Query psy8359
Match_columns 279
No_of_seqs 146 out of 650
Neff 7.5
Searched_HMMs 46136
Date Fri Aug 16 16:39:32 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8359.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8359hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2167|consensus 100.0 6E-59 1.3E-63 439.9 16.0 258 19-279 307-661 (661)
2 COG5647 Cullin, a subunit of E 100.0 7.2E-57 1.6E-61 434.1 16.9 266 6-279 407-773 (773)
3 KOG2166|consensus 100.0 4.6E-55 1E-59 434.3 17.6 257 6-277 371-725 (725)
4 KOG2284|consensus 100.0 1.2E-51 2.6E-56 377.5 10.9 257 16-279 398-728 (728)
5 KOG2285|consensus 100.0 3.4E-40 7.5E-45 304.7 15.1 260 17-279 395-777 (777)
6 PF00888 Cullin: Cullin family 99.9 3.9E-26 8.4E-31 225.8 12.8 163 19-181 326-588 (588)
7 PF10557 Cullin_Nedd8: Cullin 99.9 3.8E-23 8.3E-28 148.7 3.8 66 208-273 1-68 (68)
8 smart00182 CULLIN Cullin. 99.8 1.4E-19 3E-24 148.4 9.5 73 50-122 1-73 (142)
9 KOG2165|consensus 98.0 5.3E-05 1.1E-09 75.0 11.3 127 50-181 448-665 (765)
10 PF09012 FeoC: FeoC like trans 93.7 0.073 1.6E-06 37.8 3.1 45 220-270 5-49 (69)
11 TIGR02698 CopY_TcrY copper tra 90.0 0.87 1.9E-05 36.6 5.7 60 217-279 6-65 (130)
12 PF03965 Penicillinase_R: Peni 88.8 0.52 1.1E-05 36.8 3.5 60 217-279 5-64 (115)
13 COG3682 Predicted transcriptio 88.5 0.84 1.8E-05 36.4 4.5 62 215-279 6-67 (123)
14 PF01978 TrmB: Sugar-specific 87.8 0.48 1E-05 33.2 2.5 51 222-278 15-65 (68)
15 PF13463 HTH_27: Winged helix 86.8 2.1 4.6E-05 29.5 5.4 51 217-273 5-58 (68)
16 PF08220 HTH_DeoR: DeoR-like h 83.5 1.8 3.9E-05 29.5 3.6 47 218-270 3-49 (57)
17 smart00550 Zalpha Z-DNA-bindin 83.0 3.9 8.4E-05 28.9 5.3 53 217-275 8-62 (68)
18 smart00418 HTH_ARSR helix_turn 78.3 5.9 0.00013 26.1 4.8 45 221-272 3-47 (66)
19 PF01726 LexA_DNA_bind: LexA D 76.0 6.1 0.00013 27.7 4.4 25 248-272 39-63 (65)
20 PF02186 TFIIE_beta: TFIIE bet 74.8 3.8 8.1E-05 28.9 3.0 55 217-279 7-61 (65)
21 PF12802 MarR_2: MarR family; 73.5 4 8.7E-05 27.5 2.9 47 218-270 8-56 (62)
22 PF09756 DDRGK: DDRGK domain; 72.7 3.3 7.1E-05 35.5 2.8 58 216-279 100-157 (188)
23 smart00420 HTH_DEOR helix_turn 72.5 7.6 0.00017 24.8 4.0 45 220-270 5-49 (53)
24 PF13412 HTH_24: Winged helix- 70.8 7.3 0.00016 25.0 3.6 44 217-266 5-48 (48)
25 PF01047 MarR: MarR family; I 69.8 3.2 7E-05 27.8 1.7 46 218-269 6-51 (59)
26 cd07153 Fur_like Ferric uptake 69.4 15 0.00033 28.1 5.7 57 220-277 6-63 (116)
27 smart00344 HTH_ASNC helix_turn 69.1 7.7 0.00017 29.4 3.9 47 216-268 4-50 (108)
28 smart00347 HTH_MARR helix_turn 60.9 20 0.00044 26.0 4.8 48 217-270 12-59 (101)
29 COG3355 Predicted transcriptio 57.0 29 0.00063 27.8 5.2 51 223-279 36-90 (126)
30 PF12395 DUF3658: Protein of u 55.7 34 0.00075 26.5 5.4 62 215-277 48-109 (111)
31 TIGR01610 phage_O_Nterm phage 54.8 29 0.00063 26.0 4.7 39 226-270 44-82 (95)
32 COG1522 Lrp Transcriptional re 53.0 24 0.00053 28.3 4.4 49 215-269 8-56 (154)
33 PRK10434 srlR DNA-bindng trans 51.4 18 0.00038 32.4 3.6 46 218-269 8-53 (256)
34 smart00346 HTH_ICLR helix_turn 49.8 46 0.001 24.0 5.1 44 221-270 11-55 (91)
35 PF09339 HTH_IclR: IclR helix- 49.4 35 0.00075 22.3 3.9 34 230-269 19-52 (52)
36 TIGR02404 trehalos_R_Bsub treh 48.8 28 0.00061 30.2 4.4 39 231-276 26-64 (233)
37 PRK10079 phosphonate metabolis 48.1 27 0.00059 30.5 4.2 39 231-276 37-75 (241)
38 PRK11512 DNA-binding transcrip 47.9 38 0.00082 27.1 4.7 38 226-269 51-88 (144)
39 TIGR01889 Staph_reg_Sar staphy 47.2 44 0.00096 25.5 4.8 46 226-277 40-88 (109)
40 PRK11169 leucine-responsive tr 46.6 42 0.00092 27.7 4.9 46 216-267 15-60 (164)
41 smart00345 HTH_GNTR helix_turn 45.8 55 0.0012 21.2 4.6 38 227-270 17-55 (60)
42 PF12108 SF3a60_bindingd: Spli 45.8 17 0.00036 21.3 1.6 15 51-65 3-17 (28)
43 cd00090 HTH_ARSR Arsenical Res 45.7 48 0.001 22.2 4.5 44 221-271 13-56 (78)
44 PF02334 RTP: Replication term 45.2 28 0.00062 27.2 3.3 51 216-267 19-72 (122)
45 cd07977 TFIIE_beta_winged_heli 45.0 28 0.00062 25.1 3.2 56 215-279 9-70 (75)
46 PF09860 DUF2087: Uncharacteri 44.5 26 0.00056 25.1 2.8 43 225-275 25-68 (71)
47 PRK14999 histidine utilization 44.4 45 0.00097 29.2 5.0 47 223-276 29-76 (241)
48 PRK11402 DNA-binding transcrip 43.6 37 0.00081 29.6 4.4 42 228-276 32-73 (241)
49 PRK11179 DNA-binding transcrip 42.6 46 0.001 27.1 4.5 47 216-268 10-56 (153)
50 PRK10906 DNA-binding transcrip 42.5 31 0.00067 30.8 3.7 47 217-269 7-53 (252)
51 KOG3054|consensus 42.4 36 0.00078 30.4 3.9 54 220-279 205-258 (299)
52 TIGR02325 C_P_lyase_phnF phosp 41.6 41 0.00089 29.1 4.3 39 231-276 34-72 (238)
53 PRK03573 transcriptional regul 40.8 60 0.0013 25.8 4.9 25 245-269 56-80 (144)
54 COG2865 Predicted transcriptio 38.5 40 0.00087 33.1 4.0 60 214-279 401-460 (467)
55 TIGR02337 HpaR homoprotocatech 38.4 66 0.0014 24.7 4.6 47 217-269 30-76 (118)
56 PF08784 RPA_C: Replication pr 38.3 44 0.00096 25.1 3.5 46 216-267 48-97 (102)
57 TIGR03433 padR_acidobact trans 38.1 1.1E+02 0.0025 22.9 5.8 51 216-267 5-57 (100)
58 PRK09334 30S ribosomal protein 36.8 82 0.0018 23.5 4.6 35 245-279 51-85 (86)
59 COG1349 GlpR Transcriptional r 36.6 40 0.00086 30.1 3.4 46 219-270 9-54 (253)
60 PRK09462 fur ferric uptake reg 36.1 1.1E+02 0.0025 24.5 5.9 50 219-269 21-72 (148)
61 PF04492 Phage_rep_O: Bacterio 34.9 56 0.0012 25.0 3.5 36 135-180 62-97 (100)
62 PRK09802 DNA-binding transcrip 34.6 49 0.0011 29.8 3.7 48 217-270 19-66 (269)
63 TIGR02018 his_ut_repres histid 34.3 61 0.0013 28.0 4.2 39 231-276 27-65 (230)
64 TIGR01884 cas_HTH CRISPR locus 34.1 87 0.0019 26.7 5.1 46 219-270 147-192 (203)
65 COG5045 Ribosomal protein S10E 33.6 63 0.0014 24.4 3.4 22 248-269 38-59 (105)
66 PF00392 GntR: Bacterial regul 32.8 82 0.0018 21.4 3.9 38 227-270 21-59 (64)
67 PRK03902 manganese transport t 32.8 82 0.0018 25.1 4.5 45 219-269 12-56 (142)
68 PF06163 DUF977: Bacterial pro 31.8 90 0.002 25.0 4.3 51 214-270 11-61 (127)
69 PRK09764 DNA-binding transcrip 31.3 78 0.0017 27.6 4.4 45 225-276 24-69 (240)
70 PF01638 HxlR: HxlR-like helix 28.9 1.5E+02 0.0033 21.6 5.0 53 219-277 9-63 (90)
71 PRK14165 winged helix-turn-hel 28.1 1.3E+02 0.0028 26.4 5.1 50 223-278 15-64 (217)
72 PRK09954 putative kinase; Prov 28.0 74 0.0016 29.6 3.9 44 219-268 7-50 (362)
73 PF10007 DUF2250: Uncharacteri 27.7 81 0.0018 23.8 3.3 26 245-270 31-56 (92)
74 PF08221 HTH_9: RNA polymerase 27.6 1.8E+02 0.0038 20.0 4.8 53 208-266 6-58 (62)
75 PF11313 DUF3116: Protein of u 27.5 1.6E+02 0.0035 21.9 4.8 46 227-272 18-64 (85)
76 smart00419 HTH_CRP helix_turn_ 27.3 1.4E+02 0.0029 18.4 4.0 25 245-269 18-42 (48)
77 PF13601 HTH_34: Winged helix 26.5 70 0.0015 23.2 2.7 45 219-269 4-48 (80)
78 COG2188 PhnF Transcriptional r 26.2 1E+02 0.0022 27.0 4.2 31 245-276 41-71 (236)
79 PRK10870 transcriptional repre 25.4 1.6E+02 0.0034 24.6 5.1 37 228-270 70-106 (176)
80 cd07377 WHTH_GntR Winged helix 25.4 2E+02 0.0043 18.7 5.0 25 245-269 35-59 (66)
81 cd00092 HTH_CRP helix_turn_hel 25.4 2.1E+02 0.0045 18.9 4.9 36 228-269 24-59 (67)
82 PF09382 RQC: RQC domain; Int 25.1 69 0.0015 24.0 2.6 31 247-278 54-84 (106)
83 PF05732 RepL: Firmicute plasm 24.7 62 0.0013 27.0 2.4 42 136-186 84-125 (165)
84 PF13730 HTH_36: Helix-turn-he 24.6 61 0.0013 21.1 2.0 21 245-265 35-55 (55)
85 PRK00215 LexA repressor; Valid 24.4 2E+02 0.0044 24.3 5.7 45 226-276 20-65 (205)
86 PF01475 FUR: Ferric uptake re 22.9 1.6E+02 0.0034 22.6 4.4 57 220-277 13-70 (120)
87 PF01316 Arg_repressor: Argini 22.8 2.4E+02 0.0052 20.0 4.8 59 215-278 5-63 (70)
88 COG1846 MarR Transcriptional r 22.7 81 0.0018 23.5 2.6 26 245-270 46-71 (126)
89 PF14394 DUF4423: Domain of un 22.7 1.1E+02 0.0023 25.7 3.5 25 246-270 52-76 (171)
90 PF15479 DUF4639: Domain of un 22.3 1.1E+02 0.0023 30.3 3.8 28 245-272 78-105 (576)
91 PRK13509 transcriptional repre 22.0 1.3E+02 0.0029 26.6 4.2 46 219-270 9-54 (251)
92 PRK10411 DNA-binding transcrip 21.6 1.5E+02 0.0032 26.2 4.4 44 220-269 9-52 (240)
93 COG1378 Predicted transcriptio 21.5 85 0.0018 28.0 2.8 33 247-279 42-74 (247)
94 PF09957 DUF2191: Uncharacteri 21.1 1.4E+02 0.003 19.4 3.0 31 233-263 9-39 (47)
95 PF09114 MotA_activ: Transcrip 21.0 1.9E+02 0.0041 21.9 4.0 33 238-270 35-67 (96)
96 PF14947 HTH_45: Winged helix- 20.9 1.2E+02 0.0027 21.5 3.1 24 245-268 29-52 (77)
97 PF02082 Rrf2: Transcriptional 20.9 93 0.002 22.4 2.5 39 135-180 33-71 (83)
No 1
>KOG2167|consensus
Probab=100.00 E-value=6e-59 Score=439.88 Aligned_cols=258 Identities=63% Similarity=0.865 Sum_probs=235.8
Q ss_pred cchhhHHHHhhhcccCCCCCCCCCCCc-c--------cccccCChhHHHHHHHHHHHhHhcCCCCCChHHHHHHHHHHHH
Q psy8359 19 KSKTRAWNRDTCSSLFPPRKQALSTHE-K--------SPIQISIKVNVSSVEKVDLAKRLLVGKSASVDAEKSMLSKLKQ 89 (279)
Q Consensus 19 ~~~~p~~lA~Y~D~ll~~~~~~~~~~~-~--------~~i~l~~KD~Fe~~Y~~~LakRLL~~~s~s~~~E~~~I~~Lk~ 89 (279)
.++.++++|+|.|.+++.+.++.++.+ . .|.||..||+||.||++.||+|||.++|+|.|+|..|+++||.
T Consensus 307 ~~rpAelIak~~dt~Lr~gnk~~~d~~l~~~~d~i~~lfr~i~gkdvfeA~ykkdLakrLLl~kSAsvdae~~ml~~lk~ 386 (661)
T KOG2167|consen 307 RNRPAELIAKYVDTKLRAGNKETSDEELEFVLDKILVLFRFIHGKDVFEAFYKKDLAKRLLLGKSASVDAEKSMLSKLKL 386 (661)
T ss_pred cCCHHHHHHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHhccchhhcchhHHHHHhhh
Confidence 356889999999999999876666654 2 2459999999999999999999999999999999999999999
Q ss_pred hcCCchhHhHHHHHhhHHHhHHHHHHHHHHHhc-CC---------------CC----------CC---------------
Q psy8359 90 ECGGGFTSKLEGMFKDMELSKDINVAFKQYMGN-LK---------------ED----------KE--------------- 128 (279)
Q Consensus 90 ~cG~~~t~kle~M~~D~~~S~~l~~~F~~~~~~-~~---------------~~----------~d--------------- 128 (279)
+||..||+||++||+|+..|++++..|+.+... .. +| ++
T Consensus 387 ecgs~ft~kLegMfkdme~sk~i~~~f~~~~~~~~~~~~~l~~v~vlt~~yWpty~~~ev~Lp~em~~~~e~F~~fyl~k 466 (661)
T KOG2167|consen 387 ECGSAFTYKLEGMFKDMELSKEINRAFKQSKGANNRLEGNLLTVNVLTMGYWPTYPPMEVLLPKEMRDCQEIFKKFYLGK 466 (661)
T ss_pred hcchHHHHHHHHhhhhHHHHHHHHHHHHHHHHhhccCcCCceEEEeecccccCCCCchhccCCHHHHHHHHHHHHhcccc
Confidence 999999999999999999999999999997322 11 11 00
Q ss_pred --------------------cc------------------cccc---------cCCCCCHHHHHHHHhHhhcCCceeeee
Q psy8359 129 --------------------ST------------------SNNA---------LGIDLTDADLRRTLQSLACGKTRVLKK 161 (279)
Q Consensus 129 --------------------~~------------------FN~~---------~~t~i~~~~l~~~L~sL~~~k~~iL~~ 161 (279)
|. ||+. ++|+|.+.+|.++|+||+|++.++|.+
T Consensus 467 ~sgrklqW~~~lg~~v~ka~f~~gkkel~~slfq~~vll~fn~~~~~s~~ei~~~t~i~d~el~rtlqsl~cgr~rvl~~ 546 (661)
T KOG2167|consen 467 HSGRKLQWQDSLGHCVLKAEFKEGKKELQVSLFQTLVLLMFNEGEGLSYEEIKESTGIEDIELRRTLQSLACGRARVLQK 546 (661)
T ss_pred ccCcceeeecCCcchhhhhhccCCchHHHHHHHHHhHhhccCCCCcccHHHHHHhccccHHHHHHHHHHHhcccceeeee
Confidence 00 7865 899999999999999999999999999
Q ss_pred CCCCCCCCCCCeEEEecCCCCceeeEEeeccccccchHHHHHHHHHHHhhhhhhhhhhhhhhhccCCCCCHHHHHHHHHH
Q psy8359 162 TPASRDIEDCDRFRFNNDFTFKLFRIKINQIQMKETNEEQKATEERVFQDRQYQIDAAIVRIMKMRKTLSHNLLLSELFN 241 (279)
Q Consensus 162 ~~~~~~i~~~~~f~~N~~F~~k~~ki~i~~~~~k~~~~e~~~~~~~i~~~R~~~I~AaIVRIMK~~K~l~~~~L~~eV~~ 241 (279)
.|.|+.+.+|+.|.+|..|++|..||+|+++..|++.+|+..+.++|.+||.+.||||||||||.||+|+|+.|+.|+.+
T Consensus 547 ~pkg~~~~~~~~f~~n~~f~~kl~rikinqi~~ke~~ee~~~~~e~v~~drqy~idaaivrimk~rk~l~h~~l~~el~~ 626 (661)
T KOG2167|consen 547 VPKGKEVEDGDKFIVNDKFTHKLYRIKINQIQMKETVEENKSTTERVFQDRQYQIDAAIVRIMKMRKTLSHNLLVTELFN 626 (661)
T ss_pred CCCCCCCCCCCEEEechhhcchhheehHhhhhHHHHHHhhhhhHHHHHhhhhHHHHHHHHHHHHHHHhhchhHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcCCCCChHHHHHHHHhhhhcCceeecCCCCCceEecC
Q psy8359 242 QLKFPVKPADLKKRIESLIDRDYMERDKDKANSYNYMA 279 (279)
Q Consensus 242 ~l~F~p~~~~iK~~Ie~LIekeYi~R~~~d~~~y~Yva 279 (279)
+++|+..+ ++|+|||+||+|||++|| ++ +.|.|||
T Consensus 627 qlkfpv~~-d~kkriesli~rey~erd-~n-~~y~yva 661 (661)
T KOG2167|consen 627 QLKFPVKP-DLKKRIESLIDREYLERD-DN-NIYNYVA 661 (661)
T ss_pred hcCCCCCh-hHHHHHHHHHhHHHhccc-cc-ccccccC
Confidence 99999998 999999999999999999 44 9999997
No 2
>COG5647 Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=7.2e-57 Score=434.11 Aligned_cols=266 Identities=38% Similarity=0.485 Sum_probs=228.6
Q ss_pred EeccCcccccccCcchhhHHHHhhhcccCCCCCCC-CCCCcc--------cccccCChhHHHHHHHHHHHhHhcCCCCCC
Q psy8359 6 LISSNGISSVSLNKSKTRAWNRDTCSSLFPPRKQA-LSTHEK--------SPIQISIKVNVSSVEKVDLAKRLLVGKSAS 76 (279)
Q Consensus 6 ~~~~~~~~~~~~~~~~~p~~lA~Y~D~ll~~~~~~-~~~~~~--------~~i~l~~KD~Fe~~Y~~~LakRLL~~~s~s 76 (279)
|||.| ++..+..|++||.|.|.++++.+.. .+...+ .|.|+.+||+|+++|+++||||||+++|.|
T Consensus 407 fin~~-----~sa~~~~~e~Laky~D~~lkk~~k~s~~~~i~~~l~~iitLfryv~~KDvFe~~Yk~~laKRLL~g~S~s 481 (773)
T COG5647 407 FINGN-----ESADSGPSEYLAKYIDGLLKKDGKQSFIGKIKDLLQDIITLFRYVEEKDVFEKYYKKLLAKRLLNGRSAS 481 (773)
T ss_pred Hhccc-----cccccccHHHHHHHhHHHhhccccccccccHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHhcCCCcc
Confidence 55655 5566789999999999999987532 122111 245999999999999999999999999999
Q ss_pred hHHHHHHHHHHHHhcCCchhHhHHHHHhhHHHhHHHHHHHHHHHhcC--------------CCC-----------CCcc-
Q psy8359 77 VDAEKSMLSKLKQECGGGFTSKLEGMFKDMELSKDINVAFKQYMGNL--------------KED-----------KEST- 130 (279)
Q Consensus 77 ~~~E~~~I~~Lk~~cG~~~t~kle~M~~D~~~S~~l~~~F~~~~~~~--------------~~~-----------~d~~- 130 (279)
.++|..||++||++||.+||+|||+||+||.+|.+++..|+..-... -+| +++.
