Query 024762
Match_columns 263
No_of_seqs 168 out of 337
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 07:12:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024762.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024762hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2829 E2F-like protein [Tran 100.0 5E-62 1.1E-66 449.1 20.2 169 92-260 38-207 (326)
2 PF08781 DP: Transcription fac 99.9 3E-24 6.5E-29 181.7 9.5 76 185-260 1-76 (142)
3 KOG2577 Transcription factor E 99.7 7.5E-18 1.6E-22 159.8 10.9 69 94-183 67-138 (354)
4 PF02319 E2F_TDP: E2F/DP famil 99.7 1.4E-18 3E-23 130.5 3.2 67 96-178 2-71 (71)
5 KOG2578 Transcription factor E 98.8 2.6E-09 5.7E-14 101.2 4.8 56 137-193 44-100 (388)
6 KOG2578 Transcription factor E 96.1 0.0027 5.8E-08 61.1 1.8 72 98-180 159-239 (388)
7 PF01978 TrmB: Sugar-specific 94.0 0.086 1.9E-06 38.2 3.9 59 98-177 4-63 (68)
8 COG1378 Predicted transcriptio 93.0 0.54 1.2E-05 43.2 8.3 34 149-182 42-76 (247)
9 PF05402 PqqD: Coenzyme PQQ sy 91.1 0.43 9.4E-06 34.2 4.3 55 99-168 14-68 (68)
10 smart00420 HTH_DEOR helix_turn 78.8 4.7 0.0001 26.4 4.2 48 106-174 4-51 (53)
11 COG3355 Predicted transcriptio 73.9 18 0.00039 30.8 7.4 56 98-174 23-79 (126)
12 cd07153 Fur_like Ferric uptake 71.2 11 0.00024 29.4 5.2 48 106-169 5-53 (116)
13 PF14338 Mrr_N: Mrr N-terminal 65.9 8.8 0.00019 29.6 3.6 66 103-172 5-75 (92)
14 PF09012 FeoC: FeoC like trans 65.9 12 0.00026 27.4 4.2 43 106-169 4-46 (69)
15 smart00346 HTH_ICLR helix_turn 65.5 16 0.00034 27.0 4.8 45 105-170 8-53 (91)
16 smart00418 HTH_ARSR helix_turn 65.5 9.4 0.0002 25.3 3.3 41 107-169 2-42 (66)
17 cd08768 Cdc6_C Winged-helix do 64.3 4.1 8.9E-05 30.3 1.5 20 150-169 45-64 (87)
18 PF14193 DUF4315: Domain of un 63.4 26 0.00056 27.8 5.8 36 186-221 2-37 (83)
19 PF13412 HTH_24: Winged helix- 63.4 23 0.00049 23.7 4.9 45 103-168 4-48 (48)
20 PRK09462 fur ferric uptake reg 62.4 20 0.00043 29.8 5.4 56 98-169 11-70 (148)
21 PF09079 Cdc6_C: CDC6, C termi 61.5 5 0.00011 30.2 1.5 20 150-169 38-57 (85)
22 cd00890 Prefoldin Prefoldin is 61.0 73 0.0016 25.1 8.2 55 169-223 67-125 (129)
23 PF09339 HTH_IclR: IclR helix- 60.2 12 0.00026 25.9 3.1 45 105-170 6-51 (52)
24 smart00347 HTH_MARR helix_turn 59.8 65 0.0014 23.4 7.6 52 98-170 6-57 (101)
25 PRK03947 prefoldin subunit alp 59.5 59 0.0013 26.7 7.6 57 167-223 72-132 (140)
26 TIGR00293 prefoldin, archaeal 58.8 59 0.0013 26.1 7.4 66 155-220 52-121 (126)
27 PF00392 GntR: Bacterial regul 56.0 11 0.00023 27.0 2.3 55 119-173 2-61 (64)
28 TIGR02337 HpaR homoprotocatech 53.8 1E+02 0.0022 24.2 7.8 51 99-170 25-75 (118)
29 PF01475 FUR: Ferric uptake re 53.6 38 0.00082 26.8 5.4 55 99-169 3-60 (120)
30 PF03836 RasGAP_C: RasGAP C-te 53.4 4.4 9.6E-05 34.0 0.0 65 149-216 4-78 (142)
31 PF13404 HTH_AsnC-type: AsnC-t 53.0 24 0.00053 24.1 3.6 25 102-126 3-27 (42)
32 PF07334 IFP_35_N: Interferon- 51.8 51 0.0011 26.0 5.6 60 187-261 2-65 (76)
33 PF03979 Sigma70_r1_1: Sigma-7 51.7 16 0.00035 27.9 2.9 22 106-127 11-32 (82)
34 PRK10411 DNA-binding transcrip 50.9 1.2E+02 0.0026 27.4 8.8 53 105-178 7-60 (240)
35 PF08279 HTH_11: HTH domain; 50.4 56 0.0012 22.2 5.2 48 106-174 4-54 (55)
36 COG0735 Fur Fe2+/Zn2+ uptake r 49.9 57 0.0012 27.5 6.2 56 105-176 24-82 (145)
37 PF11594 Med28: Mediator compl 49.5 60 0.0013 27.1 6.0 36 188-223 38-73 (106)
38 PF11315 Med30: Mediator compl 49.4 67 0.0015 28.1 6.6 31 186-216 105-135 (150)
39 smart00344 HTH_ASNC helix_turn 48.7 33 0.00072 26.3 4.3 45 104-169 5-49 (108)
40 cd00584 Prefoldin_alpha Prefol 47.9 1.5E+02 0.0032 23.9 8.4 53 170-222 68-124 (129)
41 smart00550 Zalpha Z-DNA-bindin 46.7 43 0.00093 24.7 4.4 52 105-177 9-63 (68)
42 PRK10434 srlR DNA-bindng trans 45.9 93 0.002 28.3 7.3 45 105-170 8-52 (256)
43 PRK14127 cell division protein 45.1 37 0.0008 28.2 4.2 53 162-216 7-68 (109)
44 PF06717 DUF1202: Protein of u 44.8 89 0.0019 30.4 7.2 58 164-223 119-176 (308)
45 TIGR00589 ogt O-6-methylguanin 43.8 29 0.00062 26.9 3.2 25 102-126 2-29 (80)
46 PF10473 CENP-F_leu_zip: Leuci 43.7 84 0.0018 27.1 6.3 40 185-224 73-112 (140)
47 PF01035 DNA_binding_1: 6-O-me 42.9 19 0.0004 27.8 2.0 25 102-126 2-29 (85)
48 PF12840 HTH_20: Helix-turn-he 42.4 56 0.0012 23.1 4.3 45 105-170 13-57 (61)
49 PF07544 Med9: RNA polymerase 40.1 64 0.0014 25.0 4.6 49 149-213 32-80 (83)
50 smart00338 BRLZ basic region l 38.9 1.4E+02 0.0031 21.5 6.1 35 187-221 28-62 (65)
51 PF02996 Prefoldin: Prefoldin 38.0 1.5E+02 0.0032 23.2 6.5 70 156-225 44-117 (120)
52 PF01022 HTH_5: Bacterial regu 37.9 56 0.0012 22.1 3.6 42 106-169 6-47 (47)
53 cd00090 HTH_ARSR Arsenical Res 37.3 1.2E+02 0.0026 20.3 5.3 45 103-169 8-52 (78)
54 PF08317 Spc7: Spc7 kinetochor 37.1 1E+02 0.0022 29.2 6.4 34 186-219 210-243 (325)
55 KOG2264 Exostosin EXT1L [Signa 37.0 73 0.0016 34.1 5.7 9 238-246 154-162 (907)
56 PF08317 Spc7: Spc7 kinetochor 36.9 1.3E+02 0.0028 28.5 7.0 40 186-225 231-270 (325)
57 smart00345 HTH_GNTR helix_turn 36.2 48 0.001 22.0 3.1 21 149-169 32-52 (60)
58 cd06445 ATase The DNA repair p 35.9 39 0.00085 25.5 2.8 23 104-126 2-27 (79)
59 COG5625 Predicted transcriptio 35.5 95 0.0021 26.1 5.1 63 112-195 32-97 (113)
60 TIGR02894 DNA_bind_RsfA transc 35.0 1.8E+02 0.0039 25.9 7.1 43 186-228 105-154 (161)
61 smart00787 Spc7 Spc7 kinetocho 34.8 1.1E+02 0.0024 29.4 6.2 17 49-65 5-21 (312)
62 PRK07037 extracytoplasmic-func 34.5 31 0.00068 27.9 2.2 34 114-164 123-156 (163)
63 PRK11179 DNA-binding transcrip 34.4 58 0.0013 27.2 3.8 51 98-169 5-55 (153)
64 cd00092 HTH_CRP helix_turn_hel 34.3 1.5E+02 0.0032 20.4 5.4 40 114-174 23-63 (67)
65 PRK06798 fliD flagellar cappin 33.9 1.1E+02 0.0023 30.7 6.1 64 148-223 357-421 (440)
66 COG3937 Uncharacterized conser 33.2 1.4E+02 0.003 25.1 5.7 11 149-159 65-75 (108)
67 PRK11169 leucine-responsive tr 33.2 60 0.0013 27.4 3.8 52 97-169 9-60 (164)
68 KOG2077 JNK/SAPK-associated pr 33.1 1.1E+02 0.0024 32.7 6.3 77 144-229 22-99 (832)
69 PF09766 FimP: Fms-interacting 33.1 1.3E+02 0.0027 29.2 6.4 37 185-221 108-144 (355)
70 PF14817 HAUS5: HAUS augmin-li 32.5 1.7E+02 0.0037 31.0 7.6 49 168-216 53-110 (632)
71 PF05529 Bap31: B-cell recepto 32.5 1E+02 0.0023 26.6 5.2 29 189-217 158-186 (192)
72 PF08220 HTH_DeoR: DeoR-like h 32.2 1.1E+02 0.0024 21.6 4.5 49 105-174 3-51 (57)
73 PF07195 FliD_C: Flagellar hoo 32.0 2.4E+02 0.0052 25.3 7.6 61 147-223 169-235 (239)
74 PF10186 Atg14: UV radiation r 31.8 2.1E+02 0.0045 25.5 7.1 12 148-159 37-48 (302)
75 PF12958 DUF3847: Protein of u 31.7 2E+02 0.0044 23.0 6.3 33 186-218 2-34 (86)
76 PF01047 MarR: MarR family; I 31.3 91 0.002 21.3 3.9 44 105-169 6-49 (59)
77 PF12269 zf-CpG_bind_C: CpG bi 31.2 1.3E+02 0.0028 28.2 5.9 51 176-229 16-66 (236)
78 PF14394 DUF4423: Domain of un 31.1 3.5E+02 0.0077 23.5 9.4 59 98-176 16-79 (171)
79 PRK11639 zinc uptake transcrip 31.0 1.1E+02 0.0025 26.2 5.2 53 107-175 31-86 (169)
80 PF01726 LexA_DNA_bind: LexA D 30.9 1E+02 0.0022 22.9 4.2 46 107-172 15-61 (65)
81 PF04977 DivIC: Septum formati 30.8 1.7E+02 0.0036 21.1 5.4 30 187-216 19-48 (80)
82 PF02050 FliJ: Flagellar FliJ 30.7 2.3E+02 0.0049 21.1 7.4 44 185-228 59-102 (123)
83 PF04492 Phage_rep_O: Bacterio 30.5 38 0.00083 27.4 2.1 25 150-174 67-91 (100)
84 TIGR01242 26Sp45 26S proteasom 30.5 1.6E+02 0.0035 27.7 6.6 40 189-228 3-42 (364)
85 PF04380 BMFP: Membrane fusoge 30.5 1.1E+02 0.0024 23.5 4.5 49 147-213 30-78 (79)
86 smart00419 HTH_CRP helix_turn_ 30.3 49 0.0011 21.3 2.2 25 150-174 21-45 (48)
87 PRK00888 ftsB cell division pr 30.3 1.7E+02 0.0036 23.7 5.7 34 186-219 28-61 (105)
88 COG0350 Ada Methylated DNA-pro 30.0 51 0.0011 28.7 2.9 26 102-127 88-116 (168)
89 PRK10803 tol-pal system protei 29.9 1.7E+02 0.0036 27.1 6.4 45 183-227 59-104 (263)
90 PRK09954 putative kinase; Prov 29.6 90 0.0019 29.1 4.6 46 103-169 4-49 (362)
91 PRK00901 methylated-DNA--prote 29.6 54 0.0012 28.4 3.0 25 102-126 73-100 (155)
92 PF10828 DUF2570: Protein of u 28.7 3.1E+02 0.0068 22.0 7.1 64 151-225 2-65 (110)
93 PF10481 CENP-F_N: Cenp-F N-te 28.6 1.3E+02 0.0029 29.2 5.6 37 176-212 8-45 (307)
94 TIGR02263 benz_CoA_red_C benzo 28.3 5.5E+02 0.012 24.8 10.1 67 151-224 106-180 (380)
95 PF11853 DUF3373: Protein of u 28.0 56 0.0012 33.6 3.2 29 200-228 32-60 (489)
96 PF13730 HTH_36: Helix-turn-he 27.7 39 0.00085 23.0 1.5 19 149-167 37-55 (55)
97 COG3883 Uncharacterized protei 27.4 2.3E+02 0.005 27.0 6.9 42 187-228 61-103 (265)
98 PRK10884 SH3 domain-containing 27.2 2.7E+02 0.006 25.2 7.2 33 190-222 137-169 (206)
99 PF04156 IncA: IncA protein; 27.1 3E+02 0.0065 23.4 7.1 40 189-228 148-187 (191)
100 PRK13777 transcriptional regul 27.1 4.4E+02 0.0096 23.3 9.3 61 98-179 41-105 (185)
101 PF13463 HTH_27: Winged helix 26.9 86 0.0019 21.8 3.2 42 107-169 8-50 (68)
102 PF12802 MarR_2: MarR family; 26.7 1.6E+02 0.0036 20.0 4.5 51 99-170 2-54 (62)
103 PRK07720 fliJ flagellar biosyn 26.6 2.8E+02 0.006 22.8 6.6 43 186-228 79-121 (146)
104 PRK09802 DNA-binding transcrip 26.4 3.4E+02 0.0074 25.0 7.8 48 105-173 20-68 (269)
105 PRK10884 SH3 domain-containing 26.2 2.7E+02 0.0059 25.2 6.9 6 239-244 189-194 (206)
106 PF05103 DivIVA: DivIVA protei 25.8 14 0.00031 29.4 -1.2 47 174-220 13-67 (131)
107 PRK05771 V-type ATP synthase s 25.7 1.1E+02 0.0023 31.6 4.7 18 116-133 11-28 (646)
108 KOG1962 B-cell receptor-associ 25.5 1.8E+02 0.0039 27.0 5.7 39 186-224 152-190 (216)
109 PRK13923 putative spore coat p 25.4 3E+02 0.0064 24.7 6.8 44 186-229 112-155 (170)
110 PF04568 IATP: Mitochondrial A 25.1 2.1E+02 0.0045 23.5 5.4 10 204-213 88-97 (100)
111 PRK15090 DNA-binding transcrip 25.1 5E+02 0.011 23.2 8.4 45 105-170 17-61 (257)
112 PHA02047 phage lambda Rz1-like 25.0 1.5E+02 0.0032 24.7 4.5 52 173-227 25-80 (101)
113 PF08664 YcbB: YcbB domain; I 24.9 73 0.0016 27.3 2.9 61 106-168 23-89 (134)
114 smart00787 Spc7 Spc7 kinetocho 24.7 2.8E+02 0.006 26.6 7.0 35 189-223 208-242 (312)
115 PF07571 DUF1546: Protein of u 24.4 1.2E+02 0.0026 23.8 3.8 61 95-165 17-77 (92)
116 TIGR02147 Fsuc_second hypothet 24.4 6E+02 0.013 23.9 10.5 60 98-177 114-178 (271)
117 TIGR02473 flagell_FliJ flagell 24.2 3.4E+02 0.0074 21.6 6.5 43 185-227 75-117 (141)
118 KOG3478 Prefoldin subunit 6, K 24.2 1.6E+02 0.0034 25.1 4.7 23 157-179 38-60 (120)
119 PRK13509 transcriptional repre 24.2 3.9E+02 0.0084 24.2 7.6 44 105-169 8-51 (251)
120 TIGR02894 DNA_bind_RsfA transc 24.1 2.3E+02 0.005 25.2 5.9 26 189-214 101-126 (161)
121 TIGR02431 pcaR_pcaU beta-ketoa 24.0 1.6E+02 0.0035 26.1 5.1 50 105-175 12-62 (248)
122 PRK13922 rod shape-determining 23.9 2.4E+02 0.0051 25.7 6.2 20 186-205 70-89 (276)
123 PRK07737 fliD flagellar cappin 23.8 2.3E+02 0.0049 28.8 6.5 75 145-224 410-484 (501)
124 PRK05689 fliJ flagellar biosyn 23.8 3.3E+02 0.0072 22.3 6.6 44 185-228 78-121 (147)
125 PRK09834 DNA-binding transcrip 23.7 1.7E+02 0.0037 26.4 5.2 51 104-175 13-66 (263)
126 TIGR03859 PQQ_PqqD coenzyme PQ 23.6 1.6E+02 0.0034 22.5 4.2 55 98-168 27-81 (81)
127 PF03962 Mnd1: Mnd1 family; I 23.4 4.9E+02 0.011 23.0 7.9 50 154-204 32-88 (188)
128 PF13094 CENP-Q: CENP-Q, a CEN 23.1 3.3E+02 0.0071 22.9 6.5 41 185-225 41-81 (160)
129 PF07106 TBPIP: Tat binding pr 22.8 4.7E+02 0.01 22.1 11.5 87 107-212 6-106 (169)
130 PF09457 RBD-FIP: FIP domain ; 22.8 3E+02 0.0065 19.8 5.8 25 189-213 4-28 (48)
131 COG1522 Lrp Transcriptional re 22.6 96 0.0021 25.0 3.1 55 100-175 6-60 (154)
132 PF10234 Cluap1: Clusterin-ass 22.6 2E+02 0.0044 27.3 5.6 20 187-206 185-204 (267)
133 PRK13182 racA polar chromosome 22.4 2.8E+02 0.006 24.5 6.1 35 185-219 85-119 (175)
134 PRK03992 proteasome-activating 22.1 7E+02 0.015 24.1 9.3 72 188-259 4-82 (389)
135 PF04977 DivIC: Septum formati 22.1 3E+02 0.0065 19.7 5.4 38 184-221 23-60 (80)
136 PRK10079 phosphonate metabolis 22.1 1E+02 0.0022 27.2 3.3 53 117-169 12-67 (241)
137 PF04156 IncA: IncA protein; 22.0 3.4E+02 0.0074 23.1 6.5 16 149-164 99-114 (191)
138 TIGR02338 gimC_beta prefoldin, 22.0 3.5E+02 0.0075 21.6 6.1 59 156-214 35-96 (110)
139 PF14282 FlxA: FlxA-like prote 21.8 2.8E+02 0.0061 22.3 5.6 18 203-220 48-65 (106)
140 cd00632 Prefoldin_beta Prefold 21.6 4.1E+02 0.0088 20.9 6.6 69 149-220 27-98 (105)
141 TIGR00498 lexA SOS regulatory 21.5 1.5E+02 0.0032 25.4 4.2 51 104-174 8-63 (199)
142 PRK11402 DNA-binding transcrip 21.3 1E+02 0.0022 27.1 3.3 54 116-169 8-65 (241)
143 PRK10163 DNA-binding transcrip 21.3 6.3E+02 0.014 23.0 8.4 45 105-170 28-73 (271)
144 TIGR02404 trehalos_R_Bsub treh 20.9 1.1E+02 0.0023 26.8 3.2 51 119-169 2-56 (233)
145 COG1730 GIM5 Predicted prefold 20.8 5.6E+02 0.012 22.2 9.0 40 185-224 94-133 (145)
146 KOG3856 Uncharacterized conser 20.8 2.8E+02 0.0061 24.1 5.6 44 183-226 8-52 (135)
147 KOG0240 Kinesin (SMY1 subfamil 20.6 9.3E+02 0.02 25.7 10.2 23 110-132 351-373 (607)
148 PF10557 Cullin_Nedd8: Cullin 20.3 1.5E+02 0.0032 21.8 3.4 55 104-171 10-64 (68)
149 PF01638 HxlR: HxlR-like helix 20.3 1.5E+02 0.0032 22.6 3.6 45 104-169 7-51 (90)
150 COG1938 Archaeal enzymes of AT 20.2 2.8E+02 0.0061 26.1 5.9 27 186-212 205-231 (244)
151 KOG2264 Exostosin EXT1L [Signa 20.0 2.4E+02 0.0051 30.5 5.9 40 187-226 109-152 (907)
No 1
>KOG2829 consensus E2F-like protein [Transcription]
Probab=100.00 E-value=5e-62 Score=449.10 Aligned_cols=169 Identities=59% Similarity=0.895 Sum_probs=161.5
Q ss_pred CCCcCCcchhhHHHHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCC-CCCCCccccccccchhhhhhHHHHhhhccccccc
Q 024762 92 GGDKSGRGLRQFSMKVCEKVESKGRTTYNEVADELVAEFADPSNS-LATPDQQQYDEKNIRRRVYDALNVLMAMDIISKD 170 (263)
Q Consensus 92 ~~~k~~kGLR~fS~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~-~~~~~~~~~deKniKRRVYDalNVL~ai~lI~K~ 170 (263)
.++++++|||||||+|||||++||.||||||||+||++|..+++. ...++++.||+|||||||||||||||||+||+|+
T Consensus 38 ks~k~g~gLRhfs~kVCeKve~Kg~TtYneVADelVaef~~~n~~~~i~~n~~~yd~KNIRRRVYDALNVlmAmnIIsKd 117 (326)
T KOG2829|consen 38 KSDKAGGGLRHFSMKVCEKVERKGTTTYNEVADELVAEFAGANNYSHICPNEQEYDQKNIRRRVYDALNVLMAMNIISKD 117 (326)
T ss_pred CCCCCCcchhhhhHHHHHHHHhcCCccHHHHHHHHHHHHhccccccccCccccccchHHHHHHHHHHHHHHHHHHHHhcc
Confidence 367899999999999999999999999999999999999988762 4467889999999999999999999999999999
Q ss_pred CCeeeeccCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCccccceEEEEcCC
Q 024762 171 KKEIQWKGLPRTSLNDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQRNERLYSSGNAPSGGVALPFILVQVDI 250 (263)
Q Consensus 171 Kk~I~W~G~~~~s~~~~~~Lk~E~~~l~erI~~Kk~~LqEL~~Q~~alknLI~RNk~~~~~~~~ps~~I~LPFIlV~T~~ 250 (263)
||+|+|+|+|.++.+++++|++|+.+++++|++|+++||||++|+++|++||+||+.++.++.+|...|+||||||+|++
T Consensus 118 KKEIrW~GLP~~ss~dv~~le~Er~k~~erI~kK~a~lqEl~~q~~~fknLV~RN~~~e~~~~~P~~~i~LPFiiinT~k 197 (326)
T KOG2829|consen 118 KKEIRWIGLPATSSQDVSELEEERKKRMERIKKKAAQLQELIEQVSAFKNLVQRNRHAESQGQPPSENIHLPFIIINTSK 197 (326)
T ss_pred cceeeeeccCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhccCCCCcccccceEEEecCC
Confidence 99999999999999999999999999999999999999999999999999999999999988888888999999999999
Q ss_pred CceEEeEeee
Q 024762 251 RQLFSCIMAS 260 (263)
Q Consensus 251 ~tvI~C~iss 260 (263)
+|+|+|+|++
T Consensus 198 ~a~Ieceise 207 (326)
T KOG2829|consen 198 KAVIECEISE 207 (326)
T ss_pred CceEEEEecc
Confidence 9999999986
No 2
>PF08781 DP: Transcription factor DP; InterPro: IPR014889 DP forms a heterodimer with E2F and regulates genes involved in cell cycle progression. The transcriptional activity of E2F is inhibited by the retinoblastoma protein which binds to the E2F-DP heterodimer [] and negatively regulates the G1-S transition. ; PDB: 2AZE_A.
Probab=99.91 E-value=3e-24 Score=181.73 Aligned_cols=76 Identities=46% Similarity=0.698 Sum_probs=67.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCccccceEEEEcCCCceEEeEeee
Q 024762 185 NDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQRNERLYSSGNAPSGGVALPFILVQVDIRQLFSCIMAS 260 (263)
Q Consensus 185 ~~~~~Lk~E~~~l~erI~~Kk~~LqEL~~Q~~alknLI~RNk~~~~~~~~ps~~I~LPFIlV~T~~~tvI~C~iss 260 (263)
++|++|++|+.++++||++|+++||||+.|+++|+|||+||+++++++.+|+++|+||||||+|+++|+|+|+||.
