Query psy5242
Match_columns 217
No_of_seqs 131 out of 189
Neff 6.3
Searched_HMMs 46136
Date Fri Aug 16 21:22:09 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5242.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5242hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3252|consensus 100.0 5.6E-81 1.2E-85 514.5 17.1 214 3-216 2-216 (217)
2 PF10075 PCI_Csn8: COP9 signal 100.0 2E-35 4.2E-40 237.1 10.2 137 61-199 3-143 (143)
3 PF03399 SAC3_GANP: SAC3/GANP/ 99.7 2E-16 4.4E-21 132.3 8.9 144 19-162 1-203 (204)
4 KOG4414|consensus 99.7 1E-16 2.2E-21 129.5 5.7 106 78-184 52-164 (197)
5 KOG3151|consensus 97.8 9E-05 2E-09 64.5 7.9 121 65-185 103-226 (260)
6 PF01399 PCI: PCI domain; Int 97.3 0.0022 4.8E-08 47.2 8.3 75 100-175 2-83 (105)
7 KOG1861|consensus 97.1 0.0063 1.4E-07 57.7 11.4 167 25-191 347-519 (540)
8 smart00088 PINT motif in prote 95.6 0.029 6.3E-07 40.6 5.1 60 130-190 3-69 (88)
9 smart00753 PAM PCI/PINT associ 95.6 0.029 6.3E-07 40.6 5.1 60 130-190 3-69 (88)
10 KOG0687|consensus 92.8 0.93 2E-05 41.8 9.4 95 99-194 257-366 (393)
11 COG5187 RPN7 26S proteasome re 91.2 0.99 2.1E-05 41.2 7.6 98 95-193 267-379 (412)
12 KOG2581|consensus 88.7 1 2.2E-05 42.6 5.8 168 7-175 188-401 (493)
13 KOG2758|consensus 86.1 1.4 3.1E-05 40.7 5.0 48 127-175 325-372 (432)
14 PF07037 DUF1323: Putative tra 84.7 1.2 2.6E-05 35.2 3.4 28 153-181 2-29 (122)
15 KOG2072|consensus 82.7 6.2 0.00013 40.4 8.2 53 123-175 419-471 (988)
16 PF05687 DUF822: Plant protein 81.4 1.4 3.1E-05 35.8 2.8 22 167-188 49-70 (150)
17 PF10537 WAC_Acf1_DNA_bd: ATP- 78.8 1.3 2.7E-05 33.9 1.6 60 97-158 19-85 (102)
18 PF10255 Paf67: RNA polymerase 69.8 43 0.00093 31.7 9.7 92 80-174 221-343 (404)
19 smart00874 B5 tRNA synthetase 67.3 11 0.00024 25.9 4.1 31 151-181 5-36 (71)
20 KOG1464|consensus 64.7 31 0.00068 31.6 7.3 83 93-176 299-388 (440)
21 COG5484 Uncharacterized conser 63.8 6.7 0.00015 34.9 2.9 29 151-180 19-47 (279)
22 PF14555 UBA_4: UBA-like domai 59.8 10 0.00023 23.9 2.6 27 154-181 4-30 (43)
23 PF08727 P3A: Poliovirus 3A pr 58.0 4.2 9.1E-05 28.0 0.5 24 158-181 21-44 (57)
24 PF13412 HTH_24: Winged helix- 56.2 46 0.001 20.9 5.3 42 135-178 2-46 (48)
25 PF13545 HTH_Crp_2: Crp-like h 56.0 24 0.00053 24.1 4.2 40 151-191 28-70 (76)
26 PF09494 Slx4: Slx4 endonuclea 55.5 14 0.00031 25.5 2.9 33 147-179 20-60 (64)
27 KOG1498|consensus 53.6 18 0.0004 34.2 4.1 81 94-175 286-376 (439)
28 PF03484 B5: tRNA synthetase B 52.3 22 0.00048 24.7 3.5 32 151-182 5-37 (70)
29 PF06056 Terminase_5: Putative 51.4 21 0.00046 24.3 3.2 31 149-180 11-41 (58)
30 cd07377 WHTH_GntR Winged helix 51.1 26 0.00056 22.8 3.6 44 135-179 8-55 (66)
31 PF01022 HTH_5: Bacterial regu 50.9 36 0.00078 21.6 4.1 41 135-178 1-44 (47)
32 COG1724 Predicted RNA binding 50.7 16 0.00035 25.9 2.5 21 159-180 3-23 (66)
33 COG5071 RPN5 26S proteasome re 50.0 32 0.0007 31.8 4.9 44 135-179 333-383 (439)
34 KOG1076|consensus 49.9 25 0.00055 35.6 4.6 75 99-175 655-741 (843)
35 PF14821 Thr_synth_N: Threonin 49.6 17 0.00037 26.1 2.6 36 140-175 41-77 (79)
36 KOG0686|consensus 48.6 67 0.0014 30.7 6.9 126 41-174 230-387 (466)
37 PF06627 DUF1153: Protein of u 48.0 53 0.0011 24.7 5.0 38 137-175 35-72 (90)
38 PF03374 ANT: Phage antirepres 47.2 46 0.001 24.8 4.8 35 146-181 19-53 (111)
39 COG2522 Predicted transcriptio 47.1 50 0.0011 26.0 5.1 43 132-177 5-48 (119)
40 PF13463 HTH_27: Winged helix 46.9 42 0.00091 22.3 4.2 41 139-180 6-49 (68)
41 PF12728 HTH_17: Helix-turn-he 46.9 28 0.0006 22.2 3.1 23 152-175 2-24 (51)
42 PF06043 Reo_P9: Reovirus P9-l 46.0 18 0.00039 32.8 2.6 143 9-178 54-272 (333)
43 PF04800 ETC_C1_NDUFA4: ETC co 44.3 29 0.00063 26.5 3.2 40 164-208 56-95 (101)
44 TIGR01764 excise DNA binding d 43.4 32 0.0007 21.0 2.9 23 152-175 2-24 (49)
45 PF13730 HTH_36: Helix-turn-he 42.0 40 0.00087 21.7 3.3 25 153-178 27-54 (55)
46 PF10668 Phage_terminase: Phag 41.2 63 0.0014 22.4 4.2 46 138-184 9-54 (60)
47 PRK11161 fumarate/nitrate redu 40.8 73 0.0016 26.5 5.6 39 151-190 184-225 (235)
48 PF12840 HTH_20: Helix-turn-he 40.1 84 0.0018 20.8 4.8 47 131-179 5-54 (61)
49 PF01466 Skp1: Skp1 family, di 39.6 1.1E+02 0.0025 21.5 5.7 47 130-180 28-77 (78)
50 PF13986 DUF4224: Domain of un 39.5 91 0.002 20.3 4.7 29 152-180 3-31 (47)
51 PF08279 HTH_11: HTH domain; 39.1 91 0.002 19.9 4.7 41 139-180 3-46 (55)
52 PF03693 RHH_2: Uncharacterise 39.1 22 0.00048 25.8 1.8 29 26-54 10-40 (80)
53 cd04762 HTH_MerR-trunc Helix-T 38.8 43 0.00092 20.2 3.0 22 153-175 2-23 (49)
54 TIGR02606 antidote_CC2985 puta 38.4 27 0.00059 24.5 2.2 31 25-55 6-38 (69)
55 PF13977 TetR_C_6: Bacterial t 38.1 55 0.0012 23.6 3.9 49 113-161 26-79 (115)
56 COG1654 BirA Biotin operon rep 37.8 1.3E+02 0.0029 21.8 5.7 48 144-192 12-65 (79)
57 smart00550 Zalpha Z-DNA-bindin 37.4 1.2E+02 0.0026 20.8 5.4 46 134-180 4-53 (68)
58 PF03793 PASTA: PASTA domain; 37.3 48 0.001 21.9 3.2 21 159-180 5-25 (63)
59 PRK13918 CRP/FNR family transc 37.1 1E+02 0.0023 24.8 5.8 40 151-191 149-191 (202)
60 cd04761 HTH_MerR-SF Helix-Turn 34.9 50 0.0011 20.4 2.8 24 153-178 2-25 (49)
61 PF01329 Pterin_4a: Pterin 4 a 34.8 55 0.0012 24.2 3.5 19 164-182 5-24 (95)
62 smart00345 HTH_GNTR helix_turn 34.1 64 0.0014 20.4 3.3 28 151-179 19-50 (60)
63 KOG1463|consensus 33.6 1.8E+02 0.0039 27.4 7.1 79 94-174 281-367 (411)
64 cd00092 HTH_CRP helix_turn_hel 33.2 1.4E+02 0.003 19.4 5.2 31 150-181 24-57 (67)
65 PRK15325 type III secretion sy 33.1 42 0.00091 24.7 2.4 40 4-49 23-63 (80)
66 smart00513 SAP Putative DNA-bi 32.6 46 0.00099 19.9 2.2 21 163-183 3-23 (35)
67 COG4004 Uncharacterized protei 32.2 50 0.0011 24.9 2.8 20 165-184 13-32 (96)
68 smart00419 HTH_CRP helix_turn_ 32.1 1.2E+02 0.0026 18.3 4.9 33 151-184 8-43 (48)
69 PF04539 Sigma70_r3: Sigma-70 31.5 1.5E+02 0.0032 20.3 5.1 38 137-175 6-43 (78)
70 PF06971 Put_DNA-bind_N: Putat 31.4 1E+02 0.0022 20.4 3.9 32 139-171 16-47 (50)
71 PF08565 CDC37_M: Cdc37 Hsp90 31.1 1.1E+02 0.0023 25.5 4.9 89 55-148 70-162 (173)
72 PLN03238 probable histone acet 30.3 1.3E+02 0.0029 27.2 5.7 52 139-191 211-263 (290)
73 KOG3389|consensus 30.1 38 0.00082 27.8 2.0 38 164-206 132-169 (178)
74 PF08280 HTH_Mga: M protein tr 29.9 1.6E+02 0.0035 19.5 4.8 35 140-176 9-43 (59)
75 PF00165 HTH_AraC: Bacterial r 29.6 92 0.002 19.0 3.4 30 150-180 7-37 (42)
76 PF00325 Crp: Bacterial regula 28.7 88 0.0019 18.8 3.0 23 152-175 3-25 (32)
77 PF08672 APC2: Anaphase promot 28.6 89 0.0019 21.4 3.4 35 10-44 16-53 (60)
78 TIGR01889 Staph_reg_Sar staphy 28.3 1.7E+02 0.0037 21.7 5.3 67 112-180 2-74 (109)
79 PF07927 YcfA: YcfA-like prote 28.2 1.4E+02 0.0031 19.2 4.3 15 167-181 2-16 (56)
80 PF01418 HTH_6: Helix-turn-hel 28.0 1.3E+02 0.0028 21.1 4.3 29 149-178 32-60 (77)
81 PF09339 HTH_IclR: IclR helix- 27.9 95 0.0021 19.9 3.3 40 140-180 7-49 (52)
82 PF04801 Sin_N: Sin-like prote 27.2 36 0.00078 31.8 1.6 96 76-180 282-387 (421)
83 PRK09391 fixK transcriptional 27.2 1.7E+02 0.0037 24.5 5.7 40 151-191 179-222 (230)
84 PRK11511 DNA-binding transcrip 26.6 2E+02 0.0043 22.1 5.5 76 137-215 11-95 (127)
85 PF13542 HTH_Tnp_ISL3: Helix-t 26.5 1.7E+02 0.0037 18.3 5.3 41 131-175 10-50 (52)
86 KOG2582|consensus 26.5 2.7E+02 0.0059 26.4 7.1 58 135-195 301-366 (422)
87 cd01104 HTH_MlrA-CarA Helix-Tu 26.2 94 0.002 20.6 3.2 24 153-177 2-25 (68)
88 PF02042 RWP-RK: RWP-RK domain 26.0 1.3E+02 0.0028 20.2 3.7 29 148-177 12-40 (52)
89 KOG2745|consensus 25.0 83 0.0018 28.6 3.4 43 112-163 129-171 (321)
90 PF13384 HTH_23: Homeodomain-l 25.0 1.3E+02 0.0028 18.7 3.6 35 137-175 6-40 (50)
91 smart00422 HTH_MERR helix_turn 24.9 1.1E+02 0.0023 20.4 3.3 24 153-178 2-25 (70)
92 PF04147 Nop14: Nop14-like fam 24.1 4.8E+02 0.01 27.0 9.1 23 93-115 558-581 (840)
93 PF03683 UPF0175: Uncharacteri 23.9 1.2E+02 0.0026 21.5 3.5 47 132-180 16-62 (76)
94 PF04967 HTH_10: HTH DNA bindi 23.8 1.2E+02 0.0027 20.2 3.3 24 150-174 22-45 (53)
95 PRK10219 DNA-binding transcrip 23.3 2.5E+02 0.0054 20.4 5.3 65 147-214 17-90 (107)
96 PRK13696 hypothetical protein; 23.2 2.3E+02 0.005 19.8 4.6 38 131-174 23-60 (62)
97 COG4199 Uncharacterized protei 23.0 1.7E+02 0.0037 25.0 4.7 106 100-212 63-176 (201)
98 PF14791 DNA_pol_B_thumb: DNA 22.7 1.4E+02 0.003 20.6 3.5 27 158-186 3-32 (64)
99 PF05295 Luciferase_N: Lucifer 22.7 22 0.00049 25.9 -0.5 26 110-135 32-61 (82)
100 PF01978 TrmB: Sugar-specific 22.7 2.5E+02 0.0053 18.8 5.2 46 132-180 5-53 (68)
101 PF14561 TPR_20: Tetratricopep 22.5 1.9E+02 0.0041 21.1 4.4 58 22-80 18-75 (90)
102 PF13518 HTH_28: Helix-turn-he 22.3 2E+02 0.0044 17.8 4.1 25 150-175 11-35 (52)
103 PRK15365 type III secretion sy 22.2 2.1E+02 0.0045 21.9 4.6 36 25-60 27-64 (107)
104 PTZ00429 beta-adaptin; Provisi 22.2 3.9E+02 0.0084 27.4 7.9 28 44-71 158-186 (746)
105 PRK10402 DNA-binding transcrip 22.0 2.6E+02 0.0057 23.2 5.8 52 136-188 150-208 (226)
106 smart00420 HTH_DEOR helix_turn 21.9 2E+02 0.0043 17.4 5.1 31 149-180 12-45 (53)
107 PF08220 HTH_DeoR: DeoR-like h 21.8 2.4E+02 0.0051 18.6 4.5 39 139-179 3-44 (57)
108 PF04699 P16-Arc: ARP2/3 compl 21.5 4.5E+02 0.0098 21.4 7.5 71 99-174 38-108 (152)
109 PF10410 DnaB_bind: DnaB-helic 21.4 49 0.0011 21.6 1.0 52 116-168 5-58 (59)
110 PF15297 CKAP2_C: Cytoskeleton 21.3 62 0.0013 30.1 1.9 61 78-138 103-168 (353)
111 smart00418 HTH_ARSR helix_turn 21.2 2.2E+02 0.0047 17.6 4.4 31 149-180 8-41 (66)
112 PF06708 DUF1195: Protein of u 21.0 73 0.0016 25.9 2.0 84 60-143 37-141 (157)
113 KOG2140|consensus 21.0 2.8E+02 0.0061 27.7 6.3 102 64-180 198-306 (739)
114 PF04760 IF2_N: Translation in 20.9 90 0.002 20.3 2.2 28 151-179 3-31 (54)
115 PF08784 RPA_C: Replication pr 20.9 2.1E+02 0.0045 21.0 4.4 43 135-178 46-94 (102)
116 COG2074 2-phosphoglycerate kin 20.6 85 0.0018 28.4 2.5 44 98-142 128-173 (299)
117 COG1753 Predicted antotoxin, c 20.6 2.3E+02 0.005 20.4 4.3 40 130-175 23-62 (74)
118 PF13411 MerR_1: MerR HTH fami 20.4 1.2E+02 0.0026 20.1 2.9 22 153-175 2-23 (69)
119 cd04764 HTH_MlrA-like_sg1 Heli 20.3 1.5E+02 0.0033 19.8 3.3 24 153-177 2-25 (67)
No 1
>KOG3252|consensus
Probab=100.00 E-value=5.6e-81 Score=514.52 Aligned_cols=214 Identities=58% Similarity=0.985 Sum_probs=211.0
Q ss_pred hHHHHHHHHHHHhccccCCCCCchhHHHHHHHHHHhccccchHhhHHHHHhhhcCCC-CChHHHHHHHHHHhhcCCCcch
Q psy5242 3 QAELMKGSVDQLLVGIERYNPEHLSTLEKYVEVQCAENVYDLEANLAVLKLYQFHQN-YNMKITSQILLKALTNFPHTDF 81 (217)
Q Consensus 3 ~~~~~~~~i~~~l~g~~rYnp~~l~~Le~yv~~Q~~~~~Yd~~aNlalLKLYqfnP~-~~~~vv~~ILlkaL~~~P~~DF 81 (217)
++|+|+..++++|.|++|||||||++||.||+.|+++|+||++||||+||||||||+ ||.++++.||+||||++|||||
T Consensus 2 ~feq~qs~~~e~l~ginryNPE~latLe~yVq~qak~ntYdleanL~vLkLYQfnP~~~nt~itaqILlKaL~~lP~tDF 81 (217)
T KOG3252|consen 2 QFEQMQSNVGELLVGINRYNPENLATLENYVQAQAKENTYDLEANLAVLKLYQFNPEFFNTTITAQILLKALTNLPHTDF 81 (217)
T ss_pred cchHHHHHHHHHHHhcccCChhHHHHHHHHHHHHHhccccchhHHHHHHHHHhcCHHHhhhHHHHHHHHHHHhcCCCcch
Confidence 689999999999999999999999999999999999999999999999999999999 9999999999999999999999
Q ss_pred hhhhhccCCCCCCCccHHHHHHHHHHHHhCChHHHHHHhhcCCchhhhccchHHHHHHHHHHHHHHhcccccHHHHHHhh
Q psy5242 82 ILCKCLLSKDLCKEDPIDQIIYLADLLESCKFTQFWSRMHTIPDLFLNIEGFNDSIRKFVCHVVGITFQTIDKKLLSELL 161 (217)
Q Consensus 82 ~lc~~LIp~~~~~~~~i~~l~~L~~lLe~c~F~~FW~~l~~~~~l~~~i~gFed~IR~~I~~vVs~tyqsIs~~~La~~L 161 (217)
+||+||||++.+.++++++|+.||+.||+|+|+.||.+.+.+++++..|+||||+||+|+|||||.|||+|+++.|+++|
T Consensus 82 ~l~kcli~~~~~~ee~~r~ii~L~~~LEt~~Fq~FW~~~~~N~~mle~itGFedsvr~yachvv~iTyQkI~k~lLaell 161 (217)
T KOG3252|consen 82 TLAKCLIDERVQMEEPFRSIIDLGDYLETCRFQQFWQEADENRDMLEGITGFEDSVRKYACHVVGITYQKIDKWLLAELL 161 (217)
T ss_pred hHHHHhcCHHHhcccchhHHHhHHHHHhhchHHHHhhhhccchHHhcCCCcHHHHHHHHHHHheechHhhchHHHHHHhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCHHHHHHHHHHcCceEeCCceEEeCCCCccccccccccccccchHHHHhhhc
Q psy5242 162 DGVEDSTLRLWVKKYGWKELDNGYIFIANQDENIKTKNITEKIEFENAATIMTSN 216 (217)
Q Consensus 162 G~ls~~el~~~v~~~GWt~~~~g~v~p~n~en~~k~~~i~E~i~~~~~~~~~~~~ 216 (217)
|+++|++++.|++++||..+++|++|++++|.++|+|||.|||+||+|+++|++.
