Query 040084
Match_columns 127
No_of_seqs 111 out of 579
Neff 7.5
Searched_HMMs 46136
Date Fri Mar 29 04:58:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040084.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040084hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02362 B3: B3 DNA binding do 99.9 3.9E-26 8.5E-31 151.0 10.4 93 13-105 1-100 (100)
2 PF03754 DUF313: Domain of unk 96.9 0.0056 1.2E-07 41.8 7.1 67 12-78 23-114 (114)
3 PF04014 Antitoxin-MazE: Antid 87.8 2.2 4.7E-05 24.0 4.8 30 73-102 13-42 (47)
4 PLN03148 Blue copper-like prot 82.9 1.1 2.4E-05 32.6 2.4 38 76-113 41-80 (167)
5 PF08922 DUF1905: Domain of un 79.6 13 0.00028 23.4 7.7 64 25-91 13-80 (80)
6 PF02298 Cu_bind_like: Plastoc 75.3 2.1 4.4E-05 27.4 1.6 36 76-112 14-52 (85)
7 smart00536 AXH domain in Ataxi 68.5 5 0.00011 27.5 2.4 27 62-88 75-111 (116)
8 TIGR01439 lp_hng_hel_AbrB loop 68.3 16 0.00035 19.4 4.5 24 73-96 13-36 (43)
9 PF12195 End_beta_barrel: Beta 58.0 5.6 0.00012 25.3 1.0 17 77-93 24-40 (83)
10 PRK09798 antitoxin MazE; Provi 57.8 15 0.00032 23.5 3.0 51 24-79 12-62 (82)
11 TIGR02609 doc_partner putative 47.5 39 0.00084 20.8 3.7 31 73-104 16-46 (74)
12 PF08517 AXH: Ataxin-1 and HBP 46.6 4.3 9.3E-05 27.7 -0.9 25 64-88 76-110 (115)
13 COG2336 MazE Growth regulator 45.2 56 0.0012 21.0 4.1 38 24-61 11-48 (82)
14 PF11976 Rad60-SLD: Ubiquitin- 44.7 26 0.00056 20.8 2.5 47 44-93 2-48 (72)
15 PRK11347 antitoxin ChpS; Provi 41.0 36 0.00079 21.7 2.8 30 24-53 11-40 (83)
16 cd08313 Death_TNFR1 Death doma 40.0 10 0.00023 24.1 0.2 17 70-86 12-28 (80)
17 cd06555 ASCH_PF0470_like ASC-1 39.8 47 0.001 22.4 3.3 24 79-102 30-54 (109)
18 COG2002 AbrB Regulators of sta 39.8 47 0.001 21.1 3.3 37 63-102 13-50 (89)
19 TIGR02219 phage_NlpC_fam putat 38.9 46 0.00099 22.8 3.3 30 77-106 73-103 (134)
20 PF14326 DUF4384: Domain of un 38.7 45 0.00098 20.7 3.0 33 81-113 3-38 (83)
21 PF05382 Amidase_5: Bacterioph 38.4 11 0.00023 26.8 0.1 42 68-109 61-107 (145)
22 PF06071 YchF-GTPase_C: Protei 37.3 20 0.00044 23.1 1.2 15 77-91 69-83 (84)
23 KOG4146 Ubiquitin-like protein 37.2 22 0.00048 23.5 1.4 14 77-90 82-95 (101)
24 cd08316 Death_FAS_TNFRSF6 Deat 36.7 13 0.00029 24.4 0.3 17 70-86 21-37 (97)
25 cd08356 Glo_EDI_BRP_like_17 Th 36.1 37 0.0008 21.8 2.4 16 43-58 97-112 (113)
26 TIGR03511 GldH_lipo gliding mo 36.0 26 0.00056 25.1 1.7 32 43-74 76-111 (156)
27 KOG0260 RNA polymerase II, lar 35.9 58 0.0013 31.0 4.2 77 13-93 341-440 (1605)
28 PRK09974 putative regulator Pr 33.8 1.2E+02 0.0025 20.6 4.5 28 73-100 24-51 (111)
29 KOG1114 Tripeptidyl peptidase 33.7 1.6E+02 0.0035 27.6 6.5 91 25-120 224-316 (1304)
30 PF02938 GAD: GAD domain; Int 33.4 39 0.00084 21.7 2.1 25 69-93 63-87 (95)
31 cd08306 Death_FADD Fas-associa 33.2 11 0.00024 24.0 -0.5 21 68-88 12-32 (86)
32 PF11320 DUF3122: Protein of u 32.9 1.1E+02 0.0024 21.5 4.4 19 44-62 18-36 (134)
33 cd09012 Glo_EDI_BRP_like_24 Th 32.4 57 0.0012 21.0 2.9 16 44-59 108-123 (124)
34 PF09147 DUF1933: Domain of un 32.2 59 0.0013 24.1 3.1 24 77-100 93-116 (201)
35 cd04867 TGS_YchF_C TGS_YchF_C: 32.0 19 0.00041 23.2 0.4 14 78-91 70-83 (83)
36 cd08355 Glo_EDI_BRP_like_14 Th 31.5 53 0.0011 21.0 2.6 16 43-58 105-120 (122)
37 PF01568 Molydop_binding: Moly 30.7 1.4E+02 0.0031 18.8 5.9 48 26-74 31-82 (110)
38 COG1525 Micrococcal nuclease ( 30.4 56 0.0012 23.5 2.8 43 80-122 48-90 (192)
39 PF04225 OapA: Opacity-associa 30.1 59 0.0013 20.6 2.5 33 80-112 42-74 (85)
40 PF08916 Phe_ZIP: Phenylalanin 29.6 32 0.00069 20.7 1.1 10 70-79 1-10 (59)
41 cd07235 MRD Mitomycin C resist 29.5 56 0.0012 20.8 2.4 16 43-58 106-121 (122)
42 cd07254 Glo_EDI_BRP_like_20 Th 29.3 89 0.0019 19.8 3.4 19 43-61 100-118 (120)
43 PF01052 SpoA: Surface present 28.7 64 0.0014 19.5 2.5 27 75-101 23-49 (77)
44 PF12681 Glyoxalase_2: Glyoxal 28.7 59 0.0013 20.0 2.4 15 43-57 93-107 (108)
45 PRK06033 hypothetical protein; 28.7 61 0.0013 20.6 2.4 26 74-99 21-46 (83)
46 COG5131 URM1 Ubiquitin-like pr 28.0 39 0.00085 22.1 1.4 24 69-92 68-92 (96)
47 PF14109 GldH_lipo: GldH lipop 27.9 54 0.0012 22.5 2.2 58 42-100 53-113 (131)
48 cd07246 Glo_EDI_BRP_like_8 Thi 27.7 67 0.0014 20.2 2.5 17 42-58 104-120 (122)
49 cd03548 Rieske_RO_Alpha_OMO_CA 27.5 34 0.00073 23.4 1.1 38 66-106 9-46 (136)
50 PF07494 Reg_prop: Two compone 27.5 74 0.0016 15.0 2.1 13 44-56 8-20 (24)
51 PF02381 MraZ: MraZ protein; 27.2 88 0.0019 18.7 2.9 42 25-78 14-55 (72)
52 TIGR01643 YD_repeat_2x YD repe 26.9 1.1E+02 0.0023 16.0 3.6 21 42-62 5-25 (42)
53 cd04459 Rho_CSD Rho_CSD: Rho p 26.6 70 0.0015 19.6 2.3 24 64-90 27-50 (68)
54 PF00877 NLPC_P60: NlpC/P60 fa 26.4 46 0.00099 21.3 1.6 32 74-106 45-76 (105)
55 KOG3995 3-hydroxyanthranilate 26.4 39 0.00084 25.8 1.3 25 76-100 45-69 (279)
56 COG5285 Protein involved in bi 26.2 27 0.00058 27.7 0.4 44 45-92 165-208 (299)
57 TIGR02228 sigpep_I_arch signal 25.7 86 0.0019 22.3 3.0 16 79-94 59-74 (158)
58 cd09011 Glo_EDI_BRP_like_23 Th 25.6 84 0.0018 20.0 2.8 16 43-58 102-117 (120)
59 cd07262 Glo_EDI_BRP_like_19 Th 25.5 77 0.0017 20.2 2.5 15 44-58 108-122 (123)
60 cd08357 Glo_EDI_BRP_like_18 Th 25.5 91 0.002 19.6 2.9 17 43-59 108-124 (125)
61 cd08350 BLMT_like BLMT, a bleo 25.4 77 0.0017 20.3 2.5 16 43-58 102-117 (120)
62 cd07267 THT_Oxygenase_N N-term 25.1 1E+02 0.0022 19.5 3.0 18 43-60 93-110 (113)
63 cd08344 MhqB_like_N N-terminal 25.1 84 0.0018 19.8 2.6 17 43-59 92-108 (112)
64 cd07261 Glo_EDI_BRP_like_11 Th 24.9 85 0.0018 19.6 2.7 16 43-58 98-113 (114)
65 cd08777 Death_RIP1 Death Domai 24.7 18 0.00038 23.2 -0.7 23 68-90 12-34 (86)
66 cd07265 2_3_CTD_N N-terminal d 24.7 1.1E+02 0.0025 19.4 3.3 18 43-60 102-119 (122)
67 PRK03760 hypothetical protein; 24.3 81 0.0018 21.3 2.5 21 68-91 96-116 (117)
68 PF14186 Aida_C2: Cytoskeletal 23.9 63 0.0014 23.0 1.9 49 44-92 36-90 (147)
69 PF02972 Phycoerythr_ab: Phyco 23.9 37 0.0008 20.2 0.7 12 98-109 4-15 (57)
70 cd08359 Glo_EDI_BRP_like_22 Th 23.4 89 0.0019 19.6 2.6 15 43-57 103-117 (119)
71 cd02786 MopB_CT_3 The MopB_CT_ 23.1 2.1E+02 0.0047 18.3 5.6 47 25-72 31-81 (116)
72 cd06530 S26_SPase_I The S26 Ty 22.8 1E+02 0.0023 18.6 2.7 16 79-94 30-45 (85)
73 TIGR02480 fliN flagellar motor 22.7 86 0.0019 19.3 2.2 22 75-96 23-44 (77)
74 COG3400 Uncharacterized protei 22.3 2.4E+02 0.0051 23.5 5.1 44 40-89 149-205 (471)
75 PRK00809 hypothetical protein; 21.9 1.5E+02 0.0033 20.7 3.6 26 66-93 22-47 (144)
76 PF14191 YodL: YodL-like 21.8 88 0.0019 20.8 2.2 34 65-98 49-89 (103)
77 cd08315 Death_TRAILR_DR4_DR5 D 21.8 32 0.00069 22.4 0.1 17 70-86 20-36 (96)
78 PF06052 3-HAO: 3-hydroxyanthr 21.7 64 0.0014 23.1 1.6 25 76-100 45-69 (151)
79 cd08354 Glo_EDI_BRP_like_13 Th 21.5 1E+02 0.0022 19.3 2.5 17 42-58 104-120 (122)
80 COG3607 Predicted lactoylgluta 21.2 1.1E+02 0.0023 21.5 2.6 17 44-60 111-127 (133)
81 PF03221 HTH_Tnp_Tc5: Tc5 tran 20.8 58 0.0013 18.7 1.1 20 64-83 44-64 (66)
82 PRK06724 hypothetical protein; 20.8 1.3E+02 0.0028 20.0 3.0 17 43-59 106-122 (128)
83 cd07252 BphC1-RGP6_N_like N-te 20.8 1.3E+02 0.0029 19.1 3.0 17 43-59 100-116 (120)
84 PF11604 CusF_Ec: Copper bindi 20.7 1.8E+02 0.004 17.5 3.4 24 78-101 40-65 (70)
85 cd00175 SNc Staphylococcal nuc 20.6 1.9E+02 0.004 18.9 3.7 33 81-113 2-34 (129)
86 cd07251 Glo_EDI_BRP_like_10 Th 20.5 1.3E+02 0.0029 18.7 2.9 17 43-59 104-120 (121)
87 cd08361 PpCmtC_N N-terminal do 20.3 1.4E+02 0.003 19.4 3.0 17 44-60 103-119 (124)
88 PF02643 DUF192: Uncharacteriz 20.3 76 0.0017 20.9 1.7 20 68-90 88-107 (108)
89 PRK08433 flagellar motor switc 20.1 1.1E+02 0.0023 20.7 2.4 27 74-100 46-72 (111)
90 cd07247 SgaA_N_like N-terminal 20.1 1.2E+02 0.0025 18.9 2.5 15 43-57 98-112 (114)
No 1
>PF02362 B3: B3 DNA binding domain; InterPro: IPR003340 Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana contain two distinct amino acid sequence domains found only in higher plant species. The N-terminal regions of RAV1 and RAV2 are homologous to the AP2 DNA-binding domain (see IPR001471 from INTERPRO) present in a family of transcription factors, while the C-terminal region exhibits homology to the highly conserved C-terminal domain, designated B3, of VP1/ABI3 transcription factors []. The AP2 and B3-like domains of RAV1 bind autonomously to the CAACA and CACCTG motifs, respectively, and together achieve a high affinity and specificity of binding. It has been suggested that the AP2 and B3-like domains of RAV1 are connected by a highly flexible structure enabling the two domains to bind to the CAACA and CACCTG motifs in various spacings and orientations [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1WID_A 1YEL_A.
Probab=99.94 E-value=3.9e-26 Score=150.96 Aligned_cols=93 Identities=30% Similarity=0.592 Sum_probs=70.1
Q ss_pred EEEeccCCccC-CCceeccHHHHHhcccC--CCceEEEEcCCCCEEEEEEE--EeCCEEEecccHHHHHhHhCCCCCCEE
Q 040084 13 FVKAVLPSTLR-DQKPRIPNKIVRKFSHE--LSDVAHITIPNGYVWQVKLK--KEGRKVWFDDGWQDFVEAYSTFVGSLV 87 (127)
Q Consensus 13 F~k~i~~~~~~-~~~L~IP~~F~~~~~~~--~~~~v~L~~~~G~~W~V~l~--~~~~~~~~~~GW~~Fv~~~~L~~GD~l 87 (127)
|+|+|++++.. .+.|.||..|++.|+.. .+..++|++++|+.|+|++. +..++++|++||++||++|+|++||+|
T Consensus 1 F~K~l~~s~~~~~~~l~iP~~f~~~~~~~~~~~~~v~l~~~~g~~W~v~~~~~~~~~~~~l~~GW~~Fv~~n~L~~GD~~ 80 (100)
T PF02362_consen 1 FFKVLKPSDVSSSCRLIIPKEFAKKHGGNKRKSREVTLKDPDGRSWPVKLKYRKNSGRYYLTGGWKKFVRDNGLKEGDVC 80 (100)
T ss_dssp EEEE--TTCCCCTT-EEE-HHHHTTTS--SS--CEEEEEETTTEEEEEEEEEECCTTEEEEETTHHHHHHHCT--TT-EE
T ss_pred CEEEEEccCcCCCCEEEeCHHHHHHhCCCcCCCeEEEEEeCCCCEEEEEEEEEccCCeEEECCCHHHHHHHcCCCCCCEE
Confidence 89999887654 47899999999999754 57799999999999999995 456789999999999999999999999
Q ss_pred EEEEecCcEE--EEEEECCC
Q 040084 88 LFEYESNSTF--QAHIYDET 105 (127)
Q Consensus 88 vF~~~~~~~F--~V~If~~~ 105 (127)
+|++++++.| .|+||+++
T Consensus 81 ~F~~~~~~~~~~~v~i~~~~ 100 (100)
T PF02362_consen 81 VFELIGNSNFTLKVHIFRKS 100 (100)
T ss_dssp EEEE-SSSCE-EEEEEE---
T ss_pred EEEEecCCCceEEEEEEECc
Confidence 9999987665 99999864
No 2
>PF03754 DUF313: Domain of unknown function (DUF313) ; InterPro: IPR005508 This is a family of proteins from Arabidopsis thaliana (Mouse-ear cress) with uncharacterised function.
