Query 037688
Match_columns 103
No_of_seqs 104 out of 573
Neff 6.3
Searched_HMMs 46136
Date Fri Mar 29 03:26:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037688.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037688hhsearch_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 8.4E-36 1.8E-40 213.1 9.2 96 6-102 36-158 (162)
2 COG5201 SKP1 SCF ubiquitin lig 100.0 1.8E-35 4E-40 205.0 8.4 100 2-102 28-153 (158)
3 PF01466 Skp1: Skp1 family, di 100.0 1.1E-28 2.3E-33 157.3 7.8 70 32-102 5-74 (78)
4 smart00512 Skp1 Found in Skp1 99.5 2.6E-14 5.7E-19 94.5 3.0 54 2-56 28-104 (104)
5 PF03931 Skp1_POZ: Skp1 family 98.0 8.7E-07 1.9E-11 53.7 -0.8 26 3-28 28-61 (62)
6 PHA02790 Kelch-like protein; P 95.0 0.045 9.8E-07 44.6 4.8 49 17-73 74-122 (480)
7 PHA03098 kelch-like protein; P 94.7 0.079 1.7E-06 43.1 5.6 55 17-79 59-113 (534)
8 KOG3433 Protein involved in me 94.4 0.1 2.3E-06 38.5 5.0 38 48-90 161-200 (203)
9 COG5124 Protein predicted to b 93.7 0.081 1.7E-06 39.0 3.3 31 55-90 174-204 (209)
10 PHA02713 hypothetical protein; 93.0 0.23 5E-06 41.4 5.4 56 17-82 79-134 (557)
11 smart00225 BTB Broad-Complex, 93.0 0.11 2.5E-06 30.7 2.7 40 17-64 51-90 (90)
12 KOG3473 RNA polymerase II tran 92.3 0.18 3.9E-06 33.9 3.1 42 13-56 64-112 (112)
13 KOG4441 Proteins containing BT 91.3 0.43 9.4E-06 40.1 5.1 48 17-72 88-135 (571)
14 PF00651 BTB: BTB/POZ domain; 91.3 0.55 1.2E-05 29.7 4.5 45 17-69 64-109 (111)
15 PF03962 Mnd1: Mnd1 family; I 88.3 0.68 1.5E-05 33.8 3.6 43 43-90 143-187 (188)
16 KOG2716 Polymerase delta-inter 81.9 3.4 7.3E-05 31.4 4.8 52 17-74 57-108 (230)
17 PF13921 Myb_DNA-bind_6: Myb-l 75.0 6.2 0.00013 22.7 3.6 34 64-97 20-60 (60)
18 KOG4682 Uncharacterized conser 73.1 4.9 0.00011 33.3 3.7 47 40-89 139-185 (488)
19 PF03656 Pam16: Pam16; InterP 72.6 3.3 7.2E-05 28.6 2.2 27 70-96 51-77 (127)
20 PF11822 DUF3342: Domain of un 66.7 3.1 6.8E-05 33.0 1.3 32 40-71 73-104 (317)
21 cd00167 SANT 'SWI3, ADA2, N-Co 66.2 7.6 0.00016 20.1 2.4 21 64-84 22-42 (45)
22 PF00249 Myb_DNA-binding: Myb- 65.5 9.1 0.0002 21.2 2.8 21 63-83 23-44 (48)
23 smart00717 SANT SANT SWI3, AD 63.8 9.1 0.0002 20.1 2.5 21 64-84 24-44 (49)
24 PF09713 A_thal_3526: Plant pr 63.7 11 0.00023 22.5 2.9 31 73-103 12-46 (54)
25 PF01843 DIL: DIL domain; Int 63.3 1.7 3.7E-05 28.2 -0.7 60 17-84 37-97 (105)
26 PRK05365 malonic semialdehyde 62.2 6.4 0.00014 28.0 2.1 34 47-90 131-164 (195)
27 PF12556 CobS_N: Cobaltochelat 61.7 4.8 0.0001 22.1 1.1 12 79-90 14-25 (36)
28 PF11978 MVP_shoulder: Shoulde 61.4 6 0.00013 27.2 1.7 28 47-74 36-63 (118)
29 PF13798 PCYCGC: Protein of un 60.0 14 0.0003 26.6 3.4 24 60-83 118-141 (158)
30 cd02148 Nitroreductase_5 Nitro 59.3 7.6 0.00016 27.3 2.0 34 47-90 124-157 (185)
31 PRK11053 dihydropteridine redu 57.2 9.7 0.00021 27.4 2.4 34 46-89 149-183 (217)
32 PF15063 TC1: Thyroid cancer p 56.8 13 0.00027 23.8 2.5 33 65-97 28-60 (79)
33 PRK11325 scaffold protein; Pro 56.1 19 0.0004 24.4 3.5 37 48-84 53-90 (127)
34 TIGR03419 NifU_clost FeS clust 55.6 21 0.00046 23.9 3.7 38 47-84 46-84 (121)
35 PF01592 NifU_N: NifU-like N t 55.3 17 0.00036 24.4 3.1 21 61-81 65-85 (126)
36 TIGR01999 iscU FeS cluster ass 55.0 20 0.00044 24.1 3.5 37 48-84 51-88 (124)
37 PF02214 BTB_2: BTB/POZ domain 54.2 18 0.00039 22.5 3.0 41 17-63 53-94 (94)
38 KOG3442 Uncharacterized conser 54.1 14 0.00031 25.7 2.6 25 72-96 54-78 (132)
39 PF06851 DUF1247: Protein of u 53.6 28 0.0006 24.8 4.0 62 23-86 61-134 (148)
40 TIGR03147 cyt_nit_nrfF cytochr 49.3 19 0.00041 24.9 2.6 19 65-83 64-83 (126)
41 PF11569 Homez: Homeodomain le 49.2 47 0.001 19.9 4.0 35 44-84 13-47 (56)
42 PF11103 DUF2887: Protein of u 48.1 28 0.00061 25.8 3.5 29 55-83 172-200 (200)
43 cd06664 IscU_like Iron-sulfur 47.3 35 0.00076 22.4 3.7 38 47-84 47-85 (123)
44 COG4957 Predicted transcriptio 47.0 18 0.00038 25.7 2.2 19 72-90 97-115 (148)
45 COG0822 IscU NifU homolog invo 45.6 37 0.0008 23.9 3.7 35 49-83 55-90 (150)
46 PF13518 HTH_28: Helix-turn-he 45.6 39 0.00084 18.3 3.2 21 66-86 5-25 (52)
47 PF10892 DUF2688: Protein of u 45.6 26 0.00056 21.2 2.5 25 76-100 30-56 (60)
48 PF13384 HTH_23: Homeodomain-l 44.5 28 0.0006 19.0 2.4 16 72-87 16-31 (50)
49 PF11460 DUF3007: Protein of u 44.5 23 0.00049 23.8 2.4 23 75-100 79-101 (104)
50 PF08671 SinI: Anti-repressor 44.0 20 0.00044 18.7 1.6 13 72-84 15-27 (30)
51 TIGR02698 CopY_TcrY copper tra 43.9 92 0.002 21.0 5.4 42 58-99 71-112 (130)
52 PF03918 CcmH: Cytochrome C bi 43.6 23 0.0005 24.9 2.4 18 66-83 65-83 (148)
53 cd02140 Nitroreductase_4 Nitro 43.5 17 0.00037 25.6 1.8 38 45-90 128-165 (192)
54 cd03370 NADH_oxidase NADPH_oxi 43.2 19 0.00041 24.5 1.9 19 71-89 112-131 (156)
55 PF05443 ROS_MUCR: ROS/MUCR tr 43.2 12 0.00026 26.0 0.9 18 73-90 94-111 (132)
56 TIGR01994 SUF_scaf_2 SUF syste 41.8 48 0.001 22.7 3.7 37 48-84 51-88 (137)
57 KOG4244 Failed axon connection 41.8 27 0.00059 27.3 2.7 24 76-99 111-134 (281)
58 TIGR02476 BluB cob(II)yrinic a 41.6 24 0.00052 25.2 2.3 36 45-90 135-170 (205)
59 cd02144 iodotyrosine_dehalogen 41.6 25 0.00054 24.3 2.4 36 46-91 131-167 (193)
60 COG1710 Uncharacterized protei 40.9 20 0.00044 25.0 1.7 16 72-87 108-123 (139)
61 PF03883 DUF328: Protein of un 40.8 27 0.00059 26.1 2.6 37 61-97 28-64 (237)
62 PF11198 DUF2857: Protein of u 39.9 1E+02 0.0022 22.2 5.4 58 40-97 59-131 (180)
63 PF04355 SmpA_OmlA: SmpA / Oml 39.8 20 0.00042 21.4 1.4 21 67-87 9-29 (71)
64 PRK10144 formate-dependent nit 39.6 33 0.00071 23.8 2.6 19 65-83 64-83 (126)
65 cd05029 S-100A6 S-100A6: S-100 38.7 90 0.0019 19.6 4.4 44 56-99 9-58 (88)
66 PLN03212 Transcription repress 38.2 48 0.001 25.6 3.5 35 65-99 49-91 (249)
67 PF14098 SSPI: Small, acid-sol 37.9 38 0.00083 20.9 2.5 20 65-84 5-24 (65)
68 PRK15019 CsdA-binding activato 37.6 62 0.0013 22.8 3.8 38 51-92 83-128 (147)
69 PRK13696 hypothetical protein; 37.4 83 0.0018 19.2 3.9 26 72-100 36-61 (62)
70 PF11165 DUF2949: Protein of u 37.2 26 0.00056 21.1 1.6 16 11-26 31-58 (58)
71 KOG1665 AFH1-interacting prote 37.1 45 0.00097 25.9 3.2 41 17-64 64-104 (302)
72 PF03750 DUF310: Protein of un 35.3 65 0.0014 21.5 3.5 34 54-88 8-43 (119)
73 PF06514 PsbU: Photosystem II 34.3 14 0.0003 24.4 0.1 46 50-99 22-67 (93)
74 PF14748 P5CR_dimer: Pyrroline 34.2 1.2E+02 0.0026 19.7 4.6 55 46-100 26-87 (107)
75 PF11399 DUF3192: Protein of u 33.9 46 0.00099 22.3 2.5 27 64-91 25-51 (102)
76 cd07013 S14_ClpP Caseinolytic 33.8 1.2E+02 0.0026 21.0 4.9 37 58-95 118-154 (162)
77 PF00690 Cation_ATPase_N: Cati 33.7 71 0.0015 18.7 3.2 28 74-101 4-33 (69)
78 smart00385 CYCLIN domain prese 33.4 94 0.002 17.5 4.9 40 56-98 37-78 (83)
79 PF03979 Sigma70_r1_1: Sigma-7 32.8 1E+02 0.0023 19.0 4.0 26 72-98 19-45 (82)
80 PF07671 DUF1601: Protein of u 32.8 49 0.0011 18.1 2.1 30 53-82 7-36 (37)
81 PF00196 GerE: Bacterial regul 32.8 61 0.0013 18.3 2.7 22 65-86 10-31 (58)
82 COG1460 Uncharacterized protei 32.6 71 0.0015 21.8 3.3 55 40-97 49-104 (114)
83 TIGR03553 F420_FbiB_CTERM F420 32.6 25 0.00053 24.7 1.1 17 74-90 149-165 (194)
84 cd02138 Nitroreductase_2 Nitro 32.6 45 0.00098 23.2 2.5 38 44-91 108-145 (181)
85 PF02796 HTH_7: Helix-turn-hel 32.5 65 0.0014 17.6 2.7 16 71-86 19-34 (45)
86 smart00421 HTH_LUXR helix_turn 32.5 76 0.0016 16.8 3.0 17 71-87 16-32 (58)
87 TIGR03391 FeS_syn_CsdE cystein 32.3 90 0.002 21.6 3.9 34 55-92 82-123 (138)
88 PRK13742 replication protein; 32.1 53 0.0012 24.8 3.0 34 57-90 163-199 (245)
89 COG2996 Predicted RNA-bindinin 31.9 29 0.00064 27.2 1.5 13 75-87 248-260 (287)
90 PF04282 DUF438: Family of unk 31.4 91 0.002 19.4 3.4 28 72-99 11-39 (71)
91 PF05871 ESCRT-II: ESCRT-II co 31.4 34 0.00074 23.8 1.7 14 17-30 26-39 (139)
92 PF03131 bZIP_Maf: bZIP Maf tr 30.8 62 0.0014 20.5 2.8 27 70-99 5-31 (92)
93 PRK12551 ATP-dependent Clp pro 30.8 1.3E+02 0.0027 22.0 4.7 37 58-95 143-179 (196)
94 smart00497 IENR1 Intron encode 30.7 50 0.0011 18.1 2.0 26 44-75 17-42 (53)
95 PF15120 DUF4561: Domain of un 30.4 1.3E+02 0.0028 22.0 4.5 18 13-30 40-59 (171)
96 PF06777 DUF1227: Protein of u 30.2 2E+02 0.0043 20.3 5.4 52 17-72 66-117 (146)
97 PRK09296 cysteine desufuration 30.2 81 0.0017 21.9 3.4 30 63-92 81-118 (138)
98 TIGR01044 rplV_bact ribosomal 29.5 67 0.0015 21.0 2.8 20 65-84 14-33 (103)
99 cd02145 BluB Subfamily of the 29.5 37 0.0008 23.9 1.7 19 72-90 143-161 (196)
100 TIGR02000 NifU_proper Fe-S clu 29.2 60 0.0013 25.2 2.9 37 48-84 52-89 (290)
101 PF13010 pRN1_helical: Primase 29.2 29 0.00064 24.2 1.0 14 69-82 24-37 (135)
102 PRK14512 ATP-dependent Clp pro 29.2 2.2E+02 0.0048 20.6 5.7 36 58-94 141-176 (197)
103 PRK13379 protocatechuate 4,5-d 28.4 63 0.0014 22.2 2.5 32 56-87 86-117 (119)
104 PF09382 RQC: RQC domain; Int 28.3 89 0.0019 19.6 3.2 38 61-98 19-63 (106)
105 KOG0437 Leucyl-tRNA synthetase 28.2 41 0.0009 30.3 2.0 22 81-102 109-130 (1080)
106 CHL00028 clpP ATP-dependent Cl 27.4 1.6E+02 0.0035 21.5 4.7 49 44-95 137-185 (200)
107 COG2865 Predicted transcriptio 27.4 1.6E+02 0.0034 24.7 5.1 27 62-88 405-431 (467)
108 PF08281 Sigma70_r4_2: Sigma-7 27.0 42 0.00091 18.6 1.3 18 70-87 23-40 (54)
109 TIGR01589 A_thal_3526 uncharac 26.6 53 0.0012 19.7 1.7 30 74-103 16-49 (57)
110 PF04255 DUF433: Protein of un 26.2 1.4E+02 0.003 17.1 4.1 23 71-96 29-51 (56)
111 PF12674 Zn_ribbon_2: Putative 26.1 1.4E+02 0.003 18.8 3.7 28 56-84 44-71 (81)
112 PRK11548 outer membrane biogen 25.7 79 0.0017 20.8 2.6 23 65-87 41-63 (113)
113 PF10607 CLTH: CTLH/CRA C-term 25.6 1.2E+02 0.0026 20.0 3.6 14 17-30 17-30 (145)
114 PRK14981 DNA-directed RNA poly 25.4 2.1E+02 0.0045 18.9 6.1 44 55-99 61-105 (112)
115 TIGR02937 sigma70-ECF RNA poly 25.3 90 0.002 19.7 2.8 27 62-88 114-141 (158)
116 PF10507 DUF2453: Protein of u 25.0 1.4E+02 0.003 20.3 3.7 38 59-96 35-80 (111)
117 PF06056 Terminase_5: Putative 25.0 1.2E+02 0.0025 17.9 3.0 21 67-87 7-27 (58)
118 cd02062 Nitro_FMN_reductase Pr 24.9 83 0.0018 19.7 2.6 35 45-89 76-112 (122)
119 PF02657 SufE: Fe-S metabolism 24.8 1.6E+02 0.0036 19.8 4.1 33 56-92 69-108 (125)
120 PF05225 HTH_psq: helix-turn-h 24.7 1.3E+02 0.0029 16.5 3.5 23 65-87 7-30 (45)
121 PRK11566 hdeB acid-resistance 24.7 51 0.0011 22.1 1.5 14 17-30 74-87 (102)
122 PF08727 P3A: Poliovirus 3A pr 24.6 52 0.0011 19.8 1.4 12 18-29 30-41 (57)
123 PRK03094 hypothetical protein; 24.6 52 0.0011 21.0 1.5 13 71-83 63-75 (80)
124 KOG0743 AAA+-type ATPase [Post 24.5 65 0.0014 26.9 2.4 40 48-88 377-418 (457)
125 PF11338 DUF3140: Protein of u 24.5 50 0.0011 21.7 1.4 15 16-30 61-75 (92)
126 PF15628 RRM_DME: RRM in Demet 24.4 70 0.0015 21.4 2.1 20 65-84 57-76 (103)
127 cd02137 Nitroreductase_1 Nitro 23.8 77 0.0017 21.1 2.3 19 72-90 104-122 (148)
128 PF06411 HdeA: HdeA/HdeB famil 23.5 54 0.0012 20.8 1.5 14 17-30 76-89 (94)
129 PF03698 UPF0180: Uncharacteri 23.4 57 0.0012 20.8 1.5 13 71-83 63-75 (80)
130 PHA03098 kelch-like protein; P 23.3 3.6E+02 0.0079 21.8 6.5 61 17-84 90-159 (534)
131 cd07022 S49_Sppa_36K_type Sign 23.1 1.7E+02 0.0037 21.1 4.2 35 56-93 159-193 (214)
132 PF05409 Peptidase_C30: Corona 23.1 1.2E+02 0.0027 23.8 3.6 58 32-94 208-265 (293)
133 PF02885 Glycos_trans_3N: Glyc 23.0 1.3E+02 0.0029 17.6 3.1 23 60-82 35-57 (66)
134 cd06170 LuxR_C_like C-terminal 23.0 1.3E+02 0.0029 15.9 3.0 17 71-87 13-29 (57)
135 PRK12552 ATP-dependent Clp pro 22.9 2.1E+02 0.0046 21.5 4.7 50 43-95 154-203 (222)
136 cd00068 GGL G protein gamma su 22.9 72 0.0016 18.7 1.8 18 12-29 18-38 (57)
137 PRK10828 putative oxidoreducta 22.7 45 0.00098 23.4 1.0 34 46-89 117-152 (183)
138 PF09883 DUF2110: Uncharacteri 22.7 69 0.0015 24.4 2.0 17 74-90 112-128 (225)
139 PRK14514 ATP-dependent Clp pro 22.5 2.1E+02 0.0045 21.4 4.6 36 59-95 173-208 (221)
140 cd00394 Clp_protease_like Case 22.5 2E+02 0.0043 19.3 4.3 39 57-96 116-154 (161)
141 KOG0783 Uncharacterized conser 22.4 3.4E+02 0.0074 25.2 6.5 67 12-81 754-825 (1267)
142 TIGR01038 L22_arch ribosomal p 22.3 1E+02 0.0022 21.8 2.8 21 64-84 26-46 (150)
143 PF09324 DUF1981: Domain of un 22.3 1.1E+02 0.0024 19.2 2.7 32 36-68 53-84 (86)
144 PF09278 MerR-DNA-bind: MerR, 22.2 61 0.0013 18.6 1.4 17 72-88 13-29 (65)
145 PF01476 LysM: LysM domain; I 22.1 1.3E+02 0.0027 15.6 2.6 20 63-83 8-27 (44)
146 cd00336 Ribosomal_L22 Ribosoma 22.0 1.1E+02 0.0024 19.6 2.8 20 65-84 16-35 (105)
147 PRK13723 conjugal transfer pil 22.0 2.9E+02 0.0064 23.0 5.7 66 32-99 328-398 (451)
148 TIGR03879 near_KaiC_dom probab 21.9 1.5E+02 0.0033 18.5 3.2 19 69-87 28-46 (73)
149 PRK02101 hypothetical protein; 21.7 87 0.0019 23.7 2.5 42 56-98 24-65 (255)
150 PF00134 Cyclin_N: Cyclin, N-t 21.7 1.7E+02 0.0036 18.5 3.6 42 58-99 74-116 (127)
151 cd07925 LigA_like_1 The A subu 21.7 88 0.0019 21.1 2.2 30 56-85 74-103 (106)
152 cd03735 SOCS_SOCS1 SOCS (suppr 21.5 55 0.0012 18.4 1.0 19 56-74 3-21 (43)
153 PF07638 Sigma70_ECF: ECF sigm 21.1 2.6E+02 0.0057 19.5 4.8 47 40-88 119-166 (185)
154 PRK02866 cyanate hydratase; Va 21.1 2E+02 0.0042 20.4 4.0 35 63-98 20-54 (147)
155 TIGR00493 clpP ATP-dependent C 21.0 2.6E+02 0.0057 20.0 4.8 30 64-94 150-179 (191)
156 KOG4350 Uncharacterized conser 20.9 41 0.00088 28.3 0.6 36 39-79 145-180 (620)
157 PF00574 CLP_protease: Clp pro 20.9 1.2E+02 0.0027 21.0 3.0 49 44-95 122-170 (182)
158 KOG1534 Putative transcription 20.6 2.2E+02 0.0048 22.1 4.4 70 13-87 114-193 (273)
159 PRK04223 rpl22p 50S ribosomal 20.6 1.2E+02 0.0025 21.6 2.8 21 64-84 30-50 (153)
160 cd02149 NfsB_like_nitroreducta 20.6 89 0.0019 21.1 2.2 18 71-88 111-128 (157)
161 CHL00034 rpl22 ribosomal prote 20.5 1.2E+02 0.0026 20.4 2.7 21 64-84 24-44 (117)
162 KOG0028 Ca2+-binding protein ( 20.5 1.3E+02 0.0027 22.0 2.9 35 50-87 82-116 (172)
163 PF14403 CP_ATPgrasp_2: Circul 20.3 2E+02 0.0043 23.9 4.4 34 59-99 65-98 (445)
164 COG4224 Uncharacterized protei 20.2 85 0.0018 20.0 1.8 17 85-101 57-73 (77)
165 TIGR03209 P21_Cbot clostridium 20.1 1.5E+02 0.0033 19.3 3.2 24 64-87 112-137 (142)
166 PF13833 EF-hand_8: EF-hand do 20.1 1.4E+02 0.0031 16.1 2.7 22 75-97 6-30 (54)
167 PF15101 DUF4557: Domain of un 20.1 41 0.00088 25.3 0.4 26 67-92 174-200 (212)
168 PRK00565 rplV 50S ribosomal pr 20.0 1.3E+02 0.0028 19.9 2.8 22 64-85 17-38 (112)
No 1
>KOG1724 consensus SCF ubiquitin ligase, Skp1 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=8.4e-36 Score=213.13 Aligned_cols=96 Identities=44% Similarity=0.641 Sum_probs=87.8
Q ss_pred CCCCCCC--ccCc-------HHHHHHHHHhcCCc-----------c-------hhhcccCCchhHHHHHHHhhhhhchHH
Q 037688 6 DDTSEDM--VVPQ-------LPYIIKFCKAHGVS-----------K-------ENEFGKGKSNDELKEMLLVANYLNIKE 58 (103)
Q Consensus 6 e~~~~~~--~IPl-------L~~Vie~c~~h~~~-----------k-------D~~F~~~~~~~~L~~li~AA~yL~I~~ 58 (103)
+..+.++ +||| |++||+||+||+++ + |++|+++ ++++||+|+.|||||+|++
T Consensus 36 ~~~~~~~~~~IPl~nV~~~iL~kVIewC~~Hk~d~~~~~~~~~~~~~~~i~~WD~~Flk~-d~~tLfdli~AAnyLdi~g 114 (162)
T KOG1724|consen 36 EDGCADENDPIPLPNVTSKILKKVIEWCKKHKDDDPANPEDKELPEETDIPEWDAEFLKV-DQGTLFDLILAANYLDIKG 114 (162)
T ss_pred HcCCCccCCccccCccCHHHHHHHHHHHHHcccccccccccccccccCCccHHHHHHHhc-CHHHHHHHHHHhhhcccHH
Confidence 3334444 8998 99999999999975 1 9999996 9999999999999999999
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHHHhCCCCCCChHHHHHHhhhhC
Q 037688 59 MLDYLTKTLANRIKNKSVEYIRKFFGIQTNFMPEEEEATRKESF 102 (103)
Q Consensus 59 Ll~l~~~~vA~~i~gKt~eeiR~~f~I~~d~t~eee~~i~~e~~ 102 (103)
|+++||++||+|++||||+|||..|||++|+||+|+++++++|.
