Query 023374
Match_columns 283
No_of_seqs 135 out of 206
Neff 5.7
Searched_HMMs 46136
Date Fri Mar 29 03:33:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023374.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023374hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3095 Transcription initiati 100.0 4.7E-64 1E-68 458.4 18.5 274 1-282 3-282 (284)
2 COG5174 TFA2 Transcription ini 100.0 2.5E-53 5.3E-58 378.6 20.0 213 58-282 65-283 (285)
3 PF02186 TFIIE_beta: TFIIE bet 99.7 3.1E-17 6.7E-22 121.9 5.2 63 72-136 1-65 (65)
4 cd07977 TFIIE_beta_winged_heli 99.6 1.2E-15 2.5E-20 116.5 6.2 70 68-137 1-75 (75)
5 PHA02943 hypothetical protein; 93.2 0.11 2.4E-06 45.1 4.0 72 138-213 12-87 (165)
6 PF08784 RPA_C: Replication pr 89.9 0.64 1.4E-05 36.6 4.9 43 139-181 49-98 (102)
7 PF07106 TBPIP: Tat binding pr 87.5 3.2 6.9E-05 35.7 7.9 90 79-174 4-100 (169)
8 PF04703 FaeA: FaeA-like prote 87.0 0.38 8.2E-06 35.5 1.6 46 80-125 4-49 (62)
9 PF04703 FaeA: FaeA-like prote 84.2 3.2 6.9E-05 30.6 5.4 53 139-192 2-58 (62)
10 PF09339 HTH_IclR: IclR helix- 84.2 0.75 1.6E-05 31.9 1.9 49 77-125 4-52 (52)
11 COG3355 Predicted transcriptio 82.3 3.5 7.6E-05 34.6 5.5 83 81-175 32-121 (126)
12 PF07106 TBPIP: Tat binding pr 82.3 6.6 0.00014 33.8 7.5 96 139-236 3-112 (169)
13 PF05158 RNA_pol_Rpc34: RNA po 79.3 14 0.0003 35.7 9.3 140 74-213 7-177 (327)
14 smart00550 Zalpha Z-DNA-bindin 74.4 4.8 0.00011 29.6 3.7 47 79-125 9-56 (68)
15 smart00346 HTH_ICLR helix_turn 74.3 6.6 0.00014 29.5 4.6 49 77-125 6-54 (91)
16 TIGR02431 pcaR_pcaU beta-ketoa 71.3 8.3 0.00018 34.9 5.3 55 75-129 8-62 (248)
17 TIGR03820 lys_2_3_AblA lysine- 67.5 17 0.00037 36.3 6.9 94 74-180 139-249 (417)
18 PF12324 HTH_15: Helix-turn-he 66.7 6.9 0.00015 30.2 3.1 45 78-125 25-69 (77)
19 PF04157 EAP30: EAP30/Vps36 fa 66.4 23 0.00049 31.9 7.0 160 5-180 26-222 (223)
20 PRK06474 hypothetical protein; 62.7 31 0.00067 30.2 6.9 62 139-200 13-82 (178)
21 COG1803 MgsA Methylglyoxal syn 62.4 10 0.00022 32.2 3.6 52 152-212 50-101 (142)
22 PF01726 LexA_DNA_bind: LexA D 60.7 9.5 0.00021 28.1 2.8 49 78-126 12-61 (65)
23 COG3682 Predicted transcriptio 60.6 24 0.00052 29.6 5.5 94 80-174 10-114 (123)
24 KOG4603 TBP-1 interacting prot 60.5 14 0.00031 32.8 4.3 62 138-201 8-76 (201)
25 PF05158 RNA_pol_Rpc34: RNA po 60.4 21 0.00046 34.4 5.9 45 139-183 11-62 (327)
26 TIGR02702 SufR_cyano iron-sulf 59.6 29 0.00062 30.6 6.3 58 138-196 2-65 (203)
27 PF08220 HTH_DeoR: DeoR-like h 59.0 32 0.00069 24.3 5.3 42 140-182 3-48 (57)
28 PF08279 HTH_11: HTH domain; 58.8 44 0.00095 22.8 5.9 37 140-176 3-43 (55)
29 COG3357 Predicted transcriptio 58.6 17 0.00036 29.1 4.0 37 77-115 4-40 (97)
30 smart00550 Zalpha Z-DNA-bindin 58.4 39 0.00085 24.7 5.8 44 138-181 7-55 (68)
31 PF08279 HTH_11: HTH domain; 58.0 10 0.00023 26.0 2.6 49 78-126 2-51 (55)
32 TIGR00988 hip integration host 55.9 69 0.0015 24.6 7.2 45 138-182 2-46 (94)
33 PRK00199 ihfB integration host 55.1 70 0.0015 24.7 7.1 45 138-182 2-46 (94)
34 PF06757 Ins_allergen_rp: Inse 55.1 10 0.00022 33.1 2.5 32 203-235 43-75 (179)
35 cd00092 HTH_CRP helix_turn_hel 54.7 30 0.00066 24.1 4.6 44 89-132 23-67 (67)
36 PRK10163 DNA-binding transcrip 52.9 33 0.0007 31.7 5.7 56 71-126 20-75 (271)
37 PF12802 MarR_2: MarR family; 50.2 81 0.0018 21.6 6.5 45 141-185 9-58 (62)
38 PRK09834 DNA-binding transcrip 49.6 34 0.00073 31.4 5.2 58 74-131 9-68 (263)
39 smart00420 HTH_DEOR helix_turn 48.8 31 0.00068 22.5 3.7 46 79-125 3-48 (53)
40 PF08672 APC2: Anaphase promot 47.3 51 0.0011 24.0 4.8 42 77-129 16-59 (60)
41 PF11181 YflT: Heat induced st 46.8 29 0.00062 27.4 3.8 70 164-236 11-87 (103)
42 PF01316 Arg_repressor: Argini 43.9 75 0.0016 23.9 5.4 53 134-197 17-69 (70)
43 PF04558 tRNA_synt_1c_R1: Glut 43.2 23 0.0005 30.9 2.9 35 75-109 84-119 (164)
44 PRK04172 pheS phenylalanyl-tRN 42.8 3.7E+02 0.0081 27.1 12.2 146 77-234 7-169 (489)
45 PRK11569 transcriptional repre 42.4 56 0.0012 30.1 5.5 56 75-130 27-84 (274)
46 COG1414 IclR Transcriptional r 41.8 37 0.0008 31.1 4.2 55 78-132 6-62 (246)
47 PF04282 DUF438: Family of unk 40.4 19 0.00042 27.3 1.7 34 201-235 17-50 (71)
48 PHA00738 putative HTH transcri 40.3 59 0.0013 26.7 4.6 57 139-198 14-74 (108)
49 PF05066 HARE-HTH: HB1, ASXL, 39.4 16 0.00036 26.8 1.2 26 76-101 2-27 (72)
50 smart00418 HTH_ARSR helix_turn 39.2 66 0.0014 21.4 4.3 41 81-123 2-42 (66)
51 PF04239 DUF421: Protein of un 38.5 13 0.00028 29.5 0.6 91 114-232 3-95 (99)
52 PF08220 HTH_DeoR: DeoR-like h 38.0 67 0.0014 22.6 4.1 48 78-126 2-49 (57)
53 TIGR02337 HpaR homoprotocatech 36.4 56 0.0012 25.9 4.0 54 142-196 33-91 (118)
54 cd00090 HTH_ARSR Arsenical Res 36.2 70 0.0015 21.9 4.1 44 79-124 10-53 (78)
55 COG0735 Fur Fe2+/Zn2+ uptake r 35.7 96 0.0021 26.1 5.5 63 68-130 13-83 (145)
56 PRK10512 selenocysteinyl-tRNA- 35.6 1.4E+02 0.0029 31.4 7.6 83 79-168 496-582 (614)
57 TIGR02698 CopY_TcrY copper tra 34.7 1.3E+02 0.0028 24.9 6.0 60 81-144 9-74 (130)
58 smart00347 HTH_MARR helix_turn 34.6 1.3E+02 0.0027 22.2 5.5 46 141-187 14-63 (101)
59 PF01978 TrmB: Sugar-specific 34.3 28 0.0006 25.0 1.7 55 77-132 9-64 (68)
60 COG3357 Predicted transcriptio 33.2 1.2E+02 0.0027 24.3 5.2 59 138-196 4-72 (97)
61 PF08679 DsrD: Dissimilatory s 33.2 1.8E+02 0.0038 22.0 5.8 44 139-182 3-54 (67)
62 PRK15090 DNA-binding transcrip 33.1 97 0.0021 28.1 5.5 59 73-132 11-71 (257)
63 TIGR02844 spore_III_D sporulat 32.2 66 0.0014 24.8 3.6 31 74-106 4-34 (80)
64 smart00419 HTH_CRP helix_turn_ 32.1 59 0.0013 21.0 2.9 40 90-129 7-46 (48)
65 COG2442 Uncharacterized conser 32.0 52 0.0011 25.4 2.9 46 117-165 9-56 (79)
66 cd07153 Fur_like Ferric uptake 32.0 1.3E+02 0.0028 23.6 5.4 54 79-132 4-65 (116)
67 PF09106 SelB-wing_2: Elongati 31.9 1.7E+02 0.0036 20.6 5.5 42 141-182 4-54 (59)
68 PRK10512 selenocysteinyl-tRNA- 31.8 2.9E+02 0.0062 29.0 9.3 111 90-213 376-498 (614)
69 PF13412 HTH_24: Winged helix- 31.8 65 0.0014 21.4 3.1 39 78-117 5-43 (48)
70 TIGR00160 MGSA methylglyoxal s 31.7 64 0.0014 27.7 3.7 52 152-212 48-99 (143)
71 PRK10141 DNA-binding transcrip 31.1 1.6E+02 0.0034 24.2 5.9 81 140-229 19-103 (117)
72 PF13034 DUF3895: Protein of u 30.4 54 0.0012 25.4 2.8 30 161-190 46-75 (78)
73 smart00342 HTH_ARAC helix_turn 29.8 72 0.0016 22.4 3.3 30 76-107 37-67 (84)
74 PRK11050 manganese transport r 29.6 1.1E+02 0.0024 25.8 4.9 72 54-125 14-85 (152)
75 PF05584 Sulfolobus_pRN: Sulfo 28.8 1.1E+02 0.0024 23.4 4.1 62 77-143 6-72 (72)
76 PRK00285 ihfA integration host 28.4 2.8E+02 0.0061 21.4 6.8 45 138-183 4-48 (99)
77 PTZ00448 hypothetical protein; 28.1 2.8E+02 0.006 27.5 7.8 169 64-235 94-288 (373)
78 PF09066 B2-adapt-app_C: Beta2 27.7 47 0.001 26.3 2.2 33 203-235 9-54 (114)
79 PRK10434 srlR DNA-bindng trans 27.0 1.4E+02 0.003 27.4 5.5 43 139-182 7-53 (256)
80 PRK13239 alkylmercury lyase; P 27.0 1.5E+02 0.0032 27.0 5.5 42 80-125 26-67 (206)
81 PRK10753 transcriptional regul 26.9 3E+02 0.0064 21.2 6.9 44 138-182 2-45 (90)
82 PF14947 HTH_45: Winged helix- 26.3 91 0.002 23.3 3.4 54 78-133 8-61 (77)
83 PRK03573 transcriptional regul 26.2 1.6E+02 0.0035 24.0 5.2 65 134-198 27-97 (144)
84 TIGR01261 hisB_Nterm histidino 25.8 76 0.0016 27.0 3.3 27 161-187 30-57 (161)
85 PRK09802 DNA-binding transcrip 25.8 1.4E+02 0.003 27.7 5.2 42 140-182 20-65 (269)
86 PF01047 MarR: MarR family; I 25.7 2E+02 0.0044 19.5 4.9 45 142-187 8-56 (59)
87 PF01022 HTH_5: Bacterial regu 25.4 54 0.0012 22.0 1.8 38 80-119 6-43 (47)
88 COG0820 Predicted Fe-S-cluster 25.1 76 0.0016 31.1 3.4 68 58-125 222-291 (349)
89 PF12840 HTH_20: Helix-turn-he 25.0 2E+02 0.0043 20.1 4.8 43 139-182 12-58 (61)
90 KOG3095 Transcription initiati 24.9 1.1E+02 0.0024 29.2 4.3 42 187-234 179-223 (284)
91 PF13601 HTH_34: Winged helix 24.6 2.3E+02 0.005 21.4 5.4 51 141-192 4-59 (80)
92 PF01475 FUR: Ferric uptake re 24.3 2.1E+02 0.0046 22.6 5.4 46 139-184 10-64 (120)
93 PRK10026 arsenate reductase; P 24.3 2E+02 0.0043 24.5 5.4 22 70-91 7-28 (141)
94 TIGR02716 C20_methyl_CrtF C-20 24.0 90 0.002 28.9 3.7 51 80-132 14-64 (306)
95 cd00591 HU_IHF Integration hos 23.8 1.9E+02 0.0041 21.5 4.8 45 138-183 1-45 (87)
96 PRK09462 fur ferric uptake reg 23.5 1.9E+02 0.0041 24.0 5.2 61 71-131 12-81 (148)
97 PF09724 DUF2036: Uncharacteri 23.4 3.4E+02 0.0073 25.6 7.5 144 75-226 167-324 (325)
98 PF13463 HTH_27: Winged helix 23.1 2.6E+02 0.0057 19.3 6.4 51 141-191 7-62 (68)
99 PF01475 FUR: Ferric uptake re 22.8 1.3E+02 0.0027 23.9 3.8 59 74-132 6-72 (120)
100 COG2425 Uncharacterized protei 22.7 1.7E+02 0.0036 29.7 5.4 67 113-182 303-374 (437)
101 cd07153 Fur_like Ferric uptake 21.7 3.4E+02 0.0074 21.0 6.1 48 139-186 3-59 (116)
102 TIGR00987 himA integration hos 21.7 3.8E+02 0.0083 20.6 6.6 44 138-182 3-46 (96)
103 PRK00215 LexA repressor; Valid 21.7 1.7E+02 0.0037 25.4 4.8 45 81-125 13-58 (205)
104 TIGR00498 lexA SOS regulatory 21.7 1.5E+02 0.0033 25.7 4.4 50 78-127 8-62 (199)
105 COG5114 Histone acetyltransfer 21.7 4.3E+02 0.0094 26.0 7.7 109 9-117 297-424 (432)
106 COG1510 Predicted transcriptio 21.5 1.4E+02 0.003 26.6 4.0 33 80-112 30-62 (177)
107 PF03551 PadR: Transcriptional 21.4 2E+02 0.0044 20.9 4.5 29 164-192 33-63 (75)
108 PF08461 HTH_12: Ribonuclease 21.0 96 0.0021 22.7 2.5 27 80-106 2-31 (66)
109 COG4742 Predicted transcriptio 20.8 1.9E+02 0.0042 27.2 5.1 66 79-146 16-83 (260)
110 TIGR01741 staph_tand_hypo cons 20.6 1.7E+02 0.0036 25.6 4.3 61 175-237 39-100 (157)
111 COG0064 GatB Asp-tRNAAsn/Glu-t 20.4 1.8E+02 0.0038 29.9 5.0 53 182-235 266-320 (483)
112 cd08810 CARD_BCL10 Caspase act 20.3 1.5E+02 0.0033 23.1 3.6 42 78-120 18-61 (84)
113 PRK11511 DNA-binding transcrip 20.2 1.4E+02 0.0031 24.1 3.7 33 75-107 8-41 (127)
114 PRK13777 transcriptional regul 20.1 2.6E+02 0.0057 24.7 5.6 63 134-197 41-109 (185)
No 1
>KOG3095 consensus Transcription initiation factor IIE, beta subunit [Transcription]
Probab=100.00 E-value=4.7e-64 Score=458.44 Aligned_cols=274 Identities=34% Similarity=0.536 Sum_probs=236.0
Q ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCCC-ccCCCCCCCCCccccccchhhhcccccCCChhHHHHH
Q 023374 1 MALQEKLDRFKKQQEKCQETLSNIAAKSGASRATTTSRPTPA-AASTAARSSPPVKFSNDTERLQHINSIRKSPVGAQIK 79 (283)
Q Consensus 1 ~~~~~~~~~f~~qq~~~~~tl~s~a~~~~~~~~~~~~~~~~~-~~~~~~~~~~~v~~s~~~~~~q~~nt~~~~~v~tqi~ 79 (283)
|+|-++|+.|++++++|+.++.++|.+. .++++|+..+. +++++.+..+.++++.++.+++.++.++++++|++++
T Consensus 3 ~~Ll~ql~aFkK~~~~~p~v~~~~~ps~---~~t~ss~~~~~~~~~~~~p~~~~lk~~~~s~~~~~ls~~~~~~fgt~~k 79 (284)
T KOG3095|consen 3 PALLRQLEAFKKKAASTPVVAKKSAPSR---FPTPSSRANSNKASKASKPNLPRLKKDANSSNLKSLSNSSQSHFGTHAK 79 (284)
T ss_pred HHHHHHHHHHHHHHhcCcccccCCCCCC---CCCCcchhcchhhhccCCCCCcccccccchhhHHhhcCcccccchhHHH
Confidence 6899999999999999999888844432 12333444333 3555556677788888899999999999999999999
Q ss_pred HHHHHHhccCCCCCH-HHHhhhhCCCC-CCcHHHHHhhhCCCceEEeCCeeeeecCCCCCCHHHHHHHHhhCC--CCeeh
Q 023374 80 RVIDRLLETRQAFTP-EEINRDCYVDV-NANKAVFDSLRNNPKVHYDGKRFSYKSKHDLKDKSQLLVLVRKFP--EGIAV 155 (283)
Q Consensus 80 ~vvd~Lk~~~~plt~-~eI~~~~~~di-~~~~~l~e~L~~npKI~~d~~~f~yKP~y~Ik~k~~LL~lL~k~~--~Gi~v 155 (283)
.|+.++.++..+++. ++|.|.|++|+ ..+..++|+|++||||+||++||+|||.|+|+|+++||.+|++|. +||+|
T Consensus 80 iv~~~~~~h~~~~~~PE~i~E~~~~d~~~~n~~l~esLkkNpri~~d~~~FsfKp~y~Ird~~~Ll~llr~~~~~~GI~v 159 (284)
T KOG3095|consen 80 IVIYLLTEHLRGLTHPEIIDELQHYDLKHKNWLLLESLKKNPRIEYDPRTFSFKPTYNIRDKKQLLKLLRKHDTLGGILV 159 (284)
T ss_pred HHHHHHHHHHhcCCcHHHHHHHHHHHhhhccHHHHHHHhhCCceEecCceeeccCccccCCHHHHHHHHHhcCccCceeh
Confidence 999999999999999 77799999999 777889999999999999999999999999999999999999998 69999
Q ss_pred hhHhhhhhcHHHHHHHHHHcCcEEEE-ecCCCCceeEecCCCCCCCCCCHHHHHHhhhcCCCCChhHHHHHHHHCCCCCc
Q 023374 156 IDLKDSYPTVMEDLQALKAAGQIWLL-SNFDSQEDIAYPNDPRVPIKADDDLKLLFRDIALPSDMLDIEKDLQKNGMKPA 234 (283)
Q Consensus 156 ~dLkD~~p~~~~~I~~Le~~g~Ilvl-~~kd~~~~ivf~ND~~~~~~VD~efk~lW~~v~vP~d~~Di~k~L~~~Glkp~ 234 (283)
+||+||||+|+++|++|++.|+|||+ +.+|++++||||||.+|.+.|||||+.|||+|.||.++.||++||+++||+||
T Consensus 160 ~DL~d~~pNv~~~lk~L~~s~eIl~l~t~~d~k~kivf~ND~~~~~~VDdEFk~LWr~V~Ip~~~~dle~eL~k~GLkp~ 239 (284)
T KOG3095|consen 160 SDLKDAWPNVDEDLKELEKSGEILVLRTPKDDKPKIVFYNDKSCSFSVDDEFKKLWRSVTIPSMELDLEEELQKQGLKPM 239 (284)
T ss_pred HHhhhcccchHHHHHHHhcCCcEEEEeccCCCCCceEEecCCCCCcccCHHHHHHHHhCCCChHHHHHHHHHHHhCCCcc
Confidence 99999999999999999999999988 55689999999999999999999999999999999878999999999999999
Q ss_pred cchhhhHHHHHhhcccCCCCcccccccccCCCcccCCchHHHHhhhcC
Q 023374 235 TNTQKRRAAAQIQGISSKNKPKKKKHEISKRTKLTNAHLPELFQKLNG 282 (283)
Q Consensus 235 ~~~~~r~~~~~~~~~~~k~k~kkKKr~~~rr~K~TNtHm~~llkd~s~ 282 (283)
++.++++++.+ ..++-++|||++++|++|+|||||. ++.||+.
T Consensus 240 ~~v~p~~~~~~----~~~k~~~Kkk~~~~r~~kitnthl~-~l~d~~~ 282 (284)
T KOG3095|consen 240 KDVDPKKAAPQ----QRKKDKKKKKFKKTRRNKITNTHLK-ILEDYSS 282 (284)
T ss_pred cccchHHhhhh----hhhhhhhhhhhcccccchhhhhHHH-HHHhhcc
Confidence 97666665531 1111123455677789999999999 7788864
No 2
>COG5174 TFA2 Transcription initiation factor IIE, beta subunit [Transcription]
Probab=100.00 E-value=2.5e-53 Score=378.58 Aligned_cols=213 Identities=21% Similarity=0.393 Sum_probs=194.0
Q ss_pred ccchhhhcccccCCChhHHHHHHHHHHHhccCCCCCHHHHhhhhCCCCCCcHHHHHhhhCCCceEEeC--CeeeeecCCC
Q 023374 58 NDTERLQHINSIRKSPVGAQIKRVIDRLLETRQAFTPEEINRDCYVDVNANKAVFDSLRNNPKVHYDG--KRFSYKSKHD 135 (283)
Q Consensus 58 ~~~~~~q~~nt~~~~~v~tqi~~vvd~Lk~~~~plt~~eI~~~~~~di~~~~~l~e~L~~npKI~~d~--~~f~yKP~y~ 135 (283)
.|-.+.|++++|.++|-.+++|++++||+++++|++|+||.+++.+|++. .+++.|+.+.+|.||+ +||.|+|.|+
T Consensus 65 ~~~~~~q~~d~gv~~H~~s~lh~aieylk~~~~P~~~eEi~dyls~~l~~--~~v~Llkk~~ri~~d~~~~Tf~fkply~ 142 (285)
T COG5174 65 MDRDRIQSIDRGVQRHTNSYLHAAIEYLKQHDRPLSFEEIKDYLSIDLHN--NYVLLLKKKRRIRIDATHSTFMFKPLYS 142 (285)
T ss_pred hhHhhhccccccccccchHHHHHHHHHHHHcCCcccHHHHHHHhcCccch--hHHHHHhhccCceeccCCceEEeecccc
Confidence 34445599999999999999999999999999999999999988888876 7889999999999997 4999999999
Q ss_pred CCCHHHHHHHHhhCC--CCeehhhHhhhhhcHHHHHHHHHHcCcEEEEe-cCCCCceeEecCCCCCCCCCCHHHHHHhhh
Q 023374 136 LKDKSQLLVLVRKFP--EGIAVIDLKDSYPTVMEDLQALKAAGQIWLLS-NFDSQEDIAYPNDPRVPIKADDDLKLLFRD 212 (283)
Q Consensus 136 Ik~k~~LL~lL~k~~--~Gi~v~dLkD~~p~~~~~I~~Le~~g~Ilvl~-~kd~~~~ivf~ND~~~~~~VD~efk~lW~~ 212 (283)
|++.++||.+|+.+. .||++++|+||||+|...|++||+.++|+|++ .+||.+++||+|+..|.++||+||+.||+.
