Query 017244
Match_columns 375
No_of_seqs 164 out of 1140
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 06:52:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/017244.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/017244hhsearch_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 4.1E-84 8.9E-89 590.8 18.9 181 177-359 1-183 (187)
2 TIGR00624 tag DNA-3-methyladen 100.0 5.9E-82 1.3E-86 573.2 18.4 177 178-358 1-179 (179)
3 PF03352 Adenine_glyco: Methyl 100.0 2.6E-80 5.7E-85 562.4 15.1 177 182-360 1-179 (179)
4 COG2818 Tag 3-methyladenine DN 100.0 4.8E-80 1E-84 562.6 16.7 184 177-361 1-186 (188)
5 PRK13913 3-methyladenine DNA g 95.9 0.15 3.3E-06 48.6 12.4 105 210-344 31-140 (218)
6 TIGR01083 nth endonuclease III 95.8 0.15 3.2E-06 46.7 11.5 70 209-280 26-95 (191)
7 TIGR03252 uncharacterized HhH- 95.7 0.29 6.2E-06 45.7 13.0 115 209-346 18-136 (177)
8 cd00056 ENDO3c endonuclease II 95.2 0.41 9E-06 41.6 11.8 104 210-346 1-104 (158)
9 smart00478 ENDO3c endonuclease 95.1 0.25 5.4E-06 42.6 10.1 88 222-345 5-92 (149)
10 PRK10702 endonuclease III; Pro 94.0 0.39 8.5E-06 45.3 9.4 70 209-280 29-98 (211)
11 PF00730 HhH-GPD: HhH-GPD supe 93.4 0.47 1E-05 38.7 7.9 63 217-279 4-66 (108)
12 COG0177 Nth Predicted EndoIII- 92.5 2.4 5.2E-05 40.6 12.1 104 207-346 27-130 (211)
13 PRK10880 adenine DNA glycosyla 88.5 2.6 5.5E-05 43.0 9.0 69 208-279 29-97 (350)
14 TIGR01084 mutY A/G-specific ad 87.3 2.9 6.3E-05 41.1 8.4 69 208-279 25-93 (275)
15 PRK01229 N-glycosylase/DNA lya 84.6 8.1 0.00018 36.8 9.6 66 205-278 33-100 (208)
16 COG2231 Uncharacterized protei 78.4 20 0.00043 34.8 9.8 86 189-279 14-99 (215)
17 COG1393 ArsC Arsenate reductas 71.1 4 8.6E-05 35.4 2.9 67 192-265 26-92 (117)
18 PF10023 DUF2265: Predicted am 67.4 14 0.00029 38.0 6.2 108 252-366 33-167 (337)
19 cd00166 SAM Sterile alpha moti 61.9 20 0.00044 25.7 4.7 43 232-274 17-61 (63)
20 PF02142 MGS: MGS-like domain 59.9 7.6 0.00016 31.5 2.4 30 319-348 3-32 (95)
21 COG0122 AlkA 3-methyladenine D 51.1 68 0.0015 31.8 7.8 69 207-279 103-179 (285)
22 COG0632 RuvA Holliday junction 51.1 53 0.0011 31.4 6.8 78 193-287 55-134 (201)
23 PF00536 SAM_1: SAM domain (St 50.4 30 0.00065 25.6 4.1 42 232-274 18-62 (64)
24 PRK10308 3-methyl-adenine DNA 49.5 78 0.0017 31.3 7.9 118 198-348 102-231 (283)
25 PF13495 Phage_int_SAM_4: Phag 44.5 1.2E+02 0.0027 23.1 6.9 53 209-261 1-53 (85)
26 PF07647 SAM_2: SAM domain (St 44.4 30 0.00065 25.7 3.3 43 232-274 19-64 (66)
27 PF07862 Nif11: Nitrogen fixat 40.0 32 0.00068 25.0 2.7 40 249-289 1-44 (49)
28 PF13276 HTH_21: HTH-like doma 39.7 35 0.00075 25.4 3.0 30 319-348 24-53 (60)
29 PTZ00411 transaldolase-like pr 37.9 44 0.00096 34.1 4.3 62 267-345 114-175 (333)
30 smart00851 MGS MGS-like domain 35.8 32 0.0007 27.4 2.5 28 320-347 4-31 (90)
31 PF05075 DUF684: Protein of un 35.7 68 0.0015 32.4 5.2 76 206-281 115-212 (345)
32 KOG2198 tRNA cytosine-5-methyl 34.7 56 0.0012 34.2 4.5 99 224-335 19-120 (375)
33 PRK13344 spxA transcriptional 32.2 39 0.00084 29.6 2.6 54 204-265 37-91 (132)
34 KOG1921 Endonuclease III [Repl 31.9 4.6E+02 0.0099 26.6 10.0 92 240-365 108-200 (286)
35 TIGR01529 argR_whole arginine 31.9 48 0.0011 29.7 3.2 31 318-349 19-49 (146)
36 cd00532 MGS-like MGS-like doma 31.7 50 0.0011 27.6 3.1 32 316-347 12-43 (112)
37 cd03678 MM_CoA_mutase_1 Coenzy 30.6 16 0.00035 39.2 -0.1 60 229-293 144-226 (495)
38 PF13068 DUF3932: Protein of u 30.5 11 0.00024 30.9 -1.1 32 278-309 4-36 (81)
39 PRK10548 flagellar biosynthesi 29.7 1.3E+02 0.0028 26.6 5.3 76 208-290 16-111 (121)
40 PF00289 CPSase_L_chain: Carba 28.9 77 0.0017 27.0 3.8 21 317-337 87-107 (110)
41 smart00454 SAM Sterile alpha m 28.8 1.6E+02 0.0035 21.0 5.0 42 234-275 21-65 (68)
42 PHA02517 putative transposase 28.8 60 0.0013 30.6 3.4 30 319-349 49-78 (277)
43 cd01424 MGS_CPS_II Methylglyox 27.7 67 0.0015 26.4 3.1 32 316-347 13-44 (110)
44 cd00052 EH Eps15 homology doma 27.2 32 0.00069 24.8 1.0 30 234-263 1-30 (67)
45 cd03023 DsbA_Com1_like DsbA fa 27.1 3.3E+02 0.0071 22.3 7.2 29 248-276 82-110 (154)
46 PRK05269 transaldolase B; Prov 27.0 89 0.0019 31.6 4.4 63 267-346 104-166 (318)
47 cd02762 MopB_1 The MopB_1 CD i 26.9 1.9E+02 0.0041 30.4 7.0 56 204-259 217-279 (539)
48 TIGR00588 ogg 8-oxoguanine DNA 26.2 2.9E+02 0.0062 27.6 7.8 88 187-279 98-198 (310)
49 PRK12309 transaldolase/EF-hand 25.8 95 0.0021 32.3 4.5 63 267-346 108-170 (391)
50 cd03036 ArsC_like Arsenate Red 24.9 59 0.0013 27.2 2.3 53 210-265 38-92 (111)
51 PF12401 DUF3662: Protein of u 24.8 39 0.00084 29.2 1.2 25 315-339 76-100 (116)
52 cd00956 Transaldolase_FSA Tran 24.6 40 0.00086 31.8 1.4 34 310-345 83-116 (211)
53 cd04883 ACT_AcuB C-terminal AC 24.6 49 0.0011 24.5 1.6 19 318-336 54-72 (72)
54 PRK12346 transaldolase A; Prov 24.1 1.1E+02 0.0024 31.1 4.5 63 267-346 103-165 (316)
55 PF12583 TPPII_N: Tripeptidyl 23.9 36 0.00078 31.1 0.9 31 228-258 69-99 (139)
56 cd00957 Transaldolase_TalAB Tr 23.8 1E+02 0.0023 31.2 4.2 63 267-346 102-164 (313)
57 COG4081 Uncharacterized protei 23.6 58 0.0013 29.9 2.2 26 308-333 11-36 (148)
58 cd01422 MGS Methylglyoxal synt 23.6 83 0.0018 26.8 3.0 32 316-347 12-46 (115)
59 PRK01172 ski2-like helicase; P 23.5 1.7E+02 0.0037 31.8 6.0 47 232-281 623-671 (674)
60 TIGR00874 talAB transaldolase. 23.0 1.2E+02 0.0027 30.8 4.5 63 267-346 102-164 (317)
61 PF11460 DUF3007: Protein of u 22.7 83 0.0018 27.5 2.8 33 228-260 65-101 (104)
62 cd00439 Transaldolase Transald 22.4 84 0.0018 30.6 3.1 57 267-345 98-154 (252)
63 PF12023 DUF3511: Domain of un 22.3 41 0.00089 25.6 0.8 21 139-162 7-27 (47)
64 PF03960 ArsC: ArsC family; I 22.0 49 0.0011 27.5 1.3 53 205-265 34-88 (110)
65 PF05920 Homeobox_KN: Homeobox 21.8 95 0.0021 22.2 2.6 28 250-277 12-39 (40)
66 smart00027 EH Eps15 homology d 20.1 45 0.00097 26.9 0.6 45 228-272 6-50 (96)
No 1
>PRK10353 3-methyl-adenine DNA glycosylase I; Provisional
Probab=100.00 E-value=4.1e-84 Score=590.78 Aligned_cols=181 Identities=41% Similarity=0.789 Sum_probs=177.3
Q ss_pred CCCCCCCCCCCCchhhhhhhcCCCccccChHHHHHHHHHHHHhhcccHHHHHHHHHHHHHHhcCCCHHHHhcCCHHHHHH
Q 017244 177 EKRCSFITPNSDPIYVAYHDEEWGVPVHDDKLLFELLVLTAAQVGSDWTSVLKKRQAFREAFSGFDAEVVAKFTEKKMTS 256 (375)
Q Consensus 177 ~~RC~W~~~~~dply~~YHD~EWG~Pv~DDr~LFEmL~LEgfQAGLSW~tVLkKReafReAF~gFD~ekVA~~tEedIer 256 (375)
|.||.|++ +||+|++|||+|||+|+|||+.|||+||||+|||||||.|||+||++||+||+||||++||+|+|+|||+
T Consensus 1 m~rC~W~~--~~~l~~~YHD~eWG~P~~dd~~LFE~L~Le~~QAGLSW~tIL~Kre~fr~aF~~Fd~~~VA~~~e~die~ 78 (187)
T PRK10353 1 MERCGWVS--QDPLYIAYHDNEWGVPETDSKKLFEMICLEGQQAGLSWITVLKKRENYRACFHQFDPVKVAAMQEEDVER 78 (187)
T ss_pred CCCCCCCC--CChHHHHhhhccCCCcCCCcHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHcCCCHHHHhCCCHHHHHH
Confidence 46999985 8999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhcCcchhH--HHHHHHHhhHHHHHHHHHhhCCHHHhcccccCCccccCCCCCCCCCCCCCHHHHHHHHHHHHcCCCccc
Q 017244 257 LSANYAIDL--SQVRGIVDNSIRILEVKKQFGSFDKYLWGFVNHKPINTQYRSSQKIPVKTSKSEAISKDMVKKGFRFVG 334 (375)
Q Consensus 257 Ll~D~gIIR--~KI~AVI~NArail~i~~E~GSF~~ylWsFv~~kpi~~~~~~~~~iP~~t~lS~~iSKdLKKrGFkFVG 334 (375)
||+|++||| +||+|||+||+++++|++|||||++|||+||+++||++++.+..++|++|++|++|||+||||||+|||
T Consensus 79 Ll~d~~IIRnr~KI~Avi~NA~~~l~i~~e~gSf~~ylW~fv~~~p~~~~~~~~~~~P~~t~~S~~lskdLKkrGFkFvG 158 (187)
T PRK10353 79 LVQDAGIIRHRGKIQAIIGNARAYLQMEQNGEPFADFVWSFVNHQPQVTQATTLSEIPTSTPASDALSKALKKRGFKFVG 158 (187)
T ss_pred HhcCchhHHhHHHHHHHHHHHHHHHHHHHhcCCHHHHHhhccCCCcccCCccchhcCCCCCHHHHHHHHHHHHcCCcccC
Confidence 999999997 799999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhHHHHHHHhcccccccccCcchh
Q 017244 335 PTVIHSFMQAAGLTNDHLITCTRHL 359 (375)
Q Consensus 335 PTtiYSFMQAvG~VNDHl~~C~~~~ 359 (375)
||||||||||+||||||+++|+++.
T Consensus 159 pt~~ysfmqA~G~vndH~~~C~~~~ 183 (187)
T PRK10353 159 TTICYSFMQACGLVNDHVVGCCCHP 183 (187)
T ss_pred cHHHHHHHHHHCCccccccCccccC
Confidence 9999999999999999999999884
No 2
>TIGR00624 tag DNA-3-methyladenine glycosylase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=100.00 E-value=5.9e-82 Score=573.24 Aligned_cols=177 Identities=40% Similarity=0.769 Sum_probs=173.3
Q ss_pred CCCCCCCCCCCchhhhhhhcCCCccccChHHHHHHHHHHHHhhcccHHHHHHHHHHHHHHhcCCCHHHHhcCCHHHHHHh
Q 017244 178 KRCSFITPNSDPIYVAYHDEEWGVPVHDDKLLFELLVLTAAQVGSDWTSVLKKRQAFREAFSGFDAEVVAKFTEKKMTSL 257 (375)
Q Consensus 178 ~RC~W~~~~~dply~~YHD~EWG~Pv~DDr~LFEmL~LEgfQAGLSW~tVLkKReafReAF~gFD~ekVA~~tEedIerL 257 (375)
.||.|++ +||+|++|||+|||+|+|||+.|||+||||+|||||||.|||+||++||+||+||||++||+|+|+|||+|
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 4899985 89999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcCcchhH--HHHHHHHhhHHHHHHHHHhhCCHHHhcccccCCccccCCCCCCCCCCCCCHHHHHHHHHHHHcCCCccch
Q 017244 258 SANYAIDL--SQVRGIVDNSIRILEVKKQFGSFDKYLWGFVNHKPINTQYRSSQKIPVKTSKSEAISKDMVKKGFRFVGP 335 (375)
Q Consensus 258 l~D~gIIR--~KI~AVI~NArail~i~~E~GSF~~ylWsFv~~kpi~~~~~~~~~iP~~t~lS~~iSKdLKKrGFkFVGP 335 (375)
|+|++||| +||+|||+||+++++|++| ||++|||+||+++||++++....++|++|++|++|||+||||||+||||
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 99999997 6999999999999999888 9999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHHhcccccccccCcch
Q 017244 336 TVIHSFMQAAGLTNDHLITCTRH 358 (375)
Q Consensus 336 TtiYSFMQAvG~VNDHl~~C~~~ 358 (375)
||||+||||+||||||+++|+++
T Consensus 157 t~~ysfmqA~G~vndH~~~C~~~ 179 (179)
T TIGR00624 157 TICYALMQATGMVDDHIQGCWVY 179 (179)
T ss_pred HHHHHHHHHHCCccccccCCcCC
Confidence 99999999999999999999975
No 3
>PF03352 Adenine_glyco: Methyladenine glycosylase; InterPro: IPR005019 This family of methyladenine glycosylases includes DNA-3-methyladenine glycosylase I (3.2.2.20 from EC) which acts as a base excision repair enzyme by severing the glycosylic bond of numerous damaged bases. The enzyme is constitutively expressed and is specific for the alkylated 3-methyladenine DNA.; GO: 0008725 DNA-3-methyladenine glycosylase I activity, 0006284 base-excision repair; PDB: 2OFI_A 2OFK_A 2JG6_A 4AIA_E 4AI5_C 4AI4_A 1LMZ_A 1P7M_A 1NKU_A.
