Query psy3865
Match_columns 107
No_of_seqs 113 out of 396
Neff 6.2
Searched_HMMs 46136
Date Fri Aug 16 19:25:21 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3865.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3865hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02359 CDC48_N: Cell divisio 99.8 5.9E-20 1.3E-24 120.1 6.0 71 13-85 13-85 (87)
2 TIGR01243 CDC48 AAA family ATP 99.6 1E-14 2.2E-19 124.5 9.8 85 14-101 15-102 (733)
3 KOG0730|consensus 98.6 5.3E-08 1.2E-12 83.2 3.9 87 18-107 30-116 (693)
4 PF02359 CDC48_N: Cell divisio 97.4 0.00014 3E-09 47.2 3.1 39 1-39 25-82 (87)
5 cd02786 MopB_CT_3 The MopB_CT_ 97.3 0.00077 1.7E-08 44.9 6.0 49 16-65 31-79 (116)
6 PF01568 Molydop_binding: Moly 97.3 0.00048 1E-08 45.3 4.9 53 16-69 30-82 (110)
7 cd02787 MopB_CT_ydeP The MopB_ 97.3 0.0008 1.7E-08 44.8 5.6 47 16-63 31-82 (112)
8 cd02788 MopB_CT_NDH-1_NuoG2-N7 97.3 0.0012 2.5E-08 43.3 6.2 49 17-66 30-78 (96)
9 cd02790 MopB_CT_Formate-Dh_H F 97.2 0.0012 2.7E-08 43.6 6.0 49 16-65 35-83 (116)
10 cd02775 MopB_CT Molybdopterin- 97.2 0.0015 3.3E-08 41.9 6.1 50 16-66 23-72 (101)
11 cd02789 MopB_CT_FmdC-FwdD The 97.2 0.0014 3E-08 43.9 6.0 49 17-66 32-80 (106)
12 cd02794 MopB_CT_DmsA-EC The Mo 97.2 0.0012 2.6E-08 44.5 5.8 48 17-65 31-78 (121)
13 cd02777 MopB_CT_DMSOR-like The 97.2 0.0014 3.1E-08 44.5 5.8 50 16-66 34-83 (127)
14 cd02785 MopB_CT_4 The MopB_CT_ 97.1 0.0019 4.1E-08 43.7 6.3 49 17-66 33-81 (124)
15 cd02792 MopB_CT_Formate-Dh-Na- 97.1 0.0023 5E-08 42.7 6.1 49 16-65 35-83 (122)
16 cd00508 MopB_CT_Fdh-Nap-like T 97.1 0.0025 5.5E-08 42.2 6.2 49 16-65 35-83 (120)
17 cd02781 MopB_CT_Acetylene-hydr 97.1 0.0024 5.2E-08 43.3 6.2 49 17-66 34-82 (130)
18 cd02778 MopB_CT_Thiosulfate-R- 97.1 0.0025 5.3E-08 42.7 6.2 50 16-66 30-79 (123)
19 cd02793 MopB_CT_DMSOR-BSOR-TMA 97.0 0.0024 5.2E-08 43.7 5.9 49 17-66 34-82 (129)
20 cd02791 MopB_CT_Nitrate-R-NapA 96.9 0.0032 7E-08 42.0 5.7 49 16-65 35-83 (122)
21 cd02779 MopB_CT_Arsenite-Ox Th 96.9 0.0039 8.5E-08 41.8 6.1 49 17-66 34-82 (115)
22 cd02782 MopB_CT_1 The MopB_CT_ 96.9 0.0041 8.9E-08 42.2 6.0 49 17-66 34-82 (129)
23 cd02776 MopB_CT_Nitrate-R-NarG 96.8 0.0044 9.4E-08 43.6 6.2 50 17-67 32-81 (141)
24 cd02784 MopB_CT_PHLH The MopB_ 96.7 0.0057 1.2E-07 43.1 5.9 48 17-65 39-86 (137)
25 cd02780 MopB_CT_Tetrathionate_ 96.7 0.0076 1.6E-07 41.8 6.4 50 16-66 30-79 (143)
26 cd02783 MopB_CT_2 The MopB_CT_ 96.6 0.007 1.5E-07 43.0 6.0 46 17-63 33-78 (156)
27 COG1153 FwdD Formylmethanofura 96.6 0.0092 2E-07 41.8 6.1 66 10-76 25-90 (128)
28 PRK05449 aspartate alpha-decar 95.9 0.06 1.3E-06 37.8 7.3 69 15-89 23-95 (126)
29 cd06919 Asp_decarbox Aspartate 95.8 0.08 1.7E-06 36.4 7.4 68 15-88 22-93 (111)
30 TIGR00223 panD L-aspartate-alp 95.5 0.11 2.4E-06 36.5 7.4 67 15-87 23-93 (126)
31 PF03152 UFD1: Ubiquitin fusio 95.3 0.058 1.3E-06 39.7 5.7 83 18-102 28-114 (176)
32 KOG1816|consensus 95.2 0.038 8.3E-07 43.8 4.9 84 15-98 83-179 (308)
33 TIGR02693 arsenite_ox_L arseni 95.0 0.068 1.5E-06 47.1 6.2 48 17-65 726-773 (806)
34 PRK15102 trimethylamine N-oxid 94.9 0.056 1.2E-06 47.4 5.6 48 18-66 712-759 (825)
35 COG0853 PanD Aspartate 1-decar 94.7 0.28 6.1E-06 34.4 7.6 66 16-87 23-92 (126)
36 TIGR02166 dmsA_ynfE anaerobic 94.7 0.08 1.7E-06 45.9 5.8 48 17-65 706-753 (797)
37 TIGR02164 torA trimethylamine- 94.6 0.084 1.8E-06 46.3 5.8 48 18-66 709-756 (822)
38 PF02261 Asp_decarbox: Asparta 94.6 0.17 3.6E-06 35.1 6.1 64 16-85 24-91 (116)
39 TIGR03479 DMSO_red_II_alp DMSO 94.5 0.099 2.1E-06 46.5 6.1 50 17-67 811-860 (912)
40 COG0243 BisC Anaerobic dehydro 94.4 0.088 1.9E-06 45.7 5.5 48 15-63 670-717 (765)
41 PRK14990 anaerobic dimethyl su 94.2 0.11 2.3E-06 45.4 5.6 48 17-65 723-770 (814)
42 TIGR00509 bisC_fam molybdopter 94.1 0.13 2.8E-06 44.7 5.8 49 17-66 658-706 (770)
43 TIGR01591 Fdh-alpha formate de 93.9 0.17 3.7E-06 42.9 6.0 48 17-65 593-640 (671)
44 TIGR01243 CDC48 AAA family ATP 93.2 0.11 2.3E-06 45.1 3.9 40 1-40 26-85 (733)
45 PRK15488 thiosulfate reductase 93.2 0.22 4.7E-06 43.2 5.7 49 17-66 667-715 (759)
46 PRK08166 NADH dehydrogenase su 92.9 0.27 5.8E-06 43.4 6.0 48 17-65 778-825 (847)
47 PRK07860 NADH dehydrogenase su 92.8 0.28 6.1E-06 43.2 5.9 50 16-67 718-767 (797)
48 TIGR01701 Fdhalpha-like oxidor 91.9 0.46 1E-05 41.5 6.1 48 17-64 660-711 (743)
49 TIGR03327 AMP_phos AMP phospho 91.7 0.76 1.7E-05 38.9 6.9 65 19-84 17-82 (500)
50 PRK14991 tetrathionate reducta 91.5 0.5 1.1E-05 42.9 6.0 47 17-64 917-963 (1031)
51 TIGR01706 NAPA periplasmic nit 91.3 0.54 1.2E-05 41.4 6.0 48 16-64 746-795 (830)
52 PF04014 Antitoxin-MazE: Antid 91.2 0.31 6.6E-06 27.9 3.0 28 15-42 6-33 (47)
53 TIGR02645 ARCH_P_rylase putati 91.1 1.1 2.4E-05 37.9 7.3 63 21-84 18-81 (493)
54 PRK04350 thymidine phosphoryla 90.8 1.1 2.3E-05 38.0 6.9 61 23-84 14-76 (490)
55 TIGR01580 narG respiratory nit 90.6 0.69 1.5E-05 43.0 6.1 63 4-72 1109-1171(1235)
56 PRK13532 nitrate reductase cat 90.5 0.73 1.6E-05 40.5 6.0 49 16-65 746-796 (830)
57 PF04014 Antitoxin-MazE: Antid 90.1 1.2 2.6E-05 25.4 4.9 39 58-100 6-44 (47)
58 PRK09129 NADH dehydrogenase su 90.0 0.68 1.5E-05 40.4 5.3 56 16-72 708-763 (776)
59 PF08922 DUF1905: Domain of un 89.8 1.4 3.1E-05 28.1 5.5 61 18-82 15-79 (80)
60 TIGR00008 infA translation ini 89.6 1.6 3.4E-05 27.5 5.4 26 59-84 30-56 (68)
61 TIGR01439 lp_hng_hel_AbrB loop 89.4 0.59 1.3E-05 25.6 3.1 25 15-39 6-30 (43)
62 PRK15070 propanediol utilizati 89.3 3.1 6.7E-05 31.6 7.7 71 11-83 136-210 (211)
63 TIGR01439 lp_hng_hel_AbrB loop 88.5 1.8 3.8E-05 23.6 4.6 38 57-98 5-42 (43)
64 TIGR02609 doc_partner putative 87.8 0.76 1.6E-05 28.9 3.1 25 17-41 11-35 (74)
65 PRK11347 antitoxin ChpS; Provi 87.6 0.78 1.7E-05 29.8 3.2 25 18-42 14-38 (83)
66 COG0361 InfA Translation initi 86.8 0.51 1.1E-05 30.4 1.9 26 59-84 32-58 (75)
67 PF03459 TOBE: TOBE domain; I 86.6 0.74 1.6E-05 27.3 2.5 24 17-40 34-57 (64)
68 PLN03086 PRLI-interacting fact 86.2 6.9 0.00015 33.8 8.9 86 16-103 92-197 (567)
69 PF03152 UFD1: Ubiquitin fusio 85.9 0.32 7E-06 35.8 0.7 66 16-83 72-144 (176)
70 COG2002 AbrB Regulators of sta 85.9 1.1 2.4E-05 29.1 3.2 30 11-40 9-38 (89)
71 PRK12442 translation initiatio 85.2 3 6.5E-05 27.5 5.0 26 59-84 32-58 (87)
72 TIGR01553 formate-DH-alph form 84.9 2.3 5.1E-05 38.7 5.8 42 16-58 913-954 (1009)
73 PRK08577 hypothetical protein; 84.7 2.9 6.3E-05 28.8 5.1 26 14-39 11-36 (136)
74 PRK09798 antitoxin MazE; Provi 84.4 1.5 3.2E-05 28.4 3.2 25 18-42 15-39 (82)
75 PLN03086 PRLI-interacting fact 83.8 2.8 6E-05 36.1 5.5 81 15-95 150-246 (567)
76 TIGR02609 doc_partner putative 83.7 2.3 4.9E-05 26.7 3.8 37 59-100 10-46 (74)
77 cd04459 Rho_CSD Rho_CSD: Rho p 83.2 1.3 2.9E-05 27.7 2.6 22 18-39 29-50 (68)
78 COG1974 LexA SOS-response tran 81.8 1.4 3E-05 33.1 2.6 64 19-105 116-180 (201)
79 COG1974 LexA SOS-response tran 80.7 5.1 0.00011 30.0 5.4 29 1-39 122-150 (201)
80 PF09263 PEX-2N: Peroxisome bi 80.4 8.5 0.00018 25.4 5.6 66 18-84 16-85 (87)
81 COG3383 Uncharacterized anaero 79.9 4 8.7E-05 36.8 5.2 53 18-71 857-913 (978)
82 PF08605 Rad9_Rad53_bind: Fung 79.8 2 4.4E-05 30.2 2.8 28 16-43 46-73 (131)
83 PRK08577 hypothetical protein; 79.5 6.1 0.00013 27.2 5.1 44 57-103 11-54 (136)
84 KOG1816|consensus 79.4 15 0.00034 29.3 7.9 88 16-105 38-129 (308)
85 TIGR03595 Obg_CgtA_exten Obg f 79.2 2 4.3E-05 26.8 2.3 18 23-40 47-64 (69)
86 PRK11347 antitoxin ChpS; Provi 78.2 4.8 0.0001 26.1 4.0 36 59-99 12-47 (83)
87 PRK09939 putative oxidoreducta 78.0 2.2 4.9E-05 37.7 3.1 25 16-40 672-696 (759)
88 COG2002 AbrB Regulators of sta 76.9 7.6 0.00016 25.0 4.7 42 57-101 12-53 (89)
89 PF06130 PduL: Propanediol uti 76.8 3.1 6.7E-05 26.4 2.7 24 17-40 10-33 (71)
90 COG2336 MazE Growth regulator 76.4 3.4 7.4E-05 27.0 2.9 22 18-39 14-35 (82)
91 PF09269 DUF1967: Domain of un 75.6 2.4 5.3E-05 26.3 2.0 18 23-40 47-64 (69)
92 cd05793 S1_IF1A S1_IF1A: Trans 75.3 4 8.7E-05 26.0 3.0 27 58-84 24-50 (77)
93 PF03120 DNA_ligase_OB: NAD-de 72.1 4.2 9E-05 26.4 2.5 19 21-39 41-59 (82)
94 COG5140 UFD1 Ubiquitin fusion- 71.1 9.4 0.0002 30.2 4.7 69 15-83 91-164 (331)
95 cd04456 S1_IF1A_like S1_IF1A_l 70.3 9.6 0.00021 24.3 3.9 28 57-84 23-50 (78)
96 TIGR02851 spore_V_T stage V sp 70.0 13 0.00029 27.2 5.1 39 57-99 11-49 (180)
97 PRK09974 putative regulator Pr 69.2 13 0.00028 25.6 4.5 39 57-99 16-54 (111)
98 TIGR02851 spore_V_T stage V sp 68.2 5.6 0.00012 29.1 2.8 25 15-39 12-36 (180)
99 KOG0735|consensus 68.1 14 0.00031 33.4 5.6 53 51-103 52-105 (952)
100 PRK09974 putative regulator Pr 67.0 25 0.00055 24.1 5.6 29 11-39 13-41 (111)
101 COG5013 NarG Nitrate reductase 65.9 13 0.00027 34.4 4.9 89 4-99 1103-1191(1227)
102 PRK04350 thymidine phosphoryla 65.5 9.3 0.0002 32.4 3.9 40 1-40 16-75 (490)
103 KOG1625|consensus 64.4 4.6 0.0001 34.9 1.9 26 17-42 282-307 (600)
104 PTZ00329 eukaryotic translatio 64.2 6.5 0.00014 28.5 2.4 27 58-84 56-82 (155)
105 PF04076 BOF: Bacterial OB fol 63.3 14 0.0003 24.9 3.7 38 4-41 29-86 (103)
106 PF07497 Rho_RNA_bind: Rho ter 63.0 2 4.2E-05 27.8 -0.4 20 18-37 31-50 (78)
107 PRK04012 translation initiatio 62.9 9.7 0.00021 25.5 2.9 27 58-84 45-71 (100)
108 TIGR00523 eIF-1A eukaryotic/ar 62.9 16 0.00034 24.4 4.0 38 57-95 42-82 (99)
109 COG3138 AstA Arginine/ornithin 61.6 8 0.00017 31.1 2.7 24 16-39 311-334 (336)
110 PRK05892 nucleoside diphosphat 60.7 41 0.0009 24.0 6.1 69 29-97 82-156 (158)
111 TIGR00638 Mop molybdenum-pteri 60.1 16 0.00035 21.5 3.3 25 18-42 37-61 (69)
112 smart00652 eIF1a eukaryotic tr 59.7 10 0.00022 24.5 2.5 27 58-84 29-55 (83)
113 COG5214 POL12 DNA polymerase a 59.5 6.5 0.00014 33.3 1.9 25 18-42 241-265 (581)
114 PRK09798 antitoxin MazE; Provi 59.4 20 0.00043 23.1 3.8 36 59-99 13-48 (82)
115 PF12857 TOBE_3: TOBE-like dom 59.2 14 0.00031 21.8 2.9 21 18-39 36-56 (58)
116 TIGR01461 greB transcription e 57.7 24 0.00053 25.1 4.4 63 21-83 75-140 (156)
117 PRK14720 transcript cleavage f 57.5 32 0.00069 31.5 6.0 74 26-99 827-904 (906)
118 PRK01885 greB transcription el 56.5 36 0.00077 24.3 5.1 63 21-83 77-142 (157)
119 PRK08493 NADH dehydrogenase su 56.3 16 0.00036 32.8 4.0 29 15-43 746-774 (819)
120 PF04246 RseC_MucC: Positive r 56.0 33 0.00073 23.3 4.8 48 32-83 5-62 (135)
121 PRK11507 ribosome-associated p 55.9 10 0.00022 24.0 1.9 28 56-83 34-63 (70)
122 TIGR03243 arg_catab_AOST argin 54.6 13 0.00028 30.1 2.9 23 16-38 310-332 (335)
123 PF00717 Peptidase_S24: Peptid 54.0 15 0.00033 21.5 2.5 29 4-42 9-37 (70)
124 PRK10456 arginine succinyltran 51.2 16 0.00035 29.7 2.9 25 16-40 312-336 (344)
125 COG0782 Uncharacterized conser 51.0 32 0.00069 24.4 4.1 62 21-83 71-136 (151)
126 PRK12423 LexA repressor; Provi 50.0 25 0.00055 25.7 3.6 21 19-39 118-138 (202)
127 COG5140 UFD1 Ubiquitin fusion- 49.9 1.3E+02 0.0027 24.0 7.5 83 14-100 44-132 (331)
128 COG3127 Predicted ABC-type tra 48.6 17 0.00036 32.7 2.8 33 52-84 590-622 (829)
129 TIGR03244 arg_catab_AstA argin 48.2 19 0.00042 29.2 2.9 23 16-38 311-333 (336)
130 PF08845 SymE_toxin: Toxin Sym 48.2 21 0.00046 21.5 2.4 27 16-42 24-50 (57)
131 TIGR03245 arg_AOST_alph argini 47.5 20 0.00044 29.0 2.9 24 16-39 311-334 (336)
132 PRK05753 nucleoside diphosphat 47.5 41 0.00089 23.4 4.2 54 30-83 55-112 (137)
133 PF01176 eIF-1a: Translation i 47.3 25 0.00054 21.3 2.7 27 58-84 27-53 (65)
134 TIGR03327 AMP_phos AMP phospho 47.2 33 0.00072 29.3 4.3 39 2-40 24-81 (500)
135 COG2501 S4-like RNA binding pr 46.9 15 0.00032 23.5 1.7 26 57-82 35-62 (73)
136 PF01982 CTP-dep_RFKase: Domai 46.8 16 0.00034 25.4 2.0 17 23-39 104-120 (121)
137 PRK09555 feoA ferrous iron tra 46.5 66 0.0014 20.1 4.7 38 4-41 1-42 (74)
138 TIGR00498 lexA SOS regulatory 46.5 33 0.00071 24.7 3.7 21 19-39 115-135 (199)
139 COG0186 RpsQ Ribosomal protein 46.2 32 0.00069 22.7 3.2 29 69-97 52-80 (87)
140 TIGR01462 greA transcription e 43.9 1.1E+02 0.0024 21.4 6.1 55 29-83 80-138 (151)
141 PRK09570 rpoH DNA-directed RNA 43.8 22 0.00047 23.0 2.1 19 24-42 46-64 (79)
142 PF14250 AbrB-like: AbrB-like 43.7 21 0.00046 22.7 2.0 22 21-42 44-66 (71)
143 PF11302 DUF3104: Protein of u 43.4 19 0.0004 23.2 1.7 16 27-42 3-18 (75)
144 PF01191 RNA_pol_Rpb5_C: RNA p 42.3 41 0.00088 21.4 3.2 20 23-42 42-61 (74)
145 PRK04183 glutamyl-tRNA(Gln) am 42.0 79 0.0017 26.2 5.6 54 28-84 1-54 (419)
146 PRK14132 riboflavin kinase; Pr 41.5 24 0.00052 24.7 2.2 17 23-39 109-125 (126)
147 COG4869 PduL Propanediol utili 41.0 48 0.001 24.9 3.8 36 3-39 127-162 (210)
148 PF04023 FeoA: FeoA domain; I 39.8 51 0.0011 19.6 3.3 37 5-41 5-44 (74)
149 COG2012 RPB5 DNA-directed RNA 39.5 46 0.00099 21.7 3.1 20 24-43 49-68 (80)
150 cd00989 PDZ_metalloprotease PD 39.2 41 0.00088 19.9 2.8 34 4-39 3-39 (79)
151 TIGR02988 YaaA_near_RecF S4 do 39.1 23 0.00049 20.7 1.6 25 57-81 32-58 (59)
152 PF05899 Cupin_3: Protein of u 38.8 10 0.00022 23.5 -0.0 28 12-39 30-57 (74)
153 PRK00226 greA transcription el 38.3 1.1E+02 0.0024 21.4 5.3 62 22-83 78-143 (157)
154 smart00532 LIGANc Ligase N fam 37.9 32 0.0007 28.7 2.8 18 22-39 355-372 (441)
155 PF08206 OB_RNB: Ribonuclease 37.6 41 0.00088 19.8 2.5 19 19-39 23-41 (58)
156 cd04473 S1_RecJ_like S1_RecJ_l 37.5 96 0.0021 18.8 4.7 37 58-98 41-77 (77)
157 TIGR02645 ARCH_P_rylase putati 37.0 58 0.0013 27.8 4.2 39 2-40 23-80 (493)
158 COG1153 FwdD Formylmethanofura 36.9 80 0.0017 22.2 4.2 39 58-100 30-68 (128)
159 PLN00208 translation initiatio 36.8 26 0.00057 25.1 1.9 27 57-83 55-81 (145)
160 cd06462 Peptidase_S24_S26 The 36.4 55 0.0012 19.4 3.1 25 6-39 14-38 (84)
161 KOG0730|consensus 36.4 15 0.00033 32.4 0.7 37 1-39 37-91 (693)
162 TIGR03243 arg_catab_AOST argin 36.1 2.2E+02 0.0048 23.1 7.2 29 55-83 306-334 (335)
163 TIGR00156 conserved hypothetic 35.8 44 0.00096 23.4 2.8 24 18-41 86-109 (126)
164 PRK05610 rpsQ 30S ribosomal pr 35.3 70 0.0015 20.7 3.5 24 72-95 53-76 (84)
165 PF04958 AstA: Arginine N-succ 35.0 26 0.00057 28.4 1.8 23 16-38 317-339 (342)
166 TIGR03635 S17_bact 30S ribosom 34.8 58 0.0013 20.4 3.0 13 72-84 48-60 (71)
167 PRK11642 exoribonuclease R; Pr 33.9 2.1E+02 0.0045 25.9 7.3 85 4-97 116-215 (813)
168 CHL00142 rps17 ribosomal prote 33.3 80 0.0017 20.5 3.6 22 72-93 50-71 (84)
169 PRK14165 winged helix-turn-hel 32.3 37 0.00081 25.7 2.2 17 23-39 198-214 (217)
170 PF00240 ubiquitin: Ubiquitin 32.2 40 0.00088 19.7 1.9 28 15-42 41-68 (69)
171 TIGR01003 PTS_HPr_family Phosp 31.8 84 0.0018 19.7 3.5 34 7-40 29-65 (82)
172 KOG1740|consensus 31.8 29 0.00063 23.7 1.3 26 73-98 50-75 (107)
173 cd06529 S24_LexA-like Peptidas 30.9 62 0.0013 19.2 2.7 10 30-39 28-37 (81)
174 PF09926 DUF2158: Uncharacteri 30.4 1.2E+02 0.0026 17.9 4.2 18 31-50 2-21 (53)
175 COG4013 Uncharacterized protei 30.0 1.1E+02 0.0024 20.2 3.8 21 19-39 7-30 (91)
176 cd01614 EutN_CcmL Ethanolamine 29.9 15 0.00032 23.9 -0.3 45 56-105 37-81 (83)
177 PF01472 PUA: PUA domain; Int 29.6 1.2E+02 0.0025 18.5 3.8 34 9-49 16-49 (74)
178 PRK10862 SoxR reducing system 29.3 43 0.00092 23.8 1.9 17 67-83 53-69 (154)
179 COG2274 SunT ABC-type bacterio 29.3 18 0.0004 31.9 0.0 56 27-82 493-560 (709)
180 PRK08395 fumarate hydratase; P 28.4 66 0.0014 23.5 2.8 20 20-41 7-26 (162)
181 PHA02451 hypothetical protein 28.4 36 0.00078 20.5 1.2 15 92-106 3-17 (54)
182 PRK08097 ligB NAD-dependent DN 28.3 57 0.0012 28.2 2.8 19 21-39 351-369 (562)
183 COG1158 Rho Transcription term 27.9 51 0.0011 27.4 2.3 22 18-39 82-103 (422)
184 PRK06342 transcription elongat 27.9 1E+02 0.0022 22.1 3.7 54 28-81 93-149 (160)
185 PRK05659 sulfur carrier protei 27.8 82 0.0018 18.5 2.8 17 22-38 43-59 (66)
186 PRK13782 phosphocarrier protei 27.6 1.1E+02 0.0024 19.1 3.5 34 6-39 28-64 (82)
187 cd04486 YhcR_OBF_like YhcR_OBF 27.5 72 0.0016 20.0 2.6 15 27-41 42-56 (78)
188 smart00326 SH3 Src homology 3 27.3 58 0.0012 17.5 1.9 19 23-41 14-32 (58)
189 PF07244 Surf_Ag_VNR: Surface 27.3 30 0.00066 20.5 0.8 27 11-37 5-33 (78)
190 PF08497 Radical_SAM_N: Radica 27.3 61 0.0013 26.0 2.6 22 20-41 4-25 (302)
191 PF13742 tRNA_anti_2: OB-fold 27.2 1E+02 0.0022 20.0 3.3 36 6-42 45-81 (99)
192 PF01336 tRNA_anti-codon: OB-f 27.1 52 0.0011 19.1 1.8 19 23-41 38-56 (75)
193 PRK01191 rpl24p 50S ribosomal 26.8 1.1E+02 0.0024 21.2 3.6 51 18-70 29-85 (120)
194 PF13275 S4_2: S4 domain; PDB: 26.8 32 0.00069 21.3 0.8 25 58-82 32-58 (65)
195 COG1339 Transcriptional regula 26.4 55 0.0012 25.0 2.1 17 23-39 195-211 (214)
196 PTZ00194 60S ribosomal protein 26.4 1.3E+02 0.0028 21.5 4.0 53 18-72 30-88 (143)
197 KOG3447|consensus 26.2 59 0.0013 23.3 2.2 34 73-107 58-97 (150)
198 TIGR00575 dnlj DNA ligase, NAD 25.9 66 0.0014 28.2 2.8 18 22-39 348-365 (652)
199 PRK07956 ligA NAD-dependent DN 25.8 66 0.0014 28.3 2.8 19 21-39 359-377 (665)
200 PRK09376 rho transcription ter 25.7 80 0.0017 26.4 3.1 22 18-39 79-100 (416)
201 PRK14350 ligA NAD-dependent DN 25.7 66 0.0014 28.4 2.8 19 21-39 356-374 (669)
202 COG1101 PhnK ABC-type uncharac 25.6 28 0.0006 27.3 0.4 39 27-65 26-67 (263)
203 PLN00051 RNA-binding S4 domain 25.5 80 0.0017 24.6 3.0 34 6-43 212-245 (267)
204 cd00367 PTS-HPr_like Histidine 25.4 1.5E+02 0.0032 18.0 3.7 33 7-39 25-60 (77)
205 PRK12281 rplX 50S ribosomal pr 25.4 49 0.0011 21.0 1.5 15 27-41 4-19 (76)
206 PRK03760 hypothetical protein; 25.3 66 0.0014 21.9 2.3 17 23-39 99-115 (117)
207 COG1363 FrvX Cellulase M and r 24.9 65 0.0014 26.2 2.5 21 21-41 145-165 (355)
208 COG5417 Uncharacterized small 24.7 59 0.0013 21.1 1.7 31 8-38 48-80 (81)
209 TIGR00767 rho transcription te 24.7 70 0.0015 26.7 2.6 21 18-38 79-99 (415)
210 COG0272 Lig NAD-dependent DNA 24.6 94 0.002 27.6 3.5 17 23-39 361-377 (667)
211 CHL00010 infA translation init 24.5 1.1E+02 0.0024 19.2 3.0 25 60-84 33-58 (78)
212 KOG0741|consensus 24.1 1.5E+02 0.0032 26.4 4.5 33 52-84 53-85 (744)
213 TIGR00451 unchar_dom_2 unchara 24.0 1.4E+02 0.0031 19.4 3.6 36 8-49 45-80 (107)
214 COG3377 Uncharacterized conser 23.9 47 0.001 22.2 1.2 25 12-36 54-88 (95)
215 PF07653 SH3_2: Variant SH3 do 23.6 43 0.00094 19.1 0.9 12 28-39 16-27 (55)
216 COG0261 RplU Ribosomal protein 23.4 1.1E+02 0.0024 20.8 2.9 25 71-96 12-36 (103)
217 TIGR02212 lolCE lipoprotein re 23.4 2.4E+02 0.0053 21.9 5.4 22 18-39 145-166 (411)
218 PRK14351 ligA NAD-dependent DN 23.3 78 0.0017 28.0 2.8 19 21-39 381-399 (689)
219 PF01835 A2M_N: MG2 domain; I 23.3 82 0.0018 19.7 2.3 13 8-20 13-25 (99)
220 TIGR01683 thiS thiamine biosyn 23.2 1E+02 0.0023 18.1 2.6 11 28-38 47-57 (64)
221 PRK10850 PTS system phosphohis 23.2 1.6E+02 0.0034 18.7 3.6 34 7-40 29-65 (85)
222 cd01812 BAG1_N Ubiquitin-like 23.1 94 0.002 18.1 2.4 20 21-40 51-70 (71)
223 PRK05863 sulfur carrier protei 23.1 1.1E+02 0.0024 18.2 2.8 15 23-38 44-58 (65)
224 TIGR03095 rusti_cyanin rusticy 23.0 2.1E+02 0.0046 20.0 4.6 50 33-84 18-67 (148)
225 PRK06842 fumarate hydratase; P 23.0 93 0.002 23.2 2.8 20 20-41 9-28 (185)
226 PF13567 DUF4131: Domain of un 23.0 58 0.0013 21.5 1.6 13 29-41 128-140 (176)
227 PRK07696 sulfur carrier protei 22.6 1.1E+02 0.0023 18.5 2.6 16 23-38 45-60 (67)
228 PRK08228 L(+)-tartrate dehydra 22.5 95 0.0021 23.5 2.8 20 20-41 10-29 (204)
229 cd06196 FNR_like_1 Ferredoxin 22.4 1.5E+02 0.0032 21.1 3.8 56 27-83 25-91 (218)
230 PRK03818 putative transporter; 22.4 57 0.0012 27.8 1.7 41 2-42 307-349 (552)
231 PF02938 GAD: GAD domain; Int 22.3 69 0.0015 20.6 1.8 18 23-40 68-85 (95)
232 COG4591 LolE ABC-type transpor 22.2 96 0.0021 25.6 3.0 27 58-84 143-169 (408)
233 CHL00141 rpl24 ribosomal prote 21.8 59 0.0013 20.9 1.4 37 28-66 7-44 (83)
234 PRK00276 infA translation init 21.7 1.4E+02 0.003 18.3 3.0 25 60-84 33-58 (72)
235 PF14345 GDYXXLXY: GDYXXLXY pr 21.7 57 0.0012 22.5 1.4 62 5-68 34-101 (144)
236 TIGR02063 RNase_R ribonuclease 21.6 5.5E+02 0.012 22.5 9.0 76 4-87 101-185 (709)
237 smart00532 LIGANc Ligase N fam 21.6 80 0.0017 26.4 2.4 17 71-87 361-377 (441)
238 PF12704 MacB_PCD: MacB-like p 21.3 1.4E+02 0.003 20.4 3.3 25 58-82 140-167 (232)
239 PTZ00241 40S ribosomal protein 21.3 1.5E+02 0.0033 21.5 3.6 26 70-95 114-139 (158)
240 cd00565 ThiS ThiaminS ubiquiti 21.2 1.3E+02 0.0027 17.7 2.7 11 28-38 48-58 (65)
241 PF13550 Phage-tail_3: Putativ 21.2 79 0.0017 21.3 2.0 16 26-41 136-151 (164)
242 cd00988 PDZ_CTP_protease PDZ d 21.1 1.5E+02 0.0033 17.6 3.2 29 8-38 11-39 (85)
243 TIGR03106 trio_M42_hydro hydro 21.1 85 0.0018 25.1 2.4 21 21-41 148-168 (343)
244 COG3111 Periplasmic protein wi 21.1 1.7E+02 0.0037 20.6 3.6 39 3-41 51-109 (128)
245 TIGR02657 amicyanin amicyanin. 21.0 70 0.0015 19.8 1.6 26 13-42 2-27 (83)
246 COG1224 TIP49 DNA helicase TIP 20.9 1.1E+02 0.0024 25.8 3.0 18 23-40 180-197 (450)
247 cd00990 PDZ_glycyl_aminopeptid 20.9 1.7E+02 0.0037 17.2 3.3 30 9-40 11-40 (80)
248 PF11976 Rad60-SLD: Ubiquitin- 20.9 72 0.0016 18.9 1.6 19 21-39 53-71 (72)
249 PRK06944 sulfur carrier protei 20.7 1.4E+02 0.003 17.4 2.8 9 24-32 21-29 (65)
250 PF11543 UN_NPL4: Nuclear pore 20.7 48 0.001 21.0 0.8 17 23-39 62-78 (80)
251 PF00380 Ribosomal_S9: Ribosom 20.6 63 0.0014 22.3 1.4 21 44-66 4-24 (121)
252 PRK06043 fumarate hydratase; P 20.5 1.1E+02 0.0024 22.9 2.8 20 20-41 9-28 (192)
253 PRK12297 obgE GTPase CgtA; Rev 20.4 80 0.0017 26.1 2.2 18 23-40 400-417 (424)
254 COG0272 Lig NAD-dependent DNA 20.4 82 0.0018 28.0 2.3 25 71-95 366-391 (667)
255 PF05683 Fumerase_C: Fumarase 20.3 93 0.002 23.6 2.3 21 19-41 34-54 (205)
256 smart00739 KOW KOW (Kyprides, 20.2 1.2E+02 0.0026 14.3 3.0 20 30-49 2-21 (28)
257 cd06198 FNR_like_3 NAD(P) bind 20.2 1.3E+02 0.0028 21.4 3.1 56 28-83 21-84 (216)
258 TIGR00358 3_prime_RNase VacB a 20.1 3.5E+02 0.0076 23.6 6.1 24 59-83 107-130 (654)
No 1
>PF02359 CDC48_N: Cell division protein 48 (CDC48), N-terminal domain; InterPro: IPR003338 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport. Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. The VAT protein of the archaebacterium Thermoplasma acidophilum, like all other members of the Cdc48/p97 family of AAA ATPases, has two ATPase domains and a 185-residue amino-terminal substrate-recognition domain, VAT-N. VAT shows activity in protein folding and unfolding and thus shares the common function of these ATPases in disassembly and/or degradation of protein complexes. VAT-N is composed of two equally sized subdomains. The amino-terminal subdomain VAT-Nn forms a double-psi beta-barrel whose pseudo-twofold symmetry is mirrored by an internal sequence repeat of 42 residues. The carboxy-terminal subdomain VAT-Nc forms a novel six-stranded beta-clam fold []. Together, VAT-Nn and VAT-Nc form a kidney-shaped structure, in close agreement with results from electron microscopy. VAT-Nn is related to numerous proteins including prokaryotic transcription factors, metabolic enzymes, the protease cofactors UFD1 and PrlF, and aspartic proteinases. ; GO: 0005524 ATP binding; PDB: 1CZ4_A 1CZ5_A 3CF3_C 3CF1_A 3CF2_A 1S3S_D 1E32_A 1R7R_A 2PJH_B 1CR5_B ....
Probab=99.80 E-value=5.9e-20 Score=120.06 Aligned_cols=71 Identities=35% Similarity=0.539 Sum_probs=60.0
Q ss_pred EEeEEEecCHHHHhhCCCCCCCEEEEEeccCCcEEEEeccCCCC--CCCeEEEeHhhhhcccccCCCeEEEEeCC
Q psy3865 13 LLRGKRRKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSDDTC--PDEKIRMNRVMRNNLRVRLSDVVSLVPCP 85 (107)
Q Consensus 13 ~~rGiari~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai~~~~~d~--~~~~Irid~~~R~N~~v~igD~V~V~~~~ 85 (107)
..+++|+|||++|++||++.||+|+|.|++ +|+|++++.+.. +.+.|+||+.+|+||++++||.|+|++++
T Consensus 13 ~~~n~v~v~~~~m~~l~l~~gd~v~i~g~~--~tv~~v~~~~~~~~~~g~I~l~~~~R~n~~v~igd~V~V~~~~ 85 (87)
T PF02359_consen 13 AGTNCVRVSPEDMEELGLFPGDVVLISGKR--KTVAFVFPDRPDDSPPGVIRLSGIQRKNAGVSIGDRVTVRPYD 85 (87)
T ss_dssp HCTTEEEEEHHHHHCTTT-TTEEEEEETTT--EEEEEEEEECCSTTCTTEEEE-HHHHHHCT--TTSEEEEEEET
T ss_pred CCCCEEEEcHHHHHHcCCCCccEEEEeCCc--eEEEEEEECCCCCCCCCEEEECHHHHhhCCcCCCCEEEEEECC
Confidence 457899999999999999999999999955 499999877543 79999999999999999999999999973
No 2
>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily. This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.
Probab=99.57 E-value=1e-14 Score=124.47 Aligned_cols=85 Identities=27% Similarity=0.348 Sum_probs=76.4
Q ss_pred EeEEEecCHHHHhhCCCCCCCEEEEE-eccCCcEEEEecc--CCCCCCCeEEEeHhhhhcccccCCCeEEEEeCCCCCCc
Q psy3865 14 LRGKRRKESAKMDELNLFRGDTVLLR-GKRRKESVCIVLS--DDTCPDEKIRMNRVMRNNLRVRLSDVVSLVPCPGIVYG 90 (107)
Q Consensus 14 ~rGiari~~~~m~~Lgl~~GD~V~I~-Gkr~~~tvai~~~--~~d~~~~~Irid~~~R~N~~v~igD~V~V~~~~~~~~a 90 (107)
=+|++||+|+.|++||+.+||+|+|+ |++ .++|++|+ .++++.+.|+||+.+|+|+|+++||.|+|+++ ++++|
T Consensus 15 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~ 91 (733)
T TIGR01243 15 GRGIVRIDRQTAARLGVEPGDFVEIEKGDR--SVVAIVWPLRPDDEGRGIIRMDGYLRANAGVTIGDTVTVERA-EVKEA 91 (733)
T ss_pred CCCeEeeCHHHHHhcCCCCCCEEEEecCCC--ceeEEEEecCccccCCCEEeecHHHHhhcCCCCCCeEEEeec-CCCcc
Confidence 47999999999999999999999999 777 46777775 46889999999999999999999999999996 79999
Q ss_pred cEEEEccCCcc
Q psy3865 91 KRIHVLPIDDS 101 (107)
Q Consensus 91 ~~V~l~P~~dt 101 (107)
++|+++|....
T Consensus 92 ~~~~~~~~~~~ 102 (733)
T TIGR01243 92 KKVVLAPTQPI 102 (733)
T ss_pred ceEeecccccc
Confidence 99999997544
No 3
>KOG0730|consensus
Probab=98.56 E-value=5.3e-08 Score=83.17 Aligned_cols=87 Identities=40% Similarity=0.654 Sum_probs=79.4
Q ss_pred EecCHHHHhhCCCCCCCEEEEEeccCCcEEEEeccCCCCCCCeEEEeHhhhhcccccCCCeEEEEeCCCCCCccEEEEcc
Q psy3865 18 RRKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSDDTCPDEKIRMNRVMRNNLRVRLSDVVSLVPCPGIVYGKRIHVLP 97 (107)
Q Consensus 18 ari~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai~~~~~d~~~~~Irid~~~R~N~~v~igD~V~V~~~~~~~~a~~V~l~P 97 (107)
+-+++.+|++++++.| |.++|+++..+++.....++ ....+++....|+|+.++.|+.+.+++++.++++.+++++|
T Consensus 30 ~~~~~~~~~~~~l~~g--~~~~g~~~~~~~~~~~~~~~-~~~~~~~~~~~r~~l~~~~~~~~~~~~~p~v~~~~~i~~l~ 106 (693)
T KOG0730|consen 30 VVLSEGAMDKLGLLRG--VLLDGKKRREPVDAVVQDET-SELIGRQTMVSRSNLRLQLGRLLHSSDCPSVKRPARIAVLP 106 (693)
T ss_pred heecHHHHhhhcCCcc--eEEECccccCCccceeccCC-ccccchhhheeccchhhcccceecccCCCCccccceeeeee
Confidence 4568899999999999 99999998888888766666 88999999999999999999999999999999999999999
Q ss_pred CCccccCCCC
Q psy3865 98 IDDSVQGLTG 107 (107)
Q Consensus 98 ~~dti~~~~g 107 (107)
.++|.+++++
T Consensus 107 ~~~~~~~i~~ 116 (693)
T KOG0730|consen 107 VDDTSEGIAG 116 (693)
T ss_pred hhhccccchh
Confidence 9999999864
No 4
>PF02359 CDC48_N: Cell division protein 48 (CDC48), N-terminal domain; InterPro: IPR003338 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport. Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. The VAT protein of the archaebacterium Thermoplasma acidophilum, like all other members of the Cdc48/p97 family of AAA ATPases, has two ATPase domains and a 185-residue amino-terminal substrate-recognition domain, VAT-N. VAT shows activity in protein folding and unfolding and thus shares the common function of these ATPases in disassembly and/or degradation of protein complexes. VAT-N is composed of two equally sized subdomains. The amino-terminal subdomain VAT-Nn forms a double-psi beta-barrel whose pseudo-twofold symmetry is mirrored by an internal sequence repeat of 42 residues. The carboxy-terminal subdomain VAT-Nc forms a novel six-stranded beta-clam fold []. Together, VAT-Nn and VAT-Nc form a kidney-shaped structure, in close agreement with results from electron microscopy. VAT-Nn is related to numerous proteins including prokaryotic transcription factors, metabolic enzymes, the protease cofactors UFD1 and PrlF, and aspartic proteinases. ; GO: 0005524 ATP binding; PDB: 1CZ4_A 1CZ5_A 3CF3_C 3CF1_A 3CF2_A 1S3S_D 1E32_A 1R7R_A 2PJH_B 1CR5_B ....