T Consensus 482 ~~~E~~mis~LKk~~g~~fT~Kle~Mf~DIsLS~e~~~af~~s~~s~~~~~Dl~v~VLt~a~WP~sp~~~~~~lP~~l~p 561 (773)
T COG5647 482 AQAELKMISMLKKVCGQEFTSKLEGMFRDISLSSEFTEAFQHSPQSYNKYLDLFVWVLTQAYWPLSPEEVSIRLPKELVP 561 (773)
T ss_pred hHHHHHHHHHHHHHhhhHHHHHHHHHHHhcchhHHHHHHHhhCchhhccccchhHHHHHHhcCCCCccccccCCChHHHH
Confidence 99999999999999999999999999999999999999997743111 122 1110
Q ss_pred -------------------------------------------------------cccc---------cCCCCCHHHHHH
Q psy8359 131 -------------------------------------------------------SNNA---------LGIDLTDADLRR 146 (279)
Q Consensus 131 -------------------------------------------------------FN~~---------~~t~i~~~~l~~ 146 (279)
||+. +.|+|+..++++
T Consensus 562 ~le~f~~~Y~sKhngRkL~W~~hLg~~evkarf~~~~~~~~is~~s~~q~~vfll~n~~e~lt~eei~e~T~l~~~dl~~ 641 (773)
T COG5647 562 ILEGFKKFYSSKHNGRKLKWYWHLGSGEVKARFNEGQKYLEISTFSVYQLLVFLLFNDHEELTFEEILELTKLSTDDLKR 641 (773)
T ss_pred HHHHHHHHHHHhccCceEEeeeccccEEEEeeccCCccceehhHHHHHHHHHHHHhcCccceeHHHHHhhcCCChhhHHH
Confidence 5555 899999999999
Q ss_pred HHhHhhcCCceeeeeCCCCCCCCCCCeEEEecCCCCceeeEEeeccccccchHHHHHHHHHHHhhhhhhhhhhhhhhhcc
Q psy8359 147 TLQSLACGKTRVLKKTPASRDIEDCDRFRFNNDFTFKLFRIKINQIQMKETNEEQKATEERVFQDRQYQIDAAIVRIMKM 226 (279)
Q Consensus 147 ~L~sL~~~k~~iL~~~~~~~~i~~~~~f~~N~~F~~k~~ki~i~~~~~k~~~~e~~~~~~~i~~~R~~~I~AaIVRIMK~ 226 (279)
+|+||++.|..++ .++++.+.|++.|++|.+|++++.+|+++.+...+..+++.++++++++||...+|||||||||+
T Consensus 642 ~L~sl~~ak~~~l--~~~~~~~~p~~~fy~ne~f~~~~~rIki~~~~~~~~~q~~~~~h~~v~edR~~~lqA~IVRIMK~ 719 (773)
T COG5647 642 VLQSLSCAKLVVL--LKDDKLVSPNTKFYVNENFSSKLERIKINYIAESECMQDNLDTHETVEEDRQAELQACIVRIMKA 719 (773)
T ss_pred HHHHHHhhheeee--ccccccCCCCceEEEccccccccceeeecccccchhhccchhhHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999995554444 44478899999999999999999999999887766666777888999999999999999999999
Q ss_pred CCCCCHHHHHHHHHHhcC--CCCChHHHHHHHHhhhhcCceeecCCCCCceEecC
Q psy8359 227 RKTLSHNLLLSELFNQLK--FPVKPADLKKRIESLIDRDYMERDKDKANSYNYMA 279 (279)
Q Consensus 227 ~K~l~~~~L~~eV~~~l~--F~p~~~~iK~~Ie~LIekeYi~R~~~d~~~y~Yva 279 (279)
||+|.|++|++||+.++. |.|++.+||+||+.|||||||+|.++| ..|+|+|
T Consensus 720 rk~l~H~~Lv~e~i~q~~~Rf~p~vsmvKr~Ie~LiEKeYLeR~~dd-~iY~YLa 773 (773)
T COG5647 720 RKKLKHGDLVKEVIAQHKSRFEPKVSMVKRAIETLIEKEYLERQADD-EIYVYLA 773 (773)
T ss_pred hccCcHHHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHHHHhccCC-ceeeecC
Confidence 999999999999999998 999999999999999999999999988 8999997
No 3
>KOG2166|consensus
Probab=100.00 E-value=4.6e-55 Score=434.34 Aligned_cols=257 Identities=44% Similarity=0.605 Sum_probs=225.5
Q ss_pred EeccCcccccccCcchhhHHHHhhhcccCCCCCCCCCCCcc---------cccccCChhHHHHHHHHHHHhHhcCCCCCC
Q psy8359 6 LISSNGISSVSLNKSKTRAWNRDTCSSLFPPRKQALSTHEK---------SPIQISIKVNVSSVEKVDLAKRLLVGKSAS 76 (279)
Q Consensus 6 ~~~~~~~~~~~~~~~~~p~~lA~Y~D~ll~~~~~~~~~~~~---------~~i~l~~KD~Fe~~Y~~~LakRLL~~~s~s 76 (279)
|||.|+.++ |++||.|||.+++++....++.+. -+.|+.+||+|+.+|+++||||||+++|.|
T Consensus 371 fin~n~~~~--------~E~la~y~D~~lkk~~k~~~e~~ie~~l~~v~~l~~yisdKdvF~~~Ykk~lakRLl~~~S~s 442 (725)
T KOG2166|consen 371 FINKNVATS--------AELLATYCDDILKKGSKKLSDEAIEDTLEKVVKLLKYISDKDVFAEFYKKVLARRLLFDRSAS 442 (725)
T ss_pred HHcccCCCc--------HHHHHHHhHHHhcccccCCchhHHHhHhhcceeeeeeccHHHHHHHHHHHHHHHHHhhcCccc
Confidence 677777664 899999999999996544333222 245999999999999999999999999999
Q ss_pred hHHHHHHHHHHHHhcCCchhHhHHHHHhhHHHhHHHHHHHHHHHh---cC------------CCCC----Ccc-------
Q psy8359 77 VDAEKSMLSKLKQECGGGFTSKLEGMFKDMELSKDINVAFKQYMG---NL------------KEDK----EST------- 130 (279)
Q Consensus 77 ~~~E~~~I~~Lk~~cG~~~t~kle~M~~D~~~S~~l~~~F~~~~~---~~------------~~~~----d~~------- 130 (279)
+++|+.||.+|+++||.+||+||++||+|+.+|++++.+|.++.. +. .+|. +++
T Consensus 443 dd~E~~mIsklk~~~g~~~T~kL~~Mf~D~~~s~~l~~~F~~~~~~~~~~~~df~v~VLt~g~WP~~~~~~~~LP~el~~ 522 (725)
T KOG2166|consen 443 DDHEKSLITKLKNLCGEQFTSKLEGMFTDLTLSRELQTAFADYANYSANLGIDFTVTVLTTGFWPSYKSTDINLPSEMSD 522 (725)
T ss_pred hHHHHHHHHHHHHHHHhHHHHHHHhhcccHHHHHHHHHHHHhhhchhccCCCceeEEEeecCCcCCccCCCCCCChhHHH
Confidence 999999999999999999999999999999999999999997611 11 1220 111
Q ss_pred ----------------------------------------------------cccc---------cCCCCCHHHHHHHHh
Q psy8359 131 ----------------------------------------------------SNNA---------LGIDLTDADLRRTLQ 149 (279)
Q Consensus 131 ----------------------------------------------------FN~~---------~~t~i~~~~l~~~L~ 149 (279)
||+. ++|+|+.++|.+.|+
T Consensus 523 ~~e~F~~~Y~~kh~gR~L~w~~~l~~~ei~~~~~~~~~~l~vst~Qm~VLlLFN~~d~lt~~eI~~~t~i~~~~l~~~L~ 602 (725)
T KOG2166|consen 523 CVEMFKGFYATKHNGRRLTWIYSLGTGEINGKFDKKTVELQVSTYQMAVLLLFNNTEKLTYEEILEQTNLGHEDLARLLQ 602 (725)
T ss_pred HHHHHHHHHhhccCCCeeeeeeccCceEEEEEecCceEEEEEEhHHHHHHHHccchhhccHHHHHHHhCCCHHHHHHHHH
Confidence 7776 899999999999999
Q ss_pred HhhcCCceeeeeCCCCCCCCCCCeEEEecCCCCceeeEEeeccccccchHHHHHHHHHHHhhhhhhhhhhhhhhhccCCC
Q psy8359 150 SLACGKTRVLKKTPASRDIEDCDRFRFNNDFTFKLFRIKINQIQMKETNEEQKATEERVFQDRQYQIDAAIVRIMKMRKT 229 (279)
Q Consensus 150 sL~~~k~~iL~~~~~~~~i~~~~~f~~N~~F~~k~~ki~i~~~~~k~~~~e~~~~~~~i~~~R~~~I~AaIVRIMK~~K~ 229 (279)
||++.|.+++.. |.++. .+++.|.+|.+|+++.+|++++.+..+ |.+.+.+.+++||++.||||||||||+||.
T Consensus 603 Sl~~~K~~v~~~-~~s~~-~~~~~~~~N~~f~sk~~Rv~i~~~~~~----e~~~~~~~ve~dRk~~i~AaIVRIMK~rK~ 676 (725)
T KOG2166|consen 603 SLSCLKYKILLK-PMSRT-SPNDEFAFNSKFTSKMRRVKIPLPPMD----ERKKVVEDVDKDRKYAIDAAIVRIMKSRKV 676 (725)
T ss_pred HHHHHhHhhccC-ccccC-CCCcEEEeeccccCcceeeccCCCCch----hHHHHHhhhhhHHHHHHHHHHHHHHHhhcc
Confidence 998878667766 66667 899999999999999999999976654 667789999999999999999999999999
Q ss_pred CCHHHHHHHHHHhcC--CCCChHHHHHHHHhhhhcCceeecCCCCCceEe
Q psy8359 230 LSHNLLLSELFNQLK--FPVKPADLKKRIESLIDRDYMERDKDKANSYNY 277 (279)
Q Consensus 230 l~~~~L~~eV~~~l~--F~p~~~~iK~~Ie~LIekeYi~R~~~d~~~y~Y 277 (279)
+.|++|+.||++|++ |.|++.+||+|||.|||||||+|| +|+++|+|
T Consensus 677 l~h~~Lv~Ev~~ql~~RF~p~v~~IKk~Ie~LIEkeYleR~-~~~~~Y~Y 725 (725)
T KOG2166|consen 677 LGHQQLVSEVVEQLSERFKPDIKMIKKRIEDLIEREYLERD-ENPNIYRY 725 (725)
T ss_pred ccHHHHHHHHHHHHhhhcCCCHHHHHHHHHHHHHHHHHhcc-CCCCcccC
Confidence 999999999999999 999999999999999999999999 89999998
No 4
>KOG2284|consensus
Probab=100.00 E-value=1.2e-51 Score=377.47 Aligned_cols=257 Identities=31% Similarity=0.417 Sum_probs=229.9
Q ss_pred ccCcchhhHHHHhhhcccCCCCCCCCCCCcc-----c----ccccCChhHHHHHHHHHHHhHhcCCCCCChHHHHHHHHH
Q psy8359 16 SLNKSKTRAWNRDTCSSLFPPRKQALSTHEK-----S----PIQISIKVNVSSVEKVDLAKRLLVGKSASVDAEKSMLSK 86 (279)
Q Consensus 16 ~~~~~~~p~~lA~Y~D~ll~~~~~~~~~~~~-----~----~i~l~~KD~Fe~~Y~~~LakRLL~~~s~s~~~E~~~I~~ 86 (279)
|.+-.+-|+.||+|||++++++.+++++.+. + |.||.|||+|.+||.++||+||+.+.|.|.|.|..||++
T Consensus 398 g~sv~ka~e~la~y~d~llkks~kg~se~~~e~~l~s~i~if~yi~dkdifqkfys~mla~rli~~~s~smd~ee~mink 477 (728)
T KOG2284|consen 398 GQSVPKASERLARYTDGLLKKSTKGLSETDLEAKLDSAIVIFRYIEDKDIFQKFYSKMLANRLIASTSISMDAEELMINK 477 (728)
T ss_pred CccccchHHHHHHHhhhHHhhhhcCCChhhHHHhhhcceeeeeecccHHHHHHHHHHHHHHHHHhhcccccchHHHHHHH
Confidence 3555678999999999999999877766543 3 349999999999999999999999999999999999999
Q ss_pred HHHhcCCchhHhHHHHHhhHHHhHHHHHHHHHHHhcCCCCCC--------------------cc----------------
Q psy8359 87 LKQECGGGFTSKLEGMFKDMELSKDINVAFKQYMGNLKEDKE--------------------ST---------------- 130 (279)
Q Consensus 87 Lk~~cG~~~t~kle~M~~D~~~S~~l~~~F~~~~~~~~~~~d--------------------~~---------------- 130 (279)
||++||.+||+++. +.|+++|.+|+.+|.+.+.+-.+|.. ++
T Consensus 478 lkqacgyefts~~~--~td~~~s~~lnn~f~~~i~nf~~pq~l~~~iq~fe~fyt~~~~grkltwl~~~~~g~v~~~yl~ 555 (728)
T KOG2284|consen 478 LKQACGYEFTSSWP--LTDPQLSTNLNNQFAQDIANFHLPQILQPVIQEFEKFYTGKHNGRKLTWLFNMSQGDVRLTYLD 555 (728)
T ss_pred HHHHhCceecccCC--CCChhhccccchhHHHHHHhccchHHHHHHHHHHHHHhccccCCceehhhhhhcccceeeeecC
Confidence 99999999999999 99999999999999999888766510 00
Q ss_pred -----------------cccc---------cCCCCCHHHHHHHHhHhhcCCceeeeeCCCCCCCCCCCeEEEecCCCCce
Q psy8359 131 -----------------SNNA---------LGIDLTDADLRRTLQSLACGKTRVLKKTPASRDIEDCDRFRFNNDFTFKL 184 (279)
Q Consensus 131 -----------------FN~~---------~~t~i~~~~l~~~L~sL~~~k~~iL~~~~~~~~i~~~~~f~~N~~F~~k~ 184 (279)
||.+ +.+|++.++|.+++.+|. ..++|.+.. .++..+..|++|++|++|+
T Consensus 556 k~yva~~~~yqma~ll~f~~~~~i~~k~i~~~~~~~~~~l~kti~til--dv~~~~~d~--~~~~a~s~~~lnm~~tskr 631 (728)
T KOG2284|consen 556 KQYVAQMYVYQMAALLCFERRDAILVKDIGEEIGVSGDYLLKTIRTIL--DVTLLTCDD--QNLTADSLVRLNMSMTSKR 631 (728)
T ss_pred chHHHHHHHHHHHHHHHhcccccchHHhhhhhhCccHHHHHHHHHHHH--hceeecccc--cccChhhhhhccccccccc
Confidence 7766 789999999999999999 788888754 4778888999999999999
Q ss_pred eeEEeeccc-cccchHHHHHHHHHHHhhhhhhhhhhhhhhhccCCCCCHHHHHHHHHHhcC--CCCChHHHHHHHHhhhh
Q psy8359 185 FRIKINQIQ-MKETNEEQKATEERVFQDRQYQIDAAIVRIMKMRKTLSHNLLLSELFNQLK--FPVKPADLKKRIESLID 261 (279)
Q Consensus 185 ~ki~i~~~~-~k~~~~e~~~~~~~i~~~R~~~I~AaIVRIMK~~K~l~~~~L~~eV~~~l~--F~p~~~~iK~~Ie~LIe 261 (279)
.|+++..++ .|.+++|..++...+.+||++.+|||||||||.||.+.|+-|+.||+.|.+ |.|++++||+|||.||+
T Consensus 632 ~kf~~~~p~~~k~~~~e~e~~~~~v~~drk~y~~~aivrimk~rkvl~hnalv~ei~~qt~~rf~p~v~~ikk~ie~li~ 711 (728)
T KOG2284|consen 632 MKFRLQAPQVNKAVEKEQEAVANTVSQDRKYYMECAIVRIMKTRKVLKHNALVTEIMDQTKGRFSPDVPFIKKSIEDLIE 711 (728)
T ss_pred eeeEecchhhccccHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHhhcccCCCCchHHHHHHHHHHH
Confidence 999998765 457777888899999999999999999999999999999999999999999 99999999999999999
Q ss_pred cCceeecCCCCCceEecC
Q psy8359 262 RDYMERDKDKANSYNYMA 279 (279)
Q Consensus 262 keYi~R~~~d~~~y~Yva 279 (279)
+.||+|...+ +.|.|+|
T Consensus 712 k~yi~rt~~~-dey~y~a 728 (728)
T KOG2284|consen 712 KMYIQRTDQN-DEYQYLA 728 (728)
T ss_pred HHHHhhcccc-ccchhcC
Confidence 9999999765 8999997
No 5
>KOG2285|consensus
Probab=100.00 E-value=3.4e-40 Score=304.68 Aligned_cols=260 Identities=32% Similarity=0.450 Sum_probs=215.5
Q ss_pred cCcchhhHHHHhhhcccCCCCCCCCCCCc----c-----cc----cccCChhHHHHHHHHHHHhHhcCCCCCChHHHHHH
Q psy8359 17 LNKSKTRAWNRDTCSSLFPPRKQALSTHE----K-----SP----IQISIKVNVSSVEKVDLAKRLLVGKSASVDAEKSM 83 (279)
Q Consensus 17 ~~~~~~p~~lA~Y~D~ll~~~~~~~~~~~----~-----~~----i~l~~KD~Fe~~Y~~~LakRLL~~~s~s~~~E~~~ 83 (279)
.|+|+||+.||.|||.++|+. +++... . .+ .|+.+||+|+.|++.||++||+.+.|++.+.|..|
T Consensus 395 ~pESKCpELLANYCDmLLRkT--pLSKkLTSEeIdakL~~VLLVLKYV~NKDVFMRyHkaHLtRRLIL~~SADsEkEE~m 472 (777)
T KOG2285|consen 395 APESKCPELLANYCDMLLRKT--PLSKKLTSEEIDAKLNQVLLVLKYVENKDVFMRYHKAHLTRRLILEMSADSEKEEMM 472 (777)
T ss_pred CcccccHHHHHHHHHHHHhcC--ccchhccHHHHHHHHHhHhhHhHhhcccHHHHHHHHHHHHHHHHHhcccchhHHHHH
Confidence 599999999999999999874 343322 1 12 39999999999999999999999999999999999
Q ss_pred HHHHHHhcC--CchhHhHHHHHhhHHHhHHHHHHHHHHHhcCCC----------------------------C-------
Q psy8359 84 LSKLKQECG--GGFTSKLEGMFKDMELSKDINVAFKQYMGNLKE----------------------------D------- 126 (279)
Q Consensus 84 I~~Lk~~cG--~~~t~kle~M~~D~~~S~~l~~~F~~~~~~~~~----------------------------~------- 126 (279)
+..|+ +|| .+|++||.+||+|+++|++++..|+..+...+. |
T Consensus 473 VewLR-EvGMPaDyVNkLaRMfQDIkvseDlN~~Fk~~~~~~~~~~~aDsiNiKiLNaGAW~R~SErv~vSLP~ELED~i 551 (777)
T KOG2285|consen 473 VEWLR-EVGMPADYVNKLARMFQDIKVSEDLNSSFKKALTGTNNNSIADSINIKILNAGAWGRGSERVRVSLPRELEDFI 551 (777)
T ss_pred HHHHH-HcCCcHHHHHHHHHHHhhccccHHHHHHHHHHHhCCCCCCcccceeeeeecccccccccceEEEeCchhHHHhC
Confidence 99998 788 579999999999999999999999997654310 1
Q ss_pred CC---cc-------------------------------------------cccc-----------cCCCCCHHHHHHHHh
Q psy8359 127 KE---ST-------------------------------------------SNNA-----------LGIDLTDADLRRTLQ 149 (279)
Q Consensus 127 ~d---~~-------------------------------------------FN~~-----------~~t~i~~~~l~~~L~ 149 (279)
|| |. ||++ -+|.+|+.+|.++|.
