Query 041076
Match_columns 420
No_of_seqs 155 out of 1139
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 03:34:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041076.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041076hhsearch_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 2.6E-83 5.7E-88 591.9 19.0 181 209-391 1-183 (187)
2 TIGR00624 tag DNA-3-methyladen 100.0 4E-81 8.6E-86 574.1 18.5 177 210-390 1-179 (179)
3 COG2818 Tag 3-methyladenine DN 100.0 2.1E-79 4.5E-84 564.9 16.8 184 209-393 1-186 (188)
4 PF03352 Adenine_glyco: Methyl 100.0 1.3E-79 2.8E-84 564.0 15.2 177 214-392 1-179 (179)
5 TIGR01083 nth endonuclease III 95.9 0.12 2.6E-06 47.9 11.4 102 240-377 25-126 (191)
6 TIGR03252 uncharacterized HhH- 95.6 0.26 5.7E-06 46.6 12.6 115 241-378 18-136 (177)
7 cd00056 ENDO3c endonuclease II 95.4 0.23 4.9E-06 43.7 10.9 104 242-378 1-104 (158)
8 smart00478 ENDO3c endonuclease 95.2 0.2 4.4E-06 43.7 10.0 88 254-377 5-92 (149)
9 PRK13913 3-methyladenine DNA g 95.2 0.17 3.7E-06 48.9 10.1 105 242-376 31-140 (218)
10 PRK10702 endonuclease III; Pro 94.3 0.35 7.6E-06 46.2 9.8 70 241-312 29-98 (211)
11 PF00730 HhH-GPD: HhH-GPD supe 93.5 0.45 9.7E-06 39.3 7.9 63 249-311 4-66 (108)
12 COG0177 Nth Predicted EndoIII- 88.1 3 6.5E-05 40.5 8.8 76 239-319 27-102 (211)
13 PRK10880 adenine DNA glycosyla 86.5 4 8.7E-05 42.2 9.2 68 241-311 30-97 (350)
14 TIGR01084 mutY A/G-specific ad 85.6 4.2 9.1E-05 40.5 8.5 69 240-311 25-93 (275)
15 PRK01229 N-glycosylase/DNA lya 83.3 8.1 0.00017 37.4 9.1 66 237-310 33-100 (208)
16 COG2231 Uncharacterized protei 78.3 20 0.00044 35.3 9.9 79 221-304 14-92 (215)
17 COG1393 ArsC Arsenate reductas 76.0 2.6 5.7E-05 37.1 3.0 67 224-297 26-92 (117)
18 PF02142 MGS: MGS-like domain 59.1 8.3 0.00018 31.8 2.5 29 352-380 4-32 (95)
19 PF10023 DUF2265: Predicted am 58.0 30 0.00065 36.1 6.8 104 284-392 33-161 (337)
20 cd00166 SAM Sterile alpha moti 56.6 28 0.0006 25.4 4.7 43 264-306 17-61 (63)
21 COG0122 AlkA 3-methyladenine D 46.3 93 0.002 31.3 8.0 69 239-311 103-179 (285)
22 PRK10308 3-methyl-adenine DNA 43.0 1.1E+02 0.0024 30.6 8.0 120 229-381 101-232 (283)
23 PF00536 SAM_1: SAM domain (St 42.4 51 0.0011 24.8 4.3 42 264-306 18-62 (64)
24 COG0632 RuvA Holliday junction 41.4 90 0.0019 30.3 6.8 78 224-318 54-133 (201)
25 PRK13344 spxA transcriptional 41.0 25 0.00053 31.3 2.8 80 209-297 7-91 (132)
26 KOG2198 tRNA cytosine-5-methyl 40.6 37 0.0008 36.0 4.3 112 256-380 19-146 (375)
27 PTZ00411 transaldolase-like pr 40.1 43 0.00092 34.7 4.7 63 299-378 114-176 (333)
28 PF07647 SAM_2: SAM domain (St 39.0 44 0.00095 25.2 3.5 43 264-306 19-64 (66)
29 PF13495 Phage_int_SAM_4: Phag 38.9 1.5E+02 0.0033 22.9 6.7 52 241-292 1-52 (85)
30 smart00851 MGS MGS-like domain 36.0 35 0.00076 27.7 2.7 28 352-379 4-31 (90)
31 PF13276 HTH_21: HTH-like doma 33.4 49 0.0011 25.0 3.0 30 351-380 24-53 (60)
32 TIGR00588 ogg 8-oxoguanine DNA 33.2 1.9E+02 0.0041 29.3 7.9 88 219-311 98-198 (310)
33 TIGR01529 argR_whole arginine 32.5 45 0.00098 30.3 3.1 30 351-381 20-49 (146)
34 cd00532 MGS-like MGS-like doma 31.9 51 0.0011 28.0 3.2 32 348-379 12-43 (112)
35 cd03678 MM_CoA_mutase_1 Coenzy 30.8 16 0.00035 39.8 -0.1 59 262-325 145-226 (495)
36 PF00289 CPSase_L_chain: Carba 29.2 77 0.0017 27.4 3.9 21 349-369 87-107 (110)
37 PF13068 DUF3932: Protein of u 28.8 12 0.00025 31.2 -1.2 30 310-339 4-34 (81)
38 PRK05269 transaldolase B; Prov 28.4 89 0.0019 32.1 4.7 64 299-379 104-167 (318)
39 cd03023 DsbA_Com1_like DsbA fa 28.1 3.2E+02 0.0069 22.7 7.3 29 280-308 82-110 (154)
40 PF07862 Nif11: Nitrogen fixat 28.0 65 0.0014 23.7 2.8 37 281-318 1-40 (49)
41 cd00052 EH Eps15 homology doma 27.8 35 0.00075 25.0 1.3 30 266-295 1-30 (67)
42 PRK10548 flagellar biosynthesi 27.7 1.3E+02 0.0029 26.9 5.1 80 241-322 17-111 (121)
43 cd01424 MGS_CPS_II Methylglyox 27.6 69 0.0015 26.8 3.2 31 349-379 14-44 (110)
44 cd03036 ArsC_like Arsenate Red 27.5 56 0.0012 27.8 2.7 57 238-297 34-92 (111)
45 PRK12309 transaldolase/EF-hand 26.7 98 0.0021 32.7 4.8 64 299-379 108-171 (391)
46 PHA02517 putative transposase 26.6 68 0.0015 30.7 3.4 30 351-381 49-78 (277)
47 smart00454 SAM Sterile alpha m 26.3 1.9E+02 0.0041 21.0 5.0 42 266-307 21-65 (68)
48 PF03960 ArsC: ArsC family; I 25.4 37 0.00079 28.6 1.2 54 236-297 33-88 (110)
49 cd04883 ACT_AcuB C-terminal AC 24.6 51 0.0011 24.8 1.7 19 350-368 54-72 (72)
50 COG4081 Uncharacterized protei 24.0 57 0.0012 30.4 2.2 26 340-365 11-36 (148)
51 PF07755 DUF1611: Protein of u 23.3 54 0.0012 33.6 2.1 47 349-396 129-178 (301)
52 PF12401 DUF3662: Protein of u 22.7 44 0.00096 29.3 1.2 25 347-371 76-100 (116)
53 PF05075 DUF684: Protein of un 22.3 1.1E+02 0.0024 31.3 4.2 76 238-313 115-212 (345)
54 cd01422 MGS Methylglyoxal synt 22.2 92 0.002 26.9 3.1 32 348-379 12-46 (115)
55 PF12583 TPPII_N: Tripeptidyl 21.8 41 0.0009 31.2 0.9 30 260-289 69-98 (139)
56 PLN02764 glycosyltransferase f 21.1 1.3E+02 0.0028 32.2 4.5 83 231-329 359-441 (453)
57 PF13348 Y_phosphatase3C: Tyro 20.9 80 0.0017 24.4 2.2 20 309-328 34-53 (68)
58 cd00956 Transaldolase_FSA Tran 20.8 54 0.0012 31.3 1.4 34 342-377 83-116 (211)
59 smart00027 EH Eps15 homology d 20.3 47 0.001 27.1 0.9 45 260-304 6-50 (96)
60 PF14493 HTH_40: Helix-turn-he 20.2 3E+02 0.0065 22.5 5.5 43 244-288 4-57 (91)
61 PRK14606 ruvA Holliday junctio 20.0 2.5E+02 0.0055 26.7 5.7 80 222-317 47-132 (188)
No 1
>PRK10353 3-methyl-adenine DNA glycosylase I; Provisional
Probab=100.00 E-value=2.6e-83 Score=591.93 Aligned_cols=181 Identities=37% Similarity=0.775 Sum_probs=177.0
Q ss_pred CCCCcCccCCCChhhhhhhhcCCCcccCChHHHHHHHHHHHHhccccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHH
Q 041076 209 EKRCSFITAYSDPIFVAYHDEEWGVPVRNDNMLFELLVLSGAQVGSDWTSILKKRQGFRDAFSGFEAETVAKLSDKQMMS 288 (420)
Q Consensus 209 ~~RC~W~~~~~dply~~YHD~EWG~Pv~DDr~LFEmL~LEgFQAGLSW~tVLkKReafReAF~gFDpekVA~~~EedIer 288 (420)
|.||.|++ +||+|++|||+|||+|+|||+.|||+||||+|||||||.|||+||++||+||+||||++||+|+|+|||+
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 041076 289 ISTEYSIDM--SRVRGVVDNSNRILEVKRVFGSFEKYIWGFVNHKPISTQYKFGHKIPVKTSKSESISKDMVRRGFRFVG 366 (420)
Q Consensus 289 Ll~D~gIIR--~KI~AVI~NAraiL~I~~E~GSF~~yLWsFv~~kpI~~~~~~~~~iP~~T~lS~~LSKdLKKrGFkFVG 366 (420)
||+|++||| +||+|||+|||++++|++|||||++|||+||+++||++++....++|++|++|++|||+||||||+|||
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 999999996 799999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhHHHHHHHhcccccccccccccc
Q 041076 367 PTVVHSFMQAAGLTNDHLIICHRHL 391 (420)
Q Consensus 367 PTtvYSFMQAiGlVNDHl~~C~~~~ 391 (420)
|||||+||||+||||||+++|+++.