T Consensus 162 G~~sDs~le~~~~~~GW~a~e~G~ifv~~qE~~iKtkNi~EkI~fd~Va~ima~~ 216 (217)
T KOG3252|consen 162 GGLSDSQLEVWMTKYGWIADESGQIFVASQEEEIKTKNIVEKIDFDHVASIMASL 216 (217)
T ss_pred CcccHHHHHHHHHHccceecCCceEEEeccccccccCCccccCCcchHHHHHHhc
Confidence 9999999999999999999999999999999999999999999999999999864
No 2
>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=100.00 E-value=2e-35 Score=237.10 Aligned_cols=137 Identities=29% Similarity=0.503 Sum_probs=113.0
Q ss_pred ChHHHHHHHHHHhhcCCCcchhhhhhccCCCCCC-CccHHHHHHHHHHHHhCChHHHHHHhhcC---CchhhhccchHHH
Q psy5242 61 NMKITSQILLKALTNFPHTDFILCKCLLSKDLCK-EDPIDQIIYLADLLESCKFTQFWSRMHTI---PDLFLNIEGFNDS 136 (217)
Q Consensus 61 ~~~vv~~ILlkaL~~~P~~DF~lc~~LIp~~~~~-~~~i~~l~~L~~lLe~c~F~~FW~~l~~~---~~l~~~i~gFed~ 136 (217)
++++++.+|+|+|++.|.+||.+|.++||++++. +|+|+.+|.|+++||+|+|++||+.++++ +++...|+||+|+
T Consensus 3 ~~~~~~~~Ll~~L~~~~~~df~~~~~rip~~~~~~~~~i~~i~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~ 82 (143)
T PF10075_consen 3 NPEIYALILLKYLMQNDLSDFRLLWKRIPEELKQSDPEIKAIWSLGQALWEGDYSKFWQALRSNPWSPDYKPFVPGFEDT 82 (143)
T ss_dssp -HHHHHHHHHHHHHTTTSTHHHHHHHTS-HHHHTS-TTHHHHHHHHHHHHTT-HHHHHHHS-TT----HHHHTSTTHHHH
T ss_pred chhHHHHHHHHHHHcCCchHHHHHHHcCCHHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHhccchHHHHHHHHHHHHH
Confidence 6789999999999999999999999999999987 59999999999999999999999999986 8899999999999
Q ss_pred HHHHHHHHHHHhcccccHHHHHHhhcCCCHHHHHHHHHHcCceEeCCceEEeCCCCccccccc
Q psy5242 137 IRKFVCHVVGITFQTIDKKLLSELLDGVEDSTLRLWVKKYGWKELDNGYIFIANQDENIKTKN 199 (217)
Q Consensus 137 IR~~I~~vVs~tyqsIs~~~La~~LG~ls~~el~~~v~~~GWt~~~~g~v~p~n~en~~k~~~ 199 (217)
||++|+++|+.||++|+.+.+++||| ++++++.++++++||++++++++++.||+ ++|+||
T Consensus 83 iR~~i~~~i~~aY~sIs~~~la~~Lg-~~~~el~~~~~~~gW~~d~~~~~~~~~~~-~~k~k~ 143 (143)
T PF10075_consen 83 IRERIAHLISKAYSSISLSDLAEMLG-LSEEELEKFIKSRGWTVDGDGVLFPPNPE-EIKSKN 143 (143)
T ss_dssp HHHHHHHHHHHH-SEE-HHHHHHHTT-S-HHHHHHHHHHHT-EE-----EE---HH-HTS---
T ss_pred HHHHHHHHHHHHHhHcCHHHHHHHhC-CCHHHHHHHHHHcCCEECCCccEEecCCc-ccCCCC
Confidence 99999999999999999999999998 88999999999999999988899999999 899886
No 3
>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=99.67 E-value=2e-16 Score=132.28 Aligned_cols=144 Identities=22% Similarity=0.305 Sum_probs=114.3
Q ss_pred cCCCCCchhHHH-------------------HHHHHHHhccccchHh-------hHHHHH-----------hhhcC----
Q psy5242 19 ERYNPEHLSTLE-------------------KYVEVQCAENVYDLEA-------NLAVLK-----------LYQFH---- 57 (217)
Q Consensus 19 ~rYnp~~l~~Le-------------------~yv~~Q~~~~~Yd~~a-------NlalLK-----------LYqfn---- 57 (217)
|++||+.+-.++ +|+.+|.+.--+|+.+ .+.++. ++||+
T Consensus 1 ~~p~p~~vRp~~vL~~t~~~l~~~~~~~~~y~fi~drlRsiRqDl~vQ~~~~~~~i~v~E~~ar~~i~~~d~~qf~~c~~ 80 (204)
T PF03399_consen 1 DEPNPSDVRPPEVLKKTLNYLLRKIPFKDDYNFIWDRLRSIRQDLTVQNIENDFAIKVYERIARFAIESGDLEQFNQCLS 80 (204)
T ss_dssp ----------HHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHTT--SHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCChHhCCCHHHHHHHHHHHHHHhhhhhhhHHHHHHhHHHHhhHHHHhcCCHHHHHHHHHHHHHHhhcCCHHHHHHHHH
Confidence 688999998888 9999999999999999 999999 99999
Q ss_pred -------------CC-CChHHHHHHHHHHhhcCCCcchhhhhhccCCCCCCCccHHHHHHHHHHHHhCChHHHHHHh--h
Q psy5242 58 -------------QN-YNMKITSQILLKALTNFPHTDFILCKCLLSKDLCKEDPIDQIIYLADLLESCKFTQFWSRM--H 121 (217)
Q Consensus 58 -------------P~-~~~~vv~~ILlkaL~~~P~~DF~lc~~LIp~~~~~~~~i~~l~~L~~lLe~c~F~~FW~~l--~ 121 (217)
|. ...++++..|+..|++-+.+||..++..+|+....+|.|+....+...+.+++|..||..+ +
T Consensus 81 ~L~~lY~~~~~~~~~~~~~ef~~y~lL~~l~~~~~~~~~~~l~~l~~~~~~~~~i~~al~l~~a~~~gny~~ff~l~~~~ 160 (204)
T PF03399_consen 81 QLKELYDDLRDLPPSPNEAEFIAYYLLYLLCQNNIPDFHMELELLPSEILSSPYIQFALELCRALMEGNYVRFFRLYRSK 160 (204)
T ss_dssp HHHHHHHHHHHT---TTHHHHHHHHHHHTT-T---THHHHHHTTS-HHHHTSHHHHHHHHHHHHH--TTHHHHHHHHT-T
T ss_pred HHHHHHHhhccCCCCCCHHHHHHHHHHHHHHcccchHHHHHHHHCchhhhcCHHHHHHHHHHHHHHcCCHHHHHHHHhcc
Confidence 88 9999999999999999999999999999998888999999999999999999999999999 4
Q ss_pred cCCchhhh-ccchHHHHHHHHHHHHHHhccc-ccHHHHHHhhc
Q psy5242 122 TIPDLFLN-IEGFNDSIRKFVCHVVGITFQT-IDKKLLSELLD 162 (217)
Q Consensus 122 ~~~~l~~~-i~gFed~IR~~I~~vVs~tyqs-Is~~~La~~LG 162 (217)
+.+.+... +..|.+.||..+++.++.||++ |+++.|++|||
T Consensus 161 ~~~~l~~~l~~~~~~~iR~~al~~i~~ay~~~i~l~~l~~~L~ 203 (204)
T PF03399_consen 161 SAPYLFACLMERFFNRIRLRALQSISKAYRSSIPLSFLAELLG 203 (204)
T ss_dssp TS-HHHHHHHGGGHHHHHHHHHHHHHHHS-T-EEHHHHHHHTT
T ss_pred CCChHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcC
Confidence 44544444 4449999999999999999999 99999999997
No 4
>KOG4414|consensus
Probab=99.66 E-value=1e-16 Score=129.46 Aligned_cols=106 Identities=11% Similarity=0.180 Sum_probs=94.8
Q ss_pred Ccchhhhhhc---cCCCCC-CCccHHHHHHHHHHHHhCChHHHHHHhhcC---CchhhhccchHHHHHHHHHHHHHHhcc
Q psy5242 78 HTDFILCKCL---LSKDLC-KEDPIDQIIYLADLLESCKFTQFWSRMHTI---PDLFLNIEGFNDSIRKFVCHVVGITFQ 150 (217)
Q Consensus 78 ~~DF~lc~~L---Ip~~~~-~~~~i~~l~~L~~lLe~c~F~~FW~~l~~~---~~l~~~i~gFed~IR~~I~~vVs~tyq 150 (217)
+.|..-..+| ||+.++ ..||+..+|.+|+.+|+++|++.+++++.. .+....|..|.|..|+|.+.++.++|+
T Consensus 52 ~dD~dnARfLWKRIP~AIKe~k~El~aaWgiGQkiWq~Df~GiYeaI~~~dWSeeak~imaAf~D~~~kR~FaLl~qAYs 131 (197)
T KOG4414|consen 52 HDDCDNARFLWKRIPPAIKEAKPELGAAWGIGQKIWQHDFAGIYEAINAHDWSEEAKDIMAAFRDATRKRAFALLLQAYS 131 (197)
T ss_pred hccchhHHHHHHhCCHHHhhcCchhhhhhhhhHHHHhcccchHHHHHhhhcchHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4444444443 889988 678999999999999999999999999984 678899999999999999999999999
Q ss_pred cccHHHHHHhhcCCCHHHHHHHHHHcCceEeCCc
Q psy5242 151 TIDKKLLSELLDGVEDSTLRLWVKKYGWKELDNG 184 (217)
Q Consensus 151 sIs~~~La~~LG~ls~~el~~~v~~~GWt~~~~g 184 (217)
+|..++++.||| |++++..+.+.++||++|...
T Consensus 132 sI~~~D~A~FlG-l~~ddAtk~ilEnGWqaDaas 164 (197)
T KOG4414|consen 132 SIIADDFAAFLG-LPEDDATKGILENGWQADAAS 164 (197)
T ss_pred HHHHHHHHHHhC-CCHHHHHHHHHHcccchhhHH
Confidence 999999999998 999999999999999997654
No 5
>KOG3151|consensus
Probab=97.79 E-value=9e-05 Score=64.45 Aligned_cols=121 Identities=17% Similarity=0.224 Sum_probs=99.2
Q ss_pred HHHHHHHHhhcCCCcchhhhhhccCCCCCCC-ccHHHHHHHHHHHHhCChHHHHHHhhcCC--chhhhccchHHHHHHHH
Q psy5242 65 TSQILLKALTNFPHTDFILCKCLLSKDLCKE-DPIDQIIYLADLLESCKFTQFWSRMHTIP--DLFLNIEGFNDSIRKFV 141 (217)
Q Consensus 65 v~~ILlkaL~~~P~~DF~lc~~LIp~~~~~~-~~i~~l~~L~~lLe~c~F~~FW~~l~~~~--~l~~~i~gFed~IR~~I 141 (217)
+.-=|+--|.+=--+||-.-+-++|...+.+ |-|...+.|-+.+=...|.+.|.+.++.+ .+.--|.=..+.||..|
T Consensus 103 ~GLnLL~LLsqNRiaeFHteLe~lp~~~l~~~~~I~~~v~LEq~~MEGaYnKv~~a~~s~p~~~y~~FmdIl~~tiRdEI 182 (260)
T KOG3151|consen 103 LGLNLLYLLSQNRIAEFHTELELLPKKILQHNPYISHPVSLEQSLMEGAYNKVLSAKQSIPSEEYTYFMDILLDTIRDEI 182 (260)
T ss_pred HHHHHHHHHHhccHHHHHHHHHhccHHHhhccchhhhHHHHHHHHHhhHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHH
Confidence 3333444444445699999999999998744 78899999999999999999999998864 34444555568899999
Q ss_pred HHHHHHhcccccHHHHHHhhcCCCHHHHHHHHHHcCceEeCCce
Q psy5242 142 CHVVGITFQTIDKKLLSELLDGVEDSTLRLWVKKYGWKELDNGY 185 (217)
Q Consensus 142 ~~vVs~tyqsIs~~~La~~LG~ls~~el~~~v~~~GWt~~~~g~ 185 (217)
+.++-.+|..|+.++-..+|+.-++++++++..+.+|.++..++
T Consensus 183 A~c~EKsYd~l~~s~a~~~L~f~~~~e~~~~~~~r~W~l~~~~~ 226 (260)
T KOG3151|consen 183 AGCIEKSYDKLSASDATQMLLFNNDKELKKFATERQWPLDEKGV 226 (260)
T ss_pred HHHHHHHHhhcCHHHHHHHHhcCChHHHHHHHHhcCCccccccc
Confidence 99999999999999999999755678999999999999975443
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=97.26 E-value=0.0022 Score=47.19 Aligned_cols=75 Identities=13% Similarity=0.170 Sum_probs=62.8
Q ss_pred HHHHHHHHHHhCChHHHHHHhhcC-------CchhhhccchHHHHHHHHHHHHHHhcccccHHHHHHhhcCCCHHHHHHH
Q psy5242 100 QIIYLADLLESCKFTQFWSRMHTI-------PDLFLNIEGFNDSIRKFVCHVVGITFQTIDKKLLSELLDGVEDSTLRLW 172 (217)
Q Consensus 100 ~l~~L~~lLe~c~F~~FW~~l~~~-------~~l~~~i~gFed~IR~~I~~vVs~tyqsIs~~~La~~LG~ls~~el~~~ 172 (217)
.+..|-+.+.+++|..|-+.++.. +.+...+..+...+|+..+.-++..|++|+.+.+++.+| ++.++++.+
T Consensus 2 ~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~~l~~~i~~~~l~~l~~~y~~i~~~~ia~~l~-~~~~~vE~~ 80 (105)
T PF01399_consen 2 PYSELLRAFRSGDLQEFEEFLEKHSESLFKDPFLAEYVEQLKEKIRRRNLRQLSKPYSSISISEIAKALQ-LSEEEVESI 80 (105)
T ss_dssp HHHHHHHHHHCT-HHHHHHHHHHTCHHHHHCTTHHHHHHHHHHHHHHHHHHHHHHC-SEEEHHHHHHHHT-CCHHHHHHH
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHHHHHHHhcccchHHHHHHhc-cchHHHHHH
Confidence 355677889999999999888765 344567788899999999999999999999999999997 999999999
Q ss_pred HHH
Q psy5242 173 VKK 175 (217)
Q Consensus 173 v~~ 175 (217)
+.+
T Consensus 81 l~~ 83 (105)
T PF01399_consen 81 LID 83 (105)
T ss_dssp HHH
T ss_pred HHH
Confidence 885
No 7
>KOG1861|consensus
Probab=97.11 E-value=0.0063 Score=57.74 Aligned_cols=167 Identities=13% Similarity=0.131 Sum_probs=122.2
Q ss_pred chhHHHHHHHHHHhcc-ccchHhhHHHHH-hhhcCCC-CChHHHHHHHHHHhhcCCCcchhhhhhccCCCCCCCccHHHH
Q psy5242 25 HLSTLEKYVEVQCAEN-VYDLEANLAVLK-LYQFHQN-YNMKITSQILLKALTNFPHTDFILCKCLLSKDLCKEDPIDQI 101 (217)
Q Consensus 25 ~l~~Le~yv~~Q~~~~-~Yd~~aNlalLK-LYqfnP~-~~~~vv~~ILlkaL~~~P~~DF~lc~~LIp~~~~~~~~i~~l 101 (217)
.+.+-|-+-+..+++| .=.+.-+.+-|| ||-+.-. --.+-++.-+|=-+--=-.+|.+..+.=|.+..+++|-|.-.
T Consensus 347 TveVYEtHARIALEkGD~~EfNQCQtQLk~LY~egipg~~~EF~AYriLY~i~tkN~~di~sll~~lt~E~ked~~V~hA 426 (540)
T KOG1861|consen 347 TVEVYETHARIALEKGDLEEFNQCQTQLKALYSEGIPGAYLEFTAYRILYYIFTKNYPDILSLLRDLTEEDKEDEAVAHA 426 (540)
T ss_pred eeeeehhhhHHHHhcCCHHHHHHHHHHHHHHHccCCCCchhhHHHHHHHHHHHhcCchHHHHHHHhccHhhccCHHHHHH
Confidence 3445555555566654 223344556666 6744333 334444444444443333459999999999999999999999
Q ss_pred HHHHHHHHhCChHHHHHHhhcCCchh-hhccchHHHHHHHHHHHHHHhcc-cccHHHHHHhhcCCCHHHHHHHHHHcCce
Q psy5242 102 IYLADLLESCKFTQFWSRMHTIPDLF-LNIEGFNDSIRKFVCHVVGITFQ-TIDKKLLSELLDGVEDSTLRLWVKKYGWK 179 (217)
Q Consensus 102 ~~L~~lLe~c~F~~FW~~l~~~~~l~-~~i~gFed~IR~~I~~vVs~tyq-sIs~~~La~~LG~ls~~el~~~v~~~GWt 179 (217)
..+....-..+|-.|+..+..-+.+- -.|.-|.|.-|+.++.++..+|+ +|+.+-+++.|...+.++...|..+++|+
T Consensus 427 L~vR~A~~~GNY~kFFrLY~~AP~M~~yLmdlF~erER~~Al~ii~KsyrP~i~~~fi~~~laf~~~e~c~~~l~~~~~~ 506 (540)
T KOG1861|consen 427 LEVRSAVTLGNYHKFFRLYLTAPNMSGYLMDLFLERERKKALTIICKSYRPTITVDFIASELAFDSMEDCVNFLNEQNLT 506 (540)
T ss_pred HHHHHHHHhccHHHHHHHHhhcccchhHHHHHHHHHHHHHHHHHHHHHcCCCccHHHHhhhhhhchHHHHHHHHhccCcc
Confidence 99999999999999999997644432 35678999999999999999999 99999999999644448899999999999
Q ss_pred EeCCc-eEEeCCC
Q psy5242 180 ELDNG-YIFIANQ 191 (217)
Q Consensus 180 ~~~~g-~v~p~n~ 191 (217)
-+..| .+.+.|.
T Consensus 507 ~~~~g~~~~~~~~ 519 (540)
T KOG1861|consen 507 YDSLGPQILDKNA 519 (540)
T ss_pred ccccCCccccccc
Confidence 87655 5555554
No 8
>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=95.61 E-value=0.029 Score=40.57 Aligned_cols=60 Identities=22% Similarity=0.217 Sum_probs=48.0
Q ss_pred ccchHHHHHHHHHHHHHHhcccccHHHHHHhhcCCCHHHHHHHHHH---cC---ceEeC-CceEEeCC
Q psy5242 130 IEGFNDSIRKFVCHVVGITFQTIDKKLLSELLDGVEDSTLRLWVKK---YG---WKELD-NGYIFIAN 190 (217)
Q Consensus 130 i~gFed~IR~~I~~vVs~tyqsIs~~~La~~LG~ls~~el~~~v~~---~G---Wt~~~-~g~v~p~n 190 (217)
++.+...+|...+.-++.+|++|+.+.+++.+| ++.++++.++.+ .| .++|. +|.+....
T Consensus 3 ~~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~-l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~ 69 (88)
T smart00088 3 VERLQRKIRLTNLLQLSEPYSSISLSDLAKLLG-LSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEE 69 (88)
T ss_pred HHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhC-cCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECC
Confidence 456788899999999999999999999999997 899999999885 33 66764 45554433
No 9
>smart00753 PAM PCI/PINT associated module.
Probab=95.61 E-value=0.029 Score=40.57 Aligned_cols=60 Identities=22% Similarity=0.217 Sum_probs=48.0
Q ss_pred ccchHHHHHHHHHHHHHHhcccccHHHHHHhhcCCCHHHHHHHHHH---cC---ceEeC-CceEEeCC
Q psy5242 130 IEGFNDSIRKFVCHVVGITFQTIDKKLLSELLDGVEDSTLRLWVKK---YG---WKELD-NGYIFIAN 190 (217)
Q Consensus 130 i~gFed~IR~~I~~vVs~tyqsIs~~~La~~LG~ls~~el~~~v~~---~G---Wt~~~-~g~v~p~n 190 (217)
++.+...+|...+.-++.+|++|+.+.+++.+| ++.++++.++.+ .| .++|. +|.+....
T Consensus 3 ~~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~-l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~ 69 (88)
T smart00753 3 VERLQRKIRLTNLLQLSEPYSSISLSDLAKLLG-LSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEE 69 (88)
T ss_pred HHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhC-cCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECC
Confidence 456788899999999999999999999999997 899999999885 33 66764 45554433
No 10
>KOG0687|consensus
Probab=92.83 E-value=0.93 Score=41.82 Aligned_cols=95 Identities=13% Similarity=0.222 Sum_probs=68.2
Q ss_pred HHHHHHHHHHHhCChHHHHHHhhcC-------Cchh-hhccchHHHHHHHHHHHHHHhcccccHHHHHHhhcCCCH----
Q psy5242 99 DQIIYLADLLESCKFTQFWSRMHTI-------PDLF-LNIEGFNDSIRKFVCHVVGITFQTIDKKLLSELLDGVED---- 166 (217)
Q Consensus 99 ~~l~~L~~lLe~c~F~~FW~~l~~~-------~~l~-~~i~gFed~IR~~I~~vVs~tyqsIs~~~La~~LG~ls~---- 166 (217)
+.+..+..-|-.|+|..|+..+... ..+. +..-=|..-+|.++-.=+--+|++.+++.+|+-.| +|-
T Consensus 257 ~~~~q~l~SLY~C~Y~~Ff~~L~~~~~~~lk~D~~l~~h~~yyvREMR~rvY~QlLESYrsl~l~~MA~aFg-VSVefiD 335 (393)
T KOG0687|consen 257 PSVSQLLNSLYECDYSDFFNDLAAVEAKQLKDDRYLGPHYRYYVREMRRRVYAQLLESYRSLTLESMAKAFG-VSVEFID 335 (393)
T ss_pred chHHHHHHHHHhccHHHHHHHHHHHHHHhhccchhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC-chHHHHH
Confidence 3455667778899999999998431 1222 22233446688888888888999999999999998 885
Q ss_pred HHHHHHHHH-cCce-EeC-CceEEeCCCCcc
Q psy5242 167 STLRLWVKK-YGWK-ELD-NGYIFIANQDEN 194 (217)
Q Consensus 167 ~el~~~v~~-~GWt-~~~-~g~v~p~n~en~ 194 (217)
.+|..||.. +=|. +|. +|+|....||+.
T Consensus 336 reL~rFI~~grL~ckIDrVnGVVEtNrpD~K 366 (393)
T KOG0687|consen 336 RELGRFIAAGRLHCKIDRVNGVVETNRPDEK 366 (393)
T ss_pred hHHHHhhccCceeeeeecccceeecCCcccc
Confidence 467788775 4464 442 678888888773
No 11
>COG5187 RPN7 26S proteasome regulatory complex component, contains PCI domain [Posttranslational modification, protein turnover, chaperones]
Probab=91.20 E-value=0.99 Score=41.24 Aligned_cols=98 Identities=15% Similarity=0.236 Sum_probs=73.1
Q ss_pred CccHHHHHHHHHHHHhCChHHHHHHhhcC------Cc-h-hhhccchHHHHHHHHHHHHHHhcccccHHHHHHhhcCCCH
Q psy5242 95 EDPIDQIIYLADLLESCKFTQFWSRMHTI------PD-L-FLNIEGFNDSIRKFVCHVVGITFQTIDKKLLSELLDGVED 166 (217)
Q Consensus 95 ~~~i~~l~~L~~lLe~c~F~~FW~~l~~~------~~-l-~~~i~gFed~IR~~I~~vVs~tyqsIs~~~La~~LG~ls~ 166 (217)
.+.++.|..|..-|..|+|.+|+-.+-.. ++ + -..+.=|..-+|+++-.-+--+|+..+++.+|+-.| +|-
T Consensus 267 ~e~l~sl~~l~~SLy~cdY~~~F~~ll~~~~n~L~~d~fl~rh~d~fvREMRrrvYaQlLESYr~lsl~sMA~tFg-VSV 345 (412)
T COG5187 267 SEKLGSLVQLATSLYECDYGGDFMNLLYLFCNSLQDDVFLGRHVDLFVREMRRRVYAQLLESYRLLSLESMAQTFG-VSV 345 (412)
T ss_pred hhhhhhHHHHHHHHHHhccchhhHHHHHHHHhhccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhC-ccH
Confidence 34568888999999999999887766431 22 2 233444566788888888889999999999999998 776
Q ss_pred H----HHHHHHHH-cCceEeC--CceEEeCCCCc
Q psy5242 167 S----TLRLWVKK-YGWKELD--NGYIFIANQDE 193 (217)
Q Consensus 167 ~----el~~~v~~-~GWt~~~--~g~v~p~n~en 193 (217)
+ +|.+|+-+ +=|.+-+ +|+|....|||
T Consensus 346 ~yvdrDLg~FIp~~~LncvIDRvnGvVetnrpde 379 (412)
T COG5187 346 EYVDRDLGEFIPEGRLNCVIDRVNGVVETNRPDE 379 (412)
T ss_pred HHHhhhHHhhCCCCceeeeeecccceEeccCcch
Confidence 4 56777764 4576633 68999888887
No 12
>KOG2581|consensus
Probab=88.67 E-value=1 Score=42.61 Aligned_cols=168 Identities=14% Similarity=0.224 Sum_probs=107.8
Q ss_pred HHHHHHHHhcccc-CCCCCchhHHHHHHHHH-HhccccchHhhHHH------------HHhhhcCCC------CChHHHH
Q psy5242 7 MKGSVDQLLVGIE-RYNPEHLSTLEKYVEVQ-CAENVYDLEANLAV------------LKLYQFHQN------YNMKITS 66 (217)
Q Consensus 7 ~~~~i~~~l~g~~-rYnp~~l~~Le~yv~~Q-~~~~~Yd~~aNlal------------LKLYqfnP~------~~~~vv~ 66 (217)
.+..++.++.... |=|-+...+|-.++-.- +.++.||--.+|-. .-=|-||-. .+-+-..
T Consensus 188 ~rs~l~~~lrtAtLrhd~e~qavLiN~LLr~yL~n~lydqa~~lvsK~~~pe~~snne~ARY~yY~GrIkaiqldYssA~ 267 (493)
T KOG2581|consen 188 IRSFLHALLRTATLRHDEEGQAVLINLLLRNYLHNKLYDQADKLVSKSVYPEAASNNEWARYLYYLGRIKAIQLDYSSAL 267 (493)
T ss_pred HHHHHHHHHHHhhhcCcchhHHHHHHHHHHHHhhhHHHHHHHHHhhcccCccccccHHHHHHHHHHhhHHHhhcchhHHH
Confidence 3445555555555 55677777777665544 44456666665532 222333332 1334556
Q ss_pred HHHHHHhhcCCC----------cchhhhhhcc----CCCCC-CCc----cHHHHHHHHHHHHhCChHHHHHHhhcC----
Q psy5242 67 QILLKALTNFPH----------TDFILCKCLL----SKDLC-KED----PIDQIIYLADLLESCKFTQFWSRMHTI---- 123 (217)
Q Consensus 67 ~ILlkaL~~~P~----------~DF~lc~~LI----p~~~~-~~~----~i~~l~~L~~lLe~c~F~~FW~~l~~~---- 123 (217)
+-++.|+--.|+ .-..+|..|+ |++.. ..| .+.--+.|.+.....+-+.|=+.+.++
T Consensus 268 ~~~~qa~rkapq~~alGf~q~v~k~~ivv~ll~geiPers~F~Qp~~~ksL~~Yf~Lt~AVr~gdlkkF~~~leq~k~~f 347 (493)
T KOG2581|consen 268 EYFLQALRKAPQHAALGFRQQVNKLMIVVELLLGEIPERSVFRQPGMRKSLRPYFKLTQAVRLGDLKKFNETLEQFKDKF 347 (493)
T ss_pred HHHHHHHHhCcchhhhhHHHHHHHHHHHHHHHcCCCcchhhhcCccHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHH
Confidence 677888888885 1123344443 33322 233 566667899999999999999999875
Q ss_pred --CchhhhccchHHHHHHHHHHHHHHhcccccHHHHHHhhcCCCH-HHHHHHHHH
Q psy5242 124 --PDLFLNIEGFNDSIRKFVCHVVGITFQTIDKKLLSELLDGVED-STLRLWVKK 175 (217)
Q Consensus 124 --~~l~~~i~gFed~IR~~I~~vVs~tyqsIs~~~La~~LG~ls~-~el~~~v~~ 175 (217)
.+...-+..+.-.|=+--.+-||.+|++||..+.+.-|| ++. ++++-.|++
T Consensus 348 ~~D~ty~LivRLR~NVIkTgIR~ISlsYSRISl~DIA~kL~-l~Seed~EyiVak 401 (493)
T KOG2581|consen 348 QADGTYTLIVRLRHNVIKTGIRKISLSYSRISLQDIAKKLG-LNSEEDAEYIVAK 401 (493)
T ss_pred hhCCcchHHHHHHHHHHHHhhhheeeeeeeccHHHHHHHhc-CCCchhHHHHHHH
Confidence 344455666666666777888999999999999999998 555 557666664
No 13
>KOG2758|consensus
Probab=86.06 E-value=1.4 Score=40.69 Aligned_cols=48 Identities=15% Similarity=0.309 Sum_probs=44.2
Q ss_pred hhhccchHHHHHHHHHHHHHHhcccccHHHHHHhhcCCCHHHHHHHHHH
Q psy5242 127 FLNIEGFNDSIRKFVCHVVGITFQTIDKKLLSELLDGVEDSTLRLWVKK 175 (217)
Q Consensus 127 ~~~i~gFed~IR~~I~~vVs~tyqsIs~~~La~~LG~ls~~el~~~v~~ 175 (217)
.+-...|.+.-|.+|+..-..-.|.|+.+.||.=| +|++++++.|+..