T Consensus 552 PdveEfykk~hsgrkl~w~h~msNG~itf~n~~GryDLevTTFQmAVLFawNqR~hdKIS~EnLrLATELPDaELrRTLw 631 (777)
T KOG2285|consen 552 PDVEEFYKKKHSGRKLQWYHHMSNGTITFVNNFGRYDLEVTTFQMAVLFAWNQRAHDKISLENLRLATELPDAELRRTLW 631 (777)
T ss_pred ccHHHHHhcccCccchhhhhhccCCeeEeecccccceeeeehhhHHHHHHhccccccccchHhhhhhhcCCCHHHHHHHH
Confidence 00 00 6665 689999999999999
Q ss_pred HhhcC---CceeeeeCCCC----CCCCCCCeEEEecCCCC-c----eeeEEeeccccc--cchHHHHHHHHHHHhhhhhh
Q psy8359 150 SLACG---KTRVLKKTPAS----RDIEDCDRFRFNNDFTF-K----LFRIKINQIQMK--ETNEEQKATEERVFQDRQYQ 215 (279)
Q Consensus 150 sL~~~---k~~iL~~~~~~----~~i~~~~~f~~N~~F~~-k----~~ki~i~~~~~k--~~~~e~~~~~~~i~~~R~~~ 215 (279)
||+.- |..||..+|.. +++.+++.|.+|.+|+- | ..+.+++.+..- .+.....+.++.|.+-|-..
T Consensus 632 SLVAfPK~k~QiLL~ep~~~~spkDFte~T~F~iNqeF~vvKNgKsQ~RGKvNLIGRLQLstEr~~eeenesIVqLRiLR 711 (777)
T KOG2285|consen 632 SLVAFPKMKYQILLCEPPTTVSPKDFTESTKFLINQEFNVVKNGKSQQRGKVNLIGRLQLSTERNAEEENESIVQLRILR 711 (777)
T ss_pred HHHhhhhhhhheeeecCcccCCcccccccceEEeechhhhhhccchhhcccceeeeeeeehhhhhhhhhcchhHHHHHHH
Confidence 99863 45788888753 67888999999999963 1 134445544321 22222345677899999999
Q ss_pred hhhhhhhhhccCCCCCHHHHHHHHHHhcC--CCCChHHHHHHHHhhhhcCceeecCCCCCceEecC
Q psy8359 216 IDAAIVRIMKMRKTLSHNLLLSELFNQLK--FPVKPADLKKRIESLIDRDYMERDKDKANSYNYMA 279 (279)
Q Consensus 216 I~AaIVRIMK~~K~l~~~~L~~eV~~~l~--F~p~~~~iK~~Ie~LIekeYi~R~~~d~~~y~Yva 279 (279)
.|-+|++|||.||+++..+|-.|.++-|+ |-|+..+||..||+|||..|++||++|-|+|+|+|
T Consensus 712 tQEaIikImK~RK~~~nAqLq~ELveILKnmFlP~kKmIKEQieWLIEnKYmrRd~dDINtFiYia 777 (777)
T KOG2285|consen 712 TQEAIIKIMKTRKTYTNAQLQMELVEILKNMFLPNKKMIKEQIEWLIENKYMRRDADDINTFIYIA 777 (777)
T ss_pred HHHHHHHHHHHHHHhhHHHHHHHHHHHHHHccCCcHHHHHHHHHHHHhhhhhccchhhccceeeeC
Confidence 99999999999999999999999999999 99999999999999999999999999999999997
No 6
>PF00888 Cullin: Cullin family; InterPro: IPR001373 Cullins are a family of hydrophobic proteins that act as scaffolds for ubiquitin ligases (E3). Cullins are found throughout eukaryotes. Humans express seven cullins (Cul1, 2, 3, 4A, 4B, 5 and 7), each forming part of a multi-subunit ubiquitin complex. Cullin-RING ubiquitin ligases (CRLs), such as Cul1 (SCF) [], play an essential role in targeting proteins for ubiquitin-mediated destruction; as such, they are diverse in terms of composition and function, regulating many different processes from glucose sensing and DNA replication to limb patterning and circadian rhythms. The catalytic core of CRLs consists of a RING protein and a cullin family member. For Cul1, the C-terminal cullin-homology domain binds the RING protein. The RING protein appears to function as a docking site for ubiquitin-conjugating enzymes (E2s). Other proteins contain a cullin-homology domain, such as the APC2 subunit of the anaphase-promoting complex/cyclosome and the p53 cytoplasmic anchor PARC; both APC2 and PARC have ubiquitin ligase activity. The N-terminal region of cullins is more variable, and is used to interact with specific adaptor proteins [, , ]. This entry represents the N-terminal region of cullin proteins, which consists of several domains, including cullin repeat domain, a 4-helical bundle domain, an alpha+beta domain, and a winged helix-like domain.; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 2WZK_A 3DQV_D 3DPL_C 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_A 1U6G_A 4A0K_A ....
Probab=99.93 E-value=3.9e-26 Score=225.80 Aligned_cols=163 Identities=39% Similarity=0.466 Sum_probs=126.0
Q ss_pred cchhhHHHHhhhcccCCCCCCCCCCCcc---------cccccCChhHHHHHHHHHHHhHhcCCCCCChHHHHHHHHHHHH
Q psy8359 19 KSKTRAWNRDTCSSLFPPRKQALSTHEK---------SPIQISIKVNVSSVEKVDLAKRLLVGKSASVDAEKSMLSKLKQ 89 (279)
Q Consensus 19 ~~~~p~~lA~Y~D~ll~~~~~~~~~~~~---------~~i~l~~KD~Fe~~Y~~~LakRLL~~~s~s~~~E~~~I~~Lk~ 89 (279)
..++|++||+|||.+++++....++.+. -+.|+++||+|+.+|+++||+|||.+++.+.+.|+.||++|+.
T Consensus 326 ~~~~~e~La~y~d~~l~~~~~~~~~~~~~~~~~~i~~l~~~l~~Kd~F~~~Y~~~L~~RLl~~~~~~~~~E~~~i~~Lk~ 405 (588)
T PF00888_consen 326 NNKIPELLAKYCDSLLRKSNKKLSEEEIEQKLDDIVKLFSYLSDKDVFEKYYKKLLAKRLLSNKSFSEDAEKSMIEKLKK 405 (588)
T ss_dssp TSHHHHHHHHHHHHHHBSSCCCS-HCCHHHHHHHHHHHHTTSSTHHHHHHHHHHHHHHHHHTT-BS-HHHHHHHHHHHHH
T ss_pred CcchHHHHHHHhhHhhhhcccccchHHHHHHhhhhEEEeeecchhHHHHHHHHHHHHHHHhcccccccHHHHHHHHHHhc
Confidence 6889999999999999987633322222 1349999999999999999999999999999999999999999
Q ss_pred hcCCchhHhHHHHHhhHHHhHHHHHHHHHHHhcCC------------------CCC----C-cc----------------
Q psy8359 90 ECGGGFTSKLEGMFKDMELSKDINVAFKQYMGNLK------------------EDK----E-ST---------------- 130 (279)
Q Consensus 90 ~cG~~~t~kle~M~~D~~~S~~l~~~F~~~~~~~~------------------~~~----d-~~---------------- 130 (279)
+||.+||++|++|++|++.|++++++|+++..+.+ +|. + +.
T Consensus 406 ~~g~~~~~kl~~M~~D~~~S~~~~~~f~~~~~~~~~~~~~~~~~~~~vls~~~Wp~~~~~~~~~lP~~l~~~~~~f~~~Y 485 (588)
T PF00888_consen 406 ECGSSYTSKLEVMLKDIKNSKELNEEFKQKQSQNNIQLIPPFDFNVKVLSKGYWPKYPSENNIKLPPELQQALDSFEKFY 485 (588)
T ss_dssp TCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTT-SS--CCEEEEEEEETTTS-S-S-SS-----HHHHHHHHHHHHHH
T ss_pred ccCchhHHHHHHHHHHHhhcHHHHHHHHHHhhhccccccCCCceEEEEecCCCCCCCCCCccccCCHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999875421 110 0 11
Q ss_pred -------------------------------------------cccc---------cCCCCCHHHHHHHHhHhhcCCcee
Q psy8359 131 -------------------------------------------SNNA---------LGIDLTDADLRRTLQSLACGKTRV 158 (279)
Q Consensus 131 -------------------------------------------FN~~---------~~t~i~~~~l~~~L~sL~~~k~~i 158 (279)
||+. +.||++.++|+++|.+|+..+..+
T Consensus 486 ~~~~~~R~L~w~~~l~~~~i~~~~~~~~~~l~~s~~q~~iLl~Fn~~~~~t~~ei~~~~~~~~~~l~~~L~~l~~~~~l~ 565 (588)
T PF00888_consen 486 KEKHKGRKLTWLPSLSSVEIEFNFNNGKYELTVSTLQAAILLLFNDNDSLTVEEISEKTGISEEELKRALKSLVKSKILI 565 (588)
T ss_dssp HTTSTTEEEEEEGGGEEEEEEEESSSSEEEEEEEHHHHHHHHGGGSSSEEEHHHHHHHC---HHHHHHHHHCCCTTTTCS
T ss_pred HhcCCCcEEEEecccCcEEEEEEecCCceeEEeeHHHHHHHHHHccCCCccHHHHHHHHCcCHHHHHHHHHHHHhCCcce
Confidence 7776 789999999999999999554444
Q ss_pred eeeCCCCCCCCCCCeEEEecCCC
Q psy8359 159 LKKTPASRDIEDCDRFRFNNDFT 181 (279)
Q Consensus 159 L~~~~~~~~i~~~~~f~~N~~F~ 181 (279)
+.+.++++++++++.|++|.+|+
T Consensus 566 ~~~~~~~~~~~~~~~f~~N~~F~ 588 (588)
T PF00888_consen 566 LLKEPNSKSFSDNDEFSVNENFT 588 (588)
T ss_dssp EEETTTSSS--TT-EEEE-TT--
T ss_pred eecCCccCCCCCCCEEEeCCCCC
Confidence 44778889999999999999996
No 7
>PF10557 Cullin_Nedd8: Cullin protein neddylation domain; InterPro: IPR019559 This is the neddylation site of cullin proteins, which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae (Baker's yeast), and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue []. ; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_B 1U6G_A 3O6B_J 3O2P_E 4A0K_A 2HYE_C ....
Probab=99.87 E-value=3.8e-23 Score=148.68 Aligned_cols=66 Identities=61% Similarity=0.954 Sum_probs=60.5
Q ss_pred HHhhhhhhhhhhhhhhhccCCCCCHHHHHHHHHHhcC--CCCChHHHHHHHHhhhhcCceeecCCCCC
Q psy8359 208 VFQDRQYQIDAAIVRIMKMRKTLSHNLLLSELFNQLK--FPVKPADLKKRIESLIDRDYMERDKDKAN 273 (279)
Q Consensus 208 i~~~R~~~I~AaIVRIMK~~K~l~~~~L~~eV~~~l~--F~p~~~~iK~~Ie~LIekeYi~R~~~d~~ 273 (279)
|+++|.+.|+||||||||++|+++|++|+.+|.++++ |.|+..+||++||+||++|||+||++|+|
T Consensus 1 i~~~R~~~I~AaIVrimK~~k~~~~~~L~~~v~~~l~~~f~~~~~~ik~~Ie~LIekeyi~Rd~~d~n 68 (68)
T PF10557_consen 1 IEQDRKYQIDAAIVRIMKQEKKLSHDELINEVIEELKKRFPPSVSDIKKRIESLIEKEYIERDEDDPN 68 (68)
T ss_dssp CHHHHHHHHHHHHHHHHHHSSEEEHHHHHHHHHHHTTTTS---HHHHHHHHHHHHHTTSEEEESSECT
T ss_pred CcchhhhhhhhheehhhhhcCceeHHHHHHHHHHHhcCCcCCCHHHHHHHHHHHHHhhhhhcCCCCCC
Confidence 4678999999999999999999999999999999997 99999999999999999999999999876
No 8
>smart00182 CULLIN Cullin.
Probab=99.80 E-value=1.4e-19 Score=148.40 Aligned_cols=73 Identities=53% Similarity=0.715 Sum_probs=70.9
Q ss_pred ccCChhHHHHHHHHHHHhHhcCCCCCChHHHHHHHHHHHHhcCCchhHhHHHHHhhHHHhHHHHHHHHHHHhc
Q psy8359 50 QISIKVNVSSVEKVDLAKRLLVGKSASVDAEKSMLSKLKQECGGGFTSKLEGMFKDMELSKDINVAFKQYMGN 122 (279)
Q Consensus 50 ~l~~KD~Fe~~Y~~~LakRLL~~~s~s~~~E~~~I~~Lk~~cG~~~t~kle~M~~D~~~S~~l~~~F~~~~~~ 122 (279)
||++||+|+.+|+++||+|||.+++.+.+.|..||++||.+||.+||+||++||+|++.|++++++|++++.+
T Consensus 1 y~~~Kd~F~~~Y~~~La~RLL~~~~~~~~~E~~~i~~Lk~~~G~~~~~kle~Ml~Di~~S~~l~~~f~~~~~~ 73 (142)
T smart00182 1 YIQDKDVFEKYYKKHLAKRLILNRSASDDAEENMITKLKQECGYEFTSKLERMFRDISLSKDLNQSFKDMLEN 73 (142)
T ss_pred CCCchHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 7899999999999999999999999999999999999999999999999999999999999999999998765
No 9
>KOG2165|consensus
Probab=98.01 E-value=5.3e-05 Score=75.03 Aligned_cols=127 Identities=20% Similarity=0.129 Sum_probs=103.2
Q ss_pred ccCChhHHHHHHHHHHHhHhcCCCCCChHHHHHHHHHHHHhcCCchhHhHHHHHhhHHHhHHHHHHHHHH--HhcC--C-
Q psy8359 50 QISIKVNVSSVEKVDLAKRLLVGKSASVDAEKSMLSKLKQECGGGFTSKLEGMFKDMELSKDINVAFKQY--MGNL--K- 124 (279)
Q Consensus 50 ~l~~KD~Fe~~Y~~~LakRLL~~~s~s~~~E~~~I~~Lk~~cG~~~t~kle~M~~D~~~S~~l~~~F~~~--~~~~--~- 124 (279)
...+|+.|..-||.+||.||+....++.|.|..=++-||-.+|..--..++.|++|+.-|.+.++.++.. .... .
T Consensus 448 IygSKElfv~EyRnLLAdRLl~~~dy~~E~E~R~leLLKlrFgEt~lq~CevML~Dv~dS~~id~~i~~~~~~~r~~e~~ 527 (765)
T KOG2165|consen 448 IYGSKELFVKEYRNLLADRLLTLTDYDPEKEIRNLELLKLRFGETSLQGCEVMLNDVIDSRRIDQSIHNESELSRGAEEV 527 (765)
T ss_pred HHcchHHHHHHHHHHHHHHHhhhcccCHHHHHHHHHHHHhhcccchHHHHHHHHHhhhhhhhhhhhhhhhhhhhcccccC
Confidence 4589999999999999999999999999999999999999999998999999999999999999999883 2211 0
Q ss_pred --------------CCC----------Ccc--------------------------------------------------
Q psy8359 125 --------------EDK----------EST-------------------------------------------------- 130 (279)
Q Consensus 125 --------------~~~----------d~~-------------------------------------------------- 130 (279)
+|+ ++.
T Consensus 528 ~~~~i~~~IlS~~fWP~~~~~~~~lP~pl~~el~~Y~~~Y~~~K~~RkL~w~~~lG~Veieie~~DRtl~~tVsp~qA~i 607 (765)
T KOG2165|consen 528 PDFGISATILSSLFWPPLCDEAFHLPGPLEAELDKYAEIYEQLKRGRKLQWLKNLGKVEIEIEFEDRTLVLTVSPEQAAI 607 (765)
T ss_pred CCCchhhhhhhhhcCCccccccccCChhHHHHHHHHHHHHHHhccCCeeeeecccCeEEEEEEEcCeEEEEeeCHHHHHH
Confidence 111 100
Q ss_pred ---cccc---------cCCCCCHHHHHHHHhHhhcCCceeeeeCCCCCCCCCCCeEEEecCCC
Q psy8359 131 ---SNNA---------LGIDLTDADLRRTLQSLACGKTRVLKKTPASRDIEDCDRFRFNNDFT 181 (279)
Q Consensus 131 ---FN~~---------~~t~i~~~~l~~~L~sL~~~k~~iL~~~~~~~~i~~~~~f~~N~~F~ 181 (279)
|.+. +.+|||..-|.+.|.=.. +.++|+.+|. +++..+|++++.=.
