Query psy5629
Match_columns 203
No_of_seqs 68 out of 70
Neff 4.8
Searched_HMMs 46136
Date Fri Aug 16 22:32:12 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5629.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5629hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd04750 Commd2 COMM_Domain con 100.0 1.4E-43 3.1E-48 292.8 15.9 152 26-181 1-166 (166)
2 cd04752 Commd4 COMM_Domain con 99.9 1.2E-20 2.6E-25 156.9 16.1 151 25-179 7-173 (174)
3 PF07258 HCaRG: HCaRG protein; 99.8 2.6E-23 5.5E-28 167.0 -7.3 163 13-179 1-177 (178)
4 cd04758 Commd10 COMM_Domain co 99.4 9.3E-12 2E-16 104.3 16.7 165 11-179 3-185 (186)
5 cd04751 Commd3 COMM_Domain con 99.3 6.1E-12 1.3E-16 95.8 8.2 76 101-178 2-91 (95)
6 cd04756 Commd8 COMM_Domain con 99.1 6.8E-09 1.5E-13 87.0 15.5 156 12-177 2-173 (176)
7 cd04755 Commd7 COMM_Domain con 99.0 2.2E-08 4.9E-13 84.7 17.3 160 14-178 2-179 (180)
8 cd04753 Commd5_HCaRG COMM_Doma 98.9 4.7E-09 1E-13 82.4 8.5 91 89-186 1-107 (110)
9 cd04748 Commd COMM_Domain, a f 98.8 9.5E-09 2.1E-13 76.3 6.2 71 105-176 1-86 (87)
10 cd04757 Commd9 COMM_Domain con 98.7 3E-08 6.4E-13 77.9 7.0 78 92-172 1-98 (108)
11 cd04749 Commd1_MURR1 COMM_Doma 98.6 1.2E-06 2.6E-11 74.0 12.2 123 52-178 31-172 (174)
12 PF05225 HTH_psq: helix-turn-h 86.8 1.6 3.5E-05 28.8 4.4 37 27-66 4-40 (45)
13 cd04754 Commd6 COMM_Domain con 82.2 3.8 8.2E-05 31.3 5.2 53 123-175 31-83 (86)
14 cd08783 Death_MALT1 Death doma 69.7 23 0.0005 27.7 6.5 77 16-120 1-80 (97)
15 KOG3334|consensus 67.4 8.5 0.00018 32.1 4.0 50 16-66 28-78 (148)
16 PF08769 Spo0A_C: Sporulation 59.2 32 0.0007 26.7 5.7 45 27-72 20-70 (106)
17 PF08279 HTH_11: HTH domain; 58.3 16 0.00035 23.9 3.4 38 32-70 6-43 (55)
18 PF14490 HHH_4: Helix-hairpin- 58.2 20 0.00043 26.7 4.3 52 23-75 28-89 (94)
19 PF06896 DUF1268: Protein of u 54.5 23 0.0005 28.1 4.2 45 2-50 65-109 (114)
20 cd07377 WHTH_GntR Winged helix 53.8 27 0.00059 22.8 4.0 46 21-67 4-50 (66)
21 PF08784 RPA_C: Replication pr 49.2 34 0.00074 25.4 4.3 43 24-67 45-90 (102)
22 cd08315 Death_TRAILR_DR4_DR5 D 46.8 36 0.00078 25.8 4.1 36 26-62 4-39 (96)
23 cd08054 gp6 Head-Tail Connecto 46.2 55 0.0012 23.1 4.9 64 7-72 3-66 (91)
24 PF00126 HTH_1: Bacterial regu 45.7 18 0.00039 24.5 2.1 28 40-68 12-39 (60)
25 TIGR01560 put_DNA_pack unchara 44.7 83 0.0018 23.1 5.7 60 7-72 3-62 (91)
26 PF14502 HTH_41: Helix-turn-he 44.0 29 0.00063 23.8 2.8 29 37-66 2-30 (48)
27 PRK11050 manganese transport r 41.2 46 0.001 26.8 4.2 60 7-68 17-77 (152)
28 PF02627 CMD: Carboxymuconolac 40.8 67 0.0015 21.9 4.5 49 19-69 21-70 (85)
29 TIGR00987 himA integration hos 38.9 54 0.0012 24.4 4.0 34 43-77 7-40 (96)
30 PF04218 CENP-B_N: CENP-B N-te 37.0 50 0.0011 22.2 3.2 30 31-64 15-44 (53)
31 PRK00285 ihfA integration host 36.8 64 0.0014 24.0 4.1 34 43-77 8-41 (99)
32 PF13542 HTH_Tnp_ISL3: Helix-t 36.1 77 0.0017 20.3 4.0 34 27-64 16-49 (52)
33 PF05402 PqqD: Coenzyme PQQ sy 35.9 1.2E+02 0.0027 20.4 5.2 48 23-72 14-63 (68)
34 PF09607 BrkDBD: Brinker DNA-b 35.3 71 0.0015 22.7 3.8 35 26-61 9-44 (58)
35 PF09339 HTH_IclR: IclR helix- 35.1 51 0.0011 21.6 3.0 37 31-68 8-44 (52)
36 PF08280 HTH_Mga: M protein tr 34.9 34 0.00073 23.3 2.1 41 32-74 11-51 (59)
37 PF13404 HTH_AsnC-type: AsnC-t 34.3 44 0.00095 21.6 2.5 26 40-66 16-41 (42)
38 smart00345 HTH_GNTR helix_turn 34.1 77 0.0017 20.1 3.7 25 43-68 22-46 (60)
39 PRK11482 putative DNA-binding 34.0 95 0.0021 27.2 5.4 49 11-68 21-69 (317)
40 smart00421 HTH_LUXR helix_turn 33.9 1.2E+02 0.0025 18.7 4.7 32 32-67 12-43 (58)
41 PF10668 Phage_terminase: Phag 33.7 48 0.001 23.6 2.7 30 31-61 12-41 (60)
42 smart00346 HTH_ICLR helix_turn 32.9 82 0.0018 22.2 4.0 36 31-67 10-45 (91)
43 PF05135 Phage_connect_1: Phag 32.5 1.2E+02 0.0026 21.9 4.9 61 7-71 7-67 (101)
44 PF05678 VQ: VQ motif; InterP 32.2 49 0.0011 20.6 2.3 17 155-171 7-23 (31)
45 PF13518 HTH_28: Helix-turn-he 32.0 81 0.0018 19.9 3.5 29 32-64 6-34 (52)
46 cd05030 calgranulins Calgranul 31.9 77 0.0017 23.1 3.8 31 58-88 2-37 (88)
47 PF13613 HTH_Tnp_4: Helix-turn 31.9 1.2E+02 0.0026 20.0 4.5 43 29-75 10-52 (53)
48 PF13384 HTH_23: Homeodomain-l 31.7 55 0.0012 20.8 2.6 29 31-63 10-38 (50)
49 smart00418 HTH_ARSR helix_turn 31.5 95 0.0021 19.4 3.8 34 32-68 3-36 (66)
50 smart00411 BHL bacterial (prok 31.0 88 0.0019 22.4 3.9 33 43-76 6-38 (90)
51 PF12244 DUF3606: Protein of u 31.0 37 0.0008 23.5 1.8 22 44-66 23-44 (57)
52 PRK10753 transcriptional regul 30.7 95 0.0021 23.0 4.1 33 43-76 6-38 (90)
