Query psy9642
Match_columns 437
No_of_seqs 212 out of 712
Neff 7.2
Searched_HMMs 46136
Date Sat Aug 17 00:55:20 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9642.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9642hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2582|consensus 100.0 2.5E-80 5.4E-85 600.7 33.0 416 1-427 1-416 (422)
2 KOG2581|consensus 100.0 2.7E-43 5.8E-48 346.3 26.9 333 52-405 123-462 (493)
3 KOG1498|consensus 99.9 3.1E-23 6.7E-28 204.5 20.6 239 145-396 172-424 (439)
4 KOG1463|consensus 99.8 8E-18 1.7E-22 163.7 22.6 285 78-370 66-393 (411)
5 COG5071 RPN5 26S proteasome re 99.8 1.5E-18 3.3E-23 166.3 12.4 237 145-395 172-423 (439)
6 PF01399 PCI: PCI domain; Int 99.7 1.7E-16 3.7E-21 132.3 12.4 104 263-367 1-105 (105)
7 COG5159 RPN6 26S proteasome re 99.7 4.9E-14 1.1E-18 134.9 24.0 246 124-374 146-395 (421)
8 KOG1464|consensus 99.6 9.1E-15 2E-19 139.2 14.9 197 187-388 231-431 (440)
9 KOG1497|consensus 99.6 4.4E-12 9.5E-17 123.0 30.0 232 143-395 143-383 (399)
10 COG5600 Transcription-associat 99.4 9E-12 2E-16 123.3 19.7 212 148-369 181-405 (413)
11 KOG2688|consensus 99.4 1.8E-12 3.8E-17 130.7 12.3 179 181-369 199-386 (394)
12 smart00753 PAM PCI/PINT associ 99.3 4.1E-11 8.8E-16 97.3 10.4 73 299-372 2-74 (88)
13 smart00088 PINT motif in prote 99.3 4.1E-11 8.8E-16 97.3 10.4 73 299-372 2-74 (88)
14 KOG2908|consensus 99.1 2E-07 4.3E-12 91.8 27.4 276 78-370 53-342 (380)
15 KOG1076|consensus 98.3 0.00016 3.5E-09 77.2 22.0 271 79-369 465-765 (843)
16 KOG0687|consensus 98.2 0.00023 4.9E-09 70.3 20.6 183 186-370 180-365 (393)
17 COG5187 RPN7 26S proteasome re 98.1 0.0023 5E-08 62.5 25.4 257 103-370 116-379 (412)
18 PF10255 Paf67: RNA polymerase 98.1 0.0042 9E-08 64.1 27.9 186 148-343 126-342 (404)
19 KOG0686|consensus 98.0 0.00086 1.9E-08 68.1 20.2 218 146-369 189-412 (466)
20 KOG2072|consensus 97.9 0.002 4.3E-08 70.1 21.9 71 297-367 423-493 (988)
21 KOG2753|consensus 97.5 0.14 3E-06 51.1 28.8 269 79-367 63-339 (378)
22 PF08375 Rpn3_C: Proteasome re 97.4 0.00016 3.5E-09 55.7 3.7 43 370-412 1-44 (68)
23 PF10075 PCI_Csn8: COP9 signal 96.5 0.0073 1.6E-07 53.5 6.8 109 233-346 10-121 (143)
24 KOG2758|consensus 96.3 0.025 5.3E-07 56.2 9.6 105 264-369 290-396 (432)
25 PF14938 SNAP: Soluble NSF att 95.8 0.17 3.8E-06 49.8 13.2 203 78-295 53-268 (282)
26 PF13432 TPR_16: Tetratricopep 95.0 0.073 1.6E-06 39.7 5.8 61 149-218 2-63 (65)
27 PF13371 TPR_9: Tetratricopept 94.6 0.079 1.7E-06 40.4 5.2 59 152-219 3-62 (73)
28 PF13414 TPR_11: TPR repeat; P 94.6 0.14 3.1E-06 38.5 6.6 63 146-217 5-69 (69)
29 PF12895 Apc3: Anaphase-promot 94.3 0.14 3.1E-06 40.4 6.4 58 146-213 27-84 (84)
30 PF09976 TPR_21: Tetratricopep 94.2 0.2 4.3E-06 44.0 7.7 89 115-214 57-145 (145)
31 TIGR02552 LcrH_SycD type III s 94.1 0.69 1.5E-05 39.3 10.6 87 121-220 32-119 (135)
32 PF07719 TPR_2: Tetratricopept 93.9 0.1 2.3E-06 33.4 3.9 31 188-218 2-33 (34)
33 TIGR02795 tol_pal_ybgF tol-pal 93.4 1.1 2.3E-05 36.7 10.4 94 119-219 15-109 (119)
34 PF13424 TPR_12: Tetratricopep 93.1 0.4 8.7E-06 37.0 6.9 68 146-215 7-74 (78)
35 PF00515 TPR_1: Tetratricopept 92.8 0.21 4.5E-06 32.2 4.0 31 188-218 2-33 (34)
36 PF08784 RPA_C: Replication pr 92.7 0.1 2.2E-06 43.4 3.0 37 321-358 65-101 (102)
37 PF09012 FeoC: FeoC like trans 92.4 0.37 7.9E-06 37.1 5.6 48 311-359 4-51 (69)
38 cd00189 TPR Tetratricopeptide 92.0 1.6 3.4E-05 32.5 8.9 83 120-215 14-96 (100)
39 PF09295 ChAPs: ChAPs (Chs5p-A 91.8 1.1 2.3E-05 46.6 9.8 82 118-212 212-293 (395)
40 PRK15359 type III secretion sy 91.7 1.8 3.8E-05 38.1 10.0 89 118-219 36-125 (144)
41 PLN03088 SGT1, suppressor of 91.2 1.7 3.7E-05 44.4 10.6 89 119-220 15-104 (356)
42 PRK12370 invasion protein regu 90.9 5.2 0.00011 43.3 14.5 84 123-219 321-405 (553)
43 PF13174 TPR_6: Tetratricopept 90.8 0.42 9.2E-06 30.2 3.7 29 190-218 3-32 (33)
44 PF13181 TPR_8: Tetratricopept 90.2 0.43 9.3E-06 30.6 3.4 30 188-217 2-32 (34)
45 PRK10803 tol-pal system protei 87.6 3.8 8.2E-05 40.2 9.5 92 122-220 159-251 (263)
46 PF13412 HTH_24: Winged helix- 87.2 2.4 5.3E-05 29.7 5.9 43 310-353 6-48 (48)
47 PLN03218 maturation of RBCL 1; 86.9 20 0.00043 42.1 16.3 17 335-351 769-785 (1060)
48 TIGR02521 type_IV_pilW type IV 86.6 23 0.0005 31.6 14.2 87 119-218 44-130 (234)
49 PRK15359 type III secretion sy 85.6 3.8 8.3E-05 36.0 7.6 64 147-219 27-91 (144)
50 PF12569 NARP1: NMDA receptor- 85.6 14 0.0003 39.9 13.2 62 146-216 196-257 (517)
51 PRK10370 formate-dependent nit 85.5 7.3 0.00016 36.3 9.9 108 104-228 75-186 (198)
52 TIGR03302 OM_YfiO outer membra 85.4 11 0.00025 35.2 11.3 93 120-219 47-148 (235)
53 PF09986 DUF2225: Uncharacteri 85.2 7.8 0.00017 36.8 10.0 87 141-227 115-205 (214)
54 PF14559 TPR_19: Tetratricopep 84.9 1.4 3.1E-05 32.7 3.9 56 155-219 2-58 (68)
55 PRK11788 tetratricopeptide rep 84.3 40 0.00086 33.9 15.5 88 119-215 82-169 (389)
56 KOG4414|consensus 84.0 2.9 6.2E-05 37.2 5.8 44 299-343 110-153 (197)
57 smart00028 TPR Tetratricopepti 83.5 2.8 6.1E-05 24.6 4.3 27 189-215 3-29 (34)
58 TIGR02552 LcrH_SycD type III s 83.4 6.6 0.00014 33.2 8.0 66 145-219 18-84 (135)
59 PF14853 Fis1_TPR_C: Fis1 C-te 83.0 3.7 8E-05 30.1 5.2 32 188-219 2-34 (53)
60 PLN03218 maturation of RBCL 1; 82.3 24 0.00053 41.4 14.3 17 335-351 734-750 (1060)
61 cd00189 TPR Tetratricopeptide 82.2 7.5 0.00016 28.6 7.2 63 148-219 4-67 (100)
62 PF10602 RPN7: 26S proteasome 82.0 41 0.00089 30.8 14.8 127 81-218 18-144 (177)
63 smart00550 Zalpha Z-DNA-bindin 81.6 5.1 0.00011 30.7 5.9 44 310-354 9-54 (68)
64 PF12802 MarR_2: MarR family; 80.6 8.9 0.00019 28.0 6.8 50 310-360 8-59 (62)
65 PF01047 MarR: MarR family; I 80.5 8.3 0.00018 28.0 6.6 51 309-360 5-55 (59)
66 PF03399 SAC3_GANP: SAC3/GANP/ 80.5 5.9 0.00013 36.6 7.1 64 266-333 139-204 (204)
67 PF14938 SNAP: Soluble NSF att 79.6 14 0.00029 36.3 9.7 137 78-223 92-233 (282)
68 PF13176 TPR_7: Tetratricopept 79.3 2.6 5.7E-05 27.7 3.2 25 191-215 3-27 (36)
69 PRK10747 putative protoheme IX 78.4 10 0.00022 39.2 8.8 94 125-219 244-361 (398)
70 KOG0543|consensus 78.2 7.1 0.00015 40.3 7.2 69 142-219 255-324 (397)
71 KOG3677|consensus 78.2 45 0.00098 34.8 12.8 236 150-399 241-523 (525)
72 PF09756 DDRGK: DDRGK domain; 77.8 6.1 0.00013 36.7 6.2 46 320-366 112-157 (188)
73 PF13414 TPR_11: TPR repeat; P 77.5 3.5 7.6E-05 30.7 3.8 33 187-219 3-36 (69)
74 PF13424 TPR_12: Tetratricopep 76.7 4.1 8.9E-05 31.2 4.1 33 184-216 2-34 (78)
75 TIGR02917 PEP_TPR_lipo putativ 76.7 36 0.00078 37.6 13.1 90 117-219 136-226 (899)
76 PLN03081 pentatricopeptide (PP 76.4 85 0.0018 34.9 15.9 57 147-215 161-217 (697)
77 TIGR03302 OM_YfiO outer membra 74.9 15 0.00032 34.4 8.2 74 141-220 30-104 (235)
78 KOG1840|consensus 74.6 65 0.0014 34.7 13.7 109 106-215 241-353 (508)
79 TIGR02521 type_IV_pilW type IV 74.3 18 0.0004 32.3 8.5 90 118-218 77-167 (234)
80 PRK11179 DNA-binding transcrip 74.3 8.4 0.00018 34.3 6.0 38 320-358 22-62 (153)
81 CHL00033 ycf3 photosystem I as 74.3 31 0.00067 30.6 9.8 94 119-215 48-141 (168)
82 PF02082 Rrf2: Transcriptional 74.1 12 0.00026 29.5 6.3 55 322-378 26-80 (83)
83 PRK11189 lipoprotein NlpI; Pro 74.1 12 0.00027 36.9 7.7 64 146-218 100-164 (296)
84 PF13512 TPR_18: Tetratricopep 74.0 39 0.00083 30.0 9.9 93 120-219 24-132 (142)
85 PRK11169 leucine-responsive tr 73.7 7.4 0.00016 35.1 5.5 49 309-358 16-67 (164)
86 PF12895 Apc3: Anaphase-promot 72.6 7.3 0.00016 30.4 4.6 49 157-212 2-50 (84)
87 KOG3250|consensus 72.3 35 0.00076 32.4 9.6 96 261-365 58-153 (258)
88 PRK15331 chaperone protein Sic 72.2 48 0.001 30.2 10.2 124 79-219 9-137 (165)
89 cd00092 HTH_CRP helix_turn_hel 72.1 14 0.00031 27.2 6.0 33 321-354 25-57 (67)
90 COG1522 Lrp Transcriptional re 71.4 12 0.00026 32.8 6.3 48 310-358 11-61 (154)
91 PRK02603 photosystem I assembl 71.3 16 0.00034 32.8 7.2 68 146-219 37-105 (172)
92 PF01726 LexA_DNA_bind: LexA D 70.8 7.8 0.00017 29.6 4.2 32 322-353 26-57 (65)
93 PRK15179 Vi polysaccharide bio 70.6 56 0.0012 36.6 12.5 128 78-218 47-186 (694)
94 PRK02603 photosystem I assembl 69.5 71 0.0015 28.5 11.1 74 119-202 48-121 (172)
95 smart00419 HTH_CRP helix_turn_ 69.3 9.4 0.0002 26.2 4.1 32 321-353 8-39 (48)
96 PRK11788 tetratricopeptide rep 69.3 25 0.00055 35.3 8.9 92 119-218 120-212 (389)
97 TIGR00990 3a0801s09 mitochondr 69.3 20 0.00043 39.2 8.7 88 119-219 344-432 (615)
98 PLN03077 Protein ECB2; Provisi 69.2 2.1E+02 0.0046 32.6 18.9 53 149-215 227-281 (857)
99 PRK10049 pgaA outer membrane p 69.0 31 0.00068 38.9 10.3 93 115-220 368-461 (765)
100 TIGR02010 IscR iron-sulfur clu 68.5 11 0.00024 32.7 5.3 62 321-384 25-86 (135)
101 PF13428 TPR_14: Tetratricopep 68.4 7.5 0.00016 26.6 3.4 30 190-219 4-34 (44)
102 PF12688 TPR_5: Tetratrico pep 68.2 39 0.00086 28.9 8.5 96 113-215 8-103 (120)
103 TIGR02795 tol_pal_ybgF tol-pal 67.5 22 0.00047 28.7 6.7 65 149-219 7-72 (119)
104 PRK09782 bacteriophage N4 rece 67.4 22 0.00047 41.5 8.7 82 120-215 590-671 (987)
105 PRK15174 Vi polysaccharide exp 67.2 36 0.00079 37.7 10.2 88 119-219 297-385 (656)
106 smart00344 HTH_ASNC helix_turn 66.7 18 0.00038 29.8 6.0 35 318-353 14-48 (108)
107 cd00090 HTH_ARSR Arsenical Res 66.6 34 0.00073 25.1 7.1 45 322-367 21-65 (78)
108 TIGR02917 PEP_TPR_lipo putativ 66.3 85 0.0019 34.6 13.1 125 78-218 21-157 (899)
109 TIGR00540 hemY_coli hemY prote 65.8 33 0.00071 35.5 9.0 94 115-218 272-369 (409)
110 PF12840 HTH_20: Helix-turn-he 65.7 31 0.00068 25.4 6.6 47 308-355 11-57 (61)
111 PF00325 Crp: Bacterial regula 65.5 13 0.00027 24.4 3.7 31 321-352 2-32 (32)
112 cd05804 StaR_like StaR_like; a 65.2 84 0.0018 31.1 11.7 89 118-215 126-214 (355)
113 PF04703 FaeA: FaeA-like prote 65.1 17 0.00036 27.6 4.9 35 319-354 13-47 (62)
114 PF09976 TPR_21: Tetratricopep 64.9 92 0.002 26.9 10.9 69 138-212 42-110 (145)
115 PRK11189 lipoprotein NlpI; Pro 64.9 48 0.001 32.6 9.7 25 147-171 135-159 (296)
116 PRK11906 transcriptional regul 64.8 99 0.0022 32.8 12.1 73 135-219 332-405 (458)
117 smart00418 HTH_ARSR helix_turn 64.8 19 0.00041 25.7 5.3 43 320-363 9-51 (66)
118 PRK15431 ferrous iron transpor 63.8 27 0.00058 27.8 6.0 51 312-363 7-57 (78)
119 KOG2076|consensus 63.7 22 0.00047 40.3 7.4 66 146-219 416-482 (895)
120 PF09339 HTH_IclR: IclR helix- 63.6 12 0.00026 26.7 3.8 37 316-353 13-49 (52)
121 PF13429 TPR_15: Tetratricopep 62.8 15 0.00032 35.6 5.6 90 118-219 89-179 (280)
122 TIGR00990 3a0801s09 mitochondr 62.8 25 0.00053 38.5 7.8 88 118-218 377-465 (615)
123 CHL00033 ycf3 photosystem I as 62.6 35 0.00077 30.2 7.6 68 143-216 34-101 (168)
124 PRK10803 tol-pal system protei 62.4 32 0.0007 33.6 7.8 62 152-219 151-213 (263)
125 COG2345 Predicted transcriptio 62.4 21 0.00047 33.9 6.2 49 309-358 13-61 (218)
126 TIGR02944 suf_reg_Xantho FeS a 61.9 16 0.00035 31.3 5.1 35 321-356 25-59 (130)
127 COG1497 Predicted transcriptio 61.8 13 0.00029 35.8 4.7 50 304-354 7-57 (260)
128 COG3071 HemY Uncharacterized e 61.7 57 0.0012 33.7 9.5 56 154-218 304-360 (400)
129 PRK10370 formate-dependent nit 61.3 74 0.0016 29.5 9.7 66 146-219 75-143 (198)
130 PF13374 TPR_10: Tetratricopep 61.3 13 0.00029 24.2 3.5 27 190-216 5-31 (42)
131 PLN03088 SGT1, suppressor of 61.1 20 0.00043 36.6 6.3 61 150-219 8-69 (356)
132 PLN03081 pentatricopeptide (PP 61.1 2.7E+02 0.0058 30.9 20.1 53 149-215 264-318 (697)
133 cd07377 WHTH_GntR Winged helix 60.8 21 0.00045 26.0 4.8 32 321-353 24-56 (66)
134 KOG1126|consensus 60.6 9.8 0.00021 41.4 4.0 34 186-219 488-522 (638)
135 PRK15363 pathogenicity island 60.6 45 0.00098 30.1 7.7 60 151-219 42-102 (157)
136 TIGR03879 near_KaiC_dom probab 60.3 17 0.00038 28.5 4.3 42 310-352 21-62 (73)
137 KOG2316|consensus 60.2 15 0.00033 35.0 4.7 44 314-358 115-163 (277)
138 PRK15363 pathogenicity island 59.5 71 0.0015 28.9 8.8 76 128-215 56-131 (157)
139 PF13432 TPR_16: Tetratricopep 59.5 12 0.00025 27.5 3.3 29 191-219 1-30 (65)
140 PLN03098 LPA1 LOW PSII ACCUMUL 58.3 29 0.00063 36.6 6.9 67 142-216 73-141 (453)
141 PF13429 TPR_15: Tetratricopep 58.1 14 0.0003 35.8 4.4 93 114-219 154-247 (280)
142 PF05331 DUF742: Protein of un 57.8 21 0.00046 30.4 4.9 46 309-357 45-90 (114)
143 TIGR00738 rrf2_super rrf2 fami 57.0 18 0.00039 30.9 4.5 61 321-383 25-85 (132)
144 PF08220 HTH_DeoR: DeoR-like h 56.9 32 0.0007 25.2 5.2 42 310-352 3-44 (57)
145 PLN03077 Protein ECB2; Provisi 56.4 3.5E+02 0.0076 30.8 19.0 142 197-352 564-723 (857)
146 KOG0553|consensus 56.1 1.5E+02 0.0032 29.7 11.0 148 192-353 86-249 (304)
147 smart00420 HTH_DEOR helix_turn 55.8 54 0.0012 22.4 6.2 34 320-354 13-46 (53)
148 PF13463 HTH_27: Winged helix 55.4 72 0.0016 23.5 7.1 40 318-358 15-54 (68)
149 PF13404 HTH_AsnC-type: AsnC-t 55.3 33 0.00072 23.6 4.7 27 319-346 15-41 (42)
150 PRK10866 outer membrane biogen 54.5 2E+02 0.0044 27.5 13.9 65 149-219 37-102 (243)
151 PF12569 NARP1: NMDA receptor- 54.3 3.1E+02 0.0067 29.7 14.1 65 147-220 7-72 (517)
152 TIGR02337 HpaR homoprotocatech 54.2 95 0.0021 25.9 8.4 43 318-361 39-81 (118)
153 PRK10857 DNA-binding transcrip 54.0 24 0.00052 32.0 4.9 62 321-384 25-86 (164)
154 KOG3054|consensus 54.0 31 0.00066 33.3 5.6 48 318-366 211-258 (299)
155 PRK15174 Vi polysaccharide exp 53.6 55 0.0012 36.3 8.7 87 119-218 89-176 (656)
156 PF10037 MRP-S27: Mitochondria 53.3 43 0.00093 35.3 7.2 62 142-215 101-166 (429)
157 cd05804 StaR_like StaR_like; a 52.9 1.2E+02 0.0025 30.0 10.2 74 136-218 106-180 (355)
158 PRK10049 pgaA outer membrane p 52.8 98 0.0021 35.0 10.6 103 116-219 282-392 (765)
159 PF13525 YfiO: Outer membrane 52.6 1.9E+02 0.0041 26.6 12.1 94 119-219 18-123 (203)
160 PF01325 Fe_dep_repress: Iron 52.6 47 0.001 24.8 5.5 38 315-353 16-53 (60)
161 PRK09954 putative kinase; Prov 52.4 50 0.0011 33.4 7.6 54 311-365 7-63 (362)
162 TIGR02702 SufR_cyano iron-sulf 52.2 1E+02 0.0022 28.6 9.1 46 310-356 4-49 (203)
163 PF00392 GntR: Bacterial regul 51.7 35 0.00076 25.4 4.8 35 319-354 21-56 (64)
164 PF13545 HTH_Crp_2: Crp-like h 50.7 28 0.00061 26.4 4.3 42 321-367 28-69 (76)
165 PF08631 SPO22: Meiosis protei 50.3 1.4E+02 0.0031 29.0 10.2 63 153-216 2-65 (278)
166 PF01022 HTH_5: Bacterial regu 50.3 59 0.0013 22.6 5.5 33 320-353 14-46 (47)
167 TIGR01764 excise DNA binding d 50.3 35 0.00075 23.2 4.3 38 322-366 2-39 (49)
168 PF04492 Phage_rep_O: Bacterio 50.3 46 0.00099 27.7 5.6 32 320-352 53-84 (100)
169 PF06163 DUF977: Bacterial pro 49.5 51 0.0011 28.6 5.8 65 311-388 16-81 (127)
170 PRK14574 hmsH outer membrane p 49.4 91 0.002 35.7 9.6 101 118-219 339-449 (822)
171 PF04762 IKI3: IKI3 family; I 49.3 94 0.002 36.1 9.8 54 146-213 874-927 (928)
172 smart00345 HTH_GNTR helix_turn 49.0 39 0.00085 23.9 4.6 32 321-353 19-51 (60)
173 PF12862 Apc5: Anaphase-promot 49.0 1.2E+02 0.0026 24.3 7.9 74 152-226 6-80 (94)
174 PRK15179 Vi polysaccharide bio 48.7 3.9E+02 0.0084 30.1 14.2 117 76-217 102-218 (694)
175 PF12793 SgrR_N: Sugar transpo 47.8 1.5E+02 0.0033 25.2 8.6 50 320-370 18-70 (115)
176 TIGR00540 hemY_coli hemY prote 47.7 84 0.0018 32.4 8.5 90 115-216 127-216 (409)
177 PF12070 DUF3550: Protein of u 46.9 55 0.0012 35.2 6.9 52 186-240 70-133 (513)
178 PRK11920 rirA iron-responsive 46.8 67 0.0014 28.7 6.6 48 321-370 24-71 (153)
179 PF10602 RPN7: 26S proteasome 46.6 1.8E+02 0.0039 26.5 9.5 72 145-222 37-108 (177)
180 PRK10747 putative protoheme IX 46.2 94 0.002 32.0 8.5 90 116-217 128-217 (398)
181 PF13591 MerR_2: MerR HTH fami 46.1 54 0.0012 26.1 5.3 72 322-402 1-79 (84)
182 PRK06266 transcription initiat 46.0 2.4E+02 0.0052 25.9 11.0 109 320-435 35-152 (178)
183 PRK12370 invasion protein regu 45.4 70 0.0015 34.6 7.7 84 119-215 351-434 (553)
184 KOG3364|consensus 45.3 47 0.001 29.5 5.1 38 182-219 66-104 (149)
185 PRK09782 bacteriophage N4 rece 45.3 1E+02 0.0022 36.1 9.4 84 120-220 58-142 (987)
186 TIGR01610 phage_O_Nterm phage 44.5 1.1E+02 0.0025 24.8 7.1 46 318-366 44-89 (95)
187 smart00347 HTH_MARR helix_turn 44.4 1.5E+02 0.0033 23.1 8.4 38 320-358 23-60 (101)
188 KOG2796|consensus 44.0 3.4E+02 0.0074 27.0 12.8 116 97-219 168-285 (366)
189 COG1729 Uncharacterized protei 43.7 1.9E+02 0.0041 28.5 9.5 89 127-222 162-251 (262)
190 PRK10153 DNA-binding transcrip 43.6 56 0.0012 35.2 6.5 65 145-219 421-486 (517)
191 PRK10265 chaperone-modulator p 42.9 62 0.0013 26.8 5.4 75 319-402 5-87 (101)
192 TIGR00498 lexA SOS regulatory 42.8 56 0.0012 30.1 5.7 44 322-366 26-69 (199)
193 PF01978 TrmB: Sugar-specific 42.4 53 0.0012 24.6 4.5 39 318-357 19-57 (68)
194 PF13730 HTH_36: Helix-turn-he 42.1 39 0.00084 24.1 3.6 30 322-352 26-55 (55)
195 PRK14165 winged helix-turn-hel 41.4 1.2E+02 0.0025 29.0 7.6 48 319-367 19-66 (217)
196 PRK11447 cellulose synthase su 40.9 1.2E+02 0.0026 36.0 9.3 60 151-219 358-418 (1157)
197 PRK10512 selenocysteinyl-tRNA- 39.7 1.8E+02 0.0039 32.2 9.8 86 319-417 504-591 (614)
198 PF10345 Cohesin_load: Cohesin 39.7 5.4E+02 0.012 28.2 14.8 154 48-215 52-207 (608)
199 PRK10141 DNA-binding transcrip 39.6 2.1E+02 0.0045 24.4 8.2 45 320-367 29-73 (117)
200 PF13525 YfiO: Outer membrane 39.3 1.1E+02 0.0023 28.3 7.0 65 150-220 11-76 (203)
201 PRK11014 transcriptional repre 39.0 70 0.0015 27.9 5.4 59 321-381 25-83 (141)
202 TIGR01889 Staph_reg_Sar staphy 38.8 1.8E+02 0.0038 24.1 7.6 41 320-361 42-82 (109)
203 KOG1126|consensus 38.7 88 0.0019 34.4 6.9 60 151-219 530-590 (638)
204 PHA02943 hypothetical protein; 38.7 2E+02 0.0044 25.9 8.0 49 318-368 21-69 (165)
205 COG2956 Predicted N-acetylgluc 38.6 70 0.0015 32.5 5.7 76 134-218 168-246 (389)
206 PF09295 ChAPs: ChAPs (Chs5p-A 38.5 1.6E+02 0.0034 30.7 8.7 64 147-219 203-267 (395)
207 PRK11512 DNA-binding transcrip 38.5 1E+02 0.0022 26.8 6.3 45 320-365 53-97 (144)
208 COG3107 LppC Putative lipoprot 38.4 5.6E+02 0.012 27.9 13.5 210 114-358 71-288 (604)
209 KOG2047|consensus 38.1 6.2E+02 0.013 28.4 15.4 114 120-238 361-483 (835)
210 KOG2140|consensus 37.9 2.1E+02 0.0046 31.0 9.3 53 47-102 202-256 (739)
211 PRK03573 transcriptional regul 37.6 1.3E+02 0.0027 26.1 6.8 44 321-365 46-89 (144)
212 KOG2002|consensus 37.3 1.4E+02 0.003 34.5 8.3 85 125-219 255-340 (1018)
213 PRK03902 manganese transport t 37.3 2.7E+02 0.0059 24.0 10.8 38 315-353 16-53 (142)
214 PF10345 Cohesin_load: Cohesin 37.1 4.9E+02 0.011 28.5 12.8 68 146-213 363-430 (608)
215 KOG1129|consensus 36.8 2.5E+02 0.0054 28.8 9.2 94 111-218 228-322 (478)
216 KOG0548|consensus 36.7 2.6E+02 0.0057 30.2 9.9 46 185-233 424-470 (539)
217 PF12728 HTH_17: Helix-turn-he 36.6 58 0.0012 22.8 3.7 38 322-366 2-39 (51)
218 PF09613 HrpB1_HrpK: Bacterial 36.5 80 0.0017 28.6 5.4 32 186-217 43-74 (160)
219 KOG1861|consensus 36.3 3.9E+02 0.0084 28.6 10.8 196 129-338 284-495 (540)
220 PRK11447 cellulose synthase su 35.9 2.3E+02 0.005 33.7 10.6 87 115-214 470-556 (1157)
221 COG1959 Predicted transcriptio 35.8 99 0.0021 27.5 5.9 70 311-382 13-84 (150)
222 smart00346 HTH_ICLR helix_turn 35.2 1E+02 0.0022 24.1 5.3 34 320-354 19-52 (91)
223 PRK09210 RNA polymerase sigma 35.2 3.6E+02 0.0078 27.6 10.7 146 266-412 117-345 (367)
224 KOG3151|consensus 34.9 4.4E+02 0.0094 25.6 15.6 51 294-344 164-215 (260)
225 COG4235 Cytochrome c biogenesi 34.6 4.8E+02 0.01 26.0 11.1 110 104-227 158-268 (287)
226 COG1729 Uncharacterized protei 34.2 1E+02 0.0022 30.3 6.0 102 154-280 151-253 (262)
227 COG5124 Protein predicted to b 34.1 1.9E+02 0.0042 26.6 7.3 67 336-413 42-109 (209)
228 KOG1174|consensus 33.7 1.9E+02 0.004 30.6 8.0 67 144-220 438-505 (564)
229 PF07721 TPR_4: Tetratricopept 33.6 51 0.0011 19.9 2.6 23 189-211 3-25 (26)
230 COG3355 Predicted transcriptio 33.5 3.2E+02 0.007 23.7 9.7 63 320-386 41-105 (126)
231 PRK10434 srlR DNA-bindng trans 33.0 97 0.0021 30.0 5.8 46 308-354 6-51 (256)
232 PRK14574 hmsH outer membrane p 32.5 8.3E+02 0.018 28.1 16.4 51 300-350 296-357 (822)
233 PRK14720 transcript cleavage f 32.1 5.8E+02 0.012 29.7 12.4 61 146-217 33-93 (906)
234 PF08279 HTH_11: HTH domain; 32.0 1.8E+02 0.004 20.4 6.9 29 321-350 15-43 (55)
235 cd04762 HTH_MerR-trunc Helix-T 31.8 68 0.0015 21.4 3.4 39 322-366 1-39 (49)
236 PF10300 DUF3808: Protein of u 31.4 6.6E+02 0.014 26.7 12.7 105 125-243 252-356 (468)
237 PF03704 BTAD: Bacterial trans 31.0 2.3E+02 0.0051 24.1 7.5 80 143-231 61-144 (146)
238 cd06171 Sigma70_r4 Sigma70, re 30.6 1.7E+02 0.0036 19.5 5.5 45 301-346 5-50 (55)
239 PRK10046 dpiA two-component re 30.5 1.4E+02 0.003 27.8 6.3 45 314-359 170-214 (225)
240 PF03704 BTAD: Bacterial trans 30.2 1.5E+02 0.0032 25.4 6.0 64 103-170 59-122 (146)
241 PF07106 TBPIP: Tat binding pr 29.8 4.1E+02 0.0089 23.8 9.9 84 313-402 11-102 (169)
242 PLN02789 farnesyltranstransfer 29.8 5.9E+02 0.013 25.6 11.2 107 97-218 29-140 (320)
243 KOG4162|consensus 29.3 3.8E+02 0.0083 30.3 9.9 60 148-215 722-782 (799)
244 PRK13509 transcriptional repre 29.2 1.3E+02 0.0028 29.1 5.9 46 308-354 6-51 (251)
245 COG3413 Predicted DNA binding 29.1 98 0.0021 29.0 5.0 41 306-347 155-203 (215)
246 KOG1840|consensus 28.8 7.7E+02 0.017 26.6 15.8 98 117-215 336-437 (508)
247 PRK10906 DNA-binding transcrip 28.8 1.3E+02 0.0028 29.1 5.8 45 308-353 6-50 (252)
248 PF09862 DUF2089: Protein of u 28.7 41 0.00089 28.7 2.1 34 321-354 67-105 (113)
249 TIGR01884 cas_HTH CRISPR locus 28.6 1.4E+02 0.003 27.7 5.9 36 320-356 156-191 (203)
250 PF04545 Sigma70_r4: Sigma-70, 28.5 1.1E+02 0.0023 21.4 4.0 29 319-348 18-46 (50)
251 KOG0547|consensus 28.2 4.1E+02 0.009 28.7 9.6 27 193-219 121-148 (606)
252 PRK10870 transcriptional repre 28.0 2.1E+02 0.0045 26.0 6.8 43 321-364 71-113 (176)
253 TIGR02561 HrpB1_HrpK type III 28.0 96 0.0021 27.9 4.3 59 150-217 16-74 (153)
254 PF08679 DsrD: Dissimilatory s 27.6 1.1E+02 0.0023 23.7 3.8 34 319-352 17-50 (67)
255 PLN03098 LPA1 LOW PSII ACCUMUL 27.6 1E+02 0.0022 32.6 5.1 36 184-219 72-108 (453)
256 COG2956 Predicted N-acetylgluc 27.5 6.9E+02 0.015 25.6 12.0 96 114-219 44-139 (389)
257 COG1321 TroR Mn-dependent tran 27.2 1.3E+02 0.0028 27.0 5.1 55 310-368 13-67 (154)
258 PRK13777 transcriptional regul 27.1 5E+02 0.011 23.9 9.3 43 319-362 57-99 (185)
259 PF08672 APC2: Anaphase promot 26.9 84 0.0018 23.6 3.2 37 319-355 9-54 (60)
260 PF08631 SPO22: Meiosis protei 26.9 5.1E+02 0.011 25.1 9.8 29 186-214 245-273 (278)
261 KOG1125|consensus 26.8 88 0.0019 33.9 4.5 111 119-233 332-491 (579)
262 PF04967 HTH_10: HTH DNA bindi 26.7 98 0.0021 22.6 3.5 26 321-347 23-48 (53)
263 PF14559 TPR_19: Tetratricopep 26.5 1.5E+02 0.0032 21.4 4.6 49 120-172 5-53 (68)
264 PF07720 TPR_3: Tetratricopept 26.4 1.4E+02 0.0029 19.9 3.9 24 188-211 2-25 (36)
265 PF09743 DUF2042: Uncharacteri 26.4 2.6E+02 0.0056 27.5 7.5 90 312-415 2-93 (272)
266 COG2976 Uncharacterized protei 26.3 1.9E+02 0.0041 27.3 6.1 87 119-217 102-189 (207)
267 KOG0547|consensus 26.2 7.2E+02 0.016 26.9 10.9 89 189-288 396-486 (606)
268 PF08281 Sigma70_r4_2: Sigma-7 25.3 2.1E+02 0.0045 20.1 5.1 47 300-347 4-51 (54)
269 KOG1585|consensus 25.2 6.7E+02 0.015 24.8 13.7 96 184-286 145-252 (308)
270 KOG2911|consensus 24.8 4.5E+02 0.0097 27.7 9.0 95 322-416 174-270 (439)
271 PRK09802 DNA-binding transcrip 24.3 5.4E+02 0.012 25.0 9.4 45 308-353 18-62 (269)
272 PF00403 HMA: Heavy-metal-asso 24.2 2.8E+02 0.006 19.9 6.0 42 337-380 14-55 (62)
273 PF14947 HTH_45: Winged helix- 24.2 3.2E+02 0.0069 21.1 6.3 33 319-352 17-49 (77)
274 PRK11753 DNA-binding transcrip 24.1 3.3E+02 0.0072 24.6 7.6 32 321-353 168-199 (211)
275 KOG2376|consensus 23.7 2.7E+02 0.0059 30.5 7.4 69 147-215 113-203 (652)
276 PF09743 DUF2042: Uncharacteri 23.6 1.6E+02 0.0034 29.1 5.4 50 305-358 179-228 (272)
277 PRK13916 plasmid segregation p 23.5 1.9E+02 0.0042 23.3 4.8 48 195-249 9-56 (97)
278 KOG1129|consensus 23.2 1.8E+02 0.0038 29.9 5.6 107 120-244 338-446 (478)
279 cd04766 HTH_HspR Helix-Turn-He 23.1 1.9E+02 0.0042 23.0 5.0 75 322-404 2-83 (91)
280 PF13512 TPR_18: Tetratricopep 22.8 2.6E+02 0.0057 24.8 6.1 65 149-219 15-80 (142)
281 smart00422 HTH_MERR helix_turn 22.6 1.6E+02 0.0034 21.8 4.2 40 322-366 1-40 (70)
282 TIGR00373 conserved hypothetic 22.5 5.6E+02 0.012 22.9 11.3 109 320-435 27-144 (158)
283 KOG1173|consensus 22.5 6.3E+02 0.014 27.7 9.8 98 126-235 434-535 (611)
284 PRK00215 LexA repressor; Valid 22.5 2.1E+02 0.0045 26.4 5.9 38 321-358 23-60 (205)
285 PRK10866 outer membrane biogen 22.2 6.9E+02 0.015 23.8 10.9 103 123-235 49-170 (243)
286 PF14493 HTH_40: Helix-turn-he 22.1 1.2E+02 0.0026 24.3 3.6 30 321-351 13-42 (91)
287 PF13601 HTH_34: Winged helix 21.8 4E+02 0.0086 20.9 7.0 48 312-360 5-52 (80)
288 PRK10411 DNA-binding transcrip 20.8 7.4E+02 0.016 23.6 11.1 46 308-354 5-50 (240)
289 PRK05657 RNA polymerase sigma 20.8 5.6E+02 0.012 25.7 8.9 133 266-401 74-266 (325)
290 TIGR00475 selB selenocysteine- 20.5 3.2E+02 0.0069 29.9 7.5 78 319-417 486-565 (581)
291 PF14711 Nitr_red_bet_C: Respi 20.2 1.5E+02 0.0033 23.8 3.7 29 320-348 28-56 (83)
No 1
>KOG2582|consensus
Probab=100.00 E-value=2.5e-80 Score=600.70 Aligned_cols=416 Identities=47% Similarity=0.772 Sum_probs=403.1
Q ss_pred CchhHHHHHHHHhhhccCCCHHHHHHHHHhhHHHHHhccccchhhhhccCcchhhHHHHHHHHHHhccccCCCCCCccHH
Q psy9642 1 MATALEQFVNNVRQLSAQGSFRELTEIIQKSMDVLTKYGQHLDNVLETLETFQHSLGILAILSAKLTLLSSSNTGSEYQE 80 (437)
Q Consensus 1 ~~~~l~~~v~~v~~~s~~~~~~~L~~~l~~~~~~l~~~~~~~~~~L~~ldp~~hsl~~L~vL~~~~~~~~~~~~~~~~~~ 80 (437)
|++.++..+++++++|++++.++|.+.|.++.+.+.+++.+++++|..|||++||+|++|+|.+++..+.+ .++++
T Consensus 1 ~gs~l~a~i~~~~~~~~~~~~~eL~~~i~~~~ell~k~~~~~~~~L~~ld~~~hSlgml~~l~~~f~~~~~----~~~~~ 76 (422)
T KOG2582|consen 1 LGSMLEAAINELCSLSHSSNVGELAELIVKSKELLAKNSSDLDAVLLHLDPQVHSLGMLAVLKVKFHTPSA----NPDPE 76 (422)
T ss_pred CcHHHHHHHHHHHhhhcCCcHHHHHHHHHhhHHHHHhCcchHHHHHHhcCccccchhhhhhhhccccCccc----CCCHH
Confidence 56789999999999999999999999999999999999999999999999999999999999999988764 47889
Q ss_pred HHHHHHHHHHHhcChhhhhhhHHHHHHHHHHHHHHHhhhCCCCcchHHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCc
Q psy9642 81 ELFSQIQEFLNMCNPDQIRHAGDLYAELSHQYTKTVMDLKTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNF 160 (437)
Q Consensus 81 ~~~~~~~~fl~~fd~~Qir~a~~~~~~l~~~~~~~~~~~~~~~~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y 160 (437)
.+++++.+|+.+||.+|+|+|+..|..+|+.+++++...++|.+|+.++..|+.+++|++.++|++|.+++++||.+++|
T Consensus 77 ~li~~~~~FV~~~n~eqlr~as~~f~~lc~~l~~~~~~~~~p~~gi~ii~~av~k~~~~~~qlT~~H~~l~~~~L~ak~y 156 (422)
T KOG2582|consen 77 TLIELLNDFVDENNGEQLRLASEIFFPLCHDLTEAVVKKNKPLRGIRIIMQAVDKMQPSNGQLTSIHADLLQLCLEAKDY 156 (422)
T ss_pred HHHHHHHHHHHhcChHHHhhHHHHHHHHHHHHHHHHHhcCCccccchHHHHHHHHhccCccchhhhHHHHHHHHHHhhcc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhcccccccCHHHHHHHHHHHHHHHHHh
Q psy9642 161 KPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIITTPALAVSHIMLEGYKKYLLIYLIVY 240 (437)
Q Consensus 161 ~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~~P~~~~s~i~vea~Kk~iLv~Lil~ 240 (437)
..++|++|.+|.++|..++..+++.++.|+||||||++++|||++|..||+.|+++|+.+++.++.||||||+||+||+.
T Consensus 157 ~~~~p~ld~divei~~~n~h~~~k~fL~Y~yYgg~iciglk~fe~Al~~~e~~v~~Pa~~vs~~hlEaYkkylLvsLI~~ 236 (422)
T KOG2582|consen 157 ASVLPYLDDDIVEICKANPHLDPKYFLLYLYYGGMICIGLKRFERALYLLEICVTTPAMAVSHIHLEAYKKYLLVSLILT 236 (422)
T ss_pred cccCCccchhHHHHhccCCCCCHHHHHHHHHhcceeeeccccHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHHHHhhhc
Confidence 99999999999999998889999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCccccHHHhHhhccCCHHHHHHHHHHhcCCHHHHHHHHHhccccccccchhhHHHHHHHHHHHHHHHHHHHhhc
Q psy9642 241 GKAPNLPKNVSQAICRYIKPLSQPYLDLVSVYTNNNSTELQHLLLKYADVFSRDENTGLTKQIVASLYKNNIKRLTKTFL 320 (437)
Q Consensus 241 G~~~~lp~~~s~~~~r~~k~~~~pY~~L~~af~~~d~~~~~~~~~~~~~~f~~D~n~~Lv~~l~~~v~r~~I~~l~k~Ys 320 (437)
||+..+|+.+|+.+.|.+|+...||++|+++|.++...+++.++.+|.+.|.+|||+|++++++..+++|+|++++|+|+
T Consensus 237 GK~~ql~k~ts~~~~r~~K~ms~pY~ef~~~Y~~~~~~eLr~lVk~~~~rF~kDnnt~l~k~av~sl~k~nI~rltktF~ 316 (422)
T KOG2582|consen 237 GKVFQLPKNTSQNAGRFFKPMSNPYHEFLNVYLKDSSTELRTLVKKHSERFTKDNNTGLAKQAVSSLYKKNIQRLTKTFL 316 (422)
T ss_pred CceeeccccchhhhHHhcccCCchHHHHHHHHhcCCcHHHHHHHHHHHHHHhhcCcHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCCCEEEEccCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy9642 321 TLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVFNDNPQRFNNPLTFAQIESNIRACMHLDGKFQAMEE 400 (437)
Q Consensus 321 ~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~g~v~F~~~~~~~~~~e~~~~l~~~i~~~~~L~~~~~~~d~ 400 (437)
+|+|+|||++++|.+.+|||++|.+||++|+|.|.|| |||.|.+++++|.++|+... .|..|.+|.+++++||+
T Consensus 317 sLsL~dIA~~vQLa~~qevek~Ilqmie~~~i~a~iN---G~v~f~~n~e~~~SpeM~~n---k~~~~~~L~e~l~~~e~ 390 (422)
T KOG2582|consen 317 SLSLSDIASRVQLASAQEVEKYILQMIEDGEIFASIN---GMVFFTDNPEKYNSPEMHEN---KIDLCIQLIEALKAMEE 390 (422)
T ss_pred HhhHHHHHHHHHhcchHHHHHHHHHHhccCceEEEec---ceEEEecCcccCCCHHHHhh---HHHHHHHHHHHHHhcch
Confidence 9999999999999999999999999999999999997 99999999999999988765 89999999999999999
Q ss_pred HhhCCHHHHHHhcCCCCcccCCCCCCC
Q psy9642 401 EILVNPLYVKKAASPSDEETGSSKPGG 427 (437)
Q Consensus 401 ~l~~~~~yi~k~~~~~~~~~~~~~~~~ 427 (437)
.+.++|-|++|+++.|.++ +|++|..
T Consensus 391 si~l~s~~~~K~m~~~~d~-~~~~p~t 416 (422)
T KOG2582|consen 391 SIRLNSVYVSKSMGSQEDD-GGSMPPT 416 (422)
T ss_pred heeeCceeeehhhhhhhcc-ccCCCCc
Confidence 9999999999999999988 8887754
No 2
>KOG2581|consensus
Probab=100.00 E-value=2.7e-43 Score=346.29 Aligned_cols=333 Identities=17% Similarity=0.261 Sum_probs=275.4
Q ss_pred chhhHHHHHHHHHHhccccCCCCCCccHHHHHHHHHHHHHhcChhhhhhhH---HHHHHHHHHHHHHHhhhCCCCcchH-
Q psy9642 52 FQHSLGILAILSAKLTLLSSSNTGSEYQEELFSQIQEFLNMCNPDQIRHAG---DLYAELSHQYTKTVMDLKTPQRGIP- 127 (437)
Q Consensus 52 ~~hsl~~L~vL~~~~~~~~~~~~~~~~~~~~~~~~~~fl~~fd~~Qir~a~---~~~~~l~~~~~~~~~~~~~~~~~i~- 127 (437)
+..-+.||.++...+++.. ..+...+.+....=+..+|.+-+.+.+ .+|..|+++....+.. +|+..
T Consensus 123 Ei~aY~~lLv~Lfl~d~K~-----~kea~~~~~~~l~~i~~~nrRtlD~i~ak~~fy~~l~~E~~~~l~~----~rs~l~ 193 (493)
T KOG2581|consen 123 EIEAYLYLLVLLFLIDQKE-----YKEADKISDALLASISIQNRRTLDLIAAKLYFYLYLSYELEGRLAD----IRSFLH 193 (493)
T ss_pred HHHHHHHHHHHHHHHhhHH-----HHHHHHHHHHHHHHHHhcchhhHHHHHHHHHHHHHHHHHhhcchHH----HHHHHH
Confidence 3444444444444444333 334556667777778899999998766 3455566555443333 34433
Q ss_pred -HHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHH
Q psy9642 128 -LIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERA 206 (437)
Q Consensus 128 -~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A 206 (437)
.|++|.+|.+ ...-..+...++|..|..+.|..|-.++++..+. ...++++.++|+||.|+|.+.+.||.+|
T Consensus 194 ~~lrtAtLrhd--~e~qavLiN~LLr~yL~n~lydqa~~lvsK~~~p-----e~~snne~ARY~yY~GrIkaiqldYssA 266 (493)
T KOG2581|consen 194 ALLRTATLRHD--EEGQAVLINLLLRNYLHNKLYDQADKLVSKSVYP-----EAASNNEWARYLYYLGRIKAIQLDYSSA 266 (493)
T ss_pred HHHHHhhhcCc--chhHHHHHHHHHHHHhhhHHHHHHHHHhhcccCc-----cccccHHHHHHHHHHhhHHHhhcchhHH
Confidence 4666666654 3445568899999999999999998888876552 2345668999999999999999999999
Q ss_pred HHHHHHHhc-ccccccCHHHHHHHHHHHHHHHHHhCCCCCCCccccHHHhHhhccCCHHHHHHHHHHhcCCHHHHHHHHH
Q psy9642 207 LYFFEVIIT-TPALAVSHIMLEGYKKYLLIYLIVYGKAPNLPKNVSQAICRYIKPLSQPYLDLVSVYTNNNSTELQHLLL 285 (437)
Q Consensus 207 ~~~~~~ai~-~P~~~~s~i~vea~Kk~iLv~Lil~G~~~~lp~~~s~~~~r~~k~~~~pY~~L~~af~~~d~~~~~~~~~ 285 (437)
.++|.+|++ +|.. .+-.+.+...||++|.-++.|.+|.+..|+.|. +++.+.||..|++|++.||++.|..+++
T Consensus 267 ~~~~~qa~rkapq~-~alGf~q~v~k~~ivv~ll~geiPers~F~Qp~----~~ksL~~Yf~Lt~AVr~gdlkkF~~~le 341 (493)
T KOG2581|consen 267 LEYFLQALRKAPQH-AALGFRQQVNKLMIVVELLLGEIPERSVFRQPG----MRKSLRPYFKLTQAVRLGDLKKFNETLE 341 (493)
T ss_pred HHHHHHHHHhCcch-hhhhHHHHHHHHHHHHHHHcCCCcchhhhcCcc----HHHHHHHHHHHHHHHHHhhHHHHHHHHH
Confidence 999999999 9984 345566666788888888999999998887664 4445789999999999999999999999
Q ss_pred hccccccccchhhHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCCCEEEE
Q psy9642 286 KYADVFSRDENTGLTKQIVASLYKNNIKRLTKTFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVF 365 (437)
Q Consensus 286 ~~~~~f~~D~n~~Lv~~l~~~v~r~~I~~l~k~Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~g~v~F 365 (437)
++.+.|..||++.|+.+++++|+|.+||+|+-+|||||+.|||++|+|+|+++||.+|++.|.||.|.|+||+++|+|..
T Consensus 342 q~k~~f~~D~ty~LivRLR~NVIkTgIR~ISlsYSRISl~DIA~kL~l~Seed~EyiVakAIRDGvIea~Id~~~g~m~s 421 (493)
T KOG2581|consen 342 QFKDKFQADGTYTLIVRLRHNVIKTGIRKISLSYSRISLQDIAKKLGLNSEEDAEYIVAKAIRDGVIEAKIDHEDGFMQS 421 (493)
T ss_pred HHHHHHhhCCcchHHHHHHHHHHHHhhhheeeeeeeccHHHHHHHhcCCCchhHHHHHHHHHHhccceeeeccccCceeh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCCCCchHHHHHHHHHHHHHHHHHH-HHHHHHHHhhCC
Q psy9642 366 NDNPQRFNNPLTFAQIESNIRACMHLDG-KFQAMEEEILVN 405 (437)
Q Consensus 366 ~~~~~~~~~~e~~~~l~~~i~~~~~L~~-~~~~~d~~l~~~ 405 (437)
.+..+.|++.|++..|+.+|++|++||+ .+++|+..--..
T Consensus 422 kE~~diy~t~epQ~~f~~rI~fCl~LhN~~vkamRyPp~~~ 462 (493)
T KOG2581|consen 422 KETFDIYSTREPQTAFDERIRFCLQLHNEAVKAMRYPPKKK 462 (493)
T ss_pred hhhhhhhccCCchhhHhHHHHHHHHHHHHHHHHhcCCCcch
Confidence 9999999999999999999999999999 999998776544
No 3
>KOG1498|consensus
Probab=99.91 E-value=3.1e-23 Score=204.50 Aligned_cols=239 Identities=18% Similarity=0.264 Sum_probs=197.2
Q ss_pred hHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHH--hhHHHHHHHHHHHhcccccccC
Q psy9642 145 SLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLAL--KNYERALYFFEVIITTPALAVS 222 (437)
Q Consensus 145 ~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~--k~y~~A~~~~~~ai~~P~~~~s 222 (437)
.++++++|||+..++|..| .|++++|....-+. +..+.++..||..||.+++ +.|-+++++|+.++.+|..+.+
T Consensus 172 ~fiLEQmrKOG~~~D~vra-~i~skKI~~K~F~~---~~~~~lKlkyY~lmI~l~lh~~~Yl~v~~~Yraiy~t~~vk~d 247 (439)
T KOG1498|consen 172 AFILEQMRLCLLRLDYVRA-QIISKKINKKFFEK---PDVQELKLKYYELMIRLGLHDRAYLNVCRSYRAIYDTGNVKED 247 (439)
T ss_pred HHHHHHHHHHHHhhhHHHH-HHHHHHhhHHhcCC---ccHHHHHHHHHHHHHHhcccccchhhHHHHHHHHhcccccccC
Confidence 3789999999999999999 99999998643221 3356899999999999986 5999999999999999998654
Q ss_pred -HHHHHHHHHHHHHHHHHhCCCCCCCccccHHHhHhhc----cCCHHHHHHHHHHhcCCHHHHHHHHHhcccccccc---
Q psy9642 223 -HIMLEGYKKYLLIYLIVYGKAPNLPKNVSQAICRYIK----PLSQPYLDLVSVYTNNNSTELQHLLLKYADVFSRD--- 294 (437)
Q Consensus 223 -~i~vea~Kk~iLv~Lil~G~~~~lp~~~s~~~~r~~k----~~~~pY~~L~~af~~~d~~~~~~~~~~~~~~f~~D--- 294 (437)
..+.+.....++ .-...|...-.+..+.+.-. ...+.|.++++.|.++++..|..+.+.+...+.++
T Consensus 248 ~~kw~~vL~~iv~-----f~~LAp~dneQsdll~~is~dKkL~e~p~~k~lLklfv~~EL~rw~s~~~~yg~~l~~~~~~ 322 (439)
T KOG1498|consen 248 PEKWIEVLRSIVS-----FCVLAPHDNEQSDLLARISNDKKLSELPDYKELLKLFVTMELIRWVSLVESYGDELRTNDFF 322 (439)
T ss_pred hhhhhhhhhhhee-----EEeecCCCcHHHHHHHHHhcccccccCccHHHHHHHHHhcceeeehhHhhhhHHHHhhcccc
Confidence 455665444333 22223333333444443221 24789999999999999999999999998888766
Q ss_pred -c---hhhHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCCCEEEEccCCC
Q psy9642 295 -E---NTGLTKQIVASLYKNNIKRLTKTFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVFNDNPQ 370 (437)
Q Consensus 295 -~---n~~Lv~~l~~~v~r~~I~~l~k~Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~g~v~F~~~~~ 370 (437)
+ +-+.|.++..|+++||||.++++|++|++.+++..++++ ++++|.+|+.||..|.|+|+||+|.|++.|..+.+
T Consensus 323 ~~~~~gek~~~dL~~RIiEHNiRiiA~yYSrIt~~rl~eLLdl~-~ee~E~~LS~lv~t~ti~aKidrpsgII~F~k~K~ 401 (439)
T KOG1498|consen 323 DGGEEGEKRWSDLKLRIIEHNIRIIAKYYSRITLKRLAELLDLP-VEEMEKFLSDLVVTGTIYAKIDRPSGIINFQKVKD 401 (439)
T ss_pred cccchhhhHHHHHHHHHHHHHHHHHHHHHhhccHHHHHHHhCCC-HHHHHHHHHHHHhccceEEEecCCCceEEEEeccc
Confidence 2 345899999999999999999999999999999999998 89999999999999999999999999999998774
Q ss_pred CCCchHHHHHHHHHHHHHHHHHHHHH
Q psy9642 371 RFNNPLTFAQIESNIRACMHLDGKFQ 396 (437)
Q Consensus 371 ~~~~~e~~~~l~~~i~~~~~L~~~~~ 396 (437)
..+.+++|+.++..++.+.++..
T Consensus 402 ---~~~~LneW~~nve~L~~ll~K~~ 424 (439)
T KOG1498|consen 402 ---SNEILNEWASNVEKLLGLLEKVS 424 (439)
T ss_pred ---HHHHHHHHHhhHHHHHHHHHHHH
Confidence 67999999999999999988654
No 4
>KOG1463|consensus
Probab=99.80 E-value=8e-18 Score=163.71 Aligned_cols=285 Identities=16% Similarity=0.242 Sum_probs=211.9
Q ss_pred cHHHHHHHHHHHHHhcChhhhhhhHHHHHHHHHHHHHHHhhhCCCCcchHHHHHHHHHhCCCCcch--hhHHHHHHHHHH
Q psy9642 78 YQEELFSQIQEFLNMCNPDQIRHAGDLYAELSHQYTKTVMDLKTPQRGIPLIQTAIKKIQTSDSQL--TSLHSDLCQLCL 155 (437)
Q Consensus 78 ~~~~~~~~~~~fl~~fd~~Qir~a~~~~~~l~~~~~~~~~~~~~~~~~i~~l~~ai~rl~~~~~~l--T~~h~~l~~l~L 155 (437)
+-.+++.++-.|+..+...- +....+.|++.+...=. +. -.-|..+..-|..-.....+| -++...+++|.+
T Consensus 66 ~lr~li~~~Rpf~~~v~Kak---aaKlvR~Lvd~~~~~~~--~~-~~~i~l~~~cIeWA~~ekRtFLRq~Learli~Ly~ 139 (411)
T KOG1463|consen 66 ELRDLITSLRPFLSSVSKAK---AAKLVRSLVDMFLKIDD--GT-GDQIELCTECIEWAKREKRTFLRQSLEARLIRLYN 139 (411)
T ss_pred HHHHHHHHHHHHHHHhhhHH---HHHHHHHHHHHHccCCC--Cc-chHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHH
Confidence 45678888888888765332 12334444433321100 00 122344444443332222222 246778899999
Q ss_pred HhCCchHHHhhhhHhhhhhhc---C-----------------------------------CCCCChHhhHHHHHHHHHHH
Q psy9642 156 LAQNFKPALEFLDVDITTIAN---E-----------------------------------GPQFDTKYFLQYFYYGGMIY 197 (437)
Q Consensus 156 ~~~~y~~Al~il~~~I~~~~~---~-----------------------------------~~~~~~~~~l~Y~Yy~G~I~ 197 (437)
.++.|..|++.+..-+-++.+ + ...++|..+......+|+++
T Consensus 140 d~~~YteAlaL~~~L~rElKKlDDK~lLvev~llESK~y~~l~Nl~KakasLTsART~AnaiYcpPqlQa~lDLqSGIlh 219 (411)
T KOG1463|consen 140 DTKRYTEALALINDLLRELKKLDDKILLVEVHLLESKAYHALRNLPKAKASLTSARTTANAIYCPPQLQATLDLQSGILH 219 (411)
T ss_pred hhHHHHHHHHHHHHHHHHHHhcccccceeeehhhhhHHHHHHhcchhHHHHHHHHHHhhcccccCHHHHHHHHHhcccee
Confidence 999999999988765555411 0 12578889999999999999
Q ss_pred HHHhhHHHHHHHHHHHhcccccccC-HHHHHHHHHHHHHHHHHhCCCCCCCccccHH-HhHhhccCCHHHHHHHHHHhcC
Q psy9642 198 LALKNYERALYFFEVIITTPALAVS-HIMLEGYKKYLLIYLIVYGKAPNLPKNVSQA-ICRYIKPLSQPYLDLVSVYTNN 275 (437)
Q Consensus 198 ~~~k~y~~A~~~~~~ai~~P~~~~s-~i~vea~Kk~iLv~Lil~G~~~~lp~~~s~~-~~r~~k~~~~pY~~L~~af~~~ 275 (437)
++.+||..|+.||..||+-.....+ .....++|+.+| |-|+-+.........+.. ..+.-.+.+...+.++.||.++
T Consensus 220 a~ekDykTafSYFyEAfEgf~s~~~~v~A~~sLKYMlL-cKIMln~~ddv~~lls~K~~l~y~g~~i~AmkavAeA~~nR 298 (411)
T KOG1463|consen 220 AAEKDYKTAFSYFYEAFEGFDSLDDDVKALTSLKYMLL-CKIMLNLPDDVAALLSAKLALKYAGRDIDAMKAVAEAFGNR 298 (411)
T ss_pred ecccccchHHHHHHHHHccccccCCcHHHHHHHHHHHH-HHHHhcCHHHHHHHHhhHHHHhccCcchHHHHHHHHHhcCC
Confidence 9999999999999999996665444 477788866555 666766666654443322 2332235688999999999999
Q ss_pred CHHHHHHHHHhccccccccchh-hHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEE
Q psy9642 276 NSTELQHLLLKYADVFSRDENT-GLTKQIVASLYKNNIKRLTKTFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYA 354 (437)
Q Consensus 276 d~~~~~~~~~~~~~~f~~D~n~-~Lv~~l~~~v~r~~I~~l~k~Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A 354 (437)
++..|...+..|..+...|... ....-+..++.+.||-|+..+||++.++.||+.+|++ ...+|+-+++||.|+.++|
T Consensus 299 SLkdF~~AL~~yk~eL~~D~ivr~Hl~~Lyd~lLEknl~riIEPyS~Vei~hIA~~IGl~-~~~VEkKLsqMILDKkf~G 377 (411)
T KOG1463|consen 299 SLKDFEKALADYKKELAEDPIVRSHLQSLYDNLLEKNLCRIIEPYSRVEISHIAEVIGLD-VPQVEKKLSQMILDKKFYG 377 (411)
T ss_pred cHHHHHHHHHHhHHHHhcChHHHHHHHHHHHHHHHHhHHHHcCchhhhhHHHHHHHHCCC-cHHHHHHHHHHHHHHHhhc
Confidence 9999999999999999999965 4677799999999999999999999999999999998 7899999999999999999
Q ss_pred EEecCCCEEEEccCCC
Q psy9642 355 TINKKDGMVVFNDNPQ 370 (437)
Q Consensus 355 ~Id~~~g~v~F~~~~~ 370 (437)
++||.+|++...+.++
T Consensus 378 ~LDQg~g~Liv~~e~~ 393 (411)
T KOG1463|consen 378 TLDQGEGCLIVFEEPP 393 (411)
T ss_pred ccccCCCeEEEeCCCC
Confidence 9999999998776654
No 5
>COG5071 RPN5 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=99.78 E-value=1.5e-18 Score=166.27 Aligned_cols=237 Identities=13% Similarity=0.220 Sum_probs=177.1
Q ss_pred hHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHH--hhHHHHHHHHHHHhccccccc-
Q psy9642 145 SLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLAL--KNYERALYFFEVIITTPALAV- 221 (437)
Q Consensus 145 ~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~--k~y~~A~~~~~~ai~~P~~~~- 221 (437)
.++++++|||+..++|.+| .+..++|....-+. +....++..||...+.+++ +.|.+|+.||+.++.+-++..