T Consensus 115 Ll~~~ck~va~mikgktpeEir~~f~I~~d~t~eE~~~~~~e~~ 158 (162)
T KOG1724|consen 115 LLDLTCKTVANMIKGKTPEEIREIFNIENDETPEEEEAIRKENE 158 (162)
T ss_pred HHHHHHHHHHHHHccCCHHHHHHHcCCCCCCChhHHHHHhhccc
Confidence 99999999999999999999999999999999999999999875
No 2
>COG5201 SKP1 SCF ubiquitin ligase, SKP1 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.8e-35 Score=205.02 Aligned_cols=100 Identities=37% Similarity=0.506 Sum_probs=92.4
Q ss_pred CCCCCCCCC-CCccCc-------HHHHHHHHHhcCCc-----------c-------hhhcccCCchhHHHHHHHhhhhhc
Q 037688 2 SSMSDDTSE-DMVVPQ-------LPYIIKFCKAHGVS-----------K-------ENEFGKGKSNDELKEMLLVANYLN 55 (103)
Q Consensus 2 ~~m~e~~~~-~~~IPl-------L~~Vie~c~~h~~~-----------k-------D~~F~~~~~~~~L~~li~AA~yL~ 55 (103)
|+|+.++.+ +-|||+ |.+|++||+||++. | |+.|+++ |+++|++++.|||||+
T Consensus 28 kN~l~d~~~~n~p~p~pnVrSsvl~kv~ew~ehh~~s~sede~d~~~rks~p~D~wdr~Fm~v-DqemL~eI~laaNYL~ 106 (158)
T COG5201 28 KNMLCDSTACNYPIPAPNVRSSVLMKVQEWMEHHTSSLSEDENDLEIRKSKPSDFWDRFFMEV-DQEMLLEICLAANYLE 106 (158)
T ss_pred HHHhccccccCCCCcccchhHHHHHHHHHHHHhccccCCCccChHhhhccCCccHHHHHHHHh-hHHHHHHHHHhhcccc
Confidence 567887764 578887 99999999999986 1 8899999 9999999999999999
Q ss_pred hHHHHHHHHHHHHHHhcCCCHHHHHHHhCCCCCCChHHHHHHhhhhC
Q 037688 56 IKEMLDYLTKTLANRIKNKSVEYIRKFFGIQTNFMPEEEEATRKESF 102 (103)
Q Consensus 56 I~~Ll~l~~~~vA~~i~gKt~eeiR~~f~I~~d~t~eee~~i~~e~~ 102 (103)
|++|+++||+.||.||+||||+|||++|||++||||||+++||+||.
T Consensus 107 ikpLLd~gCKivaemirgkSpeeir~tfni~ndfTpEEe~~irkEnE 153 (158)
T COG5201 107 IKPLLDLGCKIVAEMIRGKSPEEIRETFNIENDFTPEEERRIRKENE 153 (158)
T ss_pred chHHHHHHHHHHHHHHccCCHHHHHHHhCCCCCCCHHHHHHHHHhcc
Confidence 99999999999999999999999999999999999999999999984
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=99.95 E-value=1.1e-28 Score=157.26 Aligned_cols=70 Identities=53% Similarity=0.732 Sum_probs=61.6
Q ss_pred hhhcccCCchhHHHHHHHhhhhhchHHHHHHHHHHHHHHhcCCCHHHHHHHhCCCCCCChHHHHHHhhhhC
Q 037688 32 ENEFGKGKSNDELKEMLLVANYLNIKEMLDYLTKTLANRIKNKSVEYIRKFFGIQTNFMPEEEEATRKESF 102 (103)
Q Consensus 32 D~~F~~~~~~~~L~~li~AA~yL~I~~Ll~l~~~~vA~~i~gKt~eeiR~~f~I~~d~t~eee~~i~~e~~ 102 (103)
|++|+++ +.+.|++|+.||+||+|++|+++||++||++++||||+|||++|||++|+|+||++++|++|+
T Consensus 5 D~~F~~~-~~~~L~~l~~AA~yL~I~~L~~~~~~~iA~~i~gks~eeir~~fgi~~d~t~eee~~i~~e~~ 74 (78)
T PF01466_consen 5 DQEFLDV-DNDELFDLLNAANYLDIKGLLDLCCKYIANMIKGKSPEEIRKYFGIENDLTPEEEEEIRKENE 74 (78)
T ss_dssp HHHHT-S--HHHHHHHHHHHHHHT-HHHHHHHHHHHHHHHTTS-HHHHHHHHT---TSSHHHHHHHHHHCC
T ss_pred HHHHHHc-CHHHHHHHHHHHHHHcchHHHHHHHHHHHHHhcCCCHHHHHHHcCCCCCCCHHHHHHHHHHcc
Confidence 8999977 999999999999999999999999999999999999999999999999999999999999986
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=99.47 E-value=2.6e-14 Score=94.54 Aligned_cols=54 Identities=35% Similarity=0.585 Sum_probs=44.8
Q ss_pred CCCCCCCCCC----CccCc-------HHHHHHHHHhcCCcc------------hhhcccCCchhHHHHHHHhhhhhch
Q 037688 2 SSMSDDTSED----MVVPQ-------LPYIIKFCKAHGVSK------------ENEFGKGKSNDELKEMLLVANYLNI 56 (103)
Q Consensus 2 ~~m~e~~~~~----~~IPl-------L~~Vie~c~~h~~~k------------D~~F~~~~~~~~L~~li~AA~yL~I 56 (103)
++|+++.+.. .+||+ |++|++||+||+.++ |++|+++ +++.|++|+.|||||+|
T Consensus 28 ~~~l~~~~~~~~~~~~Ipl~~v~~~~L~~Vi~yc~~h~~~~~~~~~~~~~~~wD~~F~~~-d~~~l~dLl~AAnyL~I 104 (104)
T smart00512 28 KAMIEDLGVDDENNNPIPLPNVTSKILSKVIEYCEHHVDDPPSVADKDDIPTWDAEFLKI-DQETLFELILAANYLDI 104 (104)
T ss_pred HHHHHccCcccCCCCCccCCCcCHHHHHHHHHHHHHcccCCCCccccccccHHHHHHHcC-CHHHHHHHHHHHHhhCC
Confidence 3566665432 47888 999999999998761 8899996 99999999999999997
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=97.99 E-value=8.7e-07 Score=53.75 Aligned_cols=26 Identities=27% Similarity=0.632 Sum_probs=20.7
Q ss_pred CCCCCCCCCC-ccCc-------HHHHHHHHHhcC
Q 037688 3 SMSDDTSEDM-VVPQ-------LPYIIKFCKAHG 28 (103)
Q Consensus 3 ~m~e~~~~~~-~IPl-------L~~Vie~c~~h~ 28 (103)
+|+++.+.++ +||+ |++|++||+||+
T Consensus 28 ~ml~~~~~~~~~Ipl~~v~~~~L~kViewc~~H~ 61 (62)
T PF03931_consen 28 NMLEDLGDEDEPIPLPNVSSRILKKVIEWCEHHK 61 (62)
T ss_dssp HHHHCTCCCGTEEEETTS-HHHHHHHHHHHHHHH
T ss_pred HHHhhhcccccccccCccCHHHHHHHHHHHHhcC
Confidence 5677766544 5888 999999999996
No 6
>PHA02790 Kelch-like protein; Provisional
Probab=94.98 E-value=0.045 Score=44.55 Aligned_cols=49 Identities=6% Similarity=0.059 Sum_probs=40.0
Q ss_pred HHHHHHHHHhcCCcchhhcccCCchhHHHHHHHhhhhhchHHHHHHHHHHHHHHhcC
Q 037688 17 LPYIIKFCKAHGVSKENEFGKGKSNDELKEMLLVANYLNIKEMLDYLTKTLANRIKN 73 (103)
Q Consensus 17 L~~Vie~c~~h~~~kD~~F~~~~~~~~L~~li~AA~yL~I~~Ll~l~~~~vA~~i~g 73 (103)
|+.||+|+-.-+ +.. +.+.+.+|+.||++|+|+.+++.||+.+...+.-
T Consensus 74 l~~lldy~YTg~-------l~i-t~~nV~~ll~aA~~Lqi~~v~~~C~~fL~~~l~~ 122 (480)
T PHA02790 74 LTSIVIYSYTGK-------VYI-DSHNVVNLLRASILTSVEFIIYTCINFILRDFRK 122 (480)
T ss_pred HHHHHHhheeee-------EEE-ecccHHHHHHHHHHhChHHHHHHHHHHHHhhCCc
Confidence 999999973322 445 6788999999999999999999999998876553
No 7
>PHA03098 kelch-like protein; Provisional
Probab=94.72 E-value=0.079 Score=43.08 Aligned_cols=55 Identities=20% Similarity=0.298 Sum_probs=42.0
Q ss_pred HHHHHHHHHhcCCcchhhcccCCchhHHHHHHHhhhhhchHHHHHHHHHHHHHHhcCCCHHHH
Q 037688 17 LPYIIKFCKAHGVSKENEFGKGKSNDELKEMLLVANYLNIKEMLDYLTKTLANRIKNKSVEYI 79 (103)
Q Consensus 17 L~~Vie~c~~h~~~kD~~F~~~~~~~~L~~li~AA~yL~I~~Ll~l~~~~vA~~i~gKt~eei 79 (103)
|+.|++|+-.-. +.. +.+.+.+|+.||++|+++.|.+.|++.+...+.-.+.-++
T Consensus 59 ~~~~l~y~Ytg~-------~~i-~~~~~~~ll~~A~~l~~~~l~~~C~~~l~~~l~~~nc~~~ 113 (534)
T PHA03098 59 FNEVIKYIYTGK-------INI-TSNNVKDILSIANYLIIDFLINLCINYIIKIIDDNNCIDI 113 (534)
T ss_pred HHHHHHHhcCCc-------eEE-cHHHHHHHHHHHHHhCcHHHHHHHHHHHHHhCCHhHHHHH
Confidence 777777765422 344 6678999999999999999999999999887654443333
No 8
>KOG3433 consensus Protein involved in meiotic recombination/predicted coiled-coil protein [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=94.38 E-value=0.1 Score=38.51 Aligned_cols=38 Identities=37% Similarity=0.399 Sum_probs=30.4
Q ss_pred HHhhhh--hchHHHHHHHHHHHHHHhcCCCHHHHHHHhCCCCCCC
Q 037688 48 LLVANY--LNIKEMLDYLTKTLANRIKNKSVEYIRKFFGIQTNFM 90 (103)
Q Consensus 48 i~AA~y--L~I~~Ll~l~~~~vA~~i~gKt~eeiR~~f~I~~d~t 90 (103)
..|||. =||--|.+++|+. .|.-+.+||+.||||+||.
T Consensus 161 ~eaanrwtDnI~il~dy~~rk-----f~~e~nqi~~~fgIPed~d 200 (203)
T KOG3433|consen 161 AEAANRWTDNIFILIDYLYRK-----FGLEPNQIRKEFGIPEDFD 200 (203)
T ss_pred HHHHhhhhhhHHHHHHHHHHh-----cCCCHHHHhHhcCCCcccc
Confidence 345553 3888899999864 4889999999999999984
No 9
>COG5124 Protein predicted to be involved in meiotic recombination [Cell division and chromosome partitioning / General function prediction only]
Probab=93.71 E-value=0.081 Score=39.03 Aligned_cols=31 Identities=42% Similarity=0.532 Sum_probs=26.0
Q ss_pred chHHHHHHHHHHHHHHhcCCCHHHHHHHhCCCCCCC
Q 037688 55 NIKEMLDYLTKTLANRIKNKSVEYIRKFFGIQTNFM 90 (103)
Q Consensus 55 ~I~~Ll~l~~~~vA~~i~gKt~eeiR~~f~I~~d~t 90 (103)
||--|+++.|+. .|..|+|||+.||||+||.
T Consensus 174 nI~ilidy~c~k-----f~~~~~qir~~fgIPedld 204 (209)
T COG5124 174 NIEILIDYLCKK-----FFLKPEQIRKEFGIPEDLD 204 (209)
T ss_pred hHHHHHHHHHHH-----cCCCHHHHHHhcCCCcchh
Confidence 678888877753 4788999999999999974
No 10
>PHA02713 hypothetical protein; Provisional
Probab=93.04 E-value=0.23 Score=41.37 Aligned_cols=56 Identities=14% Similarity=0.263 Sum_probs=45.5
Q ss_pred HHHHHHHHHhcCCcchhhcccCCchhHHHHHHHhhhhhchHHHHHHHHHHHHHHhcCCCHHHHHHH
Q 037688 17 LPYIIKFCKAHGVSKENEFGKGKSNDELKEMLLVANYLNIKEMLDYLTKTLANRIKNKSVEYIRKF 82 (103)
Q Consensus 17 L~~Vie~c~~h~~~kD~~F~~~~~~~~L~~li~AA~yL~I~~Ll~l~~~~vA~~i~gKt~eeiR~~ 82 (103)
|+.|++|+-.. + ++.+.+.+|+.||++|+|+.|.+.||..+...+.-.+-=+|...
T Consensus 79 ~~~ll~y~Yt~---------~-i~~~nv~~ll~aA~~lqi~~l~~~C~~~l~~~l~~~NCl~i~~~ 134 (557)
T PHA02713 79 VKNIVQYLYNR---------H-ISSMNVIDVLKCADYLLIDDLVTDCESYIKDYTNHDTCIYMYHR 134 (557)
T ss_pred HHHHHHHhcCC---------C-CCHHHHHHHHHHHHHHCHHHHHHHHHHHHHhhCCccchHHHHHH
Confidence 88888887552 1 36778999999999999999999999999988777666666543
No 11
>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=92.97 E-value=0.11 Score=30.74 Aligned_cols=40 Identities=18% Similarity=0.348 Sum_probs=31.9
Q ss_pred HHHHHHHHHhcCCcchhhcccCCchhHHHHHHHhhhhhchHHHHHHHH
Q 037688 17 LPYIIKFCKAHGVSKENEFGKGKSNDELKEMLLVANYLNIKEMLDYLT 64 (103)
Q Consensus 17 L~~Vie~c~~h~~~kD~~F~~~~~~~~L~~li~AA~yL~I~~Ll~l~~ 64 (103)
++.+++|+-.-. +.. ....+.+++.+|.++++++|.+.|+
T Consensus 51 f~~~l~~ly~~~-------~~~-~~~~~~~l~~~a~~~~~~~l~~~c~ 90 (90)
T smart00225 51 FRALLEFLYTGK-------LDL-PEENVEELLELADYLQIPGLVELCE 90 (90)
T ss_pred HHHHHHeecCce-------eec-CHHHHHHHHHHHHHHCcHHHHhhhC
Confidence 888999987632 233 4558899999999999999998874
No 12
>KOG3473 consensus RNA polymerase II transcription elongation factor Elongin/SIII, subunit elongin C [Transcription]
Probab=92.25 E-value=0.18 Score=33.94 Aligned_cols=42 Identities=24% Similarity=0.304 Sum_probs=31.6
Q ss_pred ccCc--HHHHHHHHHhcCCcc-----hhhcccCCchhHHHHHHHhhhhhch
Q 037688 13 VVPQ--LPYIIKFCKAHGVSK-----ENEFGKGKSNDELKEMLLVANYLNI 56 (103)
Q Consensus 13 ~IPl--L~~Vie~c~~h~~~k-----D~~F~~~~~~~~L~~li~AA~yL~I 56 (103)
.||- |.||.+|..+....+ -.+| ++ ..++.++|+.|||||++
T Consensus 64 di~shiLeKvc~Yl~Yk~rY~~~s~eiPeF-~I-ppemaleLL~aAn~Lec 112 (112)
T KOG3473|consen 64 DIPSHILEKVCEYLAYKVRYTNSSTEIPEF-DI-PPEMALELLMAANYLEC 112 (112)
T ss_pred cchHHHHHHHHHHhhheeeeccccccCCCC-CC-CHHHHHHHHHHhhhhcC
Confidence 4564 999999997644332 2354 56 78999999999999974
No 13
>KOG4441 consensus Proteins containing BTB/POZ and Kelch domains, involved in regulatory/signal transduction processes [Signal transduction mechanisms; General function prediction only]
Probab=91.29 E-value=0.43 Score=40.08 Aligned_cols=48 Identities=23% Similarity=0.354 Sum_probs=39.2
Q ss_pred HHHHHHHHHhcCCcchhhcccCCchhHHHHHHHhhhhhchHHHHHHHHHHHHHHhc
Q 037688 17 LPYIIKFCKAHGVSKENEFGKGKSNDELKEMLLVANYLNIKEMLDYLTKTLANRIK 72 (103)
Q Consensus 17 L~~Vie~c~~h~~~kD~~F~~~~~~~~L~~li~AA~yL~I~~Ll~l~~~~vA~~i~ 72 (103)
|+.+++|+-... +.. +.+.+-+|+.||.+|+|+++.+.||..+...+-
T Consensus 88 l~~ll~y~Yt~~-------i~i-~~~nVq~ll~aA~~lQi~~v~~~C~~fL~~~l~ 135 (571)
T KOG4441|consen 88 LELLLDYAYTGK-------LEI-SEDNVQELLEAASLLQIPEVVDACCEFLESQLD 135 (571)
T ss_pred HHHHHHHhhcce-------EEe-chHhHHHHHHHHHHhhhHHHHHHHHHHHHhcCC
Confidence 777777765533 555 788999999999999999999999998877544
No 14
>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=91.25 E-value=0.55 Score=29.65 Aligned_cols=45 Identities=18% Similarity=0.249 Sum_probs=36.4
Q ss_pred HHHHHHHHHhcCCcchhhcccCCc-hhHHHHHHHhhhhhchHHHHHHHHHHHHH
Q 037688 17 LPYIIKFCKAHGVSKENEFGKGKS-NDELKEMLLVANYLNIKEMLDYLTKTLAN 69 (103)
Q Consensus 17 L~~Vie~c~~h~~~kD~~F~~~~~-~~~L~~li~AA~yL~I~~Ll~l~~~~vA~ 69 (103)
+..+++||-... +.. + .+.+.+++..|++++++.|.+.|+..+..
T Consensus 64 ~~~~l~~~Y~~~-------~~~-~~~~~~~~ll~lA~~~~~~~L~~~~~~~l~~ 109 (111)
T PF00651_consen 64 FEAFLEYMYTGE-------IEI-NSDENVEELLELADKLQIPELKKACEKFLQE 109 (111)
T ss_dssp HHHHHHHHHHSE-------EEE-E-TTTHHHHHHHHHHTTBHHHHHHHHHHHHH
T ss_pred cccccccccCCc-------ccC-CHHHHHHHHHHHHHHhCcHHHHHHHHHHHHh
Confidence 999999994311 222 3 67899999999999999999999998754
No 15
>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=88.32 E-value=0.68 Score=33.75 Aligned_cols=43 Identities=40% Similarity=0.410 Sum_probs=32.9
Q ss_pred HHHHHHHhhhhh--chHHHHHHHHHHHHHHhcCCCHHHHHHHhCCCCCCC
Q 037688 43 ELKEMLLVANYL--NIKEMLDYLTKTLANRIKNKSVEYIRKFFGIQTNFM 90 (103)
Q Consensus 43 ~L~~li~AA~yL--~I~~Ll~l~~~~vA~~i~gKt~eeiR~~f~I~~d~t 90 (103)
.+.....|||.- ||-.|..++++. .|.+.+++|+.||||+||.
T Consensus 143 ~~~~~~~~anrwTDNI~~l~~~~~~k-----~~~~~~~i~k~f~Ip~d~d 187 (188)
T PF03962_consen 143 EIKIAKEAANRWTDNIFSLKSYLKKK-----FGMDEEDIRKEFGIPEDFD 187 (188)
T ss_pred HHHHHHHHHHHHHhhHHHHHHHHHHh-----cCCCHHHHHHHcCCccccC
Confidence 344455577665 777888877763 5899999999999999984
No 16
>KOG2716 consensus Polymerase delta-interacting protein PDIP1 and related proteins, contain BTB/POZ domain [Inorganic ion transport and metabolism]
Probab=81.88 E-value=3.4 Score=31.35 Aligned_cols=52 Identities=21% Similarity=0.292 Sum_probs=41.4
Q ss_pred HHHHHHHHHhcCCcchhhcccCCchhHHHHHHHhhhhhchHHHHHHHHHHHHHHhcCC
Q 037688 17 LPYIIKFCKAHGVSKENEFGKGKSNDELKEMLLVANYLNIKEMLDYLTKTLANRIKNK 74 (103)
Q Consensus 17 L~~Vie~c~~h~~~kD~~F~~~~~~~~L~~li~AA~yL~I~~Ll~l~~~~vA~~i~gK 74 (103)
+..|+.|++-=. ..+=. +...|-+|..=|.|..+.+|+++|..+++..+++.
T Consensus 57 F~~ILNfmRdGd-----v~LPe-~~kel~El~~EA~fYlL~~Lv~~C~~~i~~~~~~~ 108 (230)
T KOG2716|consen 57 FDTILNFMRDGD-----VDLPE-SEKELKELLREAEFYLLDGLVELCQSAIARLIRGY 108 (230)
T ss_pred HHHHHHhhhccc-----ccCcc-chHHHHHHHHHHHHhhHHHHHHHHHHHhhhcccCc
Confidence 888888876311 11333 56789999999999999999999999999998874
No 17
>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=74.97 E-value=6.2 Score=22.71 Aligned_cols=34 Identities=18% Similarity=0.249 Sum_probs=23.7
Q ss_pred HHHHHHHhcCCCHHHHHHHhCC------C-CCCChHHHHHH
Q 037688 64 TKTLANRIKNKSVEYIRKFFGI------Q-TNFMPEEEEAT 97 (103)
Q Consensus 64 ~~~vA~~i~gKt~eeiR~~f~I------~-~d~t~eee~~i 97 (103)
=..||..+..+|+.+++..|.- . ..+|++|++++
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 4578888844999999887652 2 25888888764
No 18
>KOG4682 consensus Uncharacterized conserved protein, contains BTB/POZ domain [General function prediction only]
Probab=73.10 E-value=4.9 Score=33.28 Aligned_cols=47 Identities=9% Similarity=0.215 Sum_probs=35.6
Q ss_pred chhHHHHHHHhhhhhchHHHHHHHHHHHHHHhcCCCHHHHHHHhCCCCCC
Q 037688 40 SNDELKEMLLVANYLNIKEMLDYLTKTLANRIKNKSVEYIRKFFGIQTNF 89 (103)
Q Consensus 40 ~~~~L~~li~AA~yL~I~~Ll~l~~~~vA~~i~gKt~eeiR~~f~I~~d~ 89 (103)
+.+.+..++.||.+|..++|++-|...+-..+ ||+-+.+++....-|
T Consensus 139 ~l~dv~gvlAaA~~lqldgl~qrC~evMie~l---spkta~~yYea~ckY 185 (488)
T KOG4682|consen 139 KLSDVVGVLAAACLLQLDGLIQRCGEVMIETL---SPKTACGYYEAACKY 185 (488)
T ss_pred cHHHHHHHHHHHHHHHHhhHHHHHHHHHHHhc---ChhhhhHhhhhhhhh
Confidence 66789999999999999999999998765555 444555665554433
No 19
>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=72.57 E-value=3.3 Score=28.63 Aligned_cols=27 Identities=15% Similarity=0.294 Sum_probs=14.5
Q ss_pred HhcCCCHHHHHHHhCCCCCCChHHHHH
Q 037688 70 RIKNKSVEYIRKFFGIQTNFMPEEEEA 96 (103)
Q Consensus 70 ~i~gKt~eeiR~~f~I~~d~t~eee~~ 96 (103)
..+|+|++|-++++||++..++|+-.+
T Consensus 51 ~~~~Mtl~EA~~ILnv~~~~~~eeI~k 77 (127)
T PF03656_consen 51 NSKGMTLDEARQILNVKEELSREEIQK 77 (127)
T ss_dssp ------HHHHHHHHT--G--SHHHHHH
T ss_pred hcCCCCHHHHHHHcCCCCccCHHHHHH
Confidence 356899999999999999888877543
No 20
>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=66.67 E-value=3.1 Score=32.97 Aligned_cols=32 Identities=6% Similarity=0.321 Sum_probs=27.3
Q ss_pred chhHHHHHHHhhhhhchHHHHHHHHHHHHHHh
Q 037688 40 SNDELKEMLLVANYLNIKEMLDYLTKTLANRI 71 (103)
Q Consensus 40 ~~~~L~~li~AA~yL~I~~Ll~l~~~~vA~~i 71 (103)
+.+...-|+..|+||++++|++-|-.++...+
T Consensus 73 ~~~NvvsIliSS~FL~M~~Lve~cl~y~~~~~ 104 (317)
T PF11822_consen 73 TPSNVVSILISSEFLQMESLVEECLQYCHDHM 104 (317)
T ss_pred CcCcEEEeEehhhhhccHHHHHHHHHHHHHhH
Confidence 66778889999999999999999988875544
No 21
>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=66.22 E-value=7.6 Score=20.10 Aligned_cols=21 Identities=10% Similarity=0.207 Sum_probs=17.2
Q ss_pred HHHHHHHhcCCCHHHHHHHhC
Q 037688 64 TKTLANRIKNKSVEYIRKFFG 84 (103)
Q Consensus 64 ~~~vA~~i~gKt~eeiR~~f~ 84 (103)
-..||..+.++|+.+++..+.