T Consensus 159 pt~~ysfmqA~G~vndH~~~C~~~~ 183 (187)
T PRK10353 159 TTICYSFMQACGLVNDHVVGCCCHP 183 (187)
T ss_pred cHHHHHHHHHHCCccccccCccccC
Confidence 9999999999999999999999883
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=4e-81 Score=574.08 Aligned_cols=177 Identities=37% Similarity=0.777 Sum_probs=173.0
Q ss_pred CCCcCccCCCChhhhhhhhcCCCcccCChHHHHHHHHHHHHhccccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHh
Q 041076 210 KRCSFITAYSDPIFVAYHDEEWGVPVRNDNMLFELLVLSGAQVGSDWTSILKKRQGFRDAFSGFEAETVAKLSDKQMMSI 289 (420)
Q Consensus 210 ~RC~W~~~~~dply~~YHD~EWG~Pv~DDr~LFEmL~LEgFQAGLSW~tVLkKReafReAF~gFDpekVA~~~EedIerL 289 (420)
.||.|++ +||+|++|||+|||+|+|||+.|||+||||+|||||||.|||+||++||+||+||||++||.|+|+|||+|
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 041076 290 STEYSIDM--SRVRGVVDNSNRILEVKRVFGSFEKYIWGFVNHKPISTQYKFGHKIPVKTSKSESISKDMVRRGFRFVGP 367 (420)
Q Consensus 290 l~D~gIIR--~KI~AVI~NAraiL~I~~E~GSF~~yLWsFv~~kpI~~~~~~~~~iP~~T~lS~~LSKdLKKrGFkFVGP 367 (420)
|+|++||| +||+|||+|||++++|++| ||++|||+||+++||++++....++|++|++|++|||+||||||+||||
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 99999996 6999999999999999888 9999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHHhccccccccccccc
Q 041076 368 TVVHSFMQAAGLTNDHLIICHRH 390 (420)
Q Consensus 368 TtvYSFMQAiGlVNDHl~~C~~~ 390 (420)
||||+||||+||||||+++|+++
T Consensus 157 t~~ysfmqA~G~vndH~~~C~~~ 179 (179)
T TIGR00624 157 TICYALMQATGMVDDHIQGCWVY 179 (179)
T ss_pred HHHHHHHHHHCCccccccCCcCC
Confidence 99999999999999999999875
No 3
>COG2818 Tag 3-methyladenine DNA glycosylase [DNA replication, recombination, and repair]
Probab=100.00 E-value=2.1e-79 Score=564.85 Aligned_cols=184 Identities=41% Similarity=0.821 Sum_probs=178.6
Q ss_pred CCCCcCccCCCChhhhhhhhcCCCcccCChHHHHHHHHHHHHhccccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHH
Q 041076 209 EKRCSFITAYSDPIFVAYHDEEWGVPVRNDNMLFELLVLSGAQVGSDWTSILKKRQGFRDAFSGFEAETVAKLSDKQMMS 288 (420)
Q Consensus 209 ~~RC~W~~~~~dply~~YHD~EWG~Pv~DDr~LFEmL~LEgFQAGLSW~tVLkKReafReAF~gFDpekVA~~~EedIer 288 (420)
+.||.|+. ..||+|.+|||+|||+|++||+.|||+||||+|||||||.|||+||++||+||++|||++||.|+|+|||+
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 47999985 34899999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhcCcChhH--HHHHHHHhhHHHHHHHHHhhCCHhHhccccCCCcccccccccCCCCCCCChHHHHHHHHHHHcCCcccc
Q 041076 289 ISTEYSIDM--SRVRGVVDNSNRILEVKRVFGSFEKYIWGFVNHKPISTQYKFGHKIPVKTSKSESISKDMVRRGFRFVG 366 (420)
Q Consensus 289 Ll~D~gIIR--~KI~AVI~NAraiL~I~~E~GSF~~yLWsFv~~kpI~~~~~~~~~iP~~T~lS~~LSKdLKKrGFkFVG 366 (420)
||+|+|||| +||+|+|+|||++|+|++|||||++|||+|++++|+.+++.+..++|+.|++|++|||+||||||+|||
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 hhhHHHHHHHhccccccccccccccch
Q 041076 367 PTVVHSFMQAAGLTNDHLIICHRHLPC 393 (420)
Q Consensus 367 PTtvYSFMQAiGlVNDHl~~C~~~~~~ 393 (420)
|||||+||||+||||||+.+|+++..+
T Consensus 160 pTt~yafmqA~G~vndH~~~C~~~~~~ 186 (188)
T COG2818 160 PTTVYAFMQATGLVNDHAEGCPCRREI 186 (188)
T ss_pred cHHHHHHHHHHcchHHHHhcCCCcccc
Confidence 999999999999999999999988653
No 4
>PF03352 Adenine_glyco: Methyladenine glycosylase; InterPro: IPR005019 This family of methyladenine glycosylases includes DNA-3-methyladenine glycosylase I (3.2.2.20 from EC) which acts as a base excision repair enzyme by severing the glycosylic bond of numerous damaged bases. The enzyme is constitutively expressed and is specific for the alkylated 3-methyladenine DNA.; GO: 0008725 DNA-3-methyladenine glycosylase I activity, 0006284 base-excision repair; PDB: 2OFI_A 2OFK_A 2JG6_A 4AIA_E 4AI5_C 4AI4_A 1LMZ_A 1P7M_A 1NKU_A.
Probab=100.00 E-value=1.3e-79 Score=564.01 Aligned_cols=177 Identities=48% Similarity=0.927 Sum_probs=152.8
Q ss_pred CccCCCChhhhhhhhcCCCcccCChHHHHHHHHHHHHhccccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhhcCc
Q 041076 214 FITAYSDPIFVAYHDEEWGVPVRNDNMLFELLVLSGAQVGSDWTSILKKRQGFRDAFSGFEAETVAKLSDKQMMSISTEY 293 (420)
Q Consensus 214 W~~~~~dply~~YHD~EWG~Pv~DDr~LFEmL~LEgFQAGLSW~tVLkKReafReAF~gFDpekVA~~~EedIerLl~D~ 293 (420)
|+. ++|+|++|||+|||+|+|||+.|||+||||+|||||||.+||+||++||+||+||||++||+|+|+||++||+|+
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 799999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ChhH--HHHHHHHhhHHHHHHHHHhhCCHhHhccccCCCcccccccccCCCCCCCChHHHHHHHHHHHcCCcccchhhHH
Q 041076 294 SIDM--SRVRGVVDNSNRILEVKRVFGSFEKYIWGFVNHKPISTQYKFGHKIPVKTSKSESISKDMVRRGFRFVGPTVVH 371 (420)
Q Consensus 294 gIIR--~KI~AVI~NAraiL~I~~E~GSF~~yLWsFv~~kpI~~~~~~~~~iP~~T~lS~~LSKdLKKrGFkFVGPTtvY 371 (420)
+||| +||+|||+||+++++|++|||||++|||+|++++||++.+....++|++|++|++|||+||||||+||||||||
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 9986 79999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhccccccccccccccc
Q 041076 372 SFMQAAGLTNDHLIICHRHLP 392 (420)
Q Consensus 372 SFMQAiGlVNDHl~~C~~~~~ 392 (420)
|||||+||||||+++|++|.+
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 5
>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=95.87 E-value=0.12 Score=47.88 Aligned_cols=102 Identities=15% Similarity=0.261 Sum_probs=79.3
Q ss_pred HHHHHHHHHHHhccccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhhcCcChhHHHHHHHHhhHHHHHHHHHhhCC
Q 041076 240 MLFELLVLSGAQVGSDWTSILKKRQGFRDAFSGFEAETVAKLSDKQMMSISTEYSIDMSRVRGVVDNSNRILEVKRVFGS 319 (420)
Q Consensus 240 ~LFEmL~LEgFQAGLSW~tVLkKReafReAF~gFDpekVA~~~EedIerLl~D~gIIR~KI~AVI~NAraiL~I~~E~GS 319 (420)
--||.|+-++.-.-.+|..+.+-...+.+.|- +++.|+..+++++++++.--|+-+.|.+.+++=|+.+++ ++|+
T Consensus 25 dpf~~Li~~ILsqqt~~~~~~~~~~~l~~~~p--t~~~l~~~~~~~L~~~ir~~G~~~~Ka~~i~~~a~~i~~---~~~~ 99 (191)
T TIGR01083 25 NPFELLVATILSAQATDKSVNKATKKLFEVYP--TPQALAQAGLEELEEYIKSIGLYRNKAKNIIALCRILVE---RYGG 99 (191)
T ss_pred CHHHHHHHHHHHhhCcHHHHHHHHHHHHHHCC--CHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHH---HcCC
Confidence 35999999999889999999988888887764 899999999999999999999999999988888887754 3332
Q ss_pred HhHhccccCCCcccccccccCCCCCCCChHHHHHHHHHHHcCCcccchhhHHHHHHHh
Q 041076 320 FEKYIWGFVNHKPISTQYKFGHKIPVKTSKSESISKDMVRRGFRFVGPTVVHSFMQAA 377 (420)
Q Consensus 320 F~~yLWsFv~~kpI~~~~~~~~~iP~~T~lS~~LSKdLKKrGFkFVGPTtvYSFMQAi 377 (420)
++|. .-+.|.+ ++-|||.|+..+|...
T Consensus 100 ----------------------~~~~-------~~~~L~~--l~GIG~ktA~~ill~~ 126 (191)
T TIGR01083 100 ----------------------EVPE-------DREELVK--LPGVGRKTANVVLNVA 126 (191)
T ss_pred ----------------------CCch-------HHHHHHh--CCCCcHHHHHHHHHHH
Confidence 0110 1234544 7889999998887543
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=95.59 E-value=0.26 Score=46.58 Aligned_cols=115 Identities=13% Similarity=0.179 Sum_probs=83.0
Q ss_pred HHHHHHHHHHhccccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhhcCc----ChhHHHHHHHHhhHHHHHHHHHh
Q 041076 241 LFELLVLSGAQVGSDWTSILKKRQGFRDAFSGFEAETVAKLSDKQMMSISTEY----SIDMSRVRGVVDNSNRILEVKRV 316 (420)
Q Consensus 241 LFEmL~LEgFQAGLSW~tVLkKReafReAF~gFDpekVA~~~EedIerLl~D~----gIIR~KI~AVI~NAraiL~I~~E 316 (420)
-||+|+-.+.-+--+|..|.+=-+.+.+.+...|++.++.++.++|++++... |.-++|=+-+++=|+.++ ++
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 39999999999999999999877777544444899999999999999999863 555688777777777763 45
Q ss_pred hCCHhHhccccCCCcccccccccCCCCCCCChHHHHHHHHHHHcCCcccchhhHHHHHHHhc
Q 041076 317 FGSFEKYIWGFVNHKPISTQYKFGHKIPVKTSKSESISKDMVRRGFRFVGPTVVHSFMQAAG 378 (420)
Q Consensus 317 ~GSF~~yLWsFv~~kpI~~~~~~~~~iP~~T~lS~~LSKdLKKrGFkFVGPTtvYSFMQAiG 378 (420)
||+=-.-||.... | . ...+-++|.+ ++-|||.|+--||.-.|
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 6543334453210 1 1 1112244544 78999999999998877
No 7
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=95.38 E-value=0.23 Score=43.72 Aligned_cols=104 Identities=13% Similarity=0.172 Sum_probs=80.6
Q ss_pred HHHHHHHHHhccccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhhcCcChhHHHHHHHHhhHHHHHHHHHhhCCHh
Q 041076 242 FELLVLSGAQVGSDWTSILKKRQGFRDAFSGFEAETVAKLSDKQMMSISTEYSIDMSRVRGVVDNSNRILEVKRVFGSFE 321 (420)
Q Consensus 242 FEmL~LEgFQAGLSW~tVLkKReafReAF~gFDpekVA~~~EedIerLl~D~gIIR~KI~AVI~NAraiL~I~~E~GSF~ 321 (420)
||.|+-.++..-.+|..+.+-...|.+.|. .+++.|+..+++++.++...-| -+.|.+.++.=|+.+. ++++++.