T Consensus 608 I~~Fqek~twt~eelse~l~ip~~~lrrrL~fWi--~~GvL~e~~~---~s~tgt~T~iEse~ 665 (765)
T KOG2165|consen 608 INLFQEKNTWTLEELSESLGIPVPALRRRLSFWI--QKGVLREEPI---ISDTGTLTVIESEM 665 (765)
T ss_pred HHHhcCcccccHHHHHHHhCCCHHHHHHHHHHHH--HcCeeecCCC---CCCCceeeeccccc
Confidence 4443 788999999999998888 7788887653 36778899998543
No 10
>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=93.66 E-value=0.073 Score=37.83 Aligned_cols=45 Identities=24% Similarity=0.409 Sum_probs=37.7
Q ss_pred hhhhhccCCCCCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeecCC
Q psy8359 220 IVRIMKMRKTLSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERDKD 270 (279)
Q Consensus 220 IVRIMK~~K~l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~~ 270 (279)
|-.+|+.++.++..+|-.+ |..+++.+...++.|+.+|||++...
T Consensus 5 i~~~l~~~~~~S~~eLa~~------~~~s~~~ve~mL~~l~~kG~I~~~~~ 49 (69)
T PF09012_consen 5 IRDYLRERGRVSLAELARE------FGISPEAVEAMLEQLIRKGYIRKVDM 49 (69)
T ss_dssp HHHHHHHS-SEEHHHHHHH------TT--HHHHHHHHHHHHCCTSCEEEEE
T ss_pred HHHHHHHcCCcCHHHHHHH------HCcCHHHHHHHHHHHHHCCcEEEecC
Confidence 4567899999999999888 99999999999999999999999754
No 11
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=90.02 E-value=0.87 Score=36.58 Aligned_cols=60 Identities=13% Similarity=0.259 Sum_probs=42.9
Q ss_pred hhhhhhhhccCCCCCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeecCCCCCceEecC
Q psy8359 217 DAAIVRIMKMRKTLSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERDKDKANSYNYMA 279 (279)
Q Consensus 217 ~AaIVRIMK~~K~l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~~d~~~y~Yva 279 (279)
+..|++++-..+.++..+++...-+. ..+...-|...|..|.+||||+|..+ ...|.|-|
T Consensus 6 E~~VM~vlW~~~~~t~~eI~~~l~~~--~~~~~tTv~T~L~rL~~KG~v~~~k~-gr~~~Y~p 65 (130)
T TIGR02698 6 EWEVMRVVWTLGETTSRDIIRILAEK--KDWSDSTIKTLLGRLVDKGCLTTEKE-GRKFIYTA 65 (130)
T ss_pred HHHHHHHHHcCCCCCHHHHHHHHhhc--cCCcHHHHHHHHHHHHHCCceeeecC-CCcEEEEe
Confidence 34466677666777766554442221 56788899999999999999999864 45788865
No 12
>PF03965 Penicillinase_R: Penicillinase repressor; InterPro: IPR005650 Proteins in this entry are transcriptional regulators found in a variety of bacteria and a small number of archaea. Many are BlaI/MecI proteins which regulate resistance to penicillins (beta-lactams), though at least one protein (Q47839 from SWISSPROT) appears to be involved in the regulation of copper homeostasis []. BlaI regulators repress the expression of penicillin-degrading enzymes (penicillinases) until the cell encounters the antiobiotic, at which point repression ceases and penicillinase expression occurs, allowing cell growth []. MecI regulators repress the expression of MecA, a cell-wall biosynthetic enzyme not inhibited by penicillins at clinically achievable concentrations, until the presence of the antibiotic is detected []. At this point repression ends and MecA expression occurs which, together with the switching off of the penicillin-sensitive enzymes, allows the cell to grow despite the presence of antibiotic.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G9W_A 2K4B_A 1XSD_A 1SD4_A 1SD7_A 1SD6_A 2P7C_B 1P6R_A 1OKR_B 2D45_B ....
Probab=88.76 E-value=0.52 Score=36.82 Aligned_cols=60 Identities=13% Similarity=0.254 Sum_probs=41.7
Q ss_pred hhhhhhhhccCCCCCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeecCCCCCceEecC
Q psy8359 217 DAAIVRIMKMRKTLSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERDKDKANSYNYMA 279 (279)
Q Consensus 217 ~AaIVRIMK~~K~l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~~d~~~y~Yva 279 (279)
+..|++++=..+.++..++....-+. ..+....|...+..|.+||||.|... ...|.|-|
T Consensus 5 E~~IM~~lW~~~~~t~~eI~~~l~~~--~~~~~sTv~t~L~rL~~Kg~l~~~~~-gr~~~Y~p 64 (115)
T PF03965_consen 5 ELEIMEILWESGEATVREIHEALPEE--RSWAYSTVQTLLNRLVEKGFLTREKI-GRAYVYSP 64 (115)
T ss_dssp HHHHHHHHHHHSSEEHHHHHHHHCTT--SS--HHHHHHHHHHHHHTTSEEEEEE-TTCEEEEE
T ss_pred HHHHHHHHHhCCCCCHHHHHHHHHhc--cccchhHHHHHHHHHHhCCceeEeec-CCceEEEe
Confidence 34456666666667766554443222 67789999999999999999999974 45788865
No 13
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=88.49 E-value=0.84 Score=36.38 Aligned_cols=62 Identities=16% Similarity=0.288 Sum_probs=52.0
Q ss_pred hhhhhhhhhhccCCCCCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeecCCCCCceEecC
Q psy8359 215 QIDAAIVRIMKMRKTLSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERDKDKANSYNYMA 279 (279)
Q Consensus 215 ~I~AaIVRIMK~~K~l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~~d~~~y~Yva 279 (279)
..++.+++||=+++..+..+++.++.+. +.++...|+--|..|..||+|.|..+ ...|.|-|
T Consensus 6 ~aE~eVM~ilW~~~~~t~~eI~~~l~~~--~ews~sTV~TLl~RL~KKg~l~~~kd-gr~~~y~p 67 (123)
T COG3682 6 AAEWEVMEILWSRGPATVREIIEELPAD--REWSYSTVKTLLNRLVKKGLLTRKKD-GRAFRYSP 67 (123)
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHhhc--ccccHHHHHHHHHHHHhccchhhhhc-CCeeeeec
Confidence 3577889999999999999877776655 78888999999999999999999974 46787754
No 14
>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=87.75 E-value=0.48 Score=33.24 Aligned_cols=51 Identities=12% Similarity=0.272 Sum_probs=39.4
Q ss_pred hhhccCCCCCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeecCCCCCceEec
Q psy8359 222 RIMKMRKTLSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERDKDKANSYNYM 278 (279)
Q Consensus 222 RIMK~~K~l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~~d~~~y~Yv 278 (279)
..+=.++.++..+|... ...+...+-+.++.|.++|+++|..+.+..|..+
T Consensus 15 ~~Ll~~~~~t~~eIa~~------l~i~~~~v~~~L~~L~~~GlV~~~~~~~~~Y~a~ 65 (68)
T PF01978_consen 15 LALLKNGPATAEEIAEE------LGISRSTVYRALKSLEEKGLVEREEGRPKVYRAV 65 (68)
T ss_dssp HHHHHHCHEEHHHHHHH------HTSSHHHHHHHHHHHHHTTSEEEEEECCEEEEEE
T ss_pred HHHHHcCCCCHHHHHHH------HCcCHHHHHHHHHHHHHCCCEEEEcCceEEEEEe
Confidence 33336667777777666 3788999999999999999999998776666554
No 15
>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=86.81 E-value=2.1 Score=29.47 Aligned_cols=51 Identities=10% Similarity=0.267 Sum_probs=35.9
Q ss_pred hhhhhhhhc-cCCCCCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeec--CCCCC
Q psy8359 217 DAAIVRIMK-MRKTLSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERD--KDKAN 273 (279)
Q Consensus 217 ~AaIVRIMK-~~K~l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~--~~d~~ 273 (279)
|..|.+.+. ....++..+|... +..+.+.+-+.|..|.++|||++. +.|..
T Consensus 5 q~~vL~~l~~~~~~~t~~~l~~~------~~~~~~~vs~~i~~L~~~glv~~~~~~~d~R 58 (68)
T PF13463_consen 5 QWQVLRALAHSDGPMTQSDLAER------LGISKSTVSRIIKKLEEKGLVEKERDPHDKR 58 (68)
T ss_dssp HHHHHHHHT--TS-BEHHHHHHH------TT--HHHHHHHHHHHHHTTSEEEEEESSCTT
T ss_pred HHHHHHHHHccCCCcCHHHHHHH------HCcCHHHHHHHHHHHHHCCCEEecCCCCcCC
Confidence 445566666 7777777777776 688888999999999999999765 44444
No 16
>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=83.53 E-value=1.8 Score=29.48 Aligned_cols=47 Identities=19% Similarity=0.376 Sum_probs=42.4
Q ss_pred hhhhhhhccCCCCCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeecCC
Q psy8359 218 AAIVRIMKMRKTLSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERDKD 270 (279)
Q Consensus 218 AaIVRIMK~~K~l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~~ 270 (279)
..|..+++.++.++..+|... |..+...|.+=+..|-++|+|.|-.+
T Consensus 3 ~~Il~~l~~~~~~s~~ela~~------~~VS~~TiRRDl~~L~~~g~i~r~~G 49 (57)
T PF08220_consen 3 QQILELLKEKGKVSVKELAEE------FGVSEMTIRRDLNKLEKQGLIKRTHG 49 (57)
T ss_pred HHHHHHHHHcCCEEHHHHHHH------HCcCHHHHHHHHHHHHHCCCEEEEcC
Confidence 357888899999999999888 89999999999999999999999754
No 17
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=82.99 E-value=3.9 Score=28.87 Aligned_cols=53 Identities=8% Similarity=0.140 Sum_probs=42.3
Q ss_pred hhhhhhhhccCCC--CCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeecCCCCCce
Q psy8359 217 DAAIVRIMKMRKT--LSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERDKDKANSY 275 (279)
Q Consensus 217 ~AaIVRIMK~~K~--l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~~d~~~y 275 (279)
+..|...|+.+.. ++-.+|..+ .-.+...+.+.+..|.++|||.++.+.|..|
T Consensus 8 ~~~IL~~L~~~g~~~~ta~eLa~~------lgl~~~~v~r~L~~L~~~G~V~~~~~~~~~W 62 (68)
T smart00550 8 EEKILEFLENSGDETSTALQLAKN------LGLPKKEVNRVLYSLEKKGKVCKQGGTPPLW 62 (68)
T ss_pred HHHHHHHHHHCCCCCcCHHHHHHH------HCCCHHHHHHHHHHHHHCCCEEecCCCCCce
Confidence 3456778888877 888877776 4677789999999999999999987665554
No 18
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=78.29 E-value=5.9 Score=26.13 Aligned_cols=45 Identities=9% Similarity=0.220 Sum_probs=33.4
Q ss_pred hhhhccCCCCCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeecCCCC
Q psy8359 221 VRIMKMRKTLSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERDKDKA 272 (279)
Q Consensus 221 VRIMK~~K~l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~~d~ 272 (279)
++.+. ...++..++... +..+.+.+.+.|+.|.++|++.+....+
T Consensus 3 l~~l~-~~~~~~~~i~~~------l~is~~~v~~~l~~L~~~g~i~~~~~~~ 47 (66)
T smart00418 3 LKLLA-EGELCVCELAEI------LGLSQSTVSHHLKKLREAGLVESRREGK 47 (66)
T ss_pred HHHhh-cCCccHHHHHHH------HCCCHHHHHHHHHHHHHCCCeeeeecCC
Confidence 44444 566777766555 4578888999999999999999876433
No 19
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=75.96 E-value=6.1 Score=27.75 Aligned_cols=25 Identities=24% Similarity=0.561 Sum_probs=21.7
Q ss_pred ChHHHHHHHHhhhhcCceeecCCCC
Q psy8359 248 KPADLKKRIESLIDRDYMERDKDKA 272 (279)
Q Consensus 248 ~~~~iK~~Ie~LIekeYi~R~~~d~ 272 (279)
++.-+..-++.|.++|||+|+++-+
T Consensus 39 S~~tv~~~L~~Le~kG~I~r~~~~~ 63 (65)
T PF01726_consen 39 STSTVQRHLKALERKGYIRRDPGKA 63 (65)
T ss_dssp SHHHHHHHHHHHHHTTSEEEGCCSC
T ss_pred ChHHHHHHHHHHHHCcCccCCCCCC
Confidence 6888889999999999999997643
No 20
>PF02186 TFIIE_beta: TFIIE beta subunit core domain; InterPro: IPR003166 Initiation of eukaryotic mRNA transcription requires melting of promoter DNA with the help of the general transcription factors TFIIE and TFIIH. In higher eukaryotes, the general transcription factor TFIIE consists of two subunits: the large alpha subunit (IPR002853 from INTERPRO) and the small beta (IPR003166 from INTERPRO). TFIIE beta has been found to bind to the region where the promoter starts to open to be single-stranded upon transcription initiation by RNA polymerase II. The approximately 120-residue central core domain of TFIIE beta plays a role in double-stranded DNA binding of TFIIE []. The TFIIE beta central core DNA-binding domain consists of three helices with a beta hairpin at the C terminus, resembling the winged helix proteins. It shows a novel double-stranded DNA-binding activity where the DNA-binding surface locates on the opposite side to the previously reported winged helix motif by forming a positively charged furrow []. This entry represents the beta subunit of the transcription factor TFIIE.; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005673 transcription factor TFIIE complex; PDB: 1D8K_A 1D8J_A.
Probab=74.82 E-value=3.8 Score=28.92 Aligned_cols=55 Identities=29% Similarity=0.405 Sum_probs=30.9
Q ss_pred hhhhhhhhccCCCCCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeecCCCCCceEecC
Q psy8359 217 DAAIVRIMKMRKTLSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERDKDKANSYNYMA 279 (279)
Q Consensus 217 ~AaIVRIMK~~K~l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~~d~~~y~Yva 279 (279)
=|.||..||++ .+---+.++.+.+++..+ +..++.|-+.+=|+-++ +.++|.|.|
T Consensus 7 l~~~VeymK~r---~~Plt~~eI~d~l~~d~~----~~~~~~Lk~npKI~~d~-~~~~f~fkp 61 (65)
T PF02186_consen 7 LAKAVEYMKKR---DHPLTLEEILDYLSLDIG----KKLKQWLKNNPKIEYDP-DGNTFSFKP 61 (65)
T ss_dssp HHHHHHHHHHH----S-B-HHHHHHHHTSSS-----HHHHHHHHH-TTEEEE--TT-CEEE--
T ss_pred HHHHHHHHHhc---CCCcCHHHHHHHHcCCCC----HHHHHHHHcCCCEEEec-CCCEEEecc
Confidence 36788999986 333334455555664443 34556777888888887 457999986
No 21
>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=73.54 E-value=4 Score=27.51 Aligned_cols=47 Identities=13% Similarity=0.301 Sum_probs=33.4
Q ss_pred hhhhhhhccCCC--CCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeecCC
Q psy8359 218 AAIVRIMKMRKT--LSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERDKD 270 (279)
Q Consensus 218 AaIVRIMK~~K~--l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~~ 270 (279)
..+...+..... ++..+|... +..+.+.+-+.|..|.++|||+|..+
T Consensus 8 ~~vL~~l~~~~~~~~t~~~la~~------l~~~~~~vs~~v~~L~~~Glv~r~~~ 56 (62)
T PF12802_consen 8 FRVLMALARHPGEELTQSELAER------LGISKSTVSRIVKRLEKKGLVERERD 56 (62)
T ss_dssp HHHHHHHHHSTTSGEEHHHHHHH------HTS-HHHHHHHHHHHHHTTSEEEEE-
T ss_pred HHHHHHHHHCCCCCcCHHHHHHH------HCcCHHHHHHHHHHHHHCCCEEEeCC
Confidence 334444444444 666666666 57788999999999999999999754
No 22
>PF09756 DDRGK: DDRGK domain; InterPro: IPR019153 This is a family of proteins of approximately 300 residues. They contain a highly conserved DDRGK motif. The function is unknown. ; PDB: 1WI9_A.
Probab=72.74 E-value=3.3 Score=35.55 Aligned_cols=58 Identities=19% Similarity=0.322 Sum_probs=42.1
Q ss_pred hhhhhhhhhccCCCCCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeecCCCCCceEecC
Q psy8359 216 IDAAIVRIMKMRKTLSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERDKDKANSYNYMA 279 (279)
Q Consensus 216 I~AaIVRIMK~~K~l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~~d~~~y~Yva 279 (279)
+=...|-..|.+|.....+|-.+ |..+++++-.+|..|...|-|.=--+|...|+||.
T Consensus 100 lL~~Fi~yIK~~Kvv~ledla~~------f~l~t~~~i~ri~~L~~~g~ltGv~DdrGkfIyIs 157 (188)
T PF09756_consen 100 LLQEFINYIKEHKVVNLEDLAAE------FGLRTQDVINRIQELEAEGRLTGVIDDRGKFIYIS 157 (188)
T ss_dssp HHHHHHHHHHH-SEE-HHHHHHH------H-S-HHHHHHHHHHHHHHSSS-EEE-TT--EEE--
T ss_pred HHHHHHHHHHHcceeeHHHHHHH------cCCCHHHHHHHHHHHHHCCCceeeEcCCCCeEEec
Confidence 33445788899999999998888 99999999999999999998888778889999984
No 23
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=72.49 E-value=7.6 Score=24.79 Aligned_cols=45 Identities=13% Similarity=0.271 Sum_probs=35.6
Q ss_pred hhhhhccCCCCCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeecCC
Q psy8359 220 IVRIMKMRKTLSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERDKD 270 (279)
Q Consensus 220 IVRIMK~~K~l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~~ 270 (279)
|.+.+..+..++..+|... |..+...+.+.|..|.++|+|.+..+
T Consensus 5 il~~l~~~~~~s~~~l~~~------l~~s~~tv~~~l~~L~~~g~i~~~~~ 49 (53)
T smart00420 5 ILELLAQQGKVSVEELAEL------LGVSEMTIRRDLNKLEEQGLLTRVHG 49 (53)
T ss_pred HHHHHHHcCCcCHHHHHHH------HCCCHHHHHHHHHHHHHCCCEEEeec
Confidence 4455555666777777766 67899999999999999999998753
No 24
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=70.76 E-value=7.3 Score=25.02 Aligned_cols=44 Identities=11% Similarity=0.322 Sum_probs=35.5
Q ss_pred hhhhhhhhccCCCCCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCcee
Q psy8359 217 DAAIVRIMKMRKTLSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYME 266 (279)
Q Consensus 217 ~AaIVRIMK~~K~l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~ 266 (279)
+-.|+..+.....++..+|...+ -.+.+.+.+.+..|.++|||+
T Consensus 5 ~~~Il~~l~~~~~~t~~ela~~~------~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 5 QRKILNYLRENPRITQKELAEKL------GISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHHCTTS-HHHHHHHH------TS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHcCCCCHHHHHHHh------CCCHHHHHHHHHHHHHCcCcC
Confidence 44567777888889998888874 789999999999999999986
No 25
>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=69.81 E-value=3.2 Score=27.83 Aligned_cols=46 Identities=17% Similarity=0.349 Sum_probs=33.9
Q ss_pred hhhhhhhccCCCCCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeecC
Q psy8359 218 AAIVRIMKMRKTLSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERDK 269 (279)
Q Consensus 218 AaIVRIMK~~K~l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~ 269 (279)
..+..+.-....++..+|-.. +..+.+.+-+.|..|.++|||+|..