T Consensus 1 q~~~~Le~ek~~~~~rI~~K~~~LqEL~~Q~va~knLv~RN~~~~~~~~~p~~~i~LPFIlV~T~~~a~I~ceiS~ 76 (142)
T PF08781_consen 1 QECEELEEEKQRRRERIKKKKEQLQELILQQVAFKNLVQRNRQLEQSGNAPSSGIQLPFILVNTSKKAVIECEISE 76 (142)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSSS--GEEESS-EEEEEESS--EEEEE-T
T ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCeeecCEEEEEecCCcEEEEEEcC
Confidence 5799999999999999999999999999999999999999999999888888999999999999999999999985
No 3
>KOG2577 consensus Transcription factor E2F/dimerization partner (TDP) [Transcription]
Probab=99.74 E-value=7.5e-18 Score=159.84 Aligned_cols=69 Identities=32% Similarity=0.494 Sum_probs=62.0
Q ss_pred CcCCcchhhHHHHHHHHHHhc--CCCcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhcccccc-c
Q 024762 94 DKSGRGLRQFSMKVCEKVESK--GRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK-D 170 (263)
Q Consensus 94 ~k~~kGLR~fS~KVcekVk~k--g~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~K-~ 170 (263)
-+..+.|-.+.+|+.++|++. |....|++|+.| ++.|||||||||||||||||+| +
T Consensus 67 ~R~d~SLglLTkKFv~Llq~s~dGvldLn~aA~~L---------------------~VqKRRIYDITNVLEGI~LIeKks 125 (354)
T KOG2577|consen 67 TRSDTSLGLLTKKFVDLLQESPDGVLDLNKAAEVL---------------------NVQKRRIYDITNVLEGIGLIEKKS 125 (354)
T ss_pred ccchhhHHHHHHHHHHHHHhCCCceeeHHHHHHHh---------------------ccccceeeehhhhhhcccceeecc
Confidence 345678999999999999984 599999999997 2779999999999999999999 9
Q ss_pred CCeeeeccCCCCC
Q 024762 171 KKEIQWKGLPRTS 183 (263)
Q Consensus 171 Kk~I~W~G~~~~s 183 (263)
||+|+|+|.+.+.
T Consensus 126 KN~IqW~G~~~~~ 138 (354)
T KOG2577|consen 126 KNNIQWIGGDFNS 138 (354)
T ss_pred ccceeeecCCCcc
Confidence 9999999988764
No 4
>PF02319 E2F_TDP: E2F/DP family winged-helix DNA-binding domain; InterPro: IPR003316 The mammalian transcription factor E2F plays an important role in regulating the expression of genes that are required for passage through the cell cycle. Multiple E2F family members have been identified that bind to DNA as heterodimers, interacting with proteins known as DP - the dimerisation partners [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005667 transcription factor complex; PDB: 1CF7_B.
Probab=99.73 E-value=1.4e-18 Score=130.46 Aligned_cols=67 Identities=36% Similarity=0.644 Sum_probs=57.2
Q ss_pred CCcchhhHHHHHHHHHHh--cCCCcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhcccccc-cCC
Q 024762 96 SGRGLRQFSMKVCEKVES--KGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK-DKK 172 (263)
Q Consensus 96 ~~kGLR~fS~KVcekVk~--kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~K-~Kk 172 (263)
..+||.+++.++.+.+.. .+.+++++||++|+.+ +.|+.|||||||+|||+|+|||+| .|+
T Consensus 2 ~~~sL~~lt~~fi~~~~~~~~~~i~l~~ia~~l~~~----------------~~k~~~RRlYDI~NVLealgli~K~~k~ 65 (71)
T PF02319_consen 2 KEKSLKLLTQRFIQLFESSPDKSISLNEIADKLISE----------------NVKTQRRRLYDIINVLEALGLIEKQSKN 65 (71)
T ss_dssp TTTHHHHHHHHHHHHHHHCCCTEEEHHHHHHHCHHH----------------CCHHHCHHHHHHHHHHHHCTSEEEEETT
T ss_pred CcCCHHHHHHHHHHHHHHCCCCcccHHHHHHHHccc----------------ccccccchhhHHHHHHHHhCceeecCCC
Confidence 458999999995555543 4899999999999988 367899999999999999999999 999
Q ss_pred eeeecc
Q 024762 173 EIQWKG 178 (263)
Q Consensus 173 ~I~W~G 178 (263)
.|+|.|
T Consensus 66 ~~~W~G 71 (71)
T PF02319_consen 66 SYKWIG 71 (71)
T ss_dssp EEEE--
T ss_pred ceEecC
Confidence 999998
No 5
>KOG2578 consensus Transcription factor E2F/dimerization partner (TDP)-like proteins [Transcription]
Probab=98.84 E-value=2.6e-09 Score=101.18 Aligned_cols=56 Identities=30% Similarity=0.513 Sum_probs=44.2
Q ss_pred CCCCCccccccccchhhhhhHHHHhhhcccccc-cCCeeeeccCCCCChhHHHHHHHH
Q 024762 137 LATPDQQQYDEKNIRRRVYDALNVLMAMDIISK-DKKEIQWKGLPRTSLNDIEELKAE 193 (263)
Q Consensus 137 ~~~~~~~~~deKniKRRVYDalNVL~ai~lI~K-~Kk~I~W~G~~~~s~~~~~~Lk~E 193 (263)
+...++.+...-+-|||||||.||||+||++.| .||.|+|+|+.... ..+.+|++|
T Consensus 44 lvgLddaA~KlgVErRRIYDiVNvlEsig~var~~KnqYsWkGf~aiP-ral~eLqeE 100 (388)
T KOG2578|consen 44 LVGLDDAARKLGVERRRIYDIVNVLESIGAVARRGKNQYSWKGFGAIP-RALFELQEE 100 (388)
T ss_pred eechhhHHHhcCchHHHHHHHHHHHHHHHHHHhcccCcccccchhhhh-HHHHHHHHH
Confidence 344556666677889999999999999999999 99999999996442 245566665
No 6
>KOG2578 consensus Transcription factor E2F/dimerization partner (TDP)-like proteins [Transcription]
Probab=96.12 E-value=0.0027 Score=61.10 Aligned_cols=72 Identities=24% Similarity=0.375 Sum_probs=47.6
Q ss_pred cchhhHHHHHHHHHHh---cCCCcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhccccccc----
Q 024762 98 RGLRQFSMKVCEKVES---KGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKD---- 170 (263)
Q Consensus 98 kGLR~fS~KVcekVk~---kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~K~---- 170 (263)
+.|-.+...+....-. ....|+...|.-|+.+-.+++ ..-.-=||+|||-|||-+|+||+|.
T Consensus 159 kSL~lL~qnFvklflcs~~~~lvslD~Aak~Ll~ds~~~~-----------~mRtkvRRLYDIANVlssm~LIeKtH~l~ 227 (388)
T KOG2578|consen 159 KSLWLLAQNFVKLFLCSDDDILVSLDSAAKALLKDSEDEP-----------PMRTKVRRLYDIANVLSSMNLIEKTHYLF 227 (388)
T ss_pred hHHHHHHHHHHHheeccccceEEeecHHHHHHhcCCCCCc-----------cHHHHHHHHHHHHHHHHHhhhhhhhcccc
Confidence 6777777765544433 225677666777765522211 1112349999999999999999992
Q ss_pred --CCeeeeccCC
Q 024762 171 --KKEIQWKGLP 180 (263)
Q Consensus 171 --Kk~I~W~G~~ 180 (263)
|--++|.|..
T Consensus 228 trkPafrwlG~~ 239 (388)
T KOG2578|consen 228 TRKPAFRWLGSK 239 (388)
T ss_pred cccchhheeCCC
Confidence 6678998864
No 7
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=93.95 E-value=0.086 Score=38.21 Aligned_cols=59 Identities=27% Similarity=0.374 Sum_probs=48.9
Q ss_pred cchhhHHHHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhcccccc-cCCeeee
Q 024762 98 RGLRQFSMKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK-DKKEIQW 176 (263)
Q Consensus 98 kGLR~fS~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~K-~Kk~I~W 176 (263)
-||...=.+|+..+-..+..|-.|||+++= .-|..||++|+-|+..|+|++ ..+...|
T Consensus 4 ~gLs~~E~~vy~~Ll~~~~~t~~eIa~~l~---------------------i~~~~v~~~L~~L~~~GlV~~~~~~~~~Y 62 (68)
T PF01978_consen 4 LGLSENEAKVYLALLKNGPATAEEIAEELG---------------------ISRSTVYRALKSLEEKGLVEREEGRPKVY 62 (68)
T ss_dssp HCHHHHHHHHHHHHHHHCHEEHHHHHHHHT---------------------SSHHHHHHHHHHHHHTTSEEEEEECCEEE
T ss_pred CCcCHHHHHHHHHHHHcCCCCHHHHHHHHC---------------------cCHHHHHHHHHHHHHCCCEEEEcCceEEE
Confidence 477778889999998999999999999861 447899999999999999999 5555555
Q ss_pred c
Q 024762 177 K 177 (263)
Q Consensus 177 ~ 177 (263)
.
T Consensus 63 ~ 63 (68)
T PF01978_consen 63 R 63 (68)
T ss_dssp E
T ss_pred E
Confidence 4
No 8
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=93.00 E-value=0.54 Score=43.15 Aligned_cols=34 Identities=21% Similarity=0.438 Sum_probs=28.0
Q ss_pred cchhhhhhHHHHhhhcccccc-cCCeeeeccCCCC
Q 024762 149 NIRRRVYDALNVLMAMDIISK-DKKEIQWKGLPRT 182 (263)
Q Consensus 149 niKRRVYDalNVL~ai~lI~K-~Kk~I~W~G~~~~ 182 (263)
.-+=||||+|+.|+.-|+|+. .++--.++-.|+.
T Consensus 42 vP~~kvY~vl~sLe~kG~v~~~~g~P~~y~av~p~ 76 (247)
T COG1378 42 VPRPKVYDVLRSLEKKGLVEVIEGRPKKYRAVPPE 76 (247)
T ss_pred CCchhHHHHHHHHHHCCCEEeeCCCCceEEeCCHH
Confidence 557899999999999999999 7777777766543
No 9
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=91.07 E-value=0.43 Score=34.25 Aligned_cols=55 Identities=24% Similarity=0.323 Sum_probs=39.8
Q ss_pred chhhHHHHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhccccc
Q 024762 99 GLRQFSMKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIIS 168 (263)
Q Consensus 99 GLR~fS~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~ 168 (263)
.|-..+..|++.+ .|..|..||++.|..+|.. +...++..|...++-|...|||+
T Consensus 14 ~Ln~~a~~Iw~~~--~g~~t~~ei~~~l~~~y~~-------------~~~~~~~dv~~fl~~L~~~glIe 68 (68)
T PF05402_consen 14 TLNETAAFIWELL--DGPRTVEEIVDALAEEYDV-------------DPEEAEEDVEEFLEQLREKGLIE 68 (68)
T ss_dssp ---THHHHHHHH----SSS-HHHHHHHHHHHTT---------------HHHHHHHHHHHHHHHHHTT---
T ss_pred cccHHHHHHHHHc--cCCCCHHHHHHHHHHHcCC-------------CHHHHHHHHHHHHHHHHHCcCcC
Confidence 7888899999999 4779999999999999844 23467999999999999999985
No 10
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=78.77 E-value=4.7 Score=26.41 Aligned_cols=48 Identities=17% Similarity=0.255 Sum_probs=38.1
Q ss_pred HHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhcccccccCCee
Q 024762 106 KVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKDKKEI 174 (263)
Q Consensus 106 KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~K~Kk~I 174 (263)
.|++.+.+++.++-.++|+.| ..-++.||..+.-|+..|+|.+..+.+
T Consensus 4 ~il~~l~~~~~~s~~~l~~~l---------------------~~s~~tv~~~l~~L~~~g~i~~~~~~~ 51 (53)
T smart00420 4 QILELLAQQGKVSVEELAELL---------------------GVSEMTIRRDLNKLEEQGLLTRVHGGA 51 (53)
T ss_pred HHHHHHHHcCCcCHHHHHHHH---------------------CCCHHHHHHHHHHHHHCCCEEEeecCc
Confidence 467777788889998888886 134688999999999999999865554
No 11
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=73.87 E-value=18 Score=30.77 Aligned_cols=56 Identities=25% Similarity=0.460 Sum_probs=44.5
Q ss_pred cchhhHHHHHHHHHH-hcCCCcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhcccccccCCee
Q 024762 98 RGLRQFSMKVCEKVE-SKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKDKKEI 174 (263)
Q Consensus 98 kGLR~fS~KVcekVk-~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~K~Kk~I 174 (263)
-||...=..|..++- +.+..|-.|+|.+|= --|-.||-+||=|+..|||.|.|-.+
T Consensus 23 ~GLs~~Dv~v~~~LL~~~~~~tvdelae~ln---------------------r~rStv~rsl~~L~~~GlV~Rek~~~ 79 (126)
T COG3355 23 YGLSELDVEVYKALLEENGPLTVDELAEILN---------------------RSRSTVYRSLQNLLEAGLVEREKVNL 79 (126)
T ss_pred hCCcHHHHHHHHHHHhhcCCcCHHHHHHHHC---------------------ccHHHHHHHHHHHHHcCCeeeeeecc
Confidence 366777777777777 688888888888862 33678999999999999999977665
No 12
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=71.18 E-value=11 Score=29.40 Aligned_cols=48 Identities=19% Similarity=0.241 Sum_probs=36.3
Q ss_pred HHHHHHHh-cCCCcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhcccccc
Q 024762 106 KVCEKVES-KGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (263)
Q Consensus 106 KVcekVk~-kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~K 169 (263)
.|.+.+.+ .+..|-.||.+.|-.+.. .--+--||-+|+.|+..|+|.+
T Consensus 5 ~Il~~l~~~~~~~sa~ei~~~l~~~~~----------------~i~~~TVYR~L~~L~~~Gli~~ 53 (116)
T cd07153 5 AILEVLLESDGHLTAEEIYERLRKKGP----------------SISLATVYRTLELLEEAGLVRE 53 (116)
T ss_pred HHHHHHHhCCCCCCHHHHHHHHHhcCC----------------CCCHHHHHHHHHHHHhCCCEEE
Confidence 46777766 456888888888865521 1234679999999999999999
No 13
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=65.93 E-value=8.8 Score=29.58 Aligned_cols=66 Identities=14% Similarity=0.259 Sum_probs=46.1
Q ss_pred HHHHHHHHHHh-cCCCcHHHHHHHHHHHhcCCCCCCCCCCccc--ccc--ccchhhhhhHHHHhhhcccccccCC
Q 024762 103 FSMKVCEKVES-KGRTTYNEVADELVAEFADPSNSLATPDQQQ--YDE--KNIRRRVYDALNVLMAMDIISKDKK 172 (263)
Q Consensus 103 fS~KVcekVk~-kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~--~de--KniKRRVYDalNVL~ai~lI~K~Kk 172 (263)
|-.-|.+-+.. .+..+..||.+.+...|.-..... ... ... ...+.||.=++.-|...|+|++.+.
T Consensus 5 ~~~piL~~L~~~g~~~~~~ei~~~v~~~~~ls~e~~----~~~~~sg~~~~~~~~ri~Wa~~~L~~aGli~~~~r 75 (92)
T PF14338_consen 5 LMPPILEALKDLGGSASRKEIYERVAERFGLSDEER----NERLPSGQGYSRFKNRIRWARSYLKKAGLIERPKR 75 (92)
T ss_pred HHHHHHHHHHHcCCCcCHHHHHHHHHHHhCCCHHHH----HHHcccCCcchhHHHhHHHHHHHHHHCCCccCCCC
Confidence 33446777888 889999999999988764321100 000 111 2578999999999999999999443
No 14
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=65.86 E-value=12 Score=27.38 Aligned_cols=43 Identities=23% Similarity=0.299 Sum_probs=34.9
Q ss_pred HHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhcccccc
Q 024762 106 KVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (263)
Q Consensus 106 KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~K 169 (263)
.|.+.++.++.+|..|+|.+|= .-..-|=+.|.+|+..|.|+|
T Consensus 4 ~i~~~l~~~~~~S~~eLa~~~~---------------------~s~~~ve~mL~~l~~kG~I~~ 46 (69)
T PF09012_consen 4 EIRDYLRERGRVSLAELAREFG---------------------ISPEAVEAMLEQLIRKGYIRK 46 (69)
T ss_dssp HHHHHHHHS-SEEHHHHHHHTT-----------------------HHHHHHHHHHHHCCTSCEE
T ss_pred HHHHHHHHcCCcCHHHHHHHHC---------------------cCHHHHHHHHHHHHHCCcEEE
Confidence 5778899999999999998852 224667899999999999999
No 15
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=65.54 E-value=16 Score=27.02 Aligned_cols=45 Identities=22% Similarity=0.313 Sum_probs=37.1
Q ss_pred HHHHHHHHhc-CCCcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhccccccc
Q 024762 105 MKVCEKVESK-GRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKD 170 (263)
Q Consensus 105 ~KVcekVk~k-g~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~K~ 170 (263)
..|.+.+... +..|..|+|+++= .-+..||-.++.|+..|+|.+.
T Consensus 8 ~~Il~~l~~~~~~~t~~~ia~~l~---------------------i~~~tv~r~l~~L~~~g~l~~~ 53 (91)
T smart00346 8 LAVLRALAEEPGGLTLAELAERLG---------------------LSKSTAHRLLNTLQELGYVEQD 53 (91)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHhC---------------------CCHHHHHHHHHHHHHCCCeeec
Confidence 5677888776 7899999999871 2357899999999999999995
No 16
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=65.53 E-value=9.4 Score=25.27 Aligned_cols=41 Identities=17% Similarity=0.188 Sum_probs=31.7
Q ss_pred HHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhcccccc
Q 024762 107 VCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (263)
Q Consensus 107 VcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~K 169 (263)
|.+.+. .+..+.+|+++.|- .-+..||++++.|..-|+|..
T Consensus 2 il~~l~-~~~~~~~~i~~~l~---------------------is~~~v~~~l~~L~~~g~i~~ 42 (66)
T smart00418 2 ILKLLA-EGELCVCELAEILG---------------------LSQSTVSHHLKKLREAGLVES 42 (66)
T ss_pred HHHHhh-cCCccHHHHHHHHC---------------------CCHHHHHHHHHHHHHCCCeee
Confidence 345555 77789999888862 224579999999999999997
No 17
>cd08768 Cdc6_C Winged-helix domain of essential DNA replication protein Cell division control protein (Cdc6), which mediates DNA binding. This model characterizes the winged-helix, C-terminal domain of the Cell division control protein (Cdc6_C). Cdc6 (also known as Cell division cycle 6 or Cdc18) functions as a regulator at the early stages of DNA replication, by helping to recruit and load the Minichromosome Maintenance Complex (MCM) onto DNA and may have additional roles in the control of mitotic entry. Precise duplication of chromosomal DNA is required for genomic stability during replication. Cdc6 has an essential role in DNA replication and irregular expression of Cdc6 may lead to genomic instability. Cdc6 over-expression is observed in many cancerous lesions. DNA replication begins when an origin recognition complex (ORC) binds to a replication origin site on the chromatin. Studies indicate that Cdc6 interacts with ORC through the Orc1 subunit, and that this association increases
Probab=64.31 E-value=4.1 Score=30.26 Aligned_cols=20 Identities=25% Similarity=0.469 Sum_probs=18.3
Q ss_pred chhhhhhHHHHhhhcccccc
Q 024762 150 IRRRVYDALNVLMAMDIISK 169 (263)
Q Consensus 150 iKRRVYDalNVL~ai~lI~K 169 (263)
-.||++|++|-|+.+|||+-
T Consensus 45 ~~~~~~~~l~~L~~~gli~~ 64 (87)
T cd08768 45 TQRRISDLLSELEMLGLLET 64 (87)
T ss_pred cHHHHHHHHHHHHHcCCeEE
Confidence 35999999999999999986
No 18
>PF14193 DUF4315: Domain of unknown function (DUF4315)
Probab=63.45 E-value=26 Score=27.78 Aligned_cols=36 Identities=33% Similarity=0.421 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024762 186 DIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNL 221 (263)
Q Consensus 186 ~~~~Lk~E~~~l~erI~~Kk~~LqEL~~Q~~alknL 221 (263)
.++.+..++.+.+++|...+++|.+|..|+.-..|+
T Consensus 2 KleKi~~eieK~k~Kiae~Q~rlK~Le~qk~E~EN~ 37 (83)
T PF14193_consen 2 KLEKIRAEIEKTKEKIAELQARLKELEAQKTEAENL 37 (83)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 467788888888888988899999999888877665
No 19
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=63.41 E-value=23 Score=23.74 Aligned_cols=45 Identities=24% Similarity=0.221 Sum_probs=36.1
Q ss_pred HHHHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhccccc
Q 024762 103 FSMKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIIS 168 (263)
Q Consensus 103 fS~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~ 168 (263)
.-.+|...+.+++.+|-.|+|+.+= .-+..|+.+++-|+.-|+|+
T Consensus 4 ~~~~Il~~l~~~~~~t~~ela~~~~---------------------is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 4 TQRKILNYLRENPRITQKELAEKLG---------------------ISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHHHCTTS-HHHHHHHHT---------------------S-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHhC---------------------CCHHHHHHHHHHHHHCcCcC
Confidence 3467889999999999999999862 33678999999999999985
No 20
>PRK09462 fur ferric uptake regulator; Provisional
Probab=62.42 E-value=20 Score=29.77 Aligned_cols=56 Identities=18% Similarity=0.222 Sum_probs=40.7
Q ss_pred cchhhHHH--HHHHHHHh--cCCCcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhcccccc
Q 024762 98 RGLRQFSM--KVCEKVES--KGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (263)
Q Consensus 98 kGLR~fS~--KVcekVk~--kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~K 169 (263)
.|||.=.. .|.+.+.+ .+..|-.||.+.|..+... .-+=-||.+|+.|+..|||.+
T Consensus 11 ~glr~T~qR~~Il~~l~~~~~~h~sa~eI~~~l~~~~~~----------------i~~aTVYR~L~~L~e~Gli~~ 70 (148)
T PRK09462 11 AGLKVTLPRLKILEVLQEPDNHHVSAEDLYKRLIDMGEE----------------IGLATVYRVLNQFDDAGIVTR 70 (148)
T ss_pred cCCCCCHHHHHHHHHHHhCCCCCCCHHHHHHHHHhhCCC----------------CCHHHHHHHHHHHHHCCCEEE
Confidence 35553333 48888886 3688988988888765321 224679999999999999998
No 21
>PF09079 Cdc6_C: CDC6, C terminal ; InterPro: IPR015163 The C-terminal domain of CDC6 assumes a winged helix fold, with a five alpha-helical bundle (alpha15-alpha19) structure, backed on one side by three beta strands (beta6-beta8). It has been shown that this domain acts as a DNA-localisation factor, however its exact function is, as yet, unknown. Putative functions include: (1) mediation of protein-protein interactions and (2) regulation of nucleotide binding and hydrolysis. Mutagenesis studies have shown that this domain is essential for appropriate Cdc6 activity []. ; PDB: 2QBY_A 2V1U_A 1W5T_A 1W5S_B 1FNN_B.
Probab=61.45 E-value=5 Score=30.23 Aligned_cols=20 Identities=30% Similarity=0.348 Sum_probs=17.9
Q ss_pred chhhhhhHHHHhhhcccccc
Q 024762 150 IRRRVYDALNVLMAMDIISK 169 (263)
Q Consensus 150 iKRRVYDalNVL~ai~lI~K 169 (263)
-.||+||.++-|+.+|||+-
T Consensus 38 s~~r~~~~l~eL~~~gli~~ 57 (85)
T PF09079_consen 38 SYRRFSDYLSELEMLGLIES 57 (85)
T ss_dssp -HHHHHHHHHHHHHTTSEEE
T ss_pred CHHHHHHHHHHHHhCCCeEE
Confidence 35999999999999999986
No 22
>cd00890 Prefoldin Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils.
