Query 040816
Match_columns 128
No_of_seqs 110 out of 738
Neff 7.5
Searched_HMMs 46136
Date Fri Mar 29 12:06:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040816.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040816hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1724 SCF ubiquitin ligase, 100.0 7E-46 1.5E-50 266.6 13.0 128 1-128 22-161 (162)
2 COG5201 SKP1 SCF ubiquitin lig 100.0 9.3E-44 2E-48 244.5 12.0 126 2-127 20-155 (158)
3 PF01466 Skp1: Skp1 family, di 100.0 1.2E-32 2.6E-37 176.9 7.8 77 52-128 1-77 (78)
4 smart00512 Skp1 Found in Skp1 99.9 1.3E-24 2.8E-29 146.1 7.4 79 1-79 19-104 (104)
5 PF03931 Skp1_POZ: Skp1 family 99.5 7.2E-15 1.6E-19 90.3 3.8 44 1-44 18-62 (62)
6 KOG3473 RNA polymerase II tran 99.3 4.3E-12 9.4E-17 83.8 6.2 74 1-79 34-112 (112)
7 smart00225 BTB Broad-Complex, 98.0 2E-05 4.3E-10 49.0 5.8 69 3-87 19-90 (90)
8 PF00651 BTB: BTB/POZ domain; 97.9 9.4E-05 2E-09 48.6 7.5 75 3-92 31-109 (111)
9 PHA03098 kelch-like protein; P 97.9 8.7E-05 1.9E-09 61.8 8.5 83 3-102 31-113 (534)
10 PHA02713 hypothetical protein; 97.8 0.00012 2.5E-09 62.0 9.0 84 3-104 46-133 (557)
11 PHA02790 Kelch-like protein; P 97.6 0.00017 3.8E-09 59.8 7.0 79 3-97 41-123 (480)
12 KOG4441 Proteins containing BT 97.5 0.0004 8.6E-09 59.1 7.6 77 3-95 56-135 (571)
13 KOG4682 Uncharacterized conser 94.5 0.15 3.2E-06 42.1 6.6 91 4-113 89-186 (488)
14 KOG3433 Protein involved in me 93.8 0.18 3.9E-06 37.2 5.2 31 78-113 170-200 (203)
15 COG5124 Protein predicted to b 92.0 0.19 4.2E-06 37.0 3.2 31 78-113 174-204 (209)
16 KOG2716 Polymerase delta-inter 87.5 6.4 0.00014 30.1 8.5 79 4-97 25-108 (230)
17 PF03962 Mnd1: Mnd1 family; I 85.9 1.1 2.5E-05 33.0 3.7 42 67-113 144-187 (188)
18 KOG4350 Uncharacterized conser 85.2 6.8 0.00015 32.8 8.0 89 3-91 64-174 (620)
19 PF11822 DUF3342: Domain of un 78.1 2.8 6.1E-05 33.5 3.4 75 5-95 26-105 (317)
20 PF03656 Pam16: Pam16; InterP 72.1 2.9 6.3E-05 29.1 1.9 26 93-118 51-76 (127)
21 KOG1665 AFH1-interacting prote 63.1 16 0.00035 28.2 4.5 48 26-88 58-105 (302)
22 KOG3442 Uncharacterized conser 62.4 8 0.00017 26.9 2.5 25 94-118 53-77 (132)
23 PF13921 Myb_DNA-bind_6: Myb-l 60.7 15 0.00032 21.3 3.2 34 87-120 20-60 (60)
24 PF12556 CobS_N: Cobaltochelat 59.5 5.6 0.00012 21.6 1.0 12 102-113 14-25 (36)
25 PF02214 BTB_2: BTB/POZ domain 57.2 16 0.00034 23.1 3.1 52 20-86 42-94 (94)
26 PF05409 Peptidase_C30: Corona 55.1 23 0.00049 28.0 4.1 96 19-118 160-266 (293)
27 cd05029 S-100A6 S-100A6: S-100 55.0 31 0.00067 22.0 4.2 45 79-123 9-59 (88)
28 PF11198 DUF2857: Protein of u 54.3 55 0.0012 23.8 5.9 59 62-120 58-131 (180)
29 PF07957 DUF3294: Protein of u 53.9 44 0.00095 25.4 5.4 86 7-94 92-209 (216)
30 PRK05365 malonic semialdehyde 52.0 10 0.00022 27.4 1.8 34 70-113 131-164 (195)
31 cd00167 SANT 'SWI3, ADA2, N-Co 51.7 16 0.00034 19.1 2.1 20 88-107 23-42 (45)
32 smart00717 SANT SANT SWI3, AD 50.8 17 0.00036 19.2 2.2 20 88-107 25-44 (49)
33 PF10892 DUF2688: Protein of u 50.6 18 0.00039 21.7 2.3 25 99-123 30-56 (60)
34 cd02148 Nitroreductase_5 Nitro 49.5 11 0.00025 26.9 1.6 34 70-113 124-157 (185)
35 PF05321 HHA: Haemolysin expre 48.5 53 0.0011 19.7 4.1 30 28-76 8-37 (57)
36 PF00249 Myb_DNA-binding: Myb- 48.3 21 0.00045 19.8 2.3 20 87-106 24-44 (48)
37 PF11978 MVP_shoulder: Shoulde 48.0 13 0.00029 25.5 1.7 27 71-97 37-63 (118)
38 PRK11053 dihydropteridine redu 47.8 14 0.00031 27.1 2.0 34 69-112 149-183 (217)
39 PF06851 DUF1247: Protein of u 46.8 68 0.0015 22.8 5.1 68 38-109 61-134 (148)
40 PF11338 DUF3140: Protein of u 45.6 24 0.00052 23.2 2.5 33 24-56 54-88 (92)
41 PF11460 DUF3007: Protein of u 45.1 20 0.00043 24.1 2.1 23 98-123 79-101 (104)
42 KOG0511 Ankyrin repeat protein 44.9 1E+02 0.0022 25.8 6.5 72 22-96 336-432 (516)
43 KOG2075 Topoisomerase TOP1-int 43.8 1.8E+02 0.0038 25.0 7.9 92 4-95 140-251 (521)
44 COG4957 Predicted transcriptio 43.0 22 0.00048 25.1 2.2 18 96-113 98-115 (148)
45 PF01592 NifU_N: NifU-like N t 42.7 36 0.00078 23.1 3.2 22 83-104 64-85 (126)
46 PRK11325 scaffold protein; Pro 42.4 40 0.00086 23.0 3.4 38 70-107 52-90 (127)
47 smart00385 CYCLIN domain prese 42.4 68 0.0015 18.5 4.9 40 79-121 37-78 (83)
48 TIGR03419 NifU_clost FeS clust 42.1 45 0.00097 22.6 3.6 37 70-106 46-83 (121)
49 TIGR01999 iscU FeS cluster ass 41.9 42 0.00091 22.8 3.5 38 70-107 50-88 (124)
50 PF09713 A_thal_3526: Plant pr 41.3 37 0.0008 20.1 2.7 30 96-125 12-45 (54)
51 TIGR01589 A_thal_3526 uncharac 40.3 79 0.0017 18.9 4.0 29 97-125 16-48 (57)
52 PF13798 PCYCGC: Protein of un 39.8 44 0.00095 24.1 3.4 25 82-106 117-141 (158)
53 PF02084 Bindin: Bindin; Inte 39.6 45 0.00098 25.5 3.5 17 28-44 126-142 (238)
54 PF05443 ROS_MUCR: ROS/MUCR tr 39.4 14 0.0003 25.8 0.8 18 96-113 94-111 (132)
55 PRK15019 CsdA-binding activato 39.1 57 0.0012 23.2 3.9 34 81-114 86-127 (147)
56 PF08671 SinI: Anti-repressor 39.0 24 0.00052 18.3 1.5 14 94-107 14-27 (30)
57 PRK09296 cysteine desufuration 39.0 63 0.0014 22.6 4.1 33 82-114 77-117 (138)
58 PF03883 DUF328: Protein of un 39.0 27 0.0006 26.5 2.4 37 83-119 27-63 (237)
59 PRK13379 protocatechuate 4,5-d 38.9 77 0.0017 21.8 4.3 25 86-110 93-117 (119)
60 PRK13503 transcriptional activ 38.7 1.6E+02 0.0035 21.9 9.1 81 27-111 168-251 (278)
61 TIGR03147 cyt_nit_nrfF cytochr 38.4 30 0.00065 24.0 2.3 19 88-106 64-83 (126)
62 PF04355 SmpA_OmlA: SmpA / Oml 37.4 16 0.00036 22.0 0.8 21 90-110 9-29 (71)
63 COG1710 Uncharacterized protei 37.3 24 0.00052 24.5 1.6 20 90-109 102-122 (139)
64 PF03750 DUF310: Protein of un 37.0 53 0.0012 22.2 3.3 33 77-110 8-42 (119)
65 PF07671 DUF1601: Protein of u 37.0 41 0.00089 18.3 2.2 30 76-105 7-36 (37)
66 PRK13742 replication protein; 36.9 35 0.00075 26.1 2.7 34 80-113 163-199 (245)
67 PF13518 HTH_28: Helix-turn-he 36.8 55 0.0012 17.8 3.0 21 89-109 5-25 (52)
68 KOG0783 Uncharacterized conser 35.7 1.7E+02 0.0037 27.2 6.9 66 27-104 758-825 (1267)
69 TIGR01044 rplV_bact ribosomal 34.9 42 0.00092 22.2 2.5 22 87-108 13-34 (103)
70 TIGR03391 FeS_syn_CsdE cystein 34.9 76 0.0017 22.2 3.9 33 82-114 82-122 (138)
71 PF13384 HTH_23: Homeodomain-l 34.7 40 0.00086 18.5 2.1 15 95-109 16-30 (50)
72 cd02140 Nitroreductase_4 Nitro 34.3 31 0.00068 24.7 2.0 39 67-113 127-165 (192)
73 PF03918 CcmH: Cytochrome C bi 34.1 34 0.00073 24.3 2.0 18 89-106 65-83 (148)
74 PF11103 DUF2887: Protein of u 33.7 65 0.0014 24.1 3.6 29 78-106 172-200 (200)
75 cd06664 IscU_like Iron-sulfur 33.4 73 0.0016 21.2 3.6 39 69-107 46-85 (123)
76 cd00068 GGL G protein gamma su 33.0 53 0.0011 19.3 2.5 18 29-46 23-40 (57)
77 KOG4244 Failed axon connection 32.9 46 0.00099 26.2 2.7 22 100-121 112-133 (281)
78 TIGR02476 BluB cob(II)yrinic a 32.7 37 0.00081 24.7 2.2 37 67-113 134-170 (205)
79 cd02144 iodotyrosine_dehalogen 32.6 38 0.00083 23.9 2.2 36 69-114 131-167 (193)
80 TIGR02698 CopY_TcrY copper tra 32.5 1.5E+02 0.0033 20.1 5.1 36 87-122 77-112 (130)
81 KOG4591 Uncharacterized conser 32.0 1.3E+02 0.0027 23.1 4.8 31 62-92 134-164 (280)
82 PF11795 DUF3322: Uncharacteri 31.5 54 0.0012 23.9 2.8 46 26-71 141-188 (190)
83 PF09382 RQC: RQC domain; Int 31.5 1.1E+02 0.0024 19.5 4.1 39 84-122 19-64 (106)
84 cd03370 NADH_oxidase NADPH_oxi 31.4 37 0.0008 23.5 1.9 20 93-112 111-131 (156)
85 PF13725 tRNA_bind_2: Possible 30.9 1.4E+02 0.0031 18.9 5.7 69 26-110 28-97 (101)
86 PF10415 FumaraseC_C: Fumarase 30.0 1.2E+02 0.0026 17.7 3.9 32 87-121 14-47 (55)
87 PF15063 TC1: Thyroid cancer p 29.9 52 0.0011 20.9 2.2 32 89-120 29-60 (79)
88 PRK07394 hypothetical protein; 29.9 74 0.0016 25.6 3.6 33 96-128 128-161 (342)
89 COG4565 CitB Response regulato 29.8 1.2E+02 0.0025 23.2 4.4 27 18-45 145-172 (224)
90 PF14098 SSPI: Small, acid-sol 29.6 61 0.0013 19.9 2.4 20 88-107 5-24 (65)
91 PF00196 GerE: Bacterial regul 29.4 63 0.0014 18.4 2.4 23 87-109 9-31 (58)
92 PRK10144 formate-dependent nit 29.1 53 0.0011 22.8 2.3 19 88-106 64-83 (126)
93 TIGR01994 SUF_scaf_2 SUF syste 28.9 97 0.0021 21.4 3.7 37 71-107 51-88 (137)
94 PRK11548 outer membrane biogen 28.7 64 0.0014 21.5 2.6 23 88-110 41-63 (113)
95 COG1460 Uncharacterized protei 28.7 1.9E+02 0.0042 19.7 5.0 61 58-121 44-105 (114)
96 PF05871 ESCRT-II: ESCRT-II co 28.7 38 0.00083 23.8 1.6 12 34-45 28-39 (139)
97 PRK09071 hypothetical protein; 28.6 70 0.0015 25.5 3.2 31 98-128 123-153 (323)
98 PF04751 DUF615: Protein of un 28.6 1.7E+02 0.0037 20.9 4.9 57 51-107 97-153 (157)
99 PRK13696 hypothetical protein; 28.4 1.4E+02 0.0031 18.1 4.0 25 96-123 37-61 (62)
100 COG0822 IscU NifU homolog invo 28.1 99 0.0021 21.9 3.6 38 69-106 52-90 (150)
101 PF09010 AsiA: Anti-Sigma Fact 27.9 1.1E+02 0.0023 20.1 3.4 59 65-126 6-76 (91)
102 smart00421 HTH_LUXR helix_turn 27.9 86 0.0019 16.8 2.8 17 93-109 15-31 (58)
103 cd00412 pyrophosphatase Inorga 27.8 1.3E+02 0.0027 21.6 4.1 46 24-75 108-154 (155)
104 cd07921 PCA_45_Doxase_A_like S 27.7 1.2E+02 0.0026 20.4 3.7 22 87-108 82-103 (106)
105 PRK09246 amidophosphoribosyltr 27.7 68 0.0015 27.2 3.1 26 19-44 359-386 (501)
106 PLN03212 Transcription repress 27.7 83 0.0018 24.4 3.3 35 88-122 49-91 (249)
107 smart00875 BACK BTB And C-term 27.3 1.5E+02 0.0033 18.0 5.0 39 69-107 3-50 (101)
108 PRK14981 DNA-directed RNA poly 27.2 1.8E+02 0.0039 19.4 4.6 42 80-122 63-105 (112)
109 PF00134 Cyclin_N: Cyclin, N-t 27.0 96 0.0021 20.1 3.3 42 81-122 74-116 (127)
110 cd07925 LigA_like_1 The A subu 27.0 1.2E+02 0.0027 20.4 3.7 23 86-108 81-103 (106)
111 TIGR02792 PCA_ligA protocatech 25.8 1.3E+02 0.0027 20.7 3.6 21 86-106 86-106 (117)
112 PF08006 DUF1700: Protein of u 25.8 1.9E+02 0.0041 20.6 4.9 36 76-111 19-55 (181)
113 smart00224 GGL G protein gamma 25.7 78 0.0017 18.9 2.4 18 29-46 23-40 (63)
114 PF07707 BACK: BTB And C-termi 25.7 1.1E+02 0.0025 18.9 3.3 40 68-107 2-50 (103)
115 PF02796 HTH_7: Helix-turn-hel 25.6 97 0.0021 16.9 2.6 17 93-109 18-34 (45)
116 cd00336 Ribosomal_L22 Ribosoma 25.3 67 0.0014 21.0 2.2 22 87-108 15-36 (105)
117 COG4680 Uncharacterized protei 25.1 50 0.0011 21.8 1.5 17 96-112 35-51 (98)
118 CHL00034 rpl22 ribosomal prote 25.0 74 0.0016 21.6 2.4 22 87-108 24-45 (117)
119 TIGR03879 near_KaiC_dom probab 24.9 1.1E+02 0.0023 19.2 2.9 20 90-109 26-45 (73)
120 PF03131 bZIP_Maf: bZIP Maf tr 24.8 92 0.002 19.9 2.8 27 93-122 5-31 (92)
121 PF15628 RRM_DME: RRM in Demet 24.8 61 0.0013 21.7 1.9 20 88-107 57-76 (103)
122 PF01726 LexA_DNA_bind: LexA D 24.6 1.5E+02 0.0032 17.8 3.5 33 81-113 10-42 (65)
123 PLN02373 soluble inorganic pyr 24.6 1.4E+02 0.003 22.1 4.0 46 25-76 131-176 (188)
124 cd07923 Gallate_dioxygenase_C 24.5 1.6E+02 0.0035 19.4 3.8 19 87-105 74-92 (94)
125 PRK13378 protocatechuate 4,5-d 24.3 1.5E+02 0.0031 20.4 3.7 21 86-106 92-112 (117)
126 COG0091 RplV Ribosomal protein 24.0 81 0.0018 21.7 2.5 21 87-107 25-45 (120)
127 PF00690 Cation_ATPase_N: Cati 23.9 88 0.0019 18.5 2.4 28 97-124 4-33 (69)
128 PRK07631 amidophosphoribosyltr 23.9 1.4E+02 0.0031 25.2 4.3 26 19-44 349-376 (475)
129 PF08281 Sigma70_r4_2: Sigma-7 23.9 53 0.0012 18.3 1.4 18 92-109 22-39 (54)
130 PF07638 Sigma70_ECF: ECF sigm 23.8 1.9E+02 0.0041 20.6 4.6 47 62-110 118-165 (185)
131 PF07079 DUF1347: Protein of u 23.8 2.2E+02 0.0049 24.4 5.4 77 30-108 243-323 (549)
132 PF09384 UTP15_C: UTP15 C term 23.7 1.1E+02 0.0025 21.3 3.3 23 24-46 68-90 (148)
133 PRK08136 glycosyl transferase 23.7 89 0.0019 24.9 3.0 31 98-128 125-155 (317)
134 cd02138 Nitroreductase_2 Nitro 23.6 73 0.0016 22.6 2.3 38 66-113 107-144 (181)
135 TIGR01038 L22_arch ribosomal p 23.6 81 0.0018 22.5 2.5 21 87-107 26-46 (150)
136 PRK10945 gene expression modul 23.3 2E+02 0.0043 18.0 5.0 26 62-91 35-60 (72)
137 PRK04223 rpl22p 50S ribosomal 23.0 84 0.0018 22.5 2.5 21 87-107 30-50 (153)
138 PF04255 DUF433: Protein of un 22.9 1.6E+02 0.0036 16.9 3.8 25 92-119 27-51 (56)
139 PF12674 Zn_ribbon_2: Putative 22.9 1.6E+02 0.0034 18.7 3.5 30 77-107 42-71 (81)
140 PRK13377 protocatechuate 4,5-d 22.8 1.6E+02 0.0035 20.6 3.7 21 86-106 92-112 (129)
141 PF10075 PCI_Csn8: COP9 signal 22.7 1.8E+02 0.0039 19.8 4.1 45 79-127 76-124 (143)
142 PRK14621 hypothetical protein; 22.5 2.5E+02 0.0055 18.9 5.2 53 55-108 56-109 (111)
143 PRK00565 rplV 50S ribosomal pr 22.5 90 0.002 20.9 2.5 22 87-108 17-38 (112)
144 PRK03094 hypothetical protein; 21.9 54 0.0012 21.0 1.2 14 93-106 62-75 (80)
145 PRK05255 hypothetical protein; 21.9 2.6E+02 0.0055 20.4 4.8 56 52-107 109-164 (171)
146 PHA03098 kelch-like protein; P 21.8 4.2E+02 0.0091 22.0 6.8 76 27-107 73-159 (534)
147 PF14748 P5CR_dimer: Pyrroline 21.5 2.3E+02 0.005 18.5 4.3 55 69-123 26-87 (107)
148 PTZ00100 DnaJ chaperone protei 21.4 1.7E+02 0.0038 19.9 3.7 23 96-118 61-83 (116)
149 KOG4350 Uncharacterized conser 21.4 68 0.0015 27.1 1.9 7 22-28 108-114 (620)
150 KOG0027 Calmodulin and related 21.3 2.8E+02 0.006 18.9 5.5 60 63-122 42-112 (151)
151 PF09278 MerR-DNA-bind: MerR, 21.2 35 0.00076 19.9 0.2 19 93-111 11-29 (65)
152 cd02145 BluB Subfamily of the 21.0 62 0.0013 23.2 1.5 34 69-112 127-160 (196)
153 PF11399 DUF3192: Protein of u 20.8 97 0.0021 20.7 2.3 25 88-113 26-50 (102)
154 cd06170 LuxR_C_like C-terminal 20.8 1.4E+02 0.0031 16.0 2.8 17 94-110 13-29 (57)
155 cd08054 gp6 Head-Tail Connecto 20.7 1.5E+02 0.0032 18.1 3.1 20 98-117 1-20 (91)
156 PF05225 HTH_psq: helix-turn-h 20.5 1.7E+02 0.0037 16.1 3.1 22 88-109 7-29 (45)
157 PRK11187 replication initiatio 20.4 1E+02 0.0022 22.8 2.5 26 86-111 10-38 (182)
158 PF02885 Glycos_trans_3N: Glyc 20.3 1.5E+02 0.0034 17.5 3.0 22 83-104 35-56 (66)
159 PF07064 RIC1: RIC1; InterPro 20.2 2.2E+02 0.0048 21.9 4.5 55 26-80 137-205 (258)
160 PF06514 PsbU: Photosystem II 20.2 26 0.00057 23.1 -0.5 46 73-122 22-67 (93)
161 PF03698 UPF0180: Uncharacteri 20.2 62 0.0013 20.6 1.2 14 93-106 62-75 (80)
No 1
>KOG1724 consensus SCF ubiquitin ligase, Skp1 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=7e-46 Score=266.57 Aligned_cols=128 Identities=56% Similarity=0.850 Sum_probs=118.4
Q ss_pred ChhhhhHHHHHHHhcCCC-CC--ceecCCCCHHHHHHHHHHHHhcccCCC---------CcccccchhhhhhccChHHHH
Q 040816 1 AVMLESQTIKHMVEDGCA-DS--VIPLLNVRGTILSMVIEYLKKHVEAKT---------TEDDLKNWDVDFAKLGQDTLF 68 (128)
Q Consensus 1 ~aa~~S~~i~~~l~~~~~-~~--~Ipl~~v~~~~L~~Vi~~c~~h~~~~~---------~~~~~~~wd~~Fl~~~~~~l~ 68 (128)
++|++|.+|++++.+.+. .. +||||+|+|.+|++||+||+||+++++ ....++.||++|++++.+.||
T Consensus 22 ~~a~~s~~i~~~~~~~~~~~~~~~IPl~nV~~~iL~kVIewC~~Hk~d~~~~~~~~~~~~~~~i~~WD~~Flk~d~~tLf 101 (162)
T KOG1724|consen 22 EVARQSQTISAHMIEDGCADENDPIPLPNVTSKILKKVIEWCKKHKDDDPANPEDKELPEETDIPEWDAEFLKVDQGTLF 101 (162)
T ss_pred HHHHHhHHHHHHHHHcCCCccCCccccCccCHHHHHHHHHHHHHcccccccccccccccccCCccHHHHHHHhcCHHHHH
Confidence 479999999999988763 34 899999999999999999999998742 233489999999999999999
Q ss_pred HHHHHhhhccHHHHHHHHHHHHHHHhcCCCHHHHHhhcCCCCCCCHHHHHHHhhhCCCCC
Q 040816 69 DLLMAANYLDIKSLLDLLCQTVADMIKGKSPEEIRQTFHIQNDFTPEEEEEIRTETPRAF 128 (128)
Q Consensus 69 ~li~AA~~L~i~~L~~l~~~~ia~~i~gkt~eeir~~f~i~~d~t~eee~~i~~e~~W~f 128 (128)
+|+.|||||+|++|+++||+.||++++||||+|||+.|||++|+|+||+++++++|.|+|
T Consensus 102 dli~AAnyLdi~gLl~~~ck~va~mikgktpeEir~~f~I~~d~t~eE~~~~~~e~~~~~ 161 (162)
T KOG1724|consen 102 DLILAANYLDIKGLLDLTCKTVANMIKGKTPEEIREIFNIENDETPEEEEAIRKENEWAF 161 (162)
T ss_pred HHHHHhhhcccHHHHHHHHHHHHHHHccCCHHHHHHHcCCCCCCChhHHHHHhhcccccc
Confidence 999999999999999999999999999999999999999999999999999999999997
No 2
>COG5201 SKP1 SCF ubiquitin ligase, SKP1 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=9.3e-44 Score=244.54 Aligned_cols=126 Identities=47% Similarity=0.731 Sum_probs=117.6
Q ss_pred hhhhhHHHHHHHhcCCC-CCceecCCCCHHHHHHHHHHHHhcccCCC---------CcccccchhhhhhccChHHHHHHH
Q 040816 2 VMLESQTIKHMVEDGCA-DSVIPLLNVRGTILSMVIEYLKKHVEAKT---------TEDDLKNWDVDFAKLGQDTLFDLL 71 (128)
Q Consensus 2 aa~~S~~i~~~l~~~~~-~~~Ipl~~v~~~~L~~Vi~~c~~h~~~~~---------~~~~~~~wd~~Fl~~~~~~l~~li 71 (128)
+|..|-+|++|+.+.++ +-|||+|+|+|.+|.+|++||+||+.... ...+.+.||+.|+.+|+++|++++
T Consensus 20 iAerSiLikN~l~d~~~~n~p~p~pnVrSsvl~kv~ew~ehh~~s~sede~d~~~rks~p~D~wdr~Fm~vDqemL~eI~ 99 (158)
T COG5201 20 IAERSILIKNMLCDSTACNYPIPAPNVRSSVLMKVQEWMEHHTSSLSEDENDLEIRKSKPSDFWDRFFMEVDQEMLLEIC 99 (158)
T ss_pred HHHHHHHHHHHhccccccCCCCcccchhHHHHHHHHHHHHhccccCCCccChHhhhccCCccHHHHHHHHhhHHHHHHHH
Confidence 57889999999998875 78999999999999999999999998531 234577899999999999999999
Q ss_pred HHhhhccHHHHHHHHHHHHHHHhcCCCHHHHHhhcCCCCCCCHHHHHHHhhhCCCC
Q 040816 72 MAANYLDIKSLLDLLCQTVADMIKGKSPEEIRQTFHIQNDFTPEEEEEIRTETPRA 127 (128)
Q Consensus 72 ~AA~~L~i~~L~~l~~~~ia~~i~gkt~eeir~~f~i~~d~t~eee~~i~~e~~W~ 127 (128)
+|||||+|++|+++||+.||.+|+||||+|||++|||++||||||+++|++||.|+
T Consensus 100 laaNYL~ikpLLd~gCKivaemirgkSpeeir~tfni~ndfTpEEe~~irkEnEWa 155 (158)
T COG5201 100 LAANYLEIKPLLDLGCKIVAEMIRGKSPEEIRETFNIENDFTPEEERRIRKENEWA 155 (158)
T ss_pred HhhccccchHHHHHHHHHHHHHHccCCHHHHHHHhCCCCCCCHHHHHHHHHhcccc
Confidence 99999999999999999999999999999999999999999999999999999997
No 3
>PF01466 Skp1: Skp1 family, dimerisation domain; InterPro: IPR016072 SKP1 (together with SKP2) was identified as an essential component of the cyclin A-CDK2 S phase kinase complex []. It was found to bind several F-box containing proteins (e.g., Cdc4, Skp2, cyclin F) and to be involved in the ubiquitin protein degradation pathway. A yeast homologue of SKP1 (P52286) was identified in the centromere bound kinetochore complex [] and is also involved in the ubiquitin pathway []. In Dictyostelium discoideum (Slime mold) FP21 was shown to be glycosylated in the cytosol and has homology to SKP1 []. This entry represents a dimerisation domain found at the C-terminal of SKP1 proteins [], as well as in subunit D of the centromere DNA-binding protein complex Cbf3 []. This domain is multi-helical in structure, and consists of an interlocked herterodimer in F-box proteins.; GO: 0006511 ubiquitin-dependent protein catabolic process; PDB: 2P1O_A 3OGL_G 3OGM_A 3C6O_A 2P1N_A 2P1Q_A 3OGK_I 3C6N_A 3C6P_A 2P1P_A ....
Probab=99.98 E-value=1.2e-32 Score=176.90 Aligned_cols=77 Identities=66% Similarity=1.050 Sum_probs=68.4
Q ss_pred ccchhhhhhccChHHHHHHHHHhhhccHHHHHHHHHHHHHHHhcCCCHHHHHhhcCCCCCCCHHHHHHHhhhCCCCC
Q 040816 52 LKNWDVDFAKLGQDTLFDLLMAANYLDIKSLLDLLCQTVADMIKGKSPEEIRQTFHIQNDFTPEEEEEIRTETPRAF 128 (128)
Q Consensus 52 ~~~wd~~Fl~~~~~~l~~li~AA~~L~i~~L~~l~~~~ia~~i~gkt~eeir~~f~i~~d~t~eee~~i~~e~~W~f 128 (128)
+++||++|++++.+.|++|+.||+||+|++|+++||++||++++|||++|||++|||++|+|+||+++++++|+|+|
T Consensus 1 l~~wD~~F~~~~~~~L~~l~~AA~yL~I~~L~~~~~~~iA~~i~gks~eeir~~fgi~~d~t~eee~~i~~e~~w~~ 77 (78)
T PF01466_consen 1 LPEWDQEFLDVDNDELFDLLNAANYLDIKGLLDLCCKYIANMIKGKSPEEIRKYFGIENDLTPEEEEEIRKENEWAF 77 (78)
T ss_dssp HHHHHHHHT-S-HHHHHHHHHHHHHHT-HHHHHHHHHHHHHHHTTS-HHHHHHHHT---TSSHHHHHHHHHHCCCTB
T ss_pred CCHHHHHHHHcCHHHHHHHHHHHHHHcchHHHHHHHHHHHHHhcCCCHHHHHHHcCCCCCCCHHHHHHHHHHcchhc
Confidence 47899999999999999999999999999999999999999999999999999999999999999999999999997
No 4
>smart00512 Skp1 Found in Skp1 protein family. Family of Skp1 (kinetochore protein required for cell cycle progression) and elongin C (subunit of RNA polymerase II transcription factor SIII) homologues.