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 7999999999999999988887 6778888888887774 3444433
Q ss_pred HhccccCCCcccccccccCCCCCCCChHHHHHHHHHHHcCCcccchhhHHHHHHHhc
Q 041076 322 KYIWGFVNHKPISTQYKFGHKIPVKTSKSESISKDMVRRGFRFVGPTVVHSFMQAAG 378 (420)
Q Consensus 322 ~yLWsFv~~kpI~~~~~~~~~iP~~T~lS~~LSKdLKKrGFkFVGPTtvYSFMQAiG 378 (420)
. +. +.+-+.|. .++-|||-|+-.+|.-..
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 10 01234455 479999999998887654
No 8
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=95.24 E-value=0.2 Score=43.73 Aligned_cols=88 Identities=11% Similarity=0.290 Sum_probs=68.8
Q ss_pred ccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhhcCcChhHHHHHHHHhhHHHHHHHHHhhCCHhHhccccCCCccc
Q 041076 254 SDWTSILKKRQGFRDAFSGFEAETVAKLSDKQMMSISTEYSIDMSRVRGVVDNSNRILEVKRVFGSFEKYIWGFVNHKPI 333 (420)
Q Consensus 254 LSW~tVLkKReafReAF~gFDpekVA~~~EedIerLl~D~gIIR~KI~AVI~NAraiL~I~~E~GSF~~yLWsFv~~kpI 333 (420)
.+|..+.+-...|.+.|- +|+.|+..++++|++++..-|.-++|.+.+++.|+.+.+ ++++
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 578888888888999887 799999999999999999888888899999999988754 3221
Q ss_pred ccccccCCCCCCCChHHHHHHHHHHHcCCcccchhhHHHHHHHh
Q 041076 334 STQYKFGHKIPVKTSKSESISKDMVRRGFRFVGPTVVHSFMQAA 377 (420)
Q Consensus 334 ~~~~~~~~~iP~~T~lS~~LSKdLKKrGFkFVGPTtvYSFMQAi 377 (420)
++| + ..+.|.+ ++-|||-++-.||...
T Consensus 66 --------~~~------~-~~~~L~~--l~GIG~~tA~~~l~~~ 92 (149)
T smart00478 66 --------EVP------D-DREELLK--LPGVGRKTANAVLSFA 92 (149)
T ss_pred --------Ccc------H-HHHHHHc--CCCCcHHHHHHHHHHH
Confidence 011 1 2345653 8999999998887765
No 9
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=95.16 E-value=0.17 Score=48.90 Aligned_cols=105 Identities=16% Similarity=0.271 Sum_probs=79.8
Q ss_pred HHHHHHHHHhccccHHHHHHhHHHHHHHhc-----CCCHHHHhcCCHHHHHHhhcCcChhHHHHHHHHhhHHHHHHHHHh
Q 041076 242 FELLVLSGAQVGSDWTSILKKRQGFRDAFS-----GFEAETVAKLSDKQMMSISTEYSIDMSRVRGVVDNSNRILEVKRV 316 (420)
Q Consensus 242 FEmL~LEgFQAGLSW~tVLkKReafReAF~-----gFDpekVA~~~EedIerLl~D~gIIR~KI~AVI~NAraiL~I~~E 316 (420)
||.|+-.+.-.--+|..|.+--+.++++|. .-+++.|+..++++|++++.-.|+-|+|.+.+.+=|+.++ ++
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 2389999999999999999999999999999988888874 46
Q ss_pred hCCHhHhccccCCCcccccccccCCCCCCCChHHHHHHHHHHHcCCcccchhhHHHHHHH
Q 041076 317 FGSFEKYIWGFVNHKPISTQYKFGHKIPVKTSKSESISKDMVRRGFRFVGPTVVHSFMQA 376 (420)
Q Consensus 317 ~GSF~~yLWsFv~~kpI~~~~~~~~~iP~~T~lS~~LSKdLKKrGFkFVGPTtvYSFMQA 376 (420)
+|+++.+. . + + .-++|.+ .+-||+-|+-++|--
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 77766321 1 0 0 1133443 677888888887763
No 10
>PRK10702 endonuclease III; Provisional
Probab=94.29 E-value=0.35 Score=46.21 Aligned_cols=70 Identities=16% Similarity=0.131 Sum_probs=61.6
Q ss_pred HHHHHHHHHHhccccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhhcCcChhHHHHHHHHhhHHHHHH
Q 041076 241 LFELLVLSGAQVGSDWTSILKKRQGFRDAFSGFEAETVAKLSDKQMMSISTEYSIDMSRVRGVVDNSNRILE 312 (420)
Q Consensus 241 LFEmL~LEgFQAGLSW~tVLkKReafReAF~gFDpekVA~~~EedIerLl~D~gIIR~KI~AVI~NAraiL~ 312 (420)
-||.|+-++.-+--+|..|.+--+.+.+.| .+++.++..++++|++++.--|.-+.|-+.+++.|+.+++
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 4789999999999999999999988888889999998753
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=93.50 E-value=0.45 Score=39.30 Aligned_cols=63 Identities=10% Similarity=0.117 Sum_probs=57.2
Q ss_pred HHhccccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhhcCcChhHHHHHHHHhhHHHHH
Q 041076 249 GAQVGSDWTSILKKRQGFRDAFSGFEAETVAKLSDKQMMSISTEYSIDMSRVRGVVDNSNRIL 311 (420)
Q Consensus 249 gFQAGLSW~tVLkKReafReAF~gFDpekVA~~~EedIerLl~D~gIIR~KI~AVI~NAraiL 311 (420)
++..-.+|..+.+-...|.+.|...+++.|+..++++|++++..-|+-+.|-+.+++=|+.++
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 445567899999999999999999999999999999999999999999999999999999997
No 12
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=88.14 E-value=3 Score=40.54 Aligned_cols=76 Identities=13% Similarity=0.213 Sum_probs=56.6
Q ss_pred HHHHHHHHHHHHhccccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhhcCcChhHHHHHHHHhhHHHHHHHHHhhC
Q 041076 239 NMLFELLVLSGAQVGSDWTSILKKRQGFRDAFSGFEAETVAKLSDKQMMSISTEYSIDMSRVRGVVDNSNRILEVKRVFG 318 (420)
Q Consensus 239 r~LFEmL~LEgFQAGLSW~tVLkKReafReAF~gFDpekVA~~~EedIerLl~D~gIIR~KI~AVI~NAraiL~I~~E~G 318 (420)
.--||+|+--+.-+--+=..|-+=-+.+.+.|. +++.++..++++|+.++..-|+-|+|-+.++.=|+.++ ++||
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 345888866555554444455444444444444 59999999999999999999999999999999888874 6676
Q ss_pred C
Q 041076 319 S 319 (420)
Q Consensus 319 S 319 (420)
+
T Consensus 102 g 102 (211)
T COG0177 102 G 102 (211)
T ss_pred C
Confidence 5
No 13
>PRK10880 adenine DNA glycosylase; Provisional
Probab=86.49 E-value=4 Score=42.16 Aligned_cols=68 Identities=9% Similarity=0.130 Sum_probs=58.3
Q ss_pred HHHHHHHHHHhccccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhhcCcChhHHHHHHHHhhHHHHH
Q 041076 241 LFELLVLSGAQVGSDWTSILKKRQGFRDAFSGFEAETVAKLSDKQMMSISTEYSIDMSRVRGVVDNSNRIL 311 (420)
Q Consensus 241 LFEmL~LEgFQAGLSW~tVLkKReafReAF~gFDpekVA~~~EedIerLl~D~gIIR~KI~AVI~NAraiL 311 (420)
-|+.|+-|++-.=-+|.+|+.-.+.|.+.| .|++.+|..++++|.++..--|.-+ |.+-+..-|+.+.
T Consensus 30 py~ilVseILlQQT~v~~v~~~~~rl~~~f--Pt~~~La~a~~eel~~~~~glGyy~-RAr~L~~~A~~i~ 97 (350)
T PRK10880 30 PYKVWLSEVMLQQTQVATVIPYFERFMARF--PTVTDLANAPLDEVLHLWTGLGYYA-RARNLHKAAQQVA 97 (350)
T ss_pred HHHHHHHHHHHhhccHHHHHHHHHHHHHHC--cCHHHHHCcCHHHHHHHHHcCChHH-HHHHHHHHHHHHH
Confidence 488998998888889999999999999987 4799999999999999999988864 7777777777664
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=85.58 E-value=4.2 Score=40.54 Aligned_cols=69 Identities=7% Similarity=0.196 Sum_probs=57.9
Q ss_pred HHHHHHHHHHHhccccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhhcCcChhHHHHHHHHhhHHHHH
Q 041076 240 MLFELLVLSGAQVGSDWTSILKKRQGFRDAFSGFEAETVAKLSDKQMMSISTEYSIDMSRVRGVVDNSNRIL 311 (420)
Q Consensus 240 ~LFEmL~LEgFQAGLSW~tVLkKReafReAF~gFDpekVA~~~EedIerLl~D~gIIR~KI~AVI~NAraiL 311 (420)
-.|+.|+-|++-.=.+|.+|+.-.+.|.+.|- +++.+|..++++|.++...-|.- +|.+.+.+=|+.+.
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--TVQALANAPQDEVLKLWEGLGYY-ARARNLHKAAQEVV 93 (275)
T ss_pred CHHHHHHHHHHHhhccHHHHHHHHHHHHHhCC--CHHHHHCcCHHHHHHHHHHCCcH-HHHHHHHHHHHHHH
Confidence 36999999999888999999999999999884 69999999999999999888886 35666665566553
No 15
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=83.27 E-value=8.1 Score=37.39 Aligned_cols=66 Identities=15% Similarity=0.132 Sum_probs=53.3
Q ss_pred ChHHHHHHHHHHHHhccccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhhcCcC--hhHHHHHHHHhhHHHH
Q 041076 237 NDNMLFELLVLSGAQVGSDWTSILKKRQGFRDAFSGFEAETVAKLSDKQMMSISTEYS--IDMSRVRGVVDNSNRI 310 (420)
Q Consensus 237 DDr~LFEmL~LEgFQAGLSW~tVLkKReafReAF~gFDpekVA~~~EedIerLl~D~g--IIR~KI~AVI~NArai 310 (420)
|+.-+||.|+..+.-+.-+|..+.+--+.+. ++.+ .+++++|++++.--| .-++|=+-++.-++.+
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 7788866666666554
No 16
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=78.32 E-value=20 Score=35.28 Aligned_cols=79 Identities=11% Similarity=0.285 Sum_probs=61.3
Q ss_pred hhhhhhhhcCCCcccCChHHHHHHHHHHHHhccccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhhcCcChhHHHH
Q 041076 221 PIFVAYHDEEWGVPVRNDNMLFELLVLSGAQVGSDWTSILKKRQGFRDAFSGFEAETVAKLSDKQMMSISTEYSIDMSRV 300 (420)
Q Consensus 221 ply~~YHD~EWG~Pv~DDr~LFEmL~LEgFQAGLSW~tVLkKReafReAF~gFDpekVA~~~EedIerLl~D~gIIR~KI 300 (420)
.++.-|+|.-|=--..+| |.++=-+.-=--||.-|++.-++++..+. +|+++|..+++++++.|..-.|.-+.|.
