Query 027271
Match_columns 225
No_of_seqs 120 out of 585
Neff 6.8
Searched_HMMs 46136
Date Fri Mar 29 07:27:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027271.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027271hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3250 COP9 signalosome, subu 100.0 4.3E-50 9.4E-55 335.1 15.0 222 1-223 1-222 (258)
2 KOG2908 26S proteasome regulat 100.0 1.6E-34 3.5E-39 255.9 15.7 182 9-192 178-375 (380)
3 KOG2753 Uncharacterized conser 100.0 8E-35 1.7E-39 256.8 12.9 171 8-183 185-367 (378)
4 PF01399 PCI: PCI domain; Int 99.6 1.2E-14 2.6E-19 108.7 7.7 95 60-156 1-105 (105)
5 smart00753 PAM PCI/PINT associ 99.5 1.5E-14 3.3E-19 106.1 7.3 86 88-177 3-88 (88)
6 smart00088 PINT motif in prote 99.5 1.5E-14 3.3E-19 106.1 7.3 86 88-177 3-88 (88)
7 KOG1464 COP9 signalosome, subu 98.9 3E-09 6.4E-14 93.8 8.1 124 60-191 305-438 (440)
8 KOG2581 26S proteasome regulat 97.8 3E-05 6.5E-10 71.6 5.7 91 60-153 319-420 (493)
9 KOG2758 Translation initiation 97.4 0.0012 2.6E-08 59.7 9.2 100 87-193 327-426 (432)
10 KOG1497 COP9 signalosome, subu 97.0 0.0033 7.2E-08 56.8 8.1 151 25-190 227-389 (399)
11 KOG0686 COP9 signalosome, subu 96.5 0.021 4.7E-07 53.1 9.9 109 62-172 308-426 (466)
12 KOG1498 26S proteasome regulat 96.1 0.056 1.2E-06 50.1 10.3 124 59-194 287-426 (439)
13 KOG2582 COP9 signalosome, subu 95.6 0.084 1.8E-06 48.6 9.2 105 60-168 259-372 (422)
14 COG5071 RPN5 26S proteasome re 95.1 0.17 3.8E-06 45.8 9.2 74 105-190 349-422 (439)
15 KOG2688 Transcription-associat 94.6 0.079 1.7E-06 49.3 6.1 97 61-158 273-386 (394)
16 KOG0687 26S proteasome regulat 93.7 1 2.2E-05 41.2 11.0 112 43-157 241-363 (393)
17 COG5600 Transcription-associat 92.9 0.24 5.2E-06 45.8 5.9 98 60-159 289-406 (413)
18 KOG1463 26S proteasome regulat 92.8 0.29 6.3E-06 44.9 6.2 101 55-157 281-391 (411)
19 PF09756 DDRGK: DDRGK domain; 92.7 0.18 4E-06 42.4 4.5 58 96-155 100-157 (188)
20 KOG2072 Translation initiation 92.6 5.1 0.00011 40.7 14.9 50 105-155 443-492 (988)
21 PF10075 PCI_Csn8: COP9 signal 91.8 1.1 2.5E-05 35.3 7.9 108 24-132 5-119 (143)
22 COG5159 RPN6 26S proteasome re 89.3 0.85 1.8E-05 41.3 5.5 97 59-157 283-389 (421)
23 COG3355 Predicted transcriptio 89.0 3.4 7.3E-05 32.6 8.1 80 105-190 38-120 (126)
24 PF09012 FeoC: FeoC like trans 88.8 0.36 7.8E-06 33.6 2.3 47 99-147 4-50 (69)
25 PF02082 Rrf2: Transcriptional 87.2 1.8 3.9E-05 31.0 5.3 59 95-156 11-69 (83)
26 KOG3054 Uncharacterized conser 85.4 1.5 3.3E-05 38.4 4.7 55 99-155 204-258 (299)
27 PHA01750 hypothetical protein 82.7 5.5 0.00012 27.9 5.6 38 184-221 36-73 (75)
28 TIGR02010 IscR iron-sulfur clu 81.1 4.4 9.5E-05 31.7 5.5 47 95-143 11-57 (135)
29 PRK11179 DNA-binding transcrip 80.6 2.6 5.7E-05 33.7 4.1 47 99-147 13-62 (153)
30 PF13412 HTH_24: Winged helix- 80.5 3.4 7.3E-05 26.2 3.9 42 99-142 7-48 (48)
31 COG1777 Predicted transcriptio 78.2 20 0.00043 30.8 8.8 109 111-222 29-157 (217)
32 PRK14165 winged helix-turn-hel 78.1 9.1 0.0002 32.9 6.9 61 93-155 5-65 (217)
33 smart00344 HTH_ASNC helix_turn 78.0 4.5 9.7E-05 30.0 4.5 37 105-143 13-49 (108)
34 COG5187 RPN7 26S proteasome re 77.8 32 0.00069 31.5 10.3 64 92-157 314-377 (412)
35 PRK10857 DNA-binding transcrip 76.6 6.5 0.00014 32.2 5.4 48 95-144 11-58 (164)
36 TIGR01410 tatB twin arginine-t 76.2 11 0.00024 27.2 5.9 38 161-198 18-55 (80)
37 PRK11169 leucine-responsive tr 76.2 5.3 0.00012 32.3 4.8 43 99-143 18-60 (164)
38 COG1522 Lrp Transcriptional re 75.5 4.4 9.4E-05 31.8 4.0 42 101-144 14-55 (154)
39 PF09339 HTH_IclR: IclR helix- 75.4 6.6 0.00014 25.4 4.2 45 96-142 4-49 (52)
40 PF01726 LexA_DNA_bind: LexA D 75.0 5.7 0.00012 27.5 3.9 37 105-142 21-57 (65)
41 TIGR00738 rrf2_super rrf2 fami 74.4 12 0.00026 28.7 6.1 49 94-144 10-58 (132)
42 smart00346 HTH_ICLR helix_turn 74.2 7.2 0.00016 27.7 4.5 46 96-143 6-52 (91)
43 PRK01919 tatB sec-independent 73.3 19 0.00041 29.8 7.2 59 161-220 19-77 (169)
44 PF03962 Mnd1: Mnd1 family; I 72.9 41 0.00089 28.1 9.4 71 109-188 11-85 (188)
45 PRK04654 sec-independent trans 72.8 22 0.00048 30.5 7.7 35 161-195 19-53 (214)
46 PF07389 DUF1500: Protein of u 72.1 7 0.00015 29.0 3.9 40 97-139 36-75 (100)
47 PRK04098 sec-independent trans 71.4 31 0.00067 28.3 8.0 58 161-218 19-79 (158)
48 COG1959 Predicted transcriptio 71.1 12 0.00025 30.1 5.5 51 95-147 11-61 (150)
49 PRK03573 transcriptional regul 68.7 36 0.00078 26.4 7.8 57 100-158 37-93 (144)
50 PRK10141 DNA-binding transcrip 67.8 11 0.00025 29.1 4.6 46 107-154 28-73 (117)
51 PF07106 TBPIP: Tat binding pr 67.6 64 0.0014 26.1 13.4 109 105-218 12-137 (169)
52 smart00550 Zalpha Z-DNA-bindin 67.6 10 0.00022 26.2 3.9 33 109-143 22-54 (68)
53 TIGR02944 suf_reg_Xantho FeS a 67.2 15 0.00032 28.3 5.2 47 95-144 12-58 (130)
54 PRK11920 rirA iron-responsive 66.6 15 0.00033 29.5 5.4 49 95-146 11-59 (153)
55 PRK11014 transcriptional repre 66.1 16 0.00035 28.6 5.3 51 95-147 11-61 (141)
56 PRK04214 rbn ribonuclease BN/u 66.0 49 0.0011 30.9 9.3 79 105-192 306-393 (412)
57 PF07889 DUF1664: Protein of u 65.4 52 0.0011 25.9 7.9 54 167-220 45-98 (126)
58 PF12840 HTH_20: Helix-turn-he 65.2 12 0.00026 25.0 3.8 38 105-144 20-57 (61)
59 PRK01770 sec-independent trans 64.4 33 0.00071 28.5 6.9 34 161-194 19-52 (171)
60 PF13730 HTH_36: Helix-turn-he 64.0 28 0.0006 22.4 5.3 47 93-141 7-55 (55)
61 KOG1076 Translation initiation 63.9 17 0.00036 36.6 5.9 96 62-159 657-766 (843)
62 PF01325 Fe_dep_repress: Iron 63.7 18 0.0004 24.4 4.5 43 98-142 11-53 (60)
63 PF08220 HTH_DeoR: DeoR-like h 63.5 11 0.00024 25.0 3.4 43 97-141 2-44 (57)
64 TIGR02702 SufR_cyano iron-sulf 63.3 87 0.0019 26.0 11.1 37 107-145 13-49 (203)
65 PF08280 HTH_Mga: M protein tr 62.9 7.4 0.00016 26.1 2.4 36 96-132 6-41 (59)
66 PF01022 HTH_5: Bacterial regu 61.3 22 0.00048 22.4 4.4 33 108-142 14-46 (47)
67 PF04967 HTH_10: HTH DNA bindi 61.1 29 0.00063 23.1 5.0 30 105-136 19-48 (53)
68 smart00345 HTH_GNTR helix_turn 61.0 34 0.00074 21.7 5.4 36 105-142 15-51 (60)
69 PF13404 HTH_AsnC-type: AsnC-t 60.6 6.3 0.00014 24.8 1.6 29 100-129 8-36 (42)
70 PF08281 Sigma70_r4_2: Sigma-7 60.3 12 0.00027 24.0 3.1 27 108-136 25-51 (54)
71 cd00090 HTH_ARSR Arsenical Res 58.9 38 0.00082 22.0 5.5 36 110-147 21-56 (78)
72 PF14947 HTH_45: Winged helix- 58.4 31 0.00066 24.3 5.1 50 99-155 10-59 (77)
73 PF08279 HTH_11: HTH domain; 57.7 16 0.00035 23.5 3.3 35 97-132 2-37 (55)
74 PF08784 RPA_C: Replication pr 57.5 24 0.00053 25.9 4.7 50 96-147 51-101 (102)
75 PRK10265 chaperone-modulator p 57.3 24 0.00052 26.4 4.6 38 106-149 4-41 (101)
76 TIGR02337 HpaR homoprotocatech 57.2 79 0.0017 23.6 8.5 48 106-155 39-86 (118)
77 smart00347 HTH_MARR helix_turn 56.8 65 0.0014 22.5 8.2 43 107-151 22-64 (101)
78 PRK14858 tatA twin arginine tr 56.7 79 0.0017 24.3 7.3 34 161-194 19-52 (108)
79 PF04545 Sigma70_r4: Sigma-70, 54.8 45 0.00097 21.0 5.0 28 107-136 18-45 (50)
80 PRK09954 putative kinase; Prov 54.3 17 0.00036 32.9 4.0 54 100-155 8-64 (362)
81 PF01920 Prefoldin_2: Prefoldi 54.1 55 0.0012 23.8 6.1 57 154-224 47-103 (106)
82 PF13601 HTH_34: Winged helix 54.0 15 0.00033 26.2 2.9 51 98-150 3-53 (80)
83 PF12802 MarR_2: MarR family; 53.7 50 0.0011 21.4 5.3 40 108-149 20-59 (62)
84 cd04786 HTH_MerR-like_sg7 Heli 53.7 1.1E+02 0.0023 24.0 8.4 106 111-225 2-120 (131)
85 PF05377 FlaC_arch: Flagella a 53.1 46 0.001 22.4 4.9 34 188-221 5-38 (55)
86 PRK10870 transcriptional repre 52.8 1E+02 0.0022 25.1 8.1 51 106-158 68-118 (176)
87 TIGR02051 MerR Hg(II)-responsi 52.2 66 0.0014 24.7 6.5 96 111-215 1-108 (124)
88 PF05331 DUF742: Protein of un 52.1 26 0.00056 27.1 4.1 42 99-144 47-88 (114)
89 smart00418 HTH_ARSR helix_turn 51.4 55 0.0012 20.6 5.2 38 107-146 8-45 (66)
90 smart00420 HTH_DEOR helix_turn 51.2 39 0.00084 20.8 4.3 35 107-143 12-46 (53)
91 PF11945 WASH_WAHD: WAHD domai 50.9 1.4E+02 0.003 27.0 9.1 66 156-221 8-74 (297)
92 PF01978 TrmB: Sugar-specific 50.2 23 0.0005 24.0 3.3 38 106-145 19-56 (68)
93 PRK00708 sec-independent trans 48.6 81 0.0018 27.0 6.9 37 161-197 19-55 (209)
94 cd04784 HTH_CadR-PbrR Helix-Tu 47.7 54 0.0012 25.2 5.4 26 111-142 2-27 (127)
95 PF01047 MarR: MarR family; I 47.7 33 0.00072 22.2 3.6 43 106-150 14-56 (59)
96 COG1497 Predicted transcriptio 47.2 2E+02 0.0044 25.4 10.1 84 99-195 15-98 (260)
97 COG4575 ElaB Uncharacterized c 45.6 98 0.0021 23.6 6.2 57 159-221 2-58 (104)
98 cd01109 HTH_YyaN Helix-Turn-He 44.9 95 0.002 23.3 6.3 45 111-170 2-47 (113)
99 KOG2629 Peroxisomal membrane a 44.8 94 0.002 28.0 6.9 83 128-219 85-169 (300)
100 cd06445 ATase The DNA repair p 44.7 25 0.00054 25.0 2.8 26 97-122 5-30 (79)
101 PF13518 HTH_28: Helix-turn-he 44.4 36 0.00078 21.3 3.3 43 99-146 4-46 (52)
102 PF13815 Dzip-like_N: Iguana/D 43.3 1.5E+02 0.0032 22.6 8.3 51 171-221 68-118 (118)
103 PF03399 SAC3_GANP: SAC3/GANP/ 43.2 1.1E+02 0.0025 24.8 7.0 62 59-120 135-203 (204)
104 PF04703 FaeA: FaeA-like prote 43.2 29 0.00063 23.8 2.8 34 107-142 13-46 (62)
105 TIGR03879 near_KaiC_dom probab 42.6 37 0.00081 24.2 3.4 24 108-132 31-54 (73)
106 KOG2166 Cullins [Cell cycle co 42.4 3.7E+02 0.008 27.4 11.5 118 95-221 566-695 (725)
107 PF06163 DUF977: Bacterial pro 42.3 40 0.00087 26.6 3.8 43 97-141 14-56 (127)
108 PRK15090 DNA-binding transcrip 41.7 52 0.0011 28.3 4.9 46 96-143 15-60 (257)
109 PF04539 Sigma70_r3: Sigma-70 41.4 28 0.0006 24.1 2.6 27 105-132 16-42 (78)
110 cd00092 HTH_CRP helix_turn_hel 41.3 54 0.0012 21.4 4.0 35 107-143 23-57 (67)
111 PRK00404 tatB sec-independent 41.3 1.7E+02 0.0037 23.6 7.3 34 161-194 19-52 (141)
112 smart00419 HTH_CRP helix_turn_ 41.2 53 0.0012 19.9 3.7 33 109-143 8-40 (48)
113 PRK10884 SH3 domain-containing 41.1 1.8E+02 0.0039 24.7 7.9 35 185-219 120-154 (206)
114 PF03979 Sigma70_r1_1: Sigma-7 40.8 23 0.00049 25.4 2.1 33 99-132 11-46 (82)
115 PF10828 DUF2570: Protein of u 39.8 1.6E+02 0.0035 22.2 8.5 55 171-225 38-92 (110)
116 TIGR01884 cas_HTH CRISPR locus 39.8 86 0.0019 26.0 5.8 52 100-154 148-199 (203)
117 PF10975 DUF2802: Protein of u 38.1 35 0.00076 24.0 2.7 20 110-130 45-64 (70)
118 PF02002 TFIIE_alpha: TFIIE al 38.1 35 0.00075 25.3 2.8 36 107-144 25-60 (105)
119 PRK03100 sec-independent trans 38.1 1.1E+02 0.0024 24.4 5.8 34 161-194 20-53 (136)
120 PF06394 Pepsin-I3: Pepsin inh 38.0 13 0.00029 26.7 0.5 37 149-185 27-66 (76)
121 PHA02943 hypothetical protein; 37.6 79 0.0017 26.0 4.9 45 95-142 11-55 (165)
122 PF13463 HTH_27: Winged helix 37.2 1.2E+02 0.0026 19.9 5.6 49 101-151 10-58 (68)
123 PF01638 HxlR: HxlR-like helix 37.1 1.5E+02 0.0034 21.1 6.8 75 98-180 9-85 (90)
124 PF13591 MerR_2: MerR HTH fami 37.1 52 0.0011 23.6 3.5 32 110-147 1-32 (84)
125 PF10668 Phage_terminase: Phag 36.5 40 0.00086 23.1 2.6 24 106-130 19-42 (60)
126 cd04789 HTH_Cfa Helix-Turn-Hel 35.9 1.8E+02 0.0039 21.5 6.8 89 110-219 2-93 (102)
127 COG1595 RpoE DNA-directed RNA 35.3 44 0.00096 26.9 3.3 28 107-136 141-168 (182)
128 PRK13182 racA polar chromosome 34.9 1.6E+02 0.0034 24.5 6.5 21 111-132 2-22 (175)
129 cd07377 WHTH_GntR Winged helix 34.5 1.3E+02 0.0027 19.3 6.0 36 105-142 20-56 (66)
130 PF12324 HTH_15: Helix-turn-he 34.2 64 0.0014 23.3 3.5 34 98-132 27-60 (77)
131 cd04769 HTH_MerR2 Helix-Turn-H 33.8 2.1E+02 0.0045 21.6 7.7 99 111-217 2-113 (116)
132 COG3413 Predicted DNA binding 33.8 57 0.0012 27.4 3.8 83 61-146 127-212 (215)
133 PF14480 DNA_pol3_a_NI: DNA po 33.5 1.5E+02 0.0032 20.3 5.3 61 111-176 2-62 (76)
134 PRK10411 DNA-binding transcrip 33.2 69 0.0015 27.6 4.3 46 95-142 4-49 (240)
135 TIGR02431 pcaR_pcaU beta-ketoa 32.9 86 0.0019 26.7 4.9 45 96-142 10-55 (248)
136 PRK00182 tatB sec-independent 31.7 1.7E+02 0.0037 24.1 6.0 33 161-193 20-52 (160)
137 KOG3431 Apoptosis-related prot 31.4 30 0.00065 27.2 1.5 22 125-147 70-91 (129)
138 PRK12537 RNA polymerase sigma 31.1 55 0.0012 26.3 3.2 27 108-136 148-174 (182)
139 TIGR01764 excise DNA binding d 31.1 1.2E+02 0.0026 18.1 5.8 30 110-145 2-31 (49)
140 PRK10434 srlR DNA-bindng trans 31.0 69 0.0015 27.8 4.0 45 95-141 5-49 (256)
141 PF12999 PRKCSH-like: Glucosid 30.9 2.2E+02 0.0047 23.8 6.6 20 202-221 151-170 (176)
142 cd01282 HTH_MerR-like_sg3 Heli 30.7 2.3E+02 0.005 21.2 7.9 44 111-169 2-45 (112)
143 cd01107 HTH_BmrR Helix-Turn-He 30.6 2.3E+02 0.0049 21.1 6.7 46 111-170 2-48 (108)
144 TIGR02338 gimC_beta prefoldin, 30.6 1.6E+02 0.0035 22.1 5.5 36 186-221 70-105 (110)
145 TIGR03541 reg_near_HchA LuxR f 30.6 88 0.0019 26.6 4.5 22 110-132 187-208 (232)
146 PRK15418 transcriptional regul 29.9 78 0.0017 28.5 4.2 39 109-149 29-67 (318)
147 PRK13509 transcriptional repre 29.8 87 0.0019 27.1 4.4 47 95-143 5-51 (251)
148 PF09202 Rio2_N: Rio2, N-termi 29.7 1.3E+02 0.0028 21.7 4.6 49 95-145 9-58 (82)
149 TIGR02999 Sig-70_X6 RNA polyme 29.7 63 0.0014 25.7 3.3 28 107-136 148-175 (183)
150 PF09743 DUF2042: Uncharacteri 29.7 94 0.002 27.6 4.6 42 105-148 126-167 (272)
151 PRK12523 RNA polymerase sigma 29.4 64 0.0014 25.6 3.3 27 108-136 134-160 (172)
152 PF13542 HTH_Tnp_ISL3: Helix-t 29.3 77 0.0017 19.9 3.1 31 99-132 19-49 (52)
153 PF10007 DUF2250: Uncharacteri 28.9 72 0.0016 23.7 3.2 27 114-142 26-52 (92)
154 PHA02763 hypothetical protein; 28.8 75 0.0016 23.6 3.1 51 109-162 52-102 (102)
155 PRK09802 DNA-binding transcrip 28.6 84 0.0018 27.6 4.1 47 94-142 16-62 (269)
156 KOG2235 Uncharacterized conser 28.6 1.2E+02 0.0026 30.3 5.4 46 106-155 130-175 (776)
157 cd00632 Prefoldin_beta Prefold 28.5 2.1E+02 0.0045 21.2 5.8 19 202-220 82-100 (105)
158 PRK12529 RNA polymerase sigma 28.1 69 0.0015 25.7 3.3 27 108-136 142-168 (178)
159 smart00502 BBC B-Box C-termina 28.1 1.8E+02 0.0038 21.3 5.4 14 203-216 56-69 (127)
160 PRK09651 RNA polymerase sigma 27.9 68 0.0015 25.5 3.2 28 107-136 133-160 (172)
161 PF07464 ApoLp-III: Apolipopho 27.8 2.5E+02 0.0055 22.8 6.4 52 167-221 29-80 (155)
162 cd04766 HTH_HspR Helix-Turn-He 27.8 2.3E+02 0.005 20.2 7.1 89 110-222 2-90 (91)
163 PF06056 Terminase_5: Putative 27.7 67 0.0015 21.6 2.6 23 109-132 13-35 (58)
164 PF13384 HTH_23: Homeodomain-l 27.6 63 0.0014 20.2 2.4 23 109-132 17-39 (50)
165 KOG3438 DNA-directed RNA polym 27.5 1.8E+02 0.0039 22.2 5.0 43 156-199 61-103 (105)
166 PRK09642 RNA polymerase sigma 27.5 74 0.0016 24.8 3.3 28 107-136 120-147 (160)
167 PRK12543 RNA polymerase sigma 27.2 73 0.0016 25.5 3.2 27 108-136 132-158 (179)
168 PRK06759 RNA polymerase factor 27.1 77 0.0017 24.4 3.3 27 108-136 121-147 (154)
169 PRK15396 murein lipoprotein; P 26.7 2.5E+02 0.0054 20.2 7.1 53 165-217 25-77 (78)
170 PRK10884 SH3 domain-containing 26.6 4E+02 0.0086 22.6 8.2 8 156-163 79-86 (206)
171 COG2390 DeoR Transcriptional r 26.6 90 0.002 28.4 4.0 38 108-147 25-62 (321)
172 PF14394 DUF4423: Domain of un 26.6 1.4E+02 0.003 24.5 4.8 34 111-146 41-76 (171)
173 PRK09047 RNA polymerase factor 26.6 79 0.0017 24.5 3.3 27 108-136 121-147 (161)
174 TIGR02919 accessory Sec system 26.4 2.6E+02 0.0057 26.4 7.3 88 111-202 340-433 (438)
175 KOG3809 Microtubule-binding pr 26.4 1.7E+02 0.0036 28.2 5.7 59 162-220 504-562 (583)
176 cd04774 HTH_YfmP Helix-Turn-He 26.2 2.3E+02 0.005 20.7 5.5 45 111-170 2-46 (96)
177 PF01765 RRF: Ribosome recycli 26.2 1.5E+02 0.0032 24.0 4.8 62 134-198 62-127 (165)
178 PRK10163 DNA-binding transcrip 26.0 1.3E+02 0.0029 26.1 4.9 54 96-153 26-80 (271)
179 cd04775 HTH_Cfa-like Helix-Tur 25.9 2.7E+02 0.0059 20.4 6.5 45 110-169 2-46 (102)
180 PF01035 DNA_binding_1: 6-O-me 25.9 60 0.0013 23.4 2.3 26 97-122 7-32 (85)
181 PF01984 dsDNA_bind: Double-st 25.7 37 0.00081 25.9 1.2 22 125-147 62-83 (107)
182 PRK11512 DNA-binding transcrip 25.6 2.2E+02 0.0048 22.0 5.7 51 107-159 52-102 (144)
183 PRK04239 hypothetical protein; 25.6 38 0.00083 26.1 1.2 22 125-147 67-88 (110)
184 COG1414 IclR Transcriptional r 25.6 1.3E+02 0.0028 26.0 4.7 56 96-155 5-61 (246)
185 PRK10188 DNA-binding transcrip 25.6 1.2E+02 0.0026 26.0 4.5 22 110-132 195-216 (240)
186 PF05791 Bacillus_HBL: Bacillu 25.5 3.3E+02 0.0072 22.4 7.0 58 166-223 125-182 (184)
187 PRK12520 RNA polymerase sigma 25.4 82 0.0018 25.4 3.3 27 108-136 146-172 (191)
188 PRK12527 RNA polymerase sigma 25.3 86 0.0019 24.4 3.3 28 107-136 119-146 (159)
189 PRK12525 RNA polymerase sigma 25.0 83 0.0018 24.9 3.2 28 107-136 132-159 (168)
190 smart00421 HTH_LUXR helix_turn 24.9 1.1E+02 0.0024 18.7 3.3 22 110-132 19-40 (58)
191 PRK11569 transcriptional repre 24.9 1.4E+02 0.003 26.0 4.8 45 96-142 29-74 (274)
192 PRK07037 extracytoplasmic-func 24.9 87 0.0019 24.4 3.3 27 108-136 124-150 (163)
193 TIGR02947 SigH_actino RNA poly 24.0 88 0.0019 25.3 3.2 28 107-136 145-172 (193)
194 PRK12514 RNA polymerase sigma 23.8 91 0.002 24.8 3.2 27 108-136 144-170 (179)
195 PF15397 DUF4618: Domain of un 23.6 2.3E+02 0.005 25.1 5.8 37 165-201 63-99 (258)
196 PRK12547 RNA polymerase sigma 23.6 94 0.002 24.4 3.2 27 108-136 127-153 (164)
197 TIGR02983 SigE-fam_strep RNA p 23.5 96 0.0021 24.1 3.3 27 108-136 125-151 (162)
198 PF12728 HTH_17: Helix-turn-he 23.4 2E+02 0.0042 17.9 6.0 37 110-154 2-38 (51)
199 TIGR00589 ogt O-6-methylguanin 23.4 95 0.0021 22.2 2.9 26 97-122 7-32 (80)
200 TIGR02047 CadR-PbrR Cd(II)/Pb( 23.4 2.7E+02 0.0059 21.3 5.7 27 111-143 2-28 (127)
201 PF07926 TPR_MLP1_2: TPR/MLP1/ 23.3 3.5E+02 0.0077 20.9 7.7 54 167-220 61-114 (132)
202 cd06170 LuxR_C_like C-terminal 23.1 1.3E+02 0.0028 18.5 3.3 23 109-132 15-37 (57)
203 PRK12513 RNA polymerase sigma 22.9 97 0.0021 25.0 3.3 28 107-136 153-180 (194)
204 cd04788 HTH_NolA-AlbR Helix-Tu 22.8 3E+02 0.0066 19.9 6.3 45 111-169 2-46 (96)
205 PF10779 XhlA: Haemolysin XhlA 22.5 2.7E+02 0.0058 19.2 7.1 48 170-221 4-51 (71)
206 PRK13729 conjugal transfer pil 22.4 3.6E+02 0.0078 26.1 7.2 67 152-221 52-121 (475)
207 TIGR02844 spore_III_D sporulat 22.4 92 0.002 22.5 2.6 31 96-128 7-37 (80)
208 cd04773 HTH_TioE_rpt2 Second H 22.4 3.3E+02 0.0072 20.2 7.0 31 110-146 1-31 (108)
209 PRK14861 tatA twin arginine tr 22.4 2.3E+02 0.005 19.3 4.5 33 161-193 20-52 (61)
210 PF02416 MttA_Hcf106: mttA/Hcf 22.3 2.4E+02 0.0052 18.5 4.5 31 161-191 16-46 (53)
211 PRK12528 RNA polymerase sigma 22.3 1.1E+02 0.0023 23.9 3.3 27 108-136 128-154 (161)
212 PF02646 RmuC: RmuC family; I 22.2 5.2E+02 0.011 23.0 8.0 53 169-221 10-65 (304)
213 PF05565 Sipho_Gp157: Siphovir 22.1 4.2E+02 0.0091 21.3 8.0 36 185-220 49-84 (162)
214 PRK09343 prefoldin subunit bet 22.0 2.6E+02 0.0057 21.4 5.4 35 146-180 48-82 (121)
215 PF05615 THOC7: Tho complex su 21.9 3.8E+02 0.0083 20.7 8.2 56 165-220 42-97 (139)
216 TIGR00373 conserved hypothetic 21.9 4.2E+02 0.0092 21.3 10.3 35 106-142 25-59 (158)
217 PF08317 Spc7: Spc7 kinetochor 21.9 4.6E+02 0.0099 23.6 7.7 60 161-220 205-267 (325)
218 PRK14857 tatA twin arginine tr 21.8 2.3E+02 0.0051 20.9 4.7 37 161-197 21-57 (90)
219 PRK12522 RNA polymerase sigma 21.7 1.1E+02 0.0023 24.2 3.3 27 108-136 134-160 (173)
220 cd07627 BAR_Vps5p The Bin/Amph 21.6 2.9E+02 0.0064 23.2 6.0 35 190-224 143-177 (216)
221 PF09341 Pcc1: Transcription f 21.6 2.8E+02 0.0061 19.1 5.5 47 138-190 30-76 (76)
222 PRK09646 RNA polymerase sigma 21.4 1.1E+02 0.0023 24.9 3.2 27 108-136 157-183 (194)
223 PRK12530 RNA polymerase sigma 21.3 1.1E+02 0.0024 24.8 3.3 27 108-136 149-175 (189)
224 PRK12511 RNA polymerase sigma 21.2 1.1E+02 0.0024 24.8 3.3 27 108-136 126-152 (182)
225 PRK00478 scpA segregation and 21.2 7.6E+02 0.017 23.9 9.5 98 107-205 360-463 (505)
226 PRK12536 RNA polymerase sigma 21.1 1.1E+02 0.0024 24.4 3.3 27 108-136 144-170 (181)
227 PF00046 Homeobox: Homeobox do 21.1 1E+02 0.0022 19.7 2.5 23 109-132 27-49 (57)
228 PRK09645 RNA polymerase sigma 21.1 1.1E+02 0.0024 24.0 3.2 27 108-136 133-159 (173)
229 PF08221 HTH_9: RNA polymerase 21.1 1.4E+02 0.0031 20.1 3.3 36 106-143 24-59 (62)
230 PRK12512 RNA polymerase sigma 21.0 1.1E+02 0.0025 24.3 3.3 27 108-136 146-172 (184)
231 cd00592 HTH_MerR-like Helix-Tu 20.9 1.9E+02 0.0042 20.8 4.2 44 111-169 2-45 (100)
232 PRK12539 RNA polymerase sigma 20.9 1.1E+02 0.0024 24.5 3.2 27 108-136 146-172 (184)
233 PRK09647 RNA polymerase sigma 20.8 1.1E+02 0.0024 25.3 3.3 27 108-136 153-179 (203)
234 PRK10430 DNA-binding transcrip 20.8 2.4E+02 0.0052 23.4 5.4 39 107-147 176-214 (239)
235 COG5647 Cullin, a subunit of E 20.8 3.1E+02 0.0066 28.0 6.6 59 95-155 608-670 (773)
236 PRK12545 RNA polymerase sigma 20.8 1.1E+02 0.0024 25.1 3.2 28 107-136 153-180 (201)
237 KOG1760 Molecular chaperone Pr 20.7 2.9E+02 0.0064 21.8 5.3 41 168-222 80-120 (131)
238 PRK10046 dpiA two-component re 20.6 1.7E+02 0.0038 24.1 4.4 37 109-147 177-213 (225)
239 TIGR02787 codY_Gpos GTP-sensin 20.5 1.8E+02 0.0038 25.7 4.4 36 107-144 196-231 (251)
240 cd04762 HTH_MerR-trunc Helix-T 20.4 1.2E+02 0.0026 18.0 2.6 28 110-143 1-28 (49)
241 PF04218 CENP-B_N: CENP-B N-te 20.3 1.1E+02 0.0025 19.9 2.6 30 99-131 14-43 (53)
242 PRK03887 methylated-DNA--prote 20.2 3.1E+02 0.0068 22.8 5.7 66 59-128 61-128 (175)
243 PF05920 Homeobox_KN: Homeobox 20.2 1.3E+02 0.0028 18.6 2.7 21 113-135 17-37 (40)
244 PRK08301 sporulation sigma fac 20.2 1.2E+02 0.0025 25.5 3.3 28 107-136 196-223 (234)
245 TIGR02950 SigM_subfam RNA poly 20.1 1.3E+02 0.0027 23.1 3.2 28 107-136 119-146 (154)
No 1
>KOG3250 consensus COP9 signalosome, subunit CSN7 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=100.00 E-value=4.3e-50 Score=335.14 Aligned_cols=222 Identities=43% Similarity=0.661 Sum_probs=218.6
Q ss_pred CchhHHHHHHHHHHHHhccCccHHHHHHHHHHHhcCCCcccchhhhcCchhhhccCCCchHHHHHHHHHhcCChhhhhhh
Q 027271 1 MDIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNN 80 (225)
Q Consensus 1 ~~~~~~~~~~l~~~l~~~~~~~~~~a~~li~~aL~~p~iy~f~eLl~~p~v~~L~~~~~~~l~~LL~iF~~G~~~d~~~~ 80 (225)
||+||++++.+++|+.++++.++.+...+|.+|+.+|++|.|+|||.+|+|..|..+.++.+++||++|++|||.||.++
T Consensus 1 m~~ek~~~~~~eqfvllak~~kg~al~~lIsqale~P~vf~F~ELl~l~nv~qlae~~dsa~lrlL~lFa~Gt~~Dy~ae 80 (258)
T KOG3250|consen 1 MDIEKKQAEIIEQFVLLAKTCKGEALEELISQALEAPGVFVFGELLILPNVVQLAEPIDSAYLRLLELFAYGTYRDYSAE 80 (258)
T ss_pred CCcchhhHHHHHHHHHHHhccchhHHHHHHHHHhcCCCeeeHHHHHhhhhHHHHcccccHHHHHHHHHHhcCchhhhhhh
Confidence 89999999999999999999999999999999999999999999999999999998889999999999999999999999
Q ss_pred hCCCCCcchHHHHHHHHHHhhhhccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeeccC
Q 027271 81 AGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGR 160 (225)
Q Consensus 81 ~~~~~~L~~~~~~Klr~LtLlsL~~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq~~~~v~V~~~~~R 160 (225)
+-.+|.|+.+++.||+.|+++++++..+.|+|..+.+.+...+..++|++|| +||+++++.|||||.+++++|.|+..|
T Consensus 81 a~rlp~Ls~~q~~kLk~ltV~slas~~k~lpy~~Ll~~l~~~nvrelEd~ii-eamya~IlrGkldqr~q~leV~faigR 159 (258)
T KOG3250|consen 81 ALRLPKLSLAQLNKLKHLTVVSLASFEKCLPYLVLLRLLPSRNVRELEDLII-EAMYADILRGKLDQRNQTLEVDFAIGR 159 (258)
T ss_pred hhcCCCCCHHHHHhhhcceehhhhhhchhhhHHHHHhhccCCchhHHHHHHH-HHHHHHHHHhhHHhhcceEeechhhcc
Confidence 9999999999999999999999999999999999999999999999999999 999999999999999999999999999
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhcccc
Q 027271 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSHK 223 (225)
Q Consensus 161 ~~~~~q~~~L~~~L~~W~~~v~~~l~~ie~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 223 (225)
++++.++.+|...|++|++.|.+++..|++++.+||++++...+++++.+..|+++||++|..
T Consensus 160 dlr~k~i~nm~~TL~~w~~~cenvL~~ie~qv~~anq~~e~~~r~~qq~e~ev~~~kKtlk~~ 222 (258)
T KOG3250|consen 160 DLRSKDIDNMKYTLDEWCEGCENVLFGIEAQVPRANQSKERASRMSQQDEIEVMNFKKTLKPT 222 (258)
T ss_pred cccHhHHHHHHHHHHHHHHHHHHHHHHHHhccchhhhHHHHHHhhhhhhhhhHHhhhcccCCC
Confidence 999999999999999999999999999999999999999999999999999999999999865
No 2
>KOG2908 consensus 26S proteasome regulatory complex, subunit RPN9/PSMD13 [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.6e-34 Score=255.87 Aligned_cols=182 Identities=18% Similarity=0.355 Sum_probs=166.1
Q ss_pred HHHHHHHHhc------cCccHHHHHHHHHHHhcCCCcccchhhhcCchhhhccCCCchHHHHHHHHHhcCChhhhhhh--
Q 027271 9 ELIDHFVKQA------SNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNN-- 80 (225)
Q Consensus 9 ~~l~~~l~~~------~~~~~~~a~~li~~aL~~p~iy~f~eLl~~p~v~~L~~~~~~~l~~LL~iF~~G~~~d~~~~-- 80 (225)
-....||... .+++.+.|..+..+||.+.++||||||+.||+..+|.||+++|++++|.+|+.||+..|++.