Probab=97.44 E-value=0.00014 Score=47.16 Aligned_cols=39 Identities=38% Similarity=0.582 Sum_probs=29.2
Q ss_pred CcccCcccCCeEEEeE-------------------EEecCHHHHhhCCCCCCCEEEEE
Q psy3865 1 MDELNLFRGDTVLLRG-------------------KRRKESAKMDELNLFRGDTVLLR 39 (107)
Q Consensus 1 ~~~~~~~~~d~~~~rG-------------------iari~~~~m~~Lgl~~GD~V~I~ 39 (107)
|++|+||.||+|.+.| ..+||...++++++..||.|.|+
T Consensus 25 m~~l~l~~gd~v~i~g~~~tv~~v~~~~~~~~~~g~I~l~~~~R~n~~v~igd~V~V~ 82 (87)
T PF02359_consen 25 MEELGLFPGDVVLISGKRKTVAFVFPDRPDDSPPGVIRLSGIQRKNAGVSIGDRVTVR 82 (87)
T ss_dssp HHCTTT-TTEEEEEETTTEEEEEEEEECCSTTCTTEEEE-HHHHHHCT--TTSEEEEE
T ss_pred HHHcCCCCccEEEEeCCceEEEEEEECCCCCCCCCEEEECHHHHhhCCcCCCCEEEEE
Confidence 6899999999999986 23344477889999999999996
No 5
>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=97.35 E-value=0.00077 Score=44.85 Aligned_cols=49 Identities=14% Similarity=0.092 Sum_probs=41.7
Q ss_pred EEEecCHHHHhhCCCCCCCEEEEEeccCCcEEEEeccCCCCCCCeEEEeH
Q psy3865 16 GKRRKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSDDTCPDEKIRMNR 65 (107)
Q Consensus 16 Giari~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai~~~~~d~~~~~Irid~ 65 (107)
..+.|+|+++++|||..||.|+|+..+. +..+.+...+.+..+.|.|..
T Consensus 31 ~~v~i~p~dA~~lgi~~Gd~V~v~s~~G-~~~~~v~~~~~i~~g~v~~~~ 79 (116)
T cd02786 31 PTLLIHPADAAARGIADGDLVVVFNDRG-SVTLRAKVTDDVPPGVVVAEG 79 (116)
T ss_pred CEEEECHHHHHHcCCCCCCEEEEEcCCe-EEEEEEEECCCCCCCEEEeec
Confidence 3589999999999999999999997664 556677788889999999875
No 6
>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=97.34 E-value=0.00048 Score=45.29 Aligned_cols=53 Identities=17% Similarity=0.086 Sum_probs=42.4
Q ss_pred EEEecCHHHHhhCCCCCCCEEEEEeccCCcEEEEeccCCCCCCCeEEEeHhhhh
Q psy3865 16 GKRRKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSDDTCPDEKIRMNRVMRN 69 (107)
Q Consensus 16 Giari~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai~~~~~d~~~~~Irid~~~R~ 69 (107)
..++|+|+++++|||..||.|+|+.+.. +..+.+...+.+.++.|.|...--.
T Consensus 30 ~~v~inp~dA~~~Gi~~Gd~V~v~s~~G-~v~~~v~~~~~v~~g~v~~~~~~~~ 82 (110)
T PF01568_consen 30 PFVEINPEDAAKLGIKDGDWVRVSSPRG-SVEVRVKVTDGVPPGVVFMPHGWGG 82 (110)
T ss_dssp EEEEEEHHHHHHCT--TTCEEEEEETTE-EEEEEEEEETTS-TTEEEEESTHTT
T ss_pred CEEEEcHHHHHHhcCcCCCEEEEEeccc-eEeeeeEEecCCcCCEEEEeccccc
Confidence 3689999999999999999999997765 6666777888899999999876655
No 7
>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=97.29 E-value=0.0008 Score=44.81 Aligned_cols=47 Identities=15% Similarity=0.092 Sum_probs=39.0
Q ss_pred EEEecCHHHHhhCCCCCCCEEEEEeccCCcEEEEeccCC-----CCCCCeEEE
Q psy3865 16 GKRRKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSDD-----TCPDEKIRM 63 (107)
Q Consensus 16 Giari~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai~~~~~-----d~~~~~Iri 63 (107)
..+.|+|+++++|||..||.|+|..++. +..+.+...+ .+..+.|.|
T Consensus 31 ~~v~i~p~dA~~lgI~dGd~V~v~s~~G-~i~~~a~v~~~~~~~~i~~g~v~~ 82 (112)
T cd02787 31 DVVFMNPDDIARLGLKAGDRVDLESAFG-DGQGRIVRGFRVVEYDIPRGCLAA 82 (112)
T ss_pred cEEEECHHHHHHhCCCCCCEEEEEecCC-CCeEEEEeccceeecCCCCCcEEE
Confidence 4589999999999999999999998775 4445565665 889999988
No 8
>cd02788 MopB_CT_NDH-1_NuoG2-N7 MopB_CT_NDH-1_NuoG2-N7: C-terminal region of the NuoG-like subunit (of the variant with a [4Fe-4S] cluster, N7) of the NADH-quinone oxidoreductase/NADH dehydrogenase-1 (NDH-1) found in various bacteria. The NDH-1 is the first energy-transducting complex in the respiratory chain and functions as a redox pump that uses the redox energy to translocate H+ ions across the membrane, resulting in a significant contribution to energy production. In Escherichia coli NDH-1, the largest subunit is encoded by the nuoG gene, and is part of the 14 distinct subunits constituting the functional enzyme. The NuoG subunit is made of two domains: the first contains three binding sites for FeS clusters (the fer2 domain), the second domain, is of unknown function or, as postulated, has lost an ancestral formate dehydrogenase activity that became redundant during the evolution of the complex I enzyme. Unique to this group, compared to the other prokaryotic and eukaryotic groups
Probab=97.28 E-value=0.0012 Score=43.27 Aligned_cols=49 Identities=18% Similarity=0.062 Sum_probs=41.5
Q ss_pred EEecCHHHHhhCCCCCCCEEEEEeccCCcEEEEeccCCCCCCCeEEEeHh
Q psy3865 17 KRRKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSDDTCPDEKIRMNRV 66 (107)
Q Consensus 17 iari~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai~~~~~d~~~~~Irid~~ 66 (107)
.+.|+|+++++||+..||.|.|+..+. +..+.+...+....+.+.|..-
T Consensus 30 ~v~inp~dA~~lGi~~Gd~V~v~s~~G-~i~~~v~v~~~v~~g~V~~p~g 78 (96)
T cd02788 30 YARLSPADAARLGLADGDLVEFSLGDG-TLTLPVQISKYLPAGVVGLPLG 78 (96)
T ss_pred EEEECHHHHHHcCCCCCCEEEEEECCe-EEEEEEEECCCCCCCEEEEecC
Confidence 589999999999999999999997664 4556677788899999988754
No 9
>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=97.23 E-value=0.0012 Score=43.62 Aligned_cols=49 Identities=14% Similarity=0.149 Sum_probs=40.7
Q ss_pred EEEecCHHHHhhCCCCCCCEEEEEeccCCcEEEEeccCCCCCCCeEEEeH
Q psy3865 16 GKRRKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSDDTCPDEKIRMNR 65 (107)
Q Consensus 16 Giari~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai~~~~~d~~~~~Irid~ 65 (107)
..+.|+|+++++|||..||.|+|+.... +..+.+...+.+..+.|.|..
T Consensus 35 ~~v~in~~dA~~lgi~~Gd~V~v~~~~G-~~~~~v~i~~~i~~g~v~~~~ 83 (116)
T cd02790 35 EYVEINPEDAKRLGIEDGEKVRVSSRRG-SVEVRARVTDRVPEGVVFMPF 83 (116)
T ss_pred cEEEECHHHHHHcCCCCCCEEEEEcCCE-EEEEEEEECCCcCCCEEEEec
Confidence 3589999999999999999999997664 445566777889999998864
No 10
>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=97.21 E-value=0.0015 Score=41.90 Aligned_cols=50 Identities=16% Similarity=0.138 Sum_probs=41.6
Q ss_pred EEEecCHHHHhhCCCCCCCEEEEEeccCCcEEEEeccCCCCCCCeEEEeHh
Q psy3865 16 GKRRKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSDDTCPDEKIRMNRV 66 (107)
Q Consensus 16 Giari~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai~~~~~d~~~~~Irid~~ 66 (107)
..++|+|+++++||+..||.|+|+.... +..+.+...+.+..+.|.|..-
T Consensus 23 ~~v~~~~~da~~lgl~~Gd~v~v~~~~g-~~~~~v~~~~~v~~g~v~~~~~ 72 (101)
T cd02775 23 PVVEINPEDAAALGIKDGDLVRVESRRG-SVVLRAKVTDGVPPGVVFLPHG 72 (101)
T ss_pred CEEEECHHHHHHcCCCCCCEEEEEcCCc-EEEEEEEECCCcCCCEEEeeCc
Confidence 4689999999999999999999997765 4555677777788888888764
No 11
>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=97.21 E-value=0.0014 Score=43.86 Aligned_cols=49 Identities=14% Similarity=0.121 Sum_probs=41.8
Q ss_pred EEecCHHHHhhCCCCCCCEEEEEeccCCcEEEEeccCCCCCCCeEEEeHh
Q psy3865 17 KRRKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSDDTCPDEKIRMNRV 66 (107)
Q Consensus 17 iari~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai~~~~~d~~~~~Irid~~ 66 (107)
.+.|+|+++++||+..||.|.|+.... +..+.+...+.+..+.|.|...
T Consensus 32 ~v~i~p~dA~~lgi~~Gd~V~v~~~~G-~v~~~v~~~~~v~~g~v~~~~g 80 (106)
T cd02789 32 YCEINPEDYKLLGKPEGDKVKVTSEFG-EVVVFAKENEGVPEGMVFIPMG 80 (106)
T ss_pred EEEECHHHHHHcCCCCCCEEEEEcCCE-EEEEEEEECCCCCCCEEEEecc
Confidence 689999999999999999999997664 4566777788899999998653
No 12
>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=97.20 E-value=0.0012 Score=44.50 Aligned_cols=48 Identities=13% Similarity=0.104 Sum_probs=40.9
Q ss_pred EEecCHHHHhhCCCCCCCEEEEEeccCCcEEEEeccCCCCCCCeEEEeH
Q psy3865 17 KRRKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSDDTCPDEKIRMNR 65 (107)
Q Consensus 17 iari~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai~~~~~d~~~~~Irid~ 65 (107)
.+.|+|+++++||+..||.|+|+-.+. +..+.+...+.+..+.|.|..
T Consensus 31 ~v~i~p~~A~~~gi~~Gd~V~v~s~~g-~i~~~a~~~~~v~~g~v~~~~ 78 (121)
T cd02794 31 EVWINPLDAAARGIKDGDRVLVFNDRG-KVIRPVKVTERIMPGVVALPQ 78 (121)
T ss_pred CEEECHHHHHHcCCCCCCEEEEEcCCc-eEEEEEEECCCccCCEEEecC
Confidence 368999999999999999999997665 566677788889999998864
No 13
>cd02777 MopB_CT_DMSOR-like The MopB_CT_DMSOR-like 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. Also included in this group is the pyrogallol-phloroglucinol transhydroxylase from Pelobacter acidigallici. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB hom
Probab=97.15 E-value=0.0014 Score=44.51 Aligned_cols=50 Identities=10% Similarity=-0.011 Sum_probs=41.5
Q ss_pred EEEecCHHHHhhCCCCCCCEEEEEeccCCcEEEEeccCCCCCCCeEEEeHh
Q psy3865 16 GKRRKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSDDTCPDEKIRMNRV 66 (107)
Q Consensus 16 Giari~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai~~~~~d~~~~~Irid~~ 66 (107)
..+.|+|+++++||+..||.|+|+..+. +..+.+...+.+..+.|.|..-
T Consensus 34 ~~v~i~p~dA~~lgi~~Gd~V~v~s~~g-~i~~~v~i~~~v~~g~v~~~~g 83 (127)
T cd02777 34 EPVWINPLDAAARGIKDGDIVRVFNDRG-AVLAGARVTDRIMPGVVALPEG 83 (127)
T ss_pred CeEEECHHHHHHcCCCCCCEEEEEcCCe-EEEEEEEECCCcCCCEEEeCcc
Confidence 3489999999999999999999997654 5556677777899999988753
No 14
>cd02785 MopB_CT_4 The MopB_CT_4 CD includes a group of related uncharacterized bacterial and archaeal 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=97.15 E-value=0.0019 Score=43.71 Aligned_cols=49 Identities=16% Similarity=0.205 Sum_probs=42.1
Q ss_pred EEecCHHHHhhCCCCCCCEEEEEeccCCcEEEEeccCCCCCCCeEEEeHh
Q psy3865 17 KRRKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSDDTCPDEKIRMNRV 66 (107)
Q Consensus 17 iari~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai~~~~~d~~~~~Irid~~ 66 (107)
.+.|+|++.++|||..||.|+|...+. +..+.+...+.+..+.|.|..-
T Consensus 33 ~v~i~p~dA~~~gi~~Gd~V~v~s~~G-~i~~~a~~~~~v~~g~v~~~~g 81 (124)
T cd02785 33 RVKINPIDAAARGIAHGDLVEVYNDRG-SVVCKAKVDDGIQPGVVTAEQG 81 (124)
T ss_pred eEEECHHHHHHcCCCCCCEEEEEeCCC-EEEEEEEECCCcCCCEEEeecc
Confidence 579999999999999999999997765 5666777888999999998754
No 15
>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=97.07 E-value=0.0023 Score=42.72 Aligned_cols=49 Identities=14% Similarity=0.087 Sum_probs=41.5
Q ss_pred EEEecCHHHHhhCCCCCCCEEEEEeccCCcEEEEeccCCCCCCCeEEEeH
Q psy3865 16 GKRRKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSDDTCPDEKIRMNR 65 (107)
Q Consensus 16 Giari~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai~~~~~d~~~~~Irid~ 65 (107)
..+.|+|+++++|||..||.|+|+..+. +..+.+...+.+..+.|.|..
T Consensus 35 ~~v~i~p~dA~~lgi~~Gd~V~v~s~~G-~~~~~v~v~~~i~~g~v~~~~ 83 (122)
T cd02792 35 MFVEISPELAAERGIKNGDMVWVSSPRG-KIKVKALVTDRVKPHEVGIPY 83 (122)
T ss_pred cEEEECHHHHHHcCCCCCCEEEEEcCCc-eEEEEEEECCCcCCCEEEEec
Confidence 3588999999999999999999997664 455667777889999999985
No 16
>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=97.07 E-value=0.0025 Score=42.18 Aligned_cols=49 Identities=16% Similarity=0.102 Sum_probs=40.7
Q ss_pred EEEecCHHHHhhCCCCCCCEEEEEeccCCcEEEEeccCCCCCCCeEEEeH
Q psy3865 16 GKRRKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSDDTCPDEKIRMNR 65 (107)
Q Consensus 16 Giari~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai~~~~~d~~~~~Irid~ 65 (107)
..+.|+|+++++|||..||.|+|+.... +..+.+...+++..+.|.|..
T Consensus 35 ~~v~inp~dA~~lgi~~Gd~V~v~~~~G-~~~~~v~~~~~i~~g~v~~~~ 83 (120)
T cd00508 35 PFVEIHPEDAARLGIKDGDLVRVSSRRG-SVVVRARVTDRVRPGTVFMPF 83 (120)
T ss_pred CEEEECHHHHHHcCCCCCCEEEEEeCCE-EEEEEEEECCCcCCCEEEEec
Confidence 4589999999999999999999997664 445566677788999999874
No 17
>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=97.07 E-value=0.0024 Score=43.28 Aligned_cols=49 Identities=12% Similarity=0.043 Sum_probs=41.5
Q ss_pred EEecCHHHHhhCCCCCCCEEEEEeccCCcEEEEeccCCCCCCCeEEEeHh
Q psy3865 17 KRRKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSDDTCPDEKIRMNRV 66 (107)
Q Consensus 17 iari~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai~~~~~d~~~~~Irid~~ 66 (107)
.+.|+|+++++|||..||.|+|..... +..+.+...+.+..+.|.|..-
T Consensus 34 ~v~inp~dA~~~gi~~Gd~V~v~s~~G-~~~~~v~v~~~i~~g~v~~~~g 82 (130)
T cd02781 34 VAEINPETAAKLGIADGDWVWVETPRG-RARQKARLTPGIRPGVVRAEHG 82 (130)
T ss_pred EEEECHHHHHHcCCCCCCEEEEECCCC-EEEEEEEECCCCCCCEEEEecc
Confidence 488999999999999999999997664 5566677788899999999753
No 18
>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=97.06 E-value=0.0025 Score=42.73 Aligned_cols=50 Identities=12% Similarity=0.070 Sum_probs=41.8
Q ss_pred EEEecCHHHHhhCCCCCCCEEEEEeccCCcEEEEeccCCCCCCCeEEEeHh
Q psy3865 16 GKRRKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSDDTCPDEKIRMNRV 66 (107)
Q Consensus 16 Giari~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai~~~~~d~~~~~Irid~~ 66 (107)
..+.|+|+++++||+..||.|+|+-.+. +..+.+...+.+..+.|.|...
T Consensus 30 ~~v~i~p~dA~~~gi~~Gd~V~v~s~~G-~i~~~v~v~~~v~~g~v~~~~g 79 (123)
T cd02778 30 NTLWINPETAARLGIKDGDRVEVSSARG-KVTGKARLTEGIRPDTVFMPHG 79 (123)
T ss_pred CeEEECHHHHHHcCCCCCCEEEEEeCCC-cEEEEEEEcCCcCCCEEEEecc
Confidence 3578999999999999999999997664 5566677788899999988853
No 19
>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=97.02 E-value=0.0024 Score=43.70 Aligned_cols=49 Identities=14% Similarity=0.104 Sum_probs=41.8
Q ss_pred EEecCHHHHhhCCCCCCCEEEEEeccCCcEEEEeccCCCCCCCeEEEeHh
Q psy3865 17 KRRKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSDDTCPDEKIRMNRV 66 (107)
Q Consensus 17 iari~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai~~~~~d~~~~~Irid~~ 66 (107)
.+.|+|+++++||+..||.|+|...+. +..+.+...+.+..+.|.|..-
T Consensus 34 ~v~i~p~dA~~~gi~~Gd~V~v~s~~G-~~~~~~~~~~~v~~g~v~~~~g 82 (129)
T cd02793 34 PIRINPADAAARGIADGDIVRVFNDRG-ACLAGAVVTDGIMPGVVQLPTG 82 (129)
T ss_pred EEEECHHHHHHcCCCCCCEEEEEcCCE-EEEEEEEECCCcCCCEEEEccc
Confidence 489999999999999999999997764 5566677788899999998754
No 20
>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=96.91 E-value=0.0032 Score=42.00 Aligned_cols=49 Identities=20% Similarity=0.158 Sum_probs=40.6
Q ss_pred EEEecCHHHHhhCCCCCCCEEEEEeccCCcEEEEeccCCCCCCCeEEEeH
Q psy3865 16 GKRRKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSDDTCPDEKIRMNR 65 (107)
Q Consensus 16 Giari~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai~~~~~d~~~~~Irid~ 65 (107)
..++|+|+++++||+..||.|.|+..+. +..+.+...+.+..+.|.|..
T Consensus 35 ~~v~in~~dA~~lgi~~Gd~V~v~~~~G-~~~~~v~~~~~i~~g~v~~~~ 83 (122)
T cd02791 35 PYVEIHPEDAARLGLKEGDLVRVTSRRG-EVVLRVRVTDRVRPGEVFVPM 83 (122)
T ss_pred CEEEECHHHHHHcCCCCCCEEEEEcCCE-EEEEEEEECCCcCCCeEEEec
Confidence 4589999999999999999999997664 445566677788999999864
No 21
>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=96.90 E-value=0.0039 Score=41.76 Aligned_cols=49 Identities=12% Similarity=0.052 Sum_probs=40.3
Q ss_pred EEecCHHHHhhCCCCCCCEEEEEeccCCcEEEEeccCCCCCCCeEEEeHh
Q psy3865 17 KRRKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSDDTCPDEKIRMNRV 66 (107)
Q Consensus 17 iari~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai~~~~~d~~~~~Irid~~ 66 (107)
.+.|+|+++++|||..||.|+|...+. +..+.+...+.+..+.|.|...
T Consensus 34 ~v~in~~dA~~lgi~~Gd~V~v~s~~G-~i~~~~~~~~~i~~g~v~~p~g 82 (115)
T cd02779 34 YIEVNPEDAKREGLKNGDLVEVYNDYG-STTAMAYVTNTVKPGQTFMLMA 82 (115)
T ss_pred EEEECHHHHHHcCCCCCCEEEEEeCCE-EEEEEEEECCCcCCCeEEEEcc
Confidence 478999999999999999999997664 4455666777889999988653
No 22
>cd02782 MopB_CT_1 The MopB_CT_1 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=96.87 E-value=0.0041 Score=42.20 Aligned_cols=49 Identities=16% Similarity=0.097 Sum_probs=41.1
Q ss_pred EEecCHHHHhhCCCCCCCEEEEEeccCCcEEEEeccCCCCCCCeEEEeHh
Q psy3865 17 KRRKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSDDTCPDEKIRMNRV 66 (107)
Q Consensus 17 iari~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai~~~~~d~~~~~Irid~~ 66 (107)
.+.|+|+++++||+..||.|.|+..+. +..+.+...+.+..+.|.|...
T Consensus 34 ~v~i~p~dA~~~gi~~Gd~V~v~s~~g-~~~~~~~~~~~v~~g~v~~~~g 82 (129)
T cd02782 34 TLRIHPDDAAALGLADGDKVRVTSAAG-SVEAEVEVTDDMMPGVVSLPHG 82 (129)
T ss_pred eEEECHHHHHHcCCCCCCEEEEEcCCC-eEEEEEEECCCcCCCeEEeecC
Confidence 488999999999999999999997664 4556677778899999998754
No 23
>cd02776 MopB_CT_Nitrate-R-NarG-like Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate to nitrite and forms part of a redox loop generating a proton-motive force. Found in prokaryotes and some archaea, NarGHI usually functions as a heterotrimer. The alpha chain contains the molybdenum cofactor-containing Mo-bisMGD catalytic subunit. This CD (MopB_CT_Nitrate-R-NarG-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=96.84 E-value=0.0044 Score=43.60 Aligned_cols=50 Identities=14% Similarity=0.037 Sum_probs=41.7
Q ss_pred EEecCHHHHhhCCCCCCCEEEEEeccCCcEEEEeccCCCCCCCeEEEeHhh
Q psy3865 17 KRRKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSDDTCPDEKIRMNRVM 67 (107)
Q Consensus 17 iari~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai~~~~~d~~~~~Irid~~~ 67 (107)
.+.|+|++.++|||..||.|+|.-.+. +..+.+...+.+..+.|.|..-.
T Consensus 32 ~v~inp~dA~~lgI~dGd~V~v~~~~G-~v~~~a~v~~~i~~g~v~~~~g~ 81 (141)
T cd02776 32 VVWMNPKDAAELGIKDNDWVEVFNDNG-VVVARAKVSPRIPRGTVFMYHAQ 81 (141)
T ss_pred EEEECHHHHHHcCCCCCCEEEEEeCCe-EEEEEEEECCCcCCCeEEEeccc
Confidence 488999999999999999999997654 55566777888999999986543
No 24
>cd02784 MopB_CT_PHLH The MopB_CT_PHLH CD includes a group of related uncharacterized putative hydrogenase-like homologs (PHLH) of molybdopterin binding proteins. This CD is of the PHLH region homologous to the conserved molybdopterin-binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=96.71 E-value=0.0057 Score=43.06 Aligned_cols=48 Identities=17% Similarity=0.163 Sum_probs=40.8
Q ss_pred EEecCHHHHhhCCCCCCCEEEEEeccCCcEEEEeccCCCCCCCeEEEeH
Q psy3865 17 KRRKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSDDTCPDEKIRMNR 65 (107)
Q Consensus 17 iari~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai~~~~~d~~~~~Irid~ 65 (107)
.+.|+|++.++|||..||.|+|...+. +..+.+...+.+.++.|.|..
T Consensus 39 ~v~InP~dA~~lGI~dGD~V~V~s~~G-~i~~~a~vt~~i~pgvV~i~~ 86 (137)
T cd02784 39 AALVSPRTAEALGLLQGDVVRIRRGGR-TIELPVWIQPGHAEGVVLLAL 86 (137)
T ss_pred eEEECHHHHHHcCCCCCCEEEEEeCCe-EEEEEEEECCCcCCCEEEEec
Confidence 488999999999999999999997665 556677788889999998854
No 25
>cd02780 MopB_CT_Tetrathionate_Arsenate-R This CD contains the molybdopterin_binding C-terminal (MopB_CT) region of tetrathionate reductase, subunit A, (TtrA); respiratory arsenate As(V) reductase, catalytic subunit (ArrA); and other related proteins.
Probab=96.68 E-value=0.0076 Score=41.84 Aligned_cols=50 Identities=10% Similarity=0.032 Sum_probs=41.2
Q ss_pred EEEecCHHHHhhCCCCCCCEEEEEeccCCcEEEEeccCCCCCCCeEEEeHh
Q psy3865 16 GKRRKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSDDTCPDEKIRMNRV 66 (107)
Q Consensus 16 Giari~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai~~~~~d~~~~~Irid~~ 66 (107)
..+.|+|++.++|||..||.|+|+-.+. +..+.+...+.+..+.|.|...
T Consensus 30 ~~v~inp~dA~~lgI~~Gd~V~v~s~~G-~i~~~v~i~~~i~~g~V~~p~g 79 (143)
T cd02780 30 NPVWINPEDAAKLGIKTGDRVRVVTPGG-SVVGKAKVTEGVRPGVVAIEHG 79 (143)
T ss_pred CEEEECHHHHHHcCCCCCCEEEEEeCCc-eEEEEEEECCCcCCCEEEEecc
Confidence 3589999999999999999999997665 4455666778899999988654
No 26
>cd02783 MopB_CT_2 The MopB_CT_2 CD includes a group of related uncharacterized bacterial and archaeal 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=96.64 E-value=0.007 Score=43.03 Aligned_cols=46 Identities=13% Similarity=0.030 Sum_probs=39.7
Q ss_pred EEecCHHHHhhCCCCCCCEEEEEeccCCcEEEEeccCCCCCCCeEEE
Q psy3865 17 KRRKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSDDTCPDEKIRM 63 (107)
Q Consensus 17 iari~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai~~~~~d~~~~~Iri 63 (107)
.+.|+|++.++|||..||.|+|+-.+. +..+.+...+.+..+.|.|
T Consensus 33 ~v~inp~dA~~~GI~dGd~V~v~s~~G-~~~~~a~v~~~i~~g~v~~ 78 (156)
T cd02783 33 YLYMHPKTAKELGIKDGDWVWVESVNG-RVKGQARFTETVEPGTVWT 78 (156)
T ss_pred EEEECHHHHHHcCCCCCCEEEEEcCCe-eEEEEEEECCCcCCCeEEE
Confidence 578999999999999999999997664 5566777788899999987
No 27
>COG1153 FwdD Formylmethanofuran dehydrogenase subunit D [Energy production and conversion]
Probab=96.58 E-value=0.0092 Score=41.76 Aligned_cols=66 Identities=14% Similarity=0.079 Sum_probs=51.3
Q ss_pred CeEEEeEEEecCHHHHhhCCCCCCCEEEEEeccCCcEEEEeccCCCCCCCeEEEeHhhhhcccccCC
Q psy3865 10 DTVLLRGKRRKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSDDTCPDEKIRMNRVMRNNLRVRLS 76 (107)
Q Consensus 10 d~~~~rGiari~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai~~~~~d~~~~~Irid~~~R~N~~v~ig 76 (107)
+++-.-.+..|||++|++||+..||.|.++-+-. +.|..+-.++...++.|.|..-.=.|.=+..+
T Consensus 25 ~Y~~a~a~~~inp~D~~~Lgv~EGD~VkVkse~G-eVVV~Ak~~~~~~pG~vfiPmgpWaN~vi~P~ 90 (128)
T COG1153 25 EYFNACAVCEINPEDMKQLGVSEGDKVKVKSEFG-EVVVKAKEADGVQPGMVFIPMGPWANVVIDPD 90 (128)
T ss_pred hhhhheeEEEECHHHHHHhCCCcCCeEEEEecCc-cEEEEEeeCCCCCCCeEEecCCcccceeeCCC
Confidence 3444567889999999999999999999996554 66666766666667999998877777655543
No 28
>PRK05449 aspartate alpha-decarboxylase; Provisional
Probab=95.90 E-value=0.06 Score=37.82 Aligned_cols=69 Identities=17% Similarity=0.217 Sum_probs=55.3
Q ss_pred eEEEecCHHHHhhCCCCCCCEEEEE----eccCCcEEEEeccCCCCCCCeEEEeHhhhhcccccCCCeEEEEeCCCCCC
Q psy3865 15 RGKRRKESAKMDELNLFRGDTVLLR----GKRRKESVCIVLSDDTCPDEKIRMNRVMRNNLRVRLSDVVSLVPCPGIVY 89 (107)
Q Consensus 15 rGiari~~~~m~~Lgl~~GD~V~I~----Gkr~~~tvai~~~~~d~~~~~Irid~~~R~N~~v~igD~V~V~~~~~~~~ 89 (107)
.|..-||++-|+.-|+.+++-|.|- |.|. +|+++.. ..+.+.|.++|..=+ -+..||.|.|-.......
T Consensus 23 ~GSitID~~Ll~aagi~p~E~V~V~Nv~NG~Rf-~TYvI~g---~~GSg~I~lNGAAAr--~~~~GD~vII~ay~~~~~ 95 (126)
T PRK05449 23 EGSITIDEDLLDAAGILENEKVQIVNVNNGARF-ETYVIAG---ERGSGVICLNGAAAR--LVQVGDLVIIAAYAQMDE 95 (126)
T ss_pred ceeEEECHHHHHhcCCCCCCEEEEEECCCCcEE-EEEEEEc---CCCCCEEEeCCHHHh--cCCCCCEEEEEECccCCH
Confidence 3667789999999999999999998 6676 8888865 457799999997544 267899999987654433
No 29
>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=95.76 E-value=0.08 Score=36.45 Aligned_cols=68 Identities=16% Similarity=0.128 Sum_probs=54.9
Q ss_pred eEEEecCHHHHhhCCCCCCCEEEEE----eccCCcEEEEeccCCCCCCCeEEEeHhhhhcccccCCCeEEEEeCCCCC
Q psy3865 15 RGKRRKESAKMDELNLFRGDTVLLR----GKRRKESVCIVLSDDTCPDEKIRMNRVMRNNLRVRLSDVVSLVPCPGIV 88 (107)
Q Consensus 15 rGiari~~~~m~~Lgl~~GD~V~I~----Gkr~~~tvai~~~~~d~~~~~Irid~~~R~N~~v~igD~V~V~~~~~~~ 88 (107)
.|.--||++-|+.-|+.+++-|.|- |.|. +|+++.. ..+.+.|.++|..=+ -+..||.|.|-......
T Consensus 22 eGSitID~~Ll~aagi~~~E~V~I~Nv~NG~Rf-~TYvI~g---~~gSg~I~lNGAAAr--~~~~GD~vII~sy~~~~ 93 (111)
T cd06919 22 EGSITIDEDLLEAAGILPYEKVLVVNVNNGARF-ETYVIPG---ERGSGVICLNGAAAR--LGQPGDRVIIMAYALMD 93 (111)
T ss_pred ceeEEECHHHHHhcCCCCCCEEEEEECCCCcEE-EEEEEEc---CCCCCEEEeCCHHHh--cCCCCCEEEEEECccCC
Confidence 3667789999999999999999998 6666 8888765 457899999997544 36789999998765444
No 30
>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=95.51 E-value=0.11 Score=36.52 Aligned_cols=67 Identities=18% Similarity=0.229 Sum_probs=54.5
Q ss_pred eEEEecCHHHHhhCCCCCCCEEEEE----eccCCcEEEEeccCCCCCCCeEEEeHhhhhcccccCCCeEEEEeCCCC
Q psy3865 15 RGKRRKESAKMDELNLFRGDTVLLR----GKRRKESVCIVLSDDTCPDEKIRMNRVMRNNLRVRLSDVVSLVPCPGI 87 (107)
Q Consensus 15 rGiari~~~~m~~Lgl~~GD~V~I~----Gkr~~~tvai~~~~~d~~~~~Irid~~~R~N~~v~igD~V~V~~~~~~ 87 (107)
.|..-||++-|+.-|+.+++-|.|- |.|. +|+++.. ..+.+.|.++|..=+ -+..||.|.|-.....
T Consensus 23 ~GSItID~~Lm~aagi~p~E~V~V~Nv~NG~Rf-~TYvI~G---~~GSg~I~lNGAAAr--l~~~GD~VII~sy~~~ 93 (126)
T TIGR00223 23 EGSITIDEDLLDAAGILENEKVDIVNVNNGKRF-STYAIAG---KRGSRIICVNGAAAR--CVSVGDIVIIASYVTM 93 (126)
T ss_pred ceeEEECHHHHHhcCCCCCCEEEEEECCCCcEE-EEEEEEc---CCCCCEEEeCCHHHh--cCCCCCEEEEEECCcC
Confidence 3677889999999999999999998 6666 8888865 557899999997644 2678999999876544
No 31
>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=95.29 E-value=0.058 Score=39.73 Aligned_cols=83 Identities=18% Similarity=0.202 Sum_probs=50.1
Q ss_pred EecCHHHHh---hCCCCCCCEEEEEec-cCCcEEEEeccCCCCCCCeEEEeHhhhhcccccCCCeEEEEeCCCCCCccEE
Q psy3865 18 RRKESAKMD---ELNLFRGDTVLLRGK-RRKESVCIVLSDDTCPDEKIRMNRVMRNNLRVRLSDVVSLVPCPGIVYGKRI 93 (107)
Q Consensus 18 ari~~~~m~---~Lgl~~GD~V~I~Gk-r~~~tvai~~~~~d~~~~~Irid~~~R~N~~v~igD~V~V~~~~~~~~a~~V 93 (107)
+.+.|.+++ ++.+..-=+-+|+.. ..+.|.|-+..- +-+.|.|-|..-+.+||++.-||.|.|+-+ ..|.|+.|
T Consensus 28 iiLP~s~L~~L~~~~~~~P~~F~i~n~~~~~~th~GVlEF-sA~eG~i~lP~wmm~~L~l~~g~~V~v~~~-~LPkgt~v 105 (176)
T PF03152_consen 28 IILPPSALDELSRLNIPYPMLFEISNPDNGKRTHCGVLEF-SAEEGTIYLPPWMMQNLGLQEGDIVRVEYV-SLPKGTFV 105 (176)
T ss_dssp EEE-HHHHHHHHHTT--SS-EEEEEETTTTEEEEEEEEEE---CTTEEEE-CHHHHHHT--TTEEEEEEEE-E----SEE
T ss_pred EEcCHHHHHHHHhccCCCCEEEEEecCCCCcEEEEEEEEe-EcCCCeEEeCccHHhhcCCCCCCEEEEEEe-ECCCCCEE
Confidence 445665555 344444445667654 233456555321 335699999999999999999999999975 99999999
Q ss_pred EEccCCccc
Q psy3865 94 HVLPIDDSV 102 (107)
Q Consensus 94 ~l~P~~dti 102 (107)
.|.|-+..+
T Consensus 106 kLqP~~~~F 114 (176)
T PF03152_consen 106 KLQPQSSDF 114 (176)
T ss_dssp EEEESCHHH
T ss_pred EEeECCCcc
Confidence 999987654
No 32
>KOG1816|consensus
Probab=95.23 E-value=0.038 Score=43.83 Aligned_cols=84 Identities=18% Similarity=0.185 Sum_probs=63.5
Q ss_pred eEEEecCHHHHhhCCCCCCCEEEEEecc-CCcEEEEeccC--C--CCCCCeEEEeHhhhhcccccCCCeEEEEe------
Q psy3865 15 RGKRRKESAKMDELNLFRGDTVLLRGKR-RKESVCIVLSD--D--TCPDEKIRMNRVMRNNLRVRLSDVVSLVP------ 83 (107)
Q Consensus 15 rGiari~~~~m~~Lgl~~GD~V~I~Gkr-~~~tvai~~~~--~--d~~~~~Irid~~~R~N~~v~igD~V~V~~------ 83 (107)
-|.+++.-=-|++|.+.+||+|.|+--. -+-|.+.+.|+ + |+......+....|+-+.+..||.+.|.=
T Consensus 83 EG~vyLP~WMmq~L~le~gdlv~i~~v~lpkgtyvKLqP~s~dFLDItNpKAvLE~~LRn~acLT~gDvi~i~Yn~k~y~ 162 (308)
T KOG1816|consen 83 EGRVYLPYWMMQNLLLEEGDLVRIRSVTLPKGTYVKLQPHSVDFLDITNPKAVLENALRNYACLTTGDVILINYNEKTYE 162 (308)
T ss_pred CceEEeehHhhhhccCCCCCeEEEEEeeccccceeeeccCCCCccccCChHHHHHHHHhhccccccCCEEEEecCCeEEE
Confidence 3778888888999999999999999521 11256666555 2 77888888999999999999999997642
Q ss_pred --CCCCCCccEEEEccC
Q psy3865 84 --CPGIVYGKRIHVLPI 98 (107)
Q Consensus 84 --~~~~~~a~~V~l~P~ 98 (107)
+.+++||+.|.|.-.
T Consensus 163 i~V~e~kPa~aVsIiEt 179 (308)
T KOG1816|consen 163 LKVVETKPANAVSIIET 179 (308)
T ss_pred EEEEEecCCceeEEEEc
Confidence 225677777776543
No 33
>TIGR02693 arsenite_ox_L arsenite oxidase, large subunit. This model represents the large subunit of an arsenite oxidase complex. The small subunit is a Rieske protein. Homologs to both large and small subunits that score in the gray zone between the set trusted and noise bit score cutoffs for the respective models are found in Aeropyrum pernix K1 and in Sulfolobus tokodaii str. 7. This enzyme acts in energy metabolim by arsenite oxidation, rather than detoxification by reduction of arsenate to arsenite prior to export.
Probab=94.96 E-value=0.068 Score=47.06 Aligned_cols=48 Identities=15% Similarity=0.110 Sum_probs=41.5
Q ss_pred EEecCHHHHhhCCCCCCCEEEEEeccCCcEEEEeccCCCCCCCeEEEeH
Q psy3865 17 KRRKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSDDTCPDEKIRMNR 65 (107)
Q Consensus 17 iari~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai~~~~~d~~~~~Irid~ 65 (107)
.+.|+|+++++|||..||.|+|.-.+. +..+.+...+.+.++.|.|..
T Consensus 726 ~v~InP~DA~~lGI~dGD~V~V~n~~G-~v~~~a~vt~~i~pG~V~~~~ 773 (806)
T TIGR02693 726 YIEVNPEDAKRLGLKSGDLVEVYNDEG-NTTAMAYPTDAVKPGTTFMLF 773 (806)
T ss_pred EEEECHHHHHHcCCCCCCEEEEEcCCc-eEEEEEEECCCCCCCcEEEEe
Confidence 478999999999999999999997765 566677778889999999875
No 34
>PRK15102 trimethylamine N-oxide reductase I catalytic subunit; Provisional
Probab=94.95 E-value=0.056 Score=47.38 Aligned_cols=48 Identities=17% Similarity=0.185 Sum_probs=41.4
Q ss_pred EecCHHHHhhCCCCCCCEEEEEeccCCcEEEEeccCCCCCCCeEEEeHh
Q psy3865 18 RRKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSDDTCPDEKIRMNRV 66 (107)
Q Consensus 18 ari~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai~~~~~d~~~~~Irid~~ 66 (107)
+.|+|++.+++||..||.|+|...+. +..+.+...+.+.++.|.|..-
T Consensus 712 v~InP~DA~~~GI~dGD~V~V~n~rG-~~~~~a~vt~~i~pGvV~~~~G 759 (825)
T PRK15102 712 VYINPQDAKARGIKDGDVVRVFNDRG-QVLAGAVVSDRYPPGVIRIHEG 759 (825)
T ss_pred EEECHHHHHHcCCCCCCEEEEECCCe-EEEEeEEECCCcCCCeEEecCc
Confidence 78999999999999999999997765 5566677778889999998876
No 35
>COG0853 PanD Aspartate 1-decarboxylase [Coenzyme metabolism]
Probab=94.73 E-value=0.28 Score=34.41 Aligned_cols=66 Identities=17% Similarity=0.228 Sum_probs=54.0
Q ss_pred EEEecCHHHHhhCCCCCCCEEEEE----eccCCcEEEEeccCCCCCCCeEEEeHhhhhcccccCCCeEEEEeCCCC
Q psy3865 16 GKRRKESAKMDELNLFRGDTVLLR----GKRRKESVCIVLSDDTCPDEKIRMNRVMRNNLRVRLSDVVSLVPCPGI 87 (107)
Q Consensus 16 Giari~~~~m~~Lgl~~GD~V~I~----Gkr~~~tvai~~~~~d~~~~~Irid~~~R~N~~v~igD~V~V~~~~~~ 87 (107)
|..-||++-|+.-|+.++.-|.|- |.|. +|.+++. ..+.+.|.++|..-+= +..||.|.|-.....
T Consensus 23 GSitID~dlldaagile~EkV~I~N~nNGaRf-~TYvI~g---~rGSg~I~lNGAAArl--~~~GD~VII~sy~~~ 92 (126)
T COG0853 23 GSITIDEDLLDAAGILENEKVDIVNVNNGARF-STYVIAG---ERGSGVICLNGAAARL--VQVGDLVIIMSYAQM 92 (126)
T ss_pred EeEEECHHHHhhcCCCCCceEEEEECCCCcEE-EEEEEEc---cCCCcEEEechHHHhh--CCCCCEEEEEEcccC
Confidence 677899999999999999999998 5665 7888865 5678999999976543 678999999765444
No 36
>TIGR02166 dmsA_ynfE anaerobic dimethyl sulfoxide reductase, A subunit, DmsA/YnfE family. Members of this family include known and probable dimethyl sulfoxide reductase (DMSO reductase) A chains. In E. coli, dmsA encodes the canonical anaerobic DMSO reductase A chain. The paralog ynfE, as part of ynfFGH expressed from a multicopy plasmid, could complement a dmsABC deletion, suggesting a similar function and some overlap in specificity, although YnfE could not substitute for DmsA in a mixed complex.