Probab=99.91 E-value=1.3e-24 Score=146.06 Aligned_cols=79 Identities=52% Similarity=0.817 Sum_probs=70.3
Q ss_pred ChhhhhHHHHHHHhcCCCC----CceecCCCCHHHHHHHHHHHHhcccCCCCc---ccccchhhhhhccChHHHHHHHHH
Q 040816 1 AVMLESQTIKHMVEDGCAD----SVIPLLNVRGTILSMVIEYLKKHVEAKTTE---DDLKNWDVDFAKLGQDTLFDLLMA 73 (128)
Q Consensus 1 ~aa~~S~~i~~~l~~~~~~----~~Ipl~~v~~~~L~~Vi~~c~~h~~~~~~~---~~~~~wd~~Fl~~~~~~l~~li~A 73 (128)
++|++|++|++|+++.+.. .+||+|+|+|.+|++|++||+||+.++... ..+++||.+|++++++.|++|+.|
T Consensus 19 ~~a~~S~~i~~~l~~~~~~~~~~~~Ipl~~v~~~~L~~Vi~yc~~h~~~~~~~~~~~~~~~wD~~F~~~d~~~l~dLl~A 98 (104)
T smart00512 19 EVARQSKTIKAMIEDLGVDDENNNPIPLPNVTSKILSKVIEYCEHHVDDPPSVADKDDIPTWDAEFLKIDQETLFELILA 98 (104)
T ss_pred HHHHHHHHHHHHHHccCcccCCCCCccCCCcCHHHHHHHHHHHHHcccCCCCccccccccHHHHHHHcCCHHHHHHHHHH
Confidence 4789999999999987632 489999999999999999999999886422 358999999999999999999999
Q ss_pred hhhccH
Q 040816 74 ANYLDI 79 (128)
Q Consensus 74 A~~L~i 79 (128)
|+||+|
T Consensus 99 AnyL~I 104 (104)
T smart00512 99 ANYLDI 104 (104)
T ss_pred HHhhCC
Confidence 999997
No 5
>PF03931 Skp1_POZ: Skp1 family, tetramerisation domain; InterPro: IPR016073 SKP1 (together with SKP2) was identified as an essential component of the cyclin A-CDK2 S phase kinase complex []. It was found to bind several F-box containing proteins (e.g., Cdc4, Skp2, cyclin F) and to be involved in the ubiquitin protein degradation pathway. A yeast homologue of SKP1 (P52286) was identified in the centromere bound kinetochore complex [] and is also involved in the ubiquitin pathway []. In Dictyostelium discoideum (Slime mold) FP21 was shown to be glycosylated in the cytosol and has homology to SKP1 []. This entry represents a POZ domain with a core structure consisting of beta(2)/alpha(2)/beta(2)/alpha(2) in two layers, alpha/beta. This domain is found at the N-terminal of SKP1 proteins [] as well as in subunit D of the centromere DNA-binding protein complex Cbf3 []. ; GO: 0006511 ubiquitin-dependent protein catabolic process; PDB: 1LM8_C 2XAI_E 1VCB_E 3ZRC_K 3ZRF_E 3DCG_B 2C9W_C 1LQB_B 2IZV_C 1HV2_A ....
Probab=99.53 E-value=7.2e-15 Score=90.26 Aligned_cols=44 Identities=41% Similarity=0.535 Sum_probs=38.6
Q ss_pred ChhhhhHHHHHHHhcCCCCC-ceecCCCCHHHHHHHHHHHHhccc
Q 040816 1 AVMLESQTIKHMVEDGCADS-VIPLLNVRGTILSMVIEYLKKHVE 44 (128)
Q Consensus 1 ~aa~~S~~i~~~l~~~~~~~-~Ipl~~v~~~~L~~Vi~~c~~h~~ 44 (128)
++|++|++|++|+++.+... +||||+|+|++|++|++||+||++
T Consensus 18 ~~a~~S~~i~~ml~~~~~~~~~Ipl~~v~~~~L~kViewc~~H~~ 62 (62)
T PF03931_consen 18 EAAKQSKTIKNMLEDLGDEDEPIPLPNVSSRILKKVIEWCEHHKN 62 (62)
T ss_dssp HHHTTSHHHHHHHHCTCCCGTEEEETTS-HHHHHHHHHHHHHHHH
T ss_pred HHHHHhHHHHHHHhhhcccccccccCccCHHHHHHHHHHHHhcCC
Confidence 37999999999999987644 599999999999999999999974
No 6
>KOG3473 consensus RNA polymerase II transcription elongation factor Elongin/SIII, subunit elongin C [Transcription]
Probab=99.32 E-value=4.3e-12 Score=83.84 Aligned_cols=74 Identities=27% Similarity=0.441 Sum_probs=64.1
Q ss_pred ChhhhhHHHHHHHhcCC-----CCCceecCCCCHHHHHHHHHHHHhcccCCCCcccccchhhhhhccChHHHHHHHHHhh
Q 040816 1 AVMLESQTIKHMVEDGC-----ADSVIPLLNVRGTILSMVIEYLKKHVEAKTTEDDLKNWDVDFAKLGQDTLFDLLMAAN 75 (128)
Q Consensus 1 ~aa~~S~~i~~~l~~~~-----~~~~Ipl~~v~~~~L~~Vi~~c~~h~~~~~~~~~~~~wd~~Fl~~~~~~l~~li~AA~ 75 (128)
++|+.|+|||.|+++.+ ....+-+++++|.+|+||++|+.+...+......+++|| +.+++.++|+.|||
T Consensus 34 e~AmtSgTiraml~gpg~~se~~~n~v~f~di~shiLeKvc~Yl~Yk~rY~~~s~eiPeF~-----IppemaleLL~aAn 108 (112)
T KOG3473|consen 34 EHAMTSGTIRAMLSGPGVFSEAEKNEVYFRDIPSHILEKVCEYLAYKVRYTNSSTEIPEFD-----IPPEMALELLMAAN 108 (112)
T ss_pred hhhhhhhHHHHHHcCCccccccccceEEeccchHHHHHHHHHHhhheeeeccccccCCCCC-----CCHHHHHHHHHHhh
Confidence 47899999999999865 256799999999999999999999777654557889985 99999999999999
Q ss_pred hccH
Q 040816 76 YLDI 79 (128)
Q Consensus 76 ~L~i 79 (128)
||++
T Consensus 109 ~Lec 112 (112)
T KOG3473|consen 109 YLEC 112 (112)
T ss_pred hhcC
Confidence 9974
No 7
>smart00225 BTB Broad-Complex, Tramtrack and Bric a brac. Domain in Broad-Complex, Tramtrack and Bric a brac. Also known as POZ (poxvirus and zinc finger) domain. Known to be a protein-protein interaction motif found at the N-termini of several C2H2-type transcription factors as well as Shaw-type potassium channels. Known structure reveals a tightly intertwined dimer formed via interactions between N-terminal strand and helix structures. However in a subset of BTB/POZ domains, these two secondary structures appear to be missing. Be aware SMART predicts BTB/POZ domains without the beta1- and alpha1-secondary structures.
Probab=98.01 E-value=2e-05 Score=48.96 Aligned_cols=69 Identities=25% Similarity=0.268 Sum_probs=55.6
Q ss_pred hhhhHHHHHHHhcCC---CCCceecCCCCHHHHHHHHHHHHhcccCCCCcccccchhhhhhccChHHHHHHHHHhhhccH
Q 040816 3 MLESQTIKHMVEDGC---ADSVIPLLNVRGTILSMVIEYLKKHVEAKTTEDDLKNWDVDFAKLGQDTLFDLLMAANYLDI 79 (128)
Q Consensus 3 a~~S~~i~~~l~~~~---~~~~Ipl~~v~~~~L~~Vi~~c~~h~~~~~~~~~~~~wd~~Fl~~~~~~l~~li~AA~~L~i 79 (128)
+..|..++.|+.... ....|++++++..+++.+++|+....- .++...+.+++.+|+++++
T Consensus 19 ~~~s~~f~~~~~~~~~~~~~~~i~l~~~~~~~f~~~l~~ly~~~~----------------~~~~~~~~~l~~~a~~~~~ 82 (90)
T smart00225 19 AACSPYFKALFSGDFKESKKSEIYLDDVSPEDFRALLEFLYTGKL----------------DLPEENVEELLELADYLQI 82 (90)
T ss_pred hhcCHHHHHHHcCCCccCCCCEEEecCCCHHHHHHHHHeecCcee----------------ecCHHHHHHHHHHHHHHCc
Confidence 345889999998754 356899999999999999999987322 1334478899999999999
Q ss_pred HHHHHHHH
Q 040816 80 KSLLDLLC 87 (128)
Q Consensus 80 ~~L~~l~~ 87 (128)
++|.+.|+
T Consensus 83 ~~l~~~c~ 90 (90)
T smart00225 83 PGLVELCE 90 (90)
T ss_pred HHHHhhhC
Confidence 99998874
No 8
>PF00651 BTB: BTB/POZ domain; InterPro: IPR013069 The BTB (for BR-C, ttk and bab) [] or POZ (for Pox virus and Zinc finger) [] domain is present near the N terminus of a fraction of zinc finger (IPR007087 from INTERPRO) proteins and in proteins that contain the IPR006652 from INTERPRO motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation []. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule []. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT [, , ]. The POZ or BTB domain is also known as BR-C/Ttk or ZiN.; GO: 0005515 protein binding; PDB: 3M5B_A 1R28_B 3LBZ_A 3E4U_F 3BIM_B 1R2B_A 1R29_A 2VPK_A 2YY9_B 3GA1_A ....
Probab=97.88 E-value=9.4e-05 Score=48.60 Aligned_cols=75 Identities=17% Similarity=0.227 Sum_probs=60.1
Q ss_pred hhhhHHHHHHHhcCC-C-C--CceecCCCCHHHHHHHHHHHHhcccCCCCcccccchhhhhhccChHHHHHHHHHhhhcc
Q 040816 3 MLESQTIKHMVEDGC-A-D--SVIPLLNVRGTILSMVIEYLKKHVEAKTTEDDLKNWDVDFAKLGQDTLFDLLMAANYLD 78 (128)
Q Consensus 3 a~~S~~i~~~l~~~~-~-~--~~Ipl~~v~~~~L~~Vi~~c~~h~~~~~~~~~~~~wd~~Fl~~~~~~l~~li~AA~~L~ 78 (128)
+..|..+++|+...+ . . ..|++++++...+..+++||...... ++ +.+.+.+++..|++|+
T Consensus 31 ~~~S~~F~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~l~~~Y~~~~~------~~---------~~~~~~~ll~lA~~~~ 95 (111)
T PF00651_consen 31 AARSPYFRNLFEGSKFKESTVPEISLPDVSPEAFEAFLEYMYTGEIE------IN---------SDENVEELLELADKLQ 95 (111)
T ss_dssp HHHBHHHHHHHTTTTSTTSSEEEEEETTSCHHHHHHHHHHHHHSEEE------EE----------TTTHHHHHHHHHHTT
T ss_pred hccchhhhhcccccccccccccccccccccccccccccccccCCccc------CC---------HHHHHHHHHHHHHHhC
Confidence 567999999999983 2 2 35889999999999999999542221 11 3667999999999999
Q ss_pred HHHHHHHHHHHHHH
Q 040816 79 IKSLLDLLCQTVAD 92 (128)
Q Consensus 79 i~~L~~l~~~~ia~ 92 (128)
++.|.+.|+..+..
T Consensus 96 ~~~L~~~~~~~l~~ 109 (111)
T PF00651_consen 96 IPELKKACEKFLQE 109 (111)
T ss_dssp BHHHHHHHHHHHHH
T ss_pred cHHHHHHHHHHHHh
Confidence 99999999998864
No 9
>PHA03098 kelch-like protein; Provisional
Probab=97.86 E-value=8.7e-05 Score=61.77 Aligned_cols=83 Identities=23% Similarity=0.285 Sum_probs=66.4
Q ss_pred hhhhHHHHHHHhcCCCCCceecCCCCHHHHHHHHHHHHhcccCCCCcccccchhhhhhccChHHHHHHHHHhhhccHHHH
Q 040816 3 MLESQTIKHMVEDGCADSVIPLLNVRGTILSMVIEYLKKHVEAKTTEDDLKNWDVDFAKLGQDTLFDLLMAANYLDIKSL 82 (128)
Q Consensus 3 a~~S~~i~~~l~~~~~~~~Ipl~~v~~~~L~~Vi~~c~~h~~~~~~~~~~~~wd~~Fl~~~~~~l~~li~AA~~L~i~~L 82 (128)
|..|...+.|+...-.+..|.|+. +..+|+.|++|+..-+- .++.+.+.+|+.||++|+++.|
T Consensus 31 aa~S~yF~~mf~~~~~~~~i~l~~-~~~~~~~~l~y~Ytg~~----------------~i~~~~~~~ll~~A~~l~~~~l 93 (534)
T PHA03098 31 SSSSEYFKKMFKNNFKENEINLNI-DYDSFNEVIKYIYTGKI----------------NITSNNVKDILSIANYLIIDFL 93 (534)
T ss_pred HhhhHHHHHHHhCCCCCceEEecC-CHHHHHHHHHHhcCCce----------------EEcHHHHHHHHHHHHHhCcHHH
Confidence 456899999998754467799988 99999999999876321 2556779999999999999999
Q ss_pred HHHHHHHHHHHhcCCCHHHH
Q 040816 83 LDLLCQTVADMIKGKSPEEI 102 (128)
Q Consensus 83 ~~l~~~~ia~~i~gkt~eei 102 (128)
.+.|++++...+.-.+.-++
T Consensus 94 ~~~C~~~l~~~l~~~nc~~~ 113 (534)
T PHA03098 94 INLCINYIIKIIDDNNCIDI 113 (534)
T ss_pred HHHHHHHHHHhCCHhHHHHH
Confidence 99999999887765443333
No 10
>PHA02713 hypothetical protein; Provisional
Probab=97.83 E-value=0.00012 Score=61.98 Aligned_cols=84 Identities=14% Similarity=0.172 Sum_probs=68.1
Q ss_pred hhhhHHHHHHHhcCC----CCCceecCCCCHHHHHHHHHHHHhcccCCCCcccccchhhhhhccChHHHHHHHHHhhhcc
Q 040816 3 MLESQTIKHMVEDGC----ADSVIPLLNVRGTILSMVIEYLKKHVEAKTTEDDLKNWDVDFAKLGQDTLFDLLMAANYLD 78 (128)
Q Consensus 3 a~~S~~i~~~l~~~~----~~~~Ipl~~v~~~~L~~Vi~~c~~h~~~~~~~~~~~~wd~~Fl~~~~~~l~~li~AA~~L~ 78 (128)
|-.|...+.|+...- ....|.|.+|+..+|+.|++|+.... ++.+.+.+|+.||++|+
T Consensus 46 aa~S~YF~amF~~~~~e~~~~~~v~l~~v~~~~~~~ll~y~Yt~~------------------i~~~nv~~ll~aA~~lq 107 (557)
T PHA02713 46 AAGSKYFRTLFTTPMIIRDLVTRVNLQMFDKDAVKNIVQYLYNRH------------------ISSMNVIDVLKCADYLL 107 (557)
T ss_pred hhcCHHHHHHhcCCchhhccCceEEeccCCHHHHHHHHHHhcCCC------------------CCHHHHHHHHHHHHHHC
Confidence 446999999997642 14569999999999999999987621 34567999999999999
Q ss_pred HHHHHHHHHHHHHHHhcCCCHHHHHh
Q 040816 79 IKSLLDLLCQTVADMIKGKSPEEIRQ 104 (128)
Q Consensus 79 i~~L~~l~~~~ia~~i~gkt~eeir~ 104 (128)
|+.|.+.||.++...+.-.+-=+|..
T Consensus 108 i~~l~~~C~~~l~~~l~~~NCl~i~~ 133 (557)
T PHA02713 108 IDDLVTDCESYIKDYTNHDTCIYMYH 133 (557)
T ss_pred HHHHHHHHHHHHHhhCCccchHHHHH
Confidence 99999999999998877666555554
No 11
>PHA02790 Kelch-like protein; Provisional
Probab=97.64 E-value=0.00017 Score=59.77 Aligned_cols=79 Identities=9% Similarity=0.087 Sum_probs=59.5
Q ss_pred hhhhHHHHHHHhcCC--CCCceec--CCCCHHHHHHHHHHHHhcccCCCCcccccchhhhhhccChHHHHHHHHHhhhcc
Q 040816 3 MLESQTIKHMVEDGC--ADSVIPL--LNVRGTILSMVIEYLKKHVEAKTTEDDLKNWDVDFAKLGQDTLFDLLMAANYLD 78 (128)
Q Consensus 3 a~~S~~i~~~l~~~~--~~~~Ipl--~~v~~~~L~~Vi~~c~~h~~~~~~~~~~~~wd~~Fl~~~~~~l~~li~AA~~L~ 78 (128)
|..|...+.|+...- ....|.+ .+|+..+|+.|++|+.--+ +.++.+.+.+|+.||++|+
T Consensus 41 Aa~S~YFraMF~~~~~Es~~~v~~~~~~v~~~~l~~lldy~YTg~----------------l~it~~nV~~ll~aA~~Lq 104 (480)
T PHA02790 41 KKLSPYFRTHLRQKYTKNKDPVTRVCLDLDIHSLTSIVIYSYTGK----------------VYIDSHNVVNLLRASILTS 104 (480)
T ss_pred hhcCHHHHHHhcCCccccccceEEEecCcCHHHHHHHHHhheeee----------------EEEecccHHHHHHHHHHhC
Confidence 556899999997642 1233444 3899999999999984411 1255667999999999999
Q ss_pred HHHHHHHHHHHHHHHhcCC
Q 040816 79 IKSLLDLLCQTVADMIKGK 97 (128)
Q Consensus 79 i~~L~~l~~~~ia~~i~gk 97 (128)
|+.+.+.||+++...+.-.
T Consensus 105 i~~v~~~C~~fL~~~l~~~ 123 (480)
T PHA02790 105 VEFIIYTCINFILRDFRKE 123 (480)
T ss_pred hHHHHHHHHHHHHhhCCcc
Confidence 9999999999887765543
No 12
>KOG4441 consensus Proteins containing BTB/POZ and Kelch domains, involved in regulatory/signal transduction processes [Signal transduction mechanisms; General function prediction only]
Probab=97.51 E-value=0.0004 Score=59.08 Aligned_cols=77 Identities=22% Similarity=0.347 Sum_probs=64.8
Q ss_pred hhhhHHHHHHHhcCC---CCCceecCCCCHHHHHHHHHHHHhcccCCCCcccccchhhhhhccChHHHHHHHHHhhhccH
Q 040816 3 MLESQTIKHMVEDGC---ADSVIPLLNVRGTILSMVIEYLKKHVEAKTTEDDLKNWDVDFAKLGQDTLFDLLMAANYLDI 79 (128)
Q Consensus 3 a~~S~~i~~~l~~~~---~~~~Ipl~~v~~~~L~~Vi~~c~~h~~~~~~~~~~~~wd~~Fl~~~~~~l~~li~AA~~L~i 79 (128)
|-.|..++.|+...- ....|.+.+|++.+|+.+++|+...+- .++.+.+-+|+.||++|+|
T Consensus 56 Aa~S~YFraMFt~~l~e~~~~~i~l~~v~~~~l~~ll~y~Yt~~i----------------~i~~~nVq~ll~aA~~lQi 119 (571)
T KOG4441|consen 56 AACSPYFRAMFTSGLKESKQKEINLEGVDPETLELLLDYAYTGKL----------------EISEDNVQELLEAASLLQI 119 (571)
T ss_pred HhccHHHHHHhcCCcccccceEEEEecCCHHHHHHHHHHhhcceE----------------EechHhHHHHHHHHHHhhh
Confidence 456899999998642 367899999999999999999877443 3678889999999999999
Q ss_pred HHHHHHHHHHHHHHhc
Q 040816 80 KSLLDLLCQTVADMIK 95 (128)
Q Consensus 80 ~~L~~l~~~~ia~~i~ 95 (128)
+.+.+.||.++...+-
T Consensus 120 ~~v~~~C~~fL~~~l~ 135 (571)
T KOG4441|consen 120 PEVVDACCEFLESQLD 135 (571)
T ss_pred HHHHHHHHHHHHhcCC
Confidence 9999999998876543
No 13
>KOG4682 consensus Uncharacterized conserved protein, contains BTB/POZ domain [General function prediction only]
Probab=94.48 E-value=0.15 Score=42.06 Aligned_cols=91 Identities=15% Similarity=0.216 Sum_probs=69.3
Q ss_pred hhhHHHHHHHhcCCC-------CCceecCCCCHHHHHHHHHHHHhcccCCCCcccccchhhhhhccChHHHHHHHHHhhh
Q 040816 4 LESQTIKHMVEDGCA-------DSVIPLLNVRGTILSMVIEYLKKHVEAKTTEDDLKNWDVDFAKLGQDTLFDLLMAANY 76 (128)
Q Consensus 4 ~~S~~i~~~l~~~~~-------~~~Ipl~~v~~~~L~~Vi~~c~~h~~~~~~~~~~~~wd~~Fl~~~~~~l~~li~AA~~ 76 (128)
.||+.+..|+.++-. +-.||=|+|+...|..++.=+.+.. +.++.+.+..++.||.+
T Consensus 89 ~QS~yf~smf~Gtw~es~~~iIqleI~Dp~Id~~al~~a~gsLY~dE----------------veI~l~dv~gvlAaA~~ 152 (488)
T KOG4682|consen 89 FQSEYFKSMFSGTWKESSMNIIQLEIPDPNIDVVALQVAFGSLYRDE----------------VEIKLSDVVGVLAAACL 152 (488)
T ss_pred eccHHHHHHhccccChhhCceEEEEcCCCcccHHHHHHHHhhhhhhh----------------eeccHHHHHHHHHHHHH
Confidence 589999999998642 2356778999999998887665511 24788999999999999
Q ss_pred ccHHHHHHHHHHHHHHHhcCCCHHHHHhhcCCCCCCC
Q 040816 77 LDIKSLLDLLCQTVADMIKGKSPEEIRQTFHIQNDFT 113 (128)
Q Consensus 77 L~i~~L~~l~~~~ia~~i~gkt~eeir~~f~i~~d~t 113 (128)
|...+|++-|...+-..++-|| +.+++....-+.
T Consensus 153 lqldgl~qrC~evMie~lspkt---a~~yYea~ckYg 186 (488)
T KOG4682|consen 153 LQLDGLIQRCGEVMIETLSPKT---ACGYYEAACKYG 186 (488)
T ss_pred HHHhhHHHHHHHHHHHhcChhh---hhHhhhhhhhhh
Confidence 9999999999998877765554 555665544443
No 14
>KOG3433 consensus Protein involved in meiotic recombination/predicted coiled-coil protein [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=93.77 E-value=0.18 Score=37.23 Aligned_cols=31 Identities=39% Similarity=0.697 Sum_probs=26.5
Q ss_pred cHHHHHHHHHHHHHHHhcCCCHHHHHhhcCCCCCCC
Q 040816 78 DIKSLLDLLCQTVADMIKGKSPEEIRQTFHIQNDFT 113 (128)
Q Consensus 78 ~i~~L~~l~~~~ia~~i~gkt~eeir~~f~i~~d~t 113 (128)
+|--|.+.||+.. |.-+++||+.||||.||.
T Consensus 170 nI~il~dy~~rkf-----~~e~nqi~~~fgIPed~d 200 (203)
T KOG3433|consen 170 NIFILIDYLYRKF-----GLEPNQIRKEFGIPEDFD 200 (203)
T ss_pred hHHHHHHHHHHhc-----CCCHHHHhHhcCCCcccc
Confidence 7777888888764 789999999999999984
No 15
>COG5124 Protein predicted to be involved in meiotic recombination [Cell division and chromosome partitioning / General function prediction only]
Probab=91.96 E-value=0.19 Score=36.99 Aligned_cols=31 Identities=39% Similarity=0.722 Sum_probs=24.8
Q ss_pred cHHHHHHHHHHHHHHHhcCCCHHHHHhhcCCCCCCC
Q 040816 78 DIKSLLDLLCQTVADMIKGKSPEEIRQTFHIQNDFT 113 (128)
Q Consensus 78 ~i~~L~~l~~~~ia~~i~gkt~eeir~~f~i~~d~t 113 (128)
+|.-|.++.|+.+ +.-++|||+.||||.||.
T Consensus 174 nI~ilidy~c~kf-----~~~~~qir~~fgIPedld 204 (209)
T COG5124 174 NIEILIDYLCKKF-----FLKPEQIRKEFGIPEDLD 204 (209)
T ss_pred hHHHHHHHHHHHc-----CCCHHHHHHhcCCCcchh
Confidence 5666777666654 678999999999999975
No 16
>KOG2716 consensus Polymerase delta-interacting protein PDIP1 and related proteins, contain BTB/POZ domain [Inorganic ion transport and metabolism]
Probab=87.46 E-value=6.4 Score=30.09 Aligned_cols=79 Identities=19% Similarity=0.302 Sum_probs=58.8
Q ss_pred hhhHHHHHHHhcCCC-----CCceecCCCCHHHHHHHHHHHHhcccCCCCcccccchhhhhhccChHHHHHHHHHhhhcc
Q 040816 4 LESQTIKHMVEDGCA-----DSVIPLLNVRGTILSMVIEYLKKHVEAKTTEDDLKNWDVDFAKLGQDTLFDLLMAANYLD 78 (128)
Q Consensus 4 ~~S~~i~~~l~~~~~-----~~~Ipl~~v~~~~L~~Vi~~c~~h~~~~~~~~~~~~wd~~Fl~~~~~~l~~li~AA~~L~ 78 (128)
+..+.++.|++.... .+.|=+ +=+++=++.|+-||+--- ..++ -+..+|-+|+.-|.|..
T Consensus 25 k~dg~fk~m~e~~i~~~~d~s~~IFI-DRSpKHF~~ILNfmRdGd------v~LP--------e~~kel~El~~EA~fYl 89 (230)
T KOG2716|consen 25 KFDGFFKTMLETDIPVEKDESGCIFI-DRSPKHFDTILNFMRDGD------VDLP--------ESEKELKELLREAEFYL 89 (230)
T ss_pred hhhhHHHHHhhcCCccccCCcCcEEe-cCChhHHHHHHHhhhccc------ccCc--------cchHHHHHHHHHHHHhh
Confidence 456677888887531 233433 567888999999987411 1233 24678999999999999
Q ss_pred HHHHHHHHHHHHHHHhcCC
Q 040816 79 IKSLLDLLCQTVADMIKGK 97 (128)
Q Consensus 79 i~~L~~l~~~~ia~~i~gk 97 (128)
+.+|+++|...++..+++.
T Consensus 90 L~~Lv~~C~~~i~~~~~~~ 108 (230)
T KOG2716|consen 90 LDGLVELCQSAIARLIRGY 108 (230)
T ss_pred HHHHHHHHHHHhhhcccCc
Confidence 9999999999999998875
No 17
>PF03962 Mnd1: Mnd1 family; InterPro: IPR005647 This family of proteins includes meiotic nuclear division protein 1 (MND1) from Saccharomyces cerevisiae (Baker's yeast). The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair [].
Probab=85.92 E-value=1.1 Score=32.97 Aligned_cols=42 Identities=36% Similarity=0.375 Sum_probs=30.4
Q ss_pred HHHHHHHhhhc--cHHHHHHHHHHHHHHHhcCCCHHHHHhhcCCCCCCC
Q 040816 67 LFDLLMAANYL--DIKSLLDLLCQTVADMIKGKSPEEIRQTFHIQNDFT 113 (128)
Q Consensus 67 l~~li~AA~~L--~i~~L~~l~~~~ia~~i~gkt~eeir~~f~i~~d~t 113 (128)
+.....|||.- ||..|...|++. .|.+.+++++.||||+||.
T Consensus 144 ~~~~~~~anrwTDNI~~l~~~~~~k-----~~~~~~~i~k~f~Ip~d~d 187 (188)
T PF03962_consen 144 IKIAKEAANRWTDNIFSLKSYLKKK-----FGMDEEDIRKEFGIPEDFD 187 (188)
T ss_pred HHHHHHHHHHHHhhHHHHHHHHHHh-----cCCCHHHHHHHcCCccccC
Confidence 34444466554 566666666664 4899999999999999984
No 18
>KOG4350 consensus Uncharacterized conserved protein, contains BTB/POZ domain [General function prediction only]
Probab=85.22 E-value=6.8 Score=32.84 Aligned_cols=89 Identities=15% Similarity=0.209 Sum_probs=61.2
Q ss_pred hhhhHHHHHHHhcCC---CCCceecCCCCHHHHHHHHHHHHhcccCCCC--------------cc---cccchhhhhhc-
Q 040816 3 MLESQTIKHMVEDGC---ADSVIPLLNVRGTILSMVIEYLKKHVEAKTT--------------ED---DLKNWDVDFAK- 61 (128)
Q Consensus 3 a~~S~~i~~~l~~~~---~~~~Ipl~~v~~~~L~~Vi~~c~~h~~~~~~--------------~~---~~~~wd~~Fl~- 61 (128)
|-.|...|.|+-..- .+..|||..-++..++.+++|+..-+-+-.. .. ++..=-.+|+.