T Consensus 325 va~l~~F~E~ARl~ifEtfCRIHqcIti~mLA~kL-nm~~eeaErwivn 372 (432)
T KOG2758|consen 325 VALLDEFLENARLLIFETFCRIHQCITIDMLADKL-NMDPEEAERWIVN 372 (432)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHheeHHHHHHHh-cCCHHHHHHHHHH
Confidence 46677899999999999999999999999999999 5999999999875
No 14
>PF07037 DUF1323: Putative transcription regulator (DUF1323); InterPro: IPR010749 This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. The function of this family is unknown.
Probab=84.72 E-value=1.2 Score=35.17 Aligned_cols=28 Identities=36% Similarity=0.639 Sum_probs=25.0
Q ss_pred cHHHHHHhhcCCCHHHHHHHHHHcCceEe
Q psy5242 153 DKKLLSELLDGVEDSTLRLWVKKYGWKEL 181 (217)
Q Consensus 153 s~~~La~~LG~ls~~el~~~v~~~GWt~~ 181 (217)
..+.||+++| ++...+.+|+.+.||+-+
T Consensus 2 T~eELA~~tG-~srQTINrWvRkegW~T~ 29 (122)
T PF07037_consen 2 TPEELAELTG-YSRQTINRWVRKEGWKTE 29 (122)
T ss_pred CHHHHHHHhC-ccHHHHHHHHHhcCceec
Confidence 4578999998 899999999999999874
No 15
>KOG2072|consensus
Probab=82.67 E-value=6.2 Score=40.40 Aligned_cols=53 Identities=19% Similarity=0.123 Sum_probs=47.0
Q ss_pred CCchhhhccchHHHHHHHHHHHHHHhcccccHHHHHHhhcCCCHHHHHHHHHH
Q psy5242 123 IPDLFLNIEGFNDSIRKFVCHVVGITFQTIDKKLLSELLDGVEDSTLRLWVKK 175 (217)
Q Consensus 123 ~~~l~~~i~gFed~IR~~I~~vVs~tyqsIs~~~La~~LG~ls~~el~~~v~~ 175 (217)
.++..+.|+.+.+-+=.+.++-||+-|++|+.+.|..+--..+.-++++++.+
T Consensus 419 ~~~~~QYI~sLq~v~~~RllqQvSqiY~sIs~~~l~~La~F~~~~~lEk~~v~ 471 (988)
T KOG2072|consen 419 SPDKSQYIPSLQDVIILRLLQQVSQIYESISFERLYKLAPFFSAFELEKLLVE 471 (988)
T ss_pred CCCccccchhHHHHHHHHHHHHHHHHHHHHhHHHHHHHHhhcCHHHHHHHHHH
Confidence 46778899999999999999999999999999999888777788899998764
No 16
>PF05687 DUF822: Plant protein of unknown function (DUF822); InterPro: IPR008540 This group of proteins contains members of the BZR1/LAT61 family of plant transcriptional repressors involved in controlling the response to Brassinosteroids (BRs). BRs are plant hormones that play essential roles in growth and development. BZR1 binds directly to DNA repressing the synthesis of genes involved in BR synthesis. Phosphorylation of BZR1 by BIN1 targets BZR1 to the 20S proteosome, while dephosphorylation leads to nuclear accumulation of BZR1 [].
Probab=81.39 E-value=1.4 Score=35.82 Aligned_cols=22 Identities=18% Similarity=0.474 Sum_probs=18.8
Q ss_pred HHHHHHHHHcCceEeCCceEEe
Q psy5242 167 STLRLWVKKYGWKELDNGYIFI 188 (217)
Q Consensus 167 ~el~~~v~~~GWt~~~~g~v~p 188 (217)
+-|+++|.+.||+|++||..+.
T Consensus 49 eVLkALc~eAGw~Ve~DGTtyr 70 (150)
T PF05687_consen 49 EVLKALCREAGWTVEPDGTTYR 70 (150)
T ss_pred HHHHHHHHhCCEEEccCCCeec
Confidence 5588889999999999997775
No 17
>PF10537 WAC_Acf1_DNA_bd: ATP-utilising chromatin assembly and remodelling N-terminal; InterPro: IPR013136 ACF (for ATP-utilising chromatin assembly and remodeling factor) is a chromatin-remodeling complex that catalyzes the ATP-dependent assembly of periodic nucleosome arrays. This reaction utilises the energy of ATP hydrolysis by ISWI, the smaller of the two subunits of ACF. Acf1, the large subunit of ACF, is essential for the full activity of the complex. The WAC (WSTF/Acf1/cbp146) domain is an ~110-residue module present at the N-termini of Acf1-related proteins in a variety of organisms. It is found in association with other domains such as the bromodomain, the PHD-type zinc finger, DDT or WAKS. The DNA-binding region of Acf1 includes the WAC domain, which is necessary for the efficient binding of ACF complex to DNA. It seems probable that the WAC domain will be involved in DNA binding in other related factors [, ]. Some proteins known to contain a WAC domain are the Drosophila melanogaster (Fruit fly) ATP-dependent chromatin assembly factor large subunit Acf1, human WSTF (Williams syndrome transcription factor), mouse cbp146, yeast imitation switch two complex protein 1 (ITC1 or YGL133w), and yeast protein YPL216w.
Probab=78.79 E-value=1.3 Score=33.95 Aligned_cols=60 Identities=17% Similarity=0.327 Sum_probs=49.4
Q ss_pred cHHHHHHHHHHHHhCChHH-----HHHHhhcCCchhhhccc-hHHHHHHHHHHHHHHhccccc-HHHHH
Q psy5242 97 PIDQIIYLADLLESCKFTQ-----FWSRMHTIPDLFLNIEG-FNDSIRKFVCHVVGITFQTID-KKLLS 158 (217)
Q Consensus 97 ~i~~l~~L~~lLe~c~F~~-----FW~~l~~~~~l~~~i~g-Fed~IR~~I~~vVs~tyqsIs-~~~La 158 (217)
=+.++....+..|+|...+ |.++++|...-...+.. |-+..|+-|++.|. |++++ .+.|.
T Consensus 19 Y~~R~~~y~~~vwtC~~TGk~~LTy~eAl~SE~~a~~~l~~~fP~~l~~piL~~v~--~s~~~rld~Lv 85 (102)
T PF10537_consen 19 YLKRMILYNQRVWTCEITGKSNLTYFEALESEKEARKKLEERFPEELREPILRLVQ--FSTRSRLDDLV 85 (102)
T ss_pred HHHHHHHHhCCeeEEecCCCCCCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHH--ccccccHHHHH
Confidence 3688888999999999987 89999887766777888 99999999999998 66666 44443
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=69.82 E-value=43 Score=31.69 Aligned_cols=92 Identities=17% Similarity=0.260 Sum_probs=58.3
Q ss_pred chhhhhhccCCCCCCCccHHHHH--HHH---HHHHhCChHHHHHHhhc-CCchhhhc---------------------cc
Q psy5242 80 DFILCKCLLSKDLCKEDPIDQII--YLA---DLLESCKFTQFWSRMHT-IPDLFLNI---------------------EG 132 (217)
Q Consensus 80 DF~lc~~LIp~~~~~~~~i~~l~--~L~---~lLe~c~F~~FW~~l~~-~~~l~~~i---------------------~g 132 (217)
.+..|.+|-|.++ ++.|.... +-| ..|...+-..||+.... +|.+++.+ .-
T Consensus 221 LlAic~~l~p~~l--de~i~~~lkeky~ek~~kmq~gd~~~f~elF~~acPKFIsp~~pp~~~~~~~~~~~e~~~~Ql~~ 298 (404)
T PF10255_consen 221 LLAICLSLCPQRL--DESISSQLKEKYGEKMEKMQRGDEEAFEELFSFACPKFISPVSPPDYDGPSQNKNKEPYRRQLKL 298 (404)
T ss_pred HHHHHHHhCCCCC--CHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHhhCCCccCCCCCCCcccccchhhhhHHHHHHHH
Confidence 4677888888874 34442222 111 22666788889988864 35554433 12
Q ss_pred hHHHHHH----HHHHHHHHhcccccHHHHHHhhcCCCHHHHHHHHH
Q psy5242 133 FNDSIRK----FVCHVVGITFQTIDKKLLSELLDGVEDSTLRLWVK 174 (217)
Q Consensus 133 Fed~IR~----~I~~vVs~tyqsIs~~~La~~LG~ls~~el~~~v~ 174 (217)
|.+.|+. ...+..-.=|++|+++.||++|+ ++++++...+.
T Consensus 299 Fl~eV~~q~~l~~lRSyLKLYtti~l~KLA~fl~-vd~~~lr~~Ll 343 (404)
T PF10255_consen 299 FLDEVKQQQKLPTLRSYLKLYTTIPLEKLASFLD-VDEEELRSQLL 343 (404)
T ss_pred HHHHHHHhhhhhHHHHHHHhhcCCCHHHHHHHcC-CCHHHHHHHHH
Confidence 3333332 23444556799999999999996 89998887765
No 19
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=67.26 E-value=11 Score=25.92 Aligned_cols=31 Identities=16% Similarity=0.365 Sum_probs=26.5
Q ss_pred cccHHHHHHhhc-CCCHHHHHHHHHHcCceEe
Q psy5242 151 TIDKKLLSELLD-GVEDSTLRLWVKKYGWKEL 181 (217)
Q Consensus 151 sIs~~~La~~LG-~ls~~el~~~v~~~GWt~~ 181 (217)
+++.+.+.++|| .++.+++.+.+++.|.+++
T Consensus 5 ~~~~~~i~~llG~~i~~~ei~~~L~~lg~~~~ 36 (71)
T smart00874 5 TLRRERINRLLGLDLSAEEIEEILKRLGFEVE 36 (71)
T ss_pred EecHHHHHHHHCCCCCHHHHHHHHHHCCCeEE
Confidence 467888999998 5677899999999999885
No 20
>KOG1464|consensus
Probab=64.71 E-value=31 Score=31.60 Aligned_cols=83 Identities=14% Similarity=0.131 Sum_probs=69.0
Q ss_pred CCCccHHHHHHHHHHHHhCChHHHHHHhhcCC-------chhhhccchHHHHHHHHHHHHHHhcccccHHHHHHhhcCCC
Q psy5242 93 CKEDPIDQIIYLADLLESCKFTQFWSRMHTIP-------DLFLNIEGFNDSIRKFVCHVVGITFQTIDKKLLSELLDGVE 165 (217)
Q Consensus 93 ~~~~~i~~l~~L~~lLe~c~F~~FW~~l~~~~-------~l~~~i~gFed~IR~~I~~vVs~tyqsIs~~~La~~LG~ls 165 (217)
+.+|+|-....|-+.-+..+-.+|=.-+++++ =+-..+..+...||.-++--+-.-|..|.++-++.-|+ ++
T Consensus 299 KNdPEIlAMTnlv~aYQ~NdI~eFE~Il~~~~~~IM~DpFIReh~EdLl~niRTQVLlkLIkPYt~i~Ipfis~~Ln-v~ 377 (440)
T KOG1464|consen 299 KNDPEILAMTNLVAAYQNNDIIEFERILKSNRSNIMDDPFIREHIEDLLRNIRTQVLLKLIKPYTNIGIPFISKELN-VP 377 (440)
T ss_pred CCCHHHHHHHHHHHHHhcccHHHHHHHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHhccccccCchhhHhhcC-CC
Confidence 37889999999999999999999998888752 23456667777788887777788999999999999994 99
Q ss_pred HHHHHHHHHHc
Q psy5242 166 DSTLRLWVKKY 176 (217)
Q Consensus 166 ~~el~~~v~~~ 176 (217)
+.++++.+..+
T Consensus 378 ~~dV~~LLV~~ 388 (440)
T KOG1464|consen 378 EADVESLLVSC 388 (440)
T ss_pred HHHHHHHHHHH
Confidence 99999988764
No 21
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=63.77 E-value=6.7 Score=34.89 Aligned_cols=29 Identities=28% Similarity=0.624 Sum_probs=26.1
Q ss_pred cccHHHHHHhhcCCCHHHHHHHHHHcCceE
Q psy5242 151 TIDKKLLSELLDGVEDSTLRLWVKKYGWKE 180 (217)
Q Consensus 151 sIs~~~La~~LG~ls~~el~~~v~~~GWt~ 180 (217)
.....++++.|| .++..+.+|....||+.
T Consensus 19 gmk~~dIAeklG-vspntiksWKrr~gWs~ 47 (279)
T COG5484 19 GMKLKDIAEKLG-VSPNTIKSWKRRDGWSA 47 (279)
T ss_pred hccHHHHHHHhC-CChHHHHHHHHhcCCCc
Confidence 377889999998 99999999999999974
No 22
>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A.
Probab=59.82 E-value=10 Score=23.91 Aligned_cols=27 Identities=4% Similarity=0.174 Sum_probs=20.8
Q ss_pred HHHHHHhhcCCCHHHHHHHHHHcCceEe
Q psy5242 154 KKLLSELLDGVEDSTLRLWVKKYGWKEL 181 (217)
Q Consensus 154 ~~~La~~LG~ls~~el~~~v~~~GWt~~ 181 (217)
+..+.+..| .+++....+++.++|-++
T Consensus 4 i~~F~~iTg-~~~~~A~~~L~~~~wdle 30 (43)
T PF14555_consen 4 IAQFMSITG-ADEDVAIQYLEANNWDLE 30 (43)
T ss_dssp HHHHHHHH--SSHHHHHHHHHHTTT-HH
T ss_pred HHHHHHHHC-cCHHHHHHHHHHcCCCHH
Confidence 356777887 799999999999999875
No 23
>PF08727 P3A: Poliovirus 3A protein like; InterPro: IPR014838 The 3A protein is found in positive-strand RNA viruses. It is a critical component of the poliovirus replication complex, and is also an inhibitor of host cell ER to Golgi transport. ; GO: 0003968 RNA-directed RNA polymerase activity, 0004197 cysteine-type endopeptidase activity, 0017111 nucleoside-triphosphatase activity; PDB: 1NG7_A.
Probab=58.01 E-value=4.2 Score=27.98 Aligned_cols=24 Identities=25% Similarity=0.570 Sum_probs=14.9
Q ss_pred HHhhcCCCHHHHHHHHHHcCceEe
Q psy5242 158 SELLDGVEDSTLRLWVKKYGWKEL 181 (217)
Q Consensus 158 a~~LG~ls~~el~~~v~~~GWt~~ 181 (217)
+.+|--++.+++.+||+++||-+.
T Consensus 21 ~DLL~SV~~~eV~~YC~~~GWIip 44 (57)
T PF08727_consen 21 ADLLRSVDSPEVREYCEEQGWIIP 44 (57)
T ss_dssp HHHHHHH--HHHHHHHHHHT--TT
T ss_pred HHHHHhcCCHHHHHHHHHCCcccc
Confidence 444533466889999999999874
No 24
>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=56.19 E-value=46 Score=20.88 Aligned_cols=42 Identities=26% Similarity=0.333 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHHHhcccccHHHHHHhhcCCCHHHHHHHHHH---cCc
Q psy5242 135 DSIRKFVCHVVGITFQTIDKKLLSELLDGVEDSTLRLWVKK---YGW 178 (217)
Q Consensus 135 d~IR~~I~~vVs~tyqsIs~~~La~~LG~ls~~el~~~v~~---~GW 178 (217)
|..+..|...+.. -..++...+++-+| ++...+...+++ .||
T Consensus 2 ~~~~~~Il~~l~~-~~~~t~~ela~~~~-is~~tv~~~l~~L~~~g~ 46 (48)
T PF13412_consen 2 DETQRKILNYLRE-NPRITQKELAEKLG-ISRSTVNRYLKKLEEKGL 46 (48)
T ss_dssp -HHHHHHHHHHHH-CTTS-HHHHHHHHT-S-HHHHHHHHHHHHHTTS
T ss_pred CHHHHHHHHHHHH-cCCCCHHHHHHHhC-CCHHHHHHHHHHHHHCcC
Confidence 4567788887777 45599999999997 999988888774 566
No 25
>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=56.03 E-value=24 Score=24.09 Aligned_cols=40 Identities=23% Similarity=0.384 Sum_probs=29.0
Q ss_pred cccHHHHHHhhcCCCHHHHHHHHH---HcCceEeCCceEEeCCC
Q psy5242 151 TIDKKLLSELLDGVEDSTLRLWVK---KYGWKELDNGYIFIANQ 191 (217)
Q Consensus 151 sIs~~~La~~LG~ls~~el~~~v~---~~GWt~~~~g~v~p~n~ 191 (217)
.++.+.+|+++| ++...+...++ +.||-.-..+.+.+.++
T Consensus 28 ~lt~~~iA~~~g-~sr~tv~r~l~~l~~~g~I~~~~~~i~I~d~ 70 (76)
T PF13545_consen 28 PLTQEEIADMLG-VSRETVSRILKRLKDEGIIEVKRGKIIILDP 70 (76)
T ss_dssp ESSHHHHHHHHT-SCHHHHHHHHHHHHHTTSEEEETTEEEESSH
T ss_pred cCCHHHHHHHHC-CCHHHHHHHHHHHHHCCCEEEcCCEEEECCH
Confidence 468999999998 89987777666 58996544555555554
No 26
>PF09494 Slx4: Slx4 endonuclease; InterPro: IPR018574 The Slx4 protein is a heteromeric structure-specific endonuclease found in fungi. Slx4 with Slx1 acts as a nuclease on branched DNA substrates, particularly simple-Y, 5'-flap, or replication fork structures by cleaving the strand bearing the 5' non-homologous arm at the branch junction and thus generating ligatable nicked products from 5'-flap or replication fork substrates [].
Probab=55.50 E-value=14 Score=25.46 Aligned_cols=33 Identities=24% Similarity=0.501 Sum_probs=27.1
Q ss_pred HhcccccHHHHHHhhc--------CCCHHHHHHHHHHcCce
Q psy5242 147 ITFQTIDKKLLSELLD--------GVEDSTLRLWVKKYGWK 179 (217)
Q Consensus 147 ~tyqsIs~~~La~~LG--------~ls~~el~~~v~~~GWt 179 (217)
.+|+-|..+.|.++|. ..+...+.+|+.++|=+
T Consensus 20 L~YePI~L~el~~~L~~~g~~~~~~~~~~~l~~~lD~~gIt 60 (64)
T PF09494_consen 20 LMYEPINLEELHAWLKASGIGFDRKVDPSKLKEWLDSQGIT 60 (64)
T ss_pred HcCCCccHHHHHHHHHHcCCCccceeCHHHHHHHHHHCCce
Confidence 4799999999999994 34678899999988844
No 27
>KOG1498|consensus
Probab=53.58 E-value=18 Score=34.17 Aligned_cols=81 Identities=14% Similarity=0.155 Sum_probs=51.9
Q ss_pred CCccHHHHHHHHHHHHhCChHHHHHHhhcC---Cch---hh----hccchHHHHHHHHHHHHHHhcccccHHHHHHhhcC
Q psy5242 94 KEDPIDQIIYLADLLESCKFTQFWSRMHTI---PDL---FL----NIEGFNDSIRKFVCHVVGITFQTIDKKLLSELLDG 163 (217)
Q Consensus 94 ~~~~i~~l~~L~~lLe~c~F~~FW~~l~~~---~~l---~~----~i~gFed~IR~~I~~vVs~tyqsIs~~~La~~LG~ 163 (217)
+.|.-..+..|=--.|--+|+.+|+..... .++ .. ....+...|=+-=.++++.-|++|+..+++++||
T Consensus 286 e~p~~k~lLklfv~~EL~rw~s~~~~yg~~l~~~~~~~~~~~gek~~~dL~~RIiEHNiRiiA~yYSrIt~~rl~eLLd- 364 (439)
T KOG1498|consen 286 ELPDYKELLKLFVTMELIRWVSLVESYGDELRTNDFFDGGEEGEKRWSDLKLRIIEHNIRIIAKYYSRITLKRLAELLD- 364 (439)
T ss_pred cCccHHHHHHHHHhcceeeehhHhhhhHHHHhhcccccccchhhhHHHHHHHHHHHHHHHHHHHHHhhccHHHHHHHhC-
Confidence 334455555555555566777777665331 111 11 1122222333334689999999999999999996
Q ss_pred CCHHHHHHHHHH
Q psy5242 164 VEDSTLRLWVKK 175 (217)
Q Consensus 164 ls~~el~~~v~~ 175 (217)
++.++.++++..
T Consensus 365 l~~ee~E~~LS~ 376 (439)
T KOG1498|consen 365 LPVEEMEKFLSD 376 (439)
T ss_pred CCHHHHHHHHHH
Confidence 899999999884
No 28
>PF03484 B5: tRNA synthetase B5 domain; InterPro: IPR005147 Domain B5 is found in phenylalanine-tRNA synthetase beta subunits. This domain has been shown to bind DNA through a winged helix-turn-helix motif []. Phenylalanine-tRNA synthetase may influence common cellular processes via DNA binding, in addition to its aminoacylation function.; GO: 0000287 magnesium ion binding, 0003723 RNA binding, 0005524 ATP binding, 0006432 phenylalanyl-tRNA aminoacylation; PDB: 2AKW_B 1B70_B 1B7Y_B 2ALY_B 2IY5_B 2AMC_B 3PCO_D 2CXI_C 1JJC_B 1EIY_B ....
Probab=52.30 E-value=22 Score=24.71 Aligned_cols=32 Identities=19% Similarity=0.280 Sum_probs=24.1
Q ss_pred cccHHHHHHhhcC-CCHHHHHHHHHHcCceEeC
Q psy5242 151 TIDKKLLSELLDG-VEDSTLRLWVKKYGWKELD 182 (217)
Q Consensus 151 sIs~~~La~~LG~-ls~~el~~~v~~~GWt~~~ 182 (217)
+++.+.+.++||. ++.+++.+.++..|-+++.