T Consensus 6 ~~iL~~l~~~~~~~~~~la~~------~~~~~~~~t~~i~~L~~~g~I~r~~ 51 (59)
T PF01047_consen 6 FRILRILYENGGITQSELAEK------LGISRSTVTRIIKRLEKKGLIERER 51 (59)
T ss_dssp HHHHHHHHHHSSEEHHHHHHH------HTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHcCCCCHHHHHHH------HCCChhHHHHHHHHHHHCCCEEecc
Confidence 344445555666666666555 5789999999999999999999964
No 26
>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=69.36 E-value=15 Score=28.11 Aligned_cols=57 Identities=12% Similarity=0.130 Sum_probs=42.6
Q ss_pred hhhhhcc-CCCCCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeecCCCCCceEe
Q psy8359 220 IVRIMKM-RKTLSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERDKDKANSYNY 277 (279)
Q Consensus 220 IVRIMK~-~K~l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~~d~~~y~Y 277 (279)
|..+|.. .+-++.++|...+.++. ..++.+.|=+.++.|.+.|+|.|-..+...+.|
T Consensus 6 Il~~l~~~~~~~sa~ei~~~l~~~~-~~i~~~TVYR~L~~L~~~Gli~~~~~~~~~~~y 63 (116)
T cd07153 6 ILEVLLESDGHLTAEEIYERLRKKG-PSISLATVYRTLELLEEAGLVREIELGDGKARY 63 (116)
T ss_pred HHHHHHhCCCCCCHHHHHHHHHhcC-CCCCHHHHHHHHHHHHhCCCEEEEEeCCCceEE
Confidence 4444444 56799999988887654 567899999999999999999997544333444
No 27
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=69.05 E-value=7.7 Score=29.40 Aligned_cols=47 Identities=17% Similarity=0.297 Sum_probs=40.9
Q ss_pred hhhhhhhhhccCCCCCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeec
Q psy8359 216 IDAAIVRIMKMRKTLSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERD 268 (279)
Q Consensus 216 I~AaIVRIMK~~K~l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~ 268 (279)
+|-.|++.+.....++..+|..+ +-.+.+.+.++|..|.++|+|+|-
T Consensus 4 ~D~~il~~L~~~~~~~~~~la~~------l~~s~~tv~~~l~~L~~~g~i~~~ 50 (108)
T smart00344 4 IDRKILEELQKDARISLAELAKK------VGLSPSTVHNRVKRLEEEGVIKGY 50 (108)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHH------HCcCHHHHHHHHHHHHHCCCeece
Confidence 45678888888889999888887 589999999999999999999963
No 28
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=60.86 E-value=20 Score=25.97 Aligned_cols=48 Identities=19% Similarity=0.302 Sum_probs=37.2
Q ss_pred hhhhhhhhccCCCCCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeecCC
Q psy8359 217 DAAIVRIMKMRKTLSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERDKD 270 (279)
Q Consensus 217 ~AaIVRIMK~~K~l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~~ 270 (279)
+..|...+.....++..+|... +..+.+.+.+.|..|.++|||.+..+
T Consensus 12 ~~~il~~l~~~~~~~~~~la~~------~~~s~~~i~~~l~~L~~~g~v~~~~~ 59 (101)
T smart00347 12 QFLVLRILYEEGPLSVSELAKR------LGVSPSTVTRVLDRLEKKGLIRRLPS 59 (101)
T ss_pred HHHHHHHHHHcCCcCHHHHHHH------HCCCchhHHHHHHHHHHCCCeEecCC
Confidence 4455666666677887777665 56788889999999999999997643
No 29
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=57.00 E-value=29 Score=27.80 Aligned_cols=51 Identities=18% Similarity=0.313 Sum_probs=38.0
Q ss_pred hhccCCCCCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeecCCC----CCceEecC
Q psy8359 223 IMKMRKTLSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERDKDK----ANSYNYMA 279 (279)
Q Consensus 223 IMK~~K~l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~~d----~~~y~Yva 279 (279)
++..+..++.++|-..+ .-+.+.+.+.+..|++.|.+.|.... +-.|.|.|
T Consensus 36 LL~~~~~~tvdelae~l------nr~rStv~rsl~~L~~~GlV~Rek~~~~~Ggy~yiY~~ 90 (126)
T COG3355 36 LLEENGPLTVDELAEIL------NRSRSTVYRSLQNLLEAGLVEREKVNLKGGGYYYLYKP 90 (126)
T ss_pred HHhhcCCcCHHHHHHHH------CccHHHHHHHHHHHHHcCCeeeeeeccCCCceeEEEec
Confidence 34467778877777664 78899999999999999999996432 34466643
No 30
>PF12395 DUF3658: Protein of unknown function ; InterPro: IPR022123 This domain family is found in bacteria, and is approximately 110 amino acids in length. The family is found in association with PF08874 from PFAM. There are two completely conserved residues (D and R) that may be functionally important.
Probab=55.70 E-value=34 Score=26.48 Aligned_cols=62 Identities=18% Similarity=0.179 Sum_probs=43.3
Q ss_pred hhhhhhhhhhccCCCCCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeecCCCCCceEe
Q psy8359 215 QIDAAIVRIMKMRKTLSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERDKDKANSYNY 277 (279)
Q Consensus 215 ~I~AaIVRIMK~~K~l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~~d~~~y~Y 277 (279)
.+|+.|.+- -...-..-..++.+|+..+...++...+--||+.||+.|.|+=..+-.++-.|
T Consensus 48 ~yD~~Il~~-~~~~~~~~arvIg~vl~~~~~~i~D~f~~~Ri~~Li~~G~le~~g~~~~mr~~ 109 (111)
T PF12395_consen 48 YYDDFILEQ-APDEFQKAARVIGEVLGHSDQGIGDWFLEYRIRELISQGVLEIKGDPKDMRHY 109 (111)
T ss_pred HhhHHHHhc-CCccccHHHHHHHHHHHhcCcCCChHHHHHHHHHHHHCCCEEEecCCCccccC
Confidence 355555551 11222345688899999988448899999999999999999988754444433
No 31
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=54.79 E-value=29 Score=26.00 Aligned_cols=39 Identities=13% Similarity=0.166 Sum_probs=32.6
Q ss_pred cCCCCCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeecCC
Q psy8359 226 MRKTLSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERDKD 270 (279)
Q Consensus 226 ~~K~l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~~ 270 (279)
....+++.+|...+ -.+.+.+-+.|..|.++|+|+|..+
T Consensus 44 ~~~~is~~eLa~~~------g~sr~tVsr~L~~Le~~GlI~r~~~ 82 (95)
T TIGR01610 44 KQDRVTATVIAELT------GLSRTHVSDAIKSLARRRIIFRQGM 82 (95)
T ss_pred cCCccCHHHHHHHH------CcCHHHHHHHHHHHHHCCCeeeecC
Confidence 56778888777763 6788899999999999999999763
No 32
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=52.99 E-value=24 Score=28.27 Aligned_cols=49 Identities=20% Similarity=0.382 Sum_probs=43.5
Q ss_pred hhhhhhhhhhccCCCCCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeecC
Q psy8359 215 QIDAAIVRIMKMRKTLSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERDK 269 (279)
Q Consensus 215 ~I~AaIVRIMK~~K~l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~ 269 (279)
.+|..|.+++.....+++.+|-.++ -.+.+.+..+|+.|.+.|.|++..
T Consensus 8 ~~D~~IL~~L~~d~r~~~~eia~~l------glS~~~v~~Ri~~L~~~GiI~~~~ 56 (154)
T COG1522 8 DIDRRILRLLQEDARISNAELAERV------GLSPSTVLRRIKRLEEEGVIKGYT 56 (154)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHH------CCCHHHHHHHHHHHHHCCceeeEE
Confidence 4677889999999999999888886 689999999999999999999864
No 33
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=51.43 E-value=18 Score=32.36 Aligned_cols=46 Identities=20% Similarity=0.181 Sum_probs=41.2
Q ss_pred hhhhhhhccCCCCCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeecC
Q psy8359 218 AAIVRIMKMRKTLSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERDK 269 (279)
Q Consensus 218 AaIVRIMK~~K~l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~ 269 (279)
..|...++.++.++..||... |..+...|.+-|+.|-++|.|.|..
T Consensus 8 ~~Il~~L~~~~~v~v~eLa~~------l~VS~~TIRRDL~~Le~~g~l~r~~ 53 (256)
T PRK10434 8 AAILEYLQKQGKTSVEELAQY------FDTTGTTIRKDLVILEHAGTVIRTY 53 (256)
T ss_pred HHHHHHHHHcCCEEHHHHHHH------HCCCHHHHHHHHHHHHHCCCEEEEE
Confidence 456778899999999999888 8999999999999999999999964
No 34
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=49.83 E-value=46 Score=23.97 Aligned_cols=44 Identities=16% Similarity=0.288 Sum_probs=35.0
Q ss_pred hhhhccC-CCCCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeecCC
Q psy8359 221 VRIMKMR-KTLSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERDKD 270 (279)
Q Consensus 221 VRIMK~~-K~l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~~ 270 (279)
...+... ..++..+|..+ +..+.+.+.+.+..|.+.|||.++..
T Consensus 11 l~~l~~~~~~~t~~~ia~~------l~i~~~tv~r~l~~L~~~g~l~~~~~ 55 (91)
T smart00346 11 LRALAEEPGGLTLAELAER------LGLSKSTAHRLLNTLQELGYVEQDGQ 55 (91)
T ss_pred HHHHHhCCCCcCHHHHHHH------hCCCHHHHHHHHHHHHHCCCeeecCC
Confidence 3444444 67888888887 47889999999999999999999753
No 35
>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=49.44 E-value=35 Score=22.31 Aligned_cols=34 Identities=21% Similarity=0.473 Sum_probs=26.7
Q ss_pred CCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeecC
Q psy8359 230 LSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERDK 269 (279)
Q Consensus 230 l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~ 269 (279)
++..+|..++ -.+..-+-+-+..|.+.||++||+
T Consensus 19 ~t~~eia~~~------gl~~stv~r~L~tL~~~g~v~~dp 52 (52)
T PF09339_consen 19 LTLSEIARAL------GLPKSTVHRLLQTLVEEGYVERDP 52 (52)
T ss_dssp EEHHHHHHHH------TS-HHHHHHHHHHHHHTTSEEECS
T ss_pred CCHHHHHHHH------CcCHHHHHHHHHHHHHCcCeecCc
Confidence 6777666663 567778889999999999999985
No 36
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.
Probab=48.78 E-value=28 Score=30.22 Aligned_cols=39 Identities=15% Similarity=0.334 Sum_probs=31.6
Q ss_pred CHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeecCCCCCceE
Q psy8359 231 SHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERDKDKANSYN 276 (279)
Q Consensus 231 ~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~~d~~~y~ 276 (279)
+-.+|+.+ |..+...|.++|+.|.+.|||.|..+ ..+|+
T Consensus 26 sE~eLa~~------~gVSR~TVR~Al~~L~~eGli~r~~G-~GTfV 64 (233)
T TIGR02404 26 SEHELMDQ------YGASRETVRKALNLLTEAGYIQKIQG-KGSIV 64 (233)
T ss_pred CHHHHHHH------HCCCHHHHHHHHHHHHHCCCEEEeCC-ceEEE
Confidence 45555555 89999999999999999999999875 45554
No 37
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=48.12 E-value=27 Score=30.52 Aligned_cols=39 Identities=15% Similarity=0.437 Sum_probs=31.3
Q ss_pred CHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeecCCCCCceE
Q psy8359 231 SHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERDKDKANSYN 276 (279)
Q Consensus 231 ~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~~d~~~y~ 276 (279)
+-.+|+.+ |..+...|+++|+.|.+.|||.|..+ ..+|+
T Consensus 37 sE~eLa~~------~~VSR~TVR~Al~~L~~eGli~r~~G-~GtfV 75 (241)
T PRK10079 37 AEQQLAAR------YEVNRHTLRRAIDQLVEKGWVQRRQG-VGVLV 75 (241)
T ss_pred CHHHHHHH------HCCCHHHHHHHHHHHHHCCCEEEecC-CEEEE
Confidence 44455555 99999999999999999999999875 34554
No 38
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=47.86 E-value=38 Score=27.11 Aligned_cols=38 Identities=16% Similarity=0.235 Sum_probs=30.7
Q ss_pred cCCCCCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeecC
Q psy8359 226 MRKTLSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERDK 269 (279)
Q Consensus 226 ~~K~l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~ 269 (279)
.+..++..+|... +..+.+.+-+.|+.|.++|||+|..
T Consensus 51 ~~~~~t~~eLa~~------l~i~~~tvsr~l~~Le~~GlI~R~~ 88 (144)
T PRK11512 51 CAACITPVELKKV------LSVDLGALTRMLDRLVCKGWVERLP 88 (144)
T ss_pred HcCCCCHHHHHHH------HCCCHHHHHHHHHHHHHCCCEEecc
Confidence 3555666666665 6789999999999999999999964
No 39
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=47.24 E-value=44 Score=25.47 Aligned_cols=46 Identities=20% Similarity=0.325 Sum_probs=33.9
Q ss_pred cCCCCCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeec--CCCC-CceEe
Q psy8359 226 MRKTLSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERD--KDKA-NSYNY 277 (279)
Q Consensus 226 ~~K~l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~--~~d~-~~y~Y 277 (279)
....++..+|... ...+.+.+-+.|..|.++|||.|. +.|. ..+.|
T Consensus 40 ~~~~~t~~eL~~~------l~~~~stvs~~i~~Le~kg~I~r~~~~~D~R~~~i~ 88 (109)
T TIGR01889 40 NEGKLTLKEIIKE------ILIKQSALVKIIKKLSKKGYLSKERSEDDERKVIIS 88 (109)
T ss_pred cCCcCcHHHHHHH------HCCCHHHHHHHHHHHHHCCCEeccCCcccCCeEEEE
Confidence 4456777766666 578899999999999999999974 4443 34444
No 40
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=46.58 E-value=42 Score=27.68 Aligned_cols=46 Identities=17% Similarity=0.307 Sum_probs=42.2
Q ss_pred hhhhhhhhhccCCCCCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceee
Q psy8359 216 IDAAIVRIMKMRKTLSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMER 267 (279)
Q Consensus 216 I~AaIVRIMK~~K~l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R 267 (279)
+|-.|.+++.....+++.+|-.+| -.+.+.+.+||..|.+.|.|++
T Consensus 15 ~D~~IL~~Lq~d~R~s~~eiA~~l------glS~~tv~~Ri~rL~~~GvI~~ 60 (164)
T PRK11169 15 IDRNILNELQKDGRISNVELSKRV------GLSPTPCLERVRRLERQGFIQG 60 (164)
T ss_pred HHHHHHHHhccCCCCCHHHHHHHH------CcCHHHHHHHHHHHHHCCCeEE
Confidence 677889999999999999888885 7899999999999999999986
No 41
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=45.84 E-value=55 Score=21.15 Aligned_cols=38 Identities=16% Similarity=0.260 Sum_probs=30.1
Q ss_pred CCCC-CHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeecCC
Q psy8359 227 RKTL-SHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERDKD 270 (279)
Q Consensus 227 ~K~l-~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~~ 270 (279)
...+ +..+|... |..+.+.+.+.+..|.+.|+|.+..+
T Consensus 17 ~~~l~s~~~la~~------~~vs~~tv~~~l~~L~~~g~i~~~~~ 55 (60)
T smart00345 17 GDKLPSERELAAQ------LGVSRTTVREALSRLEAEGLVQRRPG 55 (60)
T ss_pred CCcCcCHHHHHHH------HCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 3345 56555555 78899999999999999999998764
No 42
>PF12108 SF3a60_bindingd: Splicing factor SF3a60 binding domain; InterPro: IPR021966 This domain is found in eukaryotes. This domain is about 30 amino acids in length. This domain has a single completely conserved residue Y that may be functionally important. SF3a60 makes up the SF3a complex with SF3a66 and SF3a120. This domain is the binding site of SF3a60 for SF3a120. The SF3a complex is part of the spliceosome, a protein complex involved in splicing mRNA after transcription. ; PDB: 2DT7_A.
Probab=45.77 E-value=17 Score=21.28 Aligned_cols=15 Identities=20% Similarity=-0.223 Sum_probs=9.1
Q ss_pred cCChhHHHHHHHHHH
Q psy8359 51 ISIKVNVSSVEKVDL 65 (279)
Q Consensus 51 l~~KD~Fe~~Y~~~L 65 (279)
++..|.|.+||.++=
T Consensus 3 is~~d~f~eFY~rlk 17 (28)
T PF12108_consen 3 ISGGDPFSEFYERLK 17 (28)
T ss_dssp --S--HHHHHHHHHH
T ss_pred CCCCChHHHHHHHHH
Confidence 467899999998763
No 43
>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=45.71 E-value=48 Score=22.17 Aligned_cols=44 Identities=11% Similarity=0.277 Sum_probs=31.9
Q ss_pred hhhhccCCCCCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeecCCC
Q psy8359 221 VRIMKMRKTLSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERDKDK 271 (279)
Q Consensus 221 VRIMK~~K~l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~~d 271 (279)
...+.... ++..++... +..+...+.+.++.|.+.|+|.+....
T Consensus 13 l~~l~~~~-~~~~ei~~~------~~i~~~~i~~~l~~L~~~g~i~~~~~~ 56 (78)
T cd00090 13 LRLLLEGP-LTVSELAER------LGLSQSTVSRHLKKLEEAGLVESRREG 56 (78)
T ss_pred HHHHHHCC-cCHHHHHHH------HCcCHhHHHHHHHHHHHCCCeEEEEec
Confidence 33333444 777665544 567889999999999999999987544
No 44
>PF02334 RTP: Replication terminator protein; InterPro: IPR003432 The bacterial replication terminator protein (RTP) plays a role in the termination of DNA replication by impeding replication fork movement. Two RTP dimers bind to the two inverted repeat regions at the termination site.; GO: 0003677 DNA binding, 0006274 DNA replication termination; PDB: 2DPU_A 2DPD_A 1F4K_A 1J0R_B 2EFW_F 2DQR_B 1BM9_B.
