Query 018827
Match_columns 350
No_of_seqs 185 out of 375
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 04:22:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018827.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018827hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2829 E2F-like protein [Tran 100.0 5.2E-66 1.1E-70 491.2 21.8 203 93-296 39-243 (326)
2 KOG2577 Transcription factor E 100.0 6.1E-33 1.3E-37 271.6 17.5 157 94-277 67-240 (354)
3 PF08781 DP: Transcription fac 100.0 7.7E-32 1.7E-36 236.1 7.7 125 185-309 1-125 (142)
4 PF02319 E2F_TDP: E2F/DP famil 99.7 9.1E-19 2E-23 136.7 3.4 67 96-178 2-71 (71)
5 KOG2578 Transcription factor E 98.8 5.7E-09 1.2E-13 102.1 5.2 69 124-193 31-100 (388)
6 KOG2578 Transcription factor E 96.7 0.00054 1.2E-08 67.9 1.2 74 96-180 157-239 (388)
7 PF01978 TrmB: Sugar-specific 91.5 0.17 3.7E-06 38.3 2.7 57 99-176 5-62 (68)
8 PF05402 PqqD: Coenzyme PQQ sy 85.4 1.4 3E-05 33.0 4.0 55 99-168 14-68 (68)
9 COG1378 Predicted transcriptio 84.2 3.3 7.1E-05 39.8 6.9 36 146-181 39-75 (247)
10 COG3355 Predicted transcriptio 75.7 12 0.00026 33.0 7.0 55 99-174 24-79 (126)
11 smart00420 HTH_DEOR helix_turn 73.0 5.2 0.00011 27.4 3.4 48 106-174 4-51 (53)
12 PF11315 Med30: Mediator compl 67.7 28 0.00061 31.7 7.7 66 152-224 65-140 (150)
13 smart00418 HTH_ARSR helix_turn 64.7 6.8 0.00015 27.3 2.6 42 107-170 2-43 (66)
14 smart00346 HTH_ICLR helix_turn 60.5 15 0.00033 28.4 4.1 45 105-170 8-53 (91)
15 PF09012 FeoC: FeoC like trans 60.4 7.6 0.00016 29.7 2.3 43 106-169 4-46 (69)
16 PF07106 TBPIP: Tat binding pr 60.1 83 0.0018 28.0 9.3 27 106-132 5-32 (169)
17 cd00890 Prefoldin Prefoldin is 59.1 64 0.0014 26.7 7.9 52 169-220 67-122 (129)
18 PF13412 HTH_24: Winged helix- 57.9 20 0.00042 25.2 4.0 44 104-168 5-48 (48)
19 cd08768 Cdc6_C Winged-helix do 57.8 4.6 0.0001 31.4 0.8 21 149-169 44-64 (87)
20 TIGR02337 HpaR homoprotocatech 56.0 56 0.0012 26.9 7.0 51 99-170 25-75 (118)
21 PRK03947 prefoldin subunit alp 55.1 59 0.0013 28.0 7.2 56 167-222 72-131 (140)
22 PF09079 Cdc6_C: CDC6, C termi 55.1 5.4 0.00012 31.4 0.7 20 150-169 38-57 (85)
23 TIGR00293 prefoldin, archaeal 53.4 62 0.0013 27.2 7.0 67 152-218 49-119 (126)
24 PF14338 Mrr_N: Mrr N-terminal 52.6 14 0.0003 29.7 2.8 63 105-171 7-74 (92)
25 smart00347 HTH_MARR helix_turn 51.4 84 0.0018 23.9 7.0 53 97-170 5-57 (101)
26 PF09339 HTH_IclR: IclR helix- 49.6 14 0.00031 26.6 2.2 45 105-170 6-51 (52)
27 cd07153 Fur_like Ferric uptake 44.1 41 0.00089 27.4 4.4 48 106-169 5-53 (116)
28 PRK10411 DNA-binding transcrip 43.8 1.2E+02 0.0026 28.7 8.0 53 105-178 7-60 (240)
29 PF03979 Sigma70_r1_1: Sigma-7 43.2 20 0.00043 28.6 2.3 22 106-127 11-32 (82)
30 smart00550 Zalpha Z-DNA-bindin 42.8 37 0.00081 26.1 3.7 52 105-177 9-63 (68)
31 TIGR00589 ogt O-6-methylguanin 42.8 29 0.00063 28.0 3.2 26 102-127 2-30 (80)
32 smart00344 HTH_ASNC helix_turn 42.7 32 0.0007 27.6 3.5 45 104-169 5-49 (108)
33 PF01035 DNA_binding_1: 6-O-me 40.1 20 0.00043 28.9 1.8 26 102-127 2-30 (85)
34 PF03836 RasGAP_C: RasGAP C-te 39.9 9.6 0.00021 33.4 0.0 26 149-175 4-29 (142)
35 PRK14127 cell division protein 39.8 40 0.00087 29.1 3.8 51 161-213 6-65 (109)
36 PF12840 HTH_20: Helix-turn-he 39.0 42 0.00091 24.8 3.3 44 105-169 13-56 (61)
37 PF14193 DUF4315: Domain of un 38.6 1E+02 0.0023 25.3 5.8 35 186-220 2-36 (83)
38 PRK11512 DNA-binding transcrip 38.6 2E+02 0.0043 24.5 8.0 63 98-181 36-102 (144)
39 smart00419 HTH_CRP helix_turn_ 38.2 32 0.0007 23.3 2.5 25 150-174 21-45 (48)
40 cd00584 Prefoldin_alpha Prefol 37.8 2.1E+02 0.0045 24.1 7.8 46 169-214 67-116 (129)
41 PF07334 IFP_35_N: Interferon- 37.6 86 0.0019 25.7 5.1 25 187-211 2-26 (76)
42 PRK13182 racA polar chromosome 36.6 87 0.0019 28.9 5.7 42 183-224 83-124 (175)
43 TIGR02049 gshA_ferroox glutama 35.6 1.9E+02 0.0041 30.4 8.3 22 240-261 256-281 (403)
44 cd06445 ATase The DNA repair p 35.1 42 0.00092 26.5 3.0 24 104-127 2-28 (79)
45 PRK13777 transcriptional regul 34.9 2.5E+02 0.0053 26.0 8.4 77 98-195 41-121 (185)
46 PRK09462 fur ferric uptake reg 34.6 69 0.0015 27.8 4.5 56 98-169 11-70 (148)
47 COG0735 Fur Fe2+/Zn2+ uptake r 34.3 81 0.0018 27.8 4.9 63 98-176 15-82 (145)
48 PF13404 HTH_AsnC-type: AsnC-t 33.4 67 0.0015 22.8 3.5 26 102-127 3-28 (42)
49 TIGR01242 26Sp45 26S proteasom 33.4 1.2E+02 0.0026 30.0 6.5 71 189-259 3-73 (364)
50 TIGR02894 DNA_bind_RsfA transc 33.1 1.9E+02 0.004 26.8 7.1 43 186-228 105-154 (161)
51 PF01022 HTH_5: Bacterial regu 32.9 46 0.001 23.5 2.6 42 106-169 6-47 (47)
52 COG5174 TFA2 Transcription ini 32.3 88 0.0019 30.9 5.1 74 52-128 28-110 (285)
53 PF01475 FUR: Ferric uptake re 31.9 81 0.0018 26.1 4.3 64 98-177 2-71 (120)
54 COG3105 Uncharacterized protei 31.4 2.2E+02 0.0048 25.7 7.1 49 182-230 31-80 (138)
55 PRK10803 tol-pal system protei 31.2 1.4E+02 0.003 28.9 6.3 32 184-215 60-91 (263)
56 cd00090 HTH_ARSR Arsenical Res 30.9 98 0.0021 21.8 4.2 44 104-169 9-52 (78)
57 PRK10434 srlR DNA-bindng trans 30.1 1.5E+02 0.0031 28.3 6.2 45 105-170 8-52 (256)
58 smart00338 BRLZ basic region l 30.0 2.2E+02 0.0047 21.4 6.0 31 188-218 29-59 (65)
59 cd00092 HTH_CRP helix_turn_hel 30.0 1.1E+02 0.0024 22.0 4.4 40 114-174 23-63 (67)
60 PRK09834 DNA-binding transcrip 28.8 2.9E+02 0.0062 26.2 8.0 50 105-175 14-66 (263)
61 PF04977 DivIC: Septum formati 28.3 1.4E+02 0.003 22.6 4.8 32 187-218 19-50 (80)
62 PF11594 Med28: Mediator compl 28.2 2.1E+02 0.0045 24.9 6.2 38 188-225 38-75 (106)
63 PF08279 HTH_11: HTH domain; 27.8 77 0.0017 22.5 3.1 39 106-165 4-43 (55)
64 PRK00901 methylated-DNA--prote 27.7 59 0.0013 29.3 3.0 27 101-127 72-101 (155)
65 COG1522 Lrp Transcriptional re 27.0 78 0.0017 26.8 3.5 51 100-171 6-56 (154)
66 COG0350 Ada Methylated DNA-pro 26.9 58 0.0013 29.6 2.8 27 102-128 88-117 (168)
67 PF12252 SidE: Dot/Icm substra 26.8 1.4E+02 0.003 35.3 6.2 73 145-220 1121-1193(1439)
68 PF00392 GntR: Bacterial regul 26.7 1.1E+02 0.0023 22.7 3.8 51 119-169 2-56 (64)
69 PF01047 MarR: MarR family; I 26.4 71 0.0015 22.9 2.7 44 105-169 6-49 (59)
70 PF14931 IFT20: Intraflagellar 26.3 69 0.0015 27.9 3.1 35 188-222 76-110 (120)
71 PRK15090 DNA-binding transcrip 26.0 4.2E+02 0.009 24.8 8.5 52 98-170 8-61 (257)
72 PF08317 Spc7: Spc7 kinetochor 25.9 2.3E+02 0.0051 28.0 7.1 37 187-223 211-247 (325)
73 TIGR02147 Fsuc_second hypothet 25.6 5.9E+02 0.013 25.0 9.7 24 153-177 155-178 (271)
74 PF06295 DUF1043: Protein of u 25.6 3.3E+02 0.0072 23.6 7.2 45 185-229 25-70 (128)
75 PF08886 GshA: Glutamate-cyste 25.5 1.6E+02 0.0034 30.9 5.9 22 240-261 259-284 (404)
76 PF07195 FliD_C: Flagellar hoo 25.2 1.7E+02 0.0037 27.5 5.7 35 186-223 201-235 (239)
77 KOG2264 Exostosin EXT1L [Signa 24.8 1.7E+02 0.0036 32.6 6.1 15 304-318 278-293 (907)
78 PF02996 Prefoldin: Prefoldin 24.8 1.3E+02 0.0029 24.6 4.4 68 156-223 44-115 (120)
79 PF05529 Bap31: B-cell recepto 24.7 1.6E+02 0.0034 26.7 5.2 29 188-216 157-185 (192)
80 PF08220 HTH_DeoR: DeoR-like h 24.6 89 0.0019 23.1 3.0 46 105-171 3-48 (57)
81 PF14394 DUF4423: Domain of un 24.4 5.4E+02 0.012 23.4 8.9 21 152-172 56-76 (171)
82 TIGR02431 pcaR_pcaU beta-ketoa 24.4 3.5E+02 0.0077 25.1 7.6 50 105-175 12-62 (248)
83 PRK11179 DNA-binding transcrip 24.2 1.1E+02 0.0023 26.8 3.9 51 98-169 5-55 (153)
84 PF12958 DUF3847: Protein of u 24.1 3.9E+02 0.0084 22.3 6.9 44 187-230 3-48 (86)
85 PF08317 Spc7: Spc7 kinetochor 23.8 2.1E+02 0.0046 28.3 6.3 81 187-271 232-320 (325)
86 PRK09954 putative kinase; Prov 23.5 1E+02 0.0023 30.1 4.1 46 103-169 4-49 (362)
87 PRK06798 fliD flagellar cappin 23.5 1.6E+02 0.0035 30.6 5.7 36 186-224 387-422 (440)
88 PF10186 Atg14: UV radiation r 23.3 1.9E+02 0.0041 27.0 5.6 15 274-288 189-203 (302)
89 KOG2264 Exostosin EXT1L [Signa 22.8 1.7E+02 0.0037 32.5 5.7 39 187-225 109-151 (907)
90 PRK11169 leucine-responsive tr 22.7 1.2E+02 0.0026 26.8 4.0 52 97-169 9-60 (164)
91 PF13463 HTH_27: Winged helix 22.4 75 0.0016 23.1 2.3 42 107-169 8-50 (68)
92 PF07544 Med9: RNA polymerase 22.3 1.8E+02 0.0039 23.4 4.6 25 187-211 54-78 (83)
93 PF02050 FliJ: Flagellar FliJ 21.9 3.9E+02 0.0085 20.8 7.5 43 185-227 59-101 (123)
94 PRK13509 transcriptional repre 21.7 3.3E+02 0.0072 25.8 7.0 44 105-169 8-51 (251)
95 COG5374 Uncharacterized conser 21.4 2.1E+02 0.0046 27.2 5.4 74 145-224 89-175 (192)
96 PF12802 MarR_2: MarR family; 21.4 1.4E+02 0.0031 21.3 3.6 49 100-169 3-53 (62)
97 PF01920 Prefoldin_2: Prefoldi 21.3 4.2E+02 0.0091 21.0 7.8 66 150-217 24-94 (106)
98 PF10234 Cluap1: Clusterin-ass 21.3 2.1E+02 0.0045 28.4 5.6 35 186-220 184-218 (267)
99 PRK10163 DNA-binding transcrip 20.8 7.2E+02 0.016 23.7 9.1 52 98-170 19-73 (271)
100 PF11853 DUF3373: Protein of u 20.6 91 0.002 33.4 3.2 27 200-226 32-58 (489)
101 PF04568 IATP: Mitochondrial A 20.5 2.7E+02 0.0058 23.8 5.4 13 201-213 85-97 (100)
102 PF14830 Haemocyan_bet_s: Haem 20.0 39 0.00085 29.0 0.3 22 155-176 58-79 (103)
No 1
>KOG2829 consensus E2F-like protein [Transcription]
Probab=100.00 E-value=5.2e-66 Score=491.21 Aligned_cols=203 Identities=58% Similarity=0.845 Sum_probs=193.9
Q ss_pred ccccCccchhhHHHHHHHHHhcCCCCHHHHHHHHHHhhcCCCC-CCCCCChhhhhccccchhhhhhhhhhhhccchhcCC
Q 018827 93 GDKSGRGLRQFSMKVCEKVESKGRTTYNEVADELVAEFADPSN-SLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKDK 171 (350)
Q Consensus 93 ~~k~~~GLR~fS~KVcekVk~kg~TTYnEVAdeLV~E~~~~~~-~~~~~~~~~~DeKniKRRVYDItNVLegIgLIeKsK 171 (350)
++++++||||||++|||||++||.|||||||||||++|..+++ ....++++.||+|||||||||||||||||+||.|+|
T Consensus 39 s~k~g~gLRhfs~kVCeKve~Kg~TtYneVADelVaef~~~n~~~~i~~n~~~yd~KNIRRRVYDALNVlmAmnIIsKdK 118 (326)
T KOG2829|consen 39 SDKAGGGLRHFSMKVCEKVERKGTTTYNEVADELVAEFAGANNYSHICPNEQEYDQKNIRRRVYDALNVLMAMNIISKDK 118 (326)
T ss_pred CCCCCcchhhhhHHHHHHHHhcCCccHHHHHHHHHHHHhccccccccCccccccchHHHHHHHHHHHHHHHHHHHHhccc
Confidence 5889999999999999999999999999999999999998876 245678999999999999999999999999999999
Q ss_pred CceeecCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCcccceEEEEcCCC
Q 018827 172 KEIQWKGLPRTSLNDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQRNERLYSSGNAPSGGVALPFILVQTRPH 251 (350)
Q Consensus 172 k~IqW~G~~~~s~~~~~~Lk~El~~L~e~I~~K~~~LqEL~~q~~aLknLierNk~ly~s~~~~~e~i~LPfIaVkAP~~ 251 (350)
|+|+|+|+|.++.+++++|++|..+++++|++|+++|+||+.|+.+|++|++||+.++..+..|.+.++||||+|.|.++
T Consensus 119 KEIrW~GLP~~ss~dv~~le~Er~k~~erI~kK~a~lqEl~~q~~~fknLV~RN~~~e~~~~~P~~~i~LPFiiinT~k~ 198 (326)
T KOG2829|consen 119 KEIRWIGLPATSSQDVSELEEERKKRMERIKKKAAQLQELIEQVSAFKNLVQRNRHAESQGQPPSENIHLPFIIINTSKK 198 (326)
T ss_pred ceeeeeccCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhccCCCCcccccceEEEecCCC
Confidence 99999999999999999999999999999999999999999999999999999999998778888889999999999999
Q ss_pred cEEEeccCCCcEEEEEEeCCCCeEEecChhhhhhhccc-cccCCCC
Q 018827 252 ATVEVEISEDMQLVHFDFNSTPFKLHDDNSVLKAMKFC-ERQQSDD 296 (350)
Q Consensus 252 T~LEVp~peD~~qv~fks~~gPieV~DD~~iLK~m~~~-~~~~~~~ 296 (350)
|+|+|++++|+++|||+|++ +|+||||++|||+|+++ +.+++.|
T Consensus 199 a~IeceiseDks~~~F~Fnk-tFevHDD~eILK~m~~~~~le~~~~ 243 (326)
T KOG2829|consen 199 AVIECEISEDKSEYLFKFNK-TFEVHDDIEILKRMGENCGLEQGNC 243 (326)
T ss_pred ceEEEEecccceeeeeecCC-ceeeccHHHHHHHHHhhcccccCCC
Confidence 99999999999999999998 59999999999999994 8888888
No 2
>KOG2577 consensus Transcription factor E2F/dimerization partner (TDP) [Transcription]
Probab=100.00 E-value=6.1e-33 Score=271.55 Aligned_cols=157 Identities=26% Similarity=0.352 Sum_probs=126.3
Q ss_pred cccCccchhhHHHHHHHHHh--cCCCCHHHHHHHHHHhhcCCCCCCCCCChhhhhccccchhhhhhhhhhhhccchhc-C
Q 018827 94 DKSGRGLRQFSMKVCEKVES--KGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK-D 170 (350)
Q Consensus 94 ~k~~~GLR~fS~KVcekVk~--kg~TTYnEVAdeLV~E~~~~~~~~~~~~~~~~DeKniKRRVYDItNVLegIgLIeK-s 170 (350)
-+..++|-.+++||.++|++ -|+..+|++|+.|- ++|||||||||||||||||+| +
T Consensus 67 ~R~d~SLglLTkKFv~Llq~s~dGvldLn~aA~~L~---------------------VqKRRIYDITNVLEGI~LIeKks 125 (354)
T KOG2577|consen 67 TRSDTSLGLLTKKFVDLLQESPDGVLDLNKAAEVLN---------------------VQKRRIYDITNVLEGIGLIEKKS 125 (354)
T ss_pred ccchhhHHHHHHHHHHHHHhCCCceeeHHHHHHHhc---------------------cccceeeehhhhhhcccceeecc
Confidence 34557899999999999999 47999999999984 899999999999999999999 9
Q ss_pred CCceeecCCCCCC----hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHH-hhh------cCCCCCC
Q 018827 171 KKEIQWKGLPRTS----LNDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQR--NER-LYS------SGNAPSG 237 (350)
Q Consensus 171 Kk~IqW~G~~~~s----~~~~~~Lk~El~~L~e~I~~K~~~LqEL~~q~~aLknLier--Nk~-ly~------s~~~~~e 237 (350)
||+|||+|.+.+. ..+++.|++|+++|....+...+.+..+ +..|++|.++ |.. .|+ .+..|.+
T Consensus 126 KN~IqW~G~~~~~~~~~~e~~~~l~~e~~~L~~~E~~LD~~i~~~---q~~L~~lted~~n~~laYVT~eDI~~i~~f~~ 202 (354)
T KOG2577|consen 126 KNNIQWIGGDFNSTGGVPERLNGLEAEVEDLSQEEDDLDQLIRDC---QQNLRLLTEDVENRRLAYVTYEDIRSIPGFDE 202 (354)
T ss_pred ccceeeecCCCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHhcchhcccceeeeHHHHhhccccCC
Confidence 9999999998764 3556667777777655443333332222 3356666664 443 365 2456899
Q ss_pred CcccceEEEEcCCCcEEEeccC-CCcEEEEEEeCCCCeEEe
Q 018827 238 GVALPFILVQTRPHATVEVEIS-EDMQLVHFDFNSTPFKLH 277 (350)
Q Consensus 238 ~i~LPfIaVkAP~~T~LEVp~p-eD~~qv~fks~~gPieV~ 277 (350)
+| +|+||||++|+||||++ +++++|+|++++|||+||
T Consensus 203 q~---vi~vkap~et~levp~~~~~~~~i~L~s~~GpI~v~ 240 (354)
T KOG2577|consen 203 QT---VIAVKAPPETRLEVPDPDEDRYQIRLKSNQGPIDVY 240 (354)
T ss_pred ce---EEEEecCCcceEecccCCCCceEEEeccCCCceeEE
Confidence 99 99999999999999999 778999999999999998
No 3
>PF08781 DP: Transcription factor DP; InterPro: IPR014889 DP forms a heterodimer with E2F and regulates genes involved in cell cycle progression. The transcriptional activity of E2F is inhibited by the retinoblastoma protein which binds to the E2F-DP heterodimer [] and negatively regulates the G1-S transition. ; PDB: 2AZE_A.
