Query 032632
Match_columns 137
No_of_seqs 150 out of 585
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 03:56:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032632.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032632hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00151 SWIB SWI complex, B 100.0 1.5E-28 3.3E-33 169.1 7.7 77 58-135 1-77 (77)
2 PF02201 SWIB: SWIB/MDM2 domai 100.0 7.1E-30 1.5E-34 175.3 -0.3 76 58-134 1-76 (76)
3 KOG1946 RNA polymerase I trans 99.9 1.1E-27 2.4E-32 196.0 6.4 81 55-136 97-177 (240)
4 COG5531 SWIB-domain-containing 99.9 1.2E-23 2.7E-28 171.8 7.3 81 54-135 117-197 (237)
5 PRK14724 DNA topoisomerase III 99.9 3.8E-23 8.3E-28 194.6 8.7 76 58-134 912-987 (987)
6 KOG2570 SWI/SNF transcription 99.7 1E-17 2.3E-22 145.5 5.6 78 58-136 205-282 (420)
7 PRK06319 DNA topoisomerase I/S 99.6 1.4E-15 3E-20 142.0 5.3 77 58-135 784-860 (860)
8 KOG2522 Filamentous baseplate 94.8 0.048 1E-06 49.4 5.0 58 58-115 357-420 (560)
9 PRK05350 acyl carrier protein; 86.7 0.62 1.4E-05 31.5 2.5 53 77-133 2-54 (82)
10 PRK05828 acyl carrier protein; 83.8 1.6 3.5E-05 30.4 3.5 53 77-133 1-53 (84)
11 CHL00124 acpP acyl carrier pro 78.1 1.9 4.1E-05 28.8 2.2 53 77-133 1-53 (82)
12 PRK12449 acyl carrier protein; 77.8 3.8 8.1E-05 27.2 3.6 53 77-133 1-53 (80)
13 PTZ00171 acyl carrier protein; 73.5 4 8.6E-05 31.4 3.1 57 73-133 62-118 (148)
14 cd04762 HTH_MerR-trunc Helix-T 67.6 9.4 0.0002 21.8 3.3 24 66-96 4-27 (49)
15 PF08463 EcoEI_R_C: EcoEI R pr 66.0 3.8 8.2E-05 30.7 1.6 69 63-133 88-163 (164)
16 PF13545 HTH_Crp_2: Crp-like h 64.5 4.9 0.00011 25.9 1.7 52 57-112 22-75 (76)
17 cd01104 HTH_MlrA-CarA Helix-Tu 63.0 19 0.00041 22.7 4.3 57 66-129 4-67 (68)
18 PF07587 PSD1: Protein of unkn 55.7 15 0.00032 30.3 3.5 58 67-136 5-65 (266)
19 PRK00071 nadD nicotinic acid m 55.4 8.1 0.00018 30.1 1.8 31 66-96 171-201 (203)
20 PLN02945 nicotinamide-nucleoti 54.7 9 0.0002 31.0 2.0 32 65-96 204-235 (236)
21 PLN00129 succinate dehydrogena 54.0 9.7 0.00021 32.1 2.2 27 1-27 1-28 (276)
22 TIGR00482 nicotinate (nicotina 53.7 9.5 0.00021 29.6 1.9 32 65-96 162-193 (193)
23 PF08225 Antimicrobial19: Pseu 53.3 10 0.00023 20.7 1.4 20 109-133 4-23 (23)
24 TIGR03697 NtcA_cyano global ni 52.9 22 0.00047 26.3 3.7 49 62-114 142-192 (193)
25 PRK06973 nicotinic acid mononu 50.5 11 0.00023 31.0 1.8 32 65-96 202-241 (243)
26 smart00667 LisH Lissencephaly 48.9 13 0.00029 19.9 1.5 21 78-98 2-22 (34)
27 TIGR01764 excise DNA binding d 48.0 24 0.00053 20.2 2.7 26 66-98 5-30 (49)
28 PRK09392 ftrB transcriptional 48.0 29 0.00062 26.9 3.8 52 59-115 169-222 (236)
29 PRK07117 acyl carrier protein; 46.5 21 0.00046 24.4 2.5 51 77-132 1-52 (79)
30 PRK08558 adenine phosphoribosy 46.5 6.2 0.00013 32.2 -0.1 31 66-103 27-57 (238)
31 PF01047 MarR: MarR family; I 45.3 4.9 0.00011 24.8 -0.7 35 67-104 22-59 (59)
32 PRK13918 CRP/FNR family transc 44.5 27 0.00059 26.1 3.1 46 66-115 153-199 (202)
33 PF12728 HTH_17: Helix-turn-he 40.6 26 0.00057 21.1 2.1 27 66-99 5-31 (51)
34 TIGR00517 acyl_carrier acyl ca 40.2 25 0.00054 23.0 2.1 50 80-133 2-51 (77)
35 PRK07639 acyl carrier protein; 39.1 36 0.00077 23.4 2.8 54 77-133 1-54 (86)
36 cd02165 NMNAT Nicotinamide/nic 37.9 24 0.00052 27.1 1.9 33 64-96 160-192 (192)
37 COG1654 BirA Biotin operon rep 37.5 26 0.00057 24.3 1.9 21 65-92 22-42 (79)
38 cd09286 NMNAT_Eukarya Nicotina 36.4 25 0.00054 28.3 1.9 32 65-96 194-225 (225)
39 PRK08887 nicotinic acid mononu 36.3 28 0.0006 26.8 2.1 32 66-97 140-171 (174)
40 TIGR02057 PAPS_reductase phosp 35.4 21 0.00046 28.7 1.4 12 85-96 172-183 (226)
41 PRK05883 acyl carrier protein; 34.2 50 0.0011 23.0 2.9 55 75-133 8-62 (91)
42 PF08513 LisH: LisH; InterPro 33.2 27 0.00058 19.2 1.2 17 81-97 2-18 (27)
43 PF13950 Epimerase_Csub: UDP-g 32.9 70 0.0015 20.8 3.3 37 57-93 20-58 (62)
44 cd04763 HTH_MlrA-like Helix-Tu 32.3 1E+02 0.0023 19.5 4.1 58 66-130 4-68 (68)
45 KOG0995 Centromere-associated 32.1 1.9E+02 0.0041 27.3 7.0 53 41-98 35-91 (581)
46 TIGR02055 APS_reductase thiore 31.8 27 0.00058 27.2 1.4 12 85-96 136-147 (191)
47 PRK12563 sulfate adenylyltrans 31.6 26 0.00057 30.1 1.4 24 85-108 203-238 (312)
48 COG1846 MarR Transcriptional r 31.0 46 0.001 22.2 2.3 40 63-102 36-76 (126)
49 KOG0747 Putative NAD+-dependen 30.4 1.1E+02 0.0023 26.9 4.9 54 75-129 252-319 (331)
50 PF14838 INTS5_C: Integrator c 29.8 26 0.00057 33.4 1.2 43 64-109 618-665 (696)
51 COG5577 Spore coat protein [Ce 29.4 40 0.00088 26.0 1.9 37 64-100 85-121 (145)
52 PF13333 rve_2: Integrase core 29.1 54 0.0012 20.2 2.2 20 75-94 16-35 (52)
53 PF01726 LexA_DNA_bind: LexA D 29.0 54 0.0012 21.6 2.3 20 79-99 8-27 (65)
54 TIGR02854 spore_II_GA sigma-E 28.9 65 0.0014 26.9 3.3 34 82-115 140-204 (288)
55 PF08938 HBS1_N: HBS1 N-termin 28.4 20 0.00043 24.4 0.1 28 62-89 29-56 (79)
56 PRK09391 fixK transcriptional 27.9 62 0.0013 25.3 2.8 48 62-113 178-228 (230)
57 PRK05253 sulfate adenylyltrans 27.4 34 0.00074 29.0 1.4 13 85-97 193-205 (301)
58 PRK11161 fumarate/nitrate redu 27.2 64 0.0014 24.8 2.8 50 62-115 183-234 (235)
59 cd04761 HTH_MerR-SF Helix-Turn 27.2 1.1E+02 0.0025 17.6 3.3 24 66-96 4-27 (49)
60 PF13758 Prefoldin_3: Prefoldi 25.5 1.3E+02 0.0028 22.0 3.9 38 56-93 40-83 (99)
61 PF07308 DUF1456: Protein of u 25.5 1.3E+02 0.0028 20.2 3.6 40 66-114 17-58 (68)
62 PRK10402 DNA-binding transcrip 25.4 70 0.0015 24.8 2.7 46 66-115 173-219 (226)
63 PF10924 DUF2711: Protein of u 25.3 39 0.00084 27.9 1.3 59 56-115 65-126 (217)
64 TIGR00434 cysH phosophoadenyly 24.8 42 0.00092 26.1 1.4 12 85-96 157-168 (212)
65 PF13401 AAA_22: AAA domain; P 24.8 1.2E+02 0.0025 20.7 3.5 44 62-111 52-98 (131)
66 PLN02309 5'-adenylylsulfate re 24.8 40 0.00087 30.4 1.3 13 84-96 261-273 (457)
67 PRK07152 nadD putative nicotin 24.3 42 0.0009 28.4 1.3 16 82-97 170-185 (342)
68 PF01507 PAPS_reduct: Phosphoa 24.2 41 0.00089 24.4 1.1 12 85-96 143-154 (174)
69 PF13867 SAP30_Sin3_bdg: Sin3 24.0 77 0.0017 20.1 2.2 14 84-97 4-17 (53)
70 TIGR02039 CysD sulfate adenyly 23.5 45 0.00097 28.4 1.4 13 85-97 185-197 (294)
71 PF12368 DUF3650: Protein of u 23.4 41 0.00088 19.3 0.7 10 88-97 9-18 (28)
72 COG1057 NadD Nicotinic acid mo 23.3 60 0.0013 26.0 2.0 32 65-96 164-195 (197)
73 PF07037 DUF1323: Putative tra 22.8 99 0.0022 23.5 2.9 45 65-116 3-54 (122)
74 smart00422 HTH_MERR helix_turn 22.5 1.6E+02 0.0035 18.3 3.6 24 66-96 4-27 (70)
75 KOG2076 RNA polymerase III tra 22.4 1.7E+02 0.0037 29.0 5.1 78 52-136 123-205 (895)
76 PF12213 Dpoe2NT: DNA polymera 22.4 79 0.0017 21.5 2.1 43 56-98 16-59 (73)
77 KOG4144 Arylalkylamine N-acety 22.3 50 0.0011 26.6 1.3 34 82-115 119-152 (190)
78 PRK00982 acpP acyl carrier pro 22.3 73 0.0016 20.6 1.9 50 80-133 2-51 (78)
79 PF04636 PA26: PA26 p53-induce 21.7 1.2E+02 0.0027 27.4 3.8 56 56-131 317-389 (450)
80 cd04764 HTH_MlrA-like_sg1 Heli 21.4 2.2E+02 0.0048 17.8 4.3 57 66-129 4-66 (67)
81 TIGR00424 APS_reduc 5'-adenyly 21.4 51 0.0011 29.8 1.3 12 85-96 267-278 (463)
82 PF02650 HTH_WhiA: WhiA C-term 20.9 46 0.00099 23.3 0.8 45 85-136 24-71 (85)
83 COG0175 CysH 3'-phosphoadenosi 20.7 55 0.0012 26.9 1.3 12 85-96 184-195 (261)
84 PF00010 HLH: Helix-loop-helix 20.7 1.3E+02 0.0028 18.3 2.8 18 75-92 36-53 (55)
85 PF05643 DUF799: Putative bact 20.7 28 0.00062 28.6 -0.4 38 85-124 76-113 (215)
86 KOG4068 Uncharacterized conser 20.4 1.1E+02 0.0024 24.5 2.8 23 80-102 68-90 (174)
87 PF12487 DUF3703: Protein of u 20.3 1E+02 0.0023 22.8 2.6 19 54-72 93-111 (112)
No 1
>smart00151 SWIB SWI complex, BAF60b domains.
Probab=99.95 E-value=1.5e-28 Score=169.09 Aligned_cols=77 Identities=52% Similarity=0.978 Sum_probs=74.3
Q ss_pred CCccccCCHHHHhhhCCCCcCHHHHHHHHHHHHhHcCCCCCCCCcccccchhHHhhhCCCCccCHHHHHHHhcccCCC
Q 032632 58 ISKVSPVSPALAKFLGAPEASRSDAVRQIWAHVKTHNLQNPENKREILCDEKLKAIFEGKNAVGFLEIGKLLSPHFVK 135 (137)
Q Consensus 58 ~~k~~~lSpeLa~fLG~~e~SR~eVvk~LW~YIK~nnLQDP~nKr~I~cDekLk~LFgg~d~v~~~el~klL~~Hl~k 135 (137)
++++|.||++|++|+|..++||+||++.||+|||.||||||+|++.|+||+.|++||| ++++.|++|+++|++||.+
T Consensus 1 ~~~~~~ls~~L~~~lg~~~~tr~ev~~~lw~YIk~n~L~d~~~k~~i~~D~~L~~l~~-~~~v~~~~~~~ll~~Hl~~ 77 (77)
T smart00151 1 ITKKVTLSPELAKVLGAPEMTRTEIIKRLWEYIKEHNLQDPQNKREILCDSKLEQIFG-KDRMDMFEMNKLLTPHLIK 77 (77)
T ss_pred CCCcccCCHHHHHHhCCCcCcHHHHHHHHHHHHHHhcccCCccCCEEecCHHHHHHHC-cCeecHHHHHHHHHHHcCC
Confidence 5789999999999999999999999999999999999999999999999999999997 7899999999999999975
No 2
>PF02201 SWIB: SWIB/MDM2 domain; InterPro: IPR003121 The SWI/SNF family of complexes, which are conserved from yeast to humans, are ATP-dependent chromatin-remodelling proteins that facilitate transcription activation []. The mammalian complexes are made up of 9-12 proteins called BAFs (BRG1-associated factors). The BAF60 family have at least three members: BAF60a, which is ubiquitous, BAF60b and BAF60c, which are expressed in muscle and pancreatic tissues, respectively. BAF60b is present in alternative forms of the SWI/SNF complex, including complex B (SWIB), which lacks BAF60a. The SWIB domain is a conserved region found within the BAF60b proteins [], and can be found fused to the C terminus of DNA topoisomerase in Chlamydia. MDM2 is an oncoprotein that acts as a cellular inhibitor of the p53 tumour suppressor by binding to the transactivation domain of p53 and suppressing its ability to activate transcription []. p53 acts in response to DNA damage, inducing cell cycle arrest and apoptosis. Inactivation of p53 is a common occurrence in neoplastic transformations. The core of MDM2 folds into an open bundle of four helices, which is capped by two small 3-stranded beta-sheets. It consists of a duplication of two structural repeats. MDM2 has a deep hydrophobic cleft on which the p53 alpha-helix binds; p53 residues involved in transactivation are buried deep within the cleft of MDM2, thereby concealing the p53 transactivation domain. The SWIB and MDM2 domains are homologous and share a common fold.; GO: 0005515 protein binding; PDB: 1V31_A 3FE7_A 3JZQ_B 3EQY_B 2VYR_A 3JZO_A 3DAB_E 3LBJ_E 3FEA_A 3FDO_A ....