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 467788988885444443 55544445556789999999999998765 6799999999999999999999987665
Q ss_pred HHHH
Q 041076 301 RGVV 304 (420)
Q Consensus 301 ~AVI 304 (420)
.-.+
T Consensus 89 ~rLk 92 (215)
T COG2231 89 KRLK 92 (215)
T ss_pred HHHH
Confidence 4443
No 17
>COG1393 ArsC Arsenate reductase and related proteins, glutaredoxin family [Inorganic ion transport and metabolism]
Probab=75.97 E-value=2.6 Score=37.06 Aligned_cols=67 Identities=9% Similarity=0.123 Sum_probs=50.5
Q ss_pred hhhhhcCCCcccCChHHHHHHHHHHHHhccccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhhcCcChhH
Q 041076 224 VAYHDEEWGVPVRNDNMLFELLVLSGAQVGSDWTSILKKRQGFRDAFSGFEAETVAKLSDKQMMSISTEYSIDM 297 (420)
Q Consensus 224 ~~YHD~EWG~Pv~DDr~LFEmL~LEgFQAGLSW~tVLkKReafReAF~gFDpekVA~~~EedIerLl~D~gIIR 297 (420)
++|+-+....--.+...|-+++ -++|..|..++++|..+-+... .++....+++.++.||.++.+||
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 4454444555555666666666 6889999999999998877776 55667778888999999998775
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=59.13 E-value=8.3 Score=31.76 Aligned_cols=29 Identities=17% Similarity=0.444 Sum_probs=25.7
Q ss_pred HHHHHHHHcCCcccchhhHHHHHHHhccc
Q 041076 352 SISKDMVRRGFRFVGPTVVHSFMQAAGLT 380 (420)
Q Consensus 352 ~LSKdLKKrGFkFVGPTtvYSFMQAiGlV 380 (420)
.++|.|.+.||++++.-..+.||+..|+-
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 57899999999999999999999999984
No 19
>PF10023 DUF2265: Predicted aminopeptidase (DUF2265); InterPro: IPR014553 This group represents a predicted aminopeptidase.
Probab=58.01 E-value=30 Score=36.06 Aligned_cols=104 Identities=15% Similarity=0.287 Sum_probs=64.3
Q ss_pred HHHHHhhcCcChh---HHHHHHHHhhHHHH----HHHHHhhCCHhHhc--------cccCCCcc-----cccccccCCCC
Q 041076 284 KQMMSISTEYSID---MSRVRGVVDNSNRI----LEVKRVFGSFEKYI--------WGFVNHKP-----ISTQYKFGHKI 343 (420)
Q Consensus 284 edIerLl~D~gII---R~KI~AVI~NArai----L~I~~E~GSF~~yL--------WsFv~~kp-----I~~~~~~~~~i 343 (420)
+.|+++++|+.+- |.|| ..+..+|.| |.+ .+.+||..|. |..+--.+ ...-+.-.+-|
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 4589999999983 6666 334445555 222 2456777763 43321111 11111111222
Q ss_pred CC----CChHHHHHHHHHHHcCC-cccchhhHHHHHHHhccccccccccccccc
Q 041076 344 PV----KTSKSESISKDMVRRGF-RFVGPTVVHSFMQAAGLTNDHLIICHRHLP 392 (420)
Q Consensus 344 P~----~T~lS~~LSKdLKKrGF-kFVGPTtvYSFMQAiGlVNDHl~~C~~~~~ 392 (420)
|= .-...+..++.|++.|+ .+||++..||= .|+.+|=+.+-+.+..
T Consensus 111 ~YrGyF~~~~A~~~a~~L~~~GlDv~v~gV~AYST---LGwF~DPlLSt~l~~~ 161 (337)
T PF10023_consen 111 PYRGYFDEADARAEAAELRAQGLDVYVGGVPAYST---LGWFDDPLLSTMLRYP 161 (337)
T ss_pred cccCcCCHHHHHHHHHHHHHcCCceeEeccccccc---ccccCCcccccccCCC
Confidence 21 13456778899999999 59999999997 5999999998876544
No 20
>cd00166 SAM Sterile alpha motif.; Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerization.
Probab=56.59 E-value=28 Score=25.37 Aligned_cols=43 Identities=9% Similarity=0.327 Sum_probs=30.2
Q ss_pred HHHHHHh--cCCCHHHHhcCCHHHHHHhhcCcChhHHHHHHHHhh
Q 041076 264 QGFRDAF--SGFEAETVAKLSDKQMMSISTEYSIDMSRVRGVVDN 306 (420)
Q Consensus 264 eafReAF--~gFDpekVA~~~EedIerLl~D~gIIR~KI~AVI~N 306 (420)
+.|.+.| .++|-+.+..++++|+.++=-..--.|.||...|..
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 5677777 578999999999999884433222347788766653
No 21
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=46.34 E-value=93 Score=31.35 Aligned_cols=69 Identities=10% Similarity=0.056 Sum_probs=61.2
Q ss_pred HHHHHHHHHHHHhccccHHHHHHhHHHHHHHhcC--------CCHHHHhcCCHHHHHHhhcCcChhHHHHHHHHhhHHHH
Q 041076 239 NMLFELLVLSGAQVGSDWTSILKKRQGFRDAFSG--------FEAETVAKLSDKQMMSISTEYSIDMSRVRGVVDNSNRI 310 (420)
Q Consensus 239 r~LFEmL~LEgFQAGLSW~tVLkKReafReAF~g--------FDpekVA~~~EedIerLl~D~gIIR~KI~AVI~NArai 310 (420)
.-+||.|+--+.+.=+|=..+-+-+..|.+.|.+ =.|+.|+..+++++. .-++-+.|.+.+++=|+++
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 5799999999999999999999999999999984 589999999999887 4567789999999999988
Q ss_pred H
Q 041076 311 L 311 (420)
Q Consensus 311 L 311 (420)
.
T Consensus 179 ~ 179 (285)
T COG0122 179 A 179 (285)
T ss_pred H
Confidence 4
No 22
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=43.00 E-value=1.1e+02 Score=30.63 Aligned_cols=120 Identities=14% Similarity=0.121 Sum_probs=75.6
Q ss_pred cCCCcccCChHHHHHHHHHHHHhccccHHHHHHhHHHHHHHhc----------CC-CHHHHhcCCHHHHHHhhcCcChhH
Q 041076 229 EEWGVPVRNDNMLFELLVLSGAQVGSDWTSILKKRQGFRDAFS----------GF-EAETVAKLSDKQMMSISTEYSIDM 297 (420)
Q Consensus 229 ~EWG~Pv~DDr~LFEmL~LEgFQAGLSW~tVLkKReafReAF~----------gF-DpekVA~~~EedIerLl~D~gIIR 297 (420)
..=|.-+.-..-+||+|+..+.---.|=..+.+-...+-+.|. -| +++.|+..+++++..+ |+-+
T Consensus 101 ~~~GlR~p~~~d~fE~lv~aIigQqisv~~a~~~~~rlv~~~G~~l~~~~~~~~FPtpe~La~~~~~eL~~~----Gl~~ 176 (283)
T PRK10308 101 ARPGLRLPGSVDAFEQGVRAILGQLVSVAMAAKLTAKVAQLYGERLDDFPEYVCFPTPERLAAADPQALKAL----GMPL 176 (283)
T ss_pred hCCCCcCCCCCCHHHHHHHHHHHhHHHHHHHHHHHHHHHHHhCccccCCCCccCCCCHHHHHcCCHHHHHHC----CCCH
Confidence 3446666556778999988765444444333333444444433 34 7999999999988753 7778
Q ss_pred HHHHHHHhhHHHHHHHHHhhCCHhHhccccCCCcccccccccCCCCCCCChHHHHHHHHHHHcCCcccchhhH-HHHHHH
Q 041076 298 SRVRGVVDNSNRILEVKRVFGSFEKYIWGFVNHKPISTQYKFGHKIPVKTSKSESISKDMVRRGFRFVGPTVV-HSFMQA 376 (420)
Q Consensus 298 ~KI~AVI~NAraiL~I~~E~GSF~~yLWsFv~~kpI~~~~~~~~~iP~~T~lS~~LSKdLKKrGFkFVGPTtv-YSFMQA 376 (420)
.|.+.++.=|+++.+ |.++ + ... . +. +.+-++|.+ ++-|||-|+ |-.|.+
T Consensus 177 ~Ra~~L~~lA~~i~~-----g~l~-----l---~~~-------~------~~-~~~~~~L~~--LpGIGpwTA~~vllr~ 227 (283)
T PRK10308 177 KRAEALIHLANAALE-----GTLP-----L---TIP-------G------DV-EQAMKTLQT--FPGIGRWTANYFALRG 227 (283)
T ss_pred HHHHHHHHHHHHHHc-----CCCC-----c---ccc-------C------CH-HHHHHHHhc--CCCcCHHHHHHHHHHh
Confidence 899999988888853 3332 0 000 0 11 223455655 899999888 666777
Q ss_pred hcccc
Q 041076 377 AGLTN 381 (420)
Q Consensus 377 iGlVN 381 (420)
.|-.+
T Consensus 228 lg~~D 232 (283)
T PRK10308 228 WQAKD 232 (283)
T ss_pred CCCCC
Confidence 77543
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=42.36 E-value=51 Score=24.81 Aligned_cols=42 Identities=7% Similarity=0.322 Sum_probs=30.3
Q ss_pred HHHHHHh-cCC-CHHHHhcCCHHHHHHhhcCcCh-hHHHHHHHHhh
Q 041076 264 QGFRDAF-SGF-EAETVAKLSDKQMMSISTEYSI-DMSRVRGVVDN 306 (420)
Q Consensus 264 eafReAF-~gF-DpekVA~~~EedIerLl~D~gI-IR~KI~AVI~N 306 (420)
+.|.+.| .++ |-+.+..++++|+++ |.=..+ .|.||...|..
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 5677777 444 999999999999988 544443 47888776653
No 24
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=41.37 E-value=90 Score=30.29 Aligned_cols=78 Identities=21% Similarity=0.317 Sum_probs=52.6
Q ss_pred hhhhhcCCCcccCChHHHHHHHHHHHHhccccHHHHHHhHHHHHHHhcCCCHHHHh-cCCHHHHHHhhcCcChhHHHHHH
Q 041076 224 VAYHDEEWGVPVRNDNMLFELLVLSGAQVGSDWTSILKKRQGFRDAFSGFEAETVA-KLSDKQMMSISTEYSIDMSRVRG 302 (420)
Q Consensus 224 ~~YHD~EWG~Pv~DDr~LFEmL~LEgFQAGLSW~tVLkKReafReAF~gFDpekVA-~~~EedIerLl~D~gIIR~KI~A 302 (420)
++.+-.-+|....++|.||+.| +.+-=.|= .+-| .....+|++.++ ....+|+..|.+=|||-+.