T Consensus 64 AaRs~yFRAlLYgGm~Es~q~~ipLq~t~~eAF~~lLrYiYtg~~~l~~~~ed~lld~LslAh~Ygf~~Le~aiSeYl~~ 143 (620)
T KOG4350|consen 64 AARSSYFRALLYGGMQESHQQLIPLQETNSEAFRALLRYIYTGKIDLAGVEEDILLDYLSLAHRYGFIQLETAISEYLKE 143 (620)
T ss_pred HHHHHHHHHHHhhhhhhhhhcccccccccHHHHHHHHHHHhhcceecccchHHHHHHHHHHHHhcCcHHHHHHHHHHHHH
Confidence 445888999988643 2678999888999999999998764443110 00 01111123332
Q ss_pred -cChHHHHHHHHHhhhccHHHHHHHHHHHHH
Q 040816 62 -LGQDTLFDLLMAANYLDIKSLLDLLCQTVA 91 (128)
Q Consensus 62 -~~~~~l~~li~AA~~L~i~~L~~l~~~~ia 91 (128)
+..+.++-++.||.+.+.+.|.++||.++-
T Consensus 144 iL~~~NvCmifdaA~ly~l~~Lt~~C~mfmD 174 (620)
T KOG4350|consen 144 ILKNENVCMIFDAAYLYQLTDLTDYCMMFMD 174 (620)
T ss_pred HHcccceeeeeeHHHHhcchHHHHHHHHHHh
Confidence 455667778889999999999999998763
No 19
>PF11822 DUF3342: Domain of unknown function (DUF3342); InterPro: IPR021777 This family of proteins are functionally uncharacterised. This family is found in bacteria. This presumed domain is typically between 170 to 303 amino acids in length. The N-terminal half of this family is a BTB-like domain.
Probab=78.11 E-value=2.8 Score=33.50 Aligned_cols=75 Identities=17% Similarity=0.287 Sum_probs=49.2
Q ss_pred hhHHHHHHHhc----CCCCCceecC-CCCHHHHHHHHHHHHhcccCCCCcccccchhhhhhccChHHHHHHHHHhhhccH
Q 040816 5 ESQTIKHMVED----GCADSVIPLL-NVRGTILSMVIEYLKKHVEAKTTEDDLKNWDVDFAKLGQDTLFDLLMAANYLDI 79 (128)
Q Consensus 5 ~S~~i~~~l~~----~~~~~~Ipl~-~v~~~~L~~Vi~~c~~h~~~~~~~~~~~~wd~~Fl~~~~~~l~~li~AA~~L~i 79 (128)
..+..+..+.. ....++|++- .-+=.|++=+++|++. ..| .++++.++-|+-.|+||+|
T Consensus 26 ~M~YF~~~l~~~~~~~~~~~~idisVhCDv~iF~WLm~yv~~--~~p--------------~l~~~NvvsIliSS~FL~M 89 (317)
T PF11822_consen 26 EMRYFAEYLSRYINDSQRWEEIDISVHCDVHIFEWLMRYVKG--EPP--------------SLTPSNVVSILISSEFLQM 89 (317)
T ss_pred hhHHHHHHHhhcccccCcCCCcceEEecChhHHHHHHHHhhc--CCC--------------cCCcCcEEEeEehhhhhcc
Confidence 34556666643 1223445542 3456677777777766 111 2556778888999999999
Q ss_pred HHHHHHHHHHHHHHhc
Q 040816 80 KSLLDLLCQTVADMIK 95 (128)
Q Consensus 80 ~~L~~l~~~~ia~~i~ 95 (128)
++|++.|-.++...+.
T Consensus 90 ~~Lve~cl~y~~~~~~ 105 (317)
T PF11822_consen 90 ESLVEECLQYCHDHMS 105 (317)
T ss_pred HHHHHHHHHHHHHhHH
Confidence 9999999988855543
No 20
>PF03656 Pam16: Pam16; InterPro: IPR005341 The Pam16 protein is the fifth essential subunit of the pre-sequence translocase-associated protein import motor (PAM) []. In Saccharomyces cerevisiae (Baker's yeast), Pam16 is required for preprotein translocation into the matrix, but not for protein insertion into the inner membrane [].; PDB: 2GUZ_J.
Probab=72.09 E-value=2.9 Score=29.07 Aligned_cols=26 Identities=27% Similarity=0.464 Sum_probs=13.8
Q ss_pred HhcCCCHHHHHhhcCCCCCCCHHHHH
Q 040816 93 MIKGKSPEEIRQTFHIQNDFTPEEEE 118 (128)
Q Consensus 93 ~i~gkt~eeir~~f~i~~d~t~eee~ 118 (128)
..+|+|.+|-+++||++...++|+..
T Consensus 51 ~~~~Mtl~EA~~ILnv~~~~~~eeI~ 76 (127)
T PF03656_consen 51 NSKGMTLDEARQILNVKEELSREEIQ 76 (127)
T ss_dssp ------HHHHHHHHT--G--SHHHHH
T ss_pred hcCCCCHHHHHHHcCCCCccCHHHHH
Confidence 44689999999999999988877654
No 21
>KOG1665 consensus AFH1-interacting protein FIP2, contains BTB/POZ domain and pentapeptide repeats [General function prediction only]
Probab=63.10 E-value=16 Score=28.25 Aligned_cols=48 Identities=21% Similarity=0.332 Sum_probs=32.9
Q ss_pred CCCHHHHHHHHHHHHhcccCCCCcccccchhhhhhccChHHHHHHHHHhhhccHHHHHHHHHH
Q 040816 26 NVRGTILSMVIEYLKKHVEAKTTEDDLKNWDVDFAKLGQDTLFDLLMAANYLDIKSLLDLLCQ 88 (128)
Q Consensus 26 ~v~~~~L~~Vi~~c~~h~~~~~~~~~~~~wd~~Fl~~~~~~l~~li~AA~~L~i~~L~~l~~~ 88 (128)
+=++.-++-|+-|+.+- +|...+.-.+++++.+|.|.+|-+|.+..-.
T Consensus 58 DRsp~yFepIlNyLr~G---------------q~~~~s~i~~lgvLeeArff~i~sL~~hle~ 105 (302)
T KOG1665|consen 58 DRSPKYFEPILNYLRDG---------------QIPSLSDIDCLGVLEEARFFQILSLKDHLED 105 (302)
T ss_pred ccCchhhHHHHHHHhcC---------------ceeecCCccHHHHHHHhhHHhhHhHHhHHhh
Confidence 44555566666665541 1223456678999999999999999986543
No 22
>KOG3442 consensus Uncharacterized conserved protein [Function unknown]
Probab=62.44 E-value=8 Score=26.90 Aligned_cols=25 Identities=20% Similarity=0.240 Sum_probs=20.6
Q ss_pred hcCCCHHHHHhhcCCCCCCCHHHHH
Q 040816 94 IKGKSPEEIRQTFHIQNDFTPEEEE 118 (128)
Q Consensus 94 i~gkt~eeir~~f~i~~d~t~eee~ 118 (128)
..|+|.+|-++++||.++++.||.+
T Consensus 53 ~~~iTlqEa~qILnV~~~ln~eei~ 77 (132)
T KOG3442|consen 53 NGKITLQEAQQILNVKEPLNREEIE 77 (132)
T ss_pred cccccHHHHhhHhCCCCCCCHHHHH
Confidence 3457999999999999988876654
No 23
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=60.72 E-value=15 Score=21.27 Aligned_cols=34 Identities=18% Similarity=0.491 Sum_probs=22.2
Q ss_pred HHHHHHHhcCCCHHHHHhhcCC------C-CCCCHHHHHHH
Q 040816 87 CQTVADMIKGKSPEEIRQTFHI------Q-NDFTPEEEEEI 120 (128)
Q Consensus 87 ~~~ia~~i~gkt~eeir~~f~i------~-~d~t~eee~~i 120 (128)
=..||..+..+|+.+++..|.- . ..+|++|.+++
T Consensus 20 W~~Ia~~l~~Rt~~~~~~r~~~~l~~~~~~~~wt~eEd~~L 60 (60)
T PF13921_consen 20 WKKIAEHLGNRTPKQCRNRWRNHLRPKISRGPWTKEEDQRL 60 (60)
T ss_dssp HHHHHHHSTTS-HHHHHHHHHHTTSTTSTSSSSSHHHHHHH
T ss_pred HHHHHHHHCcCCHHHHHHHHHHHCcccccCCCcCHHHHhcC
Confidence 3578888844999999766542 1 24777777654
No 24
>PF12556 CobS_N: Cobaltochelatase CobS subunit N terminal
Probab=59.52 E-value=5.6 Score=21.63 Aligned_cols=12 Identities=33% Similarity=0.758 Sum_probs=10.4
Q ss_pred HHhhcCCCCCCC
Q 040816 102 IRQTFHIQNDFT 113 (128)
Q Consensus 102 ir~~f~i~~d~t 113 (128)
+|+.|||..|++
T Consensus 14 vre~FGiDsDm~ 25 (36)
T PF12556_consen 14 VREVFGIDSDMK 25 (36)
T ss_pred HHHhcCCCcCCe
Confidence 599999999975
No 25
>PF02214 BTB_2: BTB/POZ domain; InterPro: IPR003131 Potassium channels are the most diverse group of the ion channel family [, ]. They are important in shaping the action potential, and in neuronal excitability and plasticity []. The potassium channel family is composed of several functionally distinct isoforms, which can be broadly separated into 2 groups []: the practically non-inactivating 'delayed' group and the rapidly inactivating 'transient' group. These are all highly similar proteins, with only small amino acid changes causing the diversity of the voltage-dependent gating mechanism, channel conductance and toxin binding properties. Each type of K+ channel is activated by different signals and conditions depending on their type of regulation: some open in response to depolarisation of the plasma membrane; others in response to hyperpolarisation or an increase in intracellular calcium concentration; some can be regulated by binding of a transmitter, together with intracellular kinases; while others are regulated by GTP-binding proteins or other second messengers []. In eukaryotic cells, K+ channels are involved in neural signalling and generation of the cardiac rhythm, act as effectors in signal transduction pathways involving G protein-coupled receptors (GPCRs) and may have a role in target cell lysis by cytotoxic T-lymphocytes []. In prokaryotic cells, they play a role in the maintenance of ionic homeostasis []. All K+ channels discovered so far possess a core of alpha subunits, each comprising either one or two copies of a highly conserved pore loop domain (P-domain). The P-domain contains the sequence (T/SxxTxGxG), which has been termed the K+ selectivity sequence. In families that contain one P-domain, four subunits assemble to form a selective pathway for K+ across the membrane. However, it remains unclear how the 2 P-domain subunits assemble to form a selective pore. The functional diversity of these families can arise through homo- or hetero-associations of alpha subunits or association with auxiliary cytoplasmic beta subunits. K+ channel subunits containing one pore domain can be assigned into one of two superfamilies: those that possess six transmembrane (TM) domains and those that possess only two TM domains. The six TM domain superfamily can be further subdivided into conserved gene families: the voltage-gated (Kv) channels; the KCNQ channels (originally known as KvLQT channels); the EAG-like K+ channels; and three types of calcium (Ca)-activated K+ channels (BK, IK and SK) []. The 2TM domain family comprises inward-rectifying K+ channels. In addition, there are K+ channel alpha-subunits that possess two P-domains. These are usually highly regulated K+ selective leak channels. The Kv family can be divided into several subfamilies on the basis of sequence similarity and function. Four of these subfamilies, Kv1 (Shaker), Kv2 (Shab), Kv3 (Shaw) and Kv4 (Shal), consist of pore-forming alpha subunits that associate with different types of beta subunit. Each alpha subunit comprises six hydrophobic TM domains with a P-domain between the fifth and sixth, which partially resides in the membrane. The fourth TM domain has positively charged residues at every third residue and acts as a voltage sensor, which triggers the conformational change that opens the channel pore in response to a displacement in membrane potential []. More recently, 4 new electrically-silent alpha subunits have been cloned: Kv5 (KCNF), Kv6 (KCNG), Kv8 and Kv9 (KCNS). These subunits do not themselves possess any functional activity, but appear to form heteromeric channels with Kv2 subunits, and thus modulate Shab channel activity []. When highly expressed, they inhibit channel activity, but at lower levels show more specific modulatory actions. The N-terminal, cytoplasmic tetramerization domain (T1) of voltage-gated potassium channels encodes molecular determinants for subfamily-specific assembly of alpha-subunits into functional tetrameric channels []. This domain is found in a subset of a larger group of proteins that contain the BTB/POZ domain.; GO: 0005249 voltage-gated potassium channel activity, 0006813 potassium ion transport, 0008076 voltage-gated potassium channel complex, 0016020 membrane; PDB: 1NN7_A 3KVT_A 1EXB_E 1QDV_A 1DSX_E 1QDW_F 3LUT_B 3LNM_B 2A79_B 3DRY_C ....
Probab=57.24 E-value=16 Score=23.12 Aligned_cols=52 Identities=15% Similarity=0.253 Sum_probs=34.1
Q ss_pred CceecCCCCHHHHHHHHHHHHhcccCCCCcccccchhhhhhccChHHHHHHHHHhhhccHHHH-HHHH
Q 040816 20 SVIPLLNVRGTILSMVIEYLKKHVEAKTTEDDLKNWDVDFAKLGQDTLFDLLMAANYLDIKSL-LDLL 86 (128)
Q Consensus 20 ~~Ipl~~v~~~~L~~Vi~~c~~h~~~~~~~~~~~~wd~~Fl~~~~~~l~~li~AA~~L~i~~L-~~l~ 86 (128)
..+=+ +-++..++.|+.|++.. .. ++. -+...+..+...|.|.+|+.| ++.|
T Consensus 42 ~~~fi-DRdp~~F~~IL~ylr~~-~~------l~~-------~~~~~~~~l~~Ea~fy~l~~l~i~~c 94 (94)
T PF02214_consen 42 GEYFI-DRDPELFEYILNYLRTG-GK------LPI-------PDEICLEELLEEAEFYGLDELFIEDC 94 (94)
T ss_dssp TEEEE-SS-HHHHHHHHHHHHHT-SS------B----------TTS-HHHHHHHHHHHT-HHHHBHHC
T ss_pred ceEEe-ccChhhhhHHHHHHhhc-Cc------cCC-------CCchhHHHHHHHHHHcCCCccccCCC
Confidence 44434 67999999999999984 11 110 123457788999999999999 6654
No 26
>PF05409 Peptidase_C30: Coronavirus endopeptidase C30; InterPro: IPR008740 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. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases correspond to MEROPS peptidase family C30 (clan PA(C)). These peptidases are related to serine endopeptidases of family S1 and are restricted to RNA viruses, where they are involved in viral polyprotein processing during replication [, , ]. This entry represents the CoV M-pro which comprises three domains. Domains I and II are six-stranded antiparallel beta barrels and together resemble the architecture of chymotrypsin and of picornaviruses 3C proteinases. The substrate-binding site is located in a cleft between these two domains. The catalytic site is situated at the centre of the cleft. A long loop connects domain II to the C-terminal domain (domain III). This latter domain, a globular cluster of five helices, has been implicated in the proteolytic activity of M-pro. In the active site of M-pro, Cys and His form a catalytic dyad. In contrast to serine proteinases and other cysteine proteinases, which have a catalytic triad, there is no third catalytic residue present [, , , ]. ; GO: 0019082 viral protein processing; PDB: 2VJ1_B 2K7X_A 2Q6D_B 2Q6F_A 1P9U_E 1LVO_B 2AMP_B 1P9S_A 2ZU2_A 3D23_A ....
Probab=55.14 E-value=23 Score=27.97 Aligned_cols=96 Identities=22% Similarity=0.417 Sum_probs=55.3
Q ss_pred CCceecCCCCHHHHHHHHHHHHhcccCC------C---Ccccccchhh--hhhccChHHHHHHHHHhhhccHHHHHHHHH
Q 040816 19 DSVIPLLNVRGTILSMVIEYLKKHVEAK------T---TEDDLKNWDV--DFAKLGQDTLFDLLMAANYLDIKSLLDLLC 87 (128)
Q Consensus 19 ~~~Ipl~~v~~~~L~~Vi~~c~~h~~~~------~---~~~~~~~wd~--~Fl~~~~~~l~~li~AA~~L~i~~L~~l~~ 87 (128)
++...++.-+.-.-.-|+.|+.-|--.. + ..++..+|-. .|-+......++.+.|..-.++.+|+...-
T Consensus 160 ~~~~Q~~~~~~~~T~NVvA~LYAalln~~~w~l~~~~~svedFN~WA~~N~ft~~~~~~~~~~Laa~TgVsV~rlLaaI~ 239 (293)
T PF05409_consen 160 EEVAQLEGADQYITDNVVAWLYAALLNGCPWWLSSQRISVEDFNEWAMNNGFTSFSSDDAFDMLAAKTGVSVERLLAAIQ 239 (293)
T ss_dssp SSSSTTTTS-SB-HHHHHHHHHHHHHTT--TTSSSS---HHHHHHHHHHTTB--SSHHHHHHHHHHHHT--HHHHHHHHH
T ss_pred chhhhhcCccceeehhHHHHHHHHHHcCCCeeeccceecHHHHHHHHHhCCCcccchhhHHHHHHHHhCCcHHHHHHHHH
Confidence 3444455455555567788887655432 1 2234455633 344577788899999999999999998766
Q ss_pred HHHHHHhcCCCHHHHHhhcCCCCCCCHHHHH
Q 040816 88 QTVADMIKGKSPEEIRQTFHIQNDFTPEEEE 118 (128)
Q Consensus 88 ~~ia~~i~gkt~eeir~~f~i~~d~t~eee~ 118 (128)
+ +..-..|++ |--...+++||||++--
T Consensus 240 ~-L~~g~~G~~---IlG~~~ledE~Tp~~V~ 266 (293)
T PF05409_consen 240 R-LHKGFGGRT---ILGSCSLEDEFTPEMVY 266 (293)
T ss_dssp H-HHHTTTTT----BTTBSS--TSS-HHHHH
T ss_pred H-HhcCCCCCc---ccccccccccCCHHHHh
Confidence 5 566556665 44455577889997654
No 27
>cd05029 S-100A6 S-100A6: S-100A6 domain found in proteins similar to S100A6. S100A6 is a member of the S100 domain family within EF-hand Ca2+-binding proteins superfamily. Note that the S-100 hierarchy, to which this S-100A6 group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100 proteins exhibit unique patterns of tissue- and cell type-specific expression and have been implicated in the Ca2+-dependent regulation of diverse physiological processes, including cell cycle regulation, differentiation, growth, and metabolic control . S100A6 is normally expressed in the G1 phase of the cell cycle in neuronal cells. The function of S100A6 remains unclear, but evidence suggests that it is involved in cell cycle regulation and exocytosis. S100A6 may also be involved in tumorigenesis; the protein is overexpressed in several tumors. Ca2+ binding to S100A6 leads to a conformational change in the protein, which exposes a hydrophobic surface for interact
Probab=55.01 E-value=31 Score=21.97 Aligned_cols=45 Identities=16% Similarity=0.237 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHHHHHh-cCC-CHHHHHhhcC----CCCCCCHHHHHHHhhh
Q 040816 79 IKSLLDLLCQTVADMI-KGK-SPEEIRQTFH----IQNDFTPEEEEEIRTE 123 (128)
Q Consensus 79 i~~L~~l~~~~ia~~i-~gk-t~eeir~~f~----i~~d~t~eee~~i~~e 123 (128)
|..|+.+..++-++-= .|. |.+|+|+.+. +....|++|.+++-++
T Consensus 9 ~~~~i~~F~~y~~~~~~~g~Is~~EL~~~l~~~~~lg~k~t~~ev~~m~~~ 59 (88)
T cd05029 9 IGLLVAIFHKYSGREGDKNTLSKKELKELIQKELTIGSKLQDAEIAKLMED 59 (88)
T ss_pred HHHHHHHHHHHHccCCCCCEECHHHHHHHHHHHHhcCCCCCHHHHHHHHHH
Confidence 4566666666666322 343 7888888883 4455777777766543
No 28
>PF11198 DUF2857: Protein of unknown function (DUF2857); InterPro: IPR021364 This is a bacterial family of uncharacterised proteins.
Probab=54.27 E-value=55 Score=23.81 Aligned_cols=59 Identities=29% Similarity=0.311 Sum_probs=39.6
Q ss_pred cChHHHHHHHHHhh-----hccHHHHHHHH-HHHHHHHhcCCCHHHH---HhhcCCCCCC------CHHHHHHH
Q 040816 62 LGQDTLFDLLMAAN-----YLDIKSLLDLL-CQTVADMIKGKSPEEI---RQTFHIQNDF------TPEEEEEI 120 (128)
Q Consensus 62 ~~~~~l~~li~AA~-----~L~i~~L~~l~-~~~ia~~i~gkt~eei---r~~f~i~~d~------t~eee~~i 120 (128)
+|.+.|-.++.-|. .--|+.++.++ +..+-..+-|.|+.|+ |+.+|++..- |+|++.++
T Consensus 58 in~~~l~~~L~~~~~~~~~~~~idr~L~lGAS~~mm~~~FGls~~ev~~rR~llgi~~~~GR~~~~~ee~~~~i 131 (180)
T PF11198_consen 58 INHDVLWRLLEQARREQQEQQLIDRALRLGASIEMMQRLFGLSSAEVAARRRLLGIPVRKGRPPALSEEEEAAI 131 (180)
T ss_pred eCHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHhCCCCCCCCCCCcCHHHHHHH
Confidence 67777776666554 34555666655 4667777789998888 8899998653 44555554
No 29
>PF07957 DUF3294: Protein of unknown function (DUF3294); InterPro: IPR012917 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 [, ]. This is a family of mitochondrial ribosomal proteins, which appears to be fungal specific [].
Probab=53.87 E-value=44 Score=25.36 Aligned_cols=86 Identities=16% Similarity=0.207 Sum_probs=45.3
Q ss_pred HHHHHHHhcCCC---CCceecCCCCHHHH-------------------HHHHHHHHhcccCCCCcccccchhhhhhc---
Q 040816 7 QTIKHMVEDGCA---DSVIPLLNVRGTIL-------------------SMVIEYLKKHVEAKTTEDDLKNWDVDFAK--- 61 (128)
Q Consensus 7 ~~i~~~l~~~~~---~~~Ipl~~v~~~~L-------------------~~Vi~~c~~h~~~~~~~~~~~~wd~~Fl~--- 61 (128)
..||+++..+.. .-.-||||.+|.+- .+++++|+++.--|| ...-..++ +|++
T Consensus 92 RsiRR~~NS~~~~~~d~laPlpn~DGe~P~~~~~~fP~TL~eF~~l~~~~l~~L~~FYellpp-~~e~e~~~-~~Le~~~ 169 (216)
T PF07957_consen 92 RSIRRTVNSTKTDDDDLLAPLPNADGEIPPGKDFLFPKTLKEFKNLDDVKLIKLAKFYELLPP-LKEQEEFE-EFLEGKV 169 (216)
T ss_pred HHHHHHHhcccCCcccccccCCCCCCCCCCCCcccChhhHHHHHhccHHHHHHHHHHHHhcCC-cccHHHHH-HHHhccc
Confidence 456776666531 23445555554333 247788887665554 22233333 4442
Q ss_pred -------cChHHHHHHHHHhhhccHHHHHHHHHHHHHHHh
Q 040816 62 -------LGQDTLFDLLMAANYLDIKSLLDLLCQTVADMI 94 (128)
Q Consensus 62 -------~~~~~l~~li~AA~~L~i~~L~~l~~~~ia~~i 94 (128)
.++..+-+.+...+-=++..+++-.++|++-..
T Consensus 170 e~~~i~~~~d~~i~~~~k~~s~~eld~ifdelARylGlr~ 209 (216)
T PF07957_consen 170 EDFHINEESDEEIEKELKKYSKEELDEIFDELARYLGLRS 209 (216)
T ss_pred cccccCCCChHHHHHHHHhcCHHHHHHHHHHHHHHhCchh
Confidence 234556666665555556666666665554433
No 30
>PRK05365 malonic semialdehyde reductase; Provisional
Probab=52.00 E-value=10 Score=27.41 Aligned_cols=34 Identities=18% Similarity=0.322 Sum_probs=26.2
Q ss_pred HHHHhhhccHHHHHHHHHHHHHHHhcCCCHHHHHhhcCCCCCCC
Q 040816 70 LLMAANYLDIKSLLDLLCQTVADMIKGKSPEEIRQTFHIQNDFT 113 (128)
Q Consensus 70 li~AA~~L~i~~L~~l~~~~ia~~i~gkt~eeir~~f~i~~d~t 113 (128)
|+.||.-+|+... .+.|-..+.+++.|||++++.
T Consensus 131 l~LaA~~~Glgs~----------~~~g~~~~~v~~~l~ip~~~~ 164 (195)
T PRK05365 131 LILAARALGLDAG----------PMSGFDAAAVDAEFFAGTTWK 164 (195)
T ss_pred HHHHHHHcCCccC----------CccccCHHHHHHHhCCCCCee
Confidence 7888888887762 345678899999999997653
No 31
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=51.73 E-value=16 Score=19.06 Aligned_cols=20 Identities=20% Similarity=0.644 Sum_probs=16.4
Q ss_pred HHHHHHhcCCCHHHHHhhcC
Q 040816 88 QTVADMIKGKSPEEIRQTFH 107 (128)
Q Consensus 88 ~~ia~~i~gkt~eeir~~f~ 107 (128)
..||..+.++|..+++..+.
T Consensus 23 ~~Ia~~~~~rs~~~~~~~~~ 42 (45)
T cd00167 23 EKIAKELPGRTPKQCRERWR 42 (45)
T ss_pred HHHHhHcCCCCHHHHHHHHH
Confidence 67888888899999988763
No 32
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=50.82 E-value=17 Score=19.25 Aligned_cols=20 Identities=20% Similarity=0.572 Sum_probs=16.4
Q ss_pred HHHHHHhcCCCHHHHHhhcC
Q 040816 88 QTVADMIKGKSPEEIRQTFH 107 (128)
Q Consensus 88 ~~ia~~i~gkt~eeir~~f~ 107 (128)
..||..+.++|+.+++..+.
T Consensus 25 ~~Ia~~~~~rt~~~~~~~~~ 44 (49)
T smart00717 25 EKIAKELPGRTAEQCRERWN 44 (49)
T ss_pred HHHHHHcCCCCHHHHHHHHH
Confidence 56788888999999988764
No 33
>PF10892 DUF2688: Protein of unknown function (DUF2688); InterPro: IPR024392 Members of this protein family are annotated as KleB, and may play a role in the regulation of transcription in plasmids.
Probab=50.58 E-value=18 Score=21.68 Aligned_cols=25 Identities=36% Similarity=0.611 Sum_probs=18.9
Q ss_pred HHHHHhhcC-CCCC-CCHHHHHHHhhh
Q 040816 99 PEEIRQTFH-IQND-FTPEEEEEIRTE 123 (128)
Q Consensus 99 ~eeir~~f~-i~~d-~t~eee~~i~~e 123 (128)
.+++|.-|| |=.+ +||||..+|.+.
T Consensus 30 ad~lr~klG~IC~~CitpEE~~~I~e~ 56 (60)
T PF10892_consen 30 ADDLRVKLGGICGDCITPEEDREILEA 56 (60)
T ss_pred hHHHHHHHcchhhccCCHHHHHHHHHH
Confidence 578888887 4444 899999988753
No 34
>cd02148 Nitroreductase_5 Nitroreductase-like family 5. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and nitroimidazoles. This process requires NAD(P)H as electron donor in an obligatory two-electron transfer and uses FMN as cofactor. The enzyme is typically a homodimer. Members of this family are also called NADH dehydrogenase, oxygen-insensitive NAD(P)H nitrogenase or dihydropteridine reductase.
Probab=49.52 E-value=11 Score=26.92 Aligned_cols=34 Identities=15% Similarity=0.315 Sum_probs=25.6
Q ss_pred HHHHhhhccHHHHHHHHHHHHHHHhcCCCHHHHHhhcCCCCCCC
Q 040816 70 LLMAANYLDIKSLLDLLCQTVADMIKGKSPEEIRQTFHIQNDFT 113 (128)
Q Consensus 70 li~AA~~L~i~~L~~l~~~~ia~~i~gkt~eeir~~f~i~~d~t 113 (128)
|+.||.-||+... .+.|-..+++++.||+++++.
T Consensus 124 l~LaA~~lGlgs~----------~~~g~d~~~~~~~L~lp~~~~ 157 (185)
T cd02148 124 FILAARALGLDAG----------PMSGFDAAAVDAEFFADTRWR 157 (185)
T ss_pred HHHHHHHcCCCcC----------CCcccCHHHHHHHhCCCCCeE
Confidence 7777777777652 345677899999999998763
No 35
>PF05321 HHA: Haemolysin expression modulating protein; InterPro: IPR007985 This family consists of haemolysin expression modulating protein (Hha) from Escherichia coli and its enterobacterial homologues, such as YmoA from Yersinia enterocolitica, and RmoA encoded on the R100 plasmid. These proteins act as modulators of bacterial gene expression. Members of the Hha/YmoA/RmoA family act in conjunction with members of the H-NS family, participating in the thermoregulation of different virulence factors and in plasmid transfer []. Hha, along with the chromatin-associated protein H-NS, is involved in the regulation of expression of the toxin alpha-haemolysin in response to osmolarity and temperature []. YmoA modulates the expression of various virulence factors, such as Yop proteins and YadA adhesin, in response to temperature. RmoA is a plasmid R100 modulator involved in plasmid transfer []. The HHA family of proteins display striking similarity to the oligomerization domain of the H-NS proteins.; PDB: 1JW2_A 2K5S_A 2JQT_A.
Probab=48.54 E-value=53 Score=19.67 Aligned_cols=30 Identities=33% Similarity=0.200 Sum_probs=20.3
Q ss_pred CHHHHHHHHHHHHhcccCCCCcccccchhhhhhccChHHHHHHHHHhhh
Q 040816 28 RGTILSMVIEYLKKHVEAKTTEDDLKNWDVDFAKLGQDTLFDLLMAANY 76 (128)
Q Consensus 28 ~~~~L~~Vi~~c~~h~~~~~~~~~~~~wd~~Fl~~~~~~l~~li~AA~~ 76 (128)
+.++|++|++..++ +++.+++..+..||++
T Consensus 8 s~dtLEkv~e~~~~-------------------~L~~~e~~~f~~AaDH 37 (57)
T PF05321_consen 8 SLDTLEKVIEHNRY-------------------KLTDDELEAFNSAADH 37 (57)
T ss_dssp -HHHHHHHHHHHHH-------------------HS-HHHHHHHHHHHHH
T ss_pred CHhhHHHHHHHhhC-------------------cCCHHHHHHHHHHHHH
Confidence 45788888887766 2445677777778775
No 36
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=48.34 E-value=21 Score=19.81 Aligned_cols=20 Identities=15% Similarity=0.492 Sum_probs=16.8
Q ss_pred HHHHHHHhc-CCCHHHHHhhc
Q 040816 87 CQTVADMIK-GKSPEEIRQTF 106 (128)
Q Consensus 87 ~~~ia~~i~-gkt~eeir~~f 106 (128)
=..||..+. |+|+.++|..+
T Consensus 24 W~~Ia~~~~~~Rt~~qc~~~~ 44 (48)
T PF00249_consen 24 WKKIAKRMPGGRTAKQCRSRY 44 (48)
T ss_dssp HHHHHHHHSSSSTHHHHHHHH
T ss_pred HHHHHHHcCCCCCHHHHHHHH
Confidence 467888888 99999998765
No 37
>PF11978 MVP_shoulder: Shoulder domain; InterPro: IPR021870 This domain is found in the Major Vault Protein and has been called the shoulder domain []. This family includes two bacterial proteins A6FXE2 from SWISSPROT and A1ZGE7 from SWISSPROT. This suggests that some bacteria may possess vault particles. ; PDB: 2ZUO_G 2QZV_B 2ZV5_c 2ZV4_Y.