Probab=60.95 E-value=73 Score=25.11 Aligned_cols=55 Identities=33% Similarity=0.281 Sum_probs=30.3
Q ss_pred ccCCeeeeccCCCCC----hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024762 169 KDKKEIQWKGLPRTS----LNDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQ 223 (263)
Q Consensus 169 K~Kk~I~W~G~~~~s----~~~~~~Lk~E~~~l~erI~~Kk~~LqEL~~Q~~alknLI~ 223 (263)
...+-+.|.|.+... ....+.|+..+..+..+++...+.+.++..+...++.-++
T Consensus 67 ~~~~v~v~iG~~~~ve~~~~eA~~~l~~r~~~l~~~~~~l~~~~~~~~~~~~~l~~~l~ 125 (129)
T cd00890 67 DDDKVLVDLGTGVYVEKSLEEAIEFLKKRLETLEKQIEKLEKQLEKLQDQITELQEELQ 125 (129)
T ss_pred CCCEEEEEecCCEEEEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456678889865322 2233444455555555555555566666655555554443
No 23
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=60.25 E-value=12 Score=25.85 Aligned_cols=45 Identities=22% Similarity=0.330 Sum_probs=34.2
Q ss_pred HHHHHHHHhcCC-CcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhccccccc
Q 024762 105 MKVCEKVESKGR-TTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKD 170 (263)
Q Consensus 105 ~KVcekVk~kg~-TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~K~ 170 (263)
+.|.+.+.+.+. .|..|||+++= --|--+|.+|+.|+..|+|+++
T Consensus 6 l~iL~~l~~~~~~~t~~eia~~~g---------------------l~~stv~r~L~tL~~~g~v~~d 51 (52)
T PF09339_consen 6 LRILEALAESGGPLTLSEIARALG---------------------LPKSTVHRLLQTLVEEGYVERD 51 (52)
T ss_dssp HHHHHCHHCTBSCEEHHHHHHHHT---------------------S-HHHHHHHHHHHHHTTSEEEC
T ss_pred HHHHHHHHcCCCCCCHHHHHHHHC---------------------cCHHHHHHHHHHHHHCcCeecC
Confidence 456666666555 68999988862 3356799999999999999985
No 24
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=59.81 E-value=65 Score=23.40 Aligned_cols=52 Identities=21% Similarity=0.176 Sum_probs=42.1
Q ss_pred cchhhHHHHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhccccccc
Q 024762 98 RGLRQFSMKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKD 170 (263)
Q Consensus 98 kGLR~fS~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~K~ 170 (263)
-||-..-..|...+...+.++..++|+.+- .-+..|+.+++-|+..|+|++.
T Consensus 6 ~~l~~~~~~il~~l~~~~~~~~~~la~~~~---------------------~s~~~i~~~l~~L~~~g~v~~~ 57 (101)
T smart00347 6 LGLTPTQFLVLRILYEEGPLSVSELAKRLG---------------------VSPSTVTRVLDRLEKKGLIRRL 57 (101)
T ss_pred cCCCHHHHHHHHHHHHcCCcCHHHHHHHHC---------------------CCchhHHHHHHHHHHCCCeEec
Confidence 567777888889999899999999988751 1135689999999999999974
No 25
>PRK03947 prefoldin subunit alpha; Reviewed
Probab=59.49 E-value=59 Score=26.71 Aligned_cols=57 Identities=25% Similarity=0.239 Sum_probs=32.4
Q ss_pred ccccCCeeeeccCCCC----ChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024762 167 ISKDKKEIQWKGLPRT----SLNDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQ 223 (263)
Q Consensus 167 I~K~Kk~I~W~G~~~~----s~~~~~~Lk~E~~~l~erI~~Kk~~LqEL~~Q~~alknLI~ 223 (263)
|....+-+-|.|.+.- ....++.|+..+..+.+.++.-.+.|.++..+...+..-++
T Consensus 72 v~~~~kV~v~lG~g~~vE~~~~eA~~~l~~~~~~l~~~~~~l~~~l~~~~~~~~~~~~~l~ 132 (140)
T PRK03947 72 VKDKDKVIVSLGAGYSAEKDLDEAIEILDKRKEELEKALEKLEEALQKLASRIAQLAQELQ 132 (140)
T ss_pred ecCCCeEEEEcCCCEEEEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3345677788887632 23344555555555655666666666666655555544443
No 26
>TIGR00293 prefoldin, archaeal alpha subunit/eukaryotic subunit 5. This model finds a set of small proteins from the Archaea and from Aquifex aeolicus that may represent two orthologous groups. The proteins are predicted to be mostly coiled coil, and may hit large numbers of proteins that contain coiled coil regions.
Probab=58.83 E-value=59 Score=26.10 Aligned_cols=66 Identities=21% Similarity=0.086 Sum_probs=38.0
Q ss_pred hhHHHHhhhcccccccCCeeeeccCCCC----ChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024762 155 YDALNVLMAMDIISKDKKEIQWKGLPRT----SLNDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQN 220 (263)
Q Consensus 155 YDalNVL~ai~lI~K~Kk~I~W~G~~~~----s~~~~~~Lk~E~~~l~erI~~Kk~~LqEL~~Q~~alkn 220 (263)
+-+..-+..=+-|...++-+-|.|.... .....+-|+..+..+.+.+++-.+.+.++..+...+..
T Consensus 52 v~lg~~~~v~~~v~~~~~v~v~iG~g~~vE~~~~eA~~~l~~~~~~l~~~~~~l~~~l~~l~~~~~~i~~ 121 (126)
T TIGR00293 52 VPVGAGSFVKAKVKDTDKVLVSIGSGYYVEKDAEEAIEFLKKRIEELEKAIEKLQEALAELASRAQQLEQ 121 (126)
T ss_pred EEcCCCeEEEEEeCCCCEEEEEcCCCEEEEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3333333334445556778889997632 23344555666666666666666666666666655543
No 27
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=55.95 E-value=11 Score=27.02 Aligned_cols=55 Identities=18% Similarity=0.178 Sum_probs=35.4
Q ss_pred HHHHHHHHHHHhcCCCCCCC----CCCccccccccchhhhhhHHHHhhhcccccc-cCCe
Q 024762 119 YNEVADELVAEFADPSNSLA----TPDQQQYDEKNIRRRVYDALNVLMAMDIISK-DKKE 173 (263)
Q Consensus 119 YnEVAdeLV~e~~~~~~~~~----~~~~~~~deKniKRRVYDalNVL~ai~lI~K-~Kk~ 173 (263)
|..|++.|...+....-..+ +..+-+.....-|.-|.+|++.|++.|+|++ .++.
T Consensus 2 ~~~i~~~l~~~I~~g~~~~g~~lps~~~la~~~~vsr~tvr~al~~L~~~g~i~~~~~~G 61 (64)
T PF00392_consen 2 YEQIYDQLRQAILSGRLPPGDRLPSERELAERYGVSRTTVREALRRLEAEGLIERRPGRG 61 (64)
T ss_dssp HHHHHHHHHHHHHTTSS-TTSBE--HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTTE
T ss_pred HHHHHHHHHHHHHcCCCCCCCEeCCHHHHHHHhccCCcHHHHHHHHHHHCCcEEEECCce
Confidence 77788888877765322111 1112233445678889999999999999998 5443
No 28
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=53.79 E-value=1e+02 Score=24.19 Aligned_cols=51 Identities=14% Similarity=0.288 Sum_probs=36.6
Q ss_pred chhhHHHHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhccccccc
Q 024762 99 GLRQFSMKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKD 170 (263)
Q Consensus 99 GLR~fS~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~K~ 170 (263)
||-.--..|...+...+.+|.+|+|+.+- .-+--|+-+++-|+.-|+|++.
T Consensus 25 ~lt~~q~~iL~~l~~~~~~t~~ela~~~~---------------------~~~~tvs~~l~~Le~~GlI~r~ 75 (118)
T TIGR02337 25 GLTEQQWRILRILAEQGSMEFTQLANQAC---------------------ILRPSLTGILARLERDGLVTRL 75 (118)
T ss_pred CCCHHHHHHHHHHHHcCCcCHHHHHHHhC---------------------CCchhHHHHHHHHHHCCCEEec
Confidence 44444445667777778888888887753 2234578899999999999993
No 29
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=53.56 E-value=38 Score=26.79 Aligned_cols=55 Identities=25% Similarity=0.309 Sum_probs=38.6
Q ss_pred chhhHHH--HHHHHHHhc-CCCcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhcccccc
Q 024762 99 GLRQFSM--KVCEKVESK-GRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (263)
Q Consensus 99 GLR~fS~--KVcekVk~k-g~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~K 169 (263)
|||-=.. .|.+.+.+. +..|-.||.+.|-.+.. ..-+=-||.+|+.|+..|||.|
T Consensus 3 glr~T~~R~~Il~~l~~~~~~~ta~ei~~~l~~~~~----------------~is~~TVYR~L~~L~e~Gli~~ 60 (120)
T PF01475_consen 3 GLRLTPQRLAILELLKESPEHLTAEEIYDKLRKKGP----------------RISLATVYRTLDLLEEAGLIRK 60 (120)
T ss_dssp THHHHHHHHHHHHHHHHHSSSEEHHHHHHHHHHTTT----------------T--HHHHHHHHHHHHHTTSEEE
T ss_pred CCCCCHHHHHHHHHHHcCCCCCCHHHHHHHhhhccC----------------CcCHHHHHHHHHHHHHCCeEEE
Confidence 4554333 377777774 58888888888874411 1224569999999999999999
No 30
>PF03836 RasGAP_C: RasGAP C-terminus; InterPro: IPR000593 Ras GTPase-activating protein (rasGAP) is a major contributor to the down-regulation of ras by facilitating GTP hydrolysis of activated ras. In addition, GAP participates in the down-stream effector system of the ras signalling pathway. Abnormal signal transduction involving activated ras genes plays a major role in the development of a variety of tumours. Depending on the precise genetic alteration, its location within the gene and the effects it exerts on protein function, rasGAP can theoretically function as either an oncogene or as a tumour suppressor gene [].; GO: 0005099 Ras GTPase activator activity, 0007264 small GTPase mediated signal transduction, 0005622 intracellular; PDB: 3ISU_A 3IEZ_A 4EZA_B 1X0H_A.
Probab=53.37 E-value=4.4 Score=33.99 Aligned_cols=65 Identities=25% Similarity=0.406 Sum_probs=0.0
Q ss_pred cchhhhhhHHHHhhhcccccccCCeeeeccCCCCChhHH-------HHHHHHHHHHH---HHHHHHHHHHHHHHHHHH
Q 024762 149 NIRRRVYDALNVLMAMDIISKDKKEIQWKGLPRTSLNDI-------EELKAERLGLR---NRIEKKTAYLQELEDQFV 216 (263)
Q Consensus 149 niKRRVYDalNVL~ai~lI~K~Kk~I~W~G~~~~s~~~~-------~~Lk~E~~~l~---erI~~Kk~~LqEL~~Q~~ 216 (263)
..|+++-+-|..||.+|+|+++ |.++=. =...+.++ +..+.|+..|+ ..|.+|..+|++-..++.
T Consensus 4 ~lk~~~l~~l~~LE~~G~v~~~-n~yQ~l--ln~IA~dI~~~~~~r~~r~~El~~l~~tl~~L~~k~~~l~~ql~~Y~ 78 (142)
T PF03836_consen 4 ELKKKILENLKELESLGIVSRS-NNYQDL--LNDIAKDIRNKRRYREQRKQELEKLRQTLKNLNEKNKFLEEQLDSYN 78 (142)
T ss_dssp ------------------------------------------------------------------------------
T ss_pred HHHHHHHHHHHHHHHCCCCCCc-ccHHHH--HHHHHHHHhChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4678899999999999999998 777621 11112222 22333444443 345666777766555444
No 31
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=53.03 E-value=24 Score=24.07 Aligned_cols=25 Identities=32% Similarity=0.640 Sum_probs=20.2
Q ss_pred hHHHHHHHHHHhcCCCcHHHHHHHH
Q 024762 102 QFSMKVCEKVESKGRTTYNEVADEL 126 (263)
Q Consensus 102 ~fS~KVcekVk~kg~TTYnEVAdeL 126 (263)
.+=.++...++..+.++|.+||.++
T Consensus 3 ~~D~~Il~~Lq~d~r~s~~~la~~l 27 (42)
T PF13404_consen 3 ELDRKILRLLQEDGRRSYAELAEEL 27 (42)
T ss_dssp HHHHHHHHHHHH-TTS-HHHHHHHH
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHH
Confidence 4567889999999999999999987
No 32
>PF07334 IFP_35_N: Interferon-induced 35 kDa protein (IFP 35) N-terminus; InterPro: IPR009938 This entry represents the N terminus of interferon-induced 35 kDa protein (IFP 35) (approximately 80 residues long), which contains a leucine zipper motif in an alpha helical configuration []. This group of proteins also includes N-myc-interactor (Nmi), a homologous interferon-induced protein.
Probab=51.80 E-value=51 Score=25.98 Aligned_cols=60 Identities=23% Similarity=0.288 Sum_probs=35.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCccccceEEEE----cCCCceEEeEeeee
Q 024762 187 IEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQRNERLYSSGNAPSGGVALPFILVQ----VDIRQLFSCIMASI 261 (263)
Q Consensus 187 ~~~Lk~E~~~l~erI~~Kk~~LqEL~~Q~~alknLI~RNk~~~~~~~~ps~~I~LPFIlV~----T~~~tvI~C~iss~ 261 (263)
+.+|.+|-.+|+.+|++.++.||++. |+.+.. ...|. -.+||..+. ++..-.|.|++.+.
T Consensus 2 i~ei~eEn~~Lk~eiqkle~ELq~~~-----------~~~qIk--~diPe--~kvkFts~E~p~~d~q~~niscsf~v~ 65 (76)
T PF07334_consen 2 IHEIQEENARLKEEIQKLEAELQQNK-----------REFQIK--EDIPE--KKVKFTSPEVPEDDQQFLNISCSFQVT 65 (76)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHH-----------hhhhhc--cCCcc--ccCcCCCCCCCCCccccCCCCeEEEee
Confidence 45677888888888877777776533 332221 12343 345665554 44555678877654
No 33
>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=51.65 E-value=16 Score=27.88 Aligned_cols=22 Identities=45% Similarity=0.625 Sum_probs=16.4
Q ss_pred HHHHHHHhcCCCcHHHHHHHHH
Q 024762 106 KVCEKVESKGRTTYNEVADELV 127 (263)
Q Consensus 106 KVcekVk~kg~TTYnEVAdeLV 127 (263)
++.++-+++|..||.||.+.|-
T Consensus 11 ~Li~~gK~~G~lT~~eI~~~L~ 32 (82)
T PF03979_consen 11 KLIEKGKKKGYLTYDEINDALP 32 (82)
T ss_dssp HHHHHHHHHSS-BHHHHHHH-S
T ss_pred HHHHHHhhcCcCCHHHHHHHcC
Confidence 3557778899999999998875
No 34
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=50.88 E-value=1.2e+02 Score=27.39 Aligned_cols=53 Identities=13% Similarity=0.120 Sum_probs=38.9
Q ss_pred HHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhcccccc-cCCeeeecc
Q 024762 105 MKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK-DKKEIQWKG 178 (263)
Q Consensus 105 ~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~K-~Kk~I~W~G 178 (263)
.++.+.|++.+.+++.|+|+.|= .-.+.|..-|+.|+..|+|.+ .+.-+.+.+
T Consensus 7 ~~Il~~l~~~~~~~~~eLa~~l~---------------------VS~~TiRRdL~~L~~~~~l~r~~Gga~~~~~ 60 (240)
T PRK10411 7 QAIVDLLLNHTSLTTEALAEQLN---------------------VSKETIRRDLNELQTQGKILRNHGRAKYIHR 60 (240)
T ss_pred HHHHHHHHHcCCCcHHHHHHHHC---------------------cCHHHHHHHHHHHHHCCCEEEecCeEEEecC
Confidence 35789999999999999999971 223556666788888888887 555555543
No 35
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=50.37 E-value=56 Score=22.24 Aligned_cols=48 Identities=27% Similarity=0.278 Sum_probs=33.1
Q ss_pred HHHHHH-HhcCCCcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhcc-cccc-cCCee
Q 024762 106 KVCEKV-ESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMD-IISK-DKKEI 174 (263)
Q Consensus 106 KVcekV-k~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~-lI~K-~Kk~I 174 (263)
++...+ +.++.+|..|+|++| ..-+|-||.-++-|...+ .|.. .++.|
T Consensus 4 ~il~~L~~~~~~it~~eLa~~l---------------------~vS~rTi~~~i~~L~~~~~~I~~~~~~GY 54 (55)
T PF08279_consen 4 QILKLLLESKEPITAKELAEEL---------------------GVSRRTIRRDIKELREWGIPIESKRGKGY 54 (55)
T ss_dssp HHHHHHHHTTTSBEHHHHHHHC---------------------TS-HHHHHHHHHHHHHTT-EEEEETTTEE
T ss_pred HHHHHHHHcCCCcCHHHHHHHh---------------------CCCHHHHHHHHHHHHHCCCeEEeeCCCCc
Confidence 445556 667779999999885 255788999999998888 3333 44443
No 36
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=49.90 E-value=57 Score=27.48 Aligned_cols=56 Identities=20% Similarity=0.196 Sum_probs=39.0
Q ss_pred HHHHHHHHhc-CCCcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhcccccc--cCCeeee
Q 024762 105 MKVCEKVESK-GRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK--DKKEIQW 176 (263)
Q Consensus 105 ~KVcekVk~k-g~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~K--~Kk~I~W 176 (263)
.+|.+.+.+. +..|-.||-++|..+.... -.=-||.+|+.|...|||.+ ..+...|
T Consensus 24 ~~vl~~L~~~~~~~sAeei~~~l~~~~p~i----------------slaTVYr~L~~l~e~Glv~~~~~~~~~~~ 82 (145)
T COG0735 24 LAVLELLLEADGHLSAEELYEELREEGPGI----------------SLATVYRTLKLLEEAGLVHRLEFEGGKTR 82 (145)
T ss_pred HHHHHHHHhcCCCCCHHHHHHHHHHhCCCC----------------CHhHHHHHHHHHHHCCCEEEEEeCCCEEE
Confidence 3477888765 4577777777776642221 13579999999999999999 4454444
No 37
>PF11594 Med28: Mediator complex subunit 28; InterPro: IPR021640 Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species [],[]. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function []. Subunit Med28 of the Mediator may function as a scaffolding protein within Mediator by maintaining the stability of a submodule within the head module, and components of this submodule act together in a gene-regulatory programme to suppress smooth muscle cell differentiation. Thus, mammalian Mediator subunit Med28 functions as a repressor of smooth muscle-cell differentiation, which could have implications for disorders associated with abnormalities in smooth muscle cell growth and differentiation, including atherosclerosis, asthma, hypertension, and smooth muscle tumours [].
Probab=49.52 E-value=60 Score=27.07 Aligned_cols=36 Identities=22% Similarity=0.306 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024762 188 EELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQ 223 (263)
Q Consensus 188 ~~Lk~E~~~l~erI~~Kk~~LqEL~~Q~~alknLI~ 223 (263)
..|++|...|++.+..|.+.++.+......+++|+.
T Consensus 38 ~~lkEEi~eLK~ElqRKe~Ll~Kh~~kI~~w~~lL~ 73 (106)
T PF11594_consen 38 QVLKEEINELKEELQRKEQLLQKHYEKIDYWEKLLS 73 (106)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 457888888888899999999999988888888865
No 38
>PF11315 Med30: Mediator complex subunit 30; InterPro: IPR021019 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Med30 is a metazoan-specific subunit of Mediator [], having no homologues in yeasts.
Probab=49.43 E-value=67 Score=28.12 Aligned_cols=31 Identities=29% Similarity=0.427 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024762 186 DIEELKAERLGLRNRIEKKTAYLQELEDQFV 216 (263)
Q Consensus 186 ~~~~Lk~E~~~l~erI~~Kk~~LqEL~~Q~~ 216 (263)
+...+.+|+.++.+++.+|.++|.+++.|.-
T Consensus 105 ~~~~~~~er~el~e~v~~KN~qLk~iid~lR 135 (150)
T PF11315_consen 105 EYRQLLEERKELIEQVKQKNQQLKEIIDQLR 135 (150)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5666888999999999999999999998744
No 39
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=48.72 E-value=33 Score=26.30 Aligned_cols=45 Identities=18% Similarity=0.223 Sum_probs=36.1
Q ss_pred HHHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhcccccc
Q 024762 104 SMKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (263)
Q Consensus 104 S~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~K 169 (263)
=.+|...++..+.+||+|+|+.+= .-..-|+..++-|+.-|+|.+
T Consensus 5 D~~il~~L~~~~~~~~~~la~~l~---------------------~s~~tv~~~l~~L~~~g~i~~ 49 (108)
T smart00344 5 DRKILEELQKDARISLAELAKKVG---------------------LSPSTVHNRVKRLEEEGVIKG 49 (108)
T ss_pred HHHHHHHHHHhCCCCHHHHHHHHC---------------------cCHHHHHHHHHHHHHCCCeec
Confidence 357888999999999999999871 123567777899999999996
No 40
>cd00584 Prefoldin_alpha Prefoldin alpha subunit; Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils.
Probab=47.87 E-value=1.5e+02 Score=23.91 Aligned_cols=53 Identities=26% Similarity=0.178 Sum_probs=27.7
Q ss_pred cCCeeeeccCCCCC----hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024762 170 DKKEIQWKGLPRTS----LNDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLI 222 (263)
Q Consensus 170 ~Kk~I~W~G~~~~s----~~~~~~Lk~E~~~l~erI~~Kk~~LqEL~~Q~~alknLI 222 (263)
.++-+-|.|.+... ....+-++..+..+.+.+++.++.+..+..+...+..-+
T Consensus 68 ~~~v~v~iG~g~~vE~~~~eA~~~l~~r~~~l~~~~~~l~~~l~~l~~~~~~~~~~l 124 (129)
T cd00584 68 TDKVLVDLGTGYYVEKDLEEAIEFLDKKIEELTKQIEKLQKELAKLKDQINTLEAEL 124 (129)
T ss_pred CCEEEEEcCCCEEEEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45667788876322 223334444555555555555555555555555444433
No 41
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=46.65 E-value=43 Score=24.65 Aligned_cols=52 Identities=25% Similarity=0.280 Sum_probs=40.2
Q ss_pred HHHHHHHHhcCC--CcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhcccccccC-Ceeeec
Q 024762 105 MKVCEKVESKGR--TTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKDK-KEIQWK 177 (263)
Q Consensus 105 ~KVcekVk~kg~--TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~K~K-k~I~W~ 177 (263)
.+|++.+.+.+. .|-.|+|.+|= .-++-|.-+|.-|+..|+|.+.. +-=.|.
T Consensus 9 ~~IL~~L~~~g~~~~ta~eLa~~lg---------------------l~~~~v~r~L~~L~~~G~V~~~~~~~~~W~ 63 (68)
T smart00550 9 EKILEFLENSGDETSTALQLAKNLG---------------------LPKKEVNRVLYSLEKKGKVCKQGGTPPLWK 63 (68)
T ss_pred HHHHHHHHHCCCCCcCHHHHHHHHC---------------------CCHHHHHHHHHHHHHCCCEEecCCCCCceE
Confidence 578999999887 89889888862 23567888899999999999943 424664
No 42
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=45.90 E-value=93 Score=28.33 Aligned_cols=45 Identities=20% Similarity=0.321 Sum_probs=36.3
Q ss_pred HHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhccccccc
Q 024762 105 MKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKD 170 (263)
Q Consensus 105 ~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~K~ 170 (263)
.++.+.+++++..+.+|+|+.|= ..+..|||. |+.|+.-|+|.|-
T Consensus 8 ~~Il~~L~~~~~v~v~eLa~~l~-----------------VS~~TIRRD----L~~Le~~g~l~r~ 52 (256)
T PRK10434 8 AAILEYLQKQGKTSVEELAQYFD-----------------TTGTTIRKD----LVILEHAGTVIRT 52 (256)
T ss_pred HHHHHHHHHcCCEEHHHHHHHHC-----------------CCHHHHHHH----HHHHHHCCCEEEE
Confidence 46889999999999999999862 123478776 7889999999984
No 43
>PRK14127 cell division protein GpsB; Provisional
Probab=45.15 E-value=37 Score=28.17 Aligned_cols=53 Identities=25% Similarity=0.323 Sum_probs=32.3
Q ss_pred hhcccccc-cCCeeeeccCCCCC--------hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024762 162 MAMDIISK-DKKEIQWKGLPRTS--------LNDIEELKAERLGLRNRIEKKTAYLQELEDQFV 216 (263)
Q Consensus 162 ~ai~lI~K-~Kk~I~W~G~~~~s--------~~~~~~Lk~E~~~l~erI~~Kk~~LqEL~~Q~~ 216 (263)
-.++|..| =++ .++|++... ..+++.|..|...|++++...++.|.++..+..