T Consensus 172 ~fiLEQ~rL~vl~~Dy~~A-~~~~kKI~KK~Fe~---~d~~slKlkyYeL~V~i~Lh~R~Yl~v~~y~~~vY~t~~~~~d 247 (439)
T COG5071 172 AFILEQVRLFLLRSDYYMA-STYTKKINKKFFEK---EDVQSLKLKYYELKVRIGLHDRAYLDVCKYYRAVYDTAVVQED 247 (439)
T ss_pred HHHHHHHHHHHhccchHHH-HHHHHHHHHHHhcc---ccHHHHHHHHHHHhheeecccHHHHHHHHHHHHHHHHHHhccC
Confidence 4789999999999999999 99999998643222 2234677778888877776 699999999999998655422
Q ss_pred CHHHHHHHHHHHHHHHHHhCCCCCCCccccHHHhHh-----hccCCHHHHHHHHHHhcCCHHHHHHHHHhccccccc---
Q psy9642 222 SHIMLEGYKKYLLIYLIVYGKAPNLPKNVSQAICRY-----IKPLSQPYLDLVSVYTNNNSTELQHLLLKYADVFSR--- 293 (437)
Q Consensus 222 s~i~vea~Kk~iLv~Lil~G~~~~lp~~~s~~~~r~-----~k~~~~pY~~L~~af~~~d~~~~~~~~~~~~~~f~~--- 293 (437)
.+.+.+.+-..+. .+++ .|-..-....+.|. ++ ..+.-.++++.|..+++.+|..+...+.++...
T Consensus 248 ~Akwk~VLS~~v~-F~iL----tpy~neq~dlvhKi~~d~kl~-sl~~~~~lVk~f~vNelmrwp~V~~~y~~~l~~~~f 321 (439)
T COG5071 248 PAKWKEVLSNVVC-FALL----TPYDNEQADLLHKINADHKLN-SLPLLQQLVKCFIVNELMRWPKVAEIYGSALRSNVF 321 (439)
T ss_pred cccccchhhccee-eEEe----cccccHHHHHHHHhhhhhhhc-cchhhhhHHHHHHHHHHHhhhHHHHHhHHHHHhhhh
Confidence 2222222211110 1111 11111111122221 22 256678999999999999998888877655433
Q ss_pred ----cchhhHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCCCEEEEccCC
Q psy9642 294 ----DENTGLTKQIVASLYKNNIKRLTKTFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVFNDNP 369 (437)
Q Consensus 294 ----D~n~~Lv~~l~~~v~r~~I~~l~k~Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~g~v~F~~~~ 369 (437)
|.+-..|..++.++++||+|.|+.+||+|++.+|...++++ +.++|.+|+.|+..|-++|+|+||.|+|.|..+.
T Consensus 322 aF~~e~~~~~w~DL~krviEHN~RvI~~yYSrI~~~rl~~lld~~-~s~te~~ISdlVN~G~~yaKiNrpa~Ii~FEK~~ 400 (439)
T COG5071 322 AFNDEKGEKRWSDLRKRVIEHNIRVIANYYSRIHCSRLGVLLDMS-PSETEQFISDLVNKGHFYAKINRPAQIISFEKSQ 400 (439)
T ss_pred hhccchhhhhHHHHHHHHHHhhHhHHHHHhhhhhHHHHHHHHcCC-HHHHHHHHHHHHhcCcEEEEecCccceEEeeccc
Confidence 45566899999999999999999999999999999999998 8999999999999999999999999999999876
Q ss_pred CCCCchHHHHHHHHHHHHHHHHHHHH
Q psy9642 370 QRFNNPLTFAQIESNIRACMHLDGKF 395 (437)
Q Consensus 370 ~~~~~~e~~~~l~~~i~~~~~L~~~~ 395 (437)
. ..+.+++|..++..+++--..+
T Consensus 401 n---~~~~lneW~~NV~ellgklek~ 423 (439)
T COG5071 401 N---VQEQLNEWGSNVTELLGKLEKV 423 (439)
T ss_pred c---HHHHHHHhcccHHHHHHHHHHH
Confidence 4 6789999999988777655444
No 6
>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=99.70 E-value=1.7e-16 Score=132.26 Aligned_cols=104 Identities=24% Similarity=0.480 Sum_probs=96.8
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHhc-cccccccchhhHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHhCCCChHHHHH
Q psy9642 263 QPYLDLVSVYTNNNSTELQHLLLKY-ADVFSRDENTGLTKQIVASLYKNNIKRLTKTFLTLSLADVASRVQLGTPVQAEI 341 (437)
Q Consensus 263 ~pY~~L~~af~~~d~~~~~~~~~~~-~~~f~~D~n~~Lv~~l~~~v~r~~I~~l~k~Ys~IsL~dIa~~l~L~~~~eaE~ 341 (437)
++|.+|.++|.+||+..|.+.++++ ...|.+++...+++++...+++++++++++.|++|++++||+.++++ .+++|.
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 6899999999999999999999999 77778888889999999999999999999999999999999999998 799999
Q ss_pred HHHHhHHcCceEEEEecCCCEEEEcc
Q psy9642 342 YILKMISQNEIYATINKKDGMVVFND 367 (437)
Q Consensus 342 ~l~~mI~~G~I~A~Id~~~g~v~F~~ 367 (437)
+|.+||.+|.|.|+|||.+|+|+|..
T Consensus 80 ~l~~~I~~~~i~~~ID~~~~~v~~~k 105 (105)
T PF01399_consen 80 ILIDLISNGLIKAKIDQVNGVVVFSK 105 (105)
T ss_dssp HHHHHHHTTSSEEEEETTTTEEEE-S
T ss_pred HHHHHHHCCCEEEEEECCCCEEEecC
Confidence 99999999999999999999999973
No 7
>COG5159 RPN6 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=99.65 E-value=4.9e-14 Score=134.92 Aligned_cols=246 Identities=15% Similarity=0.207 Sum_probs=187.6
Q ss_pred cchHHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhH
Q psy9642 124 RGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNY 203 (437)
Q Consensus 124 ~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y 203 (437)
.-|.|+.+.+.|+|.-++ |+..|+.--+....-++...+-.-|... ........+++.-+.......|+.++..+||
T Consensus 146 alIn~ll~ElKk~DDK~~-Li~vhllESKvyh~irnv~KskaSLTaA--rt~Ans~YCPpqlqa~lDL~sGIlhcdd~dy 222 (421)
T COG5159 146 ALINPLLHELKKYDDKIN-LITVHLLESKVYHEIRNVSKSKASLTAA--RTLANSAYCPPQLQAQLDLLSGILHCDDRDY 222 (421)
T ss_pred HHHHHHHHHHHhhcCccc-eeehhhhhHHHHHHHHhhhhhhhHHHHH--HHHhhccCCCHHHHHHHHHhccceeeccccc
Confidence 347788899999986554 4458887777766666554432222111 0011134677888999999999999999999
Q ss_pred HHHHHHHHHHhccccc-ccCHHHHHHHHHHHHHHHHHhCCCCCCCcc-ccHHHhHhhc-cCCHHHHHHHHHHhcCCHHHH
Q psy9642 204 ERALYFFEVIITTPAL-AVSHIMLEGYKKYLLIYLIVYGKAPNLPKN-VSQAICRYIK-PLSQPYLDLVSVYTNNNSTEL 280 (437)
Q Consensus 204 ~~A~~~~~~ai~~P~~-~~s~i~vea~Kk~iLv~Lil~G~~~~lp~~-~s~~~~r~~k-~~~~pY~~L~~af~~~d~~~~ 280 (437)
..|..||..+++-.+. .........+|+. |++-|+.......... +.....++|. +.+.....+++||.++++..|
T Consensus 223 ktA~SYF~Ea~Egft~l~~d~kAc~sLkYm-lLSkIMlN~~~evk~vl~~K~t~~~y~~r~I~am~avaea~~NRsL~df 301 (421)
T COG5159 223 KTASSYFIEALEGFTLLKMDVKACVSLKYM-LLSKIMLNRREEVKAVLRNKNTLKHYDDRMIRAMLAVAEAFGNRSLKDF 301 (421)
T ss_pred hhHHHHHHHHHhccccccchHHHHHHHHHH-HHHHHHHhhHHHHHHHHccchhHhhhhhhhHHHHHHHHHHhCCCcHhhH
Confidence 9999999999996654 3445666667554 4466654444332211 2222233332 346788999999999999999
Q ss_pred HHHHHhccccccccchh-hHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecC
Q psy9642 281 QHLLLKYADVFSRDENT-GLTKQIVASLYKNNIKRLTKTFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKK 359 (437)
Q Consensus 281 ~~~~~~~~~~f~~D~n~-~Lv~~l~~~v~r~~I~~l~k~Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~ 359 (437)
...+..|.+....|.-. ....-+...+.+.|+-++..+|+++.++.||..+|++ ...+|..+++||.|+.++|++||.
T Consensus 302 ~~aL~qY~~el~~D~~iRsHl~~LYD~LLe~Nl~kiiEPfs~VeishIa~viGld-t~qvEgKLsqMILDKifyG~LDqg 380 (421)
T COG5159 302 SDALAQYSDELHQDSFIRSHLQYLYDVLLEKNLVKIIEPFSVVEISHIADVIGLD-TNQVEGKLSQMILDKIFYGTLDQG 380 (421)
T ss_pred HHHHHHhhHHhccCHHHHHHHHHHHHHHHHhhhhhhcCcceeeehhHHHHHhccc-HHHHHHHHHHHHHHHHHHhhhccC
Confidence 99999999999999865 4678899999999999999999999999999999998 799999999999999999999999
Q ss_pred CCEEEEccCCCCCCc
Q psy9642 360 DGMVVFNDNPQRFNN 374 (437)
Q Consensus 360 ~g~v~F~~~~~~~~~ 374 (437)
+|++...+.|.+-.+
T Consensus 381 ~gcLivy~ep~qd~t 395 (421)
T COG5159 381 DGCLIVYGEPAQDNT 395 (421)
T ss_pred CceEEEeCCccccch
Confidence 999999988765433
No 8
>KOG1464|consensus
Probab=99.62 E-value=9.1e-15 Score=139.20 Aligned_cols=197 Identities=12% Similarity=0.141 Sum_probs=168.9
Q ss_pred HHHHHHHHHHHHHHhhHHHHHHHHHHHhcccccccCHHHHHHHHHHHHHHHHHhCCCCCCCccccHHHhHhhcc--CCHH
Q psy9642 187 LQYFYYGGMIYLALKNYERALYFFEVIITTPALAVSHIMLEGYKKYLLIYLIVYGKAPNLPKNVSQAICRYIKP--LSQP 264 (437)
Q Consensus 187 l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~~P~~~~s~i~vea~Kk~iLv~Lil~G~~~~lp~~~s~~~~r~~k~--~~~p 264 (437)
-...=+||.+++..++|++|+.-|..||.....++|+....|+|++||..+++...+.|+... . .|-||. .+.+
T Consensus 231 GvIRECGGKMHlreg~fe~AhTDFFEAFKNYDEsGspRRttCLKYLVLANMLmkS~iNPFDsQ---E-AKPyKNdPEIlA 306 (440)
T KOG1464|consen 231 GVIRECGGKMHLREGEFEKAHTDFFEAFKNYDESGSPRRTTCLKYLVLANMLMKSGINPFDSQ---E-AKPYKNDPEILA 306 (440)
T ss_pred hHHHHcCCccccccchHHHHHhHHHHHHhcccccCCcchhHHHHHHHHHHHHHHcCCCCCccc---c-cCCCCCCHHHHH
Confidence 344558999999999999999999999999999999999999999999999998888887543 1 233553 3567
Q ss_pred HHHHHHHHhcCCHHHHHHHHHhccccccccchh-hHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHhCCCChHHHHHHH
Q psy9642 265 YLDLVSVYTNNNSTELQHLLLKYADVFSRDENT-GLTKQIVASLYKNNIKRLTKTFLTLSLADVASRVQLGTPVQAEIYI 343 (437)
Q Consensus 265 Y~~L~~af~~~d~~~~~~~~~~~~~~f~~D~n~-~Lv~~l~~~v~r~~I~~l~k~Ys~IsL~dIa~~l~L~~~~eaE~~l 343 (437)
+..++.||..+|+.+|++++..+++....|... ..++.+..+++-..+.+|.++|++|.+.-|++.|.++ +.+|+.++
T Consensus 307 MTnlv~aYQ~NdI~eFE~Il~~~~~~IM~DpFIReh~EdLl~niRTQVLlkLIkPYt~i~Ipfis~~Lnv~-~~dV~~LL 385 (440)
T KOG1464|consen 307 MTNLVAAYQNNDIIEFERILKSNRSNIMDDPFIREHIEDLLRNIRTQVLLKLIKPYTNIGIPFISKELNVP-EADVESLL 385 (440)
T ss_pred HHHHHHHHhcccHHHHHHHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHhccccccCchhhHhhcCCC-HHHHHHHH
Confidence 889999999999999999999999999888866 4788899999999999999999999999999999998 89999999
Q ss_pred HHhHHcCceEEEEecCCCEEEEccCCCCCCc-hHHHHHHHHHHHHH
Q psy9642 344 LKMISQNEIYATINKKDGMVVFNDNPQRFNN-PLTFAQIESNIRAC 388 (437)
Q Consensus 344 ~~mI~~G~I~A~Id~~~g~v~F~~~~~~~~~-~e~~~~l~~~i~~~ 388 (437)
.+.|.|..|.|+||+.++++...+.....+. -..+..|..++..+
T Consensus 386 V~~ILD~~i~g~Ide~n~~l~~~~~~~s~~k~~~al~kW~~ql~Sl 431 (440)
T KOG1464|consen 386 VSCILDDTIDGRIDEVNQYLELDKSKNSGSKLYKALDKWNNQLKSL 431 (440)
T ss_pred HHHHhccccccchHHhhhHhccCccCCcchHHHHHHHHHHHHHHHH
Confidence 9999999999999999999998766543222 35667777776543
No 9
>KOG1497|consensus
Probab=99.58 E-value=4.4e-12 Score=123.02 Aligned_cols=232 Identities=16% Similarity=0.202 Sum_probs=175.7
Q ss_pred hhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhcccccccC
Q psy9642 143 LTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIITTPALAVS 222 (437)
Q Consensus 143 lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~~P~~~~s 222 (437)
.-..-..+.+++|..++-..|..++.+.-.-...+ -+..-.+.|.-+-+++.-..++|.+|...|...-..-. ...
T Consensus 143 kl~l~iriarlyLe~~d~veae~~inRaSil~a~~---~Ne~Lqie~kvc~ARvlD~krkFlEAAqrYyels~~ki-~~e 218 (399)
T KOG1497|consen 143 KLLLCIRIARLYLEDDDKVEAEAYINRASILQAES---SNEQLQIEYKVCYARVLDYKRKFLEAAQRYYELSQRKI-VDE 218 (399)
T ss_pred HHHHHHHHHHHHHhcCcHHHHHHHHHHHHHhhhcc---cCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-cch
Confidence 33455667889999999888878877764433221 24455888998999999999999997766665443222 223
Q ss_pred HHHHHHHHHHHHHHHHHhCCCCCCCccccHHHhHhhc----cCCHHHHHHHHHHh-----cCCHHHHHHHHHhccccccc
Q psy9642 223 HIMLEGYKKYLLIYLIVYGKAPNLPKNVSQAICRYIK----PLSQPYLDLVSVYT-----NNNSTELQHLLLKYADVFSR 293 (437)
Q Consensus 223 ~i~vea~Kk~iLv~Lil~G~~~~lp~~~s~~~~r~~k----~~~~pY~~L~~af~-----~~d~~~~~~~~~~~~~~f~~ 293 (437)
.+..+|+||.+. |.|+-+--|. ++..++..+| +.++.|.-+.+.|. ..++..|...+..|+..=..
T Consensus 219 ~~~~~aL~~a~~-CtlLA~~gpq----rsr~Latlfkder~~~l~~y~ileKmyl~riI~k~el~ef~~~L~pHQka~~~ 293 (399)
T KOG1497|consen 219 SERLEALKKALQ-CTLLASAGPQ----RSRMLATLFKDERCQKLPAYGILEKMYLERIIRKEELQEFEAFLQPHQKAHTM 293 (399)
T ss_pred HHHHHHHHHhHh-heeecCCChH----HHHHHHHHhcCcccccccchHHHHHHHHHHHhcchhHHHHHHHhcchhhhccc
Confidence 478899998665 5555543333 3444555554 34788888887775 46788999999999887767
Q ss_pred cchhhHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCCCEEEEccCCCCCC
Q psy9642 294 DENTGLTKQIVASLYKNNIKRLTKTFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVFNDNPQRFN 373 (437)
Q Consensus 294 D~n~~Lv~~l~~~v~r~~I~~l~k~Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~g~v~F~~~~~~~~ 373 (437)
||.. -+-..+++|||..+++-|..||.+.+++.++++ ++.||.+.++||..|+++|.|||.+|+|+|.+.
T Consensus 294 dgss----il~ra~~EhNlls~Skly~nisf~~Lg~ll~i~-~ekaekiaa~MI~qeRmng~IDQ~egiihFe~~----- 363 (399)
T KOG1497|consen 294 DGSS----ILDRAVIEHNLLSASKLYNNISFEELGALLKID-AEKAEKIAAQMITQERMNGSIDQIEGIIHFEDR----- 363 (399)
T ss_pred Ccch----hhhhHHHHHhHHHHHHHHHhccHHHHHHHhCCC-HHHHHHHHHHHHhHHHhccchHhhcceEeecch-----
Confidence 7633 334578999999999999999999999999998 899999999999999999999999999999963
Q ss_pred chHHHHHHHHHHHHHHHHHHHH
Q psy9642 374 NPLTFAQIESNIRACMHLDGKF 395 (437)
Q Consensus 374 ~~e~~~~l~~~i~~~~~L~~~~ 395 (437)
+.+..|+++|..+..-.|.+
T Consensus 364 --e~l~~wdkqi~sl~~qvNki 383 (399)
T KOG1497|consen 364 --EELPQWDKQIQSLCNQVNKI 383 (399)
T ss_pred --hhhhhhhHHHHHHHHHHHHH
Confidence 35789999998665555544
No 10
>COG5600 Transcription-associated recombination protein [DNA replication, recombination, and repair]
Probab=99.44 E-value=9e-12 Score=123.28 Aligned_cols=212 Identities=18% Similarity=0.234 Sum_probs=148.2
Q ss_pred HHHHHHHHHhCCchHHHhhhhHhhhhhh-cCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhc-cccc-ccCHH
Q psy9642 148 SDLCQLCLLAQNFKPALEFLDVDITTIA-NEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIIT-TPAL-AVSHI 224 (437)
Q Consensus 148 ~~l~~l~L~~~~y~~Al~il~~~I~~~~-~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~-~P~~-~~s~i 224 (437)
..+.++++.-++++-+-.++..-.. +. +...-..-.++..|+||.|++|+.+.++.+|...|..||. +|.- .....
T Consensus 181 NlL~~iY~Rl~~~~l~~n~lka~~~-vs~~Di~~~~~sq~v~f~YYLG~~~l~~en~heA~~~L~~aFl~c~~l~~~n~~ 259 (413)
T COG5600 181 NLLFQIYLRLGRFKLCENFLKASKE-VSMPDISEYQKSQVVVFHYYLGIYYLLNENFHEAFLHLNEAFLQCPWLITRNRK 259 (413)
T ss_pred HHHHHHHHHhccHHHHHHHHHhccc-ccccccchhhhcceeehhhHHHHHHHHHHhHHHHHHHHHHHHHhChhhhhcchh
Confidence 4455666666666665434322111 00 0001123557999999999999999999999999999998 8872 22222
Q ss_pred HHHHHHHHHHHHHHHhCCCCCCCccccHHHhHhhccCCHHHHHHHHHHhcCCHHHHHHHHHhccccccccchhh-HHHHH
Q psy9642 225 MLEGYKKYLLIYLIVYGKAPNLPKNVSQAICRYIKPLSQPYLDLVSVYTNNNSTELQHLLLKYADVFSRDENTG-LTKQI 303 (437)
Q Consensus 225 ~vea~Kk~iLv~Lil~G~~~~lp~~~s~~~~r~~k~~~~pY~~L~~af~~~d~~~~~~~~~~~~~~f~~D~n~~-Lv~~l 303 (437)
. ..-.|+-.+|+.++..|..+ + +.| ++. +..|.-|+++++.||++.|...++.++..|.+-|-+- +...+
T Consensus 260 r--Il~~~ipt~Llv~~~~Ptk~-~----L~r-~~~-~s~~~~LvkavrsGni~~~~~~l~~ner~~~~~~l~ltl~~~~ 330 (413)
T COG5600 260 R--ILPYYIPTSLLVNKFPPTKD-L----LER-FKR-CSVYSPLVKAVRSGNIEDFDLALSRNERKFAKRGLYLTLLAHY 330 (413)
T ss_pred e--ehhHHhhHHHHhCCCCCchH-H----HHh-ccc-cchhHHHHHHHHcCCHHHHHHHHHHhHHHHHHcchHHHHHhhc
Confidence 2 22357888998888886554 3 344 554 8899999999999999999999999998888877664 34434
Q ss_pred HHHHHHHHHHHHHHh---hccccHHHH--HHHhCCCC----hHHHHHHHHHhHHcCceEEEEecCCCEEEEccCC
Q psy9642 304 VASLYKNNIKRLTKT---FLTLSLADV--ASRVQLGT----PVQAEIYILKMISQNEIYATINKKDGMVVFNDNP 369 (437)
Q Consensus 304 ~~~v~r~~I~~l~k~---Ys~IsL~dI--a~~l~L~~----~~eaE~~l~~mI~~G~I~A~Id~~~g~v~F~~~~ 369 (437)
.-.+.|..+|+.... =++++++-+ +.++.-.+ .+++|++++.||..|.++|.|.|...+|+|+..+
T Consensus 331 ~~V~~RNL~rk~w~~~~~qsrlp~sil~~~~qls~~dn~~~~~~VEciL~tlI~~G~lrgYis~s~~~vV~sk~~ 405 (413)
T COG5600 331 PLVCFRNLFRKIWRLHGKQSRLPLSILLIVLQLSAIDNFHSFKEVECILVTLIGLGLLRGYISHSRRTVVFSKKD 405 (413)
T ss_pred cHHHHHHHHHHHHhhccccccCcHHHHHHHHHccCCCcccChHHHHHHHHHHHhhhhhhheecccceEEEEecCC
Confidence 444555555533222 245455544 44444333 6899999999999999999999999999998543
No 11
>KOG2688|consensus
Probab=99.40 E-value=1.8e-12 Score=130.74 Aligned_cols=179 Identities=16% Similarity=0.199 Sum_probs=149.0
Q ss_pred CChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhc-ccccccCHHHHHHHHHHHHHHHHHhCCCCCCCccccHHHhHhhc
Q psy9642 181 FDTKYFLQYFYYGGMIYLALKNYERALYFFEVIIT-TPALAVSHIMLEGYKKYLLIYLIVYGKAPNLPKNVSQAICRYIK 259 (437)
Q Consensus 181 ~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~-~P~~~~s~i~vea~Kk~iLv~Lil~G~~~~lp~~~s~~~~r~~k 259 (437)
..-.++..|+||-|...+...||.+|...|..++. +|..... .+-....+++- ..+..|.+|.. +.+.+ +.
T Consensus 199 ~~l~~~v~y~YylGr~a~~~~d~~~A~~~L~~af~~cp~~~~~-n~~~iliylip-~~~llg~~Pt~-----~lL~~-~~ 270 (394)
T KOG2688|consen 199 FPLAQLVVYHYYLGRYAMFESDFLNAFLQLNEAFRLCPDLLLK-NKRLILIYLIP-TGLLLGRIPTK-----ELLDF-YT 270 (394)
T ss_pred cccccceeeeeeeeeehhhhhhHHHHHHHHHHHHHhCcHHHHh-hhhhHHHHHhH-HHHHhccCcch-----hhHhH-hh
Confidence 34567999999999999999999999999999999 8976322 12222333443 44467776543 22333 33
Q ss_pred cCCHHHHHHHHHHhcCCHHHHHHHHHhccccccccchhhHHHHHHHHHHHHHHHHHHHhh---ccccHHHHHHHhCCCC-
Q psy9642 260 PLSQPYLDLVSVYTNNNSTELQHLLLKYADVFSRDENTGLTKQIVASLYKNNIKRLTKTF---LTLSLADVASRVQLGT- 335 (437)
Q Consensus 260 ~~~~pY~~L~~af~~~d~~~~~~~~~~~~~~f~~D~n~~Lv~~l~~~v~r~~I~~l~k~Y---s~IsL~dIa~~l~L~~- 335 (437)
+..|..++++++.||+..|+..++.++..|.+-|-+..+..+...+++..++++.+.- ++++++.+...++..+
T Consensus 271 --~~~~~~lv~aVr~Gnl~~f~~al~~~E~~f~~~gi~l~l~~l~lv~yrnL~kkv~~~~~~~~~lpls~~~~al~~~~~ 348 (394)
T KOG2688|consen 271 --LDKYSPLVQAVRSGNLRLFDLALADNERFFIRSGIYLTLEKLPLVVYRNLFKKVIQLWGKTSQLPLSRFLTALQFSGV 348 (394)
T ss_pred --HHhHHHHHHHHHhccHHHHHHHHhhhHHHHHHhccHHHhhhhhHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHhhcCC
Confidence 7789999999999999999999999999999999999888899999999999999999 9999999999988764
Q ss_pred ----hHHHHHHHHHhHHcCceEEEEecCCCEEEEccCC
Q psy9642 336 ----PVQAEIYILKMISQNEIYATINKKDGMVVFNDNP 369 (437)
Q Consensus 336 ----~~eaE~~l~~mI~~G~I~A~Id~~~g~v~F~~~~ 369 (437)
.+|+|+++++||.+|.|+|+|+|....++|+...
T Consensus 349 ~~~~~deveciLa~lI~~G~ikgYish~~~~~V~sK~~ 386 (394)
T KOG2688|consen 349 TDVDLDEVECILANLIDLGRIKGYISHQLQTLVFSKKD 386 (394)
T ss_pred CCCchhhHHHHHHhhhhhccccchhchhhheEEEecCC
Confidence 7899999999999999999999999999987543
No 12
>smart00753 PAM PCI/PINT associated module.
Probab=99.26 E-value=4.1e-11 Score=97.31 Aligned_cols=73 Identities=26% Similarity=0.415 Sum_probs=67.9
Q ss_pred HHHHHHHHHHHHHHHHHHHhhccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCCCEEEEccCCCCC
Q psy9642 299 LTKQIVASLYKNNIKRLTKTFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVFNDNPQRF 372 (437)
Q Consensus 299 Lv~~l~~~v~r~~I~~l~k~Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~g~v~F~~~~~~~ 372 (437)
.++.+...++++++..++++|++|++++|++.++++ .+++|..|.+||.+|.|.|+||+.+|+|.|..+.+.+
T Consensus 2 ~~~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~-~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~~~r~ 74 (88)
T smart00753 2 LVERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLS-VPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVDPRR 74 (88)
T ss_pred hHHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcC-HHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCCchhh
Confidence 577899999999999999999999999999999998 6799999999999999999999999999999776543
No 13
>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=99.26 E-value=4.1e-11 Score=97.31 Aligned_cols=73 Identities=26% Similarity=0.415 Sum_probs=67.9
Q ss_pred HHHHHHHHHHHHHHHHHHHhhccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCCCEEEEccCCCCC
Q psy9642 299 LTKQIVASLYKNNIKRLTKTFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVFNDNPQRF 372 (437)
Q Consensus 299 Lv~~l~~~v~r~~I~~l~k~Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~g~v~F~~~~~~~ 372 (437)
.++.+...++++++..++++|++|++++|++.++++ .+++|..|.+||.+|.|.|+||+.+|+|.|..+.+.+
T Consensus 2 ~~~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~-~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~~~r~ 74 (88)
T smart00088 2 LVERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLS-VPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVDPRR 74 (88)
T ss_pred hHHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcC-HHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCCchhh
Confidence 577899999999999999999999999999999998 6799999999999999999999999999999776543
No 14
>KOG2908|consensus
Probab=99.07 E-value=2e-07 Score=91.81 Aligned_cols=276 Identities=13% Similarity=0.147 Sum_probs=171.2
Q ss_pred cHHHHHHHHHHHHHhcChhhhhhhHHHHHHHHHHHHHHHhhhCCCCcchHHHHHHHHHhCCCCc--chhhHHHHHHHHHH
Q psy9642 78 YQEELFSQIQEFLNMCNPDQIRHAGDLYAELSHQYTKTVMDLKTPQRGIPLIQTAIKKIQTSDS--QLTSLHSDLCQLCL 155 (437)
Q Consensus 78 ~~~~~~~~~~~fl~~fd~~Qir~a~~~~~~l~~~~~~~~~~~~~~~~~i~~l~~ai~rl~~~~~--~lT~~h~~l~~l~L 155 (437)
..+.+.+...+|+..|-+.-=.+ ++|+.+.-...+.+.+..++..|..-+..++...+ ..--+|+...++.|
T Consensus 53 ~~~~~l~lY~NFvsefe~kINpl------slvei~l~~~~~~~D~~~al~~Le~i~~~~~~~~e~~av~~~~t~~~r~~L 126 (380)
T KOG2908|consen 53 AGDLLLQLYLNFVSEFETKINPL------SLVEILLVVSEQISDKDEALEFLEKIIEKLKEYKEPDAVIYILTEIARLKL 126 (380)
T ss_pred cchHHHHHHHHHHHHHhhccChH------HHHHHHHHHHHHhccHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHHH
Confidence 34557777788887763321110 11222212222233455677777777777765544 66668999999999
Q ss_pred HhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhcccc-c--ccCHHHHHHHHHH
Q psy9642 156 LAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIITTPA-L--AVSHIMLEGYKKY 232 (437)
Q Consensus 156 ~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~~P~-~--~~s~i~vea~Kk~ 232 (437)
..++...+-++|+.--..++. ...+++.-.-.||..+..-|=..+||..++++--.=+.+-. . +.+..+..|+ -+
T Consensus 127 ~i~DLk~~kk~ldd~~~~ld~-~~~v~~~Vh~~fY~lssqYyk~~~d~a~yYr~~L~YL~~~d~~~l~~se~~~lA~-~L 204 (380)
T KOG2908|consen 127 EINDLKEIKKLLDDLKSMLDS-LDGVTSNVHSSFYSLSSQYYKKIGDFASYYRHALLYLGCSDIDDLSESEKQDLAF-DL 204 (380)
T ss_pred hcccHHHHHHHHHHHHHHHhc-ccCCChhhhhhHHHHHHHHHHHHHhHHHHHHHHHHHhccccccccCHHHHHHHHH-HH
Confidence 999999998887764333322 34566666777777777777777888877666555555432 2 2333334443 23
Q ss_pred HHHHHHHhCCCCCCCcc-ccHHHhHhhc-cCCHHHHHHHHHHhcCCHHHHHHHHHhccccccccchhhHHHHHHHHHHHH
Q psy9642 233 LLIYLIVYGKAPNLPKN-VSQAICRYIK-PLSQPYLDLVSVYTNNNSTELQHLLLKYADVFSRDENTGLTKQIVASLYKN 310 (437)
Q Consensus 233 iLv~Lil~G~~~~lp~~-~s~~~~r~~k-~~~~pY~~L~~af~~~d~~~~~~~~~~~~~~f~~D~n~~Lv~~l~~~v~r~ 310 (437)
.+..++-. .+-.+-.. ..|.+.. ++ ..-..-.++..||..||+.+|......+.. -. -|.++.-.-..|-
T Consensus 205 ~~aALLGe-~iyNfGELL~HPiles-L~gT~~eWL~dll~Afn~Gdl~~f~~l~~~~~~----~p--~L~~~e~~L~qKI 276 (380)
T KOG2908|consen 205 SLAALLGE-NIYNFGELLAHPILES-LKGTNREWLKDLLIAFNSGDLKRFESLKGVWGK----QP--DLASNEDFLLQKI 276 (380)
T ss_pred HHHHHhcc-ccccHHHHHhhHHHHH-hcCCcHHHHHHHHHHhccCCHHHHHHHHHHhcc----Cc--hHHHHHHHHHHHH
Confidence 33333222 13222211 1222222 32 234667899999999999999998776544 00 1222222222222
Q ss_pred HHHHH-HHhhcc------ccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCCCEEEEccCCC
Q psy9642 311 NIKRL-TKTFLT------LSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVFNDNPQ 370 (437)
Q Consensus 311 ~I~~l-~k~Ys~------IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~g~v~F~~~~~ 370 (437)
++..| --+|++ ||+++||+++.++ .++||.+|.+.+.-|-|.|.||+.+|.|.+....+
T Consensus 277 ~LmaLiEi~F~rpa~~R~lsf~~Ia~~tkip-~~eVE~LVMKAlslgLikG~Idqv~~~v~~swvqP 342 (380)
T KOG2908|consen 277 RLLALIEITFSRPANERTLSFKEIAEATKIP-NKEVELLVMKALSLGLIKGSIDQVEGVVYMSWVQP 342 (380)
T ss_pred HHHHHHHHHhcCcchhccccHHHHHHHhCCC-HHHHHHHHHHHHhccceeeeecccccEEEEecccc
Confidence 22222 234665 9999999999998 69999999999999999999999999999986554
No 15
>KOG1076|consensus
Probab=98.27 E-value=0.00016 Score=77.17 Aligned_cols=271 Identities=17% Similarity=0.182 Sum_probs=150.9
Q ss_pred HHHHHHHHHHHHHhcChhhhhhhHHHHHHHHHHHHHHHhhhCCCCcchHH---HHHHHHHhCCCCcchhhHHHHHHH-HH
Q psy9642 79 QEELFSQIQEFLNMCNPDQIRHAGDLYAELSHQYTKTVMDLKTPQRGIPL---IQTAIKKIQTSDSQLTSLHSDLCQ-LC 154 (437)
Q Consensus 79 ~~~~~~~~~~fl~~fd~~Qir~a~~~~~~l~~~~~~~~~~~~~~~~~i~~---l~~ai~rl~~~~~~lT~~h~~l~~-l~ 154 (437)
...+.+.+..|+-.-|..-+| .=.-||+.+-.++.+.+...|.+.+ |+.-|...|++...|--.--.++- ++
T Consensus 465 ~~~lmd~Lc~~iY~~~d~r~r----tRAmLchIYh~AL~d~f~~ARDlLLMSHlQdnI~h~D~stQIL~NRtmvQLGLCA 540 (843)
T KOG1076|consen 465 SDALMDGLCKYIYKNDDDRLR----TRAMLCHIYHHALHDNFYTARDLLLMSHLQDNIQHADISTQILFNRTMVQLGLCA 540 (843)
T ss_pred HHHHHHHHHHHHHhcchHHHH----HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhhccChhHHHHHHHHHHHHHHHH
Confidence 334677777777665554333 2344777776666665555666554 344444455544433212122222 33
Q ss_pred HHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhccccc-ccCHHHHHHHHHHH
Q psy9642 155 LLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIITTPAL-AVSHIMLEGYKKYL 233 (437)
Q Consensus 155 L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~~P~~-~~s~i~vea~Kk~i 233 (437)
...|....|-..|..-.. ..-++=..-.|...-..++...=.+-.+..-..|-. -.+-..+||. |+
T Consensus 541 FR~Gmi~EaH~~L~dl~s-----------t~r~kELLgQgv~~~~~he~t~eQe~~eR~rQlPyHmHINLELlEcV--yL 607 (843)
T KOG1076|consen 541 FRQGMIKEAHQCLSDLQS-----------TGRVKELLGQGVLQRRQHEKTAEQEKIERRRQLPYHMHINLELLECV--YL 607 (843)
T ss_pred HHcccHHHHHHHHHHHHh-----------cchHHHHHhhhhhhhhhhccChhhHHHHHhhcCchhhhccHHHHHHH--HH
Confidence 455555666444433211 012222222333333233333333334444444543 3445566663 44
Q ss_pred HHHHHHhCCCCCCC--------ccccHHHhHhhcc-----------CCHHH-HHHHHHHhcCCHHHHHHHHHhccccccc
Q psy9642 234 LIYLIVYGKAPNLP--------KNVSQAICRYIKP-----------LSQPY-LDLVSVYTNNNSTELQHLLLKYADVFSR 293 (437)
Q Consensus 234 Lv~Lil~G~~~~lp--------~~~s~~~~r~~k~-----------~~~pY-~~L~~af~~~d~~~~~~~~~~~~~~f~~ 293 (437)
.+++|+ ++|.+. ++.|..+.+.++. ....| ..-++|...|||..-...+..+.++|.=
T Consensus 608 tcaMLl--EIP~MAA~~~d~Rrr~iSk~frr~Le~serqsf~gPPEn~RehVvaAsKAm~~Gnw~~c~~fi~nn~KvW~L 685 (843)
T KOG1076|consen 608 TCAMLL--EIPYMAAHESDARRRMISKSFRRQLEHSERQSFTGPPENTREHVVAASKAMQKGNWQKCFEFIVNNIKVWDL 685 (843)
T ss_pred HHHHHH--hhhHHhhhhhhhhcccccHHHHHHHHHHhhccccCCchhHHHHHHHHHHHHhcCCHHHHHHHHHhhhhHHHh
Confidence 444443 232221 2222222222210 01122 3556788899999888866666667744
Q ss_pred cchhh-----HHHHHHHHHHHHHHHHHHHhhccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCCCEEEEccC
Q psy9642 294 DENTG-----LTKQIVASLYKNNIKRLTKTFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVFNDN 368 (437)
Q Consensus 294 D~n~~-----Lv~~l~~~v~r~~I~~l~k~Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~g~v~F~~~ 368 (437)
=.|.. |++++..--.|+-+-..+..|.+|||+.+|.+..|+ +..|-.+|++||-..+|.|++|++.++++|+..
T Consensus 686 fpn~d~V~~Ml~~rIqEEsLRTYLftYss~Y~SvSl~~LA~mFdLp-~~~VhsIiSkmiineEl~AslDqpt~~iv~hrv 764 (843)
T KOG1076|consen 686 FPNADTVLDMLTERIQEESLRTYLFTYSSVYDSVSLAKLADMFDLP-EPKVHSIISKMIINEELHASLDQPTQCIVMHRV 764 (843)
T ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhccHHHHHHHhCCC-chhHHHHHHHHHHHHHhhhccCCCcceEEEeec
Confidence 33333 344444444455555677788899999999999998 789999999999999999999999999999974
Q ss_pred C
Q psy9642 369 P 369 (437)
Q Consensus 369 ~ 369 (437)
.
T Consensus 765 E 765 (843)
T KOG1076|consen 765 E 765 (843)
T ss_pred c
Confidence 3
No 16
>KOG0687|consensus
Probab=98.23 E-value=0.00023 Score=70.29 Aligned_cols=183 Identities=13% Similarity=0.132 Sum_probs=122.9
Q ss_pred hHHHHHHHHHHHHHHhhHHHHHHHHHHHhcccccccCHHHHHHHHHHHHHHHHHhCCCCCCCcc-ccHHHhHhhccCCHH
Q psy9642 186 FLQYFYYGGMIYLALKNYERALYFFEVIITTPALAVSHIMLEGYKKYLLIYLIVYGKAPNLPKN-VSQAICRYIKPLSQP 264 (437)
Q Consensus 186 ~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~~P~~~~s~i~vea~Kk~iLv~Lil~G~~~~lp~~-~s~~~~r~~k~~~~p 264 (437)
-=+|.-|.|+-.++.+||.+|...|..++++.++..-----....+-+++++|.....+-..+. .+|.+.-.+.. +++
T Consensus 180 rNRlKvY~Gly~msvR~Fk~Aa~Lfld~vsTFtS~El~~Y~~~v~Ytv~~g~i~leR~dlktKVi~~~Evl~vl~~-l~~ 258 (393)
T KOG0687|consen 180 RNRLKVYQGLYCMSVRNFKEAADLFLDSVSTFTSYELMSYETFVRYTVITGLIALERVDLKTKVIKCPEVLEVLHK-LPS 258 (393)
T ss_pred hhhHHHHHHHHHHHHHhHHHHHHHHHHHcccccceecccHHHHHHHHHHHhhheeccchHHhhhcCcHHHHHHhhc-Cch
Confidence 4467779999999999999999999999997765211111122234567777755444333332 23333333332 455
Q ss_pred HHHHHHHHhcCCHHHHHHHH-Hhccccccccchhh-HHHHHHHHHHHHHHHHHHHhhccccHHHHHHHhCCCChHHHHHH
Q psy9642 265 YLDLVSVYTNNNSTELQHLL-LKYADVFSRDENTG-LTKQIVASLYKNNIKRLTKTFLTLSLADVASRVQLGTPVQAEIY 342 (437)
Q Consensus 265 Y~~L~~af~~~d~~~~~~~~-~~~~~~f~~D~n~~-Lv~~l~~~v~r~~I~~l~k~Ys~IsL~dIa~~l~L~~~~eaE~~ 342 (437)
-.+++...=..+-..|-..+ ......+..|.-.+ .+.--..-++++.--.+-..|.+++|.-+|+..|++ .+=+++-
T Consensus 259 ~~q~l~SLY~C~Y~~Ff~~L~~~~~~~lk~D~~l~~h~~yyvREMR~rvY~QlLESYrsl~l~~MA~aFgVS-VefiDre 337 (393)
T KOG0687|consen 259 VSQLLNSLYECDYSDFFNDLAAVEAKQLKDDRYLGPHYRYYVREMRRRVYAQLLESYRSLTLESMAKAFGVS-VEFIDRE 337 (393)
T ss_pred HHHHHHHHHhccHHHHHHHHHHHHHHhhccchhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCch-HHHHHhH
Confidence 55665555455666654444 44456676666444 333333334444445566789999999999999997 8888899
Q ss_pred HHHhHHcCceEEEEecCCCEEEEccCCC
Q psy9642 343 ILKMISQNEIYATINKKDGMVVFNDNPQ 370 (437)
Q Consensus 343 l~~mI~~G~I~A~Id~~~g~v~F~~~~~ 370 (437)
+.+-|.+|.++++||+-+|+|.-..+.+
T Consensus 338 L~rFI~~grL~ckIDrVnGVVEtNrpD~ 365 (393)
T KOG0687|consen 338 LGRFIAAGRLHCKIDRVNGVVETNRPDE 365 (393)
T ss_pred HHHhhccCceeeeeecccceeecCCccc
Confidence 9999999999999999999998875544
No 17
>COG5187 RPN7 26S proteasome regulatory complex component, contains PCI domain [Posttranslational modification, protein turnover, chaperones]
Probab=98.15 E-value=0.0023 Score=62.50 Aligned_cols=257 Identities=16% Similarity=0.164 Sum_probs=156.0
Q ss_pred HHHHHHHHHHHHHHhhhCCCCcchHHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhH--hhhhhhcCCCC
Q psy9642 103 DLYAELSHQYTKTVMDLKTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDV--DITTIANEGPQ 180 (437)
Q Consensus 103 ~~~~~l~~~~~~~~~~~~~~~~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~--~I~~~~~~~~~ 180 (437)
+.+..+++.+++.... -.|.+.++..+.+-- +.+.---+...-+|+.+--++-...-+-|+. +|.+. .
T Consensus 116 ea~~n~aeyY~qi~D~----~ng~~~~~~~~~~a~-stg~KiDv~l~kiRlg~~y~d~~vV~e~lE~~~~~iEk-----G 185 (412)
T COG5187 116 EADRNIAEYYCQIMDI----QNGFEWMRRLMRDAM-STGLKIDVFLCKIRLGLIYGDRKVVEESLEVADDIIEK-----G 185 (412)
T ss_pred HHHHHHHHHHHHHhhh----hhHHHHHHHHHHHHH-hcccchhhHHHHHHHHHhhccHHHHHHHHHHHHHHHHh-----C
Confidence 4555566666554443 235555544444321 1111111333445666666654433333322 33321 2
Q ss_pred CChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhcccccccCHHHHHHHHHHHHHHHHHhCCCCCCCcc-ccHHHhHhhc
Q psy9642 181 FDTKYFLQYFYYGGMIYLALKNYERALYFFEVIITTPALAVSHIMLEGYKKYLLIYLIVYGKAPNLPKN-VSQAICRYIK 259 (437)
Q Consensus 181 ~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~~P~~~~s~i~vea~Kk~iLv~Lil~G~~~~lp~~-~s~~~~r~~k 259 (437)
.+-+--=+|.-|.||-.+..++|.+|...|..++.+.....---.-.+..+.+..+++-....+--.+. -+|.+-..+.
T Consensus 186 gDWeRrNRyK~Y~Gi~~m~~RnFkeAa~Ll~d~l~tF~S~El~sY~~~vrYa~~~Gl~~leR~diktki~dspevl~vi~ 265 (412)
T COG5187 186 GDWERRNRYKVYKGIFKMMRRNFKEAAILLSDILPTFESSELISYSRAVRYAIFCGLLRLERRDIKTKILDSPEVLDVIG 265 (412)
T ss_pred CCHHhhhhHHHHHHHHHHHHHhhHHHHHHHHHHhccccccccccHHHHHHHHHHhhhheeehhhhhhhhcCCHHHHHhcc
Confidence 234445688899999999999999999999999986654321122334455677777754444332222 2333322222
Q ss_pred cC--CHHHHHHHHHHhcCCHH-HHHHHHHhccccccccchhh-HHHHHHHHHHHHHHHHHHHhhccccHHHHHHHhCCCC
Q psy9642 260 PL--SQPYLDLVSVYTNNNST-ELQHLLLKYADVFSRDENTG-LTKQIVASLYKNNIKRLTKTFLTLSLADVASRVQLGT 335 (437)
Q Consensus 260 ~~--~~pY~~L~~af~~~d~~-~~~~~~~~~~~~f~~D~n~~-Lv~~l~~~v~r~~I~~l~k~Ys~IsL~dIa~~l~L~~ 335 (437)
.. +..-.+++...-..|.. -|...+..+-+.+..|.-.+ .+.-...-++++.--.+-..|..+||..+|+..|++
T Consensus 266 ~~e~l~sl~~l~~SLy~cdY~~~F~~ll~~~~n~L~~d~fl~rh~d~fvREMRrrvYaQlLESYr~lsl~sMA~tFgVS- 344 (412)
T COG5187 266 SSEKLGSLVQLATSLYECDYGGDFMNLLYLFCNSLQDDVFLGRHVDLFVREMRRRVYAQLLESYRLLSLESMAQTFGVS- 344 (412)
T ss_pred chhhhhhHHHHHHHHHHhccchhhHHHHHHHHhhccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhCcc-
Confidence 11 12222333322223333 57777777777777777665 344455556666666788899999999999999997
Q ss_pred hHHHHHHHHHhHHcCceEEEEecCCCEEEEccCCC
Q psy9642 336 PVQAEIYILKMISQNEIYATINKKDGMVVFNDNPQ 370 (437)
Q Consensus 336 ~~eaE~~l~~mI~~G~I~A~Id~~~g~v~F~~~~~ 370 (437)
.+=++.=+.+-|-+|.++..||+-+|+|.-..+.+
T Consensus 345 V~yvdrDLg~FIp~~~LncvIDRvnGvVetnrpde 379 (412)
T COG5187 345 VEYVDRDLGEFIPEGRLNCVIDRVNGVVETNRPDE 379 (412)
T ss_pred HHHHhhhHHhhCCCCceeeeeecccceEeccCcch
Confidence 88899999999999999999999999987765543
No 18
>PF10255 Paf67: RNA polymerase I-associated factor PAF67; InterPro: IPR019382 RNA polymerase I is a multi-subunit enzyme and its transcription competence is dependent on the presence of PAF67 [].
Probab=98.10 E-value=0.0042 Score=64.15 Aligned_cols=186 Identities=17% Similarity=0.236 Sum_probs=117.6
Q ss_pred HHHHHHHHHhCCchHHHhhhhHhhhhhhcCC-CCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhccccc-------
Q psy9642 148 SDLCQLCLLAQNFKPALEFLDVDITTIANEG-PQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIITTPAL------- 219 (437)
Q Consensus 148 ~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~-~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~~P~~------- 219 (437)
.-++|+-..-|+|..|+++++.--. .+.. -.--+...+..+||.|-.|+.+++|.+|.+.|..++..=..
T Consensus 126 igLlRvh~LLGDY~~Alk~l~~idl--~~~~l~~~V~~~~is~~YyvGFaylMlrRY~DAir~f~~iL~yi~r~k~~~~~ 203 (404)
T PF10255_consen 126 IGLLRVHCLLGDYYQALKVLENIDL--NKKGLYTKVPACHISTYYYVGFAYLMLRRYADAIRTFSQILLYIQRTKNQYHQ 203 (404)
T ss_pred HHHHHHHHhccCHHHHHHHhhccCc--ccchhhccCcchheehHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcc
Confidence 3457888888999999999876311 1110 01234568889999999999999999999999999873211
Q ss_pred ---ccCHHHHHHHHHHHHHHHHHhCCCCCCCccccHHHhHhhccCCHHHHHHHHHHhcCCHHHHHHHHHhccccccccc-
Q psy9642 220 ---AVSHIMLEGYKKYLLIYLIVYGKAPNLPKNVSQAICRYIKPLSQPYLDLVSVYTNNNSTELQHLLLKYADVFSRDE- 295 (437)
Q Consensus 220 ---~~s~i~vea~Kk~iLv~Lil~G~~~~lp~~~s~~~~r~~k~~~~pY~~L~~af~~~d~~~~~~~~~~~~~~f~~D~- 295 (437)
.-+.+....=|-+.|+.+-+. -.|.. .+..+...++. -|.+=......||.+.|++.....-+.|..-.
T Consensus 204 ~~~q~d~i~K~~eqMyaLlAic~~-l~p~~---lde~i~~~lke---ky~ek~~kmq~gd~~~f~elF~~acPKFIsp~~ 276 (404)
T PF10255_consen 204 RSYQYDQINKKNEQMYALLAICLS-LCPQR---LDESISSQLKE---KYGEKMEKMQRGDEEAFEELFSFACPKFISPVS 276 (404)
T ss_pred ccchhhHHHhHHHHHHHHHHHHHH-hCCCC---CCHHHHHHHHH---HHHHHHHHHHccCHHHHHHHHHhhCCCccCCCC
Confidence 112233333333333332221 11211 22333444442 26555555678999999999998877775511
Q ss_pred ---------hh---h-------HHHHHHHHHHHHHHHHHHHhhccccHHHHHHHhCCCChHHHHHHH
Q psy9642 296 ---------NT---G-------LTKQIVASLYKNNIKRLTKTFLTLSLADVASRVQLGTPVQAEIYI 343 (437)
Q Consensus 296 ---------n~---~-------Lv~~l~~~v~r~~I~~l~k~Ys~IsL~dIa~~l~L~~~~eaE~~l 343 (437)
|. . ..+++.+...-.+||..-|-|++|+++.+|..++++ ++++...+
T Consensus 277 pp~~~~~~~~~~~e~~~~Ql~~Fl~eV~~q~~l~~lRSyLKLYtti~l~KLA~fl~vd-~~~lr~~L 342 (404)
T PF10255_consen 277 PPDYDGPSQNKNKEPYRRQLKLFLDEVKQQQKLPTLRSYLKLYTTIPLEKLASFLDVD-EEELRSQL 342 (404)
T ss_pred CCCcccccchhhhhHHHHHHHHHHHHHHHhhhhhHHHHHHHhhcCCCHHHHHHHcCCC-HHHHHHHH
Confidence 11 1 133444555556788999999999999999999996 56554433
No 19
>KOG0686|consensus
Probab=98.01 E-value=0.00086 Score=68.06 Aligned_cols=218 Identities=11% Similarity=0.132 Sum_probs=144.7
Q ss_pred HHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhccccc---ccC
Q psy9642 146 LHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIITTPAL---AVS 222 (437)
Q Consensus 146 ~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~~P~~---~~s 222 (437)
+-...++.++-.++|..-+.+.++-...-.. ......+-..+..-+.|.....+++|..|..+|-.+...-.. -++
T Consensus 189 m~ln~i~VSI~~~nw~hv~sy~~~A~st~~~-~~~~~q~v~~kl~C~agLa~L~lkkyk~aa~~fL~~~~~~~d~~~ivt 267 (466)
T KOG0686|consen 189 MCLNLILVSIYMGNWGHVLSYISKAESTPDA-NENLAQEVPAKLKCAAGLANLLLKKYKSAAKYFLLAEFDHCDYPEIVT 267 (466)
T ss_pred HHHHHHHHHHhhcchhhhhhHHHHHHhCchh-hhhHHHhcCcchHHHHHHHHHHHHHHHHHHHHHHhCCCCccCccceec
Confidence 3445677888888888887777776543100 011122223456678999999999999999999877652221 123
Q ss_pred HHHHHHHHHHHHHHHHH-hCCCCCC-CccccHHHhHhhccCCHHHHHHHHHHhcCCHHHHHHHHHhccccccccchh-hH
Q psy9642 223 HIMLEGYKKYLLIYLIV-YGKAPNL-PKNVSQAICRYIKPLSQPYLDLVSVYTNNNSTELQHLLLKYADVFSRDENT-GL 299 (437)
Q Consensus 223 ~i~vea~Kk~iLv~Lil-~G~~~~l-p~~~s~~~~r~~k~~~~pY~~L~~af~~~d~~~~~~~~~~~~~~f~~D~n~-~L 299 (437)
+.=+..| ..++-+. .+.-.-. ....+..+ |.|-...+.-.++...|-++.....-+.+.+.++.+.=|--. .-
T Consensus 268 psdv~iY---ggLcALAtfdr~~Lk~~vi~n~~F-k~flel~Pqlr~il~~fy~sky~~cl~~L~~~k~~llLD~yLaph 343 (466)
T KOG0686|consen 268 PSDVAIY---GGLCALATFDRQDLKLNVIKNESF-KLFLELEPQLREILFKFYSSKYASCLELLREIKPRLLLDMYLAPH 343 (466)
T ss_pred chhhHHH---HhhHhhccCCHHHHHHHHHcchhh-hhHHhcChHHHHHHHHHhhhhHHHHHHHHHHhccceeechhcchh
Confidence 3333333 2222221 1000000 00001111 112223455667888888887777777777776666555433 36
Q ss_pred HHHHHHHHHHHHHHHHHHhhccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCCCEEEEccCC
Q psy9642 300 TKQIVASLYKNNIKRLTKTFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVFNDNP 369 (437)
Q Consensus 300 v~~l~~~v~r~~I~~l~k~Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~g~v~F~~~~ 369 (437)
|..+..-++.+.+.+....|+++.++.+|...+.+ ....|.-|.++|.+|.|.|+||...++|.-.+..
T Consensus 344 Vd~Ly~~IR~r~llqy~~py~s~~m~~mA~af~~s-v~~le~~l~~LI~~~~i~~rIDs~~ki~~~~~~~ 412 (466)
T KOG0686|consen 344 VDNLYSLIRNRALLQYLSPYSSADMSKMAEAFNTS-VAILESELLELILEGKISGRIDSHNKILYARDAD 412 (466)
T ss_pred HHHHHHHHHHhhHHHhcCccccchHHHHHHHhccc-HHHHHHHHHHHHHccchheeeccccceeeecccc
Confidence 88888888999999999999999999999999987 7899999999999999999999999999887653
No 20
>KOG2072|consensus
Probab=97.91 E-value=0.002 Score=70.13 Aligned_cols=71 Identities=8% Similarity=0.215 Sum_probs=66.5
Q ss_pred hhHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCCCEEEEcc
Q psy9642 297 TGLTKQIVASLYKNNIKRLTKTFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVFND 367 (437)
Q Consensus 297 ~~Lv~~l~~~v~r~~I~~l~k~Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~g~v~F~~ 367 (437)
..-|..|....+.+.++.++++|.+|+++.|.+..-.-+.-++|+++.+....+.+..+|||..+.|.|..
T Consensus 423 ~QYI~sLq~v~~~RllqQvSqiY~sIs~~~l~~La~F~~~~~lEk~~v~a~k~~~v~iriDH~~~~v~Fgs 493 (988)
T KOG2072|consen 423 SQYIPSLQDVIILRLLQQVSQIYESISFERLYKLAPFFSAFELEKLLVEAAKHNDVSIRIDHESNSVSFGS 493 (988)
T ss_pred cccchhHHHHHHHHHHHHHHHHHHHHhHHHHHHHHhhcCHHHHHHHHHHHHhccceeEEeccccceeeecc
Confidence 45788899999999999999999999999999998877789999999999999999999999999999984
No 21
>KOG2753|consensus
Probab=97.48 E-value=0.14 Score=51.07 Aligned_cols=269 Identities=10% Similarity=0.128 Sum_probs=153.4
Q ss_pred HHHHHHHHHHHHHhcChhhhhhhHHHHHHHHHHHHHHHhhhCCCCcchHHHHHHHHHhCC-CCcchhhHHHHHHHHHHHh
Q psy9642 79 QEELFSQIQEFLNMCNPDQIRHAGDLYAELSHQYTKTVMDLKTPQRGIPLIQTAIKKIQT-SDSQLTSLHSDLCQLCLLA 157 (437)
Q Consensus 79 ~~~~~~~~~~fl~~fd~~Qir~a~~~~~~l~~~~~~~~~~~~~~~~~i~~l~~ai~rl~~-~~~~lT~~h~~l~~l~L~~ 157 (437)
-+..+.-++..+..-.|++.- ..+.+.|+.++..-. ...|...+..|...-.-++. +|..++ +...++++|-..
T Consensus 63 le~vlnsi~sLi~~~~~e~~e---~~v~a~~ekva~q~n-~~~~~l~L~vLsnLfn~~d~~~~aR~~-Vy~~lv~la~~~ 137 (378)
T KOG2753|consen 63 LECVLNSIVSLIKNAPPEKVE---EMVKAICEKVAKQPN-DKTASLRLQVLSNLFNGVDKPTPARYQ-VYMSLVTLAASC 137 (378)
T ss_pred HHHHHHHHHHHHHhCCHHHhH---HHHHHHHHHHhcCcc-CCCcccHHHHHHHHHhccCCCchHHHH-HHHHHHHHHhhc
Confidence 445566666666664444432 233333333322111 11233345555554444432 233333 455667777777
Q ss_pred CCchHH---HhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhcccccccCHHHHHHHHHHHH
Q psy9642 158 QNFKPA---LEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIITTPALAVSHIMLEGYKKYLL 234 (437)
Q Consensus 158 ~~y~~A---l~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~~P~~~~s~i~vea~Kk~iL 234 (437)
+....- ++-++.-+.+ -.++.+++=+++-.-..+.-..+.-+++...+..-+.+.+......+.|..-+.|.
T Consensus 138 ~~~~~i~~~lk~~~~~lke-----w~~~vedqrel~r~v~~al~~~k~~~~s~kvmt~lLgtyt~dnas~AredA~rcV~ 212 (378)
T KOG2753|consen 138 KLIEYIVPNLKQLDDWLKE-----WNISVEDQRELLRAVHKALKDNKSVDESSKVMTELLGTYTEDNASEAREDAMRCVV 212 (378)
T ss_pred ceeeeecccHHHHHHHHHh-----CCCCHHHHHHHHHHHHHHHHhcchhhhHHHHHHHHHHHhcccchhHHHHHHHHHHH
Confidence 754433 2223322221 23455665555444444444444555677777777766665332233333334343
Q ss_pred HHHHHhCCCCCCCcc-ccHHHhHhhccCCHHHHHHHHHHhcCCHHHHHHHHHhccccccccchhhHHHHHHHHHHHHHH-
Q psy9642 235 IYLIVYGKAPNLPKN-VSQAICRYIKPLSQPYLDLVSVYTNNNSTELQHLLLKYADVFSRDENTGLTKQIVASLYKNNI- 312 (437)
Q Consensus 235 v~Lil~G~~~~lp~~-~s~~~~r~~k~~~~pY~~L~~af~~~d~~~~~~~~~~~~~~f~~D~n~~Lv~~l~~~v~r~~I- 312 (437)
-.+ ..-++..+... +-+. -+.++. .+.++|.+.|.+|-+..+.+...++..-.. .+|++.+ ..+.|-.+
T Consensus 213 ~av-~dP~~F~fD~Ll~L~p-V~qLE~--d~i~qLL~IF~s~~L~aYveF~~~N~~Fvq---s~gl~~E--~~~~KMRLL 283 (378)
T KOG2753|consen 213 EAV-KDPKIFLFDHLLTLPP-VKQLEG--DLIHQLLKIFVSGKLDAYVEFVAANSGFVQ---SQGLVHE--QNMAKMRLL 283 (378)
T ss_pred HHH-cCCceeccchhccCch-HHHhcc--chHHHHHHHHHhcchHHHHHHHHhChHHHH---HhcccHH--HHHHHHHHH
Confidence 222 33233222211 2222 233543 347899999999999999888888765443 3456555 33444443
Q ss_pred --HHHHHhhccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCCCEEEEcc
Q psy9642 313 --KRLTKTFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVFND 367 (437)
Q Consensus 313 --~~l~k~Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~g~v~F~~ 367 (437)
..|+..=..||+.+|++.|++. ++|+|..|-+.|..|.+.|+|||-+..|+-+.
T Consensus 284 Tlm~LA~es~eisy~~l~k~LqI~-edeVE~fVIdaI~aklV~~kidq~~~~viVs~ 339 (378)
T KOG2753|consen 284 TLMSLAEESNEISYDTLAKELQIN-EDEVELFVIDAIRAKLVEGKIDQMNRTVIVSS 339 (378)
T ss_pred HHHHHhccCCCCCHHHHHHHhccC-HHHHHHHHHHHHHHHHHHhhHHhhcceEEeeh
Confidence 4555556689999999999998 78999999999999999999999887777653
No 22
>PF08375 Rpn3_C: Proteasome regulatory subunit C-terminal; InterPro: IPR013586 Intracellular proteins, including short-lived proteins such as cyclin, Mos, Myc, p53, NF-kappaB, and IkappaB, are degraded by the ubiquitin-proteasome system. The 26S proteasome is a self-compartmentalising protease responsible for the regulated degradation of intracellular proteins in eukaryotes [, ]. This giant intracellular protease is formed by several subunits arranged into two 19S polar caps, where protein recognition and ATP-dependent unfolding occur, flanking a 20S central barrel-shaped structure with an inner proteolytic chamber. This overall structure is highly conserved among eukaryotes and is essential for cell viability. Proteins targeted to the 26S proteasome are conjugated with a polyubiquitin chain by an enzymatic cascade before delivery to the 26S proteasome for degradation into oligopeptides. The 19S component is divided into a "base" subunit containing six ATPases (Rpt proteins) and two non-ATPases (Rpn1, Rpn2), and a "lid" subunit composed of eight stoichiometric proteins (Rpn3, Rpn5, Rpn6, Rpn7, Rpn8, Rpn9, Rpn11, Rpn12) []. Additional non-essential and species specific proteins may also be present. The 19S unit performs several essential functions including binding the specific protein substrates, unfolding them, cleaving the attached ubiquitin chains, opening the 20S subunit, and driving the unfolded polypeptide into the proteolytic chamber for degradation. The 26s proteasome and 19S regulator are of medical interest due to their involvement in burn rehabilitation []. This eukaryotic domain is found at the C terminus of 26S proteasome regulatory subunits such as the non-ATPase Rpn3 subunit which is essential for proteasomal function []. It occurs together with the PCI/PINT domain (IPR000717 from INTERPRO). ; GO: 0030234 enzyme regulator activity, 0042176 regulation of protein catabolic process, 0000502 proteasome complex
Probab=97.41 E-value=0.00016 Score=55.67 Aligned_cols=43 Identities=14% Similarity=0.174 Sum_probs=38.1
Q ss_pred CCCCchHHHHHHHHHHHHHHHHHH-HHHHHHHHhhCCHHHHHHh
Q psy9642 370 QRFNNPLTFAQIESNIRACMHLDG-KFQAMEEEILVNPLYVKKA 412 (437)
Q Consensus 370 ~~~~~~e~~~~l~~~i~~~~~L~~-~~~~~d~~l~~~~~yi~k~ 412 (437)
+.|+|.+|+..|++||++|+.||+ .|++|+..-...+.-..+.
