Query 043432
Match_columns 105
No_of_seqs 106 out of 350
Neff 6.7
Searched_HMMs 46136
Date Fri Mar 29 05:01:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043432.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043432hhsearch_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 99.8 5.8E-20 1.2E-24 118.7 11.2 86 11-101 1-87 (100)
2 PF03754 DUF313: Domain of unk 99.1 4.9E-10 1.1E-14 75.6 6.9 78 6-84 19-113 (114)
3 PF09217 EcoRII-N: Restriction 98.6 2.7E-07 5.9E-12 64.9 7.2 88 9-97 8-110 (156)
4 cd06919 Asp_decarbox Aspartate 93.9 1.2 2.6E-05 30.0 8.9 77 11-98 10-88 (111)
5 PRK05449 aspartate alpha-decar 93.9 1.1 2.4E-05 30.7 9.0 76 12-98 12-89 (126)
6 TIGR00223 panD L-aspartate-alp 93.6 1.2 2.7E-05 30.5 8.8 76 12-98 12-89 (126)
7 PF02261 Asp_decarbox: Asparta 92.7 2.2 4.7E-05 28.9 9.3 77 10-97 10-88 (116)
8 PF10844 DUF2577: Protein of u 92.5 0.32 6.8E-06 31.7 4.5 75 8-105 18-94 (100)
9 PF14250 AbrB-like: AbrB-like 81.5 4.6 0.0001 25.0 4.4 39 55-98 25-63 (71)
10 PF04014 Antitoxin-MazE: Antid 78.1 4.2 9.1E-05 22.5 3.3 22 80-101 13-34 (47)
11 PF03120 DNA_ligase_OB: NAD-de 77.8 2.3 4.9E-05 27.0 2.3 21 80-100 42-62 (82)
12 PRK09570 rpoH DNA-directed RNA 77.6 3.3 7.2E-05 26.2 3.0 26 80-105 44-70 (79)
13 COG0853 PanD Aspartate 1-decar 76.2 22 0.00048 24.4 7.9 78 10-98 9-88 (126)
14 PF09853 DUF2080: Putative tra 74.9 4.9 0.00011 23.6 3.0 31 3-35 10-42 (53)
15 cd04459 Rho_CSD Rho_CSD: Rho p 66.7 4.5 9.7E-05 24.8 1.7 18 80-97 33-50 (68)
16 PRK03760 hypothetical protein; 65.9 22 0.00048 23.7 5.1 29 70-98 88-116 (117)
17 PF12195 End_beta_barrel: Beta 59.3 7.2 0.00016 24.7 1.6 21 83-103 23-43 (83)
18 COG5569 Uncharacterized conser 58.3 7.4 0.00016 25.8 1.7 22 83-104 79-100 (108)
19 PRK11507 ribosome-associated p 56.3 8.3 0.00018 23.8 1.6 19 78-96 43-61 (70)
20 PF02643 DUF192: Uncharacteriz 56.2 50 0.0011 21.4 5.4 25 72-96 82-106 (108)
21 COG3466 ISA1214 Putative trans 56.0 9.5 0.00021 22.2 1.7 29 4-34 14-42 (52)
22 TIGR02609 doc_partner putative 54.5 31 0.00067 21.0 4.0 33 64-100 4-36 (74)
23 TIGR01439 lp_hng_hel_AbrB loop 53.0 24 0.00053 18.4 3.0 20 80-99 13-32 (43)
24 PF14453 ThiS-like: ThiS-like 52.6 13 0.00028 22.0 1.9 16 84-99 41-56 (57)
25 PF01878 EVE: EVE domain; Int 51.5 10 0.00022 25.5 1.6 15 86-100 38-52 (143)
26 PF07497 Rho_RNA_bind: Rho ter 50.9 11 0.00023 23.7 1.5 15 81-95 36-50 (78)
27 PF13275 S4_2: S4 domain; PDB: 50.6 7.1 0.00015 23.7 0.6 20 77-96 38-57 (65)
28 PF01191 RNA_pol_Rpb5_C: RNA p 50.5 21 0.00046 22.2 2.7 23 80-102 41-63 (74)
29 PF14604 SH3_9: Variant SH3 do 50.2 14 0.0003 20.6 1.8 19 85-103 12-30 (49)
30 TIGR01643 YD_repeat_2x YD repe 49.9 31 0.00066 18.0 3.1 22 44-66 4-25 (42)
31 COG4043 Preprotein translocase 49.1 14 0.00029 24.7 1.8 19 80-98 26-44 (111)
32 TIGR03595 Obg_CgtA_exten Obg f 48.6 16 0.00035 22.1 2.0 20 78-97 44-63 (69)
33 COG1977 MoaD Molybdopterin con 48.0 16 0.00035 22.7 2.0 19 85-103 66-84 (84)
34 COG2002 AbrB Regulators of sta 48.0 29 0.00063 21.8 3.2 23 81-103 21-43 (89)
35 cd06555 ASCH_PF0470_like ASC-1 46.8 16 0.00034 24.3 1.9 14 86-99 30-43 (109)
36 PF07076 DUF1344: Protein of u 46.3 25 0.00054 21.2 2.5 20 85-104 35-54 (61)
37 PRK06461 single-stranded DNA-b 46.1 60 0.0013 21.8 4.7 33 46-97 42-74 (129)
38 cd00989 PDZ_metalloprotease PD 45.4 17 0.00037 21.3 1.7 14 83-96 25-38 (79)
39 PRK01777 hypothetical protein; 45.3 16 0.00035 23.6 1.7 14 85-98 62-75 (95)
40 PRK11347 antitoxin ChpS; Provi 44.6 69 0.0015 20.1 4.5 35 62-100 4-38 (83)
41 PRK06488 sulfur carrier protei 43.2 28 0.0006 20.3 2.4 18 86-103 48-65 (65)
42 PRK06944 sulfur carrier protei 42.8 28 0.0006 20.1 2.3 17 87-103 49-65 (65)
43 cd04498 hPOT1_OB2 hPOT1_OB2: A 42.3 26 0.00056 23.9 2.4 16 80-97 71-86 (123)
44 PF05593 RHS_repeat: RHS Repea 42.0 52 0.0011 17.1 3.2 21 44-65 4-24 (38)
45 cd01756 PLAT_repeat PLAT/LH2 d 41.6 50 0.0011 21.6 3.7 48 18-69 59-106 (120)
46 PRK00809 hypothetical protein; 41.6 24 0.00053 24.4 2.3 18 81-100 30-47 (144)
47 smart00532 LIGANc Ligase N fam 41.4 29 0.00063 28.4 3.0 20 80-99 355-374 (441)
48 PLN03111 DNA-directed RNA poly 41.3 35 0.00076 25.3 3.1 26 80-105 173-199 (206)
49 PF14478 DUF4430: Domain of un 41.3 10 0.00022 22.6 0.2 17 81-97 52-68 (68)
50 PF11792 Baculo_LEF5_C: Baculo 41.1 5.7 0.00012 22.3 -0.8 13 83-95 19-31 (43)
51 PF09269 DUF1967: Domain of un 40.9 27 0.00058 21.1 2.1 20 78-97 44-63 (69)
52 cd01764 Urm1 Urm1-like ubuitin 40.6 26 0.00055 22.4 2.1 19 85-103 76-94 (94)
53 PTZ00061 DNA-directed RNA poly 40.2 36 0.00079 25.2 3.1 26 80-105 172-198 (205)
54 cd01752 PLAT_polycystin PLAT/L 40.1 38 0.00082 22.2 2.9 22 47-68 84-105 (120)
55 TIGR02219 phage_NlpC_fam putat 39.9 20 0.00043 24.2 1.6 15 83-97 72-86 (134)
56 PRK05659 sulfur carrier protei 39.8 31 0.00068 19.9 2.3 18 86-103 49-66 (66)
57 cd00565 ThiS ThiaminS ubiquiti 39.7 34 0.00073 19.9 2.4 17 87-103 49-65 (65)
58 smart00326 SH3 Src homology 3 39.5 40 0.00086 17.8 2.6 18 85-102 18-35 (58)
59 PRK05863 sulfur carrier protei 39.1 34 0.00074 20.1 2.4 16 88-103 50-65 (65)
60 PRK14699 replication factor A; 38.9 1.5E+02 0.0032 24.6 6.7 36 47-96 97-132 (484)
61 cd00991 PDZ_archaeal_metallopr 38.7 24 0.00053 21.1 1.7 13 84-96 24-36 (79)
62 smart00536 AXH domain in Ataxi 38.4 17 0.00036 24.6 1.0 26 71-96 76-112 (116)
63 cd01757 PLAT_RAB6IP1 PLAT/LH2 37.7 39 0.00085 22.5 2.7 21 47-67 75-95 (114)
64 cd00174 SH3 Src homology 3 dom 37.5 45 0.00098 17.4 2.6 19 85-103 15-33 (54)
65 smart00306 HintN Hint (Hedgeho 37.5 30 0.00065 21.0 2.0 15 82-96 84-98 (100)
66 PRK11130 moaD molybdopterin sy 37.3 31 0.00067 21.0 2.1 19 85-103 63-81 (81)
67 cd01234 PH_CADPS CADPS (Ca2+-d 36.7 17 0.00037 24.5 0.8 17 86-102 81-97 (117)
68 PRK02268 hypothetical protein; 36.7 26 0.00057 24.4 1.8 13 86-98 34-46 (141)
69 cd05829 Sortase_E Sortase E (S 36.5 42 0.00092 22.8 2.8 27 72-98 50-83 (144)
70 PF13180 PDZ_2: PDZ domain; PD 36.4 21 0.00045 21.5 1.1 13 83-95 27-39 (82)
71 TIGR01683 thiS thiamine biosyn 36.1 41 0.0009 19.5 2.4 17 87-103 48-64 (64)
72 PRK08053 sulfur carrier protei 36.0 41 0.00089 19.7 2.4 17 87-103 50-66 (66)
73 PF01568 Molydop_binding: Moly 35.9 32 0.0007 21.5 2.0 19 81-99 37-55 (110)
74 PRK06437 hypothetical protein; 35.7 40 0.00087 20.0 2.3 20 84-103 48-67 (67)
75 PF03658 Ub-RnfH: RnfH family 35.7 25 0.00055 22.4 1.5 14 85-98 59-72 (84)
76 TIGR00686 phnA alkylphosphonat 35.3 33 0.00072 23.0 2.0 14 86-99 49-62 (109)
77 PF00018 SH3_1: SH3 domain; I 34.4 35 0.00076 18.5 1.8 18 85-102 13-30 (48)
78 cd00136 PDZ PDZ domain, also c 34.4 33 0.00071 19.5 1.8 13 84-96 27-39 (70)
79 COG2012 RPB5 DNA-directed RNA 33.7 52 0.0011 20.8 2.6 21 81-101 48-68 (80)
80 PRK08364 sulfur carrier protei 33.2 42 0.0009 20.0 2.1 19 85-103 52-70 (70)
81 PF08922 DUF1905: Domain of un 33.1 1.2E+02 0.0026 18.6 8.3 79 11-97 1-79 (80)
82 PTZ00194 60S ribosomal protein 33.0 31 0.00068 24.2 1.7 23 82-104 41-63 (143)
83 PRK06033 hypothetical protein; 32.8 33 0.00072 21.5 1.7 15 84-98 24-38 (83)
84 cd00990 PDZ_glycyl_aminopeptid 32.8 34 0.00073 20.0 1.7 13 83-95 25-37 (80)
85 PF11604 CusF_Ec: Copper bindi 32.7 31 0.00067 20.8 1.5 17 84-100 39-55 (70)
86 PRK08097 ligB NAD-dependent DN 32.4 47 0.001 28.1 2.9 22 78-99 350-371 (562)
87 TIGR02988 YaaA_near_RecF S4 do 32.3 33 0.00072 19.6 1.5 12 85-96 47-58 (59)
88 COG2501 S4-like RNA binding pr 32.2 25 0.00055 21.9 1.0 16 81-96 46-61 (73)
89 PF02298 Cu_bind_like: Plastoc 32.0 30 0.00066 21.6 1.4 21 80-100 11-31 (85)
90 PF03831 PhnA: PhnA protein; 31.6 14 0.00031 21.9 -0.2 15 85-99 7-21 (56)
91 PF07680 DoxA: TQO small subun 31.5 71 0.0015 22.1 3.2 40 24-64 90-132 (133)
92 PRK01191 rpl24p 50S ribosomal 31.3 38 0.00083 23.0 1.9 23 82-104 40-62 (120)
93 PRK07956 ligA NAD-dependent DN 31.2 51 0.0011 28.4 3.0 20 80-99 360-379 (665)
94 PF01477 PLAT: PLAT/LH2 domain 31.0 1.1E+02 0.0023 19.0 3.9 24 47-70 80-103 (113)
95 PF07591 PT-HINT: Pretoxin HIN 31.0 22 0.00048 23.9 0.7 16 81-96 70-85 (130)
96 PF10377 ATG11: Autophagy-rela 30.8 53 0.0012 22.2 2.5 22 82-103 37-58 (129)
97 PF04225 OapA: Opacity-associa 30.8 41 0.0009 21.1 1.9 16 86-101 41-56 (85)
98 cd00992 PDZ_signaling PDZ doma 30.6 39 0.00086 19.6 1.7 15 83-97 39-53 (82)
99 PF11948 DUF3465: Protein of u 30.1 41 0.00089 23.3 1.8 53 43-97 41-95 (131)
100 TIGR00638 Mop molybdenum-pteri 30.0 63 0.0014 18.4 2.5 21 80-100 41-61 (69)
101 PF08797 HIRAN: HIRAN domain; 30.0 49 0.0011 21.0 2.2 21 82-102 17-37 (107)
102 smart00228 PDZ Domain present 29.9 42 0.0009 19.5 1.7 14 83-96 39-52 (85)
103 COG0272 Lig NAD-dependent DNA 29.8 53 0.0011 28.5 2.8 20 80-99 360-379 (667)
104 PRK14350 ligA NAD-dependent DN 29.7 55 0.0012 28.3 2.9 20 80-99 357-376 (669)
105 COG1917 Uncharacterized conser 29.6 23 0.0005 23.2 0.6 25 74-99 69-97 (131)
106 TIGR00575 dnlj DNA ligase, NAD 29.6 56 0.0012 28.0 3.0 20 80-99 348-367 (652)
107 cd00986 PDZ_LON_protease PDZ d 29.2 39 0.00084 20.0 1.5 10 87-96 24-33 (79)
108 cd02790 MopB_CT_Formate-Dh_H F 29.2 53 0.0011 20.7 2.2 19 81-99 42-60 (116)
109 PRK08577 hypothetical protein; 29.2 69 0.0015 21.4 2.9 25 80-104 19-43 (136)
110 PLN02799 Molybdopterin synthas 29.1 50 0.0011 19.9 2.0 19 85-103 64-82 (82)
111 TIGR01682 moaD molybdopterin c 29.0 52 0.0011 19.8 2.1 19 85-103 62-80 (80)
112 PF01052 SpoA: Surface present 29.0 37 0.0008 20.3 1.4 15 85-99 26-40 (77)
113 PLN02311 chalcone isomerase 28.6 68 0.0015 24.7 3.0 24 78-101 192-215 (271)
114 PRK14725 pyruvate kinase; Prov 28.5 91 0.002 26.8 4.0 57 43-100 270-347 (608)
115 cd02779 MopB_CT_Arsenite-Ox Th 28.3 56 0.0012 20.9 2.2 19 81-99 40-58 (115)
116 PLN00212 glutelin; Provisional 28.3 42 0.00092 28.0 2.0 57 37-96 340-405 (493)
117 COG1430 Uncharacterized conser 28.1 62 0.0014 22.1 2.5 29 72-100 95-123 (126)
118 cd00754 MoaD Ubiquitin domain 28.0 55 0.0012 19.3 2.0 20 84-103 61-80 (80)
119 cd04491 SoSSB_OBF SoSSB_OBF: A 28.0 1.4E+02 0.003 17.8 4.7 34 46-97 25-58 (82)
120 cd05828 Sortase_D_4 Sortase D 27.9 66 0.0014 21.2 2.6 28 72-99 44-73 (127)
121 PRK14351 ligA NAD-dependent DN 27.9 62 0.0013 28.1 2.9 20 80-99 382-401 (689)
122 cd02775 MopB_CT Molybdopterin- 27.9 58 0.0013 19.8 2.2 20 81-100 30-49 (101)
123 PF02938 GAD: GAD domain; Int 27.8 63 0.0014 20.3 2.4 28 73-100 59-87 (95)
124 cd00988 PDZ_CTP_protease PDZ d 27.1 50 0.0011 19.5 1.7 13 84-96 27-39 (85)
125 smart00739 KOW KOW (Kyprides, 26.9 80 0.0017 14.6 2.6 16 88-103 2-17 (28)
126 cd00987 PDZ_serine_protease PD 26.7 49 0.0011 19.6 1.7 14 83-96 37-50 (90)
127 KOG3218 RNA polymerase, 25-kDa 26.6 69 0.0015 23.8 2.6 31 75-105 170-201 (208)
128 PRK08433 flagellar motor switc 26.6 48 0.001 22.1 1.7 14 85-98 50-63 (111)
129 PF07237 DUF1428: Protein of u 26.5 54 0.0012 21.7 1.9 21 79-99 50-70 (103)
130 PRK10220 hypothetical protein; 26.4 58 0.0013 21.9 2.0 14 86-99 50-63 (111)
131 TIGR02480 fliN flagellar motor 26.2 46 0.001 20.2 1.4 14 85-98 26-39 (77)
132 PF02597 ThiS: ThiS family; I 26.0 40 0.00087 19.7 1.1 19 85-103 59-77 (77)
133 PF08541 ACP_syn_III_C: 3-Oxoa 25.8 59 0.0013 19.7 1.9 21 79-99 57-77 (90)
134 TIGR01687 moaD_arch MoaD famil 25.5 65 0.0014 19.6 2.1 18 86-103 71-88 (88)
135 PF00313 CSD: 'Cold-shock' DNA 25.4 1.2E+02 0.0026 17.4 3.1 28 76-103 27-56 (66)
136 cd02787 MopB_CT_ydeP The MopB_ 25.4 87 0.0019 19.8 2.7 23 78-101 36-58 (112)
137 PF11520 Cren7: Chromatin prot 25.3 44 0.00094 20.0 1.1 17 89-105 34-50 (60)
138 cd02778 MopB_CT_Thiosulfate-R- 25.3 85 0.0018 20.0 2.7 20 81-100 37-56 (123)
139 cd00508 MopB_CT_Fdh-Nap-like T 25.2 68 0.0015 20.2 2.2 19 81-99 42-60 (120)
140 PF01272 GreA_GreB: Transcript 25.1 1.6E+02 0.0035 17.6 6.0 55 44-98 8-63 (77)
141 PRK07440 hypothetical protein; 25.0 77 0.0017 19.0 2.3 17 87-103 54-70 (70)
142 smart00308 LH2 Lipoxygenase ho 25.0 1.1E+02 0.0024 19.0 3.2 21 47-67 82-102 (105)
143 cd02786 MopB_CT_3 The MopB_CT_ 24.9 66 0.0014 20.3 2.1 20 81-100 38-57 (116)
144 PF13123 DUF3978: Protein of u 24.9 77 0.0017 22.1 2.5 50 4-53 49-100 (145)
145 COG4519 Uncharacterized protei 24.4 1.1E+02 0.0024 19.6 3.0 30 44-85 49-78 (95)
146 cd02791 MopB_CT_Nitrate-R-NapA 24.3 69 0.0015 20.4 2.1 20 81-100 42-61 (122)
147 PRK10838 spr outer membrane li 24.3 48 0.0011 24.0 1.5 16 82-97 123-138 (190)
148 PF02887 PK_C: Pyruvate kinase 24.2 1.3E+02 0.0028 19.3 3.4 21 79-99 80-101 (117)
149 cd02792 MopB_CT_Formate-Dh-Na- 24.1 75 0.0016 20.2 2.3 19 81-99 42-60 (122)
150 cd04458 CSP_CDS Cold-Shock Pro 24.1 1.5E+02 0.0033 16.9 4.5 25 79-103 30-56 (65)
151 PRK07696 sulfur carrier protei 24.1 83 0.0018 18.6 2.3 17 87-103 51-67 (67)
152 TIGR03784 marine_sortase sorta 24.0 75 0.0016 22.6 2.4 30 71-100 90-121 (174)
153 PRK06083 sulfur carrier protei 23.8 82 0.0018 19.8 2.3 18 86-103 67-84 (84)
154 PF07653 SH3_2: Variant SH3 do 23.7 67 0.0014 17.8 1.7 13 85-97 15-27 (55)
155 cd02781 MopB_CT_Acetylene-hydr 23.7 75 0.0016 20.6 2.2 20 81-100 40-59 (130)
156 PF12519 DUF3722: Protein of u 23.4 1.3E+02 0.0029 23.0 3.8 14 23-36 88-101 (260)
157 PRK09838 periplasmic copper-bi 23.1 77 0.0017 21.2 2.2 18 84-101 85-102 (115)
158 PF00278 Orn_DAP_Arg_deC: Pyri 23.1 59 0.0013 20.5 1.6 12 87-98 82-93 (116)
159 PF15057 DUF4537: Domain of un 22.7 66 0.0014 21.6 1.8 21 85-105 53-73 (124)
160 PRK09798 antitoxin MazE; Provi 22.6 2E+02 0.0044 17.9 4.1 33 63-99 6-38 (82)
161 PF02431 Chalcone: Chalcone-fl 22.5 63 0.0014 23.0 1.8 23 80-102 121-144 (199)
162 PF12436 USP7_ICP0_bdg: ICP0-b 22.5 68 0.0015 23.9 2.0 15 85-99 138-152 (249)
163 PF00595 PDZ: PDZ domain (Also 22.4 51 0.0011 19.5 1.1 12 85-96 40-51 (81)
164 COG2208 RsbU Serine phosphatas 22.4 49 0.0011 25.7 1.3 22 78-99 283-304 (367)
165 TIGR01080 rplX_A_E ribosomal p 22.2 67 0.0015 21.5 1.7 22 83-104 37-58 (114)
166 KOG4146 Ubiquitin-like protein 22.1 93 0.002 20.4 2.3 17 83-99 81-97 (101)
167 COG2824 PhnA Uncharacterized Z 22.1 63 0.0014 21.7 1.5 14 86-99 51-64 (112)
168 KOG1765 Regulator of ribosome 22.1 50 0.0011 23.9 1.2 62 37-105 60-121 (181)
169 cd04497 hPOT1_OB1_like hPOT1_O 22.0 1.7E+02 0.0036 19.7 3.7 11 88-98 69-79 (138)
170 PRK11479 hypothetical protein; 21.8 56 0.0012 25.2 1.5 17 81-97 58-74 (274)
171 PF02080 TrkA_C: TrkA-C domain 21.7 44 0.00096 19.1 0.7 14 86-99 46-59 (71)
172 cd02793 MopB_CT_DMSOR-BSOR-TMA 21.7 87 0.0019 20.5 2.2 19 81-99 40-58 (129)
173 PF00877 NLPC_P60: NlpC/P60 fa 21.5 50 0.0011 20.7 1.0 18 81-98 45-62 (105)
174 PF03459 TOBE: TOBE domain; I 21.2 1E+02 0.0023 17.3 2.3 22 79-100 38-59 (64)
175 cd02789 MopB_CT_FmdC-FwdD The 21.2 92 0.002 19.9 2.2 19 81-99 38-56 (106)
176 cd02794 MopB_CT_DmsA-EC The Mo 21.2 99 0.0021 19.9 2.4 19 81-99 37-55 (121)
177 PRK09681 putative type II secr 21.1 1E+02 0.0023 23.7 2.8 22 74-95 209-232 (276)
178 cd01753 PLAT_LOX PLAT domain o 21.1 1.2E+02 0.0025 19.8 2.7 47 18-69 58-104 (113)
179 COG2947 Uncharacterized conser 21.0 1.2E+02 0.0026 21.5 2.8 19 80-100 36-54 (156)
180 cd00113 PLAT PLAT (Polycystin- 20.9 1.2E+02 0.0026 19.2 2.8 22 47-68 83-104 (116)
181 PF03152 UFD1: Ubiquitin fusio 20.6 3.3E+02 0.0072 19.5 7.2 77 16-97 18-95 (176)
182 cd02899 PLAT_SR Scavenger rece 20.5 1.2E+02 0.0025 20.0 2.6 46 16-68 52-97 (109)
183 PF12791 RsgI_N: Anti-sigma fa 20.4 57 0.0012 18.4 1.0 27 73-99 8-37 (56)
184 PRK06788 flagellar motor switc 20.3 73 0.0016 21.5 1.6 13 86-98 53-65 (119)
185 PF13356 DUF4102: Domain of un 20.3 1.6E+02 0.0035 18.0 3.1 34 43-79 22-55 (89)
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=99.84 E-value=5.8e-20 Score=118.68 Aligned_cols=86 Identities=24% Similarity=0.367 Sum_probs=63.7
Q ss_pred EEEecccCCCCCCCcEEeehhhhhccCCCCCCCCCEEEEEEECCCCeEEEEEEEEcCCCCCcceeec-ChHHHHhhcCCC
Q 043432 11 FEKQLKNSDVNAAGRIVLPKKLAETYLPPVNEKAGFWMHLEDMDFNKVWTFKFRFWPNNRGRMYIFE-NTRAFIKRYCLE 89 (105)
Q Consensus 11 f~K~LT~SDv~~~~rl~iPk~~ae~~lP~l~~~~~~~l~~~D~~~g~~W~fr~~~~~~~~s~~y~l~-gW~~fV~~k~L~ 89 (105)
|.|+|++||+.+.++|.||++.++++ .+....++.+.+.|. .|++|.++++++. .++.++|+ ||.+||++++|+
T Consensus 1 F~K~l~~s~~~~~~~l~iP~~f~~~~--~~~~~~~~~v~l~~~-~g~~W~v~~~~~~--~~~~~~l~~GW~~Fv~~n~L~ 75 (100)
T PF02362_consen 1 FFKVLKPSDVSSSCRLIIPKEFAKKH--GGNKRKSREVTLKDP-DGRSWPVKLKYRK--NSGRYYLTGGWKKFVRDNGLK 75 (100)
T ss_dssp EEEE--TTCCCCTT-EEE-HHHHTTT--S--SS--CEEEEEET-TTEEEEEEEEEEC--CTTEEEEETTHHHHHHHCT--
T ss_pred CEEEEEccCcCCCCEEEeCHHHHHHh--CCCcCCCeEEEEEeC-CCCEEEEEEEEEc--cCCeEEECCCHHHHHHHcCCC
Confidence 78999999999888999999999888 222235689999998 5999999999874 44457888 799999999999
Q ss_pred CCCEEEEEEcCC
Q 043432 90 LGDYIMVYKDEL 101 (105)
Q Consensus 90 ~GD~i~f~~~~~ 101 (105)
+||.|+|+....
T Consensus 76 ~GD~~~F~~~~~ 87 (100)
T PF02362_consen 76 EGDVCVFELIGN 87 (100)
T ss_dssp TT-EEEEEE-SS
T ss_pred CCCEEEEEEecC
Confidence 999999998753
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=99.08 E-value=4.9e-10 Score=75.55 Aligned_cols=78 Identities=22% Similarity=0.434 Sum_probs=62.7
Q ss_pred ccceeEEEecccCCCC-CCCcEEeehhhhh--ccCCC-----C-------CCCCCEEEEEEECCCCeEEEEEEEEcCC-C
Q 043432 6 LMRFLFEKQLKNSDVN-AAGRIVLPKKLAE--TYLPP-----V-------NEKAGFWMHLEDMDFNKVWTFKFRFWPN-N 69 (105)
Q Consensus 6 ~~~~~f~K~LT~SDv~-~~~rl~iPk~~ae--~~lP~-----l-------~~~~~~~l~~~D~~~g~~W~fr~~~~~~-~ 69 (105)
....++.|+|++|||. ..+||.||-.... .+|-+ + ....|+.+.+.|+. ++.|.++++.|.. +
T Consensus 19 d~kli~~K~L~~tDv~~~qsRLsmP~~qi~~~dFLt~eE~~~i~~~~~~~~~~~Gv~V~lvdp~-~~~~~m~lkkW~mg~ 97 (114)
T PF03754_consen 19 DPKLIIEKTLFKTDVDPHQSRLSMPFNQIIDNDFLTEEEKRIIKEEKKNNDKKKGVEVILVDPS-LRKWTMRLKKWNMGN 97 (114)
T ss_pred CCeEEEeeeecccCCCCCCceeeccHHHhcccccCCHHHHHHHHHhhccCcccCCceEEEECCc-CcEEEEEEEEecccC
Confidence 4578999999999999 5899999976653 23322 2 23578999999995 8999999999987 4
Q ss_pred CCcceeec-ChHHHHh
Q 043432 70 RGRMYIFE-NTRAFIK 84 (105)
Q Consensus 70 ~s~~y~l~-gW~~fV~ 84 (105)
.+-.|+|. ||.++|.