Probab=99.95 E-value=7.1e-30 Score=175.31 Aligned_cols=76 Identities=51% Similarity=0.916 Sum_probs=70.8
Q ss_pred CCccccCCHHHHhhhCCCCcCHHHHHHHHHHHHhHcCCCCCCCCcccccchhHHhhhCCCCccCHHHHHHHhcccCC
Q 032632 58 ISKVSPVSPALAKFLGAPEASRSDAVRQIWAHVKTHNLQNPENKREILCDEKLKAIFEGKNAVGFLEIGKLLSPHFV 134 (137)
Q Consensus 58 ~~k~~~lSpeLa~fLG~~e~SR~eVvk~LW~YIK~nnLQDP~nKr~I~cDekLk~LFgg~d~v~~~el~klL~~Hl~ 134 (137)
|+++|+||++|++|+|..++||+||++.||+||++||||||+|++.|+||+.|+.||+ .++|++++|+++|++||+
T Consensus 1 ~~k~~~ls~~L~~~lg~~~~sr~~v~~~lw~YIk~~~L~dp~~k~~I~cD~~L~~lf~-~~~v~~~~i~~~l~~hl~ 76 (76)
T PF02201_consen 1 FPKRFKLSPELAEFLGEDELSRSEVVKRLWQYIKENNLQDPKDKRIIICDEKLKKLFG-KDSVNFFEIPKLLKPHLI 76 (76)
T ss_dssp -EEEEHHHHHHHHHTT-SCEEHHHHHHHHHHHHHHTTSBESSSTTEEE-TTSHHHHHH-TSECSEEETTHHHHHHHE
T ss_pred CCCCccCCHHHHHHhCCCCCCHHHHHHHHHHHHHHhcCCCcccCceEecCHHHHHHhC-CCeecHhhHHHHHHHhcC
Confidence 5789999999999999999999999999999999999999999999999999999999 599999999999999984
No 3
>KOG1946 consensus RNA polymerase I transcription factor UAF [Transcription]
Probab=99.94 E-value=1.1e-27 Score=195.98 Aligned_cols=81 Identities=57% Similarity=0.976 Sum_probs=77.6
Q ss_pred CCCCCccccCCHHHHhhhCCCCcCHHHHHHHHHHHHhHcCCCCCCCCcccccchhHHhhhCCCCccCHHHHHHHhcccCC
Q 032632 55 PTGISKVSPVSPALAKFLGAPEASRSDAVRQIWAHVKTHNLQNPENKREILCDEKLKAIFEGKNAVGFLEIGKLLSPHFV 134 (137)
Q Consensus 55 ~~G~~k~~~lSpeLa~fLG~~e~SR~eVvk~LW~YIK~nnLQDP~nKr~I~cDekLk~LFgg~d~v~~~el~klL~~Hl~ 134 (137)
+.|+++.+.||++|++|+|.++++|.||++.||+|||+||||||.||+.|+|||+|+.||++ +.|+|++|.+||.+||+
T Consensus 97 ~~g~~kl~~ls~~L~~~~G~~~lsR~~vvk~iw~YIke~nLqDP~nkr~IlCDekL~~iF~~-k~v~~fem~KLL~~H~~ 175 (240)
T KOG1946|consen 97 SWGSTKLIPLSPSLARFVGTSELSRTDVVKKIWAYIKEHNLQDPKNKREILCDEKLKSIFGK-KRVGMFEMLKLLTKHFL 175 (240)
T ss_pred CcCcccccccCHHHHhhcccccccHHHHHHHHHHHHHHhccCCccccCeeeeHHHHHHHhcc-CccceeeHHHHHHHhcc
Confidence 37999999999999999999999999999999999999999999999999999999999994 56999999999999998
Q ss_pred CC
Q 032632 135 KT 136 (137)
Q Consensus 135 k~ 136 (137)
+.
T Consensus 176 ~~ 177 (240)
T KOG1946|consen 176 KN 177 (240)
T ss_pred Cc
Confidence 74
No 4
>COG5531 SWIB-domain-containing proteins implicated in chromatin remodeling [Chromatin structure and dynamics]
Probab=99.89 E-value=1.2e-23 Score=171.82 Aligned_cols=81 Identities=41% Similarity=0.757 Sum_probs=77.8
Q ss_pred CCCCCCccccCCHHHHhhhCCCCcCHHHHHHHHHHHHhHcCCCCCCCCcccccchhHHhhhCCCCccCHHHHHHHhcccC
Q 032632 54 RPTGISKVSPVSPALAKFLGAPEASRSDAVRQIWAHVKTHNLQNPENKREILCDEKLKAIFEGKNAVGFLEIGKLLSPHF 133 (137)
Q Consensus 54 ~~~G~~k~~~lSpeLa~fLG~~e~SR~eVvk~LW~YIK~nnLQDP~nKr~I~cDekLk~LFgg~d~v~~~el~klL~~Hl 133 (137)
.++-..+.|.+|+.|+.|||..++||+|||+.||+|||.||||||+||++|.||++|+.||| .+.+.||+|.+.|.+|+
T Consensus 117 ~~~~~~~~~~lS~~La~ilG~~~~tr~~~v~~lw~YIk~h~lq~~~nkr~I~~D~~L~~v~g-~~p~~mf~~~k~l~~hl 195 (237)
T COG5531 117 KNSPSGEKVKLSPKLAAILGLEPGTRPEAVKKLWKYIKKHNLQDPNNKRLILCDSKLKKVLG-SDPIDMFELTKPLSPHL 195 (237)
T ss_pred cccCCCCceecCHHHHHHhCCCCCCccHHHHHHHHHHHHhcCCCccccceecccHHHHHHhC-CCchhhhhhhcccccce
Confidence 35667899999999999999999999999999999999999999999999999999999999 89999999999999999
Q ss_pred CC
Q 032632 134 VK 135 (137)
Q Consensus 134 ~k 135 (137)
++
T Consensus 196 ~~ 197 (237)
T COG5531 196 IK 197 (237)
T ss_pred ec
Confidence 87
No 5
>PRK14724 DNA topoisomerase III; Provisional
Probab=99.88 E-value=3.8e-23 Score=194.63 Aligned_cols=76 Identities=32% Similarity=0.595 Sum_probs=73.9
Q ss_pred CCccccCCHHHHhhhCCCCcCHHHHHHHHHHHHhHcCCCCCCCCcccccchhHHhhhCCCCccCHHHHHHHhcccCC
Q 032632 58 ISKVSPVSPALAKFLGAPEASRSDAVRQIWAHVKTHNLQNPENKREILCDEKLKAIFEGKNAVGFLEIGKLLSPHFV 134 (137)
Q Consensus 58 ~~k~~~lSpeLa~fLG~~e~SR~eVvk~LW~YIK~nnLQDP~nKr~I~cDekLk~LFgg~d~v~~~el~klL~~Hl~ 134 (137)
+..+|.|||+|++|||..++||++|++.||+|||+||||||.||+.|+||++|+.||| +++|.|++|+++|++||.
T Consensus 912 ~~~~~~ls~~La~~lg~~~~~r~~v~~~lW~YIK~~~Lqdp~~k~~i~cD~~L~~vfg-~~~~~~~~~~~~l~~hl~ 987 (987)
T PRK14724 912 PAAGLKPSAALAAVIGAEPVARPEVIKKLWDYIKANNLQDPADKRAINADAKLRPVFG-KDQVTMFELAGIVGKHLS 987 (987)
T ss_pred cccccCCCHHHHHHhCCCcCCHHHHHHHHHHHHHHccCCCcccCCeeccchHHHHHhC-CCcccHHHHHHHHHHhcC
Confidence 7789999999999999999999999999999999999999999999999999999998 899999999999999984
No 6
>KOG2570 consensus SWI/SNF transcription activation complex subunit [Chromatin structure and dynamics; Transcription]
Probab=99.70 E-value=1e-17 Score=145.50 Aligned_cols=78 Identities=35% Similarity=0.602 Sum_probs=74.1
Q ss_pred CCccccCCHHHHhhhCCCCcCHHHHHHHHHHHHhHcCCCCCCCCcccccchhHHhhhCCCCccCHHHHHHHhcccCCCC
Q 032632 58 ISKVSPVSPALAKFLGAPEASRSDAVRQIWAHVKTHNLQNPENKREILCDEKLKAIFEGKNAVGFLEIGKLLSPHFVKT 136 (137)
Q Consensus 58 ~~k~~~lSpeLa~fLG~~e~SR~eVvk~LW~YIK~nnLQDP~nKr~I~cDekLk~LFgg~d~v~~~el~klL~~Hl~k~ 136 (137)
-...|++||.|+.+||+.+.||++|+..||+|||.|+||||+++.+|.||..|+++|| ++++.|.+|+.+|++||.+.
T Consensus 205 ~P~~fklsp~La~lLGi~t~Trp~iI~alWqYIk~n~Lqd~~e~~~incD~~l~qif~-~~rl~F~elp~~l~~lL~P~ 282 (420)
T KOG2570|consen 205 QPEEFKLSPRLANLLGIHTGTRPDIVTALWQYIKTNKLQDPEDSDFINCDKALEQIFG-VDRLKFPELPQLLNPLLSPP 282 (420)
T ss_pred CCcccccCHHHHHHhhhccCcchHHHHHHHHHHHHhccCCcccchhhcchHHHHHhhc-ccccccccchhhhhhccCCC
Confidence 3455999999999999999999999999999999999999999999999999999998 99999999999999999863
No 7
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=99.58 E-value=1.4e-15 Score=142.00 Aligned_cols=77 Identities=35% Similarity=0.658 Sum_probs=73.1
Q ss_pred CCccccCCHHHHhhhCCCCcCHHHHHHHHHHHHhHcCCCCCCCCcccccchhHHhhhCCCCccCHHHHHHHhcccCCC
Q 032632 58 ISKVSPVSPALAKFLGAPEASRSDAVRQIWAHVKTHNLQNPENKREILCDEKLKAIFEGKNAVGFLEIGKLLSPHFVK 135 (137)
Q Consensus 58 ~~k~~~lSpeLa~fLG~~e~SR~eVvk~LW~YIK~nnLQDP~nKr~I~cDekLk~LFgg~d~v~~~el~klL~~Hl~k 135 (137)
...+|.+|++|+.++|..+++|.++++.||+|||+|+||||+||+.|.||++|+++|+ ++.+.|++|+++|++||.|
T Consensus 784 ~~~~~~~S~~La~~~g~~~~sr~~~~~~lw~yIk~~~lqdp~~Kr~i~~d~kl~kvf~-~~~~~~~~~~k~l~~hl~~ 860 (860)
T PRK06319 784 AGPLYTPSPALAAMIGAEPVGRGEATKKVWDYIKEHGLQSPENKKLIIPDSKLQGVIG-PDPIDMFQLSKKLSQHLIK 860 (860)
T ss_pred cccccccccccccccCcCccCchHHHHHHHHHHHHhcccCccccccCCCchhhhhhhC-cCccchhhhHHHHHhhhcC
Confidence 3456889999999999999999999999999999999999999999999999999998 8999999999999999875
No 8
>KOG2522 consensus Filamentous baseplate protein Ligatin, contains PUA domain [Translation, ribosomal structure and biogenesis]
Probab=94.85 E-value=0.048 Score=49.43 Aligned_cols=58 Identities=16% Similarity=0.154 Sum_probs=48.1
Q ss_pred CCccccCCHHHHhhh---CC---CCcCHHHHHHHHHHHHhHcCCCCCCCCcccccchhHHhhhC
Q 032632 58 ISKVSPVSPALAKFL---GA---PEASRSDAVRQIWAHVKTHNLQNPENKREILCDEKLKAIFE 115 (137)
Q Consensus 58 ~~k~~~lSpeLa~fL---G~---~e~SR~eVvk~LW~YIK~nnLQDP~nKr~I~cDekLk~LFg 115 (137)
+...|+.+.-...++ |. +-.|-+||...+.+||+.|||-|+.||..|+.|+-|.+...
T Consensus 357 i~~lYk~~~~~~~Lf~evg~~kg~lyt~seir~~V~kYi~knnLad~~nKg~VrLDpILfd~~~ 420 (560)
T KOG2522|consen 357 ILTLYKPFNLAKDLFKEVGLAKGTLYTSSEIRSAVSKYISKNNLADTKNKGKVRLDPILFDMVN 420 (560)
T ss_pred eeeeeccchHHHHHHHhcCccccceeeHHHHHHHHHHHhhhhhccccccCCcEEeccHHHHHHH
Confidence 456677776555555 54 46899999999999999999999999999999999988665
No 9
>PRK05350 acyl carrier protein; Provisional
Probab=86.74 E-value=0.62 Score=31.54 Aligned_cols=53 Identities=9% Similarity=0.137 Sum_probs=43.6
Q ss_pred cCHHHHHHHHHHHHhHcCCCCCCCCcccccchhHHhhhCCCCccCHHHHHHHhcccC
Q 032632 77 ASRSDAVRQIWAHVKTHNLQNPENKREILCDEKLKAIFEGKNAVGFLEIGKLLSPHF 133 (137)
Q Consensus 77 ~SR~eVvk~LW~YIK~nnLQDP~nKr~I~cDekLk~LFgg~d~v~~~el~klL~~Hl 133 (137)
++|.++...|+++|.+. +.-+ ...|.+|..|..-+| -|++.+.+|.-.|..+|
T Consensus 2 m~~~~i~~~v~~ii~~~-~~~~--~~~i~~d~~l~~dlg-~DSld~veli~~lE~~f 54 (82)
T PRK05350 2 MTREEILERLRAILVEL-FEID--PEDITPEANLYEDLD-LDSIDAVDLVVHLQKLT 54 (82)
T ss_pred CCHHHHHHHHHHHHHHH-hCCC--HHHCCCCccchhhcC-CCHHHHHHHHHHHHHHH
Confidence 68999999999999987 4322 236999999988886 89999999988888776
No 10
>PRK05828 acyl carrier protein; Validated
Probab=83.84 E-value=1.6 Score=30.39 Aligned_cols=53 Identities=13% Similarity=0.161 Sum_probs=41.6
Q ss_pred cCHHHHHHHHHHHHhHcCCCCCCCCcccccchhHHhhhCCCCccCHHHHHHHhcccC
Q 032632 77 ASRSDAVRQIWAHVKTHNLQNPENKREILCDEKLKAIFEGKNAVGFLEIGKLLSPHF 133 (137)
Q Consensus 77 ~SR~eVvk~LW~YIK~nnLQDP~nKr~I~cDekLk~LFgg~d~v~~~el~klL~~Hl 133 (137)
|||.+|..+|-+.|.+.++.-+. ..|.+|..|.+ +| -|++.+.+|.-.|..+|
T Consensus 1 m~~~eI~~~i~~ii~e~~~~~~~--d~i~~~~~~~d-Lg-~DSLd~velv~~lE~~f 53 (84)
T PRK05828 1 MQEMEILLKIKEIAKKKNFAVTL--DESNINKPYRE-LK-IDSLDMFSIIVSLESEF 53 (84)
T ss_pred CCHHHHHHHHHHHHHHhccCCCc--ccccCCCCHHh-cC-CCHHHHHHHHHHHHHHH
Confidence 68999999999999886554322 25778888877 76 78999988888877665
No 11
>CHL00124 acpP acyl carrier protein; Validated
Probab=78.09 E-value=1.9 Score=28.79 Aligned_cols=53 Identities=11% Similarity=0.194 Sum_probs=41.9
Q ss_pred cCHHHHHHHHHHHHhHcCCCCCCCCcccccchhHHhhhCCCCccCHHHHHHHhcccC
Q 032632 77 ASRSDAVRQIWAHVKTHNLQNPENKREILCDEKLKAIFEGKNAVGFLEIGKLLSPHF 133 (137)
Q Consensus 77 ~SR~eVvk~LW~YIK~nnLQDP~nKr~I~cDekLk~LFgg~d~v~~~el~klL~~Hl 133 (137)
|+|.+|...|-++|.+.-=.+|+ .|.+|..|...+| -|++.+.+|.-.|..+|
T Consensus 1 M~~~~i~~~l~~ii~~~~~~~~~---~i~~d~~l~~dlg-~DSl~~~eli~~le~~f 53 (82)
T CHL00124 1 MTKNDIFEKVQSIVAEQLGIEKS---EVTLDANFTRDLG-ADSLDVVELVMAIEEKF 53 (82)
T ss_pred CCHHHHHHHHHHHHHHHHCCCHH---HCCCCcchhhhcC-CcHHHHHHHHHHHHHHH
Confidence 67899999999999887433433 5999999999887 78888888887776654
No 12
>PRK12449 acyl carrier protein; Provisional
Probab=77.84 E-value=3.8 Score=27.21 Aligned_cols=53 Identities=11% Similarity=0.147 Sum_probs=41.2
Q ss_pred cCHHHHHHHHHHHHhHcCCCCCCCCcccccchhHHhhhCCCCccCHHHHHHHhcccC
Q 032632 77 ASRSDAVRQIWAHVKTHNLQNPENKREILCDEKLKAIFEGKNAVGFLEIGKLLSPHF 133 (137)
Q Consensus 77 ~SR~eVvk~LW~YIK~nnLQDP~nKr~I~cDekLk~LFgg~d~v~~~el~klL~~Hl 133 (137)
|+|.+|...|-+++.+.-=.++. .|.+|..|..-+| -|++.+.+|.-.|...|
T Consensus 1 m~~~~i~~~l~~il~~~~~~~~~---~i~~~~~l~~dlg-~DSl~~~~li~~lE~~f 53 (80)
T PRK12449 1 MTREEIFERLINLIQKQRSYLSL---AITEQTHLKDDLA-VDSIELVEFIINVEDEF 53 (80)
T ss_pred CCHHHHHHHHHHHHHHHhCCCcc---ccCCCCcHHHHcC-CcHHHHHHHHHHHHHHh
Confidence 57889999999999875433333 5999999999997 88898888877776544
No 13
>PTZ00171 acyl carrier protein; Provisional
Probab=73.52 E-value=4 Score=31.42 Aligned_cols=57 Identities=12% Similarity=0.155 Sum_probs=45.6
Q ss_pred CCCCcCHHHHHHHHHHHHhHcCCCCCCCCcccccchhHHhhhCCCCccCHHHHHHHhcccC
Q 032632 73 GAPEASRSDAVRQIWAHVKTHNLQNPENKREILCDEKLKAIFEGKNAVGFLEIGKLLSPHF 133 (137)
Q Consensus 73 G~~e~SR~eVvk~LW~YIK~nnLQDP~nKr~I~cDekLk~LFgg~d~v~~~el~klL~~Hl 133 (137)
|...+++.+|...|+++|.+.-=.|++ .|.+|..|..-+| -|++.+.||.-.|+.+|
T Consensus 62 ~~~~~~~~~v~~~l~eiiae~l~vd~~---~I~~ds~~~~dLg-~DSLd~veLv~~LEdeF 118 (148)
T PTZ00171 62 KQYLLSKEDVLTRVKKVVKNFEKVDAS---KITPESNFVKDLG-ADSLDVVELLIAIEQEF 118 (148)
T ss_pred cccccCHHHHHHHHHHHHHHHhCCCHh---hCCCCcchhhhcC-CCHHHHHHHHHHHHHHH
Confidence 346789999999999999988533443 5888999988887 78888888887777665
No 14
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=67.63 E-value=9.4 Score=21.81 Aligned_cols=24 Identities=25% Similarity=0.372 Sum_probs=19.1
Q ss_pred HHHHhhhCCCCcCHHHHHHHHHHHHhHcCCC
Q 032632 66 PALAKFLGAPEASRSDAVRQIWAHVKTHNLQ 96 (137)
Q Consensus 66 peLa~fLG~~e~SR~eVvk~LW~YIK~nnLQ 96 (137)
.++++.+|++.- .||.|++...+.