Probab=96.94 E-value=0.0056 Score=41.78 Aligned_cols=67 Identities=18% Similarity=0.346 Sum_probs=48.8
Q ss_pred eEEEeccCCccC--CCceeccHHHHHh--c----------------ccCCCceEEEEcCCCCEEEEEEEEeCC-----EE
Q 040084 12 RFVKAVLPSTLR--DQKPRIPNKIVRK--F----------------SHELSDVAHITIPNGYVWQVKLKKEGR-----KV 66 (127)
Q Consensus 12 ~F~k~i~~~~~~--~~~L~IP~~F~~~--~----------------~~~~~~~v~L~~~~G~~W~V~l~~~~~-----~~ 66 (127)
-+.|.|..+++. ..+|.||..=+.. + .....-.|+|.+|+++.|.+.+++-.- .+
T Consensus 23 i~~K~L~~tDv~~~qsRLsmP~~qi~~~dFLt~eE~~~i~~~~~~~~~~~Gv~V~lvdp~~~~~~m~lkkW~mg~~~~~Y 102 (114)
T PF03754_consen 23 IIEKTLFKTDVDPHQSRLSMPFNQIIDNDFLTEEEKRIIKEEKKNNDKKKGVEVILVDPSLRKWTMRLKKWNMGNGTSNY 102 (114)
T ss_pred EEeeeecccCCCCCCceeeccHHHhcccccCCHHHHHHHHHhhccCcccCCceEEEECCcCcEEEEEEEEecccCCceEE
Confidence 455678888775 3778888664411 1 123356899999999999999998532 67
Q ss_pred EecccHHHHHhH
Q 040084 67 WFDDGWQDFVEA 78 (127)
Q Consensus 67 ~~~~GW~~Fv~~ 78 (127)
.|..||.++|++
T Consensus 103 vL~~gWn~VV~~ 114 (114)
T PF03754_consen 103 VLNSGWNKVVED 114 (114)
T ss_pred EEEcChHhhccC
Confidence 899999999864
No 3
>PF04014 Antitoxin-MazE: Antidote-toxin recognition MazE; InterPro: IPR007159 This domain is found in AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation []. AbrB is thought to interact directly with the transcription initiation regions of genes under its control []. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins []. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator []. DNA-binding activity in this AbrB homologue requires hexamerisation []. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins [].; PDB: 2L66_A 2GLW_A 3TND_D 2W1T_B 2RO5_B 2FY9_A 2RO3_B 1UB4_C 3ZVK_G 1YFB_B ....
Probab=87.84 E-value=2.2 Score=24.00 Aligned_cols=30 Identities=17% Similarity=0.126 Sum_probs=24.6
Q ss_pred HHHHhHhCCCCCCEEEEEEecCcEEEEEEE
Q 040084 73 QDFVEAYSTFVGSLVLFEYESNSTFQAHIY 102 (127)
Q Consensus 73 ~~Fv~~~~L~~GD~lvF~~~~~~~F~V~If 102 (127)
++++...+|+.||.+.+...++....+.-+
T Consensus 13 k~~~~~l~l~~Gd~v~i~~~~~g~i~i~p~ 42 (47)
T PF04014_consen 13 KEIREKLGLKPGDEVEIEVEGDGKIVIRPV 42 (47)
T ss_dssp HHHHHHTTSSTTTEEEEEEETTSEEEEEES
T ss_pred HHHHHHcCCCCCCEEEEEEeCCCEEEEEEC
Confidence 578899999999999999999875555433
No 4
>PLN03148 Blue copper-like protein; Provisional
Probab=82.91 E-value=1.1 Score=32.57 Aligned_cols=38 Identities=18% Similarity=0.437 Sum_probs=26.4
Q ss_pred HhHhCCCCCCEEEEEEecC--cEEEEEEECCCCeEEecCC
Q 040084 76 VEAYSTFVGSLVLFEYESN--STFQAHIYDETACEINYPS 113 (127)
Q Consensus 76 v~~~~L~~GD~lvF~~~~~--~~F~V~If~~~~ce~~~~~ 113 (127)
+..+....||.|+|.|..+ ++.+|.==+-+.|...-|.
T Consensus 41 A~~k~F~VGD~LvF~Y~~~~hnV~~V~~~~Y~~C~~~~pi 80 (167)
T PLN03148 41 ANNQTFYVGDLISFRYQKTQYNVFEVNQTGYDNCTTEGAA 80 (167)
T ss_pred hcCCCCccCCEEEEEecCCCceEEEEChHHcCcccCCCCc
Confidence 5678889999999999875 5666643333567654443
No 5
>PF08922 DUF1905: Domain of unknown function (DUF1905); InterPro: IPR015018 This family consist of hypothetical bacterial proteins. ; PDB: 2D9R_A.
Probab=79.56 E-value=13 Score=23.41 Aligned_cols=64 Identities=14% Similarity=0.111 Sum_probs=39.2
Q ss_pred CceeccHHHHHhcccC--CCceEEEEcCCCCEEEEEEEEe-CCEEEe-cccHHHHHhHhCCCCCCEEEEEE
Q 040084 25 QKPRIPNKIVRKFSHE--LSDVAHITIPNGYVWQVKLKKE-GRKVWF-DDGWQDFVEAYSTFVGSLVLFEY 91 (127)
Q Consensus 25 ~~L~IP~~F~~~~~~~--~~~~v~L~~~~G~~W~V~l~~~-~~~~~~-~~GW~~Fv~~~~L~~GD~lvF~~ 91 (127)
..+.||..-++.+... -+-.|..+- +|..|+-.+... ++.++| -+ ++..+.-++..||.+.+++
T Consensus 13 ~fv~vP~~v~~~l~~~~~g~v~V~~tI-~g~~~~~sl~p~g~G~~~Lpv~--~~vRk~~g~~~Gd~V~v~l 80 (80)
T PF08922_consen 13 TFVEVPFDVAEELGEGGWGRVPVRGTI-DGHPWRTSLFPMGNGGYILPVK--AAVRKAIGKEAGDTVEVTL 80 (80)
T ss_dssp EEEE--S-HHHHH--S--S-EEEEEEE-TTEEEEEEEEESSTT-EEEEE---HHHHHHHT--TTSEEEEEE
T ss_pred EEEEeCHHHHHHhccccCCceEEEEEE-CCEEEEEEEEECCCCCEEEEEc--HHHHHHcCCCCCCEEEEEC
Confidence 5678999988887766 334444443 678999988773 344444 33 7899999999999998764
No 6
>PF02298 Cu_bind_like: Plastocyanin-like domain; InterPro: IPR003245 Blue (type 1) copper proteins are small proteins which bind a single copper atom and which are characterised by an intense electronic absorption band near 600 nm [, ]. The most well known members of this class of proteins are the plant chloroplastic plastocyanins, which exchange electrons with cytochrome c6, and the distantly related bacterial azurins, which exchange electrons with cytochrome c551. This family of proteins also includes amicyanin from bacteria such as Methylobacterium extorquens or Paracoccus versutus (Thiobacillus versutus) that can grow on methylamine; auracyanins A and B from Chloroflexus aurantiacus []; blue copper protein from Alcaligenes faecalis; cupredoxin (CPC) from Cucumis sativus (Cucumber) peelings []; cusacyanin (basic blue protein; plantacyanin, CBP) from cucumber; halocyanin from Natronomonas pharaonis (Natronobacterium pharaonis) [], a membrane associated copper-binding protein; pseudoazurin from Pseudomonas; rusticyanin from Thiobacillus ferrooxidans []; stellacyanin from Rhus vernicifera (Japanese lacquer tree); umecyanin from the roots of Armoracia rusticana (Horseradish); and allergen Ra3 from ragweed. Although there is an appreciable amount of divergence in the sequences of all these proteins, the copper ligand sites are conserved. This domain is found in a variety of plant cyanins and pollern allergen. Some of the proteins in this family are allergens. Allergies are hypersensitivity reactions of the immune system to specific substances called allergens (such as pollen, stings, drugs, or food) that, in most people, result in no symptoms. A nomenclature system has been established for antigens (allergens) that cause IgE-mediated atopic allergies in humans [WHO/IUIS Allergen Nomenclature Subcommittee King T.P., Hoffmann D., Loewenstein H., Marsh D.G., Platts-Mills T.A.E., Thomas W. Bull. World Health Organ. 72:797-806(1994)]. This nomenclature system is defined by a designation that is composed of the first three letters of the genus; a space; the first letter of the species name; a space and an arabic number. In the event that two species names have identical designations, they are discriminated from one another by adding one or more letters (as necessary) to each species designation. The allergens in this family include allergens with the following designations: Amb a 3.; GO: 0005507 copper ion binding, 0009055 electron carrier activity; PDB: 1JER_A 1WS7_A 1WS8_D 1F56_B 1X9R_B 1X9U_A 2CBP_A.
Probab=75.30 E-value=2.1 Score=27.41 Aligned_cols=36 Identities=22% Similarity=0.479 Sum_probs=19.9
Q ss_pred HhHhCCCCCCEEEEEEecC--cEEEEEEECC-CCeEEecC
Q 040084 76 VEAYSTFVGSLVLFEYESN--STFQAHIYDE-TACEINYP 112 (127)
Q Consensus 76 v~~~~L~~GD~lvF~~~~~--~~F~V~If~~-~~ce~~~~ 112 (127)
+....+..||.|+|.+... ++++|. -.. +.|...-|
T Consensus 14 a~~~~F~vGD~LvF~y~~~~h~V~~V~-~~~y~~C~~~~~ 52 (85)
T PF02298_consen 14 ASGKTFRVGDTLVFNYDSGQHSVVEVS-KADYDSCNSSNP 52 (85)
T ss_dssp HCTS-BETTEEEEEE--TTTB-EEEES-HHHHHHT--STT
T ss_pred hcCCcEeCCCEEEEEecCCCCeEEecC-hhhCccCCCCCc
Confidence 4566788999999999974 566665 211 45655444
No 7
>smart00536 AXH domain in Ataxins and HMG containing proteins. unknown function
Probab=68.53 E-value=5 Score=27.47 Aligned_cols=27 Identities=22% Similarity=0.304 Sum_probs=19.6
Q ss_pred eCCEEEecccHHHHHh----------HhCCCCCCEEE
Q 040084 62 EGRKVWFDDGWQDFVE----------AYSTFVGSLVL 88 (127)
Q Consensus 62 ~~~~~~~~~GW~~Fv~----------~~~L~~GD~lv 88 (127)
...-++..+||..|.- -+.|++||+|+
T Consensus 75 eHPfFV~gqGWsSc~P~lT~~~ygL~C~~L~vGDVCl 111 (116)
T smart00536 75 EHPFFVKGKGWSSCYPSLTVQLYGLPCCELQVGDVCL 111 (116)
T ss_pred CCCeEEcCccccccChhhhhhhcCCcceecccCCEEe
Confidence 3456677999988753 24578899986
No 8
>TIGR01439 lp_hng_hel_AbrB looped-hinge helix DNA binding domain, AbrB family. This DNA-binding domain family includes AbrB, a transition state regulator in Bacillus subtilis, whose DNA-binding domain structure in solution was determined by NMR. The domain binds DNA as a dimer in what is termed a looped-hinge helix fold. Some members of the family have two copies of the domain in tandem. The domain is found usually at the N-terminus of a small protein. This model excludes members of family TIGR02609.
Probab=68.26 E-value=16 Score=19.41 Aligned_cols=24 Identities=8% Similarity=0.011 Sum_probs=19.4
Q ss_pred HHHHhHhCCCCCCEEEEEEecCcE
Q 040084 73 QDFVEAYSTFVGSLVLFEYESNST 96 (127)
Q Consensus 73 ~~Fv~~~~L~~GD~lvF~~~~~~~ 96 (127)
++|.+..+++.||.+++....+..
T Consensus 13 ~~~r~~l~~~~gd~~~i~~~~~~~ 36 (43)
T TIGR01439 13 KEIREKLGLKEGDRLEVIRVEDGE 36 (43)
T ss_pred HHHHHHcCcCCCCEEEEEEeCCCE
Confidence 578999999999999998654443
No 9
>PF12195 End_beta_barrel: Beta barrel domain of bacteriophage endosialidase; InterPro: IPR024427 This entry represents the beta barrel domain of endosialidases which is nested in a beta propeller domain. This beta barrel domain is approximately 80 amino acids in length and represents one of the two sialic acid binding sites of the enzyme [].; PDB: 1V0E_B 1V0F_E 3JU4_A 3GVL_A 3GVK_B 3GVJ_A.
Probab=58.02 E-value=5.6 Score=25.28 Aligned_cols=17 Identities=29% Similarity=0.462 Sum_probs=9.1
Q ss_pred hHhCCCCCCEEEEEEec
Q 040084 77 EAYSTFVGSLVLFEYES 93 (127)
Q Consensus 77 ~~~~L~~GD~lvF~~~~ 93 (127)
.+|+|..||.+.|.-.+
T Consensus 24 ~~HGl~vGD~VnFsnsa 40 (83)
T PF12195_consen 24 TDHGLFVGDFVNFSNSA 40 (83)
T ss_dssp TT----TT-EEEEES-S
T ss_pred ccCceeecceEEEeccc
Confidence 57999999999997654
No 10
>PRK09798 antitoxin MazE; Provisional
Probab=57.77 E-value=15 Score=23.45 Aligned_cols=51 Identities=14% Similarity=0.270 Sum_probs=32.5
Q ss_pred CCceeccHHHHHhcccCCCceEEEEcCCCCEEEEEEEEeCCEEEecccHHHHHhHh
Q 040084 24 DQKPRIPNKIVRKFSHELSDVAHITIPNGYVWQVKLKKEGRKVWFDDGWQDFVEAY 79 (127)
Q Consensus 24 ~~~L~IP~~F~~~~~~~~~~~v~L~~~~G~~W~V~l~~~~~~~~~~~GW~~Fv~~~ 79 (127)
+.-++||+.|++.++-.....+.+...+|+- .++...... ..+|.+....+
T Consensus 12 S~~vRIPk~~l~~l~l~~g~~vei~v~~~~i---iI~p~~~~~--r~~l~eLla~~ 62 (82)
T PRK09798 12 SPAVRIPATLMQALNLNIDDEVKIDLVDGKL---IIEPVRKEP--VFTLAELVNDI 62 (82)
T ss_pred cceEEcCHHHHHHcCCCCCCEEEEEEECCEE---EEEECCCCC--CCCHHHHHhcC
Confidence 3778999999999888777887777655542 222211110 23688876654
No 11
>TIGR02609 doc_partner putative addiction module antidote. Members of this protein family are putative addiction module antidote proteins that appear recurringly in two-gene operons with members of the Doc (death-on-curing) family TIGR01550. Members of this family contain a SpoVT/AbrB-like domain (pfam04014). Note that the gene pairs with a member of this family tend to be found on bacterial chromosomes, not on plasmids.
Probab=47.48 E-value=39 Score=20.84 Aligned_cols=31 Identities=16% Similarity=0.334 Sum_probs=23.6
Q ss_pred HHHHhHhCCCCCCEEEEEEecCcEEEEEEECC
Q 040084 73 QDFVEAYSTFVGSLVLFEYESNSTFQAHIYDE 104 (127)
Q Consensus 73 ~~Fv~~~~L~~GD~lvF~~~~~~~F~V~If~~ 104 (127)
++++...+|..||.+.+...++. +.+...++
T Consensus 16 k~i~~~lgl~~Gd~v~v~~~~~~-iii~~~~~ 46 (74)
T TIGR02609 16 KEVLESLGLKEGDTLYVDEEEGG-LKLKRFDE 46 (74)
T ss_pred HHHHHHcCcCCCCEEEEEEECCE-EEEEECCC
Confidence 67899999999999988777653 55555544
No 12
>PF08517 AXH: Ataxin-1 and HBP1 module (AXH); InterPro: IPR013723 AXH is a protein-protein and RNA binding motif found in Ataxin-1 (ATX1)[]. ATX1 is responsible for the autosomal-dominant neurodegenerative disorder Spinocerebellar ataxia type-1 (SCA1) in humans. The AXH module has also been identified in the apparently unrelated transcription factor HBP1 which is thought to be involved in the architectural regulation of chromatin and in specific gene expression []. ; GO: 0005488 binding; PDB: 1OA8_C 3QVE_C 1V06_A.