Probab=45.19 E-value=28 Score=27.24 Aligned_cols=51 Identities=16% Similarity=0.382 Sum_probs=30.2
Q ss_pred hhhhhhhhhccCCCCCHHHHHHHHHHhcC---CCCChHHHHHHHHhhhhcCceee
Q psy8359 216 IDAAIVRIMKMRKTLSHNLLLSELFNQLK---FPVKPADLKKRIESLIDRDYMER 267 (279)
Q Consensus 216 I~AaIVRIMK~~K~l~~~~L~~eV~~~l~---F~p~~~~iK~~Ie~LIekeYi~R 267 (279)
+.-.|+.+.-+++--.. +++.+.-++.+ |.|..+.|=+++..|++-||++|
T Consensus 19 lKlYiitm~e~~r~Yg~-q~Ld~lr~EFk~~Gy~P~hsEvYraLHeL~~dGilk~ 72 (122)
T PF02334_consen 19 LKLYIITMVEQERGYGL-QLLDELRSEFKPLGYRPNHSEVYRALHELVDDGILKQ 72 (122)
T ss_dssp HHHHHHHHHHTT-EBCT-CHHHHHHHHHTTTT----HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHhhhhcccchHH-HHHHHHHHHhhhcCCCCCHHHHHHHHHHHHhhhHHHH
Confidence 34445555555553222 24444444555 99999999999999999999966
No 45
>cd07977 TFIIE_beta_winged_helix TFIIE_beta_winged_helix domain, located at the central core region of TFIIE beta, with double-stranded DNA binding activity. Transcription Factor IIE (TFIIE) beta winged-helix (or forkhead) domain is located at the central core region of TFIIE beta. The winged-helix is a form of helix-turn-helix (HTH) domain which typically binds DNA with the 3rd helix. The winged-helix domain is distinguished by the presence of a C-terminal beta-strand hairpin unit (the wing) that packs against the cleft of the tri-helical core. Although most winged-helix domains are multi-member families, TFIIE beta winged-helix domain is typically found as a single orthologous group. TFIIE is one of the six eukaryotic general transcription factors (TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH) that are required for transcription initiation of protein-coding genes. TFIIE is a heterotetramer consisting of two copies each of alpha and beta subunits. TFIIE beta contains several functional
Probab=44.97 E-value=28 Score=25.12 Aligned_cols=56 Identities=27% Similarity=0.375 Sum_probs=31.1
Q ss_pred hhhhhhhhhhccCC--CCCHHHHHHHHHHhcC-CCCChHHHHHHHHhhhhcCce---eecCCCCCceEecC
Q psy8359 215 QIDAAIVRIMKMRK--TLSHNLLLSELFNQLK-FPVKPADLKKRIESLIDRDYM---ERDKDKANSYNYMA 279 (279)
Q Consensus 215 ~I~AaIVRIMK~~K--~l~~~~L~~eV~~~l~-F~p~~~~iK~~Ie~LIekeYi---~R~~~d~~~y~Yva 279 (279)
..=|.||-.||++. .++.+|++.+ ++ +..... ++ +.|-+-.-+ +-+.. .++|.|.|
T Consensus 9 t~l~~aV~ymK~r~~~Plt~~EIl~~----ls~~d~~~~-~~---~~L~~~~~~~n~~~~~~-~~tf~fkP 70 (75)
T cd07977 9 TQLAKIVDYMKKRHQHPLTLDEILDY----LSLLDIGPK-LK---EWLKSEALVNNPKIDPK-DGTFSFKP 70 (75)
T ss_pred hhHHHHHHHHHhcCCCCccHHHHHHH----HhccCccHH-HH---HHHHhhhhccCceeccC-CCEEEecc
Confidence 34577899999976 6666655555 44 443321 22 333322223 33332 46899976
No 46
>PF09860 DUF2087: Uncharacterized protein conserved in bacteria (DUF2087); InterPro: IPR018656 This domain, found in various hypothetical prokaryotic proteins and transcriptional activators, has no known function.
Probab=44.52 E-value=26 Score=25.10 Aligned_cols=43 Identities=30% Similarity=0.447 Sum_probs=27.4
Q ss_pred ccCCCCCHHHHHHHHHHhcC-CCCChHHHHHHHHhhhhcCceeecCCCCCce
Q psy8359 225 KMRKTLSHNLLLSELFNQLK-FPVKPADLKKRIESLIDRDYMERDKDKANSY 275 (279)
Q Consensus 225 K~~K~l~~~~L~~eV~~~l~-F~p~~~~iK~~Ie~LIekeYi~R~~~d~~~y 275 (279)
...+..+-. ||-+.|. |-.+...+.+ .||+-|||+|+.+ .+.|
T Consensus 25 ~~g~~y~E~----EVN~~L~~~~~D~a~LRR---~LVd~g~L~R~~d-g~~Y 68 (71)
T PF09860_consen 25 EPGREYSEK----EVNEILKRFFDDYATLRR---YLVDYGLLERTRD-GSRY 68 (71)
T ss_pred CCCCccCHH----HHHHHHHHHcccHHHHHH---HHHHcCCeeecCC-CCee
Confidence 445555554 3333333 4556666665 7999999999974 4556
No 47
>PRK14999 histidine utilization repressor; Provisional
Probab=44.37 E-value=45 Score=29.16 Aligned_cols=47 Identities=11% Similarity=0.321 Sum_probs=36.9
Q ss_pred hhccCCCC-CHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeecCCCCCceE
Q psy8359 223 IMKMRKTL-SHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERDKDKANSYN 276 (279)
Q Consensus 223 IMK~~K~l-~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~~d~~~y~ 276 (279)
..+....| +-.+|+.+ |..+...|+++|+.|.+.|+|.|..+ ..+|+
T Consensus 29 ~~~~G~~LPsE~eLa~~------~gVSR~TVR~Al~~L~~eGli~r~~G-kGTfV 76 (241)
T PRK14999 29 VWQPHDRIPSEAELVAQ------YGFSRMTINRALRELTDEGWLVRLQG-VGTFV 76 (241)
T ss_pred CCCCCCcCCCHHHHHHH------HCCCHHHHHHHHHHHHHCCCEEEecC-cEEEE
Confidence 34444455 67777777 99999999999999999999999874 45554
No 48
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=43.59 E-value=37 Score=29.63 Aligned_cols=42 Identities=17% Similarity=0.296 Sum_probs=32.9
Q ss_pred CCCCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeecCCCCCceE
Q psy8359 228 KTLSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERDKDKANSYN 276 (279)
Q Consensus 228 K~l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~~d~~~y~ 276 (279)
|--+-.+|..+ |..+...++++|+.|.+.|+|.|..+ ..+|+
T Consensus 32 kLPsE~eLa~~------~~VSR~TvR~Al~~L~~eGli~r~~G-~GTfV 73 (241)
T PRK11402 32 QIPTENELCTQ------YNVSRITIRKAISDLVADGVLIRWQG-KGTFV 73 (241)
T ss_pred cCcCHHHHHHH------HCCCHHHHHHHHHHHHHCCCEEEecC-ceeEE
Confidence 34445555555 99999999999999999999999875 45554
No 49
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=42.55 E-value=46 Score=27.06 Aligned_cols=47 Identities=15% Similarity=0.266 Sum_probs=41.0
Q ss_pred hhhhhhhhhccCCCCCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeec
Q psy8359 216 IDAAIVRIMKMRKTLSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERD 268 (279)
Q Consensus 216 I~AaIVRIMK~~K~l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~ 268 (279)
+|-.|.+.+......++.+|-.++ -.+.+.+..||+.|.+.|+|++-
T Consensus 10 ~D~~Il~~Lq~d~R~s~~eiA~~l------glS~~tV~~Ri~rL~~~GvI~~~ 56 (153)
T PRK11179 10 LDRGILEALMENARTPYAELAKQF------GVSPGTIHVRVEKMKQAGIITGT 56 (153)
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHH------CcCHHHHHHHHHHHHHCCCeeeE
Confidence 566788888888999999888875 78999999999999999999863
No 50
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=42.48 E-value=31 Score=30.76 Aligned_cols=47 Identities=21% Similarity=0.473 Sum_probs=41.6
Q ss_pred hhhhhhhhccCCCCCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeecC
Q psy8359 217 DAAIVRIMKMRKTLSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERDK 269 (279)
Q Consensus 217 ~AaIVRIMK~~K~l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~ 269 (279)
+..|..++++++.++..+|.+. |..+...|.+-+..|-++|+|.|--
T Consensus 7 ~~~Il~~l~~~~~~~~~ela~~------l~vS~~TiRRdL~~Le~~g~l~r~~ 53 (252)
T PRK10906 7 HDAIIELVKQQGYVSTEELVEH------FSVSPQTIRRDLNDLAEQNKILRHH 53 (252)
T ss_pred HHHHHHHHHHcCCEeHHHHHHH------hCCCHHHHHHHHHHHHHCCCEEEec
Confidence 3457788899999999998887 8999999999999999999999964
No 51
>KOG3054|consensus
Probab=42.40 E-value=36 Score=30.44 Aligned_cols=54 Identities=24% Similarity=0.388 Sum_probs=45.0
Q ss_pred hhhhhccCCCCCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeecCCCCCceEecC
Q psy8359 220 IVRIMKMRKTLSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERDKDKANSYNYMA 279 (279)
Q Consensus 220 IVRIMK~~K~l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~~d~~~y~Yva 279 (279)
.|-..|..|.....||-.+ |....++.--+|..|+.-|.|.---+|+..|+||.
T Consensus 205 Fv~YIk~nKvV~ledLas~------f~Lrtqd~inriq~~l~eg~ltGVmDDRGKfIYIS 258 (299)
T KOG3054|consen 205 FVEYIKKNKVVPLEDLASE------FGLRTQDSINRIQELLAEGLLTGVMDDRGKFIYIS 258 (299)
T ss_pred HHHHHHhcCeeeHHHHHHH------hCccHHHHHHHHHHHHHhhhheeeecCCCceEEec
Confidence 4556677777777666665 88888998899999999999999999999999984
No 52
>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF. All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.
Probab=41.60 E-value=41 Score=29.10 Aligned_cols=39 Identities=15% Similarity=0.398 Sum_probs=31.9
Q ss_pred CHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeecCCCCCceE
Q psy8359 231 SHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERDKDKANSYN 276 (279)
Q Consensus 231 ~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~~d~~~y~ 276 (279)
+-.+|+.+ |..+...+.++|+.|.+.|||.|..+ ..+|+
T Consensus 34 sE~eLa~~------~~VSR~TvR~Al~~L~~eGli~r~~G-~GtfV 72 (238)
T TIGR02325 34 AEMQLAER------FGVNRHTVRRAIAALVERGLLRAEQG-RGTFV 72 (238)
T ss_pred CHHHHHHH------HCCCHHHHHHHHHHHHHCCCEEEecC-CEEEE
Confidence 55566665 99999999999999999999999875 34554
No 53
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=40.77 E-value=60 Score=25.80 Aligned_cols=25 Identities=12% Similarity=0.401 Sum_probs=22.1
Q ss_pred CCCChHHHHHHHHhhhhcCceeecC
Q psy8359 245 FPVKPADLKKRIESLIDRDYMERDK 269 (279)
Q Consensus 245 F~p~~~~iK~~Ie~LIekeYi~R~~ 269 (279)
+..+.+.+-+.|..|.++|||+|..
T Consensus 56 l~~~~~tvt~~v~~Le~~GlV~r~~ 80 (144)
T PRK03573 56 IGIEQPSLVRTLDQLEEKGLISRQT 80 (144)
T ss_pred hCCChhhHHHHHHHHHHCCCEeeec
Confidence 5677888999999999999999974
No 54
>COG2865 Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]
Probab=38.50 E-value=40 Score=33.07 Aligned_cols=60 Identities=13% Similarity=0.274 Sum_probs=51.2
Q ss_pred hhhhhhhhhhhccCCCCCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeecCCCCCceEecC
Q psy8359 214 YQIDAAIVRIMKMRKTLSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERDKDKANSYNYMA 279 (279)
Q Consensus 214 ~~I~AaIVRIMK~~K~l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~~d~~~y~Yva 279 (279)
..-+.+|++.++....++-.+|-+. |..+...+-+.|..|+.+|++++-..+...+.||+
T Consensus 401 ~~~~~~il~~~~en~~~T~~~L~~~------l~is~~~i~r~i~~Lv~~g~~~~~g~~~~g~~~v~ 460 (467)
T COG2865 401 SERQEKILELIKENGKVTARELREI------LGISSETIRRRIANLVKRGLLKQLGSSGRGTWYVK 460 (467)
T ss_pred hHHHHHHHHHHhhccccCHHHHHHH------hCcchhhHHHHHHHHhcccHHHHhCcCCCCcEEec
Confidence 3445899999999999999877766 66899999999999999999999887777788874
No 55
>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=38.43 E-value=66 Score=24.67 Aligned_cols=47 Identities=17% Similarity=0.183 Sum_probs=33.5
Q ss_pred hhhhhhhhccCCCCCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeecC
Q psy8359 217 DAAIVRIMKMRKTLSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERDK 269 (279)
Q Consensus 217 ~AaIVRIMK~~K~l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~ 269 (279)
|..|...+.....++..+|... ...+.+.+-+.|..|.++|||+|..
T Consensus 30 q~~iL~~l~~~~~~t~~ela~~------~~~~~~tvs~~l~~Le~~GlI~r~~ 76 (118)
T TIGR02337 30 QWRILRILAEQGSMEFTQLANQ------ACILRPSLTGILARLERDGLVTRLK 76 (118)
T ss_pred HHHHHHHHHHcCCcCHHHHHHH------hCCCchhHHHHHHHHHHCCCEEecc
Confidence 3344455556677777666655 3556667889999999999999954
No 56
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=38.29 E-value=44 Score=25.11 Aligned_cols=46 Identities=9% Similarity=0.255 Sum_probs=31.2
Q ss_pred hhhhhhhhhcc----CCCCCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceee
Q psy8359 216 IDAAIVRIMKM----RKTLSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMER 267 (279)
Q Consensus 216 I~AaIVRIMK~----~K~l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R 267 (279)
++..|..++|. .--++.++|... | ..+...|+++|+.|++.|+|=-
T Consensus 48 ~~~~Vl~~i~~~~~~~~Gv~v~~I~~~----l--~~~~~~v~~al~~L~~eG~IYs 97 (102)
T PF08784_consen 48 LQDKVLNFIKQQPNSEEGVHVDEIAQQ----L--GMSENEVRKALDFLSNEGHIYS 97 (102)
T ss_dssp HHHHHHHHHHC----TTTEEHHHHHHH----S--TS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHHhcCCCCCcccHHHHHHH----h--CcCHHHHHHHHHHHHhCCeEec
Confidence 44445555555 445666655544 3 6679999999999999998743
No 57
>TIGR03433 padR_acidobact transcriptional regulator, Acidobacterial, PadR-family. Members of this protein family are putative transcriptional regulators of the PadR family, as found in species of the Acidobacteria. This family of proteins has expanded greatly in this lineage, and where it regularly is found in the vicinity of a putative transporter protein
Probab=38.14 E-value=1.1e+02 Score=22.86 Aligned_cols=51 Identities=14% Similarity=0.211 Sum_probs=42.3
Q ss_pred hhhhhhhhhccCCCCCHHHHHHHHHHhcC--CCCChHHHHHHHHhhhhcCceee
Q psy8359 216 IDAAIVRIMKMRKTLSHNLLLSELFNQLK--FPVKPADLKKRIESLIDRDYMER 267 (279)
Q Consensus 216 I~AaIVRIMK~~K~l~~~~L~~eV~~~l~--F~p~~~~iK~~Ie~LIekeYi~R 267 (279)
++-+|..++. .+.++=-+|.+++-+... +.++...+=..+..|-++|+|++
T Consensus 5 l~~~iL~~L~-~~~~~GYei~~~l~~~~~~~~~i~~gtlY~~L~rLe~~GlI~~ 57 (100)
T TIGR03433 5 LDLLILKTLS-LGPLHGYGIAQRIQQISEDVLQVEEGSLYPALHRLERRGWIAA 57 (100)
T ss_pred HHHHHHHHHh-cCCCCHHHHHHHHHHHcCCccccCCCcHHHHHHHHHHCCCeEE
Confidence 4556666776 467788899999877765 78899999999999999999998
No 58
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=36.83 E-value=82 Score=23.50 Aligned_cols=35 Identities=17% Similarity=0.190 Sum_probs=31.5
Q ss_pred CCCChHHHHHHHHhhhhcCceeecCCCCCceEecC
Q psy8359 245 FPVKPADLKKRIESLIDRDYMERDKDKANSYNYMA 279 (279)
Q Consensus 245 F~p~~~~iK~~Ie~LIekeYi~R~~~d~~~y~Yva 279 (279)
+......-+++|..|-++|-|..-..+...-+|.|
T Consensus 51 lkI~~SlAr~~Lr~L~~kG~Ik~V~~~~~q~IYt~ 85 (86)
T PRK09334 51 YGIKISVAKKVLRELEKRGVLVLYSKNRRTPIYVP 85 (86)
T ss_pred hcchHHHHHHHHHHHHHCCCEEEEecCCCeEEecc
Confidence 78899999999999999999998877778888876
No 59
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=36.57 E-value=40 Score=30.09 Aligned_cols=46 Identities=17% Similarity=0.307 Sum_probs=41.5
Q ss_pred hhhhhhccCCCCCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeecCC
Q psy8359 219 AIVRIMKMRKTLSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERDKD 270 (279)
Q Consensus 219 aIVRIMK~~K~l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~~ 270 (279)
.|+.++++++.++.++|... |..+...|.+=|..|=++|+|.|..+
T Consensus 9 ~Il~~l~~~g~v~v~eLa~~------~~VS~~TIRRDL~~Le~~g~l~R~hG 54 (253)
T COG1349 9 KILELLKEKGKVSVEELAEL------FGVSEMTIRRDLNELEEQGLLLRVHG 54 (253)
T ss_pred HHHHHHHHcCcEEHHHHHHH------hCCCHHHHHHhHHHHHHCCcEEEEeC
Confidence 47888899999999998888 99999999999999999999999543
No 60
>PRK09462 fur ferric uptake regulator; Provisional
Probab=36.12 E-value=1.1e+02 Score=24.53 Aligned_cols=50 Identities=14% Similarity=0.197 Sum_probs=39.7
Q ss_pred hhhhhhcc--CCCCCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeecC
Q psy8359 219 AIVRIMKM--RKTLSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERDK 269 (279)
Q Consensus 219 aIVRIMK~--~K~l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~ 269 (279)
+|.+++.. .+-++.++|...+.+.. ...+.+.|=+.++.|-+.|.|.+-.
T Consensus 21 ~Il~~l~~~~~~h~sa~eI~~~l~~~~-~~i~~aTVYR~L~~L~e~Gli~~~~ 72 (148)
T PRK09462 21 KILEVLQEPDNHHVSAEDLYKRLIDMG-EEIGLATVYRVLNQFDDAGIVTRHN 72 (148)
T ss_pred HHHHHHHhCCCCCCCHHHHHHHHHhhC-CCCCHHHHHHHHHHHHHCCCEEEEE
Confidence 44555554 36899999988876655 5678899999999999999998864
No 61
>PF04492 Phage_rep_O: Bacteriophage replication protein O ; InterPro: IPR006497 This entry is represented by the N-terminal domain of Bacteriophage lambda, GpO. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; GO: 0006260 DNA replication
Probab=34.95 E-value=56 Score=25.01 Aligned_cols=36 Identities=17% Similarity=0.288 Sum_probs=29.4
Q ss_pred cCCCCCHHHHHHHHhHhhcCCceeeeeCCCCCCCCCCCeEEEecCC
Q psy8359 135 LGIDLTDADLRRTLQSLACGKTRVLKKTPASRDIEDCDRFRFNNDF 180 (279)
Q Consensus 135 ~~t~i~~~~l~~~L~sL~~~k~~iL~~~~~~~~i~~~~~f~~N~~F 180 (279)
+.||++...+.+++..|+ +.++|... +..+.+|.+.
T Consensus 62 e~tg~~~~~V~~al~~Li--~~~vI~~~--------g~~~G~N~~i 97 (100)
T PF04492_consen 62 EMTGLSRDHVSKALNELI--RRGVIIRD--------GKRIGVNKNI 97 (100)
T ss_pred HHHCcCHHHHHHHHHHHH--HCCCEEeC--------CcEEeeeccc
Confidence 679999999999999999 88899763 4566677654
No 62
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=34.59 E-value=49 Score=29.79 Aligned_cols=48 Identities=13% Similarity=0.195 Sum_probs=42.4
Q ss_pred hhhhhhhhccCCCCCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeecCC
Q psy8359 217 DAAIVRIMKMRKTLSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERDKD 270 (279)
Q Consensus 217 ~AaIVRIMK~~K~l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~~ 270 (279)
+..|+..+++++.++..+|... |..+..-|.+=|..|-++|++.|..+
T Consensus 19 ~~~Il~~L~~~~~vtv~eLa~~------l~VS~~TIRRDL~~Le~~G~l~r~~G 66 (269)
T PRK09802 19 REQIIQRLRQQGSVQVNDLSAL------YGVSTVTIRNDLAFLEKQGIAVRAYG 66 (269)
T ss_pred HHHHHHHHHHcCCEeHHHHHHH------HCCCHHHHHHHHHHHHhCCCeEEEeC
Confidence 4457888899999999999888 89999999999999999999999653
No 63
>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial. This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.