Probab=100.00 E-value=2.6e-80 Score=562.38 Aligned_cols=177 Identities=53% Similarity=0.970 Sum_probs=153.0
Q ss_pred CCCCCCCchhhhhhhcCCCccccChHHHHHHHHHHHHhhcccHHHHHHHHHHHHHHhcCCCHHHHhcCCHHHHHHhhcCc
Q 017244 182 FITPNSDPIYVAYHDEEWGVPVHDDKLLFELLVLTAAQVGSDWTSVLKKRQAFREAFSGFDAEVVAKFTEKKMTSLSANY 261 (375)
Q Consensus 182 W~~~~~dply~~YHD~EWG~Pv~DDr~LFEmL~LEgfQAGLSW~tVLkKReafReAF~gFD~ekVA~~tEedIerLl~D~ 261 (375)
|+. ++|+|++|||+|||+|+|||+.|||+||||+|||||||.|||+||++||+||+||||++||+|+|+||++||+|+
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 874 899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred chhH--HHHHHHHhhHHHHHHHHHhhCCHHHhcccccCCccccCCCCCCCCCCCCCHHHHHHHHHHHHcCCCccchhhHH
Q 017244 262 AIDL--SQVRGIVDNSIRILEVKKQFGSFDKYLWGFVNHKPINTQYRSSQKIPVKTSKSEAISKDMVKKGFRFVGPTVIH 339 (375)
Q Consensus 262 gIIR--~KI~AVI~NArail~i~~E~GSF~~ylWsFv~~kpi~~~~~~~~~iP~~t~lS~~iSKdLKKrGFkFVGPTtiY 339 (375)
+||| +||+|||+||+++++|++|||||++|||+|++++||++.+.+..++|++|++|++|||+||||||+||||||||
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 9997 79999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhcccccccccCcchhh
Q 017244 340 SFMQAAGLTNDHLITCTRHLQ 360 (375)
Q Consensus 340 SFMQAvG~VNDHl~~C~~~~~ 360 (375)
|||||+||||||+++|++|.+
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 999999999999999999853
No 4
>COG2818 Tag 3-methyladenine DNA glycosylase [DNA replication, recombination, and repair]
Probab=100.00 E-value=4.8e-80 Score=562.58 Aligned_cols=184 Identities=47% Similarity=0.863 Sum_probs=178.7
Q ss_pred CCCCCCCCCCCCchhhhhhhcCCCccccChHHHHHHHHHHHHhhcccHHHHHHHHHHHHHHhcCCCHHHHhcCCHHHHHH
Q 017244 177 EKRCSFITPNSDPIYVAYHDEEWGVPVHDDKLLFELLVLTAAQVGSDWTSVLKKRQAFREAFSGFDAEVVAKFTEKKMTS 256 (375)
Q Consensus 177 ~~RC~W~~~~~dply~~YHD~EWG~Pv~DDr~LFEmL~LEgfQAGLSW~tVLkKReafReAF~gFD~ekVA~~tEedIer 256 (375)
+.||.|+. +.||+|.+|||+|||+|++||+.|||+||||+|||||||.|||+|||+||+||++|||++||.|+|+|||+
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 47999995 34899999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhcCcchhH--HHHHHHHhhHHHHHHHHHhhCCHHHhcccccCCccccCCCCCCCCCCCCCHHHHHHHHHHHHcCCCccc
Q 017244 257 LSANYAIDL--SQVRGIVDNSIRILEVKKQFGSFDKYLWGFVNHKPINTQYRSSQKIPVKTSKSEAISKDMVKKGFRFVG 334 (375)
Q Consensus 257 Ll~D~gIIR--~KI~AVI~NArail~i~~E~GSF~~ylWsFv~~kpi~~~~~~~~~iP~~t~lS~~iSKdLKKrGFkFVG 334 (375)
||+|+|||| +||+|+|+|||++++|++|||||++|||+|++++|..+++.+..++|++|++|++|||+||||||+|||
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 999999996 799999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhHHHHHHHhcccccccccCcchhhh
Q 017244 335 PTVIHSFMQAAGLTNDHLITCTRHLQC 361 (375)
Q Consensus 335 PTtiYSFMQAvG~VNDHl~~C~~~~~~ 361 (375)
|||||+||||+|+||||+.+|+++..+
T Consensus 160 pTt~yafmqA~G~vndH~~~C~~~~~~ 186 (188)
T COG2818 160 PTTVYAFMQATGLVNDHAEGCPCRREI 186 (188)
T ss_pred cHHHHHHHHHHcchHHHHhcCCCcccc
Confidence 999999999999999999999998653
No 5
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=95.89 E-value=0.15 Score=48.58 Aligned_cols=105 Identities=18% Similarity=0.268 Sum_probs=80.0
Q ss_pred HHHHHHHHHhhcccHHHHHHHHHHHHHHhc-----CCCHHHHhcCCHHHHHHhhcCcchhHHHHHHHHhhHHHHHHHHHh
Q 017244 210 FELLVLTAAQVGSDWTSVLKKRQAFREAFS-----GFDAEVVAKFTEKKMTSLSANYAIDLSQVRGIVDNSIRILEVKKQ 284 (375)
Q Consensus 210 FEmL~LEgfQAGLSW~tVLkKReafReAF~-----gFD~ekVA~~tEedIerLl~D~gIIR~KI~AVI~NArail~i~~E 284 (375)
||.|+-.+.-.--+|..|.+--+.++++|. .-+++.|+..++++|++++.-.|.-|.|.+.+.+=|+.++ ++
T Consensus 31 fevLV~aILsQqT~~~~v~~a~~~L~~~~~~~~~~~~t~e~L~~a~~eeL~~~Irp~Gf~~~KA~~Lk~la~~i~---~~ 107 (218)
T PRK13913 31 FEALLGAVLTQNTKFEAVEKSLENLKNAFILENDDEINLKKIAYIEFSKLAECVRPSGFYNQKAKRLIDLSENIL---KD 107 (218)
T ss_pred HHHHHHHHHHhhhhHHHHHHHHHHHHHhcccccccCCCHHHHHcCCHHHHHHHHHhcCCHHHHHHHHHHHHHHHH---HH
Confidence 888888877777889999888888877763 2389999999999999999999999999999988888875 46
Q ss_pred hCCHHHhcccccCCccccCCCCCCCCCCCCCHHHHHHHHHHHHcCCCccchhhHHHHHHH
Q 017244 285 FGSFDKYLWGFVNHKPINTQYRSSQKIPVKTSKSEAISKDMVKKGFRFVGPTVIHSFMQA 344 (375)
Q Consensus 285 ~GSF~~ylWsFv~~kpi~~~~~~~~~iP~~t~lS~~iSKdLKKrGFkFVGPTtiYSFMQA 344 (375)
+|+++.+. . + . .-++|.+ .+=|||-|+-++|--
T Consensus 108 ~g~~~~~~----~--~----------------~---~re~Ll~--l~GIG~kTAd~iLly 140 (218)
T PRK13913 108 FGSFENFK----Q--E----------------V---TREWLLD--QKGIGKESADAILCY 140 (218)
T ss_pred cCCchhcc----C--c----------------h---HHHHHHc--CCCccHHHHHHHHHH
Confidence 67765321 0 0 0 1134443 677899888888763
No 6
>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=95.76 E-value=0.15 Score=46.68 Aligned_cols=70 Identities=19% Similarity=0.215 Sum_probs=61.9
Q ss_pred HHHHHHHHHHhhcccHHHHHHHHHHHHHHhcCCCHHHHhcCCHHHHHHhhcCcchhHHHHHHHHhhHHHHHH
Q 017244 209 LFELLVLTAAQVGSDWTSVLKKRQAFREAFSGFDAEVVAKFTEKKMTSLSANYAIDLSQVRGIVDNSIRILE 280 (375)
Q Consensus 209 LFEmL~LEgfQAGLSW~tVLkKReafReAF~gFD~ekVA~~tEedIerLl~D~gIIR~KI~AVI~NArail~ 280 (375)
-||.|+-++.-.-.+|..+.+-...+.+.|- +++.|+..+++++++++.--|+-+.|.+.+++=|+.+++
T Consensus 26 pf~~Li~~ILsqqt~~~~~~~~~~~l~~~~p--t~~~l~~~~~~~L~~~ir~~G~~~~Ka~~i~~~a~~i~~ 95 (191)
T TIGR01083 26 PFELLVATILSAQATDKSVNKATKKLFEVYP--TPQALAQAGLEELEEYIKSIGLYRNKAKNIIALCRILVE 95 (191)
T ss_pred HHHHHHHHHHHhhCcHHHHHHHHHHHHHHCC--CHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHH
Confidence 5999999999889999999988888887764 799999999999999999999988899988888888754
No 7
>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=95.66 E-value=0.29 Score=45.69 Aligned_cols=115 Identities=13% Similarity=0.179 Sum_probs=82.4
Q ss_pred HHHHHHHHHHhhcccHHHHHHHHHHHHHHhcCCCHHHHhcCCHHHHHHhhcC-c---chhHHHHHHHHhhHHHHHHHHHh
Q 017244 209 LFELLVLTAAQVGSDWTSVLKKRQAFREAFSGFDAEVVAKFTEKKMTSLSAN-Y---AIDLSQVRGIVDNSIRILEVKKQ 284 (375)
Q Consensus 209 LFEmL~LEgfQAGLSW~tVLkKReafReAF~gFD~ekVA~~tEedIerLl~D-~---gIIR~KI~AVI~NArail~i~~E 284 (375)
-||+|+-.+.-+--+|..|.+=-+.+.+.+...|++.+++++.++|++++.. | |.-+.|=+-+++=|+.++ ++
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 4999999999999999999987777754444489999999999999999985 3 455678777777777764 45
Q ss_pred hCCHHHhcccccCCccccCCCCCCCCCCCCCHHHHHHHHHHHHcCCCccchhhHHHHHHHhc
Q 017244 285 FGSFDKYLWGFVNHKPINTQYRSSQKIPVKTSKSEAISKDMVKKGFRFVGPTVIHSFMQAAG 346 (375)
Q Consensus 285 ~GSF~~ylWsFv~~kpi~~~~~~~~~iP~~t~lS~~iSKdLKKrGFkFVGPTtiYSFMQAvG 346 (375)
||+=-+-||.... | . ...+-++|.+ ++=|||.|+--||.-.|
T Consensus 95 y~G~v~~L~~~~~--p------------~----t~~lre~Ll~--LpGVG~KTAnvVL~~l~ 136 (177)
T TIGR03252 95 YDGDATAVWTEGD--P------------D----GKELLRRLKA--LPGFGKQKAKIFLALLG 136 (177)
T ss_pred hCCChhhhhcccC--C------------C----cHHHHHHHHc--CCCCCHHHHHHHHHHHH
Confidence 5543233453210 1 1 1122345543 68899999999988777
No 8
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=95.18 E-value=0.41 Score=41.59 Aligned_cols=104 Identities=16% Similarity=0.183 Sum_probs=79.6
Q ss_pred HHHHHHHHHhhcccHHHHHHHHHHHHHHhcCCCHHHHhcCCHHHHHHhhcCcchhHHHHHHHHhhHHHHHHHHHhhCCHH
Q 017244 210 FELLVLTAAQVGSDWTSVLKKRQAFREAFSGFDAEVVAKFTEKKMTSLSANYAIDLSQVRGIVDNSIRILEVKKQFGSFD 289 (375)
Q Consensus 210 FEmL~LEgfQAGLSW~tVLkKReafReAF~gFD~ekVA~~tEedIerLl~D~gIIR~KI~AVI~NArail~i~~E~GSF~ 289 (375)
||.|+-.++..-.+|..+.+-...|.+.|. .+++.|+..+++++.++...-| -+.|.+.++.=|+.+. ++++++.
T Consensus 1 ~e~Li~~il~q~~s~~~a~~~~~~l~~~~g-pt~~~l~~~~~~~l~~~~~~~G-~~~kA~~i~~~a~~~~---~~~~~~~ 75 (158)
T cd00056 1 FEVLVSEILSQQTTDKAVNKAYERLFERYG-PTPEALAAADEEELRELIRSLG-YRRKAKYLKELARAIV---EGFGGLV 75 (158)
T ss_pred CHHHHHHHHHhcccHHHHHHHHHHHHHHhC-CCHHHHHCCCHHHHHHHHHhcC-hHHHHHHHHHHHHHHH---HHcCCcc
Confidence 688888888889999999999999999985 7899999999999999888777 5678888888787764 3344333
Q ss_pred HhcccccCCccccCCCCCCCCCCCCCHHHHHHHHHHHHcCCCccchhhHHHHHHHhc
Q 017244 290 KYLWGFVNHKPINTQYRSSQKIPVKTSKSEAISKDMVKKGFRFVGPTVIHSFMQAAG 346 (375)
Q Consensus 290 ~ylWsFv~~kpi~~~~~~~~~iP~~t~lS~~iSKdLKKrGFkFVGPTtiYSFMQAvG 346 (375)
. +. +.+-+.|. .++=|||-|+-.+|.-..