T Consensus 98 ~~~~YvL~~gWn~VV~ 113 (114)
T PF03754_consen 98 GTSNYVLNSGWNKVVE 113 (114)
T ss_pred CceEEEEEcChHhhcc
Confidence 55679999 8999886
No 3
>PF09217 EcoRII-N: Restriction endonuclease EcoRII, N-terminal; InterPro: IPR023372 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry represents the N-terminal effector-binding domain of the type II restriction endonuclease EcoRII, which has a DNA recognition fold, allowing for binding to 5'-CCWGG sequences. It assumes a structure composed of an eight-stranded beta-sheet with the strands in the order of b2, b5, b4, b3, b7, b6, b1 and b8. They are mostly antiparallel to each other except that b3 is parallel to b7. Alternatively, it may also be viewed as consisting of two mini beta-sheets of four antiparallel beta-strands, sheet I from beta-strands b2, b5, b4, b3 and sheet II from strands b7, b6, b1, b8, folded into an open mixed beta-barrel with a novel topology. Sheet I has a simple Greek key motif while sheet II does not []. The domain represented by this entry is only found in bacterial proteins.; PDB: 3HQF_A 1NA6_A.
Probab=98.58 E-value=2.7e-07 Score=64.95 Aligned_cols=88 Identities=19% Similarity=0.320 Sum_probs=55.3
Q ss_pred eeEEEecccCCCCC----CCcEEeehhhhhccCCCCC----CCCCEEEEEEECCCC--eEEEEEEEEcCC----CCCcce
Q 043432 9 FLFEKQLKNSDVNA----AGRIVLPKKLAETYLPPVN----EKAGFWMHLEDMDFN--KVWTFKFRFWPN----NRGRMY 74 (105)
Q Consensus 9 ~~f~K~LT~SDv~~----~~rl~iPk~~ae~~lP~l~----~~~~~~l~~~D~~~g--~~W~fr~~~~~~----~~s~~y 74 (105)
.+|.|.|++.|++. ..++.|||..++.+||.+. .++.+.|.+.+.. + ..+.+|++|..| +.+..|
T Consensus 8 ~~~~K~LSaNDtGaTGgHQaGiyIpk~~~~~lFp~~~~~~~~Np~~~~~~~~~s-~~~~~~~~r~iYYnn~~~~gTRNE~ 86 (156)
T PF09217_consen 8 AIYCKRLSANDTGATGGHQAGIYIPKSAAELLFPSINHTKEENPDIWLKARWQS-HFVTDSQVRFIYYNNRLFGGTRNEY 86 (156)
T ss_dssp EEEEEE--CCCCTTTSSS--EEEE-HHHHHHH-GGG-SSSSSS-EEEEEEEETT-TT---EEEEEEEE-CCCTTSS--EE
T ss_pred EEEEEEccCCCCCCcCcccceeEecccHHHHhCCCCCcccccCCceeEEEEECC-CCccceeEEEEEEcccccCCCcCce
Confidence 57999999999984 4489999999988998764 2466888888773 4 668899999966 345679
Q ss_pred eecChHHHHhhcC-CCCCCEEEEE
Q 043432 75 IFENTRAFIKRYC-LELGDYIMVY 97 (105)
Q Consensus 75 ~l~gW~~fV~~k~-L~~GD~i~f~ 97 (105)
.||.|.....-.+ =.+||.++|.
T Consensus 87 RIT~~G~~~~~~~~~~tGaL~vla 110 (156)
T PF09217_consen 87 RITRFGRGFPLQNPENTGALLVLA 110 (156)
T ss_dssp EEE---TTSGGG-GGGTT-EEEEE
T ss_pred EEeeecCCCccCCccccccEEEEE
Confidence 9999865554333 3679998886
No 4
>cd06919 Asp_decarbox Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production. Decarboxylation of aspartate is the major route of beta-alanine production in bacteria, and is catalyzed by the enzyme L-aspartate decarboxylase (ADC), EC:4.1.1.11 which requires a pyruvoyl group for its activity. The pyruvoyl cofactor is covalently bound to the enzyme. The protein is synthesized as a proenzyme and cleaved via self-processing at Gly23-Ser24 to yield an alpha chain (C-terminal fragment) and beta chain (N-terminal fragment), and the pyruvoyl group. Beta-alanine is required for the biosynthesis of pantothenate, in which the enzyme plays a critical regulatory role. The active site of the tetrameric enzyme is located at the interface of two subunits, with a Lysine and a Histidine from the beta chain of one subunit forming the active site with residues from the alpha chain of the adjacent subunit. This alignment
Probab=93.89 E-value=1.2 Score=29.95 Aligned_cols=77 Identities=13% Similarity=0.198 Sum_probs=58.0
Q ss_pred EEEecccCCCCCCCcEEeehhhhhc--cCCCCCCCCCEEEEEEECCCCeEEEEEEEEcCCCCCcceeecChHHHHhhcCC
Q 043432 11 FEKQLKNSDVNAAGRIVLPKKLAET--YLPPVNEKAGFWMHLEDMDFNKVWTFKFRFWPNNRGRMYIFENTRAFIKRYCL 88 (105)
Q Consensus 11 f~K~LT~SDv~~~~rl~iPk~~ae~--~lP~l~~~~~~~l~~~D~~~g~~W~fr~~~~~~~~s~~y~l~gW~~fV~~k~L 88 (105)
=.-..|..|+..-|.+.|..+..++ ++|. ..|.+++..+|..|+ .|.+.....|+.-.|.| .-++..
T Consensus 10 HratVT~a~L~YeGSitID~~Ll~aagi~~~------E~V~I~Nv~NG~Rf~-TYvI~g~~gSg~I~lNG----AAAr~~ 78 (111)
T cd06919 10 HRATVTEADLNYEGSITIDEDLLEAAGILPY------EKVLVVNVNNGARFE-TYVIPGERGSGVICLNG----AAARLG 78 (111)
T ss_pred cceEEeccccccceeEEECHHHHHhcCCCCC------CEEEEEECCCCcEEE-EEEEEcCCCCCEEEeCC----HHHhcC
Confidence 3456899999988999999988765 3554 478999987787665 45566445577778888 567788
Q ss_pred CCCCEEEEEE
Q 043432 89 ELGDYIMVYK 98 (105)
Q Consensus 89 ~~GD~i~f~~ 98 (105)
++||.|++.-
T Consensus 79 ~~GD~vII~s 88 (111)
T cd06919 79 QPGDRVIIMA 88 (111)
T ss_pred CCCCEEEEEE
Confidence 9999999853
No 5
>PRK05449 aspartate alpha-decarboxylase; Provisional
Probab=93.89 E-value=1.1 Score=30.74 Aligned_cols=76 Identities=11% Similarity=0.239 Sum_probs=57.8
Q ss_pred EEecccCCCCCCCcEEeehhhhhc--cCCCCCCCCCEEEEEEECCCCeEEEEEEEEcCCCCCcceeecChHHHHhhcCCC
Q 043432 12 EKQLKNSDVNAAGRIVLPKKLAET--YLPPVNEKAGFWMHLEDMDFNKVWTFKFRFWPNNRGRMYIFENTRAFIKRYCLE 89 (105)
Q Consensus 12 ~K~LT~SDv~~~~rl~iPk~~ae~--~lP~l~~~~~~~l~~~D~~~g~~W~fr~~~~~~~~s~~y~l~gW~~fV~~k~L~ 89 (105)
.-..|..|+..-|.+.|..+..++ ++|. -.|.+++..+|..|+ .|.+.....|+.-.|.| .-++..+
T Consensus 12 ratVT~a~L~Y~GSitID~~Ll~aagi~p~------E~V~V~Nv~NG~Rf~-TYvI~g~~GSg~I~lNG----AAAr~~~ 80 (126)
T PRK05449 12 RATVTEADLNYEGSITIDEDLLDAAGILEN------EKVQIVNVNNGARFE-TYVIAGERGSGVICLNG----AAARLVQ 80 (126)
T ss_pred ceEEeccccccceeEEECHHHHHhcCCCCC------CEEEEEECCCCcEEE-EEEEEcCCCCCEEEeCC----HHHhcCC
Confidence 456899999988999999998875 4554 378999987788665 45566445577778888 5678889
Q ss_pred CCCEEEEEE
Q 043432 90 LGDYIMVYK 98 (105)
Q Consensus 90 ~GD~i~f~~ 98 (105)
+||.|++.-
T Consensus 81 ~GD~vII~a 89 (126)
T PRK05449 81 VGDLVIIAA 89 (126)
T ss_pred CCCEEEEEE
Confidence 999999853
No 6
>TIGR00223 panD L-aspartate-alpha-decarboxylase. Members of this family are aspartate 1-decarboxylase, the enzyme that makes beta-alanine and C02 from aspartate. Beta-alanine is then used to make the vitamin pantothenate, from which coenzyme A is made. Aspartate 1-decarboxylase is synthesized as a proenzyme, then cleaved to an alpha (C-terminal) and beta (N-terminal) subunit with a pyruvoyl group.
Probab=93.64 E-value=1.2 Score=30.50 Aligned_cols=76 Identities=13% Similarity=0.325 Sum_probs=57.7
Q ss_pred EEecccCCCCCCCcEEeehhhhhc--cCCCCCCCCCEEEEEEECCCCeEEEEEEEEcCCCCCcceeecChHHHHhhcCCC
Q 043432 12 EKQLKNSDVNAAGRIVLPKKLAET--YLPPVNEKAGFWMHLEDMDFNKVWTFKFRFWPNNRGRMYIFENTRAFIKRYCLE 89 (105)
Q Consensus 12 ~K~LT~SDv~~~~rl~iPk~~ae~--~lP~l~~~~~~~l~~~D~~~g~~W~fr~~~~~~~~s~~y~l~gW~~fV~~k~L~ 89 (105)
....|..|+..-|.+.|..+..++ ++|. -.|.+.|..+|..|+ .|.+.....|+.-.|.| .-++..+
T Consensus 12 ratVT~a~L~Y~GSItID~~Lm~aagi~p~------E~V~V~Nv~NG~Rf~-TYvI~G~~GSg~I~lNG----AAArl~~ 80 (126)
T TIGR00223 12 RATVTHANLNYEGSITIDEDLLDAAGILEN------EKVDIVNVNNGKRFS-TYAIAGKRGSRIICVNG----AAARCVS 80 (126)
T ss_pred ceEEeccccccceeEEECHHHHHhcCCCCC------CEEEEEECCCCcEEE-EEEEEcCCCCCEEEeCC----HHHhcCC
Confidence 456789999988999999988764 4554 378899987788665 45566545577778888 5677889
Q ss_pred CCCEEEEEE
Q 043432 90 LGDYIMVYK 98 (105)
Q Consensus 90 ~GD~i~f~~ 98 (105)
+||.|++.-
T Consensus 81 ~GD~VII~s 89 (126)
T TIGR00223 81 VGDIVIIAS 89 (126)
T ss_pred CCCEEEEEE
Confidence 999999853
No 7
>PF02261 Asp_decarbox: Aspartate decarboxylase; InterPro: IPR003190 Decarboxylation of aspartate is the major route of alanine production in bacteria, and is catalysed by the enzyme aspartate decarboxylase. The enzyme is translated as an inactive proenzyme of two chains, A and B. This family contains both chains of aspartate decarboxylase.; GO: 0004068 aspartate 1-decarboxylase activity, 0006523 alanine biosynthetic process; PDB: 1PYU_C 1AW8_A 1PYQ_B 3TM7_C 1PT1_A 1PQH_A 1PPY_B 1PT0_B 1PQF_A 1PQE_A ....
Probab=92.66 E-value=2.2 Score=28.92 Aligned_cols=77 Identities=12% Similarity=0.276 Sum_probs=50.5
Q ss_pred eEEEecccCCCCCCCcEEeehhhhhc--cCCCCCCCCCEEEEEEECCCCeEEEEEEEEcCCCCCcceeecChHHHHhhcC
Q 043432 10 LFEKQLKNSDVNAAGRIVLPKKLAET--YLPPVNEKAGFWMHLEDMDFNKVWTFKFRFWPNNRGRMYIFENTRAFIKRYC 87 (105)
Q Consensus 10 ~f~K~LT~SDv~~~~rl~iPk~~ae~--~lP~l~~~~~~~l~~~D~~~g~~W~fr~~~~~~~~s~~y~l~gW~~fV~~k~ 87 (105)
+=..+.|..|+...|.+.|..+..++ ++|. -.|.+.+..+|..|+ .|.+.....|+.-.|.| .-++.
T Consensus 10 iHratVT~a~L~Y~GSitID~~Ll~aagi~p~------E~V~V~Nv~nG~Rf~-TYvI~g~~GSg~I~lNG----aAArl 78 (116)
T PF02261_consen 10 IHRATVTEADLNYEGSITIDEDLLDAAGILPY------EQVQVVNVNNGERFE-TYVIPGERGSGVICLNG----AAARL 78 (116)
T ss_dssp EEEEE--EEETTSTSCEEEEHHHHHHCT--TT------BEEEEEETTT--EEE-EEEEEESTTTT-EEEEG----GGGGC
T ss_pred hcceEEeccccccceeeEECHHHHHHcCCCcC------CEEEEEECCCCcEEE-EEEEEccCCCcEEEECC----HHHhc
Confidence 33457899999988999999988764 4554 478999988788665 34455444566777777 56788
Q ss_pred CCCCCEEEEE
Q 043432 88 LELGDYIMVY 97 (105)
Q Consensus 88 L~~GD~i~f~ 97 (105)
.++||.|++.
T Consensus 79 ~~~GD~vII~ 88 (116)
T PF02261_consen 79 VQVGDRVIIM 88 (116)
T ss_dssp S-TT-EEEEE
T ss_pred cCCCCEEEEE
Confidence 8999999884
No 8
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=92.52 E-value=0.32 Score=31.72 Aligned_cols=75 Identities=12% Similarity=0.191 Sum_probs=45.4
Q ss_pred ceeEEEecccCCCC-C-CCcEEeehhhhhccCCCCCCCCCEEEEEEECCCCeEEEEEEEEcCCCCCcceeecChHHHHhh
Q 043432 8 RFLFEKQLKNSDVN-A-AGRIVLPKKLAETYLPPVNEKAGFWMHLEDMDFNKVWTFKFRFWPNNRGRMYIFENTRAFIKR 85 (105)
Q Consensus 8 ~~~f~K~LT~SDv~-~-~~rl~iPk~~ae~~lP~l~~~~~~~l~~~D~~~g~~W~fr~~~~~~~~s~~y~l~gW~~fV~~ 85 (105)
...|.++++.+-+. + .+++.||++.. ++|..-......+.+.... ... +. .+.-.
T Consensus 18 ~i~~G~V~s~~PL~I~i~~~liL~~~~L--~i~~~l~~~~~~~~~~~~~-~~~----------~~----------~i~~~ 74 (100)
T PF10844_consen 18 DIVIGTVVSVPPLKIKIDQKLILDKDFL--IIPELLKDYTRDITIEHNS-ETD----------NI----------TITFT 74 (100)
T ss_pred eeEEEEEEecccEEEEECCeEEEchHHE--EeehhccceEEEEEEeccc-ccc----------ce----------eEEEe
Confidence 34788999998754 2 34588887654 4555323333444443321 110 00 05556
Q ss_pred cCCCCCCEEEEEEcCCCCCC
Q 043432 86 YCLELGDYIMVYKDELEGSY 105 (105)
Q Consensus 86 k~L~~GD~i~f~~~~~~g~~ 105 (105)
.+|++||.|.+.+..++.+|
T Consensus 75 ~~Lk~GD~V~ll~~~~gQ~y 94 (100)
T PF10844_consen 75 DGLKVGDKVLLLRVQGGQKY 94 (100)
T ss_pred cCCcCCCEEEEEEecCCCEE
Confidence 78999999999997777665
No 9
>PF14250 AbrB-like: AbrB-like transcriptional regulator
Probab=81.46 E-value=4.6 Score=25.05 Aligned_cols=39 Identities=15% Similarity=0.217 Sum_probs=30.7
Q ss_pred CCeEEEEEEEEcCCCCCcceeecChHHHHhhcCCCCCCEEEEEE
Q 043432 55 FNKVWTFKFRFWPNNRGRMYIFENTRAFIKRYCLELGDYIMVYK 98 (105)
Q Consensus 55 ~g~~W~fr~~~~~~~~s~~y~l~gW~~fV~~k~L~~GD~i~f~~ 98 (105)
.|++=+||.+...|++ +|-| ..|-+..+|++||++.+--
T Consensus 25 ~GR~~syr~~Vq~NGn----LLIG-~AYT~~m~L~PGdEFeI~L 63 (71)
T PF14250_consen 25 RGRKASYRVSVQGNGN----LLIG-SAYTKQMGLKPGDEFEIKL 63 (71)
T ss_pred CCcCceEEEEEecCCC----EEEc-HHHHHHhCCCCCCEEEEEe
Confidence 5888889988886544 4555 6899999999999987743
No 10
>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=78.14 E-value=4.2 Score=22.53 Aligned_cols=22 Identities=14% Similarity=0.190 Sum_probs=18.7
Q ss_pred HHHHhhcCCCCCCEEEEEEcCC
Q 043432 80 RAFIKRYCLELGDYIMVYKDEL 101 (105)
Q Consensus 80 ~~fV~~k~L~~GD~i~f~~~~~ 101 (105)
.++.+..+|++||.|.+.-+.+
T Consensus 13 k~~~~~l~l~~Gd~v~i~~~~~ 34 (47)
T PF04014_consen 13 KEIREKLGLKPGDEVEIEVEGD 34 (47)
T ss_dssp HHHHHHTTSSTTTEEEEEEETT
T ss_pred HHHHHHcCCCCCCEEEEEEeCC
Confidence 4788889999999999988744
No 11
>PF03120 DNA_ligase_OB: NAD-dependent DNA ligase OB-fold domain; InterPro: IPR004150 DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This family is a small domain found after the adenylation domain DNA_ligase_N in NAD+-dependent ligases (IPR001679 from INTERPRO). OB-fold domains generally are involved in nucleic acid binding.; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 2OWO_A 1TAE_A 3UQ8_A 1DGS_A 1V9P_B 3SGI_A.
Probab=77.81 E-value=2.3 Score=27.04 Aligned_cols=21 Identities=24% Similarity=0.505 Sum_probs=17.0
Q ss_pred HHHHhhcCCCCCCEEEEEEcC
Q 043432 80 RAFIKRYCLELGDYIMVYKDE 100 (105)
Q Consensus 80 ~~fV~~k~L~~GD~i~f~~~~ 100 (105)
.+|+++++|..||.|.++|..
T Consensus 42 ~~~i~~~~i~~Gd~V~V~raG 62 (82)
T PF03120_consen 42 YDYIKELDIRIGDTVLVTRAG 62 (82)
T ss_dssp HHHHHHTT-BBT-EEEEEEET
T ss_pred HHHHHHcCCCCCCEEEEEECC
Confidence 589999999999999999863
No 12
>PRK09570 rpoH DNA-directed RNA polymerase subunit H; Reviewed
Probab=77.56 E-value=3.3 Score=26.18 Aligned_cols=26 Identities=19% Similarity=0.273 Sum_probs=20.1
Q ss_pred HHHHhhcCCCCCCEEEEEEcCCC-CCC
Q 043432 80 RAFIKRYCLELGDYIMVYKDELE-GSY 105 (105)
Q Consensus 80 ~~fV~~k~L~~GD~i~f~~~~~~-g~~ 105 (105)
...++..+|+.||+|-+.|...+ |+|
T Consensus 44 DPv~r~~g~k~GdVvkI~R~S~taG~~ 70 (79)
T PRK09570 44 DPVVKAIGAKPGDVIKIVRKSPTAGEA 70 (79)
T ss_pred ChhhhhcCCCCCCEEEEEECCCCCCcc
Confidence 35677889999999999997544 554
No 13
>COG0853 PanD Aspartate 1-decarboxylase [Coenzyme metabolism]
Probab=76.25 E-value=22 Score=24.38 Aligned_cols=78 Identities=10% Similarity=0.259 Sum_probs=54.7
Q ss_pred eEEEecccCCCCCCCcEEeehhhhhc--cCCCCCCCCCEEEEEEECCCCeEEEEEEEEcCCCCCcceeecChHHHHhhcC
Q 043432 10 LFEKQLKNSDVNAAGRIVLPKKLAET--YLPPVNEKAGFWMHLEDMDFNKVWTFKFRFWPNNRGRMYIFENTRAFIKRYC 87 (105)
Q Consensus 10 ~f~K~LT~SDv~~~~rl~iPk~~ae~--~lP~l~~~~~~~l~~~D~~~g~~W~fr~~~~~~~~s~~y~l~gW~~fV~~k~ 87 (105)
+=.-+.|+.|+...|.+.|-.+..++ .+|. -.+.+++..+|...+ .|.+.....|+.--|.| .-++-
T Consensus 9 iHratVT~A~L~Y~GSitID~dlldaagile~------EkV~I~N~nNGaRf~-TYvI~g~rGSg~I~lNG----AAArl 77 (126)
T COG0853 9 IHRATVTEADLNYVGSITIDEDLLDAAGILEN------EKVDIVNVNNGARFS-TYVIAGERGSGVICLNG----AAARL 77 (126)
T ss_pred eeeeEEeecccceEEeEEECHHHHhhcCCCCC------ceEEEEECCCCcEEE-EEEEEccCCCcEEEech----HHHhh
Confidence 44567899999988999999888764 4554 367888886666332 34455444566666666 55777
Q ss_pred CCCCCEEEEEE
Q 043432 88 LELGDYIMVYK 98 (105)
Q Consensus 88 L~~GD~i~f~~ 98 (105)
.++||.|+++-
T Consensus 78 ~~~GD~VII~s 88 (126)
T COG0853 78 VQVGDLVIIMS 88 (126)
T ss_pred CCCCCEEEEEE
Confidence 89999999864
No 14
>PF09853 DUF2080: Putative transposon-encoded protein (DUF2080); InterPro: IPR019205 This entry, found in various hypothetical archaeal proteins, has no known function.
Probab=74.88 E-value=4.9 Score=23.58 Aligned_cols=31 Identities=23% Similarity=0.280 Sum_probs=25.9
Q ss_pred CccccceeEEEecccCCCCCCCcEE--eehhhhhc
Q 043432 3 NPFLMRFLFEKQLKNSDVNAAGRIV--LPKKLAET 35 (105)
Q Consensus 3 ~~~~~~~~f~K~LT~SDv~~~~rl~--iPk~~ae~ 35 (105)
-++++...|.+..++. ++.+++. +|+++.-+
T Consensus 10 k~~~i~~~~~~~vk~~--Gnsa~v~p~lPkeyiGK 42 (53)
T PF09853_consen 10 KPRNIEPTFIGVVKPF--GNSARVYPSLPKEYIGK 42 (53)
T ss_pred ceeeEEEEEEEEEEec--CcceeEcCCCChHHcCc
Confidence 3567888999999998 7778999 99998743
No 15
>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=66.74 E-value=4.5 Score=24.75 Aligned_cols=18 Identities=28% Similarity=0.455 Sum_probs=15.5
Q ss_pred HHHHhhcCCCCCCEEEEE
Q 043432 80 RAFIKRYCLELGDYIMVY 97 (105)
Q Consensus 80 ~~fV~~k~L~~GD~i~f~ 97 (105)
..-||..+|+.||.|.=.
T Consensus 33 ~~~Irr~~LR~GD~V~G~ 50 (68)
T cd04459 33 PSQIRRFNLRTGDTVVGQ 50 (68)
T ss_pred HHHHHHhCCCCCCEEEEE
Confidence 468999999999999754
No 16
>PRK03760 hypothetical protein; Provisional
Probab=65.87 E-value=22 Score=23.72 Aligned_cols=29 Identities=28% Similarity=0.321 Sum_probs=21.6
Q ss_pred CCcceeecChHHHHhhcCCCCCCEEEEEE
Q 043432 70 RGRMYIFENTRAFIKRYCLELGDYIMVYK 98 (105)
Q Consensus 70 ~s~~y~l~gW~~fV~~k~L~~GD~i~f~~ 98 (105)
.+-.|+|+==...+.+.++++||.|.|-+
T Consensus 88 ~~a~~VLEl~aG~~~~~gi~~Gd~v~~~~ 116 (117)
T PRK03760 88 KPARYIIEGPVGKIRVLKVEVGDEIEWID 116 (117)
T ss_pred ccceEEEEeCCChHHHcCCCCCCEEEEee
Confidence 34558999223457789999999998865
No 17
>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=59.29 E-value=7.2 Score=24.69 Aligned_cols=21 Identities=19% Similarity=0.404 Sum_probs=10.4
Q ss_pred HhhcCCCCCCEEEEEEcCCCC
Q 043432 83 IKRYCLELGDYIMVYKDELEG 103 (105)
Q Consensus 83 V~~k~L~~GD~i~f~~~~~~g 103 (105)
+-+++|.+||.|.|.-....|
T Consensus 23 l~~HGl~vGD~VnFsnsa~tG 43 (83)
T PF12195_consen 23 LTDHGLFVGDFVNFSNSAVTG 43 (83)
T ss_dssp -TT----TT-EEEEES-SSTT
T ss_pred EccCceeecceEEEecccccc
Confidence 568999999999997654443
No 18
>COG5569 Uncharacterized conserved protein [Function unknown]
Probab=58.30 E-value=7.4 Score=25.83 Aligned_cols=22 Identities=23% Similarity=0.262 Sum_probs=18.1
Q ss_pred HhhcCCCCCCEEEEEEcCCCCC
Q 043432 83 IKRYCLELGDYIMVYKDELEGS 104 (105)
Q Consensus 83 V~~k~L~~GD~i~f~~~~~~g~ 104 (105)
..=.+|++||.|.|--+..+|+
T Consensus 79 a~lsglKeGdkV~fvferv~gk 100 (108)
T COG5569 79 AKLSGLKEGDKVEFVFERVNGK 100 (108)
T ss_pred HHhhccccCCcEEEEEEeeCCE
Confidence 4456899999999988877775
No 19
>PRK11507 ribosome-associated protein; Provisional
Probab=56.29 E-value=8.3 Score=23.83 Aligned_cols=19 Identities=16% Similarity=0.109 Sum_probs=16.0
Q ss_pred ChHHHHhhcCCCCCCEEEE
Q 043432 78 NTRAFIKRYCLELGDYIMV 96 (105)
Q Consensus 78 gW~~fV~~k~L~~GD~i~f 96 (105)
|=.+.-|.++|+.||+|.|
T Consensus 43 Geve~rRgkKl~~GD~V~~ 61 (70)
T PRK11507 43 GAVETRKRCKIVAGQTVSF 61 (70)
T ss_pred CEEecccCCCCCCCCEEEE
Confidence 4457778899999999988
No 20
>PF02643 DUF192: Uncharacterized ACR, COG1430; InterPro: IPR003795 This entry describes proteins of unknown function.; PDB: 3M7A_B 3PJY_B.
Probab=56.16 E-value=50 Score=21.44 Aligned_cols=25 Identities=16% Similarity=0.501 Sum_probs=16.7
Q ss_pred cceeecChHHHHhhcCCCCCCEEEE
Q 043432 72 RMYIFENTRAFIKRYCLELGDYIMV 96 (105)
Q Consensus 72 ~~y~l~gW~~fV~~k~L~~GD~i~f 96 (105)
-.|+|+==..++.+.++++||.|.|
T Consensus 82 a~~vLE~~aG~~~~~~i~~Gd~v~~ 106 (108)
T PF02643_consen 82 ARYVLELPAGWFEKLGIKVGDRVRI 106 (108)
T ss_dssp ECEEEEEETTHHHHHT--TT-EEE-
T ss_pred cCEEEEcCCCchhhcCCCCCCEEEe
Confidence 4689993356788999999999986
No 21
>COG3466 ISA1214 Putative transposon-encoded protein [Function unknown]
Probab=56.02 E-value=9.5 Score=22.21 Aligned_cols=29 Identities=17% Similarity=0.328 Sum_probs=24.0
Q ss_pred ccccceeEEEecccCCCCCCCcEEeehhhhh
Q 043432 4 PFLMRFLFEKQLKNSDVNAAGRIVLPKKLAE 34 (105)
Q Consensus 4 ~~~~~~~f~K~LT~SDv~~~~rl~iPk~~ae 34 (105)
+.+.+..|+|..|+- ++.+-..+||++..