T Consensus 4 ~e~a~~lgvs~~-------tl~~~~~~g~~~ 27 (49)
T cd04762 4 KEAAELLGVSPS-------TLRRWVKEGKLK 27 (49)
T ss_pred HHHHHHHCcCHH-------HHHHHHHcCCCC
Confidence 578888888765 799999987764
No 15
>PF08463 EcoEI_R_C: EcoEI R protein C-terminal; InterPro: IPR013670 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type I restriction endonucleases are components of prokaryotic DNA restriction-modification mechanisms that protects the organism against invading foreign DNA. Type I enzymes have three different subunits subunits - M (modification), S (specificity) and R (restriction) - that form multifunctional enzymes with restriction (3.1.21.3 from EC), methylase (2.1.1.72 from EC) and ATPase activities [, ]. The S subunit is required for both restriction and modification and is responsible for recognition of the DNA sequence specific for the system. The M subunit is necessary for modification, and the R subunit is required for restriction. These enzymes use S-Adenosyl-L-methionine (AdoMet) as the methyl group donor in the methylation reaction, and have a requirement for ATP. They recognise asymmetric DNA sequences split into two domains of specific sequence, one 3-4 bp long and another 4-5 bp long, separated by a nonspecific spacer 6-8 bp in length. Cleavage occurs a considerable distance from the recognition sites, rarely less than 400 bp away and up to 7000 bp away. Adenosyl residues are methylated, one on each strand of the recognition sequence. These enzymes are widespread in eubacteria and archaea. In enteric bacteria they have been subdivide into four families: types IA, IB, IC and ID. Type III restriction endonucleases (3.1.21.5 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. Type III enzymes are hetero-oligomeric, multifunctional proteins composed of two subunits, Res and Mod. The Mod subunit recognises the DNA sequence specific for the system and is a modification methyltransferase; as such it is functionally equivalent to the M and S subunits of type I restriction endonuclease. Res is required for restriction, although it has no enzymatic activity on its own. Type III enzymes recognise short 5-6 bp long asymmetric DNA sequences and cleave 25-27 bp downstream to leave short, single-stranded 5' protrusions. They require the presence of two inversely oriented unmethylated recognition sites for restriction to occur. These enzymes methylate only one strand of the DNA, at the N-6 position of adenosyl residues, so newly replicated DNA will have only one strand methylated, which is sufficient to protect against restriction. Type III enzymes belong to the beta-subfamily of N6 adenine methyltransferases, containing the nine motifs that characterise this family, including motif I, the AdoMet binding pocket (FXGXG), and motif IV, the catalytic region (S/D/N (PP) Y/F) [, ]. This entry represents the C-terminal domain found in both the R subunit of type I enzymes and the Res subunit of type III enzymes. The type I enzyme represented is EcoEI, which recognises 5'-GAGN(7)ATGC-3; the R protein (HsdR) is required for both nuclease and ATPase activity [, ]. ; GO: 0003677 DNA binding, 0003824 catalytic activity, 0006304 DNA modification
Probab=65.97 E-value=3.8 Score=30.74 Aligned_cols=69 Identities=23% Similarity=0.338 Sum_probs=48.3
Q ss_pred cCCHHHHhhhCCCC--cCHHHHHHHHHHHHhHcCCCCCCCCcccccc-----hhHHhhhCCCCccCHHHHHHHhcccC
Q 032632 63 PVSPALAKFLGAPE--ASRSDAVRQIWAHVKTHNLQNPENKREILCD-----EKLKAIFEGKNAVGFLEIGKLLSPHF 133 (137)
Q Consensus 63 ~lSpeLa~fLG~~e--~SR~eVvk~LW~YIK~nnLQDP~nKr~I~cD-----ekLk~LFgg~d~v~~~el~klL~~Hl 133 (137)
.+....+.|++... ..+-+++..|-+|+..++..++++=...-+. ..+..+||+.+ .+.++-.-|+.+|
T Consensus 88 rv~~~~~~~l~~~~~~~~Q~~~L~~i~~~~~~~G~~~~~~l~~~pF~~~G~~~~~~~~Fg~~~--~l~~~~~~l~~~L 163 (164)
T PF08463_consen 88 RVEEAFSKFLNQHQFNAEQREFLERILDYYAQNGIIEPEDLKEPPFSDLGGPGGIIRVFGGKE--QLDEILNELNKNL 163 (164)
T ss_pred HHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHhCcccHHHhCCCchhhcCCHHHHHHHcCCHH--HHHHHHHHHHhhc
Confidence 34445667776554 6678899999999999999987664444333 45788898533 6667777776665
No 16
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=64.53 E-value=4.9 Score=25.90 Aligned_cols=52 Identities=25% Similarity=0.456 Sum_probs=34.4
Q ss_pred CCCccccCC-HHHHhhhCCCCcCHHHHHHHHHHHHhHcCCCCCCCCcccccc-hhHHh
Q 032632 57 GISKVSPVS-PALAKFLGAPEASRSDAVRQIWAHVKTHNLQNPENKREILCD-EKLKA 112 (137)
Q Consensus 57 G~~k~~~lS-peLa~fLG~~e~SR~eVvk~LW~YIK~nnLQDP~nKr~I~cD-ekLk~ 112 (137)
|..-.+.+| .+|++++|.+..+ +..+....++.++.+-.++++++.| +.|++
T Consensus 22 ~~~~~~~lt~~~iA~~~g~sr~t----v~r~l~~l~~~g~I~~~~~~i~I~d~~~L~~ 75 (76)
T PF13545_consen 22 GIRIPLPLTQEEIADMLGVSRET----VSRILKRLKDEGIIEVKRGKIIILDPERLEE 75 (76)
T ss_dssp EEEEEEESSHHHHHHHHTSCHHH----HHHHHHHHHHTTSEEEETTEEEESSHHHHHH
T ss_pred CceEEecCCHHHHHHHHCCCHHH----HHHHHHHHHHCCCEEEcCCEEEECCHHHHhc
Confidence 333344444 5789999986443 4455556677788888888888888 55554
No 17
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=62.99 E-value=19 Score=22.68 Aligned_cols=57 Identities=14% Similarity=0.227 Sum_probs=34.2
Q ss_pred HHHHhhhCCCCcCHHHHHHHHHHHHhHcCCCCCCC---CcccccchhHHhhhC----CCCccCHHHHHHHh
Q 032632 66 PALAKFLGAPEASRSDAVRQIWAHVKTHNLQNPEN---KREILCDEKLKAIFE----GKNAVGFLEIGKLL 129 (137)
Q Consensus 66 peLa~fLG~~e~SR~eVvk~LW~YIK~nnLQDP~n---Kr~I~cDekLk~LFg----g~d~v~~~el~klL 129 (137)
.++++.+|++.- .|+.|++..++..|.. ......++.+..+-. ...-+++.+|.++|
T Consensus 4 ~eva~~~gvs~~-------tlr~w~~~~g~~~~~r~~~~~r~yt~~~v~~l~~i~~l~~~g~~l~~i~~~~ 67 (68)
T cd01104 4 GAVARLTGVSPD-------TLRAWERRYGLPAPQRTDGGHRLYSEADVARLRLIRRLTSEGVRISQAAALA 67 (68)
T ss_pred HHHHHHHCcCHH-------HHHHHHHhCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHCCCCHHHHHHHh
Confidence 578888888765 7888998878876622 223445554433221 01335666776665
No 18
>PF07587 PSD1: Protein of unknown function (DUF1553); InterPro: IPR022655 The function is not known. It is found associated with IPR011444 from INTERPRO It is also found associated with the Planctomycete cytochrome C domain IPR011429 from INTERPRO.
Probab=55.69 E-value=15 Score=30.28 Aligned_cols=58 Identities=26% Similarity=0.393 Sum_probs=44.7
Q ss_pred HHHhhhCC--CCcCHHHHHHHHHHHHhHcCCCCCCCCcccccchhHHhhhCC-CCccCHHHHHHHhcccCCCC
Q 032632 67 ALAKFLGA--PEASRSDAVRQIWAHVKTHNLQNPENKREILCDEKLKAIFEG-KNAVGFLEIGKLLSPHFVKT 136 (137)
Q Consensus 67 eLa~fLG~--~e~SR~eVvk~LW~YIK~nnLQDP~nKr~I~cDekLk~LFgg-~d~v~~~el~klL~~Hl~k~ 136 (137)
+|++.|-. ...+---+|.+||.|.--.+|-+|-|- ||. ...-..+||-++|..+|++.
T Consensus 5 ~LA~wlt~~~Np~faRv~VNRvW~~~fGrGlV~p~dD------------~g~~~~~PshPeLLd~La~~F~~~ 65 (266)
T PF07587_consen 5 ALADWLTSPDNPLFARVIVNRVWQHLFGRGLVEPVDD------------FGPQGNPPSHPELLDWLAAEFVEH 65 (266)
T ss_pred HHHHHhcCCCCcchHHHHHHHHHHHHcCCcCcCCHhh------------ccCCCCCCCCHHHHHHHHHHHHHc
Confidence 67888744 567778899999999999999999762 442 24466789999988888764
No 19
>PRK00071 nadD nicotinic acid mononucleotide adenylyltransferase; Provisional
Probab=55.40 E-value=8.1 Score=30.12 Aligned_cols=31 Identities=13% Similarity=0.117 Sum_probs=20.6
Q ss_pred HHHHhhhCCCCcCHHHHHHHHHHHHhHcCCC
Q 032632 66 PALAKFLGAPEASRSDAVRQIWAHVKTHNLQ 96 (137)
Q Consensus 66 peLa~fLG~~e~SR~eVvk~LW~YIK~nnLQ 96 (137)
.++.+.+.....-+.-|-..+++||++|+|.
T Consensus 171 T~IR~~l~~g~~~~~lvp~~V~~YI~~~~LY 201 (203)
T PRK00071 171 TAIRERIKEGRPIRYLLPEAVLDYIEKHGLY 201 (203)
T ss_pred HHHHHHHHcCCChhHhCCHHHHHHHHHhCcc
Confidence 3444445443334455667899999999986
No 20
>PLN02945 nicotinamide-nucleotide adenylyltransferase/nicotinate-nucleotide adenylyltransferase
Probab=54.75 E-value=9 Score=30.95 Aligned_cols=32 Identities=13% Similarity=0.102 Sum_probs=22.2
Q ss_pred CHHHHhhhCCCCcCHHHHHHHHHHHHhHcCCC
Q 032632 65 SPALAKFLGAPEASRSDAVRQIWAHVKTHNLQ 96 (137)
Q Consensus 65 SpeLa~fLG~~e~SR~eVvk~LW~YIK~nnLQ 96 (137)
|.++.+.+.....-+..|-..|++||++|+|.
T Consensus 204 ST~IR~~l~~g~~i~~lvP~~V~~YI~~~~LY 235 (236)
T PLN02945 204 STRVRECISRGLSVKYLTPDGVIDYIKEHGLY 235 (236)
T ss_pred HHHHHHHHHcCCCchhhCCHHHHHHHHHcCCC
Confidence 45555555443444566777899999999985
No 21
>PLN00129 succinate dehydrogenase [ubiquinone] iron-sulfur subunit
Probab=54.00 E-value=9.7 Score=32.14 Aligned_cols=27 Identities=41% Similarity=0.586 Sum_probs=14.2
Q ss_pred Cchhhhhhhhhh-hhhhccchhhhhhhh
Q 032632 1 MSSAAARVFNGC-RALLAPAKSSAAASS 27 (137)
Q Consensus 1 ~~~~~~~~~~~~-~~~~~~a~~~~~~~~ 27 (137)
|.+..-|-..|. --|++||++++++++
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 28 (276)
T PLN00129 1 MAAGLLRRLAGAKAGLLAPAAAASAAAS 28 (276)
T ss_pred Cchhhhhhhhcccccccccchhhhhhhc
Confidence 333333444444 446778777665433
No 22
>TIGR00482 nicotinate (nicotinamide) nucleotide adenylyltransferase. This model represents the predominant bacterial/eukaryotic adenylyltransferase for nicotinamide-nucleotide, its deamido form nicotinate nucleotide, or both. The first activity, nicotinamide-nucleotide adenylyltransferase (EC 2.7.7.1), synthesizes NAD by the salvage pathway, while the second, nicotinate-nucleotide adenylyltransferase (EC 2.7.7.18) synthesizes the immediate precursor of NAD by the de novo pathway. In E. coli, NadD activity is biased toward the de novo pathway while salvage activity is channeled through the multifunctional NadR protein, but this division of labor may be exceptional. The given name of this model, nicotinate (nicotinamide) nucleotide adenylyltransferase, reflects the lack of absolute specificity with respect to substrate amidation state in most species.