T Consensus 5 ~~~~~~i~~~lG~~i~~~~i~~~L~~lg~~~~~ 37 (70)
T PF03484_consen 5 TLSLDKINKLLGIDISPEEIIKILKRLGFKVEK 37 (70)
T ss_dssp EEEHHHHHHHHTS---HHHHHHHHHHTT-EEEE
T ss_pred EecHHHHHHHhCCCCCHHHHHHHHHHCCCEEEE
Confidence 4677889999983 4678999999999988864
No 29
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=51.39 E-value=21 Score=24.28 Aligned_cols=31 Identities=35% Similarity=0.595 Sum_probs=26.9
Q ss_pred cccccHHHHHHhhcCCCHHHHHHHHHHcCceE
Q psy5242 149 FQTIDKKLLSELLDGVEDSTLRLWVKKYGWKE 180 (217)
Q Consensus 149 yqsIs~~~La~~LG~ls~~el~~~v~~~GWt~ 180 (217)
.+--+....++.|| ++...+..|+...||.-
T Consensus 11 ~~G~~~~eIA~~Lg-~~~~TV~~W~~r~~W~~ 41 (58)
T PF06056_consen 11 LQGWSIKEIAEELG-VPRSTVYSWKDRYKWDE 41 (58)
T ss_pred HcCCCHHHHHHHHC-CChHHHHHHHHhhCccc
Confidence 35667888999997 89999999999999964
No 30
>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=51.08 E-value=26 Score=22.83 Aligned_cols=44 Identities=20% Similarity=0.175 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHHHhccccc-HHHHHHhhcCCCHHHHHHHHH---HcCce
Q psy5242 135 DSIRKFVCHVVGITFQTID-KKLLSELLDGVEDSTLRLWVK---KYGWK 179 (217)
Q Consensus 135 d~IR~~I~~vVs~tyqsIs-~~~La~~LG~ls~~el~~~v~---~~GWt 179 (217)
+.+++.+....-..-..++ ...|++.+| ++...+.+.++ +.||-
T Consensus 8 ~~i~~~i~~~~~~~~~~~~~~~~la~~~~-is~~~v~~~l~~L~~~G~i 55 (66)
T cd07377 8 DQLREAILSGELKPGDRLPSERELAEELG-VSRTTVREALRELEAEGLV 55 (66)
T ss_pred HHHHHHHHcCCCCCCCCCCCHHHHHHHHC-CCHHHHHHHHHHHHHCCCE
Confidence 3444444433222333455 899999997 89988888877 47993
No 31
>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=50.89 E-value=36 Score=21.57 Aligned_cols=41 Identities=22% Similarity=0.256 Sum_probs=32.9
Q ss_pred HHHHHHHHHHHHHhcccccHHHHHHhhcCCCHHHHHHHHH---HcCc
Q psy5242 135 DSIRKFVCHVVGITFQTIDKKLLSELLDGVEDSTLRLWVK---KYGW 178 (217)
Q Consensus 135 d~IR~~I~~vVs~tyqsIs~~~La~~LG~ls~~el~~~v~---~~GW 178 (217)
|..|..|+..+.. ...+...+++-+| ++...+-..++ +.|+
T Consensus 1 d~~R~~Il~~L~~--~~~~~~el~~~l~-~s~~~vs~hL~~L~~~gl 44 (47)
T PF01022_consen 1 DPTRLRILKLLSE--GPLTVSELAEELG-LSQSTVSHHLKKLREAGL 44 (47)
T ss_dssp SHHHHHHHHHHTT--SSEEHHHHHHHHT-S-HHHHHHHHHHHHHTTS
T ss_pred CHHHHHHHHHHHh--CCCchhhHHHhcc-ccchHHHHHHHHHHHCcC
Confidence 3578889888888 8888999999997 99998888876 3565
No 32
>COG1724 Predicted RNA binding protein (dsRBD-like fold), HicA family [General function prediction only]
Probab=50.67 E-value=16 Score=25.85 Aligned_cols=21 Identities=14% Similarity=0.178 Sum_probs=17.7
Q ss_pred HhhcCCCHHHHHHHHHHcCceE
Q psy5242 159 ELLDGVEDSTLRLWVKKYGWKE 180 (217)
Q Consensus 159 ~~LG~ls~~el~~~v~~~GWt~ 180 (217)
.++. |+..++.+.+++.||..
T Consensus 3 ~lp~-~~~ke~ik~Le~~Gf~~ 23 (66)
T COG1724 3 KLPR-MKAKEVIKALEKDGFQL 23 (66)
T ss_pred cCCc-CCHHHHHHHHHhCCcEE
Confidence 3454 88999999999999987
No 33
>COG5071 RPN5 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=49.96 E-value=32 Score=31.82 Aligned_cols=44 Identities=25% Similarity=0.319 Sum_probs=36.2
Q ss_pred HHHHHHH----HHHHHHhcccccHHHHHHhhcCCCHHHHHHHHHH---cCce
Q psy5242 135 DSIRKFV----CHVVGITFQTIDKKLLSELLDGVEDSTLRLWVKK---YGWK 179 (217)
Q Consensus 135 d~IR~~I----~~vVs~tyqsIs~~~La~~LG~ls~~el~~~v~~---~GWt 179 (217)
+..|++| +++|+.-|++|+..+|..+|+ +++++.++++.. +|.-
T Consensus 333 ~DL~krviEHN~RvI~~yYSrI~~~rl~~lld-~~~s~te~~ISdlVN~G~~ 383 (439)
T COG5071 333 SDLRKRVIEHNIRVIANYYSRIHCSRLGVLLD-MSPSETEQFISDLVNKGHF 383 (439)
T ss_pred HHHHHHHHHhhHhHHHHHhhhhhHHHHHHHHc-CCHHHHHHHHHHHHhcCcE
Confidence 3355555 689999999999999999995 999999999874 6763
No 34
>KOG1076|consensus
Probab=49.87 E-value=25 Score=35.61 Aligned_cols=75 Identities=7% Similarity=0.273 Sum_probs=52.5
Q ss_pred HHHHHHHHHHHhCChHHHHHHhhc----------CCchhhhccch--HHHHHHHHHHHHHHhcccccHHHHHHhhcCCCH
Q psy5242 99 DQIIYLADLLESCKFTQFWSRMHT----------IPDLFLNIEGF--NDSIRKFVCHVVGITFQTIDKKLLSELLDGVED 166 (217)
Q Consensus 99 ~~l~~L~~lLe~c~F~~FW~~l~~----------~~~l~~~i~gF--ed~IR~~I~~vVs~tyqsIs~~~La~~LG~ls~ 166 (217)
..+...+..|...+|..-.+.+.. ...+..-+..+ +++.|.|.+. -+..|.++|++.||.+.. ++.
T Consensus 655 ehVvaAsKAm~~Gnw~~c~~fi~nn~KvW~Lfpn~d~V~~Ml~~rIqEEsLRTYLft-Yss~Y~SvSl~~LA~mFd-Lp~ 732 (843)
T KOG1076|consen 655 EHVVAASKAMQKGNWQKCFEFIVNNIKVWDLFPNADTVLDMLTERIQEESLRTYLFT-YSSVYDSVSLAKLADMFD-LPE 732 (843)
T ss_pred HHHHHHHHHHhcCCHHHHHHHHHhhhhHHHhcccHHHHHHHHHHHHHHHHHHHHHHH-hhhhhhhccHHHHHHHhC-CCc
Confidence 456677888888888765553332 23344444444 5777777776 456699999999999994 999
Q ss_pred HHHHHHHHH
Q psy5242 167 STLRLWVKK 175 (217)
Q Consensus 167 ~el~~~v~~ 175 (217)
..+-..+.+
T Consensus 733 ~~VhsIiSk 741 (843)
T KOG1076|consen 733 PKVHSIISK 741 (843)
T ss_pred hhHHHHHHH
Confidence 888877764
No 35
>PF14821 Thr_synth_N: Threonine synthase N terminus; PDB: 3V7N_A 1VB3_A 1KL7_A.
Probab=49.58 E-value=17 Score=26.14 Aligned_cols=36 Identities=17% Similarity=0.368 Sum_probs=29.6
Q ss_pred HHHHHHHHhcccccHHHHHHhh-cCCCHHHHHHHHHH
Q psy5242 140 FVCHVVGITFQTIDKKLLSELL-DGVEDSTLRLWVKK 175 (217)
Q Consensus 140 ~I~~vVs~tyqsIs~~~La~~L-G~ls~~el~~~v~~ 175 (217)
.+-.+...+|+.|....|+.|+ +.+++++|++.|.+
T Consensus 41 ~l~~l~~~sy~elA~~il~~f~~~di~~~~L~~ii~~ 77 (79)
T PF14821_consen 41 ELEELKNLSYAELAFEILSPFLGDDIPEEELKEIIEK 77 (79)
T ss_dssp HHHHHTTS-HHHHHHHHHHHHCCCCS-HHHHHHHHHH
T ss_pred HHHHHHCCCHHHHHHHHHHHHHccCCCHHHHHHHHHH
Confidence 4667788999999999999999 67899999998875
No 36
>KOG0686|consensus
Probab=48.65 E-value=67 Score=30.74 Aligned_cols=126 Identities=17% Similarity=0.132 Sum_probs=86.6
Q ss_pred ccchHhhHHHHHhh--------hc--------CCC--CChHHHHHHHHHHhhcCCCcchhhhhhccCCCCCCCccHHHHH
Q psy5242 41 VYDLEANLAVLKLY--------QF--------HQN--YNMKITSQILLKALTNFPHTDFILCKCLLSKDLCKEDPIDQII 102 (217)
Q Consensus 41 ~Yd~~aNlalLKLY--------qf--------nP~--~~~~vv~~ILlkaL~~~P~~DF~lc~~LIp~~~~~~~~i~~l~ 102 (217)
.-+|-|=||.|+|= ++ +|. ...|++....+.||.-|-..|.-+- +-..+..+...
T Consensus 230 kl~C~agLa~L~lkkyk~aa~~fL~~~~~~~d~~~ivtpsdv~iYggLcALAtfdr~~Lk~~-------vi~n~~Fk~fl 302 (466)
T KOG0686|consen 230 KLKCAAGLANLLLKKYKSAAKYFLLAEFDHCDYPEIVTPSDVAIYGGLCALATFDRQDLKLN-------VIKNESFKLFL 302 (466)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHhCCCCccCccceecchhhHHHHhhHhhccCCHHHHHHH-------HHcchhhhhHH
Confidence 56788888888764 22 344 3468889999999988887773221 11233344444
Q ss_pred HHHHH-------HHhCChHHHHHHhhcC-------CchhhhccchHHHHHHHHHHHHHHhcccccHHHHHHhhcCCCHHH
Q psy5242 103 YLADL-------LESCKFTQFWSRMHTI-------PDLFLNIEGFNDSIRKFVCHVVGITFQTIDKKLLSELLDGVEDST 168 (217)
Q Consensus 103 ~L~~l-------Le~c~F~~FW~~l~~~-------~~l~~~i~gFed~IR~~I~~vVs~tyqsIs~~~La~~LG~ls~~e 168 (217)
.|--. --..+|..--+.+++. .-+.+.|..+-+.||++..-=.-+-|.+++-+.++.-.| .+...
T Consensus 303 el~Pqlr~il~~fy~sky~~cl~~L~~~k~~llLD~yLaphVd~Ly~~IR~r~llqy~~py~s~~m~~mA~af~-~sv~~ 381 (466)
T KOG0686|consen 303 ELEPQLREILFKFYSSKYASCLELLREIKPRLLLDMYLAPHVDNLYSLIRNRALLQYLSPYSSADMSKMAEAFN-TSVAI 381 (466)
T ss_pred hcChHHHHHHHHHhhhhHHHHHHHHHHhccceeechhcchhHHHHHHHHHHhhHHHhcCccccchHHHHHHHhc-ccHHH
Confidence 44444 4456666666666663 224577889999999999999999999999999999996 77755
Q ss_pred HHHHHH
Q psy5242 169 LRLWVK 174 (217)
Q Consensus 169 l~~~v~ 174 (217)
+++=+.
T Consensus 382 le~~l~ 387 (466)
T KOG0686|consen 382 LESELL 387 (466)
T ss_pred HHHHHH
Confidence 544433
No 37
>PF06627 DUF1153: Protein of unknown function (DUF1153); InterPro: IPR009534 This family consists of several short, hypothetical bacterial proteins of unknown function.; PDB: 2OA4_A 2JRT_A.
Probab=47.99 E-value=53 Score=24.65 Aligned_cols=38 Identities=11% Similarity=0.157 Sum_probs=33.4
Q ss_pred HHHHHHHHHHHhcccccHHHHHHhhcCCCHHHHHHHHHH
Q psy5242 137 IRKFVCHVVGITFQTIDKKLLSELLDGVEDSTLRLWVKK 175 (217)
Q Consensus 137 IR~~I~~vVs~tyqsIs~~~La~~LG~ls~~el~~~v~~ 175 (217)
+|+.+.-|.+..|--|+.+.-.+--| |+++|++.|...
T Consensus 35 a~RKAaVV~aV~~Glis~~EA~~rY~-Ls~eEf~~W~~a 72 (90)
T PF06627_consen 35 ARRKAAVVRAVRGGLISVEEACRRYG-LSEEEFESWQRA 72 (90)
T ss_dssp HHHHHHHHHHHHCTTS-HHHHHHCTT-SSHHHHHHHHHH
T ss_pred hhHHHHHHHHHHcCCCCHHHHHHHhC-CCHHHHHHHHHH
Confidence 67888888999999999999999996 999999999875
No 38
>PF03374 ANT: Phage antirepressor protein KilAC domain; InterPro: IPR005039 This entry is represented by Bacteriophage P1, Ant1 C-terminal domain, which represents the processed Ant2 chain. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Prophages P1 and P7 exist as unit copy DNA plasmids in the bacterial cell. Maintenance of the prophage state requires the continuous expression of two repressors: (i) C1 is a protein which negatively regulates the expression of lytic genes including the C1 inactivator gene coi, and (ii) C4 is an antisense RNA which specifically inhibits the synthesis of an anti-repressor Ant.; GO: 0003677 DNA binding
Probab=47.19 E-value=46 Score=24.79 Aligned_cols=35 Identities=17% Similarity=0.265 Sum_probs=30.3
Q ss_pred HHhcccccHHHHHHhhcCCCHHHHHHHHHHcCceEe
Q psy5242 146 GITFQTIDKKLLSELLDGVEDSTLRLWVKKYGWKEL 181 (217)
Q Consensus 146 s~tyqsIs~~~La~~LG~ls~~el~~~v~~~GWt~~ 181 (217)
..+=-.++...+|..|| +...+|-+|+.+.||-..
T Consensus 19 ~~~~~~~ti~~~AK~L~-i~~~~l~~~Lr~~g~l~~ 53 (111)
T PF03374_consen 19 VDSDGLYTIREAAKLLG-IGRNKLFQWLREKGWLYR 53 (111)
T ss_pred HcCCCCccHHHHHHHhC-CCHHHHHHHHHhCCceEE
Confidence 33337899999999997 999999999999999876
No 39
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=47.09 E-value=50 Score=25.96 Aligned_cols=43 Identities=12% Similarity=0.227 Sum_probs=36.3
Q ss_pred chHHHHHHHHHHHHHHhcccccHHHHHHhhcCCCHHHHHHHHHH-cC
Q psy5242 132 GFNDSIRKFVCHVVGITFQTIDKKLLSELLDGVEDSTLRLWVKK-YG 177 (217)
Q Consensus 132 gFed~IR~~I~~vVs~tyqsIs~~~La~~LG~ls~~el~~~v~~-~G 177 (217)
-|.-+||..+++.+..- -.|....|.+|| ++...+-+|++. .|
T Consensus 5 ~vlPaiRa~lA~~L~ee--G~Sq~~iA~LLG-ltqaAVS~Yls~krg 48 (119)
T COG2522 5 EVLPAIRALLAKELIEE--GLSQYRIAKLLG-LTQAAVSQYLSGKRG 48 (119)
T ss_pred HHHHHHHHHHHHHHHHc--CCcHHHHHHHhC-CCHHHHHHHHccCCc
Confidence 35568999999887665 889999999998 999999999986 45
No 40
>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=46.91 E-value=42 Score=22.26 Aligned_cols=41 Identities=22% Similarity=0.187 Sum_probs=28.8
Q ss_pred HHHHHHHHHhcccccHHHHHHhhcCCCHHHHHHHHH---HcCceE
Q psy5242 139 KFVCHVVGITFQTIDKKLLSELLDGVEDSTLRLWVK---KYGWKE 180 (217)
Q Consensus 139 ~~I~~vVs~tyqsIs~~~La~~LG~ls~~el~~~v~---~~GWt~ 180 (217)
-.|.+.|......++...|++.+| ++...+-..++ +.||-.
T Consensus 6 ~~vL~~l~~~~~~~t~~~l~~~~~-~~~~~vs~~i~~L~~~glv~ 49 (68)
T PF13463_consen 6 WQVLRALAHSDGPMTQSDLAERLG-ISKSTVSRIIKKLEEKGLVE 49 (68)
T ss_dssp HHHHHHHT--TS-BEHHHHHHHTT---HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHccCCCcCHHHHHHHHC-cCHHHHHHHHHHHHHCCCEE
Confidence 456677777889999999999997 89888777777 479963
No 41
>PF12728 HTH_17: Helix-turn-helix domain
Probab=46.85 E-value=28 Score=22.20 Aligned_cols=23 Identities=30% Similarity=0.582 Sum_probs=20.0
Q ss_pred ccHHHHHHhhcCCCHHHHHHHHHH
Q psy5242 152 IDKKLLSELLDGVEDSTLRLWVKK 175 (217)
Q Consensus 152 Is~~~La~~LG~ls~~el~~~v~~ 175 (217)
++.+..+++|| ++...+..|+.+
T Consensus 2 lt~~e~a~~l~-is~~tv~~~~~~ 24 (51)
T PF12728_consen 2 LTVKEAAELLG-ISRSTVYRWIRQ 24 (51)
T ss_pred CCHHHHHHHHC-cCHHHHHHHHHc
Confidence 46788999997 999999999875
No 42
>PF06043 Reo_P9: Reovirus P9-like family; InterPro: IPR009268 These proteins of unknown function are found in Rice black streaked dwarf virus (RBSDV) and other viruses.; PDB: 3VJJ_B.
Probab=45.97 E-value=18 Score=32.78 Aligned_cols=143 Identities=23% Similarity=0.329 Sum_probs=57.2
Q ss_pred HHHHHHhcccc-------CCCCCchhHHHH-------HHHHHHhc-------cccchHhhHHHHHhhhcCCCCChHHHHH
Q psy5242 9 GSVDQLLVGIE-------RYNPEHLSTLEK-------YVEVQCAE-------NVYDLEANLAVLKLYQFHQNYNMKITSQ 67 (217)
Q Consensus 9 ~~i~~~l~g~~-------rYnp~~l~~Le~-------yv~~Q~~~-------~~Yd~~aNlalLKLYqfnP~~~~~vv~~ 67 (217)
+-++.+++|.. -||=+++|.||. ||..|.+= +.||++.|..+-
T Consensus 54 ~Ll~~Ll~G~tfeks~y~GfdYshlPnLer~FntAS~YVn~~~~i~~e~~~l~~y~~~~~isv~---------------- 117 (333)
T PF06043_consen 54 ELLNYLLNGTTFEKSHYCGFDYSHLPNLERDFNTASAYVNENYEICFEEADLDGYDRQKNISVK---------------- 117 (333)
T ss_dssp HHHHHHHHT--GGGSTT-SS---SSTTHHHHHHHHHHHHHHHHHHHHSSS------------------------------
T ss_pred HHHHHHhcCccccceeecccccccCcchhhhhHHHHHHHhcceeEEeccccccccccccceeEe----------------
Confidence 45778888875 399999999994 88888652 345555554433
Q ss_pred HHHHHhhcCCCcchhhhhhccCCCCC----------------------------CC-----ccHHHHHHHHHHHHhCChH
Q psy5242 68 ILLKALTNFPHTDFILCKCLLSKDLC----------------------------KE-----DPIDQIIYLADLLESCKFT 114 (217)
Q Consensus 68 ILlkaL~~~P~~DF~lc~~LIp~~~~----------------------------~~-----~~i~~l~~L~~lLe~c~F~ 114 (217)
+|||++|+..+-.+.+ ++ ++|..-..+-+++.- =-.
T Consensus 118 ----------~P~ft~~lef~K~~~e~~~~~~eN~~~~~~~~kiv~~ll~~~nre~ed~~~e~ieGe~A~i~l~Km-fit 186 (333)
T PF06043_consen 118 ----------SPDFTFSLEFLKNKVESQRNPYENEQLKPLTAKIVTSLLPLFNRESEDSTSEQIEGEIAVINLFKM-FIT 186 (333)
T ss_dssp -----------------------------------EEE-TTTTEE-ES-CCC-SSS-----HHHHHHHHHHHHHHH-HHH
T ss_pred ----------cCCceEEEEEecccccccCCCcccccccccchhhhhhhccccCchhhhcchhhhcchhHHHHHHHH-HHH
Confidence 6888888877654432 11 122222222221110 013
Q ss_pred HHHHHhhc-------------CCchhhhccchHHHH-----HHHHHHH--HHHhcccccHHHHHHhhc-CC-CHHHHHHH
Q psy5242 115 QFWSRMHT-------------IPDLFLNIEGFNDSI-----RKFVCHV--VGITFQTIDKKLLSELLD-GV-EDSTLRLW 172 (217)
Q Consensus 115 ~FW~~l~~-------------~~~l~~~i~gFed~I-----R~~I~~v--Vs~tyqsIs~~~La~~LG-~l-s~~el~~~ 172 (217)
+|--.+.. .+++...|.||+=.+ -+.+-|+ .-.||..-+.+.|.--|- .+ .++...+-
T Consensus 187 gFL~hLg~n~~~yD~qL~iekYrpllv~Ivgye~l~~~~v~~kk~n~iyy~latF~nypf~~lR~~L~s~is~p~~i~q~ 266 (333)
T PF06043_consen 187 GFLVHLGENPNSYDRQLNIEKYRPLLVSIVGYEWLVGTRVPNKKINHIYYQLATFDNYPFDLLRFQLSSLISVPNSILQR 266 (333)
T ss_dssp HHHHHHHC---TTGGG-BSGGGHHHHHHHHHHHHHHHHTSS-----HHHHHHHH-TT-BHHHHHHH-SS-----HHHHHH
T ss_pred HHHHHHcCCCCccchhhhhhhhcchheeeecchheecccccccccccceeeeecCCCCcHHHHHHHhhhhcCChHHHHHH
Confidence 34444433 357788999999766 3333222 335788888888866652 12 23567777
Q ss_pred HHHcCc
Q psy5242 173 VKKYGW 178 (217)
Q Consensus 173 v~~~GW 178 (217)
+++.|-
T Consensus 267 i~k~GL 272 (333)
T PF06043_consen 267 IAKDGL 272 (333)
T ss_dssp HHHS-S
T ss_pred HHhcCc
Confidence 777774
No 43
>PF04800 ETC_C1_NDUFA4: ETC complex I subunit conserved region; InterPro: IPR006885 This entry represents prokaryotic NADH-ubiquinone oxidoreductase subunits (1.6.5.3 from EC, 1.6.99.3 from EC) from complex I of the electron transport chain initially identified in Neurospora crassa as a 21 kDa protein [].; GO: 0016651 oxidoreductase activity, acting on NADH or NADPH, 0022900 electron transport chain, 0005743 mitochondrial inner membrane; PDB: 2JYA_A 2LJU_A.
Probab=44.26 E-value=29 Score=26.49 Aligned_cols=40 Identities=8% Similarity=0.174 Sum_probs=16.1
Q ss_pred CCHHHHHHHHHHcCceEeCCceEEeCCCCccccccccccccccch
Q psy5242 164 VEDSTLRLWVKKYGWKELDNGYIFIANQDENIKTKNITEKIEFEN 208 (217)
Q Consensus 164 ls~~el~~~v~~~GWt~~~~g~v~p~n~en~~k~~~i~E~i~~~~ 208 (217)
-+.+++.+||+++||..+ +.-|. +-..+.|...+++.++.