Probab=48.05 E-value=13 Score=25.49 Aligned_cols=27 Identities=22% Similarity=0.431 Sum_probs=24.4
Q ss_pred HHHhhhccHHHHHHHHHHHHHHHhcCC
Q 040816 71 LMAANYLDIKSLLDLLCQTVADMIKGK 97 (128)
Q Consensus 71 i~AA~~L~i~~L~~l~~~~ia~~i~gk 97 (128)
-.|+....++..+..+|+.||++|||.
T Consensus 37 ~~~~k~F~VpDFVGd~Ck~iaSRIR~a 63 (118)
T PF11978_consen 37 EDAAKLFSVPDFVGDACKAIASRIRGA 63 (118)
T ss_dssp HHHHHTTSSTTHHHHHHHHHHHHHHHH
T ss_pred hHHHHhcCCcchHHHHHHHHHHHHHHH
Confidence 378899999999999999999999974
No 38
>PRK11053 dihydropteridine reductase; Provisional
Probab=47.76 E-value=14 Score=27.09 Aligned_cols=34 Identities=24% Similarity=0.404 Sum_probs=22.9
Q ss_pred HHHHHhhhccHHHHHHHHHHHHHHHhcCCCHHHHHhhcCCCC-CC
Q 040816 69 DLLMAANYLDIKSLLDLLCQTVADMIKGKSPEEIRQTFHIQN-DF 112 (128)
Q Consensus 69 ~li~AA~~L~i~~L~~l~~~~ia~~i~gkt~eeir~~f~i~~-d~ 112 (128)
.|+.||.-||+.+. .+.|...+.+++.|||++ ++
T Consensus 149 ~lmLaA~~~Glgs~----------~i~g~~~~~v~~~l~ip~~~~ 183 (217)
T PRK11053 149 NLLLGAAALGIDAT----------PIEGFDAAILDAEFGLREKGL 183 (217)
T ss_pred HHHHHHHHcCCCCC----------CcCCcCHHHHHHHhCCCCcCc
Confidence 45555555555433 345678899999999985 45
No 39
>PF06851 DUF1247: Protein of unknown function (DUF1247); InterPro: IPR009657 This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf2; it is a family of uncharacterised viral proteins.
Probab=46.80 E-value=68 Score=22.82 Aligned_cols=68 Identities=16% Similarity=0.319 Sum_probs=42.4
Q ss_pred HHHhcccCCCC---cccccchhhhhhc--cChHHHHHHHHHhhhccHHHHHHHHHHHHHHHhcC-CCHHHHHhhcCCC
Q 040816 38 YLKKHVEAKTT---EDDLKNWDVDFAK--LGQDTLFDLLMAANYLDIKSLLDLLCQTVADMIKG-KSPEEIRQTFHIQ 109 (128)
Q Consensus 38 ~c~~h~~~~~~---~~~~~~wd~~Fl~--~~~~~l~~li~AA~~L~i~~L~~l~~~~ia~~i~g-kt~eeir~~f~i~ 109 (128)
||.+|+.+-=. .....++ -+|++ ++.-.+.|+- =.||..+. ....++.+-..+.| .|..++-..+|-+
T Consensus 61 rC~FHkkyif~~~~~~~~deY-v~fLNSeMGiIS~VElY--Y~yLs~~~-wk~~a~~~l~dLTgF~s~~~LL~~Yny~ 134 (148)
T PF06851_consen 61 RCDFHKKYIFTKDRKTHYDEY-VEFLNSEMGIISFVELY--YTYLSVDF-WKITAKRVLRDLTGFESLKDLLTHYNYE 134 (148)
T ss_pred hhhHhHhhhccCCcccCHHHH-HHHHccccchhhhHHHH--HHHHcccc-cHHHHHHHHHHhhCcccHHHHHHHcCCC
Confidence 67777765211 1112222 36776 3333444443 35777765 77888888888888 5899999888866
No 40
>PF11338 DUF3140: Protein of unknown function (DUF3140); InterPro: IPR021487 Some members in this family of proteins are annotated as DNA binding proteins. No function is currently known.
Probab=45.60 E-value=24 Score=23.19 Aligned_cols=33 Identities=18% Similarity=0.401 Sum_probs=22.1
Q ss_pred cCCCCHHHHHHHHHHHHhcccC-CCC-cccccchh
Q 040816 24 LLNVRGTILSMVIEYLKKHVEA-KTT-EDDLKNWD 56 (128)
Q Consensus 24 l~~v~~~~L~~Vi~~c~~h~~~-~~~-~~~~~~wd 56 (128)
|..=+-..|++|+.||..|... .|. ...-+.|-
T Consensus 54 ltddD~~hMrkVV~yv~rhlaq~~p~~~~~ds~wr 88 (92)
T PF11338_consen 54 LTDDDYEHMRKVVGYVKRHLAQGEPKGDVEDSRWR 88 (92)
T ss_pred CCHHHHHHHHHHHHHHHHHHhccCCCCCccccchH
Confidence 4444567899999999999987 332 22344564
No 41
>PF11460 DUF3007: Protein of unknown function (DUF3007); InterPro: IPR021562 This is a family of uncharacterised proteins found in bacteria and eukaryotes.
Probab=45.13 E-value=20 Score=24.14 Aligned_cols=23 Identities=30% Similarity=0.668 Sum_probs=15.4
Q ss_pred CHHHHHhhcCCCCCCCHHHHHHHhhh
Q 040816 98 SPEEIRQTFHIQNDFTPEEEEEIRTE 123 (128)
Q Consensus 98 t~eeir~~f~i~~d~t~eee~~i~~e 123 (128)
+.+|+.+.|. .+||||.+++..|
T Consensus 79 ~~~~lqkRle---~l~~eE~~~L~~e 101 (104)
T PF11460_consen 79 TNEELQKRLE---ELSPEELEALQAE 101 (104)
T ss_pred hHHHHHHHHH---hCCHHHHHHHHHH
Confidence 3345666664 5788888887765
No 42
>KOG0511 consensus Ankyrin repeat protein [General function prediction only]
Probab=44.94 E-value=1e+02 Score=25.84 Aligned_cols=72 Identities=11% Similarity=0.120 Sum_probs=53.1
Q ss_pred eecCCCCHHHHHHHHHHHHhcccCCC-------------------------CcccccchhhhhhccChHHHHHHHHHhhh
Q 040816 22 IPLLNVRGTILSMVIEYLKKHVEAKT-------------------------TEDDLKNWDVDFAKLGQDTLFDLLMAANY 76 (128)
Q Consensus 22 Ipl~~v~~~~L~~Vi~~c~~h~~~~~-------------------------~~~~~~~wd~~Fl~~~~~~l~~li~AA~~ 76 (128)
..||+..+.+.+.+.+|..-|+.+-+ ....+.+|. +| ++.-.+++++.-|--
T Consensus 336 lslp~~~~~vveI~lr~lY~d~tdi~~~~A~dvll~ad~lal~~dr~Lkt~as~~itq~~-e~--id~y~V~dIl~~~wd 412 (516)
T KOG0511|consen 336 LSLPSLADVVVEIDLRNLYCDQTDIIFDVASDVLLFADKLALADDRLLKTAASAEITQWL-EL--IDMYGVLDILEYCWD 412 (516)
T ss_pred cccchHHHHHHHHHHHHhhcccccchHHHHhhHHHHhhHhhhhhhhhhhhhhhHHHHHHH-HH--HHhhhHHHHHHHHHH
Confidence 34889999999999999988888741 111233331 11 345568899999999
Q ss_pred ccHHHHHHHHHHHHHHHhcC
Q 040816 77 LDIKSLLDLLCQTVADMIKG 96 (128)
Q Consensus 77 L~i~~L~~l~~~~ia~~i~g 96 (128)
+...+|=..+..++|+.+.-
T Consensus 413 ~~~~rlEqfa~~~~a~hl~~ 432 (516)
T KOG0511|consen 413 LVACRLEQFAETHEARHLLL 432 (516)
T ss_pred hhhHHHHHHHHHHHHHHHHH
Confidence 99999999999999987763
No 43
>KOG2075 consensus Topoisomerase TOP1-interacting protein BTBD1 [Function unknown]
Probab=43.80 E-value=1.8e+02 Score=25.00 Aligned_cols=92 Identities=17% Similarity=0.238 Sum_probs=61.2
Q ss_pred hhhHHHHHHHhcCC--C-CCceecCCCCHHHHHHHHHHHHh--cccCCC---------C---cccccchhhhhhc---cC
Q 040816 4 LESQTIKHMVEDGC--A-DSVIPLLNVRGTILSMVIEYLKK--HVEAKT---------T---EDDLKNWDVDFAK---LG 63 (128)
Q Consensus 4 ~~S~~i~~~l~~~~--~-~~~Ipl~~v~~~~L~~Vi~~c~~--h~~~~~---------~---~~~~~~wd~~Fl~---~~ 63 (128)
.-|.+...|+...- + ..+|.+|+|..+.+...+.|+.- -+.++. . ...+..=--+|+. +.
T Consensus 140 ~gS~VFdaMf~g~~a~~~s~ei~lpdvepaaFl~~L~flYsdev~~~~dtvi~tl~~AkKY~VpaLer~CVkflr~~l~~ 219 (521)
T KOG2075|consen 140 DGSDVFDAMFYGGLAEDASLEIRLPDVEPAAFLAFLRFLYSDEVKLAADTVITTLYAAKKYLVPALERQCVKFLRKNLMA 219 (521)
T ss_pred cchHHHHHHhccCcccccCceeecCCcChhHhHHHHHHHhcchhhhhHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhcCC
Confidence 34677777887643 2 56899999999999887776644 222220 0 0112222234664 57
Q ss_pred hHHHHHHHHHhhhccHHHHHHHHHHHHHHHhc
Q 040816 64 QDTLFDLLMAANYLDIKSLLDLLCQTVADMIK 95 (128)
Q Consensus 64 ~~~l~~li~AA~~L~i~~L~~l~~~~ia~~i~ 95 (128)
.+.+.+|-..|..++=+.|+..|.+.|+....
T Consensus 220 ~naf~~L~q~A~lf~ep~Li~~c~e~id~~~~ 251 (521)
T KOG2075|consen 220 DNAFLELFQRAKLFDEPSLISICLEVIDKSFE 251 (521)
T ss_pred hHHHHHHHHHHHhhcCHHHHHHHHHHhhhHHH
Confidence 77788888879999999999999988865443
No 44
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=43.02 E-value=22 Score=25.13 Aligned_cols=18 Identities=28% Similarity=0.696 Sum_probs=17.0
Q ss_pred CCCHHHHHhhcCCCCCCC
Q 040816 96 GKSPEEIRQTFHIQNDFT 113 (128)
Q Consensus 96 gkt~eeir~~f~i~~d~t 113 (128)
|+||+|-|.-.|++.|+.
T Consensus 98 gmTPd~YR~KW~LP~dYP 115 (148)
T COG4957 98 GLTPDEYRAKWGLPPDYP 115 (148)
T ss_pred CCCHHHHHHhcCCCCCCC
Confidence 799999999999999985
No 45
>PF01592 NifU_N: NifU-like N terminal domain; InterPro: IPR002871 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] []. FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins [, ]. It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly []. The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA []. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA [], acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins []. Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen []. This entry represents the N-terminal of NifU and homologous proteins. NifU contains two domains: an N-terminal and a C-terminal domain (IPR001075 from INTERPRO) []. These domains exist either together or on different polypeptides, both domains being found in organisms that do not fix nitrogen (e.g. yeast), so they have a broader significance in the cell than nitrogen fixation. ; GO: 0005506 iron ion binding, 0051536 iron-sulfur cluster binding, 0016226 iron-sulfur cluster assembly; PDB: 3LVL_A 4EB5_C 4EB7_C 1WFZ_A 2Z7E_C 2AZH_A 1XJS_A 1Q48_A 1R9P_A 2KQK_A ....
Probab=42.70 E-value=36 Score=23.08 Aligned_cols=22 Identities=27% Similarity=0.311 Sum_probs=16.5
Q ss_pred HHHHHHHHHHHhcCCCHHHHHh
Q 040816 83 LDLLCQTVADMIKGKSPEEIRQ 104 (128)
Q Consensus 83 ~~l~~~~ia~~i~gkt~eeir~ 104 (128)
.-.++..++.+++|||.+|+.+
T Consensus 64 ~~Asas~~~~~i~gk~l~ea~~ 85 (126)
T PF01592_consen 64 SIASASMMCELIKGKTLEEALK 85 (126)
T ss_dssp HHHHHHHHHHHHTTSBHHHHHC
T ss_pred HHHHHHHHHHHHcCCCHHHHHH
Confidence 3445667788999999988854
No 46
>PRK11325 scaffold protein; Provisional
Probab=42.42 E-value=40 Score=23.04 Aligned_cols=38 Identities=16% Similarity=0.204 Sum_probs=23.7
Q ss_pred HHHHhhhccHHHHHHHH-HHHHHHHhcCCCHHHHHhhcC
Q 040816 70 LLMAANYLDIKSLLDLL-CQTVADMIKGKSPEEIRQTFH 107 (128)
Q Consensus 70 li~AA~~L~i~~L~~l~-~~~ia~~i~gkt~eeir~~f~ 107 (128)
.+.-+.|-.-=--...+ +..++.+++|||++|.+.+-+
T Consensus 52 ~I~d~~f~~~GC~is~Asas~~~e~~~Gktl~ea~~i~~ 90 (127)
T PRK11325 52 IIEDAKFKTYGCGSAIASSSLVTEWVKGKTLDEALAIKN 90 (127)
T ss_pred eEEEEEEEeeCCHHHHHHHHHHHHHHcCCCHHHHHhcCH
Confidence 34444444443334444 455688999999999887644
No 47
>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma. A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.
Probab=42.40 E-value=68 Score=18.53 Aligned_cols=40 Identities=20% Similarity=0.106 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHHHHHhcCC--CHHHHHhhcCCCCCCCHHHHHHHh
Q 040816 79 IKSLLDLLCQTVADMIKGK--SPEEIRQTFHIQNDFTPEEEEEIR 121 (128)
Q Consensus 79 i~~L~~l~~~~ia~~i~gk--t~eeir~~f~i~~d~t~eee~~i~ 121 (128)
-+.++-.+|=++|.++.+. +..++....|. +|.++..+..
T Consensus 37 ~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~---~~~~~i~~~~ 78 (83)
T smart00385 37 SPSLIAAAALYLAAKTEEIPPWTKELVHYTGY---FTEEEILRME 78 (83)
T ss_pred CHHHHHHHHHHHHHHHhcCCCCchhHhHhhCC---CCHHHHHHHH
Confidence 3455666677778877764 56777777665 6666655443
No 48
>TIGR03419 NifU_clost FeS cluster assembly scaffold protein NifU, Clostridium type. NifU and NifS form a pair of iron-sulfur (FeS) cluster biosynthesis proteins much simpler than the ISC and SUF systems. Members of this protein family are a distinct group of NifU-like proteins, found always to a NifS-like protein and restricted to species that lack a SUF system. Typically, NIF systems service a smaller number of FeS-containing proteins than do ISC or SUF. Members of this particular branch typically are found, almost half the time, near the mnmA gene, involved in the carboxymethylaminomethyl modification of U34 in some tRNAs (see GenProp0704). While other NifU proteins are associated with nitrogen fixation, this family is not.
Probab=42.10 E-value=45 Score=22.55 Aligned_cols=37 Identities=19% Similarity=0.273 Sum_probs=22.9
Q ss_pred HHHHhhhccHHHHHHHH-HHHHHHHhcCCCHHHHHhhc
Q 040816 70 LLMAANYLDIKSLLDLL-CQTVADMIKGKSPEEIRQTF 106 (128)
Q Consensus 70 li~AA~~L~i~~L~~l~-~~~ia~~i~gkt~eeir~~f 106 (128)
.+.-+.|-.-=--.-.+ +..++.++.|||++|..++-
T Consensus 46 ~I~d~~f~~~GC~is~Asas~~~e~i~Gk~l~ea~~i~ 83 (121)
T TIGR03419 46 IIKDVKFKTFGCGAAIASSSMATEMIKGKTLEEAWELT 83 (121)
T ss_pred EEEEEEEEEeccHHHHHHHHHHHHHHcCCCHHHHHHhh
Confidence 34444444443334444 45568899999999977664
No 49
>TIGR01999 iscU FeS cluster assembly scaffold IscU. This model represents IscU, a homolog of the N-terminal region of NifU, an Fe-S cluster assembly protein found mostly in nitrogen-fixing bacteria. IscU is considered part of the IscSUA-hscAB-fdx system of Fe-S assembly, whereas NifU is found in nitrogenase-containing (nitrogen-fixing) species. A NifU-type protein is also found in Helicobacter and Campylobacter. IscU and NifU are considered scaffold proteins on which Fe-S clusters are assembled before transfer to apoproteins. This model excludes true NifU proteins as in Klebsiella pneumoniae and Anabaena sp. as well as archaeal homologs. It includes largely proteobacterial and eukaryotic forms.
Probab=41.93 E-value=42 Score=22.77 Aligned_cols=38 Identities=21% Similarity=0.260 Sum_probs=23.8
Q ss_pred HHHHhhhccHHHHHHHH-HHHHHHHhcCCCHHHHHhhcC
Q 040816 70 LLMAANYLDIKSLLDLL-CQTVADMIKGKSPEEIRQTFH 107 (128)
Q Consensus 70 li~AA~~L~i~~L~~l~-~~~ia~~i~gkt~eeir~~f~ 107 (128)
.+.-+.|-.-=--.-.+ +..++.++.|||.+|.+.+-+
T Consensus 50 ~I~d~~f~~~GC~~s~Asas~~~e~i~Gktl~ea~~i~~ 88 (124)
T TIGR01999 50 IIEDAKFKTFGCGSAIASSSLATELIKGKSLEEALKIKN 88 (124)
T ss_pred eEEEEEEEecCcHHHHHHHHHHHHHHcCCCHHHHHhccH
Confidence 34444444433333333 456688999999999887644
No 50
>PF09713 A_thal_3526: Plant protein 1589 of unknown function (A_thal_3526); InterPro: IPR006476 This plant-specific family of proteins are defined by an uncharacterised region 57 residues in length. It is found toward the N terminus of most proteins that contain it. Examples include at least several proteins from Arabidopsis thaliana (Mouse-ear cress) and Oryza sativa (Rice). The function of the proteins are unknown.
Probab=41.29 E-value=37 Score=20.08 Aligned_cols=30 Identities=27% Similarity=0.269 Sum_probs=23.5
Q ss_pred CCCHHHHH----hhcCCCCCCCHHHHHHHhhhCC
Q 040816 96 GKSPEEIR----QTFHIQNDFTPEEEEEIRTETP 125 (128)
Q Consensus 96 gkt~eeir----~~f~i~~d~t~eee~~i~~e~~ 125 (128)
.+|.+|+- +..||+..+|.-=+.+++++|+
T Consensus 12 yMsk~E~v~~L~~~a~I~P~~T~~VW~~Le~eN~ 45 (54)
T PF09713_consen 12 YMSKEECVRALQKQANIEPVFTSTVWQKLEKENP 45 (54)
T ss_pred cCCHHHHHHHHHHHcCCChHHHHHHHHHHHHHCH
Confidence 46666664 4458999999989999999986
No 51
>TIGR01589 A_thal_3526 uncharacterized plant-specific domain TIGR01589. This model represents an uncharacterized plant-specific domain 57 residues in length. It is found toward the N-terminus of most proteins that contain it. Examples include at least 10 proteins from Arabidopsis thaliana and at least one from Oryza sativa.
Probab=40.31 E-value=79 Score=18.90 Aligned_cols=29 Identities=24% Similarity=0.078 Sum_probs=23.3
Q ss_pred CCHHHH----HhhcCCCCCCCHHHHHHHhhhCC
Q 040816 97 KSPEEI----RQTFHIQNDFTPEEEEEIRTETP 125 (128)
Q Consensus 97 kt~eei----r~~f~i~~d~t~eee~~i~~e~~ 125 (128)
+|.+|+ .+-.||+..+|.-=+.++++||+
T Consensus 16 Msk~E~v~~L~~~a~I~P~~T~~VW~~LekeN~ 48 (57)
T TIGR01589 16 MSKEETVSFLFENAGISPKFTRFVWYLLEKENA 48 (57)
T ss_pred CCHHHHHHHHHHHcCCCchhHHHHHHHHHHHHH
Confidence 565555 56689999999988999999886
No 52
>PF13798 PCYCGC: Protein of unknown function with PCYCGC motif
Probab=39.83 E-value=44 Score=24.14 Aligned_cols=25 Identities=48% Similarity=0.618 Sum_probs=18.7
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHhhc
Q 040816 82 LLDLLCQTVADMIKGKSPEEIRQTF 106 (128)
Q Consensus 82 L~~l~~~~ia~~i~gkt~eeir~~f 106 (128)
-++.+-..+...=+|||+.|||+.-
T Consensus 117 Cl~ia~~a~~~~~~Gks~~eIR~~I 141 (158)
T PF13798_consen 117 CLDIAVQAVQMYQEGKSPKEIRQYI 141 (158)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 3455666666677899999999863
No 53
>PF02084 Bindin: Bindin; InterPro: IPR000775 Bindin, the major protein component of the acrosome granule of sea urchin sperm, mediates species-specific adhesion of sperm to the egg surface during fertilisation [, ]. The protein coats the acrosomal process after externalisation by the acrosome reaction; it binds to sulphated, fucose-containing polysaccharides on the vitelline-layer receptor proteoglycans that cover the egg plasma membrane. Bindins from different genera show high levels of sequence similarity in both the mature bindin domain and in the probindin precursor region. The most highly conserved region is a 42-residue segment in the central portion of the mature bindin protein. This domain may be responsible for conserved functions of bindin, while the more highly divergent flanking regions may be responsible for its species-specific properties [].; GO: 0007342 fusion of sperm to egg plasma membrane
Probab=39.62 E-value=45 Score=25.54 Aligned_cols=17 Identities=18% Similarity=0.307 Sum_probs=10.5
Q ss_pred CHHHHHHHHHHHHhccc
Q 040816 28 RGTILSMVIEYLKKHVE 44 (128)
Q Consensus 28 ~~~~L~~Vi~~c~~h~~ 44 (128)
+.--|-++++.++||..
T Consensus 126 DPYDlGLLLRhLRHHSN 142 (238)
T PF02084_consen 126 DPYDLGLLLRHLRHHSN 142 (238)
T ss_pred ChhhHHHHHHHHHHHHH
Confidence 34456666666666665
No 54
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=39.42 E-value=14 Score=25.83 Aligned_cols=18 Identities=33% Similarity=0.744 Sum_probs=12.6
Q ss_pred CCCHHHHHhhcCCCCCCC
Q 040816 96 GKSPEEIRQTFHIQNDFT 113 (128)
Q Consensus 96 gkt~eeir~~f~i~~d~t 113 (128)
|.|++|=|+.||++.|+.
T Consensus 94 gltp~eYR~kwGlp~dyp 111 (132)
T PF05443_consen 94 GLTPEEYRAKWGLPKDYP 111 (132)
T ss_dssp -S-HHHHHHHTT-GGG--
T ss_pred CCCHHHHHHHhCcCCCCc
Confidence 899999999999999864
No 55
>PRK15019 CsdA-binding activator; Provisional
Probab=39.09 E-value=57 Score=23.15 Aligned_cols=34 Identities=12% Similarity=0.342 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHHHhcCCCHHHHHh--------hcCCCCCCCH
Q 040816 81 SLLDLLCQTVADMIKGKSPEEIRQ--------TFHIQNDFTP 114 (128)
Q Consensus 81 ~L~~l~~~~ia~~i~gkt~eeir~--------~f~i~~d~t~ 114 (128)
.++.-.+..+...++|+||+||.+ -+|+...+||
T Consensus 86 ~IvkGl~alL~~~~~g~tp~eIl~~d~~~~~~~lGL~~~LSp 127 (147)
T PRK15019 86 RIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSA 127 (147)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHhcCHHHHHHHCCchhhcCc
Confidence 344445566677779999999864 4577777776
No 56
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=39.05 E-value=24 Score=18.28 Aligned_cols=14 Identities=43% Similarity=0.508 Sum_probs=9.6
Q ss_pred hcCCCHHHHHhhcC
Q 040816 94 IKGKSPEEIRQTFH 107 (128)
Q Consensus 94 i~gkt~eeir~~f~ 107 (128)
-.|-|.+|+|+++.
T Consensus 14 ~~Gls~eeir~FL~ 27 (30)
T PF08671_consen 14 ESGLSKEEIREFLE 27 (30)
T ss_dssp HTT--HHHHHHHHH
T ss_pred HcCCCHHHHHHHHH
Confidence 35899999999874
No 57
>PRK09296 cysteine desufuration protein SufE; Provisional
Probab=39.05 E-value=63 Score=22.60 Aligned_cols=33 Identities=18% Similarity=0.359 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHh--------hcCCCCCCCH
Q 040816 82 LLDLLCQTVADMIKGKSPEEIRQ--------TFHIQNDFTP 114 (128)
Q Consensus 82 L~~l~~~~ia~~i~gkt~eeir~--------~f~i~~d~t~ 114 (128)
++.-.+..+...++|+||+||.+ .+|+...+||
T Consensus 77 ivkGl~alL~~~~~g~tp~eIl~~d~~~~~~~lGL~~~LSp 117 (138)
T PRK09296 77 IVKGLIAVVFILYQQMTPQDIVNFDVRPWFEKLALTQHLTP 117 (138)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHhCChHHHHHHcCcccccCc
Confidence 44445566677789999999863 4577777776
No 58
>PF03883 DUF328: Protein of unknown function (DUF328); InterPro: IPR005583 The members of this family are functionally uncharacterised. They are about 250 amino acids in length.
Probab=39.04 E-value=27 Score=26.49 Aligned_cols=37 Identities=16% Similarity=0.279 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHhcCCCHHHHHhhcCCCCCCCHHHHHH
Q 040816 83 LDLLCQTVADMIKGKSPEEIRQTFHIQNDFTPEEEEE 119 (128)
Q Consensus 83 ~~l~~~~ia~~i~gkt~eeir~~f~i~~d~t~eee~~ 119 (128)
+.-..+.++..++..|.+|+++.|+|...+..+..++
T Consensus 27 f~~~~~~l~~~L~~~s~~el~~l~~is~~la~~~~~~ 63 (237)
T PF03883_consen 27 FLEKTEELLEALKSLSEEELKKLMKISDKLAEENYQR 63 (237)
T ss_pred hHHHHHHHHHHHHhcCHHHHHHHHCCCHHHHHHHHHH
Confidence 3344666777778888899999999886665544443
No 59
>PRK13379 protocatechuate 4,5-dioxygenase subunit alpha; Provisional
Probab=38.89 E-value=77 Score=21.82 Aligned_cols=25 Identities=24% Similarity=0.316 Sum_probs=21.0
Q ss_pred HHHHHHHHhcCCCHHHHHhhcCCCC
Q 040816 86 LCQTVADMIKGKSPEEIRQTFHIQN 110 (128)
Q Consensus 86 ~~~~ia~~i~gkt~eeir~~f~i~~ 110 (128)
.-+.|...++|+|.||.++.=++++
T Consensus 93 s~q~i~a~mtG~t~eeF~~tr~~~~ 117 (119)
T PRK13379 93 TNLQVYAIMRGETFEEFMQTRRVPD 117 (119)
T ss_pred cHHHHHHHhcCCcHHHHHHHccCCC
Confidence 3478889999999999999887764
No 60
>PRK13503 transcriptional activator RhaS; Provisional
Probab=38.74 E-value=1.6e+02 Score=21.86 Aligned_cols=81 Identities=16% Similarity=0.180 Sum_probs=50.2
Q ss_pred CCHHHHHHHHHHHHhcccCCCCcccccchhhhhhccChHHHHHHHHHhhhccHHHHHHHHHH-HHHHHh--cCCCHHHHH
Q 040816 27 VRGTILSMVIEYLKKHVEAKTTEDDLKNWDVDFAKLGQDTLFDLLMAANYLDIKSLLDLLCQ-TVADMI--KGKSPEEIR 103 (128)
Q Consensus 27 v~~~~L~~Vi~~c~~h~~~~~~~~~~~~wd~~Fl~~~~~~l~~li~AA~~L~i~~L~~l~~~-~ia~~i--~gkt~eeir 103 (128)
.....+.++++|.+.|...+ ..++++ ++.+.++...+..+.....-.-....+.-.-= ....++ .+.|+.||-
T Consensus 168 ~~~~~i~~~~~~I~~~~~~~---~tl~~l-A~~~~lS~~~l~r~Fk~~~G~S~~~yi~~~Rl~~A~~LL~~~~~sI~eIA 243 (278)
T PRK13503 168 NSDARLNQLLAWLEDHFAEE---VNWEAL-ADQFSLSLRTLHRQLKQQTGLTPQRYLNRLRLLKARHLLRHSDASVTDIA 243 (278)
T ss_pred ccHHHHHHHHHHHHHhhcCC---CCHHHH-HHHHCCCHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHHHcCCCCHHHHH
Confidence 45566889999999887654 245555 45556888888888886644443333332211 111222 357888888
Q ss_pred hhcCCCCC
Q 040816 104 QTFHIQND 111 (128)
Q Consensus 104 ~~f~i~~d 111 (128)
..+|..+-
T Consensus 244 ~~~GF~~~ 251 (278)
T PRK13503 244 YRCGFGDS 251 (278)
T ss_pred HHhCCCCH
Confidence 88887654
No 61
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=38.43 E-value=30 Score=24.02 Aligned_cols=19 Identities=32% Similarity=0.482 Sum_probs=14.4
Q ss_pred HHHHHHhc-CCCHHHHHhhc
Q 040816 88 QTVADMIK-GKSPEEIRQTF 106 (128)
Q Consensus 88 ~~ia~~i~-gkt~eeir~~f 106 (128)
+.|..++. |+|.+||+++|
T Consensus 64 ~~Vr~~i~~G~Sd~eI~~~~ 83 (126)
T TIGR03147 64 HEVYSMVNEGKSNQQIIDFM 83 (126)
T ss_pred HHHHHHHHcCCCHHHHHHHH
Confidence 45555555 99999999876
No 62
>PF04355 SmpA_OmlA: SmpA / OmlA family; InterPro: IPR007450 This is a bacterial outer membrane lipoprotein, possibly involved in maintaining the structural integrity of the cell envelope []. The lipid attachment site is a conserved N-terminal cysteine residue sometimes found adjacent to the OmpA domain (IPR006665 from INTERPRO).; GO: 0019867 outer membrane; PDB: 4DM5_C 2PXG_A 2YH9_B 2KXX_A 2KM7_A.