T Consensus 22 w~~Ia~~~~~rs~~~~~~~~~ 42 (45)
T cd00167 22 WEKIAKELPGRTPKQCRERWR 42 (45)
T ss_pred HHHHHhHcCCCCHHHHHHHHH
Confidence 367888888899999998764
No 22
>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=65.51 E-value=9.1 Score=21.20 Aligned_cols=21 Identities=19% Similarity=0.306 Sum_probs=17.7
Q ss_pred HHHHHHHHhc-CCCHHHHHHHh
Q 037688 63 LTKTLANRIK-NKSVEYIRKFF 83 (103)
Q Consensus 63 ~~~~vA~~i~-gKt~eeiR~~f 83 (103)
--..||..+. |+|+.++|..|
T Consensus 23 ~W~~Ia~~~~~~Rt~~qc~~~~ 44 (48)
T PF00249_consen 23 NWKKIAKRMPGGRTAKQCRSRY 44 (48)
T ss_dssp HHHHHHHHHSSSSTHHHHHHHH
T ss_pred HHHHHHHHcCCCCCHHHHHHHH
Confidence 3567888888 99999999876
No 23
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=63.76 E-value=9.1 Score=20.06 Aligned_cols=21 Identities=14% Similarity=0.297 Sum_probs=17.2
Q ss_pred HHHHHHHhcCCCHHHHHHHhC
Q 037688 64 TKTLANRIKNKSVEYIRKFFG 84 (103)
Q Consensus 64 ~~~vA~~i~gKt~eeiR~~f~ 84 (103)
-..||..+.++|+.+++..+.
T Consensus 24 w~~Ia~~~~~rt~~~~~~~~~ 44 (49)
T smart00717 24 WEKIAKELPGRTAEQCRERWN 44 (49)
T ss_pred HHHHHHHcCCCCHHHHHHHHH
Confidence 356788888999999998774
No 24
>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=63.69 E-value=11 Score=22.48 Aligned_cols=31 Identities=19% Similarity=0.057 Sum_probs=24.4
Q ss_pred CCCHHHHHHH----hCCCCCCChHHHHHHhhhhCC
Q 037688 73 NKSVEYIRKF----FGIQTNFMPEEEEATRKESFD 103 (103)
Q Consensus 73 gKt~eeiR~~----f~I~~d~t~eee~~i~~e~~~ 103 (103)
.+|.+|+-.. .||+..||.-=-.+++++|++
T Consensus 12 yMsk~E~v~~L~~~a~I~P~~T~~VW~~Le~eN~e 46 (54)
T PF09713_consen 12 YMSKEECVRALQKQANIEPVFTSTVWQKLEKENPE 46 (54)
T ss_pred cCCHHHHHHHHHHHcCCChHHHHHHHHHHHHHCHH
Confidence 4666666544 489999999999999999874
No 25
>PF01843 DIL: DIL domain; InterPro: IPR018444 Dilute encodes a novel type of myosin heavy chain, with a tail, or C-terminal, region that has elements of both type II (alpha-helical coiled-coil) and type I (non-coiled-coil) myosin heavy chains. The DIL non alpha-helical domain is found in dilute myosin heavy chain proteins and other myosins. In mouse the dilute protein may play a role in the elaboration, maintenance, or function of cellular processes of melanocytes and neurons []. The MYO2 protein of Saccharomyces cerevisiae is implicated in vectorial vesicle transport and is homologous to the dilute protein over practically its entire length [].; PDB: 3MMI_B 2F6H_X.
Probab=63.25 E-value=1.7 Score=28.20 Aligned_cols=60 Identities=20% Similarity=0.358 Sum_probs=36.1
Q ss_pred HHHHHHHHHhcCCcchhhcccCCchhHHHHHHHhhhhhchHH-HHHHHHHHHHHHhcCCCHHHHHHHhC
Q 037688 17 LPYIIKFCKAHGVSKENEFGKGKSNDELKEMLLVANYLNIKE-MLDYLTKTLANRIKNKSVEYIRKFFG 84 (103)
Q Consensus 17 L~~Vie~c~~h~~~kD~~F~~~~~~~~L~~li~AA~yL~I~~-Ll~l~~~~vA~~i~gKt~eeiR~~f~ 84 (103)
|..|-+||+.+.- ...-...|-.+.+||+.|.++. .++ --..+-..--.-||.+|++.+.
T Consensus 37 ls~l~~W~~~~~l-------~~~~~~~l~~l~Qa~~lL~~~k~~~~-d~~~~~~~c~~Ln~~Qi~~iL~ 97 (105)
T PF01843_consen 37 LSELEDWARSHGL-------EEAAEEHLQPLSQAANLLQLRKSTLQ-DWDSLRETCPSLNPAQIRKILS 97 (105)
T ss_dssp HHHHHHCCCCTTS-------TTH-HHHCHHHHHHHHHCCC--SSHH-HHHHHCCCTTTS-HHHHHHHHC
T ss_pred HHHHHHHHHhccc-------chhHHHHHHHHHHHHHHHHhcCcchh-HHHHHHHHcccCCHHHHHHHHH
Confidence 7888899988762 2202567788999999999842 222 2222222333467888877765
No 26
>PRK05365 malonic semialdehyde reductase; Provisional
Probab=62.22 E-value=6.4 Score=27.98 Aligned_cols=34 Identities=15% Similarity=0.175 Sum_probs=26.2
Q ss_pred HHHhhhhhchHHHHHHHHHHHHHHhcCCCHHHHHHHhCCCCCCC
Q 037688 47 MLLVANYLNIKEMLDYLTKTLANRIKNKSVEYIRKFFGIQTNFM 90 (103)
Q Consensus 47 li~AA~yL~I~~Ll~l~~~~vA~~i~gKt~eeiR~~f~I~~d~t 90 (103)
|+.||.-+|+.. | .+.|-..+.+++.|||++++.
T Consensus 131 l~LaA~~~Glgs-----~-----~~~g~~~~~v~~~l~ip~~~~ 164 (195)
T PRK05365 131 LILAARALGLDA-----G-----PMSGFDAAAVDAEFFAGTTWK 164 (195)
T ss_pred HHHHHHHcCCcc-----C-----CccccCHHHHHHHhCCCCCee
Confidence 777888887766 1 345678899999999997753
No 27
>PF12556 CobS_N: Cobaltochelatase CobS subunit N terminal
Probab=61.71 E-value=4.8 Score=22.06 Aligned_cols=12 Identities=33% Similarity=0.875 Sum_probs=10.6
Q ss_pred HHHHhCCCCCCC
Q 037688 79 IRKFFGIQTNFM 90 (103)
Q Consensus 79 iR~~f~I~~d~t 90 (103)
+|+.|||..|++
T Consensus 14 vre~FGiDsDm~ 25 (36)
T PF12556_consen 14 VREVFGIDSDMK 25 (36)
T ss_pred HHHhcCCCcCCe
Confidence 699999999975
No 28
>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=61.37 E-value=6 Score=27.16 Aligned_cols=28 Identities=18% Similarity=0.269 Sum_probs=24.8
Q ss_pred HHHhhhhhchHHHHHHHHHHHHHHhcCC
Q 037688 47 MLLVANYLNIKEMLDYLTKTLANRIKNK 74 (103)
Q Consensus 47 li~AA~yL~I~~Ll~l~~~~vA~~i~gK 74 (103)
--.|+....++..+..+|+++|++|+|.
T Consensus 36 ~~~~~k~F~VpDFVGd~Ck~iaSRIR~a 63 (118)
T PF11978_consen 36 PEDAAKLFSVPDFVGDACKAIASRIRGA 63 (118)
T ss_dssp HHHHHHTTSSTTHHHHHHHHHHHHHHHH
T ss_pred hhHHHHhcCCcchHHHHHHHHHHHHHHH
Confidence 3478889999999999999999999984
No 29
>PF13798 PCYCGC: Protein of unknown function with PCYCGC motif
Probab=60.03 E-value=14 Score=26.62 Aligned_cols=24 Identities=25% Similarity=0.343 Sum_probs=17.7
Q ss_pred HHHHHHHHHHHhcCCCHHHHHHHh
Q 037688 60 LDYLTKTLANRIKNKSVEYIRKFF 83 (103)
Q Consensus 60 l~l~~~~vA~~i~gKt~eeiR~~f 83 (103)
++.+...+...=+|||+.|||++-
T Consensus 118 l~ia~~a~~~~~~Gks~~eIR~~I 141 (158)
T PF13798_consen 118 LDIAVQAVQMYQEGKSPKEIRQYI 141 (158)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHH
Confidence 344556666666899999999874
No 30
>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=59.35 E-value=7.6 Score=27.32 Aligned_cols=34 Identities=15% Similarity=0.154 Sum_probs=25.9
Q ss_pred HHHhhhhhchHHHHHHHHHHHHHHhcCCCHHHHHHHhCCCCCCC
Q 037688 47 MLLVANYLNIKEMLDYLTKTLANRIKNKSVEYIRKFFGIQTNFM 90 (103)
Q Consensus 47 li~AA~yL~I~~Ll~l~~~~vA~~i~gKt~eeiR~~f~I~~d~t 90 (103)
++.||.-||+..- ++.|-..+++++.||+++++.
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 7777777777651 356678899999999998763
No 31
>PRK11053 dihydropteridine reductase; Provisional
Probab=57.21 E-value=9.7 Score=27.45 Aligned_cols=34 Identities=24% Similarity=0.357 Sum_probs=23.5
Q ss_pred HHHHhhhhhchHHHHHHHHHHHHHHhcCCCHHHHHHHhCCCC-CC
Q 037688 46 EMLLVANYLNIKEMLDYLTKTLANRIKNKSVEYIRKFFGIQT-NF 89 (103)
Q Consensus 46 ~li~AA~yL~I~~Ll~l~~~~vA~~i~gKt~eeiR~~f~I~~-d~ 89 (103)
.|+.||.-||+.+- .+.|-.++.+++.|||++ ++
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 55556666555432 345678999999999985 55
No 32
>PF15063 TC1: Thyroid cancer protein 1
Probab=56.83 E-value=13 Score=23.82 Aligned_cols=33 Identities=21% Similarity=0.301 Sum_probs=21.5
Q ss_pred HHHHHHhcCCCHHHHHHHhCCCCCCChHHHHHH
Q 037688 65 KTLANRIKNKSVEYIRKFFGIQTNFMPEEEEAT 97 (103)
Q Consensus 65 ~~vA~~i~gKt~eeiR~~f~I~~d~t~eee~~i 97 (103)
+.+|+...+-..+++++.|.-..|--.||-++|
T Consensus 28 kasaNIFe~vn~~qlqrLF~~sGD~kAEeRA~i 60 (79)
T PF15063_consen 28 KASANIFENVNLDQLQRLFQKSGDKKAEERARI 60 (79)
T ss_pred hhhhhhhhccCHHHHHHHHHHccchhHHHHHHH
Confidence 346666677777777777776666666665554
No 33
>PRK11325 scaffold protein; Provisional
Probab=56.07 E-value=19 Score=24.43 Aligned_cols=37 Identities=8% Similarity=0.012 Sum_probs=23.3
Q ss_pred HHhhhhhchHHHHHHH-HHHHHHHhcCCCHHHHHHHhC
Q 037688 48 LLVANYLNIKEMLDYL-TKTLANRIKNKSVEYIRKFFG 84 (103)
Q Consensus 48 i~AA~yL~I~~Ll~l~-~~~vA~~i~gKt~eeiR~~f~ 84 (103)
|.-+.|-.-=.-+-.+ +..++.+++|||++|.+.+-+
T Consensus 53 I~d~~f~~~GC~is~Asas~~~e~~~Gktl~ea~~i~~ 90 (127)
T PRK11325 53 IEDAKFKTYGCGSAIASSSLVTEWVKGKTLDEALAIKN 90 (127)
T ss_pred EEEEEEEeeCCHHHHHHHHHHHHHHcCCCHHHHHhcCH
Confidence 3344444443344444 455778899999999987744
No 34
>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=55.63 E-value=21 Score=23.88 Aligned_cols=38 Identities=11% Similarity=0.075 Sum_probs=24.0
Q ss_pred HHHhhhhhchHHHHHHH-HHHHHHHhcCCCHHHHHHHhC
Q 037688 47 MLLVANYLNIKEMLDYL-TKTLANRIKNKSVEYIRKFFG 84 (103)
Q Consensus 47 li~AA~yL~I~~Ll~l~-~~~vA~~i~gKt~eeiR~~f~ 84 (103)
.|.-+.|-.--.-+-.+ +..++.+++|||++|..++..
T Consensus 46 ~I~d~~f~~~GC~is~Asas~~~e~i~Gk~l~ea~~i~~ 84 (121)
T TIGR03419 46 IIKDVKFKTFGCGAAIASSSMATEMIKGKTLEEAWELTN 84 (121)
T ss_pred EEEEEEEEEeccHHHHHHHHHHHHHHcCCCHHHHHHhhh
Confidence 34444444444444444 455778899999999877643
No 35
>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=55.33 E-value=17 Score=24.42 Aligned_cols=21 Identities=24% Similarity=0.148 Sum_probs=16.4
Q ss_pred HHHHHHHHHHhcCCCHHHHHH
Q 037688 61 DYLTKTLANRIKNKSVEYIRK 81 (103)
Q Consensus 61 ~l~~~~vA~~i~gKt~eeiR~ 81 (103)
-.++..++.+++|||++|+.+
T Consensus 65 ~Asas~~~~~i~gk~l~ea~~ 85 (126)
T PF01592_consen 65 IASASMMCELIKGKTLEEALK 85 (126)
T ss_dssp HHHHHHHHHHHTTSBHHHHHC
T ss_pred HHHHHHHHHHHcCCCHHHHHH
Confidence 345667888999999998854
No 36
>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=55.04 E-value=20 Score=24.05 Aligned_cols=37 Identities=19% Similarity=0.050 Sum_probs=23.5
Q ss_pred HHhhhhhchHHHHHHH-HHHHHHHhcCCCHHHHHHHhC
Q 037688 48 LLVANYLNIKEMLDYL-TKTLANRIKNKSVEYIRKFFG 84 (103)
Q Consensus 48 i~AA~yL~I~~Ll~l~-~~~vA~~i~gKt~eeiR~~f~ 84 (103)
|.-+.|-.--.-.-.+ +..++.+++|||++|.+.+-.
T Consensus 51 I~d~~f~~~GC~~s~Asas~~~e~i~Gktl~ea~~i~~ 88 (124)
T TIGR01999 51 IEDAKFKTFGCGSAIASSSLATELIKGKSLEEALKIKN 88 (124)
T ss_pred EEEEEEEecCcHHHHHHHHHHHHHHcCCCHHHHHhccH
Confidence 3334444433334444 466788999999999987754
No 37
>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=54.20 E-value=18 Score=22.52 Aligned_cols=41 Identities=20% Similarity=0.333 Sum_probs=27.8
Q ss_pred HHHHHHHHHhcCCcchhhcccCCchhHHHHHHHhhhhhchHHH-HHHH
Q 037688 17 LPYIIKFCKAHGVSKENEFGKGKSNDELKEMLLVANYLNIKEM-LDYL 63 (103)
Q Consensus 17 L~~Vie~c~~h~~~kD~~F~~~~~~~~L~~li~AA~yL~I~~L-l~l~ 63 (103)
++.|+.|++.-. -+..-+...+..+...|.|.+|+.| ++.|
T Consensus 53 F~~IL~ylr~~~------~l~~~~~~~~~~l~~Ea~fy~l~~l~i~~c 94 (94)
T PF02214_consen 53 FEYILNYLRTGG------KLPIPDEICLEELLEEAEFYGLDELFIEDC 94 (94)
T ss_dssp HHHHHHHHHHTS------SB---TTS-HHHHHHHHHHHT-HHHHBHHC
T ss_pred hhHHHHHHhhcC------ccCCCCchhHHHHHHHHHHcCCCccccCCC
Confidence 899999998731 1222134577899999999999999 6654
No 38
>KOG3442 consensus Uncharacterized conserved protein [Function unknown]
Probab=54.13 E-value=14 Score=25.72 Aligned_cols=25 Identities=12% Similarity=0.211 Sum_probs=21.0
Q ss_pred cCCCHHHHHHHhCCCCCCChHHHHH
Q 037688 72 KNKSVEYIRKFFGIQTNFMPEEEEA 96 (103)
Q Consensus 72 ~gKt~eeiR~~f~I~~d~t~eee~~ 96 (103)
.|.|.+|-++++||.+++.++|.++
T Consensus 54 ~~iTlqEa~qILnV~~~ln~eei~k 78 (132)
T KOG3442|consen 54 GKITLQEAQQILNVKEPLNREEIEK 78 (132)
T ss_pred ccccHHHHhhHhCCCCCCCHHHHHH
Confidence 4579999999999999888877654
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=53.64 E-value=28 Score=24.76 Aligned_cols=62 Identities=16% Similarity=0.226 Sum_probs=42.1
Q ss_pred HHHhcCCc---c------h--hhcccCCchhHHHHHHHhhhhhchHHHHHHHHHHHHHHhcC-CCHHHHHHHhCCC
Q 037688 23 FCKAHGVS---K------E--NEFGKGKSNDELKEMLLVANYLNIKEMLDYLTKTLANRIKN-KSVEYIRKFFGIQ 86 (103)
Q Consensus 23 ~c~~h~~~---k------D--~~F~~~~~~~~L~~li~AA~yL~I~~Ll~l~~~~vA~~i~g-Kt~eeiR~~f~I~ 86 (103)
||..|+.. + | -+|++. +.+.+-=+=.==.||.++. ....++.+-..+.| .|+.++-..+|-+
T Consensus 61 rC~FHkkyif~~~~~~~~deYv~fLNS-eMGiIS~VElYY~yLs~~~-wk~~a~~~l~dLTgF~s~~~LL~~Yny~ 134 (148)
T PF06851_consen 61 RCDFHKKYIFTKDRKTHYDEYVEFLNS-EMGIISFVELYYTYLSVDF-WKITAKRVLRDLTGFESLKDLLTHYNYE 134 (148)
T ss_pred hhhHhHhhhccCCcccCHHHHHHHHcc-ccchhhhHHHHHHHHcccc-cHHHHHHHHHHhhCcccHHHHHHHcCCC
Confidence 88888876 2 3 277775 4443332333346777765 77788887777888 8899998888866
No 40
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=49.29 E-value=19 Score=24.95 Aligned_cols=19 Identities=21% Similarity=0.308 Sum_probs=14.8
Q ss_pred HHHHHHhc-CCCHHHHHHHh
Q 037688 65 KTLANRIK-NKSVEYIRKFF 83 (103)
Q Consensus 65 ~~vA~~i~-gKt~eeiR~~f 83 (103)
..|..++. |+|.+||+++|
T Consensus 64 ~~Vr~~i~~G~Sd~eI~~~~ 83 (126)
T TIGR03147 64 HEVYSMVNEGKSNQQIIDFM 83 (126)
T ss_pred HHHHHHHHcCCCHHHHHHHH
Confidence 45666655 99999999887
No 41
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=49.17 E-value=47 Score=19.87 Aligned_cols=35 Identities=20% Similarity=0.353 Sum_probs=19.7
Q ss_pred HHHHHHhhhhhchHHHHHHHHHHHHHHhcCCCHHHHHHHhC
Q 037688 44 LKEMLLVANYLNIKEMLDYLTKTLANRIKNKSVEYIRKFFG 84 (103)
Q Consensus 44 L~~li~AA~yL~I~~Ll~l~~~~vA~~i~gKt~eeiR~~f~ 84 (103)
|-+-..+-.+|.=..|-.||-+ .|.|.++||..|.
T Consensus 13 L~~Yy~~h~~L~E~DL~~L~~k------S~ms~qqVr~WFa 47 (56)
T PF11569_consen 13 LEDYYLKHKQLQEEDLDELCDK------SRMSYQQVRDWFA 47 (56)
T ss_dssp HHHHHHHT----TTHHHHHHHH------TT--HHHHHHHHH
T ss_pred HHHHHHHcCCccHhhHHHHHHH------HCCCHHHHHHHHH
Confidence 4444455555555556666654 7899999999995
No 42
>PF11103 DUF2887: Protein of unknown function (DUF2887); InterPro: IPR022573 This bacterial group of proteins has no known function.
Probab=48.12 E-value=28 Score=25.82 Aligned_cols=29 Identities=21% Similarity=0.345 Sum_probs=26.1
Q ss_pred chHHHHHHHHHHHHHHhcCCCHHHHHHHh
Q 037688 55 NIKEMLDYLTKTLANRIKNKSVEYIRKFF 83 (103)
Q Consensus 55 ~I~~Ll~l~~~~vA~~i~gKt~eeiR~~f 83 (103)
.=..|+++.-..++.+...+|.|||.+||
T Consensus 172 ~~~~lleLIEtIlvyKfp~lSreEIeaMl 200 (200)
T PF11103_consen 172 QQRELLELIETILVYKFPQLSREEIEAML 200 (200)
T ss_pred HHHHHHHHHHHHHHHHccccCHHHHHHhC
Confidence 45679999999999999999999999987
No 43
>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=47.29 E-value=35 Score=22.44 Aligned_cols=38 Identities=16% Similarity=0.204 Sum_probs=24.5
Q ss_pred HHHhhhhhchHHHHHHH-HHHHHHHhcCCCHHHHHHHhC
Q 037688 47 MLLVANYLNIKEMLDYL-TKTLANRIKNKSVEYIRKFFG 84 (103)
Q Consensus 47 li~AA~yL~I~~Ll~l~-~~~vA~~i~gKt~eeiR~~f~ 84 (103)
.+..+.|-.--..+-.+ +..++.+++|||++|+..+.+
T Consensus 47 ~I~d~~f~~~GC~i~~Asas~~~~~~~Gk~~~ea~~i~~ 85 (123)
T cd06664 47 RITDAKFQGFGCAISIASASLLTELIKGKTLDEALKLLN 85 (123)
T ss_pred EEEEEEEEecCcHHHHHHHHHHHHHHcCCcHHHHHHHHH
Confidence 44444444444444444 445778899999999988764
No 44
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=47.00 E-value=18 Score=25.68 Aligned_cols=19 Identities=11% Similarity=0.247 Sum_probs=17.3
Q ss_pred cCCCHHHHHHHhCCCCCCC
Q 037688 72 KNKSVEYIRKFFGIQTNFM 90 (103)
Q Consensus 72 ~gKt~eeiR~~f~I~~d~t 90 (103)
-|.||+|-|.-+|++.||.
T Consensus 97 ~gmTPd~YR~KW~LP~dYP 115 (148)
T COG4957 97 YGLTPDEYRAKWGLPPDYP 115 (148)
T ss_pred cCCCHHHHHHhcCCCCCCC
Confidence 3899999999999999985
No 45
>COG0822 IscU NifU homolog involved in Fe-S cluster formation [Energy production and conversion]
Probab=45.62 E-value=37 Score=23.88 Aligned_cols=35 Identities=11% Similarity=0.125 Sum_probs=21.6
Q ss_pred HhhhhhchHHHHHH-HHHHHHHHhcCCCHHHHHHHh
Q 037688 49 LVANYLNIKEMLDY-LTKTLANRIKNKSVEYIRKFF 83 (103)
Q Consensus 49 ~AA~yL~I~~Ll~l-~~~~vA~~i~gKt~eeiR~~f 83 (103)
..|.|...=.=+-. .+..+..+++|||.+|.+++-
T Consensus 55 ~d~~F~~~GC~is~ASss~~te~v~Gkti~EAl~i~ 90 (150)
T COG0822 55 EDAKFKGFGCAISIASSSMMTELVKGKTLDEALKIT 90 (150)
T ss_pred EEEEeeecCcHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 33444443333333 344567789999999998876
No 46
>PF13518 HTH_28: Helix-turn-helix domain
Probab=45.60 E-value=39 Score=18.30 Aligned_cols=21 Identities=29% Similarity=0.403 Sum_probs=16.7
Q ss_pred HHHHHhcCCCHHHHHHHhCCC
Q 037688 66 TLANRIKNKSVEYIRKFFGIQ 86 (103)
Q Consensus 66 ~vA~~i~gKt~eeiR~~f~I~ 86 (103)
.|.....|.|..++-+.|||.