T Consensus 178 r~~L~YL~~~d~~~l~~se~~~lA~~L~~aALLGe~iyNfGELL~HPilesL~gT~~eWL~dll~Afn~Gdl~~f~~l~~ 257 (380)
T KOG2908|consen 178 RHALLYLGCSDIDDLSESEKQDLAFDLSLAALLGENIYNFGELLAHPILESLKGTNREWLKDLLIAFNSGDLKRFESLKG 257 (380)
T ss_pred HHHHHHhccccccccCHHHHHHHHHHHHHHHHhccccccHHHHHhhHHHHHhcCCcHHHHHHHHHHhccCCHHHHHHHHH
Confidence 3456788777 55567899999999999999999999999999999999999999999999999999999984
Q ss_pred -hCCCCCcchH---HHHHHHHHHhhhhc----cCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEE
Q 027271 81 -AGHLPQLVPD---QVLKLKQLTVLTLA----ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCF 152 (225)
Q Consensus 81 -~~~~~~L~~~---~~~Klr~LtLlsL~----~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq~~~~v 152 (225)
++..|.|.+. ..+|+++++|+.+| .+.|.+||++||++++|| .++||.+|| +|++.|||+|.|||++|+|
T Consensus 258 ~~~~~p~L~~~e~~L~qKI~LmaLiEi~F~rpa~~R~lsf~~Ia~~tkip-~~eVE~LVM-KAlslgLikG~Idqv~~~v 335 (380)
T KOG2908|consen 258 VWGKQPDLASNEDFLLQKIRLLALIEITFSRPANERTLSFKEIAEATKIP-NKEVELLVM-KALSLGLIKGSIDQVEGVV 335 (380)
T ss_pred HhccCchHHHHHHHHHHHHHHHHHHHHHhcCcchhccccHHHHHHHhCCC-HHHHHHHHH-HHHhccceeeeecccccEE
Confidence 3567777643 37899999999998 378999999999999998 999999999 9999999999999999999
Q ss_pred EEEeeccCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 027271 153 EVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQEKI 192 (225)
Q Consensus 153 ~V~~~~~R~~~~~q~~~L~~~L~~W~~~v~~~l~~ie~~~ 192 (225)
+++|++||.++.+|+..|+++++.|.+.++++...|+++-
T Consensus 336 ~~swvqPRvl~~~qI~~Mk~rl~~W~~~v~~me~~ve~~~ 375 (380)
T KOG2908|consen 336 YMSWVQPRVLDRSQIVKMKDRLDEWNKDVKSMEGLVEHRG 375 (380)
T ss_pred EEecccccccCHHHHHhHHHHHHHHHHHHHHHHHHHHHhc
Confidence 9999999999999999999999999999999999988754
No 3
>KOG2753 consensus Uncharacterized conserved protein, contains PCI domain [General function prediction only]
Probab=100.00 E-value=8e-35 Score=256.78 Aligned_cols=171 Identities=25% Similarity=0.494 Sum_probs=151.8
Q ss_pred HHHHHHHHHhccCcc----HHHHHHHHHHHhcCCCcccchhhhcCchhhhccCCCchHHHHHHHHHhcCChhhhhhh---
Q 027271 8 AELIDHFVKQASNQK----GAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNN--- 80 (225)
Q Consensus 8 ~~~l~~~l~~~~~~~----~~~a~~li~~aL~~p~iy~f~eLl~~p~v~~L~~~~~~~l~~LL~iF~~G~~~d~~~~--- 80 (225)
+..|-.||..+...+ -++|.+||+.|+.+|++|.|++|+.+|+|+.|+++ .+|+||.||..|.+++|..+
T Consensus 185 ~kvmt~lLgtyt~dnas~AredA~rcV~~av~dP~~F~fD~Ll~L~pV~qLE~d---~i~qLL~IF~s~~L~aYveF~~~ 261 (378)
T KOG2753|consen 185 SKVMTELLGTYTEDNASEAREDAMRCVVEAVKDPKIFLFDHLLTLPPVKQLEGD---LIHQLLKIFVSGKLDAYVEFVAA 261 (378)
T ss_pred HHHHHHHHHHhcccchhHHHHHHHHHHHHHHcCCceeccchhccCchHHHhccc---hHHHHHHHHHhcchHHHHHHHHh
Confidence 456777777776544 26799999999999999999999999999999886 48999999999999999974
Q ss_pred -hCCCCC--cc-hHHHHHHHHHHhhhhccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEe
Q 027271 81 -AGHLPQ--LV-PDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQF 156 (225)
Q Consensus 81 -~~~~~~--L~-~~~~~Klr~LtLlsL~~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq~~~~v~V~~ 156 (225)
++++.. +. +...+|||+||||+||..+.+|||++|++.|+|. .+|||.||| +||+.|+|.|||||.+++|.|++
T Consensus 262 N~~Fvqs~gl~~E~~~~KMRLLTlm~LA~es~eisy~~l~k~LqI~-edeVE~fVI-daI~aklV~~kidq~~~~viVs~ 339 (378)
T KOG2753|consen 262 NSGFVQSQGLVHEQNMAKMRLLTLMSLAEESNEISYDTLAKELQIN-EDEVELFVI-DAIRAKLVEGKIDQMNRTVIVSS 339 (378)
T ss_pred ChHHHHHhcccHHHHHHHHHHHHHHHHhccCCCCCHHHHHHHhccC-HHHHHHHHH-HHHHHHHHHhhHHhhcceEEeeh
Confidence 444443 33 5678999999999999999999999999999997 999999999 99999999999999999999999
Q ss_pred eccCCCCCCcHHHHHHHHHHHH-HHHHH
Q 027271 157 AAGRDLRPGQLGSMIQTLSNWL-TTSDN 183 (225)
Q Consensus 157 ~~~R~~~~~q~~~L~~~L~~W~-~~v~~ 183 (225)
+++|.||..||+.|+++|..|. +++.+
T Consensus 340 ~~hR~FG~~qW~~L~~kL~aw~k~~~st 367 (378)
T KOG2753|consen 340 STHRTFGKQQWQQLRDKLAAWGKQNLST 367 (378)
T ss_pred hhhhhcccHHHHHHHHHHHHHHhhhhHH
Confidence 9999999999999999999995 44333
No 4
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=99.56 E-value=1.2e-14 Score=108.68 Aligned_cols=95 Identities=19% Similarity=0.384 Sum_probs=80.6
Q ss_pred hHHHHHHHHHhcCChhhhhhhhCCC----------CCcchHHHHHHHHHHhhhhccCCcccChHHHHHHcCCCChHHHHH
Q 027271 60 SKYLDMLRLFAHGTWSDYKNNAGHL----------PQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELED 129 (225)
Q Consensus 60 ~~l~~LL~iF~~G~~~d~~~~~~~~----------~~L~~~~~~Klr~LtLlsL~~~~~~isy~~I~~~L~i~~~~evE~ 129 (225)
+|+.+|+++|..|++..|...-... ..+.+....+++..++..++..++.+++++|++.|+++ .++||.
T Consensus 1 ~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~~l~~~i~~~~l~~l~~~y~~i~~~~ia~~l~~~-~~~vE~ 79 (105)
T PF01399_consen 1 PPYSELLRAFRSGDLQEFEEFLEKHSESLFKDPFLAEYVEQLKEKIRRRNLRQLSKPYSSISISEIAKALQLS-EEEVES 79 (105)
T ss_dssp HHHHHHHHHHHCT-HHHHHHHHHHTCHHHHHCTTHHHHHHHHHHHHHHHHHHHHHHC-SEEEHHHHHHHHTCC-HHHHHH
T ss_pred CHHHHHHHHHHhCCHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHHHHHHHhcccchHHHHHHhccc-hHHHHH
Confidence 4789999999999999998732211 12335567899999999999999999999999999998 899999
Q ss_pred HHHHHhHhcCccEEEecCCCCEEEEEe
Q 027271 130 FLINECMYTGIVRGKLDQLRRCFEVQF 156 (225)
Q Consensus 130 lvI~~AI~~gLI~gkIDq~~~~v~V~~ 156 (225)
+++ +||..|.|.|+|||.+|+|+++|
T Consensus 80 ~l~-~~I~~~~i~~~ID~~~~~v~~~k 105 (105)
T PF01399_consen 80 ILI-DLISNGLIKAKIDQVNGVVVFSK 105 (105)
T ss_dssp HHH-HHHHTTSSEEEEETTTTEEEE-S
T ss_pred HHH-HHHHCCCEEEEEECCCCEEEecC
Confidence 999 99999999999999999999875
No 5
>smart00753 PAM PCI/PINT associated module.
Probab=99.55 E-value=1.5e-14 Score=106.06 Aligned_cols=86 Identities=22% Similarity=0.335 Sum_probs=80.1
Q ss_pred chHHHHHHHHHHhhhhccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeeccCCCCCCcH
Q 027271 88 VPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQL 167 (225)
Q Consensus 88 ~~~~~~Klr~LtLlsL~~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq~~~~v~V~~~~~R~~~~~q~ 167 (225)
.+...+++|.+++..++..+++|+|++|++.++++ .+++|.+|+ ++|..|.|.|+|||.+++|.+.+..+|. .++|
T Consensus 3 ~~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~-~~~vE~~i~-~~i~~~~l~~~ID~~~~~v~~~~~~~r~--~~~~ 78 (88)
T smart00753 3 VERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLS-VPEVEKLVS-KAIRDGEISAKIDQVNGIVEFEEVDPRR--SEPL 78 (88)
T ss_pred HHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcC-HHHHHHHHH-HHHHCCCeEEEEcCcCCEEEECCCchhh--hhHH
Confidence 34567899999999999999999999999999998 889999999 9999999999999999999999999997 7789
Q ss_pred HHHHHHHHHH
Q 027271 168 GSMIQTLSNW 177 (225)
Q Consensus 168 ~~L~~~L~~W 177 (225)
..+.+++..|
T Consensus 79 ~~~~~~l~~~ 88 (88)
T smart00753 79 AQFAETLKKL 88 (88)
T ss_pred HHHHHHhhcC
Confidence 9999998887
No 6
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=99.55 E-value=1.5e-14 Score=106.06 Aligned_cols=86 Identities=22% Similarity=0.335 Sum_probs=80.1
Q ss_pred chHHHHHHHHHHhhhhccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeeccCCCCCCcH
Q 027271 88 VPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQL 167 (225)
Q Consensus 88 ~~~~~~Klr~LtLlsL~~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq~~~~v~V~~~~~R~~~~~q~ 167 (225)
.+...+++|.+++..++..+++|+|++|++.++++ .+++|.+|+ ++|..|.|.|+|||.+++|.+.+..+|. .++|
T Consensus 3 ~~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~-~~~vE~~i~-~~i~~~~l~~~ID~~~~~v~~~~~~~r~--~~~~ 78 (88)
T smart00088 3 VERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLS-VPEVEKLVS-KAIRDGEISAKIDQVNGIVEFEEVDPRR--SEPL 78 (88)
T ss_pred HHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcC-HHHHHHHHH-HHHHCCCeEEEEcCcCCEEEECCCchhh--hhHH
Confidence 34567899999999999999999999999999998 889999999 9999999999999999999999999997 7789
Q ss_pred HHHHHHHHHH
Q 027271 168 GSMIQTLSNW 177 (225)
Q Consensus 168 ~~L~~~L~~W 177 (225)
..+.+++..|
T Consensus 79 ~~~~~~l~~~ 88 (88)
T smart00088 79 AQFAETLKKL 88 (88)
T ss_pred HHHHHHhhcC
Confidence 9999998887
No 7
>KOG1464 consensus COP9 signalosome, subunit CSN2 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=98.93 E-value=3e-09 Score=93.84 Aligned_cols=124 Identities=14% Similarity=0.355 Sum_probs=102.9
Q ss_pred hHHHHHHHHHhcCChhhhhh----hhCC------CCCcchHHHHHHHHHHhhhhccCCcccChHHHHHHcCCCChHHHHH
Q 027271 60 SKYLDMLRLFAHGTWSDYKN----NAGH------LPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELED 129 (225)
Q Consensus 60 ~~l~~LL~iF~~G~~~d~~~----~~~~------~~~L~~~~~~Klr~LtLlsL~~~~~~isy~~I~~~L~i~~~~evE~ 129 (225)
-.+.+|+..+...|+.+|+. +++. +....++.++++|...|+.|..++..|.+..|+++|+|+ ..+||.
T Consensus 305 lAMTnlv~aYQ~NdI~eFE~Il~~~~~~IM~DpFIReh~EdLl~niRTQVLlkLIkPYt~i~Ipfis~~Lnv~-~~dV~~ 383 (440)
T KOG1464|consen 305 LAMTNLVAAYQNNDIIEFERILKSNRSNIMDDPFIREHIEDLLRNIRTQVLLKLIKPYTNIGIPFISKELNVP-EADVES 383 (440)
T ss_pred HHHHHHHHHHhcccHHHHHHHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHhccccccCchhhHhhcCCC-HHHHHH
Confidence 35788999999999999997 3322 222347779999999999999999999999999999998 999999
Q ss_pred HHHHHhHhcCccEEEecCCCCEEEEEeeccCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHH
Q 027271 130 FLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQEK 191 (225)
Q Consensus 130 lvI~~AI~~gLI~gkIDq~~~~v~V~~~~~R~~~~~q~~~L~~~L~~W~~~v~~~l~~ie~~ 191 (225)
+++ +||-..-|+|+||++++.+....... .-..+.+.|+.|.++++.+.+.|-.+
T Consensus 384 LLV-~~ILD~~i~g~Ide~n~~l~~~~~~~------s~~k~~~al~kW~~ql~Sl~~~i~sr 438 (440)
T KOG1464|consen 384 LLV-SCILDDTIDGRIDEVNQYLELDKSKN------SGSKLYKALDKWNNQLKSLQSNIVSR 438 (440)
T ss_pred HHH-HHHhccccccchHHhhhHhccCccCC------cchHHHHHHHHHHHHHHHHHHHHHhh
Confidence 999 99999999999999999988753321 12237899999999999887766544
No 8
>KOG2581 consensus 26S proteasome regulatory complex, subunit RPN3/PSMD3 [Posttranslational modification, protein turnover, chaperones]
Probab=97.82 E-value=3e-05 Score=71.59 Aligned_cols=91 Identities=10% Similarity=0.346 Sum_probs=67.3
Q ss_pred hHHHHHHHHHhcCChhhhhhhhCCCCC-cch----HHHHHHHH------HHhhhhccCCcccChHHHHHHcCCCChHHHH
Q 027271 60 SKYLDMLRLFAHGTWSDYKNNAGHLPQ-LVP----DQVLKLKQ------LTVLTLAETNKVLPYDELMEELDVTNVRELE 128 (225)
Q Consensus 60 ~~l~~LL~iF~~G~~~d~~~~~~~~~~-L~~----~~~~Klr~------LtLlsL~~~~~~isy~~I~~~L~i~~~~evE 128 (225)
.+++.|=.....||++-|...-..+.. +-. ...-.||+ +..+|| .++.||+.+|+..|+|+|.+++|
T Consensus 319 ~~Yf~Lt~AVr~gdlkkF~~~leq~k~~f~~D~ty~LivRLR~NVIkTgIR~ISl--sYSRISl~DIA~kL~l~Seed~E 396 (493)
T KOG2581|consen 319 RPYFKLTQAVRLGDLKKFNETLEQFKDKFQADGTYTLIVRLRHNVIKTGIRKISL--SYSRISLQDIAKKLGLNSEEDAE 396 (493)
T ss_pred HHHHHHHHHHHHhhHHHHHHHHHHHHHHHhhCCcchHHHHHHHHHHHHhhhheee--eeeeccHHHHHHHhcCCCchhHH
Confidence 479999999999999999874332221 110 01122222 222333 57889999999999999888999
Q ss_pred HHHHHHhHhcCccEEEecCCCCEEE
Q 027271 129 DFLINECMYTGIVRGKLDQLRRCFE 153 (225)
Q Consensus 129 ~lvI~~AI~~gLI~gkIDq~~~~v~ 153 (225)
.+|= +||+.|+|+|+||..+|.+.
T Consensus 397 yiVa-kAIRDGvIea~Id~~~g~m~ 420 (493)
T KOG2581|consen 397 YIVA-KAIRDGVIEAKIDHEDGFMQ 420 (493)
T ss_pred HHHH-HHHHhccceeeeccccCcee
Confidence 9999 99999999999999998443
No 9
>KOG2758 consensus Translation initiation factor 3, subunit e (eIF-3e) [Translation, ribosomal structure and biogenesis]
Probab=97.37 E-value=0.0012 Score=59.72 Aligned_cols=100 Identities=17% Similarity=0.243 Sum_probs=79.5
Q ss_pred cchHHHHHHHHHHhhhhccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeeccCCCCCCc
Q 027271 87 LVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQ 166 (225)
Q Consensus 87 L~~~~~~Klr~LtLlsL~~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq~~~~v~V~~~~~R~~~~~q 166 (225)
+-++=+..-|++-+=+.|.-+.+|+.+-+|+.|+++ .++.|.|++ +.|+...+++|||..-|.|.+....+- -
T Consensus 327 ~l~~F~E~ARl~ifEtfCRIHqcIti~mLA~kLnm~-~eeaErwiv-nlIr~~rl~AkidSklg~Vvmg~~~~s-----~ 399 (432)
T KOG2758|consen 327 LLDEFLENARLLIFETFCRIHQCITIDMLADKLNMD-PEEAERWIV-NLIRTARLDAKIDSKLGHVVMGHPTVS-----P 399 (432)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHheeHHHHHHHhcCC-HHHHHHHHH-HHHHHhhhhhhhccccCceeecCCCCC-----H
Confidence 334446778899999999999999999999999997 999999999 999999999999999999988643322 2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 027271 167 LGSMIQTLSNWLTTSDNLLISIQEKIK 193 (225)
Q Consensus 167 ~~~L~~~L~~W~~~v~~~l~~ie~~~~ 193 (225)
-+.+.++.++..-+...+-..++.+++
T Consensus 400 ~qQ~ie~tksLS~rsq~la~~lek~~~ 426 (432)
T KOG2758|consen 400 HQQLIEKTKSLSFRSQNLAQQLEKKIQ 426 (432)
T ss_pred HHHHHHhccccchhHHHHHHHHHHHHH
Confidence 355666666666666666666665544
No 10
>KOG1497 consensus COP9 signalosome, subunit CSN4 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=97.00 E-value=0.0033 Score=56.83 Aligned_cols=151 Identities=11% Similarity=0.134 Sum_probs=95.1
Q ss_pred HHHHHHHHHhcCCCcccc-hhhhcCchhhhccCCCchHHHHH-----HHHHhcC-Chhhhhhhh-C----CCCCcchHHH
Q 027271 25 ALGSVIVEATSQPSLFAF-SEILAVPNIAEFEGTENSKYLDM-----LRLFAHG-TWSDYKNNA-G----HLPQLVPDQV 92 (225)
Q Consensus 25 ~a~~li~~aL~~p~iy~f-~eLl~~p~v~~L~~~~~~~l~~L-----L~iF~~G-~~~d~~~~~-~----~~~~L~~~~~ 92 (225)
.|..|.+-|.-+|.+-.| ..|...|.++.+. .|.+ |+-|..+ +.+.|...- + ..+.=+...-
T Consensus 227 ~a~~CtlLA~~gpqrsr~Latlfkder~~~l~------~y~ileKmyl~riI~k~el~ef~~~L~pHQka~~~dgssil~ 300 (399)
T KOG1497|consen 227 KALQCTLLASAGPQRSRMLATLFKDERCQKLP------AYGILEKMYLERIIRKEELQEFEAFLQPHQKAHTMDGSSILD 300 (399)
T ss_pred HhHhheeecCCChHHHHHHHHHhcCccccccc------chHHHHHHHHHHHhcchhHHHHHHHhcchhhhcccCcchhhh
Confidence 466677777777776654 3555566666553 2333 3444444 466666521 1 1111011111
Q ss_pred HHHHHHHhhhhccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeeccCCCCCCcHHHHHH
Q 027271 93 LKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQ 172 (225)
Q Consensus 93 ~Klr~LtLlsL~~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq~~~~v~V~~~~~R~~~~~q~~~L~~ 172 (225)
+-+.-..|+++.+-+..|||+++...|+|+ ...+|..+= +.|..|-+.|.|||.++.+++-- |. ...+|+ .
T Consensus 301 ra~~EhNlls~Skly~nisf~~Lg~ll~i~-~ekaekiaa-~MI~qeRmng~IDQ~egiihFe~---~e-~l~~wd---k 371 (399)
T KOG1497|consen 301 RAVIEHNLLSASKLYNNISFEELGALLKID-AEKAEKIAA-QMITQERMNGSIDQIEGIIHFED---RE-ELPQWD---K 371 (399)
T ss_pred hHHHHHhHHHHHHHHHhccHHHHHHHhCCC-HHHHHHHHH-HHHhHHHhccchHhhcceEeecc---hh-hhhhhh---H
Confidence 234445677777778889999999999997 999999999 99999999999999999999852 11 012343 3
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 027271 173 TLSNWLTTSDNLLISIQE 190 (225)
Q Consensus 173 ~L~~W~~~v~~~l~~ie~ 190 (225)
+....++.++++++.|..
T Consensus 372 qi~sl~~qvNki~~~i~~ 389 (399)
T KOG1497|consen 372 QIQSLCNQVNKILDKISH 389 (399)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 344445566666666554
No 11
>KOG0686 consensus COP9 signalosome, subunit CSN1 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=96.52 E-value=0.021 Score=53.10 Aligned_cols=109 Identities=15% Similarity=0.184 Sum_probs=80.7
Q ss_pred HHHHHHHHhcCChhhhhhh----hCCCC---Ccc---hHHHHHHHHHHhhhhccCCcccChHHHHHHcCCCChHHHHHHH
Q 027271 62 YLDMLRLFAHGTWSDYKNN----AGHLP---QLV---PDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFL 131 (225)
Q Consensus 62 l~~LL~iF~~G~~~d~~~~----~~~~~---~L~---~~~~~Klr~LtLlsL~~~~~~isy~~I~~~L~i~~~~evE~lv 131 (225)
+.++|.-|..+-++.-... ++.+. -|. .+...++|.=+++.--.++.++.++.+|.+.+.+ ...+|.=|
T Consensus 308 lr~il~~fy~sky~~cl~~L~~~k~~llLD~yLaphVd~Ly~~IR~r~llqy~~py~s~~m~~mA~af~~s-v~~le~~l 386 (466)
T KOG0686|consen 308 LREILFKFYSSKYASCLELLREIKPRLLLDMYLAPHVDNLYSLIRNRALLQYLSPYSSADMSKMAEAFNTS-VAILESEL 386 (466)
T ss_pred HHHHHHHHhhhhHHHHHHHHHHhccceeechhcchhHHHHHHHHHHhhHHHhcCccccchHHHHHHHhccc-HHHHHHHH
Confidence 5556666766666643331 11111 122 3456789999999999999999999999999996 99999999
Q ss_pred HHHhHhcCccEEEecCCCCEEEEEeeccCCCCCCcHHHHHH
Q 027271 132 INECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQ 172 (225)
Q Consensus 132 I~~AI~~gLI~gkIDq~~~~v~V~~~~~R~~~~~q~~~L~~ 172 (225)
. +.|-.|.|.||||+.++.+++.-...|.=+-++...|.+
T Consensus 387 ~-~LI~~~~i~~rIDs~~ki~~~~~~~~en~~fe~~~~~~~ 426 (466)
T KOG0686|consen 387 L-ELILEGKISGRIDSHNKILYARDADSENATFERVLPMGK 426 (466)
T ss_pred H-HHHHccchheeeccccceeeecccccccchhhhcchhhH
Confidence 9 999999999999999999999866665544444444433
No 12
>KOG1498 consensus 26S proteasome regulatory complex, subunit RPN5/PSMD12 [Posttranslational modification, protein turnover, chaperones]
Probab=96.13 E-value=0.056 Score=50.13 Aligned_cols=124 Identities=21% Similarity=0.302 Sum_probs=90.1
Q ss_pred chHHHHHHHHHhcCChhhhhhhh---------CCCCC---cchHHH--HHHHH--HHhhhhccCCcccChHHHHHHcCCC
Q 027271 59 NSKYLDMLRLFAHGTWSDYKNNA---------GHLPQ---LVPDQV--LKLKQ--LTVLTLAETNKVLPYDELMEELDVT 122 (225)
Q Consensus 59 ~~~l~~LL~iF~~G~~~d~~~~~---------~~~~~---L~~~~~--~Klr~--LtLlsL~~~~~~isy~~I~~~L~i~ 122 (225)
.+.+-.+|..|..|-+--|.... +.+.. ..+... -+.|. .-+-=.+.-++.|++..+++-++.|
T Consensus 287 ~p~~k~lLklfv~~EL~rw~s~~~~yg~~l~~~~~~~~~~~gek~~~dL~~RIiEHNiRiiA~yYSrIt~~rl~eLLdl~ 366 (439)
T KOG1498|consen 287 LPDYKELLKLFVTMELIRWVSLVESYGDELRTNDFFDGGEEGEKRWSDLKLRIIEHNIRIIAKYYSRITLKRLAELLDLP 366 (439)
T ss_pred CccHHHHHHHHHhcceeeehhHhhhhHHHHhhcccccccchhhhHHHHHHHHHHHHHHHHHHHHHhhccHHHHHHHhCCC
Confidence 44566799999998876555311 11111 111111 12332 4444445678899999999999998
Q ss_pred ChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeeccCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 027271 123 NVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKW 194 (225)
Q Consensus 123 ~~~evE~lvI~~AI~~gLI~gkIDq~~~~v~V~~~~~R~~~~~q~~~L~~~L~~W~~~v~~~l~~ie~~~~~ 194 (225)
.++.|.++= +.+..|-+.+|||...+.+.+..+ ..+.+.|..|..++++++..++.--+-
T Consensus 367 -~ee~E~~LS-~lv~t~ti~aKidrpsgII~F~k~----------K~~~~~LneW~~nve~L~~ll~K~~HL 426 (439)
T KOG1498|consen 367 -VEEMEKFLS-DLVVTGTIYAKIDRPSGIINFQKV----------KDSNEILNEWASNVEKLLGLLEKVSHL 426 (439)
T ss_pred -HHHHHHHHH-HHHhccceEEEecCCCceEEEEec----------ccHHHHHHHHHhhHHHHHHHHHHHHHH
Confidence 999999999 899999999999999999998754 347888999999999998888754433
No 13
>KOG2582 consensus COP9 signalosome, subunit CSN3 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=95.65 E-value=0.084 Score=48.64 Aligned_cols=105 Identities=11% Similarity=0.249 Sum_probs=78.3
Q ss_pred hHHHHHHHHHhcCChhhhhh----hhCCCC-----CcchHHHHHHHHHHhhhhccCCcccChHHHHHHcCCCChHHHHHH
Q 027271 60 SKYLDMLRLFAHGTWSDYKN----NAGHLP-----QLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDF 130 (225)
Q Consensus 60 ~~l~~LL~iF~~G~~~d~~~----~~~~~~-----~L~~~~~~Klr~LtLlsL~~~~~~isy~~I~~~L~i~~~~evE~l 130 (225)
.++.++++++..+...+... +++.+. .+....+.-+.+-+|..|.+...+++.++||+..++.+..|||..
T Consensus 259 ~pY~ef~~~Y~~~~~~eLr~lVk~~~~rF~kDnnt~l~k~av~sl~k~nI~rltktF~sLsL~dIA~~vQLa~~qevek~ 338 (422)
T KOG2582|consen 259 NPYHEFLNVYLKDSSTELRTLVKKHSERFTKDNNTGLAKQAVSSLYKKNIQRLTKTFLSLSLSDIASRVQLASAQEVEKY 338 (422)
T ss_pred chHHHHHHHHhcCCcHHHHHHHHHHHHHHhhcCcHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcchHHHHHH
Confidence 37899999999998886654 332221 122333445666677777788889999999997777778999999
Q ss_pred HHHHhHhcCccEEEecCCCCEEEEEeeccCCCCCCcHH
Q 027271 131 LINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLG 168 (225)
Q Consensus 131 vI~~AI~~gLI~gkIDq~~~~v~V~~~~~R~~~~~q~~ 168 (225)
|+ ..|..|=|-+.|| |.|..+.-...+.+++...
T Consensus 339 Il-qmie~~~i~a~iN---G~v~f~~n~e~~~SpeM~~ 372 (422)
T KOG2582|consen 339 IL-QMIEDGEIFASIN---GMVFFTDNPEKYNSPEMHE 372 (422)
T ss_pred HH-HHhccCceEEEec---ceEEEecCcccCCCHHHHh
Confidence 99 9999999999999 7777765555555655444
No 14
>COG5071 RPN5 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=95.06 E-value=0.17 Score=45.78 Aligned_cols=74 Identities=16% Similarity=0.267 Sum_probs=64.3
Q ss_pred cCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeeccCCCCCCcHHHHHHHHHHHHHHHHHH
Q 027271 105 ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNL 184 (225)
Q Consensus 105 ~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq~~~~v~V~~~~~R~~~~~q~~~L~~~L~~W~~~v~~~ 184 (225)
.-++.|+-..|..-++.| ..+.|.++= +.+..|.+-+||++..+.|.+... ++..+.|..|..++..+
T Consensus 349 ~yYSrI~~~rl~~lld~~-~s~te~~IS-dlVN~G~~yaKiNrpa~Ii~FEK~----------~n~~~~lneW~~NV~el 416 (439)
T COG5071 349 NYYSRIHCSRLGVLLDMS-PSETEQFIS-DLVNKGHFYAKINRPAQIISFEKS----------QNVQEQLNEWGSNVTEL 416 (439)
T ss_pred HHhhhhhHHHHHHHHcCC-HHHHHHHHH-HHHhcCcEEEEecCccceEEeecc----------ccHHHHHHHhcccHHHH
Confidence 457789999999999998 999999999 899999999999999999987532 23577899999999999
Q ss_pred HHHHHH
Q 027271 185 LISIQE 190 (225)
Q Consensus 185 l~~ie~ 190 (225)
+..++.
T Consensus 417 lgklek 422 (439)
T COG5071 417 LGKLEK 422 (439)
T ss_pred HHHHHH
Confidence 988875
No 15
>KOG2688 consensus Transcription-associated recombination protein - Thp1p [Cell cycle control, cell division, chromosome partitioning]
Probab=94.62 E-value=0.079 Score=49.27 Aligned_cols=97 Identities=14% Similarity=0.191 Sum_probs=69.8
Q ss_pred HHHHHHHHHhcCChhhhhhh----hCCCCCcchH-HHHHHHHHHhhhhc-------cCCcccChHHHHHHcCCCC-----
Q 027271 61 KYLDMLRLFAHGTWSDYKNN----AGHLPQLVPD-QVLKLKQLTVLTLA-------ETNKVLPYDELMEELDVTN----- 123 (225)
Q Consensus 61 ~l~~LL~iF~~G~~~d~~~~----~~~~~~L~~~-~~~Klr~LtLlsL~-------~~~~~isy~~I~~~L~i~~----- 123 (225)
.+..|+.....||+..|... ...+....-- .+.|+++++.=.|. .....+|++.+..+++..+
T Consensus 273 ~~~~lv~aVr~Gnl~~f~~al~~~E~~f~~~gi~l~l~~l~lv~yrnL~kkv~~~~~~~~~lpls~~~~al~~~~~~~~~ 352 (394)
T KOG2688|consen 273 KYSPLVQAVRSGNLRLFDLALADNERFFIRSGIYLTLEKLPLVVYRNLFKKVIQLWGKTSQLPLSRFLTALQFSGVTDVD 352 (394)
T ss_pred hHHHHHHHHHhccHHHHHHHHhhhHHHHHHhccHHHhhhhhHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHhhcCCCCCc
Confidence 56678999999999999852 2112111100 12234444444443 2567899999999987764
Q ss_pred hHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeec
Q 027271 124 VRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAA 158 (225)
Q Consensus 124 ~~evE~lvI~~AI~~gLI~gkIDq~~~~v~V~~~~ 158 (225)
.++||-.+. .+|+.|.|+|.|+...+++.++...
T Consensus 353 ~deveciLa-~lI~~G~ikgYish~~~~~V~sK~~ 386 (394)
T KOG2688|consen 353 LDEVECILA-NLIDLGRIKGYISHQLQTLVFSKKD 386 (394)
T ss_pred hhhHHHHHH-hhhhhccccchhchhhheEEEecCC
Confidence 689999999 9999999999999999999998643
No 16
>KOG0687 consensus 26S proteasome regulatory complex, subunit RPN7/PSMD6 [Posttranslational modification, protein turnover, chaperones]
Probab=93.73 E-value=1 Score=41.24 Aligned_cols=112 Identities=18% Similarity=0.289 Sum_probs=77.2
Q ss_pred hhhhcCchhhhccCCCchHHHHHHHHHhcCChhhhhhhh-----CCCC-C--cchHH---HHHHHHHHhhhhccCCcccC
Q 027271 43 SEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNNA-----GHLP-Q--LVPDQ---VLKLKQLTVLTLAETNKVLP 111 (225)
Q Consensus 43 ~eLl~~p~v~~L~~~~~~~l~~LL~iF~~G~~~d~~~~~-----~~~~-~--L~~~~---~~Klr~LtLlsL~~~~~~is 111 (225)
+-.+..|.|...-.. -+.+.+++.-+-.-+|++|-..- ..+. . +.+.- .+-||...--.+-+.+|.++
T Consensus 241 tKVi~~~Evl~vl~~-l~~~~q~l~SLY~C~Y~~Ff~~L~~~~~~~lk~D~~l~~h~~yyvREMR~rvY~QlLESYrsl~ 319 (393)
T KOG0687|consen 241 TKVIKCPEVLEVLHK-LPSVSQLLNSLYECDYSDFFNDLAAVEAKQLKDDRYLGPHYRYYVREMRRRVYAQLLESYRSLT 319 (393)
T ss_pred hhhcCcHHHHHHhhc-CchHHHHHHHHHhccHHHHHHHHHHHHHHhhccchhcchHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344555555442221 23455555555555666665421 1111 1 22321 56788888888889999999
Q ss_pred hHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEee
Q 027271 112 YDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFA 157 (225)
Q Consensus 112 y~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq~~~~v~V~~~ 157 (225)
.+.+|++.|++ .+-++.=+= +-|.+|-+.++||-++|+|.+++-
T Consensus 320 l~~MA~aFgVS-VefiDreL~-rFI~~grL~ckIDrVnGVVEtNrp 363 (393)
T KOG0687|consen 320 LESMAKAFGVS-VEFIDRELG-RFIAAGRLHCKIDRVNGVVETNRP 363 (393)
T ss_pred HHHHHHHhCch-HHHHHhHHH-HhhccCceeeeeecccceeecCCc
Confidence 99999999997 888887777 788899999999999999999854
No 17
>COG5600 Transcription-associated recombination protein [DNA replication, recombination, and repair]
Probab=92.94 E-value=0.24 Score=45.84 Aligned_cols=98 Identities=20% Similarity=0.321 Sum_probs=61.6
Q ss_pred hHHHHHHHHHhcCChhhhhhhh----CCCCC------cc---hH-HHHHHHHHHhhhhccCCcccChHHH--HHHcCCCC
Q 027271 60 SKYLDMLRLFAHGTWSDYKNNA----GHLPQ------LV---PD-QVLKLKQLTVLTLAETNKVLPYDEL--MEELDVTN 123 (225)
Q Consensus 60 ~~l~~LL~iF~~G~~~d~~~~~----~~~~~------L~---~~-~~~Klr~LtLlsL~~~~~~isy~~I--~~~L~i~~ 123 (225)
+.+.-|..+..+|++++|..-- ..+-+ +. +. ..+.+.. ....++-....+|++.+ +..+...+
T Consensus 289 s~~~~LvkavrsGni~~~~~~l~~ner~~~~~~l~ltl~~~~~~V~~RNL~r-k~w~~~~~qsrlp~sil~~~~qls~~d 367 (413)
T COG5600 289 SVYSPLVKAVRSGNIEDFDLALSRNERKFAKRGLYLTLLAHYPLVCFRNLFR-KIWRLHGKQSRLPLSILLIVLQLSAID 367 (413)
T ss_pred chhHHHHHHHHcCCHHHHHHHHHHhHHHHHHcchHHHHHhhccHHHHHHHHH-HHHhhccccccCcHHHHHHHHHccCCC
Confidence 3455688899999999998621 11110 00 00 1111111 22333334444555554 44454443
Q ss_pred ----hHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecc
Q 027271 124 ----VRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAG 159 (225)
Q Consensus 124 ----~~evE~lvI~~AI~~gLI~gkIDq~~~~v~V~~~~~ 159 (225)
.++||..++ .+|..|+++|.|-...++|.++...|
T Consensus 368 n~~~~~~VEciL~-tlI~~G~lrgYis~s~~~vV~sk~~p 406 (413)
T COG5600 368 NFHSFKEVECILV-TLIGLGLLRGYISHSRRTVVFSKKDP 406 (413)
T ss_pred cccChHHHHHHHH-HHHhhhhhhheecccceEEEEecCCC
Confidence 578999999 99999999999999999999987654
No 18
>KOG1463 consensus 26S proteasome regulatory complex, subunit RPN6/PSMD11 [Posttranslational modification, protein turnover, chaperones]
Probab=92.82 E-value=0.29 Score=44.90 Aligned_cols=101 Identities=16% Similarity=0.242 Sum_probs=75.6
Q ss_pred cCCCchHHHHHHHHHhcCChhhhhhhhCCCC-Ccc-----hHHHH----HHHHHHhhhhccCCcccChHHHHHHcCCCCh
Q 027271 55 EGTENSKYLDMLRLFAHGTWSDYKNNAGHLP-QLV-----PDQVL----KLKQLTVLTLAETNKVLPYDELMEELDVTNV 124 (225)
Q Consensus 55 ~~~~~~~l~~LL~iF~~G~~~d~~~~~~~~~-~L~-----~~~~~----Klr~LtLlsL~~~~~~isy~~I~~~L~i~~~ 124 (225)
.+..-..+...=+.|..-++.||+..-..++ +|. ..++. .|----|+.+.++.+.+..+-||+-+|++ .