Probab=53.72 E-value=9.5 Score=29.56 Aligned_cols=32 Identities=13% Similarity=0.086 Sum_probs=21.0
Q ss_pred CHHHHhhhCCCCcCHHHHHHHHHHHHhHcCCC
Q 032632 65 SPALAKFLGAPEASRSDAVRQIWAHVKTHNLQ 96 (137)
Q Consensus 65 SpeLa~fLG~~e~SR~eVvk~LW~YIK~nnLQ 96 (137)
|.++.+-+.....-+.-|-..|++||++|+|.
T Consensus 162 ST~IR~~l~~g~~~~~lvP~~V~~YI~~~~LY 193 (193)
T TIGR00482 162 STEIRQRIRQGKSIEYLLPDPVIKYIKQHGLY 193 (193)
T ss_pred HHHHHHHHHcCCCchhhCCHHHHHHHHHhCCC
Confidence 34445555443444556677899999999983
No 23
>PF08225 Antimicrobial19: Pseudin antimicrobial peptide; InterPro: IPR013156 Pseudins are a subfamily of the FSAP family (Frog Secreted Active Peptides) extracted from the skin of the paradoxical frog Pseudis paradoxa (Paradoxical frog). The pseudins belong to the class of cationic, amphipathic-helical antimicrobial peptides [].; GO: 0006952 defense response
Probab=53.26 E-value=10 Score=20.65 Aligned_cols=20 Identities=40% Similarity=0.728 Sum_probs=15.9
Q ss_pred hHHhhhCCCCccCHHHHHHHhcccC
Q 032632 109 KLKAIFEGKNAVGFLEIGKLLSPHF 133 (137)
Q Consensus 109 kLk~LFgg~d~v~~~el~klL~~Hl 133 (137)
.|+++|.| +.|..+++++|.
T Consensus 4 tlkkv~qg-----lhe~ikli~nh~ 23 (23)
T PF08225_consen 4 TLKKVFQG-----LHEVIKLINNHV 23 (23)
T ss_pred HHHHHHHH-----HHHHHHHHhcCC
Confidence 57888863 789999999883
No 24
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=52.87 E-value=22 Score=26.32 Aligned_cols=49 Identities=18% Similarity=0.314 Sum_probs=33.8
Q ss_pred ccCC-HHHHhhhCCCCcCHHHHHHHHHHHHhHcCCCCCCCCcccccc-hhHHhhh
Q 032632 62 SPVS-PALAKFLGAPEASRSDAVRQIWAHVKTHNLQNPENKREILCD-EKLKAIF 114 (137)
Q Consensus 62 ~~lS-peLa~fLG~~e~SR~eVvk~LW~YIK~nnLQDP~nKr~I~cD-ekLk~LF 114 (137)
++++ .+|++++|.+.. .+.++-.-.++.|+..-..++++++| ++|++.+
T Consensus 142 ~~~t~~~iA~~lG~tre----tvsR~l~~l~~~g~I~~~~~~i~I~d~~~L~~~~ 192 (193)
T TIGR03697 142 LRLSHQAIAEAIGSTRV----TITRLLGDLRKKKLISIHKKKITVHDPIALGQRF 192 (193)
T ss_pred CCCCHHHHHHHhCCcHH----HHHHHHHHHHHCCCEEecCCEEEEeCHHHHHHhc
Confidence 4443 789999996433 34445556678888888888899998 5666543
No 25
>PRK06973 nicotinic acid mononucleotide adenylyltransferase; Provisional
Probab=50.48 E-value=11 Score=31.02 Aligned_cols=32 Identities=25% Similarity=0.384 Sum_probs=23.5
Q ss_pred CHHHHhhhCCC--------CcCHHHHHHHHHHHHhHcCCC
Q 032632 65 SPALAKFLGAP--------EASRSDAVRQIWAHVKTHNLQ 96 (137)
Q Consensus 65 SpeLa~fLG~~--------e~SR~eVvk~LW~YIK~nnLQ 96 (137)
|.++.+.+... ..-+.-|=..|++||++|+|.
T Consensus 202 ST~IR~~l~~g~~~~~~~~~~i~~lvP~~V~~YI~~~~LY 241 (243)
T PRK06973 202 ATDIRAHLRACIARRAQVPDASAEHVPAAVWAYILQHRLY 241 (243)
T ss_pred HHHHHHHHHcCCCcccccCCChhHhCCHHHHHHHHHcCCC
Confidence 45666666554 455566777899999999996
No 26
>smart00667 LisH Lissencephaly type-1-like homology motif. Alpha-helical motif present in Lis1, treacle, Nopp140, some katanin p60 subunits, muskelin, tonneau, LEUNIG and numerous WD40 repeat-containing proteins. It is suggested that LisH motifs contribute to the regulation of microtubule dynamics, either by mediating dimerisation, or else by binding cytoplasmic dynein heavy chain or microtubules directly.
Probab=48.94 E-value=13 Score=19.88 Aligned_cols=21 Identities=24% Similarity=0.262 Sum_probs=17.5
Q ss_pred CHHHHHHHHHHHHhHcCCCCC
Q 032632 78 SRSDAVRQIWAHVKTHNLQNP 98 (137)
Q Consensus 78 SR~eVvk~LW~YIK~nnLQDP 98 (137)
.+.++.+.|++|...+|+.+.
T Consensus 2 ~~~~l~~lI~~yL~~~g~~~t 22 (34)
T smart00667 2 SRSELNRLILEYLLRNGYEET 22 (34)
T ss_pred cHHHHHHHHHHHHHHcCHHHH
Confidence 467899999999999997653
No 27
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=48.01 E-value=24 Score=20.20 Aligned_cols=26 Identities=15% Similarity=0.350 Sum_probs=20.4
Q ss_pred HHHHhhhCCCCcCHHHHHHHHHHHHhHcCCCCC
Q 032632 66 PALAKFLGAPEASRSDAVRQIWAHVKTHNLQNP 98 (137)
Q Consensus 66 peLa~fLG~~e~SR~eVvk~LW~YIK~nnLQDP 98 (137)
++.+++||++.- .|+.+|++..+.-+
T Consensus 5 ~e~a~~lgis~~-------ti~~~~~~g~i~~~ 30 (49)
T TIGR01764 5 EEAAEYLGVSKD-------TVYRLIHEGELPAY 30 (49)
T ss_pred HHHHHHHCCCHH-------HHHHHHHcCCCCeE
Confidence 578899998765 79999998876643
No 28
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=47.98 E-value=29 Score=26.86 Aligned_cols=52 Identities=19% Similarity=0.287 Sum_probs=34.2
Q ss_pred CccccCC-HHHHhhhCCCCcCHHHHHHHHHHHHhHcCCCCCCCCcccccc-hhHHhhhC
Q 032632 59 SKVSPVS-PALAKFLGAPEASRSDAVRQIWAHVKTHNLQNPENKREILCD-EKLKAIFE 115 (137)
Q Consensus 59 ~k~~~lS-peLa~fLG~~e~SR~eVvk~LW~YIK~nnLQDP~nKr~I~cD-ekLk~LFg 115 (137)
.-.+.++ .+|++++|+...| |...|-+ .++.|+ .-..++++++| +.|+++.+
T Consensus 169 ~~~i~~t~~~iA~~lG~tret---vsR~l~~-L~~~gl-~~~~~~i~I~d~~~L~~~~~ 222 (236)
T PRK09392 169 VVTLPYEKRVLASYLGMTPEN---LSRAFAA-LASHGV-HVDGSAVTITDPAGLARFAK 222 (236)
T ss_pred EEEeeCCHHHHHHHhCCChhH---HHHHHHH-HHhCCe-EeeCCEEEEcCHHHHHHhhc
Confidence 3344555 7999999985444 3333333 566668 45567788888 78888776
No 29
>PRK07117 acyl carrier protein; Validated
Probab=46.50 E-value=21 Score=24.39 Aligned_cols=51 Identities=10% Similarity=0.082 Sum_probs=38.5
Q ss_pred cCHHHHHHHHHHHHhHcC-CCCCCCCcccccchhHHhhhCCCCccCHHHHHHHhccc
Q 032632 77 ASRSDAVRQIWAHVKTHN-LQNPENKREILCDEKLKAIFEGKNAVGFLEIGKLLSPH 132 (137)
Q Consensus 77 ~SR~eVvk~LW~YIK~nn-LQDP~nKr~I~cDekLk~LFgg~d~v~~~el~klL~~H 132 (137)
|+|.+|...|-+-|.+.- =-+| ..|..|..|+. || -|++.+.+|.-.|...
T Consensus 1 M~~~ei~~~v~~ii~e~~p~i~~---~~I~~~~~l~D-Lg-~DSlD~veiv~~led~ 52 (79)
T PRK07117 1 MDKQRIFDILVRHIREVLPDLDQ---HQFQPEDSLVD-LG-ANSMDRAEIVIMTLES 52 (79)
T ss_pred CCHHHHHHHHHHHHHHHcCCCCH---HHCCCCCChhh-cC-CChHHHHHHHHHHHHH
Confidence 578888888888888864 1333 46899999988 87 8889888887666543
No 30
>PRK08558 adenine phosphoribosyltransferase; Provisional
Probab=46.47 E-value=6.2 Score=32.23 Aligned_cols=31 Identities=32% Similarity=0.416 Sum_probs=22.3
Q ss_pred HHHHhhhCCCCcCHHHHHHHHHHHHhHcCCCCCCCCcc
Q 032632 66 PALAKFLGAPEASRSDAVRQIWAHVKTHNLQNPENKRE 103 (137)
Q Consensus 66 peLa~fLG~~e~SR~eVvk~LW~YIK~nnLQDP~nKr~ 103 (137)
.||++++|.++- .||.|+.-|-|-..+.-+.
T Consensus 27 ~el~~~~g~p~~-------~l~RYv~g~~~P~~~~a~~ 57 (238)
T PRK08558 27 EELSSITGLPES-------VLNRYVNGHVLPSVERARE 57 (238)
T ss_pred HHHHHHHCCCHH-------HHHHHHcCCcCCCHHHHHH
Confidence 689999998776 7788887766665554333
No 31
>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=45.27 E-value=4.9 Score=24.80 Aligned_cols=35 Identities=29% Similarity=0.436 Sum_probs=19.7
Q ss_pred HHHhhhCCCCcCHHHHHHHHHHHHhH---cCCCCCCCCccc
Q 032632 67 ALAKFLGAPEASRSDAVRQIWAHVKT---HNLQNPENKREI 104 (137)
Q Consensus 67 eLa~fLG~~e~SR~eVvk~LW~YIK~---nnLQDP~nKr~I 104 (137)
+|++++|.+. +.+...+..-++. ..-+||+|+|.|
T Consensus 22 ~la~~~~~~~---~~~t~~i~~L~~~g~I~r~~~~~D~R~v 59 (59)
T PF01047_consen 22 ELAEKLGISR---STVTRIIKRLEKKGLIERERDPDDRRQV 59 (59)
T ss_dssp HHHHHHTS-H---HHHHHHHHHHHHTTSEEEEEETTETTSE
T ss_pred HHHHHHCCCh---hHHHHHHHHHHHCCCEEeccCCCCCCcC
Confidence 7888887754 4444444444443 234577777654
No 32
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=44.53 E-value=27 Score=26.13 Aligned_cols=46 Identities=15% Similarity=0.208 Sum_probs=33.1
Q ss_pred HHHHhhhCCCCcCHHHHHHHHHHHHhHcCCCCCCCCcccccc-hhHHhhhC
Q 032632 66 PALAKFLGAPEASRSDAVRQIWAHVKTHNLQNPENKREILCD-EKLKAIFE 115 (137)
Q Consensus 66 peLa~fLG~~e~SR~eVvk~LW~YIK~nnLQDP~nKr~I~cD-ekLk~LFg 115 (137)
.+|++++|.+..|=+ ++-.-.++.++.+-..++++++| ++|+++.+
T Consensus 153 ~~iA~~lG~tretvs----R~l~~l~~~g~I~~~~~~i~I~d~~~L~~~~~ 199 (202)
T PRK13918 153 DELAAAVGSVRETVT----KVIGELSREGYIRSGYGKIQLLDLKGLEELAE 199 (202)
T ss_pred HHHHHHhCccHHHHH----HHHHHHHHCCCEEcCCCEEEEECHHHHHHHHh
Confidence 589999998654333 33344568888887778888888 67887765
No 33
>PF12728 HTH_17: Helix-turn-helix domain
Probab=40.64 E-value=26 Score=21.06 Aligned_cols=27 Identities=11% Similarity=0.318 Sum_probs=20.9
Q ss_pred HHHHhhhCCCCcCHHHHHHHHHHHHhHcCCCCCC
Q 032632 66 PALAKFLGAPEASRSDAVRQIWAHVKTHNLQNPE 99 (137)
Q Consensus 66 peLa~fLG~~e~SR~eVvk~LW~YIK~nnLQDP~ 99 (137)
+|.+++||++.- .|+++|+...+.-..
T Consensus 5 ~e~a~~l~is~~-------tv~~~~~~g~i~~~~ 31 (51)
T PF12728_consen 5 KEAAELLGISRS-------TVYRWIRQGKIPPFK 31 (51)
T ss_pred HHHHHHHCcCHH-------HHHHHHHcCCCCeEE
Confidence 688999998655 688999888776553
No 34
>TIGR00517 acyl_carrier acyl carrier protein. S (Ser) at position 37 in the seed alignment, in the motif DSLD, is the phosphopantetheine attachment site.
Probab=40.17 E-value=25 Score=23.00 Aligned_cols=50 Identities=12% Similarity=0.163 Sum_probs=36.9
Q ss_pred HHHHHHHHHHHhHcCCCCCCCCcccccchhHHhhhCCCCccCHHHHHHHhcccC
Q 032632 80 SDAVRQIWAHVKTHNLQNPENKREILCDEKLKAIFEGKNAVGFLEIGKLLSPHF 133 (137)
Q Consensus 80 ~eVvk~LW~YIK~nnLQDP~nKr~I~cDekLk~LFgg~d~v~~~el~klL~~Hl 133 (137)
.++...|.++|.+.-=.+| ..|.+|..|..-+| -|++.+.+|.-.|..+|
T Consensus 2 ~~i~~~l~~il~~~~~~~~---~~i~~~~~l~~dlg-lDSl~~veli~~lE~~f 51 (77)
T TIGR00517 2 QEIFEKVKAIIKEQLNVDE---DQVTPDASFVEDLG-ADSLDTVELVMALEEEF 51 (77)
T ss_pred hHHHHHHHHHHHHHHCCCH---HHCCCCcchhhhcC-CcHHHHHHHHHHHHHHH
Confidence 4677788888888632343 35888988887787 78898888888777665
No 35
>PRK07639 acyl carrier protein; Provisional
Probab=39.10 E-value=36 Score=23.43 Aligned_cols=54 Identities=7% Similarity=-0.004 Sum_probs=38.9
Q ss_pred cCHHHHHHHHHHHHhHcCCCCCCCCcccccchhHHhhhCCCCccCHHHHHHHhcccC
Q 032632 77 ASRSDAVRQIWAHVKTHNLQNPENKREILCDEKLKAIFEGKNAVGFLEIGKLLSPHF 133 (137)
Q Consensus 77 ~SR~eVvk~LW~YIK~nnLQDP~nKr~I~cDekLk~LFgg~d~v~~~el~klL~~Hl 133 (137)
|+|.+|...|-+.|.+.==.++. ..|..|..|..=+| -|++.+.++.-.|+.+|
T Consensus 1 M~~~ei~~~i~~il~e~l~~~~~--~~i~~d~~l~edL~-lDSld~velv~~lE~~f 54 (86)
T PRK07639 1 MRREALKNAVLKIMEEKLELKNV--THLEETMRLNEDLY-IDSVMMLQLIVYIEMDV 54 (86)
T ss_pred CCHHHHHHHHHHHHHHHhCCCcc--ccCCCCCCcccccC-CChHHHHHHHHHHHHHH
Confidence 57888888888888875311221 25788888877665 68888888887777655
No 36
>cd02165 NMNAT Nicotinamide/nicotinate mononucleotide adenylyltransferase. Nicotinamide/nicotinate mononucleotide (NMN/ NaMN)adenylyltransferase (NMNAT). NMNAT represents the primary bacterial and eukaryotic adenylyltransferases for nicotinamide-nucleotide and for the deamido form, nicotinate nucleotide. It is an indispensable enzyme in the biosynthesis of NAD(+) and NADP(+). Nicotinamide-nucleotide adenylyltransferase synthesizes NAD via the salvage pathway, while nicotinate-nucleotide adenylyltransferase synthesizes the immediate precursor of NAD via the de novo pathway. Human NMNAT displays unique dual substrate specificity toward both NMN and NaMN, and can participate in both de novo and salvage pathways of NAD synthesis.