53 PF14908 DUF4496: Domain of un 30.7 85 0.0018 24.7 4.1 38 37-75 77-115 (140)
54 smart00005 DEATH DEATH domain, 30.6 83 0.0018 22.2 3.7 29 32-61 8-36 (88)
55 PF00046 Homeobox: Homeobox do 30.2 49 0.0011 21.6 2.3 23 39-62 25-47 (57)
56 cd06170 LuxR_C_like C-terminal 30.1 1.4E+02 0.0031 18.5 4.7 31 32-66 9-39 (57)
57 cd00090 HTH_ARSR Arsenical Res 29.8 99 0.0021 19.9 3.7 34 31-67 12-45 (78)
58 PF13624 SurA_N_3: SurA N-term 29.7 88 0.0019 24.3 4.0 53 39-95 84-138 (154)
59 PF04792 LcrV: V antigen (LcrV 29.6 1E+02 0.0022 28.8 4.8 67 52-122 88-161 (323)
60 PF00196 GerE: Bacterial regul 29.3 88 0.0019 20.7 3.4 35 31-69 11-45 (58)
61 PF05942 PaREP1: Archaeal PaRE 28.8 1.3E+02 0.0028 23.1 4.7 39 24-70 6-44 (115)
62 PF13556 HTH_30: PucR C-termin 28.3 1E+02 0.0022 20.8 3.6 35 32-70 6-40 (59)
63 PF09862 DUF2089: Protein of u 27.9 1.7E+02 0.0038 23.2 5.3 45 16-68 31-75 (113)
64 PF13412 HTH_24: Winged helix- 27.6 1.2E+02 0.0026 19.2 3.7 35 31-67 8-42 (48)
65 PHA02591 hypothetical protein; 27.1 1.2E+02 0.0027 23.0 4.1 35 26-64 47-81 (83)
66 cd08794 Death_IRAK1 Death doma 27.1 47 0.001 25.3 1.9 16 15-30 2-17 (84)
67 PF10410 DnaB_bind: DnaB-helic 27.1 1.4E+02 0.003 19.5 4.1 38 20-58 17-58 (59)
68 KOG0869|consensus 26.9 2.3E+02 0.005 24.1 6.1 39 57-95 58-104 (168)
69 PF13730 HTH_36: Helix-turn-he 26.4 1.8E+02 0.004 18.7 5.3 25 43-68 27-51 (55)
70 COG3355 Predicted transcriptio 26.1 1E+02 0.0022 25.0 3.7 27 42-69 43-69 (126)
71 KOG0275|consensus 25.2 1.9E+02 0.004 27.8 5.8 99 26-141 9-107 (508)
72 cd07979 TAF9 TATA Binding Prot 25.1 1.2E+02 0.0025 23.9 3.9 51 17-68 17-68 (117)
73 cd08306 Death_FADD Fas-associa 25.0 82 0.0018 23.2 2.9 31 31-63 4-34 (86)
74 PF09312 SurA_N: SurA N-termin 24.9 1.5E+02 0.0032 22.8 4.4 49 40-95 52-102 (118)
75 PRK11013 DNA-binding transcrip 24.8 1.6E+02 0.0036 25.3 5.2 40 18-66 3-42 (309)
76 PRK00117 recX recombination re 24.6 3.6E+02 0.0077 21.4 8.3 83 19-105 5-101 (157)
77 PF03333 PapB: Adhesin biosynt 24.5 1.2E+02 0.0026 23.3 3.7 52 10-65 25-76 (91)
78 PF00216 Bac_DNA_binding: Bact 24.1 1.3E+02 0.0028 21.4 3.8 32 43-75 6-37 (90)
79 PF01726 LexA_DNA_bind: LexA D 24.0 1.6E+02 0.0034 20.8 4.0 35 32-67 16-51 (65)
80 cd08311 Death_p75NR Death doma 23.8 83 0.0018 23.1 2.7 27 36-63 10-36 (77)
81 cd00086 homeodomain Homeodomai 23.8 92 0.002 20.0 2.7 23 39-62 25-47 (59)
82 PF01325 Fe_dep_repress: Iron 23.6 2.5E+02 0.0055 19.2 5.0 42 24-67 6-47 (60)
83 PRK10664 transcriptional regul 23.3 1.5E+02 0.0032 22.0 4.0 33 43-76 6-38 (90)
84 PRK10086 DNA-binding transcrip 23.3 1.6E+02 0.0035 25.5 4.8 45 15-68 10-54 (311)
85 PF08440 Poty_PP: Potyviridae 23.2 2.1E+02 0.0044 26.0 5.6 73 81-181 103-175 (274)
86 PF10083 DUF2321: Uncharacteri 23.2 2.8E+02 0.006 23.5 5.9 63 13-78 92-158 (158)
87 PRK11062 nhaR transcriptional 23.2 1.7E+02 0.0037 25.0 5.0 39 20-67 5-43 (296)
88 TIGR00122 birA_repr_reg BirA b 23.1 1.4E+02 0.0031 20.4 3.7 32 33-67 7-38 (69)
89 smart00576 BTP Bromodomain tra 22.9 1.4E+02 0.0031 21.3 3.8 46 18-64 23-69 (77)
90 PF09012 FeoC: FeoC like trans 22.8 1.1E+02 0.0025 21.1 3.1 32 33-66 7-38 (69)
91 cd00591 HU_IHF Integration hos 22.7 1.6E+02 0.0034 20.9 3.9 32 43-75 5-36 (87)
92 PF04545 Sigma70_r4: Sigma-70, 22.4 1.8E+02 0.004 18.5 3.9 25 39-64 18-42 (50)
93 smart00088 PINT motif in prote 22.3 2.6E+02 0.0057 19.6 5.0 42 23-65 6-47 (88)
94 smart00753 PAM PCI/PINT associ 22.3 2.6E+02 0.0057 19.6 5.0 42 23-65 6-47 (88)
95 PF05589 DUF768: Protein of un 22.0 1.3E+02 0.0029 21.6 3.3 30 43-73 34-63 (64)
96 KOG0478|consensus 21.8 1.2E+02 0.0027 31.4 4.2 88 1-90 695-788 (804)
97 PF11248 DUF3046: Protein of u 21.8 73 0.0016 22.9 2.0 34 22-55 26-61 (63)
98 PF01486 K-box: K-box region; 21.6 1.2E+02 0.0025 22.7 3.2 38 157-194 45-83 (100)
99 PF06784 UPF0240: Uncharacteri 21.2 95 0.0021 26.3 2.9 35 28-63 120-157 (179)
100 PF14394 DUF4423: Domain of un 21.1 3.3E+02 0.0071 22.6 6.1 72 43-120 78-154 (171)
101 PF14842 FliG_N: FliG N-termin 21.1 2.3E+02 0.0049 21.6 4.8 59 46-106 41-99 (108)
102 PF00632 HECT: HECT-domain (ub 21.0 5.7E+02 0.012 22.4 10.5 152 18-177 142-310 (317)
103 PF00531 Death: Death domain; 20.9 90 0.0019 21.6 2.3 27 37-64 8-34 (83)
104 PF14394 DUF4423: Domain of un 20.5 1.7E+02 0.0038 24.2 4.3 47 22-69 19-68 (171)
105 TIGR02395 rpoN_sigma RNA polym 20.3 2E+02 0.0043 27.5 5.1 27 42-69 183-209 (429)
106 PRK14135 recX recombination re 20.1 5.7E+02 0.012 22.0 8.5 77 26-106 58-149 (263)