T Consensus 1 DvYsT~ePq~aF~~RI~FCL~lHneaVkAMRyP~~~~~~~~~~~ 44 (68)
T PF08375_consen 1 DVYSTNEPQEAFHQRIAFCLQLHNEAVKAMRYPPDAHKKELESA 44 (68)
T ss_pred CCcchhhHHHHHHHHHHHHHHHHHHHHHHhcCCCCccchhhhhH
Confidence 479999999999999999999999 9999999888877666554
No 23
>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=96.51 E-value=0.0073 Score=53.47 Aligned_cols=109 Identities=12% Similarity=0.188 Sum_probs=69.7
Q ss_pred HHHHHHHhCCCCCCCcc---ccHHHhHhhccCCHHHHHHHHHHhcCCHHHHHHHHHhccccccccchhhHHHHHHHHHHH
Q psy9642 233 LLIYLIVYGKAPNLPKN---VSQAICRYIKPLSQPYLDLVSVYTNNNSTELQHLLLKYADVFSRDENTGLTKQIVASLYK 309 (437)
Q Consensus 233 iLv~Lil~G~~~~lp~~---~s~~~~r~~k~~~~pY~~L~~af~~~d~~~~~~~~~~~~~~f~~D~n~~Lv~~l~~~v~r 309 (437)
+|+..|..+.++++.-. .++.+.. -.+.+..-..|.++..+|+..+|-..+..+ .|. +.-..+|..+.+.+++
T Consensus 10 ~Ll~~L~~~~~~df~~~~~rip~~~~~-~~~~i~~i~~l~~~L~~~~~~~~~~~~~~~--~~~-~~~~~~v~~~~~~iR~ 85 (143)
T PF10075_consen 10 ILLKYLMQNDLSDFRLLWKRIPEELKQ-SDPEIKAIWSLGQALWEGDYSKFWQALRSN--PWS-PDYKPFVPGFEDTIRE 85 (143)
T ss_dssp HHHHHHHTTTSTHHHHHHHTS-HHHHT-S-TTHHHHHHHHHHHHTT-HHHHHHHS-TT-------HHHHTSTTHHHHHHH
T ss_pred HHHHHHHcCCchHHHHHHHcCCHHHHh-hhHHHHHHHHHHHHHHCCCHHHHHHHHHhc--cch-HHHHHHHHHHHHHHHH
Confidence 55566666666543211 1111111 113345556888888899888777665543 332 2334567888999999
Q ss_pred HHHHHHHHhhccccHHHHHHHhCCCChHHHHHHHHHh
Q psy9642 310 NNIKRLTKTFLTLSLADVASRVQLGTPVQAEIYILKM 346 (437)
Q Consensus 310 ~~I~~l~k~Ys~IsL~dIa~~l~L~~~~eaE~~l~~m 346 (437)
+-+..++++|++|+++++++.||++ +++++.++.+-
T Consensus 86 ~i~~~i~~aY~sIs~~~la~~Lg~~-~~el~~~~~~~ 121 (143)
T PF10075_consen 86 RIAHLISKAYSSISLSDLAEMLGLS-EEELEKFIKSR 121 (143)
T ss_dssp HHHHHHHHH-SEE-HHHHHHHTTS--HHHHHHHHHHH
T ss_pred HHHHHHHHHHhHcCHHHHHHHhCCC-HHHHHHHHHHc
Confidence 9999999999999999999999998 88888888765
No 24
>KOG2758|consensus
Probab=96.31 E-value=0.025 Score=56.16 Aligned_cols=105 Identities=18% Similarity=0.281 Sum_probs=76.6
Q ss_pred HHHHHHHHH-hcCCHHHHHHHHHhccccccccchh-hHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHhCCCChHHHHH
Q psy9642 264 PYLDLVSVY-TNNNSTELQHLLLKYADVFSRDENT-GLTKQIVASLYKNNIKRLTKTFLTLSLADVASRVQLGTPVQAEI 341 (437)
Q Consensus 264 pY~~L~~af-~~~d~~~~~~~~~~~~~~f~~D~n~-~Lv~~l~~~v~r~~I~~l~k~Ys~IsL~dIa~~l~L~~~~eaE~ 341 (437)
|-.++..|. ..-|.+.-+..+.+-+++..+|--. .+....+++.+.--.-...++-.+|+++=+|.+|.++ ++|+|+
T Consensus 290 PiteFl~clyvn~DFdgAq~kl~eCeeVl~nDfFLva~l~~F~E~ARl~ifEtfCRIHqcIti~mLA~kLnm~-~eeaEr 368 (432)
T KOG2758|consen 290 PITEFLECLYVNYDFDGAQKKLRECEEVLVNDFFLVALLDEFLENARLLIFETFCRIHQCITIDMLADKLNMD-PEEAER 368 (432)
T ss_pred cHHHHHHHHhhccchHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHHHHHHHHHHHHheeHHHHHHHhcCC-HHHHHH
Confidence 444555543 4456666666666667777777643 3444455555554445555566679999999999998 899999
Q ss_pred HHHHhHHcCceEEEEecCCCEEEEccCC
Q psy9642 342 YILKMISQNEIYATINKKDGMVVFNDNP 369 (437)
Q Consensus 342 ~l~~mI~~G~I~A~Id~~~g~v~F~~~~ 369 (437)
-+.++|.+..|.|+||.+-|-|+...++
T Consensus 369 wivnlIr~~rl~AkidSklg~Vvmg~~~ 396 (432)
T KOG2758|consen 369 WIVNLIRTARLDAKIDSKLGHVVMGHPT 396 (432)
T ss_pred HHHHHHHHhhhhhhhccccCceeecCCC
Confidence 9999999999999999999999987544
No 25
>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A.
Probab=95.80 E-value=0.17 Score=49.76 Aligned_cols=203 Identities=18% Similarity=0.254 Sum_probs=119.5
Q ss_pred cHHHHHHHHHHHHHhcChhhhhhhHHHHHHHHHHHHHHHhhhCCCCcchHHHHHHHHHhCCCC--cchhhHHHHHHHHHH
Q psy9642 78 YQEELFSQIQEFLNMCNPDQIRHAGDLYAELSHQYTKTVMDLKTPQRGIPLIQTAIKKIQTSD--SQLTSLHSDLCQLCL 155 (437)
Q Consensus 78 ~~~~~~~~~~~fl~~fd~~Qir~a~~~~~~l~~~~~~~~~~~~~~~~~i~~l~~ai~rl~~~~--~~lT~~h~~l~~l~L 155 (437)
+....+.+..+.....+-. .-++..|...+..+.. ..|..++..+..|+.-+...+ ......+..+.+++-
T Consensus 53 ~A~~ay~kAa~~~~~~~~~--~~Aa~~~~~Aa~~~k~-----~~~~~Ai~~~~~A~~~y~~~G~~~~aA~~~~~lA~~ye 125 (282)
T PF14938_consen 53 KAAEAYEKAADCYEKLGDK--FEAAKAYEEAANCYKK-----GDPDEAIECYEKAIEIYREAGRFSQAAKCLKELAEIYE 125 (282)
T ss_dssp HHHHHHHHHHHHHHHTT-H--HHHHHHHHHHHHHHHH-----TTHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHC
T ss_pred hhHHHHHHHHHHHHHcCCH--HHHHHHHHHHHHHHHh-----hCHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHH
Confidence 4445555555555442221 1233444443333322 256678888999888775443 444557777788887
Q ss_pred Hh-CCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhccccc-ccCH-HHHHHHHHH
Q psy9642 156 LA-QNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIITTPAL-AVSH-IMLEGYKKY 232 (437)
Q Consensus 156 ~~-~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~~P~~-~~s~-i~vea~Kk~ 232 (437)
.. +++..|+....+-+..+.... .+......+--.|.+++..++|.+|.+.|+.+...+.. .... ...+.+=+.
T Consensus 126 ~~~~d~e~Ai~~Y~~A~~~y~~e~---~~~~a~~~~~~~A~l~~~l~~y~~A~~~~e~~~~~~l~~~l~~~~~~~~~l~a 202 (282)
T PF14938_consen 126 EQLGDYEKAIEYYQKAAELYEQEG---SPHSAAECLLKAADLYARLGRYEEAIEIYEEVAKKCLENNLLKYSAKEYFLKA 202 (282)
T ss_dssp CTT--HHHHHHHHHHHHHHHHHTT----HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTCCCHCTTGHHHHHHHHHH
T ss_pred HHcCCHHHHHHHHHHHHHHHHHCC---ChhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhhcccccchhHHHHHHHH
Confidence 87 899999988877665544432 34456666667889999999999999999999985543 2222 334444455
Q ss_pred HHHHHHHhCCCCCCCccccHHHhHhh------cc--CCHHHHHHHHHHhcCCHHHHHHHHHhccccccccc
Q psy9642 233 LLIYLIVYGKAPNLPKNVSQAICRYI------KP--LSQPYLDLVSVYTNNNSTELQHLLLKYADVFSRDE 295 (437)
Q Consensus 233 iLv~Lil~G~~~~lp~~~s~~~~r~~------k~--~~~pY~~L~~af~~~d~~~~~~~~~~~~~~f~~D~ 295 (437)
+||.| ..|.... ....+.+.. .. .+.--.+|.+||..||.+.|...+..|..+=.-|+
T Consensus 203 ~l~~L-~~~D~v~----A~~~~~~~~~~~~~F~~s~E~~~~~~l~~A~~~~D~e~f~~av~~~d~~~~ld~ 268 (282)
T PF14938_consen 203 ILCHL-AMGDYVA----ARKALERYCSQDPSFASSREYKFLEDLLEAYEEGDVEAFTEAVAEYDSISRLDN 268 (282)
T ss_dssp HHHHH-HTT-HHH----HHHHHHHHGTTSTTSTTSHHHHHHHHHHHHHHTT-CCCHHHHCHHHTTSS---H
T ss_pred HHHHH-HcCCHHH----HHHHHHHHHhhCCCCCCcHHHHHHHHHHHHHHhCCHHHHHHHHHHHcccCccHH
Confidence 66666 4443211 111122211 10 12334689999999999999999999877765554
No 26
>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B.
Probab=94.98 E-value=0.073 Score=39.75 Aligned_cols=61 Identities=16% Similarity=0.309 Sum_probs=50.4
Q ss_pred HHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhc-ccc
Q psy9642 149 DLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIIT-TPA 218 (437)
Q Consensus 149 ~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~-~P~ 218 (437)
.+.+..+..++|..|+..++.-+.. ..+.....|.-|.++..+++|.+|..+|+.++. .|.
T Consensus 2 ~~a~~~~~~g~~~~A~~~~~~~l~~---------~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~P~ 63 (65)
T PF13432_consen 2 ALARALYQQGDYDEAIAAFEQALKQ---------DPDNPEAWYLLGRILYQQGRYDEALAYYERALELDPD 63 (65)
T ss_dssp HHHHHHHHCTHHHHHHHHHHHHHCC---------STTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT
T ss_pred hHHHHHHHcCCHHHHHHHHHHHHHH---------CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcC
Confidence 3567788999999999998886652 234788899999999999999999999999997 675
No 27
>PF13371 TPR_9: Tetratricopeptide repeat
Probab=94.58 E-value=0.079 Score=40.37 Aligned_cols=59 Identities=24% Similarity=0.310 Sum_probs=49.6
Q ss_pred HHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhc-cccc
Q psy9642 152 QLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIIT-TPAL 219 (437)
Q Consensus 152 ~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~-~P~~ 219 (437)
.+++..++|..|+.++++-+.. +| +....++..|.++...++|.+|.+.|+.++. .|..
T Consensus 3 ~~~~~~~~~~~A~~~~~~~l~~--------~p-~~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~~~p~~ 62 (73)
T PF13371_consen 3 QIYLQQEDYEEALEVLERALEL--------DP-DDPELWLQRARCLFQLGRYEEALEDLERALELSPDD 62 (73)
T ss_pred HHHHhCCCHHHHHHHHHHHHHh--------Cc-ccchhhHHHHHHHHHhccHHHHHHHHHHHHHHCCCc
Confidence 5678899999999999998763 22 2566677899999999999999999999998 7854
No 28
>PF13414 TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2PL2_B 3IEG_B 2FBN_A ....
Probab=94.56 E-value=0.14 Score=38.49 Aligned_cols=63 Identities=25% Similarity=0.487 Sum_probs=51.9
Q ss_pred HHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHh-hHHHHHHHHHHHhc-cc
Q psy9642 146 LHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALK-NYERALYFFEVIIT-TP 217 (437)
Q Consensus 146 ~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k-~y~~A~~~~~~ai~-~P 217 (437)
.+..+.......++|..|+...++-|-. ++. ....+|.-|.++..++ +|.+|..+|..++. .|
T Consensus 5 ~~~~~g~~~~~~~~~~~A~~~~~~ai~~--------~p~-~~~~~~~~g~~~~~~~~~~~~A~~~~~~al~l~P 69 (69)
T PF13414_consen 5 AWYNLGQIYFQQGDYEEAIEYFEKAIEL--------DPN-NAEAYYNLGLAYMKLGKDYEEAIEDFEKALKLDP 69 (69)
T ss_dssp HHHHHHHHHHHTTHHHHHHHHHHHHHHH--------STT-HHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHST
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHHc--------CCC-CHHHHHHHHHHHHHhCccHHHHHHHHHHHHHcCc
Confidence 4566778889999999999999887763 222 5668899999999998 89999999999987 44
No 29
>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A.
Probab=94.34 E-value=0.14 Score=40.41 Aligned_cols=58 Identities=21% Similarity=0.241 Sum_probs=44.8
Q ss_pred HHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHH
Q psy9642 146 LHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVI 213 (437)
Q Consensus 146 ~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~a 213 (437)
....+.+++...++|..|++++++ .... + ......|..|.++..+++|++|...|+.+
T Consensus 27 ~~~~la~~~~~~~~y~~A~~~~~~--~~~~-------~-~~~~~~~l~a~~~~~l~~y~eAi~~l~~~ 84 (84)
T PF12895_consen 27 YLYNLAQCYFQQGKYEEAIELLQK--LKLD-------P-SNPDIHYLLARCLLKLGKYEEAIKALEKA 84 (84)
T ss_dssp HHHHHHHHHHHTTHHHHHHHHHHC--HTHH-------H-CHHHHHHHHHHHHHHTT-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHH--hCCC-------C-CCHHHHHHHHHHHHHhCCHHHHHHHHhcC
Confidence 344478999999999999999988 2221 1 24566667799999999999999999864
No 30
>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=94.25 E-value=0.2 Score=44.03 Aligned_cols=89 Identities=17% Similarity=0.188 Sum_probs=66.5
Q ss_pred HHhhhCCCCcchHHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHH
Q psy9642 115 TVMDLKTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGG 194 (437)
Q Consensus 115 ~~~~~~~~~~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G 194 (437)
...+.+..-.++..|..++..- |++..-......+.++++..+.|..|+..|+. +. +....-.+....|
T Consensus 57 ~~~~~g~~~~A~~~l~~~~~~~-~d~~l~~~a~l~LA~~~~~~~~~d~Al~~L~~-~~---------~~~~~~~~~~~~G 125 (145)
T PF09976_consen 57 AAYEQGDYDEAKAALEKALANA-PDPELKPLARLRLARILLQQGQYDEALATLQQ-IP---------DEAFKALAAELLG 125 (145)
T ss_pred HHHHCCCHHHHHHHHHHHHhhC-CCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHh-cc---------CcchHHHHHHHHH
Confidence 3344555566778888877764 55555555678899999999999999999965 11 1112344677899
Q ss_pred HHHHHHhhHHHHHHHHHHHh
Q psy9642 195 MIYLALKNYERALYFFEVII 214 (437)
Q Consensus 195 ~I~~~~k~y~~A~~~~~~ai 214 (437)
.|+...++|++|...|+.++
T Consensus 126 di~~~~g~~~~A~~~y~~Al 145 (145)
T PF09976_consen 126 DIYLAQGDYDEARAAYQKAL 145 (145)
T ss_pred HHHHHCCCHHHHHHHHHHhC
Confidence 99999999999999999875
No 31
>TIGR02552 LcrH_SycD type III secretion low calcium response chaperone LcrH/SycD. ScyD/LcrH contains three central tetratricopeptide-like repeats that are predicted to fold into an all-alpha-helical array.
Probab=94.07 E-value=0.69 Score=39.33 Aligned_cols=87 Identities=15% Similarity=0.165 Sum_probs=62.2
Q ss_pred CCCcchHHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHH
Q psy9642 121 TPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLAL 200 (437)
Q Consensus 121 ~~~~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~ 200 (437)
+...++..+..++. ++|. -+..+..+..++...+++..|++++..-+.. . .+....+|+.|.++...
T Consensus 32 ~~~~A~~~~~~~~~-~~p~---~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~--------~-p~~~~~~~~la~~~~~~ 98 (135)
T TIGR02552 32 RYDEALKLFQLLAA-YDPY---NSRYWLGLAACCQMLKEYEEAIDAYALAAAL--------D-PDDPRPYFHAAECLLAL 98 (135)
T ss_pred cHHHHHHHHHHHHH-hCCC---cHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc--------C-CCChHHHHHHHHHHHHc
Confidence 33344445555443 3333 2456777888888999999999988875442 1 12456678899999999
Q ss_pred hhHHHHHHHHHHHhc-ccccc
Q psy9642 201 KNYERALYFFEVIIT-TPALA 220 (437)
Q Consensus 201 k~y~~A~~~~~~ai~-~P~~~ 220 (437)
++|.+|..+|..++. .|...
T Consensus 99 g~~~~A~~~~~~al~~~p~~~ 119 (135)
T TIGR02552 99 GEPESALKALDLAIEICGENP 119 (135)
T ss_pred CCHHHHHHHHHHHHHhccccc
Confidence 999999999999999 67653
No 32
>PF07719 TPR_2: Tetratricopeptide repeat; InterPro: IPR013105 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]. It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. This repeat includes outlying Tetratricopeptide-like repeats (TPR) that are not matched by IPR001440 from INTERPRO.; PDB: 1XNF_B 3Q15_A 4ABN_A 1OUV_A 3U4T_A 3MA5_C 2KCV_A 2KCL_A 2XEV_A 3NF1_A ....
Probab=93.89 E-value=0.1 Score=33.42 Aligned_cols=31 Identities=39% Similarity=0.762 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHHHhhHHHHHHHHHHHhc-ccc
Q psy9642 188 QYFYYGGMIYLALKNYERALYFFEVIIT-TPA 218 (437)
Q Consensus 188 ~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~-~P~ 218 (437)
+++|+-|.++..+++|.+|.++|+.++. .|.
T Consensus 2 ~~~~~lg~~~~~~~~~~~A~~~~~~al~l~p~ 33 (34)
T PF07719_consen 2 EAWYYLGQAYYQLGNYEEAIEYFEKALELDPN 33 (34)
T ss_dssp HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHHHHCcC
Confidence 5789999999999999999999999998 664
No 33
>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF. Members of this protein family are the product of one of seven genes regularly clustered in operons to encode the proteins of the tol-pal system, which is critical for maintaining the integrity of the bacterial outer membrane. The gene for this periplasmic protein has been designated orf2 and ybgF. All members of the seed alignment were from unique tol-pal gene regions from completed bacterial genomes. The architecture of this protein is a signal sequence, a low-complexity region usually rich in Asn and Gln, a well-conserved region with tandem repeats that resemble the tetratricopeptide (TPR) repeat, involved in protein-protein interaction.
Probab=93.43 E-value=1.1 Score=36.71 Aligned_cols=94 Identities=15% Similarity=0.085 Sum_probs=67.7
Q ss_pred hCCCCcchHHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHH
Q psy9642 119 LKTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYL 198 (437)
Q Consensus 119 ~~~~~~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~ 198 (437)
.++.-.++..+..++... |........+..+.++....++|..|+..+..-+.... +........+..|.++.
T Consensus 15 ~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p------~~~~~~~~~~~~~~~~~ 87 (119)
T TIGR02795 15 AGDYADAIQAFQAFLKKY-PKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYP------KSPKAPDALLKLGMSLQ 87 (119)
T ss_pred cCCHHHHHHHHHHHHHHC-CCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCC------CCCcccHHHHHHHHHHH
Confidence 444555677777777654 43323344677789999999999999998887664311 11123455788899999
Q ss_pred HHhhHHHHHHHHHHHhc-cccc
Q psy9642 199 ALKNYERALYFFEVIIT-TPAL 219 (437)
Q Consensus 199 ~~k~y~~A~~~~~~ai~-~P~~ 219 (437)
..+++.+|..+|..++. .|..
T Consensus 88 ~~~~~~~A~~~~~~~~~~~p~~ 109 (119)
T TIGR02795 88 ELGDKEKAKATLQQVIKRYPGS 109 (119)
T ss_pred HhCChHHHHHHHHHHHHHCcCC
Confidence 99999999999999998 6653
No 34
>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H ....
Probab=93.13 E-value=0.4 Score=36.99 Aligned_cols=68 Identities=16% Similarity=0.242 Sum_probs=53.5
Q ss_pred HHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhc
Q psy9642 146 LHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIIT 215 (437)
Q Consensus 146 ~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~ 215 (437)
....+..+....++|..|++...+-+.- ....+ -+..+.+.-++--|.++...++|++|..+|+.|++
T Consensus 7 ~~~~la~~~~~~~~~~~A~~~~~~al~~-~~~~~-~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al~ 74 (78)
T PF13424_consen 7 AYNNLARVYRELGRYDEALDYYEKALDI-EEQLG-DDHPDTANTLNNLGECYYRLGDYEEALEYYQKALD 74 (78)
T ss_dssp HHHHHHHHHHHTT-HHHHHHHHHHHHHH-HHHTT-THHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHHH-HHHHC-CCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence 4567778889999999999999886654 22111 13445788899999999999999999999999986
No 35
>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]. It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs packing in a parallel fashion, resulting in a spiral of repeating anti-parallel alpha-helices []. The two helices are denoted helix A and helix B. The packing angle between helix A and helix B is ~24 degrees; within a single TPR and generates a right-handed superhelical shape. Helix A interacts with helix B and with helix A' of the next TPR. Two protein surfaces are generated: the inner concave surface is contributed to mainly by residue on helices A, and the other surface presents residues from both helices A and B. ; GO: 0005515 protein binding; PDB: 3SF4_C 2LNI_A 1ELW_A 2C0M_A 1FCH_B 3R9A_B 2J9Q_A 2C0L_A 1KT1_A 3FWV_A ....
Probab=92.76 E-value=0.21 Score=32.22 Aligned_cols=31 Identities=29% Similarity=0.640 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHHHhhHHHHHHHHHHHhc-ccc
Q psy9642 188 QYFYYGGMIYLALKNYERALYFFEVIIT-TPA 218 (437)
Q Consensus 188 ~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~-~P~ 218 (437)
+-+|..|.++..+++|.+|..+|+.|+. .|.
T Consensus 2 ~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~ 33 (34)
T PF00515_consen 2 EAYYNLGNAYFQLGDYEEALEYYQRALELDPD 33 (34)
T ss_dssp HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT
T ss_pred HHHHHHHHHHHHhCCchHHHHHHHHHHHHCcC
Confidence 4578899999999999999999999998 563
No 36
>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=92.72 E-value=0.1 Score=43.36 Aligned_cols=37 Identities=14% Similarity=0.300 Sum_probs=34.0
Q ss_pred cccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEec
Q psy9642 321 TLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINK 358 (437)
Q Consensus 321 ~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~ 358 (437)
=+++.+|+++++++ .++++..|..|+.+|.|+.+||.
T Consensus 65 Gv~v~~I~~~l~~~-~~~v~~al~~L~~eG~IYsTiDd 101 (102)
T PF08784_consen 65 GVHVDEIAQQLGMS-ENEVRKALDFLSNEGHIYSTIDD 101 (102)
T ss_dssp TEEHHHHHHHSTS--HHHHHHHHHHHHHTTSEEESSST
T ss_pred cccHHHHHHHhCcC-HHHHHHHHHHHHhCCeEecccCC
Confidence 49999999999997 89999999999999999999984
No 37
>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=92.44 E-value=0.37 Score=37.09 Aligned_cols=48 Identities=19% Similarity=0.225 Sum_probs=37.8
Q ss_pred HHHHHHHhhccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecC
Q psy9642 311 NIKRLTKTFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKK 359 (437)
Q Consensus 311 ~I~~l~k~Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~ 359 (437)
.|+.+-+---++|+++||..++++ ++.+|.+|..||..|.|...-...
T Consensus 4 ~i~~~l~~~~~~S~~eLa~~~~~s-~~~ve~mL~~l~~kG~I~~~~~~~ 51 (69)
T PF09012_consen 4 EIRDYLRERGRVSLAELAREFGIS-PEAVEAMLEQLIRKGYIRKVDMSS 51 (69)
T ss_dssp HHHHHHHHS-SEEHHHHHHHTT---HHHHHHHHHHHHCCTSCEEEEEE-
T ss_pred HHHHHHHHcCCcCHHHHHHHHCcC-HHHHHHHHHHHHHCCcEEEecCCC
Confidence 355666667889999999999998 899999999999999998666543
No 38
>cd00189 TPR Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and C
Probab=92.05 E-value=1.6 Score=32.50 Aligned_cols=83 Identities=17% Similarity=0.241 Sum_probs=57.1
Q ss_pred CCCCcchHHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHH
Q psy9642 120 KTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLA 199 (437)
Q Consensus 120 ~~~~~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~ 199 (437)
+....++..+..++... |... ..+..+..++...+++..|...+..-+.. . +. .-..++..|.++..
T Consensus 14 ~~~~~A~~~~~~~~~~~-~~~~---~~~~~~~~~~~~~~~~~~a~~~~~~~~~~-~-------~~-~~~~~~~~~~~~~~ 80 (100)
T cd00189 14 GDYDEALEYYEKALELD-PDNA---DAYYNLAAAYYKLGKYEEALEDYEKALEL-D-------PD-NAKAYYNLGLAYYK 80 (100)
T ss_pred hcHHHHHHHHHHHHhcC-CccH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhC-C-------Cc-chhHHHHHHHHHHH
Confidence 44445566666665443 3222 45777788888889999998887765442 1 11 11566788889999
Q ss_pred HhhHHHHHHHHHHHhc
Q psy9642 200 LKNYERALYFFEVIIT 215 (437)
Q Consensus 200 ~k~y~~A~~~~~~ai~ 215 (437)
.++|.+|..+|..++.
T Consensus 81 ~~~~~~a~~~~~~~~~ 96 (100)
T cd00189 81 LGKYEEALEAYEKALE 96 (100)
T ss_pred HHhHHHHHHHHHHHHc
Confidence 9999999999999887
No 39
>PF09295 ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); InterPro: IPR015374 ChAPs (Chs5p-Arf1p-binding proteins) are required for the export of specialised cargo from the Golgi. They physically interact with Chs3, Chs5 and the small GTPase Arf1, and they also form interactions with each other [].
Probab=91.76 E-value=1.1 Score=46.59 Aligned_cols=82 Identities=20% Similarity=0.295 Sum_probs=64.0
Q ss_pred hhCCCCcchHHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHH
Q psy9642 118 DLKTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIY 197 (437)
Q Consensus 118 ~~~~~~~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~ 197 (437)
..+....+|..+..++... |.. ..+-..+++.++..++|+.|+++..+-+.- .|. ..+..|+-+.+|
T Consensus 212 ~~~~E~~AI~ll~~aL~~~-p~d---~~LL~~Qa~fLl~k~~~~lAL~iAk~av~l--------sP~-~f~~W~~La~~Y 278 (395)
T PF09295_consen 212 LMNEEVEAIRLLNEALKEN-PQD---SELLNLQAEFLLSKKKYELALEIAKKAVEL--------SPS-EFETWYQLAECY 278 (395)
T ss_pred hcCcHHHHHHHHHHHHHhC-CCC---HHHHHHHHHHHHhcCCHHHHHHHHHHHHHh--------Cch-hHHHHHHHHHHH
Confidence 3566788999999998654 333 445568899999999999999998887652 333 566667899999
Q ss_pred HHHhhHHHHHHHHHH
Q psy9642 198 LALKNYERALYFFEV 212 (437)
Q Consensus 198 ~~~k~y~~A~~~~~~ 212 (437)
+..++|++|.-.+..
T Consensus 279 i~~~d~e~ALlaLNs 293 (395)
T PF09295_consen 279 IQLGDFENALLALNS 293 (395)
T ss_pred HhcCCHHHHHHHHhc
Confidence 999999999976653
No 40
>PRK15359 type III secretion system chaperone protein SscB; Provisional
Probab=91.73 E-value=1.8 Score=38.11 Aligned_cols=89 Identities=15% Similarity=0.102 Sum_probs=68.5
Q ss_pred hhCCCCcchHHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHH
Q psy9642 118 DLKTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIY 197 (437)
Q Consensus 118 ~~~~~~~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~ 197 (437)
..+..-.++..++.++ +++|.. ...|..+..+|...++|..|+....+-+.- ++ +....+|..|.++
T Consensus 36 ~~g~~~~A~~~~~~al-~~~P~~---~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l--------~p-~~~~a~~~lg~~l 102 (144)
T PRK15359 36 QEGDYSRAVIDFSWLV-MAQPWS---WRAHIALAGTWMMLKEYTTAINFYGHALML--------DA-SHPEPVYQTGVCL 102 (144)
T ss_pred HcCCHHHHHHHHHHHH-HcCCCc---HHHHHHHHHHHHHHhhHHHHHHHHHHHHhc--------CC-CCcHHHHHHHHHH
Confidence 3444455666777664 445543 347788899999999999999988887652 22 3567788999999
Q ss_pred HHHhhHHHHHHHHHHHhc-cccc
Q psy9642 198 LALKNYERALYFFEVIIT-TPAL 219 (437)
Q Consensus 198 ~~~k~y~~A~~~~~~ai~-~P~~ 219 (437)
..++++.+|..+|..++. .|..
T Consensus 103 ~~~g~~~eAi~~~~~Al~~~p~~ 125 (144)
T PRK15359 103 KMMGEPGLAREAFQTAIKMSYAD 125 (144)
T ss_pred HHcCCHHHHHHHHHHHHHhCCCC
Confidence 999999999999999999 7765
No 41
>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional
Probab=91.21 E-value=1.7 Score=44.38 Aligned_cols=89 Identities=19% Similarity=0.194 Sum_probs=68.5
Q ss_pred hCCCCcchHHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHH
Q psy9642 119 LKTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYL 198 (437)
Q Consensus 119 ~~~~~~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~ 198 (437)
.+....++..+..|+.. +|.. ...+..+..+++..+.|..|+..+++-+.- .+ +....+|..|.++.
T Consensus 15 ~~~~~~Ai~~~~~Al~~-~P~~---~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l--------~P-~~~~a~~~lg~~~~ 81 (356)
T PLN03088 15 DDDFALAVDLYTQAIDL-DPNN---AELYADRAQANIKLGNFTEAVADANKAIEL--------DP-SLAKAYLRKGTACM 81 (356)
T ss_pred cCCHHHHHHHHHHHHHh-CCCC---HHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--------Cc-CCHHHHHHHHHHHH
Confidence 34455677788887654 5543 346788889999999999999998887652 22 24556778899999
Q ss_pred HHhhHHHHHHHHHHHhc-ccccc
Q psy9642 199 ALKNYERALYFFEVIIT-TPALA 220 (437)
Q Consensus 199 ~~k~y~~A~~~~~~ai~-~P~~~ 220 (437)
.+++|.+|..+|+.++. .|...
T Consensus 82 ~lg~~~eA~~~~~~al~l~P~~~ 104 (356)
T PLN03088 82 KLEEYQTAKAALEKGASLAPGDS 104 (356)
T ss_pred HhCCHHHHHHHHHHHHHhCCCCH
Confidence 99999999999999999 77764
No 42
>PRK12370 invasion protein regulator; Provisional
Probab=90.91 E-value=5.2 Score=43.32 Aligned_cols=84 Identities=11% Similarity=0.059 Sum_probs=63.1
Q ss_pred CcchHHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhh
Q psy9642 123 QRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKN 202 (437)
Q Consensus 123 ~~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~ 202 (437)
..++..++.|+ .++|.. ...|..+..++...+++..|+..+++-+.- ++. ....+|+.|.++...++
T Consensus 321 ~~A~~~~~~Al-~ldP~~---~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l--------~P~-~~~a~~~lg~~l~~~G~ 387 (553)
T PRK12370 321 IKAKEHAIKAT-ELDHNN---PQALGLLGLINTIHSEYIVGSLLFKQANLL--------SPI-SADIKYYYGWNLFMAGQ 387 (553)
T ss_pred HHHHHHHHHHH-hcCCCC---HHHHHHHHHHHHHccCHHHHHHHHHHHHHh--------CCC-CHHHHHHHHHHHHHCCC
Confidence 34566666664 446653 346778888889999999999999887652 222 33456778999999999
Q ss_pred HHHHHHHHHHHhc-cccc
Q psy9642 203 YERALYFFEVIIT-TPAL 219 (437)
Q Consensus 203 y~~A~~~~~~ai~-~P~~ 219 (437)
|++|..+|+.++. .|..
T Consensus 388 ~~eAi~~~~~Al~l~P~~ 405 (553)
T PRK12370 388 LEEALQTINECLKLDPTR 405 (553)
T ss_pred HHHHHHHHHHHHhcCCCC
Confidence 9999999999999 7764
No 43
>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A.
Probab=90.78 E-value=0.42 Score=30.17 Aligned_cols=29 Identities=28% Similarity=0.590 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHhhHHHHHHHHHHHhc-ccc
Q psy9642 190 FYYGGMIYLALKNYERALYFFEVIIT-TPA 218 (437)
Q Consensus 190 ~Yy~G~I~~~~k~y~~A~~~~~~ai~-~P~ 218 (437)
.|..|+++...++|.+|...|+.++. .|.
T Consensus 3 ~~~~a~~~~~~g~~~~A~~~~~~~~~~~P~ 32 (33)
T PF13174_consen 3 LYRLARCYYKLGDYDEAIEYFQRLIKRYPD 32 (33)
T ss_dssp HHHHHHHHHHHCHHHHHHHHHHHHHHHSTT
T ss_pred HHHHHHHHHHccCHHHHHHHHHHHHHHCcC
Confidence 47889999999999999999999998 775
No 44
>PF13181 TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_C 2KCV_A 2KCL_A 3FP3_A 3LCA_A 3FP4_A 3FP2_A 1W3B_B 1ELW_A ....
Probab=90.19 E-value=0.43 Score=30.58 Aligned_cols=30 Identities=40% Similarity=0.724 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHHHhhHHHHHHHHHHHhc-cc
Q psy9642 188 QYFYYGGMIYLALKNYERALYFFEVIIT-TP 217 (437)
Q Consensus 188 ~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~-~P 217 (437)
+.+|.-|.++..+++|++|.++|+.++. .|
T Consensus 2 ~~~~~lg~~y~~~~~~~~A~~~~~~a~~~~~ 32 (34)
T PF13181_consen 2 EAYYNLGKIYEQLGDYEEALEYFEKALELNP 32 (34)
T ss_dssp HHHHHHHHHHHHTTSHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHHhhCC
Confidence 5678899999999999999999999997 44
No 45
>PRK10803 tol-pal system protein YbgF; Provisional
Probab=87.60 E-value=3.8 Score=40.16 Aligned_cols=92 Identities=14% Similarity=0.112 Sum_probs=64.4
Q ss_pred CCcchHHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHh
Q psy9642 122 PQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALK 201 (437)
Q Consensus 122 ~~~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k 201 (437)
.-.++..+...+.++ |.+...-..|-.+.++.+..++|..|+....+-+...... ...-.-.|.-|.++...+
T Consensus 159 y~~Ai~af~~fl~~y-P~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~s------~~~~dAl~klg~~~~~~g 231 (263)
T PRK10803 159 QDDAIVAFQNFVKKY-PDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKNYPKS------PKAADAMFKVGVIMQDKG 231 (263)
T ss_pred HHHHHHHHHHHHHHC-cCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCC------cchhHHHHHHHHHHHHcC
Confidence 345666677777666 4444444567788888899999999988877766543221 123344556788888889
Q ss_pred hHHHHHHHHHHHhc-ccccc
Q psy9642 202 NYERALYFFEVIIT-TPALA 220 (437)
Q Consensus 202 ~y~~A~~~~~~ai~-~P~~~ 220 (437)
++.+|...|+.++. .|...
T Consensus 232 ~~~~A~~~~~~vi~~yP~s~ 251 (263)
T PRK10803 232 DTAKAKAVYQQVIKKYPGTD 251 (263)
T ss_pred CHHHHHHHHHHHHHHCcCCH
Confidence 99999999999987 77653
No 46
>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=87.20 E-value=2.4 Score=29.74 Aligned_cols=43 Identities=12% Similarity=0.190 Sum_probs=32.4
Q ss_pred HHHHHHHHhhccccHHHHHHHhCCCChHHHHHHHHHhHHcCceE
Q psy9642 310 NNIKRLTKTFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIY 353 (437)
Q Consensus 310 ~~I~~l~k~Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~ 353 (437)
+.|...-.-=..++..+||+.+|++ ...+-.++.+|+++|.|.
T Consensus 6 ~~Il~~l~~~~~~t~~ela~~~~is-~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 6 RKILNYLRENPRITQKELAEKLGIS-RSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHCTTS-HHHHHHHHTS--HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHcCCCCHHHHHHHhCCC-HHHHHHHHHHHHHCcCcC
Confidence 3333333335679999999999998 789999999999999874
No 47
>PLN03218 maturation of RBCL 1; Provisional
Probab=86.92 E-value=20 Score=42.13 Aligned_cols=17 Identities=0% Similarity=-0.232 Sum_probs=12.6
Q ss_pred ChHHHHHHHHHhHHcCc
Q psy9642 335 TPVQAEIYILKMISQNE 351 (437)
Q Consensus 335 ~~~eaE~~l~~mI~~G~ 351 (437)
..++++.+...|+..|.
T Consensus 769 ~le~A~~l~~~M~k~Gi 785 (1060)
T PLN03218 769 DADVGLDLLSQAKEDGI 785 (1060)
T ss_pred CHHHHHHHHHHHHHcCC
Confidence 45778888888887763
No 48
>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW. Members of this family are designated PilF in ref (PubMed:8973346) and PilW in ref (PubMed:15612916). This outer membrane protein is required both for pilus stability and for pilus function such as adherence to human cells. Members of this family contain copies of the TPR (tetratricopeptide repeat) domain.
Probab=86.61 E-value=23 Score=31.65 Aligned_cols=87 Identities=15% Similarity=0.095 Sum_probs=60.8
Q ss_pred hCCCCcchHHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHH
Q psy9642 119 LKTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYL 198 (437)
Q Consensus 119 ~~~~~~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~ 198 (437)
.+....++..+..++.. +|.. ...+..+..++...+++..|+..+.+-+.. . +. ....++..|.++.
T Consensus 44 ~~~~~~A~~~~~~~l~~-~p~~---~~~~~~la~~~~~~~~~~~A~~~~~~al~~-~-------~~-~~~~~~~~~~~~~ 110 (234)
T TIGR02521 44 QGDLEVAKENLDKALEH-DPDD---YLAYLALALYYQQLGELEKAEDSFRRALTL-N-------PN-NGDVLNNYGTFLC 110 (234)
T ss_pred CCCHHHHHHHHHHHHHh-Cccc---HHHHHHHHHHHHHcCCHHHHHHHHHHHHhh-C-------CC-CHHHHHHHHHHHH
Confidence 34444556666666543 3322 246777888999999999998888776542 1 11 2245566788999
Q ss_pred HHhhHHHHHHHHHHHhcccc
Q psy9642 199 ALKNYERALYFFEVIITTPA 218 (437)
Q Consensus 199 ~~k~y~~A~~~~~~ai~~P~ 218 (437)
..++|.+|..+|..++..|.
T Consensus 111 ~~g~~~~A~~~~~~~~~~~~ 130 (234)
T TIGR02521 111 QQGKYEQAMQQFEQAIEDPL 130 (234)
T ss_pred HcccHHHHHHHHHHHHhccc
Confidence 99999999999999998653
No 49
>PRK15359 type III secretion system chaperone protein SscB; Provisional
Probab=85.58 E-value=3.8 Score=35.95 Aligned_cols=64 Identities=9% Similarity=0.074 Sum_probs=51.8
Q ss_pred HHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhc-cccc
Q psy9642 147 HSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIIT-TPAL 219 (437)
Q Consensus 147 h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~-~P~~ 219 (437)
+..........+.|..|+....+-+.. ++ ....+++.-|.++...++|.+|..+|..++. .|..
T Consensus 27 ~~~~g~~~~~~g~~~~A~~~~~~al~~--------~P-~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~p~~ 91 (144)
T PRK15359 27 VYASGYASWQEGDYSRAVIDFSWLVMA--------QP-WSWRAHIALAGTWMMLKEYTTAINFYGHALMLDASH 91 (144)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHc--------CC-CcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCC
Confidence 345677888999999998888776542 22 2667888999999999999999999999998 6754
No 50
>PF12569 NARP1: NMDA receptor-regulated protein 1 ; InterPro: IPR021183 This group represents N-terminal acetyltransferase A (NatA) auxiliary subunit and represents a non-catalytic component of the NatA N-terminal acetyltransferase, which catalyzes acetylation of proteins beginning with Met-Ser, Met-Gly and Met-Ala. N-terminal acetylation plays a role in normal eukaryotic translation and processing, protect against proteolytic degradation and protein turnover. NAT1 anchors ARD1 and NAT5 to the ribosome and may present the N- terminal of nascent polypeptides for acetylation [], [].
Probab=85.56 E-value=14 Score=39.86 Aligned_cols=62 Identities=15% Similarity=0.121 Sum_probs=53.6
Q ss_pred HHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhcc
Q psy9642 146 LHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIITT 216 (437)
Q Consensus 146 ~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~~ 216 (437)
++-.+.+..-..|+|..|+.++++-|.. +| ....+|+..|.|+-..|++.+|.++++.|-..
T Consensus 196 ~~~~lAqhyd~~g~~~~Al~~Id~aI~h--------tP-t~~ely~~KarilKh~G~~~~Aa~~~~~Ar~L 257 (517)
T PF12569_consen 196 TLYFLAQHYDYLGDYEKALEYIDKAIEH--------TP-TLVELYMTKARILKHAGDLKEAAEAMDEAREL 257 (517)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHHhc--------CC-CcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhC
Confidence 4566678888999999999999999874 22 26889999999999999999999999999874
No 51
>PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional
Probab=85.49 E-value=7.3 Score=36.26 Aligned_cols=108 Identities=12% Similarity=0.183 Sum_probs=70.6
Q ss_pred HHHHHHHHHHHHHhhhCCCCcchHHHHHHHHHhCCCCcchhhHHHHHHHH-HHHhCC--chHHHhhhhHhhhhhhcCCCC
Q psy9642 104 LYAELSHQYTKTVMDLKTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQL-CLLAQN--FKPALEFLDVDITTIANEGPQ 180 (437)
Q Consensus 104 ~~~~l~~~~~~~~~~~~~~~~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l-~L~~~~--y~~Al~il~~~I~~~~~~~~~ 180 (437)
.|..|+..+ ...+..-.++..+..|+. ++|+.. .++..+... +...+. +..|..++++-+..
T Consensus 75 ~w~~Lg~~~----~~~g~~~~A~~a~~~Al~-l~P~~~---~~~~~lA~aL~~~~g~~~~~~A~~~l~~al~~------- 139 (198)
T PRK10370 75 QWALLGEYY----LWRNDYDNALLAYRQALQ-LRGENA---ELYAALATVLYYQAGQHMTPQTREMIDKALAL------- 139 (198)
T ss_pred HHHHHHHHH----HHCCCHHHHHHHHHHHHH-hCCCCH---HHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHh-------
Confidence 455544433 335555667778877654 445432 245565653 466666 58898888887653
Q ss_pred CChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhc-ccccccCHHHHHH
Q psy9642 181 FDTKYFLQYFYYGGMIYLALKNYERALYFFEVIIT-TPALAVSHIMLEG 228 (437)
Q Consensus 181 ~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~-~P~~~~s~i~vea 228 (437)
++. ....++..|+++...++|++|..+|+.++. .|.......++++
T Consensus 140 -dP~-~~~al~~LA~~~~~~g~~~~Ai~~~~~aL~l~~~~~~r~~~i~~ 186 (198)
T PRK10370 140 -DAN-EVTALMLLASDAFMQADYAQAIELWQKVLDLNSPRVNRTQLVES 186 (198)
T ss_pred -CCC-ChhHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCccHHHHHHH
Confidence 222 556778999999999999999999999998 5554323344444
No 52
>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO. Members of this protein family include YfiO, a near-essential protein of the outer membrane, part of a complex involved in protein insertion into the bacterial outer membrane. Many proteins in this family are annotated as ComL, based on the involvement of this protein in natural transformation with exogenous DNA in Neisseria gonorrhoeae. This protein family shows sequence similarity to, but is distinct from, the tol-pal system protein YbgF (TIGR02795).
Probab=85.40 E-value=11 Score=35.16 Aligned_cols=93 Identities=14% Similarity=0.089 Sum_probs=63.7
Q ss_pred CCCCcchHHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHH
Q psy9642 120 KTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLA 199 (437)
Q Consensus 120 ~~~~~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~ 199 (437)
++.-.++..+..++.. .|.+......+..+..+....++|..|+..+++-+..... . ...-...|..|+++..
T Consensus 47 ~~~~~A~~~~~~~~~~-~p~~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~~p~-~-----~~~~~a~~~~g~~~~~ 119 (235)
T TIGR03302 47 GDYTEAIKYFEALESR-YPFSPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRLHPN-H-----PDADYAYYLRGLSNYN 119 (235)
T ss_pred CCHHHHHHHHHHHHHh-CCCchhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcC-C-----CchHHHHHHHHHHHHH
Confidence 3344455566665444 3443333446777888999999999999999887653221 1 1122346788888887
Q ss_pred H--------hhHHHHHHHHHHHhc-cccc
Q psy9642 200 L--------KNYERALYFFEVIIT-TPAL 219 (437)
Q Consensus 200 ~--------k~y~~A~~~~~~ai~-~P~~ 219 (437)
. +++.+|.+.|..++. .|..
T Consensus 120 ~~~~~~~~~~~~~~A~~~~~~~~~~~p~~ 148 (235)
T TIGR03302 120 QIDRVDRDQTAAREAFEAFQELIRRYPNS 148 (235)
T ss_pred hcccccCCHHHHHHHHHHHHHHHHHCCCC
Confidence 6 899999999999998 7775
No 53
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=85.17 E-value=7.8 Score=36.77 Aligned_cols=87 Identities=18% Similarity=0.157 Sum_probs=56.6
Q ss_pred cchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhh----cCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhcc
Q psy9642 141 SQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIA----NEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIITT 216 (437)
Q Consensus 141 ~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~----~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~~ 216 (437)
+....+.+.+..++=..++-.....++.+-...+. .+..+....+.....|+.|-+....+++++|.++|..++..
T Consensus 115 s~~A~l~LrlAWlyR~~~~~~~E~~fl~~Al~~y~~a~~~e~~~~~~~~~~~l~YLigeL~rrlg~~~eA~~~fs~vi~~ 194 (214)
T PF09986_consen 115 SKKAGLCLRLAWLYRDLGDEENEKRFLRKALEFYEEAYENEDFPIEGMDEATLLYLIGELNRRLGNYDEAKRWFSRVIGS 194 (214)
T ss_pred HHHHHHHHHHHHHhhccCCHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC
Confidence 34444555555666666664444444444333331 12223345567888999999999999999999999999999
Q ss_pred cccccCHHHHH
Q psy9642 217 PALAVSHIMLE 227 (437)
Q Consensus 217 P~~~~s~i~ve 227 (437)
|.....+.+++
T Consensus 195 ~~~s~~~~l~~ 205 (214)
T PF09986_consen 195 KKASKEPKLKD 205 (214)
T ss_pred CCCCCcHHHHH
Confidence 98754334443
No 54
>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A ....
Probab=84.87 E-value=1.4 Score=32.72 Aligned_cols=56 Identities=18% Similarity=0.245 Sum_probs=44.0
Q ss_pred HHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhc-cccc
Q psy9642 155 LLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIIT-TPAL 219 (437)
Q Consensus 155 L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~-~P~~ 219 (437)
+..++|..|+.++.+-+.. ..+.....+.-|.+++..++|++|...|..+.. .|..
T Consensus 2 l~~~~~~~A~~~~~~~l~~---------~p~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~ 58 (68)
T PF14559_consen 2 LKQGDYDEAIELLEKALQR---------NPDNPEARLLLAQCYLKQGQYDEAEELLERLLKQDPDN 58 (68)
T ss_dssp HHTTHHHHHHHHHHHHHHH---------TTTSHHHHHHHHHHHHHTT-HHHHHHHHHCCHGGGTTH
T ss_pred hhccCHHHHHHHHHHHHHH---------CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCH
Confidence 5678899999998887653 122556667889999999999999999999998 6763
No 55
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=84.33 E-value=40 Score=33.88 Aligned_cols=88 Identities=17% Similarity=0.039 Sum_probs=48.8
Q ss_pred hCCCCcchHHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHH
Q psy9642 119 LKTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYL 198 (437)
Q Consensus 119 ~~~~~~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~ 198 (437)
.++...++..+..++..-+..+......+..+..++...+++..|+.++++-+.. ++. ....+..-+.++.
T Consensus 82 ~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~La~~~~~~g~~~~A~~~~~~~l~~--------~~~-~~~~~~~la~~~~ 152 (389)
T PRK11788 82 RGEVDRAIRIHQNLLSRPDLTREQRLLALQELGQDYLKAGLLDRAEELFLQLVDE--------GDF-AEGALQQLLEIYQ 152 (389)
T ss_pred cCcHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHcC--------Ccc-hHHHHHHHHHHHH
Confidence 3444455555555543211111112235566677777788888887776664321 111 1222334556677
Q ss_pred HHhhHHHHHHHHHHHhc
Q psy9642 199 ALKNYERALYFFEVIIT 215 (437)
Q Consensus 199 ~~k~y~~A~~~~~~ai~ 215 (437)
..++|.+|.+.|..++.
T Consensus 153 ~~g~~~~A~~~~~~~~~ 169 (389)
T PRK11788 153 QEKDWQKAIDVAERLEK 169 (389)
T ss_pred HhchHHHHHHHHHHHHH
Confidence 77888888888887776
No 56
>KOG4414|consensus
Probab=83.96 E-value=2.9 Score=37.15 Aligned_cols=44 Identities=16% Similarity=0.113 Sum_probs=37.6
Q ss_pred HHHHHHHHHHHHHHHHHHHhhccccHHHHHHHhCCCChHHHHHHH
Q psy9642 299 LTKQIVASLYKNNIKRLTKTFLTLSLADVASRVQLGTPVQAEIYI 343 (437)
Q Consensus 299 Lv~~l~~~v~r~~I~~l~k~Ys~IsL~dIa~~l~L~~~~eaE~~l 343 (437)
.+.-++....|+...-+.+.|++|...|+|..+||+ ++++-..|
T Consensus 110 imaAf~D~~~kR~FaLl~qAYssI~~~D~A~FlGl~-~ddAtk~i 153 (197)
T KOG4414|consen 110 IMAAFRDATRKRAFALLLQAYSSIIADDFAAFLGLP-EDDATKGI 153 (197)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC-HHHHHHHH
Confidence 566678888999999999999999999999999998 56665544
No 57
>smart00028 TPR Tetratricopeptide repeats. Repeats present in 4 or more copies in proteins. Contain a minimum of 34 amino acids each and self-associate via a "knobs and holes" mechanism.
Probab=83.52 E-value=2.8 Score=24.59 Aligned_cols=27 Identities=33% Similarity=0.624 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHHhhHHHHHHHHHHHhc
Q psy9642 189 YFYYGGMIYLALKNYERALYFFEVIIT 215 (437)
Q Consensus 189 Y~Yy~G~I~~~~k~y~~A~~~~~~ai~ 215 (437)
.++..|.++...++|++|..+|..++.
T Consensus 3 ~~~~~a~~~~~~~~~~~a~~~~~~~~~ 29 (34)
T smart00028 3 ALYNLGNAYLKLGDYDEALEYYEKALE 29 (34)
T ss_pred HHHHHHHHHHHHhhHHHHHHHHHHHHc
Confidence 457789999999999999999999987
No 58
>TIGR02552 LcrH_SycD type III secretion low calcium response chaperone LcrH/SycD. ScyD/LcrH contains three central tetratricopeptide-like repeats that are predicted to fold into an all-alpha-helical array.
Probab=83.41 E-value=6.6 Score=33.16 Aligned_cols=66 Identities=17% Similarity=0.180 Sum_probs=51.9
Q ss_pred hHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhc-cccc
Q psy9642 145 SLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIIT-TPAL 219 (437)
Q Consensus 145 ~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~-~P~~ 219 (437)
.....+...++..+++..|+..+.+-+.. . + +....++..|.++...++|.+|..+|..++. .|..
T Consensus 18 ~~~~~~a~~~~~~~~~~~A~~~~~~~~~~-~-------p-~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~p~~ 84 (135)
T TIGR02552 18 EQIYALAYNLYQQGRYDEALKLFQLLAAY-D-------P-YNSRYWLGLAACCQMLKEYEEAIDAYALAAALDPDD 84 (135)
T ss_pred HHHHHHHHHHHHcccHHHHHHHHHHHHHh-C-------C-CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCC
Confidence 45677888999999999999888775442 1 1 2456667889999999999999999999988 5543
No 59
>PF14853 Fis1_TPR_C: Fis1 C-terminal tetratricopeptide repeat; PDB: 1IYG_A 1PC2_A 1NZN_A 3UUX_C 1Y8M_A 2PQR_A 2PQN_A 3O48_A.
Probab=82.98 E-value=3.7 Score=30.06 Aligned_cols=32 Identities=22% Similarity=0.445 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHHHhhHHHHHHHHHHHhc-cccc
Q psy9642 188 QYFYYGGMIYLALKNYERALYFFEVIIT-TPAL 219 (437)
Q Consensus 188 ~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~-~P~~ 219 (437)
.|.||.+.-++.+++|.+|.++.+.++. -|.+
T Consensus 2 d~lY~lAig~ykl~~Y~~A~~~~~~lL~~eP~N 34 (53)
T PF14853_consen 2 DCLYYLAIGHYKLGEYEKARRYCDALLEIEPDN 34 (53)
T ss_dssp HHHHHHHHHHHHTT-HHHHHHHHHHHHHHTTS-
T ss_pred hhHHHHHHHHHHhhhHHHHHHHHHHHHhhCCCc
Confidence 4789999999999999999999999999 6875
No 60
>PLN03218 maturation of RBCL 1; Provisional
Probab=82.34 E-value=24 Score=41.43 Aligned_cols=17 Identities=12% Similarity=-0.132 Sum_probs=12.3
Q ss_pred ChHHHHHHHHHhHHcCc
Q psy9642 335 TPVQAEIYILKMISQNE 351 (437)
Q Consensus 335 ~~~eaE~~l~~mI~~G~ 351 (437)
..++|..++.+|...|.
T Consensus 734 ~~eeAlelf~eM~~~Gi 750 (1060)
T PLN03218 734 QLPKALEVLSEMKRLGL 750 (1060)
T ss_pred CHHHHHHHHHHHHHcCC
Confidence 45778888888877663
No 61
>cd00189 TPR Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and C
Probab=82.24 E-value=7.5 Score=28.62 Aligned_cols=63 Identities=22% Similarity=0.333 Sum_probs=46.9
Q ss_pred HHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhc-cccc
Q psy9642 148 SDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIIT-TPAL 219 (437)
Q Consensus 148 ~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~-~P~~ 219 (437)
..+.......+.+..|++.+..-+.. . +. ....++..|.++...++|.+|..+|..++. .|..
T Consensus 4 ~~~a~~~~~~~~~~~A~~~~~~~~~~-~-------~~-~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~ 67 (100)
T cd00189 4 LNLGNLYYKLGDYDEALEYYEKALEL-D-------PD-NADAYYNLAAAYYKLGKYEEALEDYEKALELDPDN 67 (100)
T ss_pred HHHHHHHHHHhcHHHHHHHHHHHHhc-C-------Cc-cHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcc
Confidence 34556677788999998887765432 1 11 125678899999999999999999999998 5543
No 62
>PF10602 RPN7: 26S proteasome subunit RPN7; InterPro: IPR019585 This entry represents the regulatory subunit RPN7 (known as the non-ATPase regulatory subunit 6 in higher eukaryotes) of the 26S proteasome. This entry also matches the evolutionarily related subunit 1 of the COP9 signalosome complex (CSN) from Arabidopsis []. The 26S proteasome plays a major role in ATP-dependent degradation of ubiquitinated proteins. Substrate specificity is conferred by the regulatory particle (RP), which can dissociate into stable lid and base subcomplexes. The regulatory subunit RPN7 is one of the lid subunits of the 26S proteasome and has been shown in Saccharomyces cerevisiae (Baker's yeast) to be required for structural integrity []. The COP9 signalosome is a conserved protein complex composed of eight subunits, where Individual subunits of the complex have been linked to various signal transduction pathways leading to gene expression and cell cycle control []. The overall organisation and the amino acid sequences of the COP9 signalosome subunits resemble the lid subcomplex of the 19 S regulatory particle for the 26 S proteasome []. COP9 subunit 1 (CSN1 or GPS1) of the COP9 complex is an essential subunit of the complex with regard to both structural integrity and functionality. The N-terminal region of subunit 1 (CSN1-N) can inhibit c-fos expression from either a transfected template or a chromosomal transgene (fos-lacZ), and may contain the activity domain that confers most of the repression functions of CSN1. The C-terminal region of subunit 1 (CSN1-C) allows integration of the protein into the COP9 signalosome.
Probab=82.01 E-value=41 Score=30.77 Aligned_cols=127 Identities=15% Similarity=0.213 Sum_probs=79.6
Q ss_pred HHHHHHHHHHHhcChhhhhhhHHHHHHHHHHHHHHHhhhCCCCcchHHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCc
Q psy9642 81 ELFSQIQEFLNMCNPDQIRHAGDLYAELSHQYTKTVMDLKTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNF 160 (437)
Q Consensus 81 ~~~~~~~~fl~~fd~~Qir~a~~~~~~l~~~~~~~~~~~~~~~~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y 160 (437)
.+=..+.+.-.+..-+.+|-+ +..+++.+.+... . -.+++.+.. ++....++.+.--+...++|+++.-++|
T Consensus 18 ~Le~elk~~~~n~~kesir~~---~~~l~~~~~~~Gd-~---~~A~k~y~~-~~~~~~~~~~~id~~l~~irv~i~~~d~ 89 (177)
T PF10602_consen 18 KLEAELKDAKSNLGKESIRMA---LEDLADHYCKIGD-L---EEALKAYSR-ARDYCTSPGHKIDMCLNVIRVAIFFGDW 89 (177)
T ss_pred HHHHHHHHHHhccchHHHHHH---HHHHHHHHHHhhh-H---HHHHHHHHH-HhhhcCCHHHHHHHHHHHHHHHHHhCCH
Confidence 344445555556666667642 3333333322211 1 123334333 2223344556666778889999999999
Q ss_pred hHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhcccc
Q psy9642 161 KPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIITTPA 218 (437)
Q Consensus 161 ~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~~P~ 218 (437)
..+...+++--..+.. .-+..---++.-|.|+.+++.++|.+|.+.|..+..+.+
T Consensus 90 ~~v~~~i~ka~~~~~~---~~d~~~~nrlk~~~gL~~l~~r~f~~AA~~fl~~~~t~~ 144 (177)
T PF10602_consen 90 SHVEKYIEKAESLIEK---GGDWERRNRLKVYEGLANLAQRDFKEAAELFLDSLSTFT 144 (177)
T ss_pred HHHHHHHHHHHHHHhc---cchHHHHHHHHHHHHHHHHHhchHHHHHHHHHccCcCCC
Confidence 9998888775433322 112344566788999999999999999999999987553
No 63
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=81.62 E-value=5.1 Score=30.68 Aligned_cols=44 Identities=7% Similarity=0.080 Sum_probs=34.4
Q ss_pred HHHHHHHHhhcc--ccHHHHHHHhCCCChHHHHHHHHHhHHcCceEE
Q psy9642 310 NNIKRLTKTFLT--LSLADVASRVQLGTPVQAEIYILKMISQNEIYA 354 (437)
Q Consensus 310 ~~I~~l~k~Ys~--IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A 354 (437)
..|..+-+.--. ++..+||+.+|++ ...+.+++..|..+|.|.-
T Consensus 9 ~~IL~~L~~~g~~~~ta~eLa~~lgl~-~~~v~r~L~~L~~~G~V~~ 54 (68)
T smart00550 9 EKILEFLENSGDETSTALQLAKNLGLP-KKEVNRVLYSLEKKGKVCK 54 (68)
T ss_pred HHHHHHHHHCCCCCcCHHHHHHHHCCC-HHHHHHHHHHHHHCCCEEe
Confidence 334333344444 9999999999998 6799999999999998754
No 64
>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=80.64 E-value=8.9 Score=28.03 Aligned_cols=50 Identities=8% Similarity=0.081 Sum_probs=37.8
Q ss_pred HHHHHHHHhhcc--ccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCC
Q psy9642 310 NNIKRLTKTFLT--LSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKD 360 (437)
Q Consensus 310 ~~I~~l~k~Ys~--IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~ 360 (437)
+.|...-..+-. ++..+||+.++++ ...+-..|..|+..|.|.-.-+..+
T Consensus 8 ~~vL~~l~~~~~~~~t~~~la~~l~~~-~~~vs~~v~~L~~~Glv~r~~~~~D 59 (62)
T PF12802_consen 8 FRVLMALARHPGEELTQSELAERLGIS-KSTVSRIVKRLEKKGLVERERDPGD 59 (62)
T ss_dssp HHHHHHHHHSTTSGEEHHHHHHHHTS--HHHHHHHHHHHHHTTSEEEEE-SSS
T ss_pred HHHHHHHHHCCCCCcCHHHHHHHHCcC-HHHHHHHHHHHHHCCCEEEeCCCCC
Confidence 344433444455 9999999999998 7899999999999999988776544
No 65
>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=80.51 E-value=8.3 Score=28.00 Aligned_cols=51 Identities=12% Similarity=0.117 Sum_probs=41.2
Q ss_pred HHHHHHHHHhhccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCC
Q psy9642 309 KNNIKRLTKTFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKD 360 (437)
Q Consensus 309 r~~I~~l~k~Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~ 360 (437)
++.+..+-..+-.++..+||+.++++ ..-+-..+.+|+..|.|.-.-+..+
T Consensus 5 q~~iL~~l~~~~~~~~~~la~~~~~~-~~~~t~~i~~L~~~g~I~r~~~~~D 55 (59)
T PF01047_consen 5 QFRILRILYENGGITQSELAEKLGIS-RSTVTRIIKRLEKKGLIERERDPDD 55 (59)
T ss_dssp HHHHHHHHHHHSSEEHHHHHHHHTS--HHHHHHHHHHHHHTTSEEEEEETTE
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHCCC-hhHHHHHHHHHHHCCCEEeccCCCC
Confidence 44555555567789999999999998 7888999999999999988887654
No 66
>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=80.47 E-value=5.9 Score=36.59 Aligned_cols=64 Identities=13% Similarity=0.182 Sum_probs=46.0
Q ss_pred HHHHHHHhcCCHHHHHHHHHhccccccccchh-hHHHHHHHHHHHHHHHHHHHhhcc-ccHHHHHHHhCC
Q psy9642 266 LDLVSVYTNNNSTELQHLLLKYADVFSRDENT-GLTKQIVASLYKNNIKRLTKTFLT-LSLADVASRVQL 333 (437)
Q Consensus 266 ~~L~~af~~~d~~~~~~~~~~~~~~f~~D~n~-~Lv~~l~~~v~r~~I~~l~k~Ys~-IsL~dIa~~l~L 333 (437)
.++.+++..||..+|-+.+..... .... -++......++.+.++.++++|.. |+++.+++.|+.