Probab=37.91 E-value=24 Score=27.11 Aligned_cols=33 Identities=18% Similarity=0.099 Sum_probs=22.0
Q ss_pred CCHHHHhhhCCCCcCHHHHHHHHHHHHhHcCCC
Q 032632 64 VSPALAKFLGAPEASRSDAVRQIWAHVKTHNLQ 96 (137)
Q Consensus 64 lSpeLa~fLG~~e~SR~eVvk~LW~YIK~nnLQ 96 (137)
=|.++.+.+.....-..-|-..+.+||++|+|.
T Consensus 160 SST~IR~~~~~g~~~~~lvp~~V~~yI~~~~lY 192 (192)
T cd02165 160 SSTEIRERLKNGKSIRYLLPPAVADYIKEHGLY 192 (192)
T ss_pred CHHHHHHHHHcCCChhHhCCHHHHHHHHHccCC
Confidence 345556666544334455667899999999983
No 37
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=37.53 E-value=26 Score=24.31 Aligned_cols=21 Identities=29% Similarity=0.662 Sum_probs=16.0
Q ss_pred CHHHHhhhCCCCcCHHHHHHHHHHHHhH
Q 032632 65 SPALAKFLGAPEASRSDAVRQIWAHVKT 92 (137)
Q Consensus 65 SpeLa~fLG~~e~SR~eVvk~LW~YIK~ 92 (137)
-++|++-||++.. .||++|+.
T Consensus 22 Ge~La~~LgiSRt-------aVwK~Iq~ 42 (79)
T COG1654 22 GEKLAEELGISRT-------AVWKHIQQ 42 (79)
T ss_pred HHHHHHHHCccHH-------HHHHHHHH
Confidence 3678888887765 78998874
No 38
>cd09286 NMNAT_Eukarya Nicotinamide/nicotinate mononucleotide adenylyltransferase, Eukaryotic. Nicotinamide/nicotinate mononucleotide (NMN/ NaMN)adenylyltransferase (NMNAT). NMNAT represents the primary bacterial and eukaryotic adenylyltransferases for nicotinamide-nucleotide and for the deamido form, nicotinate nucleotide. It is an indispensable enzyme in the biosynthesis of NAD(+) and NADP(+). Nicotinamide-nucleotide adenylyltransferase synthesizes NAD via the salvage pathway, while nicotinate-nucleotide adenylyltransferase synthesizes the immediate precursor of NAD via the de novo pathway. Human NMNAT displays unique dual substrate specificity toward both NMN and NaMN, and can participate in both de novo and salvage pathways of NAD synthesis. This subfamily consists strictly of eukaryotic members and includes secondary structural elements not found in all NMNATs.
Probab=36.38 E-value=25 Score=28.31 Aligned_cols=32 Identities=13% Similarity=0.087 Sum_probs=21.2
Q ss_pred CHHHHhhhCCCCcCHHHHHHHHHHHHhHcCCC
Q 032632 65 SPALAKFLGAPEASRSDAVRQIWAHVKTHNLQ 96 (137)
Q Consensus 65 SpeLa~fLG~~e~SR~eVvk~LW~YIK~nnLQ 96 (137)
|.++.+-+.....-+..+-..|.+||++|+|.
T Consensus 194 ST~IR~~l~~g~~~~~llp~~V~~YI~~~~LY 225 (225)
T cd09286 194 STKVRRALRRGMSVKYLLPDPVIEYIEQHQLY 225 (225)
T ss_pred hHHHHHHHHcCCCchhcCCHHHHHHHHHcCCC
Confidence 44455555444444456777899999999983
No 39
>PRK08887 nicotinic acid mononucleotide adenylyltransferase; Provisional
Probab=36.35 E-value=28 Score=26.84 Aligned_cols=32 Identities=13% Similarity=0.069 Sum_probs=19.3
Q ss_pred HHHHhhhCCCCcCHHHHHHHHHHHHhHcCCCC
Q 032632 66 PALAKFLGAPEASRSDAVRQIWAHVKTHNLQN 97 (137)
Q Consensus 66 peLa~fLG~~e~SR~eVvk~LW~YIK~nnLQD 97 (137)
.++.+.+.....-..-|-..+.+||++|+|..
T Consensus 140 T~IR~~l~~g~~i~~lvp~~V~~yI~~~~LY~ 171 (174)
T PRK08887 140 TDIRNALQNGKDISHLTTPGVARLLKEHQLYT 171 (174)
T ss_pred HHHHHHHHcCCChhHhCCHHHHHHHHHccccC
Confidence 33444443322233555667899999999974
No 40
>TIGR02057 PAPS_reductase phosphoadenosine phosphosulfate reductase, thioredoxin dependent. Requiring thioredoxin as an electron donor, phosphoadenosine phosphosulfate reductase catalyzes the reduction of 3'-phosphoadenylylsulfate (PAPS) to sulfite and phospho-adenosine-phosphate (PAP). Found in enterobacteria, cyanobacteria, and yeast, PAPS reductase is related to a group of plant (TIGR00424) and bacterial (TIGR02055) enzymes preferring 5'-adenylylsulfate (APS) over PAPS as a substrate for reduction to sulfite.
Probab=35.43 E-value=21 Score=28.69 Aligned_cols=12 Identities=25% Similarity=0.606 Sum_probs=10.5
Q ss_pred HHHHHHhHcCCC
Q 032632 85 QIWAHVKTHNLQ 96 (137)
Q Consensus 85 ~LW~YIK~nnLQ 96 (137)
-||+||++|||-
T Consensus 172 dVw~Yi~~~~lP 183 (226)
T TIGR02057 172 QVYQYLDAHNVP 183 (226)
T ss_pred HHHHHHHHcCCC
Confidence 579999999985
No 41
>PRK05883 acyl carrier protein; Validated
Probab=34.22 E-value=50 Score=22.97 Aligned_cols=55 Identities=11% Similarity=0.039 Sum_probs=42.9
Q ss_pred CCcCHHHHHHHHHHHHhHcCCCCCCCCcccccchhHHhhhCCCCccCHHHHHHHhcccC
Q 032632 75 PEASRSDAVRQIWAHVKTHNLQNPENKREILCDEKLKAIFEGKNAVGFLEIGKLLSPHF 133 (137)
Q Consensus 75 ~e~SR~eVvk~LW~YIK~nnLQDP~nKr~I~cDekLk~LFgg~d~v~~~el~klL~~Hl 133 (137)
...+..+|...|-++|.+.==.+|+ .|..|..|...+| -|++.+.+|.-.|..+|
T Consensus 8 ~~~~~~~I~~~l~~iia~~l~v~~~---~I~~d~~l~~dlg-~DSL~~v~lv~~lE~~f 62 (91)
T PRK05883 8 MTSSPSTVSATLLSILRDDLNVDLT---RVTPDARLVDDVG-LDSVAFAVGMVAIEERL 62 (91)
T ss_pred CCCCHHHHHHHHHHHHHHHhCCChh---hCCCCCchhhccC-CChHHHHHHHHHHHHHH
Confidence 3578899999999999876323443 5999999999998 78888877777777665
No 42
>PF08513 LisH: LisH; InterPro: IPR013720 The LisH motif is found in a large number of eukaryotic proteins, from metazoa, fungi and plants that have a wide range of functions. The recently solved structure of the LisH domain in the N-terminal region of LIS1 depicted it as a novel dimerization motif, and that other structural elements are likely to play an important role in dimerisation [, , ]. The LisH (lis homology) domain mediates protein dimerisation and tetramerisation. The LisH domain is found in Sif2, a component of the Set3 complex which is responsible for repressing meiotic genes. It has been shown that the LisH domain helps mediate interaction with components of the Set3 complex []. ; PDB: 2XTE_L 2XTC_B 2XTD_A 1UUJ_B.
Probab=33.19 E-value=27 Score=19.22 Aligned_cols=17 Identities=6% Similarity=0.174 Sum_probs=13.5
Q ss_pred HHHHHHHHHHhHcCCCC
Q 032632 81 DAVRQIWAHVKTHNLQN 97 (137)
Q Consensus 81 eVvk~LW~YIK~nnLQD 97 (137)
++-..||+|...+|+++
T Consensus 2 ~Ln~lI~~YL~~~Gy~~ 18 (27)
T PF08513_consen 2 ELNQLIYDYLVENGYKE 18 (27)
T ss_dssp HHHHHHHHHHHHCT-HH
T ss_pred HHHHHHHHHHHHCCcHH
Confidence 56788999999999764
No 43
>PF13950 Epimerase_Csub: UDP-glucose 4-epimerase C-term subunit; PDB: 1EK5_A 1I3K_B 1I3M_B 1HZJ_A 1EK6_A 1I3N_A 1I3L_A 2CNB_B 1GY8_D 1NAI_A ....
Probab=32.87 E-value=70 Score=20.79 Aligned_cols=37 Identities=24% Similarity=0.330 Sum_probs=22.8
Q ss_pred CCCccccCCHH-HHhhhC-CCCcCHHHHHHHHHHHHhHc
Q 032632 57 GISKVSPVSPA-LAKFLG-APEASRSDAVRQIWAHVKTH 93 (137)
Q Consensus 57 G~~k~~~lSpe-La~fLG-~~e~SR~eVvk~LW~YIK~n 93 (137)
|-...+..+.. ..+.|| ..+.+=.|++...|++.+.|
T Consensus 20 GD~~~~~Ad~~kA~~~LgW~p~~~L~~~i~~~w~W~~~n 58 (62)
T PF13950_consen 20 GDPAHLVADISKAREELGWKPKYSLEDMIRDAWNWQKKN 58 (62)
T ss_dssp T--SEE-B--HHHHHHC----SSSHHHHHHHHHHHHHHS
T ss_pred CchhhhhCCHHHHHHHhCCCcCCCHHHHHHHHHHHHHHC
Confidence 44444444444 447788 46779999999999999887
No 44
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=32.30 E-value=1e+02 Score=19.47 Aligned_cols=58 Identities=24% Similarity=0.335 Sum_probs=33.2
Q ss_pred HHHHhhhCCCCcCHHHHHHHHHHHHhHcCCCCCC---CCcccccchhHHhhhCC----CCccCHHHHHHHhc
Q 032632 66 PALAKFLGAPEASRSDAVRQIWAHVKTHNLQNPE---NKREILCDEKLKAIFEG----KNAVGFLEIGKLLS 130 (137)
Q Consensus 66 peLa~fLG~~e~SR~eVvk~LW~YIK~nnLQDP~---nKr~I~cDekLk~LFgg----~d~v~~~el~klL~ 130 (137)
.++++.+|++.- .|+.|.++-+|..|. +..-+..++.+..+-.- ..-+++.+|.++|+
T Consensus 4 ~e~A~~~gVs~~-------tlr~ye~~~gl~~~~r~~~g~R~yt~~di~~l~~i~~l~~~g~~l~~i~~~l~ 68 (68)
T cd04763 4 GEVALLTGIKPH-------VLRAWEREFGLLKPQRSDGGHRLFNDADIDRILEIKRWIDNGVQVSKVKKLLS 68 (68)
T ss_pred HHHHHHHCcCHH-------HHHHHHHhcCCCCCCcCCCCCcccCHHHHHHHHHHHHHHHcCCCHHHHHHHhC
Confidence 578888888766 778887776777652 22233444433332210 13356667766653
No 45
>KOG0995 consensus Centromere-associated protein HEC1 [Cell cycle control, cell division, chromosome partitioning]
Probab=32.05 E-value=1.9e+02 Score=27.30 Aligned_cols=53 Identities=17% Similarity=0.138 Sum_probs=30.9
Q ss_pred CCCCCCCCCCCCCCCCCCCccccCCHHHHhhhCCCCcC----HHHHHHHHHHHHhHcCCCCC
Q 032632 41 PRAKSPVKRGAPTRPTGISKVSPVSPALAKFLGAPEAS----RSDAVRQIWAHVKTHNLQNP 98 (137)
Q Consensus 41 ~~~~~~~~r~~~~~~~G~~k~~~lSpeLa~fLG~~e~S----R~eVvk~LW~YIK~nnLQDP 98 (137)
+.+.|.++|. ++=..++.+.+.-....+.+.++ |++++..|++|..+||--+|
T Consensus 35 ~~valf~~r~-----S~~s~~~~~~~~~~s~~dpRpl~dk~~~s~c~~~I~~fL~engf~~~ 91 (581)
T KOG0995|consen 35 TSVALFDRRP-----SLHSSRLSSFNTSNSIRDPRPLSDKRYRSQCIRQIYNFLVENGFSHP 91 (581)
T ss_pred cccccCCCCc-----ccccccccccCchhccCCCCCcccHHHHHHHHHHHHHHHHHcCCCCC
Confidence 4555555552 23222344444444444444333 78999999999998865433
No 46
>TIGR02055 APS_reductase thioredoxin-dependent adenylylsulfate APS reductase. This model describes recently identified adenosine 5'-phosphosulfate (APS) reductase activity found in sulfate-assimilatory prokaryotes, thus separating it from the traditionally described phosphoadenosine 5'-phosphosulfate (PAPS) reductases found in bacteria and fungi. Homologous to PAPS reductase in enterobacteria, cyanobacteria, and yeast, APS reductase here clusters with, and demonstrates greater homology to plant APS reductase. Additionally, the presence of two conserved C-terminal motifs (CCXXRKXXPL & SXGCXXCT) distinguishes APS substrate specificity and serves as a FeS cluster.
Probab=31.77 E-value=27 Score=27.18 Aligned_cols=12 Identities=17% Similarity=0.684 Sum_probs=10.7
Q ss_pred HHHHHHhHcCCC
Q 032632 85 QIWAHVKTHNLQ 96 (137)
Q Consensus 85 ~LW~YIK~nnLQ 96 (137)
-||+||++|||.
