Query psy7153
Match_columns 131
No_of_seqs 176 out of 598
Neff 3.5
Searched_HMMs 46136
Date Fri Aug 16 19:32:48 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7153.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7153hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0519 GuaA GMP synthase, PP- 100.0 1.8E-44 3.9E-49 303.4 5.8 102 10-117 122-223 (315)
2 KOG1622|consensus 100.0 2.1E-39 4.6E-44 286.1 7.4 126 2-130 327-454 (552)
3 PLN02347 GMP synthetase 100.0 6.1E-33 1.3E-37 245.1 7.4 112 8-121 334-448 (536)
4 cd01997 GMP_synthase_C The C-t 99.9 6.8E-27 1.5E-31 193.6 7.1 106 10-119 101-206 (295)
5 TIGR00884 guaA_Cterm GMP synth 99.9 1.3E-26 2.7E-31 192.7 5.8 105 10-120 118-222 (311)
6 PRK00919 GMP synthase subunit 99.9 7.6E-24 1.6E-28 176.9 6.7 101 9-119 119-219 (307)
7 PRK00074 guaA GMP synthase; Re 99.9 3.1E-23 6.6E-28 181.4 7.1 106 9-119 316-421 (511)
8 PF02540 NAD_synthase: NAD syn 99.6 4.7E-16 1E-20 125.2 3.2 63 54-122 145-208 (242)
9 PRK13980 NAD synthetase; Provi 99.5 1.8E-14 3.8E-19 116.1 5.5 62 55-121 157-219 (265)
10 PRK00876 nadE NAD synthetase; 99.4 1E-13 2.2E-18 117.2 5.3 60 54-118 213-275 (326)
11 PRK00768 nadE NAD synthetase; 99.4 4.6E-13 9.9E-18 110.9 4.7 62 54-117 176-238 (268)
12 cd00553 NAD_synthase NAD+ synt 99.4 6.2E-13 1.3E-17 105.6 5.0 63 54-121 154-217 (248)
13 COG0171 NadE NAD synthase [Coe 99.3 9.3E-13 2E-17 109.2 5.1 64 52-120 159-226 (268)
14 TIGR00552 nadE NAD+ synthetase 99.3 3.4E-12 7.4E-17 101.7 5.3 61 55-120 153-214 (250)
15 PTZ00323 NAD+ synthase; Provis 99.3 6.6E-12 1.4E-16 104.8 5.9 68 54-126 187-255 (294)
16 PRK13981 NAD synthetase; Provi 99.2 1.8E-11 3.9E-16 106.7 5.1 62 55-122 412-481 (540)
17 PRK02628 nadE NAD synthetase; 98.7 2E-08 4.4E-13 91.0 4.6 64 55-124 501-583 (679)
18 PLN02339 NAD+ synthase (glutam 98.2 1.4E-06 3E-11 79.9 5.0 61 55-120 534-606 (700)
19 TIGR00268 conserved hypothetic 96.9 0.0011 2.4E-08 53.2 3.9 60 55-118 134-197 (252)
20 cd01998 tRNA_Me_trans tRNA met 96.6 0.0025 5.4E-08 53.9 4.0 77 9-89 113-191 (349)
21 cd01990 Alpha_ANH_like_I This 95.6 0.025 5.5E-07 43.0 4.7 40 54-97 121-162 (202)
22 PF03054 tRNA_Me_trans: tRNA m 95.5 0.0098 2.1E-07 51.5 2.5 76 9-89 116-195 (356)
23 cd01993 Alpha_ANH_like_II This 95.4 0.0049 1.1E-07 45.2 0.4 76 9-89 106-183 (185)
24 TIGR02432 lysidine_TilS_N tRNA 95.1 0.0065 1.4E-07 45.5 0.3 65 9-79 99-167 (189)
25 cd01992 PP-ATPase N-terminal d 94.6 0.011 2.3E-07 43.8 0.3 65 9-79 96-163 (185)
26 KOG2805|consensus 94.2 0.033 7.2E-07 49.1 2.5 33 55-89 169-201 (377)
27 cd01712 ThiI ThiI is required 93.9 0.098 2.1E-06 39.2 4.2 29 54-82 133-161 (177)
28 PRK00143 mnmA tRNA-specific 2- 93.1 0.066 1.4E-06 45.4 2.3 33 55-89 158-190 (346)
29 PRK08349 hypothetical protein; 92.9 0.62 1.3E-05 35.9 7.3 79 33-118 105-192 (198)
30 TIGR00364 exsB protein. This p 92.8 0.079 1.7E-06 40.7 2.2 24 55-78 151-177 (201)
31 PRK14664 tRNA-specific 2-thiou 92.5 0.08 1.7E-06 45.9 2.1 34 55-89 153-186 (362)
32 PRK14665 mnmA tRNA-specific 2- 92.4 0.11 2.4E-06 44.7 2.9 34 55-89 158-191 (360)
33 PRK01565 thiamine biosynthesis 91.0 0.19 4.2E-06 43.3 2.8 35 54-89 309-343 (394)
34 PRK11106 queuosine biosynthesi 90.4 0.19 4.2E-06 40.9 2.2 26 54-79 154-180 (231)
35 PF02568 ThiI: Thiamine biosyn 89.3 0.18 3.9E-06 40.5 1.2 57 8-79 107-163 (197)
36 cd01995 ExsB ExsB is a transcr 87.9 0.4 8.6E-06 35.4 2.2 28 54-81 115-142 (169)
37 TIGR00420 trmU tRNA (5-methyla 87.8 0.38 8.2E-06 41.2 2.2 33 55-89 162-194 (352)
38 COG0482 TrmU Predicted tRNA(5- 87.4 0.41 8.9E-06 42.0 2.3 33 55-89 161-193 (356)
39 cd01999 Argininosuccinate_Synt 86.9 0.5 1.1E-05 41.3 2.5 45 53-97 134-182 (385)
40 PRK14561 hypothetical protein; 84.7 3.6 7.7E-05 32.1 6.1 47 55-118 126-173 (194)
41 KOG2303|consensus 81.5 2 4.4E-05 40.5 4.1 59 54-114 533-601 (706)
42 PRK00509 argininosuccinate syn 81.2 1.2 2.7E-05 39.3 2.5 36 53-88 137-175 (399)
43 PF01171 ATP_bind_3: PP-loop f 80.7 0.87 1.9E-05 34.4 1.3 62 9-78 96-162 (182)
44 TIGR00342 thiazole biosynthesi 78.8 1.6 3.4E-05 37.4 2.3 32 54-86 305-336 (371)
45 PF06508 QueC: Queuosine biosy 74.6 1.7 3.8E-05 34.5 1.4 30 53-82 151-180 (209)
46 PRK13820 argininosuccinate syn 74.0 2.7 5.9E-05 37.1 2.6 42 54-95 136-180 (394)
47 PF01680 SOR_SNZ: SOR/SNZ fami 70.2 3.1 6.6E-05 34.5 1.9 51 33-83 138-193 (208)
48 COG1606 ATP-utilizing enzymes 68.1 3.7 8E-05 35.2 2.0 39 55-97 140-180 (269)
49 PLN00200 argininosuccinate syn 67.8 4.3 9.3E-05 36.0 2.5 28 53-80 141-171 (404)
50 PF07498 Rho_N: Rho terminatio 65.4 3.3 7.2E-05 25.6 1.0 18 61-78 3-20 (43)
51 PF15599 Imm38: Immunity prote 62.6 13 0.00027 27.6 3.8 57 65-121 4-73 (124)
52 PRK08384 thiamine biosynthesis 60.6 5.9 0.00013 34.7 2.0 59 54-120 314-373 (381)
53 PRK10696 tRNA 2-thiocytidine b 58.9 7.7 0.00017 31.2 2.2 24 55-78 173-196 (258)
54 cd01713 PAPS_reductase This do 52.9 15 0.00033 25.6 2.7 35 54-88 136-170 (173)
55 PF02037 SAP: SAP domain; Int 49.9 15 0.00033 21.6 1.9 20 60-79 1-20 (35)
56 TIGR00032 argG argininosuccina 49.5 12 0.00026 32.9 2.1 35 53-87 134-170 (394)
57 PF10288 DUF2392: Protein of u 49.1 12 0.00027 26.6 1.8 31 53-83 31-61 (107)
58 TIGR00014 arsC arsenate reduct 45.3 22 0.00048 25.5 2.6 57 62-128 35-93 (114)
59 PF04031 Las1: Las1-like ; In 44.3 14 0.00031 28.4 1.5 29 55-83 90-119 (154)
60 PF14265 DUF4355: Domain of un 42.8 29 0.00064 24.9 2.9 47 64-121 70-116 (125)
61 PF11007 CotJA: Spore coat ass 42.7 7.1 0.00015 24.0 -0.3 12 12-23 22-33 (36)
62 COG0603 Predicted PP-loop supe 40.9 20 0.00043 29.8 2.0 27 56-82 157-183 (222)
63 TIGR01565 homeo_ZF_HD homeobox 36.6 34 0.00074 22.8 2.2 20 63-82 30-49 (58)
64 PF02567 PhzC-PhzF: Phenazine 36.1 34 0.00073 27.2 2.6 39 62-100 22-61 (281)
65 PF13936 HTH_38: Helix-turn-he 34.3 24 0.00052 21.5 1.2 17 68-84 23-39 (44)
66 PF08815 Nuc_rec_co-act: Nucle 33.3 7.7 0.00017 25.9 -1.2 31 56-87 13-43 (51)
67 COG0214 SNZ1 Pyridoxine biosyn 33.3 26 0.00056 30.4 1.6 50 34-83 145-199 (296)
68 smart00513 SAP Putative DNA-bi 33.1 46 0.00099 19.3 2.2 19 61-79 2-20 (35)
69 PF10668 Phage_terminase: Phag 32.8 25 0.00055 23.7 1.1 18 67-84 24-41 (60)
70 PF13384 HTH_23: Homeodomain-l 32.6 26 0.00056 20.9 1.1 19 66-84 18-36 (50)
71 TIGR00654 PhzF_family phenazin 31.3 68 0.0015 26.0 3.6 46 62-107 29-76 (297)
72 cd04762 HTH_MerR-trunc Helix-T 31.0 32 0.00068 19.4 1.3 18 68-85 3-20 (49)
73 PF02952 Fucose_iso_C: L-fucos 30.9 33 0.00071 25.0 1.6 16 64-79 123-138 (142)
74 COG1513 CynS Cyanate lyase [In 30.8 42 0.00092 26.7 2.3 46 61-112 46-97 (151)
75 PRK01269 tRNA s(4)U8 sulfurtra 30.5 39 0.00084 30.0 2.3 26 54-79 310-335 (482)
76 PF00046 Homeobox: Homeobox do 30.3 49 0.0011 20.1 2.1 24 60-83 22-45 (57)
77 PF12116 SpoIIID: Stage III sp 30.0 29 0.00062 25.2 1.1 22 64-85 18-39 (82)
78 PF02786 CPSase_L_D2: Carbamoy 29.8 41 0.00089 26.8 2.1 46 63-111 25-70 (211)
79 PF10534 CRIC_ras_sig: Connect 29.2 18 0.0004 26.4 0.0 35 80-129 57-92 (95)
80 smart00550 Zalpha Z-DNA-bindin 28.4 29 0.00063 22.8 0.9 18 68-85 25-42 (68)
81 PRK10026 arsenate reductase; P 28.1 61 0.0013 24.8 2.7 57 62-128 38-95 (141)
82 cd03286 ABC_MSH6_euk MutS6 hom 27.4 37 0.0008 27.2 1.5 18 68-85 201-218 (218)
83 PF07453 NUMOD1: NUMOD1 domain 27.3 45 0.00097 19.3 1.5 17 68-84 19-35 (37)
84 cd03034 ArsC_ArsC Arsenate Red 26.8 58 0.0013 23.1 2.3 57 62-128 35-92 (112)
85 cd08205 RuBisCO_IV_RLP Ribulos 26.8 65 0.0014 27.9 2.9 48 74-123 100-160 (367)
86 PF04428 Choline_kin_N: Cholin 25.8 55 0.0012 21.7 1.8 17 63-79 27-43 (53)
87 PF01832 Glucosaminidase: Mann 25.7 9 0.0002 27.3 -2.1 36 3-48 11-46 (136)
88 cd03036 ArsC_like Arsenate Red 25.5 70 0.0015 22.6 2.5 59 62-128 35-94 (111)
89 PF04760 IF2_N: Translation in 25.5 31 0.00068 21.4 0.6 16 68-83 6-21 (54)
90 PF09339 HTH_IclR: IclR helix- 25.1 42 0.0009 20.6 1.1 17 68-84 21-37 (52)
91 PF06056 Terminase_5: Putative 24.8 45 0.00097 21.9 1.3 17 68-84 16-32 (58)
92 TIGR00269 conserved hypothetic 24.8 2.1E+02 0.0047 20.2 4.9 32 57-89 4-35 (104)
93 COG0045 SucC Succinyl-CoA synt 24.2 56 0.0012 29.4 2.1 29 55-83 145-173 (387)
94 cd03287 ABC_MSH3_euk MutS3 hom 24.0 48 0.001 26.6 1.5 17 69-85 206-222 (222)
95 cd01986 Alpha_ANH_like Adenine 24.0 13 0.00028 25.4 -1.5 42 9-60 61-102 (103)
96 PF08442 ATP-grasp_2: ATP-gras 23.9 59 0.0013 26.0 2.0 27 56-82 147-173 (202)
97 PRK13617 psbV cytochrome c-550 23.9 74 0.0016 25.6 2.6 40 37-76 96-153 (170)
98 PF00382 TFIIB: Transcription 23.8 46 0.00099 21.5 1.2 17 68-84 1-17 (71)
99 cd00086 homeodomain Homeodomai 23.5 70 0.0015 19.1 1.9 24 60-83 22-45 (59)
100 TIGR01764 excise DNA binding d 23.4 54 0.0012 18.6 1.3 17 68-84 4-20 (49)
101 cd08779 Death_PIDD Death Domai 23.3 37 0.0008 23.6 0.7 25 60-84 8-32 (86)
102 cd03033 ArsC_15kD Arsenate Red 22.8 74 0.0016 23.0 2.2 56 62-128 36-91 (113)
103 PF03960 ArsC: ArsC family; I 22.2 1E+02 0.0022 21.5 2.8 57 63-128 33-90 (110)
104 PF15508 NAAA-beta: beta subun 22.2 67 0.0015 22.4 1.8 18 64-81 68-85 (95)
105 PF01381 HTH_3: Helix-turn-hel 22.1 83 0.0018 18.8 2.0 22 60-81 33-54 (55)
106 COG4189 Predicted transcriptio 22.0 55 0.0012 28.5 1.6 18 66-83 38-55 (308)
107 PF02245 Pur_DNA_glyco: Methyl 22.0 34 0.00074 27.4 0.3 41 61-105 2-42 (184)
108 PF12244 DUF3606: Protein of u 21.9 67 0.0015 20.9 1.7 22 63-84 18-39 (57)
109 PF02796 HTH_7: Helix-turn-hel 21.8 58 0.0013 19.7 1.3 18 67-84 23-40 (45)
110 cd08306 Death_FADD Fas-associa 21.3 39 0.00085 23.4 0.5 24 60-83 8-31 (86)
111 cd08313 Death_TNFR1 Death doma 21.2 70 0.0015 22.4 1.7 19 66-84 12-30 (80)
112 PRK02866 cyanate hydratase; Va 20.7 86 0.0019 24.6 2.3 48 60-112 42-94 (147)
113 cd00569 HTH_Hin_like Helix-tur 20.5 78 0.0017 15.4 1.5 18 67-84 23-40 (42)
114 cd04761 HTH_MerR-SF Helix-Turn 20.4 64 0.0014 18.7 1.2 18 68-85 3-20 (49)
115 PRK10853 putative reductase; P 20.3 93 0.002 22.7 2.3 58 62-128 36-93 (118)
116 PF01022 HTH_5: Bacterial regu 20.1 45 0.00098 20.1 0.5 18 68-85 18-35 (47)
117 PF00440 TetR_N: Bacterial reg 20.0 48 0.001 19.9 0.6 19 67-85 18-36 (47)
No 1
>COG0519 GuaA GMP synthase, PP-ATPase domain/subunit [Nucleotide transport and metabolism]
Probab=100.00 E-value=1.8e-44 Score=303.39 Aligned_cols=102 Identities=46% Similarity=0.764 Sum_probs=89.7
Q ss_pred CceeeccccccceeeccCCCCCCCCCccccccCCchHHHHHhhcccccccccccchHHHHHHHHHcCCChhhhccCCCCC
Q psy7153 10 QTLLCQGTLRPDLIESASHLASNKADVIKTHHNDSPLIRALREQGKVIEPLKDFHKDEVRKLGLDLGLTPEVVMRHPFPG 89 (131)
Q Consensus 10 ~~~l~QGTiypD~iES~~~~~~~~a~~IKtHHNv~~l~~~~~~~~kdiePL~~L~KdEVR~Lg~~LGlP~~Ii~k~PfpG 89 (131)
..||+|||||||||||++ +++.+|||||||||||++|+ ++++|||++|||||||+||++||||++|++||||||
T Consensus 122 ~~~LaQGTiYpDvIES~~----g~~~~IKSHHNVGGLP~~m~--lkLvEPLr~LfKDEVR~lg~~LGlp~~iv~RhPFPG 195 (315)
T COG0519 122 AEFLAQGTIYPDVIESGT----GKAGTIKSHHNVGGLPEDMK--LKLVEPLRELFKDEVRELGRELGLPEEIVYRHPFPG 195 (315)
T ss_pred cceEEecccccceeeecC----CCCCccccccccCCCccccc--eeeeHHHHHHhHHHHHHHHHHhCCCHHHhccCCCCC
Confidence 789999999999999993 34589999999999999996 589999999999999999999999999999999999
Q ss_pred CCceeeeccCcccccccChHHHHHHHHH
Q psy7153 90 PGLAIRVICGEERYIEKDYSETQVLVKI 117 (131)
Q Consensus 90 PGLaiR~~g~~e~~l~~~y~~~d~iL~~ 117 (131)
|||||||+|.-.+|-..--.+.|.|+..
T Consensus 196 PGLaiRilGevt~Ekl~ilR~Ad~I~~e 223 (315)
T COG0519 196 PGLAVRILGEVTREKLEILREADAIVEE 223 (315)
T ss_pred CCeEEEeecccCHHHHHHHHHHhHHHHH
Confidence 9999999999655544445555666544
No 2
>KOG1622|consensus
Probab=100.00 E-value=2.1e-39 Score=286.11 Aligned_cols=126 Identities=56% Similarity=0.846 Sum_probs=118.5
Q ss_pred ccCCCCCCCc--eeeccccccceeeccCCCCCCCCCccccccCCchHHHHHhhcccccccccccchHHHHHHHHHcCCCh
Q psy7153 2 EELKLDPNQT--LLCQGTLRPDLIESASHLASNKADVIKTHHNDSPLIRALREQGKVIEPLKDFHKDEVRKLGLDLGLTP 79 (131)
Q Consensus 2 ~~~~~~~~~~--~l~QGTiypD~iES~~~~~~~~a~~IKtHHNv~~l~~~~~~~~kdiePL~~L~KdEVR~Lg~~LGlP~ 79 (131)
++++.+++.. ||||||||||+|||++..+++++++||||||+++|++.||..+|.+|||++|+|||||+||+.||+|+
T Consensus 327 ~~l~~k~~~~~~flaQgtL~Pd~ieS~s~~g~~~a~tIKThhn~~~L~r~lrklgK~ieplk~~~kDEvr~lgk~lGlp~ 406 (552)
T KOG1622|consen 327 SELNKKHGEKESFLAQGTLRPDLIESASVYGSGHAETIKTHHNDTGLIRDLRKLGKVIEPLKDFHKDEVRELGKDLGLPE 406 (552)
T ss_pred HHhhhccCccceeeecccccchhhhhccccCCchhhhhhcccccchHHHHHHHhcccCchhHHHHHHHHHHhhhhcCCch
Confidence 4677888877 99999999999999999888899999999999999999988889999999999999999999999999
Q ss_pred hhhccCCCCCCCceeeeccCcccccccChHHHHHHHHHHHhhhhhhhhcCC
Q psy7153 80 EVVMRHPFPGPGLAIRVICGEERYIEKDYSETQVLVKIIVEYDQMFKKIYP 130 (131)
Q Consensus 80 ~Ii~k~PfpGPGLaiR~~g~~e~~l~~~y~~~d~iL~~~~~~~~~~~k~~~ 130 (131)
++++||||||||||||++|+.+.. +|..++.+.+....+.++.+|+|.
T Consensus 407 ~Lv~rhPfpGPgLaIRvL~~~~~~---~~~~~~ii~~~~~~f~~~i~~~~g 454 (552)
T KOG1622|consen 407 SLVPRHPFPGPGLAIRVLCAVTAR---DLPQLEIIRKVDRIFIKSIRKDHG 454 (552)
T ss_pred hhhccCCCCCCCeEEEEeeccccc---cchHHHHHHHHHHHHHHHhcccch
Confidence 999999999999999999998765 899999999999999999998875
No 3
>PLN02347 GMP synthetase
Probab=99.98 E-value=6.1e-33 Score=245.09 Aligned_cols=112 Identities=41% Similarity=0.597 Sum_probs=95.2
Q ss_pred CCCceeeccccccceeeccCCCCC--CCCCccccccCCchHHHHHhhcccccccccccchHHHHHHHHHcCCChhhhccC
Q psy7153 8 PNQTLLCQGTLRPDLIESASHLAS--NKADVIKTHHNDSPLIRALREQGKVIEPLKDFHKDEVRKLGLDLGLTPEVVMRH 85 (131)
Q Consensus 8 ~~~~~l~QGTiypD~iES~~~~~~--~~a~~IKtHHNv~~l~~~~~~~~kdiePL~~L~KdEVR~Lg~~LGlP~~Ii~k~ 85 (131)
.+..||+|||+|||+|||+...+. ++|++|||||||++||..+. .+.++||++|+|+|||++|++||||++|++|+
T Consensus 334 ~~~~~l~qGt~~~D~~es~~r~g~~~~~~~~ik~hhn~~~l~~~~~--~~ii~PL~~l~K~eVR~la~~lgl~~~~~~~~ 411 (536)
T PLN02347 334 KKPAFLVQGTLYPDVIESCPPPGSGRTHSHTIKSHHNVGGLPKDMK--LKLIEPLKLLFKDEVRKLGRLLGVPEAFLKRH 411 (536)
T ss_pred CCCcEEccCCcccccccccCCCCCccccccceeeecccccChHHHH--CccccchhhCcHHHHHHHHHHcCCCHHHhcCC
Confidence 345899999999999999643323 35899999999999999874 57999999999999999999999999999999
Q ss_pred CCCCCCceeeeccCc-ccccccChHHHHHHHHHHHhh
Q psy7153 86 PFPGPGLAIRVICGE-ERYIEKDYSETQVLVKIIVEY 121 (131)
Q Consensus 86 PfpGPGLaiR~~g~~-e~~l~~~y~~~d~iL~~~~~~ 121 (131)
||||||||+||+|.. .++...-.++.|.|+...+..