T Consensus 143 irS~~~llk~lrsq~t~~Gls~k~L~Dgwpnv~~~veeLek~~eIliLrt~kDg~p~~vW~n~~n~~c~vD~ef~~~W~~ 222 (285)
T COG5174 143 IRSVEDLLKVLRSQGTEEGLSMKKLMDGWPNVVPFVEELEKSNEILILRTDKDGSPVVVWNNTQNLECPVDPEFKSLWNQ 222 (285)
T ss_pred ccCHHHHHHHHHhhcccccccHHHhhcCCCcccHHHHHHhhcCcEEEEeecCCCCceEEEeCCCCcCCCCCHHHHHHHHh
Confidence 999999999999986 89999999999999999999999999999996 789999999999999999999999999999
Q ss_pred cCCCCChhHHHHHHHHCCCCCccchhhhHHHHHhhcccCCCCcc-cccccccCCCcccCCchHHHHhhhcC
Q 023374 213 IALPSDMLDIEKDLQKNGMKPATNTQKRRAAAQIQGISSKNKPK-KKKHEISKRTKLTNAHLPELFQKLNG 282 (283)
Q Consensus 213 v~vP~d~~Di~k~L~~~Glkp~~~~~~r~~~~~~~~~~~k~k~k-kKKr~~~rr~K~TNtHm~~llkd~s~ 282 (283)
|.||. ..||.++|..+||+|++.++. ..+++..+ |+||+++|++|||||||.|||.|||+
T Consensus 223 V~ip~-~~dL~reL~~~GLKptsvdp~---------t~KR~t~~ik~kk~~~RkgkITNTH~~gil~dys~ 283 (285)
T COG5174 223 VRIPT-YHDLIRELNTAGLKPTSVDPN---------TKKRPTIKIKKKKRSRRKGKITNTHVKGILLDYSQ 283 (285)
T ss_pred CCCch-HHHHHHHHHhcCCCccccCcc---------hhccccccccccccccccccccchhhhhhhccccc
Confidence 99997 899999999999999998873 12223222 56677789999999999999999986
No 3
>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=99.68 E-value=3.1e-17 Score=121.94 Aligned_cols=63 Identities=30% Similarity=0.458 Sum_probs=49.3
Q ss_pred ChhHHHHHHHHHHHhccCCCCCHHHHhhhhCCCCCCcHHHHHhhhCCCceEEeC--CeeeeecCCCC
Q 023374 72 SPVGAQIKRVIDRLLETRQAFTPEEINRDCYVDVNANKAVFDSLRNNPKVHYDG--KRFSYKSKHDL 136 (283)
Q Consensus 72 ~~v~tqi~~vvd~Lk~~~~plt~~eI~~~~~~di~~~~~l~e~L~~npKI~~d~--~~f~yKP~y~I 136 (283)
++.++||++||+|||++++|+|++||+++|++|++ +.+++.|++||||+||+ ++|+|||+|+|
T Consensus 1 ~~~~tql~~~VeymK~r~~Plt~~eI~d~l~~d~~--~~~~~~Lk~npKI~~d~~~~~f~fkp~ynI 65 (65)
T PF02186_consen 1 SHKFTQLAKAVEYMKKRDHPLTLEEILDYLSLDIG--KKLKQWLKNNPKIEYDPDGNTFSFKPKYNI 65 (65)
T ss_dssp -TTHHHHHHHHHHHHHH-S-B-HHHHHHHHTSSS---HHHHHHHHH-TTEEEE-TT-CEEE--TTT-
T ss_pred CchhhHHHHHHHHHHhcCCCcCHHHHHHHHcCCCC--HHHHHHHHcCCCEEEecCCCEEEeccCCCC
Confidence 35789999999999999999999999999998885 58999999999999994 49999999997
No 4
>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=99.60 E-value=1.2e-15 Score=116.51 Aligned_cols=70 Identities=23% Similarity=0.370 Sum_probs=59.9
Q ss_pred ccCCChhHHHHHHHHHHHhccC-CCCCHHHHhhhhC-CCCCCcH-HHH--HhhhCCCceEEeCCeeeeecCCCCC
Q 023374 68 SIRKSPVGAQIKRVIDRLLETR-QAFTPEEINRDCY-VDVNANK-AVF--DSLRNNPKVHYDGKRFSYKSKHDLK 137 (283)
Q Consensus 68 t~~~~~v~tqi~~vvd~Lk~~~-~plt~~eI~~~~~-~di~~~~-~l~--e~L~~npKI~~d~~~f~yKP~y~Ik 137 (283)
+|+|.++.+||++||+|||++. .|+|++||+++|+ +|+.... +|+ +++.+||++....|+|+|||+|+||
T Consensus 1 tg~g~~~~t~l~~aV~ymK~r~~~Plt~~EIl~~ls~~d~~~~~~~~L~~~~~~~n~~~~~~~~tf~fkP~y~Ir 75 (75)
T cd07977 1 TGSGTHVFTQLAKIVDYMKKRHQHPLTLDEILDYLSLLDIGPKLKEWLKSEALVNNPKIDPKDGTFSFKPKYNIR 75 (75)
T ss_pred CCCCcchhhhHHHHHHHHHhcCCCCccHHHHHHHHhccCccHHHHHHHHhhhhccCceeccCCCEEEeccCCCCC
Confidence 5889999999999999999999 9999999999999 9988653 344 3566666666667899999999996
No 5
>PHA02943 hypothetical protein; Provisional
Probab=93.22 E-value=0.11 Score=45.05 Aligned_cols=72 Identities=13% Similarity=0.046 Sum_probs=56.0
Q ss_pred CHHHHHHHHhhCCCCeehhhHhh----hhhcHHHHHHHHHHcCcEEEEecCCCCceeEecCCCCCCCCCCHHHHHHhhhc
Q 023374 138 DKSQLLVLVRKFPEGIAVIDLKD----SYPTVMEDLQALKAAGQIWLLSNFDSQEDIAYPNDPRVPIKADDDLKLLFRDI 213 (283)
Q Consensus 138 ~k~~LL~lL~k~~~Gi~v~dLkD----~~p~~~~~I~~Le~~g~Ilvl~~kd~~~~ivf~ND~~~~~~VD~efk~lW~~v 213 (283)
-+++.|++| ..|+.+..++.+ ||-.+.-.|.-||.+|.|.-++. |...+.+.||..+..-|++=|+++|+=|
T Consensus 12 R~~eILE~L--k~G~~TtseIAkaLGlS~~qa~~~LyvLErEG~VkrV~~--G~~tyw~l~~day~~~v~~~~Relwrlv 87 (165)
T PHA02943 12 RMIKTLRLL--ADGCKTTSRIANKLGVSHSMARNALYQLAKEGMVLKVEI--GRAAIWCLDEDAYTNLVFEIKRELWRLV 87 (165)
T ss_pred HHHHHHHHH--hcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCceEEEee--cceEEEEEChHHHHHHHHHHHHHHHHHH
Confidence 367889999 556666665544 68889999999999999988763 6666666677666667999999999865
No 6
>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=89.94 E-value=0.64 Score=36.61 Aligned_cols=43 Identities=21% Similarity=0.405 Sum_probs=35.7
Q ss_pred HHHHHHHHhhC---CCCeehhhHhhhh----hcHHHHHHHHHHcCcEEEE
Q 023374 139 KSQLLVLVRKF---PEGIAVIDLKDSY----PTVMEDLQALKAAGQIWLL 181 (283)
Q Consensus 139 k~~LL~lL~k~---~~Gi~v~dLkD~~----p~~~~~I~~Le~~g~Ilvl 181 (283)
.+.+|++|+.. ..||.|++|.... ..+.++|+.|..+|.||-.
T Consensus 49 ~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT 98 (102)
T PF08784_consen 49 QDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSNEGHIYST 98 (102)
T ss_dssp HHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTTSEEES
T ss_pred HHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhCCeEecc
Confidence 57789999983 3899999999887 3478999999999999864
No 7
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=87.48 E-value=3.2 Score=35.74 Aligned_cols=90 Identities=17% Similarity=0.332 Sum_probs=62.6
Q ss_pred HHHHHHHhccCCCCCHHHHhhhhCCCCCCc--HHHHHhhhCCCceEEe--CCeeeeec---CCCCCCHHHHHHHHhhCCC
Q 023374 79 KRVIDRLLETRQAFTPEEINRDCYVDVNAN--KAVFDSLRNNPKVHYD--GKRFSYKS---KHDLKDKSQLLVLVRKFPE 151 (283)
Q Consensus 79 ~~vvd~Lk~~~~plt~~eI~~~~~~di~~~--~~l~e~L~~npKI~~d--~~~f~yKP---~y~Ik~k~~LL~lL~k~~~ 151 (283)
..|++||++.+.|++..||...++-.++.. ...++.|...-+|..- |..-.|-+ .+.+-+.++|-.+=..
T Consensus 4 ~~Il~y~~~qNRPys~~di~~nL~~~~~K~~v~k~Ld~L~~~g~i~~K~~GKqkiY~~~Q~~~~~~s~eel~~ld~e--- 80 (169)
T PF07106_consen 4 DAILEYMKEQNRPYSAQDIFDNLHNKVGKTAVQKALDSLVEEGKIVEKEYGKQKIYFANQDELEVPSPEELAELDAE--- 80 (169)
T ss_pred HHHHHHHHHcCCCCcHHHHHHHHHhhccHHHHHHHHHHHHhCCCeeeeeecceEEEeeCccccCCCCchhHHHHHHH---
Confidence 468999999999999999988776555543 4688999999999984 44433433 3455567765544322
Q ss_pred CeehhhHhhhhhcHHHHHHHHHH
Q 023374 152 GIAVIDLKDSYPTVMEDLQALKA 174 (283)
Q Consensus 152 Gi~v~dLkD~~p~~~~~I~~Le~ 174 (283)
+.+|++-.......+..|++
T Consensus 81 ---i~~L~~el~~l~~~~k~l~~ 100 (169)
T PF07106_consen 81 ---IKELREELAELKKEVKSLEA 100 (169)
T ss_pred ---HHHHHHHHHHHHHHHHHHHH
Confidence 56666666666666666643
No 8
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=86.99 E-value=0.38 Score=35.50 Aligned_cols=46 Identities=13% Similarity=0.244 Sum_probs=40.0
Q ss_pred HHHHHHhccCCCCCHHHHhhhhCCCCCCcHHHHHhhhCCCceEEeC
Q 023374 80 RVIDRLLETRQAFTPEEINRDCYVDVNANKAVFDSLRNNPKVHYDG 125 (283)
Q Consensus 80 ~vvd~Lk~~~~plt~~eI~~~~~~di~~~~~l~e~L~~npKI~~d~ 125 (283)
.|++||++.+.|++-.||.+.|++++..-..+++.|..--+|+-.+
T Consensus 4 ~Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~~~~ 49 (62)
T PF04703_consen 4 KILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLEKEGKVERSP 49 (62)
T ss_dssp CHHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEES
T ss_pred HHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEec
Confidence 4899999999999999999999999998888999999999998754
No 9
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=84.24 E-value=3.2 Score=30.59 Aligned_cols=53 Identities=11% Similarity=0.152 Sum_probs=40.7
Q ss_pred HHHHHHHHhhCCCCeehhhHhhhhh----cHHHHHHHHHHcCcEEEEecCCCCceeEe
Q 023374 139 KSQLLVLVRKFPEGIAVIDLKDSYP----TVMEDLQALKAAGQIWLLSNFDSQEDIAY 192 (283)
Q Consensus 139 k~~LL~lL~k~~~Gi~v~dLkD~~p----~~~~~I~~Le~~g~Ilvl~~kd~~~~ivf 192 (283)
|+++|++|+.+.++++-.|+.|+.- .+-..|..|+.+|.|--....-|.. .+|
T Consensus 2 ke~Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~~~~~~rG~~-~~W 58 (62)
T PF04703_consen 2 KEKILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLEKEGKVERSPVRRGKS-TYW 58 (62)
T ss_dssp HHCHHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEES-SSSSS--EE
T ss_pred cHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCCCCcc-eee
Confidence 6789999999999999999999765 4678899999999997775444554 455
No 10
>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=84.19 E-value=0.75 Score=31.91 Aligned_cols=49 Identities=20% Similarity=0.248 Sum_probs=39.6
Q ss_pred HHHHHHHHHhccCCCCCHHHHhhhhCCCCCCcHHHHHhhhCCCceEEeC
Q 023374 77 QIKRVIDRLLETRQAFTPEEINRDCYVDVNANKAVFDSLRNNPKVHYDG 125 (283)
Q Consensus 77 qi~~vvd~Lk~~~~plt~~eI~~~~~~di~~~~~l~e~L~~npKI~~d~ 125 (283)
....|+++|.....++++.||.+.++++-+.-..++..|...--|+.||
T Consensus 4 ral~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~~g~v~~dp 52 (52)
T PF09339_consen 4 RALRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVEEGYVERDP 52 (52)
T ss_dssp HHHHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEECS
T ss_pred HHHHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCcCeecCc
Confidence 3467899999999999999999999998887777888887776666554
No 11
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=82.27 E-value=3.5 Score=34.65 Aligned_cols=83 Identities=18% Similarity=0.258 Sum_probs=56.5
Q ss_pred HHHHHhccCCCCCHHHHhhhhCCCCCCcHHHHHhh-----hCCCceEEeCC--eeeeecCCCCCCHHHHHHHHhhCCCCe
Q 023374 81 VIDRLLETRQAFTPEEINRDCYVDVNANKAVFDSL-----RNNPKVHYDGK--RFSYKSKHDLKDKSQLLVLVRKFPEGI 153 (283)
Q Consensus 81 vvd~Lk~~~~plt~~eI~~~~~~di~~~~~l~e~L-----~~npKI~~d~~--~f~yKP~y~Ik~k~~LL~lL~k~~~Gi 153 (283)
|.-.|.+.+.|+|.+||.+.++.+-+.-..-+..| ..-.++.+++| .|.|+|.. .+++-..+
T Consensus 32 v~~~LL~~~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek~~~~~Ggy~yiY~~i~----~ee~k~~i------- 100 (126)
T COG3355 32 VYKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVEREKVNLKGGGYYYLYKPID----PEEIKKKI------- 100 (126)
T ss_pred HHHHHHhhcCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeeeeeeccCCCceeEEEecCC----HHHHHHHH-------
Confidence 34445558899999999998988887655433333 23455556666 67777755 66665444
Q ss_pred ehhhHhhhhhcHHHHHHHHHHc
Q 023374 154 AVIDLKDSYPTVMEDLQALKAA 175 (283)
Q Consensus 154 ~v~dLkD~~p~~~~~I~~Le~~ 175 (283)
.++|.+.|-.+...|++.+..
T Consensus 101 -~~~l~~w~~~~~~~i~~~~~~ 121 (126)
T COG3355 101 -LKDLDEWYDKMKQLIEEFEKK 121 (126)
T ss_pred -HHHHHHHHHHHHHHHHHHhcc
Confidence 457888888888888887543
No 12
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=82.25 E-value=6.6 Score=33.76 Aligned_cols=96 Identities=19% Similarity=0.325 Sum_probs=61.3
Q ss_pred HHHHHHHHhhCCCCeehhhHhhhhhc------HHHHHHHHHHcCcEEEEecCCCCceeEecCCCCCCCC-------CCHH
Q 023374 139 KSQLLVLVRKFPEGIAVIDLKDSYPT------VMEDLQALKAAGQIWLLSNFDSQEDIAYPNDPRVPIK-------ADDD 205 (283)
Q Consensus 139 k~~LL~lL~k~~~Gi~v~dLkD~~p~------~~~~I~~Le~~g~Ilvl~~kd~~~~ivf~ND~~~~~~-------VD~e 205 (283)
.+.+|.||+++..-.++-||-+..-+ |...|+.|.++|+|.+-.- |+-+|.|+|...+... +|.+
T Consensus 3 e~~Il~y~~~qNRPys~~di~~nL~~~~~K~~v~k~Ld~L~~~g~i~~K~~--GKqkiY~~~Q~~~~~~s~eel~~ld~e 80 (169)
T PF07106_consen 3 EDAILEYMKEQNRPYSAQDIFDNLHNKVGKTAVQKALDSLVEEGKIVEKEY--GKQKIYFANQDELEVPSPEELAELDAE 80 (169)
T ss_pred HHHHHHHHHHcCCCCcHHHHHHHHHhhccHHHHHHHHHHHHhCCCeeeeee--cceEEEeeCccccCCCCchhHHHHHHH
Confidence 35789999998877777777776644 6889999999999988753 7778999997665432 3334
Q ss_pred HHHHhhhcC-CCCChhHHHHHHHHCCCCCccc
Q 023374 206 LKLLFRDIA-LPSDMLDIEKDLQKNGMKPATN 236 (283)
Q Consensus 206 fk~lW~~v~-vP~d~~Di~k~L~~~Glkp~~~ 236 (283)
+..|=..+. +-.+...+..+|....-.|+.+
T Consensus 81 i~~L~~el~~l~~~~k~l~~eL~~L~~~~t~~ 112 (169)
T PF07106_consen 81 IKELREELAELKKEVKSLEAELASLSSEPTNE 112 (169)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcCCCHH
Confidence 333332221 1112223555555555555543
No 13
>PF05158 RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; InterPro: IPR007832 The family comprises a subunit specific to RNA Pol III, the tRNA specific polymerase. The C34 subunit of Saccharomyces cerevisiae RNA Pol III is part of a subcomplex of three subunits which have no counterpart in the other two nuclear RNA polymerases. This subunit interacts with TFIIIB70 and therefore participates in Pol III recruitment [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2DK8_A 2DK5_A 2YU3_A.
Probab=79.26 E-value=14 Score=35.68 Aligned_cols=140 Identities=17% Similarity=0.256 Sum_probs=73.9
Q ss_pred hHHHHHHHHHHHhcc--CCCCCHHHHhhh-hCCCCCCcHHHHHhhhCCCceEE--eCCeeeeecC-------C-CCCCHH
Q 023374 74 VGAQIKRVIDRLLET--RQAFTPEEINRD-CYVDVNANKAVFDSLRNNPKVHY--DGKRFSYKSK-------H-DLKDKS 140 (283)
Q Consensus 74 v~tqi~~vvd~Lk~~--~~plt~~eI~~~-~~~di~~~~~l~e~L~~npKI~~--d~~~f~yKP~-------y-~Ik~k~ 140 (283)
+...-.++++.+++. ...+|.+||.+. .+.|+..--.++..|-+.-+|.. .++...|+.. + ++.+-+
T Consensus 7 ~~~~~~~l~~~~~~~~~~~~~~~~~L~~~~~~~~~~~~~~~in~Ll~~~~~~~~~~~~~l~~~~~~~~~a~k~~~l~~~e 86 (327)
T PF05158_consen 7 LSELEKKLLELCRENPSPKGFSQEDLQQLIPGLDLQELVKAINELLSSGLLKLLKKGGGLSYKAVSEEEAKKLKGLSDEE 86 (327)
T ss_dssp HHHHHHHHHHHHHH---SS-EEHHHHHHH-TTS-HHHHHHHHHHHHHHTSEEEEE-SSSEEEEE--SSS-----SSSCCH
T ss_pred HHHHHHHHHHHHHHhcCCCCcCHHHHHhhcCCCCHHHHHHHHHHHHhCCCEEEEEcCCEEEEEEeCHHHHhhhcCCCHHH
Confidence 344456788888887 889999999876 34555443456677777777776 3455666643 2 333333
Q ss_pred -HHHHHHhhC-CCCeehhhHhhhhh----cHHHHHHHHHHcCcEEEEecCCCCce---eEecCCCCCC---------CCC
Q 023374 141 -QLLVLVRKF-PEGIAVIDLKDSYP----TVMEDLQALKAAGQIWLLSNFDSQED---IAYPNDPRVP---------IKA 202 (283)
Q Consensus 141 -~LL~lL~k~-~~Gi~v~dLkD~~p----~~~~~I~~Le~~g~Ilvl~~kd~~~~---ivf~ND~~~~---------~~V 202 (283)
-++.+++.- ..||-.+||+..-. .+...|+.||..+-|=-+++-....| |+|--.|+-. -.+
T Consensus 87 ~lvy~~I~~ag~~GIw~~~i~~~t~l~~~~~~k~lk~Le~k~lIK~vksv~~~~rK~Yml~~l~Ps~eiTGG~wy~d~e~ 166 (327)
T PF05158_consen 87 RLVYQLIEEAGNKGIWTKDIKKKTNLHQTQLTKILKSLESKKLIKSVKSVKNPNRKVYMLYDLEPSEEITGGPWYTDGEF 166 (327)
T ss_dssp HHHHHHHHHHTTT-EEHHHHHHHCT--HHHHHHHHHHHHHTTSEEEE--SS-SS--EEEESSS-----------------
T ss_pred HHHHHHHHHhCCCCCcHHHHHHHcCCCHHHHHHHHHHHHhCCCEEEecCcCCCCeEEEEEccCCcCcccCCCCcccCCcc
Confidence 456677654 49999999988653 46888999999998887765322222 4444455432 368
Q ss_pred CHHHHHHhhhc
Q 023374 203 DDDLKLLFRDI 213 (283)
Q Consensus 203 D~efk~lW~~v 213 (283)
|.||.+-++.+
T Consensus 167 D~efi~~l~~~ 177 (327)
T PF05158_consen 167 DTEFIDVLREQ 177 (327)
T ss_dssp -----------
T ss_pred cHHHHHHHHHH
Confidence 99998887764
No 14
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=74.45 E-value=4.8 Score=29.64 Aligned_cols=47 Identities=17% Similarity=0.231 Sum_probs=40.8
Q ss_pred HHHHHHHhccCC-CCCHHHHhhhhCCCCCCcHHHHHhhhCCCceEEeC
Q 023374 79 KRVIDRLLETRQ-AFTPEEINRDCYVDVNANKAVFDSLRNNPKVHYDG 125 (283)
Q Consensus 79 ~~vvd~Lk~~~~-plt~~eI~~~~~~di~~~~~l~e~L~~npKI~~d~ 125 (283)
..|+++|+..+. +++..||.+.++++-..-..++..|...-.|..++
T Consensus 9 ~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~~~ 56 (68)
T smart00550 9 EKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCKQG 56 (68)
T ss_pred HHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence 478999999877 49999999999999887678889999999999864
No 15
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=74.34 E-value=6.6 Score=29.45 Aligned_cols=49 Identities=18% Similarity=0.205 Sum_probs=40.6
Q ss_pred HHHHHHHHHhccCCCCCHHHHhhhhCCCCCCcHHHHHhhhCCCceEEeC
Q 023374 77 QIKRVIDRLLETRQAFTPEEINRDCYVDVNANKAVFDSLRNNPKVHYDG 125 (283)
Q Consensus 77 qi~~vvd~Lk~~~~plt~~eI~~~~~~di~~~~~l~e~L~~npKI~~d~ 125 (283)
....|+++|.+...++++.||.+.++++...-...+..|..+--|..++
T Consensus 6 r~~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~~~ 54 (91)
T smart00346 6 RGLAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQDG 54 (91)
T ss_pred HHHHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeeecC
Confidence 4567899998876799999999999888777678888898888887764
No 16
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=71.33 E-value=8.3 Score=34.91 Aligned_cols=55 Identities=20% Similarity=0.139 Sum_probs=45.6
Q ss_pred HHHHHHHHHHHhccCCCCCHHHHhhhhCCCCCCcHHHHHhhhCCCceEEeCCeee
Q 023374 75 GAQIKRVIDRLLETRQAFTPEEINRDCYVDVNANKAVFDSLRNNPKVHYDGKRFS 129 (283)
Q Consensus 75 ~tqi~~vvd~Lk~~~~plt~~eI~~~~~~di~~~~~l~e~L~~npKI~~d~~~f~ 129 (283)
......|+++|-..+.|+++.||.+.+++.-+.-..++..|...-=|+.++++|.
T Consensus 8 l~ral~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~~~G~l~~~~~~Y~ 62 (248)
T TIGR02431 8 LARGLAVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLVELGYVTSDGRLFW 62 (248)
T ss_pred HHHHHHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeCCCEEE
Confidence 3455678888888889999999999999998888889999988888888766543
No 17
>TIGR03820 lys_2_3_AblA lysine-2,3-aminomutase. This model describes lysine-2,3-aminomutase as found along with beta-lysine acetyltransferase in a two-enzyme pathway for making the compatible solute N-epsilon-acetyl-beta-lysine. This compatible solute, or osmolyte, is known to protect a number of methanogenic archaea against salt stress. The trusted cutoff distinguishes a tight clade with essentially full-length homology from additional homologs that are shorter or highly diverged in the C-terminal region. All members of this family have the radical SAM motif CXXXCXXC, while some but not all have a second copy of the motif in the C-terminal region.