Probab=37.38 E-value=16 Score=21.95 Aligned_cols=21 Identities=14% Similarity=0.338 Sum_probs=15.6
Q ss_pred HHHHhcCCCHHHHHhhcCCCC
Q 040816 90 VADMIKGKSPEEIRQTFHIQN 110 (128)
Q Consensus 90 ia~~i~gkt~eeir~~f~i~~ 110 (128)
++..-.|+|.+|++..||-|.
T Consensus 9 ~~~i~~GmTk~qV~~lLG~P~ 29 (71)
T PF04355_consen 9 LAQIKPGMTKDQVRALLGSPS 29 (71)
T ss_dssp HTTT-TTSBHHHHHHHHTS-S
T ss_pred HHhhcCCCCHHHHHHhcCCCC
Confidence 444556999999999999775
No 63
>COG1710 Uncharacterized protein conserved in archaea [Function unknown]
Probab=37.30 E-value=24 Score=24.49 Aligned_cols=20 Identities=35% Similarity=0.793 Sum_probs=16.1
Q ss_pred HHHHhc-CCCHHHHHhhcCCC
Q 040816 90 VADMIK-GKSPEEIRQTFHIQ 109 (128)
Q Consensus 90 ia~~i~-gkt~eeir~~f~i~ 109 (128)
|-.+++ ||+|.||.+.+||+
T Consensus 102 i~emlr~gk~preIsk~lGIp 122 (139)
T COG1710 102 IREMLRNGKTPREISKDLGIP 122 (139)
T ss_pred HHHHHHcCCCHHHHHHhhCCc
Confidence 344444 89999999999997
No 64
>PF03750 DUF310: Protein of unknown function (DUF310); InterPro: IPR010149 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. This entry represents the C-terminal domain of a minor family of CRISPR-associated proteins. These proteins are found adjacent to a characteristic short, palindromic repeat cluster termed CRISPR, a probable mobile DNA element.
Probab=37.04 E-value=53 Score=22.19 Aligned_cols=33 Identities=24% Similarity=0.393 Sum_probs=20.9
Q ss_pred ccHHHHHHHHHHHHHHHhc--CCCHHHHHhhcCCCC
Q 040816 77 LDIKSLLDLLCQTVADMIK--GKSPEEIRQTFHIQN 110 (128)
Q Consensus 77 L~i~~L~~l~~~~ia~~i~--gkt~eeir~~f~i~~ 110 (128)
++++.|.+.+.+ +|..++ +.|+.+||++|+--.
T Consensus 8 ~~~~~~~~~Ae~-~~k~l~~~~lttsQlRkf~~~v~ 42 (119)
T PF03750_consen 8 LDIELLVDYAEK-IAKELKKNKLTTSQLRKFYDEVK 42 (119)
T ss_pred cCHHHHHHHHHH-HHHHHHhCCCCHHHHHHHHHHHH
Confidence 445555555544 444444 479999999998433
No 65
>PF07671 DUF1601: Protein of unknown function (DUF1601); InterPro: IPR011632 This repeat is found in a small number of proteins and is apparently limited to Coxiella burnetii.
Probab=36.98 E-value=41 Score=18.27 Aligned_cols=30 Identities=33% Similarity=0.427 Sum_probs=24.1
Q ss_pred hccHHHHHHHHHHHHHHHhcCCCHHHHHhh
Q 040816 76 YLDIKSLLDLLCQTVADMIKGKSPEEIRQT 105 (128)
Q Consensus 76 ~L~i~~L~~l~~~~ia~~i~gkt~eeir~~ 105 (128)
||.-++|-+.....|+..+..-++++|-..
T Consensus 7 ~l~~q~L~~~L~~aV~~~a~~Fn~QeiaNt 36 (37)
T PF07671_consen 7 YLEEQRLSDRLLDAVRRNAEQFNPQEIANT 36 (37)
T ss_pred hhhhccchHHHHHHHHHHHHHcCHHHHhhc
Confidence 677788888888888888888888887543
No 66
>PRK13742 replication protein; Provisional
Probab=36.94 E-value=35 Score=26.14 Aligned_cols=34 Identities=18% Similarity=0.271 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHHHHhcC---CCHHHHHhhcCCCCCCC
Q 040816 80 KSLLDLLCQTVADMIKG---KSPEEIRQTFHIQNDFT 113 (128)
Q Consensus 80 ~~L~~l~~~~ia~~i~g---kt~eeir~~f~i~~d~t 113 (128)
.+|++++|++-...-.| -+.+++|..||+++.+.
T Consensus 163 ~RLYelL~q~~~~~~~g~~~i~i~elr~~l~~~~~Y~ 199 (245)
T PRK13742 163 MRLYESLCQYRKPDGSGIVSLKIDWIIERYQLPQSYQ 199 (245)
T ss_pred HHHHHHHHHhhhhccCCeEEEEHHHHHHHhCCccccc
Confidence 36788888876543234 47999999999988774
No 67
>PF13518 HTH_28: Helix-turn-helix domain
Probab=36.84 E-value=55 Score=17.83 Aligned_cols=21 Identities=33% Similarity=0.468 Sum_probs=16.9
Q ss_pred HHHHHhcCCCHHHHHhhcCCC
Q 040816 89 TVADMIKGKSPEEIRQTFHIQ 109 (128)
Q Consensus 89 ~ia~~i~gkt~eeir~~f~i~ 109 (128)
.|.....|.|..++.+.|||.
T Consensus 5 iv~~~~~g~s~~~~a~~~gis 25 (52)
T PF13518_consen 5 IVELYLEGESVREIAREFGIS 25 (52)
T ss_pred HHHHHHcCCCHHHHHHHHCCC
Confidence 344556799999999999994
No 68
>KOG0783 consensus Uncharacterized conserved protein, contains ankyrin and BTB/POZ domains [Function unknown]
Probab=35.68 E-value=1.7e+02 Score=27.19 Aligned_cols=66 Identities=23% Similarity=0.299 Sum_probs=48.6
Q ss_pred CCHHHHHHHHHHHHhcccCCCCcccccchhhhhhc--cChHHHHHHHHHhhhccHHHHHHHHHHHHHHHhcCCCHHHHHh
Q 040816 27 VRGTILSMVIEYLKKHVEAKTTEDDLKNWDVDFAK--LGQDTLFDLLMAANYLDIKSLLDLLCQTVADMIKGKSPEEIRQ 104 (128)
Q Consensus 27 v~~~~L~~Vi~~c~~h~~~~~~~~~~~~wd~~Fl~--~~~~~l~~li~AA~~L~i~~L~~l~~~~ia~~i~gkt~eeir~ 104 (128)
++++.|+-|++|...--. .+|++ .+.+-+|+++..|+-|=|..|-+.|-..+-+++.=|+..++-+
T Consensus 758 ~~~e~m~ivLdylYs~d~------------~~~~k~~~~~dF~~~il~iaDqlli~~Lk~Ice~~ll~kl~lk~~~~lle 825 (1267)
T KOG0783|consen 758 LTVEHMSIVLDYLYSDDK------------VELFKDLKESDFMFEILSIADQLLILELKSICEQSLLRKLNLKTLPTLLE 825 (1267)
T ss_pred chHHHHHHHHHHHHccch------------HHHHhccchhhhhHHHHHHHHHHHHHHHHHHHHHHHHhHhcccchHHHHH
Confidence 579999999999753111 23333 3445688999999999999999999888888888777655543
No 69
>TIGR01044 rplV_bact ribosomal protein L22, bacterial type. This model decribes bacterial and chloroplast ribosomal protein L22.
Probab=34.95 E-value=42 Score=22.15 Aligned_cols=22 Identities=32% Similarity=0.511 Sum_probs=18.7
Q ss_pred HHHHHHHhcCCCHHHHHhhcCC
Q 040816 87 CQTVADMIKGKSPEEIRQTFHI 108 (128)
Q Consensus 87 ~~~ia~~i~gkt~eeir~~f~i 108 (128)
+..||+.|+|+++++-..++..
T Consensus 13 ~~~va~~IrG~~v~~A~~~L~f 34 (103)
T TIGR01044 13 ARLVADLIRGKSVSQALDILRF 34 (103)
T ss_pred HHHHHHHHcCCcHHHHHHHHhh
Confidence 4678999999999999888874
No 70
>TIGR03391 FeS_syn_CsdE cysteine desulfurase, sulfur acceptor subunit CsdE. Members of this protein family are CsdE, formerly called YgdK. This protein, found as a paralog to SufE in Escherichia coli, Yersinia pestis, Photorhabdus luminescens, and related species, works together and physically interacts with CsdA (a paralog of SufS). CsdA has cysteine desulfurase activity that is enhanced by this protein (CsdE), in which Cys-61 (numbered as in E. coli) is a sulfur acceptor site. This gene pair, although involved in FeS cluster biosynthesis, is not found next to other such genes as are its paralogs from the Suf or Isc systems.
Probab=34.89 E-value=76 Score=22.19 Aligned_cols=33 Identities=15% Similarity=0.407 Sum_probs=22.8
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHh--------hcCCCCCCCH
Q 040816 82 LLDLLCQTVADMIKGKSPEEIRQ--------TFHIQNDFTP 114 (128)
Q Consensus 82 L~~l~~~~ia~~i~gkt~eeir~--------~f~i~~d~t~ 114 (128)
++.-.+..+....+|+||+||.+ .+|+...+||
T Consensus 82 IvkGl~alL~~~~~g~tp~eI~~~d~~~~~~~lGL~~~LSp 122 (138)
T TIGR03391 82 IVRGLLAVLLTAVEGKTPEQLLAQDPLALFDELGLRAQLSA 122 (138)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHCCHHHHHHHcCchhccCc
Confidence 44444556667779999999863 3567777776
No 71
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=34.74 E-value=40 Score=18.50 Aligned_cols=15 Identities=27% Similarity=0.368 Sum_probs=10.5
Q ss_pred cCCCHHHHHhhcCCC
Q 040816 95 KGKSPEEIRQTFHIQ 109 (128)
Q Consensus 95 ~gkt~eeir~~f~i~ 109 (128)
.|+|..+|-+.||++
T Consensus 16 ~G~s~~~ia~~lgvs 30 (50)
T PF13384_consen 16 EGWSIREIAKRLGVS 30 (50)
T ss_dssp HT--HHHHHHHHTS-
T ss_pred CCCCHHHHHHHHCcC
Confidence 489999999999985
No 72
>cd02140 Nitroreductase_4 Nitroreductase-like family 4. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and nitroimidazoles. This process requires NAD(P)H as electron donor in an obligatory two-electron transfer and uses FMN as cofactor. The enzyme is typically a homodimer. Members of this family are also called NADH dehydrogenase, oxygen-insensitive NAD(P)H nitrogenase or dihydropteridine reductase.
Probab=34.32 E-value=31 Score=24.74 Aligned_cols=39 Identities=15% Similarity=0.181 Sum_probs=24.4
Q ss_pred HHHHHHHhhhccHHHHHHHHHHHHHHHhcCCCHHHHHhhcCCCCCCC
Q 040816 67 LFDLLMAANYLDIKSLLDLLCQTVADMIKGKSPEEIRQTFHIQNDFT 113 (128)
Q Consensus 67 l~~li~AA~~L~i~~L~~l~~~~ia~~i~gkt~eeir~~f~i~~d~t 113 (128)
+-.|+.||.-+|+-+.+... .....+.+|+.|||++++.
T Consensus 127 ~~nl~LaA~~~GlGs~~~~~--------~~~~~~~v~~~l~ip~~~~ 165 (192)
T cd02140 127 QIAVWTALAAEGIGANLQHY--------NPLIDEEVAKKWNIPSNWK 165 (192)
T ss_pred HHHHHHHHHhCCCcccHHHh--------CccCCHHHHHhcCCCccce
Confidence 34677777777776532110 0123589999999998753
No 73
>PF03918 CcmH: Cytochrome C biogenesis protein; InterPro: IPR005616 Members of this family include NrfF, CcmH, CycL, Ccl2.; PDB: 2KW0_A 2HL7_A.
Probab=34.11 E-value=34 Score=24.28 Aligned_cols=18 Identities=44% Similarity=0.732 Sum_probs=10.9
Q ss_pred HHHHHh-cCCCHHHHHhhc
Q 040816 89 TVADMI-KGKSPEEIRQTF 106 (128)
Q Consensus 89 ~ia~~i-~gkt~eeir~~f 106 (128)
.|..++ .|+|.+||+++|
T Consensus 65 ~I~~~l~~G~s~~eI~~~~ 83 (148)
T PF03918_consen 65 EIREMLAEGKSDEEIIDYF 83 (148)
T ss_dssp HHHHHHHHT--HHHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHH
Confidence 444444 499999998875
No 74
>PF11103 DUF2887: Protein of unknown function (DUF2887); InterPro: IPR022573 This bacterial group of proteins has no known function.
Probab=33.65 E-value=65 Score=24.10 Aligned_cols=29 Identities=24% Similarity=0.288 Sum_probs=25.8
Q ss_pred cHHHHHHHHHHHHHHHhcCCCHHHHHhhc
Q 040816 78 DIKSLLDLLCQTVADMIKGKSPEEIRQTF 106 (128)
Q Consensus 78 ~i~~L~~l~~~~ia~~i~gkt~eeir~~f 106 (128)
.=..|+++.-..+..+...+|.+||..||
T Consensus 172 ~~~~lleLIEtIlvyKfp~lSreEIeaMl 200 (200)
T PF11103_consen 172 QQRELLELIETILVYKFPQLSREEIEAML 200 (200)
T ss_pred HHHHHHHHHHHHHHHHccccCHHHHHHhC
Confidence 35678999999999999999999999986
No 75
>cd06664 IscU_like Iron-sulfur cluster scaffold-like proteins. IscU_like and NifU_like proteins. IscU and NifU function as a scaffold for the assembly of [2Fe-2S] clusters before they are transferred to apo target proteins. They are highly conserved and play vital roles in the ISC and NIF systems of Fe-S protein maturation. NIF genes participate in nitrogen fixation in several isolated bacterial species. The NifU domain, however, is also found in bacteria that do not fix nitrogen, so it may have wider significance in the cell. Human IscU interacts with frataxin, the Friedreich ataxia gene product, and incorrectly spliced IscU has been shown to disrupt iron homeostasis in skeletal muscle and cause myopathy.
Probab=33.41 E-value=73 Score=21.18 Aligned_cols=39 Identities=15% Similarity=0.347 Sum_probs=24.6
Q ss_pred HHHHHhhhccHHHHHHHH-HHHHHHHhcCCCHHHHHhhcC
Q 040816 69 DLLMAANYLDIKSLLDLL-CQTVADMIKGKSPEEIRQTFH 107 (128)
Q Consensus 69 ~li~AA~~L~i~~L~~l~-~~~ia~~i~gkt~eeir~~f~ 107 (128)
+.+..+.|-.-=-.+-.+ +..++.+++|||.+|...+.+
T Consensus 46 ~~I~d~~f~~~GC~i~~Asas~~~~~~~Gk~~~ea~~i~~ 85 (123)
T cd06664 46 GRITDAKFQGFGCAISIASASLLTELIKGKTLDEALKLLN 85 (123)
T ss_pred CEEEEEEEEecCcHHHHHHHHHHHHHHcCCcHHHHHHHHH
Confidence 344444554444444444 445588999999999987654
No 76
>cd00068 GGL G protein gamma subunit-like motifs, the alpha-helical G-gamma chain dimerizes with the G-beta propeller subunit as part of the heterotrimeric G-protein complex; involved in signal transduction via G-protein-coupled receptors
Probab=32.95 E-value=53 Score=19.29 Aligned_cols=18 Identities=11% Similarity=0.326 Sum_probs=14.8
Q ss_pred HHHHHHHHHHHHhcccCC
Q 040816 29 GTILSMVIEYLKKHVEAK 46 (128)
Q Consensus 29 ~~~L~~Vi~~c~~h~~~~ 46 (128)
|.+..-++.||+.|....
T Consensus 23 S~a~~~l~~y~e~~~~~D 40 (57)
T cd00068 23 SKAAAELLKYCEQNAEND 40 (57)
T ss_pred HHHHHHHHHHHHhcCCCC
Confidence 778889999999996653
No 77
>KOG4244 consensus Failed axon connections (fax) protein/glutathione S-transferase-like protein [Signal transduction mechanisms]
Probab=32.91 E-value=46 Score=26.22 Aligned_cols=22 Identities=27% Similarity=0.670 Sum_probs=18.1
Q ss_pred HHHHhhcCCCCCCCHHHHHHHh
Q 040816 100 EEIRQTFHIQNDFTPEEEEEIR 121 (128)
Q Consensus 100 eeir~~f~i~~d~t~eee~~i~ 121 (128)
..+|+-|++++++++||+.+.+
T Consensus 112 ~~L~~hf~~~~~L~~e~~a~s~ 133 (281)
T KOG4244|consen 112 DRLRKHFKIPDDLSAEQRAQSR 133 (281)
T ss_pred HHHHHHcCCCCCCCHHHHHHHH
Confidence 3567899999999999988654
No 78
>TIGR02476 BluB cob(II)yrinic acid a,c-diamide reductase. The BluB protein is related to the nitroreductase family (pfam0881), and is found to substitute for the FldA cobalt reductase in aerobic species (by phylogenetic profiling). BluB is also found to be preceded by B12 promoter elements elements. The gene in R. capsulatus has been shown to be essential for cobalamin biosynthesis.
Probab=32.71 E-value=37 Score=24.66 Aligned_cols=37 Identities=14% Similarity=0.248 Sum_probs=26.0
Q ss_pred HHHHHHHhhhccHHHHHHHHHHHHHHHhcCCCHHHHHhhcCCCCCCC
Q 040816 67 LFDLLMAANYLDIKSLLDLLCQTVADMIKGKSPEEIRQTFHIQNDFT 113 (128)
Q Consensus 67 l~~li~AA~~L~i~~L~~l~~~~ia~~i~gkt~eeir~~f~i~~d~t 113 (128)
+-.++.||.-+|+-.. .+.+-..+++++.|||+.++.
T Consensus 134 ~~nl~LaA~~~GlGs~----------~~~~~~~~~v~~~L~lp~~~~ 170 (205)
T TIGR02476 134 IQNLWLAARAEGLGVG----------WVSILDPDAVRRLLGVPEGWR 170 (205)
T ss_pred HHHHHHHHHHCCCcce----------eecccChHHHHHHhCcCCCce
Confidence 4467777887777652 123445789999999998754
No 79
>cd02144 iodotyrosine_dehalogenase Iodotyrosine dehalogenase catalyzes the removal of iodine from the 3, 5 positions of L-tyosine in thyroid, liver and kidney, using NADPH as electron donor. This enzyme is a homolog of the nitroreductase family. These enzymes are usually homodimers.
Probab=32.55 E-value=38 Score=23.92 Aligned_cols=36 Identities=11% Similarity=-0.011 Sum_probs=24.9
Q ss_pred HHHHHhhhccHHHHHHHHHHHHHHHhcCCCH-HHHHhhcCCCCCCCH
Q 040816 69 DLLMAANYLDIKSLLDLLCQTVADMIKGKSP-EEIRQTFHIQNDFTP 114 (128)
Q Consensus 69 ~li~AA~~L~i~~L~~l~~~~ia~~i~gkt~-eeir~~f~i~~d~t~ 114 (128)
.++.||.-+|+-.. .+.+... +.+++.|||++++.+
T Consensus 131 ~l~LaA~~~Glgs~----------~~~~~~~~~~v~~~l~ip~~~~~ 167 (193)
T cd02144 131 LLLAALQNAGLGTV----------TTTPLNMGPFLRRLLGRPANEKL 167 (193)
T ss_pred HHHHHHHHCCCcee----------ecCCcchhHHHHHHhCCCCCCce
Confidence 47778888887762 1234344 899999999987543
No 80
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=32.46 E-value=1.5e+02 Score=20.13 Aligned_cols=36 Identities=8% Similarity=0.132 Sum_probs=20.2
Q ss_pred HHHHHHHhcCCCHHHHHhhcCCCCCCCHHHHHHHhh
Q 040816 87 CQTVADMIKGKSPEEIRQTFHIQNDFTPEEEEEIRT 122 (128)
Q Consensus 87 ~~~ia~~i~gkt~eeir~~f~i~~d~t~eee~~i~~ 122 (128)
.+.+.+.+-|-++..+-..|--.+.+++||.+++++
T Consensus 77 ~~~~~~~~f~gs~~~ll~~l~~~~~ls~eele~L~~ 112 (130)
T TIGR02698 77 AQELFSRICSRKVGAVIADLIEESPLSQTDIEKLEK 112 (130)
T ss_pred HHHHHHHHHCCCHHHHHHHHHhcCCCCHHHHHHHHH
Confidence 344444445555555444442245678888877765
No 81
>KOG4591 consensus Uncharacterized conserved protein, contains BTB/POZ domain [General function prediction only]
Probab=31.96 E-value=1.3e+02 Score=23.10 Aligned_cols=31 Identities=16% Similarity=0.176 Sum_probs=19.1
Q ss_pred cChHHHHHHHHHhhhccHHHHHHHHHHHHHH
Q 040816 62 LGQDTLFDLLMAANYLDIKSLLDLLCQTVAD 92 (128)
Q Consensus 62 ~~~~~l~~li~AA~~L~i~~L~~l~~~~ia~ 92 (128)
.++..|.+|+.-|+..+.+-|-+.|-+-+..
T Consensus 134 ~dD~~L~el~e~An~FqLe~Lke~C~k~l~a 164 (280)
T KOG4591|consen 134 EDDEFLLELCELANRFQLELLKERCEKGLGA 164 (280)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 4555666666666666666666666554443
No 82
>PF11795 DUF3322: Uncharacterized protein conserved in bacteria N-term (DUF3322); InterPro: IPR024537 This domain, found in various hypothetical bacterial proteins, has no known function. The family represents just the N terminus.
Probab=31.51 E-value=54 Score=23.94 Aligned_cols=46 Identities=20% Similarity=0.222 Sum_probs=31.8
Q ss_pred CCCHHHHHHHHHHHHhcccCC--CCcccccchhhhhhccChHHHHHHH
Q 040816 26 NVRGTILSMVIEYLKKHVEAK--TTEDDLKNWDVDFAKLGQDTLFDLL 71 (128)
Q Consensus 26 ~v~~~~L~~Vi~~c~~h~~~~--~~~~~~~~wd~~Fl~~~~~~l~~li 71 (128)
..+..-|-.|+.|+..|.... ....+++-.|.+||+-....|-+|+
T Consensus 141 ~~d~~~l~~vl~wl~~h~~~g~ylRqlpi~GvDTKfiE~h~~ll~~Ll 188 (190)
T PF11795_consen 141 DDDFERLLAVLDWLRPHPRSGLYLRQLPIPGVDTKFIERHRGLLAALL 188 (190)
T ss_pred HhhHHHHHHHHHHHhcCCCCCCchhhCCcCCcchHHHHHHHHHHHHHh
Confidence 344467888999998887653 2456678889999984444454543
No 83
>PF09382 RQC: RQC domain; InterPro: IPR018982 This entry represents the RQC domain, which is a DNA-binding domain found only in RecQ family enzymes. RecQ family helicases can unwind G4 DNA, and play important roles at G-rich domains of the genome, including the telomeres, rDNA, and immunoglobulin switch regions. This domain has a helix-turn-helix structure and acts as a high affinity G4 DNA binding domain []. Binding of RecQ to Holliday junctions involves both the RQC and the HRDC domains.; GO: 0043140 ATP-dependent 3'-5' DNA helicase activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1OYW_A 1OYY_A 3AAF_A 2AXL_A 2V1X_B 2WWY_B.
Probab=31.46 E-value=1.1e+02 Score=19.48 Aligned_cols=39 Identities=21% Similarity=0.458 Sum_probs=27.6
Q ss_pred HHHHHHHHHHhcCCCHHHHHh-------hcCCCCCCCHHHHHHHhh
Q 040816 84 DLLCQTVADMIKGKSPEEIRQ-------TFHIQNDFTPEEEEEIRT 122 (128)
Q Consensus 84 ~l~~~~ia~~i~gkt~eeir~-------~f~i~~d~t~eee~~i~~ 122 (128)
.++...+++.++|...+.+++ .||+-.+++..+.+++-.
T Consensus 19 ~~~~~~ivdvlrGs~~~~i~~~~~~~l~~yG~gk~~~~~~~~~li~ 64 (106)
T PF09382_consen 19 RFGLSQIVDVLRGSKSKKIREKGHDQLPTYGIGKDMSKDDWERLIR 64 (106)
T ss_dssp -S-HHHHHHHHTT-S-CCCHHTTGGGSTTTTTTTTS-HHHHHHHHH
T ss_pred cccHHHHHHHHHhccchhhhhcCCCcCcccCCcccCCHHHHHHHHH
Confidence 577888999999988777765 499999999888887643
No 84
>cd03370 NADH_oxidase NADPH_oxidase. Nitroreductase family containing NADH oxidase and other, uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and nitroimidazoles. This process requires NAD(P)H as electron donor in an obligatory two-electron transfer and uses FMN as cofactor. The enzyme is typically a homodimer. Members of this family are also called NADH dehydrogenase, oxygen-insensitive NAD(P)H nitrogenase or dihydropteridine reductase.
Probab=31.42 E-value=37 Score=23.45 Aligned_cols=20 Identities=15% Similarity=0.360 Sum_probs=15.6
Q ss_pred HhcCCCHHHHHhhcCCCC-CC
Q 040816 93 MIKGKSPEEIRQTFHIQN-DF 112 (128)
Q Consensus 93 ~i~gkt~eeir~~f~i~~-d~ 112 (128)
++.|...+.+++.||++. ++
T Consensus 111 ~i~~~~~~~v~~~l~l~~~~~ 131 (156)
T cd03370 111 PMTGFDEEKVKEALGLPGRDR 131 (156)
T ss_pred cCcCcCHHHHHHHhCcCCcCc
Confidence 345677899999999986 54
No 85
>PF13725 tRNA_bind_2: Possible tRNA binding domain; PDB: 2ZPA_B.
Probab=30.89 E-value=1.4e+02 Score=18.90 Aligned_cols=69 Identities=19% Similarity=0.205 Sum_probs=31.8
Q ss_pred CCCHHHHHHHHHHHHhcccCCCCcccccchhhhhhccChHHHHHHHHHhhhccHHHHHHHHH-HHHHHHhcCCCHHHHHh
Q 040816 26 NVRGTILSMVIEYLKKHVEAKTTEDDLKNWDVDFAKLGQDTLFDLLMAANYLDIKSLLDLLC-QTVADMIKGKSPEEIRQ 104 (128)
Q Consensus 26 ~v~~~~L~~Vi~~c~~h~~~~~~~~~~~~wd~~Fl~~~~~~l~~li~AA~~L~i~~L~~l~~-~~ia~~i~gkt~eeir~ 104 (128)
.++..-++++-.|+..+..+.. + ...+-.++.....-. ..|-.... --|+.-+.+||.+++.+
T Consensus 28 ~ls~~d~~rL~~ya~g~~~y~~----v-----------~~~l~~l~~~~~~~~-~~Ls~~q~~lLi~k~LQ~ksw~~~a~ 91 (101)
T PF13725_consen 28 SLSPIDLQRLERYARGGRDYES----V-----------APALWRLAFQYFLSP-VSLSELQQALLIAKGLQGKSWEEVAK 91 (101)
T ss_dssp ---HHHHHHHHHHHHS---TCC----C-----------HHHHHHHHHH-----------S--HHHHHHHCS---HHHHHH
T ss_pred cCCHHHHHHHHHHHcCCCCHHH----H-----------HHHHHHHHHHccccc-hhhHHHHHHHHHHHHHCCCCHHHHHH
Confidence 5788999999999988776531 1 222333333332211 33333332 23577788999999999
Q ss_pred hcCCCC
Q 040816 105 TFHIQN 110 (128)
Q Consensus 105 ~f~i~~ 110 (128)
.||++.
T Consensus 92 ~l~l~g 97 (101)
T PF13725_consen 92 ELGLPG 97 (101)
T ss_dssp HCT-SS
T ss_pred HcCCCC
Confidence 999873
No 86
>PF10415 FumaraseC_C: Fumarase C C-terminus; InterPro: IPR018951 Fumarase C catalyses the stereo-specific interconversion of fumarate to L-malate as part of the Krebs cycle. The full-length protein forms a tetramer with visible globular shape. FumaraseC_C is the C-terminal 65 residues referred to as domain 3. The core of the molecule consists of a bundle of 20 alpha-helices from the five-helix bundle of domain 2. The projections from the core of the tetramer are generated from domains 1 and 3 of each subunit []. This entry does not appear to be part of either the active site or the activation site but is helical in structure forming a little bundle. ; GO: 0016829 lyase activity, 0006099 tricarboxylic acid cycle; PDB: 3RRP_A 3OCE_D 3OCF_D 3E04_B 3GTD_A 3R6V_F 3R6Q_F 1J3U_B 1FUR_A 1YFE_A ....