T Consensus 14 ~~~ve~~~ek~Vtpf--GnsakVdvPK~yiG 42 (52)
T COG3466 14 KEEVEVVFEKRVTPF--GNSAKVDVPKRYIG 42 (52)
T ss_pred chheEEEEEEEEEec--CCcceeeCchHHcC
Confidence 456788999999987 66689999999873
No 22
>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=54.46 E-value=31 Score=20.99 Aligned_cols=33 Identities=18% Similarity=0.256 Sum_probs=23.2
Q ss_pred EEcCCCCCcceeecChHHHHhhcCCCCCCEEEEEEcC
Q 043432 64 RFWPNNRGRMYIFENTRAFIKRYCLELGDYIMVYKDE 100 (105)
Q Consensus 64 ~~~~~~~s~~y~l~gW~~fV~~k~L~~GD~i~f~~~~ 100 (105)
..|. +| +.++==.+++.+-+|.+||.|.+..+.
T Consensus 4 ~k~G--NS--~~vtIPk~i~~~lgl~~Gd~v~v~~~~ 36 (74)
T TIGR02609 4 RKVG--NS--LVVTLPKEVLESLGLKEGDTLYVDEEE 36 (74)
T ss_pred EEEC--Ce--eEEEECHHHHHHcCcCCCCEEEEEEEC
Confidence 4563 35 444422588999999999999886653
No 23
>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=52.96 E-value=24 Score=18.41 Aligned_cols=20 Identities=20% Similarity=0.308 Sum_probs=17.7
Q ss_pred HHHHhhcCCCCCCEEEEEEc
Q 043432 80 RAFIKRYCLELGDYIMVYKD 99 (105)
Q Consensus 80 ~~fV~~k~L~~GD~i~f~~~ 99 (105)
..|.+..++..||.|.+...
T Consensus 13 ~~~r~~l~~~~gd~~~i~~~ 32 (43)
T TIGR01439 13 KEIREKLGLKEGDRLEVIRV 32 (43)
T ss_pred HHHHHHcCcCCCCEEEEEEe
Confidence 58899999999999999865
No 24
>PF14453 ThiS-like: ThiS-like ubiquitin
Probab=52.60 E-value=13 Score=22.04 Aligned_cols=16 Identities=25% Similarity=0.370 Sum_probs=13.1
Q ss_pred hhcCCCCCCEEEEEEc
Q 043432 84 KRYCLELGDYIMVYKD 99 (105)
Q Consensus 84 ~~k~L~~GD~i~f~~~ 99 (105)
....|++||.|+|.+.
T Consensus 41 ~d~~L~e~D~v~~Ikk 56 (57)
T PF14453_consen 41 EDIELKEGDEVFLIKK 56 (57)
T ss_pred CccccCCCCEEEEEeC
Confidence 4667999999999763
No 25
>PF01878 EVE: EVE domain; InterPro: IPR002740 The EVE domain is part of the wider PUA domain superfamily. The function of this domain is not known but, given the structural similarities to PUA, is likely to involve RNA binding []. ; PDB: 2G2X_B 2AR1_A 3EOP_A 2EVE_A 2HD9_A 2ZBN_A 1WMM_A 2P5D_A 2GBS_A 1ZCE_A.
Probab=51.48 E-value=10 Score=25.53 Aligned_cols=15 Identities=20% Similarity=0.454 Sum_probs=10.7
Q ss_pred cCCCCCCEEEEEEcC
Q 043432 86 YCLELGDYIMVYKDE 100 (105)
Q Consensus 86 k~L~~GD~i~f~~~~ 100 (105)
+.+++||.|+||...
T Consensus 38 ~~mk~GD~vifY~s~ 52 (143)
T PF01878_consen 38 KRMKPGDKVIFYHSG 52 (143)
T ss_dssp HC--TT-EEEEEETS
T ss_pred hcCCCCCEEEEEEcC
Confidence 499999999999976
No 26
>PF07497 Rho_RNA_bind: Rho termination factor, RNA-binding domain; InterPro: IPR011113 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers [].; GO: 0003723 RNA binding, 0006353 transcription termination, DNA-dependent; PDB: 1A8V_B 1PVO_A 1PV4_D 3ICE_A 1XPU_C 1XPO_D 1XPR_F 2A8V_B 2HT1_B 1A63_A ....
Probab=50.95 E-value=11 Score=23.72 Aligned_cols=15 Identities=33% Similarity=0.634 Sum_probs=11.0
Q ss_pred HHHhhcCCCCCCEEE
Q 043432 81 AFIKRYCLELGDYIM 95 (105)
Q Consensus 81 ~fV~~k~L~~GD~i~ 95 (105)
.-+|..+|+.||.|.
T Consensus 36 ~qIrrf~LR~GD~V~ 50 (78)
T PF07497_consen 36 SQIRRFGLRTGDLVE 50 (78)
T ss_dssp CCCCCTT--TTEEEE
T ss_pred HHHHHcCCCCCCEEE
Confidence 457899999999987
No 27
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=50.59 E-value=7.1 Score=23.69 Aligned_cols=20 Identities=15% Similarity=0.134 Sum_probs=9.7
Q ss_pred cChHHHHhhcCCCCCCEEEE
Q 043432 77 ENTRAFIKRYCLELGDYIMV 96 (105)
Q Consensus 77 ~gW~~fV~~k~L~~GD~i~f 96 (105)
.|=.+.-|.++|++||+|.|
T Consensus 38 NGe~e~rrg~Kl~~GD~V~~ 57 (65)
T PF13275_consen 38 NGEVETRRGKKLRPGDVVEI 57 (65)
T ss_dssp TTB----SS----SSEEEEE
T ss_pred CCEEccccCCcCCCCCEEEE
Confidence 34566778899999999998
No 28
>PF01191 RNA_pol_Rpb5_C: RNA polymerase Rpb5, C-terminal domain; InterPro: IPR000783 Prokaryotes contain a single DNA-dependent RNA polymerase (RNAP; 2.7.7.6 from EC) that is responsible for the transcription of all genes, while eukaryotes have three classes of RNAPs (I-III) that transcribe different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. Certain subunits of RNAPs, including RPB5 (POLR2E in mammals), are common to all three eukaryotic polymerases. RPB5 plays a role in the transcription activation process. Eukaryotic RPB5 has a bipartite structure consisting of a unique N-terminal region (IPR005571 from INTERPRO), plus a C-terminal region that is structurally homologous to the prokaryotic RPB5 homologue, subunit H (gene rpoH) [, , , ]. This entry represents prokaryotic subunit H and the C-terminal domain of eukaryotic RPB5, which share a two-layer alpha/beta fold, with a core structure of beta/alpha/beta/alpha/beta(2). ; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1EIK_A 2Y0S_Z 1DZF_A 3GTG_E 2VUM_E 3GTP_E 3GTO_E 3S17_E 3S1R_E 1I3Q_E ....
Probab=50.48 E-value=21 Score=22.20 Aligned_cols=23 Identities=9% Similarity=0.157 Sum_probs=17.1
Q ss_pred HHHHhhcCCCCCCEEEEEEcCCC
Q 043432 80 RAFIKRYCLELGDYIMVYKDELE 102 (105)
Q Consensus 80 ~~fV~~k~L~~GD~i~f~~~~~~ 102 (105)
...++..+++.||+|-+.|...+
T Consensus 41 DPv~r~~g~k~GdVvkI~R~S~t 63 (74)
T PF01191_consen 41 DPVARYLGAKPGDVVKIIRKSET 63 (74)
T ss_dssp SHHHHHTT--TTSEEEEEEEETT
T ss_pred ChhhhhcCCCCCCEEEEEecCCC
Confidence 46788889999999999996543
No 29
>PF14604 SH3_9: Variant SH3 domain; PDB: 2CRE_A 2E5K_A 2CT3_A 2DE0_X 2D8H_A 2DA9_A 2X3X_E 2X3W_D 2KRN_A 2ED0_A ....
Probab=50.25 E-value=14 Score=20.58 Aligned_cols=19 Identities=26% Similarity=0.454 Sum_probs=12.8
Q ss_pred hcCCCCCCEEEEEEcCCCC
Q 043432 85 RYCLELGDYIMVYKDELEG 103 (105)
Q Consensus 85 ~k~L~~GD~i~f~~~~~~g 103 (105)
+-.|++||.|.+....++|
T Consensus 12 ELs~~~Gd~i~v~~~~~~~ 30 (49)
T PF14604_consen 12 ELSFKKGDVITVLEKSDDG 30 (49)
T ss_dssp B-EB-TTEEEEEEEESSTS
T ss_pred EeeEcCCCEEEEEEeCCCC
Confidence 4568999999998765443
No 30
>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=49.87 E-value=31 Score=18.00 Aligned_cols=22 Identities=18% Similarity=0.161 Sum_probs=16.4
Q ss_pred CCEEEEEEECCCCeEEEEEEEEc
Q 043432 44 AGFWMHLEDMDFNKVWTFKFRFW 66 (105)
Q Consensus 44 ~~~~l~~~D~~~g~~W~fr~~~~ 66 (105)
.|..+.+.|+. |..|+|.|--.
T Consensus 4 ~g~l~~~~~p~-G~~~~~~YD~~ 25 (42)
T TIGR01643 4 AGRLTGSTDAD-GTTTRYTYDAA 25 (42)
T ss_pred CCCEEEEECCC-CCEEEEEECCC
Confidence 45677888994 89999887543
No 31
>COG4043 Preprotein translocase subunit Sec61beta [Intracellular trafficking, secretion, and vesicular transport]
Probab=49.11 E-value=14 Score=24.72 Aligned_cols=19 Identities=32% Similarity=0.209 Sum_probs=15.6
Q ss_pred HHHHhhcCCCCCCEEEEEE
Q 043432 80 RAFIKRYCLELGDYIMVYK 98 (105)
Q Consensus 80 ~~fV~~k~L~~GD~i~f~~ 98 (105)
...-+.++.+.||.|+|-.
T Consensus 26 l~d~krr~ik~GD~IiF~~ 44 (111)
T COG4043 26 LADPKRRQIKPGDKIIFNG 44 (111)
T ss_pred ecCHhhcCCCCCCEEEEcC
Confidence 4567788999999999963
No 32
>TIGR03595 Obg_CgtA_exten Obg family GTPase CgtA, C-terminal extension. CgtA (see model TIGR02729) is a broadly conserved member of the obg family of GTPases associated with ribosome maturation. This model represents a unique C-terminal domain found in some but not all sequences of CgtA. This region is preceded, and may be followed, by a region of low-complexity sequence.
Probab=48.56 E-value=16 Score=22.07 Aligned_cols=20 Identities=10% Similarity=0.137 Sum_probs=16.1
Q ss_pred ChHHHHhhcCCCCCCEEEEE
Q 043432 78 NTRAFIKRYCLELGDYIMVY 97 (105)
Q Consensus 78 gW~~fV~~k~L~~GD~i~f~ 97 (105)
|-.+=.++++.+.||+|.+.
T Consensus 44 Gv~~~L~~~G~~~GD~V~Ig 63 (69)
T TIGR03595 44 GVEDALRKAGAKDGDTVRIG 63 (69)
T ss_pred CHHHHHHHcCCCCCCEEEEc
Confidence 34556789999999999875
No 33
>COG1977 MoaD Molybdopterin converting factor, small subunit [Coenzyme metabolism]
Probab=48.05 E-value=16 Score=22.72 Aligned_cols=19 Identities=21% Similarity=0.223 Sum_probs=14.9
Q ss_pred hcCCCCCCEEEEEEcCCCC
Q 043432 85 RYCLELGDYIMVYKDELEG 103 (105)
Q Consensus 85 ~k~L~~GD~i~f~~~~~~g 103 (105)
+..|+.||+|.|+.-..+|
T Consensus 66 ~t~L~dGDeVa~~PPVsGG 84 (84)
T COG1977 66 DTPLKDGDEVAFFPPVSGG 84 (84)
T ss_pred cccCCCCCEEEEeCCCCCC
Confidence 3568999999999866554
No 34
>COG2002 AbrB Regulators of stationary/sporulation gene expression [Transcription]
Probab=48.05 E-value=29 Score=21.81 Aligned_cols=23 Identities=17% Similarity=0.231 Sum_probs=19.0
Q ss_pred HHHhhcCCCCCCEEEEEEcCCCC
Q 043432 81 AFIKRYCLELGDYIMVYKDELEG 103 (105)
Q Consensus 81 ~fV~~k~L~~GD~i~f~~~~~~g 103 (105)
..-+..++++||.+.|+.+...|
T Consensus 21 eiR~~lgi~~Gd~lei~~~~~~~ 43 (89)
T COG2002 21 EIREALGIKEGDVLEIIVDGDGG 43 (89)
T ss_pred HHHHHhCCCCCCEEEEEEeCCCC
Confidence 55677899999999999987654
No 35
>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=46.80 E-value=16 Score=24.33 Aligned_cols=14 Identities=21% Similarity=0.309 Sum_probs=11.9
Q ss_pred cCCCCCCEEEEEEc
Q 043432 86 YCLELGDYIMVYKD 99 (105)
Q Consensus 86 k~L~~GD~i~f~~~ 99 (105)
.++++||.|+|..-
T Consensus 30 ~~ikvGD~I~f~~~ 43 (109)
T cd06555 30 QQIKVGDKILFNDL 43 (109)
T ss_pred hcCCCCCEEEEEEc
Confidence 67999999999663
No 36
>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Probab=46.26 E-value=25 Score=21.18 Aligned_cols=20 Identities=30% Similarity=0.451 Sum_probs=16.8
Q ss_pred hcCCCCCCEEEEEEcCCCCC
Q 043432 85 RYCLELGDYIMVYKDELEGS 104 (105)
Q Consensus 85 ~k~L~~GD~i~f~~~~~~g~ 104 (105)
--+|++|..|.++.+..+|+
T Consensus 35 ~~~L~~G~kV~V~yd~~~gk 54 (61)
T PF07076_consen 35 FDGLKPGMKVVVFYDEVDGK 54 (61)
T ss_pred ccccCCCCEEEEEEEccCCc
Confidence 56899999999988887774
No 37
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=46.14 E-value=60 Score=21.75 Aligned_cols=33 Identities=15% Similarity=0.244 Sum_probs=22.6
Q ss_pred EEEEEEECCCCeEEEEEEEEcCCCCCcceeecChHHHHhhcCCCCCCEEEEE
Q 043432 46 FWMHLEDMDFNKVWTFKFRFWPNNRGRMYIFENTRAFIKRYCLELGDYIMVY 97 (105)
Q Consensus 46 ~~l~~~D~~~g~~W~fr~~~~~~~~s~~y~l~gW~~fV~~k~L~~GD~i~f~ 97 (105)
..+.+.|. ||. .+++.|. . .+..|++||+|.+.
T Consensus 42 ~~~~l~D~-TG~---I~~tlW~--~-------------~a~~l~~GdvV~I~ 74 (129)
T PRK06461 42 SEAVVGDE-TGR---VKLTLWG--E-------------QAGSLKEGEVVEIE 74 (129)
T ss_pred EEEEEECC-CCE---EEEEEeC--C-------------ccccCCCCCEEEEE
Confidence 35677888 675 6778883 2 12368889988875
No 38
>cd00989 PDZ_metalloprotease PDZ domain of bacterial and plant zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=45.38 E-value=17 Score=21.25 Aligned_cols=14 Identities=29% Similarity=0.423 Sum_probs=10.8
Q ss_pred HhhcCCCCCCEEEE
Q 043432 83 IKRYCLELGDYIMV 96 (105)
Q Consensus 83 V~~k~L~~GD~i~f 96 (105)
....+|++||+|+=
T Consensus 25 a~~~gl~~GD~I~~ 38 (79)
T cd00989 25 AAKAGLKAGDRILA 38 (79)
T ss_pred HHHcCCCCCCEEEE
Confidence 34578999999863
No 39
>PRK01777 hypothetical protein; Validated
Probab=45.29 E-value=16 Score=23.63 Aligned_cols=14 Identities=29% Similarity=0.515 Sum_probs=12.4
Q ss_pred hcCCCCCCEEEEEE
Q 043432 85 RYCLELGDYIMVYK 98 (105)
Q Consensus 85 ~k~L~~GD~i~f~~ 98 (105)
+.-|+.||.|.+|+
T Consensus 62 d~~L~dGDRVeIyr 75 (95)
T PRK01777 62 TDVLRDGDRVEIYR 75 (95)
T ss_pred CCcCCCCCEEEEec
Confidence 55799999999998
No 40
>PRK11347 antitoxin ChpS; Provisional
Probab=44.58 E-value=69 Score=20.10 Aligned_cols=35 Identities=14% Similarity=0.276 Sum_probs=24.9
Q ss_pred EEEEcCCCCCcceeecChHHHHhhcCCCCCCEEEEEEcC
Q 043432 62 KFRFWPNNRGRMYIFENTRAFIKRYCLELGDYIMVYKDE 100 (105)
Q Consensus 62 r~~~~~~~~s~~y~l~gW~~fV~~k~L~~GD~i~f~~~~ 100 (105)
+.+.|.| |..-.|- ..++++-+|.+||.|.+.-..
T Consensus 4 ~v~kwGN--S~~vriP--k~il~~l~l~~G~~v~i~v~~ 38 (83)
T PRK11347 4 TIKRWGN--SAGMVIP--NIVMKELNLQPGQSVEAQVSN 38 (83)
T ss_pred EEEEEcC--ceeEEeC--HHHHHHcCCCCCCEEEEEEEC
Confidence 4567844 5334444 489999999999999886543
No 41
>PRK06488 sulfur carrier protein ThiS; Validated
Probab=43.21 E-value=28 Score=20.30 Aligned_cols=18 Identities=28% Similarity=0.425 Sum_probs=14.5
Q ss_pred cCCCCCCEEEEEEcCCCC
Q 043432 86 YCLELGDYIMVYKDELEG 103 (105)
Q Consensus 86 k~L~~GD~i~f~~~~~~g 103 (105)
..|+.||.|.|..-..+|
T Consensus 48 ~~L~dgD~Ieiv~~V~GG 65 (65)
T PRK06488 48 FVLHEGDRIEILSPMQGG 65 (65)
T ss_pred cccCCCCEEEEEEeccCC
Confidence 469999999998866655
No 42
>PRK06944 sulfur carrier protein ThiS; Provisional
Probab=42.79 E-value=28 Score=20.08 Aligned_cols=17 Identities=24% Similarity=0.331 Sum_probs=13.9
Q ss_pred CCCCCCEEEEEEcCCCC
Q 043432 87 CLELGDYIMVYKDELEG 103 (105)
Q Consensus 87 ~L~~GD~i~f~~~~~~g 103 (105)
-|+.||.|-++.-..+|
T Consensus 49 ~L~~gD~vei~~~v~GG 65 (65)
T PRK06944 49 ALAAGDRLDLVQPVAGG 65 (65)
T ss_pred cCCCCCEEEEEeeccCC
Confidence 39999999999866655
No 43
>cd04498 hPOT1_OB2 hPOT1_OB2: A subfamily of OB folds similar to the second OB fold (OB2) of human protection of telomeres 1 protein (hPOT1). POT1 proteins bind to the single-stranded (ss) 3-prime ends of the telomere. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB2) which cooperate to bind telomeric ssDNA. OB1 makes more extensive contact with the ssDNA than OB2. OB2 protects the 3' end of the ssDNA. hPOT1 is implicated in telomere length regulation.
Probab=42.28 E-value=26 Score=23.85 Aligned_cols=16 Identities=31% Similarity=0.704 Sum_probs=13.8
Q ss_pred HHHHhhcCCCCCCEEEEE
Q 043432 80 RAFIKRYCLELGDYIMVY 97 (105)
Q Consensus 80 ~~fV~~k~L~~GD~i~f~ 97 (105)
..|+|+ |++||.|.++
T Consensus 71 ~~~ar~--lK~GdfV~L~ 86 (123)
T cd04498 71 VELAKS--LKPGDFVRIY 86 (123)
T ss_pred HHHHhh--CCCCCEEEEE
Confidence 578888 9999999885
No 44
>PF05593 RHS_repeat: RHS Repeat; InterPro: IPR006530 These sequences contain two tandem copies of a 21-residue extracellular repeat that is 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=42.02 E-value=52 Score=17.12 Aligned_cols=21 Identities=10% Similarity=0.132 Sum_probs=15.4
Q ss_pred CCEEEEEEECCCCeEEEEEEEE
Q 043432 44 AGFWMHLEDMDFNKVWTFKFRF 65 (105)
Q Consensus 44 ~~~~l~~~D~~~g~~W~fr~~~ 65 (105)
.|..+.+.|. .|.+|+|.|--
T Consensus 4 ~G~l~~~~d~-~G~~~~y~YD~ 24 (38)
T PF05593_consen 4 NGRLTSVTDP-DGRTTRYTYDA 24 (38)
T ss_pred CCCEEEEEcC-CCCEEEEEECC
Confidence 4567788899 48999777553
No 45
>cd01756 PLAT_repeat PLAT/LH2 domain repeats of family of proteins with unknown function. In general, PLAT/LH2 consists of an eight stranded beta-barrel and it's proposed function is to mediate interaction with lipids or membrane bound proteins.
Probab=41.62 E-value=50 Score=21.60 Aligned_cols=48 Identities=10% Similarity=0.079 Sum_probs=27.9
Q ss_pred CCCCCCCcEEeehhhhhccCCCCCCCCCEEEEEEECCCCeEEEEEEEEcCCC
Q 043432 18 SDVNAAGRIVLPKKLAETYLPPVNEKAGFWMHLEDMDFNKVWTFKFRFWPNN 69 (105)
Q Consensus 18 SDv~~~~rl~iPk~~ae~~lP~l~~~~~~~l~~~D~~~g~~W~fr~~~~~~~ 69 (105)
.|++...++.|=.+... .-|.- .=-.|.|.|..+|+.|.|-|..|-..
T Consensus 59 ~~lG~l~~i~i~~d~~g-~~~~W---~~~~V~V~~~~~~~~~~F~~~~Wl~~ 106 (120)
T cd01756 59 VDLGKLKKIRIGHDNSG-LGAGW---FLDKVEIREPGTGDEYTFPCNRWLDK 106 (120)
T ss_pred cCCCCeEEEEEEECCCC-CCCCc---EEeEEEEEECCCceEEEEEeCCccCC
Confidence 56665555655543321 11110 00366788887789999998888543
No 46
>PRK00809 hypothetical protein; Provisional
Probab=41.61 E-value=24 Score=24.39 Aligned_cols=18 Identities=22% Similarity=0.593 Sum_probs=15.0
Q ss_pred HHHhhcCCCCCCEEEEEEcC
Q 043432 81 AFIKRYCLELGDYIMVYKDE 100 (105)
Q Consensus 81 ~fV~~k~L~~GD~i~f~~~~ 100 (105)
+++++ +++||.|+||-..
T Consensus 30 n~lr~--Mk~GD~v~fYhs~ 47 (144)
T PRK00809 30 NTIEK--VKPGDKLIIYVSQ 47 (144)
T ss_pred hHHhh--CCCCCEEEEEECC
Confidence 66666 9999999999865
No 47
>smart00532 LIGANc Ligase N family.
Probab=41.41 E-value=29 Score=28.37 Aligned_cols=20 Identities=25% Similarity=0.353 Sum_probs=18.6
Q ss_pred HHHHhhcCCCCCCEEEEEEc
Q 043432 80 RAFIKRYCLELGDYIMVYKD 99 (105)
Q Consensus 80 ~~fV~~k~L~~GD~i~f~~~ 99 (105)
.+++++++|+.||.|.+.|.
T Consensus 355 ~~~i~~~~i~iGd~V~V~ra 374 (441)
T smart00532 355 EDEIEEKDIRIGDTVVVRKA 374 (441)
T ss_pred HHHHHHcCCCCCCEEEEEEC
Confidence 68999999999999999985
No 48
>PLN03111 DNA-directed RNA polymerase II subunit family protein; Provisional
Probab=41.35 E-value=35 Score=25.30 Aligned_cols=26 Identities=23% Similarity=0.499 Sum_probs=20.9
Q ss_pred HHHHhhcCCCCCCEEEEEEc-CCCCCC
Q 043432 80 RAFIKRYCLELGDYIMVYKD-ELEGSY 105 (105)
Q Consensus 80 ~~fV~~k~L~~GD~i~f~~~-~~~g~~ 105 (105)
...++..+|+.||+|-+.|. +-.|+|
T Consensus 173 DPvary~g~k~G~vvkI~R~S~taG~~ 199 (206)
T PLN03111 173 DPIARYYGLKRGQVVKIIRPSETAGRY 199 (206)
T ss_pred ChhhHhcCCCCCCEEEEEECCCCCCCc
Confidence 57788999999999999996 444554
No 49
>PF14478 DUF4430: Domain of unknown function (DUF4430); PDB: 3U7Z_B 2BB5_A.
Probab=41.31 E-value=10 Score=22.59 Aligned_cols=17 Identities=35% Similarity=0.331 Sum_probs=10.2
Q ss_pred HHHhhcCCCCCCEEEEE
Q 043432 81 AFIKRYCLELGDYIMVY 97 (105)
Q Consensus 81 ~fV~~k~L~~GD~i~f~ 97 (105)
.=+.+..|+.||.|+|+
T Consensus 52 ~ga~~~~l~~GD~i~~~ 68 (68)
T PF14478_consen 52 VGAGSYKLKDGDKITWY 68 (68)
T ss_dssp S-CCC-B--TTEEEEE-
T ss_pred cCcceeEeCCCCEEEeC
Confidence 45677899999999985
No 50
>PF11792 Baculo_LEF5_C: Baculoviridae late expression factor 5 C-terminal domain; InterPro: IPR021758 This C-terminal domain is likely to be a zinc-binding domain.
Probab=41.13 E-value=5.7 Score=22.34 Aligned_cols=13 Identities=23% Similarity=0.151 Sum_probs=10.3
Q ss_pred HhhcCCCCCCEEE
Q 043432 83 IKRYCLELGDYIM 95 (105)
Q Consensus 83 V~~k~L~~GD~i~ 95 (105)
+-+++|++||+.+
T Consensus 19 ~~E~Q~RAGDE~V 31 (43)
T PF11792_consen 19 TIEKQLRAGDEAV 31 (43)
T ss_pred ehhhhhcccchHH
Confidence 5679999999753
No 51
>PF09269 DUF1967: Domain of unknown function (DUF1967); InterPro: IPR015349 The Obg family comprises a group of ancient P-loop small G proteins (GTPases) belonging to the TRAFAC (for translation factors) class and can be subdivided into several distinct protein subfamilies []. OBG GTPases have been found in both prokaryotes and eukaryotes []. The structure of the OBG GTPase from Thermus thermophilus has been determined []. This entry represents a C-terminal domain found in certain OBG GTPases. This domain contains a four-stranded beta sheet and three alpha helices flanked by an additional beta strand. It is predominantly found in the bacterial GTP-binding protein Obg, and is functionally uncharacterised. ; GO: 0000166 nucleotide binding; PDB: 1UDX_A.
Probab=40.94 E-value=27 Score=21.08 Aligned_cols=20 Identities=10% Similarity=0.155 Sum_probs=13.8
Q ss_pred ChHHHHhhcCCCCCCEEEEE
Q 043432 78 NTRAFIKRYCLELGDYIMVY 97 (105)
Q Consensus 78 gW~~fV~~k~L~~GD~i~f~ 97 (105)
|-.+-.++++.++||+|.+.
T Consensus 44 Gv~~~L~~~G~~~GD~V~Ig 63 (69)
T PF09269_consen 44 GVEKALRKAGAKEGDTVRIG 63 (69)
T ss_dssp THHHHHHTTT--TT-EEEET
T ss_pred CHHHHHHHcCCCCCCEEEEc
Confidence 55778889999999999873
No 52
>cd01764 Urm1 Urm1-like ubuitin domain. Urm1 (Ubiquitin-Related Modifier1) The Urm1 fold, like those of two closely related proteins MoaD (molybdopterin synthase) and ThiS (sulfur carrier protein), is similar to that of ubiquitin although there is little or no sequence similarity. The C-terminal glycines of Urm1 are conjugated to an E1-like protein Uba4 as part of a novel conjugation system in yeast. The Urm1 fold is found only in eukaryotes.