T Consensus 281 ~g~~i~AmkavAeA~~nRSLkdF~~AL~~yk~eL~~D~ivr~Hl~~Lyd~lLEknl~riIEPyS~Vei~hIA~~IGl~-~ 359 (411)
T KOG1463|consen 281 AGRDIDAMKAVAEAFGNRSLKDFEKALADYKKELAEDPIVRSHLQSLYDNLLEKNLCRIIEPYSRVEISHIAEVIGLD-V 359 (411)
T ss_pred cCcchHHHHHHHHHhcCCcHHHHHHHHHHhHHHHhcChHHHHHHHHHHHHHHHHhHHHHcCchhhhhHHHHHHHHCCC-c
Confidence 3444456777888899999999987322111 222 22222 22224577778999999999999999997 9
Q ss_pred HHHHHHHHHHhHhcCccEEEecCCCCEEEEEee
Q 027271 125 RELEDFLINECMYTGIVRGKLDQLRRCFEVQFA 157 (225)
Q Consensus 125 ~evE~lvI~~AI~~gLI~gkIDq~~~~v~V~~~ 157 (225)
..||.=+= +.|-.+.+.|.+||.+|++.|.--
T Consensus 360 ~~VEkKLs-qMILDKkf~G~LDQg~g~Liv~~e 391 (411)
T KOG1463|consen 360 PQVEKKLS-QMILDKKFYGTLDQGEGCLIVFEE 391 (411)
T ss_pred HHHHHHHH-HHHHHHHhhcccccCCCeEEEeCC
Confidence 99999888 899999999999999999999643
No 19
>PF09756 DDRGK: DDRGK domain; InterPro: IPR019153 This is a family of proteins of approximately 300 residues. They contain a highly conserved DDRGK motif. The function is unknown. ; PDB: 1WI9_A.
Probab=92.74 E-value=0.18 Score=42.40 Aligned_cols=58 Identities=14% Similarity=0.251 Sum_probs=42.4
Q ss_pred HHHHhhhhccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEE
Q 027271 96 KQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ 155 (225)
Q Consensus 96 r~LtLlsL~~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq~~~~v~V~ 155 (225)
-+-.++..++..+.+..++||..+|+. ..++-+-|- +....|.|.|-||....-|+|+
T Consensus 100 lL~~Fi~yIK~~Kvv~ledla~~f~l~-t~~~i~ri~-~L~~~g~ltGv~DdrGkfIyIs 157 (188)
T PF09756_consen 100 LLQEFINYIKEHKVVNLEDLAAEFGLR-TQDVINRIQ-ELEAEGRLTGVIDDRGKFIYIS 157 (188)
T ss_dssp HHHHHHHHHHH-SEE-HHHHHHHH-S--HHHHHHHHH-HHHHHSSS-EEE-TT--EEE--
T ss_pred HHHHHHHHHHHcceeeHHHHHHHcCCC-HHHHHHHHH-HHHHCCCceeeEcCCCCeEEec
Confidence 345677788899999999999999997 888888888 8999999999999998888887
No 20
>KOG2072 consensus Translation initiation factor 3, subunit a (eIF-3a) [Translation, ribosomal structure and biogenesis]
Probab=92.62 E-value=5.1 Score=40.70 Aligned_cols=50 Identities=16% Similarity=0.219 Sum_probs=43.3
Q ss_pred cCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEE
Q 027271 105 ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ 155 (225)
Q Consensus 105 ~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq~~~~v~V~ 155 (225)
.-+.+|+|+.|.+-.-.=|.-++|.++| +|...+.+..+||...++|.+.
T Consensus 443 qiY~sIs~~~l~~La~F~~~~~lEk~~v-~a~k~~~v~iriDH~~~~v~Fg 492 (988)
T KOG2072|consen 443 QIYESISFERLYKLAPFFSAFELEKLLV-EAAKHNDVSIRIDHESNSVSFG 492 (988)
T ss_pred HHHHHHhHHHHHHHHhhcCHHHHHHHHH-HHHhccceeEEeccccceeeec
Confidence 4678899998877544445789999999 9999999999999999999997
No 21
>PF10075 PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro: IPR019280 The photomorphogenic 9 (COP9) signalosome or CSN complex is composed of eight subunits: Cops1/GPS1, Cops2, Cops3, Cops4, Cops5, Cop6, Cops7 (Cops7A or Cops7B) and Cops8. In the complex, Cops8, which is the smallest subunit, probably interacts directly with Cops3, Cops4 and Cops7 (Cops7A or Cops7B). This signalosome is homologous to the lid subcomplex of the 26S proteasome and regulates the ubiquitin-proteasome pathway. It functions as a structural scaffold for subunit-subunit interactions within the complex and is a key regulator of photomorphogenic development [].; PDB: 1RZ4_A.
Probab=91.79 E-value=1.1 Score=35.32 Aligned_cols=108 Identities=15% Similarity=0.187 Sum_probs=72.1
Q ss_pred HHHHHHHHHHhcCCCcccchhhhcCchhhhccC-CCchHHHHHHHHHhcCChhhhhhhhCCC---CC---cchHHHHHHH
Q 027271 24 AALGSVIVEATSQPSLFAFSEILAVPNIAEFEG-TENSKYLDMLRLFAHGTWSDYKNNAGHL---PQ---LVPDQVLKLK 96 (225)
Q Consensus 24 ~~a~~li~~aL~~p~iy~f~eLl~~p~v~~L~~-~~~~~l~~LL~iF~~G~~~d~~~~~~~~---~~---L~~~~~~Klr 96 (225)
.........+|..-..-+|.-+|..-+-..... .+-..+..|...+-.|++..|....... +. +.+.-..++|
T Consensus 5 ~~~~~~Ll~~L~~~~~~df~~~~~rip~~~~~~~~~i~~i~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~iR 84 (143)
T PF10075_consen 5 EIYALILLKYLMQNDLSDFRLLWKRIPEELKQSDPEIKAIWSLGQALWEGDYSKFWQALRSNPWSPDYKPFVPGFEDTIR 84 (143)
T ss_dssp HHHHHHHHHHHHTTTSTHHHHHHHTS-HHHHTS-TTHHHHHHHHHHHHTT-HHHHHHHS-TT----HHHHTSTTHHHHHH
T ss_pred hHHHHHHHHHHHcCCchHHHHHHHcCCHHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHhccchHHHHHHHHHHHHHHH
Confidence 444555566666666788888877443333332 3456678899999999999998732211 11 2234456788
Q ss_pred HHHhhhhccCCcccChHHHHHHcCCCChHHHHHHHH
Q 027271 97 QLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLI 132 (225)
Q Consensus 97 ~LtLlsL~~~~~~isy~~I~~~L~i~~~~evE~lvI 132 (225)
.-.+-.+...+..|+.+.+++-||++ .++++.++.
T Consensus 85 ~~i~~~i~~aY~sIs~~~la~~Lg~~-~~el~~~~~ 119 (143)
T PF10075_consen 85 ERIAHLISKAYSSISLSDLAEMLGLS-EEELEKFIK 119 (143)
T ss_dssp HHHHHHHHHH-SEE-HHHHHHHTTS--HHHHHHHHH
T ss_pred HHHHHHHHHHHhHcCHHHHHHHhCCC-HHHHHHHHH
Confidence 87777777889999999999999998 999999877
No 22
>COG5159 RPN6 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=89.34 E-value=0.85 Score=41.29 Aligned_cols=97 Identities=16% Similarity=0.250 Sum_probs=71.9
Q ss_pred chHHHHHHHHHhcCChhhhhhhhCC-CCCcc-----hHHHH----HHHHHHhhhhccCCcccChHHHHHHcCCCChHHHH
Q 027271 59 NSKYLDMLRLFAHGTWSDYKNNAGH-LPQLV-----PDQVL----KLKQLTVLTLAETNKVLPYDELMEELDVTNVRELE 128 (225)
Q Consensus 59 ~~~l~~LL~iF~~G~~~d~~~~~~~-~~~L~-----~~~~~----Klr~LtLlsL~~~~~~isy~~I~~~L~i~~~~evE 128 (225)
-..+...-+.|...++.||...-.+ -+++. -.+++ .|---.|+.+.++...+...-|++-+|++ ..+||
T Consensus 283 I~am~avaea~~NRsL~df~~aL~qY~~el~~D~~iRsHl~~LYD~LLe~Nl~kiiEPfs~VeishIa~viGld-t~qvE 361 (421)
T COG5159 283 IRAMLAVAEAFGNRSLKDFSDALAQYSDELHQDSFIRSHLQYLYDVLLEKNLVKIIEPFSVVEISHIADVIGLD-TNQVE 361 (421)
T ss_pred HHHHHHHHHHhCCCcHhhHHHHHHHhhHHhccCHHHHHHHHHHHHHHHHhhhhhhcCcceeeehhHHHHHhccc-HHHHH
Confidence 3456677788888889999873222 12222 11111 22223566677899999999999999996 99999
Q ss_pred HHHHHHhHhcCccEEEecCCCCEEEEEee
Q 027271 129 DFLINECMYTGIVRGKLDQLRRCFEVQFA 157 (225)
Q Consensus 129 ~lvI~~AI~~gLI~gkIDq~~~~v~V~~~ 157 (225)
-=+= +.|-.+++-|.+||.++++.|.--
T Consensus 362 gKLs-qMILDKifyG~LDqg~gcLivy~e 389 (421)
T COG5159 362 GKLS-QMILDKIFYGTLDQGDGCLIVYGE 389 (421)
T ss_pred HHHH-HHHHHHHHHhhhccCCceEEEeCC
Confidence 8888 889999999999999999999754
No 23
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=88.99 E-value=3.4 Score=32.63 Aligned_cols=80 Identities=19% Similarity=0.316 Sum_probs=58.9
Q ss_pred cCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecC--CCCEEEEEeeccCCCCCCcHH-HHHHHHHHHHHHH
Q 027271 105 ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQ--LRRCFEVQFAAGRDLRPGQLG-SMIQTLSNWLTTS 181 (225)
Q Consensus 105 ~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq--~~~~v~V~~~~~R~~~~~q~~-~L~~~L~~W~~~v 181 (225)
+.++..+-++||+.++++ ...|..-|= +.+..|+|.=.=.. ..|-.++. +..+++++. .+...|+.|.+++
T Consensus 38 ~~~~~~tvdelae~lnr~-rStv~rsl~-~L~~~GlV~Rek~~~~~Ggy~yiY----~~i~~ee~k~~i~~~l~~w~~~~ 111 (126)
T COG3355 38 EENGPLTVDELAEILNRS-RSTVYRSLQ-NLLEAGLVEREKVNLKGGGYYYLY----KPIDPEEIKKKILKDLDEWYDKM 111 (126)
T ss_pred hhcCCcCHHHHHHHHCcc-HHHHHHHHH-HHHHcCCeeeeeeccCCCceeEEE----ecCCHHHHHHHHHHHHHHHHHHH
Confidence 467799999999999996 889998888 99999998654333 22333333 233445555 3688999999999
Q ss_pred HHHHHHHHH
Q 027271 182 DNLLISIQE 190 (225)
Q Consensus 182 ~~~l~~ie~ 190 (225)
...+...+.
T Consensus 112 ~~~i~~~~~ 120 (126)
T COG3355 112 KQLIEEFEK 120 (126)
T ss_pred HHHHHHHhc
Confidence 988877653
No 24
>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=88.77 E-value=0.36 Score=33.56 Aligned_cols=47 Identities=15% Similarity=0.203 Sum_probs=35.7
Q ss_pred HhhhhccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecC
Q 027271 99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQ 147 (225)
Q Consensus 99 tLlsL~~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq 147 (225)
.|.+....++.+|+++||.+++++ .+.||.++= ..+..|-|+-.-+.
T Consensus 4 ~i~~~l~~~~~~S~~eLa~~~~~s-~~~ve~mL~-~l~~kG~I~~~~~~ 50 (69)
T PF09012_consen 4 EIRDYLRERGRVSLAELAREFGIS-PEAVEAMLE-QLIRKGYIRKVDMS 50 (69)
T ss_dssp HHHHHHHHS-SEEHHHHHHHTT---HHHHHHHHH-HHHCCTSCEEEEEE
T ss_pred HHHHHHHHcCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCcEEEecCC
Confidence 344555677899999999999997 999999988 89999999844433
No 25
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=87.16 E-value=1.8 Score=30.99 Aligned_cols=59 Identities=17% Similarity=0.219 Sum_probs=40.7
Q ss_pred HHHHHhhhhccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEe
Q 027271 95 LKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQF 156 (225)
Q Consensus 95 lr~LtLlsL~~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq~~~~v~V~~ 156 (225)
++.|..+.....++.++.++|++.++++ ...++..+= +....|+|+.. -..++-+...+
T Consensus 11 l~~l~~la~~~~~~~~s~~eiA~~~~i~-~~~l~kil~-~L~~~Gli~s~-~G~~GGy~L~~ 69 (83)
T PF02082_consen 11 LRILLYLARHPDGKPVSSKEIAERLGIS-PSYLRKILQ-KLKKAGLIESS-RGRGGGYRLAR 69 (83)
T ss_dssp HHHHHHHHCTTTSC-BEHHHHHHHHTS--HHHHHHHHH-HHHHTTSEEEE-TSTTSEEEESS
T ss_pred HHHHHHHHhCCCCCCCCHHHHHHHHCcC-HHHHHHHHH-HHhhCCeeEec-CCCCCceeecC
Confidence 3444444333444569999999999998 999999887 88899998665 34556665543
No 26
>KOG3054 consensus Uncharacterized conserved protein [Function unknown]
Probab=85.36 E-value=1.5 Score=38.37 Aligned_cols=55 Identities=18% Similarity=0.393 Sum_probs=45.2
Q ss_pred HhhhhccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEE
Q 027271 99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ 155 (225)
Q Consensus 99 tLlsL~~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq~~~~v~V~ 155 (225)
-++..++.+++++.++++.+.++. ..++=.-+= +.+..|++.|-||...+-|+|+
T Consensus 204 eFv~YIk~nKvV~ledLas~f~Lr-tqd~inriq-~~l~eg~ltGVmDDRGKfIYIS 258 (299)
T KOG3054|consen 204 EFVEYIKKNKVVPLEDLASEFGLR-TQDSINRIQ-ELLAEGLLTGVMDDRGKFIYIS 258 (299)
T ss_pred HHHHHHHhcCeeeHHHHHHHhCcc-HHHHHHHHH-HHHHhhhheeeecCCCceEEec
Confidence 355566889999999999999998 444444455 6777899999999999999997
No 27
>PHA01750 hypothetical protein
Probab=82.67 E-value=5.5 Score=27.92 Aligned_cols=38 Identities=21% Similarity=0.234 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhcc
Q 027271 184 LLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLS 221 (225)
Q Consensus 184 ~l~~ie~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 221 (225)
+-+.+.+++++...+.+....++++++++|.++|+.+-
T Consensus 36 vkeIV~~ELdNL~~ei~~~kikqDnl~~qv~eik~k~d 73 (75)
T PHA01750 36 VKEIVNSELDNLKTEIEELKIKQDELSRQVEEIKRKLD 73 (75)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhhc
Confidence 34456778899999998899999999999999998753
No 28
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=81.12 E-value=4.4 Score=31.73 Aligned_cols=47 Identities=15% Similarity=0.299 Sum_probs=36.2
Q ss_pred HHHHHhhhhccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE
Q 027271 95 LKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (225)
Q Consensus 95 lr~LtLlsL~~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~g 143 (225)
+|.|..+....+++.++-++|++.++|| ...++.++= ..-..|+|..
T Consensus 11 l~~l~~La~~~~~~~~s~~~ia~~~~ip-~~~l~kil~-~L~~~glv~s 57 (135)
T TIGR02010 11 VTAMLDLALNAETGPVTLADISERQGIS-LSYLEQLFA-KLRKAGLVKS 57 (135)
T ss_pred HHHHHHHHhCCCCCcCcHHHHHHHHCcC-HHHHHHHHH-HHHHCCceEE
Confidence 3333333333455689999999999998 999999888 8888999985
No 29
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=80.62 E-value=2.6 Score=33.71 Aligned_cols=47 Identities=21% Similarity=0.348 Sum_probs=37.6
Q ss_pred HhhhhccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE---EecC
Q 027271 99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG---KLDQ 147 (225)
Q Consensus 99 tLlsL~~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~g---kIDq 147 (225)
.|+.+-..+...||.+||+.+|++ ...|-.-+= +....|+|+| .+|.
T Consensus 13 ~Il~~Lq~d~R~s~~eiA~~lglS-~~tV~~Ri~-rL~~~GvI~~~~~~v~~ 62 (153)
T PRK11179 13 GILEALMENARTPYAELAKQFGVS-PGTIHVRVE-KMKQAGIITGTRVDVNP 62 (153)
T ss_pred HHHHHHHHcCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCeeeEEEEECH
Confidence 344444666899999999999997 899988877 8899999984 4565
No 30
>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=80.52 E-value=3.4 Score=26.18 Aligned_cols=42 Identities=19% Similarity=0.360 Sum_probs=30.6
Q ss_pred HhhhhccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 027271 99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (225)
Q Consensus 99 tLlsL~~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~ 142 (225)
.++.....+..+|..+||+.++++ ...|-..+= +....|+|+
T Consensus 7 ~Il~~l~~~~~~t~~ela~~~~is-~~tv~~~l~-~L~~~g~I~ 48 (48)
T PF13412_consen 7 KILNYLRENPRITQKELAEKLGIS-RSTVNRYLK-KLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHCTTS-HHHHHHHHTS--HHHHHHHHH-HHHHTTSEE
T ss_pred HHHHHHHHcCCCCHHHHHHHhCCC-HHHHHHHHH-HHHHCcCcC
Confidence 344444445569999999999997 888887766 888888875
No 31
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=78.23 E-value=20 Score=30.82 Aligned_cols=109 Identities=18% Similarity=0.263 Sum_probs=63.3
Q ss_pred Ch-HHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCC-----EEEEE--------------eeccCCCCCCcHHHH
Q 027271 111 PY-DELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRR-----CFEVQ--------------FAAGRDLRPGQLGSM 170 (225)
Q Consensus 111 sy-~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq~~~-----~v~V~--------------~~~~R~~~~~q~~~L 170 (225)
.| .+|++.+|++.-.-++.+=+ .-.+|||+.+++-+.+ ..+++ |+...+....+.+..
T Consensus 29 ~yvsEiS~~lgvsqkAVl~HL~~--LE~AGlveS~ie~~~Rg~~rKYY~Is~~~rleV~lsp~~f~~~~~~~~~~~l~~~ 106 (217)
T COG1777 29 CYVSEISRELGVSQKAVLKHLRI--LERAGLVESRIEKIPRGRPRKYYMISRNLRLEVTLSPNFFGAERFDLEEDDLESE 106 (217)
T ss_pred hHHHHHHhhcCcCHHHHHHHHHH--HHHcCCchhhccccccCCCcceeeccCCeEEEEEecCcccceeccCccccchhhh
Confidence 44 47899999984444577766 4679999999998877 33333 222233333323332
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhccc
Q 027271 171 IQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSH 222 (225)
Q Consensus 171 ~~~L~~W~~~v~~~l~~ie~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 222 (225)
+..+..-.. -..-+..+..+...+|...+.--+.+.+++....++.+++|.
T Consensus 107 r~~~~~~~~-s~~~~~~l~srl~~~~~~~e~l~~~~~~L~~~~~el~~rik~ 157 (217)
T COG1777 107 RSEVSKLFK-SPEGISELISRLLEINREIEELSRAQTELQKQLNELMDRIKE 157 (217)
T ss_pred hcchhhhcc-cchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 222211111 122244455566666766666677777777777777776664
No 32
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=78.14 E-value=9.1 Score=32.92 Aligned_cols=61 Identities=11% Similarity=0.151 Sum_probs=49.9
Q ss_pred HHHHHHHhhhhccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEE
Q 027271 93 LKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ 155 (225)
Q Consensus 93 ~Klr~LtLlsL~~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq~~~~v~V~ 155 (225)
.-|..+.++....+...+|..+|++.++++ ...+=..+- +.-..|+|.-..+...+.+.+|
T Consensus 5 ~~Lk~iallg~l~~~~~IS~~eLA~~L~iS-~~Tvsr~Lk-~LEe~GlI~R~~~~r~~~v~LT 65 (217)
T PRK14165 5 EALKKLALLGAVNNTVKISSSEFANHTGTS-SKTAARILK-QLEDEGYITRTIVPRGQLITIT 65 (217)
T ss_pred HHHHHHHHHhccCCCCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEEEEcCCceEEEEC
Confidence 346666777766777789999999999997 888888877 8888999999999877666665
No 33
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=78.05 E-value=4.5 Score=29.95 Aligned_cols=37 Identities=11% Similarity=0.308 Sum_probs=31.6
Q ss_pred cCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE
Q 027271 105 ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (225)
Q Consensus 105 ~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~g 143 (225)
..+..+|+.+|++.++++ ...+-..+- .....|+|.+
T Consensus 13 ~~~~~~~~~~la~~l~~s-~~tv~~~l~-~L~~~g~i~~ 49 (108)
T smart00344 13 QKDARISLAELAKKVGLS-PSTVHNRVK-RLEEEGVIKG 49 (108)
T ss_pred HHhCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCeec
Confidence 444579999999999997 889988888 8888999884
No 34
>COG5187 RPN7 26S proteasome regulatory complex component, contains PCI domain [Posttranslational modification, protein turnover, chaperones]
Probab=77.76 E-value=32 Score=31.46 Aligned_cols=64 Identities=17% Similarity=0.265 Sum_probs=55.0
Q ss_pred HHHHHHHHhhhhccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEee
Q 027271 92 VLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFA 157 (225)
Q Consensus 92 ~~Klr~LtLlsL~~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq~~~~v~V~~~ 157 (225)
.+-||.-.-..|-+.++.++.+.+|+..|++ .+-|+.=+= +-|-.|-+.+.||-++|+|..++-
T Consensus 314 vREMRrrvYaQlLESYr~lsl~sMA~tFgVS-V~yvdrDLg-~FIp~~~LncvIDRvnGvVetnrp 377 (412)
T COG5187 314 VREMRRRVYAQLLESYRLLSLESMAQTFGVS-VEYVDRDLG-EFIPEGRLNCVIDRVNGVVETNRP 377 (412)
T ss_pred HHHHHHHHHHHHHHHHHHhhHHHHHHHhCcc-HHHHhhhHH-hhCCCCceeeeeecccceEeccCc
Confidence 4667777777777899999999999999996 888887777 778889999999999999998854
No 35
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=76.56 E-value=6.5 Score=32.16 Aligned_cols=48 Identities=15% Similarity=0.280 Sum_probs=38.2
Q ss_pred HHHHHhhhhccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEE
Q 027271 95 LKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (225)
Q Consensus 95 lr~LtLlsL~~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gk 144 (225)
+|.+..+....+++.++-++|++.+++| ..-++..+- ..-..|||...
T Consensus 11 l~~l~~lA~~~~~~~vs~~eIA~~~~ip-~~~l~kIl~-~L~~aGLv~s~ 58 (164)
T PRK10857 11 VTAMLDVALNSEAGPVPLADISERQGIS-LSYLEQLFS-RLRKNGLVSSV 58 (164)
T ss_pred HHHHHHHHhCCCCCcCcHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEeC
Confidence 4444444444556789999999999998 999999988 88999999973
No 36
>TIGR01410 tatB twin arginine-targeting protein translocase TatB. This model represents the TatB protein of a Sec-independent system for transporting folded proteins, often with a bound redox cofactor, across the bacterial inner membrane. TatC is the multiple membrane spanning component. TatB, like the related TatA/E proteins, appears to span the membrane one time. The tat system recognizes proteins with an elongated signal sequence containing a conserved R-R in a motif approximated by RRxFLK N-terminal to the transmembrane helix. TIGRFAMs model TIGR01409 describes this twin-Arg signal sequence. A similar system, termed Delta-pH-dependent transport, operates on chloroplast-encoded proteins.
Probab=76.17 E-value=11 Score=27.23 Aligned_cols=38 Identities=11% Similarity=0.200 Sum_probs=31.7
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 027271 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSM 198 (225)
Q Consensus 161 ~~~~~q~~~L~~~L~~W~~~v~~~l~~ie~~~~~~~~~ 198 (225)
.|+|+.++.+...+..|..++......+++.+...-..
T Consensus 18 v~GP~kLP~~~r~~G~~i~~~r~~~~~~~~~~~~e~~~ 55 (80)
T TIGR01410 18 VLGPERLPVAIRAVGKFVRRLRGMASDVKNELDEELKA 55 (80)
T ss_pred eECchHHHHHHHHHHHHHHHHHHhhHhHHHHHHHHhch
Confidence 46899999999999999999999888888877654443
No 37
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=76.17 E-value=5.3 Score=32.32 Aligned_cols=43 Identities=12% Similarity=0.179 Sum_probs=35.6
Q ss_pred HhhhhccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE
Q 027271 99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (225)
Q Consensus 99 tLlsL~~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~g 143 (225)
.|+.+-..+..+||.+||+.+|++ ...|-.-+= +....|+|+|
T Consensus 18 ~IL~~Lq~d~R~s~~eiA~~lglS-~~tv~~Ri~-rL~~~GvI~~ 60 (164)
T PRK11169 18 NILNELQKDGRISNVELSKRVGLS-PTPCLERVR-RLERQGFIQG 60 (164)
T ss_pred HHHHHhccCCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCeEE
Confidence 445555778899999999999997 888887777 8888999975
No 38
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=75.52 E-value=4.4 Score=31.83 Aligned_cols=42 Identities=17% Similarity=0.270 Sum_probs=33.5
Q ss_pred hhhccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEE
Q 027271 101 LTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (225)
Q Consensus 101 lsL~~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gk 144 (225)
+.+-+.+..+||.+|++.+|++ ...|=.-+= +....|+|+|-
T Consensus 14 L~~L~~d~r~~~~eia~~lglS-~~~v~~Ri~-~L~~~GiI~~~ 55 (154)
T COG1522 14 LRLLQEDARISNAELAERVGLS-PSTVLRRIK-RLEEEGVIKGY 55 (154)
T ss_pred HHHHHHhCCCCHHHHHHHHCCC-HHHHHHHHH-HHHHCCceeeE
Confidence 3333445559999999999997 888887777 88889999875
No 39
>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=75.36 E-value=6.6 Score=25.42 Aligned_cols=45 Identities=20% Similarity=0.306 Sum_probs=33.4
Q ss_pred HHHHhhhhc-cCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 027271 96 KQLTVLTLA-ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (225)
Q Consensus 96 r~LtLlsL~-~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~ 142 (225)
|-+.++... .....++..+|++.+++| ...+-.++- .....|+++
T Consensus 4 ral~iL~~l~~~~~~~t~~eia~~~gl~-~stv~r~L~-tL~~~g~v~ 49 (52)
T PF09339_consen 4 RALRILEALAESGGPLTLSEIARALGLP-KSTVHRLLQ-TLVEEGYVE 49 (52)
T ss_dssp HHHHHHHCHHCTBSCEEHHHHHHHHTS--HHHHHHHHH-HHHHTTSEE
T ss_pred HHHHHHHHHHcCCCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCcCee
Confidence 445666654 445558999999999998 888888877 777777764
No 40
>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=74.97 E-value=5.7 Score=27.48 Aligned_cols=37 Identities=19% Similarity=0.240 Sum_probs=28.7
Q ss_pred cCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 027271 105 ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (225)
Q Consensus 105 ~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~ 142 (225)
..+..-|+.+|++.+|+.|...|-..|- ..-..|+|+
T Consensus 21 ~~G~~Pt~rEIa~~~g~~S~~tv~~~L~-~Le~kG~I~ 57 (65)
T PF01726_consen 21 ENGYPPTVREIAEALGLKSTSTVQRHLK-ALERKGYIR 57 (65)
T ss_dssp HHSS---HHHHHHHHTSSSHHHHHHHHH-HHHHTTSEE
T ss_pred HcCCCCCHHHHHHHhCCCChHHHHHHHH-HHHHCcCcc
Confidence 4667789999999999998999998887 777778775
No 41
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=74.45 E-value=12 Score=28.68 Aligned_cols=49 Identities=22% Similarity=0.269 Sum_probs=38.0
Q ss_pred HHHHHHhhhhccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEE
Q 027271 94 KLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (225)
Q Consensus 94 Klr~LtLlsL~~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gk 144 (225)
-++.+..+....+...++..+|++.+++| ...|...+= .....|+|...
T Consensus 10 al~~l~~la~~~~~~~~s~~eia~~~~i~-~~~v~~il~-~L~~~gli~~~ 58 (132)
T TIGR00738 10 ALRALLDLALNPDEGPVSVKEIAERQGIS-RSYLEKILR-TLRRAGLVESV 58 (132)
T ss_pred HHHHHHHHHhCCCCCcCcHHHHHHHHCcC-HHHHHHHHH-HHHHCCcEEec
Confidence 35555555543345589999999999998 999999888 88889998753
No 42
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=74.15 E-value=7.2 Score=27.69 Aligned_cols=46 Identities=24% Similarity=0.232 Sum_probs=36.2
Q ss_pred HHHHhhhhccCC-cccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE
Q 027271 96 KQLTVLTLAETN-KVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (225)
Q Consensus 96 r~LtLlsL~~~~-~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~g 143 (225)
|.+.++.+.... +.++..+|++.++++ ...|-..+- .....|+|..
T Consensus 6 r~~~Il~~l~~~~~~~t~~~ia~~l~i~-~~tv~r~l~-~L~~~g~l~~ 52 (91)
T smart00346 6 RGLAVLRALAEEPGGLTLAELAERLGLS-KSTAHRLLN-TLQELGYVEQ 52 (91)
T ss_pred HHHHHHHHHHhCCCCcCHHHHHHHhCCC-HHHHHHHHH-HHHHCCCeee
Confidence 345556555433 689999999999998 889988887 7788999976
No 43
>PRK01919 tatB sec-independent translocase; Provisional
Probab=73.27 E-value=19 Score=29.80 Aligned_cols=59 Identities=10% Similarity=0.263 Sum_probs=39.3
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhc
Q 027271 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSL 220 (225)
Q Consensus 161 ~~~~~q~~~L~~~L~~W~~~v~~~l~~ie~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 220 (225)
.|+++.++.+...+..|..++......+.+.+..--+. .+..+.+++++....+++.++
T Consensus 19 V~GPekLP~~aRtlGk~i~k~Rr~~~d~K~ev~~E~e~-dElrk~~~~~e~~~~~v~~si 77 (169)
T PRK01919 19 VIGPERLPRVARTAGALFGRAQRYINDVKAEVSREIEL-DELRKMKTDFESAARDVENTI 77 (169)
T ss_pred eeCchHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH-HHHHHHHHHHHHHHHHHHHHH
Confidence 47899999999999999999999988888777644322 222233344444444444443
No 44
>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=72.93 E-value=41 Score=28.11 Aligned_cols=71 Identities=14% Similarity=0.095 Sum_probs=42.2
Q ss_pred ccChHHH----HHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeeccCCCCCCcHHHHHHHHHHHHHHHHHH
Q 027271 109 VLPYDEL----MEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNL 184 (225)
Q Consensus 109 ~isy~~I----~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq~~~~v~V~~~~~R~~~~~q~~~L~~~L~~W~~~v~~~ 184 (225)
..+..+| .+.+||. ...|.++|- ..+..|+|.. ..=|+-.+.|+-|- +....+...+......+..+
T Consensus 11 ~y~lKELEK~~pK~~gI~-~~~VKdvlq-~LvDDglV~~---EKiGssn~YWsFps----~~~~~~~~~~~~l~~~~~~~ 81 (188)
T PF03962_consen 11 FYTLKELEKLAPKEKGIV-SMSVKDVLQ-SLVDDGLVHV---EKIGSSNYYWSFPS----QAKQKRQNKLEKLQKEIEEL 81 (188)
T ss_pred cccHHHHHHHcccccCCc-hhhHHHHHH-HHhccccchh---hhccCeeEEEecCh----HHHHHHHHHHHHHHHHHHHH
Confidence 4455554 3448997 889999888 7777666643 13367777887553 34444555555555444444
Q ss_pred HHHH
Q 027271 185 LISI 188 (225)
Q Consensus 185 l~~i 188 (225)
...+
T Consensus 82 ~~~i 85 (188)
T PF03962_consen 82 EKKI 85 (188)
T ss_pred HHHH
Confidence 3333
No 45
>PRK04654 sec-independent translocase; Provisional
Probab=72.78 E-value=22 Score=30.51 Aligned_cols=35 Identities=14% Similarity=0.241 Sum_probs=29.1
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 027271 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWA 195 (225)
Q Consensus 161 ~~~~~q~~~L~~~L~~W~~~v~~~l~~ie~~~~~~ 195 (225)
.|+++++..+...+..|..++++....+.+.+.+-
T Consensus 19 V~GPerLPe~aRtlGk~irk~R~~~~~vk~El~~E 53 (214)
T PRK04654 19 VLGPERLPKAARFAGLWVRRARMQWDSVKQELERE 53 (214)
T ss_pred hcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 47899999999999999999888877777666543
No 46
>PF07389 DUF1500: Protein of unknown function (DUF1500); InterPro: IPR009974 This family consists of several Orthopoxvirus specific proteins, which include Vaccinia virus, B6 protein, they are around 100 residues in length. The function of this family is unknown.
Probab=72.14 E-value=7 Score=28.98 Aligned_cols=40 Identities=15% Similarity=0.387 Sum_probs=29.6
Q ss_pred HHHhhhhccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcC
Q 027271 97 QLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTG 139 (225)
Q Consensus 97 ~LtLlsL~~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~g 139 (225)
...+..+.+.-..++|++|-+. +|+.+.||+||| +.+..+
T Consensus 36 lhNIyrlftr~~vi~Fd~iVr~--mpNes~v~qWV~-dtln~i 75 (100)
T PF07389_consen 36 LHNIYRLFTRCAVIPFDDIVRT--MPNESRVKQWVI-DTLNDI 75 (100)
T ss_pred HHHHHHHHHhhccccHHHHHHh--CCCHHHHHHHHH-HHHHhH
Confidence 3344455555567899999998 677899999999 876433
No 47
>PRK04098 sec-independent translocase; Provisional
Probab=71.36 E-value=31 Score=28.30 Aligned_cols=58 Identities=19% Similarity=0.279 Sum_probs=40.1
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---hhhHHHHHHHHHHHHHHHHHHH
Q 027271 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWAD---SMNEMDKKHRKDLEEKVEEAKK 218 (225)
Q Consensus 161 ~~~~~q~~~L~~~L~~W~~~v~~~l~~ie~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~ 218 (225)
.||++.++.+...+..|...+......+...+...- .-+++...-++.++...+++++
T Consensus 19 vfGP~KLP~~~r~lGk~ir~~K~~~~~~k~~l~~Ei~~~elk~e~~k~k~~l~~~~~~l~~ 79 (158)
T PRK04098 19 FLGPDKLPQAMVDIAKFFKAVKKTINDAKSTLDKEINIEEIKEEALKYKKEFESAVESLKK 79 (158)
T ss_pred hcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHh
Confidence 478999999999999999988888877766555332 2222223345666777777766
No 48
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=71.06 E-value=12 Score=30.14 Aligned_cols=51 Identities=22% Similarity=0.269 Sum_probs=38.6
Q ss_pred HHHHHhhhhccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecC
Q 027271 95 LKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQ 147 (225)
Q Consensus 95 lr~LtLlsL~~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq 147 (225)
++.|..++.-..++.++-++||+..+|| ..-++.++- ..-.+|||+..=-.
T Consensus 11 l~~L~~LA~~~~~~~~s~~~IA~~~~is-~~~L~kil~-~L~kaGlV~S~rG~ 61 (150)
T COG1959 11 LRALLYLALLPGGGPVSSAEIAERQGIS-PSYLEKILS-KLRKAGLVKSVRGK 61 (150)
T ss_pred HHHHHHHHhCCCCCcccHHHHHHHhCcC-HHHHHHHHH-HHHHcCCEEeecCC
Confidence 3334444443455588999999999998 999999998 89999999876443
No 49
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=68.74 E-value=36 Score=26.40 Aligned_cols=57 Identities=9% Similarity=-0.013 Sum_probs=42.8
Q ss_pred hhhhccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeec
Q 027271 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAA 158 (225)
Q Consensus 100 LlsL~~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq~~~~v~V~~~~ 158 (225)
|..+...+..++-.+|++.++++ ...|=..|= .....|+|.-.-|+.++....-..+
T Consensus 37 L~~l~~~~~~~t~~eLa~~l~~~-~~tvt~~v~-~Le~~GlV~r~~~~~DrR~~~l~LT 93 (144)
T PRK03573 37 LHNIHQLPPEQSQIQLAKAIGIE-QPSLVRTLD-QLEEKGLISRQTCASDRRAKRIKLT 93 (144)
T ss_pred HHHHHHcCCCCCHHHHHHHhCCC-hhhHHHHHH-HHHHCCCEeeecCCCCcCeeeeEEC
Confidence 33444333457789999999997 777777776 8889999999999887776655544
No 50
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=67.76 E-value=11 Score=29.13 Aligned_cols=46 Identities=13% Similarity=0.120 Sum_probs=33.8
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEE
Q 027271 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEV 154 (225)
Q Consensus 107 ~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq~~~~v~V 154 (225)
+...+..+|++.++++ ...|-.-+= ..-.+|||..+-+.......+
T Consensus 28 ~~~~~v~ela~~l~ls-qstvS~HL~-~L~~AGLV~~~r~Gr~~~Y~l 73 (117)
T PRK10141 28 SGELCVCDLCTALDQS-QPKISRHLA-LLRESGLLLDRKQGKWVHYRL 73 (117)
T ss_pred cCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCceEEEEEcCEEEEEE
Confidence 3468899999999997 777765544 456699999998865544433
No 51
>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=67.59 E-value=64 Score=26.05 Aligned_cols=109 Identities=17% Similarity=0.205 Sum_probs=64.9
Q ss_pred cCCcccChHHHHHHcC--CCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeeccCC---CCCCcHHHHHHHHHHHHH
Q 027271 105 ETNKVLPYDELMEELD--VTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRD---LRPGQLGSMIQTLSNWLT 179 (225)
Q Consensus 105 ~~~~~isy~~I~~~L~--i~~~~evE~lvI~~AI~~gLI~gkIDq~~~~v~V~~~~~R~---~~~~q~~~L~~~L~~W~~ 179 (225)
..+|+.+..+|...|+ ++ -..|...+= .+...|.|.+|.=. .-.|.++.... .++++...|...+....+
T Consensus 12 ~qNRPys~~di~~nL~~~~~-K~~v~k~Ld-~L~~~g~i~~K~~G---KqkiY~~~Q~~~~~~s~eel~~ld~ei~~L~~ 86 (169)
T PF07106_consen 12 EQNRPYSAQDIFDNLHNKVG-KTAVQKALD-SLVEEGKIVEKEYG---KQKIYFANQDELEVPSPEELAELDAEIKELRE 86 (169)
T ss_pred HcCCCCcHHHHHHHHHhhcc-HHHHHHHHH-HHHhCCCeeeeeec---ceEEEeeCccccCCCCchhHHHHHHHHHHHHH
Confidence 5789999999999995 54 456666555 66678999999643 33444443333 457777777777777766
Q ss_pred HHHHHHHHH---HHHHHHHHh---------hhHHHHHHHHHHHHHHHHHHH
Q 027271 180 TSDNLLISI---QEKIKWADS---------MNEMDKKHRKDLEEKVEEAKK 218 (225)
Q Consensus 180 ~v~~~l~~i---e~~~~~~~~---------~~~~~~~~~~~~~~~~~~~~~ 218 (225)
.+..+-..+ +.++...+. ...+....-..++++++..+.