Probab=99.97 E-value=7.7e-32 Score=236.13 Aligned_cols=125 Identities=48% Similarity=0.625 Sum_probs=103.8
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCcccceEEEEcCCCcEEEeccCCCcEE
Q 018827 185 NDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQRNERLYSSGNAPSGGVALPFILVQTRPHATVEVEISEDMQL 264 (350)
Q Consensus 185 ~~~~~Lk~El~~L~e~I~~K~~~LqEL~~q~~aLknLierNk~ly~s~~~~~e~i~LPfIaVkAP~~T~LEVp~peD~~q 264 (350)
++|++|++|+.+++++|++|+++|+||+.|+++|+||++||+.++..+..|.+.|+||||+|+|.++|+|+|++++|+.+
T Consensus 1 q~~~~Le~ek~~~~~rI~~K~~~LqEL~~Q~va~knLv~RN~~~~~~~~~p~~~i~LPFIlV~T~~~a~I~ceiS~D~~~ 80 (142)
T PF08781_consen 1 QECEELEEEKQRRRERIKKKKEQLQELILQQVAFKNLVQRNRQLEQSGNAPSSGIQLPFILVNTSKKAVIECEISEDKSE 80 (142)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSSS--GEEESS-EEEEEESS--EEEEE-TTSSE
T ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCeeecCEEEEEecCCcEEEEEEcCCccE
Confidence 47899999999999999999999999999999999999999999988777789999999999999999999999999999
Q ss_pred EEEEeCCCCeEEecChhhhhhhccccccCCCCCccCCCCCCCCCC
Q 018827 265 VHFDFNSTPFKLHDDNSVLKAMKFCERQQSDDMAQSFPADDGEGS 309 (350)
Q Consensus 265 v~fks~~gPieV~DD~~iLK~m~~~~~~~~~~~~~~~~~~~~~~s 309 (350)
|||+|++.||+||||++|||+|||+...+.+..+.++...+...+
T Consensus 81 ~~F~Fn~~pFeIhDD~eVLK~m~~~~~~~~~~~~~~~~~~~~s~~ 125 (142)
T PF08781_consen 81 YHFDFNSTPFEIHDDIEVLKRMGLAFGLESGSCTPEDLAKAKSLV 125 (142)
T ss_dssp EEEEESS--EEEEEHHHHHHHTTTTTTGGGT---HHHHHHHHHTS
T ss_pred EEEEcCCCceeeechHHHHHHHHhhcCCCCCCCCccchhcccccC
Confidence 999999988999999999999999766554433777766555443
No 4
>PF02319 E2F_TDP: E2F/DP family winged-helix DNA-binding domain; InterPro: IPR003316 The mammalian transcription factor E2F plays an important role in regulating the expression of genes that are required for passage through the cell cycle. Multiple E2F family members have been identified that bind to DNA as heterodimers, interacting with proteins known as DP - the dimerisation partners [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005667 transcription factor complex; PDB: 1CF7_B.
Probab=99.74 E-value=9.1e-19 Score=136.70 Aligned_cols=67 Identities=36% Similarity=0.644 Sum_probs=58.1
Q ss_pred cCccchhhHHHHHHHHHh--cCCCCHHHHHHHHHHhhcCCCCCCCCCChhhhhccccchhhhhhhhhhhhccchhc-CCC
Q 018827 96 SGRGLRQFSMKVCEKVES--KGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK-DKK 172 (350)
Q Consensus 96 ~~~GLR~fS~KVcekVk~--kg~TTYnEVAdeLV~E~~~~~~~~~~~~~~~~DeKniKRRVYDItNVLegIgLIeK-sKk 172 (350)
..+||..++.+|.+.+.. .+.+++++||++|+.+ +.|++|||||||+|||+|+|||+| +|+
T Consensus 2 ~~~sL~~lt~~fi~~~~~~~~~~i~l~~ia~~l~~~----------------~~k~~~RRlYDI~NVLealgli~K~~k~ 65 (71)
T PF02319_consen 2 KEKSLKLLTQRFIQLFESSPDKSISLNEIADKLISE----------------NVKTQRRRLYDIINVLEALGLIEKQSKN 65 (71)
T ss_dssp TTTHHHHHHHHHHHHHHHCCCTEEEHHHHHHHCHHH----------------CCHHHCHHHHHHHHHHHHCTSEEEEETT
T ss_pred CcCCHHHHHHHHHHHHHHCCCCcccHHHHHHHHccc----------------ccccccchhhHHHHHHHHhCceeecCCC
Confidence 568999999997776664 4899999999999976 346899999999999999999999 999
Q ss_pred ceeecC
Q 018827 173 EIQWKG 178 (350)
Q Consensus 173 ~IqW~G 178 (350)
.|+|.|
T Consensus 66 ~~~W~G 71 (71)
T PF02319_consen 66 SYKWIG 71 (71)
T ss_dssp EEEE--
T ss_pred ceEecC
Confidence 999998
No 5
>KOG2578 consensus Transcription factor E2F/dimerization partner (TDP)-like proteins [Transcription]
Probab=98.79 E-value=5.7e-09 Score=102.11 Aligned_cols=69 Identities=25% Similarity=0.431 Sum_probs=51.7
Q ss_pred HHHHHhhcCCCCCCCCCChhhhhccccchhhhhhhhhhhhccchhc-CCCceeecCCCCCChhhHHHHHHH
Q 018827 124 DELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK-DKKEIQWKGLPRTSLNDIEELKAE 193 (350)
Q Consensus 124 deLV~E~~~~~~~~~~~~~~~~DeKniKRRVYDItNVLegIgLIeK-sKk~IqW~G~~~~s~~~~~~Lk~E 193 (350)
..++-.|......+..+++.+....+-|||||||.||||+||++.| -||.++|+|+... -.-+.+|++|
T Consensus 31 ~nfl~lynr~dvdlvgLddaA~KlgVErRRIYDiVNvlEsig~var~~KnqYsWkGf~ai-Pral~eLqeE 100 (388)
T KOG2578|consen 31 QNFLILYNRSDVDLVGLDDAARKLGVERRRIYDIVNVLESIGAVARRGKNQYSWKGFGAI-PRALFELQEE 100 (388)
T ss_pred HHHHHHhcCCCcceechhhHHHhcCchHHHHHHHHHHHHHHHHHHhcccCcccccchhhh-hHHHHHHHHH
Confidence 3334445555555566778888899999999999999999999999 8999999999642 1223455554
No 6
>KOG2578 consensus Transcription factor E2F/dimerization partner (TDP)-like proteins [Transcription]
Probab=96.75 E-value=0.00054 Score=67.88 Aligned_cols=74 Identities=23% Similarity=0.366 Sum_probs=50.5
Q ss_pred cCccchhhHHHHHHHHHh--cC-CCCHHHHHHHHHHhhcCCCCCCCCCChhhhhccccchhhhhhhhhhhhccchhc---
Q 018827 96 SGRGLRQFSMKVCEKVES--KG-RTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK--- 169 (350)
Q Consensus 96 ~~~GLR~fS~KVcekVk~--kg-~TTYnEVAdeLV~E~~~~~~~~~~~~~~~~DeKniKRRVYDItNVLegIgLIeK--- 169 (350)
..++|-.++..|....-. +- ..|+-..|.-|+.+-.+. .-...-=||+|||-|||-+|+||+|
T Consensus 157 kekSL~lL~qnFvklflcs~~~~lvslD~Aak~Ll~ds~~~-----------~~mRtkvRRLYDIANVlssm~LIeKtH~ 225 (388)
T KOG2578|consen 157 KEKSLWLLAQNFVKLFLCSDDDILVSLDSAAKALLKDSEDE-----------PPMRTKVRRLYDIANVLSSMNLIEKTHY 225 (388)
T ss_pred hhhHHHHHHHHHHHheeccccceEEeecHHHHHHhcCCCCC-----------ccHHHHHHHHHHHHHHHHHhhhhhhhcc
Confidence 347888888877665544 22 567766666666432221 1122344999999999999999999
Q ss_pred ---CCCceeecCCC
Q 018827 170 ---DKKEIQWKGLP 180 (350)
Q Consensus 170 ---sKk~IqW~G~~ 180 (350)
-|--++|.|.-
T Consensus 226 l~trkPafrwlG~~ 239 (388)
T KOG2578|consen 226 LFTRKPAFRWLGSK 239 (388)
T ss_pred cccccchhheeCCC
Confidence 26788999874
No 7
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=91.50 E-value=0.17 Score=38.26 Aligned_cols=57 Identities=28% Similarity=0.384 Sum_probs=45.8
Q ss_pred cchhhHHHHHHHHHhcCCCCHHHHHHHHHHhhcCCCCCCCCCChhhhhccccchhhhhhhhhhhhccchhc-CCCceee
Q 018827 99 GLRQFSMKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK-DKKEIQW 176 (350)
Q Consensus 99 GLR~fS~KVcekVk~kg~TTYnEVAdeLV~E~~~~~~~~~~~~~~~~DeKniKRRVYDItNVLegIgLIeK-sKk~IqW 176 (350)
||...=.+|...+-..|..|-.|||+++- .-|..||++++-|+.-|+|++ ..+...|
T Consensus 5 gLs~~E~~vy~~Ll~~~~~t~~eIa~~l~---------------------i~~~~v~~~L~~L~~~GlV~~~~~~~~~Y 62 (68)
T PF01978_consen 5 GLSENEAKVYLALLKNGPATAEEIAEELG---------------------ISRSTVYRALKSLEEKGLVEREEGRPKVY 62 (68)
T ss_dssp CHHHHHHHHHHHHHHHCHEEHHHHHHHHT---------------------SSHHHHHHHHHHHHHTTSEEEEEECCEEE
T ss_pred CcCHHHHHHHHHHHHcCCCCHHHHHHHHC---------------------cCHHHHHHHHHHHHHCCCEEEEcCceEEE
Confidence 56666678888887889899999998874 567899999999999999999 4444444
No 8
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=85.38 E-value=1.4 Score=33.05 Aligned_cols=55 Identities=24% Similarity=0.323 Sum_probs=39.1
Q ss_pred cchhhHHHHHHHHHhcCCCCHHHHHHHHHHhhcCCCCCCCCCChhhhhccccchhhhhhhhhhhhccchh
Q 018827 99 GLRQFSMKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIIS 168 (350)
Q Consensus 99 GLR~fS~KVcekVk~kg~TTYnEVAdeLV~E~~~~~~~~~~~~~~~~DeKniKRRVYDItNVLegIgLIe 168 (350)
.|-..+..|++.+ .|..|..|+++.|..+|.. +.+..++.|...++-|...|||+
T Consensus 14 ~Ln~~a~~Iw~~~--~g~~t~~ei~~~l~~~y~~-------------~~~~~~~dv~~fl~~L~~~glIe 68 (68)
T PF05402_consen 14 TLNETAAFIWELL--DGPRTVEEIVDALAEEYDV-------------DPEEAEEDVEEFLEQLREKGLIE 68 (68)
T ss_dssp ---THHHHHHHH----SSS-HHHHHHHHHHHTT---------------HHHHHHHHHHHHHHHHHTT---
T ss_pred cccHHHHHHHHHc--cCCCCHHHHHHHHHHHcCC-------------CHHHHHHHHHHHHHHHHHCcCcC
Confidence 7888889999999 3678899999999998844 23467999999999999999985
No 9
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=84.22 E-value=3.3 Score=39.76 Aligned_cols=36 Identities=19% Similarity=0.404 Sum_probs=28.3
Q ss_pred hccccchhhhhhhhhhhhccchhc-CCCceeecCCCC
Q 018827 146 DEKNIRRRVYDALNVLMAMDIISK-DKKEIQWKGLPR 181 (350)
Q Consensus 146 DeKniKRRVYDItNVLegIgLIeK-sKk~IqW~G~~~ 181 (350)
...+=+=||||+|+.|++-|+++. .++--.++..+.
T Consensus 39 ~sgvP~~kvY~vl~sLe~kG~v~~~~g~P~~y~av~p 75 (247)
T COG1378 39 ASGVPRPKVYDVLRSLEKKGLVEVIEGRPKKYRAVPP 75 (247)
T ss_pred HcCCCchhHHHHHHHHHHCCCEEeeCCCCceEEeCCH
Confidence 344667899999999999999999 666666665554
No 10
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=75.68 E-value=12 Score=33.04 Aligned_cols=55 Identities=25% Similarity=0.479 Sum_probs=41.4
Q ss_pred cchhhHHHHHHHHH-hcCCCCHHHHHHHHHHhhcCCCCCCCCCChhhhhccccchhhhhhhhhhhhccchhcCCCce
Q 018827 99 GLRQFSMKVCEKVE-SKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKDKKEI 174 (350)
Q Consensus 99 GLR~fS~KVcekVk-~kg~TTYnEVAdeLV~E~~~~~~~~~~~~~~~~DeKniKRRVYDItNVLegIgLIeKsKk~I 174 (350)
||...=..|..++- +.+..|-.|+|.+|- --|-.||=++|=|+..|||.|.|-.+
T Consensus 24 GLs~~Dv~v~~~LL~~~~~~tvdelae~ln---------------------r~rStv~rsl~~L~~~GlV~Rek~~~ 79 (126)
T COG3355 24 GLSELDVEVYKALLEENGPLTVDELAEILN---------------------RSRSTVYRSLQNLLEAGLVEREKVNL 79 (126)
T ss_pred CCcHHHHHHHHHHHhhcCCcCHHHHHHHHC---------------------ccHHHHHHHHHHHHHcCCeeeeeecc
Confidence 55555556665555 577777777777763 35678999999999999999988777
No 11
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=73.00 E-value=5.2 Score=27.45 Aligned_cols=48 Identities=17% Similarity=0.240 Sum_probs=37.5
Q ss_pred HHHHHHHhcCCCCHHHHHHHHHHhhcCCCCCCCCCChhhhhccccchhhhhhhhhhhhccchhcCCCce
Q 018827 106 KVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKDKKEI 174 (350)
Q Consensus 106 KVcekVk~kg~TTYnEVAdeLV~E~~~~~~~~~~~~~~~~DeKniKRRVYDItNVLegIgLIeKsKk~I 174 (350)
.|++.+.+++..+..++|+.|- .-++-||.++.-|+..|+|.+..+.|
T Consensus 4 ~il~~l~~~~~~s~~~l~~~l~---------------------~s~~tv~~~l~~L~~~g~i~~~~~~~ 51 (53)
T smart00420 4 QILELLAQQGKVSVEELAELLG---------------------VSEMTIRRDLNKLEEQGLLTRVHGGA 51 (53)
T ss_pred HHHHHHHHcCCcCHHHHHHHHC---------------------CCHHHHHHHHHHHHHCCCEEEeecCc
Confidence 4677777777788888888761 45688999999999999999855544
No 12
>PF11315 Med30: Mediator complex subunit 30; InterPro: IPR021019 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Med30 is a metazoan-specific subunit of Mediator [], having no homologues in yeasts.
Probab=67.75 E-value=28 Score=31.66 Aligned_cols=66 Identities=33% Similarity=0.458 Sum_probs=43.0
Q ss_pred hhhhhhhhh----hhhccchhcCCCceeecCCCCC------ChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 018827 152 RRVYDALNV----LMAMDIISKDKKEIQWKGLPRT------SLNDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNL 221 (350)
Q Consensus 152 RRVYDItNV----LegIgLIeKsKk~IqW~G~~~~------s~~~~~~Lk~El~~L~e~I~~K~~~LqEL~~q~~aLknL 221 (350)
|-|||-.|= |+...+= .-|-|++-+.. +..+...+.+|+.++.+.+..|.++|.+++++ ++++
T Consensus 65 RlIYekCne~~~~l~~~~iE----sLIP~~~~~~~k~e~~~~s~~~~~~~~er~el~e~v~~KN~qLk~iid~---lR~~ 137 (150)
T PF11315_consen 65 RLIYEKCNENCQGLEPTPIE----SLIPYKEEPRNKEEERDSSEEYRQLLEERKELIEQVKQKNQQLKEIIDQ---LRNI 137 (150)
T ss_pred HHHHHHHHHhccCCCCCCHH----HhccccCCccccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHH
Confidence 777887776 4433331 23344433321 12356678889999999999999999999887 4555
Q ss_pred HHH
Q 018827 222 IQR 224 (350)
Q Consensus 222 ier 224 (350)
+.+
T Consensus 138 iwe 140 (150)
T PF11315_consen 138 IWE 140 (150)
T ss_pred HHH
Confidence 554
No 13
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=64.72 E-value=6.8 Score=27.31 Aligned_cols=42 Identities=17% Similarity=0.181 Sum_probs=32.4
Q ss_pred HHHHHHhcCCCCHHHHHHHHHHhhcCCCCCCCCCChhhhhccccchhhhhhhhhhhhccchhcC
Q 018827 107 VCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKD 170 (350)
Q Consensus 107 VcekVk~kg~TTYnEVAdeLV~E~~~~~~~~~~~~~~~~DeKniKRRVYDItNVLegIgLIeKs 170 (350)
|.+.+. .+..+.+++++.|- .-+..||++++.|+.-|+|++.