No 1
>cd04750 Commd2 COMM_Domain containing protein 2. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=100.00 E-value=1.4e-43 Score=292.81 Aligned_cols=152 Identities=34% Similarity=0.599 Sum_probs=147.3
Q ss_pred HHHHHHHHHHhcCCchhhHHHHHhhcCCCchHHHHHHHHHHHHHHHHHhhccCChhhhhhhhhhcCCCChhHHHHHHHHH
Q psy5629 26 DFCTLTTNYLKDGPNQKLYKSVSKKLSLPSADNVQDSVEGLVYFLLLATILNISEYDFCNTLYHMGFTQDDKCEKILYEF 105 (203)
Q Consensus 26 efckiAiefl~~G~n~K~y~~aA~KL~v~~~~~Vq~~Ve~L~~Ll~essK~~ise~dF~dsl~~l~F~ee~~~~~vL~q~ 105 (203)
||||+|+|||++|||+|+|+.+|+|||+++ ++|+++|+||.+|+++|+|+++++.+|.+++..+|||++ +.++|+++
T Consensus 1 e~~~~a~~~l~~g~n~~~~~~~A~~l~i~~-~~vk~~v~aL~~ll~~a~K~~l~~~~~~~~L~~l~~~~e--~~~~l~~~ 77 (166)
T cd04750 1 EFCKLAIEFLFKGINQKKYEGAARKLEVEV-ETVQHGVEALVYLLIESTKLKLSERDFQDSIEFLGFSDD--LNEILLQL 77 (166)
T ss_pred CHHHHHHHHHHcCCChHHHHHHHHHhCCCH-HHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHcCCCHH--HHHHHHHH
Confidence 799999999999999999999999999999 999999999999999999999999999999999999999 99999999
Q ss_pred HHHHHHhHHHHhhhhhh--------------heecccccccccCceEEEEEeecCCCcccccceeecChhHHHHHHHHHH
Q psy5629 106 YTQEKYNLYRTLISEYI--------------SVVATRSHLNQCEPKFTIRLHLENPDEQEKQIDLEMDVRSVLNITQILE 171 (203)
Q Consensus 106 y~~~r~~I~r~iLs~~~--------------vqiASRsl~~q~~P~vtmkL~l~~~~~~~~~~~LqTDp~~L~hl~~~LE 171 (203)
|.+||..| |..+++.+ |++|||+++++.+|.|+|+|++++++.+.+.++|||||.+|.||+++||
T Consensus 78 y~~~~~~l-~~~l~~~~~~lp~l~dleWRvDv~isS~~l~~~~~P~i~mkL~l~~~~~~~~~~~l~td~~~l~~l~~eLe 156 (166)
T cd04750 78 YESNRKEI-RNILKELSPDLPHYHNLEWRLDVQIASRSLRSQVKPVITMKLHLEDENKKIETHLLQTDPANLVHLTQTLE 156 (166)
T ss_pred HHHHHHHH-HHHHHhcCCCCccccCCceeEEeEEcchhhHhhcCceEEEEEEecCCCCcccceEEEeCHHHHHHHHHHHH
Confidence 99999999 99998874 9999999999999999999999988776667899999999999999999
Q ss_pred HHHHHhhhhh
Q psy5629 172 EALSHAKLNQ 181 (203)
Q Consensus 172 ~AL~e~kT~h 181 (203)
+||++|+|+|
T Consensus 157 ~Al~~~~t~~ 166 (166)
T cd04750 157 QALQESKTLH 166 (166)
T ss_pred HHHHHhhccC
Confidence 9999999987
No 2
>cd04752 Commd4 COMM_Domain containing protein 4. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=99.86 E-value=1.2e-20 Score=156.87 Aligned_cols=151 Identities=15% Similarity=0.216 Sum_probs=133.0
Q ss_pred HHHHHHHHHHHhcC-CchhhHHHHHhhcCCCchHHHHHHHHHHHHHHHHHhhccCChhhhhhhhhhcCCCChhHHHHHHH
Q psy5629 25 QDFCTLTTNYLKDG-PNQKLYKSVSKKLSLPSADNVQDSVEGLVYFLLLATILNISEYDFCNTLYHMGFTQDDKCEKILY 103 (203)
Q Consensus 25 ~efckiAiefl~~G-~n~K~y~~aA~KL~v~~~~~Vq~~Ve~L~~Ll~essK~~ise~dF~dsl~~l~F~ee~~~~~vL~ 103 (203)
.=.|-..+.+|..+ .+...+...-+..+++. ++++.+|+||.++|.+|+|+++++.+|.+.|..+|||++ +.+.|.
T Consensus 7 k~~~~~v~~~~~~~~~~~~~~~kl~~~~~~~~-~~lk~~va~l~fiL~~A~k~n~~~~~l~~eL~~lglp~e--~~~~l~ 83 (174)
T cd04752 7 KLLCAQVLKDLLGEGIDYEKVLKLTADAKFES-GDVKASIAVLSFILSSAAKYNVDGESLSSELQQLGLPKE--HATSLC 83 (174)
T ss_pred HHHHHHHHHHHHhccCCHHHHHHHHHHhCCCH-hhHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHcCCCHH--HHHHHH
Confidence 34566656555444 55556667777789999 999999999999999999999999999999999999999 999999
Q ss_pred HHHHHHHHhHHHHhhhhhh--------------heecccccccccCceEEEEEeecCCC-cccccceeecChhHHHHHHH
Q psy5629 104 EFYTQEKYNLYRTLISEYI--------------SVVATRSHLNQCEPKFTIRLHLENPD-EQEKQIDLEMDVRSVLNITQ 168 (203)
Q Consensus 104 q~y~~~r~~I~r~iLs~~~--------------vqiASRsl~~q~~P~vtmkL~l~~~~-~~~~~~~LqTDp~~L~hl~~ 168 (203)
+.|.++|.+| |..+.... +++||+++++...|.++|+|++.+++ +..+.+.++||+..|.+|+.
T Consensus 84 ~~~~~~~~~l-~~~l~~~~l~~~~L~d~~WRld~~lsSs~l~~~~~P~~~l~L~v~~~~~~~~~~v~~e~s~~ql~~L~~ 162 (174)
T cd04752 84 RSYEEKQSKL-QESLRANSLRLSRLESVDWRVDYILSSSELQEVNEPLVQLRLKVRNADTGEITPHPFSVSADKFRVLLA 162 (174)
T ss_pred HHHHHHHHHH-HHHHHhcCCCCCcccccceeeEEEEcchhhhhcCCCeEEEEEeeecCCCCCcceEEEEecHHHHHHHHH
Confidence 9999999999 98888774 89999999999999999999999755 34456799999999999999
Q ss_pred HHHHHHHHhhh
Q psy5629 169 ILEEALSHAKL 179 (203)
Q Consensus 169 ~LE~AL~e~kT 179 (203)
+||+|.+.|++
T Consensus 163 eLe~A~~~m~~ 173 (174)
T cd04752 163 ELKQAQTLMET 173 (174)
T ss_pred HHHHHHHHHhc
Confidence 99999999986
No 3
>PF07258 HCaRG: HCaRG protein; InterPro: IPR009886 This family consists of several mammalian HCaRG(hypertension-related, calcium-regulated gene) proteins. HCaRG is negatively regulated by extracellular calcium concentration, and its basal mRNA levels are higher in hypertensive animals. HCaRG is a nuclear protein potentially involved in the control of cell proliferation [].; PDB: 2H2M_A.