Probab=34.26 E-value=61 Score=28.03 Aligned_cols=39 Identities=15% Similarity=0.382 Sum_probs=32.1
Q ss_pred CHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeecCCCCCceE
Q psy8359 231 SHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERDKDKANSYN 276 (279)
Q Consensus 231 ~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~~d~~~y~ 276 (279)
+..+|..+ |..+...|.++|..|.+.|+|.|..+ ..+|+
T Consensus 27 sE~eLa~~------~~VSR~TVR~Al~~L~~eGli~r~~G-~GtfV 65 (230)
T TIGR02018 27 SEHELVAQ------YGCSRMTVNRALRELTDAGLLERRQG-VGTFV 65 (230)
T ss_pred CHHHHHHH------HCCCHHHHHHHHHHHHHCCCEEEecC-CEEEE
Confidence 56666666 99999999999999999999999875 34553
No 64
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein. Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.
Probab=34.09 E-value=87 Score=26.69 Aligned_cols=46 Identities=9% Similarity=0.211 Sum_probs=36.3
Q ss_pred hhhhhhccCCCCCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeecCC
Q psy8359 219 AIVRIMKMRKTLSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERDKD 270 (279)
Q Consensus 219 aIVRIMK~~K~l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~~ 270 (279)
.|...+..+..++..+|... +..+.+.+-+.+..|.++|||+|...
T Consensus 147 ~IL~~l~~~g~~s~~eia~~------l~is~stv~r~L~~Le~~GlI~r~~~ 192 (203)
T TIGR01884 147 KVLEVLKAEGEKSVKNIAKK------LGKSLSTISRHLRELEKKGLVEQKGR 192 (203)
T ss_pred HHHHHHHHcCCcCHHHHHHH------HCcCHHHHHHHHHHHHHCCCEEEEcC
Confidence 45555666667788777766 46778889999999999999999974
No 65
>COG5045 Ribosomal protein S10E [Translation, ribosomal structure and biogenesis]
Probab=33.57 E-value=63 Score=24.42 Aligned_cols=22 Identities=23% Similarity=0.311 Sum_probs=18.3
Q ss_pred ChHHHHHHHHhhhhcCceeecC
Q psy8359 248 KPADLKKRIESLIDRDYMERDK 269 (279)
Q Consensus 248 ~~~~iK~~Ie~LIekeYi~R~~ 269 (279)
..-.++++..+||.+||+++--
T Consensus 38 pNL~vika~qsl~S~GYvkt~~ 59 (105)
T COG5045 38 PNLHVIKAMQSLISYGYVKTIH 59 (105)
T ss_pred CchHHHHHHHHHhhcceeEEEe
Confidence 4456778899999999999975
No 66
>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=32.83 E-value=82 Score=21.36 Aligned_cols=38 Identities=18% Similarity=0.292 Sum_probs=29.0
Q ss_pred CCCC-CHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeecCC
Q psy8359 227 RKTL-SHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERDKD 270 (279)
Q Consensus 227 ~K~l-~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~~ 270 (279)
...+ +..+|... |..+...+.+++..|.+.|+|.+.+.
T Consensus 21 g~~lps~~~la~~------~~vsr~tvr~al~~L~~~g~i~~~~~ 59 (64)
T PF00392_consen 21 GDRLPSERELAER------YGVSRTTVREALRRLEAEGLIERRPG 59 (64)
T ss_dssp TSBE--HHHHHHH------HTS-HHHHHHHHHHHHHTTSEEEETT
T ss_pred CCEeCCHHHHHHH------hccCCcHHHHHHHHHHHCCcEEEECC
Confidence 3445 55555555 88999999999999999999999874
No 67
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=32.77 E-value=82 Score=25.13 Aligned_cols=45 Identities=16% Similarity=0.290 Sum_probs=34.3
Q ss_pred hhhhhhccCCCCCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeecC
Q psy8359 219 AIVRIMKMRKTLSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERDK 269 (279)
Q Consensus 219 aIVRIMK~~K~l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~ 269 (279)
+|.++.......+..+|... +..+.+.+-..|..|.++|||.+..
T Consensus 12 ~I~~l~~~~~~~~~~ela~~------l~vs~~svs~~l~~L~~~Gli~~~~ 56 (142)
T PRK03902 12 QIYLLIEEKGYARVSDIAEA------LSVHPSSVTKMVQKLDKDEYLIYEK 56 (142)
T ss_pred HHHHHHhcCCCcCHHHHHHH------hCCChhHHHHHHHHHHHCCCEEEec
Confidence 45566677776766555554 6778999999999999999999753
No 68
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=31.81 E-value=90 Score=25.02 Aligned_cols=51 Identities=16% Similarity=0.281 Sum_probs=45.2
Q ss_pred hhhhhhhhhhhccCCCCCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeecCC
Q psy8359 214 YQIDAAIVRIMKMRKTLSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERDKD 270 (279)
Q Consensus 214 ~~I~AaIVRIMK~~K~l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~~ 270 (279)
..|.+-||-+.+.++.++..+|... +-.+...++..+..|.+.|.|-+...
T Consensus 11 ~eLk~rIvElVRe~GRiTi~ql~~~------TGasR~Tvk~~lreLVa~G~l~~~G~ 61 (127)
T PF06163_consen 11 EELKARIVELVREHGRITIKQLVAK------TGASRNTVKRYLRELVARGDLYRHGR 61 (127)
T ss_pred HHHHHHHHHHHHHcCCccHHHHHHH------HCCCHHHHHHHHHHHHHcCCeEeCCC
Confidence 4588899999999999999999988 57899999999999999999988653
No 69
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=31.27 E-value=78 Score=27.61 Aligned_cols=45 Identities=20% Similarity=0.409 Sum_probs=34.8
Q ss_pred ccCCCC-CHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeecCCCCCceE
Q psy8359 225 KMRKTL-SHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERDKDKANSYN 276 (279)
Q Consensus 225 K~~K~l-~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~~d~~~y~ 276 (279)
+....| +-.+|..+ |..+...|+++|+.|...|+|.|..+ ..+|+
T Consensus 24 ~~G~~LPsE~eL~~~------~~VSR~TvR~Al~~L~~eGli~r~~G-~GtfV 69 (240)
T PRK09764 24 KPGDALPTESALQTE------FGVSRVTVRQALRQLVEQQILESIQG-SGTYV 69 (240)
T ss_pred CCCCcCCCHHHHHHH------HCCCHHHHHHHHHHHHHCCCEEEecC-ceeEE
Confidence 334445 55666666 89999999999999999999999875 34554
No 70
>PF01638 HxlR: HxlR-like helix-turn-helix; InterPro: IPR002577 The hxlR-type HTH domain is a domain of ~90-100 amino acids present in putative transcription regulators with a winged helix-turn-helix (wHTH) structure. The domain is named after Bacillus subtilis hxlR, a transcription activator of the hxlAB operon involved in the detoxification of formaldehyde []. The hxlR-type domain forms the core of putative transcription regulators and of hypothetical proteins occurring in eubacteria as well as in archaea. The sequence and structure of hxlR-type proteins show similarities with the marR-type wHTH []. The crystal structure of ytfH resembles the DNA-binding domains of winged helix proteins, containing a three helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-H2-B1-H3-H4-B2-B3-H5-H6. This topology corresponds with that of the marR-type DNA-binding domain, wherein helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. ; PDB: 2F2E_B 3DF8_A 1Z7U_B 1YYV_A 4A5M_D 4A5N_B 2FSW_A 2HZT_D.
Probab=28.94 E-value=1.5e+02 Score=21.61 Aligned_cols=53 Identities=21% Similarity=0.275 Sum_probs=38.1
Q ss_pred hhhhhhccCCCCCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeecCC--CCCceEe
Q psy8359 219 AIVRIMKMRKTLSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERDKD--KANSYNY 277 (279)
Q Consensus 219 aIVRIMK~~K~l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~~--d~~~y~Y 277 (279)
.|++.+.. +.+.+.+|...+ =..+...+-+++..|.+.|.|.|... .|....|
T Consensus 9 ~IL~~l~~-g~~rf~el~~~l-----~~is~~~L~~~L~~L~~~GLv~r~~~~~~p~~v~Y 63 (90)
T PF01638_consen 9 LILRALFQ-GPMRFSELQRRL-----PGISPKVLSQRLKELEEAGLVERRVYPEVPPRVEY 63 (90)
T ss_dssp HHHHHHTT-SSEEHHHHHHHS-----TTS-HHHHHHHHHHHHHTTSEEEEEESSSSSEEEE
T ss_pred HHHHHHHh-CCCcHHHHHHhc-----chhHHHHHHHHHHHHHHcchhhcccccCCCCCCcc
Confidence 45555666 788888887774 13578899999999999999999743 3444555
No 71
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=28.09 E-value=1.3e+02 Score=26.42 Aligned_cols=50 Identities=10% Similarity=0.105 Sum_probs=36.8
Q ss_pred hhccCCCCCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeecCCCCCceEec
Q psy8359 223 IMKMRKTLSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERDKDKANSYNYM 278 (279)
Q Consensus 223 IMK~~K~l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~~d~~~y~Yv 278 (279)
.++..-.++..+|... ...+.+.+-+.+..|-++|||+|..+....+.|+
T Consensus 15 ~l~~~~~IS~~eLA~~------L~iS~~Tvsr~Lk~LEe~GlI~R~~~~r~~~v~L 64 (217)
T PRK14165 15 AVNNTVKISSSEFANH------TGTSSKTAARILKQLEDEGYITRTIVPRGQLITI 64 (217)
T ss_pred ccCCCCCcCHHHHHHH------HCcCHHHHHHHHHHHHHCCCEEEEEcCCceEEEE
Confidence 3444555666666666 5779999999999999999999987544445443
No 72
>PRK09954 putative kinase; Provisional
Probab=28.02 E-value=74 Score=29.56 Aligned_cols=44 Identities=11% Similarity=0.270 Sum_probs=38.7
Q ss_pred hhhhhhccCCCCCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeec
Q psy8359 219 AIVRIMKMRKTLSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERD 268 (279)
Q Consensus 219 aIVRIMK~~K~l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~ 268 (279)
-|.++++....++..+|-.. +..+...+.++|..|.++|||+..
T Consensus 7 ~il~~l~~~~~~s~~~la~~------l~~s~~~v~~~i~~L~~~g~i~~~ 50 (362)
T PRK09954 7 EILAILRRNPLIQQNEIADI------LQISRSRVAAHIMDLMRKGRIKGK 50 (362)
T ss_pred HHHHHHHHCCCCCHHHHHHH------HCCCHHHHHHHHHHHHHCCCcCCc
Confidence 37899999999999988877 579999999999999999999754
No 73
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=27.71 E-value=81 Score=23.79 Aligned_cols=26 Identities=15% Similarity=0.358 Sum_probs=23.0
Q ss_pred CCCChHHHHHHHHhhhhcCceeecCC
Q psy8359 245 FPVKPADLKKRIESLIDRDYMERDKD 270 (279)
Q Consensus 245 F~p~~~~iK~~Ie~LIekeYi~R~~~ 270 (279)
+..+...|..+++.|.+.|+|+|..+
T Consensus 31 l~~~~~~v~~~l~~Le~~GLler~~g 56 (92)
T PF10007_consen 31 LKIPLEEVREALEKLEEMGLLERVEG 56 (92)
T ss_pred HCCCHHHHHHHHHHHHHCCCeEEecC
Confidence 45688899999999999999999875
No 74
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.
Probab=27.62 E-value=1.8e+02 Score=19.96 Aligned_cols=53 Identities=17% Similarity=0.308 Sum_probs=40.4
Q ss_pred HHhhhhhhhhhhhhhhhccCCCCCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCcee
Q psy8359 208 VFQDRQYQIDAAIVRIMKMRKTLSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYME 266 (279)
Q Consensus 208 i~~~R~~~I~AaIVRIMK~~K~l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~ 266 (279)
+.++.--.+=|.|...+-+++.++..+|...+ ..++..||+++-.||..+++.
T Consensus 6 ii~~~fG~~~~~V~~~Ll~~G~ltl~~i~~~t------~l~~~~Vk~~L~~LiQh~~v~ 58 (62)
T PF08221_consen 6 IIEEHFGEIVAKVGEVLLSRGRLTLREIVRRT------GLSPKQVKKALVVLIQHNLVQ 58 (62)
T ss_dssp HHHHHHHHHHHHHHHHHHHC-SEEHHHHHHHH------T--HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHcChHHHHHHHHHHHcCCcCHHHHHHHh------CCCHHHHHHHHHHHHHcCCee
Confidence 34444455667888999999999999998876 377889999999999998775
No 75
>PF11313 DUF3116: Protein of unknown function (DUF3116); InterPro: IPR021464 This family of proteins with unknown function appears to be restricted to Bacillales.
Probab=27.50 E-value=1.6e+02 Score=21.87 Aligned_cols=46 Identities=17% Similarity=0.213 Sum_probs=37.2
Q ss_pred CCCCCHHHHHHHHHHhcC-CCCChHHHHHHHHhhhhcCceeecCCCC
Q psy8359 227 RKTLSHNLLLSELFNQLK-FPVKPADLKKRIESLIDRDYMERDKDKA 272 (279)
Q Consensus 227 ~K~l~~~~L~~eV~~~l~-F~p~~~~iK~~Ie~LIekeYi~R~~~d~ 272 (279)
.......+|..++++.-. -.++-..+-.++=.|=+.|||.|+..+.
T Consensus 18 ~~~~~i~~L~~e~~~~~~~~~~TKNelL~~vYWLE~ngyI~R~~~~~ 64 (85)
T PF11313_consen 18 DPNATINHLTFEFIDFPGAYDFTKNELLYTVYWLEENGYIFRDNNNN 64 (85)
T ss_pred CccccHHHHHHHHHhccccccccHHHHHHHHHHHhhcCeeEeecCCC
Confidence 345566788888777666 7789999999999999999999997553
No 76
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=27.28 E-value=1.4e+02 Score=18.36 Aligned_cols=25 Identities=8% Similarity=0.280 Sum_probs=22.1
Q ss_pred CCCChHHHHHHHHhhhhcCceeecC
Q psy8359 245 FPVKPADLKKRIESLIDRDYMERDK 269 (279)
Q Consensus 245 F~p~~~~iK~~Ie~LIekeYi~R~~ 269 (279)
+..+.+.+.+.+..|.++|+|+++.
T Consensus 18 l~~s~~tv~~~l~~L~~~g~l~~~~ 42 (48)
T smart00419 18 LGLTRETVSRTLKRLEKEGLISREG 42 (48)
T ss_pred HCCCHHHHHHHHHHHHHCCCEEEeC
Confidence 5678889999999999999999874
No 77
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=26.49 E-value=70 Score=23.18 Aligned_cols=45 Identities=22% Similarity=0.390 Sum_probs=34.6
Q ss_pred hhhhhhccCCCCCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeecC
Q psy8359 219 AIVRIMKMRKTLSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERDK 269 (279)
Q Consensus 219 aIVRIMK~~K~l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~ 269 (279)
+|+-++.....+++.+|-.. ...+...+-+.+..|.+.|||++..
T Consensus 4 ~Il~~L~~~~~~~f~~L~~~------l~lt~g~Ls~hL~~Le~~GyV~~~k 48 (80)
T PF13601_consen 4 AILALLYANEEATFSELKEE------LGLTDGNLSKHLKKLEEAGYVEVEK 48 (80)
T ss_dssp HHHHHHHHHSEEEHHHHHHH------TT--HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHhhcCCCCHHHHHHH------hCcCHHHHHHHHHHHHHCCCEEEEE
Confidence 45556666777888777766 5789999999999999999999863
No 78
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=26.16 E-value=1e+02 Score=27.02 Aligned_cols=31 Identities=16% Similarity=0.446 Sum_probs=27.2
Q ss_pred CCCChHHHHHHHHhhhhcCceeecCCCCCceE
Q psy8359 245 FPVKPADLKKRIESLIDRDYMERDKDKANSYN 276 (279)
Q Consensus 245 F~p~~~~iK~~Ie~LIekeYi~R~~~d~~~y~ 276 (279)
|..+...++++|..|.+.|+|.|..+ ..+|+
T Consensus 41 f~VSR~TvRkAL~~L~~eGli~r~~G-~GtfV 71 (236)
T COG2188 41 FGVSRMTVRKALDELVEEGLIVRRQG-KGTFV 71 (236)
T ss_pred HCCcHHHHHHHHHHHHHCCcEEEEec-CeeEE
Confidence 89999999999999999999999874 35554
No 79
>PRK10870 transcriptional repressor MprA; Provisional
Probab=25.42 E-value=1.6e+02 Score=24.62 Aligned_cols=37 Identities=14% Similarity=0.269 Sum_probs=29.0
Q ss_pred CCCCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeecCC
Q psy8359 228 KTLSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERDKD 270 (279)
Q Consensus 228 K~l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~~ 270 (279)
..++..+|... +..+.+.+-+.|..|.++|||+|..+
T Consensus 70 ~~it~~eLa~~------l~l~~~tvsr~v~rLe~kGlV~R~~~ 106 (176)
T PRK10870 70 HSIQPSELSCA------LGSSRTNATRIADELEKRGWIERRES 106 (176)
T ss_pred CCcCHHHHHHH------HCCCHHHHHHHHHHHHHCCCEEecCC
Confidence 45565665555 56788999999999999999999643
No 80
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=25.40 E-value=2e+02 Score=18.75 Aligned_cols=25 Identities=16% Similarity=0.303 Sum_probs=23.0
Q ss_pred CCCChHHHHHHHHhhhhcCceeecC
Q psy8359 245 FPVKPADLKKRIESLIDRDYMERDK 269 (279)
Q Consensus 245 F~p~~~~iK~~Ie~LIekeYi~R~~ 269 (279)
|..+.+.+.+.+..|-++|||.+..
T Consensus 35 ~~is~~~v~~~l~~L~~~G~i~~~~ 59 (66)
T cd07377 35 LGVSRTTVREALRELEAEGLVERRP 59 (66)
T ss_pred HCCCHHHHHHHHHHHHHCCCEEecC
Confidence 6789999999999999999999875
No 81
>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=25.36 E-value=2.1e+02 Score=18.93 Aligned_cols=36 Identities=8% Similarity=0.205 Sum_probs=29.4
Q ss_pred CCCCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeecC
Q psy8359 228 KTLSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERDK 269 (279)
Q Consensus 228 K~l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~ 269 (279)
..++..+|... +-.+.+.+.+.+..|.++|+|.+..