T Consensus 2 il~~l~-~~~~~~~~i~~~l~---------------------is~~~v~~~l~~L~~~g~i~~~ 43 (66)
T smart00418 2 ILKLLA-EGELCVCELAEILG---------------------LSQSTVSHHLKKLREAGLVESR 43 (66)
T ss_pred HHHHhh-cCCccHHHHHHHHC---------------------CCHHHHHHHHHHHHHCCCeeee
Confidence 345555 67788999888873 2345699999999999999973
No 14
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=60.54 E-value=15 Score=28.42 Aligned_cols=45 Identities=22% Similarity=0.313 Sum_probs=37.2
Q ss_pred HHHHHHHHhc-CCCCHHHHHHHHHHhhcCCCCCCCCCChhhhhccccchhhhhhhhhhhhccchhcC
Q 018827 105 MKVCEKVESK-GRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKD 170 (350)
Q Consensus 105 ~KVcekVk~k-g~TTYnEVAdeLV~E~~~~~~~~~~~~~~~~DeKniKRRVYDItNVLegIgLIeKs 170 (350)
..|++.+... +..|..|+|+++- .-+.-||-.++.|+..|+|+++
T Consensus 8 ~~Il~~l~~~~~~~t~~~ia~~l~---------------------i~~~tv~r~l~~L~~~g~l~~~ 53 (91)
T smart00346 8 LAVLRALAEEPGGLTLAELAERLG---------------------LSKSTAHRLLNTLQELGYVEQD 53 (91)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHhC---------------------CCHHHHHHHHHHHHHCCCeeec
Confidence 5677778776 7899999999882 3467899999999999999995
No 15
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=60.38 E-value=7.6 Score=29.72 Aligned_cols=43 Identities=23% Similarity=0.315 Sum_probs=34.8
Q ss_pred HHHHHHHhcCCCCHHHHHHHHHHhhcCCCCCCCCCChhhhhccccchhhhhhhhhhhhccchhc
Q 018827 106 KVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (350)
Q Consensus 106 KVcekVk~kg~TTYnEVAdeLV~E~~~~~~~~~~~~~~~~DeKniKRRVYDItNVLegIgLIeK 169 (350)
.|.+.++.++.+|..|+|.+|-. -..-|=+.|.+|+..|.|+|
T Consensus 4 ~i~~~l~~~~~~S~~eLa~~~~~---------------------s~~~ve~mL~~l~~kG~I~~ 46 (69)
T PF09012_consen 4 EIRDYLRERGRVSLAELAREFGI---------------------SPEAVEAMLEQLIRKGYIRK 46 (69)
T ss_dssp HHHHHHHHS-SEEHHHHHHHTT-----------------------HHHHHHHHHHHHCCTSCEE
T ss_pred HHHHHHHHcCCcCHHHHHHHHCc---------------------CHHHHHHHHHHHHHCCcEEE
Confidence 57888999999999999999852 23456689999999999999
No 16
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=60.10 E-value=83 Score=27.97 Aligned_cols=27 Identities=11% Similarity=0.197 Sum_probs=19.6
Q ss_pred HHHHHHHh-cCCCCHHHHHHHHHHhhcC
Q 018827 106 KVCEKVES-KGRTTYNEVADELVAEFAD 132 (350)
Q Consensus 106 KVcekVk~-kg~TTYnEVAdeLV~E~~~ 132 (350)
.|.+-+++ ...-+.++|.+.|-..|..
T Consensus 5 ~Il~y~~~qNRPys~~di~~nL~~~~~K 32 (169)
T PF07106_consen 5 AILEYMKEQNRPYSAQDIFDNLHNKVGK 32 (169)
T ss_pred HHHHHHHHcCCCCcHHHHHHHHHhhccH
Confidence 35555555 6888999999999865554
No 17
>cd00890 Prefoldin Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils.
Probab=59.14 E-value=64 Score=26.72 Aligned_cols=52 Identities=35% Similarity=0.323 Sum_probs=25.6
Q ss_pred cCCCceeecCCCCCC---h-hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 018827 169 KDKKEIQWKGLPRTS---L-NDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQN 220 (350)
Q Consensus 169 KsKk~IqW~G~~~~s---~-~~~~~Lk~El~~L~e~I~~K~~~LqEL~~q~~aLkn 220 (350)
.+.+-+.|+|.+.-. . .-.+.|++.+..+..+++.....+.++..+...++.
T Consensus 67 ~~~~v~v~iG~~~~ve~~~~eA~~~l~~r~~~l~~~~~~l~~~~~~~~~~~~~l~~ 122 (129)
T cd00890 67 DDDKVLVDLGTGVYVEKSLEEAIEFLKKRLETLEKQIEKLEKQLEKLQDQITELQE 122 (129)
T ss_pred CCCEEEEEecCCEEEEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456678899976321 1 122333444444444444444555555444444433
No 18
>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=57.89 E-value=20 Score=25.16 Aligned_cols=44 Identities=25% Similarity=0.243 Sum_probs=35.5
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhhcCCCCCCCCCChhhhhccccchhhhhhhhhhhhccchh
Q 018827 104 SMKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIIS 168 (350)
Q Consensus 104 S~KVcekVk~kg~TTYnEVAdeLV~E~~~~~~~~~~~~~~~~DeKniKRRVYDItNVLegIgLIe 168 (350)
-.+|...+.+++.+|-.|+|+.+- .-+..|+.+++-|+.-|+|+
T Consensus 5 ~~~Il~~l~~~~~~t~~ela~~~~---------------------is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 5 QRKILNYLRENPRITQKELAEKLG---------------------ISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHHCTTS-HHHHHHHHT---------------------S-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHcCCCCHHHHHHHhC---------------------CCHHHHHHHHHHHHHCcCcC
Confidence 467888999999999999999974 34577889999999999885
No 19
>cd08768 Cdc6_C Winged-helix domain of essential DNA replication protein Cell division control protein (Cdc6), which mediates DNA binding. This model characterizes the winged-helix, C-terminal domain of the Cell division control protein (Cdc6_C). Cdc6 (also known as Cell division cycle 6 or Cdc18) functions as a regulator at the early stages of DNA replication, by helping to recruit and load the Minichromosome Maintenance Complex (MCM) onto DNA and may have additional roles in the control of mitotic entry. Precise duplication of chromosomal DNA is required for genomic stability during replication. Cdc6 has an essential role in DNA replication and irregular expression of Cdc6 may lead to genomic instability. Cdc6 over-expression is observed in many cancerous lesions. DNA replication begins when an origin recognition complex (ORC) binds to a replication origin site on the chromatin. Studies indicate that Cdc6 interacts with ORC through the Orc1 subunit, and that this association increases
Probab=57.84 E-value=4.6 Score=31.42 Aligned_cols=21 Identities=24% Similarity=0.400 Sum_probs=18.7
Q ss_pred ccchhhhhhhhhhhhccchhc
Q 018827 149 NIRRRVYDALNVLMAMDIISK 169 (350)
Q Consensus 149 niKRRVYDItNVLegIgLIeK 169 (350)
--.||++|++|-|+..|||+-
T Consensus 44 l~~~~~~~~l~~L~~~gli~~ 64 (87)
T cd08768 44 LTQRRISDLLSELEMLGLLET 64 (87)
T ss_pred CcHHHHHHHHHHHHHcCCeEE
Confidence 345999999999999999986
No 20
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=56.01 E-value=56 Score=26.89 Aligned_cols=51 Identities=14% Similarity=0.288 Sum_probs=36.7
Q ss_pred cchhhHHHHHHHHHhcCCCCHHHHHHHHHHhhcCCCCCCCCCChhhhhccccchhhhhhhhhhhhccchhcC
Q 018827 99 GLRQFSMKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKD 170 (350)
Q Consensus 99 GLR~fS~KVcekVk~kg~TTYnEVAdeLV~E~~~~~~~~~~~~~~~~DeKniKRRVYDItNVLegIgLIeKs 170 (350)
||-.--..|...+...+.+|.+|+|+.+. .-+--|+=+++-|+.-|+|++.
T Consensus 25 ~lt~~q~~iL~~l~~~~~~t~~ela~~~~---------------------~~~~tvs~~l~~Le~~GlI~r~ 75 (118)
T TIGR02337 25 GLTEQQWRILRILAEQGSMEFTQLANQAC---------------------ILRPSLTGILARLERDGLVTRL 75 (118)
T ss_pred CCCHHHHHHHHHHHHcCCcCHHHHHHHhC---------------------CCchhHHHHHHHHHHCCCEEec
Confidence 44444455667777777788888888765 2334577889999999999993
No 21
>PRK03947 prefoldin subunit alpha; Reviewed
Probab=55.14 E-value=59 Score=27.98 Aligned_cols=56 Identities=23% Similarity=0.246 Sum_probs=30.4
Q ss_pred hhcCCCceeecCCCCCC----hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 018827 167 ISKDKKEIQWKGLPRTS----LNDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLI 222 (350)
Q Consensus 167 IeKsKk~IqW~G~~~~s----~~~~~~Lk~El~~L~e~I~~K~~~LqEL~~q~~aLknLi 222 (350)
|....+-|-|.|.+--. ..-++.|++.+..|.+.++.....|.++..+...+...+
T Consensus 72 v~~~~kV~v~lG~g~~vE~~~~eA~~~l~~~~~~l~~~~~~l~~~l~~~~~~~~~~~~~l 131 (140)
T PRK03947 72 VKDKDKVIVSLGAGYSAEKDLDEAIEILDKRKEELEKALEKLEEALQKLASRIAQLAQEL 131 (140)
T ss_pred ecCCCeEEEEcCCCEEEEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33456778899887432 223344555555555555555555555555544444333
No 22
>PF09079 Cdc6_C: CDC6, C terminal ; InterPro: IPR015163 The C-terminal domain of CDC6 assumes a winged helix fold, with a five alpha-helical bundle (alpha15-alpha19) structure, backed on one side by three beta strands (beta6-beta8). It has been shown that this domain acts as a DNA-localisation factor, however its exact function is, as yet, unknown. Putative functions include: (1) mediation of protein-protein interactions and (2) regulation of nucleotide binding and hydrolysis. Mutagenesis studies have shown that this domain is essential for appropriate Cdc6 activity []. ; PDB: 2QBY_A 2V1U_A 1W5T_A 1W5S_B 1FNN_B.
Probab=55.09 E-value=5.4 Score=31.44 Aligned_cols=20 Identities=30% Similarity=0.348 Sum_probs=17.9
Q ss_pred cchhhhhhhhhhhhccchhc
Q 018827 150 IRRRVYDALNVLMAMDIISK 169 (350)
Q Consensus 150 iKRRVYDItNVLegIgLIeK 169 (350)
-.||+||+++-|+.+|||+-
T Consensus 38 s~~r~~~~l~eL~~~gli~~ 57 (85)
T PF09079_consen 38 SYRRFSDYLSELEMLGLIES 57 (85)
T ss_dssp -HHHHHHHHHHHHHTTSEEE
T ss_pred CHHHHHHHHHHHHhCCCeEE
Confidence 45999999999999999976
No 23
>TIGR00293 prefoldin, archaeal alpha subunit/eukaryotic subunit 5. This model finds a set of small proteins from the Archaea and from Aquifex aeolicus that may represent two orthologous groups. The proteins are predicted to be mostly coiled coil, and may hit large numbers of proteins that contain coiled coil regions.
Probab=53.42 E-value=62 Score=27.20 Aligned_cols=67 Identities=21% Similarity=0.072 Sum_probs=37.9
Q ss_pred hhhhhhhhhhhhccchhcCCCceeecCCCCCC----hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 018827 152 RRVYDALNVLMAMDIISKDKKEIQWKGLPRTS----LNDIEELKAERLGLRNRIEKKTAYLQELEDQFVGL 218 (350)
Q Consensus 152 RRVYDItNVLegIgLIeKsKk~IqW~G~~~~s----~~~~~~Lk~El~~L~e~I~~K~~~LqEL~~q~~aL 218 (350)
...+-+..-+..=+-|...++-+-|+|.+-.. ..-.+-|+..+..+.+.++...+.|.++..+...+
T Consensus 49 ~~lv~lg~~~~v~~~v~~~~~v~v~iG~g~~vE~~~~eA~~~l~~~~~~l~~~~~~l~~~l~~l~~~~~~i 119 (126)
T TIGR00293 49 ETLVPVGAGSFVKAKVKDTDKVLVSIGSGYYVEKDAEEAIEFLKKRIEELEKAIEKLQEALAELASRAQQL 119 (126)
T ss_pred eEEEEcCCCeEEEEEeCCCCEEEEEcCCCEEEEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44555555555555566678889999987432 22234445555555555555555555555544433
No 24
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=52.59 E-value=14 Score=29.74 Aligned_cols=63 Identities=14% Similarity=0.261 Sum_probs=44.4
Q ss_pred HHHHHHHHh-cCCCCHHHHHHHHHHhhcCCCCCCCCCChhh--hhc--cccchhhhhhhhhhhhccchhcCC
Q 018827 105 MKVCEKVES-KGRTTYNEVADELVAEFADPSNSLATPDQQQ--YDE--KNIRRRVYDALNVLMAMDIISKDK 171 (350)
Q Consensus 105 ~KVcekVk~-kg~TTYnEVAdeLV~E~~~~~~~~~~~~~~~--~De--KniKRRVYDItNVLegIgLIeKsK 171 (350)
.-|.+-+.. .|..+..||.+.+...+.-.... . ... ... ...+.||.=++.-|...|+|++.+
T Consensus 7 ~piL~~L~~~g~~~~~~ei~~~v~~~~~ls~e~---~-~~~~~sg~~~~~~~~ri~Wa~~~L~~aGli~~~~ 74 (92)
T PF14338_consen 7 PPILEALKDLGGSASRKEIYERVAERFGLSDEE---R-NERLPSGQGYSRFKNRIRWARSYLKKAGLIERPK 74 (92)
T ss_pred HHHHHHHHHcCCCcCHHHHHHHHHHHhCCCHHH---H-HHHcccCCcchhHHHhHHHHHHHHHHCCCccCCC
Confidence 346777788 88999999999998766432110 0 001 111 268899999999999999999944
No 25
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=51.41 E-value=84 Score=23.94 Aligned_cols=53 Identities=21% Similarity=0.162 Sum_probs=42.0
Q ss_pred CccchhhHHHHHHHHHhcCCCCHHHHHHHHHHhhcCCCCCCCCCChhhhhccccchhhhhhhhhhhhccchhcC
Q 018827 97 GRGLRQFSMKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKD 170 (350)
Q Consensus 97 ~~GLR~fS~KVcekVk~kg~TTYnEVAdeLV~E~~~~~~~~~~~~~~~~DeKniKRRVYDItNVLegIgLIeKs 170 (350)
..||-..-..+...+...+..+..++|+.+- .-+.-|+-+++-|+..|+|++.
T Consensus 5 ~~~l~~~~~~il~~l~~~~~~~~~~la~~~~---------------------~s~~~i~~~l~~L~~~g~v~~~ 57 (101)
T smart00347 5 PLGLTPTQFLVLRILYEEGPLSVSELAKRLG---------------------VSPSTVTRVLDRLEKKGLIRRL 57 (101)
T ss_pred ccCCCHHHHHHHHHHHHcCCcCHHHHHHHHC---------------------CCchhHHHHHHHHHHCCCeEec
Confidence 3566777788888998888899999887752 1245589999999999999984
No 26
>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=49.58 E-value=14 Score=26.57 Aligned_cols=45 Identities=22% Similarity=0.331 Sum_probs=33.6
Q ss_pred HHHHHHHHhcC-CCCHHHHHHHHHHhhcCCCCCCCCCChhhhhccccchhhhhhhhhhhhccchhcC
Q 018827 105 MKVCEKVESKG-RTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKD 170 (350)
Q Consensus 105 ~KVcekVk~kg-~TTYnEVAdeLV~E~~~~~~~~~~~~~~~~DeKniKRRVYDItNVLegIgLIeKs 170 (350)
..|.+.+.+.+ ..+..|+|+++- .-|--+|-+++.|+..|+|+|+
T Consensus 6 l~iL~~l~~~~~~~t~~eia~~~g---------------------l~~stv~r~L~tL~~~g~v~~d 51 (52)
T PF09339_consen 6 LRILEALAESGGPLTLSEIARALG---------------------LPKSTVHRLLQTLVEEGYVERD 51 (52)
T ss_dssp HHHHHCHHCTBSCEEHHHHHHHHT---------------------S-HHHHHHHHHHHHHTTSEEEC
T ss_pred HHHHHHHHcCCCCCCHHHHHHHHC---------------------cCHHHHHHHHHHHHHCcCeecC
Confidence 45566666644 468999998874 2355689999999999999874
No 27
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=44.06 E-value=41 Score=27.40 Aligned_cols=48 Identities=19% Similarity=0.241 Sum_probs=35.3
Q ss_pred HHHHHHHh-cCCCCHHHHHHHHHHhhcCCCCCCCCCChhhhhccccchhhhhhhhhhhhccchhc
Q 018827 106 KVCEKVES-KGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (350)
Q Consensus 106 KVcekVk~-kg~TTYnEVAdeLV~E~~~~~~~~~~~~~~~~DeKniKRRVYDItNVLegIgLIeK 169 (350)
.|.+.+.+ .+..|-.||.+.|..+.. ..-+-=||=+|+.|+..|||.|
T Consensus 5 ~Il~~l~~~~~~~sa~ei~~~l~~~~~----------------~i~~~TVYR~L~~L~~~Gli~~ 53 (116)
T cd07153 5 AILEVLLESDGHLTAEEIYERLRKKGP----------------SISLATVYRTLELLEEAGLVRE 53 (116)
T ss_pred HHHHHHHhCCCCCCHHHHHHHHHhcCC----------------CCCHHHHHHHHHHHHhCCCEEE
Confidence 46777766 456788788888765321 1234569999999999999999
No 28
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=43.84 E-value=1.2e+02 Score=28.73 Aligned_cols=53 Identities=13% Similarity=0.120 Sum_probs=38.4
Q ss_pred HHHHHHHHhcCCCCHHHHHHHHHHhhcCCCCCCCCCChhhhhccccchhhhhhhhhhhhccchhc-CCCceeecC
Q 018827 105 MKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK-DKKEIQWKG 178 (350)
Q Consensus 105 ~KVcekVk~kg~TTYnEVAdeLV~E~~~~~~~~~~~~~~~~DeKniKRRVYDItNVLegIgLIeK-sKk~IqW~G 178 (350)
.++.+.+++.+.+++.|+|+.|- +-.+.|+--++.|+..++|.+ .+.-+.+.+
T Consensus 7 ~~Il~~l~~~~~~~~~eLa~~l~---------------------VS~~TiRRdL~~L~~~~~l~r~~Gga~~~~~ 60 (240)
T PRK10411 7 QAIVDLLLNHTSLTTEALAEQLN---------------------VSKETIRRDLNELQTQGKILRNHGRAKYIHR 60 (240)
T ss_pred HHHHHHHHHcCCCcHHHHHHHHC---------------------cCHHHHHHHHHHHHHCCCEEEecCeEEEecC
Confidence 35789999999999999999982 223455556777877888887 555555543
No 29
>PF03979 Sigma70_r1_1: Sigma-70 factor, region 1.1; InterPro: IPR007127 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. This entry represents Region 1.1 which modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase [, ]. Region 1.1 is also involved in promoter binding.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2K6X_A.