Probab=99.83 E-value=2.6e-23 Score=167.01 Aligned_cols=163 Identities=22% Similarity=0.388 Sum_probs=72.0
Q ss_pred hccccCCChHHHHHHHHHHHHHHhcCCchhhHHHHHhhcCCCchHHHHHHHHHHHHHHHHHhhccCChhhhhhhhhhcCC
Q psy5629 13 LSVLFQLPPEVIQDFCTLTTNYLKDGPNQKLYKSVSKKLSLPSADNVQDSVEGLVYFLLLATILNISEYDFCNTLYHMGF 92 (203)
Q Consensus 13 L~fL~~~~~~vv~efckiAiefl~~G~n~K~y~~aA~KL~v~~~~~Vq~~Ve~L~~Ll~essK~~ise~dF~dsl~~l~F 92 (203)
+++|..++.+.+..||+.+++|+.+|++++.+..+++.++++. +.+++++.++.+++.+++|+.+++.+|...+..+||
T Consensus 1 ~~~l~~l~~~~~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~l~~ll~~a~k~~~~~~~l~~~L~~lgl 79 (178)
T PF07258_consen 1 ISLLSKLSSEKFKQLCKRAIDFLLGGDNESEISKLAEDLQLSE-EELKQLVAALSYLLREAAKYDLSEEDLRQELEQLGL 79 (178)
T ss_dssp -THHHHT---SSS--SS--HHHHHHHH-SS----------S-S-STHHHHHTTTSTTHHHHTTT---TTTSTTTHHHTT-
T ss_pred CCchhhCCHHHHHHHHHHHHHHHccCCCcccccchhhcccCCH-HHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHcCC
Confidence 4678899999999999999999999999889999999999999 999999999999999999999999999999999999
Q ss_pred CChhHHHHHHHHHHHHHHHhHHHHhhhhhh--------------heecccccccccCceEEEEEeecCCCcccccceeec
Q psy5629 93 TQDDKCEKILYEFYTQEKYNLYRTLISEYI--------------SVVATRSHLNQCEPKFTIRLHLENPDEQEKQIDLEM 158 (203)
Q Consensus 93 ~ee~~~~~vL~q~y~~~r~~I~r~iLs~~~--------------vqiASRsl~~q~~P~vtmkL~l~~~~~~~~~~~LqT 158 (203)
|++ +.+.|.++|..++..| +..+.... ++++|++..+...|+++|+|++.++++..+.+.+++
T Consensus 80 ~~e--~~~~l~~~~~~~~~~l-~~~l~~~~~~~~~l~d~~Wrl~~~~~s~~~~~~~~p~~~l~L~~~~~~~~~~~~~~e~ 156 (178)
T PF07258_consen 80 PEE--HAEALCKVYEQNREEL-RKALSSTSFSFPHLVDVDWRLDVQVSSSSLAKINEPVVILQLKTQNGNGKEETVTFEL 156 (178)
T ss_dssp -HH--HHHHHTTTTTTTSSSS-S---------------------------------------------------------
T ss_pred CHH--HHHHHHHHHHhccHHH-HHHHhcccccccccCCCcEEEEeeecccHhhhccCcEEEEEEEecCCCCcCceEEEEE
Confidence 999 9999999999999999 88777663 899999999999999999999998866666789999
Q ss_pred ChhHHHHHHHHHHHHHHHhhh
Q psy5629 159 DVRSVLNITQILEEALSHAKL 179 (203)
Q Consensus 159 Dp~~L~hl~~~LE~AL~e~kT 179 (203)
|+..|.+|.++|+.|.+++.+
T Consensus 157 ~~~~l~~l~~~L~~a~~~l~~ 177 (178)
T PF07258_consen 157 SKEELQDLLNELKDAQKQLDQ 177 (178)
T ss_dssp ---------------------
T ss_pred CHHHHHHHHHHHHHHHHHHhc
Confidence 999999999999999998764
No 4
>cd04758 Commd10 COMM_Domain containing protein 10. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=99.43 E-value=9.3e-12 Score=104.32 Aligned_cols=165 Identities=14% Similarity=0.178 Sum_probs=143.5
Q ss_pred hhhccccCCChHHHHHHHHHHHHHHhcCCch----hhHHHHHhhcCCCchHHHHHHHHHHHHHHHHHhhccCChhhhhhh
Q psy5629 11 EHLSVLFQLPPEVIQDFCTLTTNYLKDGPNQ----KLYKSVSKKLSLPSADNVQDSVEGLVYFLLLATILNISEYDFCNT 86 (203)
Q Consensus 11 ehL~fL~~~~~~vv~efckiAiefl~~G~n~----K~y~~aA~KL~v~~~~~Vq~~Ve~L~~Ll~essK~~ise~dF~ds 86 (203)
+=+..|..+|.+-+..+|...++++.....+ ..-+...+-.+++. ++++..++++.++|-.++|+++++..+..-
T Consensus 3 ~av~~ln~l~~~~f~~ll~~i~~~l~~~~~~~~s~~~~~kl~~~~~~~~-~~l~~vi~~l~~il~~A~k~nl~~~~L~~~ 81 (186)
T cd04758 3 EAVSLINSIDTEKFPRLLSRLFQKLHLKAERSFSEEEEEKLQEAFKLLS-QDLKLLLETISFILEQAAYHNLKPSNLQQQ 81 (186)
T ss_pred hHHHHHhcCCHHHHHHHHHHHHHHhcccccCCccHHHHHHHHHHhCCCh-HHHHHHHHHHHHHHHHHHHhcCCHHHHHHH
Confidence 3456789999999999999999999865553 22345556668999 999999999999999999999999999999
Q ss_pred hhhcCCCChhHHHHHHHHHHHHHHHhHHHHhhhhhh--------------heecccccccccCceEEEEEeecCCCcccc
Q psy5629 87 LYHMGFTQDDKCEKILYEFYTQEKYNLYRTLISEYI--------------SVVATRSHLNQCEPKFTIRLHLENPDEQEK 152 (203)
Q Consensus 87 l~~l~F~ee~~~~~vL~q~y~~~r~~I~r~iLs~~~--------------vqiASRsl~~q~~P~vtmkL~l~~~~~~~~ 152 (203)
|..+|++++ +...+.+.|..++..+ +..+.... ++++|-.+...-.|.+.|.|.+..+++..+
T Consensus 82 L~~l~l~~e--~~~~~~~~w~~~~~~l-~~~l~~~~l~~~~L~D~~Wrl~~~~sSs~~~~~~~P~~~L~L~~~~~~g~~e 158 (186)
T cd04758 82 LRNILLLED--KASAFVNAWEAEGEDV-LEKLRSRILAPNQLEDVSWRLNLQMSSSTQAKLKSPLAVLELGVTSEDGNLE 158 (186)
T ss_pred HHHcCCCHH--HHHHHHHHHHHHHHHH-HHHHHhccCCCCccccccceEEEEEccchhhhhcCCcEEEEeecCCCCCCcc
Confidence 999999999 9999999999999999 77765442 899998888888899999999998666666
Q ss_pred cceeecChhHHHHHHHHHHHHHHHhhh
Q psy5629 153 QIDLEMDVRSVLNITQILEEALSHAKL 179 (203)
Q Consensus 153 ~~~LqTDp~~L~hl~~~LE~AL~e~kT 179 (203)
.+.++++-.-|.++..+||+|=++..+
T Consensus 159 ~v~~E~t~~el~~l~~~le~~q~~ld~ 185 (186)
T cd04758 159 KINLEFNHEELLEFYNQLESIQEQLDS 185 (186)
T ss_pred ceEEEEcHHHHHHHHHHHHHHHHHhcc
Confidence 789999999999999999999877654
No 5
>cd04751 Commd3 COMM_Domain containing protein 3. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=99.32 E-value=6.1e-12 Score=95.84 Aligned_cols=76 Identities=18% Similarity=0.296 Sum_probs=70.0
Q ss_pred HHHHHHHHHHHhHHHHhhhhhh--------------heecccccccccCceEEEEEeecCCCcccccceeecChhHHHHH
Q psy5629 101 ILYEFYTQEKYNLYRTLISEYI--------------SVVATRSHLNQCEPKFTIRLHLENPDEQEKQIDLEMDVRSVLNI 166 (203)
Q Consensus 101 vL~q~y~~~r~~I~r~iLs~~~--------------vqiASRsl~~q~~P~vtmkL~l~~~~~~~~~~~LqTDp~~L~hl 166 (203)
+|.++|.+||+.| |.+|++.+ .+++||+++++..|+++|+|++.++++ .+.+.|+|||..|.||
T Consensus 2 ~l~~~Y~~~r~~l-~~~l~~~~~~~p~l~dv~WRld~~lsS~~l~~~~~p~~~i~L~~~~~~~-~~~i~f~c~~e~L~~L 79 (95)
T cd04751 2 IFAKQYQKKKEVL-ENKLKSIGISFPHITDVNWRLDYVVSSKHLGKVNQPIYLIQLSTENGEN-KPDINFTCTLEQLQDL 79 (95)
T ss_pred hHHHHHHHhHHHH-HHHHHHhCCCCCceecCceEEEEEEcccccCcccceeEEEEEeccCCCC-cceEEEEeCHHHHHHH
Confidence 6899999999999 99999985 899999999999999999999997666 5577999999999999
Q ss_pred HHHHHHHHHHhh
Q psy5629 167 TQILEEALSHAK 178 (203)
Q Consensus 167 ~~~LE~AL~e~k 178 (203)
+++|++|-+.+.