T Consensus 139 l~l~~a~~~gny~~ff~l~~~~~~----~~l~~~l~~~~~~~iR~~al~~i~~ay~~~i~l~~l~~~L~F 204 (204)
T PF03399_consen 139 LELCRALMEGNYVRFFRLYRSKSA----PYLFACLMERFFNRIRLRALQSISKAYRSSIPLSFLAELLGF 204 (204)
T ss_dssp HHHHHHH--TTHHHHHHHHT-TTS-----HHHHHHHGGGHHHHHHHHHHHHHHHS-T-EEHHHHHHHTT-
T ss_pred HHHHHHHHcCCHHHHHHHHhccCC----ChHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCC
Confidence 478899999999988887732111 1122 256668889999999999999999 999999998863
No 67
>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A.
Probab=79.57 E-value=14 Score=36.32 Aligned_cols=137 Identities=15% Similarity=0.123 Sum_probs=88.8
Q ss_pred cHHHHHHHHHHHHHhcC-hhhhhhhHHHHHHHHHHHHHHHhhh-CCCCcchHHHHHHHHHhCCCC--cchhhHHHHHHHH
Q psy9642 78 YQEELFSQIQEFLNMCN-PDQIRHAGDLYAELSHQYTKTVMDL-KTPQRGIPLIQTAIKKIQTSD--SQLTSLHSDLCQL 153 (437)
Q Consensus 78 ~~~~~~~~~~~fl~~fd-~~Qir~a~~~~~~l~~~~~~~~~~~-~~~~~~i~~l~~ai~rl~~~~--~~lT~~h~~l~~l 153 (437)
+....+.+.++.....+ +.+ ++..+.. +++...+. +.+-.++.....|+.-+...+ ............+
T Consensus 92 ~Ai~~~~~A~~~y~~~G~~~~---aA~~~~~----lA~~ye~~~~d~e~Ai~~Y~~A~~~y~~e~~~~~a~~~~~~~A~l 164 (282)
T PF14938_consen 92 EAIECYEKAIEIYREAGRFSQ---AAKCLKE----LAEIYEEQLGDYEKAIEYYQKAAELYEQEGSPHSAAECLLKAADL 164 (282)
T ss_dssp HHHHHHHHHHHHHHHCT-HHH---HHHHHHH----HHHHHCCTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhcCcHHH---HHHHHHH----HHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChhhHHHHHHHHHHH
Confidence 34445555555554322 222 2333333 33344444 567789999999999886554 4446666778899
Q ss_pred HHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhc-ccccccCH
Q psy9642 154 CLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIIT-TPALAVSH 223 (437)
Q Consensus 154 ~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~-~P~~~~s~ 223 (437)
+...+.|..|+.+.++-+..... ..+..-..=.|++-.+++++..+|+..|.+.|..... .|+-..|.
T Consensus 165 ~~~l~~y~~A~~~~e~~~~~~l~--~~l~~~~~~~~~l~a~l~~L~~~D~v~A~~~~~~~~~~~~~F~~s~ 233 (282)
T PF14938_consen 165 YARLGRYEEAIEIYEEVAKKCLE--NNLLKYSAKEYFLKAILCHLAMGDYVAARKALERYCSQDPSFASSR 233 (282)
T ss_dssp HHHTT-HHHHHHHHHHHHHTCCC--HCTTGHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHGTTSTTSTTSH
T ss_pred HHHhCCHHHHHHHHHHHHHHhhc--ccccchhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCCCcH
Confidence 99999999999999876553211 1122223556888899999999999999999999987 68765553
No 68
>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A.
Probab=79.35 E-value=2.6 Score=27.73 Aligned_cols=25 Identities=28% Similarity=0.509 Sum_probs=20.9
Q ss_pred HHHHHHHHHHhhHHHHHHHHHHHhc
Q psy9642 191 YYGGMIYLALKNYERALYFFEVIIT 215 (437)
Q Consensus 191 Yy~G~I~~~~k~y~~A~~~~~~ai~ 215 (437)
..-|.+|...++|++|.++|++++.
T Consensus 3 ~~Lg~~~~~~g~~~~Ai~~y~~aL~ 27 (36)
T PF13176_consen 3 NNLGRIYRQQGDYEKAIEYYEQALA 27 (36)
T ss_dssp HHHHHHHHHCT-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHH
Confidence 4568999999999999999999664
No 69
>PRK10747 putative protoheme IX biogenesis protein; Provisional
Probab=78.44 E-value=10 Score=39.18 Aligned_cols=94 Identities=9% Similarity=0.078 Sum_probs=60.6
Q ss_pred chHHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcC-----------CCCC------------
Q psy9642 125 GIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANE-----------GPQF------------ 181 (437)
Q Consensus 125 ~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~-----------~~~~------------ 181 (437)
+...+......+...-.....++..+++..+..++...|..++.+... .... ....
T Consensus 244 ~~~~l~~~w~~lp~~~~~~~~~~~~~A~~l~~~g~~~~A~~~L~~~l~-~~~~~~l~~l~~~l~~~~~~~al~~~e~~lk 322 (398)
T PRK10747 244 GSEGLKRWWKNQSRKTRHQVALQVAMAEHLIECDDHDTAQQIILDGLK-RQYDERLVLLIPRLKTNNPEQLEKVLRQQIK 322 (398)
T ss_pred CHHHHHHHHHhCCHHHhCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHh-cCCCHHHHHHHhhccCCChHHHHHHHHHHHh
Confidence 345555555555322223455777777777777777777777765433 1000 0000
Q ss_pred ChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhc-cccc
Q psy9642 182 DTKYFLQYFYYGGMIYLALKNYERALYFFEVIIT-TPAL 219 (437)
Q Consensus 182 ~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~-~P~~ 219 (437)
...+...+++.-|.+++..++|.+|.++|+.++. .|+.
T Consensus 323 ~~P~~~~l~l~lgrl~~~~~~~~~A~~~le~al~~~P~~ 361 (398)
T PRK10747 323 QHGDTPLLWSTLGQLLMKHGEWQEASLAFRAALKQRPDA 361 (398)
T ss_pred hCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCH
Confidence 1123456788999999999999999999999999 5764
No 70
>KOG0543|consensus
Probab=78.21 E-value=7.1 Score=40.28 Aligned_cols=69 Identities=23% Similarity=0.275 Sum_probs=56.7
Q ss_pred chhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhc-cccc
Q psy9642 142 QLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIIT-TPAL 219 (437)
Q Consensus 142 ~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~-~P~~ 219 (437)
..++.|+.++-++++-+.|..|+.--++-... ++ ...+=.|=.|++++.+++|+.|...|..|+. -|.+
T Consensus 255 ~k~~~~lNlA~c~lKl~~~~~Ai~~c~kvLe~--------~~-~N~KALyRrG~A~l~~~e~~~A~~df~ka~k~~P~N 324 (397)
T KOG0543|consen 255 LKLACHLNLAACYLKLKEYKEAIESCNKVLEL--------DP-NNVKALYRRGQALLALGEYDLARDDFQKALKLEPSN 324 (397)
T ss_pred HHHHHhhHHHHHHHhhhhHHHHHHHHHHHHhc--------CC-CchhHHHHHHHHHHhhccHHHHHHHHHHHHHhCCCc
Confidence 45678999999999999999997766654431 11 2566678999999999999999999999999 8987
No 71
>KOG3677|consensus
Probab=78.16 E-value=45 Score=34.82 Aligned_cols=236 Identities=15% Similarity=0.188 Sum_probs=122.4
Q ss_pred HHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhcccccccCHHHHHHH
Q psy9642 150 LCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIITTPALAVSHIMLEGY 229 (437)
Q Consensus 150 l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~~P~~~~s~i~vea~ 229 (437)
++|.-..-|++...++++|-.=-++ -+--+...+. ||-|-.|+..++|.+|.+.|..++..=..+.+-...-+|
T Consensus 241 LlR~H~lLgDhQat~q~idi~pk~i----y~t~p~c~VT--Y~VGFayLmmrryadai~~F~niLlyIqrtks~~~~~~y 314 (525)
T KOG3677|consen 241 LLRMHILLGDHQATSQILDIMPKEI----YGTEPMCRVT--YQVGFAYLMMRRYADAIRVFLNILLYIQRTKSMFSRTTY 314 (525)
T ss_pred HHHHHHHhhhhHhhhhhhhcCchhh----cCcccceeEe--eehhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcchhh
Confidence 4566666677655555544321111 0112223333 899999999999999999999888631111110011111
Q ss_pred H----------HHHHHHHHHhCCCCCCCccccHHHhHhhccCCHHHHHHHHHHhcCCHHHHHHHHHhccccccc------
Q psy9642 230 K----------KYLLIYLIVYGKAPNLPKNVSQAICRYIKPLSQPYLDLVSVYTNNNSTELQHLLLKYADVFSR------ 293 (437)
Q Consensus 230 K----------k~iLv~Lil~G~~~~lp~~~s~~~~r~~k~~~~pY~~L~~af~~~d~~~~~~~~~~~~~~f~~------ 293 (437)
+ -+-|+...+. .-|......+...+. +-|.+=.--...|+...|+..+.-....|..
T Consensus 315 ~~d~inKq~eqm~~llai~l~----~yPq~iDESi~s~l~---Ek~~d~ml~mqng~~q~~ks~f~y~cpkflsp~~~~~ 387 (525)
T KOG3677|consen 315 QYDMINKQNEQMHHLLAICLS----MYPQMIDESIHSQLA---EKYGDKMLPMQNGDPQVFKSLFSYLCPKFLSPVVPNY 387 (525)
T ss_pred hHhhhhhhHHHHHHHHHHHHH----hCchhhhHHHHHHHH---HHhcchhhhhhcCChHHHHHHHHHcCccccCCCCccc
Confidence 1 1111111111 111111222222221 1122111112358899999888887777754
Q ss_pred cchhh------HHHH-------HHHHHHHHHHHHHHHhhccccHHHHHHHhCCCChHHHHHHHHHh----------H-Hc
Q psy9642 294 DENTG------LTKQ-------IVASLYKNNIKRLTKTFLTLSLADVASRVQLGTPVQAEIYILKM----------I-SQ 349 (437)
Q Consensus 294 D~n~~------Lv~~-------l~~~v~r~~I~~l~k~Ys~IsL~dIa~~l~L~~~~eaE~~l~~m----------I-~~ 349 (437)
||.+. +..| +.+...---++..-|-|++++..-+|..+.+++ ++-.+.+..+ + .+
T Consensus 388 dgv~~~y~kePl~~qlq~fld~v~qq~dl~~~rsylklyTt~P~kkla~F~D~~d-~~~dk~li~Ll~~khkm~nlv~~s 466 (525)
T KOG3677|consen 388 DGVLPNYHKEPLLQQLQVFLDEVSQQADLPTIRSYLKLYTTLPVKKLASFLDLTD-QERDKFLIQLLVFKHKMKNLVWTS 466 (525)
T ss_pred ccccccccccHHHHHHHHHhHHHhhhccchHHHHHHHHHHhccHHHhhhccCCch-hhhhhhHHHHHHHHHHHHHHHHhc
Confidence 33222 2222 222333345677778899999999999999873 4422332222 2 23
Q ss_pred CceEEEEe-cCCCEEEEccCCCCC---C---chHHHHHHHHHHHHHHHHHHHHHHHH
Q psy9642 350 NEIYATIN-KKDGMVVFNDNPQRF---N---NPLTFAQIESNIRACMHLDGKFQAME 399 (437)
Q Consensus 350 G~I~A~Id-~~~g~v~F~~~~~~~---~---~~e~~~~l~~~i~~~~~L~~~~~~~d 399 (437)
|-+.+.++ .+...|-|.-+.+.. + ..+...-+-.+|.+..+++..+|.++
T Consensus 467 g~s~~d~~f~~~s~idfyid~dmi~iaDtkv~r~~gd~fir~i~kf~El~~vLK~i~ 523 (525)
T KOG3677|consen 467 GPSDLDDAFFSRSEIDFYIDKDMIHIADTKVARRYGDIFIRQIHKFEELNRVLKLIT 523 (525)
T ss_pred CCccccccccCcceeeEEechhHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 55555555 345566675433321 1 12455556677788888888777654
No 72
>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=77.80 E-value=6.1 Score=36.74 Aligned_cols=46 Identities=13% Similarity=0.234 Sum_probs=32.8
Q ss_pred ccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCCCEEEEc
Q psy9642 320 LTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVFN 366 (437)
Q Consensus 320 s~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~g~v~F~ 366 (437)
.-+.|.|||...||. .+++...|..+..+|.|.|.||..+.+|...
T Consensus 112 Kvv~ledla~~f~l~-t~~~i~ri~~L~~~g~ltGv~DdrGkfIyIs 157 (188)
T PF09756_consen 112 KVVNLEDLAAEFGLR-TQDVINRIQELEAEGRLTGVIDDRGKFIYIS 157 (188)
T ss_dssp SEE-HHHHHHHH-S--HHHHHHHHHHHHHHSSS-EEE-TT--EEE--
T ss_pred ceeeHHHHHHHcCCC-HHHHHHHHHHHHHCCCceeeEcCCCCeEEec
Confidence 458999999999998 7899999999999999999999855454444
No 73
>PF13414 TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2PL2_B 3IEG_B 2FBN_A ....
Probab=77.48 E-value=3.5 Score=30.68 Aligned_cols=33 Identities=33% Similarity=0.589 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHHHHhhHHHHHHHHHHHhc-cccc
Q psy9642 187 LQYFYYGGMIYLALKNYERALYFFEVIIT-TPAL 219 (437)
Q Consensus 187 l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~-~P~~ 219 (437)
...++.-|.+++..++|.+|..+|..++. .|..
T Consensus 3 a~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~p~~ 36 (69)
T PF13414_consen 3 AEAWYNLGQIYFQQGDYEEAIEYFEKAIELDPNN 36 (69)
T ss_dssp HHHHHHHHHHHHHTTHHHHHHHHHHHHHHHSTTH
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCC
Confidence 35678899999999999999999999999 7764
No 74
>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H ....
Probab=76.74 E-value=4.1 Score=31.17 Aligned_cols=33 Identities=18% Similarity=0.287 Sum_probs=28.6
Q ss_pred HhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhcc
Q psy9642 184 KYFLQYFYYGGMIYLALKNYERALYFFEVIITT 216 (437)
Q Consensus 184 ~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~~ 216 (437)
.+.+..+..-|.++..+++|++|..+|+.|+..
T Consensus 2 ~~~a~~~~~la~~~~~~~~~~~A~~~~~~al~~ 34 (78)
T PF13424_consen 2 PDTANAYNNLARVYRELGRYDEALDYYEKALDI 34 (78)
T ss_dssp HHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence 356778889999999999999999999999986
No 75
>TIGR02917 PEP_TPR_lipo putative PEP-CTERM system TPR-repeat lipoprotein. This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.
Probab=76.73 E-value=36 Score=37.56 Aligned_cols=90 Identities=21% Similarity=0.217 Sum_probs=65.4
Q ss_pred hhhCCCCcchHHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHH
Q psy9642 117 MDLKTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMI 196 (437)
Q Consensus 117 ~~~~~~~~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I 196 (437)
...+.+-.++..+..++.. +|.. ...+..+.++.+..++|..|+.++++-+.. + + .....+++.|.+
T Consensus 136 ~~~~~~~~A~~~~~~a~~~-~~~~---~~~~~~la~~~~~~~~~~~A~~~~~~~~~~-~-------~-~~~~~~~~~~~~ 202 (899)
T TIGR02917 136 LGLGQLELAQKSYEQALAI-DPRS---LYAKLGLAQLALAENRFDEARALIDEVLTA-D-------P-GNVDALLLKGDL 202 (899)
T ss_pred HHcCCHHHHHHHHHHHHhc-CCCC---hhhHHHHHHHHHHCCCHHHHHHHHHHHHHh-C-------C-CChHHHHHHHHH
Confidence 3455666777777777643 4432 225677888899999999999998885542 1 1 134566778999
Q ss_pred HHHHhhHHHHHHHHHHHhc-cccc
Q psy9642 197 YLALKNYERALYFFEVIIT-TPAL 219 (437)
Q Consensus 197 ~~~~k~y~~A~~~~~~ai~-~P~~ 219 (437)
+...++|.+|..+|+.++. .|..
T Consensus 203 ~~~~g~~~~A~~~~~~a~~~~p~~ 226 (899)
T TIGR02917 203 LLSLGNIELALAAYRKAIALRPNN 226 (899)
T ss_pred HHhcCCHHHHHHHHHHHHhhCCCC
Confidence 9999999999999999998 6654
No 76
>PLN03081 pentatricopeptide (PPR) repeat-containing protein; Provisional
Probab=76.36 E-value=85 Score=34.87 Aligned_cols=57 Identities=11% Similarity=0.019 Sum_probs=32.0
Q ss_pred HHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhc
Q psy9642 147 HSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIIT 215 (437)
Q Consensus 147 h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~ 215 (437)
...++..+...++++.|..+++.-.. .+...| ..-...|+..+++++|.+.|.....
T Consensus 161 ~n~Li~~y~k~g~~~~A~~lf~~m~~-----------~~~~t~-n~li~~~~~~g~~~~A~~lf~~M~~ 217 (697)
T PLN03081 161 MNRVLLMHVKCGMLIDARRLFDEMPE-----------RNLASW-GTIIGGLVDAGNYREAFALFREMWE 217 (697)
T ss_pred HHHHHHHHhcCCCHHHHHHHHhcCCC-----------CCeeeH-HHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 44556667777777777666554210 111111 1112234445788888888888765
No 77
>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO. Members of this protein family include YfiO, a near-essential protein of the outer membrane, part of a complex involved in protein insertion into the bacterial outer membrane. Many proteins in this family are annotated as ComL, based on the involvement of this protein in natural transformation with exogenous DNA in Neisseria gonorrhoeae. This protein family shows sequence similarity to, but is distinct from, the tol-pal system protein YbgF (TIGR02795).
Probab=74.86 E-value=15 Score=34.37 Aligned_cols=74 Identities=12% Similarity=0.086 Sum_probs=56.4
Q ss_pred cchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhc-cccc
Q psy9642 141 SQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIIT-TPAL 219 (437)
Q Consensus 141 ~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~-~P~~ 219 (437)
..-...+..+.+.++..++|..|+..+++-+... + +......-+|..|.++...++|.+|...|..+++ .|..
T Consensus 30 ~~~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~-p-----~~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~ 103 (235)
T TIGR03302 30 EWPAEELYEEAKEALDSGDYTEAIKYFEALESRY-P-----FSPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRLHPNH 103 (235)
T ss_pred cCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-C-----CchhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCC
Confidence 3444577888889999999999999888755431 1 1122334567889999999999999999999998 7865
Q ss_pred c
Q psy9642 220 A 220 (437)
Q Consensus 220 ~ 220 (437)
.
T Consensus 104 ~ 104 (235)
T TIGR03302 104 P 104 (235)
T ss_pred C
Confidence 3
No 78
>KOG1840|consensus
Probab=74.64 E-value=65 Score=34.70 Aligned_cols=109 Identities=13% Similarity=0.122 Sum_probs=82.0
Q ss_pred HHHHHHHHHHHhhhCCCCcchHHHHHHHHHhC----CCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCC
Q psy9642 106 AELSHQYTKTVMDLKTPQRGIPLIQTAIKKIQ----TSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQF 181 (437)
Q Consensus 106 ~~l~~~~~~~~~~~~~~~~~i~~l~~ai~rl~----~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~ 181 (437)
...++.++....+.++..-++..+..|+.-+. ++....-.+|..+..+....+.|+.|.+..++-+. |-......
T Consensus 241 a~~l~~~a~~y~~~~k~~eAv~ly~~AL~i~e~~~G~~h~~va~~l~nLa~ly~~~GKf~EA~~~~e~Al~-I~~~~~~~ 319 (508)
T KOG1840|consen 241 ASMLNILALVYRSLGKYDEAVNLYEEALTIREEVFGEDHPAVAATLNNLAVLYYKQGKFAEAEEYCERALE-IYEKLLGA 319 (508)
T ss_pred HHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHhccCChHHHHHHHHHHHH-HHHHhhcc
Confidence 33444455555567777788888888887765 55556666888999999999999999777776432 22222345
Q ss_pred ChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhc
Q psy9642 182 DTKYFLQYFYYGGMIYLALKNYERALYFFEVIIT 215 (437)
Q Consensus 182 ~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~ 215 (437)
++.++...+-..+.++...++|++|..+|..++.
T Consensus 320 ~~~~v~~~l~~~~~~~~~~~~~Eea~~l~q~al~ 353 (508)
T KOG1840|consen 320 SHPEVAAQLSELAAILQSMNEYEEAKKLLQKALK 353 (508)
T ss_pred ChHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHH
Confidence 6777889999999999999999999999998776
No 79
>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW. Members of this family are designated PilF in ref (PubMed:8973346) and PilW in ref (PubMed:15612916). This outer membrane protein is required both for pilus stability and for pilus function such as adherence to human cells. Members of this family contain copies of the TPR (tetratricopeptide repeat) domain.
Probab=74.33 E-value=18 Score=32.35 Aligned_cols=90 Identities=9% Similarity=0.134 Sum_probs=63.7
Q ss_pred hhCCCCcchHHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHH
Q psy9642 118 DLKTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIY 197 (437)
Q Consensus 118 ~~~~~~~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~ 197 (437)
..+..-.++..+..++... |.. ...+..+..++...+++..|+..+.+-+... .........+..|.++
T Consensus 77 ~~~~~~~A~~~~~~al~~~-~~~---~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~-------~~~~~~~~~~~l~~~~ 145 (234)
T TIGR02521 77 QLGELEKAEDSFRRALTLN-PNN---GDVLNNYGTFLCQQGKYEQAMQQFEQAIEDP-------LYPQPARSLENAGLCA 145 (234)
T ss_pred HcCCHHHHHHHHHHHHhhC-CCC---HHHHHHHHHHHHHcccHHHHHHHHHHHHhcc-------ccccchHHHHHHHHHH
Confidence 3455566777888777654 322 2356677888899999999999888866421 0112333455679999
Q ss_pred HHHhhHHHHHHHHHHHhc-ccc
Q psy9642 198 LALKNYERALYFFEVIIT-TPA 218 (437)
Q Consensus 198 ~~~k~y~~A~~~~~~ai~-~P~ 218 (437)
...+++.+|..+|..++. .|.
T Consensus 146 ~~~g~~~~A~~~~~~~~~~~~~ 167 (234)
T TIGR02521 146 LKAGDFDKAEKYLTRALQIDPQ 167 (234)
T ss_pred HHcCCHHHHHHHHHHHHHhCcC
Confidence 999999999999999998 454
No 80
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=74.28 E-value=8.4 Score=34.27 Aligned_cols=38 Identities=18% Similarity=0.239 Sum_probs=34.4
Q ss_pred ccccHHHHHHHhCCCChHHHHHHHHHhHHcCceE---EEEec
Q psy9642 320 LTLSLADVASRVQLGTPVQAEIYILKMISQNEIY---ATINK 358 (437)
Q Consensus 320 s~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~---A~Id~ 358 (437)
.|+|.++||+.+|++ +..+..-+.+|.++|.|. |.+|+
T Consensus 22 ~R~s~~eiA~~lglS-~~tV~~Ri~rL~~~GvI~~~~~~v~~ 62 (153)
T PRK11179 22 ARTPYAELAKQFGVS-PGTIHVRVEKMKQAGIITGTRVDVNP 62 (153)
T ss_pred CCCCHHHHHHHHCcC-HHHHHHHHHHHHHCCCeeeEEEEECH
Confidence 899999999999998 889999999999999996 45665
No 81
>CHL00033 ycf3 photosystem I assembly protein Ycf3
Probab=74.26 E-value=31 Score=30.61 Aligned_cols=94 Identities=10% Similarity=0.000 Sum_probs=59.0
Q ss_pred hCCCCcchHHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHH
Q psy9642 119 LKTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYL 198 (437)
Q Consensus 119 ~~~~~~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~ 198 (437)
.+....++..++.|+.- .|++......|..+..++...+.+..|+....+-+.. .+.. .-........++..|..+.
T Consensus 48 ~g~~~~A~~~~~~al~l-~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~-~~~~-~~~~~~la~i~~~~~~~~~ 124 (168)
T CHL00033 48 EGEYAEALQNYYEAMRL-EIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQALER-NPFL-PQALNNMAVICHYRGEQAI 124 (168)
T ss_pred cCCHHHHHHHHHHHHhc-cccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-CcCc-HHHHHHHHHHHHHhhHHHH
Confidence 45556677777777654 3444444457888999999999999999988776542 1110 0111223444555555566
Q ss_pred HHhhHHHHHHHHHHHhc
Q psy9642 199 ALKNYERALYFFEVIIT 215 (437)
Q Consensus 199 ~~k~y~~A~~~~~~ai~ 215 (437)
..++|.+|..+|..++.
T Consensus 125 ~~g~~~~A~~~~~~a~~ 141 (168)
T CHL00033 125 EQGDSEIAEAWFDQAAE 141 (168)
T ss_pred HcccHHHHHHHHHHHHH
Confidence 88888866666665554
No 82
>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=74.09 E-value=12 Score=29.53 Aligned_cols=55 Identities=15% Similarity=0.169 Sum_probs=41.5
Q ss_pred ccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCCCEEEEccCCCCCCchHHH
Q psy9642 322 LSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVFNDNPQRFNNPLTF 378 (437)
Q Consensus 322 IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~g~v~F~~~~~~~~~~e~~ 378 (437)
++..+||+.++++ +..+++++.++...|-|..+= -++|-.....+++..+-.++.
T Consensus 26 ~s~~eiA~~~~i~-~~~l~kil~~L~~~Gli~s~~-G~~GGy~L~~~~~~Itl~dI~ 80 (83)
T PF02082_consen 26 VSSKEIAERLGIS-PSYLRKILQKLKKAGLIESSR-GRGGGYRLARPPEEITLLDIV 80 (83)
T ss_dssp BEHHHHHHHHTS--HHHHHHHHHHHHHTTSEEEET-STTSEEEESS-CCGSBHHHHH
T ss_pred CCHHHHHHHHCcC-HHHHHHHHHHHhhCCeeEecC-CCCCceeecCCHHHCCHHHHH
Confidence 9999999999998 899999999999999876553 335777777777655543443
No 83
>PRK11189 lipoprotein NlpI; Provisional
Probab=74.06 E-value=12 Score=36.87 Aligned_cols=64 Identities=20% Similarity=0.167 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhc-ccc
Q psy9642 146 LHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIIT-TPA 218 (437)
Q Consensus 146 ~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~-~P~ 218 (437)
.+..+...+...++|..|+...++-+. + ++. ....++..|.++...++|++|.+.|+.++. .|.
T Consensus 100 a~~~lg~~~~~~g~~~~A~~~~~~Al~-l-------~P~-~~~a~~~lg~~l~~~g~~~eA~~~~~~al~~~P~ 164 (296)
T PRK11189 100 AYNYLGIYLTQAGNFDAAYEAFDSVLE-L-------DPT-YNYAYLNRGIALYYGGRYELAQDDLLAFYQDDPN 164 (296)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHHHH-h-------CCC-CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC
Confidence 344445555555555555555444432 1 111 222334455555555555555555555555 443
No 84
>PF13512 TPR_18: Tetratricopeptide repeat
Probab=74.04 E-value=39 Score=30.04 Aligned_cols=93 Identities=16% Similarity=0.211 Sum_probs=66.5
Q ss_pred CCCCcchHHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHH
Q psy9642 120 KTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLA 199 (437)
Q Consensus 120 ~~~~~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~ 199 (437)
++-..++..+...-.|+ |.+..-.-.-+.+.-....+++|..|+...++=|-- .+....++. =+|..|++++.
T Consensus 24 ~~Y~~A~~~le~L~~ry-P~g~ya~qAqL~l~yayy~~~~y~~A~a~~~rFirL-hP~hp~vdY-----a~Y~~gL~~~~ 96 (142)
T PF13512_consen 24 GNYEEAIKQLEALDTRY-PFGEYAEQAQLDLAYAYYKQGDYEEAIAAYDRFIRL-HPTHPNVDY-----AYYMRGLSYYE 96 (142)
T ss_pred CCHHHHHHHHHHHHhcC-CCCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHh-CCCCCCccH-----HHHHHHHHHHH
Confidence 33344566666666666 667777778889999999999999999888886542 222222222 24688999999
Q ss_pred Hhh---------------HHHHHHHHHHHhc-cccc
Q psy9642 200 LKN---------------YERALYFFEVIIT-TPAL 219 (437)
Q Consensus 200 ~k~---------------y~~A~~~~~~ai~-~P~~ 219 (437)
+.+ ..+|...|+..++ .|.+
T Consensus 97 ~~~~~~~~~~~~drD~~~~~~A~~~f~~lv~~yP~S 132 (142)
T PF13512_consen 97 QDEGSLQSFFRSDRDPTPARQAFRDFEQLVRRYPNS 132 (142)
T ss_pred HhhhHHhhhcccccCcHHHHHHHHHHHHHHHHCcCC
Confidence 887 7888888888888 7765
No 85
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=73.73 E-value=7.4 Score=35.11 Aligned_cols=49 Identities=22% Similarity=0.187 Sum_probs=39.7
Q ss_pred HHHHHHHHHhhccccHHHHHHHhCCCChHHHHHHHHHhHHcCceE---EEEec
Q psy9642 309 KNNIKRLTKTFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIY---ATINK 358 (437)
Q Consensus 309 r~~I~~l~k~Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~---A~Id~ 358 (437)
-+.|..+-+-=.|+|.++||+++|++ +..+-.-+.+|.++|.|. |.+|+
T Consensus 16 D~~IL~~Lq~d~R~s~~eiA~~lglS-~~tv~~Ri~rL~~~GvI~~~~~~v~p 67 (164)
T PRK11169 16 DRNILNELQKDGRISNVELSKRVGLS-PTPCLERVRRLERQGFIQGYTALLNP 67 (164)
T ss_pred HHHHHHHhccCCCCCHHHHHHHHCcC-HHHHHHHHHHHHHCCCeEEEEEEECH
Confidence 34455555566899999999999998 789999999999999985 44564
No 86
>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A.
Probab=72.62 E-value=7.3 Score=30.43 Aligned_cols=49 Identities=16% Similarity=0.328 Sum_probs=37.9
Q ss_pred hCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHH
Q psy9642 157 AQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEV 212 (437)
Q Consensus 157 ~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ 212 (437)
.++|+.|+.+.++-+..-.. ++ .-.|.|.-|.+++..++|.+|..++..
T Consensus 2 ~~~y~~Ai~~~~k~~~~~~~-----~~--~~~~~~~la~~~~~~~~y~~A~~~~~~ 50 (84)
T PF12895_consen 2 QGNYENAIKYYEKLLELDPT-----NP--NSAYLYNLAQCYFQQGKYEEAIELLQK 50 (84)
T ss_dssp TT-HHHHHHHHHHHHHHHCG-----TH--HHHHHHHHHHHHHHTTHHHHHHHHHHC
T ss_pred CccHHHHHHHHHHHHHHCCC-----Ch--hHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence 57899999988887664211 11 555778899999999999999999988
No 87
>KOG3250|consensus
Probab=72.29 E-value=35 Score=32.44 Aligned_cols=96 Identities=11% Similarity=0.163 Sum_probs=65.4
Q ss_pred CCHHHHHHHHHHhcCCHHHHHHHHHhccccccccchhhHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHhCCCChHHHH
Q psy9642 261 LSQPYLDLVSVYTNNNSTELQHLLLKYADVFSRDENTGLTKQIVASLYKNNIKRLTKTFLTLSLADVASRVQLGTPVQAE 340 (437)
Q Consensus 261 ~~~pY~~L~~af~~~d~~~~~~~~~~~~~~f~~D~n~~Lv~~l~~~v~r~~I~~l~k~Ys~IsL~dIa~~l~L~~~~eaE 340 (437)
.-..|..+.+.|.-|++..+...... |-+=....+.+ +....|-.++..-..|+-..+-..+.+.+..++|
T Consensus 58 ~dsa~lrlL~lFa~Gt~~Dy~aea~r----lp~Ls~~q~~k-----Lk~ltV~slas~~k~lpy~~Ll~~l~~~nvrelE 128 (258)
T KOG3250|consen 58 IDSAYLRLLELFAYGTYRDYSAEALR----LPKLSLAQLNK-----LKHLTVVSLASFEKCLPYLVLLRLLPSRNVRELE 128 (258)
T ss_pred ccHHHHHHHHHHhcCchhhhhhhhhc----CCCCCHHHHHh-----hhcceehhhhhhchhhhHHHHHhhccCCchhHHH
Confidence 45789999999999998877665432 21111111111 1111223344444567777777788888889999
Q ss_pred HHHHHhHHcCceEEEEecCCCEEEE
Q psy9642 341 IYILKMISQNEIYATINKKDGMVVF 365 (437)
Q Consensus 341 ~~l~~mI~~G~I~A~Id~~~g~v~F 365 (437)
.+|.+.+..+.+.|+||+.+.++.-
T Consensus 129 d~iieamya~IlrGkldqr~q~leV 153 (258)
T KOG3250|consen 129 DLIIEAMYADILRGKLDQRNQTLEV 153 (258)
T ss_pred HHHHHHHHHHHHHhhHHhhcceEee
Confidence 9999999999999999998887763
No 88
>PRK15331 chaperone protein SicA; Provisional
Probab=72.21 E-value=48 Score=30.23 Aligned_cols=124 Identities=12% Similarity=0.146 Sum_probs=74.8
Q ss_pred HHHHHHHHHHHHHh-cChhhhhhhH----HHHHHHHHHHHHHHhhhCCCCcchHHHHHHHHHhCCCCcchhhHHHHHHHH
Q psy9642 79 QEELFSQIQEFLNM-CNPDQIRHAG----DLYAELSHQYTKTVMDLKTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQL 153 (437)
Q Consensus 79 ~~~~~~~~~~fl~~-fd~~Qir~a~----~~~~~l~~~~~~~~~~~~~~~~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l 153 (437)
.+.+.+.+.+++.. -...+++=.+ +.++..+..+.+ .++-. .-.-+-..+..+||.... ...-|.-+
T Consensus 9 ~~~~~~~i~~al~~G~tlk~l~gis~~~le~iY~~Ay~~y~----~Gk~~-eA~~~F~~L~~~d~~n~~---Y~~GLaa~ 80 (165)
T PRK15331 9 EERVAEMIWDAVSEGATLKDVHGIPQDMMDGLYAHAYEFYN----QGRLD-EAETFFRFLCIYDFYNPD---YTMGLAAV 80 (165)
T ss_pred HHHHHHHHHHHHHCCCCHHHHhCCCHHHHHHHHHHHHHHHH----CCCHH-HHHHHHHHHHHhCcCcHH---HHHHHHHH
Confidence 44566666677663 3444444222 234444443322 11111 122334455557765533 45667777
Q ss_pred HHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhccccc
Q psy9642 154 CLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIITTPAL 219 (437)
Q Consensus 154 ~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~~P~~ 219 (437)
|-..+.|..|+..-..-..- .. . .-+-.||.|.+++.+++-..|.++|+.|+..|..
T Consensus 81 ~Q~~k~y~~Ai~~Y~~A~~l-~~-~-------dp~p~f~agqC~l~l~~~~~A~~~f~~a~~~~~~ 137 (165)
T PRK15331 81 CQLKKQFQKACDLYAVAFTL-LK-N-------DYRPVFFTGQCQLLMRKAAKARQCFELVNERTED 137 (165)
T ss_pred HHHHHHHHHHHHHHHHHHHc-cc-C-------CCCccchHHHHHHHhCCHHHHHHHHHHHHhCcch
Confidence 88888999998765544331 11 1 1122689999999999999999999999998764
No 89
>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=72.07 E-value=14 Score=27.23 Aligned_cols=33 Identities=12% Similarity=0.103 Sum_probs=30.3
Q ss_pred cccHHHHHHHhCCCChHHHHHHHHHhHHcCceEE
Q psy9642 321 TLSLADVASRVQLGTPVQAEIYILKMISQNEIYA 354 (437)
Q Consensus 321 ~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A 354 (437)
.++.++||+.+|++ ...+..++..|..+|.|..
T Consensus 25 ~~s~~ela~~~g~s-~~tv~r~l~~L~~~g~i~~ 57 (67)
T cd00092 25 PLTRQEIADYLGLT-RETVSRTLKELEEEGLISR 57 (67)
T ss_pred CcCHHHHHHHHCCC-HHHHHHHHHHHHHCCCEEe
Confidence 58999999999997 7899999999999998864
No 90
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=71.43 E-value=12 Score=32.76 Aligned_cols=48 Identities=27% Similarity=0.293 Sum_probs=38.1
Q ss_pred HHHHHHHHhhccccHHHHHHHhCCCChHHHHHHHHHhHHcCceE---EEEec
Q psy9642 310 NNIKRLTKTFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIY---ATINK 358 (437)
Q Consensus 310 ~~I~~l~k~Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~---A~Id~ 358 (437)
..|.++-+.=.++|+.+||+++|++ +..+-..|.+|..+|.|. |.+|.
T Consensus 11 ~~IL~~L~~d~r~~~~eia~~lglS-~~~v~~Ri~~L~~~GiI~~~~~~v~~ 61 (154)
T COG1522 11 RRILRLLQEDARISNAELAERVGLS-PSTVLRRIKRLEEEGVIKGYTAVLDP 61 (154)
T ss_pred HHHHHHHHHhCCCCHHHHHHHHCCC-HHHHHHHHHHHHHCCceeeEEEEECH
Confidence 3444444555779999999999998 789999999999999874 55654
No 91
>PRK02603 photosystem I assembly protein Ycf3; Provisional
Probab=71.34 E-value=16 Score=32.78 Aligned_cols=68 Identities=16% Similarity=0.204 Sum_probs=52.0
Q ss_pred HHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhc-cccc
Q psy9642 146 LHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIIT-TPAL 219 (437)
Q Consensus 146 ~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~-~P~~ 219 (437)
.+..+...+...++|..|+....+-+.. .+ ++.+...+++.-|.++...++|++|..+|..++. .|..
T Consensus 37 ~~~~lg~~~~~~g~~~~A~~~~~~al~~-~~-----~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~ 105 (172)
T PRK02603 37 VYYRDGMSAQADGEYAEALENYEEALKL-EE-----DPNDRSYILYNMGIIYASNGEHDKALEYYHQALELNPKQ 105 (172)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHHH-hh-----ccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCccc
Confidence 3456677888889999999988876542 11 1223456778899999999999999999999998 5653
No 92
>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=70.80 E-value=7.8 Score=29.56 Aligned_cols=32 Identities=9% Similarity=0.120 Sum_probs=28.5
Q ss_pred ccHHHHHHHhCCCChHHHHHHHHHhHHcCceE
Q psy9642 322 LSLADVASRVQLGTPVQAEIYILKMISQNEIY 353 (437)
Q Consensus 322 IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~ 353 (437)
-|+.+||+.+|+.|..-|..+|..|...|.|.
T Consensus 26 Pt~rEIa~~~g~~S~~tv~~~L~~Le~kG~I~ 57 (65)
T PF01726_consen 26 PTVREIAEALGLKSTSTVQRHLKALERKGYIR 57 (65)
T ss_dssp --HHHHHHHHTSSSHHHHHHHHHHHHHTTSEE
T ss_pred CCHHHHHHHhCCCChHHHHHHHHHHHHCcCcc
Confidence 69999999999999999999999999999885
No 93
>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional
Probab=70.62 E-value=56 Score=36.63 Aligned_cols=128 Identities=9% Similarity=0.055 Sum_probs=78.5
Q ss_pred cHHHHHHHHHHHHHhcChhhhhhhH-HHHHHHHHH----------HHHHHhhhCCCCcchHHHHHHHHHhCCCCcchhhH
Q psy9642 78 YQEELFSQIQEFLNMCNPDQIRHAG-DLYAELSHQ----------YTKTVMDLKTPQRGIPLIQTAIKKIQTSDSQLTSL 146 (437)
Q Consensus 78 ~~~~~~~~~~~fl~~fd~~Qir~a~-~~~~~l~~~----------~~~~~~~~~~~~~~i~~l~~ai~rl~~~~~~lT~~ 146 (437)
.+..+..+...-++..-..|+-.+. .+.-.+++. +.+...+.+..--+...+..+ ..+.|. ....
T Consensus 47 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~La~i~~~~g~~~ea~~~l~~~-~~~~Pd---~~~a 122 (694)
T PRK15179 47 AGRELLQQARQVLERHAAVHKPAAALPELLDYVRRYPHTELFQVLVARALEAAHRSDEGLAVWRGI-HQRFPD---SSEA 122 (694)
T ss_pred HHHHHHHHHHHHHHHhhhhcchHhhHHHHHHHHHhccccHHHHHHHHHHHHHcCCcHHHHHHHHHH-HhhCCC---cHHH
Confidence 3456777777777777777664332 111111111 222223333333344444444 334443 2336
Q ss_pred HHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhc-ccc
Q psy9642 147 HSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIIT-TPA 218 (437)
Q Consensus 147 h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~-~P~ 218 (437)
+..+.+.+.+.+.++.|+....+-.-. ..+.....+..|+.....++|++|...|+.++. .|.
T Consensus 123 ~~~~a~~L~~~~~~eeA~~~~~~~l~~---------~p~~~~~~~~~a~~l~~~g~~~~A~~~y~~~~~~~p~ 186 (694)
T PRK15179 123 FILMLRGVKRQQGIEAGRAEIELYFSG---------GSSSAREILLEAKSWDEIGQSEQADACFERLSRQHPE 186 (694)
T ss_pred HHHHHHHHHHhccHHHHHHHHHHHhhc---------CCCCHHHHHHHHHHHHHhcchHHHHHHHHHHHhcCCC
Confidence 677777888888888887776665431 234677888999999999999999999999997 554
No 94
>PRK02603 photosystem I assembly protein Ycf3; Provisional
Probab=69.50 E-value=71 Score=28.46 Aligned_cols=74 Identities=11% Similarity=0.061 Sum_probs=47.8
Q ss_pred hCCCCcchHHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHH
Q psy9642 119 LKTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYL 198 (437)
Q Consensus 119 ~~~~~~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~ 198 (437)
.+..-.++..+..++.. .|.+......+..+..++...++|..|+..+.+-+.. . +. ....++..|.++.
T Consensus 48 ~g~~~~A~~~~~~al~~-~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~-~-------p~-~~~~~~~lg~~~~ 117 (172)
T PRK02603 48 DGEYAEALENYEEALKL-EEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALEL-N-------PK-QPSALNNIAVIYH 117 (172)
T ss_pred cCCHHHHHHHHHHHHHH-hhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-C-------cc-cHHHHHHHHHHHH
Confidence 34445677777777654 3433333457888899999999999999988876652 1 11 2333445577766
Q ss_pred HHhh
Q psy9642 199 ALKN 202 (437)
Q Consensus 199 ~~k~ 202 (437)
..++
T Consensus 118 ~~g~ 121 (172)
T PRK02603 118 KRGE 121 (172)
T ss_pred HcCC
Confidence 6544
No 95
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=69.34 E-value=9.4 Score=26.17 Aligned_cols=32 Identities=13% Similarity=0.120 Sum_probs=29.3
Q ss_pred cccHHHHHHHhCCCChHHHHHHHHHhHHcCceE
Q psy9642 321 TLSLADVASRVQLGTPVQAEIYILKMISQNEIY 353 (437)
Q Consensus 321 ~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~ 353 (437)
.++..+||+.++++ ...+.+.+..|.+.|.|.
T Consensus 8 ~~s~~~la~~l~~s-~~tv~~~l~~L~~~g~l~ 39 (48)
T smart00419 8 PLTRQEIAELLGLT-RETVSRTLKRLEKEGLIS 39 (48)
T ss_pred ccCHHHHHHHHCCC-HHHHHHHHHHHHHCCCEE
Confidence 47899999999997 789999999999999985
No 96
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=69.28 E-value=25 Score=35.32 Aligned_cols=92 Identities=9% Similarity=0.082 Sum_probs=56.6
Q ss_pred hCCCCcchHHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHH
Q psy9642 119 LKTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYL 198 (437)
Q Consensus 119 ~~~~~~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~ 198 (437)
.+..-.++..+..++.. +| .-...+..++.++...++|..|+...++-+.. .+.. .......|++..|.++.
T Consensus 120 ~g~~~~A~~~~~~~l~~-~~---~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~-~~~~---~~~~~~~~~~~la~~~~ 191 (389)
T PRK11788 120 AGLLDRAEELFLQLVDE-GD---FAEGALQQLLEIYQQEKDWQKAIDVAERLEKL-GGDS---LRVEIAHFYCELAQQAL 191 (389)
T ss_pred CCCHHHHHHHHHHHHcC-Cc---chHHHHHHHHHHHHHhchHHHHHHHHHHHHHh-cCCc---chHHHHHHHHHHHHHHH
Confidence 34444556666665432 22 22345677788888888888888887775542 1110 11123344555677777
Q ss_pred HHhhHHHHHHHHHHHhc-ccc
Q psy9642 199 ALKNYERALYFFEVIIT-TPA 218 (437)
Q Consensus 199 ~~k~y~~A~~~~~~ai~-~P~ 218 (437)
..+++.+|..+|..++. .|.
T Consensus 192 ~~~~~~~A~~~~~~al~~~p~ 212 (389)
T PRK11788 192 ARGDLDAARALLKKALAADPQ 212 (389)
T ss_pred hCCCHHHHHHHHHHHHhHCcC
Confidence 78888888888888887 454
No 97
>TIGR00990 3a0801s09 mitochondrial precursor proteins import receptor (72 kDa mitochondrial outermembrane protein) (mitochondrial import receptor for the ADP/ATP carrier) (translocase of outermembrane tom70).
Probab=69.27 E-value=20 Score=39.22 Aligned_cols=88 Identities=11% Similarity=0.071 Sum_probs=64.9
Q ss_pred hCCCCcchHHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHH
Q psy9642 119 LKTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYL 198 (437)
Q Consensus 119 ~~~~~~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~ 198 (437)
.+.+-.++..+..++.. +|. ....+..+..++...++|..|+..+++-+.. . + +....+|..|.++.
T Consensus 344 ~g~~~eA~~~~~kal~l-~P~---~~~~~~~la~~~~~~g~~~eA~~~~~~al~~-~-------p-~~~~~~~~lg~~~~ 410 (615)
T TIGR00990 344 KGKHLEALADLSKSIEL-DPR---VTQSYIKRASMNLELGDPDKAEEDFDKALKL-N-------S-EDPDIYYHRAQLHF 410 (615)
T ss_pred cCCHHHHHHHHHHHHHc-CCC---cHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh-C-------C-CCHHHHHHHHHHHH
Confidence 45555677777776543 442 3346777788888999999999988876542 1 1 13456788899999
Q ss_pred HHhhHHHHHHHHHHHhc-cccc
Q psy9642 199 ALKNYERALYFFEVIIT-TPAL 219 (437)
Q Consensus 199 ~~k~y~~A~~~~~~ai~-~P~~ 219 (437)
..++|.+|..+|+.++. .|..
T Consensus 411 ~~g~~~~A~~~~~kal~l~P~~ 432 (615)
T TIGR00990 411 IKGEFAQAGKDYQKSIDLDPDF 432 (615)
T ss_pred HcCCHHHHHHHHHHHHHcCccC
Confidence 99999999999999998 6654
No 98
>PLN03077 Protein ECB2; Provisional
Probab=69.24 E-value=2.1e+02 Score=32.61 Aligned_cols=53 Identities=13% Similarity=0.060 Sum_probs=28.8
Q ss_pred HHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHH--HhhHHHHHHHHHHHhc
Q psy9642 149 DLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLA--LKNYERALYFFEVIIT 215 (437)
Q Consensus 149 ~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~--~k~y~~A~~~~~~ai~ 215 (437)
.++..+...+++..|..+.+.-. ..+... |..||... .+++.+|.+.|.....
T Consensus 227 ~Li~~y~k~g~~~~A~~lf~~m~-----------~~d~~s---~n~li~~~~~~g~~~eAl~lf~~M~~ 281 (857)
T PLN03077 227 ALITMYVKCGDVVSARLVFDRMP-----------RRDCIS---WNAMISGYFENGECLEGLELFFTMRE 281 (857)
T ss_pred HHHHHHhcCCCHHHHHHHHhcCC-----------CCCcch---hHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 34455556666666655554421 011111 34444433 3688888888888766
No 99
>PRK10049 pgaA outer membrane protein PgaA; Provisional
Probab=69.01 E-value=31 Score=38.94 Aligned_cols=93 Identities=8% Similarity=-0.030 Sum_probs=68.3
Q ss_pred HHhhhCCCCcchHHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHH
Q psy9642 115 TVMDLKTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGG 194 (437)
Q Consensus 115 ~~~~~~~~~~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G 194 (437)
.+...+..-.++..+..++... |.. ..++..+..+....+.+..|+..+++-+.. .| +...+.|..|
T Consensus 368 ~l~~~g~~~eA~~~l~~al~~~-P~n---~~l~~~lA~l~~~~g~~~~A~~~l~~al~l--------~P-d~~~l~~~~a 434 (765)
T PRK10049 368 VAKYSNDLPQAEMRARELAYNA-PGN---QGLRIDYASVLQARGWPRAAENELKKAEVL--------EP-RNINLEVEQA 434 (765)
T ss_pred HHHHcCCHHHHHHHHHHHHHhC-CCC---HHHHHHHHHHHHhcCCHHHHHHHHHHHHhh--------CC-CChHHHHHHH
Confidence 3334555566677777775543 433 347888888888999999999888876552 12 3555788999
Q ss_pred HHHHHHhhHHHHHHHHHHHhc-ccccc
Q psy9642 195 MIYLALKNYERALYFFEVIIT-TPALA 220 (437)
Q Consensus 195 ~I~~~~k~y~~A~~~~~~ai~-~P~~~ 220 (437)
+++...++|.+|...+..++. .|...
T Consensus 435 ~~al~~~~~~~A~~~~~~ll~~~Pd~~ 461 (765)
T PRK10049 435 WTALDLQEWRQMDVLTDDVVAREPQDP 461 (765)
T ss_pred HHHHHhCCHHHHHHHHHHHHHhCCCCH
Confidence 999999999999999999998 67654
No 100
>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=68.53 E-value=11 Score=32.73 Aligned_cols=62 Identities=11% Similarity=0.145 Sum_probs=46.0
Q ss_pred cccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCCCEEEEccCCCCCCchHHHHHHHHH
Q psy9642 321 TLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVFNDNPQRFNNPLTFAQIESN 384 (437)
Q Consensus 321 ~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~g~v~F~~~~~~~~~~e~~~~l~~~ 384 (437)
.++.++||+.++++ ...+++++.+|...|-|..+=- +.|-.....+++..+-.++.+.++..
T Consensus 25 ~~s~~~ia~~~~ip-~~~l~kil~~L~~~glv~s~~G-~~Ggy~l~~~~~~Itl~dv~~a~eg~ 86 (135)
T TIGR02010 25 PVTLADISERQGIS-LSYLEQLFAKLRKAGLVKSVRG-PGGGYQLGRPAEDISVADIIDAVDES 86 (135)
T ss_pred cCcHHHHHHHHCcC-HHHHHHHHHHHHHCCceEEEeC-CCCCEeccCCHHHCcHHHHHHHhCCC
Confidence 59999999999998 8999999999999999876433 34445566666555555555555443
No 101
>PF13428 TPR_14: Tetratricopeptide repeat
Probab=68.39 E-value=7.5 Score=26.63 Aligned_cols=30 Identities=13% Similarity=0.110 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHhhHHHHHHHHHHHhc-cccc
Q psy9642 190 FYYGGMIYLALKNYERALYFFEVIIT-TPAL 219 (437)
Q Consensus 190 ~Yy~G~I~~~~k~y~~A~~~~~~ai~-~P~~ 219 (437)
++.-|..|..++++++|...|+.++. .|..
T Consensus 4 ~~~la~~~~~~G~~~~A~~~~~~~l~~~P~~ 34 (44)
T PF13428_consen 4 WLALARAYRRLGQPDEAERLLRRALALDPDD 34 (44)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHHCcCC
Confidence 35668899999999999999999999 8876
No 102
>PF12688 TPR_5: Tetratrico peptide repeat
Probab=68.17 E-value=39 Score=28.92 Aligned_cols=96 Identities=15% Similarity=0.174 Sum_probs=67.2
Q ss_pred HHHHhhhCCCCcchHHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHH
Q psy9642 113 TKTVMDLKTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYY 192 (437)
Q Consensus 113 ~~~~~~~~~~~~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy 192 (437)
.......+.+-.+|...+.|+.. ..++....-.-..+....-.-|.++.|+.++...+..+... +...-++ +.
T Consensus 8 A~a~d~~G~~~~Ai~~Y~~Al~~-gL~~~~~~~a~i~lastlr~LG~~deA~~~L~~~~~~~p~~----~~~~~l~--~f 80 (120)
T PF12688_consen 8 AWAHDSLGREEEAIPLYRRALAA-GLSGADRRRALIQLASTLRNLGRYDEALALLEEALEEFPDD----ELNAALR--VF 80 (120)
T ss_pred HHHHHhcCCHHHHHHHHHHHHHc-CCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCc----cccHHHH--HH
Confidence 34455578888999999999774 34444444344445566677789999999999887653221 1123444 45
Q ss_pred HHHHHHHHhhHHHHHHHHHHHhc
Q psy9642 193 GGMIYLALKNYERALYFFEVIIT 215 (437)
Q Consensus 193 ~G~I~~~~k~y~~A~~~~~~ai~ 215 (437)
.+|.....+++++|.+++..++.
T Consensus 81 ~Al~L~~~gr~~eAl~~~l~~la 103 (120)
T PF12688_consen 81 LALALYNLGRPKEALEWLLEALA 103 (120)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHH
Confidence 67899999999999999988775
No 103
>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF. Members of this protein family are the product of one of seven genes regularly clustered in operons to encode the proteins of the tol-pal system, which is critical for maintaining the integrity of the bacterial outer membrane. The gene for this periplasmic protein has been designated orf2 and ybgF. All members of the seed alignment were from unique tol-pal gene regions from completed bacterial genomes. The architecture of this protein is a signal sequence, a low-complexity region usually rich in Asn and Gln, a well-conserved region with tandem repeats that resemble the tetratricopeptide (TPR) repeat, involved in protein-protein interaction.
Probab=67.49 E-value=22 Score=28.70 Aligned_cols=65 Identities=22% Similarity=0.326 Sum_probs=47.6
Q ss_pred HHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhc-cccc
Q psy9642 149 DLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIIT-TPAL 219 (437)
Q Consensus 149 ~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~-~P~~ 219 (437)
.++...+..++|..|...+..-+..... ......-.|.-|.++...++|.+|..+|..++. .|..
T Consensus 7 ~~~~~~~~~~~~~~A~~~~~~~~~~~~~------~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~ 72 (119)
T TIGR02795 7 DAALLVLKAGDYADAIQAFQAFLKKYPK------STYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKS 72 (119)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHHCCC------ccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCC
Confidence 4556678889999999888776643111 111233456789999999999999999999998 6654
No 104
>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional
Probab=67.42 E-value=22 Score=41.54 Aligned_cols=82 Identities=11% Similarity=0.070 Sum_probs=38.5
Q ss_pred CCCCcchHHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHH
Q psy9642 120 KTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLA 199 (437)
Q Consensus 120 ~~~~~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~ 199 (437)
+.+-.++..++.|+ +++|+ ...+..+..++...+.+..|+..+.+-+.. +| +...+++.-|+++..
T Consensus 590 Gr~~eAl~~~~~AL-~l~P~----~~a~~~LA~~l~~lG~~deA~~~l~~AL~l--------~P-d~~~a~~nLG~aL~~ 655 (987)
T PRK09782 590 GQPELALNDLTRSL-NIAPS----ANAYVARATIYRQRHNVPAAVSDLRAALEL--------EP-NNSNYQAALGYALWD 655 (987)
T ss_pred CCHHHHHHHHHHHH-HhCCC----HHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--------CC-CCHHHHHHHHHHHHH
Confidence 34444555555554 23342 234555556666666666666655554331 11 122333444444444
Q ss_pred HhhHHHHHHHHHHHhc
Q psy9642 200 LKNYERALYFFEVIIT 215 (437)
Q Consensus 200 ~k~y~~A~~~~~~ai~ 215 (437)
.+++++|..+|+.++.
T Consensus 656 ~G~~eeAi~~l~~AL~ 671 (987)
T PRK09782 656 SGDIAQSREMLERAHK 671 (987)
T ss_pred CCCHHHHHHHHHHHHH
Confidence 4444444444444444
No 105
>PRK15174 Vi polysaccharide export protein VexE; Provisional
Probab=67.25 E-value=36 Score=37.71 Aligned_cols=88 Identities=13% Similarity=0.101 Sum_probs=49.9
Q ss_pred hCCCCcchHHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHH
Q psy9642 119 LKTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYL 198 (437)
Q Consensus 119 ~~~~~~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~ 198 (437)
.+..-.++..++.++. ++|... ..+..+.......++|..|+..+.+-+.. ++. ...+.++.|.++.
T Consensus 297 ~g~~~eA~~~l~~al~-l~P~~~---~a~~~La~~l~~~G~~~eA~~~l~~al~~--------~P~-~~~~~~~~a~al~ 363 (656)
T PRK15174 297 TGQNEKAIPLLQQSLA-THPDLP---YVRAMYARALRQVGQYTAASDEFVQLARE--------KGV-TSKWNRYAAAALL 363 (656)
T ss_pred CCCHHHHHHHHHHHHH-hCCCCH---HHHHHHHHHHHHCCCHHHHHHHHHHHHHh--------Ccc-chHHHHHHHHHHH
Confidence 3444445555555443 333321 23445556666666666666665543321 121 2345555677777
Q ss_pred HHhhHHHHHHHHHHHhc-cccc
Q psy9642 199 ALKNYERALYFFEVIIT-TPAL 219 (437)
Q Consensus 199 ~~k~y~~A~~~~~~ai~-~P~~ 219 (437)
..+++++|..+|..++. .|..
T Consensus 364 ~~G~~deA~~~l~~al~~~P~~ 385 (656)
T PRK15174 364 QAGKTSEAESVFEHYIQARASH 385 (656)
T ss_pred HCCCHHHHHHHHHHHHHhChhh
Confidence 88888888888888887 5654
No 106
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=66.70 E-value=18 Score=29.79 Aligned_cols=35 Identities=23% Similarity=0.294 Sum_probs=31.8
Q ss_pred hhccccHHHHHHHhCCCChHHHHHHHHHhHHcCceE
Q psy9642 318 TFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIY 353 (437)
Q Consensus 318 ~Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~ 353 (437)
.-.+++.++||+.+|++ +..+-..+.+|..+|.|.
T Consensus 14 ~~~~~~~~~la~~l~~s-~~tv~~~l~~L~~~g~i~ 48 (108)
T smart00344 14 KDARISLAELAKKVGLS-PSTVHNRVKRLEEEGVIK 48 (108)
T ss_pred HhCCCCHHHHHHHHCcC-HHHHHHHHHHHHHCCCee
Confidence 34689999999999998 789999999999999886
No 107
>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=66.59 E-value=34 Score=25.10 Aligned_cols=45 Identities=13% Similarity=0.181 Sum_probs=37.1
Q ss_pred ccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCCCEEEEcc
Q psy9642 322 LSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVFND 367 (437)
Q Consensus 322 IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~g~v~F~~ 367 (437)
++.++|++.++++ ...+...+..|...|.|.+.-+...+...+.+
T Consensus 21 ~~~~ei~~~~~i~-~~~i~~~l~~L~~~g~i~~~~~~~~~~~~~~~ 65 (78)
T cd00090 21 LTVSELAERLGLS-QSTVSRHLKKLEEAGLVESRREGRRVYYSLTD 65 (78)
T ss_pred cCHHHHHHHHCcC-HhHHHHHHHHHHHCCCeEEEEeccEEEEEeCC
Confidence 9999999999997 78899999999999999987765445544443
No 108
>TIGR02917 PEP_TPR_lipo putative PEP-CTERM system TPR-repeat lipoprotein. This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.
Probab=66.30 E-value=85 Score=34.58 Aligned_cols=125 Identities=18% Similarity=0.175 Sum_probs=74.8
Q ss_pred cHHHHHHHHHHHHHhcChhhhhhh--------H---HHHHHHHHHHHHHHhhhCCCCcchHHHHHHHHHhCCCCcchhhH
Q psy9642 78 YQEELFSQIQEFLNMCNPDQIRHA--------G---DLYAELSHQYTKTVMDLKTPQRGIPLIQTAIKKIQTSDSQLTSL 146 (437)
Q Consensus 78 ~~~~~~~~~~~fl~~fd~~Qir~a--------~---~~~~~l~~~~~~~~~~~~~~~~~i~~l~~ai~rl~~~~~~lT~~ 146 (437)
.....+.....++..-+.....-. | ..++.++ ......+....++..+..++.. .|.+ ...
T Consensus 21 ~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~l~----~~~~~~g~~~~A~~~~~~~~~~-~~~~---~~~ 92 (899)
T TIGR02917 21 SPESLIEAAKSYLQKNKYKAAIIQLKNALQKDPNDAEARFLLG----KIYLALGDYAAAEKELRKALSL-GYPK---NQV 92 (899)
T ss_pred CHHHHHHHHHHHHHcCChHhHHHHHHHHHHhCCCCHHHHHHHH----HHHHHcCCHHHHHHHHHHHHHc-CCCh---hhh
Confidence 445566677777766555443211 1 1222222 2223345555677777776543 3332 234
Q ss_pred HHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhc-ccc
Q psy9642 147 HSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIIT-TPA 218 (437)
Q Consensus 147 h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~-~P~ 218 (437)
+..+.+.....++|..|+..+..-. ..+.......++..|.++...++|.+|..+|..++. .|.