Probab=46.58 E-value=4.3 Score=27.72 Aligned_cols=25 Identities=20% Similarity=0.274 Sum_probs=14.4
Q ss_pred CEEEecccHHHHH-----hH-----hCCCCCCEEE
Q 040084 64 RKVWFDDGWQDFV-----EA-----YSTFVGSLVL 88 (127)
Q Consensus 64 ~~~~~~~GW~~Fv-----~~-----~~L~~GD~lv 88 (127)
.-++..+||..|. .- +.|++||+|+
T Consensus 76 PFFV~gkGWsS~~P~~T~~~ygL~C~~L~vGDvCl 110 (115)
T PF08517_consen 76 PFFVKGKGWSSCNPSLTVQLYGLPCRQLQVGDVCL 110 (115)
T ss_dssp EEEETTTEEEESSHHHHHHHHTS--EE--TT-EEE
T ss_pred ceEEeCCcccccCcchhceecCCcccccccCCEEe
Confidence 3455699996553 33 4567899986
No 13
>COG2336 MazE Growth regulator [Signal transduction mechanisms]
Probab=45.23 E-value=56 Score=20.98 Aligned_cols=38 Identities=13% Similarity=0.323 Sum_probs=30.8
Q ss_pred CCceeccHHHHHhcccCCCceEEEEcCCCCEEEEEEEE
Q 040084 24 DQKPRIPNKIVRKFSHELSDVAHITIPNGYVWQVKLKK 61 (127)
Q Consensus 24 ~~~L~IP~~F~~~~~~~~~~~v~L~~~~G~~W~V~l~~ 61 (127)
+-.++||...++..+-..+..++++..++..--+.-++
T Consensus 11 S~avrIP~~l~kql~l~~g~~v~v~v~n~~~i~~~p~r 48 (82)
T COG2336 11 SAAVRIPAALLKQLNLTIGDEVEVEVGNDQSILIRPVR 48 (82)
T ss_pred cceeeccHHHHHHhCCCcCceEEEEEcCCcEEEecccc
Confidence 36789999999999888899999998777666665554
No 14
>PF11976 Rad60-SLD: Ubiquitin-2 like Rad60 SUMO-like; InterPro: IPR022617 This entry includes small ubiquitin-related modifier (SUMO) proteins. SUMOs are small proteins that are covalently attached to lysines as post-translational modifications and are used to control multiple cellular process including signal transduction, nuclear transport and DNA replication and repair []. Unlike ubiquitin, they are not involved in protein degradation. This entry also contains the C-terminal Rad60 DNA repair protein SUMO-like domain.; PDB: 3RD2_A 2JXX_A 3RCZ_A 3GOE_A 3A4S_D 3A4R_B 2IO1_D 1U4A_A 2K1F_A 1WZ0_A ....
Probab=44.67 E-value=26 Score=20.82 Aligned_cols=47 Identities=9% Similarity=0.091 Sum_probs=33.7
Q ss_pred eEEEEcCCCCEEEEEEEEeCCEEEecccHHHHHhHhCCCCCCEEEEEEec
Q 040084 44 VAHITIPNGYVWQVKLKKEGRKVWFDDGWQDFVEAYSTFVGSLVLFEYES 93 (127)
Q Consensus 44 ~v~L~~~~G~~W~V~l~~~~~~~~~~~GW~~Fv~~~~L~~GD~lvF~~~~ 93 (127)
+++|++.+|+.-.+.+... .-+..=...|++..++..-..+.|.++|
T Consensus 2 ~i~v~~~~~~~~~~~v~~~---~~~~~l~~~~~~~~~i~~~~~~~l~fdG 48 (72)
T PF11976_consen 2 TIKVRSQDGKEIKFKVKPT---TTVSKLIEKYCEKKGIPPEESIRLIFDG 48 (72)
T ss_dssp EEEEEETTSEEEEEEEETT---SCCHHHHHHHHHHHTTTT-TTEEEEETT
T ss_pred EEEEEeCCCCEEEEEECCC---CcHHHHHHHHHHhhCCCccceEEEEECC
Confidence 5788998888666666432 2367777999999999995666677766
No 15
>PRK11347 antitoxin ChpS; Provisional
Probab=41.00 E-value=36 Score=21.66 Aligned_cols=30 Identities=13% Similarity=0.258 Sum_probs=24.3
Q ss_pred CCceeccHHHHHhcccCCCceEEEEcCCCC
Q 040084 24 DQKPRIPNKIVRKFSHELSDVAHITIPNGY 53 (127)
Q Consensus 24 ~~~L~IP~~F~~~~~~~~~~~v~L~~~~G~ 53 (127)
+.-++||+.+++.++-....++.|...+|.
T Consensus 11 S~~vriPk~il~~l~l~~G~~v~i~v~~~~ 40 (83)
T PRK11347 11 SAGMVIPNIVMKELNLQPGQSVEAQVSNNQ 40 (83)
T ss_pred ceeEEeCHHHHHHcCCCCCCEEEEEEECCE
Confidence 377899999999998888888888765553
No 16
>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=40.00 E-value=10 Score=24.06 Aligned_cols=17 Identities=18% Similarity=0.474 Sum_probs=14.4
Q ss_pred ccHHHHHhHhCCCCCCE
Q 040084 70 DGWQDFVEAYSTFVGSL 86 (127)
Q Consensus 70 ~GW~~Fv~~~~L~~GD~ 86 (127)
.-|++|++..+|.++++
T Consensus 12 ~~wk~~~R~LGlse~~I 28 (80)
T cd08313 12 RRWKEFVRRLGLSDNEI 28 (80)
T ss_pred HHHHHHHHHcCCCHHHH
Confidence 56999999999998753
No 17
>cd06555 ASCH_PF0470_like ASC-1 homology domain, subfamily similar to Pyrococcus furiosus Pf0470. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation.
Probab=39.80 E-value=47 Score=22.36 Aligned_cols=24 Identities=17% Similarity=0.232 Sum_probs=16.0
Q ss_pred hCCCCCCEEEEEEec-CcEEEEEEE
Q 040084 79 YSTFVGSLVLFEYES-NSTFQAHIY 102 (127)
Q Consensus 79 ~~L~~GD~lvF~~~~-~~~F~V~If 102 (127)
-.++.||.|+|.-.. +..+.|.|-
T Consensus 30 ~~ikvGD~I~f~~~~~~~~l~v~V~ 54 (109)
T cd06555 30 QQIKVGDKILFNDLDTGQQLLVKVV 54 (109)
T ss_pred hcCCCCCEEEEEEcCCCcEEEEEEE
Confidence 467999999996543 344555544
No 18
>COG2002 AbrB Regulators of stationary/sporulation gene expression [Transcription]
Probab=39.76 E-value=47 Score=21.12 Aligned_cols=37 Identities=11% Similarity=0.166 Sum_probs=26.8
Q ss_pred CCEEEecccHHHHHhHhCCCCCCEEEEEEecC-cEEEEEEE
Q 040084 63 GRKVWFDDGWQDFVEAYSTFVGSLVLFEYESN-STFQAHIY 102 (127)
Q Consensus 63 ~~~~~~~~GW~~Fv~~~~L~~GD~lvF~~~~~-~~F~V~If 102 (127)
.+++.+=. +..+..+|+.||.+.|...++ ...-+.=+
T Consensus 13 ~GqIvIPk---eiR~~lgi~~Gd~lei~~~~~~~~ivl~k~ 50 (89)
T COG2002 13 KGQIVIPK---EIREALGIKEGDVLEIIVDGDGGRIVLKKY 50 (89)
T ss_pred CceEEecH---HHHHHhCCCCCCEEEEEEeCCCCEEEEEEC
Confidence 46677665 456788999999999999986 45444433
No 19
>TIGR02219 phage_NlpC_fam putative phage cell wall peptidase, NlpC/P60 family. Members of this family show sequence similarity to members of the NlpC/P60 family described by Pfam model pfam00877 and by Anantharaman and Aravind (PubMed:12620121). The NlpC/P60 family includes a number of characterized bacterial cell wall hydrolases. Members of this related family are all found in prophage regions of bacterial genomes.
Probab=38.93 E-value=46 Score=22.77 Aligned_cols=30 Identities=13% Similarity=0.261 Sum_probs=21.9
Q ss_pred hHhCCCCCCEEEEEEecC-cEEEEEEECCCC
Q 040084 77 EAYSTFVGSLVLFEYESN-STFQAHIYDETA 106 (127)
Q Consensus 77 ~~~~L~~GD~lvF~~~~~-~~F~V~If~~~~ 106 (127)
....|+.||++.|...+. ..-+|=||-.++
T Consensus 73 ~~~~~qpGDlvff~~~~~~~~~HvGIy~G~g 103 (134)
T TIGR02219 73 PCDAAQPGDVLVFRWRPGAAAKHAAIAASPT 103 (134)
T ss_pred chhcCCCCCEEEEeeCCCCCCcEEEEEeCCC
Confidence 345799999999986543 346888886655
No 20
>PF14326 DUF4384: Domain of unknown function (DUF4384)
Probab=38.67 E-value=45 Score=20.73 Aligned_cols=33 Identities=24% Similarity=0.327 Sum_probs=22.9
Q ss_pred CCCCCEEEEEEecCcEEEEEEE--CCCC-eEEecCC
Q 040084 81 TFVGSLVLFEYESNSTFQAHIY--DETA-CEINYPS 113 (127)
Q Consensus 81 L~~GD~lvF~~~~~~~F~V~If--~~~~-ce~~~~~ 113 (127)
++.||.+.|.+..+..-.|.|| +.+| ....+|.
T Consensus 3 ~~~Ge~v~~~~~~~~~~Yl~l~~~~~~G~v~~L~Pn 38 (83)
T PF14326_consen 3 YRVGERVRFRVTSNRDGYLYLFYIDADGKVTLLFPN 38 (83)
T ss_pred ccCCCEEEEEEEeCCCeEEEEEEECCCCCEEEEecC
Confidence 6789999999998655445555 5566 4556665
No 21
>PF05382 Amidase_5: Bacteriophage peptidoglycan hydrolase ; InterPro: IPR008044 This entry is represented by Bacteriophage SFi21, lysin (Cell wall hydrolase; 3.5.1.28 from EC). At least one of proteins in this entry, the Pal protein from the pneumococcal bacteriophage Dp-1 (O03979 from SWISSPROT) has been shown to be an N-acetylmuramoyl-L-alanine amidase []. According to the known modular structure of this and other peptidoglycan hydrolases from the pneumococcal system, the active site should reside within this domain while a C-terminal domain binds to the choline residues of the cell wall teichoic acids [, ].
Probab=38.42 E-value=11 Score=26.76 Aligned_cols=42 Identities=17% Similarity=0.307 Sum_probs=26.0
Q ss_pred ecccHHHHHhH--hCCCCCCEEEEEEecCc---EEEEEEECCCCeEE
Q 040084 68 FDDGWQDFVEA--YSTFVGSLVLFEYESNS---TFQAHIYDETACEI 109 (127)
Q Consensus 68 ~~~GW~~Fv~~--~~L~~GD~lvF~~~~~~---~F~V~If~~~~ce~ 109 (127)
...||++.... ..++.||+|++...+.+ -=++-||-....-+
T Consensus 61 ~~~G~~~I~~~~~~~~q~GDI~I~g~~g~S~G~~GHtgif~~~~~iI 107 (145)
T PF05382_consen 61 KKNGFKKISENVDWNLQRGDIFIWGRRGNSAGAGGHTGIFMDNDTII 107 (145)
T ss_pred hhCCcEEeccCCcccccCCCEEEEcCCCCCCCCCCeEEEEeCCCcEE
Confidence 36677666544 48999999999877633 12444554444333
No 22
>PF06071 YchF-GTPase_C: Protein of unknown function (DUF933); InterPro: IPR013029 This domain is found at the C terminus of family of conserved hypothetical proteins found in both prokaryotes and eukaryotes. While the function of these proteins is not known, the crystal structure of P44681 from SWISSPROT from Haemophilus influenzae has been determined []. This protein consists of three domains: an N-terminal domain which has a mononucleotide binding fold typical for the P-loop NTPases, a central domain which forms an alpha-helical coiled coil, and this C-terminal domain which is composed of a six-stranded half-barrel curved around an alpha helix. The central domain and this domain are topologically similar to RNA-binding proteins, while the N-terminal region contains the features typical of GTP-dependent molecular switches. The purified protein was capable of binding both double-stranded nucleic acid and GTP. It was suggested, therefore, that this protein might be part of a nucleoprotein complex and could function as a GTP-dependent translation factor.; PDB: 1NI3_A 1JAL_A 2DWQ_B 2DBY_A 2OHF_A.
Probab=37.35 E-value=20 Score=23.11 Aligned_cols=15 Identities=20% Similarity=0.556 Sum_probs=9.9
Q ss_pred hHhCCCCCCEEEEEE
Q 040084 77 EAYSTFVGSLVLFEY 91 (127)
Q Consensus 77 ~~~~L~~GD~lvF~~ 91 (127)
++|-++.||++.|+.
T Consensus 69 K~YivqDGDIi~f~f 83 (84)
T PF06071_consen 69 KDYIVQDGDIIHFRF 83 (84)
T ss_dssp TT-B--TTEEEEEEE
T ss_pred CceeEeCCCEEEEEc
Confidence 467789999999975
No 23
>KOG4146 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=37.16 E-value=22 Score=23.45 Aligned_cols=14 Identities=29% Similarity=0.425 Sum_probs=12.4
Q ss_pred hHhCCCCCCEEEEE
Q 040084 77 EAYSTFVGSLVLFE 90 (127)
Q Consensus 77 ~~~~L~~GD~lvF~ 90 (127)
.+|.|+.||.++|.
T Consensus 82 edy~ledgD~ivfi 95 (101)
T KOG4146|consen 82 EDYPLEDGDHIVFI 95 (101)
T ss_pred cccCcccCCEEEEE
Confidence 47899999999995
No 24
>cd08316 Death_FAS_TNFRSF6 Death domain of FAS or TNF receptor superfamily member 6. Death Domain (DD) found in the FS7-associated cell surface antigen (FAS). FAS, also known as TNFRSF6 (TNF receptor superfamily member 6), APT1, CD95, FAS1, or APO-1, together with FADD (Fas-associating via Death Domain) and caspase 8, is an integral part of the death inducing signalling complex (DISC), which plays an important role in the induction of apoptosis and is activated by binding of the ligand FasL to FAS. FAS also plays a critical role in self-tolerance by eliminating cell types (autoreactive T and B cells) that contribute to autoimmunity. 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), DED (Death Effector Domain), and PYRIN. They serve as adaptors in sign
Probab=36.73 E-value=13 Score=24.45 Aligned_cols=17 Identities=12% Similarity=0.085 Sum_probs=14.4
Q ss_pred ccHHHHHhHhCCCCCCE
Q 040084 70 DGWQDFVEAYSTFVGSL 86 (127)
Q Consensus 70 ~GW~~Fv~~~~L~~GD~ 86 (127)
.-|++||...+|.++++
T Consensus 21 ~~wK~faR~lglse~~I 37 (97)
T cd08316 21 KDVKKFVRKSGLSEPKI 37 (97)
T ss_pred HHHHHHHHHcCCCHHHH
Confidence 46999999999998753
No 25
>cd08356 Glo_EDI_BRP_like_17 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping.