T Consensus 412 p~p~p~La~Ri~g~~~~~~~l~~~~~ad~i~~~~~~~ 448 (536)
T PLN02347 412 PFPGPGLAVRVLGDVTEGNALDILRQVDEIFINSIKD 448 (536)
T ss_pred CcCCCCEEeeeCCccCCHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999985 444345678888888776544
No 4
>cd01997 GMP_synthase_C The C-terminal domain of GMP synthetase. It contains two subdomains; the ATP pyrophosphatase domain which closes to the N-termial and the dimerization domain at C-terminal end. The ATP-PPase is a twisted, five-stranded parallel beta-sheet sandwiched between helical layers. It has a signature nucleotide-binding motif, or P-loop, at the end of the first-beta strand.The dimerization domain formed by the C-terminal 115 amino acid for prokaryotic proteins. It is adjacent to teh ATP-binding site of the ATP-PPase subdomain. The largest difference between the primary sequence of prokaryotic and eukaryotic GMP synthetase map to the dimerization domain.Eukaryotic GMP synthetase has several large insertions relative to prokaryotes.
Probab=99.93 E-value=6.8e-27 Score=193.58 Aligned_cols=106 Identities=47% Similarity=0.712 Sum_probs=88.7
Q ss_pred CceeeccccccceeeccCCCCCCCCCccccccCCchHHHHHhhcccccccccccchHHHHHHHHHcCCChhhhccCCCCC
Q psy7153 10 QTLLCQGTLRPDLIESASHLASNKADVIKTHHNDSPLIRALREQGKVIEPLKDFHKDEVRKLGLDLGLTPEVVMRHPFPG 89 (131)
Q Consensus 10 ~~~l~QGTiypD~iES~~~~~~~~a~~IKtHHNv~~l~~~~~~~~kdiePL~~L~KdEVR~Lg~~LGlP~~Ii~k~PfpG 89 (131)
..+++|||.|||++||..... .+++||+|||+++++... ..++++||.+|+|+|||++|++||||.++++|+||||
T Consensus 101 ~~~Ia~Gh~~dD~~Es~~~~~--~~~~IKs~~n~~Gl~a~~--~~~vi~PL~~l~K~EVR~lar~lGLp~~~~~~~Pfp~ 176 (295)
T cd01997 101 AEYLAQGTLYPDVIESGSGKG--SADTIKSHHNVGGLPEDM--KLKLIEPLRDLFKDEVRELGRELGLPEEIVERHPFPG 176 (295)
T ss_pred CCEEEECCcccchhhhccccc--ccccccccccccccchHh--hCCcccccccCcHHHHHHHHHHcCCCchhhCCCCCCC
Confidence 569999999999999986432 278999999999999764 3689999999999999999999999999999999999
Q ss_pred CCceeeeccCcccccccChHHHHHHHHHHH
Q psy7153 90 PGLAIRVICGEERYIEKDYSETQVLVKIIV 119 (131)
Q Consensus 90 PGLaiR~~g~~e~~l~~~y~~~d~iL~~~~ 119 (131)
||||+|++|+..++-..--++.+.++..-.
T Consensus 177 p~La~Ri~g~it~e~l~~~~~ae~~~~~~~ 206 (295)
T cd01997 177 PGLAVRILGEVTEEKLEILREADAIVEEEL 206 (295)
T ss_pred CcceeEEecCCCHHHHHHHHHHHHHHHHHH
Confidence 999999999655544444555555555533
No 5
>TIGR00884 guaA_Cterm GMP synthase (glutamine-hydrolyzing), C-terminal domain or B subunit. This protein of purine de novo biosynthesis is well-conserved. However, it appears to split into two separate polypeptide chains in most of the Archaea. This C-terminal region would be the larger subunit
Probab=99.93 E-value=1.3e-26 Score=192.72 Aligned_cols=105 Identities=46% Similarity=0.722 Sum_probs=89.6
Q ss_pred CceeeccccccceeeccCCCCCCCCCccccccCCchHHHHHhhcccccccccccchHHHHHHHHHcCCChhhhccCCCCC
Q psy7153 10 QTLLCQGTLRPDLIESASHLASNKADVIKTHHNDSPLIRALREQGKVIEPLKDFHKDEVRKLGLDLGLTPEVVMRHPFPG 89 (131)
Q Consensus 10 ~~~l~QGTiypD~iES~~~~~~~~a~~IKtHHNv~~l~~~~~~~~kdiePL~~L~KdEVR~Lg~~LGlP~~Ii~k~PfpG 89 (131)
..+++|||.|||++||.. +.+++||||||+++++..+. .++++||.+|+|+|||++|+.||||.++++|+||||
T Consensus 118 ~~~la~Gt~~dD~~Es~~----G~~~~iks~~~~~gl~~~~~--~~ii~PL~~l~K~EVr~la~~lgLp~~~~~~~Pf~~ 191 (311)
T TIGR00884 118 AEYLAQGTIYPDVIESAA----GTAHVIKSHHNVGGLPEDMK--LKLVEPLRELFKDEVRKLGKELGLPEEIVWRHPFPG 191 (311)
T ss_pred CCEEEECCCChhhhhhcc----ChhHhhhccCccccCChhhc--CceEEEcccCcHHHHHHHHHHcCCCHHHhhCCCCCC
Confidence 569999999999999974 34678999999999998764 579999999999999999999999999999999999
Q ss_pred CCceeeeccCcccccccChHHHHHHHHHHHh
Q psy7153 90 PGLAIRVICGEERYIEKDYSETQVLVKIIVE 120 (131)
Q Consensus 90 PGLaiR~~g~~e~~l~~~y~~~d~iL~~~~~ 120 (131)
||||+||+|.-.++...--.+.+.++...+.
T Consensus 192 p~La~Ri~g~it~e~l~~~~~ae~~~~~~~~ 222 (311)
T TIGR00884 192 PGLAVRVLGEVTKEKLEILRRADAIVIEELK 222 (311)
T ss_pred CceEeeeecccCHHHHHHHHHHHHHHHHHHH
Confidence 9999999995455555556666776665443
No 6
>PRK00919 GMP synthase subunit B; Validated
Probab=99.89 E-value=7.6e-24 Score=176.88 Aligned_cols=101 Identities=43% Similarity=0.622 Sum_probs=85.5
Q ss_pred CCceeeccccccceeeccCCCCCCCCCccccccCCchHHHHHhhcccccccccccchHHHHHHHHHcCCChhhhccCCCC
Q psy7153 9 NQTLLCQGTLRPDLIESASHLASNKADVIKTHHNDSPLIRALREQGKVIEPLKDFHKDEVRKLGLDLGLTPEVVMRHPFP 88 (131)
Q Consensus 9 ~~~~l~QGTiypD~iES~~~~~~~~a~~IKtHHNv~~l~~~~~~~~kdiePL~~L~KdEVR~Lg~~LGlP~~Ii~k~Pfp 88 (131)
+..+++|||.|||++|+.+ .||+|||++++|..+. .++++||.+|+|+|||++|+.||||.++++|+|||
T Consensus 119 g~~~Ia~Gtn~dD~iE~r~--------~iks~~nv~gl~~~~~--~~Ii~PL~~l~K~EVr~la~~lGLp~~~~~r~p~~ 188 (307)
T PRK00919 119 GAEYLVQGTIAPDWIESEG--------GIKSHHNVGGLPEGMV--LKIVEPLRDLYKDEVREVARALGLPEEISERMPFP 188 (307)
T ss_pred CCCEEEECCCCcchhhccC--------cccccccccccChhhc--CCcccCchhCcHHHHHHHHHHcCCChhhhCCCCCC
Confidence 4569999999999999864 3999999999987663 57999999999999999999999999999999999
Q ss_pred CCCceeeeccCcccccccChHHHHHHHHHHH
Q psy7153 89 GPGLAIRVICGEERYIEKDYSETQVLVKIIV 119 (131)
Q Consensus 89 GPGLaiR~~g~~e~~l~~~y~~~d~iL~~~~ 119 (131)
|||||+||.|.-.++-..--++.+.++..-+
T Consensus 189 ~pcLa~Ri~g~vt~e~l~~v~~ae~~~~~~~ 219 (307)
T PRK00919 189 GPGLAVRIIGEVTEEKLEIVREANAIVEEEV 219 (307)
T ss_pred CCceeEEeecccCHHHHHHHHHHHHHHHHHH
Confidence 9999999999645554455566666665533
No 7
>PRK00074 guaA GMP synthase; Reviewed
Probab=99.88 E-value=3.1e-23 Score=181.41 Aligned_cols=106 Identities=46% Similarity=0.720 Sum_probs=87.2
Q ss_pred CCceeeccccccceeeccCCCCCCCCCccccccCCchHHHHHhhcccccccccccchHHHHHHHHHcCCChhhhccCCCC
Q psy7153 9 NQTLLCQGTLRPDLIESASHLASNKADVIKTHHNDSPLIRALREQGKVIEPLKDFHKDEVRKLGLDLGLTPEVVMRHPFP 88 (131)
Q Consensus 9 ~~~~l~QGTiypD~iES~~~~~~~~a~~IKtHHNv~~l~~~~~~~~kdiePL~~L~KdEVR~Lg~~LGlP~~Ii~k~Pfp 88 (131)
+..+++|||.|+|++||.... .+++||+|||++|++.... .+.++||.+|+|+|||++|+.+|||.++++|+|||
T Consensus 316 g~~~latGhn~dD~~Et~~~~---~~~~ik~~~~l~Gl~~~~~--~~ii~PL~~l~K~EIr~~a~~~gLp~~~~~~~p~p 390 (511)
T PRK00074 316 GVKFLAQGTLYPDVIESGGTK---KAATIKSHHNVGGLPEDMK--LKLVEPLRELFKDEVRKLGLELGLPEEIVYRHPFP 390 (511)
T ss_pred CCCEEEECCCcchhhhhcCCC---CccccccccCccCcChhHh--cccccchhhcCHHHHHHHHHHcCCCHHHhCCCCCC
Confidence 567999999999999997432 5779999999999998653 46999999999999999999999999999999999
Q ss_pred CCCceeeeccCcccccccChHHHHHHHHHHH
Q psy7153 89 GPGLAIRVICGEERYIEKDYSETQVLVKIIV 119 (131)
Q Consensus 89 GPGLaiR~~g~~e~~l~~~y~~~d~iL~~~~ 119 (131)
|||||+||+|.-.++...--++.+.++...+
T Consensus 391 ~~~la~Ri~g~it~e~l~~~~~ae~~~~~~~ 421 (511)
T PRK00074 391 GPGLAIRILGEVTKEKLDILREADAIFIEEL 421 (511)
T ss_pred CCceeeEEecccCHHHHHHHHHHHHHHHHHH
Confidence 9999999999744444344455555554433
No 8
>PF02540 NAD_synthase: NAD synthase; InterPro: IPR022310 NAD+ synthase (6.3.5.1 from EC) catalyzes the last step in the biosynthesis of nicotinamide adenine dinucleotide and is induced by stress factors such as heat shock and glucose limitation. The three-dimensional structure of NH3-dependent NAD+ synthetase from Bacillus subtilis, in its free form and in complex with ATP shows that the enzyme consists of a tight homodimer with alpha/beta subunit topology []. Catalyzes the synthesis of GMP from XMP. The protein is a homodimer, but in the archaea it is a heterodimer composed of a glutamine amidotransferase subunit (A) and a GMP-binding subunit (B). This entry contains the GMP-binding subunit (B). ; PDB: 2VXO_A 3UOW_B 3N05_A 2DPL_B 3A4I_A 3SEQ_D 3SZG_A 3SYT_A 3SDB_A 3SEZ_C ....
Probab=99.59 E-value=4.7e-16 Score=125.20 Aligned_cols=63 Identities=29% Similarity=0.454 Sum_probs=54.6
Q ss_pred ccccccccccchHHHHHHHHHcCCChhhhccCCCCCCCceeeeccCc-ccccccChHHHHHHHHHHHhhh
Q psy7153 54 GKVIEPLKDFHKDEVRKLGLDLGLTPEVVMRHPFPGPGLAIRVICGE-ERYIEKDYSETQVLVKIIVEYD 122 (131)
Q Consensus 54 ~kdiePL~~L~KdEVR~Lg~~LGlP~~Ii~k~PfpGPGLaiR~~g~~-e~~l~~~y~~~d~iL~~~~~~~ 122 (131)
.-|++||++|||+|||+||++||+|++|++|+|||| | |.||+ |.++|.+|+++|.+|+ +++..
T Consensus 145 ~~d~~Pi~~L~K~eV~~la~~l~ip~~ii~k~Psa~--L---~~gqtDE~elg~~Y~~lD~~l~-~~~~~ 208 (242)
T PF02540_consen 145 AGDIAPIADLYKTEVRELARYLGIPEEIIEKPPSAG--L---WPGQTDEDELGFSYEELDAILR-LIEEG 208 (242)
T ss_dssp SSSBETTTTS-HHHHHHHHHHTTCGHHHHCS--BHH--S---STT-BHHHHHTSTHHHHHHHHH-HHTSS
T ss_pred cccceeeCCcCHHHHHHHHHHHhhHHHHhcCCCCCC--C---CCCCCCHHHhCCCHHHHHHHHH-HHHcC
Confidence 469999999999999999999999999999999998 9 89996 9999999999999999 66554
No 9
>PRK13980 NAD synthetase; Provisional
Probab=99.51 E-value=1.8e-14 Score=116.05 Aligned_cols=62 Identities=19% Similarity=0.352 Sum_probs=58.0
Q ss_pred cccccccccchHHHHHHHHHcCCChhhhccCCCCCCCceeeeccCc-ccccccChHHHHHHHHHHHhh
Q psy7153 55 KVIEPLKDFHKDEVRKLGLDLGLTPEVVMRHPFPGPGLAIRVICGE-ERYIEKDYSETQVLVKIIVEY 121 (131)
Q Consensus 55 kdiePL~~L~KdEVR~Lg~~LGlP~~Ii~k~PfpGPGLaiR~~g~~-e~~l~~~y~~~d~iL~~~~~~ 121 (131)
.++.||++|+|+|||+||++||+|++|++|+|||| | |.||+ |.++|++|+++|.+|+..++.
T Consensus 157 ~~l~Pl~~l~K~eV~~la~~lgip~~i~~k~psa~--L---~~~q~De~~lg~~Y~~lD~~l~~~~~~ 219 (265)
T PRK13980 157 VDLNPIGDLYKTQVRELARHLGVPEDIIEKPPSAD--L---WEGQTDEGELGFSYETIDEILYLLFDK 219 (265)
T ss_pred cCcccCCCCcHHHHHHHHHHHCchHHHhCCCCCcC--C---CCCCCCHHHcCCCHHHHHHHHHHHHHc
Confidence 48999999999999999999999999999999999 8 68996 999999999999999887654
No 10
>PRK00876 nadE NAD synthetase; Reviewed
Probab=99.44 E-value=1e-13 Score=117.17 Aligned_cols=60 Identities=18% Similarity=0.325 Sum_probs=54.6
Q ss_pred ccccccccccchHHHHHHHHHcCCChhhhccCCCCCCCceeee-ccCc-ccc-cccChHHHHHHHHHH
Q psy7153 54 GKVIEPLKDFHKDEVRKLGLDLGLTPEVVMRHPFPGPGLAIRV-ICGE-ERY-IEKDYSETQVLVKII 118 (131)
Q Consensus 54 ~kdiePL~~L~KdEVR~Lg~~LGlP~~Ii~k~PfpGPGLaiR~-~g~~-e~~-l~~~y~~~d~iL~~~ 118 (131)
.-|++||++|||+|||+||++||+|++|++|+|||| | | .||+ |.+ +|++|+++|.+|+.+
T Consensus 213 ~~d~~Pi~~L~Kt~V~~La~~l~vP~~Ii~k~PSa~--L---~~~~q~de~~~~g~~Y~~lD~~L~~~ 275 (326)
T PRK00876 213 AADLKPIAHLYKTQVYALAEHLGVPEEIRRRPPTTD--T---YSLPQTQEEFYFALPYDRMDLCLYAL 275 (326)
T ss_pred cccchhccCCCHHHHHHHHHHhCCCHHHhcCCCCcc--c---CCCCCChhhhhcCCCHHHHHHHHHHh
Confidence 468999999999999999999999999999999998 8 6 4775 666 899999999999876
No 11
>PRK00768 nadE NAD synthetase; Reviewed
Probab=99.37 E-value=4.6e-13 Score=110.95 Aligned_cols=62 Identities=21% Similarity=0.155 Sum_probs=58.1
Q ss_pred ccccccccccchHHHHHHHHHcCCChhhhccCCCCCCCceeeeccCc-ccccccChHHHHHHHHH
Q psy7153 54 GKVIEPLKDFHKDEVRKLGLDLGLTPEVVMRHPFPGPGLAIRVICGE-ERYIEKDYSETQVLVKI 117 (131)
Q Consensus 54 ~kdiePL~~L~KdEVR~Lg~~LGlP~~Ii~k~PfpGPGLaiR~~g~~-e~~l~~~y~~~d~iL~~ 117 (131)
.-|+.||++|+|+|||+||++||+|++|++|+|+|| |+=|..||+ |.++|.+|+++|.+|..
T Consensus 176 ~~d~~pi~~L~KteV~~La~~l~vP~~ii~k~Psa~--L~~~~~gq~DE~~lg~~Y~~lD~~L~~ 238 (268)
T PRK00768 176 GADILPLFGLNKRQGRALLAALGAPEHLYEKVPTAD--LEDDRPGLPDEVALGVTYDQIDDYLEG 238 (268)
T ss_pred cccchhhcCCcHHHHHHHHHHhCCCHHHhcCCCCCC--cCCCCCCCCChhhcCCCHHHHHHHHhc
Confidence 359999999999999999999999999999999999 977778996 99999999999999976
No 12
>cd00553 NAD_synthase NAD+ synthase is a homodimer, which catalyzes the final step in de novo nicotinamide adenine dinucleotide (NAD+) biosynthesis, an amide transfer from either ammonia or glutamine to nicotinic acid adenine dinucleotide (NaAD). The conversion of NaAD to NAD+ occurs via an NAD-adenylate intermediate and requires ATP and Mg2+. The intemediate is subsequently cleaved into NAD+ and AMP. In many prokaryotes, such as E. coli , NAD synthetase consists of a single domain and is strictly ammonia dependent. In contrast, eukaryotes and other prokaryotes have an additional N-terminal amidohydrolase domain that prefer glutamine, Interestingly, NAD+ synthases in these prokaryotes, can also utilize ammonia as an amide source .
Probab=99.36 E-value=6.2e-13 Score=105.62 Aligned_cols=63 Identities=24% Similarity=0.321 Sum_probs=58.5
Q ss_pred ccccccccccchHHHHHHHHHcCCChhhhccCCCCCCCceeeeccCc-ccccccChHHHHHHHHHHHhh
Q psy7153 54 GKVIEPLKDFHKDEVRKLGLDLGLTPEVVMRHPFPGPGLAIRVICGE-ERYIEKDYSETQVLVKIIVEY 121 (131)
Q Consensus 54 ~kdiePL~~L~KdEVR~Lg~~LGlP~~Ii~k~PfpGPGLaiR~~g~~-e~~l~~~y~~~d~iL~~~~~~ 121 (131)
..++.||++|+|+|||++|+++|+|+.|++|+|||| | |.||+ |.++|++|+++|.+|+..++.
T Consensus 154 ~~~i~Pl~~l~K~eV~~la~~~~ip~~i~~k~psa~--l---~~~q~de~~lg~~Y~~lD~~l~~~~~~ 217 (248)
T cd00553 154 AADINPIGDLYKTQVRELARYLGVPESIIDKPPSAE--L---WPGQTDEDELGMPYEELDQFLYLRLEG 217 (248)
T ss_pred ccCccccCCCcHHHHHHHHHHHCchHHHhcCCCCcc--c---CCCCCCHHHhCCCHHHHHHHHHHHHhc
Confidence 359999999999999999999999999999999999 8 67996 999999999999999987654
No 13
>COG0171 NadE NAD synthase [Coenzyme metabolism]
Probab=99.35 E-value=9.3e-13 Score=109.24 Aligned_cols=64 Identities=23% Similarity=0.327 Sum_probs=58.4
Q ss_pred hcccccccccccchHHHHHHHHHcCCChhhhccCCCCCCCceeeecc---Cc-ccccccChHHHHHHHHHHHh
Q psy7153 52 EQGKVIEPLKDFHKDEVRKLGLDLGLTPEVVMRHPFPGPGLAIRVIC---GE-ERYIEKDYSETQVLVKIIVE 120 (131)
Q Consensus 52 ~~~kdiePL~~L~KdEVR~Lg~~LGlP~~Ii~k~PfpGPGLaiR~~g---~~-e~~l~~~y~~~d~iL~~~~~ 120 (131)
..+-|++||++|||+||++|++.||+|++|++|+|+|+ | |.+ |+ |.++|++|+++|.+|+.+++
T Consensus 159 Dg~~d~~Pi~~L~KtqV~~La~~l~ipe~I~~k~PTAe--L---~~~~~~q~DE~~lg~~Y~~lD~~L~~~~~ 226 (268)
T COG0171 159 DGAVDINPIADLYKTQVYALARHLGIPEEILKKPPTAD--L---WPDEPGQTDEAELGMPYEELDDILYGLLE 226 (268)
T ss_pred CcccChhhhcCCcHHHHHHHHHHcCCCHHHhcCCCCcc--c---cCCCCCCCCHHHhCCCHHHHHHHHHHhhh
Confidence 34579999999999999999999999999999999999 8 674 86 99999999999999998853
No 14
>TIGR00552 nadE NAD+ synthetase. NAD+ synthetase is a nearly ubiquitous enzyme for the final step in the biosynthesis of the essensial cofactor NAD. The member of this family from Bacillus subtilis is a strictly NH(3)-dependent NAD(+) synthetase of 272 amino acids. Proteins consisting only of the domain modeled here may be named as NH3-dependent NAD+ synthetase. Amidotransferase activity may reside in a separate protein, or not be present. Some other members of the family, such as from Mycobacterium tuberculosis, are considerably longer, contain an apparent amidotransferase domain, and show glutamine-dependent as well as NH(3)-dependent activity.