T Consensus 93 ~~~~a~~~~~~g~~~~a~~~~~~~~--------~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~ 157 (899)
T TIGR02917 93 LPLLARAYLLQGKFQQVLDELPGKT--------LLDDEGAAELLALRGLAYLGLGQLELAQKSYEQALAIDPR 157 (899)
T ss_pred HHHHHHHHHHCCCHHHHHHhhcccc--------cCCchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCC
Confidence 5667778888888888877664321 112334566677888888888888888888888887 554
No 109
>TIGR00540 hemY_coli hemY protein. This is an uncharacterized protein encoded next to a heme-biosynthetic enzyme in two gamma division proteobacteria (E. coli and H. influenzae). It is known in no other species. The gene symbol hemY is unfortunate in that an unrelated protein, protoporphyrinogen oxidase, is designated as HemG in E. coli but as HemY in Bacillus subtilis.
Probab=65.77 E-value=33 Score=35.51 Aligned_cols=94 Identities=10% Similarity=0.060 Sum_probs=51.7
Q ss_pred HHhhhCCCCcchHHHHHHHHHhCCCCcchhhHHHHHHHH-HHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHH
Q psy9642 115 TVMDLKTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQL-CLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYG 193 (437)
Q Consensus 115 ~~~~~~~~~~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l-~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~ 193 (437)
.+...+.+-.++..+..++.+..+ +.... +..+.+. .+..++...++..+++-... .+-++ .+.+...-
T Consensus 272 ~l~~~g~~~~A~~~l~~~l~~~pd-~~~~~--~~~l~~~~~l~~~~~~~~~~~~e~~lk~-----~p~~~--~~~ll~sL 341 (409)
T TIGR00540 272 HLIDCDDHDSAQEIIFDGLKKLGD-DRAIS--LPLCLPIPRLKPEDNEKLEKLIEKQAKN-----VDDKP--KCCINRAL 341 (409)
T ss_pred HHHHCCChHHHHHHHHHHHhhCCC-cccch--hHHHHHhhhcCCCChHHHHHHHHHHHHh-----CCCCh--hHHHHHHH
Confidence 344455566666666666665432 22111 1111111 12234455555555443321 01111 14677788
Q ss_pred HHHHHHHhhHHHHHHHHH--HHhc-ccc
Q psy9642 194 GMIYLALKNYERALYFFE--VIIT-TPA 218 (437)
Q Consensus 194 G~I~~~~k~y~~A~~~~~--~ai~-~P~ 218 (437)
|.+++..++|.+|.++|+ .++. .|.
T Consensus 342 g~l~~~~~~~~~A~~~le~a~a~~~~p~ 369 (409)
T TIGR00540 342 GQLLMKHGEFIEAADAFKNVAACKEQLD 369 (409)
T ss_pred HHHHHHcccHHHHHHHHHHhHHhhcCCC
Confidence 999999999999999999 5776 564
No 110
>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=65.68 E-value=31 Score=25.38 Aligned_cols=47 Identities=13% Similarity=0.136 Sum_probs=38.1
Q ss_pred HHHHHHHHHHhhccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEE
Q psy9642 308 YKNNIKRLTKTFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYAT 355 (437)
Q Consensus 308 ~r~~I~~l~k~Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~ 355 (437)
.|..|.+.-..-...+..+||+.++++ ...+-.++..|.+.|.|...
T Consensus 11 ~R~~Il~~L~~~~~~t~~ela~~l~~~-~~t~s~hL~~L~~aGli~~~ 57 (61)
T PF12840_consen 11 TRLRILRLLASNGPMTVSELAEELGIS-QSTVSYHLKKLEEAGLIEVE 57 (61)
T ss_dssp HHHHHHHHHHHCSTBEHHHHHHHHTS--HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHHCCC-HHHHHHHHHHHHHCCCeEEe
Confidence 455555555677899999999999998 78899999999999988754
No 111
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=65.54 E-value=13 Score=24.39 Aligned_cols=31 Identities=19% Similarity=0.186 Sum_probs=25.0
Q ss_pred cccHHHHHHHhCCCChHHHHHHHHHhHHcCce
Q psy9642 321 TLSLADVASRVQLGTPVQAEIYILKMISQNEI 352 (437)
Q Consensus 321 ~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I 352 (437)
.++-.|||..+|++ .+-+-+.+.++-.+|.|
T Consensus 2 ~mtr~diA~~lG~t-~ETVSR~l~~l~~~glI 32 (32)
T PF00325_consen 2 PMTRQDIADYLGLT-RETVSRILKKLERQGLI 32 (32)
T ss_dssp E--HHHHHHHHTS--HHHHHHHHHHHHHTTSE
T ss_pred CcCHHHHHHHhCCc-HHHHHHHHHHHHHcCCC
Confidence 36778999999998 88899999999999876
No 112
>cd05804 StaR_like StaR_like; a well-conserved protein found in bacteria, plants, and animals. A family member from Streptomyces toyocaensis, StaR is part of a gene cluster involved in the biosynthesis of glycopeptide antibiotics (GPAs), specifically A47934. It has been speculated that StaR could be a flavoprotein hydroxylating a tyrosine sidechain. Some family members have been annotated as proteins containing tetratricopeptide (TPR) repeats, which may at least indicate mostly alpha-helical secondary structure.
Probab=65.22 E-value=84 Score=31.08 Aligned_cols=89 Identities=16% Similarity=0.215 Sum_probs=61.1
Q ss_pred hhCCCCcchHHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHH
Q psy9642 118 DLKTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIY 197 (437)
Q Consensus 118 ~~~~~~~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~ 197 (437)
..+..-.++..++.++.. .|.. ...|..+..++...+.++.|...+++-+..... ++......++.-|.++
T Consensus 126 ~~G~~~~A~~~~~~al~~-~p~~---~~~~~~la~i~~~~g~~~eA~~~l~~~l~~~~~-----~~~~~~~~~~~la~~~ 196 (355)
T cd05804 126 EAGQYDRAEEAARRALEL-NPDD---AWAVHAVAHVLEMQGRFKEGIAFMESWRDTWDC-----SSMLRGHNWWHLALFY 196 (355)
T ss_pred HcCCHHHHHHHHHHHHhh-CCCC---cHHHHHHHHHHHHcCCHHHHHHHHHhhhhccCC-----CcchhHHHHHHHHHHH
Confidence 345555677777777665 3433 235677788889999999998888776542111 1222334556778889
Q ss_pred HHHhhHHHHHHHHHHHhc
Q psy9642 198 LALKNYERALYFFEVIIT 215 (437)
Q Consensus 198 ~~~k~y~~A~~~~~~ai~ 215 (437)
..++++++|...|..++.
T Consensus 197 ~~~G~~~~A~~~~~~~~~ 214 (355)
T cd05804 197 LERGDYEAALAIYDTHIA 214 (355)
T ss_pred HHCCCHHHHHHHHHHHhc
Confidence 999999999999999875
No 113
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=65.05 E-value=17 Score=27.57 Aligned_cols=35 Identities=20% Similarity=0.226 Sum_probs=30.4
Q ss_pred hccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEE
Q psy9642 319 FLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYA 354 (437)
Q Consensus 319 Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A 354 (437)
..-++-.|||+.+|++ .-.|..+|..+..+|.|.-
T Consensus 13 ~~p~~T~eiA~~~gls-~~~aR~yL~~Le~eG~V~~ 47 (62)
T PF04703_consen 13 NGPLKTREIADALGLS-IYQARYYLEKLEKEGKVER 47 (62)
T ss_dssp TS-EEHHHHHHHHTS--HHHHHHHHHHHHHCTSEEE
T ss_pred CCCCCHHHHHHHhCCC-HHHHHHHHHHHHHCCCEEE
Confidence 6779999999999998 7899999999999999853
No 114
>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=64.90 E-value=92 Score=26.87 Aligned_cols=69 Identities=14% Similarity=0.066 Sum_probs=49.6
Q ss_pred CCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHH
Q psy9642 138 TSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEV 212 (437)
Q Consensus 138 ~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ 212 (437)
|++..-......+.+.+...++|..|...+..-+..- -++.-.-.-.+.-+.|++..++|.+|...+..
T Consensus 42 ~~s~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~------~d~~l~~~a~l~LA~~~~~~~~~d~Al~~L~~ 110 (145)
T PF09976_consen 42 PSSPYAALAALQLAKAAYEQGDYDEAKAALEKALANA------PDPELKPLARLRLARILLQQGQYDEALATLQQ 110 (145)
T ss_pred CCChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhC------CCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHh
Confidence 4443445566778899999999999999988866531 12222222344678999999999999999966
No 115
>PRK11189 lipoprotein NlpI; Provisional
Probab=64.86 E-value=48 Score=32.63 Aligned_cols=25 Identities=8% Similarity=-0.173 Sum_probs=12.4
Q ss_pred HHHHHHHHHHhCCchHHHhhhhHhh
Q psy9642 147 HSDLCQLCLLAQNFKPALEFLDVDI 171 (437)
Q Consensus 147 h~~l~~l~L~~~~y~~Al~il~~~I 171 (437)
+..+..+....+.|..|+..+++-+
T Consensus 135 ~~~lg~~l~~~g~~~eA~~~~~~al 159 (296)
T PRK11189 135 YLNRGIALYYGGRYELAQDDLLAFY 159 (296)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3344444445555555555555543
No 116
>PRK11906 transcriptional regulator; Provisional
Probab=64.84 E-value=99 Score=32.78 Aligned_cols=73 Identities=15% Similarity=0.220 Sum_probs=55.3
Q ss_pred HhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHh
Q psy9642 135 KIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVII 214 (437)
Q Consensus 135 rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai 214 (437)
.++|.... .|..+..+....+.+..|...+++-.. ++|+ ...-+||+|.+....++.++|.++++.|+
T Consensus 332 eld~~Da~---a~~~~g~~~~~~~~~~~a~~~f~rA~~--------L~Pn-~A~~~~~~~~~~~~~G~~~~a~~~i~~al 399 (458)
T PRK11906 332 DITTVDGK---ILAIMGLITGLSGQAKVSHILFEQAKI--------HSTD-IASLYYYRALVHFHNEKIEEARICIDKSL 399 (458)
T ss_pred hcCCCCHH---HHHHHHHHHHhhcchhhHHHHHHHHhh--------cCCc-cHHHHHHHHHHHHHcCCHHHHHHHHHHHh
Confidence 35665433 455555655666679999998888765 2333 66677899999999999999999999999
Q ss_pred c-cccc
Q psy9642 215 T-TPAL 219 (437)
Q Consensus 215 ~-~P~~ 219 (437)
+ .|..
T Consensus 400 rLsP~~ 405 (458)
T PRK11906 400 QLEPRR 405 (458)
T ss_pred ccCchh
Confidence 9 7875
No 117
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=64.76 E-value=19 Score=25.68 Aligned_cols=43 Identities=12% Similarity=0.044 Sum_probs=34.4
Q ss_pred ccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCCCEE
Q psy9642 320 LTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMV 363 (437)
Q Consensus 320 s~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~g~v 363 (437)
..+++.+|++.++++ ...+...+..|...|.|...-+...++.
T Consensus 9 ~~~~~~~i~~~l~is-~~~v~~~l~~L~~~g~i~~~~~~~~~~~ 51 (66)
T smart00418 9 GELCVCELAEILGLS-QSTVSHHLKKLREAGLVESRREGKRVYY 51 (66)
T ss_pred CCccHHHHHHHHCCC-HHHHHHHHHHHHHCCCeeeeecCCEEEE
Confidence 568999999999997 6889999999999999986544333333
No 118
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=63.78 E-value=27 Score=27.77 Aligned_cols=51 Identities=10% Similarity=0.120 Sum_probs=40.6
Q ss_pred HHHHHHhhccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCCCEE
Q psy9642 312 IKRLTKTFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMV 363 (437)
Q Consensus 312 I~~l~k~Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~g~v 363 (437)
||..-.-+-+.++.+|+..++.+ ++-+|.++..++..|.|.-.-..+.|+.
T Consensus 7 lRd~l~~~gr~s~~~Ls~~~~~p-~~~VeaMLe~l~~kGkverv~~~~~gC~ 57 (78)
T PRK15431 7 VRDLLALRGRMEAAQISQTLNTP-QPMINAMLQQLESMGKAVRIQEEPDGCL 57 (78)
T ss_pred HHHHHHHcCcccHHHHHHHHCcC-HHHHHHHHHHHHHCCCeEeeccCCCCCC
Confidence 45555667899999999999998 8999999999999999876542334444
No 119
>KOG2076|consensus
Probab=63.65 E-value=22 Score=40.25 Aligned_cols=66 Identities=24% Similarity=0.289 Sum_probs=53.1
Q ss_pred HHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhc-cccc
Q psy9642 146 LHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIIT-TPAL 219 (437)
Q Consensus 146 ~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~-~P~~ 219 (437)
+..+++++....+.|+.|+++++.-+..- ..+..-++|--|.+|+.++.|++|.++|+.|+. .|..
T Consensus 416 L~~d~a~al~~~~~~~~Al~~l~~i~~~~--------~~~~~~vw~~~a~c~~~l~e~e~A~e~y~kvl~~~p~~ 482 (895)
T KOG2076|consen 416 LYLDLADALTNIGKYKEALRLLSPITNRE--------GYQNAFVWYKLARCYMELGEYEEAIEFYEKVLILAPDN 482 (895)
T ss_pred HHHHHHHHHHhcccHHHHHHHHHHHhcCc--------cccchhhhHHHHHHHHHHhhHHHHHHHHHHHHhcCCCc
Confidence 55567788899999999999988765431 112356788899999999999999999999998 8875
No 120
>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=63.57 E-value=12 Score=26.74 Aligned_cols=37 Identities=11% Similarity=0.170 Sum_probs=30.3
Q ss_pred HHhhccccHHHHHHHhCCCChHHHHHHHHHhHHcCceE
Q psy9642 316 TKTFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIY 353 (437)
Q Consensus 316 ~k~Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~ 353 (437)
+..=..+++++||+.+|++ ...+-+++..|...|.+.
T Consensus 13 ~~~~~~~t~~eia~~~gl~-~stv~r~L~tL~~~g~v~ 49 (52)
T PF09339_consen 13 AESGGPLTLSEIARALGLP-KSTVHRLLQTLVEEGYVE 49 (52)
T ss_dssp HCTBSCEEHHHHHHHHTS--HHHHHHHHHHHHHTTSEE
T ss_pred HcCCCCCCHHHHHHHHCcC-HHHHHHHHHHHHHCcCee
Confidence 3344458999999999998 789999999999999764
No 121
>PF13429 TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2_B.
Probab=62.85 E-value=15 Score=35.56 Aligned_cols=90 Identities=18% Similarity=0.192 Sum_probs=44.8
Q ss_pred hhCCCCcchHHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHH
Q psy9642 118 DLKTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIY 197 (437)
Q Consensus 118 ~~~~~~~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~ 197 (437)
..+.|..++..+..+..+. +++..+. ..+.++...+++..+..+++.-... . ...+...+++..|.++
T Consensus 89 ~~~~~~~A~~~~~~~~~~~-~~~~~l~----~~l~~~~~~~~~~~~~~~l~~~~~~-----~--~~~~~~~~~~~~a~~~ 156 (280)
T PF13429_consen 89 QDGDPEEALKLAEKAYERD-GDPRYLL----SALQLYYRLGDYDEAEELLEKLEEL-----P--AAPDSARFWLALAEIY 156 (280)
T ss_dssp ----------------------------------H-HHHTT-HHHHHHHHHHHHH------T-----T-HHHHHHHHHHH
T ss_pred ccccccccccccccccccc-cccchhh----HHHHHHHHHhHHHHHHHHHHHHHhc-----c--CCCCCHHHHHHHHHHH
Confidence 3566777777777776654 4444443 3557788899999998888874321 1 1235677888999999
Q ss_pred HHHhhHHHHHHHHHHHhc-cccc
Q psy9642 198 LALKNYERALYFFEVIIT-TPAL 219 (437)
Q Consensus 198 ~~~k~y~~A~~~~~~ai~-~P~~ 219 (437)
...+++.+|.++|+.++. .|..
T Consensus 157 ~~~G~~~~A~~~~~~al~~~P~~ 179 (280)
T PF13429_consen 157 EQLGDPDKALRDYRKALELDPDD 179 (280)
T ss_dssp HHCCHHHHHHHHHHHHHHH-TT-
T ss_pred HHcCCHHHHHHHHHHHHHcCCCC
Confidence 999999999999999999 8874
No 122
>TIGR00990 3a0801s09 mitochondrial precursor proteins import receptor (72 kDa mitochondrial outermembrane protein) (mitochondrial import receptor for the ADP/ATP carrier) (translocase of outermembrane tom70).
Probab=62.84 E-value=25 Score=38.46 Aligned_cols=88 Identities=17% Similarity=0.194 Sum_probs=54.5
Q ss_pred hhCCCCcchHHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHH
Q psy9642 118 DLKTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIY 197 (437)
Q Consensus 118 ~~~~~~~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~ 197 (437)
..+..-.++..+..++. ++|.. ..++..+..++...++|..|+..+.+-+.. .+ +....++..|.++
T Consensus 377 ~~g~~~eA~~~~~~al~-~~p~~---~~~~~~lg~~~~~~g~~~~A~~~~~kal~l--------~P-~~~~~~~~la~~~ 443 (615)
T TIGR00990 377 ELGDPDKAEEDFDKALK-LNSED---PDIYYHRAQLHFIKGEFAQAGKDYQKSIDL--------DP-DFIFSHIQLGVTQ 443 (615)
T ss_pred HCCCHHHHHHHHHHHHH-hCCCC---HHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--------Cc-cCHHHHHHHHHHH
Confidence 34555566667776644 34432 235666777788888888888877765542 11 1233345566777
Q ss_pred HHHhhHHHHHHHHHHHhc-ccc
Q psy9642 198 LALKNYERALYFFEVIIT-TPA 218 (437)
Q Consensus 198 ~~~k~y~~A~~~~~~ai~-~P~ 218 (437)
..+++|.+|...|..++. .|.
T Consensus 444 ~~~g~~~eA~~~~~~al~~~P~ 465 (615)
T TIGR00990 444 YKEGSIASSMATFRRCKKNFPE 465 (615)
T ss_pred HHCCCHHHHHHHHHHHHHhCCC
Confidence 777777777777777776 454
No 123
>CHL00033 ycf3 photosystem I assembly protein Ycf3
Probab=62.56 E-value=35 Score=30.23 Aligned_cols=68 Identities=12% Similarity=-0.041 Sum_probs=51.3
Q ss_pred hhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhcc
Q psy9642 143 LTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIITT 216 (437)
Q Consensus 143 lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~~ 216 (437)
-...+.....++...+.|..|+..+.+-+... . ++.+...-++.-|.++...+++.+|..+|+.++..
T Consensus 34 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~l~-~-----~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~ 101 (168)
T CHL00033 34 EAFTYYRDGMSAQSEGEYAEALQNYYEAMRLE-I-----DPYDRSYILYNIGLIHTSNGEHTKALEYYFQALER 101 (168)
T ss_pred HHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcc-c-----cchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence 34466777888889999999999888765421 1 12223345577899999999999999999999984
No 124
>PRK10803 tol-pal system protein YbgF; Provisional
Probab=62.44 E-value=32 Score=33.65 Aligned_cols=62 Identities=15% Similarity=0.207 Sum_probs=45.8
Q ss_pred HHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhc-cccc
Q psy9642 152 QLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIIT-TPAL 219 (437)
Q Consensus 152 ~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~-~P~~ 219 (437)
.+.+..++|..|+..+..=+.....+ ...-.-+|+-|.+|...++|.+|..+|..++. .|..
T Consensus 151 ~l~~~~~~y~~Ai~af~~fl~~yP~s------~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~s 213 (263)
T PRK10803 151 ALVQDKSRQDDAIVAFQNFVKKYPDS------TYQPNANYWLGQLNYNKGKKDDAAYYFASVVKNYPKS 213 (263)
T ss_pred HHHHhcCCHHHHHHHHHHHHHHCcCC------cchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCC
Confidence 34455789999988877766543321 11223457999999999999999999999998 6754
No 125
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=62.40 E-value=21 Score=33.95 Aligned_cols=49 Identities=12% Similarity=0.165 Sum_probs=41.4
Q ss_pred HHHHHHHHHhhccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEec
Q psy9642 309 KNNIKRLTKTFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINK 358 (437)
Q Consensus 309 r~~I~~l~k~Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~ 358 (437)
|..|..+-+-=..+|..+||+.||++ ...|..++.+++.+|.+....-+
T Consensus 13 r~~il~lL~~~g~~sa~elA~~Lgis-~~avR~HL~~Le~~Glv~~~~~~ 61 (218)
T COG2345 13 RERILELLKKSGPVSADELAEELGIS-PMAVRRHLDDLEAEGLVEVERQQ 61 (218)
T ss_pred HHHHHHHHhccCCccHHHHHHHhCCC-HHHHHHHHHHHHhCcceeeeecc
Confidence 45566666666789999999999998 79999999999999999988544
No 126
>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=61.91 E-value=16 Score=31.30 Aligned_cols=35 Identities=11% Similarity=0.111 Sum_probs=31.9
Q ss_pred cccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEE
Q psy9642 321 TLSLADVASRVQLGTPVQAEIYILKMISQNEIYATI 356 (437)
Q Consensus 321 ~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~I 356 (437)
.++..+||++++++ ..-+.+++..|...|.|.++-
T Consensus 25 ~~s~~eia~~l~is-~~~v~~~l~~L~~~Gli~~~~ 59 (130)
T TIGR02944 25 PYSAAEIAEQTGLN-APTVSKILKQLSLAGIVTSKR 59 (130)
T ss_pred CccHHHHHHHHCcC-HHHHHHHHHHHHHCCcEEecC
Confidence 58999999999998 789999999999999997753
No 127
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=61.81 E-value=13 Score=35.75 Aligned_cols=50 Identities=10% Similarity=0.052 Sum_probs=42.8
Q ss_pred HHHHHHHHHHHHHHhh-ccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEE
Q psy9642 304 VASLYKNNIKRLTKTF-LTLSLADVASRVQLGTPVQAEIYILKMISQNEIYA 354 (437)
Q Consensus 304 ~~~v~r~~I~~l~k~Y-s~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A 354 (437)
.....|.+|......| -+++.+|||..+|+. ++.+-.++-+||.+|.|.-
T Consensus 7 kk~~t~fqIL~ei~~~qp~v~q~eIA~~lgiT-~QaVsehiK~Lv~eG~i~~ 57 (260)
T COG1497 7 KKNLTRFQILSEIAVRQPRVKQKEIAKKLGIT-LQAVSEHIKELVKEGLIEK 57 (260)
T ss_pred cccchHHHHHHHHHHhCCCCCHHHHHHHcCCC-HHHHHHHHHHHHhccceee
Confidence 3456777887777777 689999999999998 8999999999999998865
No 128
>COG3071 HemY Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]
Probab=61.69 E-value=57 Score=33.71 Aligned_cols=56 Identities=14% Similarity=0.078 Sum_probs=39.6
Q ss_pred HHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhc-ccc
Q psy9642 154 CLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIIT-TPA 218 (437)
Q Consensus 154 ~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~-~P~ 218 (437)
|+..+++.+=++.+++-+... +.+- ..+++-|+.+...+.|.+|..+|+.++. -|+
T Consensus 304 ~l~~~d~~~l~k~~e~~l~~h--------~~~p-~L~~tLG~L~~k~~~w~kA~~~leaAl~~~~s 360 (400)
T COG3071 304 RLRPGDPEPLIKAAEKWLKQH--------PEDP-LLLSTLGRLALKNKLWGKASEALEAALKLRPS 360 (400)
T ss_pred hcCCCCchHHHHHHHHHHHhC--------CCCh-hHHHHHHHHHHHhhHHHHHHHHHHHHHhcCCC
Confidence 455555666555555554431 1112 5678999999999999999999999998 555
No 129
>PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional
Probab=61.35 E-value=74 Score=29.46 Aligned_cols=66 Identities=9% Similarity=0.062 Sum_probs=49.3
Q ss_pred HHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhh--HHHHHHHHHHHhc-cccc
Q psy9642 146 LHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKN--YERALYFFEVIIT-TPAL 219 (437)
Q Consensus 146 ~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~--y~~A~~~~~~ai~-~P~~ 219 (437)
.+..+.++++..+++..|+..+++-+.- .+.+.-.+..|+...+...++ +.+|...|..++. .|..
T Consensus 75 ~w~~Lg~~~~~~g~~~~A~~a~~~Al~l--------~P~~~~~~~~lA~aL~~~~g~~~~~~A~~~l~~al~~dP~~ 143 (198)
T PRK10370 75 QWALLGEYYLWRNDYDNALLAYRQALQL--------RGENAELYAALATVLYYQAGQHMTPQTREMIDKALALDANE 143 (198)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHHHHh--------CCCCHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHhCCCC
Confidence 7889999999999999999999876652 233333334444444566666 5999999999999 6765
No 130
>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A.
Probab=61.29 E-value=13 Score=24.20 Aligned_cols=27 Identities=26% Similarity=0.254 Sum_probs=22.3
Q ss_pred HHHHHHHHHHHhhHHHHHHHHHHHhcc
Q psy9642 190 FYYGGMIYLALKNYERALYFFEVIITT 216 (437)
Q Consensus 190 ~Yy~G~I~~~~k~y~~A~~~~~~ai~~ 216 (437)
..--|.+|..+++|.+|..+++.++..
T Consensus 5 ~~~la~~~~~~g~~~~A~~~~~~al~~ 31 (42)
T PF13374_consen 5 LNNLANAYRAQGRYEEALELLEEALEI 31 (42)
T ss_dssp HHHHHHHHHHCT-HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHhhhhcchhhHHHHHHHHH
Confidence 345688999999999999999999874
No 131
>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional
Probab=61.08 E-value=20 Score=36.59 Aligned_cols=61 Identities=16% Similarity=0.221 Sum_probs=50.2
Q ss_pred HHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhc-cccc
Q psy9642 150 LCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIIT-TPAL 219 (437)
Q Consensus 150 l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~-~P~~ 219 (437)
..+.++..++|..|+..+++-|.. ++ +...+++..|.++..+++|.+|...+..++. .|..
T Consensus 8 ~a~~a~~~~~~~~Ai~~~~~Al~~--------~P-~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~P~~ 69 (356)
T PLN03088 8 KAKEAFVDDDFALAVDLYTQAIDL--------DP-NNAELYADRAQANIKLGNFTEAVADANKAIELDPSL 69 (356)
T ss_pred HHHHHHHcCCHHHHHHHHHHHHHh--------CC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCC
Confidence 457788999999999999888753 12 2456778999999999999999999999999 6754
No 132
>PLN03081 pentatricopeptide (PPR) repeat-containing protein; Provisional
Probab=61.08 E-value=2.7e+02 Score=30.92 Aligned_cols=53 Identities=17% Similarity=0.165 Sum_probs=29.6
Q ss_pred HHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHH--HHHHhhHHHHHHHHHHHhc
Q psy9642 149 DLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMI--YLALKNYERALYFFEVIIT 215 (437)
Q Consensus 149 ~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I--~~~~k~y~~A~~~~~~ai~ 215 (437)
.++..+.+.++++.|..+++.- ...+... |..+| |...+++++|.+.|.....
T Consensus 264 ~Li~~y~k~g~~~~A~~vf~~m-----------~~~~~vt---~n~li~~y~~~g~~~eA~~lf~~M~~ 318 (697)
T PLN03081 264 ALIDMYSKCGDIEDARCVFDGM-----------PEKTTVA---WNSMLAGYALHGYSEEALCLYYEMRD 318 (697)
T ss_pred HHHHHHHHCCCHHHHHHHHHhC-----------CCCChhH---HHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4455566666666666555432 1112222 33333 3445788999998888765
No 133
>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=60.76 E-value=21 Score=26.03 Aligned_cols=32 Identities=6% Similarity=0.093 Sum_probs=28.2
Q ss_pred ccc-HHHHHHHhCCCChHHHHHHHHHhHHcCceE
Q psy9642 321 TLS-LADVASRVQLGTPVQAEIYILKMISQNEIY 353 (437)
Q Consensus 321 ~Is-L~dIa~~l~L~~~~eaE~~l~~mI~~G~I~ 353 (437)
.++ ..+||+.++++ ...+...+..|...|.|.
T Consensus 24 ~~~~~~~la~~~~is-~~~v~~~l~~L~~~G~i~ 56 (66)
T cd07377 24 RLPSERELAEELGVS-RTTVREALRELEAEGLVE 56 (66)
T ss_pred CCCCHHHHHHHHCCC-HHHHHHHHHHHHHCCCEE
Confidence 344 99999999997 789999999999999875
No 134
>KOG1126|consensus
Probab=60.62 E-value=9.8 Score=41.44 Aligned_cols=34 Identities=24% Similarity=0.420 Sum_probs=30.7
Q ss_pred hHHHHHHHHHHHHHHhhHHHHHHHHHHHhc-cccc
Q psy9642 186 FLQYFYYGGMIYLALKNYERALYFFEVIIT-TPAL 219 (437)
Q Consensus 186 ~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~-~P~~ 219 (437)
...=.|=.||||..+++|+.|..+|+.|+. .|.+
T Consensus 488 hYnAwYGlG~vy~Kqek~e~Ae~~fqkA~~INP~n 522 (638)
T KOG1126|consen 488 HYNAWYGLGTVYLKQEKLEFAEFHFQKAVEINPSN 522 (638)
T ss_pred hhHHHHhhhhheeccchhhHHHHHHHhhhcCCccc
Confidence 566678889999999999999999999999 7876
No 135
>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional
Probab=60.56 E-value=45 Score=30.14 Aligned_cols=60 Identities=15% Similarity=0.245 Sum_probs=45.4
Q ss_pred HHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhc-cccc
Q psy9642 151 CQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIIT-TPAL 219 (437)
Q Consensus 151 ~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~-~P~~ 219 (437)
.-+....|++..|..+..--.. + ++ .+..|+|--|+++=.+++|.+|..+|..++. .|..
T Consensus 42 A~~ly~~G~l~~A~~~f~~L~~-~-------Dp-~~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~~dd 102 (157)
T PRK15363 42 AMQLMEVKEFAGAARLFQLLTI-Y-------DA-WSFDYWFRLGECCQAQKHWGEAIYAYGRAAQIKIDA 102 (157)
T ss_pred HHHHHHCCCHHHHHHHHHHHHH-h-------Cc-ccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCC
Confidence 3455678889998655443222 1 22 3889999999999999999999999999999 5644
No 136
>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=60.26 E-value=17 Score=28.45 Aligned_cols=42 Identities=5% Similarity=-0.012 Sum_probs=33.8
Q ss_pred HHHHHHHHhhccccHHHHHHHhCCCChHHHHHHHHHhHHcCce
Q psy9642 310 NNIKRLTKTFLTLSLADVASRVQLGTPVQAEIYILKMISQNEI 352 (437)
Q Consensus 310 ~~I~~l~k~Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I 352 (437)
..+-.+++.+.-.|.++||+.+|++ +.-+...+..+...|.+
T Consensus 21 r~af~L~R~~eGlS~kEIAe~LGIS-~~TVk~~l~~~~~~~~~ 62 (73)
T TIGR03879 21 EAAAALAREEAGKTASEIAEELGRT-EQTVRNHLKGETKAGGL 62 (73)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCcC-HHHHHHHHhcCcccchH
Confidence 4455666778999999999999998 78888888877776653
No 137
>KOG2316|consensus
Probab=60.24 E-value=15 Score=34.97 Aligned_cols=44 Identities=23% Similarity=0.270 Sum_probs=35.0
Q ss_pred HHHHhhccccHHHHHHHhCCCC-----hHHHHHHHHHhHHcCceEEEEec
Q psy9642 314 RLTKTFLTLSLADVASRVQLGT-----PVQAEIYILKMISQNEIYATINK 358 (437)
Q Consensus 314 ~l~k~Ys~IsL~dIa~~l~L~~-----~~eaE~~l~~mI~~G~I~A~Id~ 358 (437)
.|-..|.|+..+.|+++|+|-+ ..+-|.++.+||.+| ++|.|-.
T Consensus 115 AIlS~YQr~RVEnVC~RL~L~~Ls~LW~rdQ~~LL~eMi~~g-~~AiiiK 163 (277)
T KOG2316|consen 115 AILSDYQRTRVENVCSRLGLVSLSYLWQRDQEELLQEMILSG-LDAIIIK 163 (277)
T ss_pred hhHhHHHHHHHHHHHhhhCceeehHHHhccHHHHHHHHHHcC-CCeEEEE
Confidence 4556799999999999999753 245578999999999 7888753
No 138
>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional
Probab=59.55 E-value=71 Score=28.88 Aligned_cols=76 Identities=12% Similarity=0.056 Sum_probs=57.3
Q ss_pred HHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHH
Q psy9642 128 LIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERAL 207 (437)
Q Consensus 128 ~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~ 207 (437)
-+-..+.++||.. ...+--|.-.|-..++|..|+..-.+-+.- ++ +.-+-+++.|.+++..++-..|.
T Consensus 56 ~~f~~L~~~Dp~~---~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L--------~~-ddp~~~~~ag~c~L~lG~~~~A~ 123 (157)
T PRK15363 56 RLFQLLTIYDAWS---FDYWFRLGECCQAQKHWGEAIYAYGRAAQI--------KI-DAPQAPWAAAECYLACDNVCYAI 123 (157)
T ss_pred HHHHHHHHhCccc---HHHHHHHHHHHHHHhhHHHHHHHHHHHHhc--------CC-CCchHHHHHHHHHHHcCCHHHHH
Confidence 3445566777643 335566667777888999998877776552 22 35566789999999999999999
Q ss_pred HHHHHHhc
Q psy9642 208 YFFEVIIT 215 (437)
Q Consensus 208 ~~~~~ai~ 215 (437)
..|+.|+.
T Consensus 124 ~aF~~Ai~ 131 (157)
T PRK15363 124 KALKAVVR 131 (157)
T ss_pred HHHHHHHH
Confidence 99999998
No 139
>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B.
Probab=59.48 E-value=12 Score=27.47 Aligned_cols=29 Identities=21% Similarity=0.296 Sum_probs=25.4
Q ss_pred HHHHHHHHHHhhHHHHHHHHHHHhc-cccc
Q psy9642 191 YYGGMIYLALKNYERALYFFEVIIT-TPAL 219 (437)
Q Consensus 191 Yy~G~I~~~~k~y~~A~~~~~~ai~-~P~~ 219 (437)
|-.|+.++..++|.+|...|+.++. .|..
T Consensus 1 ~~~a~~~~~~g~~~~A~~~~~~~l~~~P~~ 30 (65)
T PF13432_consen 1 YALARALYQQGDYDEAIAAFEQALKQDPDN 30 (65)
T ss_dssp HHHHHHHHHCTHHHHHHHHHHHHHCCSTTH
T ss_pred ChHHHHHHHcCCHHHHHHHHHHHHHHCCCC
Confidence 4568999999999999999999999 6653
No 140
>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional
Probab=58.33 E-value=29 Score=36.59 Aligned_cols=67 Identities=9% Similarity=0.012 Sum_probs=54.0
Q ss_pred chhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhh-H-HHHHHHHHHHHHHhhHHHHHHHHHHHhcc
Q psy9642 142 QLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYF-L-QYFYYGGMIYLALKNYERALYFFEVIITT 216 (437)
Q Consensus 142 ~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~-l-~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~~ 216 (437)
.....|..+...+...+.|+.|+...++-+.- ++.+. . --+|..|++|..++++++|..+|+.|+..
T Consensus 73 ~~a~a~~NLG~AL~~lGryeEAIa~f~rALeL--------~Pd~aeA~~A~yNLAcaya~LGr~dEAla~LrrALel 141 (453)
T PLN03098 73 KTAEDAVNLGLSLFSKGRVKDALAQFETALEL--------NPNPDEAQAAYYNKACCHAYREEGKKAADCLRTALRD 141 (453)
T ss_pred CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--------CCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence 44557888889999999999999999887653 22211 1 33689999999999999999999999984
No 141
>PF13429 TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2_B.
Probab=58.13 E-value=14 Score=35.85 Aligned_cols=93 Identities=20% Similarity=0.277 Sum_probs=62.0
Q ss_pred HHHhhhCCCCcchHHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHH
Q psy9642 114 KTVMDLKTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYG 193 (437)
Q Consensus 114 ~~~~~~~~~~~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~ 193 (437)
......+.+-.++..++.|+..- |.... +...++.+.+..+++..+.+++..-.-.... ++ .+...-
T Consensus 154 ~~~~~~G~~~~A~~~~~~al~~~-P~~~~---~~~~l~~~li~~~~~~~~~~~l~~~~~~~~~-----~~----~~~~~l 220 (280)
T PF13429_consen 154 EIYEQLGDPDKALRDYRKALELD-PDDPD---ARNALAWLLIDMGDYDEAREALKRLLKAAPD-----DP----DLWDAL 220 (280)
T ss_dssp HHHHHCCHHHHHHHHHHHHHHH--TT-HH---HHHHHHHHHCTTCHHHHHHHHHHHHHHH-HT-----SC----CHCHHH
T ss_pred HHHHHcCCHHHHHHHHHHHHHcC-CCCHH---HHHHHHHHHHHCCChHHHHHHHHHHHHHCcC-----HH----HHHHHH
Confidence 34445677778899999987664 54322 4556777888899998876666654332111 11 133345
Q ss_pred HHHHHHHhhHHHHHHHHHHHhc-cccc
Q psy9642 194 GMIYLALKNYERALYFFEVIIT-TPAL 219 (437)
Q Consensus 194 G~I~~~~k~y~~A~~~~~~ai~-~P~~ 219 (437)
|.++..++++++|..+|+.+.. .|..
T Consensus 221 a~~~~~lg~~~~Al~~~~~~~~~~p~d 247 (280)
T PF13429_consen 221 AAAYLQLGRYEEALEYLEKALKLNPDD 247 (280)
T ss_dssp HHHHHHHT-HHHHHHHHHHHHHHSTT-
T ss_pred HHHhccccccccccccccccccccccc
Confidence 9999999999999999999998 6653
No 142
>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=57.79 E-value=21 Score=30.43 Aligned_cols=46 Identities=17% Similarity=0.248 Sum_probs=37.4
Q ss_pred HHHHHHHHHhhccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEe
Q psy9642 309 KNNIKRLTKTFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATIN 357 (437)
Q Consensus 309 r~~I~~l~k~Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id 357 (437)
.+.|..++.. .+|+++||..++++ ..-+.-++++|+..|.+...--
T Consensus 45 ~~~Il~lC~~--~~SVAEiAA~L~lP-lgVvrVLvsDL~~~G~v~v~~p 90 (114)
T PF05331_consen 45 HRAILELCRR--PLSVAEIAARLGLP-LGVVRVLVSDLADAGLVRVRAP 90 (114)
T ss_pred HHHHHHHHCC--CccHHHHHHhhCCC-chhhhhhHHHHHhCCCEEEeCC
Confidence 3455566666 89999999999998 6788889999999998877553
No 143
>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=57.03 E-value=18 Score=30.95 Aligned_cols=61 Identities=11% Similarity=0.127 Sum_probs=43.7
Q ss_pred cccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCCCEEEEccCCCCCCchHHHHHHHH
Q psy9642 321 TLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVFNDNPQRFNNPLTFAQIES 383 (437)
Q Consensus 321 ~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~g~v~F~~~~~~~~~~e~~~~l~~ 383 (437)
.++.++||+.++++ ...+.+++..|...|.|...-.. +|-.....+++..+-.++.+.++.
T Consensus 25 ~~s~~eia~~~~i~-~~~v~~il~~L~~~gli~~~~g~-~ggy~l~~~~~~itl~~I~~~~e~ 85 (132)
T TIGR00738 25 PVSVKEIAERQGIS-RSYLEKILRTLRRAGLVESVRGP-GGGYRLARPPEEITVGDVVRAVEG 85 (132)
T ss_pred cCcHHHHHHHHCcC-HHHHHHHHHHHHHCCcEEeccCC-CCCccCCCCHHHCCHHHHHHHHcC
Confidence 68999999999998 89999999999999998764333 333444555554444455555443
No 144
>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=56.91 E-value=32 Score=25.18 Aligned_cols=42 Identities=19% Similarity=0.154 Sum_probs=35.0
Q ss_pred HHHHHHHHhhccccHHHHHHHhCCCChHHHHHHHHHhHHcCce
Q psy9642 310 NNIKRLTKTFLTLSLADVASRVQLGTPVQAEIYILKMISQNEI 352 (437)
Q Consensus 310 ~~I~~l~k~Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I 352 (437)
..|..+-+.-..++++++|+.++.+ +.-+..-+..|-..|.|
T Consensus 3 ~~Il~~l~~~~~~s~~ela~~~~VS-~~TiRRDl~~L~~~g~i 44 (57)
T PF08220_consen 3 QQILELLKEKGKVSVKELAEEFGVS-EMTIRRDLNKLEKQGLI 44 (57)
T ss_pred HHHHHHHHHcCCEEHHHHHHHHCcC-HHHHHHHHHHHHHCCCE
Confidence 3455555667889999999999997 78999999999999974
No 145
>PLN03077 Protein ECB2; Provisional
Probab=56.40 E-value=3.5e+02 Score=30.81 Aligned_cols=142 Identities=12% Similarity=0.053 Sum_probs=67.6
Q ss_pred HHHHhhHHHHHHHHHHHhc---ccccccCHHHHHHHHHHHHHHHHHhCCCCCCCccccHHH-hHhhccCCHHHHHHHHHH
Q psy9642 197 YLALKNYERALYFFEVIIT---TPALAVSHIMLEGYKKYLLIYLIVYGKAPNLPKNVSQAI-CRYIKPLSQPYLDLVSVY 272 (437)
Q Consensus 197 ~~~~k~y~~A~~~~~~ai~---~P~~~~s~i~vea~Kk~iLv~Lil~G~~~~lp~~~s~~~-~r~~k~~~~pY~~L~~af 272 (437)
|...+++++|.+.|+.... .|....-..++.++- ..|.+..--.+-.... ...+.+....|.-++.++
T Consensus 564 ~~~~G~~~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~--------~~g~v~ea~~~f~~M~~~~gi~P~~~~y~~lv~~l 635 (857)
T PLN03077 564 YVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACS--------RSGMVTQGLEYFHSMEEKYSITPNLKHYACVVDLL 635 (857)
T ss_pred HHHcCCHHHHHHHHHHHHHcCCCCCcccHHHHHHHHh--------hcChHHHHHHHHHHHHHHhCCCCchHHHHHHHHHH
Confidence 3344788888888888776 344321112222221 1222211111101111 011234556788888888
Q ss_pred h-cCCHHHHHHHHHhccccccccchhhHHHHHHHHHHHHHHH--------HHHH-----hhccccHHHHHHHhCCCChHH
Q psy9642 273 T-NNNSTELQHLLLKYADVFSRDENTGLTKQIVASLYKNNIK--------RLTK-----TFLTLSLADVASRVQLGTPVQ 338 (437)
Q Consensus 273 ~-~~d~~~~~~~~~~~~~~f~~D~n~~Lv~~l~~~v~r~~I~--------~l~k-----~Ys~IsL~dIa~~l~L~~~~e 338 (437)
. .|.+++-.+.+++.. +..| ...|.-++..+..|+=. ++-+ +-.-+.++.+-...| .-++
T Consensus 636 ~r~G~~~eA~~~~~~m~--~~pd--~~~~~aLl~ac~~~~~~e~~e~~a~~l~~l~p~~~~~y~ll~n~ya~~g--~~~~ 709 (857)
T PLN03077 636 GRAGKLTEAYNFINKMP--ITPD--PAVWGALLNACRIHRHVELGELAAQHIFELDPNSVGYYILLCNLYADAG--KWDE 709 (857)
T ss_pred HhCCCHHHHHHHHHHCC--CCCC--HHHHHHHHHHHHHcCChHHHHHHHHHHHhhCCCCcchHHHHHHHHHHCC--ChHH
Confidence 4 577777777766542 2222 23333344333322111 1111 001123333433444 3578
Q ss_pred HHHHHHHhHHcCce
Q psy9642 339 AEIYILKMISQNEI 352 (437)
Q Consensus 339 aE~~l~~mI~~G~I 352 (437)
|+.+...|.+.|.-
T Consensus 710 a~~vr~~M~~~g~~ 723 (857)
T PLN03077 710 VARVRKTMRENGLT 723 (857)
T ss_pred HHHHHHHHHHcCCC
Confidence 99999999988753
No 146
>KOG0553|consensus
Probab=56.09 E-value=1.5e+02 Score=29.68 Aligned_cols=148 Identities=16% Similarity=0.150 Sum_probs=82.8
Q ss_pred HHHHHHHHHhhHHHHHHHHHHHhc-ccccccCHHH-HHHHHHHHHHHHHHhCCCCC-CCccccHHHhHhhc-cCCHHHHH
Q psy9642 192 YGGMIYLALKNYERALYFFEVIIT-TPALAVSHIM-LEGYKKYLLIYLIVYGKAPN-LPKNVSQAICRYIK-PLSQPYLD 267 (437)
Q Consensus 192 y~G~I~~~~k~y~~A~~~~~~ai~-~P~~~~s~i~-vea~Kk~iLv~Lil~G~~~~-lp~~~s~~~~r~~k-~~~~pY~~ 267 (437)
..|-=.+..++|++|...|..||. .|..++---. -.|| ..| |+..+ +....+. .+ +. ...+.|..
T Consensus 86 ~eGN~~m~~~~Y~eAv~kY~~AI~l~P~nAVyycNRAAAy-----~~L---g~~~~AVkDce~A--l~-iDp~yskay~R 154 (304)
T KOG0553|consen 86 NEGNKLMKNKDYQEAVDKYTEAIELDPTNAVYYCNRAAAY-----SKL---GEYEDAVKDCESA--LS-IDPHYSKAYGR 154 (304)
T ss_pred HHHHHHHHhhhHHHHHHHHHHHHhcCCCcchHHHHHHHHH-----HHh---cchHHHHHHHHHH--Hh-cChHHHHHHHH
Confidence 467778899999999999999999 8987643211 1222 122 21110 0000000 00 11 12578889
Q ss_pred HHHHHhcCCHHHHHHHHHhccccccccchhhHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHhCC-C-----------C
Q psy9642 268 LVSVYTNNNSTELQHLLLKYADVFSRDENTGLTKQIVASLYKNNIKRLTKTFLTLSLADVASRVQL-G-----------T 335 (437)
Q Consensus 268 L~~af~~~d~~~~~~~~~~~~~~f~~D~n~~Lv~~l~~~v~r~~I~~l~k~Ys~IsL~dIa~~l~L-~-----------~ 335 (437)
|..||...+ ++...++.|+..+.=|++..-+|.-+... +..++.-...=.++.-.|++..++. + +
T Consensus 155 LG~A~~~~g--k~~~A~~aykKaLeldP~Ne~~K~nL~~A-e~~l~e~~~~~~~~~~~d~~~~ig~~Pd~~s~~~~~l~n 231 (304)
T KOG0553|consen 155 LGLAYLALG--KYEEAIEAYKKALELDPDNESYKSNLKIA-EQKLNEPKSSAQASGSFDMAGLIGAFPDSRSMFNGDLMN 231 (304)
T ss_pred HHHHHHccC--cHHHHHHHHHhhhccCCCcHHHHHHHHHH-HHHhcCCCcccccccchhhhhhccCCccchhhhcccccc
Confidence 999987643 56777777888777777666444332211 1222222222356677777777775 1 2
Q ss_pred hHHHHHHHHHhHHcCceE
Q psy9642 336 PVQAEIYILKMISQNEIY 353 (437)
Q Consensus 336 ~~eaE~~l~~mI~~G~I~ 353 (437)
...+-.....|+.+|.+.
T Consensus 232 np~l~~~~~~m~~~~~~~ 249 (304)
T KOG0553|consen 232 NPQLMQLASQMMKDGALN 249 (304)
T ss_pred CHHHHHHHHHHhhccccc
Confidence 344555666777655443
No 147
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=55.83 E-value=54 Score=22.45 Aligned_cols=34 Identities=12% Similarity=0.089 Sum_probs=30.3
Q ss_pred ccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEE
Q psy9642 320 LTLSLADVASRVQLGTPVQAEIYILKMISQNEIYA 354 (437)
Q Consensus 320 s~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A 354 (437)
..++..+|++.++++ ...+...+..|...|.|..
T Consensus 13 ~~~s~~~l~~~l~~s-~~tv~~~l~~L~~~g~i~~ 46 (53)
T smart00420 13 GKVSVEELAELLGVS-EMTIRRDLNKLEEQGLLTR 46 (53)
T ss_pred CCcCHHHHHHHHCCC-HHHHHHHHHHHHHCCCEEE
Confidence 458999999999997 7899999999999998864
No 148
>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=55.38 E-value=72 Score=23.47 Aligned_cols=40 Identities=13% Similarity=0.115 Sum_probs=31.5
Q ss_pred hhccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEec
Q psy9642 318 TFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINK 358 (437)
Q Consensus 318 ~Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~ 358 (437)
..-.++..+|++.++++ ...+-..|.+|++.|-|.=.-|.
T Consensus 15 ~~~~~t~~~l~~~~~~~-~~~vs~~i~~L~~~glv~~~~~~ 54 (68)
T PF13463_consen 15 SDGPMTQSDLAERLGIS-KSTVSRIIKKLEEKGLVEKERDP 54 (68)
T ss_dssp -TS-BEHHHHHHHTT---HHHHHHHHHHHHHTTSEEEEEES
T ss_pred cCCCcCHHHHHHHHCcC-HHHHHHHHHHHHHCCCEEecCCC
Confidence 56789999999999998 78888999999999999666554
No 149
>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=55.32 E-value=33 Score=23.65 Aligned_cols=27 Identities=19% Similarity=0.102 Sum_probs=19.8
Q ss_pred hccccHHHHHHHhCCCChHHHHHHHHHh
Q psy9642 319 FLTLSLADVASRVQLGTPVQAEIYILKM 346 (437)
Q Consensus 319 Ys~IsL~dIa~~l~L~~~~eaE~~l~~m 346 (437)
=.+.|..+||+.+|++ +..+-.-+.+|
T Consensus 15 d~r~s~~~la~~lglS-~~~v~~Ri~rL 41 (42)
T PF13404_consen 15 DGRRSYAELAEELGLS-ESTVRRRIRRL 41 (42)
T ss_dssp -TTS-HHHHHHHHTS--HHHHHHHHHHH
T ss_pred cCCccHHHHHHHHCcC-HHHHHHHHHHh
Confidence 3899999999999998 67776666554
No 150
>PRK10866 outer membrane biogenesis protein BamD; Provisional
Probab=54.54 E-value=2e+02 Score=27.52 Aligned_cols=65 Identities=18% Similarity=0.044 Sum_probs=49.2
Q ss_pred HHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhc-cccc
Q psy9642 149 DLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIIT-TPAL 219 (437)
Q Consensus 149 ~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~-~P~~ 219 (437)
.....++..++|..|...++.-+..... +...-.=.|..|.++...++|.+|..+|+..+. .|..
T Consensus 37 ~~A~~~~~~g~y~~Ai~~f~~l~~~yP~------s~~a~~a~l~la~ayy~~~~y~~A~~~~e~fi~~~P~~ 102 (243)
T PRK10866 37 ATAQQKLQDGNWKQAITQLEALDNRYPF------GPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTH 102 (243)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHhCCC------ChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCcCC
Confidence 5567788999999998887775553221 112222256889999999999999999999998 7876
No 151
>PF12569 NARP1: NMDA receptor-regulated protein 1 ; InterPro: IPR021183 This group represents N-terminal acetyltransferase A (NatA) auxiliary subunit and represents a non-catalytic component of the NatA N-terminal acetyltransferase, which catalyzes acetylation of proteins beginning with Met-Ser, Met-Gly and Met-Ala. N-terminal acetylation plays a role in normal eukaryotic translation and processing, protect against proteolytic degradation and protein turnover. NAT1 anchors ARD1 and NAT5 to the ribosome and may present the N- terminal of nascent polypeptides for acetylation [], [].
Probab=54.30 E-value=3.1e+02 Score=29.70 Aligned_cols=65 Identities=20% Similarity=0.132 Sum_probs=52.6
Q ss_pred HHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhc-ccccc
Q psy9642 147 HSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIIT-TPALA 220 (437)
Q Consensus 147 h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~-~P~~~ 220 (437)
.+-...+...+|.|..||..|......+ -|.+.+.=..|.+++.++++++|...|..-|. .|.+.
T Consensus 7 lLY~~~il~e~g~~~~AL~~L~~~~~~I---------~Dk~~~~E~rA~ll~kLg~~~eA~~~y~~Li~rNPdn~ 72 (517)
T PF12569_consen 7 LLYKNSILEEAGDYEEALEHLEKNEKQI---------LDKLAVLEKRAELLLKLGRKEEAEKIYRELIDRNPDNY 72 (517)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHhhhhhC---------CCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCcH
Confidence 3445567788999999999997765543 23666777899999999999999999999998 89763
No 152
>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=54.18 E-value=95 Score=25.90 Aligned_cols=43 Identities=5% Similarity=-0.007 Sum_probs=36.6
Q ss_pred hhccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCCC
Q psy9642 318 TFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDG 361 (437)
Q Consensus 318 ~Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~g 361 (437)
..-.++.++||+.++++ ...+-..|.+|..+|.|...-|..++
T Consensus 39 ~~~~~t~~ela~~~~~~-~~tvs~~l~~Le~~GlI~r~~~~~D~ 81 (118)
T TIGR02337 39 EQGSMEFTQLANQACIL-RPSLTGILARLERDGLVTRLKASNDQ 81 (118)
T ss_pred HcCCcCHHHHHHHhCCC-chhHHHHHHHHHHCCCEEeccCCCCC
Confidence 35679999999999998 46788999999999999998876553
No 153
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=54.04 E-value=24 Score=32.02 Aligned_cols=62 Identities=10% Similarity=0.169 Sum_probs=45.9
Q ss_pred cccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCCCEEEEccCCCCCCchHHHHHHHHH
Q psy9642 321 TLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVFNDNPQRFNNPLTFAQIESN 384 (437)
Q Consensus 321 ~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~g~v~F~~~~~~~~~~e~~~~l~~~ 384 (437)
.+++++||+.++++ ..-+++++..|...|-+.++--. +|-.....+++..+-.++.+.++..
T Consensus 25 ~vs~~eIA~~~~ip-~~~l~kIl~~L~~aGLv~s~rG~-~GGy~Lar~p~~Itl~dIl~aieg~ 86 (164)
T PRK10857 25 PVPLADISERQGIS-LSYLEQLFSRLRKNGLVSSVRGP-GGGYLLGKDASSIAVGEVISAVDES 86 (164)
T ss_pred cCcHHHHHHHHCcC-HHHHHHHHHHHHHCCCEEeCCCC-CCCeeccCCHHHCCHHHHHHHHcCC
Confidence 59999999999998 89999999999999998874333 3444555555555555666655543
No 154
>KOG3054|consensus
Probab=53.97 E-value=31 Score=33.33 Aligned_cols=48 Identities=13% Similarity=0.220 Sum_probs=41.5
Q ss_pred hhccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCCCEEEEc
Q psy9642 318 TFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVFN 366 (437)
Q Consensus 318 ~Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~g~v~F~ 366 (437)
.-..+.|.|+|...||- .+++-.-+.+++.+|.|.|.||.-..++..+
T Consensus 211 ~nKvV~ledLas~f~Lr-tqd~inriq~~l~eg~ltGVmDDRGKfIYIS 258 (299)
T KOG3054|consen 211 KNKVVPLEDLASEFGLR-TQDSINRIQELLAEGLLTGVMDDRGKFIYIS 258 (299)
T ss_pred hcCeeeHHHHHHHhCcc-HHHHHHHHHHHHHhhhheeeecCCCceEEec
Confidence 34569999999999998 5788889999999999999999877777665
No 155
>PRK15174 Vi polysaccharide export protein VexE; Provisional
Probab=53.64 E-value=55 Score=36.29 Aligned_cols=87 Identities=7% Similarity=0.035 Sum_probs=52.8
Q ss_pred hCCCCcchHHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHH
Q psy9642 119 LKTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYL 198 (437)
Q Consensus 119 ~~~~~~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~ 198 (437)
.+++-.++..+..++.. +|... ..|..+..+....+++..|+..+++-+.. . .+...+++..|.++.
T Consensus 89 ~g~~~~A~~~l~~~l~~-~P~~~---~a~~~la~~l~~~g~~~~Ai~~l~~Al~l--------~-P~~~~a~~~la~~l~ 155 (656)
T PRK15174 89 SSQPDAVLQVVNKLLAV-NVCQP---EDVLLVASVLLKSKQYATVADLAEQAWLA--------F-SGNSQIFALHLRTLV 155 (656)
T ss_pred cCCHHHHHHHHHHHHHh-CCCCh---HHHHHHHHHHHHcCCHHHHHHHHHHHHHh--------C-CCcHHHHHHHHHHHH
Confidence 45555566666655433 44322 24566667777777777777777665542 1 123445566677777
Q ss_pred HHhhHHHHHHHHHHHhc-ccc
Q psy9642 199 ALKNYERALYFFEVIIT-TPA 218 (437)
Q Consensus 199 ~~k~y~~A~~~~~~ai~-~P~ 218 (437)
..+++++|...+..+.. .|.
T Consensus 156 ~~g~~~eA~~~~~~~~~~~P~ 176 (656)
T PRK15174 156 LMDKELQAISLARTQAQEVPP 176 (656)
T ss_pred HCCChHHHHHHHHHHHHhCCC
Confidence 77788888777776655 443
No 156
>PF10037 MRP-S27: Mitochondrial 28S ribosomal protein S27; InterPro: IPR019266 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents a family of small ribosomal proteins possessing one of three conserved sequence blocks found in proteins that stimulate the dissociation of guanine nucleotides from G-proteins. This leaves open the possibility that they may be functional partners of GTP-binding ribosomal proteins [].
Probab=53.33 E-value=43 Score=35.27 Aligned_cols=62 Identities=23% Similarity=0.258 Sum_probs=43.0
Q ss_pred chhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHH----HHHHhhHHHHHHHHHHHhc
Q psy9642 142 QLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMI----YLALKNYERALYFFEVIIT 215 (437)
Q Consensus 142 ~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I----~~~~k~y~~A~~~~~~ai~ 215 (437)
.+.+.|..++|.|+..+..+.++.+|..++.. +-+.. . |.+.+ ++..++|..|.+-....+-
T Consensus 101 ~~~~t~ha~vR~~l~~~~~~~~l~~L~n~~~y-----GiF~D--~-----~s~n~Lmd~fl~~~~~~~A~~V~~~~~l 166 (429)
T PF10037_consen 101 LLPSTHHALVRQCLELGAEDELLELLKNRLQY-----GIFPD--N-----FSFNLLMDHFLKKGNYKSAAKVATEMML 166 (429)
T ss_pred ccCccHHHHHHHHHhcCCHHHHHHHHhChhhc-----ccCCC--h-----hhHHHHHHHHhhcccHHHHHHHHHHHHH
Confidence 44566779999999999999999999887663 11111 1 33333 3344799999887776654
No 157
>cd05804 StaR_like StaR_like; a well-conserved protein found in bacteria, plants, and animals. A family member from Streptomyces toyocaensis, StaR is part of a gene cluster involved in the biosynthesis of glycopeptide antibiotics (GPAs), specifically A47934. It has been speculated that StaR could be a flavoprotein hydroxylating a tyrosine sidechain. Some family members have been annotated as proteins containing tetratricopeptide (TPR) repeats, which may at least indicate mostly alpha-helical secondary structure.
Probab=52.91 E-value=1.2e+02 Score=30.05 Aligned_cols=74 Identities=9% Similarity=-0.063 Sum_probs=52.3
Q ss_pred hCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhc
Q psy9642 136 IQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIIT 215 (437)
Q Consensus 136 l~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~ 215 (437)
..+........+..+...+...+++..|.....+-+.- .+.+ ...++.-|.++...++|++|..+|..++.
T Consensus 106 ~~~~~~~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~--------~p~~-~~~~~~la~i~~~~g~~~eA~~~l~~~l~ 176 (355)
T cd05804 106 WAPENPDYWYLLGMLAFGLEEAGQYDRAEEAARRALEL--------NPDD-AWAVHAVAHVLEMQGRFKEGIAFMESWRD 176 (355)
T ss_pred cCcCCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--------CCCC-cHHHHHHHHHHHHcCCHHHHHHHHHhhhh
Confidence 33433333345556667888999999998888776652 1222 34455669999999999999999999998
Q ss_pred -ccc
Q psy9642 216 -TPA 218 (437)
Q Consensus 216 -~P~ 218 (437)
.|.
T Consensus 177 ~~~~ 180 (355)
T cd05804 177 TWDC 180 (355)
T ss_pred ccCC
Confidence 453
No 158
>PRK10049 pgaA outer membrane protein PgaA; Provisional
Probab=52.82 E-value=98 Score=34.99 Aligned_cols=103 Identities=13% Similarity=0.051 Sum_probs=68.9
Q ss_pred HhhhCCCCcchHHHHHHHHHhCCCC-cchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcC------CCCCChHhhHH
Q psy9642 116 VMDLKTPQRGIPLIQTAIKKIQTSD-SQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANE------GPQFDTKYFLQ 188 (437)
Q Consensus 116 ~~~~~~~~~~i~~l~~ai~rl~~~~-~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~------~~~~~~~~~l~ 188 (437)
....++|-.++..++.++ ..+|.. ...-..+..+....+..+.+..|+..+++-...-... ....+..+.+.
T Consensus 282 yl~~g~~e~A~~~l~~~l-~~~p~~~~~~~~~~~~L~~a~~~~g~~~eA~~~l~~~~~~~P~~~~~~~~~~~~p~~~~~~ 360 (765)
T PRK10049 282 YLKLHQPEKAQSILTELF-YHPETIADLSDEELADLFYSLLESENYPGALTVTAHTINNSPPFLRLYGSPTSIPNDDWLQ 360 (765)
T ss_pred HHhcCCcHHHHHHHHHHh-hcCCCCCCCChHHHHHHHHHHHhcccHHHHHHHHHHHhhcCCceEeecCCCCCCCCchHHH
Confidence 334666777777777755 344433 1112345666667789999999988877644321100 01112224577
Q ss_pred HHHHHHHHHHHHhhHHHHHHHHHHHhc-cccc
Q psy9642 189 YFYYGGMIYLALKNYERALYFFEVIIT-TPAL 219 (437)
Q Consensus 189 Y~Yy~G~I~~~~k~y~~A~~~~~~ai~-~P~~ 219 (437)
..+..|.++...+++.+|...|+.++. .|..
T Consensus 361 a~~~~a~~l~~~g~~~eA~~~l~~al~~~P~n 392 (765)
T PRK10049 361 GQSLLSQVAKYSNDLPQAEMRARELAYNAPGN 392 (765)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCC
Confidence 888999999999999999999999998 8876
No 159
>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A.