Probab=43.22 E-value=20 Score=28.60 Aligned_cols=22 Identities=45% Similarity=0.625 Sum_probs=16.3
Q ss_pred HHHHHHHhcCCCCHHHHHHHHH
Q 018827 106 KVCEKVESKGRTTYNEVADELV 127 (350)
Q Consensus 106 KVcekVk~kg~TTYnEVAdeLV 127 (350)
++.++-+.+|..||.||.+.|-
T Consensus 11 ~Li~~gK~~G~lT~~eI~~~L~ 32 (82)
T PF03979_consen 11 KLIEKGKKKGYLTYDEINDALP 32 (82)
T ss_dssp HHHHHHHHHSS-BHHHHHHH-S
T ss_pred HHHHHHhhcCcCCHHHHHHHcC
Confidence 4566677799999999999886
No 30
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=42.85 E-value=37 Score=26.07 Aligned_cols=52 Identities=25% Similarity=0.280 Sum_probs=40.3
Q ss_pred HHHHHHHHhcCC--CCHHHHHHHHHHhhcCCCCCCCCCChhhhhccccchhhhhhhhhhhhccchhcC-CCceeec
Q 018827 105 MKVCEKVESKGR--TTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKD-KKEIQWK 177 (350)
Q Consensus 105 ~KVcekVk~kg~--TTYnEVAdeLV~E~~~~~~~~~~~~~~~~DeKniKRRVYDItNVLegIgLIeKs-Kk~IqW~ 177 (350)
.+|++.++..|. .+-.|+|.+|- .-++-|.-+|.-|+.-|+|.+. .+-=.|.
T Consensus 9 ~~IL~~L~~~g~~~~ta~eLa~~lg---------------------l~~~~v~r~L~~L~~~G~V~~~~~~~~~W~ 63 (68)
T smart00550 9 EKILEFLENSGDETSTALQLAKNLG---------------------LPKKEVNRVLYSLEKKGKVCKQGGTPPLWK 63 (68)
T ss_pred HHHHHHHHHCCCCCcCHHHHHHHHC---------------------CCHHHHHHHHHHHHHCCCEEecCCCCCceE
Confidence 578999999877 88889888874 3456788889999999999993 3324663
No 31
>TIGR00589 ogt O-6-methylguanine DNA methyltransferase. All proteins in this family for which functions are known are involved alkyl-DNA transferases which remove alkyl groups from DNA as part of alkylation DNA repair. Some of the proteins in this family are also transcription regulators and have a distinct transcription regulatory domain. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=42.83 E-value=29 Score=27.98 Aligned_cols=26 Identities=15% Similarity=0.377 Sum_probs=21.5
Q ss_pred hhHHHHHHHHHh---cCCCCHHHHHHHHH
Q 018827 102 QFSMKVCEKVES---KGRTTYNEVADELV 127 (350)
Q Consensus 102 ~fS~KVcekVk~---kg~TTYnEVAdeLV 127 (350)
.|..+|.+.|.+ ..++||.+||..+-
T Consensus 2 ~f~~~V~~~l~~IP~G~v~TYg~iA~~~g 30 (80)
T TIGR00589 2 PFQQRVWQALRTIPYGETKSYGQLAARIG 30 (80)
T ss_pred hHHHHHHHHHhCCCCCCcCCHHHHHHHhC
Confidence 377888888888 67999999999863
No 32
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=42.67 E-value=32 Score=27.65 Aligned_cols=45 Identities=18% Similarity=0.223 Sum_probs=35.9
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhhcCCCCCCCCCChhhhhccccchhhhhhhhhhhhccchhc
Q 018827 104 SMKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (350)
Q Consensus 104 S~KVcekVk~kg~TTYnEVAdeLV~E~~~~~~~~~~~~~~~~DeKniKRRVYDItNVLegIgLIeK 169 (350)
=.+|...++..+.++++|+|+.+- .-..-|+..++-|+.-|+|.+
T Consensus 5 D~~il~~L~~~~~~~~~~la~~l~---------------------~s~~tv~~~l~~L~~~g~i~~ 49 (108)
T smart00344 5 DRKILEELQKDARISLAELAKKVG---------------------LSPSTVHNRVKRLEEEGVIKG 49 (108)
T ss_pred HHHHHHHHHHhCCCCHHHHHHHHC---------------------cCHHHHHHHHHHHHHCCCeec
Confidence 367888999999999999999983 123456667899999999986
No 33
>PF01035 DNA_binding_1: 6-O-methylguanine DNA methyltransferase, DNA binding domain; InterPro: IPR014048 Synonym(s): 6-O-methylguanine-DNA methyltransferase, O-6-methylguanine-DNA-alkyltransferase This entry represents the DNA binding region of 6-O-methylguanine-DNA methyltransferases. The repair of DNA containing O6-alkylated guanine is carried out by DNA-[protein]-cysteine S-methyltransferase (2.1.1.63 from EC). The major mutagenic and carcinogenic effect of methylating agents in DNA is the formation of O6-alkylguanine. The alkyl group at the O-6 position is transferred to a cysteine residue in the enzyme []. This is a suicide reaction since the enzyme is irreversibly inactivated and the methylated protein accumulates as a dead-end product. Most, but not all of the methyltransferases are also able to repair O-4-methylthymine. DNA-[protein]-cysteine S-methyltransferases are widely distributed and are found in various prokaryotic and eukaryotic sources [].; GO: 0003824 catalytic activity, 0006281 DNA repair; PDB: 1SFE_A 1T39_B 1T38_A 1EH7_A 1EH6_A 1YFH_C 1EH8_A 1QNT_A 2KIM_A 2KIF_A ....
Probab=40.10 E-value=20 Score=28.92 Aligned_cols=26 Identities=38% Similarity=0.428 Sum_probs=20.8
Q ss_pred hhHHHHHHHHHh---cCCCCHHHHHHHHH
Q 018827 102 QFSMKVCEKVES---KGRTTYNEVADELV 127 (350)
Q Consensus 102 ~fS~KVcekVk~---kg~TTYnEVAdeLV 127 (350)
.|..+|.+.|.+ ..++||.+||..+-
T Consensus 2 ~f~~~V~~~v~~IP~G~v~TYg~iA~~~g 30 (85)
T PF01035_consen 2 PFQRRVWEAVRQIPYGKVTTYGEIARLLG 30 (85)
T ss_dssp HHHHHHHHHHTTS-TT-BEEHHHHHHHTT
T ss_pred hHHHHHHHHHHcCCCCceEeHHHHHHHHh
Confidence 377888888888 67999999998864
No 34
>PF03836 RasGAP_C: RasGAP C-terminus; InterPro: IPR000593 Ras GTPase-activating protein (rasGAP) is a major contributor to the down-regulation of ras by facilitating GTP hydrolysis of activated ras. In addition, GAP participates in the down-stream effector system of the ras signalling pathway. Abnormal signal transduction involving activated ras genes plays a major role in the development of a variety of tumours. Depending on the precise genetic alteration, its location within the gene and the effects it exerts on protein function, rasGAP can theoretically function as either an oncogene or as a tumour suppressor gene [].; GO: 0005099 Ras GTPase activator activity, 0007264 small GTPase mediated signal transduction, 0005622 intracellular; PDB: 3ISU_A 3IEZ_A 4EZA_B 1X0H_A.
Probab=39.87 E-value=9.6 Score=33.40 Aligned_cols=26 Identities=19% Similarity=0.544 Sum_probs=0.0
Q ss_pred ccchhhhhhhhhhhhccchhcCCCcee
Q 018827 149 NIRRRVYDALNVLMAMDIISKDKKEIQ 175 (350)
Q Consensus 149 niKRRVYDItNVLegIgLIeKsKk~Iq 175 (350)
..|++|-+-+..||.+|+|.++ |.+|
T Consensus 4 ~lk~~~l~~l~~LE~~G~v~~~-n~yQ 29 (142)
T PF03836_consen 4 ELKKKILENLKELESLGIVSRS-NNYQ 29 (142)
T ss_dssp ---------------------------
T ss_pred HHHHHHHHHHHHHHHCCCCCCc-ccHH
Confidence 4688999999999999999998 7776
No 35
>PRK14127 cell division protein GpsB; Provisional
Probab=39.83 E-value=40 Score=29.08 Aligned_cols=51 Identities=25% Similarity=0.350 Sum_probs=28.6
Q ss_pred hhhccchhc-CCCceeecCCCCCC--------hhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 018827 161 LMAMDIISK-DKKEIQWKGLPRTS--------LNDIEELKAERLGLRNRIEKKTAYLQELED 213 (350)
Q Consensus 161 LegIgLIeK-sKk~IqW~G~~~~s--------~~~~~~Lk~El~~L~e~I~~K~~~LqEL~~ 213 (350)
|-.++|..| =|+ .|+|++... ..+++.|.+|...|++++...++.|.++..
T Consensus 6 LTp~DI~~KeF~~--~~RGYd~~EVD~FLd~V~~dye~l~~e~~~Lk~e~~~l~~~l~e~~~ 65 (109)
T PRK14127 6 LTPKDILEKEFKT--SMRGYDQDEVDKFLDDVIKDYEAFQKEIEELQQENARLKAQVDELTK 65 (109)
T ss_pred CCHHHHhhCccCC--CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345566677 222 256887532 344556666666666666665555555543
No 36
>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=38.98 E-value=42 Score=24.80 Aligned_cols=44 Identities=25% Similarity=0.279 Sum_probs=35.5
Q ss_pred HHHHHHHHhcCCCCHHHHHHHHHHhhcCCCCCCCCCChhhhhccccchhhhhhhhhhhhccchhc
Q 018827 105 MKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (350)
Q Consensus 105 ~KVcekVk~kg~TTYnEVAdeLV~E~~~~~~~~~~~~~~~~DeKniKRRVYDItNVLegIgLIeK 169 (350)
.+|+..+...+..|..|+|++|- .-+--+|-=+++|+..|||+.
T Consensus 13 ~~Il~~L~~~~~~t~~ela~~l~---------------------~~~~t~s~hL~~L~~aGli~~ 56 (61)
T PF12840_consen 13 LRILRLLASNGPMTVSELAEELG---------------------ISQSTVSYHLKKLEEAGLIEV 56 (61)
T ss_dssp HHHHHHHHHCSTBEHHHHHHHHT---------------------S-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHhcCCCCCHHHHHHHHC---------------------CCHHHHHHHHHHHHHCCCeEE
Confidence 56788887889999999999983 122348888999999999987
No 37
>PF14193 DUF4315: Domain of unknown function (DUF4315)
Probab=38.64 E-value=1e+02 Score=25.35 Aligned_cols=35 Identities=31% Similarity=0.395 Sum_probs=25.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 018827 186 DIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQN 220 (350)
Q Consensus 186 ~~~~Lk~El~~L~e~I~~K~~~LqEL~~q~~aLkn 220 (350)
.++++.+++++.+++|......|.+|..|+.-+-|
T Consensus 2 KleKi~~eieK~k~Kiae~Q~rlK~Le~qk~E~EN 36 (83)
T PF14193_consen 2 KLEKIRAEIEKTKEKIAELQARLKELEAQKTEAEN 36 (83)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 36677888888888887777788888776655444
No 38
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=38.63 E-value=2e+02 Score=24.50 Aligned_cols=63 Identities=14% Similarity=0.066 Sum_probs=43.7
Q ss_pred ccchhhHHHHHHHHHhcCCCCHHHHHHHHHHhhcCCCCCCCCCChhhhhccccchhhhhhhhhhhhccchhc----CCCc
Q 018827 98 RGLRQFSMKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK----DKKE 173 (350)
Q Consensus 98 ~GLR~fS~KVcekVk~kg~TTYnEVAdeLV~E~~~~~~~~~~~~~~~~DeKniKRRVYDItNVLegIgLIeK----sKk~ 173 (350)
-||-.--..|...+...+.+|-.|+|+.+.- -+--|--+++-|+.-|+|+| ..+.
T Consensus 36 ~glt~~q~~vL~~l~~~~~~t~~eLa~~l~i---------------------~~~tvsr~l~~Le~~GlI~R~~~~~DrR 94 (144)
T PRK11512 36 LDITAAQFKVLCSIRCAACITPVELKKVLSV---------------------DLGALTRMLDRLVCKGWVERLPNPNDKR 94 (144)
T ss_pred cCCCHHHHHHHHHHHHcCCCCHHHHHHHHCC---------------------CHHHHHHHHHHHHHCCCEEeccCcccCC
Confidence 4565555667777777777888888888752 23345567889999999999 2356
Q ss_pred eeecCCCC
Q 018827 174 IQWKGLPR 181 (350)
Q Consensus 174 IqW~G~~~ 181 (350)
..+.-+..
T Consensus 95 ~~~l~LT~ 102 (144)
T PRK11512 95 GVLVKLTT 102 (144)
T ss_pred eeEeEECh
Confidence 66665544
No 39
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=38.18 E-value=32 Score=23.26 Aligned_cols=25 Identities=28% Similarity=0.337 Sum_probs=20.7
Q ss_pred cchhhhhhhhhhhhccchhcCCCce
Q 018827 150 IRRRVYDALNVLMAMDIISKDKKEI 174 (350)
Q Consensus 150 iKRRVYDItNVLegIgLIeKsKk~I 174 (350)
-+..|+.+++.|+..|+|++.++.|
T Consensus 21 s~~tv~~~l~~L~~~g~l~~~~~~~ 45 (48)
T smart00419 21 TRETVSRTLKRLEKEGLISREGGRI 45 (48)
T ss_pred CHHHHHHHHHHHHHCCCEEEeCCEE
Confidence 4567899999999999999866544
No 40
>cd00584 Prefoldin_alpha Prefoldin alpha subunit; Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils.
Probab=37.80 E-value=2.1e+02 Score=24.12 Aligned_cols=46 Identities=30% Similarity=0.235 Sum_probs=21.4
Q ss_pred cCCCceeecCCCCCC---h-hhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 018827 169 KDKKEIQWKGLPRTS---L-NDIEELKAERLGLRNRIEKKTAYLQELEDQ 214 (350)
Q Consensus 169 KsKk~IqW~G~~~~s---~-~~~~~Lk~El~~L~e~I~~K~~~LqEL~~q 214 (350)
..++-+-|+|.+-.. . .-.+-++..+..|++.++.....+..+..+
T Consensus 67 ~~~~v~v~iG~g~~vE~~~~eA~~~l~~r~~~l~~~~~~l~~~l~~l~~~ 116 (129)
T cd00584 67 DTDKVLVDLGTGYYVEKDLEEAIEFLDKKIEELTKQIEKLQKELAKLKDQ 116 (129)
T ss_pred CCCEEEEEcCCCEEEEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 346667888887321 1 112233333444444444444444444433
No 41
>PF07334 IFP_35_N: Interferon-induced 35 kDa protein (IFP 35) N-terminus; InterPro: IPR009938 This entry represents the N terminus of interferon-induced 35 kDa protein (IFP 35) (approximately 80 residues long), which contains a leucine zipper motif in an alpha helical configuration []. This group of proteins also includes N-myc-interactor (Nmi), a homologous interferon-induced protein.
Probab=37.56 E-value=86 Score=25.66 Aligned_cols=25 Identities=36% Similarity=0.452 Sum_probs=18.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 018827 187 IEELKAERLGLRNRIEKKTAYLQEL 211 (350)
Q Consensus 187 ~~~Lk~El~~L~e~I~~K~~~LqEL 211 (350)
+.+|.+|-.+|+++|++..+.|+++
T Consensus 2 i~ei~eEn~~Lk~eiqkle~ELq~~ 26 (76)
T PF07334_consen 2 IHEIQEENARLKEEIQKLEAELQQN 26 (76)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3567788888888887777777764
No 42
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=36.59 E-value=87 Score=28.89 Aligned_cols=42 Identities=31% Similarity=0.360 Sum_probs=30.5
Q ss_pred ChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 018827 183 SLNDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQR 224 (350)
Q Consensus 183 s~~~~~~Lk~El~~L~e~I~~K~~~LqEL~~q~~aLknLier 224 (350)
.....+-|+..++.+.++|++..+.|..+.++.+.++-|-+|
T Consensus 83 ~~~R~~lLe~~~~~l~~ri~eLe~~l~~kad~vvsYqll~hr 124 (175)
T PRK13182 83 SSVDFEQLEAQLNTITRRLDELERQLQQKADDVVSYQLLQHR 124 (175)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHhH
Confidence 335566777777888888887777777777777777766665
No 43
>TIGR02049 gshA_ferroox glutamate--cysteine ligase, T. ferrooxidans family. This family consists of a rare family of glutamate--cysteine ligases, demonstrated first in Thiobacillus ferrooxidans and present in a few other Proteobacteria. It is the first of two enzymes for glutathione biosynthesis. It is also called gamma-glutamylcysteine synthetase.