T Consensus 56 ~skE~Ai~yaer~G~~Y~---V~~p~--~r~~~~ksY~dNF~~~r 95 (101)
T PF04800_consen 56 DSKEDAIAYAERNGWDYE---VEEPK--KRKRRPKSYADNFSWNR 95 (101)
T ss_dssp SSHHHHHHHHHHCT-EEE---EE-ST--T----------------
T ss_pred CCHHHHHHHHHHcCCeEE---EeCCC--CCcCCcccHHHhCCcCC
Confidence 377899999999999874 22232 23466777777776553
No 44
>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=43.44 E-value=32 Score=20.97 Aligned_cols=23 Identities=17% Similarity=0.237 Sum_probs=20.0
Q ss_pred ccHHHHHHhhcCCCHHHHHHHHHH
Q psy5242 152 IDKKLLSELLDGVEDSTLRLWVKK 175 (217)
Q Consensus 152 Is~~~La~~LG~ls~~el~~~v~~ 175 (217)
++....+++|| ++...+.+|+++
T Consensus 2 lt~~e~a~~lg-is~~ti~~~~~~ 24 (49)
T TIGR01764 2 LTVEEAAEYLG-VSKDTVYRLIHE 24 (49)
T ss_pred CCHHHHHHHHC-CCHHHHHHHHHc
Confidence 46788999997 999999999865
No 45
>PF13730 HTH_36: Helix-turn-helix domain
Probab=41.97 E-value=40 Score=21.69 Aligned_cols=25 Identities=24% Similarity=0.304 Sum_probs=21.5
Q ss_pred cHHHHHHhhcCCCHHHHHHHHHH---cCc
Q psy5242 153 DKKLLSELLDGVEDSTLRLWVKK---YGW 178 (217)
Q Consensus 153 s~~~La~~LG~ls~~el~~~v~~---~GW 178 (217)
|.+.|++.+| ++...+.+++++ .||
T Consensus 27 S~~~la~~~g-~s~~Tv~~~i~~L~~~G~ 54 (55)
T PF13730_consen 27 SQETLAKDLG-VSRRTVQRAIKELEEKGL 54 (55)
T ss_pred CHHHHHHHHC-cCHHHHHHHHHHHHHCcC
Confidence 7889999997 899889888874 687
No 46
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=41.16 E-value=63 Score=22.38 Aligned_cols=46 Identities=28% Similarity=0.406 Sum_probs=34.2
Q ss_pred HHHHHHHHHHhcccccHHHHHHhhcCCCHHHHHHHHHHcCceEeCCc
Q psy5242 138 RKFVCHVVGITFQTIDKKLLSELLDGVEDSTLRLWVKKYGWKELDNG 184 (217)
Q Consensus 138 R~~I~~vVs~tyqsIs~~~La~~LG~ls~~el~~~v~~~GWt~~~~g 184 (217)
|..++.+--.+=..|..-.+|+-|| +++..+..|=.+-.|...-+|
T Consensus 9 rdkA~e~y~~~~g~i~lkdIA~~Lg-vs~~tIr~WK~~dkW~~~~~~ 54 (60)
T PF10668_consen 9 RDKAFEIYKESNGKIKLKDIAEKLG-VSESTIRKWKSRDKWDEKLKG 54 (60)
T ss_pred HHHHHHHHHHhCCCccHHHHHHHHC-CCHHHHHHHhhhcchhhHhcc
Confidence 3444444444445799999999997 999999999888899764333
No 47
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=40.75 E-value=73 Score=26.47 Aligned_cols=39 Identities=23% Similarity=0.313 Sum_probs=27.8
Q ss_pred cccHHHHHHhhcCCCHHHHHHHHH---HcCceEeCCceEEeCC
Q psy5242 151 TIDKKLLSELLDGVEDSTLRLWVK---KYGWKELDNGYIFIAN 190 (217)
Q Consensus 151 sIs~~~La~~LG~ls~~el~~~v~---~~GWt~~~~g~v~p~n 190 (217)
.++...+|++|| ++.+.+-..++ +.||-.-..+.+.+.|
T Consensus 184 ~lt~~~iA~~lG-~sr~tvsR~l~~l~~~g~I~~~~~~i~i~d 225 (235)
T PRK11161 184 TMTRGDIGNYLG-LTVETISRLLGRFQKSGMLAVKGKYITIEN 225 (235)
T ss_pred cccHHHHHHHhC-CcHHHHHHHHHHHHHCCCEEecCCEEEEcC
Confidence 478889999998 89988777665 4799554444454444
No 48
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=40.10 E-value=84 Score=20.83 Aligned_cols=47 Identities=21% Similarity=0.275 Sum_probs=37.9
Q ss_pred cchHHHHHHHHHHHHHHhcccccHHHHHHhhcCCCHHHHHHHHHH---cCce
Q psy5242 131 EGFNDSIRKFVCHVVGITFQTIDKKLLSELLDGVEDSTLRLWVKK---YGWK 179 (217)
Q Consensus 131 ~gFed~IR~~I~~vVs~tyqsIs~~~La~~LG~ls~~el~~~v~~---~GWt 179 (217)
..+.+..|..|+..+ ..-...+...+++-|| ++...+-..++. .|+-
T Consensus 5 ~aL~~p~R~~Il~~L-~~~~~~t~~ela~~l~-~~~~t~s~hL~~L~~aGli 54 (61)
T PF12840_consen 5 KALSDPTRLRILRLL-ASNGPMTVSELAEELG-ISQSTVSYHLKKLEEAGLI 54 (61)
T ss_dssp HHHTSHHHHHHHHHH-HHCSTBEHHHHHHHHT-S-HHHHHHHHHHHHHTTSE
T ss_pred HHhCCHHHHHHHHHH-hcCCCCCHHHHHHHHC-CCHHHHHHHHHHHHHCCCe
Confidence 345578999999999 7888999999999997 899888887774 6773
No 49
>PF01466 Skp1: Skp1 family, dimerisation domain; InterPro: IPR016072 SKP1 (together with SKP2) was identified as an essential component of the cyclin A-CDK2 S phase kinase complex []. It was found to bind several F-box containing proteins (e.g., Cdc4, Skp2, cyclin F) and to be involved in the ubiquitin protein degradation pathway. A yeast homologue of SKP1 (P52286) was identified in the centromere bound kinetochore complex [] and is also involved in the ubiquitin pathway []. In Dictyostelium discoideum (Slime mold) FP21 was shown to be glycosylated in the cytosol and has homology to SKP1 []. This entry represents a dimerisation domain found at the C-terminal of SKP1 proteins [], as well as in subunit D of the centromere DNA-binding protein complex Cbf3 []. This domain is multi-helical in structure, and consists of an interlocked herterodimer in F-box proteins.; GO: 0006511 ubiquitin-dependent protein catabolic process; PDB: 2P1O_A 3OGL_G 3OGM_A 3C6O_A 2P1N_A 2P1Q_A 3OGK_I 3C6N_A 3C6P_A 2P1P_A ....
Probab=39.59 E-value=1.1e+02 Score=21.53 Aligned_cols=47 Identities=13% Similarity=0.261 Sum_probs=29.8
Q ss_pred ccchHHHHHHHHHHHHHHhcccccHHHHHHhhc---CCCHHHHHHHHHHcCceE
Q psy5242 130 IEGFNDSIRKFVCHVVGITFQTIDKKLLSELLD---GVEDSTLRLWVKKYGWKE 180 (217)
Q Consensus 130 i~gFed~IR~~I~~vVs~tyqsIs~~~La~~LG---~ls~~el~~~v~~~GWt~ 180 (217)
|+++.+ ..|+.|+..-+.-+.+.+..++| +.++++.++.=+++-|..
T Consensus 28 I~~L~~----~~~~~iA~~i~gks~eeir~~fgi~~d~t~eee~~i~~e~~w~~ 77 (78)
T PF01466_consen 28 IKGLLD----LCCKYIANMIKGKSPEEIRKYFGIENDLTPEEEEEIRKENEWAF 77 (78)
T ss_dssp -HHHHH----HHHHHHHHHHTTS-HHHHHHHHT---TSSHHHHHHHHHHCCCTB
T ss_pred chHHHH----HHHHHHHHHhcCCCHHHHHHHcCCCCCCCHHHHHHHHHHcchhc
Confidence 555555 45555555556789999999998 234466666555788854
No 50
>PF13986 DUF4224: Domain of unknown function (DUF4224)
Probab=39.54 E-value=91 Score=20.27 Aligned_cols=29 Identities=21% Similarity=0.263 Sum_probs=24.8
Q ss_pred ccHHHHHHhhcCCCHHHHHHHHHHcCceE
Q psy5242 152 IDKKLLSELLDGVEDSTLRLWVKKYGWKE 180 (217)
Q Consensus 152 Is~~~La~~LG~ls~~el~~~v~~~GWt~ 180 (217)
++.+.|.++.|....+.-.+|+.++||-.
T Consensus 3 LT~~El~elTG~k~~~~Q~~~L~~~Gi~~ 31 (47)
T PF13986_consen 3 LTDEELQELTGYKRPSKQIRWLRRNGIPF 31 (47)
T ss_pred CCHHHHHHHHCCCCHHHHHHHHHHCCCee
Confidence 57789999999777788889999999976
No 51
>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=39.08 E-value=91 Score=19.93 Aligned_cols=41 Identities=27% Similarity=0.263 Sum_probs=28.7
Q ss_pred HHHHHHHHHhcccccHHHHHHhhcCCCHHHHHHHHHH---cCceE
Q psy5242 139 KFVCHVVGITFQTIDKKLLSELLDGVEDSTLRLWVKK---YGWKE 180 (217)
Q Consensus 139 ~~I~~vVs~tyqsIs~~~La~~LG~ls~~el~~~v~~---~GWt~ 180 (217)
..|...+..+=..++...|++.|| +|...+...++. .|..+
T Consensus 3 ~~il~~L~~~~~~it~~eLa~~l~-vS~rTi~~~i~~L~~~~~~I 46 (55)
T PF08279_consen 3 KQILKLLLESKEPITAKELAEELG-VSRRTIRRDIKELREWGIPI 46 (55)
T ss_dssp HHHHHHHHHTTTSBEHHHHHHHCT-S-HHHHHHHHHHHHHTT-EE
T ss_pred HHHHHHHHHcCCCcCHHHHHHHhC-CCHHHHHHHHHHHHHCCCeE
Confidence 355666644444599999999997 999888888774 56444
No 52
>PF03693 RHH_2: Uncharacterised protein family (UPF0156); InterPro: IPR022789 This family of proteins are about 80 amino acids in length and their function is unknown. The proteins contain a conserved GRY motif. This family appears to be related to ribbon-helix-helix DNA-binding proteins. ; PDB: 3KXE_C.
Probab=39.06 E-value=22 Score=25.78 Aligned_cols=29 Identities=31% Similarity=0.416 Sum_probs=19.6
Q ss_pred hhHHHHHHHHHHhccccch--HhhHHHHHhh
Q psy5242 26 LSTLEKYVEVQCAENVYDL--EANLAVLKLY 54 (217)
Q Consensus 26 l~~Le~yv~~Q~~~~~Yd~--~aNlalLKLY 54 (217)
-+.+|+||++|++.|.|.- +.-.+.|+|-
T Consensus 10 ~~~~~~~i~~~V~sG~Y~s~SEvvR~aLRll 40 (80)
T PF03693_consen 10 TPELEAFIEEQVASGRYSSASEVVREALRLL 40 (80)
T ss_dssp -HHHHHHHHHHHCTTS-SSHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence 3679999999999999864 3334455543
No 53
>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=38.82 E-value=43 Score=20.22 Aligned_cols=22 Identities=55% Similarity=0.730 Sum_probs=19.1
Q ss_pred cHHHHHHhhcCCCHHHHHHHHHH
Q psy5242 153 DKKLLSELLDGVEDSTLRLWVKK 175 (217)
Q Consensus 153 s~~~La~~LG~ls~~el~~~v~~ 175 (217)
+...++++|| ++...+..|+++
T Consensus 2 s~~e~a~~lg-vs~~tl~~~~~~ 23 (49)
T cd04762 2 TTKEAAELLG-VSPSTLRRWVKE 23 (49)
T ss_pred CHHHHHHHHC-cCHHHHHHHHHc
Confidence 5678999997 999999999875
No 54
>TIGR02606 antidote_CC2985 putative addiction module antidote protein, CC2985 family. This bacterial protein family has a very similar seed alignment to that of Pfam model pfam03693 but is a more stringent model with higher cutoff scores. Proteins that score above the trusted cutoff to this model almost invariably are found adjacent to a ParE family protein (pfam05016), where ParE is the killing partner of an addiction module for plasmid stabilization. Members of this family, therefore, are putative addiction module antidote proteins. Some are encoded on plasmids or in prophage regions, but others appear chromosomal. A genome may contain several identical copies, such as the four in Magnetococcus sp. MC-1. This family is named for one member, CC2985 of Caulobacter crescentus CB15.
Probab=38.43 E-value=27 Score=24.51 Aligned_cols=31 Identities=26% Similarity=0.324 Sum_probs=22.1
Q ss_pred chhHHHHHHHHHHhccccch--HhhHHHHHhhh
Q psy5242 25 HLSTLEKYVEVQCAENVYDL--EANLAVLKLYQ 55 (217)
Q Consensus 25 ~l~~Le~yv~~Q~~~~~Yd~--~aNlalLKLYq 55 (217)
--+.+|+|++.|++.|.|.- +.-.+.|++.+
T Consensus 6 L~~~~~~~i~~~V~sG~Y~s~SEVir~aLR~le 38 (69)
T TIGR02606 6 LGEHLESFIRSQVQSGRYGSASEVVRAALRLLE 38 (69)
T ss_pred cCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH
Confidence 34689999999999999864 33445555544
No 55
>PF13977 TetR_C_6: Bacterial transcriptional repressor; PDB: 2NX4_C 3CRJ_C 3E7Q_B 2NP5_A 3QBM_B 2G3B_B 2GFN_A.
Probab=38.11 E-value=55 Score=23.56 Aligned_cols=49 Identities=16% Similarity=0.337 Sum_probs=38.4
Q ss_pred hHHHHHHhhcCCchhhhccchHHHHHHHHHHHHHHhcc-----cccHHHHHHhh
Q psy5242 113 FTQFWSRMHTIPDLFLNIEGFNDSIRKFVCHVVGITFQ-----TIDKKLLSELL 161 (217)
Q Consensus 113 F~~FW~~l~~~~~l~~~i~gFed~IR~~I~~vVs~tyq-----sIs~~~La~~L 161 (217)
|.+||.....++++...+..+.+.+|..+..++..... ..+...++..|
T Consensus 26 ~~~~~~~a~~~p~l~~~~~~~~~~~~~~l~~~l~~~~~g~~~~~~~~~~~A~~l 79 (115)
T PF13977_consen 26 WLEFWAEARRDPELRALLREAYARWRSRLAELLRRAVAGGIRADVDPERLARML 79 (115)
T ss_dssp HHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTSSSTTSTHHHHHHHH
T ss_pred HHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCHHHHHHHH
Confidence 56788888788899999999999999999998887665 56666666655
No 56
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=37.82 E-value=1.3e+02 Score=21.79 Aligned_cols=48 Identities=17% Similarity=0.234 Sum_probs=36.6
Q ss_pred HHHHhcccccHHHHHHhhcCCCHHHHHHHHHH---cCceEeC---CceEEeCCCC
Q psy5242 144 VVGITFQTIDKKLLSELLDGVEDSTLRLWVKK---YGWKELD---NGYIFIANQD 192 (217)
Q Consensus 144 vVs~tyqsIs~~~La~~LG~ls~~el~~~v~~---~GWt~~~---~g~v~p~n~e 192 (217)
+.-.++.-+|=+.|++-|| +|...+.+.|++ .|-.++. .|...|..++
T Consensus 12 l~~~~~~~~SGe~La~~Lg-iSRtaVwK~Iq~Lr~~G~~I~s~~~kGY~L~~~~~ 65 (79)
T COG1654 12 LLLLTGNFVSGEKLAEELG-ISRTAVWKHIQQLREEGVDIESVRGKGYLLPQLPD 65 (79)
T ss_pred HHHcCCCcccHHHHHHHHC-ccHHHHHHHHHHHHHhCCceEecCCCceeccCccc
Confidence 3445777899999999998 999999998884 6888763 3666665554
No 57
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=37.39 E-value=1.2e+02 Score=20.81 Aligned_cols=46 Identities=15% Similarity=0.064 Sum_probs=37.1
Q ss_pred HHHHHHHHHHHHHHhcc-cccHHHHHHhhcCCCHHHHHHHHH---HcCceE
Q psy5242 134 NDSIRKFVCHVVGITFQ-TIDKKLLSELLDGVEDSTLRLWVK---KYGWKE 180 (217)
Q Consensus 134 ed~IR~~I~~vVs~tyq-sIs~~~La~~LG~ls~~el~~~v~---~~GWt~ 180 (217)
.+..++.|+..+...=. .++...|+.-|| ++...+...+. +.|+-.
T Consensus 4 ~~~~~~~IL~~L~~~g~~~~ta~eLa~~lg-l~~~~v~r~L~~L~~~G~V~ 53 (68)
T smart00550 4 QDSLEEKILEFLENSGDETSTALQLAKNLG-LPKKEVNRVLYSLEKKGKVC 53 (68)
T ss_pred chHHHHHHHHHHHHCCCCCcCHHHHHHHHC-CCHHHHHHHHHHHHHCCCEE
Confidence 36678899999987634 399999999997 99999888876 478854
No 58
>PF03793 PASTA: PASTA domain; InterPro: IPR005543 The PASTA domain is found at the C-termini of several Penicillin-binding proteins (PBP) and bacterial serine/threonine kinases. It binds the beta-lactam stem, which implicates it in sensing D-alanyl-D-alanine - the PBP transpeptidase substrate. In PknB of Mycobacterium tuberculosis (P71584 from SWISSPROT), all of the extracellular portion is predicted to be made up of four PASTA domains, which strongly suggests that it is a signal-binding sensor domain. The domain has also been found in proteins involved in cell wall biosynthesis, where it is implicated in localizing the biosynthesis complex to unlinked peptidoglycan. PASTA is a small globular fold consisting of 3 beta-sheets and an alpha-helix, with a loop region of variable length between the first and second beta-strands. The name PASTA is derived from PBP and Serine/Threonine kinase Associated domain [].; GO: 0008658 penicillin binding; PDB: 2ZC3_C 1QME_A 1RP5_B 2Z2M_C 2Z2L_F 2ZC4_C 1QMF_A 3M9G_A 3PY9_A 1K25_B ....
Probab=37.27 E-value=48 Score=21.93 Aligned_cols=21 Identities=10% Similarity=0.158 Sum_probs=17.1
Q ss_pred HhhcCCCHHHHHHHHHHcCceE
Q psy5242 159 ELLDGVEDSTLRLWVKKYGWKE 180 (217)
Q Consensus 159 ~~LG~ls~~el~~~v~~~GWt~ 180 (217)
.+.| ++-+++.+.+++.||++
T Consensus 5 d~~g-~~~~~a~~~l~~~g~~~ 25 (63)
T PF03793_consen 5 DLVG-MTYDEAKSILEAAGLTV 25 (63)
T ss_dssp TTTT-SBHHHHHHHHHHTT-EE
T ss_pred CcCC-CcHHHHHHHHHHCCCEE
Confidence 4566 89999999999999965
No 59
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=37.13 E-value=1e+02 Score=24.77 Aligned_cols=40 Identities=13% Similarity=0.115 Sum_probs=28.7
Q ss_pred cccHHHHHHhhcCCCHHHHHHHHH---HcCceEeCCceEEeCCC
Q psy5242 151 TIDKKLLSELLDGVEDSTLRLWVK---KYGWKELDNGYIFIANQ 191 (217)
Q Consensus 151 sIs~~~La~~LG~ls~~el~~~v~---~~GWt~~~~g~v~p~n~ 191 (217)
.++...+|++|| ++.+.+-..++ +.||-.-+.+.+.+.++
T Consensus 149 ~~t~~~iA~~lG-~tretvsR~l~~l~~~g~I~~~~~~i~I~d~ 191 (202)
T PRK13918 149 YATHDELAAAVG-SVRETVTKVIGELSREGYIRSGYGKIQLLDL 191 (202)
T ss_pred cCCHHHHHHHhC-ccHHHHHHHHHHHHHCCCEEcCCCEEEEECH
Confidence 478999999998 89988777666 47996644454544443
No 60
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=34.86 E-value=50 Score=20.39 Aligned_cols=24 Identities=33% Similarity=0.411 Sum_probs=19.3
Q ss_pred cHHHHHHhhcCCCHHHHHHHHHHcCc
Q psy5242 153 DKKLLSELLDGVEDSTLRLWVKKYGW 178 (217)
Q Consensus 153 s~~~La~~LG~ls~~el~~~v~~~GW 178 (217)
+...+++++| ++...+..|.+ .|+
T Consensus 2 ~~~e~a~~~g-v~~~tlr~~~~-~g~ 25 (49)
T cd04761 2 TIGELAKLTG-VSPSTLRYYER-IGL 25 (49)
T ss_pred cHHHHHHHHC-cCHHHHHHHHH-CCC
Confidence 5678999997 99999999954 444
No 61
>PF01329 Pterin_4a: Pterin 4 alpha carbinolamine dehydratase; InterPro: IPR001533 DCoH is the dimerisation cofactor of hepatocyte nuclear factor 1 (HNF-1) that functions as both a transcriptional coactivator and a pterin dehydratase []. X-ray crystallographic studies have shown that the ligand binds at four sites per tetrameric enzyme, with little apparent conformational change in the protein.; GO: 0008124 4-alpha-hydroxytetrahydrobiopterin dehydratase activity, 0006729 tetrahydrobiopterin biosynthetic process; PDB: 2V6T_B 2V6U_A 2V6S_B 2EBB_A 1USM_A 1F93_B 1DCP_C 1DCH_E 3HXA_E 1DCO_C ....
Probab=34.84 E-value=55 Score=24.16 Aligned_cols=19 Identities=16% Similarity=0.307 Sum_probs=15.6
Q ss_pred CCHHHHHHHHHH-cCceEeC
Q psy5242 164 VEDSTLRLWVKK-YGWKELD 182 (217)
Q Consensus 164 ls~~el~~~v~~-~GWt~~~ 182 (217)
++++|+.+.+++ .||++.+
T Consensus 5 Ls~~ei~~~L~~l~~W~~~~ 24 (95)
T PF01329_consen 5 LSEEEIAEALAELPGWKLDG 24 (95)
T ss_dssp -THHHHHHHHHTSTTSEEET
T ss_pred CCHHHHHHhhhcCcCCEECC
Confidence 678899999887 6999976
No 62
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=34.10 E-value=64 Score=20.41 Aligned_cols=28 Identities=21% Similarity=0.270 Sum_probs=22.7
Q ss_pred cc-cHHHHHHhhcCCCHHHHHHHHH---HcCce
Q psy5242 151 TI-DKKLLSELLDGVEDSTLRLWVK---KYGWK 179 (217)
Q Consensus 151 sI-s~~~La~~LG~ls~~el~~~v~---~~GWt 179 (217)
.+ +...|++.+| +|...+.+.+. +.||-
T Consensus 19 ~l~s~~~la~~~~-vs~~tv~~~l~~L~~~g~i 50 (60)
T smart00345 19 KLPSERELAAQLG-VSRTTVREALSRLEAEGLV 50 (60)
T ss_pred cCcCHHHHHHHHC-CCHHHHHHHHHHHHHCCCE
Confidence 46 7999999997 89888887776 47994
No 63
>KOG1463|consensus
Probab=33.56 E-value=1.8e+02 Score=27.41 Aligned_cols=79 Identities=10% Similarity=0.292 Sum_probs=59.3
Q ss_pred CCccHHHHHHHHHHHHhCChHHHHHHhhcC------Cchh-hhccchHHH-HHHHHHHHHHHhcccccHHHHHHhhcCCC
Q psy5242 94 KEDPIDQIIYLADLLESCKFTQFWSRMHTI------PDLF-LNIEGFNDS-IRKFVCHVVGITFQTIDKKLLSELLDGVE 165 (217)
Q Consensus 94 ~~~~i~~l~~L~~lLe~c~F~~FW~~l~~~------~~l~-~~i~gFed~-IR~~I~~vVs~tyqsIs~~~La~~LG~ls 165 (217)
..+.|..+..+++.-.++....|=.++..+ ..++ .....+.|. .-+-+|++| --|+.+.++..++.+| ++
T Consensus 281 ~g~~i~AmkavAeA~~nRSLkdF~~AL~~yk~eL~~D~ivr~Hl~~Lyd~lLEknl~riI-EPyS~Vei~hIA~~IG-l~ 358 (411)
T KOG1463|consen 281 AGRDIDAMKAVAEAFGNRSLKDFEKALADYKKELAEDPIVRSHLQSLYDNLLEKNLCRII-EPYSRVEISHIAEVIG-LD 358 (411)
T ss_pred cCcchHHHHHHHHHhcCCcHHHHHHHHHHhHHHHhcChHHHHHHHHHHHHHHHHhHHHHc-CchhhhhHHHHHHHHC-CC
Confidence 667889999999999999999999999764 2222 223334443 456778866 4799999999999998 88
Q ss_pred HHHHHHHHH
Q psy5242 166 DSTLRLWVK 174 (217)
Q Consensus 166 ~~el~~~v~ 174 (217)
-..+++-+.