T Consensus 76 ~------~~--------------------~~~~~~L~--~l~GIG~~tA~~~l~~~~ 104 (158)
T cd00056 76 L------DD--------------------PDAREELL--ALPGVGRKTANVVLLFAL 104 (158)
T ss_pred C------CC--------------------cccHHHHH--cCCCCCHHHHHHHHHHHC
Confidence 2 00 11234554 478899999988887553
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=95.10 E-value=0.25 Score=42.65 Aligned_cols=88 Identities=17% Similarity=0.278 Sum_probs=67.6
Q ss_pred ccHHHHHHHHHHHHHHhcCCCHHHHhcCCHHHHHHhhcCcchhHHHHHHHHhhHHHHHHHHHhhCCHHHhcccccCCccc
Q 017244 222 SDWTSVLKKRQAFREAFSGFDAEVVAKFTEKKMTSLSANYAIDLSQVRGIVDNSIRILEVKKQFGSFDKYLWGFVNHKPI 301 (375)
Q Consensus 222 LSW~tVLkKReafReAF~gFD~ekVA~~tEedIerLl~D~gIIR~KI~AVI~NArail~i~~E~GSF~~ylWsFv~~kpi 301 (375)
.+|..+.+-...|.+.|- +++.++..++++|++++..-|.-+.|.+.+++.|+.+.+ ++++
T Consensus 5 ~~~~~a~~~~~~l~~~~~--~~~~l~~~~~~eL~~~l~~~g~~~~ka~~i~~~a~~~~~---~~~~-------------- 65 (149)
T smart00478 5 TSDEAVNKATERLFEKFP--TPEDLAAADEEELEELIRPLGFYRRKAKYLIELARILVE---EYGG-------------- 65 (149)
T ss_pred ccHHHHHHHHHHHHHHCC--CHHHHHCCCHHHHHHHHHHcCChHHHHHHHHHHHHHHHH---HHCC--------------
Confidence 478888888888888887 799999999999999998888878899999999988754 2221
Q ss_pred cCCCCCCCCCCCCCHHHHHHHHHHHHcCCCccchhhHHHHHHHh
Q 017244 302 NTQYRSSQKIPVKTSKSEAISKDMVKKGFRFVGPTVIHSFMQAA 345 (375)
Q Consensus 302 ~~~~~~~~~iP~~t~lS~~iSKdLKKrGFkFVGPTtiYSFMQAv 345 (375)
++| ...+.|.+ ++=|||-|+-.||.-.
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 12345643 8889999998887765
No 10
>PRK10702 endonuclease III; Provisional
Probab=93.99 E-value=0.39 Score=45.28 Aligned_cols=70 Identities=14% Similarity=0.130 Sum_probs=61.3
Q ss_pred HHHHHHHHHHhhcccHHHHHHHHHHHHHHhcCCCHHHHhcCCHHHHHHhhcCcchhHHHHHHHHhhHHHHHH
Q 017244 209 LFELLVLTAAQVGSDWTSVLKKRQAFREAFSGFDAEVVAKFTEKKMTSLSANYAIDLSQVRGIVDNSIRILE 280 (375)
Q Consensus 209 LFEmL~LEgfQAGLSW~tVLkKReafReAF~gFD~ekVA~~tEedIerLl~D~gIIR~KI~AVI~NArail~ 280 (375)
-||.|+-++.-+--+|..|.+--+.+.+.| .+++.+++.++++|+.++.--|.-+.|-+.+++.|+.+++
T Consensus 29 p~e~lvs~iLsq~t~~~~v~~~~~~L~~~~--pt~e~l~~a~~~~l~~~i~~~G~y~~kA~~l~~~a~~i~~ 98 (211)
T PRK10702 29 PFELLIAVLLSAQATDVSVNKATAKLYPVA--NTPAAMLELGVEGVKTYIKTIGLYNSKAENVIKTCRILLE 98 (211)
T ss_pred hHHHHHHHHHHhhcCHHHHHHHHHHHHHHc--CCHHHHHCCCHHHHHHHHHHcCCHHHHHHHHHHHHHHHHH
Confidence 599999999888899999998888887665 4799999999999999999889888888889999998764
No 11
>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=93.44 E-value=0.47 Score=38.67 Aligned_cols=63 Identities=14% Similarity=0.131 Sum_probs=56.8
Q ss_pred HHhhcccHHHHHHHHHHHHHHhcCCCHHHHhcCCHHHHHHhhcCcchhHHHHHHHHhhHHHHH
Q 017244 217 AAQVGSDWTSVLKKRQAFREAFSGFDAEVVAKFTEKKMTSLSANYAIDLSQVRGIVDNSIRIL 279 (375)
Q Consensus 217 gfQAGLSW~tVLkKReafReAF~gFD~ekVA~~tEedIerLl~D~gIIR~KI~AVI~NArail 279 (375)
++..-.+|..+.+-...|.+.|...+++.|+..++++|++++..-|+-+.|-+.+++=|+.++
T Consensus 4 Il~qq~s~~~a~~~~~~l~~~~g~pt~~~l~~~~~~el~~~i~~~G~~~~ka~~i~~~a~~~~ 66 (108)
T PF00730_consen 4 ILSQQTSIKAARKIYRRLFERYGFPTPEALAEASEEELRELIRPLGFSRRKAKYIIELARAIL 66 (108)
T ss_dssp HHCTTS-HHHHHHHHHHHHHHHSCSSHHHHHCSHHHHHHHHHTTSTSHHHHHHHHHHHHHHHH
T ss_pred eecCcCcHHHHHHHHHHHHHHhcCCCHHHHHhCCHHHHHHHhhccCCCHHHHHHHHHHHHHhh
Confidence 445567899999999999999998999999999999999999999999899999999999987
No 12
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=92.48 E-value=2.4 Score=40.63 Aligned_cols=104 Identities=19% Similarity=0.243 Sum_probs=72.5
Q ss_pred HHHHHHHHHHHHhhcccHHHHHHHHHHHHHHhcCCCHHHHhcCCHHHHHHhhcCcchhHHHHHHHHhhHHHHHHHHHhhC
Q 017244 207 KLLFELLVLTAAQVGSDWTSVLKKRQAFREAFSGFDAEVVAKFTEKKMTSLSANYAIDLSQVRGIVDNSIRILEVKKQFG 286 (375)
Q Consensus 207 r~LFEmL~LEgfQAGLSW~tVLkKReafReAF~gFD~ekVA~~tEedIerLl~D~gIIR~KI~AVI~NArail~i~~E~G 286 (375)
.--||+|+--+.-+--+=..|-+=-+.+.+.|. +++.++..++++|+.++..-|+-|+|-..|+.=|+.++ ++||
T Consensus 27 ~~pf~lLva~iLSaqttD~~vn~at~~Lf~~~~--t~e~l~~a~~~~l~~~I~~iGlyr~KAk~I~~~~~~l~---e~~~ 101 (211)
T COG0177 27 KDPFELLVAVILSAQTTDEVVNKATPALFKRYP--TPEDLLNADEEELEELIKSIGLYRNKAKNIKELARILL---EKFG 101 (211)
T ss_pred CCcHHHHHHHHHhccCchHHHHHHHHHHHHHcC--CHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHH---HHcC
Confidence 345888865555554444455444444544444 49999999999999999999999999999999888874 5666
Q ss_pred CHHHhcccccCCccccCCCCCCCCCCCCCHHHHHHHHHHHHcCCCccchhhHHHHHHHhc
Q 017244 287 SFDKYLWGFVNHKPINTQYRSSQKIPVKTSKSEAISKDMVKKGFRFVGPTVIHSFMQAAG 346 (375)
Q Consensus 287 SF~~ylWsFv~~kpi~~~~~~~~~iP~~t~lS~~iSKdLKKrGFkFVGPTtiYSFMQAvG 346 (375)
+ ++|. .+ ++|.+ .-=||+.|++-.|.-+.
T Consensus 102 g----------------------~vP~------~~-~eL~~--LPGVGrKTAnvVL~~a~ 130 (211)
T COG0177 102 G----------------------EVPD------TR-EELLS--LPGVGRKTANVVLSFAF 130 (211)
T ss_pred C----------------------CCCc------hH-HHHHh--CCCcchHHHHHHHHhhc
Confidence 5 1221 11 23333 35699999999987643
No 13
>PRK10880 adenine DNA glycosylase; Provisional
Probab=88.49 E-value=2.6 Score=42.99 Aligned_cols=69 Identities=9% Similarity=0.082 Sum_probs=59.0
Q ss_pred HHHHHHHHHHHhhcccHHHHHHHHHHHHHHhcCCCHHHHhcCCHHHHHHhhcCcchhHHHHHHHHhhHHHHH
Q 017244 208 LLFELLVLTAAQVGSDWTSVLKKRQAFREAFSGFDAEVVAKFTEKKMTSLSANYAIDLSQVRGIVDNSIRIL 279 (375)
Q Consensus 208 ~LFEmL~LEgfQAGLSW~tVLkKReafReAF~gFD~ekVA~~tEedIerLl~D~gIIR~KI~AVI~NArail 279 (375)
--|+.|+-|++-.=-+|.+|+.-.+.|.+.| .|++.+|..++++|.++..--|.-+ |.+-+..-|+.+.
T Consensus 29 dpy~ilVseILlQQT~v~~v~~~~~rl~~~f--Pt~~~La~a~~eel~~~~~glGyy~-RAr~L~~~A~~i~ 97 (350)
T PRK10880 29 TPYKVWLSEVMLQQTQVATVIPYFERFMARF--PTVTDLANAPLDEVLHLWTGLGYYA-RARNLHKAAQQVA 97 (350)
T ss_pred CHHHHHHHHHHHhhccHHHHHHHHHHHHHHC--cCHHHHHCcCHHHHHHHHHcCChHH-HHHHHHHHHHHHH
Confidence 3489999999888889999999999999987 4699999999999999998888864 7777777777764
No 14
>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=87.33 E-value=2.9 Score=41.09 Aligned_cols=69 Identities=10% Similarity=0.166 Sum_probs=58.1
Q ss_pred HHHHHHHHHHHhhcccHHHHHHHHHHHHHHhcCCCHHHHhcCCHHHHHHhhcCcchhHHHHHHHHhhHHHHH
Q 017244 208 LLFELLVLTAAQVGSDWTSVLKKRQAFREAFSGFDAEVVAKFTEKKMTSLSANYAIDLSQVRGIVDNSIRIL 279 (375)
Q Consensus 208 ~LFEmL~LEgfQAGLSW~tVLkKReafReAF~gFD~ekVA~~tEedIerLl~D~gIIR~KI~AVI~NArail 279 (375)
-.||.|+-|++-.=.+|.+|+.-.+.|.+.|- +++.+|..++++|..+..--|.-+ |.+.+.+=|+.+.
T Consensus 25 dpy~vlvseIL~QQT~v~~v~~~~~rl~~~fp--t~~~La~a~~eeL~~~~~~lG~y~-RAr~L~~~A~~i~ 93 (275)
T TIGR01084 25 TPYRVWLSEVMLQQTQVATVIPYFERFLERFP--TVQALANAPQDEVLKLWEGLGYYA-RARNLHKAAQEVV 93 (275)
T ss_pred CHHHHHHHHHHHhhccHHHHHHHHHHHHHhCC--CHHHHHCcCHHHHHHHHHHCCcHH-HHHHHHHHHHHHH
Confidence 35999999999999999999999999999884 699999999999999988888863 6666666666553
No 15
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=84.61 E-value=8.1 Score=36.84 Aligned_cols=66 Identities=14% Similarity=0.130 Sum_probs=52.9
Q ss_pred ChHHHHHHHHHHHHhhcccHHHHHHHHHHHHHHhcCCCHHHHhcCCHHHHHHhhcCcc--hhHHHHHHHHhhHHHH
Q 017244 205 DDKLLFELLVLTAAQVGSDWTSVLKKRQAFREAFSGFDAEVVAKFTEKKMTSLSANYA--IDLSQVRGIVDNSIRI 278 (375)
Q Consensus 205 DDr~LFEmL~LEgfQAGLSW~tVLkKReafReAF~gFD~ekVA~~tEedIerLl~D~g--IIR~KI~AVI~NArai 278 (375)
|+.-+||.|+..+.-+.-+|..+.+--+.+. ++.+ .+++++|++++.--| .-++|=+.++.-++.+
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 8889999999999999999999988766663 3445 789999999998774 7777766666666554
No 16
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=78.44 E-value=20 Score=34.79 Aligned_cols=86 Identities=14% Similarity=0.250 Sum_probs=63.9
Q ss_pred chhhhhhhcCCCccccChHHHHHHHHHHHHhhcccHHHHHHHHHHHHHHhcCCCHHHHhcCCHHHHHHhhcCcchhHHHH
Q 017244 189 PIYVAYHDEEWGVPVHDDKLLFELLVLTAAQVGSDWTSVLKKRQAFREAFSGFDAEVVAKFTEKKMTSLSANYAIDLSQV 268 (375)
Q Consensus 189 ply~~YHD~EWG~Pv~DDr~LFEmL~LEgfQAGLSW~tVLkKReafReAF~gFD~ekVA~~tEedIerLl~D~gIIR~KI 268 (375)
.++..|+|.-|=--..+| |.++=-+.-=--+|.-|++.-+.++..+. +|+++|..+++++++.+..-.|--+.|.
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 466789998886544444 55544444446789999999999998765 6799999999999999999999987665
Q ss_pred HHHHhhHHHHH
Q 017244 269 RGIVDNSIRIL 279 (375)
Q Consensus 269 ~AVI~NArail 279 (375)
.-++.=.+.+.