T Consensus 5 iv~~~~~g~s~~~~a~~~gis 25 (52)
T PF13518_consen 5 IVELYLEGESVREIAREFGIS 25 (52)
T ss_pred HHHHHHcCCCHHHHHHHHCCC
Confidence 344556789999999999994
No 47
>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=45.58 E-value=26 Score=21.20 Aligned_cols=25 Identities=24% Similarity=0.408 Sum_probs=19.0
Q ss_pred HHHHHHHhC-CCCC-CChHHHHHHhhh
Q 037688 76 VEYIRKFFG-IQTN-FMPEEEEATRKE 100 (103)
Q Consensus 76 ~eeiR~~f~-I~~d-~t~eee~~i~~e 100 (103)
.+++|.-|| |=.+ +||||..+|.+.
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 4455 899999998764
No 48
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=44.52 E-value=28 Score=19.00 Aligned_cols=16 Identities=25% Similarity=0.339 Sum_probs=10.7
Q ss_pred cCCCHHHHHHHhCCCC
Q 037688 72 KNKSVEYIRKFFGIQT 87 (103)
Q Consensus 72 ~gKt~eeiR~~f~I~~ 87 (103)
.|+|..+|-+.||++.
T Consensus 16 ~G~s~~~ia~~lgvs~ 31 (50)
T PF13384_consen 16 EGWSIREIAKRLGVSR 31 (50)
T ss_dssp HT--HHHHHHHHTS-H
T ss_pred CCCCHHHHHHHHCcCH
Confidence 4899999999998763
No 49
>PF11460 DUF3007: Protein of unknown function (DUF3007); InterPro: IPR021562 This is a family of uncharacterised proteins found in bacteria and eukaryotes.
Probab=44.48 E-value=23 Score=23.83 Aligned_cols=23 Identities=35% Similarity=0.416 Sum_probs=16.6
Q ss_pred CHHHHHHHhCCCCCCChHHHHHHhhh
Q 037688 75 SVEYIRKFFGIQTNFMPEEEEATRKE 100 (103)
Q Consensus 75 t~eeiR~~f~I~~d~t~eee~~i~~e 100 (103)
+.+++.+.|. .+||||.+++..|
T Consensus 79 ~~~~lqkRle---~l~~eE~~~L~~e 101 (104)
T PF11460_consen 79 TNEELQKRLE---ELSPEELEALQAE 101 (104)
T ss_pred hHHHHHHHHH---hCCHHHHHHHHHH
Confidence 4455666664 6889998888765
No 50
>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=43.99 E-value=20 Score=18.74 Aligned_cols=13 Identities=38% Similarity=0.460 Sum_probs=9.4
Q ss_pred cCCCHHHHHHHhC
Q 037688 72 KNKSVEYIRKFFG 84 (103)
Q Consensus 72 ~gKt~eeiR~~f~ 84 (103)
.|-|.+|+|+++.
T Consensus 15 ~Gls~eeir~FL~ 27 (30)
T PF08671_consen 15 SGLSKEEIREFLE 27 (30)
T ss_dssp TT--HHHHHHHHH
T ss_pred cCCCHHHHHHHHH
Confidence 6899999999874
No 51
>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=43.88 E-value=92 Score=21.03 Aligned_cols=42 Identities=17% Similarity=0.146 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHHHhcCCCHHHHHHHhCCCCCCChHHHHHHhh
Q 037688 58 EMLDYLTKTLANRIKNKSVEYIRKFFGIQTNFMPEEEEATRK 99 (103)
Q Consensus 58 ~Ll~l~~~~vA~~i~gKt~eeiR~~f~I~~d~t~eee~~i~~ 99 (103)
.......+.+.+.+-|-++..+-..|--.+.+|++|.+++++
T Consensus 71 e~~~~~~~~~~~~~f~gs~~~ll~~l~~~~~ls~eele~L~~ 112 (130)
T TIGR02698 71 EAVENAAQELFSRICSRKVGAVIADLIEESPLSQTDIEKLEK 112 (130)
T ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHhcCCCCHHHHHHHHH
Confidence 344445566666666667666655554356799999999986
No 52
>PF03918 CcmH: Cytochrome C biogenesis protein; InterPro: IPR005616 Members of this family include NrfF, CcmH, CycL, Ccl2.; PDB: 2KW0_A 2HL7_A.
Probab=43.58 E-value=23 Score=24.90 Aligned_cols=18 Identities=28% Similarity=0.433 Sum_probs=11.3
Q ss_pred HHHHHh-cCCCHHHHHHHh
Q 037688 66 TLANRI-KNKSVEYIRKFF 83 (103)
Q Consensus 66 ~vA~~i-~gKt~eeiR~~f 83 (103)
.|..++ .|+|.+||+++|
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 344444 599999999876
No 53
>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=43.54 E-value=17 Score=25.62 Aligned_cols=38 Identities=16% Similarity=0.060 Sum_probs=24.1
Q ss_pred HHHHHhhhhhchHHHHHHHHHHHHHHhcCCCHHHHHHHhCCCCCCC
Q 037688 45 KEMLLVANYLNIKEMLDYLTKTLANRIKNKSVEYIRKFFGIQTNFM 90 (103)
Q Consensus 45 ~~li~AA~yL~I~~Ll~l~~~~vA~~i~gKt~eeiR~~f~I~~d~t 90 (103)
-.|+.||.-+|+-.-+... .....+.+|+.|||+++++
T Consensus 128 ~nl~LaA~~~GlGs~~~~~--------~~~~~~~v~~~l~ip~~~~ 165 (192)
T cd02140 128 IAVWTALAAEGIGANLQHY--------NPLIDEEVAKKWNIPSNWK 165 (192)
T ss_pred HHHHHHHHhCCCcccHHHh--------CccCCHHHHHhcCCCccce
Confidence 4677777777776522110 0123589999999998753
No 54
>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=43.22 E-value=19 Score=24.47 Aligned_cols=19 Identities=11% Similarity=0.240 Sum_probs=15.5
Q ss_pred hcCCCHHHHHHHhCCCC-CC
Q 037688 71 IKNKSVEYIRKFFGIQT-NF 89 (103)
Q Consensus 71 i~gKt~eeiR~~f~I~~-d~ 89 (103)
+.|...+.+++.||+++ ++
T Consensus 112 i~~~~~~~v~~~l~l~~~~~ 131 (156)
T cd03370 112 MTGFDEEKVKEALGLPGRDR 131 (156)
T ss_pred CcCcCHHHHHHHhCcCCcCc
Confidence 45678899999999997 54
No 55
>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=43.21 E-value=12 Score=26.03 Aligned_cols=18 Identities=17% Similarity=0.316 Sum_probs=12.7
Q ss_pred CCCHHHHHHHhCCCCCCC
Q 037688 73 NKSVEYIRKFFGIQTNFM 90 (103)
Q Consensus 73 gKt~eeiR~~f~I~~d~t 90 (103)
|.||+|=|+.||++.|+.
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 56
>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=41.83 E-value=48 Score=22.66 Aligned_cols=37 Identities=14% Similarity=0.083 Sum_probs=24.5
Q ss_pred HHhhhhhchHHHHHHHH-HHHHHHhcCCCHHHHHHHhC
Q 037688 48 LLVANYLNIKEMLDYLT-KTLANRIKNKSVEYIRKFFG 84 (103)
Q Consensus 48 i~AA~yL~I~~Ll~l~~-~~vA~~i~gKt~eeiR~~f~ 84 (103)
|..+.|-.--.-+-.+| ..++.+++|||++|+..+..
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 44444444444444444 55788899999999987764
No 57
>KOG4244 consensus Failed axon connections (fax) protein/glutathione S-transferase-like protein [Signal transduction mechanisms]
Probab=41.82 E-value=27 Score=27.30 Aligned_cols=24 Identities=25% Similarity=0.469 Sum_probs=20.2
Q ss_pred HHHHHHHhCCCCCCChHHHHHHhh
Q 037688 76 VEYIRKFFGIQTNFMPEEEEATRK 99 (103)
Q Consensus 76 ~eeiR~~f~I~~d~t~eee~~i~~ 99 (103)
...+|+-|++++++|+||+++.+.
T Consensus 111 ~~~L~~hf~~~~~L~~e~~a~s~A 134 (281)
T KOG4244|consen 111 EDRLRKHFKIPDDLSAEQRAQSRA 134 (281)
T ss_pred HHHHHHHcCCCCCCCHHHHHHHHH
Confidence 346789999999999999988764
No 58
>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=41.60 E-value=24 Score=25.18 Aligned_cols=36 Identities=11% Similarity=0.234 Sum_probs=25.0
Q ss_pred HHHHHhhhhhchHHHHHHHHHHHHHHhcCCCHHHHHHHhCCCCCCC
Q 037688 45 KEMLLVANYLNIKEMLDYLTKTLANRIKNKSVEYIRKFFGIQTNFM 90 (103)
Q Consensus 45 ~~li~AA~yL~I~~Ll~l~~~~vA~~i~gKt~eeiR~~f~I~~d~t 90 (103)
-.++.||..+|+-.- ++.+-..+.+++.|||+++++
T Consensus 135 ~nl~LaA~~~GlGs~----------~~~~~~~~~v~~~L~lp~~~~ 170 (205)
T TIGR02476 135 QNLWLAARAEGLGVG----------WVSILDPDAVRRLLGVPEGWR 170 (205)
T ss_pred HHHHHHHHHCCCcce----------eecccChHHHHHHhCcCCCce
Confidence 366677777777642 123445789999999998764
No 59
>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=41.57 E-value=25 Score=24.33 Aligned_cols=36 Identities=11% Similarity=0.204 Sum_probs=24.9
Q ss_pred HHHHhhhhhchHHHHHHHHHHHHHHhcCCCH-HHHHHHhCCCCCCCh
Q 037688 46 EMLLVANYLNIKEMLDYLTKTLANRIKNKSV-EYIRKFFGIQTNFMP 91 (103)
Q Consensus 46 ~li~AA~yL~I~~Ll~l~~~~vA~~i~gKt~-eeiR~~f~I~~d~t~ 91 (103)
.++.||.-+|+... .+.|-.. +.+++.|||++++.+
T Consensus 131 ~l~LaA~~~Glgs~----------~~~~~~~~~~v~~~l~ip~~~~~ 167 (193)
T cd02144 131 LLLAALQNAGLGTV----------TTTPLNMGPFLRRLLGRPANEKL 167 (193)
T ss_pred HHHHHHHHCCCcee----------ecCCcchhHHHHHHhCCCCCCce
Confidence 47778888877752 1234344 899999999987643
No 60
>COG1710 Uncharacterized protein conserved in archaea [Function unknown]
Probab=40.89 E-value=20 Score=24.97 Aligned_cols=16 Identities=31% Similarity=0.337 Sum_probs=14.3
Q ss_pred cCCCHHHHHHHhCCCC
Q 037688 72 KNKSVEYIRKFFGIQT 87 (103)
Q Consensus 72 ~gKt~eeiR~~f~I~~ 87 (103)
+||+|.||.+.+||+=
T Consensus 108 ~gk~preIsk~lGIpi 123 (139)
T COG1710 108 NGKTPREISKDLGIPI 123 (139)
T ss_pred cCCCHHHHHHhhCCch
Confidence 4899999999999973
No 61
>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=40.76 E-value=27 Score=26.15 Aligned_cols=37 Identities=22% Similarity=0.221 Sum_probs=27.9
Q ss_pred HHHHHHHHHHhcCCCHHHHHHHhCCCCCCChHHHHHH
Q 037688 61 DYLTKTLANRIKNKSVEYIRKFFGIQTNFMPEEEEAT 97 (103)
Q Consensus 61 ~l~~~~vA~~i~gKt~eeiR~~f~I~~d~t~eee~~i 97 (103)
.-.++.|+..++..|++|+++.|+|.+.+..+.-+..
T Consensus 28 ~~~~~~l~~~L~~~s~~el~~l~~is~~la~~~~~~~ 64 (237)
T PF03883_consen 28 LEKTEELLEALKSLSEEELKKLMKISDKLAEENYQRN 64 (237)
T ss_pred HHHHHHHHHHHHhcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 3456778888899999999999999987655444443
No 62
>PF11198 DUF2857: Protein of unknown function (DUF2857); InterPro: IPR021364 This is a bacterial family of uncharacterised proteins.
Probab=39.87 E-value=1e+02 Score=22.15 Aligned_cols=58 Identities=26% Similarity=0.279 Sum_probs=33.9
Q ss_pred chhHHHHHHHhhh-----hhchHHHHHHHH-HHHHHHhcCCCHHHH---HHHhCCCCC------CChHHHHHH
Q 037688 40 SNDELKEMLLVAN-----YLNIKEMLDYLT-KTLANRIKNKSVEYI---RKFFGIQTN------FMPEEEEAT 97 (103)
Q Consensus 40 ~~~~L~~li~AA~-----yL~I~~Ll~l~~-~~vA~~i~gKt~eei---R~~f~I~~d------~t~eee~~i 97 (103)
|.+.|-.++.-|. .--|+.++.+++ ..+-...-|.|+.|+ |+++||+.. .|+|++.+|
T Consensus 59 n~~~l~~~L~~~~~~~~~~~~idr~L~lGAS~~mm~~~FGls~~ev~~rR~llgi~~~~GR~~~~~ee~~~~i 131 (180)
T PF11198_consen 59 NHDVLWRLLEQARREQQEQQLIDRALRLGASIEMMQRLFGLSSAEVAARRRLLGIPVRKGRPPALSEEEEAAI 131 (180)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHhCCCCCCCCCCCcCHHHHHHH
Confidence 5566665555443 344555555543 334455678887777 777888753 345555544
No 63
>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=39.79 E-value=20 Score=21.39 Aligned_cols=21 Identities=19% Similarity=0.308 Sum_probs=15.6
Q ss_pred HHHHhcCCCHHHHHHHhCCCC
Q 037688 67 LANRIKNKSVEYIRKFFGIQT 87 (103)
Q Consensus 67 vA~~i~gKt~eeiR~~f~I~~ 87 (103)
++..-.|+|.+|++.++|-|.
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 444456999999999999775
No 64
>PRK10144 formate-dependent nitrite reductase complex subunit NrfF; Provisional
Probab=39.62 E-value=33 Score=23.77 Aligned_cols=19 Identities=16% Similarity=0.127 Sum_probs=14.4
Q ss_pred HHHHHHhc-CCCHHHHHHHh
Q 037688 65 KTLANRIK-NKSVEYIRKFF 83 (103)
Q Consensus 65 ~~vA~~i~-gKt~eeiR~~f 83 (103)
..|..++. |+|.+||+.+|
T Consensus 64 ~~Vr~~i~~G~sd~eI~~~~ 83 (126)
T PRK10144 64 HQVYSMVAEGKSEVEIIGWM 83 (126)
T ss_pred HHHHHHHHcCCCHHHHHHHH
Confidence 44555555 99999999886
No 65
>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=38.71 E-value=90 Score=19.59 Aligned_cols=44 Identities=16% Similarity=0.140 Sum_probs=23.2
Q ss_pred hHHHHHHHHHHHHHHh-cC-CCHHHHHHHhC----CCCCCChHHHHHHhh
Q 037688 56 IKEMLDYLTKTLANRI-KN-KSVEYIRKFFG----IQTNFMPEEEEATRK 99 (103)
Q Consensus 56 I~~Ll~l~~~~vA~~i-~g-Kt~eeiR~~f~----I~~d~t~eee~~i~~ 99 (103)
|..|+.+..++.++-- +| -|.+|+|+++. ....+|++|-.++-+
T Consensus 9 ~~~~i~~F~~y~~~~~~~g~Is~~EL~~~l~~~~~lg~k~t~~ev~~m~~ 58 (88)
T cd05029 9 IGLLVAIFHKYSGREGDKNTLSKKELKELIQKELTIGSKLQDAEIAKLME 58 (88)
T ss_pred HHHHHHHHHHHHccCCCCCEECHHHHHHHHHHHHhcCCCCCHHHHHHHHH
Confidence 3445555555555221 23 36677777662 334466666665543
No 66
>PLN03212 Transcription repressor MYB5; Provisional
Probab=38.22 E-value=48 Score=25.56 Aligned_cols=35 Identities=14% Similarity=0.213 Sum_probs=27.4
Q ss_pred HHHHHHh-cCCCHHHHHHHhC------CCC-CCChHHHHHHhh
Q 037688 65 KTLANRI-KNKSVEYIRKFFG------IQT-NFMPEEEEATRK 99 (103)
Q Consensus 65 ~~vA~~i-~gKt~eeiR~~f~------I~~-d~t~eee~~i~~ 99 (103)
..||..+ .|+|+.+.|+.+. |.. .+|+||++.|.+
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 4577776 4899999999884 666 699999987754
No 67
>PF14098 SSPI: Small, acid-soluble spore protein I
Probab=37.95 E-value=38 Score=20.88 Aligned_cols=20 Identities=15% Similarity=0.298 Sum_probs=15.8
Q ss_pred HHHHHHhcCCCHHHHHHHhC
Q 037688 65 KTLANRIKNKSVEYIRKFFG 84 (103)
Q Consensus 65 ~~vA~~i~gKt~eeiR~~f~ 84 (103)
++|-..++|+|.+|++.+-.
T Consensus 5 ~AI~~nv~g~s~~el~~~I~ 24 (65)
T PF14098_consen 5 QAIIHNVKGSSKEELKDTIE 24 (65)
T ss_pred HHHHHHccCCCHHHHHHHHH
Confidence 45666789999999998753
No 68
>PRK15019 CsdA-binding activator; Provisional
Probab=37.60 E-value=62 Score=22.78 Aligned_cols=38 Identities=11% Similarity=0.249 Sum_probs=23.7
Q ss_pred hhhhchHHHHHHHHHHHHHHhcCCCHHHHHH--------HhCCCCCCChH
Q 037688 51 ANYLNIKEMLDYLTKTLANRIKNKSVEYIRK--------FFGIQTNFMPE 92 (103)
Q Consensus 51 A~yL~I~~Ll~l~~~~vA~~i~gKt~eeiR~--------~f~I~~d~t~e 92 (103)
+...=+++|+-+ +.....|+||+||.+ -+|+...+||.
T Consensus 83 SDA~IvkGl~al----L~~~~~g~tp~eIl~~d~~~~~~~lGL~~~LSps 128 (147)
T PRK15019 83 SEGRIVRGLLAV----LLTAVEGKTAAELQAQSPLALFDELGLRAQLSAS 128 (147)
T ss_pred CccHHHHHHHHH----HHHHHcCCCHHHHHhcCHHHHHHHCCchhhcCcc
Confidence 333344555544 444568999999975 34677677664
No 69
>PRK13696 hypothetical protein; Provisional
Probab=37.41 E-value=83 Score=19.18 Aligned_cols=26 Identities=38% Similarity=0.585 Sum_probs=19.9
Q ss_pred cCCCHHHHHHHhCCCCCCChHHHHHHhhh
Q 037688 72 KNKSVEYIRKFFGIQTNFMPEEEEATRKE 100 (103)
Q Consensus 72 ~gKt~eeiR~~f~I~~d~t~eee~~i~~e 100 (103)
+..+...+.++||+-+| ||-++++++
T Consensus 36 ~~~~~~~l~~~~Gil~d---ee~~e~~~~ 61 (62)
T PRK13696 36 KKGNLDKLMKAFGILSE---EEAEELKKE 61 (62)
T ss_pred hhccHHHHHHHHCCCCH---HHHHHHHhh
Confidence 34578899999999864 777777764
No 70
>PF11165 DUF2949: Protein of unknown function (DUF2949); InterPro: IPR021336 This family of proteins with unknown function appear to be restricted to Cyanobacteria.
Probab=37.19 E-value=26 Score=21.09 Aligned_cols=16 Identities=19% Similarity=0.295 Sum_probs=13.0
Q ss_pred CCccCc------------HHHHHHHHHh
Q 037688 11 DMVVPQ------------LPYIIKFCKA 26 (103)
Q Consensus 11 ~~~IPl------------L~~Vie~c~~ 26 (103)
.+|+|+ |.+|++|+++
T Consensus 31 ~~pLPmiLWqyGLItL~QL~~i~DWl~~ 58 (58)
T PF11165_consen 31 QGPLPMILWQYGLITLEQLDQIFDWLEN 58 (58)
T ss_pred CCCcchHHHHhccccHHHHHHHHHHHhC
Confidence 467886 9999999874
No 71
>KOG1665 consensus AFH1-interacting protein FIP2, contains BTB/POZ domain and pentapeptide repeats [General function prediction only]
Probab=37.09 E-value=45 Score=25.90 Aligned_cols=41 Identities=17% Similarity=0.235 Sum_probs=32.5
Q ss_pred HHHHHHHHHhcCCcchhhcccCCchhHHHHHHHhhhhhchHHHHHHHH
Q 037688 17 LPYIIKFCKAHGVSKENEFGKGKSNDELKEMLLVANYLNIKEMLDYLT 64 (103)
Q Consensus 17 L~~Vie~c~~h~~~kD~~F~~~~~~~~L~~li~AA~yL~I~~Ll~l~~ 64 (103)
++-|+.|..+ -+|.-. +.-.+..++.+|.|.+|-+|.+-.-
T Consensus 64 FepIlNyLr~------Gq~~~~-s~i~~lgvLeeArff~i~sL~~hle 104 (302)
T KOG1665|consen 64 FEPILNYLRD------GQIPSL-SDIDCLGVLEEARFFQILSLKDHLE 104 (302)
T ss_pred hHHHHHHHhc------Cceeec-CCccHHHHHHHhhHHhhHhHHhHHh
Confidence 8888888764 445544 6678999999999999999988654
No 72
>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=35.33 E-value=65 Score=21.53 Aligned_cols=34 Identities=29% Similarity=0.567 Sum_probs=21.5
Q ss_pred hchHHHHHHHHHHHHHHhc--CCCHHHHHHHhCCCCC
Q 037688 54 LNIKEMLDYLTKTLANRIK--NKSVEYIRKFFGIQTN 88 (103)
Q Consensus 54 L~I~~Ll~l~~~~vA~~i~--gKt~eeiR~~f~I~~d 88 (103)
+++..|.+.+.+ +|..++ +-|+-|||++|+--..
T Consensus 8 ~~~~~~~~~Ae~-~~k~l~~~~lttsQlRkf~~~v~~ 43 (119)
T PF03750_consen 8 LDIELLVDYAEK-IAKELKKNKLTTSQLRKFYDEVKR 43 (119)
T ss_pred cCHHHHHHHHHH-HHHHHHhCCCCHHHHHHHHHHHHH
Confidence 445555555544 445454 4799999999984433
No 73
>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=34.28 E-value=14 Score=24.37 Aligned_cols=46 Identities=20% Similarity=0.280 Sum_probs=30.2
Q ss_pred hhhhhchHHHHHHHHHHHHHHhcCCCHHHHHHHhCCCCCCChHHHHHHhh
Q 037688 50 VANYLNIKEMLDYLTKTLANRIKNKSVEYIRKFFGIQTNFMPEEEEATRK 99 (103)
Q Consensus 50 AA~yL~I~~Ll~l~~~~vA~~i~gKt~eeiR~~f~I~~d~t~eee~~i~~ 99 (103)
...|-+.+++.-..+.+|+...--+|++++ +.|+ ++|+.|.+.+++
T Consensus 22 vr~f~~~pGmYPtlA~kIv~naPY~sveDv---l~ip-gLse~qK~~lk~ 67 (93)
T PF06514_consen 22 VRAFRQFPGMYPTLAGKIVSNAPYKSVEDV---LNIP-GLSERQKALLKK 67 (93)
T ss_dssp GGGGCCSTTTTCCHHHHHHHS---SSGGGG---CCST-T--HHHHHHHHH
T ss_pred HHHHHHCCCCCHHHHHHHHhCCCCCCHHHH---Hhcc-CCCHHHHHHHHH
Confidence 456788888888777777775555787765 5555 688888887765
No 74
>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=34.25 E-value=1.2e+02 Score=19.73 Aligned_cols=55 Identities=11% Similarity=-0.025 Sum_probs=34.7
Q ss_pred HHHHhhhhhchHH-----HHHHHHHHHHHHhc--CCCHHHHHHHhCCCCCCChHHHHHHhhh
Q 037688 46 EMLLVANYLNIKE-----MLDYLTKTLANRIK--NKSVEYIRKFFGIQTNFMPEEEEATRKE 100 (103)
Q Consensus 46 ~li~AA~yL~I~~-----Ll~l~~~~vA~~i~--gKt~eeiR~~f~I~~d~t~eee~~i~~e 100 (103)
.++.|+-..+|++ |+--+..-.|.++. +++|+++|+..-.|...|.+-.+.+++.