T Consensus 7 Tp~DI~~KeF~~--~~RGYd~~EVD~FLd~V~~dye~l~~e~~~Lk~e~~~l~~~l~e~~~~~~ 68 (109)
T PRK14127 7 TPKDILEKEFKT--SMRGYDQDEVDKFLDDVIKDYEAFQKEIEELQQENARLKAQVDELTKQVS 68 (109)
T ss_pred CHHHHhhCccCC--CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 34556666 333 356887653 245666666777777777666666666665544
No 44
>PF06717 DUF1202: Protein of unknown function (DUF1202); InterPro: IPR009592 This family consists of several hypothetical bacterial proteins of around 335 residues in length. Members of this family are found exclusively in Escherichia coli and Salmonella species and are often referred to as YggM proteins. The function of this family is unknown.
Probab=44.75 E-value=89 Score=30.39 Aligned_cols=58 Identities=16% Similarity=0.177 Sum_probs=41.0
Q ss_pred cccccccCCeeeeccCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024762 164 MDIISKDKKEIQWKGLPRTSLNDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQ 223 (263)
Q Consensus 164 i~lI~K~Kk~I~W~G~~~~s~~~~~~Lk~E~~~l~erI~~Kk~~LqEL~~Q~~alknLI~ 223 (263)
+..|....|-+.|.+- .....+..++.+....+..|...++++.+|..|.++++.-+.
T Consensus 119 v~~i~tn~KYLIvn~~--~F~~rf~~Ied~~~~kK~~I~~L~~qisaLdkqi~ai~Kkid 176 (308)
T PF06717_consen 119 VPDIKTNDKYLIVNDQ--DFNYRFNQIEDEYNRKKNKIPGLNKQISALDKQIVAINKKID 176 (308)
T ss_pred CCccccCCcEEEecch--hHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567776688888874 334567777777777777777777777777777777665543
No 45
>TIGR00589 ogt O-6-methylguanine DNA methyltransferase. All proteins in this family for which functions are known are involved alkyl-DNA transferases which remove alkyl groups from DNA as part of alkylation DNA repair. Some of the proteins in this family are also transcription regulators and have a distinct transcription regulatory domain. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=43.76 E-value=29 Score=26.88 Aligned_cols=25 Identities=16% Similarity=0.436 Sum_probs=20.8
Q ss_pred hHHHHHHHHHHh---cCCCcHHHHHHHH
Q 024762 102 QFSMKVCEKVES---KGRTTYNEVADEL 126 (263)
Q Consensus 102 ~fS~KVcekVk~---kg~TTYnEVAdeL 126 (263)
.|-.+|++.|.+ -.++||.+||..+
T Consensus 2 ~f~~~V~~~l~~IP~G~v~TYg~iA~~~ 29 (80)
T TIGR00589 2 PFQQRVWQALRTIPYGETKSYGQLAARI 29 (80)
T ss_pred hHHHHHHHHHhCCCCCCcCCHHHHHHHh
Confidence 377889998887 5689999999885
No 46
>PF10473 CENP-F_leu_zip: Leucine-rich repeats of kinetochore protein Cenp-F/LEK1; InterPro: IPR019513 Cenp-F, a centromeric kinetochore, microtubule-binding protein consisting of two 1,600-amino acid-long coils, is essential for the full functioning of the mitotic checkpoint pathway [, ]. There are several leucine-rich repeats along the sequence of LEK1 that are considered to be zippers, though they do not appear to be binding DNA directly in this instance []. ; GO: 0008134 transcription factor binding, 0042803 protein homodimerization activity, 0045502 dynein binding
Probab=43.74 E-value=84 Score=27.11 Aligned_cols=40 Identities=30% Similarity=0.487 Sum_probs=32.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024762 185 NDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQR 224 (263)
Q Consensus 185 ~~~~~Lk~E~~~l~erI~~Kk~~LqEL~~Q~~alknLI~R 224 (263)
.++..|..|...|...+++++.+..+|..-...+.++|+.
T Consensus 73 ~EL~~l~sEk~~L~k~lq~~q~kv~eLE~~~~~~~~~l~~ 112 (140)
T PF10473_consen 73 LELDTLRSEKENLDKELQKKQEKVSELESLNSSLENLLQE 112 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH
Confidence 4566677777788888899999999999988888888874
No 47
>PF01035 DNA_binding_1: 6-O-methylguanine DNA methyltransferase, DNA binding domain; InterPro: IPR014048 Synonym(s): 6-O-methylguanine-DNA methyltransferase, O-6-methylguanine-DNA-alkyltransferase This entry represents the DNA binding region of 6-O-methylguanine-DNA methyltransferases. The repair of DNA containing O6-alkylated guanine is carried out by DNA-[protein]-cysteine S-methyltransferase (2.1.1.63 from EC). The major mutagenic and carcinogenic effect of methylating agents in DNA is the formation of O6-alkylguanine. The alkyl group at the O-6 position is transferred to a cysteine residue in the enzyme []. This is a suicide reaction since the enzyme is irreversibly inactivated and the methylated protein accumulates as a dead-end product. Most, but not all of the methyltransferases are also able to repair O-4-methylthymine. DNA-[protein]-cysteine S-methyltransferases are widely distributed and are found in various prokaryotic and eukaryotic sources [].; GO: 0003824 catalytic activity, 0006281 DNA repair; PDB: 1SFE_A 1T39_B 1T38_A 1EH7_A 1EH6_A 1YFH_C 1EH8_A 1QNT_A 2KIM_A 2KIF_A ....
Probab=42.93 E-value=19 Score=27.85 Aligned_cols=25 Identities=40% Similarity=0.489 Sum_probs=20.1
Q ss_pred hHHHHHHHHHHh---cCCCcHHHHHHHH
Q 024762 102 QFSMKVCEKVES---KGRTTYNEVADEL 126 (263)
Q Consensus 102 ~fS~KVcekVk~---kg~TTYnEVAdeL 126 (263)
.|..+|++.|.+ -..+||.|||..+
T Consensus 2 ~f~~~V~~~v~~IP~G~v~TYg~iA~~~ 29 (85)
T PF01035_consen 2 PFQRRVWEAVRQIPYGKVTTYGEIARLL 29 (85)
T ss_dssp HHHHHHHHHHTTS-TT-BEEHHHHHHHT
T ss_pred hHHHHHHHHHHcCCCCceEeHHHHHHHH
Confidence 377889998887 4689999999875
No 48
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=42.40 E-value=56 Score=23.06 Aligned_cols=45 Identities=24% Similarity=0.293 Sum_probs=36.3
Q ss_pred HHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhccccccc
Q 024762 105 MKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKD 170 (263)
Q Consensus 105 ~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~K~ 170 (263)
.+|+..+...+..|..|+|++|= --.-.+|-=|++|+..|||+..
T Consensus 13 ~~Il~~L~~~~~~t~~ela~~l~---------------------~~~~t~s~hL~~L~~aGli~~~ 57 (61)
T PF12840_consen 13 LRILRLLASNGPMTVSELAEELG---------------------ISQSTVSYHLKKLEEAGLIEVE 57 (61)
T ss_dssp HHHHHHHHHCSTBEHHHHHHHHT---------------------S-HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHhcCCCCCHHHHHHHHC---------------------CCHHHHHHHHHHHHHCCCeEEe
Confidence 56778888899999999999971 1134588999999999999873
No 49
>PF07544 Med9: RNA polymerase II transcription mediator complex subunit 9; InterPro: IPR011425 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. This entry represents subunit Med9 of the Mediator complex. Subunit Med9 is part of the middle module of the Mediator complex []; this associates with the core polymerase subunits to form the RNA polymerase II holoenzyme. Med9 alternatively known as the chromosome segregation protein, CSE2 (P33308 from SWISSPROT) is required, along with CSE1 (P33307 from SWISSPROT) for accurate mitotic chromosome segregation in Saccharomyces cerevisiae (Baker's yeast) [].; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=40.08 E-value=64 Score=24.98 Aligned_cols=49 Identities=22% Similarity=0.354 Sum_probs=30.8
Q ss_pred cchhhhhhHHHHhhhcccccccCCeeeeccCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024762 149 NIRRRVYDALNVLMAMDIISKDKKEIQWKGLPRTSLNDIEELKAERLGLRNRIEKKTAYLQELED 213 (263)
Q Consensus 149 niKRRVYDalNVL~ai~lI~K~Kk~I~W~G~~~~s~~~~~~Lk~E~~~l~erI~~Kk~~LqEL~~ 213 (263)
.||-|+==+-+++.++.=|+ ..+++.+.++..|+++|+.|++.|+.+-.
T Consensus 32 ~lk~Klq~ar~~i~~lpgi~----------------~s~eeq~~~i~~Le~~i~~k~~~L~~~~~ 80 (83)
T PF07544_consen 32 SLKHKLQKARAAIRELPGID----------------RSVEEQEEEIEELEEQIRKKREVLQKFKE 80 (83)
T ss_pred HHHHHHHHHHHHHHhCCCcc----------------CCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45666666666665553222 12456667777788888888888876654
No 50
>smart00338 BRLZ basic region leucin zipper.
Probab=38.90 E-value=1.4e+02 Score=21.45 Aligned_cols=35 Identities=23% Similarity=0.263 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024762 187 IEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNL 221 (263)
Q Consensus 187 ~~~Lk~E~~~l~erI~~Kk~~LqEL~~Q~~alknL 221 (263)
++.|+.++..|..........+..|..+...++++
T Consensus 28 ~~~Le~~~~~L~~en~~L~~~~~~l~~e~~~lk~~ 62 (65)
T smart00338 28 IEELERKVEQLEAENERLKKEIERLRRELEKLKSE 62 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44455555555555555555555555555544443
No 51
>PF02996 Prefoldin: Prefoldin subunit; InterPro: IPR004127 This entry comprises of several prefoldin subunits. Prefoldin (PFD) is a chaperone that interacts exclusively with type II chaperonins, hetero-oligomers lacking an obligate co-chaperonin that are found only in eukaryotes (chaperonin-containing T-complex polypeptide-1 (CCT)) and archaea. Eukaryotic PFD is a multi-subunit complex containing six polypeptides in the molecular mass range of 14-23 kDa. In archaea, on the other hand, PFD is composed of two types of subunits, two alpha and four beta. The six subunits associate to form two back-to-back up-and-down eight-stranded barrels, from which hang six coiled coils. Each subunit contributes one (beta subunits) or two (alpha subunits) beta hairpin turns to the barrels. The coiled coils are formed by the N and C termini of an individual subunit. Overall, this unique arrangement resembles a jellyfish. The eukaryotic PFD hexamer is composed of six different subunits; however, these can be grouped into two alpha-like (PFD3 and -5) and four beta-like (PFD1, -2, -4, and -6) subunits based on amino acid sequence similarity with their archaeal counterparts. Eukaryotic PFD has a six-legged structure similar to that seen in the archaeal homologue [, ]. This family contains the archaeal alpha subunit, eukaryotic prefoldin subunits 3 and 5 and the UXT (ubiquitously expressed transcript) family. Eukaryotic PFD has been shown to bind both actin and tubulin co-translationally. The chaperone then delivers the target protein to CCT, interacting with the chaperonin through the tips of the coiled coils. No authentic target proteins of any archaeal PFD have been identified, to date.; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0016272 prefoldin complex; PDB: 1FXK_C 2ZDI_C.
Probab=37.99 E-value=1.5e+02 Score=23.24 Aligned_cols=70 Identities=23% Similarity=0.136 Sum_probs=41.1
Q ss_pred hHHHHhhhcccccccCCeeeeccCCCC----ChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024762 156 DALNVLMAMDIISKDKKEIQWKGLPRT----SLNDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQRN 225 (263)
Q Consensus 156 DalNVL~ai~lI~K~Kk~I~W~G~~~~----s~~~~~~Lk~E~~~l~erI~~Kk~~LqEL~~Q~~alknLI~RN 225 (263)
++-..+..-|-|....+-+-|.|.+.. ..+..+-|+..+..+.+.+++....+.++..+...+...+++-
T Consensus 44 plg~~~~v~g~i~~~~~vlV~lG~~~~vE~s~~eA~~~l~~r~~~l~~~~~~l~~~~~~~~~~~~~~~~~l~~~ 117 (120)
T PF02996_consen 44 PLGSGVFVPGKIPDTDKVLVSLGAGYYVEMSLEEAIEFLKKRIKELEEQLEKLEKELAELQAQIEQLEQTLQQL 117 (120)
T ss_dssp EECTTEEEEEE-SSTTEEEEEEETTEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHH
T ss_pred cCCCCeEEEEEeCCCCEEEEEeeCCeEEEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333444444556566777788886532 2234445555666666666666777777777777666666543
No 52
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=37.93 E-value=56 Score=22.07 Aligned_cols=42 Identities=24% Similarity=0.308 Sum_probs=30.2
Q ss_pred HHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhcccccc
Q 024762 106 KVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (263)
Q Consensus 106 KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~K 169 (263)
+|...+.. +..+..|+|+.|- .-+--|+--|+.|+..|||+|
T Consensus 6 ~Il~~L~~-~~~~~~el~~~l~---------------------~s~~~vs~hL~~L~~~glV~~ 47 (47)
T PF01022_consen 6 RILKLLSE-GPLTVSELAEELG---------------------LSQSTVSHHLKKLREAGLVEK 47 (47)
T ss_dssp HHHHHHTT-SSEEHHHHHHHHT---------------------S-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHh-CCCchhhHHHhcc---------------------ccchHHHHHHHHHHHCcCeeC
Confidence 34455544 8888888888862 234567778999999999986
No 53
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=37.31 E-value=1.2e+02 Score=20.25 Aligned_cols=45 Identities=16% Similarity=0.146 Sum_probs=33.8
Q ss_pred HHHHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhcccccc
Q 024762 103 FSMKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (263)
Q Consensus 103 fS~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~K 169 (263)
...+|.+.+...+ .++.|+|+.+- .-+..||-+++.|...|+|.+
T Consensus 8 ~~~~il~~l~~~~-~~~~ei~~~~~---------------------i~~~~i~~~l~~L~~~g~i~~ 52 (78)
T cd00090 8 TRLRILRLLLEGP-LTVSELAERLG---------------------LSQSTVSRHLKKLEEAGLVES 52 (78)
T ss_pred HHHHHHHHHHHCC-cCHHHHHHHHC---------------------cCHhHHHHHHHHHHHCCCeEE
Confidence 3456777776666 88999888751 123667888999999999998
No 54
>PF08317 Spc7: Spc7 kinetochore protein; InterPro: IPR013253 This entry consists of cell division proteins which are required for kinetochore-spindle association [].
Probab=37.08 E-value=1e+02 Score=29.16 Aligned_cols=34 Identities=29% Similarity=0.465 Sum_probs=16.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024762 186 DIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQ 219 (263)
Q Consensus 186 ~~~~Lk~E~~~l~erI~~Kk~~LqEL~~Q~~alk 219 (263)
+++.|+.++..+...|+.+++.|.+|..+...++
T Consensus 210 eL~~lr~eL~~~~~~i~~~k~~l~el~~el~~l~ 243 (325)
T PF08317_consen 210 ELEALRQELAEQKEEIEAKKKELAELQEELEELE 243 (325)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4445555555554555544444444444444333
No 55
>KOG2264 consensus Exostosin EXT1L [Signal transduction mechanisms]
Probab=37.04 E-value=73 Score=34.08 Aligned_cols=9 Identities=44% Similarity=0.777 Sum_probs=6.0
Q ss_pred ccccceEEE
Q 024762 238 GVALPFILV 246 (263)
Q Consensus 238 ~I~LPFIlV 246 (263)
++.|||=+.
T Consensus 154 kl~LP~sll 162 (907)
T KOG2264|consen 154 KLFLPFSLL 162 (907)
T ss_pred ceeeccccC
Confidence 577777643
No 56
>PF08317 Spc7: Spc7 kinetochore protein; InterPro: IPR013253 This entry consists of cell division proteins which are required for kinetochore-spindle association [].
Probab=36.94 E-value=1.3e+02 Score=28.47 Aligned_cols=40 Identities=23% Similarity=0.288 Sum_probs=22.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024762 186 DIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQRN 225 (263)
Q Consensus 186 ~~~~Lk~E~~~l~erI~~Kk~~LqEL~~Q~~alknLI~RN 225 (263)
++.+|+.++..+.+.|+...++.+++..+...++...+.+
T Consensus 231 ~l~el~~el~~l~~~i~~~~~~k~~l~~eI~e~~~~~~~~ 270 (325)
T PF08317_consen 231 ELAELQEELEELEEKIEELEEQKQELLAEIAEAEKIREEC 270 (325)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3445555555555566666666666665555555555444
No 57
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=36.23 E-value=48 Score=22.03 Aligned_cols=21 Identities=29% Similarity=0.338 Sum_probs=18.0
Q ss_pred cchhhhhhHHHHhhhcccccc
Q 024762 149 NIRRRVYDALNVLMAMDIISK 169 (263)
Q Consensus 149 niKRRVYDalNVL~ai~lI~K 169 (263)
.-+--|..+++.|+.-|+|.+
T Consensus 32 vs~~tv~~~l~~L~~~g~i~~ 52 (60)
T smart00345 32 VSRTTVREALSRLEAEGLVQR 52 (60)
T ss_pred CCHHHHHHHHHHHHHCCCEEE
Confidence 446678999999999999987
No 58
>cd06445 ATase The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases are specific for repair of guanines with O6-alkyl adducts, however human ATase is not limited to O6-methylguanine, repairing many other adducts at the O6-position of guanine as well. ATase is widely distributed among species. Most ATases have N- and C-terminal domains. The C-terminal domain contains the conserved active-site cysteine motif (PCHR), the O6-alkylguanine binding channel, and the helix-turn-helix (HTH) DNA-binding motif. The active site is located near the recognition helix of the HTH motif. While the C-terminal domain of ATase contains residues that are necessary for DNA binding and alkyl transfer, the function of the N-terminal domain is still unknown. Removal of the N-terminal domain abolishes the activity of
Probab=35.90 E-value=39 Score=25.53 Aligned_cols=23 Identities=26% Similarity=0.293 Sum_probs=17.7
Q ss_pred HHHHHHHHH---hcCCCcHHHHHHHH
Q 024762 104 SMKVCEKVE---SKGRTTYNEVADEL 126 (263)
Q Consensus 104 S~KVcekVk---~kg~TTYnEVAdeL 126 (263)
-.+|++.|. .-..+||.+||+.+
T Consensus 2 ~~~V~~~v~~IP~G~v~TYg~iA~~~ 27 (79)
T cd06445 2 QRRVWEALRQIPYGEVTTYGQIAKLA 27 (79)
T ss_pred HHHHHHHHhcCCCCCcCcHHHHHHHH
Confidence 356667766 46799999999986
No 59
>COG5625 Predicted transcription regulator containing HTH domain [Transcription]
Probab=35.52 E-value=95 Score=26.15 Aligned_cols=63 Identities=22% Similarity=0.334 Sum_probs=41.7
Q ss_pred HhcCCCcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhcccccccCCeeeeccCCCCC---hhHHH
Q 024762 112 ESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKDKKEIQWKGLPRTS---LNDIE 188 (263)
Q Consensus 112 k~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~K~Kk~I~W~G~~~~s---~~~~~ 188 (263)
+..+.+--.||+.||. -..|-|.|++-||---|++.++==+--|.|+--.. ..-++
T Consensus 32 e~~~~mri~ei~rEl~---------------------is~rtvr~~v~~l~rrGll~relvqkgWvGYiya~~~P~k~le 90 (113)
T COG5625 32 EKGRGMRIREIQRELG---------------------ISERTVRAAVAVLLRRGLLARELVQKGWVGYIYATTPPPKPLE 90 (113)
T ss_pred HhcCCchHHHHHHHHh---------------------HHHHHHHHHHHHHHHhhHHHHHHHhccceeeEecCCCCchHHH
Confidence 3444588889888875 22588999999999888988854444588863222 23455
Q ss_pred HHHHHHH
Q 024762 189 ELKAERL 195 (263)
Q Consensus 189 ~Lk~E~~ 195 (263)
+.+++..
T Consensus 91 ei~~~i~ 97 (113)
T COG5625 91 EIEEEIM 97 (113)
T ss_pred HHHHHHH
Confidence 5555443
No 60
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=35.02 E-value=1.8e+02 Score=25.93 Aligned_cols=43 Identities=26% Similarity=0.448 Sum_probs=24.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHh
Q 024762 186 DIEELKAERLGLRNRIEKKTA-------YLQELEDQFVGLQNLIQRNERL 228 (263)
Q Consensus 186 ~~~~Lk~E~~~l~erI~~Kk~-------~LqEL~~Q~~alknLI~RNk~~ 228 (263)
+.+.|+.|...|.++++..+. .+..+...+.+|-.++.|=+.+
T Consensus 105 e~~~l~~e~~~l~~~~e~Le~e~~~L~~~~~~~~eDY~~L~~Im~RARkl 154 (161)
T TIGR02894 105 ENERLKNQNESLQKRNEELEKELEKLRQRLSTIEEDYQTLIDIMDRARKL 154 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444555555555544444444 4444456677777788776655
No 61
>smart00787 Spc7 Spc7 kinetochore protein. This domain is found in cell division proteins which are required for kinetochore-spindle association.
Probab=34.77 E-value=1.1e+02 Score=29.38 Aligned_cols=17 Identities=24% Similarity=0.387 Sum_probs=10.3
Q ss_pred CCCCCCcccchhhcccc
Q 024762 49 SMATPASDSTFLRLNHL 65 (263)
Q Consensus 49 ~~~~~~~~~~~~~l~~~ 65 (263)
+...|-+.+-||..-++
T Consensus 5 ~~~~~isL~dFL~~t~I 21 (312)
T smart00787 5 PPTEPISLQDFLNMTGI 21 (312)
T ss_pred CCCCCccHHHHHHHcCc
Confidence 35667777777644443
No 62
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=34.51 E-value=31 Score=27.90 Aligned_cols=34 Identities=21% Similarity=0.075 Sum_probs=26.6
Q ss_pred cCCCcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhc
Q 024762 114 KGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAM 164 (263)
Q Consensus 114 kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai 164 (263)
-...+|.|||++|= ....++++++|.++..|...
T Consensus 123 ~~~~s~~EIA~~lg-----------------is~~tV~~~l~ra~~~lr~~ 156 (163)
T PRK07037 123 LHGETQKDIARELG-----------------VSPTLVNFMIRDALVHCRKC 156 (163)
T ss_pred HcCCCHHHHHHHHC-----------------CCHHHHHHHHHHHHHHHHHH
Confidence 35778999999862 23569999999999999753
No 63
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=34.40 E-value=58 Score=27.16 Aligned_cols=51 Identities=20% Similarity=0.317 Sum_probs=39.8
Q ss_pred cchhhHHHHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhcccccc
Q 024762 98 RGLRQFSMKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (263)
Q Consensus 98 kGLR~fS~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~K 169 (263)
..|-.+=.++.+.++..++++|.|+|++|= . .+..++|| ++=|+.-|+|.+
T Consensus 5 ~~lD~~D~~Il~~Lq~d~R~s~~eiA~~lg---------l--------S~~tV~~R----i~rL~~~GvI~~ 55 (153)
T PRK11179 5 YQIDNLDRGILEALMENARTPYAELAKQFG---------V--------SPGTIHVR----VEKMKQAGIITG 55 (153)
T ss_pred cccCHHHHHHHHHHHHcCCCCHHHHHHHHC---------c--------CHHHHHHH----HHHHHHCCCeee
Confidence 346778889999999999999999999971 0 23356666 477888888886
No 64
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=34.25 E-value=1.5e+02 Score=20.37 Aligned_cols=40 Identities=28% Similarity=0.201 Sum_probs=30.0
Q ss_pred cCCCcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhcccccccC-Cee
Q 024762 114 KGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKDK-KEI 174 (263)
Q Consensus 114 kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~K~K-k~I 174 (263)
....|..|+|+.+- .-+.-|+.+++.|+.-|+|.+.. +.|
T Consensus 23 ~~~~s~~ela~~~g---------------------~s~~tv~r~l~~L~~~g~i~~~~~~~~ 63 (67)
T cd00092 23 QLPLTRQEIADYLG---------------------LTRETVSRTLKELEEEGLISRRGRGKY 63 (67)
T ss_pred cCCcCHHHHHHHHC---------------------CCHHHHHHHHHHHHHCCCEEecCCCeE
Confidence 44577777777651 34678999999999999999955 444
No 65
>PRK06798 fliD flagellar capping protein; Validated
Probab=33.87 E-value=1.1e+02 Score=30.65 Aligned_cols=64 Identities=14% Similarity=0.305 Sum_probs=29.7
Q ss_pred ccchhhhhhHHHHhhh-cccccccCCeeeeccCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024762 148 KNIRRRVYDALNVLMA-MDIISKDKKEIQWKGLPRTSLNDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQ 223 (263)
Q Consensus 148 KniKRRVYDalNVL~a-i~lI~K~Kk~I~W~G~~~~s~~~~~~Lk~E~~~l~erI~~Kk~~LqEL~~Q~~alknLI~ 223 (263)
..+-.|+||+|+=+.+ -|+|....+ ....+++.|+.+++++++|+++++ +.|..|+.++..+|.