T Consensus 89 ~rLk~l~k~l~ 99 (215)
T COG2231 89 KRLKALSKNLA 99 (215)
T ss_pred HHHHHHHHHHH
Confidence 55543333343
No 17
>COG1393 ArsC Arsenate reductase and related proteins, glutaredoxin family [Inorganic ion transport and metabolism]
Probab=71.10 E-value=4 Score=35.42 Aligned_cols=67 Identities=12% Similarity=0.133 Sum_probs=48.6
Q ss_pred hhhhhcCCCccccChHHHHHHHHHHHHhhcccHHHHHHHHHHHHHHhcCCCHHHHhcCCHHHHHHhhcCcchhH
Q 017244 192 VAYHDEEWGVPVHDDKLLFELLVLTAAQVGSDWTSVLKKRQAFREAFSGFDAEVVAKFTEKKMTSLSANYAIDL 265 (375)
Q Consensus 192 ~~YHD~EWG~Pv~DDr~LFEmL~LEgfQAGLSW~tVLkKReafReAF~gFD~ekVA~~tEedIerLl~D~gIIR 265 (375)
++|+-.....--.+...|-+++ -++|..|..++++|..+-+... .++..-.+++.++.|+.++.+||
T Consensus 26 i~~~~~~y~~~~~s~~eL~~~l----~~~g~~~~~li~t~~~~~r~L~---~~~~~~~~~~~~~~i~~~~~Lik 92 (117)
T COG1393 26 IEYTFIDYLKTPPSREELKKIL----SKLGDGVEELINTRGTTYRELN---LDKEDLSDEELIEALLENPSLIK 92 (117)
T ss_pred CCcEEEEeecCCCCHHHHHHHH----HHcCccHHHHHHhccchHHHcC---CcccccChHHHHHHHHhChhhcc
Confidence 3443333444444555666665 7889999999999998877776 55566778888999999997775
No 18
>PF10023 DUF2265: Predicted aminopeptidase (DUF2265); InterPro: IPR014553 This group represents a predicted aminopeptidase.
Probab=67.36 E-value=14 Score=37.98 Aligned_cols=108 Identities=19% Similarity=0.272 Sum_probs=66.9
Q ss_pred HHHHHhhcCcchh---HHHHHHHHhhHHHH----HHHHHhhCCHHHhc--------ccccCCc-----------cccCCC
Q 017244 252 KKMTSLSANYAID---LSQVRGIVDNSIRI----LEVKKQFGSFDKYL--------WGFVNHK-----------PINTQY 305 (375)
Q Consensus 252 edIerLl~D~gII---R~KI~AVI~NArai----l~i~~E~GSF~~yl--------WsFv~~k-----------pi~~~~ 305 (375)
+-|+++++|+.+- |.|+ ..+..+|.+ |.+ .+.+||..|. |..+--. ||..-.
T Consensus 33 ~pv~~vl~dp~~~~~lr~rL-~~~~~iR~FA~~~L~L-pdn~sY~~YadL~Rp~vvWnV~Aap~~sl~~~~WcFPi~Gcv 110 (337)
T PF10023_consen 33 RPVDDVLADPATPPALRARL-RLAQQIRRFASEELGL-PDNGSYRSYADLDRPYVVWNVFAAPEFSLEPKTWCFPIVGCV 110 (337)
T ss_pred CcHHHHhhCCCCCHHHHHHH-HHHHHHHHHHHHhcCC-CCCCChhhhhhcCCCcEEEEEEecCcccCCcceeeccccccc
Confidence 4588889999883 4555 233444444 222 2446666663 3332211 343322
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHcCC-CccchhhHHHHHHHhcccccccccCcchhhhhhhhc
Q 017244 306 RSSQKIPVKTSKSEAISKDMVKKGF-RFVGPTVIHSFMQAAGLTNDHLITCTRHLQCTALAS 366 (375)
Q Consensus 306 ~~~~~iP~~t~lS~~iSKdLKKrGF-kFVGPTtiYSFMQAvG~VNDHl~~C~~~~~~~~~~~ 366 (375)
...+= -...-.+..++.|++.|+ .+||+|.+||- .|+.+|=+.+-+.+..-..||.
T Consensus 111 ~YrGy--F~~~~A~~~a~~L~~~GlDv~v~gV~AYST---LGwF~DPlLSt~l~~~~~~LA~ 167 (337)
T PF10023_consen 111 PYRGY--FDEADARAEAAELRAQGLDVYVGGVPAYST---LGWFDDPLLSTMLRYPDGELAR 167 (337)
T ss_pred cccCc--CCHHHHHHHHHHHHHcCCceeEeccccccc---ccccCCcccccccCCCchHHHH
Confidence 22111 113456778899999999 69999999998 7999999998887644444544
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=61.87 E-value=20 Score=25.72 Aligned_cols=43 Identities=14% Similarity=0.356 Sum_probs=30.4
Q ss_pred HHHHHHh--cCCCHHHHhcCCHHHHHHhhcCcchhHHHHHHHHhh
Q 017244 232 QAFREAF--SGFDAEVVAKFTEKKMTSLSANYAIDLSQVRGIVDN 274 (375)
Q Consensus 232 eafReAF--~gFD~ekVA~~tEedIerLl~D~gIIR~KI~AVI~N 274 (375)
+.|.+.| .++|-..+..++++|+.++=-...-.|.||...|..
T Consensus 17 ~~y~~~f~~~~i~g~~L~~l~~~dL~~lgi~~~g~r~~i~~~i~~ 61 (63)
T cd00166 17 GQYADNFRENGIDGDLLLLLTEEDLKELGITLPGHRKKILKAIQK 61 (63)
T ss_pred HHHHHHHHHcCCCHHHHhHCCHHHHHHcCCCCHHHHHHHHHHHHH
Confidence 6677777 568999999999999884433332356787766643
No 20
>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=59.86 E-value=7.6 Score=31.54 Aligned_cols=30 Identities=17% Similarity=0.410 Sum_probs=26.1
Q ss_pred HHHHHHHHHcCCCccchhhHHHHHHHhccc
Q 017244 319 EAISKDMVKKGFRFVGPTVIHSFMQAAGLT 348 (375)
Q Consensus 319 ~~iSKdLKKrGFkFVGPTtiYSFMQAvG~V 348 (375)
..+++.|.+.||++++.-..+.||+..|+-
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 358899999999999999999999999974
No 21
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=51.12 E-value=68 Score=31.82 Aligned_cols=69 Identities=13% Similarity=0.050 Sum_probs=60.8
Q ss_pred HHHHHHHHHHHHhhcccHHHHHHHHHHHHHHhcC--------CCHHHHhcCCHHHHHHhhcCcchhHHHHHHHHhhHHHH
Q 017244 207 KLLFELLVLTAAQVGSDWTSVLKKRQAFREAFSG--------FDAEVVAKFTEKKMTSLSANYAIDLSQVRGIVDNSIRI 278 (375)
Q Consensus 207 r~LFEmL~LEgfQAGLSW~tVLkKReafReAF~g--------FD~ekVA~~tEedIerLl~D~gIIR~KI~AVI~NArai 278 (375)
.-+||.|+--+.+.=+|=..+-+-+..|.+.|.+ =.|+.++..+++++. .-++-+.|.+.+++=|+++
T Consensus 103 ~d~fe~lv~aI~~QqvS~~~A~~i~~rl~~~~g~~~~~~~~fptpe~l~~~~~~~l~----~~g~s~~Ka~yi~~~A~~~ 178 (285)
T COG0122 103 PDPFEALVRAILSQQVSVAAAAKIWARLVSLYGNALEIYHSFPTPEQLAAADEEALR----RCGLSGRKAEYIISLARAA 178 (285)
T ss_pred CCHHHHHHHHHHHhHhhHHHHHHHHHHHHHHhCCccccccCCCCHHHHHhcCHHHHH----HhCCcHHHHHHHHHHHHHH
Confidence 5789999999999999999999999999999984 479999999999887 4466778999999999997
Q ss_pred H
Q 017244 279 L 279 (375)
Q Consensus 279 l 279 (375)
.
T Consensus 179 ~ 179 (285)
T COG0122 179 A 179 (285)
T ss_pred H
Confidence 4
No 22
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=51.06 E-value=53 Score=31.39 Aligned_cols=78 Identities=22% Similarity=0.353 Sum_probs=52.6
Q ss_pred hhhhcCCCccccChHHHHHHHHHHHHhhcccHHHHHHHHHHHHHHhcCCCHHHHh-cCCHHHHHHhhcCcchhHHHHHHH
Q 017244 193 AYHDEEWGVPVHDDKLLFELLVLTAAQVGSDWTSVLKKRQAFREAFSGFDAEVVA-KFTEKKMTSLSANYAIDLSQVRGI 271 (375)
Q Consensus 193 ~YHD~EWG~Pv~DDr~LFEmL~LEgfQAGLSW~tVLkKReafReAF~gFD~ekVA-~~tEedIerLl~D~gIIR~KI~AV 271 (375)
+.+-.-+|....++|.||+.| +.+-=.|= .+-| .....+|++.++ ....+|+..|.+=|||-.+
T Consensus 55 Ed~~~LyGF~~~~ER~lF~~L-isVnGIGp--K~AL-------aiLs~~~~~~l~~aI~~~d~~~L~k~PGIGkK----- 119 (201)
T COG0632 55 EDAHLLYGFLTEEERELFRLL-ISVNGIGP--KLAL-------AILSNLDPEELAQAIANEDVKALSKIPGIGKK----- 119 (201)
T ss_pred hhHHHHcCCCCHHHHHHHHHH-HccCCccH--HHHH-------HHHcCCCHHHHHHHHHhcChHhhhcCCCCCHH-----
Confidence 344567999999999999999 55543443 3322 245677777776 4477888888888888752
Q ss_pred HhhH-HHHHHHHHhhCC
Q 017244 272 VDNS-IRILEVKKQFGS 287 (375)
Q Consensus 272 I~NA-rail~i~~E~GS 287 (375)
+| |.+++++.++..
T Consensus 120 --tAerivleLk~K~~~ 134 (201)
T COG0632 120 --TAERIVLELKGKLAA 134 (201)
T ss_pred --HHHHHHHHHhhhhhh
Confidence 34 456677765443
No 23
>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=50.43 E-value=30 Score=25.65 Aligned_cols=42 Identities=14% Similarity=0.327 Sum_probs=30.6
Q ss_pred HHHHHHh-cCC-CHHHHhcCCHHHHHHhhcCcch-hHHHHHHHHhh
Q 017244 232 QAFREAF-SGF-DAEVVAKFTEKKMTSLSANYAI-DLSQVRGIVDN 274 (375)
Q Consensus 232 eafReAF-~gF-D~ekVA~~tEedIerLl~D~gI-IR~KI~AVI~N 274 (375)
+.|.+.| .++ |-+.+..++++|+++ |.=..+ .|.||...|..
T Consensus 18 ~~y~~~F~~~~i~g~~L~~lt~~dL~~-lgi~~~ghr~ki~~~i~~ 62 (64)
T PF00536_consen 18 EQYAENFEKNYIDGEDLLSLTEEDLEE-LGITKLGHRKKILRAIQK 62 (64)
T ss_dssp GGGHHHHHHTTSSHHHHTTSCHHHHHH-TT-SSHHHHHHHHHHHHH
T ss_pred HHHHHHHHcCCchHHHHHhcCHHHHHH-cCCCCHHHHHHHHHHHHH
Confidence 6677777 444 999999999999988 544443 57788777653
No 24
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=49.53 E-value=78 Score=31.27 Aligned_cols=118 Identities=14% Similarity=0.099 Sum_probs=74.0
Q ss_pred CCCccccChHHHHHHHHHHHHhhcccHHHHHHHHHHHHHHhc----------CC-CHHHHhcCCHHHHHHhhcCcchhHH
Q 017244 198 EWGVPVHDDKLLFELLVLTAAQVGSDWTSVLKKRQAFREAFS----------GF-DAEVVAKFTEKKMTSLSANYAIDLS 266 (375)
Q Consensus 198 EWG~Pv~DDr~LFEmL~LEgfQAGLSW~tVLkKReafReAF~----------gF-D~ekVA~~tEedIerLl~D~gIIR~ 266 (375)
.=|.-+.-..-.||+|+..+.-.-.|=..+-+-...+-+.|. -| +++.|+..+++++..+ |+-+.
T Consensus 102 ~~GlR~p~~~d~fE~lv~aIigQqisv~~a~~~~~rlv~~~G~~l~~~~~~~~FPtpe~La~~~~~eL~~~----Gl~~~ 177 (283)
T PRK10308 102 RPGLRLPGSVDAFEQGVRAILGQLVSVAMAAKLTAKVAQLYGERLDDFPEYVCFPTPERLAAADPQALKAL----GMPLK 177 (283)
T ss_pred CCCCcCCCCCCHHHHHHHHHHHhHHHHHHHHHHHHHHHHHhCccccCCCCccCCCCHHHHHcCCHHHHHHC----CCCHH
Confidence 346656555677999987765444443333333344444433 24 7999999999988753 77778
Q ss_pred HHHHHHhhHHHHHHHHHhhCCHHHhcccccCCccccCCCCCCCCCCCCCHHHHHHHHHHHHcCCCccchhhH-HHHHHHh
Q 017244 267 QVRGIVDNSIRILEVKKQFGSFDKYLWGFVNHKPINTQYRSSQKIPVKTSKSEAISKDMVKKGFRFVGPTVI-HSFMQAA 345 (375)
Q Consensus 267 KI~AVI~NArail~i~~E~GSF~~ylWsFv~~kpi~~~~~~~~~iP~~t~lS~~iSKdLKKrGFkFVGPTti-YSFMQAv 345 (375)
|.+.++.=|+++.+ |.++ + ... . +. +.+-+.|.+ ++=|||-|+ |-.|.+.
T Consensus 178 Ra~~L~~lA~~i~~-----g~l~-----l---~~~-----------~--~~-~~~~~~L~~--LpGIGpwTA~~vllr~l 228 (283)
T PRK10308 178 RAEALIHLANAALE-----GTLP-----L---TIP-----------G--DV-EQAMKTLQT--FPGIGRWTANYFALRGW 228 (283)
T ss_pred HHHHHHHHHHHHHc-----CCCC-----c---ccc-----------C--CH-HHHHHHHhc--CCCcCHHHHHHHHHHhC
Confidence 99999999988753 3322 0 000 0 11 234456655 889999888 6677777
Q ss_pred ccc
Q 017244 346 GLT 348 (375)
Q Consensus 346 G~V 348 (375)
|-.