Probab=52.62 E-value=1.9e+02 Score=26.63 Aligned_cols=94 Identities=16% Similarity=0.155 Sum_probs=63.0
Q ss_pred hCCCCcchHHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHH
Q psy9642 119 LKTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYL 198 (437)
Q Consensus 119 ~~~~~~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~ 198 (437)
.++...++..+...+.++ |.+.........++..+...++|..|....++=|...... +. .-.=.|..|+.++
T Consensus 18 ~g~y~~Ai~~f~~l~~~~-P~s~~a~~A~l~la~a~y~~~~y~~A~~~~~~fi~~yP~~----~~--~~~A~Y~~g~~~~ 90 (203)
T PF13525_consen 18 QGDYEEAIKLFEKLIDRY-PNSPYAPQAQLMLAYAYYKQGDYEEAIAAYERFIKLYPNS----PK--ADYALYMLGLSYY 90 (203)
T ss_dssp CT-HHHHHHHHHHHHHH--TTSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-----TT--HHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHC-CCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCC----cc--hhhHHHHHHHHHH
Confidence 455666778888877776 5566666677888999999999999988888877654332 11 2223567788776
Q ss_pred HHh-----------hHHHHHHHHHHHhc-cccc
Q psy9642 199 ALK-----------NYERALYFFEVIIT-TPAL 219 (437)
Q Consensus 199 ~~k-----------~y~~A~~~~~~ai~-~P~~ 219 (437)
.+. ...+|...|+..+. .|.+
T Consensus 91 ~~~~~~~~~~~D~~~~~~A~~~~~~li~~yP~S 123 (203)
T PF13525_consen 91 KQIPGILRSDRDQTSTRKAIEEFEELIKRYPNS 123 (203)
T ss_dssp HHHHHHH-TT---HHHHHHHHHHHHHHHH-TTS
T ss_pred HhCccchhcccChHHHHHHHHHHHHHHHHCcCc
Confidence 652 34578888888887 7764
No 160
>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=52.59 E-value=47 Score=24.75 Aligned_cols=38 Identities=13% Similarity=0.204 Sum_probs=30.7
Q ss_pred HHHhhccccHHHHHHHhCCCChHHHHHHHHHhHHcCceE
Q psy9642 315 LTKTFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIY 353 (437)
Q Consensus 315 l~k~Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~ 353 (437)
+..-=..++..+||+.++++ +.-|-..+.+|..+|.+.
T Consensus 16 l~~~~~~v~~~~iA~~L~vs-~~tvt~ml~~L~~~GlV~ 53 (60)
T PF01325_consen 16 LSEEGGPVRTKDIAERLGVS-PPTVTEMLKRLAEKGLVE 53 (60)
T ss_dssp HHHCTSSBBHHHHHHHHTS--HHHHHHHHHHHHHTTSEE
T ss_pred HHcCCCCccHHHHHHHHCCC-hHHHHHHHHHHHHCCCEE
Confidence 33334679999999999998 788889999999999764
No 161
>PRK09954 putative kinase; Provisional
Probab=52.36 E-value=50 Score=33.40 Aligned_cols=54 Identities=13% Similarity=0.223 Sum_probs=40.9
Q ss_pred HHHHHHHhhccccHHHHHHHhCCCChHHHHHHHHHhHHcCceE---EEEecCCCEEEE
Q psy9642 311 NIKRLTKTFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIY---ATINKKDGMVVF 365 (437)
Q Consensus 311 ~I~~l~k~Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~---A~Id~~~g~v~F 365 (437)
.|.++-+--.++|.++||+.|+++ ...+...|.+|.++|.|. ..++++..++.+
T Consensus 7 ~il~~l~~~~~~s~~~la~~l~~s-~~~v~~~i~~L~~~g~i~~~~~~l~~~~~v~vi 63 (362)
T PRK09954 7 EILAILRRNPLIQQNEIADILQIS-RSRVAAHIMDLMRKGRIKGKGYILTEQEYCVVV 63 (362)
T ss_pred HHHHHHHHCCCCCHHHHHHHHCCC-HHHHHHHHHHHHHCCCcCCcEEEEcCCccEEEE
Confidence 344554555799999999999998 789999999999999884 334455555444
No 162
>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=52.23 E-value=1e+02 Score=28.60 Aligned_cols=46 Identities=11% Similarity=0.049 Sum_probs=37.5
Q ss_pred HHHHHHHHhhccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEE
Q psy9642 310 NNIKRLTKTFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATI 356 (437)
Q Consensus 310 ~~I~~l~k~Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~I 356 (437)
..|..+-.....++..+||+.++++ ..-+-.++..|..+|.|.-+-
T Consensus 4 ~~IL~~L~~~~~~t~~eLA~~lgis-~~tV~~~L~~Le~~GlV~r~~ 49 (203)
T TIGR02702 4 EDILSYLLKQGQATAAALAEALAIS-PQAVRRHLKDLETEGLIEYEA 49 (203)
T ss_pred HHHHHHHHHcCCCCHHHHHHHHCcC-HHHHHHHHHHHHHCCCeEEee
Confidence 4444444455779999999999997 789999999999999997663
No 163
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=51.72 E-value=35 Score=25.36 Aligned_cols=35 Identities=14% Similarity=0.045 Sum_probs=29.1
Q ss_pred hccc-cHHHHHHHhCCCChHHHHHHHHHhHHcCceEE
Q psy9642 319 FLTL-SLADVASRVQLGTPVQAEIYILKMISQNEIYA 354 (437)
Q Consensus 319 Ys~I-sL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A 354 (437)
=.++ +..+||++++++ ..-+..-+..+..+|.|.-
T Consensus 21 g~~lps~~~la~~~~vs-r~tvr~al~~L~~~g~i~~ 56 (64)
T PF00392_consen 21 GDRLPSERELAERYGVS-RTTVREALRRLEAEGLIER 56 (64)
T ss_dssp TSBE--HHHHHHHHTS--HHHHHHHHHHHHHTTSEEE
T ss_pred CCEeCCHHHHHHHhccC-CcHHHHHHHHHHHCCcEEE
Confidence 3589 999999999998 7889999999999998764
No 164
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=50.71 E-value=28 Score=26.43 Aligned_cols=42 Identities=14% Similarity=0.270 Sum_probs=34.7
Q ss_pred cccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCCCEEEEcc
Q psy9642 321 TLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVFND 367 (437)
Q Consensus 321 ~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~g~v~F~~ 367 (437)
.++..+||..+|++ .+.+-+.+..|..+|.|. + ..+.+...|
T Consensus 28 ~lt~~~iA~~~g~s-r~tv~r~l~~l~~~g~I~--~--~~~~i~I~d 69 (76)
T PF13545_consen 28 PLTQEEIADMLGVS-RETVSRILKRLKDEGIIE--V--KRGKIIILD 69 (76)
T ss_dssp ESSHHHHHHHHTSC-HHHHHHHHHHHHHTTSEE--E--ETTEEEESS
T ss_pred cCCHHHHHHHHCCC-HHHHHHHHHHHHHCCCEE--E--cCCEEEECC
Confidence 47899999999998 789999999999999887 3 345666554
No 165
>PF08631 SPO22: Meiosis protein SPO22/ZIP4 like; InterPro: IPR013940 SPO22 is a meiosis-specific protein with similarity to phospholipase A2, involved in completion of nuclear divisions during meiosis; induced early in meiosis []. It is also involved in sporulation [].
Probab=50.35 E-value=1.4e+02 Score=29.04 Aligned_cols=63 Identities=16% Similarity=0.133 Sum_probs=43.6
Q ss_pred HHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHh-hHHHHHHHHHHHhcc
Q psy9642 153 LCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALK-NYERALYFFEVIITT 216 (437)
Q Consensus 153 l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k-~y~~A~~~~~~ai~~ 216 (437)
++...++++.|....+|- ........+-......+-+|--|.=....+ +|++|..|+++++..
T Consensus 2 ~A~~~~~~~~A~~~~~K~-~~~~~~~~~~~~~~La~~~yn~G~~l~~~~~~~~~a~~wL~~a~~~ 65 (278)
T PF08631_consen 2 LAWKQGDLDLAEHMYSKA-KDLLNSLDPDMAEELARVCYNIGKSLLSKKDKYEEAVKWLQRAYDI 65 (278)
T ss_pred cchhhCCHHHHHHHHHHh-hhHHhcCCcHHHHHHHHHHHHHHHHHHHcCCChHHHHHHHHHHHHH
Confidence 566778888885555542 111111111233457778888999999999 999999999999995
No 166
>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=50.35 E-value=59 Score=22.59 Aligned_cols=33 Identities=12% Similarity=0.141 Sum_probs=29.1
Q ss_pred ccccHHHHHHHhCCCChHHHHHHHHHhHHcCceE
Q psy9642 320 LTLSLADVASRVQLGTPVQAEIYILKMISQNEIY 353 (437)
Q Consensus 320 s~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~ 353 (437)
...+..+|++.++++ ...+-.++..|.+.|.|.
T Consensus 14 ~~~~~~el~~~l~~s-~~~vs~hL~~L~~~glV~ 46 (47)
T PF01022_consen 14 GPLTVSELAEELGLS-QSTVSHHLKKLREAGLVE 46 (47)
T ss_dssp SSEEHHHHHHHHTS--HHHHHHHHHHHHHTTSEE
T ss_pred CCCchhhHHHhcccc-chHHHHHHHHHHHCcCee
Confidence 678899999999998 789999999999999874
No 167
>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=50.35 E-value=35 Score=23.15 Aligned_cols=38 Identities=13% Similarity=0.143 Sum_probs=29.4
Q ss_pred ccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCCCEEEEc
Q psy9642 322 LSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVFN 366 (437)
Q Consensus 322 IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~g~v~F~ 366 (437)
+++.++|+.+|++ . ..|.+++.+|.|.+... ++...|.
T Consensus 2 lt~~e~a~~lgis-~----~ti~~~~~~g~i~~~~~--g~~~~~~ 39 (49)
T TIGR01764 2 LTVEEAAEYLGVS-K----DTVYRLIHEGELPAYRV--GRHYRIP 39 (49)
T ss_pred CCHHHHHHHHCCC-H----HHHHHHHHcCCCCeEEe--CCeEEEe
Confidence 5789999999997 3 46778899999988654 4555664
No 168
>PF04492 Phage_rep_O: Bacteriophage replication protein O ; InterPro: IPR006497 This entry is represented by the N-terminal domain of Bacteriophage lambda, GpO. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; GO: 0006260 DNA replication
Probab=50.35 E-value=46 Score=27.70 Aligned_cols=32 Identities=16% Similarity=0.129 Sum_probs=30.0
Q ss_pred ccccHHHHHHHhCCCChHHHHHHHHHhHHcCce
Q psy9642 320 LTLSLADVASRVQLGTPVQAEIYILKMISQNEI 352 (437)
Q Consensus 320 s~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I 352 (437)
-+|+.+.++++.|++ ...+..-+..+|+.|.|
T Consensus 53 d~Is~sq~~e~tg~~-~~~V~~al~~Li~~~vI 84 (100)
T PF04492_consen 53 DRISNSQIAEMTGLS-RDHVSKALNELIRRGVI 84 (100)
T ss_pred ceeeHHHHHHHHCcC-HHHHHHHHHHHHHCCCE
Confidence 389999999999998 78999999999999999
No 169
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=49.55 E-value=51 Score=28.65 Aligned_cols=65 Identities=9% Similarity=0.253 Sum_probs=47.3
Q ss_pred HHHHHHHhhccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCC-CEEEEccCCCCCCchHHHHHHHHHHHHH
Q psy9642 311 NIKRLTKTFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKD-GMVVFNDNPQRFNNPLTFAQIESNIRAC 388 (437)
Q Consensus 311 ~I~~l~k~Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~-g~v~F~~~~~~~~~~e~~~~l~~~i~~~ 388 (437)
.|..+.+-=-++++.++...+|++ -..++.++.++++.|.|.- ++. | .|.++..-.+|+..-+.+
T Consensus 16 rIvElVRe~GRiTi~ql~~~TGas-R~Tvk~~lreLVa~G~l~~---~G~~G---------vF~seqA~~dw~~~~~~~ 81 (127)
T PF06163_consen 16 RIVELVREHGRITIKQLVAKTGAS-RNTVKRYLRELVARGDLYR---HGRSG---------VFPSEQARKDWDKARKKL 81 (127)
T ss_pred HHHHHHHHcCCccHHHHHHHHCCC-HHHHHHHHHHHHHcCCeEe---CCCcc---------ccccHHHHHHHHHhHHhh
Confidence 344444555799999999999998 7899999999999998753 322 3 233556678887766543
No 170
>PRK14574 hmsH outer membrane protein; Provisional
Probab=49.40 E-value=91 Score=35.74 Aligned_cols=101 Identities=14% Similarity=0.071 Sum_probs=73.5
Q ss_pred hhCCCCcchHHHHHHHHHhCC---CCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhc------CCCCCChHhhHH
Q psy9642 118 DLKTPQRGIPLIQTAIKKIQT---SDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIAN------EGPQFDTKYFLQ 188 (437)
Q Consensus 118 ~~~~~~~~i~~l~~ai~rl~~---~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~------~~~~~~~~~~l~ 188 (437)
..++|.++...++.++.--.+ .+..+. .+..|.-..+.+..|..|..++++-...-.. .....++.+...
T Consensus 339 ~~~~P~kA~~l~~~~~~~~~~~~~~~~~~~-~~~~L~yA~ld~e~~~~A~~~l~~~~~~~p~~~~~~~~~~~~pn~d~~~ 417 (822)
T PRK14574 339 DRRLPEKAAPILSSLYYSDGKTFRNSDDLL-DADDLYYSLNESEQLDKAYQFAVNYSEQTPYQVGVYGLPGKEPNDDWIE 417 (822)
T ss_pred hcCCcHHHHHHHHHHhhccccccCCCcchH-HHHHHHHHHHhcccHHHHHHHHHHHHhcCCcEEeccCCCCCCCCccHHH
Confidence 367788887777776543211 111121 1467888999999999999998886542110 022456677899
Q ss_pred HHHHHHHHHHHHhhHHHHHHHHHHHhc-cccc
Q psy9642 189 YFYYGGMIYLALKNYERALYFFEVIIT-TPAL 219 (437)
Q Consensus 189 Y~Yy~G~I~~~~k~y~~A~~~~~~ai~-~P~~ 219 (437)
+++..+++++..+++.+|.+.++.... +|.+
T Consensus 418 ~~~l~a~~~~~~gdl~~Ae~~le~l~~~aP~n 449 (822)
T PRK14574 418 GQTLLVQSLVALNDLPTAQKKLEDLSSTAPAN 449 (822)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCC
Confidence 999999999999999999999999987 9986
No 171
>PF04762 IKI3: IKI3 family; InterPro: IPR006849 Members of this family are components of the elongator multi-subunit component of a novel RNA polymerase II holoenzyme for transcriptional elongation [].
Probab=49.32 E-value=94 Score=36.14 Aligned_cols=54 Identities=26% Similarity=0.193 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHH
Q psy9642 146 LHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVI 213 (437)
Q Consensus 146 ~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~a 213 (437)
+.+.++=.--..++.+.+||+|.+--. +++ .|-.-.|-..+|+|++|.+++..|
T Consensus 874 l~Lal~VAq~SQkDPKEYLPfL~~L~~--------l~~------~~rry~ID~hLkRy~kAL~~L~~~ 927 (928)
T PF04762_consen 874 LELALMVAQQSQKDPKEYLPFLQELQK--------LPP------LYRRYKIDDHLKRYEKALRHLSAC 927 (928)
T ss_pred HHHHHHHHHHhccChHHHHHHHHHHHh--------CCh------hheeeeHhhhhCCHHHHHHHHHhh
Confidence 444444444456788999999876311 111 234557889999999999998764
No 172
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=49.04 E-value=39 Score=23.93 Aligned_cols=32 Identities=9% Similarity=0.162 Sum_probs=28.9
Q ss_pred cc-cHHHHHHHhCCCChHHHHHHHHHhHHcCceE
Q psy9642 321 TL-SLADVASRVQLGTPVQAEIYILKMISQNEIY 353 (437)
Q Consensus 321 ~I-sL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~ 353 (437)
.+ |..+||+.++++ ..-+...+..|..+|.|.
T Consensus 19 ~l~s~~~la~~~~vs-~~tv~~~l~~L~~~g~i~ 51 (60)
T smart00345 19 KLPSERELAAQLGVS-RTTVREALSRLEAEGLVQ 51 (60)
T ss_pred cCcCHHHHHHHHCCC-HHHHHHHHHHHHHCCCEE
Confidence 46 899999999997 789999999999999875
No 173
>PF12862 Apc5: Anaphase-promoting complex subunit 5
Probab=48.96 E-value=1.2e+02 Score=24.35 Aligned_cols=74 Identities=19% Similarity=0.138 Sum_probs=46.2
Q ss_pred HHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHH-HHHHHHHHHHHhhHHHHHHHHHHHhcccccccCHHHH
Q psy9642 152 QLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQY-FYYGGMIYLALKNYERALYFFEVIITTPALAVSHIML 226 (437)
Q Consensus 152 ~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y-~Yy~G~I~~~~k~y~~A~~~~~~ai~~P~~~~s~i~v 226 (437)
-.++..++|..|++-+.+-. +.+...........+.| ....|.++...+++++|...++.+++.-....+...+
T Consensus 6 ~~~~~~~dy~~A~d~L~~~f-D~~~~~~~~~~~~~~~~all~lA~~~~~~G~~~~A~~~l~eAi~~Are~~D~~~l 80 (94)
T PF12862_consen 6 LNALRSGDYSEALDALHRYF-DYAKQSNNSSSNSGLAYALLNLAELHRRFGHYEEALQALEEAIRLARENGDRRCL 80 (94)
T ss_pred HHHHHcCCHHHHHHHHHHHH-HHHhhcccchhhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHCCHHHH
Confidence 35788999999988877643 22221111110112222 2346778888899999999999999954444444443
No 174
>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional
Probab=48.72 E-value=3.9e+02 Score=30.08 Aligned_cols=117 Identities=9% Similarity=-0.104 Sum_probs=75.1
Q ss_pred CccHHHHHHHHHHHHHhcChhhhhhhHHHHHHHHHHHHHHHhhhCCCCcchHHHHHHHHHhCCCCcchhhHHHHHHHHHH
Q psy9642 76 SEYQEELFSQIQEFLNMCNPDQIRHAGDLYAELSHQYTKTVMDLKTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCL 155 (437)
Q Consensus 76 ~~~~~~~~~~~~~fl~~fd~~Qir~a~~~~~~l~~~~~~~~~~~~~~~~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L 155 (437)
.++...+|..+..|...+....+-++ ..+...+..-.++...+.+ ++-.|...+ .|..+..++.
T Consensus 102 ~~ea~~~l~~~~~~~Pd~~~a~~~~a------------~~L~~~~~~eeA~~~~~~~---l~~~p~~~~-~~~~~a~~l~ 165 (694)
T PRK15179 102 SDEGLAVWRGIHQRFPDSSEAFILML------------RGVKRQQGIEAGRAEIELY---FSGGSSSAR-EILLEAKSWD 165 (694)
T ss_pred cHHHHHHHHHHHhhCCCcHHHHHHHH------------HHHHHhccHHHHHHHHHHH---hhcCCCCHH-HHHHHHHHHH
Confidence 56777788877776555443333332 2222222222333344443 333455565 7778889999
Q ss_pred HhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhccc
Q psy9642 156 LAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIITTP 217 (437)
Q Consensus 156 ~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~~P 217 (437)
..+.|..|....++-+.. . .+.-.-.+--|..+...++.++|...|+.++..-
T Consensus 166 ~~g~~~~A~~~y~~~~~~--~-------p~~~~~~~~~a~~l~~~G~~~~A~~~~~~a~~~~ 218 (694)
T PRK15179 166 EIGQSEQADACFERLSRQ--H-------PEFENGYVGWAQSLTRRGALWRARDVLQAGLDAI 218 (694)
T ss_pred HhcchHHHHHHHHHHHhc--C-------CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhh
Confidence 999999999999887752 1 1222333455888889999999999999999843
No 175
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=47.79 E-value=1.5e+02 Score=25.17 Aligned_cols=50 Identities=16% Similarity=0.199 Sum_probs=40.2
Q ss_pred ccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecC---CCEEEEccCCC
Q psy9642 320 LTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKK---DGMVVFNDNPQ 370 (437)
Q Consensus 320 s~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~---~g~v~F~~~~~ 370 (437)
..++|++||..+.-+ +..|..+|.+|.+.|-|.=+=-.+ .+.++|..+++
T Consensus 18 ~~vtl~elA~~l~cS-~Rn~r~lLkkm~~~gWi~W~pg~GRG~~S~L~~l~~~~ 70 (115)
T PF12793_consen 18 VEVTLDELAELLFCS-RRNARTLLKKMQEEGWITWQPGRGRGNRSQLTFLKSPE 70 (115)
T ss_pred cceeHHHHHHHhCCC-HHHHHHHHHHHHHCCCeeeeCCCCCCCCCeeEEeeCHH
Confidence 368999999999987 899999999999999985443332 47888886653
No 176
>TIGR00540 hemY_coli hemY protein. This is an uncharacterized protein encoded next to a heme-biosynthetic enzyme in two gamma division proteobacteria (E. coli and H. influenzae). It is known in no other species. The gene symbol hemY is unfortunate in that an unrelated protein, protoporphyrinogen oxidase, is designated as HemG in E. coli but as HemY in Bacillus subtilis.
Probab=47.74 E-value=84 Score=32.44 Aligned_cols=90 Identities=8% Similarity=0.056 Sum_probs=59.1
Q ss_pred HHhhhCCCCcchHHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHH
Q psy9642 115 TVMDLKTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGG 194 (437)
Q Consensus 115 ~~~~~~~~~~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G 194 (437)
.+...+.+-.+...+..+..+. |.+.. .+....+++.+..++|..|+..++.-... .|. .-.-.+..|
T Consensus 127 aa~~~g~~~~A~~~l~~a~~~~-p~~~l--~~~~~~a~l~l~~~~~~~Al~~l~~l~~~--------~P~-~~~~l~ll~ 194 (409)
T TIGR00540 127 AAQQRGDEARANQHLEEAAELA-GNDNI--LVEIARTRILLAQNELHAARHGVDKLLEM--------APR-HKEVLKLAE 194 (409)
T ss_pred HHHHCCCHHHHHHHHHHHHHhC-CcCch--HHHHHHHHHHHHCCCHHHHHHHHHHHHHh--------CCC-CHHHHHHHH
Confidence 3444566666777777776544 43321 13444578888899999888877665432 111 123355788
Q ss_pred HHHHHHhhHHHHHHHHHHHhcc
Q psy9642 195 MIYLALKNYERALYFFEVIITT 216 (437)
Q Consensus 195 ~I~~~~k~y~~A~~~~~~ai~~ 216 (437)
.++...+||++|.+.+......
T Consensus 195 ~~~~~~~d~~~a~~~l~~l~k~ 216 (409)
T TIGR00540 195 EAYIRSGAWQALDDIIDNMAKA 216 (409)
T ss_pred HHHHHHhhHHHHHHHHHHHHHc
Confidence 8899999999999998888864
No 177
>PF12070 DUF3550: Protein of unknown function (DUF3550/UPF0682); InterPro: IPR022709 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 249 to 606 amino acids in length.
Probab=46.91 E-value=55 Score=35.16 Aligned_cols=52 Identities=25% Similarity=0.443 Sum_probs=34.5
Q ss_pred hHHHHHHHHHHHHHHhhHHH-HHHHHHHHhc--ccc--cc--cC-----HHHHHHHHHHHHHHHHHh
Q psy9642 186 FLQYFYYGGMIYLALKNYER-ALYFFEVIIT--TPA--LA--VS-----HIMLEGYKKYLLIYLIVY 240 (437)
Q Consensus 186 ~l~Y~Yy~G~I~~~~k~y~~-A~~~~~~ai~--~P~--~~--~s-----~i~vea~Kk~iLv~Lil~ 240 (437)
+|-|+|| +....-+|.. |+.+|+.+.+ ... .. .+ ...+.-|-++|+|+|+++
T Consensus 70 QLYyhyY---LRTse~~yL~Ea~~FY~AI~~R~Yf~~~~~~~~~dl~~~~K~LR~~ARFivVcLlLn 133 (513)
T PF12070_consen 70 QLYYHYY---LRTSETNYLNEAYIFYEAIRSRGYFKDASKEEKPDLMVPNKQLRYYARFIVVCLLLN 133 (513)
T ss_pred HHHHHHH---HHhccccHHHHHHHHHHHHHhhhhccccccccccccchhHHHHHHHHHHHHHHHHhh
Confidence 7888888 6777777764 7777765554 211 11 11 145577889999999876
No 178
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=46.81 E-value=67 Score=28.65 Aligned_cols=48 Identities=6% Similarity=0.083 Sum_probs=37.0
Q ss_pred cccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCCCEEEEccCCC
Q psy9642 321 TLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVFNDNPQ 370 (437)
Q Consensus 321 ~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~g~v~F~~~~~ 370 (437)
.++.++||+..+++ ..-+++++..|...|-|...-=. +|-..+..+++
T Consensus 24 ~~s~~eIA~~~~is-~~~L~kIl~~L~~aGlv~S~rG~-~GGy~La~~p~ 71 (153)
T PRK11920 24 LSRIPEIARAYGVS-ELFLFKILQPLVEAGLVETVRGR-NGGVRLGRPAA 71 (153)
T ss_pred cCcHHHHHHHHCcC-HHHHHHHHHHHHHCCCEEeecCC-CCCeeecCCHH
Confidence 47999999999998 88999999999999988776643 33344443333
No 179
>PF10602 RPN7: 26S proteasome subunit RPN7; InterPro: IPR019585 This entry represents the regulatory subunit RPN7 (known as the non-ATPase regulatory subunit 6 in higher eukaryotes) of the 26S proteasome. This entry also matches the evolutionarily related subunit 1 of the COP9 signalosome complex (CSN) from Arabidopsis []. The 26S proteasome plays a major role in ATP-dependent degradation of ubiquitinated proteins. Substrate specificity is conferred by the regulatory particle (RP), which can dissociate into stable lid and base subcomplexes. The regulatory subunit RPN7 is one of the lid subunits of the 26S proteasome and has been shown in Saccharomyces cerevisiae (Baker's yeast) to be required for structural integrity []. The COP9 signalosome is a conserved protein complex composed of eight subunits, where Individual subunits of the complex have been linked to various signal transduction pathways leading to gene expression and cell cycle control []. The overall organisation and the amino acid sequences of the COP9 signalosome subunits resemble the lid subcomplex of the 19 S regulatory particle for the 26 S proteasome []. COP9 subunit 1 (CSN1 or GPS1) of the COP9 complex is an essential subunit of the complex with regard to both structural integrity and functionality. The N-terminal region of subunit 1 (CSN1-N) can inhibit c-fos expression from either a transfected template or a chromosomal transgene (fos-lacZ), and may contain the activity domain that confers most of the repression functions of CSN1. The C-terminal region of subunit 1 (CSN1-C) allows integration of the protein into the COP9 signalosome.
Probab=46.56 E-value=1.8e+02 Score=26.52 Aligned_cols=72 Identities=7% Similarity=-0.025 Sum_probs=58.9
Q ss_pred hHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhcccccccC
Q psy9642 145 SLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIITTPALAVS 222 (437)
Q Consensus 145 ~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~~P~~~~s 222 (437)
-.|..+.......|++..|++...+ ..+.|. ++.+.+..++.--.+.+..+||..+..+...+-..+....+
T Consensus 37 ~~~~~l~~~~~~~Gd~~~A~k~y~~-~~~~~~-----~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka~~~~~~~~d 108 (177)
T PF10602_consen 37 MALEDLADHYCKIGDLEEALKAYSR-ARDYCT-----SPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKAESLIEKGGD 108 (177)
T ss_pred HHHHHHHHHHHHhhhHHHHHHHHHH-HhhhcC-----CHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhccch
Confidence 3688889999999999999999888 444443 56778888888888888889999999999999887766433
No 180
>PRK10747 putative protoheme IX biogenesis protein; Provisional
Probab=46.17 E-value=94 Score=32.01 Aligned_cols=90 Identities=9% Similarity=0.076 Sum_probs=63.0
Q ss_pred HhhhCCCCcchHHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHH
Q psy9642 116 VMDLKTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGM 195 (437)
Q Consensus 116 ~~~~~~~~~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~ 195 (437)
+...+.+-.+...+..|.. .+|+.. ........++.+..+++..|+..+++-... .| +.....+..+.
T Consensus 128 A~~~g~~~~A~~~l~~A~~-~~~~~~--~~~~l~~a~l~l~~g~~~~Al~~l~~~~~~--------~P-~~~~al~ll~~ 195 (398)
T PRK10747 128 AQQRGDEARANQHLERAAE-LADNDQ--LPVEITRVRIQLARNENHAARHGVDKLLEV--------AP-RHPEVLRLAEQ 195 (398)
T ss_pred HHHCCCHHHHHHHHHHHHh-cCCcch--HHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--------CC-CCHHHHHHHHH
Confidence 3556777777788887753 344332 223344578999999999999988776432 11 13345567789
Q ss_pred HHHHHhhHHHHHHHHHHHhccc
Q psy9642 196 IYLALKNYERALYFFEVIITTP 217 (437)
Q Consensus 196 I~~~~k~y~~A~~~~~~ai~~P 217 (437)
+|+..++|++|.+.|......-
T Consensus 196 ~~~~~gdw~~a~~~l~~l~k~~ 217 (398)
T PRK10747 196 AYIRTGAWSSLLDILPSMAKAH 217 (398)
T ss_pred HHHHHHhHHHHHHHHHHHHHcC
Confidence 9999999999999998888743
No 181
>PF13591 MerR_2: MerR HTH family regulatory protein
Probab=46.06 E-value=54 Score=26.10 Aligned_cols=72 Identities=11% Similarity=0.252 Sum_probs=46.2
Q ss_pred ccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCCCEEEEccCCCCCCchHHHHHHHH-------HHHHHHHHHHH
Q psy9642 322 LSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVFNDNPQRFNNPLTFAQIES-------NIRACMHLDGK 394 (437)
Q Consensus 322 IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~g~v~F~~~~~~~~~~e~~~~l~~-------~i~~~~~L~~~ 394 (437)
|++.+++...|++ + ..|..+++.|-|......+ --.|....- ..-+-..+|+. .+.-+++|-++
T Consensus 1 is~~e~~~~~~i~-~----~~l~~lve~Gli~p~~~~~--~~~f~~~~l--~rl~~~~rL~~Dl~in~~gi~lil~LLd~ 71 (84)
T PF13591_consen 1 ISLEEFCEACGIE-P----EFLRELVEEGLIEPEGEEE--EWYFSEEDL--ARLRRIRRLHRDLGINLEGIALILDLLDR 71 (84)
T ss_pred CCHHHHHHHHCcC-H----HHHHHHHHCCCeeecCCCC--eeeECHHHH--HHHHHHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 7899999999997 3 5788999999999877653 233653210 01123333333 23566777777
Q ss_pred HHHHHHHh
Q psy9642 395 FQAMEEEI 402 (437)
Q Consensus 395 ~~~~d~~l 402 (437)
+..++.++
T Consensus 72 i~~L~~el 79 (84)
T PF13591_consen 72 IEQLRREL 79 (84)
T ss_pred HHHHHHHH
Confidence 77777766
No 182
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=46.01 E-value=2.4e+02 Score=25.88 Aligned_cols=109 Identities=12% Similarity=0.021 Sum_probs=63.8
Q ss_pred ccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEec--CCCEEEEccCCCCCCchHHHHHHHHHHHHHHHHHHHHHH
Q psy9642 320 LTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINK--KDGMVVFNDNPQRFNNPLTFAQIESNIRACMHLDGKFQA 397 (437)
Q Consensus 320 s~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~--~~g~v~F~~~~~~~~~~e~~~~l~~~i~~~~~L~~~~~~ 397 (437)
..++-.+||+.+|++ ..++.+++.++-++|-+..+--+ +.|..++.-.. +..++-..+..++.++ .+.++.
T Consensus 35 g~~tdeeLA~~Lgi~-~~~VRk~L~~L~e~gLv~~~r~r~~~~Gr~~y~w~l---~~~~i~d~ik~~~~~~---~~klk~ 107 (178)
T PRK06266 35 GEVTDEEIAEQTGIK-LNTVRKILYKLYDARLADYKREKDEETNWYTYTWKP---ELEKLPEIIKKKKMEE---LKKLKE 107 (178)
T ss_pred CCcCHHHHHHHHCCC-HHHHHHHHHHHHHCCCeEEeeeeccCCCcEEEEEEe---CHHHHHHHHHHHHHHH---HHHHHH
Confidence 469999999999998 79999999999999998754433 34555553221 2334555555555433 222222
Q ss_pred HHHHhhCCHHHHHHhcCCC-------CcccCCCCCCCcccccccc
Q psy9642 398 MEEEILVNPLYVKKAASPS-------DEETGSSKPGGRVMEVENS 435 (437)
Q Consensus 398 ~d~~l~~~~~yi~k~~~~~-------~~~~~~~~~~~~~~~~~~~ 435 (437)
.=+.-..+..|+=-..+.. +.+-++..=|+++.+.+|+
T Consensus 108 ~l~~e~~~~~Y~Cp~C~~rytf~eA~~~~F~Cp~Cg~~L~~~dn~ 152 (178)
T PRK06266 108 QLEEEENNMFFFCPNCHIRFTFDEAMEYGFRCPQCGEMLEEYDNS 152 (178)
T ss_pred HhhhccCCCEEECCCCCcEEeHHHHhhcCCcCCCCCCCCeecccH
Confidence 2111122333431111110 0112666889999999886
No 183
>PRK12370 invasion protein regulator; Provisional
Probab=45.41 E-value=70 Score=34.58 Aligned_cols=84 Identities=11% Similarity=-0.020 Sum_probs=59.6
Q ss_pred hCCCCcchHHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHH
Q psy9642 119 LKTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYL 198 (437)
Q Consensus 119 ~~~~~~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~ 198 (437)
.+.+-.++..+..|+. ++|+.. ..|..+..++...|.+..|+..+++-+.- ++. ...+.++.+.++.
T Consensus 351 ~g~~~~A~~~~~~Al~-l~P~~~---~a~~~lg~~l~~~G~~~eAi~~~~~Al~l--------~P~-~~~~~~~~~~~~~ 417 (553)
T PRK12370 351 HSEYIVGSLLFKQANL-LSPISA---DIKYYYGWNLFMAGQLEEALQTINECLKL--------DPT-RAAAGITKLWITY 417 (553)
T ss_pred ccCHHHHHHHHHHHHH-hCCCCH---HHHHHHHHHHHHCCCHHHHHHHHHHHHhc--------CCC-ChhhHHHHHHHHH
Confidence 4555667778887754 456543 26788889999999999999999886552 222 1223334455666
Q ss_pred HHhhHHHHHHHHHHHhc
Q psy9642 199 ALKNYERALYFFEVIIT 215 (437)
Q Consensus 199 ~~k~y~~A~~~~~~ai~ 215 (437)
..++|++|..++..++.
T Consensus 418 ~~g~~eeA~~~~~~~l~ 434 (553)
T PRK12370 418 YHTGIDDAIRLGDELRS 434 (553)
T ss_pred hccCHHHHHHHHHHHHH
Confidence 78899999999999986
No 184
>KOG3364|consensus
Probab=45.33 E-value=47 Score=29.46 Aligned_cols=38 Identities=21% Similarity=0.405 Sum_probs=33.3
Q ss_pred ChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhcc-ccc
Q psy9642 182 DTKYFLQYFYYGGMIYLALKNYERALYFFEVIITT-PAL 219 (437)
Q Consensus 182 ~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~~-P~~ 219 (437)
++...-.|.||-+.-++..|+|++|.++....+++ |.+
T Consensus 66 ~~~~rRe~lyYLAvg~yRlkeY~~s~~yvd~ll~~e~~n 104 (149)
T KOG3364|consen 66 HPERRRECLYYLAVGHYRLKEYSKSLRYVDALLETEPNN 104 (149)
T ss_pred CcccchhhhhhhHHHHHHHhhHHHHHHHHHHHHhhCCCc
Confidence 46668889999999999999999999999999994 554
No 185
>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional
Probab=45.29 E-value=1e+02 Score=36.09 Aligned_cols=84 Identities=10% Similarity=-0.048 Sum_probs=61.1
Q ss_pred CCCCcchHHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHH
Q psy9642 120 KTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLA 199 (437)
Q Consensus 120 ~~~~~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~ 199 (437)
+..-.++..+++|+ +++|.. ..++..+.+..+..+.+..|+..+.+-+.. ++. ...|+-..|.|
T Consensus 58 Gd~~~A~~~l~~Al-~~dP~n---~~~~~~LA~~yl~~g~~~~A~~~~~kAv~l--------dP~-n~~~~~~La~i--- 121 (987)
T PRK09782 58 NDEATAIREFEYIH-QQVPDN---IPLTLYLAEAYRHFGHDDRARLLLEDQLKR--------HPG-DARLERSLAAI--- 121 (987)
T ss_pred CCHHHHHHHHHHHH-HhCCCC---HHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--------Ccc-cHHHHHHHHHh---
Confidence 44446777888875 446655 557799999999999999998888876652 332 33333333444
Q ss_pred HhhHHHHHHHHHHHhc-ccccc
Q psy9642 200 LKNYERALYFFEVIIT-TPALA 220 (437)
Q Consensus 200 ~k~y~~A~~~~~~ai~-~P~~~ 220 (437)
++|.+|...|+..+. .|...
T Consensus 122 -~~~~kA~~~ye~l~~~~P~n~ 142 (987)
T PRK09782 122 -PVEVKSVTTVEELLAQQKACD 142 (987)
T ss_pred -ccChhHHHHHHHHHHhCCCCh
Confidence 999999999999998 78763
No 186
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=44.48 E-value=1.1e+02 Score=24.75 Aligned_cols=46 Identities=15% Similarity=0.106 Sum_probs=35.8
Q ss_pred hhccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCCCEEEEc
Q psy9642 318 TFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVFN 366 (437)
Q Consensus 318 ~Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~g~v~F~ 366 (437)
.--.++-++||+++|++ .+-+-+.|.+|...|.|.- .+..|.+.-.
T Consensus 44 ~~~~is~~eLa~~~g~s-r~tVsr~L~~Le~~GlI~r--~~~~~~~~~n 89 (95)
T TIGR01610 44 KQDRVTATVIAELTGLS-RTHVSDAIKSLARRRIIFR--QGMMGIVGVN 89 (95)
T ss_pred cCCccCHHHHHHHHCcC-HHHHHHHHHHHHHCCCeee--ecCCceeecC
Confidence 34679999999999997 7889999999999999963 3334544433
No 187
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=44.37 E-value=1.5e+02 Score=23.09 Aligned_cols=38 Identities=16% Similarity=0.190 Sum_probs=33.0
Q ss_pred ccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEec
Q psy9642 320 LTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINK 358 (437)
Q Consensus 320 s~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~ 358 (437)
..++.++|++.++++ ...+...|.+|...|.|...-+.
T Consensus 23 ~~~~~~~la~~~~~s-~~~i~~~l~~L~~~g~v~~~~~~ 60 (101)
T smart00347 23 GPLSVSELAKRLGVS-PSTVTRVLDRLEKKGLIRRLPSP 60 (101)
T ss_pred CCcCHHHHHHHHCCC-chhHHHHHHHHHHCCCeEecCCC
Confidence 358999999999997 67889999999999999877654
No 188
>KOG2796|consensus
Probab=43.97 E-value=3.4e+02 Score=27.05 Aligned_cols=116 Identities=16% Similarity=0.235 Sum_probs=72.5
Q ss_pred hhhhhHHHHHHHHHHHHHHHhhhCCCCcchHHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhc
Q psy9642 97 QIRHAGDLYAELSHQYTKTVMDLKTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIAN 176 (437)
Q Consensus 97 Qir~a~~~~~~l~~~~~~~~~~~~~~~~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~ 176 (437)
-++..-.+...+-..+.+++.-.+.-..++..+..-+.+. ++.-|.+...+.+.....|+.+.|-...++ +....
T Consensus 168 sv~lW~KRl~~Vmy~~~~~llG~kEy~iS~d~~~~vi~~~---~e~~p~L~s~Lgr~~MQ~GD~k~a~~yf~~-vek~~- 242 (366)
T KOG2796|consen 168 SIRLWRKRLGRVMYSMANCLLGMKEYVLSVDAYHSVIKYY---PEQEPQLLSGLGRISMQIGDIKTAEKYFQD-VEKVT- 242 (366)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcchhhhhhHHHHHHHHHhC---CcccHHHHHHHHHHHHhcccHHHHHHHHHH-HHHHH-
Confidence 3455555555555555555554444456677777777754 345566788999999999999988444432 21111
Q ss_pred CCCCCCh-HhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhc-cccc
Q psy9642 177 EGPQFDT-KYFLQYFYYGGMIYLALKNYERALYFFEVIIT-TPAL 219 (437)
Q Consensus 177 ~~~~~~~-~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~-~P~~ 219 (437)
..++. .....-.--.+.||.+.+||.+|+.+|..|+. -|.+
T Consensus 243 --~kL~~~q~~~~V~~n~a~i~lg~nn~a~a~r~~~~i~~~D~~~ 285 (366)
T KOG2796|consen 243 --QKLDGLQGKIMVLMNSAFLHLGQNNFAEAHRFFTEILRMDPRN 285 (366)
T ss_pred --hhhhccchhHHHHhhhhhheecccchHHHHHHHhhccccCCCc
Confidence 11111 11233334566788889999999999999887 4443
No 189
>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=43.70 E-value=1.9e+02 Score=28.46 Aligned_cols=89 Identities=13% Similarity=0.073 Sum_probs=54.8
Q ss_pred HHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHH
Q psy9642 127 PLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERA 206 (437)
Q Consensus 127 ~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A 206 (437)
..++.-+.++ |.+...--.|=-+.++.+..++|..|..+..+-+-...+.+. .+.-. +=-|++...+++-++|
T Consensus 162 ~~F~~fi~~Y-P~s~~~~nA~yWLGe~~y~qg~y~~Aa~~f~~~~k~~P~s~K--Apdal----lKlg~~~~~l~~~d~A 234 (262)
T COG1729 162 QAFQAFIKKY-PNSTYTPNAYYWLGESLYAQGDYEDAAYIFARVVKDYPKSPK--APDAL----LKLGVSLGRLGNTDEA 234 (262)
T ss_pred HHHHHHHHcC-CCCcccchhHHHHHHHHHhcccchHHHHHHHHHHHhCCCCCC--ChHHH----HHHHHHHHHhcCHHHH
Confidence 3444555555 333333334555667778888888887776666555433211 12222 3458888888888888
Q ss_pred HHHHHHHhc-ccccccC
Q psy9642 207 LYFFEVIIT-TPALAVS 222 (437)
Q Consensus 207 ~~~~~~ai~-~P~~~~s 222 (437)
+..|++++. .|.+...
T Consensus 235 ~atl~qv~k~YP~t~aA 251 (262)
T COG1729 235 CATLQQVIKRYPGTDAA 251 (262)
T ss_pred HHHHHHHHHHCCCCHHH
Confidence 888888887 7776433
No 190
>PRK10153 DNA-binding transcriptional activator CadC; Provisional
Probab=43.64 E-value=56 Score=35.24 Aligned_cols=65 Identities=12% Similarity=0.102 Sum_probs=53.1
Q ss_pred hHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhc-cccc
Q psy9642 145 SLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIIT-TPAL 219 (437)
Q Consensus 145 ~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~-~P~~ 219 (437)
-.|..+.-.++..+++..|...+++-+.- .+ ....+++.|.++...+++++|.++|+.|+. .|..
T Consensus 421 ~~~~ala~~~~~~g~~~~A~~~l~rAl~L--------~p--s~~a~~~lG~~~~~~G~~~eA~~~~~~A~~L~P~~ 486 (517)
T PRK10153 421 RIYEILAVQALVKGKTDEAYQAINKAIDL--------EM--SWLNYVLLGKVYELKGDNRLAADAYSTAFNLRPGE 486 (517)
T ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHHHHc--------CC--CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCC
Confidence 35777777777889999999999987652 23 245778899999999999999999999998 7764
No 191
>PRK10265 chaperone-modulator protein CbpM; Provisional
Probab=42.95 E-value=62 Score=26.78 Aligned_cols=75 Identities=11% Similarity=0.139 Sum_probs=45.3
Q ss_pred hccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCCCEEEEcc-CCCCCCchHHHHHHHH-------HHHHHHH
Q psy9642 319 FLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVFND-NPQRFNNPLTFAQIES-------NIRACMH 390 (437)
Q Consensus 319 Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~g~v~F~~-~~~~~~~~e~~~~l~~-------~i~~~~~ 390 (437)
-.++++.+++...|++ + ..|.++|+-|-|......+ +--.|.+ ... -.+...+++. .+.-+++
T Consensus 5 ~~~lt~~Elc~~~gi~-~----~~l~eLve~GlIep~~~~~-~~~~F~~~~l~---r~~~a~rL~~dl~in~~gialvl~ 75 (101)
T PRK10265 5 TVTFTITEFCLHTGVS-E----EELNEIVGLGVIEPREIQE-TTWVFDDHAAI---VVQRAVRLRHELALDWPGIAVALT 75 (101)
T ss_pred EEEeeHHHHHHHHCcC-H----HHHHHHHHCCCeecCCCCc-ccceECHHHHH---HHHHHHHHHHHcCCCHHHHHHHHH
Confidence 3579999999999997 3 5777999999998644433 4445553 211 1122223332 2345556
Q ss_pred HHHHHHHHHHHh
Q psy9642 391 LDGKFQAMEEEI 402 (437)
Q Consensus 391 L~~~~~~~d~~l 402 (437)
|-+++.+++.++
T Consensus 76 LLd~i~~Lr~el 87 (101)
T PRK10265 76 LLDEIAHLKQEN 87 (101)
T ss_pred HHHHHHHHHHHH
Confidence 666666666555
No 192
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=42.77 E-value=56 Score=30.11 Aligned_cols=44 Identities=20% Similarity=0.172 Sum_probs=35.1
Q ss_pred ccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCCCEEEEc
Q psy9642 322 LSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVFN 366 (437)
Q Consensus 322 IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~g~v~F~ 366 (437)
.++++||+.+++++..-+...|..|..+|.|...=.... -+.|.
T Consensus 26 ~~~~ela~~~~~~s~~tv~~~l~~L~~~g~i~~~~~~~~-~~~~~ 69 (199)
T TIGR00498 26 PSIREIARAVGLRSPSAAEEHLKALERKGYIERDPGKPR-AIRIL 69 (199)
T ss_pred CcHHHHHHHhCCCChHHHHHHHHHHHHCCCEecCCCCCC-eEEeC
Confidence 889999999999867889999999999999876644433 34443
No 193
>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=42.41 E-value=53 Score=24.60 Aligned_cols=39 Identities=3% Similarity=-0.056 Sum_probs=34.1
Q ss_pred hhccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEe
Q psy9642 318 TFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATIN 357 (437)
Q Consensus 318 ~Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id 357 (437)
..-..+..+||+.++++ ...+-..|.+|...|.|.-.-.
T Consensus 19 ~~~~~t~~eIa~~l~i~-~~~v~~~L~~L~~~GlV~~~~~ 57 (68)
T PF01978_consen 19 KNGPATAEEIAEELGIS-RSTVYRALKSLEEKGLVEREEG 57 (68)
T ss_dssp HHCHEEHHHHHHHHTSS-HHHHHHHHHHHHHTTSEEEEEE
T ss_pred HcCCCCHHHHHHHHCcC-HHHHHHHHHHHHHCCCEEEEcC
Confidence 45678999999999998 8899999999999999876654
No 194
>PF13730 HTH_36: Helix-turn-helix domain
Probab=42.14 E-value=39 Score=24.10 Aligned_cols=30 Identities=13% Similarity=0.070 Sum_probs=26.9
Q ss_pred ccHHHHHHHhCCCChHHHHHHHHHhHHcCce
Q psy9642 322 LSLADVASRVQLGTPVQAEIYILKMISQNEI 352 (437)
Q Consensus 322 IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I 352 (437)
-|.++||+.+|++ ...+.+.+.++++.|-|
T Consensus 26 pS~~~la~~~g~s-~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 26 PSQETLAKDLGVS-RRTVQRAIKELEEKGLI 55 (55)
T ss_pred cCHHHHHHHHCcC-HHHHHHHHHHHHHCcCC
Confidence 4899999999998 88999999999998865
No 195
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=41.41 E-value=1.2e+02 Score=28.97 Aligned_cols=48 Identities=13% Similarity=0.181 Sum_probs=39.4
Q ss_pred hccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCCCEEEEcc
Q psy9642 319 FLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVFND 367 (437)
Q Consensus 319 Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~g~v~F~~ 367 (437)
...||.++||+.++++ ..-+-+.|.+|.+.|.|.-..+.....+...+
T Consensus 19 ~~~IS~~eLA~~L~iS-~~Tvsr~Lk~LEe~GlI~R~~~~r~~~v~LTe 66 (217)
T PRK14165 19 TVKISSSEFANHTGTS-SKTAARILKQLEDEGYITRTIVPRGQLITITE 66 (217)
T ss_pred CCCcCHHHHHHHHCcC-HHHHHHHHHHHHHCCCEEEEEcCCceEEEECH
Confidence 3469999999999997 78899999999999999988886554454443
No 196
>PRK11447 cellulose synthase subunit BcsC; Provisional
Probab=40.89 E-value=1.2e+02 Score=36.01 Aligned_cols=60 Identities=18% Similarity=0.162 Sum_probs=41.0
Q ss_pred HHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhc-cccc
Q psy9642 151 CQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIIT-TPAL 219 (437)
Q Consensus 151 ~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~-~P~~ 219 (437)
...++..+++..|+..+.+-+.. ++. ...-++.-|.++...++|++|..+|+.++. .|..
T Consensus 358 g~~~~~~g~~~eA~~~~~~Al~~--------~P~-~~~a~~~Lg~~~~~~g~~~eA~~~y~~aL~~~p~~ 418 (1157)
T PRK11447 358 GDAALKANNLAQAERLYQQARQV--------DNT-DSYAVLGLGDVAMARKDYAAAERYYQQALRMDPGN 418 (1157)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHh--------CCC-CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCC
Confidence 34556666777776666655432 122 223345679999999999999999999998 5764
No 197
>PRK10512 selenocysteinyl-tRNA-specific translation factor; Provisional
Probab=39.74 E-value=1.8e+02 Score=32.18 Aligned_cols=86 Identities=13% Similarity=-0.001 Sum_probs=63.1
Q ss_pred hccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCCCEEEEccCCCCCCchHHHHHHHHHHHHHHHHHH--HHH
Q psy9642 319 FLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVFNDNPQRFNNPLTFAQIESNIRACMHLDG--KFQ 396 (437)
Q Consensus 319 Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~g~v~F~~~~~~~~~~e~~~~l~~~i~~~~~L~~--~~~ 396 (437)
+.--.+++++..++++ ..++..++..|+..|.+. +|+ .-+.|. .+..+.+.+.+...+.-+. .+.
T Consensus 504 ~~p~~~~~~~~~l~~~-~~~~~~~l~~l~~~g~lv-~l~---~~~~~~--------~~~~~~~~~~~~~~~~~~~~~~~~ 570 (614)
T PRK10512 504 DEPWWVRDLAKETGTD-EQAMRLTLRQAAQQGIIT-AIV---KDRYYR--------NDRIVQFANMIRELDQECGSTCAA 570 (614)
T ss_pred cCCCCHHHHHHHhCCC-HHHHHHHHHHHHHCCCEE-Eec---CCEEEC--------HHHHHHHHHHHHHHHhhCCcEeHH
Confidence 5777889999999997 788999999999999775 443 233333 3455666666666555433 788
Q ss_pred HHHHHhhCCHHHHHHhcCCCC
Q psy9642 397 AMEEEILVNPLYVKKAASPSD 417 (437)
Q Consensus 397 ~~d~~l~~~~~yi~k~~~~~~ 417 (437)
+.++.+++|+.|+--.+..=|
T Consensus 571 ~~r~~~g~sRK~~i~lLE~~D 591 (614)
T PRK10512 571 DFRDRLGVGRKLAIQILEYFD 591 (614)
T ss_pred HHHHHhCccHHHHHHHHHHhc
Confidence 999999999999876665433
No 198
>PF10345 Cohesin_load: Cohesin loading factor; InterPro: IPR019440 Cohesin loading factor is a conserved protein that has been characterised in fungi. It is associated with the cohesin complex and is required in G1 for cohesin binding to chromosomes, but is dispensable in G2 when cohesion has been established. It is often referred to as Ssl3 in Schizosaccharomyces pombe (Fission yeast), and Scc4 in Saccharomyces cerevisiae (Baker's yeast). It complexes with Mis4 [].
Probab=39.73 E-value=5.4e+02 Score=28.17 Aligned_cols=154 Identities=14% Similarity=0.124 Sum_probs=96.7
Q ss_pred ccCcchhhHHHHHHHHHHhccccCCCCCCccHHHHHHHHHHHHHhcChhhhhhhHHHHHHHHHHHHHHHhhhCCCCcchH
Q psy9642 48 TLETFQHSLGILAILSAKLTLLSSSNTGSEYQEELFSQIQEFLNMCNPDQIRHAGDLYAELSHQYTKTVMDLKTPQRGIP 127 (437)
Q Consensus 48 ~ldp~~hsl~~L~vL~~~~~~~~~~~~~~~~~~~~~~~~~~fl~~fd~~Qir~a~~~~~~l~~~~~~~~~~~~~~~~~i~ 127 (437)
.|.|......+|=+=...+.-.. +....+..+++...-+++.+=.-++|..+.. +.+.....+ |..+..
T Consensus 52 ~l~p~~ea~~~l~la~iL~~eT~----n~~~Ae~~L~k~~~l~~~~~~~d~k~~~~~l------l~~i~~~~~-~~~a~~ 120 (608)
T PF10345_consen 52 KLSPRQEARVRLRLASILLEETE----NLDLAETYLEKAILLCERHRLTDLKFRCQFL------LARIYFKTN-PKAALK 120 (608)
T ss_pred CCCHHHHHHHHHHHHHHHHHHcC----CHHHHHHHHHHHHHhccccchHHHHHHHHHH------HHHHHHhcC-HHHHHH
Confidence 45677777776665555554332 2445667777776666653333344433332 223333333 333888
Q ss_pred HHHHHHHHhCCCCcchhhHHHHHHHH--HHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHH
Q psy9642 128 LIQTAIKKIQTSDSQLTSLHSDLCQL--CLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYER 205 (437)
Q Consensus 128 ~l~~ai~rl~~~~~~lT~~h~~l~~l--~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~ 205 (437)
.+..+|..++..+...=..+-.|++. ++..+++..|+..+..-+..-.. .-++.-.+...++.|++....+...+
T Consensus 121 ~l~~~I~~~~~~~~~~w~~~frll~~~l~~~~~d~~~Al~~L~~~~~~a~~---~~d~~~~v~~~l~~~~l~l~~~~~~d 197 (608)
T PF10345_consen 121 NLDKAIEDSETYGHSAWYYAFRLLKIQLALQHKDYNAALENLQSIAQLANQ---RGDPAVFVLASLSEALLHLRRGSPDD 197 (608)
T ss_pred HHHHHHHHHhccCchhHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhhh---cCCHHHHHHHHHHHHHHHhcCCCchh
Confidence 89999988876555554555566544 44467899999988775543211 23566688888999999998887888
Q ss_pred HHHHHHHHhc
Q psy9642 206 ALYFFEVIIT 215 (437)
Q Consensus 206 A~~~~~~ai~ 215 (437)
+.+-+..+..
T Consensus 198 ~~~~l~~~~~ 207 (608)
T PF10345_consen 198 VLELLQRAIA 207 (608)
T ss_pred HHHHHHHHHH
Confidence 8887777744
No 199
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=39.62 E-value=2.1e+02 Score=24.45 Aligned_cols=45 Identities=7% Similarity=0.041 Sum_probs=37.0
Q ss_pred ccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCCCEEEEcc
Q psy9642 320 LTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVFND 367 (437)
Q Consensus 320 s~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~g~v~F~~ 367 (437)
...+..+|++.++++ ...+-.++..|.+.|-|..+-+ ...+.+.-
T Consensus 29 ~~~~v~ela~~l~ls-qstvS~HL~~L~~AGLV~~~r~--Gr~~~Y~l 73 (117)
T PRK10141 29 GELCVCDLCTALDQS-QPKISRHLALLRESGLLLDRKQ--GKWVHYRL 73 (117)
T ss_pred CCcCHHHHHHHHCcC-HHHHHHHHHHHHHCCceEEEEE--cCEEEEEE
Confidence 358899999999998 6789999999999999999886 34455543
No 200
>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A.
Probab=39.25 E-value=1.1e+02 Score=28.35 Aligned_cols=65 Identities=17% Similarity=0.185 Sum_probs=45.6
Q ss_pred HHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhc-ccccc
Q psy9642 150 LCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIIT-TPALA 220 (437)
Q Consensus 150 l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~-~P~~~ 220 (437)
....++..|+|..|...++.-+.....+ ...... .+..|..+...++|..|...|+.-+. .|...
T Consensus 11 ~a~~~~~~g~y~~Ai~~f~~l~~~~P~s----~~a~~A--~l~la~a~y~~~~y~~A~~~~~~fi~~yP~~~ 76 (203)
T PF13525_consen 11 KALEALQQGDYEEAIKLFEKLIDRYPNS----PYAPQA--QLMLAYAYYKQGDYEEAIAAYERFIKLYPNSP 76 (203)
T ss_dssp HHHHHHHCT-HHHHHHHHHHHHHH-TTS----TTHHHH--HHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-T
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHHCCCC----hHHHHH--HHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCc
Confidence 3467889999999999988876654332 122233 35778899999999999999999998 88753
No 201
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=39.03 E-value=70 Score=27.86 Aligned_cols=59 Identities=10% Similarity=0.054 Sum_probs=43.0
Q ss_pred cccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCCCEEEEccCCCCCCchHHHHHH
Q psy9642 321 TLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVFNDNPQRFNNPLTFAQI 381 (437)
Q Consensus 321 ~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~g~v~F~~~~~~~~~~e~~~~l 381 (437)
.++.++||+.++++ ..-+++.+..+...|-|..+=-...|+.... +++..+--++...+
T Consensus 25 ~~s~~~ia~~~~is-~~~vrk~l~~L~~~Glv~s~~G~~GG~~l~~-~~~~itl~dI~~ai 83 (141)
T PRK11014 25 MTSISEVTEVYGVS-RNHMVKIINQLSRAGYVTAVRGKNGGIRLGK-PASTIRIGDVVREL 83 (141)
T ss_pred ccCHHHHHHHHCcC-HHHHHHHHHHHHhCCEEEEecCCCCCeeecC-CHHHCCHHHHHHHH
Confidence 58999999999998 7899999999999999888776655655544 44333333444433
No 202
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=38.84 E-value=1.8e+02 Score=24.06 Aligned_cols=41 Identities=12% Similarity=0.133 Sum_probs=35.6
Q ss_pred ccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCCC
Q psy9642 320 LTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDG 361 (437)
Q Consensus 320 s~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~g 361 (437)
..++..+||..++++ ...+-..|.+|...|.|.=.-|..|+
T Consensus 42 ~~~t~~eL~~~l~~~-~stvs~~i~~Le~kg~I~r~~~~~D~ 82 (109)
T TIGR01889 42 GKLTLKEIIKEILIK-QSALVKIIKKLSKKGYLSKERSEDDE 82 (109)
T ss_pred CcCcHHHHHHHHCCC-HHHHHHHHHHHHHCCCEeccCCcccC
Confidence 359999999999998 68889999999999999877776554
No 203
>KOG1126|consensus
Probab=38.69 E-value=88 Score=34.39 Aligned_cols=60 Identities=23% Similarity=0.231 Sum_probs=32.8
Q ss_pred HHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhc-cccc
Q psy9642 151 CQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIIT-TPAL 219 (437)
Q Consensus 151 ~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~-~P~~ 219 (437)
.+..-..|..+.||.++++-+. +++++.+. .|+.|.|+..+++|.+|+.-|+..-. .|..
T Consensus 530 g~~~~~~k~~d~AL~~~~~A~~--------ld~kn~l~-~~~~~~il~~~~~~~eal~~LEeLk~~vP~e 590 (638)
T KOG1126|consen 530 GRIQHQLKRKDKALQLYEKAIH--------LDPKNPLC-KYHRASILFSLGRYVEALQELEELKELVPQE 590 (638)
T ss_pred hHHHHHhhhhhHHHHHHHHHHh--------cCCCCchh-HHHHHHHHHhhcchHHHHHHHHHHHHhCcch
Confidence 3344455556666666666544 12332222 24666666666666666666666665 5654
No 204
>PHA02943 hypothetical protein; Provisional
Probab=38.69 E-value=2e+02 Score=25.93 Aligned_cols=49 Identities=6% Similarity=0.062 Sum_probs=38.4
Q ss_pred hhccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCCCEEEEccC
Q psy9642 318 TFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVFNDN 368 (437)
Q Consensus 318 ~Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~g~v~F~~~ 368 (437)
..-.-+.++||+.+|++ ..+|+.+|--+=.+|.|.- +.++...+-+.++
T Consensus 21 k~G~~TtseIAkaLGlS-~~qa~~~LyvLErEG~Vkr-V~~G~~tyw~l~~ 69 (165)
T PHA02943 21 ADGCKTTSRIANKLGVS-HSMARNALYQLAKEGMVLK-VEIGRAAIWCLDE 69 (165)
T ss_pred hcCCccHHHHHHHHCCC-HHHHHHHHHHHHHcCceEE-EeecceEEEEECh
Confidence 44567899999999998 7899999999999999865 5555555555544
No 205
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=38.56 E-value=70 Score=32.50 Aligned_cols=76 Identities=18% Similarity=0.273 Sum_probs=53.5
Q ss_pred HHhCCC--CcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHH
Q psy9642 134 KKIQTS--DSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFE 211 (437)
Q Consensus 134 ~rl~~~--~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~ 211 (437)
.++.+. .-.+.-+-.++.+..+..++.+.|...+.+-... + + ...+---..|.|++..++|+.|.+.++
T Consensus 168 ~k~~~q~~~~eIAqfyCELAq~~~~~~~~d~A~~~l~kAlqa-~-------~-~cvRAsi~lG~v~~~~g~y~~AV~~~e 238 (389)
T COG2956 168 VKLGGQTYRVEIAQFYCELAQQALASSDVDRARELLKKALQA-D-------K-KCVRASIILGRVELAKGDYQKAVEALE 238 (389)
T ss_pred HHcCCccchhHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHhh-C-------c-cceehhhhhhHHHHhccchHHHHHHHH
Confidence 444443 3445667778888888888888888887776543 1 1 133333467899999999999999999
Q ss_pred HHhc-ccc
Q psy9642 212 VIIT-TPA 218 (437)
Q Consensus 212 ~ai~-~P~ 218 (437)
.+.. .|.
T Consensus 239 ~v~eQn~~ 246 (389)
T COG2956 239 RVLEQNPE 246 (389)
T ss_pred HHHHhChH
Confidence 9888 564
No 206
>PF09295 ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); InterPro: IPR015374 ChAPs (Chs5p-Arf1p-binding proteins) are required for the export of specialised cargo from the Golgi. They physically interact with Chs3, Chs5 and the small GTPase Arf1, and they also form interactions with each other [].
Probab=38.47 E-value=1.6e+02 Score=30.72 Aligned_cols=64 Identities=19% Similarity=0.242 Sum_probs=44.4
Q ss_pred HHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhc-cccc
Q psy9642 147 HSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIIT-TPAL 219 (437)
Q Consensus 147 h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~-~P~~ 219 (437)
...++++.+..+.-..|++++.+-+.. .+.+ ....-..+..++..++|+.|......++. .|..