Probab=94.66 E-value=0.08 Score=45.94 Aligned_cols=48 Identities=10% Similarity=0.045 Sum_probs=40.9
Q ss_pred EEecCHHHHhhCCCCCCCEEEEEeccCCcEEEEeccCCCCCCCeEEEeH
Q psy3865 17 KRRKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSDDTCPDEKIRMNR 65 (107)
Q Consensus 17 iari~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai~~~~~d~~~~~Irid~ 65 (107)
-+.|+|++.++|||..||.|+|...+. +..+.+...+.+.++.|.|..
T Consensus 706 ~v~inp~dA~~lGI~dGD~V~V~s~~G-~~~~~a~vt~~i~pg~V~~~~ 753 (797)
T TIGR02166 706 ELWINPIDAQKRGITNGDMVRIFNSRG-EVEIPAKVTPRIMPGVVALGQ 753 (797)
T ss_pred cEEECHHHHHHhCCCcCCEEEEEeCCe-EEEEEEEECCCCCCCeEEecC
Confidence 378999999999999999999998765 566677778889999998854
No 37
>TIGR02164 torA trimethylamine-N-oxide reductase TorA. This very narrowly defined family represents TorA, part of a family of related molybdoenzymes that include biotin sulfoxide reductases, dimethyl sulfoxide reductases, and at least two different subfamilies of trimethylamine-N-oxide reductases. A single enzyme from the larger family may have more than one activity. TorA typically is located in the periplasm, has a Tat (twin-arginine translocation)-dependent signal sequence, and is encoded in a torCAD operon.
Probab=94.59 E-value=0.084 Score=46.29 Aligned_cols=48 Identities=15% Similarity=0.176 Sum_probs=40.3
Q ss_pred EecCHHHHhhCCCCCCCEEEEEeccCCcEEEEeccCCCCCCCeEEEeHh
Q psy3865 18 RRKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSDDTCPDEKIRMNRV 66 (107)
Q Consensus 18 ari~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai~~~~~d~~~~~Irid~~ 66 (107)
+.|+|++.+++||..||.|+|...+. +..+.+...+.+.++.|.|..-
T Consensus 709 v~InP~dA~~~GI~dGD~V~V~n~~G-~v~~~A~vt~~i~pG~V~~~~G 756 (822)
T TIGR02164 709 VYINPVDAKARGIKDGDLVRVFNDRG-QLLAGAVVSDNFPKGVVRIHEG 756 (822)
T ss_pred EEECHHHHHHcCCCCCCEEEEECCCc-EEEEEEEECCCcCCCeEEecCc
Confidence 78999999999999999999997664 5556676777888898887765
No 38
>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=94.56 E-value=0.17 Score=35.14 Aligned_cols=64 Identities=19% Similarity=0.204 Sum_probs=45.5
Q ss_pred EEEecCHHHHhhCCCCCCCEEEEE----eccCCcEEEEeccCCCCCCCeEEEeHhhhhcccccCCCeEEEEeCC
Q psy3865 16 GKRRKESAKMDELNLFRGDTVLLR----GKRRKESVCIVLSDDTCPDEKIRMNRVMRNNLRVRLSDVVSLVPCP 85 (107)
Q Consensus 16 Giari~~~~m~~Lgl~~GD~V~I~----Gkr~~~tvai~~~~~d~~~~~Irid~~~R~N~~v~igD~V~V~~~~ 85 (107)
|..-||++-|+.-|+.+++.|.|- |.|. +|+++.. ..+.+.|.++|..=+ .+..||.|.|-...
T Consensus 24 GSitID~~Ll~aagi~p~E~V~V~Nv~nG~Rf-~TYvI~g---~~GSg~I~lNGaAAr--l~~~GD~vII~sy~ 91 (116)
T PF02261_consen 24 GSITIDEDLLDAAGILPYEQVQVVNVNNGERF-ETYVIPG---ERGSGVICLNGAAAR--LVQVGDRVIIMSYA 91 (116)
T ss_dssp SCEEEEHHHHHHCT--TTBEEEEEETTT--EE-EEEEEEE---STTTT-EEEEGGGGG--CS-TT-EEEEEEEE
T ss_pred eeeEECHHHHHHcCCCcCCEEEEEECCCCcEE-EEEEEEc---cCCCcEEEECCHHHh--ccCCCCEEEEEEcc
Confidence 445679999999999999999999 6666 8888876 347799999997644 36789999987543
No 39
>TIGR03479 DMSO_red_II_alp DMSO reductase family type II enzyme, molybdopterin subunit. This model represents the molybdopterin subunit, typically called the alpha subunit, of various proteins that also contain an iron-sulfur subunit and a heme b subunit. The group includes two distinct but very closely related periplasmic proteins of anaerobic respiration, selenate reductase and chlorate reductase. Other members of this family include dimethyl sulphide dehydrogenase, ethylbenzene dehydrogenase, and an archaeal respiratory nitrate reductase. This alpha subunit has a twin-arginine translocation (TAT) signal for Sec-independent translocation across the plasma membrane.
Probab=94.51 E-value=0.099 Score=46.52 Aligned_cols=50 Identities=12% Similarity=-0.063 Sum_probs=42.4
Q ss_pred EEecCHHHHhhCCCCCCCEEEEEeccCCcEEEEeccCCCCCCCeEEEeHhh
Q psy3865 17 KRRKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSDDTCPDEKIRMNRVM 67 (107)
Q Consensus 17 iari~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai~~~~~d~~~~~Irid~~~ 67 (107)
.+.|+|++.+++||..||.|+|...+. +..+.+...+.+.++.|.|..--
T Consensus 811 ~v~inp~DA~~~GI~dGD~V~V~n~~G-~~~~~a~vt~~i~pG~v~~~~gw 860 (912)
T TIGR03479 811 VVYINPKDAAEKGIKDGDQVRIFNDLA-EFEAMAKIYPGLQPGTCIMYHGW 860 (912)
T ss_pred EEEECHHHHHHcCCCcCCEEEEEeCCc-EEEEEEEEcCCCCCCeEEEeecc
Confidence 488999999999999999999997765 56667777788999999987643
No 40
>COG0243 BisC Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]
Probab=94.42 E-value=0.088 Score=45.65 Aligned_cols=48 Identities=15% Similarity=0.127 Sum_probs=36.6
Q ss_pred eEEEecCHHHHhhCCCCCCCEEEEEeccCCcEEEEeccCCCCCCCeEEE
Q psy3865 15 RGKRRKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSDDTCPDEKIRM 63 (107)
Q Consensus 15 rGiari~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai~~~~~d~~~~~Iri 63 (107)
+..+.|+|++.++|||..||.|.|...+. +..+.+...+.+.++.+++
T Consensus 670 ~~~v~inp~DA~~~GI~~GD~V~V~~~rG-~v~~~a~vt~~~~~gv~~i 717 (765)
T COG0243 670 RPFVWINPEDAAKLGIKDGDLVRVENRRG-EVEARAKVTERIRPGVVAI 717 (765)
T ss_pred CceEEECHHHHHHcCCCcCCEEEEEcCCc-eEEEEEEECCCccCCceee
Confidence 45788999999999999999999998776 6666666666444444333
No 41
>PRK14990 anaerobic dimethyl sulfoxide reductase subunit A; Provisional
Probab=94.18 E-value=0.11 Score=45.40 Aligned_cols=48 Identities=10% Similarity=0.039 Sum_probs=41.0
Q ss_pred EEecCHHHHhhCCCCCCCEEEEEeccCCcEEEEeccCCCCCCCeEEEeH
Q psy3865 17 KRRKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSDDTCPDEKIRMNR 65 (107)
Q Consensus 17 iari~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai~~~~~d~~~~~Irid~ 65 (107)
-+.|+|++.+++||..||.|+|...+. +..+.+...+.+.++.|.|..
T Consensus 723 ~v~inp~dA~~~GI~dGD~V~V~n~~G-~v~~~a~vt~~i~pg~V~~~~ 770 (814)
T PRK14990 723 EMWINPLDAQKRGINNGDKVRIFNDRG-EVHIEAKVTPRMMPGVVALGE 770 (814)
T ss_pred cEEEcHHHHHHcCCCCCCEEEEEcCCc-eEEEEEEECCCcCCCeEEccC
Confidence 378999999999999999999997765 666677778889999998844
No 42
>TIGR00509 bisC_fam molybdopterin guanine dinucleotide-containing S/N-oxide reductases. This enzyme family shares sequence similarity and a requirement for a molydenum cofactor as the only prosthetic group. The form of the cofactor is a single molybdenum atom coordinated by two molybdopterin guanine dinucleotide molecules. Members of the family include biotin sulfoxide reductase, dimethylsulfoxide reductase, and trimethylamine-N-oxide reductase, although a single member may show all those activities and related activities; it may not be possible to resolve the primary function for members of this family by sequence comparison alone. A number of similar molybdoproteins in which the N-terminal region contains a CXXXC motif and may bind an iron-sulfur cluster are excluded from this set, including formate dehydrogenases and nitrate reductases. Also excluded is the A chain of a heteromeric, anaerobic DMSO reductase, which also contains the CXXXC motif.
Probab=94.08 E-value=0.13 Score=44.74 Aligned_cols=49 Identities=10% Similarity=0.082 Sum_probs=40.1
Q ss_pred EEecCHHHHhhCCCCCCCEEEEEeccCCcEEEEeccCCCCCCCeEEEeHh
Q psy3865 17 KRRKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSDDTCPDEKIRMNRV 66 (107)
Q Consensus 17 iari~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai~~~~~d~~~~~Irid~~ 66 (107)
.+.|+|+++++|||..||.|+|...+. +..+.+...+.+..+.|.|..-
T Consensus 658 ~v~Inp~dA~~~GI~dGD~V~V~s~~G-~~~~~a~vt~~i~pg~V~~~~g 706 (770)
T TIGR00509 658 PVMIHPDDAAARGIADGDIVRVFNARG-QCLAGAVVTDGIRKGVVQIHEG 706 (770)
T ss_pred eEEECHHHHHHcCCCCCCEEEEECCCc-eEEEEEEEcCCcCCCeEEecCc
Confidence 478999999999999999999997665 5555666677888888888554
No 43
>TIGR01591 Fdh-alpha formate dehydrogenase, alpha subunit, archaeal-type. This model is well-defined, with only a single fragmentary sequence falling between trusted and noise. The alpha subunit of a version of nitrate reductase is closely related.
Probab=93.85 E-value=0.17 Score=42.91 Aligned_cols=48 Identities=17% Similarity=0.183 Sum_probs=40.3
Q ss_pred EEecCHHHHhhCCCCCCCEEEEEeccCCcEEEEeccCCCCCCCeEEEeH
Q psy3865 17 KRRKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSDDTCPDEKIRMNR 65 (107)
Q Consensus 17 iari~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai~~~~~d~~~~~Irid~ 65 (107)
.++|||++++++||..||.|+|+..+. +..+.+...+...++.|.|..
T Consensus 593 ~v~i~p~dA~~~gl~~Gd~V~v~~~~g-~i~~~~~~~~~~~~g~v~~~~ 640 (671)
T TIGR01591 593 YVEINTEDAKKLGIKDGDLVKVKSRRG-EITLRAKVSDRVNKGAIYITM 640 (671)
T ss_pred EEEECHHHHHHcCCCCCCEEEEEeCCE-EEEEEEEECCCcCCCEEEEec
Confidence 589999999999999999999997664 555566777788889998865
No 44
>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily. This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.
Probab=93.24 E-value=0.11 Score=45.09 Aligned_cols=40 Identities=25% Similarity=0.254 Sum_probs=34.9
Q ss_pred CcccCcccCCeEEEe--------------------EEEecCHHHHhhCCCCCCCEEEEEe
Q psy3865 1 MDELNLFRGDTVLLR--------------------GKRRKESAKMDELNLFRGDTVLLRG 40 (107)
Q Consensus 1 ~~~~~~~~~d~~~~r--------------------Giari~~~~m~~Lgl~~GD~V~I~G 40 (107)
|++|+++.||+|.++ |++++|.....++|+..||.|.|+-
T Consensus 26 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 85 (733)
T TIGR01243 26 AARLGVEPGDFVEIEKGDRSVVAIVWPLRPDDEGRGIIRMDGYLRANAGVTIGDTVTVER 85 (733)
T ss_pred HHhcCCCCCCEEEEecCCCceeEEEEecCccccCCCEEeecHHHHhhcCCCCCCeEEEee
Confidence 678999999999999 4566677788899999999999973
No 45
>PRK15488 thiosulfate reductase PhsA; Provisional
Probab=93.18 E-value=0.22 Score=43.17 Aligned_cols=49 Identities=10% Similarity=0.022 Sum_probs=40.3
Q ss_pred EEecCHHHHhhCCCCCCCEEEEEeccCCcEEEEeccCCCCCCCeEEEeHh
Q psy3865 17 KRRKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSDDTCPDEKIRMNRV 66 (107)
Q Consensus 17 iari~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai~~~~~d~~~~~Irid~~ 66 (107)
.+.|+|++.++|||..||.|+|+-.+. +..+.+...+.+.++.|.|...
T Consensus 667 ~v~mnp~dA~~~GI~dGD~V~v~n~~G-~i~~~a~vt~~v~~g~v~i~~g 715 (759)
T PRK15488 667 AVWIHPQTAGKLGIKNGDEIRLENSVG-KEKGKALVTPGIRPDTLFAYMG 715 (759)
T ss_pred cEEeCHHHHHHhCCCCCCEEEEEcCCC-cEEEEEEEeCCccCCeEEEecc
Confidence 378999999999999999999997664 4556677777888888888653
No 46
>PRK08166 NADH dehydrogenase subunit G; Validated
Probab=92.95 E-value=0.27 Score=43.38 Aligned_cols=48 Identities=10% Similarity=0.001 Sum_probs=39.3
Q ss_pred EEecCHHHHhhCCCCCCCEEEEEeccCCcEEEEeccCCCCCCCeEEEeH
Q psy3865 17 KRRKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSDDTCPDEKIRMNR 65 (107)
Q Consensus 17 iari~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai~~~~~d~~~~~Irid~ 65 (107)
.+.|+|++.++|||..||.|.|+..+. +..+.+-..+.+..+.|.|..
T Consensus 778 ~v~i~p~dA~~lgI~dGd~V~v~s~~G-~v~~~a~vt~~i~~g~V~~p~ 825 (847)
T PRK08166 778 YVLLNPADAARLGVNAGARVSFSCDGQ-TLRLPVRLSEGLAAGQVGLPL 825 (847)
T ss_pred eeEECHHHHHHcCCCCCCEEEEEECCe-EEEEEEEEcCCCCCCEEEecC
Confidence 588999999999999999999997664 333456677889999998854
No 47
>PRK07860 NADH dehydrogenase subunit G; Validated
Probab=92.84 E-value=0.28 Score=43.15 Aligned_cols=50 Identities=18% Similarity=0.186 Sum_probs=39.4
Q ss_pred EEEecCHHHHhhCCCCCCCEEEEEeccCCcEEEEeccCCCCCCCeEEEeHhh
Q psy3865 16 GKRRKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSDDTCPDEKIRMNRVM 67 (107)
Q Consensus 16 Giari~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai~~~~~d~~~~~Irid~~~ 67 (107)
..+.|+|++.++|||..||.|+|+-.+.+ ..+.+... .+..|.+.|...-
T Consensus 718 ~~v~i~p~dA~~lgi~~Gd~V~v~s~~G~-i~~~v~v~-~v~~G~vf~p~h~ 767 (797)
T PRK07860 718 PVARLSAATAAEIGVADGDAVTVSTERGS-ITLPLAIT-DMPDRVVWLPLNS 767 (797)
T ss_pred CEEEECHHHHHHcCCCCCCEEEEEcCCeE-EEEEEEEc-ccCCCeEEEecCC
Confidence 36889999999999999999999976653 33344445 6999999998643
No 48
>TIGR01701 Fdhalpha-like oxidoreductase alpha (molybdopterin) subunit. This model represents a well-defined clade of oxidoreductase alpha subunits most closely related to a group of formate dehydrogenases including the E. coli FdhH protein (TIGR01591). These alpha subunits contain a molybdopterin cofactor and generally associate with two other subunits which contain iron-sulfur clusters and cytochromes. The particular subunits with which this enzyme interacts and the substrate which is reduced is unknown at this time. In Ralstonia, the gene is associated with the cbb operon, but is not essential for CO2 fixation.
Probab=91.88 E-value=0.46 Score=41.54 Aligned_cols=48 Identities=10% Similarity=0.032 Sum_probs=36.4
Q ss_pred EEecCHHHHhhCCCCCCCEEEEEeccCC----cEEEEeccCCCCCCCeEEEe
Q psy3865 17 KRRKESAKMDELNLFRGDTVLLRGKRRK----ESVCIVLSDDTCPDEKIRMN 64 (107)
Q Consensus 17 iari~~~~m~~Lgl~~GD~V~I~Gkr~~----~tvai~~~~~d~~~~~Irid 64 (107)
.+.|+|+++++|||..||.|.|+..+.. +...+....+++..+.+.+.
T Consensus 660 ~v~inp~Da~~lGi~~Gd~V~v~s~~G~~~~r~~~~~~~v~~~i~~G~v~~~ 711 (743)
T TIGR01701 660 VVFMNETDIKKLGLRNGERVDVYNQYGDGQKRKFDNLRIVFYDTPTGNAAAY 711 (743)
T ss_pred EEEECHHHHHHcCCCCcCEEEEEeCCCCCcceeEEEEEEeeCCCCCCeEEEE
Confidence 5789999999999999999999965531 22222334568888998886
No 49
>TIGR03327 AMP_phos AMP phosphorylase. This enzyme family is found, so far, strictly in the Archaea, and only in those with a type III Rubisco enzyme. Most of the members previously were annotated as thymidine phosphorylase, or DeoA. The AMP metabolized by this enzyme may be produced by ADP-dependent sugar kinases.
Probab=91.69 E-value=0.76 Score=38.93 Aligned_cols=65 Identities=23% Similarity=0.320 Sum_probs=53.8
Q ss_pred ecCHHHHhhCCCCCCCEEEEEeccCCcEEEEecc-CCCCCCCeEEEeHhhhhcccccCCCeEEEEeC
Q psy3865 19 RKESAKMDELNLFRGDTVLLRGKRRKESVCIVLS-DDTCPDEKIRMNRVMRNNLRVRLSDVVSLVPC 84 (107)
Q Consensus 19 ri~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai~~~-~~d~~~~~Irid~~~R~N~~v~igD~V~V~~~ 84 (107)
-++.+++..+|+.++|-|+|+-..+ +.+|.+.. ++-..++.+-+....=+.+++.-||.|.|+++
T Consensus 17 ~~~~~d~~~~g~~~~~rv~v~~~~~-~~~a~~~~~~~~~~~g~~gls~~~~~~l~~~~g~~v~v~~a 82 (500)
T TIGR03327 17 LLNEEDAKELGVHPGDRVRIESGGK-SVVGIVDSTDTLVEKGEIGLSHEVLEELGISEGEVVEVTPA 82 (500)
T ss_pred EEehhhhhhhCCCCCCeEEEEeCCE-EEEEEEEcccccccCCeeeccHHHHHHcCCCCCCEEEEecC
Confidence 3466788899999999999995443 56666543 35678999999999999999999999999986
No 50
>PRK14991 tetrathionate reductase subunit A; Provisional
Probab=91.46 E-value=0.5 Score=42.93 Aligned_cols=47 Identities=13% Similarity=0.063 Sum_probs=35.5
Q ss_pred EEecCHHHHhhCCCCCCCEEEEEeccCCcEEEEeccCCCCCCCeEEEe
Q psy3865 17 KRRKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSDDTCPDEKIRMN 64 (107)
Q Consensus 17 iari~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai~~~~~d~~~~~Irid 64 (107)
.+.|+|++.++|||..||.|+|...+. +..+.+...+.+.++.|.|.
T Consensus 917 ~v~InP~DA~~lGI~dGD~V~V~s~~G-~i~~~a~vt~~i~pGvV~ip 963 (1031)
T PRK14991 917 PVALNPQDAARLGIQHGDRVRISTPGG-SVVAQASVLNGVMPGVIAIE 963 (1031)
T ss_pred eEEECHHHHHHcCCCCCCEEEEEECCE-EEEEEEEECCCCCCCeEEEe
Confidence 478999999999999999999997664 33445555566666666554
No 51
>TIGR01706 NAPA periplasmic nitrate reductase, large subunit. The enzymes from Alicagenes eutrophus and Paracoccus pantotrophus have been characterized. In E. coli (as well as other organisms) this gene is part of a large nitrate reduction operon (napFDAGHBC).
Probab=91.34 E-value=0.54 Score=41.43 Aligned_cols=48 Identities=21% Similarity=0.178 Sum_probs=37.1
Q ss_pred EEEecCHHHHhhCCCCCCCEEEEEeccCCcEEEEeccCC--CCCCCeEEEe
Q psy3865 16 GKRRKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSDD--TCPDEKIRMN 64 (107)
Q Consensus 16 Giari~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai~~~~~--d~~~~~Irid 64 (107)
..+.|||++++++||..||.|+|...+. +..+.+...+ ....+.|.|.
T Consensus 746 ~~v~I~p~DA~~~GI~dGD~V~V~s~~G-~v~~~a~v~~~~~~~~G~V~~~ 795 (830)
T TIGR01706 746 ALCFMHPEDAKALGLRRGDEVWVVSRRG-EVRSRVETRGRNKPPRGLVFVP 795 (830)
T ss_pred CEEEECHHHHHHcCCcCCCEEEEEeCCe-eEEEEEEEcCCcccCCCeEEeC
Confidence 3578999999999999999999997665 4445554433 4566888886
No 52
>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=91.20 E-value=0.31 Score=27.90 Aligned_cols=28 Identities=21% Similarity=0.233 Sum_probs=23.3
Q ss_pred eEEEecCHHHHhhCCCCCCCEEEEEecc
Q psy3865 15 RGKRRKESAKMDELNLFRGDTVLLRGKR 42 (107)
Q Consensus 15 rGiari~~~~m~~Lgl~~GD~V~I~Gkr 42 (107)
++-++|..+.+++|++.+||.|++.-..
T Consensus 6 s~~v~iPk~~~~~l~l~~Gd~v~i~~~~ 33 (47)
T PF04014_consen 6 SGQVTIPKEIREKLGLKPGDEVEIEVEG 33 (47)
T ss_dssp CSEEEE-HHHHHHTTSSTTTEEEEEEET
T ss_pred CceEECCHHHHHHcCCCCCCEEEEEEeC
Confidence 3567899999999999999999999554
No 53
>TIGR02645 ARCH_P_rylase putative thymidine phosphorylase. Members of this family are closely related to characterized examples of thymidine phosphorylase (EC 2.4.2.4) and pyrimidine nucleoside phosphorylase (RC 2.4.2.2). Most examples are found in the archaea, but other examples in Legionella pneumophila str. Paris and Rhodopseudomonas palustris CGA009.
Probab=91.07 E-value=1.1 Score=37.88 Aligned_cols=63 Identities=17% Similarity=0.252 Sum_probs=52.3
Q ss_pred CHHHHhhCCCCCCCEEEEEeccCCcEEEEecc-CCCCCCCeEEEeHhhhhcccccCCCeEEEEeC
Q psy3865 21 ESAKMDELNLFRGDTVLLRGKRRKESVCIVLS-DDTCPDEKIRMNRVMRNNLRVRLSDVVSLVPC 84 (107)
Q Consensus 21 ~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai~~~-~~d~~~~~Irid~~~R~N~~v~igD~V~V~~~ 84 (107)
+.++++.+|+.++|-|+|+-..+ +.+|.+.. ++-..++.+-+....=+.+++.-||.|.|+++
T Consensus 18 ~~~d~~~~g~~~~~rv~v~~~~~-~~~a~~~~~~~~~~~~~~gl~~~~~~~l~~~~g~~v~v~~~ 81 (493)
T TIGR02645 18 NSPDLRAEGFTPQDRVEVRIGGK-SLIAILVGSDTLVEMGEIGLSVSAVETFMAREGDIVTVTPA 81 (493)
T ss_pred ehhhhhhcCCCcCCeEEEEeCCE-EEEEEEecccccccCCeeeccHHHHHHcCCCCCCEEEEecC
Confidence 44559999999999999995443 56666554 35678999999999999999999999999986
No 54
>PRK04350 thymidine phosphorylase; Provisional
Probab=90.76 E-value=1.1 Score=38.00 Aligned_cols=61 Identities=18% Similarity=0.165 Sum_probs=50.1
Q ss_pred HHHhhCCCCCCCEEEEEeccCCcEEEEeccCC--CCCCCeEEEeHhhhhcccccCCCeEEEEeC
Q psy3865 23 AKMDELNLFRGDTVLLRGKRRKESVCIVLSDD--TCPDEKIRMNRVMRNNLRVRLSDVVSLVPC 84 (107)
Q Consensus 23 ~~m~~Lgl~~GD~V~I~Gkr~~~tvai~~~~~--d~~~~~Irid~~~R~N~~v~igD~V~V~~~ 84 (107)
..++++|+.++|-|+|+...+ +.+|.+...+ -.+++.+-+....-+.+++.-||.|.|+++
T Consensus 14 ~~~~~~g~~~~~rv~v~~~~~-~~~a~~~~~~~~~~~~~~~gl~~~~~~~l~~~~g~~v~v~~a 76 (490)
T PRK04350 14 HVCRSEGFHAGDRVEVRAGGR-SIIATLNITDDDLVGPGEIGLSESAFRRLGVSEGDEVEVSHA 76 (490)
T ss_pred chhhhhCCCcCCeEEEEcCCe-EEEEEEEeccccccCCCcccccHHHHHHhCCCCCCeEEEecC
Confidence 446999999999999996443 4555544333 578999999999999999999999999986
No 55
>TIGR01580 narG respiratory nitrate reductase, alpha subunit. The Nitrate reductase enzyme complex allows bacteria to use nitrate as an electron acceptor during anaerobic growth. The enzyme complex consists of a tetramer that has an alpha, beta and 2 gamma subunits. The alpha and beta subunits have catalytic activity and the gamma subunits attach the enzyme to the membrane and is a b-type cytochrome that receives electrons from the quinone pool and transfers them to the beta subunit. This model is specific for the alpha subunit for nitrate reductase I (narG) and nitrate reductase II (narZ) for gram positive and gram negative bacteria.A few thermophiles and archaea also match the model The seed members used to make the model include Nitrate reductases from Pseudomonas fluorescens, E.coli and B.subtilis. All seed members are experimentally characterized. Some unpublished nitrate reductases, that are shorter sequences, and probably fragments fall in between the noise and trusted cutoffs. P
Probab=90.64 E-value=0.69 Score=42.97 Aligned_cols=63 Identities=16% Similarity=0.126 Sum_probs=49.4
Q ss_pred cCcccCCeEEEeEEEecCHHHHhhCCCCCCCEEEEEeccCCcEEEEeccCCCCCCCeEEEeHhhhhccc
Q psy3865 4 LNLFRGDTVLLRGKRRKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSDDTCPDEKIRMNRVMRNNLR 72 (107)
Q Consensus 4 ~~~~~~d~~~~rGiari~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai~~~~~d~~~~~Irid~~~R~N~~ 72 (107)
|-||+|..+ +-|||++.++.||..||-|++..... ..+|.+.....++.+.+.|--.--+...
T Consensus 1109 LtL~RGgp~-----vw~s~~DA~~~Gi~DnDwVEv~N~nG-~v~arAvvs~rip~g~~~myHa~er~~~ 1171 (1235)
T TIGR01580 1109 LTLGRGGPV-----VWLSEADAKDLGIADNDWIECFNSNG-ALTARAVVSQRVPAGMTMMYHAQERIVN 1171 (1235)
T ss_pred HhhccCCCe-----EEeCHHHHHHcCCCCCCEEEEEecCC-eEEEEEEEcCCCCCCeEEEecchhhhcC
Confidence 568888766 68999999999999999999996654 5667776777888899888765544333
No 56
>PRK13532 nitrate reductase catalytic subunit; Provisional
Probab=90.53 E-value=0.73 Score=40.54 Aligned_cols=49 Identities=18% Similarity=0.106 Sum_probs=37.9
Q ss_pred EEEecCHHHHhhCCCCCCCEEEEEeccCCcEEEEeccCC--CCCCCeEEEeH
Q psy3865 16 GKRRKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSDD--TCPDEKIRMNR 65 (107)
Q Consensus 16 Giari~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai~~~~~--d~~~~~Irid~ 65 (107)
..+.|+|++++++||..||.|+|.-.+. +..+.+...+ .+..+.+.|..
T Consensus 746 ~~v~inp~DA~~~GI~dGD~V~V~n~~G-~v~~~a~v~~~~~v~~Gvv~~~~ 796 (830)
T PRK13532 746 AVCFMHPEDAKARGLRRGDEVKVVSRRG-EVKSRVETRGRNKPPRGLVFVPF 796 (830)
T ss_pred CEEEECHHHHHHcCCCCCCEEEEEeCCe-eEEEEEEecCCcCCCCCeEEecc
Confidence 3478999999999999999999997664 4455554443 46789998863
No 57
>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=90.14 E-value=1.2 Score=25.36 Aligned_cols=39 Identities=18% Similarity=0.366 Sum_probs=31.1
Q ss_pred CCeEEEeHhhhhcccccCCCeEEEEeCCCCCCccEEEEccCCc
Q psy3865 58 DEKIRMNRVMRNNLRVRLSDVVSLVPCPGIVYGKRIHVLPIDD 100 (107)
Q Consensus 58 ~~~Irid~~~R~N~~v~igD~V~V~~~~~~~~a~~V~l~P~~d 100 (107)
.+.|+|...+|.-+++..||.|.++.- + . ..+.+.|+..
T Consensus 6 s~~v~iPk~~~~~l~l~~Gd~v~i~~~-~--~-g~i~i~p~~~ 44 (47)
T PF04014_consen 6 SGQVTIPKEIREKLGLKPGDEVEIEVE-G--D-GKIVIRPVKR 44 (47)
T ss_dssp CSEEEE-HHHHHHTTSSTTTEEEEEEE-T--T-SEEEEEESTT
T ss_pred CceEECCHHHHHHcCCCCCCEEEEEEe-C--C-CEEEEEECCC
Confidence 478999999999999999999999974 2 1 1788888753
No 58
>PRK09129 NADH dehydrogenase subunit G; Validated
Probab=90.01 E-value=0.68 Score=40.39 Aligned_cols=56 Identities=21% Similarity=0.222 Sum_probs=43.2
Q ss_pred EEEecCHHHHhhCCCCCCCEEEEEeccCCcEEEEeccCCCCCCCeEEEeHhhhhccc
Q psy3865 16 GKRRKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSDDTCPDEKIRMNRVMRNNLR 72 (107)
Q Consensus 16 Giari~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai~~~~~d~~~~~Irid~~~R~N~~ 72 (107)
..+.|||++.++|||..||.|.|+-.+. +..+.+...+.+..+.|.|..--..++-
T Consensus 708 ~~v~i~p~dA~~lgi~dGd~V~v~s~~G-~i~~~a~i~~~v~~g~V~~p~g~~~~~~ 763 (776)
T PRK09129 708 AAARLNPELAARLGLKEGDAVRVRQGDG-EVTLPVVLDDRLAEGVVRVAAAHPATAA 763 (776)
T ss_pred chhhcCHHHHHHcCCCCCCEEEEEcCCe-eEEEEEEEcCCCCCCEEEeecCChhhhh
Confidence 3478999999999999999999997764 3344566777889999998664444443
No 59
>PF08922 DUF1905: Domain of unknown function (DUF1905); InterPro: IPR015018 This family consist of hypothetical bacterial proteins. ; PDB: 2D9R_A.
Probab=89.79 E-value=1.4 Score=28.08 Aligned_cols=61 Identities=13% Similarity=0.087 Sum_probs=33.1
Q ss_pred EecCHHHHhhCCCCCCCEEEEEec----cCCcEEEEeccCCCCCCCeEEEeHhhhhcccccCCCeEEEE
Q psy3865 18 RRKESAKMDELNLFRGDTVLLRGK----RRKESVCIVLSDDTCPDEKIRMNRVMRNNLRVRLSDVVSLV 82 (107)
Q Consensus 18 ari~~~~m~~Lgl~~GD~V~I~Gk----r~~~tvai~~~~~d~~~~~Irid~~~R~N~~v~igD~V~V~ 82 (107)
+.+..+..++|+-.-=-.+.+++. .. +| .+ ++ .-.+.-.+-++..+|++++...||.|.|+
T Consensus 15 v~vP~~v~~~l~~~~~g~v~V~~tI~g~~~-~~-sl-~p-~g~G~~~Lpv~~~vRk~~g~~~Gd~V~v~ 79 (80)
T PF08922_consen 15 VEVPFDVAEELGEGGWGRVPVRGTIDGHPW-RT-SL-FP-MGNGGYILPVKAAVRKAIGKEAGDTVEVT 79 (80)
T ss_dssp EE--S-HHHHH--S--S-EEEEEEETTEEE-EE-EE-EE-SSTT-EEEEE-HHHHHHHT--TTSEEEEE
T ss_pred EEeCHHHHHHhccccCCceEEEEEECCEEE-EE-EE-EE-CCCCCEEEEEcHHHHHHcCCCCCCEEEEE
Confidence 566777777777541124555543 22 12 22 22 34466789999999999999999999986
No 60
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=89.58 E-value=1.6 Score=27.54 Aligned_cols=26 Identities=15% Similarity=0.184 Sum_probs=21.8
Q ss_pred CeEEEeHhhh-hcccccCCCeEEEEeC
Q psy3865 59 EKIRMNRVMR-NNLRVRLSDVVSLVPC 84 (107)
Q Consensus 59 ~~Irid~~~R-~N~~v~igD~V~V~~~ 84 (107)
-..++.|-+| +..++..||+|.|+..
T Consensus 30 vla~i~GKmr~~rI~I~~GD~V~Ve~s 56 (68)
T TIGR00008 30 VLAHISGKIRMHYIRILPGDKVKVELS 56 (68)
T ss_pred EEEEecCcchhccEEECCCCEEEEEEC
Confidence 3456888999 4999999999999975
No 61
>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=89.45 E-value=0.59 Score=25.57 Aligned_cols=25 Identities=20% Similarity=0.255 Sum_probs=23.6
Q ss_pred eEEEecCHHHHhhCCCCCCCEEEEE
Q psy3865 15 RGKRRKESAKMDELNLFRGDTVLLR 39 (107)
Q Consensus 15 rGiari~~~~m~~Lgl~~GD~V~I~ 39 (107)
+|-..|..+.+++|++..||.+.+.
T Consensus 6 kgri~iP~~~r~~l~~~~gd~~~i~ 30 (43)
T TIGR01439 6 KGQIVIPKEIREKLGLKEGDRLEVI 30 (43)
T ss_pred CCeEEecHHHHHHcCcCCCCEEEEE
Confidence 6788999999999999999999999
No 62
>PRK15070 propanediol utilization phosphotransacylase; Provisional
Probab=89.35 E-value=3.1 Score=31.63 Aligned_cols=71 Identities=13% Similarity=0.204 Sum_probs=47.3
Q ss_pred eEEEeEEEecCHHHHhhCCCCCCCEEEEE--eccCCcEEEE-e-ccCCCCCCCeEEEeHhhhhcccccCCCeEEEEe
Q psy3865 11 TVLLRGKRRKESAKMDELNLFRGDTVLLR--GKRRKESVCI-V-LSDDTCPDEKIRMNRVMRNNLRVRLSDVVSLVP 83 (107)
Q Consensus 11 ~~~~rGiari~~~~m~~Lgl~~GD~V~I~--Gkr~~~tvai-~-~~~~d~~~~~Irid~~~R~N~~v~igD~V~V~~ 83 (107)
.+.-+-...|+|++.+++|+..||.|.++ |.|. ++.- + ..-.+--.-..-||-+-=+-+++.-||.+.+-+
T Consensus 136 vIvA~RHIHm~p~dA~~~gvkdg~~V~V~v~g~R~--~if~~V~vRVs~~f~lemHIDtDEANA~~l~~~~~~~ii~ 210 (211)
T PRK15070 136 VIVAKRHIHMSPEDAEKFGVKDGDIVSVKVEGERG--LIFDNVLVRVSPDFALEMHIDTDEANAAGLKNGDKVKIIK 210 (211)
T ss_pred EEEEecccCCCHHHHHHhCCCCCCEEEEEecCCCc--eEEeeEEEEeCCCcceeeEeccchHhhcCCCCCCEEEEee
Confidence 34444556789999999999999999997 5552 2211 1 111122223456777777888899999888764
No 63
>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=88.45 E-value=1.8 Score=23.57 Aligned_cols=38 Identities=16% Similarity=0.288 Sum_probs=31.5
Q ss_pred CCCeEEEeHhhhhcccccCCCeEEEEeCCCCCCccEEEEccC
Q psy3865 57 PDEKIRMNRVMRNNLRVRLSDVVSLVPCPGIVYGKRIHVLPI 98 (107)
Q Consensus 57 ~~~~Irid~~~R~N~~v~igD~V~V~~~~~~~~a~~V~l~P~ 98 (107)
.++.+.|....|+.++...||.+.+... +...+.|.|.
T Consensus 5 ~kgri~iP~~~r~~l~~~~gd~~~i~~~----~~~~l~l~p~ 42 (43)
T TIGR01439 5 KKGQIVIPKEIREKLGLKEGDRLEVIRV----EDGEIILRPA 42 (43)
T ss_pred cCCeEEecHHHHHHcCcCCCCEEEEEEe----CCCEEEEEEC
Confidence 4689999999999999999999999964 2246888774
No 64
>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=87.78 E-value=0.76 Score=28.94 Aligned_cols=25 Identities=20% Similarity=0.276 Sum_probs=22.0
Q ss_pred EEecCHHHHhhCCCCCCCEEEEEec
Q psy3865 17 KRRKESAKMDELNLFRGDTVLLRGK 41 (107)
Q Consensus 17 iari~~~~m~~Lgl~~GD~V~I~Gk 41 (107)
-++|+.+.+++||+.+||.|.+.=.
T Consensus 11 ~vtIPk~i~~~lgl~~Gd~v~v~~~ 35 (74)
T TIGR02609 11 VVTLPKEVLESLGLKEGDTLYVDEE 35 (74)
T ss_pred EEEECHHHHHHcCcCCCCEEEEEEE
Confidence 3689999999999999999999743
No 65
>PRK11347 antitoxin ChpS; Provisional
Probab=87.59 E-value=0.78 Score=29.77 Aligned_cols=25 Identities=28% Similarity=0.213 Sum_probs=22.2
Q ss_pred EecCHHHHhhCCCCCCCEEEEEecc
Q psy3865 18 RRKESAKMDELNLFRGDTVLLRGKR 42 (107)
Q Consensus 18 ari~~~~m~~Lgl~~GD~V~I~Gkr 42 (107)
+||+.+.+++|++..||.|.|.=..