T Consensus 357 ~Gia~~l~~~l~~~~~~~G~i~~r~~---------~l~~~i~~l~~~~~~~e~rl~~~e---~~l~~qf~ale~~ms 421 (440)
T PRK06798 357 NGLGKEMEKSLDKIFGDEGIIGERSK---------SIDNRVSKLDLKITDIDTQNKQKQ---DNIVDKYQKLESTLA 421 (440)
T ss_pred CcHHHHHHHHHHhhhCCCceeehhhh---------HHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHH
Confidence 3566777877765442 112211111 112334444444444444444332 334556666666654
No 66
>COG3937 Uncharacterized conserved protein [Function unknown]
Probab=33.24 E-value=1.4e+02 Score=25.13 Aligned_cols=11 Identities=27% Similarity=0.564 Sum_probs=6.8
Q ss_pred cchhhhhhHHH
Q 024762 149 NIRRRVYDALN 159 (263)
Q Consensus 149 niKRRVYDalN 159 (263)
.+.|||-+++-
T Consensus 65 K~~r~i~~ml~ 75 (108)
T COG3937 65 KIPRKIEEMLS 75 (108)
T ss_pred hhhHHHHHHHh
Confidence 47777765543
No 67
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=33.23 E-value=60 Score=27.43 Aligned_cols=52 Identities=17% Similarity=0.304 Sum_probs=41.4
Q ss_pred CcchhhHHHHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhcccccc
Q 024762 97 GRGLRQFSMKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (263)
Q Consensus 97 ~kGLR~fS~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~K 169 (263)
.+.|-.+=.++...++..+++||.|+|++|= . .+-.++|| ++=|+.-|+|++
T Consensus 9 ~~~lD~~D~~IL~~Lq~d~R~s~~eiA~~lg---------l--------S~~tv~~R----i~rL~~~GvI~~ 60 (164)
T PRK11169 9 GKDLDRIDRNILNELQKDGRISNVELSKRVG---------L--------SPTPCLER----VRRLERQGFIQG 60 (164)
T ss_pred hhhHHHHHHHHHHHhccCCCCCHHHHHHHHC---------c--------CHHHHHHH----HHHHHHCCCeEE
Confidence 4668899999999999999999999999971 0 12345555 577999999986
No 68
>KOG2077 consensus JNK/SAPK-associated protein-1 [Signal transduction mechanisms]
Probab=33.12 E-value=1.1e+02 Score=32.74 Aligned_cols=77 Identities=22% Similarity=0.332 Sum_probs=46.4
Q ss_pred ccccccchhhhhhHHHHhhhcccccccCCeeeeccCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHH
Q 024762 144 QYDEKNIRRRVYDALNVLMAMDIISKDKKEIQWKGLPRTSLNDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQ-NLI 222 (263)
Q Consensus 144 ~~deKniKRRVYDalNVL~ai~lI~K~Kk~I~W~G~~~~s~~~~~~Lk~E~~~l~erI~~Kk~~LqEL~~Q~~alk-nLI 222 (263)
-||+..+|.=+-=+.|||++++++--+.. ...-+++-|++.-+.|.-+-+.-+..-..+.++++.+. .|+
T Consensus 22 ~~~Ee~VKeLMPLVVNVLEnLD~v~~Enq---------EhevELElLrEDNEQl~tqYErEkalR~q~eqKfie~eD~Le 92 (832)
T KOG2077|consen 22 CYDEEVVKELMPLVVNVLENLDSVLSENQ---------EHEVELELLREDNEQLITQYEREKALRTQLEQKFIEGEDQLE 92 (832)
T ss_pred hccHHHHHHHHHHHHHHHHHHHHHhhccc---------hhHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhhhcchHHHHH
Confidence 57888999999999999999987643221 12235566666555554444333344444555555554 455
Q ss_pred HHHHHhh
Q 024762 223 QRNERLY 229 (263)
Q Consensus 223 ~RNk~~~ 229 (263)
..|+.+.
T Consensus 93 ~~~kel~ 99 (832)
T KOG2077|consen 93 STAKELI 99 (832)
T ss_pred hhHHHHH
Confidence 5666553
No 69
>PF09766 FimP: Fms-interacting protein; InterPro: IPR019163 This entry represents Thoc5 which is one of the subunits of the THO complex, which additionally contains: HPR1, Thoc2, Thoc6 and Thoc7. The evolutionarily conserved multisubunit THO complex, which is recruited to actively transcribed genes is required for the efficient expression of genes that have internal tandem repeats. It is suggested that the THO complex functions to rectify aberrant structures that arise during transcription [, ] and is required for cell proliferation and for proper export of heat-shock mRNAs under heat stress []. This entry also identifies the crucial 144 N-terminal residues of the FmiP protein, which is essential for the binding of the protein to the cytoplasmic domain of activated Fms-molecules in M-CSF induced haematopoietic differentiation of macrophages. The C terminus contains a putative nuclear localisation sequence and a leucine zipper which suggest further, as yet unknown, nuclear functions. The level of FMIP expression might form a threshold that determines whether cells differentiate into macrophages or into granulocytes [].
Probab=33.09 E-value=1.3e+02 Score=29.22 Aligned_cols=37 Identities=24% Similarity=0.424 Sum_probs=26.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024762 185 NDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNL 221 (263)
Q Consensus 185 ~~~~~Lk~E~~~l~erI~~Kk~~LqEL~~Q~~alknL 221 (263)
.++++|+.++..+.+.++.|+++|..|..+...|..-
T Consensus 108 ~~~~el~~~k~~l~~~~~~k~~~L~~l~~~L~~l~~a 144 (355)
T PF09766_consen 108 EQLKELEQRKKKLQQENKKKKKFLDSLPPQLKSLKKA 144 (355)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHH
Confidence 3456666677777777888888888888777666544
No 70
>PF14817 HAUS5: HAUS augmin-like complex subunit 5
Probab=32.50 E-value=1.7e+02 Score=30.99 Aligned_cols=49 Identities=20% Similarity=0.292 Sum_probs=30.6
Q ss_pred cccCCeeeeccCCCCC---------hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024762 168 SKDKKEIQWKGLPRTS---------LNDIEELKAERLGLRNRIEKKTAYLQELEDQFV 216 (263)
Q Consensus 168 ~K~Kk~I~W~G~~~~s---------~~~~~~Lk~E~~~l~erI~~Kk~~LqEL~~Q~~ 216 (263)
+|-++.|.|.|..... ..+-.+|++|+.+|+..|...+..+..+..+..
T Consensus 53 ~~iRgNl~~~~~~~~~~~~~~~e~~~~~r~~L~~everLraei~~l~~~I~~~e~e~~ 110 (632)
T PF14817_consen 53 RKIRGNLLWYGHQQSKERKKSRENEARRRRELEKEVERLRAEIQELDKEIESREREVS 110 (632)
T ss_pred HHHHcceeeccccccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4457889998875432 234556677777777777666666655544443
No 71
>PF05529 Bap31: B-cell receptor-associated protein 31-like ; InterPro: IPR008417 Bap31 is a polytopic integral protein of the endoplasmic reticulum membrane and a substrate of caspase-8. Bap31 is cleaved within its cytosolic domain, generating pro-apoptotic p20 Bap31 [].; GO: 0006886 intracellular protein transport, 0005783 endoplasmic reticulum, 0016021 integral to membrane
Probab=32.48 E-value=1e+02 Score=26.61 Aligned_cols=29 Identities=31% Similarity=0.402 Sum_probs=15.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024762 189 ELKAERLGLRNRIEKKTAYLQELEDQFVG 217 (263)
Q Consensus 189 ~Lk~E~~~l~erI~~Kk~~LqEL~~Q~~a 217 (263)
.+++|.++++++|++++..+..|..|...
T Consensus 158 ~~~~ei~~lk~el~~~~~~~~~LkkQ~~~ 186 (192)
T PF05529_consen 158 KLSEEIEKLKKELEKKEKEIEALKKQSEG 186 (192)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455555555555555555555555443
No 72
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=32.16 E-value=1.1e+02 Score=21.64 Aligned_cols=49 Identities=29% Similarity=0.428 Sum_probs=35.7
Q ss_pred HHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhcccccccCCee
Q 024762 105 MKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKDKKEI 174 (263)
Q Consensus 105 ~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~K~Kk~I 174 (263)
.++.+.|++++..+..|+|++|- ....++|| =||.|+.-|+|.|-...+
T Consensus 3 ~~Il~~l~~~~~~s~~ela~~~~-----------------VS~~TiRR----Dl~~L~~~g~i~r~~GG~ 51 (57)
T PF08220_consen 3 QQILELLKEKGKVSVKELAEEFG-----------------VSEMTIRR----DLNKLEKQGLIKRTHGGA 51 (57)
T ss_pred HHHHHHHHHcCCEEHHHHHHHHC-----------------cCHHHHHH----HHHHHHHCCCEEEEcCEE
Confidence 35788999999999999998861 11335655 367899999998854443
No 73
>PF07195 FliD_C: Flagellar hook-associated protein 2 C-terminus; InterPro: IPR010809 The flagellar hook-associated protein 2 (HAP2 or FliD) forms the distal end of the flagella, and plays a role in mucin specific adhesion of the bacteria []. This alignment covers the C-terminal region of the flagellar hook-associated protein 2.; GO: 0007155 cell adhesion, 0009288 bacterial-type flagellum
Probab=31.99 E-value=2.4e+02 Score=25.26 Aligned_cols=61 Identities=26% Similarity=0.403 Sum_probs=29.7
Q ss_pred cccchhhhhhHHHHhhhc--ccccccCCeeeeccCCCCChhHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHH
Q 024762 147 EKNIRRRVYDALNVLMAM--DIISKDKKEIQWKGLPRTSLNDIEELKAERLGLRNRIEKKTAYLQ----ELEDQFVGLQN 220 (263)
Q Consensus 147 eKniKRRVYDalNVL~ai--~lI~K~Kk~I~W~G~~~~s~~~~~~Lk~E~~~l~erI~~Kk~~Lq----EL~~Q~~alkn 220 (263)
...+=.|++|+|+=+..- |+|. .....|..+...+.++|+..++++. .|..|+.++..
T Consensus 169 ~~Gi~~~l~~~l~~~~~~~~G~i~----------------~~~~~l~~~~~~~~~~i~~~~~rl~~~~~~l~~qf~~me~ 232 (239)
T PF07195_consen 169 TSGIATRLNDYLDSYTGSSTGSIT----------------SRIDSLNSQIKSLDKQIEDLEERLESKEERLRKQFSAMES 232 (239)
T ss_pred cccHHHHHHHHHHHHhCCCCcchh----------------hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345566677777654422 2222 2233344444444444443333332 34557777777
Q ss_pred HHH
Q 024762 221 LIQ 223 (263)
Q Consensus 221 LI~ 223 (263)
++.
T Consensus 233 ~i~ 235 (239)
T PF07195_consen 233 LIS 235 (239)
T ss_pred HHH
Confidence 764
No 74
>PF10186 Atg14: UV radiation resistance protein and autophagy-related subunit 14; InterPro: IPR018791 Class III phosphatidylinositol 3-kinase (PI3-kinase) regulates multiple membrane trafficking. In yeast, two distinct PI3-kinase complexes are known: complex I (Vps34, Vps15, Vps30/Atg6, and Atg14) is involved in autophagy, and complex II (Vps34, Vps15, Vps30/Atg6, and Vps38) functions in the vacuolar protein sorting pathway. In mammals, the counterparts of Vps34, Vps15, and Vps30/Atg6 are Vps34, p150, and Beclin 1, respectively. Mammalian UV irradiation resistance-associated gene (UVRAG) has been identified as identical to yeast Vps38 []. The Atg14 (autophagy-related protein 14) proteins are hydrophilic proteins and have a coiled-coil motif at the N terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole []. This entry represents Atg14 and UVRAG, which bind Beclin 1 to forms two distinct PI3-kinase complexes. This entry also includes Bakor (beclin-1-associated autophagy-related key regulator), also known as autophagy-related protein 14-like protein, which share sequence similarity to the yeast Atg14 protein []. Barkor positively regulates autophagy through its interaction with Beclin-1, with decreased levels of autophagosome formation observed when Barkor expression is eliminated []. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. ; GO: 0010508 positive regulation of autophagy
Probab=31.77 E-value=2.1e+02 Score=25.47 Aligned_cols=12 Identities=33% Similarity=0.728 Sum_probs=6.8
Q ss_pred ccchhhhhhHHH
Q 024762 148 KNIRRRVYDALN 159 (263)
Q Consensus 148 KniKRRVYDalN 159 (263)
..++++|=+++.
T Consensus 37 ~~l~~~i~~~l~ 48 (302)
T PF10186_consen 37 EELRRRIEEILE 48 (302)
T ss_pred HHHHHHHHHHHH
Confidence 355566666555
No 75
>PF12958 DUF3847: Protein of unknown function (DUF3847); InterPro: IPR024215 This entry represents a family of uncharacterised proteins that were found by clustering human gut metagenomic sequences [].
Probab=31.73 E-value=2e+02 Score=23.00 Aligned_cols=33 Identities=27% Similarity=0.381 Sum_probs=22.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024762 186 DIEELKAERLGLRNRIEKKTAYLQELEDQFVGL 218 (263)
Q Consensus 186 ~~~~Lk~E~~~l~erI~~Kk~~LqEL~~Q~~al 218 (263)
.+++|++|.....+.|++.+..++.|.-+..-+
T Consensus 2 ~Le~l~~e~e~~~~kl~q~e~~~k~L~nr~k~l 34 (86)
T PF12958_consen 2 TLEELQAEIEKAEKKLEQAEHKIKQLENRKKKL 34 (86)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 367777877777777777666666666655544
No 76
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=31.27 E-value=91 Score=21.28 Aligned_cols=44 Identities=20% Similarity=0.268 Sum_probs=35.2
Q ss_pred HHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhcccccc
Q 024762 105 MKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (263)
Q Consensus 105 ~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~K 169 (263)
..|...+.+.+.++..|+|+.+- .-+-.|-.+++-|+.-|+|+|
T Consensus 6 ~~iL~~l~~~~~~~~~~la~~~~---------------------~~~~~~t~~i~~L~~~g~I~r 49 (59)
T PF01047_consen 6 FRILRILYENGGITQSELAEKLG---------------------ISRSTVTRIIKRLEKKGLIER 49 (59)
T ss_dssp HHHHHHHHHHSSEEHHHHHHHHT---------------------S-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHcCCCCHHHHHHHHC---------------------CChhHHHHHHHHHHHCCCEEe
Confidence 34667788899999999998863 234667889999999999998
No 77
>PF12269 zf-CpG_bind_C: CpG binding protein zinc finger C terminal domain; InterPro: IPR022056 This domain family is found in eukaryotes, and is approximately 240 amino acids in length. This domain is the zinc finger domain of a CpG binding DNA methyltransferase protein. It contains a CxxC motif which forms the zinc finger and binds to DNA.
Probab=31.21 E-value=1.3e+02 Score=28.23 Aligned_cols=51 Identities=25% Similarity=0.392 Sum_probs=33.2
Q ss_pred eccCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 024762 176 WKGLPRTSLNDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQRNERLY 229 (263)
Q Consensus 176 W~G~~~~s~~~~~~Lk~E~~~l~erI~~Kk~~LqEL~~Q~~alknLI~RNk~~~ 229 (263)
|...|..+.. .-+..++.++.+...-+..|++|+.++.-|..+|.|=+...
T Consensus 16 w~~~p~~A~E---~~r~~Le~Ir~kq~~v~~~l~eLe~~~~el~~~i~~~k~~~ 66 (236)
T PF12269_consen 16 WQLSPCVAEE---QNRKLLEEIRKKQQKVRNRLQELEKRFKELEAIIARAKQFT 66 (236)
T ss_pred hcCCCchhhh---hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 7766654331 22233334455555667788999999999999998877653
No 78
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=31.12 E-value=3.5e+02 Score=23.47 Aligned_cols=59 Identities=17% Similarity=0.147 Sum_probs=38.2
Q ss_pred cchhhHHHHHHHHHH----hcCCC-cHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhcccccccCC
Q 024762 98 RGLRQFSMKVCEKVE----SKGRT-TYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKDKK 172 (263)
Q Consensus 98 kGLR~fS~KVcekVk----~kg~T-TYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~K~Kk 172 (263)
.-+.+|+.=.+--|+ -..-. ++.+||+.|.-. .--..|=++|+.|+-+|+|+|+++
T Consensus 16 ~~~~~~~~W~~~~ir~l~~l~~~~~d~~~iak~l~p~-------------------is~~ev~~sL~~L~~~gli~k~~~ 76 (171)
T PF14394_consen 16 DEFEYYSSWYHPAIRELLPLMPFAPDPEWIAKRLRPK-------------------ISAEEVRDSLEFLEKLGLIKKDGD 76 (171)
T ss_pred HHHHHHhhhHHHHHHHHhhcCCCCCCHHHHHHHhcCC-------------------CCHHHHHHHHHHHHHCCCeEECCC
Confidence 446666665444333 34444 777888777422 222457799999999999999665
Q ss_pred eeee
Q 024762 173 EIQW 176 (263)
Q Consensus 173 ~I~W 176 (263)
-.|
T Consensus 77 -g~y 79 (171)
T PF14394_consen 77 -GKY 79 (171)
T ss_pred -CcE
Confidence 344
No 79
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=31.00 E-value=1.1e+02 Score=26.22 Aligned_cols=53 Identities=19% Similarity=0.220 Sum_probs=36.9
Q ss_pred HHHHHHh-cCCCcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhcccccc--cCCeee
Q 024762 107 VCEKVES-KGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK--DKKEIQ 175 (263)
Q Consensus 107 VcekVk~-kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~K--~Kk~I~ 175 (263)
|.+.+.+ .+..|-.||.+.|.++... .=+=-||..|+.|+..|||.+ ..+.+.
T Consensus 31 IL~~l~~~~~hlSa~eI~~~L~~~~~~----------------is~aTVYRtL~~L~e~Glv~~~~~~~~~~ 86 (169)
T PRK11639 31 VLRLMSLQPGAISAYDLLDLLREAEPQ----------------AKPPTVYRALDFLLEQGFVHKVESTNSYV 86 (169)
T ss_pred HHHHHHhcCCCCCHHHHHHHHHhhCCC----------------CCcchHHHHHHHHHHCCCEEEEecCCcEE
Confidence 6676665 4577777877777655321 223569999999999999999 344443
No 80
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=30.94 E-value=1e+02 Score=22.88 Aligned_cols=46 Identities=28% Similarity=0.341 Sum_probs=30.9
Q ss_pred HHHHHHhcC-CCcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhcccccccCC
Q 024762 107 VCEKVESKG-RTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKDKK 172 (263)
Q Consensus 107 VcekVk~kg-~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~K~Kk 172 (263)
+++-+.+.| .-|+.|||+.|= . .-..-|++.|..|+.-|+|.+..+
T Consensus 15 I~~~~~~~G~~Pt~rEIa~~~g---------~-----------~S~~tv~~~L~~Le~kG~I~r~~~ 61 (65)
T PF01726_consen 15 IREYIEENGYPPTVREIAEALG---------L-----------KSTSTVQRHLKALERKGYIRRDPG 61 (65)
T ss_dssp HHHHHHHHSS---HHHHHHHHT---------S-----------SSHHHHHHHHHHHHHTTSEEEGCC
T ss_pred HHHHHHHcCCCCCHHHHHHHhC---------C-----------CChHHHHHHHHHHHHCcCccCCCC
Confidence 345455555 678999888862 0 124789999999999999999543
No 81
>PF04977 DivIC: Septum formation initiator; InterPro: IPR007060 DivIC, from the spore-forming, Gram-positive bacterium Bacillus subtilis, is necessary for both vegetative and sporulation septum formation []. These proteins are mainly composed of an N-terminal coiled-coil. DivIB, DivIC and FtsL inter-depend on each other for stabilisation and localisation. The latter two form a heterodimer. DivIC is always centre cell but the other two associate with it during septation [].; GO: 0007049 cell cycle
Probab=30.85 E-value=1.7e+02 Score=21.13 Aligned_cols=30 Identities=23% Similarity=0.263 Sum_probs=12.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024762 187 IEELKAERLGLRNRIEKKTAYLQELEDQFV 216 (263)
Q Consensus 187 ~~~Lk~E~~~l~erI~~Kk~~LqEL~~Q~~ 216 (263)
...++.+...+..+|++.++...+|..+..
T Consensus 19 ~~~~~~ei~~l~~~i~~l~~e~~~L~~ei~ 48 (80)
T PF04977_consen 19 YYQLNQEIAELQKEIEELKKENEELKEEIE 48 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334444444444444444444444443333
No 82
>PF02050 FliJ: Flagellar FliJ protein; InterPro: IPR012823 Many flagellar proteins are exported by a flagellum-specific export pathway. Attempts have been made to characterise the apparatus responsible for this process, by designing assays to screen for mutants with export defects []. Experiments involving filament removal from temperature-sensitive flagellar mutants of Salmonella typhimurium have shown that, while most mutants were able to regrow filaments, flhA, fliH, fliI and fliN mutants showed no or greatly reduced regrowth. This suggests that the corresponding gene products are involved in the process of flagellum-specific export. The sequences of fliH, fliI and the adjacent gene, fliJ, have been deduced. FliJ was shown to encode a protein of molecular mass 17,302 Da []. It is a membrane-associated protein that affects chemotactic events, mutations in FliJ result in failure to respond to chemotactic stimuli.; GO: 0003774 motor activity, 0001539 ciliary or flagellar motility, 0006935 chemotaxis, 0009288 bacterial-type flagellum, 0016020 membrane, 0044461 bacterial-type flagellum part; PDB: 3AJW_A.
Probab=30.75 E-value=2.3e+02 Score=21.12 Aligned_cols=44 Identities=23% Similarity=0.256 Sum_probs=33.3
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024762 185 NDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQRNERL 228 (263)
Q Consensus 185 ~~~~~Lk~E~~~l~erI~~Kk~~LqEL~~Q~~alknLI~RNk~~ 228 (263)
..+..++.++..++..++.++..|.+.......+..|.+|-...
T Consensus 59 ~~i~~~~~~~~~~~~~~~~~r~~l~~a~~~~k~~e~L~e~~~~~ 102 (123)
T PF02050_consen 59 QAIQQQQQELERLEQEVEQAREELQEARRERKKLEKLKERRREE 102 (123)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34566677777777788888888888888888888888866543
No 83
>PF04492 Phage_rep_O: Bacteriophage replication protein O ; InterPro: IPR006497 This entry is represented by the N-terminal domain of Bacteriophage lambda, GpO. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; GO: 0006260 DNA replication
Probab=30.54 E-value=38 Score=27.37 Aligned_cols=25 Identities=40% Similarity=0.494 Sum_probs=21.3
Q ss_pred chhhhhhHHHHhhhcccccccCCee
Q 024762 150 IRRRVYDALNVLMAMDIISKDKKEI 174 (263)
Q Consensus 150 iKRRVYDalNVL~ai~lI~K~Kk~I 174 (263)
-+..|.+++|.|..++||.++++.+
T Consensus 67 ~~~~V~~al~~Li~~~vI~~~g~~~ 91 (100)
T PF04492_consen 67 SRDHVSKALNELIRRGVIIRDGKRI 91 (100)
T ss_pred CHHHHHHHHHHHHHCCCEEeCCcEE
Confidence 3678999999999999998877544
No 84
>TIGR01242 26Sp45 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
Probab=30.47 E-value=1.6e+02 Score=27.72 Aligned_cols=40 Identities=20% Similarity=0.139 Sum_probs=25.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024762 189 ELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQRNERL 228 (263)
Q Consensus 189 ~Lk~E~~~l~erI~~Kk~~LqEL~~Q~~alknLI~RNk~~ 228 (263)
+|+.+.+.+++++++-+..+.++..+...++..+.+++..