T Consensus 87 el~~l~~~~k~l~~eL~~L~~~~t~~el~~~i~~l~~e~~~l~~kL~~l~~ 137 (169)
T PF07106_consen 87 ELAELKKEVKSLEAELASLSSEPTNEELREEIEELEEEIEELEEKLEKLRS 137 (169)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 655544433 334443333 333334444445555555443
No 52
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=67.56 E-value=10 Score=26.22 Aligned_cols=33 Identities=18% Similarity=0.150 Sum_probs=29.9
Q ss_pred ccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE
Q 027271 109 VLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (225)
Q Consensus 109 ~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~g 143 (225)
.++-.+|++.|||+ ...|-..+- .....|+|.-
T Consensus 22 ~~ta~eLa~~lgl~-~~~v~r~L~-~L~~~G~V~~ 54 (68)
T smart00550 22 TSTALQLAKNLGLP-KKEVNRVLY-SLEKKGKVCK 54 (68)
T ss_pred CcCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEEe
Confidence 49999999999998 889999999 8999999865
No 53
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=67.18 E-value=15 Score=28.32 Aligned_cols=47 Identities=21% Similarity=0.267 Sum_probs=36.2
Q ss_pred HHHHHhhhhccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEE
Q 027271 95 LKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (225)
Q Consensus 95 lr~LtLlsL~~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gk 144 (225)
++.|..+.- .++..++..+|++.++++ ..-|...+= .....|+|.+.
T Consensus 12 l~~l~~la~-~~~~~~s~~eia~~l~is-~~~v~~~l~-~L~~~Gli~~~ 58 (130)
T TIGR02944 12 TLVLTTLAQ-NDSQPYSAAEIAEQTGLN-APTVSKILK-QLSLAGIVTSK 58 (130)
T ss_pred HHHHHHHHh-CCCCCccHHHHHHHHCcC-HHHHHHHHH-HHHHCCcEEec
Confidence 344334432 245679999999999998 999999888 88899999874
No 54
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=66.64 E-value=15 Score=29.48 Aligned_cols=49 Identities=16% Similarity=0.133 Sum_probs=37.1
Q ss_pred HHHHHhhhhccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEec
Q 027271 95 LKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLD 146 (225)
Q Consensus 95 lr~LtLlsL~~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkID 146 (225)
+|.|..++. .+++.++-.+||+..+|| ..-++.++- ..-.+|+|+..=-
T Consensus 11 lr~L~~LA~-~~~~~~s~~eIA~~~~is-~~~L~kIl~-~L~~aGlv~S~rG 59 (153)
T PRK11920 11 IRMLMYCAA-NDGKLSRIPEIARAYGVS-ELFLFKILQ-PLVEAGLVETVRG 59 (153)
T ss_pred HHHHHHHHh-CCCCcCcHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEeecC
Confidence 444444442 344568999999999998 999999988 8888999887653
No 55
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=66.10 E-value=16 Score=28.65 Aligned_cols=51 Identities=14% Similarity=0.194 Sum_probs=38.4
Q ss_pred HHHHHhhhhccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecC
Q 027271 95 LKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQ 147 (225)
Q Consensus 95 lr~LtLlsL~~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq 147 (225)
+|.+..+.-..++..++-++|++.++|| ..-|+..+- ..-..|+|+.+=--
T Consensus 11 l~~~i~la~~~~g~~~s~~~ia~~~~is-~~~vrk~l~-~L~~~Glv~s~~G~ 61 (141)
T PRK11014 11 LRALIYMASLPEGRMTSISEVTEVYGVS-RNHMVKIIN-QLSRAGYVTAVRGK 61 (141)
T ss_pred HHHHHHHhcCCCCCccCHHHHHHHHCcC-HHHHHHHHH-HHHhCCEEEEecCC
Confidence 4444444444566788999999999997 889999888 88888988765443
No 56
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=65.97 E-value=49 Score=30.88 Aligned_cols=79 Identities=22% Similarity=0.324 Sum_probs=52.3
Q ss_pred cCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeeccCCCCCCcHHHHHHHH---------H
Q 027271 105 ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTL---------S 175 (225)
Q Consensus 105 ~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq~~~~v~V~~~~~R~~~~~q~~~L~~~L---------~ 175 (225)
..++.++.++|++.+++| .+.+++++= +....|+|. +-++ + .|+..||.+.=....+.+.+ .
T Consensus 306 ~~g~~~t~~~La~~l~~~-~~~v~~iL~-~L~~agLI~-~~~~--g----~~~l~rd~~~itL~dv~~~~~~~~~~~~~~ 376 (412)
T PRK04214 306 KHGKALDVDEIRRLEPMG-YDELGELLC-ELARIGLLR-RGER--G----QWVLARDLDSVPLAELYELFVLRPLPCRDD 376 (412)
T ss_pred hcCCCCCHHHHHHHhCCC-HHHHHHHHH-HHHhCCCeE-ecCC--C----ceEecCCHHhCcHHHHHHhCCCCcCCCccc
Confidence 356789999999999998 999998877 788889997 3332 2 26666775443333333322 2
Q ss_pred HHHHHHHHHHHHHHHHH
Q 027271 176 NWLTTSDNLLISIQEKI 192 (225)
Q Consensus 176 ~W~~~v~~~l~~ie~~~ 192 (225)
.|..+++.+++.+++..
T Consensus 377 ~~~~~~~~~l~~~~~~~ 393 (412)
T PRK04214 377 HVGQAADAALTQLRQPL 393 (412)
T ss_pred hHHHHHHHHHHHHHHHH
Confidence 56666666666655443
No 57
>PF07889 DUF1664: Protein of unknown function (DUF1664); InterPro: IPR012458 The members of this family are hypothetical plant proteins of unknown function. The region featured in this family is approximately 100 amino acids long.
Probab=65.38 E-value=52 Score=25.93 Aligned_cols=54 Identities=15% Similarity=0.255 Sum_probs=46.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhc
Q 027271 167 LGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSL 220 (225)
Q Consensus 167 ~~~L~~~L~~W~~~v~~~l~~ie~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 220 (225)
...+...|++-.+.+..+-..+.+++..++....+.....+.+.++|.+++..+
T Consensus 45 ~~~v~kql~~vs~~l~~tKkhLsqRId~vd~klDe~~ei~~~i~~eV~~v~~dv 98 (126)
T PF07889_consen 45 VASVSKQLEQVSESLSSTKKHLSQRIDRVDDKLDEQKEISKQIKDEVTEVREDV 98 (126)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHhhH
Confidence 455778888888888888888999999999999999999999999999888654
No 58
>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=65.17 E-value=12 Score=24.96 Aligned_cols=38 Identities=21% Similarity=0.292 Sum_probs=29.7
Q ss_pred cCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEE
Q 027271 105 ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (225)
Q Consensus 105 ~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gk 144 (225)
......+..+|++.++++ ...+-.=+= .....|+|+..
T Consensus 20 ~~~~~~t~~ela~~l~~~-~~t~s~hL~-~L~~aGli~~~ 57 (61)
T PF12840_consen 20 ASNGPMTVSELAEELGIS-QSTVSYHLK-KLEEAGLIEVE 57 (61)
T ss_dssp HHCSTBEHHHHHHHHTS--HHHHHHHHH-HHHHTTSEEEE
T ss_pred hcCCCCCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCeEEe
Confidence 566789999999999998 777766655 66778998764
No 59
>PRK01770 sec-independent translocase; Provisional
Probab=64.40 E-value=33 Score=28.48 Aligned_cols=34 Identities=21% Similarity=0.462 Sum_probs=29.9
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 027271 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKW 194 (225)
Q Consensus 161 ~~~~~q~~~L~~~L~~W~~~v~~~l~~ie~~~~~ 194 (225)
.||++.+..+...+..|..+++++...+++.+..
T Consensus 19 V~GPerLP~~~r~lg~~i~~~R~~~~~~k~e~~~ 52 (171)
T PRK01770 19 VLGPQRLPVAVKTVAGWIRALRSLATTVQNELTQ 52 (171)
T ss_pred hcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5789999999999999999999998888876654
No 60
>PF13730 HTH_36: Helix-turn-helix domain
Probab=63.99 E-value=28 Score=22.37 Aligned_cols=47 Identities=21% Similarity=0.311 Sum_probs=35.1
Q ss_pred HHHHHHHhhhhcc-CCccc-ChHHHHHHcCCCChHHHHHHHHHHhHhcCcc
Q 027271 93 LKLKQLTVLTLAE-TNKVL-PYDELMEELDVTNVRELEDFLINECMYTGIV 141 (225)
Q Consensus 93 ~Klr~LtLlsL~~-~~~~i-sy~~I~~~L~i~~~~evE~lvI~~AI~~gLI 141 (225)
.|+-.+.|.+.+. .+... |++.|++.+|++ .+.|-..+= +....|+|
T Consensus 7 ~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s-~~Tv~~~i~-~L~~~G~I 55 (55)
T PF13730_consen 7 AKLVYLYLASYANKNGGCFPSQETLAKDLGVS-RRTVQRAIK-ELEEKGLI 55 (55)
T ss_pred HHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCcCC
Confidence 3666678888873 22233 789999999997 889888776 77777765
No 61
>KOG1076 consensus Translation initiation factor 3, subunit c (eIF-3c) [Translation, ribosomal structure and biogenesis]
Probab=63.90 E-value=17 Score=36.59 Aligned_cols=96 Identities=10% Similarity=0.208 Sum_probs=67.4
Q ss_pred HHHHHHHHhcCChhhhhhh-------hCCCCCcc---hHHHHHHHHH----HhhhhccCCcccChHHHHHHcCCCChHHH
Q 027271 62 YLDMLRLFAHGTWSDYKNN-------AGHLPQLV---PDQVLKLKQL----TVLTLAETNKVLPYDELMEELDVTNVREL 127 (225)
Q Consensus 62 l~~LL~iF~~G~~~d~~~~-------~~~~~~L~---~~~~~Klr~L----tLlsL~~~~~~isy~~I~~~L~i~~~~ev 127 (225)
+..-=.+...|+|.+-..+ |+.+|.-. .-...+++-= .|++.++-+..+|.+.+|+-..+| ...|
T Consensus 657 VvaAsKAm~~Gnw~~c~~fi~nn~KvW~Lfpn~d~V~~Ml~~rIqEEsLRTYLftYss~Y~SvSl~~LA~mFdLp-~~~V 735 (843)
T KOG1076|consen 657 VVAASKAMQKGNWQKCFEFIVNNIKVWDLFPNADTVLDMLTERIQEESLRTYLFTYSSVYDSVSLAKLADMFDLP-EPKV 735 (843)
T ss_pred HHHHHHHHhcCCHHHHHHHHHhhhhHHHhcccHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhccHHHHHHHhCCC-chhH
Confidence 4445567788998855442 23444321 1112333331 345555679999999999999998 8888
Q ss_pred HHHHHHHhHhcCccEEEecCCCCEEEEEeecc
Q 027271 128 EDFLINECMYTGIVRGKLDQLRRCFEVQFAAG 159 (225)
Q Consensus 128 E~lvI~~AI~~gLI~gkIDq~~~~v~V~~~~~ 159 (225)
=..|= +.|-..=|.+++||+.++|.+.++.|
T Consensus 736 hsIiS-kmiineEl~AslDqpt~~iv~hrvE~ 766 (843)
T KOG1076|consen 736 HSIIS-KMIINEELHASLDQPTQCIVMHRVEP 766 (843)
T ss_pred HHHHH-HHHHHHHhhhccCCCcceEEEeeccc
Confidence 88777 88888889999999999999987654
No 62
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=63.69 E-value=18 Score=24.39 Aligned_cols=43 Identities=19% Similarity=0.302 Sum_probs=33.3
Q ss_pred HHhhhhccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 027271 98 LTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (225)
Q Consensus 98 LtLlsL~~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~ 142 (225)
.+|..|...+..++-.+||+.|+++ ...|=..+= +.-..|+|.
T Consensus 11 ~~Iy~l~~~~~~v~~~~iA~~L~vs-~~tvt~ml~-~L~~~GlV~ 53 (60)
T PF01325_consen 11 KAIYELSEEGGPVRTKDIAERLGVS-PPTVTEMLK-RLAEKGLVE 53 (60)
T ss_dssp HHHHHHHHCTSSBBHHHHHHHHTS--HHHHHHHHH-HHHHTTSEE
T ss_pred HHHHHHHcCCCCccHHHHHHHHCCC-hHHHHHHHH-HHHHCCCEE
Confidence 3455555688899999999999997 777777766 777788875
No 63
>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=63.53 E-value=11 Score=25.04 Aligned_cols=43 Identities=23% Similarity=0.286 Sum_probs=31.5
Q ss_pred HHHhhhhccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCcc
Q 027271 97 QLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIV 141 (225)
Q Consensus 97 ~LtLlsL~~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI 141 (225)
+-.|+.+....+.++..++++.++++ ...+-.=+. ..-..|+|
T Consensus 2 ~~~Il~~l~~~~~~s~~ela~~~~VS-~~TiRRDl~-~L~~~g~i 44 (57)
T PF08220_consen 2 QQQILELLKEKGKVSVKELAEEFGVS-EMTIRRDLN-KLEKQGLI 44 (57)
T ss_pred HHHHHHHHHHcCCEEHHHHHHHHCcC-HHHHHHHHH-HHHHCCCE
Confidence 34566666778899999999999997 777765555 55555653
No 64
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=63.27 E-value=87 Score=26.02 Aligned_cols=37 Identities=14% Similarity=0.175 Sum_probs=30.5
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEe
Q 027271 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKL 145 (225)
Q Consensus 107 ~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkI 145 (225)
...++..+|++.++|+ ...|=..+= .....|+|.-+-
T Consensus 13 ~~~~t~~eLA~~lgis-~~tV~~~L~-~Le~~GlV~r~~ 49 (203)
T TIGR02702 13 QGQATAAALAEALAIS-PQAVRRHLK-DLETEGLIEYEA 49 (203)
T ss_pred cCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCeEEee
Confidence 3459999999999997 888877766 778899998663
No 65
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=62.91 E-value=7.4 Score=26.09 Aligned_cols=36 Identities=28% Similarity=0.442 Sum_probs=25.4
Q ss_pred HHHHhhhhccCCcccChHHHHHHcCCCChHHHHHHHH
Q 027271 96 KQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLI 132 (225)
Q Consensus 96 r~LtLlsL~~~~~~isy~~I~~~L~i~~~~evE~lvI 132 (225)
|++.|+.+.-..+.+++++|++.++++ ...+-..+-
T Consensus 6 rq~~Ll~~L~~~~~~~~~ela~~l~~S-~rti~~~i~ 41 (59)
T PF08280_consen 6 RQLKLLELLLKNKWITLKELAKKLNIS-ERTIKNDIN 41 (59)
T ss_dssp HHHHHHHHHHHHTSBBHHHHHHHCTS--HHHHHHHHH
T ss_pred HHHHHHHHHHcCCCCcHHHHHHHHCCC-HHHHHHHHH
Confidence 445555555447789999999999997 777665543
No 66
>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=61.31 E-value=22 Score=22.39 Aligned_cols=33 Identities=27% Similarity=0.341 Sum_probs=25.8
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 027271 108 KVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (225)
Q Consensus 108 ~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~ 142 (225)
+..++.+|++.++++ ...|-.-+= .....|+|+
T Consensus 14 ~~~~~~el~~~l~~s-~~~vs~hL~-~L~~~glV~ 46 (47)
T PF01022_consen 14 GPLTVSELAEELGLS-QSTVSHHLK-KLREAGLVE 46 (47)
T ss_dssp SSEEHHHHHHHHTS--HHHHHHHHH-HHHHTTSEE
T ss_pred CCCchhhHHHhcccc-chHHHHHHH-HHHHCcCee
Confidence 679999999999997 878776655 667778775
No 67
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=61.10 E-value=29 Score=23.09 Aligned_cols=30 Identities=20% Similarity=0.379 Sum_probs=23.3
Q ss_pred cCCcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 027271 105 ETNKVLPYDELMEELDVTNVRELEDFLINECM 136 (225)
Q Consensus 105 ~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI 136 (225)
..-|.++..+||+.|||+ ...+-.-+= +|.
T Consensus 19 d~PR~~tl~elA~~lgis-~st~~~~LR-rae 48 (53)
T PF04967_consen 19 DVPRRITLEELAEELGIS-KSTVSEHLR-RAE 48 (53)
T ss_pred CCCCcCCHHHHHHHhCCC-HHHHHHHHH-HHH
Confidence 567899999999999997 777765554 443
No 68
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=60.99 E-value=34 Score=21.67 Aligned_cols=36 Identities=22% Similarity=0.280 Sum_probs=29.7
Q ss_pred cCCccc-ChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 027271 105 ETNKVL-PYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (225)
Q Consensus 105 ~~~~~i-sy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~ 142 (225)
.++..+ |..+|++.++++ ...|-..+- .....|+|.
T Consensus 15 ~~~~~l~s~~~la~~~~vs-~~tv~~~l~-~L~~~g~i~ 51 (60)
T smart00345 15 RPGDKLPSERELAAQLGVS-RTTVREALS-RLEAEGLVQ 51 (60)
T ss_pred CCCCcCcCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEE
Confidence 455567 899999999996 888988877 777788875
No 69
>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=60.55 E-value=6.3 Score=24.82 Aligned_cols=29 Identities=28% Similarity=0.430 Sum_probs=19.2
Q ss_pred hhhhccCCcccChHHHHHHcCCCChHHHHH
Q 027271 100 VLTLAETNKVLPYDELMEELDVTNVRELED 129 (225)
Q Consensus 100 LlsL~~~~~~isy~~I~~~L~i~~~~evE~ 129 (225)
|+.+-..+...||.+|++.+|++ ...|-.
T Consensus 8 Il~~Lq~d~r~s~~~la~~lglS-~~~v~~ 36 (42)
T PF13404_consen 8 ILRLLQEDGRRSYAELAEELGLS-ESTVRR 36 (42)
T ss_dssp HHHHHHH-TTS-HHHHHHHHTS--HHHHHH
T ss_pred HHHHHHHcCCccHHHHHHHHCcC-HHHHHH
Confidence 44444555789999999999997 766643
No 70
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=60.29 E-value=12 Score=24.00 Aligned_cols=27 Identities=19% Similarity=0.277 Sum_probs=20.4
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 027271 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (225)
Q Consensus 108 ~~isy~~I~~~L~i~~~~evE~lvI~~AI 136 (225)
.-.||.+||+.+|++ ...|..++- +|.
T Consensus 25 ~g~s~~eIa~~l~~s-~~~v~~~l~-ra~ 51 (54)
T PF08281_consen 25 QGMSYAEIAEILGIS-ESTVKRRLR-RAR 51 (54)
T ss_dssp S---HHHHHHHCTS--HHHHHHHHH-HHH
T ss_pred HCcCHHHHHHHHCcC-HHHHHHHHH-HHH
Confidence 468999999999997 999999887 665
No 71
>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=58.85 E-value=38 Score=22.04 Aligned_cols=36 Identities=22% Similarity=0.325 Sum_probs=30.8
Q ss_pred cChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecC
Q 027271 110 LPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQ 147 (225)
Q Consensus 110 isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq 147 (225)
+++.+|++.++++ ...+-..+= .....|+|...-+.
T Consensus 21 ~~~~ei~~~~~i~-~~~i~~~l~-~L~~~g~i~~~~~~ 56 (78)
T cd00090 21 LTVSELAERLGLS-QSTVSRHLK-KLEEAGLVESRREG 56 (78)
T ss_pred cCHHHHHHHHCcC-HhHHHHHHH-HHHHCCCeEEEEec
Confidence 9999999999997 888887776 77789999987665
No 72
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=58.41 E-value=31 Score=24.31 Aligned_cols=50 Identities=14% Similarity=0.255 Sum_probs=34.2
Q ss_pred HhhhhccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEE
Q 027271 99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ 155 (225)
Q Consensus 99 tLlsL~~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq~~~~v~V~ 155 (225)
.++..++ ....++.+|+..++++ ...+..++= ..+..|+|++ .++.+.+|
T Consensus 10 ~IL~~l~-~~~~~~t~i~~~~~L~-~~~~~~yL~-~L~~~gLI~~----~~~~Y~lT 59 (77)
T PF14947_consen 10 DILKILS-KGGAKKTEIMYKANLN-YSTLKKYLK-ELEEKGLIKK----KDGKYRLT 59 (77)
T ss_dssp HHHHHH--TT-B-HHHHHTTST---HHHHHHHHH-HHHHTTSEEE----ETTEEEE-
T ss_pred HHHHHHH-cCCCCHHHHHHHhCcC-HHHHHHHHH-HHHHCcCeeC----CCCEEEEC
Confidence 3444444 5678899999999997 899999888 8999999944 45566655
No 73
>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=57.69 E-value=16 Score=23.49 Aligned_cols=35 Identities=31% Similarity=0.400 Sum_probs=24.2
Q ss_pred HHHhhhhc-cCCcccChHHHHHHcCCCChHHHHHHHH
Q 027271 97 QLTVLTLA-ETNKVLPYDELMEELDVTNVRELEDFLI 132 (225)
Q Consensus 97 ~LtLlsL~-~~~~~isy~~I~~~L~i~~~~evE~lvI 132 (225)
+..++.+. .....+|.++||+.|+++ ...|..-+=
T Consensus 2 ~~~il~~L~~~~~~it~~eLa~~l~vS-~rTi~~~i~ 37 (55)
T PF08279_consen 2 QKQILKLLLESKEPITAKELAEELGVS-RRTIRRDIK 37 (55)
T ss_dssp HHHHHHHHHHTTTSBEHHHHHHHCTS--HHHHHHHHH
T ss_pred HHHHHHHHHHcCCCcCHHHHHHHhCCC-HHHHHHHHH
Confidence 34444444 444459999999999996 888776644
No 74
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=57.45 E-value=24 Score=25.94 Aligned_cols=50 Identities=18% Similarity=0.259 Sum_probs=37.4
Q ss_pred HHHHhhhh-ccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecC
Q 027271 96 KQLTVLTL-AETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQ 147 (225)
Q Consensus 96 r~LtLlsL-~~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq 147 (225)
+.|.++.- +....=+++++|++.|+++ .++|+..|= ..+..|.|=-.||+
T Consensus 51 ~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~-~~~v~~al~-~L~~eG~IYsTiDd 101 (102)
T PF08784_consen 51 KVLNFIKQQPNSEEGVHVDEIAQQLGMS-ENEVRKALD-FLSNEGHIYSTIDD 101 (102)
T ss_dssp HHHHHHHC----TTTEEHHHHHHHSTS--HHHHHHHHH-HHHHTTSEEESSST
T ss_pred HHHHHHHhcCCCCCcccHHHHHHHhCcC-HHHHHHHHH-HHHhCCeEecccCC
Confidence 34555554 4445569999999999997 999999877 89999999888875
No 75
>PRK10265 chaperone-modulator protein CbpM; Provisional
Probab=57.32 E-value=24 Score=26.40 Aligned_cols=38 Identities=18% Similarity=0.142 Sum_probs=28.5
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCC
Q 027271 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLR 149 (225)
Q Consensus 106 ~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq~~ 149 (225)
....++.+++.+.++++ +.||. +.+..|+|+-.-+...
T Consensus 4 ~~~~lt~~Elc~~~gi~-----~~~l~-eLve~GlIep~~~~~~ 41 (101)
T PRK10265 4 VTVTFTITEFCLHTGVS-----EEELN-EIVGLGVIEPREIQET 41 (101)
T ss_pred eEEEeeHHHHHHHHCcC-----HHHHH-HHHHCCCeecCCCCcc
Confidence 34568999999999998 44666 6777999997555533
No 76
>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=57.23 E-value=79 Score=23.60 Aligned_cols=48 Identities=10% Similarity=0.049 Sum_probs=37.9
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEE
Q 027271 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ 155 (225)
Q Consensus 106 ~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq~~~~v~V~ 155 (225)
.+..++..+|++.++++ ...+=..|- +....|+|...-|..++.....
T Consensus 39 ~~~~~t~~ela~~~~~~-~~tvs~~l~-~Le~~GlI~r~~~~~D~R~~~v 86 (118)
T TIGR02337 39 EQGSMEFTQLANQACIL-RPSLTGILA-RLERDGLVTRLKASNDQRRVYI 86 (118)
T ss_pred HcCCcCHHHHHHHhCCC-chhHHHHHH-HHHHCCCEEeccCCCCCCeeEE
Confidence 34568999999999997 667777666 8889999999998877654433
No 77
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=56.75 E-value=65 Score=22.50 Aligned_cols=43 Identities=21% Similarity=0.198 Sum_probs=35.4
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCE
Q 027271 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRC 151 (225)
Q Consensus 107 ~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq~~~~ 151 (225)
...++..+|++.++++ ...+-..+- +....|+|.-.-+..++.
T Consensus 22 ~~~~~~~~la~~~~~s-~~~i~~~l~-~L~~~g~v~~~~~~~~~r 64 (101)
T smart00347 22 EGPLSVSELAKRLGVS-PSTVTRVLD-RLEKKGLIRRLPSPEDRR 64 (101)
T ss_pred cCCcCHHHHHHHHCCC-chhHHHHHH-HHHHCCCeEecCCCCCCC
Confidence 3469999999999997 888988888 899999998776654433
No 78
>PRK14858 tatA twin arginine translocase protein A; Provisional
Probab=56.70 E-value=79 Score=24.28 Aligned_cols=34 Identities=12% Similarity=0.167 Sum_probs=29.3
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 027271 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKW 194 (225)
Q Consensus 161 ~~~~~q~~~L~~~L~~W~~~v~~~l~~ie~~~~~ 194 (225)
.|+++.++.+...+..|..+.......++..+..
T Consensus 19 vfGPkKLPelar~lGk~i~~fk~~~~d~k~~i~~ 52 (108)
T PRK14858 19 VIGPQKLPDLARSLGRGLAEFKKATDDFKQSMQE 52 (108)
T ss_pred hcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5789999999999999999999988888777653
No 79
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=54.77 E-value=45 Score=21.04 Aligned_cols=28 Identities=18% Similarity=0.313 Sum_probs=22.3
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 027271 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (225)
Q Consensus 107 ~~~isy~~I~~~L~i~~~~evE~lvI~~AI 136 (225)
....||.+|++.+|++ ...|-.+.- .|+
T Consensus 18 ~~~~t~~eIa~~lg~s-~~~V~~~~~-~al 45 (50)
T PF04545_consen 18 FEGLTLEEIAERLGIS-RSTVRRILK-RAL 45 (50)
T ss_dssp TST-SHHHHHHHHTSC-HHHHHHHHH-HHH
T ss_pred cCCCCHHHHHHHHCCc-HHHHHHHHH-HHH
Confidence 4678999999999997 888877766 665
No 80
>PRK09954 putative kinase; Provisional
Probab=54.32 E-value=17 Score=32.89 Aligned_cols=54 Identities=19% Similarity=0.438 Sum_probs=41.0
Q ss_pred hhhhccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE---EecCCCCEEEEE
Q 027271 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG---KLDQLRRCFEVQ 155 (225)
Q Consensus 100 LlsL~~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~g---kIDq~~~~v~V~ 155 (225)
|+.+...+..+|+.+|++.|+++ ...|-..+- +....|+|+| .+|.....+.|.
T Consensus 8 il~~l~~~~~~s~~~la~~l~~s-~~~v~~~i~-~L~~~g~i~~~~~~l~~~~~v~viG 64 (362)
T PRK09954 8 ILAILRRNPLIQQNEIADILQIS-RSRVAAHIM-DLMRKGRIKGKGYILTEQEYCVVVG 64 (362)
T ss_pred HHHHHHHCCCCCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCcCCcEEEEcCCccEEEEE
Confidence 44555566789999999999997 999999888 8888899875 455555554443
No 81
>PF01920 Prefoldin_2: Prefoldin subunit; InterPro: IPR002777 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 beta subunit, eukaryotic prefoldin subunits 1, 2, 4 and 6. 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: 2ZDI_B 3AEI_B 2ZQM_A 1FXK_A.
Probab=54.14 E-value=55 Score=23.78 Aligned_cols=57 Identities=26% Similarity=0.238 Sum_probs=30.7
Q ss_pred EEeeccCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhccccc
Q 027271 154 VQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSHKV 224 (225)
Q Consensus 154 V~~~~~R~~~~~q~~~L~~~L~~W~~~v~~~l~~ie~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 224 (225)
|....++.|=....+.+...|. ..+..+.............++.++.+.++.++..+
T Consensus 47 ~y~~vG~~fv~~~~~~~~~~L~--------------~~~~~~~~~i~~l~~~~~~l~~~l~~~~~~l~~~~ 103 (106)
T PF01920_consen 47 VYKSVGKMFVKQDKEEAIEELE--------------ERIEKLEKEIKKLEKQLKYLEKKLKELKKKLYELF 103 (106)
T ss_dssp EEEEETTEEEEEEHHHHHHHHH--------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_pred hHHHHhHHHHHhhHHHHHHHHH--------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3344566665555555544444 44444444444444555566666777777666543
No 82
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=54.00 E-value=15 Score=26.22 Aligned_cols=51 Identities=29% Similarity=0.315 Sum_probs=35.3
Q ss_pred HHhhhhccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCC
Q 027271 98 LTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRR 150 (225)
Q Consensus 98 LtLlsL~~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq~~~ 150 (225)
|.++++-.....++|.+|.+.|+++ ...+-.-+= .....|+|+-+-.-..+
T Consensus 3 l~Il~~L~~~~~~~f~~L~~~l~lt-~g~Ls~hL~-~Le~~GyV~~~k~~~~~ 53 (80)
T PF13601_consen 3 LAILALLYANEEATFSELKEELGLT-DGNLSKHLK-KLEEAGYVEVEKEFEGR 53 (80)
T ss_dssp HHHHHHHHHHSEEEHHHHHHHTT---HHHHHHHHH-HHHHTTSEEEEEE-SSS
T ss_pred HHHHHHHhhcCCCCHHHHHHHhCcC-HHHHHHHHH-HHHHCCCEEEEEeccCC
Confidence 3444444446789999999999997 777766666 67779999987665544
No 83
>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=53.71 E-value=50 Score=21.39 Aligned_cols=40 Identities=20% Similarity=0.236 Sum_probs=32.6
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCC
Q 027271 108 KVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLR 149 (225)
Q Consensus 108 ~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq~~ 149 (225)
..++..+|++.++++ ...|=..|= .....|+|.-.-|..+
T Consensus 20 ~~~t~~~la~~l~~~-~~~vs~~v~-~L~~~Glv~r~~~~~D 59 (62)
T PF12802_consen 20 EELTQSELAERLGIS-KSTVSRIVK-RLEKKGLVERERDPGD 59 (62)
T ss_dssp SGEEHHHHHHHHTS--HHHHHHHHH-HHHHTTSEEEEE-SSS
T ss_pred CCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEEeCCCCC
Confidence 359999999999997 888888877 8999999998877654
No 84
>cd04786 HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic su
Probab=53.70 E-value=1.1e+02 Score=23.98 Aligned_cols=106 Identities=11% Similarity=0.125 Sum_probs=61.6
Q ss_pred ChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCE-EEE----------EeeccCCCCCCcHHHHHHHHHHHH-
Q 027271 111 PYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRC-FEV----------QFAAGRDLRPGQLGSMIQTLSNWL- 178 (225)
Q Consensus 111 sy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq~~~~-v~V----------~~~~~R~~~~~q~~~L~~~L~~W~- 178 (225)
+..++++.+||+ ...+-.| + ..|||.-.-...+|. .+= .+...-.|+.+++..+ +..+.
T Consensus 2 ~Ige~a~~~gvs-~~tLRyY---E--~~GLl~p~~r~~~gyR~Y~~~~v~~l~~I~~lr~~GfsL~eI~~l---l~~~~~ 72 (131)
T cd04786 2 KIGELAKRSGMA-ASRIRFY---E--AEGLLSSVERSANGYRDYPPETVWVLEIISSAQQAGFSLDEIRQL---LPADAS 72 (131)
T ss_pred CHHHHHHHHCcC-HHHHHHH---H--HCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHH---HhcccC
Confidence 578999999997 8888877 2 268886432222322 110 0111122333333333 22221
Q ss_pred -HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhcccccC
Q 027271 179 -TTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSHKVC 225 (225)
Q Consensus 179 -~~v~~~l~~ie~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 225 (225)
.....+...+++++...+.+..+..+.+..+...+...........|
T Consensus 73 ~~~~~~~~~~l~~k~~~i~~~i~~L~~~~~~L~~~i~~~~~~~~~~~~ 120 (131)
T cd04786 73 NWQHDELLAALERKVADIEALEARLAQNKAQLLVLIDLIESKPDEMDC 120 (131)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCc
Confidence 12355666777788888888777777788888877777665555444
No 85
>PF05377 FlaC_arch: Flagella accessory protein C (FlaC); InterPro: IPR008039 Although archaeal flagella appear superficially similar to those of bacteria, they are quite distinct []. In several archaea, the flagellin genes are followed immediately by the flagellar accessory genes flaCDEFGHIJ. The gene products may have a role in translocation, secretion, or assembly of the flagellum. FlaC is a protein whose exact role is unknown but it has been shown to be membrane-associated (by immuno-blotting fractionated cells) [].
Probab=53.11 E-value=46 Score=22.44 Aligned_cols=34 Identities=18% Similarity=0.343 Sum_probs=17.6
Q ss_pred HHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhcc
Q 027271 188 IQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLS 221 (225)
Q Consensus 188 ie~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 221 (225)
|++++.........-...-+++...++.+++++|
T Consensus 5 lEn~~~~~~~~i~tvk~en~~i~~~ve~i~envk 38 (55)
T PF05377_consen 5 LENELPRIESSINTVKKENEEISESVEKIEENVK 38 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444444444444455566666666666554
No 86
>PRK10870 transcriptional repressor MprA; Provisional
Probab=52.81 E-value=1e+02 Score=25.11 Aligned_cols=51 Identities=14% Similarity=-0.001 Sum_probs=41.0
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeec
Q 027271 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAA 158 (225)
Q Consensus 106 ~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq~~~~v~V~~~~ 158 (225)
++..++..+|++.++++ ...+=..|= +....|+|+=.-|..++....-..+
T Consensus 68 ~~~~it~~eLa~~l~l~-~~tvsr~v~-rLe~kGlV~R~~~~~DrR~~~v~LT 118 (176)
T PRK10870 68 ENHSIQPSELSCALGSS-RTNATRIAD-ELEKRGWIERRESDNDRRCLHLQLT 118 (176)
T ss_pred CCCCcCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEEecCCCCCCCeeEEEEC
Confidence 45679999999999997 777766655 8888999999999988766555443
No 87
>TIGR02051 MerR Hg(II)-responsive transcriptional regulator. This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=52.22 E-value=66 Score=24.71 Aligned_cols=96 Identities=16% Similarity=0.086 Sum_probs=50.7
Q ss_pred ChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEE-----------eeccCCCCCCcHHHHHHHHHHHH-
Q 027271 111 PYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ-----------FAAGRDLRPGQLGSMIQTLSNWL- 178 (225)
Q Consensus 111 sy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq~~~~v~V~-----------~~~~R~~~~~q~~~L~~~L~~W~- 178 (225)
+..++|+.+||+ .+.+=.| - + .|||...-...++.-.-+ ....-.|+.+++.. -+..+.
T Consensus 1 ~I~e~a~~~gvs-~~tlR~Y-e-~---~GLl~~~~r~~~g~R~Y~~~~l~~l~~I~~l~~~G~sl~eI~~---~l~~~~~ 71 (124)
T TIGR02051 1 TIGELAKAAGVN-VETIRYY-E-R---KGLLPEPDRPEGGYRRYPEETVKRLRFIKRAQELGFSLEEIGG---LLGLVDG 71 (124)
T ss_pred CHHHHHHHHCcC-HHHHHHH-H-H---CCCCCCCccCCCCCEeECHHHHHHHHHHHHHHHCCCCHHHHHH---HHhcccC
Confidence 467899999997 8888766 3 3 688864333333322211 01111122223332 222222
Q ss_pred HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHH
Q 027271 179 TTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEE 215 (225)
Q Consensus 179 ~~v~~~l~~ie~~~~~~~~~~~~~~~~~~~~~~~~~~ 215 (225)
..+..+...+++++..++.+.++....+..+++.+..
T Consensus 72 ~~~~~~~~~l~~~~~~l~~~i~~L~~~~~~L~~~~~~ 108 (124)
T TIGR02051 72 THCREMYELASRKLKSVQAKMADLLRIERLLEELLEQ 108 (124)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 2344556666666666666666666666555555443
No 88
>PF05331 DUF742: Protein of unknown function (DUF742); InterPro: IPR007995 This family consists of several uncharacterised Streptomyces proteins as well as one from Mycobacterium tuberculosis. The function of these proteins is unknown.