Probab=36.12 E-value=37 Score=21.83 Aligned_cols=16 Identities=19% Similarity=0.569 Sum_probs=13.6
Q ss_pred ceEEEEcCCCCEEEEE
Q 040084 43 DVAHITIPNGYVWQVK 58 (127)
Q Consensus 43 ~~v~L~~~~G~~W~V~ 58 (127)
..+.+.||+|+.|.+.
T Consensus 97 r~f~~~DPdGn~~~~~ 112 (113)
T cd08356 97 REFFLHDPSGVLWHIG 112 (113)
T ss_pred EEEEEECCCccEEEee
Confidence 5789999999999873
No 26
>TIGR03511 GldH_lipo gliding motility-associated lipoprotein GldH. Members of this protein family are predicted lipoproteins, exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). Members include GldH, a protein linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. Not all Bacteroidetes with members of this protein family may have gliding motility.
Probab=36.01 E-value=26 Score=25.07 Aligned_cols=32 Identities=22% Similarity=0.476 Sum_probs=21.5
Q ss_pred ceEEEEcCCCCEEE---EEEEE-eCCEEEecccHHH
Q 040084 43 DVAHITIPNGYVWQ---VKLKK-EGRKVWFDDGWQD 74 (127)
Q Consensus 43 ~~v~L~~~~G~~W~---V~l~~-~~~~~~~~~GW~~ 74 (127)
-.+.++.|+|+.|. +++.- ...+.|++.||..
T Consensus 76 l~~~~~~~~~~~~~~DTl~~~Lad~~G~w~G~G~g~ 111 (156)
T TIGR03511 76 ALIHENLEDSTVIFTDTVDLTLADSTGQWTGKGWGS 111 (156)
T ss_pred EEEEEEcCCCceEEeeeeEEEeeCCCCCEEeeeecc
Confidence 45667788999983 33332 3467789999953
No 27
>KOG0260 consensus RNA polymerase II, large subunit [Transcription]
Probab=35.86 E-value=58 Score=30.95 Aligned_cols=77 Identities=17% Similarity=0.252 Sum_probs=52.0
Q ss_pred EEEeccCC-ccCCCceeccHHHHHhcc---------------------cCCCc-eEEEEcCCCCEEEEEEEEeCCEEEec
Q 040084 13 FVKAVLPS-TLRDQKPRIPNKIVRKFS---------------------HELSD-VAHITIPNGYVWQVKLKKEGRKVWFD 69 (127)
Q Consensus 13 F~k~i~~~-~~~~~~L~IP~~F~~~~~---------------------~~~~~-~v~L~~~~G~~W~V~l~~~~~~~~~~ 69 (127)
+=+||+++ +++-+.+-||...|+.+- .+.++ +-++++ +|..-...+.++.+..-|+
T Consensus 341 aRTVItgDPnl~ldevGVP~sIAk~lTfpE~Vtp~NidrLqeLV~~g~~~~pgakyiird-~G~Ridlr~~~~~~d~~Lq 419 (1605)
T KOG0260|consen 341 ARTVITGDPNLSLDEVGVPRSIAKRLTFPEHVTPFNIDRLQELVRRGLLEHPGAKYIIRD-NGDRIDLRYHKRAGDIHLQ 419 (1605)
T ss_pred eeeeecCCCCcchhcccCcHHHHhhccCcceeccccHHHHHHHhhCCCCCCCCcceeeec-CCcEEEEeecCCccccccc
Confidence 44567774 454577888988887651 11222 333443 5776666776666777899
Q ss_pred ccHHHHHhHhCCCCCCEEEEEEec
Q 040084 70 DGWQDFVEAYSTFVGSLVLFEYES 93 (127)
Q Consensus 70 ~GW~~Fv~~~~L~~GD~lvF~~~~ 93 (127)
.||+-+ -+|+.||+++|.-.-
T Consensus 420 ~G~kVe---Rhl~DGD~VlfNRqP 440 (1605)
T KOG0260|consen 420 PGYKVE---RHLMDGDVVLFNRQP 440 (1605)
T ss_pred cccEEE---EeeccCCEEEEcCCC
Confidence 999854 579999999997654
No 28
>PRK09974 putative regulator PrlF; Provisional
Probab=33.76 E-value=1.2e+02 Score=20.62 Aligned_cols=28 Identities=7% Similarity=-0.057 Sum_probs=22.3
Q ss_pred HHHHhHhCCCCCCEEEEEEecCcEEEEE
Q 040084 73 QDFVEAYSTFVGSLVLFEYESNSTFQAH 100 (127)
Q Consensus 73 ~~Fv~~~~L~~GD~lvF~~~~~~~F~V~ 100 (127)
++..+.-+|+.||.+.|....+....+.
T Consensus 24 k~IR~~Lgl~~GdkI~f~i~~dG~V~i~ 51 (111)
T PRK09974 24 APVRKALKLKKRDSIHYEILPGGQVFIC 51 (111)
T ss_pred HHHHHHcCCCCCCEEEEEEeCCCEEEEE
Confidence 5677889999999999998866655444
No 29
>KOG1114 consensus Tripeptidyl peptidase II [Posttranslational modification, protein turnover, chaperones]
Probab=33.74 E-value=1.6e+02 Score=27.57 Aligned_cols=91 Identities=15% Similarity=0.265 Sum_probs=56.4
Q ss_pred CceeccHHHHHhcccCCCceEEEEcCCCCEEEEEEEEe-CCEEEecccHHHHHhHhCCCCCCEEEEEEecCcEEEEEEEC
Q 040084 25 QKPRIPNKIVRKFSHELSDVAHITIPNGYVWQVKLKKE-GRKVWFDDGWQDFVEAYSTFVGSLVLFEYESNSTFQAHIYD 103 (127)
Q Consensus 25 ~~L~IP~~F~~~~~~~~~~~v~L~~~~G~~W~V~l~~~-~~~~~~~~GW~~Fv~~~~L~~GD~lvF~~~~~~~F~V~If~ 103 (127)
+.+..=+.++++|.+..+--=.+.-++|..|+|-+... .|.+++..--.+|-..+... .|.-..-..+.|+|||
T Consensus 224 ~kve~Lks~a~ky~D~gpvyD~vvwhdgE~Wrv~iDt~~~Gdl~~~~~L~~~~~t~e~~-----~f~~~d~l~ysV~vyd 298 (1304)
T KOG1114|consen 224 SKVEFLKSLAKKYDDPGPVYDVVVWHDGEVWRVCIDTDETGDLYLHKVLGEFNETGEYA-----TFGSLDLLSYSVNVYD 298 (1304)
T ss_pred HHHHHHHHHHHhcCCCCcceEEEEeecCCeEEEEecccccCcccccccccccccccccc-----ccccccccceeEEEcc
Confidence 34455567888888776654444557899999999764 56777666555554444333 2222223457788998
Q ss_pred C-CCeEEecCCCCCCcCC
Q 040084 104 E-TACEINYPSSNEESHT 120 (127)
Q Consensus 104 ~-~~ce~~~~~~~~~~~~ 120 (127)
. +-.+++.+++--..+.
T Consensus 299 ~gnvlsIV~~Sg~HGTHV 316 (1304)
T KOG1114|consen 299 DGNVLSIVTVSGPHGTHV 316 (1304)
T ss_pred CCceEEEEecCCCCccee
Confidence 7 5567777765444443
No 30
>PF02938 GAD: GAD domain; InterPro: IPR004115 This entry represetns an 2 layer alpha/beta insertion domain found in some glutamyl-tRNA amidotransferases and aspartyl tRNA synthetases [, ]. The function of this domain is not yet known.; GO: 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0005737 cytoplasm; PDB: 1ZQ1_D 1EQR_B 1IL2_B 1C0A_A 1L0W_A 1G51_B 1EFW_B 2D6F_D.
Probab=33.44 E-value=39 Score=21.68 Aligned_cols=25 Identities=20% Similarity=0.377 Sum_probs=18.7
Q ss_pred cccHHHHHhHhCCCCCCEEEEEEec
Q 040084 69 DDGWQDFVEAYSTFVGSLVLFEYES 93 (127)
Q Consensus 69 ~~GW~~Fv~~~~L~~GD~lvF~~~~ 93 (127)
..-=+++....+++.||.|.|--..
T Consensus 63 e~~~~~l~~~~~a~~GD~ll~~Ag~ 87 (95)
T PF02938_consen 63 EEELKALIERLGAKPGDLLLFVAGK 87 (95)
T ss_dssp HHHHHHHHHHTT--TTEEEEEEEES
T ss_pred HHHHHHHHHHhCCCCCCEEEEECCC
Confidence 5556889999999999999997543
No 31
>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=33.20 E-value=11 Score=24.03 Aligned_cols=21 Identities=5% Similarity=0.169 Sum_probs=17.5
Q ss_pred ecccHHHHHhHhCCCCCCEEE
Q 040084 68 FDDGWQDFVEAYSTFVGSLVL 88 (127)
Q Consensus 68 ~~~GW~~Fv~~~~L~~GD~lv 88 (127)
++..|++|+..-+|.++|+=.
T Consensus 12 lG~~Wk~laR~LGlse~~Id~ 32 (86)
T cd08306 12 VGRDWRKLARKLGLSETKIES 32 (86)
T ss_pred HhhhHHHHHHHcCCCHHHHHH
Confidence 567899999999999887543
No 32
>PF11320 DUF3122: Protein of unknown function (DUF3122); InterPro: IPR021469 This family of proteins with unknown function appear to be restricted to Cyanobacteria.
Probab=32.90 E-value=1.1e+02 Score=21.45 Aligned_cols=19 Identities=32% Similarity=0.449 Sum_probs=16.0
Q ss_pred eEEEEcCCCCEEEEEEEEe
Q 040084 44 VAHITIPNGYVWQVKLKKE 62 (127)
Q Consensus 44 ~v~L~~~~G~~W~V~l~~~ 62 (127)
.-.|+|-+|++|.|-+-++
T Consensus 18 ~qsLrD~~g~sWQvV~fkr 36 (134)
T PF11320_consen 18 RQSLRDQDGNSWQVVLFKR 36 (134)
T ss_pred eeeecCCCCCceEEEEEEe
Confidence 4478899999999999775
No 33
>cd09012 Glo_EDI_BRP_like_24 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping.
Probab=32.44 E-value=57 Score=20.97 Aligned_cols=16 Identities=19% Similarity=0.341 Sum_probs=13.7
Q ss_pred eEEEEcCCCCEEEEEE
Q 040084 44 VAHITIPNGYVWQVKL 59 (127)
Q Consensus 44 ~v~L~~~~G~~W~V~l 59 (127)
.+.++||+|+.|.+..
T Consensus 108 ~~~~~DPdG~~ie~~~ 123 (124)
T cd09012 108 GRSFADLDGHLWEVLW 123 (124)
T ss_pred EEEEECCCCCEEEEEE
Confidence 5789999999999864
No 34
>PF09147 DUF1933: Domain of unknown function (DUF1933); InterPro: IPR015230 This domain is predominantly found in carbapenam synthetase, and is composed of two antiparallel six-stranded beta-sheets that form a sandwich, flanked on each side by two alpha-helices. Their exact function has not, as yet, been determined []. ; PDB: 1Q19_A 1Q15_D.
Probab=32.24 E-value=59 Score=24.15 Aligned_cols=24 Identities=21% Similarity=0.245 Sum_probs=18.3
Q ss_pred hHhCCCCCCEEEEEEecCcEEEEE
Q 040084 77 EAYSTFVGSLVLFEYESNSTFQAH 100 (127)
Q Consensus 77 ~~~~L~~GD~lvF~~~~~~~F~V~ 100 (127)
.+-.|.+||+|.|.-+.+.++.|.
T Consensus 93 ~aLsLAEGdfcffiE~kng~L~l~ 116 (201)
T PF09147_consen 93 SALSLAEGDFCFFIEDKNGELTLI 116 (201)
T ss_dssp GGGGG--SSEEEEEEETTSEEEEE
T ss_pred hhhhhhcCceEEEEecCCCcEEEE
Confidence 456899999999999998888764
No 35
>cd04867 TGS_YchF_C TGS_YchF_C: This subfamily represents TGS domain-containing YchF GTP-binding protein, a universally conserved GTPase whose function is unknown. The N-terminal domain of the YchF protein belongs to the Obg-like family of GTPases, and some members of the family contain a C-terminal TGS domain. TGS is a small domain of about 50 amino acid residues with a predominantly beta-sheet structure. There is no direct information on the function of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role.
Probab=31.98 E-value=19 Score=23.20 Aligned_cols=14 Identities=21% Similarity=0.698 Sum_probs=11.4
Q ss_pred HhCCCCCCEEEEEE
Q 040084 78 AYSTFVGSLVLFEY 91 (127)
Q Consensus 78 ~~~L~~GD~lvF~~ 91 (127)
+|-++.||++.|++
T Consensus 70 ~Yiv~DGDi~~f~f 83 (83)
T cd04867 70 DYVVQDGDIIFFKF 83 (83)
T ss_pred ceEeeCCeEEEEEC
Confidence 67789999999863
No 36
>cd08355 Glo_EDI_BRP_like_14 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The structures of this family demonstrate domain swapping, which is shared by glyoxalase I and antibiotic resistance proteins.
Probab=31.49 E-value=53 Score=20.96 Aligned_cols=16 Identities=19% Similarity=0.399 Sum_probs=13.2
Q ss_pred ceEEEEcCCCCEEEEE
Q 040084 43 DVAHITIPNGYVWQVK 58 (127)
Q Consensus 43 ~~v~L~~~~G~~W~V~ 58 (127)
..+.++||+|+.|.+.
T Consensus 105 ~~~~~~DPdG~~~~l~ 120 (122)
T cd08355 105 REFTARDPEGNLWTFG 120 (122)
T ss_pred EEEEEECCCCCEEEEe
Confidence 4578999999999874
No 37
>PF01568 Molydop_binding: Molydopterin dinucleotide binding domain; InterPro: IPR006657 A domain in this entry corresponds to the C-terminal domain IV in dimethyl sulphoxide (DMSO)reductase which interacts with the 2-amino pyrimidone ring of both molybdopterin guanine dinucleotide molecules [].; GO: 0016491 oxidoreductase activity, 0030151 molybdenum ion binding, 0055114 oxidation-reduction process; PDB: 2IVF_A 1OGY_G 3ML1_A 3O5A_A 1TI2_G 1VLE_M 1VLD_U 1VLF_O 1TI4_I 1TI6_E ....
Probab=30.71 E-value=1.4e+02 Score=18.83 Aligned_cols=48 Identities=21% Similarity=0.327 Sum_probs=35.6
Q ss_pred ceeccHHHHHhcccCCCceEEEEcCCCCEEEEEEEEe----CCEEEecccHHH
Q 040084 26 KPRIPNKIVRKFSHELSDVAHITIPNGYVWQVKLKKE----GRKVWFDDGWQD 74 (127)
Q Consensus 26 ~L~IP~~F~~~~~~~~~~~v~L~~~~G~~W~V~l~~~----~~~~~~~~GW~~ 74 (127)
.+.|.+.=+++++-+..+.|.|.++.| .-.+.+... .+.+++..||..