T Consensus 359 ~~~VEkKLs 367 (411)
T KOG1463|consen 359 VPQVEKKLS 367 (411)
T ss_pred cHHHHHHHH
Confidence 777666554
No 64
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=33.22 E-value=1.4e+02 Score=19.44 Aligned_cols=31 Identities=13% Similarity=0.203 Sum_probs=25.0
Q ss_pred ccccHHHHHHhhcCCCHHHHHHHHH---HcCceEe
Q psy5242 150 QTIDKKLLSELLDGVEDSTLRLWVK---KYGWKEL 181 (217)
Q Consensus 150 qsIs~~~La~~LG~ls~~el~~~v~---~~GWt~~ 181 (217)
..++...+++.+| ++...+.+.+. +.||-..
T Consensus 24 ~~~s~~ela~~~g-~s~~tv~r~l~~L~~~g~i~~ 57 (67)
T cd00092 24 LPLTRQEIADYLG-LTRETVSRTLKELEEEGLISR 57 (67)
T ss_pred CCcCHHHHHHHHC-CCHHHHHHHHHHHHHCCCEEe
Confidence 3589999999997 89988888776 4799653
No 65
>PRK15325 type III secretion system needle complex protein PrgJ; Provisional
Probab=33.08 E-value=42 Score=24.66 Aligned_cols=40 Identities=13% Similarity=0.281 Sum_probs=29.2
Q ss_pred HHHHHHHHHHHhccccCC-CCCchhHHHHHHHHHHhccccchHhhHH
Q psy5242 4 AELMKGSVDQLLVGIERY-NPEHLSTLEKYVEVQCAENVYDLEANLA 49 (217)
Q Consensus 4 ~~~~~~~i~~~l~g~~rY-np~~l~~Le~yv~~Q~~~~~Yd~~aNla 49 (217)
.++-++.|.+.+...++. ||+.|-.|++++ +.|.+..|+.
T Consensus 23 ~~~ek~~i~~~~~~~~~~snP~~Ll~lQ~~~------~~Ysl~vslv 63 (80)
T PRK15325 23 TAVDKQTITNRIEDPNLVTDPKELAISQEMI------SDYNLYVSMV 63 (80)
T ss_pred HHHHHHHHHHHhcCCcccCCHHHHHHHHHHH------HhHhHHHHHH
Confidence 455667788888888865 888887777666 5687777764
No 66
>smart00513 SAP Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation.
Probab=32.61 E-value=46 Score=19.92 Aligned_cols=21 Identities=24% Similarity=0.166 Sum_probs=17.4
Q ss_pred CCCHHHHHHHHHHcCceEeCC
Q psy5242 163 GVEDSTLRLWVKKYGWKELDN 183 (217)
Q Consensus 163 ~ls~~el~~~v~~~GWt~~~~ 183 (217)
.|+.++|++++.+.||...|.
T Consensus 3 ~l~~~~Lk~~l~~~gl~~~G~ 23 (35)
T smart00513 3 KLKVSELKDELKKRGLSTSGT 23 (35)
T ss_pred cCcHHHHHHHHHHcCCCCCCC
Confidence 478899999999999987543
No 67
>COG4004 Uncharacterized protein conserved in archaea [Function unknown]
Probab=32.19 E-value=50 Score=24.93 Aligned_cols=20 Identities=15% Similarity=0.458 Sum_probs=15.8
Q ss_pred CHHHHHHHHHHcCceEeCCc
Q psy5242 165 EDSTLRLWVKKYGWKELDNG 184 (217)
Q Consensus 165 s~~el~~~v~~~GWt~~~~g 184 (217)
+.+-+...++++||++...|
T Consensus 13 ~~dri~~~l~e~g~~v~~eG 32 (96)
T COG4004 13 DPDRIMRGLSELGWTVSEEG 32 (96)
T ss_pred CHHHHHHHHHHhCeeEeecc
Confidence 34668999999999997555
No 68
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=32.08 E-value=1.2e+02 Score=18.32 Aligned_cols=33 Identities=24% Similarity=0.374 Sum_probs=24.9
Q ss_pred cccHHHHHHhhcCCCHHHHHHHHH---HcCceEeCCc
Q psy5242 151 TIDKKLLSELLDGVEDSTLRLWVK---KYGWKELDNG 184 (217)
Q Consensus 151 sIs~~~La~~LG~ls~~el~~~v~---~~GWt~~~~g 184 (217)
.++...+++.+| ++...+.+.+. +.||-....|
T Consensus 8 ~~s~~~la~~l~-~s~~tv~~~l~~L~~~g~l~~~~~ 43 (48)
T smart00419 8 PLTRQEIAELLG-LTRETVSRTLKRLEKEGLISREGG 43 (48)
T ss_pred ccCHHHHHHHHC-CCHHHHHHHHHHHHHCCCEEEeCC
Confidence 367889999997 89988877776 4799653333
No 69
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=31.52 E-value=1.5e+02 Score=20.31 Aligned_cols=38 Identities=11% Similarity=0.034 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHhcccccHHHHHHhhcCCCHHHHHHHHHH
Q psy5242 137 IRKFVCHVVGITFQTIDKKLLSELLDGVEDSTLRLWVKK 175 (217)
Q Consensus 137 IR~~I~~vVs~tyqsIs~~~La~~LG~ls~~el~~~v~~ 175 (217)
|++.+-++-...=+.-+...+|+.|| ++.+++...+..
T Consensus 6 i~~a~~~L~~~lgr~Pt~eEiA~~lg-is~~~v~~~l~~ 43 (78)
T PF04539_consen 6 IERARRELEQELGREPTDEEIAEELG-ISVEEVRELLQA 43 (78)
T ss_dssp HHHHHHHHHHHHSS--BHHHHHHHHT-S-HHHHHHHHHH
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHc-ccHHHHHHHHHh
Confidence 44444444444447888999999997 999999998875
No 70
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=31.39 E-value=1e+02 Score=20.45 Aligned_cols=32 Identities=13% Similarity=0.280 Sum_probs=22.3
Q ss_pred HHHHHHHHHhcccccHHHHHHhhcCCCHHHHHH
Q psy5242 139 KFVCHVVGITFQTIDKKLLSELLDGVEDSTLRL 171 (217)
Q Consensus 139 ~~I~~vVs~tyqsIs~~~La~~LG~ls~~el~~ 171 (217)
+..-++-..-...|+-..|++.+| +++.++.+
T Consensus 16 r~L~~l~~~G~~~vSS~~La~~~g-i~~~qVRK 47 (50)
T PF06971_consen 16 RYLEQLKEEGVERVSSQELAEALG-ITPAQVRK 47 (50)
T ss_dssp HHHHHHHHTT-SEE-HHHHHHHHT-S-HHHHHH
T ss_pred HHHHHHHHcCCeeECHHHHHHHHC-CCHHHhcc
Confidence 344455566778999999999998 89988765
No 71
>PF08565 CDC37_M: Cdc37 Hsp90 binding domain; InterPro: IPR013874 Cdc37 is a molecular chaperone required for the activity of numerous eukaryotic protein kinases. This entry corresponds to the Hsp90 chaperone (heat shock protein 90) binding domain of Cdc37 []. It is found between the N-terminal Cdc37 domain IPR013855 from INTERPRO, which is predominantly involved in kinase binding, and the C-terminal domain of Cdc37 IPR013873 from INTERPRO whose function is unclear. ; PDB: 1US7_B 2W0G_A 2K5B_B.
Probab=31.10 E-value=1.1e+02 Score=25.53 Aligned_cols=89 Identities=18% Similarity=0.182 Sum_probs=53.1
Q ss_pred hcCCC-CChHHHHHHHHHHhhcCCCcchhhhhhccCCCCCCCccHHHHHHHHHHHH---hCChHHHHHHhhcCCchhhhc
Q psy5242 55 QFHQN-YNMKITSQILLKALTNFPHTDFILCKCLLSKDLCKEDPIDQIIYLADLLE---SCKFTQFWSRMHTIPDLFLNI 130 (217)
Q Consensus 55 qfnP~-~~~~vv~~ILlkaL~~~P~~DF~lc~~LIp~~~~~~~~i~~l~~L~~lLe---~c~F~~FW~~l~~~~~l~~~i 130 (217)
.=+|+ ......-.+|+.|+-.-=.-|--+....+.+++ -++.+..||.-+. ..-+..|++.+.. +.--...
T Consensus 70 ~~hp~l~~E~~~d~Ll~~af~~emegk~~~~~q~vhQsl----lLqyi~eLak~~~~~pr~~v~~FF~r~~~-~~~~~~~ 144 (173)
T PF08565_consen 70 LEHPELLCEQTADALLMWAFDLEMEGKHELARQVVHQSL----LLQYIRELAKSLKRDPRDGVRLFFKRIKT-PGHPEAK 144 (173)
T ss_dssp HHCGGG-SHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHH----HHHHHHHHHHHHTS-GGGCHHHHHHHHTT--SSHHHH
T ss_pred HhCccccChhhccHHHHHHHHHHHcCCHHHHHHHHHHHH----HHHHHHHHHhcCCCChhhHHHHHHHHHHh-ccCHHHH
Confidence 56889 889999999999986432333333333333332 3566666665554 5668889999876 2223345
Q ss_pred cchHHHHHHHHHHHHHHh
Q psy5242 131 EGFNDSIRKFVCHVVGIT 148 (217)
Q Consensus 131 ~gFed~IR~~I~~vVs~t 148 (217)
.+|.+.+..+.-|+...+
T Consensus 145 ~~F~~dv~~~~~rIk~Ra 162 (173)
T PF08565_consen 145 KVFEDDVEAFYERIKERA 162 (173)
T ss_dssp HHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 566666666666655443
No 72
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=30.31 E-value=1.3e+02 Score=27.18 Aligned_cols=52 Identities=10% Similarity=0.031 Sum_probs=36.7
Q ss_pred HHHHHHHHHhcccccHHHHHHhhcCCCHHHHHHHHHHcCceEeCCc-eEEeCCC
Q psy5242 139 KFVCHVVGITFQTIDKKLLSELLDGVEDSTLRLWVKKYGWKELDNG-YIFIANQ 191 (217)
Q Consensus 139 ~~I~~vVs~tyqsIs~~~La~~LG~ls~~el~~~v~~~GWt~~~~g-~v~p~n~ 191 (217)
..|+..+.....+||++.++...| +..+++-.-++..|.-..-.| .++..++
T Consensus 211 ~~il~~L~~~~~~isi~~is~~T~-i~~~Dii~tL~~l~~l~~~~g~~~i~~~~ 263 (290)
T PLN03238 211 RVLLEQLRDVKGDVSIKDLSLATG-IRGEDIVSTLQSLNLIKYWKGQHVIHVDQ 263 (290)
T ss_pred HHHHHHHHhcCCCccHHHHHHHhC-CCHHHHHHHHHHCCcEEEECCcEEEEeCH
Confidence 344444445568999999999997 999999999999997543233 3443333
No 73
>KOG3389|consensus
Probab=30.12 E-value=38 Score=27.81 Aligned_cols=38 Identities=13% Similarity=0.243 Sum_probs=24.8
Q ss_pred CCHHHHHHHHHHcCceEeCCceEEeCCCCcccccccccccccc
Q psy5242 164 VEDSTLRLWVKKYGWKELDNGYIFIANQDENIKTKNITEKIEF 206 (217)
Q Consensus 164 ls~~el~~~v~~~GWt~~~~g~v~p~n~en~~k~~~i~E~i~~ 206 (217)
-+.+++..|++++||..+-. -| .+-.+|.|+...++..
T Consensus 132 ~tkEdA~sFaEkngW~ydve---ep--~~pk~K~KsYg~NFsW 169 (178)
T KOG3389|consen 132 DTKEDAKSFAEKNGWDYDVE---EP--NTPKLKVKSYGDNFSW 169 (178)
T ss_pred ccHHHHHHHHHHcCCccccc---CC--CCCccccccccccccc
Confidence 36788999999999987511 12 2224666666666544
No 74
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=29.85 E-value=1.6e+02 Score=19.54 Aligned_cols=35 Identities=14% Similarity=0.124 Sum_probs=28.4
Q ss_pred HHHHHHHHhcccccHHHHHHhhcCCCHHHHHHHHHHc
Q psy5242 140 FVCHVVGITFQTIDKKLLSELLDGVEDSTLRLWVKKY 176 (217)
Q Consensus 140 ~I~~vVs~tyqsIs~~~La~~LG~ls~~el~~~v~~~ 176 (217)
.++..+.. -..++...|++.|| +|...+...+.+.
T Consensus 9 ~Ll~~L~~-~~~~~~~ela~~l~-~S~rti~~~i~~L 43 (59)
T PF08280_consen 9 KLLELLLK-NKWITLKELAKKLN-ISERTIKNDINEL 43 (59)
T ss_dssp HHHHHHHH-HTSBBHHHHHHHCT-S-HHHHHHHHHHH
T ss_pred HHHHHHHc-CCCCcHHHHHHHHC-CCHHHHHHHHHHH
Confidence 45666666 78999999999997 9999999999863
No 75
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=29.60 E-value=92 Score=18.96 Aligned_cols=30 Identities=20% Similarity=0.159 Sum_probs=21.1
Q ss_pred ccccHHHHHHhhcCCCHHHHHHHHHH-cCceE
Q psy5242 150 QTIDKKLLSELLDGVEDSTLRLWVKK-YGWKE 180 (217)
Q Consensus 150 qsIs~~~La~~LG~ls~~el~~~v~~-~GWt~ 180 (217)
+.++++++|+.+| +|..-+....++ .|.|.
T Consensus 7 ~~~~l~~iA~~~g-~S~~~f~r~Fk~~~g~tp 37 (42)
T PF00165_consen 7 QKLTLEDIAEQAG-FSPSYFSRLFKKETGMTP 37 (42)
T ss_dssp SS--HHHHHHHHT-S-HHHHHHHHHHHTSS-H
T ss_pred CCCCHHHHHHHHC-CCHHHHHHHHHHHHCcCH
Confidence 5688999999998 798888888776 58763
No 76
>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=28.72 E-value=88 Score=18.84 Aligned_cols=23 Identities=17% Similarity=0.339 Sum_probs=15.7
Q ss_pred ccHHHHHHhhcCCCHHHHHHHHHH
Q psy5242 152 IDKKLLSELLDGVEDSTLRLWVKK 175 (217)
Q Consensus 152 Is~~~La~~LG~ls~~el~~~v~~ 175 (217)
++..+++.+|| ++.+.+-..+++
T Consensus 3 mtr~diA~~lG-~t~ETVSR~l~~ 25 (32)
T PF00325_consen 3 MTRQDIADYLG-LTRETVSRILKK 25 (32)
T ss_dssp --HHHHHHHHT-S-HHHHHHHHHH
T ss_pred cCHHHHHHHhC-CcHHHHHHHHHH
Confidence 67889999998 888877666653
No 77
>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=28.56 E-value=89 Score=21.41 Aligned_cols=35 Identities=11% Similarity=0.155 Sum_probs=23.8
Q ss_pred HHHHHhccc---cCCCCCchhHHHHHHHHHHhccccch
Q psy5242 10 SVDQLLVGI---ERYNPEHLSTLEKYVEVQCAENVYDL 44 (217)
Q Consensus 10 ~i~~~l~g~---~rYnp~~l~~Le~yv~~Q~~~~~Yd~ 44 (217)
.|+.+++-. ..+-+-..+.|++|++.=++++.-.+
T Consensus 16 RIh~mLkmf~~~~~~~~~s~~eL~~fL~~lv~e~~L~~ 53 (60)
T PF08672_consen 16 RIHSMLKMFPKDPGGYDISLEELQEFLDRLVEEGKLEC 53 (60)
T ss_dssp HHHHHHHHH-GGG--TT--HHHHHHHHHHHHHTTSEE-
T ss_pred HHHHHHHhccCCCCCCCCCHHHHHHHHHHHHHCCcEEe
Confidence 577777655 56777789999999999999875443
No 78
>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=28.34 E-value=1.7e+02 Score=21.69 Aligned_cols=67 Identities=10% Similarity=0.125 Sum_probs=41.4
Q ss_pred ChHHHHHHhhcCCchhhhccchHHHHHHHHHHHHH--Hhc-ccccHHHHHHhhcCCCHHHHHHHHH---HcCceE
Q psy5242 112 KFTQFWSRMHTIPDLFLNIEGFNDSIRKFVCHVVG--ITF-QTIDKKLLSELLDGVEDSTLRLWVK---KYGWKE 180 (217)
Q Consensus 112 ~F~~FW~~l~~~~~l~~~i~gFed~IR~~I~~vVs--~ty-qsIs~~~La~~LG~ls~~el~~~v~---~~GWt~ 180 (217)
+|-.||..++.-.+....--|+ ..-.-.++..+. ... ..++...|+..+| ++...+-..+. +.||-.
T Consensus 2 ~~~~~~~~~~~~~~~l~~~~~l-s~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~-~~~stvs~~i~~Le~kg~I~ 74 (109)
T TIGR01889 2 DLLSLYLYIKSLKRYLKKEFNL-SLEELLILYYLGKLENNEGKLTLKEIIKEIL-IKQSALVKIIKKLSKKGYLS 74 (109)
T ss_pred cHHHHHHHHHHHHHHHHHHcCC-CHHHHHHHHHHHhhhccCCcCcHHHHHHHHC-CCHHHHHHHHHHHHHCCCEe
Confidence 4666777765532222211233 122334666666 222 4599999999997 89988877777 489955
No 79
>PF07927 YcfA: YcfA-like protein; InterPro: IPR012933 This entry represents UPF0395, which contains viral, archaeal and bacterial proteins. It includes YncN of Escherichia coli K12. Most of these proteins are hypothetical proteins of unknown function. ; GO: 0016788 hydrolase activity, acting on ester bonds; PDB: 1WHZ_A.
Probab=28.25 E-value=1.4e+02 Score=19.18 Aligned_cols=15 Identities=27% Similarity=0.430 Sum_probs=12.1
Q ss_pred HHHHHHHHHcCceEe
Q psy5242 167 STLRLWVKKYGWKEL 181 (217)
Q Consensus 167 ~el~~~v~~~GWt~~ 181 (217)
+|+.+++++.||+..
T Consensus 2 ~el~k~L~~~G~~~~ 16 (56)
T PF07927_consen 2 RELIKLLEKAGFEEV 16 (56)
T ss_dssp HHHHHHHHHTT-EEE
T ss_pred hHHHHHHHHCCCEEe
Confidence 578999999999885
No 80
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=27.95 E-value=1.3e+02 Score=21.08 Aligned_cols=29 Identities=28% Similarity=0.331 Sum_probs=22.9
Q ss_pred cccccHHHHHHhhcCCCHHHHHHHHHHcCc
Q psy5242 149 FQTIDKKLLSELLDGVEDSTLRLWVKKYGW 178 (217)
Q Consensus 149 yqsIs~~~La~~LG~ls~~el~~~v~~~GW 178 (217)
....+...+|+-+| .|...+-.|+++.|.
T Consensus 32 ~~~~si~elA~~~~-vS~sti~Rf~kkLG~ 60 (77)
T PF01418_consen 32 IAFMSISELAEKAG-VSPSTIVRFCKKLGF 60 (77)
T ss_dssp HCT--HHHHHHHCT-S-HHHHHHHHHHCTT
T ss_pred HHHccHHHHHHHcC-CCHHHHHHHHHHhCC
Confidence 35788999999997 999999999999876
No 81
>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=27.85 E-value=95 Score=19.91 Aligned_cols=40 Identities=13% Similarity=0.164 Sum_probs=31.5
Q ss_pred HHHHHHHHhcccccHHHHHHhhcCCCHHHHHHHHH---HcCceE
Q psy5242 140 FVCHVVGITFQTIDKKLLSELLDGVEDSTLRLWVK---KYGWKE 180 (217)
Q Consensus 140 ~I~~vVs~tyqsIs~~~La~~LG~ls~~el~~~v~---~~GWt~ 180 (217)
.|+..++.+=..++...+++-+| ++...+-.++. +.||-.
T Consensus 7 ~iL~~l~~~~~~~t~~eia~~~g-l~~stv~r~L~tL~~~g~v~ 49 (52)
T PF09339_consen 7 RILEALAESGGPLTLSEIARALG-LPKSTVHRLLQTLVEEGYVE 49 (52)
T ss_dssp HHHHCHHCTBSCEEHHHHHHHHT-S-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHcCCCCCCHHHHHHHHC-cCHHHHHHHHHHHHHCcCee
Confidence 46677777778889999999997 89988877776 579954
No 82
>PF04801 Sin_N: Sin-like protein conserved region; InterPro: IPR006886 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. RNA polymerase III (Pol III) is a complex consisting of 17 subunits, which synthesizes small RNAs, such as 5S rRNA and tRNAs. Pol III is essential for efficient transcription from both the type 2 VAI and type 3 U6 RNA polymerase III promoters and plays a key role in sensing and limiting infection by intracellular bacteria and DNA viruses. Subunit c5 is a specific peripheric component of RNA polymerase III complex. ; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent, 0005634 nucleus
Probab=27.25 E-value=36 Score=31.83 Aligned_cols=96 Identities=16% Similarity=0.216 Sum_probs=64.0
Q ss_pred CCCcchhhhhhccCCCCC-CCccHHHHHHHHHHHHhCChHHHHHHhhcCCchhh-hccchHHHHHHHHHHHHHHhccccc
Q psy5242 76 FPHTDFILCKCLLSKDLC-KEDPIDQIIYLADLLESCKFTQFWSRMHTIPDLFL-NIEGFNDSIRKFVCHVVGITFQTID 153 (217)
Q Consensus 76 ~P~~DF~lc~~LIp~~~~-~~~~i~~l~~L~~lLe~c~F~~FW~~l~~~~~l~~-~i~gFed~IR~~I~~vVs~tyqsIs 153 (217)
.+---|.--..++|++.. ++.-|..|-..+-++.++ |- ++| .-+.. .-++.....|.+|+-+.+.. ..|+
T Consensus 282 ~~v~~Fs~L~~ll~~~~~~~~~lL~~L~~~AvLV~G~-----WV-~kS-~ll~~~~~~e~~~~aRD~iL~~F~~~-~~v~ 353 (421)
T PF04801_consen 282 ARVISFSELRKLLPSNSDTDEELLRALQQVAVLVQGN-----WV-VKS-ELLYPDVPAEQLCRARDYILLLFTKS-RYVK 353 (421)
T ss_pred CCcccHHHHHHHhccccchHHHHHHHHHhheEEEeee-----EE-Eeh-hhccCCCcchhhhhhHHHHHHHhcCC-Ccee
Confidence 345556667778888775 444556655555554433 21 112 11222 23568899999999999998 7799
Q ss_pred HHHHHHhhcCCCHHHHHHHHHH--------cCceE
Q psy5242 154 KKLLSELLDGVEDSTLRLWVKK--------YGWKE 180 (217)
Q Consensus 154 ~~~La~~LG~ls~~el~~~v~~--------~GWt~ 180 (217)
+..+....+ ++.++++.+++. .||++
T Consensus 354 r~~l~~~~~-l~~~~~~eiL~~~a~~~~~~~~W~l 387 (421)
T PF04801_consen 354 RKELMSATK-LPPEDVKEILKEIAVLRPSNRGWKL 387 (421)
T ss_pred HHHhhhhcC-CCHHHHHHHHHHHhhccCCCCceEE
Confidence 999999997 888777666652 47887
No 83
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=27.20 E-value=1.7e+02 Score=24.50 Aligned_cols=40 Identities=15% Similarity=0.210 Sum_probs=27.7
Q ss_pred cccHHHHHHhhcCCCHHHHHHHHH---HcCceEeCC-ceEEeCCC
Q psy5242 151 TIDKKLLSELLDGVEDSTLRLWVK---KYGWKELDN-GYIFIANQ 191 (217)
Q Consensus 151 sIs~~~La~~LG~ls~~el~~~v~---~~GWt~~~~-g~v~p~n~ 191 (217)
.++..++|++|| ++.+.+-..++ +.|+-.-.. +.+.+.++
T Consensus 179 ~lt~~~IA~~lG-isretlsR~L~~L~~~GlI~~~~~~~i~I~D~ 222 (230)
T PRK09391 179 PMSRRDIADYLG-LTIETVSRALSQLQDRGLIGLSGARQIELRNR 222 (230)
T ss_pred cCCHHHHHHHHC-CCHHHHHHHHHHHHHCCcEEecCCceEEEcCH
Confidence 367789999998 89988777665 478864333 44555443
No 84
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=26.57 E-value=2e+02 Score=22.06 Aligned_cols=76 Identities=16% Similarity=0.109 Sum_probs=44.5
Q ss_pred HHHHHHHHHHHhcccccHHHHHHhhcCCCHHHHHHHHHHc-CceEeCC--ce------EEeCCCCccccccccccccccc
Q psy5242 137 IRKFVCHVVGITFQTIDKKLLSELLDGVEDSTLRLWVKKY-GWKELDN--GY------IFIANQDENIKTKNITEKIEFE 207 (217)
Q Consensus 137 IR~~I~~vVs~tyqsIs~~~La~~LG~ls~~el~~~v~~~-GWt~~~~--g~------v~p~n~en~~k~~~i~E~i~~~ 207 (217)
|++.+..+-..-.+.++++.+++.+| ++...+....++. |=+..+= .. ..-.+.+. .-..|.+...|.