Probab=52.14 E-value=26 Score=27.13 Aligned_cols=42 Identities=19% Similarity=0.327 Sum_probs=34.3
Q ss_pred HhhhhccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEE
Q 027271 99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (225)
Q Consensus 99 tLlsL~~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gk 144 (225)
.|++||.. ..|..|||..|++| ..-+--++= +.+..|+|.-+
T Consensus 47 ~Il~lC~~--~~SVAEiAA~L~lP-lgVvrVLvs-DL~~~G~v~v~ 88 (114)
T PF05331_consen 47 AILELCRR--PLSVAEIAARLGLP-LGVVRVLVS-DLADAGLVRVR 88 (114)
T ss_pred HHHHHHCC--CccHHHHHHhhCCC-chhhhhhHH-HHHhCCCEEEe
Confidence 67888887 89999999999999 777776666 88888877543
No 89
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=51.44 E-value=55 Score=20.60 Aligned_cols=38 Identities=21% Similarity=0.219 Sum_probs=29.7
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEec
Q 027271 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLD 146 (225)
Q Consensus 107 ~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkID 146 (225)
...+++.+|++.++++ ...+-..+= .....|+|.-.-+
T Consensus 8 ~~~~~~~~i~~~l~is-~~~v~~~l~-~L~~~g~i~~~~~ 45 (66)
T smart00418 8 EGELCVCELAEILGLS-QSTVSHHLK-KLREAGLVESRRE 45 (66)
T ss_pred cCCccHHHHHHHHCCC-HHHHHHHHH-HHHHCCCeeeeec
Confidence 4678999999999997 777777655 6777899985443
No 90
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=51.22 E-value=39 Score=20.80 Aligned_cols=35 Identities=20% Similarity=0.186 Sum_probs=28.0
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE
Q 027271 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (225)
Q Consensus 107 ~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~g 143 (225)
+..++..+|++.++++ ...+-..+= .....|+|.-
T Consensus 12 ~~~~s~~~l~~~l~~s-~~tv~~~l~-~L~~~g~i~~ 46 (53)
T smart00420 12 QGKVSVEELAELLGVS-EMTIRRDLN-KLEEQGLLTR 46 (53)
T ss_pred cCCcCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEEE
Confidence 3569999999999996 888888766 6667777764
No 91
>PF11945 WASH_WAHD: WAHD domain of WASH complex; InterPro: IPR021854 This entry represents a component of the WASH complex. The WASH complex is present at the surface of endosomes and recruits and activates the Arp2/3 complex to induce actin polymerisation. The WASH complex plays a key role in the fission of tubules that serve as transport intermediates during endosome sorting []. The WASH complex's subunit structure: F-actin-capping protein subunit alpha (CAPZA1, CAPZA2 or CAPZA3), F-actin-capping protein subunit beta (CAPZB), WASH (WASH1, WASH2P, WASH3P, WASH4P, WASH5P or WASH6P), FAM21 (FAM21A, FAM21B or FAM21C), KIAA1033, KIAA0196 (strumpellin) and CCDC53. This entry represents the WASH subunit of the WASH complex. WASH genes duplicated to multiple chromosomal ends during primate evolution, with highest copy number reached in humans, whose WASH repertoires probably vary extensively among individuals []. It is therefore difficult to determine which gene is functional or not. The telomeric region of chromosome 9p is paralogous to the pericentromeric regions of chromosome 9 as well as to 2q. Paralogous regions contain 7 transcriptional units. Duplicated WASH genes are also present in the Xq/Yq pseudoautosomal region, as well as on chromosome 1 and 15. The chromosome 16 copy seems to be a pseudogene.
Probab=50.94 E-value=1.4e+02 Score=26.97 Aligned_cols=66 Identities=14% Similarity=0.137 Sum_probs=54.3
Q ss_pred eeccCCCCCCc-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhcc
Q 027271 156 FAAGRDLRPGQ-LGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLS 221 (225)
Q Consensus 156 ~~~~R~~~~~q-~~~L~~~L~~W~~~v~~~l~~ie~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 221 (225)
-..+.|++.++ +..+.+.|+....-++.+-..|.+++..-.++.+.-.+|-...+++|+.++-.-|
T Consensus 8 plI~~dLr~eEti~qi~~aL~~L~~v~~diF~rI~~Rv~~~~~~l~~i~~Ri~~~qaKi~~l~gs~k 74 (297)
T PF11945_consen 8 PLIPPDLRREETILQIADALEYLDKVSNDIFSRISARVERNRERLQAIQQRIEVAQAKIEKLQGSKK 74 (297)
T ss_pred cccCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCc
Confidence 45678887765 6678999999999999999999999998888888778888888888888765543
No 92
>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=50.21 E-value=23 Score=23.96 Aligned_cols=38 Identities=21% Similarity=0.202 Sum_probs=32.9
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEe
Q 027271 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKL 145 (225)
Q Consensus 106 ~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkI 145 (225)
..+..+..+|++.++++ ...|-..+= +....|+|+-.-
T Consensus 19 ~~~~~t~~eIa~~l~i~-~~~v~~~L~-~L~~~GlV~~~~ 56 (68)
T PF01978_consen 19 KNGPATAEEIAEELGIS-RSTVYRALK-SLEEKGLVEREE 56 (68)
T ss_dssp HHCHEEHHHHHHHHTSS-HHHHHHHHH-HHHHTTSEEEEE
T ss_pred HcCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEEEc
Confidence 44689999999999998 999998888 899999997665
No 93
>PRK00708 sec-independent translocase; Provisional
Probab=48.65 E-value=81 Score=27.03 Aligned_cols=37 Identities=11% Similarity=0.136 Sum_probs=31.4
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 027271 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADS 197 (225)
Q Consensus 161 ~~~~~q~~~L~~~L~~W~~~v~~~l~~ie~~~~~~~~ 197 (225)
+|+++++..+...+..|..+++.+...+.+.+...-.
T Consensus 19 V~GPkrLP~~~R~lGk~v~k~R~~a~e~r~~~~e~~~ 55 (209)
T PRK00708 19 VVGPKDLPPMLRAFGKMTARMRKMAGEFRRQFDEALR 55 (209)
T ss_pred hcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 5789999999999999999999888888877765444
No 94
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=47.75 E-value=54 Score=25.18 Aligned_cols=26 Identities=15% Similarity=0.339 Sum_probs=20.8
Q ss_pred ChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 027271 111 PYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (225)
Q Consensus 111 sy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~ 142 (225)
+..++|+.+||+ ...+-.| - + .|||.
T Consensus 2 ~IgevA~~~gvs-~~tLRyY-e-~---~GLl~ 27 (127)
T cd04784 2 KIGELAKKTGCS-VETIRYY-E-K---EGLLP 27 (127)
T ss_pred CHHHHHHHHCcC-HHHHHHH-H-H---CCCCC
Confidence 678999999997 8888877 2 2 68886
No 95
>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=47.68 E-value=33 Score=22.20 Aligned_cols=43 Identities=19% Similarity=0.257 Sum_probs=34.6
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCC
Q 027271 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRR 150 (225)
Q Consensus 106 ~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq~~~ 150 (225)
....++..+|++.++++ ...+=.++= .....|+|.=.-|+.++
T Consensus 14 ~~~~~~~~~la~~~~~~-~~~~t~~i~-~L~~~g~I~r~~~~~D~ 56 (59)
T PF01047_consen 14 ENGGITQSELAEKLGIS-RSTVTRIIK-RLEKKGLIERERDPDDR 56 (59)
T ss_dssp HHSSEEHHHHHHHHTS--HHHHHHHHH-HHHHTTSEEEEEETTET
T ss_pred HcCCCCHHHHHHHHCCC-hhHHHHHHH-HHHHCCCEEeccCCCCC
Confidence 34459999999999997 777777766 88889999998887664
No 96
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=47.17 E-value=2e+02 Score=25.37 Aligned_cols=84 Identities=14% Similarity=0.294 Sum_probs=52.9
Q ss_pred HhhhhccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeeccCCCCCCcHHHHHHHHHHHH
Q 027271 99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWL 178 (225)
Q Consensus 99 tLlsL~~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq~~~~v~V~~~~~R~~~~~q~~~L~~~L~~W~ 178 (225)
-|.-++-.+..+.-.+|++.++|+ ...|=+.+= +.+..|+|+- .-.+.-.|| ++-.+-|.+.+...+
T Consensus 15 IL~ei~~~qp~v~q~eIA~~lgiT-~QaVsehiK-~Lv~eG~i~~---~gR~~Y~iT--------kkG~e~l~~~~~dlr 81 (260)
T COG1497 15 ILSEIAVRQPRVKQKEIAKKLGIT-LQAVSEHIK-ELVKEGLIEK---EGRGEYEIT--------KKGAEWLLEQLSDLR 81 (260)
T ss_pred HHHHHHHhCCCCCHHHHHHHcCCC-HHHHHHHHH-HHHhccceee---cCCeeEEEe--------hhHHHHHHHHHHHHH
Confidence 344444555678999999999997 888877777 8888887764 222233343 233444666666666
Q ss_pred HHHHHHHHHHHHHHHHH
Q 027271 179 TTSDNLLISIQEKIKWA 195 (225)
Q Consensus 179 ~~v~~~l~~ie~~~~~~ 195 (225)
.-++.+...+.....|.
T Consensus 82 ~f~~ev~~~l~~~~vw~ 98 (260)
T COG1497 82 RFSEEVELVLDYVMVWT 98 (260)
T ss_pred HHHHHHHHHHhhHHHHH
Confidence 55555555555555554
No 97
>COG4575 ElaB Uncharacterized conserved protein [Function unknown]
Probab=45.61 E-value=98 Score=23.61 Aligned_cols=57 Identities=19% Similarity=0.327 Sum_probs=31.6
Q ss_pred cCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhcc
Q 027271 159 GRDLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLS 221 (225)
Q Consensus 159 ~R~~~~~q~~~L~~~L~~W~~~v~~~l~~ie~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 221 (225)
+|.+....++.+...|..-...++.++.. +......+-+..+..++..+.++++++.
T Consensus 2 ~~~~~~~~~~~l~~el~~L~d~lEevL~s------sg~~a~~e~~~lR~r~~~~Lk~~r~rl~ 58 (104)
T COG4575 2 SREFTDDAIDQLLAELQELLDTLEEVLKS------SGSLAGDEAEELRSKAESALKEARDRLG 58 (104)
T ss_pred cccchhhhHHHHHHHHHHHHHHHHHHHHh------cccchhhHHHHHHHHHHHHHHHHHHHHH
Confidence 56666666666655555555544444332 3333344455566666666666666654
No 98
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=44.90 E-value=95 Score=23.26 Aligned_cols=45 Identities=20% Similarity=0.310 Sum_probs=29.7
Q ss_pred ChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE-EecCCCCEEEEEeeccCCCCCCcHHHH
Q 027271 111 PYDELMEELDVTNVRELEDFLINECMYTGIVRG-KLDQLRRCFEVQFAAGRDLRPGQLGSM 170 (225)
Q Consensus 111 sy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~g-kIDq~~~~v~V~~~~~R~~~~~q~~~L 170 (225)
+..++|+.+||+ ...+-.| - + .|+|.. .-+. .-.|.++.+++..+
T Consensus 2 ~i~e~a~~~gvs-~~tlr~y-e-~---~gll~~~~r~~---------~gyR~Y~~~~l~~l 47 (113)
T cd01109 2 TIKEVAEKTGLS-ADTLRYY-E-K---EGLLPPVKRDE---------NGIRDFTEEDLEWL 47 (113)
T ss_pred CHHHHHHHHCcC-HHHHHHH-H-H---CCCCCCCCcCC---------CCCccCCHHHHHHH
Confidence 678999999997 8888887 2 3 577742 2121 23566776665543
No 99
>KOG2629 consensus Peroxisomal membrane anchor protein (peroxin) [Cell wall/membrane/envelope biogenesis; Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=44.81 E-value=94 Score=28.02 Aligned_cols=83 Identities=13% Similarity=0.255 Sum_probs=58.4
Q ss_pred HHHHHHHhHhcCccEEEecCCCCEEEEEeeccCCCCCCc--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHH
Q 027271 128 EDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQ--LGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKH 205 (225)
Q Consensus 128 E~lvI~~AI~~gLI~gkIDq~~~~v~V~~~~~R~~~~~q--~~~L~~~L~~W~~~v~~~l~~ie~~~~~~~~~~~~~~~~ 205 (225)
+++++ -++..|+.-|=.- |.=.|+.||.|+..+ .+..+..|+.=-..++..+.-++..+..+.+. ....
T Consensus 85 dy~vm-Avi~aGi~y~~y~-----~~K~YV~P~~l~~~~~k~e~~k~~Ld~~~~~~~~~~~~l~~~va~v~q~---~~~q 155 (300)
T KOG2629|consen 85 DYFVM-AVILAGIAYAAYR-----FVKSYVLPRFLGESKDKLEADKRQLDDQFDKAAKSLNALMDEVAQVSQL---LATQ 155 (300)
T ss_pred HHHHH-HHHHhhHHHHHHH-----HHHHHHHHHhhCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHH
Confidence 44555 7777775443221 111368899998765 47788888888888888888888877777665 4555
Q ss_pred HHHHHHHHHHHHHh
Q 027271 206 RKDLEEKVEEAKKS 219 (225)
Q Consensus 206 ~~~~~~~~~~~~~~ 219 (225)
|+++.+.++.++.+
T Consensus 156 q~Els~~L~~l~~~ 169 (300)
T KOG2629|consen 156 QSELSRALASLKNT 169 (300)
T ss_pred HHHHHHHHHHHHHH
Confidence 66888888888877
No 100
>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=44.72 E-value=25 Score=24.96 Aligned_cols=26 Identities=12% Similarity=0.127 Sum_probs=21.0
Q ss_pred HHHhhhhccCCcccChHHHHHHcCCC
Q 027271 97 QLTVLTLAETNKVLPYDELMEELDVT 122 (225)
Q Consensus 97 ~LtLlsL~~~~~~isy~~I~~~L~i~ 122 (225)
.+.++.-...++..||.+||+.++.+
T Consensus 5 V~~~v~~IP~G~v~TYg~iA~~~g~p 30 (79)
T cd06445 5 VWEALRQIPYGEVTTYGQIAKLAGTP 30 (79)
T ss_pred HHHHHhcCCCCCcCcHHHHHHHHCCC
Confidence 34455555789999999999999996
No 101
>PF13518 HTH_28: Helix-turn-helix domain
Probab=44.44 E-value=36 Score=21.28 Aligned_cols=43 Identities=12% Similarity=0.193 Sum_probs=28.4
Q ss_pred HhhhhccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEec
Q 027271 99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLD 146 (225)
Q Consensus 99 tLlsL~~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkID 146 (225)
.++.+...+ . |+.++++.++|+ ...|-.|+- .--..| +.|-.+
T Consensus 4 ~iv~~~~~g-~-s~~~~a~~~gis-~~tv~~w~~-~y~~~G-~~~l~~ 46 (52)
T PF13518_consen 4 QIVELYLEG-E-SVREIAREFGIS-RSTVYRWIK-RYREGG-IEGLKP 46 (52)
T ss_pred HHHHHHHcC-C-CHHHHHHHHCCC-HhHHHHHHH-HHHhcC-HHHhcc
Confidence 344444444 3 999999999995 899999976 433334 444433
No 102
>PF13815 Dzip-like_N: Iguana/Dzip1-like DAZ-interacting protein N-terminal
Probab=43.30 E-value=1.5e+02 Score=22.65 Aligned_cols=51 Identities=20% Similarity=0.170 Sum_probs=38.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhcc
Q 027271 171 IQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLS 221 (225)
Q Consensus 171 ~~~L~~W~~~v~~~l~~ie~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 221 (225)
.+.|-.-.+.+...+..+++.+..++...+.....-+...+++..+|+.+|
T Consensus 68 ieYLl~~q~~L~~~~~~l~~~~~~~~~~~~~l~~~~~~~~~~~k~lk~E~k 118 (118)
T PF13815_consen 68 IEYLLHCQEYLSSQLEQLEERLQELQQEIEKLKQKLKKQKEEIKKLKKESK 118 (118)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 344444456677777788888888888887778888888888888888765
No 103
>PF03399 SAC3_GANP: SAC3/GANP/Nin1/mts3/eIF-3 p25 family; InterPro: IPR005062 This large family includes diverse proteins involved in large complexes [, , ]. The alignment contains one highly conserved negatively charged residue and one highly conserved positively charged residue that are probably important for the function of these proteins. The family includes the yeast nuclear export factor Sac3 [], and mammalian GANP/MCM3-associated proteins, which facilitate the nuclear localisation of MCM3, a protein that associates with chromatin in the G1 phase of the cell-cycle. The 26S protease (or 26S proteasome) is responsible for degrading ubiquitin conjugates. It consists of 19S regulatory complexes associated with the ends of 20S proteasomes. The 19S regulatory complex is composed of about 20 different polypeptides and confers ATP-dependence and substrate specificity to the 26S enzyme. The conserved region occurs at the C-terminal of the Nin1-like regulatory subunit [, , ]. This family includes several eukaryotic translation initiation factor 3 subunit 11 (eIF-3 p25) proteins. Eukaryotic initiation factor 3 (eIF3) is a multisubunit complex that is required for binding of mRNA to 40 S ribosomal subunits, stabilisation of ternary complex binding to 40 S subunits, and dissociation of 40 and 60 S subunits [].; PDB: 3T5V_D.
Probab=43.18 E-value=1.1e+02 Score=24.84 Aligned_cols=62 Identities=15% Similarity=0.222 Sum_probs=44.2
Q ss_pred chHHHHHHHHHhcCChhhhhhhh--CCCCCcc----hHHHHHHHHHHhhhhccCCcc-cChHHHHHHcC
Q 027271 59 NSKYLDMLRLFAHGTWSDYKNNA--GHLPQLV----PDQVLKLKQLTVLTLAETNKV-LPYDELMEELD 120 (225)
Q Consensus 59 ~~~l~~LL~iF~~G~~~d~~~~~--~~~~~L~----~~~~~Klr~LtLlsL~~~~~~-isy~~I~~~L~ 120 (225)
-.-..++...+..|++..|-+.. ...|.+. +....++|..++-+++...+. ++.+.+++-|+
T Consensus 135 i~~al~l~~a~~~gny~~ff~l~~~~~~~~l~~~l~~~~~~~iR~~al~~i~~ay~~~i~l~~l~~~L~ 203 (204)
T PF03399_consen 135 IQFALELCRALMEGNYVRFFRLYRSKSAPYLFACLMERFFNRIRLRALQSISKAYRSSIPLSFLAELLG 203 (204)
T ss_dssp HHHHHHHHHHH--TTHHHHHHHHT-TTS-HHHHHHHGGGHHHHHHHHHHHHHHHS-T-EEHHHHHHHTT
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHhccCCChHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcC
Confidence 34567888999999999998855 4455433 234679999999999887777 99998888765
No 104
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=43.16 E-value=29 Score=23.82 Aligned_cols=34 Identities=21% Similarity=0.271 Sum_probs=28.2
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 027271 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (225)
Q Consensus 107 ~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~ 142 (225)
+..++=.+||++|+++ ...+-.++. ..-..|.|+
T Consensus 13 ~~p~~T~eiA~~~gls-~~~aR~yL~-~Le~eG~V~ 46 (62)
T PF04703_consen 13 NGPLKTREIADALGLS-IYQARYYLE-KLEKEGKVE 46 (62)
T ss_dssp TS-EEHHHHHHHHTS--HHHHHHHHH-HHHHCTSEE
T ss_pred CCCCCHHHHHHHhCCC-HHHHHHHHH-HHHHCCCEE
Confidence 5678889999999997 999999999 888888774
No 105
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=42.60 E-value=37 Score=24.16 Aligned_cols=24 Identities=25% Similarity=0.221 Sum_probs=20.9
Q ss_pred cccChHHHHHHcCCCChHHHHHHHH
Q 027271 108 KVLPYDELMEELDVTNVRELEDFLI 132 (225)
Q Consensus 108 ~~isy~~I~~~L~i~~~~evE~lvI 132 (225)
...||.+||+.++++ ...|..++-
T Consensus 31 eGlS~kEIAe~LGIS-~~TVk~~l~ 54 (73)
T TIGR03879 31 AGKTASEIAEELGRT-EQTVRNHLK 54 (73)
T ss_pred cCCCHHHHHHHHCcC-HHHHHHHHh
Confidence 568999999999997 888888765
No 106
>KOG2166 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=42.38 E-value=3.7e+02 Score=27.41 Aligned_cols=118 Identities=16% Similarity=0.169 Sum_probs=67.9
Q ss_pred HHHHHhhhhccCCcccChHHHHHHcCCCChHHHHHHHHHHh--HhcCccEEEe--cCCCCEEEEEee----ccCC----C
Q 027271 95 LKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINEC--MYTGIVRGKL--DQLRRCFEVQFA----AGRD----L 162 (225)
Q Consensus 95 lr~LtLlsL~~~~~~isy~~I~~~L~i~~~~evE~lvI~~A--I~~gLI~gkI--Dq~~~~v~V~~~----~~R~----~ 162 (225)
+-+++++-|-.+.-.++|++|.+.++++ ..++-..+- .. +...++.+.. |..+.++.+++. .+|+ +
T Consensus 566 t~Qm~VLlLFN~~d~lt~~eI~~~t~i~-~~~l~~~L~-Sl~~~K~~v~~~~~s~~~~~~~~~~N~~f~sk~~Rv~i~~~ 643 (725)
T KOG2166|consen 566 TYQMAVLLLFNNTEKLTYEEILEQTNLG-HEDLARLLQ-SLSCLKYKILLKPMSRTSPNDEFAFNSKFTSKMRRVKIPLP 643 (725)
T ss_pred hHHHHHHHHccchhhccHHHHHHHhCCC-HHHHHHHHH-HHHHHhHhhccCccccCCCCcEEEeeccccCcceeeccCCC
Confidence 5567777788888899999999999998 888776665 54 1211222211 145667777642 2332 2
Q ss_pred CCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhcc
Q 027271 163 RPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLS 221 (225)
Q Consensus 163 ~~~q~~~L~~~L~~W~~~v~~~l~~ie~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 221 (225)
...+-+.....++.|+.- .|++.+...=++ +....|++=+.+=++..+++++
T Consensus 644 ~~~e~~~~~~~ve~dRk~------~i~AaIVRIMK~-rK~l~h~~Lv~Ev~~ql~~RF~ 695 (725)
T KOG2166|consen 644 PMDERKKVVEDVDKDRKY------AIDAAIVRIMKS-RKVLGHQQLVSEVVEQLSERFK 695 (725)
T ss_pred CchhHHHHHhhhhhHHHH------HHHHHHHHHHHh-hccccHHHHHHHHHHHHhhhcC
Confidence 333566678888888753 233333333222 1224445555555555555554
No 107
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=42.31 E-value=40 Score=26.61 Aligned_cols=43 Identities=12% Similarity=0.254 Sum_probs=37.9
Q ss_pred HHHhhhhccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCcc
Q 027271 97 QLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIV 141 (225)
Q Consensus 97 ~LtLlsL~~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI 141 (225)
...|+.++..++.+|+.++....|++ ...++.++- ++...|-|
T Consensus 14 k~rIvElVRe~GRiTi~ql~~~TGas-R~Tvk~~lr-eLVa~G~l 56 (127)
T PF06163_consen 14 KARIVELVREHGRITIKQLVAKTGAS-RNTVKRYLR-ELVARGDL 56 (127)
T ss_pred HHHHHHHHHHcCCccHHHHHHHHCCC-HHHHHHHHH-HHHHcCCe
Confidence 36888999999999999999999997 999999999 89877743
No 108
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=41.70 E-value=52 Score=28.32 Aligned_cols=46 Identities=17% Similarity=0.196 Sum_probs=34.4
Q ss_pred HHHHhhhhccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE
Q 027271 96 KQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (225)
Q Consensus 96 r~LtLlsL~~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~g 143 (225)
|-+.|+.+....+.++..+|++.+++| ...+=.++= .....|++.=
T Consensus 15 r~l~IL~~l~~~~~l~l~eia~~lgl~-kstv~Rll~-tL~~~G~l~~ 60 (257)
T PRK15090 15 KVFGILQALGEEREIGITELSQRVMMS-KSTVYRFLQ-TMKTLGYVAQ 60 (257)
T ss_pred HHHHHHHHhhcCCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEE
Confidence 445566555445679999999999998 888887777 6777887753
No 109
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=41.45 E-value=28 Score=24.06 Aligned_cols=27 Identities=30% Similarity=0.485 Sum_probs=20.4
Q ss_pred cCCcccChHHHHHHcCCCChHHHHHHHH
Q 027271 105 ETNKVLPYDELMEELDVTNVRELEDFLI 132 (225)
Q Consensus 105 ~~~~~isy~~I~~~L~i~~~~evE~lvI 132 (225)
..+|.-+.++||+.|||+ ..+|..++-
T Consensus 16 ~lgr~Pt~eEiA~~lgis-~~~v~~~l~ 42 (78)
T PF04539_consen 16 ELGREPTDEEIAEELGIS-VEEVRELLQ 42 (78)
T ss_dssp HHSS--BHHHHHHHHTS--HHHHHHHHH
T ss_pred HhCCCCCHHHHHHHHccc-HHHHHHHHH
Confidence 357899999999999997 999997644
No 110
>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=41.28 E-value=54 Score=21.44 Aligned_cols=35 Identities=20% Similarity=0.215 Sum_probs=29.3
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE
Q 027271 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (225)
Q Consensus 107 ~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~g 143 (225)
...++..+|++.++++ ...|...+= .....|+|.-
T Consensus 23 ~~~~s~~ela~~~g~s-~~tv~r~l~-~L~~~g~i~~ 57 (67)
T cd00092 23 QLPLTRQEIADYLGLT-RETVSRTLK-ELEEEGLISR 57 (67)
T ss_pred cCCcCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEEe
Confidence 3568999999999997 889988777 7888888864
No 111
>PRK00404 tatB sec-independent translocase; Provisional
Probab=41.26 E-value=1.7e+02 Score=23.55 Aligned_cols=34 Identities=18% Similarity=0.331 Sum_probs=27.8
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 027271 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKW 194 (225)
Q Consensus 161 ~~~~~q~~~L~~~L~~W~~~v~~~l~~ie~~~~~ 194 (225)
.|+++.+..+...+..|..++.+....+.+.+..
T Consensus 19 V~GPkkLP~laR~lG~~i~~~rr~~~~~k~ei~~ 52 (141)
T PRK00404 19 VLGPERLPGAARTAGLWIGRLKRSFNAIKQEVER 52 (141)
T ss_pred hcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4789999999999999999888877776665554
No 112
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=41.19 E-value=53 Score=19.90 Aligned_cols=33 Identities=21% Similarity=0.224 Sum_probs=27.8
Q ss_pred ccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE
Q 027271 109 VLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (225)
Q Consensus 109 ~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~g 143 (225)
.++..+|++.++++ ...+-..+- .....|+|.-
T Consensus 8 ~~s~~~la~~l~~s-~~tv~~~l~-~L~~~g~l~~ 40 (48)
T smart00419 8 PLTRQEIAELLGLT-RETVSRTLK-RLEKEGLISR 40 (48)
T ss_pred ccCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEEE
Confidence 46788999999997 888888877 8888898863
No 113
>PRK10884 SH3 domain-containing protein; Provisional
Probab=41.08 E-value=1.8e+02 Score=24.72 Aligned_cols=35 Identities=23% Similarity=0.264 Sum_probs=17.2
Q ss_pred HHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHh
Q 027271 185 LISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKS 219 (225)
Q Consensus 185 l~~ie~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 219 (225)
...+++++...++...+...+-+++.++++.+++.
T Consensus 120 ~~~l~~~~~~~~~~~~~L~~~n~~L~~~l~~~~~~ 154 (206)
T PRK10884 120 TAEMQQKVAQSDSVINGLKEENQKLKNQLIVAQKK 154 (206)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444444444444444455555555555555544
No 114
>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=40.79 E-value=23 Score=25.37 Aligned_cols=33 Identities=15% Similarity=0.377 Sum_probs=22.1
Q ss_pred HhhhhccCCcccChHHHHHHcC---CCChHHHHHHHH
Q 027271 99 TVLTLAETNKVLPYDELMEELD---VTNVRELEDFLI 132 (225)
Q Consensus 99 tLlsL~~~~~~isy~~I~~~L~---i~~~~evE~lvI 132 (225)
.|+...+..+.|||++|..+|. ++ .+.++.++-
T Consensus 11 ~Li~~gK~~G~lT~~eI~~~L~~~~~~-~e~id~i~~ 46 (82)
T PF03979_consen 11 KLIEKGKKKGYLTYDEINDALPEDDLD-PEQIDEIYD 46 (82)
T ss_dssp HHHHHHHHHSS-BHHHHHHH-S-S----HHHHHHHHH
T ss_pred HHHHHHhhcCcCCHHHHHHHcCccCCC-HHHHHHHHH
Confidence 3677777777899999999986 33 667777655
No 115
>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=39.81 E-value=1.6e+02 Score=22.16 Aligned_cols=55 Identities=20% Similarity=0.315 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhcccccC
Q 027271 171 IQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSHKVC 225 (225)
Q Consensus 171 ~~~L~~W~~~v~~~l~~ie~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 225 (225)
...+.+=..-++.+...+.....-+...+....+.+++-++..+.+|+.++..-|
T Consensus 38 ~~tI~qq~~~~~~L~~~~~~~r~~~~~~~~~~qq~r~~~e~~~e~ik~~lk~d~C 92 (110)
T PF10828_consen 38 AQTIQQQEDANQELKAQLQQNRQAVEEQQKREQQLRQQSEERRESIKTALKDDPC 92 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCcc
Confidence 3334444444445555555444444444444455556666777777777777666
No 116
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein. Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.
Probab=39.79 E-value=86 Score=26.05 Aligned_cols=52 Identities=15% Similarity=0.217 Sum_probs=37.0
Q ss_pred hhhhccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEE
Q 027271 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEV 154 (225)
Q Consensus 100 LlsL~~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq~~~~v~V 154 (225)
++.....++.++..+|++.++++ ...+-..+- .....|+|.-.-+ ....+.+
T Consensus 148 IL~~l~~~g~~s~~eia~~l~is-~stv~r~L~-~Le~~GlI~r~~~-r~~~~~l 199 (203)
T TIGR01884 148 VLEVLKAEGEKSVKNIAKKLGKS-LSTISRHLR-ELEKKGLVEQKGR-KGKRYSL 199 (203)
T ss_pred HHHHHHHcCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEEEcC-CccEEEe
Confidence 33333444569999999999997 888888777 7888899986543 3444443
No 117
>PF10975 DUF2802: Protein of unknown function (DUF2802); InterPro: IPR021244 This bacterial family of proteins has no known function.
Probab=38.11 E-value=35 Score=23.97 Aligned_cols=20 Identities=35% Similarity=0.388 Sum_probs=17.4
Q ss_pred cChHHHHHHcCCCChHHHHHH
Q 027271 110 LPYDELMEELDVTNVRELEDF 130 (225)
Q Consensus 110 isy~~I~~~L~i~~~~evE~l 130 (225)
-+.++|++.|+|| ..|+|-+
T Consensus 45 a~~~el~~~CgL~-~aEAeLl 64 (70)
T PF10975_consen 45 ASVEELMEECGLS-RAEAELL 64 (70)
T ss_pred CCHHHHHHHcCCC-HHHHHHH
Confidence 6789999999998 8999954
No 118
>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024550 The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation, together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits, TFIIE-alpha and TFIIE-beta, and joins the preinitiation complex after RNA polymerase II and TFIIF []. This entry represents a helix-turn-helix (HTH) domain found in eukaryotic TFIIE-alpha []. It is also found in proteins from archaebacteria that are presumed to be TFIIE-alpha subunits [], the transcriptional regulator SarR, and also DNA-directed RNA polymerase III subunit Rpc3.; PDB: 1VD4_A 1Q1H_A.
Probab=38.11 E-value=35 Score=25.30 Aligned_cols=36 Identities=19% Similarity=0.333 Sum_probs=27.3
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEE
Q 027271 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (225)
Q Consensus 107 ~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gk 144 (225)
++.++-++|++.++++ ..+|-.++- .....|+|..+
T Consensus 25 ~~~l~de~la~~~~l~-~~~vRkiL~-~L~~~~lv~~~ 60 (105)
T PF02002_consen 25 KGELTDEDLAKKLGLK-PKEVRKILY-KLYEDGLVSYR 60 (105)
T ss_dssp H--B-HHHHHHTT-S--HHHHHHHHH-HHHHHSS-EEE
T ss_pred cCCcCHHHHHHHhCCC-HHHHHHHHH-HHHHCCCeEEE
Confidence 4579999999999998 999999998 99999999666
No 119
>PRK03100 sec-independent translocase; Provisional
Probab=38.05 E-value=1.1e+02 Score=24.40 Aligned_cols=34 Identities=15% Similarity=0.143 Sum_probs=28.6
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 027271 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKW 194 (225)
Q Consensus 161 ~~~~~q~~~L~~~L~~W~~~v~~~l~~ie~~~~~ 194 (225)
.|+++.+..+...+..|...++.....+++++..
T Consensus 20 v~GPkrLP~~~r~lG~~vr~~R~~~~~~~~~~~~ 53 (136)
T PRK03100 20 ILGPERLPGAIRWTARALRQARDYASGATSQLRE 53 (136)
T ss_pred hcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4789999999999999999988887777766653
No 120
>PF06394 Pepsin-I3: Pepsin inhibitor-3-like repeated domain; InterPro: IPR010480 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. The members of this group of proteins belong to MEROPS inhibitor family I33, clan IR; the nematode aspartyl protease inhibitors or Aspins. They are restricted to parasitic nematode species. Structural features common to the nematode Aspins include the presence of a signal peptide sequence and the conservation of all four cysteine residues in the mature protein. The Y[V.A]RDLT sequence motif has been suggested as being of crucial functional importance in several filarial nematode inhibitors [], this sequence is not conserved in Tco-API-1 from Trichostrongylus colubriformis (Black scour worm) and it has been demonstrated that Tco-API-1, is not an Aspin as it does not inhibit porcine pepsin []. Related inhibitors from Onchocerca volvulus, Ov33 [] and Ascaris suum (Pig roundworm), PI-3 [] inhibit the in vitro activity of aspartyl proteases such as pepsin and cathepsin E (MEROPS peptidase family A1). Aspin may facilitate the safe passage of the eggs of Ascaris through the host stomach without digestion by pepsin [, ]. The other parasitic nematodes known to express homologous proteins do not pass through the stomach of their hosts []. Several proteins in the family are potent allergens in mammals. The three-dimensional structures of pepsin inhibitor-3 (PI-3) from A. suum and of the complex between PI-3 and porcine pepsin at 1. 75 A and 2.45 A resolution, respectively, have revealed the mechanism of aspartic protease inhibition. PI-3 has a new fold consisting of two identical domains, each comprising an antiparallel beta-sheet flanked by an alpha-helix. In the enzyme-inhibitor complex, the N-terminal beta-strand of PI-3 pairs with one strand of the 'active site flap' (residues 70-82) of pepsin, thus forming an eight-stranded beta-sheet that spans the two proteins. PI-3 has a novel mode of inhibition, using its N-terminal residues to occupy and therefore block the first three binding pockets in pepsin for substrate residues C-terminal to the scissile bond (S1'-S3') [].; PDB: 1F32_A 1F34_B.
Probab=38.04 E-value=13 Score=26.70 Aligned_cols=37 Identities=14% Similarity=0.198 Sum_probs=25.9
Q ss_pred CCEEEEEeeccCCCCCCcHHHH---HHHHHHHHHHHHHHH
Q 027271 149 RRCFEVQFAAGRDLRPGQLGSM---IQTLSNWLTTSDNLL 185 (225)
Q Consensus 149 ~~~v~V~~~~~R~~~~~q~~~L---~~~L~~W~~~v~~~l 185 (225)
++.++|...--|++++++.+.| .+++..|++.+...+
T Consensus 27 ~nklyvng~~~R~Lt~~E~~eL~~y~~~v~~y~~~l~~~i 66 (76)
T PF06394_consen 27 NNKLYVNGKYARDLTPDEQQELKTYQKKVAAYKEQLQQQI 66 (76)
T ss_dssp TTEEEETTCEEEE--HHHHHHHHHHHHHHHHHHHHHTT--
T ss_pred CCEEEECCEeeccCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5678888888899999887766 568888888766544
No 121
>PHA02943 hypothetical protein; Provisional
Probab=37.60 E-value=79 Score=25.97 Aligned_cols=45 Identities=16% Similarity=0.206 Sum_probs=32.3
Q ss_pred HHHHHhhhhccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 027271 95 LKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (225)
Q Consensus 95 lr~LtLlsL~~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~ 142 (225)
-|+.-++.+. ..+.-|-.+||+++|++ ..+++..+- -.=+.|.|+
T Consensus 11 ~R~~eILE~L-k~G~~TtseIAkaLGlS-~~qa~~~Ly-vLErEG~Vk 55 (165)
T PHA02943 11 TRMIKTLRLL-ADGCKTTSRIANKLGVS-HSMARNALY-QLAKEGMVL 55 (165)
T ss_pred HHHHHHHHHH-hcCCccHHHHHHHHCCC-HHHHHHHHH-HHHHcCceE
Confidence 3444555554 55678889999999997 999997766 555566554
No 122
>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=37.20 E-value=1.2e+02 Score=19.86 Aligned_cols=49 Identities=16% Similarity=0.252 Sum_probs=33.5
Q ss_pred hhhccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCE
Q 027271 101 LTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRC 151 (225)
Q Consensus 101 lsL~~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq~~~~ 151 (225)
..++..++..+..+|++.++++ ...+=..|= ++...|+|+=.=|..++.
T Consensus 10 ~~l~~~~~~~t~~~l~~~~~~~-~~~vs~~i~-~L~~~glv~~~~~~~d~R 58 (68)
T PF13463_consen 10 RALAHSDGPMTQSDLAERLGIS-KSTVSRIIK-KLEEKGLVEKERDPHDKR 58 (68)
T ss_dssp HHHT--TS-BEHHHHHHHTT---HHHHHHHHH-HHHHTTSEEEEEESSCTT
T ss_pred HHHHccCCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEecCCCCcCC
Confidence 3344577889999999999997 777776655 888899997776665544
No 123
>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=37.12 E-value=1.5e+02 Score=21.11 Aligned_cols=75 Identities=19% Similarity=0.298 Sum_probs=47.4
Q ss_pred HHhhhhccCCcccChHHHHHHc-CCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEe-eccCCCCCCcHHHHHHHHH
Q 027271 98 LTVLTLAETNKVLPYDELMEEL-DVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQF-AAGRDLRPGQLGSMIQTLS 175 (225)
Q Consensus 98 LtLlsL~~~~~~isy~~I~~~L-~i~~~~evE~lvI~~AI~~gLI~gkIDq~~~~v~V~~-~~~R~~~~~q~~~L~~~L~ 175 (225)
+.|..|.. +...|.+|.+.+ +|+ ...+-.-+= +....|||.=....... ..+.+ .+++- .++..+...+.