Probab=40.59 E-value=26 Score=22.42 Aligned_cols=19 Identities=32% Similarity=0.429 Sum_probs=15.2
Q ss_pred hcCCCCCCEEEEEEcCCCC
Q 043432 85 RYCLELGDYIMVYKDELEG 103 (105)
Q Consensus 85 ~k~L~~GD~i~f~~~~~~g 103 (105)
+..|+.||.|.|+.-..+|
T Consensus 76 ~t~L~dgD~v~i~P~v~GG 94 (94)
T cd01764 76 DYILEDGDHVVFISTLHGG 94 (94)
T ss_pred ccCCCCcCEEEEECCCCCC
Confidence 4679999999999865554
No 53
>PTZ00061 DNA-directed RNA polymerase; Provisional
Probab=40.17 E-value=36 Score=25.21 Aligned_cols=26 Identities=19% Similarity=0.442 Sum_probs=20.5
Q ss_pred HHHHhhcCCCCCCEEEEEEc-CCCCCC
Q 043432 80 RAFIKRYCLELGDYIMVYKD-ELEGSY 105 (105)
Q Consensus 80 ~~fV~~k~L~~GD~i~f~~~-~~~g~~ 105 (105)
...++..+|+.||+|-+.|. +-.|+|
T Consensus 172 DPvary~g~k~G~vvkI~R~S~taG~~ 198 (205)
T PTZ00061 172 DPVARYFGLSKGQVVKIIRPSETAGRY 198 (205)
T ss_pred ChhhHhcCCCCCCEEEEEECCCCCCcc
Confidence 57788899999999999985 444544
No 54
>cd01752 PLAT_polycystin PLAT/LH2 domain of polycystin-1 like proteins. Polycystins are a large family of membrane proteins composed of multiple domains, present in fish, invertebrates, mammals, and humans that are widely expressed in various cell types and whose biological functions remain poorly defined. In human, mutations in polycystin-1 (PKD1) and polycystin-2 (PKD2) have been shown to be the cause for autosomal dominant polycystic kidney disease (ADPKD). The generally proposed function of PLAT/LH2 domains is to mediate interaction with lipids or membrane bound proteins.
Probab=40.08 E-value=38 Score=22.24 Aligned_cols=22 Identities=23% Similarity=0.498 Sum_probs=17.9
Q ss_pred EEEEEECCCCeEEEEEEEEcCC
Q 043432 47 WMHLEDMDFNKVWTFKFRFWPN 68 (105)
Q Consensus 47 ~l~~~D~~~g~~W~fr~~~~~~ 68 (105)
.|.|.|..+++.|.|.|..|-.
T Consensus 84 ~V~V~~~~t~~~~~F~~~rWl~ 105 (120)
T cd01752 84 RVIVRDLQTGKKWFFLCNDWLS 105 (120)
T ss_pred EEEEEECCCCcEEEEEeCcEEC
Confidence 5678888788999999988854
No 55
>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=39.85 E-value=20 Score=24.16 Aligned_cols=15 Identities=13% Similarity=0.204 Sum_probs=11.9
Q ss_pred HhhcCCCCCCEEEEE
Q 043432 83 IKRYCLELGDYIMVY 97 (105)
Q Consensus 83 V~~k~L~~GD~i~f~ 97 (105)
|....|++||.|.|-
T Consensus 72 v~~~~~qpGDlvff~ 86 (134)
T TIGR02219 72 VPCDAAQPGDVLVFR 86 (134)
T ss_pred cchhcCCCCCEEEEe
Confidence 455689999999775
No 56
>PRK05659 sulfur carrier protein ThiS; Validated
Probab=39.78 E-value=31 Score=19.94 Aligned_cols=18 Identities=22% Similarity=0.231 Sum_probs=14.2
Q ss_pred cCCCCCCEEEEEEcCCCC
Q 043432 86 YCLELGDYIMVYKDELEG 103 (105)
Q Consensus 86 k~L~~GD~i~f~~~~~~g 103 (105)
.-|++||.|-++.-.++|
T Consensus 49 ~~l~~gD~vei~~~vgGG 66 (66)
T PRK05659 49 TALREGDVVEIVHALGGG 66 (66)
T ss_pred ccCCCCCEEEEEEEecCC
Confidence 348999999998866655
No 57
>cd00565 ThiS ThiaminS ubiquitin-like sulfur carrier protein. ThiS (ThiaminS) is a sulfur carrier protein involved in thiamin biosynthesis in bacteria. The ThiS fold, like those of two closely related proteins MoaD and Urm1, is similar to that of ubiquitin although there is little or no sequence similarity.
Probab=39.71 E-value=34 Score=19.91 Aligned_cols=17 Identities=29% Similarity=0.225 Sum_probs=13.9
Q ss_pred CCCCCCEEEEEEcCCCC
Q 043432 87 CLELGDYIMVYKDELEG 103 (105)
Q Consensus 87 ~L~~GD~i~f~~~~~~g 103 (105)
.|+.||.|.+..-.++|
T Consensus 49 ~L~~gD~V~ii~~v~GG 65 (65)
T cd00565 49 PLQDGDRIEIVTAVGGG 65 (65)
T ss_pred ecCCCCEEEEEEeccCC
Confidence 59999999998866655
No 58
>smart00326 SH3 Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
Probab=39.52 E-value=40 Score=17.82 Aligned_cols=18 Identities=22% Similarity=0.364 Sum_probs=13.3
Q ss_pred hcCCCCCCEEEEEEcCCC
Q 043432 85 RYCLELGDYIMVYKDELE 102 (105)
Q Consensus 85 ~k~L~~GD~i~f~~~~~~ 102 (105)
+-.|++||.|.+.....+
T Consensus 18 ~l~~~~Gd~v~v~~~~~~ 35 (58)
T smart00326 18 ELSFKKGDIITVLEKSDD 35 (58)
T ss_pred CCCCCCCCEEEEEEcCCC
Confidence 346889999999876544
No 59
>PRK05863 sulfur carrier protein ThiS; Provisional
Probab=39.15 E-value=34 Score=20.08 Aligned_cols=16 Identities=25% Similarity=0.212 Sum_probs=13.6
Q ss_pred CCCCCEEEEEEcCCCC
Q 043432 88 LELGDYIMVYKDELEG 103 (105)
Q Consensus 88 L~~GD~i~f~~~~~~g 103 (105)
|+.||.|-+..-.++|
T Consensus 50 L~~gD~ieIv~~VgGG 65 (65)
T PRK05863 50 LRDGARLEVVTAVQGG 65 (65)
T ss_pred cCCCCEEEEEeeccCC
Confidence 9999999998876655
No 60
>PRK14699 replication factor A; Provisional
Probab=38.93 E-value=1.5e+02 Score=24.64 Aligned_cols=36 Identities=19% Similarity=0.349 Sum_probs=23.0
Q ss_pred EEEEEECCCCeEEEEEEEEcCCCCCcceeecChHHHHhhcCCCCCCEEEE
Q 043432 47 WMHLEDMDFNKVWTFKFRFWPNNRGRMYIFENTRAFIKRYCLELGDYIMV 96 (105)
Q Consensus 47 ~l~~~D~~~g~~W~fr~~~~~~~~s~~y~l~gW~~fV~~k~L~~GD~i~f 96 (105)
.+.+.|. ||. -+++.| +.. .+.+.+-+|++||+|-+
T Consensus 97 ~~~iaDe-TG~---ir~tlW--~~~--------a~~~~~g~l~~GDvv~I 132 (484)
T PRK14699 97 NLIVGDE-TGK---IKLTLW--DNM--------ADLIKAGKIKAGQTLQI 132 (484)
T ss_pred EEEEecC-CCe---EEEEEe--cCc--------cchhhhcCCCCCCEEEE
Confidence 3466777 673 566677 221 23455557999999987
No 61
>cd00991 PDZ_archaeal_metalloprotease PDZ domain of archaeal zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=38.66 E-value=24 Score=21.13 Aligned_cols=13 Identities=31% Similarity=0.396 Sum_probs=10.2
Q ss_pred hhcCCCCCCEEEE
Q 043432 84 KRYCLELGDYIMV 96 (105)
Q Consensus 84 ~~k~L~~GD~i~f 96 (105)
...+|++||+|+=
T Consensus 24 ~~aGL~~GDiI~~ 36 (79)
T cd00991 24 ENAVLHTGDVIYS 36 (79)
T ss_pred HhcCCCCCCEEEE
Confidence 4568999999873
No 62
>smart00536 AXH domain in Ataxins and HMG containing proteins. unknown function
Probab=38.37 E-value=17 Score=24.65 Aligned_cols=26 Identities=12% Similarity=0.198 Sum_probs=19.4
Q ss_pred Ccceeec-ChHHH----------HhhcCCCCCCEEEE
Q 043432 71 GRMYIFE-NTRAF----------IKRYCLELGDYIMV 96 (105)
Q Consensus 71 s~~y~l~-gW~~f----------V~~k~L~~GD~i~f 96 (105)
-..||.. ||+.| +....|++||++.-
T Consensus 76 HPfFV~gqGWsSc~P~lT~~~ygL~C~~L~vGDVCl~ 112 (116)
T smart00536 76 HPFFVKGKGWSSCYPSLTVQLYGLPCCELQVGDVCLS 112 (116)
T ss_pred CCeEEcCccccccChhhhhhhcCCcceecccCCEEec
Confidence 4567777 69877 45678999999864
No 63
>cd01757 PLAT_RAB6IP1 PLAT/LH2 domain present in RAB6 interacting protein 1 (Rab6IP1)_like family. PLAT/LH2 domains consists of an eight stranded beta-barrel. In RabIP1 this domain may participate in lipid-mediated modulation of Rab6IP1's function via it's generally proposed function of mediating interaction with lipids or membrane bound proteins.
Probab=37.74 E-value=39 Score=22.51 Aligned_cols=21 Identities=10% Similarity=0.308 Sum_probs=16.6
Q ss_pred EEEEEECCCCeEEEEEEEEcC
Q 043432 47 WMHLEDMDFNKVWTFKFRFWP 67 (105)
Q Consensus 47 ~l~~~D~~~g~~W~fr~~~~~ 67 (105)
.|.|.|..+|+.|.|-|-.|-
T Consensus 75 ~V~V~d~~t~~~~~FpC~rWL 95 (114)
T cd01757 75 YVMVRNEITGHTYKFPCGRWL 95 (114)
T ss_pred EEEEEeCCCCCEEEEecCcee
Confidence 567788667899999888774
No 64
>cd00174 SH3 Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
Probab=37.52 E-value=45 Score=17.39 Aligned_cols=19 Identities=26% Similarity=0.436 Sum_probs=13.9
Q ss_pred hcCCCCCCEEEEEEcCCCC
Q 043432 85 RYCLELGDYIMVYKDELEG 103 (105)
Q Consensus 85 ~k~L~~GD~i~f~~~~~~g 103 (105)
+-.|++||.|.+.....+|
T Consensus 15 ~l~~~~Gd~v~v~~~~~~~ 33 (54)
T cd00174 15 ELSFKKGDIIEVLEKSDDG 33 (54)
T ss_pred CCCCCCCCEEEEEEcCCCC
Confidence 4568899999998764443
No 65
>smart00306 HintN Hint (Hedgehog/Intein) domain N-terminal region. Hedgehog/Intein domain, N-terminal region. Domain has been split to accommodate large insertions of endonucleases.
Probab=37.46 E-value=30 Score=20.96 Aligned_cols=15 Identities=33% Similarity=0.649 Sum_probs=13.2
Q ss_pred HHhhcCCCCCCEEEE
Q 043432 82 FIKRYCLELGDYIMV 96 (105)
Q Consensus 82 fV~~k~L~~GD~i~f 96 (105)
.+++..|++||.|.+
T Consensus 84 w~~a~~l~~gd~v~~ 98 (100)
T smart00306 84 WVFASELKPGDYVLV 98 (100)
T ss_pred EEEHHHCCCCCEEEe
Confidence 588999999999875
No 66
>PRK11130 moaD molybdopterin synthase small subunit; Provisional
Probab=37.33 E-value=31 Score=21.04 Aligned_cols=19 Identities=21% Similarity=0.209 Sum_probs=15.0
Q ss_pred hcCCCCCCEEEEEEcCCCC
Q 043432 85 RYCLELGDYIMVYKDELEG 103 (105)
Q Consensus 85 ~k~L~~GD~i~f~~~~~~g 103 (105)
+--|+.||.|.|+.-..+|
T Consensus 63 ~~~l~dgDeVai~PPVsGG 81 (81)
T PRK11130 63 DHPLTDGDEVAFFPPVTGG 81 (81)
T ss_pred CCCCCCCCEEEEeCCCCCC
Confidence 4469999999999866554
No 67
>cd01234 PH_CADPS CADPS (Ca2+-dependent activator protein) Pleckstrin homology (PH) domain. CADPS (Ca2+-dependent activator protein) Pleckstrin homology (PH) domain. CADPS is a calcium-dependent activator involved in secretion. It contains a central PH domain that binds to phosphoinositide 4,5 bisphosphate containing liposomes. However, membrane association may also be mediated by binding to phosphatidlyserine via general electrostatic interactions. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=36.75 E-value=17 Score=24.49 Aligned_cols=17 Identities=18% Similarity=0.253 Sum_probs=13.5
Q ss_pred cCCCCCCEEEEEEcCCC
Q 043432 86 YCLELGDYIMVYKDELE 102 (105)
Q Consensus 86 k~L~~GD~i~f~~~~~~ 102 (105)
+.+++||.|.|--+.++
T Consensus 81 ~avkegd~~~fa~~de~ 97 (117)
T cd01234 81 NAVKEGDELKFATDDEN 97 (117)
T ss_pred heeccCcEEEEeccchH
Confidence 45899999999876654
No 68
>PRK02268 hypothetical protein; Provisional
Probab=36.70 E-value=26 Score=24.38 Aligned_cols=13 Identities=31% Similarity=0.677 Sum_probs=11.3
Q ss_pred cCCCCCCEEEEEE
Q 043432 86 YCLELGDYIMVYK 98 (105)
Q Consensus 86 k~L~~GD~i~f~~ 98 (105)
+++++||.|++|-
T Consensus 34 ~RmkpGD~ivyYs 46 (141)
T PRK02268 34 RRMKPGDWIIYYS 46 (141)
T ss_pred hcCCCCCEEEEEe
Confidence 5679999999986
No 69
>cd05829 Sortase_E Sortase E (SrtE) is a membrane transpeptidase found in gram-positive bacteria that cleaves surface proteins at a cell sorting motif and catalyzes a transpeptidation reaction in which the surface protein substrate is covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. The function of Sortase E is unknown. In two different sortase families, the N-terminus either functions as both a signal peptide for secretion and a stop-transfer signal for membrane anchoring, or it contains a signal peptide only and the C-terminus serves as a membrane anchor. Most gram-positive bacteria contain more than one sortase and it is thought that the different sortases anchor different surface protein classes. The sortase domain is a modified beta-barrel flanked by two (SrtA) or three (SrtB) short alpha-helices.
Probab=36.46 E-value=42 Score=22.84 Aligned_cols=27 Identities=19% Similarity=0.236 Sum_probs=21.1
Q ss_pred cceeecC--hHH-----HHhhcCCCCCCEEEEEE
Q 043432 72 RMYIFEN--TRA-----FIKRYCLELGDYIMVYK 98 (105)
Q Consensus 72 ~~y~l~g--W~~-----fV~~k~L~~GD~i~f~~ 98 (105)
+.++|.| +.. |-+=..|++||.|.+..
T Consensus 50 Gn~viaGH~~~~g~~~~F~~L~~l~~GD~I~v~~ 83 (144)
T cd05829 50 GTAVLAGHVDSRGGPAVFFRLGDLRKGDKVEVTR 83 (144)
T ss_pred CCEEEEEecCCCCCChhhcchhcCCCCCEEEEEE
Confidence 4566664 443 88889999999999977
No 70
>PF13180 PDZ_2: PDZ domain; PDB: 2L97_A 1Y8T_A 2Z9I_A 1LCY_A 2PZD_B 2P3W_A 1VCW_C 1TE0_B 1SOZ_C 1SOT_C ....
Probab=36.42 E-value=21 Score=21.46 Aligned_cols=13 Identities=31% Similarity=0.465 Sum_probs=9.2
Q ss_pred HhhcCCCCCCEEE
Q 043432 83 IKRYCLELGDYIM 95 (105)
Q Consensus 83 V~~k~L~~GD~i~ 95 (105)
+...+|++||+|+
T Consensus 27 A~~aGl~~GD~I~ 39 (82)
T PF13180_consen 27 AAKAGLQPGDIIL 39 (82)
T ss_dssp HHHTTS-TTEEEE
T ss_pred HHHCCCCCCcEEE
Confidence 3456799999986
No 71
>TIGR01683 thiS thiamine biosynthesis protein ThiS. This model represents ThiS, a small thiamine-biosynthesis protein related to MoaD, a molybdenum cofactor biosynthesis protein. Both proteins are involved in sulfur transfer. ThiS has a conserved Gly-Gly C-terminus that is modified, in reactions requiring ThiI, ThiF, IscS, and a sulfur atom from Cys, into the thiocarboxylate that provides the sulfur for thiazole biosynthesis.
Probab=36.14 E-value=41 Score=19.49 Aligned_cols=17 Identities=29% Similarity=0.196 Sum_probs=14.0
Q ss_pred CCCCCCEEEEEEcCCCC
Q 043432 87 CLELGDYIMVYKDELEG 103 (105)
Q Consensus 87 ~L~~GD~i~f~~~~~~g 103 (105)
.|+.||.|.++.-.++|
T Consensus 48 ~L~~gD~veii~~V~GG 64 (64)
T TIGR01683 48 ILKEGDRIEIVTFVGGG 64 (64)
T ss_pred ecCCCCEEEEEEeccCC
Confidence 59999999998866655
No 72
>PRK08053 sulfur carrier protein ThiS; Provisional
Probab=36.03 E-value=41 Score=19.72 Aligned_cols=17 Identities=24% Similarity=0.436 Sum_probs=13.9
Q ss_pred CCCCCCEEEEEEcCCCC
Q 043432 87 CLELGDYIMVYKDELEG 103 (105)
Q Consensus 87 ~L~~GD~i~f~~~~~~g 103 (105)
.|++||.|.+..-.++|
T Consensus 50 ~L~~gD~Ieii~~v~GG 66 (66)
T PRK08053 50 IVQDGDQILLFQVIAGG 66 (66)
T ss_pred ccCCCCEEEEEEEccCC
Confidence 49999999998866655
No 73
>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=35.94 E-value=32 Score=21.55 Aligned_cols=19 Identities=16% Similarity=0.225 Sum_probs=13.8
Q ss_pred HHHhhcCCCCCCEEEEEEc
Q 043432 81 AFIKRYCLELGDYIMVYKD 99 (105)
Q Consensus 81 ~fV~~k~L~~GD~i~f~~~ 99 (105)
+=+++.+|+.||.|.++-.
T Consensus 37 ~dA~~~Gi~~Gd~V~v~s~ 55 (110)
T PF01568_consen 37 EDAAKLGIKDGDWVRVSSP 55 (110)
T ss_dssp HHHHHCT--TTCEEEEEET
T ss_pred HHHHHhcCcCCCEEEEEec
Confidence 5577889999999999754
No 74
>PRK06437 hypothetical protein; Provisional
Probab=35.72 E-value=40 Score=20.03 Aligned_cols=20 Identities=10% Similarity=0.102 Sum_probs=15.5
Q ss_pred hhcCCCCCCEEEEEEcCCCC
Q 043432 84 KRYCLELGDYIMVYKDELEG 103 (105)
Q Consensus 84 ~~k~L~~GD~i~f~~~~~~g 103 (105)
.+.-|++||.|.+.+-.++|
T Consensus 48 ~~~~L~dgD~Veiv~~V~GG 67 (67)
T PRK06437 48 EDHNVKKEDDVLILEVFSGG 67 (67)
T ss_pred CceEcCCCCEEEEEecccCC
Confidence 45578999999998866655
No 75
>PF03658 Ub-RnfH: RnfH family Ubiquitin; InterPro: IPR005346 This is a small family of proteins of unknown function.; PDB: 2HJ1_B.
Probab=35.69 E-value=25 Score=22.37 Aligned_cols=14 Identities=29% Similarity=0.534 Sum_probs=8.0
Q ss_pred hcCCCCCCEEEEEE
Q 043432 85 RYCLELGDYIMVYK 98 (105)
Q Consensus 85 ~k~L~~GD~i~f~~ 98 (105)
+.-|++||.|-+||
T Consensus 59 d~~L~~GDRVEIYR 72 (84)
T PF03658_consen 59 DTVLRDGDRVEIYR 72 (84)
T ss_dssp T-B--TT-EEEEE-
T ss_pred CCcCCCCCEEEEec
Confidence 45689999999998
No 76
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=35.26 E-value=33 Score=22.97 Aligned_cols=14 Identities=36% Similarity=0.527 Sum_probs=12.1
Q ss_pred cCCCCCCEEEEEEc
Q 043432 86 YCLELGDYIMVYKD 99 (105)
Q Consensus 86 k~L~~GD~i~f~~~ 99 (105)
+-|+.||.|++.++
T Consensus 49 ~~L~dGDsV~liKD 62 (109)
T TIGR00686 49 NLLANGDSVILIKD 62 (109)
T ss_pred CCccCCCEEEEEee
Confidence 46899999999886
No 77
>PF00018 SH3_1: SH3 domain; InterPro: IPR001452 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. The crystal structure of the SH3 domain of the cytoskeletal protein spectrin, and the solution structures of SH3 domains of phospholipase C (PLC-y) and phosphatidylinositol 3-kinase p85 alpha-subunit, have been determined [, , ]. In spite of relatively limited sequence similarity, their overall structures are similar. The domains belong to the alpha+beta structural class, with 5 to 8 beta-strands forming 2 tightly-packed, anti-parallel beta-sheets arranged in a barrel-like structure, and intervening loops sometimes forming helices. Conserved aliphatic and aromatic residues form a hydrophobic core (A11, L23, A29, V34, W42, L52 and V59 in PLC-y []) and a hydrophobic pocket on the molecular surface (L12, F13, W53 and P55 in PLC-y). The conserved core is believed to stabilise the fold, while the pocket is thought to serve as a binding site for target proteins. Conserved carboxylic amino acids located in the loops, on the periphery of the pocket (D14 and E22), may be involved in protein-protein interactions via proline-rich regions. The N- and C-termini are packed in close proximity, indicating that they are independent structural modules.; GO: 0005515 protein binding; PDB: 1UHF_A 1W1F_A 1WA7_A 1SEM_A 1KFZ_A 2SEM_B 1K76_A 3SEM_B 1X2Q_A 2J06_B ....
Probab=34.39 E-value=35 Score=18.45 Aligned_cols=18 Identities=22% Similarity=0.338 Sum_probs=12.8
Q ss_pred hcCCCCCCEEEEEEcCCC
Q 043432 85 RYCLELGDYIMVYKDELE 102 (105)
Q Consensus 85 ~k~L~~GD~i~f~~~~~~ 102 (105)
+-.+++||.|.+....++
T Consensus 13 eLs~~~Gd~i~v~~~~~~ 30 (48)
T PF00018_consen 13 ELSFKKGDIIEVLEKSDD 30 (48)
T ss_dssp BSEB-TTEEEEEEEESSS
T ss_pred EEeEECCCEEEEEEecCC
Confidence 446889999999886554
No 78
>cd00136 PDZ PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(pos
Probab=34.36 E-value=33 Score=19.48 Aligned_cols=13 Identities=38% Similarity=0.598 Sum_probs=10.3
Q ss_pred hhcCCCCCCEEEE
Q 043432 84 KRYCLELGDYIMV 96 (105)
Q Consensus 84 ~~k~L~~GD~i~f 96 (105)
...+|++||.|+=
T Consensus 27 ~~~gl~~GD~I~~ 39 (70)
T cd00136 27 ERAGLQAGDVILA 39 (70)
T ss_pred HHcCCCCCCEEEE
Confidence 3468999999873
No 79
>COG2012 RPB5 DNA-directed RNA polymerase, subunit H, RpoH/RPB5 [Transcription]
Probab=33.67 E-value=52 Score=20.85 Aligned_cols=21 Identities=14% Similarity=0.207 Sum_probs=17.8
Q ss_pred HHHhhcCCCCCCEEEEEEcCC
Q 043432 81 AFIKRYCLELGDYIMVYKDEL 101 (105)
Q Consensus 81 ~fV~~k~L~~GD~i~f~~~~~ 101 (105)
..++.-+.+.||+|-+.|...
T Consensus 48 Pva~~lgak~GdvVkIvRkS~ 68 (80)
T COG2012 48 PVAKALGAKPGDVVKIVRKSP 68 (80)
T ss_pred hhHHHccCCCCcEEEEEecCC
Confidence 568888999999999999754
No 80
>PRK08364 sulfur carrier protein ThiS; Provisional
Probab=33.15 E-value=42 Score=20.01 Aligned_cols=19 Identities=26% Similarity=0.247 Sum_probs=15.1
Q ss_pred hcCCCCCCEEEEEEcCCCC
Q 043432 85 RYCLELGDYIMVYKDELEG 103 (105)
Q Consensus 85 ~k~L~~GD~i~f~~~~~~g 103 (105)
+..|++||.|.|.+-.++|
T Consensus 52 ~~~l~~gD~Veii~~V~GG 70 (70)
T PRK08364 52 DDPVKDGDYVEVIPVVSGG 70 (70)
T ss_pred CcCcCCCCEEEEEccccCC
Confidence 5569999999999876655
No 81
>PF08922 DUF1905: Domain of unknown function (DUF1905); InterPro: IPR015018 This family consist of hypothetical bacterial proteins. ; PDB: 2D9R_A.
Probab=33.07 E-value=1.2e+02 Score=18.62 Aligned_cols=79 Identities=19% Similarity=0.154 Sum_probs=39.1
Q ss_pred EEEecccCCCCCCCcEEeehhhhhccCCCCCCCCCEEEEEEECCCCeEEEEEEEEcCCCCCcceeecChHHHHhhcCCCC
Q 043432 11 FEKQLKNSDVNAAGRIVLPKKLAETYLPPVNEKAGFWMHLEDMDFNKVWTFKFRFWPNNRGRMYIFENTRAFIKRYCLEL 90 (105)
Q Consensus 11 f~K~LT~SDv~~~~rl~iPk~~ae~~lP~l~~~~~~~l~~~D~~~g~~W~fr~~~~~~~~s~~y~l~gW~~fV~~k~L~~ 90 (105)
|+.+|-+++-+ -.-+.||.+.++.+-.. +...+.|.+. . .|..|+- +..+.+ ...|+|-==.+.-++-++.+
T Consensus 1 F~a~l~~~~~~-~~fv~vP~~v~~~l~~~--~~g~v~V~~t-I-~g~~~~~--sl~p~g-~G~~~Lpv~~~vRk~~g~~~ 72 (80)
T PF08922_consen 1 FTATLWKGEGG-WTFVEVPFDVAEELGEG--GWGRVPVRGT-I-DGHPWRT--SLFPMG-NGGYILPVKAAVRKAIGKEA 72 (80)
T ss_dssp EEEE-EE-TTS--EEEE--S-HHHHH--S----S-EEEEEE-E-TTEEEEE--EEEESS-TT-EEEEE-HHHHHHHT--T
T ss_pred CeEEEEecCCc-eEEEEeCHHHHHHhccc--cCCceEEEEE-E-CCEEEEE--EEEECC-CCCEEEEEcHHHHHHcCCCC
Confidence 45555555432 23477998888765333 1233555555 3 2565555 555422 34476662267888999999
Q ss_pred CCEEEEE
Q 043432 91 GDYIMVY 97 (105)
Q Consensus 91 GD~i~f~ 97 (105)
||.|.+.