Probab=99.29 E-value=3.4e-12 Score=101.70 Aligned_cols=61 Identities=25% Similarity=0.299 Sum_probs=57.2
Q ss_pred cccccccccchHHHHHHHHHcCCChhhhccCCCCCCCceeeeccCc-ccccccChHHHHHHHHHHHh
Q psy7153 55 KVIEPLKDFHKDEVRKLGLDLGLTPEVVMRHPFPGPGLAIRVICGE-ERYIEKDYSETQVLVKIIVE 120 (131)
Q Consensus 55 kdiePL~~L~KdEVR~Lg~~LGlP~~Ii~k~PfpGPGLaiR~~g~~-e~~l~~~y~~~d~iL~~~~~ 120 (131)
.++.||.+++|.|||++|+++|+|+.|++|+|++| | |.||+ |.++|++|+++|.+|+.+.+
T Consensus 153 ~~i~PL~~l~K~eV~~lA~~~g~p~~i~~k~psa~--L---~~~q~de~~~g~~y~~~D~~l~~~~~ 214 (250)
T TIGR00552 153 CDIAPIGDLFKTQVYELAKRLNVPERIIEKPPTAD--L---FDGQTDETELGITYDELDDYLKGIEE 214 (250)
T ss_pred cCccccCCCcHHHHHHHHHHHCccHHHhCCCCCcC--C---CCCCcCHHHhCcCHHHHHHHHHHHhh
Confidence 58999999999999999999999999999999999 8 78996 99999999999999988654
No 15
>PTZ00323 NAD+ synthase; Provisional
Probab=99.26 E-value=6.6e-12 Score=104.79 Aligned_cols=68 Identities=18% Similarity=0.209 Sum_probs=61.4
Q ss_pred ccccccccccchHHHHHHHHHcCCChhhhccCCCCCCCceeeeccCc-ccccccChHHHHHHHHHHHhhhhhhh
Q psy7153 54 GKVIEPLKDFHKDEVRKLGLDLGLTPEVVMRHPFPGPGLAIRVICGE-ERYIEKDYSETQVLVKIIVEYDQMFK 126 (131)
Q Consensus 54 ~kdiePL~~L~KdEVR~Lg~~LGlP~~Ii~k~PfpGPGLaiR~~g~~-e~~l~~~y~~~d~iL~~~~~~~~~~~ 126 (131)
..++.|+++|+|+|||+||++||+|++|++|+|+|+ | |.||+ |.++|.+|+.+|.+++..+....+-+
T Consensus 187 ~~d~~pia~L~K~eVr~LAr~l~lp~~i~~kppSA~--L---~~~qtDE~elg~~Y~~lD~~~~~~~~~~~~~~ 255 (294)
T PTZ00323 187 VVDVQLISDLHKSEVFLVARELGVPENTLQAAPSAD--L---WEGQTDEDELGFPYDFVELYTEWYLKLNETEK 255 (294)
T ss_pred CcCchhhcCCcHHHHHHHHHHcCCCHHHhcCCCCcC--c---CCCCcCHhhcCCCHHHHHHHHHHHHHhhHHHH
Confidence 368999999999999999999999999999999998 8 57886 99999999999999999776665544
No 16
>PRK13981 NAD synthetase; Provisional
Probab=99.19 E-value=1.8e-11 Score=106.72 Aligned_cols=62 Identities=18% Similarity=0.225 Sum_probs=57.5
Q ss_pred cccccccccchHHHHHHHHHcC-------CChhhhccCCCCCCCceeeeccCc-ccccccChHHHHHHHHHHHhhh
Q psy7153 55 KVIEPLKDFHKDEVRKLGLDLG-------LTPEVVMRHPFPGPGLAIRVICGE-ERYIEKDYSETQVLVKIIVEYD 122 (131)
Q Consensus 55 kdiePL~~L~KdEVR~Lg~~LG-------lP~~Ii~k~PfpGPGLaiR~~g~~-e~~l~~~y~~~d~iL~~~~~~~ 122 (131)
-++.||++|+|+||++||++|| +|+.|++|+|+|+ | |.||+ |.++| +|+.+|.+|+.+++..
T Consensus 412 ~~~~pi~~l~K~~v~~la~~~~~~~~~~~vp~~i~~~~psa~--l---~~~q~de~~l~-~Y~~lD~~l~~~~~~~ 481 (540)
T PRK13981 412 GGFAPIKDVYKTLVYRLCRWRNTVSPGEVIPERIITKPPSAE--L---RPNQTDQDSLP-PYDVLDAILERLVEEE 481 (540)
T ss_pred cCccccCCCCHHHHHHHHHHHHhhcCCCcchHHHhCCCCCCC--C---CCCCcCccccC-CHHHHHHHHHHHHHcC
Confidence 5899999999999999999999 9999999999998 8 68996 99999 9999999999887654
No 17
>PRK02628 nadE NAD synthetase; Reviewed
Probab=98.67 E-value=2e-08 Score=91.01 Aligned_cols=64 Identities=14% Similarity=0.103 Sum_probs=57.4
Q ss_pred cccccccccchHHHHHHHHHc-----------CCChhhhccCCCCCCCceeeecc-------Cc-ccccccChHHHHHHH
Q psy7153 55 KVIEPLKDFHKDEVRKLGLDL-----------GLTPEVVMRHPFPGPGLAIRVIC-------GE-ERYIEKDYSETQVLV 115 (131)
Q Consensus 55 kdiePL~~L~KdEVR~Lg~~L-----------GlP~~Ii~k~PfpGPGLaiR~~g-------~~-e~~l~~~y~~~d~iL 115 (131)
-++.||++|+|++||+|++++ ++|++|++|+|||+ | +.+ |+ |.++| +|+.+|.+|
T Consensus 501 ~~~~~~~~l~Kt~v~~l~~~~~~~~~~~~~~~~ip~~i~~~~psae--L---~p~~~~g~~~q~ded~lg-pY~~~D~~l 574 (679)
T PRK02628 501 SHYNVNASVPKTLIQHLIRWVIASGQFDEAVSEVLLDILDTEISPE--L---VPADKEGEIVQSTEDIIG-PYELQDFFL 574 (679)
T ss_pred cccccccCCcHHHHHHHHHHHHhhccccccchhhHHHHhcCCCCcc--c---cCCCCCCCCCCcchhccC-CHHHHHHHH
Confidence 579999999999999999999 69999999999998 8 677 75 88888 999999999
Q ss_pred HHHHhhhhh
Q psy7153 116 KIIVEYDQM 124 (131)
Q Consensus 116 ~~~~~~~~~ 124 (131)
+..++...+
T Consensus 575 ~~~~~~~~~ 583 (679)
T PRK02628 575 YYFLRYGFR 583 (679)
T ss_pred HHHHhcCCC
Confidence 998876544
No 18
>PLN02339 NAD+ synthase (glutamine-hydrolysing)
Probab=98.22 E-value=1.4e-06 Score=79.93 Aligned_cols=61 Identities=23% Similarity=0.304 Sum_probs=52.3
Q ss_pred cccccccccchHHHHHH----HHHcCCC--hhhhccCCCCCCCceeeec-----cCc-ccccccChHHHHHHHHHHHh
Q psy7153 55 KVIEPLKDFHKDEVRKL----GLDLGLT--PEVVMRHPFPGPGLAIRVI-----CGE-ERYIEKDYSETQVLVKIIVE 120 (131)
Q Consensus 55 kdiePL~~L~KdEVR~L----g~~LGlP--~~Ii~k~PfpGPGLaiR~~-----g~~-e~~l~~~y~~~d~iL~~~~~ 120 (131)
-++.||++++|++||+| ++.+|+| ++|+.++|+|+ | +. +|+ |.+||++|++++.+.+.-..
T Consensus 534 ~~~~pi~~l~Kt~v~~l~~~~~~~~~~~il~~i~~~~pSaE--L---~p~~~~~~Q~dE~~lG~~Y~~l~~~~~l~~~ 606 (700)
T PLN02339 534 ADINPIGGISKQDLRSFLRWAATNLGYPSLAEVEAAPPTAE--L---EPIRDDYSQTDEEDMGMTYEELGVYGRLRKI 606 (700)
T ss_pred cCccccCCCcHHHHHHHHHHHHHhcCCCcHHHHhcCCCCcc--c---ccCCCCCCCCCHHHHCcCHHHHHHHHHHHhc
Confidence 47999999999999999 7778888 99999999998 7 33 575 99999999999987765443
No 19
>TIGR00268 conserved hypothetical protein TIGR00268. The N-terminal region of the model shows similarity to Argininosuccinate synthase proteins using PSI-blast and using the recognize protein identification server.
Probab=96.90 E-value=0.0011 Score=53.23 Aligned_cols=60 Identities=20% Similarity=0.249 Sum_probs=44.1
Q ss_pred cccccccc--cchHHHHHHHHHcCCChhhhccCCCCCCCceeeec-cCc-ccccccChHHHHHHHHHH
Q psy7153 55 KVIEPLKD--FHKDEVRKLGLDLGLTPEVVMRHPFPGPGLAIRVI-CGE-ERYIEKDYSETQVLVKII 118 (131)
Q Consensus 55 kdiePL~~--L~KdEVR~Lg~~LGlP~~Ii~k~PfpGPGLaiR~~-g~~-e~~l~~~y~~~d~iL~~~ 118 (131)
..+.||.+ +.|+|||++|+.+||| +.+|+++ +.|+.|+. |.. .++...-++..+..|+.+
T Consensus 134 ~~~~PL~~~~l~K~eIr~la~~~gl~--~~~~ps~--~Cl~sr~~~g~~it~~~l~~v~~~E~~l~~~ 197 (252)
T TIGR00268 134 NGVSPWAEFGITKKEIREIAKSLGIS--FPDKPSE--ACLASRFPFGREIDEEKLKMVDEAEEVLRNA 197 (252)
T ss_pred CCCCcchhcCCCHHHHHHHHHHcCCC--ccCCCCC--CceEeecCCCCcCCHHHHHHHHHHHHHHHHc
Confidence 45699986 7999999999999999 5567655 55999986 532 333334477777777763
No 20
>cd01998 tRNA_Me_trans tRNA methyl transferase. This family represents tRNA(5-methylaminomethyl-2-thiouridine)-methyltransferase which is involved in the biosynthesis of the modified nucleoside 5-methylaminomethyl-2-thiouridine present in the wobble position of some tRNAs. This family of enzyme only presents in bacteria and eukaryote. The archaeal counterpart of this enzyme performs same function, but is completely unrelated in sequence.
Probab=96.59 E-value=0.0025 Score=53.92 Aligned_cols=77 Identities=23% Similarity=0.246 Sum_probs=50.1
Q ss_pred CCceeeccccccceeec-cCCCCCCCCCccccc-cCCchHHHHHhhcccccccccccchHHHHHHHHHcCCChhhhccCC
Q psy7153 9 NQTLLCQGTLRPDLIES-ASHLASNKADVIKTH-HNDSPLIRALREQGKVIEPLKDFHKDEVRKLGLDLGLTPEVVMRHP 86 (131)
Q Consensus 9 ~~~~l~QGTiypD~iES-~~~~~~~~a~~IKtH-HNv~~l~~~~~~~~kdiePL~~L~KdEVR~Lg~~LGlP~~Ii~k~P 86 (131)
...+++.|+-.-|..|. ....-...++.-|.+ +...++++.. ..+.+.||.+++|+|||++|+.+||| +.+|+.
T Consensus 113 g~~~IatGHya~d~~~~~~~~~l~rg~d~~kdqsy~L~~~~~~~--l~~ii~PL~~~~K~eVr~~A~~~gl~--~~~k~~ 188 (349)
T cd01998 113 GADYIATGHYARIEEDNNGRYRLLRGVDPNKDQSYFLSQLSQEQ--LSRLIFPLGDLTKPEVREIAKELGLP--VAKKKD 188 (349)
T ss_pred CcCEEEECCcCCeeecCCCceEEeecCCCCCCcceEeccCCHHH--HhheeecCCCCCHHHHHHHHHHcCCC--CCCCCC
Confidence 45689999855555544 211001123333433 2333444332 14799999999999999999999999 688888
Q ss_pred CCC
Q psy7153 87 FPG 89 (131)
Q Consensus 87 fpG 89 (131)
|-|
T Consensus 189 s~~ 191 (349)
T cd01998 189 SQG 191 (349)
T ss_pred CCc
Confidence 888
No 21
>cd01990 Alpha_ANH_like_I This is a subfamily of Adenine nucleotide alpha hydrolases superfamily. Adenine nucleotide alpha hydrolases superfamily includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which binds to Adenosine group. This subfamily of proteins probably binds ATP. This domain is about 200 amino acids long with a strongly conserved motif SGGKD at the N terminus.
Probab=95.55 E-value=0.025 Score=42.97 Aligned_cols=40 Identities=33% Similarity=0.409 Sum_probs=31.8
Q ss_pred cccccccc--ccchHHHHHHHHHcCCChhhhccCCCCCCCceeeec
Q psy7153 54 GKVIEPLK--DFHKDEVRKLGLDLGLTPEVVMRHPFPGPGLAIRVI 97 (131)
Q Consensus 54 ~kdiePL~--~L~KdEVR~Lg~~LGlP~~Ii~k~PfpGPGLaiR~~ 97 (131)
.+++.||. ++.|.||+++|+++|+|. +.+++.+. ++-|..
T Consensus 121 ~~iirPL~~~~~~K~ei~~~a~~~gl~~--~~~~~~~c--~~~~~~ 162 (202)
T cd01990 121 LGVRSPLAEAGLGKAEIRELARELGLPT--WDKPAMAC--LASRIP 162 (202)
T ss_pred cCCcCchhhcCCCHHHHHHHHHHcCCCC--cCCCCcch--HHhhCc
Confidence 47999999 599999999999999986 66666655 544444
No 22
>PF03054 tRNA_Me_trans: tRNA methyl transferase; InterPro: IPR004506 tRNA-specific 2-thiouridylase catalyzes the 2-thiolation of uridine at the wobble position (U34) of tRNA, leading to the formation of s(2)U34.; GO: 0016740 transferase activity, 0008033 tRNA processing, 0005737 cytoplasm; PDB: 2DET_A 2DER_A 2DEU_A 2HMA_A.
Probab=95.46 E-value=0.0098 Score=51.46 Aligned_cols=76 Identities=21% Similarity=0.274 Sum_probs=36.4
Q ss_pred CCceeeccccccceeecc--CC-CCCCCCCccccccCCc-hHHHHHhhcccccccccccchHHHHHHHHHcCCChhhhcc
Q psy7153 9 NQTLLCQGTLRPDLIESA--SH-LASNKADVIKTHHNDS-PLIRALREQGKVIEPLKDFHKDEVRKLGLDLGLTPEVVMR 84 (131)
Q Consensus 9 ~~~~l~QGTiypD~iES~--~~-~~~~~a~~IKtHHNv~-~l~~~~~~~~kdiePL~~L~KdEVR~Lg~~LGlP~~Ii~k 84 (131)
...|+|-|. |--+.+.. +. .-....|..|-+.=.- .|++..- .+.+-||++|+|+|||++|+.+||| +.+|
T Consensus 116 g~d~iATGH-YAri~~~~~~~~~~L~r~~D~~KDQSYfL~~l~~~~L--~~~~FPLG~~~K~eVR~iA~~~gl~--~a~k 190 (356)
T PF03054_consen 116 GADYIATGH-YARIEKDEKNGRYRLLRGADPKKDQSYFLSRLPQEQL--SRLIFPLGELTKEEVREIAREAGLP--VAEK 190 (356)
T ss_dssp T-SEEE----SEEEEEES-TTEEEEEE-SSTTC--GGGGTT--HHHH--CCEE-TCCCS-HHHHHHHHHHCT-T--TTT-
T ss_pred CCCeeccce-eEEEEeeccCCceEEEecCCCCCCceEEEEecCHHHH--HhhcCCCCCCCHHHHHHHHHhcCCc--ccCc
Confidence 445777775 44444442 10 0011245556554322 3444321 3799999999999999999999999 7777
Q ss_pred CCCCC
Q psy7153 85 HPFPG 89 (131)
Q Consensus 85 ~PfpG 89 (131)
.=|-|
T Consensus 191 ~eSq~ 195 (356)
T PF03054_consen 191 KESQG 195 (356)
T ss_dssp ----S
T ss_pred cccce
Confidence 77776
No 23
>cd01993 Alpha_ANH_like_II This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases superfamily includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which binds to Adenosine group. This subfamily of proteins is predicted to bind ATP. This domainhas a strongly conserved motif SGGKD at the N terminus.
Probab=95.41 E-value=0.0049 Score=45.23 Aligned_cols=76 Identities=17% Similarity=0.072 Sum_probs=47.2
Q ss_pred CCceeeccccccceeeccCCCC--CCCCCccccccCCchHHHHHhhcccccccccccchHHHHHHHHHcCCChhhhccCC
Q psy7153 9 NQTLLCQGTLRPDLIESASHLA--SNKADVIKTHHNDSPLIRALREQGKVIEPLKDFHKDEVRKLGLDLGLTPEVVMRHP 86 (131)
Q Consensus 9 ~~~~l~QGTiypD~iES~~~~~--~~~a~~IKtHHNv~~l~~~~~~~~kdiePL~~L~KdEVR~Lg~~LGlP~~Ii~k~P 86 (131)
+..+++.|+-..|++|+.-... .+.....+.+.+. .........+-||.+++|+||+++++.+||| .+-...|
T Consensus 106 g~~~l~~Gh~~dD~~et~l~~~~~g~~~~~~~~~~~~----~~~~~~~~iirPL~~~~k~eI~~~~~~~~l~-~~~d~~~ 180 (185)
T cd01993 106 GADKLATGHNLDDEAETLLMNLLRGGILRLMRPGPIL----YLDEGDVTRIRPLVYVREKEIVLYAELNGLP-FVEEECP 180 (185)
T ss_pred CCCEEEEcCChHHHHHHHHHHHHhcCHHHHcCCCCcc----ccCCCCceEEeecccCCHHHHHHHHHHcCCC-cccCCCC
Confidence 3457899999999998642100 0011122333220 0011123689999999999999999999998 4555566
Q ss_pred CCC
Q psy7153 87 FPG 89 (131)
Q Consensus 87 fpG 89 (131)
|.+
T Consensus 181 ~~~ 183 (185)
T cd01993 181 YAG 183 (185)
T ss_pred CCC
Confidence 544
No 24
>TIGR02432 lysidine_TilS_N tRNA(Ile)-lysidine synthetase, N-terminal domain. The only examples in which the wobble position of a tRNA must discriminate between G and A of mRNA are AUA (Ile) vs. AUG (Met) and UGA (stop) vs. UGG (Trp). In all bacteria, the wobble position of the tRNA(Ile) recognizing AUA is lysidine, a lysine derivative of cytidine. This family describes a protein domain found, apparently, in all bacteria in a single copy. Eukaryotic sequences appear to be organellar. The domain archictecture of this protein family is variable; some, including characterized proteins of E. coli and B. subtilis known to be tRNA(Ile)-lysidine synthetase, include a conserved 50-residue domain that many other members lack. This protein belongs to the ATP-binding PP-loop family ( pfam01171). It appears in the literature and protein databases as TilS, YacA, and putative cell cycle protein MesJ (a misnomer).
Probab=95.11 E-value=0.0065 Score=45.50 Aligned_cols=65 Identities=18% Similarity=0.205 Sum_probs=42.2
Q ss_pred CCceeeccccccceeeccCCCCCCCCCcccc--ccCCchHHHH--HhhcccccccccccchHHHHHHHHHcCCCh
Q psy7153 9 NQTLLCQGTLRPDLIESASHLASNKADVIKT--HHNDSPLIRA--LREQGKVIEPLKDFHKDEVRKLGLDLGLTP 79 (131)
Q Consensus 9 ~~~~l~QGTiypD~iES~~~~~~~~a~~IKt--HHNv~~l~~~--~~~~~kdiePL~~L~KdEVR~Lg~~LGlP~ 79 (131)
+..+++.|+-.-|++|+.-.. ..+. ..+..+++.. .....+.+.||.+++|+||+++++.+|||-
T Consensus 99 g~~~i~~Gh~~~D~~e~~l~~------~~~g~~~~~l~~~~~~~~~~~~~~iirPL~~~~k~ei~~~~~~~~lp~ 167 (189)
T TIGR02432 99 GADYILTAHHADDQAETILLR------LLRGSGLRGLSGMKPIRILGNGGQIIRPLLGISKSEIEEYLKENGLPW 167 (189)
T ss_pred CCCEEEEcCccHHHHHHHHHH------HHcCCCcccccCCccccccCCCCEEECCCCCCCHHHHHHHHHHcCCCe
Confidence 456899999999999863100 0000 1122222211 100246899999999999999999999983
No 25
>cd01992 PP-ATPase N-terminal domain of predicted ATPase of the PP-loop faimly implicated in cell cycle control [Cell division and chromosome partitioning]. This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases superfamily includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which binds to Adenosine group. This domain has a strongly conserved motif SGGXD at the N terminus.
Probab=94.61 E-value=0.011 Score=43.81 Aligned_cols=65 Identities=17% Similarity=0.170 Sum_probs=41.1
Q ss_pred CCceeeccccccceeeccCCC--CCCCCCccccccCCchH-HHHHhhcccccccccccchHHHHHHHHHcCCCh
Q psy7153 9 NQTLLCQGTLRPDLIESASHL--ASNKADVIKTHHNDSPL-IRALREQGKVIEPLKDFHKDEVRKLGLDLGLTP 79 (131)
Q Consensus 9 ~~~~l~QGTiypD~iES~~~~--~~~~a~~IKtHHNv~~l-~~~~~~~~kdiePL~~L~KdEVR~Lg~~LGlP~ 79 (131)
+..+++.|+-+.|.+|..-.. ..+..... .++ +.......+.+-||.++.|+||+++++.+|||.