T Consensus 9 ~IL~~l~~--g~~rf~el~~~l~~is-~~~L~~~L~-~L~~~GLv~r~~~~~~p-~~v~Y~LT~~G---~~l~~~l~~l~ 80 (90)
T PF01638_consen 9 LILRALFQ--GPMRFSELQRRLPGIS-PKVLSQRLK-ELEEAGLVERRVYPEVP-PRVEYSLTEKG---KELLPVLEALE 80 (90)
T ss_dssp HHHHHHTT--SSEEHHHHHHHSTTS--HHHHHHHHH-HHHHTTSEEEEEESSSS-SEEEEEE-HHH---HHHHHHHHHHH
T ss_pred HHHHHHHh--CCCcHHHHHHhcchhH-HHHHHHHHH-HHHHcchhhcccccCCC-CCCccCCCcCH---HHHHHHHHHHH
Confidence 34444544 689999999999 886 777766666 68889999887765432 23332 22221 23445677777
Q ss_pred HHHHH
Q 027271 176 NWLTT 180 (225)
Q Consensus 176 ~W~~~ 180 (225)
.|..+
T Consensus 81 ~W~~~ 85 (90)
T PF01638_consen 81 EWGEE 85 (90)
T ss_dssp HHHHH
T ss_pred HHHHH
Confidence 77654
No 124
>PF13591 MerR_2: MerR HTH family regulatory protein
Probab=37.09 E-value=52 Score=23.62 Aligned_cols=32 Identities=19% Similarity=0.404 Sum_probs=25.7
Q ss_pred cChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecC
Q 027271 110 LPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQ 147 (225)
Q Consensus 110 isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq 147 (225)
||++++.+.++++ . .||. ..+..|+|.-...+
T Consensus 1 is~~e~~~~~~i~-~----~~l~-~lve~Gli~p~~~~ 32 (84)
T PF13591_consen 1 ISLEEFCEACGIE-P----EFLR-ELVEEGLIEPEGEE 32 (84)
T ss_pred CCHHHHHHHHCcC-H----HHHH-HHHHCCCeeecCCC
Confidence 6899999999998 4 4555 66669999987776
No 125
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=36.52 E-value=40 Score=23.11 Aligned_cols=24 Identities=17% Similarity=0.403 Sum_probs=20.4
Q ss_pred CCcccChHHHHHHcCCCChHHHHHH
Q 027271 106 TNKVLPYDELMEELDVTNVRELEDF 130 (225)
Q Consensus 106 ~~~~isy~~I~~~L~i~~~~evE~l 130 (225)
.++.+++-+||+.|+|+ ...|-.|
T Consensus 19 ~~g~i~lkdIA~~Lgvs-~~tIr~W 42 (60)
T PF10668_consen 19 SNGKIKLKDIAEKLGVS-ESTIRKW 42 (60)
T ss_pred hCCCccHHHHHHHHCCC-HHHHHHH
Confidence 45789999999999997 7777766
No 126
>cd04789 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator. Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=35.92 E-value=1.8e+02 Score=21.46 Aligned_cols=89 Identities=16% Similarity=0.233 Sum_probs=50.3
Q ss_pred cChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeeccCCCCCCcHHHHHHHHHHHHH---HHHHHHH
Q 027271 110 LPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLT---TSDNLLI 186 (225)
Q Consensus 110 isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq~~~~v~V~~~~~R~~~~~q~~~L~~~L~~W~~---~v~~~l~ 186 (225)
++..++|+.+||+ ...+-.| +- .|+|...=++ .-.|.++..++..+. .+..+++ .+..+..
T Consensus 2 ~~i~eva~~~gvs-~~tlR~y---e~--~Gll~~~r~~---------~g~R~Y~~~~l~~l~-~I~~l~~~G~~l~ei~~ 65 (102)
T cd04789 2 YTISELAEKAGIS-RSTLLYY---EK--LGLITGTRNA---------NGYRLYPDSDLQRLL-LIQQLQAGGLSLKECLA 65 (102)
T ss_pred CCHHHHHHHHCcC-HHHHHHH---HH--CCCCCCCcCC---------CCCeeCCHHHHHHHH-HHHHHHHCCCCHHHHHH
Confidence 5778999999997 8888877 22 4888753222 245667777766543 3333333 2222222
Q ss_pred HHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHh
Q 027271 187 SIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKS 219 (225)
Q Consensus 187 ~ie~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 219 (225)
.+... ...+....+.+++++++++....
T Consensus 66 ~l~~~-----~~~~~l~~~~~~l~~~i~~l~~~ 93 (102)
T cd04789 66 CLQGK-----LTRSLLLERLSSLAEQIARKQQA 93 (102)
T ss_pred HHcCC-----cHHHHHHHHHHHHHHHHHHHHHH
Confidence 22111 11234456667777777766554
No 127
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=35.33 E-value=44 Score=26.92 Aligned_cols=28 Identities=25% Similarity=0.343 Sum_probs=24.5
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 027271 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (225)
Q Consensus 107 ~~~isy~~I~~~L~i~~~~evE~lvI~~AI 136 (225)
...+||.+||+.+||| ...|...+- .|.
T Consensus 141 ~~gls~~EIA~~l~i~-~~tVks~l~-ra~ 168 (182)
T COG1595 141 LEGLSYEEIAEILGIS-VGTVKSRLH-RAR 168 (182)
T ss_pred hcCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 4579999999999998 999999887 764
No 128
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=34.93 E-value=1.6e+02 Score=24.45 Aligned_cols=21 Identities=10% Similarity=0.203 Sum_probs=17.8
Q ss_pred ChHHHHHHcCCCChHHHHHHHH
Q 027271 111 PYDELMEELDVTNVRELEDFLI 132 (225)
Q Consensus 111 sy~~I~~~L~i~~~~evE~lvI 132 (225)
+..++|+.+||+ ...+-.|.=
T Consensus 2 ti~evA~~lGVS-~~TLRrw~k 22 (175)
T PRK13182 2 KTPFVAKKLGVS-PKTVQRWVK 22 (175)
T ss_pred CHHHHHHHHCcC-HHHHHHHHH
Confidence 568999999997 889988854
No 129
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=34.55 E-value=1.3e+02 Score=19.31 Aligned_cols=36 Identities=33% Similarity=0.416 Sum_probs=28.9
Q ss_pred cCCcccC-hHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 027271 105 ETNKVLP-YDELMEELDVTNVRELEDFLINECMYTGIVR 142 (225)
Q Consensus 105 ~~~~~is-y~~I~~~L~i~~~~evE~lvI~~AI~~gLI~ 142 (225)
..+..++ -.+|++.++++ ...|-..+- ..-..|+|.
T Consensus 20 ~~~~~~~~~~~la~~~~is-~~~v~~~l~-~L~~~G~i~ 56 (66)
T cd07377 20 KPGDRLPSERELAEELGVS-RTTVREALR-ELEAEGLVE 56 (66)
T ss_pred CCCCCCCCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEE
Confidence 4444555 99999999996 889998888 788888875
No 130
>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; InterPro: IPR024259 Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.
Probab=34.19 E-value=64 Score=23.27 Aligned_cols=34 Identities=21% Similarity=0.264 Sum_probs=24.1
Q ss_pred HHhhhhccCCcccChHHHHHHcCCCChHHHHHHHH
Q 027271 98 LTVLTLAETNKVLPYDELMEELDVTNVRELEDFLI 132 (225)
Q Consensus 98 LtLlsL~~~~~~isy~~I~~~L~i~~~~evE~lvI 132 (225)
..|+.+-..++.+|-.++|.+++.+ .++|...+=
T Consensus 27 r~LLr~LA~G~PVt~~~LA~a~g~~-~e~v~~~L~ 60 (77)
T PF12324_consen 27 RPLLRLLAKGQPVTVEQLAAALGWP-VEEVRAALA 60 (77)
T ss_dssp HHHHHHHTTTS-B-HHHHHHHHT---HHHHHHHHH
T ss_pred HHHHHHHHcCCCcCHHHHHHHHCCC-HHHHHHHHH
Confidence 4566666679999999999999998 999987654
No 131
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=33.81 E-value=2.1e+02 Score=21.55 Aligned_cols=99 Identities=14% Similarity=0.092 Sum_probs=53.4
Q ss_pred ChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE-EecCCCCEEEEE----e----eccCCCCCCcHHHHHHHHHHHH---
Q 027271 111 PYDELMEELDVTNVRELEDFLINECMYTGIVRG-KLDQLRRCFEVQ----F----AAGRDLRPGQLGSMIQTLSNWL--- 178 (225)
Q Consensus 111 sy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~g-kIDq~~~~v~V~----~----~~~R~~~~~q~~~L~~~L~~W~--- 178 (225)
+..++|+.+||+ ...+-.| - + .|||.. +-+. +-..+=. | ...|.++.. ++.++.-+..+.
T Consensus 2 ~ige~a~~~gvs-~~tLryY-e-~---~GLi~p~~~~~-~yR~Y~~~d~~~l~~I~~lr~~G~s-l~eI~~~l~~~~~~~ 73 (116)
T cd04769 2 YIGELAQQTGVT-IKAIRLY-E-E---KGLLPSPKRSG-NYRVYDAQHVECLRFIKEARQLGFT-LAELKAIFAGHEGRA 73 (116)
T ss_pred CHHHHHHHHCcC-HHHHHHH-H-H---CCCCCCCCCCC-CceeeCHHHHHHHHHHHHHHHcCCC-HHHHHHHHhccccCC
Confidence 678999999997 8888877 2 3 688875 3333 2222111 0 011222211 222222222222
Q ss_pred -HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHH
Q 027271 179 -TTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAK 217 (225)
Q Consensus 179 -~~v~~~l~~ie~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 217 (225)
.....+...++++....+++.......++.+...++.++
T Consensus 74 ~~~~~~~~~~l~~~~~~l~~~i~~l~~~~~~l~~~~~~~~ 113 (116)
T cd04769 74 VLPWPHLQQALEDKKQEIRAQITELQQLLARLDAFEASLK 113 (116)
T ss_pred cCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 123445566667777777776666666666666666554
No 132
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=33.78 E-value=57 Score=27.43 Aligned_cols=83 Identities=14% Similarity=0.209 Sum_probs=53.0
Q ss_pred HHHHHHHHHhcCChhhhhhhh--C-CCCCcchHHHHHHHHHHhhhhccCCcccChHHHHHHcCCCChHHHHHHHHHHhHh
Q 027271 61 KYLDMLRLFAHGTWSDYKNNA--G-HLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMY 137 (225)
Q Consensus 61 ~l~~LL~iF~~G~~~d~~~~~--~-~~~~L~~~~~~Klr~LtLlsL~~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~ 137 (225)
.+-.+..++............ . ..+.|++.|.+=|+.-.=+..-..-|.++..+||+.+||+ ...+.+-+= +|.
T Consensus 127 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGIS-kst~~ehLR-rAe- 203 (215)
T COG3413 127 ELRDLLEILNFEDKEEVIESAFVEIGKNDLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGIS-KSTLSEHLR-RAE- 203 (215)
T ss_pred HHHHHHHHhcccceeeeccccccccccccCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCC-HHHHHHHHH-HHH-
Confidence 444556666655544333321 1 2235888876555555555555678999999999999997 778877666 555
Q ss_pred cCccEEEec
Q 027271 138 TGIVRGKLD 146 (225)
Q Consensus 138 ~gLI~gkID 146 (225)
.+|+.+-++
T Consensus 204 ~Kl~~~~~~ 212 (215)
T COG3413 204 RKLIEAYFD 212 (215)
T ss_pred HHHHHHhhh
Confidence 566555443
No 133
>PF14480 DNA_pol3_a_NI: DNA polymerase III polC-type N-terminus I
Probab=33.45 E-value=1.5e+02 Score=20.31 Aligned_cols=61 Identities=11% Similarity=0.178 Sum_probs=46.2
Q ss_pred ChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeeccCCCCCCcHHHHHHHHHH
Q 027271 111 PYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSN 176 (225)
Q Consensus 111 sy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq~~~~v~V~~~~~R~~~~~q~~~L~~~L~~ 176 (225)
.|..+.+.+++++ +....++= + ..+-+-.++..+++.++.-..++.++.+.+..+.++|..
T Consensus 2 ~F~~ll~ql~~~~-~~~~~~f~-~---~~I~kv~v~k~~~~w~f~l~~~~~l~~~~~~~~~~~l~~ 62 (76)
T PF14480_consen 2 RFFELLKQLQIPD-ELDNPLFE-D---AEIEKVTVHKKSRKWRFHLSSPHILPFEVYQKFEEKLKK 62 (76)
T ss_pred chHHHHHHcCCCc-hhhhhhhc-c---cEEEEEEEEccCCEEEEEEEeCCcCCHHHHHHHHHHHHH
Confidence 3678888999983 33344433 3 456778899999999999889999998888888777654
No 134
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=33.22 E-value=69 Score=27.58 Aligned_cols=46 Identities=22% Similarity=0.265 Sum_probs=35.2
Q ss_pred HHHHHhhhhccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 027271 95 LKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (225)
Q Consensus 95 lr~LtLlsL~~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~ 142 (225)
-|+..|+.+...++.++.++|++.++++ ...+...+- +.-..|++.
T Consensus 4 ~R~~~Il~~l~~~~~~~~~eLa~~l~VS-~~TiRRdL~-~L~~~~~l~ 49 (240)
T PRK10411 4 ARQQAIVDLLLNHTSLTTEALAEQLNVS-KETIRRDLN-ELQTQGKIL 49 (240)
T ss_pred HHHHHHHHHHHHcCCCcHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEE
Confidence 3666777777778899999999999997 888887766 544445554
No 135
>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=32.89 E-value=86 Score=26.73 Aligned_cols=45 Identities=20% Similarity=0.265 Sum_probs=36.7
Q ss_pred HHHHhhhhcc-CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 027271 96 KQLTVLTLAE-TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (225)
Q Consensus 96 r~LtLlsL~~-~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~ 142 (225)
|-+.++.+.. ..+.++..+|++.+++| ...+=.++- .....|++.
T Consensus 10 ral~IL~~l~~~~~~~~l~eia~~lglp-ksT~~RlL~-tL~~~G~l~ 55 (248)
T TIGR02431 10 RGLAVIEAFGAERPRLTLTDVAEATGLT-RAAARRFLL-TLVELGYVT 55 (248)
T ss_pred HHHHHHHHHhcCCCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEE
Confidence 4466676553 46689999999999998 888988888 788899987
No 136
>PRK00182 tatB sec-independent translocase; Provisional
Probab=31.66 E-value=1.7e+02 Score=24.06 Aligned_cols=33 Identities=12% Similarity=0.275 Sum_probs=26.4
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 027271 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIK 193 (225)
Q Consensus 161 ~~~~~q~~~L~~~L~~W~~~v~~~l~~ie~~~~ 193 (225)
.|+++.+..+...+..|...++.......+.+.
T Consensus 20 VfGPerLP~~~r~lg~~ir~~R~~~~~~k~el~ 52 (160)
T PRK00182 20 VIGPERLPRLIEDVRAALLAARTAINNAKQQLD 52 (160)
T ss_pred hcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 478999999999999999888877776555443
No 137
>KOG3431 consensus Apoptosis-related protein/predicted DNA-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=31.38 E-value=30 Score=27.21 Aligned_cols=22 Identities=32% Similarity=0.554 Sum_probs=20.1
Q ss_pred HHHHHHHHHHhHhcCccEEEecC
Q 027271 125 RELEDFLINECMYTGIVRGKLDQ 147 (225)
Q Consensus 125 ~evE~lvI~~AI~~gLI~gkIDq 147 (225)
..||.++| +++..|-|.|||++
T Consensus 70 q~VE~~li-rma~~gQvs~Kise 91 (129)
T KOG3431|consen 70 QAVENYLI-RMAQTGQVSHKISE 91 (129)
T ss_pred HHHHHHHH-HHHHhCCccccccH
Confidence 56999999 99999999999986
No 138
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=31.08 E-value=55 Score=26.33 Aligned_cols=27 Identities=7% Similarity=0.208 Sum_probs=23.9
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 027271 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (225)
Q Consensus 108 ~~isy~~I~~~L~i~~~~evE~lvI~~AI 136 (225)
...||++||+.+|++ ...|...+- .|.
T Consensus 148 ~~~s~~eIA~~lgis-~~tV~~~l~-ra~ 174 (182)
T PRK12537 148 DGCSHAEIAQRLGAP-LGTVKAWIK-RSL 174 (182)
T ss_pred cCCCHHHHHHHHCCC-hhhHHHHHH-HHH
Confidence 568999999999997 999999887 765
No 139
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=31.06 E-value=1.2e+02 Score=18.11 Aligned_cols=30 Identities=20% Similarity=0.196 Sum_probs=22.4
Q ss_pred cChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEe
Q 027271 110 LPYDELMEELDVTNVRELEDFLINECMYTGIVRGKL 145 (225)
Q Consensus 110 isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkI 145 (225)
++..++++.||++ ...+-.|+ ..|.|.+..
T Consensus 2 lt~~e~a~~lgis-~~ti~~~~-----~~g~i~~~~ 31 (49)
T TIGR01764 2 LTVEEAAEYLGVS-KDTVYRLI-----HEGELPAYR 31 (49)
T ss_pred CCHHHHHHHHCCC-HHHHHHHH-----HcCCCCeEE
Confidence 5788999999997 77777663 367777654
No 140
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=31.01 E-value=69 Score=27.80 Aligned_cols=45 Identities=20% Similarity=0.215 Sum_probs=34.1
Q ss_pred HHHHHhhhhccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCcc
Q 027271 95 LKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIV 141 (225)
Q Consensus 95 lr~LtLlsL~~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI 141 (225)
=|+..|+.+...++.++..++++.++++ ...+-.=+. ..-..|+|
T Consensus 5 eR~~~Il~~L~~~~~v~v~eLa~~l~VS-~~TIRRDL~-~Le~~g~l 49 (256)
T PRK10434 5 QRQAAILEYLQKQGKTSVEELAQYFDTT-GTTIRKDLV-ILEHAGTV 49 (256)
T ss_pred HHHHHHHHHHHHcCCEEHHHHHHHHCCC-HHHHHHHHH-HHHHCCCE
Confidence 3777888888888899999999999997 766644444 44456654
No 141
>PF12999 PRKCSH-like: Glucosidase II beta subunit-like
Probab=30.89 E-value=2.2e+02 Score=23.79 Aligned_cols=20 Identities=45% Similarity=0.712 Sum_probs=9.8
Q ss_pred HHHHHHHHHHHHHHHHHhcc
Q 027271 202 DKKHRKDLEEKVEEAKKSLS 221 (225)
Q Consensus 202 ~~~~~~~~~~~~~~~~~~~~ 221 (225)
....+++++++++++++.++
T Consensus 151 a~~~~~e~~~~l~~l~~ei~ 170 (176)
T PF12999_consen 151 AKKKREELEKKLEELEKEIQ 170 (176)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 33444555555555555443
No 142
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=30.68 E-value=2.3e+02 Score=21.19 Aligned_cols=44 Identities=23% Similarity=0.298 Sum_probs=29.5
Q ss_pred ChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeeccCCCCCCcHHH
Q 027271 111 PYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGS 169 (225)
Q Consensus 111 sy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq~~~~v~V~~~~~R~~~~~q~~~ 169 (225)
+..++++.+||+ ...+-.| - + .|||...-+. .-.|.++..++..
T Consensus 2 ~i~eva~~~gvs-~~tlR~Y-e-~---~GLl~p~r~~---------~g~R~Y~~~~~~~ 45 (112)
T cd01282 2 RIGELAARTGVS-VRSLRYY-E-E---QGLLVPERSA---------NGYRDYDEAAVDR 45 (112)
T ss_pred CHHHHHHHHCCC-HHHHHHH-H-H---CCCCCCCcCC---------CCCeecCHHHHHH
Confidence 678999999997 8888888 2 3 5888653221 2346666655443
No 143
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=30.63 E-value=2.3e+02 Score=21.06 Aligned_cols=46 Identities=15% Similarity=0.247 Sum_probs=30.2
Q ss_pred ChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEe-cCCCCEEEEEeeccCCCCCCcHHHH
Q 027271 111 PYDELMEELDVTNVRELEDFLINECMYTGIVRGKL-DQLRRCFEVQFAAGRDLRPGQLGSM 170 (225)
Q Consensus 111 sy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkI-Dq~~~~v~V~~~~~R~~~~~q~~~L 170 (225)
+..++++.+||+ ...+=.| - + .|||...- +..+ -.|.++..++..+
T Consensus 2 ~i~eva~~~gis-~~tlR~y-e-~---~GLi~p~~~~~~n--------gyR~Y~~~~i~~l 48 (108)
T cd01107 2 TIGEFAKLSNLS-IKALRYY-D-K---IGLLKPAYVDPDT--------GYRYYSAEQLERL 48 (108)
T ss_pred CHHHHHHHHCcC-HHHHHHH-H-H---cCCCCCCcCCCCC--------CccccCHHHHHHH
Confidence 678999999997 8888877 2 3 58887633 3323 2455555554443
No 144
>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=30.63 E-value=1.6e+02 Score=22.08 Aligned_cols=36 Identities=14% Similarity=0.229 Sum_probs=16.8
Q ss_pred HHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhcc
Q 027271 186 ISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLS 221 (225)
Q Consensus 186 ~~ie~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 221 (225)
..++.++...+......+...+.++.++.+..+.++
T Consensus 70 ~~l~~r~e~ie~~i~~lek~~~~l~~~l~e~q~~l~ 105 (110)
T TIGR02338 70 QELKEKKETLELRVKTLQRQEERLREQLKELQEKIQ 105 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333334444444444444445555555555555444
No 145
>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated. Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.
Probab=30.59 E-value=88 Score=26.59 Aligned_cols=22 Identities=18% Similarity=0.267 Sum_probs=18.5
Q ss_pred cChHHHHHHcCCCChHHHHHHHH
Q 027271 110 LPYDELMEELDVTNVRELEDFLI 132 (225)
Q Consensus 110 isy~~I~~~L~i~~~~evE~lvI 132 (225)
.++.+|++.|+|+ ...|+..+-
T Consensus 187 ~t~~eIa~~l~is-~~Tv~~~l~ 208 (232)
T TIGR03541 187 RRQADIAAILGIS-ERTVENHLR 208 (232)
T ss_pred CCHHHHHHHHCcC-HHHHHHHHH
Confidence 7899999999997 888876654
No 146
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=29.88 E-value=78 Score=28.54 Aligned_cols=39 Identities=23% Similarity=0.263 Sum_probs=34.8
Q ss_pred ccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCC
Q 027271 109 VLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLR 149 (225)
Q Consensus 109 ~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq~~ 149 (225)
-.+=++||+.||++ ...|=.++= +|...|+|+-+|+...
T Consensus 29 g~tQ~eIA~~lgiS-R~~VsRlL~-~Ar~~GiV~I~I~~~~ 67 (318)
T PRK15418 29 GLTQSEIGERLGLT-RLKVSRLLE-KGRQSGIIRVQINSRF 67 (318)
T ss_pred CCCHHHHHHHhCCC-HHHHHHHHH-HHHHcCcEEEEEeCCC
Confidence 47788999999997 899999988 9999999999998653
No 147
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=29.78 E-value=87 Score=27.10 Aligned_cols=47 Identities=11% Similarity=0.155 Sum_probs=37.6
Q ss_pred HHHHHhhhhccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE
Q 027271 95 LKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (225)
Q Consensus 95 lr~LtLlsL~~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~g 143 (225)
-|+..|+.+...++.++..+|++.++++ ...+-..+- +.-..|+|.-
T Consensus 5 ~R~~~Il~~l~~~~~~~~~ela~~l~vS-~~TirRdL~-~Le~~g~i~r 51 (251)
T PRK13509 5 QRHQILLELLAQLGFVTVEKVIERLGIS-PATARRDIN-KLDESGKLKK 51 (251)
T ss_pred HHHHHHHHHHHHcCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEE
Confidence 4666778888888999999999999997 888877766 6666677754
No 148
>PF09202 Rio2_N: Rio2, N-terminal; InterPro: IPR015285 This N-terminal domain is found in RIO2 kinases, and is structurally homologous to the winged helix (wHTH) domain. It adopts a structure consisting of four alpha helices followed by two beta strands and a fifth alpha helix. The domain confers DNA binding properties to the protein, as per other winged helix domains []. ; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0006468 protein phosphorylation; PDB: 1TQP_A 1ZAR_A 1TQI_A 1ZAO_A 1TQM_A.
Probab=29.75 E-value=1.3e+02 Score=21.69 Aligned_cols=49 Identities=12% Similarity=0.209 Sum_probs=37.9
Q ss_pred HHHHHhhhhc-cCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEe
Q 027271 95 LKQLTVLTLA-ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKL 145 (225)
Q Consensus 95 lr~LtLlsL~-~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkI 145 (225)
.|.|+-+-.. .++.-+|.+.|.+..+++ ..+++..+- +.+..++|.-+.
T Consensus 9 ~rvL~aiE~gmk~hE~VP~~~I~~~s~l~-~~~~~~~L~-~L~~~kLv~~~~ 58 (82)
T PF09202_consen 9 FRVLRAIEMGMKNHEWVPLELIEKISGLS-EGEVEKRLK-RLVKLKLVSRRN 58 (82)
T ss_dssp HHHHHHHHTTTTT-SSEEHHHHHHHHT---HHHHHHHHH-HHHHTTSEEEE-
T ss_pred HHHHHHHHHcccCCccCCHHHHHHHhCcC-HHHHHHHHH-HHHhcCCccccC
Confidence 5666666655 678889999999999997 999999888 899999998854
No 149
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=29.66 E-value=63 Score=25.73 Aligned_cols=28 Identities=29% Similarity=0.178 Sum_probs=23.7
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 027271 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (225)
Q Consensus 107 ~~~isy~~I~~~L~i~~~~evE~lvI~~AI 136 (225)
....||.+||+.+|++ ...|...+- .|.
T Consensus 148 ~~g~s~~EIA~~lgis-~~tVk~~l~-Rar 175 (183)
T TIGR02999 148 FAGLTVEEIAELLGVS-VRTVERDWR-FAR 175 (183)
T ss_pred HcCCCHHHHHHHhCCC-HHHHHHHHH-HHH
Confidence 3568999999999997 999998877 664
No 150
>PF09743 DUF2042: Uncharacterized conserved protein (DUF2042); InterPro: IPR018611 The ubiquitin fold modifier 1 (Ufm1) is the most recently discovered ubiquitin-like modifier whose conjugation (ufmylation) system is conserved in multicellular organisms. Ufm1 is known to covalently attach with cellular protein(s) via a specific E1-activating enzyme (Uba5), an E2-conjugating enzyme (Ufc1), and a E3-ligating enzyme []. This entry represents E3 UFM1-protein ligase 1.
Probab=29.65 E-value=94 Score=27.57 Aligned_cols=42 Identities=24% Similarity=0.336 Sum_probs=36.3
Q ss_pred cCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCC
Q 027271 105 ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQL 148 (225)
Q Consensus 105 ~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq~ 148 (225)
...+.++..++++..++| .+-+-..++ ++...++|+|++|..
T Consensus 126 qe~G~vsi~eLa~~~~Lp-~efl~~~li-~~~lg~~I~g~~d~~ 167 (272)
T PF09743_consen 126 QESGQVSISELAKQYDLP-SEFLKEELI-SKRLGKIIKGRLDGD 167 (272)
T ss_pred HHcCeEeHHHHHHhcCCc-HHHHHHHHh-hhhcCcceeEEEeCC
Confidence 355799999999999998 677776788 888899999999997
No 151
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=29.44 E-value=64 Score=25.60 Aligned_cols=27 Identities=22% Similarity=0.398 Sum_probs=23.7
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 027271 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (225)
Q Consensus 108 ~~isy~~I~~~L~i~~~~evE~lvI~~AI 136 (225)
...||.+||+.+|++ ...|...+- .|+
T Consensus 134 ~g~s~~EIA~~lgis-~~tV~~~l~-ra~ 160 (172)
T PRK12523 134 DGMGHAEIAERLGVS-VSRVRQYLA-QGL 160 (172)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 468999999999997 999998887 765
No 152
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=29.29 E-value=77 Score=19.91 Aligned_cols=31 Identities=16% Similarity=0.304 Sum_probs=22.9
Q ss_pred HhhhhccCCcccChHHHHHHcCCCChHHHHHHHH
Q 027271 99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFLI 132 (225)
Q Consensus 99 tLlsL~~~~~~isy~~I~~~L~i~~~~evE~lvI 132 (225)
.++.++... .|+.+||+.+|++ ...|..++-
T Consensus 19 ~i~~~~~~~--~s~~~vA~~~~vs-~~TV~ri~~ 49 (52)
T PF13542_consen 19 YILKLLRES--RSFKDVARELGVS-WSTVRRIFD 49 (52)
T ss_pred HHHHHHhhc--CCHHHHHHHHCCC-HHHHHHHHH
Confidence 344444444 7999999999997 888887654
No 153
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=28.89 E-value=72 Score=23.70 Aligned_cols=27 Identities=15% Similarity=0.329 Sum_probs=23.9
Q ss_pred HHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 027271 114 ELMEELDVTNVRELEDFLINECMYTGIVR 142 (225)
Q Consensus 114 ~I~~~L~i~~~~evE~lvI~~AI~~gLI~ 142 (225)
.||..++++ .++|+..+- +....|||+
T Consensus 26 ~ia~~l~~~-~~~v~~~l~-~Le~~GLle 52 (92)
T PF10007_consen 26 SIARRLKIP-LEEVREALE-KLEEMGLLE 52 (92)
T ss_pred HHHHHHCCC-HHHHHHHHH-HHHHCCCeE
Confidence 478889998 999999988 999999986
No 154
>PHA02763 hypothetical protein; Provisional
Probab=28.85 E-value=75 Score=23.57 Aligned_cols=51 Identities=20% Similarity=0.228 Sum_probs=40.3
Q ss_pred ccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeeccCCC
Q 027271 109 VLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDL 162 (225)
Q Consensus 109 ~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq~~~~v~V~~~~~R~~ 162 (225)
.++-+-+++-++-+.-+.||.|+= +| ..|=.-+||...=.+.|.|+..|-|
T Consensus 52 p~t~~~LsKYv~~SGFe~VEeWl~-eA--rrLh~~~id~~ryeiivi~in~~~f 102 (102)
T PHA02763 52 PVTEYCLSKYVKFSGFENVEEWLN-EA--RRLHNDKIDPERYEIIVIWINGRLF 102 (102)
T ss_pred CchHHHHHHHhhhcchhhHHHHHH-HH--HHHhcCCCChhheEEEEEEEcCccC
Confidence 455566777777776789999998 77 5677889999999999999877643
No 155
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=28.59 E-value=84 Score=27.55 Aligned_cols=47 Identities=11% Similarity=0.085 Sum_probs=36.2
Q ss_pred HHHHHHhhhhccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 027271 94 KLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (225)
Q Consensus 94 Klr~LtLlsL~~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~ 142 (225)
.-|+..|+.+...++.++..+|++.++++ ...+-.=+. ..-..|++.
T Consensus 16 ~eR~~~Il~~L~~~~~vtv~eLa~~l~VS-~~TIRRDL~-~Le~~G~l~ 62 (269)
T PRK09802 16 SERREQIIQRLRQQGSVQVNDLSALYGVS-TVTIRNDLA-FLEKQGIAV 62 (269)
T ss_pred HHHHHHHHHHHHHcCCEeHHHHHHHHCCC-HHHHHHHHH-HHHhCCCeE
Confidence 45788888888877789999999999997 776655555 444567776
No 156
>KOG2235 consensus Uncharacterized conserved protein [Function unknown]
Probab=28.57 E-value=1.2e+02 Score=30.34 Aligned_cols=46 Identities=22% Similarity=0.381 Sum_probs=39.2
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEE
Q 027271 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ 155 (225)
Q Consensus 106 ~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq~~~~v~V~ 155 (225)
..+.++.++++..+++| .+-+...++ +=....+|+|++|. ++++-.
T Consensus 130 E~gqvtiaeLakq~dl~-sellqs~l~-ek~lg~iikgr~dg--gviyT~ 175 (776)
T KOG2235|consen 130 EQGQVTIAELAKQWDLP-SELLQSLLI-EKLLGSIIKGRVDG--GVIYTS 175 (776)
T ss_pred HhcchHHHHHHHhcCCc-HHHHHHHHH-HHhhccceeeeecC--CEEeeH
Confidence 46789999999999999 678899999 76678899999999 676654
No 157
>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=28.48 E-value=2.1e+02 Score=21.16 Aligned_cols=19 Identities=26% Similarity=0.543 Sum_probs=8.0
Q ss_pred HHHHHHHHHHHHHHHHHhc
Q 027271 202 DKKHRKDLEEKVEEAKKSL 220 (225)
Q Consensus 202 ~~~~~~~~~~~~~~~~~~~ 220 (225)
-....+.++.++.+.++.|
T Consensus 82 l~~~~~~l~~~~~elk~~l 100 (105)
T cd00632 82 LERQEEDLQEKLKELQEKI 100 (105)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3333444444444444443
No 158
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=28.14 E-value=69 Score=25.70 Aligned_cols=27 Identities=7% Similarity=0.361 Sum_probs=23.5
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 027271 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (225)
Q Consensus 108 ~~isy~~I~~~L~i~~~~evE~lvI~~AI 136 (225)
...||++||+.+|++ ...|...+- .|+
T Consensus 142 ~g~s~~EIA~~lgis-~~tVk~~l~-rAl 168 (178)
T PRK12529 142 DGMKQKDIAQALDIA-LPTVKKYIH-QAY 168 (178)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 468999999999997 999998877 665
No 159
>smart00502 BBC B-Box C-terminal domain. Coiled coil region C-terminal to (some) B-Box domains
Probab=28.08 E-value=1.8e+02 Score=21.30 Aligned_cols=14 Identities=43% Similarity=0.608 Sum_probs=5.7
Q ss_pred HHHHHHHHHHHHHH
Q 027271 203 KKHRKDLEEKVEEA 216 (225)
Q Consensus 203 ~~~~~~~~~~~~~~ 216 (225)
..+++.+-.+++..
T Consensus 56 ~~~e~~ll~~l~~~ 69 (127)
T smart00502 56 NKRKKQLLEDLEEQ 69 (127)
T ss_pred HHHHHHHHHHHHHH
Confidence 33444444444433
No 160
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=27.88 E-value=68 Score=25.53 Aligned_cols=28 Identities=21% Similarity=0.441 Sum_probs=24.1
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 027271 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (225)
Q Consensus 107 ~~~isy~~I~~~L~i~~~~evE~lvI~~AI 136 (225)
....||++||+.+|++ ...|...+- .|+
T Consensus 133 ~~g~s~~EIA~~lgis-~~tV~~~l~-Ra~ 160 (172)
T PRK09651 133 LDGLTYSEIAHKLGVS-VSSVKKYVA-KAT 160 (172)
T ss_pred ccCCCHHHHHHHhCCC-HHHHHHHHH-HHH
Confidence 4678999999999997 999998877 765
No 161
>PF07464 ApoLp-III: Apolipophorin-III precursor (apoLp-III); InterPro: IPR010009 This family consists of several insect apolipoprotein-III sequences. Exchangeable apolipoproteins constitute a functionally important family of proteins that play critical roles in lipid transport and lipoprotein metabolism. Apolipophorin III (apoLp-III) is a prototypical exchangeable apolipoprotein found in many insect species that functions in transport of diacylglycerol (DAG) from the fat body lipid storage depot to flight muscles in the adult life stage [].; GO: 0008289 lipid binding, 0006869 lipid transport, 0005576 extracellular region; PDB: 1EQ1_A.
Probab=27.82 E-value=2.5e+02 Score=22.80 Aligned_cols=52 Identities=25% Similarity=0.279 Sum_probs=35.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhcc
Q 027271 167 LGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLS 221 (225)
Q Consensus 167 ~~~L~~~L~~W~~~v~~~l~~ie~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 221 (225)
.+.|++.-+....++..+...|+++++.+|.. -...-.++-.++.++...|+
T Consensus 29 ~~aik~~sd~~~~~l~~~~~~l~eeik~~n~~---~~e~l~~~~~kl~et~~~L~ 80 (155)
T PF07464_consen 29 VKAIKEQSDSVAQQLQNVSSSLQEEIKDANPE---AEEALKQLKTKLEETAEKLR 80 (155)
T ss_dssp SHHHHHHHHHHHHHHHHHHHHHHHHHTT-SST---HHHHHHHHHHHHHHHHHGGG
T ss_pred HHHHHHhHHHHHHHHHHHHHHHHHHHHhcChh---HHHHHHHHHHHHHHHHHHHH
Confidence 45678888888888888888888888887766 33334455555666555555
No 162
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=27.81 E-value=2.3e+02 Score=20.23 Aligned_cols=89 Identities=9% Similarity=0.136 Sum_probs=49.0
Q ss_pred cChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeeccCCCCCCcHHHHHHHHHHHHHHHHHHHHHHH
Q 027271 110 LPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQ 189 (225)
Q Consensus 110 isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq~~~~v~V~~~~~R~~~~~q~~~L~~~L~~W~~~v~~~l~~ie 189 (225)
.+..++|+.+||+ ...+-.| . + .|+|...=++ -..|.++..++..+ ..+..+.....--+..|.