Probab=29.95 E-value=1.2e+02 Score=17.66 Aligned_cols=32 Identities=25% Similarity=0.319 Sum_probs=18.8
Q ss_pred HHHHHHH--hcCCCHHHHHhhcCCCCCCCHHHHHHHh
Q 040816 87 CQTVADM--IKGKSPEEIRQTFHIQNDFTPEEEEEIR 121 (128)
Q Consensus 87 ~~~ia~~--i~gkt~eeir~~f~i~~d~t~eee~~i~ 121 (128)
+..||.. -.|+|+.|+-.-.|+ +|++|.+++.
T Consensus 14 aa~iAk~A~~~g~svre~v~~~g~---lt~ee~d~ll 47 (55)
T PF10415_consen 14 AAEIAKEALAEGRSVREVVLEEGL---LTEEELDELL 47 (55)
T ss_dssp HHHHHHHHHHHT--HHHHHHHTTS---S-HHHHHHHT
T ss_pred HHHHHHHHHHcCCCHHHHHHHcCC---CCHHHHHHHc
Confidence 3444443 358999999887774 5777777653
No 87
>PF15063 TC1: Thyroid cancer protein 1
Probab=29.94 E-value=52 Score=20.90 Aligned_cols=32 Identities=19% Similarity=0.372 Sum_probs=16.6
Q ss_pred HHHHHhcCCCHHHHHhhcCCCCCCCHHHHHHH
Q 040816 89 TVADMIKGKSPEEIRQTFHIQNDFTPEEEEEI 120 (128)
Q Consensus 89 ~ia~~i~gkt~eeir~~f~i~~d~t~eee~~i 120 (128)
..|+...+-+-.+++++|.-..|--.||-.++
T Consensus 29 asaNIFe~vn~~qlqrLF~~sGD~kAEeRA~i 60 (79)
T PF15063_consen 29 ASANIFENVNLDQLQRLFQKSGDKKAEERARI 60 (79)
T ss_pred hhhhhhhccCHHHHHHHHHHccchhHHHHHHH
Confidence 34555555555555555555555544444443
No 88
>PRK07394 hypothetical protein; Provisional
Probab=29.87 E-value=74 Score=25.59 Aligned_cols=33 Identities=24% Similarity=0.142 Sum_probs=28.8
Q ss_pred CCCHHHHHhhcCCCCCC-CHHHHHHHhhhCCCCC
Q 040816 96 GKSPEEIRQTFHIQNDF-TPEEEEEIRTETPRAF 128 (128)
Q Consensus 96 gkt~eeir~~f~i~~d~-t~eee~~i~~e~~W~f 128 (128)
|-|..++-+.+||+-+. |+++-.+..++..|+|
T Consensus 128 GvtsaDvLe~LGv~~~~~~~~~~~~~l~~~g~~F 161 (342)
T PRK07394 128 GVPLVELWQGLGVDLTGLSLEQVQEGFEQTGLAF 161 (342)
T ss_pred CchHHHHHHHCCCCCCCCCHHHHHHHHHHcCcee
Confidence 44579999999999997 9999999888888876
No 89
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=29.82 E-value=1.2e+02 Score=23.22 Aligned_cols=27 Identities=22% Similarity=0.118 Sum_probs=21.9
Q ss_pred CCCceecC-CCCHHHHHHHHHHHHhcccC
Q 040816 18 ADSVIPLL-NVRGTILSMVIEYLKKHVEA 45 (128)
Q Consensus 18 ~~~~Ipl~-~v~~~~L~~Vi~~c~~h~~~ 45 (128)
...+.+|| ++++.||.+|.+|.+ +.+.
T Consensus 145 ~~~~~~LPkGi~~~Tl~~i~~~~~-~~~~ 172 (224)
T COG4565 145 EQPPDDLPKGLDELTLQKVREALK-EPDQ 172 (224)
T ss_pred ccCcccCCCCcCHHHHHHHHHHHh-CcCC
Confidence 35677788 799999999999999 4543
No 90
>PF14098 SSPI: Small, acid-soluble spore protein I
Probab=29.57 E-value=61 Score=19.90 Aligned_cols=20 Identities=35% Similarity=0.599 Sum_probs=15.8
Q ss_pred HHHHHHhcCCCHHHHHhhcC
Q 040816 88 QTVADMIKGKSPEEIRQTFH 107 (128)
Q Consensus 88 ~~ia~~i~gkt~eeir~~f~ 107 (128)
+.|-..++|+|.+|++.+-.
T Consensus 5 ~AI~~nv~g~s~~el~~~I~ 24 (65)
T PF14098_consen 5 QAIIHNVKGSSKEELKDTIE 24 (65)
T ss_pred HHHHHHccCCCHHHHHHHHH
Confidence 45667789999999998753
No 91
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=29.44 E-value=63 Score=18.45 Aligned_cols=23 Identities=22% Similarity=0.320 Sum_probs=17.1
Q ss_pred HHHHHHHhcCCCHHHHHhhcCCC
Q 040816 87 CQTVADMIKGKSPEEIRQTFHIQ 109 (128)
Q Consensus 87 ~~~ia~~i~gkt~eeir~~f~i~ 109 (128)
...+.-+..|+|+.||-+.+||+
T Consensus 9 ~~vl~~l~~G~~~~eIA~~l~is 31 (58)
T PF00196_consen 9 LEVLRLLAQGMSNKEIAEELGIS 31 (58)
T ss_dssp HHHHHHHHTTS-HHHHHHHHTSH
T ss_pred HHHHHHHHhcCCcchhHHhcCcc
Confidence 34566677899999999888875
No 92
>PRK10144 formate-dependent nitrite reductase complex subunit NrfF; Provisional
Probab=29.09 E-value=53 Score=22.81 Aligned_cols=19 Identities=37% Similarity=0.384 Sum_probs=14.0
Q ss_pred HHHHHHhc-CCCHHHHHhhc
Q 040816 88 QTVADMIK-GKSPEEIRQTF 106 (128)
Q Consensus 88 ~~ia~~i~-gkt~eeir~~f 106 (128)
..|..++. |+|.+||+.+|
T Consensus 64 ~~Vr~~i~~G~sd~eI~~~~ 83 (126)
T PRK10144 64 HQVYSMVAEGKSEVEIIGWM 83 (126)
T ss_pred HHHHHHHHcCCCHHHHHHHH
Confidence 34555555 99999998876
No 93
>TIGR01994 SUF_scaf_2 SUF system FeS assembly protein, NifU family. Three iron-sulfur cluster assembly systems are known so far. ISC is broadly distributed while NIF tends to be associated with nitrogenase in nitrogen-fixing bacteria. The most recently described is SUF, believed to be important to maintain the function during aerobic stress of enzymes with labile Fe-S clusters. It is fairly widely distributed. This family represents one of two different proteins proposed to act as a scaffold on which the Fe-S cluster is built and from which it is transferred.
Probab=28.93 E-value=97 Score=21.36 Aligned_cols=37 Identities=16% Similarity=0.220 Sum_probs=23.2
Q ss_pred HHHhhhccHHHHHHHHH-HHHHHHhcCCCHHHHHhhcC
Q 040816 71 LMAANYLDIKSLLDLLC-QTVADMIKGKSPEEIRQTFH 107 (128)
Q Consensus 71 i~AA~~L~i~~L~~l~~-~~ia~~i~gkt~eeir~~f~ 107 (128)
+..+.|-.-=--+-.+| ..++.++.|||.+|+.....
T Consensus 51 I~d~~f~~~GCais~Asas~~~e~i~Gk~~~ea~~l~~ 88 (137)
T TIGR01994 51 IEDIAFEGEGCSISQASASMMTELIKGKTVEEALSLVE 88 (137)
T ss_pred EEEEEEEecccHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 34444444333344444 55688999999999977763
No 94
>PRK11548 outer membrane biogenesis protein BamE; Provisional
Probab=28.74 E-value=64 Score=21.52 Aligned_cols=23 Identities=17% Similarity=0.239 Sum_probs=18.8
Q ss_pred HHHHHHhcCCCHHHHHhhcCCCC
Q 040816 88 QTVADMIKGKSPEEIRQTFHIQN 110 (128)
Q Consensus 88 ~~ia~~i~gkt~eeir~~f~i~~ 110 (128)
..++..-.|+|.+|++..||-|.
T Consensus 41 ~~l~~l~~GmTk~qV~~lLGtP~ 63 (113)
T PRK11548 41 NDVAKIHVGMTQQQVAYTLGTPM 63 (113)
T ss_pred HHHHHhcCCCCHHHHHHHcCCCc
Confidence 34566667999999999999874
No 95
>COG1460 Uncharacterized protein conserved in archaea [Function unknown]
Probab=28.70 E-value=1.9e+02 Score=19.70 Aligned_cols=61 Identities=25% Similarity=0.427 Sum_probs=37.4
Q ss_pred hhhccChHHHHHHHHHhhhccHHHHHHHHHHHHHHHhcCCCHHHHHhhcCCCCC-CCHHHHHHHh
Q 040816 58 DFAKLGQDTLFDLLMAANYLDIKSLLDLLCQTVADMIKGKSPEEIRQTFHIQND-FTPEEEEEIR 121 (128)
Q Consensus 58 ~Fl~~~~~~l~~li~AA~~L~i~~L~~l~~~~ia~~i~gkt~eeir~~f~i~~d-~t~eee~~i~ 121 (128)
.|-.+|++..-++..= .++|..+-+-...+||+. .=.|+.|+|..|--..- .|+|+..+|.
T Consensus 44 kFakldpe~a~e~veE--L~~i~~~~e~~avkIadI-~P~t~~ElRsIla~e~~~~s~E~l~~Il 105 (114)
T COG1460 44 KFAKLDPEKARELVEE--LLSIVKMSEKIAVKIADI-MPRTPDELRSILAKERVMLSDEELDKIL 105 (114)
T ss_pred HHhcCCHHHHHHHHHH--HHhhccccHHHHHHHHHh-CCCCHHHHHHHHHHccCCCCHHHHHHHH
Confidence 5666777666555442 233333444555555553 45799999999986654 5677776653
No 96
>PF05871 ESCRT-II: ESCRT-II complex subunit; InterPro: IPR008570 This entry represents the vps25 subunit (vacuolar protein sorting-associated protein 25) of the endosome-associated complex ESCRT-II (Endosomal Sorting Complexes Required for Transport protein II). ESCRT (ESCRT-I, -II, -III) complexes orchestrate efficient sorting of ubiquitinated transmembrane receptors to lysosomes via multivesicular bodies (MVBs) []. ESCRT-II recruits the transport machinery for protein sorting at MVB []. In addition, the human ESCRT-II has been shown to form a complex with RNA polymerase II elongation factor ELL in order to exert transcriptional control activity. ESCRT-II transiently associates with the endosomal membrane and thereby initiates the formation of ESCRT-III, a membrane-associated protein complex that functions immediately downstream of ESCRT-II during sorting of MVB cargo. ESCRT-II in turn functions downstream of ESCRT-I, a protein complex that binds to ubiquitinated endosomal cargo []. ESCRT-II is a trilobal complex composed of two copies of vps25, one copy of vps22 and the C-terminal region of vps36. The crystal structure of vps25 revealed two winged-helix domains, the N-terminal domain of vps25 interacting with vps22 and vps35 [].; PDB: 1W7P_B 1U5T_D 1XB4_D 3HTU_E 3CUQ_C 2ZME_D.
Probab=28.67 E-value=38 Score=23.78 Aligned_cols=12 Identities=17% Similarity=0.564 Sum_probs=9.7
Q ss_pred HHHHHHHhcccC
Q 040816 34 MVIEYLKKHVEA 45 (128)
Q Consensus 34 ~Vi~~c~~h~~~ 45 (128)
.|+.||+||+-.
T Consensus 28 lIl~y~~~~k~~ 39 (139)
T PF05871_consen 28 LILDYCRHHKIF 39 (139)
T ss_dssp HHHHHHHHTT-S
T ss_pred HHHHHHHHhcee
Confidence 599999999876
No 97
>PRK09071 hypothetical protein; Validated
Probab=28.62 E-value=70 Score=25.54 Aligned_cols=31 Identities=19% Similarity=0.174 Sum_probs=27.3
Q ss_pred CHHHHHhhcCCCCCCCHHHHHHHhhhCCCCC
Q 040816 98 SPEEIRQTFHIQNDFTPEEEEEIRTETPRAF 128 (128)
Q Consensus 98 t~eeir~~f~i~~d~t~eee~~i~~e~~W~f 128 (128)
+..++-+.+||+-+.++++-.+..++.-|+|
T Consensus 123 ~saDvLeaLGv~~~~~~~~~~~~l~~~g~~f 153 (323)
T PRK09071 123 YTEQLLEALGIPIARSWQEAEQALEEHNIAY 153 (323)
T ss_pred cHHHHHHHCCCCCCCCHHHHHHHHHhcCeEE
Confidence 3899999999999999999988888887775
No 98
>PF04751 DUF615: Protein of unknown function (DUF615); InterPro: IPR006839 The proteins in this entry are functionally uncharacterised. The entry contains the Escherichia coli (strain K12) protein YjgA (P0A8X0 from SWISSPROT), which has been shown to comigrate with the mature 50S ribosome subunit. Therefore it either represents a novel ribosome-associated protein or it is associated with a different oligomeric complex that comigrates with ribosomal particles [].; PDB: 2P0T_A.
Probab=28.56 E-value=1.7e+02 Score=20.93 Aligned_cols=57 Identities=19% Similarity=0.296 Sum_probs=42.2
Q ss_pred cccchhhhhhccChHHHHHHHHHhhhccHHHHHHHHHHHHHHHhcCCCHHHHHhhcC
Q 040816 51 DLKNWDVDFAKLGQDTLFDLLMAANYLDIKSLLDLLCQTVADMIKGKSPEEIRQTFH 107 (128)
Q Consensus 51 ~~~~wd~~Fl~~~~~~l~~li~AA~~L~i~~L~~l~~~~ia~~i~gkt~eeir~~f~ 107 (128)
.+..|-...+.-+...+-+++..-.-.|...|-.++-..-...-.+|+|.--|+.|.
T Consensus 97 ~lE~wRdrLi~~~~~al~e~~~~~p~~D~Q~LRqLiR~a~ke~~~~k~~ka~R~Lfr 153 (157)
T PF04751_consen 97 RLERWRDRLIADDDSALTEFLAEYPDADRQQLRQLIRNARKEREANKPPKAYRELFR 153 (157)
T ss_dssp HHHHHHHHHHHS-HHHHHHHHHHSTTS-HHHHHHHHHHHHHHHHTT---HHHHHHHH
T ss_pred HHHHHHHHHHhCChHHHHHHHHHCChhhHHHHHHHHHHHHHHHHcCCCchhHHHHHH
Confidence 456787778877778888888887778899988888888888888999988888774
No 99
>PRK13696 hypothetical protein; Provisional
Probab=28.41 E-value=1.4e+02 Score=18.09 Aligned_cols=25 Identities=28% Similarity=0.482 Sum_probs=18.4
Q ss_pred CCCHHHHHhhcCCCCCCCHHHHHHHhhh
Q 040816 96 GKSPEEIRQTFHIQNDFTPEEEEEIRTE 123 (128)
Q Consensus 96 gkt~eeir~~f~i~~d~t~eee~~i~~e 123 (128)
..+...+.++||+- ++||-++++++
T Consensus 37 ~~~~~~l~~~~Gil---~dee~~e~~~~ 61 (62)
T PRK13696 37 KGNLDKLMKAFGIL---SEEEAEELKKE 61 (62)
T ss_pred hccHHHHHHHHCCC---CHHHHHHHHhh
Confidence 45688899999985 56676777654
No 100
>COG0822 IscU NifU homolog involved in Fe-S cluster formation [Energy production and conversion]
Probab=28.11 E-value=99 Score=21.89 Aligned_cols=38 Identities=13% Similarity=0.327 Sum_probs=23.5
Q ss_pred HHHHHhhhccHHHHHHHH-HHHHHHHhcCCCHHHHHhhc
Q 040816 69 DLLMAANYLDIKSLLDLL-CQTVADMIKGKSPEEIRQTF 106 (128)
Q Consensus 69 ~li~AA~~L~i~~L~~l~-~~~ia~~i~gkt~eeir~~f 106 (128)
+.+..|.|...=-=.-.+ +..+..++.|||.+|.+++-
T Consensus 52 ~~I~d~~F~~~GC~is~ASss~~te~v~Gkti~EAl~i~ 90 (150)
T COG0822 52 GVIEDAKFKGFGCAISIASSSMMTELVKGKTLDEALKIT 90 (150)
T ss_pred CEEEEEEeeecCcHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 344445555444333333 34557889999999988765
No 101
>PF09010 AsiA: Anti-Sigma Factor A; InterPro: IPR015100 Anti-sigma factor A is a transcriptional inhibitor that inhibits sigma 70-directed transcription by weakening its interaction with the core of the host's RNA polymerase. It is an all-helical protein, composed of six helical segments and intervening loops and turns, as well as a helix-turn-helix DNA binding motif, although neither free anti-sigma factor nor anti-sigma factor bound to sigma-70 has been shown to interact directly with DNA. In solution, the protein forms a symmetric dimer of small (10.59 kDa) protomers, which are composed of helix and coil regions and are devoid of beta-strand/sheet secondary structural elements []. ; PDB: 1TKV_A 1JR5_B 1TLH_A 1TL6_A.
Probab=27.93 E-value=1.1e+02 Score=20.11 Aligned_cols=59 Identities=24% Similarity=0.339 Sum_probs=34.3
Q ss_pred HHHHHHHHHhhhc---------cHHHHHHHHHHHHHHHh-cCC--CHHHHHhhcCCCCCCCHHHHHHHhhhCCC
Q 040816 65 DTLFDLLMAANYL---------DIKSLLDLLCQTVADMI-KGK--SPEEIRQTFHIQNDFTPEEEEEIRTETPR 126 (128)
Q Consensus 65 ~~l~~li~AA~~L---------~i~~L~~l~~~~ia~~i-~gk--t~eeir~~f~i~~d~t~eee~~i~~e~~W 126 (128)
+.+.+++..|+-| +-+.++-.-+..+.-+- .|+ |..-.|++++ ++|++|.+++..++.|
T Consensus 6 E~v~eIia~aSiLIKfg~ddIl~~q~~FIaFLNElG~r~~~G~~~t~~sfr~m~~---~lt~~ek~elieeFn~ 76 (91)
T PF09010_consen 6 EIVKEIIAVASILIKFGRDDILENQELFIAFLNELGFRTPTGKEFTQMSFRQMFK---RLTQEEKEELIEEFNE 76 (91)
T ss_dssp HHHHHHHHHHHHHHHTTTHHHHTSHHHHHHHHHHHT-ES-SSSE--HHHHHHHHH---TS-HHHHHHHHHHSHH
T ss_pred HHHHHHHHHHHHHHHcChHHHHHhHHHHHHHHHHhcccccCCcchhHHHHHHHHH---HcCHHHHHHHHHHHhh
Confidence 4556666666543 33333333344444333 565 5666688876 7899999999888765
No 102
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=27.92 E-value=86 Score=16.82 Aligned_cols=17 Identities=24% Similarity=0.448 Sum_probs=13.4
Q ss_pred HhcCCCHHHHHhhcCCC
Q 040816 93 MIKGKSPEEIRQTFHIQ 109 (128)
Q Consensus 93 ~i~gkt~eeir~~f~i~ 109 (128)
...|+|..||-+.+|++
T Consensus 15 ~~~g~s~~eia~~l~is 31 (58)
T smart00421 15 LAEGLTNKEIAERLGIS 31 (58)
T ss_pred HHcCCCHHHHHHHHCCC
Confidence 34688888888888875
No 103
>cd00412 pyrophosphatase Inorganic pyrophosphatase. These enzymes hydrolyze inorganic pyrophosphate (PPi) to two molecules of orthophosphates (Pi). The reaction requires bivalent cations. The enzymes in general exist as homooligomers.
Probab=27.76 E-value=1.3e+02 Score=21.57 Aligned_cols=46 Identities=9% Similarity=0.291 Sum_probs=32.2
Q ss_pred cCCCCHHHHHHHHHHHHhcccCCC-CcccccchhhhhhccChHHHHHHHHHhh
Q 040816 24 LLNVRGTILSMVIEYLKKHVEAKT-TEDDLKNWDVDFAKLGQDTLFDLLMAAN 75 (128)
Q Consensus 24 l~~v~~~~L~~Vi~~c~~h~~~~~-~~~~~~~wd~~Fl~~~~~~l~~li~AA~ 75 (128)
+.+++...++.|-.|.++++.-.+ ....+..| .+.+...+++..|.
T Consensus 108 l~Dl~~~~l~~I~~fF~~YK~le~~k~~~~~g~------~~~~~A~~~I~~~~ 154 (155)
T cd00412 108 ISDVPPHLLDEIKHFFEHYKDLEGKKEVKVAGW------KDKEEALKIIKESI 154 (155)
T ss_pred hHHCCHHHHHHHHHHHHHhcccCCCCceEECcC------cCHHHHHHHHHHHh
Confidence 344779999999999999987542 22334444 46777777777663
No 104
>cd07921 PCA_45_Doxase_A_like Subunit A of the Class III Extradiol dioxygenase, Protocatechuate 4,5-dioxygenase, and similar enzymes. This subfamily includes the A subunit of protocatechuate (PCA) 4,5-dioxygenase (LigAB) and two subfamilies of unknown function. The A subunit is the smaller, non-catalytic subunit of LigAB. PCA 4,5-dioxygenase catalyzes the oxidization and subsequent ring-opening of PCA (or 3,4-dihydroxybenzoic acid), which is an intermediate in the breakdown of lignin and other compounds. PCA 4,5-dioxygenase is one of the aromatic ring opening dioxygenases which play key roles in the degradation of aromatic compounds. As members of the Class III extradiol dioxygenase family, the enzymes use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. LigAB-like class III enzymes are usually composed of two subunits, designated A and B, which form a tetramer composed of two copies of each subunit.
Probab=27.74 E-value=1.2e+02 Score=20.44 Aligned_cols=22 Identities=23% Similarity=0.362 Sum_probs=18.2
Q ss_pred HHHHHHHhcCCCHHHHHhhcCC
Q 040816 87 CQTVADMIKGKSPEEIRQTFHI 108 (128)
Q Consensus 87 ~~~ia~~i~gkt~eeir~~f~i 108 (128)
-+.|...++|+|.||.+++...
T Consensus 82 ~~~~~a~mtG~t~eef~~~~~~ 103 (106)
T cd07921 82 MQDIGAQMTGMTEEEFRAMMVA 103 (106)
T ss_pred HHHHHHHhcCCCHHHHHHHHHc
Confidence 4788889999999998887653
No 105
>PRK09246 amidophosphoribosyltransferase; Provisional
Probab=27.71 E-value=68 Score=27.17 Aligned_cols=26 Identities=19% Similarity=0.326 Sum_probs=19.7
Q ss_pred CCceecCC--CCHHHHHHHHHHHHhccc
Q 040816 19 DSVIPLLN--VRGTILSMVIEYLKKHVE 44 (128)
Q Consensus 19 ~~~Ipl~~--v~~~~L~~Vi~~c~~h~~ 44 (128)
..++-+.+ ++|.||+.+++.+.....
T Consensus 359 K~VlLVDDvitTGaTl~~~~~~L~~aGA 386 (501)
T PRK09246 359 KNVLLVDDSIVRGTTSEQIVQMAREAGA 386 (501)
T ss_pred CeEEEEeccccccHHHHHHHHHHHHcCC
Confidence 34555555 699999999999987654
No 106
>PLN03212 Transcription repressor MYB5; Provisional
Probab=27.67 E-value=83 Score=24.41 Aligned_cols=35 Identities=14% Similarity=0.236 Sum_probs=26.4
Q ss_pred HHHHHHhc-CCCHHHHHhhcC------CCC-CCCHHHHHHHhh
Q 040816 88 QTVADMIK-GKSPEEIRQTFH------IQN-DFTPEEEEEIRT 122 (128)
Q Consensus 88 ~~ia~~i~-gkt~eeir~~f~------i~~-d~t~eee~~i~~ 122 (128)
..||..+. |+|..+.|+.+. |.. .+|+||.+.|.+
T Consensus 49 ~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgpWT~EED~lLle 91 (249)
T PLN03212 49 RSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGITSDEEDLILR 91 (249)
T ss_pred HHHHHhhhcCCCcchHHHHHHHhhchhcccCCCChHHHHHHHH
Confidence 45777774 899999999874 655 499988886654
No 107
>smart00875 BACK BTB And C-terminal Kelch. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues.
Probab=27.28 E-value=1.5e+02 Score=17.97 Aligned_cols=39 Identities=13% Similarity=0.106 Sum_probs=28.0
Q ss_pred HHHHHhhhccHHHHHHHHHHHHHHH---------hcCCCHHHHHhhcC
Q 040816 69 DLLMAANYLDIKSLLDLLCQTVADM---------IKGKSPEEIRQTFH 107 (128)
Q Consensus 69 ~li~AA~~L~i~~L~~l~~~~ia~~---------i~gkt~eeir~~f~ 107 (128)
++...|...+.+.|.+.|-++++.. ....+.++++.+++
T Consensus 3 ~i~~~a~~~~~~~L~~~~~~~i~~nf~~~~~~~~f~~L~~~~l~~iL~ 50 (101)
T smart00875 3 GIRRFAELYGLEELLEKALRFILKNFLEVAQSEEFLELSLEQLLSLLS 50 (101)
T ss_pred hHHHHHHHhChHHHHHHHHHHHHHHHHHHhcCcHHhcCCHHHHHHHhC
Confidence 4566777778888888888887663 33456777777776
No 108
>PRK14981 DNA-directed RNA polymerase subunit F; Provisional
Probab=27.19 E-value=1.8e+02 Score=19.42 Aligned_cols=42 Identities=24% Similarity=0.429 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHHHhcCCCHHHHHhhcCCCC-CCCHHHHHHHhh
Q 040816 80 KSLLDLLCQTVADMIKGKSPEEIRQTFHIQN-DFTPEEEEEIRT 122 (128)
Q Consensus 80 ~~L~~l~~~~ia~~i~gkt~eeir~~f~i~~-d~t~eee~~i~~ 122 (128)
..|-+-....||+. .=.|++|+|..|.-.. -+++|+.++|..
T Consensus 63 ~~l~e~~a~~I~nL-~P~~~dElrai~~~~~~~~~~e~l~~ILd 105 (112)
T PRK14981 63 EKMKEKTAVKIADI-LPETRDELRAIFAKERYTLSPEELDEILD 105 (112)
T ss_pred cCCCHHHHHHHHhc-CCCCHHHHHHHHHHhccCCCHHHHHHHHH
Confidence 33444444555553 3479999999997653 388888888754
No 109
>PF00134 Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR006671 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. Cyclins contain two domains of similar all-alpha fold, of which this entry is associated with the N-terminal domain.; PDB: 2W2H_B 3RGF_B 1KXU_A 1JKW_A 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D ....
Probab=27.03 E-value=96 Score=20.09 Aligned_cols=42 Identities=24% Similarity=0.454 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHHHhcCCCHHHHHhhcCCCC-CCCHHHHHHHhh
Q 040816 81 SLLDLLCQTVADMIKGKSPEEIRQTFHIQN-DFTPEEEEEIRT 122 (128)
Q Consensus 81 ~L~~l~~~~ia~~i~gkt~eeir~~f~i~~-d~t~eee~~i~~ 122 (128)
.|+-++|-.+|.++.+..+--+.....+.+ .+|.++..+.+.
T Consensus 74 ~li~~~cl~lA~K~~e~~~~~~~~~~~~~~~~~~~~~i~~~E~ 116 (127)
T PF00134_consen 74 QLIALACLFLASKMEEDNPPSISDLIRISDNTFTKKDILEMER 116 (127)
T ss_dssp HHHHHHHHHHHHHHHTSS--HHHHHHHHTTTSSHHHHHHHHHH
T ss_pred hhhhhhHHHHhhhhhccccchHHHHHHHHcCCCCHHHHHHHHH
Confidence 577788889999998775555666555544 477776655543
No 110
>cd07925 LigA_like_1 The A subunit of Uncharacterized proteins with similarity to Protocatechuate 4,5-dioxygenase (LigAB). The proteins of unknown function in this subfamily are similar to the A subunit of the Protocatechuate (PCA) 4,5-dioxygenase (LigAB). LigAB belongs to the class III extradiol dioxygenase family, composed of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Dioxygenases play key roles in the degradation of aromatic compounds. PCA 4,5-dioxygenase catalyzes the oxidization and subsequent ring-opening of PCA (or 3,4-dihydroxybenzoic acid), which is an intermediate in the breakdown of lignin and other compounds.
Probab=26.98 E-value=1.2e+02 Score=20.38 Aligned_cols=23 Identities=22% Similarity=0.296 Sum_probs=18.7
Q ss_pred HHHHHHHHhcCCCHHHHHhhcCC
Q 040816 86 LCQTVADMIKGKSPEEIRQTFHI 108 (128)
Q Consensus 86 ~~~~ia~~i~gkt~eeir~~f~i 108 (128)
.-+.|...++|+|.||.+++..-
T Consensus 81 s~q~i~a~mtG~t~eef~~~~~~ 103 (106)
T cd07925 81 NMQDIGGLQTGMSTEEFKAMLVA 103 (106)
T ss_pred cHHHHHHHhcCCCHHHHHHHHHh
Confidence 34788899999999999887653
No 111
>TIGR02792 PCA_ligA protocatechuate 4,5-dioxygenase, alpha subunit. Protocatechuate (PCA) 4,5-dioxygenase is the first enzyme in the PCA 4,5-cleavage pathway that is an alternative to PCA 3,4-cleavage and PCA 2,3 cleavage pathways. PCA is an intermediate in the breakdown of lignin (hence the gene symbol ligA) and other compounds. Members of this family are the alpha chain of PCA 4,5-dioxygenase, or the equivalent domain of a fusion protein.