T Consensus 24 ~~~s~~ela~~------~g~s~~tv~r~l~~L~~~g~i~~~~ 59 (67)
T cd00092 24 LPLTRQEIADY------LGLTRETVSRTLKELEEEGLISRRG 59 (67)
T ss_pred CCcCHHHHHHH------HCCCHHHHHHHHHHHHHCCCEEecC
Confidence 44666666665 5678999999999999999999976
No 82
>PF09382 RQC: RQC domain; InterPro: IPR018982 This entry represents the RQC domain, which is a DNA-binding domain found only in RecQ family enzymes. RecQ family helicases can unwind G4 DNA, and play important roles at G-rich domains of the genome, including the telomeres, rDNA, and immunoglobulin switch regions. This domain has a helix-turn-helix structure and acts as a high affinity G4 DNA binding domain []. Binding of RecQ to Holliday junctions involves both the RQC and the HRDC domains.; GO: 0043140 ATP-dependent 3'-5' DNA helicase activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1OYW_A 1OYY_A 3AAF_A 2AXL_A 2V1X_B 2WWY_B.
Probab=25.15 E-value=69 Score=23.96 Aligned_cols=31 Identities=26% Similarity=0.504 Sum_probs=23.1
Q ss_pred CChHHHHHHHHhhhhcCceeecCCCCCceEec
Q psy8359 247 VKPADLKKRIESLIDRDYMERDKDKANSYNYM 278 (279)
Q Consensus 247 p~~~~iK~~Ie~LIekeYi~R~~~d~~~y~Yv 278 (279)
-+...+++.|..|+..|||..+.+. ..|.|+
T Consensus 54 ~~~~~~~~li~~Li~~g~L~~~~~~-~~~~~l 84 (106)
T PF09382_consen 54 MSKDDWERLIRQLILEGYLSEDNGG-FAYPYL 84 (106)
T ss_dssp S-HHHHHHHHHHHHHTTSEEEEECC-CCTEEE
T ss_pred CCHHHHHHHHHHHHHcCCceecCCc-ccccEE
Confidence 4899999999999999999776542 344443
No 83
>PF05732 RepL: Firmicute plasmid replication protein (RepL); InterPro: IPR008813 This entry consists of proteins thought to be involved in plasmid replication. ; GO: 0006260 DNA replication, 0006276 plasmid maintenance
Probab=24.72 E-value=62 Score=27.03 Aligned_cols=42 Identities=21% Similarity=0.419 Sum_probs=33.6
Q ss_pred CCCCCHHHHHHHHhHhhcCCceeeeeCCCCCCCCCCCeEEEecCCCCceee
Q psy8359 136 GIDLTDADLRRTLQSLACGKTRVLKKTPASRDIEDCDRFRFNNDFTFKLFR 186 (279)
Q Consensus 136 ~t~i~~~~l~~~L~sL~~~k~~iL~~~~~~~~i~~~~~f~~N~~F~~k~~k 186 (279)
.++++...+.+++..|. +.++|.+.. ...|.+|++|-.+..+
T Consensus 84 ~l~iS~~Tv~r~ik~L~--e~~iI~k~~-------~G~Y~iNP~~~~kG~~ 125 (165)
T PF05732_consen 84 KLGISKPTVSRAIKELE--EKNIIKKIR-------NGAYMINPNFFFKGDR 125 (165)
T ss_pred HhCCCHHHHHHHHHHHH--hCCcEEEcc-------CCeEEECcHHheeCcH
Confidence 36899999999999999 788888742 3589999998765443
No 84
>PF13730 HTH_36: Helix-turn-helix domain
Probab=24.62 E-value=61 Score=21.12 Aligned_cols=21 Identities=14% Similarity=0.358 Sum_probs=18.1
Q ss_pred CCCChHHHHHHHHhhhhcCce
Q psy8359 245 FPVKPADLKKRIESLIDRDYM 265 (279)
Q Consensus 245 F~p~~~~iK~~Ie~LIekeYi 265 (279)
...+...|.+.|..|.++|||
T Consensus 35 ~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 35 LGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred HCcCHHHHHHHHHHHHHCcCC
Confidence 356788999999999999986
No 85
>PRK00215 LexA repressor; Validated
Probab=24.42 E-value=2e+02 Score=24.28 Aligned_cols=45 Identities=11% Similarity=0.317 Sum_probs=33.7
Q ss_pred cCCCCCHHHHHHHHHHhcCCCC-ChHHHHHHHHhhhhcCceeecCCCCCceE
Q psy8359 226 MRKTLSHNLLLSELFNQLKFPV-KPADLKKRIESLIDRDYMERDKDKANSYN 276 (279)
Q Consensus 226 ~~K~l~~~~L~~eV~~~l~F~p-~~~~iK~~Ie~LIekeYi~R~~~d~~~y~ 276 (279)
....++..+|... +-. +.+-+-..|..|.++|||+|+.+++..+.
T Consensus 20 ~~~~~s~~ela~~------~~~~~~~tv~~~l~~L~~~g~i~~~~~~~r~~~ 65 (205)
T PRK00215 20 TGYPPSRREIADA------LGLRSPSAVHEHLKALERKGFIRRDPGRSRAIE 65 (205)
T ss_pred hCCCCCHHHHHHH------hCCCChHHHHHHHHHHHHCCCEEeCCCCcceEE
Confidence 3445666666666 566 77888899999999999999987654443
No 86
>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=22.94 E-value=1.6e+02 Score=22.58 Aligned_cols=57 Identities=12% Similarity=0.181 Sum_probs=39.7
Q ss_pred hhhhhcc-CCCCCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeecCCCCCceEe
Q psy8359 220 IVRIMKM-RKTLSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERDKDKANSYNY 277 (279)
Q Consensus 220 IVRIMK~-~K~l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~~d~~~y~Y 277 (279)
|..+++. .+-++.++|...+.+.- ..++.+.|=+.|+.|.+.|.|.+-..+.....|
T Consensus 13 Il~~l~~~~~~~ta~ei~~~l~~~~-~~is~~TVYR~L~~L~e~Gli~~~~~~~~~~~Y 70 (120)
T PF01475_consen 13 ILELLKESPEHLTAEEIYDKLRKKG-PRISLATVYRTLDLLEEAGLIRKIEFGDGESRY 70 (120)
T ss_dssp HHHHHHHHSSSEEHHHHHHHHHHTT-TT--HHHHHHHHHHHHHTTSEEEEEETTSEEEE
T ss_pred HHHHHHcCCCCCCHHHHHHHhhhcc-CCcCHHHHHHHHHHHHHCCeEEEEEcCCCcceE
Confidence 3444444 56888888888776322 677889999999999999999997655444444
No 87
>PF01316 Arg_repressor: Arginine repressor, DNA binding domain; InterPro: IPR020900 The arginine dihydrolase (AD) pathway is found in many prokaryotes and some primitive eukaryotes, an example of the latter being Giardia lamblia (Giardia intestinalis) []. The three-enzyme anaerobic pathway breaks down L-arginine to form 1 mol of ATP, carbon dioxide and ammonia. In simpler bacteria, the first enzyme, arginine deiminase, can account for up to 10% of total cell protein []. Most prokaryotic arginine deiminase pathways are under the control of a repressor gene, termed ArgR []. This is a negative regulator, and will only release the arginine deiminase operon for expression in the presence of arginine []. The crystal structure of apo-ArgR from Bacillus stearothermophilus has been determined to 2.5A by means of X-ray crystallography []. The protein exists as a hexamer of identical subunits, and is shown to have six DNA-binding domains, clustered around a central oligomeric core when bound to arginine. It predominantly interacts with A.T residues in ARG boxes. This hexameric protein binds DNA at its N terminus to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbour-joining tree, some of these paralogous sequences show long branches and differ significantly from the well-conserved C-terminal region. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0006525 arginine metabolic process; PDB: 1AOY_A 3V4G_A 3LAJ_D 3FHZ_A 3LAP_B 3ERE_D 2P5L_C 1F9N_D 2P5K_A 1B4A_A ....
Probab=22.82 E-value=2.4e+02 Score=20.04 Aligned_cols=59 Identities=17% Similarity=0.280 Sum_probs=38.7
Q ss_pred hhhhhhhhhhccCCCCCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeecCCCCCceEec
Q psy8359 215 QIDAAIVRIMKMRKTLSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERDKDKANSYNYM 278 (279)
Q Consensus 215 ~I~AaIVRIMK~~K~l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~~d~~~y~Yv 278 (279)
.-+++|-.|.+.+..-+..+|+....++ .|..+-+.|-+=|..| +-++-. +..+.|.|.
T Consensus 5 ~R~~~I~~li~~~~i~sQ~eL~~~L~~~-Gi~vTQaTiSRDLkeL---~~vKv~-~~~g~~~Y~ 63 (70)
T PF01316_consen 5 KRQELIKELISEHEISSQEELVELLEEE-GIEVTQATISRDLKEL---GAVKVP-DGNGKYRYV 63 (70)
T ss_dssp HHHHHHHHHHHHS---SHHHHHHHHHHT-T-T--HHHHHHHHHHH---T-EEEE-CTTSSEEEE
T ss_pred HHHHHHHHHHHHCCcCCHHHHHHHHHHc-CCCcchhHHHHHHHHc---CcEEee-CCCCCEEEE
Confidence 4577889999999999999998886554 6999999998877776 444433 344668885
No 88
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=22.74 E-value=81 Score=23.46 Aligned_cols=26 Identities=19% Similarity=0.413 Sum_probs=23.0
Q ss_pred CCCChHHHHHHHHhhhhcCceeecCC
Q psy8359 245 FPVKPADLKKRIESLIDRDYMERDKD 270 (279)
Q Consensus 245 F~p~~~~iK~~Ie~LIekeYi~R~~~ 270 (279)
...+.+.+-+.|..|.++|||+|..+
T Consensus 46 l~i~~~~vt~~l~~Le~~glv~r~~~ 71 (126)
T COG1846 46 LGLDRSTVTRLLKRLEDKGLIERLRD 71 (126)
T ss_pred HCCCHHHHHHHHHHHHHCCCeeecCC
Confidence 56788899999999999999999754
No 89
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=22.70 E-value=1.1e+02 Score=25.67 Aligned_cols=25 Identities=16% Similarity=0.380 Sum_probs=23.0
Q ss_pred CCChHHHHHHHHhhhhcCceeecCC
Q psy8359 246 PVKPADLKKRIESLIDRDYMERDKD 270 (279)
Q Consensus 246 ~p~~~~iK~~Ie~LIekeYi~R~~~ 270 (279)
..+...++.+|+.|.+-|+|+++++
T Consensus 52 ~is~~ev~~sL~~L~~~gli~k~~~ 76 (171)
T PF14394_consen 52 KISAEEVRDSLEFLEKLGLIKKDGD 76 (171)
T ss_pred CCCHHHHHHHHHHHHHCCCeEECCC
Confidence 5689999999999999999999985
No 90
>PF15479 DUF4639: Domain of unknown function (DUF4639)
Probab=22.27 E-value=1.1e+02 Score=30.27 Aligned_cols=28 Identities=14% Similarity=0.463 Sum_probs=25.3
Q ss_pred CCCChHHHHHHHHhhhhcCceeecCCCC
Q psy8359 245 FPVKPADLKKRIESLIDRDYMERDKDKA 272 (279)
Q Consensus 245 F~p~~~~iK~~Ie~LIekeYi~R~~~d~ 272 (279)
++-++..-+.++-.+||=.||.||++..
T Consensus 78 iPfTV~qArdamLqiiewrFLarD~GE~ 105 (576)
T PF15479_consen 78 IPFTVSQARDAMLQIIEWRFLARDEGES 105 (576)
T ss_pred cceeHHHHHHHHHHHhheeeeeccCCCC
Confidence 6778999999999999999999998764
No 91
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=21.95 E-value=1.3e+02 Score=26.63 Aligned_cols=46 Identities=9% Similarity=0.292 Sum_probs=40.6
Q ss_pred hhhhhhccCCCCCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeecCC
Q psy8359 219 AIVRIMKMRKTLSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERDKD 270 (279)
Q Consensus 219 aIVRIMK~~K~l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~~ 270 (279)
.|.+.++.++.++..+|... |..+..-|.+-+..|-++|.|.|-.+
T Consensus 9 ~Il~~l~~~~~~~~~ela~~------l~vS~~TirRdL~~Le~~g~i~r~~g 54 (251)
T PRK13509 9 ILLELLAQLGFVTVEKVIER------LGISPATARRDINKLDESGKLKKVRN 54 (251)
T ss_pred HHHHHHHHcCCcCHHHHHHH------HCcCHHHHHHHHHHHHHCCCEEEecC
Confidence 37888899999999999888 78999999999999999999998543
No 92
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=21.62 E-value=1.5e+02 Score=26.15 Aligned_cols=44 Identities=16% Similarity=0.341 Sum_probs=39.2
Q ss_pred hhhhhccCCCCCHHHHHHHHHHhcCCCCChHHHHHHHHhhhhcCceeecC
Q psy8359 220 IVRIMKMRKTLSHNLLLSELFNQLKFPVKPADLKKRIESLIDRDYMERDK 269 (279)
Q Consensus 220 IVRIMK~~K~l~~~~L~~eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~ 269 (279)
|..+++.++.++..+|... |..+..-|++-+..|-+++.|.|..
T Consensus 9 Il~~l~~~~~~~~~eLa~~------l~VS~~TiRRdL~~L~~~~~l~r~~ 52 (240)
T PRK10411 9 IVDLLLNHTSLTTEALAEQ------LNVSKETIRRDLNELQTQGKILRNH 52 (240)
T ss_pred HHHHHHHcCCCcHHHHHHH------HCcCHHHHHHHHHHHHHCCCEEEec
Confidence 7888889999999998888 7899999999999999999998854
No 93
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=21.50 E-value=85 Score=28.01 Aligned_cols=33 Identities=15% Similarity=0.237 Sum_probs=27.8
Q ss_pred CChHHHHHHHHhhhhcCceeecCCCCCceEecC
Q psy8359 247 VKPADLKKRIESLIDRDYMERDKDKANSYNYMA 279 (279)
Q Consensus 247 p~~~~iK~~Ie~LIekeYi~R~~~d~~~y~Yva 279 (279)
...+.|=..+++|..|||++..++.|..|..++
T Consensus 42 vP~~kvY~vl~sLe~kG~v~~~~g~P~~y~av~ 74 (247)
T COG1378 42 VPRPKVYDVLRSLEKKGLVEVIEGRPKKYRAVP 74 (247)
T ss_pred CCchhHHHHHHHHHHCCCEEeeCCCCceEEeCC
Confidence 344557788999999999999999999998774
No 94
>PF09957 DUF2191: Uncharacterized protein conserved in bacteria (DUF2191); InterPro: IPR019239 This entry, found in various hypothetical prokaryotic proteins, has no known function.
Probab=21.06 E-value=1.4e+02 Score=19.45 Aligned_cols=31 Identities=23% Similarity=0.292 Sum_probs=25.0
Q ss_pred HHHHHHHHHhcCCCCChHHHHHHHHhhhhcC
Q psy8359 233 NLLLSELFNQLKFPVKPADLKKRIESLIDRD 263 (279)
Q Consensus 233 ~~L~~eV~~~l~F~p~~~~iK~~Ie~LIeke 263 (279)
++|+.++.....+....+.|..+++.||.++
T Consensus 9 d~Ll~eA~~l~g~~tk~~~V~~ALr~~i~r~ 39 (47)
T PF09957_consen 9 DELLAEAMRLTGTKTKKEAVNEALRELIRRR 39 (47)
T ss_pred HHHHHHHHHHhCCCCHHHHHHHHHHHHHHHH
Confidence 4788888776668888899999999888764
No 95
>PF09114 MotA_activ: Transcription factor MotA, activation domain; InterPro: IPR015198 Transcription factor MotA is required for the activation of middle promoters in Bacteriophage T4, in addition to phage T4 co-activator AsiA, and sigma-70-containing Escherichia coli RNA polymerase. Phage T4 middle promoters have the sigma70 -10 DNA element, but not the -35 element; instead, they have a MotA box at -30 to which the transcription factor MotA binds []. MotA and AsiA interact with the C-terminal of sigma70 (region 4), which normally binds the -35 element and the beta-flap, thereby diverting sigma70 away from host promoters that require -35 element-binding to phage T4 middle promoters. Transcription factor MotA has two domains: an N-terminal domain required for binding to sigma70, and a C-terminal domain required for binding to the -30 MotA box element in the phage T4 middle promoter. This entry represents the N-terminal (activation) domain of MotA factors that binds sigma70. The N-terminal domain adopts an almost completely alpha-helical topology, with five alpha-helices and a short, two-stranded, beta-ribbon. Four alpha helices (alpha1, alpha3, alpha4 and alpha5) are amphipathic and pack their hydrophobic surfaces around the central helix alpha2 [].; PDB: 1BJA_B 1I1S_A.
Probab=20.99 E-value=1.9e+02 Score=21.87 Aligned_cols=33 Identities=24% Similarity=0.384 Sum_probs=23.5
Q ss_pred HHHHhcCCCCChHHHHHHHHhhhhcCceeecCC
Q psy8359 238 ELFNQLKFPVKPADLKKRIESLIDRDYMERDKD 270 (279)
Q Consensus 238 eV~~~l~F~p~~~~iK~~Ie~LIekeYi~R~~~ 270 (279)
+|.+.+.=..+.+.+-..|-.||.+|||+...+
T Consensus 35 ev~e~l~~~~~~~~V~SNIGvLIKkglIEKSGD 67 (96)
T PF09114_consen 35 EVREALATEMNKASVNSNIGVLIKKGLIEKSGD 67 (96)
T ss_dssp HHHH-T-TTS-HHHHHHHHHHHHHTTSEEEETT
T ss_pred HHHHHHHHHhhhhHHHHhHHHHHHcCcccccCC
Confidence 344444334577889999999999999999874
No 96
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=20.93 E-value=1.2e+02 Score=21.53 Aligned_cols=24 Identities=17% Similarity=0.333 Sum_probs=19.2
Q ss_pred CCCChHHHHHHHHhhhhcCceeec
Q psy8359 245 FPVKPADLKKRIESLIDRDYMERD 268 (279)
Q Consensus 245 F~p~~~~iK~~Ie~LIekeYi~R~ 268 (279)
-..+...+.+-|+.|.++|+|+.+
T Consensus 29 ~~L~~~~~~~yL~~L~~~gLI~~~ 52 (77)
T PF14947_consen 29 ANLNYSTLKKYLKELEEKGLIKKK 52 (77)
T ss_dssp ST--HHHHHHHHHHHHHTTSEEEE
T ss_pred hCcCHHHHHHHHHHHHHCcCeeCC
Confidence 357888999999999999999763
No 97
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=20.89 E-value=93 Score=22.36 Aligned_cols=39 Identities=18% Similarity=0.310 Sum_probs=28.7
Q ss_pred cCCCCCHHHHHHHHhHhhcCCceeeeeCCCCCCCCCCCeEEEecCC
Q psy8359 135 LGIDLTDADLRRTLQSLACGKTRVLKKTPASRDIEDCDRFRFNNDF 180 (279)
Q Consensus 135 ~~t~i~~~~l~~~L~sL~~~k~~iL~~~~~~~~i~~~~~f~~N~~F 180 (279)
+.++++...+.+.|+.|. +.+++....+ ++.-|.++.+.
T Consensus 33 ~~~~i~~~~l~kil~~L~--~~Gli~s~~G-----~~GGy~L~~~~ 71 (83)
T PF02082_consen 33 ERLGISPSYLRKILQKLK--KAGLIESSRG-----RGGGYRLARPP 71 (83)
T ss_dssp HHHTS-HHHHHHHHHHHH--HTTSEEEETS-----TTSEEEESS-C
T ss_pred HHHCcCHHHHHHHHHHHh--hCCeeEecCC-----CCCceeecCCH
Confidence 457899999999999999 8888876542 45677777653
Done!