T Consensus 229 g~~ 231 (283)
T PRK10308 229 QAK 231 (283)
T ss_pred CCC
Confidence 744
No 25
>PF13495 Phage_int_SAM_4: Phage integrase, N-terminal SAM-like domain; PDB: 2A3V_A.
Probab=44.53 E-value=1.2e+02 Score=23.07 Aligned_cols=53 Identities=9% Similarity=0.054 Sum_probs=36.3
Q ss_pred HHHHHHHHHHhhcccHHHHHHHHHHHHHHhcCCCHHHHhcCCHHHHHHhhcCc
Q 017244 209 LFELLVLTAAQVGSDWTSVLKKRQAFREAFSGFDAEVVAKFTEKKMTSLSANY 261 (375)
Q Consensus 209 LFEmL~LEgfQAGLSW~tVLkKReafReAF~gFD~ekVA~~tEedIerLl~D~ 261 (375)
|++.+....-..|+|=.||-.-+-.++.-..-|+-..+..++.+||+..+..-
T Consensus 1 Ll~~f~~~l~~~~~s~~Ti~~Y~~~l~~f~~~~~~~~~~~it~~~i~~y~~~l 53 (85)
T PF13495_consen 1 LLEEFLEYLRLKGLSEKTIKNYRYHLKRFLRFLGNKPPDEITPEDIEQYLNYL 53 (85)
T ss_dssp -HHHHHHHHHHTT--HHHHHHHHHHHHHHHTTSSS--GGG--HHHHHHHHHHH
T ss_pred CHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcccCccchhHHHHHHHHHHHH
Confidence 34445455566999999999999999987777776788999999998777543
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=44.43 E-value=30 Score=25.74 Aligned_cols=43 Identities=16% Similarity=0.345 Sum_probs=29.7
Q ss_pred HHHHHHhc--CCCH-HHHhcCCHHHHHHhhcCcchhHHHHHHHHhh
Q 017244 232 QAFREAFS--GFDA-EVVAKFTEKKMTSLSANYAIDLSQVRGIVDN 274 (375)
Q Consensus 232 eafReAF~--gFD~-ekVA~~tEedIerLl~D~gIIR~KI~AVI~N 274 (375)
+.|.+.|. ++|- +.++.++++++.++=-.....|.||-..|++
T Consensus 19 ~~y~~~f~~~~i~g~~~L~~l~~~~L~~lGI~~~~~r~kll~~i~~ 64 (66)
T PF07647_consen 19 EQYADNFRENGIDGLEDLLQLTEEDLKELGITNLGHRRKLLSAIQE 64 (66)
T ss_dssp GGGHHHHHHTTCSHHHHHTTSCHHHHHHTTTTHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHcCCcHHHHHhhCCHHHHHHcCCCCHHHHHHHHHHHHH
Confidence 56667776 5666 7799999999975544333456777766654
No 27
>PF07862 Nif11: Nitrogen fixation protein of unknown function; InterPro: IPR012903 This domain is found in the cyanobacteria, and the nitrogen-fixing proteobacterium Azotobacter vinelandii and may be involved in nitrogen fixation, but no role has been assigned [].
Probab=39.97 E-value=32 Score=24.96 Aligned_cols=40 Identities=10% Similarity=0.223 Sum_probs=26.8
Q ss_pred CCHHHHHHhhcCcch---hHHHHHHHHhhHHHHHHHHHhhC-CHH
Q 017244 249 FTEKKMTSLSANYAI---DLSQVRGIVDNSIRILEVKKQFG-SFD 289 (375)
Q Consensus 249 ~tEedIerLl~D~gI---IR~KI~AVI~NArail~i~~E~G-SF~ 289 (375)
|+.+++++++..-.- .|.|+.++- |...+++|.++.| +|.
T Consensus 1 MS~~~l~~Fl~~~~~d~~l~~~l~~~~-~~~e~~~lA~~~Gy~ft 44 (49)
T PF07862_consen 1 MSIESLKAFLEKVKSDPELREQLKACQ-NPEEVVALAREAGYDFT 44 (49)
T ss_pred CCHHHHHHHHHHHhcCHHHHHHHHhcC-CHHHHHHHHHHcCCCCC
Confidence 556666665544322 356888754 8899999999988 443
No 28
>PF13276 HTH_21: HTH-like domain
Probab=39.73 E-value=35 Score=25.40 Aligned_cols=30 Identities=20% Similarity=0.283 Sum_probs=26.0
Q ss_pred HHHHHHHHHcCCCccchhhHHHHHHHhccc
Q 017244 319 EAISKDMVKKGFRFVGPTVIHSFMQAAGLT 348 (375)
Q Consensus 319 ~~iSKdLKKrGFkFVGPTtiYSFMQAvG~V 348 (375)
..|..+|.+.|---||-.+|+-+|+..||.
T Consensus 24 rri~~~L~~~~~~~v~~krV~RlM~~~gL~ 53 (60)
T PF13276_consen 24 RRIWAELRREGGIRVSRKRVRRLMREMGLR 53 (60)
T ss_pred hHHHHHHhccCcccccHHHHHHHHHHcCCc
Confidence 478899999965579999999999999985
No 29
>PTZ00411 transaldolase-like protein; Provisional
Probab=37.87 E-value=44 Score=34.12 Aligned_cols=62 Identities=23% Similarity=0.344 Sum_probs=46.5
Q ss_pred HHHHHHhhHHHHHHHHHhhCCHHHhcccccCCccccCCCCCCCCCCCCCHHHHHHHHHHHHcCCCccchhhHHHHHHHh
Q 017244 267 QVRGIVDNSIRILEVKKQFGSFDKYLWGFVNHKPINTQYRSSQKIPVKTSKSEAISKDMVKKGFRFVGPTVIHSFMQAA 345 (375)
Q Consensus 267 KI~AVI~NArail~i~~E~GSF~~ylWsFv~~kpi~~~~~~~~~iP~~t~lS~~iSKdLKKrGFkFVGPTtiYSFMQAv 345 (375)
-.+++|..|+.+.++-++.| ++...+ +=+||++ ...-+-++.|.+.|.+--. |.+|++.||+
T Consensus 114 d~e~~i~~A~~l~~l~~~~g---------i~~~ri------lIKIPaT-~eGi~Aa~~L~~eGI~~N~-TlvFS~~QA~ 175 (333)
T PTZ00411 114 DKQAMVDKARKIIKMYEEAG---------ISKDRI------LIKLAST-WEGIQAAKALEKEGIHCNL-TLLFSFAQAV 175 (333)
T ss_pred CHHHHHHHHHHHHHhhhhhc---------CCCCcE------EEEeCCC-HHHHHHHHHHHHCCCceeE-eEecCHHHHH
Confidence 46889999999988855533 222222 3478865 7777788999999999877 8899999985
No 30
>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=35.80 E-value=32 Score=27.45 Aligned_cols=28 Identities=29% Similarity=0.565 Sum_probs=24.8
Q ss_pred HHHHHHHHcCCCccchhhHHHHHHHhcc
Q 017244 320 AISKDMVKKGFRFVGPTVIHSFMQAAGL 347 (375)
Q Consensus 320 ~iSKdLKKrGFkFVGPTtiYSFMQAvG~ 347 (375)
.+++.|.+.||+.+.-...+.||+..|+
T Consensus 4 ~~~~~l~~lG~~i~AT~gTa~~L~~~Gi 31 (90)
T smart00851 4 ELAKRLAELGFELVATGGTAKFLREAGL 31 (90)
T ss_pred HHHHHHHHCCCEEEEccHHHHHHHHCCC
Confidence 5788999999999988888999999885
No 31
>PF05075 DUF684: Protein of unknown function (DUF684); InterPro: IPR007767 This family contains uncharacterised proteins from Caenorhabditis elegans.
Probab=35.67 E-value=68 Score=32.41 Aligned_cols=76 Identities=18% Similarity=0.223 Sum_probs=48.1
Q ss_pred hHHHHHHHHHHHHhhcc-------cHHHHHHHHHHHHHHhcCCCHHHH--hcCCHHHHHHhhcC-----cch--------
Q 017244 206 DKLLFELLVLTAAQVGS-------DWTSVLKKRQAFREAFSGFDAEVV--AKFTEKKMTSLSAN-----YAI-------- 263 (375)
Q Consensus 206 Dr~LFEmL~LEgfQAGL-------SW~tVLkKReafReAF~gFD~ekV--A~~tEedIerLl~D-----~gI-------- 263 (375)
+..|-.+|.||+|.+|| .+..|+.+-..+.+..+.|+-+.. ..|=++.++.++.+ ..+
T Consensus 115 ~~vl~q~l~lEafa~Gl~~~~n~~~~~~L~e~~~~~~~~~~~w~~~Y~~~~~yWp~~v~~~v~~~~d~~~~~sn~eKAd~ 194 (345)
T PF05075_consen 115 DGVLGQLLFLEAFASGLFKDKNMYDPDRLIEKIEEINEKMDKWKEEYKKDESYWPDNVKKFVEEVQDNNSHLSNEEKADE 194 (345)
T ss_pred HHHHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhhccccccchHHHHHHHHHHHHhcCCCChHHHHHH
Confidence 56799999999999999 678888888777777776665552 23333444444322 211
Q ss_pred hHHHHHHHHhhHHHHHHH
Q 017244 264 DLSQVRGIVDNSIRILEV 281 (375)
Q Consensus 264 IR~KI~AVI~NArail~i 281 (375)
|+.+++.+.+|-..++=|
T Consensus 195 Ik~~Le~ilTnDsFYIiV 212 (345)
T PF05075_consen 195 IKKKLEKILTNDSFYIIV 212 (345)
T ss_pred HHHHHHhhCCCCcEEEEE
Confidence 345666666665544433
No 32
>KOG2198 consensus tRNA cytosine-5-methylases and related enzymes of the NOL1/NOP2/sun superfamily [Translation, ribosomal structure and biogenesis]
Probab=34.65 E-value=56 Score=34.18 Aligned_cols=99 Identities=14% Similarity=0.154 Sum_probs=65.9
Q ss_pred HHHHHHHHHHHHHHhcCCCHHHHhcCCHHHHHHhhcCcchh---HHHHHHHHhhHHHHHHHHHhhCCHHHhcccccCCcc
Q 017244 224 WTSVLKKRQAFREAFSGFDAEVVAKFTEKKMTSLSANYAID---LSQVRGIVDNSIRILEVKKQFGSFDKYLWGFVNHKP 300 (375)
Q Consensus 224 W~tVLkKReafReAF~gFD~ekVA~~tEedIerLl~D~gII---R~KI~AVI~NArail~i~~E~GSF~~ylWsFv~~kp 300 (375)
|..--.+.+.|+++.++||. +++.+.++..-+.. .-++.+.++|+-+++.+.+++-.-..|--.. .+
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 55566778899999999986 77777777654443 3699999999999999977654322222111 11
Q ss_pred ccCCCCCCCCCCCCCHHHHHHHHHHHHcCCCccch
Q 017244 301 INTQYRSSQKIPVKTSKSEAISKDMVKKGFRFVGP 335 (375)
Q Consensus 301 i~~~~~~~~~iP~~t~lS~~iSKdLKKrGFkFVGP 335 (375)
..+....+.|- .|..-+..++.++-+|+-.+|
T Consensus 89 --~~~e~~~~~p~-~p~~~a~~~~~~~~~~r~~~~ 120 (375)
T KOG2198|consen 89 --LKFEAPFELPW-YPDNLAFEKDVKLDEIRKSPP 120 (375)
T ss_pred --cccCccccCCC-CcccchhhhcCcccccccCCc
Confidence 12333344443 255667778888888888774
No 33
>PRK13344 spxA transcriptional regulator Spx; Reviewed
Probab=32.18 E-value=39 Score=29.62 Aligned_cols=54 Identities=11% Similarity=0.242 Sum_probs=36.8
Q ss_pred cChHHHHHHHHHHHHhhcccHHHHHHHHHHHHHHhcCCCHHHHhcCCHHH-HHHhhcCcchhH
Q 017244 204 HDDKLLFELLVLTAAQVGSDWTSVLKKRQAFREAFSGFDAEVVAKFTEKK-MTSLSANYAIDL 265 (375)
Q Consensus 204 ~DDr~LFEmL~LEgfQAGLSW~tVLkKReafReAF~gFD~ekVA~~tEed-IerLl~D~gIIR 265 (375)
.+...|-+++ -+.|..|..++++|..+.+... .+. ..+++++ ++-|+++|.+|+
T Consensus 37 ~s~~eL~~~l----~~~~~~~~~lin~~~~~~k~L~-~~~---~~ls~~e~i~ll~~~P~Lik 91 (132)
T PRK13344 37 LTKEEILAIL----TKTENGIESIVSSKNRYAKALD-CDI---EELSVNEVIDLIQENPRILK 91 (132)
T ss_pred CCHHHHHHHH----HHhCCCHHHhhccCcHHHHhCC-cch---hcCCHHHHHHHHHhCcccee
Confidence 3444555555 4568899999999998877543 332 4566554 677788898875
No 34
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=31.87 E-value=4.6e+02 Score=26.64 Aligned_cols=92 Identities=22% Similarity=0.273 Sum_probs=63.4
Q ss_pred CCCHHHHhcCCHHHHHHhhcCcchhHHHHHHHHhhHHHHHHHHHhhCCHHHhcccccCCccccCCCCCCCCCCCCCHHHH
Q 017244 240 GFDAEVVAKFTEKKMTSLSANYAIDLSQVRGIVDNSIRILEVKKQFGSFDKYLWGFVNHKPINTQYRSSQKIPVKTSKSE 319 (375)
Q Consensus 240 gFD~ekVA~~tEedIerLl~D~gIIR~KI~AVI~NArail~i~~E~GSF~~ylWsFv~~kpi~~~~~~~~~iP~~t~lS~ 319 (375)
|.-++.|.+++|..|+.|+.--|...+|-.=+-.-|+.++ ++|+ ++||.+
T Consensus 108 gLT~e~v~~~de~~l~~LI~~VgFy~rKA~ylkkta~IL~---d~f~----------------------gDIP~~----- 157 (286)
T KOG1921|consen 108 GLTLEAVLKIDEPTLNELIYPVGFYTRKAKYLKKTAKILQ---DKFD----------------------GDIPDT----- 157 (286)
T ss_pred CCCHHHHhccChHhHHhhhhhccchHHHHHHHHHHHHHHH---HHhC----------------------CCCchh-----
Confidence 7899999999999999999998988778666655555542 3322 233331
Q ss_pred HHHHHHHHcCCCccchhhHHHHHH-HhcccccccccCcchhhhhhhh
Q 017244 320 AISKDMVKKGFRFVGPTVIHSFMQ-AAGLTNDHLITCTRHLQCTALA 365 (375)
Q Consensus 320 ~iSKdLKKrGFkFVGPTtiYSFMQ-AvG~VNDHl~~C~~~~~~~~~~ 365 (375)
-+|| .+.--|||..+|-.|| |.|-|-.--+|-+.|.-|..++
T Consensus 158 --v~dL--lsLPGVGPKMa~L~m~~AWn~i~GI~VDtHVHRi~nrlg 200 (286)
T KOG1921|consen 158 --VEDL--LSLPGVGPKMAHLTMQVAWNKIVGICVDTHVHRICNRLG 200 (286)
T ss_pred --HHHH--hcCCCCchHHHHHHHHHHhccceeEEeehHHHHHHHHhc
Confidence 1344 2567899999999998 4565555555556666666554
No 35
>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=31.87 E-value=48 Score=29.66 Aligned_cols=31 Identities=13% Similarity=0.231 Sum_probs=26.7
Q ss_pred HHHHHHHHHHcCCCccchhhHHHHHHHhcccc
Q 017244 318 SEAISKDMVKKGFRFVGPTVIHSFMQAAGLTN 349 (375)
Q Consensus 318 S~~iSKdLKKrGFkFVGPTtiYSFMQAvG~VN 349 (375)
.+.|...|+++||. |.-.|+|-.|...|++-
T Consensus 19 qeeL~~~L~~~G~~-vsqaTIsRdL~elglvk 49 (146)
T TIGR01529 19 QEELVALLKAEGIE-VTQATVSRDLRELGAVK 49 (146)
T ss_pred HHHHHHHHHHhCCC-cCHHHHHHHHHHcCCEE
Confidence 34677889999999 88889999999999974
No 36
>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=31.71 E-value=50 Score=27.60 Aligned_cols=32 Identities=13% Similarity=0.270 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHHcCCCccchhhHHHHHHHhcc
Q 017244 316 SKSEAISKDMVKKGFRFVGPTVIHSFMQAAGL 347 (375)
Q Consensus 316 ~lS~~iSKdLKKrGFkFVGPTtiYSFMQAvG~ 347 (375)
+....+++.|.+.||+.++.-..+.||+..|+
T Consensus 12 ~~~~~~a~~l~~~G~~i~AT~gTa~~L~~~Gi 43 (112)
T cd00532 12 AMLVDLAPKLSSDGFPLFATGGTSRVLADAGI 43 (112)
T ss_pred HHHHHHHHHHHHCCCEEEECcHHHHHHHHcCC
Confidence 45567899999999999998889999998885
No 37
>cd03678 MM_CoA_mutase_1 Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM) family, unknown subfamily 1; composed of uncharacterized bacterial proteins containing a C-terminal MCM domain. MCM catalyzes the isomerization of methylmalonyl-CoA to succinyl-CoA. The reaction proceeds via radical intermediates beginning with a substrate-induced homolytic cleavage of the Co-C bond of coenzyme B12 to produce cob(II)alamin and the deoxyadenosyl radical. MCM plays an important role in the conversion of propionyl-CoA to succinyl-CoA during the degradation of propionate for the Krebs cycle. In some bacteria, MCM is involved in the reverse metabolic reaction, the rearrangement of succinyl-CoA to methylmalonyl-CoA. Members of this subfamily also contain an N-terminal coenzyme B12 binding domain followed by a domain similar to the E. coli ArgK membrane ATPase.
