHHHHhhhcCCCCccCCCCC
Q 016657 261 QISKVIDEFG-SFNNYIWSFVSHKPIVSRFRY 291 (385)
Q Consensus 261 ailkI~~E~G-SF~~ylWsFv~~kpiv~~~~~ 291 (385)
.+..+|-.|. ||+.|+-+||.+.|..-.|..
T Consensus 3 evfrlqtdfsssfdrwvssfvsdhpaql~wtt 34 (81)
T PF13068_consen 3 EVFRLQTDFSSSFDRWVSSFVSDHPAQLEWTT 34 (81)
T ss_pred hhhhhhcchhhHHHHHHHHHhcCCccccchhH
Confidence 3456777876 699999999988887666643
No 40
>TIGR00588 ogg 8-oxoguanine DNA-glycosylase (ogg). All proteins in this family for which functions are known are 8-oxo-guanaine DNA glycosylases that function in base excision repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is distantly realted to the Nth-MutY superfamily.
Probab=23.57 E-value=7.5e+02 Score=24.76 Aligned_cols=129 Identities=19% Similarity=0.175 Sum_probs=76.3
Q ss_pred ChhhhhhhhcCCCccccchHHHHHHHHHHHHhcCCcHHHHHHhHHHHHHHhc------------CC-CHHHHhcCCHH-H
Q 016657 170 DPCYAAFHDEEWGVPVHDDKKLFELLVLSGALSELTWPAILSKRHIFREVFV------------GF-DPIAVSKLNEK-K 235 (385)
Q Consensus 170 dply~~YHD~EWG~Pv~DDr~LFE~L~LEgfQAGLSW~tILkKRe~fReAF~------------~F-Dp~kVA~~~E~-d 235 (385)
||.+..--+.--|..+.-. -.||.|+-.+...-.|+..|.+-...+.+.|- .| +|+.|+..+.+ +
T Consensus 99 D~~l~~~~~~~~GlRi~~~-d~fE~lv~~IlsQq~si~~a~~~~~rL~~~~G~~~~~~~g~~~~~FPtp~~La~~~~e~~ 177 (310)
T TIGR00588 99 DKHFQYVAQKFQGVRLLRQ-DPFECLISFICSSNNNIARITRMVERLCQAFGPRLITLDGVTYHGFPSLHALTGPEAEAH 177 (310)
T ss_pred CHHHHHHHHhCCCCCCCCC-CHHHHHHHHHHhCCCCHHHHHHHHHHHHHHhCCCcccCCCcccccCCCHHHHhCCChHHH
Confidence 4544433444567544433 57999999999999999999999999988765 23 47777775433 3
Q ss_pred HHHhccccccccchhHHHHHHHHHHHHHHHHHhcCCHHHHHhhhcCCCCccCCCCCCCCCCCCChhHHHHHHHHHHcCCc
Q 016657 236 LLAAGSAASSLLSELKLRAIIENARQISKVIDEFGSFNNYIWSFVSHKPIVSRFRYPRQVPVKTPKADVISKDLVRRGFR 315 (385)
Q Consensus 236 Ie~Lm~d~~IIRNr~KI~AVI~NArailkI~~E~GSF~~ylWsFv~~kpiv~~~~~~~~vP~~T~lS~~ISKdLKkrGFk 315 (385)
|..+ ++ . .|.+.|+.=|+++.+ .+|+.. ++..+ ... +. +.+-+.|.+ ++
T Consensus 178 Lr~~----G~-g--~Ra~~I~~~A~~i~~---~~~~~~-~l~~l-~~~----------------~~-~~~~~~L~~--l~ 226 (310)
T TIGR00588 178 LRKL----GL-G--YRARYIRETARALLE---EQGGRA-WLQQI-RGA----------------SY-EDAREALCE--LP 226 (310)
T ss_pred HHHc----CC-H--HHHHHHHHHHHHHHh---ccCCch-hHHhh-ccC----------------Ch-HHHHHHHHh--CC
Confidence 3332 22 1 246677777776643 333321 11111 111 11 134455555 89
Q ss_pred ccchhhHHH-HHHHhc
Q 016657 316 SVGPTIIYS-FMQVAG 330 (385)
Q Consensus 316 FVGPTtvYS-FMQAvG 330 (385)
-|||-|+-- .|.+.|
T Consensus 227 GIG~~tAd~vll~~l~ 242 (310)
T TIGR00588 227 GVGPKVADCICLMGLD 242 (310)
T ss_pred CccHHHHHHHHHHhCC
Confidence 999988754 445555
No 41
>PHA02543 regA translation repressor protein; Provisional
Probab=23.50 E-value=29 Score=31.24 Aligned_cols=58 Identities=19% Similarity=0.241 Sum_probs=42.5
Q ss_pred HHHHHHHHhcCCcHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhccccccccchhH
Q 016657 193 ELLVLSGALSELTWPAILSKRHIFREVFVGFDPIAVSKLNEKKLLAAGSAASSLLSELK 251 (385)
Q Consensus 193 E~L~LEgfQAGLSW~tILkKRe~fReAF~~FDp~kVA~~~E~dIe~Lm~d~~IIRNr~K 251 (385)
|||.|.|-|.+|++..|++ |...-+...+++.-.|..=+.-.--...++-++|+|+.|
T Consensus 55 eLl~lDG~~~~~~~eDi~R-rn~Ia~LL~~Wgl~~iv~~~~~~~~~~~n~frVishkqK 112 (125)
T PHA02543 55 ELLALDGRQVDLTEEDIQR-RNNIAKLLEDWGLIEIVDPDQMEEVSPTNNFRVISHKQK 112 (125)
T ss_pred HHHhhcCcccCCCHHHHHH-HHHHHHHHHhCCceEEeccchhcccCCcCceEEEEeccc
Confidence 7899999999999999975 566677788887666654322122246778888888876
No 42
>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=22.95 E-value=98 Score=25.43 Aligned_cols=31 Identities=26% Similarity=0.498 Sum_probs=25.6
Q ss_pred HHHHHHHHHHcCCcccchhhHHH---HHHHhcccc
Q 016657 302 ADVISKDLVRRGFRSVGPTIIYS---FMQVAGVTN 333 (385)
Q Consensus 302 S~~ISKdLKkrGFkFVGPTtvYS---FMQAvGivN 333 (385)
++.|.+.|+++|. -++++|||- +|...|+|.