Probab=35.55 E-value=1.9e+02 Score=30.36 Aligned_cols=22 Identities=14% Similarity=0.427 Sum_probs=16.8
Q ss_pred ccceEEEEcCCCc----EEEeccCCC
Q 018827 240 ALPFILVQTRPHA----TVEVEISED 261 (350)
Q Consensus 240 ~LPfIaVkAP~~T----~LEVp~peD 261 (350)
.-||++|||..|| .+.|-..+|
T Consensus 256 e~PfViVKADaGTYGMGImtv~~~~e 281 (403)
T TIGR02049 256 TQPYVIVKADAGTYGMGIMTATSGEE 281 (403)
T ss_pred CCCeEEEEcCCCCCCceEEEecCHHH
Confidence 3489999999999 466666555
No 44
>cd06445 ATase The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases are specific for repair of guanines with O6-alkyl adducts, however human ATase is not limited to O6-methylguanine, repairing many other adducts at the O6-position of guanine as well. ATase is widely distributed among species. Most ATases have N- and C-terminal domains. The C-terminal domain contains the conserved active-site cysteine motif (PCHR), the O6-alkylguanine binding channel, and the helix-turn-helix (HTH) DNA-binding motif. The active site is located near the recognition helix of the HTH motif. While the C-terminal domain of ATase contains residues that are necessary for DNA binding and alkyl transfer, the function of the N-terminal domain is still unknown. Removal of the N-terminal domain abolishes the activity of
Probab=35.06 E-value=42 Score=26.47 Aligned_cols=24 Identities=25% Similarity=0.264 Sum_probs=18.6
Q ss_pred HHHHHHHHHh---cCCCCHHHHHHHHH
Q 018827 104 SMKVCEKVES---KGRTTYNEVADELV 127 (350)
Q Consensus 104 S~KVcekVk~---kg~TTYnEVAdeLV 127 (350)
-.+|.+.|.+ ...+||.+||+.+-
T Consensus 2 ~~~V~~~v~~IP~G~v~TYg~iA~~~g 28 (79)
T cd06445 2 QRRVWEALRQIPYGEVTTYGQIAKLAG 28 (79)
T ss_pred HHHHHHHHhcCCCCCcCcHHHHHHHHC
Confidence 3466666664 78999999999875
No 45
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=34.91 E-value=2.5e+02 Score=26.04 Aligned_cols=77 Identities=13% Similarity=-0.009 Sum_probs=47.2
Q ss_pred ccchhhHHHHHHHHHhcCCCCHHHHHHHHHHhhcCCCCCCCCCChhhhhccccchhhhhhhhhhhhccchhc----CCCc
Q 018827 98 RGLRQFSMKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK----DKKE 173 (350)
Q Consensus 98 ~GLR~fS~KVcekVk~kg~TTYnEVAdeLV~E~~~~~~~~~~~~~~~~DeKniKRRVYDItNVLegIgLIeK----sKk~ 173 (350)
-||..--..|...+...+.+|-.|+|+.+... +--|=-+++-||.-|+|+| +.++
T Consensus 41 ~gLt~~q~~iL~~L~~~~~itq~eLa~~l~l~---------------------~sTvtr~l~rLE~kGlI~R~~~~~DrR 99 (185)
T PRK13777 41 YDLNINEHHILWIAYHLKGASISEIAKFGVMH---------------------VSTAFNFSKKLEERGYLTFSKKEDDKR 99 (185)
T ss_pred CCCCHHHHHHHHHHHhCCCcCHHHHHHHHCCC---------------------HhhHHHHHHHHHHCCCEEecCCCCCCC
Confidence 45665556677777777778888888865421 0113336778999999998 3467
Q ss_pred eeecCCCCCChhhHHHHHHHHH
Q 018827 174 IQWKGLPRTSLNDIEELKAERL 195 (350)
Q Consensus 174 IqW~G~~~~s~~~~~~Lk~El~ 195 (350)
..++-+......-.+++.....
T Consensus 100 ~~~I~LTekG~~l~~~l~~~~~ 121 (185)
T PRK13777 100 NTYIELTEKGEELLLETMEEYD 121 (185)
T ss_pred eeEEEECHHHHHHHHHHHHHHH
Confidence 7776665433333334433333
No 46
>PRK09462 fur ferric uptake regulator; Provisional
Probab=34.56 E-value=69 Score=27.78 Aligned_cols=56 Identities=18% Similarity=0.253 Sum_probs=41.1
Q ss_pred ccchhhH--HHHHHHHHh--cCCCCHHHHHHHHHHhhcCCCCCCCCCChhhhhccccchhhhhhhhhhhhccchhc
Q 018827 98 RGLRQFS--MKVCEKVES--KGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (350)
Q Consensus 98 ~GLR~fS--~KVcekVk~--kg~TTYnEVAdeLV~E~~~~~~~~~~~~~~~~DeKniKRRVYDItNVLegIgLIeK 169 (350)
+|||.-. ..|.+.+.+ .+..|-.||.+.|..+... .-+==||-+|+.|+..|||.|
T Consensus 11 ~glr~T~qR~~Il~~l~~~~~~h~sa~eI~~~l~~~~~~----------------i~~aTVYR~L~~L~e~Gli~~ 70 (148)
T PRK09462 11 AGLKVTLPRLKILEVLQEPDNHHVSAEDLYKRLIDMGEE----------------IGLATVYRVLNQFDDAGIVTR 70 (148)
T ss_pred cCCCCCHHHHHHHHHHHhCCCCCCCHHHHHHHHHhhCCC----------------CCHHHHHHHHHHHHHCCCEEE
Confidence 4666544 458898986 3588888888887754321 223459999999999999998
No 47
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=34.29 E-value=81 Score=27.76 Aligned_cols=63 Identities=22% Similarity=0.234 Sum_probs=42.2
Q ss_pred ccchhhH--HHHHHHHHhc-CCCCHHHHHHHHHHhhcCCCCCCCCCChhhhhccccchhhhhhhhhhhhccchhc--CCC
Q 018827 98 RGLRQFS--MKVCEKVESK-GRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK--DKK 172 (350)
Q Consensus 98 ~GLR~fS--~KVcekVk~k-g~TTYnEVAdeLV~E~~~~~~~~~~~~~~~~DeKniKRRVYDItNVLegIgLIeK--sKk 172 (350)
+|||.=- .+|.+.+.+. +..|-.||-++|..++... -.==||-+|+.|+..|||.+ ..+
T Consensus 15 ~glr~T~qR~~vl~~L~~~~~~~sAeei~~~l~~~~p~i----------------slaTVYr~L~~l~e~Glv~~~~~~~ 78 (145)
T COG0735 15 AGLRLTPQRLAVLELLLEADGHLSAEELYEELREEGPGI----------------SLATVYRTLKLLEEAGLVHRLEFEG 78 (145)
T ss_pred cCCCcCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCC----------------CHhHHHHHHHHHHHCCCEEEEEeCC
Confidence 5565544 4588888864 5577767777766532221 13359999999999999999 445
Q ss_pred ceee
Q 018827 173 EIQW 176 (350)
Q Consensus 173 ~IqW 176 (350)
...|
T Consensus 79 ~~~~ 82 (145)
T COG0735 79 GKTR 82 (145)
T ss_pred CEEE
Confidence 4444
No 48
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=33.44 E-value=67 Score=22.78 Aligned_cols=26 Identities=31% Similarity=0.574 Sum_probs=20.5
Q ss_pred hhHHHHHHHHHhcCCCCHHHHHHHHH
Q 018827 102 QFSMKVCEKVESKGRTTYNEVADELV 127 (350)
Q Consensus 102 ~fS~KVcekVk~kg~TTYnEVAdeLV 127 (350)
.+=.++...++..++.+|.++|.++-
T Consensus 3 ~~D~~Il~~Lq~d~r~s~~~la~~lg 28 (42)
T PF13404_consen 3 ELDRKILRLLQEDGRRSYAELAEELG 28 (42)
T ss_dssp HHHHHHHHHHHH-TTS-HHHHHHHHT
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHC
Confidence 35578899999999999999999974
No 49
>TIGR01242 26Sp45 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
Probab=33.40 E-value=1.2e+02 Score=30.03 Aligned_cols=71 Identities=15% Similarity=0.054 Sum_probs=34.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCcccceEEEEcCCCcEEEeccC
Q 018827 189 ELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQRNERLYSSGNAPSGGVALPFILVQTRPHATVEVEIS 259 (350)
Q Consensus 189 ~Lk~El~~L~e~I~~K~~~LqEL~~q~~aLknLierNk~ly~s~~~~~e~i~LPfIaVkAP~~T~LEVp~p 259 (350)
+|+.+.+.|++.++....++.++..+...++..+++++..........+.+.-=-++|++..++.+-+...
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 (364)
T TIGR01242 3 ELDVRIRKLEDEKRSLEKEKIRLERELERLRSEIERLRSPPLIVGTVLEVLDDNRVVVKSSTGPNFVVNVS 73 (364)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeEEEEEEEEecCCEEEEEeCCCCEEEEecc
Confidence 34455555555555555555555555555555555544321100000011111145788888888766543
No 50
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=33.07 E-value=1.9e+02 Score=26.83 Aligned_cols=43 Identities=26% Similarity=0.462 Sum_probs=24.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHh
Q 018827 186 DIEELKAERLGLRNRIEKKTAYLQE-------LEDQFVGLQNLIQRNERL 228 (350)
Q Consensus 186 ~~~~Lk~El~~L~e~I~~K~~~LqE-------L~~q~~aLknLierNk~l 228 (350)
+.+.|+.|+.+|+++++.....+.+ +...+.+|-.+++|-..+
T Consensus 105 e~~~l~~e~~~l~~~~e~Le~e~~~L~~~~~~~~eDY~~L~~Im~RARkl 154 (161)
T TIGR02894 105 ENERLKNQNESLQKRNEELEKELEKLRQRLSTIEEDYQTLIDIMDRARKL 154 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445555555555444444444444 455677777777776554
No 51
>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=32.92 E-value=46 Score=23.49 Aligned_cols=42 Identities=24% Similarity=0.308 Sum_probs=29.2
Q ss_pred HHHHHHHhcCCCCHHHHHHHHHHhhcCCCCCCCCCChhhhhccccchhhhhhhhhhhhccchhc
Q 018827 106 KVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (350)
Q Consensus 106 KVcekVk~kg~TTYnEVAdeLV~E~~~~~~~~~~~~~~~~DeKniKRRVYDItNVLegIgLIeK 169 (350)
++...+.+ |..+..|+|+.|- .-+--|+==++.|+..|||+|
T Consensus 6 ~Il~~L~~-~~~~~~el~~~l~---------------------~s~~~vs~hL~~L~~~glV~~ 47 (47)
T PF01022_consen 6 RILKLLSE-GPLTVSELAEELG---------------------LSQSTVSHHLKKLREAGLVEK 47 (47)
T ss_dssp HHHHHHTT-SSEEHHHHHHHHT---------------------S-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHh-CCCchhhHHHhcc---------------------ccchHHHHHHHHHHHCcCeeC
Confidence 34555554 7888888888874 223345667889999999976
No 52
>COG5174 TFA2 Transcription initiation factor IIE, beta subunit [Transcription]
Probab=32.32 E-value=88 Score=30.87 Aligned_cols=74 Identities=27% Similarity=0.256 Sum_probs=39.7
Q ss_pred CCCCccch-hhcccccccCCCCCCCCcccccccccCCCC--CC--CccccCccchhhHHH---HHHHHHhc-CCCCHHHH
Q 018827 52 TPASDSTF-LRLNHLDIHGDDAGSQGAVVGGKKKKRGQR--AG--GGDKSGRGLRQFSMK---VCEKVESK-GRTTYNEV 122 (350)
Q Consensus 52 ~~~~~~~~-~~~~~~~~~~~~~~s~~~~~~~~kk~~~~~--~~--~~~k~~~GLR~fS~K---VcekVk~k-g~TTYnEV 122 (350)
.+|+.-+| .-||--|-|.-.+-|.++.. + ||+|-.+ ++ -+--.+-+ +|.+.+ +.|.++++ ...+++|+
T Consensus 28 r~asp~~~e~~LnsndghsS~a~s~gs~~-~-kk~R~~~~~~~~~q~~d~gv~-~H~~s~lh~aieylk~~~~P~~~eEi 104 (285)
T COG5174 28 RMASPCHFEVGLNSNDGHSSTAWSKGSSP-T-KKARIPRMDRDRIQSIDRGVQ-RHTNSYLHAAIEYLKQHDRPLSFEEI 104 (285)
T ss_pred ccCCccchhcccccCCCCcccccccCCCc-c-ccccccchhHhhhcccccccc-ccchHHHHHHHHHHHHcCCcccHHHH
Confidence 34555455 25555454444455554333 3 4444222 11 22233344 666644 56777775 57899999
Q ss_pred HHHHHH
Q 018827 123 ADELVA 128 (350)
Q Consensus 123 AdeLV~ 128 (350)
+|-|-.
T Consensus 105 ~dyls~ 110 (285)
T COG5174 105 KDYLSI 110 (285)
T ss_pred HHHhcC
Confidence 998853
No 53
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=31.88 E-value=81 Score=26.06 Aligned_cols=64 Identities=23% Similarity=0.321 Sum_probs=42.5
Q ss_pred ccchhhH--HHHHHHHHh-cCCCCHHHHHHHHHHhhcCCCCCCCCCChhhhhccccchhhhhhhhhhhhccchhc---CC
Q 018827 98 RGLRQFS--MKVCEKVES-KGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK---DK 171 (350)
Q Consensus 98 ~GLR~fS--~KVcekVk~-kg~TTYnEVAdeLV~E~~~~~~~~~~~~~~~~DeKniKRRVYDItNVLegIgLIeK---sK 171 (350)
+|||.=. ..|.+.+.+ .+..|-.||.+.|-.+.. ..-+==||-+|+.|+..|||.| ..
T Consensus 2 ~glr~T~~R~~Il~~l~~~~~~~ta~ei~~~l~~~~~----------------~is~~TVYR~L~~L~e~Gli~~~~~~~ 65 (120)
T PF01475_consen 2 AGLRLTPQRLAILELLKESPEHLTAEEIYDKLRKKGP----------------RISLATVYRTLDLLEEAGLIRKIEFGD 65 (120)
T ss_dssp TTHHHHHHHHHHHHHHHHHSSSEEHHHHHHHHHHTTT----------------T--HHHHHHHHHHHHHTTSEEEEEETT
T ss_pred CCCCCCHHHHHHHHHHHcCCCCCCHHHHHHHhhhccC----------------CcCHHHHHHHHHHHHHCCeEEEEEcCC
Confidence 3555544 347787877 458888888888774311 1223459999999999999999 33
Q ss_pred Cceeec
Q 018827 172 KEIQWK 177 (350)
Q Consensus 172 k~IqW~ 177 (350)
+...+.
T Consensus 66 ~~~~Y~ 71 (120)
T PF01475_consen 66 GESRYE 71 (120)
T ss_dssp SEEEEE
T ss_pred CcceEe
Confidence 444443
No 54
>COG3105 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.44 E-value=2.2e+02 Score=25.75 Aligned_cols=49 Identities=18% Similarity=0.217 Sum_probs=34.9
Q ss_pred CChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHhhh
Q 018827 182 TSLNDIEELKAERLGLRNRIEKKTAYLQELEDQ-FVGLQNLIQRNERLYS 230 (350)
Q Consensus 182 ~s~~~~~~Lk~El~~L~e~I~~K~~~LqEL~~q-~~aLknLierNk~ly~ 230 (350)
.......+++.|+++++.++++-+++|...-.+ -.-|++|..+-+.+|.
T Consensus 31 ~~~k~q~~~q~ELe~~K~~ld~~rqel~~HFa~sAeLlktl~~dYqklyq 80 (138)
T COG3105 31 RKLKQQQKLQYELEKVKAQLDEYRQELVKHFARSAELLKTLAQDYQKLYQ 80 (138)
T ss_pred hhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445667789999999998888777666544433 3457888888777764
No 55
>PRK10803 tol-pal system protein YbgF; Provisional
Probab=31.19 E-value=1.4e+02 Score=28.90 Aligned_cols=32 Identities=13% Similarity=0.255 Sum_probs=22.2
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 018827 184 LNDIEELKAERLGLRNRIEKKTAYLQELEDQF 215 (350)
Q Consensus 184 ~~~~~~Lk~El~~L~e~I~~K~~~LqEL~~q~ 215 (350)
..+++.|+.|+.+|+..|++..-+|+++..++
T Consensus 60 ~~ql~~lq~ev~~LrG~~E~~~~~l~~~~~rq 91 (263)
T PRK10803 60 QQQLSDNQSDIDSLRGQIQENQYQLNQVVERQ 91 (263)
T ss_pred HHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHH
Confidence 35667777777777777777777777666544
No 56
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=30.89 E-value=98 Score=21.79 Aligned_cols=44 Identities=16% Similarity=0.166 Sum_probs=33.2
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhhcCCCCCCCCCChhhhhccccchhhhhhhhhhhhccchhc
Q 018827 104 SMKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (350)
Q Consensus 104 S~KVcekVk~kg~TTYnEVAdeLV~E~~~~~~~~~~~~~~~~DeKniKRRVYDItNVLegIgLIeK 169 (350)
..+|...+...+ .++.|+|+.|- .-+.-||=+++.|+..|+|.+
T Consensus 9 ~~~il~~l~~~~-~~~~ei~~~~~---------------------i~~~~i~~~l~~L~~~g~i~~ 52 (78)
T cd00090 9 RLRILRLLLEGP-LTVSELAERLG---------------------LSQSTVSRHLKKLEEAGLVES 52 (78)
T ss_pred HHHHHHHHHHCC-cCHHHHHHHHC---------------------cCHhHHHHHHHHHHHCCCeEE
Confidence 456777766666 88999888762 123567888999999999998
No 57
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=30.06 E-value=1.5e+02 Score=28.34 Aligned_cols=45 Identities=20% Similarity=0.321 Sum_probs=36.7
Q ss_pred HHHHHHHHhcCCCCHHHHHHHHHHhhcCCCCCCCCCChhhhhccccchhhhhhhhhhhhccchhcC
Q 018827 105 MKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKD 170 (350)
Q Consensus 105 ~KVcekVk~kg~TTYnEVAdeLV~E~~~~~~~~~~~~~~~~DeKniKRRVYDItNVLegIgLIeKs 170 (350)
.++.+.+++++..+.+|+|+.|- ..+.++||. |+.|+.-|+|.|-
T Consensus 8 ~~Il~~L~~~~~v~v~eLa~~l~-----------------VS~~TIRRD----L~~Le~~g~l~r~ 52 (256)
T PRK10434 8 AAILEYLQKQGKTSVEELAQYFD-----------------TTGTTIRKD----LVILEHAGTVIRT 52 (256)
T ss_pred HHHHHHHHHcCCEEHHHHHHHHC-----------------CCHHHHHHH----HHHHHHCCCEEEE
Confidence 46899999999999999999884 123478887 6889999999883
No 58
>smart00338 BRLZ basic region leucin zipper.