T Consensus 2 ~~i~e~A~~~gvs-~~tLr~y-e-~---~Gli~p~r~~---------~g~R~y~~~dv~~l-~~i~~L~~d~g~~l~~i~ 65 (91)
T cd04766 2 YVISVAAELSGMH-PQTLRLY-E-R---LGLLSPSRTD---------GGTRRYSERDIERL-RRIQRLTQELGVNLAGVK 65 (91)
T ss_pred cCHHHHHHHHCcC-HHHHHHH-H-H---CCCcCCCcCC---------CCCeeECHHHHHHH-HHHHHHHHHcCCCHHHHH
Confidence 4778999999997 8888887 3 3 6888752121 13456666666543 223333331111222222
Q ss_pred HHHHHHHhhhHHHHHHHHHHHHHHHHHHHhccc
Q 027271 190 EKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSH 222 (225)
Q Consensus 190 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 222 (225)
.-+. ..++-..++++++++++.++.
T Consensus 66 ~~l~--------l~~~~~~l~~~l~~l~~~~~~ 90 (91)
T cd04766 66 RILE--------LEEELAELRAELDELRARLRR 90 (91)
T ss_pred HHHH--------HHHHHHHHHHHHHHHHHHhcc
Confidence 2221 344455666666666666653
No 163
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=27.73 E-value=67 Score=21.59 Aligned_cols=23 Identities=22% Similarity=0.172 Sum_probs=19.7
Q ss_pred ccChHHHHHHcCCCChHHHHHHHH
Q 027271 109 VLPYDELMEELDVTNVRELEDFLI 132 (225)
Q Consensus 109 ~isy~~I~~~L~i~~~~evE~lvI 132 (225)
-.++.+||+.|+++ ...|-.|.=
T Consensus 13 G~~~~eIA~~Lg~~-~~TV~~W~~ 35 (58)
T PF06056_consen 13 GWSIKEIAEELGVP-RSTVYSWKD 35 (58)
T ss_pred CCCHHHHHHHHCCC-hHHHHHHHH
Confidence 47899999999998 888888854
No 164
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=27.57 E-value=63 Score=20.16 Aligned_cols=23 Identities=13% Similarity=0.183 Sum_probs=17.6
Q ss_pred ccChHHHHHHcCCCChHHHHHHHH
Q 027271 109 VLPYDELMEELDVTNVRELEDFLI 132 (225)
Q Consensus 109 ~isy~~I~~~L~i~~~~evE~lvI 132 (225)
-.|+.+|++.||++ ...|-.|+=
T Consensus 17 G~s~~~ia~~lgvs-~~Tv~~w~k 39 (50)
T PF13384_consen 17 GWSIREIAKRLGVS-RSTVYRWIK 39 (50)
T ss_dssp T--HHHHHHHHTS--HHHHHHHHT
T ss_pred CCCHHHHHHHHCcC-HHHHHHHHH
Confidence 57999999999997 999998854
No 165
>KOG3438 consensus DNA-directed RNA polymerase, subunit L [Transcription]
Probab=27.54 E-value=1.8e+02 Score=22.19 Aligned_cols=43 Identities=14% Similarity=0.146 Sum_probs=35.7
Q ss_pred eeccCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 027271 156 FAAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMN 199 (225)
Q Consensus 156 ~~~~R~~~~~q~~~L~~~L~~W~~~v~~~l~~ie~~~~~~~~~~ 199 (225)
+++.|+ +..-.+.|+++|..-.+-++.+.+..++++..-+.++
T Consensus 61 RIQt~~-~~~A~evl~kgl~el~~~c~~v~~kF~~~i~~~k~~~ 103 (105)
T KOG3438|consen 61 RIQTRD-GDPAVEVLKKGLEELMQLCDHVRSKFEEEIEEYKDQK 103 (105)
T ss_pred EEEecC-CCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhc
Confidence 566666 5566889999999999999999999999998776654
No 166
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=27.52 E-value=74 Score=24.76 Aligned_cols=28 Identities=18% Similarity=0.195 Sum_probs=23.6
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 027271 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (225)
Q Consensus 107 ~~~isy~~I~~~L~i~~~~evE~lvI~~AI 136 (225)
....||++||+.+|++ ...|...+- .|.
T Consensus 120 ~~g~s~~EIA~~lgis-~~tV~~~l~-Rar 147 (160)
T PRK09642 120 LEEKSYQEIALQEKIE-VKTVEMKLY-RAR 147 (160)
T ss_pred HhCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 3568999999999997 999988876 654
No 167
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=27.19 E-value=73 Score=25.50 Aligned_cols=27 Identities=7% Similarity=0.224 Sum_probs=22.7
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 027271 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (225)
Q Consensus 108 ~~isy~~I~~~L~i~~~~evE~lvI~~AI 136 (225)
...||++||+.+|++ ...|...+- .|.
T Consensus 132 e~~s~~EIA~~lgis-~~tV~~~l~-ra~ 158 (179)
T PRK12543 132 HDYSQEEIAQLLQIP-IGTVKSRIH-AAL 158 (179)
T ss_pred ccCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 467999999999998 889888776 654
No 168
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=27.08 E-value=77 Score=24.38 Aligned_cols=27 Identities=11% Similarity=0.056 Sum_probs=23.3
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 027271 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (225)
Q Consensus 108 ~~isy~~I~~~L~i~~~~evE~lvI~~AI 136 (225)
...|+.+||+.+|++ ...|...+- .|+
T Consensus 121 ~~~s~~EIA~~l~is-~~tV~~~~~-ra~ 147 (154)
T PRK06759 121 VGKTMGEIALETEMT-YYQVRWIYR-QAL 147 (154)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 458999999999997 999998877 665
No 169
>PRK15396 murein lipoprotein; Provisional
Probab=26.67 E-value=2.5e+02 Score=20.23 Aligned_cols=53 Identities=6% Similarity=0.129 Sum_probs=37.7
Q ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHH
Q 027271 165 GQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAK 217 (225)
Q Consensus 165 ~q~~~L~~~L~~W~~~v~~~l~~ie~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 217 (225)
.+++.|...++.-..+++.+...+......+...+++.+|.-+.|-..+.+-|
T Consensus 25 ~kvd~LssqV~~L~~kvdql~~dv~~~~~~~~~a~~eA~raN~RlDn~~~sy~ 77 (78)
T PRK15396 25 AKIDQLSSDVQTLNAKVDQLSNDVNAMRSDVQAAKDDAARANQRLDNQATKYR 77 (78)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 36777888888888888888887777777777777767666666655555444
No 170
>PRK10884 SH3 domain-containing protein; Provisional
Probab=26.65 E-value=4e+02 Score=22.61 Aligned_cols=8 Identities=13% Similarity=0.256 Sum_probs=4.2
Q ss_pred eeccCCCC
Q 027271 156 FAAGRDLR 163 (225)
Q Consensus 156 ~~~~R~~~ 163 (225)
|+..+.+.
T Consensus 79 WV~~~~Ls 86 (206)
T PRK10884 79 WIPLKQLS 86 (206)
T ss_pred eEEHHHhc
Confidence 55555554
No 171
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=26.62 E-value=90 Score=28.42 Aligned_cols=38 Identities=21% Similarity=0.336 Sum_probs=34.1
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecC
Q 027271 108 KVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQ 147 (225)
Q Consensus 108 ~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq 147 (225)
..++=++||+.|||+ ..-|=.++= +|...|+|+-+|+.
T Consensus 25 ~gltQ~eIA~~LgiS-R~~v~rlL~-~Ar~~GiV~I~i~~ 62 (321)
T COG2390 25 EGLTQSEIAERLGIS-RATVSRLLA-KAREEGIVKISINS 62 (321)
T ss_pred cCCCHHHHHHHhCCC-HHHHHHHHH-HHHHCCeEEEEeCC
Confidence 457788999999997 889999988 99999999999984
No 172
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=26.61 E-value=1.4e+02 Score=24.46 Aligned_cols=34 Identities=18% Similarity=0.208 Sum_probs=28.7
Q ss_pred ChHHHHHHc--CCCChHHHHHHHHHHhHhcCccEEEec
Q 027271 111 PYDELMEEL--DVTNVRELEDFLINECMYTGIVRGKLD 146 (225)
Q Consensus 111 sy~~I~~~L--~i~~~~evE~lvI~~AI~~gLI~gkID 146 (225)
.+..|++.| +|+ .++|+.-+- -....|+|+=.=|
T Consensus 41 d~~~iak~l~p~is-~~ev~~sL~-~L~~~gli~k~~~ 76 (171)
T PF14394_consen 41 DPEWIAKRLRPKIS-AEEVRDSLE-FLEKLGLIKKDGD 76 (171)
T ss_pred CHHHHHHHhcCCCC-HHHHHHHHH-HHHHCCCeEECCC
Confidence 899999999 997 999998777 7888999975444
No 173
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=26.61 E-value=79 Score=24.46 Aligned_cols=27 Identities=4% Similarity=0.030 Sum_probs=22.8
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 027271 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (225)
Q Consensus 108 ~~isy~~I~~~L~i~~~~evE~lvI~~AI 136 (225)
...||++||+.||++ ...|...+- .|.
T Consensus 121 ~g~s~~EIA~~lgis-~~tV~~~l~-ra~ 147 (161)
T PRK09047 121 EDMDVAETAAAMGCS-EGSVKTHCS-RAT 147 (161)
T ss_pred hcCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 568999999999997 999988776 654
No 174
>TIGR02919 accessory Sec system glycosyltransferase GtfB. Members of this protein family are found only in Gram-positive bacteria of the Firmicutes lineage, including several species of Staphylococcus, Streptococcus, and Lactobacillus.
Probab=26.44 E-value=2.6e+02 Score=26.42 Aligned_cols=88 Identities=11% Similarity=0.206 Sum_probs=58.8
Q ss_pred ChHHHHHHcCC----CChHHHHHHHHHHhHhcCccEEEecCC--CCEEEEEeeccCCCCCCcHHHHHHHHHHHHHHHHHH
Q 027271 111 PYDELMEELDV----TNVRELEDFLINECMYTGIVRGKLDQL--RRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNL 184 (225)
Q Consensus 111 sy~~I~~~L~i----~~~~evE~lvI~~AI~~gLI~gkIDq~--~~~v~V~~~~~R~~~~~q~~~L~~~L~~W~~~v~~~ 184 (225)
..+++-+.|++ +..+++...++ +|+..|+.----|.. .+.+... ...+...+.+.|.+++..-...-+.+
T Consensus 340 ~l~~ly~~~dlyLdin~~e~~~~al~-eA~~~G~pI~afd~t~~~~~~i~~---g~l~~~~~~~~m~~~i~~lL~d~~~~ 415 (438)
T TIGR02919 340 KIQELYQTCDIYLDINHGNEILNAVR-RAFEYNLLILGFEETAHNRDFIAS---ENIFEHNEVDQLISKLKDLLNDPNQF 415 (438)
T ss_pred HHHHHHHhccEEEEccccccHHHHHH-HHHHcCCcEEEEecccCCcccccC---CceecCCCHHHHHHHHHHHhcCHHHH
Confidence 34455555543 43578888888 999999988777765 3222222 45577788899988888776555555
Q ss_pred HHHHHHHHHHHHhhhHHH
Q 027271 185 LISIQEKIKWADSMNEMD 202 (225)
Q Consensus 185 l~~ie~~~~~~~~~~~~~ 202 (225)
-..++.+...||....+.
T Consensus 416 ~~~~~~q~~~a~~~~~~~ 433 (438)
T TIGR02919 416 RELLEQQREHANDISKEQ 433 (438)
T ss_pred HHHHHHHHHHhccCCHHH
Confidence 666667777777665443
No 175
>KOG3809 consensus Microtubule-binding protein MIP-T3 [Cytoskeleton]
Probab=26.40 E-value=1.7e+02 Score=28.17 Aligned_cols=59 Identities=12% Similarity=0.169 Sum_probs=37.2
Q ss_pred CCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhc
Q 027271 162 LRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSL 220 (225)
Q Consensus 162 ~~~~q~~~L~~~L~~W~~~v~~~l~~ie~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 220 (225)
|-++++++|..-|..|+..-..--..++++..--....+-....-++++..+...++.|
T Consensus 504 ~i~eD~daMq~EL~mWrse~rq~~~elq~eq~~t~~a~epL~~~la~lq~~I~d~~e~i 562 (583)
T KOG3809|consen 504 FINEDIDAMQKELEMWRSEQRQNEQELQNEQAATFGASEPLYNILANLQKEINDTKEEI 562 (583)
T ss_pred hhhhhHHHHHHHHHHHHHHHHHhHHHHHhhhhcccccchHHHHHHHHHHHHHHHHHHHH
Confidence 34578999999999999766655555655554444444444455555666666555544
No 176
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=26.22 E-value=2.3e+02 Score=20.69 Aligned_cols=45 Identities=24% Similarity=0.313 Sum_probs=30.5
Q ss_pred ChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeeccCCCCCCcHHHH
Q 027271 111 PYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSM 170 (225)
Q Consensus 111 sy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq~~~~v~V~~~~~R~~~~~q~~~L 170 (225)
+..++++.+||+ ...+-.| . + .|++...=++ .-.|.++..++..+
T Consensus 2 ~I~e~a~~~gvs-~~tLR~y-e-~---~Gll~p~r~~---------~g~R~Y~~~dv~~l 46 (96)
T cd04774 2 KVDEVAKRLGLT-KRTLKYY-E-E---IGLVSPERSE---------GRYRLYSEEDLKRL 46 (96)
T ss_pred CHHHHHHHHCcC-HHHHHHH-H-H---CCCCCCCcCC---------CCCEEECHHHHHHH
Confidence 568999999997 8899988 3 3 5887632221 24566666666544
No 177
>PF01765 RRF: Ribosome recycling factor; InterPro: IPR023584 The ribosome recycling factor or ribosome release factor (RRF) dissociates ribosomes from mRNA after termination of translation, and is essential for bacterial growth []. Thus ribosomes are 'recycled' and ready for another round of protein synthesis. This entry represents a domain found in ribosome recycling factors.; PDB: 3R8N_Y 1Y69_8 1ISE_A 1EK8_A 1DD5_A 1WIH_A 2Z4L_6 2QBE_6 2V46_Y 1EH1_A ....
Probab=26.20 E-value=1.5e+02 Score=24.05 Aligned_cols=62 Identities=6% Similarity=-0.051 Sum_probs=36.1
Q ss_pred HhHhcCccEEEecCCCCEEEEEeeccCCCCCCc----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 027271 134 ECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQ----LGSMIQTLSNWLTTSDNLLISIQEKIKWADSM 198 (225)
Q Consensus 134 ~AI~~gLI~gkIDq~~~~v~V~~~~~R~~~~~q----~~~L~~~L~~W~~~v~~~l~~ie~~~~~~~~~ 198 (225)
+||...=+.-.......++.|. .|+ ++.+. ....+...+.|+..+.++-......+......
T Consensus 62 kAI~~s~l~l~p~~d~~~i~v~--iP~-~T~E~R~~l~k~~k~~~E~~k~~iR~iR~~~~~~lkk~~~~ 127 (165)
T PF01765_consen 62 KAIQKSNLNLNPQNDGNTIRVP--IPP-PTEERRKELVKQAKKIAEEAKVSIRNIRRDAMKKLKKLKKS 127 (165)
T ss_dssp HHHHHTTSSSEEEEETTEEEEE----S-SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred HHHHHCCCCCCcccCCcEEEEE--CCC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence 4444322233333334677765 333 23333 34457778889999999888888888777653
No 178
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=26.01 E-value=1.3e+02 Score=26.12 Aligned_cols=54 Identities=13% Similarity=0.148 Sum_probs=38.1
Q ss_pred HHHHhhhhcc-CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEE
Q 027271 96 KQLTVLTLAE-TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFE 153 (225)
Q Consensus 96 r~LtLlsL~~-~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq~~~~v~ 153 (225)
|-+.|+.+.. ..+.++..+|++.+++| ...+=.++- .....|++.= |...+...
T Consensus 26 r~l~IL~~~~~~~~~~tl~eIa~~lglp-kStv~RlL~-tL~~~G~l~~--~~~~~~Y~ 80 (271)
T PRK10163 26 RGIAILQYLEKSGGSSSVSDISLNLDLP-LSTTFRLLK-VLQAADFVYQ--DSQLGWWH 80 (271)
T ss_pred HHHHHHHHHHhCCCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEE--cCCCCeEE
Confidence 4456666553 44679999999999998 888888877 7788888843 44444433
No 179
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil
Probab=25.90 E-value=2.7e+02 Score=20.42 Aligned_cols=45 Identities=11% Similarity=0.157 Sum_probs=29.1
Q ss_pred cChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeeccCCCCCCcHHH
Q 027271 110 LPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGS 169 (225)
Q Consensus 110 isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq~~~~v~V~~~~~R~~~~~q~~~ 169 (225)
.+..++|+.+||+ ...+=.|- + .|++...-+.. -.|.++.+++..
T Consensus 2 ~~i~eva~~~gvs-~~tLR~ye--~---~Gll~~~r~~~---------g~R~Y~~~dl~~ 46 (102)
T cd04775 2 YTIGQMSRKFGVS-RSTLLYYE--S---IGLIPSARSEA---------NYRLYSEADLSR 46 (102)
T ss_pred CCHHHHHHHHCcC-HHHHHHHH--H---CCCCCCCCCCC---------CCeeeCHHHHHH
Confidence 5788999999997 88887762 2 58884332221 345556565554
No 180
>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=25.89 E-value=60 Score=23.36 Aligned_cols=26 Identities=19% Similarity=0.179 Sum_probs=18.6
Q ss_pred HHHhhhhccCCcccChHHHHHHcCCC
Q 027271 97 QLTVLTLAETNKVLPYDELMEELDVT 122 (225)
Q Consensus 97 ~LtLlsL~~~~~~isy~~I~~~L~i~ 122 (225)
.+..+.-...++..||.+||+.++-+
T Consensus 7 V~~~v~~IP~G~v~TYg~iA~~~g~p 32 (85)
T PF01035_consen 7 VWEAVRQIPYGKVTTYGEIARLLGRP 32 (85)
T ss_dssp HHHHHTTS-TT-BEEHHHHHHHTT-T
T ss_pred HHHHHHcCCCCceEeHHHHHHHHhhc
Confidence 35555566789999999999999954
No 181
>PF01984 dsDNA_bind: Double-stranded DNA-binding domain; InterPro: IPR002836 This protein family is found in archaea and eukaryota. The human TFAR19 (TF-1 cell apoptosis-related protein 19) encodes a protein which shares significant homology to the corresponding proteins of species ranging from yeast to mice. TFAR19 exhibits a ubiquitous expression pattern and its expression is up-regulated in the tumour cells undergoing apoptosis. TFAR19 may play a general role in the apoptotic process []. Also included in this family is a DNA-binding protein from the archaea, Methanobacterium thermoautotrophicum.; GO: 0003677 DNA binding; PDB: 1EIJ_A 2K6B_A 2CRU_A 1YYB_A 2JXN_A 2FH0_A.
Probab=25.66 E-value=37 Score=25.87 Aligned_cols=22 Identities=41% Similarity=0.729 Sum_probs=18.3
Q ss_pred HHHHHHHHHHhHhcCccEEEecC
Q 027271 125 RELEDFLINECMYTGIVRGKLDQ 147 (225)
Q Consensus 125 ~evE~lvI~~AI~~gLI~gkIDq 147 (225)
..||+.+| .....|-|.|+||.
T Consensus 62 ~~VE~~Li-qlaq~G~l~~kI~d 83 (107)
T PF01984_consen 62 RQVENQLI-QLAQSGQLRGKIDD 83 (107)
T ss_dssp HHHHHHHH-HHHHCTSSSS-B-H
T ss_pred HHHHHHHH-HHHHcCCCCCCcCH
Confidence 57999999 89999999999986
No 182
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=25.65 E-value=2.2e+02 Score=21.95 Aligned_cols=51 Identities=16% Similarity=0.045 Sum_probs=41.1
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecc
Q 027271 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAG 159 (225)
Q Consensus 107 ~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq~~~~v~V~~~~~ 159 (225)
...++-.+|++.++++ ...|=..|= .....|+|.=.-|+.++....-+.++
T Consensus 52 ~~~~t~~eLa~~l~i~-~~tvsr~l~-~Le~~GlI~R~~~~~DrR~~~l~LT~ 102 (144)
T PRK11512 52 AACITPVELKKVLSVD-LGALTRMLD-RLVCKGWVERLPNPNDKRGVLVKLTT 102 (144)
T ss_pred cCCCCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEEeccCcccCCeeEeEECh
Confidence 4569999999999997 777766655 78889999999998887777666554
No 183
>PRK04239 hypothetical protein; Provisional
Probab=25.64 E-value=38 Score=26.07 Aligned_cols=22 Identities=27% Similarity=0.551 Sum_probs=20.0
Q ss_pred HHHHHHHHHHhHhcCccEEEecC
Q 027271 125 RELEDFLINECMYTGIVRGKLDQ 147 (225)
Q Consensus 125 ~evE~lvI~~AI~~gLI~gkIDq 147 (225)
..||+.+| .+...|-|.|+||.
T Consensus 67 ~~VE~~li-qlAq~G~i~~ki~e 88 (110)
T PRK04239 67 EQVEQQLI-QLAQSGRIQGPIDD 88 (110)
T ss_pred HHHHHHHH-HHHHcCCCCCCcCH
Confidence 57999999 89999999999987
No 184
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=25.61 E-value=1.3e+02 Score=25.99 Aligned_cols=56 Identities=21% Similarity=0.268 Sum_probs=39.0
Q ss_pred HHHHhhhhcc-CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEE
Q 027271 96 KQLTVLTLAE-TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ 155 (225)
Q Consensus 96 r~LtLlsL~~-~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq~~~~v~V~ 155 (225)
|-|.|+++.. ....+++.+|++.+++| ...+=.++. .....|+++= |...++..+.
T Consensus 5 ral~iL~~l~~~~~~l~l~ela~~~glp-ksT~~RlL~-tL~~~G~v~~--d~~~g~Y~Lg 61 (246)
T COG1414 5 RALAILDLLAEGPGGLSLAELAERLGLP-KSTVHRLLQ-TLVELGYVEQ--DPEDGRYRLG 61 (246)
T ss_pred HHHHHHHHHHhCCCCCCHHHHHHHhCcC-HHHHHHHHH-HHHHCCCEEE--cCCCCcEeeh
Confidence 3355666543 33348999999999998 889988888 7888888753 3334455543
No 185
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=25.58 E-value=1.2e+02 Score=25.99 Aligned_cols=22 Identities=9% Similarity=-0.019 Sum_probs=17.1
Q ss_pred cChHHHHHHcCCCChHHHHHHHH
Q 027271 110 LPYDELMEELDVTNVRELEDFLI 132 (225)
Q Consensus 110 isy~~I~~~L~i~~~~evE~lvI 132 (225)
.+..+|++.|+|+ ...|+.-+-
T Consensus 195 ~t~~eIa~~l~is-~~TV~~h~~ 216 (240)
T PRK10188 195 KTSAEIAMILSIS-ENTVNFHQK 216 (240)
T ss_pred CCHHHHHHHhCCC-HHHHHHHHH
Confidence 6788999999996 777775443
No 186
>PF05791 Bacillus_HBL: Bacillus haemolytic enterotoxin (HBL); InterPro: IPR008414 This family consists of several Bacillus haemolytic enterotoxins (HblC, HblD, HblA, NheA, and NheB), which can cause food poisoning in humans []. Haemolysin BL (encoded by HBL) and non-haemolytic enterotoxin (encoded by NHE), represent the major enterotoxins produced by Bacillus cereus. Most of the cytotoxic activity of B. cereus isolates has been attributed to the level of Nhe, which may indicate a highly diarrheic potential []. The exact mechanism by which B. cereus causes diarrhoea is unknown. Hbl, cytotoxin K (CytK) and Nhe are all putative causes. Both Hbl and Nhe are three-component cytotoxins and maximal cytotoxicity of Nhe against epithelia is dependent on all three components. Nhe has haemolytic activity against erythrocytes from a variety of species. It is possible that the common structural and functional properties of these toxins indicate that the Hbl/Nhe and ClyA families of toxins constitute a superfamily of pore-forming cytotoxins []. The high virulence of some strains is thought to be due to the greater cytotoxic activity of CytK-1 compared to CytK-2, and to a high level of cytK expression []. Haemolysin BL and non-haemolytic enterotoxin production are both influenced by pH and micro []. This entry is found in cytotoxic proteins that form part of the enterotoxin complex and bind to erythrocytes. HblA is composed of a binding component, B, and two lytic components, L1 and L2. All three subunits act synergically to cause hemolysis.; GO: 0009405 pathogenesis, 0016020 membrane; PDB: 2NRJ_A.
Probab=25.50 E-value=3.3e+02 Score=22.39 Aligned_cols=58 Identities=9% Similarity=0.204 Sum_probs=43.6
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhcccc
Q 027271 166 QLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSHK 223 (225)
Q Consensus 166 q~~~L~~~L~~W~~~v~~~l~~ie~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 223 (225)
..+.+...|..|+..+..=...+......+..--......-..++.++.+.++.++..
T Consensus 125 ~~~~~i~~L~~f~~~l~~D~~~l~~~~~~l~~~l~~~~g~I~~L~~~I~~~~~~I~~~ 182 (184)
T PF05791_consen 125 KVQALINELNDFKDKLQKDSRNLKTDVDELQSILAGENGDIPQLQKQIENLNEEIKKD 182 (184)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHTGGG-GG
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHhcccCCHHHHHHHHHHHHHHHHhh
Confidence 4567888899999888888888888777777777777777788888888888877653
No 187
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=25.40 E-value=82 Score=25.44 Aligned_cols=27 Identities=22% Similarity=0.230 Sum_probs=22.8
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 027271 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (225)
Q Consensus 108 ~~isy~~I~~~L~i~~~~evE~lvI~~AI 136 (225)
...||++||+.+|++ ...|...+- .|.
T Consensus 146 ~g~s~~EIA~~lgis-~~tV~~~l~-Rar 172 (191)
T PRK12520 146 LELETEEICQELQIT-ATNAWVLLY-RAR 172 (191)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 458999999999997 999998876 653
No 188
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=25.27 E-value=86 Score=24.37 Aligned_cols=28 Identities=18% Similarity=0.322 Sum_probs=23.4
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 027271 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (225)
Q Consensus 107 ~~~isy~~I~~~L~i~~~~evE~lvI~~AI 136 (225)
....||++||+.+|++ ...|...+- .|.
T Consensus 119 ~~~~s~~eIA~~lgis-~~tv~~~l~-ra~ 146 (159)
T PRK12527 119 LEGLSHQQIAEHLGIS-RSLVEKHIV-NAM 146 (159)
T ss_pred HcCCCHHHHHHHhCCC-HHHHHHHHH-HHH
Confidence 3568999999999997 899988776 664
No 189
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=25.04 E-value=83 Score=24.88 Aligned_cols=28 Identities=25% Similarity=0.508 Sum_probs=23.8
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 027271 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (225)
Q Consensus 107 ~~~isy~~I~~~L~i~~~~evE~lvI~~AI 136 (225)
....||++||+.+|++ ...|...+- .|+
T Consensus 132 ~eg~s~~EIA~~l~is-~~tV~~~l~-ra~ 159 (168)
T PRK12525 132 LEGLTYVEIGERLGVS-LSRIHQYMV-EAF 159 (168)
T ss_pred HcCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 3568999999999997 999988877 665
No 190
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=24.93 E-value=1.1e+02 Score=18.67 Aligned_cols=22 Identities=23% Similarity=0.416 Sum_probs=19.5
Q ss_pred cChHHHHHHcCCCChHHHHHHHH
Q 027271 110 LPYDELMEELDVTNVRELEDFLI 132 (225)
Q Consensus 110 isy~~I~~~L~i~~~~evE~lvI 132 (225)
.++.+|++.++++ ...|..++-
T Consensus 19 ~s~~eia~~l~is-~~tv~~~~~ 40 (58)
T smart00421 19 LTNKEIAERLGIS-EKTVKTHLS 40 (58)
T ss_pred CCHHHHHHHHCCC-HHHHHHHHH
Confidence 6999999999997 899988765
No 191
>PRK11569 transcriptional repressor IclR; Provisional
Probab=24.93 E-value=1.4e+02 Score=26.01 Aligned_cols=45 Identities=22% Similarity=0.325 Sum_probs=35.7
Q ss_pred HHHHhhhhc-cCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 027271 96 KQLTVLTLA-ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (225)
Q Consensus 96 r~LtLlsL~-~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~ 142 (225)
|-|.|+.+. ...+.++..+|++.++++ ...+=.++- .....|++.
T Consensus 29 ral~IL~~l~~~~~~~~lseia~~lglp-ksTv~RlL~-tL~~~G~l~ 74 (274)
T PRK11569 29 RGLKLLEWIAESNGSVALTELAQQAGLP-NSTTHRLLT-TMQQQGFVR 74 (274)
T ss_pred HHHHHHHHHHhCCCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEE
Confidence 446666654 446679999999999998 888888888 788889885
No 192
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=24.92 E-value=87 Score=24.36 Aligned_cols=27 Identities=11% Similarity=0.158 Sum_probs=22.7
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 027271 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (225)
Q Consensus 108 ~~isy~~I~~~L~i~~~~evE~lvI~~AI 136 (225)
...||++||+.+|++ ...|...+- .|+
T Consensus 124 ~~~s~~EIA~~lgis-~~tV~~~l~-ra~ 150 (163)
T PRK07037 124 HGETQKDIARELGVS-PTLVNFMIR-DAL 150 (163)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 468999999999997 999998866 654
No 193
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=24.04 E-value=88 Score=25.29 Aligned_cols=28 Identities=14% Similarity=0.163 Sum_probs=23.6
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 027271 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (225)
Q Consensus 107 ~~~isy~~I~~~L~i~~~~evE~lvI~~AI 136 (225)
....||.+||+.+|++ ...|...+- .|.
T Consensus 145 ~~g~s~~EIA~~lgis-~~tVk~~l~-Rar 172 (193)
T TIGR02947 145 VEGFAYKEIAEIMGTP-IGTVMSRLH-RGR 172 (193)
T ss_pred hcCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 3568999999999997 999998877 664
No 194
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=23.79 E-value=91 Score=24.78 Aligned_cols=27 Identities=30% Similarity=0.513 Sum_probs=22.5
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 027271 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (225)
Q Consensus 108 ~~isy~~I~~~L~i~~~~evE~lvI~~AI 136 (225)
...||++||+.+|++ ...|...+- .|.
T Consensus 144 ~g~s~~eIA~~lgis-~~tV~~~l~-Rar 170 (179)
T PRK12514 144 EGLSYKELAERHDVP-LNTMRTWLR-RSL 170 (179)
T ss_pred cCCCHHHHHHHHCCC-hHHHHHHHH-HHH
Confidence 357999999999997 999988776 654
No 195
>PF15397 DUF4618: Domain of unknown function (DUF4618)
Probab=23.57 E-value=2.3e+02 Score=25.09 Aligned_cols=37 Identities=19% Similarity=0.298 Sum_probs=31.2
Q ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHH
Q 027271 165 GQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEM 201 (225)
Q Consensus 165 ~q~~~L~~~L~~W~~~v~~~l~~ie~~~~~~~~~~~~ 201 (225)
.+.+.+...|..|.++...-+..++.++..++.....
T Consensus 63 ~~l~~ak~eLqe~eek~e~~l~~Lq~ql~~l~akI~k 99 (258)
T PF15397_consen 63 KQLQQAKAELQEWEEKEESKLSKLQQQLEQLDAKIQK 99 (258)
T ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHH
Confidence 5688899999999999999999999888887776544
No 196
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=23.55 E-value=94 Score=24.43 Aligned_cols=27 Identities=7% Similarity=0.123 Sum_probs=23.4
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 027271 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (225)
Q Consensus 108 ~~isy~~I~~~L~i~~~~evE~lvI~~AI 136 (225)
...||++||+.+|++ ...|...+- +|.
T Consensus 127 ~g~s~~eIA~~lgis-~~tV~~~l~-Rar 153 (164)
T PRK12547 127 SGFSYEDAAAICGCA-VGTIKSRVS-RAR 153 (164)
T ss_pred cCCCHHHHHHHhCCC-HHHHHHHHH-HHH
Confidence 568999999999997 999998877 664
No 197
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=23.48 E-value=96 Score=24.08 Aligned_cols=27 Identities=19% Similarity=0.289 Sum_probs=23.4
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 027271 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (225)
Q Consensus 108 ~~isy~~I~~~L~i~~~~evE~lvI~~AI 136 (225)
...||.+||+.+|++ ...|...+- .|.
T Consensus 125 ~g~s~~eIA~~lgis-~~tV~~~l~-ra~ 151 (162)
T TIGR02983 125 EDLSEAQVAEALGIS-VGTVKSRLS-RAL 151 (162)
T ss_pred hcCCHHHHHHHhCCC-HHHHHHHHH-HHH
Confidence 468999999999997 999998877 664
No 198
>PF12728 HTH_17: Helix-turn-helix domain
Probab=23.42 E-value=2e+02 Score=17.94 Aligned_cols=37 Identities=16% Similarity=0.266 Sum_probs=24.7
Q ss_pred cChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEE
Q 027271 110 LPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEV 154 (225)
Q Consensus 110 isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq~~~~v~V 154 (225)
++.+++++.|+|+ ...+..|+= .|-|.+- ...+.+.+
T Consensus 2 lt~~e~a~~l~is-~~tv~~~~~-----~g~i~~~--~~g~~~~~ 38 (51)
T PF12728_consen 2 LTVKEAAELLGIS-RSTVYRWIR-----QGKIPPF--KIGRKWRI 38 (51)
T ss_pred CCHHHHHHHHCcC-HHHHHHHHH-----cCCCCeE--EeCCEEEE
Confidence 5788999999997 777776643 5666554 14444444
No 199
>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=23.36 E-value=95 Score=22.23 Aligned_cols=26 Identities=12% Similarity=0.146 Sum_probs=20.8
Q ss_pred HHHhhhhccCCcccChHHHHHHcCCC
Q 027271 97 QLTVLTLAETNKVLPYDELMEELDVT 122 (225)
Q Consensus 97 ~LtLlsL~~~~~~isy~~I~~~L~i~ 122 (225)
.+..+.-...++..||.+||+.++-+
T Consensus 7 V~~~l~~IP~G~v~TYg~iA~~~g~p 32 (80)
T TIGR00589 7 VWQALRTIPYGETKSYGQLAARIGNP 32 (80)
T ss_pred HHHHHhCCCCCCcCCHHHHHHHhCCC
Confidence 34555556789999999999999976
No 200
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator. This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=23.35 E-value=2.7e+02 Score=21.33 Aligned_cols=27 Identities=19% Similarity=0.333 Sum_probs=21.1
Q ss_pred ChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE
Q 027271 111 PYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (225)
Q Consensus 111 sy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~g 143 (225)
+..++|+.+||+ ...+-.|- + .||+..
T Consensus 2 ~I~e~a~~~gvs-~~tlR~Ye--~---~GLl~~ 28 (127)
T TIGR02047 2 KIGELAQKTGVS-VETIRFYE--K---QGLLPP 28 (127)
T ss_pred cHHHHHHHHCcC-HHHHHHHH--H---CCCCCC
Confidence 578999999997 88888772 2 688863
No 201
>PF07926 TPR_MLP1_2: TPR/MLP1/MLP2-like protein; InterPro: IPR012929 This domain is found in a number of proteins, including TPR protein (P12270 from SWISSPROT) and yeast myosin-like proteins 1 (MLP1, Q02455 from SWISSPROT) and 2 (MLP2, P40457 from SWISSPROT). These proteins share a number of features; for example, they all have coiled-coil regions and all three are associated with nuclear pores [, , ]. TPR is thought to be a component of nuclear pore complex- attached intranuclear filaments [], and is implicated in nuclear protein import []. Moreover, its N-terminal region is involved in the activation of oncogenic kinases, possibly by mediating the dimerisation of kinase domains or by targeting these kinases to the nuclear pore complex []. MLP1 and MLP2 are involved in the process of telomere length regulation, where they are thought to interact with proteins such as Tel1p and modulate their activity []. ; GO: 0006606 protein import into nucleus, 0005643 nuclear pore
Probab=23.31 E-value=3.5e+02 Score=20.87 Aligned_cols=54 Identities=11% Similarity=0.169 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhc
Q 027271 167 LGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSL 220 (225)
Q Consensus 167 ~~~L~~~L~~W~~~v~~~l~~ie~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 220 (225)
+..++..+..-...+..+-..++............-+.++..++.++.++++++
T Consensus 61 L~~lr~e~~~~~~~~~~l~~~~~~a~~~l~~~e~sw~~qk~~le~e~~~~~~r~ 114 (132)
T PF07926_consen 61 LQQLREELQELQQEINELKAEAESAKAELEESEASWEEQKEQLEKELSELEQRI 114 (132)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHH
Confidence 344555555555555555555555555555555555666666777776666654
No 202
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=23.10 E-value=1.3e+02 Score=18.54 Aligned_cols=23 Identities=13% Similarity=0.196 Sum_probs=20.0
Q ss_pred ccChHHHHHHcCCCChHHHHHHHH
Q 027271 109 VLPYDELMEELDVTNVRELEDFLI 132 (225)
Q Consensus 109 ~isy~~I~~~L~i~~~~evE~lvI 132 (225)
..++.+|++.++++ ...|..++=
T Consensus 15 ~~s~~eia~~l~~s-~~tv~~~~~ 37 (57)
T cd06170 15 GKTNKEIADILGIS-EKTVKTHLR 37 (57)
T ss_pred CCCHHHHHHHHCCC-HHHHHHHHH
Confidence 36999999999997 899998865
No 203
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=22.93 E-value=97 Score=25.01 Aligned_cols=28 Identities=18% Similarity=0.158 Sum_probs=23.1
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 027271 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (225)
Q Consensus 107 ~~~isy~~I~~~L~i~~~~evE~lvI~~AI 136 (225)
....||.+||+.+|++ ...|...+- .|.