T Consensus 14 vriPk~il~~l~l~~G~~v~i~v~~ 38 (83)
T PRK11347 14 MVIPNIVMKELNLQPGQSVEAQVSN 38 (83)
T ss_pred EEeCHHHHHHcCCCCCCEEEEEEEC
Confidence 6899999999999999999998433
No 66
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=86.77 E-value=0.51 Score=30.37 Aligned_cols=26 Identities=23% Similarity=0.290 Sum_probs=22.2
Q ss_pred CeEEEeHhhhh-cccccCCCeEEEEeC
Q psy3865 59 EKIRMNRVMRN-NLRVRLSDVVSLVPC 84 (107)
Q Consensus 59 ~~Irid~~~R~-N~~v~igD~V~V~~~ 84 (107)
..-+|.|-+|+ +..+..||.|.|++-
T Consensus 32 ~~ahI~GKmr~~~i~I~~GD~V~Ve~~ 58 (75)
T COG0361 32 RLAHISGKMRKNRIRILPGDVVLVELS 58 (75)
T ss_pred EEEEccCcchheeEEeCCCCEEEEEec
Confidence 34567888999 999999999999975
No 67
>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=86.60 E-value=0.74 Score=27.27 Aligned_cols=24 Identities=29% Similarity=0.293 Sum_probs=19.3
Q ss_pred EEecCHHHHhhCCCCCCCEEEEEe
Q psy3865 17 KRRKESAKMDELNLFRGDTVLLRG 40 (107)
Q Consensus 17 iari~~~~m~~Lgl~~GD~V~I~G 40 (107)
.|+++++..++|++.+||.|.+.=
T Consensus 34 ~a~it~~~~~~L~L~~G~~V~~~i 57 (64)
T PF03459_consen 34 TARITPESAEELGLKPGDEVYASI 57 (64)
T ss_dssp EEEEEHHHHHHCT-STT-EEEEEE
T ss_pred EEEEcHHHHHHcCCCCCCEEEEEE
Confidence 388999999999999999998753
No 68
>PLN03086 PRLI-interacting factor K; Provisional
Probab=86.23 E-value=6.9 Score=33.79 Aligned_cols=86 Identities=15% Similarity=0.069 Sum_probs=59.5
Q ss_pred EEEecCHHHHh---hCCCC-CC-CEEEEEec------------cCCcEEEEeccCCCCCCCeEEEeHhhhhcccccC---
Q psy3865 16 GKRRKESAKMD---ELNLF-RG-DTVLLRGK------------RRKESVCIVLSDDTCPDEKIRMNRVMRNNLRVRL--- 75 (107)
Q Consensus 16 Giari~~~~m~---~Lgl~-~G-D~V~I~Gk------------r~~~tvai~~~~~d~~~~~Irid~~~R~N~~v~i--- 75 (107)
|++-|.|.+.+ .+++. ++ =+-+|+.. ..+.|.|=+.- -+-+.|.|-|..-+.+||+..-
T Consensus 92 dKI~LPpSaL~~L~~~~~~~~~Pm~F~l~~~~~~~~~~~~~~~~~~~th~GVlE-F~A~EG~v~lP~wm~~~L~~~~~~~ 170 (567)
T PLN03086 92 DKIKLPPSCFTELSDQGAFDKGPLYFRLSVVHQEGSGEMKDTDSQKTTHSGVLE-FTAEEGSVGLPPHVWSNLFPSDPPD 170 (567)
T ss_pred CeEEcCHHHHHHHHhcCCCCCCCeEEEEeccccccccccccccCCcEEEEEEEE-EEcCCCeEEcCHHHHhhcCCCCCCC
Confidence 35667887777 44441 11 23455531 23356665532 1345699999999999999753
Q ss_pred CCeEEEEeCCCCCCccEEEEccCCcccc
Q psy3865 76 SDVVSLVPCPGIVYGKRIHVLPIDDSVQ 103 (107)
Q Consensus 76 gD~V~V~~~~~~~~a~~V~l~P~~dti~ 103 (107)
|+.|+|+.+ .+|.|+-|.|.|-+..+-
T Consensus 171 ~~~v~v~~~-~Lpkgt~vklqP~~~~f~ 197 (567)
T PLN03086 171 VPLVEVRYI-WLPKGTYAKLQPDGVGFS 197 (567)
T ss_pred CCeEEEEEe-ecCCCCEEEEeeccCCcC
Confidence 789999986 999999999999876553
No 69
>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=85.87 E-value=0.32 Score=35.80 Aligned_cols=66 Identities=20% Similarity=0.226 Sum_probs=44.9
Q ss_pred EEEecCHHHHhhCCCCCCCEEEEEec---cCCcEEEEeccCC----CCCCCeEEEeHhhhhcccccCCCeEEEEe
Q psy3865 16 GKRRKESAKMDELNLFRGDTVLLRGK---RRKESVCIVLSDD----TCPDEKIRMNRVMRNNLRVRLSDVVSLVP 83 (107)
Q Consensus 16 Giari~~~~m~~Lgl~~GD~V~I~Gk---r~~~tvai~~~~~----d~~~~~Irid~~~R~N~~v~igD~V~V~~ 83 (107)
|.+.|++--|++|++.+||.|.|+.. +. |.+.+.|.+ +...-.-.+....|+-.-+..||++.|.-
T Consensus 72 G~i~lP~wmm~~L~l~~g~~V~v~~~~LPkg--t~vkLqP~~~~F~~i~n~KavLE~~Lr~ystLT~Gd~I~i~~ 144 (176)
T PF03152_consen 72 GTIYLPPWMMQNLGLQEGDIVRVEYVSLPKG--TFVKLQPQSSDFLDISNPKAVLERALRNYSTLTKGDTISIEY 144 (176)
T ss_dssp TEEEE-CHHHHHHT--TTEEEEEEEEE------SEEEEEESCHHHHCSS-HHHHHHHHHCC-SEEETTSEEEEEC
T ss_pred CeEEeCccHHhhcCCCCCCEEEEEEeECCCC--CEEEEeECCCccccccchHHHHHhhcccCceeecCCEEEEEe
Confidence 66788889999999999999999953 32 233333322 45555556888999999999999999983
No 70
>COG2002 AbrB Regulators of stationary/sporulation gene expression [Transcription]
Probab=85.86 E-value=1.1 Score=29.07 Aligned_cols=30 Identities=17% Similarity=0.133 Sum_probs=26.4
Q ss_pred eEEEeEEEecCHHHHhhCCCCCCCEEEEEe
Q psy3865 11 TVLLRGKRRKESAKMDELNLFRGDTVLLRG 40 (107)
Q Consensus 11 ~~~~rGiari~~~~m~~Lgl~~GD~V~I~G 40 (107)
.|.-+|-.-|..+..+.||+.+||.+++.-
T Consensus 9 kV~~~GqIvIPkeiR~~lgi~~Gd~lei~~ 38 (89)
T COG2002 9 KVDRKGQIVIPKEIREALGIKEGDVLEIIV 38 (89)
T ss_pred EECcCceEEecHHHHHHhCCCCCCEEEEEE
Confidence 355678899999999999999999999984
No 71
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=85.20 E-value=3 Score=27.55 Aligned_cols=26 Identities=23% Similarity=0.217 Sum_probs=21.8
Q ss_pred CeEEEeHhhhh-cccccCCCeEEEEeC
Q psy3865 59 EKIRMNRVMRN-NLRVRLSDVVSLVPC 84 (107)
Q Consensus 59 ~~Irid~~~R~-N~~v~igD~V~V~~~ 84 (107)
-...+.|-+|+ .+++-.||+|+|+.-
T Consensus 32 vla~isGKmR~~rIrIl~GD~V~VE~s 58 (87)
T PRK12442 32 VGAYASGRMRKHRIRILAGDRVTLELS 58 (87)
T ss_pred EEEEeccceeeeeEEecCCCEEEEEEC
Confidence 34567888888 899999999999964
No 72
>TIGR01553 formate-DH-alph formate dehydrogenase, alpha subunit, proteobacterial-type. This model is well-defined, with a large, unpopulated trusted/noise gap.
Probab=84.89 E-value=2.3 Score=38.71 Aligned_cols=42 Identities=14% Similarity=0.071 Sum_probs=32.0
Q ss_pred EEEecCHHHHhhCCCCCCCEEEEEeccCCcEEEEeccCCCCCC
Q psy3865 16 GKRRKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSDDTCPD 58 (107)
Q Consensus 16 Giari~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai~~~~~d~~~ 58 (107)
..+-|+|+..++|||+.||.|.|+..|. +..+.+...+.+..
T Consensus 913 ~fveI~p~~A~~~GI~~Gd~V~v~s~rG-~i~~~a~vt~ri~p 954 (1009)
T TIGR01553 913 MFCEISEELATEKGIQNGDKVILESVRG-KIWAKAIVTKRIKP 954 (1009)
T ss_pred cEEEECHHHHHHcCCcCCCEEEEEcCCe-eEEEEEEEcCCccc
Confidence 3577999999999999999999998875 55555555544433
No 73
>PRK08577 hypothetical protein; Provisional
Probab=84.74 E-value=2.9 Score=28.79 Aligned_cols=26 Identities=23% Similarity=0.215 Sum_probs=23.8
Q ss_pred EeEEEecCHHHHhhCCCCCCCEEEEE
Q psy3865 14 LRGKRRKESAKMDELNLFRGDTVLLR 39 (107)
Q Consensus 14 ~rGiari~~~~m~~Lgl~~GD~V~I~ 39 (107)
=+|-..|+.+..+.||+.+||.+++.
T Consensus 11 ~~g~i~ip~~~r~~l~~~~g~~~~~~ 36 (136)
T PRK08577 11 SKGRITIPLEIREALGIREGMYVLLI 36 (136)
T ss_pred cCCeEEecHHHHHHcCcCCCCEEEEE
Confidence 36888899999999999999999997
No 74
>PRK09798 antitoxin MazE; Provisional
Probab=84.43 E-value=1.5 Score=28.40 Aligned_cols=25 Identities=28% Similarity=0.179 Sum_probs=22.1
Q ss_pred EecCHHHHhhCCCCCCCEEEEEecc
Q psy3865 18 RRKESAKMDELNLFRGDTVLLRGKR 42 (107)
Q Consensus 18 ari~~~~m~~Lgl~~GD~V~I~Gkr 42 (107)
.||++..+++||+..||.|+|+=..
T Consensus 15 vRIPk~~l~~l~l~~g~~vei~v~~ 39 (82)
T PRK09798 15 VRIPATLMQALNLNIDDEVKIDLVD 39 (82)
T ss_pred EEcCHHHHHHcCCCCCCEEEEEEEC
Confidence 6899999999999999999998543
No 75
>PLN03086 PRLI-interacting factor K; Provisional
Probab=83.80 E-value=2.8 Score=36.12 Aligned_cols=81 Identities=15% Similarity=0.085 Sum_probs=56.3
Q ss_pred eEEEecCHHHHhhCCCCC---CCEEEEEecc-CCcEEEEeccC---C-CCCCCeEEEeHhhhhcccccCCCeEEEE----
Q psy3865 15 RGKRRKESAKMDELNLFR---GDTVLLRGKR-RKESVCIVLSD---D-TCPDEKIRMNRVMRNNLRVRLSDVVSLV---- 82 (107)
Q Consensus 15 rGiari~~~~m~~Lgl~~---GD~V~I~Gkr-~~~tvai~~~~---~-d~~~~~Irid~~~R~N~~v~igD~V~V~---- 82 (107)
-|.+.|++--|++|++.. |++|.|+... -+-|.+.+-|. . +...-.-.+-...|+-.-+..||++.|.
T Consensus 150 EG~v~lP~wm~~~L~~~~~~~~~~v~v~~~~Lpkgt~vklqP~~~~f~di~npKavLE~~Lr~~stLT~Gd~i~i~~~~~ 229 (567)
T PLN03086 150 EGSVGLPPHVWSNLFPSDPPDVPLVEVRYIWLPKGTYAKLQPDGVGFSDLPNHKAVLETALRQHATLSEDDVLVVNYGQL 229 (567)
T ss_pred CCeEEcCHHHHhhcCCCCCCCCCeEEEEEeecCCCCEEEEeeccCCcCCcccHHHHHHHHhhcCccccCCCEEEEecCCE
Confidence 378899999999999874 8999998641 01234444332 1 5555666678899999999999999987
Q ss_pred ----eCCCCCCccEEEE
Q psy3865 83 ----PCPGIVYGKRIHV 95 (107)
Q Consensus 83 ----~~~~~~~a~~V~l 95 (107)
.+.+++|+..|.|
T Consensus 230 ~y~~~V~ev~P~~aVsi 246 (567)
T PLN03086 230 TYKLKVLELKPASSVSV 246 (567)
T ss_pred EEEEEEEEEcCCCeeEE
Confidence 2334455555544
No 76
>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=83.71 E-value=2.3 Score=26.74 Aligned_cols=37 Identities=8% Similarity=0.138 Sum_probs=31.4
Q ss_pred CeEEEeHhhhhcccccCCCeEEEEeCCCCCCccEEEEccCCc
Q psy3865 59 EKIRMNRVMRNNLRVRLSDVVSLVPCPGIVYGKRIHVLPIDD 100 (107)
Q Consensus 59 ~~Irid~~~R~N~~v~igD~V~V~~~~~~~~a~~V~l~P~~d 100 (107)
-.|+|.+.++..+|+..||.|.+..- + ..+.+.|...
T Consensus 10 ~~vtIPk~i~~~lgl~~Gd~v~v~~~-~----~~iii~~~~~ 46 (74)
T TIGR02609 10 LVVTLPKEVLESLGLKEGDTLYVDEE-E----GGLKLKRFDE 46 (74)
T ss_pred eEEEECHHHHHHcCcCCCCEEEEEEE-C----CEEEEEECCC
Confidence 57899999999999999999999863 2 4588888876
No 77
>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=83.19 E-value=1.3 Score=27.74 Aligned_cols=22 Identities=27% Similarity=0.341 Sum_probs=19.1
Q ss_pred EecCHHHHhhCCCCCCCEEEEE
Q psy3865 18 RRKESAKMDELNLFRGDTVLLR 39 (107)
Q Consensus 18 ari~~~~m~~Lgl~~GD~V~I~ 39 (107)
+++++..+++.+++.||.|+=.
T Consensus 29 vyVs~~~Irr~~LR~GD~V~G~ 50 (68)
T cd04459 29 IYVSPSQIRRFNLRTGDTVVGQ 50 (68)
T ss_pred EEECHHHHHHhCCCCCCEEEEE
Confidence 4688999999999999998754
No 78
>COG1974 LexA SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]
Probab=81.83 E-value=1.4 Score=33.08 Aligned_cols=64 Identities=14% Similarity=0.224 Sum_probs=37.2
Q ss_pred ecCHHHHhhCCCCCCCEEEEEeccCCcEEEEeccCCCCCCCeEEEeHhhhhcccccCCC-eEEEEeCCCCCCccEEEEcc
Q psy3865 19 RKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSDDTCPDEKIRMNRVMRNNLRVRLSD-VVSLVPCPGIVYGKRIHVLP 97 (107)
Q Consensus 19 ri~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai~~~~~d~~~~~Irid~~~R~N~~v~igD-~V~V~~~~~~~~a~~V~l~P 97 (107)
|+.-+.|.+-|+..||+|.|+-.. +...|-|.+ +.++| ..++++. ...+..|.|.|
T Consensus 116 ~V~GdSM~~~gi~dGDlvvV~~~~------------~a~~GdiVv---------A~i~g~e~TvKrl--~~~g~~i~L~p 172 (201)
T COG1974 116 RVSGDSMIDAGILDGDLVVVDPTE------------DAENGDIVV---------ALIDGEEATVKRL--YRDGNQILLKP 172 (201)
T ss_pred EecCCccccCcCCCCCEEEEcCCC------------CCCCCCEEE---------EEcCCCcEEEEEE--EEeCCEEEEEe
Confidence 356678888888888888887322 111222222 23333 3666664 24556677777
Q ss_pred CCccccCC
Q psy3865 98 IDDSVQGL 105 (107)
Q Consensus 98 ~~dti~~~ 105 (107)
.+.+.+.+
T Consensus 173 ~Np~~~~i 180 (201)
T COG1974 173 ENPAYPPI 180 (201)
T ss_pred CCCCCCCc
Confidence 76666544
No 79
>COG1974 LexA SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]
Probab=80.71 E-value=5.1 Score=30.01 Aligned_cols=29 Identities=24% Similarity=0.345 Sum_probs=16.6
Q ss_pred CcccCcccCCeEEEeEEEecCHHHHhhCCCCCCCEEEEE
Q psy3865 1 MDELNLFRGDTVLLRGKRRKESAKMDELNLFRGDTVLLR 39 (107)
Q Consensus 1 ~~~~~~~~~d~~~~rGiari~~~~m~~Lgl~~GD~V~I~ 39 (107)
|.+-|+++||+|.|+ .+-.+.+||+|-..
T Consensus 122 M~~~gi~dGDlvvV~----------~~~~a~~GdiVvA~ 150 (201)
T COG1974 122 MIDAGILDGDLVVVD----------PTEDAENGDIVVAL 150 (201)
T ss_pred cccCcCCCCCEEEEc----------CCCCCCCCCEEEEE
Confidence 445566666666666 34455566665444
No 80
>PF09263 PEX-2N: Peroxisome biogenesis factor 1, N-terminal ; InterPro: IPR015343 This domain adopts a Cdc48 domain 2-like fold, with a beta-alpha-beta(3) arrangement. It has been suggested that this domain may be involved in interactions with ubiquitin, ubiquitin-like protein modifiers, or ubiquitin-like domains, such as Ubx. Furthermore, the domain may possess a putative adaptor or substrate binding site, allowing for peroxisomal biogenesis, membrane fusion and protein translocation []. ; PDB: 1WLF_A.
Probab=80.36 E-value=8.5 Score=25.39 Aligned_cols=66 Identities=18% Similarity=0.239 Sum_probs=40.4
Q ss_pred EecCHHHHhhCCCCCCCEEEEEeccCCcEEEEeccC----CCCCCCeEEEeHhhhhcccccCCCeEEEEeC
Q psy3865 18 RRKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSD----DTCPDEKIRMNRVMRNNLRVRLSDVVSLVPC 84 (107)
Q Consensus 18 ari~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai~~~~----~d~~~~~Irid~~~R~N~~v~igD~V~V~~~ 84 (107)
-++++.-..+|.+..+.-|++.--.. ..+.+-|.. .+.+.+.+.|++..=+-||.+-|+.|-++||
T Consensus 16 L~Lp~~l~~~L~L~q~qAvEvsWg~~-~pvfLSW~e~r~~~~~~en~~EinrqlgeKLGl~dGeQvfLrpC 85 (87)
T PF09263_consen 16 LHLPSRLASQLHLQQNQAVEVSWGHQ-SPVFLSWVEGRSFSDQGENVAEINRQLGEKLGLSDGEQVFLRPC 85 (87)
T ss_dssp EEE-HHHHHHTT--TT--EEEESSS----EEE-EEE-SS-------EEEEEHHHHHHTT--TT-EEEEEE-
T ss_pred EECCHHHHHHHHHhhCceEEEEeCCC-CcEEEEeecccccCCccccHHHHHHHHHHhhCCCcCCeEeeeeC
Confidence 46788999999999999999994332 355555643 2457799999999999999999999999997
No 81
>COG3383 Uncharacterized anaerobic dehydrogenase [General function prediction only]
Probab=79.90 E-value=4 Score=36.79 Aligned_cols=53 Identities=19% Similarity=0.098 Sum_probs=42.1
Q ss_pred EecCHHHHhhCCCCCCCEEEEEeccCCcEEEEeccCCCCCCCeEEEeHh----hhhcc
Q psy3865 18 RRKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSDDTCPDEKIRMNRV----MRNNL 71 (107)
Q Consensus 18 ari~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai~~~~~d~~~~~Irid~~----~R~N~ 71 (107)
+-|||+..+++|+..||.|+++-+.. ++.+.+...+.+..+.|.|.-. .+-|.
T Consensus 857 vEispelA~~rgi~dGd~Vrl~S~~G-~~~~ralVtdRv~~~evy~p~n~~~~~~~N~ 913 (978)
T COG3383 857 VEISPELAAERGIEDGDLVRLTSEFG-EIKLRALVTDRVKGGEVYMPMNDHPETAANV 913 (978)
T ss_pred eeeCHHHHhhcCCCCCCEEEEecCCC-cEEEEEEEecccCCCeEEEeccCCccchhhh
Confidence 45799999999999999999997665 6666777777888888877655 55554
No 82
>PF08605 Rad9_Rad53_bind: Fungal Rad9-like Rad53-binding; InterPro: IPR013914 In Saccharomyces cerevisiae (Baker s yeast), the Rad9 is a key adaptor protein in DNA damage checkpoint pathways. DNA damage induces Rad9 phosphorylation, and Rad53 specifically associates with this region of Rad9, when phosphorylated, via the Rad53 IPR000253 from INTERPRO domain []. There is no clear higher eukaryotic ortholog to Rad9.
Probab=79.85 E-value=2 Score=30.22 Aligned_cols=28 Identities=29% Similarity=0.395 Sum_probs=23.3
Q ss_pred EEEecCHHHHhhCCCCCCCEEEEEeccC
Q psy3865 16 GKRRKESAKMDELNLFRGDTVLLRGKRR 43 (107)
Q Consensus 16 Giari~~~~m~~Lgl~~GD~V~I~Gkr~ 43 (107)
|...++.+++..|.|+.||+|.+.++|.
T Consensus 46 g~~~i~~~dv~~LDlRIGD~Vkv~~~k~ 73 (131)
T PF08605_consen 46 GTYEIKNEDVKYLDLRIGDTVKVDGPKV 73 (131)
T ss_pred CceEeCcccEeeeeeecCCEEEECCCCc
Confidence 3356677888999999999999999764
No 83
>PRK08577 hypothetical protein; Provisional
Probab=79.50 E-value=6.1 Score=27.15 Aligned_cols=44 Identities=25% Similarity=0.268 Sum_probs=34.7
Q ss_pred CCCeEEEeHhhhhcccccCCCeEEEEeCCCCCCccEEEEccCCcccc
Q psy3865 57 PDEKIRMNRVMRNNLRVRLSDVVSLVPCPGIVYGKRIHVLPIDDSVQ 103 (107)
Q Consensus 57 ~~~~Irid~~~R~N~~v~igD~V~V~~~~~~~~a~~V~l~P~~dti~ 103 (107)
.+|.|.|...+|+-+|+..||.+.+..- + .-.+|++.|.....+
T Consensus 11 ~~g~i~ip~~~r~~l~~~~g~~~~~~~~-~--~~~~~~~~~~~~~~k 54 (136)
T PRK08577 11 SKGRITIPLEIREALGIREGMYVLLIAD-T--DKKEIHLEPIALPGK 54 (136)
T ss_pred cCCeEEecHHHHHHcCcCCCCEEEEEEE-C--CCCEEEEEEcCCCCc
Confidence 4689999999999999999999999952 2 234688888765443
No 84
>KOG1816|consensus
Probab=79.44 E-value=15 Score=29.34 Aligned_cols=88 Identities=19% Similarity=0.220 Sum_probs=62.6
Q ss_pred EEEecCHHHHh---hCCCCCCCEEEEEec-cCCcEEEEeccCCCCCCCeEEEeHhhhhcccccCCCeEEEEeCCCCCCcc
Q psy3865 16 GKRRKESAKMD---ELNLFRGDTVLLRGK-RRKESVCIVLSDDTCPDEKIRMNRVMRNNLRVRLSDVVSLVPCPGIVYGK 91 (107)
Q Consensus 16 Giari~~~~m~---~Lgl~~GD~V~I~Gk-r~~~tvai~~~~~d~~~~~Irid~~~R~N~~v~igD~V~V~~~~~~~~a~ 91 (107)
|+.-|.|.+.. .|.+.-=-+-+++.. ..+.|.|=+.. -.-+.|.|-+.--+-.|+...-||.|.|+-+ .+|.|+
T Consensus 38 gKIilPPSaL~~Ls~lnI~yPMlFkLtn~~~~r~THcGVLE-F~AeEG~vyLP~WMmq~L~le~gdlv~i~~v-~lpkgt 115 (308)
T KOG1816|consen 38 GKIILPPSALDRLSSLNITYPMLFKLTNVDVDRVTHCGVLE-FTAEEGRVYLPYWMMQNLLLEEGDLVRIRSV-TLPKGT 115 (308)
T ss_pred CeEEeCHHHHHHHHHhcCCCceEEEEeccccceeeeeeEEE-EEecCceEEeehHhhhhccCCCCCeEEEEEe-eccccc
Confidence 45667776655 455555555566532 11256665531 1334589999999999999999999999996 999999
Q ss_pred EEEEccCCccccCC
Q psy3865 92 RIHVLPIDDSVQGL 105 (107)
Q Consensus 92 ~V~l~P~~dti~~~ 105 (107)
-|.|.|-+-.+=.|
T Consensus 116 yvKLqP~s~dFLDI 129 (308)
T KOG1816|consen 116 YVKLQPHSVDFLDI 129 (308)
T ss_pred eeeeccCCCCcccc
Confidence 99999976554444
No 85
>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=79.19 E-value=2 Score=26.79 Aligned_cols=18 Identities=22% Similarity=0.267 Sum_probs=15.9
Q ss_pred HHHhhCCCCCCCEEEEEe
Q psy3865 23 AKMDELNLFRGDTVLLRG 40 (107)
Q Consensus 23 ~~m~~Lgl~~GD~V~I~G 40 (107)
+++++.|+.+||+|.|-+
T Consensus 47 ~~L~~~G~~~GD~V~Ig~ 64 (69)
T TIGR03595 47 DALRKAGAKDGDTVRIGD 64 (69)
T ss_pred HHHHHcCCCCCCEEEEcc
Confidence 677899999999999965
No 86
>PRK11347 antitoxin ChpS; Provisional
Probab=78.16 E-value=4.8 Score=26.06 Aligned_cols=36 Identities=11% Similarity=0.249 Sum_probs=30.3
Q ss_pred CeEEEeHhhhhcccccCCCeEEEEeCCCCCCccEEEEccCC
Q psy3865 59 EKIRMNRVMRNNLRVRLSDVVSLVPCPGIVYGKRIHVLPID 99 (107)
Q Consensus 59 ~~Irid~~~R~N~~v~igD~V~V~~~~~~~~a~~V~l~P~~ 99 (107)
.-|||.+.+.+.+++..||.|.|... + ..+.|.|..
T Consensus 12 ~~vriPk~il~~l~l~~G~~v~i~v~-~----~~iii~p~~ 47 (83)
T PRK11347 12 AGMVIPNIVMKELNLQPGQSVEAQVS-N----NQLILTPIS 47 (83)
T ss_pred eeEEeCHHHHHHcCCCCCCEEEEEEE-C----CEEEEEECC
Confidence 57899999999999999999999974 3 458888863
No 87
>PRK09939 putative oxidoreductase; Provisional
Probab=77.98 E-value=2.2 Score=37.66 Aligned_cols=25 Identities=12% Similarity=0.009 Sum_probs=22.7
Q ss_pred EEEecCHHHHhhCCCCCCCEEEEEe
Q psy3865 16 GKRRKESAKMDELNLFRGDTVLLRG 40 (107)
Q Consensus 16 Giari~~~~m~~Lgl~~GD~V~I~G 40 (107)
..+-|+|+++++|||..||.|.|..
T Consensus 672 ~~v~mnp~Da~~lGi~~Gd~V~v~s 696 (759)
T PRK09939 672 DVVFMSAKQAKICRVKNGERVNLIA 696 (759)
T ss_pred CEEEECHHHHHHcCCCCCCEEEEEE
Confidence 3578999999999999999999994
No 88
>COG2002 AbrB Regulators of stationary/sporulation gene expression [Transcription]
Probab=76.93 E-value=7.6 Score=25.05 Aligned_cols=42 Identities=21% Similarity=0.360 Sum_probs=33.5
Q ss_pred CCCeEEEeHhhhhcccccCCCeEEEEeCCCCCCccEEEEccCCcc
Q psy3865 57 PDEKIRMNRVMRNNLRVRLSDVVSLVPCPGIVYGKRIHVLPIDDS 101 (107)
Q Consensus 57 ~~~~Irid~~~R~N~~v~igD~V~V~~~~~~~~a~~V~l~P~~dt 101 (107)
..+.|-|...+|+-+|...||.+.+..- . ...++.|.|..+.
T Consensus 12 ~~GqIvIPkeiR~~lgi~~Gd~lei~~~-~--~~~~ivl~k~~~~ 53 (89)
T COG2002 12 RKGQIVIPKEIREALGIKEGDVLEIIVD-G--DGGRIVLKKYKPA 53 (89)
T ss_pred cCceEEecHHHHHHhCCCCCCEEEEEEe-C--CCCEEEEEECCcc
Confidence 3589999999999999999999999964 2 2233788887763
No 89
>PF06130 PduL: Propanediol utilisation protein PduL; InterPro: IPR008300 Salmonella enterica subsp. enterica serovar Typhimurium degrades 1,2-propanediol by a pathway that requires coenzyme B12, adenosylcobalamin (AdoCbl). Proteins required for 1,2-propanediol degradation are encoded by the pdu operon []. PduL functions in this pathway, but its exact role is not yet determined. Propanediol degradation is thought to be important for the natural Salmonella populations, since propanediol is produced by the fermentation of the common plant sugars rhamnose and fucose [, ]. More than 1% of the Salmonella enterica genome is devoted to the utilization of propanediol and cobalamin biosynthesis. In vivo expression technology has indicated that propanediol utilization (pdu) genes may be important for growth in host tissues, and competitive index studies with mice have shown that pdu mutations confer a virulence defect [, ]. The pdu operon is contiguous and coregulated with the cobalamin (B12) biosynthesis cob operon, indicating that propanediol catabolism may be the primary reason for de novo B12 synthesis in Salmonella [, , ]. Please see IPR003207 from INTERPRO, IPR010254 from INTERPRO and IPR009204 from INTERPRO for more details on the propanediol utilization pathway and the pdu operon.; GO: 0016747 transferase activity, transferring acyl groups other than amino-acyl groups
Probab=76.75 E-value=3.1 Score=26.36 Aligned_cols=24 Identities=13% Similarity=0.014 Sum_probs=20.8
Q ss_pred EEecCHHHHhhCCCCCCCEEEEEe
Q psy3865 17 KRRKESAKMDELNLFRGDTVLLRG 40 (107)
Q Consensus 17 iari~~~~m~~Lgl~~GD~V~I~G 40 (107)
-..|+|++.+.|++.+||+|.++=
T Consensus 10 HIHms~~da~~l~~~dg~~v~ve~ 33 (71)
T PF06130_consen 10 HIHMSPEDAEKLFGQDGQFVSVEV 33 (71)
T ss_pred ccCCCHHHHHHhCCCCCCEEEEEE
Confidence 356899999999999999998863
No 90
>COG2336 MazE Growth regulator [Signal transduction mechanisms]
Probab=76.42 E-value=3.4 Score=27.01 Aligned_cols=22 Identities=36% Similarity=0.421 Sum_probs=20.8
Q ss_pred EecCHHHHhhCCCCCCCEEEEE
Q psy3865 18 RRKESAKMDELNLFRGDTVLLR 39 (107)
Q Consensus 18 ari~~~~m~~Lgl~~GD~V~I~ 39 (107)
+||.+..|++|++..||-|++.
T Consensus 14 vrIP~~l~kql~l~~g~~v~v~ 35 (82)
T COG2336 14 VRIPAALLKQLNLTIGDEVEVE 35 (82)
T ss_pred eeccHHHHHHhCCCcCceEEEE
Confidence 6899999999999999999988
No 91
>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=75.62 E-value=2.4 Score=26.34 Aligned_cols=18 Identities=22% Similarity=0.278 Sum_probs=12.6
Q ss_pred HHHhhCCCCCCCEEEEEe
Q psy3865 23 AKMDELNLFRGDTVLLRG 40 (107)
Q Consensus 23 ~~m~~Lgl~~GD~V~I~G 40 (107)
+++++.|+.+||+|.|-+
T Consensus 47 ~~L~~~G~~~GD~V~Ig~ 64 (69)
T PF09269_consen 47 KALRKAGAKEGDTVRIGD 64 (69)
T ss_dssp HHHHTTT--TT-EEEETT
T ss_pred HHHHHcCCCCCCEEEEcC
Confidence 677899999999999854
No 92
>cd05793 S1_IF1A S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A in archaea, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=75.32 E-value=4 Score=26.02 Aligned_cols=27 Identities=22% Similarity=0.389 Sum_probs=23.9
Q ss_pred CCeEEEeHhhhhcccccCCCeEEEEeC
Q psy3865 58 DEKIRMNRVMRNNLRVRLSDVVSLVPC 84 (107)
Q Consensus 58 ~~~Irid~~~R~N~~v~igD~V~V~~~ 84 (107)
.-..+|.+-+|+++.+..||.|.|.+-
T Consensus 24 ~~la~i~gK~rk~iwI~~GD~V~Ve~~ 50 (77)
T cd05793 24 KRLCRIRGKMRKRVWINEGDIVLVAPW 50 (77)
T ss_pred EEEEEEchhhcccEEEcCCCEEEEEec
Confidence 356789999999999999999999965
No 93
>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=72.13 E-value=4.2 Score=26.45 Aligned_cols=19 Identities=37% Similarity=0.517 Sum_probs=15.4
Q ss_pred CHHHHhhCCCCCCCEEEEE
Q psy3865 21 ESAKMDELNLFRGDTVLLR 39 (107)
Q Consensus 21 ~~~~m~~Lgl~~GD~V~I~ 39 (107)
+.+.++++++..||.|.|.
T Consensus 41 N~~~i~~~~i~~Gd~V~V~ 59 (82)
T PF03120_consen 41 NYDYIKELDIRIGDTVLVT 59 (82)
T ss_dssp SHHHHHHTT-BBT-EEEEE
T ss_pred CHHHHHHcCCCCCCEEEEE
Confidence 4689999999999999997
No 94
>COG5140 UFD1 Ubiquitin fusion-degradation protein [Posttranslational modification, protein turnover, chaperones]
Probab=71.13 E-value=9.4 Score=30.18 Aligned_cols=69 Identities=23% Similarity=0.240 Sum_probs=50.5
Q ss_pred eEEEecCHHHHhhCCCCCCCEEEEEecc--CCcEEEEeccC-C--CCCCCeEEEeHhhhhcccccCCCeEEEEe
Q psy3865 15 RGKRRKESAKMDELNLFRGDTVLLRGKR--RKESVCIVLSD-D--TCPDEKIRMNRVMRNNLRVRLSDVVSLVP 83 (107)
Q Consensus 15 rGiari~~~~m~~Lgl~~GD~V~I~Gkr--~~~tvai~~~~-~--d~~~~~Irid~~~R~N~~v~igD~V~V~~ 83 (107)
.|-+++..=-|+.|++++||.|.|+--. -.+-|-+.+.. + ++......+....|+---+..||.+.+.-
T Consensus 91 EGrVylP~WMm~tLs~epgdlv~~~~td~plG~fVKL~PqSVdFLdI~dpkavLEn~LRNfstLt~~D~iei~y 164 (331)
T COG5140 91 EGRVYLPSWMMQTLSMEPGDLVVLRYTDFPLGKFVKLIPQSVDFLDIEDPKAVLENCLRNFSTLTEGDEIEIQY 164 (331)
T ss_pred CCcEeehHHHHHhccCCCCcEEEEEeccccccceEEecccccceEeccChHHHHHHHHhhccccccCCEEEEEE
Confidence 4667888888999999999999998421 00123222222 2 67777888889999999999999998875
No 95
>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=70.30 E-value=9.6 Score=24.32 Aligned_cols=28 Identities=14% Similarity=0.324 Sum_probs=24.6
Q ss_pred CCCeEEEeHhhhhcccccCCCeEEEEeC
Q psy3865 57 PDEKIRMNRVMRNNLRVRLSDVVSLVPC 84 (107)
Q Consensus 57 ~~~~Irid~~~R~N~~v~igD~V~V~~~ 84 (107)
..-..+|.+-+|+|+.+..||.|.|.+.
T Consensus 23 ~~~l~~i~gK~Rk~iwI~~GD~VlV~~~ 50 (78)
T cd04456 23 QRRLVSIPGKLRKNIWIKRGDFLIVDPI 50 (78)
T ss_pred CEEEEEEchhhccCEEEcCCCEEEEEec
Confidence 3456789999999999999999999975
No 96
>TIGR02851 spore_V_T stage V sporulation protein T. Members of this protein family are the stage V sporulation protein T (SpoVT), a protein of the sporulation/germination program in Bacillus subtilis and related species. The amino-terminal 50 amino acids are nearly perfectly conserved across all endospore-forming bacteria. SpoVT is a DNA-binding transcriptional regulator related to AbrB (See PFAM model pfam04014).
Probab=70.00 E-value=13 Score=27.15 Aligned_cols=39 Identities=13% Similarity=0.198 Sum_probs=31.0
Q ss_pred CCCeEEEeHhhhhcccccCCCeEEEEeCCCCCCccEEEEccCC
Q psy3865 57 PDEKIRMNRVMRNNLRVRLSDVVSLVPCPGIVYGKRIHVLPID 99 (107)
Q Consensus 57 ~~~~Irid~~~R~N~~v~igD~V~V~~~~~~~~a~~V~l~P~~ 99 (107)
..|.|.|...+|+.+|++.||.+.++.- + . ..|.|-+++
T Consensus 11 ~~Gri~iP~~iR~~l~i~~gd~~~~~~~-~--~-~~iil~k~~ 49 (180)
T TIGR02851 11 DLGRVVIPKEIRRTLRIREGDPLEIFTD-R--E-GEVILKKYS 49 (180)
T ss_pred CCCcEEEeHHHHHHcCCCCCCeEEEEEe-C--C-CEEEEEECC
Confidence 4689999999999999999999999863 2 1 347776665
No 97
>PRK09974 putative regulator PrlF; Provisional
Probab=69.24 E-value=13 Score=25.58 Aligned_cols=39 Identities=10% Similarity=0.207 Sum_probs=30.9
Q ss_pred CCCeEEEeHhhhhcccccCCCeEEEEeCCCCCCccEEEEccCC
Q psy3865 57 PDEKIRMNRVMRNNLRVRLSDVVSLVPCPGIVYGKRIHVLPID 99 (107)
Q Consensus 57 ~~~~Irid~~~R~N~~v~igD~V~V~~~~~~~~a~~V~l~P~~ 99 (107)
.++.|.|...+|+-+|++.||+|.+.-. +...|.+.|..
T Consensus 16 sKGQvTIPk~IR~~Lgl~~GdkI~f~i~----~dG~V~i~~~~ 54 (111)
T PRK09974 16 DRGQTTVPAPVRKALKLKKRDSIHYEIL----PGGQVFICRLG 54 (111)
T ss_pred cCCCEeccHHHHHHcCCCCCCEEEEEEe----CCCEEEEEECC
Confidence 5689999999999999999999998743 22446666653
No 98
>TIGR02851 spore_V_T stage V sporulation protein T. Members of this protein family are the stage V sporulation protein T (SpoVT), a protein of the sporulation/germination program in Bacillus subtilis and related species. The amino-terminal 50 amino acids are nearly perfectly conserved across all endospore-forming bacteria. SpoVT is a DNA-binding transcriptional regulator related to AbrB (See PFAM model pfam04014).
Probab=68.17 E-value=5.6 Score=29.15 Aligned_cols=25 Identities=16% Similarity=0.145 Sum_probs=22.3
Q ss_pred eEEEecCHHHHhhCCCCCCCEEEEE
Q psy3865 15 RGKRRKESAKMDELNLFRGDTVLLR 39 (107)
Q Consensus 15 rGiari~~~~m~~Lgl~~GD~V~I~ 39 (107)
+|..-|+.+.++.||+.+||.+++.
T Consensus 12 ~Gri~iP~~iR~~l~i~~gd~~~~~ 36 (180)
T TIGR02851 12 LGRVVIPKEIRRTLRIREGDPLEIF 36 (180)
T ss_pred CCcEEEeHHHHHHcCCCCCCeEEEE
Confidence 5677788899999999999999996
No 99
>KOG0735|consensus
Probab=68.10 E-value=14 Score=33.39 Aligned_cols=53 Identities=19% Similarity=0.248 Sum_probs=46.9
Q ss_pred ccCCCCCCCeEEEeHhhhhcccccCCCeEEEEeCCCCCCccEEEEccC-Ccccc
Q psy3865 51 LSDDTCPDEKIRMNRVMRNNLRVRLSDVVSLVPCPGIVYGKRIHVLPI-DDSVQ 103 (107)
Q Consensus 51 ~~~~d~~~~~Irid~~~R~N~~v~igD~V~V~~~~~~~~a~~V~l~P~-~dti~ 103 (107)
+.+.+...+.|-|++..-.-+++.-|+.|.++.++.+..|+.|++-|. +|.+|
T Consensus 52 g~~s~~se~~ieIn~~~A~~l~L~e~~~V~l~~~~~v~~~~~V~VeP~TsdDWE 105 (952)
T KOG0735|consen 52 GHGSGSSENVIEINRVYAHTLGLAENQEVKLSIIDHVHEATQVEVEPVTSDDWE 105 (952)
T ss_pred ccCCCCccceEEeehhhHhhccCCCCCeEEEEEcCCccceeEEEEeeccCccHH
Confidence 444577889999999999999999999999999999999999999995 56654
No 100
>PRK09974 putative regulator PrlF; Provisional
Probab=67.03 E-value=25 Score=24.12 Aligned_cols=29 Identities=17% Similarity=0.235 Sum_probs=26.3
Q ss_pred eEEEeEEEecCHHHHhhCCCCCCCEEEEE
Q psy3865 11 TVLLRGKRRKESAKMDELNLFRGDTVLLR 39 (107)
Q Consensus 11 ~~~~rGiari~~~~m~~Lgl~~GD~V~I~ 39 (107)
+|+=||=..|..+.++.||+.+||-|...
T Consensus 13 tvTsKGQvTIPk~IR~~Lgl~~GdkI~f~ 41 (111)
T PRK09974 13 KLTDRGQTTVPAPVRKALKLKKRDSIHYE 41 (111)
T ss_pred EEecCCCEeccHHHHHHcCCCCCCEEEEE
Confidence 46778889999999999999999999986
No 101
>COG5013 NarG Nitrate reductase alpha subunit [Energy production and conversion]
Probab=65.88 E-value=13 Score=34.39 Aligned_cols=89 Identities=18% Similarity=0.098 Sum_probs=60.3
Q ss_pred cCcccCCeEEEeEEEecCHHHHhhCCCCCCCEEEEEeccCCcEEEEeccCCCCCCCeEEEeHhhhhcccccCCCeEEEEe
Q psy3865 4 LNLFRGDTVLLRGKRRKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSDDTCPDEKIRMNRVMRNNLRVRLSDVVSLVP 83 (107)
Q Consensus 4 ~~~~~~d~~~~rGiari~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai~~~~~d~~~~~Irid~~~R~N~~v~igD~V~V~~ 83 (107)
|-||+|..| +-||+++.+.+||...|-|++-.... ..+|.+..+.-++.|...|--..-+-+.+-..++ +=.+
T Consensus 1103 LtL~RGGp~-----vW~s~~DA~~~gi~DNDWvEv~N~NG-~~~aRavvS~Rip~G~~~MyHAQer~v~~Pgse~-tg~R 1175 (1227)
T COG5013 1103 LTLSRGGPV-----VWISEEDAKKLGIADNDWVEVFNANG-ALTARAVVSQRVPKGMTFMYHAQERIVNVPGSEI-TGKR 1175 (1227)
T ss_pred EEecCCCce-----EEeccccHHHcCCccCceeEEeccCC-eEEEEEeecccCCCCcEEEeeeccccccCCCCcc-cCCc
Confidence 678999887 67899999999999999999996554 5566666677888888888766655555443322 1111
Q ss_pred CCCCCCccEEEEccCC
Q psy3865 84 CPGIVYGKRIHVLPID 99 (107)
Q Consensus 84 ~~~~~~a~~V~l~P~~ 99 (107)
-..-..-++|++-|..
T Consensus 1176 GG~HNsvTRi~~KPth 1191 (1227)
T COG5013 1176 GGIHNSVTRIHPKPTH 1191 (1227)
T ss_pred CcccCccceEecccce
Confidence 1111233566666653
No 102
>PRK04350 thymidine phosphorylase; Provisional
Probab=65.48 E-value=9.3 Score=32.42 Aligned_cols=40 Identities=23% Similarity=0.310 Sum_probs=33.3
Q ss_pred CcccCcccCCeEEEe--------------------EEEecCHHHHhhCCCCCCCEEEEEe
Q psy3865 1 MDELNLFRGDTVLLR--------------------GKRRKESAKMDELNLFRGDTVLLRG 40 (107)
Q Consensus 1 ~~~~~~~~~d~~~~r--------------------Giari~~~~m~~Lgl~~GD~V~I~G 40 (107)
|.++|+..+|-|.|+ |-+.++....++|++..||.|.|.-
T Consensus 16 ~~~~g~~~~~rv~v~~~~~~~~a~~~~~~~~~~~~~~~gl~~~~~~~l~~~~g~~v~v~~ 75 (490)
T PRK04350 16 CRSEGFHAGDRVEVRAGGRSIIATLNITDDDLVGPGEIGLSESAFRRLGVSEGDEVEVSH 75 (490)
T ss_pred hhhhCCCcCCeEEEEcCCeEEEEEEEeccccccCCCcccccHHHHHHhCCCCCCeEEEec
Confidence 367899999999887 3455677889999999999999984
No 103
>KOG1625|consensus
Probab=64.35 E-value=4.6 Score=34.89 Aligned_cols=26 Identities=27% Similarity=0.617 Sum_probs=23.4
Q ss_pred EEecCHHHHhhCCCCCCCEEEEEecc
Q psy3865 17 KRRKESAKMDELNLFRGDTVLLRGKR 42 (107)
Q Consensus 17 iari~~~~m~~Lgl~~GD~V~I~Gkr 42 (107)
.+|++-..|+++.+|+|++|.+||+.