T Consensus 96 ~~~~i~~Gh~~dD~~e~~l~~l~~g~~~~~l------~~~~~~~~~~~~~virPl~~~~k~eI~~~~~~~~l~~ 163 (185)
T cd01992 96 GADVLLTAHHADDQAETVLMRLLRGSGLRGL------AGMPARIPFGGGRLIRPLLGITRAEIEAYLRENGLPW 163 (185)
T ss_pred CCCEEEEcCCcHHHHHHHHHHHHccCCcccc------cCCCcccCCCCCeEECCCCCCCHHHHHHHHHHcCCCe
Confidence 456899999999998863110 00000111 011 000112347899999999999999999999973
No 26
>KOG2805|consensus
Probab=94.23 E-value=0.033 Score=49.15 Aligned_cols=33 Identities=27% Similarity=0.409 Sum_probs=30.9
Q ss_pred cccccccccchHHHHHHHHHcCCChhhhccCCCCC
Q psy7153 55 KVIEPLKDFHKDEVRKLGLDLGLTPEVVMRHPFPG 89 (131)
Q Consensus 55 kdiePL~~L~KdEVR~Lg~~LGlP~~Ii~k~PfpG 89 (131)
+.+-||..|.|+|||.||++.|+| +.+|+-|-|
T Consensus 169 r~lfPlg~~~K~eVk~lA~~~gf~--~aeK~eSqG 201 (377)
T KOG2805|consen 169 RLLFPLGCLTKSEVKKLAKQAGFP--NAEKPESQG 201 (377)
T ss_pred hhhccCcccCHHHHHHHHHhcCCc--cccCcccce
Confidence 578899999999999999999999 999998887
No 27
>cd01712 ThiI ThiI is required for thiazole synthesis in the thiamine biosynthesis pathway. It belongs to the Adenosine Nucleotide Hydrolysis suoerfamily and predicted to bind to Adenosine nucleotide.
Probab=93.89 E-value=0.098 Score=39.16 Aligned_cols=29 Identities=21% Similarity=0.382 Sum_probs=25.7
Q ss_pred ccccccccccchHHHHHHHHHcCCChhhh
Q psy7153 54 GKVIEPLKDFHKDEVRKLGLDLGLTPEVV 82 (131)
Q Consensus 54 ~kdiePL~~L~KdEVR~Lg~~LGlP~~Ii 82 (131)
.+.+.||.++.|.||+++|+.+|+|.-..
T Consensus 133 ~~i~rPl~~~~K~eI~~~a~~~gl~~~~~ 161 (177)
T cd01712 133 LPILRPLIGFDKEEIIGIARRIGTYDISI 161 (177)
T ss_pred CeEECCCCCCCHHHHHHHHHHcCCcceec
Confidence 46899999999999999999999996543
No 28
>PRK00143 mnmA tRNA-specific 2-thiouridylase MnmA; Reviewed
Probab=93.09 E-value=0.066 Score=45.43 Aligned_cols=33 Identities=33% Similarity=0.558 Sum_probs=28.1
Q ss_pred cccccccccchHHHHHHHHHcCCChhhhccCCCCC
Q psy7153 55 KVIEPLKDFHKDEVRKLGLDLGLTPEVVMRHPFPG 89 (131)
Q Consensus 55 kdiePL~~L~KdEVR~Lg~~LGlP~~Ii~k~PfpG 89 (131)
+.+-||.+++|+|||++|+.+||| ..+|.-+-|
T Consensus 158 ~~i~PL~~~~K~eVr~~A~~~gl~--~~~k~~s~~ 190 (346)
T PRK00143 158 KLLFPLGELTKPEVREIAEEAGLP--VAKKKDSQG 190 (346)
T ss_pred ceeccCccCCHHHHHHHHHHcCCC--cCCCCCCCc
Confidence 789999999999999999999998 355555555
No 29
>PRK08349 hypothetical protein; Validated
Probab=92.87 E-value=0.62 Score=35.89 Aligned_cols=79 Identities=18% Similarity=0.265 Sum_probs=47.8
Q ss_pred CCCccccccCCchHHHHHh---------hcccccccccccchHHHHHHHHHcCCChhhhccCCCCCCCceeeeccCcccc
Q psy7153 33 KADVIKTHHNDSPLIRALR---------EQGKVIEPLKDFHKDEVRKLGLDLGLTPEVVMRHPFPGPGLAIRVICGEERY 103 (131)
Q Consensus 33 ~a~~IKtHHNv~~l~~~~~---------~~~kdiePL~~L~KdEVR~Lg~~LGlP~~Ii~k~PfpGPGLaiR~~g~~e~~ 103 (131)
+++.|=+=||.+....... ...+.+.||.+++|+|++++|+.+|++ ++..+++..=| + ....+.
T Consensus 105 g~~~I~tG~~~~d~a~~~l~nl~~~~~~~~i~i~rPL~~~~K~eI~~~a~~~g~~-~~~~~~~~~C~-~-----~~~~~~ 177 (198)
T PRK08349 105 GASAIITGDSLGQVASQTLDNLMVISTATDLPVLRPLIGLDKEEIVKIAKEIGTF-EISIEPEPPCP-F-----VPKYPV 177 (198)
T ss_pred CCCEEEEecCCchHHHHHHHHHhccccccCCeEEcCCCCCCHHHHHHHHHHcCCh-hhhhCCCCCCc-C-----CCCCCc
Confidence 3555666566665433211 113689999999999999999999965 44443333222 1 122444
Q ss_pred cccChHHHHHHHHHH
Q psy7153 104 IEKDYSETQVLVKII 118 (131)
Q Consensus 104 l~~~y~~~d~iL~~~ 118 (131)
......++..+++.+
T Consensus 178 ~~~~~~~~~~~~~~~ 192 (198)
T PRK08349 178 VRASLGEFEKILEEV 192 (198)
T ss_pred CCCCHHHHHHHHHHH
Confidence 455666666766655
No 30
>TIGR00364 exsB protein. This protein family is represented by a single member in nearly every completed large ( 1000 genes) prokaryotic genome. In Rhizobium meliloti, a species in which the exo genes make succinoglycan, a symbiotically important exopolysaccharide, exsB is located nearby and affects succinoglycan levels, probably through polar effects on exsA expression or the same polycistronic mRNA. In Arthrobacter viscosus, the homologous gene is designated ALU1 and is associated with an aluminum tolerance phenotype. The function is unknown.
Probab=92.76 E-value=0.079 Score=40.65 Aligned_cols=24 Identities=42% Similarity=0.659 Sum_probs=22.4
Q ss_pred cccccccccchHHHHHHHHHcC---CC
Q psy7153 55 KVIEPLKDFHKDEVRKLGLDLG---LT 78 (131)
Q Consensus 55 kdiePL~~L~KdEVR~Lg~~LG---lP 78 (131)
+++.|+.++.|.||+++|+++| +|
T Consensus 151 ~i~~Pl~~~~K~eI~~la~~~g~~~~~ 177 (201)
T TIGR00364 151 KIRAPLMDLTKAEIVQLADELGVLDLV 177 (201)
T ss_pred EEEECCcCCCHHHHHHHHHHcCCcccc
Confidence 5899999999999999999999 65
No 31
>PRK14664 tRNA-specific 2-thiouridylase MnmA; Provisional
Probab=92.51 E-value=0.08 Score=45.87 Aligned_cols=34 Identities=21% Similarity=0.225 Sum_probs=27.9
Q ss_pred cccccccccchHHHHHHHHHcCCChhhhccCCCCC
Q psy7153 55 KVIEPLKDFHKDEVRKLGLDLGLTPEVVMRHPFPG 89 (131)
Q Consensus 55 kdiePL~~L~KdEVR~Lg~~LGlP~~Ii~k~PfpG 89 (131)
+.+-||++++|+|||++|+..|||. ..+|.=|-|
T Consensus 153 ~~ifPLg~~~K~evr~~A~~~gl~~-~a~k~dSq~ 186 (362)
T PRK14664 153 RCIFPLGNYTKQTVREYLREKGYEA-KSKEGESME 186 (362)
T ss_pred HHhccCccCCHHHHHHHHHHcCCCC-CCCCCCCCc
Confidence 6899999999999999999999972 245555555
No 32
>PRK14665 mnmA tRNA-specific 2-thiouridylase MnmA; Provisional
Probab=92.39 E-value=0.11 Score=44.74 Aligned_cols=34 Identities=21% Similarity=0.417 Sum_probs=28.8
Q ss_pred cccccccccchHHHHHHHHHcCCChhhhccCCCCC
Q psy7153 55 KVIEPLKDFHKDEVRKLGLDLGLTPEVVMRHPFPG 89 (131)
Q Consensus 55 kdiePL~~L~KdEVR~Lg~~LGlP~~Ii~k~PfpG 89 (131)
+.+-||.++.|.|||++|+++|++ .+.+|.-|-|
T Consensus 158 ~~ifPLg~~~K~eVr~~A~~~gl~-~~a~k~eSq~ 191 (360)
T PRK14665 158 RMLLPMGGMTKSEARAYAAERGFE-KVAKKRDSLG 191 (360)
T ss_pred heeccCcCCCHHHHHHHHHHCCCC-ccCcCCCCCc
Confidence 579999999999999999999985 3466666666
No 33
>PRK01565 thiamine biosynthesis protein ThiI; Provisional
Probab=90.97 E-value=0.19 Score=43.25 Aligned_cols=35 Identities=17% Similarity=0.278 Sum_probs=27.7
Q ss_pred ccccccccccchHHHHHHHHHcCCChhhhccCCCCC
Q psy7153 54 GKVIEPLKDFHKDEVRKLGLDLGLTPEVVMRHPFPG 89 (131)
Q Consensus 54 ~kdiePL~~L~KdEVR~Lg~~LGlP~~Ii~k~PfpG 89 (131)
..++.||..|+|.||+++|+++|++ ++-++++.+.
T Consensus 309 ~~V~rPLig~~K~EI~~lAr~iG~~-~~s~~p~~~c 343 (394)
T PRK01565 309 LPVLRPLIGMDKEEIIEIAKEIGTY-DISILPYEDC 343 (394)
T ss_pred cEEEECCCCCCHHHHHHHHHHhCCH-HHhcCCCcCe
Confidence 3579999999999999999999965 4545555543
No 34
>PRK11106 queuosine biosynthesis protein QueC; Provisional
Probab=90.40 E-value=0.19 Score=40.94 Aligned_cols=26 Identities=27% Similarity=0.184 Sum_probs=23.9
Q ss_pred ccccccccccchHHHHHHHHHcC-CCh
Q psy7153 54 GKVIEPLKDFHKDEVRKLGLDLG-LTP 79 (131)
Q Consensus 54 ~kdiePL~~L~KdEVR~Lg~~LG-lP~ 79 (131)
.++..|+.+|.|.||+++|++|| +|-
T Consensus 154 i~I~aPl~~lsK~eI~~l~~~lg~v~~ 180 (231)
T PRK11106 154 IRFETPLMWLNKAETWALADYYGQLDL 180 (231)
T ss_pred cEEEecCCCCCHHHHHHHHHHcCCccc
Confidence 57899999999999999999999 864
No 35
>PF02568 ThiI: Thiamine biosynthesis protein (ThiI); InterPro: IPR020536 Thiamine pyrophosphate (TPP) is synthesized de novo in many bacteria and is a required cofactor for many enzymes in the cell. ThiI is required for thiazole synthesis in the thiamine biosynthesis pathway []. Almost all proteins containing this entry have an N-terminal THUMP domain (see IPR004114 from INTERPRO).; GO: 0003723 RNA binding, 0009228 thiamine biosynthetic process, 0005737 cytoplasm; PDB: 1VBK_B 2C5S_A.
Probab=89.25 E-value=0.18 Score=40.46 Aligned_cols=57 Identities=25% Similarity=0.346 Sum_probs=29.9
Q ss_pred CCCceeeccccccceeeccCCCCCCCCCccccccCCchHHHHHhhcccccccccccchHHHHHHHHHcCCCh
Q psy7153 8 PNQTLLCQGTLRPDLIESASHLASNKADVIKTHHNDSPLIRALREQGKVIEPLKDFHKDEVRKLGLDLGLTP 79 (131)
Q Consensus 8 ~~~~~l~QGTiypD~iES~~~~~~~~a~~IKtHHNv~~l~~~~~~~~kdiePL~~L~KdEVR~Lg~~LGlP~ 79 (131)
.+..+++.| ||-+..+| .|.+|.....+.. .+-++-||..+.|+|+.++||+.|..+
T Consensus 107 ~ga~~IvTG-------EsLGQvaS------QTl~nL~~i~~~~--~~pIlRPLig~dK~EIi~~Ar~Igtye 163 (197)
T PF02568_consen 107 EGADAIVTG-------ESLGQVAS------QTLENLRVIESAS--DLPILRPLIGFDKEEIIEIARKIGTYE 163 (197)
T ss_dssp TT--EEE-----------SSSTTS--------HHHHHHHGGG----S-EE-TTTT--HHHHHHHHHHTT-HH
T ss_pred CCCCEEEeC-------chhHHHHh------hhHHHHhhhhccc--CCceeCCcCCCCHHHHHHHHHHhCchh
Confidence 355688999 66554333 4455543333322 346899999999999999999999974
No 36
>cd01995 ExsB ExsB is a transcription regulator related protein. It is a subfamily of a Adenosine nucleotide binding superfamily of proteins. This protein family is represented by a single member in nearly every completed large ( 1000 genes) prokaryotic genome. In Rhizobium meliloti, a species in which the exo genes make succinoglycan, a symbiotically important exopolysaccharide, exsB is located nearby and affects succinoglycan levels, probably through polar effects on exsA expression or the same polycistronic mRNA. In Arthrobacter viscosus, the homologous gene is designated ALU1 and is associated with an aluminum tolerance phenotype. The function is unknown
Probab=87.91 E-value=0.4 Score=35.43 Aligned_cols=28 Identities=39% Similarity=0.600 Sum_probs=24.9
Q ss_pred ccccccccccchHHHHHHHHHcCCChhh
Q psy7153 54 GKVIEPLKDFHKDEVRKLGLDLGLTPEV 81 (131)
Q Consensus 54 ~kdiePL~~L~KdEVR~Lg~~LGlP~~I 81 (131)
.+.+.||..+.|.||++.++++|+|-..
T Consensus 115 ~~v~~PL~~~~K~ei~~~~~~~g~~~~~ 142 (169)
T cd01995 115 IKIHAPLIDLSKAEIVRLGGELGVPLEL 142 (169)
T ss_pred eEEEeCcccCCHHHHHHHHhHcCCChhh
Confidence 4689999999999999999999998554
No 37
>TIGR00420 trmU tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase. tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase (trmU, asuE, or mnmA) is involved in the biosynthesis of the modified nucleoside 5-methylaminomethyl-2-thiouridine (mnm5s2U34) present in the wobble position of some tRNAs. This enzyme appears not to occur in the Archaea.
Probab=87.81 E-value=0.38 Score=41.18 Aligned_cols=33 Identities=30% Similarity=0.507 Sum_probs=28.5
Q ss_pred cccccccccchHHHHHHHHHcCCChhhhccCCCCC
Q psy7153 55 KVIEPLKDFHKDEVRKLGLDLGLTPEVVMRHPFPG 89 (131)
Q Consensus 55 kdiePL~~L~KdEVR~Lg~~LGlP~~Ii~k~PfpG 89 (131)
+.+-||.+++|.|||++|+..||| ..+|+-|-|
T Consensus 162 ~~i~PL~~~~K~EVr~~A~~~gl~--~~~k~~Sq~ 194 (352)
T TIGR00420 162 KLLFPLGELLKPEVRQIAKNAGLP--TAEKKDSQG 194 (352)
T ss_pred hhcccCCCCCHHHHHHHHHHcCCC--CCCCCCCCC
Confidence 589999999999999999999998 355766666
No 38
>COG0482 TrmU Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]
Probab=87.36 E-value=0.41 Score=42.04 Aligned_cols=33 Identities=30% Similarity=0.502 Sum_probs=26.8
Q ss_pred cccccccccchHHHHHHHHHcCCChhhhccCCCCC
Q psy7153 55 KVIEPLKDFHKDEVRKLGLDLGLTPEVVMRHPFPG 89 (131)
Q Consensus 55 kdiePL~~L~KdEVR~Lg~~LGlP~~Ii~k~PfpG 89 (131)
+.+-||++|.|.|||+||++.||| ...|.=|-|
T Consensus 161 ~~lFPlG~l~K~evR~iA~~~gL~--~a~KkdS~~ 193 (356)
T COG0482 161 RLLFPLGDLEKLEVRPIAAEKGLP--TAKKKDSQG 193 (356)
T ss_pred hccccCCCCCHHHHHHHHHHcCCC--ccCcccCCc
Confidence 678999999999999999999998 334444444
No 39
>cd01999 Argininosuccinate_Synthase Argininosuccinate synthase. The Argininosuccinate synthase is a urea cycle enzyme that catalyzes the penultimate step in arginine biosynthesis: the ATP-dependent ligation of citrulline to aspartate to form argininosuccinate, AMP and pyrophosphate . In humans, a defect in the AS gene causes citrullinemia, a genetic disease characterized by severe vomiting spells and mental retardation. AS is a homotetrameric enzyme of chains of about 400 amino-acid residues. An arginine seems to be important for the enzyme's catalytic mechanism. The sequences of AS from various prokaryotes, archaebacteria and eukaryotes show significant similarity
Probab=86.92 E-value=0.5 Score=41.33 Aligned_cols=45 Identities=24% Similarity=0.431 Sum_probs=35.6
Q ss_pred ccccccccccc---chHHHHHHHHHcCCChhhhccCCCC-CCCceeeec
Q psy7153 53 QGKVIEPLKDF---HKDEVRKLGLDLGLTPEVVMRHPFP-GPGLAIRVI 97 (131)
Q Consensus 53 ~~kdiePL~~L---~KdEVR~Lg~~LGlP~~Ii~k~Pfp-GPGLaiR~~ 97 (131)
..+++.|++++ .|+|+|++|+.+|||-..-.+.||. .-.|+=|-+
T Consensus 134 el~ViaPlre~~~~sr~ev~~~A~~~Gip~~~~~~~pyS~d~nl~~~s~ 182 (385)
T cd01999 134 DLKIIAPWRDWEFLSREEEIEYAEEHGIPVPVTKKKPYSIDENLWGRSI 182 (385)
T ss_pred CCEEEcchhhhhcCCHHHHHHHHHHcCCCCcccCCCCCccCCCcceeec
Confidence 45799999999 9999999999999998766567765 455655533
No 40
>PRK14561 hypothetical protein; Provisional
Probab=84.69 E-value=3.6 Score=32.12 Aligned_cols=47 Identities=26% Similarity=0.365 Sum_probs=34.5
Q ss_pred cccccccccchHHHHHHHHHcCCChhhhccCCCCCCCceeeeccCcccccccChH-HHHHHHHHH
Q psy7153 55 KVIEPLKDFHKDEVRKLGLDLGLTPEVVMRHPFPGPGLAIRVICGEERYIEKDYS-ETQVLVKII 118 (131)
Q Consensus 55 kdiePL~~L~KdEVR~Lg~~LGlP~~Ii~k~PfpGPGLaiR~~g~~e~~l~~~y~-~~d~iL~~~ 118 (131)
+.+.||..+.|.|||++++.| |-|. .|+++..--.||+ ++..++...
T Consensus 126 ~iirPL~~~~K~eI~~la~~l----------------~~~~-~~~~~~~~~~~~~~~~~~~~~~~ 173 (194)
T PRK14561 126 QYIRPLLGFGRKTIDRLVERL----------------FEIE-EGESEEIPKSDYETELRELLRER 173 (194)
T ss_pred EEEeeCCCCCHHHHHHHHHhh----------------EEEE-eccCCCcCccchHHHHHHHHHHh
Confidence 469999999999999999998 5432 3555555566774 566666554
No 41
>KOG2303|consensus
Probab=81.47 E-value=2 Score=40.47 Aligned_cols=59 Identities=20% Similarity=0.300 Sum_probs=45.6
Q ss_pred ccccccccccchHHHHHHH----HHcCCC--hhhhccCCCCCCCceeeecc---C-cccccccChHHHHHH
Q psy7153 54 GKVIEPLKDFHKDEVRKLG----LDLGLT--PEVVMRHPFPGPGLAIRVIC---G-EERYIEKDYSETQVL 114 (131)
Q Consensus 54 ~kdiePL~~L~KdEVR~Lg----~~LGlP--~~Ii~k~PfpGPGLaiR~~g---~-~e~~l~~~y~~~d~i 114 (131)
.-||.||+...|..+|..- +.+|+| ++|+.-+|.+- |-==.-| | +|.+|||+|+|+-..
T Consensus 533 SADINPIGgISK~DLr~Fl~~a~~~~~lp~L~~il~a~pTAE--LePl~~g~~~QtDE~dmGmTY~ELsv~ 601 (706)
T KOG2303|consen 533 SADINPIGGISKTDLRRFLQYAKEKFGLPALQSILDAPPTAE--LEPLTDGDYSQTDEADMGMTYAELSVF 601 (706)
T ss_pred ccccCCccCccHHHHHHHHHHHHHhcCchHHHHHhcCCCccc--ccccccCcccccchhhhCccHHHHHHh
Confidence 3699999999999999864 457888 68999999986 4211223 3 499999999998654
No 42
>PRK00509 argininosuccinate synthase; Provisional
Probab=81.25 E-value=1.2 Score=39.31 Aligned_cols=36 Identities=22% Similarity=0.494 Sum_probs=28.8
Q ss_pred ccccccccccc---chHHHHHHHHHcCCChhhhccCCCC
Q psy7153 53 QGKVIEPLKDF---HKDEVRKLGLDLGLTPEVVMRHPFP 88 (131)
Q Consensus 53 ~~kdiePL~~L---~KdEVR~Lg~~LGlP~~Ii~k~Pfp 88 (131)
..+++.|++++ .|+|+|++|+.+|||-..-.+.|+-
T Consensus 137 el~VisPlre~~~~tK~eir~~A~~~Gipv~~~~~~~yS 175 (399)
T PRK00509 137 DLKVIAPWREWDLKSREELIAYAEEHGIPIPVTKKSPYS 175 (399)
T ss_pred CCeeecchhhcCCCCHHHHHHHHHHcCCCCCCCCCCCCc
Confidence 34799999998 9999999999999996544444443
No 43
>PF01171 ATP_bind_3: PP-loop family; InterPro: IPR011063 This entry represents the PP-loop motif superfamily [,]. The PP-loop motif appears to be a modified version of the P-loop of nucleotide binding domain that is involved in phosphate binding []. Named PP-motif, since it appears to be a part of a previously uncharacterised ATP pyrophophatase domain. ATP sulfurylases, Escherichia coli NtrL, and Bacillus subtilis OutB consist of this domain alone. In other proteins, the pyrophosphatase domain is associated with amidotransferase domains (type I or type II), a putative citrulline-aspartate ligase domain or a nitrilase/amidase domain.; PDB: 3A2K_A 2E89_B 2E21_D 1WY5_B 1NI5_A.