T Consensus 11 i~~~~~~I~~~~~~~~sl~~lA~~~g-~S~~~l~r~Fk~~~G~s~~~~l~~~Rl~~A~~~L~~t~~--~i~eIA~~~Gf~ 87 (127)
T PRK11511 11 IHSILDWIEDNLESPLSLEKVSERSG-YSKWHLQRMFKKETGHSLGQYIRSRKMTEIAQKLKESNE--PILYLAERYGFE 87 (127)
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHC-cCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHcCCC--CHHHHHHHhCCC
Confidence 34333343344447799999999997 9999998888864 7544100 00 00112222 234677777777
Q ss_pred hHHHHhhh
Q psy5242 208 NAATIMTS 215 (217)
Q Consensus 208 ~~~~~~~~ 215 (217)
+.+...+.
T Consensus 88 s~s~F~r~ 95 (127)
T PRK11511 88 SQQTLTRT 95 (127)
T ss_pred CHHHHHHH
Confidence 76665543
No 85
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=26.51 E-value=1.7e+02 Score=18.34 Aligned_cols=41 Identities=15% Similarity=0.154 Sum_probs=29.5
Q ss_pred cchHHHHHHHHHHHHHHhcccccHHHHHHhhcCCCHHHHHHHHHH
Q psy5242 131 EGFNDSIRKFVCHVVGITFQTIDKKLLSELLDGVEDSTLRLWVKK 175 (217)
Q Consensus 131 ~gFed~IR~~I~~vVs~tyqsIs~~~La~~LG~ls~~el~~~v~~ 175 (217)
..+-...+..|...+... .+....+..+| ++.+.+..++..
T Consensus 10 ~r~T~~~~~~i~~~~~~~---~s~~~vA~~~~-vs~~TV~ri~~~ 50 (52)
T PF13542_consen 10 CRITKRLEQYILKLLRES---RSFKDVARELG-VSWSTVRRIFDR 50 (52)
T ss_pred CcHHHHHHHHHHHHHhhc---CCHHHHHHHHC-CCHHHHHHHHHh
Confidence 445555666666655544 78899999997 999988887654
No 86
>KOG2582|consensus
Probab=26.47 E-value=2.7e+02 Score=26.39 Aligned_cols=58 Identities=17% Similarity=0.236 Sum_probs=37.8
Q ss_pred HHHHHHHHHHHHHhcccccHHHHHH--hhcCCCHHHHHHHHHH---cC--ceEeCCc-eEEeCCCCccc
Q psy5242 135 DSIRKFVCHVVGITFQTIDKKLLSE--LLDGVEDSTLRLWVKK---YG--WKELDNG-YIFIANQDENI 195 (217)
Q Consensus 135 d~IR~~I~~vVs~tyqsIs~~~La~--~LG~ls~~el~~~v~~---~G--Wt~~~~g-~v~p~n~en~~ 195 (217)
.+.-++-..-...||.+++++..++ .|+ +.+|++++|-+ .| .+. -+| +.|--||+...
T Consensus 301 ~sl~k~nI~rltktF~sLsL~dIA~~vQLa--~~qevek~Ilqmie~~~i~a~-iNG~v~f~~n~e~~~ 366 (422)
T KOG2582|consen 301 SSLYKKNIQRLTKTFLSLSLSDIASRVQLA--SAQEVEKYILQMIEDGEIFAS-INGMVFFTDNPEKYN 366 (422)
T ss_pred HHHHHHHHHHHHHHHHHhhHHHHHHHHHhc--chHHHHHHHHHHhccCceEEE-ecceEEEecCcccCC
Confidence 3344444455889999999999999 564 56677777664 23 333 346 56666765543
No 87
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=26.16 E-value=94 Score=20.64 Aligned_cols=24 Identities=33% Similarity=0.656 Sum_probs=20.2
Q ss_pred cHHHHHHhhcCCCHHHHHHHHHHcC
Q psy5242 153 DKKLLSELLDGVEDSTLRLWVKKYG 177 (217)
Q Consensus 153 s~~~La~~LG~ls~~el~~~v~~~G 177 (217)
+...+++.+| ++...+..|.++.|
T Consensus 2 s~~eva~~~g-vs~~tlr~w~~~~g 25 (68)
T cd01104 2 TIGAVARLTG-VSPDTLRAWERRYG 25 (68)
T ss_pred CHHHHHHHHC-cCHHHHHHHHHhCC
Confidence 5678999997 99999999987654
No 88
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=25.99 E-value=1.3e+02 Score=20.20 Aligned_cols=29 Identities=21% Similarity=0.284 Sum_probs=23.6
Q ss_pred hcccccHHHHHHhhcCCCHHHHHHHHHHcC
Q psy5242 148 TFQTIDKKLLSELLDGVEDSTLRLWVKKYG 177 (217)
Q Consensus 148 tyqsIs~~~La~~LG~ls~~el~~~v~~~G 177 (217)
.|=..+....|.-|| ++...|+..|.+.|
T Consensus 12 ~~fhlp~~eAA~~Lg-v~~T~LKr~CR~~G 40 (52)
T PF02042_consen 12 QYFHLPIKEAAKELG-VSVTTLKRRCRRLG 40 (52)
T ss_pred HHhCCCHHHHHHHhC-CCHHHHHHHHHHcC
Confidence 355678888888887 88889999999877
No 89
>KOG2745|consensus
Probab=25.04 E-value=83 Score=28.57 Aligned_cols=43 Identities=19% Similarity=0.338 Sum_probs=37.8
Q ss_pred ChHHHHHHhhcCCchhhhccchHHHHHHHHHHHHHHhcccccHHHHHHhhcC
Q psy5242 112 KFTQFWSRMHTIPDLFLNIEGFNDSIRKFVCHVVGITFQTIDKKLLSELLDG 163 (217)
Q Consensus 112 ~F~~FW~~l~~~~~l~~~i~gFed~IR~~I~~vVs~tyqsIs~~~La~~LG~ 163 (217)
+...||..++. +|.|++++-++.+++.-|.=|+.-.++++.|.
T Consensus 129 ~~~sF~~vik~---------t~rd~v~~~~~v~~ahPFhVi~~R~maQfVGr 171 (321)
T KOG2745|consen 129 DAESFKKVIKR---------TFRDSVIRVVAVVAAHPFHVISLRQMAQFVGR 171 (321)
T ss_pred HHHHHHHHHHH---------hHHHHHHHHHHHhhcCceeeeeHHHHHHHHcc
Confidence 55668877764 78999999999999999999999999999984
No 90
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=24.96 E-value=1.3e+02 Score=18.74 Aligned_cols=35 Identities=20% Similarity=0.318 Sum_probs=21.8
Q ss_pred HHHHHHHHHHHhcccccHHHHHHhhcCCCHHHHHHHHHH
Q psy5242 137 IRKFVCHVVGITFQTIDKKLLSELLDGVEDSTLRLWVKK 175 (217)
Q Consensus 137 IR~~I~~vVs~tyqsIs~~~La~~LG~ls~~el~~~v~~ 175 (217)
.|..|..++.. -.+...++..|| +|...+..|++.
T Consensus 6 ~R~~ii~l~~~---G~s~~~ia~~lg-vs~~Tv~~w~kr 40 (50)
T PF13384_consen 6 RRAQIIRLLRE---GWSIREIAKRLG-VSRSTVYRWIKR 40 (50)
T ss_dssp ----HHHHHHH---T--HHHHHHHHT-S-HHHHHHHHT-
T ss_pred HHHHHHHHHHC---CCCHHHHHHHHC-cCHHHHHHHHHH
Confidence 34455555544 788889999997 999999999875
No 91
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=24.90 E-value=1.1e+02 Score=20.41 Aligned_cols=24 Identities=25% Similarity=0.318 Sum_probs=19.7
Q ss_pred cHHHHHHhhcCCCHHHHHHHHHHcCc
Q psy5242 153 DKKLLSELLDGVEDSTLRLWVKKYGW 178 (217)
Q Consensus 153 s~~~La~~LG~ls~~el~~~v~~~GW 178 (217)
+...+++.+| ++.+.+..|.+ .||
T Consensus 2 s~~eva~~~g-vs~~tlr~~~~-~gl 25 (70)
T smart00422 2 TIGEVAKLAG-VSVRTLRYYER-IGL 25 (70)
T ss_pred CHHHHHHHHC-cCHHHHHHHHH-CCC
Confidence 5678999997 99999999965 455
No 92
>PF04147 Nop14: Nop14-like family ; InterPro: IPR007276 Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production [].
Probab=24.13 E-value=4.8e+02 Score=27.02 Aligned_cols=23 Identities=9% Similarity=0.478 Sum_probs=17.7
Q ss_pred CCCccH-HHHHHHHHHHHhCChHH
Q psy5242 93 CKEDPI-DQIIYLADLLESCKFTQ 115 (217)
Q Consensus 93 ~~~~~i-~~l~~L~~lLe~c~F~~ 115 (217)
..||-+ +.+..++++|.+|++..
T Consensus 558 ~~HpVVTPalllm~~~L~q~~v~s 581 (840)
T PF04147_consen 558 FRHPVVTPALLLMSEYLSQCRVRS 581 (840)
T ss_pred ccCcchhHHHHHHHHHHhcCCCCC
Confidence 345544 77899999999998863
No 93
>PF03683 UPF0175: Uncharacterised protein family (UPF0175); InterPro: IPR005368 This entry contains small proteins of unknown function.
Probab=23.94 E-value=1.2e+02 Score=21.47 Aligned_cols=47 Identities=15% Similarity=0.098 Sum_probs=33.2
Q ss_pred chHHHHHHHHHHHHHHhcccccHHHHHHhhcCCCHHHHHHHHHHcCceE
Q psy5242 132 GFNDSIRKFVCHVVGITFQTIDKKLLSELLDGVEDSTLRLWVKKYGWKE 180 (217)
Q Consensus 132 gFed~IR~~I~~vVs~tyqsIs~~~La~~LG~ls~~el~~~v~~~GWt~ 180 (217)
.|+..+|..++-.. =--.+||...-++++| ++--++.+.+.+.|=.+
T Consensus 16 e~~~~~r~~~Ai~l-Y~~g~iS~gkAAelag-~s~~eF~~~L~~~gI~~ 62 (76)
T PF03683_consen 16 EFEQELREELAIKL-YEEGKISLGKAAELAG-MSRWEFLELLKERGIPI 62 (76)
T ss_pred HHHHHHHHHHHHHH-HHcCCCCHHHHHHHhC-CCHHHHHHHHHHCCCCC
Confidence 45555554433211 1345799999999998 99999999999988543
No 94
>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=23.77 E-value=1.2e+02 Score=20.22 Aligned_cols=24 Identities=25% Similarity=0.315 Sum_probs=20.1
Q ss_pred ccccHHHHHHhhcCCCHHHHHHHHH
Q psy5242 150 QTIDKKLLSELLDGVEDSTLRLWVK 174 (217)
Q Consensus 150 qsIs~~~La~~LG~ls~~el~~~v~ 174 (217)
+.++...||+-|| ++...+...+.
T Consensus 22 R~~tl~elA~~lg-is~st~~~~LR 45 (53)
T PF04967_consen 22 RRITLEELAEELG-ISKSTVSEHLR 45 (53)
T ss_pred CcCCHHHHHHHhC-CCHHHHHHHHH
Confidence 4788999999997 89988877665
No 95
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=23.29 E-value=2.5e+02 Score=20.41 Aligned_cols=65 Identities=8% Similarity=0.003 Sum_probs=41.1
Q ss_pred HhcccccHHHHHHhhcCCCHHHHHHHHHH-cCceEeC--Cce------EEeCCCCccccccccccccccchHHHHhh
Q psy5242 147 ITFQTIDKKLLSELLDGVEDSTLRLWVKK-YGWKELD--NGY------IFIANQDENIKTKNITEKIEFENAATIMT 214 (217)
Q Consensus 147 ~tyqsIs~~~La~~LG~ls~~el~~~v~~-~GWt~~~--~g~------v~p~n~en~~k~~~i~E~i~~~~~~~~~~ 214 (217)
.-...++.+.++.-+| +|...+....++ .|.+..+ ... -.-.+++ ..-+.|.+...|.+-+.+.+
T Consensus 17 ~~~~~~~~~~lA~~~~-~S~~~l~r~f~~~~g~s~~~~i~~~Rl~~a~~~L~~~~--~~i~~iA~~~Gf~~~s~f~~ 90 (107)
T PRK10219 17 HIDQPLNIDVVAKKSG-YSKWYLQRMFRTVTHQTLGDYIRQRRLLLAAVELRTTE--RPIFDIAMDLGYVSQQTFSR 90 (107)
T ss_pred hcCCCCCHHHHHHHHC-CCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHccC--CCHHHHHHHHCCCCHHHHHH
Confidence 3345699999999997 999999888887 4887621 000 0011222 22345777777776665544
No 96
>PRK13696 hypothetical protein; Provisional
Probab=23.23 E-value=2.3e+02 Score=19.78 Aligned_cols=38 Identities=13% Similarity=0.201 Sum_probs=27.9
Q ss_pred cchHHHHHHHHHHHHHHhcccccHHHHHHhhcCCCHHHHHHHHH
Q psy5242 131 EGFNDSIRKFVCHVVGITFQTIDKKLLSELLDGVEDSTLRLWVK 174 (217)
Q Consensus 131 ~gFed~IR~~I~~vVs~tyqsIs~~~La~~LG~ls~~el~~~v~ 174 (217)
..|.|-||+.+ .. ..-....|..+.|-++++++++.-.
T Consensus 23 ~SFSevi~~L~-~~-----~~~~~~~l~~~~Gil~dee~~e~~~ 60 (62)
T PRK13696 23 KSFSEVIRELI-EK-----KKGNLDKLMKAFGILSEEEAEELKK 60 (62)
T ss_pred CCHHHHHHHHH-HH-----hhccHHHHHHHHCCCCHHHHHHHHh
Confidence 37888888877 32 2334778889999889999887643
No 97
>COG4199 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.99 E-value=1.7e+02 Score=25.05 Aligned_cols=106 Identities=20% Similarity=0.396 Sum_probs=62.1
Q ss_pred HHHHHHHHHHhCChHHHHHHhhcCCc-hhhhccchHHHHHHHHHHHHHHhccccc----HHHHHHhhcCCCHHHHHHHHH
Q psy5242 100 QIIYLADLLESCKFTQFWSRMHTIPD-LFLNIEGFNDSIRKFVCHVVGITFQTID----KKLLSELLDGVEDSTLRLWVK 174 (217)
Q Consensus 100 ~l~~L~~lLe~c~F~~FW~~l~~~~~-l~~~i~gFed~IR~~I~~vVs~tyqsIs----~~~La~~LG~ls~~el~~~v~ 174 (217)
.+-.|.+++..-+|.+.+-....+.+ +++.+|. .|..++.-.-+ ..|+.-+ ..+|+.+|| .+.+.+...++
T Consensus 63 ~~~~l~~~~~e~~f~rIYf~~~~~e~~yltg~pt-Rd~Fa~lYk~i--~kf~eFdi~k~~~~La~~l~-~~~e~l~fM~K 138 (201)
T COG4199 63 SLEQLSNLFQEKDFSRIYFKFDISEDYYLTGIPT-RDHFAKLYKFI--YKFPEFDIRKKGKRLAQYLG-WNKETLVFMIK 138 (201)
T ss_pred cHHHHHHHHhccCcceEEEEeccCCCeeecCCCc-HHHHHHHHHHH--HhcCCccHHHHHHHHHHHcC-CCHHHHHHHHH
Confidence 35567888888899886655544333 3333332 33344332222 2233322 467999997 88888777766
Q ss_pred ---HcCceEeCCceEEeCCCCccccccccccccccchHHHH
Q psy5242 175 ---KYGWKELDNGYIFIANQDENIKTKNITEKIEFENAATI 212 (217)
Q Consensus 175 ---~~GWt~~~~g~v~p~n~en~~k~~~i~E~i~~~~~~~~ 212 (217)
+.|.---+||++.+.. .+++++|.|...+-+....
T Consensus 139 VF~eL~FVtiddGlitvn~---~a~KR~ideS~iYQ~kqe~ 176 (201)
T COG4199 139 VFFELGFVTIDDGLITVNQ---QAEKREIDESQIYQQKQEL 176 (201)
T ss_pred HHHHcceeEeeCCeEEecc---CccccCCcHHHHHHHHHHH
Confidence 5898544678655533 2566677666555444443
No 98
>PF14791 DNA_pol_B_thumb: DNA polymerase beta thumb ; PDB: 1HUZ_A 3K75_D 1HUO_A 2BPC_A 1RPL_A 1NOM_A 1ZQX_A 1ZQU_A 1ZQZ_A 1ZQV_A ....
Probab=22.75 E-value=1.4e+02 Score=20.64 Aligned_cols=27 Identities=26% Similarity=0.309 Sum_probs=19.3
Q ss_pred HHhhcCCCH---HHHHHHHHHcCceEeCCceE
Q psy5242 158 SELLDGVED---STLRLWVKKYGWKELDNGYI 186 (217)
Q Consensus 158 a~~LG~ls~---~el~~~v~~~GWt~~~~g~v 186 (217)
--|.| |. ..++.++.+.||++++.|..
T Consensus 3 l~~TG--s~~fnr~lR~~A~~~g~~L~~~Gl~ 32 (64)
T PF14791_consen 3 LYFTG--SKEFNRDLRQYAKKKGMKLSEYGLF 32 (64)
T ss_dssp HHHHS---HHHHHHHHHHHHHTTEEEESSEEE
T ss_pred ccccC--CHHHHHHHHHHHHHcCCeeCccccc
Confidence 34666 33 46889999999999877743
No 99
>PF05295 Luciferase_N: Luciferase/LBP N-terminal domain; InterPro: IPR007959 Proteins in this entry belong to a family of dinoflagellate luciferase and luciferin binding proteins. Luciferase is involved in catalysing the light emitting reaction in bioluminescence and luciferin binding protein (LBP) is known to bind to luciferin (the substrate for luciferase) to stop it reacting with the enzyme and therefore switching off the bioluminescence function. The expression of these two proteins is controlled by a circadian clock at the translational level, with synthesis and degradation occurring on a daily basis []. This entry consists of a presumed N-terminal domain that is conserved between dinoflagellate luciferase and luciferin binding proteins. This domain is not, however, the catalytic part of the protein. It has been suggested that this region may mediate an interaction between LBP and Luciferase or their association with the vacuolar membrane []. More information about these proteins can be found at Protein of the Month: Luciferase [].
Probab=22.72 E-value=22 Score=25.92 Aligned_cols=26 Identities=15% Similarity=0.560 Sum_probs=18.8
Q ss_pred hCChHHHHHHhhcC----CchhhhccchHH
Q psy5242 110 SCKFTQFWSRMHTI----PDLFLNIEGFND 135 (217)
Q Consensus 110 ~c~F~~FW~~l~~~----~~l~~~i~gFed 135 (217)
-.+|+.||+.-+.+ .|++..+++|.+
T Consensus 32 vsDFAn~WTs~eyE~GvqdDIi~kv~~f~~ 61 (82)
T PF05295_consen 32 VSDFANYWTSAEYEKGVQDDIISKVAAFQN 61 (82)
T ss_pred HHHHHhhhhHHHHHhhhHHHHHHHhhcccc
Confidence 36899999987643 567777777763
No 100
>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=22.70 E-value=2.5e+02 Score=18.80 Aligned_cols=46 Identities=20% Similarity=0.213 Sum_probs=34.7
Q ss_pred chHHHHHHHHHHHHHHhcccccHHHHHHhhcCCCHHHHHHHHH---HcCceE
Q psy5242 132 GFNDSIRKFVCHVVGITFQTIDKKLLSELLDGVEDSTLRLWVK---KYGWKE 180 (217)
Q Consensus 132 gFed~IR~~I~~vVs~tyqsIs~~~La~~LG~ls~~el~~~v~---~~GWt~ 180 (217)
||.+.=.+....++ .....+...+++-+| ++...+...++ +.||-.
T Consensus 5 gLs~~E~~vy~~Ll--~~~~~t~~eIa~~l~-i~~~~v~~~L~~L~~~GlV~ 53 (68)
T PF01978_consen 5 GLSENEAKVYLALL--KNGPATAEEIAEELG-ISRSTVYRALKSLEEKGLVE 53 (68)
T ss_dssp CHHHHHHHHHHHHH--HHCHEEHHHHHHHHT-SSHHHHHHHHHHHHHTTSEE
T ss_pred CcCHHHHHHHHHHH--HcCCCCHHHHHHHHC-cCHHHHHHHHHHHHHCCCEE
Confidence 55555445455555 788899999999997 99988888877 479954
No 101
>PF14561 TPR_20: Tetratricopeptide repeat; PDB: 3QOU_A 2R5S_A 3QDN_B.
Probab=22.54 E-value=1.9e+02 Score=21.10 Aligned_cols=58 Identities=22% Similarity=0.289 Sum_probs=43.3
Q ss_pred CCCchhHHHHHHHHHHhccccchHhhHHHHHhhhcCCCCChHHHHHHHHHHhhcCCCcc
Q psy5242 22 NPEHLSTLEKYVEVQCAENVYDLEANLAVLKLYQFHQNYNMKITSQILLKALTNFPHTD 80 (217)
Q Consensus 22 np~~l~~Le~yv~~Q~~~~~Yd~~aNlalLKLYqfnP~~~~~vv~~ILlkaL~~~P~~D 80 (217)
||.++...-+.-...+..|.|. +|-=.+|++.+-+|+++.+...+-||..+..++..|
T Consensus 18 ~P~D~~ar~~lA~~~~~~g~~e-~Al~~Ll~~v~~dr~~~~~~ar~~ll~~f~~lg~~~ 75 (90)
T PF14561_consen 18 NPDDLDARYALADALLAAGDYE-EALDQLLELVRRDRDYEDDAARKRLLDIFELLGPGD 75 (90)
T ss_dssp STT-HHHHHHHHHHHHHTT-HH-HHHHHHHHHHCC-TTCCCCHHHHHHHHHHHHH-TT-
T ss_pred CCCCHHHHHHHHHHHHHCCCHH-HHHHHHHHHHHhCccccccHHHHHHHHHHHHcCCCC
Confidence 7888887777777777777775 455567888899999999999999999998888765
No 102
>PF13518 HTH_28: Helix-turn-helix domain
Probab=22.27 E-value=2e+02 Score=17.75 Aligned_cols=25 Identities=16% Similarity=0.387 Sum_probs=21.5
Q ss_pred ccccHHHHHHhhcCCCHHHHHHHHHH
Q psy5242 150 QTIDKKLLSELLDGVEDSTLRLWVKK 175 (217)
Q Consensus 150 qsIs~~~La~~LG~ls~~el~~~v~~ 175 (217)
+.-+...++.-+| ++...+..|++.