T Consensus 73 Gd~V~v~ 79 (80)
T PF08922_consen 73 GDTVEVT 79 (80)
T ss_dssp TSEEEEE
T ss_pred CCEEEEE
Confidence 9999763
No 82
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=32.96 E-value=31 Score=24.16 Aligned_cols=23 Identities=17% Similarity=0.291 Sum_probs=18.3
Q ss_pred HHhhcCCCCCCEEEEEEcCCCCC
Q 043432 82 FIKRYCLELGDYIMVYKDELEGS 104 (105)
Q Consensus 82 fV~~k~L~~GD~i~f~~~~~~g~ 104 (105)
-+|+..++.||.|.+......|+
T Consensus 41 ~~Rs~~IkkGD~V~Vi~Gk~KGk 63 (143)
T PTZ00194 41 NVRSMPVRKDDEVMVVRGHHKGR 63 (143)
T ss_pred CCccceeecCCEEEEecCCCCCC
Confidence 45666899999999998777664
No 83
>PRK06033 hypothetical protein; Validated
Probab=32.85 E-value=33 Score=21.51 Aligned_cols=15 Identities=13% Similarity=0.058 Sum_probs=11.6
Q ss_pred hhcCCCCCCEEEEEE
Q 043432 84 KRYCLELGDYIMVYK 98 (105)
Q Consensus 84 ~~k~L~~GD~i~f~~ 98 (105)
.=-+|++||+|.|-+
T Consensus 24 dlL~L~~GDVI~L~~ 38 (83)
T PRK06033 24 QVLRMGRGAVIPLDA 38 (83)
T ss_pred HHhCCCCCCEEEeCC
Confidence 335799999999854
No 84
>cd00990 PDZ_glycyl_aminopeptidase PDZ domain associated with archaeal and bacterial M61 glycyl-aminopeptidases. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand is presumed to form the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=32.82 E-value=34 Score=20.04 Aligned_cols=13 Identities=23% Similarity=0.312 Sum_probs=10.2
Q ss_pred HhhcCCCCCCEEE
Q 043432 83 IKRYCLELGDYIM 95 (105)
Q Consensus 83 V~~k~L~~GD~i~ 95 (105)
....+|++||+|+
T Consensus 25 a~~aGl~~GD~I~ 37 (80)
T cd00990 25 ADKAGLVAGDELV 37 (80)
T ss_pred HHHhCCCCCCEEE
Confidence 3456899999986
No 85
>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=32.67 E-value=31 Score=20.75 Aligned_cols=17 Identities=18% Similarity=0.112 Sum_probs=10.9
Q ss_pred hhcCCCCCCEEEEEEcC
Q 043432 84 KRYCLELGDYIMVYKDE 100 (105)
Q Consensus 84 ~~k~L~~GD~i~f~~~~ 100 (105)
--.+|++||.|.|.-..
T Consensus 39 ~l~~l~~Gd~V~F~~~~ 55 (70)
T PF11604_consen 39 DLAGLKPGDKVRFTFER 55 (70)
T ss_dssp EESS-STT-EEEEEEEE
T ss_pred hhhcCCCCCEEEEEEEE
Confidence 34679999999996543
No 86
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=32.38 E-value=47 Score=28.14 Aligned_cols=22 Identities=14% Similarity=0.203 Sum_probs=19.7
Q ss_pred ChHHHHhhcCCCCCCEEEEEEc
Q 043432 78 NTRAFIKRYCLELGDYIMVYKD 99 (105)
Q Consensus 78 gW~~fV~~k~L~~GD~i~f~~~ 99 (105)
+..+++++++|+.||.|.+.|.
T Consensus 350 hN~~~i~~~~I~iGD~V~V~ra 371 (562)
T PRK08097 350 GSVRRWQQWDIAPGDQVLVSLA 371 (562)
T ss_pred CCHHHHHHcCCCCCCEEEEEec
Confidence 4579999999999999999985
No 87
>TIGR02988 YaaA_near_RecF S4 domain protein YaaA. This small protein has a single S4 domain (pfam01479), as do bacterial ribosomal protein S4, some pseudouridine synthases, tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein family are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members of this family that are not near recF are found instead near dnaA and/or dnaN, the usual neighbors of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage.
Probab=32.35 E-value=33 Score=19.56 Aligned_cols=12 Identities=33% Similarity=0.235 Sum_probs=9.8
Q ss_pred hcCCCCCCEEEE
Q 043432 85 RYCLELGDYIMV 96 (105)
Q Consensus 85 ~k~L~~GD~i~f 96 (105)
+..|++||.|.+
T Consensus 47 ~~~l~~Gd~v~i 58 (59)
T TIGR02988 47 GKKLYPGDVIEI 58 (59)
T ss_pred CCCCCCCCEEEe
Confidence 567899999876
No 88
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=32.21 E-value=25 Score=21.87 Aligned_cols=16 Identities=19% Similarity=0.148 Sum_probs=12.5
Q ss_pred HHHhhcCCCCCCEEEE
Q 043432 81 AFIKRYCLELGDYIMV 96 (105)
Q Consensus 81 ~fV~~k~L~~GD~i~f 96 (105)
+=-|.++|+.||.|.|
T Consensus 46 EtRRgkKlr~gd~V~i 61 (73)
T COG2501 46 ETRRGKKLRDGDVVEI 61 (73)
T ss_pred eeccCCEeecCCEEEE
Confidence 3346788999999987
No 89
>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=31.95 E-value=30 Score=21.58 Aligned_cols=21 Identities=14% Similarity=0.292 Sum_probs=14.7
Q ss_pred HHHHhhcCCCCCCEEEEEEcC
Q 043432 80 RAFIKRYCLELGDYIMVYKDE 100 (105)
Q Consensus 80 ~~fV~~k~L~~GD~i~f~~~~ 100 (105)
...+..+..++||+++|-.+.
T Consensus 11 ~~Wa~~~~F~vGD~LvF~y~~ 31 (85)
T PF02298_consen 11 TDWASGKTFRVGDTLVFNYDS 31 (85)
T ss_dssp HHHHCTS-BETTEEEEEE--T
T ss_pred hHhhcCCcEeCCCEEEEEecC
Confidence 455678899999999996654
No 90
>PF03831 PhnA: PhnA protein; InterPro: IPR013988 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the C-terminal domain of PhnA.; PDB: 2AKK_A 2AKL_A.
Probab=31.57 E-value=14 Score=21.88 Aligned_cols=15 Identities=33% Similarity=0.383 Sum_probs=9.2
Q ss_pred hcCCCCCCEEEEEEc
Q 043432 85 RYCLELGDYIMVYKD 99 (105)
Q Consensus 85 ~k~L~~GD~i~f~~~ 99 (105)
-+-|+.||.|++.++
T Consensus 7 Gn~L~dGDsV~~iKD 21 (56)
T PF03831_consen 7 GNELQDGDSVTLIKD 21 (56)
T ss_dssp S-B--TTEEEEESS-
T ss_pred CCCccCCCEEEEEee
Confidence 356899999999775
No 91
>PF07680 DoxA: TQO small subunit DoxA; InterPro: IPR011636 Thiosulphate:quinone oxidoreductase (TQO) catalyses one of the early steps in elemental sulphur oxidation. A novel TQO enzyme was purified from the thermo-acidophilic archaeon Acidianus ambivalens and shown to consist of a large subunit (DoxD) and a smaller subunit (DoxA). The DoxD- and DoxA-like two subunits are fused together in a single polypeptide in Q8AAF0 from SWISSPROT.
Probab=31.46 E-value=71 Score=22.05 Aligned_cols=40 Identities=20% Similarity=0.351 Sum_probs=26.4
Q ss_pred CcEEeehhh-hhccCCCCC--CCCCEEEEEEECCCCeEEEEEEE
Q 043432 24 GRIVLPKKL-AETYLPPVN--EKAGFWMHLEDMDFNKVWTFKFR 64 (105)
Q Consensus 24 ~rl~iPk~~-ae~~lP~l~--~~~~~~l~~~D~~~g~~W~fr~~ 64 (105)
-.|++|--. |.-.||... ......|.+.|+. |..|.-..+
T Consensus 90 ~gl~vpLGakA~i~L~~~~~l~~g~Y~l~L~dis-G~~w~~~~~ 132 (133)
T PF07680_consen 90 HGLVVPLGAKATITLPLPDHLPPGTYTLKLYDIS-GITWSAGIT 132 (133)
T ss_pred eeEEEEcCCcEEEEecCCCccCCCcEEEEEEcCC-CCeeeeccc
Confidence 378999644 333454421 3455889999994 999986654
No 92
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=31.29 E-value=38 Score=23.01 Aligned_cols=23 Identities=22% Similarity=0.408 Sum_probs=18.6
Q ss_pred HHhhcCCCCCCEEEEEEcCCCCC
Q 043432 82 FIKRYCLELGDYIMVYKDELEGS 104 (105)
Q Consensus 82 fV~~k~L~~GD~i~f~~~~~~g~ 104 (105)
-+++-.++.||.|.+......|+
T Consensus 40 ~ir~~~IkkGD~V~VisG~~KGk 62 (120)
T PRK01191 40 GIRSLPVRKGDTVKVMRGDFKGE 62 (120)
T ss_pred CCccceEeCCCEEEEeecCCCCc
Confidence 46667899999999998877664
No 93
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=31.24 E-value=51 Score=28.40 Aligned_cols=20 Identities=25% Similarity=0.399 Sum_probs=18.4
Q ss_pred HHHHhhcCCCCCCEEEEEEc
Q 043432 80 RAFIKRYCLELGDYIMVYKD 99 (105)
Q Consensus 80 ~~fV~~k~L~~GD~i~f~~~ 99 (105)
.+++++++|+.||.|.+.|.
T Consensus 360 ~~~i~~~~i~iGD~V~V~ra 379 (665)
T PRK07956 360 ADEIERKDIRIGDTVVVRRA 379 (665)
T ss_pred HHHHHHcCCCCCCEEEEEEC
Confidence 58999999999999999985
No 94
>PF01477 PLAT: PLAT/LH2 domain; InterPro: IPR001024 Lipoxygenases (1.13.11.- from EC) are a class of iron-containing dioxygenases which catalyses the hydroperoxidation of lipids, containing a cis,cis-1,4-pentadiene structure. They are common in plants where they may be involved in a number of diverse aspects of plant physiology including growth and development, pest resistance, and senescence or responses to wounding. In mammals a number of lipoxygenases isozymes are involved in the metabolism of prostaglandins and leukotrienes []. Sequence data is available for the following lipoxygenases: Plant lipoxygenases (1.13.11.12 from EC, IPR001246 from INTERPRO). Plants express a variety of cytosolic isozymes as well as what seems to be a chloroplast isozyme []. Mammalian arachidonate 5-lipoxygenase (1.13.11.34 from EC, IPR001885 from INTERPRO). Mammalian arachidonate 12-lipoxygenase (1.13.11.31 from EC, IPR001885 from INTERPRO). Mammalian erythroid cell-specific 15-lipoxygenase (1.13.11.33 from EC, IPR001885 from INTERPRO). The iron atom in lipoxygenases is bound by four ligands, three of which are histidine residues []. Six histidines are conserved in all lipoxygenase sequences, five of them are found clustered in a stretch of 40 amino acids. This region contains two of the three iron-ligands; the other histidines have been shown [] to be important for the activity of lipoxygenases. This entry represents a domain found in lipoxygenases and other enzymes. It is known as the PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology) domain, is found in a variety of membrane or lipid associated proteins. Structurally, this domain forms a beta-sandwich composed of two sheets of four strands each [, , ]. The most highly conserved regions coincide with the beta-strands, with most of the highly conserved residues being buried within the protein. An exception to this is a surface lysine or arginine that occurs on the surface of the fifth beta-strand of the eukaryotic domains. In pancreatic lipase, the lysine in this position forms a salt bridge with the procolipase protein. The conservation of a charged surface residue may indicate the location of a conserved ligand-binding site. It is thought that this domain may mediate membrane attachment via other protein binding partners.; GO: 0005515 protein binding; PDB: 3FG3_D 3FG1_C 3FG4_D 3DY5_A 2FNQ_B 3O8Y_B 3V99_B 3V92_A 3V98_B 1HPL_A ....
Probab=31.03 E-value=1.1e+02 Score=19.04 Aligned_cols=24 Identities=17% Similarity=0.348 Sum_probs=18.6
Q ss_pred EEEEEECCCCeEEEEEEEEcCCCC
Q 043432 47 WMHLEDMDFNKVWTFKFRFWPNNR 70 (105)
Q Consensus 47 ~l~~~D~~~g~~W~fr~~~~~~~~ 70 (105)
.|.|.+..+++.|.|.|.-|-...
T Consensus 80 ~V~V~~~~~~~~~~F~~~~Wl~~~ 103 (113)
T PF01477_consen 80 SVVVTDGETGRTYTFPCNRWLDPD 103 (113)
T ss_dssp EEEEEETTTSEEEEEEEEEEESTT
T ss_pred EEEEEeCCCCcEEEEEcCCEECCC
Confidence 567788667899999999986543
No 95
>PF07591 PT-HINT: Pretoxin HINT domain; InterPro: IPR011451 This entry represents a cluster of homologous proteins identified in Leptospira interrogans. One member (Q8EZX6 from SWISSPROT) has been predicted to be a phenazine biosynthesis family protein.; PDB: 2JNQ_A 2JMZ_A.
Probab=31.02 E-value=22 Score=23.91 Aligned_cols=16 Identities=19% Similarity=0.501 Sum_probs=10.4
Q ss_pred HHHhhcCCCCCCEEEE
Q 043432 81 AFIKRYCLELGDYIMV 96 (105)
Q Consensus 81 ~fV~~k~L~~GD~i~f 96 (105)
.+|++..|++||.+.-
T Consensus 70 gWv~A~~L~~GD~L~~ 85 (130)
T PF07591_consen 70 GWVEAEDLKVGDRLLT 85 (130)
T ss_dssp --EEGGG--TTSEEEE
T ss_pred hhhhHhhCCCCCEEEc
Confidence 5799999999999753
No 96
>PF10377 ATG11: Autophagy-related protein 11; InterPro: IPR019460 This family consists of proteins involved in telomere maintenance. In Schizosaccharomyces pombe (fission yeast) this protein is called Taf1 (taz1 interacting factor) and is part of the telomere cap complex. In Saccharomyces cerevisiae (baker's yeast) this protein is called ATG11 and is known to be involved in vacuolar targeting and peroxisome degradation [, ].
Probab=30.81 E-value=53 Score=22.25 Aligned_cols=22 Identities=14% Similarity=0.220 Sum_probs=16.9
Q ss_pred HHhhcCCCCCCEEEEEEcCCCC
Q 043432 82 FIKRYCLELGDYIMVYKDELEG 103 (105)
Q Consensus 82 fV~~k~L~~GD~i~f~~~~~~g 103 (105)
=+.-++.++||.+.|.++..+.
T Consensus 37 kIs~~~f~~GDlvLflpt~~~~ 58 (129)
T PF10377_consen 37 KISFRNFQVGDLVLFLPTRNHN 58 (129)
T ss_pred cEEEecCCCCCEEEEEecCCCC
Confidence 3445678999999999986654
No 97
>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=30.80 E-value=41 Score=21.05 Aligned_cols=16 Identities=25% Similarity=0.123 Sum_probs=9.6
Q ss_pred cCCCCCCEEEEEEcCC
Q 043432 86 YCLELGDYIMVYKDEL 101 (105)
Q Consensus 86 k~L~~GD~i~f~~~~~ 101 (105)
.+|++||.|.|.-+.+
T Consensus 41 ~~L~pGq~l~f~~d~~ 56 (85)
T PF04225_consen 41 TRLKPGQTLEFQLDED 56 (85)
T ss_dssp GG--TT-EEEEEE-TT
T ss_pred hhCCCCCEEEEEECCC
Confidence 3689999999998753
No 98
>cd00992 PDZ_signaling PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
Probab=30.61 E-value=39 Score=19.64 Aligned_cols=15 Identities=33% Similarity=0.414 Sum_probs=11.4
Q ss_pred HhhcCCCCCCEEEEE
Q 043432 83 IKRYCLELGDYIMVY 97 (105)
Q Consensus 83 V~~k~L~~GD~i~f~ 97 (105)
+...+|++||.|+=.
T Consensus 39 a~~~gl~~GD~I~~i 53 (82)
T cd00992 39 AERGGLRVGDRILEV 53 (82)
T ss_pred HHhCCCCCCCEEEEE
Confidence 445799999998743
No 99
>PF11948 DUF3465: Protein of unknown function (DUF3465); InterPro: IPR021856 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 131 to 151 amino acids in length. This protein has a conserved HWTH sequence motif.
Probab=30.05 E-value=41 Score=23.26 Aligned_cols=53 Identities=17% Similarity=0.162 Sum_probs=27.7
Q ss_pred CCCEEEEEE-ECCCCeEEEEEEEEcCCCCCcceeecChHHH-HhhcCCCCCCEEEEE
Q 043432 43 KAGFWMHLE-DMDFNKVWTFKFRFWPNNRGRMYIFENTRAF-IKRYCLELGDYIMVY 97 (105)
Q Consensus 43 ~~~~~l~~~-D~~~g~~W~fr~~~~~~~~s~~y~l~gW~~f-V~~k~L~~GD~i~f~ 97 (105)
..|..+.+. |...|.. +-+|..+-.+.....+-.+ .+. =+-..|++||.|.|+
T Consensus 41 g~G~V~~vLpdd~~Gsr-HQ~Fiv~l~~g~tllIahN-IDlaprip~l~~GD~V~f~ 95 (131)
T PF11948_consen 41 GCGTVVKVLPDDNKGSR-HQRFIVRLSSGQTLLIAHN-IDLAPRIPWLQKGDQVEFY 95 (131)
T ss_pred ccEEEEEECcccCCCCc-ceEEEEEeCCCCEEEEEec-cCccccCcCcCCCCEEEEE
Confidence 355555553 3223554 6677766433322222113 222 344569999999995
No 100
>TIGR00638 Mop molybdenum-pterin binding domain. This model describes a multigene family of molybdenum-pterin binding proteins of about 70 amino acids in Clostridium pasteurianum, as a tandemly-repeated domain C-terminal to an unrelated domain in ModE, a molybdate transport gene repressor of E. coli, and in single or tandemly paired domains in several related proteins.
Probab=30.00 E-value=63 Score=18.42 Aligned_cols=21 Identities=10% Similarity=0.061 Sum_probs=17.1
Q ss_pred HHHHhhcCCCCCCEEEEEEcC
Q 043432 80 RAFIKRYCLELGDYIMVYKDE 100 (105)
Q Consensus 80 ~~fV~~k~L~~GD~i~f~~~~ 100 (105)
..=+.+-+|++||.|.++...
T Consensus 41 ~~~~~~l~l~~G~~v~~~ik~ 61 (69)
T TIGR00638 41 LESVAELGLKPGKEVYAVIKA 61 (69)
T ss_pred HHHHhhCCCCCCCEEEEEEEC
Confidence 466788999999999987754
No 101
>PF08797 HIRAN: HIRAN domain; InterPro: IPR014905 The HIRAN protein (HIP116, Rad5p N-terminal) is found in the N-terminal regions of the SWI2/SNF2 proteins typified by HIP116 and Rad5p. HIRAN is found as a standalone protein in several bacteria and prophages, or fused to other catalytic domains, such as a nuclease of the restriction endonuclease fold and TDP1-like DNA phosphoesterases, in the eukaryotes []. It has been predicted that this protein functions as a DNA-binding domain that probably recognises features associated with damaged DNA or stalled replication forks [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides; PDB: 2L1I_A 3K2Y_C.
Probab=29.96 E-value=49 Score=21.04 Aligned_cols=21 Identities=19% Similarity=0.199 Sum_probs=14.8
Q ss_pred HHhhcCCCCCCEEEEEEcCCC
Q 043432 82 FIKRYCLELGDYIMVYKDELE 102 (105)
Q Consensus 82 fV~~k~L~~GD~i~f~~~~~~ 102 (105)
......|+.||.|.|.|+.+|
T Consensus 17 ~~~~~~l~~g~~v~L~re~~N 37 (107)
T PF08797_consen 17 RAGRGKLKPGDRVVLVREPDN 37 (107)
T ss_dssp HHCCTT--TTSEEEEEEETT-
T ss_pred cccccccCCCCEEEEEEcCCC
Confidence 345678899999999998776
No 102
>smart00228 PDZ Domain present in PSD-95, Dlg, and ZO-1/2. Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.
Probab=29.86 E-value=42 Score=19.47 Aligned_cols=14 Identities=29% Similarity=0.463 Sum_probs=10.1
Q ss_pred HhhcCCCCCCEEEE
Q 043432 83 IKRYCLELGDYIMV 96 (105)
Q Consensus 83 V~~k~L~~GD~i~f 96 (105)
....+|++||.|+=
T Consensus 39 a~~~gl~~GD~I~~ 52 (85)
T smart00228 39 AAKAGLKVGDVILE 52 (85)
T ss_pred HHHcCCCCCCEEEE
Confidence 33455999999864
No 103
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=29.83 E-value=53 Score=28.50 Aligned_cols=20 Identities=35% Similarity=0.418 Sum_probs=18.3
Q ss_pred HHHHhhcCCCCCCEEEEEEc
Q 043432 80 RAFIKRYCLELGDYIMVYKD 99 (105)
Q Consensus 80 ~~fV~~k~L~~GD~i~f~~~ 99 (105)
.+++++++++.||+|+++|.
T Consensus 360 ~d~I~rkdIrIGDtV~V~kA 379 (667)
T COG0272 360 VDEIKRKDIRIGDTVVVRKA 379 (667)
T ss_pred HHHHHhcCCCCCCEEEEEec
Confidence 58899999999999999985
No 104
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=29.67 E-value=55 Score=28.28 Aligned_cols=20 Identities=20% Similarity=0.502 Sum_probs=18.6
Q ss_pred HHHHhhcCCCCCCEEEEEEc
Q 043432 80 RAFIKRYCLELGDYIMVYKD 99 (105)
Q Consensus 80 ~~fV~~k~L~~GD~i~f~~~ 99 (105)
.+++++++|+.||.|.+.|.
T Consensus 357 ~~~I~~~di~iGD~V~V~ra 376 (669)
T PRK14350 357 QDYIDSIGLNVGDVVKISRR 376 (669)
T ss_pred HHHHHHcCCCCCCEEEEEec
Confidence 68999999999999999985
No 105
>COG1917 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]
Probab=29.56 E-value=23 Score=23.22 Aligned_cols=25 Identities=24% Similarity=0.390 Sum_probs=19.5
Q ss_pred eeecC----hHHHHhhcCCCCCCEEEEEEc
Q 043432 74 YIFEN----TRAFIKRYCLELGDYIMVYKD 99 (105)
Q Consensus 74 y~l~g----W~~fV~~k~L~~GD~i~f~~~ 99 (105)
|+|.| |.+ =..+.|++||.|.+-..
T Consensus 69 ~Vl~G~~~~~~~-g~~~~l~~Gd~i~ip~g 97 (131)
T COG1917 69 YVLEGEGTVQLE-GEKKELKAGDVIIIPPG 97 (131)
T ss_pred EEEecEEEEEec-CCceEecCCCEEEECCC
Confidence 77775 466 78889999999988554
No 106
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=29.55 E-value=56 Score=28.05 Aligned_cols=20 Identities=25% Similarity=0.388 Sum_probs=18.5
Q ss_pred HHHHhhcCCCCCCEEEEEEc
Q 043432 80 RAFIKRYCLELGDYIMVYKD 99 (105)
Q Consensus 80 ~~fV~~k~L~~GD~i~f~~~ 99 (105)
.+++++++|+.||.|.++|.
T Consensus 348 ~~~i~~~~i~iGD~V~V~ra 367 (652)
T TIGR00575 348 EDEIEELDIRIGDTVVVRKA 367 (652)
T ss_pred HHHHHHcCCCCCCEEEEEec
Confidence 68999999999999999985
No 107
>cd00986 PDZ_LON_protease PDZ domain of ATP-dependent LON serine proteases. Most PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this bacterial subfamily of protease-associated PDZ domains a C-terminal beta-strand is thought to form the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=29.24 E-value=39 Score=19.98 Aligned_cols=10 Identities=40% Similarity=0.564 Sum_probs=8.6
Q ss_pred CCCCCCEEEE
Q 043432 87 CLELGDYIMV 96 (105)
Q Consensus 87 ~L~~GD~i~f 96 (105)
+|++||+|.=
T Consensus 24 gL~~GD~I~~ 33 (79)
T cd00986 24 KLKAGDHIIA 33 (79)
T ss_pred CCCCCCEEEE
Confidence 7999999874
No 108
>cd02790 MopB_CT_Formate-Dh_H Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is a monomer composed of a single polypeptide chain with a Mo active site region and a [4Fe-4S] center. This CD (MopB_CT_Formate-Dh_H) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=29.18 E-value=53 Score=20.69 Aligned_cols=19 Identities=26% Similarity=0.228 Sum_probs=15.7
Q ss_pred HHHhhcCCCCCCEEEEEEc
Q 043432 81 AFIKRYCLELGDYIMVYKD 99 (105)
Q Consensus 81 ~fV~~k~L~~GD~i~f~~~ 99 (105)
+=.++.+|+.||.|.+.-.
T Consensus 42 ~dA~~lgi~~Gd~V~v~~~ 60 (116)
T cd02790 42 EDAKRLGIEDGEKVRVSSR 60 (116)
T ss_pred HHHHHcCCCCCCEEEEEcC
Confidence 4578899999999998754
No 109
>PRK08577 hypothetical protein; Provisional
Probab=29.16 E-value=69 Score=21.41 Aligned_cols=25 Identities=12% Similarity=0.193 Sum_probs=20.2
Q ss_pred HHHHhhcCCCCCCEEEEEEcCCCCC
Q 043432 80 RAFIKRYCLELGDYIMVYKDELEGS 104 (105)
Q Consensus 80 ~~fV~~k~L~~GD~i~f~~~~~~g~ 104 (105)
.+.-+.-+|++||.+.|+-+.+.|+
T Consensus 19 ~~~r~~l~~~~g~~~~~~~~~~~~~ 43 (136)
T PRK08577 19 LEIREALGIREGMYVLLIADTDKKE 43 (136)
T ss_pred HHHHHHcCcCCCCEEEEEEECCCCE
Confidence 3667788999999999998776654
No 110
>PLN02799 Molybdopterin synthase sulfur carrier subunit
Probab=29.11 E-value=50 Score=19.95 Aligned_cols=19 Identities=21% Similarity=0.214 Sum_probs=14.6
Q ss_pred hcCCCCCCEEEEEEcCCCC
Q 043432 85 RYCLELGDYIMVYKDELEG 103 (105)
Q Consensus 85 ~k~L~~GD~i~f~~~~~~g 103 (105)
+.-|+.||.|.|+.-..+|
T Consensus 64 ~~~l~dgDeVai~PpvsGG 82 (82)
T PLN02799 64 SAALKDGDELAIIPPISGG 82 (82)
T ss_pred CcCcCCCCEEEEeCCCCCC
Confidence 4568999999998765554
No 111
>TIGR01682 moaD molybdopterin converting factor, subunit 1, non-archaeal. The C-terminal Gly-Gly of this model is critical to function.
Probab=29.01 E-value=52 Score=19.80 Aligned_cols=19 Identities=21% Similarity=0.160 Sum_probs=15.5
Q ss_pred hcCCCCCCEEEEEEcCCCC
Q 043432 85 RYCLELGDYIMVYKDELEG 103 (105)
Q Consensus 85 ~k~L~~GD~i~f~~~~~~g 103 (105)
+..|+.||.|.|+.-..+|
T Consensus 62 ~~~l~dgDevai~PpvsGG 80 (80)
T TIGR01682 62 DALLNEGDEVAFIPPVSGG 80 (80)
T ss_pred CcCcCCCCEEEEeCCCCCC
Confidence 5789999999999866554
No 112
>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=28.96 E-value=37 Score=20.28 Aligned_cols=15 Identities=33% Similarity=0.363 Sum_probs=8.8
Q ss_pred hcCCCCCCEEEEEEc
Q 043432 85 RYCLELGDYIMVYKD 99 (105)
Q Consensus 85 ~k~L~~GD~i~f~~~ 99 (105)
=.+|++||+|.+-..
T Consensus 26 l~~L~~Gdvi~l~~~ 40 (77)
T PF01052_consen 26 LLNLKVGDVIPLDKP 40 (77)
T ss_dssp HHC--TT-EEEECCE
T ss_pred HhcCCCCCEEEeCCC
Confidence 357999999988554
No 113
>PLN02311 chalcone isomerase
Probab=28.59 E-value=68 Score=24.70 Aligned_cols=24 Identities=17% Similarity=0.159 Sum_probs=18.7
Q ss_pred ChHHHHhhcCCCCCCEEEEEEcCC
Q 043432 78 NTRAFIKRYCLELGDYIMVYKDEL 101 (105)
Q Consensus 78 gW~~fV~~k~L~~GD~i~f~~~~~ 101 (105)
.-..+.+...|++||+|.|.+...