T Consensus 80 i~~Lk~A~~~~e 91 (95)
T cd04751 80 VNKLKDAAKNIE 91 (95)
T ss_pred HHHHHHHHHHHH
Confidence 999999988765
No 6
>cd04756 Commd8 COMM_Domain containing protein 8. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=99.08 E-value=6.8e-09 Score=87.04 Aligned_cols=156 Identities=15% Similarity=0.163 Sum_probs=133.0
Q ss_pred hhccccCCChHHHHHHHHHHHHHHhcCCchhhHHHHHhhcCCCchHHHHHHHHHHHHHHHHHhhccCChhhhhhhhhhcC
Q psy5629 12 HLSVLFQLPPEVIQDFCTLTTNYLKDGPNQKLYKSVSKKLSLPSADNVQDSVEGLVYFLLLATILNISEYDFCNTLYHMG 91 (203)
Q Consensus 12 hL~fL~~~~~~vv~efckiAiefl~~G~n~K~y~~aA~KL~v~~~~~Vq~~Ve~L~~Ll~essK~~ise~dF~dsl~~l~ 91 (203)
|+-++..+|+.-+..+|--.++.|-.+.-++ |.-+.. .|+. +++.+.++++.+++..++|+++++..-...|. |
T Consensus 2 ~~~~i~~l~~~~~~~Ll~~vv~~l~~~~~~~-~~~~~~--~~s~-~e~~~~l~~l~~i~~~a~~~~l~~~~l~~~L~--~ 75 (176)
T cd04756 2 PPELINLLPVAQIVKLLHRVVDGVCGRAYPR-YQDYSA--IWSL-EEWTEVLESLATLFKQAVGKNSNDEEAKAQLS--D 75 (176)
T ss_pred hhhhhhcCCHHHHHHHHHHHHHHHhcccCCc-hhhhcc--cCCH-HHHHHHHHHHHHHHHHHHccCCCHHHHHHHHh--c
Confidence 5567788999999999999999997655544 333332 8889 99999999999999999999999999988775 8
Q ss_pred CCChhHHHHHHHHHHHHHHHhHHHHhhhhh----------------hheecccccccccCceEEEEEeecCCCcccccce
Q psy5629 92 FTQDDKCEKILYEFYTQEKYNLYRTLISEY----------------ISVVATRSHLNQCEPKFTIRLHLENPDEQEKQID 155 (203)
Q Consensus 92 F~ee~~~~~vL~q~y~~~r~~I~r~iLs~~----------------~vqiASRsl~~q~~P~vtmkL~l~~~~~~~~~~~ 155 (203)
++.+ +.+.+.+.|..++.+| +..|.+. ...+||=++.+.-.|.++|+|.+. +++..+.+.
T Consensus 76 L~~~--~~~a~~~~~~~~~~ei-~~~L~~~~~~is~~~L~d~dWrv~l~lSSd~~~~l~~P~~~L~L~v~-~~~~~~~v~ 151 (176)
T cd04756 76 LSSS--HQEALLKCVKSRKEEI-RQALVNKTNSISSAQLQDFDWQLKLALSSDKLSSLQEPLLNLDLDVK-ENGILKPVS 151 (176)
T ss_pred CCHH--HHHHHHHHHHHhhHHH-HHHHHHHHhccCchhhccccCeeeeeechhhHHHhcCCeEEEEEEec-CCCCeeEEE
Confidence 9999 9999999999999999 8877422 178888889999999999999999 555556789
Q ss_pred eecChhHHHHHHHHHHHHHHHh
Q psy5629 156 LEMDVRSVLNITQILEEALSHA 177 (203)
Q Consensus 156 LqTDp~~L~hl~~~LE~AL~e~ 177 (203)
++.+-..|..|+.+||+|=+-|
T Consensus 152 ~Ems~eel~~li~~Le~a~~~~ 173 (176)
T cd04756 152 IEMNKEELQNLISSLEAANKVV 173 (176)
T ss_pred EEEcHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999996543
No 7
>cd04755 Commd7 COMM_Domain containing protein 7. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=99.04 E-value=2.2e-08 Score=84.67 Aligned_cols=160 Identities=10% Similarity=0.140 Sum_probs=133.8
Q ss_pred ccccCCChHHHHHHHHHHHHHHhcCCc-hh---hHHHHHhhcCCCchHHHHHHHHHHHHHHHHHhhccCChhhhhhhhhh
Q psy5629 14 SVLFQLPPEVIQDFCTLTTNYLKDGPN-QK---LYKSVSKKLSLPSADNVQDSVEGLVYFLLLATILNISEYDFCNTLYH 89 (203)
Q Consensus 14 ~fL~~~~~~vv~efckiAiefl~~G~n-~K---~y~~aA~KL~v~~~~~Vq~~Ve~L~~Ll~essK~~ise~dF~dsl~~ 89 (203)
+-++.++++-+.++|-+.+.||.--.. .. ..+..|...+++. .+++..|++|.+++..++|+++++.....-+..
T Consensus 2 ~~in~l~~~~f~~l~~~i~~~L~~~k~~~~~~~~~~ef~~~~~~~~-~dlk~vi~~l~fi~~~A~k~nv~~~~L~~eL~~ 80 (180)
T cd04755 2 QNLNQLSEQQFSRLTEILFEFLLEPKESERLLNQLDEFAGENGISL-GPLKNIVKSILLVPNGALKRNLTAEQLREDLIQ 80 (180)
T ss_pred CccccCCHHHHHHHHHHHHHHHhccchHhHHHHHHHHHHHhcCCCH-HHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 347789999999999999999994333 22 2345677889999 999999999999999999999999999999999
Q ss_pred cCCCChhHHHHHHHHHHHHHHHhHHHHhhhhh--------------hheecccccccccCceEEEEEeecCCCcccccce
Q psy5629 90 MGFTQDDKCEKILYEFYTQEKYNLYRTLISEY--------------ISVVATRSHLNQCEPKFTIRLHLENPDEQEKQID 155 (203)
Q Consensus 90 l~F~ee~~~~~vL~q~y~~~r~~I~r~iLs~~--------------~vqiASRsl~~q~~P~vtmkL~l~~~~~~~~~~~ 155 (203)
+|.|++ +...+.+.|.++...+ +..+..- .+++||=.+++-=.|.+.|||...+++. .+.++
T Consensus 81 lgL~~e--ka~~~~~~w~~~~~~L-~~~~~~~tL~~~qL~d~~Wr~~~~~sSS~~~~~~~p~vqLkl~~~~~~~-~e~v~ 156 (180)
T cd04755 81 LGLSEE--KASYFSEQWKQHYSTL-SRSAVGQTLMVNQLVDMEWKFGVTAGSSELQKVGSIFLQLKLVVRKGNQ-TENVY 156 (180)
T ss_pred cCCCHH--HHHHHHHHHHHhHHHH-HHHHHHcccCccccccccceeeeEecchhhhhcCCcEEEEEEEecCCCC-ceeEE
Confidence 999999 9999999999999999 5554333 2888886666656699999999864433 34668
Q ss_pred eecChhHHHHHHHHHHHHHHHhh
Q psy5629 156 LEMDVRSVLNITQILEEALSHAK 178 (203)
Q Consensus 156 LqTDp~~L~hl~~~LE~AL~e~k 178 (203)
++...+-+..+..+||+|=+.|.
T Consensus 157 ~E~t~~qF~~f~~elk~a~a~me 179 (180)
T cd04755 157 MELTLPQFYSFLHEMERAKASLE 179 (180)
T ss_pred EEEcHHHHHHHHHHHHHHHHHhc
Confidence 99999999999999999976653
No 8
>cd04753 Commd5_HCaRG COMM_Domain containing protein 5, also called HCaRG (hypertension-related, calcium-regulated gene). HCaRG is a nuclear protein that might be involved in cell proliferation; it is negatively regulated by extracellular calcium concentration, and its basal mRNA levels are higher in hypertensive animals. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=98.94 E-value=4.7e-09 Score=82.42 Aligned_cols=91 Identities=13% Similarity=0.117 Sum_probs=78.8
Q ss_pred hcCCCChhHHHHHHH-HHHHHHHHhHHHHhhhhhh--------------heecccccccccCceEEEEEeecCCCccccc
Q psy5629 89 HMGFTQDDKCEKILY-EFYTQEKYNLYRTLISEYI--------------SVVATRSHLNQCEPKFTIRLHLENPDEQEKQ 153 (203)
Q Consensus 89 ~l~F~ee~~~~~vL~-q~y~~~r~~I~r~iLs~~~--------------vqiASRsl~~q~~P~vtmkL~l~~~~~~~~~ 153 (203)
.+|||+| +.+.|+ ++|..+|..+ ++++.+.. |.+|||++.++.+|.|+|+|++++++ .