Probab=30.00 E-value=2.2e+02 Score=21.44 Aligned_cols=31 Identities=23% Similarity=0.258 Sum_probs=13.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 018827 188 EELKAERLGLRNRIEKKTAYLQELEDQFVGL 218 (350)
Q Consensus 188 ~~Lk~El~~L~e~I~~K~~~LqEL~~q~~aL 218 (350)
..|+.++..|..........+..|..+...|
T Consensus 29 ~~Le~~~~~L~~en~~L~~~~~~l~~e~~~l 59 (65)
T smart00338 29 EELERKVEQLEAENERLKKEIERLRRELEKL 59 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444444444444444444444333333
No 59
>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=29.99 E-value=1.1e+02 Score=21.99 Aligned_cols=40 Identities=28% Similarity=0.201 Sum_probs=30.1
Q ss_pred cCCCCHHHHHHHHHHhhcCCCCCCCCCChhhhhccccchhhhhhhhhhhhccchhcCC-Cce
Q 018827 114 KGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKDK-KEI 174 (350)
Q Consensus 114 kg~TTYnEVAdeLV~E~~~~~~~~~~~~~~~~DeKniKRRVYDItNVLegIgLIeKsK-k~I 174 (350)
.+..+..|+|+.+- .-+.-|+-+++.|+.-|+|++.. +.|
T Consensus 23 ~~~~s~~ela~~~g---------------------~s~~tv~r~l~~L~~~g~i~~~~~~~~ 63 (67)
T cd00092 23 QLPLTRQEIADYLG---------------------LTRETVSRTLKELEEEGLISRRGRGKY 63 (67)
T ss_pred cCCcCHHHHHHHHC---------------------CCHHHHHHHHHHHHHCCCEEecCCCeE
Confidence 34567777777763 34677899999999999999954 444
No 60
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=28.84 E-value=2.9e+02 Score=26.15 Aligned_cols=50 Identities=16% Similarity=0.153 Sum_probs=37.7
Q ss_pred HHHHHHHHhc-CCCCHHHHHHHHHHhhcCCCCCCCCCChhhhhccccchhhhhhhhhhhhccchhcC--CCcee
Q 018827 105 MKVCEKVESK-GRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKD--KKEIQ 175 (350)
Q Consensus 105 ~KVcekVk~k-g~TTYnEVAdeLV~E~~~~~~~~~~~~~~~~DeKniKRRVYDItNVLegIgLIeKs--Kk~Iq 175 (350)
..|.+.+-.. +..+..|+|+++- .-|--||-+|+-|+..|+|+++ .+.++
T Consensus 14 l~iL~~l~~~~~~ls~~eia~~lg---------------------l~kstv~RlL~tL~~~g~v~~~~~~~~Y~ 66 (263)
T PRK09834 14 LMVLRALNRLDGGATVGLLAELTG---------------------LHRTTVRRLLETLQEEGYVRRSASDDSFR 66 (263)
T ss_pred HHHHHHHHhcCCCCCHHHHHHHHC---------------------cCHHHHHHHHHHHHHCCCEEEecCCCcEE
Confidence 5567777554 4488999999883 2356799999999999999993 55555
No 61
>PF04977 DivIC: Septum formation initiator; InterPro: IPR007060 DivIC, from the spore-forming, Gram-positive bacterium Bacillus subtilis, is necessary for both vegetative and sporulation septum formation []. These proteins are mainly composed of an N-terminal coiled-coil. DivIB, DivIC and FtsL inter-depend on each other for stabilisation and localisation. The latter two form a heterodimer. DivIC is always centre cell but the other two associate with it during septation [].; GO: 0007049 cell cycle
Probab=28.30 E-value=1.4e+02 Score=22.56 Aligned_cols=32 Identities=25% Similarity=0.278 Sum_probs=14.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 018827 187 IEELKAERLGLRNRIEKKTAYLQELEDQFVGL 218 (350)
Q Consensus 187 ~~~Lk~El~~L~e~I~~K~~~LqEL~~q~~aL 218 (350)
...++.++..++..+++.++...+|..+...|
T Consensus 19 ~~~~~~ei~~l~~~i~~l~~e~~~L~~ei~~l 50 (80)
T PF04977_consen 19 YYQLNQEIAELQKEIEELKKENEELKEEIERL 50 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 34455555555544444444444444433333
No 62
>PF11594 Med28: Mediator complex subunit 28; InterPro: IPR021640 Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species [],[]. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function []. Subunit Med28 of the Mediator may function as a scaffolding protein within Mediator by maintaining the stability of a submodule within the head module, and components of this submodule act together in a gene-regulatory programme to suppress smooth muscle cell differentiation. Thus, mammalian Mediator subunit Med28 functions as a repressor of smooth muscle-cell differentiation, which could have implications for disorders associated with abnormalities in smooth muscle cell growth and differentiation, including atherosclerosis, asthma, hypertension, and smooth muscle tumours [].
Probab=28.20 E-value=2.1e+02 Score=24.87 Aligned_cols=38 Identities=21% Similarity=0.285 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 018827 188 EELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQRN 225 (350)
Q Consensus 188 ~~Lk~El~~L~e~I~~K~~~LqEL~~q~~aLknLierN 225 (350)
..|++|..+|++.+..|.+.++.+......+++|+..-
T Consensus 38 ~~lkEEi~eLK~ElqRKe~Ll~Kh~~kI~~w~~lL~d~ 75 (106)
T PF11594_consen 38 QVLKEEINELKEELQRKEQLLQKHYEKIDYWEKLLSDA 75 (106)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35677777777777888888888877777788877653
No 63
>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=27.80 E-value=77 Score=22.55 Aligned_cols=39 Identities=28% Similarity=0.306 Sum_probs=28.8
Q ss_pred HHHHHH-HhcCCCCHHHHHHHHHHhhcCCCCCCCCCChhhhhccccchhhhhhhhhhhhcc
Q 018827 106 KVCEKV-ESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMD 165 (350)
Q Consensus 106 KVcekV-k~kg~TTYnEVAdeLV~E~~~~~~~~~~~~~~~~DeKniKRRVYDItNVLegIg 165 (350)
++...+ +.++.+|..|+|++|- +-+|=||--++-|...+
T Consensus 4 ~il~~L~~~~~~it~~eLa~~l~---------------------vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 4 QILKLLLESKEPITAKELAEELG---------------------VSRRTIRRDIKELREWG 43 (55)
T ss_dssp HHHHHHHHTTTSBEHHHHHHHCT---------------------S-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHcCCCcCHHHHHHHhC---------------------CCHHHHHHHHHHHHHCC
Confidence 455566 6677799999998873 56777888888888877
No 64
>PRK00901 methylated-DNA--protein-cysteine methyltransferase; Provisional
Probab=27.73 E-value=59 Score=29.34 Aligned_cols=27 Identities=22% Similarity=0.394 Sum_probs=23.3
Q ss_pred hhhHHHHHHHHHh---cCCCCHHHHHHHHH
Q 018827 101 RQFSMKVCEKVES---KGRTTYNEVADELV 127 (350)
Q Consensus 101 R~fS~KVcekVk~---kg~TTYnEVAdeLV 127 (350)
--|-.+|++.+.+ ..++||.|||..|-
T Consensus 72 t~fq~~Vw~~l~~Ip~G~t~tY~~lA~~~g 101 (155)
T PRK00901 72 TEFQKKVWKALQEIPYGETRSYKEIAVNIG 101 (155)
T ss_pred ChHHHHHHHHHccCCCCCcCCHHHHHHHHC
Confidence 3789999999988 67999999999865
No 65
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=26.97 E-value=78 Score=26.81 Aligned_cols=51 Identities=16% Similarity=0.262 Sum_probs=37.5
Q ss_pred chhhHHHHHHHHHhcCCCCHHHHHHHHHHhhcCCCCCCCCCChhhhhccccchhhhhhhhhhhhccchhcCC
Q 018827 100 LRQFSMKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKDK 171 (350)
Q Consensus 100 LR~fS~KVcekVk~kg~TTYnEVAdeLV~E~~~~~~~~~~~~~~~~DeKniKRRVYDItNVLegIgLIeKsK 171 (350)
|--+=.++.+.++..++++|.|+|++|-- .....+|| +.-|+.-|||.+-.
T Consensus 6 lD~~D~~IL~~L~~d~r~~~~eia~~lgl-----------------S~~~v~~R----i~~L~~~GiI~~~~ 56 (154)
T COG1522 6 LDDIDRRILRLLQEDARISNAELAERVGL-----------------SPSTVLRR----IKRLEEEGVIKGYT 56 (154)
T ss_pred ccHHHHHHHHHHHHhCCCCHHHHHHHHCC-----------------CHHHHHHH----HHHHHHCCceeeEE
Confidence 34455789999999999999999999851 11234444 45689999999843
No 66
>COG0350 Ada Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]
Probab=26.85 E-value=58 Score=29.58 Aligned_cols=27 Identities=26% Similarity=0.364 Sum_probs=23.6
Q ss_pred hhHHHHHHHHHh---cCCCCHHHHHHHHHH
Q 018827 102 QFSMKVCEKVES---KGRTTYNEVADELVA 128 (350)
Q Consensus 102 ~fS~KVcekVk~---kg~TTYnEVAdeLV~ 128 (350)
-|-.+|.+.+++ ..++||.|+|..|-.
T Consensus 88 ~Fq~~Vw~aL~~IP~Get~TY~eiA~~ig~ 117 (168)
T COG0350 88 GFQGRVWQALREIPYGETVTYGEIARRLGR 117 (168)
T ss_pred hHHHHHHHHHhcCCCCCcEeHHHHHHHhCC
Confidence 688999999988 678999999999863
No 67
>PF12252 SidE: Dot/Icm substrate protein; InterPro: IPR021014 This entry represents bacterial proteins that are typically between 397 and 1543 amino acids in length including SidE protein in the Dot/Icm pathway of Legionella pneumophila bacteria. There is little literature describing the family.
Probab=26.82 E-value=1.4e+02 Score=35.27 Aligned_cols=73 Identities=19% Similarity=0.395 Sum_probs=56.1
Q ss_pred hhccccchhhhhhhhhhhhccchhcCCCceeecCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 018827 145 YDEKNIRRRVYDALNVLMAMDIISKDKKEIQWKGLPRTSLNDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQN 220 (350)
Q Consensus 145 ~DeKniKRRVYDItNVLegIgLIeKsKk~IqW~G~~~~s~~~~~~Lk~El~~L~e~I~~K~~~LqEL~~q~~aLkn 220 (350)
.+..++|.-|+|.-|..+.+.|+..+|.... .|...--.+++++|+++++.+...+ ...+|-+.++|..+|..
T Consensus 1121 ~~l~~ikK~ia~lnnlqqElklLRnEK~Rmh-~~~dkVDFSDIEkLE~qLq~~~~kL--~dAyl~eitKqIsaLe~ 1193 (1439)
T PF12252_consen 1121 DNLDSIKKAIANLNNLQQELKLLRNEKIRMH-SGTDKVDFSDIEKLEKQLQVIHTKL--YDAYLVEITKQISALEK 1193 (1439)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHhHHHhhc-cCCCcccHHHHHHHHHHHHHhhhhh--HHHHHHHHHHHHHHHHh
Confidence 4566899999999999999999998887766 3444455789999999988776654 45677777777666654
No 68
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=26.72 E-value=1.1e+02 Score=22.73 Aligned_cols=51 Identities=20% Similarity=0.191 Sum_probs=34.4
Q ss_pred HHHHHHHHHHhhcCCCCCCC----CCChhhhhccccchhhhhhhhhhhhccchhc
Q 018827 119 YNEVADELVAEFADPSNSLA----TPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (350)
Q Consensus 119 YnEVAdeLV~E~~~~~~~~~----~~~~~~~DeKniKRRVYDItNVLegIgLIeK 169 (350)
|.+|++.|...+....-..+ +..+-....++-+.=|..|++.|+..|+|++
T Consensus 2 ~~~i~~~l~~~I~~g~~~~g~~lps~~~la~~~~vsr~tvr~al~~L~~~g~i~~ 56 (64)
T PF00392_consen 2 YEQIYDQLRQAILSGRLPPGDRLPSERELAERYGVSRTTVREALRRLEAEGLIER 56 (64)
T ss_dssp HHHHHHHHHHHHHTTSS-TTSBE--HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHHHHHcCCCCCCCEeCCHHHHHHHhccCCcHHHHHHHHHHHCCcEEE
Confidence 66777777776654322111 1224455667888889999999999999988
No 69
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=26.44 E-value=71 Score=22.86 Aligned_cols=44 Identities=20% Similarity=0.268 Sum_probs=34.8
Q ss_pred HHHHHHHHhcCCCCHHHHHHHHHHhhcCCCCCCCCCChhhhhccccchhhhhhhhhhhhccchhc
Q 018827 105 MKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (350)
Q Consensus 105 ~KVcekVk~kg~TTYnEVAdeLV~E~~~~~~~~~~~~~~~~DeKniKRRVYDItNVLegIgLIeK 169 (350)
..|...+.+.+.++..|+|+.+- .-+--|-.+++=|+.-|+|+|
T Consensus 6 ~~iL~~l~~~~~~~~~~la~~~~---------------------~~~~~~t~~i~~L~~~g~I~r 49 (59)
T PF01047_consen 6 FRILRILYENGGITQSELAEKLG---------------------ISRSTVTRIIKRLEKKGLIER 49 (59)
T ss_dssp HHHHHHHHHHSSEEHHHHHHHHT---------------------S-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHcCCCCHHHHHHHHC---------------------CChhHHHHHHHHHHHCCCEEe
Confidence 45677788888899999999875 234556778899999999998
No 70
>PF14931 IFT20: Intraflagellar transport complex B, subunit 20
Probab=26.29 E-value=69 Score=27.94 Aligned_cols=35 Identities=23% Similarity=0.343 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 018827 188 EELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLI 222 (350)
Q Consensus 188 ~~Lk~El~~L~e~I~~K~~~LqEL~~q~~aLknLi 222 (350)
+.-+.+...|...|.+|+.+|..|..++.+|+.+-
T Consensus 76 k~R~~~~q~lq~~I~Ek~~eLERl~~E~~sL~kve 110 (120)
T PF14931_consen 76 KQREAQQQQLQALIAEKKMELERLRSEYESLQKVE 110 (120)
T ss_pred HhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33445556777889999999999999988887753
No 71
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=26.01 E-value=4.2e+02 Score=24.84 Aligned_cols=52 Identities=8% Similarity=0.249 Sum_probs=39.2
Q ss_pred ccchhhH--HHHHHHHHhcCCCCHHHHHHHHHHhhcCCCCCCCCCChhhhhccccchhhhhhhhhhhhccchhcC
Q 018827 98 RGLRQFS--MKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKD 170 (350)
Q Consensus 98 ~GLR~fS--~KVcekVk~kg~TTYnEVAdeLV~E~~~~~~~~~~~~~~~~DeKniKRRVYDItNVLegIgLIeKs 170 (350)
.++.-+. ..|.+.+.+.+..+..|+|+++- -=|=-+|-+++.|+..|+++++
T Consensus 8 ~~v~sl~r~l~IL~~l~~~~~l~l~eia~~lg---------------------l~kstv~Rll~tL~~~G~l~~~ 61 (257)
T PRK15090 8 DSVSSVLKVFGILQALGEEREIGITELSQRVM---------------------MSKSTVYRFLQTMKTLGYVAQE 61 (257)
T ss_pred cccHHHHHHHHHHHHhhcCCCCCHHHHHHHHC---------------------cCHHHHHHHHHHHHHCCCEEEc
Confidence 4444444 56777777666788999988874 2345689999999999999993
No 72
>PF08317 Spc7: Spc7 kinetochore protein; InterPro: IPR013253 This entry consists of cell division proteins which are required for kinetochore-spindle association [].
Probab=25.86 E-value=2.3e+02 Score=28.01 Aligned_cols=37 Identities=30% Similarity=0.443 Sum_probs=19.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 018827 187 IEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQ 223 (350)
Q Consensus 187 ~~~Lk~El~~L~e~I~~K~~~LqEL~~q~~aLknLie 223 (350)
+..++.++..+...|..+++.|.+|..+...++.-++
T Consensus 211 L~~lr~eL~~~~~~i~~~k~~l~el~~el~~l~~~i~ 247 (325)
T PF08317_consen 211 LEALRQELAEQKEEIEAKKKELAELQEELEELEEKIE 247 (325)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444555555555566566666666655555444443
No 73
>TIGR02147 Fsuc_second hypothetical protein, TIGR02147. This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.
Probab=25.64 E-value=5.9e+02 Score=25.00 Aligned_cols=24 Identities=25% Similarity=0.512 Sum_probs=18.5
Q ss_pred hhhhhhhhhhhccchhcCCCceeec
Q 018827 153 RVYDALNVLMAMDIISKDKKEIQWK 177 (350)
Q Consensus 153 RVYDItNVLegIgLIeKsKk~IqW~ 177 (350)
.|=|+|..|+-+|||+|+.+. .|.
T Consensus 155 ev~~sL~~L~~~glikk~~~g-~y~ 178 (271)
T TIGR02147 155 QVKESLDLLERLGLIKKNEDG-FYK 178 (271)
T ss_pred HHHHHHHHHHHCCCeeECCCC-cEE
Confidence 355899999999999996543 554
No 74
>PF06295 DUF1043: Protein of unknown function (DUF1043); InterPro: IPR009386 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=25.55 E-value=3.3e+02 Score=23.56 Aligned_cols=45 Identities=20% Similarity=0.213 Sum_probs=29.3
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHhh
Q 018827 185 NDIEELKAERLGLRNRIEKKTAYLQELED-QFVGLQNLIQRNERLY 229 (350)
Q Consensus 185 ~~~~~Lk~El~~L~e~I~~K~~~LqEL~~-q~~aLknLierNk~ly 229 (350)
.+...|+.|+++.+..+++-++.+.+... ....|.+|.+.-+.+|
T Consensus 25 ~~q~~l~~eL~~~k~el~~yk~~V~~HF~~ta~Ll~~l~~~Y~~l~ 70 (128)
T PF06295_consen 25 QKQAKLEQELEQAKQELEQYKQEVNDHFAQTAELLDNLTQDYQKLY 70 (128)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44568888888888888777777766443 3344566666555554
No 75
>PF08886 GshA: Glutamate-cysteine ligase; InterPro: IPR011718 This entry represents a rare family of glutamate--cysteine ligases, demonstrated first in Thiobacillus ferrooxidans and present in a few other Proteobacteria []. It is the first of two enzymes for glutathione biosynthesis. It is also called gamma-glutamylcysteine synthetase.; PDB: 3K1T_A.