T Consensus 192 kF~~~F~~~~l~kGd~I~~~~~p~ 215 (271)
T PLN02311 192 TFRSIFQNRSLNKGTVIFLTWINP 215 (271)
T ss_pred HHHHHhcCCCCCCCCEEEEEEeCC
Confidence 345666678999999999998754
No 114
>PRK14725 pyruvate kinase; Provisional
Probab=28.53 E-value=91 Score=26.82 Aligned_cols=57 Identities=16% Similarity=0.237 Sum_probs=37.3
Q ss_pred CCCEEEEEEECCCCeEEEEEEEEcCCC------CCcceeecChHHHHh---------------hcCCCCCCEEEEEEcC
Q 043432 43 KAGFWMHLEDMDFNKVWTFKFRFWPNN------RGRMYIFENTRAFIK---------------RYCLELGDYIMVYKDE 100 (105)
Q Consensus 43 ~~~~~l~~~D~~~g~~W~fr~~~~~~~------~s~~y~l~gW~~fV~---------------~k~L~~GD~i~f~~~~ 100 (105)
..|-.+.+.|. .|+.-.|+..--... ...-|+-+|..-..+ .-.|++||.+.|.++.
T Consensus 270 ~~Gd~i~~~Da-Rg~~R~l~V~~~~~~~~~~~~~~~~Y~~~G~~l~~~~~~~~~v~~~p~~~~~i~L~~Gd~l~lt~~~ 347 (608)
T PRK14725 270 EPGDELRFTDA-RGKKRKLTVTEVDDEGVLAEGSQTAYLANGTLLRLGRHDSTRVGGLPPVEQKLRLKVGDRLVLTRDD 347 (608)
T ss_pred CCCceeeeeec-cccceeeeEEeecCceeEEeecceeeeccCceeeeccccccccccccccCcceEecCCCEEEEecCC
Confidence 56778899998 488888776632111 112255556433334 5689999999999874
No 115
>cd02779 MopB_CT_Arsenite-Ox This CD contains the molybdopterin_binding C-terminal (MopB_CT) region of Arsenite oxidase (Arsenite-Ox) and related proteins. Arsenite oxidase oxidizes arsenite to the less toxic arsenate; it transfers the electrons obtained from the oxidation of arsenite towards the soluble periplasmic electron carriers cytochrome c and/or amicyanin.
Probab=28.29 E-value=56 Score=20.94 Aligned_cols=19 Identities=42% Similarity=0.513 Sum_probs=15.7
Q ss_pred HHHhhcCCCCCCEEEEEEc
Q 043432 81 AFIKRYCLELGDYIMVYKD 99 (105)
Q Consensus 81 ~fV~~k~L~~GD~i~f~~~ 99 (105)
+=+++.+|+.||.|.++-.
T Consensus 40 ~dA~~lgi~~Gd~V~v~s~ 58 (115)
T cd02779 40 EDAKREGLKNGDLVEVYND 58 (115)
T ss_pred HHHHHcCCCCCCEEEEEeC
Confidence 4578899999999998754
No 116
>PLN00212 glutelin; Provisional
Probab=28.26 E-value=42 Score=27.97 Aligned_cols=57 Identities=14% Similarity=0.190 Sum_probs=34.3
Q ss_pred CCCCCCCCCEEEEEEECCCCeEEEEEEEEcCCCCCcceeecC--hHHHHhhc-------CCCCCCEEEE
Q 043432 37 LPPVNEKAGFWMHLEDMDFNKVWTFKFRFWPNNRGRMYIFEN--TRAFIKRY-------CLELGDYIMV 96 (105)
Q Consensus 37 lP~l~~~~~~~l~~~D~~~g~~W~fr~~~~~~~~s~~y~l~g--W~~fV~~k-------~L~~GD~i~f 96 (105)
||.|. .-++.+...|...|-+-..- +.+|..+-.|++.| +..||..+ .|++||++++
T Consensus 340 ~P~L~-~L~LSa~rv~L~~gam~~PH--wn~nA~eI~yV~rG~g~vqvV~~~g~~vf~~~L~~GdvfVV 405 (493)
T PLN00212 340 FPILN-LIQMSATRVNLYQNALLSPF--WNVNAHSVVYITQGRARVQVVSNNGKTVFNGVLRPGQLLII 405 (493)
T ss_pred Ccccc-ccCeeEEEEEEcCCcccCCe--ecCCCCEEEEEeecceEEEEEcCCCCEEEEEEEcCCCEEEE
Confidence 67774 23344444454323332222 22334456688886 78888766 7999999987
No 117
>COG1430 Uncharacterized conserved protein [Function unknown]
Probab=28.11 E-value=62 Score=22.08 Aligned_cols=29 Identities=17% Similarity=0.280 Sum_probs=22.4
Q ss_pred cceeecChHHHHhhcCCCCCCEEEEEEcC
Q 043432 72 RMYIFENTRAFIKRYCLELGDYIMVYKDE 100 (105)
Q Consensus 72 ~~y~l~gW~~fV~~k~L~~GD~i~f~~~~ 100 (105)
..|+|+-=...+++.+++.||.|.|....
T Consensus 95 ~~yvLEl~~G~~~~~~i~vGd~v~~~~~~ 123 (126)
T COG1430 95 VRYVLELPAGWAARLGIKVGDRVEFRPLG 123 (126)
T ss_pred ccEEEEecCCchhhcCCccCCEEEecccC
Confidence 35999943455788999999999987643
No 118
>cd00754 MoaD Ubiquitin domain of MoaD-like proteins. MoaD family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor of a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and eukaryotes. Moco contains a tricyclic pyranopterin, termed molybdopterin (MPT), that contains the cis-dithiolene group responsible for molybdenum ligation. This dithiolene group is generated by MPT synthase, the second major step in Moco biosynthesis. MPT synthase consists of a large (MoeE) and small (MoaD) subunit. The small subunit is inserted into the lare subunit to form the active site. The small subunit, which is structurally similar to ubiquitin, contains a C-terminal thiocarboxylated glycine residue that serves as a sulfur donor for the synthesis of the MPT dithiolene group.
Probab=27.99 E-value=55 Score=19.27 Aligned_cols=20 Identities=20% Similarity=0.130 Sum_probs=15.6
Q ss_pred hhcCCCCCCEEEEEEcCCCC
Q 043432 84 KRYCLELGDYIMVYKDELEG 103 (105)
Q Consensus 84 ~~k~L~~GD~i~f~~~~~~g 103 (105)
.+..|+.||.|.|+.-..+|
T Consensus 61 ~~~~l~~gD~v~i~ppv~GG 80 (80)
T cd00754 61 LDTPLKDGDEVAIIPPVSGG 80 (80)
T ss_pred CCcccCCCCEEEEeCCCCCC
Confidence 45679999999998765554
No 119
>cd04491 SoSSB_OBF SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB). SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is limiting, and supporting transcription when TBP is absent. SSoSSB selectively melts the duplex DNA of promoter sequences. It also relieves transcriptional repression by the chromatin Alba. In addition, SSoSSB activates reverse gyrase activity, which involves DNA binding, DNA cleavage, strand passage and ligation. SSoSSB stimulates all these steps in the presence of the chromatin protein, Sul7d. SSoSSB antagonizes the inhibitory effect of Sul7d on reverse gyrase supercoiling activity. It also physically and functionally interacts with Mini-chromosome Maintenance (MCM), stimulating
Probab=27.96 E-value=1.4e+02 Score=17.80 Aligned_cols=34 Identities=26% Similarity=0.339 Sum_probs=22.9
Q ss_pred EEEEEEECCCCeEEEEEEEEcCCCCCcceeecChHHHHhhcCCCCCCEEEEE
Q 043432 46 FWMHLEDMDFNKVWTFKFRFWPNNRGRMYIFENTRAFIKRYCLELGDYIMVY 97 (105)
Q Consensus 46 ~~l~~~D~~~g~~W~fr~~~~~~~~s~~y~l~gW~~fV~~k~L~~GD~i~f~ 97 (105)
..+.+.|. +| +.+++.| +.. . ...+++||.|.+.
T Consensus 25 ~~~~l~D~-TG---~i~~~~W--~~~---------~---~~~~~~G~vv~i~ 58 (82)
T cd04491 25 QSGLVGDE-TG---TIRFTLW--DEK---------A---ADDLEPGDVVRIE 58 (82)
T ss_pred EEEEEECC-CC---EEEEEEE--Cch---------h---cccCCCCCEEEEE
Confidence 56677887 57 4677888 332 1 4558889988775
No 120
>cd05828 Sortase_D_4 Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at the cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Class D sortases are further classified into subfamilies 4 and 5. This group contains a subset of Class D sortases belonging to subfamily-4. These sortases recognize a unique sorting signal (LPXTA) and they constitute a specialized sorting pathway found in bacilli. Their substrates are predicted to be predominantly enzymes such as 5'-nucleotidases, glycosyl hydrolase, and subtilase.
Probab=27.93 E-value=66 Score=21.22 Aligned_cols=28 Identities=21% Similarity=0.088 Sum_probs=23.0
Q ss_pred cceeecC--hHHHHhhcCCCCCCEEEEEEc
Q 043432 72 RMYIFEN--TRAFIKRYCLELGDYIMVYKD 99 (105)
Q Consensus 72 ~~y~l~g--W~~fV~~k~L~~GD~i~f~~~ 99 (105)
..++|.| ..-|-+=..|+.||.|.+...
T Consensus 44 gn~vIaGH~~~~F~~L~~l~~Gd~i~v~~~ 73 (127)
T cd05828 44 GNIVIAGHRDTHFRFLGELEPGDIITLQTL 73 (127)
T ss_pred CcEEEEEeCchhhhChhcCCCCCEEEEEEC
Confidence 4577775 578999999999999999865
No 121
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=27.91 E-value=62 Score=28.07 Aligned_cols=20 Identities=25% Similarity=0.340 Sum_probs=18.4
Q ss_pred HHHHhhcCCCCCCEEEEEEc
Q 043432 80 RAFIKRYCLELGDYIMVYKD 99 (105)
Q Consensus 80 ~~fV~~k~L~~GD~i~f~~~ 99 (105)
.+++++++|+.||.|.+.|.
T Consensus 382 ~~~i~~~di~iGD~V~V~ra 401 (689)
T PRK14351 382 PAEIEELGVNVGDRVRVKRA 401 (689)
T ss_pred HHHHHHcCCCCCCEEEEEec
Confidence 57999999999999999985
No 122
>cd02775 MopB_CT Molybdopterin-Binding, C-terminal (MopB_CT) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and tungsten-containing enzymes, including formate dehydrogenase-H (Fdh-H) and -N (Fdh-N), several forms of nitrate reductase (Nap, Nas, NarG), dimethylsulfoxide reductase (DMSOR), thiosulfate reductase, formylmethanofuran dehydrogenase, and arsenite oxidase. Molybdenum is present in most of these enzymes in the form of molybdopterin, a modified pterin ring with a dithiolene side chain, which is responsible for ligating the Mo. In many bacterial and archaeal species, molybdopterin is in the form of a dinucleotide, with two molybdopterin dinucleotide units per molybdenum. These proteins can function as monomers, heterodimers, or heterotrimers, depending on the protein and organism. Also included in the MopB superfamily is
Probab=27.87 E-value=58 Score=19.79 Aligned_cols=20 Identities=15% Similarity=0.091 Sum_probs=15.6
Q ss_pred HHHhhcCCCCCCEEEEEEcC
Q 043432 81 AFIKRYCLELGDYIMVYKDE 100 (105)
Q Consensus 81 ~fV~~k~L~~GD~i~f~~~~ 100 (105)
+=+++.+|+.||.|.++-..
T Consensus 30 ~da~~lgl~~Gd~v~v~~~~ 49 (101)
T cd02775 30 EDAAALGIKDGDLVRVESRR 49 (101)
T ss_pred HHHHHcCCCCCCEEEEEcCC
Confidence 45678899999999887543
No 123
>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=27.80 E-value=63 Score=20.32 Aligned_cols=28 Identities=21% Similarity=0.434 Sum_probs=20.2
Q ss_pred ceeecC-hHHHHhhcCCCCCCEEEEEEcC
Q 043432 73 MYIFEN-TRAFIKRYCLELGDYIMVYKDE 100 (105)
Q Consensus 73 ~y~l~g-W~~fV~~k~L~~GD~i~f~~~~ 100 (105)
.++... -...+..-++++||.|.|.-++
T Consensus 59 kfl~e~~~~~l~~~~~a~~GD~ll~~Ag~ 87 (95)
T PF02938_consen 59 KFLSEEELKALIERLGAKPGDLLLFVAGK 87 (95)
T ss_dssp CCCHHHHHHHHHHHTT--TTEEEEEEEES
T ss_pred ccCCHHHHHHHHHHhCCCCCCEEEEECCC
Confidence 354444 6899999999999999997654
No 124
>cd00988 PDZ_CTP_protease PDZ domain of C-terminal processing-, tail-specific-, and tricorn proteases, which function in posttranslational protein processing, maturation, and disassembly or degradation, in Bacteria, Archaea, and plant chloroplasts. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=27.11 E-value=50 Score=19.47 Aligned_cols=13 Identities=23% Similarity=0.442 Sum_probs=10.1
Q ss_pred hhcCCCCCCEEEE
Q 043432 84 KRYCLELGDYIMV 96 (105)
Q Consensus 84 ~~k~L~~GD~i~f 96 (105)
...+|++||.|+=
T Consensus 27 ~~~gl~~GD~I~~ 39 (85)
T cd00988 27 AKAGIKAGDIIVA 39 (85)
T ss_pred HHcCCCCCCEEEE
Confidence 3449999999874
No 125
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=26.86 E-value=80 Score=14.64 Aligned_cols=16 Identities=31% Similarity=0.623 Sum_probs=12.1
Q ss_pred CCCCCEEEEEEcCCCC
Q 043432 88 LELGDYIMVYKDELEG 103 (105)
Q Consensus 88 L~~GD~i~f~~~~~~g 103 (105)
+++||.|.+......|
T Consensus 2 ~~~G~~V~I~~G~~~g 17 (28)
T smart00739 2 FEVGDTVRVIAGPFKG 17 (28)
T ss_pred CCCCCEEEEeECCCCC
Confidence 5789999888766555
No 126
>cd00987 PDZ_serine_protease PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=26.71 E-value=49 Score=19.58 Aligned_cols=14 Identities=29% Similarity=0.413 Sum_probs=10.6
Q ss_pred HhhcCCCCCCEEEE
Q 043432 83 IKRYCLELGDYIMV 96 (105)
Q Consensus 83 V~~k~L~~GD~i~f 96 (105)
....+|++||+|+=
T Consensus 37 a~~~gl~~GD~I~~ 50 (90)
T cd00987 37 AAKAGLKPGDVILA 50 (90)
T ss_pred HHHcCCCcCCEEEE
Confidence 44568999999863
No 127
>KOG3218 consensus RNA polymerase, 25-kDa subunit (common to polymerases I, II and III) [Transcription]
Probab=26.60 E-value=69 Score=23.76 Aligned_cols=31 Identities=19% Similarity=0.435 Sum_probs=24.2
Q ss_pred eecChHHHHhhcCCCCCCEEEEEE-cCCCCCC
Q 043432 75 IFENTRAFIKRYCLELGDYIMVYK-DELEGSY 105 (105)
Q Consensus 75 ~l~gW~~fV~~k~L~~GD~i~f~~-~~~~g~~ 105 (105)
.+..-..++|-.||+.|++|-+.| ++-.|+|
T Consensus 170 RIq~~DpvaRYyGLKrGqVVKI~r~setag~y 201 (208)
T KOG3218|consen 170 RIQKKDPVARYYGLKRGQVVKIIRRSETAGRY 201 (208)
T ss_pred eeeccChHHhhhccccCcEEEEEecCccCcce
Confidence 344446899999999999998866 5667776
No 128
>PRK08433 flagellar motor switch protein; Validated
Probab=26.58 E-value=48 Score=22.13 Aligned_cols=14 Identities=29% Similarity=0.183 Sum_probs=11.3
Q ss_pred hcCCCCCCEEEEEE
Q 043432 85 RYCLELGDYIMVYK 98 (105)
Q Consensus 85 ~k~L~~GD~i~f~~ 98 (105)
=-+|++||+|.+=+
T Consensus 50 lL~Lq~GDVI~Ld~ 63 (111)
T PRK08433 50 ILKFEKGSVIDLEK 63 (111)
T ss_pred HhCCCCCCEEEeCC
Confidence 35799999999854
No 129
>PF07237 DUF1428: Protein of unknown function (DUF1428); InterPro: IPR009874 This family consists of several hypothetical bacterial and one archaeal sequence of around 120 residues in length. The function of this family is unknown.; PDB: 2OKQ_A.
Probab=26.50 E-value=54 Score=21.68 Aligned_cols=21 Identities=5% Similarity=-0.034 Sum_probs=15.4
Q ss_pred hHHHHhhcCCCCCCEEEEEEc
Q 043432 79 TRAFIKRYCLELGDYIMVYKD 99 (105)
Q Consensus 79 W~~fV~~k~L~~GD~i~f~~~ 99 (105)
...|-++-++++|.+|+|.|-
T Consensus 50 ~TsF~~Av~a~~~E~VVFSWi 70 (103)
T PF07237_consen 50 VTSFPRAVKAKPDETVVFSWI 70 (103)
T ss_dssp S--HHHHTT--TTEEEEEEEE
T ss_pred cCCHHHHhcCCCCCEEEEEEE
Confidence 579999999999999999874
No 130
>PRK10220 hypothetical protein; Provisional
Probab=26.35 E-value=58 Score=21.88 Aligned_cols=14 Identities=36% Similarity=0.451 Sum_probs=12.0
Q ss_pred cCCCCCCEEEEEEc
Q 043432 86 YCLELGDYIMVYKD 99 (105)
Q Consensus 86 k~L~~GD~i~f~~~ 99 (105)
+-|..||.|++.++
T Consensus 50 ~~L~dGDsV~viKD 63 (111)
T PRK10220 50 NLLADGDSVTIVKD 63 (111)
T ss_pred CCccCCCEEEEEee
Confidence 56889999999886
No 131
>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=26.20 E-value=46 Score=20.24 Aligned_cols=14 Identities=29% Similarity=0.135 Sum_probs=11.1
Q ss_pred hcCCCCCCEEEEEE
Q 043432 85 RYCLELGDYIMVYK 98 (105)
Q Consensus 85 ~k~L~~GD~i~f~~ 98 (105)
=.+|++||+|.+-+
T Consensus 26 ll~L~~Gdvi~L~~ 39 (77)
T TIGR02480 26 LLKLGEGSVIELDK 39 (77)
T ss_pred HhcCCCCCEEEcCC
Confidence 35799999999854
No 132
>PF02597 ThiS: ThiS family; InterPro: IPR003749 ThiS (thiaminS) is a 66 aa protein involved in sulphur transfer. ThiS is coded in the thiCEFSGH operon in Escherichia coli. This family of proteins have two conserved Glycines at the COOH terminus. Thiocarboxylate is formed at the last G in the activation process. Sulphur is transferred from ThiI to ThiS in a reaction catalysed by IscS []. MoaD, a protein involved in sulphur transfer during molybdopterin synthesis, is about the same length and shows limited sequence similarity to ThiS. Both have the conserved GG at the COOH end.; PDB: 1JW9_D 1JWB_D 1JWA_D 3BII_D 1NVI_D 1FMA_D 1FM0_D 2QIE_G 2Q5W_D 2K5P_A ....
Probab=25.98 E-value=40 Score=19.70 Aligned_cols=19 Identities=21% Similarity=0.186 Sum_probs=14.8
Q ss_pred hcCCCCCCEEEEEEcCCCC
Q 043432 85 RYCLELGDYIMVYKDELEG 103 (105)
Q Consensus 85 ~k~L~~GD~i~f~~~~~~g 103 (105)
+..|+.||.|.|+.-..+|
T Consensus 59 ~~~l~~gD~V~i~ppvsGG 77 (77)
T PF02597_consen 59 DTPLKDGDEVAILPPVSGG 77 (77)
T ss_dssp TSBEETTEEEEEEESTSTS
T ss_pred CcCcCCCCEEEEECCCCCC
Confidence 4567999999998866555
No 133
>PF08541 ACP_syn_III_C: 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal ; InterPro: IPR013747 This domain is found on 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III 2.3.1.41 from EC, the enzyme responsible for initiating the chain of reactions of the fatty acid synthase in plants and bacteria. ; GO: 0016747 transferase activity, transferring acyl groups other than amino-acyl groups, 0008610 lipid biosynthetic process; PDB: 3IL3_A 1ZOW_C 3GWE_B 3GWA_B 1UB7_B 3LED_B 2EBD_A 1HNJ_A 2EFT_B 1HN9_B ....
Probab=25.77 E-value=59 Score=19.73 Aligned_cols=21 Identities=10% Similarity=0.096 Sum_probs=17.1
Q ss_pred hHHHHhhcCCCCCCEEEEEEc
Q 043432 79 TRAFIKRYCLELGDYIMVYKD 99 (105)
Q Consensus 79 W~~fV~~k~L~~GD~i~f~~~ 99 (105)
-...+++..+++||.|.+.--
T Consensus 57 L~~~~~~g~~~~Gd~vl~~~~ 77 (90)
T PF08541_consen 57 LADALEEGRIKPGDRVLLVGF 77 (90)
T ss_dssp HHHHHHTTSSCTTEEEEEEEE
T ss_pred HHHHHHcCCCCCCCEEEEEEE
Confidence 357788889999999998753
No 134
>TIGR01687 moaD_arch MoaD family protein, archaeal. Members of this family appear to be archaeal versions of MoaD, subunit 1 of molybdopterin converting factor. This model has been split from the bacterial/eukaryotic equivalog model TIGR01682 because the presence of two members of this family in a substantial number of archaeal species suggests that roles might not be interchangeable.
Probab=25.46 E-value=65 Score=19.62 Aligned_cols=18 Identities=22% Similarity=0.327 Sum_probs=14.3
Q ss_pred cCCCCCCEEEEEEcCCCC
Q 043432 86 YCLELGDYIMVYKDELEG 103 (105)
Q Consensus 86 k~L~~GD~i~f~~~~~~g 103 (105)
..|+.||.|.|+.-..+|
T Consensus 71 ~~l~dgdev~i~PpvsGG 88 (88)
T TIGR01687 71 TELKDGDVVAIFPPVSGG 88 (88)
T ss_pred CCCCCCCEEEEeCCCcCC
Confidence 479999999998765554
No 135
>PF00313 CSD: 'Cold-shock' DNA-binding domain; InterPro: IPR002059 When Escherichia coli is exposed to a temperature drop from 37 to 10 degrees centigrade, a 4-5 hour lag phase occurs, after which growth is resumed at a reduced rate []. During the lag phase, the expression of around 13 proteins, which contain specific DNA-binding regions [], is increased 2-10 fold. These so-called 'cold shock' proteins are thought to help the cell to survive in temperatures lower than optimum growth temperature, by contrast with heat shock proteins, which help the cell to survive in temperatures greater than the optimum, possibly by condensation of the chromosome and organisation of the prokaryotic nucleoid []. A conserved domain of about 70 amino acids has been found in prokaryotic and eukaryotic DNA-binding proteins [, , ]. This domain is known as the 'cold-shock domain' (CSD), part of which is highly similar [] to the RNP-1 RNA-binding motif.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1HZC_A 1I5F_A 1HZ9_B 1C9O_B 1HZB_B 1HZA_A 2HAX_B 2L15_A 2LSS_A 3I2Z_B ....
Probab=25.43 E-value=1.2e+02 Score=17.36 Aligned_cols=28 Identities=18% Similarity=0.140 Sum_probs=17.3
Q ss_pred ecChHHHHhh--cCCCCCCEEEEEEcCCCC
Q 043432 76 FENTRAFIKR--YCLELGDYIMVYKDELEG 103 (105)
Q Consensus 76 l~gW~~fV~~--k~L~~GD~i~f~~~~~~g 103 (105)
+-..+++... ..|++||.|.|.-....+
T Consensus 27 Ffh~s~~~~~~~~~l~~G~~V~F~~~~~~~ 56 (66)
T PF00313_consen 27 FFHISDLSGNGFRSLKEGDRVEFEVEEGKK 56 (66)
T ss_dssp EEEGGGBCSSSSTS--TTSEEEEEEEECTT
T ss_pred EeccccccccccccCCCCCEEEEEEEECCC
Confidence 3344555555 489999999998765544
No 136
>cd02787 MopB_CT_ydeP The MopB_CT_ydeP CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative 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=25.39 E-value=87 Score=19.83 Aligned_cols=23 Identities=26% Similarity=0.202 Sum_probs=17.9
Q ss_pred ChHHHHhhcCCCCCCEEEEEEcCC
Q 043432 78 NTRAFIKRYCLELGDYIMVYKDEL 101 (105)
Q Consensus 78 gW~~fV~~k~L~~GD~i~f~~~~~ 101 (105)
+-.+ +++.+|+.||.|.++-..+
T Consensus 36 ~p~d-A~~lgI~dGd~V~v~s~~G 58 (112)
T cd02787 36 NPDD-IARLGLKAGDRVDLESAFG 58 (112)
T ss_pred CHHH-HHHhCCCCCCEEEEEecCC
Confidence 4444 8899999999999986543
No 137
>PF11520 Cren7: Chromatin protein Cren7; InterPro: IPR020906 Cren7 is a chromatin protein found in Crenarchaeota and has a higher affinity for double-stranded DNA than for single-stranded DNA. The protein contains negative DNA supercoils and is associated with genomic DNA in vivo. Cren7 interacts with duplex DNA through a beta-sheet and a long flexible loop. Its binding to double-stranded DNA is without sequence specificity. There is approximately 1 Cren7 molecule for 12 bp of DNA. The function of Cren7 has not been completely determined but it is thought that the protein may have a role similar to that of archaeal proteins in Euryarchaea [].; GO: 0003690 double-stranded DNA binding, 0005737 cytoplasm; PDB: 3KXT_A 3LWH_A 3LWI_A 2JTM_A.
Probab=25.33 E-value=44 Score=20.04 Aligned_cols=17 Identities=35% Similarity=0.516 Sum_probs=10.4
Q ss_pred CCCCEEEEEEcCCCCCC
Q 043432 89 ELGDYIMVYKDELEGSY 105 (105)
Q Consensus 89 ~~GD~i~f~~~~~~g~~ 105 (105)
+.|=.|.++++.++|+|
T Consensus 34 rkGV~igLFk~P~tGk~ 50 (60)
T PF11520_consen 34 RKGVKIGLFKDPETGKY 50 (60)
T ss_dssp S--EEEEEEE-TTT--E
T ss_pred CCceEEEEEeCCCCCcc
Confidence 56788999999999986
No 138
>cd02778 MopB_CT_Thiosulfate-R-like The MopB_CT_Thiosulfate-R-like CD contains thiosulfate-, sulfur-, and polysulfide-reductases, and other related proteins. Thiosulfate reductase catalyzes the cleavage of sulfur-sulfur bonds in thiosulfate. Polysulfide reductase is a membrane-bound enzyme that catalyzes the reduction of polysulfide using either hydrogen or formate as the electron donor. Also included in this CD is the phenylacetyl-CoA:acceptor oxidoreductase, large subunit (PadB2), which has been characterized as a membrane-bound molybdenum-iron-sulfur enzyme involved in anaerobic metabolism of phenylalanine in the denitrifying bacterium Thauera aromatica. The MopB_CT_Thiosulfate-R-like CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=25.30 E-value=85 Score=20.00 Aligned_cols=20 Identities=20% Similarity=0.195 Sum_probs=16.1
Q ss_pred HHHhhcCCCCCCEEEEEEcC
Q 043432 81 AFIKRYCLELGDYIMVYKDE 100 (105)
Q Consensus 81 ~fV~~k~L~~GD~i~f~~~~ 100 (105)
+=.++.+|+.||.|.++-+.