T Consensus 153 ~~g~s~~EIA~~lgis-~~tV~~~l~-ra~ 180 (194)
T PRK12513 153 HGDLELEEIAELTGVP-EETVKSRLR-YAL 180 (194)
T ss_pred ccCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 3568999999999997 999987766 554
No 204
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=22.79 E-value=3e+02 Score=19.90 Aligned_cols=45 Identities=16% Similarity=0.197 Sum_probs=30.4
Q ss_pred ChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeeccCCCCCCcHHH
Q 027271 111 PYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGS 169 (225)
Q Consensus 111 sy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq~~~~v~V~~~~~R~~~~~q~~~ 169 (225)
+..++|+.+||+ ...+-.| - + .|||.......++ .|.++.+++..
T Consensus 2 ~i~eva~~~gvs-~~tlR~y-e-~---~Gll~p~~r~~~g--------yR~Y~~~~l~~ 46 (96)
T cd04788 2 KIGELARRTGLS-VRTLHHY-D-H---IGLLSPSQRTEGG--------HRLYDRADIRR 46 (96)
T ss_pred CHHHHHHHHCcC-HHHHHHH-H-H---CCCCCCCccCCCC--------ceeeCHHHHHH
Confidence 578999999997 8888888 2 3 6888764333332 46666666544
No 205
>PF10779 XhlA: Haemolysin XhlA; InterPro: IPR019715 Haemolysin XhlA is a cell-surface associated haemolysin that lyses the two most prevalent types of insect immune cells (granulocytes and plasmatocytes) as well as rabbit and horse erythrocytes [].
Probab=22.53 E-value=2.7e+02 Score=19.19 Aligned_cols=48 Identities=23% Similarity=0.324 Sum_probs=27.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhcc
Q 027271 170 MIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLS 221 (225)
Q Consensus 170 L~~~L~~W~~~v~~~l~~ie~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 221 (225)
+.+++..=..++++ ++..+.......+..+...+.+.+++.+++.+.|
T Consensus 4 i~e~l~~ie~~l~~----~~~~i~~lE~~~~~~e~~i~~~~~~l~~I~~n~k 51 (71)
T PF10779_consen 4 IKEKLNRIETKLDN----HEERIDKLEKRDAANEKDIKNLNKQLEKIKSNTK 51 (71)
T ss_pred HHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444444444333 5555555555555556666777777777776543
No 206
>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional
Probab=22.43 E-value=3.6e+02 Score=26.08 Aligned_cols=67 Identities=7% Similarity=0.030 Sum_probs=39.2
Q ss_pred EEEEeeccCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---hhhHHHHHHHHHHHHHHHHHHHhcc
Q 027271 152 FEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWAD---SMNEMDKKHRKDLEEKVEEAKKSLS 221 (225)
Q Consensus 152 v~V~~~~~R~~~~~q~~~L~~~L~~W~~~v~~~l~~ie~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~ 221 (225)
+.++-+..+.|+.. .=..+|.++..+...+-..++.....++ .+..+.+++-++++++++.+++.++
T Consensus 52 ~~~~~vV~~~Fddk---VnqSALteqQ~kasELEKqLaaLrqElq~~saq~~dle~KIkeLEaE~~~Lk~Ql~ 121 (475)
T PRK13729 52 PDMTGVVDTTFDDK---VRQHATTEMQVTAAQMQKQYEEIRRELDVLNKQRGDDQRRIEKLGQDNAALAEQVK 121 (475)
T ss_pred CCccceecchhHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHH
Confidence 44444444554322 1245677777776666555555444444 5555566666777777777777663
No 207
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=22.42 E-value=92 Score=22.47 Aligned_cols=31 Identities=10% Similarity=0.057 Sum_probs=24.9
Q ss_pred HHHHhhhhccCCcccChHHHHHHcCCCChHHHH
Q 027271 96 KQLTVLTLAETNKVLPYDELMEELDVTNVRELE 128 (225)
Q Consensus 96 r~LtLlsL~~~~~~isy~~I~~~L~i~~~~evE 128 (225)
|+.-|+.+... +.++..+|++.+|++ ...|=
T Consensus 7 R~~~I~e~l~~-~~~ti~dvA~~~gvS-~~TVs 37 (80)
T TIGR02844 7 RVLEIGKYIVE-TKATVRETAKVFGVS-KSTVH 37 (80)
T ss_pred HHHHHHHHHHH-CCCCHHHHHHHhCCC-HHHHH
Confidence 66777887777 899999999999997 55543
No 208
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=22.42 E-value=3.3e+02 Score=20.20 Aligned_cols=31 Identities=19% Similarity=0.318 Sum_probs=23.3
Q ss_pred cChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEec
Q 027271 110 LPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLD 146 (225)
Q Consensus 110 isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkID 146 (225)
++..++|+.+||+ ...+-.|- + .|+|...-+
T Consensus 1 ~~i~eva~~~gvs-~~tlR~ye--~---~Gll~p~~~ 31 (108)
T cd04773 1 MTIGELAHLLGVP-PSTLRHWE--K---EGLLSPDRE 31 (108)
T ss_pred CCHHHHHHHHCcC-HHHHHHHH--H---CCCCCCCcC
Confidence 3678999999997 88888882 2 588865433
No 209
>PRK14861 tatA twin arginine translocase protein A; Provisional
Probab=22.37 E-value=2.3e+02 Score=19.34 Aligned_cols=33 Identities=12% Similarity=0.069 Sum_probs=24.6
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 027271 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIK 193 (225)
Q Consensus 161 ~~~~~q~~~L~~~L~~W~~~v~~~l~~ie~~~~ 193 (225)
.|+++.++.+...+..|....+.....+++...
T Consensus 20 vfGp~kLP~l~r~~G~~~~~fk~~~~~~~~~~~ 52 (61)
T PRK14861 20 IFGPKKLPELGKALGKTLREFKKATKELTDDDF 52 (61)
T ss_pred hcCchHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 478888999999998888777776666555443
No 210
>PF02416 MttA_Hcf106: mttA/Hcf106 family; InterPro: IPR003369 Members of this protein family are involved in a sec-independent translocation mechanism. This pathway has been called the DeltapH pathway in chloroplasts []. Members of this family in Escherichia coli are involved in export of redox proteins with a "twin arginine" leader motif (S/T-R-R-X-F-L-K) []. This sec-independent pathway is termed TAT for twin-arginine translocation system. This system mainly transports proteins with bound cofactors that require folding prior to export.; GO: 0008565 protein transporter activity, 0015031 protein transport; PDB: 2L16_A.
Probab=22.28 E-value=2.4e+02 Score=18.51 Aligned_cols=31 Identities=13% Similarity=0.214 Sum_probs=23.3
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHH
Q 027271 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEK 191 (225)
Q Consensus 161 ~~~~~q~~~L~~~L~~W~~~v~~~l~~ie~~ 191 (225)
.|+++.++.+...+.+|.....+..+..++.
T Consensus 16 lfGp~kLP~~~r~lG~~ir~fk~~~~~~~~~ 46 (53)
T PF02416_consen 16 LFGPKKLPELARSLGKAIREFKKAINEAKEE 46 (53)
T ss_dssp HS-TTTHHHHHHHHHHHHHHHHHHHHHHHH-
T ss_pred HhCchHHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence 3788999999999999988877766666554
No 211
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=22.27 E-value=1.1e+02 Score=23.90 Aligned_cols=27 Identities=22% Similarity=0.452 Sum_probs=23.4
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 027271 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (225)
Q Consensus 108 ~~isy~~I~~~L~i~~~~evE~lvI~~AI 136 (225)
...||.+||+.+|++ ...|...+- .|.
T Consensus 128 ~g~s~~EIA~~l~is-~~tV~~~l~-ra~ 154 (161)
T PRK12528 128 DGLGYGEIATELGIS-LATVKRYLN-KAA 154 (161)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 578999999999997 999998877 664
No 212
>PF02646 RmuC: RmuC family; InterPro: IPR003798 This protein contains several bacterial RmuC DNA recombination proteins. The function of the RMUC protein is unknown but it is suspected that it is either a structural protein that protects DNA against nuclease action, or is itself involved in DNA cleavage at the regions of DNA secondary structures []. Proteins in this family are predicted to contain a central endonuclease-like fold domain, surrounded by coiled coils, consistent with a direct role in DNA cleavage [, ].
Probab=22.17 E-value=5.2e+02 Score=23.02 Aligned_cols=53 Identities=8% Similarity=0.090 Sum_probs=37.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHH---HHHHHHHHHHHHhcc
Q 027271 169 SMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHR---KDLEEKVEEAKKSLS 221 (225)
Q Consensus 169 ~L~~~L~~W~~~v~~~l~~ie~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~ 221 (225)
.+.++|....+++..+-....+......++.+...... +++...+.++.++|+
T Consensus 10 pl~e~l~~~~~~l~~~~~~~~~~~~~L~~~l~~l~~~~~~~~~l~~~~~~L~~aL~ 65 (304)
T PF02646_consen 10 PLKEQLEKFEKRLEESFEQRSEEFGSLKEQLKQLSEANGEIQQLSQEASNLTSALK 65 (304)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHh
Confidence 35667777777777766666666666666665555566 788888888888876
No 213
>PF05565 Sipho_Gp157: Siphovirus Gp157; InterPro: IPR008840 This family contains both viral and bacterial proteins which are related to the Gp157 protein of the Streptococcus thermophilus SFi bacteriophage. It is thought that bacteria possessing the gene coding for this protein have an increased resistance to the bacteriophage [].
Probab=22.14 E-value=4.2e+02 Score=21.32 Aligned_cols=36 Identities=14% Similarity=0.288 Sum_probs=19.4
Q ss_pred HHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhc
Q 027271 185 LISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSL 220 (225)
Q Consensus 185 l~~ie~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 220 (225)
+..+++.+...+........+++..+.++..+|..+
T Consensus 49 Ik~~ea~~e~~k~E~krL~~rkk~~e~~~~~Lk~yL 84 (162)
T PF05565_consen 49 IKNLEADIEAIKAEIKRLQERKKSIENRIDRLKEYL 84 (162)
T ss_pred HHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333344444555555555556666666666666554
No 214
>PRK09343 prefoldin subunit beta; Provisional
Probab=21.97 E-value=2.6e+02 Score=21.44 Aligned_cols=35 Identities=11% Similarity=-0.021 Sum_probs=15.8
Q ss_pred cCCCCEEEEEeeccCCCCCCcHHHHHHHHHHHHHH
Q 027271 146 DQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTT 180 (225)
Q Consensus 146 Dq~~~~v~V~~~~~R~~~~~q~~~L~~~L~~W~~~ 180 (225)
+.+..--.|....+|.|=+.+.+.+...|..=.+.
T Consensus 48 ~~L~~d~~VYk~VG~vlv~qd~~e~~~~l~~r~E~ 82 (121)
T PRK09343 48 EKLPDDTPIYKIVGNLLVKVDKTKVEKELKERKEL 82 (121)
T ss_pred HcCCCcchhHHHhhHHHhhccHHHHHHHHHHHHHH
Confidence 33333333444455665455555554444433333
No 215
>PF05615 THOC7: Tho complex subunit 7; InterPro: IPR008501 The Tho complex (THOC) is involved in transcription elongation and mRNA export from the nucleus []. This entry represents the subunit THOC7, which is found in higher eukaryotes, and the non-homologous subunit Mft1p found in yeast. The funtions of these subunits are unknown, and it is not known if these subunits are functionally equivalent.
Probab=21.94 E-value=3.8e+02 Score=20.72 Aligned_cols=56 Identities=16% Similarity=0.195 Sum_probs=29.3
Q ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhc
Q 027271 165 GQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSL 220 (225)
Q Consensus 165 ~q~~~L~~~L~~W~~~v~~~l~~ie~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 220 (225)
+++..+.+.+..+...+.--+...+.-......+.+.=.....+|+.+++++|+.+
T Consensus 42 e~~~~~~e~~l~~l~~~e~~~~k~q~~~~~n~~e~e~Y~~~~~~i~~~i~~~k~~i 97 (139)
T PF05615_consen 42 EESQFLYERLLKELAQFEFSILKSQLILEMNKRERENYEQLNEEIEQEIEQAKKEI 97 (139)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45556666666665555555544443332222233333555666677666666654
No 216
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=21.92 E-value=4.2e+02 Score=21.26 Aligned_cols=35 Identities=17% Similarity=0.259 Sum_probs=31.1
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 027271 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (225)
Q Consensus 106 ~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~ 142 (225)
.++.++=++||+.|||+ ..+|=..+- .....||+.
T Consensus 25 ~~~~~tdEeLa~~Lgi~-~~~VRk~L~-~L~e~~Lv~ 59 (158)
T TIGR00373 25 IKGEFTDEEISLELGIK-LNEVRKALY-ALYDAGLAD 59 (158)
T ss_pred ccCCCCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCce
Confidence 44589999999999997 999999988 899999994
No 217
>PF08317 Spc7: Spc7 kinetochore protein; InterPro: IPR013253 This entry consists of cell division proteins which are required for kinetochore-spindle association [].
Probab=21.89 E-value=4.6e+02 Score=23.57 Aligned_cols=60 Identities=18% Similarity=0.204 Sum_probs=42.6
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhc
Q 027271 161 DLRPGQLGSMIQTLSNWLTTSDN---LLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSL 220 (225)
Q Consensus 161 ~~~~~q~~~L~~~L~~W~~~v~~---~l~~ie~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 220 (225)
..++.++..++..|..=...+.. -+..++.++...+...+.....+.++.++++++++..
T Consensus 205 ~~D~~eL~~lr~eL~~~~~~i~~~k~~l~el~~el~~l~~~i~~~~~~k~~l~~eI~e~~~~~ 267 (325)
T PF08317_consen 205 SCDQEELEALRQELAEQKEEIEAKKKELAELQEELEELEEKIEELEEQKQELLAEIAEAEKIR 267 (325)
T ss_pred hcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34556777888888777766653 3455566777777777778888888888888877654
No 218
>PRK14857 tatA twin arginine translocase protein A; Provisional
Probab=21.76 E-value=2.3e+02 Score=20.93 Aligned_cols=37 Identities=16% Similarity=0.153 Sum_probs=29.7
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 027271 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADS 197 (225)
Q Consensus 161 ~~~~~q~~~L~~~L~~W~~~v~~~l~~ie~~~~~~~~ 197 (225)
.|+++.+..+...+..|...++.....+++.+...-.
T Consensus 21 vfGP~KLP~lar~lGk~i~~fkk~~~~~~~e~~~~~~ 57 (90)
T PRK14857 21 VFGPKKLPEIGRSLGKTLKGFQEASKEFENEIKREMA 57 (90)
T ss_pred HcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4788999999999999999988888877766554433
No 219
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=21.67 E-value=1.1e+02 Score=24.22 Aligned_cols=27 Identities=19% Similarity=0.252 Sum_probs=22.8
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 027271 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (225)
Q Consensus 108 ~~isy~~I~~~L~i~~~~evE~lvI~~AI 136 (225)
...||.+||+.+|++ ...|...+- .|.
T Consensus 134 ~~~s~~EIA~~lgis-~~tV~~~l~-Ra~ 160 (173)
T PRK12522 134 EQYSYKEMSEILNIP-IGTVKYRLN-YAK 160 (173)
T ss_pred cCCCHHHHHHHhCCC-HHHHHHHHH-HHH
Confidence 568999999999997 999988776 654
No 220
>cd07627 BAR_Vps5p The Bin/Amphiphysin/Rvs (BAR) domain of yeast Sorting Nexin Vps5p. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. Vsp5p is the yeast counterpart of human SNX1 and is part of the retromer complex, which functions in the endosome-to-Golgi retrieval of vacuolar protein sorting receptor Vps10p, the Golgi-resident membrane protein A-ALP, and endopeptidase Kex2. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in
Probab=21.59 E-value=2.9e+02 Score=23.17 Aligned_cols=35 Identities=20% Similarity=0.259 Sum_probs=19.3
Q ss_pred HHHHHHHhhhHHHHHHHHHHHHHHHHHHHhccccc
Q 027271 190 EKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSHKV 224 (225)
Q Consensus 190 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 224 (225)
.++..++......+++.+....+-+++.+++|.++
T Consensus 143 ~K~~~~~~ei~~~e~~~~~a~~~~e~is~~~k~El 177 (216)
T cd07627 143 EKLNSLLSELEEAERRASELKKEFEEVSELIKSEL 177 (216)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34445555555555555555556666655555543
No 221
>PF09341 Pcc1: Transcription factor Pcc1; InterPro: IPR015419 Pcc1 is a proposed transcription factor involved in the expression of genes regulated by alpha-factor and galactose; component of the EKC/KEOPS protein complex with Kae1, Gon7, Bud32, and Cgi121; related to human cancer-testis antigens [].; PDB: 2BNR_C 2P5W_C 3KLA_C 2F54_C 2P5E_C 2F53_C 3ENO_E 3ENC_B.
Probab=21.55 E-value=2.8e+02 Score=19.08 Aligned_cols=47 Identities=17% Similarity=0.164 Sum_probs=36.4
Q ss_pred cCccEEEecCCCCEEEEEeeccCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHH
Q 027271 138 TGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQE 190 (225)
Q Consensus 138 ~gLI~gkIDq~~~~v~V~~~~~R~~~~~q~~~L~~~L~~W~~~v~~~l~~ie~ 190 (225)
.+-++..++-.++.+.|.+.. .+...|+..+..|...+.-+...+++
T Consensus 30 ~~~~~~~~~~~~~~L~i~~~A------~d~~~LRasvns~l~~l~l~~~~i~e 76 (76)
T PF09341_consen 30 PSRVKRELSVDGNKLVITIEA------EDLRSLRASVNSFLDLLKLAEETIEE 76 (76)
T ss_dssp S-SSEEEEEEESSEEEEEEEE------SSHHHHHHHHHHHHHHHHHHCHHH--
T ss_pred CCcEEEEEEEeCCEEEEEEEE------CCHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 467888888888899988754 55788999999999988877776653
No 222
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=21.40 E-value=1.1e+02 Score=24.91 Aligned_cols=27 Identities=22% Similarity=0.341 Sum_probs=22.9
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 027271 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (225)
Q Consensus 108 ~~isy~~I~~~L~i~~~~evE~lvI~~AI 136 (225)
...||++||+.||++ ...|...+- .|.
T Consensus 157 ~~~s~~EIA~~Lgis-~~tVk~~l~-ra~ 183 (194)
T PRK09646 157 GGLTYREVAERLAVP-LGTVKTRMR-DGL 183 (194)
T ss_pred cCCCHHHHHHHhCCC-hHhHHHHHH-HHH
Confidence 458999999999997 999998876 653
No 223
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=21.31 E-value=1.1e+02 Score=24.79 Aligned_cols=27 Identities=19% Similarity=0.305 Sum_probs=22.8
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 027271 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (225)
Q Consensus 108 ~~isy~~I~~~L~i~~~~evE~lvI~~AI 136 (225)
...||++||+.+|++ ...|...+= .|.
T Consensus 149 ~g~s~~EIA~~lgis-~~tVk~~l~-RAr 175 (189)
T PRK12530 149 LELSSEQICQECDIS-TSNLHVLLY-RAR 175 (189)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 468999999999997 999988766 554
No 224
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=21.19 E-value=1.1e+02 Score=24.78 Aligned_cols=27 Identities=19% Similarity=0.211 Sum_probs=23.3
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 027271 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (225)
Q Consensus 108 ~~isy~~I~~~L~i~~~~evE~lvI~~AI 136 (225)
...||++||+.+|++ ...|...+- .|.
T Consensus 126 eg~s~~EIA~~lgis-~~tV~~~l~-Rar 152 (182)
T PRK12511 126 EGLSYQEAAAVLGIP-IGTLMSRIG-RAR 152 (182)
T ss_pred cCCCHHHHHHHhCcC-HHHHHHHHH-HHH
Confidence 468999999999997 999998876 664
No 225
>PRK00478 scpA segregation and condensation protein A/unknown domain fusion protein; Provisional
Probab=21.18 E-value=7.6e+02 Score=23.94 Aligned_cols=98 Identities=6% Similarity=-0.024 Sum_probs=66.9
Q ss_pred CcccChHHHHHHcC-CCChHH---HHHHHHHHhHhcCccEEEecCCCCEEEEEeec-cCCCCCC-cHHHHHHHHHHHHHH
Q 027271 107 NKVLPYDELMEELD-VTNVRE---LEDFLINECMYTGIVRGKLDQLRRCFEVQFAA-GRDLRPG-QLGSMIQTLSNWLTT 180 (225)
Q Consensus 107 ~~~isy~~I~~~L~-i~~~~e---vE~lvI~~AI~~gLI~gkIDq~~~~v~V~~~~-~R~~~~~-q~~~L~~~L~~W~~~ 180 (225)
++.++|.++-..+. -++..+ .=--|. +.++.|.|...=+..-+.+.|.+.. .|..+.+ ..+.|.++...=...
T Consensus 360 ~~~~~F~~L~~~~~~~~sr~evVvtFLAlL-EL~K~~~I~i~Q~~~f~~I~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 438 (505)
T PRK00478 360 YNQVSLKRVLLKINHKISLMYFVTAFVALL-VLVNNQKIDLEQKNDDEELYICLLDPTKIVNSQESPQEMVQRQQEQEQA 438 (505)
T ss_pred CCeEEhHHHhhhcccCCCcceEehHHHHHH-HHhccCeEEEEEcCCCCeEEEEEcCcchhhhhhhCHHHHHHHHHHHHHH
Confidence 45799999987542 112222 124456 7889999999888888899987754 3444333 256777887777777
Q ss_pred HHHHHHHHHHHHHHHHhhhHHHHHH
Q 027271 181 SDNLLISIQEKIKWADSMNEMDKKH 205 (225)
Q Consensus 181 v~~~l~~ie~~~~~~~~~~~~~~~~ 205 (225)
....+..+++..+..|.++.+..-.
T Consensus 439 ~~~~~~~~~~~~~~~~~~~~~~~~~ 463 (505)
T PRK00478 439 LKESIKQIQEERAISNFQKREEYLK 463 (505)
T ss_pred HHHHHHHHHHHHHHhhHHHHHHHHH
Confidence 7888888888777777776655433
No 226
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=21.10 E-value=1.1e+02 Score=24.42 Aligned_cols=27 Identities=7% Similarity=-0.021 Sum_probs=22.8
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 027271 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (225)
Q Consensus 108 ~~isy~~I~~~L~i~~~~evE~lvI~~AI 136 (225)
...||++||+.+|++ ...|...+- .|.
T Consensus 144 ~g~s~~EIA~~l~is-~~tV~~~l~-rar 170 (181)
T PRK12536 144 EGLSVAETAQLTGLS-ESAVKVGIH-RGL 170 (181)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 468999999999997 999988876 654
No 227
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=21.08 E-value=1e+02 Score=19.72 Aligned_cols=23 Identities=26% Similarity=0.427 Sum_probs=18.9
Q ss_pred ccChHHHHHHcCCCChHHHHHHHH
Q 027271 109 VLPYDELMEELDVTNVRELEDFLI 132 (225)
Q Consensus 109 ~isy~~I~~~L~i~~~~evE~lvI 132 (225)
.-....||..|||+ ...|..|.=
T Consensus 27 ~~~~~~la~~l~l~-~~~V~~WF~ 49 (57)
T PF00046_consen 27 KEEREELAKELGLT-ERQVKNWFQ 49 (57)
T ss_dssp HHHHHHHHHHHTSS-HHHHHHHHH
T ss_pred cccccccccccccc-ccccccCHH
Confidence 44577899999997 899998864
No 228
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=21.06 E-value=1.1e+02 Score=24.04 Aligned_cols=27 Identities=7% Similarity=0.131 Sum_probs=22.9
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 027271 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (225)
Q Consensus 108 ~~isy~~I~~~L~i~~~~evE~lvI~~AI 136 (225)
...||.+||+.||++ ...|...+- .|.
T Consensus 133 ~g~s~~EIA~~lgis-~~tV~~~l~-ra~ 159 (173)
T PRK09645 133 RGWSTAQIAADLGIP-EGTVKSRLH-YAL 159 (173)
T ss_pred cCCCHHHHHHHHCcC-HHHHHHHHH-HHH
Confidence 468999999999998 999988776 664
No 229
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and 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 []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.
Probab=21.06 E-value=1.4e+02 Score=20.09 Aligned_cols=36 Identities=11% Similarity=0.238 Sum_probs=27.7
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE
Q 027271 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (225)
Q Consensus 106 ~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~g 143 (225)
..+..|..+|.+..+++ .++|-.-++ -.|..|++.-
T Consensus 24 ~~G~ltl~~i~~~t~l~-~~~Vk~~L~-~LiQh~~v~y 59 (62)
T PF08221_consen 24 SRGRLTLREIVRRTGLS-PKQVKKALV-VLIQHNLVQY 59 (62)
T ss_dssp HC-SEEHHHHHHHHT---HHHHHHHHH-HHHHTTSEEE
T ss_pred HcCCcCHHHHHHHhCCC-HHHHHHHHH-HHHHcCCeee
Confidence 34578999999999998 899977777 6899998864
No 230
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=21.01 E-value=1.1e+02 Score=24.33 Aligned_cols=27 Identities=11% Similarity=0.057 Sum_probs=23.2
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 027271 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (225)
Q Consensus 108 ~~isy~~I~~~L~i~~~~evE~lvI~~AI 136 (225)
...||++||+.+|++ ...|...+- .|.
T Consensus 146 ~g~s~~eIA~~l~is-~~tV~~~l~-ra~ 172 (184)
T PRK12512 146 EGASIKETAAKLSMS-EGAVRVALH-RGL 172 (184)
T ss_pred cCCCHHHHHHHhCCC-HHHHHHHHH-HHH
Confidence 478999999999998 999998876 664
No 231
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=20.92 E-value=1.9e+02 Score=20.77 Aligned_cols=44 Identities=23% Similarity=0.258 Sum_probs=29.5
Q ss_pred ChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeeccCCCCCCcHHH
Q 027271 111 PYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGS 169 (225)
Q Consensus 111 sy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq~~~~v~V~~~~~R~~~~~q~~~ 169 (225)
+..++++.+||+ ...+-.| . + .|++...-+.. -.|.|+..++..
T Consensus 2 ~~~eva~~~gi~-~~tlr~~-~-~---~Gll~~~~~~~---------g~r~y~~~dv~~ 45 (100)
T cd00592 2 TIGEVAKLLGVS-VRTLRYY-E-E---KGLLPPERSEN---------GYRLYSEEDLER 45 (100)
T ss_pred CHHHHHHHHCcC-HHHHHHH-H-H---CCCcCCCcCCC---------CCcccCHHHHHH
Confidence 567899999998 8888877 3 3 68876544332 235566665554
No 232
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=20.90 E-value=1.1e+02 Score=24.51 Aligned_cols=27 Identities=7% Similarity=0.003 Sum_probs=23.2
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 027271 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (225)
Q Consensus 108 ~~isy~~I~~~L~i~~~~evE~lvI~~AI 136 (225)
...||++||+.+|+| ...|...+= .|.
T Consensus 146 ~g~s~~eIA~~lgis-~~tV~~~l~-ra~ 172 (184)
T PRK12539 146 EGLSVAEAATRSGMS-ESAVKVSVH-RGL 172 (184)
T ss_pred cCCcHHHHHHHHCcC-HHHHHHHHH-HHH
Confidence 568999999999997 999998876 664
No 233
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=20.84 E-value=1.1e+02 Score=25.32 Aligned_cols=27 Identities=19% Similarity=0.292 Sum_probs=23.2
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 027271 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (225)
Q Consensus 108 ~~isy~~I~~~L~i~~~~evE~lvI~~AI 136 (225)
.-.+|.+||+.+|++ ...|...+- .|.
T Consensus 153 ~g~s~~EIA~~Lgis-~~tV~~~l~-RAr 179 (203)
T PRK09647 153 EGLSYEEIAATLGVK-LGTVRSRIH-RGR 179 (203)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 568999999999997 899998877 664
No 234
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=20.81 E-value=2.4e+02 Score=23.42 Aligned_cols=39 Identities=15% Similarity=0.208 Sum_probs=33.4
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecC
Q 027271 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQ 147 (225)
Q Consensus 107 ~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq 147 (225)
..-.+..+||+.++++ ...|+..+. .+...|++.-+++-
T Consensus 176 ~~g~s~~eIA~~l~iS-~~Tv~~~~~-~~~~~~~~~~~~~~ 214 (239)
T PRK10430 176 DYEFSTDELANAVNIS-RVSCRKYLI-WLVNCHILFTSIHY 214 (239)
T ss_pred CCCcCHHHHHHHhCch-HHHHHHHHH-HHHhCCEEEEEeec
Confidence 4567999999999997 999999999 99999988666654
No 235
>COG5647 Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=20.79 E-value=3.1e+02 Score=28.04 Aligned_cols=59 Identities=24% Similarity=0.311 Sum_probs=44.1
Q ss_pred HHHHHhhhhccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE----EEecCCCCEEEEE
Q 027271 95 LKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR----GKLDQLRRCFEVQ 155 (225)
Q Consensus 95 lr~LtLlsL~~~~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~----gkIDq~~~~v~V~ 155 (225)
.-++.++.|+..+.+++|++|.+-.+++ .+++-..+. ..+.+.++. ++.-..+-.++++
T Consensus 608 ~~q~~vfll~n~~e~lt~eei~e~T~l~-~~dl~~~L~-sl~~ak~~~l~~~~~~~~p~~~fy~n 670 (773)
T COG5647 608 VYQLLVFLLFNDHEELTFEEILELTKLS-TDDLKRVLQ-SLSCAKLVVLLKDDKLVSPNTKFYVN 670 (773)
T ss_pred HHHHHHHHHhcCccceeHHHHHhhcCCC-hhhHHHHHH-HHHhhheeeeccccccCCCCceEEEc
Confidence 3456777788999999999999999998 889888877 766666554 2333455556665
No 236
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=20.78 E-value=1.1e+02 Score=25.08 Aligned_cols=28 Identities=18% Similarity=0.179 Sum_probs=23.3
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 027271 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (225)
Q Consensus 107 ~~~isy~~I~~~L~i~~~~evE~lvI~~AI 136 (225)
....||.+||+.+|++ ...|...+- .|.
T Consensus 153 ~eg~s~~EIA~~lgis-~~tVk~~l~-RAr 180 (201)
T PRK12545 153 FLDFEIDDICTELTLT-ANHCSVLLY-RAR 180 (201)
T ss_pred HcCCCHHHHHHHHCcC-HHHHHHHHH-HHH
Confidence 4568999999999997 999988776 654
No 237
>KOG1760 consensus Molecular chaperone Prefoldin, subunit 4 [Posttranslational modification, protein turnover, chaperones]
Probab=20.74 E-value=2.9e+02 Score=21.79 Aligned_cols=41 Identities=15% Similarity=0.217 Sum_probs=22.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhccc
Q 027271 168 GSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSH 222 (225)
Q Consensus 168 ~~L~~~L~~W~~~v~~~l~~ie~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 222 (225)
+.+.+.|..=++++...+..++ .+.+.|.+..+++|+-|=+
T Consensus 80 ~~~~~~LEe~ke~l~k~i~~le--------------s~~e~I~~~m~~LK~~LYa 120 (131)
T KOG1760|consen 80 DKLQDQLEEKKETLEKEIEELE--------------SELESISARMDELKKVLYA 120 (131)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHHHHHHH
Confidence 3455555555555555444444 4455566666666665543
No 238
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=20.55 E-value=1.7e+02 Score=24.08 Aligned_cols=37 Identities=8% Similarity=0.204 Sum_probs=31.3
Q ss_pred ccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecC
Q 027271 109 VLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQ 147 (225)
Q Consensus 109 ~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gkIDq 147 (225)
-.+..+||+.|+|+ ...|+..+= -.-..|++.-.+.=
T Consensus 177 g~s~~eIa~~l~iS-~~Tv~~~~~-~~~~~~~~~~~~~~ 213 (225)
T PRK10046 177 QHTAETVAQALTIS-RTTARRYLE-YCASRHLIIAEIVH 213 (225)
T ss_pred CcCHHHHHHHhCcc-HHHHHHHHH-HHHhCCeEEEEeec
Confidence 47899999999997 999998887 77788988877653
No 239
>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY. This model represents the full length of CodY, a pleiotropic repressor in Bacillus subtilis and other Firmicutes (low-GC Gram-positive bacteria) that responds to intracellular levels of GTP and branched chain amino acids. The C-terminal helix-turn-helix DNA-binding region is modeled by pfam08222 in Pfam.
Probab=20.47 E-value=1.8e+02 Score=25.69 Aligned_cols=36 Identities=11% Similarity=0.252 Sum_probs=28.8
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEE
Q 027271 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (225)
Q Consensus 107 ~~~isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~gk 144 (225)
...++..+||+.+||+ ..-+=.-+- ..-..|+|+++
T Consensus 196 egrlse~eLAerlGVS-Rs~ireAlr-kLE~aGvIe~r 231 (251)
T TIGR02787 196 EGLLVASKIADRVGIT-RSVIVNALR-KLESAGVIESR 231 (251)
T ss_pred cccccHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEEec
Confidence 4789999999999997 666555555 67778999886
No 240
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=20.41 E-value=1.2e+02 Score=17.98 Aligned_cols=28 Identities=25% Similarity=0.345 Sum_probs=20.7
Q ss_pred cChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE
Q 027271 110 LPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (225)
Q Consensus 110 isy~~I~~~L~i~~~~evE~lvI~~AI~~gLI~g 143 (225)
++..++++.|+|+ ...+-.|+= .|.+.+
T Consensus 1 ~s~~e~a~~lgvs-~~tl~~~~~-----~g~~~~ 28 (49)
T cd04762 1 LTTKEAAELLGVS-PSTLRRWVK-----EGKLKA 28 (49)
T ss_pred CCHHHHHHHHCcC-HHHHHHHHH-----cCCCCc
Confidence 4678999999997 888887744 455544
No 241
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=20.34 E-value=1.1e+02 Score=19.87 Aligned_cols=30 Identities=13% Similarity=0.292 Sum_probs=19.8
Q ss_pred HhhhhccCCcccChHHHHHHcCCCChHHHHHHH
Q 027271 99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFL 131 (225)
Q Consensus 99 tLlsL~~~~~~isy~~I~~~L~i~~~~evE~lv 131 (225)
.++.....+. +..+||+.+||+ ...|-.++
T Consensus 14 ~iI~~~e~g~--s~~~ia~~fgv~-~sTv~~I~ 43 (53)
T PF04218_consen 14 EIIKRLEEGE--SKRDIAREFGVS-RSTVSTIL 43 (53)
T ss_dssp HHHHHHHCTT---HHHHHHHHT---CCHHHHHH
T ss_pred HHHHHHHcCC--CHHHHHHHhCCC-HHHHHHHH
Confidence 4555556665 999999999998 77776653
No 242
>PRK03887 methylated-DNA--protein-cysteine methyltransferase; Provisional
Probab=20.20 E-value=3.1e+02 Score=22.84 Aligned_cols=66 Identities=20% Similarity=0.267 Sum_probs=39.5
Q ss_pred chHHHHHHHHHhcCChhhhhhhhC-CCCCcchHHHHHHHHHH-hhhhccCCcccChHHHHHHcCCCChHHHH
Q 027271 59 NSKYLDMLRLFAHGTWSDYKNNAG-HLPQLVPDQVLKLKQLT-VLTLAETNKVLPYDELMEELDVTNVRELE 128 (225)
Q Consensus 59 ~~~l~~LL~iF~~G~~~d~~~~~~-~~~~L~~~~~~Klr~Lt-LlsL~~~~~~isy~~I~~~L~i~~~~evE 128 (225)
+..+-+++.-+..|...++..... .+..+++= .-+... |+.-+..+++.||.+||+.++.+ ...|=
T Consensus 61 ~~~~~~~l~~~l~g~~~~~~~~~~l~~~g~T~F---q~rV~~~Lv~~IP~G~v~TYgqIA~~~G~a-aRAVG 128 (175)
T PRK03887 61 PSDYPELVFKVLIGKISNEEGLEELSFEGLTPF---ERKVYEWLTKNVKRGEVITYGELAKALNTS-PRAVG 128 (175)
T ss_pred ChhHHHHHHHHHcCCccccccCcccCcCCCCHH---HHHHHHHHHHhCCCCCCCcHHHHHHHHCch-HHHHH
Confidence 345667777777888877642211 11111222 223333 45556889999999999999964 44443
No 243
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=20.19 E-value=1.3e+02 Score=18.57 Aligned_cols=21 Identities=14% Similarity=0.528 Sum_probs=16.7
Q ss_pred HHHHHHcCCCChHHHHHHHHHHh
Q 027271 113 DELMEELDVTNVRELEDFLINEC 135 (225)
Q Consensus 113 ~~I~~~L~i~~~~evE~lvI~~A 135 (225)
+.|+...|++ ..+|..|++ .|
T Consensus 17 ~~L~~~tgls-~~Qi~~WF~-Na 37 (40)
T PF05920_consen 17 EELAKQTGLS-RKQISNWFI-NA 37 (40)
T ss_dssp HHHHHHHTS--HHHHHHHHH-HH
T ss_pred HHHHHHcCCC-HHHHHHHHH-Hh
Confidence 4578889996 999999998 65
No 244
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=20.15 E-value=1.2e+02 Score=25.54 Aligned_cols=28 Identities=7% Similarity=0.095 Sum_probs=23.8
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 027271 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (225)
Q Consensus 107 ~~~isy~~I~~~L~i~~~~evE~lvI~~AI 136 (225)
....||.+||+.+|++ ...|...+- .|+
T Consensus 196 ~eg~s~~EIA~~lgis-~~tVk~~~~-rA~ 223 (234)
T PRK08301 196 GEEKTQKEVADMLGIS-QSYISRLEK-RII 223 (234)
T ss_pred CCCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 4678999999999997 999988876 664
No 245
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=20.14 E-value=1.3e+02 Score=23.09 Aligned_cols=28 Identities=21% Similarity=0.381 Sum_probs=22.6
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 027271 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (225)
Q Consensus 107 ~~~isy~~I~~~L~i~~~~evE~lvI~~AI 136 (225)
..-.||.+||+.+|++ ...|...+= .|.
T Consensus 119 ~~g~s~~eIA~~lgis-~~tv~~~l~-Ra~ 146 (154)
T TIGR02950 119 FKEFSYKEIAELLNLS-LAKVKSNLF-RAR 146 (154)
T ss_pred hccCcHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 3568999999999998 888887765 543
Done!