T Consensus 282 ~Vrldls~l~e~SiFPGQIVavkG~N 307 (600)
T KOG1625|consen 282 RVRLDLSRLKEYSIFPGQIVAVKGKN 307 (600)
T ss_pred eEEeehhhccceeecCCcEEEEeeec
Confidence 36788999999999999999999973
No 104
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=64.22 E-value=6.5 Score=28.55 Aligned_cols=27 Identities=11% Similarity=0.254 Sum_probs=23.7
Q ss_pred CCeEEEeHhhhhcccccCCCeEEEEeC
Q psy3865 58 DEKIRMNRVMRNNLRVRLSDVVSLVPC 84 (107)
Q Consensus 58 ~~~Irid~~~R~N~~v~igD~V~V~~~ 84 (107)
.-..+|.+-+|+++.+..||+|.|.+-
T Consensus 56 ~rLa~I~GKmRK~IWI~~GD~VlVel~ 82 (155)
T PTZ00329 56 KRLCHIRGKMRKRVWINIGDIILVSLR 82 (155)
T ss_pred EEEEEeeccceeeEEecCCCEEEEecc
Confidence 356789999999999999999999863
No 105
>PF04076 BOF: Bacterial OB fold (BOF) protein; InterPro: IPR005220 Proteins in this entry have an OB-fold fold (oligonucleotide/oligosaccharide binding motif). Analysis of the predicted nucleotide-binding site of the OB-fold suggests that they lack nucleic acid-binding properties. They contain an predicted N-terminal signal peptide which indicates that they localise to the periplasm where they may function to bind proteins, small molecules, or other typical OB-fold ligands. As hypothesised for the distantly related OB-fold containing bacterial enterotoxins, the loss of nucleotide-binding function and the rapid evolution of the OB-fold ligand-binding site may be associated with the presence of members in mobile genetic elements and their potential role in bacterial pathogenicity [].; PDB: 1NNX_A.
Probab=63.32 E-value=14 Score=24.88 Aligned_cols=38 Identities=18% Similarity=0.182 Sum_probs=22.5
Q ss_pred cCcccCCeEEEeEE--------------------EecCHHHHhhCCCCCCCEEEEEec
Q psy3865 4 LNLFRGDTVLLRGK--------------------RRKESAKMDELNLFRGDTVLLRGK 41 (107)
Q Consensus 4 ~~~~~~d~~~~rGi--------------------ari~~~~m~~Lgl~~GD~V~I~Gk 41 (107)
+..+++-.|.|+|. +-|+++...-+.+.+.|.|+|.|+
T Consensus 29 ~~~~Dd~~V~L~G~Iv~~l~~d~Y~F~D~TG~I~VeId~~~w~g~~vt~~~~Vri~Ge 86 (103)
T PF04076_consen 29 KNAKDDTPVTLEGNIVKQLGDDKYLFRDATGEIEVEIDDDVWRGQTVTPDDKVRISGE 86 (103)
T ss_dssp TTS-SSEEEEEEEEEEEEEETTEEEEEETTEEEEEE--GGGSTT----TTSEEEEEEE
T ss_pred hhCcCCCeEEEEEEEEEEecCCEEEEECCCCcEEEEEChhhcCCcccCCCCEEEEEEE
Confidence 45567777777775 345667777788888888888885
No 106
>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=63.00 E-value=2 Score=27.76 Aligned_cols=20 Identities=20% Similarity=0.233 Sum_probs=15.2
Q ss_pred EecCHHHHhhCCCCCCCEEE
Q psy3865 18 RRKESAKMDELNLFRGDTVL 37 (107)
Q Consensus 18 ari~~~~m~~Lgl~~GD~V~ 37 (107)
+++++..+++++++.||.|+
T Consensus 31 vYVs~~qIrrf~LR~GD~V~ 50 (78)
T PF07497_consen 31 VYVSPSQIRRFGLRTGDLVE 50 (78)
T ss_dssp EEE-CCCCCCTT--TTEEEE
T ss_pred EEECHHHHHHcCCCCCCEEE
Confidence 56788899999999999998
No 107
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=62.92 E-value=9.7 Score=25.55 Aligned_cols=27 Identities=26% Similarity=0.417 Sum_probs=23.9
Q ss_pred CCeEEEeHhhhhcccccCCCeEEEEeC
Q psy3865 58 DEKIRMNRVMRNNLRVRLSDVVSLVPC 84 (107)
Q Consensus 58 ~~~Irid~~~R~N~~v~igD~V~V~~~ 84 (107)
.-..+|.+-+|+.+.+..||.|.|.+-
T Consensus 45 ~~la~i~GK~Rk~IwI~~GD~VlVe~~ 71 (100)
T PRK04012 45 ERMGRIPGKMKKRMWIREGDVVIVAPW 71 (100)
T ss_pred EEEEEEchhhcccEEecCCCEEEEEec
Confidence 356789999999999999999999964
No 108
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=62.85 E-value=16 Score=24.44 Aligned_cols=38 Identities=16% Similarity=0.172 Sum_probs=29.5
Q ss_pred CCCeEEEeHhhhhcccccCCCeEEEEeCCCCC---CccEEEE
Q psy3865 57 PDEKIRMNRVMRNNLRVRLSDVVSLVPCPGIV---YGKRIHV 95 (107)
Q Consensus 57 ~~~~Irid~~~R~N~~v~igD~V~V~~~~~~~---~a~~V~l 95 (107)
..-..+|.+-+|+.+.+..||.|.|++. +.. .|.-++.
T Consensus 42 ~~~la~i~GK~Rk~iwI~~GD~VlVsp~-d~~~~~kg~Iv~r 82 (99)
T TIGR00523 42 KTRLGRIPGKLKKRIWIREGDVVIVKPW-EFQGDDKCDIVWR 82 (99)
T ss_pred CEEEEEEchhhcccEEecCCCEEEEEEc-cCCCCccEEEEEE
Confidence 3456789999999999999999999875 544 4554444
No 109
>COG3138 AstA Arginine/ornithine N-succinyltransferase beta subunit [Amino acid transport and metabolism]
Probab=61.60 E-value=8 Score=31.10 Aligned_cols=24 Identities=25% Similarity=0.227 Sum_probs=21.3
Q ss_pred EEEecCHHHHhhCCCCCCCEEEEE
Q psy3865 16 GKRRKESAKMDELNLFRGDTVLLR 39 (107)
Q Consensus 16 Giari~~~~m~~Lgl~~GD~V~I~ 39 (107)
+.++++++.++.||+..||.|.+.
T Consensus 311 e~~~l~~~~a~ALgv~~G~~vR~v 334 (336)
T COG3138 311 ERLILTAEAADALGVGAGDSVRLV 334 (336)
T ss_pred CcEEEcHHHHhhhCCCCCCeEEEe
Confidence 347899999999999999999874
No 110
>PRK05892 nucleoside diphosphate kinase regulator; Provisional
Probab=60.65 E-value=41 Score=24.03 Aligned_cols=69 Identities=17% Similarity=0.103 Sum_probs=44.2
Q ss_pred CCCCCCEEEEEec-cCCcEEEEeccCC-CC---CCCeEEEeH-hhhhcccccCCCeEEEEeCCCCCCccEEEEcc
Q psy3865 29 NLFRGDTVLLRGK-RRKESVCIVLSDD-TC---PDEKIRMNR-VMRNNLRVRLSDVVSLVPCPGIVYGKRIHVLP 97 (107)
Q Consensus 29 gl~~GD~V~I~Gk-r~~~tvai~~~~~-d~---~~~~Irid~-~~R~N~~v~igD~V~V~~~~~~~~a~~V~l~P 97 (107)
.+.-|-+|.++.. ....++.++...+ +. ..+.|-... ..|.=+|-+.||.|+|........-+-+.+.|
T Consensus 82 ~V~~Gs~Vtl~~~~g~~~~~~IVg~~e~d~~~~~~~~IS~~SPlG~ALlGk~vGD~v~v~~p~g~~~~eI~~I~~ 156 (158)
T PRK05892 82 TLPGGTEVTLRFPDGEVETMHVISVVEETPVGREAETLTADSPLGQALAGHQAGDTVTYSTPQGPAQVELLAVKL 156 (158)
T ss_pred EEEcCcEEEEEECCCCEEEEEEeCchhcCcccccCCEEccCCHHHHHHhCCCCCCEEEEEcCCCcEEEEEEEEEc
Confidence 4677999999843 2335666665543 22 367776655 78888999999999998432322334444444
No 111
>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=60.07 E-value=16 Score=21.47 Aligned_cols=25 Identities=24% Similarity=0.104 Sum_probs=21.4
Q ss_pred EecCHHHHhhCCCCCCCEEEEEecc
Q psy3865 18 RRKESAKMDELNLFRGDTVLLRGKR 42 (107)
Q Consensus 18 ari~~~~m~~Lgl~~GD~V~I~Gkr 42 (107)
|.++++..++|++.+||-|.+.=|.
T Consensus 37 a~i~~~~~~~l~l~~G~~v~~~ik~ 61 (69)
T TIGR00638 37 AVITLESVAELGLKPGKEVYAVIKA 61 (69)
T ss_pred EEecHHHHhhCCCCCCCEEEEEEEC
Confidence 5788999999999999998876544
No 112
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=59.74 E-value=10 Score=24.51 Aligned_cols=27 Identities=26% Similarity=0.436 Sum_probs=23.9
Q ss_pred CCeEEEeHhhhhcccccCCCeEEEEeC
Q psy3865 58 DEKIRMNRVMRNNLRVRLSDVVSLVPC 84 (107)
Q Consensus 58 ~~~Irid~~~R~N~~v~igD~V~V~~~ 84 (107)
.-..+|.+-+|+++.+..||.|.|.+.
T Consensus 29 ~~la~ipgK~Rk~iwI~~GD~VlVe~~ 55 (83)
T smart00652 29 ERLARIPGKMRKKVWIRRGDIVLVDPW 55 (83)
T ss_pred EEEEEEchhhcccEEEcCCCEEEEEec
Confidence 356789999999999999999999964
No 113
>COG5214 POL12 DNA polymerase alpha-primase complex, polymerase-associated subunit B [DNA replication, recombination, and repair]
Probab=59.48 E-value=6.5 Score=33.25 Aligned_cols=25 Identities=28% Similarity=0.521 Sum_probs=23.3
Q ss_pred EecCHHHHhhCCCCCCCEEEEEecc
Q psy3865 18 RRKESAKMDELNLFRGDTVLLRGKR 42 (107)
Q Consensus 18 ari~~~~m~~Lgl~~GD~V~I~Gkr 42 (107)
+|++-+..+++.+++|++|.+|||.
T Consensus 241 VRL~l~~l~~yS~FpGQIVavKGkN 265 (581)
T COG5214 241 VRLNLAHLQRYSVFPGQIVAVKGKN 265 (581)
T ss_pred EEeehhhccccccccccEEEEeccc
Confidence 7899999999999999999999984
No 114
>PRK09798 antitoxin MazE; Provisional
Probab=59.38 E-value=20 Score=23.06 Aligned_cols=36 Identities=14% Similarity=0.335 Sum_probs=30.5
Q ss_pred CeEEEeHhhhhcccccCCCeEEEEeCCCCCCccEEEEccCC
Q psy3865 59 EKIRMNRVMRNNLRVRLSDVVSLVPCPGIVYGKRIHVLPID 99 (107)
Q Consensus 59 ~~Irid~~~R~N~~v~igD~V~V~~~~~~~~a~~V~l~P~~ 99 (107)
--|||.+.+-+.+++..||.|.|+.- ..++.|.|..
T Consensus 13 ~~vRIPk~~l~~l~l~~g~~vei~v~-----~~~iiI~p~~ 48 (82)
T PRK09798 13 PAVRIPATLMQALNLNIDDEVKIDLV-----DGKLIIEPVR 48 (82)
T ss_pred ceEEcCHHHHHHcCCCCCCEEEEEEE-----CCEEEEEECC
Confidence 46899999999999999999999963 3668888864
No 115
>PF12857 TOBE_3: TOBE-like domain; InterPro: IPR024765 The TOBE (transport-associated OB) domain [] always occurs as a dimer and it is found in ABC transporters immediately after the ATPase domain. This entry represents a TOBE-like domain, found in the C terminus of ATPase subunit CysA. CysA is part of the CysATWP ABC transporter complex, involved in sulphate/thiosulphate import [, ].
Probab=59.18 E-value=14 Score=21.78 Aligned_cols=21 Identities=33% Similarity=0.442 Sum_probs=17.7
Q ss_pred EecCHHHHhhCCCCCCCEEEEE
Q psy3865 18 RRKESAKMDELNLFRGDTVLLR 39 (107)
Q Consensus 18 ari~~~~m~~Lgl~~GD~V~I~ 39 (107)
+-|+.+. .+|++..||.|.++
T Consensus 36 vel~~~~-~~l~l~~G~~V~l~ 56 (58)
T PF12857_consen 36 VELPRER-RQLGLQPGDRVYLR 56 (58)
T ss_pred EEeCHhH-HhcCCCCCCEEEEE
Confidence 4578888 99999999999875
No 116
>TIGR01461 greB transcription elongation factor GreB. The GreA and GreB transcription elongation factors enable to continuation of RNA transcription past template-encoded arresting sites. Among the Proteobacteria, distinct clades of GreA and GreB are found. GreB differs functionally in that it releases larger oligonucleotides. This model describes proteobacterial GreB.
Probab=57.71 E-value=24 Score=25.15 Aligned_cols=63 Identities=21% Similarity=0.208 Sum_probs=44.1
Q ss_pred CHHHHhhCCCCCCCEEEEEec-cCCcEEEEeccCC-CCCCCeEEEeH-hhhhcccccCCCeEEEEe
Q psy3865 21 ESAKMDELNLFRGDTVLLRGK-RRKESVCIVLSDD-TCPDEKIRMNR-VMRNNLRVRLSDVVSLVP 83 (107)
Q Consensus 21 ~~~~m~~Lgl~~GD~V~I~Gk-r~~~tvai~~~~~-d~~~~~Irid~-~~R~N~~v~igD~V~V~~ 83 (107)
++..+..-.+.-|-+|+++.. ....++.++.+.+ +...+.|-... ..+.=+|-..||.|+|..
T Consensus 75 d~~~~~~~~V~~Gs~V~l~d~~~~~~~~~iVgp~ead~~~~~IS~~SPlG~ALlGk~~GD~v~v~~ 140 (156)
T TIGR01461 75 DYSPQQEGKVFFGAWVELENDDGVTHRFRIVGYDEIDGRKNYISIDSPLARALLKKEVGDEVVVNT 140 (156)
T ss_pred CCCCCCCCEEecCeEEEEEECCCCEEEEEEEChHHhCcCCCeECCCCHHHHHHcCCCCCCEEEEEc
Confidence 455555556778999999843 2224565665554 55667776554 788889999999999974
No 117
>PRK14720 transcript cleavage factor/unknown domain fusion protein; Provisional
Probab=57.55 E-value=32 Score=31.45 Aligned_cols=74 Identities=14% Similarity=0.053 Sum_probs=50.6
Q ss_pred hhCCCCCCCEEEEEec--cCCcEEEEeccCC-CCCCCeEEEeH-hhhhcccccCCCeEEEEeCCCCCCccEEEEccCC
Q psy3865 26 DELNLFRGDTVLLRGK--RRKESVCIVLSDD-TCPDEKIRMNR-VMRNNLRVRLSDVVSLVPCPGIVYGKRIHVLPID 99 (107)
Q Consensus 26 ~~Lgl~~GD~V~I~Gk--r~~~tvai~~~~~-d~~~~~Irid~-~~R~N~~v~igD~V~V~~~~~~~~a~~V~l~P~~ 99 (107)
..=.+..|-+|+++.. ....+..++.+.+ +...+.|-+.. ..+.=+|-+.||.|+|........-+.+.+.|++
T Consensus 827 ~~d~V~~GS~Vtl~d~d~~ee~ty~IVGp~EaD~~~g~IS~~SPLGkALLGkkvGD~V~v~~P~g~~~yeIl~I~~~~ 904 (906)
T PRK14720 827 KTSKVGFGTKVKLKNEDTGEEESYSILGPWESDPEEGIISYQSPLGKSLLGKKEGDSLEFVINDTETRYTVLKIERAS 904 (906)
T ss_pred CCCEEEeCCEEEEEECCCCCEEEEEEEChhhcCcCCCeECCCCHHHHHHcCCCCCCEEEEEECCceEEEEEEEEEeec
Confidence 3345678999999843 2224677776664 66778877665 7888899999999999853232334556666664
No 118
>PRK01885 greB transcription elongation factor GreB; Reviewed
Probab=56.51 E-value=36 Score=24.32 Aligned_cols=63 Identities=19% Similarity=0.247 Sum_probs=42.9
Q ss_pred CHHHHhhCCCCCCCEEEEEecc-CCcEEEEeccCC-CCCCCeEEEeH-hhhhcccccCCCeEEEEe
Q psy3865 21 ESAKMDELNLFRGDTVLLRGKR-RKESVCIVLSDD-TCPDEKIRMNR-VMRNNLRVRLSDVVSLVP 83 (107)
Q Consensus 21 ~~~~m~~Lgl~~GD~V~I~Gkr-~~~tvai~~~~~-d~~~~~Irid~-~~R~N~~v~igD~V~V~~ 83 (107)
++..+..=.+.-|-+|+++... ...++-++.+.+ +...+.|.+.. ..|.=+|-+.||.|++..
T Consensus 77 d~~~~~~~~V~~Gs~V~l~d~~~~~~~~~iVgp~e~d~~~~~IS~~SPlG~ALlGk~vGd~v~v~~ 142 (157)
T PRK01885 77 DYSPQQEGKVFFGAWVEIENEDGEEKRFRIVGPDEIDGRKGYISIDSPMARALLKKEVGDEVTVNT 142 (157)
T ss_pred CCCCCCCCEEEeCCEEEEEECCCCEEEEEEEChHHhCcCCCeEeccCHHHHHHhCCCCCCEEEEEc
Confidence 3434444467789999998422 224454665553 66667777655 778889999999999984
No 119
>PRK08493 NADH dehydrogenase subunit G; Validated
Probab=56.33 E-value=16 Score=32.76 Aligned_cols=29 Identities=28% Similarity=0.347 Sum_probs=25.8
Q ss_pred eEEEecCHHHHhhCCCCCCCEEEEEeccC
Q psy3865 15 RGKRRKESAKMDELNLFRGDTVLLRGKRR 43 (107)
Q Consensus 15 rGiari~~~~m~~Lgl~~GD~V~I~Gkr~ 43 (107)
++..++|++.+++|++..||.|+|+-++.
T Consensus 746 ~~~l~~S~~fa~~l~l~~Gd~v~l~~~~~ 774 (819)
T PRK08493 746 KAGLYVSEAFLKKLNLKDGDNVTLKKEEE 774 (819)
T ss_pred ccceEecHHHHHHcCCCCCCEEEEecCCc
Confidence 56689999999999999999999997763
No 120
>PF04246 RseC_MucC: Positive regulator of sigma(E), RseC/MucC; InterPro: IPR007359 This bacterial family of integral membrane proteins represents a positive regulator of the sigma(E) transcription factor, namely RseC/MucC. The sigma(E) transcription factor is up-regulated by cell envelope protein misfolding, and regulates the expression of genes that are collectively termed ECF (devoted to Extra-Cellular Functions) []. In Pseudomonas aeruginosa, derepression of sigma(E) is associated with the alginate-overproducing phenotype characteristic of chronic respiratory tract colonization in cystic fibrosis patients. The mechanism by which RseC/MucC positively regulates the sigma(E) transcription factor is unknown. RseC is also thought to have a role in thiamine biosynthesis in Salmonella typhimurium []. In addition, this family also includes an N-terminal part of RnfF, a Rhodobacter capsulatus protein, of unknown function, that is essential for nitrogen fixation. This protein also contains a domain found in ApbE protein IPR003374 from INTERPRO, which is itself involved in thiamine biosynthesis.
Probab=56.00 E-value=33 Score=23.33 Aligned_cols=48 Identities=21% Similarity=0.314 Sum_probs=29.9
Q ss_pred CCCEEEEEeccCCcEEEEecc-CCCCC---------CCeEEEeHhhhhcccccCCCeEEEEe
Q psy3865 32 RGDTVLLRGKRRKESVCIVLS-DDTCP---------DEKIRMNRVMRNNLRVRLSDVVSLVP 83 (107)
Q Consensus 32 ~GD~V~I~Gkr~~~tvai~~~-~~d~~---------~~~Irid~~~R~N~~v~igD~V~V~~ 83 (107)
.||.+.++-.+. +.|--+. ...|+ .....+ ...++.++..||.|+|.-
T Consensus 5 ~~~~~~V~~~r~--saC~~C~~~~~Cg~~~~~~~~~~~~~~~--~~~~~~~~~~GD~V~v~i 62 (135)
T PF04246_consen 5 EGGIAWVEVQRS--SACGSCSASGGCGTGLLAKLFSGKPITF--RAPNPIGAKVGDRVEVEI 62 (135)
T ss_pred eCCEEEEEEccC--CcCcccCCCCCCCcchhhhhcCCCcEEE--EecCCCCCCCCCEEEEEe
Confidence 467888886553 3343333 34666 122222 337888999999999985
No 121
>PRK11507 ribosome-associated protein; Provisional
Probab=55.90 E-value=10 Score=24.03 Aligned_cols=28 Identities=11% Similarity=0.275 Sum_probs=23.9
Q ss_pred CCCCeEEEeH--hhhhcccccCCCeEEEEe
Q psy3865 56 CPDEKIRMNR--VMRNNLRVRLSDVVSLVP 83 (107)
Q Consensus 56 ~~~~~Irid~--~~R~N~~v~igD~V~V~~ 83 (107)
+..+.|.+|+ .+|+...++.||.|++.-
T Consensus 34 I~eg~V~VNGeve~rRgkKl~~GD~V~~~g 63 (70)
T PRK11507 34 IAEGQVKVDGAVETRKRCKIVAGQTVSFAG 63 (70)
T ss_pred HHcCceEECCEEecccCCCCCCCCEEEECC
Confidence 4568999999 689999999999999863
No 122
>TIGR03243 arg_catab_AOST arginine and ornithine succinyltransferase subunits. In many bacteria, the sole member of this protein family is arginine N-succinyltransferase (EC 2.3.1.109), the AstA protein of the arginine succinyltransferase (ast) pathway. However, in Pseudomonas aeruginosa and several other species, a tandem gene pair encodes alpha and beta subunits of a heterodimer that is designated arginine and ornithine succinyltransferase (AOST).
Probab=54.64 E-value=13 Score=30.12 Aligned_cols=23 Identities=30% Similarity=0.367 Sum_probs=21.0
Q ss_pred EEEecCHHHHhhCCCCCCCEEEE
Q psy3865 16 GKRRKESAKMDELNLFRGDTVLL 38 (107)
Q Consensus 16 Giari~~~~m~~Lgl~~GD~V~I 38 (107)
+.+.++++.++.|++.+||.|.+
T Consensus 310 ~~~~l~~~~a~aL~v~~Gd~Vr~ 332 (335)
T TIGR03243 310 GTLILSADAADALGVSEGDTVRV 332 (335)
T ss_pred CeeecCHHHHHhcCCCCCCeEEE
Confidence 56789999999999999999986
No 123
>PF00717 Peptidase_S24: Peptidase S24-like peptidase classification. ; InterPro: IPR019759 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ].; PDB: 1KCA_H 3BDN_A 1F39_A 1JHH_A 1JHE_B 3JSP_A 1JHF_B 1JHC_A 3JSO_B 1B12_D ....
Probab=54.04 E-value=15 Score=21.52 Aligned_cols=29 Identities=24% Similarity=0.297 Sum_probs=19.4
Q ss_pred cCcccCCeEEEeEEEecCHHHHhhCCCCCCCEEEEEecc
Q psy3865 4 LNLFRGDTVLLRGKRRKESAKMDELNLFRGDTVLLRGKR 42 (107)
Q Consensus 4 ~~~~~~d~~~~rGiari~~~~m~~Lgl~~GD~V~I~Gkr 42 (107)
=.|.+||+|++.-.. .+..||+|.++-..
T Consensus 9 P~i~~Gd~v~v~~~~----------~~~~gdivv~~~~~ 37 (70)
T PF00717_consen 9 PTIKDGDIVLVDPSS----------EPKDGDIVVVKIDG 37 (70)
T ss_dssp GTSSTTEEEEEEETS-------------TTSEEEEEETT
T ss_pred cCeeCCCEEEEEEcC----------CCccCeEEEEEECC
Confidence 457889999887333 77889999998544
No 124
>PRK10456 arginine succinyltransferase; Provisional
Probab=51.16 E-value=16 Score=29.68 Aligned_cols=25 Identities=28% Similarity=0.315 Sum_probs=21.8
Q ss_pred EEEecCHHHHhhCCCCCCCEEEEEe
Q psy3865 16 GKRRKESAKMDELNLFRGDTVLLRG 40 (107)
Q Consensus 16 Giari~~~~m~~Lgl~~GD~V~I~G 40 (107)
+.+.++++.++.|++.+||.|.+-.
T Consensus 312 ~~~~l~~~~a~aL~v~~Gd~Vr~~~ 336 (344)
T PRK10456 312 ERLILTAAQLDALKCHAGDRVRLVR 336 (344)
T ss_pred CeEecCHHHHHhcCCCCCCeEEEEe
Confidence 4568899999999999999998764
No 125
>COG0782 Uncharacterized conserved protein, YhbC family [Function unknown]
Probab=51.01 E-value=32 Score=24.45 Aligned_cols=62 Identities=23% Similarity=0.260 Sum_probs=45.1
Q ss_pred CHHHHhhCCCCCCCEEEEEe--ccCCcEEEEeccCC-CCCCCeEEEeH-hhhhcccccCCCeEEEEe
Q psy3865 21 ESAKMDELNLFRGDTVLLRG--KRRKESVCIVLSDD-TCPDEKIRMNR-VMRNNLRVRLSDVVSLVP 83 (107)
Q Consensus 21 ~~~~m~~Lgl~~GD~V~I~G--kr~~~tvai~~~~~-d~~~~~Irid~-~~R~N~~v~igD~V~V~~ 83 (107)
+++.... .+.-|-+|.++. .....++-++.+.+ +...+.|-++. ..|.=+|-+.||.|.+.-
T Consensus 71 ~~~~~~~-~V~~Gs~V~~~~~~~ge~~~~~iVg~~ead~~~~~IS~~SPig~aLlGk~vGd~v~v~~ 136 (151)
T COG0782 71 DDEKPPD-VVTFGSTVTLENLDDGEEVTYTIVGPDEADPAKGKISVDSPLGRALLGKKVGDTVEVNT 136 (151)
T ss_pred CCCCCCC-EEecCCEEEEEECCCCCEEEEEEEcccccccccCceeccCHHHHHHhCCCCCCEEEEec
Confidence 4445555 788999999992 23335666676654 55667777665 778889999999999984
No 126
>PRK12423 LexA repressor; Provisional
Probab=49.96 E-value=25 Score=25.67 Aligned_cols=21 Identities=19% Similarity=0.275 Sum_probs=16.4
Q ss_pred ecCHHHHhhCCCCCCCEEEEE
Q psy3865 19 RKESAKMDELNLFRGDTVLLR 39 (107)
Q Consensus 19 ri~~~~m~~Lgl~~GD~V~I~ 39 (107)
+++-+.|..-++..||+|.|.
T Consensus 118 ~V~GdSM~~~~i~~Gd~viv~ 138 (202)
T PRK12423 118 QVQGDSMIDDGILDGDLVGVH 138 (202)
T ss_pred EEecCcCCCCCcCCCCEEEEe
Confidence 566677877788888888887
No 127
>COG5140 UFD1 Ubiquitin fusion-degradation protein [Posttranslational modification, protein turnover, chaperones]
Probab=49.86 E-value=1.3e+02 Score=23.99 Aligned_cols=83 Identities=17% Similarity=0.136 Sum_probs=61.6
Q ss_pred EeEEEecCHHHHh---hCCCCCCCEEEEEe---ccCCcEEEEeccCCCCCCCeEEEeHhhhhcccccCCCeEEEEeCCCC
Q psy3865 14 LRGKRRKESAKMD---ELNLFRGDTVLLRG---KRRKESVCIVLSDDTCPDEKIRMNRVMRNNLRVRLSDVVSLVPCPGI 87 (107)
Q Consensus 14 ~rGiari~~~~m~---~Lgl~~GD~V~I~G---kr~~~tvai~~~~~d~~~~~Irid~~~R~N~~v~igD~V~V~~~~~~ 87 (107)
--|++-+.|.++. .|+++.=-+-+|.. -+ .|.+-+.. -.-+.+.+.+..-+-.-|+...||.|.++-. ++
T Consensus 44 fGGKvilPpSaL~kLs~lni~yPmlF~~s~~~~~~--~THgGVLE-FiaEEGrVylP~WMm~tLs~epgdlv~~~~t-d~ 119 (331)
T COG5140 44 FGGKVILPPSALVKLSSLNIQYPMLFEISHSDGIY--RTHGGVLE-FIAEEGRVYLPSWMMQTLSMEPGDLVVLRYT-DF 119 (331)
T ss_pred cCceEEcCHHHHHHHHhhccCCceEEEEeccccee--EecccEEE-EeecCCcEeehHHHHHhccCCCCcEEEEEec-cc
Confidence 4477888886665 56677777777773 23 24444321 1234588999999999999999999999984 99
Q ss_pred CCccEEEEccCCc
Q psy3865 88 VYGKRIHVLPIDD 100 (107)
Q Consensus 88 ~~a~~V~l~P~~d 100 (107)
+-++-|.|.|-+=
T Consensus 120 plG~fVKL~PqSV 132 (331)
T COG5140 120 PLGKFVKLIPQSV 132 (331)
T ss_pred cccceEEeccccc
Confidence 9999999999653
No 128
>COG3127 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=48.63 E-value=17 Score=32.72 Aligned_cols=33 Identities=15% Similarity=0.310 Sum_probs=27.3
Q ss_pred cCCCCCCCeEEEeHhhhhcccccCCCeEEEEeC
Q psy3865 52 SDDTCPDEKIRMNRVMRNNLRVRLSDVVSLVPC 84 (107)
Q Consensus 52 ~~~d~~~~~Irid~~~R~N~~v~igD~V~V~~~ 84 (107)
++++-+.-.+-|....=+|+|+++||+|++.-.
T Consensus 590 ~~~~~g~P~VS~e~~~A~~LglKLGDtvTf~v~ 622 (829)
T COG3127 590 PKNDSGEPEVSMEEGEAKRLGLKLGDTVTFMVL 622 (829)
T ss_pred CCCCCCCCccchhHhHHHHhCCccCCEEEEEec
Confidence 334446668999999999999999999999854
No 129
>TIGR03244 arg_catab_AstA arginine N-succinyltransferase. In many bacteria, the arginine succinyltransferase (ast) pathway operon consists of five genes, including this protein, arginine N-succinyltransferase (EC 2.3.1.109). In a few species, such as Pseudomonas aeruginosa, the member of this family is encoded adjacent to a paralog, and the two polypeptides form a heterodimeric enzyme, active on both arginine and ornithine. In such species, this polypeptide may be treated as the beta subunit of an enzyme that may be named either arginine N-succinyltransferase (AST) or arginine and orthithine N-succinyltransferase (AOST).
Probab=48.18 E-value=19 Score=29.15 Aligned_cols=23 Identities=30% Similarity=0.394 Sum_probs=20.8
Q ss_pred EEEecCHHHHhhCCCCCCCEEEE
Q psy3865 16 GKRRKESAKMDELNLFRGDTVLL 38 (107)
Q Consensus 16 Giari~~~~m~~Lgl~~GD~V~I 38 (107)
+.+.++++.++.|++.+||.|.+
T Consensus 311 ~~~~l~~~~a~aL~v~~Gd~Vr~ 333 (336)
T TIGR03244 311 GELVLTAAQADALRVSAGDLVRI 333 (336)
T ss_pred CeEecCHHHHHhcCCCCCCeEEE
Confidence 55689999999999999999986
No 130
>PF08845 SymE_toxin: Toxin SymE, type I toxin-antitoxin system; InterPro: IPR014944 This entry represents a SOS-induced gene whose product shows homology to the antitoxin MazE (SymE), the coding region contains a cis-encoded antisense RNA. The small antisense RNA and the gene have the all the hallmarks of a toxin-antitoxin module. The synthesis of the SymE is tightly repressed at multiple levels; at the transcriptional level by the LexA repressor, at the level of mRNA stability and translation by the SymR RNA and at the level of protein stability by the Lon protease. SymE co-purifies with ribosomes and overproduction of the protein leads to cell growth inhibition, decreased protein synthesis and increased RNA degradation. These properties are shared with several RNA endonuclease toxins of toxin-antitoxin modules. It seems probable that the SymE protein represents an evolutionary derivative of a toxin containing the AbrB fold, whose representatives are typically antitoxins. The SymE promoted cleavage of RNA cleavage may be important for the recycling of RNAs damaged under SOS-inducing conditions []. ; GO: 0003723 RNA binding, 0016788 hydrolase activity, acting on ester bonds, 0016070 RNA metabolic process, 0005737 cytoplasm
Probab=48.16 E-value=21 Score=21.50 Aligned_cols=27 Identities=22% Similarity=0.209 Sum_probs=21.9
Q ss_pred EEEecCHHHHhhCCCCCCCEEEEEecc
Q psy3865 16 GKRRKESAKMDELNLFRGDTVLLRGKR 42 (107)
Q Consensus 16 Giari~~~~m~~Lgl~~GD~V~I~Gkr 42 (107)
.-.+|+-..++++|+..||-|.|+=..
T Consensus 24 p~i~L~G~WL~~aGF~~G~~v~V~v~~ 50 (57)
T PF08845_consen 24 PEIRLKGKWLEEAGFTIGDPVKVRVMP 50 (57)
T ss_pred ceEEEchhhhHHhCCCCCCEEEEEEEC
Confidence 445677789999999999999998433
No 131
>TIGR03245 arg_AOST_alph arginine/ornithine succinyltransferase, alpha subunit. In some bacteria, including Pseudomonas aeruginosa, the astB gene (arginine N-succinyltransferase) is replaced by tandem paralogs that form a heterodimer. This heterodimer from P. aeruginosa is characterized as arginine and ornithine N-2 succinyltransferase (AOST). Members of this protein family represent the less widespread paralog, designated AruI, or arginine/ornithine succinyltransferase, alpha subunit.
Probab=47.50 E-value=20 Score=29.05 Aligned_cols=24 Identities=21% Similarity=0.264 Sum_probs=21.0
Q ss_pred EEEecCHHHHhhCCCCCCCEEEEE
Q psy3865 16 GKRRKESAKMDELNLFRGDTVLLR 39 (107)
Q Consensus 16 Giari~~~~m~~Lgl~~GD~V~I~ 39 (107)
+.+.++++.++.|++.+||.|.+-
T Consensus 311 ~~~~l~~~~a~aL~v~~Gd~Vr~~ 334 (336)
T TIGR03245 311 DLLRLKRDAAEALGVSEGDNVRFA 334 (336)
T ss_pred CeeecCHHHHHhcCCCCCCeEEEe
Confidence 456899999999999999999863
No 132
>PRK05753 nucleoside diphosphate kinase regulator; Provisional
Probab=47.49 E-value=41 Score=23.42 Aligned_cols=54 Identities=11% Similarity=0.113 Sum_probs=39.4
Q ss_pred CCCCCEEEEEe--ccCCcEEEEeccCC-CCCCCeEEEeH-hhhhcccccCCCeEEEEe
Q psy3865 30 LFRGDTVLLRG--KRRKESVCIVLSDD-TCPDEKIRMNR-VMRNNLRVRLSDVVSLVP 83 (107)
Q Consensus 30 l~~GD~V~I~G--kr~~~tvai~~~~~-d~~~~~Irid~-~~R~N~~v~igD~V~V~~ 83 (107)
+.-|-.|+++. .....++.++.+.+ +...+.|-+.. ..+.=+|.+.||.|.+..
T Consensus 55 V~~Gs~V~~~~~~~~~~~~~~iVg~~Ead~~~~~ISi~SPlG~ALlG~~~Gd~v~v~~ 112 (137)
T PRK05753 55 VTMNSRVRFRDLSSGEERVRTLVYPADADDSEGQLSVLAPVGAALLGLSVGQSIDWPL 112 (137)
T ss_pred EEeCCEEEEEECCCCCEEEEEEEChhHcCccCCcCcccCHHHHHHcCCCCCCEEEEEC
Confidence 56677788873 33346777877654 55567777655 788889999999999984
No 133
>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.
Probab=47.28 E-value=25 Score=21.29 Aligned_cols=27 Identities=19% Similarity=0.373 Sum_probs=19.6
Q ss_pred CCeEEEeHhhhhcccccCCCeEEEEeC
Q psy3865 58 DEKIRMNRVMRNNLRVRLSDVVSLVPC 84 (107)
Q Consensus 58 ~~~Irid~~~R~N~~v~igD~V~V~~~ 84 (107)
.-..+|.+-.|++..+..||.|.|.+-
T Consensus 27 ~~l~~i~gK~r~~iwI~~GD~V~V~~~ 53 (65)
T PF01176_consen 27 ERLARIPGKFRKRIWIKRGDFVLVEPS 53 (65)
T ss_dssp EEEEEE-HHHHTCC---TTEEEEEEES
T ss_pred EEEEEeccceeeeEecCCCCEEEEEec
Confidence 346778899999999999999999974
No 134
>TIGR03327 AMP_phos AMP phosphorylase. This enzyme family is found, so far, strictly in the Archaea, and only in those with a type III Rubisco enzyme. Most of the members previously were annotated as thymidine phosphorylase, or DeoA. The AMP metabolized by this enzyme may be produced by ADP-dependent sugar kinases.
Probab=47.25 E-value=33 Score=29.26 Aligned_cols=39 Identities=23% Similarity=0.369 Sum_probs=30.2
Q ss_pred cccCcccCCeEEEeE-------------------EEecCHHHHhhCCCCCCCEEEEEe
Q psy3865 2 DELNLFRGDTVLLRG-------------------KRRKESAKMDELNLFRGDTVLLRG 40 (107)
Q Consensus 2 ~~~~~~~~d~~~~rG-------------------iari~~~~m~~Lgl~~GD~V~I~G 40 (107)
.++|+..+|-|.|+. -+-++....++|++.+||.|.|.-
T Consensus 24 ~~~g~~~~~rv~v~~~~~~~~a~~~~~~~~~~~g~~gls~~~~~~l~~~~g~~v~v~~ 81 (500)
T TIGR03327 24 KELGVHPGDRVRIESGGKSVVGIVDSTDTLVEKGEIGLSHEVLEELGISEGEVVEVTP 81 (500)
T ss_pred hhhCCCCCCeEEEEeCCEEEEEEEEcccccccCCeeeccHHHHHHcCCCCCCEEEEec
Confidence 456788888887763 333456888999999999999984
No 135
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=46.90 E-value=15 Score=23.49 Aligned_cols=26 Identities=23% Similarity=0.420 Sum_probs=22.4
Q ss_pred CCCeEEEeH--hhhhcccccCCCeEEEE
Q psy3865 57 PDEKIRMNR--VMRNNLRVRLSDVVSLV 82 (107)
Q Consensus 57 ~~~~Irid~--~~R~N~~v~igD~V~V~ 82 (107)
..+.|.+|+ .+|++..++.||.|.+.
T Consensus 35 ~eg~V~vNGe~EtRRgkKlr~gd~V~i~ 62 (73)
T COG2501 35 AEGEVKVNGEVETRRGKKLRDGDVVEIP 62 (73)
T ss_pred HCCeEEECCeeeeccCCEeecCCEEEEC
Confidence 357888888 68999999999999886
No 136
>PF01982 CTP-dep_RFKase: Domain of unknown function DUF120; InterPro: IPR023602 Riboflavin is converted into catalytically active cofactors (FAD and FMN) by the actions of riboflavin kinase (2.7.1.26 from EC), which converts it into FMN, and FAD synthetase (2.7.7.2 from EC), which adenylates FMN to FAD. Eukaryotes usually have two separate enzymes, while most prokaryotes have a single bifunctional protein that can carry out both catalyses, although exceptions occur in both cases. While eukaryotic monofunctional riboflavin kinase is orthologous to the bifunctional prokaryotic enzyme [], the monofunctional FAD synthetase differs from its prokaryotic counterpart, and is instead related to the PAPS-reductase family []. The bacterial FAD synthetase that is part of the bifunctional enzyme has remote similarity to nucleotidyl transferases and, hence, it may be involved in the adenylylation reaction of FAD synthetases []. This entry represents a CTP-dependent riboflavin kinase domain, found primarily in archaea, that catalyses the phosphorylation of riboflavin to form flavin mononucleotide in riboflavin biosynthesis. Its structure resembles a RIFT barrel, structurally similar to but topologically distinct from bacterial and eukaryotic examples []. The N-terminal is a winged helix-turn-helix DNA-binding domain, and the C-terminal half is most similar in sequence to a group of cradle-loop barrels.; GO: 0016773 phosphotransferase activity, alcohol group as acceptor; PDB: 2VBV_A 2VBU_A 2VBS_A 2VBT_A 2P3M_A 2OYN_A 3CTA_A.
Probab=46.80 E-value=16 Score=25.44 Aligned_cols=17 Identities=35% Similarity=0.378 Sum_probs=10.5
Q ss_pred HHHhhCCCCCCCEEEEE
Q psy3865 23 AKMDELNLFRGDTVLLR 39 (107)
Q Consensus 23 ~~m~~Lgl~~GD~V~I~ 39 (107)
.-++.|++..||.|+|+
T Consensus 104 ~LR~~L~L~DGD~V~v~ 120 (121)
T PF01982_consen 104 KLRDTLGLKDGDEVEVE 120 (121)
T ss_dssp -HHHHTT--TT-EEEEE
T ss_pred chHhhcCCCCCCEEEEE
Confidence 44567999999999985
No 137
>PRK09555 feoA ferrous iron transport protein A; Reviewed
Probab=46.53 E-value=66 Score=20.06 Aligned_cols=38 Identities=16% Similarity=0.211 Sum_probs=29.7
Q ss_pred cCcccCCeEEEeEEEe-cCH---HHHhhCCCCCCCEEEEEec
Q psy3865 4 LNLFRGDTVLLRGKRR-KES---AKMDELNLFRGDTVLLRGK 41 (107)
Q Consensus 4 ~~~~~~d~~~~rGiar-i~~---~~m~~Lgl~~GD~V~I~Gk 41 (107)
++|-.|+...|.++.- .++ ..+-.||+.+|..|.+..+
T Consensus 1 ~~l~~G~~~~I~~~~~~~~~~~~~rL~~mGl~pG~~V~v~~~ 42 (74)
T PRK09555 1 MQLTPDTAYKITGFSREISPAYRQKLLSLGMLPGSSFNVVRV 42 (74)
T ss_pred CCCCCCCEEEEEEEccCCChHHHHHHHHcCCCCCCEEEEEEE
Confidence 4677899999999943 333 6667999999999999753
No 138
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=46.48 E-value=33 Score=24.66 Aligned_cols=21 Identities=19% Similarity=0.403 Sum_probs=15.1
Q ss_pred ecCHHHHhhCCCCCCCEEEEE
Q psy3865 19 RKESAKMDELNLFRGDTVLLR 39 (107)
Q Consensus 19 ri~~~~m~~Lgl~~GD~V~I~ 39 (107)
+++-+.|...++..||+|.+.