T Consensus 37 ~dA~~~gi~~Gd~V~v~s~~ 56 (123)
T cd02778 37 ETAARLGIKDGDRVEVSSAR 56 (123)
T ss_pred HHHHHcCCCCCCEEEEEeCC
Confidence 45778999999999987653
No 139
>cd00508 MopB_CT_Fdh-Nap-like This CD includes formate dehydrogenases (Fdh) H and N; nitrate reductases, Nap and Nas; and other related proteins. Formate dehydrogenase H is a component of the anaerobic formate hydrogen lyase complex and catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. Formate dehydrogenase N (alpha subunit) is the major electron donor to the bacterial nitrate respiratory chain and nitrate reductases, Nap and Nas, catalyze the reduction of nitrate to nitrite. This CD (MopB_CT_Fdh-Nap-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=25.19 E-value=68 Score=20.19 Aligned_cols=19 Identities=21% Similarity=0.195 Sum_probs=15.6
Q ss_pred HHHhhcCCCCCCEEEEEEc
Q 043432 81 AFIKRYCLELGDYIMVYKD 99 (105)
Q Consensus 81 ~fV~~k~L~~GD~i~f~~~ 99 (105)
+=+++.+|+.||.|.++-+
T Consensus 42 ~dA~~lgi~~Gd~V~v~~~ 60 (120)
T cd00508 42 EDAARLGIKDGDLVRVSSR 60 (120)
T ss_pred HHHHHcCCCCCCEEEEEeC
Confidence 4467899999999998864
No 140
>PF01272 GreA_GreB: Transcription elongation factor, GreA/GreB, C-term; InterPro: IPR001437 Bacterial proteins greA and greB are necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites. Arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked DNA/RNA/ polymerase ternary complexes. Cleavage of the nascent transcript by cleavage factors, such as greA or greB, allows the resumption of elongation from the new 3' terminus [, ]. Escherichia coli GreA and GreB are sequence homologues and have homologues in every known bacterial genome []. GreA induces cleavage two or three nucleotides behind the terminus and can only prevent the formation of arrested complexes while greB releases longer sequences up to eighteen nucleotides in length and can rescue preexisting arrested complexes. These functional differences correlate with a distinctive structural feature, the distribution of positively charged residues on one face of the N-terminal coiled coil. Remarkably, despite close functional similarity, the prokaryotic Gre factors have no sequence or structural similarity with eukaryotic TFIIS. ; GO: 0003677 DNA binding, 0032784 regulation of transcription elongation, DNA-dependent; PDB: 2P4V_E 2ETN_B 3BMB_B 2PN0_D 1GRJ_A 2EUL_C 3AOH_Y 3AOI_X 2F23_A.
Probab=25.09 E-value=1.6e+02 Score=17.58 Aligned_cols=55 Identities=16% Similarity=0.014 Sum_probs=33.7
Q ss_pred CCEEEEEEECCCCeEEEEEEEEcCCCCCcceeecChHHHHhh-cCCCCCCEEEEEE
Q 043432 44 AGFWMHLEDMDFNKVWTFKFRFWPNNRGRMYIFENTRAFIKR-YCLELGDYIMVYK 98 (105)
Q Consensus 44 ~~~~l~~~D~~~g~~W~fr~~~~~~~~s~~y~l~gW~~fV~~-k~L~~GD~i~f~~ 98 (105)
-|-.+.+.|..++..-.|.+..-...+...-.++-.+..-++ .+.++||.|.+.-
T Consensus 8 ~Gs~V~l~~~~~~~~~~~~lv~~~~~~~~~~~IS~~SPLG~ALlG~~~Gd~v~~~~ 63 (77)
T PF01272_consen 8 IGSTVTLKDLDDGEEETYTLVGPDEADPDNGKISIDSPLGKALLGKKVGDEVEVEL 63 (77)
T ss_dssp TTEEEEEEETTTTEEEEEEEE-GGG-BSTSTEEETTSHHHHHHTT-BTT-EEEEEE
T ss_pred eCCEEEEEECCCCCEEEEEEEeEhHhCCceeEEEecCHHHHHhcCCCCCCEEEEEe
Confidence 467788898656888888877543333222345544566555 5889999998864
No 141
>PRK07440 hypothetical protein; Provisional
Probab=25.03 E-value=77 Score=18.98 Aligned_cols=17 Identities=18% Similarity=0.137 Sum_probs=13.4
Q ss_pred CCCCCCEEEEEEcCCCC
Q 043432 87 CLELGDYIMVYKDELEG 103 (105)
Q Consensus 87 ~L~~GD~i~f~~~~~~g 103 (105)
.|++||.|-+..-.++|
T Consensus 54 ~L~~gD~IEIv~~v~GG 70 (70)
T PRK07440 54 QVQPGDRLEIVTIVGGG 70 (70)
T ss_pred ecCCCCEEEEEEEecCC
Confidence 49999999998766554
No 142
>smart00308 LH2 Lipoxygenase homology 2 (beta barrel) domain.
Probab=24.98 E-value=1.1e+02 Score=19.02 Aligned_cols=21 Identities=14% Similarity=0.373 Sum_probs=13.9
Q ss_pred EEEEEECCCCeEEEEEEEEcC
Q 043432 47 WMHLEDMDFNKVWTFKFRFWP 67 (105)
Q Consensus 47 ~l~~~D~~~g~~W~fr~~~~~ 67 (105)
.|.|+|..+++.|.|-|.-|.
T Consensus 82 ~V~V~~~~~~~~~~F~c~~Wl 102 (105)
T smart00308 82 SITVKDLPTGGKYHFPCNSWV 102 (105)
T ss_pred EEEEEECCCCCEEEEEcCcee
Confidence 456677555777777776663
No 143
>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=24.93 E-value=66 Score=20.35 Aligned_cols=20 Identities=25% Similarity=0.360 Sum_probs=15.6
Q ss_pred HHHhhcCCCCCCEEEEEEcC
Q 043432 81 AFIKRYCLELGDYIMVYKDE 100 (105)
Q Consensus 81 ~fV~~k~L~~GD~i~f~~~~ 100 (105)
+=..+.+|+.||.|.++-..
T Consensus 38 ~dA~~lgi~~Gd~V~v~s~~ 57 (116)
T cd02786 38 ADAAARGIADGDLVVVFNDR 57 (116)
T ss_pred HHHHHcCCCCCCEEEEEcCC
Confidence 44678999999999887543
No 144
>PF13123 DUF3978: Protein of unknown function (DUF3978)
Probab=24.88 E-value=77 Score=22.06 Aligned_cols=50 Identities=12% Similarity=0.228 Sum_probs=31.0
Q ss_pred ccccceeEEEecccCCCCC-CCcEEeehhhhhccCCCCCCCC-CEEEEEEEC
Q 043432 4 PFLMRFLFEKQLKNSDVNA-AGRIVLPKKLAETYLPPVNEKA-GFWMHLEDM 53 (105)
Q Consensus 4 ~~~~~~~f~K~LT~SDv~~-~~rl~iPk~~ae~~lP~l~~~~-~~~l~~~D~ 53 (105)
+.+++..++|.....-.+- +...+||..+..-+||.++..+ .+.|.++-.
T Consensus 49 kenikI~~Kk~~n~~~e~~~~k~yiIPtk~FhY~lp~Ise~~~~~~iQ~qsf 100 (145)
T PF13123_consen 49 KENIKIETKKTINSRQESMIGKSYIIPTKAFHYLLPIISEGEDEMNIQVQSF 100 (145)
T ss_pred ccceEEEEEecCCCChHHhhhheeeeehhheeeEeceeecCccceeeEEEec
Confidence 4556666776553221111 3578999888877789987654 556666543
No 145
>COG4519 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.35 E-value=1.1e+02 Score=19.62 Aligned_cols=30 Identities=10% Similarity=0.130 Sum_probs=19.4
Q ss_pred CCEEEEEEECCCCeEEEEEEEEcCCCCCcceeecChHHHHhh
Q 043432 44 AGFWMHLEDMDFNKVWTFKFRFWPNNRGRMYIFENTRAFIKR 85 (105)
Q Consensus 44 ~~~~l~~~D~~~g~~W~fr~~~~~~~~s~~y~l~gW~~fV~~ 85 (105)
-|+.+.+.-. | .+ +....|.|+.|..|-++
T Consensus 49 lgi~l~FvQ~--G--------~R--nn~GyYql~dWGp~~~~ 78 (95)
T COG4519 49 LGIVLEFVQE--G--------AR--NNQGYYQLRDWGPVRRE 78 (95)
T ss_pred CCeEEEeeec--c--------cc--cCCCceEeeeccchhHH
Confidence 3577777654 3 23 44567999999776554
No 146
>cd02791 MopB_CT_Nitrate-R-NapA-like Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol oxidation via a membrane-anchored tetraheme cytochrome. This CD (MopB_CT_Nitrate-R-Nap) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs
Probab=24.32 E-value=69 Score=20.37 Aligned_cols=20 Identities=25% Similarity=0.232 Sum_probs=16.1
Q ss_pred HHHhhcCCCCCCEEEEEEcC
Q 043432 81 AFIKRYCLELGDYIMVYKDE 100 (105)
Q Consensus 81 ~fV~~k~L~~GD~i~f~~~~ 100 (105)
+=.++.+++.||.|.++-+.
T Consensus 42 ~dA~~lgi~~Gd~V~v~~~~ 61 (122)
T cd02791 42 EDAARLGLKEGDLVRVTSRR 61 (122)
T ss_pred HHHHHcCCCCCCEEEEEcCC
Confidence 45778899999999987654
No 147
>PRK10838 spr outer membrane lipoprotein; Provisional
Probab=24.31 E-value=48 Score=24.04 Aligned_cols=16 Identities=25% Similarity=0.397 Sum_probs=12.5
Q ss_pred HHhhcCCCCCCEEEEE
Q 043432 82 FIKRYCLELGDYIMVY 97 (105)
Q Consensus 82 fV~~k~L~~GD~i~f~ 97 (105)
-|....|++||.|.|-
T Consensus 123 ~V~~~~lqpGDLVfF~ 138 (190)
T PRK10838 123 SVSRSKLRTGDLVLFR 138 (190)
T ss_pred CcccCCCCCCcEEEEC
Confidence 4566789999998774
No 148
>PF02887 PK_C: Pyruvate kinase, alpha/beta domain; InterPro: IPR015795 Pyruvate kinase (2.7.1.40 from EC) (PK) catalyses the final step in glycolysis [], the conversion of phosphoenolpyruvate to pyruvate with concomitant phosphorylation of ADP to ATP: ADP + phosphoenolpyruvate = ATP + pyruvate The enzyme, which is found in all living organisms, requires both magnesium and potassium ions for its activity. In vertebrates, there are four tissue-specific isozymes: L (liver), R (red cells), M1 (muscle, heart and brain), and M2 (early foetal tissue). In plants, PK exists as cytoplasmic and plastid isozymes, while most bacteria and lower eukaryotes have one form, except in certain bacteria, such as Escherichia coli, that have two isozymes. All isozymes appear to be tetramers of identical subunits of ~500 residues. PK helps control the rate of glycolysis, along with phosphofructokinase (IPR000023 from INTERPRO) and hexokinase (IPR001312 from INTERPRO). PK possesses allosteric sites for numerous effectors, yet the isozymes respond differently, in keeping with their different tissue distributions []. The activity of L-type (liver) PK is increased by fructose-1,6-bisphosphate (F1,6BP) and lowered by ATP and alanine (gluconeogenic precursor), therefore when glucose levels are high, glycolysis is promoted, and when levels are low, gluconeogenesis is promoted. L-type PK is also hormonally regulated, being activated by insulin and inhibited by glucagon, which covalently modifies the PK enzyme. M1-type (muscle, brain) PK is inhibited by ATP, but F1,6BP and alanine have no effect, which correlates with the function of muscle and brain, as opposed to the liver. The structure of several pyruvate kinases from various organisms have been determined [, ]. The protein comprises three-four domains: a small N-terminal helical domain (absent in bacterial PK), a beta/alpha-barrel domain, a beta-barrel domain (inserted within the beta/alpha-barrel domain), and a 3-layer alpha/beta/alpha sandwich domain. This entry represents the 3-layer alpha/beta/alpha sandwich domain. This domain has a similar topology to the archaeal hypothetical protein, MTH1675 from Methanobacterium thermoautotrophicum.; PDB: 3QTG_B 1VP8_A 1T57_C 3N25_A 1AQF_C 2G50_B 1F3X_G 1A5U_F 1A49_E 1F3W_C ....
Probab=24.16 E-value=1.3e+02 Score=19.31 Aligned_cols=21 Identities=24% Similarity=0.339 Sum_probs=15.7
Q ss_pred hHHHHhhcCC-CCCCEEEEEEc
Q 043432 79 TRAFIKRYCL-ELGDYIMVYKD 99 (105)
Q Consensus 79 W~~fV~~k~L-~~GD~i~f~~~ 99 (105)
-.++.++++| +.||.|++...
T Consensus 80 a~~~~~~~g~~~~gd~vVv~~g 101 (117)
T PF02887_consen 80 ALEYAKERGLLKPGDKVVVVAG 101 (117)
T ss_dssp HHHHHHHTTSS-TTSEEEEEEE
T ss_pred HHHHHHHcCCCCCCCEEEEEeC
Confidence 3566777777 88999998876
No 149
>cd02792 MopB_CT_Formate-Dh-Na-like Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the major electron donor to the nitrate respiratory chain. Also included in this CD is the Desulfovibrio gigas tungsten formate dehydrogenase, DgW-FDH. In contrast to Fdh-N, which is a functional heterotrimer, DgW-FDH is a heterodimer. The DgW-FDH complex is composed of a large subunit carrying the W active site and one [4Fe-4S] center, and a small subunit that harbors a series of three [4Fe-4S] clusters as well as a putative vacant binding site for a fourth cluster. The smaller subunit is not included in this alignment. This CD (MopB_CT_Formate-Dh-Na-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=24.10 E-value=75 Score=20.20 Aligned_cols=19 Identities=16% Similarity=0.221 Sum_probs=15.4
Q ss_pred HHHhhcCCCCCCEEEEEEc
Q 043432 81 AFIKRYCLELGDYIMVYKD 99 (105)
Q Consensus 81 ~fV~~k~L~~GD~i~f~~~ 99 (105)
+=.++.+|+.||.|.++-+
T Consensus 42 ~dA~~lgi~~Gd~V~v~s~ 60 (122)
T cd02792 42 ELAAERGIKNGDMVWVSSP 60 (122)
T ss_pred HHHHHcCCCCCCEEEEEcC
Confidence 4477889999999988754
No 150
>cd04458 CSP_CDS Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA. CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription.
Probab=24.09 E-value=1.5e+02 Score=16.86 Aligned_cols=25 Identities=24% Similarity=0.162 Sum_probs=18.5
Q ss_pred hHHHHhh--cCCCCCCEEEEEEcCCCC
Q 043432 79 TRAFIKR--YCLELGDYIMVYKDELEG 103 (105)
Q Consensus 79 W~~fV~~--k~L~~GD~i~f~~~~~~g 103 (105)
-+++... ..|++||.|.|......+
T Consensus 30 ~~~~~~~~~~~~~~G~~V~f~~~~~~~ 56 (65)
T cd04458 30 ISALEGDGFRSLEEGDRVEFELEEGDK 56 (65)
T ss_pred hhHhhccCCCcCCCCCEEEEEEEECCC
Confidence 3566665 789999999997765443
No 151
>PRK07696 sulfur carrier protein ThiS; Provisional
Probab=24.06 E-value=83 Score=18.59 Aligned_cols=17 Identities=24% Similarity=0.055 Sum_probs=13.3
Q ss_pred CCCCCCEEEEEEcCCCC
Q 043432 87 CLELGDYIMVYKDELEG 103 (105)
Q Consensus 87 ~L~~GD~i~f~~~~~~g 103 (105)
.|+.||.|-+..-.++|
T Consensus 51 ~L~~gD~iEIv~~VgGG 67 (67)
T PRK07696 51 SVFDGDQIEIVTFVGGG 67 (67)
T ss_pred ecCCCCEEEEEEEecCC
Confidence 48999999998766554
No 152
>TIGR03784 marine_sortase sortase, marine proteobacterial type. Members of this protein family are sortase enzymes, cysteine transpeptidases involved in protein sorting activities. Members of this family tend to be found in proteobacteria, rather than in Gram-positive bacteria where sortases attach proteins to the Gram-positive cell wall or participate in pilin cross-linking. Many species with this sortase appear to contain a signal target sequence, a protein with a Vault protein inter-alpha-trypsin domain (pfam08487) and a von Willebrand factor type A domain (pfam00092), encoded by an adjacent gene. These sortases are designated subfamily 6 according to Comfort and Clubb (2004).
Probab=23.96 E-value=75 Score=22.59 Aligned_cols=30 Identities=17% Similarity=0.115 Sum_probs=23.5
Q ss_pred CcceeecC--hHHHHhhcCCCCCCEEEEEEcC
Q 043432 71 GRMYIFEN--TRAFIKRYCLELGDYIMVYKDE 100 (105)
Q Consensus 71 s~~y~l~g--W~~fV~~k~L~~GD~i~f~~~~ 100 (105)
...++|.| -..|-.=.+|++||.|.+....
T Consensus 90 ~Gn~VIAGHrdt~F~~L~~L~~GD~I~v~~~~ 121 (174)
T TIGR03784 90 QGNSVIAGHRDTHFAFLQELRPGDVIRLQTPD 121 (174)
T ss_pred CCcEEEEeeCCccCCChhhCCCCCEEEEEECC
Confidence 34578875 4569999999999999998643
No 153
>PRK06083 sulfur carrier protein ThiS; Provisional
Probab=23.81 E-value=82 Score=19.78 Aligned_cols=18 Identities=28% Similarity=0.407 Sum_probs=14.1
Q ss_pred cCCCCCCEEEEEEcCCCC
Q 043432 86 YCLELGDYIMVYKDELEG 103 (105)
Q Consensus 86 k~L~~GD~i~f~~~~~~g 103 (105)
..|++||.|-+..-.++|
T Consensus 67 t~L~egD~IEIv~~VgGG 84 (84)
T PRK06083 67 TVLSSGDAISLFQAIAGG 84 (84)
T ss_pred ccCCCCCEEEEEEEecCC
Confidence 349999999998866655
No 154
>PF07653 SH3_2: Variant SH3 domain; InterPro: IPR011511 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. This entry represents a variant of the SH3 domain.; PDB: 1I1J_B 1K0X_A 1HJD_A 2KEA_A 1KJW_A 1JXM_A 1JXO_B 2EBP_A 2DL3_A 2EYX_A ....
Probab=23.73 E-value=67 Score=17.84 Aligned_cols=13 Identities=31% Similarity=0.442 Sum_probs=9.4
Q ss_pred hcCCCCCCEEEEE
Q 043432 85 RYCLELGDYIMVY 97 (105)
Q Consensus 85 ~k~L~~GD~i~f~ 97 (105)
+-.+++||+|.+.
T Consensus 15 ~Ls~~~Gd~i~v~ 27 (55)
T PF07653_consen 15 ELSFKKGDVIEVL 27 (55)
T ss_dssp B-EB-TTEEEEEE
T ss_pred ceEEecCCEEEEE
Confidence 3568899999998
No 155
>cd02781 MopB_CT_Acetylene-hydratase The MopB_CT_Acetylene-hydratase CD contains acetylene hydratase (Ahy) and other related proteins. The acetylene hydratase of Pelobacter acetylenicus is a tungsten iron-sulfur protein involved in the fermentation of acetylene to ethanol and acetate. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=23.71 E-value=75 Score=20.55 Aligned_cols=20 Identities=15% Similarity=0.237 Sum_probs=16.1
Q ss_pred HHHhhcCCCCCCEEEEEEcC
Q 043432 81 AFIKRYCLELGDYIMVYKDE 100 (105)
Q Consensus 81 ~fV~~k~L~~GD~i~f~~~~ 100 (105)
+=.++.+|+.||.|.++-..
T Consensus 40 ~dA~~~gi~~Gd~V~v~s~~ 59 (130)
T cd02781 40 ETAAKLGIADGDWVWVETPR 59 (130)
T ss_pred HHHHHcCCCCCCEEEEECCC
Confidence 45778999999999887643
No 156
>PF12519 DUF3722: Protein of unknown function (DUF3722) ; InterPro: IPR022197 This family of proteins is found in eukaryotes. Proteins in this family are typically between 415 and 473 amino acids in length.
Probab=23.36 E-value=1.3e+02 Score=23.00 Aligned_cols=14 Identities=36% Similarity=0.551 Sum_probs=11.0
Q ss_pred CCcEEeehhhhhcc
Q 043432 23 AGRIVLPKKLAETY 36 (105)
Q Consensus 23 ~~rl~iPk~~ae~~ 36 (105)
.|||.+|....|+.
T Consensus 88 YGRmylP~s~LeAl 101 (260)
T PF12519_consen 88 YGRMYLPSSRLEAL 101 (260)
T ss_pred EEEEecChhhhhhh
Confidence 47899998887764
No 157
>PRK09838 periplasmic copper-binding protein; Provisional
Probab=23.11 E-value=77 Score=21.18 Aligned_cols=18 Identities=17% Similarity=0.067 Sum_probs=13.4
Q ss_pred hhcCCCCCCEEEEEEcCC
Q 043432 84 KRYCLELGDYIMVYKDEL 101 (105)
Q Consensus 84 ~~k~L~~GD~i~f~~~~~ 101 (105)
.-.+|++||.|.|.-...
T Consensus 85 ~l~~lk~G~~V~F~~~~~ 102 (115)
T PRK09838 85 KMSEIKTGDKVAFNFVQQ 102 (115)
T ss_pred hhccCCCCCEEEEEEEEc
Confidence 456899999999954333
No 158
>PF00278 Orn_DAP_Arg_deC: Pyridoxal-dependent decarboxylase, C-terminal sheet domain; InterPro: IPR022643 These enzymes are collectively known as group IV decarboxylases []. Pyridoxal-dependent decarboxylases acting on ornithine, lysine, arginine and related substrates can be classified into two different families on the basis of sequence similarities [, ]. Members of this family while most probably evolutionary related, do not share extensive regions of sequence similarities. The proteins contain a conserved lysine residue which is known, in mouse ODC [], to be the site of attachment of the pyridoxal-phosphate group. The proteins also contain a stretch of three consecutive glycine residues and has been proposed to be part of a substrate- binding region []. This entry represents the C-terminal region of the Orn/DAP/Arg decarboxylases.; GO: 0003824 catalytic activity; PDB: 1TWI_B 1TUF_A 3MT1_A 3N2B_C 2O0T_A 1HKW_A 1HKV_A 3VAB_A 3N2O_A 7ODC_A ....
Probab=23.06 E-value=59 Score=20.53 Aligned_cols=12 Identities=33% Similarity=0.678 Sum_probs=9.5
Q ss_pred CCCCCCEEEEEE
Q 043432 87 CLELGDYIMVYK 98 (105)
Q Consensus 87 ~L~~GD~i~f~~ 98 (105)
.|++||.|+|.-
T Consensus 82 ~l~~GD~l~f~~ 93 (116)
T PF00278_consen 82 ELEVGDWLVFEN 93 (116)
T ss_dssp TTTTT-EEEESS
T ss_pred CCCCCCEEEEec
Confidence 899999999954
No 159
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=22.65 E-value=66 Score=21.57 Aligned_cols=21 Identities=24% Similarity=0.401 Sum_probs=16.2
Q ss_pred hcCCCCCCEEEEEEcCCCCCC
Q 043432 85 RYCLELGDYIMVYKDELEGSY 105 (105)
Q Consensus 85 ~k~L~~GD~i~f~~~~~~g~~ 105 (105)
+..|++||.|.--++..+-+|
T Consensus 53 ~~~L~~GD~VLA~~~~~~~~Y 73 (124)
T PF15057_consen 53 RHSLQVGDKVLAPWEPDDCRY 73 (124)
T ss_pred cCcCCCCCEEEEecCcCCCEE
Confidence 899999999887776655443
No 160
>PRK09798 antitoxin MazE; Provisional
Probab=22.63 E-value=2e+02 Score=17.87 Aligned_cols=33 Identities=12% Similarity=0.226 Sum_probs=23.1
Q ss_pred EEEcCCCCCcceeecChHHHHhhcCCCCCCEEEEEEc
Q 043432 63 FRFWPNNRGRMYIFENTRAFIKRYCLELGDYIMVYKD 99 (105)
Q Consensus 63 ~~~~~~~~s~~y~l~gW~~fV~~k~L~~GD~i~f~~~ 99 (105)
...|.| |..-.+- ..|+++-+|..||.|.+.-+
T Consensus 6 v~KwGN--S~~vRIP--k~~l~~l~l~~g~~vei~v~ 38 (82)
T PRK09798 6 VKRWGN--SPAVRIP--ATLMQALNLNIDDEVKIDLV 38 (82)
T ss_pred EEEEcC--cceEEcC--HHHHHHcCCCCCCEEEEEEE
Confidence 456754 4332232 48999999999999988664
No 161
>PF02431 Chalcone: Chalcone-flavanone isomerase; InterPro: IPR003466 Chalcone isomerase (5.5.1.6 from EC) also known as chalcone-flavanone isomerase, is a plant enzyme responsible for the isomerisation of chalcone to naringenin a key step in the biosynthesis of flavonoids. The Petunia hybrida (Petunia) genome contains two genes coding for very similar enzymes, ChiA and ChiB, but only the first seems to encode a functional chalcone isomerase. Chalcone isomerase has a core 2-layer alpha/beta structure consisting of beta(3)-alpha(2)-beta-alpha(2)-beta(3) []. This entry represents a subgroup of Chalcone isomerase.; GO: 0016872 intramolecular lyase activity, 0042398 cellular modified amino acid biosynthetic process; PDB: 1JX0_B 1JEP_A 1EYP_B 1JX1_B 1EYQ_B 1FM8_A 1FM7_A 4DOL_A 4DOI_A 4DOK_B ....
Probab=22.54 E-value=63 Score=22.98 Aligned_cols=23 Identities=17% Similarity=0.179 Sum_probs=16.0
Q ss_pred HHHHhhc-CCCCCCEEEEEEcCCC
Q 043432 80 RAFIKRY-CLELGDYIMVYKDELE 102 (105)
Q Consensus 80 ~~fV~~k-~L~~GD~i~f~~~~~~ 102 (105)
..+...+ .+++||.|.|.|..++
T Consensus 121 ~~~F~~~g~~~kG~~i~l~~~~~g 144 (199)
T PF02431_consen 121 KSLFKSKGSVPKGDVITLTWSPDG 144 (199)
T ss_dssp HHHHTTB-EE-TT-EEEEEEETTT
T ss_pred HHHhcccccccCCCEEEEEECCCC
Confidence 4555566 8999999999997654
No 162
>PF12436 USP7_ICP0_bdg: ICP0-binding domain of Ubiquitin-specific protease 7; InterPro: IPR024729 This domain is found in eukaryotes, and is approximately 40 amino acids in length. It is found in proteins of the peptidase C19 family, which contains contains ubiquitinyl hydrolases like ubiquitin-specific protease 7 (USP7). USP7 regulates the turnover of p53 [].; PDB: 2KVR_A 2YLM_A.
Probab=22.52 E-value=68 Score=23.92 Aligned_cols=15 Identities=27% Similarity=0.306 Sum_probs=9.8
Q ss_pred hcCCCCCCEEEEEEc
Q 043432 85 RYCLELGDYIMVYKD 99 (105)
Q Consensus 85 ~k~L~~GD~i~f~~~ 99 (105)
...|+-||+|+|.+.
T Consensus 138 ~~el~~GdIi~fQ~~ 152 (249)
T PF12436_consen 138 KAELQDGDIICFQRA 152 (249)
T ss_dssp HTT--TTEEEEEEE-
T ss_pred hcccCCCCEEEEEec
Confidence 378888888888884
No 163
>PF00595 PDZ: PDZ domain (Also known as DHR or GLGF) Coordinates are not yet available; InterPro: IPR001478 PDZ domains are found in diverse signalling proteins in bacteria, yeasts, plants, insects and vertebrates [, ]. PDZ domains can occur in one or multiple copies and are nearly always found in cytoplasmic proteins. They bind either the carboxyl-terminal sequences of proteins or internal peptide sequences []. In most cases, interaction between a PDZ domain and its target is constitutive, with a binding affinity of 1 to 10 microns. However, agonist-dependent activation of cell surface receptors is sometimes required to promote interaction with a PDZ protein. PDZ domain proteins are frequently associated with the plasma membrane, a compartment where high concentrations of phosphatidylinositol 4,5-bisphosphate (PIP2) are found. Direct interaction between PIP2 and a subset of class II PDZ domains (syntenin, CASK, Tiam-1) has been demonstrated. PDZ domains consist of 80 to 90 amino acids comprising six beta-strands (beta-A to beta-F) and two alpha-helices, A and B, compactly arranged in a globular structure. Peptide binding of the ligand takes place in an elongated surface groove as an anti-parallel beta-strand interacts with the beta-B strand and the B helix. The structure of PDZ domains allows binding to a free carboxylate group at the end of a peptide through a carboxylate-binding loop between the beta-A and beta-B strands.; GO: 0005515 protein binding; PDB: 3AXA_A 1WF8_A 1QAV_B 1QAU_A 1B8Q_A 1MC7_A 2KAW_A 1I16_A 1VB7_A 1WI4_A ....