T Consensus 54 REd~~~LyGF~~~~ER~lF~~L-isVnGIGp--K~AL-------aiLs~~~~~~l~~aI~~~d~~~L~k~PGIGkK---- 119 (201)
T COG0632 54 REDAHLLYGFLTEEERELFRLL-ISVNGIGP--KLAL-------AILSNLDPEELAQAIANEDVKALSKIPGIGKK---- 119 (201)
T ss_pred hhhHHHHcCCCCHHHHHHHHHH-HccCCccH--HHHH-------HHHcCCCHHHHHHHHHhcChHhhhcCCCCCHH----
Confidence 3444567999999999999999 66554443 3322 345677877776 4477888888888888643
Q ss_pred HHhhH-HHHHHHHHhhC
Q 041076 303 VVDNS-NRILEVKRVFG 318 (420)
Q Consensus 303 VI~NA-raiL~I~~E~G 318 (420)
+| |.+++++.++.
T Consensus 120 ---tAerivleLk~K~~ 133 (201)
T COG0632 120 ---TAERIVLELKGKLA 133 (201)
T ss_pred ---HHHHHHHHHhhhhh
Confidence 23 45567765533
No 25
>PRK13344 spxA transcriptional regulator Spx; Reviewed
Probab=41.01 E-value=25 Score=31.30 Aligned_cols=80 Identities=14% Similarity=0.229 Sum_probs=47.2
Q ss_pred CCCCcCccCCCChh----hhhhhhcCCCcccCChHHHHHHHHHHHHhccccHHHHHHhHHHHHHHhcCCCHHHHhcCCHH
Q 041076 209 EKRCSFITAYSDPI----FVAYHDEEWGVPVRNDNMLFELLVLSGAQVGSDWTSILKKRQGFRDAFSGFEAETVAKLSDK 284 (420)
Q Consensus 209 ~~RC~W~~~~~dpl----y~~YHD~EWG~Pv~DDr~LFEmL~LEgFQAGLSW~tVLkKReafReAF~gFDpekVA~~~Ee 284 (420)
..+|++|... -.. -++|.-...-.--.+...|-+++ -+.|..|..++++|..+.+.-. .+. ..++++
T Consensus 7 ~~~C~~crkA-~~~L~~~~i~~~~~d~~~~~~s~~eL~~~l----~~~~~~~~~lin~~~~~~k~L~-~~~---~~ls~~ 77 (132)
T PRK13344 7 ISSCTSCKKA-KTWLNAHQLSYKEQNLGKEPLTKEEILAIL----TKTENGIESIVSSKNRYAKALD-CDI---EELSVN 77 (132)
T ss_pred CCCCHHHHHH-HHHHHHcCCCeEEEECCCCCCCHHHHHHHH----HHhCCCHHHhhccCcHHHHhCC-cch---hcCCHH
Confidence 4578777421 111 12333333333334444555555 4568899999999998776543 332 456655
Q ss_pred H-HHHhhcCcChhH
Q 041076 285 Q-MMSISTEYSIDM 297 (420)
Q Consensus 285 d-IerLl~D~gIIR 297 (420)
+ ++-|+++|.+|+
T Consensus 78 e~i~ll~~~P~Lik 91 (132)
T PRK13344 78 EVIDLIQENPRILK 91 (132)
T ss_pred HHHHHHHhCcccee
Confidence 4 677778898875
No 26
>KOG2198 consensus tRNA cytosine-5-methylases and related enzymes of the NOL1/NOP2/sun superfamily [Translation, ribosomal structure and biogenesis]
Probab=40.62 E-value=37 Score=35.97 Aligned_cols=112 Identities=12% Similarity=0.090 Sum_probs=74.1
Q ss_pred HHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhhcCcChh---HHHHHHHHhhHHHHHHHHHhhCCHhHhccccCCCcc
Q 041076 256 WTSILKKRQGFRDAFSGFEAETVAKLSDKQMMSISTEYSID---MSRVRGVVDNSNRILEVKRVFGSFEKYIWGFVNHKP 332 (420)
Q Consensus 256 W~tVLkKReafReAF~gFDpekVA~~~EedIerLl~D~gII---R~KI~AVI~NAraiL~I~~E~GSF~~yLWsFv~~kp 332 (420)
|...-.+.+.|+++.++||. +++.+.++..-+.. .-++.+.++|+-+++.+.+++-.-..|--.. .+
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 55556678899999999986 77888887765543 4799999999999999977653222222111 11
Q ss_pred cccccccCCCCCCCChHHHHHHHHHHHcCCcccch-------------hhHHHHHHHhccc
Q 041076 333 ISTQYKFGHKIPVKTSKSESISKDMVRRGFRFVGP-------------TVVHSFMQAAGLT 380 (420)
Q Consensus 333 I~~~~~~~~~iP~~T~lS~~LSKdLKKrGFkFVGP-------------TtvYSFMQAiGlV 380 (420)
..++.....|- .|..-+..+++++-+|+-.+| +..|..|.|+-|+
T Consensus 89 --~~~e~~~~~p~-~p~~~a~~~~~~~~~~r~~~~l~rf~~fl~~e~~vg~i~rqeavSml 146 (375)
T KOG2198|consen 89 --LKFEAPFELPW-YPDNLAFEKDVKLDEIRKSPPLSRFHGFLKLETGVGNIYRQEAVSML 146 (375)
T ss_pred --cccCccccCCC-CcccchhhhcCcccccccCCchhhcchHhhhhcccccchhhhhhhcc
Confidence 22333444443 356667778888888888764 4456666666665
No 27
>PTZ00411 transaldolase-like protein; Provisional
Probab=40.11 E-value=43 Score=34.73 Aligned_cols=63 Identities=21% Similarity=0.286 Sum_probs=46.7
Q ss_pred HHHHHHhhHHHHHHHHHhhCCHhHhccccCCCcccccccccCCCCCCCChHHHHHHHHHHHcCCcccchhhHHHHHHHhc
Q 041076 299 RVRGVVDNSNRILEVKRVFGSFEKYIWGFVNHKPISTQYKFGHKIPVKTSKSESISKDMVRRGFRFVGPTVVHSFMQAAG 378 (420)
Q Consensus 299 KI~AVI~NAraiL~I~~E~GSF~~yLWsFv~~kpI~~~~~~~~~iP~~T~lS~~LSKdLKKrGFkFVGPTtvYSFMQAiG 378 (420)
-.+++|..|+.+.++-++.| . +...+ +=+||++ ....+.++.|++.|.+--. |.+|++.||+-
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--------I-SKDRI------LIKLAST-WEGIQAAKALEKEGIHCNL-TLLFSFAQAVA 176 (333)
T ss_pred CHHHHHHHHHHHHHhhhhhc--------C-CCCcE------EEEeCCC-HHHHHHHHHHHHCCCceeE-eEecCHHHHHH
Confidence 46888999999988855433 1 22222 2368865 7778888999999999777 88999999863
No 28
>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=39.02 E-value=44 Score=25.22 Aligned_cols=43 Identities=12% Similarity=0.354 Sum_probs=29.3
Q ss_pred HHHHHHhc--CCCH-HHHhcCCHHHHHHhhcCcChhHHHHHHHHhh
Q 041076 264 QGFRDAFS--GFEA-ETVAKLSDKQMMSISTEYSIDMSRVRGVVDN 306 (420)
Q Consensus 264 eafReAF~--gFDp-ekVA~~~EedIerLl~D~gIIR~KI~AVI~N 306 (420)
+.|.+.|. ++|- +.++.++++++.++=-.....|.||...|++
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 45666666 6666 7799999999975533333357788766654
No 29
>PF13495 Phage_int_SAM_4: Phage integrase, N-terminal SAM-like domain; PDB: 2A3V_A.
Probab=38.90 E-value=1.5e+02 Score=22.91 Aligned_cols=52 Identities=10% Similarity=0.025 Sum_probs=35.6
Q ss_pred HHHHHHHHHHhccccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhhcC
Q 041076 241 LFELLVLSGAQVGSDWTSILKKRQGFRDAFSGFEAETVAKLSDKQMMSISTE 292 (420)
Q Consensus 241 LFEmL~LEgFQAGLSW~tVLkKReafReAF~gFDpekVA~~~EedIerLl~D 292 (420)
|++......-..|+|=.||-.-+-.++.-..-|+-..+..++.+||+..+..
T Consensus 1 Ll~~f~~~l~~~~~s~~Ti~~Y~~~l~~f~~~~~~~~~~~it~~~i~~y~~~ 52 (85)
T PF13495_consen 1 LLEEFLEYLRLKGLSEKTIKNYRYHLKRFLRFLGNKPPDEITPEDIEQYLNY 52 (85)
T ss_dssp -HHHHHHHHHHTT--HHHHHHHHHHHHHHHTTSSS--GGG--HHHHHHHHHH
T ss_pred CHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcccCccchhHHHHHHHHHHH
Confidence 3444445556699999999999999998777777678899999999877754
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=35.97 E-value=35 Score=27.65 Aligned_cols=28 Identities=29% Similarity=0.564 Sum_probs=25.1
Q ss_pred HHHHHHHHcCCcccchhhHHHHHHHhcc
Q 041076 352 SISKDMVRRGFRFVGPTVVHSFMQAAGL 379 (420)
Q Consensus 352 ~LSKdLKKrGFkFVGPTtvYSFMQAiGl 379 (420)
.+++.|.+.||+.+.....+.||+..|+
T Consensus 4 ~~~~~l~~lG~~i~AT~gTa~~L~~~Gi 31 (90)
T smart00851 4 ELAKRLAELGFELVATGGTAKFLREAGL 31 (90)
T ss_pred HHHHHHHHCCCEEEEccHHHHHHHHCCC
Confidence 4778999999999998888999999886
No 31
>PF13276 HTH_21: HTH-like domain
Probab=33.39 E-value=49 Score=24.97 Aligned_cols=30 Identities=27% Similarity=0.304 Sum_probs=25.7
Q ss_pred HHHHHHHHHcCCcccchhhHHHHHHHhccc
Q 041076 351 ESISKDMVRRGFRFVGPTVVHSFMQAAGLT 380 (420)
Q Consensus 351 ~~LSKdLKKrGFkFVGPTtvYSFMQAiGlV 380 (420)
..|..+|.+.|---||-.+|+-+|+..||.