Probab=67.47 E-value=17 Score=36.33 Aligned_cols=94 Identities=15% Similarity=0.120 Sum_probs=62.3
Q ss_pred hHHHHHHHHHHHhcc----------CCCCCHHH-HhhhhCCCCCCcHHHHHhhhCCCceEEe---CCeeeeecCCCCCCH
Q 023374 74 VGAQIKRVIDRLLET----------RQAFTPEE-INRDCYVDVNANKAVFDSLRNNPKVHYD---GKRFSYKSKHDLKDK 139 (283)
Q Consensus 74 v~tqi~~vvd~Lk~~----------~~plt~~e-I~~~~~~di~~~~~l~e~L~~npKI~~d---~~~f~yKP~y~Ik~k 139 (283)
-..++..+++||+.+ +.||.+.+ +++ .+++.|+..|.|+.. ...-.+-| +-|.
T Consensus 139 s~eei~~~i~yI~~~p~I~~VlLSGGDPLll~d~~L~----------~iL~~L~~IphV~~IRI~TR~pvv~P-~RIT-- 205 (417)
T TIGR03820 139 SKEQILEGIEYIRNTPQIRDVLLSGGDPLLLSDDYLD----------WILTELRAIPHVEVIRIGTRVPVVLP-QRIT-- 205 (417)
T ss_pred CHHHHHHHHHHHHhcCCCCEEEEeCCccccCChHHHH----------HHHHHHhhcCCCceEEEeeccccccc-cccC--
Confidence 356888999999875 34554433 222 356777777777632 23333333 2343
Q ss_pred HHHHHHHhhCC---CCeehhhHhhhhhcHHHHHHHHHHcCcEEE
Q 023374 140 SQLLVLVRKFP---EGIAVIDLKDSYPTVMEDLQALKAAGQIWL 180 (283)
Q Consensus 140 ~~LL~lL~k~~---~Gi~v~dLkD~~p~~~~~I~~Le~~g~Ilv 180 (283)
++|++.|+++. =++.+.--.|-.+.+.++|+.|.+.|-.+.
T Consensus 206 ~ell~~Lk~~~~~~v~~h~nhp~Eit~~a~~Al~~L~~aGI~l~ 249 (417)
T TIGR03820 206 DELVAILKKHHPVWLNTHFNHPREITASSKKALAKLADAGIPLG 249 (417)
T ss_pred HHHHHHHHhcCCeEEEEeCCChHhChHHHHHHHHHHHHcCCEEE
Confidence 59999998875 355666566779999999999999994433
No 18
>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; InterPro: IPR024259 Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.
Probab=66.65 E-value=6.9 Score=30.23 Aligned_cols=45 Identities=29% Similarity=0.323 Sum_probs=30.9
Q ss_pred HHHHHHHHhccCCCCCHHHHhhhhCCCCCCcHHHHHhhhCCCceEEeC
Q 023374 78 IKRVIDRLLETRQAFTPEEINRDCYVDVNANKAVFDSLRNNPKVHYDG 125 (283)
Q Consensus 78 i~~vvd~Lk~~~~plt~~eI~~~~~~di~~~~~l~e~L~~npKI~~d~ 125 (283)
|.+.+-.+...++|+|.++|..+++.++. ++..+|..-|-++||+
T Consensus 25 L~r~LLr~LA~G~PVt~~~LA~a~g~~~e---~v~~~L~~~p~tEyD~ 69 (77)
T PF12324_consen 25 LLRPLLRLLAKGQPVTVEQLAAALGWPVE---EVRAALAAMPDTEYDD 69 (77)
T ss_dssp HHHHHHHHHTTTS-B-HHHHHHHHT--HH---HHHHHHHH-TTSEEET
T ss_pred HHHHHHHHHHcCCCcCHHHHHHHHCCCHH---HHHHHHHhCCCceEcC
Confidence 44444444455999999999999998775 5778888889999985
No 19
>PF04157 EAP30: EAP30/Vps36 family; InterPro: IPR007286 EAP30 is a subunit of the ELL complex. The ELL is an 80kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity. ; PDB: 2ZME_A 3CUQ_A 1W7P_D 1U5T_B.
Probab=66.42 E-value=23 Score=31.92 Aligned_cols=160 Identities=16% Similarity=0.242 Sum_probs=91.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCC-------------CCCCCccCCCCCCCCCccccccchhhhcccccCC
Q 023374 5 EKLDRFKKQQEKCQETLSNIAAKSGASRATTTS-------------RPTPAAASTAARSSPPVKFSNDTERLQHINSIRK 71 (283)
Q Consensus 5 ~~~~~f~~qq~~~~~tl~s~a~~~~~~~~~~~~-------------~~~~~~~~~~~~~~~~v~~s~~~~~~q~~nt~~~ 71 (283)
+.|+.+..|-..|++.+...|.+..+....-|. ..|++.+. .+| +.. ++-+
T Consensus 26 ~dl~~L~~qa~~~~~~l~~fa~k~~~~i~~~~~~r~~f~~~~~~lGvdp~~s~~---------~~s------~~l-~~~~ 89 (223)
T PF04157_consen 26 QDLEALMSQAKDFVELLENFARKHKSEIKSDPEFRSQFQSMCASLGVDPLASSK---------FWS------ESL-KGSG 89 (223)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCSHHHHHHHHHHHHHHT--CHCCTT---------CCC------CCC-SCHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhccccCCchHHHHHHHHHHHcCCCcccchh---------hhh------hcc-ccch
Confidence 478889999999999999999887643322111 01111111 233 111 0111
Q ss_pred ---ChhHHHHHHHHHHHhc-cCCCCCHHHHhhhh-----CCCCCCcHHHHHh------hhCCCce-EEeCC-eeeeecC-
Q 023374 72 ---SPVGAQIKRVIDRLLE-TRQAFTPEEINRDC-----YVDVNANKAVFDS------LRNNPKV-HYDGK-RFSYKSK- 133 (283)
Q Consensus 72 ---~~v~tqi~~vvd~Lk~-~~~plt~~eI~~~~-----~~di~~~~~l~e~------L~~npKI-~~d~~-~f~yKP~- 133 (283)
..++.||..+..-.+. ++.-+++.|+.... +.++-...+++.+ |-..=+| .|..+ +|.--+.
T Consensus 90 ~f~~ELa~qi~e~c~~~~~~~GGii~L~dl~~~~nr~R~g~~lISp~Di~~A~~~l~~lg~g~~l~~~~sg~~vv~s~~~ 169 (223)
T PF04157_consen 90 DFYYELAVQIAEVCLATRSKNGGIISLSDLYCRYNRARGGSELISPEDILRACKLLEVLGLGFRLRKFGSGVKVVQSVPY 169 (223)
T ss_dssp HHHHHHHHHHHHHHHHHCCTTTSEEEHHHHHHHHHHCTTTSST--HHHHHHHHHHHCCCTSSEEEEEETTTEEEEECST-
T ss_pred hHHHHHHHHHHHHHHHHHhcCCCEEEHHHHHHHHHHhcccCCCcCHHHHHHHHHHHHHcCCCeEEEEeCCCcEEEEeCCc
Confidence 1255555555333333 34568999986544 3333333444433 3223222 23435 4544445
Q ss_pred CCC-CCHHHHHHHH-hhCCCCeehhhHhh--hhhc--HHHHHHHHHHcCcEEE
Q 023374 134 HDL-KDKSQLLVLV-RKFPEGIAVIDLKD--SYPT--VMEDLQALKAAGQIWL 180 (283)
Q Consensus 134 y~I-k~k~~LL~lL-~k~~~Gi~v~dLkD--~~p~--~~~~I~~Le~~g~Ilv 180 (283)
... .+...+|+++ ....+|+++.+|.+ +|+- |.+.|+.|+.+|-+|+
T Consensus 170 ~e~~~~~~~il~~~~~~~~g~vt~~~l~~~~~ws~~~a~~~L~~~~~~G~l~~ 222 (223)
T PF04157_consen 170 SELSKDQSRILELAEEENGGGVTASELAEKLGWSVERAKEALEELEREGLLWR 222 (223)
T ss_dssp CHH-HHHHHHHHHH--TTTSEEEHHHHHHHHTB-HHHHHHHHHHHHHTTSEEE
T ss_pred hhhhHHHHHHHHHHHhhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCEee
Confidence 344 7778899999 56669999999976 5665 6889999999999986
No 20
>PRK06474 hypothetical protein; Provisional
Probab=62.69 E-value=31 Score=30.15 Aligned_cols=62 Identities=15% Similarity=0.250 Sum_probs=46.2
Q ss_pred HHHHHHHHhhCCCCeehhhHhhhhhc-----HHHHHHHHHHcCcEEEEecC---CCCceeEecCCCCCCC
Q 023374 139 KSQLLVLVRKFPEGIAVIDLKDSYPT-----VMEDLQALKAAGQIWLLSNF---DSQEDIAYPNDPRVPI 200 (283)
Q Consensus 139 k~~LL~lL~k~~~Gi~v~dLkD~~p~-----~~~~I~~Le~~g~Ilvl~~k---d~~~~ivf~ND~~~~~ 200 (283)
+..+|.+|..+.+++++.+|-+...+ +-..|+.|++.|-|.++... ++.+++...|...+.+
T Consensus 13 R~~Il~~L~~~~~~~ta~el~~~l~~is~aTvYrhL~~L~e~GLI~~~~~~~~~~~~ek~y~~~~~~~~~ 82 (178)
T PRK06474 13 RMKICQVLMRNKEGLTPLELVKILKDVPQATLYRHLQTMVDSGILHVVKEKKVRSVSEKYYAINEEDAKI 82 (178)
T ss_pred HHHHHHHHHhCCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEEeecccccCceeEEEEeccceeee
Confidence 45678888877666999998876643 45689999999999998542 4566677777776654
No 21
>COG1803 MgsA Methylglyoxal synthase [Carbohydrate transport and metabolism]
Probab=62.41 E-value=10 Score=32.23 Aligned_cols=52 Identities=31% Similarity=0.328 Sum_probs=45.7
Q ss_pred CeehhhHhhhhhcHHHHHHHHHHcCcEEEEecCCCCceeEecCCCCCCCCCCHHHHHHhhh
Q 023374 152 GIAVIDLKDSYPTVMEDLQALKAAGQIWLLSNFDSQEDIAYPNDPRVPIKADDDLKLLFRD 212 (283)
Q Consensus 152 Gi~v~dLkD~~p~~~~~I~~Le~~g~Ilvl~~kd~~~~ivf~ND~~~~~~VD~efk~lW~~ 212 (283)
|+.|.-++-|.-|-..-|-+|.++|+|-+ ++|+-||-.-.+=|+|++.|-|=
T Consensus 50 gL~v~~~~SGPmGGDQQiGa~Iaeg~id~---------lIFf~DPLtaqPHdpDVkAL~Rl 101 (142)
T COG1803 50 GLNVHRLKSGPMGGDQQIGALIAEGKIDV---------LIFFWDPLTAQPHDPDVKALLRL 101 (142)
T ss_pred CCceEEeecCCCCccHHHHHHHhcCcceE---------EEEEecCCCCCCCCcCHHHHHHH
Confidence 78888899999999999999999999866 57888888888899999998875
No 22
>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=60.72 E-value=9.5 Score=28.11 Aligned_cols=49 Identities=12% Similarity=0.091 Sum_probs=32.8
Q ss_pred HHHHHHHHhccCCCCCHHHHhhhhCCC-CCCcHHHHHhhhCCCceEEeCC
Q 023374 78 IKRVIDRLLETRQAFTPEEINRDCYVD-VNANKAVFDSLRNNPKVHYDGK 126 (283)
Q Consensus 78 i~~vvd~Lk~~~~plt~~eI~~~~~~d-i~~~~~l~e~L~~npKI~~d~~ 126 (283)
+.+|.+|+.+++.|-|+.||.+++|+. .+.-...+++|..-=-|..+++
T Consensus 12 L~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~kG~I~r~~~ 61 (65)
T PF01726_consen 12 LEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKALERKGYIRRDPG 61 (65)
T ss_dssp HHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHHHHTTSEEEGCC
T ss_pred HHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCcCccCCCC
Confidence 445666667789999999999999886 3333467788877766776654
No 23
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=60.58 E-value=24 Score=29.56 Aligned_cols=94 Identities=22% Similarity=0.272 Sum_probs=59.0
Q ss_pred HHHHHHhccCCCCCHHHHhhhhCCC--CCCc--HHHHHhhhCCCceE-E-eCCeeeeecCCCCCCHHHHH--HHHhhC-C
Q 023374 80 RVIDRLLETRQAFTPEEINRDCYVD--VNAN--KAVFDSLRNNPKVH-Y-DGKRFSYKSKHDLKDKSQLL--VLVRKF-P 150 (283)
Q Consensus 80 ~vvd~Lk~~~~plt~~eI~~~~~~d--i~~~--~~l~e~L~~npKI~-~-d~~~f~yKP~y~Ik~k~~LL--~lL~k~-~ 150 (283)
.|.++|=... |.|..||.+.+.-+ .+.. ..|+..|-.--=|. + |++.|.|.|.++...-.++. .+|.+- .
T Consensus 10 eVM~ilW~~~-~~t~~eI~~~l~~~~ews~sTV~TLl~RL~KKg~l~~~kdgr~~~y~pL~~~~~~~~~~~~~~l~k~~d 88 (123)
T COG3682 10 EVMEILWSRG-PATVREIIEELPADREWSYSTVKTLLNRLVKKGLLTRKKDGRAFRYSPLLTRDQYVAGESQDLLDKICD 88 (123)
T ss_pred HHHHHHHHcC-CccHHHHHHHHhhcccccHHHHHHHHHHHHhccchhhhhcCCeeeeecccCHHHHHHHHHHHHHHHHHc
Confidence 3455555544 99999998887644 4433 25666665443333 3 67899999998655544333 345543 3
Q ss_pred CCee--hhhHhhhhhcHHHHHHHHHH
Q 023374 151 EGIA--VIDLKDSYPTVMEDLQALKA 174 (283)
Q Consensus 151 ~Gi~--v~dLkD~~p~~~~~I~~Le~ 174 (283)
+|+. |....|.-+--.++|++|++
T Consensus 89 ~~~~~lv~~F~~~~~l~~~eie~L~~ 114 (123)
T COG3682 89 GGLASLVAHFAEKEKLTADEIEALKA 114 (123)
T ss_pred ccchHHHHHHHHhccCCHHHHHHHHH
Confidence 5652 57777776666667777654
No 24
>KOG4603 consensus TBP-1 interacting protein [Signal transduction mechanisms]
Probab=60.54 E-value=14 Score=32.83 Aligned_cols=62 Identities=13% Similarity=0.173 Sum_probs=38.3
Q ss_pred CHHHHHHHHhhCCCCeehhhHhhhh-------hcHHHHHHHHHHcCcEEEEecCCCCceeEecCCCCCCCC
Q 023374 138 DKSQLLVLVRKFPEGIAVIDLKDSY-------PTVMEDLQALKAAGQIWLLSNFDSQEDIAYPNDPRVPIK 201 (283)
Q Consensus 138 ~k~~LL~lL~k~~~Gi~v~dLkD~~-------p~~~~~I~~Le~~g~Ilvl~~kd~~~~ivf~ND~~~~~~ 201 (283)
+..-+|++|+++..-.+-.|+-+.+ .-|.+.|+.|.+.|+|..-. =|+.+|.|.|.-.+++.
T Consensus 8 ~e~ivl~~~~eqNrP~ssq~v~~~lq~e~lgktavqk~Ld~La~~Gki~~K~--YGKqKIY~a~QDqF~~~ 76 (201)
T KOG4603|consen 8 AEGIVLRYLQEQNRPYSSQDVFGNLQREHLGKTAVQKTLDQLAQQGKIKEKM--YGKQKIYFADQDQFDMV 76 (201)
T ss_pred cHHHHHHHHHHhcCCCchHHHHHHHHHHhccchHHHHHHHHHHHcCchhHHh--ccceeeEeecHHhhcCC
Confidence 3456777777765333333322222 23678899999999986443 37778888886555443
No 25
>PF05158 RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; InterPro: IPR007832 The family comprises a subunit specific to RNA Pol III, the tRNA specific polymerase. The C34 subunit of Saccharomyces cerevisiae RNA Pol III is part of a subcomplex of three subunits which have no counterpart in the other two nuclear RNA polymerases. This subunit interacts with TFIIIB70 and therefore participates in Pol III recruitment [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2DK8_A 2DK5_A 2YU3_A.
Probab=60.39 E-value=21 Score=34.39 Aligned_cols=45 Identities=29% Similarity=0.511 Sum_probs=36.7
Q ss_pred HHHHHHHHhhC--CCCeehhhHhhhhhc-----HHHHHHHHHHcCcEEEEec
Q 023374 139 KSQLLVLVRKF--PEGIAVIDLKDSYPT-----VMEDLQALKAAGQIWLLSN 183 (283)
Q Consensus 139 k~~LL~lL~k~--~~Gi~v~dLkD~~p~-----~~~~I~~Le~~g~Ilvl~~ 183 (283)
++.||++++.+ ++|++.+||.+..|+ ....|+.|...|.|-++..
T Consensus 11 ~~~l~~~~~~~~~~~~~~~~~L~~~~~~~~~~~~~~~in~Ll~~~~~~~~~~ 62 (327)
T PF05158_consen 11 EKKLLELCRENPSPKGFSQEDLQQLIPGLDLQELVKAINELLSSGLLKLLKK 62 (327)
T ss_dssp HHHHHHHHHH---SS-EEHHHHHHH-TTS-HHHHHHHHHHHHHHTSEEEEE-
T ss_pred HHHHHHHHHHhcCCCCcCHHHHHhhcCCCCHHHHHHHHHHHHhCCCEEEEEc
Confidence 57899999998 699999999999776 4788999999999999983
No 26
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=59.64 E-value=29 Score=30.62 Aligned_cols=58 Identities=17% Similarity=0.169 Sum_probs=42.7
Q ss_pred CHHHHHHHHhhCCCCeehhhHhhhh----hcHHHHHHHHHHcCcEEEEe--cCCCCceeEecCCC
Q 023374 138 DKSQLLVLVRKFPEGIAVIDLKDSY----PTVMEDLQALKAAGQIWLLS--NFDSQEDIAYPNDP 196 (283)
Q Consensus 138 ~k~~LL~lL~k~~~Gi~v~dLkD~~----p~~~~~I~~Le~~g~Ilvl~--~kd~~~~ivf~ND~ 196 (283)
++..+|.+|..+ +++++.+|.+.. +.+-..|+.|++.|-|.... ...|.+.++|.--+
T Consensus 2 tr~~IL~~L~~~-~~~t~~eLA~~lgis~~tV~~~L~~Le~~GlV~r~~~~~~~gRp~~~y~LT~ 65 (203)
T TIGR02702 2 TKEDILSYLLKQ-GQATAAALAEALAISPQAVRRHLKDLETEGLIEYEAVVQGMGRPQYHYQLSR 65 (203)
T ss_pred HHHHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEeecccCCCCCceEEEECc
Confidence 567899999876 568998887754 56788999999999886553 23567767765433
No 27
>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=58.97 E-value=32 Score=24.30 Aligned_cols=42 Identities=26% Similarity=0.393 Sum_probs=32.4
Q ss_pred HHHHHHHhhCCCCeehhhHhhhh----hcHHHHHHHHHHcCcEEEEe
Q 023374 140 SQLLVLVRKFPEGIAVIDLKDSY----PTVMEDLQALKAAGQIWLLS 182 (283)
Q Consensus 140 ~~LL~lL~k~~~Gi~v~dLkD~~----p~~~~~I~~Le~~g~Ilvl~ 182 (283)
..+|++|+.+ +-+++.||.+-+ ..+-.||+.|++.|.|..+.
T Consensus 3 ~~Il~~l~~~-~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~i~r~~ 48 (57)
T PF08220_consen 3 QQILELLKEK-GKVSVKELAEEFGVSEMTIRRDLNKLEKQGLIKRTH 48 (57)
T ss_pred HHHHHHHHHc-CCEEHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEc
Confidence 5688888765 567888877755 45788999999999876554
No 28
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=58.82 E-value=44 Score=22.78 Aligned_cols=37 Identities=27% Similarity=0.408 Sum_probs=31.2
Q ss_pred HHHHHHHhhCCCCeehhhHhhhh----hcHHHHHHHHHHcC
Q 023374 140 SQLLVLVRKFPEGIAVIDLKDSY----PTVMEDLQALKAAG 176 (283)
Q Consensus 140 ~~LL~lL~k~~~Gi~v~dLkD~~----p~~~~~I~~Le~~g 176 (283)
.++|.+|..+.++++..+|.+.. ..+..+|+.|++.+
T Consensus 3 ~~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 3 KQILKLLLESKEPITAKELAEELGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp HHHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 47889998888779999998865 45789999999999
No 29
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=58.64 E-value=17 Score=29.11 Aligned_cols=37 Identities=30% Similarity=0.384 Sum_probs=28.1
Q ss_pred HHHHHHHHHhccCCCCCHHHHhhhhCCCCCCcHHHHHhh
Q 023374 77 QIKRVIDRLLETRQAFTPEEINRDCYVDVNANKAVFDSL 115 (283)
Q Consensus 77 qi~~vvd~Lk~~~~plt~~eI~~~~~~di~~~~~l~e~L 115 (283)
.--+|+.+|.+++.|+|+.+|.+.++.+ ...++++.|
T Consensus 4 ~rEkii~lL~e~~eplt~~ei~~~~~~~--~~~~v~~~L 40 (97)
T COG3357 4 TREKIISLLLESDEPLTVAEIFELLNGE--KEKEVYDHL 40 (97)
T ss_pred HHHHHHHHHHcCCCcchHHHHHHHHcCC--chHHHHHHH
Confidence 3468999999999999999999877766 333444444
No 30
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=58.36 E-value=39 Score=24.73 Aligned_cols=44 Identities=14% Similarity=0.198 Sum_probs=35.4
Q ss_pred CHHHHHHHHhhCCC-CeehhhHhhhh----hcHHHHHHHHHHcCcEEEE
Q 023374 138 DKSQLLVLVRKFPE-GIAVIDLKDSY----PTVMEDLQALKAAGQIWLL 181 (283)
Q Consensus 138 ~k~~LL~lL~k~~~-Gi~v~dLkD~~----p~~~~~I~~Le~~g~Ilvl 181 (283)
.++.+|.+|.++.+ |+...||.+.. ..+-..|..|+++|.|...
T Consensus 7 ~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~~ 55 (68)
T smart00550 7 LEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCKQ 55 (68)
T ss_pred HHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence 36789999999875 89999987754 3578889999999987543
No 31
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=58.01 E-value=10 Score=25.99 Aligned_cols=49 Identities=18% Similarity=0.255 Sum_probs=31.6
Q ss_pred HHHHHHHHhccCCCCCHHHHhhhhCCCCCCcHHHHHhhhCC-CceEEeCC
Q 023374 78 IKRVIDRLLETRQAFTPEEINRDCYVDVNANKAVFDSLRNN-PKVHYDGK 126 (283)
Q Consensus 78 i~~vvd~Lk~~~~plt~~eI~~~~~~di~~~~~l~e~L~~n-pKI~~d~~ 126 (283)
...|+.+|.+.+.++|.+||.+.++++-..=..-++.|+.. -.|...++
T Consensus 2 ~~~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~~~I~~~~~ 51 (55)
T PF08279_consen 2 QKQILKLLLESKEPITAKELAEELGVSRRTIRRDIKELREWGIPIESKRG 51 (55)
T ss_dssp HHHHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT-EEEEETT
T ss_pred HHHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeEEeeCC
Confidence 45789999888888999999998887655433333444332 24444443
No 32
>TIGR00988 hip integration host factor, beta subunit. This protein forms a site-specific DNA-binding heterodimer with the homologous integration host factor alpha subunit. It is closely related to the DNA-binding protein HU.