T Consensus 115 ~V~GdSM~~~~i~~Gd~v~v~ 135 (199)
T TIGR00498 115 KVMGDSMVDAGICDGDLLIVR 135 (199)
T ss_pred EecCCCCCCCCCCCCCEEEEe
Confidence 455567777777888888776
No 139
>COG0186 RpsQ Ribosomal protein S17 [Translation, ribosomal structure and biogenesis]
Probab=46.22 E-value=32 Score=22.70 Aligned_cols=29 Identities=17% Similarity=0.256 Sum_probs=21.1
Q ss_pred hcccccCCCeEEEEeCCCCCCccEEEEcc
Q psy3865 69 NNLRVRLSDVVSLVPCPGIVYGKRIHVLP 97 (107)
Q Consensus 69 ~N~~v~igD~V~V~~~~~~~~a~~V~l~P 97 (107)
.|..+++||.|+|..+..+..-++-.|..
T Consensus 52 e~~~~k~GD~V~I~EtRPLSKtK~~~vv~ 80 (87)
T COG0186 52 ECNEAKVGDIVRIAETRPLSKTKRFVVVE 80 (87)
T ss_pred ccccCCCCCEEEEEEccccCCcceEEEEE
Confidence 56779999999999886555555555543
No 140
>TIGR01462 greA transcription elongation factor GreA. In the Chlamydias and some spirochetes, the region described by this model is found as the C-terminal region of a much larger protein.
Probab=43.88 E-value=1.1e+02 Score=21.37 Aligned_cols=55 Identities=22% Similarity=0.230 Sum_probs=39.2
Q ss_pred CCCCCCEEEEEecc--CCcEEEEeccCC-CCCCCeEEEe-HhhhhcccccCCCeEEEEe
Q psy3865 29 NLFRGDTVLLRGKR--RKESVCIVLSDD-TCPDEKIRMN-RVMRNNLRVRLSDVVSLVP 83 (107)
Q Consensus 29 gl~~GD~V~I~Gkr--~~~tvai~~~~~-d~~~~~Irid-~~~R~N~~v~igD~V~V~~ 83 (107)
.+..|-.|.++... ...++.++.+.+ +...+.|-+. -..|.=+|-+.||.|.+..
T Consensus 80 ~V~~Gs~V~l~~~~~g~~~~~~lVgp~e~d~~~~~IS~~SPlG~ALlG~~~Gd~v~v~~ 138 (151)
T TIGR01462 80 VVGFGSTVTIKDLDTGEEETYTIVGSWEADPKEGKISIDSPLGKALIGKKVGDVVEVQT 138 (151)
T ss_pred EEeeCCEEEEEECCCCCEEEEEEECchhcCccCCeecCCCHHHHHHcCCCCCCEEEEEe
Confidence 56678889998542 225676776654 5555666654 4788889999999999985
No 141
>PRK09570 rpoH DNA-directed RNA polymerase subunit H; Reviewed
Probab=43.77 E-value=22 Score=22.99 Aligned_cols=19 Identities=16% Similarity=0.235 Sum_probs=15.3
Q ss_pred HHhhCCCCCCCEEEEEecc
Q psy3865 24 KMDELNLFRGDTVLLRGKR 42 (107)
Q Consensus 24 ~m~~Lgl~~GD~V~I~Gkr 42 (107)
..+.+|+.+||+|.|.-+.
T Consensus 46 v~r~~g~k~GdVvkI~R~S 64 (79)
T PRK09570 46 VVKAIGAKPGDVIKIVRKS 64 (79)
T ss_pred hhhhcCCCCCCEEEEEECC
Confidence 4457899999999997553
No 142
>PF14250 AbrB-like: AbrB-like transcriptional regulator
Probab=43.73 E-value=21 Score=22.69 Aligned_cols=22 Identities=27% Similarity=0.490 Sum_probs=17.7
Q ss_pred CHHHHhhCCCCCCCEEEEE-ecc
Q psy3865 21 ESAKMDELNLFRGDTVLLR-GKR 42 (107)
Q Consensus 21 ~~~~m~~Lgl~~GD~V~I~-Gkr 42 (107)
...--++|++.|||--+|+ |++
T Consensus 44 G~AYT~~m~L~PGdEFeI~LgrK 66 (71)
T PF14250_consen 44 GSAYTKQMGLKPGDEFEIKLGRK 66 (71)
T ss_pred cHHHHHHhCCCCCCEEEEEeCcc
Confidence 3455689999999999999 554
No 143
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=43.38 E-value=19 Score=23.19 Aligned_cols=16 Identities=31% Similarity=0.515 Sum_probs=13.2
Q ss_pred hCCCCCCCEEEEEecc
Q psy3865 27 ELNLFRGDTVLLRGKR 42 (107)
Q Consensus 27 ~Lgl~~GD~V~I~Gkr 42 (107)
-|.+.+||+|.++...
T Consensus 3 FL~Vk~Gd~ViV~~~~ 18 (75)
T PF11302_consen 3 FLSVKPGDTVIVQDEQ 18 (75)
T ss_pred ccccCCCCEEEEecCc
Confidence 3788999999998755
No 144
>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=42.35 E-value=41 Score=21.40 Aligned_cols=20 Identities=25% Similarity=0.150 Sum_probs=14.4
Q ss_pred HHHhhCCCCCCCEEEEEecc
Q psy3865 23 AKMDELNLFRGDTVLLRGKR 42 (107)
Q Consensus 23 ~~m~~Lgl~~GD~V~I~Gkr 42 (107)
-..+.||+.+||+|.|.-+.
T Consensus 42 Pv~r~~g~k~GdVvkI~R~S 61 (74)
T PF01191_consen 42 PVARYLGAKPGDVVKIIRKS 61 (74)
T ss_dssp HHHHHTT--TTSEEEEEEEE
T ss_pred hhhhhcCCCCCCEEEEEecC
Confidence 35568999999999998654
No 145
>PRK04183 glutamyl-tRNA(Gln) amidotransferase subunit D; Validated
Probab=41.96 E-value=79 Score=26.23 Aligned_cols=54 Identities=15% Similarity=0.175 Sum_probs=37.6
Q ss_pred CCCCCCCEEEEEeccCCcEEEEeccCCCCCCCeEEEeHhhhhcccccCCCeEEEEeC
Q psy3865 28 LNLFRGDTVLLRGKRRKESVCIVLSDDTCPDEKIRMNRVMRNNLRVRLSDVVSLVPC 84 (107)
Q Consensus 28 Lgl~~GD~V~I~Gkr~~~tvai~~~~~d~~~~~Irid~~~R~N~~v~igD~V~V~~~ 84 (107)
+++..||.|+|+-+.. .--.+++|..+ .++|.|.=.-.-|+|+.+++...++.+
T Consensus 1 ~~~~~gd~v~~~~~~~-~~~g~~~p~~~--~~~~~~kl~~gyn~g~~~~~~~~~~~~ 54 (419)
T PRK04183 1 LGMEVGDRVRVEKDDV-VYEGILMPSYE--DDHIVIKLDNGYNIGIDIDKIAEIELL 54 (419)
T ss_pred CCCCCCCEEEEEECCe-EEEEEEecCCC--CCEEEEEcCCCceeeeccccccceEEc
Confidence 3678899999985431 22233455444 678888888889999999996666654
No 146
>PRK14132 riboflavin kinase; Provisional
Probab=41.50 E-value=24 Score=24.74 Aligned_cols=17 Identities=35% Similarity=0.276 Sum_probs=13.8
Q ss_pred HHHhhCCCCCCCEEEEE
Q psy3865 23 AKMDELNLFRGDTVLLR 39 (107)
Q Consensus 23 ~~m~~Lgl~~GD~V~I~ 39 (107)
.-++.|++..||.|+|+
T Consensus 109 ~LR~~L~LkDGD~V~I~ 125 (126)
T PRK14132 109 KLRKFLNLKDGDVVKIV 125 (126)
T ss_pred chHhhcCCCCCCEEEEE
Confidence 34557999999999985
No 147
>COG4869 PduL Propanediol utilization protein [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=40.97 E-value=48 Score=24.87 Aligned_cols=36 Identities=19% Similarity=0.297 Sum_probs=26.9
Q ss_pred ccCcccCCeEEEeEEEecCHHHHhhCCCCCCCEEEEE
Q psy3865 3 ELNLFRGDTVLLRGKRRKESAKMDELNLFRGDTVLLR 39 (107)
Q Consensus 3 ~~~~~~~d~~~~rGiari~~~~m~~Lgl~~GD~V~I~ 39 (107)
||.|-.|=. .-|-...|+|++.+.+|+..||.|.+.
T Consensus 127 ~l~l~kGvI-vAkRHIHm~p~dA~~~~Vkq~diVsV~ 162 (210)
T COG4869 127 ELQLPKGVI-VAKRHIHMTPEDAAKYGVKQGDIVSVK 162 (210)
T ss_pred eEecccceE-EEeeeccCCHHHHHHhCcccCcEEEEE
Confidence 344444433 345556789999999999999999987
No 148
>PF04023 FeoA: FeoA domain; InterPro: IPR007167 This entry represents the core domain of the ferrous iron (Fe2+) transport protein FeoA found in bacteria. This domain also occurs at the C terminus in related proteins. The transporter Feo is composed of three proteins: FeoA a small, soluble SH3-domain protein probably located in the cytosol; FeoB, a large protein with a cytosolic N-terminal G-protein domain and a C-terminal integral inner-membrane domain containing two 'Gate' motifs which likely functions as the Fe2+ permease; and FeoC, a small protein apparently functioning as an [Fe-S]-dependent transcriptional repressor [, ]. Feo allows the bacterial cell to acquire iron from its environment. ; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 1G3T_A 1C0W_B 1BI3_A 1QVP_A 1BI1_A 1BYM_A 2QQB_A ....
Probab=39.78 E-value=51 Score=19.63 Aligned_cols=37 Identities=16% Similarity=0.287 Sum_probs=27.4
Q ss_pred CcccCCeEEEeEEEecCH---HHHhhCCCCCCCEEEEEec
Q psy3865 5 NLFRGDTVLLRGKRRKES---AKMDELNLFRGDTVLLRGK 41 (107)
Q Consensus 5 ~~~~~d~~~~rGiari~~---~~m~~Lgl~~GD~V~I~Gk 41 (107)
++=.|+.+.|..+.-=++ ..+.+||+.+|..|.+..+
T Consensus 5 ~~~~g~~~~I~~i~~~d~~~~~~L~~lGl~~G~~i~v~~~ 44 (74)
T PF04023_consen 5 ELPPGERARIVRISDEDPELLRRLADLGLTPGSEITVIRK 44 (74)
T ss_dssp GSSTTEEEEEEEESTSSHHHHHHHHHCT-STTEEEEEEEE
T ss_pred HCCCCCEEEEEEEECCCHHHHHHHHHCCCCCCCEEEEEEe
Confidence 345688888887774345 5566999999999999864
No 149
>COG2012 RPB5 DNA-directed RNA polymerase, subunit H, RpoH/RPB5 [Transcription]
Probab=39.45 E-value=46 Score=21.65 Aligned_cols=20 Identities=25% Similarity=0.195 Sum_probs=15.6
Q ss_pred HHhhCCCCCCCEEEEEeccC
Q psy3865 24 KMDELNLFRGDTVLLRGKRR 43 (107)
Q Consensus 24 ~m~~Lgl~~GD~V~I~Gkr~ 43 (107)
....||..+||+|+|.-+..
T Consensus 49 va~~lgak~GdvVkIvRkS~ 68 (80)
T COG2012 49 VAKALGAKPGDVVKIVRKSP 68 (80)
T ss_pred hHHHccCCCCcEEEEEecCC
Confidence 45689999999999976543
No 150
>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=39.18 E-value=41 Score=19.89 Aligned_cols=34 Identities=18% Similarity=0.212 Sum_probs=20.4
Q ss_pred cCcccCCe---EEEeEEEecCHHHHhhCCCCCCCEEEEE
Q psy3865 4 LNLFRGDT---VLLRGKRRKESAKMDELNLFRGDTVLLR 39 (107)
Q Consensus 4 ~~~~~~d~---~~~rGiari~~~~m~~Lgl~~GD~V~I~ 39 (107)
|+++-|.. +.|..+..=+ .+.+.|+.+||.+.=-
T Consensus 3 ~~~~~g~~~~~~~V~~v~~~s--~a~~~gl~~GD~I~~i 39 (79)
T cd00989 3 LGFVPGGPPIEPVIGEVVPGS--PAAKAGLKAGDRILAI 39 (79)
T ss_pred eeEeccCCccCcEEEeECCCC--HHHHcCCCCCCEEEEE
Confidence 44445533 5555443323 3567899999988644
No 151
>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=39.08 E-value=23 Score=20.75 Aligned_cols=25 Identities=12% Similarity=0.332 Sum_probs=19.6
Q ss_pred CCCeEEEeHhhh--hcccccCCCeEEE
Q psy3865 57 PDEKIRMNRVMR--NNLRVRLSDVVSL 81 (107)
Q Consensus 57 ~~~~Irid~~~R--~N~~v~igD~V~V 81 (107)
..+.|.+|+... .|..+..||.|+|
T Consensus 32 ~~G~V~VNg~~~~~~~~~l~~Gd~v~i 58 (59)
T TIGR02988 32 QENEVLVNGELENRRGKKLYPGDVIEI 58 (59)
T ss_pred HcCCEEECCEEccCCCCCCCCCCEEEe
Confidence 567888888653 4889999999876
No 152
>PF05899 Cupin_3: Protein of unknown function (DUF861); InterPro: IPR008579 The function of the proteins in this entry are unknown. They contain the conserved barrel domain of the 'cupin' superfamily and members are specific to plants and bacteria.; PDB: 1RC6_A 3MYX_A 1O5U_A 2K9Z_A 1LKN_A 3ES4_A 1SFN_B 3BCW_A.
Probab=38.84 E-value=10 Score=23.48 Aligned_cols=28 Identities=18% Similarity=0.312 Sum_probs=24.5
Q ss_pred EEEeEEEecCHHHHhhCCCCCCCEEEEE
Q psy3865 12 VLLRGKRRKESAKMDELNLFRGDTVLLR 39 (107)
Q Consensus 12 ~~~rGiari~~~~m~~Lgl~~GD~V~I~ 39 (107)
..|.|.+++..+.=+...+.+||.+.+.
T Consensus 30 ~vleG~v~it~~~G~~~~~~aGD~~~~p 57 (74)
T PF05899_consen 30 YVLEGEVTITDEDGETVTFKAGDAFFLP 57 (74)
T ss_dssp EEEEEEEEEEETTTEEEEEETTEEEEE-
T ss_pred EEEEeEEEEEECCCCEEEEcCCcEEEEC
Confidence 5789999999988888999999999986
No 153
>PRK00226 greA transcription elongation factor GreA; Reviewed
Probab=38.33 E-value=1.1e+02 Score=21.41 Aligned_cols=62 Identities=24% Similarity=0.305 Sum_probs=41.6
Q ss_pred HHHHhhCCCCCCCEEEEEecc--CCcEEEEeccCC-CCCCCeEEEeH-hhhhcccccCCCeEEEEe
Q psy3865 22 SAKMDELNLFRGDTVLLRGKR--RKESVCIVLSDD-TCPDEKIRMNR-VMRNNLRVRLSDVVSLVP 83 (107)
Q Consensus 22 ~~~m~~Lgl~~GD~V~I~Gkr--~~~tvai~~~~~-d~~~~~Irid~-~~R~N~~v~igD~V~V~~ 83 (107)
+..+..=.+..|-.|.++... ...++-++.+.+ +...+.|-+.. ..+.=+|-+.||.|.+..
T Consensus 78 ~~~~~~~~V~~Gs~V~l~~~~~~~~~~~~lvg~~e~d~~~~~IS~~SPlG~aLlGk~~Gd~v~~~~ 143 (157)
T PRK00226 78 PSKLSGGKVKFGSTVTLKDLDTDEEETYQIVGSDEADPKQGKISIESPIARALIGKKVGDTVEVTT 143 (157)
T ss_pred cccCCCCEEecCCEEEEEECCCCCEEEEEEEChhhcCccCCeeccCChHHHHHhCCCCCCEEEEEc
Confidence 333334456779999997422 234566665543 55566766554 778889999999999985
No 154
>smart00532 LIGANc Ligase N family.
Probab=37.92 E-value=32 Score=28.65 Aligned_cols=18 Identities=33% Similarity=0.606 Sum_probs=17.0
Q ss_pred HHHHhhCCCCCCCEEEEE
Q psy3865 22 SAKMDELNLFRGDTVLLR 39 (107)
Q Consensus 22 ~~~m~~Lgl~~GD~V~I~ 39 (107)
.+.+++++|..||+|.|+
T Consensus 355 ~~~i~~~~i~iGd~V~V~ 372 (441)
T smart00532 355 EDEIEEKDIRIGDTVVVR 372 (441)
T ss_pred HHHHHHcCCCCCCEEEEE
Confidence 589999999999999998
No 155
>PF08206 OB_RNB: Ribonuclease B OB domain; InterPro: IPR013223 This domain includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.; PDB: 2ID0_D 2IX1_A 2IX0_A.
Probab=37.63 E-value=41 Score=19.79 Aligned_cols=19 Identities=26% Similarity=0.450 Sum_probs=11.5
Q ss_pred ecCHHHHhhCCCCCCCEEEEE
Q psy3865 19 RKESAKMDELNLFRGDTVLLR 39 (107)
Q Consensus 19 ri~~~~m~~Lgl~~GD~V~I~ 39 (107)
.|+++.|+ +...||.|+++
T Consensus 23 fIp~~~l~--~A~~gD~V~v~ 41 (58)
T PF08206_consen 23 FIPPRNLN--GAMDGDKVLVR 41 (58)
T ss_dssp EE-HHHHT--TS-TT-EEEEE
T ss_pred EECHHHHC--CCCCCCEEEEE
Confidence 34555554 89999999986
No 156
>cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.
Probab=37.46 E-value=96 Score=18.85 Aligned_cols=37 Identities=16% Similarity=0.182 Sum_probs=24.5
Q ss_pred CCeEEEeHhhhhcccccCCCeEEEEeCCCCCCccEEEEccC
Q psy3865 58 DEKIRMNRVMRNNLRVRLSDVVSLVPCPGIVYGKRIHVLPI 98 (107)
Q Consensus 58 ~~~Irid~~~R~N~~v~igD~V~V~~~~~~~~a~~V~l~P~ 98 (107)
.+.+.++.. +-..++||.++++-. .+....++.++|.
T Consensus 41 ~Glv~~se~---~~~~~iGd~v~v~I~-~i~e~~~i~l~~~ 77 (77)
T cd04473 41 RGLIHRSNL---LRDYEVGDEVIVQVT-DIPENGNIDLIPV 77 (77)
T ss_pred EEEEEchhc---cCcCCCCCEEEEEEE-EECCCCcEEEEEC
Confidence 344444443 234899999999964 5555678888774
No 157
>TIGR02645 ARCH_P_rylase putative thymidine phosphorylase. Members of this family are closely related to characterized examples of thymidine phosphorylase (EC 2.4.2.4) and pyrimidine nucleoside phosphorylase (RC 2.4.2.2). Most examples are found in the archaea, but other examples in Legionella pneumophila str. Paris and Rhodopseudomonas palustris CGA009.
Probab=36.98 E-value=58 Score=27.79 Aligned_cols=39 Identities=18% Similarity=0.188 Sum_probs=29.2
Q ss_pred cccCcccCCeEEEe-------------------EEEecCHHHHhhCCCCCCCEEEEEe
Q psy3865 2 DELNLFRGDTVLLR-------------------GKRRKESAKMDELNLFRGDTVLLRG 40 (107)
Q Consensus 2 ~~~~~~~~d~~~~r-------------------Giari~~~~m~~Lgl~~GD~V~I~G 40 (107)
.++|+..+|-|.|+ |-+-++....++|++.+||.|.|.-
T Consensus 23 ~~~g~~~~~rv~v~~~~~~~~a~~~~~~~~~~~~~~gl~~~~~~~l~~~~g~~v~v~~ 80 (493)
T TIGR02645 23 RAEGFTPQDRVEVRIGGKSLIAILVGSDTLVEMGEIGLSVSAVETFMAREGDIVTVTP 80 (493)
T ss_pred hhcCCCcCCeEEEEeCCEEEEEEEecccccccCCeeeccHHHHHHcCCCCCCEEEEec
Confidence 45677777777766 3333455888999999999999984
No 158
>COG1153 FwdD Formylmethanofuran dehydrogenase subunit D [Energy production and conversion]
Probab=36.87 E-value=80 Score=22.21 Aligned_cols=39 Identities=18% Similarity=0.120 Sum_probs=29.9
Q ss_pred CCeEEEeHhhhhcccccCCCeEEEEeCCCCCCccEEEEccCCc
Q psy3865 58 DEKIRMNRVMRNNLRVRLSDVVSLVPCPGIVYGKRIHVLPIDD 100 (107)
Q Consensus 58 ~~~Irid~~~R~N~~v~igD~V~V~~~~~~~~a~~V~l~P~~d 100 (107)
-.++.||-.--+-||+.-||.|+|.. .+++.|+.+--+|
T Consensus 30 ~a~~~inp~D~~~Lgv~EGD~VkVks----e~GeVVV~Ak~~~ 68 (128)
T COG1153 30 CAVCEINPEDMKQLGVSEGDKVKVKS----EFGEVVVKAKEAD 68 (128)
T ss_pred eeEEEECHHHHHHhCCCcCCeEEEEe----cCccEEEEEeeCC
Confidence 37889999999999999999999986 2555555554443
No 159
>PLN00208 translation initiation factor (eIF); Provisional
Probab=36.75 E-value=26 Score=25.13 Aligned_cols=27 Identities=11% Similarity=0.200 Sum_probs=23.7
Q ss_pred CCCeEEEeHhhhhcccccCCCeEEEEe
Q psy3865 57 PDEKIRMNRVMRNNLRVRLSDVVSLVP 83 (107)
Q Consensus 57 ~~~~Irid~~~R~N~~v~igD~V~V~~ 83 (107)
..-..+|.+-+|+++.+..||.|.|..
T Consensus 55 ~~rLa~IpGKmRKrIWI~~GD~VlVel 81 (145)
T PLN00208 55 TKRLCHIRGKMRKKVWIAAGDIILVGL 81 (145)
T ss_pred CEEEEEEeccceeeEEecCCCEEEEEc
Confidence 345678999999999999999999985
No 160
>cd06462 Peptidase_S24_S26 The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The S26 type I signal peptidase (SPase) family also includes mitochondrial inner membrane protease (IMP)-like members. SPases are essential membrane-bound proteases which function to cleave away the amino-terminal signal peptide from the translocated pre-protein, thus playing a crucial role in the tr
Probab=36.37 E-value=55 Score=19.36 Aligned_cols=25 Identities=36% Similarity=0.497 Sum_probs=13.1
Q ss_pred cccCCeEEEeEEEecCHHHHhhCCCCCCCEEEEE
Q psy3865 6 LFRGDTVLLRGKRRKESAKMDELNLFRGDTVLLR 39 (107)
Q Consensus 6 ~~~~d~~~~rGiari~~~~m~~Lgl~~GD~V~I~ 39 (107)
|.+||.+.+..... .+..||++.++
T Consensus 14 i~~gd~v~i~~~~~---------~~~~G~iv~~~ 38 (84)
T cd06462 14 IPDGDLVLVDKSSY---------EPKRGDIVVFR 38 (84)
T ss_pred ccCCCEEEEEecCC---------CCcCCEEEEEE
Confidence 45566666553222 45556666655
No 161
>KOG0730|consensus
Probab=36.37 E-value=15 Score=32.41 Aligned_cols=37 Identities=43% Similarity=0.657 Sum_probs=31.2
Q ss_pred CcccCcccCCeEEEeEEEecCH------------------HHHhhCCCCCCCEEEEE
Q psy3865 1 MDELNLFRGDTVLLRGKRRKES------------------AKMDELNLFRGDTVLLR 39 (107)
Q Consensus 1 ~~~~~~~~~d~~~~rGiari~~------------------~~m~~Lgl~~GD~V~I~ 39 (107)
|+++++|+| |.+.|.-|.++ ....+|.++.|+++.+.
T Consensus 37 ~~~~~l~~g--~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~r~~l~~~~~~~~~~~ 91 (693)
T KOG0730|consen 37 MDKLGLLRG--VLLDGKKRREPVDAVVQDETSELIGRQTMVSRSNLRLQLGRLLHSS 91 (693)
T ss_pred HhhhcCCcc--eEEECccccCCccceeccCCccccchhhheeccchhhcccceeccc
Confidence 689999999 99999987766 44458889999999988
No 162
>TIGR03243 arg_catab_AOST arginine and ornithine succinyltransferase subunits. In many bacteria, the sole member of this protein family is arginine N-succinyltransferase (EC 2.3.1.109), the AstA protein of the arginine succinyltransferase (ast) pathway. However, in Pseudomonas aeruginosa and several other species, a tandem gene pair encodes alpha and beta subunits of a heterodimer that is designated arginine and ornithine succinyltransferase (AOST).
Probab=36.07 E-value=2.2e+02 Score=23.13 Aligned_cols=29 Identities=21% Similarity=0.300 Sum_probs=25.1
Q ss_pred CCCCCeEEEeHhhhhcccccCCCeEEEEe
Q psy3865 55 TCPDEKIRMNRVMRNNLRVRLSDVVSLVP 83 (107)
Q Consensus 55 d~~~~~Irid~~~R~N~~v~igD~V~V~~ 83 (107)
.+..+.+.++..+...|++..||.|.+-+
T Consensus 306 ~~~~~~~~l~~~~a~aL~v~~Gd~Vr~~~ 334 (335)
T TIGR03243 306 SADAGTLILSADAADALGVSEGDTVRVVP 334 (335)
T ss_pred cCCCCeeecCHHHHHhcCCCCCCeEEEee
Confidence 44668899999999999999999998754
No 163
>TIGR00156 conserved hypothetical protein TIGR00156. As of the last revision, this family consists only of two proteins from Escherichia coli and one from the related species Haemophilus influenzae.
Probab=35.76 E-value=44 Score=23.36 Aligned_cols=24 Identities=17% Similarity=0.076 Sum_probs=20.3
Q ss_pred EecCHHHHhhCCCCCCCEEEEEec
Q psy3865 18 RRKESAKMDELNLFRGDTVLLRGK 41 (107)
Q Consensus 18 ari~~~~m~~Lgl~~GD~V~I~Gk 41 (107)
+-|+.+..+-+.+.++|.|+|.|+
T Consensus 86 VeId~~~w~G~~v~p~d~V~I~Ge 109 (126)
T TIGR00156 86 VVIPAAVWNGREVQPKDMVNISGS 109 (126)
T ss_pred EEECHHHcCCCcCCCCCEEEEEEE
Confidence 456778888899999999999996
No 164
>PRK05610 rpsQ 30S ribosomal protein S17; Reviewed
Probab=35.28 E-value=70 Score=20.70 Aligned_cols=24 Identities=21% Similarity=0.358 Sum_probs=16.6
Q ss_pred cccCCCeEEEEeCCCCCCccEEEE
Q psy3865 72 RVRLSDVVSLVPCPGIVYGKRIHV 95 (107)
Q Consensus 72 ~v~igD~V~V~~~~~~~~a~~V~l 95 (107)
.+.+||.|.|..+..+...++-.|
T Consensus 53 ~~k~GD~V~I~e~rPlSK~K~~~v 76 (84)
T PRK05610 53 EAKIGDVVRIMETRPLSKTKRWRL 76 (84)
T ss_pred CCCCCCEEEEEEcccCCCCEEEEE
Confidence 489999999998754444444333
No 165
>PF04958 AstA: Arginine N-succinyltransferase beta subunit; InterPro: IPR007041 Arginine N-succinyltransferase catalyses the transfer of succinyl-CoA to arginine to produce succinylarginine. This is the first step in arginine catabolism via the arginine succinyltransferase pathway. Six major L-arginine-degrading pathways have been described for prokaryotes []. Many bacteria arginine succinyltransferase 2.3.1.109 from EC, which is the AstA protein of the succinyltransferase (ast) pathway operon consists of five genes. In a few species, such as Pseudomonas aeruginosa, a tandem gene pair encodes alpha and beta subunits of a heterodimer that is designated arginine and ornithine succinyltransferase (AOST). This entry represents the family of proteins that make up the beta subunit of the heterodimer of Ast and AOST.; GO: 0008791 arginine N-succinyltransferase activity, 0006527 arginine catabolic process; PDB: 1YLE_A.
Probab=35.01 E-value=26 Score=28.43 Aligned_cols=23 Identities=22% Similarity=0.244 Sum_probs=16.0
Q ss_pred EEEecCHHHHhhCCCCCCCEEEE
Q psy3865 16 GKRRKESAKMDELNLFRGDTVLL 38 (107)
Q Consensus 16 Giari~~~~m~~Lgl~~GD~V~I 38 (107)
+-+.++++.++.|++.+||.|.+
T Consensus 317 ~~~~l~~~~a~~L~v~~Gd~Vr~ 339 (342)
T PF04958_consen 317 DQLVLSPEVADALQVSEGDPVRV 339 (342)
T ss_dssp S-EEE-HHHHHHHT--TT-EEEE
T ss_pred CeEEcCHHHHhhcCCCCCCEEEE
Confidence 56778999999999999999976
No 166
>TIGR03635 S17_bact 30S ribosomal protein S17. This model describes the bacterial ribosomal small subunit protein S17, while excluding cytosolic eukaryotic homologs and archaeal homologs. The model finds many, but not, chloroplast and mitochondrial counterparts to bacterial S17.
Probab=34.78 E-value=58 Score=20.36 Aligned_cols=13 Identities=23% Similarity=0.552 Sum_probs=11.7
Q ss_pred cccCCCeEEEEeC
Q psy3865 72 RVRLSDVVSLVPC 84 (107)
Q Consensus 72 ~v~igD~V~V~~~ 84 (107)
.+.+||.|.|..+
T Consensus 48 ~~k~GD~V~I~ec 60 (71)
T TIGR03635 48 ECKVGDVVRIIET 60 (71)
T ss_pred CCCCCCEEEEEEc
Confidence 3899999999987
No 167
>PRK11642 exoribonuclease R; Provisional
Probab=33.87 E-value=2.1e+02 Score=25.87 Aligned_cols=85 Identities=19% Similarity=0.097 Sum_probs=48.2
Q ss_pred cCcccCCeEEEeEEEecCHHHHhhCCCCCCCEEEEEeccCCcEEEEe---------ccCCCCCCCeEEEeHhhhhccccc
Q psy3865 4 LNLFRGDTVLLRGKRRKESAKMDELNLFRGDTVLLRGKRRKESVCIV---------LSDDTCPDEKIRMNRVMRNNLRVR 74 (107)
Q Consensus 4 ~~~~~~d~~~~rGiari~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai~---------~~~~d~~~~~Irid~~~R~N~~v~ 74 (107)
.+-|.||.|.++ +.+-+. . +=..|-+|+|--+..+..++.+ .|.+..-...|.+...... ++.
T Consensus 116 ~~A~~GD~V~v~-i~~~~~---~--~r~eg~Vv~IleR~~~~~vG~~~~~~~~~~v~P~d~r~~~~i~i~~~~~~--~~~ 187 (813)
T PRK11642 116 KTCIHGDQVLAQ-PLGADR---K--GRREARIVRVLVPKTSQIVGRYFTDAGVGFVVPDDSRLSFDILIPPEQIM--GAR 187 (813)
T ss_pred ccCCCCCEEEEE-EccCCC---C--CCcEEEEEEEEecCCCEEEEEEEEeCCeEEEEECCCCCCCcEEecccccc--CCC
Confidence 356889999988 322111 1 1147888888755544555532 2333333445666543333 566
Q ss_pred CCCeEEEEeCCCCCC------ccEEEEcc
Q psy3865 75 LSDVVSLVPCPGIVY------GKRIHVLP 97 (107)
Q Consensus 75 igD~V~V~~~~~~~~------a~~V~l~P 97 (107)
.||.|.|+-. .+|. ++-+.++-
T Consensus 188 ~gd~V~v~I~-~~p~~~~~~~g~iv~vLG 215 (813)
T PRK11642 188 MGFVVVVELT-QRPTRRTKAVGKIVEVLG 215 (813)
T ss_pred CCCEEEEEEe-cCCCcCCCCCEEEEEEec
Confidence 7899999964 5433 45555543
No 168
>CHL00142 rps17 ribosomal protein S17; Validated
Probab=33.32 E-value=80 Score=20.49 Aligned_cols=22 Identities=18% Similarity=0.161 Sum_probs=15.8
Q ss_pred cccCCCeEEEEeCCCCCCccEE
Q psy3865 72 RVRLSDVVSLVPCPGIVYGKRI 93 (107)
Q Consensus 72 ~v~igD~V~V~~~~~~~~a~~V 93 (107)
.+.+||.|.|..+..+..-++-
T Consensus 50 ~~~~GD~V~I~e~RPlSKtK~~ 71 (84)
T CHL00142 50 ECNIGDQVLIEETRPLSKTKRW 71 (84)
T ss_pred CCCCCCEEEEEEcCCCCCcEEE
Confidence 4899999999988544444433
No 169
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=32.35 E-value=37 Score=25.67 Aligned_cols=17 Identities=41% Similarity=0.346 Sum_probs=14.0
Q ss_pred HHHhhCCCCCCCEEEEE
Q psy3865 23 AKMDELNLFRGDTVLLR 39 (107)
Q Consensus 23 ~~m~~Lgl~~GD~V~I~ 39 (107)
.-.+.|++..||.|+|+
T Consensus 198 ~LR~~l~l~dgd~v~i~ 214 (217)
T PRK14165 198 YLRKELNLKDGDRVEVL 214 (217)
T ss_pred hhHHhcCCCCCCEEEEE
Confidence 34557999999999986
No 170
>PF00240 ubiquitin: Ubiquitin family; InterPro: IPR000626 Ubiquitinylation is an ATP-dependent process that involves the action of at least three enzymes: a ubiquitin-activating enzyme (E1, IPR000011 from INTERPRO), a ubiquitin-conjugating enzyme (E2, IPR000608 from INTERPRO), and a ubiquitin ligase (E3, IPR000569 from INTERPRO, IPR003613 from INTERPRO), which work sequentially in a cascade. There are many different E3 ligases, which are responsible for the type of ubiquitin chain formed, the specificity of the target protein, and the regulation of the ubiquitinylation process []. Ubiquitinylation is an important regulatory tool that controls the concentration of key signalling proteins, such as those involved in cell cycle control, as well as removing misfolded, damaged or mutant proteins that could be harmful to the cell. Several ubiquitin-like molecules have been discovered, such as Ufm1 (IPR005375 from INTERPRO), SUMO1 (IPR003653 from INTERPRO), NEDD8, Rad23 (IPR004806 from INTERPRO), Elongin B and Parkin (IPR003977 from INTERPRO), the latter being involved in Parkinson's disease []. Ubiquitin is a protein of 76 amino acid residues, found in all eukaryotic cells and whose sequence is extremely well conserved from protozoan to vertebrates. Ubiquitin acts through its post-translational attachment (ubiquitinylation) to other proteins, where these modifications alter the function, location or trafficking of the protein, or targets it for destruction by the 26S proteasome []. The terminal glycine in the C-terminal 4-residue tail of ubiquitin can form an isopeptide bond with a lysine residue in the target protein, or with a lysine in another ubiquitin molecule to form a ubiquitin chain that attaches itself to a target protein. Ubiquitin has seven lysine residues, any one of which can be used to link ubiquitin molecules together, resulting in different structures that alter the target protein in different ways. It appears that Lys(11)-, Lys(29) and Lys(48)-linked poly-ubiquitin chains target the protein to the proteasome for degradation, while mono-ubiquitinylated and Lys(6)- or Lys(63)-linked poly-ubiquitin chains signal reversible modifications in protein activity, location or trafficking []. For example, Lys(63)-linked poly-ubiquitinylation is known to be involved in DNA damage tolerance, inflammatory response, protein trafficking and signal transduction through kinase activation []. In addition, the length of the ubiquitin chain alters the fate of the target protein. Regulatory proteins such as transcription factors and histones are frequent targets of ubquitinylation [].; GO: 0005515 protein binding; PDB: 2DZI_A 2XEW_E 3NOB_E 2KWU_B 2Y5B_F 3PHD_G 2KWV_B 2KOX_A 2XK5_B 3NHE_B ....
Probab=32.23 E-value=40 Score=19.70 Aligned_cols=28 Identities=21% Similarity=0.334 Sum_probs=21.2
Q ss_pred eEEEecCHHHHhhCCCCCCCEEEEEecc
Q psy3865 15 RGKRRKESAKMDELNLFRGDTVLLRGKR 42 (107)
Q Consensus 15 rGiari~~~~m~~Lgl~~GD~V~I~Gkr 42 (107)
+|..-=+...+.++|+.+|++|.+..+.
T Consensus 41 ~G~~L~d~~tL~~~~i~~~~~I~l~~k~ 68 (69)
T PF00240_consen 41 NGKELDDDKTLSDYGIKDGSTIHLVIKP 68 (69)
T ss_dssp TTEEESTTSBTGGGTTSTTEEEEEEESS
T ss_pred eeecccCcCcHHHcCCCCCCEEEEEEec
Confidence 3444447788889999999999887764
No 171
>TIGR01003 PTS_HPr_family Phosphotransferase System HPr (HPr) Family. The HPr family are bacterial proteins (or domains of proteins) which function in phosphoryl transfer system (PTS) systems. They include energy-coupling components which catalyze sugar uptake via a group translocation mechanism. The functions of most of these proteins are not known, but they presumably function in PTS-related regulatory capacities. All seed members are stand-alone HPr proteins, although the model also recognizes HPr domains of PTS fusion proteins. This family includes the related NPr protein.
Probab=31.77 E-value=84 Score=19.66 Aligned_cols=34 Identities=15% Similarity=0.229 Sum_probs=22.6
Q ss_pred ccCCeEEEeEEEecCH---HHHhhCCCCCCCEEEEEe
Q psy3865 7 FRGDTVLLRGKRRKES---AKMDELNLFRGDTVLLRG 40 (107)
Q Consensus 7 ~~~d~~~~rGiari~~---~~m~~Lgl~~GD~V~I~G 40 (107)
|+.|....++-...|. -.+-.||+..||.++|.-
T Consensus 29 f~s~I~i~~~~~~~dakSil~ll~Lg~~~G~~i~i~~ 65 (82)
T TIGR01003 29 FDSEITLTKNGKEVNAKSIMGIMMLGAGQGTEVTVSA 65 (82)
T ss_pred CCCEEEEEECCEEEehHhHHHHHhcCCCCCCEEEEEE
Confidence 6666655544344444 334488999999999983
No 172
>KOG1740|consensus
Probab=31.76 E-value=29 Score=23.66 Aligned_cols=26 Identities=23% Similarity=0.287 Sum_probs=18.7
Q ss_pred ccCCCeEEEEeCCCCCCccEEEEccC
Q psy3865 73 VRLSDVVSLVPCPGIVYGKRIHVLPI 98 (107)
Q Consensus 73 v~igD~V~V~~~~~~~~a~~V~l~P~ 98 (107)
+.+||.|++.++.....-|.-.++|+
T Consensus 50 cnvGD~VrlepsRPlSk~K~f~i~eI 75 (107)
T KOG1740|consen 50 CNVGDRVRLEPSRPLSKTKHFIIAEI 75 (107)
T ss_pred ccccceEEeccCCcccccceeehHHH
Confidence 68999999999755555565555553
No 173
>cd06529 S24_LexA-like Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The LexA-like proteins contain two-domains: an N-terminal DNA binding domain and a C-terminal domain (CTD) that provides LexA dimerization as well as cleavage activity. They undergo autolysis, cleaving at an Ala-Gly or a Cys-Gly bond, separating the DNA-binding domain from the rest of the
Probab=30.93 E-value=62 Score=19.22 Aligned_cols=10 Identities=40% Similarity=0.454 Sum_probs=5.3
Q ss_pred CCCCCEEEEE
Q psy3865 30 LFRGDTVLLR 39 (107)
Q Consensus 30 l~~GD~V~I~ 39 (107)
+..||++.++
T Consensus 28 ~~~g~i~~~~ 37 (81)
T cd06529 28 PRDGDIVVAR 37 (81)
T ss_pred CCCCCEEEEE
Confidence 4455555555
No 174
>PF09926 DUF2158: Uncharacterized small protein (DUF2158); InterPro: IPR019226 This entry represents a family of predominantly prokaryotic proteins with no known function.
Probab=30.39 E-value=1.2e+02 Score=17.89 Aligned_cols=18 Identities=44% Similarity=0.517 Sum_probs=13.1
Q ss_pred CCCCEEEEE--eccCCcEEEEe
Q psy3865 31 FRGDTVLLR--GKRRKESVCIV 50 (107)
Q Consensus 31 ~~GD~V~I~--Gkr~~~tvai~ 50 (107)
.+||+|.+| |.+ -||.-+
T Consensus 2 ~~GDvV~LKSGGp~--MTV~~v 21 (53)
T PF09926_consen 2 KIGDVVQLKSGGPR--MTVTEV 21 (53)
T ss_pred CCCCEEEEccCCCC--eEEEEc
Confidence 579999999 444 577644
No 175
>COG4013 Uncharacterized protein conserved in archaea [Function unknown]
Probab=30.00 E-value=1.1e+02 Score=20.18 Aligned_cols=21 Identities=24% Similarity=0.148 Sum_probs=14.4
Q ss_pred ecCHHHHh---hCCCCCCCEEEEE
Q psy3865 19 RKESAKMD---ELNLFRGDTVLLR 39 (107)
Q Consensus 19 ri~~~~m~---~Lgl~~GD~V~I~ 39 (107)
+++|+..- +-.+.+||+|++.