Probab=80.74 E-value=0.87 Score=34.37 Aligned_cols=62 Identities=21% Similarity=0.153 Sum_probs=35.8
Q ss_pred CCceeeccccccceeeccCCC---CC--CCCCccccccCCchHHHHHhhcccccccccccchHHHHHHHHHcCCC
Q psy7153 9 NQTLLCQGTLRPDLIESASHL---AS--NKADVIKTHHNDSPLIRALREQGKVIEPLKDFHKDEVRKLGLDLGLT 78 (131)
Q Consensus 9 ~~~~l~QGTiypD~iES~~~~---~~--~~a~~IKtHHNv~~l~~~~~~~~kdiePL~~L~KdEVR~Lg~~LGlP 78 (131)
+..+++.|+-..|.+|+--.. .+ ..-..++..... ...+.+-||-.+.|+|+++.++..|+|
T Consensus 96 g~~~i~~GHh~dD~~ET~l~~l~rg~~~~~l~~~~~~~~~--------~~~~~iRPLl~~~k~ei~~~~~~~~i~ 162 (182)
T PF01171_consen 96 GCNKIALGHHLDDQAETFLMNLLRGSGLRGLAGMPPVSPF--------KGIKLIRPLLYVSKDEIRAYAKENGIP 162 (182)
T ss_dssp T-CEEE---BHHHHHHHHHHHHHHT--CCCCC-S-SEEEE--------TTCEEE-GGGCS-HHHHHHHHHHTT-S
T ss_pred cccceeecCcCCccHHHHHHHHHHhccchhhccccccccc--------cCcccCCcchhCCHHHHHHHHHHCCCc
Confidence 456899999999999985110 00 111222222211 125799999999999999999999998
No 44
>TIGR00342 thiazole biosynthesis/tRNA modification protein ThiI. The protein product of the thiI gene is required for the synthesis of the thiazole moiety in thiamine biosynthesis. It also acts in the generation of 4-thiouridine in tRNA, and may occur in species (such as Mycoplasma genitalium) that lack de novo thiamine biosynthesis.
Probab=78.82 E-value=1.6 Score=37.43 Aligned_cols=32 Identities=22% Similarity=0.473 Sum_probs=25.7
Q ss_pred ccccccccccchHHHHHHHHHcCCChhhhccCC
Q psy7153 54 GKVIEPLKDFHKDEVRKLGLDLGLTPEVVMRHP 86 (131)
Q Consensus 54 ~kdiePL~~L~KdEVR~Lg~~LGlP~~Ii~k~P 86 (131)
..++.||..+.|+||+++|+.+|.. ++-++++
T Consensus 305 ~~I~rPLi~~~K~EIi~~a~~iG~~-~~s~~~~ 336 (371)
T TIGR00342 305 TPILRPLIGMDKEEIIELAKEIGTY-EISIEPH 336 (371)
T ss_pred CCEEeCCCCCCHHHHHHHHHHhCCc-ceeecCC
Confidence 4589999999999999999999954 4444444
No 45
>PF06508 QueC: Queuosine biosynthesis protein QueC; InterPro: IPR018317 This protein family is represented by a single member in nearly every completed large (> 1000 genes) prokaryotic genome. In Rhizobium meliloti (Sinorhizobium meliloti), a species in which the exo genes make succinoglycan, a symbiotically important exopolysaccharide, exsB is located nearby and affects succinoglycan levels, probably through polar effects on exsA expression or the same polycistronic mRNA [, ]. In Arthrobacter viscosus, the homologous gene is designated alu1 and is associated with an aluminum tolerance phenotype. When expressed in Escherichia coli, it conferred aliminium tolerance []. The entry also contains the gene queC, which is responsible for the conversion of GTP to 7-cyano-7-deazaguanine (preQ0). The biosynthesis of hypermodified tRNA nucleoside queuosine only occurs in eubacteria. It occupies the wobble position for all known tRNAs that are specific for Asp, Asn, His or Tyr [].; PDB: 3BL5_B 2PG3_A.
Probab=74.64 E-value=1.7 Score=34.53 Aligned_cols=30 Identities=37% Similarity=0.633 Sum_probs=21.8
Q ss_pred cccccccccccchHHHHHHHHHcCCChhhh
Q psy7153 53 QGKVIEPLKDFHKDEVRKLGLDLGLTPEVV 82 (131)
Q Consensus 53 ~~kdiePL~~L~KdEVR~Lg~~LGlP~~Ii 82 (131)
..++..|+.++.|.||.++|..||+|-+.-
T Consensus 151 ~v~i~~P~~~~tK~eiv~~~~~lg~~~~~T 180 (209)
T PF06508_consen 151 PVRIETPLIDLTKAEIVKLGVELGVPLELT 180 (209)
T ss_dssp --EEE-TTTT--HHHHHHHHHHTTHHHHH-
T ss_pred CEEEEecCCCCCHHHHHHHHHHcCCCHHHc
Confidence 458999999999999999999999776554
No 46
>PRK13820 argininosuccinate synthase; Provisional
Probab=74.00 E-value=2.7 Score=37.09 Aligned_cols=42 Identities=19% Similarity=0.299 Sum_probs=32.2
Q ss_pred ccccccccc--cchHHHHHHHHHcCCChhhhccCCC-CCCCceee
Q psy7153 54 GKVIEPLKD--FHKDEVRKLGLDLGLTPEVVMRHPF-PGPGLAIR 95 (131)
Q Consensus 54 ~kdiePL~~--L~KdEVR~Lg~~LGlP~~Ii~k~Pf-pGPGLaiR 95 (131)
.+.+.|+++ +.|+|+|++++..|||-..-.+.|+ -.-.|+-|
T Consensus 136 l~viaP~re~~ltK~ei~~ya~~~gip~~~~~~~~yS~d~nlw~~ 180 (394)
T PRK13820 136 LEVIAPIRELNLTREWEIEYAKEKGIPVPVGKEKPWSIDENLWSR 180 (394)
T ss_pred CeeeCchhccCCCHHHHHHHHHHcCCCCCcCCCCCcccccccccc
Confidence 578999999 8999999999999999765445554 34456433
No 47
>PF01680 SOR_SNZ: SOR/SNZ family; InterPro: IPR001852 Snz1p is a highly conserved protein involved in growth arrest in Saccharomyces cerevisiae (Baker's yeast) []. Sor1 (singlet oxygen resistance) is essential in pyridoxine (vitamin B6) synthesis in Cercospora nicotianae and Aspergillus flavus. Pyridoxine quenches singlet oxygen at a rate comparable to that of vitamins C and E, two of the most highly efficient biological antioxidants, suggesting a previously unknown role for pyridoxine in active oxygen resistance [].; GO: 0042823 pyridoxal phosphate biosynthetic process; PDB: 2ISS_A 1ZNN_B 2ZBT_B 2NV2_I 2NV1_C 4ADS_C 4ADU_B 4ADT_B 3FEM_F 3O07_A ....
Probab=70.18 E-value=3.1 Score=34.53 Aligned_cols=51 Identities=24% Similarity=0.348 Sum_probs=40.3
Q ss_pred CCCccccc-----cCCchHHHHHhhcccccccccccchHHHHHHHHHcCCChhhhc
Q psy7153 33 KADVIKTH-----HNDSPLIRALREQGKVIEPLKDFHKDEVRKLGLDLGLTPEVVM 83 (131)
Q Consensus 33 ~a~~IKtH-----HNv~~l~~~~~~~~kdiePL~~L~KdEVR~Lg~~LGlP~~Ii~ 83 (131)
.|..|+|+ .||..-.+++|.-.+.|.-|..+..+|+...|+.++.|-+++.
T Consensus 138 GAaMIRtKGEaGTGnvveAVrH~R~i~~eI~~l~~~~~~el~~~Ak~~~ap~eLv~ 193 (208)
T PF01680_consen 138 GAAMIRTKGEAGTGNVVEAVRHMRTINGEIRRLQNMDDEELFAFAKEIGAPYELVK 193 (208)
T ss_dssp T-SEEEEETTTTST-THHHHHHHHHHHHHHHHHHTS-HHHHHHHHHHHTCGHHHHH
T ss_pred hhhhhcccCCCCCCcHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHCCCHHHHH
Confidence 35678776 5777777888876678888999999999999999999999875
No 48
>COG1606 ATP-utilizing enzymes of the PP-loop superfamily [General function prediction only]
Probab=68.08 E-value=3.7 Score=35.21 Aligned_cols=39 Identities=31% Similarity=0.508 Sum_probs=27.7
Q ss_pred ccccccccc--chHHHHHHHHHcCCChhhhccCCCCCCCceeeec
Q psy7153 55 KVIEPLKDF--HKDEVRKLGLDLGLTPEVVMRHPFPGPGLAIRVI 97 (131)
Q Consensus 55 kdiePL~~L--~KdEVR~Lg~~LGlP~~Ii~k~PfpGPGLaiR~~ 97 (131)
..-.|+.+| .|.|+|++|+.||+|- -+|++-+= |+.|+.
T Consensus 140 gi~sPl~e~gitk~eIre~a~~lgl~~--~~kp~~aC--l~sr~p 180 (269)
T COG1606 140 GIRSPLAEFGITKKEIREIAKSLGLPT--WDKPSMAC--LASRIP 180 (269)
T ss_pred CCCChHHHhCCcHHHHHHHHHHcCCCc--ccCccccc--cccccC
Confidence 467888765 9999999999999994 33444333 555543
No 49
>PLN00200 argininosuccinate synthase; Provisional
Probab=67.83 E-value=4.3 Score=36.03 Aligned_cols=28 Identities=11% Similarity=0.359 Sum_probs=24.4
Q ss_pred cccccccccccc---hHHHHHHHHHcCCChh
Q psy7153 53 QGKVIEPLKDFH---KDEVRKLGLDLGLTPE 80 (131)
Q Consensus 53 ~~kdiePL~~L~---KdEVR~Lg~~LGlP~~ 80 (131)
..+++.|++++. |+|+|++|+..|||-.
T Consensus 141 el~ViaPlre~~~~~r~e~~~~A~~~Gipv~ 171 (404)
T PLN00200 141 ELKVVAPWREWDIKGREDLIEYAKKHNIPVP 171 (404)
T ss_pred CCeeeCchhhcCCCCHHHHHHHHHHcCCCCC
Confidence 457999999985 9999999999999843
No 50
>PF07498 Rho_N: Rho termination factor, N-terminal domain; InterPro: IPR011112 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers []. This domain is found to the N terminus of the RNA binding domain (IPR011113 from INTERPRO).; GO: 0006353 transcription termination, DNA-dependent; PDB: 1A8V_B 1PVO_A 1PV4_D 3ICE_A 1XPU_C 1XPO_D 1XPR_F 2A8V_B 2HT1_B 1A63_A ....
Probab=65.43 E-value=3.3 Score=25.57 Aligned_cols=18 Identities=28% Similarity=0.591 Sum_probs=14.1
Q ss_pred cccchHHHHHHHHHcCCC
Q psy7153 61 KDFHKDEVRKLGLDLGLT 78 (131)
Q Consensus 61 ~~L~KdEVR~Lg~~LGlP 78 (131)
..+...|+|++|+.+||+
T Consensus 3 ~~~~~~eL~~iAk~lgI~ 20 (43)
T PF07498_consen 3 KSMTLSELREIAKELGIE 20 (43)
T ss_dssp HCS-HHHHHHHHHCTT-T
T ss_pred ccCCHHHHHHHHHHcCCC
Confidence 456788999999999998
No 51
>PF15599 Imm38: Immunity protein 38
Probab=62.62 E-value=13 Score=27.62 Aligned_cols=57 Identities=18% Similarity=0.113 Sum_probs=37.3
Q ss_pred hHHHHHHHHHcCCChhhhccCCCCCC---Cce-eeeccCc----cccccc-----ChHHHHHHHHHHHhh
Q psy7153 65 KDEVRKLGLDLGLTPEVVMRHPFPGP---GLA-IRVICGE----ERYIEK-----DYSETQVLVKIIVEY 121 (131)
Q Consensus 65 KdEVR~Lg~~LGlP~~Ii~k~PfpGP---GLa-iR~~g~~----e~~l~~-----~y~~~d~iL~~~~~~ 121 (131)
|.+|-+||+.+|+|+..+......+| |.. |.+-+.. -.|-|. .....|.+||-+++.
T Consensus 4 k~~i~~l~~k~g~~~~~~~~~~~~~~~~dg~~~i~~~~~~Y~~~~~ERG~~~~~r~T~~~dEllYwi~~d 73 (124)
T PF15599_consen 4 KAEIDELARKIGAPDNEYPLFFRDDPFGDGSPYIEIDNDGYHYVFYERGKEFSDRRTTDLDELLYWILDD 73 (124)
T ss_pred HHHHHHHHHHhCCCcccccccccCCCCCCCceEEEEeCCEEEEEEEecCceeeecccCCHHHHHHHHHHH
Confidence 67899999999999976666555544 777 6555542 112222 335678888876654
No 52
>PRK08384 thiamine biosynthesis protein ThiI; Provisional
Probab=60.60 E-value=5.9 Score=34.70 Aligned_cols=59 Identities=19% Similarity=0.267 Sum_probs=39.6
Q ss_pred ccccccccccchHHHHHHHHHcC-CChhhhccCCCCCCCceeeeccCcccccccChHHHHHHHHHHHh
Q psy7153 54 GKVIEPLKDFHKDEVRKLGLDLG-LTPEVVMRHPFPGPGLAIRVICGEERYIEKDYSETQVLVKIIVE 120 (131)
Q Consensus 54 ~kdiePL~~L~KdEVR~Lg~~LG-lP~~Ii~k~PfpGPGLaiR~~g~~e~~l~~~y~~~d~iL~~~~~ 120 (131)
...+-||..+.|+|++++|+.+| .+-+ ..|..+ . +.-...+..-.+.+.+..+-..++.
T Consensus 314 lpilRPLi~~dK~EIi~~Ar~iGT~~~s---~~~~~d--c---~f~pk~P~t~~~~~~~~~~e~~~~~ 373 (381)
T PRK08384 314 LPIYRPLIGMDKEEIVAIAKTIGTFELS---TLPEDE--I---PFIPKHPVIRGSWEEFRKLYKAIFG 373 (381)
T ss_pred CcEEeeCCCCCHHHHHHHHHHcCCcccc---cCCCCc--e---EEeCCCCcCCCCHHHHHHHHHHHhc
Confidence 36899999999999999999999 4433 245433 1 1113355666666666666666653
No 53
>PRK10696 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional
Probab=58.93 E-value=7.7 Score=31.20 Aligned_cols=24 Identities=21% Similarity=0.283 Sum_probs=23.1
Q ss_pred cccccccccchHHHHHHHHHcCCC
Q psy7153 55 KVIEPLKDFHKDEVRKLGLDLGLT 78 (131)
Q Consensus 55 kdiePL~~L~KdEVR~Lg~~LGlP 78 (131)
..+-||.++.|.|+++.++..|+|
T Consensus 173 ~iiRPLl~~~k~eI~~y~~~~~lp 196 (258)
T PRK10696 173 IVIRPLAYVAEKDIIKFAEAKEFP 196 (258)
T ss_pred eEEecCccCCHHHHHHHHHHcCCC
Confidence 589999999999999999999999
No 54
>cd01713 PAPS_reductase This domain is found in phosphoadenosine phosphosulphate (PAPS) reductase enzymes or PAPS sulphotransferase. PAPS reductase is part of the adenine nucleotide alpha hydrolases superfamily also including N type ATP PPases and ATP sulphurylases. A highly modified version of the P loop, the fingerprint peptide of mononucleotide-binding proteins, is present in the active site of the protein, which appears to be a positively charged cleft containing a number of conserved arginine and lysine residues. Although PAPS reductase has no ATPase activity, it shows a striking similarity to the structure of the ATP pyrophosphatase (ATP PPase) domain of GMP synthetase, indicating that both enzyme families have evolved from a common ancestral nucleotide-binding fold. The enzyme uses thioredoxin as an electron donor for the reduction of PAPS to phospho-adenosine-phosphate (PAP) . It is also found in NodP nodulation protein P from Rhizobium meliloti which has ATP sulphurylase acti
Probab=52.89 E-value=15 Score=25.65 Aligned_cols=35 Identities=17% Similarity=0.210 Sum_probs=29.4
Q ss_pred ccccccccccchHHHHHHHHHcCCChhhhccCCCC
Q psy7153 54 GKVIEPLKDFHKDEVRKLGLDLGLTPEVVMRHPFP 88 (131)
Q Consensus 54 ~kdiePL~~L~KdEVR~Lg~~LGlP~~Ii~k~Pfp 88 (131)
...+.||.++.+.+|++..+..|+|-.-+++.-|.
T Consensus 136 ~~~~~Pl~~w~~~di~~~~~~~~l~~~~ly~~g~~ 170 (173)
T cd01713 136 ILKVNPLLDWTYEDVWAYLARHGLPYNPLYDQGYR 170 (173)
T ss_pred cEEEcchhcCCHHHHHHHHHHcCCCCCHHHHcCCC
Confidence 35799999999999999999999997766665443
No 55
>PF02037 SAP: SAP domain; InterPro: IPR003034 The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA binding domain found in diverse nuclear proteins involved in chromosomal organisation [], including in apoptosis []. In yeast, SAP is found in the most distal N-terminal region of E3 SUMO-protein ligase SIZ1, where it is involved in nuclear localization [].; GO: 0003676 nucleic acid binding; PDB: 2RNN_A 1JEQ_A 2KW9_A 2KVU_A 2DO1_A 1ZBU_B 1ZBH_A 2DO5_A 2RNO_A 1H1J_S ....
Probab=49.86 E-value=15 Score=21.64 Aligned_cols=20 Identities=20% Similarity=0.285 Sum_probs=16.2
Q ss_pred ccccchHHHHHHHHHcCCCh
Q psy7153 60 LKDFHKDEVRKLGLDLGLTP 79 (131)
Q Consensus 60 L~~L~KdEVR~Lg~~LGlP~ 79 (131)
+..|...|+|++.+.+|+|.
T Consensus 1 l~~l~v~eLk~~l~~~gL~~ 20 (35)
T PF02037_consen 1 LSKLTVAELKEELKERGLST 20 (35)
T ss_dssp TTTSHHHHHHHHHHHTTS-S
T ss_pred CCcCcHHHHHHHHHHCCCCC
Confidence 35678899999999999984
No 56
>TIGR00032 argG argininosuccinate synthase. argG in bacteria, ARG1 in Saccharomyces cerevisiae. There is a very unusual clustering in the alignment, with a deep split between one cohort of E. coli, H. influenzae, and Streptomyces, and the other cohort of eukaryotes, archaea, and the rest of the eubacteria.
Probab=49.54 E-value=12 Score=32.92 Aligned_cols=35 Identities=26% Similarity=0.529 Sum_probs=29.5
Q ss_pred cccccccccc--cchHHHHHHHHHcCCChhhhccCCC
Q psy7153 53 QGKVIEPLKD--FHKDEVRKLGLDLGLTPEVVMRHPF 87 (131)
Q Consensus 53 ~~kdiePL~~--L~KdEVR~Lg~~LGlP~~Ii~k~Pf 87 (131)
..+.+.|+++ +.|.|+++.++..|+|-.+....|+
T Consensus 134 ~l~viaPLrew~l~r~ei~~ya~~~Gip~~~~~~~py 170 (394)
T TIGR00032 134 DLKVIAPWRDLNFTREEEIEYAIQCGIPYPMSKEKPY 170 (394)
T ss_pred CCeEECchhhcCCCHHHHHHHHHHcCCCeeEecCCCC
Confidence 3579999955 9999999999999999887665665
No 57
>PF10288 DUF2392: Protein of unknown function (DUF2392); InterPro: IPR019407 Cytoplasmic thiouridylase is a highly conserved complex responsible for the 2-thiolation of cytosolic tRNAs []. Inactivation of this complex leads to a loss of thiolation on tRNAs, decreased viability and aberrant cell development. This entry represents the second subunit of this complex.
Probab=49.11 E-value=12 Score=26.61 Aligned_cols=31 Identities=32% Similarity=0.401 Sum_probs=26.9
Q ss_pred cccccccccccchHHHHHHHHHcCCChhhhc
Q psy7153 53 QGKVIEPLKDFHKDEVRKLGLDLGLTPEVVM 83 (131)
Q Consensus 53 ~~kdiePL~~L~KdEVR~Lg~~LGlP~~Ii~ 83 (131)
..+.+-||+++.+.|+...++..|++...+.
T Consensus 31 ~i~~~rPLRd~l~kEi~~Y~~~~~l~~~~~~ 61 (107)
T PF10288_consen 31 DIKIIRPLRDLLKKEIAFYNRLCGLESVLVP 61 (107)
T ss_pred CceEEeehHhCCHHHHHHHHHHhCcchhhcc
Confidence 3478999999999999999999999866654
No 58
>TIGR00014 arsC arsenate reductase (glutaredoxin). composed of two polypeptides, the products of the arsA and arsB genes. The pump alone produces resistance to arsenite and antimonite. This protein, ArsC, catalyzes the reduction of arsenate to arsenite, and thus extends resistance to include arsenate.
Probab=45.34 E-value=22 Score=25.47 Aligned_cols=57 Identities=21% Similarity=0.186 Sum_probs=35.8
Q ss_pred ccchHHHHHHHHHcCCC--hhhhccCCCCCCCceeeeccCcccccccChHHHHHHHHHHHhhhhhhhhc
Q psy7153 62 DFHKDEVRKLGLDLGLT--PEVVMRHPFPGPGLAIRVICGEERYIEKDYSETQVLVKIIVEYDQMFKKI 128 (131)
Q Consensus 62 ~L~KdEVR~Lg~~LGlP--~~Ii~k~PfpGPGLaiR~~g~~e~~l~~~y~~~d~iL~~~~~~~~~~~k~ 128 (131)
.+.++|++++.+.+|++ .+++++.-..=-.| +-... +.+ .+.++..|+.....+++|
T Consensus 35 p~t~~el~~~l~~~g~~~~~~lin~~~~~~~~l-----~~~~~----~ls-~~e~i~~l~~~P~LikRP 93 (114)
T TIGR00014 35 PPTKSELEAIFAKLGLTVAREMIRTKEALYKEL-----GLSDP----NLS-DQELLDAMVAHPILLERP 93 (114)
T ss_pred CcCHHHHHHHHHHcCCchHHHHHhcCCcHHHHc-----CCCcc----CCC-HHHHHHHHHHCcCcccCC
Confidence 46899999999999997 47886543221111 11111 122 355778888777777776
No 59
>PF04031 Las1: Las1-like ; InterPro: IPR007174 Las1 is an essential nuclear protein involved in cell morphogenesis and cell surface growth [].