Probab=25.84 E-value=1.3e+02 Score=20.70 Aligned_cols=21 Identities=33% Similarity=0.417 Sum_probs=17.2
Q ss_pred HHHHHHHHhcCCCHHHHHhhc
Q 040816 86 LCQTVADMIKGKSPEEIRQTF 106 (128)
Q Consensus 86 ~~~~ia~~i~gkt~eeir~~f 106 (128)
.-+.|+..++|+|.||.++++
T Consensus 86 s~q~i~a~mtG~t~eef~~mm 106 (117)
T TIGR02792 86 SFQQMAGSMTGMTEEEYRQMM 106 (117)
T ss_pred cHHHHHHHhcCCCHHHHHHHH
Confidence 347888899999999988764
No 112
>PF08006 DUF1700: Protein of unknown function (DUF1700); InterPro: IPR012963 This family contains many hypothetical bacterial proteins and two putative membrane proteins (Q6GFD0 from SWISSPROT and Q6G806 from SWISSPROT).
Probab=25.84 E-value=1.9e+02 Score=20.59 Aligned_cols=36 Identities=22% Similarity=0.234 Sum_probs=26.6
Q ss_pred hccHHHHHHHHHHHHHHHh-cCCCHHHHHhhcCCCCC
Q 040816 76 YLDIKSLLDLLCQTVADMI-KGKSPEEIRQTFHIQND 111 (128)
Q Consensus 76 ~L~i~~L~~l~~~~ia~~i-~gkt~eeir~~f~i~~d 111 (128)
.=+.+..++....++.+.. .|+|.||+-+-||=|.+
T Consensus 19 ~~e~~e~l~~Y~e~f~d~~~~G~sEeeii~~LG~P~~ 55 (181)
T PF08006_consen 19 EEEREEILEYYEEYFDDAGEEGKSEEEIIAELGSPKE 55 (181)
T ss_pred HHHHHHHHHHHHHHHHHhhhCCCCHHHHHHHcCCHHH
Confidence 3356666777778887755 48999999999995443
No 113
>smart00224 GGL G protein gamma subunit-like motifs.
Probab=25.73 E-value=78 Score=18.95 Aligned_cols=18 Identities=17% Similarity=0.381 Sum_probs=15.0
Q ss_pred HHHHHHHHHHHHhcccCC
Q 040816 29 GTILSMVIEYLKKHVEAK 46 (128)
Q Consensus 29 ~~~L~~Vi~~c~~h~~~~ 46 (128)
|.....++.||+.|....
T Consensus 23 S~a~~~li~y~e~~~~~D 40 (63)
T smart00224 23 SKAAEELLAYCEQHAEED 40 (63)
T ss_pred HHHHHHHHHHHHcCCCCC
Confidence 778889999999877754
No 114
>PF07707 BACK: BTB And C-terminal Kelch; InterPro: IPR011705 This domain is found associated with (IPR000210 from INTERPRO) and (IPR006652 from INTERPRO). BTB (broad-complex, tramtrack and bric a brac) is a Kelch related domain, also known as the POZ domain []. BTB proteins are divided into subgroups depending on what domain lies at the C terminus. Despite the divergence in sequences, the BTB fold is highly conserved. BTB-Kelch proteins have Kelch repeats that form a beta-propeller that can interact with actin filaments []. BTB and C-terminal Kelch (BACK) together constitute a novel conserved domain, which is thought to have a possible role in substrate orientation in Cullin3-based E3 ligase complexes. Four domains, namely the BTB domain, a kelch domain, a BACK domain, and an intervening region (IVR) make up the aryl hydrocarbon receptor (AHR); a ligand-activated transcription factor []. This entry represents the domain associated with BTB and Kelch.; PDB: 3HVE_A 2EQX_A 3I3N_A 4AP2_A 4APF_A.
Probab=25.70 E-value=1.1e+02 Score=18.89 Aligned_cols=40 Identities=8% Similarity=0.131 Sum_probs=29.1
Q ss_pred HHHHHHhhhccHHHHHHHHHHHHHHHhc---------CCCHHHHHhhcC
Q 040816 68 FDLLMAANYLDIKSLLDLLCQTVADMIK---------GKSPEEIRQTFH 107 (128)
Q Consensus 68 ~~li~AA~~L~i~~L~~l~~~~ia~~i~---------gkt~eeir~~f~ 107 (128)
+++...|...+.+.|.+.|-++|+..+. .-+.+++..+++
T Consensus 2 ~~i~~~A~~~~~~~L~~~~~~~i~~nf~~v~~~~~f~~L~~~~l~~iL~ 50 (103)
T PF07707_consen 2 LSIYRLAEKYGLEELAEACLRFIAKNFNEVSKSDEFLELPFDQLIEILS 50 (103)
T ss_dssp HHHHHHHHHTT-HHHHHHHHHHHHHTHHHHTTSHHHHCS-HHHHHHHHH
T ss_pred hhHHHHHHHcChHHHHHHHHHHHHHHHHHHccchhhhcCCHHHHHHHHh
Confidence 4678899999999999999999986553 235666666665
No 115
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=25.64 E-value=97 Score=16.89 Aligned_cols=17 Identities=29% Similarity=0.440 Sum_probs=11.6
Q ss_pred HhcCCCHHHHHhhcCCC
Q 040816 93 MIKGKSPEEIRQTFHIQ 109 (128)
Q Consensus 93 ~i~gkt~eeir~~f~i~ 109 (128)
.-.|.|+.+|-+.|||.
T Consensus 18 ~~~G~si~~IA~~~gvs 34 (45)
T PF02796_consen 18 YAEGMSIAEIAKQFGVS 34 (45)
T ss_dssp HHTT--HHHHHHHTTS-
T ss_pred HHCCCCHHHHHHHHCcC
Confidence 34589999999999985
No 116
>cd00336 Ribosomal_L22 Ribosomal protein L22/L17e. L22 (L17 in eukaryotes) is a core protein of the large ribosomal subunit. It is the only ribosomal protein that interacts with all six domains of 23S rRNA, and is one of the proteins important for directing the proper folding and stabilizing the conformation of 23S rRNA. L22 is the largest protein contributor to the surface of the polypeptide exit channel, the tunnel through which the polypeptide product passes. L22 is also one of six proteins located at the putative translocon binding site on the exterior surface of the ribosome.
Probab=25.30 E-value=67 Score=20.98 Aligned_cols=22 Identities=27% Similarity=0.422 Sum_probs=17.4
Q ss_pred HHHHHHHhcCCCHHHHHhhcCC
Q 040816 87 CQTVADMIKGKSPEEIRQTFHI 108 (128)
Q Consensus 87 ~~~ia~~i~gkt~eeir~~f~i 108 (128)
+..+++.|+|++.+|-..++..
T Consensus 15 ~~~v~~~Irg~~v~~A~~~L~~ 36 (105)
T cd00336 15 ARLVARLIRGMSVDEALAQLEF 36 (105)
T ss_pred HHHHHHHHcCCcHHHHHHHHHh
Confidence 3568999999999997777664
No 117
>COG4680 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.09 E-value=50 Score=21.83 Aligned_cols=17 Identities=35% Similarity=0.505 Sum_probs=14.1
Q ss_pred CCCHHHHHhhcCCCCCC
Q 040816 96 GKSPEEIRQTFHIQNDF 112 (128)
Q Consensus 96 gkt~eeir~~f~i~~d~ 112 (128)
=++|++|+.+|+..+++
T Consensus 35 w~~P~diK~~f~~d~~~ 51 (98)
T COG4680 35 WKKPEDIKSVFPLDNFK 51 (98)
T ss_pred cCCHHHHHHhcCcccce
Confidence 37999999999976664
No 118
>CHL00034 rpl22 ribosomal protein L22
Probab=24.98 E-value=74 Score=21.59 Aligned_cols=22 Identities=32% Similarity=0.443 Sum_probs=18.3
Q ss_pred HHHHHHHhcCCCHHHHHhhcCC
Q 040816 87 CQTVADMIKGKSPEEIRQTFHI 108 (128)
Q Consensus 87 ~~~ia~~i~gkt~eeir~~f~i 108 (128)
+..||+.|+|+++++-..++..
T Consensus 24 ~r~va~~IRG~~v~~A~~~L~~ 45 (117)
T CHL00034 24 ARRVIDQIRGRSYEEALMILEF 45 (117)
T ss_pred HHHHHHHHcCCcHHHHHHHHHH
Confidence 4678999999999998888774
No 119
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=24.86 E-value=1.1e+02 Score=19.18 Aligned_cols=20 Identities=25% Similarity=0.292 Sum_probs=16.4
Q ss_pred HHHHhcCCCHHHHHhhcCCC
Q 040816 90 VADMIKGKSPEEIRQTFHIQ 109 (128)
Q Consensus 90 ia~~i~gkt~eeir~~f~i~ 109 (128)
+.....|+|..||-+.+|++
T Consensus 26 L~R~~eGlS~kEIAe~LGIS 45 (73)
T TIGR03879 26 LAREEAGKTASEIAEELGRT 45 (73)
T ss_pred HHHHHcCCCHHHHHHHHCcC
Confidence 34556899999999999986
No 120
>PF03131 bZIP_Maf: bZIP Maf transcription factor; InterPro: IPR004826 There are several different types of Maf transcription factors with different roles in the cell. MafG and MafH are small Mafs which lack a putative transactivation domain. They behave as transcriptional repressors when they dimerize among themselves. However they also serve as transcriptional activators by dimerizing with other (usually larger) basic-zipper proteins and recruiting them to specific DNA-binding sites. Maf transcription factors contain a conserved basic region leucine zipper (bZIP) domain, which mediates their dimerization and DNA binding property. Neural retina-specific leucine zipper proteins also belong to this family. Together with the basic region, the Maf extended homology region (EHR), conserved only within the Maf family, defines the DNA binding specific to Mafs. This structure enables Mafs to make a broader area of contact with DNA and to recognise longer DNA sequences. In particular, the two residues at the beginning of helix H2 are positioned to recognise the flanking region []. Small Maf proteins heterodimerize with Fos and may act as competitive repressors of the NF2-E2 transcription factor. In mouse, Maf1 may play an early role in axial patterning. Defects in these proteins are a cause of autosomal dominant retinitis pigmentosa. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2KZ5_A 3A5T_A 1K1V_A 1SKN_P 2WT7_B 2WTY_B.
Probab=24.83 E-value=92 Score=19.93 Aligned_cols=27 Identities=19% Similarity=0.274 Sum_probs=19.0
Q ss_pred HhcCCCHHHHHhhcCCCCCCCHHHHHHHhh
Q 040816 93 MIKGKSPEEIRQTFHIQNDFTPEEEEEIRT 122 (128)
Q Consensus 93 ~i~gkt~eeir~~f~i~~d~t~eee~~i~~ 122 (128)
.|..+|++|+..++ ..+|+++...++.
T Consensus 5 eL~~m~v~efn~~L---~~lt~~q~~~lK~ 31 (92)
T PF03131_consen 5 ELVSMSVREFNRLL---RGLTEEQIAELKQ 31 (92)
T ss_dssp HHHHS-HHHHHHHC---TTS-HHHHHHHHH
T ss_pred HHhhCCHHHHHHHH---HcCCHHHHHHHHH
Confidence 34567889998888 6788888877654
No 121
>PF15628 RRM_DME: RRM in Demeter
Probab=24.80 E-value=61 Score=21.68 Aligned_cols=20 Identities=40% Similarity=0.660 Sum_probs=17.1
Q ss_pred HHHHHHhcCCCHHHHHhhcC
Q 040816 88 QTVADMIKGKSPEEIRQTFH 107 (128)
Q Consensus 88 ~~ia~~i~gkt~eeir~~f~ 107 (128)
-.++...+|+|.+||...|-
T Consensus 57 tsv~SIfrGls~~eIq~cF~ 76 (103)
T PF15628_consen 57 TSVSSIFRGLSREEIQQCFW 76 (103)
T ss_pred CcHHHHhcccCHHHHHHHHh
Confidence 46788899999999998874
No 122
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=24.58 E-value=1.5e+02 Score=17.78 Aligned_cols=33 Identities=12% Similarity=0.212 Sum_probs=20.9
Q ss_pred HHHHHHHHHHHHHhcCCCHHHHHhhcCCCCCCC
Q 040816 81 SLLDLLCQTVADMIKGKSPEEIRQTFHIQNDFT 113 (128)
Q Consensus 81 ~L~~l~~~~ia~~i~gkt~eeir~~f~i~~d~t 113 (128)
..++..+.++...-..=|..||.+.||+.+.-|
T Consensus 10 ~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~t 42 (65)
T PF01726_consen 10 EVLEFIREYIEENGYPPTVREIAEALGLKSTST 42 (65)
T ss_dssp HHHHHHHHHHHHHSS---HHHHHHHHTSSSHHH
T ss_pred HHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHH
Confidence 345666677766433447899999999985443
No 123
>PLN02373 soluble inorganic pyrophosphatase
Probab=24.57 E-value=1.4e+02 Score=22.09 Aligned_cols=46 Identities=7% Similarity=0.136 Sum_probs=31.9
Q ss_pred CCCCHHHHHHHHHHHHhcccCCCCcccccchhhhhhccChHHHHHHHHHhhh
Q 040816 25 LNVRGTILSMVIEYLKKHVEAKTTEDDLKNWDVDFAKLGQDTLFDLLMAANY 76 (128)
Q Consensus 25 ~~v~~~~L~~Vi~~c~~h~~~~~~~~~~~~wd~~Fl~~~~~~l~~li~AA~~ 76 (128)
.++....++.|..|.++++.-......+..| .+.+...+++.+|.-
T Consensus 131 ~Dl~~~~l~~I~~fF~~YK~legK~v~v~g~------~~~~~A~~~I~~~~~ 176 (188)
T PLN02373 131 KELPPHRLAEIRRFFEDYKKNENKEVAVNDF------LPAEAAIEAIQYSMD 176 (188)
T ss_pred HHCCHHHHHHHHHHHHHhcccCCCeEEeCCc------cCHHHHHHHHHHHHH
Confidence 3567899999999999998754222223333 567888888877743
No 124
>cd07923 Gallate_dioxygenase_C The C-terminal domain of Gallate Dioxygenase, which catalyzes the oxidization and subsequent ring-opening of gallate. Gallate Dioxygenase catalyzes the oxidization and subsequent ring-opening of gallate, an intermediate in the degradation of the aromatic compound, syringate. The reaction product of gallate dioxygenase is 4-oxalomesaconate. The amino acid sequence of the N-terminal and C-terminal regions of gallate dioxygenase exhibits homology with the sequence of the PCA 4,5-dioxygenase B (catalytic) and A subunits, respectively. This model represents the C-terminal domain, which is similar to the A subunit of PCA 4,5-dioxygenase (or LigAB). The enzyme is estimated to be a homodimer according to the Escherichia coli enzyme. Since enzymes in this subfamily have fused A and B subunits, the dimer interface may resemble the tetramer interface of classical LigAB enzymes. This enzyme belongs to the class III extradiol dioxygenase family, composed of enzymes whi
Probab=24.51 E-value=1.6e+02 Score=19.38 Aligned_cols=19 Identities=32% Similarity=0.406 Sum_probs=15.3
Q ss_pred HHHHHHHhcCCCHHHHHhh
Q 040816 87 CQTVADMIKGKSPEEIRQT 105 (128)
Q Consensus 87 ~~~ia~~i~gkt~eeir~~ 105 (128)
-+.|...++|+|.||.++.
T Consensus 74 ~~~~~a~m~G~t~eef~~t 92 (94)
T cd07923 74 NLHVYAAMRGESLEEFQKT 92 (94)
T ss_pred HHHHHHHhhCCCHHHHHHh
Confidence 4678888899999998764
No 125
>PRK13378 protocatechuate 4,5-dioxygenase subunit alpha; Provisional
Probab=24.28 E-value=1.5e+02 Score=20.42 Aligned_cols=21 Identities=19% Similarity=0.275 Sum_probs=17.0
Q ss_pred HHHHHHHHhcCCCHHHHHhhc
Q 040816 86 LCQTVADMIKGKSPEEIRQTF 106 (128)
Q Consensus 86 ~~~~ia~~i~gkt~eeir~~f 106 (128)
.-+.|...++|+|.||.++++
T Consensus 92 s~q~i~a~mtG~t~eef~~mm 112 (117)
T PRK13378 92 DMQDIGAQQTGMTKEEFKAKL 112 (117)
T ss_pred cHHHHHHHhcCCCHHHHHHHH
Confidence 347888899999999988764
No 126
>COG0091 RplV Ribosomal protein L22 [Translation, ribosomal structure and biogenesis]
Probab=24.05 E-value=81 Score=21.68 Aligned_cols=21 Identities=33% Similarity=0.493 Sum_probs=17.8
Q ss_pred HHHHHHHhcCCCHHHHHhhcC
Q 040816 87 CQTVADMIKGKSPEEIRQTFH 107 (128)
Q Consensus 87 ~~~ia~~i~gkt~eeir~~f~ 107 (128)
.+.||+.|+|++.++-++++.
T Consensus 25 ~r~Va~~IrG~~v~~A~~~L~ 45 (120)
T COG0091 25 ARLVADLIRGKKVAEALAILE 45 (120)
T ss_pred HHHHHHHHcCCcHHHHHHHHH
Confidence 457899999999999988865
No 127
>PF00690 Cation_ATPase_N: Cation transporter/ATPase, N-terminus; InterPro: IPR004014 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. P-ATPases (sometime known as E1-E2 ATPases) (3.6.3.- from EC) are found in bacteria and in a number of eukaryotic plasma membranes and organelles []. P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, each of which transports a specific type of ion: H+, Na+, K+, Mg2+, Ca2+, Ag+ and Ag2+, Zn2+, Co2+, Pb2+, Ni2+, Cd2+, Cu+ and Cu2+. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2. This entry represents the conserved N-terminal region found in several classes of cation-transporting P-type ATPases, including those that transport H+ (3.6.3.6 from EC), Na+ (3.6.3.7 from EC), Ca2+ (3.6.3.8 from EC), Na+/K+ (3.6.3.9 from EC), and H+/K+ (3.6.3.10 from EC). In the H+/K+- and Na+/K+-exchange P-ATPases, this domain is found in the catalytic alpha chain. In gastric H+/K+-ATPases, this domain undergoes reversible sequential phosphorylation inducing conformational changes that may be important for regulating the function of these ATPases [, ]. More information about this protein can be found at Protein of the Month: ATP Synthases [].; PDB: 3KDP_C 3N2F_A 3B8E_A 3N23_A 2XZB_A 1MHS_B 3A3Y_A 2ZXE_A 3B8C_A 3B9B_A ....
Probab=23.92 E-value=88 Score=18.50 Aligned_cols=28 Identities=29% Similarity=0.351 Sum_probs=17.8
Q ss_pred CCHHHHHhhcCCC--CCCCHHHHHHHhhhC
Q 040816 97 KSPEEIRQTFHIQ--NDFTPEEEEEIRTET 124 (128)
Q Consensus 97 kt~eeir~~f~i~--~d~t~eee~~i~~e~ 124 (128)
++++++.+.|+.. +-+|++|-++.++++
T Consensus 4 ~~~~~v~~~l~t~~~~GLs~~ev~~r~~~~ 33 (69)
T PF00690_consen 4 LSVEEVLKRLNTSSSQGLSSEEVEERRKKY 33 (69)
T ss_dssp SSHHHHHHHHTTBTSSBBTHHHHHHHHHHH
T ss_pred CCHHHHHHHHCcCCCCCCCHHHHHHHHHhc
Confidence 5778888888632 237777666655543
No 128
>PRK07631 amidophosphoribosyltransferase; Provisional
Probab=23.91 E-value=1.4e+02 Score=25.22 Aligned_cols=26 Identities=23% Similarity=0.344 Sum_probs=18.7
Q ss_pred CCceecCC--CCHHHHHHHHHHHHhccc
Q 040816 19 DSVIPLLN--VRGTILSMVIEYLKKHVE 44 (128)
Q Consensus 19 ~~~Ipl~~--v~~~~L~~Vi~~c~~h~~ 44 (128)
..++-+.+ ++|.||+.+++=+.....
T Consensus 349 k~VlLVDDsittGtTl~~~~~~L~~aGA 376 (475)
T PRK07631 349 KRVVMVDDSIVRGTTSRRIVTMLREAGA 376 (475)
T ss_pred ceEEEEeeeeccHHHHHHHHHHHHHcCC
Confidence 34455555 699999999998876443
No 129
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=23.90 E-value=53 Score=18.29 Aligned_cols=18 Identities=28% Similarity=0.357 Sum_probs=11.5
Q ss_pred HHhcCCCHHHHHhhcCCC
Q 040816 92 DMIKGKSPEEIRQTFHIQ 109 (128)
Q Consensus 92 ~~i~gkt~eeir~~f~i~ 109 (128)
..+.|+|.+||-+.+|++
T Consensus 22 ~~~~g~s~~eIa~~l~~s 39 (54)
T PF08281_consen 22 RYFQGMSYAEIAEILGIS 39 (54)
T ss_dssp HHTS---HHHHHHHCTS-
T ss_pred HHHHCcCHHHHHHHHCcC
Confidence 356789999999999985
No 130
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=23.84 E-value=1.9e+02 Score=20.58 Aligned_cols=47 Identities=26% Similarity=0.205 Sum_probs=34.2
Q ss_pred cChHHHHHHHHHhhhccHHHHHHHHHHHHHH-HhcCCCHHHHHhhcCCCC
Q 040816 62 LGQDTLFDLLMAANYLDIKSLLDLLCQTVAD-MIKGKSPEEIRQTFHIQN 110 (128)
Q Consensus 62 ~~~~~l~~li~AA~~L~i~~L~~l~~~~ia~-~i~gkt~eeir~~f~i~~ 110 (128)
-+...+.++-.|.+-|.- |-.-.++.|.- .+.|.|.+||-+.+||+.
T Consensus 118 ~~~~~~~~l~e~l~~L~~--l~~~~~~~v~l~~~~Gls~~EIA~~lgiS~ 165 (185)
T PF07638_consen 118 PSPEELLELEEALERLLA--LDPRQRRVVELRFFEGLSVEEIAERLGISE 165 (185)
T ss_pred CCHHHHHHHHHHHHHHHc--cCHHHHHHHHHHHHCCCCHHHHHHHHCcCH
Confidence 455677777776665433 66666777755 568999999999999974
No 131
>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length. Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.
Probab=23.77 E-value=2.2e+02 Score=24.42 Aligned_cols=77 Identities=12% Similarity=0.151 Sum_probs=52.3
Q ss_pred HHHHHHHHHHHhcccCCCCcccccchhhhhhccChHHHHHHHHHhhhccHHHHHHHHHHH----HHHHhcCCCHHHHHhh
Q 040816 30 TILSMVIEYLKKHVEAKTTEDDLKNWDVDFAKLGQDTLFDLLMAANYLDIKSLLDLLCQT----VADMIKGKSPEEIRQT 105 (128)
Q Consensus 30 ~~L~~Vi~~c~~h~~~~~~~~~~~~wd~~Fl~~~~~~l~~li~AA~~L~i~~L~~l~~~~----ia~~i~gkt~eeir~~ 105 (128)
.-+..+-.| ++|+.+|...-.+..-+.+|++ +.+.+..+.+|=-++.|.+|-+-.... +...++.-.+++..++
T Consensus 243 ~~mq~l~~W-e~~yv~p~~~LVi~~L~~~f~~-~~e~~~~~ce~ia~~~i~~Lke~li~~F~~~Ls~~Vk~~~T~~a~q~ 320 (549)
T PF07079_consen 243 PLMQILENW-ENFYVHPNYDLVIEPLKQQFMS-DPEQVGHFCEAIASSKIEKLKEELIDRFGNLLSFKVKQVQTEEAKQY 320 (549)
T ss_pred HHHHHHHHH-HhhccCCchhHHHHHHHHHHhc-ChHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHH
Confidence 345556667 8888777556667888889998 888888888888888898887655443 3444443345555555
Q ss_pred cCC
Q 040816 106 FHI 108 (128)
Q Consensus 106 f~i 108 (128)
+++
T Consensus 321 l~l 323 (549)
T PF07079_consen 321 LAL 323 (549)
T ss_pred HHH
Confidence 543
No 132
>PF09384 UTP15_C: UTP15 C terminal; InterPro: IPR018983 This entry represents the C-terminal domain of the U3 small nucleolar RNA-associated protein 15 (UTP15). This protein is involved in nucleolar processing of pre-18S ribosomal RNA, and is required for optimal pre-ribosomal RNA transcription by RNA polymerase I together with a subset of U3 proteins required for transcription (t-UTPs). UTP15 is a component of the ribosomal small subunit (SSU) processome, which is a large ribonucleoprotein (RNP) required for processing of precursors to the small subunit RNA, the 18S, of the ribosome [, ]. This domain is found C-terminal to the WD40 repeat (IPR001680 from INTERPRO). UTP15 associates with U3 snoRNA, which is ubiquitous in eukaryotes and is required for nucleolar processing of pre-18S ribosomal RNA []. ; GO: 0006364 rRNA processing, 0005730 nucleolus
Probab=23.73 E-value=1.1e+02 Score=21.32 Aligned_cols=23 Identities=17% Similarity=0.300 Sum_probs=20.3
Q ss_pred cCCCCHHHHHHHHHHHHhcccCC
Q 040816 24 LLNVRGTILSMVIEYLKKHVEAK 46 (128)
Q Consensus 24 l~~v~~~~L~~Vi~~c~~h~~~~ 46 (128)
|-+-+...|..|+.|+.+|-.+|
T Consensus 68 L~~Rde~~L~piL~Fl~k~i~~p 90 (148)
T PF09384_consen 68 LAGRDEESLEPILKFLIKNITDP 90 (148)
T ss_pred HHhCCHHHHHHHHHHHHHhCCCc
Confidence 66789999999999999998875
No 133
>PRK08136 glycosyl transferase family protein; Provisional
Probab=23.71 E-value=89 Score=24.91 Aligned_cols=31 Identities=19% Similarity=0.295 Sum_probs=28.0
Q ss_pred CHHHHHhhcCCCCCCCHHHHHHHhhhCCCCC
Q 040816 98 SPEEIRQTFHIQNDFTPEEEEEIRTETPRAF 128 (128)
Q Consensus 98 t~eeir~~f~i~~d~t~eee~~i~~e~~W~f 128 (128)
...++-+.+||+-+.++++-++..++.-|+|
T Consensus 125 gsadvleaLGi~~~~~~~~~~~~l~~~g~~f 155 (317)
T PRK08136 125 TSAEIFEALGIPPTLHADQAQAKLAEGQPAF 155 (317)
T ss_pred cHHHHHHHcCCCCCCCHHHHHHHHHhcCeEE
Confidence 5799999999999999999999998888876
No 134
>cd02138 Nitroreductase_2 Nitroreductase-like family 2. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and nitroimidazoles. This process requires NAD(P)H as electron donor in an obligatory two-electron transfer and uses FMN as cofactor. The enzyme is typically a homodimer. Members of this family are also called NADH dehydrogenase, oxygen-insensitive NAD(P)H nitrogenase or dihydropteridine reductase.
Probab=23.57 E-value=73 Score=22.55 Aligned_cols=38 Identities=16% Similarity=0.344 Sum_probs=26.0
Q ss_pred HHHHHHHHhhhccHHHHHHHHHHHHHHHhcCCCHHHHHhhcCCCCCCC
Q 040816 66 TLFDLLMAANYLDIKSLLDLLCQTVADMIKGKSPEEIRQTFHIQNDFT 113 (128)
Q Consensus 66 ~l~~li~AA~~L~i~~L~~l~~~~ia~~i~gkt~eeir~~f~i~~d~t 113 (128)
.+-.++.||.-|++-.. .+.|...+++++.||++++..
T Consensus 107 a~~nl~Laa~~lGlgt~----------~~~~~~~~~l~~~l~l~~~~~ 144 (181)
T cd02138 107 AWGNLALQATAMGLAAH----------QMGGFDADKAREELNIPEDYE 144 (181)
T ss_pred HHHHHHHHHHHcCcccc----------eecCcCHHHHHHHhCCCCCce
Confidence 34467777777776542 233567789999999998643
No 135
>TIGR01038 L22_arch ribosomal protein L22(archaeal)/L17(eukaryotic/archaeal). This model describes the ribosomal protein of the eukaryotic cytosol and of the Archaea, variously designated as L17, L22, and L23. The corresponding bacterial homolog, described by a separate model, is designated L22.
Probab=23.56 E-value=81 Score=22.48 Aligned_cols=21 Identities=19% Similarity=0.365 Sum_probs=17.6
Q ss_pred HHHHHHHhcCCCHHHHHhhcC
Q 040816 87 CQTVADMIKGKSPEEIRQTFH 107 (128)
Q Consensus 87 ~~~ia~~i~gkt~eeir~~f~ 107 (128)
+..+|+.|+|++.++-..+|.
T Consensus 26 ~r~va~~IrG~~v~~A~~~L~ 46 (150)
T TIGR01038 26 ARETARAIRGMELDKARKYLE 46 (150)
T ss_pred HHHHHHHHcCCcHHHHHHHHH
Confidence 467899999999999888775
No 136
>PRK10945 gene expression modulator; Provisional
Probab=23.29 E-value=2e+02 Score=18.01 Aligned_cols=26 Identities=27% Similarity=0.278 Sum_probs=16.8
Q ss_pred cChHHHHHHHHHhhhccHHHHHHHHHHHHH
Q 040816 62 LGQDTLFDLLMAANYLDIKSLLDLLCQTVA 91 (128)
Q Consensus 62 ~~~~~l~~li~AA~~L~i~~L~~l~~~~ia 91 (128)
++.+++..+..||++ ++.++++.++-
T Consensus 35 L~~~E~~~f~~AaDH----R~AEL~~~KLy 60 (72)
T PRK10945 35 LSDDELAVFYSAADH----RLAELTMNKLY 60 (72)
T ss_pred CCHHHHHHHHHHHHH----HHHHHHhchhH
Confidence 556778888888886 45555554443
No 137
>PRK04223 rpl22p 50S ribosomal protein L22P; Reviewed
Probab=23.01 E-value=84 Score=22.46 Aligned_cols=21 Identities=19% Similarity=0.317 Sum_probs=17.6
Q ss_pred HHHHHHHhcCCCHHHHHhhcC
Q 040816 87 CQTVADMIKGKSPEEIRQTFH 107 (128)
Q Consensus 87 ~~~ia~~i~gkt~eeir~~f~ 107 (128)
+..+|+.|+|++.++-.+++.