T Consensus 31 ~v~inp~dA~~~Gi~~Gd~V~v~s~~G-~v~~~v~~~~~v~~g~v~~~~~~~~ 82 (110)
T PF01568_consen 31 FVEINPEDAAKLGIKDGDWVRVSSPRG-SVEVRVKVTDGVPPGVVFMPHGWGG 82 (110)
T ss_dssp EEEEEHHHHHHCT--TTCEEEEEETTE-EEEEEEEEETTS-TTEEEEESTHTT
T ss_pred EEEEcHHHHHHhcCcCCCEEEEEeccc-eEeeeeEEecCCcCCEEEEeccccc
Confidence 678888889999988899999999988 334444433 578888888876
No 38
>COG1525 Micrococcal nuclease (thermonuclease) homologs [DNA replication, recombination, and repair]
Probab=30.35 E-value=56 Score=23.49 Aligned_cols=43 Identities=14% Similarity=0.128 Sum_probs=32.6
Q ss_pred CCCCCCEEEEEEecCcEEEEEEECCCCeEEecCCCCCCcCCCC
Q 040084 80 STFVGSLVLFEYESNSTFQAHIYDETACEINYPSSNEESHTNG 122 (127)
Q Consensus 80 ~L~~GD~lvF~~~~~~~F~V~If~~~~ce~~~~~~~~~~~~~~ 122 (127)
.+..||.+.....+...-+|.+.+-+.+|...++.+...+-+|
T Consensus 48 ~v~dGDT~~v~~~~~~~~~iRl~gIdaPe~~~~~~~~~~~~~G 90 (192)
T COG1525 48 RVIDGDTLKVRGEGGQAVKIRLAGIDAPETKQTCAGGKSQPCG 90 (192)
T ss_pred EecCCCeEEEecCCCceeEEEEeccCCCcccccCCcccccchH
Confidence 3467888888888888999999999999988776444444444
No 39
>PF04225 OapA: Opacity-associated protein A LysM-like domain; InterPro: IPR007340 This entry includes the Haemophilus influenzae opacity-associated protein. This protein is required for efficient nasopharyngeal mucosal colonization, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation [].; PDB: 2GU1_A.
Probab=30.14 E-value=59 Score=20.62 Aligned_cols=33 Identities=15% Similarity=0.267 Sum_probs=17.9
Q ss_pred CCCCCCEEEEEEecCcEEEEEEECCCCeEEecC
Q 040084 80 STFVGSLVLFEYESNSTFQAHIYDETACEINYP 112 (127)
Q Consensus 80 ~L~~GD~lvF~~~~~~~F~V~If~~~~ce~~~~ 112 (127)
.|+.||.|.|.++.+..+.-.-+..+.-+..|.
T Consensus 42 ~L~pGq~l~f~~d~~g~L~~L~~~~~~~~~~~~ 74 (85)
T PF04225_consen 42 RLKPGQTLEFQLDEDGQLTALRYERSPKTTLYT 74 (85)
T ss_dssp G--TT-EEEEEE-TTS-EEEEEEEEETTEEEEE
T ss_pred hCCCCCEEEEEECCCCCEEEEEEEcCCcEEEEE
Confidence 589999999999987766544444433344443
No 40
>PF08916 Phe_ZIP: Phenylalanine zipper; InterPro: IPR015012 The phenylalanine zipper consists of aromatic side chains from ten phenylalanine residues that are stacked within a hydrophobic core. This zipper mediates dimerisation of various proteins, such as APS, SH2-B and Lnk []. ; GO: 0004871 signal transducer activity, 0035556 intracellular signal transduction; PDB: 1Q2H_B.
Probab=29.63 E-value=32 Score=20.71 Aligned_cols=10 Identities=40% Similarity=1.069 Sum_probs=6.4
Q ss_pred ccHHHHHhHh
Q 040084 70 DGWQDFVEAY 79 (127)
Q Consensus 70 ~GW~~Fv~~~ 79 (127)
.||.+|+.-|
T Consensus 1 ~~W~EFCE~H 10 (59)
T PF08916_consen 1 PGWREFCERH 10 (59)
T ss_dssp --HHHHHHHH
T ss_pred CCHHHHHHHH
Confidence 3899998755
No 41
>cd07235 MRD Mitomycin C resistance protein (MRD). Mitomycin C (MC) is a naturally occurring antibiotic, and antitumor agent used in the treatment of cancer. Its antitumor activity is exerted primarily through monofunctional and bifunctional alkylation of DNA. MRD binds to MC and functions as a component of the MC exporting system. MC is bound to MRD by a stacking interaction between a His and a Trp. MRD adopts a structural fold similar to bleomycin resistance protein, glyoxalase I, and extradiol dioxygenases; and it has binding sites at an identical location to binding sites in these evolutionarily related enzymes.
Probab=29.45 E-value=56 Score=20.80 Aligned_cols=16 Identities=19% Similarity=0.248 Sum_probs=13.1
Q ss_pred ceEEEEcCCCCEEEEE
Q 040084 43 DVAHITIPNGYVWQVK 58 (127)
Q Consensus 43 ~~v~L~~~~G~~W~V~ 58 (127)
..+.++||+|+.|.+-
T Consensus 106 ~~~~~~DPdG~~iel~ 121 (122)
T cd07235 106 RYAIVKDPDGNLVDLF 121 (122)
T ss_pred EEEEEECCCCCEEEEe
Confidence 3568999999999874
No 42
>cd07254 Glo_EDI_BRP_like_20 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and types I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping.
Probab=29.27 E-value=89 Score=19.79 Aligned_cols=19 Identities=32% Similarity=0.615 Sum_probs=15.7
Q ss_pred ceEEEEcCCCCEEEEEEEE
Q 040084 43 DVAHITIPNGYVWQVKLKK 61 (127)
Q Consensus 43 ~~v~L~~~~G~~W~V~l~~ 61 (127)
..+.++||+|+.|.+....
T Consensus 100 ~~~~~~DP~G~~ie~~~~~ 118 (120)
T cd07254 100 DKVWVTDPDGNAWEVFVTL 118 (120)
T ss_pred ceEEEECCCCCEEEEEEee
Confidence 3588999999999998743
No 43
>PF01052 SpoA: Surface presentation of antigens (SPOA); InterPro: IPR001543 Proteins in this group are involved in a secretory pathway responsible for the surface presentation of invasion plasmid antigen needed for the entry of Salmonella and other species into mammalian cells [, ].They could play a role in preserving the translocation competence of the IPA antigens and are required for secretion of the three IPA proteins []. The C-terminal region of flagellar motor switch proteins FliN and FliM is also included in this entry. ; PDB: 3UEP_A 1O9Y_B 1YAB_A.
Probab=28.74 E-value=64 Score=19.51 Aligned_cols=27 Identities=11% Similarity=0.255 Sum_probs=17.3
Q ss_pred HHhHhCCCCCCEEEEEEecCcEEEEEE
Q 040084 75 FVEAYSTFVGSLVLFEYESNSTFQAHI 101 (127)
Q Consensus 75 Fv~~~~L~~GD~lvF~~~~~~~F~V~I 101 (127)
...-.+|+.||++.+...-+....|.+
T Consensus 23 l~el~~L~~Gdvi~l~~~~~~~v~l~v 49 (77)
T PF01052_consen 23 LGELLNLKVGDVIPLDKPADEPVELRV 49 (77)
T ss_dssp HHHHHC--TT-EEEECCESSTEEEEEE
T ss_pred HHHHhcCCCCCEEEeCCCCCCCEEEEE
Confidence 345678999999999888666666654
No 44
>PF12681 Glyoxalase_2: Glyoxalase-like domain; PDB: 3G12_B 1JIF_B 1JIE_B 1QTO_A 3OXH_A 2PJS_A 2RBB_A 3SK1_B 3SK2_B 3RRI_A ....
Probab=28.71 E-value=59 Score=20.00 Aligned_cols=15 Identities=13% Similarity=0.087 Sum_probs=11.1
Q ss_pred ceEEEEcCCCCEEEE
Q 040084 43 DVAHITIPNGYVWQV 57 (127)
Q Consensus 43 ~~v~L~~~~G~~W~V 57 (127)
..+.++||+|+.|.+
T Consensus 93 ~~~~~~DPdG~~ie~ 107 (108)
T PF12681_consen 93 RSFYFIDPDGNRIEF 107 (108)
T ss_dssp EEEEEE-TTS-EEEE
T ss_pred EEEEEECCCCCEEEe
Confidence 588999999999876
No 45
>PRK06033 hypothetical protein; Validated
Probab=28.68 E-value=61 Score=20.57 Aligned_cols=26 Identities=4% Similarity=0.024 Sum_probs=17.4
Q ss_pred HHHhHhCCCCCCEEEEEEecCcEEEE
Q 040084 74 DFVEAYSTFVGSLVLFEYESNSTFQA 99 (127)
Q Consensus 74 ~Fv~~~~L~~GD~lvF~~~~~~~F~V 99 (127)
.+..--+|++||++.+....+....|
T Consensus 21 ~l~dlL~L~~GDVI~L~~~~~~~v~v 46 (83)
T PRK06033 21 PIHQVLRMGRGAVIPLDATEADEVWI 46 (83)
T ss_pred cHHHHhCCCCCCEEEeCCCCCCcEEE
Confidence 34556789999999997654433333
No 46
>COG5131 URM1 Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=28.04 E-value=39 Score=22.14 Aligned_cols=24 Identities=21% Similarity=0.440 Sum_probs=16.5
Q ss_pred cccHHHHHh-HhCCCCCCEEEEEEe
Q 040084 69 DDGWQDFVE-AYSTFVGSLVLFEYE 92 (127)
Q Consensus 69 ~~GW~~Fv~-~~~L~~GD~lvF~~~ 92 (127)
...|.-.-+ ++.|+.||.++|.-.
T Consensus 68 d~DWeLleke~y~ledgDiIvfist 92 (96)
T COG5131 68 DMDWELLEKERYPLEDGDIIVFIST 92 (96)
T ss_pred CccHhhhhcccccCCCCCEEEEEec
Confidence 344554443 688999999999643
No 47
>PF14109 GldH_lipo: GldH lipoprotein
Probab=27.91 E-value=54 Score=22.51 Aligned_cols=58 Identities=21% Similarity=0.250 Sum_probs=35.0
Q ss_pred CceEEEEcCCCCEEEEEEEE---eCCEEEecccHHHHHhHhCCCCCCEEEEEEecCcEEEEE
Q 040084 42 SDVAHITIPNGYVWQVKLKK---EGRKVWFDDGWQDFVEAYSTFVGSLVLFEYESNSTFQAH 100 (127)
Q Consensus 42 ~~~v~L~~~~G~~W~V~l~~---~~~~~~~~~GW~~Fv~~~~L~~GD~lvF~~~~~~~F~V~ 100 (127)
--.+.+..|+|+...=.+.. ...+-|++.||.. +.++.+-.-.-+.|...|.-+|.|.
T Consensus 53 ~l~v~~~~p~~~~~~dtl~~~Lad~~G~w~G~G~~~-~~e~~~~~~~~~~f~~~G~Y~~~i~ 113 (131)
T PF14109_consen 53 WLIVELTDPDGKKVTDTLECELADPDGKWLGKGIGD-LYEYKLPYKENVRFPRKGSYTFTIE 113 (131)
T ss_pred EEEEEEEcCCCCEEeeeEEEEEECCCCcEeeeeEeE-eEEEEEEeecceecCCCCcEEEEEE
Confidence 34677778888874433332 2456788999887 5555555544555554555555544
No 48
>cd07246 Glo_EDI_BRP_like_8 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The structures of this family demonstrate domain swapping, which is shared by glyoxalase I and antibiotic resistance proteins.
Probab=27.66 E-value=67 Score=20.15 Aligned_cols=17 Identities=18% Similarity=0.362 Sum_probs=13.9
Q ss_pred CceEEEEcCCCCEEEEE
Q 040084 42 SDVAHITIPNGYVWQVK 58 (127)
Q Consensus 42 ~~~v~L~~~~G~~W~V~ 58 (127)
...+.++||+|..|.+.
T Consensus 104 ~~~~~~~DP~G~~~~l~ 120 (122)
T cd07246 104 DRYGGVRDPFGHRWWIA 120 (122)
T ss_pred ceEEEEECCCCCEEEEe
Confidence 35889999999999864
No 49
>cd03548 Rieske_RO_Alpha_OMO_CARDO Rieske non-heme iron oxygenase (RO) family, 2-Oxoquinoline 8-monooxygenase (OMO) and Carbazole 1,9a-dioxygenase (CARDO) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. OMO catalyzes the NADH-dependent oxidation of the N-heterocyclic aromatic compound 2-oxoquinoline to 8-hydroxy-2-oxoquinoline, the second step in the bacterial degradation of quinoline. OMO consists of a reductase component (OMR) and an oxygenase component (OMO) that together function to shuttle electrons from the
Probab=27.51 E-value=34 Score=23.44 Aligned_cols=38 Identities=8% Similarity=-0.026 Sum_probs=27.4
Q ss_pred EEecccHHHHHhHhCCCCCCEEEEEEecCcEEEEEEECCCC
Q 040084 66 VWFDDGWQDFVEAYSTFVGSLVLFEYESNSTFQAHIYDETA 106 (127)
Q Consensus 66 ~~~~~GW~~Fv~~~~L~~GD~lvF~~~~~~~F~V~If~~~~ 106 (127)
.-|..+|-..+....|..|+...|++.+.. +.|++.+|
T Consensus 9 ~~~~~~W~~v~~~~el~~g~~~~~~~~g~~---i~l~r~~g 46 (136)
T cd03548 9 WGFRNHWYPALFSHELEEGEPKGIQLCGEP---ILLRRVDG 46 (136)
T ss_pred cCcccCcEEEEEHHHCCCCCeEEEEECCcE---EEEEecCC
Confidence 356788887788888999999999987654 34444443
No 50
>PF07494 Reg_prop: Two component regulator propeller; InterPro: IPR011110 A large group of two component regulator proteins appear to have the same N-terminal structure of 14 tandem repeats. These repeats show homology to members of IPR002372 from INTERPRO and IPR001680 from INTERPRO indicating that they are likely to form a beta-propeller. This family has been built with artificially high cut-offs in order to avoid overlaps with other beta-propeller families. The fourteen repeats are likely to form two propellers; it is not clear if these structures are likely to recruit other proteins or interact with DNA.; PDB: 3V9F_D 3VA6_B 3OTT_B 4A2M_D 4A2L_B.
Probab=27.49 E-value=74 Score=15.01 Aligned_cols=13 Identities=15% Similarity=0.389 Sum_probs=8.8
Q ss_pred eEEEEcCCCCEEE
Q 040084 44 VAHITIPNGYVWQ 56 (127)
Q Consensus 44 ~v~L~~~~G~~W~ 56 (127)
...++|++|+-|-
T Consensus 8 ~~i~~D~~G~lWi 20 (24)
T PF07494_consen 8 YSIYEDSDGNLWI 20 (24)
T ss_dssp EEEEE-TTSCEEE
T ss_pred EEEEEcCCcCEEE
Confidence 4567888888884
No 51
>PF02381 MraZ: MraZ protein; InterPro: IPR020603 this entry represents the 70 amino acid region found duplicated in the bacterial proteins MraZ. These proteins may be DNA-binding transcription factors, its members are probably enzymes containing a conserved DXXXR motif that probably forms part of the active site.; PDB: 1N0F_E 1N0E_F 1N0G_A.
Probab=27.19 E-value=88 Score=18.71 Aligned_cols=42 Identities=14% Similarity=0.336 Sum_probs=25.7
Q ss_pred CceeccHHHHHhcccCCCceEEEEcCCCCEEEEEEEEeCCEEEecccHHHHHhH
Q 040084 25 QKPRIPNKIVRKFSHELSDVAHITIPNGYVWQVKLKKEGRKVWFDDGWQDFVEA 78 (127)
Q Consensus 25 ~~L~IP~~F~~~~~~~~~~~v~L~~~~G~~W~V~l~~~~~~~~~~~GW~~Fv~~ 78 (127)
.++.||..|-+..+.. ..+++.+.++ +- .+|=...|.++...