Probab=25.52 E-value=1.6e+02 Score=30.94 Aligned_cols=22 Identities=18% Similarity=0.483 Sum_probs=14.6
Q ss_pred ccceEEEEcCCCc----EEEeccCCC
Q 018827 240 ALPFILVQTRPHA----TVEVEISED 261 (350)
Q Consensus 240 ~LPfIaVkAP~~T----~LEVp~peD 261 (350)
.-||++|||..|| .+.|-+.+|
T Consensus 259 e~PfV~VKAD~GTYGMGImtV~~~~e 284 (404)
T PF08886_consen 259 EKPFVFVKADAGTYGMGIMTVKSGDE 284 (404)
T ss_dssp S---EEEEEE-GGG-EEEEEESSGGG
T ss_pred CCceEEEEcCCCCCCceEEEecCHHH
Confidence 3489999999999 577777766
No 76
>PF07195 FliD_C: Flagellar hook-associated protein 2 C-terminus; InterPro: IPR010809 The flagellar hook-associated protein 2 (HAP2 or FliD) forms the distal end of the flagella, and plays a role in mucin specific adhesion of the bacteria []. This alignment covers the C-terminal region of the flagellar hook-associated protein 2.; GO: 0007155 cell adhesion, 0009288 bacterial-type flagellum
Probab=25.20 E-value=1.7e+02 Score=27.48 Aligned_cols=35 Identities=31% Similarity=0.501 Sum_probs=17.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 018827 186 DIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQ 223 (350)
Q Consensus 186 ~~~~Lk~El~~L~e~I~~K~~~LqEL~~q~~aLknLie 223 (350)
++..+..++..++++++.+.+. |..|+.+|..++.
T Consensus 201 ~~~~~~~~i~~~~~rl~~~~~~---l~~qf~~me~~i~ 235 (239)
T PF07195_consen 201 QIKSLDKQIEDLEERLESKEER---LRKQFSAMESLIS 235 (239)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHH
Confidence 3444445555555554444332 3346666666654
No 77
>KOG2264 consensus Exostosin EXT1L [Signal transduction mechanisms]
Probab=24.82 E-value=1.7e+02 Score=32.55 Aligned_cols=15 Identities=20% Similarity=0.273 Sum_probs=8.1
Q ss_pred CCCCCCCCCC-CCCCC
Q 018827 304 DDGEGSSMAG-VYQPP 318 (350)
Q Consensus 304 ~~~~~s~~~~-~~~~~ 318 (350)
|-+..|..+| +|..+
T Consensus 278 Nl~r~s~~~n~lyn~~ 293 (907)
T KOG2264|consen 278 NLGRPSDTQNLLYNFQ 293 (907)
T ss_pred EccCccccccceeEec
Confidence 4455666666 44443
No 78
>PF02996 Prefoldin: Prefoldin subunit; InterPro: IPR004127 This entry comprises of several prefoldin subunits. Prefoldin (PFD) is a chaperone that interacts exclusively with type II chaperonins, hetero-oligomers lacking an obligate co-chaperonin that are found only in eukaryotes (chaperonin-containing T-complex polypeptide-1 (CCT)) and archaea. Eukaryotic PFD is a multi-subunit complex containing six polypeptides in the molecular mass range of 14-23 kDa. In archaea, on the other hand, PFD is composed of two types of subunits, two alpha and four beta. The six subunits associate to form two back-to-back up-and-down eight-stranded barrels, from which hang six coiled coils. Each subunit contributes one (beta subunits) or two (alpha subunits) beta hairpin turns to the barrels. The coiled coils are formed by the N and C termini of an individual subunit. Overall, this unique arrangement resembles a jellyfish. The eukaryotic PFD hexamer is composed of six different subunits; however, these can be grouped into two alpha-like (PFD3 and -5) and four beta-like (PFD1, -2, -4, and -6) subunits based on amino acid sequence similarity with their archaeal counterparts. Eukaryotic PFD has a six-legged structure similar to that seen in the archaeal homologue [, ]. This family contains the archaeal alpha subunit, eukaryotic prefoldin subunits 3 and 5 and the UXT (ubiquitously expressed transcript) family. Eukaryotic PFD has been shown to bind both actin and tubulin co-translationally. The chaperone then delivers the target protein to CCT, interacting with the chaperonin through the tips of the coiled coils. No authentic target proteins of any archaeal PFD have been identified, to date.; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0016272 prefoldin complex; PDB: 1FXK_C 2ZDI_C.
Probab=24.80 E-value=1.3e+02 Score=24.62 Aligned_cols=68 Identities=24% Similarity=0.153 Sum_probs=36.6
Q ss_pred hhhhhhhhccchhcCCCceeecCCCCCC----hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 018827 156 DALNVLMAMDIISKDKKEIQWKGLPRTS----LNDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQ 223 (350)
Q Consensus 156 DItNVLegIgLIeKsKk~IqW~G~~~~s----~~~~~~Lk~El~~L~e~I~~K~~~LqEL~~q~~aLknLie 223 (350)
|+...+..=+-|....+-+-|.|.+--. ..-.+-++..+..+++.++.....+.++..+...+...++
T Consensus 44 plg~~~~v~g~i~~~~~vlV~lG~~~~vE~s~~eA~~~l~~r~~~l~~~~~~l~~~~~~~~~~~~~~~~~l~ 115 (120)
T PF02996_consen 44 PLGSGVFVPGKIPDTDKVLVSLGAGYYVEMSLEEAIEFLKKRIKELEEQLEKLEKELAELQAQIEQLEQTLQ 115 (120)
T ss_dssp EECTTEEEEEE-SSTTEEEEEEETTEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHH
T ss_pred cCCCCeEEEEEeCCCCEEEEEeeCCeEEEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5555555556666677788888876321 1222334444455555555555555555555544444444
No 79
>PF05529 Bap31: B-cell receptor-associated protein 31-like ; InterPro: IPR008417 Bap31 is a polytopic integral protein of the endoplasmic reticulum membrane and a substrate of caspase-8. Bap31 is cleaved within its cytosolic domain, generating pro-apoptotic p20 Bap31 [].; GO: 0006886 intracellular protein transport, 0005783 endoplasmic reticulum, 0016021 integral to membrane
Probab=24.74 E-value=1.6e+02 Score=26.72 Aligned_cols=29 Identities=28% Similarity=0.341 Sum_probs=16.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 018827 188 EELKAERLGLRNRIEKKTAYLQELEDQFV 216 (350)
Q Consensus 188 ~~Lk~El~~L~e~I~~K~~~LqEL~~q~~ 216 (350)
+.+++|+++|++.|+++...+..|.+|..
T Consensus 157 ~~~~~ei~~lk~el~~~~~~~~~LkkQ~~ 185 (192)
T PF05529_consen 157 KKLSEEIEKLKKELEKKEKEIEALKKQSE 185 (192)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455555666666665555555555543
No 80
>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=24.64 E-value=89 Score=23.15 Aligned_cols=46 Identities=30% Similarity=0.484 Sum_probs=34.2
Q ss_pred HHHHHHHHhcCCCCHHHHHHHHHHhhcCCCCCCCCCChhhhhccccchhhhhhhhhhhhccchhcCC
Q 018827 105 MKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKDK 171 (350)
Q Consensus 105 ~KVcekVk~kg~TTYnEVAdeLV~E~~~~~~~~~~~~~~~~DeKniKRRVYDItNVLegIgLIeKsK 171 (350)
.++.+.|++++..+..|+|++|-- .+.++||= +|.|+.-|+|.|-.
T Consensus 3 ~~Il~~l~~~~~~s~~ela~~~~V-----------------S~~TiRRD----l~~L~~~g~i~r~~ 48 (57)
T PF08220_consen 3 QQILELLKEKGKVSVKELAEEFGV-----------------SEMTIRRD----LNKLEKQGLIKRTH 48 (57)
T ss_pred HHHHHHHHHcCCEEHHHHHHHHCc-----------------CHHHHHHH----HHHHHHCCCEEEEc
Confidence 367889999999999999998741 12356653 56789899888843
No 81
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=24.45 E-value=5.4e+02 Score=23.36 Aligned_cols=21 Identities=33% Similarity=0.507 Sum_probs=17.6
Q ss_pred hhhhhhhhhhhhccchhcCCC
Q 018827 152 RRVYDALNVLMAMDIISKDKK 172 (350)
Q Consensus 152 RRVYDItNVLegIgLIeKsKk 172 (350)
-.|=++|+.|+-+|+|+|+++
T Consensus 56 ~ev~~sL~~L~~~gli~k~~~ 76 (171)
T PF14394_consen 56 EEVRDSLEFLEKLGLIKKDGD 76 (171)
T ss_pred HHHHHHHHHHHHCCCeEECCC
Confidence 345689999999999999655
No 82
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=24.36 E-value=3.5e+02 Score=25.11 Aligned_cols=50 Identities=20% Similarity=0.224 Sum_probs=37.9
Q ss_pred HHHHHHHHh-cCCCCHHHHHHHHHHhhcCCCCCCCCCChhhhhccccchhhhhhhhhhhhccchhcCCCcee
Q 018827 105 MKVCEKVES-KGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKDKKEIQ 175 (350)
Q Consensus 105 ~KVcekVk~-kg~TTYnEVAdeLV~E~~~~~~~~~~~~~~~~DeKniKRRVYDItNVLegIgLIeKsKk~Iq 175 (350)
..|.+.+.+ ....+..|+|+++- -=|=.+|-+++-|+..|+++++.+.++
T Consensus 12 l~IL~~l~~~~~~~~l~eia~~lg---------------------lpksT~~RlL~tL~~~G~l~~~~~~Y~ 62 (248)
T TIGR02431 12 LAVIEAFGAERPRLTLTDVAEATG---------------------LTRAAARRFLLTLVELGYVTSDGRLFW 62 (248)
T ss_pred HHHHHHHhcCCCCCCHHHHHHHHC---------------------cCHHHHHHHHHHHHHCCCEEeCCCEEE
Confidence 456666654 56788999999874 235679999999999999999655443
No 83
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=24.17 E-value=1.1e+02 Score=26.80 Aligned_cols=51 Identities=22% Similarity=0.316 Sum_probs=38.7
Q ss_pred ccchhhHHHHHHHHHhcCCCCHHHHHHHHHHhhcCCCCCCCCCChhhhhccccchhhhhhhhhhhhccchhc
Q 018827 98 RGLRQFSMKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (350)
Q Consensus 98 ~GLR~fS~KVcekVk~kg~TTYnEVAdeLV~E~~~~~~~~~~~~~~~~DeKniKRRVYDItNVLegIgLIeK 169 (350)
..|-.+=.++.+.++..++++|.|+|++|-- .+...+||| +=|+.-|+|++
T Consensus 5 ~~lD~~D~~Il~~Lq~d~R~s~~eiA~~lgl-----------------S~~tV~~Ri----~rL~~~GvI~~ 55 (153)
T PRK11179 5 YQIDNLDRGILEALMENARTPYAELAKQFGV-----------------SPGTIHVRV----EKMKQAGIITG 55 (153)
T ss_pred cccCHHHHHHHHHHHHcCCCCHHHHHHHHCc-----------------CHHHHHHHH----HHHHHCCCeee
Confidence 3466778899999999999999999999841 123455554 66778888875
No 84
>PF12958 DUF3847: Protein of unknown function (DUF3847); InterPro: IPR024215 This entry represents a family of uncharacterised proteins that were found by clustering human gut metagenomic sequences [].
Probab=24.11 E-value=3.9e+02 Score=22.27 Aligned_cols=44 Identities=27% Similarity=0.391 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHhhh
Q 018827 187 IEELKAERLGLRNRIEKKTAYLQELEDQFVGLQ--NLIQRNERLYS 230 (350)
Q Consensus 187 ~~~Lk~El~~L~e~I~~K~~~LqEL~~q~~aLk--nLierNk~ly~ 230 (350)
+++|++|+...++.|+++...++.|..+...|. .--+|+..++.
T Consensus 3 Le~l~~e~e~~~~kl~q~e~~~k~L~nr~k~l~k~eRK~RtHRLi~ 48 (86)
T PF12958_consen 3 LEELQAEIEKAEKKLEQAEHKIKQLENRKKKLEKKERKERTHRLIE 48 (86)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 578888888888888888877777776554442 12235555553
No 85
>PF08317 Spc7: Spc7 kinetochore protein; InterPro: IPR013253 This entry consists of cell division proteins which are required for kinetochore-spindle association [].
Probab=23.76 E-value=2.1e+02 Score=28.27 Aligned_cols=81 Identities=19% Similarity=0.221 Sum_probs=40.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-----h---hcCCCCCCCcccceEEEEcCCCcEEEecc
Q 018827 187 IEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQRNERL-----Y---SSGNAPSGGVALPFILVQTRPHATVEVEI 258 (350)
Q Consensus 187 ~~~Lk~El~~L~e~I~~K~~~LqEL~~q~~aLknLierNk~l-----y---~s~~~~~e~i~LPfIaVkAP~~T~LEVp~ 258 (350)
+.+|+.++..+.+.|+....+.+++..+...++...+.++.. . ..-...+..+.+-|+-+. ++.|.+..
T Consensus 232 l~el~~el~~l~~~i~~~~~~k~~l~~eI~e~~~~~~~~r~~t~~Ev~~Lk~~~~~Le~~~gw~~~~~~---~~~l~~~~ 308 (325)
T PF08317_consen 232 LAELQEELEELEEKIEELEEQKQELLAEIAEAEKIREECRGWTRSEVKRLKAKVDALEKLTGWKIVSIS---GSTLEFRY 308 (325)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHCcEEEEEe---CCeEEEEE
Confidence 344555555555556666666666666655666555544321 0 000000111111233333 67777777
Q ss_pred CCCcEEEEEEeCC
Q 018827 259 SEDMQLVHFDFNS 271 (350)
Q Consensus 259 peD~~qv~fks~~ 271 (350)
..+ +.+.|+|.+
T Consensus 309 ~~~-i~~~fd~~~ 320 (325)
T PF08317_consen 309 KDE-IELSFDFFK 320 (325)
T ss_pred cCE-EEEEEeccc
Confidence 655 777777654
No 86
>PRK09954 putative kinase; Provisional
Probab=23.47 E-value=1e+02 Score=30.11 Aligned_cols=46 Identities=24% Similarity=0.145 Sum_probs=35.6
Q ss_pred hHHHHHHHHHhcCCCCHHHHHHHHHHhhcCCCCCCCCCChhhhhccccchhhhhhhhhhhhccchhc
Q 018827 103 FSMKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (350)
Q Consensus 103 fS~KVcekVk~kg~TTYnEVAdeLV~E~~~~~~~~~~~~~~~~DeKniKRRVYDItNVLegIgLIeK 169 (350)
.-.+|++.+++.+.+++.|+|+.|- .-|..|+-.++=|+.-|+|.+
T Consensus 4 ~~~~il~~l~~~~~~s~~~la~~l~---------------------~s~~~v~~~i~~L~~~g~i~~ 49 (362)
T PRK09954 4 REKEILAILRRNPLIQQNEIADILQ---------------------ISRSRVAAHIMDLMRKGRIKG 49 (362)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHC---------------------CCHHHHHHHHHHHHHCCCcCC
Confidence 3467999999999999999999984 455666777777777777754
No 87
>PRK06798 fliD flagellar capping protein; Validated
Probab=23.47 E-value=1.6e+02 Score=30.64 Aligned_cols=36 Identities=11% Similarity=0.292 Sum_probs=18.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 018827 186 DIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQR 224 (350)
Q Consensus 186 ~~~~Lk~El~~L~e~I~~K~~~LqEL~~q~~aLknLier 224 (350)
+++.|+.++++++++++... +.|..|+.+|..++.+
T Consensus 387 ~i~~l~~~~~~~e~rl~~~e---~~l~~qf~ale~~ms~ 422 (440)
T PRK06798 387 RVSKLDLKITDIDTQNKQKQ---DNIVDKYQKLESTLAA 422 (440)
T ss_pred HHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHH
Confidence 34444544444444443332 3445566666666665
No 88
>PF10186 Atg14: UV radiation resistance protein and autophagy-related subunit 14; InterPro: IPR018791 Class III phosphatidylinositol 3-kinase (PI3-kinase) regulates multiple membrane trafficking. In yeast, two distinct PI3-kinase complexes are known: complex I (Vps34, Vps15, Vps30/Atg6, and Atg14) is involved in autophagy, and complex II (Vps34, Vps15, Vps30/Atg6, and Vps38) functions in the vacuolar protein sorting pathway. In mammals, the counterparts of Vps34, Vps15, and Vps30/Atg6 are Vps34, p150, and Beclin 1, respectively. Mammalian UV irradiation resistance-associated gene (UVRAG) has been identified as identical to yeast Vps38 []. The Atg14 (autophagy-related protein 14) proteins are hydrophilic proteins and have a coiled-coil motif at the N terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole []. This entry represents Atg14 and UVRAG, which bind Beclin 1 to forms two distinct PI3-kinase complexes. This entry also includes Bakor (beclin-1-associated autophagy-related key regulator), also known as autophagy-related protein 14-like protein, which share sequence similarity to the yeast Atg14 protein []. Barkor positively regulates autophagy through its interaction with Beclin-1, with decreased levels of autophagosome formation observed when Barkor expression is eliminated []. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. ; GO: 0010508 positive regulation of autophagy
Probab=23.33 E-value=1.9e+02 Score=27.02 Aligned_cols=15 Identities=20% Similarity=0.417 Sum_probs=8.6
Q ss_pred eEEecChhhhhhhcc
Q 018827 274 FKLHDDNSVLKAMKF 288 (350)
Q Consensus 274 ieV~DD~~iLK~m~~ 288 (350)
+.-+++..|--.+|+
T Consensus 189 ~~~~~~~~isaALgy 203 (302)
T PF10186_consen 189 FNSLPDEEISAALGY 203 (302)
T ss_pred cccCCHHHHHHHHHH
Confidence 444666666666655
No 89
>KOG2264 consensus Exostosin EXT1L [Signal transduction mechanisms]
Probab=22.82 E-value=1.7e+02 Score=32.48 Aligned_cols=39 Identities=28% Similarity=0.324 Sum_probs=17.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHH
Q 018827 187 IEELKAERLGLRNRIEKKTAYLQELE----DQFVGLQNLIQRN 225 (350)
Q Consensus 187 ~~~Lk~El~~L~e~I~~K~~~LqEL~----~q~~aLknLierN 225 (350)
++++...+++++..|.+++..|..|. ..+.+++.|+++|
T Consensus 109 I~~~n~kiEelk~~i~~~q~eL~~Lk~~ieqaq~~~~El~~~n 151 (907)
T KOG2264|consen 109 IEEINTKIEELKRLIPQKQLELSALKGEIEQAQRQLEELRETN 151 (907)
T ss_pred HHHHHHHHHHHHHHHHHhHHHHHHHHhHHHHHHHHHHHHHhhc
Confidence 33343334444444444444444333 1234455555554
No 90
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=22.66 E-value=1.2e+02 Score=26.81 Aligned_cols=52 Identities=15% Similarity=0.271 Sum_probs=40.3
Q ss_pred CccchhhHHHHHHHHHhcCCCCHHHHHHHHHHhhcCCCCCCCCCChhhhhccccchhhhhhhhhhhhccchhc
Q 018827 97 GRGLRQFSMKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (350)
Q Consensus 97 ~~GLR~fS~KVcekVk~kg~TTYnEVAdeLV~E~~~~~~~~~~~~~~~~DeKniKRRVYDItNVLegIgLIeK 169 (350)
...|-.+=.++...++..++++|.|+|+++-- ..-..+|| ++=|+.-|+|++
T Consensus 9 ~~~lD~~D~~IL~~Lq~d~R~s~~eiA~~lgl-----------------S~~tv~~R----i~rL~~~GvI~~ 60 (164)
T PRK11169 9 GKDLDRIDRNILNELQKDGRISNVELSKRVGL-----------------SPTPCLER----VRRLERQGFIQG 60 (164)
T ss_pred hhhHHHHHHHHHHHhccCCCCCHHHHHHHHCc-----------------CHHHHHHH----HHHHHHCCCeEE
Confidence 35678888999999999999999999999841 11244555 467888888886
No 91
>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=22.42 E-value=75 Score=23.14 Aligned_cols=42 Identities=21% Similarity=0.271 Sum_probs=30.4
Q ss_pred HHHHHH-hcCCCCHHHHHHHHHHhhcCCCCCCCCCChhhhhccccchhhhhhhhhhhhccchhc
Q 018827 107 VCEKVE-SKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (350)
Q Consensus 107 VcekVk-~kg~TTYnEVAdeLV~E~~~~~~~~~~~~~~~~DeKniKRRVYDItNVLegIgLIeK 169 (350)
|...|. +.+..+..+||+.+- .-+.-|..+++-|+..|+|+|
T Consensus 8 vL~~l~~~~~~~t~~~l~~~~~---------------------~~~~~vs~~i~~L~~~glv~~ 50 (68)
T PF13463_consen 8 VLRALAHSDGPMTQSDLAERLG---------------------ISKSTVSRIIKKLEEKGLVEK 50 (68)
T ss_dssp HHHHHT--TS-BEHHHHHHHTT-----------------------HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHccCCCcCHHHHHHHHC---------------------cCHHHHHHHHHHHHHCCCEEe
Confidence 455555 778888888888875 235567889999999999988
No 92
>PF07544 Med9: RNA polymerase II transcription mediator complex subunit 9; InterPro: IPR011425 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. This entry represents subunit Med9 of the Mediator complex. Subunit Med9 is part of the middle module of the Mediator complex []; this associates with the core polymerase subunits to form the RNA polymerase II holoenzyme. Med9 alternatively known as the chromosome segregation protein, CSE2 (P33308 from SWISSPROT) is required, along with CSE1 (P33307 from SWISSPROT) for accurate mitotic chromosome segregation in Saccharomyces cerevisiae (Baker's yeast) [].; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=22.34 E-value=1.8e+02 Score=23.43 Aligned_cols=25 Identities=36% Similarity=0.450 Sum_probs=16.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 018827 187 IEELKAERLGLRNRIEKKTAYLQEL 211 (350)
Q Consensus 187 ~~~Lk~El~~L~e~I~~K~~~LqEL 211 (350)
+++.+.+++.|+++|+.|++.|.++
T Consensus 54 ~eeq~~~i~~Le~~i~~k~~~L~~~ 78 (83)
T PF07544_consen 54 VEEQEEEIEELEEQIRKKREVLQKF 78 (83)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455566666777777776666654
No 93
>PF02050 FliJ: Flagellar FliJ protein; InterPro: IPR012823 Many flagellar proteins are exported by a flagellum-specific export pathway. Attempts have been made to characterise the apparatus responsible for this process, by designing assays to screen for mutants with export defects []. Experiments involving filament removal from temperature-sensitive flagellar mutants of Salmonella typhimurium have shown that, while most mutants were able to regrow filaments, flhA, fliH, fliI and fliN mutants showed no or greatly reduced regrowth. This suggests that the corresponding gene products are involved in the process of flagellum-specific export. The sequences of fliH, fliI and the adjacent gene, fliJ, have been deduced. FliJ was shown to encode a protein of molecular mass 17,302 Da []. It is a membrane-associated protein that affects chemotactic events, mutations in FliJ result in failure to respond to chemotactic stimuli.; GO: 0003774 motor activity, 0001539 ciliary or flagellar motility, 0006935 chemotaxis, 0009288 bacterial-type flagellum, 0016020 membrane, 0044461 bacterial-type flagellum part; PDB: 3AJW_A.