Probab=22.44 E-value=51 Score=19.47 Aligned_cols=12 Identities=42% Similarity=0.609 Sum_probs=9.0
Q ss_pred hcCCCCCCEEEE
Q 043432 85 RYCLELGDYIMV 96 (105)
Q Consensus 85 ~k~L~~GD~i~f 96 (105)
..+|++||.|+=
T Consensus 40 ~~gl~~GD~Il~ 51 (81)
T PF00595_consen 40 RAGLKVGDRILE 51 (81)
T ss_dssp HHTSSTTEEEEE
T ss_pred hcccchhhhhhe
Confidence 334999999863
No 164
>COG2208 RsbU Serine phosphatase RsbU, regulator of sigma subunit [Signal transduction mechanisms / Transcription]
Probab=22.40 E-value=49 Score=25.68 Aligned_cols=22 Identities=27% Similarity=0.474 Sum_probs=19.9
Q ss_pred ChHHHHhhcCCCCCCEEEEEEc
Q 043432 78 NTRAFIKRYCLELGDYIMVYKD 99 (105)
Q Consensus 78 gW~~fV~~k~L~~GD~i~f~~~ 99 (105)
.|..++.+..|+.||.+++|-|
T Consensus 283 ~~~~~~~~~~l~~gd~lvl~tD 304 (367)
T COG2208 283 DYQYEVASLQLEPGDLLVLYTD 304 (367)
T ss_pred CccchheeEEecCCCEEEEEcC
Confidence 5888899999999999999976
No 165
>TIGR01080 rplX_A_E ribosomal protein L24p/L26e, archaeal/eukaryotic. This model represents the archaeal and eukaryotic branch of the ribosomal protein L24p/L26e family. Bacterial and organellar forms are represented by the related TIGR01079.
Probab=22.24 E-value=67 Score=21.55 Aligned_cols=22 Identities=14% Similarity=0.389 Sum_probs=18.3
Q ss_pred HhhcCCCCCCEEEEEEcCCCCC
Q 043432 83 IKRYCLELGDYIMVYKDELEGS 104 (105)
Q Consensus 83 V~~k~L~~GD~i~f~~~~~~g~ 104 (105)
+++..++.||.|.+......|+
T Consensus 37 ~r~~~IkkGD~V~Vi~Gk~KGk 58 (114)
T TIGR01080 37 KRALPVRKGDKVRIMRGDFKGH 58 (114)
T ss_pred cccceeecCCEEEEecCCCCCC
Confidence 6777899999999998776663
No 166
>KOG4146 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=22.10 E-value=93 Score=20.44 Aligned_cols=17 Identities=35% Similarity=0.419 Sum_probs=13.4
Q ss_pred HhhcCCCCCCEEEEEEc
Q 043432 83 IKRYCLELGDYIMVYKD 99 (105)
Q Consensus 83 V~~k~L~~GD~i~f~~~ 99 (105)
-.+..|+.||.|+|.-.
T Consensus 81 kedy~ledgD~ivfiST 97 (101)
T KOG4146|consen 81 KEDYPLEDGDHIVFIST 97 (101)
T ss_pred ccccCcccCCEEEEEEe
Confidence 34568999999999754
No 167
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=22.07 E-value=63 Score=21.70 Aligned_cols=14 Identities=36% Similarity=0.430 Sum_probs=11.5
Q ss_pred cCCCCCCEEEEEEc
Q 043432 86 YCLELGDYIMVYKD 99 (105)
Q Consensus 86 k~L~~GD~i~f~~~ 99 (105)
+-|+.||.|++.++
T Consensus 51 n~L~dGDsV~lIKD 64 (112)
T COG2824 51 NLLADGDSVTLIKD 64 (112)
T ss_pred cEeccCCeEEEEEe
Confidence 45888999999886
No 168
>KOG1765 consensus Regulator of ribosome synthesis [Translation, ribosomal structure and biogenesis]
Probab=22.07 E-value=50 Score=23.89 Aligned_cols=62 Identities=16% Similarity=0.154 Sum_probs=35.6
Q ss_pred CCCCCCCCCEEEEEEECCCCeEEEEEEEEcCCCCCcceeecChHHHHhhcCCCCCCEEEEEEcCCCCCC
Q 043432 37 LPPVNEKAGFWMHLEDMDFNKVWTFKFRFWPNNRGRMYIFENTRAFIKRYCLELGDYIMVYKDELEGSY 105 (105)
Q Consensus 37 lP~l~~~~~~~l~~~D~~~g~~W~fr~~~~~~~~s~~y~l~gW~~fV~~k~L~~GD~i~f~~~~~~g~~ 105 (105)
||.-.-.+++.+.+=+. +-. | =|...-++..-.|.|..|++.||.+.--.=.+.+|+.+|-|
T Consensus 60 lp~~rt~e~vv~qLPe~-Tt~---L---PReK~lPr~k~~TkWe~FAr~KGI~krKk~~lV~DEasgew 121 (181)
T KOG1765|consen 60 LPSKRTEEGVVVQLPEP-TTR---L---PREKPLPRPKPETKWERFARKKGIEKRKKEKLVYDEASGEW 121 (181)
T ss_pred CcccccccceeEeCCCc-ccc---C---ccccCCCCCCCccHHHHHHHHcCcchhhccCcceecccccc
Confidence 34443456676666554 211 0 01111234456788999999999987444446666666643
No 169
>cd04497 hPOT1_OB1_like hPOT1_OB1_like: A subfamily of OB folds similar to the first OB fold (OB1) of human protection of telomeres 1 protein (hPOT1), the single OB fold of the N-terminal domain of Schizosaccharomyces pombe POT1 (SpPOT1), and the first OB fold of the N-terminal domain of the alpha subunit (OB1Nalpha) of Oxytricha nova telomere end binding protein (OnTEBP). POT1 proteins recognize single-stranded (ss) 3-prime ends of the telomere. A 3-prime ss overhang is conserved in ciliated protozoa, yeast, and mammals. SpPOT1 is essential for telomere maintenance. It binds specifically to the ss G-rich telomeric sequence (GGTTAC) of S. pombe. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. Deletion of the S. pombe pot1+ gene results in a rapid loss of telomere sequences, chromosome mis-segregation and chromosome circularization. hPOT1 is implicated in telomere length regulation. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB
Probab=22.01 E-value=1.7e+02 Score=19.67 Aligned_cols=11 Identities=27% Similarity=0.754 Sum_probs=9.0
Q ss_pred CCCCCEEEEEE
Q 043432 88 LELGDYIMVYK 98 (105)
Q Consensus 88 L~~GD~i~f~~ 98 (105)
+.+||+|.|.+
T Consensus 69 v~~GDVIll~~ 79 (138)
T cd04497 69 VKVGDIILLRR 79 (138)
T ss_pred CCCCCEEEEEE
Confidence 68899998865
No 170
>PRK11479 hypothetical protein; Provisional
Probab=21.80 E-value=56 Score=25.20 Aligned_cols=17 Identities=24% Similarity=0.170 Sum_probs=14.2
Q ss_pred HHHhhcCCCCCCEEEEE
Q 043432 81 AFIKRYCLELGDYIMVY 97 (105)
Q Consensus 81 ~fV~~k~L~~GD~i~f~ 97 (105)
.-|....|++||.|.|-
T Consensus 58 ~~Vs~~~LqpGDLVFfs 74 (274)
T PRK11479 58 KEITAPDLKPGDLLFSS 74 (274)
T ss_pred cccChhhCCCCCEEEEe
Confidence 46788899999998874
No 171
>PF02080 TrkA_C: TrkA-C domain; InterPro: IPR006037 The regulator of K+ conductance (RCK) domain is found in many ligand-gated K+ channels, most often attached to the intracellular carboxy terminus. The domain is prevalent among prokaryotic K+ channels, and also found in eukaryotic, high-conductance Ca2+-activated K+ channels (BK channels) [, , ]. Largely involved in redox-linked regulation of potassium channels, the N-terminal part of the RCK domain is predicted to be an active dehydrogenase at least in some cases []. Some have a conserved sequence motif (G-x-G-x-x-G-x(n)-[DE]) for NAD+ binding [], but others do not, reflecting the diversity of ligands for RCK domains. The C-terminal part is less conserved, being absent in some channels, such as the kefC antiporter from Escherichia coli. It is predicted to bind unidentified ligands and to regulate sulphate, sodium and other transporters. The X-ray structure of several RCK domains has been solved [, , ]. It reveals an alpha-beta fold similar to dehydrogenase enzymes. The domain forms a homodimer, producing a cleft between two lobes. It has a composite structure, with an N-terminal (RCK-N), and a C-terminal (RCK-C) subdomain. The RCK-N subdomain forms a Rossmann fold with two alpha helices on one side of a six stranded parallel beta sheet and three alpha helices on the other side. The RCK-C subdomain is an all-beta-strand fold. It forms an extention of the dimer interface and further stabilises the RCK homodimer [, , ]. Ca2+ is a ligand that opens the channel in a concentration-dependent manner. Two Ca2+ ions are located at the base of a cleft between two RCK domains, coordinated by the carboxylate groups of two glutamate residues, and by an aspartate residue [, , ]. RCK domains occur in at least five different contexts: As a single domain on the C terminus of some K+ channels (for example, many prokaryotic K+ channels). As two tandem RCK domains on the C terminus of some transporters that form gating rings (for example, eukaryotic BK channels). The gating ring has an arrangement of eight identical RCK domains, one from each of the four pore-forming subunits and four from the intracellular solution. As two domains, one at the N terminus and another at the C terminus of transporter (for example, the prokaryotic trk system potassium uptake protein A). As a soluble protein (not part of a K+ channel) consisting of two tandem RCK domains. As a soluble protein consisting of a single RCK domain. This entry represents the C-terminal subdomain of RCK.; GO: 0008324 cation transmembrane transporter activity, 0006813 potassium ion transport; PDB: 2BKP_A 1VCT_A 2BKO_A 2BKN_A 3L4B_C 2FY8_D 2AEF_A 1LNQ_E 3RBX_C 3KXD_A ....
Probab=21.72 E-value=44 Score=19.11 Aligned_cols=14 Identities=36% Similarity=0.581 Sum_probs=9.2
Q ss_pred cCCCCCCEEEEEEc
Q 043432 86 YCLELGDYIMVYKD 99 (105)
Q Consensus 86 k~L~~GD~i~f~~~ 99 (105)
-.|++||.+.+.-+
T Consensus 46 ~~l~~gD~l~v~g~ 59 (71)
T PF02080_consen 46 TVLQAGDILIVVGD 59 (71)
T ss_dssp -BE-TTEEEEEEEE
T ss_pred CEECCCCEEEEEEC
Confidence 35789999988643
No 172
>cd02793 MopB_CT_DMSOR-BSOR-TMAOR The MopB_DMSOR-BSOR-TMAOR CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its cellular location and oligomerization state are organism-dependent. For example, in Rhodobacter sphaeriodes and Rhodobacter capsulatus, it is an 82-kDa monomeric soluble protein found in the periplasmic space; in E. coli, it is membrane-bound and exists as a heterotrimer. BSOR catalyzes the reduction of biotin sulfixode to biotin, and is unique among Mo enzymes because no additional auxiliary proteins or cofactors are required. TMAOR is similar to DMSOR, but its only natural substrate is TMAO.This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=21.65 E-value=87 Score=20.50 Aligned_cols=19 Identities=26% Similarity=0.301 Sum_probs=15.6
Q ss_pred HHHhhcCCCCCCEEEEEEc
Q 043432 81 AFIKRYCLELGDYIMVYKD 99 (105)
Q Consensus 81 ~fV~~k~L~~GD~i~f~~~ 99 (105)
+=+.+.+|+.||.|.++-.
T Consensus 40 ~dA~~~gi~~Gd~V~v~s~ 58 (129)
T cd02793 40 ADAAARGIADGDIVRVFND 58 (129)
T ss_pred HHHHHcCCCCCCEEEEEcC
Confidence 3478999999999988754
No 173
>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=21.52 E-value=50 Score=20.68 Aligned_cols=18 Identities=22% Similarity=0.165 Sum_probs=13.8
Q ss_pred HHHhhcCCCCCCEEEEEE
Q 043432 81 AFIKRYCLELGDYIMVYK 98 (105)
Q Consensus 81 ~fV~~k~L~~GD~i~f~~ 98 (105)
.++....+++||.|.|..
T Consensus 45 ~~~~~~~~~pGDlif~~~ 62 (105)
T PF00877_consen 45 KRVPISELQPGDLIFFKG 62 (105)
T ss_dssp EHEEGGG-TTTEEEEEEG
T ss_pred cccchhcCCcccEEEEeC
Confidence 367888999999988765
No 174
>PF03459 TOBE: TOBE domain; InterPro: IPR005116 The TOBE domain [] (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner. It is probably involved in the recognition of small ligands such as molybdenum (P46930 from SWISSPROT) and sulphate (P16676 from SWISSPROT), and is found in ABC transporters immediately after the ATPase domain.; GO: 0005215 transporter activity, 0005524 ATP binding, 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0006810 transport, 0043190 ATP-binding cassette (ABC) transporter complex; PDB: 1G29_2 1H9M_B 1H9J_A 1H9K_A 1H9R_B 1O7L_C 1H9S_A 1B9N_A 1B9M_A 1GUS_C ....
Probab=21.25 E-value=1e+02 Score=17.28 Aligned_cols=22 Identities=18% Similarity=0.132 Sum_probs=15.3
Q ss_pred hHHHHhhcCCCCCCEEEEEEcC
Q 043432 79 TRAFIKRYCLELGDYIMVYKDE 100 (105)
Q Consensus 79 W~~fV~~k~L~~GD~i~f~~~~ 100 (105)
-.+-..+-+|++||.|.+.=+.
T Consensus 38 t~~~~~~L~L~~G~~V~~~ik~ 59 (64)
T PF03459_consen 38 TPESAEELGLKPGDEVYASIKA 59 (64)
T ss_dssp EHHHHHHCT-STT-EEEEEE-G
T ss_pred cHHHHHHcCCCCCCEEEEEEeh
Confidence 3578889999999999986543
No 175
>cd02789 MopB_CT_FmdC-FwdD The MopB_FmdC-FwdD CD includes the C-terminus of subunit C of molybdenum formylmethanofuran dehydrogenase (FmdC) and subunit D of tungsten formylmethanofuran dehydrogenase (FwdD), and other related proteins. Formylmethanofuran dehydrogenase catalyzes the first step in methane formation from CO2 in methanogenic archaea and some eubacteria. Members of this CD belong to the molybdopterin_binding superfamily of proteins. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=21.24 E-value=92 Score=19.86 Aligned_cols=19 Identities=21% Similarity=0.065 Sum_probs=15.4
Q ss_pred HHHhhcCCCCCCEEEEEEc
Q 043432 81 AFIKRYCLELGDYIMVYKD 99 (105)
Q Consensus 81 ~fV~~k~L~~GD~i~f~~~ 99 (105)
+=.++.+|+.||.|.++-.
T Consensus 38 ~dA~~lgi~~Gd~V~v~~~ 56 (106)
T cd02789 38 EDYKLLGKPEGDKVKVTSE 56 (106)
T ss_pred HHHHHcCCCCCCEEEEEcC
Confidence 3388999999999988743
No 176
>cd02794 MopB_CT_DmsA-EC The MopB_CT_DmsA-EC CD includes the DmsA enzyme of the dmsABC operon encoding the anaerobic dimethylsulfoxide reductase (DMSOR) of Escherichia coli and other related DMSOR-like enzymes. Unlike other DMSOR-like enzymes, this group has a predicted N-terminal iron-sulfur [4Fe-4S] cluster binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=21.23 E-value=99 Score=19.86 Aligned_cols=19 Identities=21% Similarity=0.319 Sum_probs=15.4
Q ss_pred HHHhhcCCCCCCEEEEEEc
Q 043432 81 AFIKRYCLELGDYIMVYKD 99 (105)
Q Consensus 81 ~fV~~k~L~~GD~i~f~~~ 99 (105)
+=+++.+++.||.|.++-.
T Consensus 37 ~~A~~~gi~~Gd~V~v~s~ 55 (121)
T cd02794 37 LDAAARGIKDGDRVLVFND 55 (121)
T ss_pred HHHHHcCCCCCCEEEEEcC
Confidence 3478899999999988754
No 177
>PRK09681 putative type II secretion protein GspC; Provisional
Probab=21.13 E-value=1e+02 Score=23.74 Aligned_cols=22 Identities=18% Similarity=0.398 Sum_probs=17.1
Q ss_pred eeec-C-hHHHHhhcCCCCCCEEE
Q 043432 74 YIFE-N-TRAFIKRYCLELGDYIM 95 (105)
Q Consensus 74 y~l~-g-W~~fV~~k~L~~GD~i~ 95 (105)
|.++ | =....++-+|+.||+++
T Consensus 209 Yrl~Pgkd~~lF~~~GLq~GDva~ 232 (276)
T PRK09681 209 YAVKPGADRSLFDASGFKEGDIAI 232 (276)
T ss_pred EEECCCCcHHHHHHcCCCCCCEEE
Confidence 4454 3 35889999999999986
No 178
>cd01753 PLAT_LOX PLAT domain of 12/15-lipoxygenase. As a unique subfamily of the mammalian lipoxygenases, they catalyze enzymatic lipid peroxidation in complex biological structures via direct dioxygenation of phospholipids and cholesterol esters of biomembranes and plasma lipoproteins. Both types of enzymes are cytosolic but need this domain to access their sequestered membrane or micelle bound substrates.
Probab=21.07 E-value=1.2e+02 Score=19.83 Aligned_cols=47 Identities=11% Similarity=0.116 Sum_probs=26.6
Q ss_pred CCCCCCCcEEeehhhhhccCCCCCCCCCEEEEEEECCCCeEEEEEEEEcCCC
Q 043432 18 SDVNAAGRIVLPKKLAETYLPPVNEKAGFWMHLEDMDFNKVWTFKFRFWPNN 69 (105)
Q Consensus 18 SDv~~~~rl~iPk~~ae~~lP~l~~~~~~~l~~~D~~~g~~W~fr~~~~~~~ 69 (105)
.|++...++.|=.+..- .-|.- .=-.|.|.|.. +++|.|-|..|-.+
T Consensus 58 ~~lG~l~~i~i~~d~~g-~~~~W---~l~~V~V~~~~-~~~~~F~c~rWl~~ 104 (113)
T cd01753 58 EDLGELLLVRLRKRKYL-LFDAW---FCNYITVTGPG-GDEYHFPCYRWIEG 104 (113)
T ss_pred cCCCCcEEEEEEECCCC-CCCCe---eecEEEEEcCC-CCEEEEEhHHeECC
Confidence 45665556665543321 11110 00256777885 89999988888643
No 179
>COG2947 Uncharacterized conserved protein [Function unknown]
Probab=21.00 E-value=1.2e+02 Score=21.54 Aligned_cols=19 Identities=26% Similarity=0.726 Sum_probs=15.7
Q ss_pred HHHHhhcCCCCCCEEEEEEcC
Q 043432 80 RAFIKRYCLELGDYIMVYKDE 100 (105)
Q Consensus 80 ~~fV~~k~L~~GD~i~f~~~~ 100 (105)
.+|.|+ .+.||.+.||-..
T Consensus 36 RNfmR~--M~iGD~~fFYHSN 54 (156)
T COG2947 36 RNFMRD--MKIGDLGFFYHSN 54 (156)
T ss_pred HHHHHh--cccCceEEEEecC
Confidence 467777 8899999999864
No 180
>cd00113 PLAT PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2) domain. It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates.
Probab=20.88 E-value=1.2e+02 Score=19.17 Aligned_cols=22 Identities=23% Similarity=0.452 Sum_probs=16.5
Q ss_pred EEEEEECCCCeEEEEEEEEcCC
Q 043432 47 WMHLEDMDFNKVWTFKFRFWPN 68 (105)
Q Consensus 47 ~l~~~D~~~g~~W~fr~~~~~~ 68 (105)
.|.|+|..+|+.+.|-+..|..
T Consensus 83 ~V~V~~~~~~~~~~F~~~~Wl~ 104 (116)
T cd00113 83 SITVQALGTKKVYTFPVNRWVL 104 (116)
T ss_pred EEEEEeCCCCCEEEEEeCCCcc
Confidence 4677887667888888887754
No 181
>PF03152 UFD1: Ubiquitin fusion degradation protein UFD1; InterPro: IPR004854 Post-translational ubiquitin-protein conjugates are recognised for degradation by the ubiquitin fusion degradation (UFD) pathway. Several proteins involved in this pathway have been identified []. This family includes UFD1, a 40kDa protein that is essential for vegetative cell viability []. The human UFD1 gene is expressed at high levels during embryogenesis, especially in the eyes and in the inner ear primordia and is thought to be important in the determination of ectoderm-derived structures, including neural crest cells. In addition, this gene is deleted in the CATCH-22 (cardiac defects, abnormal facies, thymic hypoplasia, cleft palate and hypocalcaemia with deletions on chromosome 22) syndrome. This clinical syndrome is associated with a variety of developmental defects, all characterised by microdeletions on 22q11.2. Two such developmental defects are the DiGeorge syndrome OMIM:188400, and the velo-cardio- facial syndrome OMIM:145410. Several of the abnormalities associated with these conditions are thought to be due to defective neural crest cell differentiation []. ; GO: 0006511 ubiquitin-dependent protein catabolic process; PDB: 1ZC1_A 2YUJ_A.
Probab=20.64 E-value=3.3e+02 Score=19.50 Aligned_cols=77 Identities=14% Similarity=0.181 Sum_probs=39.2
Q ss_pred ccCCCCCCCcEEeehhhhhccCCCCCCCCCEEEEEEECCCCeE-EEEEEEEcCCCCCcceeecChHHHHhhcCCCCCCEE
Q 043432 16 KNSDVNAAGRIVLPKKLAETYLPPVNEKAGFWMHLEDMDFNKV-WTFKFRFWPNNRGRMYIFENTRAFIKRYCLELGDYI 94 (105)
Q Consensus 16 T~SDv~~~~rl~iPk~~ae~~lP~l~~~~~~~l~~~D~~~g~~-W~fr~~~~~~~~s~~y~l~gW~~fV~~k~L~~GD~i 94 (105)
..++++.++++++|...++... ..+-...+.+.+....+++. +-=..-|. ...+.-+|-.| ..+.-+|++||.|
T Consensus 18 ~~~~~~~gdKiiLP~s~L~~L~-~~~~~~P~~F~i~n~~~~~~th~GVlEFs--A~eG~i~lP~w--mm~~L~l~~g~~V 92 (176)
T PF03152_consen 18 DRPELEYGDKIILPPSALDELS-RLNIPYPMLFEISNPDNGKRTHCGVLEFS--AEEGTIYLPPW--MMQNLGLQEGDIV 92 (176)
T ss_dssp S-CCCCCTTEEEE-HHHHHHHH-HTT--SS-EEEEEETTTTEEEEEEEEEE----CTTEEEE-CH--HHHHHT--TTEEE
T ss_pred CCcccCCCCeEEcCHHHHHHHH-hccCCCCEEEEEecCCCCcEEEEEEEEeE--cCCCeEEeCcc--HHhhcCCCCCCEE
Confidence 4556667789999976655431 12223346677776643432 22112222 23344556678 4677899999999
Q ss_pred EEE
Q 043432 95 MVY 97 (105)
Q Consensus 95 ~f~ 97 (105)
.+-
T Consensus 93 ~v~ 95 (176)
T PF03152_consen 93 RVE 95 (176)
T ss_dssp EEE
T ss_pred EEE
Confidence 763
No 182
>cd02899 PLAT_SR Scavenger receptor protein. A subfamily of PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2) domain. It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates. This subfamily contains Toxoplasma gondii Scavenger protein TgSR1.
Probab=20.46 E-value=1.2e+02 Score=20.05 Aligned_cols=46 Identities=20% Similarity=0.330 Sum_probs=27.7
Q ss_pred ccCCCCCCCcEEeehhhhhccCCCCCCCCCEEEEEEECCCCeEEEEEEEEcCC
Q 043432 16 KNSDVNAAGRIVLPKKLAETYLPPVNEKAGFWMHLEDMDFNKVWTFKFRFWPN 68 (105)
Q Consensus 16 T~SDv~~~~rl~iPk~~ae~~lP~l~~~~~~~l~~~D~~~g~~W~fr~~~~~~ 68 (105)
++.|++.+..|.|-+.- ..=+..- -.|.|.|. +|+.|.|-|..|-.
T Consensus 52 ~~~dLG~l~~i~l~n~g--~~~~Wf~----~~V~V~~~-~g~~~~Fpc~rWla 97 (109)
T cd02899 52 RAADVGDINAIILSNTA--LNDPWYC----DYVRIKSE-DGKVFAFNVKRWIG 97 (109)
T ss_pred CccccCceEEEEEECCC--CCCCcee----eEEEEECC-CCCEEEEEcceeeC
Confidence 47777766666663211 0001110 25677886 68999999999953
No 183
>PF12791 RsgI_N: Anti-sigma factor N-terminus; InterPro: IPR024449 The heat shock genes in Bacillus subtilis can be classified into several groups according to their regulation [], and the sigma gene, sigI, of Bacillus subtilis belongs to the group IV heat-shock response genes and has many orthologues in the bacterial phylum Firmicutes []. Regulation of sigma factor I is carried out by RsgI from the same operon. This entry represents the N-terminal cytoplasmic portion of RsgI ('upstream' of the single transmembrane helix) which has been shown to interact directly with Sigma-I [].
Probab=20.45 E-value=57 Score=18.36 Aligned_cols=27 Identities=11% Similarity=0.153 Sum_probs=17.8
Q ss_pred ceeec--C-hHHHHhhcCCCCCCEEEEEEc
Q 043432 73 MYIFE--N-TRAFIKRYCLELGDYIMVYKD 99 (105)
Q Consensus 73 ~y~l~--g-W~~fV~~k~L~~GD~i~f~~~ 99 (105)
..+|| | ....-+..+.+.||.|.|...
T Consensus 8 aiVlT~dGeF~~ik~~~~~~vG~eI~~~~~ 37 (56)
T PF12791_consen 8 AIVLTPDGEFIKIKRKPGMEVGQEIEFDEK 37 (56)
T ss_pred EEEEcCCCcEEEEeCCCCCcccCEEEEech
Confidence 35666 3 444445556888999998764
No 184
>PRK06788 flagellar motor switch protein; Validated
Probab=20.33 E-value=73 Score=21.54 Aligned_cols=13 Identities=38% Similarity=0.447 Sum_probs=10.6
Q ss_pred cCCCCCCEEEEEE
Q 043432 86 YCLELGDYIMVYK 98 (105)
Q Consensus 86 k~L~~GD~i~f~~ 98 (105)
.+|++||+|.+=+
T Consensus 53 L~L~vGDVI~Ldk 65 (119)
T PRK06788 53 KQLKVGDVLEVEK 65 (119)
T ss_pred hCCCCCCEEEeCC
Confidence 4799999999843
No 185
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=20.26 E-value=1.6e+02 Score=17.98 Aligned_cols=34 Identities=15% Similarity=0.346 Sum_probs=19.1
Q ss_pred CCCEEEEEEECCCCeEEEEEEEEcCCCCCcceeecCh
Q 043432 43 KAGFWMHLEDMDFNKVWTFKFRFWPNNRGRMYIFENT 79 (105)
Q Consensus 43 ~~~~~l~~~D~~~g~~W~fr~~~~~~~~s~~y~l~gW 79 (105)
..|..|.|.-. +.+.|.|+|..- ++.+...|..|
T Consensus 22 ~~GL~l~v~~~-G~kt~~~r~~~~--gk~~~~~lG~~ 55 (89)
T PF13356_consen 22 VPGLYLRVTPS-GSKTFYFRYRIN--GKRRRITLGRY 55 (89)
T ss_dssp STTEEEEE-TT-S-EEEEEEEEET--TEEEEEEEEEC
T ss_pred CCCcEEEEEeC-CCeEEEEEEEec--ceEEEeccCCC
Confidence 35777788744 468899888543 55444333325
Done!