Probab=44.32 E-value=14 Score=28.40 Aligned_cols=29 Identities=17% Similarity=0.313 Sum_probs=23.5
Q ss_pred ccccccc-ccchHHHHHHHHHcCCChhhhc
Q psy7153 55 KVIEPLK-DFHKDEVRKLGLDLGLTPEVVM 83 (131)
Q Consensus 55 kdiePL~-~L~KdEVR~Lg~~LGlP~~Ii~ 83 (131)
-.+.|.. ..+..=|..+|+.+|||..||+
T Consensus 90 gl~D~~Q~~~~a~si~~~A~~iglP~~lVd 119 (154)
T PF04031_consen 90 GLVDPSQQGKYARSIASLAKEIGLPSWLVD 119 (154)
T ss_pred HhhhHhhccchhhhHHHHHHHcCCCHHHHH
Confidence 3566655 5677889999999999999985
No 60
>PF14265 DUF4355: Domain of unknown function (DUF4355)
Probab=42.81 E-value=29 Score=24.88 Aligned_cols=47 Identities=17% Similarity=0.210 Sum_probs=35.9
Q ss_pred chHHHHHHHHHcCCChhhhccCCCCCCCceeeeccCcccccccChHHHHHHHHHHHhh
Q psy7153 64 HKDEVRKLGLDLGLTPEVVMRHPFPGPGLAIRVICGEERYIEKDYSETQVLVKIIVEY 121 (131)
Q Consensus 64 ~KdEVR~Lg~~LGlP~~Ii~k~PfpGPGLaiR~~g~~e~~l~~~y~~~d~iL~~~~~~ 121 (131)
...+|+.++...|||.+++.+ ++|.++..+..+...+..++...+..
T Consensus 70 ~~~~~~~~l~e~GLp~~l~~~-----------l~g~d~e~~~~~v~~l~~~~~~~v~~ 116 (125)
T PF14265_consen 70 LRSEAKKVLAEKGLPAELADF-----------LVGDDEEETKANVKALKKLFNKAVQE 116 (125)
T ss_pred HHHHHHHHHHHcCCCHHHHHH-----------HhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 457788999999999997653 57888888877777777776666544
No 61
>PF11007 CotJA: Spore coat associated protein JA (CotJA); InterPro: IPR020256 cotJA is part of the cotJ operon, which encodes spore coat proteins. Interaction of CotJA with CotJC is required for the assembly of both CotJA and CotJC into the spore coat [].
Probab=42.75 E-value=7.1 Score=23.97 Aligned_cols=12 Identities=42% Similarity=0.661 Sum_probs=9.9
Q ss_pred eeecccccccee
Q psy7153 12 LLCQGTLRPDLI 23 (131)
Q Consensus 12 ~l~QGTiypD~i 23 (131)
-|-+|||+||+.
T Consensus 22 aL~~GTiFp~L~ 33 (36)
T PF11007_consen 22 ALKRGTIFPELY 33 (36)
T ss_pred HHhcCCcchhhc
Confidence 467899999974
No 62
>COG0603 Predicted PP-loop superfamily ATPase [General function prediction only]
Probab=40.85 E-value=20 Score=29.78 Aligned_cols=27 Identities=33% Similarity=0.557 Sum_probs=24.1
Q ss_pred ccccccccchHHHHHHHHHcCCChhhh
Q psy7153 56 VIEPLKDFHKDEVRKLGLDLGLTPEVV 82 (131)
Q Consensus 56 diePL~~L~KdEVR~Lg~~LGlP~~Ii 82 (131)
...||-+|.|.|..++|.+||+|-+.-
T Consensus 157 i~aPl~~l~Ka~iv~l~~elg~~~~~T 183 (222)
T COG0603 157 IHAPLMELTKAEIVKLADELGVPLELT 183 (222)
T ss_pred EeCCeeeccHHHHHHHHHHhCCcchhc
Confidence 489999999999999999999886654
No 63
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=36.56 E-value=34 Score=22.77 Aligned_cols=20 Identities=30% Similarity=0.551 Sum_probs=17.4
Q ss_pred cchHHHHHHHHHcCCChhhh
Q psy7153 63 FHKDEVRKLGLDLGLTPEVV 82 (131)
Q Consensus 63 L~KdEVR~Lg~~LGlP~~Ii 82 (131)
....++.+||..|||++..|
T Consensus 30 ~~~~~r~~la~~lgl~~~vv 49 (58)
T TIGR01565 30 KRREEVREFCEEIGVTRKVF 49 (58)
T ss_pred CCHHHHHHHHHHhCCCHHHe
Confidence 56779999999999998765
No 64
>PF02567 PhzC-PhzF: Phenazine biosynthesis-like protein; InterPro: IPR003719 Five genes, phzF, phzA, phzB, phzC and phzD, encode enzymes for phenazine biosynthesis in the biological control bacterium Pseudomonas chlororaphis (also known as Pseudomonas aureofaciens). Protein PhzF is similar to 3-deoxy-D-arabino-heptulosonate-7-phosphate synthases of solanaceous plants. PhzC is responsible for the conversion of phenazine-I-carboxylic acid to 2-hydroxy-phenazine-I-carboxylic acid [].; GO: 0003824 catalytic activity, 0009058 biosynthetic process; PDB: 1U0K_A 1QYA_B 1QY9_D 1SDJ_A 1U1X_A 1U1W_B 1T6K_A 1XUA_A 1XUB_A 1U1V_A ....
Probab=36.12 E-value=34 Score=27.19 Aligned_cols=39 Identities=5% Similarity=0.198 Sum_probs=30.3
Q ss_pred ccchHHHHHHHHHcCCChhhhccCC-CCCCCceeeeccCc
Q psy7153 62 DFHKDEVRKLGLDLGLTPEVVMRHP-FPGPGLAIRVICGE 100 (131)
Q Consensus 62 ~L~KdEVR~Lg~~LGlP~~Ii~k~P-fpGPGLaiR~~g~~ 100 (131)
+|.-++.++||+++++|+-..=.++ -+.....|||--..
T Consensus 22 ~l~~~~mq~iA~e~n~sET~Fv~~~~~~~~~~~vR~FTp~ 61 (281)
T PF02567_consen 22 GLSDEQMQAIAREFNLSETAFVLPSTDDEADYRVRIFTPT 61 (281)
T ss_dssp TS-HHHHHHHHHHHTSSEEEEEEEESSSTTSEEEEEEESS
T ss_pred CCCHHHHHHHHHHcCCCeeEEEEeccCCCceeEEEEEecc
Confidence 5778889999999999995544444 46777999998876
No 65
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=34.30 E-value=24 Score=21.50 Aligned_cols=17 Identities=29% Similarity=0.507 Sum_probs=12.3
Q ss_pred HHHHHHHcCCChhhhcc
Q psy7153 68 VRKLGLDLGLTPEVVMR 84 (131)
Q Consensus 68 VR~Lg~~LGlP~~Ii~k 84 (131)
+++||+.||....-|.|
T Consensus 23 ~~~IA~~lg~s~sTV~r 39 (44)
T PF13936_consen 23 IREIAKRLGRSRSTVSR 39 (44)
T ss_dssp HHHHHHHTT--HHHHHH
T ss_pred HHHHHHHHCcCcHHHHH
Confidence 58899999999887764
No 66
>PF08815 Nuc_rec_co-act: Nuclear receptor coactivator; InterPro: IPR014920 This entry represents the interlocking domain of the eukaryotic nuclear receptor coactivators Ncoa1, Ncoa2 and Ncoa3. The interlocking domain forms a 3-helical non-globular array that forms interlocked heterodimers with its target. Nuclear receptors are ligand-activated transcription factors involved in the regulation of many processes, including development, reproduction and homeostasis. Nuclear receptor coactivators act to modulate the function of nuclear receptors. Coactivators associate with promoters and enhancers primarily through protein-protein contacts to facilitate the interaction between DNA-bound transcription factors and the transcription machinery. In addition to their role as coactivators of various nuclear receptors, Ncoa1 and Ncoa3 both have histone acetyltransferase activity (2.3.1.48 from EC), but Ncoa2 does not [, ]. ; GO: 0003713 transcription coactivator activity, 0035257 nuclear hormone receptor binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2C52_B 1KBH_A.
Probab=33.26 E-value=7.7 Score=25.91 Aligned_cols=31 Identities=13% Similarity=0.220 Sum_probs=22.4
Q ss_pred ccccccccchHHHHHHHHHcCCChhhhccCCC
Q psy7153 56 VIEPLKDFHKDEVRKLGLDLGLTPEVVMRHPF 87 (131)
Q Consensus 56 diePL~~L~KdEVR~Lg~~LGlP~~Ii~k~Pf 87 (131)
+..-|+++-+.++.+|-|.|||| ++++.-..
T Consensus 13 L~s~L~~~D~~~LeEIDraLGIp-~Lv~Q~q~ 43 (51)
T PF08815_consen 13 LYSLLSNTDVTGLEEIDRALGIP-DLVGQGQA 43 (51)
T ss_dssp HHHHCCTSSGCCCHCCHHHTTCC-CCCHCTCC
T ss_pred HHHHHhccchhhHHHHHHHhCcH-HHHHccCC
Confidence 34456777788999999999997 56654433
No 67
>COG0214 SNZ1 Pyridoxine biosynthesis enzyme [Coenzyme metabolism]
Probab=33.26 E-value=26 Score=30.44 Aligned_cols=50 Identities=26% Similarity=0.329 Sum_probs=40.0
Q ss_pred CCccccc-----cCCchHHHHHhhcccccccccccchHHHHHHHHHcCCChhhhc
Q psy7153 34 ADVIKTH-----HNDSPLIRALREQGKVIEPLKDFHKDEVRKLGLDLGLTPEVVM 83 (131)
Q Consensus 34 a~~IKtH-----HNv~~l~~~~~~~~kdiePL~~L~KdEVR~Lg~~LGlP~~Ii~ 83 (131)
|+.|+|- .||..-.++||.-...|.-+..+..||++..|+.++.|-+|+.
T Consensus 145 AaMIRTKGEaGTGnv~eAVrHmr~i~~eI~~l~~~~edel~~~Ak~~~~p~elv~ 199 (296)
T COG0214 145 AAMIRTKGEAGTGNVVEAVRHMRKINGEIRRLQSMTEDELYVVAKELQAPYELVK 199 (296)
T ss_pred HHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHhCChHHHHH
Confidence 4556554 4666677788765677888889999999999999999999974
No 68
>smart00513 SAP Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation.
Probab=33.10 E-value=46 Score=19.26 Aligned_cols=19 Identities=16% Similarity=0.200 Sum_probs=16.1
Q ss_pred cccchHHHHHHHHHcCCCh
Q psy7153 61 KDFHKDEVRKLGLDLGLTP 79 (131)
Q Consensus 61 ~~L~KdEVR~Lg~~LGlP~ 79 (131)
..+...|+|+..+.+|+|.
T Consensus 2 ~~l~~~~Lk~~l~~~gl~~ 20 (35)
T smart00513 2 AKLKVSELKDELKKRGLST 20 (35)
T ss_pred CcCcHHHHHHHHHHcCCCC
Confidence 4577889999999999984
No 69
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=32.77 E-value=25 Score=23.75 Aligned_cols=18 Identities=11% Similarity=0.462 Sum_probs=15.3
Q ss_pred HHHHHHHHcCCChhhhcc
Q psy7153 67 EVRKLGLDLGLTPEVVMR 84 (131)
Q Consensus 67 EVR~Lg~~LGlP~~Ii~k 84 (131)
..++||+.||+++.-|.+
T Consensus 24 ~lkdIA~~Lgvs~~tIr~ 41 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRK 41 (60)
T ss_pred cHHHHHHHHCCCHHHHHH
Confidence 578999999999987754
No 70
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=32.58 E-value=26 Score=20.89 Aligned_cols=19 Identities=26% Similarity=0.457 Sum_probs=13.4
Q ss_pred HHHHHHHHHcCCChhhhcc
Q psy7153 66 DEVRKLGLDLGLTPEVVMR 84 (131)
Q Consensus 66 dEVR~Lg~~LGlP~~Ii~k 84 (131)
--++++|+.||++..-|.|
T Consensus 18 ~s~~~ia~~lgvs~~Tv~~ 36 (50)
T PF13384_consen 18 WSIREIAKRLGVSRSTVYR 36 (50)
T ss_dssp --HHHHHHHHTS-HHHHHH
T ss_pred CCHHHHHHHHCcCHHHHHH
Confidence 3468899999999887754
No 71
>TIGR00654 PhzF_family phenazine biosynthesis protein PhzF family. Members of this family show a distant global similarity to diaminopimelate epimerases, which can be taken as the outgroup. One member of this family has been shown to act as an enzyme in the biosynthesis of the antibiotic phenazine in Pseudomonas aureofaciens. The function in other species is unclear.
Probab=31.26 E-value=68 Score=25.95 Aligned_cols=46 Identities=9% Similarity=0.151 Sum_probs=34.7
Q ss_pred ccchHHHHHHHHHcCCChhhhccCC-CCCCCceeeeccCc-ccccccC
Q psy7153 62 DFHKDEVRKLGLDLGLTPEVVMRHP-FPGPGLAIRVICGE-ERYIEKD 107 (131)
Q Consensus 62 ~L~KdEVR~Lg~~LGlP~~Ii~k~P-fpGPGLaiR~~g~~-e~~l~~~ 107 (131)
+|.-++.++||+++|.++-+.-.+| .++-.+-+||-... |.++|-.
T Consensus 29 ~l~~~~mq~iA~~~~~~et~Fv~~~~~~~~~~~~R~Fnpg~E~~~CGh 76 (297)
T TIGR00654 29 ILSEEEMQAIANETNYSETTFLLKPSSEKYDYRLRIFTPRSELPFAGH 76 (297)
T ss_pred CCCHHHHHHHHHHhCCCceEEEcCCCCCCCceEEEEECCCCccCcCCc
Confidence 4667889999999999998887765 44445899999884 5555543
No 72
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=31.03 E-value=32 Score=19.40 Aligned_cols=18 Identities=22% Similarity=0.411 Sum_probs=13.7
Q ss_pred HHHHHHHcCCChhhhccC
Q psy7153 68 VRKLGLDLGLTPEVVMRH 85 (131)
Q Consensus 68 VR~Lg~~LGlP~~Ii~k~ 85 (131)
+.++|+.||++..-+.+-
T Consensus 3 ~~e~a~~lgvs~~tl~~~ 20 (49)
T cd04762 3 TKEAAELLGVSPSTLRRW 20 (49)
T ss_pred HHHHHHHHCcCHHHHHHH
Confidence 467899999998776653
No 73
>PF02952 Fucose_iso_C: L-fucose isomerase, C-terminal domain; InterPro: IPR015888 L-fucose isomerase (5.3.1.25 from EC) converts the aldose L-fucose into the corresponding ketose L-fuculose during the first step in fucose metabolism using Mn2+ as a cofactor. The enzyme is a hexamer, forming the largest structurally known ketol isomerase, and has no sequence or structural similarity with other ketol isomerases. The structure was determined by X-ray crystallography at 2.5 A resolution []. This entry represents the C-terminal domain of L-fucose isomerase.; GO: 0008736 L-fucose isomerase activity, 0006004 fucose metabolic process, 0005737 cytoplasm; PDB: 1FUI_E 3A9R_A 3A9T_C 3A9S_C.
Probab=30.93 E-value=33 Score=24.96 Aligned_cols=16 Identities=25% Similarity=0.428 Sum_probs=12.0
Q ss_pred chHHHHHHHHHcCCCh
Q psy7153 64 HKDEVRKLGLDLGLTP 79 (131)
Q Consensus 64 ~KdEVR~Lg~~LGlP~ 79 (131)
+.+|++++++.||++-
T Consensus 123 ~~~~l~~~~~~lgi~v 138 (142)
T PF02952_consen 123 YAEELKELAKYLGIEV 138 (142)
T ss_dssp -HHHHHHHHHHHT--E
T ss_pred HHHHHHHHHHHcCCEE
Confidence 7899999999999983
No 74
>COG1513 CynS Cyanate lyase [Inorganic ion transport and metabolism]
Probab=30.79 E-value=42 Score=26.67 Aligned_cols=46 Identities=24% Similarity=0.338 Sum_probs=32.5
Q ss_pred cccchHHHHHHHHHcCCChhhh---ccCCCCCCCceeeecc---CcccccccChHHHH
Q psy7153 61 KDFHKDEVRKLGLDLGLTPEVV---MRHPFPGPGLAIRVIC---GEERYIEKDYSETQ 112 (131)
Q Consensus 61 ~~L~KdEVR~Lg~~LGlP~~Ii---~k~PfpGPGLaiR~~g---~~e~~l~~~y~~~d 112 (131)
..+..+|+|++|..|||+++.| .-.|.-|| ++ .+.+.+-.=|+.++
T Consensus 46 a~~~~~ear~v~e~L~L~~~~v~~L~~~p~rg~------l~~~~PTDP~iYRfYE~~q 97 (151)
T COG1513 46 AALPADEARAVGEALDLDEDAILLLQMIPLRGC------LGPVIPTDPLIYRFYEMLQ 97 (151)
T ss_pred ccCCHHHHHHHHHHhCCCHHHHHHhhccCccCC------CCCCCCCChHHHHHHHHHH
Confidence 4668899999999999999865 45677662 22 34666666665554
No 75
>PRK01269 tRNA s(4)U8 sulfurtransferase; Provisional
Probab=30.54 E-value=39 Score=30.04 Aligned_cols=26 Identities=19% Similarity=0.468 Sum_probs=23.4
Q ss_pred ccccccccccchHHHHHHHHHcCCCh
Q psy7153 54 GKVIEPLKDFHKDEVRKLGLDLGLTP 79 (131)
Q Consensus 54 ~kdiePL~~L~KdEVR~Lg~~LGlP~ 79 (131)
..++-||..+.|.|+-++|+.+|+++
T Consensus 310 ~~v~rPLi~~dK~EIi~~a~~ig~~~ 335 (482)
T PRK01269 310 TLILRPLIAMDKEDIIDLAREIGTED 335 (482)
T ss_pred CceecCCcCCCHHHHHHHHHHhCChh
Confidence 45789999999999999999999853
No 76
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=30.34 E-value=49 Score=20.15 Aligned_cols=24 Identities=33% Similarity=0.297 Sum_probs=19.5
Q ss_pred ccccchHHHHHHHHHcCCChhhhc
Q psy7153 60 LKDFHKDEVRKLGLDLGLTPEVVM 83 (131)
Q Consensus 60 L~~L~KdEVR~Lg~~LGlP~~Ii~ 83 (131)
-.....+|..+||..|||+..-|.
T Consensus 22 ~~~p~~~~~~~la~~l~l~~~~V~ 45 (57)
T PF00046_consen 22 NPYPSKEEREELAKELGLTERQVK 45 (57)
T ss_dssp SSSCHHHHHHHHHHHHTSSHHHHH
T ss_pred hccccccccccccccccccccccc
Confidence 345678899999999999987653
No 77
>PF12116 SpoIIID: Stage III sporulation protein D; InterPro: IPR014208 Members of this entry represent the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if, and only if, the species is capable of endospore formation. In Bacillus subtilis SpoIIID is a DNA binding protein that is involved in gene repression as well as activation [].; PDB: 2L0K_A.
Probab=29.98 E-value=29 Score=25.18 Aligned_cols=22 Identities=23% Similarity=0.351 Sum_probs=15.7
Q ss_pred chHHHHHHHHHcCCChhhhccC
Q psy7153 64 HKDEVRKLGLDLGLTPEVVMRH 85 (131)
Q Consensus 64 ~KdEVR~Lg~~LGlP~~Ii~k~ 85 (131)
.+.=||+.|+.+|++.+-|+|-
T Consensus 18 ~~aTVR~~Ak~FGvSKSTVHkD 39 (82)
T PF12116_consen 18 TKATVRQAAKVFGVSKSTVHKD 39 (82)
T ss_dssp H---HHHHHHHHTS-HHHHHHH
T ss_pred cccHHHHHHHHHCCcHHHHHHH
Confidence 3667999999999999988763
No 78
>PF02786 CPSase_L_D2: Carbamoyl-phosphate synthase L chain, ATP binding domain; InterPro: IPR005479 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 ATP-binding domain found in the large subunit of carbamoyl phosphate synthase, as well as in related proteins.; GO: 0003824 catalytic activity, 0005524 ATP binding, 0008152 metabolic process; PDB: 3U9S_A 3U9T_A 2C00_B 2VQD_A 1W96_B 1W93_A 1M6V_C 1CS0_C 1C30_E 1C3O_G ....
Probab=29.77 E-value=41 Score=26.77 Aligned_cols=46 Identities=17% Similarity=0.411 Sum_probs=34.0
Q ss_pred cchHHHHHHHHHcCCChhhhccCCCCCCCceeeeccCcccccccChHHH
Q psy7153 63 FHKDEVRKLGLDLGLTPEVVMRHPFPGPGLAIRVICGEERYIEKDYSET 111 (131)
Q Consensus 63 L~KdEVR~Lg~~LGlP~~Ii~k~PfpGPGLaiR~~g~~e~~l~~~y~~~ 111 (131)
-..+|+++.|+.+|.| ++=|+-+.|=|-++|++- ++.++..-+...