Probab=30.62 E-value=16 Score=39.23 Aligned_cols=60 Identities=18% Similarity=0.372 Sum_probs=44.4
Q ss_pred HHHHHHHHHhcCCCHHH--------------------HhcCCHHHHHHhhcCcchh---HHHHHHHHhhHHHHHHHHHhh
Q 017244 229 KKRQAFREAFSGFDAEV--------------------VAKFTEKKMTSLSANYAID---LSQVRGIVDNSIRILEVKKQF 285 (375)
Q Consensus 229 kKReafReAF~gFD~ek--------------------VA~~tEedIerLl~D~gII---R~KI~AVI~NArail~i~~E~ 285 (375)
.-.+.|+.+|+|+|.++ ++.-.+..||..+...|+. ..|++.+|.| ++.+|+
T Consensus 144 ~sl~Dm~~lf~gi~L~~~~~s~smtin~~a~~~lAmy~a~a~~~~~~~~~~~~G~~~~~~~~l~Gtiqn-----DiLke~ 218 (495)
T cd03678 144 ATLDDMKKLYSGFDLCAPNTSVSMTINGPAPMLLAFFLNTAIDQQVEKFRRENGIRAETLRSVRGTVQA-----DILKED 218 (495)
T ss_pred CcHHHHHHHhcCCCCCCCcceeeeeecccHHHHHHHHHHHHHHhhhhhhHhhcCCCcccHhhcCccccc-----chHHHH
Confidence 44589999999999999 4444455688888899998 6799999988 444555
Q ss_pred CCHHHhcc
Q 017244 286 GSFDKYLW 293 (375)
Q Consensus 286 GSF~~ylW 293 (375)
-.-..|++
T Consensus 219 ~argt~i~ 226 (495)
T cd03678 219 QAQNTCIF 226 (495)
T ss_pred HhCCCccC
Confidence 44444443
No 38
>PF13068 DUF3932: Protein of unknown function (DUF3932)
Probab=30.53 E-value=11 Score=30.86 Aligned_cols=32 Identities=22% Similarity=0.644 Sum_probs=24.5
Q ss_pred HHHHHHhhC-CHHHhcccccCCccccCCCCCCC
Q 017244 278 ILEVKKQFG-SFDKYLWGFVNHKPINTQYRSSQ 309 (375)
Q Consensus 278 il~i~~E~G-SF~~ylWsFv~~kpi~~~~~~~~ 309 (375)
+.+++-+|. ||+.|+-+||.+.|-...|....
T Consensus 4 vfrlqtdfsssfdrwvssfvsdhpaql~wttlk 36 (81)
T PF13068_consen 4 VFRLQTDFSSSFDRWVSSFVSDHPAQLEWTTLK 36 (81)
T ss_pred hhhhhcchhhHHHHHHHHHhcCCccccchhHHH
Confidence 456777876 89999999998888766665443
No 39
>PRK10548 flagellar biosynthesis protein FliT; Provisional
Probab=29.75 E-value=1.3e+02 Score=26.57 Aligned_cols=76 Identities=18% Similarity=0.333 Sum_probs=57.2
Q ss_pred HHHHHHHHHHHhhcccHHHHHHHHHHHHHHhcCCCHHHHhc------CCHHH-------HHHhhcCcchhH-------HH
Q 017244 208 LLFELLVLTAAQVGSDWTSVLKKRQAFREAFSGFDAEVVAK------FTEKK-------MTSLSANYAIDL-------SQ 267 (375)
Q Consensus 208 ~LFEmL~LEgfQAGLSW~tVLkKReafReAF~gFD~ekVA~------~tEed-------IerLl~D~gIIR-------~K 267 (375)
.|.+-+ |+..+.| .|..+..-...|..+-+ .+.. +++.+ |.+|+.|..-|| ..
T Consensus 16 ~lS~~M-L~aA~~g-~Wd~Li~lE~~y~~~Ve-----~l~~~~~~~~l~~~~q~~~~~lL~~IL~nda~Ir~Llq~rl~e 88 (121)
T PRK10548 16 TLSQSM-LRLATEG-QWDELIEQEVAYVQAVE-----EIAHLTIPPDISTVMQEQLRPMLRQILDNEAELKQLLQQRMDE 88 (121)
T ss_pred HHHHHH-HHHHHHC-CHHHHHHHHHHHHHHHH-----HHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 355555 7888888 69999999888887744 3322 34333 567888887775 48
Q ss_pred HHHHHhhHHHHHHHHHhhCCHHH
Q 017244 268 VRGIVDNSIRILEVKKQFGSFDK 290 (375)
Q Consensus 268 I~AVI~NArail~i~~E~GSF~~ 290 (375)
+...|.+++.=..+..-||.|+.
T Consensus 89 L~~li~~~~rq~~l~~aYg~~~~ 111 (121)
T PRK10548 89 LSSLIGQSTRQKSVNSAYGQLSG 111 (121)
T ss_pred HHHHHHHhHHHHHHHHHHhcCCC
Confidence 99999999999999999999885
No 40
>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=28.88 E-value=77 Score=27.02 Aligned_cols=21 Identities=19% Similarity=0.502 Sum_probs=16.3
Q ss_pred HHHHHHHHHHHcCCCccchhh
Q 017244 317 KSEAISKDMVKKGFRFVGPTV 337 (375)
Q Consensus 317 lS~~iSKdLKKrGFkFVGPTt 337 (375)
+...+++.+.+.|.+|+||..
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 566788899999999999974
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=28.82 E-value=1.6e+02 Score=21.05 Aligned_cols=42 Identities=14% Similarity=0.308 Sum_probs=27.8
Q ss_pred HHHHh--cCCCHHHHhcCC-HHHHHHhhcCcchhHHHHHHHHhhH
Q 017244 234 FREAF--SGFDAEVVAKFT-EKKMTSLSANYAIDLSQVRGIVDNS 275 (375)
Q Consensus 234 fReAF--~gFD~ekVA~~t-EedIerLl~D~gIIR~KI~AVI~NA 275 (375)
|.+.| .++|-..+..++ +++++++=-..--.|.||...|..-
T Consensus 21 y~~~f~~~~i~g~~ll~~~~~~~l~~lgi~~~~~r~~ll~~i~~l 65 (68)
T smart00454 21 YADNFRKNGIDGALLLLLTSEEDLKELGITKLGHRKKILKAIQKL 65 (68)
T ss_pred HHHHHHHCCCCHHHHHhcChHHHHHHcCCCcHHHHHHHHHHHHHH
Confidence 66666 577888888998 7777775433323567777666553
No 42
>PHA02517 putative transposase OrfB; Reviewed
Probab=28.76 E-value=60 Score=30.64 Aligned_cols=30 Identities=20% Similarity=0.472 Sum_probs=26.1
Q ss_pred HHHHHHHHHcCCCccchhhHHHHHHHhcccc
Q 017244 319 EAISKDMVKKGFRFVGPTVIHSFMQAAGLTN 349 (375)
Q Consensus 319 ~~iSKdLKKrGFkFVGPTtiYSFMQAvG~VN 349 (375)
..|...|+++|+. ++..++|-+|+..||.-
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 4788899999986 59999999999999964
No 43
>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=27.66 E-value=67 Score=26.43 Aligned_cols=32 Identities=25% Similarity=0.530 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHHcCCCccchhhHHHHHHHhcc
Q 017244 316 SKSEAISKDMVKKGFRFVGPTVIHSFMQAAGL 347 (375)
Q Consensus 316 ~lS~~iSKdLKKrGFkFVGPTtiYSFMQAvG~ 347 (375)
+....+++.|.+.||+..+.-..+.||+..|+
T Consensus 13 ~~~~~~~~~l~~~G~~l~aT~gT~~~l~~~gi 44 (110)
T cd01424 13 PEAVEIAKRLAELGFKLVATEGTAKYLQEAGI 44 (110)
T ss_pred hHHHHHHHHHHHCCCEEEEchHHHHHHHHcCC
Confidence 34557889999999999999999999999886
No 44
>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=27.15 E-value=32 Score=24.83 Aligned_cols=30 Identities=7% Similarity=0.227 Sum_probs=24.0
Q ss_pred HHHHhcCCCHHHHhcCCHHHHHHhhcCcch
Q 017244 234 FREAFSGFDAEVVAKFTEKKMTSLSANYAI 263 (375)
Q Consensus 234 fReAF~gFD~ekVA~~tEedIerLl~D~gI 263 (375)
|+++|.-||.+.=-.++.+++..++...++
T Consensus 1 ~~~~F~~~D~~~~G~i~~~el~~~l~~~g~ 30 (67)
T cd00052 1 YDQIFRSLDPDGDGLISGDEARPFLGKSGL 30 (67)
T ss_pred ChHHHHHhCCCCCCcCcHHHHHHHHHHcCC
Confidence 578899999887777888888888866555
No 45
>cd03023 DsbA_Com1_like DsbA family, Com1-like subfamily; composed of proteins similar to Com1, a 27-kDa outer membrane-associated immunoreactive protein originally found in both acute and chronic disease strains of the pathogenic bacteria Coxiella burnetti. It contains a CXXC motif, assumed to be imbedded in a DsbA-like structure. Its homology to DsbA suggests that the protein is a protein disulfide oxidoreductase. The role of such a protein in pathogenesis is unknown.
Probab=27.15 E-value=3.3e+02 Score=22.31 Aligned_cols=29 Identities=10% Similarity=0.313 Sum_probs=21.5
Q ss_pred cCCHHHHHHhhcCcchhHHHHHHHHhhHH
Q 017244 248 KFTEKKMTSLSANYAIDLSQVRGIVDNSI 276 (375)
Q Consensus 248 ~~tEedIerLl~D~gIIR~KI~AVI~NAr 276 (375)
..+++++..++.+.|+...++.+.++...