T Consensus 7 ~~~peEl~eY~~eeV~~gd~vel~ 30 (91)
T COG4013 7 VKNPEELIEYLNEEVDVGDYVELY 30 (91)
T ss_pred hcCHHHHHHHHHhcCCCCCEEEEE
Confidence 45664332 3368999999998
No 176
>cd01614 EutN_CcmL Ethanolamine utilisation protein and carboxysome structural protein domain family. Beside the Escherichia coli ethanolamine utilization protein EutN and the Synechocystis sp. carboxysome (beta-type) structural protein CcmL, this family also includes alpha-type carboxysome structural proteins CsoS4A and CsoS4B (previously known as OrfA and OrfB), propanediol utilizationprotein PduN, and some hypothetical homologous of various bacterial microcompartments. The carboxysome, a polyhedral organelle, participates in carbon fixation by sequestering enzymes. It is the prototypical bacterial microcompartment. Its enzymatic components, ribulose bisphosphate carboxylase/oxygenase(RuBisCO) and carbonic anhydrase (CA), are surrounded by a polyhedral protein shell. Similarly, the ethanolamine utilization (eut) microcompartment, and the 1,2-propanediol utilization (pdu) microcompartment encapsulate the enzymes necessary for the process of cobalamin-dependent ethanolamine degradation,
Probab=29.89 E-value=15 Score=23.87 Aligned_cols=45 Identities=11% Similarity=0.155 Sum_probs=27.4
Q ss_pred CCCCeEEEeHhhhhcccccCCCeEEEEeCCCCCCccEEEEccCCccccCC
Q psy3865 56 CPDEKIRMNRVMRNNLRVRLSDVVSLVPCPGIVYGKRIHVLPIDDSVQGL 105 (107)
Q Consensus 56 ~~~~~Irid~~~R~N~~v~igD~V~V~~~~~~~~a~~V~l~P~~dti~~~ 105 (107)
.+.-.|-+| ++|+++||.|-+..=..++.+..=.-.|++.+|=||
T Consensus 37 ~g~~~VA~D-----~vGAG~Ge~Vlv~~Gs~Ar~~~~~~~~PiDa~IvGI 81 (83)
T cd01614 37 KGEPLVAVD-----PVGAGVGEWVLVATGSAARQAFGDKDVPIDAAIIGI 81 (83)
T ss_pred CCCEEEEEE-----CCCCCCCCEEEEeCChHHhhhcCCCCCCceEEEEEE
Confidence 445666666 579999999999853233333222235766666544
No 177
>PF01472 PUA: PUA domain; InterPro: IPR002478 The PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain was named after the proteins in which it was first found []. PUA is a highly conserved RNA-binding motif found in a wide range of archaeal, bacterial and eukaryotic proteins, including enzymes that catalyse tRNA and rRNA post-transcriptional modifications, proteins involved in ribosome biogenesis and translation, as well as in enzymes involved in proline biosynthesis [, ]. The structures of several PUA-RNA complexes reveal a common RNA recognition surface, but also some versatility in the way in which the motif binds to RNA []. PUA motifs are involved in dyskeratosis congenita and cancer, pointing to links between RNA metabolism and human diseases [].; GO: 0003723 RNA binding; PDB: 1ZE2_A 1ZE1_A 1R3E_A 2AB4_A 3R90_D 2J5T_A 2J5V_B 1Q7H_A 2APO_A 2RFK_A ....
Probab=29.64 E-value=1.2e+02 Score=18.49 Aligned_cols=34 Identities=18% Similarity=0.407 Sum_probs=20.8
Q ss_pred CCeEEEeEEEecCHHHHhhCCCCCCCEEEEEeccCCcEEEE
Q psy3865 9 GDTVLLRGKRRKESAKMDELNLFRGDTVLLRGKRRKESVCI 49 (107)
Q Consensus 9 ~d~~~~rGiari~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai 49 (107)
|--+...|+..+++ .+..||.|.|..... +.+|+
T Consensus 16 Ga~L~~~GV~~~~~------~f~~gd~V~i~~~~g-~~ia~ 49 (74)
T PF01472_consen 16 GASLFAPGVVEVDG------DFRKGDEVAIVDEDG-EVIAV 49 (74)
T ss_dssp TSEEEGGGEEEEET------T--TTSEEEEEETTS-SEEEE
T ss_pred CCCcchHHhEECCC------CcCCCCEEEEEcCCC-eEEEE
Confidence 44556666777655 358899999987642 44554
No 178
>PRK10862 SoxR reducing system protein RseC; Provisional
Probab=29.34 E-value=43 Score=23.84 Aligned_cols=17 Identities=12% Similarity=-0.021 Sum_probs=13.2
Q ss_pred hhhcccccCCCeEEEEe
Q psy3865 67 MRNNLRVRLSDVVSLVP 83 (107)
Q Consensus 67 ~R~N~~v~igD~V~V~~ 83 (107)
+-.+.++..||.|.|.-
T Consensus 53 v~~~~~~~vGD~V~v~i 69 (154)
T PRK10862 53 VPSSQPLVPGQKVELGI 69 (154)
T ss_pred ecCCCCCCCCCEEEEec
Confidence 34567789999999984
No 179
>COG2274 SunT ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]
Probab=29.31 E-value=18 Score=31.88 Aligned_cols=56 Identities=18% Similarity=0.267 Sum_probs=43.3
Q ss_pred hCCCCCCCEEEEEec--cCCcEEEEeccC-CCCCCCeEEEeH---------hhhhcccccCCCeEEEE
Q psy3865 27 ELNLFRGDTVLLRGK--RRKESVCIVLSD-DTCPDEKIRMNR---------VMRNNLRVRLSDVVSLV 82 (107)
Q Consensus 27 ~Lgl~~GD~V~I~Gk--r~~~tvai~~~~-~d~~~~~Irid~---------~~R~N~~v~igD~V~V~ 82 (107)
+|.+.+|+.|-|-|+ -.|+|.+..... +....|.|.+|+ ..|+|.++-..|..-.+
T Consensus 493 sL~I~~Ge~vaIvG~SGsGKSTL~KLL~gly~p~~G~I~~dg~dl~~i~~~~lR~~ig~V~Q~~~Lf~ 560 (709)
T COG2274 493 SLEIPPGEKVAIVGRSGSGKSTLLKLLLGLYKPQQGRILLDGVDLNDIDLASLRRQVGYVLQDPFLFS 560 (709)
T ss_pred eEEeCCCCEEEEECCCCCCHHHHHHHHhcCCCCCCceEEECCEeHHhcCHHHHHhheeEEcccchhhc
Confidence 588899999999987 445888887655 567789999998 57888887777664433
No 180
>PRK08395 fumarate hydratase; Provisional
Probab=28.42 E-value=66 Score=23.46 Aligned_cols=20 Identities=30% Similarity=0.356 Sum_probs=15.1
Q ss_pred cCHHHHhhCCCCCCCEEEEEec
Q psy3865 20 KESAKMDELNLFRGDTVLLRGK 41 (107)
Q Consensus 20 i~~~~m~~Lgl~~GD~V~I~Gk 41 (107)
+++++.++|. .||.|.+.|+
T Consensus 7 l~~e~i~~L~--~GD~V~LsG~ 26 (162)
T PRK08395 7 LSWEDVLKLK--AGDVVYLSGI 26 (162)
T ss_pred CCHHHHhhCC--CCCEEEEEEE
Confidence 4566666655 5999999995
No 181
>PHA02451 hypothetical protein
Probab=28.42 E-value=36 Score=20.49 Aligned_cols=15 Identities=40% Similarity=0.875 Sum_probs=12.4
Q ss_pred EEEEccCCccccCCC
Q psy3865 92 RIHVLPIDDSVQGLT 106 (107)
Q Consensus 92 ~V~l~P~~dti~~~~ 106 (107)
.||++|.+|.|+.-+
T Consensus 3 ~vHv~p~dDlI~H~~ 17 (54)
T PHA02451 3 TVHVLPVDDLIEHVE 17 (54)
T ss_pred ceeecccccceeecc
Confidence 589999999998754
No 182
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=28.26 E-value=57 Score=28.22 Aligned_cols=19 Identities=21% Similarity=0.428 Sum_probs=17.3
Q ss_pred CHHHHhhCCCCCCCEEEEE
Q psy3865 21 ESAKMDELNLFRGDTVLLR 39 (107)
Q Consensus 21 ~~~~m~~Lgl~~GD~V~I~ 39 (107)
+.+.++++++..||+|.|+
T Consensus 351 N~~~i~~~~I~iGD~V~V~ 369 (562)
T PRK08097 351 SVRRWQQWDIAPGDQVLVS 369 (562)
T ss_pred CHHHHHHcCCCCCCEEEEE
Confidence 4588999999999999998
No 183
>COG1158 Rho Transcription termination factor [Transcription]
Probab=27.89 E-value=51 Score=27.39 Aligned_cols=22 Identities=27% Similarity=0.289 Sum_probs=19.2
Q ss_pred EecCHHHHhhCCCCCCCEEEEE
Q psy3865 18 RRKESAKMDELNLFRGDTVLLR 39 (107)
Q Consensus 18 ari~~~~m~~Lgl~~GD~V~I~ 39 (107)
.++||..+++.+++.||.|+=+
T Consensus 82 iYvSpSQIRrf~LrtGD~v~G~ 103 (422)
T COG1158 82 IYVSPSQIRRFNLRTGDTVEGK 103 (422)
T ss_pred eEECHHHHhhccCccCCEEeee
Confidence 4789999999999999999743
No 184
>PRK06342 transcription elongation factor regulatory protein; Validated
Probab=27.86 E-value=1e+02 Score=22.15 Aligned_cols=54 Identities=26% Similarity=0.208 Sum_probs=38.2
Q ss_pred CCCCCCCEEEEEec-cCCcEEEEeccCC-CCCCCeEEEeH-hhhhcccccCCCeEEE
Q psy3865 28 LNLFRGDTVLLRGK-RRKESVCIVLSDD-TCPDEKIRMNR-VMRNNLRVRLSDVVSL 81 (107)
Q Consensus 28 Lgl~~GD~V~I~Gk-r~~~tvai~~~~~-d~~~~~Irid~-~~R~N~~v~igD~V~V 81 (107)
=.+.-|-+|.++.. ....++.++.+.+ +...+.|-+.. ..+.=+|-+.||.|.|
T Consensus 93 d~V~~Gs~V~l~~~~~~~~~~~IVg~~Ead~~~g~IS~~SPlG~ALlGk~vGD~V~v 149 (160)
T PRK06342 93 DVVAFGSTVTFSRDDGRVQTYRIVGEDEADPKAGSISYVSPVARALMGKAVGDVVSV 149 (160)
T ss_pred CEEEeCcEEEEEECCCCEEEEEEEChHHhCcCCCcccccCHHHHHHcCCCCCCEEEE
Confidence 34567889999732 2335666665553 56667777655 7788899999999998
No 185
>PRK05659 sulfur carrier protein ThiS; Validated
Probab=27.76 E-value=82 Score=18.46 Aligned_cols=17 Identities=24% Similarity=0.301 Sum_probs=7.9
Q ss_pred HHHHhhCCCCCCCEEEE
Q psy3865 22 SAKMDELNLFRGDTVLL 38 (107)
Q Consensus 22 ~~~m~~Lgl~~GD~V~I 38 (107)
+.....--+..||.|+|
T Consensus 43 r~~~~~~~l~~gD~vei 59 (66)
T PRK05659 43 RSQHASTALREGDVVEI 59 (66)
T ss_pred HHHcCcccCCCCCEEEE
Confidence 34444444555555544
No 186
>PRK13782 phosphocarrier protein Chr; Provisional
Probab=27.58 E-value=1.1e+02 Score=19.09 Aligned_cols=34 Identities=12% Similarity=0.266 Sum_probs=23.4
Q ss_pred cccCCeEEEeEEEecCHHH---HhhCCCCCCCEEEEE
Q psy3865 6 LFRGDTVLLRGKRRKESAK---MDELNLFRGDTVLLR 39 (107)
Q Consensus 6 ~~~~d~~~~rGiari~~~~---m~~Lgl~~GD~V~I~ 39 (107)
=|+.|....++-...|... +-.||+..||.|+|.
T Consensus 28 ~f~~~i~l~~~~~~vdaKSil~llsLg~~~g~~v~v~ 64 (82)
T PRK13782 28 RFHADIFIEKDGKKVNAKSIMGLMSLAIGTGSMITII 64 (82)
T ss_pred hCCCEEEEEECCeEEecHhHHHHHhcCCCCCCEEEEE
Confidence 3677666555545555433 348999999999998
No 187
>cd04486 YhcR_OBF_like YhcR_OBF_like: A subfamily of OB-fold domains similar to the OB folds of Bacillus subtilis YhcR. YhcR is a sugar-nonspecific nuclease, which is active in the presence of Ca2+ and Mn2+. It cleaves RNA endonucleolytically, producing 3'-monophosphate nucleosides. YhcR appears to be the major Ca2+ activated nuclease of B. subtilis. YhcR may be localized in the cell wall.
Probab=27.51 E-value=72 Score=19.98 Aligned_cols=15 Identities=27% Similarity=0.383 Sum_probs=12.9
Q ss_pred hCCCCCCCEEEEEec
Q psy3865 27 ELNLFRGDTVLLRGK 41 (107)
Q Consensus 27 ~Lgl~~GD~V~I~Gk 41 (107)
...+..||.|+|.|+
T Consensus 42 ~~~~~~Gd~V~vtG~ 56 (78)
T cd04486 42 GADVAVGDLVRVTGT 56 (78)
T ss_pred CCCCCCCCEEEEEEE
Confidence 567889999999986
No 188
>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=27.32 E-value=58 Score=17.46 Aligned_cols=19 Identities=32% Similarity=0.475 Sum_probs=15.4
Q ss_pred HHHhhCCCCCCCEEEEEec
Q psy3865 23 AKMDELNLFRGDTVLLRGK 41 (107)
Q Consensus 23 ~~m~~Lgl~~GD~V~I~Gk 41 (107)
..-.+|.+..||.|.+..+
T Consensus 14 ~~~~~l~~~~Gd~v~v~~~ 32 (58)
T smart00326 14 QDPDELSFKKGDIITVLEK 32 (58)
T ss_pred CCCCCCCCCCCCEEEEEEc
Confidence 4446799999999999865
No 189
>PF07244 Surf_Ag_VNR: Surface antigen variable number repeat; InterPro: IPR010827 This motif is found primarily in bacterial surface antigens, normally as variable number repeats at the N terminus. The C terminus of these proteins is normally represented by IPR000184 from INTERPRO. There may also be a relationship to haemolysin activator HlyB (IPR005565 from INTERPRO). The alignment centres on a -GY- or -GF- motif. Some members of this family are found in the mitochondria. It is predicted to have a mixed alpha/beta secondary structure.; GO: 0019867 outer membrane; PDB: 2X8X_X 3MC8_A 3OG5_A 3MC9_B 2QCZ_B 3EFC_A 3Q6B_A 2QDF_A 2V9H_A.
Probab=27.29 E-value=30 Score=20.48 Aligned_cols=27 Identities=19% Similarity=0.338 Sum_probs=19.6
Q ss_pred eEEEeE-EEecCHHHHhh-CCCCCCCEEE
Q psy3865 11 TVLLRG-KRRKESAKMDE-LNLFRGDTVL 37 (107)
Q Consensus 11 ~~~~rG-iari~~~~m~~-Lgl~~GD~V~ 37 (107)
-|.+.| ..+++++.+.+ |++.+|+...
T Consensus 5 ~I~i~Gn~~~~~~~~l~~~l~~~~G~~~~ 33 (78)
T PF07244_consen 5 EINIEGNLKKFSDEELRRELGLKPGDPFN 33 (78)
T ss_dssp EEEEESE-SSSHHHHHHHCHSS-TTSBEC
T ss_pred EEEEEcCceEeCHHHHHhhcCCCCCCEeC
Confidence 367788 47888888887 9999997665
No 190
>PF08497 Radical_SAM_N: Radical SAM N-terminal; InterPro: IPR013704 This domain tends to occur to the N terminus of PF04055 from PFAM radical SAM domain in hypothetical bacterial proteins. Proteins in this entry are radical SAM proteins, they catalyse diverse reactions, including unusual methylations, isomerization, sulphur insertion, ring formation, anaerobic oxidation and protein radical formation. Evidence exists that these proteins generate a radical species by reductive cleavage of S:-adenosylmethionine (SAM) through an unusual Fe-S centre [, ].
Probab=27.28 E-value=61 Score=26.00 Aligned_cols=22 Identities=18% Similarity=0.234 Sum_probs=20.1
Q ss_pred cCHHHHhhCCCCCCCEEEEEec
Q psy3865 20 KESAKMDELNLFRGDTVLLRGK 41 (107)
Q Consensus 20 i~~~~m~~Lgl~~GD~V~I~Gk 41 (107)
++.+.|+++|+..=|+|.|.|-
T Consensus 4 ~t~~em~~rGWd~lDvilVtGD 25 (302)
T PF08497_consen 4 TTREEMKARGWDELDVILVTGD 25 (302)
T ss_pred CCHHHHHHcCCccccEEEEeCc
Confidence 5789999999999999999974
No 191
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=27.23 E-value=1e+02 Score=20.01 Aligned_cols=36 Identities=25% Similarity=0.312 Sum_probs=21.4
Q ss_pred cccCCeEEEeEEEecCHHHHhh-CCCCCCCEEEEEecc
Q psy3865 6 LFRGDTVLLRGKRRKESAKMDE-LNLFRGDTVLLRGKR 42 (107)
Q Consensus 6 ~~~~d~~~~rGiari~~~~m~~-Lgl~~GD~V~I~Gkr 42 (107)
|-+++ ..+++...-+....-. ..+..||-|.+.|+-
T Consensus 45 LkD~~-a~i~~~~~~~~~~~i~~~~l~~G~~V~v~g~~ 81 (99)
T PF13742_consen 45 LKDEE-ASISCVIFRSRARRIRGFDLKDGDKVLVRGRV 81 (99)
T ss_pred EEcCC-cEEEEEEEHHHHhhCCCCCCCCCCEEEEEEEE
Confidence 33444 5555555433322223 458999999999963
No 192
>PF01336 tRNA_anti-codon: OB-fold nucleic acid binding domain; InterPro: IPR004365 The OB-fold (oligonucleotide/oligosaccharide-binding fold) is found in all three kingdoms and its common architecture presents a binding face that has adapted to bind different ligands. The OB-fold is a five/six-stranded closed beta-barrel formed by 70-80 amino acid residues. The strands are connected by loops of varying length which form the functional appendages of the protein. The majority of OB-fold proteins use the same face for ligand binding or as an active site. Different OB-fold proteins use this 'fold-related binding face' to, variously, bind oligosaccharides, oligonucleotides, proteins, metal ions and catalytic substrates. This entry contains OB-fold domains that bind to nucleic acids []. It includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl-tRNA synthetases (See IPR004364 from INTERPRO). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule 6.1.1 from EC. This domain is found in RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family [, ]. This domain is also found at the C terminus of bacterial DNA polymerase III alpha chain.; GO: 0003676 nucleic acid binding; PDB: 1BBU_A 1KRS_A 1BBW_A 1KRT_A 1EQR_B 1IL2_B 1C0A_A 3KFU_A 1EOV_A 1ASY_A ....
Probab=27.08 E-value=52 Score=19.08 Aligned_cols=19 Identities=37% Similarity=0.361 Sum_probs=13.6
Q ss_pred HHHhhCCCCCCCEEEEEec
Q psy3865 23 AKMDELNLFRGDTVLLRGK 41 (107)
Q Consensus 23 ~~m~~Lgl~~GD~V~I~Gk 41 (107)
.....-.+.+||.|.++|+
T Consensus 38 ~~~~~~~l~~g~~v~v~G~ 56 (75)
T PF01336_consen 38 YERFREKLKEGDIVRVRGK 56 (75)
T ss_dssp HHHHHHTS-TTSEEEEEEE
T ss_pred hhHHhhcCCCCeEEEEEEE
Confidence 3444556789999999996
No 193
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=26.79 E-value=1.1e+02 Score=21.20 Aligned_cols=51 Identities=18% Similarity=0.167 Sum_probs=30.9
Q ss_pred EecCHHHHhhCC-----CCCCCEEEEE-eccCCcEEEEeccCCCCCCCeEEEeHhhhhc
Q psy3865 18 RRKESAKMDELN-----LFRGDTVLLR-GKRRKESVCIVLSDDTCPDEKIRMNRVMRNN 70 (107)
Q Consensus 18 ari~~~~m~~Lg-----l~~GD~V~I~-Gkr~~~tvai~~~~~d~~~~~Irid~~~R~N 70 (107)
++||.|-.+++| +..||.|.|- |+.+.++--+... +...+.|.++++.+..
T Consensus 29 a~LSkeLr~~y~ir~~~IkkGD~V~VisG~~KGk~GkV~~V--~~~~~~V~VeGvn~~k 85 (120)
T PRK01191 29 APLSKELREKYGIRSLPVRKGDTVKVMRGDFKGEEGKVVEV--DLKRGRIYVEGVTVKK 85 (120)
T ss_pred CccCHHHHHHhCCccceEeCCCEEEEeecCCCCceEEEEEE--EcCCCEEEEeCcEEEC
Confidence 677777777665 5689999987 4432222212111 2234678888877766
No 194
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=26.76 E-value=32 Score=21.31 Aligned_cols=25 Identities=24% Similarity=0.441 Sum_probs=14.4
Q ss_pred CCeEEEeH--hhhhcccccCCCeEEEE
Q psy3865 58 DEKIRMNR--VMRNNLRVRLSDVVSLV 82 (107)
Q Consensus 58 ~~~Irid~--~~R~N~~v~igD~V~V~ 82 (107)
.+.|++|+ .+|++..++.||.|++.
T Consensus 32 ~g~V~VNGe~e~rrg~Kl~~GD~V~~~ 58 (65)
T PF13275_consen 32 EGEVKVNGEVETRRGKKLRPGDVVEID 58 (65)
T ss_dssp HHHHEETTB----SS----SSEEEEET
T ss_pred cCceEECCEEccccCCcCCCCCEEEEC
Confidence 36677777 68999999999999983
No 195
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=26.43 E-value=55 Score=24.98 Aligned_cols=17 Identities=47% Similarity=0.565 Sum_probs=14.4
Q ss_pred HHHhhCCCCCCCEEEEE
Q psy3865 23 AKMDELNLFRGDTVLLR 39 (107)
Q Consensus 23 ~~m~~Lgl~~GD~V~I~ 39 (107)
.-.++|++..||.|.|+
T Consensus 195 ~LR~~LnLkDGD~V~ie 211 (214)
T COG1339 195 KLRDELNLKDGDEVTIE 211 (214)
T ss_pred hHHHHhCCCCCCEEEEE
Confidence 55679999999999886
No 196
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=26.40 E-value=1.3e+02 Score=21.55 Aligned_cols=53 Identities=11% Similarity=0.146 Sum_probs=31.8
Q ss_pred EecCHHHHhhCC-----CCCCCEEEEE-eccCCcEEEEeccCCCCCCCeEEEeHhhhhccc
Q psy3865 18 RRKESAKMDELN-----LFRGDTVLLR-GKRRKESVCIVLSDDTCPDEKIRMNRVMRNNLR 72 (107)
Q Consensus 18 ari~~~~m~~Lg-----l~~GD~V~I~-Gkr~~~tvai~~~~~d~~~~~Irid~~~R~N~~ 72 (107)
|+||.|..+++| |..||.|.|- |+.+.+.=-++.. +...+.|.++++.+....
T Consensus 30 a~LSkeLr~k~~~Rs~~IkkGD~V~Vi~Gk~KGk~GkV~~V--~~k~~~ViVEgvn~~Kk~ 88 (143)
T PTZ00194 30 APLSKELRAKYNVRSMPVRKDDEVMVVRGHHKGREGKVTAV--YRKKWVIHIEKITREKAN 88 (143)
T ss_pred CccCHHHHHHhCCccceeecCCEEEEecCCCCCCceEEEEE--EcCCCEEEEeCeEEEecC
Confidence 677887777665 5679999987 4422222111111 223467888887776654
No 197
>KOG3447|consensus
Probab=26.21 E-value=59 Score=23.31 Aligned_cols=34 Identities=18% Similarity=0.312 Sum_probs=23.4
Q ss_pred ccCCCeEEEEeCCCCCCccEEE------EccCCccccCCCC
Q psy3865 73 VRLSDVVSLVPCPGIVYGKRIH------VLPIDDSVQGLTG 107 (107)
Q Consensus 73 v~igD~V~V~~~~~~~~a~~V~------l~P~~dti~~~~g 107 (107)
+.+||+|-|+.. +.++-+.|+ +-|+-+-++.+||
T Consensus 58 c~vGDtVLir~l-p~r~t~~V~H~v~~VVfk~G~IidPvTG 97 (150)
T KOG3447|consen 58 CTVGDTVLIRAL-PVRRTKHVKHEVAEVVFKVGKIIDPVTG 97 (150)
T ss_pred cccCCEEEEecC-CcchhhhhhhhhHhheeecccccCCCcC
Confidence 579999999987 455544443 3477777777665
No 198
>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=25.89 E-value=66 Score=28.16 Aligned_cols=18 Identities=39% Similarity=0.719 Sum_probs=16.9
Q ss_pred HHHHhhCCCCCCCEEEEE
Q psy3865 22 SAKMDELNLFRGDTVLLR 39 (107)
Q Consensus 22 ~~~m~~Lgl~~GD~V~I~ 39 (107)
.+.++++++..||+|.|+
T Consensus 348 ~~~i~~~~i~iGD~V~V~ 365 (652)
T TIGR00575 348 EDEIEELDIRIGDTVVVR 365 (652)
T ss_pred HHHHHHcCCCCCCEEEEE
Confidence 489999999999999998
No 199
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=25.84 E-value=66 Score=28.25 Aligned_cols=19 Identities=26% Similarity=0.550 Sum_probs=17.3
Q ss_pred CHHHHhhCCCCCCCEEEEE
Q psy3865 21 ESAKMDELNLFRGDTVLLR 39 (107)
Q Consensus 21 ~~~~m~~Lgl~~GD~V~I~ 39 (107)
+.+.++++++..||+|.|+
T Consensus 359 N~~~i~~~~i~iGD~V~V~ 377 (665)
T PRK07956 359 NADEIERKDIRIGDTVVVR 377 (665)
T ss_pred CHHHHHHcCCCCCCEEEEE
Confidence 4489999999999999998
No 200
>PRK09376 rho transcription termination factor Rho; Provisional
Probab=25.74 E-value=80 Score=26.42 Aligned_cols=22 Identities=27% Similarity=0.289 Sum_probs=19.7
Q ss_pred EecCHHHHhhCCCCCCCEEEEE
Q psy3865 18 RRKESAKMDELNLFRGDTVLLR 39 (107)
Q Consensus 18 ari~~~~m~~Lgl~~GD~V~I~ 39 (107)
.+++|..+++.+++.||.|.=.
T Consensus 79 ~yvs~~~ir~~~lr~gd~v~g~ 100 (416)
T PRK09376 79 IYVSPSQIRRFNLRTGDTVEGK 100 (416)
T ss_pred eeeCHHHHHhcCCCCCCEEEEE
Confidence 7889999999999999999743
No 201
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=25.73 E-value=66 Score=28.37 Aligned_cols=19 Identities=26% Similarity=0.412 Sum_probs=17.2
Q ss_pred CHHHHhhCCCCCCCEEEEE
Q psy3865 21 ESAKMDELNLFRGDTVLLR 39 (107)
Q Consensus 21 ~~~~m~~Lgl~~GD~V~I~ 39 (107)
+.+.++++++..||+|.|+
T Consensus 356 N~~~I~~~di~iGD~V~V~ 374 (669)
T PRK14350 356 NQDYIDSIGLNVGDVVKIS 374 (669)
T ss_pred CHHHHHHcCCCCCCEEEEE
Confidence 3489999999999999998
No 202
>COG1101 PhnK ABC-type uncharacterized transport system, ATPase component [General function prediction only]
Probab=25.58 E-value=28 Score=27.29 Aligned_cols=39 Identities=21% Similarity=0.315 Sum_probs=29.0
Q ss_pred hCCCCCCCEEEEEec--cCCcEEEEeccCC-CCCCCeEEEeH
Q psy3865 27 ELNLFRGDTVLLRGK--RRKESVCIVLSDD-TCPDEKIRMNR 65 (107)
Q Consensus 27 ~Lgl~~GD~V~I~Gk--r~~~tvai~~~~~-d~~~~~Irid~ 65 (107)
.|.+..||+|.|-|. ..++|.+-+...+ ....|.|.||+
T Consensus 26 sL~I~~g~FvtViGsNGAGKSTlln~iaG~l~~t~G~I~Idg 67 (263)
T COG1101 26 SLEIAEGDFVTVIGSNGAGKSTLLNAIAGDLKPTSGQILIDG 67 (263)
T ss_pred ceeecCCceEEEEcCCCccHHHHHHHhhCccccCCceEEECc
Confidence 678899999999975 3346766665555 55668888886
No 203
>PLN00051 RNA-binding S4 domain-containing protein; Provisional
Probab=25.49 E-value=80 Score=24.57 Aligned_cols=34 Identities=26% Similarity=0.340 Sum_probs=22.2
Q ss_pred cccCCeEEEeEEEecCHHHHhhCCCCCCCEEEEEeccC
Q psy3865 6 LFRGDTVLLRGKRRKESAKMDELNLFRGDTVLLRGKRR 43 (107)
Q Consensus 6 ~~~~d~~~~rGiari~~~~m~~Lgl~~GD~V~I~Gkr~ 43 (107)
++++..|.|=+..--+| ..-+.+||+|.|+|..+
T Consensus 212 lI~~g~V~vN~~~v~~~----s~~v~~gD~isiRG~GR 245 (267)
T PLN00051 212 LISSGDVRVNWREVTKN----GTTLKTGDVVSVSGKGR 245 (267)
T ss_pred HHHcCcEEECCEEcCCC----CCCCCCCCEEEEeeCCE
Confidence 44555555554443333 45788999999999864
No 204
>cd00367 PTS-HPr_like Histidine-containing phosphocarrier protein (HPr)-like proteins. HPr is a central component of the bacterial phosphoenolpyruvate sugar phosphotransferase system (PTS). The PTS catalyses the phosphorylation of sugar substrates during their translocation across the cell membrane. The phosphoryl group from phosphoenolpyruvate is transferred to HPr by enzyme I (EI). Phospho-HPr then transfers the phosphoryl group to one of several sugar-specific phosphoprotein intermediates. The conserved histidine in the N-terminus of HPr serves as an acceptor for the phosphoryl group of EI. In addition to the phosphotransferase proteins HPr and E1, this family also includes the closely related Carbon Catabolite Repressor (CCR) proteins which use the same phosphorylation mechanism and interact with transcriptional regulators to control expression of genes coding for utilization of less favored carbon sources.
Probab=25.42 E-value=1.5e+02 Score=18.02 Aligned_cols=33 Identities=27% Similarity=0.505 Sum_probs=22.2
Q ss_pred ccCCeEEEeEEEecCHH---HHhhCCCCCCCEEEEE
Q psy3865 7 FRGDTVLLRGKRRKESA---KMDELNLFRGDTVLLR 39 (107)
Q Consensus 7 ~~~d~~~~rGiari~~~---~m~~Lgl~~GD~V~I~ 39 (107)
|+.|.....+-...|.. .+-.||+..||.|+|.
T Consensus 25 ~~~~v~i~~~~~~vdakSil~i~~L~~~~G~~i~i~ 60 (77)
T cd00367 25 FKSDITLRKGGRKANAKSILGLMSLGAKQGDEITLS 60 (77)
T ss_pred CCCEEEEEECCEEEcHHhHHHHHHcCCCCCCEEEEE
Confidence 66665555554445543 3347899999999998
No 205
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=25.40 E-value=49 Score=20.97 Aligned_cols=15 Identities=33% Similarity=0.572 Sum_probs=10.7
Q ss_pred hCCCCCCCEEEEE-ec
Q psy3865 27 ELNLFRGDTVLLR-GK 41 (107)
Q Consensus 27 ~Lgl~~GD~V~I~-Gk 41 (107)
.+.++.||.|.|- |+
T Consensus 4 ~~~I~kGD~V~Vi~G~ 19 (76)
T PRK12281 4 KLKVKKGDMVKVIAGD 19 (76)
T ss_pred cccccCCCEEEEeEcC
Confidence 3578888888876 44
No 206
>PRK03760 hypothetical protein; Provisional
Probab=25.34 E-value=66 Score=21.86 Aligned_cols=17 Identities=24% Similarity=0.259 Sum_probs=14.5
Q ss_pred HHHhhCCCCCCCEEEEE
Q psy3865 23 AKMDELNLFRGDTVLLR 39 (107)
Q Consensus 23 ~~m~~Lgl~~GD~V~I~ 39 (107)
-..+++|+.+||.|+++
T Consensus 99 G~~~~~gi~~Gd~v~~~ 115 (117)
T PRK03760 99 GKIRVLKVEVGDEIEWI 115 (117)
T ss_pred ChHHHcCCCCCCEEEEe
Confidence 46679999999999875
No 207
>COG1363 FrvX Cellulase M and related proteins [Carbohydrate transport and metabolism]
Probab=24.94 E-value=65 Score=26.23 Aligned_cols=21 Identities=24% Similarity=0.417 Sum_probs=17.7
Q ss_pred CHHHHhhCCCCCCCEEEEEec
Q psy3865 21 ESAKMDELNLFRGDTVLLRGK 41 (107)
Q Consensus 21 ~~~~m~~Lgl~~GD~V~I~Gk 41 (107)
|.+..++||+++||+|.+...
T Consensus 145 skeea~~lGI~vGd~v~~~~~ 165 (355)
T COG1363 145 SKEEAEELGIRVGDFVVFDPR 165 (355)
T ss_pred CHHHHHhcCCCCCCEEEEcCc
Confidence 457788999999999999753
No 208
>COG5417 Uncharacterized small protein [Function unknown]
Probab=24.72 E-value=59 Score=21.11 Aligned_cols=31 Identities=16% Similarity=0.305 Sum_probs=17.7
Q ss_pred cCCeEEEeEEEec--CHHHHhhCCCCCCCEEEE
Q psy3865 8 RGDTVLLRGKRRK--ESAKMDELNLFRGDTVLL 38 (107)
Q Consensus 8 ~~d~~~~rGiari--~~~~m~~Lgl~~GD~V~I 38 (107)
+|+.+.+--++++ .....-..++..||..+|
T Consensus 48 eg~~Ikv~nKa~llsgd~kL~d~~IadGD~Lei 80 (81)
T COG5417 48 EGTQIKVMNKAQLLSGDDKLIDYQIADGDILEI 80 (81)
T ss_pred CCCEEEEeccceEecCCceEEeccccCCCEEEe
Confidence 3556666555555 334445666677776654
No 209
>TIGR00767 rho transcription termination factor Rho. Members of this family differ in the specificity of RNA binding.
Probab=24.68 E-value=70 Score=26.70 Aligned_cols=21 Identities=24% Similarity=0.256 Sum_probs=19.0
Q ss_pred EecCHHHHhhCCCCCCCEEEE
Q psy3865 18 RRKESAKMDELNLFRGDTVLL 38 (107)
Q Consensus 18 ari~~~~m~~Lgl~~GD~V~I 38 (107)
++++|..+++.+++.||.|.=
T Consensus 79 ~yvs~~~i~~~~lr~gd~v~g 99 (415)
T TIGR00767 79 IYVSPSQIRRFNLRTGDTIEG 99 (415)
T ss_pred eeeCHHHHHhcCCCCCCEEEE
Confidence 578999999999999999974
No 210
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=24.60 E-value=94 Score=27.59 Aligned_cols=17 Identities=29% Similarity=0.532 Sum_probs=16.0
Q ss_pred HHHhhCCCCCCCEEEEE
Q psy3865 23 AKMDELNLFRGDTVLLR 39 (107)
Q Consensus 23 ~~m~~Lgl~~GD~V~I~ 39 (107)
+.+++++++.||+|.|+
T Consensus 361 d~I~rkdIrIGDtV~V~ 377 (667)
T COG0272 361 DEIKRKDIRIGDTVVVR 377 (667)
T ss_pred HHHHhcCCCCCCEEEEE
Confidence 78889999999999998
No 211
>CHL00010 infA translation initiation factor 1
Probab=24.50 E-value=1.1e+02 Score=19.21 Aligned_cols=25 Identities=20% Similarity=0.189 Sum_probs=18.2
Q ss_pred eEEEeHhhhhc-ccccCCCeEEEEeC
Q psy3865 60 KIRMNRVMRNN-LRVRLSDVVSLVPC 84 (107)
Q Consensus 60 ~Irid~~~R~N-~~v~igD~V~V~~~ 84 (107)
..++-|-+|++ ...-.||.|.+++.
T Consensus 33 ~c~~rGklr~~~i~~~vGD~V~ve~~ 58 (78)
T CHL00010 33 LGYISGKIRRNSIRILPGDRVKVELS 58 (78)
T ss_pred EEEeccceecCCcccCCCCEEEEEEc
Confidence 45566677764 66778999999963
No 212
>KOG0741|consensus
Probab=24.07 E-value=1.5e+02 Score=26.39 Aligned_cols=33 Identities=18% Similarity=0.155 Sum_probs=29.9
Q ss_pred cCCCCCCCeEEEeHhhhhcccccCCCeEEEEeC
Q psy3865 52 SDDTCPDEKIRMNRVMRNNLRVRLSDVVSLVPC 84 (107)
Q Consensus 52 ~~~d~~~~~Irid~~~R~N~~v~igD~V~V~~~ 84 (107)
..-+.+++.|..+...|+=+++++||.|.|++.
T Consensus 53 ~~~~i~~g~i~fs~~qR~wa~~Sl~qev~V~~~ 85 (744)
T KOG0741|consen 53 FTPSIPPGNIGFSLPQRKWAGWSLGQEVEVKPF 85 (744)
T ss_pred ccCCCCCceeccchhhhhhhhcccCceeEEEec
Confidence 335789999999999999999999999999976
No 213
>TIGR00451 unchar_dom_2 uncharacterized domain 2. This uncharacterized domain is found a number of enzymes and uncharacterized proteins, often at the C-terminus. It is found in some but not all members of a family of related tRNA-guanine transglycosylases (tgt), which exchange a guanine base for some modified base without breaking the phosphodiester backbone of the tRNA. It is also found in rRNA pseudouridine synthase, another enzyme of RNA base modification not otherwise homologous to tgt. It is found, again at the C-terminus, in two putative glutamate 5-kinases. It is also found in a family of small, uncharacterized archaeal proteins consisting mostly of this domain.
Probab=23.96 E-value=1.4e+02 Score=19.37 Aligned_cols=36 Identities=17% Similarity=0.407 Sum_probs=21.6
Q ss_pred cCCeEEEeEEEecCHHHHhhCCCCCCCEEEEEeccCCcEEEE
Q psy3865 8 RGDTVLLRGKRRKESAKMDELNLFRGDTVLLRGKRRKESVCI 49 (107)
Q Consensus 8 ~~d~~~~rGiari~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai 49 (107)
+|-.+...|+...+. .+..||.|.|......+.+|+
T Consensus 45 ~Ga~L~~pGV~~~~~------~~~~gd~V~I~~~~~~~~iav 80 (107)
T TIGR00451 45 NGADVMRPGIVDADE------DIKEGDDVVVVDENKDRPLAV 80 (107)
T ss_pred CCccccCCeeEeCCC------CcCCCCEEEEEECCCCeEEEE
Confidence 455555566655544 567899999985432244444
No 214
>COG3377 Uncharacterized conserved protein [Function unknown]
Probab=23.92 E-value=47 Score=22.23 Aligned_cols=25 Identities=28% Similarity=0.343 Sum_probs=15.9
Q ss_pred EEEeEEEecCH----------HHHhhCCCCCCCEE
Q psy3865 12 VLLRGKRRKES----------AKMDELNLFRGDTV 36 (107)
Q Consensus 12 ~~~rGiari~~----------~~m~~Lgl~~GD~V 36 (107)
+.++|+.-++. ...++||+..|+..
T Consensus 54 ~rv~GVrt~ddml~A~i~evT~~Ae~lGI~~Gm~~ 88 (95)
T COG3377 54 VRVVGVRTFDDMLSAPIVEVTSAAEELGIKRGMKG 88 (95)
T ss_pred eEEEeeeeHHHHhcchHHHHHHHHHHhCCCccchH
Confidence 45666666654 45567788777753
No 215
>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=23.56 E-value=43 Score=19.05 Aligned_cols=12 Identities=25% Similarity=0.487 Sum_probs=5.3
Q ss_pred CCCCCCCEEEEE
Q psy3865 28 LNLFRGDTVLLR 39 (107)
Q Consensus 28 Lgl~~GD~V~I~ 39 (107)
|.+..||+|.|-
T Consensus 16 Ls~~~Gd~i~v~ 27 (55)
T PF07653_consen 16 LSFKKGDVIEVL 27 (55)
T ss_dssp -EB-TTEEEEEE
T ss_pred eEEecCCEEEEE
Confidence 445555555554
No 216
>COG0261 RplU Ribosomal protein L21 [Translation, ribosomal structure and biogenesis]
Probab=23.39 E-value=1.1e+02 Score=20.80 Aligned_cols=25 Identities=16% Similarity=0.227 Sum_probs=19.2
Q ss_pred ccccCCCeEEEEeCCCCCCccEEEEc
Q psy3865 71 LRVRLSDVVSLVPCPGIVYGKRIHVL 96 (107)
Q Consensus 71 ~~v~igD~V~V~~~~~~~~a~~V~l~ 96 (107)
-+|.-||.+.|++. +..++..|.+-
T Consensus 12 ykV~~G~~i~vEkl-~~e~g~~v~f~ 36 (103)
T COG0261 12 YKVEEGDVIKVEKL-DAEPGDKVEFD 36 (103)
T ss_pred EEEecCCEEEEEEc-CCCCCCEEEEE
Confidence 35778899999987 77777777763
No 217
>TIGR02212 lolCE lipoprotein releasing system, transmembrane protein, LolC/E family. This model describes the LolC protein, and its paralog LolE found in some species. These proteins are homologous to permease proteins of ABC transporters. In some species, two paralogs occur, designated LolC and LolE. In others, a single form is found and tends to be designated LolC.
Probab=23.37 E-value=2.4e+02 Score=21.92 Aligned_cols=22 Identities=18% Similarity=0.148 Sum_probs=19.6
Q ss_pred EecCHHHHhhCCCCCCCEEEEE
Q psy3865 18 RRKESAKMDELNLFRGDTVLLR 39 (107)
Q Consensus 18 ari~~~~m~~Lgl~~GD~V~I~ 39 (107)
+-++.+.+++||+..||.|.+.