T Consensus 24 rri~~~L~~~~~~~v~~krV~RlM~~~gL~ 53 (60)
T PF13276_consen 24 RRIWAELRREGGIRVSRKRVRRLMREMGLR 53 (60)
T ss_pred hHHHHHHhccCcccccHHHHHHHHHHcCCc
Confidence 458889999965569999999999999984
No 32
>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=33.17 E-value=1.9e+02 Score=29.33 Aligned_cols=88 Identities=16% Similarity=0.164 Sum_probs=58.3
Q ss_pred CChhhhhhhhcCCCcccCChHHHHHHHHHHHHhccccHHHHHHhHHHHHHHhcC------------C-CHHHHhcCCHHH
Q 041076 219 SDPIFVAYHDEEWGVPVRNDNMLFELLVLSGAQVGSDWTSILKKRQGFRDAFSG------------F-EAETVAKLSDKQ 285 (420)
Q Consensus 219 ~dply~~YHD~EWG~Pv~DDr~LFEmL~LEgFQAGLSW~tVLkKReafReAF~g------------F-DpekVA~~~Eed 285 (420)
.||.+..--+.--|..+.-. -.||.|+-.+...-.|+..+.+-...+.+.|-. | +++.|+..+.+
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 46666555556678655444 679999999999999999999999999988752 2 35666653322
Q ss_pred HHHhhcCcChhHHHHHHHHhhHHHHH
Q 041076 286 MMSISTEYSIDMSRVRGVVDNSNRIL 311 (420)
Q Consensus 286 IerLl~D~gIIR~KI~AVI~NAraiL 311 (420)
..|..-|+ ..|.+.++.=|+++.
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 23333444 234666666666653
No 33
>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=32.46 E-value=45 Score=30.28 Aligned_cols=30 Identities=17% Similarity=0.231 Sum_probs=26.4
Q ss_pred HHHHHHHHHcCCcccchhhHHHHHHHhcccc
Q 041076 351 ESISKDMVRRGFRFVGPTVVHSFMQAAGLTN 381 (420)
Q Consensus 351 ~~LSKdLKKrGFkFVGPTtvYSFMQAiGlVN 381 (420)
+.|...|+++||. |.-.|+|-.|...|++-
T Consensus 20 eeL~~~L~~~G~~-vsqaTIsRdL~elglvk 49 (146)
T TIGR01529 20 EELVALLKAEGIE-VTQATVSRDLRELGAVK 49 (146)
T ss_pred HHHHHHHHHhCCC-cCHHHHHHHHHHcCCEE
Confidence 4577889999999 88899999999999974
No 34
>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=31.85 E-value=51 Score=27.97 Aligned_cols=32 Identities=13% Similarity=0.273 Sum_probs=27.9
Q ss_pred hHHHHHHHHHHHcCCcccchhhHHHHHHHhcc
Q 041076 348 SKSESISKDMVRRGFRFVGPTVVHSFMQAAGL 379 (420)
Q Consensus 348 ~lS~~LSKdLKKrGFkFVGPTtvYSFMQAiGl 379 (420)
+....+++.|.+.||+.++.-..+.||+..|+
T Consensus 12 ~~~~~~a~~l~~~G~~i~AT~gTa~~L~~~Gi 43 (112)
T cd00532 12 AMLVDLAPKLSSDGFPLFATGGTSRVLADAGI 43 (112)
T ss_pred HHHHHHHHHHHHCCCEEEECcHHHHHHHHcCC
Confidence 34557889999999999999899999999886
No 35
>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=30.80 E-value=16 Score=39.76 Aligned_cols=59 Identities=20% Similarity=0.359 Sum_probs=45.4
Q ss_pred hHHHHHHHhcCCCHHH--------------------HhcCCHHHHHHhhcCcChh---HHHHHHHHhhHHHHHHHHHhhC
Q 041076 262 KRQGFRDAFSGFEAET--------------------VAKLSDKQMMSISTEYSID---MSRVRGVVDNSNRILEVKRVFG 318 (420)
Q Consensus 262 KReafReAF~gFDpek--------------------VA~~~EedIerLl~D~gII---R~KI~AVI~NAraiL~I~~E~G 318 (420)
--+.|+.+|+|+|.++ ++.-.+..||..+...|+- ..||+.+|.| ++-+||-
T Consensus 145 sl~Dm~~lf~gi~L~~~~~s~smtin~~a~~~lAmy~a~a~~~~~~~~~~~~G~~~~~~~~l~Gtiqn-----DiLke~~ 219 (495)
T cd03678 145 TLDDMKKLYSGFDLCAPNTSVSMTINGPAPMLLAFFLNTAIDQQVEKFRRENGIRAETLRSVRGTVQA-----DILKEDQ 219 (495)
T ss_pred cHHHHHHHhcCCCCCCCcceeeeeecccHHHHHHHHHHHHHHhhhhhhHhhcCCCcccHhhcCccccc-----chHHHHH
Confidence 3489999999999999 4444555688889999998 7899999998 5556665
Q ss_pred CHhHhcc
Q 041076 319 SFEKYIW 325 (420)
Q Consensus 319 SF~~yLW 325 (420)
....|++
T Consensus 220 argt~i~ 226 (495)
T cd03678 220 AQNTCIF 226 (495)
T ss_pred hCCCccC
Confidence 5555654
No 36
>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=29.17 E-value=77 Score=27.43 Aligned_cols=21 Identities=19% Similarity=0.490 Sum_probs=16.1
Q ss_pred HHHHHHHHHHHcCCcccchhh
Q 041076 349 KSESISKDMVRRGFRFVGPTV 369 (420)
Q Consensus 349 lS~~LSKdLKKrGFkFVGPTt 369 (420)
+...+++.+.+.|.+|+||..
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 456788889999999999964
No 37
>PF13068 DUF3932: Protein of unknown function (DUF3932)
Probab=28.78 E-value=12 Score=31.22 Aligned_cols=30 Identities=20% Similarity=0.597 Sum_probs=22.7
Q ss_pred HHHHHHhhC-CHhHhccccCCCccccccccc
Q 041076 310 ILEVKRVFG-SFEKYIWGFVNHKPISTQYKF 339 (420)
Q Consensus 310 iL~I~~E~G-SF~~yLWsFv~~kpI~~~~~~ 339 (420)
+..+|.+|. ||+.|+-+||.+.|..-.|..
T Consensus 4 vfrlqtdfsssfdrwvssfvsdhpaql~wtt 34 (81)
T PF13068_consen 4 VFRLQTDFSSSFDRWVSSFVSDHPAQLEWTT 34 (81)
T ss_pred hhhhhcchhhHHHHHHHHHhcCCccccchhH
Confidence 456777775 899999999987776655543
No 38
>PRK05269 transaldolase B; Provisional
Probab=28.43 E-value=89 Score=32.11 Aligned_cols=64 Identities=16% Similarity=0.225 Sum_probs=46.7
Q ss_pred HHHHHHhhHHHHHHHHHhhCCHhHhccccCCCcccccccccCCCCCCCChHHHHHHHHHHHcCCcccchhhHHHHHHHhc
Q 041076 299 RVRGVVDNSNRILEVKRVFGSFEKYIWGFVNHKPISTQYKFGHKIPVKTSKSESISKDMVRRGFRFVGPTVVHSFMQAAG 378 (420)
Q Consensus 299 KI~AVI~NAraiL~I~~E~GSF~~yLWsFv~~kpI~~~~~~~~~iP~~T~lS~~LSKdLKKrGFkFVGPTtvYSFMQAiG 378 (420)
-.+++|..|+.+.++-++.| . +...+ +=+||++ ....+-++.|.+.|.+--. |.+|++-|+.-
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-SKDRI------LIKIAST-WEGIRAAEQLEKEGINCNL-TLLFSFAQARA 166 (318)
T ss_pred CHHHHHHHHHHHHHHhhhcC--------C-CCCcE------EEEeCCC-HHHHHHHHHHHHcCCceeE-eEecCHHHHHH
Confidence 56889999999988755422 2 11112 2378865 7777778999999999877 88999999865
Q ss_pred c
Q 041076 379 L 379 (420)
Q Consensus 379 l 379 (420)
-
T Consensus 167 a 167 (318)
T PRK05269 167 C 167 (318)
T ss_pred H
Confidence 3
No 39
>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=28.12 E-value=3.2e+02 Score=22.73 Aligned_cols=29 Identities=14% Similarity=0.476 Sum_probs=21.6
Q ss_pred cCCHHHHHHhhcCcChhHHHHHHHHhhHH
Q 041076 280 KLSDKQMMSISTEYSIDMSRVRGVVDNSN 308 (420)
Q Consensus 280 ~~~EedIerLl~D~gIIR~KI~AVI~NAr 308 (420)
..+++++..++.+.|+...++.+.++...
T Consensus 82 ~~~~~~l~~~a~~~gl~~~~~~~~~~~~~ 110 (154)
T cd03023 82 RLNEESLLRIAKKAGLDEAKLKKDMDDPE 110 (154)
T ss_pred CCCHHHHHHHHHHcCCCHHHHHHHhhChH
Confidence 35778888888888887777777776543
No 40
>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=28.04 E-value=65 Score=23.69 Aligned_cols=37 Identities=11% Similarity=0.188 Sum_probs=26.6
Q ss_pred CCHHHHHHhhcCcCh---hHHHHHHHHhhHHHHHHHHHhhC
Q 041076 281 LSDKQMMSISTEYSI---DMSRVRGVVDNSNRILEVKRVFG 318 (420)
Q Consensus 281 ~~EedIerLl~D~gI---IR~KI~AVI~NAraiL~I~~E~G 318 (420)
|+.+++++++..-.- .|.||.++- |...+++|.+++|
T Consensus 1 MS~~~l~~Fl~~~~~d~~l~~~l~~~~-~~~e~~~lA~~~G 40 (49)
T PF07862_consen 1 MSIESLKAFLEKVKSDPELREQLKACQ-NPEEVVALAREAG 40 (49)
T ss_pred CCHHHHHHHHHHHhcCHHHHHHHHhcC-CHHHHHHHHHHcC
Confidence 556666666654332 477888854 8899999999988
No 41
>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=27.77 E-value=35 Score=24.99 Aligned_cols=30 Identities=7% Similarity=0.222 Sum_probs=24.5
Q ss_pred HHHHhcCCCHHHHhcCCHHHHHHhhcCcCh
Q 041076 266 FRDAFSGFEAETVAKLSDKQMMSISTEYSI 295 (420)
Q Consensus 266 fReAF~gFDpekVA~~~EedIerLl~D~gI 295 (420)
|+++|.-||.+.=-.++.+++.+++...++
T Consensus 1 ~~~~F~~~D~~~~G~i~~~el~~~l~~~g~ 30 (67)
T cd00052 1 YDQIFRSLDPDGDGLISGDEARPFLGKSGL 30 (67)
T ss_pred ChHHHHHhCCCCCCcCcHHHHHHHHHHcCC
Confidence 578899999888778888899888876665
No 42
>PRK10548 flagellar biosynthesis protein FliT; Provisional
Probab=27.74 E-value=1.3e+02 Score=26.89 Aligned_cols=80 Identities=15% Similarity=0.266 Sum_probs=56.1
Q ss_pred HHHHHHHHHHhccccHHHHHHhHHHHHHHhcCCCH-HHHhcCCHHH-------HHHhhcCcChhH-------HHHHHHHh
Q 041076 241 LFELLVLSGAQVGSDWTSILKKRQGFRDAFSGFEA-ETVAKLSDKQ-------MMSISTEYSIDM-------SRVRGVVD 305 (420)
Q Consensus 241 LFEmL~LEgFQAGLSW~tVLkKReafReAF~gFDp-ekVA~~~Eed-------IerLl~D~gIIR-------~KI~AVI~ 305 (420)
|.+-+ |+..+.| .|..+..-...|..+-..--- ..-...++.+ |.+||.|..-|| .++...|.