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 42 (364)
T TIGR01242 3 ELDVRIRKLEDEKRSLEKEKIRLERELERLRSEIERLRSP 42 (364)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 4455556666666666666666666666677777666554
No 85
>PF04380 BMFP: Membrane fusogenic activity; InterPro: IPR007475 BMFP consists of two structural domains, a coiled-coil C-terminal domain via which the protein self-associates as a trimer, and an N-terminal domain disordered at neutral pH but adopting an amphipathic alpha-helical structure in the presence of phospholipid vesicles, high ionic strength, acidic pH or SDS. BMFP interacts with phospholipid vesicles though the predicted amphipathic alpha-helix induced in the N-terminal half of the protein and promotes aggregation and fusion of vesicles in vitro.
Probab=30.47 E-value=1.1e+02 Score=23.53 Aligned_cols=49 Identities=33% Similarity=0.487 Sum_probs=34.6
Q ss_pred cccchhhhhhHHHHhhhcccccccCCeeeeccCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024762 147 EKNIRRRVYDALNVLMAMDIISKDKKEIQWKGLPRTSLNDIEELKAERLGLRNRIEKKTAYLQELED 213 (263)
Q Consensus 147 eKniKRRVYDalNVL~ai~lI~K~Kk~I~W~G~~~~s~~~~~~Lk~E~~~l~erI~~Kk~~LqEL~~ 213 (263)
++++|-++=. .|..+++++| .+.+.+++.+.+.+++|+..+++|.+|+.
T Consensus 30 e~~~r~~l~~---~l~kldlVtR---------------EEFd~q~~~L~~~r~kl~~LEarl~~LE~ 78 (79)
T PF04380_consen 30 EKNIRARLQS---ALSKLDLVTR---------------EEFDAQKAVLARTREKLEALEARLAALEA 78 (79)
T ss_pred HHHHHHHHHH---HHHHCCCCcH---------------HHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 4566666544 4445666665 46777788888888888888888888764
No 86
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=30.30 E-value=49 Score=21.34 Aligned_cols=25 Identities=28% Similarity=0.337 Sum_probs=20.9
Q ss_pred chhhhhhHHHHhhhcccccccCCee
Q 024762 150 IRRRVYDALNVLMAMDIISKDKKEI 174 (263)
Q Consensus 150 iKRRVYDalNVL~ai~lI~K~Kk~I 174 (263)
-+..|+.+++.|++.|+|++.++.|
T Consensus 21 s~~tv~~~l~~L~~~g~l~~~~~~~ 45 (48)
T smart00419 21 TRETVSRTLKRLEKEGLISREGGRI 45 (48)
T ss_pred CHHHHHHHHHHHHHCCCEEEeCCEE
Confidence 3577999999999999999866554
No 87
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=30.30 E-value=1.7e+02 Score=23.72 Aligned_cols=34 Identities=15% Similarity=0.057 Sum_probs=16.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024762 186 DIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQ 219 (263)
Q Consensus 186 ~~~~Lk~E~~~l~erI~~Kk~~LqEL~~Q~~alk 219 (263)
...+++.+...+++++++.++.-++|..+...++
T Consensus 28 ~~~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~ 61 (105)
T PRK00888 28 DYWRVNDQVAAQQQTNAKLKARNDQLFAEIDDLK 61 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3445555555555555544444444444444443
No 88
>COG0350 Ada Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]
Probab=30.01 E-value=51 Score=28.70 Aligned_cols=26 Identities=27% Similarity=0.386 Sum_probs=22.5
Q ss_pred hHHHHHHHHHHh---cCCCcHHHHHHHHH
Q 024762 102 QFSMKVCEKVES---KGRTTYNEVADELV 127 (263)
Q Consensus 102 ~fS~KVcekVk~---kg~TTYnEVAdeLV 127 (263)
.|-.+|++.+++ -.++||.|||..|-
T Consensus 88 ~Fq~~Vw~aL~~IP~Get~TY~eiA~~ig 116 (168)
T COG0350 88 GFQGRVWQALREIPYGETVTYGEIARRLG 116 (168)
T ss_pred hHHHHHHHHHhcCCCCCcEeHHHHHHHhC
Confidence 688999999988 45899999999974
No 89
>PRK10803 tol-pal system protein YbgF; Provisional
Probab=29.87 E-value=1.7e+02 Score=27.11 Aligned_cols=45 Identities=9% Similarity=0.093 Sum_probs=33.6
Q ss_pred ChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHH
Q 024762 183 SLNDIEELKAERLGLRNRIEKKTAYLQELEDQFV-GLQNLIQRNER 227 (263)
Q Consensus 183 s~~~~~~Lk~E~~~l~erI~~Kk~~LqEL~~Q~~-alknLI~RNk~ 227 (263)
..++++.|+.|+.+|+-+|++-.-+|+++.+++. -+..|=.|-+.
T Consensus 59 l~~ql~~lq~ev~~LrG~~E~~~~~l~~~~~rq~~~y~dld~r~~~ 104 (263)
T PRK10803 59 LQQQLSDNQSDIDSLRGQIQENQYQLNQVVERQKQIYLQIDSLSSG 104 (263)
T ss_pred HHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 3467889999999999999999988988887555 44455555543
No 90
>PRK09954 putative kinase; Provisional
Probab=29.57 E-value=90 Score=29.10 Aligned_cols=46 Identities=24% Similarity=0.145 Sum_probs=36.8
Q ss_pred HHHHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhcccccc
Q 024762 103 FSMKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (263)
Q Consensus 103 fS~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~K 169 (263)
.-.+|++.+++.+.+|+.|+|++|= .-|..|+..++=|+.-|+|.+
T Consensus 4 ~~~~il~~l~~~~~~s~~~la~~l~---------------------~s~~~v~~~i~~L~~~g~i~~ 49 (362)
T PRK09954 4 REKEILAILRRNPLIQQNEIADILQ---------------------ISRSRVAAHIMDLMRKGRIKG 49 (362)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHC---------------------CCHHHHHHHHHHHHHCCCcCC
Confidence 4467999999999999999999872 446777777888888887754
No 91
>PRK00901 methylated-DNA--protein-cysteine methyltransferase; Provisional
Probab=29.56 E-value=54 Score=28.36 Aligned_cols=25 Identities=24% Similarity=0.472 Sum_probs=22.0
Q ss_pred hHHHHHHHHHHh---cCCCcHHHHHHHH
Q 024762 102 QFSMKVCEKVES---KGRTTYNEVADEL 126 (263)
Q Consensus 102 ~fS~KVcekVk~---kg~TTYnEVAdeL 126 (263)
-|-.+|++.+.+ -.++||.|||..|
T Consensus 73 ~fq~~Vw~~l~~Ip~G~t~tY~~lA~~~ 100 (155)
T PRK00901 73 EFQKKVWKALQEIPYGETRSYKEIAVNI 100 (155)
T ss_pred hHHHHHHHHHccCCCCCcCCHHHHHHHH
Confidence 799999999987 4589999999985
No 92
>PF10828 DUF2570: Protein of unknown function (DUF2570); InterPro: IPR022538 This entry is represented by Bacteriophage IME08, pseT.3. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a family of proteins with unknown function.
Probab=28.67 E-value=3.1e+02 Score=22.05 Aligned_cols=64 Identities=23% Similarity=0.359 Sum_probs=36.4
Q ss_pred hhhhhhHHHHhhhcccccccCCeeeeccCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024762 151 RRRVYDALNVLMAMDIISKDKKEIQWKGLPRTSLNDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQRN 225 (263)
Q Consensus 151 KRRVYDalNVL~ai~lI~K~Kk~I~W~G~~~~s~~~~~~Lk~E~~~l~erI~~Kk~~LqEL~~Q~~alknLI~RN 225 (263)
+|.+|-++-|| .++|.-= -|. ....++.|+.+.....+.|++...-.++|..+...-+.++..+
T Consensus 2 ~~~~~~~l~~l-vl~L~~~-----l~~-----qs~~i~~L~a~n~~q~~tI~qq~~~~~~L~~~~~~~r~~~~~~ 65 (110)
T PF10828_consen 2 KKYIYIALAVL-VLGLGGW-----LWY-----QSQRIDRLRAENKAQAQTIQQQEDANQELKAQLQQNRQAVEEQ 65 (110)
T ss_pred hHHHHHHHHHH-HHHHHHH-----HHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56677777555 4443211 111 1245777888777777777776666666665554444444433
No 93
>PF10481 CENP-F_N: Cenp-F N-terminal domain; InterPro: IPR018463 Mitosin or centromere-associated protein-F (Cenp-F) is found bound across the centromere as one of the proteins of the outer layer of the kinetochore []. Most of the kinetochore/centromere functions appear to depend upon binding of the C-terminal part of the molecule, whereas the N-terminal part, here, may be a cytoplasmic player in controlling the function of microtubules and dynein [].
Probab=28.60 E-value=1.3e+02 Score=29.19 Aligned_cols=37 Identities=32% Similarity=0.623 Sum_probs=27.2
Q ss_pred e-ccCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024762 176 W-KGLPRTSLNDIEELKAERLGLRNRIEKKTAYLQELE 212 (263)
Q Consensus 176 W-~G~~~~s~~~~~~Lk~E~~~l~erI~~Kk~~LqEL~ 212 (263)
| .|+|....+.|++|+..+++|+..-++++=+|..|+
T Consensus 8 WKeGL~~~aLqKIqelE~QldkLkKE~qQrQfQleSlE 45 (307)
T PF10481_consen 8 WKEGLPTRALQKIQELEQQLDKLKKERQQRQFQLESLE 45 (307)
T ss_pred HhccCCHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHH
Confidence 5 589988889999999888888766555555554444
No 94
>TIGR02263 benz_CoA_red_C benzoyl-CoA reductase, subunit C. This model describes C subunit of benzoyl-CoA reductase, a 4-subunit enzyme. Many aromatic compounds are metabolized by way of benzoyl-CoA. This enzyme acts under anaerobic conditions.
Probab=28.27 E-value=5.5e+02 Score=24.79 Aligned_cols=67 Identities=19% Similarity=0.156 Sum_probs=42.3
Q ss_pred hhhhhhHHHHhhhcccccccCCeeeeccCCCCCh-h-HHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHH
Q 024762 151 RRRVYDALNVLMAMDIISKDKKEIQWKGLPRTSL-N-DIEELKAERLGLRNRIEKK------TAYLQELEDQFVGLQNLI 222 (263)
Q Consensus 151 KRRVYDalNVL~ai~lI~K~Kk~I~W~G~~~~s~-~-~~~~Lk~E~~~l~erI~~K------k~~LqEL~~Q~~alknLI 222 (263)
+||+|+.+-.+.. .+-+.+..+|.+.. . ..+-+.+|+.++.+.|++. .+.|++-+..+...+.++
T Consensus 106 ~k~l~~~~~~~~~-------~~~~~~ldlP~~~~~~~~~~Y~~~el~~l~~~LE~~~G~~it~e~L~~aI~~~N~~R~~~ 178 (380)
T TIGR02263 106 IRNLSGMWKLMFP-------GKGARYFDLPHNFDDDLGGEFYTAELNELCEGLEHLSGKKITDDAIRASIAVFNDNRKLI 178 (380)
T ss_pred HHHHHHHHHHhCC-------CCcEEEEeCCCCCCcHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHH
Confidence 8999998765422 12345667776432 2 2666777777777777765 566666666666666555
Q ss_pred HH
Q 024762 223 QR 224 (263)
Q Consensus 223 ~R 224 (263)
++
T Consensus 179 ~~ 180 (380)
T TIGR02263 179 QA 180 (380)
T ss_pred HH
Confidence 54
No 95
>PF11853 DUF3373: Protein of unknown function (DUF3373); InterPro: IPR021803 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 472 to 574 amino acids in length.
Probab=27.98 E-value=56 Score=33.57 Aligned_cols=29 Identities=28% Similarity=0.357 Sum_probs=19.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024762 200 RIEKKTAYLQELEDQFVGLQNLIQRNERL 228 (263)
Q Consensus 200 rI~~Kk~~LqEL~~Q~~alknLI~RNk~~ 228 (263)
+|++.+++|++|.+|+..++.-|.+++..
T Consensus 32 kie~L~kql~~Lk~q~~~l~~~v~k~e~~ 60 (489)
T PF11853_consen 32 KIEALKKQLEELKAQQDDLNDRVDKVEKH 60 (489)
T ss_pred HHHHHHHHHHHHHHhhcccccccchhhHh
Confidence 56666667777777777766666666543
No 96
>PF13730 HTH_36: Helix-turn-helix domain
Probab=27.71 E-value=39 Score=23.02 Aligned_cols=19 Identities=32% Similarity=0.321 Sum_probs=16.8
Q ss_pred cchhhhhhHHHHhhhcccc
Q 024762 149 NIRRRVYDALNVLMAMDII 167 (263)
Q Consensus 149 niKRRVYDalNVL~ai~lI 167 (263)
.-+|.|+.+++.|+..|+|
T Consensus 37 ~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 37 VSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred cCHHHHHHHHHHHHHCcCC
Confidence 3489999999999999987
No 97
>COG3883 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.40 E-value=2.3e+02 Score=27.01 Aligned_cols=42 Identities=29% Similarity=0.531 Sum_probs=21.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHh
Q 024762 187 IEELKAERLGLRNRIEKKTAYLQELEDQFVGLQ-NLIQRNERL 228 (263)
Q Consensus 187 ~~~Lk~E~~~l~erI~~Kk~~LqEL~~Q~~alk-nLI~RNk~~ 228 (263)
++++..+...++++|.+-+..+.+|..+...++ ++.+||..+
T Consensus 61 i~~~~~k~~~~~~~i~~~~~eik~l~~eI~~~~~~I~~r~~~l 103 (265)
T COG3883 61 IEEIQSKIDELQKEIDQSKAEIKKLQKEIAELKENIVERQELL 103 (265)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334444444445555555555555555555555 444566433
No 98
>PRK10884 SH3 domain-containing protein; Provisional
Probab=27.25 E-value=2.7e+02 Score=25.17 Aligned_cols=33 Identities=24% Similarity=0.202 Sum_probs=13.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024762 190 LKAERLGLRNRIEKKTAYLQELEDQFVGLQNLI 222 (263)
Q Consensus 190 Lk~E~~~l~erI~~Kk~~LqEL~~Q~~alknLI 222 (263)
|++|..+|++++...+..+.+|..+...++.-+
T Consensus 137 L~~~n~~L~~~l~~~~~~~~~l~~~~~~~~~~~ 169 (206)
T PRK10884 137 LKEENQKLKNQLIVAQKKVDAANLQLDDKQRTI 169 (206)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444444444444444444444444444433333
No 99
>PF04156 IncA: IncA protein; InterPro: IPR007285 Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion. The inclusion is nonfusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA (Inclusion membrane protein A), is functionally associated with the homotypic fusion of inclusions [].
Probab=27.14 E-value=3e+02 Score=23.37 Aligned_cols=40 Identities=25% Similarity=0.376 Sum_probs=21.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024762 189 ELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQRNERL 228 (263)
Q Consensus 189 ~Lk~E~~~l~erI~~Kk~~LqEL~~Q~~alknLI~RNk~~ 228 (263)
+|..+..+.+++++.++.++.++......+.+.++.++.+
T Consensus 148 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~l 187 (191)
T PF04156_consen 148 ELQKELQDSREEVQELRSQLERLQENLQQLEEKIQELQEL 187 (191)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3333333444555566666666655555555555555443
No 100
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=27.13 E-value=4.4e+02 Score=23.33 Aligned_cols=61 Identities=11% Similarity=-0.001 Sum_probs=40.9
Q ss_pred cchhhHHHHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhccccccc----CCe
Q 024762 98 RGLRQFSMKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKD----KKE 173 (263)
Q Consensus 98 kGLR~fS~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~K~----Kk~ 173 (263)
-||..--..|...+...+.+|-.|+|+.+... +-.|--++.-|+.-|+|+|. .++
T Consensus 41 ~gLt~~q~~iL~~L~~~~~itq~eLa~~l~l~---------------------~sTvtr~l~rLE~kGlI~R~~~~~DrR 99 (185)
T PRK13777 41 YDLNINEHHILWIAYHLKGASISEIAKFGVMH---------------------VSTAFNFSKKLEERGYLTFSKKEDDKR 99 (185)
T ss_pred CCCCHHHHHHHHHHHhCCCcCHHHHHHHHCCC---------------------HhhHHHHHHHHHHCCCEEecCCCCCCC
Confidence 45665556677777777778888888865321 11244578899999999983 356
Q ss_pred eeeccC
Q 024762 174 IQWKGL 179 (263)
Q Consensus 174 I~W~G~ 179 (263)
..+.-+
T Consensus 100 ~~~I~L 105 (185)
T PRK13777 100 NTYIEL 105 (185)
T ss_pred eeEEEE
Confidence 666544
No 101
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=26.88 E-value=86 Score=21.77 Aligned_cols=42 Identities=21% Similarity=0.271 Sum_probs=30.4
Q ss_pred HHHHHH-hcCCCcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhcccccc
Q 024762 107 VCEKVE-SKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (263)
Q Consensus 107 VcekVk-~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~K 169 (263)
|...|. +.+..+..+||+.+- --+--|.++++-|+..|+|+|
T Consensus 8 vL~~l~~~~~~~t~~~l~~~~~---------------------~~~~~vs~~i~~L~~~glv~~ 50 (68)
T PF13463_consen 8 VLRALAHSDGPMTQSDLAERLG---------------------ISKSTVSRIIKKLEEKGLVEK 50 (68)
T ss_dssp HHHHHT--TS-BEHHHHHHHTT-----------------------HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHccCCCcCHHHHHHHHC---------------------cCHHHHHHHHHHHHHCCCEEe
Confidence 445555 788888888888753 235678899999999999987
No 102
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=26.71 E-value=1.6e+02 Score=19.98 Aligned_cols=51 Identities=18% Similarity=0.221 Sum_probs=37.5
Q ss_pred chhhHHHHHHHHHHhcCC--CcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhccccccc
Q 024762 99 GLRQFSMKVCEKVESKGR--TTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKD 170 (263)
Q Consensus 99 GLR~fS~KVcekVk~kg~--TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~K~ 170 (263)
||-.--..|.-.|...+. +|-.|||+.+- .-+-.|--+++-|+..|+|++.
T Consensus 2 glt~~q~~vL~~l~~~~~~~~t~~~la~~l~---------------------~~~~~vs~~v~~L~~~Glv~r~ 54 (62)
T PF12802_consen 2 GLTPSQFRVLMALARHPGEELTQSELAERLG---------------------ISKSTVSRIVKRLEKKGLVERE 54 (62)
T ss_dssp TSTHHHHHHHHHHHHSTTSGEEHHHHHHHHT---------------------S-HHHHHHHHHHHHHTTSEEEE
T ss_pred ccCHHHHHHHHHHHHCCCCCcCHHHHHHHHC---------------------cCHHHHHHHHHHHHHCCCEEEe
Confidence 344444566777777777 89999999874 2245677789999999999983
No 103
>PRK07720 fliJ flagellar biosynthesis chaperone; Validated
Probab=26.62 E-value=2.8e+02 Score=22.84 Aligned_cols=43 Identities=12% Similarity=0.246 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024762 186 DIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQRNERL 228 (263)
Q Consensus 186 ~~~~Lk~E~~~l~erI~~Kk~~LqEL~~Q~~alknLI~RNk~~ 228 (263)
.+...+..+..+...+++++..+.+-......|..|++|-...
T Consensus 79 ~i~~q~~~v~~~~~~ve~~r~~~~ea~~~~k~~ekLker~~~~ 121 (146)
T PRK07720 79 TIDHYQLLVMQAREQMNRKQQDLTEKNIEVKKYEKMKEKKQEM 121 (146)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455556666777788888899999888999999999876543
No 104
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=26.43 E-value=3.4e+02 Score=24.97 Aligned_cols=48 Identities=15% Similarity=0.205 Sum_probs=35.8
Q ss_pred HHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhcccccc-cCCe
Q 024762 105 MKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK-DKKE 173 (263)
Q Consensus 105 ~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~K-~Kk~ 173 (263)
.++.+.+++++..+..|+|+.|= ..+.++||- |..|+..|++.| .+.-
T Consensus 20 ~~Il~~L~~~~~vtv~eLa~~l~-----------------VS~~TIRRD----L~~Le~~G~l~r~~GGa 68 (269)
T PRK09802 20 EQIIQRLRQQGSVQVNDLSALYG-----------------VSTVTIRND----LAFLEKQGIAVRAYGGA 68 (269)
T ss_pred HHHHHHHHHcCCEeHHHHHHHHC-----------------CCHHHHHHH----HHHHHhCCCeEEEeCCE
Confidence 56789999999999999999871 123456553 567899999999 4443
No 105
>PRK10884 SH3 domain-containing protein; Provisional
Probab=26.18 E-value=2.7e+02 Score=25.20 Aligned_cols=6 Identities=33% Similarity=0.827 Sum_probs=3.3
Q ss_pred cccceE
Q 024762 239 VALPFI 244 (263)
Q Consensus 239 I~LPFI 244 (263)
|=||++
T Consensus 189 lilp~l 194 (206)
T PRK10884 189 LLLPHL 194 (206)
T ss_pred HHhccc
Confidence 455554
No 106
>PF05103 DivIVA: DivIVA protein; InterPro: IPR007793 The Bacillus subtilis divIVA1 mutation causes misplacement of the septum during cell division, resulting in the formation of small, circular, anucleate minicells []. Inactivation of divIVA produces a minicell phenotype, whereas overproduction of DivIVA results in a filamentation phenotype []. These proteins appear to contain coiled-coils.; PDB: 2WUK_C 2WUJ_A.
Probab=25.78 E-value=14 Score=29.43 Aligned_cols=47 Identities=28% Similarity=0.420 Sum_probs=18.7
Q ss_pred eeeccCCCCCh--------hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024762 174 IQWKGLPRTSL--------NDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQN 220 (263)
Q Consensus 174 I~W~G~~~~s~--------~~~~~Lk~E~~~l~erI~~Kk~~LqEL~~Q~~alkn 220 (263)
..|.|+++..+ .+++.|..+...|+.++...+..|.++......+++
T Consensus 13 ~~~rGYd~~eVD~fl~~l~~~~~~l~~e~~~L~~~~~~l~~~l~~~~~~~~~l~~ 67 (131)
T PF05103_consen 13 KSMRGYDPDEVDDFLDELAEELERLQRENAELKEEIEELQAQLEELREEEESLQR 67 (131)
T ss_dssp EEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCT-------------
T ss_pred CCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhHHHHHHH
Confidence 56788876543 234455555555555555444445454444444443
No 107
>PRK05771 V-type ATP synthase subunit I; Validated
Probab=25.74 E-value=1.1e+02 Score=31.65 Aligned_cols=18 Identities=17% Similarity=0.244 Sum_probs=11.7
Q ss_pred CCcHHHHHHHHHHHhcCC
Q 024762 116 RTTYNEVADELVAEFADP 133 (263)
Q Consensus 116 ~TTYnEVAdeLV~e~~~~ 133 (263)
-..+++..|+++..+.+.
T Consensus 11 l~~~~~~~~~~l~~L~~l 28 (646)
T PRK05771 11 IVTLKSYKDEVLEALHEL 28 (646)
T ss_pred EEEEHHHHHHHHHHHHhC
Confidence 445667777777776653
No 108
>KOG1962 consensus B-cell receptor-associated protein and related proteins [Defense mechanisms]
Probab=25.54 E-value=1.8e+02 Score=26.96 Aligned_cols=39 Identities=23% Similarity=0.312 Sum_probs=24.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024762 186 DIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQR 224 (263)
Q Consensus 186 ~~~~Lk~E~~~l~erI~~Kk~~LqEL~~Q~~alknLI~R 224 (263)
+...++++..+++++++.+...|..+..+..+++.-.+.