T Consensus 145 ivl~~~~a~~l~~~~Gd~v~l~ 166 (411)
T TIGR02212 145 IIIGEQLAEKLGVSVGDKITLI 166 (411)
T ss_pred EEEhHHHHHHCCCCCCCEEEEE
Confidence 5568889999999999999996
No 218
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=23.34 E-value=78 Score=28.00 Aligned_cols=19 Identities=32% Similarity=0.555 Sum_probs=17.3
Q ss_pred CHHHHhhCCCCCCCEEEEE
Q psy3865 21 ESAKMDELNLFRGDTVLLR 39 (107)
Q Consensus 21 ~~~~m~~Lgl~~GD~V~I~ 39 (107)
+.+.+++++|..||+|.|+
T Consensus 381 N~~~i~~~di~iGD~V~V~ 399 (689)
T PRK14351 381 NPAEIEELGVNVGDRVRVK 399 (689)
T ss_pred CHHHHHHcCCCCCCEEEEE
Confidence 3589999999999999998
No 219
>PF01835 A2M_N: MG2 domain; InterPro: IPR002890 The proteinase-binding alpha-macroglobulins (A2M) [] are large glycoproteins found in the plasma of vertebrates, in the hemolymph of some invertebrates and in reptilian and avian egg white. A2M-like proteins are able to inhibit all four classes of proteinases by a 'trapping' mechanism. They have a peptide stretch, called the 'bait region', which contains specific cleavage sites for different proteinases. When a proteinase cleaves the bait region, a conformational change is induced in the protein, thus trapping the proteinase. The entrapped enzyme remains active against low molecular weight substrates, whilst its activity toward larger substrates is greatly reduced, due to steric hindrance. Following cleavage in the bait region, a thiol ester bond, formed between the side chains of a cysteine and a glutamine, is cleaved and mediates the covalent binding of the A2M-like protein to the proteinase. This family includes the N-terminal region of the alpha-2-macroglobulin family. The inhibitor domains belong to MEROPS inhibitor family I39.; GO: 0004866 endopeptidase inhibitor activity; PDB: 2B39_B 3KLS_B 3PRX_C 3KM9_B 3PVM_C 3CU7_A 4E0S_A 4A5W_A 4ACQ_C 2P9R_B ....
Probab=23.31 E-value=82 Score=19.74 Aligned_cols=13 Identities=38% Similarity=0.532 Sum_probs=11.6
Q ss_pred cCCeEEEeEEEec
Q psy3865 8 RGDTVLLRGKRRK 20 (107)
Q Consensus 8 ~~d~~~~rGiari 20 (107)
.||+|.+|+++|-
T Consensus 13 PGetV~~~~~~~~ 25 (99)
T PF01835_consen 13 PGETVHFRAIVRD 25 (99)
T ss_dssp TTSEEEEEEEEEE
T ss_pred CCCEEEEEEEEec
Confidence 6999999999884
No 220
>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=23.18 E-value=1e+02 Score=18.09 Aligned_cols=11 Identities=27% Similarity=0.341 Sum_probs=4.5
Q ss_pred CCCCCCCEEEE
Q psy3865 28 LNLFRGDTVLL 38 (107)
Q Consensus 28 Lgl~~GD~V~I 38 (107)
.-+..||.|+|
T Consensus 47 ~~L~~gD~vei 57 (64)
T TIGR01683 47 TILKEGDRIEI 57 (64)
T ss_pred eecCCCCEEEE
Confidence 33444444443
No 221
>PRK10850 PTS system phosphohistidinoprotein-hexose phosphotransferase subunit Hpr; Provisional
Probab=23.18 E-value=1.6e+02 Score=18.75 Aligned_cols=34 Identities=15% Similarity=0.346 Sum_probs=23.5
Q ss_pred ccCCeEEEeEEEecCHHHH---hhCCCCCCCEEEEEe
Q psy3865 7 FRGDTVLLRGKRRKESAKM---DELNLFRGDTVLLRG 40 (107)
Q Consensus 7 ~~~d~~~~rGiari~~~~m---~~Lgl~~GD~V~I~G 40 (107)
|+.+..+.++-...|...+ =.||+..||.|+|.-
T Consensus 29 ~~s~v~l~~~~~~~~akSil~lm~Lg~~~G~~v~i~~ 65 (85)
T PRK10850 29 FTSEITVTSNGKSASAKSLFKLQTLGLTQGTVVTISA 65 (85)
T ss_pred CCCEEEEEECCeEEchHhHHHHHhcCCCCCCEEEEEE
Confidence 6666665555455665333 389999999999983
No 222
>cd01812 BAG1_N Ubiquitin-like domain of BAG1. BAG1_N N-terminal ubiquitin-like (Ubl) domain of the BAG1 protein. This domain occurs together with the BAG domain and is closely related to the Ubl domain of a family of deubiquitinases that includes Rpn11, UBP6 (USP14), USP7 (HAUSP).
Probab=23.10 E-value=94 Score=18.12 Aligned_cols=20 Identities=20% Similarity=0.340 Sum_probs=15.3
Q ss_pred CHHHHhhCCCCCCCEEEEEe
Q psy3865 21 ESAKMDELNLFRGDTVLLRG 40 (107)
Q Consensus 21 ~~~~m~~Lgl~~GD~V~I~G 40 (107)
+......+|+.+|+.+.+-|
T Consensus 51 d~~~L~~~~i~~g~~l~v~~ 70 (71)
T cd01812 51 DAETLDMSGVKDGSKVMLLE 70 (71)
T ss_pred ccCcHHHcCCCCCCEEEEec
Confidence 45567888888888887765
No 223
>PRK05863 sulfur carrier protein ThiS; Provisional
Probab=23.06 E-value=1.1e+02 Score=18.18 Aligned_cols=15 Identities=13% Similarity=0.124 Sum_probs=8.0
Q ss_pred HHHhhCCCCCCCEEEE
Q psy3865 23 AKMDELNLFRGDTVLL 38 (107)
Q Consensus 23 ~~m~~Lgl~~GD~V~I 38 (107)
+..+.. +.+||.|+|
T Consensus 44 ~~~~~~-L~~gD~ieI 58 (65)
T PRK05863 44 SDWATK-LRDGARLEV 58 (65)
T ss_pred hHhhhh-cCCCCEEEE
Confidence 334443 566666665
No 224
>TIGR03095 rusti_cyanin rusticyanin. Rusticyanin is a blue copper protein, described in an obligate acidophilic chemolithoautroph, Acidithiobacillus ferrooxidans, as an electron transfer protein. It can constitute up to 5 percent of protein in cells grown on Fe(II) and is thought to be part of an electron chain for Fe(II) oxidation, with two c-type cytochromes, an aa3-type cytochrome oxidase, and 02 as terminal electron acceptor. It is rather closely related to sulfocyanin (TIGR03094).
Probab=23.04 E-value=2.1e+02 Score=20.04 Aligned_cols=50 Identities=8% Similarity=0.014 Sum_probs=33.8
Q ss_pred CCEEEEEeccCCcEEEEeccCCCCCCCeEEEeHhhhhcccccCCCeEEEEeC
Q psy3865 33 GDTVLLRGKRRKESVCIVLSDDTCPDEKIRMNRVMRNNLRVRLSDVVSLVPC 84 (107)
Q Consensus 33 GD~V~I~Gkr~~~tvai~~~~~d~~~~~Irid~~~R~N~~v~igD~V~V~~~ 84 (107)
++.|.-.|++ -.+-+...........+.+++..=--+.+.-||.|++.-.
T Consensus 18 ~~~v~~~g~~--v~v~~~~~~~~~~~~~f~~~~~~~P~I~v~~Gd~V~v~v~ 67 (148)
T TIGR03095 18 GSTIYYNNST--TLVVAAGPMPGPSMYSFEIHDLKNPTIVIPEGVTVHFTVI 67 (148)
T ss_pred CCEEEEcCCE--EEEEEEEcCCCCCceeEEecCCCCCEEEEcCCCEEEEEEE
Confidence 3566666654 2333333444556677888888778888999999999864
No 225
>PRK06842 fumarate hydratase; Provisional
Probab=23.00 E-value=93 Score=23.18 Aligned_cols=20 Identities=35% Similarity=0.625 Sum_probs=14.5
Q ss_pred cCHHHHhhCCCCCCCEEEEEec
Q psy3865 20 KESAKMDELNLFRGDTVLLRGK 41 (107)
Q Consensus 20 i~~~~m~~Lgl~~GD~V~I~Gk 41 (107)
++++..++|. .||.|.+.|.
T Consensus 9 l~~e~i~~L~--vGD~V~LsG~ 28 (185)
T PRK06842 9 LTEEKVKDLK--AGDSVLISGY 28 (185)
T ss_pred CCHHHHhhCC--CCCEEEEeEE
Confidence 4556666555 5999999985
No 226
>PF13567 DUF4131: Domain of unknown function (DUF4131)
Probab=22.97 E-value=58 Score=21.45 Aligned_cols=13 Identities=46% Similarity=0.746 Sum_probs=9.8
Q ss_pred CCCCCCEEEEEec
Q psy3865 29 NLFRGDTVLLRGK 41 (107)
Q Consensus 29 gl~~GD~V~I~Gk 41 (107)
.+.+||.++++|+
T Consensus 128 ~l~~Gd~i~~~g~ 140 (176)
T PF13567_consen 128 RLQPGDRIRVRGK 140 (176)
T ss_pred ccCCCCEEEEEEE
Confidence 5777888888774
No 227
>PRK07696 sulfur carrier protein ThiS; Provisional
Probab=22.60 E-value=1.1e+02 Score=18.54 Aligned_cols=16 Identities=19% Similarity=0.503 Sum_probs=6.2
Q ss_pred HHHhhCCCCCCCEEEE
Q psy3865 23 AKMDELNLFRGDTVLL 38 (107)
Q Consensus 23 ~~m~~Lgl~~GD~V~I 38 (107)
+.-.+.-+..||.|+|
T Consensus 45 ~~w~~~~L~~gD~iEI 60 (67)
T PRK07696 45 DDHTDTSVFDGDQIEI 60 (67)
T ss_pred HHcCceecCCCCEEEE
Confidence 3333333444444433
No 228
>PRK08228 L(+)-tartrate dehydratase subunit beta; Validated
Probab=22.53 E-value=95 Score=23.50 Aligned_cols=20 Identities=20% Similarity=0.551 Sum_probs=14.7
Q ss_pred cCHHHHhhCCCCCCCEEEEEec
Q psy3865 20 KESAKMDELNLFRGDTVLLRGK 41 (107)
Q Consensus 20 i~~~~m~~Lgl~~GD~V~I~Gk 41 (107)
+++++.++|. .||.|.+.|.
T Consensus 10 l~~e~i~~L~--vGD~V~LsG~ 29 (204)
T PRK08228 10 IKDEDLQDIK--VGDVIYLTGT 29 (204)
T ss_pred CCHHHHhhCC--CCCEEEEEEE
Confidence 4556666555 5999999995
No 229
>cd06196 FNR_like_1 Ferredoxin reductase-like proteins catalyze electron transfer between an NAD(P)-binding domain of the alpha/beta class and a discrete (usually N-terminal) domain which varies in orientation with respect to the NAD(P) binding domain. The N-terminal region may contain a flavin prosthetic group (as in flavoenzymes) or use flavin as a substrate. Ferredoxin is reduced in the final stage of photosystem I. The flavoprotein Ferredoxin-NADP+ reductase transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) which then transfers a hydride ion to convert NADP+ to NADPH.
Probab=22.42 E-value=1.5e+02 Score=21.07 Aligned_cols=56 Identities=11% Similarity=0.061 Sum_probs=31.4
Q ss_pred hCCCCCCCEEEEEec-----cCCcEEEEeccCCCCCC--CeEEE----eHhhhhcccccCCCeEEEEe
Q psy3865 27 ELNLFRGDTVLLRGK-----RRKESVCIVLSDDTCPD--EKIRM----NRVMRNNLRVRLSDVVSLVP 83 (107)
Q Consensus 27 ~Lgl~~GD~V~I~Gk-----r~~~tvai~~~~~d~~~--~~Iri----d~~~R~N~~v~igD~V~V~~ 83 (107)
.+...+|++|.|+-. .......++...++ +. =.|+. .+.++.-..+..||.|.++.
T Consensus 25 ~~~~~pGQ~v~l~~~~~~~~~~~r~ySi~s~~~~-~~l~~~vk~~~~~g~~s~~l~~l~~G~~v~i~g 91 (218)
T cd06196 25 GYDFTPGQATEVAIDKPGWRDEKRPFTFTSLPED-DVLEFVIKSYPDHDGVTEQLGRLQPGDTLLIED 91 (218)
T ss_pred cCCCCCCCEEEEEeeCCCCCccccccccccCCCC-CeEEEEEEEcCCCCcHhHHHHhCCCCCEEEEEC
Confidence 468999999998731 11112222222222 11 11322 23466666788999999985
No 230
>PRK03818 putative transporter; Validated
Probab=22.38 E-value=57 Score=27.85 Aligned_cols=41 Identities=24% Similarity=0.281 Sum_probs=30.9
Q ss_pred cccCcccCCeEEEeEEEecCHH--HHhhCCCCCCCEEEEEecc
Q psy3865 2 DELNLFRGDTVLLRGKRRKESA--KMDELNLFRGDTVLLRGKR 42 (107)
Q Consensus 2 ~~~~~~~~d~~~~rGiari~~~--~m~~Lgl~~GD~V~I~Gkr 42 (107)
.||++.+.--+.|-++.|-+.+ ...++-++.||++++.|.+
T Consensus 307 ~eL~~r~~~Gv~VlaI~R~g~~l~~~~d~~Lq~GD~LlVvG~~ 349 (552)
T PRK03818 307 RDLHLKNKYGVVISRLNRAGVELVASPDLSLQFGDILNLVGRP 349 (552)
T ss_pred HHhcccccCCeEEEEEeECCeecCCCCCCEEecCCEEEEEECH
Confidence 3566666667888888885443 2458889999999999976
No 231
>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=22.28 E-value=69 Score=20.56 Aligned_cols=18 Identities=28% Similarity=0.394 Sum_probs=12.9
Q ss_pred HHHhhCCCCCCCEEEEEe
Q psy3865 23 AKMDELNLFRGDTVLLRG 40 (107)
Q Consensus 23 ~~m~~Lgl~~GD~V~I~G 40 (107)
+-++.+++.+||++.+-.
T Consensus 68 ~l~~~~~a~~GD~ll~~A 85 (95)
T PF02938_consen 68 ALIERLGAKPGDLLLFVA 85 (95)
T ss_dssp HHHHHTT--TTEEEEEEE
T ss_pred HHHHHhCCCCCCEEEEEC
Confidence 456699999999999873
No 232
>COG4591 LolE ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]
Probab=22.19 E-value=96 Score=25.60 Aligned_cols=27 Identities=26% Similarity=0.349 Sum_probs=23.6
Q ss_pred CCeEEEeHhhhhcccccCCCeEEEEeC
Q psy3865 58 DEKIRMNRVMRNNLRVRLSDVVSLVPC 84 (107)
Q Consensus 58 ~~~Irid~~~R~N~~v~igD~V~V~~~ 84 (107)
...|-+-..+-+++|++.||+|++--.
T Consensus 143 ~~~iilG~~LA~~Lgv~~GD~v~li~p 169 (408)
T COG4591 143 EFGIILGSGLAEKLGVRVGDKVTLITP 169 (408)
T ss_pred CCcEEecHHHHHHcCCCCCCEEEEEee
Confidence 444899999999999999999999863
No 233
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=21.84 E-value=59 Score=20.92 Aligned_cols=37 Identities=16% Similarity=0.214 Sum_probs=18.0
Q ss_pred CCCCCCCEEEEE-eccCCcEEEEeccCCCCCCCeEEEeHh
Q psy3865 28 LNLFRGDTVLLR-GKRRKESVCIVLSDDTCPDEKIRMNRV 66 (107)
Q Consensus 28 Lgl~~GD~V~I~-Gkr~~~tvai~~~~~d~~~~~Irid~~ 66 (107)
+.++.||.|.|- |+.+.+.--+... +...+.+.+++.
T Consensus 7 ~~I~~GD~V~Vi~G~dKGK~G~V~~V--~~~~~~V~Vegv 44 (83)
T CHL00141 7 MHVKIGDTVKIISGSDKGKIGEVLKI--IKKSNKVIVKGI 44 (83)
T ss_pred CcccCCCEEEEeEcCCCCcEEEEEEE--EcCCCEEEEcCc
Confidence 467778887765 4422222212111 123356666665
No 234
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=21.74 E-value=1.4e+02 Score=18.30 Aligned_cols=25 Identities=20% Similarity=0.254 Sum_probs=17.9
Q ss_pred eEEEeHhhhh-cccccCCCeEEEEeC
Q psy3865 60 KIRMNRVMRN-NLRVRLSDVVSLVPC 84 (107)
Q Consensus 60 ~Irid~~~R~-N~~v~igD~V~V~~~ 84 (107)
..++-|-+|+ ......||.|.+++.
T Consensus 33 ~c~~~Gklr~~~i~i~vGD~V~ve~~ 58 (72)
T PRK00276 33 LAHISGKMRKNYIRILPGDKVTVELS 58 (72)
T ss_pred EEEEccceeeCCcccCCCCEEEEEEc
Confidence 3456666663 566889999999953
No 235
>PF14345 GDYXXLXY: GDYXXLXY protein
Probab=21.74 E-value=57 Score=22.52 Aligned_cols=62 Identities=26% Similarity=0.309 Sum_probs=29.8
Q ss_pred CcccCCeEEEeEEEecCHHH-HhhCCCCCCCEEEEEeccCCcEE--EE-eccC--CCCCCCeEEEeHhhh
Q psy3865 5 NLFRGDTVLLRGKRRKESAK-MDELNLFRGDTVLLRGKRRKESV--CI-VLSD--DTCPDEKIRMNRVMR 68 (107)
Q Consensus 5 ~~~~~d~~~~rGiari~~~~-m~~Lgl~~GD~V~I~Gkr~~~tv--ai-~~~~--~d~~~~~Irid~~~R 68 (107)
+||+||++.++= -++... ...-....|+.+.+.=+.....+ +. +..+ .....+.+.+-+..+
T Consensus 34 dllrGdYv~L~Y--~i~~~~~~~~~~~~~~~~vyv~L~~d~~g~~~~~~v~~~~p~~~~~~~~~l~g~~~ 101 (144)
T PF14345_consen 34 DLLRGDYVALNY--DISRVDPSEDPELKNGDTVYVVLKPDADGVARATFVSFDRPKPLAPGEVYLRGRVR 101 (144)
T ss_pred cccccceEEEEc--ccccCCccccccccCCCEEEEEEEECCCCcEEEEEEEecCCCCCCCCceEEEEEec
Confidence 689999999872 222222 22334455555544421111222 11 1111 133456666666666
No 236
>TIGR02063 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
Probab=21.63 E-value=5.5e+02 Score=22.48 Aligned_cols=76 Identities=17% Similarity=0.121 Sum_probs=42.0
Q ss_pred cCcccCCeEEEeEEEecCHHHHhhCCCCCCCEEEEEeccCCcEEEEec---------cCCCCCCCeEEEeHhhhhccccc
Q psy3865 4 LNLFRGDTVLLRGKRRKESAKMDELNLFRGDTVLLRGKRRKESVCIVL---------SDDTCPDEKIRMNRVMRNNLRVR 74 (107)
Q Consensus 4 ~~~~~~d~~~~rGiari~~~~m~~Lgl~~GD~V~I~Gkr~~~tvai~~---------~~~d~~~~~Irid~~~R~N~~v~ 74 (107)
.+.|.||.|.++=...-++ -+-..|-+++|-+......++... |.+..-...|.+...- ...+.
T Consensus 101 ~~a~~GD~Vlv~I~~~~~~-----~~~~eg~Vv~Il~r~~~~~VG~~~~~~~~~~v~p~d~~~~~~I~i~~~~--~~~~~ 173 (709)
T TIGR02063 101 NGAMHGDRVLVRITGKPDG-----GDRFEARVIKILERANDQIVGTFYIENGIGFVIPDDKRIYLDIFIPPEQ--ILGAE 173 (709)
T ss_pred CcCCCCCEEEEEEecccCC-----CCCceEEEEEEEeeCCCEEEEEEEEcCcEEEEEECCCCCCCCEEECCcc--ccCCC
Confidence 3578888888872221111 122467788887766555555332 2222222345564332 23667
Q ss_pred CCCeEEEEeCCCC
Q psy3865 75 LSDVVSLVPCPGI 87 (107)
Q Consensus 75 igD~V~V~~~~~~ 87 (107)
.||.|.++-. .+
T Consensus 174 ~g~~v~v~i~-~~ 185 (709)
T TIGR02063 174 EGDKVLVEIT-KY 185 (709)
T ss_pred CCCEEEEEEc-cC
Confidence 8999999864 55
No 237
>smart00532 LIGANc Ligase N family.
Probab=21.57 E-value=80 Score=26.36 Aligned_cols=17 Identities=18% Similarity=0.335 Sum_probs=14.5
Q ss_pred ccccCCCeEEEEeCCCC
Q psy3865 71 LRVRLSDVVSLVPCPGI 87 (107)
Q Consensus 71 ~~v~igD~V~V~~~~~~ 87 (107)
+++++||+|.|+++.++
T Consensus 361 ~~i~iGd~V~V~raGdV 377 (441)
T smart00532 361 KDIRIGDTVVVRKAGDV 377 (441)
T ss_pred cCCCCCCEEEEEECCCc
Confidence 57899999999998654
No 238
>PF12704 MacB_PCD: MacB-like periplasmic core domain; PDB: 3FTJ_A 3IS6_B.
Probab=21.34 E-value=1.4e+02 Score=20.38 Aligned_cols=25 Identities=16% Similarity=0.432 Sum_probs=22.3
Q ss_pred CCeEEEeHhhhhccccc---CCCeEEEE
Q psy3865 58 DEKIRMNRVMRNNLRVR---LSDVVSLV 82 (107)
Q Consensus 58 ~~~Irid~~~R~N~~v~---igD~V~V~ 82 (107)
.+.|-++....+.++.+ +||.|++.
T Consensus 140 ~~~ivi~~~~a~~~~~~~~~iGd~i~l~ 167 (232)
T PF12704_consen 140 ENEIVISESLAKKLGLSEDPIGDTITLN 167 (232)
T ss_dssp TTEEEEEHHHHHHCCTTS--TT-EEEET
T ss_pred cceeecchhHHHHhccCCCccceEEEEC
Confidence 78999999999999999 99999995
No 239
>PTZ00241 40S ribosomal protein S11; Provisional
Probab=21.27 E-value=1.5e+02 Score=21.55 Aligned_cols=26 Identities=23% Similarity=0.364 Sum_probs=18.1
Q ss_pred cccccCCCeEEEEeCCCCCCccEEEE
Q psy3865 70 NLRVRLSDVVSLVPCPGIVYGKRIHV 95 (107)
Q Consensus 70 N~~v~igD~V~V~~~~~~~~a~~V~l 95 (107)
+..+.+||.|+|..+..+..-++-.|
T Consensus 114 ~~~~kvGD~V~I~EcRPLSKTKrf~V 139 (158)
T PTZ00241 114 CFDVKEGDIVVVGQCRPLSKTVRFNV 139 (158)
T ss_pred cCCCCCCCEEEEEEcCCCCCceeEEE
Confidence 34589999999998855544444444
No 240
>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=21.21 E-value=1.3e+02 Score=17.75 Aligned_cols=11 Identities=27% Similarity=0.398 Sum_probs=4.7
Q ss_pred CCCCCCCEEEE
Q psy3865 28 LNLFRGDTVLL 38 (107)
Q Consensus 28 Lgl~~GD~V~I 38 (107)
--+..||.|+|
T Consensus 48 ~~L~~gD~V~i 58 (65)
T cd00565 48 TPLQDGDRIEI 58 (65)
T ss_pred eecCCCCEEEE
Confidence 33444444443
No 241
>PF13550 Phage-tail_3: Putative phage tail protein
Probab=21.21 E-value=79 Score=21.34 Aligned_cols=16 Identities=38% Similarity=0.509 Sum_probs=13.5
Q ss_pred hhCCCCCCCEEEEEec
Q psy3865 26 DELNLFRGDTVLLRGK 41 (107)
Q Consensus 26 ~~Lgl~~GD~V~I~Gk 41 (107)
+.+.+.+||+|.|...
T Consensus 136 ~~~~l~pGDvi~l~~~ 151 (164)
T PF13550_consen 136 DGLALEPGDVIALSDD 151 (164)
T ss_pred hhccCCCCCEEEEEeC
Confidence 4578999999999954
No 242
>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=21.10 E-value=1.5e+02 Score=17.56 Aligned_cols=29 Identities=7% Similarity=0.149 Sum_probs=18.6
Q ss_pred cCCeEEEeEEEecCHHHHhhCCCCCCCEEEE
Q psy3865 8 RGDTVLLRGKRRKESAKMDELNLFRGDTVLL 38 (107)
Q Consensus 8 ~~d~~~~rGiari~~~~m~~Lgl~~GD~V~I 38 (107)
+.+.+.|..+..=+| ..+.|+.+||.|.=
T Consensus 11 ~~~~~~V~~v~~~s~--a~~~gl~~GD~I~~ 39 (85)
T cd00988 11 DDGGLVITSVLPGSP--AAKAGIKAGDIIVA 39 (85)
T ss_pred cCCeEEEEEecCCCC--HHHcCCCCCCEEEE
Confidence 455566665544344 45569999999853
No 243
>TIGR03106 trio_M42_hydro hydrolase, peptidase M42 family. This model describes a subfamily of MEROPS peptidase family M42, a glutamyl aminopeptidase family that also includes the cellulase CelM from Clostridium thermocellum and deblocking aminopeptidases that can remove acylated amino acids. Members of this family occur in a three gene cassette with an amidotransferase (TIGR03104)in the asparagine synthase (glutamine-hydrolyzing) family, and a probable acetyltransferase (TIGR03103) in the GNAT family.
Probab=21.08 E-value=85 Score=25.07 Aligned_cols=21 Identities=24% Similarity=0.245 Sum_probs=16.8
Q ss_pred CHHHHhhCCCCCCCEEEEEec
Q psy3865 21 ESAKMDELNLFRGDTVLLRGK 41 (107)
Q Consensus 21 ~~~~m~~Lgl~~GD~V~I~Gk 41 (107)
|.+..++||+++||.|.....
T Consensus 148 s~ee~~~lGV~~Gd~v~~~~~ 168 (343)
T TIGR03106 148 CRADLVRLGISVGDFVAFDPQ 168 (343)
T ss_pred CHHHHHHcCCCCCCEEEECCc
Confidence 346667899999999988754
No 244
>COG3111 Periplasmic protein with OB-fold [Function unknown]
Probab=21.07 E-value=1.7e+02 Score=20.61 Aligned_cols=39 Identities=21% Similarity=0.242 Sum_probs=25.0
Q ss_pred ccCcccCCeEEEeEE--EecC------------------HHHHhhCCCCCCCEEEEEec
Q psy3865 3 ELNLFRGDTVLLRGK--RRKE------------------SAKMDELNLFRGDTVLLRGK 41 (107)
Q Consensus 3 ~~~~~~~d~~~~rGi--ari~------------------~~~m~~Lgl~~GD~V~I~Gk 41 (107)
.+.+|++=.|+|+|- .+++ .+.-+.+.+.+-|.|.|.|+
T Consensus 51 Ak~~~Dda~V~l~GnIv~qi~~D~y~FrD~sGeI~VeIdd~~w~g~tv~P~dkV~I~Ge 109 (128)
T COG3111 51 AKTLHDDAWVSLEGNIVRQIGDDRYVFRDASGEINVDIDDKVWNGQTVTPKDKVRIQGE 109 (128)
T ss_pred hhccccCCeEEEEeeEEEeeCCceEEEEcCCccEEEEecccccCCcccCcccEEEEEeE
Confidence 467888888888884 2332 24444666666666666665
No 245
>TIGR02657 amicyanin amicyanin. Members of this family are amicyanin, a type I blue copper protein that accepts electrons from the tryptophan tryptophylquinone (TTQ) cofactor of the methylamine dehydrogenase light chain and then transfers them to the heme group of cytochrome c-551i. Amicyanin, methylamine dehydrogenase, and cytochrome c-551i are periplasmic and form a complex. This system has been studied primarily in Paracoccus denitrificans and Methylobacterium extorquens. Related type I blue copper proteins include plastocyanin, pseudoazurin, halocyanin, etc.
Probab=20.99 E-value=70 Score=19.83 Aligned_cols=26 Identities=27% Similarity=0.291 Sum_probs=18.4
Q ss_pred EEeEEEecCHHHHhhCCCCCCCEEEEEecc
Q psy3865 13 LLRGKRRKESAKMDELNLFRGDTVLLRGKR 42 (107)
Q Consensus 13 ~~rGiari~~~~m~~Lgl~~GD~V~I~Gkr 42 (107)
.+.+.+. +| ..|.+.+||+|..+-..
T Consensus 2 ~i~~~~F-~P---~~i~v~~GdtVt~~N~d 27 (83)
T TIGR02657 2 DIAKMKY-ET---PELHVKVGDTVTWINRE 27 (83)
T ss_pred EEEeeEE-cC---CEEEECCCCEEEEEECC
Confidence 4555555 44 45889999999998653
No 246
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=20.93 E-value=1.1e+02 Score=25.76 Aligned_cols=18 Identities=11% Similarity=0.296 Sum_probs=15.3
Q ss_pred HHHhhCCCCCCCEEEEEe
Q psy3865 23 AKMDELNLFRGDTVLLRG 40 (107)
Q Consensus 23 ~~m~~Lgl~~GD~V~I~G 40 (107)
+.+.++++..||+|.|.-
T Consensus 180 ~ql~~~~V~~GDVI~Id~ 197 (450)
T COG1224 180 EQLVKEGVEEGDVIYIDA 197 (450)
T ss_pred HHHHHhCcccCCEEEEEc
Confidence 556689999999999983
No 247
>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=20.91 E-value=1.7e+02 Score=17.20 Aligned_cols=30 Identities=17% Similarity=0.132 Sum_probs=18.8
Q ss_pred CCeEEEeEEEecCHHHHhhCCCCCCCEEEEEe
Q psy3865 9 GDTVLLRGKRRKESAKMDELNLFRGDTVLLRG 40 (107)
Q Consensus 9 ~d~~~~rGiari~~~~m~~Lgl~~GD~V~I~G 40 (107)
++.+.|..+..=+ ...+.|+.+||.|.=-+
T Consensus 11 ~~~~~V~~V~~~s--~a~~aGl~~GD~I~~In 40 (80)
T cd00990 11 EGLGKVTFVRDDS--PADKAGLVAGDELVAVN 40 (80)
T ss_pred CCcEEEEEECCCC--hHHHhCCCCCCEEEEEC
Confidence 3446665543333 35678999999986543
No 248
>PF11976 Rad60-SLD: Ubiquitin-2 like Rad60 SUMO-like; InterPro: IPR022617 This entry includes small ubiquitin-related modifier (SUMO) proteins. SUMOs are small proteins that are covalently attached to lysines as post-translational modifications and are used to control multiple cellular process including signal transduction, nuclear transport and DNA replication and repair []. Unlike ubiquitin, they are not involved in protein degradation. This entry also contains the C-terminal Rad60 DNA repair protein SUMO-like domain.; PDB: 3RD2_A 2JXX_A 3RCZ_A 3GOE_A 3A4S_D 3A4R_B 2IO1_D 1U4A_A 2K1F_A 1WZ0_A ....
Probab=20.87 E-value=72 Score=18.85 Aligned_cols=19 Identities=21% Similarity=0.326 Sum_probs=14.1
Q ss_pred CHHHHhhCCCCCCCEEEEE
Q psy3865 21 ESAKMDELNLFRGDTVLLR 39 (107)
Q Consensus 21 ~~~~m~~Lgl~~GD~V~I~ 39 (107)
+....+.||+..||+|.+.
T Consensus 53 ~~~T~~~~~ied~d~Idv~ 71 (72)
T PF11976_consen 53 PNDTPEDLGIEDGDTIDVI 71 (72)
T ss_dssp TTSCHHHHT-STTEEEEEE
T ss_pred CCCCHHHCCCCCCCEEEEE
Confidence 3467789999999998763
No 249
>PRK06944 sulfur carrier protein ThiS; Provisional
Probab=20.67 E-value=1.4e+02 Score=17.36 Aligned_cols=9 Identities=0% Similarity=-0.101 Sum_probs=4.0
Q ss_pred HHhhCCCCC
Q psy3865 24 KMDELNLFR 32 (107)
Q Consensus 24 ~m~~Lgl~~ 32 (107)
..+.|++.+
T Consensus 21 ll~~l~~~~ 29 (65)
T PRK06944 21 ALAAYGARP 29 (65)
T ss_pred HHHhhCCCC
Confidence 334555543
No 250
>PF11543 UN_NPL4: Nuclear pore localisation protein NPL4; InterPro: IPR024682 Npl4, along with Ufd1, forms the heterodimer adaptor complex UN, which is involved in the recruitment of p97, an AAA ATPase, for tasks involving the ubiquitin pathway. Npl4 has a N-terminal ubiquitin-like domain which has within its structure a beta-grasp fold with a helical insert []. This entry represents the ubiquitin-like domain.; PDB: 2PJH_A 1WF9_A.
Probab=20.65 E-value=48 Score=21.00 Aligned_cols=17 Identities=29% Similarity=0.552 Sum_probs=8.3
Q ss_pred HHHhhCCCCCCCEEEEE
Q psy3865 23 AKMDELNLFRGDTVLLR 39 (107)
Q Consensus 23 ~~m~~Lgl~~GD~V~I~ 39 (107)
....+||+..||.|.++
T Consensus 62 ~tl~~lglkHGdmlyL~ 78 (80)
T PF11543_consen 62 KTLSSLGLKHGDMLYLK 78 (80)
T ss_dssp -CCCCT---TT-EEE--
T ss_pred CCHHHcCCCCccEEEEe
Confidence 45668999999999874
No 251
>PF00380 Ribosomal_S9: Ribosomal protein S9/S16; InterPro: IPR000754 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S9 is one of the proteins from the small ribosomal subunit. It belongs to the S9P family of ribosomal proteins which, on the basis of sequence similarities [, ], groups bacterial; algal chloroplast; cyanelle and archaeal S9 proteins; and mammalian; plant; and yeast mitochondrial ribosomal S9 proteins. These proteins adopt a beta-alpha-beta fold similar to that found in numerous RNA/DNA-binding proteins, as well as in kinases from the GHMP kinase family [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2V46_I 3T1H_I 3MR8_I 3F1G_I 3D5C_I 3D5A_I 2WDG_I 3MS0_I 2WDM_I 2J02_I ....
Probab=20.61 E-value=63 Score=22.25 Aligned_cols=21 Identities=29% Similarity=0.309 Sum_probs=16.0
Q ss_pred CcEEEEeccCCCCCCCeEEEeHh
Q psy3865 44 KESVCIVLSDDTCPDEKIRMNRV 66 (107)
Q Consensus 44 ~~tvai~~~~~d~~~~~Irid~~ 66 (107)
++++|.++..+ +.+.|.||+.
T Consensus 4 K~a~A~v~l~~--G~G~i~INg~ 24 (121)
T PF00380_consen 4 KTAIARVWLKP--GSGKIRINGK 24 (121)
T ss_dssp TTEEEEEEEEE--SSSEEEETTS
T ss_pred ceEEEEEEEEe--CceEEEECCE
Confidence 47888887644 7799999875
No 252
>PRK06043 fumarate hydratase; Provisional
Probab=20.54 E-value=1.1e+02 Score=22.90 Aligned_cols=20 Identities=30% Similarity=0.607 Sum_probs=14.8
Q ss_pred cCHHHHhhCCCCCCCEEEEEec
Q psy3865 20 KESAKMDELNLFRGDTVLLRGK 41 (107)
Q Consensus 20 i~~~~m~~Lgl~~GD~V~I~Gk 41 (107)
++.+++++|. .||.|.+.|.
T Consensus 9 l~~e~i~~L~--vGD~V~LsG~ 28 (192)
T PRK06043 9 LKKEDIEKLN--VGDIVYISGE 28 (192)
T ss_pred CCHHHHhhCC--CCCEEEEEEE
Confidence 4556666655 5999999994
No 253
>PRK12297 obgE GTPase CgtA; Reviewed
Probab=20.40 E-value=80 Score=26.12 Aligned_cols=18 Identities=28% Similarity=0.311 Sum_probs=15.7
Q ss_pred HHHhhCCCCCCCEEEEEe
Q psy3865 23 AKMDELNLFRGDTVLLRG 40 (107)
Q Consensus 23 ~~m~~Lgl~~GD~V~I~G 40 (107)
+.+++.|+.+||+|.|.+
T Consensus 400 ~~l~~~g~~~gd~v~i~~ 417 (424)
T PRK12297 400 DALREAGAKDGDTVRIGD 417 (424)
T ss_pred HHHHHCCCCCCCEEEECC
Confidence 566799999999999965
No 254
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=20.37 E-value=82 Score=27.96 Aligned_cols=25 Identities=12% Similarity=0.141 Sum_probs=18.1
Q ss_pred ccccCCCeEEEEeCCCC-CCccEEEE
Q psy3865 71 LRVRLSDVVSLVPCPGI-VYGKRIHV 95 (107)
Q Consensus 71 ~~v~igD~V~V~~~~~~-~~a~~V~l 95 (107)
..++|||+|.|+++.++ |.--.|..
T Consensus 366 kdIrIGDtV~V~kAGdVIP~V~~Vv~ 391 (667)
T COG0272 366 KDIRIGDTVVVRKAGDVIPQVVGVVL 391 (667)
T ss_pred cCCCCCCEEEEEecCCCCcceeeeec
Confidence 77899999999998665 33344443
No 255
>PF05683 Fumerase_C: Fumarase C-terminus; InterPro: IPR004647 This entry represents various Fe-S type hydro-lyases, including the beta subunit from both L-tartrate dehydratase (TtdB; EC:4.2.1.32) and class 2 fumarate hydratase (FumC; (4.2.1.2 from EC) []. A number of Fe-S cluster-containing hydro-lyases share a conserved motif, including argininosuccinate lyase, adenylosuccinate lyase, aspartase, class I fumarate hydratase (fumarase), and tartrate dehydratase (see IPR000362 from INTERPRO). Proteins in this group represent a subset of closely related proteins or modules, including the Escherichia coli tartrate dehydratase beta chain and the C-terminal region of the class I fumarase (where the N-terminal region is homologous to the tartrate dehydratase alpha chain). The activity of the archaeal proteins in this group is unknown.; GO: 0016836 hydro-lyase activity; PDB: 2ISB_A.
Probab=20.31 E-value=93 Score=23.56 Aligned_cols=21 Identities=33% Similarity=0.561 Sum_probs=12.7
Q ss_pred ecCHHHHhhCCCCCCCEEEEEec
Q psy3865 19 RKESAKMDELNLFRGDTVLLRGK 41 (107)
Q Consensus 19 ri~~~~m~~Lgl~~GD~V~I~Gk 41 (107)
=++.+.+++|.+ ||.|.|.|.
T Consensus 34 Plt~e~i~~L~v--GD~V~LsG~ 54 (205)
T PF05683_consen 34 PLTEEDIRKLKV--GDTVYLSGT 54 (205)
T ss_dssp S--HHHHHH--T--T-EEEEEEE
T ss_pred CCCHHHHhhCCC--CCEEEEeeE
Confidence 356677777765 999999995
No 256
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=20.23 E-value=1.2e+02 Score=14.32 Aligned_cols=20 Identities=30% Similarity=0.129 Sum_probs=12.4
Q ss_pred CCCCCEEEEEeccCCcEEEE
Q psy3865 30 LFRGDTVLLRGKRRKESVCI 49 (107)
Q Consensus 30 l~~GD~V~I~Gkr~~~tvai 49 (107)
+.+||.|.|.+-..+-..+.
T Consensus 2 ~~~G~~V~I~~G~~~g~~g~ 21 (28)
T smart00739 2 FEVGDTVRVIAGPFKGKVGK 21 (28)
T ss_pred CCCCCEEEEeECCCCCcEEE
Confidence 56899999985443333343
No 257
>cd06198 FNR_like_3 NAD(P) binding domain of ferredoxin reductase-like proteins catalyze electron transfer between an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) domain, which varies in orientation with respect to the NAD(P) binding domain. The N-terminal domain may contain a flavin prosthetic group (as in flavoenzymes) or use flavin as a substrate. Ferredoxin is reduced in the final stage of photosystem I. The flavoprotein Ferredoxin-NADP+ reductase transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) which then transfers a hydride ion to convert NADP+ to NADPH.
Probab=20.22 E-value=1.3e+02 Score=21.38 Aligned_cols=56 Identities=18% Similarity=0.106 Sum_probs=28.7
Q ss_pred CCCCCCCEEEEEec----cCCcEEEEeccCCCCCC--CeEEEeH-hhhhcc-cccCCCeEEEEe
Q psy3865 28 LNLFRGDTVLLRGK----RRKESVCIVLSDDTCPD--EKIRMNR-VMRNNL-RVRLSDVVSLVP 83 (107)
Q Consensus 28 Lgl~~GD~V~I~Gk----r~~~tvai~~~~~d~~~--~~Irid~-~~R~N~-~v~igD~V~V~~ 83 (107)
+...+|++|.|+-. .......++..+++-+. =.|+..+ .++.=. .+..||.|.|+.
T Consensus 21 ~~~~pGQ~v~l~~~~~~~~~~r~ySi~s~~~~~~~l~l~vk~~G~~t~~l~~~l~~G~~v~i~g 84 (216)
T cd06198 21 LGHRAGQFAFLRFDASGWEEPHPFTISSAPDPDGRLRFTIKALGDYTRRLAERLKPGTRVTVEG 84 (216)
T ss_pred CCcCCCCEEEEEeCCCCCCCCCCcEEecCCCCCCeEEEEEEeCChHHHHHHHhCCCCCEEEEEC
Confidence 78999999999832 11122333322211111 1122222 233322 467899999985
No 258
>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases. This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases.
Probab=20.12 E-value=3.5e+02 Score=23.55 Aligned_cols=24 Identities=13% Similarity=-0.009 Sum_probs=14.7
Q ss_pred CeEEEeHhhhhcccccCCCeEEEEe
Q psy3865 59 EKIRMNRVMRNNLRVRLSDVVSLVP 83 (107)
Q Consensus 59 ~~Irid~~~R~N~~v~igD~V~V~~ 83 (107)
..|.+.... .+.+...||.|.++-
T Consensus 107 ~~i~i~~~~-~~~~~~~g~~V~v~i 130 (654)
T TIGR00358 107 LDIIVPKAS-VKNELAEGDKVVVEL 130 (654)
T ss_pred CcEEEcCCc-cccCCCCCCEEEEEE
Confidence 335553321 223678899999985
Done!