T Consensus 11 ~g~s~~~~a~~~g-is~~tv~~w~~~ 35 (52)
T PF13518_consen 11 EGESVREIAREFG-ISRSTVYRWIKR 35 (52)
T ss_pred cCCCHHHHHHHHC-CCHhHHHHHHHH
Confidence 3458899999997 899999999985
No 103
>PRK15365 type III secretion system chaperone SseA; Provisional
Probab=22.16 E-value=2.1e+02 Score=21.94 Aligned_cols=36 Identities=14% Similarity=0.036 Sum_probs=31.3
Q ss_pred chhHHHHHHHHHHhc-cccchHhhHHHHHhhhcCCC-C
Q psy5242 25 HLSTLEKYVEVQCAE-NVYDLEANLAVLKLYQFHQN-Y 60 (217)
Q Consensus 25 ~l~~Le~yv~~Q~~~-~~Yd~~aNlalLKLYqfnP~-~ 60 (217)
.+..+.++|.+|+.+ ..+|-.|--++.+|=+..|+ +
T Consensus 27 Kfkq~q~~I~q~L~eRA~~d~kaRE~l~rLd~aFP~G~ 64 (107)
T PRK15365 27 KFHQIRAKVSQQLAERAESPKKSRETESILHNLFPQGV 64 (107)
T ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCcchh
Confidence 455667788888888 59999999999999999999 7
No 104
>PTZ00429 beta-adaptin; Provisional
Probab=22.16 E-value=3.9e+02 Score=27.42 Aligned_cols=28 Identities=14% Similarity=0.153 Sum_probs=20.5
Q ss_pred hHhhHHHHHhhhcCCC-CChHHHHHHHHH
Q psy5242 44 LEANLAVLKLYQFHQN-YNMKITSQILLK 71 (217)
Q Consensus 44 ~~aNlalLKLYqfnP~-~~~~vv~~ILlk 71 (217)
-.|-+|++|||+.+|+ ....-....|.+
T Consensus 158 KtAalai~Kly~~~pelv~~~~~~~~L~~ 186 (746)
T PTZ00429 158 KTAAMGLGKLFHDDMQLFYQQDFKKDLVE 186 (746)
T ss_pred HHHHHHHHHHHhhCcccccccchHHHHHH
Confidence 4578999999999999 654444455555
No 105
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=21.99 E-value=2.6e+02 Score=23.19 Aligned_cols=52 Identities=13% Similarity=0.124 Sum_probs=33.6
Q ss_pred HHHHHHHHHHHHhcc----cccHHHHHHhhcCCCHHHHHHHHH---HcCceEeCCceEEe
Q psy5242 136 SIRKFVCHVVGITFQ----TIDKKLLSELLDGVEDSTLRLWVK---KYGWKELDNGYIFI 188 (217)
Q Consensus 136 ~IR~~I~~vVs~tyq----sIs~~~La~~LG~ls~~el~~~v~---~~GWt~~~~g~v~p 188 (217)
+++.++++.+-.... ..+...+|++|| ++.+.+-..++ +.|+-.-+.+.+.+
T Consensus 150 ~~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG-~sretvsR~L~~L~~~G~I~~~~~~i~I 208 (226)
T PRK10402 150 PLENRLAAFILLTQEGDLYHEKHTQAAEYLG-VSYRHLLYVLAQFIQDGYLKKSKRGYLI 208 (226)
T ss_pred hHHHHHHHHHHhcccCCcccchHHHHHHHHC-CcHHHHHHHHHHHHHCCCEEeeCCEEEE
Confidence 456666666643211 257899999998 89988877766 47985433333333
No 106
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=21.88 E-value=2e+02 Score=17.43 Aligned_cols=31 Identities=26% Similarity=0.291 Sum_probs=24.5
Q ss_pred cccccHHHHHHhhcCCCHHHHHHHHH---HcCceE
Q psy5242 149 FQTIDKKLLSELLDGVEDSTLRLWVK---KYGWKE 180 (217)
Q Consensus 149 yqsIs~~~La~~LG~ls~~el~~~v~---~~GWt~ 180 (217)
-..++...+++.+| ++...+...+. +.||-.
T Consensus 12 ~~~~s~~~l~~~l~-~s~~tv~~~l~~L~~~g~i~ 45 (53)
T smart00420 12 QGKVSVEELAELLG-VSEMTIRRDLNKLEEQGLLT 45 (53)
T ss_pred cCCcCHHHHHHHHC-CCHHHHHHHHHHHHHCCCEE
Confidence 35689999999997 89888777766 478844
No 107
>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=21.80 E-value=2.4e+02 Score=18.59 Aligned_cols=39 Identities=21% Similarity=0.192 Sum_probs=29.2
Q ss_pred HHHHHHHHHhcccccHHHHHHhhcCCCHHHHHHHHH---HcCce
Q psy5242 139 KFVCHVVGITFQTIDKKLLSELLDGVEDSTLRLWVK---KYGWK 179 (217)
Q Consensus 139 ~~I~~vVs~tyqsIs~~~La~~LG~ls~~el~~~v~---~~GWt 179 (217)
..|...+.. -..++...|++.|| +|...+..-+. +.|.-
T Consensus 3 ~~Il~~l~~-~~~~s~~ela~~~~-VS~~TiRRDl~~L~~~g~i 44 (57)
T PF08220_consen 3 QQILELLKE-KGKVSVKELAEEFG-VSEMTIRRDLNKLEKQGLI 44 (57)
T ss_pred HHHHHHHHH-cCCEEHHHHHHHHC-cCHHHHHHHHHHHHHCCCE
Confidence 456666644 58999999999997 99987776655 46763
No 108
>PF04699 P16-Arc: ARP2/3 complex 16 kDa subunit (p16-Arc); InterPro: IPR006789 The Arp2/3 protein complex has been implicated in the control of actin polymerisation. The human complex consists of seven subunits which include the actin related proteins Arp2 and Arp3, and five others referred to as p41-Arc, p34-Arc, p21-Arc, p20-Arc, and p16-Arc. The precise function of p16-Arc is currently unknown. Its structure consists of a single domain containing a bundle of seven alpha helices [, ].; GO: 0030833 regulation of actin filament polymerization, 0005856 cytoskeleton; PDB: 3DWL_G 1TYQ_G 1U2V_G 2P9U_G 2P9L_G 1K8K_G 3DXM_G 2P9N_G 3DXK_G 2P9I_G ....
Probab=21.51 E-value=4.5e+02 Score=21.41 Aligned_cols=71 Identities=11% Similarity=0.107 Sum_probs=51.5
Q ss_pred HHHHHHHHHHHhCChHHHHHHhhcCCchhhhccchHHHHHHHHHHHHHHhcccccHHHHHHhhcCCCHHHHHHHHH
Q psy5242 99 DQIIYLADLLESCKFTQFWSRMHTIPDLFLNIEGFNDSIRKFVCHVVGITFQTIDKKLLSELLDGVEDSTLRLWVK 174 (217)
Q Consensus 99 ~~l~~L~~lLe~c~F~~FW~~l~~~~~l~~~i~gFed~IR~~I~~vVs~tyqsIs~~~La~~LG~ls~~el~~~v~ 174 (217)
.....+.++|.+.++.+-=+..-+++.+-.. +.++.....+|-....+|..+.+..+++.|+.++..-+++
T Consensus 38 ~~~~qvr~ll~~g~~~~ALk~aL~npP~~~k-----~~~K~~~~~~Vl~vL~s~k~sdI~~~v~~L~~~~~D~LMK 108 (152)
T PF04699_consen 38 PKEQQVRQLLSSGDNEEALKAALENPPYGSK-----DAVKDRALQLVLEVLTSIKSSDIENAVKSLDSDQQDILMK 108 (152)
T ss_dssp GTHHHHHHHHHCT-HHHHHHHHTSS--TT-S------HHHHHHHHHHHHHHHCS-GGGHHHHHCCS-HHHHHHHHH
T ss_pred hhHHHHHHHHhCCCHHHHHHHhccCCCcCCC-----cchHHHHHHHHHHHHHHccHHHHHHHHHhCCHHHHhHHHH
Confidence 5566778888899998866666666766544 3788888999999999999999999998899988766665
No 109
>PF10410 DnaB_bind: DnaB-helicase binding domain of primase; InterPro: IPR019475 This entry represents the C-terminal region three-helical domain of DNA primase []. Primases synthesise short RNA strands on single-stranded DNA templates, thereby generating the hybrid duplexes required for the initiation of synthesis by DNA polymerases. Primases are recruited to single-stranded DNA by helicases - this domain binds DnaB-helicase []. It is associated with the Toprim domain IPR006171 from INTERPRO, which is the central catalytic core. ; GO: 0016779 nucleotidyltransferase activity; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A.
Probab=21.40 E-value=49 Score=21.55 Aligned_cols=52 Identities=10% Similarity=0.040 Sum_probs=33.3
Q ss_pred HHHHhhcCCc--hhhhccchHHHHHHHHHHHHHHhcccccHHHHHHhhcCCCHHH
Q psy5242 116 FWSRMHTIPD--LFLNIEGFNDSIRKFVCHVVGITFQTIDKKLLSELLDGVEDST 168 (217)
Q Consensus 116 FW~~l~~~~~--l~~~i~gFed~IR~~I~~vVs~tyqsIs~~~La~~LG~ls~~e 168 (217)
+|+.+....+ -...-..|...+...|..+=+..++......+++.+| ++.++
T Consensus 5 ~~~~l~~~~dl~~~egk~~~~~~~~~~i~~i~~~i~r~~y~~~la~~~~-i~~~~ 58 (59)
T PF10410_consen 5 LIERLSKGYDLDTPEGKAEAVREAAPLIAQIPDPIERELYIRELAERLG-ISEDA 58 (59)
T ss_dssp HHHHHGGGS-TTSHHHHHHHHHHHHHHHTT--SHHHHHHHHHHHHHHCT--SSTT
T ss_pred HHHHHHhcCCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHhC-cCccc
Confidence 3444544322 2345556677777888888788899999999999997 77654
No 110
>PF15297 CKAP2_C: Cytoskeleton-associated protein 2 C-terminus
Probab=21.29 E-value=62 Score=30.11 Aligned_cols=61 Identities=15% Similarity=0.261 Sum_probs=37.5
Q ss_pred CcchhhhhhccCCCCCCCccHHHHHHHHHHH-HhCChHHHHHHhhc----CCchhhhccchHHHHH
Q psy5242 78 HTDFILCKCLLSKDLCKEDPIDQIIYLADLL-ESCKFTQFWSRMHT----IPDLFLNIEGFNDSIR 138 (217)
Q Consensus 78 ~~DF~lc~~LIp~~~~~~~~i~~l~~L~~lL-e~c~F~~FW~~l~~----~~~l~~~i~gFed~IR 138 (217)
+.=|+=|+-||.+--..++-+..|-.|-... ..-+|+.||-++.. ...+-..|+-||++|+
T Consensus 103 n~tlsECl~Li~eGcp~eei~~~L~~li~~IP~A~K~aKYWIC~Arl~~~~~~~e~vi~iyEeAi~ 168 (353)
T PF15297_consen 103 NKTLSECLNLIEEGCPKEEILATLSDLIKNIPDAKKLAKYWICLARLEPRTGPIEDVIAIYEEAIL 168 (353)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHH
Confidence 4457889999998776444333333333333 56789999987754 2334455667776654
No 111
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=21.17 E-value=2.2e+02 Score=17.64 Aligned_cols=31 Identities=26% Similarity=0.230 Sum_probs=24.6
Q ss_pred cccccHHHHHHhhcCCCHHHHHHHHH---HcCceE
Q psy5242 149 FQTIDKKLLSELLDGVEDSTLRLWVK---KYGWKE 180 (217)
Q Consensus 149 yqsIs~~~La~~LG~ls~~el~~~v~---~~GWt~ 180 (217)
-..++...+++.|| ++...+...++ +.||-.
T Consensus 8 ~~~~~~~~i~~~l~-is~~~v~~~l~~L~~~g~i~ 41 (66)
T smart00418 8 EGELCVCELAEILG-LSQSTVSHHLKKLREAGLVE 41 (66)
T ss_pred cCCccHHHHHHHHC-CCHHHHHHHHHHHHHCCCee
Confidence 56788889999997 88888877777 478854
No 112
>PF06708 DUF1195: Protein of unknown function (DUF1195); InterPro: IPR010608 This family consists of several plant specific hypothetical proteins of around 160 residues in length. The function of this family is unknown.
Probab=21.02 E-value=73 Score=25.94 Aligned_cols=84 Identities=12% Similarity=0.169 Sum_probs=54.8
Q ss_pred CChHHHHHHHHHHhhcCC---------CcchhhhhhccCCCCCCC----------ccHHHHHHHHHHHHhCChHHHHHHh
Q psy5242 60 YNMKITSQILLKALTNFP---------HTDFILCKCLLSKDLCKE----------DPIDQIIYLADLLESCKFTQFWSRM 120 (217)
Q Consensus 60 ~~~~vv~~ILlkaL~~~P---------~~DF~lc~~LIp~~~~~~----------~~i~~l~~L~~lLe~c~F~~FW~~l 120 (217)
|+.=+.+-|||.|+-.+= ..|++....=++..+.++ .-+++.|.+...=..-+.|.||+..
T Consensus 37 YK~WaLaAIlLLAfWSM~tgsvtLrwS~g~l~~~~~dl~~~~~dDlDvLEmEeREKvVr~MWDvYt~s~~vrLPrFWqEA 116 (157)
T PF06708_consen 37 YKFWALAAILLLAFWSMFTGSVTLRWSAGNLNSVSDDLDFPIHDDLDVLEMEEREKVVRHMWDVYTRSRRVRLPRFWQEA 116 (157)
T ss_pred hHHHHHHHHHHHHHHHHhheeeEEEeccCcccccccccCCcccccccHHHHHHHHHHHHHHHHHhcCCCCccCchHHHHH
Confidence 555567778888775432 244433333344444321 1468889888888889999999976
Q ss_pred hc--CCchhhhccchHHHHHHHHHH
Q psy5242 121 HT--IPDLFLNIEGFNDSIRKFVCH 143 (217)
Q Consensus 121 ~~--~~~l~~~i~gFed~IR~~I~~ 143 (217)
=+ ++++..++++..|.-=..|++
T Consensus 117 FeAAYe~L~sD~~~VrdaAisEIAk 141 (157)
T PF06708_consen 117 FEAAYEELASDVPQVRDAAISEIAK 141 (157)
T ss_pred HHHHHHHHhccCcchhHHHHHHHHH
Confidence 33 578899999988875555554
No 113
>KOG2140|consensus
Probab=21.00 E-value=2.8e+02 Score=27.70 Aligned_cols=102 Identities=17% Similarity=0.231 Sum_probs=57.9
Q ss_pred HHHHHHHHHhhcCCC--cchhhhhhccCCCCCCCccHHHHHHHHHHHHhCChHHHHHHhhcCCchhhhccchHHHHHHHH
Q psy5242 64 ITSQILLKALTNFPH--TDFILCKCLLSKDLCKEDPIDQIIYLADLLESCKFTQFWSRMHTIPDLFLNIEGFNDSIRKFV 141 (217)
Q Consensus 64 vv~~ILlkaL~~~P~--~DF~lc~~LIp~~~~~~~~i~~l~~L~~lLe~c~F~~FW~~l~~~~~l~~~i~gFed~IR~~I 141 (217)
+.|.-.+||-++-|. |=|.+..++|.... |.| |.+|-.+---.|=...+.+.. +..-++-+||
T Consensus 198 l~crsv~~aq~asp~ft~vyaALvAviNskf---P~I------gElLlkrLilqf~r~f~RnDk------~~c~~~~kfi 262 (739)
T KOG2140|consen 198 LLCRSVMQAQAASPGFTPVYAALVAVINSKF---PQI------GELLLKRLILQFKRSFRRNDK------VSCLNASKFI 262 (739)
T ss_pred hhHHHHHHHHhcCCCCcHHHHHHHHHHccCC---chH------HHHHHHHHHHHHHHHhcccch------HHHHHHHHHH
Confidence 445566777666554 44445555555443 233 333333333344444444321 1223456788
Q ss_pred HHHHHH--hcccccHHHHHHhhcCCCH---HHHHHHHHHcCceE
Q psy5242 142 CHVVGI--TFQTIDKKLLSELLDGVED---STLRLWVKKYGWKE 180 (217)
Q Consensus 142 ~~vVs~--tyqsIs~~~La~~LG~ls~---~el~~~v~~~GWt~ 180 (217)
+|+|.+ +..=+-++.|.-+|+..++ +-+-.|+++|||++
T Consensus 263 ahLinq~VahEIv~Leil~lLLe~PTddSvevaI~flkecGakL 306 (739)
T KOG2140|consen 263 AHLINQQVAHEIVALEILTLLLERPTDDSVEVAIAFLKECGAKL 306 (739)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHH
Confidence 888864 5555677788888875444 34667788999987
No 114
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=20.92 E-value=90 Score=20.29 Aligned_cols=28 Identities=21% Similarity=0.178 Sum_probs=22.2
Q ss_pred cccHHHHHHhhcCCCHHHHHHHH-HHcCce
Q psy5242 151 TIDKKLLSELLDGVEDSTLRLWV-KKYGWK 179 (217)
Q Consensus 151 sIs~~~La~~LG~ls~~el~~~v-~~~GWt 179 (217)
.|++..||.-|| ++.+++-+.+ ++.|=.
T Consensus 3 ~i~V~elAk~l~-v~~~~ii~~l~~~~Gi~ 31 (54)
T PF04760_consen 3 KIRVSELAKELG-VPSKEIIKKLFKELGIM 31 (54)
T ss_dssp EE-TTHHHHHHS-SSHHHHHHHH-HHHTS-
T ss_pred ceEHHHHHHHHC-cCHHHHHHHHHHhCCcC
Confidence 577889999997 9999988888 558876
No 115
>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=20.90 E-value=2.1e+02 Score=20.95 Aligned_cols=43 Identities=9% Similarity=0.155 Sum_probs=31.8
Q ss_pred HHHHHHHHHHHHH---hcccccHHHHHHhhcCCCHHHHHHHHHH---cCc
Q psy5242 135 DSIRKFVCHVVGI---TFQTIDKKLLSELLDGVEDSTLRLWVKK---YGW 178 (217)
Q Consensus 135 d~IR~~I~~vVs~---tyqsIs~~~La~~LG~ls~~el~~~v~~---~GW 178 (217)
..+++.|+.++.. .=.=++++.+++-|| ++.+++++.|.. .|+
T Consensus 46 ~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~-~~~~~v~~al~~L~~eG~ 94 (102)
T PF08784_consen 46 SPLQDKVLNFIKQQPNSEEGVHVDEIAQQLG-MSENEVRKALDFLSNEGH 94 (102)
T ss_dssp -HHHHHHHHHHHC----TTTEEHHHHHHHST-S-HHHHHHHHHHHHHTTS
T ss_pred CHHHHHHHHHHHhcCCCCCcccHHHHHHHhC-cCHHHHHHHHHHHHhCCe
Confidence 4478888888887 233499999999996 999999988874 565
No 116
>COG2074 2-phosphoglycerate kinase [Carbohydrate transport and metabolism]
Probab=20.56 E-value=85 Score=28.37 Aligned_cols=44 Identities=23% Similarity=0.409 Sum_probs=32.9
Q ss_pred HHHHHH--HHHHHHhCChHHHHHHhhcCCchhhhccchHHHHHHHHH
Q psy5242 98 IDQIIY--LADLLESCKFTQFWSRMHTIPDLFLNIEGFNDSIRKFVC 142 (217)
Q Consensus 98 i~~l~~--L~~lLe~c~F~~FW~~l~~~~~l~~~i~gFed~IR~~I~ 142 (217)
+.++.. +.-.|.+.-|.+ |++++..++--+.++||+|..+....
T Consensus 128 lR~ii~~~l~PtLh~Ssy~A-wkalr~~~~~~piiaGF~dqa~~V~~ 173 (299)
T COG2074 128 LRKIISPELLPTLHTSSYDA-WKALRDPTDENPIIAGFEDQASAVMV 173 (299)
T ss_pred HHHhCCHHhcchhhHhHHHH-HHHhcCCCCCcchhhhHHHHhHHHHH
Confidence 355554 777788888876 99998866666699999998775443
No 117
>COG1753 Predicted antotoxin, copG family [Signal transduction mechanisms]
Probab=20.56 E-value=2.3e+02 Score=20.43 Aligned_cols=40 Identities=18% Similarity=0.258 Sum_probs=27.6
Q ss_pred ccchHHHHHHHHHHHHHHhcccccHHHHHHhhcCCCHHHHHHHHHH
Q psy5242 130 IEGFNDSIRKFVCHVVGITFQTIDKKLLSELLDGVEDSTLRLWVKK 175 (217)
Q Consensus 130 i~gFed~IR~~I~~vVs~tyqsIs~~~La~~LG~ls~~el~~~v~~ 175 (217)
=..|.|-||+.+- -.+=..+.|+.+.|.++++++++.+.+
T Consensus 23 ~~SFSdvI~~l~~------kKr~~levl~~~~g~~s~eEvek~~~e 62 (74)
T COG1753 23 KESFSDVIRELIE------KKRGNLEVLMRAFGTLSEEEVEKIKKE 62 (74)
T ss_pred cccHHHHHHHHHH------HhhhhHHHHHHHhCCCcHHHHHHHHHH
Confidence 3466666665543 233456678888898999999998764
No 118
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=20.36 E-value=1.2e+02 Score=20.13 Aligned_cols=22 Identities=36% Similarity=0.499 Sum_probs=18.5
Q ss_pred cHHHHHHhhcCCCHHHHHHHHHH
Q psy5242 153 DKKLLSELLDGVEDSTLRLWVKK 175 (217)
Q Consensus 153 s~~~La~~LG~ls~~el~~~v~~ 175 (217)
+...++..+| ++...+..|.++
T Consensus 2 ti~eva~~~g-vs~~tlr~y~~~ 23 (69)
T PF13411_consen 2 TIKEVAKLLG-VSPSTLRYYERE 23 (69)
T ss_dssp EHHHHHHHTT-TTHHHHHHHHHT
T ss_pred cHHHHHHHHC-cCHHHHHHHHHh
Confidence 4678999997 999999999653
No 119
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=20.32 E-value=1.5e+02 Score=19.78 Aligned_cols=24 Identities=33% Similarity=0.537 Sum_probs=19.6
Q ss_pred cHHHHHHhhcCCCHHHHHHHHHHcC
Q psy5242 153 DKKLLSELLDGVEDSTLRLWVKKYG 177 (217)
Q Consensus 153 s~~~La~~LG~ls~~el~~~v~~~G 177 (217)
+...+++.+| ++...+..|.++-|
T Consensus 2 ~i~evA~~~g-vs~~tlR~~~~~g~ 25 (67)
T cd04764 2 TIKEVSEIIG-VKPHTLRYYEKEFN 25 (67)
T ss_pred CHHHHHHHHC-cCHHHHHHHHHhcC
Confidence 5678999997 99999999976533
Done!