Probab=55.94 E-value=69 Score=24.63 Aligned_cols=45 Identities=20% Similarity=0.282 Sum_probs=34.8
Q ss_pred CHHHHHHHHhhCCCCeehhhHhhhhhcHHHHHHHHHHcCcEEEEe
Q 023374 138 DKSQLLVLVRKFPEGIAVIDLKDSYPTVMEDLQALKAAGQIWLLS 182 (283)
Q Consensus 138 ~k~~LL~lL~k~~~Gi~v~dLkD~~p~~~~~I~~Le~~g~Ilvl~ 182 (283)
++++|++.|..+..|++-.|.+..+-.+.+.|.+--.+|..+.+.
T Consensus 2 ~k~eli~~i~~~~~~~s~~~v~~vv~~~~~~i~~~L~~g~~V~l~ 46 (94)
T TIGR00988 2 TKSELIERIATQQSHLPAKDVEDAVKTMLEHMASALAQGDRIEIR 46 (94)
T ss_pred CHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHcCCeEEEc
Confidence 688999999988888999999999998888886644555444443
No 33
>PRK00199 ihfB integration host factor subunit beta; Reviewed
Probab=55.15 E-value=70 Score=24.69 Aligned_cols=45 Identities=16% Similarity=0.240 Sum_probs=36.2
Q ss_pred CHHHHHHHHhhCCCCeehhhHhhhhhcHHHHHHHHHHcCcEEEEe
Q 023374 138 DKSQLLVLVRKFPEGIAVIDLKDSYPTVMEDLQALKAAGQIWLLS 182 (283)
Q Consensus 138 ~k~~LL~lL~k~~~Gi~v~dLkD~~p~~~~~I~~Le~~g~Ilvl~ 182 (283)
++.+|+..|.....|++-.|+...+-.+.+.|.+--+.|..+.+.
T Consensus 2 tk~eli~~ia~~~~~~s~~~~~~vv~~~~~~i~~~L~~g~~V~l~ 46 (94)
T PRK00199 2 TKSELIERLAARNPHLSAKDVENAVKEILEEMSDALARGDRIEIR 46 (94)
T ss_pred CHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHcCCeEEEc
Confidence 688999999887788999999999988888887766666655554
No 34
>PF06757 Ins_allergen_rp: Insect allergen related repeat, nitrile-specifier detoxification; InterPro: IPR010629 This entry represents several insect specific allergen repeats. These repeats are commonly found in various proteins from cockroaches, fruit flies and mosquitos. It has been suggested that the repeat sequences have evolved by duplication of an ancestral amino acid domain, which may have arisen from the mitochondrial energy transfer proteins []. This family exemplifies a case of novel gene evolution. The case in point is the arms-race between plants and their infective insective herbivores in the area of the glucosinolate-myrosinase system. Brassicas have developed the glucosinolate-myrosinase system as chemical defence mechanism against the insects, and consequently the insects have adapted to produce a detoxifying molecule, nitrile-specifier protein (NSP). NSP is present in the Pieris rapae (Cabbage white butterfly). NSP is structurally different from and has no amino acid homology to any known detoxifying enzymes, and it appears to have arisen by a process of domain and gene duplication of a sequence of unknown function that is widespread in insect species and referred to as insect-allergen-repeat protein. Thus this family is found either as a single domain or as a multiple repeat-domain [].
Probab=55.11 E-value=10 Score=33.08 Aligned_cols=32 Identities=22% Similarity=0.425 Sum_probs=28.2
Q ss_pred CHHHHHHhhhc-CCCCChhHHHHHHHHCCCCCcc
Q 023374 203 DDDLKLLFRDI-ALPSDMLDIEKDLQKNGMKPAT 235 (283)
Q Consensus 203 D~efk~lW~~v-~vP~d~~Di~k~L~~~Glkp~~ 235 (283)
.++|+++|+.+ .+|. ..++..||+.+|+....
T Consensus 43 s~~f~~l~~~l~~~pE-~~~l~~yL~~~gldv~~ 75 (179)
T PF06757_consen 43 SSEFKQLWQQLEALPE-VKALLDYLESAGLDVYY 75 (179)
T ss_pred ChHHHHHHHHHHcCHH-HHHHHHHHHHCCCCHHH
Confidence 56899999996 6775 89999999999999886
No 35
>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=54.69 E-value=30 Score=24.10 Aligned_cols=44 Identities=11% Similarity=0.169 Sum_probs=35.7
Q ss_pred CCCCCHHHHhhhhCCCCCCcHHHHHhhhCCCceEEeC-Ceeeeec
Q 023374 89 RQAFTPEEINRDCYVDVNANKAVFDSLRNNPKVHYDG-KRFSYKS 132 (283)
Q Consensus 89 ~~plt~~eI~~~~~~di~~~~~l~e~L~~npKI~~d~-~~f~yKP 132 (283)
..++|..||.+.++++...-...+..|.+.--|.+++ ++|...|
T Consensus 23 ~~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~~~~~~~~~l~~ 67 (67)
T cd00092 23 QLPLTRQEIADYLGLTRETVSRTLKELEEEGLISRRGRGKYRVNP 67 (67)
T ss_pred cCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCeEEeCC
Confidence 3689999999999987776667889999998899887 6776543
No 36
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=52.95 E-value=33 Score=31.68 Aligned_cols=56 Identities=9% Similarity=0.059 Sum_probs=47.2
Q ss_pred CChhHHHHHHHHHHHhccCCCCCHHHHhhhhCCCCCCcHHHHHhhhCCCceEEeCC
Q 023374 71 KSPVGAQIKRVIDRLLETRQAFTPEEINRDCYVDVNANKAVFDSLRNNPKVHYDGK 126 (283)
Q Consensus 71 ~~~v~tqi~~vvd~Lk~~~~plt~~eI~~~~~~di~~~~~l~e~L~~npKI~~d~~ 126 (283)
+.+.......|+++|-..+.++++.||.+.++++-+.-..++..|...-=|.+|+.
T Consensus 20 ~~~sl~r~l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~~~~~ 75 (271)
T PRK10163 20 GAQALERGIAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQAADFVYQDSQ 75 (271)
T ss_pred cchHHHHHHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCC
Confidence 34455667889999988888999999999999999888889999999888988753
No 37
>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=50.21 E-value=81 Score=21.64 Aligned_cols=45 Identities=16% Similarity=0.240 Sum_probs=35.4
Q ss_pred HHHHHHhhCCC-CeehhhHhhhh----hcHHHHHHHHHHcCcEEEEecCC
Q 023374 141 QLLVLVRKFPE-GIAVIDLKDSY----PTVMEDLQALKAAGQIWLLSNFD 185 (283)
Q Consensus 141 ~LL~lL~k~~~-Gi~v~dLkD~~----p~~~~~I~~Le~~g~Ilvl~~kd 185 (283)
.+|.+|..+++ ++++.||.+.+ +.+-..|+.|++.|-|......+
T Consensus 9 ~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r~~~~~ 58 (62)
T PF12802_consen 9 RVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKKGLVERERDPG 58 (62)
T ss_dssp HHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE-SS
T ss_pred HHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCCC
Confidence 57788888875 49999998876 45788899999999988776653
No 38
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=49.63 E-value=34 Score=31.35 Aligned_cols=58 Identities=10% Similarity=0.023 Sum_probs=46.9
Q ss_pred hHHHHHHHHHHHhccCCCCCHHHHhhhhCCCCCCcHHHHHhhhCCCceEEeC--Ceeeee
Q 023374 74 VGAQIKRVIDRLLETRQAFTPEEINRDCYVDVNANKAVFDSLRNNPKVHYDG--KRFSYK 131 (283)
Q Consensus 74 v~tqi~~vvd~Lk~~~~plt~~eI~~~~~~di~~~~~l~e~L~~npKI~~d~--~~f~yK 131 (283)
....-..|+++|...+.++++.||.+.++++-+.-..++..|..+-=|+.++ ++|+.=
T Consensus 9 sl~ral~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~~~g~v~~~~~~~~Y~Lg 68 (263)
T PRK09834 9 GLSRGLMVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQEEGYVRRSASDDSFRLT 68 (263)
T ss_pred HHHHHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEecCCCcEEEc
Confidence 3445667788888888889999999999999888888999999999999874 354433
No 39
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=48.80 E-value=31 Score=22.53 Aligned_cols=46 Identities=11% Similarity=0.087 Sum_probs=34.0
Q ss_pred HHHHHHHhccCCCCCHHHHhhhhCCCCCCcHHHHHhhhCCCceEEeC
Q 023374 79 KRVIDRLLETRQAFTPEEINRDCYVDVNANKAVFDSLRNNPKVHYDG 125 (283)
Q Consensus 79 ~~vvd~Lk~~~~plt~~eI~~~~~~di~~~~~l~e~L~~npKI~~d~ 125 (283)
..++++|.+. .+++..||.+.++++...-...+..|....-|....
T Consensus 3 ~~il~~l~~~-~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~~~~ 48 (53)
T smart00420 3 QQILELLAQQ-GKVSVEELAELLGVSEMTIRRDLNKLEEQGLLTRVH 48 (53)
T ss_pred HHHHHHHHHc-CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEee
Confidence 3577888765 579999999988776665556778888777776643
No 40
>PF08672 APC2: Anaphase promoting complex (APC) subunit 2; InterPro: IPR014786 The anaphase-promoting complex (APC) or cyclosome is a multi-subunit E3 protein ubiquitin ligase that regulates important events in mitosis such as the initiation of anaphase and exit from telophase. The APC, in conjunction with other enzymes, assembles multi-ubiquitin chains on a variety of regulatory proteins, thereby targeting them for proteolysis by the 26S proteasome. Anaphase is initiated when the APC triggers the destruction of securin, thereby allowing the protease, separase, to disrupt sister-chromatid cohesion. Securin ubiquitination by the APC is inhibited by cyclin-dependent kinase 1 (Cdk1)-dependent phosphorylation []. Forkhead Box M1 (FoxM1), which is a transcription factor that is over-expressed in many cancers, is degraded in late mitosis and early G1 phase by the APC/cyclosome (APC/C) E3 ubiquitin ligase []. The APC/C targets mitotic cyclins for destruction in mitosis and G1 phase and is then inactivated at S phase. It thereby generates alternating states of high and low cyclin-Cdk activity, which is required for the alternation of mitosis and DNA replication []. The APC/C is composed of at least 13 subunits that stay tightly associated throughout the cell cycle: APC1, APC2, APC4, APC5, APC9, APC11, CDC16, CDC23, CDC26, CDC27, DOC1, MND2 and SWM1[], []. In fission yeast the 13 subunits are known as: Apc1, Apc2, Nuc2, Apc4, Apc5, Cut9, Apc8, Apc10, Apc11, Hcn1, Apc13, Apc14 and Apc15 []. This entry represents a C-terminal domain found in APC subunit 2. ; PDB: 1LDD_A.
Probab=47.30 E-value=51 Score=24.00 Aligned_cols=42 Identities=17% Similarity=0.304 Sum_probs=26.3
Q ss_pred HHHHHHHHH--hccCCCCCHHHHhhhhCCCCCCcHHHHHhhhCCCceEEeCCeee
Q 023374 77 QIKRVIDRL--LETRQAFTPEEINRDCYVDVNANKAVFDSLRNNPKVHYDGKRFS 129 (283)
Q Consensus 77 qi~~vvd~L--k~~~~plt~~eI~~~~~~di~~~~~l~e~L~~npKI~~d~~~f~ 129 (283)
+||-.+..+ -...-+.|.+|+. .+++.+....++++.+|.|.
T Consensus 16 RIh~mLkmf~~~~~~~~~s~~eL~-----------~fL~~lv~e~~L~~~~G~Yk 59 (60)
T PF08672_consen 16 RIHSMLKMFPKDPGGYDISLEELQ-----------EFLDRLVEEGKLECSGGSYK 59 (60)
T ss_dssp HHHHHHHHH-GGG--TT--HHHHH-----------HHHHHHHHTTSEE--TTEEE
T ss_pred HHHHHHHhccCCCCCCCCCHHHHH-----------HHHHHHHHCCcEEecCCEEe
Confidence 455555555 2345566777775 58899999999999998885
No 41
>PF11181 YflT: Heat induced stress protein YflT
Probab=46.81 E-value=29 Score=27.44 Aligned_cols=70 Identities=20% Similarity=0.392 Sum_probs=40.8
Q ss_pred cHHHHHHHHHHcC----cEEEEe-cCCCCceeEecCCCCCCCCCCHHHHHHhhhcC--CCCChhHHHHHHHHCCCCCccc
Q 023374 164 TVMEDLQALKAAG----QIWLLS-NFDSQEDIAYPNDPRVPIKADDDLKLLFRDIA--LPSDMLDIEKDLQKNGMKPATN 236 (283)
Q Consensus 164 ~~~~~I~~Le~~g----~Ilvl~-~kd~~~~ivf~ND~~~~~~VD~efk~lW~~v~--vP~d~~Di~k~L~~~Glkp~~~ 236 (283)
.+...|++|+++| +|+|+. +++....+-..-+-.. +.+.+ ..+|.++. +....+++...|.+-|+.....
T Consensus 11 E~~~~I~~L~~~Gy~~ddI~Vva~d~~~~~~l~~~t~~~~-~~~~~--~~~~d~~~~~f~~~~d~~~~~l~~lGl~~~ea 87 (103)
T PF11181_consen 11 EALSAIEELKAQGYSEDDIYVVAKDKDRTERLADQTDTNT-VGASE--ESFWDKIKNFFTSGGDELRSKLESLGLSEDEA 87 (103)
T ss_pred HHHHHHHHHHHcCCCcccEEEEEcCchHHHHHHHhcCCce-ecccc--ccHHHHHHHhccCCcHHHHHHHHHcCCCHHHH
Confidence 4677889999877 899997 4443333332222221 12222 44555431 1123567999999999876653
No 42
>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=43.87 E-value=75 Score=23.86 Aligned_cols=53 Identities=21% Similarity=0.386 Sum_probs=0.0
Q ss_pred CCCCCHHHHHHHHhhCCCCeehhhHhhhhhcHHHHHHHHHHcCcEEEEecCCCCceeEecCCCC
Q 023374 134 HDLKDKSQLLVLVRKFPEGIAVIDLKDSYPTVMEDLQALKAAGQIWLLSNFDSQEDIAYPNDPR 197 (283)
Q Consensus 134 y~Ik~k~~LL~lL~k~~~Gi~v~dLkD~~p~~~~~I~~Le~~g~Ilvl~~kd~~~~ivf~ND~~ 197 (283)
+.|.+-++|+.+|+++ |+.|.- +.+-.||++| .|.=+++.+|....+.+++.+
T Consensus 17 ~~i~sQ~eL~~~L~~~--Gi~vTQ-----aTiSRDLkeL----~~vKv~~~~g~~~Y~l~~~~~ 69 (70)
T PF01316_consen 17 HEISSQEELVELLEEE--GIEVTQ-----ATISRDLKEL----GAVKVPDGNGKYRYVLPEETE 69 (70)
T ss_dssp S---SHHHHHHHHHHT--T-T--H-----HHHHHHHHHH----T-EEEECTTSSEEEE-TTSTT
T ss_pred CCcCCHHHHHHHHHHc--CCCcch-----hHHHHHHHHc----CcEEeeCCCCCEEEEecCcCC
No 43
>PF04558 tRNA_synt_1c_R1: Glutaminyl-tRNA synthetase, non-specific RNA binding region part 1 ; InterPro: IPR007639 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This is a domain found N-terminal to the catalytic domain of glutaminyl-tRNA synthetase (6.1.1.18 from EC) in eukaryotes but not in Escherichia coli. This domain is thought to bind RNA in a non-specific manner, enhancing interactions between the tRNA and enzyme, but is not essential for enzyme function [].; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 3TL4_X.
Probab=43.24 E-value=23 Score=30.86 Aligned_cols=35 Identities=17% Similarity=0.265 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHhccCC-CCCHHHHhhhhCCCCCCcH
Q 023374 75 GAQIKRVIDRLLETRQ-AFTPEEINRDCYVDVNANK 109 (283)
Q Consensus 75 ~tqi~~vvd~Lk~~~~-plt~~eI~~~~~~di~~~~ 109 (283)
.-|+..+++||+.+.. |+..++.+++||+.|.-.+
T Consensus 84 ~~Ql~AA~~Yl~~~~~~~~d~~~Fe~~cGVGV~VT~ 119 (164)
T PF04558_consen 84 NLQLDAALKYLKSNPSEPIDVAEFEKACGVGVVVTP 119 (164)
T ss_dssp HHHHHHHHHHHHHHGG-G--HHHHHHTTTTT----H
T ss_pred HHHHHHHHHHHHHCCCCCCCHHHHHHHcCCCeEECH
Confidence 5789999999999876 9999999999998877654
No 44
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=42.76 E-value=3.7e+02 Score=27.14 Aligned_cols=146 Identities=18% Similarity=0.168 Sum_probs=90.6
Q ss_pred HHHHHHHHHhccCCCCCHHHHhhhhCCCCCCcHHHHHhhhCCCceEEeCCe-eeeecC-----C--CCCCHHHHHHHHhh
Q 023374 77 QIKRVIDRLLETRQAFTPEEINRDCYVDVNANKAVFDSLRNNPKVHYDGKR-FSYKSK-----H--DLKDKSQLLVLVRK 148 (283)
Q Consensus 77 qi~~vvd~Lk~~~~plt~~eI~~~~~~di~~~~~l~e~L~~npKI~~d~~~-f~yKP~-----y--~Ik~k~~LL~lL~k 148 (283)
.-..|+.+|...+ +++..||.+.++++-+.-...++.|...-=|+....+ -.|.-. + ++--...|++.|..
T Consensus 7 ~e~~vL~~L~~~~-~~s~~eLA~~l~l~~~tVt~~i~~Le~kGlV~~~~~~~~~i~LTeeG~~~~~~g~pE~rl~~~l~~ 85 (489)
T PRK04172 7 NEKKVLKALKELK-EATLEELAEKLGLPPEAVMRAAEWLEEKGLVKVEERVEEVYVLTEEGKKYAEEGLPERRLLNALKD 85 (489)
T ss_pred HHHHHHHHHHhCC-CCCHHHHHHHhCcCHHHHHHHHHHHHhCCCEEEEeeeEEEEEECHHHHHHHHhcCHHHHHHHhhHh
Confidence 3467788886544 7999999998998877767788999988888886542 222221 1 34445667777762
Q ss_pred CCCCeehhhHhhh-hh--cHHHHHHHHHHcCcEEEEecCCCCceeEecCCCCCCCCCCHHHHHHhhhcC------CCCCh
Q 023374 149 FPEGIAVIDLKDS-YP--TVMEDLQALKAAGQIWLLSNFDSQEDIAYPNDPRVPIKADDDLKLLFRDIA------LPSDM 219 (283)
Q Consensus 149 ~~~Gi~v~dLkD~-~p--~~~~~I~~Le~~g~Ilvl~~kd~~~~ivf~ND~~~~~~VD~efk~lW~~v~------vP~d~ 219 (283)
.+|+.++||.+. ++ .+...+..|.+.|.|-+ . .| .+.+.... +.++...+=..+. ++...
T Consensus 86 -~~g~~~~el~~~aL~~~~~~i~~~~l~k~g~i~i--~-~G---~~i~~~~~----~~d~~~~~L~~l~~g~~~~~~~~~ 154 (489)
T PRK04172 86 -GGEVSLDELKEALLDKKEVGIALGNLARKGWAKI--E-KG---KVILKPDA----YEDPEEKALKALAEGDKEELSEED 154 (489)
T ss_pred -cCCcCHHHHHHhhccchhHHHHHHHHHHCCCeec--C-CC---ceeecCcc----cCcHHHHHHHHHhccCccccccCC
Confidence 478999999987 43 45666778888887766 1 22 34444221 2222333334332 22212
Q ss_pred hHHHHHHHHCCCCCc
Q 023374 220 LDIEKDLQKNGMKPA 234 (283)
Q Consensus 220 ~Di~k~L~~~Glkp~ 234 (283)
.++-++|++-||--.
T Consensus 155 ~~~l~~LkkRkL~~~ 169 (489)
T PRK04172 155 LKVLKELKKRKLVEE 169 (489)
T ss_pred HHHHHHHHhcCCeEE
Confidence 457788888876444
No 45
>PRK11569 transcriptional repressor IclR; Provisional
Probab=42.35 E-value=56 Score=30.12 Aligned_cols=56 Identities=7% Similarity=0.159 Sum_probs=46.9
Q ss_pred HHHHHHHHHHHhccCCCCCHHHHhhhhCCCCCCcHHHHHhhhCCCceEEeC--Ceeee
Q 023374 75 GAQIKRVIDRLLETRQAFTPEEINRDCYVDVNANKAVFDSLRNNPKVHYDG--KRFSY 130 (283)
Q Consensus 75 ~tqi~~vvd~Lk~~~~plt~~eI~~~~~~di~~~~~l~e~L~~npKI~~d~--~~f~y 130 (283)
...-..|+++|.+.+.|+++.||.+.++++-+.-..++..|...-=|+.|+ ++|.-
T Consensus 27 l~ral~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~~~G~l~~~~~~~~Y~l 84 (274)
T PRK11569 27 LTRGLKLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQQGFVRQVGELGHWAI 84 (274)
T ss_pred HHHHHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCCCCeEec
Confidence 455678888888888999999999999999888888999999999998875 35543
No 46
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=41.80 E-value=37 Score=31.08 Aligned_cols=55 Identities=15% Similarity=0.166 Sum_probs=46.3
Q ss_pred HHHHHHHHhccCCCCCHHHHhhhhCCCCCCcHHHHHhhhCCCceEEeCC--eeeeec
Q 023374 78 IKRVIDRLLETRQAFTPEEINRDCYVDVNANKAVFDSLRNNPKVHYDGK--RFSYKS 132 (283)
Q Consensus 78 i~~vvd~Lk~~~~plt~~eI~~~~~~di~~~~~l~e~L~~npKI~~d~~--~f~yKP 132 (283)
-..|+++|.....++++.||.+.++++-+.-..++..|..+-=|.+|+. +|.--|
T Consensus 6 al~iL~~l~~~~~~l~l~ela~~~glpksT~~RlL~tL~~~G~v~~d~~~g~Y~Lg~ 62 (246)
T COG1414 6 ALAILDLLAEGPGGLSLAELAERLGLPKSTVHRLLQTLVELGYVEQDPEDGRYRLGP 62 (246)
T ss_pred HHHHHHHHHhCCCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEcCCCCcEeehH
Confidence 3568899988777789999999999998888899999999999999984 555444
No 47
>PF04282 DUF438: Family of unknown function (DUF438); InterPro: IPR007380 This is a a group of uncharacterised proteins.
Probab=40.42 E-value=19 Score=27.29 Aligned_cols=34 Identities=26% Similarity=0.542 Sum_probs=27.1
Q ss_pred CCCHHHHHHhhhcCCCCChhHHHHHHHHCCCCCcc
Q 023374 201 KADDDLKLLFRDIALPSDMLDIEKDLQKNGMKPAT 235 (283)
Q Consensus 201 ~VD~efk~lW~~v~vP~d~~Di~k~L~~~Glkp~~ 235 (283)
.|-.+|.+++.+|. |.+...++++|...|+.+..