T Consensus 136 dVw~Yi~~~~lp 147 (191)
T TIGR02055 136 DVWEYIADNELP 147 (191)
T ss_pred HHHHHHHHcCCC
Confidence 689999999984
No 47
>PRK12563 sulfate adenylyltransferase subunit 2; Provisional
Probab=31.65 E-value=26 Score=30.14 Aligned_cols=24 Identities=13% Similarity=0.401 Sum_probs=17.2
Q ss_pred HHHHHHhHcCCCCC-----C-------CCcccccch
Q 032632 85 QIWAHVKTHNLQNP-----E-------NKREILCDE 108 (137)
Q Consensus 85 ~LW~YIK~nnLQDP-----~-------nKr~I~cDe 108 (137)
-||.||+.|||--. . |...|.||+
T Consensus 203 DVW~YI~~~~IP~~pLY~~~~r~~~~~~g~~~~~~~ 238 (312)
T PRK12563 203 DVWQYIAREKIPLVPLYFAKRRPVVERDGLLIMVDD 238 (312)
T ss_pred HHHHHHHHcCCCCCcchhcCCCceEEECCeEEeccc
Confidence 68999999998632 1 445667776
No 48
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=31.01 E-value=46 Score=22.21 Aligned_cols=40 Identities=20% Similarity=0.372 Sum_probs=28.9
Q ss_pred cCC-HHHHhhhCCCCcCHHHHHHHHHHHHhHcCCCCCCCCc
Q 032632 63 PVS-PALAKFLGAPEASRSDAVRQIWAHVKTHNLQNPENKR 102 (137)
Q Consensus 63 ~lS-peLa~fLG~~e~SR~eVvk~LW~YIK~nnLQDP~nKr 102 (137)
..+ .+|++.+|.+..+=+.+++.|++-==-....||+|+|
T Consensus 36 ~~~~~~la~~l~i~~~~vt~~l~~Le~~glv~r~~~~~DrR 76 (126)
T COG1846 36 GITVKELAERLGLDRSTVTRLLKRLEDKGLIERLRDPEDRR 76 (126)
T ss_pred CCcHHHHHHHHCCCHHHHHHHHHHHHHCCCeeecCCccccc
Confidence 344 8999999998888888888888632223445777765
No 49
>KOG0747 consensus Putative NAD+-dependent epimerases [Carbohydrate transport and metabolism]
Probab=30.44 E-value=1.1e+02 Score=26.87 Aligned_cols=54 Identities=19% Similarity=0.142 Sum_probs=39.7
Q ss_pred CCcCHHHHHHHHHHHHhHcCCCC-------------CCCCcccccchhHHhhhCCCCccCHH-HHHHHh
Q 032632 75 PEASRSDAVRQIWAHVKTHNLQN-------------PENKREILCDEKLKAIFEGKNAVGFL-EIGKLL 129 (137)
Q Consensus 75 ~e~SR~eVvk~LW~YIK~nnLQD-------------P~nKr~I~cDekLk~LFgg~d~v~~~-el~klL 129 (137)
.|+++-|+.+.|.++|......- -+|-|.-+|+|+++ =+|=+..+.+. .|.+.+
T Consensus 252 ~e~~~~~l~k~i~eli~~~~~~~~~~p~~~~v~dRp~nd~Ry~~~~eKik-~LGw~~~~p~~eGLrkti 319 (331)
T KOG0747|consen 252 DEMRVIDLAKDICELFEKRLPNIDTEPFIFFVEDRPYNDLRYFLDDEKIK-KLGWRPTTPWEEGLRKTI 319 (331)
T ss_pred chhhHHHHHHHHHHHHHHhccCCCCCCcceecCCCCcccccccccHHHHH-hcCCcccCcHHHHHHHHH
Confidence 68999999999999999854421 14567899999999 66646666663 455444
No 50
>PF14838 INTS5_C: Integrator complex subunit 5 C-terminus
Probab=29.83 E-value=26 Score=33.41 Aligned_cols=43 Identities=23% Similarity=0.385 Sum_probs=26.1
Q ss_pred CCHHHHhhhCC-CCcCHHHHH---HH-HHHHHhHcCCCCCCCCcccccchh
Q 032632 64 VSPALAKFLGA-PEASRSDAV---RQ-IWAHVKTHNLQNPENKREILCDEK 109 (137)
Q Consensus 64 lSpeLa~fLG~-~e~SR~eVv---k~-LW~YIK~nnLQDP~nKr~I~cDek 109 (137)
|.|+|..+... +.++-.||. .. ||+|+|+|. |..-.++.||+.
T Consensus 618 LPppL~~~~el~~~ltp~Ei~~lL~~cIW~y~kdh~---Psp~~f~~~~~~ 665 (696)
T PF14838_consen 618 LPPPLSYIHELFPYLTPHEIYLLLLSCIWNYMKDHV---PSPALFVFNDET 665 (696)
T ss_pred CCchHHHHHHHHHhcCHHHHHHHHHHHHHHHHhhCC---CCHHHHhcCccc
Confidence 44555554443 456666653 44 999999987 333346667765
No 51
>COG5577 Spore coat protein [Cell envelope biogenesis, outer membrane]
Probab=29.42 E-value=40 Score=25.98 Aligned_cols=37 Identities=14% Similarity=0.168 Sum_probs=28.2
Q ss_pred CCHHHHhhhCCCCcCHHHHHHHHHHHHhHcCCCCCCC
Q 032632 64 VSPALAKFLGAPEASRSDAVRQIWAHVKTHNLQNPEN 100 (137)
Q Consensus 64 lSpeLa~fLG~~e~SR~eVvk~LW~YIK~nnLQDP~n 100 (137)
-+|+|..+|-..-..--+-.+.||+|...|+-.-|.|
T Consensus 85 ~tP~lR~vL~~~l~~~i~~~~~v~~ym~~~g~Y~py~ 121 (145)
T COG5577 85 ATPELRAVLKDQLNQAIEMHKEVSEYMVQKGYYPPYN 121 (145)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCcCCCC
Confidence 3677777776544444556789999999999998876
No 52
>PF13333 rve_2: Integrase core domain
Probab=29.13 E-value=54 Score=20.23 Aligned_cols=20 Identities=15% Similarity=0.044 Sum_probs=17.4
Q ss_pred CCcCHHHHHHHHHHHHhHcC
Q 032632 75 PEASRSDAVRQIWAHVKTHN 94 (137)
Q Consensus 75 ~e~SR~eVvk~LW~YIK~nn 94 (137)
.-.|+.|+...|++||.-.|
T Consensus 16 ~~~t~eel~~~I~~YI~~yN 35 (52)
T PF13333_consen 16 KFKTREELKQAIDEYIDYYN 35 (52)
T ss_pred ccchHHHHHHHHHHHHHHhc
Confidence 45799999999999998764
No 53
>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=28.96 E-value=54 Score=21.57 Aligned_cols=20 Identities=10% Similarity=0.290 Sum_probs=15.2
Q ss_pred HHHHHHHHHHHHhHcCCCCCC
Q 032632 79 RSDAVRQIWAHVKTHNLQNPE 99 (137)
Q Consensus 79 R~eVvk~LW~YIK~nnLQDP~ 99 (137)
+.+|+..|.+||.+|+.- |.
T Consensus 8 Q~~vL~~I~~~~~~~G~~-Pt 27 (65)
T PF01726_consen 8 QKEVLEFIREYIEENGYP-PT 27 (65)
T ss_dssp HHHHHHHHHHHHHHHSS----
T ss_pred HHHHHHHHHHHHHHcCCC-CC
Confidence 578999999999999943 54
No 54
>TIGR02854 spore_II_GA sigma-E processing peptidase SpoIIGA. Members of this protein family are the stage II sporulation protein SpoIIGA. This protein acts as an activating protease for Sigma-E, one of several specialized sigma factors of the sporulation process in Bacillus subtilis and related endospore-forming bacteria.
Probab=28.92 E-value=65 Score=26.93 Aligned_cols=34 Identities=24% Similarity=0.449 Sum_probs=25.4
Q ss_pred HHHHHHHHHhH-----------------------------cCCCCCCCCc-ccccc-hhHHhhhC
Q 032632 82 AVRQIWAHVKT-----------------------------HNLQNPENKR-EILCD-EKLKAIFE 115 (137)
Q Consensus 82 Vvk~LW~YIK~-----------------------------nnLQDP~nKr-~I~cD-ekLk~LFg 115 (137)
+.+.+|+||+. |.|.||-+++ .+++| +.+++++.
T Consensus 140 ~~~~~~~~i~~~~~~~~~~~~v~i~~~g~~~~~~alvDTGN~L~DPlT~~PV~Ive~~~~~~~lp 204 (288)
T TIGR02854 140 FVKRRMDAIRDRAILDKQIYELEICLDGKKVTIKGFLDTGNQLRDPLTKLPVIVVEYDSLKSILP 204 (288)
T ss_pred HHHHHHHHHHHHHhhhceEEEEEEEECCEEEEEEEEEecCCcccCCCCCCCEEEEEHHHhhhhCC
Confidence 56788999995 6889996544 66666 67777775
No 55
>PF08938 HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This domain is found in various eukaryotic HBS1-like proteins. ; PDB: 1UFZ_A 3IZQ_1.
Probab=28.43 E-value=20 Score=24.40 Aligned_cols=28 Identities=14% Similarity=0.305 Sum_probs=21.2
Q ss_pred ccCCHHHHhhhCCCCcCHHHHHHHHHHH
Q 032632 62 SPVSPALAKFLGAPEASRSDAVRQIWAH 89 (137)
Q Consensus 62 ~~lSpeLa~fLG~~e~SR~eVvk~LW~Y 89 (137)
+..-+.+.+.||....+..+|..+||.|
T Consensus 29 ~~~l~~vr~~Lg~~~~~e~~i~eal~~~ 56 (79)
T PF08938_consen 29 YSCLPQVREVLGDYVPPEEQIKEALWHY 56 (79)
T ss_dssp CHHCCCHHHHCCCCC--CCHHHHHHHHT
T ss_pred HHHHHHHHHHHcccCCCHHHHHHHHHHH
Confidence 4455678888887655999999999998
No 56
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=27.93 E-value=62 Score=25.31 Aligned_cols=48 Identities=19% Similarity=0.314 Sum_probs=32.4
Q ss_pred ccCC-HHHHhhhCCCCcCHHHHHHHHHHHHhHcCCCCCCC-Ccccccch-hHHhh
Q 032632 62 SPVS-PALAKFLGAPEASRSDAVRQIWAHVKTHNLQNPEN-KREILCDE-KLKAI 113 (137)
Q Consensus 62 ~~lS-peLa~fLG~~e~SR~eVvk~LW~YIK~nnLQDP~n-Kr~I~cDe-kLk~L 113 (137)
..++ .+|++++|++..|=+. +-.-.++.|+.+-.. ++++++|. .|..+
T Consensus 178 i~lt~~~IA~~lGisretlsR----~L~~L~~~GlI~~~~~~~i~I~D~~~L~~l 228 (230)
T PRK09391 178 LPMSRRDIADYLGLTIETVSR----ALSQLQDRGLIGLSGARQIELRNRQALRNL 228 (230)
T ss_pred ecCCHHHHHHHHCCCHHHHHH----HHHHHHHCCcEEecCCceEEEcCHHHHHHh
Confidence 4455 7999999986544333 344567788887654 67888884 55554
No 57
>PRK05253 sulfate adenylyltransferase subunit 2; Provisional
Probab=27.41 E-value=34 Score=28.98 Aligned_cols=13 Identities=23% Similarity=0.636 Sum_probs=11.2
Q ss_pred HHHHHHhHcCCCC
Q 032632 85 QIWAHVKTHNLQN 97 (137)
Q Consensus 85 ~LW~YIK~nnLQD 97 (137)
-||+||+.+||.=
T Consensus 193 DIw~Yi~~~~IP~ 205 (301)
T PRK05253 193 DIWQYIERENIPI 205 (301)
T ss_pred HHHHHHHHcCCCC
Confidence 6899999999863
No 58
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=27.24 E-value=64 Score=24.83 Aligned_cols=50 Identities=10% Similarity=0.207 Sum_probs=33.7
Q ss_pred ccCC-HHHHhhhCCCCcCHHHHHHHHHHHHhHcCCCCCCCCcccccc-hhHHhhhC
Q 032632 62 SPVS-PALAKFLGAPEASRSDAVRQIWAHVKTHNLQNPENKREILCD-EKLKAIFE 115 (137)
Q Consensus 62 ~~lS-peLa~fLG~~e~SR~eVvk~LW~YIK~nnLQDP~nKr~I~cD-ekLk~LFg 115 (137)
.+++ .+|++++|++..| |.+.+ .=.++.++..-.++++++.| +.|.++.+
T Consensus 183 ~~lt~~~iA~~lG~sr~t---vsR~l-~~l~~~g~I~~~~~~i~i~d~~~L~~~~~ 234 (235)
T PRK11161 183 LTMTRGDIGNYLGLTVET---ISRLL-GRFQKSGMLAVKGKYITIENNDALAQLAG 234 (235)
T ss_pred ccccHHHHHHHhCCcHHH---HHHHH-HHHHHCCCEEecCCEEEEcCHHHHHHHhc
Confidence 4555 7999999986443 33333 34577888887778888887 56666553
No 59
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=27.21 E-value=1.1e+02 Score=17.56 Aligned_cols=24 Identities=21% Similarity=0.185 Sum_probs=19.1
Q ss_pred HHHHhhhCCCCcCHHHHHHHHHHHHhHcCCC
Q 032632 66 PALAKFLGAPEASRSDAVRQIWAHVKTHNLQ 96 (137)
Q Consensus 66 peLa~fLG~~e~SR~eVvk~LW~YIK~nnLQ 96 (137)
.++++++|++.- .||.|+++..|.
T Consensus 4 ~e~a~~~gv~~~-------tlr~~~~~g~l~ 27 (49)
T cd04761 4 GELAKLTGVSPS-------TLRYYERIGLLS 27 (49)
T ss_pred HHHHHHHCcCHH-------HHHHHHHCCCCC
Confidence 478888888766 789998887765
No 60
>PF13758 Prefoldin_3: Prefoldin subunit
Probab=25.53 E-value=1.3e+02 Score=21.97 Aligned_cols=38 Identities=13% Similarity=0.205 Sum_probs=28.4
Q ss_pred CCCCccccCCHHHHhhhCCCC---cCHHHHHHHH---HHHHhHc
Q 032632 56 TGISKVSPVSPALAKFLGAPE---ASRSDAVRQI---WAHVKTH 93 (137)
Q Consensus 56 ~G~~k~~~lSpeLa~fLG~~e---~SR~eVvk~L---W~YIK~n 93 (137)
.+|....---.++..+||... =|+.+|+..| .+||++|
T Consensus 40 r~f~g~lv~~kEi~~ilG~~~~i~Rt~~Qvv~~l~RRiDYV~~N 83 (99)
T PF13758_consen 40 RDFGGSLVTEKEIKEILGEGQGITRTREQVVDVLSRRIDYVQQN 83 (99)
T ss_pred HhcCcccccHHHHHHHhCCCCCCCcCHHHHHHHHHHHHHHHHHH
Confidence 456666666789999999854 4788887766 6899876
No 61
>PF07308 DUF1456: Protein of unknown function (DUF1456); InterPro: IPR009921 This domain occurs in several hypothetical bacterial proteins of around 150 residues in length. The function of this domain is unknown.
Probab=25.47 E-value=1.3e+02 Score=20.20 Aligned_cols=40 Identities=15% Similarity=0.248 Sum_probs=28.4
Q ss_pred HHHHhhh--CCCCcCHHHHHHHHHHHHhHcCCCCCCCCcccccchhHHhhh
Q 032632 66 PALAKFL--GAPEASRSDAVRQIWAHVKTHNLQNPENKREILCDEKLKAIF 114 (137)
Q Consensus 66 peLa~fL--G~~e~SR~eVvk~LW~YIK~nnLQDP~nKr~I~cDekLk~LF 114 (137)
+++.+++ |.-++|+.|+...+-. |+++....|++.+-.-|
T Consensus 17 ~~m~~if~l~~~~vs~~el~a~lrk---------e~~~~y~~c~D~~L~~F 58 (68)
T PF07308_consen 17 DDMIEIFALAGFEVSKAELSAWLRK---------EDEKGYKECSDQLLRNF 58 (68)
T ss_pred HHHHHHHHHcCCccCHHHHHHHHCC---------CCCccccccChHHHHHH
Confidence 4566664 5678999998876543 77778889987765544
No 62
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=25.42 E-value=70 Score=24.81 Aligned_cols=46 Identities=11% Similarity=0.142 Sum_probs=31.7
Q ss_pred HHHHhhhCCCCcCHHHHHHHHHHHHhHcCCCCCCCCcccccc-hhHHhhhC
Q 032632 66 PALAKFLGAPEASRSDAVRQIWAHVKTHNLQNPENKREILCD-EKLKAIFE 115 (137)
Q Consensus 66 peLa~fLG~~e~SR~eVvk~LW~YIK~nnLQDP~nKr~I~cD-ekLk~LFg 115 (137)
.+|++++|.+..|=+.+++. .+++|+.+...+++.++| +.|..+..