T Consensus 14 GRi~iP~~~R~~l~~~--~~v~~~g~~~-~l---------eiw~~~~w~~~~~~ 55 (72)
T PF02381_consen 14 GRISIPAKFREHLGIE--KEVVFVGFDD-CL---------EIWPPEEWEELEAR 55 (72)
T ss_dssp SEEE--CHHHHHTTSC--SEEEEEECCS-EE---------EEEEHHHHHHHHHC
T ss_pred CCEecCHHHHhhhccC--ceEEEeccCC-EE---------EEcCHHHHHHHHHH
Confidence 8899999998876665 6666665432 11 13346778777765
No 52
>TIGR01643 YD_repeat_2x YD repeat (two copies). This model describes two tandem copies of a 21-residue extracellular repeat found in Gram-negative, Gram-positive, and animal proteins. The repeat is named for a YD dipeptide, the most strongly conserved motif of the repeat. These repeats appear in general to be involved in binding carbohydrate; the chicken teneurin-1 YD-repeat region has been shown to bind heparin.
Probab=26.88 E-value=1.1e+02 Score=16.02 Aligned_cols=21 Identities=10% Similarity=0.039 Sum_probs=16.3
Q ss_pred CceEEEEcCCCCEEEEEEEEe
Q 040084 42 SDVAHITIPNGYVWQVKLKKE 62 (127)
Q Consensus 42 ~~~v~L~~~~G~~W~V~l~~~ 62 (127)
...+.+.+|+|+.|...+...
T Consensus 5 g~l~~~~~p~G~~~~~~YD~~ 25 (42)
T TIGR01643 5 GRLTGSTDADGTTTRYTYDAA 25 (42)
T ss_pred CCEEEEECCCCCEEEEEECCC
Confidence 456788889999999888543
No 53
>cd04459 Rho_CSD Rho_CSD: Rho protein cold-shock domain (CSD). Rho protein is a transcription termination factor in most bacteria. In bacteria, there are two distinct mechanisms for mRNA transcription termination. In intrinsic termination, RNA polymerase and nascent mRNA are released from DNA template by an mRNA stem loop structure, which resembles the transcription termination mechanism used by eukaryotic pol III. The second mechanism is mediated by Rho factor. Rho factor terminates transcription by using energy from ATP hydrolysis to forcibly dissociate the transcripts from RNA polymerase. Rho protein contains an N-terminal S1-like domain, which binds single-stranded RNA. Rho has a C-terminal ATPase domain which hydrolyzes ATP to provide energy to strip RNA polymerase and mRNA from the DNA template. Rho functions as a homohexamer.
Probab=26.61 E-value=70 Score=19.64 Aligned_cols=24 Identities=8% Similarity=0.246 Sum_probs=18.0
Q ss_pred CEEEecccHHHHHhHhCCCCCCEEEEE
Q 040084 64 RKVWFDDGWQDFVEAYSTFVGSLVLFE 90 (127)
Q Consensus 64 ~~~~~~~GW~~Fv~~~~L~~GD~lvF~ 90 (127)
+.++.. ...++.++|+.||.+.=.
T Consensus 27 ~DvyVs---~~~Irr~~LR~GD~V~G~ 50 (68)
T cd04459 27 DDIYVS---PSQIRRFNLRTGDTVVGQ 50 (68)
T ss_pred CCEEEC---HHHHHHhCCCCCCEEEEE
Confidence 445544 478999999999998643
No 54
>PF00877 NLPC_P60: NlpC/P60 family; InterPro: IPR000064 The Escherichia coli NLPC/Listeria P60 domain occurs at the C terminus of a number of different bacterial and viral proteins. The viral proteins are either described as tail assembly proteins or Gp19. In bacteria, the proteins are variously described as being putative tail component of prophage, invasin, invasion associated protein, putative lipoprotein, cell wall hydrolase, or putative endopeptidase. The E. coli NLPC/Listeria P60 domain is contained within the boundaries of the cysteine peptidase domain that defines the MEROPS peptidase family C40 (clan C-). A type example being dipeptidyl-peptidase VI from Bacillus sphaericus and gamma-glutamyl-diamino acid-endopeptidase precursor from Lactococcus lactis 3.4.19.11 from EC. This group also contains proteins classified as non-peptidase homologues in that they either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity of peptidases in the C40 family. ; PDB: 3PVQ_B 3GT2_A 3NPF_B 2K1G_A 3I86_A 3S0Q_A 2XIV_A 3PBC_A 3NE0_A 3M1U_B ....
Probab=26.40 E-value=46 Score=21.28 Aligned_cols=32 Identities=19% Similarity=0.185 Sum_probs=23.5
Q ss_pred HHHhHhCCCCCCEEEEEEecCcEEEEEEECCCC
Q 040084 74 DFVEAYSTFVGSLVLFEYESNSTFQAHIYDETA 106 (127)
Q Consensus 74 ~Fv~~~~L~~GD~lvF~~~~~~~F~V~If~~~~ 106 (127)
.++....++.||++.|.. +...-+|-||-.++
T Consensus 45 ~~~~~~~~~pGDlif~~~-~~~~~Hvgiy~g~~ 76 (105)
T PF00877_consen 45 KRVPISELQPGDLIFFKG-GGGISHVGIYLGDG 76 (105)
T ss_dssp EHEEGGG-TTTEEEEEEG-TGGEEEEEEEEETT
T ss_pred cccchhcCCcccEEEEeC-CccCCEeEEEEeCC
Confidence 356677899999999998 66677777776544
No 55
>KOG3995 consensus 3-hydroxyanthranilate oxygenase HAAO [Amino acid transport and metabolism]
Probab=26.35 E-value=39 Score=25.82 Aligned_cols=25 Identities=12% Similarity=0.274 Sum_probs=22.4
Q ss_pred HhHhCCCCCCEEEEEEecCcEEEEE
Q 040084 76 VEAYSTFVGSLVLFEYESNSTFQAH 100 (127)
Q Consensus 76 v~~~~L~~GD~lvF~~~~~~~F~V~ 100 (127)
.++|+|.+|.-..|+..|++.++|.
T Consensus 45 RkdyHieegeE~FyQ~KGdMvLKVi 69 (279)
T KOG3995|consen 45 RKDYHIEEGEEVFYQLKGDMVLKVL 69 (279)
T ss_pred ccccccCCcchhheeecCceEEeee
Confidence 4789999999999999999998875
No 56
>COG5285 Protein involved in biosynthesis of mitomycin antibiotics/polyketide fumonisin [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=26.22 E-value=27 Score=27.74 Aligned_cols=44 Identities=16% Similarity=0.360 Sum_probs=30.5
Q ss_pred EEEEcCCCCEEEEEEEEeCCEEEecccHHHHHhHhCCCCCCEEEEEEe
Q 040084 45 AHITIPNGYVWQVKLKKEGRKVWFDDGWQDFVEAYSTFVGSLVLFEYE 92 (127)
Q Consensus 45 v~L~~~~G~~W~V~l~~~~~~~~~~~GW~~Fv~~~~L~~GD~lvF~~~ 92 (127)
+++..|...+|.+...+.+++.|+.+- +..-.|..||.++|.-.
T Consensus 165 at~vvPgSH~~~~~~~r~d~~~y~~~~----~~pv~lekGDallF~~~ 208 (299)
T COG5285 165 ATLVVPGSHKWDVIPERPDHETYLERN----AVPVELEKGDALLFNGS 208 (299)
T ss_pred ceEEEecccccccCCCCCCccchhhhc----ceeeeecCCCEEEEcch
Confidence 366667677787776555555565443 66778899999999654
No 57
>TIGR02228 sigpep_I_arch signal peptidase I, archaeal type. This model represents signal peptidase I from most archaea, a subunit of the eukaryotic endoplasmic reticulum signal peptidase I complex, and an apparent signal peptidase I from a small number of bacteria. It is related to but does not overlap in hits with TIGR02227, the bacterial and mitochondrial signal peptidase I.
Probab=25.68 E-value=86 Score=22.29 Aligned_cols=16 Identities=13% Similarity=0.235 Sum_probs=14.1
Q ss_pred hCCCCCCEEEEEEecC
Q 040084 79 YSTFVGSLVLFEYESN 94 (127)
Q Consensus 79 ~~L~~GD~lvF~~~~~ 94 (127)
..++.||+++|+..++
T Consensus 59 ~~~~~GDIVvf~~~~~ 74 (158)
T TIGR02228 59 NDIQVGDVITYKSPGF 74 (158)
T ss_pred CCCCCCCEEEEEECCC
Confidence 5899999999998774
No 58
>cd09011 Glo_EDI_BRP_like_23 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping.
Probab=25.64 E-value=84 Score=20.00 Aligned_cols=16 Identities=19% Similarity=0.229 Sum_probs=13.0
Q ss_pred ceEEEEcCCCCEEEEE
Q 040084 43 DVAHITIPNGYVWQVK 58 (127)
Q Consensus 43 ~~v~L~~~~G~~W~V~ 58 (127)
..+.++||+|+.|.+.
T Consensus 102 r~~~~~DPdGn~iei~ 117 (120)
T cd09011 102 RVVRFYDPDKHIIEVG 117 (120)
T ss_pred EEEEEECCCCCEEEEe
Confidence 4788899999988764
No 59
>cd07262 Glo_EDI_BRP_like_19 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping.
Probab=25.51 E-value=77 Score=20.16 Aligned_cols=15 Identities=20% Similarity=0.246 Sum_probs=12.8
Q ss_pred eEEEEcCCCCEEEEE
Q 040084 44 VAHITIPNGYVWQVK 58 (127)
Q Consensus 44 ~v~L~~~~G~~W~V~ 58 (127)
.+.+.||+|+.|++.
T Consensus 108 ~~~~~DPdG~~ie~~ 122 (123)
T cd07262 108 AAYVRDPDGNKIEAV 122 (123)
T ss_pred EEEEECCCCCEEEEe
Confidence 478999999999874
No 60
>cd08357 Glo_EDI_BRP_like_18 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping.
Probab=25.48 E-value=91 Score=19.65 Aligned_cols=17 Identities=18% Similarity=0.321 Sum_probs=13.8
Q ss_pred ceEEEEcCCCCEEEEEE
Q 040084 43 DVAHITIPNGYVWQVKL 59 (127)
Q Consensus 43 ~~v~L~~~~G~~W~V~l 59 (127)
..+.++||+|+.|++..
T Consensus 108 ~~~~~~DPdG~~iE~~~ 124 (125)
T cd08357 108 ETFFLKDPSGNALEFKA 124 (125)
T ss_pred eEEEEECCCCCEEEEee
Confidence 45889999999998763
No 61
>cd08350 BLMT_like BLMT, a bleomycin resistance protein encoded on the transposon Tn5, and similar proteins. BLMT is a bleomycin (Bm) resistance protein, encoded by the ble gene on the transposon Tn5. This protein confers a survival advantage to Escherichia coli host cells. Bm is a glycopeptide antibiotic produced naturally by actinomycetes. It is a potent anti-cancer drug, which acts as a strong DNA-cutting agent, thereby causing cell death. BLMT has strong binding affinity to Bm and it protects against this lethal compound through drug sequestering. BLMT has two identically-folded subdomains, with the same alpha/beta fold; these two halves have no sequence similarity. BLMT is a dimer with two Bm-binding pockets formed at the dimer interface.
Probab=25.37 E-value=77 Score=20.26 Aligned_cols=16 Identities=13% Similarity=0.216 Sum_probs=13.4
Q ss_pred ceEEEEcCCCCEEEEE
Q 040084 43 DVAHITIPNGYVWQVK 58 (127)
Q Consensus 43 ~~v~L~~~~G~~W~V~ 58 (127)
..+.++||+|+.|.+.
T Consensus 102 ~~~~~~DPdG~~ie~~ 117 (120)
T cd08350 102 REFALVDPDGNLLRFG 117 (120)
T ss_pred eEEEEECCCCCEEEee
Confidence 4689999999999873
No 62
>cd07267 THT_Oxygenase_N N-terminal domain of 2,4,5-trihydroxytoluene (THT) oxygenase. This subfamily contains the N-terminal, non-catalytic, domain of THT oxygenase. THT oxygenase is an extradiol dioxygenase in the 2,4-dinitrotoluene (DNT) degradation pathway. It catalyzes the conversion of 2,4,5-trihydroxytoluene to an unstable ring fission product, 2,4-dihydroxy-5-methyl-6-oxo-2,4-hexadienoic acid. The native protein was determined to be a dimer by gel filtration. The enzyme belongs to the type I family of extradiol dioxygenases which contains two structurally homologous barrel-shaped domains at the N- and C-terminus of each monomer. The active-site metal is located in the C-terminal barrel. Fe(II) is required for its catalytic activity.
Probab=25.12 E-value=1e+02 Score=19.54 Aligned_cols=18 Identities=17% Similarity=0.327 Sum_probs=14.8
Q ss_pred ceEEEEcCCCCEEEEEEE
Q 040084 43 DVAHITIPNGYVWQVKLK 60 (127)
Q Consensus 43 ~~v~L~~~~G~~W~V~l~ 60 (127)
..+.+.||+|+.|++...
T Consensus 93 ~~~~~~DPdG~~iEl~~~ 110 (113)
T cd07267 93 KRVTLTDPDGFPVELVYG 110 (113)
T ss_pred eEEEEECCCCCEEEEEec
Confidence 468899999999988763
No 63
>cd08344 MhqB_like_N N-terminal domain of MhqB, a type I extradiol dioxygenase, and similar proteins. This subfamily contains the N-terminal, non-catalytic, domain of Burkholderia sp. NF100 MhqB and similar proteins. MhqB is a type I extradiol dioxygenase involved in the catabolism of methylhydroquinone, an intermediate in the degradation of fenitrothion. The purified enzyme has shown extradiol ring cleavage activity toward 3-methylcatechol. Fe2+ was suggested as a cofactor, the same as most other enzymes in the family. Burkholderia sp. NF100 MhqB is encoded on the plasmid pNF1. The type I family of extradiol dioxygenases contains two structurally homologous barrel-shaped domains at the N- and C-terminal. The active-site metal is located in the C-terminal barrel and plays an essential role in the catalytic mechanism.
Probab=25.09 E-value=84 Score=19.83 Aligned_cols=17 Identities=35% Similarity=0.489 Sum_probs=14.3
Q ss_pred ceEEEEcCCCCEEEEEE
Q 040084 43 DVAHITIPNGYVWQVKL 59 (127)
Q Consensus 43 ~~v~L~~~~G~~W~V~l 59 (127)
..+.+.||+|+.|.+..
T Consensus 92 ~~~~~~DP~Gn~iel~~ 108 (112)
T cd08344 92 DGVWFRDPDGNLLQVKV 108 (112)
T ss_pred CEEEEECCCCCEEEEec
Confidence 36899999999998874
No 64
>cd07261 Glo_EDI_BRP_like_11 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping.