T Consensus 1 ~l~lp~E--~~~dL~~~~y~~~r~~l-~~~l~~~~~rlp~l~~l~WRVDv~lSSs~l~~~~~PtI~LkLkl~dg~----~ 73 (110)
T cd04753 1 ELRIPEE--LITDLASVVYGQRRPLL-ESGALQKGVRLPHLEDFKWRVDVAISTSSLSRVLQPSILMEMKLSDGK----S 73 (110)
T ss_pred CCCCCHH--HHHHHHHHHHhccHHHH-HHHHHHhccCCcccccCcceEEEEEchhhhhcccCCeEEEEEEecCCC----e
Confidence 3899999 999996 9999999999 88877763 99999999999999999999996443 4
Q ss_pred ceeecChhHHHHHHHHHHHHHHHhhhhh-hhhHh
Q psy5629 154 IDLEMDVRSVLNITQILEEALSHAKLNQ-RKMSR 186 (203)
Q Consensus 154 ~~LqTDp~~L~hl~~~LE~AL~e~kT~h-RrI~R 186 (203)
+.+++..+..-.+.--.-..|+||..-. |.|.+
T Consensus 74 ~~fe~~~~kF~~Lry~~a~~l~em~~le~~~~~~ 107 (110)
T cd04753 74 HRFEVPVAKFHELRYNVALILKEMNDLEKRSILK 107 (110)
T ss_pred EEEEeeHHHHHHHHHHHHHHHHHHHHHHhccchh
Confidence 4889999998888888888999998888 66654
No 9
>cd04748 Commd COMM_Domain, a family of domains found at the C-terminus of HCarG, the copper metabolism gene MURR1 product, and related proteins. Presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB. Murr1/Commd1 is a protein involved in copper homeostasis, which has also been identified as a regulator of the human delta epithelial sodium channel. HCaRG, a nuclear protein that might be involved in cell proliferation, is negatively regulated by extracellular calcium concentration, and its basal mRNA levels are higher in hypertensive animals.
Probab=98.82 E-value=9.5e-09 Score=76.28 Aligned_cols=71 Identities=20% Similarity=0.302 Sum_probs=63.5
Q ss_pred HHHHHHHhHHHHhhhhhh--------------heecccccccccCceEEEEEeecCCCc-ccccceeecChhHHHHHHHH
Q psy5629 105 FYTQEKYNLYRTLISEYI--------------SVVATRSHLNQCEPKFTIRLHLENPDE-QEKQIDLEMDVRSVLNITQI 169 (203)
Q Consensus 105 ~y~~~r~~I~r~iLs~~~--------------vqiASRsl~~q~~P~vtmkL~l~~~~~-~~~~~~LqTDp~~L~hl~~~ 169 (203)
+|.++|..| |.+|.+.. +++||+++.+.-.|.++|.|++..+++ ..+.+.+++|+..|.+++++
T Consensus 1 ~~~~~~~~i-~~~l~~~s~~~~~L~d~~Wrld~~~sS~~~~~~~~P~~~~~L~l~~~~~~~~~~v~~E~~~~~l~~l~~~ 79 (87)
T cd04748 1 LLTENKAEI-EELLSKQSLSLPQLVDFDWRLDVQISSSSLAKVKQPTILVQLKLQVGDNNSSEKICFEMTKEELQNFLNK 79 (87)
T ss_pred ChhhHHHHH-HHHHHHhccCCCeeeeeeeEEEEEEchhHHHHhhCCeEEEEEEEecCCCCccceEEEEeCHHHHHHHHHH
Confidence 488999999 99998884 999999999999999999999997654 45568999999999999999
Q ss_pred HHHHHHH
Q psy5629 170 LEEALSH 176 (203)
Q Consensus 170 LE~AL~e 176 (203)
||+|.++
T Consensus 80 L~~a~~~ 86 (87)
T cd04748 80 LKKIKAQ 86 (87)
T ss_pred HHHHHhc
Confidence 9999865
No 10
>cd04757 Commd9 COMM_Domain containing protein 9. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=98.74 E-value=3e-08 Score=77.92 Aligned_cols=78 Identities=12% Similarity=0.185 Sum_probs=68.6
Q ss_pred CCChhHHHHHHHHHHHHHHHhHHHHhhhhhh--------------heecccccccccCceEEEEEeecCCCc------cc
Q psy5629 92 FTQDDKCEKILYEFYTQEKYNLYRTLISEYI--------------SVVATRSHLNQCEPKFTIRLHLENPDE------QE 151 (203)
Q Consensus 92 F~ee~~~~~vL~q~y~~~r~~I~r~iLs~~~--------------vqiASRsl~~q~~P~vtmkL~l~~~~~------~~ 151 (203)
|..+ +.++|+++|.+||+++ |+++++.. +++|||++.++..|++.|.|.+.+++. ..
T Consensus 1 f~~~--l~~lL~~~~le~r~~~-r~~~~~~~~slp~l~dldWRldv~isS~sl~r~~~P~vll~lkv~~~~~~~~~~~~~ 77 (108)
T cd04757 1 FHSN--LKNLLTKIILENRDKW-RSEASENQISLPKLVDHDWRVDIKTSSDSLGRMAVPTCLLQMKIQEAPSLCGLLPPL 77 (108)
T ss_pred CCHH--HHHHHHHHHHHhhHHH-HHHHHhcCCCchhhhCccceehhHHHHHHHHhhhcCeEEEEEEeecCccccccCCCc
Confidence 6677 9999999999999999 99998883 999999999999999999999987643 13
Q ss_pred ccceeecChhHHHHHHHHHHH
Q psy5629 152 KQIDLEMDVRSVLNITQILEE 172 (203)
Q Consensus 152 ~~~~LqTDp~~L~hl~~~LE~ 172 (203)
+.+.+|.+-.+|-.|.+-|+.
T Consensus 78 ~~v~~ELsKe~l~tml~~L~~ 98 (108)
T cd04757 78 STLTMELSKETLDTMLDGLGR 98 (108)
T ss_pred ceEEEEcCHHHHHHHHHHHHH
Confidence 457899999999999988875
No 11
>cd04749 Commd1_MURR1 COMM_Domain containing protein 1, also called Murr1. Murr1/Commd1 is a protein involved in copper homeostasis, which has also been identified as a regulator of the human delta epithelial sodium channel. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=98.57 E-value=1.2e-06 Score=73.97 Aligned_cols=123 Identities=15% Similarity=0.137 Sum_probs=110.3
Q ss_pred CCCchHHHHHHHHHHHHHHHHHhhccCChhhhhhhh-----hhcCCCChhHHHHHHHHHHHHHHHhHHHHhhhhhh----
Q psy5629 52 SLPSADNVQDSVEGLVYFLLLATILNISEYDFCNTL-----YHMGFTQDDKCEKILYEFYTQEKYNLYRTLISEYI---- 122 (203)
Q Consensus 52 ~v~~~~~Vq~~Ve~L~~Ll~essK~~ise~dF~dsl-----~~l~F~ee~~~~~vL~q~y~~~r~~I~r~iLs~~~---- 122 (203)
++++ +.+...+.++.+++..++|+......+..-| ..+|.|.+ +.+.+..||..||..| |.+|-+-+
T Consensus 31 ~~~~-ed~ka~~ak~~~ii~saa~~dvD~~~L~~~Lt~q~~qQ~Gl~~e--ha~~l~Kfwk~~~~kl-r~~l~~~S~~~~ 106 (174)
T cd04749 31 EDPL-EEFRALHNKMRGLLKSIASADMDINQLEAFLTAQTKKQGGITSL--QAAVIAKFWKVHKKKI-RESLLAQSRWEN 106 (174)
T ss_pred CCCH-HHHHHHHHHHHHHHHHHHHccCCHHHHHHHHHhhHHHhcCCChH--HHHHHHHHHHHhHHHH-HHHHHHHhhhcc
Confidence 6778 9999999999999999999999999999988 78999999 9999999999999999 98877663
Q ss_pred ----------heecccccccccCceEEEEEeecCCCcccccceeecChhHHHHHHHHHHHHHHHhh
Q psy5629 123 ----------SVVATRSHLNQCEPKFTIRLHLENPDEQEKQIDLEMDVRSVLNITQILEEALSHAK 178 (203)
Q Consensus 123 ----------vqiASRsl~~q~~P~vtmkL~l~~~~~~~~~~~LqTDp~~L~hl~~~LE~AL~e~k 178 (203)
...+|+.+.+.-.|++.++|.+..++.....+.++.|-..+.-|..+|.+|=..|.