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 4445555555543 33344444455555 6899999999999999998888877764
No 75
>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=33.85 E-value=46 Score=22.27 Aligned_cols=27 Identities=15% Similarity=0.244 Sum_probs=21.4
Q ss_pred HHHHHHHhcCCCHHHHHHHhCCCCCCCh
Q 037688 64 TKTLANRIKNKSVEYIRKFFGIQTNFMP 91 (103)
Q Consensus 64 ~~~vA~~i~gKt~eeiR~~f~I~~d~t~ 91 (103)
-+.||..--|.|.++++..+|-| |||.
T Consensus 25 r~~i~~L~lg~s~~~V~~~lG~p-dfsE 51 (102)
T PF11399_consen 25 RQNIAKLSLGMSKDQVIALLGTP-DFSE 51 (102)
T ss_pred HHHHHhcCCCCCHHHHHHHhCCC-Cchh
Confidence 35677776799999999999987 5653
No 76
>cd07013 S14_ClpP Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease. Clp protease (caseinolytic protease; ClpP; Peptidase S14) is a highly conserved serine protease present throughout in bacteria and eukaryota, but seems to be absent in archaea, mollicutes and some fungi. Clp proteases are involved in a number of cellular processes such as degradation of misfolded proteins, regulation of short-lived proteins and housekeeping removal of dysfunctional proteins. Additionally, they are implicated in the control of cell growth, targeting DNA-binding protein from starved cells. ClpP has also been linked to the tight regulation of virulence genes in the pathogens Listeria monocytogenes and Salmonella typhimurium. This enzyme belong to the family of ATP-dependent proteases; the functional Clp protease is comprised of two components: a proteolytic component and one of several regulatory ATPase components, both of which are required for effective levels of proteas
Probab=33.84 E-value=1.2e+02 Score=21.03 Aligned_cols=37 Identities=16% Similarity=0.119 Sum_probs=24.8
Q ss_pred HHHHHHHHHHHHHhcCCCHHHHHHHhCCCCCCChHHHH
Q 037688 58 EMLDYLTKTLANRIKNKSVEYIRKFFGIQTNFMPEEEE 95 (103)
Q Consensus 58 ~Ll~l~~~~vA~~i~gKt~eeiR~~f~I~~d~t~eee~ 95 (103)
.+.+...+.+|.. .|+++++|++.+.=..=||++|-.
T Consensus 118 ~~~~~~~~~~a~~-tg~~~~~i~~~~~~~~~~sa~eA~ 154 (162)
T cd07013 118 KVEGNLVSAYAHK-TGQSEEELHADLERDTWLSAREAV 154 (162)
T ss_pred HHHHHHHHHHHHH-hCcCHHHHHHHHcCCccccHHHHH
Confidence 3334444555544 689999999998755557877643
No 77
>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=33.68 E-value=71 Score=18.75 Aligned_cols=28 Identities=32% Similarity=0.280 Sum_probs=19.8
Q ss_pred CCHHHHHHHhC--CCCCCChHHHHHHhhhh
Q 037688 74 KSVEYIRKFFG--IQTNFMPEEEEATRKES 101 (103)
Q Consensus 74 Kt~eeiR~~f~--I~~d~t~eee~~i~~e~ 101 (103)
++++++-+.|+ .++.+|++|-++-++++
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 67888888886 44468887777666553
No 78
>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=33.38 E-value=94 Score=17.52 Aligned_cols=40 Identities=15% Similarity=0.154 Sum_probs=25.3
Q ss_pred hHHHHHHHHHHHHHHhcC--CCHHHHHHHhCCCCCCChHHHHHHh
Q 037688 56 IKEMLDYLTKTLANRIKN--KSVEYIRKFFGIQTNFMPEEEEATR 98 (103)
Q Consensus 56 I~~Ll~l~~~~vA~~i~g--Kt~eeiR~~f~I~~d~t~eee~~i~ 98 (103)
=+.++-.+|=.+|.++.+ .++.++....|. +|.++..+..
T Consensus 37 ~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~---~~~~~i~~~~ 78 (83)
T smart00385 37 SPSLIAAAALYLAAKTEEIPPWTKELVHYTGY---FTEEEILRME 78 (83)
T ss_pred CHHHHHHHHHHHHHHHhcCCCCchhHhHhhCC---CCHHHHHHHH
Confidence 345566677777887776 356677666665 6666655443
No 79
>PF03979 Sigma70_r1_1: Sigma-70 factor, region 1.1; InterPro: IPR007127 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 [, ]. This entry represents Region 1.1 which modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase [, ]. Region 1.1 is also involved in promoter binding.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2K6X_A.
Probab=32.84 E-value=1e+02 Score=19.01 Aligned_cols=26 Identities=15% Similarity=0.235 Sum_probs=15.7
Q ss_pred cC-CCHHHHHHHhCCCCCCChHHHHHHh
Q 037688 72 KN-KSVEYIRKFFGIQTNFMPEEEEATR 98 (103)
Q Consensus 72 ~g-Kt~eeiR~~f~I~~d~t~eee~~i~ 98 (103)
+| -|.++|...|. +.+++|++.+.+-
T Consensus 19 ~G~lT~~eI~~~L~-~~~~~~e~id~i~ 45 (82)
T PF03979_consen 19 KGYLTYDEINDALP-EDDLDPEQIDEIY 45 (82)
T ss_dssp HSS-BHHHHHHH-S--S---HHHHHHHH
T ss_pred cCcCCHHHHHHHcC-ccCCCHHHHHHHH
Confidence 44 68999999998 5568888877764
No 80
>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=32.81 E-value=49 Score=18.08 Aligned_cols=30 Identities=17% Similarity=0.213 Sum_probs=24.0
Q ss_pred hhchHHHHHHHHHHHHHHhcCCCHHHHHHH
Q 037688 53 YLNIKEMLDYLTKTLANRIKNKSVEYIRKF 82 (103)
Q Consensus 53 yL~I~~Ll~l~~~~vA~~i~gKt~eeiR~~ 82 (103)
||.-.+|-+....+|+..+..-+|++|-.+
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 677788888888888888888888887654
No 81
>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=32.77 E-value=61 Score=18.32 Aligned_cols=22 Identities=23% Similarity=0.170 Sum_probs=15.0
Q ss_pred HHHHHHhcCCCHHHHHHHhCCC
Q 037688 65 KTLANRIKNKSVEYIRKFFGIQ 86 (103)
Q Consensus 65 ~~vA~~i~gKt~eeiR~~f~I~ 86 (103)
..+.-+..|+|+.||-..+||.
T Consensus 10 ~vl~~l~~G~~~~eIA~~l~is 31 (58)
T PF00196_consen 10 EVLRLLAQGMSNKEIAEELGIS 31 (58)
T ss_dssp HHHHHHHTTS-HHHHHHHHTSH
T ss_pred HHHHHHHhcCCcchhHHhcCcc
Confidence 3445566788888888888775
No 82
>COG1460 Uncharacterized protein conserved in archaea [Function unknown]
Probab=32.56 E-value=71 Score=21.79 Aligned_cols=55 Identities=16% Similarity=0.305 Sum_probs=34.2
Q ss_pred chhHHHHHHHhhhhhchHHHHHHHHHHHHHHhcCCCHHHHHHHhCCCCC-CChHHHHHH
Q 037688 40 SNDELKEMLLVANYLNIKEMLDYLTKTLANRIKNKSVEYIRKFFGIQTN-FMPEEEEAT 97 (103)
Q Consensus 40 ~~~~L~~li~AA~yL~I~~Ll~l~~~~vA~~i~gKt~eeiR~~f~I~~d-~t~eee~~i 97 (103)
|.+..-++.. ..++|..+-+-...+||+ |.=.|+.|+|.+|.-..- .|+|+..+|
T Consensus 49 dpe~a~e~ve--EL~~i~~~~e~~avkIad-I~P~t~~ElRsIla~e~~~~s~E~l~~I 104 (114)
T COG1460 49 DPEKARELVE--ELLSIVKMSEKIAVKIAD-IMPRTPDELRSILAKERVMLSDEELDKI 104 (114)
T ss_pred CHHHHHHHHH--HHHhhccccHHHHHHHHH-hCCCCHHHHHHHHHHccCCCCHHHHHHH
Confidence 6554444433 123333345556666666 467899999999986653 467777665
No 83
>TIGR03553 F420_FbiB_CTERM F420 biosynthesis protein FbiB, C-terminal domain. Coenzyme F420 differs between the Archaea and the Actinobacteria, where the numbers of glutamate residues attached are 2 (Archaea) or 5-6 (Mycobacterium). The enzyme in the Archaea is homologous to the N-terminal domain of FbiB from Mycobacterium bovis, and is responsible for glutamate ligation. Therefore it seems likely that the C-terminal domain of FbiB, modeled by this alignment, is involved in additional glutamate ligation.
Probab=32.55 E-value=25 Score=24.67 Aligned_cols=17 Identities=6% Similarity=0.239 Sum_probs=14.2
Q ss_pred CCHHHHHHHhCCCCCCC
Q 037688 74 KSVEYIRKFFGIQTNFM 90 (103)
Q Consensus 74 Kt~eeiR~~f~I~~d~t 90 (103)
-..+.+|+.|||+.++.
T Consensus 149 ~~~~~v~~~l~lp~~~~ 165 (194)
T TIGR03553 149 FAADVVRAELDLPADWE 165 (194)
T ss_pred cCHHHHHHHhCcCCCce
Confidence 45789999999998764
No 84
>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=32.55 E-value=45 Score=23.21 Aligned_cols=38 Identities=11% Similarity=0.179 Sum_probs=25.5
Q ss_pred HHHHHHhhhhhchHHHHHHHHHHHHHHhcCCCHHHHHHHhCCCCCCCh
Q 037688 44 LKEMLLVANYLNIKEMLDYLTKTLANRIKNKSVEYIRKFFGIQTNFMP 91 (103)
Q Consensus 44 L~~li~AA~yL~I~~Ll~l~~~~vA~~i~gKt~eeiR~~f~I~~d~t~ 91 (103)
+-.++.||..||+-.. ++.|...+++++.||++++..+
T Consensus 108 ~~nl~Laa~~lGlgt~----------~~~~~~~~~l~~~l~l~~~~~~ 145 (181)
T cd02138 108 WGNLALQATAMGLAAH----------QMGGFDADKAREELNIPEDYEV 145 (181)
T ss_pred HHHHHHHHHHcCcccc----------eecCcCHHHHHHHhCCCCCceE
Confidence 3456666666666532 2345678899999999987543
No 85
>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=32.52 E-value=65 Score=17.57 Aligned_cols=16 Identities=31% Similarity=0.478 Sum_probs=11.4
Q ss_pred hcCCCHHHHHHHhCCC
Q 037688 71 IKNKSVEYIRKFFGIQ 86 (103)
Q Consensus 71 i~gKt~eeiR~~f~I~ 86 (103)
-.|.|+.+|-+.|||.
T Consensus 19 ~~G~si~~IA~~~gvs 34 (45)
T PF02796_consen 19 AEGMSIAEIAKQFGVS 34 (45)
T ss_dssp HTT--HHHHHHHTTS-
T ss_pred HCCCCHHHHHHHHCcC
Confidence 4689999999999986
No 86
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=32.46 E-value=76 Score=16.79 Aligned_cols=17 Identities=18% Similarity=0.210 Sum_probs=13.3
Q ss_pred hcCCCHHHHHHHhCCCC
Q 037688 71 IKNKSVEYIRKFFGIQT 87 (103)
Q Consensus 71 i~gKt~eeiR~~f~I~~ 87 (103)
..|+|..+|-+.+|++.
T Consensus 16 ~~g~s~~eia~~l~is~ 32 (58)
T smart00421 16 AEGLTNKEIAERLGISE 32 (58)
T ss_pred HcCCCHHHHHHHHCCCH
Confidence 46888888888888754
No 87
>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=32.33 E-value=90 Score=21.63 Aligned_cols=34 Identities=15% Similarity=0.322 Sum_probs=21.3
Q ss_pred chHHHHHHHHHHHHHHhcCCCHHHHHHH--------hCCCCCCChH
Q 037688 55 NIKEMLDYLTKTLANRIKNKSVEYIRKF--------FGIQTNFMPE 92 (103)
Q Consensus 55 ~I~~Ll~l~~~~vA~~i~gKt~eeiR~~--------f~I~~d~t~e 92 (103)
=+++|+-+ +.....|+||+||.++ +|+...+||.
T Consensus 82 IvkGl~al----L~~~~~g~tp~eI~~~d~~~~~~~lGL~~~LSps 123 (138)
T TIGR03391 82 IVRGLLAV----LLTAVEGKTPEQLLAQDPLALFDELGLRAQLSAS 123 (138)
T ss_pred HHHHHHHH----HHHHHcCCCHHHHHHCCHHHHHHHcCchhccCcc
Confidence 34444444 4445689999998733 3666666664
No 88
>PRK13742 replication protein; Provisional
Probab=32.09 E-value=53 Score=24.79 Aligned_cols=34 Identities=6% Similarity=0.170 Sum_probs=24.8
Q ss_pred HHHHHHHHHHHHHHhcC---CCHHHHHHHhCCCCCCC
Q 037688 57 KEMLDYLTKTLANRIKN---KSVEYIRKFFGIQTNFM 90 (103)
Q Consensus 57 ~~Ll~l~~~~vA~~i~g---Kt~eeiR~~f~I~~d~t 90 (103)
.+|.+++|+.-...-.| -+++++|.+||+++.+.
T Consensus 163 ~RLYelL~q~~~~~~~g~~~i~i~elr~~l~~~~~Y~ 199 (245)
T PRK13742 163 MRLYESLCQYRKPDGSGIVSLKIDWIIERYQLPQSYQ 199 (245)
T ss_pred HHHHHHHHHhhhhccCCeEEEEHHHHHHHhCCccccc
Confidence 46788888765542224 47899999999998774
No 89
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=31.86 E-value=29 Score=27.21 Aligned_cols=13 Identities=46% Similarity=0.595 Sum_probs=11.9
Q ss_pred CHHHHHHHhCCCC
Q 037688 75 SVEYIRKFFGIQT 87 (103)
Q Consensus 75 t~eeiR~~f~I~~ 87 (103)
|||+|++.|||+.
T Consensus 248 sPEdIk~~FgiSK 260 (287)
T COG2996 248 SPEDIKATFGISK 260 (287)
T ss_pred CHHHHHHHhCcCH
Confidence 6999999999985
No 90
>PF04282 DUF438: Family of unknown function (DUF438); InterPro: IPR007380 This is a a group of uncharacterised proteins.
Probab=31.41 E-value=91 Score=19.40 Aligned_cols=28 Identities=14% Similarity=0.200 Sum_probs=16.1
Q ss_pred cCCCHHHHHHHhCCC-CCCChHHHHHHhh
Q 037688 72 KNKSVEYIRKFFGIQ-TNFMPEEEEATRK 99 (103)
Q Consensus 72 ~gKt~eeiR~~f~I~-~d~t~eee~~i~~ 99 (103)
.|.+++++|+.|.=. .+.+|.|-..+.+
T Consensus 11 ~G~~~e~vk~~F~~~~~~Vs~~EI~~~Eq 39 (71)
T PF04282_consen 11 EGEDPEEVKEEFKKLFSDVSASEISAAEQ 39 (71)
T ss_pred CCCCHHHHHHHHHHHHCCCCHHHHHHHHH
Confidence 577777777776522 2455555555443
No 91
>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=31.37 E-value=34 Score=23.84 Aligned_cols=14 Identities=21% Similarity=0.672 Sum_probs=11.2
Q ss_pred HHHHHHHHHhcCCc
Q 037688 17 LPYIIKFCKAHGVS 30 (103)
Q Consensus 17 L~~Vie~c~~h~~~ 30 (103)
-+.|+.||++|+-.
T Consensus 26 ~~lIl~y~~~~k~~ 39 (139)
T PF05871_consen 26 SDLILDYCRHHKIF 39 (139)
T ss_dssp HHHHHHHHHHTT-S
T ss_pred HHHHHHHHHHhcee
Confidence 46799999999976
No 92
>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=30.83 E-value=62 Score=20.55 Aligned_cols=27 Identities=11% Similarity=0.235 Sum_probs=20.2
Q ss_pred HhcCCCHHHHHHHhCCCCCCChHHHHHHhh
Q 037688 70 RIKNKSVEYIRKFFGIQTNFMPEEEEATRK 99 (103)
Q Consensus 70 ~i~gKt~eeiR~~f~I~~d~t~eee~~i~~ 99 (103)
.+...|++|+..++ ..+|++|...|+.
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 34568999999998 7899999988865
No 93
>PRK12551 ATP-dependent Clp protease proteolytic subunit; Reviewed
Probab=30.81 E-value=1.3e+02 Score=22.03 Aligned_cols=37 Identities=19% Similarity=0.199 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHHHhcCCCHHHHHHHhCCCCCCChHHHH
Q 037688 58 EMLDYLTKTLANRIKNKSVEYIRKFFGIQTNFMPEEEE 95 (103)
Q Consensus 58 ~Ll~l~~~~vA~~i~gKt~eeiR~~f~I~~d~t~eee~ 95 (103)
.+-+...+..|.+ .|++.++|++...=..=+|++|--
T Consensus 143 ~~~~~~~~~ya~~-tG~~~~~i~~~~~rd~~msa~EA~ 179 (196)
T PRK12551 143 FLKERLNTELSER-TGQPLERIQEDTDRDFFMSPSEAV 179 (196)
T ss_pred HHHHHHHHHHHHH-HCcCHHHHHHHhhcCcCCCHHHHH
Confidence 3334455555554 599999999998776668887743
No 94
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=30.70 E-value=50 Score=18.07 Aligned_cols=26 Identities=15% Similarity=0.316 Sum_probs=17.7
Q ss_pred HHHHHHhhhhhchHHHHHHHHHHHHHHhcCCC
Q 037688 44 LKEMLLVANYLNIKEMLDYLTKTLANRIKNKS 75 (103)
Q Consensus 44 L~~li~AA~yL~I~~Ll~l~~~~vA~~i~gKt 75 (103)
.-.+-.||.+|++ .-..|+..++|+.
T Consensus 17 f~S~~eAa~~lg~------~~~~I~~~~~~~~ 42 (53)
T smart00497 17 FSSIREAAKYLGI------SHSSISKYLNTGK 42 (53)
T ss_pred ecCHHHHHHHhCC------CHHHHHHHHhCCC
Confidence 3467789999999 3455666666643
No 95
>PF15120 DUF4561: Domain of unknown function (DUF4561)
Probab=30.40 E-value=1.3e+02 Score=21.98 Aligned_cols=18 Identities=17% Similarity=0.285 Sum_probs=14.4
Q ss_pred ccCc--HHHHHHHHHhcCCc
Q 037688 13 VVPQ--LPYIIKFCKAHGVS 30 (103)
Q Consensus 13 ~IPl--L~~Vie~c~~h~~~ 30 (103)
.-|+ +..|-.||+||...
T Consensus 40 ~~pV~tI~QV~~y~eh~~~n 59 (171)
T PF15120_consen 40 TRPVSTIGQVQKYMEHHCNN 59 (171)
T ss_pred ccccccHHHHHHHHHHHhcc
Confidence 3455 99999999998764
No 96
>PF06777 DUF1227: Protein of unknown function (DUF1227); InterPro: IPR010643 This domain represents a conserved region within a number of eukaryotic DNA repair helicases.; GO: 0005634 nucleus
Probab=30.24 E-value=2e+02 Score=20.34 Aligned_cols=52 Identities=12% Similarity=0.183 Sum_probs=29.8
Q ss_pred HHHHHHHHHhcCCcchhhcccCCchhHHHHHHHhhhhhchHHHHHHHHHHHHHHhc
Q 037688 17 LPYIIKFCKAHGVSKENEFGKGKSNDELKEMLLVANYLNIKEMLDYLTKTLANRIK 72 (103)
Q Consensus 17 L~~Vie~c~~h~~~kD~~F~~~~~~~~L~~li~AA~yL~I~~Ll~l~~~~vA~~i~ 72 (103)
|+++|+|++..-. -...... +...++.-+.-..+++.++| ..|...+...++
T Consensus 66 lkR~veylk~rlr--v~~v~~e-~P~sFL~~~~~~~~id~k~L-rFc~eRL~sLl~ 117 (146)
T PF06777_consen 66 LKRFVEYLKTRLR--VQHVISE-SPLSFLQHLKDETFIDRKPL-RFCSERLSSLLR 117 (146)
T ss_pred HHHHHHHHHHHhh--hcceeec-CHHHHHHHHHHHhCCCcHHH-HHHHHHHHHHHH
Confidence 9999999987553 2222222 34444555555556665554 456666655554
No 97
>PRK09296 cysteine desufuration protein SufE; Provisional
Probab=30.17 E-value=81 Score=21.89 Aligned_cols=30 Identities=10% Similarity=0.129 Sum_probs=20.1
Q ss_pred HHHHHHHHhcCCCHHHHHH--------HhCCCCCCChH
Q 037688 63 LTKTLANRIKNKSVEYIRK--------FFGIQTNFMPE 92 (103)
Q Consensus 63 ~~~~vA~~i~gKt~eeiR~--------~f~I~~d~t~e 92 (103)
.+..+.....|+||+||.+ -+|+...+||.
T Consensus 81 l~alL~~~~~g~tp~eIl~~d~~~~~~~lGL~~~LSps 118 (138)
T PRK09296 81 LIAVVFILYQQMTPQDIVNFDVRPWFEKLALTQHLTPS 118 (138)
T ss_pred HHHHHHHHHcCCCHHHHHhCChHHHHHHcCcccccCcc
Confidence 3444555678999999874 34667667664
No 98
>TIGR01044 rplV_bact ribosomal protein L22, bacterial type. This model decribes bacterial and chloroplast ribosomal protein L22.
Probab=29.55 E-value=67 Score=21.00 Aligned_cols=20 Identities=25% Similarity=0.326 Sum_probs=17.2
Q ss_pred HHHHHHhcCCCHHHHHHHhC
Q 037688 65 KTLANRIKNKSVEYIRKFFG 84 (103)
Q Consensus 65 ~~vA~~i~gKt~eeiR~~f~ 84 (103)
..||+.|+|+++++-..++.
T Consensus 14 ~~va~~IrG~~v~~A~~~L~ 33 (103)
T TIGR01044 14 RLVADLIRGKSVSQALDILR 33 (103)
T ss_pred HHHHHHHcCCcHHHHHHHHh
Confidence 56889999999999888776
No 99
>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=29.51 E-value=37 Score=23.87 Aligned_cols=19 Identities=16% Similarity=0.323 Sum_probs=15.3
Q ss_pred cCCCHHHHHHHhCCCCCCC
Q 037688 72 KNKSVEYIRKFFGIQTNFM 90 (103)
Q Consensus 72 ~gKt~eeiR~~f~I~~d~t 90 (103)
.|-..+.+++.|||++++.
T Consensus 143 ~~~~~~~v~~~l~lp~~~~ 161 (196)
T cd02145 143 SILDPEALARLLGIPEDWE 161 (196)
T ss_pred cccChHHHHHHcCcCCCcE
Confidence 4567899999999998753
No 100
>TIGR02000 NifU_proper Fe-S cluster assembly protein NifU. Three different but partially homologous Fe-S cluster assembly systems have been described: Isc, Suf, and Nif. The latter is associated with donation of an Fe-S cluster to nitrogenase in a number of nitrogen-fixing species. NifU, described here, consists of an N-terminal domain (pfam01592) and a C-terminal domain (pfam01106). Homologs with an equivalent domain archictecture from Helicobacter and Campylobacter, however, are excluded from this model by a high trusted cutoff. The model, therefore, is specific for NifU involved in nitrogenase maturation. The related model TIGR01999 homologous to the N-terminus of this model describes IscU from the Isc system as in E. coli, Saccharomyces cerevisiae, and Homo sapiens.