Probab=24.94 E-value=85 Score=19.62 Aligned_cols=16 Identities=19% Similarity=0.005 Sum_probs=12.9
Q ss_pred ceEEEEcCCCCEEEEE
Q 040084 43 DVAHITIPNGYVWQVK 58 (127)
Q Consensus 43 ~~v~L~~~~G~~W~V~ 58 (127)
..+.++||+|+.|.+-
T Consensus 98 ~~~~~~DPdGn~ie~~ 113 (114)
T cd07261 98 YTFVALDPDGHRLRVF 113 (114)
T ss_pred cEEEEECCCCCEEEee
Confidence 4578999999998873
No 65
>cd08777 Death_RIP1 Death Domain of Receptor-Interacting Protein 1. Death domain (DD) found in Receptor-Interacting Protein 1 (RIP1) and related proteins. RIP kinases serve as essential sensors of cellular stress. Vertebrates contain several types containing a homologous N-terminal kinase domain and varying C-terminal domains. RIP1 harbors a C-terminal DD, which binds death receptors (DRs) including TNF receptor 1, Fas, TNF-related apoptosis-inducing ligand receptor 1 (TRAILR1), and TRAILR2. It also interacts with other DD-containing adaptor proteins such as TRADD and FADD. RIP1 plays a crucial role in determining a cell's fate, between survival or death, following exposure to stress signals. It is important in the signaling of NF-kappaB and MAPKs, and it links DR-associated signaling to reactive oxygen species (ROS) production. Abnormal RIP1 function may result in ROS accumulation affecting inflammatory responses, innate immunity, stress responses, and cell survival. In general, DDs ar
Probab=24.74 E-value=18 Score=23.18 Aligned_cols=23 Identities=4% Similarity=0.186 Sum_probs=19.1
Q ss_pred ecccHHHHHhHhCCCCCCEEEEE
Q 040084 68 FDDGWQDFVEAYSTFVGSLVLFE 90 (127)
Q Consensus 68 ~~~GW~~Fv~~~~L~~GD~lvF~ 90 (127)
++..|++|+..-++.+.|+=.|+
T Consensus 12 lG~~Wk~lar~LG~s~~eI~~ie 34 (86)
T cd08777 12 LGKKWKRCARKLGFTESEIEEID 34 (86)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHH
Confidence 57899999999999998765554
No 66
>cd07265 2_3_CTD_N N-terminal domain of catechol 2,3-dioxygenase. This subfamily contains the N-terminal, non-catalytic, domain of catechol 2,3-dioxygenase. Catechol 2,3-dioxygenase (2,3-CTD, catechol:oxygen 2,3-oxidoreductase) catalyzes an extradiol cleavage of catechol to form 2-hydroxymuconate semialdehyde with the insertion of two atoms of oxygen. The enzyme is a homotetramer and contains catalytically essential Fe(II) . The reaction proceeds by an ordered bi-unit mechanism. First, catechol binds to the enzyme, this is then followed by the binding of dioxygen to form a tertiary complex, and then the aromatic ring is cleaved to produce 2-hydroxymuconate semialdehyde. Catechol 2,3-dioxygenase belongs to the type I extradiol dioxygenase family. The subunit comprises the N- and C-terminal domains of similar structure fold, resulting from an ancient gene duplication. The active site is located in a funnel-shaped space of the C-terminal domain. This subfamily represents the N-terminal do
Probab=24.68 E-value=1.1e+02 Score=19.39 Aligned_cols=18 Identities=11% Similarity=0.276 Sum_probs=15.0
Q ss_pred ceEEEEcCCCCEEEEEEE
Q 040084 43 DVAHITIPNGYVWQVKLK 60 (127)
Q Consensus 43 ~~v~L~~~~G~~W~V~l~ 60 (127)
..+.++||+|+.|++...
T Consensus 102 ~~~~~~DPdG~~iE~~~~ 119 (122)
T cd07265 102 RRVRFQLPSGHTMELYAD 119 (122)
T ss_pred eEEEEECCCCCEEEEEEe
Confidence 468999999999988764
No 67
>PRK03760 hypothetical protein; Provisional
Probab=24.33 E-value=81 Score=21.30 Aligned_cols=21 Identities=14% Similarity=0.006 Sum_probs=17.1
Q ss_pred ecccHHHHHhHhCCCCCCEEEEEE
Q 040084 68 FDDGWQDFVEAYSTFVGSLVLFEY 91 (127)
Q Consensus 68 ~~~GW~~Fv~~~~L~~GD~lvF~~ 91 (127)
+..|| +..++|+.||.+.|+.
T Consensus 96 l~aG~---~~~~gi~~Gd~v~~~~ 116 (117)
T PRK03760 96 GPVGK---IRVLKVEVGDEIEWID 116 (117)
T ss_pred eCCCh---HHHcCCCCCCEEEEee
Confidence 46776 5789999999998864
No 68
>PF14186 Aida_C2: Cytoskeletal adhesion; PDB: 2QZQ_A 2QZ5_A.
Probab=23.90 E-value=63 Score=22.99 Aligned_cols=49 Identities=18% Similarity=0.201 Sum_probs=31.4
Q ss_pred eEEEEcCCCCE------EEEEEEEeCCEEEecccHHHHHhHhCCCCCCEEEEEEe
Q 040084 44 VAHITIPNGYV------WQVKLKKEGRKVWFDDGWQDFVEAYSTFVGSLVLFEYE 92 (127)
Q Consensus 44 ~v~L~~~~G~~------W~V~l~~~~~~~~~~~GW~~Fv~~~~L~~GD~lvF~~~ 92 (127)
+|.+.|.+|+- -.|...+.++.++|..+|.-=.--.+|..|-.++||+.
T Consensus 36 tVSV~D~~G~~ve~~QdTpv~~~~~~~yv~f~~~v~lqtple~lp~Gaai~fE~k 90 (147)
T PF14186_consen 36 TVSVKDGNGKDVEPPQDTPVGSRREDNYVHFNNTVHLQTPLEKLPKGAAIFFEFK 90 (147)
T ss_dssp EEEEE-TTS-BSS--EE--S-SEEETTEEEEEEEEE-SS-GGGS-TT-EEEEEEE
T ss_pred EEEEECCCCCCccccccCCCcccccCCEEEEcccEEEcCCHHHCCCceEEEEEEE
Confidence 67777877742 34444456788899999977777788999999999887
No 69
>PF02972 Phycoerythr_ab: Phycoerythrin, alpha/beta chain; InterPro: IPR004228 Cryptophytes are unicellular photosynthetic algae that use a lumenally located light-harvesting system, which is distinct from the phycobilisome structure found in cyanobacteria and red algae. One of the key components of this system is water-soluble phycoerythrin (PE) 545 whose expression is enhanced by low light levels []. Phycoerythrin (PE) 545 is a heterodimeric of alpha(1)alpha(2)betabeta subunits. Each alpha subunit carries a covalently linked 15,16-dihydrobiliverdin chromophore that probably acts as the final energy acceptor. The architecture of the heterodimer suggests that PE 545 may dock to an acceptor protein via a deep cleft and that energy may be transferred via this intermediary protein to the reaction centre [].; GO: 0030089 phycobilisome; PDB: 1XG0_B 1QGW_B 1XF6_B.
Probab=23.89 E-value=37 Score=20.20 Aligned_cols=12 Identities=25% Similarity=0.659 Sum_probs=8.2
Q ss_pred EEEEECCCCeEE
Q 040084 98 QAHIYDETACEI 109 (127)
Q Consensus 98 ~V~If~~~~ce~ 109 (127)
.|.|||.-||++
T Consensus 4 vItiFDhRGC~r 15 (57)
T PF02972_consen 4 VITIFDHRGCDR 15 (57)
T ss_dssp EEEEEE-TT-SS
T ss_pred EEEEecccccCC
Confidence 478999999965
No 70
>cd08359 Glo_EDI_BRP_like_22 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The structures of this family demonstrate domain swapping, which is shared by glyoxalase I and antibiotic resistance proteins.
Probab=23.45 E-value=89 Score=19.64 Aligned_cols=15 Identities=20% Similarity=0.295 Sum_probs=12.5
Q ss_pred ceEEEEcCCCCEEEE
Q 040084 43 DVAHITIPNGYVWQV 57 (127)
Q Consensus 43 ~~v~L~~~~G~~W~V 57 (127)
..+.++||+|+.|.+
T Consensus 103 ~~~~~~DP~G~~ie~ 117 (119)
T cd08359 103 RHFIVRDPNGVLIDI 117 (119)
T ss_pred eEEEEECCCCCEEEE
Confidence 467889999999876
No 71
>cd02786 MopB_CT_3 The MopB_CT_3 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=23.06 E-value=2.1e+02 Score=18.27 Aligned_cols=47 Identities=17% Similarity=0.120 Sum_probs=35.1
Q ss_pred CceeccHHHHHhcccCCCceEEEEcCCCCEEEEEEEEe----CCEEEecccH
Q 040084 25 QKPRIPNKIVRKFSHELSDVAHITIPNGYVWQVKLKKE----GRKVWFDDGW 72 (127)
Q Consensus 25 ~~L~IP~~F~~~~~~~~~~~v~L~~~~G~~W~V~l~~~----~~~~~~~~GW 72 (127)
..+.|.+.=+++++-+..+.|.|.++.|+. .+.+... .+.+++..||
T Consensus 31 ~~v~i~p~dA~~lgi~~Gd~V~v~s~~G~~-~~~v~~~~~i~~g~v~~~~g~ 81 (116)
T cd02786 31 PTLLIHPADAAARGIADGDLVVVFNDRGSV-TLRAKVTDDVPPGVVVAEGGW 81 (116)
T ss_pred CEEEECHHHHHHcCCCCCCEEEEEcCCeEE-EEEEEECCCCCCCEEEeeccc
Confidence 346788888888888888999999988864 3444432 4778888886
No 72
>cd06530 S26_SPase_I The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3.4.21.89) family members are essential membrane-bound serine proteases that function to cleave the amino-terminal signal peptide extension from proteins that are translocated across biological membranes. The bacterial signal peptidase I, which is the most intensively studied, has two N-terminal transmembrane segments inserted in the plasma membrane and a hydrophilic, C-terminal catalytic region that is located in the periplasmic space. Although the bacterial signal peptidase I is monomeric, signal peptidases of eukaryotic cells commonly function as oligomeric complexes containing two divergent copies of the catalytic monomer. These are the IMP1 and IMP2 signal peptidases of the mitochondrial inner membrane that remove leader peptides from nuclear- and mitochondrial-encoded proteins. Also, two components of the endoplasmic reticulum signal peptidase in mammals (18-kDa and 21-kDa
Probab=22.84 E-value=1e+02 Score=18.65 Aligned_cols=16 Identities=19% Similarity=0.328 Sum_probs=13.9
Q ss_pred hCCCCCCEEEEEEecC
Q 040084 79 YSTFVGSLVLFEYESN 94 (127)
Q Consensus 79 ~~L~~GD~lvF~~~~~ 94 (127)
..++.||+++|+..+.
T Consensus 30 ~~~~~GDiv~~~~~~~ 45 (85)
T cd06530 30 REPKRGDVVVFKSPGD 45 (85)
T ss_pred CCCCCCCEEEEeCCCC
Confidence 5688999999999984
No 73
>TIGR02480 fliN flagellar motor switch protein FliN. Proteins that consist largely of the domain described by this model can be designated flagellar motor switch protein FliN. Longer proteins in which this region is a C-terminal domain typically are designated FliY. More distantly related sequences, outside the scope of this family, are associated with type III secretion and include the surface presentation of antigens protein SpaO required or invasion of host cells by Salmonella enterica.
Probab=22.68 E-value=86 Score=19.28 Aligned_cols=22 Identities=9% Similarity=0.069 Sum_probs=14.8
Q ss_pred HHhHhCCCCCCEEEEEEecCcE
Q 040084 75 FVEAYSTFVGSLVLFEYESNST 96 (127)
Q Consensus 75 Fv~~~~L~~GD~lvF~~~~~~~ 96 (127)
+..--+|++||++.+...-+..
T Consensus 23 l~ell~L~~Gdvi~L~~~~~~~ 44 (77)
T TIGR02480 23 LGDLLKLGEGSVIELDKLAGEP 44 (77)
T ss_pred HHHHhcCCCCCEEEcCCCCCCc
Confidence 3445678999999887543333
No 74
>COG3400 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.25 E-value=2.4e+02 Score=23.50 Aligned_cols=44 Identities=14% Similarity=0.268 Sum_probs=32.7
Q ss_pred CCCceEEEEcCCC-------------CEEEEEEEEeCCEEEecccHHHHHhHhCCCCCCEEEE
Q 040084 40 ELSDVAHITIPNG-------------YVWQVKLKKEGRKVWFDDGWQDFVEAYSTFVGSLVLF 89 (127)
Q Consensus 40 ~~~~~v~L~~~~G-------------~~W~V~l~~~~~~~~~~~GW~~Fv~~~~L~~GD~lvF 89 (127)
+.++.+.+..|.| +.|+|.+..++++++|.. ...-|+.||.++-
T Consensus 149 gkGEImEI~vp~gSifaYrhi~sI~qk~~RIvl~YRN~klll~~------~slvlqp~D~lLV 205 (471)
T COG3400 149 GKGEIMEIDVPFGSIFAYRHIGSIRQKEYRIVLLYRNDKLLLST------KSLVLQPRDILLV 205 (471)
T ss_pred ccceEEEEecCCCchhhhhhhhhhhhheeEEEEEEECCEEEEec------cceEecCCCEEEE
Confidence 3456666666666 789999999999999876 3345788888753
No 75
>PRK00809 hypothetical protein; Provisional
Probab=21.94 E-value=1.5e+02 Score=20.70 Aligned_cols=26 Identities=8% Similarity=0.111 Sum_probs=21.5
Q ss_pred EEecccHHHHHhHhCCCCCCEEEEEEec
Q 040084 66 VWFDDGWQDFVEAYSTFVGSLVLFEYES 93 (127)
Q Consensus 66 ~~~~~GW~~Fv~~~~L~~GD~lvF~~~~ 93 (127)
.-+..|=+.|.++ ++.||.++|.+.+
T Consensus 22 ~g~~~~~rn~lr~--Mk~GD~v~fYhs~ 47 (144)
T PRK00809 22 WGVPERYKNTIEK--VKPGDKLIIYVSQ 47 (144)
T ss_pred eecchhhhhHHhh--CCCCCEEEEEECC
Confidence 3457777788887 9999999999987
No 76
>PF14191 YodL: YodL-like
Probab=21.83 E-value=88 Score=20.81 Aligned_cols=34 Identities=21% Similarity=0.161 Sum_probs=26.7
Q ss_pred EEEecccHHHHHhHh-------CCCCCCEEEEEEecCcEEE
Q 040084 65 KVWFDDGWQDFVEAY-------STFVGSLVLFEYESNSTFQ 98 (127)
Q Consensus 65 ~~~~~~GW~~Fv~~~-------~L~~GD~lvF~~~~~~~F~ 98 (127)
.-.|..=|.+|-.++ .|..+|+++..-.+.+.|.
T Consensus 49 ~~~Le~iy~~FN~~~P~df~GhsLSvSDVV~l~~~g~~~~y 89 (103)
T PF14191_consen 49 TETLEDIYERFNVDHPEDFKGHSLSVSDVVELYDGGKSSFY 89 (103)
T ss_pred CCCHHHHHHHhCcCCCCCCCCCccChheEEEEEcCCceEEE
Confidence 344777788888866 9999999999988866543
No 77
>cd08315 Death_TRAILR_DR4_DR5 Death domain of Tumor necrosis factor-Related Apoptosis-Inducing Ligand Receptors. Death Domain (DD) found in Tumor necrosis factor-Related Apoptosis-Inducing Ligand (TRAIL) Receptors. In mammals, this family includes TRAILR1 (also called DR4 or TNFRSF10A) and TRAILR2 (also called DR5, TNFRSF10B, or KILLER). They function as receptors for the cytokine TRAIL and are involved in apoptosis signaling pathways. TRAIL preferentially induces apoptosis in cancer cells while exhibiting little toxicity in normal cells. 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), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=21.79 E-value=32 Score=22.43 Aligned_cols=17 Identities=12% Similarity=0.419 Sum_probs=14.9
Q ss_pred ccHHHHHhHhCCCCCCE
Q 040084 70 DGWQDFVEAYSTFVGSL 86 (127)
Q Consensus 70 ~GW~~Fv~~~~L~~GD~ 86 (127)
..|++|+...+|.++|+
T Consensus 20 ~~Wk~laR~LGLse~~I 36 (96)
T cd08315 20 DSWNRLMRQLGLSENEI 36 (96)
T ss_pred HHHHHHHHHcCCCHHHH
Confidence 57999999999998864
No 78
>PF06052 3-HAO: 3-hydroxyanthranilic acid dioxygenase; InterPro: IPR010329 Members of this protein family, from both bacteria and eukaryotes, are the enzyme 3-hydroxyanthranilate 3,4-dioxygenase (1.13.11.6 from EC). It is part of the kynurenine pathway for the degradation of tryptophan and the biosynthesis of nicotinic acid [].The prokaryotic homologue is involved in the 2-nitrobenzoate degradation pathway []. The enzyme acts on the tryptophan metabolite 3-hydroxyanthranilate and produces 2-amino-3-carboxymuconate semialdehyde, which can rearrange spontaneously to quinolinic acid and feed into nicotinamide biosynthesis, or undergo further enzymatic degradation.; GO: 0000334 3-hydroxyanthranilate 3,4-dioxygenase activity, 0005506 iron ion binding, 0008152 metabolic process, 0055114 oxidation-reduction process; PDB: 1ZVF_A 1YFX_A 1YFW_A 1YFY_A 1YFU_A 2QNK_A 3FE5_A.