T Consensus 203 ~~~LA~v~l~~~~E~~AI~ll~~aL~~--------~p~d-~~LL~~Qa~fLl~k~~~~lAL~iAk~av~lsP~~ 267 (395)
T PF09295_consen 203 AVLLARVYLLMNEEVEAIRLLNEALKE--------NPQD-SELLNLQAEFLLSKKKYELALEIAKKAVELSPSE 267 (395)
T ss_pred HHHHHHHHHhcCcHHHHHHHHHHHHHh--------CCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCchh
Confidence 344667777777777777777777643 1111 22233566677788999999999999998 7875
No 207
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=38.47 E-value=1e+02 Score=26.80 Aligned_cols=45 Identities=7% Similarity=0.045 Sum_probs=38.2
Q ss_pred ccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCCCEEEE
Q psy9642 320 LTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVF 365 (437)
Q Consensus 320 s~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~g~v~F 365 (437)
-.++.++||+.++++ ..-+-..|..|+..|.|.-.-|..++-...
T Consensus 53 ~~~t~~eLa~~l~i~-~~tvsr~l~~Le~~GlI~R~~~~~DrR~~~ 97 (144)
T PRK11512 53 ACITPVELKKVLSVD-LGALTRMLDRLVCKGWVERLPNPNDKRGVL 97 (144)
T ss_pred CCCCHHHHHHHHCCC-HHHHHHHHHHHHHCCCEEeccCcccCCeeE
Confidence 469999999999998 688889999999999999988876644443
No 208
>COG3107 LppC Putative lipoprotein [General function prediction only]
Probab=38.39 E-value=5.6e+02 Score=27.93 Aligned_cols=210 Identities=14% Similarity=0.142 Sum_probs=119.8
Q ss_pred HHHhhhCCCCcchHHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHH
Q psy9642 114 KTVMDLKTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYG 193 (437)
Q Consensus 114 ~~~~~~~~~~~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~ 193 (437)
..+.+.+++.++...+...-..| ++.+---.-+..+++.+..+.+..|+..+.+.-. ..++..+..+| |.
T Consensus 71 ~al~~e~k~~qA~~Ll~ql~~~L--td~Q~~~~~LL~ael~la~~q~~~Al~~L~~~~~------~~ls~~Qq~Ry--~q 140 (604)
T COG3107 71 RALVEEGKTAQAQALLNQLPQEL--TDAQRAEKSLLAAELALAQKQPAAALQQLAKLLP------ADLSQNQQARY--YQ 140 (604)
T ss_pred HHHHHcCChHHHHHHHHhccccC--CHHHHHHHHHHHHHHHHhccChHHHHHHHhhcch------hhcCHHHHHHH--HH
Confidence 34445556666555444321111 1122222345567899999999999999887643 34555566666 56
Q ss_pred HHHHHHHh--hHHHHHHH---HHHHhcccccccCHHHHHHHHHHHHHHH-HHhCCCCCCCccccHHHhHhhccCCHHHHH
Q psy9642 194 GMIYLALK--NYERALYF---FEVIITTPALAVSHIMLEGYKKYLLIYL-IVYGKAPNLPKNVSQAICRYIKPLSQPYLD 267 (437)
Q Consensus 194 G~I~~~~k--~y~~A~~~---~~~ai~~P~~~~s~i~vea~Kk~iLv~L-il~G~~~~lp~~~s~~~~r~~k~~~~pY~~ 267 (437)
+.+-+... +--+|.+. ++..++.+. ..-.+=|-|-+++- +..|.+.+- +.+ -.-.+.-|..
T Consensus 141 ~~a~a~ea~~~~~~a~rari~~~~lL~~k~-----~q~nid~tW~ll~~~~~~~VIn~s---a~e-----~~~~L~GWL~ 207 (604)
T COG3107 141 ARADALEARGDSIDAARARIAQDPLLSGKA-----KQANIDKTWQLLSEQANTGVINNS---ADE-----GNAALQGWLD 207 (604)
T ss_pred HHHHHHhcccchHHHHHHHHHhhhhccchh-----HHHhHHHHHHHhhhhccccceecc---cCC-----cccccchHHH
Confidence 66655554 34344333 333333333 22334466888772 234444211 000 0113678999
Q ss_pred HHHHHhc--CCHHHHHHHHHhccccccccchhhHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHhCCCChHHHHHHHHH
Q psy9642 268 LVSVYTN--NNSTELQHLLLKYADVFSRDENTGLTKQIVASLYKNNIKRLTKTFLTLSLADVASRVQLGTPVQAEIYILK 345 (437)
Q Consensus 268 L~~af~~--~d~~~~~~~~~~~~~~f~~D~n~~Lv~~l~~~v~r~~I~~l~k~Ys~IsL~dIa~~l~L~~~~eaE~~l~~ 345 (437)
|++.+.+ .++.++.+.++......-+..--...-..+. . -+.|+.-+.+.||-.|=|+... ..+..
T Consensus 208 L~rv~~~~~~~p~qlk~~i~~Wq~~yPqhPaA~~~P~~l~--------~-l~~f~~~~~skiALLLPLtG~~---a~~a~ 275 (604)
T COG3107 208 LARVYKDNGSDPPQLKAGIEDWQKRYPQHPAAKMLPTALT--------N-LKNFSQASPSKIALLLPLTGQA---AVFAR 275 (604)
T ss_pred HHHHHHhcccCHHHHHHHHHHHHhcCCCCchhhhChHHHH--------h-hhhcccCCchheeEEeccCChh---HHHHH
Confidence 9999975 3677888888876655544332111111111 1 1467888999999888887422 36789
Q ss_pred hHHcCceEEEEec
Q psy9642 346 MISQNEIYATINK 358 (437)
Q Consensus 346 mI~~G~I~A~Id~ 358 (437)
-|.+|-..|+-+.
T Consensus 276 ~IqdGF~aA~~~~ 288 (604)
T COG3107 276 TIQDGFLAAKNAP 288 (604)
T ss_pred HHHHHHHHhccCc
Confidence 9999999888843
No 209
>KOG2047|consensus
Probab=38.13 E-value=6.2e+02 Score=28.37 Aligned_cols=114 Identities=12% Similarity=0.102 Sum_probs=77.4
Q ss_pred CCCCcchHHHHHHHHHhCCC--CcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHH
Q psy9642 120 KTPQRGIPLIQTAIKKIQTS--DSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIY 197 (437)
Q Consensus 120 ~~~~~~i~~l~~ai~rl~~~--~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~ 197 (437)
++|...+.+...|+++.+|. .+.++.+...|.+++-.+++.+.|-.+.++..- -..-...+...-.---|-..
T Consensus 361 ~~~~~~i~tyteAv~~vdP~ka~Gs~~~Lw~~faklYe~~~~l~~aRvifeka~~-----V~y~~v~dLa~vw~~waemE 435 (835)
T KOG2047|consen 361 GNAAEQINTYTEAVKTVDPKKAVGSPGTLWVEFAKLYENNGDLDDARVIFEKATK-----VPYKTVEDLAEVWCAWAEME 435 (835)
T ss_pred CChHHHHHHHHHHHHccCcccCCCChhhHHHHHHHHHHhcCcHHHHHHHHHHhhc-----CCccchHHHHHHHHHHHHHH
Confidence 44677789999999999998 567777889999999999999999555554321 11112333333333334455
Q ss_pred HHHhhHHHHHHHHHHHhccccccc------C-HHHHHHHHHHHHHHHH
Q psy9642 198 LALKNYERALYFFEVIITTPALAV------S-HIMLEGYKKYLLIYLI 238 (437)
Q Consensus 198 ~~~k~y~~A~~~~~~ai~~P~~~~------s-~i~vea~Kk~iLv~Li 238 (437)
+..++++.|.+..+.|...|+... + +.+...+|.+.+-+..
T Consensus 436 lrh~~~~~Al~lm~~A~~vP~~~~~~~yd~~~pvQ~rlhrSlkiWs~y 483 (835)
T KOG2047|consen 436 LRHENFEAALKLMRRATHVPTNPELEYYDNSEPVQARLHRSLKIWSMY 483 (835)
T ss_pred HhhhhHHHHHHHHHhhhcCCCchhhhhhcCCCcHHHHHHHhHHHHHHH
Confidence 566799999999999999887621 1 3444555555555544
No 210
>KOG2140|consensus
Probab=37.92 E-value=2.1e+02 Score=31.01 Aligned_cols=53 Identities=15% Similarity=0.155 Sum_probs=28.5
Q ss_pred hccCcchhhHHHHHHHHHHhccccCCCCCCccHHHHH--HHHHHHHHhcChhhhhhhH
Q psy9642 47 ETLETFQHSLGILAILSAKLTLLSSSNTGSEYQEELF--SQIQEFLNMCNPDQIRHAG 102 (437)
Q Consensus 47 ~~ldp~~hsl~~L~vL~~~~~~~~~~~~~~~~~~~~~--~~~~~fl~~fd~~Qir~a~ 102 (437)
..++.+..|.|+.-|+.|+......+ .|+.++++ ..++.|-++|.+.--..++
T Consensus 202 sv~~aq~asp~ft~vyaALvAviNsk---fP~IgElLlkrLilqf~r~f~RnDk~~c~ 256 (739)
T KOG2140|consen 202 SVMQAQAASPGFTPVYAALVAVINSK---FPQIGELLLKRLILQFKRSFRRNDKVSCL 256 (739)
T ss_pred HHHHHHhcCCCCcHHHHHHHHHHccC---CchHHHHHHHHHHHHHHHHhcccchHHHH
Confidence 34444555555555555544433321 55655543 3488899999766443333
No 211
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=37.57 E-value=1.3e+02 Score=26.06 Aligned_cols=44 Identities=9% Similarity=-0.048 Sum_probs=36.9
Q ss_pred cccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCCCEEEE
Q psy9642 321 TLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVF 365 (437)
Q Consensus 321 ~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~g~v~F 365 (437)
.++.++||+.++++ ..-+-..|.+|...|.|.-.-|..++-...
T Consensus 46 ~~t~~eLa~~l~~~-~~tvt~~v~~Le~~GlV~r~~~~~DrR~~~ 89 (144)
T PRK03573 46 EQSQIQLAKAIGIE-QPSLVRTLDQLEEKGLISRQTCASDRRAKR 89 (144)
T ss_pred CCCHHHHHHHhCCC-hhhHHHHHHHHHHCCCEeeecCCCCcCeee
Confidence 47889999999998 678889999999999999998876654443
No 212
>KOG2002|consensus
Probab=37.32 E-value=1.4e+02 Score=34.53 Aligned_cols=85 Identities=18% Similarity=0.293 Sum_probs=54.3
Q ss_pred chHHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHH
Q psy9642 125 GIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYE 204 (437)
Q Consensus 125 ~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~ 204 (437)
|+..+..|-.--..+|..++ .+..-....++|..+..+-..-|..- ....-...=||..|+.|-+++||+
T Consensus 255 ~~~ll~~ay~~n~~nP~~l~----~LAn~fyfK~dy~~v~~la~~ai~~t------~~~~~~aes~Y~~gRs~Ha~Gd~e 324 (1018)
T KOG2002|consen 255 GVQLLQRAYKENNENPVALN----HLANHFYFKKDYERVWHLAEHAIKNT------ENKSIKAESFYQLGRSYHAQGDFE 324 (1018)
T ss_pred HHHHHHHHHhhcCCCcHHHH----HHHHHHhhcccHHHHHHHHHHHHHhh------hhhHHHHHHHHHHHHHHHhhccHH
Confidence 34444444333333354444 34456677888888877766665531 112224456789999999999999
Q ss_pred HHHHHHHHHhc-cccc
Q psy9642 205 RALYFFEVIIT-TPAL 219 (437)
Q Consensus 205 ~A~~~~~~ai~-~P~~ 219 (437)
+|..||..+.. .|..
T Consensus 325 kA~~yY~~s~k~~~d~ 340 (1018)
T KOG2002|consen 325 KAFKYYMESLKADNDN 340 (1018)
T ss_pred HHHHHHHHHHccCCCC
Confidence 99999999987 5543
No 213
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=37.27 E-value=2.7e+02 Score=24.03 Aligned_cols=38 Identities=13% Similarity=0.161 Sum_probs=31.5
Q ss_pred HHHhhccccHHHHHHHhCCCChHHHHHHHHHhHHcCceE
Q psy9642 315 LTKTFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIY 353 (437)
Q Consensus 315 l~k~Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~ 353 (437)
+...-..+++++||+.++++ ...+-..|.+|...|.|.
T Consensus 16 l~~~~~~~~~~ela~~l~vs-~~svs~~l~~L~~~Gli~ 53 (142)
T PRK03902 16 LIEEKGYARVSDIAEALSVH-PSSVTKMVQKLDKDEYLI 53 (142)
T ss_pred HHhcCCCcCHHHHHHHhCCC-hhHHHHHHHHHHHCCCEE
Confidence 33444567899999999997 678889999999999886
No 214
>PF10345 Cohesin_load: Cohesin loading factor; InterPro: IPR019440 Cohesin loading factor is a conserved protein that has been characterised in fungi. It is associated with the cohesin complex and is required in G1 for cohesin binding to chromosomes, but is dispensable in G2 when cohesion has been established. It is often referred to as Ssl3 in Schizosaccharomyces pombe (Fission yeast), and Scc4 in Saccharomyces cerevisiae (Baker's yeast). It complexes with Mis4 [].
Probab=37.09 E-value=4.9e+02 Score=28.48 Aligned_cols=68 Identities=15% Similarity=0.156 Sum_probs=43.9
Q ss_pred HHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHH
Q psy9642 146 LHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVI 213 (437)
Q Consensus 146 ~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~a 213 (437)
++..++-+.+..++|..|.+.++.-.....+.+..+.......-+|..|+.+-+.++.+.|..+|..+
T Consensus 363 ~~~y~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~~~~~yL~gl~~q~~g~l~~A~~~y~~~ 430 (608)
T PF10345_consen 363 LLFYQIWCNFIRGDWSKATQELEFMRQLCQRSPSKLYESLYPLLHYLLGLYYQSTGDLEAALYQYQKP 430 (608)
T ss_pred HHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcCccchhhhhhHHHHHHHHHHHHHcCCHHHHHHHHhhh
Confidence 33444455566677878866666533322222222333445667789999999999999999999833
No 215
>KOG1129|consensus
Probab=36.76 E-value=2.5e+02 Score=28.82 Aligned_cols=94 Identities=17% Similarity=0.268 Sum_probs=65.6
Q ss_pred HHHHHHhhhCCCCcchHHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHH
Q psy9642 111 QYTKTVMDLKTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYF 190 (437)
Q Consensus 111 ~~~~~~~~~~~~~~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~ 190 (437)
.+..+....+-|-++-+-|++++..+ |.+.+ .+.+.+.+..-+....||.++..-+-.+ ...+.|.
T Consensus 228 Q~gkCylrLgm~r~AekqlqssL~q~-~~~dT----fllLskvY~ridQP~~AL~~~~~gld~f---------P~~VT~l 293 (478)
T KOG1129|consen 228 QMGKCYLRLGMPRRAEKQLQSSLTQF-PHPDT----FLLLSKVYQRIDQPERALLVIGEGLDSF---------PFDVTYL 293 (478)
T ss_pred HHHHHHHHhcChhhhHHHHHHHhhcC-CchhH----HHHHHHHHHHhccHHHHHHHHhhhhhcC---------Cchhhhh
Confidence 44555556677777877888887665 44443 3466777778888888887766543321 1245666
Q ss_pred HHHHHHHHHHhhHHHHHHHHHHHhc-ccc
Q psy9642 191 YYGGMIYLALKNYERALYFFEVIIT-TPA 218 (437)
Q Consensus 191 Yy~G~I~~~~k~y~~A~~~~~~ai~-~P~ 218 (437)
.-.++|+=+++++++|.++|..++. .|.
T Consensus 294 ~g~ARi~eam~~~~~a~~lYk~vlk~~~~ 322 (478)
T KOG1129|consen 294 LGQARIHEAMEQQEDALQLYKLVLKLHPI 322 (478)
T ss_pred hhhHHHHHHHHhHHHHHHHHHHHHhcCCc
Confidence 6667777788999999999999998 554
No 216
>KOG0548|consensus
Probab=36.66 E-value=2.6e+02 Score=30.17 Aligned_cols=46 Identities=22% Similarity=0.520 Sum_probs=36.4
Q ss_pred hhHHHHHHHHHHHHHHhhHHHHHHHHHHHhc-ccccccCHHHHHHHHHHH
Q psy9642 185 YFLQYFYYGGMIYLALKNYERALYFFEVIIT-TPALAVSHIMLEGYKKYL 233 (437)
Q Consensus 185 ~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~-~P~~~~s~i~vea~Kk~i 233 (437)
.+.+=+...|.++.++++|.+|.+.|..+.. .|.. ...++.|++-+
T Consensus 424 ~~~kgy~RKg~al~~mk~ydkAleay~eale~dp~~---~e~~~~~~rc~ 470 (539)
T KOG0548|consen 424 NFIKAYLRKGAALRAMKEYDKALEAYQEALELDPSN---AEAIDGYRRCV 470 (539)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCchh---HHHHHHHHHHH
Confidence 3777788889999999999999999999998 5653 45566666633
No 217
>PF12728 HTH_17: Helix-turn-helix domain
Probab=36.64 E-value=58 Score=22.82 Aligned_cols=38 Identities=13% Similarity=0.093 Sum_probs=28.2
Q ss_pred ccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCCCEEEEc
Q psy9642 322 LSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVFN 366 (437)
Q Consensus 322 IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~g~v~F~ 366 (437)
++.+++|+.||++ . ..+.+|+..|.|.+.- .++...|.
T Consensus 2 lt~~e~a~~l~is-~----~tv~~~~~~g~i~~~~--~g~~~~~~ 39 (51)
T PF12728_consen 2 LTVKEAAELLGIS-R----STVYRWIRQGKIPPFK--IGRKWRIP 39 (51)
T ss_pred CCHHHHHHHHCcC-H----HHHHHHHHcCCCCeEE--eCCEEEEe
Confidence 5789999999997 3 4577899999997763 34445554
No 218
>PF09613 HrpB1_HrpK: Bacterial type III secretion protein (HrpB1_HrpK); InterPro: IPR013394 This family of proteins is encoded by genes found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.
Probab=36.49 E-value=80 Score=28.63 Aligned_cols=32 Identities=13% Similarity=0.301 Sum_probs=27.4
Q ss_pred hHHHHHHHHHHHHHHhhHHHHHHHHHHHhccc
Q psy9642 186 FLQYFYYGGMIYLALKNYERALYFFEVIITTP 217 (437)
Q Consensus 186 ~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~~P 217 (437)
.-....+.|++++..++|.+|.+.|+.+...+
T Consensus 43 ~~e~~~~~~~l~i~r~~w~dA~rlLr~l~~~~ 74 (160)
T PF09613_consen 43 FPELDLFDGWLHIVRGDWDDALRLLRELEERA 74 (160)
T ss_pred chHHHHHHHHHHHHhCCHHHHHHHHHHHhccC
Confidence 44556689999999999999999999988744
No 219
>KOG1861|consensus
Probab=36.25 E-value=3.9e+02 Score=28.60 Aligned_cols=196 Identities=14% Similarity=0.175 Sum_probs=106.6
Q ss_pred HHHHHHHh--CCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcC-------C--CCCChHhhHHHHHHHHHHH
Q psy9642 129 IQTAIKKI--QTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANE-------G--PQFDTKYFLQYFYYGGMIY 197 (437)
Q Consensus 129 l~~ai~rl--~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~-------~--~~~~~~~~l~Y~Yy~G~I~ 197 (437)
|...-+|| .|+|++.-|.-..---||+..+.|+.= .+-..+|+. - ..+..+-.++-|=--++|-
T Consensus 284 lEKsyLRLTsAPdPstVRP~~VL~ksL~~vkdk~k~~-----~~Y~y~CdQ~KSiRQDLTVQ~IrneFTveVYEtHARIA 358 (540)
T KOG1861|consen 284 LEKSYLRLTSAPDPSTVRPLEVLKKSLCLVKDKWKAK-----ANYAYLCDQFKSIRQDLTVQRIRNEFTVEVYETHARIA 358 (540)
T ss_pred HHHhHhhhccCCCccccCCHHHHHHHHHHHHHHHHhh-----ccHHHHHHHHHHHhhhhhhheeccceeeeeehhhhHHH
Confidence 44445555 488888888888888888888877622 011122221 0 0111111222233446666
Q ss_pred HHHhhHHHHHHHHHHHhcccccccCHHHHHHHHHHHHHHHHHhCCCCCCCccccHHHhHhhcc--CCHHHHHHHHHHhcC
Q psy9642 198 LALKNYERALYFFEVIITTPALAVSHIMLEGYKKYLLIYLIVYGKAPNLPKNVSQAICRYIKP--LSQPYLDLVSVYTNN 275 (437)
Q Consensus 198 ~~~k~y~~A~~~~~~ai~~P~~~~s~i~vea~Kk~iLv~Lil~G~~~~lp~~~s~~~~r~~k~--~~~pY~~L~~af~~~ 275 (437)
+..+|.++=-+|-.+.....+.....-..|=.-+-|| +.|+....+.+-..... ++.-.+. ....-.++-.|...|
T Consensus 359 LEkGD~~EfNQCQtQLk~LY~egipg~~~EF~AYriL-Y~i~tkN~~di~sll~~-lt~E~ked~~V~hAL~vR~A~~~G 436 (540)
T KOG1861|consen 359 LEKGDLEEFNQCQTQLKALYSEGIPGAYLEFTAYRIL-YYIFTKNYPDILSLLRD-LTEEDKEDEAVAHALEVRSAVTLG 436 (540)
T ss_pred HhcCCHHHHHHHHHHHHHHHccCCCCchhhHHHHHHH-HHHHhcCchHHHHHHHh-ccHhhccCHHHHHHHHHHHHHHhc
Confidence 6667766655555555442222111113332222344 55554333322111000 0111111 123335677777788
Q ss_pred CHHHHHHHHHhccccccccchhh--HHHHHHHHHHHHHHHHHHHhhc-cccHHHHHHHhCCCChHH
Q psy9642 276 NSTELQHLLLKYADVFSRDENTG--LTKQIVASLYKNNIKRLTKTFL-TLSLADVASRVQLGTPVQ 338 (437)
Q Consensus 276 d~~~~~~~~~~~~~~f~~D~n~~--Lv~~l~~~v~r~~I~~l~k~Ys-~IsL~dIa~~l~L~~~~e 338 (437)
|.-.|-.. |..-.+++ |+...+++-++..+..|+|+|- +|+++-|++-+.+.+-++
T Consensus 437 NY~kFFrL-------Y~~AP~M~~yLmdlF~erER~~Al~ii~KsyrP~i~~~fi~~~laf~~~e~ 495 (540)
T KOG1861|consen 437 NYHKFFRL-------YLTAPNMSGYLMDLFLERERKKALTIICKSYRPTITVDFIASELAFDSMED 495 (540)
T ss_pred cHHHHHHH-------HhhcccchhHHHHHHHHHHHHHHHHHHHHHcCCCccHHHHhhhhhhchHHH
Confidence 86665443 22334443 8888999999999999999999 999999999888764333
No 220
>PRK11447 cellulose synthase subunit BcsC; Provisional
Probab=35.92 E-value=2.3e+02 Score=33.70 Aligned_cols=87 Identities=11% Similarity=-0.016 Sum_probs=60.8
Q ss_pred HHhhhCCCCcchHHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHH
Q psy9642 115 TVMDLKTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGG 194 (437)
Q Consensus 115 ~~~~~~~~~~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G 194 (437)
.+...+..-.++..++.|+.. +|... .++..+.+++...+++..|...+++-+.. .+ . .....|-.|
T Consensus 470 ~~~~~g~~~eA~~~~~~Al~~-~P~~~---~~~~~LA~~~~~~G~~~~A~~~l~~al~~-~P-------~-~~~~~~a~a 536 (1157)
T PRK11447 470 ALENQGKWAQAAELQRQRLAL-DPGSV---WLTYRLAQDLRQAGQRSQADALMRRLAQQ-KP-------N-DPEQVYAYG 536 (1157)
T ss_pred HHHHCCCHHHHHHHHHHHHHh-CCCCH---HHHHHHHHHHHHcCCHHHHHHHHHHHHHc-CC-------C-CHHHHHHHH
Confidence 334456667788888888654 45432 36788899999999999999998885531 11 1 122334556
Q ss_pred HHHHHHhhHHHHHHHHHHHh
Q psy9642 195 MIYLALKNYERALYFFEVII 214 (437)
Q Consensus 195 ~I~~~~k~y~~A~~~~~~ai 214 (437)
+.+...+++.+|..+|..+.
T Consensus 537 l~l~~~~~~~~Al~~l~~l~ 556 (1157)
T PRK11447 537 LYLSGSDRDRAALAHLNTLP 556 (1157)
T ss_pred HHHHhCCCHHHHHHHHHhCC
Confidence 77777899999999998754
No 221
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=35.76 E-value=99 Score=27.51 Aligned_cols=70 Identities=17% Similarity=0.152 Sum_probs=46.2
Q ss_pred HHHHHHHhhc--cccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCCCEEEEccCCCCCCchHHHHHHH
Q psy9642 311 NIKRLTKTFL--TLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVFNDNPQRFNNPLTFAQIE 382 (437)
Q Consensus 311 ~I~~l~k~Ys--~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~g~v~F~~~~~~~~~~e~~~~l~ 382 (437)
-+.-|+.-.. .+++++||++.+++ +.-+++++..|...|.+...==...|+ +...+++..+--++.+.++
T Consensus 13 ~L~~LA~~~~~~~~s~~~IA~~~~is-~~~L~kil~~L~kaGlV~S~rG~~GGy-~Lar~~~~Isl~dVv~ave 84 (150)
T COG1959 13 ALLYLALLPGGGPVSSAEIAERQGIS-PSYLEKILSKLRKAGLVKSVRGKGGGY-RLARPPEEITLGDVVRALE 84 (150)
T ss_pred HHHHHHhCCCCCcccHHHHHHHhCcC-HHHHHHHHHHHHHcCCEEeecCCCCCc-cCCCChHHCcHHHHHHHhc
Confidence 3344554444 68899999999998 899999999999999988766543333 3333333333333333333
No 222
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=35.25 E-value=1e+02 Score=24.15 Aligned_cols=34 Identities=21% Similarity=0.193 Sum_probs=30.5
Q ss_pred ccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEE
Q psy9642 320 LTLSLADVASRVQLGTPVQAEIYILKMISQNEIYA 354 (437)
Q Consensus 320 s~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A 354 (437)
..+++++||+.++++ ...+..++..|...|.|..
T Consensus 19 ~~~t~~~ia~~l~i~-~~tv~r~l~~L~~~g~l~~ 52 (91)
T smart00346 19 GGLTLAELAERLGLS-KSTAHRLLNTLQELGYVEQ 52 (91)
T ss_pred CCcCHHHHHHHhCCC-HHHHHHHHHHHHHCCCeee
Confidence 359999999999998 7899999999999998865
No 223
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=35.19 E-value=3.6e+02 Score=27.59 Aligned_cols=146 Identities=10% Similarity=0.141 Sum_probs=0.0
Q ss_pred HHHHHHHhcCCHHHHHHHHHhc-----------------cccccccchhhHHHHHH----------HHHHHHHHHHHHHh
Q psy9642 266 LDLVSVYTNNNSTELQHLLLKY-----------------ADVFSRDENTGLTKQIV----------ASLYKNNIKRLTKT 318 (437)
Q Consensus 266 ~~L~~af~~~d~~~~~~~~~~~-----------------~~~f~~D~n~~Lv~~l~----------~~v~r~~I~~l~k~ 318 (437)
.+|+..+..||...+...++.| ..-..++|++||++.+. ..+..|-|+.-..-
T Consensus 117 ~~L~~~~~~Gd~~A~~~Li~~~~~lV~~iA~~~~~~~~~~eDLiQEg~igL~~a~~~fd~~~g~~FsTyA~~wIr~aI~~ 196 (367)
T PRK09210 117 IELAKRIEEGDEEAKQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITR 196 (367)
T ss_pred HHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHH
Q ss_pred hc-------cc--------------------------cHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCCC--EE
Q psy9642 319 FL-------TL--------------------------SLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDG--MV 363 (437)
Q Consensus 319 Ys-------~I--------------------------sL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~g--~v 363 (437)
|. +| +..+||..+|++ +++++.++...-..-.+...+...++ ..
T Consensus 197 ~i~~~~r~irip~~~~~~~~~~~~~~~~l~~~lgr~pt~~EiA~~l~~~-~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~ 275 (367)
T PRK09210 197 AIADQARTIRIPVHMVETINKLIRVQRQLLQELGREPTPEEIAEEMDMP-PEKVREILKIAQEPVSLETPIGEEDDSHLG 275 (367)
T ss_pred HHHHcCCceeccHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcC-HHHHHHHHHHhcCCCCcCCCCCCCCcchhh
Q ss_pred EEccCCCCCCch-------------HHHHHHHHHHHHHHHHH--------HHHHHHHHHhhCCHHHHHHh
Q psy9642 364 VFNDNPQRFNNP-------------LTFAQIESNIRACMHLD--------GKFQAMEEEILVNPLYVKKA 412 (437)
Q Consensus 364 ~F~~~~~~~~~~-------------e~~~~l~~~i~~~~~L~--------~~~~~~d~~l~~~~~yi~k~ 412 (437)
.|..+.+..++. +.+..+..+-+.++.+. ..+++.=..++++++-|++.
T Consensus 276 d~i~d~~~~~p~~~~~~~~~~~~l~~~l~~L~~rEr~Vl~lrygl~~~~~~tl~EIa~~lgvs~erVrQi 345 (367)
T PRK09210 276 DFIEDQDATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQI 345 (367)
T ss_pred hhccCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCccHHHHHHHHCCCHHHHHHH
No 224
>KOG3151|consensus
Probab=34.90 E-value=4.4e+02 Score=25.64 Aligned_cols=51 Identities=14% Similarity=0.203 Sum_probs=36.0
Q ss_pred cchhhHHHHHHHHHHHHHH-HHHHHhhccccHHHHHHHhCCCChHHHHHHHH
Q psy9642 294 DENTGLTKQIVASLYKNNI-KRLTKTFLTLSLADVASRVQLGTPVQAEIYIL 344 (437)
Q Consensus 294 D~n~~Lv~~l~~~v~r~~I-~~l~k~Ys~IsL~dIa~~l~L~~~~eaE~~l~ 344 (437)
+..|.---+++..-+|.-| ..+-|.|..|++++.+++|.+.++++.+.+..
T Consensus 164 ~~~y~~FmdIl~~tiRdEIA~c~EKsYd~l~~s~a~~~L~f~~~~e~~~~~~ 215 (260)
T KOG3151|consen 164 SEEYTYFMDILLDTIRDEIAGCIEKSYDKLSASDATQMLLFNNDKELKKFAT 215 (260)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCHHHHHHHHhcCChHHHHHHHH
Confidence 3344433344444445555 67789999999999999999998777776554
No 225
>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]
Probab=34.61 E-value=4.8e+02 Score=26.02 Aligned_cols=110 Identities=15% Similarity=0.152 Sum_probs=68.1
Q ss_pred HHHHHHHHHHHHHhhhCCCCcchHHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCCh
Q psy9642 104 LYAELSHQYTKTVMDLKTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDT 183 (437)
Q Consensus 104 ~~~~l~~~~~~~~~~~~~~~~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~ 183 (437)
-|..|.+.+.. .+.---++..+++|++...+++..+..+=..++.-. ...+-..+-..+++-+. .++
T Consensus 158 gW~~Lg~~ym~----~~~~~~A~~AY~~A~rL~g~n~~~~~g~aeaL~~~a-~~~~ta~a~~ll~~al~--------~D~ 224 (287)
T COG4235 158 GWDLLGRAYMA----LGRASDALLAYRNALRLAGDNPEILLGLAEALYYQA-GQQMTAKARALLRQALA--------LDP 224 (287)
T ss_pred hHHHHHHHHHH----hcchhHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhc-CCcccHHHHHHHHHHHh--------cCC
Confidence 45555554432 222234677888888776666776665555543332 22233344333443332 122
Q ss_pred HhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhc-ccccccCHHHHH
Q psy9642 184 KYFLQYFYYGGMIYLALKNYERALYFFEVIIT-TPALAVSHIMLE 227 (437)
Q Consensus 184 ~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~-~P~~~~s~i~ve 227 (437)
..++=.||-|+.++.+++|.+|...++..+. .|........+|
T Consensus 225 -~~iral~lLA~~afe~g~~~~A~~~Wq~lL~~lp~~~~rr~~ie 268 (287)
T COG4235 225 -ANIRALSLLAFAAFEQGDYAEAAAAWQMLLDLLPADDPRRSLIE 268 (287)
T ss_pred -ccHHHHHHHHHHHHHcccHHHHHHHHHHHHhcCCCCCchHHHHH
Confidence 3667778999999999999999999999998 777654444444
No 226
>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.21 E-value=1e+02 Score=30.28 Aligned_cols=102 Identities=17% Similarity=0.274 Sum_probs=60.6
Q ss_pred HHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhc-ccccccCHHHHHHHHHH
Q psy9642 154 CLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIIT-TPALAVSHIMLEGYKKY 232 (437)
Q Consensus 154 ~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~-~P~~~~s~i~vea~Kk~ 232 (437)
.+.+|+|..|..-...-|-.+..+ .. .-.=+|+-|-.++.+++|.+|...|..++. .|.....+ |++=|+
T Consensus 151 ~~ksgdy~~A~~~F~~fi~~YP~s--~~----~~nA~yWLGe~~y~qg~y~~Aa~~f~~~~k~~P~s~KAp---dallKl 221 (262)
T COG1729 151 LYKSGDYAEAEQAFQAFIKKYPNS--TY----TPNAYYWLGESLYAQGDYEDAAYIFARVVKDYPKSPKAP---DALLKL 221 (262)
T ss_pred HHHcCCHHHHHHHHHHHHHcCCCC--cc----cchhHHHHHHHHHhcccchHHHHHHHHHHHhCCCCCCCh---HHHHHH
Confidence 345556777755555544433332 11 122357889999999999999999999998 88764333 233333
Q ss_pred HHHHHHHhCCCCCCCccccHHHhHhhccCCHHHHHHHHHHhcCCHHHH
Q psy9642 233 LLIYLIVYGKAPNLPKNVSQAICRYIKPLSQPYLDLVSVYTNNNSTEL 280 (437)
Q Consensus 233 iLv~Lil~G~~~~lp~~~s~~~~r~~k~~~~pY~~L~~af~~~d~~~~ 280 (437)
.+ ++--.|+... .|..|.++.+-|...+....
T Consensus 222 g~-~~~~l~~~d~---------------A~atl~qv~k~YP~t~aA~~ 253 (262)
T COG1729 222 GV-SLGRLGNTDE---------------ACATLQQVIKRYPGTDAAKL 253 (262)
T ss_pred HH-HHHHhcCHHH---------------HHHHHHHHHHHCCCCHHHHH
Confidence 33 3334444321 25566777777765544443
No 227
>COG5124 Protein predicted to be involved in meiotic recombination [Cell division and chromosome partitioning / General function prediction only]
Probab=34.12 E-value=1.9e+02 Score=26.65 Aligned_cols=67 Identities=9% Similarity=0.127 Sum_probs=47.4
Q ss_pred hHHHHHHHHHhHHcCceEEE-EecCCCEEEEccCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCHHHHHHhc
Q psy9642 336 PVQAEIYILKMISQNEIYAT-INKKDGMVVFNDNPQRFNNPLTFAQIESNIRACMHLDGKFQAMEEEILVNPLYVKKAA 413 (437)
Q Consensus 336 ~~eaE~~l~~mI~~G~I~A~-Id~~~g~v~F~~~~~~~~~~e~~~~l~~~i~~~~~L~~~~~~~d~~l~~~~~yi~k~~ 413 (437)
..-+..+|.+||.||.+.+. +-..+=+-.|.. +.++..-..|-.|.+.++.|...+.+-++||.+.-
T Consensus 42 l~tVKd~lQqlVDDgvV~~EK~GtsN~YWsF~s-----------~~~qk~~~~~~~l~~~~~~~kqdi~t~~e~i~~ek 109 (209)
T COG5124 42 LMTVKDLLQQLVDDGVVSVEKCGTSNIYWSFKS-----------QTLQKLYDSSELLKKKIQEVKQDIATYKEEIDKEK 109 (209)
T ss_pred HHHHHHHHHHHhhcCceeeeeeccceeEEecch-----------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHH
Confidence 45678899999999998763 222233444432 44555667777888888889889988899987654
No 228
>KOG1174|consensus
Probab=33.68 E-value=1.9e+02 Score=30.57 Aligned_cols=67 Identities=15% Similarity=0.215 Sum_probs=52.5
Q ss_pred hhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhc-ccccc
Q psy9642 144 TSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIIT-TPALA 220 (437)
Q Consensus 144 T~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~-~P~~~ 220 (437)
|+.-..+..||..-+.+..++.+|.+....+. ....+---|-++.+...|++|.++|..|++ -|...
T Consensus 438 ~~AV~~~AEL~~~Eg~~~D~i~LLe~~L~~~~----------D~~LH~~Lgd~~~A~Ne~Q~am~~y~~ALr~dP~~~ 505 (564)
T KOG1174|consen 438 TPAVNLIAELCQVEGPTKDIIKLLEKHLIIFP----------DVNLHNHLGDIMRAQNEPQKAMEYYYKALRQDPKSK 505 (564)
T ss_pred HHHHHHHHHHHHhhCccchHHHHHHHHHhhcc----------ccHHHHHHHHHHHHhhhHHHHHHHHHHHHhcCccch
Confidence 44556778889999999999888888765322 233445678899999999999999999999 78764
No 229
>PF07721 TPR_4: Tetratricopeptide repeat; InterPro: IPR011717 This entry includes tetratricopeptide-like repeats not detected by the IPR001440 from INTERPRO, IPR013105 from INTERPRO and IPR011716 from INTERPRO models. The tetratricopeptide repeat (TPR) motif is a protein-protein interaction module found in multiple copies in a number of functionally different proteins that facilitates specific interactions with a partner protein(s) [].; GO: 0042802 identical protein binding
Probab=33.56 E-value=51 Score=19.85 Aligned_cols=23 Identities=13% Similarity=-0.083 Sum_probs=19.9
Q ss_pred HHHHHHHHHHHHhhHHHHHHHHH
Q psy9642 189 YFYYGGMIYLALKNYERALYFFE 211 (437)
Q Consensus 189 Y~Yy~G~I~~~~k~y~~A~~~~~ 211 (437)
..+.-|.++..++++.+|...++
T Consensus 3 a~~~la~~~~~~G~~~eA~~~l~ 25 (26)
T PF07721_consen 3 ARLALARALLAQGDPDEAERLLR 25 (26)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHh
Confidence 35678999999999999999876
No 230
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=33.49 E-value=3.2e+02 Score=23.74 Aligned_cols=63 Identities=8% Similarity=0.063 Sum_probs=42.5
Q ss_pred ccccHHHHHHHhCCCChHHHHHHHHHhHHcCce-EEEEec-CCCEEEEccCCCCCCchHHHHHHHHHHH
Q psy9642 320 LTLSLADVASRVQLGTPVQAEIYILKMISQNEI-YATINK-KDGMVVFNDNPQRFNNPLTFAQIESNIR 386 (437)
Q Consensus 320 s~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I-~A~Id~-~~g~v~F~~~~~~~~~~e~~~~l~~~i~ 386 (437)
--++..+||+.++.+ ..-|.+-|.+++.-|.| +-+.+- ..|......+.+ .+++-..+.+.+.
T Consensus 41 ~~~tvdelae~lnr~-rStv~rsl~~L~~~GlV~Rek~~~~~Ggy~yiY~~i~---~ee~k~~i~~~l~ 105 (126)
T COG3355 41 GPLTVDELAEILNRS-RSTVYRSLQNLLEAGLVEREKVNLKGGGYYYLYKPID---PEEIKKKILKDLD 105 (126)
T ss_pred CCcCHHHHHHHHCcc-HHHHHHHHHHHHHcCCeeeeeeccCCCceeEEEecCC---HHHHHHHHHHHHH
Confidence 457899999999998 78899999999999997 445543 345554444432 3344444444443
No 231
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=33.03 E-value=97 Score=30.01 Aligned_cols=46 Identities=7% Similarity=-0.006 Sum_probs=40.0
Q ss_pred HHHHHHHHHHhhccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEE
Q psy9642 308 YKNNIKRLTKTFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYA 354 (437)
Q Consensus 308 ~r~~I~~l~k~Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A 354 (437)
++..|..+-+...+++++|+|+.++++ +.-+.+-|..|-+.|.|.-
T Consensus 6 R~~~Il~~L~~~~~v~v~eLa~~l~VS-~~TIRRDL~~Le~~g~l~r 51 (256)
T PRK10434 6 RQAAILEYLQKQGKTSVEELAQYFDTT-GTTIRKDLVILEHAGTVIR 51 (256)
T ss_pred HHHHHHHHHHHcCCEEHHHHHHHHCCC-HHHHHHHHHHHHHCCCEEE
Confidence 667788888889999999999999998 7888999999999997643
No 232
>PRK14574 hmsH outer membrane protein; Provisional
Probab=32.46 E-value=8.3e+02 Score=28.13 Aligned_cols=51 Identities=12% Similarity=0.188 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHHHHHHHHhhccccHHH----------H-HHHhCCCChHHHHHHHHHhHHcC
Q psy9642 300 TKQIVASLYKNNIKRLTKTFLTLSLAD----------V-ASRVQLGTPVQAEIYILKMISQN 350 (437)
Q Consensus 300 v~~l~~~v~r~~I~~l~k~Ys~IsL~d----------I-a~~l~L~~~~eaE~~l~~mI~~G 350 (437)
+-++..-..++.-..+.+.|.+|+-.- + ...+.+..++.|+.+....+.+.
T Consensus 296 ~Drl~aL~~r~r~~~vi~~y~~l~~~~~~~P~y~~~a~adayl~~~~P~kA~~l~~~~~~~~ 357 (822)
T PRK14574 296 IDRLGALLVRHQTADLIKEYEAMEAEGYKMPDYARRWAASAYIDRRLPEKAAPILSSLYYSD 357 (822)
T ss_pred HHHHHHHHHhhhHHHHHHHHHHhhhcCCCCCHHHHHHHHHHHHhcCCcHHHHHHHHHHhhcc
Confidence 455666666677777777777666222 1 12244556788888888887653
No 233
>PRK14720 transcript cleavage factor/unknown domain fusion protein; Provisional
Probab=32.07 E-value=5.8e+02 Score=29.73 Aligned_cols=61 Identities=13% Similarity=0.146 Sum_probs=47.6
Q ss_pred HHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhccc
Q psy9642 146 LHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIITTP 217 (437)
Q Consensus 146 ~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~~P 217 (437)
.-..++.+....++++.|+.+++..+.. ....+.++||.|+++...+++.+|.-. .++...
T Consensus 33 a~~~Li~~~~~~~~~deai~i~~~~l~~---------~P~~i~~yy~~G~l~~q~~~~~~~~lv--~~l~~~ 93 (906)
T PRK14720 33 ELDDLIDAYKSENLTDEAKDICEEHLKE---------HKKSISALYISGILSLSRRPLNDSNLL--NLIDSF 93 (906)
T ss_pred HHHHHHHHHHhcCCHHHHHHHHHHHHHh---------CCcceehHHHHHHHHHhhcchhhhhhh--hhhhhc
Confidence 4456777888999999999998866553 234788999999999999998888776 666643
No 234
>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=31.97 E-value=1.8e+02 Score=20.43 Aligned_cols=29 Identities=7% Similarity=0.074 Sum_probs=25.8
Q ss_pred cccHHHHHHHhCCCChHHHHHHHHHhHHcC
Q psy9642 321 TLSLADVASRVQLGTPVQAEIYILKMISQN 350 (437)
Q Consensus 321 ~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G 350 (437)
.++..+||+.++++ ..-+...|..+-..|
T Consensus 15 ~it~~eLa~~l~vS-~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 15 PITAKELAEELGVS-RRTIRRDIKELREWG 43 (55)
T ss_dssp SBEHHHHHHHCTS--HHHHHHHHHHHHHTT
T ss_pred CcCHHHHHHHhCCC-HHHHHHHHHHHHHCC
Confidence 49999999999997 789999999998888
No 235
>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=31.83 E-value=68 Score=21.44 Aligned_cols=39 Identities=15% Similarity=0.256 Sum_probs=27.9
Q ss_pred ccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCCCEEEEc
Q psy9642 322 LSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVFN 366 (437)
Q Consensus 322 IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~g~v~F~ 366 (437)
+++.++|+.+|++ . ..|..++.+|.+.+.- .+.|...|.
T Consensus 1 ~s~~e~a~~lgvs-~----~tl~~~~~~g~~~~~~-~~~~~~~~~ 39 (49)
T cd04762 1 LTTKEAAELLGVS-P----STLRRWVKEGKLKAIR-TPGGHRRFP 39 (49)
T ss_pred CCHHHHHHHHCcC-H----HHHHHHHHcCCCCcee-CCCCceecC
Confidence 4788999999997 3 5677888899987643 234555554
No 236
>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans. In humans this protein is expressed in primary breast carcinomas but not in normal breast tissue, and has a putative eukaryotic RNP-1 RNA binding region and a candidate anchoring transmembrane domain. The human protein is coordinately regulated with oestrogen receptor, but is not necessarily oestradiol-responsive []. Members of this family carry a tetratricopeptide repeat (IPR013105 from INTERPRO) at their C terminus.
Probab=31.43 E-value=6.6e+02 Score=26.65 Aligned_cols=105 Identities=14% Similarity=0.196 Sum_probs=67.3
Q ss_pred chHHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHH
Q psy9642 125 GIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYE 204 (437)
Q Consensus 125 ~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~ 204 (437)
+...|.....|+ |++.- +...-.|++...++.+.|+..+++-+..-. .. .+-....+|--|..++.+.||+
T Consensus 252 a~~lL~~~~~~y-P~s~l---fl~~~gR~~~~~g~~~~Ai~~~~~a~~~q~----~~-~Ql~~l~~~El~w~~~~~~~w~ 322 (468)
T PF10300_consen 252 AEELLEEMLKRY-PNSAL---FLFFEGRLERLKGNLEEAIESFERAIESQS----EW-KQLHHLCYFELAWCHMFQHDWE 322 (468)
T ss_pred HHHHHHHHHHhC-CCcHH---HHHHHHHHHHHhcCHHHHHHHHHHhccchh----hH-HhHHHHHHHHHHHHHHHHchHH
Confidence 344566666666 44322 334446899999999999999987653111 11 1113344567788899999999
Q ss_pred HHHHHHHHHhcccccccCHHHHHHHHHHHHHHHHHhCCC
Q psy9642 205 RALYFFEVIITTPALAVSHIMLEGYKKYLLIYLIVYGKA 243 (437)
Q Consensus 205 ~A~~~~~~ai~~P~~~~s~i~vea~Kk~iLv~Lil~G~~ 243 (437)
+|.++|......-.- | ..-|.+..=++++..|+.
T Consensus 323 ~A~~~f~~L~~~s~W--S---ka~Y~Y~~a~c~~~l~~~ 356 (468)
T PF10300_consen 323 EAAEYFLRLLKESKW--S---KAFYAYLAAACLLMLGRE 356 (468)
T ss_pred HHHHHHHHHHhcccc--H---HHHHHHHHHHHHHhhccc
Confidence 999999999973221 1 223545555666677766
No 237
>PF03704 BTAD: Bacterial transcriptional activator domain; InterPro: IPR005158 Found in the DNRI/REDD/AFSR family of regulators, this region of AFSR (P25941 from SWISSPROT) along with the C-terminal region is capable of independently directing actinorhodin production. It is important for the formation of secondary metabolites.; PDB: 2FF4_B 2FEZ_A.
Probab=30.97 E-value=2.3e+02 Score=24.07 Aligned_cols=80 Identities=16% Similarity=0.076 Sum_probs=46.9
Q ss_pred hhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhcccc----
Q psy9642 143 LTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIITTPA---- 218 (437)
Q Consensus 143 lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~~P~---- 218 (437)
.......++..++..+++..|+....+-+.. +|- .=..+...-.++...+++.+|.+.|..+-..-.
T Consensus 61 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~l~~--------dP~-~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~~elg 131 (146)
T PF03704_consen 61 YLDALERLAEALLEAGDYEEALRLLQRALAL--------DPY-DEEAYRLLMRALAAQGRRAEALRVYERYRRRLREELG 131 (146)
T ss_dssp HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH--------STT--HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS
T ss_pred HHHHHHHHHHHHHhccCHHHHHHHHHHHHhc--------CCC-CHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhC
Confidence 3446677788899999999999998887653 111 112233445566677888888888877765322
Q ss_pred cccCHHHHHHHHH
Q psy9642 219 LAVSHIMLEGYKK 231 (437)
Q Consensus 219 ~~~s~i~vea~Kk 231 (437)
...|+.+.+.|.+
T Consensus 132 ~~Ps~~~~~l~~~ 144 (146)
T PF03704_consen 132 IEPSPETRALYRE 144 (146)
T ss_dssp ----HHHHHHHHH
T ss_pred cCcCHHHHHHHHH
Confidence 2344455555443
No 238
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=30.61 E-value=1.7e+02 Score=19.53 Aligned_cols=45 Identities=11% Similarity=0.151 Sum_probs=29.2
Q ss_pred HHHHHHHHHHHHHHHHHhh-ccccHHHHHHHhCCCChHHHHHHHHHh
Q psy9642 301 KQIVASLYKNNIKRLTKTF-LTLSLADVASRVQLGTPVQAEIYILKM 346 (437)
Q Consensus 301 ~~l~~~v~r~~I~~l~k~Y-s~IsL~dIa~~l~L~~~~eaE~~l~~m 346 (437)
..+...+....-..+...| .-.+..+||+.+|++ ...+...+...
T Consensus 5 ~~~~~~l~~~~~~~~~~~~~~~~~~~~ia~~~~~s-~~~i~~~~~~~ 50 (55)
T cd06171 5 EEALDKLPEREREVILLRFGEGLSYEEIAEILGIS-RSTVRQRLHRA 50 (55)
T ss_pred HHHHHhCCHHHHHHHHHHHhcCCCHHHHHHHHCcC-HHHHHHHHHHH
Confidence 3444444444444555555 889999999999997 56665555543
No 239
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=30.52 E-value=1.4e+02 Score=27.77 Aligned_cols=45 Identities=18% Similarity=0.143 Sum_probs=37.7
Q ss_pred HHHHhhccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecC
Q psy9642 314 RLTKTFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKK 359 (437)
Q Consensus 314 ~l~k~Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~ 359 (437)
-+.+-+.-.+..+||+.++++ +.-++.++..+...|.+...+...
T Consensus 170 ~~~~g~~g~s~~eIa~~l~iS-~~Tv~~~~~~~~~~~~~~~~~~~~ 214 (225)
T PRK10046 170 LFKEPGVQHTAETVAQALTIS-RTTARRYLEYCASRHLIIAEIVHG 214 (225)
T ss_pred HHHcCCCCcCHHHHHHHhCcc-HHHHHHHHHHHHhCCeEEEEeecC
Confidence 333444457899999999998 889999999999999999999863
No 240
>PF03704 BTAD: Bacterial transcriptional activator domain; InterPro: IPR005158 Found in the DNRI/REDD/AFSR family of regulators, this region of AFSR (P25941 from SWISSPROT) along with the C-terminal region is capable of independently directing actinorhodin production. It is important for the formation of secondary metabolites.; PDB: 2FF4_B 2FEZ_A.
Probab=30.15 E-value=1.5e+02 Score=25.36 Aligned_cols=64 Identities=14% Similarity=0.198 Sum_probs=43.8
Q ss_pred HHHHHHHHHHHHHHhhhCCCCcchHHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHh
Q psy9642 103 DLYAELSHQYTKTVMDLKTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVD 170 (437)
Q Consensus 103 ~~~~~l~~~~~~~~~~~~~~~~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~ 170 (437)
..|...+..+.......+.+-.++..++.++ .++|..+. .|..++++....|++..|+.+-.+-
T Consensus 59 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~l-~~dP~~E~---~~~~lm~~~~~~g~~~~A~~~Y~~~ 122 (146)
T PF03704_consen 59 ELYLDALERLAEALLEAGDYEEALRLLQRAL-ALDPYDEE---AYRLLMRALAAQGRRAEALRVYERY 122 (146)
T ss_dssp HHHHHHHHHHHHHHHHTT-HHHHHHHHHHHH-HHSTT-HH---HHHHHHHHHHHTT-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHhccCHHHHHHHHHHHH-hcCCCCHH---HHHHHHHHHHHCcCHHHHHHHHHHH
Confidence 3455555556666666777777777776665 45675543 7899999999999999998876653
No 241
>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=29.78 E-value=4.1e+02 Score=23.77 Aligned_cols=84 Identities=14% Similarity=0.317 Sum_probs=49.0
Q ss_pred HHHHHhhccccHHHHHHHhC--CCChHHHHHHHHHhHHcCceEEEEecCCCEEEEcc--CCCCCCchHHHHHHHHHHH--
Q psy9642 313 KRLTKTFLTLSLADVASRVQ--LGTPVQAEIYILKMISQNEIYATINKKDGMVVFND--NPQRFNNPLTFAQIESNIR-- 386 (437)
Q Consensus 313 ~~l~k~Ys~IsL~dIa~~l~--L~~~~eaE~~l~~mI~~G~I~A~Id~~~g~v~F~~--~~~~~~~~e~~~~l~~~i~-- 386 (437)
+.-.++| |..||..-|+ ++ -..+...|-.++.+|.|.++.- +...|.|-. ..+.. +.+-+..++.+|.
T Consensus 11 ~~qNRPy---s~~di~~nL~~~~~-K~~v~k~Ld~L~~~g~i~~K~~-GKqkiY~~~Q~~~~~~-s~eel~~ld~ei~~L 84 (169)
T PF07106_consen 11 KEQNRPY---SAQDIFDNLHNKVG-KTAVQKALDSLVEEGKIVEKEY-GKQKIYFANQDELEVP-SPEELAELDAEIKEL 84 (169)
T ss_pred HHcCCCC---cHHHHHHHHHhhcc-HHHHHHHHHHHHhCCCeeeeee-cceEEEeeCccccCCC-CchhHHHHHHHHHHH
Confidence 3334455 4566666664 44 5788999999999999999975 344555532 22211 3344555555543
Q ss_pred --HHHHHHHHHHHHHHHh
Q psy9642 387 --ACMHLDGKFQAMEEEI 402 (437)
Q Consensus 387 --~~~~L~~~~~~~d~~l 402 (437)
.+..|...++.++.++
T Consensus 85 ~~el~~l~~~~k~l~~eL 102 (169)
T PF07106_consen 85 REELAELKKEVKSLEAEL 102 (169)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 3355555555554444
No 242
>PLN02789 farnesyltranstransferase
Probab=29.77 E-value=5.9e+02 Score=25.57 Aligned_cols=107 Identities=18% Similarity=0.213 Sum_probs=55.0
Q ss_pred hhhhhHHHHHHHHHHHHHHHhhhCCCCcchHHHHHHHHHhCCCCcchhhHHHHHHHHHHHh--CCchHHHhhhhHhhhhh
Q psy9642 97 QIRHAGDLYAELSHQYTKTVMDLKTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLA--QNFKPALEFLDVDITTI 174 (437)
Q Consensus 97 Qir~a~~~~~~l~~~~~~~~~~~~~~~~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~--~~y~~Al~il~~~I~~~ 174 (437)
++.|.+ .|......+...+...+..-+++.....+|.. +|...|.-|-. +.++.. +.+..++.++++-+..
T Consensus 29 ~i~y~~-~~~~a~~~~ra~l~~~e~serAL~lt~~aI~l---nP~~ytaW~~R--~~iL~~L~~~l~eeL~~~~~~i~~- 101 (320)
T PLN02789 29 PIAYTP-EFREAMDYFRAVYASDERSPRALDLTADVIRL---NPGNYTVWHFR--RLCLEALDADLEEELDFAEDVAED- 101 (320)
T ss_pred ceeeCH-HHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHH---CchhHHHHHHH--HHHHHHcchhHHHHHHHHHHHHHH-
Confidence 455543 34444444444444455666777777766533 34556655544 223333 2577888877775542
Q ss_pred hcCCCCCChHhhHHHHHHHHHHHHHHhh--HHHHHHHHHHHhc-ccc
Q psy9642 175 ANEGPQFDTKYFLQYFYYGGMIYLALKN--YERALYFFEVIIT-TPA 218 (437)
Q Consensus 175 ~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~--y~~A~~~~~~ai~-~P~ 218 (437)
. ++ .....++.|.+.-..++ +.++..++..++. -|.
T Consensus 102 n-------pk-nyqaW~~R~~~l~~l~~~~~~~el~~~~kal~~dpk 140 (320)
T PLN02789 102 N-------PK-NYQIWHHRRWLAEKLGPDAANKELEFTRKILSLDAK 140 (320)
T ss_pred C-------Cc-chHHhHHHHHHHHHcCchhhHHHHHHHHHHHHhCcc
Confidence 1 11 12224445555444443 3556666666665 443
No 243
>KOG4162|consensus
Probab=29.25 E-value=3.8e+02 Score=30.29 Aligned_cols=60 Identities=20% Similarity=0.232 Sum_probs=44.2
Q ss_pred HHHHHHHHHhCCchHHHh-hhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhc
Q psy9642 148 SDLCQLCLLAQNFKPALE-FLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIIT 215 (437)
Q Consensus 148 ~~l~~l~L~~~~y~~Al~-il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~ 215 (437)
..+..+.+.-|+-+-|.. .+.++-..+++ ...+-.||.|+++..+|+..+|.+||..|+.
T Consensus 722 ~Ala~~lle~G~~~la~~~~~L~dalr~dp--------~n~eaW~~LG~v~k~~Gd~~~Aaecf~aa~q 782 (799)
T KOG4162|consen 722 TALAELLLELGSPRLAEKRSLLSDALRLDP--------LNHEAWYYLGEVFKKLGDSKQAAECFQAALQ 782 (799)
T ss_pred HHHHHHHHHhCCcchHHHHHHHHHHHhhCC--------CCHHHHHHHHHHHHHccchHHHHHHHHHHHh
Confidence 345667777776666543 24444444333 2667889999999999999999999999997
No 244
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=29.20 E-value=1.3e+02 Score=29.07 Aligned_cols=46 Identities=15% Similarity=0.171 Sum_probs=39.2
Q ss_pred HHHHHHHHHHhhccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEE
Q psy9642 308 YKNNIKRLTKTFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYA 354 (437)
Q Consensus 308 ~r~~I~~l~k~Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A 354 (437)
++..|..+-+....+++.++++.++++ ..-+.+.|.+|-+.|.|.-
T Consensus 6 R~~~Il~~l~~~~~~~~~ela~~l~vS-~~TirRdL~~Le~~g~i~r 51 (251)
T PRK13509 6 RHQILLELLAQLGFVTVEKVIERLGIS-PATARRDINKLDESGKLKK 51 (251)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHHCcC-HHHHHHHHHHHHHCCCEEE
Confidence 455677777788999999999999997 7889999999999998854
No 245
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=29.12 E-value=98 Score=29.02 Aligned_cols=41 Identities=15% Similarity=0.202 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHHhhc--------cccHHHHHHHhCCCChHHHHHHHHHhH
Q psy9642 306 SLYKNNIKRLTKTFL--------TLSLADVASRVQLGTPVQAEIYILKMI 347 (437)
Q Consensus 306 ~v~r~~I~~l~k~Ys--------~IsL~dIa~~l~L~~~~eaE~~l~~mI 347 (437)
.+-.++.+.|..+|. ++++.+||+.+|++ ...+..+|.+..
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGIS-kst~~ehLRrAe 203 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGIS-KSTLSEHLRRAE 203 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCC-HHHHHHHHHHHH
Confidence 567778888888885 79999999999998 566666666554
No 246
>KOG1840|consensus
Probab=28.81 E-value=7.7e+02 Score=26.65 Aligned_cols=98 Identities=21% Similarity=0.199 Sum_probs=65.8
Q ss_pred hhhCCCCcchHHHHHHHHHhC--CC--CcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHH
Q psy9642 117 MDLKTPQRGIPLIQTAIKKIQ--TS--DSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYY 192 (437)
Q Consensus 117 ~~~~~~~~~i~~l~~ai~rl~--~~--~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy 192 (437)
...+..-.++..++.++..+. |. ...+-.+-..+..+.+..|.|..|.++..+-|.-........++ .+-....-
T Consensus 336 ~~~~~~Eea~~l~q~al~i~~~~~g~~~~~~a~~~~nl~~l~~~~gk~~ea~~~~k~ai~~~~~~~~~~~~-~~~~~l~~ 414 (508)
T KOG1840|consen 336 QSMNEYEEAKKLLQKALKIYLDAPGEDNVNLAKIYANLAELYLKMGKYKEAEELYKKAIQILRELLGKKDY-GVGKPLNQ 414 (508)
T ss_pred HHhcchhHHHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhcccCcCh-hhhHHHHH
Confidence 335555667788888877765 22 22566677889999999999999998888777644222111111 23333444
Q ss_pred HHHHHHHHhhHHHHHHHHHHHhc
Q psy9642 193 GGMIYLALKNYERALYFFEVIIT 215 (437)
Q Consensus 193 ~G~I~~~~k~y~~A~~~~~~ai~ 215 (437)
-|--|...++|.+|.+.|..++.
T Consensus 415 la~~~~~~k~~~~a~~l~~~~~~ 437 (508)
T KOG1840|consen 415 LAEAYEELKKYEEAEQLFEEAKD 437 (508)
T ss_pred HHHHHHHhcccchHHHHHHHHHH
Confidence 55666777899999999987764
No 247
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=28.78 E-value=1.3e+02 Score=29.15 Aligned_cols=45 Identities=18% Similarity=0.199 Sum_probs=39.5
Q ss_pred HHHHHHHHHHhhccccHHHHHHHhCCCChHHHHHHHHHhHHcCceE
Q psy9642 308 YKNNIKRLTKTFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIY 353 (437)
Q Consensus 308 ~r~~I~~l~k~Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~ 353 (437)
++..|..+-+...++++.+++++++++ ..-+.+-|..|-+.|.|.