Probab=29.25 E-value=60 Score=25.22 Aligned_cols=37 Identities=14% Similarity=0.087 Sum_probs=22.7
Q ss_pred HHhhhhhchHHHHHH-HHHHHHHHhcCCCHHHHHHHhC
Q 037688 48 LLVANYLNIKEMLDY-LTKTLANRIKNKSVEYIRKFFG 84 (103)
Q Consensus 48 i~AA~yL~I~~Ll~l-~~~~vA~~i~gKt~eeiR~~f~ 84 (103)
|.-+.|-..-.-... ++..++.+++|||++|..++.+
T Consensus 52 I~d~~F~~~GCais~ASAs~~~eli~Gktv~ea~~i~~ 89 (290)
T TIGR02000 52 IVDAGFQTFGCGSAIASSSALTEMIKGLTLDEALKVSN 89 (290)
T ss_pred EEEEEEEecCcHHHHHHHHHHHHHHcCCCHHHHHHhhH
Confidence 333444444333333 4456788999999999776643
No 101
>PF13010 pRN1_helical: Primase helical domain; PDB: 1RO0_A 1RNI_A 1RO2_A 3M1M_A.
Probab=29.20 E-value=29 Score=24.17 Aligned_cols=14 Identities=50% Similarity=0.643 Sum_probs=5.8
Q ss_pred HHhcCCCHHHHHHH
Q 037688 69 NRIKNKSVEYIRKF 82 (103)
Q Consensus 69 ~~i~gKt~eeiR~~ 82 (103)
++.+|||+|.||.-
T Consensus 24 drfkGKtveair~e 37 (135)
T PF13010_consen 24 DRFKGKTVEAIREE 37 (135)
T ss_dssp -------HHHHHHH
T ss_pred ccccCchHHHHHHH
Confidence 45789999999863
No 102
>PRK14512 ATP-dependent Clp protease proteolytic subunit; Provisional
Probab=29.20 E-value=2.2e+02 Score=20.64 Aligned_cols=36 Identities=8% Similarity=0.063 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHHHhcCCCHHHHHHHhCCCCCCChHHH
Q 037688 58 EMLDYLTKTLANRIKNKSVEYIRKFFGIQTNFMPEEE 94 (103)
Q Consensus 58 ~Ll~l~~~~vA~~i~gKt~eeiR~~f~I~~d~t~eee 94 (103)
.+-+......|.. .|+++++|++...=..=+|++|-
T Consensus 141 ~~~~~i~~~~a~~-tg~~~~~i~~~~~~d~~lta~EA 176 (197)
T PRK14512 141 KVKSELNDIIAKE-TGQELDKVEKDTDRDFWLDSSSA 176 (197)
T ss_pred HHHHHHHHHHHHH-hCcCHHHHHHhhhcCcccCHHHH
Confidence 3444455555554 69999999998765555677653
No 103
>PRK13379 protocatechuate 4,5-dioxygenase subunit alpha; Provisional
Probab=28.44 E-value=63 Score=22.22 Aligned_cols=32 Identities=3% Similarity=0.049 Sum_probs=24.4
Q ss_pred hHHHHHHHHHHHHHHhcCCCHHHHHHHhCCCC
Q 037688 56 IKEMLDYLTKTLANRIKNKSVEYIRKFFGIQT 87 (103)
Q Consensus 56 I~~Ll~l~~~~vA~~i~gKt~eeiR~~f~I~~ 87 (103)
+-+...+..+.|+..++|.|.||.++.=++++
T Consensus 86 l~av~G~s~q~i~a~mtG~t~eeF~~tr~~~~ 117 (119)
T PRK13379 86 FARVVRMTNLQVYAIMRGETFEEFMQTRRVPD 117 (119)
T ss_pred HHHHcCCcHHHHHHHhcCCcHHHHHHHccCCC
Confidence 44445556678888899999999999887764
No 104
>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=28.28 E-value=89 Score=19.64 Aligned_cols=38 Identities=13% Similarity=0.266 Sum_probs=26.8
Q ss_pred HHHHHHHHHHhcCCCHHHHHHH-------hCCCCCCChHHHHHHh
Q 037688 61 DYLTKTLANRIKNKSVEYIRKF-------FGIQTNFMPEEEEATR 98 (103)
Q Consensus 61 ~l~~~~vA~~i~gKt~eeiR~~-------f~I~~d~t~eee~~i~ 98 (103)
.++...+++.++|.....|++. ||+-.+++..+-+++=
T Consensus 19 ~~~~~~ivdvlrGs~~~~i~~~~~~~l~~yG~gk~~~~~~~~~li 63 (106)
T PF09382_consen 19 RFGLSQIVDVLRGSKSKKIREKGHDQLPTYGIGKDMSKDDWERLI 63 (106)
T ss_dssp -S-HHHHHHHHTT-S-CCCHHTTGGGSTTTTTTTTS-HHHHHHHH
T ss_pred cccHHHHHHHHHhccchhhhhcCCCcCcccCCcccCCHHHHHHHH
Confidence 5677888999999888887764 9999999988877653
No 105
>KOG0437 consensus Leucyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=28.23 E-value=41 Score=30.34 Aligned_cols=22 Identities=36% Similarity=0.564 Sum_probs=19.6
Q ss_pred HHhCCCCCCChHHHHHHhhhhC
Q 037688 81 KFFGIQTNFMPEEEEATRKESF 102 (103)
Q Consensus 81 ~~f~I~~d~t~eee~~i~~e~~ 102 (103)
+.||-+.||++|++++++.|.+
T Consensus 109 e~fG~ppdf~~e~eeEv~eev~ 130 (1080)
T KOG0437|consen 109 ELFGCPPDFPEEEEEEVEEEVK 130 (1080)
T ss_pred HHhCCCCCCchhhhhhhhhccc
Confidence 5899999999999999998764
No 106
>CHL00028 clpP ATP-dependent Clp protease proteolytic subunit
Probab=27.40 E-value=1.6e+02 Score=21.51 Aligned_cols=49 Identities=20% Similarity=0.209 Sum_probs=32.1
Q ss_pred HHHHHHhhhhhchHHHHHHHHHHHHHHhcCCCHHHHHHHhCCCCCCChHHHH
Q 037688 44 LKEMLLVANYLNIKEMLDYLTKTLANRIKNKSVEYIRKFFGIQTNFMPEEEE 95 (103)
Q Consensus 44 L~~li~AA~yL~I~~Ll~l~~~~vA~~i~gKt~eeiR~~f~I~~d~t~eee~ 95 (103)
.-++...|..|+ .+-+...+..|.. .|+++++|++...=+.=+|++|--
T Consensus 137 a~di~~~a~~l~--~~~~~~~~~ya~~-Tg~~~e~i~~~~~r~~~lta~EA~ 185 (200)
T CHL00028 137 ASEFVLEAEELL--KLRETITRVYAQR-TGKPLWVISEDMERDVFMSATEAK 185 (200)
T ss_pred HHHHHHHHHHHH--HHHHHHHHHHHHH-HCcCHHHHHHHhhcCccCCHHHHH
Confidence 445555555544 2444455555555 599999999998866668888643
No 107
>COG2865 Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]
Probab=27.36 E-value=1.6e+02 Score=24.74 Aligned_cols=27 Identities=15% Similarity=0.202 Sum_probs=18.7
Q ss_pred HHHHHHHHHhcCCCHHHHHHHhCCCCC
Q 037688 62 YLTKTLANRIKNKSVEYIRKFFGIQTN 88 (103)
Q Consensus 62 l~~~~vA~~i~gKt~eeiR~~f~I~~d 88 (103)
-+|-.++..-.-.|+.++|+.||++..
T Consensus 405 ~~il~~~~en~~~T~~~L~~~l~is~~ 431 (467)
T COG2865 405 EKILELIKENGKVTARELREILGISSE 431 (467)
T ss_pred HHHHHHHhhccccCHHHHHHHhCcchh
Confidence 344444444445899999999997653
No 108
>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=27.01 E-value=42 Score=18.56 Aligned_cols=18 Identities=22% Similarity=0.305 Sum_probs=11.3
Q ss_pred HhcCCCHHHHHHHhCCCC
Q 037688 70 RIKNKSVEYIRKFFGIQT 87 (103)
Q Consensus 70 ~i~gKt~eeiR~~f~I~~ 87 (103)
.+.|+|..||-+.+|++.
T Consensus 23 ~~~g~s~~eIa~~l~~s~ 40 (54)
T PF08281_consen 23 YFQGMSYAEIAEILGISE 40 (54)
T ss_dssp HTS---HHHHHHHCTS-H
T ss_pred HHHCcCHHHHHHHHCcCH
Confidence 367899999999998764
No 109
>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=26.57 E-value=53 Score=19.71 Aligned_cols=30 Identities=27% Similarity=0.051 Sum_probs=24.2
Q ss_pred CCHHHH----HHHhCCCCCCChHHHHHHhhhhCC
Q 037688 74 KSVEYI----RKFFGIQTNFMPEEEEATRKESFD 103 (103)
Q Consensus 74 Kt~eei----R~~f~I~~d~t~eee~~i~~e~~~ 103 (103)
+|.+|+ .+-.||+..||.-=-.++.+||++
T Consensus 16 Msk~E~v~~L~~~a~I~P~~T~~VW~~LekeN~e 49 (57)
T TIGR01589 16 MSKEETVSFLFENAGISPKFTRFVWYLLEKENAD 49 (57)
T ss_pred CCHHHHHHHHHHHcCCCchhHHHHHHHHHHHHHH
Confidence 565555 456799999999999999999874
No 110
>PF04255 DUF433: Protein of unknown function (DUF433); InterPro: IPR007367 This is a family of uncharacterised proteins.; PDB: 2GA1_B.
Probab=26.21 E-value=1.4e+02 Score=17.14 Aligned_cols=23 Identities=22% Similarity=0.171 Sum_probs=13.9
Q ss_pred hcCCCHHHHHHHhCCCCCCChHHHHH
Q 037688 71 IKNKSVEYIRKFFGIQTNFMPEEEEA 96 (103)
Q Consensus 71 i~gKt~eeiR~~f~I~~d~t~eee~~ 96 (103)
-.|.|++||.+-|. ++|+++-..
T Consensus 29 ~~G~s~eeI~~~yp---~Lt~~~i~a 51 (56)
T PF04255_consen 29 AAGESPEEIAEDYP---SLTLEDIRA 51 (56)
T ss_dssp HTT--HHHHHHHST---T--HHHHHH
T ss_pred HcCCCHHHHHHHCC---CCCHHHHHH
Confidence 46899999999986 466666543
No 111
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=26.09 E-value=1.4e+02 Score=18.82 Aligned_cols=28 Identities=18% Similarity=0.325 Sum_probs=20.1
Q ss_pred hHHHHHHHHHHHHHHhcCCCHHHHHHHhC
Q 037688 56 IKEMLDYLTKTLANRIKNKSVEYIRKFFG 84 (103)
Q Consensus 56 I~~Ll~l~~~~vA~~i~gKt~eeiR~~f~ 84 (103)
+..+++.+.+.++.. .+.+++++|+++.
T Consensus 44 ~eemie~~~~~~~~~-~~~~~~~a~~~~~ 71 (81)
T PF12674_consen 44 MEEMIEFCVPFMDEF-NGMTPEEARKMMP 71 (81)
T ss_pred HHHHHHHHHHHHHHh-CCCCHHHHHHHHH
Confidence 455566777777775 3489999998874
No 112
>PRK11548 outer membrane biogenesis protein BamE; Provisional
Probab=25.66 E-value=79 Score=20.84 Aligned_cols=23 Identities=9% Similarity=0.059 Sum_probs=18.8
Q ss_pred HHHHHHhcCCCHHHHHHHhCCCC
Q 037688 65 KTLANRIKNKSVEYIRKFFGIQT 87 (103)
Q Consensus 65 ~~vA~~i~gKt~eeiR~~f~I~~ 87 (103)
..++..-.|+|-+|++..+|-|.
T Consensus 41 ~~l~~l~~GmTk~qV~~lLGtP~ 63 (113)
T PRK11548 41 NDVAKIHVGMTQQQVAYTLGTPM 63 (113)
T ss_pred HHHHHhcCCCCHHHHHHHcCCCc
Confidence 34566667999999999999885
No 113
>PF10607 CLTH: CTLH/CRA C-terminal to LisH motif domain; InterPro: IPR019589 This entry represents the CRA (or CT11-RanBPM) domain, which is a protein-protein interaction domain present in crown eukaryotes (plants, animals, fungi) and which is found in Ran-binding proteins such as Ran-binding protein 9 (RanBP9 or RanBPM) and RanBP10. RanBPM is a scaffolding protein important in regulating cellular function in both the immune system and the nervous system, and may act as an adapter protein to couple membrane receptors to intracellular signaling pathways. This domain is at the C terminus of the proteins and is the binding domain for the CRA motif, which is comprised of approximately 100 amino acids at the C-terminal of RanBPM. It was found to be important for the interaction of RanBPM with fragile X mental retardation protein (FMRP), but its functional significance has yet to be determined [].
Probab=25.55 E-value=1.2e+02 Score=20.04 Aligned_cols=14 Identities=7% Similarity=0.019 Sum_probs=11.6
Q ss_pred HHHHHHHHHhcCCc
Q 037688 17 LPYIIKFCKAHGVS 30 (103)
Q Consensus 17 L~~Vie~c~~h~~~ 30 (103)
+...++||+.|...
T Consensus 17 i~~Ai~w~~~~~~~ 30 (145)
T PF10607_consen 17 IDPAIEWLNENFPE 30 (145)
T ss_pred HHHHHHHHHHcCHH
Confidence 67889999998754
No 114
>PRK14981 DNA-directed RNA polymerase subunit F; Provisional
Probab=25.36 E-value=2.1e+02 Score=18.95 Aligned_cols=44 Identities=16% Similarity=0.288 Sum_probs=30.7
Q ss_pred chHHHHHHHHHHHHHHhcCCCHHHHHHHhCCCC-CCChHHHHHHhh
Q 037688 55 NIKEMLDYLTKTLANRIKNKSVEYIRKFFGIQT-NFMPEEEEATRK 99 (103)
Q Consensus 55 ~I~~Ll~l~~~~vA~~i~gKt~eeiR~~f~I~~-d~t~eee~~i~~ 99 (103)
++..|-+.....||+. .=.|++|+|.+|.-.. -+++|+.++|-.
T Consensus 61 ~~~~l~e~~a~~I~nL-~P~~~dElrai~~~~~~~~~~e~l~~ILd 105 (112)
T PRK14981 61 ELEKMKEKTAVKIADI-LPETRDELRAIFAKERYTLSPEELDEILD 105 (112)
T ss_pred HccCCCHHHHHHHHhc-CCCCHHHHHHHHHHhccCCCHHHHHHHHH
Confidence 3334455556666663 5689999999998663 488888888753
No 115
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=25.26 E-value=90 Score=19.67 Aligned_cols=27 Identities=22% Similarity=0.284 Sum_probs=19.3
Q ss_pred HHHHHHHHH-hcCCCHHHHHHHhCCCCC
Q 037688 62 YLTKTLANR-IKNKSVEYIRKFFGIQTN 88 (103)
Q Consensus 62 l~~~~vA~~-i~gKt~eeiR~~f~I~~d 88 (103)
...+.+.-. +.|+|.++|-+.+|++..
T Consensus 114 ~~~~ii~~~~~~g~s~~eIA~~l~~s~~ 141 (158)
T TIGR02937 114 REREVLVLRYLEGLSYKEIAEILGISVG 141 (158)
T ss_pred HHHHHHhhHHhcCCCHHHHHHHHCCCHH
Confidence 333444443 689999999999998643
No 116
>PF10507 DUF2453: Protein of unknown function (DUF2453); InterPro: IPR019537 The function of these transmembrane protein is not known.
Probab=24.97 E-value=1.4e+02 Score=20.28 Aligned_cols=38 Identities=16% Similarity=0.310 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHHhcC-------CCHHHHHHHhCCCC-CCChHHHHH
Q 037688 59 MLDYLTKTLANRIKN-------KSVEYIRKFFGIQT-NFMPEEEEA 96 (103)
Q Consensus 59 Ll~l~~~~vA~~i~g-------Kt~eeiR~~f~I~~-d~t~eee~~ 96 (103)
|--++++.+.+.+.+ -.+|.+.+..|++. ++|++|.+-
T Consensus 35 iStmAAAalGN~vSDv~Gi~~~~~vE~~~~rlg~~~P~Lt~~Q~~~ 80 (111)
T PF10507_consen 35 ISTMAAAALGNLVSDVAGIGLGGYVERLAQRLGLKAPVLTPAQLNS 80 (111)
T ss_pred HHHHHHHHHhhhhhhhhhhHHHHHHHHHHHHhCCCCCCCCHHHHhC
Confidence 344455555555443 57999999999988 699998763
No 117
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=24.95 E-value=1.2e+02 Score=17.86 Aligned_cols=21 Identities=14% Similarity=0.178 Sum_probs=17.0
Q ss_pred HHHHhcCCCHHHHHHHhCCCC
Q 037688 67 LANRIKNKSVEYIRKFFGIQT 87 (103)
Q Consensus 67 vA~~i~gKt~eeiR~~f~I~~ 87 (103)
..-..+|-++.+|-+.+|++.
T Consensus 7 ~~LY~~G~~~~eIA~~Lg~~~ 27 (58)
T PF06056_consen 7 RSLYLQGWSIKEIAEELGVPR 27 (58)
T ss_pred HHHHHcCCCHHHHHHHHCCCh
Confidence 344578999999999999873
No 118
>cd02062 Nitro_FMN_reductase Proteins of this family catalyze the reduction of flavin or nitrocompounds using NAD(P)H as electron donor in a obligatory two-electron transfer, utilizing FMN or FAD as cofactor. They are often found to be homodimers. Enzymes of this family are described as NAD(P)H:FMN oxidoreductases, oxygen-insensitive nitroreductase, flavin reductase P, dihydropteridine reductase, NADH oxidase or NADH dehydrogenase.
Probab=24.95 E-value=83 Score=19.73 Aligned_cols=35 Identities=26% Similarity=0.452 Sum_probs=23.1
Q ss_pred HHHHHhhhhhchHHHHHHHHHHHHHHhcCCC--HHHHHHHhCCCCCC
Q 037688 45 KEMLLVANYLNIKEMLDYLTKTLANRIKNKS--VEYIRKFFGIQTNF 89 (103)
Q Consensus 45 ~~li~AA~yL~I~~Ll~l~~~~vA~~i~gKt--~eeiR~~f~I~~d~ 89 (103)
..++.+|..+|+..- ++.|-. .+++++.||++++.
T Consensus 76 ~~l~l~a~~~Glg~~----------~~~~~~~~~~~~~~~l~l~~~~ 112 (122)
T cd02062 76 QNILLAAHALGLGSC----------WIGGLDLVEEELRELLGIPEGY 112 (122)
T ss_pred HHHHHHHHHcCCCch----------hcCCcccchHHHHHHhCcCCCc
Confidence 355666666665432 234444 89999999999764
No 119
>PF02657 SufE: Fe-S metabolism associated domain; InterPro: IPR003808 This entry represents the core domain of SufE and related proteins. This domain of SufE shows strong structural similarity to IscU, and the sulfur-acceptor site in SufE coincides with the location of the cysteine residues mediating Fe-S cluster assembly in IscU. Thus, a conserved core structure is implicated in mediating the interactions of both SufE and IscU with the mutually homologous cysteine desulfurase enzymes present in their respective operons [].; PDB: 1MZG_B 1WLO_A 3G0M_A 1NI7_A.
Probab=24.82 E-value=1.6e+02 Score=19.80 Aligned_cols=33 Identities=21% Similarity=0.405 Sum_probs=22.4
Q ss_pred hHHHHHHHHHHHHHHhcCCCHHHHHH-------HhCCCCCCChH
Q 037688 56 IKEMLDYLTKTLANRIKNKSVEYIRK-------FFGIQTNFMPE 92 (103)
Q Consensus 56 I~~Ll~l~~~~vA~~i~gKt~eeiR~-------~f~I~~d~t~e 92 (103)
+++|+-+.+. .+.|+||+||.. .+|+...+||.
T Consensus 69 vkGl~all~~----~~~g~t~~eI~~~~~~fl~~lgl~~~Ls~s 108 (125)
T PF02657_consen 69 VKGLLALLLE----VLNGQTPEEILAFDPDFLEQLGLSQHLSPS 108 (125)
T ss_dssp HHHHHHHHHH----HTTT-BHHHHHHS-THHHHHHTSCCCSTHH
T ss_pred HHHHHHHHHH----HHcCCCHHHHHhCCHHHHHHcCcccccCch
Confidence 4555555554 558999999975 46788888875
No 120
>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=24.74 E-value=1.3e+02 Score=16.53 Aligned_cols=23 Identities=17% Similarity=0.270 Sum_probs=14.5
Q ss_pred HHHHHHhcC-CCHHHHHHHhCCCC
Q 037688 65 KTLANRIKN-KSVEYIRKFFGIQT 87 (103)
Q Consensus 65 ~~vA~~i~g-Kt~eeiR~~f~I~~ 87 (103)
++|...-.| +|.-+.-+.||||.
T Consensus 7 ~Ai~~v~~g~~S~r~AA~~ygVp~ 30 (45)
T PF05225_consen 7 KAIEAVKNGKMSIRKAAKKYGVPR 30 (45)
T ss_dssp HHHHHHHTTSS-HHHHHHHHT--H
T ss_pred HHHHHHHhCCCCHHHHHHHHCcCH
Confidence 344454567 89999999999984
No 121
>PRK11566 hdeB acid-resistance protein; Provisional
Probab=24.68 E-value=51 Score=22.07 Aligned_cols=14 Identities=29% Similarity=0.790 Sum_probs=12.3
Q ss_pred HHHHHHHHHhcCCc
Q 037688 17 LPYIIKFCKAHGVS 30 (103)
Q Consensus 17 L~~Vie~c~~h~~~ 30 (103)
-.+|++||++|.+.
T Consensus 74 tPkvie~Ckk~P~~ 87 (102)
T PRK11566 74 VPKVIEYCKKNPQK 87 (102)
T ss_pred chHHHHHHHhCCcc
Confidence 78999999999864
No 122
>PF08727 P3A: Poliovirus 3A protein like; InterPro: IPR014838 The 3A protein is found in positive-strand RNA viruses. It is a critical component of the poliovirus replication complex, and is also an inhibitor of host cell ER to Golgi transport. ; GO: 0003968 RNA-directed RNA polymerase activity, 0004197 cysteine-type endopeptidase activity, 0017111 nucleoside-triphosphatase activity; PDB: 1NG7_A.
Probab=24.61 E-value=52 Score=19.79 Aligned_cols=12 Identities=25% Similarity=0.827 Sum_probs=9.0
Q ss_pred HHHHHHHHhcCC
Q 037688 18 PYIIKFCKAHGV 29 (103)
Q Consensus 18 ~~Vie~c~~h~~ 29 (103)
..|++||+....
T Consensus 30 ~eV~~YC~~~GW 41 (57)
T PF08727_consen 30 PEVREYCEEQGW 41 (57)
T ss_dssp HHHHHHHHHHT-
T ss_pred HHHHHHHHHCCc
Confidence 479999997654
No 123
>PRK03094 hypothetical protein; Provisional
Probab=24.61 E-value=52 Score=21.02 Aligned_cols=13 Identities=8% Similarity=0.003 Sum_probs=10.9
Q ss_pred hcCCCHHHHHHHh
Q 037688 71 IKNKSVEYIRKFF 83 (103)
Q Consensus 71 i~gKt~eeiR~~f 83 (103)
..|+|+|||.+..