Probab=21.67 E-value=64 Score=23.10 Aligned_cols=25 Identities=4% Similarity=0.113 Sum_probs=18.6
Q ss_pred HhHhCCCCCCEEEEEEecCcEEEEE
Q 040084 76 VEAYSTFVGSLVLFEYESNSTFQAH 100 (127)
Q Consensus 76 v~~~~L~~GD~lvF~~~~~~~F~V~ 100 (127)
.+||++.+|+-+.+++.|++.++|.
T Consensus 45 R~DyHine~eE~FyQ~kG~m~Lkv~ 69 (151)
T PF06052_consen 45 RTDYHINETEEFFYQLKGDMCLKVV 69 (151)
T ss_dssp -SSEEE-SS-EEEEEEES-EEEEEE
T ss_pred CCccccCCcceEEEEEeCcEEEEEE
Confidence 4688899999999999999988855
No 79
>cd08354 Glo_EDI_BRP_like_13 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping.
Probab=21.54 E-value=1e+02 Score=19.31 Aligned_cols=17 Identities=12% Similarity=0.235 Sum_probs=13.7
Q ss_pred CceEEEEcCCCCEEEEE
Q 040084 42 SDVAHITIPNGYVWQVK 58 (127)
Q Consensus 42 ~~~v~L~~~~G~~W~V~ 58 (127)
...+.+.||+|..|++.
T Consensus 104 ~~~~~~~DP~G~~ie~~ 120 (122)
T cd08354 104 GRSLYFRDPDGNLLELA 120 (122)
T ss_pred eeEEEEECCCCCEEEEe
Confidence 35788999999988874
No 80
>COG3607 Predicted lactoylglutathione lyase [General function prediction only]
Probab=21.15 E-value=1.1e+02 Score=21.47 Aligned_cols=17 Identities=24% Similarity=0.442 Sum_probs=14.0
Q ss_pred eEEEEcCCCCEEEEEEE
Q 040084 44 VAHITIPNGYVWQVKLK 60 (127)
Q Consensus 44 ~v~L~~~~G~~W~V~l~ 60 (127)
-...+||+|..|++.+.
T Consensus 111 g~~fqDpDGh~wE~l~m 127 (133)
T COG3607 111 GRSFQDPDGHVWEFLWM 127 (133)
T ss_pred ceeeeCCCCCeEEEEEe
Confidence 35688999999998874
No 81
>PF03221 HTH_Tnp_Tc5: Tc5 transposase DNA-binding domain; InterPro: IPR006600 This entry represents a DNA-binding helix-turn-helix domain found in the pogo family of transposable elements, the centromere protein Cenp-B, and yeast PCD2. There is extensive sequence similarity between Cenp-B and transposase proteins encoded by the pogo superfamily of transposable elements, which includes the human Tigger and Jerky elements []. The HTH domain is composed of three alpha-helices, with the second and third helices connected via a turn comprise the helix-turn-helix motif. Helix 3 is termed the recognition helix as it binds the DNA major groove, as in other HTHs []. This conserved DNA-binding domain is found in the following proteins: Cenp-B (major centromere autoantigen B or centromere protein B), which appears to organise arrays of centromere satellite DNA into a higher order structure that then direct centromere formation and kinetochore assembly in mammalian chromosomes. The N terminus of Cenp-B contains two DNA-binding HTH domains, which bind to adjacent major grooves of DNA: a psq-type HTH domain followed by a CenpB-type HTH domain, which together bind specifically to the Cenp-B box, which occurs in alpha-satellite DNA in human centromeres []. Pogo family transposable elements includes both Tigger and Jerky elements []. Pogo contains two open reading frames flanked by inverted repeats. The N-terminal region of pogo transposase contains a Cenp-B-type HTH DNA-binding domain []. Mammalian jerky protein, involved in epileptic seizures in mice []. PDC2 (Pyruvate DeCarboxylase 2), which is a transcription factor required for the synthesis of the glycolytic enzyme pyruvate decarboxylase, required for high level expression of both the THI and the PDC genes. PDC2 may be important for a high basal level of PDC gene expression or play a positive role in the autoregulation control of PDC1 and PDC5 [, ]. ; PDB: 1HLV_A 1IUF_A.
Probab=20.81 E-value=58 Score=18.67 Aligned_cols=20 Identities=15% Similarity=0.318 Sum_probs=10.7
Q ss_pred CEEEecccH-HHHHhHhCCCC
Q 040084 64 RKVWFDDGW-QDFVEAYSTFV 83 (127)
Q Consensus 64 ~~~~~~~GW-~~Fv~~~~L~~ 83 (127)
....++.|| ..|.+.|+|..
T Consensus 44 ~~~~~s~~W~~~F~~Rh~i~~ 64 (66)
T PF03221_consen 44 PEFKASKGWLDRFKKRHGIKL 64 (66)
T ss_dssp TT-S--CHHHHHHHHHTS---
T ss_pred CcCCcccHHHHHHHHHcCCCC
Confidence 345578999 55999998763
No 82
>PRK06724 hypothetical protein; Provisional
Probab=20.78 E-value=1.3e+02 Score=20.04 Aligned_cols=17 Identities=24% Similarity=0.417 Sum_probs=13.8
Q ss_pred ceEEEEcCCCCEEEEEE
Q 040084 43 DVAHITIPNGYVWQVKL 59 (127)
Q Consensus 43 ~~v~L~~~~G~~W~V~l 59 (127)
..+.++||+|+.|++..
T Consensus 106 ~~~~f~DPdG~~iEl~~ 122 (128)
T PRK06724 106 YTIDFYDPNGFIIEVAY 122 (128)
T ss_pred EEEEEECCCCCEEEEEe
Confidence 35678999999998865
No 83
>cd07252 BphC1-RGP6_N_like N-terminal domain of 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC, EC 1.13.11.39) 1 from Rhodococcus globerulus P6 (BphC1-RGP6) and similar proteins. This subfamily contains the N-terminal, non-catalytic, domain of BphC1-RGP6 and similar proteins. BphC catalyzes the extradiol ring cleavage reaction of 2,3-dihydroxybiphenyl, the third step in the polychlorinated biphenyls (PCBs) degradation pathway (bph pathway). This subfamily of BphCs belongs to the type I extradiol dioxygenase family, which require a metal in the active site in its catalytic mechanism. Polychlorinated biphenyl degrading bacteria demonstrate a multiplicity of 2,3-dihydroxybiphenyl 1,2-dioxygenases. For example, three types of BphC enzymes have been found in Rhodococcus globerulus (BphC1-RGP6 - BphC3-RGP6), all three enzymes are type I extradiol dioxygenases. BphC1-RGP6 has an internal duplication, it is a two-domain dioxygenase which forms octamers, and has Fe(II) at the catalytic site. Its N-
Probab=20.78 E-value=1.3e+02 Score=19.14 Aligned_cols=17 Identities=12% Similarity=0.222 Sum_probs=14.5
Q ss_pred ceEEEEcCCCCEEEEEE
Q 040084 43 DVAHITIPNGYVWQVKL 59 (127)
Q Consensus 43 ~~v~L~~~~G~~W~V~l 59 (127)
..+.++||+|+.|++..
T Consensus 100 ~~~~~~DPdG~~iE~~~ 116 (120)
T cd07252 100 GLIRFADPDGNRHELFW 116 (120)
T ss_pred EEEEEECCCCCEEEEEe
Confidence 46899999999998876
No 84
>PF11604 CusF_Ec: Copper binding periplasmic protein CusF; InterPro: IPR021647 CusF is a periplasmic protein involved in copper and silver resistance in Escherichia coil. CusF forms a five-stranded beta-barrel OB fold. Cu(I) binds to H36, M47 and M49 which are conserved residues in the protein []. ; PDB: 2L55_A 2VB3_X 1ZEQ_X 2QCP_X 3E6Z_X 2VB2_X.
Probab=20.66 E-value=1.8e+02 Score=17.50 Aligned_cols=24 Identities=17% Similarity=0.252 Sum_probs=15.7
Q ss_pred HhCCCCCCEEEEEEec--CcEEEEEE
Q 040084 78 AYSTFVGSLVLFEYES--NSTFQAHI 101 (127)
Q Consensus 78 ~~~L~~GD~lvF~~~~--~~~F~V~I 101 (127)
-.+|+.||.+.|.+.. +..+.|.-
T Consensus 40 l~~l~~Gd~V~F~~~~~~~~~~~I~~ 65 (70)
T PF11604_consen 40 LAGLKPGDKVRFTFERTDDGSYVITA 65 (70)
T ss_dssp ESS-STT-EEEEEEEEETTCEEEEEE
T ss_pred hhcCCCCCEEEEEEEECCCCcEEEEE
Confidence 3578999999999986 23366553
No 85
>cd00175 SNc Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds.
Probab=20.60 E-value=1.9e+02 Score=18.94 Aligned_cols=33 Identities=12% Similarity=0.137 Sum_probs=27.5
Q ss_pred CCCCCEEEEEEecCcEEEEEEECCCCeEEecCC
Q 040084 81 TFVGSLVLFEYESNSTFQAHIYDETACEINYPS 113 (127)
Q Consensus 81 L~~GD~lvF~~~~~~~F~V~If~~~~ce~~~~~ 113 (127)
+..||.+.+...+.....|.+.+-+..|...++
T Consensus 2 V~dGDt~~v~~~~~~~~~vrL~gId~Pe~~~~~ 34 (129)
T cd00175 2 VIDGDTIRVRLPPGPLITVRLSGIDAPETARPN 34 (129)
T ss_pred eecCcEEEEEeCCCCEEEEEEEeecCccccCCc
Confidence 457999999888777889999998888887665
No 86
>cd07251 Glo_EDI_BRP_like_10 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping.
Probab=20.52 E-value=1.3e+02 Score=18.68 Aligned_cols=17 Identities=24% Similarity=0.497 Sum_probs=13.8
Q ss_pred ceEEEEcCCCCEEEEEE
Q 040084 43 DVAHITIPNGYVWQVKL 59 (127)
Q Consensus 43 ~~v~L~~~~G~~W~V~l 59 (127)
..+.+.||+|+.|.+..
T Consensus 104 ~~~~~~DP~Gn~iei~~ 120 (121)
T cd07251 104 YSGYFADPDGHLWEVAH 120 (121)
T ss_pred eEEEEECCCCCEEEEee
Confidence 46889999999998754
No 87
>cd08361 PpCmtC_N N-terminal domain of 2,3-dihydroxy-p-cumate-3,4-dioxygenase (PpCmtC). This subfamily contains the N-terminal, non-catalytic, domain of PpCmtC. 2,3-dihydroxy-p-cumate-3,4-dioxygenase (CmtC of Pseudomonas putida F1) is a dioxygenase involved in the eight-step catabolism pathway of p-cymene. CmtC acts upon the reaction intermediate 2,3-dihydroxy-p-cumate, yielding 2-hydroxy-3-carboxy-6-oxo-7-methylocta-2,4-dienoate. The CmtC belongs to the type I family of extradiol dioxygenases. Fe2+ was suggested as a cofactor, same as other enzymes in the family. The type I family of extradiol dioxygenases contains two structurally homologous barrel-shaped domains at the N- and C-terminal. The active-site metal is located in the C-terminal barrel and plays an essential role in the catalytic mechanism.
Probab=20.34 E-value=1.4e+02 Score=19.36 Aligned_cols=17 Identities=12% Similarity=0.251 Sum_probs=14.2
Q ss_pred eEEEEcCCCCEEEEEEE
Q 040084 44 VAHITIPNGYVWQVKLK 60 (127)
Q Consensus 44 ~v~L~~~~G~~W~V~l~ 60 (127)
.+.+.||+|+.|++...
T Consensus 103 ~~~f~DPdG~~iE~~~~ 119 (124)
T cd08361 103 FIAFRDPSGNSIELVVR 119 (124)
T ss_pred EEEEECcCCCEEEEEEe
Confidence 47899999999988653
No 88
>PF02643 DUF192: Uncharacterized ACR, COG1430; InterPro: IPR003795 This entry describes proteins of unknown function.; PDB: 3M7A_B 3PJY_B.
Probab=20.30 E-value=76 Score=20.89 Aligned_cols=20 Identities=35% Similarity=0.596 Sum_probs=11.4
Q ss_pred ecccHHHHHhHhCCCCCCEEEEE
Q 040084 68 FDDGWQDFVEAYSTFVGSLVLFE 90 (127)
Q Consensus 68 ~~~GW~~Fv~~~~L~~GD~lvF~ 90 (127)
+..|| +..++|+.||.+.|+
T Consensus 88 ~~aG~---~~~~~i~~Gd~v~~~ 107 (108)
T PF02643_consen 88 LPAGW---FEKLGIKVGDRVRIE 107 (108)
T ss_dssp EETTH---HHHHT--TT-EEE--
T ss_pred cCCCc---hhhcCCCCCCEEEec
Confidence 35554 678999999999875
No 89
>PRK08433 flagellar motor switch protein; Validated
Probab=20.07 E-value=1.1e+02 Score=20.69 Aligned_cols=27 Identities=15% Similarity=0.171 Sum_probs=17.5
Q ss_pred HHHhHhCCCCCCEEEEEEecCcEEEEE
Q 040084 74 DFVEAYSTFVGSLVLFEYESNSTFQAH 100 (127)
Q Consensus 74 ~Fv~~~~L~~GD~lvF~~~~~~~F~V~ 100 (127)
.+..--+|++||++.+...-+....|.
T Consensus 46 tl~dlL~Lq~GDVI~Ld~~~~e~v~v~ 72 (111)
T PRK08433 46 SLLEILKFEKGSVIDLEKPAGESVELY 72 (111)
T ss_pred cHHHHhCCCCCCEEEeCCCCCCCEEEE
Confidence 345567899999999876543333333
No 90
>cd07247 SgaA_N_like N-terminal domain of Streptomyces griseus SgaA (suppression of growth disturbance caused by A-factor at a high concentration under high osmolality during early growth phase), and similar domains. SgaA suppresses the growth disturbances caused by high osmolarity and a high concentration of A-factor, a microbial hormone, during the early growth phase in Streptomyces griseus. A-factor (2-isocapryloyl-3R-hydroxymethyl-gamma-butyrolactone) controls morphological differentiation and secondary metabolism in Streptomyces griseus. It is a chemical signaling molecule that at a very low concentration acts as a switch for yellow pigment production, aerial mycelium formation, streptomycin production, and streptomycin resistance. The structure and amino acid sequence of SgaA are closely related to a group of antibiotics resistance proteins, including bleomycin resistance protein, mitomycin resistance protein, and fosfomycin resistance proteins. SgaA might also function as a strep
Probab=20.07 E-value=1.2e+02 Score=18.93 Aligned_cols=15 Identities=27% Similarity=0.417 Sum_probs=12.0
Q ss_pred ceEEEEcCCCCEEEE
Q 040084 43 DVAHITIPNGYVWQV 57 (127)
Q Consensus 43 ~~v~L~~~~G~~W~V 57 (127)
..+.+.||+|+.|.+
T Consensus 98 ~~~~~~DPdG~~~~l 112 (114)
T cd07247 98 RFAVFADPEGAVFGL 112 (114)
T ss_pred EEEEEECCCCCEEEe
Confidence 467888899988876
Done!