T Consensus 17 lS~~M-L~aA~~g-~Wd~Li~lE~~y~~~Ve~l~~~~~~~~l~~~~q~~~~~lL~~IL~nda~Ir~Llq~rl~eL~~li~ 94 (121)
T PRK10548 17 LSQSM-LRLATEG-QWDELIEQEVAYVQAVEEIAHLTIPPDISTVMQEQLRPMLRQILDNEAELKQLLQQRMDELSSLIG 94 (121)
T ss_pred HHHHH-HHHHHHC-CHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44555 7778877 699999988888876432200 0011233322 567888888775 48999999
Q ss_pred hHHHHHHHHHhhCCHhH
Q 041076 306 NSNRILEVKRVFGSFEK 322 (420)
Q Consensus 306 NAraiL~I~~E~GSF~~ 322 (420)
+++.=..+..-||.|+.
T Consensus 95 ~~~rq~~l~~aYg~~~~ 111 (121)
T PRK10548 95 QSTRQKSVNSAYGQLSG 111 (121)
T ss_pred HhHHHHHHHHHHhcCCC
Confidence 99999999999999986
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=27.59 E-value=69 Score=26.75 Aligned_cols=31 Identities=26% Similarity=0.542 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHcCCcccchhhHHHHHHHhcc
Q 041076 349 KSESISKDMVRRGFRFVGPTVVHSFMQAAGL 379 (420)
Q Consensus 349 lS~~LSKdLKKrGFkFVGPTtvYSFMQAiGl 379 (420)
....+++.|.+.||+..+.-..+.||+..|+
T Consensus 14 ~~~~~~~~l~~~G~~l~aT~gT~~~l~~~gi 44 (110)
T cd01424 14 EAVEIAKRLAELGFKLVATEGTAKYLQEAGI 44 (110)
T ss_pred HHHHHHHHHHHCCCEEEEchHHHHHHHHcCC
Confidence 4556889999999999999999999999886
No 44
>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=27.52 E-value=56 Score=27.81 Aligned_cols=57 Identities=12% Similarity=0.121 Sum_probs=35.8
Q ss_pred hHHHHHHHHHHHHhccccHHHHHHhHH-HHHHHhcCCCHHHHhcCCHHH-HHHhhcCcChhH
Q 041076 238 DNMLFELLVLSGAQVGSDWTSILKKRQ-GFRDAFSGFEAETVAKLSDKQ-MMSISTEYSIDM 297 (420)
Q Consensus 238 Dr~LFEmL~LEgFQAGLSW~tVLkKRe-afReAF~gFDpekVA~~~Eed-IerLl~D~gIIR 297 (420)
|..-.+.|.--+-+.|..|..+++||. .|++.- .+ +++..+++++ ++.|+++|.+|+
T Consensus 34 ~~~~~~el~~~~~~~~~~~~~l~~~~~~~~~~l~--~~-~~~~~~s~~e~~~~l~~~p~Lik 92 (111)
T cd03036 34 EPPSKEELKKWLEKSGLPLKKFFNTSGKSYRELG--LK-DKLPSLSEEEALELLSSDGMLIK 92 (111)
T ss_pred CcccHHHHHHHHHHcCCCHHHHHhcCCchHHhCC--cc-cccccCCHHHHHHHHHhCcCeee
Confidence 333344443334567888999999997 455542 22 3466777665 566777888875
No 45
>PRK12309 transaldolase/EF-hand domain-containing protein; Provisional
Probab=26.67 E-value=98 Score=32.70 Aligned_cols=64 Identities=13% Similarity=0.197 Sum_probs=46.4
Q ss_pred HHHHHHhhHHHHHHHHHhhCCHhHhccccCCCcccccccccCCCCCCCChHHHHHHHHHHHcCCcccchhhHHHHHHHhc
Q 041076 299 RVRGVVDNSNRILEVKRVFGSFEKYIWGFVNHKPISTQYKFGHKIPVKTSKSESISKDMVRRGFRFVGPTVVHSFMQAAG 378 (420)
Q Consensus 299 KI~AVI~NAraiL~I~~E~GSF~~yLWsFv~~kpI~~~~~~~~~iP~~T~lS~~LSKdLKKrGFkFVGPTtvYSFMQAiG 378 (420)
-.+++|..|+.+.++-++.| ++...+ +=+||++ ....+-.+.|++.|.+--. |.+|++-||+-
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---------ISRDRV------LIKIAST-WEGIKAAEVLEKEGIHCNL-TLLFGFHQAIA 170 (391)
T ss_pred CHHHHHHHHHHHHHHhhhhc---------CCCCcE------EEEeCCC-HHHHHHHHHHHHCCCceee-eeecCHHHHHH
Confidence 46888999999987754432 111112 2378865 7777778899999999877 88999999875
Q ss_pred c
Q 041076 379 L 379 (420)
Q Consensus 379 l 379 (420)
-
T Consensus 171 a 171 (391)
T PRK12309 171 C 171 (391)
T ss_pred H
Confidence 3
No 46
>PHA02517 putative transposase OrfB; Reviewed
Probab=26.59 E-value=68 Score=30.68 Aligned_cols=30 Identities=27% Similarity=0.494 Sum_probs=26.0
Q ss_pred HHHHHHHHHcCCcccchhhHHHHHHHhcccc
Q 041076 351 ESISKDMVRRGFRFVGPTVVHSFMQAAGLTN 381 (420)
Q Consensus 351 ~~LSKdLKKrGFkFVGPTtvYSFMQAiGlVN 381 (420)
.+|...|+++|+. ++..+||-+|+..||.-
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 4578899999986 59999999999999954
No 47
>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=26.28 E-value=1.9e+02 Score=21.02 Aligned_cols=42 Identities=10% Similarity=0.276 Sum_probs=27.7
Q ss_pred HHHHh--cCCCHHHHhcCC-HHHHHHhhcCcChhHHHHHHHHhhH
Q 041076 266 FRDAF--SGFEAETVAKLS-DKQMMSISTEYSIDMSRVRGVVDNS 307 (420)
Q Consensus 266 fReAF--~gFDpekVA~~~-EedIerLl~D~gIIR~KI~AVI~NA 307 (420)
|.+.| .++|-..+..++ +++++++=-..--.|.||...|..-
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 677878888888 7777775432323477777666553
No 48
>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=25.42 E-value=37 Score=28.63 Aligned_cols=54 Identities=17% Similarity=0.222 Sum_probs=34.6
Q ss_pred CChHHHHHHHHHHHHhccccHHHHHHhHH-HHHHHhcCCCHHHHhcCCHHHH-HHhhcCcChhH
Q 041076 236 RNDNMLFELLVLSGAQVGSDWTSILKKRQ-GFRDAFSGFEAETVAKLSDKQM-MSISTEYSIDM 297 (420)
Q Consensus 236 ~DDr~LFEmL~LEgFQAGLSW~tVLkKRe-afReAF~gFDpekVA~~~EedI-erLl~D~gIIR 297 (420)
-+...|-+++ -+.|..|..+++++. .|++.. -.....++++++ +-|+++|.+|+
T Consensus 33 ~s~~el~~~l----~~~~~~~~~lin~~~~~~k~l~----~~~~~~~s~~e~i~~l~~~p~Lik 88 (110)
T PF03960_consen 33 LSREELRELL----SKLGNGPDDLINTRSKTYKELG----KLKKDDLSDEELIELLLENPKLIK 88 (110)
T ss_dssp --HHHHHHHH----HHHTSSGGGGB-TTSHHHHHTT----HHHCTTSBHHHHHHHHHHSGGGB-
T ss_pred CCHHHHHHHH----HHhcccHHHHhcCccchHhhhh----hhhhhhhhhHHHHHHHHhChhhee
Confidence 3455566665 566888999999885 455544 455678888886 55666788875
No 49
>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=24.65 E-value=51 Score=24.79 Aligned_cols=19 Identities=26% Similarity=0.567 Sum_probs=16.2
Q ss_pred HHHHHHHHHHcCCcccchh
Q 041076 350 SESISKDMVRRGFRFVGPT 368 (420)
Q Consensus 350 S~~LSKdLKKrGFkFVGPT 368 (420)
.+.+.+.|++.||++.||.
T Consensus 54 ~~~~~~~L~~~G~~v~~~~ 72 (72)
T cd04883 54 PRPIIEDLRRAGYEVLWPN 72 (72)
T ss_pred HHHHHHHHHHCCCeeeCCC
Confidence 4578899999999999983
No 50
>COG4081 Uncharacterized protein conserved in archaea [Function unknown]
Probab=24.00 E-value=57 Score=30.45 Aligned_cols=26 Identities=23% Similarity=0.432 Sum_probs=22.9
Q ss_pred CCCCCCCChHHHHHHHHHHHcCCccc
Q 041076 340 GHKIPVKTSKSESISKDMVRRGFRFV 365 (420)
Q Consensus 340 ~~~iP~~T~lS~~LSKdLKKrGFkFV 365 (420)
.-++|.+.+...-+|..||++||.-.
T Consensus 11 CPeiP~qissaiYls~klkkkgf~v~ 36 (148)
T COG4081 11 CPEIPPQISSAIYLSHKLKKKGFDVT 36 (148)
T ss_pred CCCCCccchHHHHHHHHhhccCccEE
Confidence 45789999999999999999999854
No 51
>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=23.26 E-value=54 Score=33.58 Aligned_cols=47 Identities=21% Similarity=0.209 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHcCCc--ccchhhHHHHHHH-hccccccccccccccchhhh
Q 041076 349 KSESISKDMVRRGFR--FVGPTVVHSFMQA-AGLTNDHLIICHRHLPCTLL 396 (420)
Q Consensus 349 lS~~LSKdLKKrGFk--FVGPTtvYSFMQA-iGlVNDHl~~C~~~~~~~~~ 396 (420)
.+..|-+.|+++|++ |+| |..-.+||+ .|++-|.++.+|.-+..+.+
T Consensus 129 Tal~L~~~l~~~G~~a~fva-TGQTGimia~~Gv~iDav~~DFvaGavE~~ 178 (301)
T PF07755_consen 129 TALELRRALRERGINAGFVA-TGQTGIMIAGYGVPIDAVPSDFVAGAVEAL 178 (301)
T ss_dssp HHHHHHHHHHHTT--EEEEE--SHHHHHCHSEC--GGGSBGGGHHHHHHHH
T ss_pred HHHHHHHHHHHcCCCceEEe-cCCceEEEecCCeeccchhhhhHHHHHHHH
Confidence 466788999999985 666 666677772 35899999999988776654
No 52
>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=22.66 E-value=44 Score=29.28 Aligned_cols=25 Identities=24% Similarity=0.593 Sum_probs=17.0
Q ss_pred ChHHHHHHHHHHHcCCcccchhhHH
Q 041076 347 TSKSESISKDMVRRGFRFVGPTVVH 371 (420)
Q Consensus 347 T~lS~~LSKdLKKrGFkFVGPTtvY 371 (420)
.++++.+.+....+||.|+||++|.