T Consensus 17 ~vk~~F~~~~~~Vs-~~EI~~~Eq~Li~eG~~~ee 50 (71)
T PF04282_consen 17 EVKEEFKKLFSDVS-ASEISAAEQELIQEGMPVEE 50 (71)
T ss_pred HHHHHHHHHHCCCC-HHHHHHHHHHHHHcCCCHHH
Confidence 46688999999997 44577789999999976653
No 48
>PHA00738 putative HTH transcription regulator
Probab=40.34 E-value=59 Score=26.68 Aligned_cols=57 Identities=18% Similarity=0.186 Sum_probs=40.0
Q ss_pred HHHHHHHHhhCCCCeehhhHhhh----hhcHHHHHHHHHHcCcEEEEecCCCCceeEecCCCCC
Q 023374 139 KSQLLVLVRKFPEGIAVIDLKDS----YPTVMEDLQALKAAGQIWLLSNFDSQEDIAYPNDPRV 198 (283)
Q Consensus 139 k~~LL~lL~k~~~Gi~v~dLkD~----~p~~~~~I~~Le~~g~Ilvl~~kd~~~~ivf~ND~~~ 198 (283)
.-.+|.+|... ++++|.||.+. .|.+-..|+-|++.|-|- ..++|+..++..|+..-
T Consensus 14 Rr~IL~lL~~~-e~~~V~eLae~l~lSQptVS~HLKvLreAGLV~--srK~Gr~vyY~Ln~~~~ 74 (108)
T PHA00738 14 RRKILELIAEN-YILSASLISHTLLLSYTTVLRHLKILNEQGYIE--LYKEGRTLYAKIRENSK 74 (108)
T ss_pred HHHHHHHHHHc-CCccHHHHHHhhCCCHHHHHHHHHHHHHCCceE--EEEECCEEEEEECCCcc
Confidence 45678888653 34788888776 678899999999999554 44557775555565543
No 49
>PF05066 HARE-HTH: HB1, ASXL, restriction endonuclease HTH domain; InterPro: IPR007759 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. The delta protein is a dispensable subunit of Bacillus subtilis RNA polymerase (RNAP) that has major effects on the biochemical properties of the purified enzyme. In the presence of delta, RNAP displays an increased specificity of transcription, a decreased affinity for nucleic acids, and an increased efficiency of RNA synthesis because of enhanced recycling []. The delta protein, contains two distinct regions, an N-terminal domain and a glutamate and aspartate residue-rich C-terminal region [].; GO: 0003677 DNA binding, 0006351 transcription, DNA-dependent; PDB: 2KRC_A.
Probab=39.36 E-value=16 Score=26.76 Aligned_cols=26 Identities=19% Similarity=0.134 Sum_probs=18.5
Q ss_pred HHHHHHHHHHhccCCCCCHHHHhhhh
Q 023374 76 AQIKRVIDRLLETRQAFTPEEINRDC 101 (283)
Q Consensus 76 tqi~~vvd~Lk~~~~plt~~eI~~~~ 101 (283)
|-+-.|.+.|++.+.|+++.||.+..
T Consensus 2 t~~eaa~~vL~~~~~pm~~~eI~~~i 27 (72)
T PF05066_consen 2 TFKEAAYEVLEEAGRPMTFKEIWEEI 27 (72)
T ss_dssp -HHHHHHHHHHHH-S-EEHHHHHHHH
T ss_pred CHHHHHHHHHHhcCCCcCHHHHHHHH
Confidence 34567789999999999999995543
No 50
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=39.18 E-value=66 Score=21.37 Aligned_cols=41 Identities=12% Similarity=0.066 Sum_probs=29.2
Q ss_pred HHHHHhccCCCCCHHHHhhhhCCCCCCcHHHHHhhhCCCceEE
Q 023374 81 VIDRLLETRQAFTPEEINRDCYVDVNANKAVFDSLRNNPKVHY 123 (283)
Q Consensus 81 vvd~Lk~~~~plt~~eI~~~~~~di~~~~~l~e~L~~npKI~~ 123 (283)
|+++|. +.++++.||.+.+++....-...++.|...-=|..
T Consensus 2 il~~l~--~~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~ 42 (66)
T smart00418 2 ILKLLA--EGELCVCELAEILGLSQSTVSHHLKKLREAGLVES 42 (66)
T ss_pred HHHHhh--cCCccHHHHHHHHCCCHHHHHHHHHHHHHCCCeee
Confidence 567776 78899999999888666544566666666555554
No 51
>PF04239 DUF421: Protein of unknown function (DUF421); InterPro: IPR007353 This family of uncharacterised proteins is known as YDFR family; PDB: 3C6F_D.
Probab=38.53 E-value=13 Score=29.50 Aligned_cols=91 Identities=24% Similarity=0.366 Sum_probs=37.3
Q ss_pred hhhCCCceEEeCCeeeeecC-CCCCCHHHHHHHHhhCCCCe-ehhhHhhhhhcHHHHHHHHHHcCcEEEEecCCCCceeE
Q 023374 114 SLRNNPKVHYDGKRFSYKSK-HDLKDKSQLLVLVRKFPEGI-AVIDLKDSYPTVMEDLQALKAAGQIWLLSNFDSQEDIA 191 (283)
Q Consensus 114 ~L~~npKI~~d~~~f~yKP~-y~Ik~k~~LL~lL~k~~~Gi-~v~dLkD~~p~~~~~I~~Le~~g~Ilvl~~kd~~~~iv 191 (283)
.|...|.+-+.+|.|.+.-. ..==+.++|+..||.+ |+ +++|+.-++ ||..|.|.|+...+..+ +
T Consensus 3 l~~g~p~~Li~dG~i~~~~l~~~~it~~dl~~~LR~~--gi~~l~dV~~a~---------lE~~G~lsv~~k~~~~~--~ 69 (99)
T PF04239_consen 3 LLEGKPTVLIRDGKIDEDNLRRARITEEDLLSALREQ--GIESLSDVKAAV---------LEPNGQLSVIKKEDAQP--V 69 (99)
T ss_dssp ------EEEEETTEE-HHHHHHTT--HHHHHHHHHHT--T--SGGGEEEEE---------E-TTS-EEEEE-GGGS----
T ss_pred cccCCcEEEEECCEECHHHHhHcCCCHHHHHHHHHhh--CCCCHHHcCEEE---------ECCCCCEEEEEcCCCCC--C
Confidence 35567778888888888873 3344788999999966 65 577776554 56789999997654333 1
Q ss_pred ecCCCCCCCCCCHHHHHHhhhcCCCCChhHHHHHHHHCCCC
Q 023374 192 YPNDPRVPIKADDDLKLLFRDIALPSDMLDIEKDLQKNGMK 232 (283)
Q Consensus 192 f~ND~~~~~~VD~efk~lW~~v~vP~d~~Di~k~L~~~Glk 232 (283)
.+. +. |+ .+-.|..=+.++|+++|.+
T Consensus 70 ~~~---l~--I~----------~~~~~~~wl~~~L~~~~~~ 95 (99)
T PF04239_consen 70 TPE---LN--ID----------QIGKDEEWLKEELKKQGYK 95 (99)
T ss_dssp -TT---TT---------------------------------
T ss_pred Ccc---EE--Ee----------eeccccccccccccccccc
Confidence 111 11 22 2223445589999999987
No 52
>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=37.96 E-value=67 Score=22.64 Aligned_cols=48 Identities=10% Similarity=0.140 Sum_probs=35.5
Q ss_pred HHHHHHHHhccCCCCCHHHHhhhhCCCCCCcHHHHHhhhCCCceEEeCC
Q 023374 78 IKRVIDRLLETRQAFTPEEINRDCYVDVNANKAVFDSLRNNPKVHYDGK 126 (283)
Q Consensus 78 i~~vvd~Lk~~~~plt~~eI~~~~~~di~~~~~l~e~L~~npKI~~d~~ 126 (283)
+..|++||+++ ..++.+||.+.+++....-..-+..|.+.-.|.-..|
T Consensus 2 ~~~Il~~l~~~-~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~i~r~~G 49 (57)
T PF08220_consen 2 QQQILELLKEK-GKVSVKELAEEFGVSEMTIRRDLNKLEKQGLIKRTHG 49 (57)
T ss_pred HHHHHHHHHHc-CCEEHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcC
Confidence 35789999775 6899999999887776655556677777777765443
No 53
>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=36.44 E-value=56 Score=25.88 Aligned_cols=54 Identities=13% Similarity=0.177 Sum_probs=37.8
Q ss_pred HHHHHhhCCCCeehhhHhhh----hhcHHHHHHHHHHcCcEEEEecCCC-CceeEecCCC
Q 023374 142 LLVLVRKFPEGIAVIDLKDS----YPTVMEDLQALKAAGQIWLLSNFDS-QEDIAYPNDP 196 (283)
Q Consensus 142 LL~lL~k~~~Gi~v~dLkD~----~p~~~~~I~~Le~~g~Ilvl~~kd~-~~~ivf~ND~ 196 (283)
+|..|.. .+|+++.||.+. -+.+-..|+.|++.|-|....+..+ ....|..-+.
T Consensus 33 iL~~l~~-~~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~~~~D~R~~~v~LT~~ 91 (118)
T TIGR02337 33 ILRILAE-QGSMEFTQLANQACILRPSLTGILARLERDGLVTRLKASNDQRRVYISLTPK 91 (118)
T ss_pred HHHHHHH-cCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHh
Confidence 6666654 468899999887 4567889999999998887766543 3334444443
No 54
>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=36.25 E-value=70 Score=21.85 Aligned_cols=44 Identities=18% Similarity=0.171 Sum_probs=33.6
Q ss_pred HHHHHHHhccCCCCCHHHHhhhhCCCCCCcHHHHHhhhCCCceEEe
Q 023374 79 KRVIDRLLETRQAFTPEEINRDCYVDVNANKAVFDSLRNNPKVHYD 124 (283)
Q Consensus 79 ~~vvd~Lk~~~~plt~~eI~~~~~~di~~~~~l~e~L~~npKI~~d 124 (283)
..|+.+|.... +++.||.+.++++...-...+..|....-|...
T Consensus 10 ~~il~~l~~~~--~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~ 53 (78)
T cd00090 10 LRILRLLLEGP--LTVSELAERLGLSQSTVSRHLKKLEEAGLVESR 53 (78)
T ss_pred HHHHHHHHHCC--cCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEEE
Confidence 45677777654 999999998888766656788888887777764
No 55
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=35.67 E-value=96 Score=26.13 Aligned_cols=63 Identities=16% Similarity=0.239 Sum_probs=41.2
Q ss_pred ccCCChhHHHHHHHHHHHhccCCCCCHHHHhhhh---CCCCCCc--HHHHHhhhC---CCceEEeCCeeee
Q 023374 68 SIRKSPVGAQIKRVIDRLLETRQAFTPEEINRDC---YVDVNAN--KAVFDSLRN---NPKVHYDGKRFSY 130 (283)
Q Consensus 68 t~~~~~v~tqi~~vvd~Lk~~~~plt~~eI~~~~---~~di~~~--~~l~e~L~~---npKI~~d~~~f~y 130 (283)
..+|.-+-.|=..|+++|.+...++|.+||.+.+ +.+++.. ...++.|.. -.++.+.++...|
T Consensus 13 k~~glr~T~qR~~vl~~L~~~~~~~sAeei~~~l~~~~p~islaTVYr~L~~l~e~Glv~~~~~~~~~~~y 83 (145)
T COG0735 13 KEAGLRLTPQRLAVLELLLEADGHLSAEELYEELREEGPGISLATVYRTLKLLEEAGLVHRLEFEGGKTRY 83 (145)
T ss_pred HHcCCCcCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHCCCEEEEEeCCCEEEE
Confidence 3445556677789999999999899999997766 3445433 234444444 4556666664333
No 56
>PRK10512 selenocysteinyl-tRNA-specific translation factor; Provisional
Probab=35.60 E-value=1.4e+02 Score=31.35 Aligned_cols=83 Identities=8% Similarity=0.103 Sum_probs=56.3
Q ss_pred HHHHHHHhccCCCCCHHHHhhhhCCCCCCcHHHHHhhhCCCceEE-eCCeeeeecCCCCCCHHHHHHHHhhC---CCCee
Q 023374 79 KRVIDRLLETRQAFTPEEINRDCYVDVNANKAVFDSLRNNPKVHY-DGKRFSYKSKHDLKDKSQLLVLVRKF---PEGIA 154 (283)
Q Consensus 79 ~~vvd~Lk~~~~plt~~eI~~~~~~di~~~~~l~e~L~~npKI~~-d~~~f~yKP~y~Ik~k~~LL~lL~k~---~~Gi~ 154 (283)
..+.+++. -.|.++.||.+.+++|...-.+++..|...-+|.. .++.|-....| +++.+.|+.+ .+++.
T Consensus 496 ~~l~~~~~--~~p~~~~~~~~~l~~~~~~~~~~l~~l~~~g~lv~l~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~ 568 (614)
T PRK10512 496 QKAEPLFG--DEPWWVRDLAKETGTDEQAMRLTLRQAAQQGIITAIVKDRYYRNDRI-----VQFANMIRELDQECGSTC 568 (614)
T ss_pred HHHHHHHh--cCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCCEEECHHHH-----HHHHHHHHHHHhhCCcEe
Confidence 45555555 57999999999888887666788888888777665 44444433333 3334444332 47899
Q ss_pred hhhHhhhhhcHHHH
Q 023374 155 VIDLKDSYPTVMED 168 (283)
Q Consensus 155 v~dLkD~~p~~~~~ 168 (283)
+.+++|.+.-.-+.
T Consensus 569 ~~~~r~~~g~sRK~ 582 (614)
T PRK10512 569 AADFRDRLGVGRKL 582 (614)
T ss_pred HHHHHHHhCccHHH
Confidence 99999999875443
No 57
>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=34.68 E-value=1.3e+02 Score=24.90 Aligned_cols=60 Identities=17% Similarity=0.232 Sum_probs=39.6
Q ss_pred HHHHHhccCCCCCHHHHhhhhC--CCCCCc--HHHHHhhhCCCceEE--eCCeeeeecCCCCCCHHHHHH
Q 023374 81 VIDRLLETRQAFTPEEINRDCY--VDVNAN--KAVFDSLRNNPKVHY--DGKRFSYKSKHDLKDKSQLLV 144 (283)
Q Consensus 81 vvd~Lk~~~~plt~~eI~~~~~--~di~~~--~~l~e~L~~npKI~~--d~~~f~yKP~y~Ik~k~~LL~ 144 (283)
|+.+|-+. .|.|..||.+.+. .++..+ ..++..|...-=|.. +++.|.|.|.. ++++++.
T Consensus 9 VM~vlW~~-~~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~KG~v~~~k~gr~~~Y~p~v---s~ee~~~ 74 (130)
T TIGR02698 9 VMRVVWTL-GETTSRDIIRILAEKKDWSDSTIKTLLGRLVDKGCLTTEKEGRKFIYTALV---SEDEAVE 74 (130)
T ss_pred HHHHHHcC-CCCCHHHHHHHHhhccCCcHHHHHHHHHHHHHCCceeeecCCCcEEEEecC---CHHHHHH
Confidence 55555544 4789999988764 333333 367888887776775 46689999854 4555543
No 58
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=34.60 E-value=1.3e+02 Score=22.15 Aligned_cols=46 Identities=22% Similarity=0.229 Sum_probs=32.2
Q ss_pred HHHHHHhhCCCCeehhhHhhh----hhcHHHHHHHHHHcCcEEEEecCCCC
Q 023374 141 QLLVLVRKFPEGIAVIDLKDS----YPTVMEDLQALKAAGQIWLLSNFDSQ 187 (283)
Q Consensus 141 ~LL~lL~k~~~Gi~v~dLkD~----~p~~~~~I~~Le~~g~Ilvl~~kd~~ 187 (283)
.+|.+|..++ ++.+.+|.+. .+.+-..|+.|++.|-|.......+.
T Consensus 14 ~il~~l~~~~-~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~~~~~~~ 63 (101)
T smart00347 14 LVLRILYEEG-PLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRLPSPEDR 63 (101)
T ss_pred HHHHHHHHcC-CcCHHHHHHHHCCCchhHHHHHHHHHHCCCeEecCCCCCC
Confidence 3455665543 6777776554 56789999999999988877655443
No 59
>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=34.33 E-value=28 Score=25.02 Aligned_cols=55 Identities=20% Similarity=0.205 Sum_probs=41.9
Q ss_pred HHHHHHHHHhccCCCCCHHHHhhhhCCCCCCcHHHHHhhhCCCceEEeC-Ceeeeec
Q 023374 77 QIKRVIDRLLETRQAFTPEEINRDCYVDVNANKAVFDSLRNNPKVHYDG-KRFSYKS 132 (283)
Q Consensus 77 qi~~vvd~Lk~~~~plt~~eI~~~~~~di~~~~~l~e~L~~npKI~~d~-~~f~yKP 132 (283)
.-..|..+|. ...+.|..||.+.++++-+.-...+..|...-=|+..+ +.+.|.+
T Consensus 9 ~E~~vy~~Ll-~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~~~~~~~~Y~a 64 (68)
T PF01978_consen 9 NEAKVYLALL-KNGPATAEEIAEELGISRSTVYRALKSLEEKGLVEREEGRPKVYRA 64 (68)
T ss_dssp HHHHHHHHHH-HHCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEEECCEEEEE
T ss_pred HHHHHHHHHH-HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcCceEEEEE
Confidence 3456666666 67799999999989988777677888888888888764 3556655
No 60
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=33.24 E-value=1.2e+02 Score=24.27 Aligned_cols=59 Identities=15% Similarity=0.264 Sum_probs=41.5
Q ss_pred CHHHHHHHHhhCCCCeehhhHhh---------hhhcHHHHHHHHHHcCcEEEEec-CCCCceeEecCCC
Q 023374 138 DKSQLLVLVRKFPEGIAVIDLKD---------SYPTVMEDLQALKAAGQIWLLSN-FDSQEDIAYPNDP 196 (283)
Q Consensus 138 ~k~~LL~lL~k~~~Gi~v~dLkD---------~~p~~~~~I~~Le~~g~Ilvl~~-kd~~~~ivf~ND~ 196 (283)
..+.+..+|..+++++.+.++.+ -|-+++-.-+.|+.+|..+++.- .-.+...+|..|+
T Consensus 4 ~rEkii~lL~e~~eplt~~ei~~~~~~~~~~~v~~~L~hiak~lkr~g~~Llv~Pa~CkkCGfef~~~~ 72 (97)
T COG3357 4 TREKIISLLLESDEPLTVAEIFELLNGEKEKEVYDHLEHIAKSLKRKGKRLLVRPARCKKCGFEFRDDK 72 (97)
T ss_pred HHHHHHHHHHcCCCcchHHHHHHHHcCCchHHHHHHHHHHHHHHHhCCceEEecChhhcccCccccccc
Confidence 45778888988888888877643 45556666677889999988853 3445556776644
No 61
>PF08679 DsrD: Dissimilatory sulfite reductase D (DsrD); InterPro: IPR014793 The structure of the dissimilatory sulphite reductase D (DsrD) protein has shown it to contain a winged-helix motif similar to those found in DNA binding proteins []. The structure suggests a possible role for DsrD in transcription or translation of genes, which catalyse dissimilatory sulphite reduction. ; PDB: 1WQ2_B 1UCR_B.
Probab=33.21 E-value=1.8e+02 Score=21.97 Aligned_cols=44 Identities=18% Similarity=0.278 Sum_probs=34.3
Q ss_pred HHHHHHHHhhCC---CCeehhhHhhhhhc-----HHHHHHHHHHcCcEEEEe
Q 023374 139 KSQLLVLVRKFP---EGIAVIDLKDSYPT-----VMEDLQALKAAGQIWLLS 182 (283)
Q Consensus 139 k~~LL~lL~k~~---~Gi~v~dLkD~~p~-----~~~~I~~Le~~g~Ilvl~ 182 (283)
++.+|++|+... .-..++|+..+.|+ +.+.+.+|..+|....-+
T Consensus 3 K~~Ile~L~~k~~~KskfYfkD~~k~~pd~k~R~vKKi~~~LV~Eg~l~yWS 54 (67)
T PF08679_consen 3 KQKILEFLEAKKKKKSKFYFKDFYKAFPDAKPREVKKIVNELVNEGKLEYWS 54 (67)
T ss_dssp HHHHHHHHSSCCCHSS-EEHHHHHHH-TTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHhccCCCCceeHHHHHHHCCCcCHHHHHHHHHHHHhhCeEEEEc
Confidence 678899998554 56789999999998 478899999999876654
No 62
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=33.07 E-value=97 Score=28.10 Aligned_cols=59 Identities=10% Similarity=0.181 Sum_probs=46.7
Q ss_pred hhHHHHHHHHHHHhccCCCCCHHHHhhhhCCCCCCcHHHHHhhhCCCceEEeC--Ceeeeec
Q 023374 73 PVGAQIKRVIDRLLETRQAFTPEEINRDCYVDVNANKAVFDSLRNNPKVHYDG--KRFSYKS 132 (283)
Q Consensus 73 ~v~tqi~~vvd~Lk~~~~plt~~eI~~~~~~di~~~~~l~e~L~~npKI~~d~--~~f~yKP 132 (283)
........|+++|-.. .++++.||.+.+++.-+.-..++..|...-=|+.++ ++|.-=|
T Consensus 11 ~sl~r~l~IL~~l~~~-~~l~l~eia~~lgl~kstv~Rll~tL~~~G~l~~~~~~~~Y~lG~ 71 (257)
T PRK15090 11 SSVLKVFGILQALGEE-REIGITELSQRVMMSKSTVYRFLQTMKTLGYVAQEGESEKYSLTL 71 (257)
T ss_pred HHHHHHHHHHHHhhcC-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCCCCcEEecH
Confidence 3445567788888764 589999999999999988889999999999898875 4555544
No 63
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=32.21 E-value=66 Score=24.81 Aligned_cols=31 Identities=13% Similarity=0.109 Sum_probs=25.9
Q ss_pred hHHHHHHHHHHHhccCCCCCHHHHhhhhCCCCC
Q 023374 74 VGAQIKRVIDRLLETRQAFTPEEINRDCYVDVN 106 (283)
Q Consensus 74 v~tqi~~vvd~Lk~~~~plt~~eI~~~~~~di~ 106 (283)
+......|++||.+ ..+|+.||.+.+|+...
T Consensus 4 ~~~R~~~I~e~l~~--~~~ti~dvA~~~gvS~~ 34 (80)
T TIGR02844 4 IEERVLEIGKYIVE--TKATVRETAKVFGVSKS 34 (80)
T ss_pred HHHHHHHHHHHHHH--CCCCHHHHHHHhCCCHH
Confidence 44567899999999 78899999998887765
No 64
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=32.14 E-value=59 Score=20.98 Aligned_cols=40 Identities=15% Similarity=0.164 Sum_probs=31.6
Q ss_pred CCCCHHHHhhhhCCCCCCcHHHHHhhhCCCceEEeCCeee
Q 023374 90 QAFTPEEINRDCYVDVNANKAVFDSLRNNPKVHYDGKRFS 129 (283)
Q Consensus 90 ~plt~~eI~~~~~~di~~~~~l~e~L~~npKI~~d~~~f~ 129 (283)
-|++..||.+.++++...-...+..|...--|.++++.|.
T Consensus 7 ~~~s~~~la~~l~~s~~tv~~~l~~L~~~g~l~~~~~~~~ 46 (48)
T smart00419 7 LPLTRQEIAELLGLTRETVSRTLKRLEKEGLISREGGRIV 46 (48)
T ss_pred eccCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCCEEE
Confidence 3688999999888876665678888888888888776654
No 65
>COG2442 Uncharacterized conserved protein [Function unknown]
Probab=32.01 E-value=52 Score=25.38 Aligned_cols=46 Identities=11% Similarity=0.126 Sum_probs=33.1
Q ss_pred CCCceEEeCCeeeeecCC-CCC-CHHHHHHHHhhCCCCeehhhHhhhhhcH
Q 023374 117 NNPKVHYDGKRFSYKSKH-DLK-DKSQLLVLVRKFPEGIAVIDLKDSYPTV 165 (283)
Q Consensus 117 ~npKI~~d~~~f~yKP~y-~Ik-~k~~LL~lL~k~~~Gi~v~dLkD~~p~~ 165 (283)
..+.|..+|+...=||-. +-| .-..+|..|+ .|++.+||.+-||++
T Consensus 9 ~~~~I~~~P~i~gGkP~I~GtRI~V~~Il~~l~---~G~s~eeil~dyp~L 56 (79)
T COG2442 9 LLNRIVITPGICGGKPCIRGTRIPVWDILEMLA---AGESIEEILADYPDL 56 (79)
T ss_pred ccCeeEeCCcccCCcceEeCceecHHHHHHHHH---CCCCHHHHHHhCCCC
Confidence 445788888766666632 221 3567777777 899999999999975
No 66
>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=31.99 E-value=1.3e+02 Score=23.56 Aligned_cols=54 Identities=19% Similarity=0.242 Sum_probs=35.8
Q ss_pred HHHHHHHhccCCCCCHHHHhhhhC---CCCCCc--HHHHHhhhCCCceE---EeCCeeeeec
Q 023374 79 KRVIDRLLETRQAFTPEEINRDCY---VDVNAN--KAVFDSLRNNPKVH---YDGKRFSYKS 132 (283)
Q Consensus 79 ~~vvd~Lk~~~~plt~~eI~~~~~---~di~~~--~~l~e~L~~npKI~---~d~~~f~yKP 132 (283)
..|+++|.+.+.++|.+||.+.+. ..++.. ...++.|...--|. .+++.+.|..