T Consensus 173 ~~lA~~lG~sretvsR~L~~----L~~~G~I~~~~~~i~I~d~~~L~~~~~ 219 (226)
T PRK10402 173 TQAAEYLGVSYRHLLYVLAQ----FIQDGYLKKSKRGYLIKNRKQLSGLAL 219 (226)
T ss_pred HHHHHHHCCcHHHHHHHHHH----HHHCCCEEeeCCEEEEeCHHHHHHHHH
Confidence 78999999865444444444 356777777778888898 46666553
No 63
>PF10924 DUF2711: Protein of unknown function (DUF2711); InterPro: IPR024250 Some members in this family of proteins are annotated as ywbB. The function of these proteins is unknown.
Probab=25.32 E-value=39 Score=27.94 Aligned_cols=59 Identities=19% Similarity=0.325 Sum_probs=42.6
Q ss_pred CCCCccccCCHHHHhhhCC--CCcCHHHHHHHHHHHHhHcCCCCCCC-CcccccchhHHhhhC
Q 032632 56 TGISKVSPVSPALAKFLGA--PEASRSDAVRQIWAHVKTHNLQNPEN-KREILCDEKLKAIFE 115 (137)
Q Consensus 56 ~G~~k~~~lSpeLa~fLG~--~e~SR~eVvk~LW~YIK~nnLQDP~n-Kr~I~cDekLk~LFg 115 (137)
+|+...-.|.-.|-.-+|. .+..|++..+.|-.|++. +|..|.+ .--+..=..|.+||+
T Consensus 65 ~gL~s~~Ela~AL~Tsigalr~ey~r~dla~~L~~~~~~-dlyyP~ED~~s~Fl~~~l~kvl~ 126 (217)
T PF10924_consen 65 CGLNSYKELALALMTSIGALRKEYARPDLAEKLNSYIDE-DLYYPSEDHTSLFLIPSLLKVLK 126 (217)
T ss_pred cCCCcHHHHHHHHHHHhhhhhhhhcChHHHHHHHhhccc-ccCCCCccCcchhhHHHHHHHHH
Confidence 4555555555555444443 678999999999999985 6999965 445666677888887
No 64
>TIGR00434 cysH phosophoadenylyl-sulfate reductase (thioredoxin). This enzyme, involved in the assimilation of inorganic sulfate, is designated cysH in Bacteria and MET16 in Saccharomyces cerevisiae. Synonyms include phosphoadenosine phosphosulfate reductase, PAPS reductase, and PAPS reductase, thioredoxin-dependent. In a reaction requiring reduced thioredoxin and NADPH, it converts 3(prime)-phosphoadenylylsulfate (PAPS) to sulfite and adenosine 3(prime),5(prime) diphosphate (PAP). A related family of plant enzymes, scoring below the trusted cutoff, differs in having a thioredoxin-like C-terminal domain, not requiring thioredoxin, and in having a preference for 5(prime)-adenylylsulfate (APS) over PAPS.
Probab=24.79 E-value=42 Score=26.07 Aligned_cols=12 Identities=25% Similarity=0.653 Sum_probs=10.6
Q ss_pred HHHHHHhHcCCC
Q 032632 85 QIWAHVKTHNLQ 96 (137)
Q Consensus 85 ~LW~YIK~nnLQ 96 (137)
-||+||.++||.
T Consensus 157 dVw~Yi~~~~lp 168 (212)
T TIGR00434 157 DVYQYIDAHNLP 168 (212)
T ss_pred HHHHHHHHcCCC
Confidence 469999999987
No 65
>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B.
Probab=24.76 E-value=1.2e+02 Score=20.74 Aligned_cols=44 Identities=11% Similarity=0.193 Sum_probs=31.8
Q ss_pred ccCCHHHHhhhCCC---CcCHHHHHHHHHHHHhHcCCCCCCCCcccccchhHH
Q 032632 62 SPVSPALAKFLGAP---EASRSDAVRQIWAHVKTHNLQNPENKREILCDEKLK 111 (137)
Q Consensus 62 ~~lSpeLa~fLG~~---e~SR~eVvk~LW~YIK~nnLQDP~nKr~I~cDekLk 111 (137)
..+-.+|.+.+|.. ..+..++...+|++++.++. ..|+.||-=.
T Consensus 52 ~~~~~~i~~~l~~~~~~~~~~~~l~~~~~~~l~~~~~------~~lviDe~~~ 98 (131)
T PF13401_consen 52 RDFAQEILEALGLPLKSRQTSDELRSLLIDALDRRRV------VLLVIDEADH 98 (131)
T ss_dssp HHHHHHHHHHHT-SSSSTS-HHHHHHHHHHHHHHCTE------EEEEEETTHH
T ss_pred HHHHHHHHHHhCccccccCCHHHHHHHHHHHHHhcCC------eEEEEeChHh
Confidence 34456677777764 35789999999999999985 5888887633
No 66
>PLN02309 5'-adenylylsulfate reductase
Probab=24.76 E-value=40 Score=30.41 Aligned_cols=13 Identities=15% Similarity=0.728 Sum_probs=11.1
Q ss_pred HHHHHHHhHcCCC
Q 032632 84 RQIWAHVKTHNLQ 96 (137)
Q Consensus 84 k~LW~YIK~nnLQ 96 (137)
.-||.||++|||-
T Consensus 261 ~dVw~Yi~~~~lP 273 (457)
T PLN02309 261 NEVWNFLRTMDVP 273 (457)
T ss_pred HHHHHHHHHcCCC
Confidence 3689999999985
No 67
>PRK07152 nadD putative nicotinate-nucleotide adenylyltransferase; Validated
Probab=24.32 E-value=42 Score=28.41 Aligned_cols=16 Identities=6% Similarity=-0.107 Sum_probs=13.1
Q ss_pred HHHHHHHHHhHcCCCC
Q 032632 82 AVRQIWAHVKTHNLQN 97 (137)
Q Consensus 82 Vvk~LW~YIK~nnLQD 97 (137)
|-..|++||++|+|..
T Consensus 170 vP~~V~~YI~~~~LY~ 185 (342)
T PRK07152 170 LDPKVNDYINENFLYL 185 (342)
T ss_pred CCHHHHHHHHHcCccc
Confidence 4456899999999983
No 68
>PF01507 PAPS_reduct: Phosphoadenosine phosphosulfate reductase family; InterPro: IPR002500 This domain is found in phosphoadenosine phosphosulphate (PAPS) reductase enzymes or PAPS sulphotransferase. PAPS reductase is part of the adenine nucleotide alpha hydrolases superfamily also including N type ATP PPases and ATP sulphurylases []. The enzyme uses thioredoxin as an electron donor for the reduction of PAPS to phospho-adenosine-phosphate (PAP) [, ]. It is also found in NodP nodulation protein P from Rhizobium meliloti (Sinorhizobium meliloti) which has ATP sulphurylase activity (sulphate adenylate transferase) [].; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 2GOY_C 3G5A_C 3G6K_D 3G59_A 3FWK_A 2WSI_A 2OQ2_B 1SUR_A 2O8V_A 1ZUN_A.
Probab=24.17 E-value=41 Score=24.36 Aligned_cols=12 Identities=25% Similarity=0.778 Sum_probs=9.1
Q ss_pred HHHHHHhHcCCC
Q 032632 85 QIWAHVKTHNLQ 96 (137)
Q Consensus 85 ~LW~YIK~nnLQ 96 (137)
-||+||+.++|.
T Consensus 143 dV~~yi~~~~l~ 154 (174)
T PF01507_consen 143 DVWDYIKANGLP 154 (174)
T ss_dssp HHHHHHHHHT--
T ss_pred HHHHHHHHhcCC
Confidence 579999999984
No 69
>PF13867 SAP30_Sin3_bdg: Sin3 binding region of histone deacetylase complex subunit SAP30; PDB: 2LD7_A.
Probab=24.01 E-value=77 Score=20.06 Aligned_cols=14 Identities=14% Similarity=0.050 Sum_probs=9.4
Q ss_pred HHHHHHHhHcCCCC
Q 032632 84 RQIWAHVKTHNLQN 97 (137)
Q Consensus 84 k~LW~YIK~nnLQD 97 (137)
..||.|-+.++|+.
T Consensus 4 ~tLrrY~~~~~l~~ 17 (53)
T PF13867_consen 4 PTLRRYKKHYKLPE 17 (53)
T ss_dssp HHHHHHHHHTT---
T ss_pred HHHHHHHHHhCCCC
Confidence 46899999999884
No 70
>TIGR02039 CysD sulfate adenylyltransferase, small subunit. In Escherichia coli, ATP sulfurylase is a heterodimer composed of two subunits encoded by cysD and cysN, with APS kinase encoded by cysC. These genes are located in a unidirectionally transcribed gene cluster, and have been shown to be required for the synthesis of sulfur-containing amino acids. Homologous to this E.coli activation pathway are nodPQH gene products found among members of the Rhizobiaceae family. These gene products have been shown to exhibit ATP sulfurase and APS kinase activity, yet are involved in Nod factor sulfation, and sulfation of other macromolecules.
Probab=23.51 E-value=45 Score=28.36 Aligned_cols=13 Identities=23% Similarity=0.606 Sum_probs=11.3
Q ss_pred HHHHHHhHcCCCC
Q 032632 85 QIWAHVKTHNLQN 97 (137)
Q Consensus 85 ~LW~YIK~nnLQD 97 (137)
-||.||..|||-=
T Consensus 185 DVW~YI~~~~IP~ 197 (294)
T TIGR02039 185 DIWRYIAAENIPI 197 (294)
T ss_pred HHHHHHHHcCCCC
Confidence 6899999999863
No 71
>PF12368 DUF3650: Protein of unknown function (DUF3650) ; InterPro: IPR022111 This domain family is found in bacteria, and is approximately 30 amino acids in length. The family is found in association with PF00581 from PFAM. There is a single completely conserved residue N that may be functionally important.
Probab=23.37 E-value=41 Score=19.34 Aligned_cols=10 Identities=40% Similarity=0.507 Sum_probs=8.2
Q ss_pred HHHhHcCCCC
Q 032632 88 AHVKTHNLQN 97 (137)
Q Consensus 88 ~YIK~nnLQD 97 (137)
-||++|||-+
T Consensus 9 rYV~eh~ls~ 18 (28)
T PF12368_consen 9 RYVKEHGLSE 18 (28)
T ss_pred hhHHhcCCCH
Confidence 4999999865
No 72
>COG1057 NadD Nicotinic acid mononucleotide adenylyltransferase [Coenzyme metabolism]
Probab=23.33 E-value=60 Score=25.96 Aligned_cols=32 Identities=6% Similarity=0.020 Sum_probs=23.9
Q ss_pred CHHHHhhhCCCCcCHHHHHHHHHHHHhHcCCC
Q 032632 65 SPALAKFLGAPEASRSDAVRQIWAHVKTHNLQ 96 (137)
Q Consensus 65 SpeLa~fLG~~e~SR~eVvk~LW~YIK~nnLQ 96 (137)
|.+..+.+....-....+-..+.+||++|+|.
T Consensus 164 St~IR~~~~~~~~~~~llP~~V~~YI~~~~LY 195 (197)
T COG1057 164 STEIRERIRRGASVDYLLPDSVLSYIEERGLY 195 (197)
T ss_pred hHHHHHHHhCCCCchhcCCHHHHHHHHHhccc
Confidence 44555666666666677778899999999986
No 73
>PF07037 DUF1323: Putative transcription regulator (DUF1323); InterPro: IPR010749 This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. The function of this family is unknown.
Probab=22.79 E-value=99 Score=23.46 Aligned_cols=45 Identities=20% Similarity=0.291 Sum_probs=33.8
Q ss_pred CHHHHhhhCCCCcCHHHHHHHHHHHHhHcCCCCC-------CCCcccccchhHHhhhCC
Q 032632 65 SPALAKFLGAPEASRSDAVRQIWAHVKTHNLQNP-------ENKREILCDEKLKAIFEG 116 (137)
Q Consensus 65 SpeLa~fLG~~e~SR~eVvk~LW~YIK~nnLQDP-------~nKr~I~cDekLk~LFgg 116 (137)
.+||++.+|.... .|-.+|++.|-... ..-|+|+-|+..+..+..
T Consensus 3 ~eELA~~tG~srQ-------TINrWvRkegW~T~p~pGVkGGrARLIhId~~V~efi~s 54 (122)
T PF07037_consen 3 PEELAELTGYSRQ-------TINRWVRKEGWKTEPKPGVKGGRARLIHIDEQVREFIRS 54 (122)
T ss_pred HHHHHHHhCccHH-------HHHHHHHhcCceeccCCccccccceeeeecHHHHHHHHh
Confidence 4789999998654 56778888776643 234789999999998764
No 74
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=22.50 E-value=1.6e+02 Score=18.26 Aligned_cols=24 Identities=17% Similarity=0.108 Sum_probs=17.5
Q ss_pred HHHHhhhCCCCcCHHHHHHHHHHHHhHcCCC
Q 032632 66 PALAKFLGAPEASRSDAVRQIWAHVKTHNLQ 96 (137)
Q Consensus 66 peLa~fLG~~e~SR~eVvk~LW~YIK~nnLQ 96 (137)
.++++.+|++.- .|+.|+++.-+.
T Consensus 4 ~eva~~~gvs~~-------tlr~~~~~gli~ 27 (70)
T smart00422 4 GEVAKLAGVSVR-------TLRYYERIGLLP 27 (70)
T ss_pred HHHHHHHCcCHH-------HHHHHHHCCCCC
Confidence 577888888766 788888755443
No 75
>KOG2076 consensus RNA polymerase III transcription factor TFIIIC [Transcription]
Probab=22.42 E-value=1.7e+02 Score=28.97 Aligned_cols=78 Identities=19% Similarity=0.240 Sum_probs=51.8
Q ss_pred CCCCCCCCccccCCHHHHhhhCC-----CCcCHHHHHHHHHHHHhHcCCCCCCCCcccccchhHHhhhCCCCccCHHHHH
Q 032632 52 PTRPTGISKVSPVSPALAKFLGA-----PEASRSDAVRQIWAHVKTHNLQNPENKREILCDEKLKAIFEGKNAVGFLEIG 126 (137)
Q Consensus 52 ~~~~~G~~k~~~lSpeLa~fLG~-----~e~SR~eVvk~LW~YIK~nnLQDP~nKr~I~cDekLk~LFgg~d~v~~~el~ 126 (137)
|+++++-...-.|+++|..+||. -.-...++...+.+-||. ||. .+.+=..|-.|+..+..+.-+=..
T Consensus 123 ~k~~~~~r~~~~l~~~l~~ll~eAN~lfarg~~eeA~~i~~EvIkq----dp~---~~~ay~tL~~IyEqrGd~eK~l~~ 195 (895)
T KOG2076|consen 123 KKRGRRSRGKSKLAPELRQLLGEANNLFARGDLEEAEEILMEVIKQ----DPR---NPIAYYTLGEIYEQRGDIEKALNF 195 (895)
T ss_pred CccCCCCCcccccCHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHh----Ccc---chhhHHHHHHHHHHcccHHHHHHH
Confidence 55566667778999999999996 236778888899999985 443 456667788888633222222233
Q ss_pred HHhcccCCCC
Q 032632 127 KLLSPHFVKT 136 (137)
Q Consensus 127 klL~~Hl~k~ 136 (137)
-+|.-||-++
T Consensus 196 ~llAAHL~p~ 205 (895)
T KOG2076|consen 196 WLLAAHLNPK 205 (895)
T ss_pred HHHHHhcCCC
Confidence 4555666553
No 76
>PF12213 Dpoe2NT: DNA polymerases epsilon N terminal; InterPro: IPR024639 This domain is found in the N-terminal of DNA polymerase epsilon subunit B proteins. It contains a single completely conserved phenylalanine residue that may be functionally important. It forms a primarily alpha helical structure in which four helices are arranged in two hairpins with connecting loops containing beta strands which form a short parallel sheet. DNA polymerase epsilon is required in DNA replication for synthesis of the leading strand. The N-terminal domain has close structural relation to AAA+ protein C-terminal domains [].; PDB: 2V6Z_M.