T Consensus 25 ~~~eea~~~a~~iGyP--VliKas~ggGG~gm~iv~-~~~eL~~~~~~~ 70 (211)
T PF02786_consen 25 SSVEEALEFAEEIGYP--VLIKASAGGGGRGMRIVH-NEEELEEAFERA 70 (211)
T ss_dssp SSHHHHHHHHHHH-SS--EEEEETTSSTTTSEEEES-SHHHHHHHHHHH
T ss_pred CCHHHHHHHHHhcCCc--eEEeeccccccccccccc-chhhhhhhhhhc
Confidence 3678999999999999 888999999899888875 344444444333
No 79
>PF10534 CRIC_ras_sig: Connector enhancer of kinase suppressor of ras; InterPro: IPR019555 The multi-domain protein Connector enhancer of kinase suppressor of ras (Connector enhancer of KSR) (CNK) functions as a scaffold in several signal cascades and acts on proliferation, differentiation and apoptosis. CNK connects upstream activators and downstream targets of Ras- and Rho-dependent signalling pathways and may allow cross-talk between these pathways. In invertebrates, CNK is expressed as one isoform, whereas in mammals there exists CNK1, CNK2A, and its splice variant CNK2B. CNK proteins consist of one sterile alpha motif (SAM) domain (see PDOC50105 from PROSITEDOC, IPR001660 from INTERPRO) one conserved region in CNK (CRIC) domain, one PSD-96/Dlg-A/ZO-1 (PDZ) domain (see PDOC50106 from PROSITEDOC, IPR001478 from INTERPRO) and one pleckstrin homology (PH) domain (see PDOC50003 from PROSITEDOC, IPR001849 from INTERPRO. The CRIC domain is enriched in leucine residues and functions as a protein-protein interaction domain [, ].; PDB: 1WWV_A.
Probab=29.17 E-value=18 Score=26.35 Aligned_cols=35 Identities=23% Similarity=0.451 Sum_probs=0.0
Q ss_pred hhhccCCCCCCCceeeeccCcccccccChHHHH-HHHHHHHhhhhhhhhcC
Q psy7153 80 EVVMRHPFPGPGLAIRVICGEERYIEKDYSETQ-VLVKIIVEYDQMFKKIY 129 (131)
Q Consensus 80 ~Ii~k~PfpGPGLaiR~~g~~e~~l~~~y~~~d-~iL~~~~~~~~~~~k~~ 129 (131)
.+++|.||.| ..+|..+. .|++...+....+++-.
T Consensus 57 ~WLdR~pF~~---------------~~dfs~~kn~I~~lc~eL~~~vq~d~ 92 (95)
T PF10534_consen 57 SWLDRYPFSG---------------LNDFSACKNKIIQLCLELTTIVQKDC 92 (95)
T ss_dssp ---------------------------------------------------
T ss_pred ccccCCCCCC---------------chHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 5789999999 57898888 88888888887777643
No 80
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=28.38 E-value=29 Score=22.84 Aligned_cols=18 Identities=33% Similarity=0.396 Sum_probs=14.7
Q ss_pred HHHHHHHcCCChhhhccC
Q psy7153 68 VRKLGLDLGLTPEVVMRH 85 (131)
Q Consensus 68 VR~Lg~~LGlP~~Ii~k~ 85 (131)
..+||+.|||+..-++|+
T Consensus 25 a~eLa~~lgl~~~~v~r~ 42 (68)
T smart00550 25 ALQLAKNLGLPKKEVNRV 42 (68)
T ss_pred HHHHHHHHCCCHHHHHHH
Confidence 467999999998888776
No 81
>PRK10026 arsenate reductase; Provisional
Probab=28.08 E-value=61 Score=24.83 Aligned_cols=57 Identities=18% Similarity=0.227 Sum_probs=35.8
Q ss_pred ccchHHHHHHHHHcCC-ChhhhccCCCCCCCceeeeccCcccccccChHHHHHHHHHHHhhhhhhhhc
Q psy7153 62 DFHKDEVRKLGLDLGL-TPEVVMRHPFPGPGLAIRVICGEERYIEKDYSETQVLVKIIVEYDQMFKKI 128 (131)
Q Consensus 62 ~L~KdEVR~Lg~~LGl-P~~Ii~k~PfpGPGLaiR~~g~~e~~l~~~y~~~d~iL~~~~~~~~~~~k~ 128 (131)
.+.++|++.+.+.+|+ +++++++.-..=-.| +-... .+ +.+.++..++....-+++|
T Consensus 38 ppt~~eL~~~l~~~g~~~~~lint~~~~yr~L-----~~~~~--~l---s~~e~l~ll~~~P~LIKRP 95 (141)
T PRK10026 38 PPTRDELVKLIADMGISVRALLRKNVEPYEEL-----GLAED--KF---TDDQLIDFMLQHPILINRP 95 (141)
T ss_pred CcCHHHHHHHHHhCCCCHHHHHHcCCchHHHc-----CCCcc--CC---CHHHHHHHHHhCccceeCc
Confidence 3689999999999999 588887753322112 11111 11 2356777777776666665
No 82
>cd03286 ABC_MSH6_euk MutS6 homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c
Probab=27.39 E-value=37 Score=27.17 Aligned_cols=18 Identities=28% Similarity=0.209 Sum_probs=15.4
Q ss_pred HHHHHHHcCCChhhhccC
Q psy7153 68 VRKLGLDLGLTPEVVMRH 85 (131)
Q Consensus 68 VR~Lg~~LGlP~~Ii~k~ 85 (131)
--++|+..|+|+++|+|+
T Consensus 201 al~~A~~~g~p~~vi~rA 218 (218)
T cd03286 201 GLYVALMAGIPDGVVERA 218 (218)
T ss_pred HHHHHHHhCcCHHHHhcC
Confidence 346999999999999884
No 83
>PF07453 NUMOD1: NUMOD1 domain; InterPro: IPR010896 This helix-turn-helix-containing DNA-binding domain is found associated in homing nucleases [].
Probab=27.32 E-value=45 Score=19.26 Aligned_cols=17 Identities=18% Similarity=0.427 Sum_probs=13.8
Q ss_pred HHHHHHHcCCChhhhcc
Q psy7153 68 VRKLGLDLGLTPEVVMR 84 (131)
Q Consensus 68 VR~Lg~~LGlP~~Ii~k 84 (131)
+++.|++||++..-|++
T Consensus 19 i~eAa~~l~i~~~~I~~ 35 (37)
T PF07453_consen 19 IREAARYLGISHSTISK 35 (37)
T ss_pred HHHHHHHhCCCHHHHHH
Confidence 47899999999887765
No 84
>cd03034 ArsC_ArsC Arsenate Reductase (ArsC) family, ArsC subfamily; arsenic reductases similar to that encoded by arsC on the R733 plasmid of Escherichia coli. E. coli ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], the first step in the detoxification of arsenic, using reducing equivalents derived from glutathione (GSH) via glutaredoxin (GRX). ArsC contains a single catalytic cysteine, within a thioredoxin fold, that forms a covalent thiolate-As(V) intermediate, which is reduced by GRX through a mixed GSH-arsenate intermediate. This family of predominantly bacterial enzymes is unrelated to two other families of arsenate reductases which show similarity to low-molecular-weight acid phosphatases and phosphotyrosyl phosphatases.
Probab=26.83 E-value=58 Score=23.13 Aligned_cols=57 Identities=14% Similarity=0.234 Sum_probs=35.9
Q ss_pred ccchHHHHHHHHHcCC-ChhhhccCCCCCCCceeeeccCcccccccChHHHHHHHHHHHhhhhhhhhc
Q psy7153 62 DFHKDEVRKLGLDLGL-TPEVVMRHPFPGPGLAIRVICGEERYIEKDYSETQVLVKIIVEYDQMFKKI 128 (131)
Q Consensus 62 ~L~KdEVR~Lg~~LGl-P~~Ii~k~PfpGPGLaiR~~g~~e~~l~~~y~~~d~iL~~~~~~~~~~~k~ 128 (131)
.+.++|++++...+|. +++++++.-.. .|=++-... +++ .+.++..|+.....+++|
T Consensus 35 ~~t~~el~~~l~~~~~~~~~lin~~~~~-----y~~l~~~~~----~ls-~~e~i~ll~~~P~LikRP 92 (112)
T cd03034 35 PPTAAELRELLAKLGISPRDLLRTKEAP-----YKELGLADP----ELS-DEELIDAMAAHPILIERP 92 (112)
T ss_pred CcCHHHHHHHHHHcCCCHHHHHhcCCch-----HHHcCCCcc----CCC-HHHHHHHHHhCcCcccCC
Confidence 4689999999999997 67777763211 111111111 222 466778888777777776
No 85
>cd08205 RuBisCO_IV_RLP Ribulose bisphosphate carboxylase like proteins, Rubisco-Form IV. Ribulose bisphosphate carboxylase (Rubisco) plays an important role in the Calvin reductive pentose phosphate pathway. It catalyzes the primary CO2 fixation step. Rubisco is activated by carbamylation of an active site lysine, stabilized by a divalent cation, which then catalyzes the proton abstraction from the substrate ribulose 1,5 bisphosphate (RuBP) and leads to the formation of two molecules of 3-phosphoglycerate. Members of the Rubisco family can be divided into 4 subgroups, Form I-IV, which differ in their taxonomic distribution and subunit composition. Form I-III have Rubisco activity, while Form IV, also called Rubisco-like proteins (RLP), are missing critical active site residues and therefore do not catalyze CO2 fixation. They are believed to utilize a related enzymatic mechanism, but have divergent functions, like for example 2,3-diketo-5-methylthiopentyl-1-phosphate enolase or 5-methyl
Probab=26.76 E-value=65 Score=27.93 Aligned_cols=48 Identities=25% Similarity=0.297 Sum_probs=37.1
Q ss_pred HcCCChhhhccCCCCCCCcee---e---------eccCc-ccccccChHHHHHHHHHHHhhhh
Q psy7153 74 DLGLTPEVVMRHPFPGPGLAI---R---------VICGE-ERYIEKDYSETQVLVKIIVEYDQ 123 (131)
Q Consensus 74 ~LGlP~~Ii~k~PfpGPGLai---R---------~~g~~-e~~l~~~y~~~d~iL~~~~~~~~ 123 (131)
.+.+|++++.+ |+||-++| | .++.- ++..+.|.+++..+++.+++..-
T Consensus 100 D~~~P~~~~~~--f~GP~fGi~g~R~~~gv~~rPli~Ti~kp~~gld~~~la~~~~~l~~gGv 160 (367)
T cd08205 100 DLELPDSLLAA--FPGPRFGIEGLRRLLGVHDRPLLGTIIKPSIGLSPEELAELAYELALGGI 160 (367)
T ss_pred ecCCCHHHHhh--CCCCCCCchhHHHHhCCCCCCeeeeeeCCCCCCCHHHHHHHHHHHHhcCC
Confidence 45689999988 88997775 2 23333 77889999999999999887653
No 86
>PF04428 Choline_kin_N: Choline kinase N terminus; InterPro: IPR007521 This domain is found N-terminal to choline/ethanolamine kinase regions (IPR002573 from INTERPRO) in some plant and fungal choline kinase enzymes (2.7.1.32 from EC). This region is only found in some members of the choline kinase family, and is therefore unlikely to contribute to catalysis.; GO: 0016773 phosphotransferase activity, alcohol group as acceptor
Probab=25.81 E-value=55 Score=21.71 Aligned_cols=17 Identities=18% Similarity=0.196 Sum_probs=15.5
Q ss_pred cchHHHHHHHHHcCCCh
Q psy7153 63 FHKDEVRKLGLDLGLTP 79 (131)
Q Consensus 63 L~KdEVR~Lg~~LGlP~ 79 (131)
-||.||..|...|.||.
T Consensus 27 ~fk~di~~l~htL~i~~ 43 (53)
T PF04428_consen 27 RFKQDILRLIHTLKIKK 43 (53)
T ss_pred ccHHHHHHHHHHhcccc
Confidence 49999999999999985
No 87
>PF01832 Glucosaminidase: Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase; InterPro: IPR002901 This domain is found in many different proteins including mannosyl-glycoprotein endo-beta-N-acetylglucosamidase (3.2.1.96 from EC).It is also found in flagellar protein J (P75942 from SWISSPROT), which has been shown to hydrolyse peptidoglycan [].; GO: 0004040 amidase activity, 0009253 peptidoglycan catabolic process; PDB: 3FI7_A 2ZYC_A 3K3T_A.
Probab=25.68 E-value=9 Score=27.35 Aligned_cols=36 Identities=19% Similarity=0.237 Sum_probs=22.2
Q ss_pred cCCCCCCCceeeccccccceeeccCCCCCCCCCccccccCCchHHH
Q psy7153 3 ELKLDPNQTLLCQGTLRPDLIESASHLASNKADVIKTHHNDSPLIR 48 (131)
Q Consensus 3 ~~~~~~~~~~l~QGTiypD~iES~~~~~~~~a~~IKtHHNv~~l~~ 48 (131)
+.++++ ...|+|- .+||+-. .+..-+.+||..|+--
T Consensus 11 ~~gI~~-~~~laQa-----~lESg~G----~s~~a~~~nN~fGi~~ 46 (136)
T PF01832_consen 11 KYGIPP-SLILAQA-----ILESGWG----TSRLAKEYNNFFGIKA 46 (136)
T ss_dssp HCTS-H-HHHHHHH-----HHHHTTT----TTTTTSCTT-TT--BS
T ss_pred HhCCCH-HHHHHHH-----HHHhcCC----CCccccccccccceec
Confidence 356666 5577888 7899853 3456788889887743
No 88
>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=25.50 E-value=70 Score=22.63 Aligned_cols=59 Identities=14% Similarity=0.118 Sum_probs=36.4
Q ss_pred ccchHHHHHHHHHcCCC-hhhhccCCCCCCCceeeeccCcccccccChHHHHHHHHHHHhhhhhhhhc
Q psy7153 62 DFHKDEVRKLGLDLGLT-PEVVMRHPFPGPGLAIRVICGEERYIEKDYSETQVLVKIIVEYDQMFKKI 128 (131)
Q Consensus 62 ~L~KdEVR~Lg~~LGlP-~~Ii~k~PfpGPGLaiR~~g~~e~~l~~~y~~~d~iL~~~~~~~~~~~k~ 128 (131)
.+.++|++++...+|+| .+++++....=..| +-++. + .+.+ .+.++..++.....+++|
T Consensus 35 ~~~~~el~~~~~~~~~~~~~l~~~~~~~~~~l-----~~~~~-~-~~~s-~~e~~~~l~~~p~LikRP 94 (111)
T cd03036 35 PPSKEELKKWLEKSGLPLKKFFNTSGKSYREL-----GLKDK-L-PSLS-EEEALELLSSDGMLIKRP 94 (111)
T ss_pred cccHHHHHHHHHHcCCCHHHHHhcCCchHHhC-----Ccccc-c-ccCC-HHHHHHHHHhCcCeeeCC
Confidence 45689999999999995 77777654432223 22221 1 1122 355777777777777766
No 89
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=25.49 E-value=31 Score=21.45 Aligned_cols=16 Identities=25% Similarity=0.569 Sum_probs=12.1
Q ss_pred HHHHHHHcCCChhhhc
Q psy7153 68 VRKLGLDLGLTPEVVM 83 (131)
Q Consensus 68 VR~Lg~~LGlP~~Ii~ 83 (131)
|++||+.||+|..-+-
T Consensus 6 V~elAk~l~v~~~~ii 21 (54)
T PF04760_consen 6 VSELAKELGVPSKEII 21 (54)
T ss_dssp TTHHHHHHSSSHHHHH
T ss_pred HHHHHHHHCcCHHHHH
Confidence 6789999998875443
No 90
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=25.13 E-value=42 Score=20.59 Aligned_cols=17 Identities=29% Similarity=0.485 Sum_probs=12.6
Q ss_pred HHHHHHHcCCChhhhcc
Q psy7153 68 VRKLGLDLGLTPEVVMR 84 (131)
Q Consensus 68 VR~Lg~~LGlP~~Ii~k 84 (131)
+.+|++.+|+|..-++|
T Consensus 21 ~~eia~~~gl~~stv~r 37 (52)
T PF09339_consen 21 LSEIARALGLPKSTVHR 37 (52)
T ss_dssp HHHHHHHHTS-HHHHHH
T ss_pred HHHHHHHHCcCHHHHHH
Confidence 57799999999877665
No 91
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=24.83 E-value=45 Score=21.87 Aligned_cols=17 Identities=18% Similarity=0.491 Sum_probs=13.9
Q ss_pred HHHHHHHcCCChhhhcc
Q psy7153 68 VRKLGLDLGLTPEVVMR 84 (131)
Q Consensus 68 VR~Lg~~LGlP~~Ii~k 84 (131)
+.++|+.||+|...|+.
T Consensus 16 ~~eIA~~Lg~~~~TV~~ 32 (58)
T PF06056_consen 16 IKEIAEELGVPRSTVYS 32 (58)
T ss_pred HHHHHHHHCCChHHHHH
Confidence 46799999999887764
No 92
>TIGR00269 conserved hypothetical protein TIGR00269.
Probab=24.82 E-value=2.1e+02 Score=20.19 Aligned_cols=32 Identities=22% Similarity=0.314 Sum_probs=27.1
Q ss_pred cccccccchHHHHHHHHHcCCChhhhccCCCCC
Q psy7153 57 IEPLKDFHKDEVRKLGLDLGLTPEVVMRHPFPG 89 (131)
Q Consensus 57 iePL~~L~KdEVR~Lg~~LGlP~~Ii~k~PfpG 89 (131)
|-||..+...||...|...|||-. -..=|+.+
T Consensus 4 IRPL~~v~E~ei~~ya~~~~lp~~-~~~CP~~~ 35 (104)
T TIGR00269 4 IKPLRYIPEKEVVLYAFLNELKVH-LDECPYSS 35 (104)
T ss_pred ccccccCCHHHHHHHHHHcCCCcC-CCCCCCCC
Confidence 669999999999999999999943 45577777
No 93
>COG0045 SucC Succinyl-CoA synthetase, beta subunit [Energy production and conversion]
Probab=24.16 E-value=56 Score=29.44 Aligned_cols=29 Identities=31% Similarity=0.565 Sum_probs=25.6
Q ss_pred cccccccccchHHHHHHHHHcCCChhhhc
Q psy7153 55 KVIEPLKDFHKDEVRKLGLDLGLTPEVVM 83 (131)
Q Consensus 55 kdiePL~~L~KdEVR~Lg~~LGlP~~Ii~ 83 (131)
.-|.|...|.-.+.|+++..||+|.+.+.
T Consensus 145 ~~idp~~g~~~~~aR~la~~lgl~~~~~~ 173 (387)
T COG0045 145 VSVDPLTGLRPYQARELAFKLGLEGELVK 173 (387)
T ss_pred EEeCCccCCCHHHHHHHHHHcCCCHHHHH
Confidence 46899999999999999999999987543
No 94
>cd03287 ABC_MSH3_euk MutS3 homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c
Probab=24.02 E-value=48 Score=26.60 Aligned_cols=17 Identities=18% Similarity=0.247 Sum_probs=14.9
Q ss_pred HHHHHHcCCChhhhccC
Q psy7153 69 RKLGLDLGLTPEVVMRH 85 (131)
Q Consensus 69 R~Lg~~LGlP~~Ii~k~ 85 (131)
-++|+..|+|+++|+|+
T Consensus 206 ~~~a~~~g~p~~vi~rA 222 (222)
T cd03287 206 LNVARLAGLPKSIISRA 222 (222)
T ss_pred HHHHHHhCcCHHHHhcC
Confidence 46899999999999984
No 95
>cd01986 Alpha_ANH_like Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases and ATP sulphurylases. The domain forms a apha/beta/apha fold which binds to Adenosine group..
Probab=23.95 E-value=13 Score=25.45 Aligned_cols=42 Identities=21% Similarity=0.249 Sum_probs=31.0
Q ss_pred CCceeeccccccceeeccCCCCCCCCCccccccCCchHHHHHhhcccccccc
Q psy7153 9 NQTLLCQGTLRPDLIESASHLASNKADVIKTHHNDSPLIRALREQGKVIEPL 60 (131)
Q Consensus 9 ~~~~l~QGTiypD~iES~~~~~~~~a~~IKtHHNv~~l~~~~~~~~kdiePL 60 (131)
...+++.|+-+.|++|+... .+.|+|+.+.++.. ..+.++|+
T Consensus 61 g~~~i~~g~~~~D~~~~~~~--------~~~~~~~~~~~~~~--~~~~~~Pl 102 (103)
T cd01986 61 GAETIATGTRRDDVANRALG--------LTALLNLTVTLSGA--GIQSLEPL 102 (103)
T ss_pred CCCEEEEcCCcchHHHHHHH--------HHHHhcCCCCcccC--cceEeecC
Confidence 34689999999999998742 22399988888765 24678876
No 96
>PF08442 ATP-grasp_2: ATP-grasp domain; InterPro: IPR013650 The ATP-grasp superfamily currently includes 17 groups of enzymes, catalyzing ATP-dependent ligation of a carboxylate containing molecule to an amino or thiol group-containing molecule []. They contribute predominantly to macromolecular synthesis. ATP-hydrolysis is used to activate a substrate. For example, DD-ligase transfers phosphate from ATP to D-alanine on the first step of catalysis. On the second step the resulting acylphosphate is attacked by a second D-alanine to produce a DD dipeptide following phosphate elimination []. The ATP-grasp domain contains three conserved motifs, corresponding to the phosphate binding loop and the Mg(2+) binding site []. The fold is characterised by two alpha-beta subdomains that grasp the ATP molecule between them. Each subdomain provides a variable loop that forms a part of the active site, completed by region of other domains not conserved between the various ATP-grasp enzymes []. The ATP-grasp domain represented by this entry is found primarily in succinyl-CoA synthetases (6.2.1.5 from EC).; PDB: 3PFF_A 3MWD_A 3MWE_A 1CQI_E 1SCU_B 2NU9_G 2NU6_E 1CQJ_E 2NU7_B 1JLL_E ....
Probab=23.91 E-value=59 Score=26.03 Aligned_cols=27 Identities=22% Similarity=0.450 Sum_probs=20.8
Q ss_pred ccccccccchHHHHHHHHHcCCChhhh
Q psy7153 56 VIEPLKDFHKDEVRKLGLDLGLTPEVV 82 (131)
Q Consensus 56 diePL~~L~KdEVR~Lg~~LGlP~~Ii 82 (131)
.|.|...+...++|+++..||++.+..