T Consensus 4 ~~Il~~l~~~~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~~~~~~~~~~y~~ 65 (116)
T cd07153 4 LAILEVLLESDGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREIELGDGKARYEL 65 (116)
T ss_pred HHHHHHHHhCCCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEEEEeCCCceEEEe
Confidence 468999999999999999988773 233332 35667776655444 4455555543
No 67
>PF09106 SelB-wing_2: Elongation factor SelB, winged helix ; InterPro: IPR015190 This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing []. Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 2". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity []. ; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0005525 GTP binding, 0001514 selenocysteine incorporation, 0005737 cytoplasm; PDB: 2V9V_A 1LVA_A 2PLY_A 2UWM_A.
Probab=31.93 E-value=1.7e+02 Score=20.60 Aligned_cols=42 Identities=24% Similarity=0.251 Sum_probs=30.1
Q ss_pred HHHHHHhhCC--CCeehhhHhhhhhc-------HHHHHHHHHHcCcEEEEe
Q 023374 141 QLLVLVRKFP--EGIAVIDLKDSYPT-------VMEDLQALKAAGQIWLLS 182 (283)
Q Consensus 141 ~LL~lL~k~~--~Gi~v~dLkD~~p~-------~~~~I~~Le~~g~Ilvl~ 182 (283)
.|-+|=+++| .||.-++|+-.+.. ....|+.|+++|.|.+-.
T Consensus 4 ~L~~yH~~~Plr~G~~keeLrsrl~~~~l~~k~~~~ll~~l~~~g~l~~~g 54 (59)
T PF09106_consen 4 ILAEYHRENPLRPGMPKEELRSRLFKPRLPPKLFNALLEALVAEGRLKVEG 54 (59)
T ss_dssp HHHHHHHH-TTSS-EEHHHHHHHCST-TS-HCCHHHHHHHHHHTTSEEEES
T ss_pred HHHHHHHHCcCccCcCHHHHHHHHhhccCCHHHHHHHHHHHHHCCCeeeEC
Confidence 4555556677 89999999976633 577889999999887653
No 68
>PRK10512 selenocysteinyl-tRNA-specific translation factor; Provisional
Probab=31.83 E-value=2.9e+02 Score=28.96 Aligned_cols=111 Identities=10% Similarity=0.085 Sum_probs=68.3
Q ss_pred CCCCHHHHhhhhCCCCCCcHHHHHhhhCCCceEEeCCeeeeecCCCCCCHHHHHHHHh----hCC--CCeehhhHhhhhh
Q 023374 90 QAFTPEEINRDCYVDVNANKAVFDSLRNNPKVHYDGKRFSYKSKHDLKDKSQLLVLVR----KFP--EGIAVIDLKDSYP 163 (283)
Q Consensus 90 ~plt~~eI~~~~~~di~~~~~l~e~L~~npKI~~d~~~f~yKP~y~Ik~k~~LL~lL~----k~~--~Gi~v~dLkD~~p 163 (283)
.++++.+|....++... ++.+.|...+-|.++ +.| |-+.+-=.=.+.|+.+|. ++| .|++..+|+..+.
T Consensus 376 ~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~-~~~-~~~~~~~~~~~~~~~~l~~~h~~~p~~~g~~~~~l~~~~~ 450 (614)
T PRK10512 376 GAVNLADFAWARQLNGE---GMRALLQQPGYIQAG-DSL-LSAPVAARWQRKLLDTLATYHEQHRDEPGPGRERLRRMAL 450 (614)
T ss_pred cCCCHHHHHHHhcCCHH---HHHHHhccCCeEEEc-cEE-ECHHHHHHHHHHHHHHHHHHHHHCCcccCCCHHHHHhhcc
Confidence 78899999776655432 454556555545554 332 333332223456666665 455 7999999998753
Q ss_pred c------HHHHHHHHHHcCcEEEEecCCCCceeEecCCCCCCCCCCHHHHHHhhhc
Q 023374 164 T------VMEDLQALKAAGQIWLLSNFDSQEDIAYPNDPRVPIKADDDLKLLFRDI 213 (283)
Q Consensus 164 ~------~~~~I~~Le~~g~Ilvl~~kd~~~~ivf~ND~~~~~~VD~efk~lW~~v 213 (283)
. +...|++|.++|.|.+..+ .|.. +......+++-..+|..+
T Consensus 451 ~~~~~~~~~~~l~~l~~~~~i~~~~~------~~~~--~~~~~~~~~~~~~~~~~l 498 (614)
T PRK10512 451 PMEDEALVLLLIEKMRESGDIHSHHG------WLHL--PDHKAGFSEEQQALWQKA 498 (614)
T ss_pred cCCCHHHHHHHHHHHHhCCCEEEeCC------EEEC--CCCCCCCCHHHHHHHHHH
Confidence 2 3567889988888877542 2332 444445677777777765
No 69
>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=31.82 E-value=65 Score=21.39 Aligned_cols=39 Identities=13% Similarity=0.242 Sum_probs=26.7
Q ss_pred HHHHHHHHhccCCCCCHHHHhhhhCCCCCCcHHHHHhhhC
Q 023374 78 IKRVIDRLLETRQAFTPEEINRDCYVDVNANKAVFDSLRN 117 (283)
Q Consensus 78 i~~vvd~Lk~~~~plt~~eI~~~~~~di~~~~~l~e~L~~ 117 (283)
-..|+.+|.+.. .+|..||.+.+++....-...+..|.+
T Consensus 5 ~~~Il~~l~~~~-~~t~~ela~~~~is~~tv~~~l~~L~~ 43 (48)
T PF13412_consen 5 QRKILNYLRENP-RITQKELAEKLGISRSTVNRYLKKLEE 43 (48)
T ss_dssp HHHHHHHHHHCT-TS-HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHcC-CCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 467899998854 499999999898877654445544443
No 70
>TIGR00160 MGSA methylglyoxal synthase. Methylglyoxal synthase (MGS) generates methylglyoxal (MG), a toxic metabolite (that may also be a regulatory metabolite and) that is detoxified, prinicipally, through a pathway involving glutathione and glyoxylase I. Totemeyer, et al. (MUID:98149311) propose that, during a loss of control over carbon flux, with accumulation of phosphorylated sugars and depletion of phosphate, as might happen during a rapid shift to a richer medium, MGS aids the cell by converting some dihydroxyacetone phosphate (DHAP) to MG and phosphate. This is therefore an alternative to triosephosphate isomerase and the remainder of the glycolytic pathway for the disposal of DHAP during the stress of a sudden increase in available sugars.
Probab=31.68 E-value=64 Score=27.75 Aligned_cols=52 Identities=23% Similarity=0.243 Sum_probs=42.8
Q ss_pred CeehhhHhhhhhcHHHHHHHHHHcCcEEEEecCCCCceeEecCCCCCCCCCCHHHHHHhhh
Q 023374 152 GIAVIDLKDSYPTVMEDLQALKAAGQIWLLSNFDSQEDIAYPNDPRVPIKADDDLKLLFRD 212 (283)
Q Consensus 152 Gi~v~dLkD~~p~~~~~I~~Le~~g~Ilvl~~kd~~~~ivf~ND~~~~~~VD~efk~lW~~ 212 (283)
|+.|.-++-|--|-+.-|-++.++|+|- -++|+-||-...+=|+|++.|-|-
T Consensus 48 gL~V~~~~SGplGGDqQIga~Ia~g~id---------~vIFf~DPl~~~phepDi~aLlRl 99 (143)
T TIGR00160 48 GLNINAMLSGPMGGDQQIGALIAEGKID---------AVIFFWDPLNAQPHEPDVKALLRL 99 (143)
T ss_pred CCCeEEeccCCccHHHHHHHHHHhCCCC---------EEEEecCCCCCCCCCcCHHHHHHH
Confidence 6777777888788888899998888874 478999998877889999998876
No 71
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=31.08 E-value=1.6e+02 Score=24.23 Aligned_cols=81 Identities=17% Similarity=0.253 Sum_probs=48.9
Q ss_pred HHHHHHHhhCCCCeehhhHhhh----hhcHHHHHHHHHHcCcEEEEecCCCCceeEecCCCCCCCCCCHHHHHHhhhcCC
Q 023374 140 SQLLVLVRKFPEGIAVIDLKDS----YPTVMEDLQALKAAGQIWLLSNFDSQEDIAYPNDPRVPIKADDDLKLLFRDIAL 215 (283)
Q Consensus 140 ~~LL~lL~k~~~Gi~v~dLkD~----~p~~~~~I~~Le~~g~Ilvl~~kd~~~~ivf~ND~~~~~~VD~efk~lW~~v~v 215 (283)
-++|.+|... +++.|.||.+. -|.+-..|+.|++.|-|..-+ +|.. ++|.-++...--+..=|...|..-
T Consensus 19 l~IL~~L~~~-~~~~v~ela~~l~lsqstvS~HL~~L~~AGLV~~~r--~Gr~-~~Y~l~~~~~~~~~~~~~~~w~~~-- 92 (117)
T PRK10141 19 LGIVLLLRES-GELCVCDLCTALDQSQPKISRHLALLRESGLLLDRK--QGKW-VHYRLSPHIPAWAAKIIEQAWLCE-- 92 (117)
T ss_pred HHHHHHHHHc-CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEE--EcCE-EEEEECchHHHHHHHHHHHHHHHH--
Confidence 3567777542 45777777664 567889999999999776655 3665 444444432111222255677765
Q ss_pred CCChhHHHHHHHHC
Q 023374 216 PSDMLDIEKDLQKN 229 (283)
Q Consensus 216 P~d~~Di~k~L~~~ 229 (283)
.+++..+|.+-
T Consensus 93 ---~~~l~~~l~~l 103 (117)
T PRK10141 93 ---QEDVQAIVRNL 103 (117)
T ss_pred ---HHHHHHHHHHH
Confidence 35666666543
No 72
>PF13034 DUF3895: Protein of unknown function (DUF3895)
Probab=30.40 E-value=54 Score=25.43 Aligned_cols=30 Identities=27% Similarity=0.435 Sum_probs=24.7
Q ss_pred hhhcHHHHHHHHHHcCcEEEEecCCCCcee
Q 023374 161 SYPTVMEDLQALKAAGQIWLLSNFDSQEDI 190 (283)
Q Consensus 161 ~~p~~~~~I~~Le~~g~Ilvl~~kd~~~~i 190 (283)
.||.|..-|+-|.++|.|.++.+.+-..|+
T Consensus 46 iY~~Vc~yLe~L~~eg~l~~i~~~~~~dRi 75 (78)
T PF13034_consen 46 IYPYVCNYLEYLVKEGKLSFIENDGTRDRI 75 (78)
T ss_pred eHHHHHHHHHHHHHCCeEEEEecCcchhhh
Confidence 389999999999999999999886555543
No 73
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=29.84 E-value=72 Score=22.44 Aligned_cols=30 Identities=17% Similarity=0.132 Sum_probs=24.3
Q ss_pred HHHHHHHHHHhccCCCCCHHHHhhhhCC-CCCC
Q 023374 76 AQIKRVIDRLLETRQAFTPEEINRDCYV-DVNA 107 (283)
Q Consensus 76 tqi~~vvd~Lk~~~~plt~~eI~~~~~~-di~~ 107 (283)
..+..++++|... +++++||...+|+ +.+.
T Consensus 37 ~r~~~a~~~l~~~--~~~~~~ia~~~g~~s~~~ 67 (84)
T smart00342 37 RRLERARRLLRDT--DLSVTEIALRVGFSSQSY 67 (84)
T ss_pred HHHHHHHHHHHcC--CCCHHHHHHHhCCCChHH
Confidence 3577889999877 8999999998888 6543
No 74
>PRK11050 manganese transport regulator MntR; Provisional
Probab=29.62 E-value=1.1e+02 Score=25.77 Aligned_cols=72 Identities=11% Similarity=0.121 Sum_probs=54.1
Q ss_pred ccccccchhhhcccccCCChhHHHHHHHHHHHhccCCCCCHHHHhhhhCCCCCCcHHHHHhhhCCCceEEeC
Q 023374 54 VKFSNDTERLQHINSIRKSPVGAQIKRVIDRLLETRQAFTPEEINRDCYVDVNANKAVFDSLRNNPKVHYDG 125 (283)
Q Consensus 54 v~~s~~~~~~q~~nt~~~~~v~tqi~~vvd~Lk~~~~plt~~eI~~~~~~di~~~~~l~e~L~~npKI~~d~ 125 (283)
|..-+-+|++|.....++..+......+|-.+-..+.+.+..||.+.++++-+.-..++..|....-|...+
T Consensus 14 ~~~~~~~~~~~~~~~~~~~~~~e~~l~~I~~~l~~~~~~t~~eLA~~l~is~stVsr~l~~Le~~GlI~r~~ 85 (152)
T PRK11050 14 VDVEEHVEGFRQVREAHRRELIEDYVELIADLIAEVGEARQVDIAARLGVSQPTVAKMLKRLARDGLVEMRP 85 (152)
T ss_pred CCcchhHHHHHHHHHHHhHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence 566677888998888888887777666655444556789999999989887766667888888876555443
No 75
>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.
Probab=28.82 E-value=1.1e+02 Score=23.37 Aligned_cols=62 Identities=21% Similarity=0.274 Sum_probs=38.5
Q ss_pred HHHHHHHHHhccCCCCCHHHHhhhhCCCCCCcHHHHHhhhCCCceE-----EeCCeeeeecCCCCCCHHHHH
Q 023374 77 QIKRVIDRLLETRQAFTPEEINRDCYVDVNANKAVFDSLRNNPKVH-----YDGKRFSYKSKHDLKDKSQLL 143 (283)
Q Consensus 77 qi~~vvd~Lk~~~~plt~~eI~~~~~~di~~~~~l~e~L~~npKI~-----~d~~~f~yKP~y~Ik~k~~LL 143 (283)
+--.|+..|.+. .+|++||.+.++++=+.=..-+..|..--.|. |.+.+|.= |-++.+++||
T Consensus 6 ~~~~IL~~ls~~--c~TLeeL~ekTgi~k~~LlV~LsrL~k~GiI~Rkw~~~~gkk~R~---YclK~~ee~~ 72 (72)
T PF05584_consen 6 VTQKILIILSKR--CCTLEELEEKTGISKNTLLVYLSRLAKRGIIERKWRKFGGKKYRE---YCLKYKEELL 72 (72)
T ss_pred HHHHHHHHHHhc--cCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeeeEEecCeEEEE---EEecchhhcC
Confidence 344677777666 99999999988887553223335555555554 23334432 6666677764
No 76
>PRK00285 ihfA integration host factor subunit alpha; Reviewed
Probab=28.39 E-value=2.8e+02 Score=21.44 Aligned_cols=45 Identities=18% Similarity=0.187 Sum_probs=36.0
Q ss_pred CHHHHHHHHhhCCCCeehhhHhhhhhcHHHHHHHHHHcCcEEEEec
Q 023374 138 DKSQLLVLVRKFPEGIAVIDLKDSYPTVMEDLQALKAAGQIWLLSN 183 (283)
Q Consensus 138 ~k~~LL~lL~k~~~Gi~v~dLkD~~p~~~~~I~~Le~~g~Ilvl~~ 183 (283)
++++|++.|... .|++..|++..+-.+.+.|.+.-++|..+-+..
T Consensus 4 tk~el~~~ia~~-~~~s~~~v~~vl~~~~~~i~~~L~~g~~V~l~g 48 (99)
T PRK00285 4 TKADLAEALFEK-VGLSKREAKELVELFFEEIRDALENGEQVKLSG 48 (99)
T ss_pred CHHHHHHHHHHH-hCcCHHHHHHHHHHHHHHHHHHHHcCCeEEEcC
Confidence 688999999754 779999999999999988888767776655543
No 77
>PTZ00448 hypothetical protein; Provisional
Probab=28.11 E-value=2.8e+02 Score=27.54 Aligned_cols=169 Identities=17% Similarity=0.205 Sum_probs=93.7
Q ss_pred hcccccCCChhHHHHHHHHHHHhc------cCCCCCHHHHhhhh---CCCCCCcH-------HHHHhhhCCCceEEeCCe
Q 023374 64 QHINSIRKSPVGAQIKRVIDRLLE------TRQAFTPEEINRDC---YVDVNANK-------AVFDSLRNNPKVHYDGKR 127 (283)
Q Consensus 64 q~~nt~~~~~v~tqi~~vvd~Lk~------~~~plt~~eI~~~~---~~di~~~~-------~l~e~L~~npKI~~d~~~ 127 (283)
|-..--|..-+..+...|++++-. ++.|++..-|..++ ++.|..+. +++.+|+..-=|.+.--.
T Consensus 94 Qlt~~ER~~~~E~k~r~Ii~~Ia~~~InP~T~~P~P~~rIE~Am~e~~~~Vdp~Ksak~Qalevik~L~~iiPikiera~ 173 (373)
T PTZ00448 94 QVSETERSYMLDKQFTDICHMLNRMTVNPKNNLPLSVKIIESELKDSGFSVSLNKTTKEQALKAFDILKKRIPDQIERAK 173 (373)
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHHhccCCCCCCCCCHHHHHHHHHhcCcccCCCCCHHHHHHHHHHHHHHhCCcceeEEE
Confidence 333333444566777888999965 47899998886654 45554441 355667654444454433
Q ss_pred eeeecCCCCCCHHHHHHHHhhC-CCCeehhhHhh-------hhhcHHHHHHHHHHcCcEEEEecC--CCCceeEecCCCC
Q 023374 128 FSYKSKHDLKDKSQLLVLVRKF-PEGIAVIDLKD-------SYPTVMEDLQALKAAGQIWLLSNF--DSQEDIAYPNDPR 197 (283)
Q Consensus 128 f~yKP~y~Ik~k~~LL~lL~k~-~~Gi~v~dLkD-------~~p~~~~~I~~Le~~g~Ilvl~~k--d~~~~ivf~ND~~ 197 (283)
..-+=......+..|+..|... -..+.-.|-.+ .-|+....|.+| .|.+.|+... .-..+-+--|...
T Consensus 174 m~vki~~~~~~~~~~~~~l~~~~~~~~~~e~~~~~~~~~~~idP~~yR~~~~l--~g~l~v~~~~v~~~~~~~~~~~~~~ 251 (373)
T PTZ00448 174 MMLKLSVDIVNKQNITKKLNEFNVFPISSEEKHNTYSITFLCEPRYYREIDQL--DCKLLLLDSNVKTIDKNSNQDNVEA 251 (373)
T ss_pred EEEEEecccccHHHHHHHHhhcccccccccccCCceEEEEEECCccccchhcc--CceeEEEeeeccccccccccccccc
Confidence 4333333335577888888775 23222222111 247788888888 8888888531 1011122223333
Q ss_pred CCCCCCHHHHHHhhhcCCCCChhHHHHHHHHCCCCCcc
Q 023374 198 VPIKADDDLKLLFRDIALPSDMLDIEKDLQKNGMKPAT 235 (283)
Q Consensus 198 ~~~~VD~efk~lW~~v~vP~d~~Di~k~L~~~Glkp~~ 235 (283)
..++..++--.+..+++.- ...-|-+.|++.++..-+
T Consensus 252 ~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~ 288 (373)
T PTZ00448 252 IQLELSNKSDILFNSITND-PRHIIDKKLEKTEVSIKE 288 (373)
T ss_pred cccccccccccchhccCCC-hHHHHhHhhhhhcccccc
Confidence 3444444444555555421 123478888888877743
No 78
>PF09066 B2-adapt-app_C: Beta2-adaptin appendage, C-terminal sub-domain; InterPro: IPR015151 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. These vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transport []. Clathrin coats contain both clathrin (acts as a scaffold) and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors [, ]. AP (adaptor protein) complexes are found in coated vesicles and clathrin-coated pits. AP complexes connect cargo proteins and lipids to clathrin at vesicle budding sites, as well as binding accessory proteins that regulate coat assembly and disassembly (such as AP180, epsins and auxilin). There are different AP complexes in mammals. AP1 is responsible for the transport of lysosomal hydrolases between the TGN and endosomes []. AP2 associates with the plasma membrane and is responsible for endocytosis []. AP3 is responsible for protein trafficking to lysosomes and other related organelles []. AP4 is less well characterised. AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). For example, in AP1 these subunits are gamma-1-adaptin, beta-1-adaptin, mu-1 and sigma-1, while in AP2 they are alpha-adaptin, beta-2-adaptin, mu-2 and sigma-2. Each subunit has a specific function. Adaptins recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal ear (appendage) domains. Mu recognises tyrosine-based sorting signals within the cytoplasmic domains of transmembrane cargo proteins []. One function of clathrin and AP2 complex-mediated endocytosis is to regulate the number of GABA(A) receptors available at the cell surface []. This entry represents a subdomain of the appendage (ear) domain of beta-adaptin from AP clathrin adaptor complexes. This domain has a three-layer arrangement, alpha-beta-alpha, with a bifurcated antiparallel beta-sheet []. This domain is required for binding to clathrin, and its subsequent polymerisation. Furthermore, a hydrophobic patch present in the domain also binds to a subset of D-phi-F/W motif-containing proteins that are bound by the alpha-adaptin appendage domain (epsin, AP180, eps15) []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030131 clathrin adaptor complex; PDB: 1E42_B 2G30_A 2IV9_B 2IV8_A 3HS9_A 3H1Z_A.
Probab=27.74 E-value=47 Score=26.30 Aligned_cols=33 Identities=18% Similarity=0.348 Sum_probs=23.2
Q ss_pred CHHHHHHhhhcC----------CC---CChhHHHHHHHHCCCCCcc
Q 023374 203 DDDLKLLFRDIA----------LP---SDMLDIEKDLQKNGMKPAT 235 (283)
Q Consensus 203 D~efk~lW~~v~----------vP---~d~~Di~k~L~~~Glkp~~ 235 (283)
-++|..+|.++. ++ .+.++|++.|+..||-.+.
T Consensus 9 ~~~F~~~W~sl~~~~~~e~~~~~~~~~~~~~~i~~~L~~~nI~~iA 54 (114)
T PF09066_consen 9 PEEFQEMWKSLPDSNQQELSIQLNASVPSPDAIEEKLQANNIFTIA 54 (114)
T ss_dssp HHHHHHHHHHS-GGG--EEEEEETT----HHHHHHHHHCTT-EEEE
T ss_pred HHHHHHHHHhCCcccceEEEEeccccCCcHHHHHHHHHHCCEEEEe
Confidence 368999999851 12 3566799999999998874
No 79
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=27.05 E-value=1.4e+02 Score=27.38 Aligned_cols=43 Identities=23% Similarity=0.337 Sum_probs=33.3
Q ss_pred HHHHHHHHhhCCCCeehhhHhhhh----hcHHHHHHHHHHcCcEEEEe
Q 023374 139 KSQLLVLVRKFPEGIAVIDLKDSY----PTVMEDLQALKAAGQIWLLS 182 (283)
Q Consensus 139 k~~LL~lL~k~~~Gi~v~dLkD~~----p~~~~~I~~Le~~g~Ilvl~ 182 (283)
...+|++|+++.. +++.||.+-+ ..+-.||+.|+++|.|.-+.