T Consensus 30 ~r~va~~IRG~~v~~A~~~L~ 50 (153)
T PRK04223 30 SVEIAREIRGMKLDEAKAYLE 50 (153)
T ss_pred HHHHHHHHcCCcHHHHHHHHH
Confidence 467899999999999888776
No 138
>PF04255 DUF433: Protein of unknown function (DUF433); InterPro: IPR007367 This is a family of uncharacterised proteins.; PDB: 2GA1_B.
Probab=22.94 E-value=1.6e+02 Score=16.88 Aligned_cols=25 Identities=32% Similarity=0.510 Sum_probs=14.4
Q ss_pred HHhcCCCHHHHHhhcCCCCCCCHHHHHH
Q 040816 92 DMIKGKSPEEIRQTFHIQNDFTPEEEEE 119 (128)
Q Consensus 92 ~~i~gkt~eeir~~f~i~~d~t~eee~~ 119 (128)
..-.|.|++||.+-|. ++|+++-..
T Consensus 27 ~~~~G~s~eeI~~~yp---~Lt~~~i~a 51 (56)
T PF04255_consen 27 LLAAGESPEEIAEDYP---SLTLEDIRA 51 (56)
T ss_dssp HHHTT--HHHHHHHST---T--HHHHHH
T ss_pred HHHcCCCHHHHHHHCC---CCCHHHHHH
Confidence 3456899999999886 356665443
No 139
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=22.88 E-value=1.6e+02 Score=18.65 Aligned_cols=30 Identities=17% Similarity=0.475 Sum_probs=20.6
Q ss_pred ccHHHHHHHHHHHHHHHhcCCCHHHHHhhcC
Q 040816 77 LDIKSLLDLLCQTVADMIKGKSPEEIRQTFH 107 (128)
Q Consensus 77 L~i~~L~~l~~~~ia~~i~gkt~eeir~~f~ 107 (128)
+.++.+++.+...++..- +.+++++|+++.
T Consensus 42 ~t~eemie~~~~~~~~~~-~~~~~~a~~~~~ 71 (81)
T PF12674_consen 42 ITMEEMIEFCVPFMDEFN-GMTPEEARKMMP 71 (81)
T ss_pred CCHHHHHHHHHHHHHHhC-CCCHHHHHHHHH
Confidence 345566677777776653 388998888764
No 140
>PRK13377 protocatechuate 4,5-dioxygenase subunit alpha; Provisional
Probab=22.79 E-value=1.6e+02 Score=20.56 Aligned_cols=21 Identities=33% Similarity=0.417 Sum_probs=17.5
Q ss_pred HHHHHHHHhcCCCHHHHHhhc
Q 040816 86 LCQTVADMIKGKSPEEIRQTF 106 (128)
Q Consensus 86 ~~~~ia~~i~gkt~eeir~~f 106 (128)
.-+.|+..++|+|.||.++++
T Consensus 92 s~q~i~a~mtG~t~eef~~mm 112 (129)
T PRK13377 92 SFQQMAGSMTGMTEEEYRQMM 112 (129)
T ss_pred cHHHHHHHhcCCCHHHHHHHH
Confidence 347888999999999988765
No 141
>PF10075 PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro: IPR019280 The photomorphogenic 9 (COP9) signalosome or CSN complex is composed of eight subunits: Cops1/GPS1, Cops2, Cops3, Cops4, Cops5, Cop6, Cops7 (Cops7A or Cops7B) and Cops8. In the complex, Cops8, which is the smallest subunit, probably interacts directly with Cops3, Cops4 and Cops7 (Cops7A or Cops7B). This signalosome is homologous to the lid subcomplex of the 26S proteasome and regulates the ubiquitin-proteasome pathway. It functions as a structural scaffold for subunit-subunit interactions within the complex and is a key regulator of photomorphogenic development [].; PDB: 1RZ4_A.
Probab=22.71 E-value=1.8e+02 Score=19.78 Aligned_cols=45 Identities=16% Similarity=0.248 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHHHHHhc----CCCHHHHHhhcCCCCCCCHHHHHHHhhhCCCC
Q 040816 79 IKSLLDLLCQTVADMIK----GKSPEEIRQTFHIQNDFTPEEEEEIRTETPRA 127 (128)
Q Consensus 79 i~~L~~l~~~~ia~~i~----gkt~eeir~~f~i~~d~t~eee~~i~~e~~W~ 127 (128)
|..|.+..-..++..+. .-+.+.+.+++|++ ++|..++-+...|.
T Consensus 76 v~~~~~~iR~~i~~~i~~aY~sIs~~~la~~Lg~~----~~el~~~~~~~gW~ 124 (143)
T PF10075_consen 76 VPGFEDTIRERIAHLISKAYSSISLSDLAEMLGLS----EEELEKFIKSRGWT 124 (143)
T ss_dssp STTHHHHHHHHHHHHHHHH-SEE-HHHHHHHTTS-----HHHHHHHHHHHT-E
T ss_pred HHHHHHHHHHHHHHHHHHHHhHcCHHHHHHHhCCC----HHHHHHHHHHcCCE
Confidence 45555555555555444 45899999999976 66777776666774
No 142
>PRK14621 hypothetical protein; Provisional
Probab=22.54 E-value=2.5e+02 Score=18.87 Aligned_cols=53 Identities=17% Similarity=0.298 Sum_probs=35.2
Q ss_pred hhhhhhccChHHHHHHHHHhhhccHHHHHHHHHHHHHHHhcCCC-HHHHHhhcCC
Q 040816 55 WDVDFAKLGQDTLFDLLMAANYLDIKSLLDLLCQTVADMIKGKS-PEEIRQTFHI 108 (128)
Q Consensus 55 wd~~Fl~~~~~~l~~li~AA~~L~i~~L~~l~~~~ia~~i~gkt-~eeir~~f~i 108 (128)
.|.+.++ |.+.|-+|+.||.-=-+...-+.....++....|.. |-.+...|++
T Consensus 56 Idp~lld-D~e~LeDLI~aA~NdA~~ka~~~~~e~m~~~tgGm~~p~~~~~~~~~ 109 (111)
T PRK14621 56 IDPEIMD-DVEMVQDLVVAAVNSALEESAKLAQEEISKVAGGMMNPADILKNLNL 109 (111)
T ss_pred ECHHHcC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHhhccc
Confidence 4556665 778888999999776677776666666766666653 3345444443
No 143
>PRK00565 rplV 50S ribosomal protein L22; Reviewed
Probab=22.51 E-value=90 Score=20.86 Aligned_cols=22 Identities=36% Similarity=0.543 Sum_probs=17.9
Q ss_pred HHHHHHHhcCCCHHHHHhhcCC
Q 040816 87 CQTVADMIKGKSPEEIRQTFHI 108 (128)
Q Consensus 87 ~~~ia~~i~gkt~eeir~~f~i 108 (128)
+..|++.|+|+++++-..++..
T Consensus 17 ~~~v~~~IrG~~v~~A~~~L~~ 38 (112)
T PRK00565 17 ARLVADLIRGKKVEEALAILKF 38 (112)
T ss_pred HHHHHHHHcCCcHHHHHHHHHH
Confidence 4578999999999998877764
No 144
>PRK03094 hypothetical protein; Provisional
Probab=21.88 E-value=54 Score=20.95 Aligned_cols=14 Identities=29% Similarity=0.380 Sum_probs=10.9
Q ss_pred HhcCCCHHHHHhhc
Q 040816 93 MIKGKSPEEIRQTF 106 (128)
Q Consensus 93 ~i~gkt~eeir~~f 106 (128)
-.+|+|+|||.+.+
T Consensus 62 ~A~G~TaeEI~~~v 75 (80)
T PRK03094 62 TASGLTADEICQQV 75 (80)
T ss_pred EcCCCCHHHHHHHH
Confidence 45799999997765
No 145
>PRK05255 hypothetical protein; Provisional
Probab=21.87 E-value=2.6e+02 Score=20.41 Aligned_cols=56 Identities=23% Similarity=0.405 Sum_probs=44.1
Q ss_pred ccchhhhhhccChHHHHHHHHHhhhccHHHHHHHHHHHHHHHhcCCCHHHHHhhcC
Q 040816 52 LKNWDVDFAKLGQDTLFDLLMAANYLDIKSLLDLLCQTVADMIKGKSPEEIRQTFH 107 (128)
Q Consensus 52 ~~~wd~~Fl~~~~~~l~~li~AA~~L~i~~L~~l~~~~ia~~i~gkt~eeir~~f~ 107 (128)
+..|-...++-+++.+-+++..=--+|...|-.++-..-...-.+|+|.--|+.|.
T Consensus 109 lE~wRdrLi~~~d~al~e~~~~~P~~DrQ~LRqLiR~A~kE~~~~kppk~~R~LF~ 164 (171)
T PRK05255 109 LERWRDRLLAEGDDALTEFLEEYPDADRQQLRQLIRNAKKEKAQNKPPKSFRELFQ 164 (171)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHCchhhHHHHHHHHHHHHHHHHcCCCchhHHHHHH
Confidence 55677777766777888888777678888888888777777778899888888885
No 146
>PHA03098 kelch-like protein; Provisional
Probab=21.77 E-value=4.2e+02 Score=21.97 Aligned_cols=76 Identities=11% Similarity=0.142 Sum_probs=54.9
Q ss_pred CCHHHHHHHHHHHHhcccCCCCcccccchhhhhhc--cChHHHHHHHHHhhhccHHHHHHHHHHHHHHHhc---------
Q 040816 27 VRGTILSMVIEYLKKHVEAKTTEDDLKNWDVDFAK--LGQDTLFDLLMAANYLDIKSLLDLLCQTVADMIK--------- 95 (128)
Q Consensus 27 v~~~~L~~Vi~~c~~h~~~~~~~~~~~~wd~~Fl~--~~~~~l~~li~AA~~L~i~~L~~l~~~~ia~~i~--------- 95 (128)
++.+.+..++.=..+..-. .+...-.+|+. ++.+..++++..|...+.+.|.+.|-++|+..+.
T Consensus 73 i~~~~~~~ll~~A~~l~~~-----~l~~~C~~~l~~~l~~~nc~~~~~~a~~~~~~~L~~~~~~~i~~nf~~v~~~~~f~ 147 (534)
T PHA03098 73 ITSNNVKDILSIANYLIID-----FLINLCINYIIKIIDDNNCIDIYRFSFFYGCKKLYSAAYNYIRNNIELIYNDPDFI 147 (534)
T ss_pred EcHHHHHHHHHHHHHhCcH-----HHHHHHHHHHHHhCCHhHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHhcCchhh
Confidence 3455566666665554432 34555567764 7888999999999999999999999999886543
Q ss_pred CCCHHHHHhhcC
Q 040816 96 GKSPEEIRQTFH 107 (128)
Q Consensus 96 gkt~eeir~~f~ 107 (128)
..+.+++.+++.
T Consensus 148 ~l~~~~l~~ll~ 159 (534)
T PHA03098 148 YLSKNELIKILS 159 (534)
T ss_pred cCCHHHHHHHhc
Confidence 236788888866
No 147
>PF14748 P5CR_dimer: Pyrroline-5-carboxylate reductase dimerisation; PDB: 2RCY_D 3TRI_A 2IZZ_B 2GR9_B 2GRA_B 2GER_C 1YQG_A 2AG8_A 3GT0_A 2AMF_E ....
Probab=21.48 E-value=2.3e+02 Score=18.53 Aligned_cols=55 Identities=22% Similarity=0.231 Sum_probs=33.3
Q ss_pred HHHHHhhhccHHH-----HHHHHHHHHHHHhc--CCCHHHHHhhcCCCCCCCHHHHHHHhhh
Q 040816 69 DLLMAANYLDIKS-----LLDLLCQTVADMIK--GKSPEEIRQTFHIQNDFTPEEEEEIRTE 123 (128)
Q Consensus 69 ~li~AA~~L~i~~-----L~~l~~~~ia~~i~--gkt~eeir~~f~i~~d~t~eee~~i~~e 123 (128)
.++.|+--.++++ |+--+..-.+.++. +++|+++|+....|.-.|.+-.+.+++.
T Consensus 26 al~~a~v~~Gl~~~~A~~lv~~t~~G~a~ll~~~~~~~~~l~~~v~tPgG~T~~gl~~L~~~ 87 (107)
T PF14748_consen 26 ALADAAVAQGLPREEARKLVAQTFIGAAKLLEESGRSPAELRDEVTTPGGTTIAGLEVLEKG 87 (107)
T ss_dssp HHHHHHHHTT--HHHHHHHHHHHHHHHHHHHHHCSS-HHHHHHHHS-TTSHHHHHHHHHHHT
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHccCCCHHHHhhhccCCCCcHHHHHHHHHHC
Confidence 4455555555543 33444444455555 6799999999999888888766666554
No 148
>PTZ00100 DnaJ chaperone protein; Provisional
Probab=21.42 E-value=1.7e+02 Score=19.90 Aligned_cols=23 Identities=17% Similarity=0.111 Sum_probs=16.7
Q ss_pred CCCHHHHHhhcCCCCCCCHHHHH
Q 040816 96 GKSPEEIRQTFHIQNDFTPEEEE 118 (128)
Q Consensus 96 gkt~eeir~~f~i~~d~t~eee~ 118 (128)
.+|.+|-.+.|||+.+-|.+|..
T Consensus 61 ~Ms~~eAy~ILGv~~~As~~eIk 83 (116)
T PTZ00100 61 PMSKSEAYKILNISPTASKERIR 83 (116)
T ss_pred CCCHHHHHHHcCCCCCCCHHHHH
Confidence 45677888888888887765544
No 149
>KOG4350 consensus Uncharacterized conserved protein, contains BTB/POZ domain [General function prediction only]
Probab=21.35 E-value=68 Score=27.10 Aligned_cols=7 Identities=43% Similarity=0.491 Sum_probs=2.6
Q ss_pred eecCCCC
Q 040816 22 IPLLNVR 28 (128)
Q Consensus 22 Ipl~~v~ 28 (128)
|-|.++.
T Consensus 108 ~~l~~~~ 114 (620)
T KOG4350|consen 108 IDLAGVE 114 (620)
T ss_pred eecccch
Confidence 3333333
No 150
>KOG0027 consensus Calmodulin and related proteins (EF-Hand superfamily) [Signal transduction mechanisms]
Probab=21.31 E-value=2.8e+02 Score=18.91 Aligned_cols=60 Identities=23% Similarity=0.429 Sum_probs=34.8
Q ss_pred ChHHHHHHHHHhh-----hccHHHHHHHHHHHHHHHhcC-CCHHHHHhhcCCCC---C--CCHHHHHHHhh
Q 040816 63 GQDTLFDLLMAAN-----YLDIKSLLDLLCQTVADMIKG-KSPEEIRQTFHIQN---D--FTPEEEEEIRT 122 (128)
Q Consensus 63 ~~~~l~~li~AA~-----~L~i~~L~~l~~~~ia~~i~g-kt~eeir~~f~i~~---d--~t~eee~~i~~ 122 (128)
...++-+++...+ .++...++.+..+........ .+.+++++.|.+-+ | .|.+|..++..
T Consensus 42 t~~el~~~~~~~D~dg~g~I~~~eF~~l~~~~~~~~~~~~~~~~el~eaF~~fD~d~~G~Is~~el~~~l~ 112 (151)
T KOG0027|consen 42 TEEELRDLIKEIDLDGDGTIDFEEFLDLMEKLGEEKTDEEASSEELKEAFRVFDKDGDGFISASELKKVLT 112 (151)
T ss_pred CHHHHHHHHHHhCCCCCCeEcHHHHHHHHHhhhcccccccccHHHHHHHHHHHccCCCCcCcHHHHHHHHH
Confidence 3455666666655 567777777666665444333 35667777666533 1 46666665544
No 151
>PF09278 MerR-DNA-bind: MerR, DNA binding; InterPro: IPR015358 This entry represents a family of DNA-binding domains that are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold []. ; PDB: 3QAO_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q09_A 1Q08_B 1Q0A_B 1Q07_A ....
Probab=21.24 E-value=35 Score=19.90 Aligned_cols=19 Identities=32% Similarity=0.345 Sum_probs=13.8
Q ss_pred HhcCCCHHHHHhhcCCCCC
Q 040816 93 MIKGKSPEEIRQTFHIQND 111 (128)
Q Consensus 93 ~i~gkt~eeir~~f~i~~d 111 (128)
+--|.|.+|||+++.+.++
T Consensus 11 r~lGfsL~eI~~~l~l~~~ 29 (65)
T PF09278_consen 11 RELGFSLEEIRELLELYDQ 29 (65)
T ss_dssp HHTT--HHHHHHHHHHCCS
T ss_pred HHcCCCHHHHHHHHhccCC
Confidence 3458999999999988766
No 152
>cd02145 BluB Subfamily of the nitroreductase family that includes BluB protein in Rhodobacter capsulatus is involved in the conversion of cobinamide to cobalamin in Cobalamin (vitamin B12) biosynthesis. Nitroreductases typically reduce their substrates by using NAD(P)H as electron donor and often use FMN as a cofactor.
Probab=20.96 E-value=62 Score=23.18 Aligned_cols=34 Identities=21% Similarity=0.277 Sum_probs=22.6
Q ss_pred HHHHHhhhccHHHHHHHHHHHHHHHhcCCCHHHHHhhcCCCCCC
Q 040816 69 DLLMAANYLDIKSLLDLLCQTVADMIKGKSPEEIRQTFHIQNDF 112 (128)
Q Consensus 69 ~li~AA~~L~i~~L~~l~~~~ia~~i~gkt~eeir~~f~i~~d~ 112 (128)
.|+.||.-+++-.. .+.|...+++++.|||++++
T Consensus 127 nl~LaA~~~Glgt~----------~~~~~~~~~v~~~l~lp~~~ 160 (196)
T cd02145 127 NLWLAARAEGLGVG----------WVSILDPEALARLLGIPEDW 160 (196)
T ss_pred HHHHHHHHcCCceE----------EecccChHHHHHHcCcCCCc
Confidence 55556665555431 23356789999999999765
No 153
>PF11399 DUF3192: Protein of unknown function (DUF3192); InterPro: IPR021534 Some members in this family of proteins are annotated as lipoproteins however this cannot be confirmed.
Probab=20.84 E-value=97 Score=20.74 Aligned_cols=25 Identities=24% Similarity=0.421 Sum_probs=20.6
Q ss_pred HHHHHHhcCCCHHHHHhhcCCCCCCC
Q 040816 88 QTVADMIKGKSPEEIRQTFHIQNDFT 113 (128)
Q Consensus 88 ~~ia~~i~gkt~eeir~~f~i~~d~t 113 (128)
+.|+.+--|+|.++++..+|-| |||
T Consensus 26 ~~i~~L~lg~s~~~V~~~lG~p-dfs 50 (102)
T PF11399_consen 26 QNIAKLSLGMSKDQVIALLGTP-DFS 50 (102)
T ss_pred HHHHhcCCCCCHHHHHHHhCCC-Cch
Confidence 4667777799999999999976 665
No 154
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=20.84 E-value=1.4e+02 Score=15.98 Aligned_cols=17 Identities=29% Similarity=0.491 Sum_probs=13.2
Q ss_pred hcCCCHHHHHhhcCCCC
Q 040816 94 IKGKSPEEIRQTFHIQN 110 (128)
Q Consensus 94 i~gkt~eeir~~f~i~~ 110 (128)
..|+|.++|-+.+|++.
T Consensus 13 ~~~~s~~eia~~l~~s~ 29 (57)
T cd06170 13 AEGKTNKEIADILGISE 29 (57)
T ss_pred HcCCCHHHHHHHHCCCH
Confidence 46788888888888753
No 155
>cd08054 gp6 Head-Tail Connector Protein gp6 of Bacteriophage HK97 and similar proteins. The bacteriophage HK97 gp6 protein is critical in the assembly of the connector, a specialized structure that serves as an interface for head and tail attachment, as well as a point at which DNA exits the head during infection by the bacteriophage. It forms a dodecameric ring structure that comprises the middle ring of the connector, located between the portal protein (attached to the head) and the gp7 ring (attached to the tail). It is a component of the mature phage and the absence of HK97 gp6 results in defective head-tail joining and the absence of mature phage particles. Although the crystal structure of HK97 gp6 shows an unexpected 13-mer ring, the biological form present in the mature phage is believed to be a dodecamer.
Probab=20.65 E-value=1.5e+02 Score=18.14 Aligned_cols=20 Identities=20% Similarity=0.177 Sum_probs=15.7
Q ss_pred CHHHHHhhcCCCCCCCHHHH
Q 040816 98 SPEEIRQTFHIQNDFTPEEE 117 (128)
Q Consensus 98 t~eeir~~f~i~~d~t~eee 117 (128)
|.+++|+.++|..|..++-.
T Consensus 1 ~L~~~K~~Lrid~d~dD~~i 20 (91)
T cd08054 1 TLEEAKAHLRIDHDDDDALI 20 (91)
T ss_pred CHHHHHhHcCCCCCCCHHHH
Confidence 56899999999987765443
No 156
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=20.45 E-value=1.7e+02 Score=16.12 Aligned_cols=22 Identities=9% Similarity=0.280 Sum_probs=14.0
Q ss_pred HHHHHHhcC-CCHHHHHhhcCCC
Q 040816 88 QTVADMIKG-KSPEEIRQTFHIQ 109 (128)
Q Consensus 88 ~~ia~~i~g-kt~eeir~~f~i~ 109 (128)
+.|...-.| +|..+.-+.||||
T Consensus 7 ~Ai~~v~~g~~S~r~AA~~ygVp 29 (45)
T PF05225_consen 7 KAIEAVKNGKMSIRKAAKKYGVP 29 (45)
T ss_dssp HHHHHHHTTSS-HHHHHHHHT--
T ss_pred HHHHHHHhCCCCHHHHHHHHCcC
Confidence 344455577 8999999999997
No 157
>PRK11187 replication initiation regulator SeqA; Provisional
Probab=20.42 E-value=1e+02 Score=22.83 Aligned_cols=26 Identities=23% Similarity=0.498 Sum_probs=20.8
Q ss_pred HHHHHHHHhc--CCCHHHH-HhhcCCCCC
Q 040816 86 LCQTVADMIK--GKSPEEI-RQTFHIQND 111 (128)
Q Consensus 86 ~~~~ia~~i~--gkt~eei-r~~f~i~~d 111 (128)
..+|||...+ |-|..+| |++|+++.+
T Consensus 10 LYryIAS~Tq~IGESASDILRRLL~l~~~ 38 (182)
T PRK11187 10 LYRYIASHTQHIGESASDILRRLLKLSAE 38 (182)
T ss_pred HHHHHHHccCccCCCHHHHHHHHhCCCcc
Confidence 3578888777 8898887 999998863
No 158
>PF02885 Glycos_trans_3N: Glycosyl transferase family, helical bundle domain Prosite entry for Thymidine and pyrimidine-nucleoside phosphorylases; InterPro: IPR017459 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. The glycosyl transferase family includes anthranilate phosphoribosyltransferase (TrpD, 2.4.2.18 from EC) and thymidine phosphorylase (2.4.2.2 from EC). All these proteins can transfer a phosphorylated ribose substrate. Thymidine phosphorylase (2.4.2.2 from EC) catalyses the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate. This enzyme regulates the availability of thymidine and is therefore essential to nucleic acid metabolism. This N-terminal domain is found in various family 3 glycosyl transferases, including anthranilate phosphoribosyltransferase (TrpD, 2.4.2.18 from EC) and thymidine phosphorylase (2.4.2.2 from EC). All these proteins can transfer a phosphorylated ribose substrate. Thymidine phosphorylase catalyses the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate. This enzyme regulates the availability of thymidine and is therefore essential to nucleic acid metabolism.; PDB: 2DSJ_B 2ELC_B 2BPQ_A 1ZVW_B 3QR9_B 1V8G_B 2WK5_C 2J0F_C 2WK6_B 1UOU_A ....
Probab=20.29 E-value=1.5e+02 Score=17.46 Aligned_cols=22 Identities=32% Similarity=0.431 Sum_probs=13.4
Q ss_pred HHHHHHHHHHHhcCCCHHHHHh
Q 040816 83 LDLLCQTVADMIKGKSPEEIRQ 104 (128)
Q Consensus 83 ~~l~~~~ia~~i~gkt~eeir~ 104 (128)
..+++--+|-.++|-|++|+..
T Consensus 35 ~qiaAfL~al~~kget~~Eiag 56 (66)
T PF02885_consen 35 AQIAAFLMALRMKGETPEEIAG 56 (66)
T ss_dssp HHHHHHHHHHHHH---HHHHHH
T ss_pred HHHHHHHHHHHHhCcCHHHHHH
Confidence 3455666778888999988854
No 159
>PF07064 RIC1: RIC1; InterPro: IPR009771 This entry represents RIC1 (Ribosomal control protein1) and has been identified in yeast as a Golgi protein involved in retrograde transport to the cis-Golgi network. It forms a heterodimer with Rgp1 and functions as a guanyl-nucleotide exchange factor [] which activates YPT6 by exchanging bound GDP for free GTP. RIC1 is thereby required for efficient fusion of endosome-derived vesicles with the Golgi. The RIC1-RGP1 complex participates in the recycling of SNC1, presumably by mediating fusion of endosomal vesicles with the Golgi compartment and may also be indirectly involved in the transcription of both ribosomal protein genes and ribosomal RNA [, , ].
Probab=20.24 E-value=2.2e+02 Score=21.92 Aligned_cols=55 Identities=25% Similarity=0.427 Sum_probs=37.8
Q ss_pred CCCHHHHHHHHHHHHhcccCC------CCcccccchhhhhhcc-ChHHHHHHHH-------HhhhccHH
Q 040816 26 NVRGTILSMVIEYLKKHVEAK------TTEDDLKNWDVDFAKL-GQDTLFDLLM-------AANYLDIK 80 (128)
Q Consensus 26 ~v~~~~L~~Vi~~c~~h~~~~------~~~~~~~~wd~~Fl~~-~~~~l~~li~-------AA~~L~i~ 80 (128)
......|..|++++.++.... .+..++.-|..=|-.+ ++..||+-.. ||+||-|-
T Consensus 137 ~~~~~~L~~v~~ll~~f~~~l~Ivv~C~RKtE~~~W~~LF~~lg~P~dLf~~cl~~~~l~tAa~yLlVl 205 (258)
T PF07064_consen 137 PIPDALLPRVISLLQEFPEYLEIVVNCARKTEVRYWPYLFDYLGSPRDLFEECLENGNLKTAASYLLVL 205 (258)
T ss_pred cchHHHHHHHHHHHHcCcchHHHHHHHHHhhHHHHHHHHHHhcCCHHHHHHHHHHcCcHHHHHHHHHHH
Confidence 467789999999999976653 2456788897655333 6788887554 55555443
No 160
>PF06514 PsbU: Photosystem II 12 kDa extrinsic protein (PsbU); InterPro: IPR010527 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. In PSII, the oxygen-evolving complex (OEC) is responsible for catalysing the splitting of water to O(2) and 4H+. The OEC is composed of a cluster of manganese, calcium and chloride ions bound to extrinsic proteins. In cyanobacteria there are five extrinsic proteins in OEC (PsbO, PsbP-like, PsbQ-like, PsbU and PsbV), while in plants there are only three (PsbO, PsbP and PsbQ), PsbU and PsbV having been lost during the evolution of green plants []. This family represents the PSII extrinsic protein PsbU, which forms part of the OEC in cyanobacteria and red algae. PsbU acts to stabilise the oxygen-evolving machinery of PSII against heat-induced inactivation, which is crucial for cellular thermo-tolerance [].; GO: 0015979 photosynthesis, 0042549 photosystem II stabilization, 0009523 photosystem II, 0009654 oxygen evolving complex, 0019898 extrinsic to membrane; PDB: 3BZ1_U 3KZI_U 3PRQ_U 2AXT_u 3BZ2_U 4FBY_U 3PRR_U 1S5L_U 3A0H_U 3ARC_U ....
Probab=20.21 E-value=26 Score=23.07 Aligned_cols=46 Identities=11% Similarity=0.214 Sum_probs=28.8
Q ss_pred HhhhccHHHHHHHHHHHHHHHhcCCCHHHHHhhcCCCCCCCHHHHHHHhh
Q 040816 73 AANYLDIKSLLDLLCQTVADMIKGKSPEEIRQTFHIQNDFTPEEEEEIRT 122 (128)
Q Consensus 73 AA~~L~i~~L~~l~~~~ia~~i~gkt~eeir~~f~i~~d~t~eee~~i~~ 122 (128)
...|.+.++++-..+.+|+...--+|++++- +|+ ++|+.|.+.+++
T Consensus 22 vr~f~~~pGmYPtlA~kIv~naPY~sveDvl---~ip-gLse~qK~~lk~ 67 (93)
T PF06514_consen 22 VRAFRQFPGMYPTLAGKIVSNAPYKSVEDVL---NIP-GLSERQKALLKK 67 (93)
T ss_dssp GGGGCCSTTTTCCHHHHHHHS---SSGGGGC---CST-T--HHHHHHHHH
T ss_pred HHHHHHCCCCCHHHHHHHHhCCCCCCHHHHH---hcc-CCCHHHHHHHHH
Confidence 4567788888877777777766667777754 443 577877776654
No 161
>PF03698 UPF0180: Uncharacterised protein family (UPF0180); InterPro: IPR005370 The members of this family are small uncharacterised proteins.
Probab=20.16 E-value=62 Score=20.63 Aligned_cols=14 Identities=36% Similarity=0.366 Sum_probs=10.2
Q ss_pred HhcCCCHHHHHhhc
Q 040816 93 MIKGKSPEEIRQTF 106 (128)
Q Consensus 93 ~i~gkt~eeir~~f 106 (128)
-..|+|++||.+.+
T Consensus 62 nA~G~T~eEI~~~v 75 (80)
T PF03698_consen 62 NASGLTAEEIVQEV 75 (80)
T ss_pred ecCCCCHHHHHHHH
Confidence 34799999987643
Done!