T Consensus 6 R~~~Il~~l~~~~~~~~~ela~~l~vS-~~TiRRdL~~Le~~g~l~ 50 (252)
T PRK10906 6 RHDAIIELVKQQGYVSTEELVEHFSVS-PQTIRRDLNDLAEQNKIL 50 (252)
T ss_pred HHHHHHHHHHHcCCEeHHHHHHHhCCC-HHHHHHHHHHHHHCCCEE
Confidence 566777777888999999999999997 788999999999999874
No 248
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=28.70 E-value=41 Score=28.67 Aligned_cols=34 Identities=15% Similarity=0.176 Sum_probs=24.1
Q ss_pred cccHHHHHHHhCCC-----ChHHHHHHHHHhHHcCceEE
Q psy9642 321 TLSLADVASRVQLG-----TPVQAEIYILKMISQNEIYA 354 (437)
Q Consensus 321 ~IsL~dIa~~l~L~-----~~~eaE~~l~~mI~~G~I~A 354 (437)
|-.|.+|.+++|+. ....-..-|.+|+.+|+|.+
T Consensus 67 R~rLd~ii~~lg~~~~~~~~~~~~~~~IL~~L~~GeIs~ 105 (113)
T PF09862_consen 67 RNRLDKIIEKLGYEEDEEEEEEDERKEILDKLEKGEISV 105 (113)
T ss_pred HHHHHHHHHHhCCCCCcccccchhHHHHHHHHHcCCCCH
Confidence 45688999999982 12233466888898999864
No 249
>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=28.61 E-value=1.4e+02 Score=27.67 Aligned_cols=36 Identities=6% Similarity=-0.044 Sum_probs=31.6
Q ss_pred ccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEE
Q psy9642 320 LTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATI 356 (437)
Q Consensus 320 s~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~I 356 (437)
..+++++||+.++++ ..-+...|..|.+.|.|.-.-
T Consensus 156 g~~s~~eia~~l~is-~stv~r~L~~Le~~GlI~r~~ 191 (203)
T TIGR01884 156 GEKSVKNIAKKLGKS-LSTISRHLRELEKKGLVEQKG 191 (203)
T ss_pred CCcCHHHHHHHHCcC-HHHHHHHHHHHHHCCCEEEEc
Confidence 569999999999997 678899999999999987553
No 250
>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=28.51 E-value=1.1e+02 Score=21.39 Aligned_cols=29 Identities=17% Similarity=0.355 Sum_probs=22.8
Q ss_pred hccccHHHHHHHhCCCChHHHHHHHHHhHH
Q psy9642 319 FLTLSLADVASRVQLGTPVQAEIYILKMIS 348 (437)
Q Consensus 319 Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~ 348 (437)
|...++.+||..+|++ ...+..+..+.+.
T Consensus 18 ~~~~t~~eIa~~lg~s-~~~V~~~~~~al~ 46 (50)
T PF04545_consen 18 FEGLTLEEIAERLGIS-RSTVRRILKRALK 46 (50)
T ss_dssp TST-SHHHHHHHHTSC-HHHHHHHHHHHHH
T ss_pred cCCCCHHHHHHHHCCc-HHHHHHHHHHHHH
Confidence 7889999999999997 7777777666553
No 251
>KOG0547|consensus
Probab=28.24 E-value=4.1e+02 Score=28.68 Aligned_cols=27 Identities=22% Similarity=0.475 Sum_probs=23.1
Q ss_pred HHHHHHHHhhHHHHHHHHHHHhc-cccc
Q psy9642 193 GGMIYLALKNYERALYFFEVIIT-TPAL 219 (437)
Q Consensus 193 ~G~I~~~~k~y~~A~~~~~~ai~-~P~~ 219 (437)
.|--++..|+|.+|..||..||+ +|..
T Consensus 121 ~GN~~f~~kkY~eAIkyY~~AI~l~p~e 148 (606)
T KOG0547|consen 121 KGNKFFRNKKYDEAIKYYTQAIELCPDE 148 (606)
T ss_pred hhhhhhhcccHHHHHHHHHHHHhcCCCC
Confidence 45667788999999999999999 8874
No 252
>PRK10870 transcriptional repressor MprA; Provisional
Probab=28.05 E-value=2.1e+02 Score=26.00 Aligned_cols=43 Identities=7% Similarity=0.037 Sum_probs=36.3
Q ss_pred cccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCCCEEE
Q psy9642 321 TLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVV 364 (437)
Q Consensus 321 ~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~g~v~ 364 (437)
.++..+||+.++++ ..-+-.+|.+|+..|.|.=.-+..++-..
T Consensus 71 ~it~~eLa~~l~l~-~~tvsr~v~rLe~kGlV~R~~~~~DrR~~ 113 (176)
T PRK10870 71 SIQPSELSCALGSS-RTNATRIADELEKRGWIERRESDNDRRCL 113 (176)
T ss_pred CcCHHHHHHHHCCC-HHHHHHHHHHHHHCCCEEecCCCCCCCee
Confidence 48889999999998 67888999999999999888887664443
No 253
>TIGR02561 HrpB1_HrpK type III secretion protein HrpB1/HrpK. This gene is found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.
Probab=27.95 E-value=96 Score=27.89 Aligned_cols=59 Identities=15% Similarity=0.244 Sum_probs=38.9
Q ss_pred HHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhccc
Q psy9642 150 LCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIITTP 217 (437)
Q Consensus 150 l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~~P 217 (437)
.+...+...+...+..+|+.- .+-. | ..-....+.|++++..++|.+|.+.|..+.+-+
T Consensus 16 ~~~~aL~~~d~~D~e~lLdAL--rvLr------P-~~~e~d~~dg~l~i~rg~w~eA~rvlr~l~~~~ 74 (153)
T TIGR02561 16 VLMYALRSADPYDAQAMLDAL--RVLR------P-NLKELDMFDGWLLIARGNYDEAARILRELLSSA 74 (153)
T ss_pred HHHHHHhcCCHHHHHHHHHHH--HHhC------C-CccccchhHHHHHHHcCCHHHHHHHHHhhhccC
Confidence 344555566666665555542 1111 1 123344589999999999999999999999844
No 254
>PF08679 DsrD: Dissimilatory sulfite reductase D (DsrD); InterPro: IPR014793 The structure of the dissimilatory sulphite reductase D (DsrD) protein has shown it to contain a winged-helix motif similar to those found in DNA binding proteins []. The structure suggests a possible role for DsrD in transcription or translation of genes, which catalyse dissimilatory sulphite reduction. ; PDB: 1WQ2_B 1UCR_B.
Probab=27.62 E-value=1.1e+02 Score=23.65 Aligned_cols=34 Identities=6% Similarity=0.149 Sum_probs=25.2
Q ss_pred hccccHHHHHHHhCCCChHHHHHHHHHhHHcCce
Q psy9642 319 FLTLSLADVASRVQLGTPVQAEIYILKMISQNEI 352 (437)
Q Consensus 319 Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I 352 (437)
=++.-+.|+++.+--..+.++..++.+||.+|.+
T Consensus 17 KskfYfkD~~k~~pd~k~R~vKKi~~~LV~Eg~l 50 (67)
T PF08679_consen 17 KSKFYFKDFYKAFPDAKPREVKKIVNELVNEGKL 50 (67)
T ss_dssp SS-EEHHHHHHH-TTS-HHHHHHHHHHHHHTTSE
T ss_pred CCceeHHHHHHHCCCcCHHHHHHHHHHHHhhCeE
Confidence 3567789999853322489999999999999976
No 255
>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional
Probab=27.55 E-value=1e+02 Score=32.63 Aligned_cols=36 Identities=17% Similarity=0.092 Sum_probs=31.9
Q ss_pred HhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhc-cccc
Q psy9642 184 KYFLQYFYYGGMIYLALKNYERALYFFEVIIT-TPAL 219 (437)
Q Consensus 184 ~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~-~P~~ 219 (437)
.+....++.-|.++..+++|++|..+|+.++. .|..
T Consensus 72 P~~a~a~~NLG~AL~~lGryeEAIa~f~rALeL~Pd~ 108 (453)
T PLN03098 72 VKTAEDAVNLGLSLFSKGRVKDALAQFETALELNPNP 108 (453)
T ss_pred CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCc
Confidence 34778888999999999999999999999999 6764
No 256
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=27.48 E-value=6.9e+02 Score=25.64 Aligned_cols=96 Identities=15% Similarity=0.187 Sum_probs=72.6
Q ss_pred HHHhhhCCCCcchHHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHH
Q psy9642 114 KTVMDLKTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYG 193 (437)
Q Consensus 114 ~~~~~~~~~~~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~ 193 (437)
+.+. .++|-++|..+..- .+ .+++++- .|..+-.|.-..|..+.|+.|--.-+. .+.++.++-+.-.+--
T Consensus 44 NfLL-s~Q~dKAvdlF~e~-l~--~d~~t~e-~~ltLGnLfRsRGEvDRAIRiHQ~L~~-----spdlT~~qr~lAl~qL 113 (389)
T COG2956 44 NFLL-SNQPDKAVDLFLEM-LQ--EDPETFE-AHLTLGNLFRSRGEVDRAIRIHQTLLE-----SPDLTFEQRLLALQQL 113 (389)
T ss_pred HHHh-hcCcchHHHHHHHH-Hh--cCchhhH-HHHHHHHHHHhcchHHHHHHHHHHHhc-----CCCCchHHHHHHHHHH
Confidence 4455 47788887766553 33 3445554 799999999999999999887544332 3566777777788899
Q ss_pred HHHHHHHhhHHHHHHHHHHHhccccc
Q psy9642 194 GMIYLALKNYERALYFFEVIITTPAL 219 (437)
Q Consensus 194 G~I~~~~k~y~~A~~~~~~ai~~P~~ 219 (437)
|.=|+.-+=|++|...|...+.-|..
T Consensus 114 ~~Dym~aGl~DRAE~~f~~L~de~ef 139 (389)
T COG2956 114 GRDYMAAGLLDRAEDIFNQLVDEGEF 139 (389)
T ss_pred HHHHHHhhhhhHHHHHHHHHhcchhh
Confidence 99999999999999999999987654
No 257
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=27.20 E-value=1.3e+02 Score=27.01 Aligned_cols=55 Identities=15% Similarity=0.152 Sum_probs=38.1
Q ss_pred HHHHHHHHhhccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCCCEEEEccC
Q psy9642 310 NNIKRLTKTFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVFNDN 368 (437)
Q Consensus 310 ~~I~~l~k~Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~g~v~F~~~ 368 (437)
+.|..+.+---.+...|||+.|+++ +..|-..+.+|...|.+.=. +.|.+..-+.
T Consensus 13 ~~Iy~l~~~~~~~~~~diA~~L~Vs-p~sVt~ml~rL~~~GlV~~~---~y~gi~LT~~ 67 (154)
T COG1321 13 ETIYELLEEKGFARTKDIAERLKVS-PPSVTEMLKRLERLGLVEYE---PYGGVTLTEK 67 (154)
T ss_pred HHHHHHHhccCcccHHHHHHHhCCC-cHHHHHHHHHHHHCCCeEEe---cCCCeEEChh
Confidence 3445555555678999999999998 67788888999888865321 3455555443
No 258
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=27.13 E-value=5e+02 Score=23.95 Aligned_cols=43 Identities=12% Similarity=0.038 Sum_probs=35.3
Q ss_pred hccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCCCE
Q psy9642 319 FLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGM 362 (437)
Q Consensus 319 Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~g~ 362 (437)
.-.++.++||+.++++ ..-+-.+|.+|...|.|.=..+..++-
T Consensus 57 ~~~itq~eLa~~l~l~-~sTvtr~l~rLE~kGlI~R~~~~~DrR 99 (185)
T PRK13777 57 LKGASISEIAKFGVMH-VSTAFNFSKKLEERGYLTFSKKEDDKR 99 (185)
T ss_pred CCCcCHHHHHHHHCCC-HhhHHHHHHHHHHCCCEEecCCCCCCC
Confidence 4579999999999987 567888999999999998777765543
No 259
>PF08672 APC2: Anaphase promoting complex (APC) subunit 2; InterPro: IPR014786 The anaphase-promoting complex (APC) or cyclosome is a multi-subunit E3 protein ubiquitin ligase that regulates important events in mitosis such as the initiation of anaphase and exit from telophase. The APC, in conjunction with other enzymes, assembles multi-ubiquitin chains on a variety of regulatory proteins, thereby targeting them for proteolysis by the 26S proteasome. Anaphase is initiated when the APC triggers the destruction of securin, thereby allowing the protease, separase, to disrupt sister-chromatid cohesion. Securin ubiquitination by the APC is inhibited by cyclin-dependent kinase 1 (Cdk1)-dependent phosphorylation []. Forkhead Box M1 (FoxM1), which is a transcription factor that is over-expressed in many cancers, is degraded in late mitosis and early G1 phase by the APC/cyclosome (APC/C) E3 ubiquitin ligase []. The APC/C targets mitotic cyclins for destruction in mitosis and G1 phase and is then inactivated at S phase. It thereby generates alternating states of high and low cyclin-Cdk activity, which is required for the alternation of mitosis and DNA replication []. The APC/C is composed of at least 13 subunits that stay tightly associated throughout the cell cycle: APC1, APC2, APC4, APC5, APC9, APC11, CDC16, CDC23, CDC26, CDC27, DOC1, MND2 and SWM1[], []. In fission yeast the 13 subunits are known as: Apc1, Apc2, Nuc2, Apc4, Apc5, Cut9, Apc8, Apc10, Apc11, Hcn1, Apc13, Apc14 and Apc15 []. This entry represents a C-terminal domain found in APC subunit 2. ; PDB: 1LDD_A.
Probab=26.88 E-value=84 Score=23.56 Aligned_cols=37 Identities=8% Similarity=0.231 Sum_probs=27.0
Q ss_pred hccccHHHHHHHhCCC---------ChHHHHHHHHHhHHcCceEEE
Q psy9642 319 FLTLSLADVASRVQLG---------TPVQAEIYILKMISQNEIYAT 355 (437)
Q Consensus 319 Ys~IsL~dIa~~l~L~---------~~~eaE~~l~~mI~~G~I~A~ 355 (437)
+..+++++|...+++- +.++.+.++.+++++|.+...
T Consensus 9 ~gsl~l~RIh~mLkmf~~~~~~~~~s~~eL~~fL~~lv~e~~L~~~ 54 (60)
T PF08672_consen 9 LGSLPLDRIHSMLKMFPKDPGGYDISLEELQEFLDRLVEEGKLECS 54 (60)
T ss_dssp H-SEEHHHHHHHHHHH-GGG--TT--HHHHHHHHHHHHHTTSEE--
T ss_pred CCCCCHHHHHHHHHhccCCCCCCCCCHHHHHHHHHHHHHCCcEEec
Confidence 3457888888777631 478999999999999998654
No 260
>PF08631 SPO22: Meiosis protein SPO22/ZIP4 like; InterPro: IPR013940 SPO22 is a meiosis-specific protein with similarity to phospholipase A2, involved in completion of nuclear divisions during meiosis; induced early in meiosis []. It is also involved in sporulation [].
Probab=26.87 E-value=5.1e+02 Score=25.12 Aligned_cols=29 Identities=21% Similarity=0.443 Sum_probs=24.9
Q ss_pred hHHHHHHHHHHHHHHhhHHHHHHHHHHHh
Q psy9642 186 FLQYFYYGGMIYLALKNYERALYFFEVII 214 (437)
Q Consensus 186 ~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai 214 (437)
.....+-.|.-....++|.+|.+||+.+.
T Consensus 245 ~~~LLW~~~~~~~~~k~y~~A~~w~~~al 273 (278)
T PF08631_consen 245 IHTLLWNKGKKHYKAKNYDEAIEWYELAL 273 (278)
T ss_pred HHHHHHHHHHHHHhhcCHHHHHHHHHHHH
Confidence 55666778999999999999999999776
No 261
>KOG1125|consensus
Probab=26.80 E-value=88 Score=33.89 Aligned_cols=111 Identities=19% Similarity=0.224 Sum_probs=65.5
Q ss_pred hCCCCcchHHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcC----------C----CC-CCh
Q psy9642 119 LKTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANE----------G----PQ-FDT 183 (437)
Q Consensus 119 ~~~~~~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~----------~----~~-~~~ 183 (437)
..+-.+||..|+.+ +.|||+. +..+ ..|.--..-.+.=..|+..|++-|....+. . .. .+.
T Consensus 332 NE~E~~ai~AL~rc-l~LdP~N--leaL-maLAVSytNeg~q~~Al~~L~~Wi~~~p~y~~l~~a~~~~~~~~~~s~~~~ 407 (579)
T KOG1125|consen 332 NENEQNAISALRRC-LELDPTN--LEAL-MALAVSYTNEGLQNQALKMLDKWIRNKPKYVHLVSAGENEDFENTKSFLDS 407 (579)
T ss_pred ccchHHHHHHHHHH-HhcCCcc--HHHH-HHHHHHHhhhhhHHHHHHHHHHHHHhCccchhccccCccccccCCcCCCCH
Confidence 34557788888875 5677754 2211 111111222334457888888876643110 0 01 111
Q ss_pred H---hhHHH----------------HHHHHHHHHHHhhHHHHHHHHHHHhc-cccc--------------ccCHHHHHHH
Q psy9642 184 K---YFLQY----------------FYYGGMIYLALKNYERALYFFEVIIT-TPAL--------------AVSHIMLEGY 229 (437)
Q Consensus 184 ~---~~l~Y----------------~Yy~G~I~~~~k~y~~A~~~~~~ai~-~P~~--------------~~s~i~vea~ 229 (437)
. ++.++ .---|.+|.-.++|.+|..||+.|++ -|.. .-|..+|+||
T Consensus 408 ~~l~~i~~~fLeaa~~~~~~~DpdvQ~~LGVLy~ls~efdraiDcf~~AL~v~Pnd~~lWNRLGAtLAN~~~s~EAIsAY 487 (579)
T KOG1125|consen 408 SHLAHIQELFLEAARQLPTKIDPDVQSGLGVLYNLSGEFDRAVDCFEAALQVKPNDYLLWNRLGATLANGNRSEEAISAY 487 (579)
T ss_pred HHHHHHHHHHHHHHHhCCCCCChhHHhhhHHHHhcchHHHHHHHHHHHHHhcCCchHHHHHHhhHHhcCCcccHHHHHHH
Confidence 1 12222 23457888888999999999999999 7853 1467899999
Q ss_pred HHHH
Q psy9642 230 KKYL 233 (437)
Q Consensus 230 Kk~i 233 (437)
.+.+
T Consensus 488 ~rAL 491 (579)
T KOG1125|consen 488 NRAL 491 (579)
T ss_pred HHHH
Confidence 8744
No 262
>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=26.67 E-value=98 Score=22.62 Aligned_cols=26 Identities=8% Similarity=0.172 Sum_probs=20.0
Q ss_pred cccHHHHHHHhCCCChHHHHHHHHHhH
Q psy9642 321 TLSLADVASRVQLGTPVQAEIYILKMI 347 (437)
Q Consensus 321 ~IsL~dIa~~l~L~~~~eaE~~l~~mI 347 (437)
.+++.+||+.+|++ ..-+..+|.+..
T Consensus 23 ~~tl~elA~~lgis-~st~~~~LRrae 48 (53)
T PF04967_consen 23 RITLEELAEELGIS-KSTVSEHLRRAE 48 (53)
T ss_pred cCCHHHHHHHhCCC-HHHHHHHHHHHH
Confidence 69999999999998 555655665543
No 263
>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A ....
Probab=26.47 E-value=1.5e+02 Score=21.43 Aligned_cols=49 Identities=18% Similarity=0.228 Sum_probs=34.8
Q ss_pred CCCCcchHHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhh
Q psy9642 120 KTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDIT 172 (437)
Q Consensus 120 ~~~~~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~ 172 (437)
+++-.++..++.++.+. |.. ..+...+.++++..|++..|..++++-+.
T Consensus 5 ~~~~~A~~~~~~~l~~~-p~~---~~~~~~la~~~~~~g~~~~A~~~l~~~~~ 53 (68)
T PF14559_consen 5 GDYDEAIELLEKALQRN-PDN---PEARLLLAQCYLKQGQYDEAEELLERLLK 53 (68)
T ss_dssp THHHHHHHHHHHHHHHT-TTS---HHHHHHHHHHHHHTT-HHHHHHHHHCCHG
T ss_pred cCHHHHHHHHHHHHHHC-CCC---HHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence 33445677788877664 432 33566899999999999999988887654
No 264
>PF07720 TPR_3: Tetratricopeptide repeat; InterPro: IPR011716 This entry includes tetratricopeptide-like repeats found in the LcrH/SycD-like chaperones [].; PDB: 3KS2_O 3GZ2_A 3GZ1_A 3GYZ_A 4AM9_A 2VGX_A 2VGY_A.
Probab=26.44 E-value=1.4e+02 Score=19.88 Aligned_cols=24 Identities=25% Similarity=0.563 Sum_probs=18.7
Q ss_pred HHHHHHHHHHHHHhhHHHHHHHHH
Q psy9642 188 QYFYYGGMIYLALKNYERALYFFE 211 (437)
Q Consensus 188 ~Y~Yy~G~I~~~~k~y~~A~~~~~ 211 (437)
.+.|--|..+...|+|++|.++|.
T Consensus 2 e~~y~~a~~~y~~~ky~~A~~~~~ 25 (36)
T PF07720_consen 2 EYLYGLAYNFYQKGKYDEAIHFFQ 25 (36)
T ss_dssp HHHHHHHHHHHHTT-HHHHHHHHH
T ss_pred cHHHHHHHHHHHHhhHHHHHHHHH
Confidence 466677888888899999999954
No 265
>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=26.43 E-value=2.6e+02 Score=27.55 Aligned_cols=90 Identities=13% Similarity=0.200 Sum_probs=57.9
Q ss_pred HHHHHHhhccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCCCEEEEccCCCCCCc-hHHHHHHHHHHHHHHH
Q psy9642 312 IKRLTKTFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVFNDNPQRFNN-PLTFAQIESNIRACMH 390 (437)
Q Consensus 312 I~~l~k~Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~g~v~F~~~~~~~~~-~e~~~~l~~~i~~~~~ 390 (437)
|++|.+=+.++-.++.+.+|. +..+-.+|.+||+.|.|. |.|..+...|-| ....+++...+.. .
T Consensus 2 i~~L~~~~q~~Q~~~~~~rLS---ErnciEiv~kL~~~~~ld---------li~T~dGkeyiT~~~L~~EI~~el~~--~ 67 (272)
T PF09743_consen 2 IEELQADFQRAQLASSSQRLS---ERNCIEIVNKLIEKKLLD---------LIHTTDGKEYITPEQLEKEIKDELYV--H 67 (272)
T ss_pred HHHHHHHHHHHHHHhhhhhcc---hhhHHHHHHHHHHcCCee---------EEEECCCCEEECHHHHHHHHHHHHHH--c
Confidence 456666777777777776653 667778999999999887 445444444443 3444444444311 1
Q ss_pred HHH-HHHHHHHHhhCCHHHHHHhcCC
Q psy9642 391 LDG-KFQAMEEEILVNPLYVKKAASP 415 (437)
Q Consensus 391 L~~-~~~~~d~~l~~~~~yi~k~~~~ 415 (437)
-.. .+-++-.-|..+..+|.+.+..
T Consensus 68 gGRv~~~dL~~~LnVd~~~ie~~~~~ 93 (272)
T PF09743_consen 68 GGRVNLVDLAQALNVDLDHIERRAQE 93 (272)
T ss_pred CCceEHHHHHHhcCcCHHHHHHHHHH
Confidence 111 5566777888999999887765
No 266
>COG2976 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.32 E-value=1.9e+02 Score=27.33 Aligned_cols=87 Identities=21% Similarity=0.195 Sum_probs=63.0
Q ss_pred hCCCCcchHHHHHHHHHhCCCCcchhhHH-HHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHH
Q psy9642 119 LKTPQRGIPLIQTAIKKIQTSDSQLTSLH-SDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIY 197 (437)
Q Consensus 119 ~~~~~~~i~~l~~ai~rl~~~~~~lT~~h-~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~ 197 (437)
.+.--.++.-|+.++. .|..+.|+++. ..+.|+-+..+.++.||..|+.+.- ....-++.-..|-|+
T Consensus 102 ~~~~d~A~aqL~~~l~--~t~De~lk~l~~lRLArvq~q~~k~D~AL~~L~t~~~----------~~w~~~~~elrGDil 169 (207)
T COG2976 102 ANNLDKAEAQLKQALA--QTKDENLKALAALRLARVQLQQKKADAALKTLDTIKE----------ESWAAIVAELRGDIL 169 (207)
T ss_pred hccHHHHHHHHHHHHc--cchhHHHHHHHHHHHHHHHHHhhhHHHHHHHHhcccc----------ccHHHHHHHHhhhHH
Confidence 3333334444444432 34566676554 5678999999999999999987643 334566777899999
Q ss_pred HHHhhHHHHHHHHHHHhccc
Q psy9642 198 LALKNYERALYFFEVIITTP 217 (437)
Q Consensus 198 ~~~k~y~~A~~~~~~ai~~P 217 (437)
+..+|=.+|...|+.++..-
T Consensus 170 l~kg~k~~Ar~ay~kAl~~~ 189 (207)
T COG2976 170 LAKGDKQEARAAYEKALESD 189 (207)
T ss_pred HHcCchHHHHHHHHHHHHcc
Confidence 99999999999999999863
No 267
>KOG0547|consensus
Probab=26.19 E-value=7.2e+02 Score=26.94 Aligned_cols=89 Identities=19% Similarity=0.260 Sum_probs=52.2
Q ss_pred HHHHHHHHHHHHhhHHHHHHHHHHHhc-ccccccCHHHHHHHHHHHHHHHHH-hCCCCCCCccccHHHhHhhccCCHHHH
Q psy9642 189 YFYYGGMIYLALKNYERALYFFEVIIT-TPALAVSHIMLEGYKKYLLIYLIV-YGKAPNLPKNVSQAICRYIKPLSQPYL 266 (437)
Q Consensus 189 Y~Yy~G~I~~~~k~y~~A~~~~~~ai~-~P~~~~s~i~vea~Kk~iLv~Lil-~G~~~~lp~~~s~~~~r~~k~~~~pY~ 266 (437)
-||..|-+++.+.+|++|..-|+.|++ .|...-+.+++-+ ++. .+++..--++ -..+.+.|-+....|.
T Consensus 396 vYyHRgQm~flL~q~e~A~aDF~Kai~L~pe~~~~~iQl~~--------a~Yr~~k~~~~m~~-Fee~kkkFP~~~Evy~ 466 (606)
T KOG0547|consen 396 VYYHRGQMRFLLQQYEEAIADFQKAISLDPENAYAYIQLCC--------ALYRQHKIAESMKT-FEEAKKKFPNCPEVYN 466 (606)
T ss_pred hhHhHHHHHHHHHHHHHHHHHHHHHhhcChhhhHHHHHHHH--------HHHHHHHHHHHHHH-HHHHHHhCCCCchHHH
Confidence 468999999999999999999999999 7877544444332 211 1221110000 0112233444455666
Q ss_pred HHHHHHhcCCHHHHHHHHHhcc
Q psy9642 267 DLVSVYTNNNSTELQHLLLKYA 288 (437)
Q Consensus 267 ~L~~af~~~d~~~~~~~~~~~~ 288 (437)
=++++.. |-.+|.+.++.|.
T Consensus 467 ~fAeiLt--DqqqFd~A~k~YD 486 (606)
T KOG0547|consen 467 LFAEILT--DQQQFDKAVKQYD 486 (606)
T ss_pred HHHHHHh--hHHhHHHHHHHHH
Confidence 6666654 3446666666653
No 268
>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=25.26 E-value=2.1e+02 Score=20.07 Aligned_cols=47 Identities=15% Similarity=0.145 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHHHHHHHH-hhccccHHHHHHHhCCCChHHHHHHHHHhH
Q psy9642 300 TKQIVASLYKNNIKRLTK-TFLTLSLADVASRVQLGTPVQAEIYILKMI 347 (437)
Q Consensus 300 v~~l~~~v~r~~I~~l~k-~Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI 347 (437)
+.+++..+....=..+.. ++.-.|..+||+.+|++ +..+...+....
T Consensus 4 l~~~l~~L~~~~r~i~~l~~~~g~s~~eIa~~l~~s-~~~v~~~l~ra~ 51 (54)
T PF08281_consen 4 LQQALAQLPERQREIFLLRYFQGMSYAEIAEILGIS-ESTVKRRLRRAR 51 (54)
T ss_dssp HHHHHHCS-HHHHHHHHHHHTS---HHHHHHHCTS--HHHHHHHHHHHH
T ss_pred HHHHHHCCCHHHHHHHHHHHHHCcCHHHHHHHHCcC-HHHHHHHHHHHH
Confidence 334444444443333333 56789999999999998 778887776543
No 269
>KOG1585|consensus
Probab=25.21 E-value=6.7e+02 Score=24.76 Aligned_cols=96 Identities=16% Similarity=0.272 Sum_probs=54.3
Q ss_pred HhhHHHHHHH--HHHHHHHhhHHHHHHHHHHHhccccc-ccCHHHHHHHHHHHHHHHHHh---------CCCCCCCcccc
Q psy9642 184 KYFLQYFYYG--GMIYLALKNYERALYFFEVIITTPAL-AVSHIMLEGYKKYLLIYLIVY---------GKAPNLPKNVS 251 (437)
Q Consensus 184 ~~~l~Y~Yy~--G~I~~~~k~y~~A~~~~~~ai~~P~~-~~s~i~vea~Kk~iLv~Lil~---------G~~~~lp~~~s 251 (437)
.+...|-+|| ++++...+.|.+|-.+|..-...--. ..-+..-.+|--.|||.|-.+ .+....|.+..
T Consensus 145 r~~ma~el~gk~sr~lVrl~kf~Eaa~a~lKe~~~~~~~~~y~~~~k~~va~ilv~L~~~Dyv~aekc~r~~~qip~f~~ 224 (308)
T KOG1585|consen 145 RDQMAFELYGKCSRVLVRLEKFTEAATAFLKEGVAADKCDAYNSQCKAYVAAILVYLYAHDYVQAEKCYRDCSQIPAFLK 224 (308)
T ss_pred hHHHHHHHHHHhhhHhhhhHHhhHHHHHHHHhhhHHHHHhhcccHHHHHHHHHHHHhhHHHHHHHHHHhcchhcCccccC
Confidence 3455555565 67888889999988777654432111 001112223333456666421 11112333311
Q ss_pred HHHhHhhccCCHHHHHHHHHHhcCCHHHHHHHHHh
Q psy9642 252 QAICRYIKPLSQPYLDLVSVYTNNNSTELQHLLLK 286 (437)
Q Consensus 252 ~~~~r~~k~~~~pY~~L~~af~~~d~~~~~~~~~~ 286 (437)
+ ..+..-..|..+|..||.+.+..++..
T Consensus 225 s-------ed~r~lenLL~ayd~gD~E~~~kvl~s 252 (308)
T KOG1585|consen 225 S-------EDSRSLENLLTAYDEGDIEEIKKVLSS 252 (308)
T ss_pred h-------HHHHHHHHHHHHhccCCHHHHHHHHcC
Confidence 1 135566889999999999999888764
No 270
>KOG2911|consensus
Probab=24.78 E-value=4.5e+02 Score=27.69 Aligned_cols=95 Identities=13% Similarity=0.098 Sum_probs=60.0
Q ss_pred ccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCCCEEEEccCCCCCCc--hHHHHHHHHHHHHHHHHHHHHHHHH
Q psy9642 322 LSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVFNDNPQRFNN--PLTFAQIESNIRACMHLDGKFQAME 399 (437)
Q Consensus 322 IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~g~v~F~~~~~~~~~--~e~~~~l~~~i~~~~~L~~~~~~~d 399 (437)
=-+.+.++-.+.++.+.-...+..|-..+.|.---.-+...+.|.+.+..... .+....+.+-++-...|.+++..++
T Consensus 174 nef~tlc~~~~~~~~~t~~l~l~~l~~~k~i~vg~~~g~k~~~f~~i~~~~~~~it~~D~~V~~L~~~~~~L~kqie~L~ 253 (439)
T KOG2911|consen 174 NEFQTLCSNLGKPDEETKDLVLCWLAYQKHIIVGESIGIKFLKFSQIPSQDASIITEIDGSVADLIQARAKLAKQIEFLE 253 (439)
T ss_pred HHHHHHhccCCCCcHHHHHHHHHHHHhhhheeeehhcceEEEeeccCCcccccCCccchhhHHHHHHHHHHHHHHHHHHH
Confidence 33455555556565555555555665555543222334567778876655332 2455556666666678888999999
Q ss_pred HHhhCCHHHHHHhcCCC
Q psy9642 400 EEILVNPLYVKKAASPS 416 (437)
Q Consensus 400 ~~l~~~~~yi~k~~~~~ 416 (437)
+++..+++=+...++.-
T Consensus 254 qeie~~~~~~r~~~k~g 270 (439)
T KOG2911|consen 254 QEIEKSKEKLRQALKEG 270 (439)
T ss_pred HHHHHHHHHHHHHHHhc
Confidence 99999998887776653
No 271
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=24.30 E-value=5.4e+02 Score=25.01 Aligned_cols=45 Identities=9% Similarity=0.033 Sum_probs=38.3
Q ss_pred HHHHHHHHHHhhccccHHHHHHHhCCCChHHHHHHHHHhHHcCceE
Q psy9642 308 YKNNIKRLTKTFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIY 353 (437)
Q Consensus 308 ~r~~I~~l~k~Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~ 353 (437)
++..|..+-+...++++.++|+.++++ ..-+.+-|..|-..|.+.
T Consensus 18 R~~~Il~~L~~~~~vtv~eLa~~l~VS-~~TIRRDL~~Le~~G~l~ 62 (269)
T PRK09802 18 RREQIIQRLRQQGSVQVNDLSALYGVS-TVTIRNDLAFLEKQGIAV 62 (269)
T ss_pred HHHHHHHHHHHcCCEeHHHHHHHHCCC-HHHHHHHHHHHHhCCCeE
Confidence 556667777778889999999999998 788899999998888876
No 272
>PF00403 HMA: Heavy-metal-associated domain; InterPro: IPR006121 Proteins that transport heavy metals in micro-organisms and mammals share similarities in their sequences and structures. These proteins provide an important focus for research, some being involved in bacterial resistance to toxic metals, such as lead and cadmium, while others are involved in inherited human syndromes, such as Wilson's and Menke's diseases []. A conserved domain has been found in a number of these heavy metal transport or detoxification proteins []. The domain, which has been termed Heavy-Metal-Associated (HMA), contains two conserved cysteines that are probably involved in metal binding. Structure solution of the fourth HMA domain of the Menke's copper transporting ATPase shows a well-defined structure comprising a four-stranded antiparallel beta-sheet and two alpha helices packed in an alpha-beta sandwich fold []. This fold is common to other domains and is classified as "ferredoxin-like".; GO: 0046872 metal ion binding, 0030001 metal ion transport; PDB: 2VOY_A 1P6T_A 1KQK_A 2RML_A 1JWW_A 3K7R_F 1FES_A 1CC8_A 1FD8_A 2GGP_A ....
Probab=24.22 E-value=2.8e+02 Score=19.92 Aligned_cols=42 Identities=10% Similarity=0.091 Sum_probs=27.4
Q ss_pred HHHHHHHHHhHHcCceEEEEecCCCEEEEccCCCCCCchHHHHH
Q psy9642 337 VQAEIYILKMISQNEIYATINKKDGMVVFNDNPQRFNNPLTFAQ 380 (437)
Q Consensus 337 ~eaE~~l~~mI~~G~I~A~Id~~~g~v~F~~~~~~~~~~e~~~~ 380 (437)
..++..|.++ +|.-.+.+|...+.+.+.-+++..+..++.+.
T Consensus 14 ~~v~~~l~~~--~GV~~v~vd~~~~~v~v~~~~~~~~~~~i~~~ 55 (62)
T PF00403_consen 14 KKVEKALSKL--PGVKSVKVDLETKTVTVTYDPDKTSIEKIIEA 55 (62)
T ss_dssp HHHHHHHHTS--TTEEEEEEETTTTEEEEEESTTTSCHHHHHHH
T ss_pred HHHHHHHhcC--CCCcEEEEECCCCEEEEEEecCCCCHHHHHHH
Confidence 3455555555 58899999999999988755544333333333
No 273
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=24.18 E-value=3.2e+02 Score=21.13 Aligned_cols=33 Identities=9% Similarity=0.069 Sum_probs=27.0
Q ss_pred hccccHHHHHHHhCCCChHHHHHHHHHhHHcCce
Q psy9642 319 FLTLSLADVASRVQLGTPVQAEIYILKMISQNEI 352 (437)
Q Consensus 319 Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I 352 (437)
....+.++|+...+|+ ...+..++..++..|-|
T Consensus 17 ~~~~~~t~i~~~~~L~-~~~~~~yL~~L~~~gLI 49 (77)
T PF14947_consen 17 KGGAKKTEIMYKANLN-YSTLKKYLKELEEKGLI 49 (77)
T ss_dssp TT-B-HHHHHTTST---HHHHHHHHHHHHHTTSE
T ss_pred cCCCCHHHHHHHhCcC-HHHHHHHHHHHHHCcCe
Confidence 5778899999999998 78999999999999999
No 274
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=24.12 E-value=3.3e+02 Score=24.61 Aligned_cols=32 Identities=9% Similarity=0.016 Sum_probs=29.0
Q ss_pred cccHHHHHHHhCCCChHHHHHHHHHhHHcCceE
Q psy9642 321 TLSLADVASRVQLGTPVQAEIYILKMISQNEIY 353 (437)
Q Consensus 321 ~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~ 353 (437)
+++-.+||+.+|++ .+.+-+++.+|-.+|.|.
T Consensus 168 ~~t~~~lA~~lG~t-r~tvsR~l~~l~~~gii~ 199 (211)
T PRK11753 168 KITRQEIGRIVGCS-REMVGRVLKMLEDQGLIS 199 (211)
T ss_pred CCCHHHHHHHhCCC-HHHHHHHHHHHHHCCCEE
Confidence 68889999999997 788999999999999874
No 275
>KOG2376|consensus
Probab=23.70 E-value=2.7e+02 Score=30.54 Aligned_cols=69 Identities=12% Similarity=0.117 Sum_probs=49.3
Q ss_pred HHHHHHHHHHhCCchHHHhhhhHhhh----hhhc------------------CCCCCChHhhHHHHHHHHHHHHHHhhHH
Q psy9642 147 HSDLCQLCLLAQNFKPALEFLDVDIT----TIAN------------------EGPQFDTKYFLQYFYYGGMIYLALKNYE 204 (437)
Q Consensus 147 h~~l~~l~L~~~~y~~Al~il~~~I~----~~~~------------------~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~ 204 (437)
-....|.|+..+.|..|+.|-..-+- +... +.-...+.+...-.|-.+++++..++|.
T Consensus 113 l~L~AQvlYrl~~ydealdiY~~L~kn~~dd~d~~~r~nl~a~~a~l~~~~~q~v~~v~e~syel~yN~Ac~~i~~gky~ 192 (652)
T KOG2376|consen 113 LELRAQVLYRLERYDEALDIYQHLAKNNSDDQDEERRANLLAVAAALQVQLLQSVPEVPEDSYELLYNTACILIENGKYN 192 (652)
T ss_pred HHHHHHHHHHHhhHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHhhhHHHHHhccCCCcchHHHHHHHHHHHHhcccHH
Confidence 33457999999999999887543211 1100 0112344567778899999999999999
Q ss_pred HHHHHHHHHhc
Q psy9642 205 RALYFFEVIIT 215 (437)
Q Consensus 205 ~A~~~~~~ai~ 215 (437)
+|.+.++.+..
T Consensus 193 qA~elL~kA~~ 203 (652)
T KOG2376|consen 193 QAIELLEKALR 203 (652)
T ss_pred HHHHHHHHHHH
Confidence 99999999954
No 276
>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=23.63 E-value=1.6e+02 Score=29.08 Aligned_cols=50 Identities=12% Similarity=0.189 Sum_probs=39.7
Q ss_pred HHHHHHHHHHHHHhhccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEec
Q psy9642 305 ASLYKNNIKRLTKTFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINK 358 (437)
Q Consensus 305 ~~v~r~~I~~l~k~Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~ 358 (437)
.+.+|-.+..+++ -++++.+.+..+++ +.-.-.++.++|.+|.+.|+|.-
T Consensus 179 ka~iRG~l~a~T~---Pt~l~~l~~~~~~~-~~l~~~il~~Li~~~~l~G~i~G 228 (272)
T PF09743_consen 179 KARIRGALSAITR---PTPLSSLLKRYGFE-EKLFQSILEELIKSGELPGSIVG 228 (272)
T ss_pred HHHHHHHHhcCcc---ceEHHHHHHHhCCc-HHHHHHHHHHHHhcCcceEEEEC
Confidence 3444555555554 48999999999997 67888999999999999999963
No 277
>PRK13916 plasmid segregation protein ParR; Provisional
Probab=23.54 E-value=1.9e+02 Score=23.26 Aligned_cols=48 Identities=19% Similarity=0.476 Sum_probs=36.3
Q ss_pred HHHHHHhhHHHHHHHHHHHhcccccccCHHHHHHHHHHHHHHHHHhCCCCCCCcc
Q psy9642 195 MIYLALKNYERALYFFEVIITTPALAVSHIMLEGYKKYLLIYLIVYGKAPNLPKN 249 (437)
Q Consensus 195 ~I~~~~k~y~~A~~~~~~ai~~P~~~~s~i~vea~Kk~iLv~Lil~G~~~~lp~~ 249 (437)
.+++..++|.+-++|+..+ |.-.......+++.|||= .-|..||+|.-
T Consensus 9 ~L~i~r~~~~~iF~FL~~~---P~GT~~~~iR~~L~rYI~----~~G~~~PiP~~ 56 (97)
T PRK13916 9 LLKIKKEDYPQIFDFLENV---PRGTKTAHIREALRRYIE----EIGENPPIPSK 56 (97)
T ss_pred HHHhcccccHHHHHHHHHC---CCCCccHHHHHHHHHHHH----hcCCCCCCCcc
Confidence 4567778999988888654 554555678899999885 67888999865
No 278
>KOG1129|consensus
Probab=23.18 E-value=1.8e+02 Score=29.85 Aligned_cols=107 Identities=15% Similarity=0.260 Sum_probs=70.2
Q ss_pred CCCCcchHHHHHHHHHhC-CCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHH
Q psy9642 120 KTPQRGIPLIQTAIKKIQ-TSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYL 198 (437)
Q Consensus 120 ~~~~~~i~~l~~ai~rl~-~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~ 198 (437)
++|..++...+.- +.+- .+|+ +...+.-+|+-++.|+.+|+-+.+....-. .+.+-....|--|-|..
T Consensus 338 ~~PE~AlryYRRi-LqmG~~spe----Lf~NigLCC~yaqQ~D~~L~sf~RAlstat------~~~~aaDvWYNlg~vaV 406 (478)
T KOG1129|consen 338 NNPEMALRYYRRI-LQMGAQSPE----LFCNIGLCCLYAQQIDLVLPSFQRALSTAT------QPGQAADVWYNLGFVAV 406 (478)
T ss_pred CChHHHHHHHHHH-HHhcCCChH----HHhhHHHHHHhhcchhhhHHHHHHHHhhcc------CcchhhhhhhccceeEE
Confidence 5666666665543 3332 2232 344556689999999999998888766321 13345666788999999
Q ss_pred HHhhHHHHHHHHHHHhcc-cccccCHHHHHHHHHHHHHHHHHhCCCC
Q psy9642 199 ALKNYERALYFFEVIITT-PALAVSHIMLEGYKKYLLIYLIVYGKAP 244 (437)
Q Consensus 199 ~~k~y~~A~~~~~~ai~~-P~~~~s~i~vea~Kk~iLv~Lil~G~~~ 244 (437)
.-+|+.-|.++|+.|++. |..+ ||+..+.++.. ..|++.
T Consensus 407 ~iGD~nlA~rcfrlaL~~d~~h~------ealnNLavL~~-r~G~i~ 446 (478)
T KOG1129|consen 407 TIGDFNLAKRCFRLALTSDAQHG------EALNNLAVLAA-RSGDIL 446 (478)
T ss_pred eccchHHHHHHHHHHhccCcchH------HHHHhHHHHHh-hcCchH
Confidence 999999999999999984 4432 44444433222 455554
No 279
>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=23.06 E-value=1.9e+02 Score=23.02 Aligned_cols=75 Identities=7% Similarity=0.128 Sum_probs=45.6
Q ss_pred ccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCCCEEEEccCCCCCCchHHHHHHHH-------HHHHHHHHHHH
Q psy9642 322 LSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVFNDNPQRFNNPLTFAQIES-------NIRACMHLDGK 394 (437)
Q Consensus 322 IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~g~v~F~~~~~~~~~~e~~~~l~~-------~i~~~~~L~~~ 394 (437)
.+++++|+.+|++ +.. |......|.|.+.= .++|.-.|.+.. . ..-.....+.+ .|+.++.|.++
T Consensus 2 ~~i~e~A~~~gvs-~~t----Lr~ye~~Gli~p~r-~~~g~R~y~~~d-v-~~l~~i~~L~~d~g~~l~~i~~~l~l~~~ 73 (91)
T cd04766 2 YVISVAAELSGMH-PQT----LRLYERLGLLSPSR-TDGGTRRYSERD-I-ERLRRIQRLTQELGVNLAGVKRILELEEE 73 (91)
T ss_pred cCHHHHHHHHCcC-HHH----HHHHHHCCCcCCCc-CCCCCeeECHHH-H-HHHHHHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 3789999999998 544 44456678887632 245666665321 0 01122333333 55677778888
Q ss_pred HHHHHHHhhC
Q psy9642 395 FQAMEEEILV 404 (437)
Q Consensus 395 ~~~~d~~l~~ 404 (437)
+..++.++..
T Consensus 74 ~~~l~~~l~~ 83 (91)
T cd04766 74 LAELRAELDE 83 (91)
T ss_pred HHHHHHHHHH
Confidence 8777777743
No 280
>PF13512 TPR_18: Tetratricopeptide repeat
Probab=22.79 E-value=2.6e+02 Score=24.77 Aligned_cols=65 Identities=20% Similarity=0.227 Sum_probs=45.5
Q ss_pred HHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhc-cccc
Q psy9642 149 DLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIIT-TPAL 219 (437)
Q Consensus 149 ~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~-~P~~ 219 (437)
.-.+-.+..++|..|...+..--..+... .... ..++ -.|-.|...++|.+|...++.-+. +|+.
T Consensus 15 ~~a~~~l~~~~Y~~A~~~le~L~~ryP~g--~ya~--qAqL--~l~yayy~~~~y~~A~a~~~rFirLhP~h 80 (142)
T PF13512_consen 15 QEAQEALQKGNYEEAIKQLEALDTRYPFG--EYAE--QAQL--DLAYAYYKQGDYEEAIAAYDRFIRLHPTH 80 (142)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHhcCCCC--cccH--HHHH--HHHHHHHHccCHHHHHHHHHHHHHhCCCC
Confidence 34567889999999988777655443221 1122 2222 345567788999999999999999 8986
No 281
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=22.61 E-value=1.6e+02 Score=21.76 Aligned_cols=40 Identities=10% Similarity=0.135 Sum_probs=27.2
Q ss_pred ccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCCCEEEEc
Q psy9642 322 LSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVFN 366 (437)
Q Consensus 322 IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~g~v~F~ 366 (437)
.+++++|+++|++ +. .|......|.|.+....++|.-.|.
T Consensus 1 ~s~~eva~~~gvs-~~----tlr~~~~~gli~~~~~~~~g~r~y~ 40 (70)
T smart00422 1 YTIGEVAKLAGVS-VR----TLRYYERIGLLPPPIRTEGGYRLYS 40 (70)
T ss_pred CCHHHHHHHHCcC-HH----HHHHHHHCCCCCCCccCCCCCEecC
Confidence 3689999999998 43 4556677888876533345555554
No 282
>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=22.53 E-value=5.6e+02 Score=22.89 Aligned_cols=109 Identities=7% Similarity=0.038 Sum_probs=63.8
Q ss_pred ccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEE--ecCCCEEEEccCCCCCCchHHHHHHHHHHHHHHHHHHHHHH
Q psy9642 320 LTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATI--NKKDGMVVFNDNPQRFNNPLTFAQIESNIRACMHLDGKFQA 397 (437)
Q Consensus 320 s~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~I--d~~~g~v~F~~~~~~~~~~e~~~~l~~~i~~~~~L~~~~~~ 397 (437)
.-++-.+||+.+|++ ..++.++|..+-++|.+.-+= +...|+..+.--. +..++...+..++..+. +.++.
T Consensus 27 ~~~tdEeLa~~Lgi~-~~~VRk~L~~L~e~~Lv~~~r~r~~~~gw~~Y~w~i---~~~~i~d~Ik~~~~~~~---~~lk~ 99 (158)
T TIGR00373 27 GEFTDEEISLELGIK-LNEVRKALYALYDAGLADYKRRKDDETGWYEYTWRI---NYEKALDVLKRKLEETA---KKLRE 99 (158)
T ss_pred CCCCHHHHHHHHCCC-HHHHHHHHHHHHHCCCceeeeeeecCCCcEEEEEEe---CHHHHHHHHHHHHHHHH---HHHHH
Confidence 348999999999997 799999999999999984221 2234666644211 13355555655554433 23322
Q ss_pred HHHHhhCCHHHHHHhcCCC---C----cccCCCCCCCcccccccc
Q psy9642 398 MEEEILVNPLYVKKAASPS---D----EETGSSKPGGRVMEVENS 435 (437)
Q Consensus 398 ~d~~l~~~~~yi~k~~~~~---~----~~~~~~~~~~~~~~~~~~ 435 (437)
.=..-..+..|+=-..+.. + .+-++..=|+++.+.+|+
T Consensus 100 ~l~~e~~~~~Y~Cp~c~~r~tf~eA~~~~F~Cp~Cg~~L~~~dn~ 144 (158)
T TIGR00373 100 KLEFETNNMFFICPNMCVRFTFNEAMELNFTCPRCGAMLDYLDNS 144 (158)
T ss_pred HHhhccCCCeEECCCCCcEeeHHHHHHcCCcCCCCCCEeeeccCH
Confidence 2222223334431111110 0 122666889999999886
No 283
>KOG1173|consensus
Probab=22.53 E-value=6.3e+02 Score=27.67 Aligned_cols=98 Identities=15% Similarity=0.168 Sum_probs=64.3
Q ss_pred hHHHHHHHHHhCC---CCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhh
Q psy9642 126 IPLIQTAIKKIQT---SDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKN 202 (437)
Q Consensus 126 i~~l~~ai~rl~~---~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~ 202 (437)
+..++.++.+... ....--|+-..+...|-..+.|..|+....+.+.- ......++--.|.||..+|+
T Consensus 434 ~~~f~~~l~~ik~~~~e~~~w~p~~~NLGH~~Rkl~~~~eAI~~~q~aL~l---------~~k~~~~~asig~iy~llgn 504 (611)
T KOG1173|consen 434 LKYFQKALEVIKSVLNEKIFWEPTLNNLGHAYRKLNKYEEAIDYYQKALLL---------SPKDASTHASIGYIYHLLGN 504 (611)
T ss_pred HHHHHHHHHHhhhccccccchhHHHHhHHHHHHHHhhHHHHHHHHHHHHHc---------CCCchhHHHHHHHHHHHhcC
Confidence 3445566544422 12223445556667777888888888877776652 12256666678899999999
Q ss_pred HHHHHHHHHHHhc-ccccccCHHHHHHHHHHHHH
Q psy9642 203 YERALYFFEVIIT-TPALAVSHIMLEGYKKYLLI 235 (437)
Q Consensus 203 y~~A~~~~~~ai~-~P~~~~s~i~vea~Kk~iLv 235 (437)
.+.|.++|..++- .|... ...+.+|+.|=-
T Consensus 505 ld~Aid~fhKaL~l~p~n~---~~~~lL~~aie~ 535 (611)
T KOG1173|consen 505 LDKAIDHFHKALALKPDNI---FISELLKLAIED 535 (611)
T ss_pred hHHHHHHHHHHHhcCCccH---HHHHHHHHHHHh
Confidence 9999999999998 67642 334555555444
No 284
>PRK00215 LexA repressor; Validated
Probab=22.50 E-value=2.1e+02 Score=26.37 Aligned_cols=38 Identities=13% Similarity=0.115 Sum_probs=31.6
Q ss_pred cccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEec
Q psy9642 321 TLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINK 358 (437)
Q Consensus 321 ~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~ 358 (437)
.+++++||+.+|+.+..-+-.+|..|.+.|.|.-.-+.
T Consensus 23 ~~s~~ela~~~~~~~~~tv~~~l~~L~~~g~i~~~~~~ 60 (205)
T PRK00215 23 PPSRREIADALGLRSPSAVHEHLKALERKGFIRRDPGR 60 (205)
T ss_pred CCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEeCCCC
Confidence 47999999999993367889999999999999665444
No 285
>PRK10866 outer membrane biogenesis protein BamD; Provisional
Probab=22.19 E-value=6.9e+02 Score=23.82 Aligned_cols=103 Identities=14% Similarity=0.164 Sum_probs=64.9
Q ss_pred CcchHHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHh-
Q psy9642 123 QRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALK- 201 (437)
Q Consensus 123 ~~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k- 201 (437)
-.++..+...+.+. |.+.........+....+..++|..|+...++=|...... ...=.=.|..|+++..+.
T Consensus 49 ~~Ai~~f~~l~~~y-P~s~~a~~a~l~la~ayy~~~~y~~A~~~~e~fi~~~P~~------~~~~~a~Y~~g~~~~~~~~ 121 (243)
T PRK10866 49 KQAITQLEALDNRY-PFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTH------PNIDYVLYMRGLTNMALDD 121 (243)
T ss_pred HHHHHHHHHHHHhC-CCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCcCC------CchHHHHHHHHHhhhhcch
Confidence 34566666665554 5555555567788899999999999988888866543221 112222456677653332
Q ss_pred --------------h---HHHHHHHHHHHhc-ccccccCHHHHHHHHHHHHH
Q psy9642 202 --------------N---YERALYFFEVIIT-TPALAVSHIMLEGYKKYLLI 235 (437)
Q Consensus 202 --------------~---y~~A~~~~~~ai~-~P~~~~s~i~vea~Kk~iLv 235 (437)
| -.+|...|+..+. .|.+ .-..+|-++...+
T Consensus 122 ~~~~~~~~~~~~~rD~~~~~~A~~~~~~li~~yP~S---~ya~~A~~rl~~l 170 (243)
T PRK10866 122 SALQGFFGVDRSDRDPQHARAAFRDFSKLVRGYPNS---QYTTDATKRLVFL 170 (243)
T ss_pred hhhhhccCCCccccCHHHHHHHHHHHHHHHHHCcCC---hhHHHHHHHHHHH
Confidence 2 2467888999998 7864 4455665555554
No 286
>PF14493 HTH_40: Helix-turn-helix domain
Probab=22.07 E-value=1.2e+02 Score=24.31 Aligned_cols=30 Identities=20% Similarity=0.180 Sum_probs=27.9
Q ss_pred cccHHHHHHHhCCCChHHHHHHHHHhHHcCc
Q psy9642 321 TLSLADVASRVQLGTPVQAEIYILKMISQNE 351 (437)
Q Consensus 321 ~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~ 351 (437)
-.|+.+||+.-+|. ..-++.++.+++..|.
T Consensus 13 G~si~eIA~~R~L~-~sTI~~HL~~~~~~g~ 42 (91)
T PF14493_consen 13 GLSIEEIAKIRGLK-ESTIYGHLAELIESGE 42 (91)
T ss_pred CCCHHHHHHHcCCC-HHHHHHHHHHHHHhCC
Confidence 58999999999998 7899999999999987
No 287
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=21.82 E-value=4e+02 Score=20.87 Aligned_cols=48 Identities=8% Similarity=-0.007 Sum_probs=35.7
Q ss_pred HHHHHHhhccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCC
Q psy9642 312 IKRLTKTFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKD 360 (437)
Q Consensus 312 I~~l~k~Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~ 360 (437)
|..+-..-..+++++|.+.++++ ....-.++..+.+.|.|..+-...+
T Consensus 5 Il~~L~~~~~~~f~~L~~~l~lt-~g~Ls~hL~~Le~~GyV~~~k~~~~ 52 (80)
T PF13601_consen 5 ILALLYANEEATFSELKEELGLT-DGNLSKHLKKLEEAGYVEVEKEFEG 52 (80)
T ss_dssp HHHHHHHHSEEEHHHHHHHTT---HHHHHHHHHHHHHTTSEEEEEE-SS
T ss_pred HHHHHhhcCCCCHHHHHHHhCcC-HHHHHHHHHHHHHCCCEEEEEeccC
Confidence 33333345679999999999997 6889999999999999987766543
No 288
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=20.84 E-value=7.4e+02 Score=23.63 Aligned_cols=46 Identities=13% Similarity=0.153 Sum_probs=37.6
Q ss_pred HHHHHHHHHHhhccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEE
Q psy9642 308 YKNNIKRLTKTFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYA 354 (437)
Q Consensus 308 ~r~~I~~l~k~Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A 354 (437)
++..|..+-+-...++.++||+.++++ +.-+.+.+..|...|.|..
T Consensus 5 R~~~Il~~l~~~~~~~~~eLa~~l~VS-~~TiRRdL~~L~~~~~l~r 50 (240)
T PRK10411 5 RQQAIVDLLLNHTSLTTEALAEQLNVS-KETIRRDLNELQTQGKILR 50 (240)
T ss_pred HHHHHHHHHHHcCCCcHHHHHHHHCcC-HHHHHHHHHHHHHCCCEEE
Confidence 344456666667899999999999997 7889999999999888764
No 289
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=20.80 E-value=5.6e+02 Score=25.70 Aligned_cols=133 Identities=7% Similarity=-0.058 Sum_probs=0.0
Q ss_pred HHHHHHHhcCCHHHHHHHHHhc-----------------cccccccchhhHHHHHHHHHHH----------HHHHHHHHh
Q psy9642 266 LDLVSVYTNNNSTELQHLLLKY-----------------ADVFSRDENTGLTKQIVASLYK----------NNIKRLTKT 318 (437)
Q Consensus 266 ~~L~~af~~~d~~~~~~~~~~~-----------------~~~f~~D~n~~Lv~~l~~~v~r----------~~I~~l~k~ 318 (437)
.+++..+..||...|...+..| .+-+.+|+++++++.+..-=.. |-|+.....
T Consensus 74 ~~li~~~~~Gd~~A~~~Li~~y~~~V~~~a~~~~~~~~~aeDLvQE~fi~l~~ai~~fd~~rg~~Fstyatw~iR~ai~~ 153 (325)
T PRK05657 74 VYFARRALRGDFAARQRMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIER 153 (325)
T ss_pred HHHHHHHHcCCHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCccCCCHHHHHHHHHHHHHHH
Q ss_pred h---------------------------------ccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCCCEEEE
Q psy9642 319 F---------------------------------LTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVF 365 (437)
Q Consensus 319 Y---------------------------------s~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~g~v~F 365 (437)
+ ..-++.+||..++++ ++++..++.-.-..-.+.+.++ .++...+
T Consensus 154 ~i~~~~r~ir~p~~~~~~l~~~~R~~~~l~~~l~r~~t~~eiA~~l~~~-~~~v~~~l~~~~~~~sld~~~~-~~~~~~l 231 (325)
T PRK05657 154 AIMNQTRTIRLPVHVVKELNVYLRAARELEHKLDHEPSAEEIAELLDKP-VDDVSRMLALNERITSLDTPLG-GDPEKSL 231 (325)
T ss_pred HHHHcCCccccCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcC-HHHHHHHHHhccCCcccCCCCC-CCCCcch
Q ss_pred ccCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy9642 366 NDNPQRFNNPLTFAQIESNIRACMHLDGKFQAMEEE 401 (437)
Q Consensus 366 ~~~~~~~~~~e~~~~l~~~i~~~~~L~~~~~~~d~~ 401 (437)
.+....-....+...+..+ .....|...+..+..+
T Consensus 232 ~d~l~d~~~~~pe~~~~~~-e~~~~L~~aL~~L~~~ 266 (325)
T PRK05657 232 LDILADEQENGPEDTTQDD-DMKQSIVKWLFELNDK 266 (325)
T ss_pred hhhccCCCCCCHHHHHHHH-HHHHHHHHHHHcCCHH
No 290
>TIGR00475 selB selenocysteine-specific elongation factor SelB. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3-prime or 5-prime non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation. This model describes the elongation factor SelB, a close homolog rf EF-Tu. It may function by replacing EF-Tu. A C-terminal domain not found in EF-Tu is in all SelB sequences in the seed alignment except that from Methanococcus jannaschii. This model does not find an equivalent protein for eukaryotes.
Probab=20.45 E-value=3.2e+02 Score=29.95 Aligned_cols=78 Identities=10% Similarity=-0.009 Sum_probs=56.4
Q ss_pred hccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCCCEEEEccCCCCCCchHHHHHHHHHHHHHHHHHH--HHH
Q psy9642 319 FLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVFNDNPQRFNNPLTFAQIESNIRACMHLDG--KFQ 396 (437)
Q Consensus 319 Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~g~v~F~~~~~~~~~~e~~~~l~~~i~~~~~L~~--~~~ 396 (437)
+.--.+.|++..++++ +..+..++..|+..|.+..-.+ + +.|+ ..+.....-+. .+.
T Consensus 486 ~~~~~~~~~~~~~~~~-~~~~~~~l~~l~~~g~~~~~~~--~--~~~~----------------~~~~~~~~~~~~~~~~ 544 (581)
T TIGR00475 486 TKGAWVREFAEEVNGD-EKVMLKRVRKAGHRGGETLIVK--D--RLLK----------------KYINELKEEGGTFNVQ 544 (581)
T ss_pred cCCCCHHHHHhhhCCC-HHHHHHHHHHHHhCCCEEEEeC--C--eEHH----------------HHHHHHHhcCCcCcHH
Confidence 5789999999999987 7888999999999998766553 2 2233 22222222222 688
Q ss_pred HHHHHhhCCHHHHHHhcCCCC
Q psy9642 397 AMEEEILVNPLYVKKAASPSD 417 (437)
Q Consensus 397 ~~d~~l~~~~~yi~k~~~~~~ 417 (437)
+.++.+++|+.|.--.+..=|
T Consensus 545 ~~r~~~g~sRK~~i~lle~~D 565 (581)
T TIGR00475 545 QARDKLGLGRKLLIQLLEYFD 565 (581)
T ss_pred HHHHHHCccHHHHHHHHHHhh
Confidence 899999999999977765444
No 291
>PF14711 Nitr_red_bet_C: Respiratory nitrate reductase beta C-terminal; PDB: 3IR7_B 1Y5N_B 1R27_D 3EGW_B 1Y5I_B 1Q16_B 1Y4Z_B 1Y5L_B 3IR6_B 3IR5_B ....
Probab=20.21 E-value=1.5e+02 Score=23.80 Aligned_cols=29 Identities=10% Similarity=0.218 Sum_probs=24.1
Q ss_pred ccccHHHHHHHhCCCChHHHHHHHHHhHH
Q psy9642 320 LTLSLADVASRVQLGTPVQAEIYILKMIS 348 (437)
Q Consensus 320 s~IsL~dIa~~l~L~~~~eaE~~l~~mI~ 348 (437)
.||++..+|+++-=.+++.++..+.+|+.
T Consensus 28 lRIPi~YLAnLftAGd~~~V~~~L~rL~A 56 (83)
T PF14711_consen 28 LRIPIEYLANLFTAGDEEPVRRALKRLLA 56 (83)
T ss_dssp BSS-HHHHHHHHSTT-HHHHHHHHHHHHH
T ss_pred hcccHHHHHHHHccCChHHHHHHHHHHHH
Confidence 58999999999998888899999988875
Done!