T Consensus 63 A~G~TaeEI~~~v 75 (80)
T PRK03094 63 ASGLTADEICQQV 75 (80)
T ss_pred cCCCCHHHHHHHH
Confidence 4799999998765
No 124
>KOG0743 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]
Probab=24.54 E-value=65 Score=26.94 Aligned_cols=40 Identities=23% Similarity=0.263 Sum_probs=27.8
Q ss_pred HHhhhhhchHHHHHHHHHHHHHHhcCC--CHHHHHHHhCCCCC
Q 037688 48 LLVANYLNIKEMLDYLTKTLANRIKNK--SVEYIRKFFGIQTN 88 (103)
Q Consensus 48 i~AA~yL~I~~Ll~l~~~~vA~~i~gK--t~eeiR~~f~I~~d 88 (103)
..|+|||+++. =.-.|..|...+.|- ||.|+.+.|--..+
T Consensus 377 ~La~nYL~~~~-~h~L~~eie~l~~~~~~tPA~V~e~lm~~~~ 418 (457)
T KOG0743|consen 377 TLASNYLGIEE-DHRLFDEIERLIEETEVTPAQVAEELMKNKN 418 (457)
T ss_pred HHHHHhcCCCC-CcchhHHHHHHhhcCccCHHHHHHHHhhccc
Confidence 36899999965 233344555566764 89999888876653
No 125
>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=24.51 E-value=50 Score=21.70 Aligned_cols=15 Identities=13% Similarity=0.350 Sum_probs=12.8
Q ss_pred cHHHHHHHHHhcCCc
Q 037688 16 QLPYIIKFCKAHGVS 30 (103)
Q Consensus 16 lL~~Vie~c~~h~~~ 30 (103)
.+++|+.||..|...
T Consensus 61 hMrkVV~yv~rhlaq 75 (92)
T PF11338_consen 61 HMRKVVGYVKRHLAQ 75 (92)
T ss_pred HHHHHHHHHHHHHhc
Confidence 399999999998754
No 126
>PF15628 RRM_DME: RRM in Demeter
Probab=24.43 E-value=70 Score=21.45 Aligned_cols=20 Identities=20% Similarity=0.257 Sum_probs=17.0
Q ss_pred HHHHHHhcCCCHHHHHHHhC
Q 037688 65 KTLANRIKNKSVEYIRKFFG 84 (103)
Q Consensus 65 ~~vA~~i~gKt~eeiR~~f~ 84 (103)
..|++..||.|.+||...|-
T Consensus 57 tsv~SIfrGls~~eIq~cF~ 76 (103)
T PF15628_consen 57 TSVSSIFRGLSREEIQQCFW 76 (103)
T ss_pred CcHHHHhcccCHHHHHHHHh
Confidence 45788889999999999884
No 127
>cd02137 Nitroreductase_1 Nitroreductase-like family 1. 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=23.85 E-value=77 Score=21.11 Aligned_cols=19 Identities=5% Similarity=0.289 Sum_probs=14.9
Q ss_pred cCCCHHHHHHHhCCCCCCC
Q 037688 72 KNKSVEYIRKFFGIQTNFM 90 (103)
Q Consensus 72 ~gKt~eeiR~~f~I~~d~t 90 (103)
.|-..+++++.||++++..
T Consensus 104 ~~~~~~~i~~~l~l~~~~~ 122 (148)
T cd02137 104 GGFDAEKVAELLNLPARYV 122 (148)
T ss_pred cCcCHHHHHHHhCcCCCce
Confidence 4457799999999998643
No 128
>PF06411 HdeA: HdeA/HdeB family; InterPro: IPR010486 HNS (histone-like nucleoid structuring)-dependent expression A (HdeA) protein is a stress response protein found in highly acid resistant bacteria such as Shigella flexneri and Escherichia coli, but which is lacking in mildly acid tolerant bacteria such as Salmonella []. HdeA is one of the most abundant proteins found in the periplasmic space of E. coli, where it is one of a network of proteins that confer an acid resistance phenotype essential for the pathogenesis of enteric bacteria []. HdeA is thought to act as a chaperone, functioning to prevent the aggregation of periplasmic proteins denatured under acidic conditions. The HNS protein, a chromatin-associated protein that influences the gene expression of several environmentally-induced target genes, represses the expression of HdeA. HdeB, which is encoded within the same operon, may form heterodimers with HdeA. HdeA is a single domain protein with an overall fold that is similar to the fold of the N-terminal subdomain of the GluRS anticodon-binding domain. ; PDB: 1BG8_C 1DJ8_C 2XUV_C.
Probab=23.52 E-value=54 Score=20.84 Aligned_cols=14 Identities=29% Similarity=0.740 Sum_probs=11.6
Q ss_pred HHHHHHHHHhcCCc
Q 037688 17 LPYIIKFCKAHGVS 30 (103)
Q Consensus 17 L~~Vie~c~~h~~~ 30 (103)
-.+|++||..|.+.
T Consensus 76 tp~v~~~Ckk~P~~ 89 (94)
T PF06411_consen 76 TPKVVEYCKKNPKS 89 (94)
T ss_dssp HHHHHHHHHCTTTS
T ss_pred hHHHHHHHHHCccc
Confidence 67899999998753
No 129
>PF03698 UPF0180: Uncharacterised protein family (UPF0180); InterPro: IPR005370 The members of this family are small uncharacterised proteins.
Probab=23.42 E-value=57 Score=20.76 Aligned_cols=13 Identities=15% Similarity=-0.003 Sum_probs=10.3
Q ss_pred hcCCCHHHHHHHh
Q 037688 71 IKNKSVEYIRKFF 83 (103)
Q Consensus 71 i~gKt~eeiR~~f 83 (103)
..|+||+||.+..
T Consensus 63 A~G~T~eEI~~~v 75 (80)
T PF03698_consen 63 ASGLTAEEIVQEV 75 (80)
T ss_pred cCCCCHHHHHHHH
Confidence 4799999997653
No 130
>PHA03098 kelch-like protein; Provisional
Probab=23.28 E-value=3.6e+02 Score=21.83 Aligned_cols=61 Identities=13% Similarity=0.188 Sum_probs=45.7
Q ss_pred HHHHHHHHHhcCCcchhhcccCCchhHHHHHHHhhhhhchHHHHHHHHHHHHHHhc---------CCCHHHHHHHhC
Q 037688 17 LPYIIKFCKAHGVSKENEFGKGKSNDELKEMLLVANYLNIKEMLDYLTKTLANRIK---------NKSVEYIRKFFG 84 (103)
Q Consensus 17 L~~Vie~c~~h~~~kD~~F~~~~~~~~L~~li~AA~yL~I~~Ll~l~~~~vA~~i~---------gKt~eeiR~~f~ 84 (103)
+..+.+.|..+- .+.++.+..+++...|...+...|.+.|-+.|+..+. .-+++++.+++.
T Consensus 90 ~~~l~~~C~~~l-------~~~l~~~nc~~~~~~a~~~~~~~L~~~~~~~i~~nf~~v~~~~~f~~l~~~~l~~ll~ 159 (534)
T PHA03098 90 IDFLINLCINYI-------IKIIDDNNCIDIYRFSFFYGCKKLYSAAYNYIRNNIELIYNDPDFIYLSKNELIKILS 159 (534)
T ss_pred cHHHHHHHHHHH-------HHhCCHhHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHhcCchhhcCCHHHHHHHhc
Confidence 566666666532 2344778889999999999999999999999886643 236788888765
No 131
>cd07022 S49_Sppa_36K_type Signal peptide peptidase A (SppA) 36K type, a serine protease, has catalytic Ser-Lys dyad. Signal peptide peptidase A (SppA; Peptidase S49; Protease IV) 36K type: SppA is found in all three domains of life and is involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. Members in this subfamily are all bacterial and include sohB peptidase and protein C. These are sometimes referred to as 36K type since they contain only one domain, unlike E. coli SppA that also contains an amino-terminal domain. Site-directed mutagenesis and sequence analysis have shown these SppAs to be serine proteases. The predicted active site serine for members in this family occurs in a transmembrane domain. Mutagenesis studies also suggest that the catalytic center comprises a Ser-Lys dyad and not the usual Ser-His-Asp catalytic triad found in the majority of serine proteases.
Probab=23.15 E-value=1.7e+02 Score=21.10 Aligned_cols=35 Identities=14% Similarity=0.192 Sum_probs=24.7
Q ss_pred hHHHHHHHHHHHHHHhcCCCHHHHHHHhCCCCCCChHH
Q 037688 56 IKEMLDYLTKTLANRIKNKSVEYIRKFFGIQTNFMPEE 93 (103)
Q Consensus 56 I~~Ll~l~~~~vA~~i~gKt~eeiR~~f~I~~d~t~ee 93 (103)
+..+.+.-...||.. +|.++++++..+ ..-||.++
T Consensus 159 l~~~~~~f~~~V~~~-R~~~~~~~~~~~--~~~~~~~~ 193 (214)
T cd07022 159 VDALYAMFVAAVARN-RGLSAAAVRATE--GGVFRGQE 193 (214)
T ss_pred HHHHHHHHHHHHHHh-CCCCHHHHHHhh--cCeeeHHH
Confidence 445555556666664 688999999988 45688865
No 132
>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=23.11 E-value=1.2e+02 Score=23.85 Aligned_cols=58 Identities=21% Similarity=0.335 Sum_probs=34.5
Q ss_pred hhhcccCCchhHHHHHHHhhhhhchHHHHHHHHHHHHHHhcCCCHHHHHHHhCCCCCCChHHH
Q 037688 32 ENEFGKGKSNDELKEMLLVANYLNIKEMLDYLTKTLANRIKNKSVEYIRKFFGIQTNFMPEEE 94 (103)
Q Consensus 32 D~~F~~~~~~~~L~~li~AA~yL~I~~Ll~l~~~~vA~~i~gKt~eeiR~~f~I~~d~t~eee 94 (103)
...|-+. ..+..++.+.|..-..+.+|+...-+ +..-..||+ |--....+++|||++-
T Consensus 208 ~N~ft~~-~~~~~~~~Laa~TgVsV~rlLaaI~~-L~~g~~G~~---IlG~~~ledE~Tp~~V 265 (293)
T PF05409_consen 208 NNGFTSF-SSDDAFDMLAAKTGVSVERLLAAIQR-LHKGFGGRT---ILGSCSLEDEFTPEMV 265 (293)
T ss_dssp HTTB--S-SHHHHHHHHHHHHT--HHHHHHHHHH-HHHTTTTT----BTTBSS--TSS-HHHH
T ss_pred hCCCccc-chhhHHHHHHHHhCCcHHHHHHHHHH-HhcCCCCCc---ccccccccccCCHHHH
Confidence 3455444 66778999999999999999986554 665556664 3334446667887764
No 133
>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=23.04 E-value=1.3e+02 Score=17.62 Aligned_cols=23 Identities=26% Similarity=0.261 Sum_probs=13.6
Q ss_pred HHHHHHHHHHHhcCCCHHHHHHH
Q 037688 60 LDYLTKTLANRIKNKSVEYIRKF 82 (103)
Q Consensus 60 l~l~~~~vA~~i~gKt~eeiR~~ 82 (103)
.+++.--+|-.+||-|++||..+
T Consensus 35 ~qiaAfL~al~~kget~~Eiag~ 57 (66)
T PF02885_consen 35 AQIAAFLMALRMKGETPEEIAGF 57 (66)
T ss_dssp HHHHHHHHHHHHH---HHHHHHH
T ss_pred HHHHHHHHHHHHhCcCHHHHHHH
Confidence 34555567778899999998654
No 134
>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=22.95 E-value=1.3e+02 Score=15.89 Aligned_cols=17 Identities=24% Similarity=0.382 Sum_probs=12.8
Q ss_pred hcCCCHHHHHHHhCCCC
Q 037688 71 IKNKSVEYIRKFFGIQT 87 (103)
Q Consensus 71 i~gKt~eeiR~~f~I~~ 87 (103)
..|.|..+|-+.+|++.
T Consensus 13 ~~~~s~~eia~~l~~s~ 29 (57)
T cd06170 13 AEGKTNKEIADILGISE 29 (57)
T ss_pred HcCCCHHHHHHHHCCCH
Confidence 46788888888888754
No 135
>PRK12552 ATP-dependent Clp protease-like protein; Reviewed
Probab=22.94 E-value=2.1e+02 Score=21.46 Aligned_cols=50 Identities=14% Similarity=0.164 Sum_probs=31.1
Q ss_pred HHHHHHHhhhhhchHHHHHHHHHHHHHHhcCCCHHHHHHHhCCCCCCChHHHH
Q 037688 43 ELKEMLLVANYLNIKEMLDYLTKTLANRIKNKSVEYIRKFFGIQTNFMPEEEE 95 (103)
Q Consensus 43 ~L~~li~AA~yL~I~~Ll~l~~~~vA~~i~gKt~eeiR~~f~I~~d~t~eee~ 95 (103)
.--++...|.- +..+-+...+..|.. .|++.++|.+...=..=+|++|-.
T Consensus 154 ~A~di~~~a~e--l~~~r~~l~~iya~~-TG~~~e~I~~d~~rd~wmsA~EA~ 203 (222)
T PRK12552 154 QATDIQIRAKE--VLHNKRTMLEILSRN-TGQTVEKLSKDTDRMFYLTPQEAK 203 (222)
T ss_pred CHHHHHHHHHH--HHHHHHHHHHHHHHH-HCCCHHHHHHHhcCCCcCCHHHHH
Confidence 33455444443 233334445555555 699999999999766557887754
No 136
>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=22.87 E-value=72 Score=18.66 Aligned_cols=18 Identities=11% Similarity=0.340 Sum_probs=14.0
Q ss_pred CccCc---HHHHHHHHHhcCC
Q 037688 12 MVVPQ---LPYIIKFCKAHGV 29 (103)
Q Consensus 12 ~~IPl---L~~Vie~c~~h~~ 29 (103)
..|++ ...++.||+.|..
T Consensus 18 ~RikvS~a~~~l~~y~e~~~~ 38 (57)
T cd00068 18 ERLKVSKAAAELLKYCEQNAE 38 (57)
T ss_pred chhhHHHHHHHHHHHHHhcCC
Confidence 34666 7889999999964
No 137
>PRK10828 putative oxidoreductase; Provisional
Probab=22.68 E-value=45 Score=23.40 Aligned_cols=34 Identities=15% Similarity=0.197 Sum_probs=22.0
Q ss_pred HHHHhhhhhchHHHHHHHHHHHHHHhcC--CCHHHHHHHhCCCCCC
Q 037688 46 EMLLVANYLNIKEMLDYLTKTLANRIKN--KSVEYIRKFFGIQTNF 89 (103)
Q Consensus 46 ~li~AA~yL~I~~Ll~l~~~~vA~~i~g--Kt~eeiR~~f~I~~d~ 89 (103)
.++.||.-+|+-+.+- .| -..+.+|+.|||++++
T Consensus 117 nl~LaA~a~GlGs~w~----------~~~~~~~~~~~~~L~ip~~~ 152 (183)
T PRK10828 117 AMQMAAVAQGFNGIWR----------SGAWTESPVVREAFGCREQD 152 (183)
T ss_pred HHHHHHHHCCCCeEee----------cCCCccCHHHHHHcCCCCCC
Confidence 5666666666643321 12 2457899999999875
No 138
>PF09883 DUF2110: Uncharacterized protein conserved in archaea (DUF2110); InterPro: IPR016757 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=22.66 E-value=69 Score=24.35 Aligned_cols=17 Identities=29% Similarity=0.430 Sum_probs=14.6
Q ss_pred CCHHHHHHHhCCCCCCC
Q 037688 74 KSVEYIRKFFGIQTNFM 90 (103)
Q Consensus 74 Kt~eeiR~~f~I~~d~t 90 (103)
+||.||+..||+-++++
T Consensus 112 g~~~Qi~~rFG~V~hlP 128 (225)
T PF09883_consen 112 GSPRQIRRRFGLVQHLP 128 (225)
T ss_pred CCHHHHHHHhCcccCCc
Confidence 89999999999876654
No 139
>PRK14514 ATP-dependent Clp protease proteolytic subunit; Provisional
Probab=22.54 E-value=2.1e+02 Score=21.40 Aligned_cols=36 Identities=8% Similarity=0.044 Sum_probs=24.4
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHHHhCCCCCCChHHHH
Q 037688 59 MLDYLTKTLANRIKNKSVEYIRKFFGIQTNFMPEEEE 95 (103)
Q Consensus 59 Ll~l~~~~vA~~i~gKt~eeiR~~f~I~~d~t~eee~ 95 (103)
+-+...+..|.+ .|++.++|++...=..=+|++|-.
T Consensus 173 ~~~~i~~iya~~-TG~~~e~I~~~~~rd~wmtA~EA~ 208 (221)
T PRK14514 173 LKKELYTIIADH-SGTPFDKVWADSDRDYWMTAQEAK 208 (221)
T ss_pred HHHHHHHHHHHH-HCcCHHHHHHHhhcCccCCHHHHH
Confidence 334444555554 599999999998765557877643
No 140
>cd00394 Clp_protease_like Caseinolytic protease (ClpP) is an ATP-dependent protease. Clp protease (caseinolytic protease; ClpP; endopeptidase Clp; Peptidase S14; ATP-dependent protease, ClpAP)-like enzymes are highly conserved serine proteases and belong to the ClpP/Crotonase superfamily. Included in this family are Clp proteases that are involved in a number of cellular processes such as degradation of misfolded proteins, regulation of short-lived proteins and housekeeping removal of dysfunctional proteins. They are also implicated in the control of cell growth, targeting DNA-binding protein from starved cells. The functional Clp protease is comprised of two components: a proteolytic component and one of several regulatory ATPase components, both of which are required for effective levels of protease activity in the presence of ATP. Active site consists of the triad Ser, His and Asp, preferring hydrophobic or non-polar residues at P1 or P1' positions. The protease exists as a tetradec
Probab=22.50 E-value=2e+02 Score=19.34 Aligned_cols=39 Identities=8% Similarity=0.090 Sum_probs=24.6
Q ss_pred HHHHHHHHHHHHHHhcCCCHHHHHHHhCCCCCCChHHHHH
Q 037688 57 KEMLDYLTKTLANRIKNKSVEYIRKFFGIQTNFMPEEEEA 96 (103)
Q Consensus 57 ~~Ll~l~~~~vA~~i~gKt~eeiR~~f~I~~d~t~eee~~ 96 (103)
..+.+.....++.. +|.+++++++.+.-..-+|++|-.+
T Consensus 116 ~~~~~~~~~~v~~~-r~~~~~~~~~~~~~~~~~~a~eA~~ 154 (161)
T cd00394 116 LYFIARFISLVAEN-RGQTTEKLEEDIEKDLVLTAQEALE 154 (161)
T ss_pred HHHHHHHHHHHHHh-cCCCHHHHHHHhcCCcEEcHHHHHH
Confidence 33444444555543 6789999998876555577776443
No 141
>KOG0783 consensus Uncharacterized conserved protein, contains ankyrin and BTB/POZ domains [Function unknown]
Probab=22.37 E-value=3.4e+02 Score=25.20 Aligned_cols=67 Identities=19% Similarity=0.293 Sum_probs=49.7
Q ss_pred CccCc----HHHHHHHHHhcCCcchhhcccC-CchhHHHHHHHhhhhhchHHHHHHHHHHHHHHhcCCCHHHHHH
Q 037688 12 MVVPQ----LPYIIKFCKAHGVSKENEFGKG-KSNDELKEMLLVANYLNIKEMLDYLTKTLANRIKNKSVEYIRK 81 (103)
Q Consensus 12 ~~IPl----L~~Vie~c~~h~~~kD~~F~~~-~~~~~L~~li~AA~yL~I~~Ll~l~~~~vA~~i~gKt~eeiR~ 81 (103)
...|+ |+-|+.|.---- ..+|++. ...+.+|+++..|.-|=|..|-++|-+.+-+.+.=|+...+-+
T Consensus 754 ~~~p~~~e~m~ivLdylYs~d---~~~~~k~~~~~dF~~~il~iaDqlli~~Lk~Ice~~ll~kl~lk~~~~lle 825 (1267)
T KOG0783|consen 754 NLSPLTVEHMSIVLDYLYSDD---KVELFKDLKESDFMFEILSIADQLLILELKSICEQSLLRKLNLKTLPTLLE 825 (1267)
T ss_pred ecCcchHHHHHHHHHHHHccc---hHHHHhccchhhhhHHHHHHHHHHHHHHHHHHHHHHHHhHhcccchHHHHH
Confidence 44665 888887764211 3466653 2567899999999999999999999999999888777655543
No 142
>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=22.26 E-value=1e+02 Score=21.77 Aligned_cols=21 Identities=19% Similarity=0.409 Sum_probs=17.5
Q ss_pred HHHHHHHhcCCCHHHHHHHhC
Q 037688 64 TKTLANRIKNKSVEYIRKFFG 84 (103)
Q Consensus 64 ~~~vA~~i~gKt~eeiR~~f~ 84 (103)
+..||+.|+|+++++-..++.
T Consensus 26 ~r~va~~IrG~~v~~A~~~L~ 46 (150)
T TIGR01038 26 ARETARAIRGMELDKARKYLE 46 (150)
T ss_pred HHHHHHHHcCCcHHHHHHHHH
Confidence 456889999999999888875
No 143
>PF09324 DUF1981: Domain of unknown function (DUF1981); InterPro: IPR015403 This domain is functionally uncharacterised and found in various plant and yeast protein transport proteins. It is noramlly associated with and C-termianl to the SEC7 domain. The SEC7 domain was named after the first protein found to contain such a region []. It has been shown to be linked with guanine nucleotide exchange function [, ].
Probab=22.25 E-value=1.1e+02 Score=19.19 Aligned_cols=32 Identities=13% Similarity=-0.004 Sum_probs=27.2
Q ss_pred ccCCchhHHHHHHHhhhhhchHHHHHHHHHHHH
Q 037688 36 GKGKSNDELKEMLLVANYLNIKEMLDYLTKTLA 68 (103)
Q Consensus 36 ~~~~~~~~L~~li~AA~yL~I~~Ll~l~~~~vA 68 (103)
++. +...+|+++.+|..-+-..|+..+.+.+-
T Consensus 53 i~S-GW~~if~il~~aa~~~~e~lv~~af~~~~ 84 (86)
T PF09324_consen 53 IKS-GWKVIFSILRAAAKDNDESLVRLAFQIVQ 84 (86)
T ss_pred HHh-ccHHHHHHHHHHHhCCCccHHHHHHHHHh
Confidence 445 78899999999999999999999988763
No 144
>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=22.25 E-value=61 Score=18.63 Aligned_cols=17 Identities=24% Similarity=0.292 Sum_probs=12.8
Q ss_pred cCCCHHHHHHHhCCCCC
Q 037688 72 KNKSVEYIRKFFGIQTN 88 (103)
Q Consensus 72 ~gKt~eeiR~~f~I~~d 88 (103)
-|-|.+|||+++.+..+
T Consensus 13 lGfsL~eI~~~l~l~~~ 29 (65)
T PF09278_consen 13 LGFSLEEIRELLELYDQ 29 (65)
T ss_dssp TT--HHHHHHHHHHCCS
T ss_pred cCCCHHHHHHHHhccCC
Confidence 48999999999988765
No 145
>PF01476 LysM: LysM domain; InterPro: IPR018392 This domain is about 40 residues long and is found in a variety of enzymes involved in bacterial cell wall degradation []. This domain may have a general peptidoglycan binding function.; GO: 0016998 cell wall macromolecule catabolic process; PDB: 2DJP_A 3ZQD_A 1Y7M_B 4A52_A 2L9Y_A 1E0G_A.
Probab=22.14 E-value=1.3e+02 Score=15.62 Aligned_cols=20 Identities=20% Similarity=0.177 Sum_probs=12.3
Q ss_pred HHHHHHHHhcCCCHHHHHHHh
Q 037688 63 LTKTLANRIKNKSVEYIRKFF 83 (103)
Q Consensus 63 ~~~~vA~~i~gKt~eeiR~~f 83 (103)
+|..||.+. |-|+++|++.=
T Consensus 8 tl~~IA~~~-~~~~~~l~~~N 27 (44)
T PF01476_consen 8 TLWSIAKRY-GISVDELMELN 27 (44)
T ss_dssp -HHHHHHHT-TS-HHHHHHHC
T ss_pred cHHHHHhhh-hhhHhHHHHhc
Confidence 456666664 77888887764
No 146
>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=22.02 E-value=1.1e+02 Score=19.65 Aligned_cols=20 Identities=20% Similarity=0.172 Sum_probs=15.8
Q ss_pred HHHHHHhcCCCHHHHHHHhC
Q 037688 65 KTLANRIKNKSVEYIRKFFG 84 (103)
Q Consensus 65 ~~vA~~i~gKt~eeiR~~f~ 84 (103)
..||+.|+|+++++=..++.