T Consensus 107 ~L~~l~WRVD~~tsS~~~~evn~P~~~l~L~v~~~~~~~~~v~~emd~ek~~~lL~eLk~iq~~m~ 172 (174)
T cd04749 107 SLRGLSWRVDLKTQSRHIAQINSPVAIVELELGKTGQESEFVCLEFDEAKVNRVLKQLAEIQESLD 172 (174)
T ss_pred cccCCCCeeeeecccchhhhccCCeEEEEEeeccCCCCCceEEEEecHHHHHHHHHHHHHHHHHHh
Confidence 77889999999999999999998766555578999999999999999998866553
No 12
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=86.76 E-value=1.6 Score=28.81 Aligned_cols=37 Identities=16% Similarity=0.273 Sum_probs=28.2
Q ss_pred HHHHHHHHHhcCCchhhHHHHHhhcCCCchHHHHHHHHHH
Q psy5629 27 FCTLTTNYLKDGPNQKLYKSVSKKLSLPSADNVQDSVEGL 66 (203)
Q Consensus 27 fckiAiefl~~G~n~K~y~~aA~KL~v~~~~~Vq~~Ve~L 66 (203)
=...|++.+.+|. ..+..||+++|||. .++.+-+.|.
T Consensus 4 ~l~~Ai~~v~~g~--~S~r~AA~~ygVp~-sTL~~r~~g~ 40 (45)
T PF05225_consen 4 DLQKAIEAVKNGK--MSIRKAAKKYGVPR-STLRRRLRGK 40 (45)
T ss_dssp HHHHHHHHHHTTS--S-HHHHHHHHT--H-HHHHHHHHHT
T ss_pred HHHHHHHHHHhCC--CCHHHHHHHHCcCH-HHHHHHHcCC
Confidence 3567999999887 66789999999999 9998877663
No 13
>cd04754 Commd6 COMM_Domain containing protein 6. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=82.20 E-value=3.8 Score=31.30 Aligned_cols=53 Identities=17% Similarity=0.287 Sum_probs=45.4
Q ss_pred heecccccccccCceEEEEEeecCCCcccccceeecChhHHHHHHHHHHHHHH
Q psy5629 123 SVVATRSHLNQCEPKFTIRLHLENPDEQEKQIDLEMDVRSVLNITQILEEALS 175 (203)
Q Consensus 123 vqiASRsl~~q~~P~vtmkL~l~~~~~~~~~~~LqTDp~~L~hl~~~LE~AL~ 175 (203)
+-++|=.+++-=.|.++++|.+..+.+..+...++...+-+..++.+.|+|=+
T Consensus 31 va~sSd~~~sl~~Pfl~l~L~V~~~~G~~~~~~~EmTlpEFq~f~~~~~~~~a 83 (86)
T cd04754 31 MAVSSDTCRSLNSPYVAVTLKVADPSGQVVTKSFEMTIPEFQNFSRQFKEMAA 83 (86)
T ss_pred EEEechhhhhcCCceEEEEEEEEccCCCccceEEEEcHHHHHHHHHHHHHHHH
Confidence 77888888888899999999999855555556999999999999999998743
No 14
>cd08783 Death_MALT1 Death domain similar to that found in Mucosa-associated lymphoid tissue-lymphoma-translocation gene 1. Death domain (DD) similar to that found in Malt1 (mucosa-associated lymphoid tissue-lymphoma-translocation gene 1). Malt1, together with Bcl10 (B-cell lymphoma 10), are the integral components of the CBM signalosome. 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. In general, 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 associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins
Probab=69.72 E-value=23 Score=27.66 Aligned_cols=77 Identities=12% Similarity=0.132 Sum_probs=49.3
Q ss_pred ccCCChHHHHHHHHHHHHHHhcCCchhhHHHHHhhcCCCchHHHHHHHHHHHHHHHHHhhccCChhhh-hhhhhh--cCC
Q psy5629 16 LFQLPPEVIQDFCTLTTNYLKDGPNQKLYKSVSKKLSLPSADNVQDSVEGLVYFLLLATILNISEYDF-CNTLYH--MGF 92 (203)
Q Consensus 16 L~~~~~~vv~efckiAiefl~~G~n~K~y~~aA~KL~v~~~~~Vq~~Ve~L~~Ll~essK~~ise~dF-~dsl~~--l~F 92 (203)
+.++++++++.+|+ .|.+.+..+-|...|+++|... +|.+|..|. +=|+.. .|=
T Consensus 1 ~~~L~e~~l~~L~~----lLD~~~~~~gWr~LAe~lg~~~-------------------~fr~S~~el~~cslkvl~p~g 57 (97)
T cd08783 1 LNRLREPLLRRLSE----LLDRAADGKGWRKLAELAGSRG-------------------RFRLSCLDLEQCSLKVLEPEG 57 (97)
T ss_pred CCcccHHHHHHHHH----HHhCCCccCCHHHHHHHHccCC-------------------ccccCHHHHHHHHHHHhcCCC
Confidence 35678889999997 4677777799999999998843 445555444 222222 244
Q ss_pred CChhHHHHHHHHHHHHHHHhHHHHhhhh
Q psy5629 93 TQDDKCEKILYEFYTQEKYNLYRTLISE 120 (203)
Q Consensus 93 ~ee~~~~~vL~q~y~~~r~~I~r~iLs~ 120 (203)
++. .-|++.|.+.-.-+ +..+..
T Consensus 58 SPs----k~LL~~~~~rg~Tv-~~Ll~~ 80 (97)
T cd08783 58 SPS----RSLLKLLGERGCTV-TELSEF 80 (97)
T ss_pred Cch----HHHHHHHHHcCCcH-HHHHHH
Confidence 444 56666666666555 544433
No 15
>KOG3334|consensus
Probab=67.41 E-value=8.5 Score=32.08 Aligned_cols=50 Identities=20% Similarity=0.365 Sum_probs=44.5
Q ss_pred ccCCChHHHHHHHHHHHHHHhcC-CchhhHHHHHhhcCCCchHHHHHHHHHH
Q psy5629 16 LFQLPPEVIQDFCTLTTNYLKDG-PNQKLYKSVSKKLSLPSADNVQDSVEGL 66 (203)
Q Consensus 16 L~~~~~~vv~efckiAiefl~~G-~n~K~y~~aA~KL~v~~~~~Vq~~Ve~L 66 (203)
.++.++-|+.-+..+|+.|-..= ...++|..-|+|-+++. |+|+-|+...
T Consensus 28 I~eyEprVi~qlLefa~rYtt~vL~DA~vys~HA~ka~i~~-eDVrlA~~~~ 78 (148)
T KOG3334|consen 28 IQEYEPRVINQLLEFAYRYTTTVLDDAKVYSSHAKKATIDA-EDVRLAIQMR 78 (148)
T ss_pred ccccChHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcH-HHHHHHHHHH
Confidence 35678889999999999999887 77899999999999999 9999998754
No 16
>PF08769 Spo0A_C: Sporulation initiation factor Spo0A C terminal; InterPro: IPR014879 The response regulator Spo0A is comprised of a phophoacceptor domain and a transcription activation domain. This domain corresponds to the transcription activation domain and forms an alpha helical structure comprising of 6 alpha helices. The structure contains a helix-turn-helix and binds DNA [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0005509 calcium ion binding, 0006355 regulation of transcription, DNA-dependent, 0042173 regulation of sporulation resulting in formation of a cellular spore, 0005737 cytoplasm; PDB: 1FC3_C 1LQ1_D.
Probab=59.20 E-value=32 Score=26.67 Aligned_cols=45 Identities=13% Similarity=0.301 Sum_probs=33.8
Q ss_pred HHHHHHHHHhcCC------chhhHHHHHhhcCCCchHHHHHHHHHHHHHHHH
Q psy5629 27 FCTLTTNYLKDGP------NQKLYKSVSKKLSLPSADNVQDSVEGLVYFLLL 72 (203)
Q Consensus 27 fckiAiefl~~G~------n~K~y~~aA~KL~v~~~~~Vq~~Ve~L~~Ll~e 72 (203)
+.+-|+......+ ....|...|+|.++++ ..|++++.-.+.....