Probab=21.86 E-value=3.9e+02 Score=20.83 Aligned_cols=43 Identities=23% Similarity=0.283 Sum_probs=31.7
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 018827 185 NDIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQNLIQRNER 227 (350)
Q Consensus 185 ~~~~~Lk~El~~L~e~I~~K~~~LqEL~~q~~aLknLierNk~ 227 (350)
..+..++.++..++..++.+...|.+.......+..|.++-..
T Consensus 59 ~~i~~~~~~~~~~~~~~~~~r~~l~~a~~~~k~~e~L~e~~~~ 101 (123)
T PF02050_consen 59 QAIQQQQQELERLEQEVEQAREELQEARRERKKLEKLKERRRE 101 (123)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455666777777777888888888887788888888887443
No 94
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=21.73 E-value=3.3e+02 Score=25.84 Aligned_cols=44 Identities=23% Similarity=0.215 Sum_probs=34.6
Q ss_pred HHHHHHHHhcCCCCHHHHHHHHHHhhcCCCCCCCCCChhhhhccccchhhhhhhhhhhhccchhc
Q 018827 105 MKVCEKVESKGRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (350)
Q Consensus 105 ~KVcekVk~kg~TTYnEVAdeLV~E~~~~~~~~~~~~~~~~DeKniKRRVYDItNVLegIgLIeK 169 (350)
.++.+.+++++..+-.|+|+.|-- .+.++||. |+.|+..|+|.|
T Consensus 8 ~~Il~~l~~~~~~~~~ela~~l~v-----------------S~~TirRd----L~~Le~~g~i~r 51 (251)
T PRK13509 8 QILLELLAQLGFVTVEKVIERLGI-----------------SPATARRD----INKLDESGKLKK 51 (251)
T ss_pred HHHHHHHHHcCCcCHHHHHHHHCc-----------------CHHHHHHH----HHHHHHCCCEEE
Confidence 458899999999999999998731 12356665 677999999988
No 95
>COG5374 Uncharacterized conserved protein [Function unknown]
Probab=21.40 E-value=2.1e+02 Score=27.18 Aligned_cols=74 Identities=19% Similarity=0.333 Sum_probs=49.5
Q ss_pred hhccccchhhhhhhhhhh-------------hccchhcCCCceeecCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 018827 145 YDEKNIRRRVYDALNVLM-------------AMDIISKDKKEIQWKGLPRTSLNDIEELKAERLGLRNRIEKKTAYLQEL 211 (350)
Q Consensus 145 ~DeKniKRRVYDItNVLe-------------gIgLIeKsKk~IqW~G~~~~s~~~~~~Lk~El~~L~e~I~~K~~~LqEL 211 (350)
-...++=||-|---|++. -+++++. .+.|.|.-. ..++.++++-.+++++++.+...|+.|
T Consensus 89 ~~i~~las~fy~qrnmyl~g~~L~l~~~v~~~~~~v~~---ml~~~~~~~---~k~D~~eA~~t~lk~~~~~~~~~le~L 162 (192)
T COG5374 89 TRIAVLASRFYAQRNMYLSGSALFLSIVVMRVMSIVEE---MLEENAKKG---GKIDKMEADSTDLKARLRKAQILLEGL 162 (192)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHhhhcc---cchhhhhcchHHHHHHHhhhhHHHHHH
Confidence 344567788877766543 2333332 233433221 345678888888899999888999999
Q ss_pred HHHHHHHHHHHHH
Q 018827 212 EDQFVGLQNLIQR 224 (350)
Q Consensus 212 ~~q~~aLknLier 224 (350)
..++..+.++.+.
T Consensus 163 qkn~~~~~k~~d~ 175 (192)
T COG5374 163 QKNQEELFKLLDK 175 (192)
T ss_pred HHHHHHHHHHHHH
Confidence 9888888888775
No 96
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=21.38 E-value=1.4e+02 Score=21.25 Aligned_cols=49 Identities=16% Similarity=0.167 Sum_probs=35.4
Q ss_pred chhhHHHHHHHHHhcCC--CCHHHHHHHHHHhhcCCCCCCCCCChhhhhccccchhhhhhhhhhhhccchhc
Q 018827 100 LRQFSMKVCEKVESKGR--TTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISK 169 (350)
Q Consensus 100 LR~fS~KVcekVk~kg~--TTYnEVAdeLV~E~~~~~~~~~~~~~~~~DeKniKRRVYDItNVLegIgLIeK 169 (350)
|-.--..|.-.|...+. +|-.|+|+.+. .-|-.|=-+++-|+.-|+|+|
T Consensus 3 lt~~q~~vL~~l~~~~~~~~t~~~la~~l~---------------------~~~~~vs~~v~~L~~~Glv~r 53 (62)
T PF12802_consen 3 LTPSQFRVLMALARHPGEELTQSELAERLG---------------------ISKSTVSRIVKRLEKKGLVER 53 (62)
T ss_dssp STHHHHHHHHHHHHSTTSGEEHHHHHHHHT---------------------S-HHHHHHHHHHHHHTTSEEE
T ss_pred cCHHHHHHHHHHHHCCCCCcCHHHHHHHHC---------------------cCHHHHHHHHHHHHHCCCEEE
Confidence 33344566777777666 89999999986 223445567899999999998
No 97
>PF01920 Prefoldin_2: Prefoldin subunit; InterPro: IPR002777 Prefoldin (PFD) is a chaperone that interacts exclusively with type II chaperonins, hetero-oligomers lacking an obligate co-chaperonin that are found only in eukaryotes (chaperonin-containing T-complex polypeptide-1 (CCT)) and archaea. Eukaryotic PFD is a multi-subunit complex containing six polypeptides in the molecular mass range of 14-23 kDa. In archaea, on the other hand, PFD is composed of two types of subunits, two alpha and four beta. The six subunits associate to form two back-to-back up-and-down eight-stranded barrels, from which hang six coiled coils. Each subunit contributes one (beta subunits) or two (alpha subunits) beta hairpin turns to the barrels. The coiled coils are formed by the N and C termini of an individual subunit. Overall, this unique arrangement resembles a jellyfish. The eukaryotic PFD hexamer is composed of six different subunits; however, these can be grouped into two alpha-like (PFD3 and -5) and four beta-like (PFD1, -2, -4, and -6) subunits based on amino acid sequence similarity with their archaeal counterparts. Eukaryotic PFD has a six-legged structure similar to that seen in the archaeal homologue [, ]. This family contains the archaeal beta subunit, eukaryotic prefoldin subunits 1, 2, 4 and 6. Eukaryotic PFD has been shown to bind both actin and tubulin co-translationally. The chaperone then delivers the target protein to CCT, interacting with the chaperonin through the tips of the coiled coils. No authentic target proteins of any archaeal PFD have been identified, to date.; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0016272 prefoldin complex; PDB: 2ZDI_B 3AEI_B 2ZQM_A 1FXK_A.
Probab=21.28 E-value=4.2e+02 Score=20.97 Aligned_cols=66 Identities=21% Similarity=0.269 Sum_probs=34.0
Q ss_pred cchhhhhhhhhhhhccchhcCCCceeecCCCCCC-----hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 018827 150 IRRRVYDALNVLMAMDIISKDKKEIQWKGLPRTS-----LNDIEELKAERLGLRNRIEKKTAYLQELEDQFVG 217 (350)
Q Consensus 150 iKRRVYDItNVLegIgLIeKsKk~IqW~G~~~~s-----~~~~~~Lk~El~~L~e~I~~K~~~LqEL~~q~~a 217 (350)
+.+.+..+.-|+..+..+.-+ ..-|+..+... ..-...|+.+...+...|+.+...+..+..+...
T Consensus 24 l~~~~~~~~~~~~eL~~l~~~--~~~y~~vG~~fv~~~~~~~~~~L~~~~~~~~~~i~~l~~~~~~l~~~l~~ 94 (106)
T PF01920_consen 24 LERQLRELELTLEELEKLDDD--RKVYKSVGKMFVKQDKEEAIEELEERIEKLEKEIKKLEKQLKYLEKKLKE 94 (106)
T ss_dssp HHHHHHHHHHHHHHHHTSSTT---EEEEEETTEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHhCCCc--chhHHHHhHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444455555566666666555 45555544321 1223455555556666666666666655554433
No 98
>PF10234 Cluap1: Clusterin-associated protein-1; InterPro: IPR019366 This protein of 413 amino acids contains a central coiled-coil domain, possibly the region that binds to clusterin. Cluap1 expression is highest in the nucleus and gradually increases during late S to G2/M phases of the cell cycle and returns to the basal level in the G0/G1 phases. In addition, it is upregulated in colon cancer tissues compared to corresponding non-cancerous mucosa. It thus plays a crucial role in the life of the cell [].
Probab=21.26 E-value=2.1e+02 Score=28.40 Aligned_cols=35 Identities=26% Similarity=0.437 Sum_probs=22.1
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 018827 186 DIEELKAERLGLRNRIEKKTAYLQELEDQFVGLQN 220 (350)
Q Consensus 186 ~~~~Lk~El~~L~e~I~~K~~~LqEL~~q~~aLkn 220 (350)
.+..|..+...|...|++|+..|+...+...+|++
T Consensus 184 ~l~~l~~de~~Le~KIekkk~ELER~qKRL~sLq~ 218 (267)
T PF10234_consen 184 QLNNLASDEANLEAKIEKKKQELERNQKRLQSLQS 218 (267)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 34555555666667777777777666665555554
No 99
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=20.84 E-value=7.2e+02 Score=23.66 Aligned_cols=52 Identities=19% Similarity=0.360 Sum_probs=38.4
Q ss_pred ccchhhH--HHHHHHHHhc-CCCCHHHHHHHHHHhhcCCCCCCCCCChhhhhccccchhhhhhhhhhhhccchhcC
Q 018827 98 RGLRQFS--MKVCEKVESK-GRTTYNEVADELVAEFADPSNSLATPDQQQYDEKNIRRRVYDALNVLMAMDIISKD 170 (350)
Q Consensus 98 ~GLR~fS--~KVcekVk~k-g~TTYnEVAdeLV~E~~~~~~~~~~~~~~~~DeKniKRRVYDItNVLegIgLIeKs 170 (350)
.|+.-+. ..|.+.+... +..+..|+|+++- --|=.||.+++-|+..|+++++
T Consensus 19 ~~~~sl~r~l~IL~~~~~~~~~~tl~eIa~~lg---------------------lpkStv~RlL~tL~~~G~l~~~ 73 (271)
T PRK10163 19 KGAQALERGIAILQYLEKSGGSSSVSDISLNLD---------------------LPLSTTFRLLKVLQAADFVYQD 73 (271)
T ss_pred ccchHHHHHHHHHHHHHhCCCCcCHHHHHHHHC---------------------cCHHHHHHHHHHHHHCCCEEEc
Confidence 3444443 4567777553 5688999999874 2356799999999999999994
No 100
>PF11853 DUF3373: Protein of unknown function (DUF3373); InterPro: IPR021803 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 472 to 574 amino acids in length.
Probab=20.58 E-value=91 Score=33.39 Aligned_cols=27 Identities=30% Similarity=0.373 Sum_probs=12.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 018827 200 RIEKKTAYLQELEDQFVGLQNLIQRNE 226 (350)
Q Consensus 200 ~I~~K~~~LqEL~~q~~aLknLierNk 226 (350)
+|++.+++|++|.+|+..++.-+++++
T Consensus 32 kie~L~kql~~Lk~q~~~l~~~v~k~e 58 (489)
T PF11853_consen 32 KIEALKKQLEELKAQQDDLNDRVDKVE 58 (489)
T ss_pred HHHHHHHHHHHHHHhhcccccccchhh
Confidence 344444444555555444444444443
No 101
>PF04568 IATP: Mitochondrial ATPase inhibitor, IATP; InterPro: IPR007648 ATP synthase inhibitor prevents the enzyme from switching to ATP hydrolysis during collapse of the electrochemical gradient, for example during oxygen deprivation [] ATP synthase inhibitor forms a one to one complex with the F1 ATPase, possibly by binding at the alpha-beta interface. It is thought to inhibit ATP synthesis by preventing the release of ATP []. The minimum inhibitory region for bovine inhibitor (P01096 from SWISSPROT) is from residues 39 to 72 []. The inhibitor has two oligomeric states, dimer (the active state) and tetramer. At low pH , the inhibitor forms a dimer via antiparallel coiled coil interactions between the C-terminal regions of two monomers. At high pH, the inhibitor forms tetramers and higher oligomers by coiled coil interactions involving the N terminus and inhibitory region, thus preventing the inhibitory activity []. ; GO: 0004857 enzyme inhibitor activity, 0045980 negative regulation of nucleotide metabolic process, 0005739 mitochondrion; PDB: 1GMJ_B 1OHH_H 1HF9_B 2V7Q_J.
Probab=20.48 E-value=2.7e+02 Score=23.79 Aligned_cols=13 Identities=38% Similarity=0.537 Sum_probs=6.3
Q ss_pred HHHHHHHHHHHHH
Q 018827 201 IEKKTAYLQELED 213 (350)
Q Consensus 201 I~~K~~~LqEL~~ 213 (350)
|...+++|++|..
T Consensus 85 ~~~~~k~i~~le~ 97 (100)
T PF04568_consen 85 IEHHRKEIDELEK 97 (100)
T ss_dssp HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHH
Confidence 3335555555543
No 102
>PF14830 Haemocyan_bet_s: Haemocyanin beta-sandwich; PDB: 1JS8_B 3QJO_A 1LNL_A.
Probab=20.03 E-value=39 Score=28.98 Aligned_cols=22 Identities=23% Similarity=0.321 Sum_probs=14.0
Q ss_pred hhhhhhhhhccchhcCCCceee
Q 018827 155 YDALNVLMAMDIISKDKKEIQW 176 (350)
Q Consensus 155 YDItNVLegIgLIeKsKk~IqW 176 (350)
||||.||..+||=--+.=.|++
T Consensus 58 ydIT~~l~~l~l~~~~~f~i~~ 79 (103)
T PF14830_consen 58 YDITDALKKLGLHYDDPFHIKV 79 (103)
T ss_dssp EE-HHHHHHCT--TTSSEEEEE
T ss_pred hhHHHHHHHcCCCCCCCEEEEE
Confidence 8999999999987445444544
Done!