T Consensus 7 ~~~Il~~L~~~~~-v~v~eLa~~l~VS~~TIRRDL~~Le~~g~l~r~~ 53 (256)
T PRK10434 7 QAAILEYLQKQGK-TSVEELAQYFDTTGTTIRKDLVILEHAGTVIRTY 53 (256)
T ss_pred HHHHHHHHHHcCC-EEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEE
Confidence 3568888887543 8888888754 55789999999999887665
No 80
>PRK13239 alkylmercury lyase; Provisional
Probab=27.04 E-value=1.5e+02 Score=26.96 Aligned_cols=42 Identities=17% Similarity=0.176 Sum_probs=31.7
Q ss_pred HHHHHHhccCCCCCHHHHhhhhCCCCCCcHHHHHhhhCCCceEEeC
Q 023374 80 RVIDRLLETRQAFTPEEINRDCYVDVNANKAVFDSLRNNPKVHYDG 125 (283)
Q Consensus 80 ~vvd~Lk~~~~plt~~eI~~~~~~di~~~~~l~e~L~~npKI~~d~ 125 (283)
.++..|. +++|.|..+|...++.+.. ++...|..-+-++||+
T Consensus 26 ~llr~la-~G~pvt~~~lA~~~~~~~~---~v~~~L~~l~~~~~d~ 67 (206)
T PRK13239 26 PLLRLLA-KGRPVSVTTLAAALGWPVE---EVEAVLEAMPDTEYDE 67 (206)
T ss_pred HHHHHHH-cCCCCCHHHHHHHhCCCHH---HHHHHHHhCCCeEECC
Confidence 4444444 8999999999998888876 4556666667889986
No 81
>PRK10753 transcriptional regulator HU subunit alpha; Provisional
Probab=26.95 E-value=3e+02 Score=21.21 Aligned_cols=44 Identities=14% Similarity=0.204 Sum_probs=32.9
Q ss_pred CHHHHHHHHhhCCCCeehhhHhhhhhcHHHHHHHHHHcCcEEEEe
Q 023374 138 DKSQLLVLVRKFPEGIAVIDLKDSYPTVMEDLQALKAAGQIWLLS 182 (283)
Q Consensus 138 ~k~~LL~lL~k~~~Gi~v~dLkD~~p~~~~~I~~Le~~g~Ilvl~ 182 (283)
++.+|.+.|... .|++..|.+...-.+.+.|.+--.+|+-+.++
T Consensus 2 ~K~eli~~ia~~-~~~s~~~~~~~v~~~~~~i~~~L~~g~~V~i~ 45 (90)
T PRK10753 2 NKTQLIDVIADK-AELSKTQAKAALESTLAAITESLKEGDAVQLV 45 (90)
T ss_pred CHHHHHHHHHHH-hCCCHHHHHHHHHHHHHHHHHHHHcCCeEEEc
Confidence 688999999765 57999999888888888886655555544444
No 82
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=26.27 E-value=91 Score=23.27 Aligned_cols=54 Identities=13% Similarity=0.182 Sum_probs=35.0
Q ss_pred HHHHHHHHhccCCCCCHHHHhhhhCCCCCCcHHHHHhhhCCCceEEeCCeeeeecC
Q 023374 78 IKRVIDRLLETRQAFTPEEINRDCYVDVNANKAVFDSLRNNPKVHYDGKRFSYKSK 133 (283)
Q Consensus 78 i~~vvd~Lk~~~~plt~~eI~~~~~~di~~~~~l~e~L~~npKI~~d~~~f~yKP~ 133 (283)
|..|+..|. ..+.++.+|...++++-..-...++.|.++-=|..+++.|.=-++
T Consensus 8 i~~IL~~l~--~~~~~~t~i~~~~~L~~~~~~~yL~~L~~~gLI~~~~~~Y~lTek 61 (77)
T PF14947_consen 8 IFDILKILS--KGGAKKTEIMYKANLNYSTLKKYLKELEEKGLIKKKDGKYRLTEK 61 (77)
T ss_dssp HHHHHHHH---TT-B-HHHHHTTST--HHHHHHHHHHHHHTTSEEEETTEEEE-HH
T ss_pred HHHHHHHHH--cCCCCHHHHHHHhCcCHHHHHHHHHHHHHCcCeeCCCCEEEECcc
Confidence 445555555 778899999876665555545788999999999887777765443
No 83
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=26.18 E-value=1.6e+02 Score=23.97 Aligned_cols=65 Identities=17% Similarity=0.223 Sum_probs=46.6
Q ss_pred CCCCCHH-HHHHHHhhCCCCeehhhHhhhh----hcHHHHHHHHHHcCcEEEEecC-CCCceeEecCCCCC
Q 023374 134 HDLKDKS-QLLVLVRKFPEGIAVIDLKDSY----PTVMEDLQALKAAGQIWLLSNF-DSQEDIAYPNDPRV 198 (283)
Q Consensus 134 y~Ik~k~-~LL~lL~k~~~Gi~v~dLkD~~----p~~~~~I~~Le~~g~Ilvl~~k-d~~~~ivf~ND~~~ 198 (283)
|++.... .+|..|...++|++..||.+.. +.+-..|+.|++.|-|....+. |.....|+.-+.+.
T Consensus 27 ~glt~~q~~vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~ 97 (144)
T PRK03573 27 LELTQTHWVTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQTCASDRRAKRIKLTEKAE 97 (144)
T ss_pred cCCCHHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeecCCCCcCeeeeEEChHHH
Confidence 5555544 4667776666788888887754 6688999999999998888765 55555666666553
No 84
>TIGR01261 hisB_Nterm histidinol-phosphatase. This model describes histidinol phosphatase. All known examples in the scope of this model are bifunctional proteins with a histidinol phosphatase domain followed by an imidazoleglycerol-phosphate dehydratase domain. These enzymatic domains catalyze the ninth and seventh steps, respectively, of histidine biosynthesis.
Probab=25.82 E-value=76 Score=27.05 Aligned_cols=27 Identities=30% Similarity=0.327 Sum_probs=21.8
Q ss_pred hhhcHHHHHHHHHHcC-cEEEEecCCCC
Q 023374 161 SYPTVMEDLQALKAAG-QIWLLSNFDSQ 187 (283)
Q Consensus 161 ~~p~~~~~I~~Le~~g-~Ilvl~~kd~~ 187 (283)
=||++.+.|+.|.+.| .+.|++|+.|.
T Consensus 30 ~~pgv~e~L~~L~~~g~~l~IvSN~~g~ 57 (161)
T TIGR01261 30 FEKGVIPALLKLKKAGYKFVMVTNQDGL 57 (161)
T ss_pred ECCCHHHHHHHHHHCCCeEEEEeCCccc
Confidence 3799999999999877 67777987543
No 85
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=25.80 E-value=1.4e+02 Score=27.68 Aligned_cols=42 Identities=26% Similarity=0.247 Sum_probs=0.0
Q ss_pred HHHHHHHhhCCCCeehhhHhh----hhhcHHHHHHHHHHcCcEEEEe
Q 023374 140 SQLLVLVRKFPEGIAVIDLKD----SYPTVMEDLQALKAAGQIWLLS 182 (283)
Q Consensus 140 ~~LL~lL~k~~~Gi~v~dLkD----~~p~~~~~I~~Le~~g~Ilvl~ 182 (283)
..++++|+++.. +.+.||.+ +-..+-.||..|++.|.+.-+.
T Consensus 20 ~~Il~~L~~~~~-vtv~eLa~~l~VS~~TIRRDL~~Le~~G~l~r~~ 65 (269)
T PRK09802 20 EQIIQRLRQQGS-VQVNDLSALYGVSTVTIRNDLAFLEKQGIAVRAY 65 (269)
T ss_pred HHHHHHHHHcCC-EeHHHHHHHHCCCHHHHHHHHHHHHhCCCeEEEe
No 86
>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=25.69 E-value=2e+02 Score=19.50 Aligned_cols=45 Identities=22% Similarity=0.275 Sum_probs=33.6
Q ss_pred HHHHHhhCCCCeehhhHhhhh----hcHHHHHHHHHHcCcEEEEecCCCC
Q 023374 142 LLVLVRKFPEGIAVIDLKDSY----PTVMEDLQALKAAGQIWLLSNFDSQ 187 (283)
Q Consensus 142 LL~lL~k~~~Gi~v~dLkD~~----p~~~~~I~~Le~~g~Ilvl~~kd~~ 187 (283)
+|.+|..+ +|+++.+|.+.. +.+-..|+.|++.|-|--..++++.
T Consensus 8 iL~~l~~~-~~~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~r~~~~~D~ 56 (59)
T PF01047_consen 8 ILRILYEN-GGITQSELAEKLGISRSTVTRIIKRLEKKGLIERERDPDDR 56 (59)
T ss_dssp HHHHHHHH-SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTET
T ss_pred HHHHHHHc-CCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEeccCCCCC
Confidence 45555543 569999988865 5678889999999998888776554
No 87
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=25.40 E-value=54 Score=21.97 Aligned_cols=38 Identities=18% Similarity=0.247 Sum_probs=26.4
Q ss_pred HHHHHHhccCCCCCHHHHhhhhCCCCCCcHHHHHhhhCCC
Q 023374 80 RVIDRLLETRQAFTPEEINRDCYVDVNANKAVFDSLRNNP 119 (283)
Q Consensus 80 ~vvd~Lk~~~~plt~~eI~~~~~~di~~~~~l~e~L~~np 119 (283)
.|+.+|.+ .|+++.||.+.++++-+.=..-+..|+++-
T Consensus 6 ~Il~~L~~--~~~~~~el~~~l~~s~~~vs~hL~~L~~~g 43 (47)
T PF01022_consen 6 RILKLLSE--GPLTVSELAEELGLSQSTVSHHLKKLREAG 43 (47)
T ss_dssp HHHHHHTT--SSEEHHHHHHHHTS-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHh--CCCchhhHHHhccccchHHHHHHHHHHHCc
Confidence 57777877 799999999988887654444445555443
No 88
>COG0820 Predicted Fe-S-cluster redox enzyme [General function prediction only]
Probab=25.14 E-value=76 Score=31.13 Aligned_cols=68 Identities=19% Similarity=0.131 Sum_probs=38.3
Q ss_pred ccchhhhcccccCCChhHHHHHHHHHHHhccCCCCCHHHH-hhhhCCCCCCcHHHHHhhhCCC-ceEEeC
Q 023374 58 NDTERLQHINSIRKSPVGAQIKRVIDRLLETRQAFTPEEI-NRDCYVDVNANKAVFDSLRNNP-KVHYDG 125 (283)
Q Consensus 58 ~~~~~~q~~nt~~~~~v~tqi~~vvd~Lk~~~~plt~~eI-~~~~~~di~~~~~l~e~L~~np-KI~~d~ 125 (283)
||..|.+-.--...-++..-+.-+-.|...++..+||+=+ +....-++....+|.+.|++++ +|...|
T Consensus 222 nd~lR~~L~Pink~~~~e~l~~a~r~Y~~~t~~rVt~EY~Ll~~VND~~e~A~~L~~ll~~~~~~VNLIP 291 (349)
T COG0820 222 NDELRDQLMPINKKYPIEELLEAIRYYPEKSGRRVTFEYVLLDGVNDSLEHAKELAKLLKGIPCKVNLIP 291 (349)
T ss_pred CHHHHhhhhccccCCCHHHHHHHHHhhhhccCceEEEEeeecccccCCHHHHHHHHHHhcCCCceEEEee
Confidence 5555555555555556666666666666666766666544 2211122222346778888877 555543
No 89
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=24.98 E-value=2e+02 Score=20.09 Aligned_cols=43 Identities=26% Similarity=0.303 Sum_probs=32.5
Q ss_pred HHHHHHHHhhCCCCeehhhHhhhh----hcHHHHHHHHHHcCcEEEEe
Q 023374 139 KSQLLVLVRKFPEGIAVIDLKDSY----PTVMEDLQALKAAGQIWLLS 182 (283)
Q Consensus 139 k~~LL~lL~k~~~Gi~v~dLkD~~----p~~~~~I~~Le~~g~Ilvl~ 182 (283)
.-.+|.+| ...+|+++.+|.+.. +.+-..|+.|++.|-|-+.+
T Consensus 12 R~~Il~~L-~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~aGli~~~~ 58 (61)
T PF12840_consen 12 RLRILRLL-ASNGPMTVSELAEELGISQSTVSYHLKKLEEAGLIEVER 58 (61)
T ss_dssp HHHHHHHH-HHCSTBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHH-hcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEec
Confidence 34567777 345788888887754 66888999999999887664
No 90
>KOG3095 consensus Transcription initiation factor IIE, beta subunit [Transcription]
Probab=24.85 E-value=1.1e+02 Score=29.19 Aligned_cols=42 Identities=17% Similarity=0.261 Sum_probs=21.9
Q ss_pred CceeEecCCCCCCCCCCHHHHHHhhh---cCCCCChhHHHHHHHHCCCCCc
Q 023374 187 QEDIAYPNDPRVPIKADDDLKLLFRD---IALPSDMLDIEKDLQKNGMKPA 234 (283)
Q Consensus 187 ~~~ivf~ND~~~~~~VD~efk~lW~~---v~vP~d~~Di~k~L~~~Glkp~ 234 (283)
..+|+|.+.+.- +-=+-+|.+ ...+.| ++|.+--+..-|.+|
T Consensus 179 s~eIl~l~t~~d-----~k~kivf~ND~~~~~~VD-dEFk~LWr~V~Ip~~ 223 (284)
T KOG3095|consen 179 SGEILVLRTPKD-----DKPKIVFYNDKSCSFSVD-DEFKKLWRSVTIPSM 223 (284)
T ss_pred CCcEEEEeccCC-----CCCceEEecCCCCCcccC-HHHHHHHHhCCCChH
Confidence 345777776532 111223332 233453 567777777777774
No 91
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=24.58 E-value=2.3e+02 Score=21.37 Aligned_cols=51 Identities=22% Similarity=0.356 Sum_probs=33.7
Q ss_pred HHHHHHhhCCCCeehhhHhhhh----hcHHHHHHHHHHcCcEEEEecCC-CCceeEe
Q 023374 141 QLLVLVRKFPEGIAVIDLKDSY----PTVMEDLQALKAAGQIWLLSNFD-SQEDIAY 192 (283)
Q Consensus 141 ~LL~lL~k~~~Gi~v~dLkD~~----p~~~~~I~~Le~~g~Ilvl~~kd-~~~~ivf 192 (283)
.+|.+|.. .+++...+|++.. .++-..++.|+++|-|-+-+... +.|+++|
T Consensus 4 ~Il~~L~~-~~~~~f~~L~~~l~lt~g~Ls~hL~~Le~~GyV~~~k~~~~~~p~t~~ 59 (80)
T PF13601_consen 4 AILALLYA-NEEATFSELKEELGLTDGNLSKHLKKLEEAGYVEVEKEFEGRRPRTWY 59 (80)
T ss_dssp HHHHHHHH-HSEEEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEE-SSS--EEEE
T ss_pred HHHHHHhh-cCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEEEeccCCCCeEEE
Confidence 34555655 4567777777754 56788899999999988876554 4465554
No 92
>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=24.28 E-value=2.1e+02 Score=22.62 Aligned_cols=46 Identities=26% Similarity=0.387 Sum_probs=34.6
Q ss_pred HHHHHHHHhhCCCCeehhhHhhhh----hc-----HHHHHHHHHHcCcEEEEecC
Q 023374 139 KSQLLVLVRKFPEGIAVIDLKDSY----PT-----VMEDLQALKAAGQIWLLSNF 184 (283)
Q Consensus 139 k~~LL~lL~k~~~Gi~v~dLkD~~----p~-----~~~~I~~Le~~g~Ilvl~~k 184 (283)
+..+|.+|..+++-++++||-+.. |. +=..|+.|++.|-|.-+...
T Consensus 10 R~~Il~~l~~~~~~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~~~~~ 64 (120)
T PF01475_consen 10 RLAILELLKESPEHLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRKIEFG 64 (120)
T ss_dssp HHHHHHHHHHHSSSEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEET
T ss_pred HHHHHHHHHcCCCCCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEEEEcC
Confidence 567888888887778777765544 33 57789999999988888654
No 93
>PRK10026 arsenate reductase; Provisional
Probab=24.27 E-value=2e+02 Score=24.46 Aligned_cols=22 Identities=5% Similarity=0.197 Sum_probs=13.6
Q ss_pred CCChhHHHHHHHHHHHhccCCC
Q 023374 70 RKSPVGAQIKRVIDRLLETRQA 91 (283)
Q Consensus 70 ~~~~v~tqi~~vvd~Lk~~~~p 91 (283)
++.|--+-...++.||.+++-+
T Consensus 7 Y~~p~Cst~RKA~~wL~~~gi~ 28 (141)
T PRK10026 7 YHNPACGTSRNTLEMIRNSGTE 28 (141)
T ss_pred EeCCCCHHHHHHHHHHHHCCCC
Confidence 3334444567888888877433
No 94
>TIGR02716 C20_methyl_CrtF C-20 methyltransferase BchU. Members of this protein family are the S-adenosylmethionine-depenedent C-20 methyltransferase BchU, part of the pathway of bacteriochlorophyll c production in photosynthetic green sulfur bacteria. The position modified by this enzyme represents the difference between bacteriochlorophylls c and d; strains lacking this protein can only produced bacteriochlorophyll d.
Probab=24.05 E-value=90 Score=28.95 Aligned_cols=51 Identities=10% Similarity=0.147 Sum_probs=39.7
Q ss_pred HHHHHHhccCCCCCHHHHhhhhCCCCCCcHHHHHhhhCCCceEEeCCeeeeec
Q 023374 80 RVIDRLLETRQAFTPEEINRDCYVDVNANKAVFDSLRNNPKVHYDGKRFSYKS 132 (283)
Q Consensus 80 ~vvd~Lk~~~~plt~~eI~~~~~~di~~~~~l~e~L~~npKI~~d~~~f~yKP 132 (283)
.|.|+|.+ .|.|.+||.+.++++...-..|+++|..--=++.++++|.--|
T Consensus 14 glfd~L~~--gp~t~~eLA~~~~~~~~~~~~lL~~L~~lgll~~~~~~y~~t~ 64 (306)
T TIGR02716 14 DLFSHMAE--GPKDLATLAADTGSVPPRLEMLLETLRQMRVINLEDGKWSLTE 64 (306)
T ss_pred CcHHHHhc--CCCCHHHHHHHcCCChHHHHHHHHHHHhCCCeEecCCcEecch
Confidence 35677755 5999999999898887766678899988888877776666555
No 95
>cd00591 HU_IHF Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and higher-order nucleoprotein complex assembly. The dimer subunits associate to form a compact globular core from which two beta ribbon arms (one from each subunit) protrude. The beta arms track and bind the DNA minor groove. Despite sequence and structural similarity, IHF and HU can be distinguished by their different DNA substrate preferences.
Probab=23.79 E-value=1.9e+02 Score=21.46 Aligned_cols=45 Identities=18% Similarity=0.240 Sum_probs=35.1
Q ss_pred CHHHHHHHHhhCCCCeehhhHhhhhhcHHHHHHHHHHcCcEEEEec
Q 023374 138 DKSQLLVLVRKFPEGIAVIDLKDSYPTVMEDLQALKAAGQIWLLSN 183 (283)
Q Consensus 138 ~k~~LL~lL~k~~~Gi~v~dLkD~~p~~~~~I~~Le~~g~Ilvl~~ 183 (283)
|+++|.+.|.... |++..|++.-.....+.|.+...+|..+.+.+
T Consensus 1 ~K~~l~~~ia~~~-~~~~~~v~~vl~~~~~~i~~~L~~g~~V~l~~ 45 (87)
T cd00591 1 TKSELIEAIAEKT-GLSKKDAEAAVDAFLDVITEALAKGEKVELPG 45 (87)
T ss_pred CHHHHHHHHHHHh-CcCHHHHHHHHHHHHHHHHHHHhCCCeEEEeC
Confidence 5788888887655 88999999888888888877777776665554
No 96
>PRK09462 fur ferric uptake regulator; Provisional
Probab=23.48 E-value=1.9e+02 Score=24.04 Aligned_cols=61 Identities=11% Similarity=0.245 Sum_probs=39.5
Q ss_pred CChhHHHHHHHHHHHhcc-CCCCCHHHHhhhh---CCCCCCc--HHHHHhhhCCCceE---EeCCeeeee
Q 023374 71 KSPVGAQIKRVIDRLLET-RQAFTPEEINRDC---YVDVNAN--KAVFDSLRNNPKVH---YDGKRFSYK 131 (283)
Q Consensus 71 ~~~v~tqi~~vvd~Lk~~-~~plt~~eI~~~~---~~di~~~--~~l~e~L~~npKI~---~d~~~f~yK 131 (283)
|.-+..|=..|+++|.+. ..++|.+||.+.+ +..++.. ..-++.|...--|. ..++...|.
T Consensus 12 glr~T~qR~~Il~~l~~~~~~h~sa~eI~~~l~~~~~~i~~aTVYR~L~~L~e~Gli~~~~~~~~~~~y~ 81 (148)
T PRK09462 12 GLKVTLPRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRHNFEGGKSVFE 81 (148)
T ss_pred CCCCCHHHHHHHHHHHhCCCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCCEEEEEcCCCcEEEE
Confidence 444566778899999986 5799999998776 3344433 24556666655543 344555553
No 97
>PF09724 DUF2036: Uncharacterized conserved protein (DUF2036); InterPro: IPR019128 Sister chromatid cohesion protein DCC1 is a component of the RFC-like complex CTF18-RFC. This complex is required for the efficient establishment of chromosome cohesion during S-phase and may load or unload POL30/PCNA. During a clamp loading circle, the RFC:clamp complex binds to DNA and the recognition of the double-stranded/single-stranded junction stimulates ATP hydrolysis by RFC. The complex presumably provides bipartite ATP sites in which one subunit supplies a catalytic site for hydrolysis of ATP bound to the neighbouring subunit. Dissociation of RFC from the clamp leaves the clamp encircling DNA [, ].
Probab=23.35 E-value=3.4e+02 Score=25.65 Aligned_cols=144 Identities=16% Similarity=0.210 Sum_probs=81.5
Q ss_pred HHHHHHHHHHHhccC---CCCCHHHHhhhhCCCCCCcHHHHH-hhhCCCceEEe-CCeeeeecCCCCCCHHHHHHHHhhC
Q 023374 75 GAQIKRVIDRLLETR---QAFTPEEINRDCYVDVNANKAVFD-SLRNNPKVHYD-GKRFSYKSKHDLKDKSQLLVLVRKF 149 (283)
Q Consensus 75 ~tqi~~vvd~Lk~~~---~plt~~eI~~~~~~di~~~~~l~e-~L~~npKI~~d-~~~f~yKP~y~Ik~k~~LL~lL~k~ 149 (283)
..-++.|+.++-..+ ..++++++.+.+.-+.-. ..+++ .|+..-...-+ +..|.+...--++-- =..+|+.+
T Consensus 167 ~~~L~~il~~~~~~~~~~~~~~~~~~~~~l~~~~~p-~~v~~~vl~~~~~~~~~~~~~~~Ld~~ki~~~~--a~~lL~~~ 243 (325)
T PF09724_consen 167 FEILDLILTSAVEESWDLDQFPVEEVVEALEEDEYP-REVVEHVLRKFGTREDDDDSWWKLDEDKICRWF--AIQLLKAH 243 (325)
T ss_pred HHHHHHHHHHHHHcCCCcccCCHHHHHHHhcccCCC-HHHHHHHHHHhCCCccCCCceEEcCHHHHHHHH--HHHHHHhc
Confidence 444555566665554 467788887766544211 23332 22222111111 224444332111111 12345555
Q ss_pred C-CCeehhhHhhhhhcH-------HHHHHHHHHcCcEEEEecCCCCceeEecCCCCCCCCCCHHHHHHhhhcCCCC-Chh
Q 023374 150 P-EGIAVIDLKDSYPTV-------MEDLQALKAAGQIWLLSNFDSQEDIAYPNDPRVPIKADDDLKLLFRDIALPS-DML 220 (283)
Q Consensus 150 ~-~Gi~v~dLkD~~p~~-------~~~I~~Le~~g~Ilvl~~kd~~~~ivf~ND~~~~~~VD~efk~lW~~v~vP~-d~~ 220 (283)
. +.+.++|..+.|-+. .-+++-| .|..++-... ....|.|.+...+-..+-+=|+.||+--+ . +.+
T Consensus 244 ~~~~~~~~eFl~~Wk~~lP~~~~~~~~l~~L--~G~~~~~~~~-~~~~I~y~~~~~Lp~dp~~Rf~~LF~~~~--kW~~~ 318 (325)
T PF09724_consen 244 ASSSFPLDEFLEAWKSSLPEFFGMDPDLEML--RGLALIDDRP-SPTTIQYFPESDLPTDPKERFKELFKLRP--KWTLD 318 (325)
T ss_pred ccCCCCHHHHHHHHHHhCCCcCCCCCCHHHh--CCeeEeecCC-CCCEEEEecHHHCCCCHHHHHHHHHhcCC--CCCHH
Confidence 4 478888888888654 4457777 6766655333 44568888888887788888999998763 3 567
Q ss_pred HHHHHH
Q 023374 221 DIEKDL 226 (283)
Q Consensus 221 Di~k~L 226 (283)
||.-|+
T Consensus 319 ei~Pyi 324 (325)
T PF09724_consen 319 EIEPYI 324 (325)
T ss_pred HHHHhh
Confidence 887775
No 98
>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=23.13 E-value=2.6e+02 Score=19.30 Aligned_cols=51 Identities=18% Similarity=0.130 Sum_probs=34.6
Q ss_pred HHHHHHhhCCCCeehhhHhhhhh----cHHHHHHHHHHcCcEEEEecC-CCCceeE
Q 023374 141 QLLVLVRKFPEGIAVIDLKDSYP----TVMEDLQALKAAGQIWLLSNF-DSQEDIA 191 (283)
Q Consensus 141 ~LL~lL~k~~~Gi~v~dLkD~~p----~~~~~I~~Le~~g~Ilvl~~k-d~~~~iv 191 (283)
.+|.+|....+++...+|.+.+- .+-..|++|.+.|-|--..+. |+....|
T Consensus 7 ~vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv~~~~~~~d~R~~~~ 62 (68)
T PF13463_consen 7 QVLRALAHSDGPMTQSDLAERLGISKSTVSRIIKKLEEKGLVEKERDPHDKRSKRY 62 (68)
T ss_dssp HHHHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEESSCTTSEEE
T ss_pred HHHHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecCCCCcCCeeEE
Confidence 45666664458888888887654 678999999999999777665 4443333
No 99
>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=22.78 E-value=1.3e+02 Score=23.95 Aligned_cols=59 Identities=19% Similarity=0.253 Sum_probs=36.8
Q ss_pred hHHHHHHHHHHHhccCCCCCHHHHhhhhC---CCCCCc--HHHHHhhhCCC---ceEEeCCeeeeec
Q 023374 74 VGAQIKRVIDRLLETRQAFTPEEINRDCY---VDVNAN--KAVFDSLRNNP---KVHYDGKRFSYKS 132 (283)
Q Consensus 74 v~tqi~~vvd~Lk~~~~plt~~eI~~~~~---~di~~~--~~l~e~L~~np---KI~~d~~~f~yKP 132 (283)
+..|=..|+++|.+...++|.+||.+.+. ..++.. ..-++.|...- +|..+++...|-.