Probab=22.38 E-value=79 Score=21.54 Aligned_cols=43 Identities=30% Similarity=0.326 Sum_probs=28.0
Q ss_pred CCCCccccCCHHHHhhh-CCCCcCHHHHHHHHHHHHhHcCCCCC
Q 032632 56 TGISKVSPVSPALAKFL-GAPEASRSDAVRQIWAHVKTHNLQNP 98 (137)
Q Consensus 56 ~G~~k~~~lSpeLa~fL-G~~e~SR~eVvk~LW~YIK~nnLQDP 98 (137)
.||.=+-.-+.-|.++| ..++..|.+++..|-+-|...+|.+|
T Consensus 16 ~Gl~Lr~eA~~~l~~~l~~~~~~e~e~~l~~Ii~~v~kq~Lss~ 59 (73)
T PF12213_consen 16 RGLSLRSEASKYLAEQLQSLSEEEREDWLDKIIDAVQKQPLSSS 59 (73)
T ss_dssp TT-EE-HHHHHHHHHHTTTS-TTTHHHHHHHHHHHHTTS--SSS
T ss_pred ccceecHHHHHHHHHHHccCCHHHHHHHHHHHHHHHhcCCCCCC
Confidence 34444444455555655 45788899999999999999999886
No 77
>KOG4144 consensus Arylalkylamine N-acetyltransferase [General function prediction only]
Probab=22.31 E-value=50 Score=26.60 Aligned_cols=34 Identities=18% Similarity=0.411 Sum_probs=28.3
Q ss_pred HHHHHHHHHhHcCCCCCCCCcccccchhHHhhhC
Q 032632 82 AVRQIWAHVKTHNLQNPENKREILCDEKLKAIFE 115 (137)
Q Consensus 82 Vvk~LW~YIK~nnLQDP~nKr~I~cDekLk~LFg 115 (137)
....||+|+..-+=|.-.++-..+|.+.|-....
T Consensus 119 a~~Ll~~ylq~l~~q~i~~r~~Li~h~pLvPFYE 152 (190)
T KOG4144|consen 119 APILLWRYLQHLGSQPIVRRAALICHDPLVPFYE 152 (190)
T ss_pred chhHHHHHHHHhhcCccccceeeeecCCccchhH
Confidence 3568999999999888888888999999877653
No 78
>PRK00982 acpP acyl carrier protein; Provisional
Probab=22.31 E-value=73 Score=20.64 Aligned_cols=50 Identities=10% Similarity=0.127 Sum_probs=36.0
Q ss_pred HHHHHHHHHHHhHcCCCCCCCCcccccchhHHhhhCCCCccCHHHHHHHhcccC
Q 032632 80 SDAVRQIWAHVKTHNLQNPENKREILCDEKLKAIFEGKNAVGFLEIGKLLSPHF 133 (137)
Q Consensus 80 ~eVvk~LW~YIK~nnLQDP~nKr~I~cDekLk~LFgg~d~v~~~el~klL~~Hl 133 (137)
.++...|+++|.+.= .-+ ...|..|..|..-+| -|++.+.+|...|...|
T Consensus 2 ~~i~~~l~~~l~~~l-~~~--~~~i~~d~~l~~dlg-lDSl~~~~li~~le~~f 51 (78)
T PRK00982 2 SEIFEKVKKIIVEQL-GVD--EEEVTPEASFVDDLG-ADSLDTVELVMALEEEF 51 (78)
T ss_pred hHHHHHHHHHHHHHH-CCC--HHHCCCCcchHhhcC-CCHHHHHHHHHHHHHHH
Confidence 457788888887643 322 336888999977776 78888888887776654
No 79
>PF04636 PA26: PA26 p53-induced protein (sestrin); InterPro: IPR006730 Exposure of mammalian cells to hypoxia, radiation and certain chemotherapeutic agents promotes cell cycle arrest and/or apoptosis. Activation of p53 responsive genes is believed to play an important role in mediating such responses. PA26 is differentially induced by genotoxic stress (UV, gamma-irradiation and cytotoxic drugs) in a p53-dependent manner. PA26 gene is a novel p53 target gene with properties common to the GADD family of growth arrest and DNA damage-inducible stress-response genes, and, thus, a potential novel regulator of cellular growth []. A homolgue found in Xenopus, XPA26, was initially detected in the anterior portion of developing notochord at neurula stages, and later in the entire notochord except its posterior region at tailbud stages []. ; GO: 0007050 cell cycle arrest, 0005634 nucleus
Probab=21.67 E-value=1.2e+02 Score=27.40 Aligned_cols=56 Identities=29% Similarity=0.481 Sum_probs=34.8
Q ss_pred CCCCccccCCHHHHhhhCC----------------CCcCHHHHHHHHHHHHhHcCCCCCCCCcccccchhHHhhhCC-CC
Q 032632 56 TGISKVSPVSPALAKFLGA----------------PEASRSDAVRQIWAHVKTHNLQNPENKREILCDEKLKAIFEG-KN 118 (137)
Q Consensus 56 ~G~~k~~~lSpeLa~fLG~----------------~e~SR~eVvk~LW~YIK~nnLQDP~nKr~I~cDekLk~LFgg-~d 118 (137)
.|+.-.-.+-|+++.+|+. ....=+-..++||.||. .|||- .|
T Consensus 317 hg~slvnrly~d~~~lLdekF~~v~~LTy~tm~~~~~VdTs~~R~Aiw~Yiq--------------------~i~Gi~~D 376 (450)
T PF04636_consen 317 HGFSLVNRLYPDLGQLLDEKFRVVYNLTYNTMGMHEDVDTSPFRRAIWNYIQ--------------------CIFGIRHD 376 (450)
T ss_pred chhHHHHHhhhHHHHHHHHHHHHHHHhccccccCCCCCCcHHHHHHHHHHHH--------------------HHhccccc
Confidence 3444444566788888742 22222346799999984 46652 35
Q ss_pred ccCHHHHHHHhcc
Q 032632 119 AVGFLEIGKLLSP 131 (137)
Q Consensus 119 ~v~~~el~klL~~ 131 (137)
-.++.||+++|.+
T Consensus 377 DydY~evN~lL~r 389 (450)
T PF04636_consen 377 DYDYGEVNKLLER 389 (450)
T ss_pred CCCHHHHHHHhhh
Confidence 5677888888764
No 80
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=21.43 E-value=2.2e+02 Score=17.80 Aligned_cols=57 Identities=21% Similarity=0.316 Sum_probs=32.4
Q ss_pred HHHHhhhCCCCcCHHHHHHHHHHHHhHcCCCCCC--CCcccccchhHHhhhCC----CCccCHHHHHHHh
Q 032632 66 PALAKFLGAPEASRSDAVRQIWAHVKTHNLQNPE--NKREILCDEKLKAIFEG----KNAVGFLEIGKLL 129 (137)
Q Consensus 66 peLa~fLG~~e~SR~eVvk~LW~YIK~nnLQDP~--nKr~I~cDekLk~LFgg----~d~v~~~el~klL 129 (137)
.++++++|++.- .|+-|.++-+|.-|. +..-...++.+..+-.- ..-+++.+|..+|
T Consensus 4 ~evA~~~gvs~~-------tlR~~~~~g~l~~~~~~~g~R~y~~~~l~~l~~i~~l~~~g~~l~~i~~~l 66 (67)
T cd04764 4 KEVSEIIGVKPH-------TLRYYEKEFNLYIPRTENGRRYYTDEDIELLKKIKTLLEKGLSIKEIKEIL 66 (67)
T ss_pred HHHHHHHCcCHH-------HHHHHHHhcCCCCCCCCCCceeeCHHHHHHHHHHHHHHHCCCCHHHHHHHh
Confidence 578888888765 677787765665442 23344445444433220 1235566776665
No 81
>TIGR00424 APS_reduc 5'-adenylylsulfate reductase, thioredoxin-independent. This enzyme, involved in the assimilation of inorganic sulfate, is closely related to the thioredoxin-dependent PAPS reductase of Bacteria (CysH) and Saccharomyces cerevisiae. However, it has its own C-terminal thioredoxin-like domain and is not thioredoxin-dependent. Also, it has a substrate preference for 5'-adenylylsulfate (APS) over 3'-phosphoadenylylsulfate (PAPS) so the pathway does not require an APS kinase (CysC) to convert APS to PAPS. Arabidopsis thaliana appears to have three isozymes, all able to complement E. coli CysH mutants (even in backgrounds lacking thioredoxin or APS kinase) but likely localized to different compartments in Arabidopsis.
Probab=21.38 E-value=51 Score=29.81 Aligned_cols=12 Identities=17% Similarity=0.758 Sum_probs=10.5
Q ss_pred HHHHHHhHcCCC
Q 032632 85 QIWAHVKTHNLQ 96 (137)
Q Consensus 85 ~LW~YIK~nnLQ 96 (137)
-||.||++|||-
T Consensus 267 dVw~Yi~~~~LP 278 (463)
T TIGR00424 267 DVWNFLRTMDVP 278 (463)
T ss_pred HHHHHHHHcCCC
Confidence 399999999985
No 82
>PF02650 HTH_WhiA: WhiA C-terminal HTH domain; InterPro: IPR023054 This domain is found at the C terminus of the sporulation regulator WhiA. It is predicted to form a DNA binding helix-turn-helix structure []. ; PDB: 3HYI_A.
Probab=20.94 E-value=46 Score=23.35 Aligned_cols=45 Identities=24% Similarity=0.335 Sum_probs=26.4
Q ss_pred HHHHHHhHcCCCCCCCCcccccchhHHhhhCC---CCccCHHHHHHHhcccCCCC
Q 032632 85 QIWAHVKTHNLQNPENKREILCDEKLKAIFEG---KNAVGFLEIGKLLSPHFVKT 136 (137)
Q Consensus 85 ~LW~YIK~nnLQDP~nKr~I~cDekLk~LFgg---~d~v~~~el~klL~~Hl~k~ 136 (137)
..++||.++++.| ..++.|+.++.- -...++.||.+++.+-+.|+
T Consensus 24 ~~I~~i~~~~~~~-------~l~~~l~~~a~lRl~~Pd~SL~EL~~~~~~~iSKS 71 (85)
T PF02650_consen 24 EAIEFIEENNGLD-------KLPEKLREFAELRLENPDASLKELGELLEPPISKS 71 (85)
T ss_dssp HHHHHHHHHT-GG-------GS-HHHHHHHHHHHH-TTS-HHHHHHTT--T--HH
T ss_pred HHHHHHHHhcccc-------cCCHHHHHHHHHHHHCccccHHHHHHHHcCcCcHH
Confidence 3678888888643 456778887752 24578889999988766554
No 83
>COG0175 CysH 3'-phosphoadenosine 5'-phosphosulfate sulfotransferase (PAPS reductase)/FAD synthetase and related enzymes [Amino acid transport and metabolism / Coenzyme metabolism]
Probab=20.73 E-value=55 Score=26.89 Aligned_cols=12 Identities=25% Similarity=0.700 Sum_probs=10.6
Q ss_pred HHHHHHhHcCCC
Q 032632 85 QIWAHVKTHNLQ 96 (137)
Q Consensus 85 ~LW~YIK~nnLQ 96 (137)
-||.||..|||-
T Consensus 184 dVw~Yi~~~~lp 195 (261)
T COG0175 184 DVWLYILANNLP 195 (261)
T ss_pred HHHHHHHHhCCC
Confidence 689999999975
No 84
>PF00010 HLH: Helix-loop-helix DNA-binding domain only nuclear translocator protein (Arnt).; InterPro: IPR011598 The helix-loop-helix (HLH) DNA-binding domain consists of a closed bundle of four helices in a left-handed twist with two crossover connections. The HLH domain directs dimerisation, and is juxtaposed to basic regions to create a DNA interaction interface surface that recognises specific DNA sequences. Basic region/HLH (bHLH) proteins regulate diverse biological pathways []. bHLH proteins include MyoD [], SREBPs (sterol regulatory element binding proteins) [], and yeast Pho4 (phosphatase system) []. In certain proteins the bHLH domain contains a leucine-zipper motif. The bHLH/leucine zipper (bHLHZip) domain specifies dimerisation within a network of proteins and determines sequence-specific DNA binding []. bHLHZip domains occur in the transcription factors Myc, Mad, Max and Usf [, ]. This entry is bHLHZip, which covers the bHLH domain and the leucine zipper motif, when present.; PDB: 1NLW_A 1NKP_D 1A93_A 2A93_A 1AM9_C 3U5V_A 1A0A_B 2QL2_C 1UKL_C 1AN4_B ....
Probab=20.71 E-value=1.3e+02 Score=18.32 Aligned_cols=18 Identities=11% Similarity=0.202 Sum_probs=16.2
Q ss_pred CCcCHHHHHHHHHHHHhH
Q 032632 75 PEASRSDAVRQIWAHVKT 92 (137)
Q Consensus 75 ~e~SR~eVvk~LW~YIK~ 92 (137)
...++.+|+...++||+.
T Consensus 36 ~k~~K~~iL~~ai~yI~~ 53 (55)
T PF00010_consen 36 RKLSKASILQKAIDYIKQ 53 (55)
T ss_dssp SSSSHHHHHHHHHHHHHH
T ss_pred ccCCHHHHHHHHHHHHHH
Confidence 469999999999999985
No 85
>PF05643 DUF799: Putative bacterial lipoprotein (DUF799); InterPro: IPR008517 This family consists of several bacterial proteins of unknown function. Some of the family members are described as putative lipoproteins.
Probab=20.69 E-value=28 Score=28.60 Aligned_cols=38 Identities=24% Similarity=0.378 Sum_probs=27.7
Q ss_pred HHHHHHhHcCCCCCCCCcccccchhHHhhhCCCCccCHHH
Q 032632 85 QIWAHVKTHNLQNPENKREILCDEKLKAIFEGKNAVGFLE 124 (137)
Q Consensus 85 ~LW~YIK~nnLQDP~nKr~I~cDekLk~LFgg~d~v~~~e 124 (137)
.+-+-+|+|+|.||++=..+- -++|++||| -|-+-+..
T Consensus 76 ~vde~fkqnGlt~~~~i~~v~-~~kL~eiFG-ADAvLY~~ 113 (215)
T PF05643_consen 76 LVDETFKQNGLTDAEDIHAVP-PAKLREIFG-ADAVLYIT 113 (215)
T ss_pred HHHHHHHHcCCCCHHHhccCC-HHHHHHHhC-CCEEEEEE
Confidence 344567899999999865444 689999998 67654433
No 86
>KOG4068 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.38 E-value=1.1e+02 Score=24.51 Aligned_cols=23 Identities=22% Similarity=0.511 Sum_probs=21.1
Q ss_pred HHHHHHHHHHHhHcCCCCCCCCc
Q 032632 80 SDAVRQIWAHVKTHNLQNPENKR 102 (137)
Q Consensus 80 ~eVvk~LW~YIK~nnLQDP~nKr 102 (137)
.+++..||+|....|+-.|.||+
T Consensus 68 ~~~i~~Il~~l~k~g~~e~~Dk~ 90 (174)
T KOG4068|consen 68 QEFIDEILEELEKKGLAEPTDKR 90 (174)
T ss_pred HHHHHHHHHHHHHccCCcccccC
Confidence 57889999999999999999987
No 87
>PF12487 DUF3703: Protein of unknown function (DUF3703) ; InterPro: IPR022172 This family of proteins is found in bacteria. Proteins in this family are typically between 113 and 135 amino acids in length.
Probab=20.28 E-value=1e+02 Score=22.84 Aligned_cols=19 Identities=21% Similarity=0.233 Sum_probs=16.7
Q ss_pred CCCCCCccccCCHHHHhhh
Q 032632 54 RPTGISKVSPVSPALAKFL 72 (137)
Q Consensus 54 ~~~G~~k~~~lSpeLa~fL 72 (137)
.+-|..++..|+++|+++|
T Consensus 93 anV~~f~pmpip~dl~~~l 111 (112)
T PF12487_consen 93 ANVSPFKPMPIPEDLQALL 111 (112)
T ss_pred CCCCCCCCCCCCHHHHHHh
Confidence 4678999999999999886
Done!