T Consensus 82 ~~~~~~l~~~a~~~gl~~~~~~~~~~~~~ 110 (154)
T cd03023 82 RLNEESLLRIAKKAGLDEAKLKKDMDDPE 110 (154)
T ss_pred CCCHHHHHHHHHHcCCCHHHHHHHhhChH
Confidence 35777888888888887777777776643
No 46
>PRK05269 transaldolase B; Provisional
Probab=27.05 E-value=89 Score=31.64 Aligned_cols=63 Identities=16% Similarity=0.241 Sum_probs=46.2
Q ss_pred HHHHHHhhHHHHHHHHHhhCCHHHhcccccCCccccCCCCCCCCCCCCCHHHHHHHHHHHHcCCCccchhhHHHHHHHhc
Q 017244 267 QVRGIVDNSIRILEVKKQFGSFDKYLWGFVNHKPINTQYRSSQKIPVKTSKSEAISKDMVKKGFRFVGPTVIHSFMQAAG 346 (375)
Q Consensus 267 KI~AVI~NArail~i~~E~GSF~~ylWsFv~~kpi~~~~~~~~~iP~~t~lS~~iSKdLKKrGFkFVGPTtiYSFMQAvG 346 (375)
-.+++|..|+.+.++-++.| . +... -+=+||++ ....+-++.|.+.|.+--. |.+|++.||.-
T Consensus 104 d~~~~i~~A~~l~~~~~~~g--------i-~~~~------v~IKIPaT-~eGi~A~~~L~~~GI~vn~-TlvFs~~Qa~~ 166 (318)
T PRK05269 104 DTEATIAKARKLIALYEEAG--------I-SKDR------ILIKIAST-WEGIRAAEQLEKEGINCNL-TLLFSFAQARA 166 (318)
T ss_pred CHHHHHHHHHHHHHHhhhcC--------C-CCCc------EEEEeCCC-HHHHHHHHHHHHcCCceeE-eEecCHHHHHH
Confidence 56889999999988755422 2 2212 23478876 6666677999999999877 88999999864
No 47
>cd02762 MopB_1 The MopB_1 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. These members belong to the molybdopterin_binding (MopB) superfamily of proteins.
Probab=26.89 E-value=1.9e+02 Score=30.39 Aligned_cols=56 Identities=18% Similarity=0.242 Sum_probs=43.6
Q ss_pred cChHHHHHHHHHHHHhhcc-cHHHHHHH---HHHHHHHhcCCCHHHHh---cCCHHHHHHhhc
Q 017244 204 HDDKLLFELLVLTAAQVGS-DWTSVLKK---RQAFREAFSGFDAEVVA---KFTEKKMTSLSA 259 (375)
Q Consensus 204 ~DDr~LFEmL~LEgfQAGL-SW~tVLkK---ReafReAF~gFD~ekVA---~~tEedIerLl~ 259 (375)
..|-.|+-.|+..++.-|+ ++.-|-+. .+.|++...+|+++.++ ..++++|++|..
T Consensus 217 GtD~aL~~a~~~~ii~~~~~D~~fi~~~t~Gf~~~~~~~~~~t~e~~~~~tGv~~~~I~~lA~ 279 (539)
T cd02762 217 GTDAWLLAAMLAVLLAEGLTDRRFLAEHCDGLDEVRAALAEFTPEAYAPRCGVPAETIRRLAR 279 (539)
T ss_pred CcHHHHHHHHHHHHHHCCCCChHHHHHHcCcHHHHHHHHhcCCHHHHHHHHCcCHHHHHHHHH
Confidence 5688888888888888887 45555444 67889999999999888 667888887764
No 48
>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=26.22 E-value=2.9e+02 Score=27.61 Aligned_cols=88 Identities=14% Similarity=0.139 Sum_probs=58.5
Q ss_pred CCchhhhhhhcCCCccccChHHHHHHHHHHHHhhcccHHHHHHHHHHHHHHhcC------------C-CHHHHhcCCHHH
Q 017244 187 SDPIYVAYHDEEWGVPVHDDKLLFELLVLTAAQVGSDWTSVLKKRQAFREAFSG------------F-DAEVVAKFTEKK 253 (375)
Q Consensus 187 ~dply~~YHD~EWG~Pv~DDr~LFEmL~LEgfQAGLSW~tVLkKReafReAF~g------------F-D~ekVA~~tEed 253 (375)
.||.+..--+.--|..+.-. -.||.|+-.+...-.|+..+.+-...+.+.|-. | +++.|+..+.+
T Consensus 98 ~D~~l~~~~~~~~GlRi~~~-d~fE~lv~~IlsQq~si~~a~~~~~rL~~~~G~~~~~~~g~~~~~FPtp~~La~~~~e- 175 (310)
T TIGR00588 98 VDKHFQYVAQKFQGVRLLRQ-DPFECLISFICSSNNNIARITRMVERLCQAFGPRLITLDGVTYHGFPSLHALTGPEAE- 175 (310)
T ss_pred cCHHHHHHHHhCCCCCCCCC-CHHHHHHHHHHhCCCCHHHHHHHHHHHHHHhCCCcccCCCcccccCCCHHHHhCCChH-
Confidence 46665555555668655444 679999999999999999999999999988752 2 36666664322
Q ss_pred HHHhhcCcchhHHHHHHHHhhHHHHH
Q 017244 254 MTSLSANYAIDLSQVRGIVDNSIRIL 279 (375)
Q Consensus 254 IerLl~D~gIIR~KI~AVI~NArail 279 (375)
..+..-|+ ..|.+.++.=|+++.
T Consensus 176 --~~Lr~~G~-g~Ra~~I~~~A~~i~ 198 (310)
T TIGR00588 176 --AHLRKLGL-GYRARYIRETARALL 198 (310)
T ss_pred --HHHHHcCC-HHHHHHHHHHHHHHH
Confidence 22333344 235666666666653
No 49
>PRK12309 transaldolase/EF-hand domain-containing protein; Provisional
Probab=25.83 E-value=95 Score=32.33 Aligned_cols=63 Identities=14% Similarity=0.222 Sum_probs=45.8
Q ss_pred HHHHHHhhHHHHHHHHHhhCCHHHhcccccCCccccCCCCCCCCCCCCCHHHHHHHHHHHHcCCCccchhhHHHHHHHhc
Q 017244 267 QVRGIVDNSIRILEVKKQFGSFDKYLWGFVNHKPINTQYRSSQKIPVKTSKSEAISKDMVKKGFRFVGPTVIHSFMQAAG 346 (375)
Q Consensus 267 KI~AVI~NArail~i~~E~GSF~~ylWsFv~~kpi~~~~~~~~~iP~~t~lS~~iSKdLKKrGFkFVGPTtiYSFMQAvG 346 (375)
-.+++|..|+.+.++-++.| ++... -+=+||++ ....+-++.|++.|.+--. |.+|++.||+-
T Consensus 108 d~~~~i~~A~~l~~~~~~~g---------i~~~~------v~IKIPaT-~eGi~A~~~L~~~GI~~n~-TlvFS~~QA~a 170 (391)
T PRK12309 108 DTEATIAKARKLISLYEDAG---------ISRDR------VLIKIAST-WEGIKAAEVLEKEGIHCNL-TLLFGFHQAIA 170 (391)
T ss_pred CHHHHHHHHHHHHHHhhhhc---------CCCCc------EEEEeCCC-HHHHHHHHHHHHCCCceee-eeecCHHHHHH
Confidence 56888999999887754432 12211 23478875 6667777899999999887 88999999863
No 50
>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=24.90 E-value=59 Score=27.25 Aligned_cols=53 Identities=15% Similarity=0.154 Sum_probs=34.1
Q ss_pred HHHHHHHHHhhcccHHHHHHHHH-HHHHHhcCCCHHHHhcCCHHH-HHHhhcCcchhH
Q 017244 210 FELLVLTAAQVGSDWTSVLKKRQ-AFREAFSGFDAEVVAKFTEKK-MTSLSANYAIDL 265 (375)
Q Consensus 210 FEmL~LEgfQAGLSW~tVLkKRe-afReAF~gFD~ekVA~~tEed-IerLl~D~gIIR 265 (375)
.+.|.--+-+.|..|..++++|. .|++.= .+ +++..+++++ ++.|+++|.+|+
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 33443334567888999999997 455542 22 3456777665 567777888875
No 51
>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=24.82 E-value=39 Score=29.21 Aligned_cols=25 Identities=20% Similarity=0.595 Sum_probs=16.9
Q ss_pred CHHHHHHHHHHHHcCCCccchhhHH
Q 017244 315 TSKSEAISKDMVKKGFRFVGPTVIH 339 (375)
Q Consensus 315 t~lS~~iSKdLKKrGFkFVGPTtiY 339 (375)
.++++.+.+....+||.|+||++|.
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 3577778888889999999999864
No 52
>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=24.63 E-value=40 Score=31.79 Aligned_cols=34 Identities=32% Similarity=0.390 Sum_probs=27.6
Q ss_pred CCCCCCHHHHHHHHHHHHcCCCccchhhHHHHHHHh
Q 017244 310 KIPVKTSKSEAISKDMVKKGFRFVGPTVIHSFMQAA 345 (375)
Q Consensus 310 ~iP~~t~lS~~iSKdLKKrGFkFVGPTtiYSFMQAv 345 (375)
+||.+. ..-...+.|++.|.+ +|-|+||+..||.
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 677766 555677999999977 7779999999975
No 53
>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=24.57 E-value=49 Score=24.51 Aligned_cols=19 Identities=21% Similarity=0.534 Sum_probs=16.3
Q ss_pred HHHHHHHHHHcCCCccchh
Q 017244 318 SEAISKDMVKKGFRFVGPT 336 (375)
Q Consensus 318 S~~iSKdLKKrGFkFVGPT 336 (375)
.+.+.+.|++.||++.+|.
T Consensus 54 ~~~~~~~L~~~G~~v~~~~ 72 (72)
T cd04883 54 PRPIIEDLRRAGYEVLWPN 72 (72)
T ss_pred HHHHHHHHHHCCCeeeCCC
Confidence 4578899999999999983
No 54
>PRK12346 transaldolase A; Provisional
Probab=24.11 E-value=1.1e+02 Score=31.12 Aligned_cols=63 Identities=19% Similarity=0.296 Sum_probs=45.6
Q ss_pred HHHHHHhhHHHHHHHHHhhCCHHHhcccccCCccccCCCCCCCCCCCCCHHHHHHHHHHHHcCCCccchhhHHHHHHHhc
Q 017244 267 QVRGIVDNSIRILEVKKQFGSFDKYLWGFVNHKPINTQYRSSQKIPVKTSKSEAISKDMVKKGFRFVGPTVIHSFMQAAG 346 (375)
Q Consensus 267 KI~AVI~NArail~i~~E~GSF~~ylWsFv~~kpi~~~~~~~~~iP~~t~lS~~iSKdLKKrGFkFVGPTtiYSFMQAvG 346 (375)
-.+++|..|+.+.++-++.| ++.. .-+=+||+ |....+-++.|++.|.+--. |.+||+-|+.-
T Consensus 103 d~e~~i~~A~~l~~l~~~~g---------i~~~------~i~IKIPa-T~eGi~A~~~L~~~GI~~n~-TliFS~~Qa~~ 165 (316)
T PRK12346 103 DREKSIEKARHLVDLYQQQG---------IDKS------RILIKLAS-TWEGIRAAEELEKEGINCNL-TLLFSFAQARA 165 (316)
T ss_pred CHHHHHHHHHHHHHHhhhcC---------CCCC------cEEEEeCC-CHHHHHHHHHHHHCCCceeE-EEecCHHHHHH
Confidence 56889999999988855433 1211 12347885 55666667999999999877 88999999853
No 55
>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=23.93 E-value=36 Score=31.07 Aligned_cols=31 Identities=19% Similarity=0.332 Sum_probs=23.0
Q ss_pred HHHHHHHHHHhcCCCHHHHhcCCHHHHHHhh
Q 017244 228 LKKRQAFREAFSGFDAEVVAKFTEKKMTSLS 258 (375)
Q Consensus 228 LkKReafReAF~gFD~ekVA~~tEedIerLl 258 (375)
..|++.|+|++-+|-+..|++++-+..|.|-
T Consensus 69 ktk~DeY~EaLRDfq~~~iaKle~e~Ae~vY 99 (139)
T PF12583_consen 69 KTKWDEYSEALRDFQCSWIAKLEPENAEQVY 99 (139)
T ss_dssp ---HHHHHHHHHHHHHHHHTTS-HHHHHHHH
T ss_pred cccHHHHHHHHHHHHHHHHHhhCHHHHHHHH
Confidence 3578999999999999999999886665443
No 56
>cd00957 Transaldolase_TalAB Transaldolases including both TalA and TalB. The enzyme catalyses the reversible transfer of a dyhydroxyacetone moiety, derived from fructose-6-phosphate to erythrose-4-phosphate yielding sedoheptulose-7-phosphate and glyceraldehyde-3-phosphate. The catalytic mechanism is similar to other class I aldolases. The enzyme is found in the non-oxidative branch of the pentose phosphate pathway and forms a dimer in solution.
Probab=23.75 E-value=1e+02 Score=31.16 Aligned_cols=63 Identities=17% Similarity=0.292 Sum_probs=45.6
Q ss_pred HHHHHHhhHHHHHHHHHhhCCHHHhcccccCCccccCCCCCCCCCCCCCHHHHHHHHHHHHcCCCccchhhHHHHHHHhc
Q 017244 267 QVRGIVDNSIRILEVKKQFGSFDKYLWGFVNHKPINTQYRSSQKIPVKTSKSEAISKDMVKKGFRFVGPTVIHSFMQAAG 346 (375)
Q Consensus 267 KI~AVI~NArail~i~~E~GSF~~ylWsFv~~kpi~~~~~~~~~iP~~t~lS~~iSKdLKKrGFkFVGPTtiYSFMQAvG 346 (375)
-.+++|..|+.+.++-++.| ++... -+=+||++. ...+-++.|++.|.+--. |.+||+-||.-
T Consensus 102 d~~~~i~~A~~l~~~~~~~g---------i~~~~------i~IKIPaT~-eGi~A~~~L~~~GI~vn~-TlvFS~~Qa~~ 164 (313)
T cd00957 102 DTNATIAKARKLIKLYEEAG---------IDKER------ILIKIAATW-EGIQAAKQLEKEGIHCNL-TLLFSFAQAVA 164 (313)
T ss_pred CHHHHHHHHHHHHHHhHhcC---------CCCCc------EEEEeCCCH-HHHHHHHHHHHCCCceee-eeecCHHHHHH
Confidence 56889999999988755543 22222 234788654 466667999999999877 88999999863
No 57
>COG4081 Uncharacterized protein conserved in archaea [Function unknown]
Probab=23.65 E-value=58 Score=29.87 Aligned_cols=26 Identities=31% Similarity=0.479 Sum_probs=22.8
Q ss_pred CCCCCCCCHHHHHHHHHHHHcCCCcc
Q 017244 308 SQKIPVKTSKSEAISKDMVKKGFRFV 333 (375)
Q Consensus 308 ~~~iP~~t~lS~~iSKdLKKrGFkFV 333 (375)
.-++|.+.+...-+|..||++||.-.