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 4577778888889999999999875
No 53
>PF05075 DUF684: Protein of unknown function (DUF684); InterPro: IPR007767 This family contains uncharacterised proteins from Caenorhabditis elegans.
Probab=22.31 E-value=1.1e+02 Score=31.30 Aligned_cols=76 Identities=14% Similarity=0.179 Sum_probs=48.3
Q ss_pred hHHHHHHHHHHHHhccc-------cHHHHHHhHHHHHHHhcCCCHHHH--hcCCHHHHHHhhc----C-cC--------h
Q 041076 238 DNMLFELLVLSGAQVGS-------DWTSILKKRQGFRDAFSGFEAETV--AKLSDKQMMSIST----E-YS--------I 295 (420)
Q Consensus 238 Dr~LFEmL~LEgFQAGL-------SW~tVLkKReafReAF~gFDpekV--A~~~EedIerLl~----D-~g--------I 295 (420)
+..|-.+|.||+|.+|| .+..|+.+-..+.+..+.|+-+.. ..|=++.++.++. + .. +
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 56789999999999999 678888888777777777665552 2333344444432 2 21 2
Q ss_pred hHHHHHHHHhhHHHHHHH
Q 041076 296 DMSRVRGVVDNSNRILEV 313 (420)
Q Consensus 296 IR~KI~AVI~NAraiL~I 313 (420)
|+.+++.+..|-..++=+
T Consensus 195 Ik~~Le~ilTnDsFYIiV 212 (345)
T PF05075_consen 195 IKKKLEKILTNDSFYIIV 212 (345)
T ss_pred HHHHHHhhCCCCcEEEEE
Confidence 445666666665544433
No 54
>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=22.22 E-value=92 Score=26.95 Aligned_cols=32 Identities=19% Similarity=0.208 Sum_probs=28.2
Q ss_pred hHHHHHHHHHHHc--CCcccchhhHHHHHHH-hcc
Q 041076 348 SKSESISKDMVRR--GFRFVGPTVVHSFMQA-AGL 379 (420)
Q Consensus 348 ~lS~~LSKdLKKr--GFkFVGPTtvYSFMQA-iGl 379 (420)
+....+++.|.+. ||+++.....+.||+. .|+
T Consensus 12 ~~~~~~a~~~~~ll~Gf~i~AT~gTa~~L~~~~Gi 46 (115)
T cd01422 12 EDLVEFVKQHQELLSRHRLVATGTTGLLIQEATGL 46 (115)
T ss_pred HHHHHHHHHHHHHhcCCEEEEechHHHHHHHhhCC
Confidence 4556788999999 9999999999999999 887
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=21.78 E-value=41 Score=31.20 Aligned_cols=30 Identities=20% Similarity=0.359 Sum_probs=22.6
Q ss_pred HHhHHHHHHHhcCCCHHHHhcCCHHHHHHh
Q 041076 260 LKKRQGFRDAFSGFEAETVAKLSDKQMMSI 289 (420)
Q Consensus 260 LkKReafReAF~gFDpekVA~~~EedIerL 289 (420)
..||+.|++++-+|-+..|++++-+..|.|
T Consensus 69 ktk~DeY~EaLRDfq~~~iaKle~e~Ae~v 98 (139)
T PF12583_consen 69 KTKWDEYSEALRDFQCSWIAKLEPENAEQV 98 (139)
T ss_dssp ---HHHHHHHHHHHHHHHHTTS-HHHHHHH
T ss_pred cccHHHHHHHHHHHHHHHHHhhCHHHHHHH
Confidence 458899999999999999999988665544
No 56
>PLN02764 glycosyltransferase family protein
Probab=21.09 E-value=1.3e+02 Score=32.24 Aligned_cols=83 Identities=19% Similarity=0.156 Sum_probs=55.3
Q ss_pred CCcccCChHHHHHHHHHHHHhccccHHHHHHhHHHHHHHhcCCCHHHHhcCCHHHHHHhhcCcChhHHHHHHHHhhHHHH
Q 041076 231 WGVPVRNDNMLFELLVLSGAQVGSDWTSILKKRQGFRDAFSGFEAETVAKLSDKQMMSISTEYSIDMSRVRGVVDNSNRI 310 (420)
Q Consensus 231 WG~Pv~DDr~LFEmL~LEgFQAGLSW~tVLkKReafReAF~gFDpekVA~~~EedIerLl~D~gIIR~KI~AVI~NArai 310 (420)
-+.|..-||.+...++-+..-+|+.= .+.+ ...++.+.|. +-|+++|.|.+=.+ +.+..||+.+
T Consensus 359 l~~P~~~DQ~~na~~l~~~~g~gv~~----~~~~-----~~~~~~e~i~----~av~~vm~~~~~~g---~~~r~~a~~~ 422 (453)
T PLN02764 359 VLVPQLGDQVLNTRLLSDELKVSVEV----AREE-----TGWFSKESLR----DAINSVMKRDSEIG---NLVKKNHTKW 422 (453)
T ss_pred EeCCcccchHHHHHHHHHHhceEEEe----cccc-----CCccCHHHHH----HHHHHHhcCCchhH---HHHHHHHHHH
Confidence 34688999999999966778888751 1110 0134555554 34778887764222 3356677777
Q ss_pred HHHHHhhCCHhHhccccCC
Q 041076 311 LEVKRVFGSFEKYIWGFVN 329 (420)
Q Consensus 311 L~I~~E~GSF~~yLWsFv~ 329 (420)
.+..+++||-..+|-.|++
T Consensus 423 ~~~~~~~GSS~~~l~~lv~ 441 (453)
T PLN02764 423 RETLASPGLLTGYVDNFIE 441 (453)
T ss_pred HHHHHhcCCHHHHHHHHHH
Confidence 7777899999888887774
No 57
>PF13348 Y_phosphatase3C: Tyrosine phosphatase family C-terminal region; PDB: 1YWF_A 2OZ5_B.
Probab=20.93 E-value=80 Score=24.35 Aligned_cols=20 Identities=20% Similarity=0.413 Sum_probs=14.6
Q ss_pred HHHHHHHhhCCHhHhccccC
Q 041076 309 RILEVKRVFGSFEKYIWGFV 328 (420)
Q Consensus 309 aiL~I~~E~GSF~~yLWsFv 328 (420)
++-.|.++|||+..|+=...
T Consensus 34 ~l~~i~~~yGs~e~Yl~~~l 53 (68)
T PF13348_consen 34 ALDAIDERYGSVENYLREEL 53 (68)
T ss_dssp HHHHHHHHHSSHHHHHHHT-
T ss_pred HHHHHHHHcCCHHHHHHHcC
Confidence 34467889999999995443
No 58
>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=20.76 E-value=54 Score=31.34 Aligned_cols=34 Identities=29% Similarity=0.371 Sum_probs=27.5
Q ss_pred CCCCCChHHHHHHHHHHHcCCcccchhhHHHHHHHh
Q 041076 342 KIPVKTSKSESISKDMVRRGFRFVGPTVVHSFMQAA 377 (420)
Q Consensus 342 ~iP~~T~lS~~LSKdLKKrGFkFVGPTtvYSFMQAi 377 (420)
+||.+. ......+.|++.|.+ ||-|+||+..|+.
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 577666 556677899999987 7779999999985
No 59
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=20.29 E-value=47 Score=27.13 Aligned_cols=45 Identities=7% Similarity=0.163 Sum_probs=33.2
Q ss_pred HHhHHHHHHHhcCCCHHHHhcCCHHHHHHhhcCcChhHHHHHHHH
Q 041076 260 LKKRQGFRDAFSGFEAETVAKLSDKQMMSISTEYSIDMSRVRGVV 304 (420)
Q Consensus 260 LkKReafReAF~gFDpekVA~~~EedIerLl~D~gIIR~KI~AVI 304 (420)
-.-.+.|+++|.-||.+.=-.++-+++.++|...++-...|..++
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 345678999999999888778899999999877665443343333
No 60
>PF14493 HTH_40: Helix-turn-helix domain
Probab=20.16 E-value=3e+02 Score=22.55 Aligned_cols=43 Identities=19% Similarity=0.195 Sum_probs=27.5
Q ss_pred HHHHHHHhccccHHHHHHhHH-----------HHHHHhcCCCHHHHhcCCHHHHHH
Q 041076 244 LLVLSGAQVGSDWTSILKKRQ-----------GFRDAFSGFEAETVAKLSDKQMMS 288 (420)
Q Consensus 244 mL~LEgFQAGLSW~tVLkKRe-----------afReAF~gFDpekVA~~~EedIer 288 (420)
..+++.||.|+|=..|-++|. .+-.....||++.+ +++++++.
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 456888888888887777763 44455555666655 45554443
No 61
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=20.02 E-value=2.5e+02 Score=26.68 Aligned_cols=80 Identities=19% Similarity=0.263 Sum_probs=46.6
Q ss_pred hhhhhhhcC-----CCcccCChHHHHHHHHHHHHhccccHHHHHHhHHHHHHHhcCCCHHHHh-cCCHHHHHHhhcCcCh
Q 041076 222 IFVAYHDEE-----WGVPVRNDNMLFELLVLSGAQVGSDWTSILKKRQGFRDAFSGFEAETVA-KLSDKQMMSISTEYSI 295 (420)
Q Consensus 222 ly~~YHD~E-----WG~Pv~DDr~LFEmL~LEgFQAGLSW~tVLkKReafReAF~gFDpekVA-~~~EedIerLl~D~gI 295 (420)
+|.+.|=.| +|....+++.||++| +.+-=.| =++-| .....|+++.+. ....+|+..|..=|||
T Consensus 47 l~t~~~vrEd~~~LyGF~~~~Er~lF~~L-i~V~GIG--pK~AL-------~iLs~~~~~el~~aI~~~D~~~L~~vpGI 116 (188)
T PRK14606 47 LHTFLSVSQDGITLYGFSNERKKELFLSL-TKVSRLG--PKTAL-------KIISNEDAETLVTMIASQDVEGLSKLPGI 116 (188)
T ss_pred EEEEEEEecCCceeeCCCCHHHHHHHHHH-hccCCcc--HHHHH-------HHHcCCCHHHHHHHHHhCCHHHHhhCCCC
Confidence 455555433 788889999999999 4543333 22222 233455555554 3355667777777777
Q ss_pred hHHHHHHHHhhHHHHHHHHHhh
Q 041076 296 DMSRVRGVVDNSNRILEVKRVF 317 (420)
Q Consensus 296 IR~KI~AVI~NAraiL~I~~E~ 317 (420)
=+..=+ |.+++++...
T Consensus 117 GkKtAe------rIilELkdK~ 132 (188)
T PRK14606 117 SKKTAE------RIVMELKDEF 132 (188)
T ss_pred CHHHHH------HHHHHHHHhh
Confidence 532111 4566777664
Done!