T Consensus 6 ~T~~R~~Il~~l~~~~~~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~~~~~~~~~~Y~~ 72 (120)
T PF01475_consen 6 LTPQRLAILELLKESPEHLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRKIEFGDGESRYEL 72 (120)
T ss_dssp HHHHHHHHHHHHHHHSSSEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEETTSEEEEEE
T ss_pred CCHHHHHHHHHHHcCCCCCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEEEEcCCCcceEee
Confidence 34455678999999988999999977763 344322 23455555543 3445556555554
No 100
>COG2425 Uncharacterized protein containing a von Willebrand factor type A (vWA) domain [General function prediction only]
Probab=22.68 E-value=1.7e+02 Score=29.67 Aligned_cols=67 Identities=18% Similarity=0.297 Sum_probs=49.7
Q ss_pred HhhhCCCceE---EeCCeeeeecCCCCCCHHHHHHHHhhCC-CCeehhhHhhhhhcHHHHHHHHHHc-CcEEEEe
Q 023374 113 DSLRNNPKVH---YDGKRFSYKSKHDLKDKSQLLVLVRKFP-EGIAVIDLKDSYPTVMEDLQALKAA-GQIWLLS 182 (283)
Q Consensus 113 e~L~~npKI~---~d~~~f~yKP~y~Ik~k~~LL~lL~k~~-~Gi~v~dLkD~~p~~~~~I~~Le~~-g~Ilvl~ 182 (283)
-+|+.|-++- |+...+.|+.-..+++-++++++|-... || -|+--+.-.+.++++.-+-. .+|++++
T Consensus 303 ~alaenR~~~~~lF~s~~~~~el~~k~~~~~e~i~fL~~~f~GG---TD~~~~l~~al~~~k~~~~~~adiv~IT 374 (437)
T COG2425 303 IALAENRDCYVILFDSEVIEYELYEKKIDIEELIEFLSYVFGGG---TDITKALRSALEDLKSRELFKADIVVIT 374 (437)
T ss_pred HHHHhccceEEEEecccceeeeecCCccCHHHHHHHHhhhcCCC---CChHHHHHHHHHHhhcccccCCCEEEEe
Confidence 5778887755 4778999999999999999999998876 77 57777777777776654322 2455555
No 101
>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=21.75 E-value=3.4e+02 Score=21.04 Aligned_cols=48 Identities=17% Similarity=0.217 Sum_probs=34.0
Q ss_pred HHHHHHHHhhCCCCeehhhHhhh---------hhcHHHHHHHHHHcCcEEEEecCCC
Q 023374 139 KSQLLVLVRKFPEGIAVIDLKDS---------YPTVMEDLQALKAAGQIWLLSNFDS 186 (283)
Q Consensus 139 k~~LL~lL~k~~~Gi~v~dLkD~---------~p~~~~~I~~Le~~g~Ilvl~~kd~ 186 (283)
+..+|++|....+.+++.||-+. .+.|-..|+.|++.|-|.-+...++
T Consensus 3 R~~Il~~l~~~~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~~~~~~~ 59 (116)
T cd07153 3 RLAILEVLLESDGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREIELGDG 59 (116)
T ss_pred HHHHHHHHHhCCCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEEEEeCCC
Confidence 45677777766666666665443 3557788999999999988865444
No 102
>TIGR00987 himA integration host factor, alpha subunit. This protein forms a site-specific DNA-binding heterodimer with the integration host factor beta subunit. It is closely related to the DNA-binding protein HU.
Probab=21.71 E-value=3.8e+02 Score=20.64 Aligned_cols=44 Identities=16% Similarity=0.169 Sum_probs=34.6
Q ss_pred CHHHHHHHHhhCCCCeehhhHhhhhhcHHHHHHHHHHcCcEEEEe
Q 023374 138 DKSQLLVLVRKFPEGIAVIDLKDSYPTVMEDLQALKAAGQIWLLS 182 (283)
Q Consensus 138 ~k~~LL~lL~k~~~Gi~v~dLkD~~p~~~~~I~~Le~~g~Ilvl~ 182 (283)
++.+|.+.|... .|++..|++..+-.+.+.|.+.-..|.-+.+.
T Consensus 3 tk~eli~~ia~~-~~~s~~~v~~vv~~~~~~i~~~L~~g~~V~l~ 46 (96)
T TIGR00987 3 TKAEMSEYLFDE-LGLSKREAKELVELFFEEIRRALENGEQVKLS 46 (96)
T ss_pred CHHHHHHHHHHH-hCcCHHHHHHHHHHHHHHHHHHHHcCCeEEec
Confidence 678899999764 58999999999999988888766666555554
No 103
>PRK00215 LexA repressor; Validated
Probab=21.70 E-value=1.7e+02 Score=25.44 Aligned_cols=45 Identities=18% Similarity=0.132 Sum_probs=34.9
Q ss_pred HHHHHhccCCCCCHHHHhhhhCC-CCCCcHHHHHhhhCCCceEEeC
Q 023374 81 VIDRLLETRQAFTPEEINRDCYV-DVNANKAVFDSLRNNPKVHYDG 125 (283)
Q Consensus 81 vvd~Lk~~~~plt~~eI~~~~~~-di~~~~~l~e~L~~npKI~~d~ 125 (283)
+.+|+.+.+.+.|+.||.+++++ +-+.-..++..|..+--|+.+.
T Consensus 13 i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~~~g~i~~~~ 58 (205)
T PRK00215 13 IRDHIEETGYPPSRREIADALGLRSPSAVHEHLKALERKGFIRRDP 58 (205)
T ss_pred HHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEeCC
Confidence 33344456789999999999998 7777678889998888887764
No 104
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=21.68 E-value=1.5e+02 Score=25.67 Aligned_cols=50 Identities=18% Similarity=0.179 Sum_probs=37.0
Q ss_pred HHHHHHHHh----ccCCCCCHHHHhhhhCCC-CCCcHHHHHhhhCCCceEEeCCe
Q 023374 78 IKRVIDRLL----ETRQAFTPEEINRDCYVD-VNANKAVFDSLRNNPKVHYDGKR 127 (283)
Q Consensus 78 i~~vvd~Lk----~~~~plt~~eI~~~~~~d-i~~~~~l~e~L~~npKI~~d~~~ 127 (283)
...|+++|. +...|.|..||.+.++++ -+.-...++.|...--|..+++.
T Consensus 8 q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~~g~i~~~~~~ 62 (199)
T TIGR00498 8 QQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALERKGYIERDPGK 62 (199)
T ss_pred HHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHHHCCCEecCCCC
Confidence 345555555 457789999999988888 44445788888888888887664
No 105
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=21.67 E-value=4.3e+02 Score=25.98 Aligned_cols=109 Identities=22% Similarity=0.282 Sum_probs=68.8
Q ss_pred HHHHHHHHHHHHHHHHHhhcCCC------CCC----CCC-------CCCCCccCCCC-CCCCC-ccccccchhhhccccc
Q 023374 9 RFKKQQEKCQETLSNIAAKSGAS------RAT----TTS-------RPTPAAASTAA-RSSPP-VKFSNDTERLQHINSI 69 (283)
Q Consensus 9 ~f~~qq~~~~~tl~s~a~~~~~~------~~~----~~~-------~~~~~~~~~~~-~~~~~-v~~s~~~~~~q~~nt~ 69 (283)
+++-...+|+.-++|-|++++.. .++ ++. -.|+...+.+- ..+|. --.|+|..+|=-...+
T Consensus 297 g~kyeRDk~ekf~~s~aas~~e~~~r~~~n~~~~sna~~s~~d~~ni~p~K~~t~s~~q~a~d~~llS~dEq~LC~~l~i 376 (432)
T COG5114 297 GLKYERDKFEKFGASTAASLSEGNSRYRSNSAHRSNAEYSQMDVKNILPSKNMTISDIQHAPDYALLSDDEQRLCETLNI 376 (432)
T ss_pred hhhhhhhHHHhhccchhhhhcccchhhhcccccccCcchhHHHHHhccCCCCCChhhhhccchhhhhcchHHHHHHHhCC
Confidence 34444566777788888777621 111 111 01333333221 11222 3468888788777888
Q ss_pred CCChhHHHHHHHHHHHhccCCCCCHHHHhhhhCCCCCCcHHHHHhhhC
Q 023374 70 RKSPVGAQIKRVIDRLLETRQAFTPEEINRDCYVDVNANKAVFDSLRN 117 (283)
Q Consensus 70 ~~~~v~tqi~~vvd~Lk~~~~plt~~eI~~~~~~di~~~~~l~e~L~~ 117 (283)
.-.|...--+.++.-+..++.+++-++-.+..++|...-..+.+.+.+
T Consensus 377 ~PkpyL~LK~~~is~~l~t~g~f~K~d~~~Lf~id~~ka~~~YdfF~~ 424 (432)
T COG5114 377 SPKPYLELKKEVISCFLRTRGEFTKEDFNRLFGIDLGKADGLYDFFLE 424 (432)
T ss_pred CCccHHHHHHHHHHHHHHhCCCccHHHHHHHhCcCcchhhHHHHHHHh
Confidence 777776666667777788899999999999889888877666665543
No 106
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=21.50 E-value=1.4e+02 Score=26.62 Aligned_cols=33 Identities=15% Similarity=0.148 Sum_probs=25.6
Q ss_pred HHHHHHhccCCCCCHHHHhhhhCCCCCCcHHHH
Q 023374 80 RVIDRLLETRQAFTPEEINRDCYVDVNANKAVF 112 (283)
Q Consensus 80 ~vvd~Lk~~~~plt~~eI~~~~~~di~~~~~l~ 112 (283)
+|.-.|.=.++|+|++||.+.+|+..+.-...+
T Consensus 30 ~iYgilyls~~Pmtl~Ei~E~lg~Sks~vS~~l 62 (177)
T COG1510 30 QIYGILYLSRKPLTLDEIAEALGMSKSNVSMGL 62 (177)
T ss_pred HHhhhheecCCCccHHHHHHHHCCCcchHHHHH
Confidence 555566667899999999999999888655433
No 107
>PF03551 PadR: Transcriptional regulator PadR-like family; InterPro: IPR005149 Phenolic acids, also called substituted hydroxycinnamic acids, are abundant in the plant kingdom because they are involved in the structure of plant cell walls and are present in some vacuoles. In plant-soil ecosystems they are released as free acids by hemicellulases produced by several fungi and bacteria. Of these weak acids, the most abundant are p-coumaric, ferulic, and caffeic acids, considered to be natural toxins that inhibit the growth of microorganisms, especially at low pHs. In spite of this chemical stress, some bacteria can use phenolic acids as a sole source of carbon. For other microorganisms, these compounds induce a specific response by which the organism adapts to its environment. The ubiquitous lactic acid bacterium Lactobacillus plantarum exhibits an inducible phenolic acid decarboxylase (PAD) activity which converts these substrates into less-toxic vinyl phenol derivatives. PadR acts as a repressor of padA gene expression in the phenolic acid stress response [].; PDB: 1XMA_B 2ESH_A 2DQL_B 3L9F_C 3ELK_B 4EJO_B 3L7W_A 3HHH_A 1YG2_A 3F8B_A ....
Probab=21.43 E-value=2e+02 Score=20.85 Aligned_cols=29 Identities=17% Similarity=0.155 Sum_probs=21.0
Q ss_pred cHHHHHHHHHHcCcEEEEecC--CCCceeEe
Q 023374 164 TVMEDLQALKAAGQIWLLSNF--DSQEDIAY 192 (283)
Q Consensus 164 ~~~~~I~~Le~~g~Ilvl~~k--d~~~~ivf 192 (283)
.+=..|+.|+++|-|-..... .+..+.+|
T Consensus 33 ~lY~~L~~Le~~gli~~~~~~~~~~~~rk~Y 63 (75)
T PF03551_consen 33 SLYPALKRLEEEGLIESRWEEEGNGRPRKYY 63 (75)
T ss_dssp HHHHHHHHHHHTTSEEEEEEEETTSSEEEEE
T ss_pred HHHHHHHHHHhCCCEEEeeeccCCCCCCEEE
Confidence 357789999999998777433 45555655
No 108
>PF08461 HTH_12: Ribonuclease R winged-helix domain; InterPro: IPR013668 This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaea.
Probab=20.95 E-value=96 Score=22.72 Aligned_cols=27 Identities=7% Similarity=0.198 Sum_probs=22.3
Q ss_pred HHHHHHhccCCCCCHHHHhhhh---CCCCC
Q 023374 80 RVIDRLLETRQAFTPEEINRDC---YVDVN 106 (283)
Q Consensus 80 ~vvd~Lk~~~~plt~~eI~~~~---~~di~ 106 (283)
+|+++|.+.+.|++..+|.+.+ +++++
T Consensus 2 ~IL~~L~~~~~P~g~~~l~~~L~~~g~~~s 31 (66)
T PF08461_consen 2 FILRILAESDKPLGRKQLAEELKLRGEELS 31 (66)
T ss_pred HHHHHHHHcCCCCCHHHHHHHHHhcChhhh
Confidence 6899999999999999997665 45554
No 109
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=20.79 E-value=1.9e+02 Score=27.21 Aligned_cols=66 Identities=26% Similarity=0.238 Sum_probs=45.2
Q ss_pred HHHHHHHhccCCCCCHHHHhhhhCCCCCCcHHHHHhhhCCCceEEeCCeeeeecCC--CCCCHHHHHHHH
Q 023374 79 KRVIDRLLETRQAFTPEEINRDCYVDVNANKAVFDSLRNNPKVHYDGKRFSYKSKH--DLKDKSQLLVLV 146 (283)
Q Consensus 79 ~~vvd~Lk~~~~plt~~eI~~~~~~di~~~~~l~e~L~~npKI~~d~~~f~yKP~y--~Ik~k~~LL~lL 146 (283)
+.++-+|++ .|.|++||.+.++++-..--.-+..|....=|.-+++.|+--+.- -+..-+.|++.|
T Consensus 16 k~lLllL~e--gPkti~EI~~~l~vs~~ai~pqiKkL~~~~LV~~~~~~Y~LS~~G~iiv~km~~ll~tl 83 (260)
T COG4742 16 KDLLLLLKE--GPKTIEEIKNELNVSSSAILPQIKKLKDKGLVVQEGDRYSLSSLGKIIVEKMEPLLDTL 83 (260)
T ss_pred HHHHHHHHh--CCCCHHHHHHHhCCCcHHHHHHHHHHhhCCCEEecCCEEEecchHHHHHHHHHHHHHHH
Confidence 566777777 799999999877766554333445566677788888898888753 344555555444
No 110
>TIGR01741 staph_tand_hypo conserved hypothetical protein. This model represents a tandem array of 10 proteins in Staphylococcus aureus and the C-terminal region of one protein each in Bacillus subtilis and Bacillus halodurans.
Probab=20.59 E-value=1.7e+02 Score=25.57 Aligned_cols=61 Identities=13% Similarity=0.279 Sum_probs=40.7
Q ss_pred cCcEEEEecCCCCceeEecCCCCCCCCCC-HHHHHHhhhcCCCCChhHHHHHHHHCCCCCccch
Q 023374 175 AGQIWLLSNFDSQEDIAYPNDPRVPIKAD-DDLKLLFRDIALPSDMLDIEKDLQKNGMKPATNT 237 (283)
Q Consensus 175 ~g~Ilvl~~kd~~~~ivf~ND~~~~~~VD-~efk~lW~~v~vP~d~~Di~k~L~~~Glkp~~~~ 237 (283)
+|.|+..=++.+..+.+|..|..-...|+ ++|.++|+.+- .=..+|.+....+|+.|-+.-
T Consensus 39 ~g~v~F~y~~~~~~e~~Ys~dIp~~ynVse~~f~~~~~~L~--~lf~~Lr~~Fk~n~qe~Wts~ 100 (157)
T TIGR01741 39 SGEVLFNYTTPESNQLIYYQDIPKHYNVSKDIFKTSLRELR--ELFEELREEFRNENLEPWTSC 100 (157)
T ss_pred CcEEEEEEcCCCCCceeeeecChHHcCcCHHHHHHHHHHHH--HHHHHHHHHHHHcCCCCcEEE
Confidence 45555553333555566666666566676 46899999973 124579999999999987643
No 111
>COG0064 GatB Asp-tRNAAsn/Glu-tRNAGln amidotransferase B subunit (PET112 homolog) [Translation, ribosomal structure and biogenesis]
Probab=20.39 E-value=1.8e+02 Score=29.89 Aligned_cols=53 Identities=21% Similarity=0.349 Sum_probs=40.7
Q ss_pred ecCCCCceeEecCCCCC-CCCCCHHHHHHhhhcCCCC-ChhHHHHHHHHCCCCCcc
Q 023374 182 SNFDSQEDIAYPNDPRV-PIKADDDLKLLFRDIALPS-DMLDIEKDLQKNGMKPAT 235 (283)
Q Consensus 182 ~~kd~~~~ivf~ND~~~-~~~VD~efk~lW~~v~vP~-d~~Di~k~L~~~Glkp~~ 235 (283)
|.|++..+.-|+.||.+ .+.+|+++.+-|+. .+|. -..+.+++....|++...
T Consensus 266 R~KE~a~DYRYfpePDl~p~~is~~~i~~~~~-~lPelP~~~~~r~~~~~gls~~d 320 (483)
T COG0064 266 RSKEEAEDYRYFPEPDLPPLEISDEWIEEVRA-TLPELPDEKRERYIKEYGLSEYD 320 (483)
T ss_pred cccccccccccCCCCCcCCccCCHHHHHHHHH-hCCCCCHHHHHHHHHHcCCCHHH
Confidence 45667777889999987 57899999999983 3342 136799999999998754
No 112
>cd08810 CARD_BCL10 Caspase activation and recruitment domain of B-cell lymphoma 10. Caspase activation and recruitment domain (CARD) similar to that found in BCL10 (B-cell lymphoma 10). BCL10 and Malt1 (mucosa-associated lymphoid tissue-lymphoma-translocation gene 1) are the integral components of CBM signalosomes. They associate with CARD9 to form M-CBM (CBM complex in myeloid immune cells) and with CARMA1 to form L-CBM (CBM complex in lymphoid immune cells), to mediate activation of NF-kB and MAPK by ITAM-coupled receptors expressed on immune cells. Both CARMA1 and CARD9 associate with BCL10 via a CARD-CARD interaction. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by asso
Probab=20.29 E-value=1.5e+02 Score=23.06 Aligned_cols=42 Identities=24% Similarity=0.343 Sum_probs=28.3
Q ss_pred HHHHHHHHhccCCCCCHHHHhhhhCCCCCCcH--HHHHhhhCCCc
Q 023374 78 IKRVIDRLLETRQAFTPEEINRDCYVDVNANK--AVFDSLRNNPK 120 (283)
Q Consensus 78 i~~vvd~Lk~~~~plt~~eI~~~~~~di~~~~--~l~e~L~~npK 120 (283)
..++.+||.+.+ -+|.+++++-.....+..+ .|++.|..+|+
T Consensus 18 ~~~l~d~L~s~~-ILt~~d~EeI~~~~t~~~qa~~LLdiL~rGp~ 61 (84)
T cd08810 18 ADRHFDYLRSKR-ILTRDDCEEISCRTTSRKQAGKLLDILAENPK 61 (84)
T ss_pred HHHHHHHHHHcC-CCCHHHHHHHhccCCcHHHHHHHHHHHhhCch
Confidence 357899999887 8888888776654433332 46677665554
No 113
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=20.17 E-value=1.4e+02 Score=24.13 Aligned_cols=33 Identities=9% Similarity=0.171 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHhcc-CCCCCHHHHhhhhCCCCCC
Q 023374 75 GAQIKRVIDRLLET-RQAFTPEEINRDCYVDVNA 107 (283)
Q Consensus 75 ~tqi~~vvd~Lk~~-~~plt~~eI~~~~~~di~~ 107 (283)
...+..|++||.++ .++++++||.+.+++....
T Consensus 8 ~~~i~~~~~~I~~~~~~~~sl~~lA~~~g~S~~~ 41 (127)
T PRK11511 8 AITIHSILDWIEDNLESPLSLEKVSERSGYSKWH 41 (127)
T ss_pred HHHHHHHHHHHHHhcCCCCCHHHHHHHHCcCHHH
Confidence 45578899999886 5789999999988887654
No 114
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=20.05 E-value=2.6e+02 Score=24.69 Aligned_cols=63 Identities=13% Similarity=0.160 Sum_probs=43.4
Q ss_pred CCCCCHH-HHHHHHhhCCCCeehhhHhhhh----hcHHHHHHHHHHcCcEEEEecC-CCCceeEecCCCC
Q 023374 134 HDLKDKS-QLLVLVRKFPEGIAVIDLKDSY----PTVMEDLQALKAAGQIWLLSNF-DSQEDIAYPNDPR 197 (283)
Q Consensus 134 y~Ik~k~-~LL~lL~k~~~Gi~v~dLkD~~----p~~~~~I~~Le~~g~Ilvl~~k-d~~~~ivf~ND~~ 197 (283)
|+|...+ .+|..|..+ +|++..||.+.+ +.+-..|+.||+.|-|...+++ |.....|+.=+.+
T Consensus 41 ~gLt~~q~~iL~~L~~~-~~itq~eLa~~l~l~~sTvtr~l~rLE~kGlI~R~~~~~DrR~~~I~LTekG 109 (185)
T PRK13777 41 YDLNINEHHILWIAYHL-KGASISEIAKFGVMHVSTAFNFSKKLEERGYLTFSKKEDDKRNTYIELTEKG 109 (185)
T ss_pred CCCCHHHHHHHHHHHhC-CCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHH
Confidence 4554433 345555443 589999998863 5678899999999988877665 4456667665554
Done!