T Consensus 152 ~~~~~~~~~~kL~~el~~~~~~Le~~~~~~~al~Kq~e~ 190 (216)
T KOG1962|consen 152 ENDKLKADLEKLETELEKKQKKLEKAQKKVDALKKQSEG 190 (216)
T ss_pred hHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345566666777777777777776666666655544443
No 109
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=25.41 E-value=3e+02 Score=24.70 Aligned_cols=44 Identities=20% Similarity=0.246 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 024762 186 DIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQRNERLY 229 (263)
Q Consensus 186 ~~~~Lk~E~~~l~erI~~Kk~~LqEL~~Q~~alknLI~RNk~~~ 229 (263)
++.+|+.+...|...++..+....-....+..|.+++.|++.+.
T Consensus 112 e~~kl~~~~e~L~~e~~~L~~~~~~~~eDy~~Li~Im~rark~~ 155 (170)
T PRK13923 112 QIGKLQEEEEKLSWENQTLKQELAITEEDYRALIVIMNRARRMA 155 (170)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence 34444545445544444444444455667778888898998763
No 110
>PF04568 IATP: Mitochondrial ATPase inhibitor, IATP; InterPro: IPR007648 ATP synthase inhibitor prevents the enzyme from switching to ATP hydrolysis during collapse of the electrochemical gradient, for example during oxygen deprivation [] ATP synthase inhibitor forms a one to one complex with the F1 ATPase, possibly by binding at the alpha-beta interface. It is thought to inhibit ATP synthesis by preventing the release of ATP []. The minimum inhibitory region for bovine inhibitor (P01096 from SWISSPROT) is from residues 39 to 72 []. The inhibitor has two oligomeric states, dimer (the active state) and tetramer. At low pH , the inhibitor forms a dimer via antiparallel coiled coil interactions between the C-terminal regions of two monomers. At high pH, the inhibitor forms tetramers and higher oligomers by coiled coil interactions involving the N terminus and inhibitory region, thus preventing the inhibitory activity []. ; GO: 0004857 enzyme inhibitor activity, 0045980 negative regulation of nucleotide metabolic process, 0005739 mitochondrion; PDB: 1GMJ_B 1OHH_H 1HF9_B 2V7Q_J.
Probab=25.13 E-value=2.1e+02 Score=23.48 Aligned_cols=10 Identities=30% Similarity=0.425 Sum_probs=4.3
Q ss_pred HHHHHHHHHH
Q 024762 204 KTAYLQELED 213 (263)
Q Consensus 204 Kk~~LqEL~~ 213 (263)
.+++|++|+.
T Consensus 88 ~~k~i~~le~ 97 (100)
T PF04568_consen 88 HRKEIDELEK 97 (100)
T ss_dssp HHHHHHHHHH
T ss_pred HHHHHHHHHH
Confidence 4444444443
No 111
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=25.09 E-value=5e+02 Score=23.20 Aligned_cols=45 Identities=9% Similarity=0.288 Sum_probs=35.6
Q ss_pred HHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhccccccc
Q 024762 105 MKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKD 170 (263)
Q Consensus 105 ~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~K~ 170 (263)
+.|.+.+-+.+..|..|+|++|= --|=.+|-+|+-|+..|+++++
T Consensus 17 l~IL~~l~~~~~l~l~eia~~lg---------------------l~kstv~Rll~tL~~~G~l~~~ 61 (257)
T PRK15090 17 FGILQALGEEREIGITELSQRVM---------------------MSKSTVYRFLQTMKTLGYVAQE 61 (257)
T ss_pred HHHHHHhhcCCCCCHHHHHHHHC---------------------cCHHHHHHHHHHHHHCCCEEEc
Confidence 45777776667788999888862 2356799999999999999993
No 112
>PHA02047 phage lambda Rz1-like protein
Probab=25.02 E-value=1.5e+02 Score=24.66 Aligned_cols=52 Identities=13% Similarity=0.148 Sum_probs=31.6
Q ss_pred eeeeccCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHH
Q 024762 173 EIQWKGLPRTSLNDIEELKAERLGLRNRIEKKTAYLQELEDQFV----GLQNLIQRNER 227 (263)
Q Consensus 173 ~I~W~G~~~~s~~~~~~Lk~E~~~l~erI~~Kk~~LqEL~~Q~~----alknLI~RNk~ 227 (263)
.++|-|. ...+.+.|..+++.++.+|..-+++.++|..+.. .+++-++.|+.
T Consensus 25 ~~r~~g~---~h~~a~~la~qLE~a~~r~~~~Q~~V~~l~~kae~~t~Ei~~aL~~n~~ 80 (101)
T PHA02047 25 SYRALGI---AHEEAKRQTARLEALEVRYATLQRHVQAVEARTNTQRQEVDRALDQNRP 80 (101)
T ss_pred HHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC
Confidence 4667764 3345667777777777777777777777665432 34444444443
No 113
>PF08664 YcbB: YcbB domain; InterPro: IPR013972 YcbB is a DNA-binding protein [].
Probab=24.88 E-value=73 Score=27.32 Aligned_cols=61 Identities=20% Similarity=0.313 Sum_probs=35.5
Q ss_pred HHHHHHHhcCCC------cHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhccccc
Q 024762 106 KVCEKVESKGRT------TYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIIS 168 (263)
Q Consensus 106 KVcekVk~kg~T------TYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~ 168 (263)
++|+-+.++... +.+++..++.......... -..+...-++-|||-|+-+|+-|-.+||..
T Consensus 23 ~Ii~~l~~~~~~~~~~~~~Lk~~f~~~~~~~~~~~~~--~~~e~Ka~EQRIRRai~~al~nlAsLGl~D 89 (134)
T PF08664_consen 23 KIIEYLIEQEKSFSQNFPSLKEIFEELAQKKLASDEE--IEKEKKAIEQRIRRAIKQALTNLASLGLED 89 (134)
T ss_pred HHHHHHHHhccccCcCCCcHHHHHHHHHHhhccchhh--hhHHHHHHHHHHHHHHHHHHHHHHHhCCcc
Confidence 445555554433 3366666665443111100 011234456789999999999999998754
No 114
>smart00787 Spc7 Spc7 kinetochore protein. This domain is found in cell division proteins which are required for kinetochore-spindle association.
Probab=24.67 E-value=2.8e+02 Score=26.64 Aligned_cols=35 Identities=29% Similarity=0.315 Sum_probs=14.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024762 189 ELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQ 223 (263)
Q Consensus 189 ~Lk~E~~~l~erI~~Kk~~LqEL~~Q~~alknLI~ 223 (263)
.+++++..+...|..++..+.++..|...+..-|+
T Consensus 208 ~lk~~l~~~~~ei~~~~~~l~e~~~~l~~l~~~I~ 242 (312)
T smart00787 208 RAKEKLKKLLQEIMIKVKKLEELEEELQELESKIE 242 (312)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33333333334444444444444444444443333
No 115
>PF07571 DUF1546: Protein of unknown function (DUF1546); InterPro: IPR011442 These proteins are associated with IPR004823 from INTERPRO in transcription initiation factor TFIID subunit 6 (TAF6).; GO: 0051090 regulation of sequence-specific DNA binding transcription factor activity, 0005634 nucleus
Probab=24.44 E-value=1.2e+02 Score=23.76 Aligned_cols=61 Identities=18% Similarity=0.225 Sum_probs=42.6
Q ss_pred cCCcchhhHHHHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhcc
Q 024762 95 KSGRGLRQFSMKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMD 165 (263)
Q Consensus 95 k~~kGLR~fS~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~ 165 (263)
.+.|.||.||.++...|-.+-..+|+.+--+|+..|...-. |.+.---..|=|+-=|.++|
T Consensus 17 ~~h~~LRd~AA~lL~~I~~~~~~~~~~L~~Ri~~tl~k~l~----------d~~~~~~t~YGAi~gL~~lG 77 (92)
T PF07571_consen 17 DNHWALRDFAASLLAQICRKFSSSYPTLQPRITRTLLKALL----------DPKKPLGTHYGAIVGLSALG 77 (92)
T ss_pred cchHHHHHHHHHHHHHHHHHhccccchHHHHHHHHHHHHHc----------CCCCCHHHHHHHHHHHHHHH
Confidence 56799999999999988888888888777777766654321 12223345677776666654
No 116
>TIGR02147 Fsuc_second hypothetical protein, TIGR02147. This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.
Probab=24.40 E-value=6e+02 Score=23.90 Aligned_cols=60 Identities=13% Similarity=0.166 Sum_probs=37.6
Q ss_pred cchhhHHHHHHHHHHhc-----CCCcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhcccccccCC
Q 024762 98 RGLRQFSMKVCEKVESK-----GRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKDKK 172 (263)
Q Consensus 98 kGLR~fS~KVcekVk~k-----g~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~K~Kk 172 (263)
.-+.+|+.=.+-.|++- +..+..++|+.|.-. .-=..|=|+|..|+.+|+|+|+.+
T Consensus 114 ~~~~y~~~W~~~virel~~~~~~~~~~~~ia~~l~p~-------------------is~~ev~~sL~~L~~~glikk~~~ 174 (271)
T TIGR02147 114 DQFEYYRHWYNSVIRELLGVMPFADDPEELAKRCFPK-------------------ISAEQVKESLDLLERLGLIKKNED 174 (271)
T ss_pred HHHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHhCCC-------------------CCHHHHHHHHHHHHHCCCeeECCC
Confidence 45777777666655552 233566666665311 111456699999999999999654
Q ss_pred eeeec
Q 024762 173 EIQWK 177 (263)
Q Consensus 173 ~I~W~ 177 (263)
. .|.
T Consensus 175 g-~y~ 178 (271)
T TIGR02147 175 G-FYK 178 (271)
T ss_pred C-cEE
Confidence 3 554
No 117
>TIGR02473 flagell_FliJ flagellar export protein FliJ. Members of this family are the FliJ protein found, in nearly every case, in the midst of other flagellar biosynthesis genes in bacgterial genomes. Typically the fliJ gene is found adjacent to the gene for the flagellum-specific ATPase FliI. Sequence scoring in the gray zone between trusted and noise cutoffs include both probable FliJ proteins and components of bacterial type III secretion systems.
Probab=24.22 E-value=3.4e+02 Score=21.57 Aligned_cols=43 Identities=21% Similarity=0.333 Sum_probs=31.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024762 185 NDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQRNER 227 (263)
Q Consensus 185 ~~~~~Lk~E~~~l~erI~~Kk~~LqEL~~Q~~alknLI~RNk~ 227 (263)
..+...+.++..+...++..+..|.+-......+..|.+|-..
T Consensus 75 ~~i~~q~~~l~~~~~~~e~~r~~l~~a~~~~k~lekL~ek~~~ 117 (141)
T TIGR02473 75 QRIQQQQQELALLQQEVEAKRERLLEARRELKALEKLKEKKQK 117 (141)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455566666777777888888888888888888888886543
No 118
>KOG3478 consensus Prefoldin subunit 6, KE2 family [Posttranslational modification, protein turnover, chaperones]
Probab=24.21 E-value=1.6e+02 Score=25.12 Aligned_cols=23 Identities=22% Similarity=0.302 Sum_probs=19.5
Q ss_pred HHHHhhhcccccccCCeeeeccC
Q 024762 157 ALNVLMAMDIISKDKKEIQWKGL 179 (263)
Q Consensus 157 alNVL~ai~lI~K~Kk~I~W~G~ 179 (263)
=.+||+.+++++-+-|-|+-.|-
T Consensus 38 nk~V~~Eldlle~d~~VYKliGp 60 (120)
T KOG3478|consen 38 NKIVLEELDLLEEDSNVYKLIGP 60 (120)
T ss_pred hHHHHHHHHHhcccchHHHHhcc
Confidence 35799999999999999998873
No 119
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=24.20 E-value=3.9e+02 Score=24.24 Aligned_cols=44 Identities=23% Similarity=0.215 Sum_probs=34.0
Q ss_pred HHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhcccccc
Q 024762 105 MKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (263)
Q Consensus 105 ~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~K 169 (263)
.++.+.+++++..+-+|+|+.|= ..+..+||. |+.|+..|+|.|
T Consensus 8 ~~Il~~l~~~~~~~~~ela~~l~-----------------vS~~TirRd----L~~Le~~g~i~r 51 (251)
T PRK13509 8 QILLELLAQLGFVTVEKVIERLG-----------------ISPATARRD----INKLDESGKLKK 51 (251)
T ss_pred HHHHHHHHHcCCcCHHHHHHHHC-----------------cCHHHHHHH----HHHHHHCCCEEE
Confidence 35789999999999999999861 012355554 778999999998
No 120
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=24.13 E-value=2.3e+02 Score=25.25 Aligned_cols=26 Identities=31% Similarity=0.334 Sum_probs=13.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024762 189 ELKAERLGLRNRIEKKTAYLQELEDQ 214 (263)
Q Consensus 189 ~Lk~E~~~l~erI~~Kk~~LqEL~~Q 214 (263)
.++.|...+++.+.+.+.++.+|...
T Consensus 101 ~~~~e~~~l~~e~~~l~~~~e~Le~e 126 (161)
T TIGR02894 101 ALQKENERLKNQNESLQKRNEELEKE 126 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34445555555555555555555443
No 121
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=23.99 E-value=1.6e+02 Score=26.08 Aligned_cols=50 Identities=20% Similarity=0.224 Sum_probs=38.1
Q ss_pred HHHHHHHHh-cCCCcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhcccccccCCeee
Q 024762 105 MKVCEKVES-KGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKDKKEIQ 175 (263)
Q Consensus 105 ~KVcekVk~-kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~K~Kk~I~ 175 (263)
..|.+.+-+ ....|..|||+++= --|=.+|.+|+-|+..|+++++.+.|.
T Consensus 12 l~IL~~l~~~~~~~~l~eia~~lg---------------------lpksT~~RlL~tL~~~G~l~~~~~~Y~ 62 (248)
T TIGR02431 12 LAVIEAFGAERPRLTLTDVAEATG---------------------LTRAAARRFLLTLVELGYVTSDGRLFW 62 (248)
T ss_pred HHHHHHHhcCCCCCCHHHHHHHHC---------------------cCHHHHHHHHHHHHHCCCEEeCCCEEE
Confidence 446666654 56789999998862 235789999999999999999766554
No 122
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=23.94 E-value=2.4e+02 Score=25.67 Aligned_cols=20 Identities=15% Similarity=0.268 Sum_probs=9.3
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 024762 186 DIEELKAERLGLRNRIEKKT 205 (263)
Q Consensus 186 ~~~~Lk~E~~~l~erI~~Kk 205 (263)
...+|++|-.+|++++.+.+
T Consensus 70 ~~~~l~~en~~L~~e~~~l~ 89 (276)
T PRK13922 70 SLFDLREENEELKKELLELE 89 (276)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 34455555555544443333
No 123
>PRK07737 fliD flagellar capping protein; Validated
Probab=23.81 E-value=2.3e+02 Score=28.78 Aligned_cols=75 Identities=20% Similarity=0.301 Sum_probs=43.9
Q ss_pred cccccchhhhhhHHHHhhhcccccccCCeeeeccCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024762 145 YDEKNIRRRVYDALNVLMAMDIISKDKKEIQWKGLPRTSLNDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQR 224 (263)
Q Consensus 145 ~deKniKRRVYDalNVL~ai~lI~K~Kk~I~W~G~~~~s~~~~~~Lk~E~~~l~erI~~Kk~~LqEL~~Q~~alknLI~R 224 (263)
+.+.-+=.|++|++.=+.+. +..+....+.+. .......++..+..+...+++||+++++.| ..|+.++..+|.+
T Consensus 410 ~~~~Gia~~l~~~l~~~~~~-~~~~~g~g~~~~-~~~~l~~~i~~l~~~i~~~~~rl~~~e~ry---~~qf~ale~~~s~ 484 (501)
T PRK07737 410 YNEKGIARRLRDTLKETIKS-IEQKAGNTTMTN-QQFAIGKDLNQIETQIDRFQDRLKQIEDRY---YKKFSAMEKAIQK 484 (501)
T ss_pred cccCcHHHHHHHHHHHHHhh-hhhhcCCccccc-hhHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHH
Confidence 34567888999998887653 222222221111 001122456677777777777777665544 6677777777764
No 124
>PRK05689 fliJ flagellar biosynthesis chaperone; Validated
Probab=23.78 E-value=3.3e+02 Score=22.26 Aligned_cols=44 Identities=16% Similarity=0.303 Sum_probs=32.8
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024762 185 NDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQRNERL 228 (263)
Q Consensus 185 ~~~~~Lk~E~~~l~erI~~Kk~~LqEL~~Q~~alknLI~RNk~~ 228 (263)
..+...+..+..+...+++.+..+.+-......|..|++|-...
T Consensus 78 ~~I~~q~~~v~~~~~~ve~~r~~~~~a~~~~k~lEkL~ek~~~~ 121 (147)
T PRK05689 78 KAITQQRQQLTQWTQKVDNARKYWQEKKQRLEALETLQERYQTE 121 (147)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34555566667777788888888888888888999998876543
No 125
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=23.69 E-value=1.7e+02 Score=26.38 Aligned_cols=51 Identities=14% Similarity=0.111 Sum_probs=38.2
Q ss_pred HHHHHHHHHhcC-CCcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhccccccc--CCeee
Q 024762 104 SMKVCEKVESKG-RTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKD--KKEIQ 175 (263)
Q Consensus 104 S~KVcekVk~kg-~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~K~--Kk~I~ 175 (263)
++.|.+.+-..+ ..|-.|||++|= .-|--+|.+|+-|+..|+|+++ .+.|.
T Consensus 13 al~iL~~l~~~~~~ls~~eia~~lg---------------------l~kstv~RlL~tL~~~g~v~~~~~~~~Y~ 66 (263)
T PRK09834 13 GLMVLRALNRLDGGATVGLLAELTG---------------------LHRTTVRRLLETLQEEGYVRRSASDDSFR 66 (263)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHHC---------------------cCHHHHHHHHHHHHHCCCEEEecCCCcEE
Confidence 455677775544 489999999871 2356799999999999999983 55555
No 126
>TIGR03859 PQQ_PqqD coenzyme PQQ biosynthesis protein PqqD. This model identifies PqqD, a protein involved in the final steps of the biosynthesis of pyrroloquinoline quinone, coenzyme PQQ.
Probab=23.56 E-value=1.6e+02 Score=22.46 Aligned_cols=55 Identities=20% Similarity=0.266 Sum_probs=41.9
Q ss_pred cchhhHHHHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhccccc
Q 024762 98 RGLRQFSMKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIIS 168 (263)
Q Consensus 98 kGLR~fS~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~ 168 (263)
-+|--....|++.+.. ..|-.||++.|..+|.. . +.+..+|-.-|+-|..-|+|.
T Consensus 27 ~~Ln~~g~~Iw~lldg--~~tv~eI~~~L~~~Y~~-~-------------e~~~~dV~~fL~~L~~~gli~ 81 (81)
T TIGR03859 27 VKLNDSAGEILELCDG--KRSLAEIIQELAQRFPA-A-------------EEIEDDVIAFLAVARAKHWLE 81 (81)
T ss_pred eeeChHHHHHHHHccC--CCcHHHHHHHHHHHcCC-h-------------hhHHHHHHHHHHHHHHCcCcC
Confidence 5677788889998854 55899999999999765 2 255677777778777778774
No 127
>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=23.39 E-value=4.9e+02 Score=23.05 Aligned_cols=50 Identities=28% Similarity=0.488 Sum_probs=25.8
Q ss_pred hhhHHHHhhhcccccccC---CeeeeccCCCCC----hhHHHHHHHHHHHHHHHHHHH
Q 024762 154 VYDALNVLMAMDIISKDK---KEIQWKGLPRTS----LNDIEELKAERLGLRNRIEKK 204 (263)
Q Consensus 154 VYDalNVL~ai~lI~K~K---k~I~W~G~~~~s----~~~~~~Lk~E~~~l~erI~~K 204 (263)
|=|+|--|..=|+|.-+| -.+.|. +|... ...++.|++++..++++|...
T Consensus 32 VKdvlq~LvDDglV~~EKiGssn~YWs-Fps~~~~~~~~~~~~l~~~~~~~~~~i~~l 88 (188)
T PF03962_consen 32 VKDVLQSLVDDGLVHVEKIGSSNYYWS-FPSQAKQKRQNKLEKLQKEIEELEKKIEEL 88 (188)
T ss_pred HHHHHHHHhccccchhhhccCeeEEEe-cChHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445566666667776543 577886 44321 233444555544444444333
No 128
>PF13094 CENP-Q: CENP-Q, a CENPA-CAD centromere complex subunit
Probab=23.11 E-value=3.3e+02 Score=22.91 Aligned_cols=41 Identities=27% Similarity=0.327 Sum_probs=29.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024762 185 NDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQRN 225 (263)
Q Consensus 185 ~~~~~Lk~E~~~l~erI~~Kk~~LqEL~~Q~~alknLI~RN 225 (263)
..++.|++|+.+....++.-.++|++|.........-+++-
T Consensus 41 ~~l~lLq~e~~~~e~~le~d~~~L~~Le~~~~~~~~e~~~~ 81 (160)
T PF13094_consen 41 HQLELLQEEIEKEEAALERDYEYLQELEKNAKALEREREEE 81 (160)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34567888888777777888888888887776666555533
No 129
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=22.80 E-value=4.7e+02 Score=22.11 Aligned_cols=87 Identities=24% Similarity=0.318 Sum_probs=43.8
Q ss_pred HHHHHHh-cCCCcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhcc-cccc-cCC-eeeec---cC
Q 024762 107 VCEKVES-KGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMD-IISK-DKK-EIQWK---GL 179 (263)
Q Consensus 107 VcekVk~-kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~-lI~K-~Kk-~I~W~---G~ 179 (263)
|.+-+++ ++--|.++|.+.|=..|.. =-|==+|.-|..-| |+.| -+| .|.|. .+
T Consensus 6 Il~y~~~qNRPys~~di~~nL~~~~~K-------------------~~v~k~Ld~L~~~g~i~~K~~GKqkiY~~~Q~~~ 66 (169)
T PF07106_consen 6 ILEYMKEQNRPYSAQDIFDNLHNKVGK-------------------TAVQKALDSLVEEGKIVEKEYGKQKIYFANQDEL 66 (169)
T ss_pred HHHHHHHcCCCCcHHHHHHHHHhhccH-------------------HHHHHHHHHHHhCCCeeeeeecceEEEeeCcccc
Confidence 4444444 6677888888887654433 22233455555544 5566 444 44442 33
Q ss_pred CCCChh-------HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024762 180 PRTSLN-------DIEELKAERLGLRNRIEKKTAYLQELE 212 (263)
Q Consensus 180 ~~~s~~-------~~~~Lk~E~~~l~erI~~Kk~~LqEL~ 212 (263)
+..+.. ++..|++|+..+...++..+..|..|.
T Consensus 67 ~~~s~eel~~ld~ei~~L~~el~~l~~~~k~l~~eL~~L~ 106 (169)
T PF07106_consen 67 EVPSPEELAELDAEIKELREELAELKKEVKSLEAELASLS 106 (169)
T ss_pred CCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 322222 344555555555555555555554443
No 130
>PF09457 RBD-FIP: FIP domain ; InterPro: IPR019018 The Rab11 GTPase regulates recycling of internalized plasma membrane receptors and is essential for completion of cytokinesis. A family of Rab11 interacting proteins (FIPs) that conserve a C-terminal Rab-binding domain (RBD) selectively recognise the active form of Rab11. FIPs are diverse in sequence length and composition toward their N-termini, presumably a feature that underpins their specific roles in Rab11-mediated vesicle trafficking. They have been divided into three subfamilies (classe I, II, and III)on the basis of domain architecture. Class I FIPs comprises a subfamily of three proteins (Rip11/pp75/FIP5, Rab-coupling protein (RCP), and FIP2) that possess an N- terminal C2 domain, localize to recycling endosomes, and regulate plasma membrane recycling. The class II subfamily consists of two proteins (FIP3/eferin/arfophilin and FIP4) with tandem EF hands and a proline-rich region. Class II FIPs localize to recycling endosomes, the trans-Golgi network, and have been implicated in the regulation of membrane trafficking during cytokinesis. The class III subfamily consists of a single protein, FIP1, which does not contain obvious homology domains or motifs other than the FIP-RBD [, , , ]. The FIP-RBD domain is also found in Rab6-interacting protein Erc1/Elks. Erc1 is the regulatory subunit of the IKK complex and probably recruits IkappaBalpha/NFKBIA to the complex []. It may be involved in the organisation of the cytomatrix at the nerve terminals active zone (CAZ) which regulates neurotransmitter release. It may also be involved in vesicle trafficking at the CAZ, as well as in Rab-6 regulated endosomes to Golgi transport []. The FIB-RBD domain consists of an N-terminal long alpha-helix, followed by a 90 degrees bend at a conserved proline residue, a 3(10) helix and a C-terminal short beta-strand, adopting an "L" shape. The long alpha-helix forms a parallel coiled-coil homodimer that symmetrically interacts with two Rab11 molecules on both sides, forming a quaternary Rab11-(FIP)2-Rab11 complex. The Rab11-interacting region of FIP-RBD is confined to the C-terminal 24 amino acids, which cover the C-terminal half of the long alpha-helix and the short beta-strand [, , , ]. This entry represents the FIP-RBD domain.; PDB: 2HV8_E 2D7C_D 2K6S_B 2GZD_D 2GZH_B.