T Consensus 11 CPeiP~qissaiYls~klkkkgf~v~ 36 (148)
T COG4081 11 CPEIPPQISSAIYLSHKLKKKGFDVT 36 (148)
T ss_pred CCCCCccchHHHHHHHHhhccCccEE
Confidence 45789999999999999999999853
No 58
>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=23.64 E-value=83 Score=26.84 Aligned_cols=32 Identities=19% Similarity=0.209 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHc--CCCccchhhHHHHHHH-hcc
Q 017244 316 SKSEAISKDMVKK--GFRFVGPTVIHSFMQA-AGL 347 (375)
Q Consensus 316 ~lS~~iSKdLKKr--GFkFVGPTtiYSFMQA-vG~ 347 (375)
+....+++.|.+. ||+++.....+.||+. .|+
T Consensus 12 ~~~~~~a~~~~~ll~Gf~i~AT~gTa~~L~~~~Gi 46 (115)
T cd01422 12 EDLVEFVKQHQELLSRHRLVATGTTGLLIQEATGL 46 (115)
T ss_pred HHHHHHHHHHHHHhcCCEEEEechHHHHHHHhhCC
Confidence 4566788999999 9999999999999999 886
No 59
>PRK01172 ski2-like helicase; Provisional
Probab=23.55 E-value=1.7e+02 Score=31.76 Aligned_cols=47 Identities=11% Similarity=0.248 Sum_probs=36.5
Q ss_pred HHHHHHhcC--CCHHHHhcCCHHHHHHhhcCcchhHHHHHHHHhhHHHHHHH
Q 017244 232 QAFREAFSG--FDAEVVAKFTEKKMTSLSANYAIDLSQVRGIVDNSIRILEV 281 (375)
Q Consensus 232 eafReAF~g--FD~ekVA~~tEedIerLl~D~gIIR~KI~AVI~NArail~i 281 (375)
...|+.|.. -++..|+.++++++++|+ ++-..+.+.||..|+.+++|
T Consensus 623 ~~a~~l~~~g~~~~~di~~~~~~~~~~i~---~~~~~~~~~i~~~~~~~~~~ 671 (674)
T PRK01172 623 VRARRLYDAGFKTVDDIARSSPERIKKIY---GFSDTLANAIVNRAMKISSM 671 (674)
T ss_pred HHHHHHHHcCCCCHHHHHhCCHHHHHHHh---ccCHHHHHHHHHHHHHHHHH
Confidence 444555553 368888999999999986 46668999999999999876
No 60
>TIGR00874 talAB transaldolase. This family includes the majority of known and predicted transaldolase sequences, including E. coli TalA and TalB. It excluded two other families. The first includes E. coli transaldolase-like protein TalC. The second family includes the putative transaldolases of Helicobacter pylori and Mycobacterium tuberculosis.
Probab=23.05 E-value=1.2e+02 Score=30.80 Aligned_cols=63 Identities=22% Similarity=0.335 Sum_probs=45.9
Q ss_pred HHHHHHhhHHHHHHHHHhhCCHHHhcccccCCccccCCCCCCCCCCCCCHHHHHHHHHHHHcCCCccchhhHHHHHHHhc
Q 017244 267 QVRGIVDNSIRILEVKKQFGSFDKYLWGFVNHKPINTQYRSSQKIPVKTSKSEAISKDMVKKGFRFVGPTVIHSFMQAAG 346 (375)
Q Consensus 267 KI~AVI~NArail~i~~E~GSF~~ylWsFv~~kpi~~~~~~~~~iP~~t~lS~~iSKdLKKrGFkFVGPTtiYSFMQAvG 346 (375)
-.+++|..|+.+.++-++.| ++.. .-+=+||++ .....-.+.|.+.|.+--. |.+||+-|+.-
T Consensus 102 d~~~~i~~A~~l~~l~~~~g---------i~~~------~v~IKIPaT-~eGi~A~~~L~~~GI~vN~-TliFS~~Qa~a 164 (317)
T TIGR00874 102 DTEATVEKARHLIKLYEDAG---------VDKK------RILIKIAST-WEGIRAAEELEKEGIHCNL-TLLFSFVQAIA 164 (317)
T ss_pred CHHHHHHHHHHHHHHhHhcC---------CCCC------cEEEEeCCC-HHHHHHHHHHHHCCCceee-eeecCHHHHHH
Confidence 56889999999988755433 2221 123478875 6666677999999999776 88999999863
No 61
>PF11460 DUF3007: Protein of unknown function (DUF3007); InterPro: IPR021562 This is a family of uncharacterised proteins found in bacteria and eukaryotes.
Probab=22.66 E-value=83 Score=27.53 Aligned_cols=33 Identities=18% Similarity=0.464 Sum_probs=26.2
Q ss_pred HHHHHHHHHHhcCCCHH----HHhcCCHHHHHHhhcC
Q 017244 228 LKKRQAFREAFSGFDAE----VVAKFTEKKMTSLSAN 260 (375)
Q Consensus 228 LkKReafReAF~gFD~e----kVA~~tEedIerLl~D 260 (375)
-.-|..||+|++.+--+ ++.+|+++++++|+++
T Consensus 65 ~~Q~k~Ye~a~~~~~~~~lqkRle~l~~eE~~~L~~e 101 (104)
T PF11460_consen 65 MQQRKDYEEAVDQLTNEELQKRLEELSPEELEALQAE 101 (104)
T ss_pred HHHHHHHHHHHHHHhHHHHHHHHHhCCHHHHHHHHHH
Confidence 35689999999776655 4578999999999864
No 62
>cd00439 Transaldolase Transaldolase. Enzymes found in the non-oxidative branch of the pentose phosphate pathway, that catalyze the reversible transfer of a dihydroxyacetone group from fructose-6-phosphate to erythrose-4-phosphate yielding sedoheptulose-7-phosphate and glyceraldehyde-3-phosphate. They are members of the class I aldolases, who are characterized by using a Schiff-base mechanism for stabilization of the reaction intermediates.
Probab=22.35 E-value=84 Score=30.56 Aligned_cols=57 Identities=25% Similarity=0.338 Sum_probs=40.2
Q ss_pred HHHHHHhhHHHHHHHHHhhCCHHHhcccccCCccccCCCCCCCCCCCCCHHHHHHHHHHHHcCCCccchhhHHHHHHHh
Q 017244 267 QVRGIVDNSIRILEVKKQFGSFDKYLWGFVNHKPINTQYRSSQKIPVKTSKSEAISKDMVKKGFRFVGPTVIHSFMQAA 345 (375)
Q Consensus 267 KI~AVI~NArail~i~~E~GSF~~ylWsFv~~kpi~~~~~~~~~iP~~t~lS~~iSKdLKKrGFkFVGPTtiYSFMQAv 345 (375)
-.+++|..|+.+.++..+ ++ -.=+||+ |...-+-.+.|++.|.+--+ |.||++.|+.
T Consensus 98 d~~~mi~~A~~l~~~~~~------------~n--------v~IKIPa-T~~Gl~A~~~L~~~GI~vn~-T~vfs~~Qa~ 154 (252)
T cd00439 98 DTQGMVEAAKYLSKVVNR------------RN--------IYIKIPA-TAEGIPAIKDLIAAGISVNV-TLIFSIAQYE 154 (252)
T ss_pred CHHHHHHHHHHHHHhcCc------------cc--------EEEEeCC-CHHHHHHHHHHHHCCCceee-eeecCHHHHH
Confidence 456777888887665221 01 1236886 45666677999999999887 8899999975
No 63
>PF12023 DUF3511: Domain of unknown function (DUF3511); InterPro: IPR021899 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 50 amino acids in length. This domain has two completely conserved residues (Y and K) that may be functionally important.
Probab=22.34 E-value=41 Score=25.63 Aligned_cols=21 Identities=48% Similarity=0.646 Sum_probs=15.6
Q ss_pred HHHHHhhhhccCCCCcccccCCCC
Q 017244 139 QEQRKLRIAHYGRTKSAKFEGKVP 162 (375)
Q Consensus 139 q~qrk~~iah~~~~~~~~~~~~~~ 162 (375)
..|||.|||-| |.--+||||-
T Consensus 7 E~kRkkRVA~Y---k~y~vEGKvK 27 (47)
T PF12023_consen 7 EMKRKKRVASY---KVYAVEGKVK 27 (47)
T ss_pred HHHHHHHHHhh---heeeeehHHH
Confidence 57999999999 4455677653
No 64
>PF03960 ArsC: ArsC family; InterPro: IPR006660 Several bacterial taxon have a chromosomal resistance system, encoded by the ars operon, for the detoxification of arsenate, arsenite, and antimonite []. This system transports arsenite and antimonite out of the cell. The pump is composed of two polypeptides, the products of the arsA and arsB genes. This two-subunit enzyme produces resistance to arsenite and antimonite. Arsenate, however, must first be reduced to arsenite before it is extruded. A third gene, arsC, expands the substrate specificity to allow for arsenate pumping and resistance. ArsC is an approximately 150-residue arsenate reductase that uses reduced glutathione (GSH) to convert arsenate to arsenite with a redox active cysteine residue in the active site. ArsC forms an active quaternary complex with GSH, arsenate, and glutaredoxin 1 (Grx1). The three ligands must be present simultaneously for reduction to occur []. The arsC family also comprises the Spx proteins which are GRAM-positive bacterial transcription factors that regulate the transcription of multiple genes in response to disulphide stress []. The arsC protein structure has been solved []. It belongs to the thioredoxin superfamily fold which is defined by a beta-sheet core surrounded by alpha-helices. The active cysteine residue of ArsC is located in the loop between the first beta-strand and the first helix, which is also conserved in the Spx protein and its homologues.; PDB: 2KOK_A 1SK1_A 1SK2_A 1JZW_A 1J9B_A 1S3C_A 1SD8_A 1SD9_A 1I9D_A 1SK0_A ....
Probab=22.00 E-value=49 Score=27.48 Aligned_cols=53 Identities=17% Similarity=0.231 Sum_probs=34.5
Q ss_pred ChHHHHHHHHHHHHhhcccHHHHHHHHH-HHHHHhcCCCHHHHhcCCHHHH-HHhhcCcchhH
Q 017244 205 DDKLLFELLVLTAAQVGSDWTSVLKKRQ-AFREAFSGFDAEVVAKFTEKKM-TSLSANYAIDL 265 (375)
Q Consensus 205 DDr~LFEmL~LEgfQAGLSW~tVLkKRe-afReAF~gFD~ekVA~~tEedI-erLl~D~gIIR 265 (375)
+...|-+++ .+.|..|..+++++. .|++.. -.....++++++ +-|+++|.+|+
T Consensus 34 s~~el~~~l----~~~~~~~~~lin~~~~~~k~l~----~~~~~~~s~~e~i~~l~~~p~Lik 88 (110)
T PF03960_consen 34 SREELRELL----SKLGNGPDDLINTRSKTYKELG----KLKKDDLSDEELIELLLENPKLIK 88 (110)
T ss_dssp -HHHHHHHH----HHHTSSGGGGB-TTSHHHHHTT----HHHCTTSBHHHHHHHHHHSGGGB-
T ss_pred CHHHHHHHH----HHhcccHHHHhcCccchHhhhh----hhhhhhhhhHHHHHHHHhChhhee
Confidence 445555555 566888999999884 555544 445578888886 56666888875
No 65
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=21.84 E-value=95 Score=22.24 Aligned_cols=28 Identities=14% Similarity=0.201 Sum_probs=23.8
Q ss_pred CHHHHHHhhcCcchhHHHHHHHHhhHHH
Q 017244 250 TEKKMTSLSANYAIDLSQVRGIVDNSIR 277 (375)
Q Consensus 250 tEedIerLl~D~gIIR~KI~AVI~NAra 277 (375)
++++.+.|+...|+-+..|..=..|||.
T Consensus 12 s~~ek~~L~~~tgls~~Qi~~WF~NaRr 39 (40)
T PF05920_consen 12 SKEEKEELAKQTGLSRKQISNWFINARR 39 (40)
T ss_dssp -HHHHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHcCCCHHHHHHHHHHhHc
Confidence 6788999999999999999999999985
No 66
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=20.10 E-value=45 Score=26.89 Aligned_cols=45 Identities=9% Similarity=0.165 Sum_probs=32.7
Q ss_pred HHHHHHHHHHhcCCCHHHHhcCCHHHHHHhhcCcchhHHHHHHHH
Q 017244 228 LKKRQAFREAFSGFDAEVVAKFTEKKMTSLSANYAIDLSQVRGIV 272 (375)
Q Consensus 228 LkKReafReAF~gFD~ekVA~~tEedIerLl~D~gIIR~KI~AVI 272 (375)
-.-...|+++|.-||.+.=-.++-+++.++|...++-...|+.++
T Consensus 6 ~~~~~~l~~~F~~~D~d~~G~Is~~el~~~l~~~~~~~~ev~~i~ 50 (96)
T smart00027 6 PEDKAKYEQIFRSLDKNQDGTVTGAQAKPILLKSGLPQTLLAKIW 50 (96)
T ss_pred HHHHHHHHHHHHHhCCCCCCeEeHHHHHHHHHHcCCCHHHHHHHH
Confidence 345678999999999887778889999998877665433344333
Done!