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 5689999999975 589999998 677788764
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=22.78 E-value=78 Score=30.17 Aligned_cols=31 Identities=23% Similarity=0.295 Sum_probs=28.2
Q ss_pred hHHHHHHHHHHcCCcccchhhHHHHHHHhcc
Q 016657 301 KADVISKDLVRRGFRSVGPTIIYSFMQVAGV 331 (385)
Q Consensus 301 lS~~ISKdLKkrGFkFVGPTtvYSFMQAvGi 331 (385)
....|++.|.+.||+.+.....+.||+..||
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 3568999999999999999999999999996
No 44
>KOG2198 consensus tRNA cytosine-5-methylases and related enzymes of the NOL1/NOP2/sun superfamily [Translation, ribosomal structure and biogenesis]
Probab=22.51 E-value=1.3e+02 Score=31.78 Aligned_cols=101 Identities=18% Similarity=0.206 Sum_probs=64.8
Q ss_pred HHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhccc-cccccchhHHHHHHHHHHHHHHHHHhcCCHHHHHhhhcCCCC
Q 016657 206 WPAILSKRHIFREVFVGFDPIAVSKLNEKKLLAAGSA-ASSLLSELKLRAIIENARQISKVIDEFGSFNNYIWSFVSHKP 284 (385)
Q Consensus 206 W~tILkKRe~fReAF~~FDp~kVA~~~E~dIe~Lm~d-~~IIRNr~KI~AVI~NArailkI~~E~GSF~~ylWsFv~~kp 284 (385)
|..--.+.+.|.++..+||. +++++.++.. ...+-..-++.+.++||.+++.+.+++-.-..|--.. .+
T Consensus 19 ~~~~~~~~~~~~~~l~~f~~-------~~e~~~~~~~ir~~Lps~fr~~~~~~~~~~~~~~~~~~~~~~~~~~~~-E~-- 88 (375)
T KOG2198|consen 19 IAKTNPKFEKYYKALDHFDK-------EDEFGDFWETIRKPLPSTFRYTALVNNADALLSIFEEYEFESLKDRVI-EG-- 88 (375)
T ss_pred hhccchhhHHHHHHHhcCcc-------hHHHHHHHHHHHhccchhhhHHHhccchHHHHHHHhhccchhhhhhhc-cc--
Confidence 44445677889999999986 6666655543 2234467899999999999999877753322222222 11
Q ss_pred ccCCCCCCCCCCCCChhHHHHHHHHHHcCCcccch
Q 016657 285 IVSRFRYPRQVPVKTPKADVISKDLVRRGFRSVGP 319 (385)
Q Consensus 285 iv~~~~~~~~vP~~T~lS~~ISKdLKkrGFkFVGP 319 (385)
..++...+.|-. |..-+..+++++.+|+-.+|
T Consensus 89 --~~~e~~~~~p~~-p~~~a~~~~~~~~~~r~~~~ 120 (375)
T KOG2198|consen 89 --LKFEAPFELPWY-PDNLAFEKDVKLDEIRKSPP 120 (375)
T ss_pred --cccCccccCCCC-cccchhhhcCcccccccCCc
Confidence 123334444332 55667788888888888775
No 45
>PF14493 HTH_40: Helix-turn-helix domain
Probab=22.08 E-value=2.6e+02 Score=22.61 Aligned_cols=43 Identities=16% Similarity=0.047 Sum_probs=29.5
Q ss_pred HHHHHHHhcCCcHHHHHHhH-----------HHHHHHhcCCCHHHHhcCCHHHHHH
Q 016657 194 LLVLSGALSELTWPAILSKR-----------HIFREVFVGFDPIAVSKLNEKKLLA 238 (385)
Q Consensus 194 ~L~LEgfQAGLSW~tILkKR-----------e~fReAF~~FDp~kVA~~~E~dIe~ 238 (385)
..+++.||.|+|=..|-++| ..+-.....||+..+ +++++++.