Probab=22.77 E-value=3e+02 Score=19.80 Aligned_cols=25 Identities=28% Similarity=0.270 Sum_probs=13.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 024762 189 ELKAERLGLRNRIEKKTAYLQELED 213 (263)
Q Consensus 189 ~Lk~E~~~l~erI~~Kk~~LqEL~~ 213 (263)
+|..++.++++.+.+|..+++||..
T Consensus 4 eL~~~l~~~e~~~~~k~~~v~eLe~ 28 (48)
T PF09457_consen 4 ELISLLKKQEEENARKDSRVRELED 28 (48)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4445555555555555555555553
No 131
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=22.61 E-value=96 Score=25.01 Aligned_cols=55 Identities=16% Similarity=0.283 Sum_probs=39.2
Q ss_pred hhhHHHHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhcccccccCCeee
Q 024762 100 LRQFSMKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKDKKEIQ 175 (263)
Q Consensus 100 LR~fS~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~K~Kk~I~ 175 (263)
|--+=.++.+.++..++++|.|+|++|= . ....+++| +.-|+.-|+|.+-.-.+.
T Consensus 6 lD~~D~~IL~~L~~d~r~~~~eia~~lg---------l--------S~~~v~~R----i~~L~~~GiI~~~~~~v~ 60 (154)
T COG1522 6 LDDIDRRILRLLQEDARISNAELAERVG---------L--------SPSTVLRR----IKRLEEEGVIKGYTAVLD 60 (154)
T ss_pred ccHHHHHHHHHHHHhCCCCHHHHHHHHC---------C--------CHHHHHHH----HHHHHHCCceeeEEEEEC
Confidence 4455678999999999999999999972 0 12244555 456899999988443333
No 132
>PF10234 Cluap1: Clusterin-associated protein-1; InterPro: IPR019366 This protein of 413 amino acids contains a central coiled-coil domain, possibly the region that binds to clusterin. Cluap1 expression is highest in the nucleus and gradually increases during late S to G2/M phases of the cell cycle and returns to the basal level in the G0/G1 phases. In addition, it is upregulated in colon cancer tissues compared to corresponding non-cancerous mucosa. It thus plays a crucial role in the life of the cell [].
Probab=22.58 E-value=2e+02 Score=27.30 Aligned_cols=20 Identities=30% Similarity=0.539 Sum_probs=9.2
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 024762 187 IEELKAERLGLRNRIEKKTA 206 (263)
Q Consensus 187 ~~~Lk~E~~~l~erI~~Kk~ 206 (263)
+..|..+...|..+|++|+.
T Consensus 185 l~~l~~de~~Le~KIekkk~ 204 (267)
T PF10234_consen 185 LNNLASDEANLEAKIEKKKQ 204 (267)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 33444444444445544443
No 133
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=22.43 E-value=2.8e+02 Score=24.55 Aligned_cols=35 Identities=29% Similarity=0.383 Sum_probs=19.8
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024762 185 NDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQ 219 (263)
Q Consensus 185 ~~~~~Lk~E~~~l~erI~~Kk~~LqEL~~Q~~alk 219 (263)
..++-|++.+..+.++|.+.++.|..+....+.++
T Consensus 85 ~R~~lLe~~~~~l~~ri~eLe~~l~~kad~vvsYq 119 (175)
T PRK13182 85 VDFEQLEAQLNTITRRLDELERQLQQKADDVVSYQ 119 (175)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHH
Confidence 44556666666666666666655554444444443
No 134
>PRK03992 proteasome-activating nucleotidase; Provisional
Probab=22.15 E-value=7e+02 Score=24.09 Aligned_cols=72 Identities=17% Similarity=0.131 Sum_probs=35.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc-CCCCCCC------ccccceEEEEcCCCceEEeEee
Q 024762 188 EELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQRNERLYS-SGNAPSG------GVALPFILVQVDIRQLFSCIMA 259 (263)
Q Consensus 188 ~~Lk~E~~~l~erI~~Kk~~LqEL~~Q~~alknLI~RNk~~~~-~~~~ps~------~I~LPFIlV~T~~~tvI~C~is 259 (263)
..|.+....++.++++.+..+++|..+...++..+++-+..-. -..+|.. .+.=..++|.++....+-..+.
T Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~v~~~~g~~~~~~~~ 82 (389)
T PRK03992 4 EALEERNSELEEQIRQLELKLRDLEAENEKLERELERLKSELEKLKSPPLIVATVLEVLDDGRVVVKSSGGPQFLVNVS 82 (389)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceEEEEEEEeCCCeEEEEECCCCEEEEecc
Confidence 3455555555556666666666666666666554443322111 1112221 2333446777766555444433
No 135
>PF04977 DivIC: Septum formation initiator; InterPro: IPR007060 DivIC, from the spore-forming, Gram-positive bacterium Bacillus subtilis, is necessary for both vegetative and sporulation septum formation []. These proteins are mainly composed of an N-terminal coiled-coil. DivIB, DivIC and FtsL inter-depend on each other for stabilisation and localisation. The latter two form a heterodimer. DivIC is always centre cell but the other two associate with it during septation [].; GO: 0007049 cell cycle
Probab=22.11 E-value=3e+02 Score=19.74 Aligned_cols=38 Identities=18% Similarity=0.225 Sum_probs=24.9
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024762 184 LNDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNL 221 (263)
Q Consensus 184 ~~~~~~Lk~E~~~l~erI~~Kk~~LqEL~~Q~~alknL 221 (263)
..++..|+.+...++++.++.+++++.|...-..+..+
T Consensus 23 ~~ei~~l~~~i~~l~~e~~~L~~ei~~l~~~~~~ie~~ 60 (80)
T PF04977_consen 23 NQEIAELQKEIEELKKENEELKEEIERLKNDPDYIEKV 60 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHH
Confidence 35677888888888777777777777773333333333
No 136
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=22.11 E-value=1e+02 Score=27.24 Aligned_cols=53 Identities=21% Similarity=0.270 Sum_probs=37.2
Q ss_pred CcHHHHHHHHHHHhcC---CCCCCCCCCccccccccchhhhhhHHHHhhhcccccc
Q 024762 117 TTYNEVADELVAEFAD---PSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (263)
Q Consensus 117 TTYnEVAdeLV~e~~~---~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~K 169 (263)
.-|.+|++.|...+.. +...+.+..+-+-...+-|=-|-.||+.|+.-|+|.+
T Consensus 12 p~Y~qi~~~L~~~I~~~~~~G~~LPsE~eLa~~~~VSR~TVR~Al~~L~~eGli~r 67 (241)
T PRK10079 12 TRYQEIAAKLEQELRQHYRCGDYLPAEQQLAARYEVNRHTLRRAIDQLVEKGWVQR 67 (241)
T ss_pred CHHHHHHHHHHHHHhcccCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 3499999999887753 1122222223344455778889999999999999999
No 137
>PF04156 IncA: IncA protein; InterPro: IPR007285 Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion. The inclusion is nonfusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA (Inclusion membrane protein A), is functionally associated with the homotypic fusion of inclusions [].
Probab=21.98 E-value=3.4e+02 Score=23.06 Aligned_cols=16 Identities=13% Similarity=0.285 Sum_probs=10.5
Q ss_pred cchhhhhhHHHHhhhc
Q 024762 149 NIRRRVYDALNVLMAM 164 (263)
Q Consensus 149 niKRRVYDalNVL~ai 164 (263)
...+++++...-|+.+
T Consensus 99 ~l~~~~~~~~~~l~~~ 114 (191)
T PF04156_consen 99 QLQERIQELESELEKL 114 (191)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3567777777766655
No 138
>TIGR02338 gimC_beta prefoldin, beta subunit, archaeal. Chaperonins are cytosolic, ATP-dependent molecular chaperones, with a conserved toroidal architecture, that assist in the folding of nascent and/or denatured polypeptide chains. The group I chaperonin system consists of GroEL and GroES, and is found (usually) in bacteria and organelles of bacterial origin. The group II chaperonin system, called the thermosome in Archaea and TRiC or CCT in the Eukaryota, is structurally similar but only distantly related. Prefoldin, also called GimC, is a complex in Archaea and Eukaryota, that works with group II chaperonins. Members of this protein family are the archaeal clade of the beta class of prefoldin subunit. Closely related, but outside the scope of this family are the eukaryotic beta-class prefoldin subunits, Gim-1,3,4 and 6. The alpha class prefoldin subunits are more distantly related.
Probab=21.98 E-value=3.5e+02 Score=21.58 Aligned_cols=59 Identities=20% Similarity=0.232 Sum_probs=25.3
Q ss_pred hHHHHhhhcccccccCCeeeeccCC---CCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024762 156 DALNVLMAMDIISKDKKEIQWKGLP---RTSLNDIEELKAERLGLRNRIEKKTAYLQELEDQ 214 (263)
Q Consensus 156 DalNVL~ai~lI~K~Kk~I~W~G~~---~~s~~~~~~Lk~E~~~l~erI~~Kk~~LqEL~~Q 214 (263)
..-.|+..+.-+.-+.+-|+-.|-- .+...-...|+.....+..+|+...+.+..|..+
T Consensus 35 E~~~v~~eL~~l~~d~~vyk~VG~vlv~~~~~e~~~~l~~r~e~ie~~i~~lek~~~~l~~~ 96 (110)
T TIGR02338 35 EAEKALEELERLPDDTPVYKSVGNLLVKTDKEEAIQELKEKKETLELRVKTLQRQEERLREQ 96 (110)
T ss_pred HHHHHHHHHHcCCCcchhHHHhchhhheecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455555555555555555544421 1111122344444444444444444444433333
No 139
>PF14282 FlxA: FlxA-like protein
Probab=21.81 E-value=2.8e+02 Score=22.30 Aligned_cols=18 Identities=33% Similarity=0.344 Sum_probs=9.2
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 024762 203 KKTAYLQELEDQFVGLQN 220 (263)
Q Consensus 203 ~Kk~~LqEL~~Q~~alkn 220 (263)
.|+.+.+.|..|...|+.
T Consensus 48 ~k~~q~q~Lq~QI~~Lqa 65 (106)
T PF14282_consen 48 QKQQQIQLLQAQIQQLQA 65 (106)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 444555555555555553
No 140
>cd00632 Prefoldin_beta Prefoldin beta; Prefoldin is a hexameric molecular chaperone complex, composed of two evolutionarily related subunits (alpha and beta), which are found in both eukaryotes and archaea. Prefoldin binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The hexameric structure consists of a double beta barrel assembly with six protruding coiled-coils. The alpha prefoldin subunits have two beta hairpin structures while the beta prefoldin subunits (this CD) have only one hairpin that is most similar to the second hairpin of the alpha subunit. The prefoldin hexamer consists of two alpha and four beta subunits and is assembled from the beta hairpins of all six subunits. The alpha subunits initially dimerize providing a structural nucleus for the assembly of the beta subunits. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the st
Probab=21.60 E-value=4.1e+02 Score=20.91 Aligned_cols=69 Identities=19% Similarity=0.172 Sum_probs=35.2
Q ss_pred cchhhhhhHHHHhhhcccccccCCeeeeccCC---CCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024762 149 NIRRRVYDALNVLMAMDIISKDKKEIQWKGLP---RTSLNDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQN 220 (263)
Q Consensus 149 niKRRVYDalNVL~ai~lI~K~Kk~I~W~G~~---~~s~~~~~~Lk~E~~~l~erI~~Kk~~LqEL~~Q~~alkn 220 (263)
...+...|+++-|+.+. -+.+-++-.|-- .....-...|+..+..+..+|+.....+.++..+...++.
T Consensus 27 ~~~~E~~~v~~EL~~l~---~d~~vy~~VG~vfv~~~~~ea~~~Le~~~e~le~~i~~l~~~~~~l~~~~~elk~ 98 (105)
T cd00632 27 AQLNENKKALEELEKLA---DDAEVYKLVGNVLVKQEKEEARTELKERLETIELRIKRLERQEEDLQEKLKELQE 98 (105)
T ss_pred HHHHHHHHHHHHHHcCC---CcchHHHHhhhHHhhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44566677777776664 333333333321 1112223445555555555666666666666665555543
No 141
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=21.48 E-value=1.5e+02 Score=25.45 Aligned_cols=51 Identities=16% Similarity=0.198 Sum_probs=34.6
Q ss_pred HHHHHHHHHhc----C-CCcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhcccccccCCee
Q 024762 104 SMKVCEKVESK----G-RTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKDKKEI 174 (263)
Q Consensus 104 S~KVcekVk~k----g-~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~K~Kk~I 174 (263)
=.+|.+.+++. + ..|..|+|+++-- .-+--||..|..|+..|+|++..+.+
T Consensus 8 q~~iL~~l~~~~~~~~~~~~~~ela~~~~~--------------------~s~~tv~~~l~~L~~~g~i~~~~~~~ 63 (199)
T TIGR00498 8 QQEVLDLIRAHIESTGYPPSIREIARAVGL--------------------RSPSAAEEHLKALERKGYIERDPGKP 63 (199)
T ss_pred HHHHHHHHHHHHHhcCCCCcHHHHHHHhCC--------------------CChHHHHHHHHHHHHCCCEecCCCCC
Confidence 34566666543 2 3678888887520 01456899999999999999965553
No 142
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=21.31 E-value=1e+02 Score=27.09 Aligned_cols=54 Identities=17% Similarity=0.247 Sum_probs=38.5
Q ss_pred CCcHHHHHHHHHHHhcCC----CCCCCCCCccccccccchhhhhhHHHHhhhcccccc
Q 024762 116 RTTYNEVADELVAEFADP----SNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (263)
Q Consensus 116 ~TTYnEVAdeLV~e~~~~----~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~K 169 (263)
..-|.+|++.|...+... ...+.+..+-+....+-|=-|-.||+.|..-|+|.+
T Consensus 8 ~p~y~qI~~~i~~~I~~G~~~~g~kLPsE~eLa~~~~VSR~TvR~Al~~L~~eGli~r 65 (241)
T PRK11402 8 QLLYATVRQRLLDDIAQGVYQAGQQIPTENELCTQYNVSRITIRKAISDLVADGVLIR 65 (241)
T ss_pred CcHHHHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 356999999999887642 222222223344445678889999999999999999
No 143
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=21.30 E-value=6.3e+02 Score=22.97 Aligned_cols=45 Identities=20% Similarity=0.330 Sum_probs=34.9
Q ss_pred HHHHHHHHhc-CCCcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhccccccc
Q 024762 105 MKVCEKVESK-GRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKD 170 (263)
Q Consensus 105 ~KVcekVk~k-g~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~K~ 170 (263)
..|.+.+-+. +..|..|||++|= --|=.+|.+|+-|+..|++.++
T Consensus 28 l~IL~~~~~~~~~~tl~eIa~~lg---------------------lpkStv~RlL~tL~~~G~l~~~ 73 (271)
T PRK10163 28 IAILQYLEKSGGSSSVSDISLNLD---------------------LPLSTTFRLLKVLQAADFVYQD 73 (271)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHHC---------------------cCHHHHHHHHHHHHHCCCEEEc
Confidence 3466667554 4688999998862 2367899999999999999994
No 144
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.
Probab=20.89 E-value=1.1e+02 Score=26.80 Aligned_cols=51 Identities=22% Similarity=0.293 Sum_probs=36.1
Q ss_pred HHHHHHHHHHHhcCC----CCCCCCCCccccccccchhhhhhHHHHhhhcccccc
Q 024762 119 YNEVADELVAEFADP----SNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (263)
Q Consensus 119 YnEVAdeLV~e~~~~----~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~K 169 (263)
|.+|++.|...+... ...+.+..+-+-...+-|=-|-.||+.|+.-|+|.+
T Consensus 2 y~qi~~~l~~~I~~g~~~~G~~LPsE~eLa~~~gVSR~TVR~Al~~L~~eGli~r 56 (233)
T TIGR02404 2 YEQIYQDLEQKITHGQYKEGDYLPSEHELMDQYGASRETVRKALNLLTEAGYIQK 56 (233)
T ss_pred HHHHHHHHHHHHHhCCCCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 788899988877642 222222223344445778889999999999999999
No 145
>COG1730 GIM5 Predicted prefoldin, molecular chaperone implicated in de novo protein folding [Posttranslational modification, protein turnover, chaperones]
Probab=20.82 E-value=5.6e+02 Score=22.23 Aligned_cols=40 Identities=33% Similarity=0.296 Sum_probs=30.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024762 185 NDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQR 224 (263)
Q Consensus 185 ~~~~~Lk~E~~~l~erI~~Kk~~LqEL~~Q~~alknLI~R 224 (263)
..++.|++.++.|...+++.++.|++|......+...++.
T Consensus 94 eAie~l~k~~~~l~~~~~~l~~~l~~l~~~~~~l~~~~q~ 133 (145)
T COG1730 94 EAIEFLKKRIEELEKAIEKLQQALAELAQRIEQLEQEAQQ 133 (145)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4577788888888888888888888888877766665543
No 146
>KOG3856 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.76 E-value=2.8e+02 Score=24.09 Aligned_cols=44 Identities=23% Similarity=0.311 Sum_probs=27.4
Q ss_pred ChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHH
Q 024762 183 SLNDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQ-NLIQRNE 226 (263)
Q Consensus 183 s~~~~~~Lk~E~~~l~erI~~Kk~~LqEL~~Q~~alk-nLI~RNk 226 (263)
.....+.+++|+.++.++-++..+.|..|+.|+-+|. .-++.|+
T Consensus 8 ~~~~ye~~kaEL~elikkrqe~eetl~nLe~qIY~~EgsYle~ts 52 (135)
T KOG3856|consen 8 ELKSYEDTKAELAELIKKRQELEETLANLERQIYAFEGSYLEDTS 52 (135)
T ss_pred cccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhccc
Confidence 3445677888877665555555566667777777776 3344443
No 147
>KOG0240 consensus Kinesin (SMY1 subfamily) [Cytoskeleton]
Probab=20.59 E-value=9.3e+02 Score=25.75 Aligned_cols=23 Identities=9% Similarity=0.140 Sum_probs=14.0
Q ss_pred HHHhcCCCcHHHHHHHHHHHhcC
Q 024762 110 KVESKGRTTYNEVADELVAEFAD 132 (263)
Q Consensus 110 kVk~kg~TTYnEVAdeLV~e~~~ 132 (263)
.++..+.+...+....+..++..
T Consensus 351 e~~kd~~~~~~~~~~~~~~sl~~ 373 (607)
T KOG0240|consen 351 EKKKDKNVALKEELEKLRNSLKR 373 (607)
T ss_pred HHHHhHHHHHHHHHHHHHHHHhh
Confidence 33444566666777777777663
No 148
>PF10557 Cullin_Nedd8: Cullin protein neddylation domain; InterPro: IPR019559 This is the neddylation site of cullin proteins, which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae (Baker's yeast), and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue []. ; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_B 1U6G_A 3O6B_J 3O2P_E 4A0K_A 2HYE_C ....
Probab=20.30 E-value=1.5e+02 Score=21.82 Aligned_cols=55 Identities=15% Similarity=0.355 Sum_probs=38.6
Q ss_pred HHHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhcccccccC
Q 024762 104 SMKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKDK 171 (263)
Q Consensus 104 S~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~K~K 171 (263)
-..+..+++..+..+|.|+..+++..+.... ..+...+|++ +.-|..=+.|+++.
T Consensus 10 ~AaIVrimK~~k~~~~~~L~~~v~~~l~~~f---------~~~~~~ik~~----Ie~LIekeyi~Rd~ 64 (68)
T PF10557_consen 10 DAAIVRIMKQEKKLSHDELINEVIEELKKRF---------PPSVSDIKKR----IESLIEKEYIERDE 64 (68)
T ss_dssp HHHHHHHHHHSSEEEHHHHHHHHHHHTTTTS------------HHHHHHH----HHHHHHTTSEEEES
T ss_pred hhheehhhhhcCceeHHHHHHHHHHHhcCCc---------CCCHHHHHHH----HHHHHHhhhhhcCC
Confidence 3457789999999999999999999877522 1133455554 56777777887743
No 149
>PF01638 HxlR: HxlR-like helix-turn-helix; InterPro: IPR002577 The hxlR-type HTH domain is a domain of ~90-100 amino acids present in putative transcription regulators with a winged helix-turn-helix (wHTH) structure. The domain is named after Bacillus subtilis hxlR, a transcription activator of the hxlAB operon involved in the detoxification of formaldehyde []. The hxlR-type domain forms the core of putative transcription regulators and of hypothetical proteins occurring in eubacteria as well as in archaea. The sequence and structure of hxlR-type proteins show similarities with the marR-type wHTH []. The crystal structure of ytfH resembles the DNA-binding domains of winged helix proteins, containing a three helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-H2-B1-H3-H4-B2-B3-H5-H6. This topology corresponds with that of the marR-type DNA-binding domain, wherein helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. ; PDB: 2F2E_B 3DF8_A 1Z7U_B 1YYV_A 4A5M_D 4A5N_B 2FSW_A 2HZT_D.
Probab=20.27 E-value=1.5e+02 Score=22.57 Aligned_cols=45 Identities=11% Similarity=0.207 Sum_probs=32.6
Q ss_pred HHHHHHHHHhcCCCcHHHHHHHHHHHhcCCCCCCCCCCccccccccchhhhhhHHHHhhhcccccc
Q 024762 104 SMKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (263)
Q Consensus 104 S~KVcekVk~kg~TTYnEVAdeLV~e~~~~~~~~~~~~~~~~deKniKRRVYDalNVL~ai~lI~K 169 (263)
+..|...+.. |.+.|+|+...|- ..-.+=+.+-|.-|++.|||+|
T Consensus 7 ~~~IL~~l~~-g~~rf~el~~~l~--------------------~is~~~L~~~L~~L~~~GLv~r 51 (90)
T PF01638_consen 7 TLLILRALFQ-GPMRFSELQRRLP--------------------GISPKVLSQRLKELEEAGLVER 51 (90)
T ss_dssp HHHHHHHHTT-SSEEHHHHHHHST--------------------TS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHh-CCCcHHHHHHhcc--------------------hhHHHHHHHHHHHHHHcchhhc
Confidence 3445555555 8999999877751 0224667899999999999999
No 150
>COG1938 Archaeal enzymes of ATP-grasp superfamily [General function prediction only]
Probab=20.24 E-value=2.8e+02 Score=26.15 Aligned_cols=27 Identities=26% Similarity=0.395 Sum_probs=19.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024762 186 DIEELKAERLGLRNRIEKKTAYLQELE 212 (263)
Q Consensus 186 ~~~~Lk~E~~~l~erI~~Kk~~LqEL~ 212 (263)
+.+.|.+|-+.++++|++..+++++..
T Consensus 205 ~td~L~keAe~i~~~lekl~eq~~~~~ 231 (244)
T COG1938 205 DTDKLEKEAEEIEEQLEKLAEQLEKEE 231 (244)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 356788888888777777777766554
No 151
>KOG2264 consensus Exostosin EXT1L [Signal transduction mechanisms]
Probab=20.05 E-value=2.4e+02 Score=30.46 Aligned_cols=40 Identities=30% Similarity=0.343 Sum_probs=20.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHH
Q 024762 187 IEELKAERLGLRNRIEKKTAYLQEL----EDQFVGLQNLIQRNE 226 (263)
Q Consensus 187 ~~~Lk~E~~~l~erI~~Kk~~LqEL----~~Q~~alknLI~RNk 226 (263)
++++....+.++..|.+|+..|..| ++-+.+++.|+++|.
T Consensus 109 I~~~n~kiEelk~~i~~~q~eL~~Lk~~ieqaq~~~~El~~~n~ 152 (907)
T KOG2264|consen 109 IEEINTKIEELKRLIPQKQLELSALKGEIEQAQRQLEELRETNN 152 (907)
T ss_pred HHHHHHHHHHHHHHHHHhHHHHHHHHhHHHHHHHHHHHHHhhcC
Confidence 3333333344444455555444433 234556777777774
Done!