T Consensus 147 ~id~~~g~~~~~~~~i~~~lg~~~~~~ 173 (202)
T PF08442_consen 147 PIDPTEGLTPYQAREIAKKLGLPGKLA 173 (202)
T ss_dssp EEBTTTB--HHHHHHHHHHTTS-CHHH
T ss_pred ecCCCCCCCHHHHHHHHHhccccHHHH
Confidence 478999999999999999999997653
No 97
>PRK13617 psbV cytochrome c-550; Provisional
Probab=23.86 E-value=74 Score=25.57 Aligned_cols=40 Identities=15% Similarity=0.289 Sum_probs=28.2
Q ss_pred cccccCCchHHHHHhhc--c---------------ccccc-ccccchHHHHHHHHHcC
Q psy7153 37 IKTHHNDSPLIRALREQ--G---------------KVIEP-LKDFHKDEVRKLGLDLG 76 (131)
Q Consensus 37 IKtHHNv~~l~~~~~~~--~---------------kdieP-L~~L~KdEVR~Lg~~LG 76 (131)
+-.-+|+..|.++++.. . .++.| .++|..+|++.|+.+|-
T Consensus 96 ~p~r~nv~aLv~yikdP~sydg~~s~~e~~P~~~~~~imP~~~~LsdeeL~alAayLl 153 (170)
T PRK13617 96 TPARDNVDALVDYLKDPTSYDGEYSIADLHPSMRSADLYPAMRDLNDEDLRLMAGYIL 153 (170)
T ss_pred CCCCCCHHHHHHHHhChHhhcchhhccccCccccccccCcccCCCCHHHHHHHHHHHH
Confidence 34557777887777642 1 22444 67899999999999983
No 98
>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [, ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB []. This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2PHG_A 1C9B_Q 1TFB_A 1VOL_A 3K7A_M 1AIS_B 1D3U_B.
Probab=23.81 E-value=46 Score=21.53 Aligned_cols=17 Identities=29% Similarity=0.493 Sum_probs=10.6
Q ss_pred HHHHHHHcCCChhhhcc
Q psy7153 68 VRKLGLDLGLTPEVVMR 84 (131)
Q Consensus 68 VR~Lg~~LGlP~~Ii~k 84 (131)
+.+++..||||+.+.++
T Consensus 1 I~r~~~~L~L~~~v~~~ 17 (71)
T PF00382_consen 1 IPRICSKLGLPEDVRER 17 (71)
T ss_dssp HHHHHHHTT--HHHHHH
T ss_pred ChHHHhHcCCCHHHHHH
Confidence 45678888888877653
No 99
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=23.53 E-value=70 Score=19.09 Aligned_cols=24 Identities=29% Similarity=0.290 Sum_probs=19.7
Q ss_pred ccccchHHHHHHHHHcCCChhhhc
Q psy7153 60 LKDFHKDEVRKLGLDLGLTPEVVM 83 (131)
Q Consensus 60 L~~L~KdEVR~Lg~~LGlP~~Ii~ 83 (131)
-......|..+||..+||+..-|.
T Consensus 22 ~~~P~~~~~~~la~~~~l~~~qV~ 45 (59)
T cd00086 22 NPYPSREEREELAKELGLTERQVK 45 (59)
T ss_pred CCCCCHHHHHHHHHHHCcCHHHHH
Confidence 336688999999999999987664
No 100
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=23.39 E-value=54 Score=18.62 Aligned_cols=17 Identities=29% Similarity=0.444 Sum_probs=13.2
Q ss_pred HHHHHHHcCCChhhhcc
Q psy7153 68 VRKLGLDLGLTPEVVMR 84 (131)
Q Consensus 68 VR~Lg~~LGlP~~Ii~k 84 (131)
+.++|+.||++..-+.+
T Consensus 4 ~~e~a~~lgis~~ti~~ 20 (49)
T TIGR01764 4 VEEAAEYLGVSKDTVYR 20 (49)
T ss_pred HHHHHHHHCCCHHHHHH
Confidence 46789999999886654
No 101
>cd08779 Death_PIDD Death Domain of p53-induced protein with a death domain. Death domain (DD) found in PIDD (p53-induced protein with a death domain) and similar proteins. PIDD is a component of the PIDDosome complex, which is an oligomeric caspase-activating complex involved in caspase-2 activation and plays a role in mediating stress-induced apoptosis. The PIDDosome complex is composed of three components, PIDD, RAIDD and caspase-2, which interact through their DDs and DD-like domains. The DD of PIDD interacts with the DD of RAIDD, which also contains a Caspase Activation and Recruitment Domain (CARD) that interacts with the caspase-2 CARD. Autoproteolysis of PIDD determines the downstream signaling event, between pro-survival NF-kB or pro-death caspase-2 activation. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members
Probab=23.29 E-value=37 Score=23.57 Aligned_cols=25 Identities=24% Similarity=0.325 Sum_probs=18.0
Q ss_pred ccccchHHHHHHHHHcCCChhhhcc
Q psy7153 60 LKDFHKDEVRKLGLDLGLTPEVVMR 84 (131)
Q Consensus 60 L~~L~KdEVR~Lg~~LGlP~~Ii~k 84 (131)
|++---.+-++||+.|||++.-|.+
T Consensus 8 ia~~LG~~Wk~lar~LGlse~~Id~ 32 (86)
T cd08779 8 IAGRLGLDWQAIGLHLGLSYRELQR 32 (86)
T ss_pred HHHHHhHHHHHHHHHcCCCHHHHHH
Confidence 3344445678999999999876654
No 102
>cd03033 ArsC_15kD Arsenate Reductase (ArsC) family, 15kD protein subfamily; composed of proteins of unknown function with similarity to thioredoxin-fold arsenic reductases, ArsC. It is encoded by an ORF present in a gene cluster associated with nitrogen fixation that also encodes dinitrogenase reductase ADP-ribosyltransferase (DRAT) and dinitrogenase reductase activating glycohydrolase (DRAG). ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], using reducing equivalents derived from glutathione via glutaredoxin, through a single catalytic cysteine.
Probab=22.84 E-value=74 Score=23.03 Aligned_cols=56 Identities=7% Similarity=0.070 Sum_probs=36.1
Q ss_pred ccchHHHHHHHHHcCCChhhhccCCCCCCCceeeeccCcccccccChHHHHHHHHHHHhhhhhhhhc
Q psy7153 62 DFHKDEVRKLGLDLGLTPEVVMRHPFPGPGLAIRVICGEERYIEKDYSETQVLVKIIVEYDQMFKKI 128 (131)
Q Consensus 62 ~L~KdEVR~Lg~~LGlP~~Ii~k~PfpGPGLaiR~~g~~e~~l~~~y~~~d~iL~~~~~~~~~~~k~ 128 (131)
.+.++|++++-..+|+ +.++++. | -..|-.+.... +. +.+.++..+++....+++|
T Consensus 36 p~s~~eL~~~l~~~g~-~~l~n~~---~--~~~r~~~~~~~----~l-s~~e~~~ll~~~P~LikRP 91 (113)
T cd03033 36 PWTAETLRPFFGDLPV-AEWFNPA---A--PRVKSGEVVPE----AL-DEEEALALMIADPLLIRRP 91 (113)
T ss_pred CCCHHHHHHHHHHcCH-HHHHhcc---c--HHHHhcCCCcc----CC-CHHHHHHHHHhCcceeeCC
Confidence 4689999999999997 7777765 2 33332222211 11 2355778888877777776
No 103
>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=22.23 E-value=1e+02 Score=21.51 Aligned_cols=57 Identities=18% Similarity=0.344 Sum_probs=33.5
Q ss_pred cchHHHHHHHHHcCC-ChhhhccCCCCCCCceeeeccCcccccccChHHHHHHHHHHHhhhhhhhhc
Q psy7153 63 FHKDEVRKLGLDLGL-TPEVVMRHPFPGPGLAIRVICGEERYIEKDYSETQVLVKIIVEYDQMFKKI 128 (131)
Q Consensus 63 L~KdEVR~Lg~~LGl-P~~Ii~k~PfpGPGLaiR~~g~~e~~l~~~y~~~d~iL~~~~~~~~~~~k~ 128 (131)
+.++|++++...+|. +++|+++... ..|=.+ .+..+--..+.++..|+.....+++|
T Consensus 33 ~s~~el~~~l~~~~~~~~~lin~~~~-----~~k~l~----~~~~~~~s~~e~i~~l~~~p~LikRP 90 (110)
T PF03960_consen 33 LSREELRELLSKLGNGPDDLINTRSK-----TYKELG----KLKKDDLSDEELIELLLENPKLIKRP 90 (110)
T ss_dssp --HHHHHHHHHHHTSSGGGGB-TTSH-----HHHHTT----HHHCTTSBHHHHHHHHHHSGGGB-SS
T ss_pred CCHHHHHHHHHHhcccHHHHhcCccc-----hHhhhh----hhhhhhhhhHHHHHHHHhChhheeCC
Confidence 688999999999996 6777766431 111122 01122233477888888888777776
No 104
>PF15508 NAAA-beta: beta subunit of N-acylethanolamine-hydrolyzing acid amidase
Probab=22.19 E-value=67 Score=22.39 Aligned_cols=18 Identities=17% Similarity=0.254 Sum_probs=15.8
Q ss_pred chHHHHHHHHHcCCChhh
Q psy7153 64 HKDEVRKLGLDLGLTPEV 81 (131)
Q Consensus 64 ~KdEVR~Lg~~LGlP~~I 81 (131)
|.+|+|-+|+.+|+|-..
T Consensus 68 ~~~EirGIA~~~gi~l~~ 85 (95)
T PF15508_consen 68 YAEEIRGIAKAAGIPLGD 85 (95)
T ss_pred HHHHHHHHHHHhCCCHHH
Confidence 889999999999998543
No 105
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=22.14 E-value=83 Score=18.75 Aligned_cols=22 Identities=27% Similarity=0.514 Sum_probs=17.5
Q ss_pred ccccchHHHHHHHHHcCCChhh
Q psy7153 60 LKDFHKDEVRKLGLDLGLTPEV 81 (131)
Q Consensus 60 L~~L~KdEVR~Lg~~LGlP~~I 81 (131)
-+....+.+.+|++.||+|.+.
T Consensus 33 ~~~~~~~~~~~ia~~l~~~~~~ 54 (55)
T PF01381_consen 33 KRNPSLDTLKKIAKALGVSPEY 54 (55)
T ss_dssp SSTSBHHHHHHHHHHHTSEHHH
T ss_pred CCCCCHHHHHHHHHHHCCCHHH
Confidence 3456788899999999998653
No 106
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=22.02 E-value=55 Score=28.52 Aligned_cols=18 Identities=22% Similarity=0.315 Sum_probs=15.2
Q ss_pred HHHHHHHHHcCCChhhhc
Q psy7153 66 DEVRKLGLDLGLTPEVVM 83 (131)
Q Consensus 66 dEVR~Lg~~LGlP~~Ii~ 83 (131)
--|+++|.+||||++++.
T Consensus 38 lNvneiAe~lgLpqst~s 55 (308)
T COG4189 38 LNVNEIAEALGLPQSTMS 55 (308)
T ss_pred CCHHHHHHHhCCchhhhh
Confidence 358999999999998764
No 107
>PF02245 Pur_DNA_glyco: Methylpurine-DNA glycosylase (MPG); InterPro: IPR003180 Methylpurine-DNA glycosylase is a base excision-repair protein. It is responsible for the hydrolysis of the deoxyribose N-glycosidic bond, excising 3-methyladenine and 3-methylguanine from damaged DNA []. Its action is induced by alkylating chemotherapeutics, as well as deaminated and lipid peroxidation-induced purine adducts []. MPG without an N-terminal extension excises hypoxanthine with one-third of the efficiency of full-length MPG under similar conditions, suggesting that is function may largely be attributable to the N-terminal extension [].; GO: 0003677 DNA binding, 0003905 alkylbase DNA N-glycosylase activity, 0006284 base-excision repair; PDB: 1BNK_A 1F6O_A 3QI5_A 3UBY_B 1F4R_A 1EWN_A.
Probab=21.96 E-value=34 Score=27.43 Aligned_cols=41 Identities=29% Similarity=0.448 Sum_probs=29.8
Q ss_pred cccchHHHHHHHHHcCCChhhhccCCCCCCCceeeeccCcccccc
Q psy7153 61 KDFHKDEVRKLGLDLGLTPEVVMRHPFPGPGLAIRVICGEERYIE 105 (131)
Q Consensus 61 ~~L~KdEVR~Lg~~LGlP~~Ii~k~PfpGPGLaiR~~g~~e~~l~ 105 (131)
++||...+-++|+.| |-..++.+.+--. ++.||+ ++|.++|
T Consensus 2 ~~Ff~r~~~~vA~~L-LG~~Lv~~~~~~~--~~grIv-EtEAY~g 42 (184)
T PF02245_consen 2 RDFFDRDTVEVARDL-LGKVLVRRIPGGE--LSGRIV-ETEAYLG 42 (184)
T ss_dssp -HHHSSBHHHHHHHC-TT-EEEEE-TTS---EEEEEE-EEEEE-S
T ss_pred cchhccCHHHHHHHh-CCCEEEEEeCCCe--EEEEEE-EEeeccC
Confidence 467788889999999 8899999988766 888876 4577776
No 108
>PF12244 DUF3606: Protein of unknown function (DUF3606); InterPro: IPR022037 This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=21.87 E-value=67 Score=20.95 Aligned_cols=22 Identities=27% Similarity=0.247 Sum_probs=18.1
Q ss_pred cchHHHHHHHHHcCCChhhhcc
Q psy7153 63 FHKDEVRKLGLDLGLTPEVVMR 84 (131)
Q Consensus 63 L~KdEVR~Lg~~LGlP~~Ii~k 84 (131)
=-..||+-+++.||++++-+.+
T Consensus 18 ~e~~ev~ywa~~~gvt~~~L~~ 39 (57)
T PF12244_consen 18 SEPYEVRYWAKRFGVTEEQLRE 39 (57)
T ss_pred CCHHHHHHHHHHHCcCHHHHHH
Confidence 3467999999999999887653
No 109
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=21.76 E-value=58 Score=19.70 Aligned_cols=18 Identities=17% Similarity=0.466 Sum_probs=13.4
Q ss_pred HHHHHHHHcCCChhhhcc
Q psy7153 67 EVRKLGLDLGLTPEVVMR 84 (131)
Q Consensus 67 EVR~Lg~~LGlP~~Ii~k 84 (131)
-|.++|+.+||...-|.|
T Consensus 23 si~~IA~~~gvsr~TvyR 40 (45)
T PF02796_consen 23 SIAEIAKQFGVSRSTVYR 40 (45)
T ss_dssp -HHHHHHHTTS-HHHHHH
T ss_pred CHHHHHHHHCcCHHHHHH
Confidence 468899999999877765
No 110
>cd08306 Death_FADD Fas-associated Death Domain protein-protein interaction domain. Death domain (DD) found in FAS-associated via death domain (FADD). FADD is a component of the death-inducing signaling complex (DISC) and serves as an adaptor in the signaling pathway of death receptor proteins. It modulates apoptosis as well as non-apoptotic processes such as cell cycle progression, survival, innate immune signaling, and hematopoiesis. FADD contains an N-terminal DED and a C-terminal DD. Its DD interacts with the DD of the activated death receptor, FAS, and its DED recruits the initiator caspases, caspase-8 and -10, to the DISC complex via a homotypic interaction with the N-terminal DED of the caspase. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain),
Probab=21.28 E-value=39 Score=23.39 Aligned_cols=24 Identities=25% Similarity=0.306 Sum_probs=17.3
Q ss_pred ccccchHHHHHHHHHcCCChhhhc
Q psy7153 60 LKDFHKDEVRKLGLDLGLTPEVVM 83 (131)
Q Consensus 60 L~~L~KdEVR~Lg~~LGlP~~Ii~ 83 (131)
|++--=.+-++||+.||+++.=|.
T Consensus 8 i~~~lG~~Wk~laR~LGlse~~Id 31 (86)
T cd08306 8 ICENVGRDWRKLARKLGLSETKIE 31 (86)
T ss_pred HHHHHhhhHHHHHHHcCCCHHHHH
Confidence 333344567899999999987655
No 111
>cd08313 Death_TNFR1 Death domain of Tumor Necrosis Factor Receptor 1. Death Domain (DD) found in tumor necrosis factor receptor-1 (TNFR-1). TNFR-1 has many names including TNFRSF1A, CD120a, p55, p60, and TNFR60. It activates two major intracellular signaling pathways that lead to the activation of the transcription factor NF-kB and the induction of cell death. Upon binding of its ligand TNF, TNFR-1 trimerizes which leads to the recruitment of an adaptor protein named TNFR-associated death domain protein (TRADD) through a DD/DD interaction. Mutations in the TNFRSF1A gene causes TNFR-associated periodic syndrome (TRAPS), a rare disorder characterized recurrent fever, myalgia, abdominal pain, conjunctivitis and skin eruptions. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation a
Probab=21.16 E-value=70 Score=22.37 Aligned_cols=19 Identities=21% Similarity=0.314 Sum_probs=15.7
Q ss_pred HHHHHHHHHcCCChhhhcc
Q psy7153 66 DEVRKLGLDLGLTPEVVMR 84 (131)
Q Consensus 66 dEVR~Lg~~LGlP~~Ii~k 84 (131)
.+++++||.|||.+.-|+.
T Consensus 12 ~~wk~~~R~LGlse~~Id~ 30 (80)
T cd08313 12 RRWKEFVRRLGLSDNEIER 30 (80)
T ss_pred HHHHHHHHHcCCCHHHHHH
Confidence 5678999999999877654
No 112
>PRK02866 cyanate hydratase; Validated
Probab=20.70 E-value=86 Score=24.60 Aligned_cols=48 Identities=23% Similarity=0.290 Sum_probs=32.1
Q ss_pred ccccchHHHHHHHHHcCCChhhhcc---CCCCCCCceeeecc--CcccccccChHHHH
Q psy7153 60 LKDFHKDEVRKLGLDLGLTPEVVMR---HPFPGPGLAIRVIC--GEERYIEKDYSETQ 112 (131)
Q Consensus 60 L~~L~KdEVR~Lg~~LGlP~~Ii~k---~PfpGPGLaiR~~g--~~e~~l~~~y~~~d 112 (131)
-+.+.+++...|++.||||++.+.- .|.-|. +.. .+++-+-.=|+.++
T Consensus 42 Q~~ls~e~A~kla~~LgL~~~~~~~l~~~P~rg~-----~~~~~ptdP~iYR~yE~v~ 94 (147)
T PRK02866 42 QMTLPAEEAEKVAELLGLDEDAVALLQEVPYRGS-----LPPAVPTDPLIYRFYEMVQ 94 (147)
T ss_pred CCCCCHHHHHHHHHHhCCCHHHHHHHhcCCcCCC-----CCCCCCCCcHHHHHHHHHH
Confidence 3577899999999999999997653 565551 011 24666655555443
No 113
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=20.50 E-value=78 Score=15.40 Aligned_cols=18 Identities=22% Similarity=0.455 Sum_probs=13.8
Q ss_pred HHHHHHHHcCCChhhhcc
Q psy7153 67 EVRKLGLDLGLTPEVVMR 84 (131)
Q Consensus 67 EVR~Lg~~LGlP~~Ii~k 84 (131)
-++++++.+|+...-+.+
T Consensus 23 s~~~ia~~~~is~~tv~~ 40 (42)
T cd00569 23 SVAEIARRLGVSRSTLYR 40 (42)
T ss_pred CHHHHHHHHCCCHHHHHH
Confidence 467889999998776654
No 114
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=20.36 E-value=64 Score=18.71 Aligned_cols=18 Identities=17% Similarity=0.265 Sum_probs=13.6
Q ss_pred HHHHHHHcCCChhhhccC
Q psy7153 68 VRKLGLDLGLTPEVVMRH 85 (131)
Q Consensus 68 VR~Lg~~LGlP~~Ii~k~ 85 (131)
+.++|+.+|++..-+.+-
T Consensus 3 ~~e~a~~~gv~~~tlr~~ 20 (49)
T cd04761 3 IGELAKLTGVSPSTLRYY 20 (49)
T ss_pred HHHHHHHHCcCHHHHHHH
Confidence 467888999998777654
No 115
>PRK10853 putative reductase; Provisional
Probab=20.31 E-value=93 Score=22.67 Aligned_cols=58 Identities=10% Similarity=0.162 Sum_probs=34.5
Q ss_pred ccchHHHHHHHHHcCCChhhhccCCCCCCCceeeeccCcccccccChHHHHHHHHHHHhhhhhhhhc
Q psy7153 62 DFHKDEVRKLGLDLGLTPEVVMRHPFPGPGLAIRVICGEERYIEKDYSETQVLVKIIVEYDQMFKKI 128 (131)
Q Consensus 62 ~L~KdEVR~Lg~~LGlP~~Ii~k~PfpGPGLaiR~~g~~e~~l~~~y~~~d~iL~~~~~~~~~~~k~ 128 (131)
.+.++|++++...+|+.+ ++++.-..= |=++..+.. ...+.+.++..++....-+++|
T Consensus 36 p~s~~eL~~~l~~~g~~~-l~n~~~~~~-----r~L~~~~k~---~~~~~~e~~~ll~~~P~LikRP 93 (118)
T PRK10853 36 GLDSELLQGFIDELGWEA-LLNTRGTTW-----RKLDETQRN---AITDAASAAALMLEQPAIIKRP 93 (118)
T ss_pred CcCHHHHHHHHHHcCHHH-HHhcCCchH-----HhCCHhHhh---cCCCHHHHHHHHHhCcCeeecc
Confidence 468999999999999764 776643221 111111110 0112366777888777777766
No 116
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=20.11 E-value=45 Score=20.12 Aligned_cols=18 Identities=39% Similarity=0.621 Sum_probs=13.2
Q ss_pred HHHHHHHcCCChhhhccC
Q psy7153 68 VRKLGLDLGLTPEVVMRH 85 (131)
Q Consensus 68 VR~Lg~~LGlP~~Ii~k~ 85 (131)
|.+|++.+|++..-+.+|
T Consensus 18 ~~el~~~l~~s~~~vs~h 35 (47)
T PF01022_consen 18 VSELAEELGLSQSTVSHH 35 (47)
T ss_dssp HHHHHHHHTS-HHHHHHH
T ss_pred hhhHHHhccccchHHHHH
Confidence 567999999988877654
No 117
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=20.05 E-value=48 Score=19.88 Aligned_cols=19 Identities=16% Similarity=0.317 Sum_probs=15.5
Q ss_pred HHHHHHHHcCCChhhhccC
Q psy7153 67 EVRKLGLDLGLTPEVVMRH 85 (131)
Q Consensus 67 EVR~Lg~~LGlP~~Ii~k~ 85 (131)
=++++++.+|++..-++++
T Consensus 18 s~~~Ia~~~gvs~~~~y~~ 36 (47)
T PF00440_consen 18 SIRDIARRAGVSKGSFYRY 36 (47)
T ss_dssp SHHHHHHHHTSCHHHHHHH
T ss_pred CHHHHHHHHccchhhHHHH
Confidence 4688999999998877654
Done!