T Consensus 16 ~~v~~~Irg~~v~~A~~~L~ 35 (105)
T cd00336 16 RLVARLIRGMSVDEALAQLE 35 (105)
T ss_pred HHHHHHHcCCcHHHHHHHHH
Confidence 46888999999999666655
No 147
>PRK13723 conjugal transfer pilus assembly protein TraH; Provisional
Probab=21.98 E-value=2.9e+02 Score=23.04 Aligned_cols=66 Identities=14% Similarity=0.218 Sum_probs=43.7
Q ss_pred hhhcccCCchhHHHHHHHhhhhhch-----HHHHHHHHHHHHHHhcCCCHHHHHHHhCCCCCCChHHHHHHhh
Q 037688 32 ENEFGKGKSNDELKEMLLVANYLNI-----KEMLDYLTKTLANRIKNKSVEYIRKFFGIQTNFMPEEEEATRK 99 (103)
Q Consensus 32 D~~F~~~~~~~~L~~li~AA~yL~I-----~~Ll~l~~~~vA~~i~gKt~eeiR~~f~I~~d~t~eee~~i~~ 99 (103)
++.|++. -.--++.++..+..++. ..+-++.+..++...-.....++|..++- .+++++...++++
T Consensus 328 ek~Fl~~-t~~Pv~k~l~~~~~~g~s~~~~~~~a~~IA~dll~~yL~~~l~~~~~al~~-~~~~~~~~~~~~~ 398 (451)
T PRK13723 328 EKGFISS-TTIPVFKYLVDPQMLGVSNSLIYQLTDYIGYDILLQYIQELIQQARAMLAT-GNYPEAVMDHLRE 398 (451)
T ss_pred HHHHHhc-CchhHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-CCCCHHHHHHHHH
Confidence 7899988 45667777766666664 35555555555444445678888888865 5677776666654
No 148
>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=21.86 E-value=1.5e+02 Score=18.47 Aligned_cols=19 Identities=16% Similarity=0.127 Sum_probs=15.8
Q ss_pred HHhcCCCHHHHHHHhCCCC
Q 037688 69 NRIKNKSVEYIRKFFGIQT 87 (103)
Q Consensus 69 ~~i~gKt~eeiR~~f~I~~ 87 (103)
....|.|..||-+.+|++.
T Consensus 28 R~~eGlS~kEIAe~LGIS~ 46 (73)
T TIGR03879 28 REEAGKTASEIAEELGRTE 46 (73)
T ss_pred HHHcCCCHHHHHHHHCcCH
Confidence 4468999999999999875
No 149
>PRK02101 hypothetical protein; Validated
Probab=21.74 E-value=87 Score=23.72 Aligned_cols=42 Identities=14% Similarity=0.233 Sum_probs=29.9
Q ss_pred hHHHHHHHHHHHHHHhcCCCHHHHHHHhCCCCCCChHHHHHHh
Q 037688 56 IKEMLDYLTKTLANRIKNKSVEYIRKFFGIQTNFMPEEEEATR 98 (103)
Q Consensus 56 I~~Ll~l~~~~vA~~i~gKt~eeiR~~f~I~~d~t~eee~~i~ 98 (103)
.+.|.+ ..+.|+..++..|++|+.+.|||.+....+....++
T Consensus 24 ~p~l~~-~~~~ll~~l~~~s~~el~~l~~vs~~la~~~~~~~~ 65 (255)
T PRK02101 24 QPELLD-QSQELLDALRELSPDDLASLMKISDKLAGLNAARFQ 65 (255)
T ss_pred CcChHH-HHHHHHHHHHhCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 355555 455677778889999999999999876554444443
No 150
>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=21.69 E-value=1.7e+02 Score=18.53 Aligned_cols=42 Identities=12% Similarity=0.244 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHHhcCCCHHHHHHHhCCCC-CCChHHHHHHhh
Q 037688 58 EMLDYLTKTLANRIKNKSVEYIRKFFGIQT-NFMPEEEEATRK 99 (103)
Q Consensus 58 ~Ll~l~~~~vA~~i~gKt~eeiR~~f~I~~-d~t~eee~~i~~ 99 (103)
.|+-++|-.+|.++....+-.+.....+.+ .+|+++.-+.+.
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 477788889999988776666777666554 477777666543
No 151
>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=21.69 E-value=88 Score=21.07 Aligned_cols=30 Identities=10% Similarity=0.121 Sum_probs=22.2
Q ss_pred hHHHHHHHHHHHHHHhcCCCHHHHHHHhCC
Q 037688 56 IKEMLDYLTKTLANRIKNKSVEYIRKFFGI 85 (103)
Q Consensus 56 I~~Ll~l~~~~vA~~i~gKt~eeiR~~f~I 85 (103)
+-+...+.-+.|+..++|.|.||.+++...
T Consensus 74 l~~~~G~s~q~i~a~mtG~t~eef~~~~~~ 103 (106)
T cd07925 74 LAGILGLNMQDIGGLQTGMSTEEFKAMLVA 103 (106)
T ss_pred HHHHhCCcHHHHHHHhcCCCHHHHHHHHHh
Confidence 344455566788888899999998887654
No 152
>cd03735 SOCS_SOCS1 SOCS (suppressors of cytokine signaling) box of SOCS1-like proteins. Together with CIS1, the CIS/SOCS family of proteins is characterized by the presence of a C-terminal SOCS box and a central SH2 domain. SOCS1, like CIS1 and SOCS3, is involved in the down-regulation of the JAK/STAT pathway. SOCS1 has a dual function as a direct potent JAK kinase inhibitor and as a component of an E3 ubiquitin-ligase complex recruiting substrates to the protein degradation machinery.
Probab=21.48 E-value=55 Score=18.44 Aligned_cols=19 Identities=5% Similarity=0.282 Sum_probs=15.2
Q ss_pred hHHHHHHHHHHHHHHhcCC
Q 037688 56 IKEMLDYLTKTLANRIKNK 74 (103)
Q Consensus 56 I~~Ll~l~~~~vA~~i~gK 74 (103)
+.+|.++|.++|-..+.+.
T Consensus 3 ~~sLQhLCR~tI~~~~~~~ 21 (43)
T cd03735 3 VRPLQELCRKSIVATFGRE 21 (43)
T ss_pred ccCHHHHHHHHHHHhcCcc
Confidence 5689999999998876654
No 153
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=21.11 E-value=2.6e+02 Score=19.49 Aligned_cols=47 Identities=26% Similarity=0.219 Sum_probs=32.6
Q ss_pred chhHHHHHHHhhhhhchHHHHHHHHHHHHHH-hcCCCHHHHHHHhCCCCC
Q 037688 40 SNDELKEMLLVANYLNIKEMLDYLTKTLANR-IKNKSVEYIRKFFGIQTN 88 (103)
Q Consensus 40 ~~~~L~~li~AA~yL~I~~Ll~l~~~~vA~~-i~gKt~eeiR~~f~I~~d 88 (103)
+.+.+.++-.+..-|.- |-.-.++.|.-+ +.|-|.+||-+.+||+..
T Consensus 119 ~~~~~~~l~e~l~~L~~--l~~~~~~~v~l~~~~Gls~~EIA~~lgiS~~ 166 (185)
T PF07638_consen 119 SPEELLELEEALERLLA--LDPRQRRVVELRFFEGLSVEEIAERLGISER 166 (185)
T ss_pred CHHHHHHHHHHHHHHHc--cCHHHHHHHHHHHHCCCCHHHHHHHHCcCHH
Confidence 34456666665554333 556667777665 689999999999999863
No 154
>PRK02866 cyanate hydratase; Validated
Probab=21.08 E-value=2e+02 Score=20.41 Aligned_cols=35 Identities=20% Similarity=0.104 Sum_probs=19.0
Q ss_pred HHHHHHHHhcCCCHHHHHHHhCCCCCCChHHHHHHh
Q 037688 63 LTKTLANRIKNKSVEYIRKFFGIQTNFMPEEEEATR 98 (103)
Q Consensus 63 ~~~~vA~~i~gKt~eeiR~~f~I~~d~t~eee~~i~ 98 (103)
+-+.||..+ |.|...+...|.=+..+++|+-+++.
T Consensus 20 Tw~~IA~~i-G~S~v~vaaa~lGQ~~ls~e~A~kla 54 (147)
T PRK02866 20 TWADIAEAI-GLSEVWVTAALLGQMTLPAEEAEKVA 54 (147)
T ss_pred CHHHHHHHh-CCCHHHHHHHHhCCCCCCHHHHHHHH
Confidence 334455544 55555555555555556665555543
No 155
>TIGR00493 clpP ATP-dependent Clp protease, proteolytic subunit ClpP. This model for the proteolytic subunit ClpP has been rebuilt to a higher stringency. In every bacterial genome with the ClpXP machine, a ClpP protein will be found that scores with this model. In general, this ClpP member will be encoded adjacent to the clpX gene, as were all examples used in the seed alignment. A large fraction of genomes have one or more additional ClpP paralogs, sometimes encoded nearby and sometimes elsewhere. The stringency of the trusted cutoff used here excludes the more divergent ClpP paralogs from being called authentic ClpP by this model.
Probab=21.01 E-value=2.6e+02 Score=20.04 Aligned_cols=30 Identities=30% Similarity=0.225 Sum_probs=19.8
Q ss_pred HHHHHHHhcCCCHHHHHHHhCCCCCCChHHH
Q 037688 64 TKTLANRIKNKSVEYIRKFFGIQTNFMPEEE 94 (103)
Q Consensus 64 ~~~vA~~i~gKt~eeiR~~f~I~~d~t~eee 94 (103)
.+..|.. .|++++++++...=..=+|++|-
T Consensus 150 ~~~ya~~-tg~~~~~i~~~~~~~~~lta~EA 179 (191)
T TIGR00493 150 NDILANH-TGQSLEQIEKDTERDFFMSAEEA 179 (191)
T ss_pred HHHHHHH-HCcCHHHHHHHhhCCccCcHHHH
Confidence 3334443 58999999998764444677553
No 156
>KOG4350 consensus Uncharacterized conserved protein, contains BTB/POZ domain [General function prediction only]
Probab=20.91 E-value=41 Score=28.34 Aligned_cols=36 Identities=11% Similarity=0.277 Sum_probs=0.0
Q ss_pred CchhHHHHHHHhhhhhchHHHHHHHHHHHHHHhcCCCHHHH
Q 037688 39 KSNDELKEMLLVANYLNIKEMLDYLTKTLANRIKNKSVEYI 79 (103)
Q Consensus 39 ~~~~~L~~li~AA~yL~I~~Ll~l~~~~vA~~i~gKt~eei 79 (103)
+..+.+|-++.||.+.+.+.|.++|| |...+...++
T Consensus 145 L~~~NvCmifdaA~ly~l~~Lt~~C~-----mfmDrnA~~l 180 (620)
T KOG4350|consen 145 LKNENVCMIFDAAYLYQLTDLTDYCM-----MFMDRNADQL 180 (620)
T ss_pred HcccceeeeeeHHHHhcchHHHHHHH-----HHHhcCHHhh
No 157
>PF00574 CLP_protease: Clp protease; InterPro: IPR001907 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of serine peptidases belong to the MEROPS peptidase family S14 (ClpP endopeptidase family, clan SK). ClpP is an ATP-dependent protease that cleaves a number of proteins, such as casein and albumin []. It exists as a heterodimer of ATP-binding regulatory A and catalytic P subunits, both of which are required for effective levels of protease activity in the presence of ATP [], although the P subunit alone does possess some catalytic activity. This family of sequences represent the P subunit. Proteases highly similar to ClpP have been found to be encoded in the genome of bacteria, metazoa, some viruses and in the chloroplast of plants. A number of the proteins in this family are classified as non-peptidase homologues as they have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for catalytic activity. ; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 2ZL3_L 2ZL0_F 2ZL2_M 2ZL4_C 1TG6_D 2F6I_D 3V5I_b 3V5E_M 3QWD_D 2DEO_A ....
Probab=20.87 E-value=1.2e+02 Score=21.03 Aligned_cols=49 Identities=22% Similarity=0.203 Sum_probs=31.5
Q ss_pred HHHHHHhhhhhchHHHHHHHHHHHHHHhcCCCHHHHHHHhCCCCCCChHHHH
Q 037688 44 LKEMLLVANYLNIKEMLDYLTKTLANRIKNKSVEYIRKFFGIQTNFMPEEEE 95 (103)
Q Consensus 44 L~~li~AA~yL~I~~Ll~l~~~~vA~~i~gKt~eeiR~~f~I~~d~t~eee~ 95 (103)
.-++-..+.+|. .+.+...+.+|.. .|+++++|++...-..=+||+|--
T Consensus 122 ~~~l~~~~~~l~--~~~~~~~~~~~~~-tg~~~~~i~~~~~~~~~l~a~EA~ 170 (182)
T PF00574_consen 122 ASELREQAKELE--KLNERIANIYAER-TGLSKEEIEELMDRDTWLSAEEAL 170 (182)
T ss_dssp HHHHHHHHHHHH--HHHHHHHHHHHHH-HTS-HHHHHHHCSSTEEEEHHHHH
T ss_pred cchhHHHHHHHH--HHHHHHHHHHHHH-hCCcHHHHHHHHhCCccccHHHHH
Confidence 345555555544 4556677888887 599999999987643336776543
No 158
>KOG1534 consensus Putative transcription factor FET5 [Transcription]
Probab=20.61 E-value=2.2e+02 Score=22.05 Aligned_cols=70 Identities=17% Similarity=0.335 Sum_probs=41.7
Q ss_pred ccCcHHHHHHHHHhcCCcc------hhhcccCCchhHHH----HHHHhhhhhchHHHHHHHHHHHHHHhcCCCHHHHHHH
Q 037688 13 VVPQLPYIIKFCKAHGVSK------ENEFGKGKSNDELK----EMLLVANYLNIKEMLDYLTKTLANRIKNKSVEYIRKF 82 (103)
Q Consensus 13 ~IPlL~~Vie~c~~h~~~k------D~~F~~~~~~~~L~----~li~AA~yL~I~~Ll~l~~~~vA~~i~gKt~eeiR~~ 82 (103)
-+|+|+++|+-.++..-.- |.+|+- |....+ .-+.|--.|++|.. ++.++ -+.+++|+-+++.++
T Consensus 114 H~pVm~~iv~hl~~~~F~~c~Vylldsqf~v--D~~KfiSG~lsAlsAMi~lE~P~I-NvlsK--MDLlk~~~k~~l~~F 188 (273)
T KOG1534|consen 114 HLPVMPQIVEHLKQWNFNVCVVYLLDSQFLV--DSTKFISGCLSALSAMISLEVPHI-NVLSK--MDLLKDKNKKELERF 188 (273)
T ss_pred cChhHHHHHHHHhcccCceeEEEEeccchhh--hHHHHHHHHHHHHHHHHHhcCcch-hhhhH--HHHhhhhhHHHHHHh
Confidence 4566999988887733221 888863 333322 22334445565542 22222 245788999999999
Q ss_pred hCCCC
Q 037688 83 FGIQT 87 (103)
Q Consensus 83 f~I~~ 87 (103)
++...
T Consensus 189 l~~d~ 193 (273)
T KOG1534|consen 189 LNPDE 193 (273)
T ss_pred cCCch
Confidence 98655
No 159
>PRK04223 rpl22p 50S ribosomal protein L22P; Reviewed
Probab=20.59 E-value=1.2e+02 Score=21.56 Aligned_cols=21 Identities=10% Similarity=0.335 Sum_probs=17.6
Q ss_pred HHHHHHHhcCCCHHHHHHHhC
Q 037688 64 TKTLANRIKNKSVEYIRKFFG 84 (103)
Q Consensus 64 ~~~vA~~i~gKt~eeiR~~f~ 84 (103)
+..||+.|+|+++++-.+++.
T Consensus 30 ~r~va~~IRG~~v~~A~~~L~ 50 (153)
T PRK04223 30 SVEIAREIRGMKLDEAKAYLE 50 (153)
T ss_pred HHHHHHHHcCCcHHHHHHHHH
Confidence 356889999999999888876
No 160
>cd02149 NfsB_like_nitroreductase NAD(P)H:FMN oxidoreductase family. This domain catalyzes the reduction of flavin, nitrocompound, quinones and azo compounds using NADH or NADPH as an electron donor. The enzyme is a homodimer, and each monomer binds a FMN as co-factor. This family includes FRase I in Vibrio fischeri, wihich reduces FMN into FMNH2 as part of the bioluminescent reaction. The family also includes oxygen-insensitive nitroreductases that use NADH or NADPH as an electron donor in the ping pong bi bi mechanism. This type of nitroreductase can be used in cancer chemotherapy to activate a range of prodrugs.
Probab=20.58 E-value=89 Score=21.06 Aligned_cols=18 Identities=11% Similarity=0.309 Sum_probs=14.3
Q ss_pred hcCCCHHHHHHHhCCCCC
Q 037688 71 IKNKSVEYIRKFFGIQTN 88 (103)
Q Consensus 71 i~gKt~eeiR~~f~I~~d 88 (103)
+.|-..+++++.|||+++
T Consensus 111 i~~~~~~~v~~~l~l~~~ 128 (157)
T cd02149 111 IEGFDPAKLDEILGLDEK 128 (157)
T ss_pred ccCcCHHHHHHHhCCCcc
Confidence 445678999999999863
No 161
>CHL00034 rpl22 ribosomal protein L22
Probab=20.53 E-value=1.2e+02 Score=20.39 Aligned_cols=21 Identities=14% Similarity=0.278 Sum_probs=17.2
Q ss_pred HHHHHHHhcCCCHHHHHHHhC
Q 037688 64 TKTLANRIKNKSVEYIRKFFG 84 (103)
Q Consensus 64 ~~~vA~~i~gKt~eeiR~~f~ 84 (103)
+..||+.|+|+++++-..++.
T Consensus 24 ~r~va~~IRG~~v~~A~~~L~ 44 (117)
T CHL00034 24 ARRVIDQIRGRSYEEALMILE 44 (117)
T ss_pred HHHHHHHHcCCcHHHHHHHHH
Confidence 356889999999998887776
No 162
>KOG0028 consensus Ca2+-binding protein (centrin/caltractin), EF-Hand superfamily protein [Cytoskeleton; Cell cycle control, cell division, chromosome partitioning]
Probab=20.48 E-value=1.3e+02 Score=22.03 Aligned_cols=35 Identities=17% Similarity=0.295 Sum_probs=28.0
Q ss_pred hhhhhchHHHHHHHHHHHHHHhcCCCHHHHHHHhCCCC
Q 037688 50 VANYLNIKEMLDYLTKTLANRIKNKSVEYIRKFFGIQT 87 (103)
Q Consensus 50 AA~yL~I~~Ll~l~~~~vA~~i~gKt~eeiR~~f~I~~ 87 (103)
++.++..+.+....+.+++. ++ |-+||++.|.+-+
T Consensus 82 ~~g~i~fe~f~~~mt~k~~e--~d-t~eEi~~afrl~D 116 (172)
T KOG0028|consen 82 GSGKITFEDFRRVMTVKLGE--RD-TKEEIKKAFRLFD 116 (172)
T ss_pred cCceechHHHHHHHHHHHhc--cC-cHHHHHHHHHccc
Confidence 67788888888888877765 44 9999999999554
No 163
>PF14403 CP_ATPgrasp_2: Circularly permuted ATP-grasp type 2
Probab=20.25 E-value=2e+02 Score=23.93 Aligned_cols=34 Identities=32% Similarity=0.515 Sum_probs=19.5
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHHHhCCCCCCChHHHHHHhh
Q 037688 59 MLDYLTKTLANRIKNKSVEYIRKFFGIQTNFMPEEEEATRK 99 (103)
Q Consensus 59 Ll~l~~~~vA~~i~gKt~eeiR~~f~I~~d~t~eee~~i~~ 99 (103)
|+.+.++.+...+. ++ +.|+.||+ ||++++-|..
T Consensus 65 l~~i~~kv~~~~l~--d~-~lR~~fg~----~~~~e~Li~~ 98 (445)
T PF14403_consen 65 LYSILLKVIRRYLR--DP-ELRKLFGF----SPEEEELILI 98 (445)
T ss_pred HHHHHHHHHHHHhC--CH-HHHHHhCc----CHHHHHHhcC
Confidence 33444444333333 34 99999995 4667766543
No 164
>COG4224 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.15 E-value=85 Score=19.97 Aligned_cols=17 Identities=12% Similarity=0.288 Sum_probs=14.2
Q ss_pred CCCCCChHHHHHHhhhh
Q 037688 85 IQTNFMPEEEEATRKES 101 (103)
Q Consensus 85 I~~d~t~eee~~i~~e~ 101 (103)
.-+|+||+-..++++++
T Consensus 57 ~GnDVTP~Klk~~q~~~ 73 (77)
T COG4224 57 KGNDVTPEKLKQIQRKK 73 (77)
T ss_pred CCCCCChHHHHHHHHHh
Confidence 45699999999998875
No 165
>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR. Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo.
Probab=20.15 E-value=1.5e+02 Score=19.35 Aligned_cols=24 Identities=17% Similarity=0.083 Sum_probs=18.2
Q ss_pred HHHHHHH--hcCCCHHHHHHHhCCCC
Q 037688 64 TKTLANR--IKNKSVEYIRKFFGIQT 87 (103)
Q Consensus 64 ~~~vA~~--i~gKt~eeiR~~f~I~~ 87 (103)
++.|-.+ +.|+|.+||-+.+||+.
T Consensus 112 ~r~v~~l~~~~~~s~~EIA~~l~is~ 137 (142)
T TIGR03209 112 QKKIIYMKFFEDMKEIDIAKKLHISR 137 (142)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCcCH
Confidence 4444444 68999999999999874
No 166
>PF13833 EF-hand_8: EF-hand domain pair; PDB: 3KF9_A 1TTX_A 1WLZ_A 1ALV_A 1NX3_A 1ALW_A 1NX2_A 1NX1_A 1NX0_A 1DF0_A ....
Probab=20.11 E-value=1.4e+02 Score=16.13 Aligned_cols=22 Identities=27% Similarity=0.407 Sum_probs=10.0
Q ss_pred CHHHHHHHh---CCCCCCChHHHHHH
Q 037688 75 SVEYIRKFF---GIQTNFMPEEEEAT 97 (103)
Q Consensus 75 t~eeiR~~f---~I~~d~t~eee~~i 97 (103)
|+++++..+ |+.. +|++|-..+
T Consensus 6 ~~~~~~~~l~~~g~~~-~s~~e~~~l 30 (54)
T PF13833_consen 6 TREEFRRALSKLGIKD-LSEEEVDRL 30 (54)
T ss_dssp EHHHHHHHHHHTTSSS-SCHHHHHHH
T ss_pred CHHHHHHHHHHhCCCC-CCHHHHHHH
Confidence 445555544 3322 555554443
No 167
>PF15101 DUF4557: Domain of unknown function (DUF4557)
Probab=20.05 E-value=41 Score=25.30 Aligned_cols=26 Identities=27% Similarity=0.626 Sum_probs=22.2
Q ss_pred HHHHhcC-CCHHHHHHHhCCCCCCChH
Q 037688 67 LANRIKN-KSVEYIRKFFGIQTNFMPE 92 (103)
Q Consensus 67 vA~~i~g-Kt~eeiR~~f~I~~d~t~e 92 (103)
|-+|++| -|..+|+++.|--.||+|.
T Consensus 174 vNnmVtgyisiD~mkk~~gelhdFiPg 200 (212)
T PF15101_consen 174 VNNMVTGYISIDAMKKFLGELHDFIPG 200 (212)
T ss_pred hhhheeeeeehhHhhhhcchhhhhCCC
Confidence 6678888 6999999999988889873
No 168
>PRK00565 rplV 50S ribosomal protein L22; Reviewed
Probab=20.02 E-value=1.3e+02 Score=19.93 Aligned_cols=22 Identities=23% Similarity=0.311 Sum_probs=17.0
Q ss_pred HHHHHHHhcCCCHHHHHHHhCC
Q 037688 64 TKTLANRIKNKSVEYIRKFFGI 85 (103)
Q Consensus 64 ~~~vA~~i~gKt~eeiR~~f~I 85 (103)
+..|++.|+|+++++=..++..
T Consensus 17 ~~~v~~~IrG~~v~~A~~~L~~ 38 (112)
T PRK00565 17 ARLVADLIRGKKVEEALAILKF 38 (112)
T ss_pred HHHHHHHHcCCcHHHHHHHHHH
Confidence 3568889999999887776653
Done!