T Consensus 4 ~~T~~l~~~G~si~eIA~~R~L~~sTI~~HL~~~~~~g~~~~~~~~--l~~e~~~~ 57 (91)
T PF14493_consen 4 QITYELFQKGLSIEEIAKIRGLKESTIYGHLAELIESGEPLDIEEL--LSEEEIKQ 57 (91)
T ss_pred HHHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHhCCCCCHHHh--CCHHHHHH
Confidence 36888999999988888877 344555556666666 55555543
No 46
>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=21.82 E-value=46 Score=28.85 Aligned_cols=25 Identities=24% Similarity=0.448 Sum_probs=17.0
Q ss_pred ChhHHHHHHHHHHcCCcccchhhHH
Q 016657 299 TPKADVISKDLVRRGFRSVGPTIIY 323 (385)
Q Consensus 299 T~lS~~ISKdLKkrGFkFVGPTtvY 323 (385)
..+++.+.+....+||.|+||.+|-
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 3677788888889999999999875
No 47
>PF12583 TPPII_N: Tripeptidyl peptidase II N terminal; InterPro: IPR022232 This entry represents a region of approximately 190 amino acids in length and is found in association with PF00082 from PFAM. The members are serine peptidases belonging to MEROPS peptidase family S8A, tripeptidyl peptidase II (TPPII), clan SB. They are a crucial component of the proteolytic cascade acting downstream of the 26S proteasome in the ubiquitin-proteasome pathway. It is an amino peptidase belonging to the subtilase family removing tripeptides from the free N terminus of oligopeptides. ; PDB: 3LXU_X.
Probab=21.53 E-value=50 Score=30.32 Aligned_cols=29 Identities=17% Similarity=0.190 Sum_probs=21.6
Q ss_pred HHhHHHHHHHhcCCCHHHHhcCCHHHHHH
Q 016657 210 LSKRHIFREVFVGFDPIAVSKLNEKKLLA 238 (385)
Q Consensus 210 LkKRe~fReAF~~FDp~kVA~~~E~dIe~ 238 (385)
..|++.|++++-+|.+..|++++-+..+.
T Consensus 69 ktk~DeY~EaLRDfq~~~iaKle~e~Ae~ 97 (139)
T PF12583_consen 69 KTKWDEYSEALRDFQCSWIAKLEPENAEQ 97 (139)
T ss_dssp ---HHHHHHHHHHHHHHHHTTS-HHHHHH
T ss_pred cccHHHHHHHHHHHHHHHHHhhCHHHHHH
Confidence 35789999999999999999998765544
No 48
>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=21.16 E-value=1e+02 Score=25.97 Aligned_cols=53 Identities=19% Similarity=0.092 Sum_probs=34.3
Q ss_pred HHHHHHHHHhcCCcHHHHHHhHH-HHHHHhcCCCHHHHhcCCHHHHH-Hhcccccccc
Q 016657 192 FELLVLSGALSELTWPAILSKRH-IFREVFVGFDPIAVSKLNEKKLL-AAGSAASSLL 247 (385)
Q Consensus 192 FE~L~LEgfQAGLSW~tILkKRe-~fReAF~~FDp~kVA~~~E~dIe-~Lm~d~~IIR 247 (385)
.+.|.--+.+.|..|..++++|. .|++.- .+ +++..++++++- .|..+|.+|+
T Consensus 38 ~~el~~~~~~~~~~~~~l~~~~~~~~~~l~--~~-~~~~~~s~~e~~~~l~~~p~Lik 92 (111)
T cd03036 38 KEELKKWLEKSGLPLKKFFNTSGKSYRELG--LK-DKLPSLSEEEALELLSSDGMLIK 92 (111)
T ss_pred HHHHHHHHHHcCCCHHHHHhcCCchHHhCC--cc-cccccCCHHHHHHHHHhCcCeee
Confidence 34444445677888999999996 555542 22 345677766654 5666777776
No 49
>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=20.63 E-value=49 Score=23.88 Aligned_cols=29 Identities=10% Similarity=0.205 Sum_probs=22.6
Q ss_pred HHHHhcCCCHHHHhcCCHHHHHHhccccc
Q 016657 216 FREVFVGFDPIAVSKLNEKKLLAAGSAAS 244 (385)
Q Consensus 216 fReAF~~FDp~kVA~~~E~dIe~Lm~d~~ 244 (385)
|+++|.-||.+.=-.++.+++..++..-+
T Consensus 1 ~~~~F~~~D~~~~G~i~~~el~~~l~~~g 29 (67)
T cd00052 1 YDQIFRSLDPDGDGLISGDEARPFLGKSG 29 (67)
T ss_pred ChHHHHHhCCCCCCcCcHHHHHHHHHHcC
Confidence 67889999988777788888888765433
Done!