T Consensus 20 Yl~~Ai~l~~~d~~~l~~itK~LYp~IA~k~~TT~-s~VERaIR~aI~~~w~ 70 (106)
T PF08769_consen 20 YLRDAIELVLEDPELLNSITKELYPDIAKKYGTTP-SRVERAIRHAIEVAWT 70 (106)
T ss_dssp HHHHHHHHHHHTGGGGCCTTTTHHHHHHHHTTS-H-HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHhcchhhHHHHHHHHHCCCH-HHHHHHHHHHHHHHHH
Confidence 4455666665555 4568999999999999 9999999887766555
No 17
>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=58.30 E-value=16 Score=23.88 Aligned_cols=38 Identities=11% Similarity=0.187 Sum_probs=28.5
Q ss_pred HHHHhcCCchhhHHHHHhhcCCCchHHHHHHHHHHHHHH
Q psy5629 32 TNYLKDGPNQKLYKSVSKKLSLPSADNVQDSVEGLVYFL 70 (203)
Q Consensus 32 iefl~~G~n~K~y~~aA~KL~v~~~~~Vq~~Ve~L~~Ll 70 (203)
+.+|....++-..+.+|+.|||+. -+|.+-+..|-..+
T Consensus 6 l~~L~~~~~~it~~eLa~~l~vS~-rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 6 LKLLLESKEPITAKELAEELGVSR-RTIRRDIKELREWG 43 (55)
T ss_dssp HHHHHHTTTSBEHHHHHHHCTS-H-HHHHHHHHHHHHTT
T ss_pred HHHHHHcCCCcCHHHHHHHhCCCH-HHHHHHHHHHHHCC
Confidence 456644544467889999999999 99999998886544
No 18
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=58.23 E-value=20 Score=26.68 Aligned_cols=52 Identities=19% Similarity=0.264 Sum_probs=38.8
Q ss_pred HHHHHHHHHHHHHhc----------CCchhhHHHHHhhcCCCchHHHHHHHHHHHHHHHHHhh
Q psy5629 23 VIQDFCTLTTNYLKD----------GPNQKLYKSVSKKLSLPSADNVQDSVEGLVYFLLLATI 75 (203)
Q Consensus 23 vv~efckiAiefl~~----------G~n~K~y~~aA~KL~v~~~~~Vq~~Ve~L~~Ll~essK 75 (203)
.+..|+.-|++-|.+ |..=|..+.+|+++|++. +.-++..-|+.+.|.++..
T Consensus 28 l~~~yg~~ai~~l~~nPY~L~~~i~gi~F~~aD~iA~~~g~~~-~d~~Ri~A~i~~~L~~~~~ 89 (94)
T PF14490_consen 28 LYKKYGDDAIEILKENPYRLIEDIDGIGFKTADKIALKLGIEP-DDPRRIRAAILYVLREAEE 89 (94)
T ss_dssp HHHHH-TTHHHHHHH-STCCCB-SSSSBHHHHHHHHHTTT--T-T-HHHHHHHHHHHHHHHHH
T ss_pred HHHHHhHHHHHHHHHChHHHHHHccCCCHHHHHHHHHHcCCCC-CCHHHHHHHHHHHHHHHHh
Confidence 455666667777654 556778889999999999 9999999999999998654
No 19
>PF06896 DUF1268: Protein of unknown function (DUF1268); InterPro: IPR009681 This entry is represented by Bacteriophage bIL286, Orf51. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several bacterial and phage proteins of around 115 residues in length. The function of this family is unknown.
Probab=54.51 E-value=23 Score=28.12 Aligned_cols=45 Identities=22% Similarity=0.307 Sum_probs=32.4
Q ss_pred eeecchhhHhhhccccCCChHHHHHHHHHHHHHHhcCCchhhHHHHHhh
Q psy5629 2 IINLNESHREHLSVLFQLPPEVIQDFCTLTTNYLKDGPNQKLYKSVSKK 50 (203)
Q Consensus 2 ll~Ls~~hkehL~fL~~~~~~vv~efckiAiefl~~G~n~K~y~~aA~K 50 (203)
+|-||+++.++| .++|.+.++|+...-+.+|. |-.-.-|+.++++
T Consensus 65 iL~L~dkq~ekl---~~iD~~~~~e~~~yl~~rl~-G~sD~~i~~~~~~ 109 (114)
T PF06896_consen 65 ILKLNDKQVEKL---EDIDFEDLQEIVSYLVMRLQ-GMSDEQIELAEKE 109 (114)
T ss_pred HHCCCHHHHHHH---hcCCHHHHHHHHHHHHHHHc-CCCHHHHHHHHhc
Confidence 467889999888 66899999998887777766 5555555555443
No 20
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=53.76 E-value=27 Score=22.80 Aligned_cols=46 Identities=9% Similarity=0.145 Sum_probs=30.3
Q ss_pred hHHHHHHHHHHHHHHh-cCCchhhHHHHHhhcCCCchHHHHHHHHHHH
Q psy5629 21 PEVIQDFCTLTTNYLK-DGPNQKLYKSVSKKLSLPSADNVQDSVEGLV 67 (203)
Q Consensus 21 ~~vv~efckiAiefl~-~G~n~K~y~~aA~KL~v~~~~~Vq~~Ve~L~ 67 (203)
.++...+++.-++... .|.....-..+|+.++++. .+|.+++..|.
T Consensus 4 ~~~~~~i~~~i~~~~~~~~~~~~~~~~la~~~~is~-~~v~~~l~~L~ 50 (66)
T cd07377 4 EQIADQLREAILSGELKPGDRLPSERELAEELGVSR-TTVREALRELE 50 (66)
T ss_pred HHHHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCH-HHHHHHHHHHH
Confidence 4555566665555533 3322223568999999999 99998887764
No 21
>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=49.23 E-value=34 Score=25.40 Aligned_cols=43 Identities=16% Similarity=0.394 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHHhcCCchh---hHHHHHhhcCCCchHHHHHHHHHHH
Q psy5629 24 IQDFCTLTTNYLKDGPNQK---LYKSVSKKLSLPSADNVQDSVEGLV 67 (203)
Q Consensus 24 v~efckiAiefl~~G~n~K---~y~~aA~KL~v~~~~~Vq~~Ve~L~ 67 (203)
+....+.-++||+..++.. -..-+|++|+++. +.|..+++-|+
T Consensus 45 ~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~-~~v~~al~~L~ 90 (102)
T PF08784_consen 45 LSPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSE-NEVRKALDFLS 90 (102)
T ss_dssp S-HHHHHHHHHHHC----TTTEEHHHHHHHSTS-H-HHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCH-HHHHHHHHHHH
Confidence 4667788889999843322 3789999999999 99999998775
No 22
>cd08315 Death_TRAILR_DR4_DR5 Death domain of Tumor necrosis factor-Related Apoptosis-Inducing Ligand Receptors. Death Domain (DD) found in Tumor necrosis factor-Related Apoptosis-Inducing Ligand (TRAIL) Receptors. In mammals, this family includes TRAILR1 (also called DR4 or TNFRSF10A) and TRAILR2 (also called DR5, TNFRSF10B, or KILLER). They function as receptors for the cytokine TRAIL and are involved in apoptosis signaling pathways. TRAIL preferentially induces apoptosis in cancer cells while exhibiting little toxicity in normal cells. 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 associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=46.78 E-value=36 Score=25.84 Aligned_cols=36 Identities=6% Similarity=0.115 Sum_probs=30.4
Q ss_pred HHHHHHHHHHhcCCchhhHHHHHhhcCCCchHHHHHH
Q psy5629 26 DFCTLTTNYLKDGPNQKLYKSVSKKLSLPSADNVQDS 62 (203)
Q Consensus 26 efckiAiefl~~G~n~K~y~~aA~KL~v~~~~~Vq~~ 62 (203)
|-.+.+++++...-..+.+...|++||++. ..|..+
T Consensus 4 ~~l~~~f~~i~~~V~~~~Wk~laR~LGLse-~~I~~i 39 (96)
T cd08315 4 ETLRRSFDHFIKEVPFDSWNRLMRQLGLSE-NEIDVA 39 (96)
T ss_pred hHHHHHHHHHHHHCCHHHHHHHHHHcCCCH-HHHHHH
Confidence 456778999999988899999999999998 777654
No 23
>cd08054 gp6 Head-Tail Connector Protein gp6 of Bacteriophage HK97 and similar proteins. The bacteriophage HK97 gp6 protein is critical in the assembly of the connector, a specialized structure that serves as an interface for head and tail attachment, as well as a point at which DNA exits the head during infection by the bacteriophage. It forms a dodecameric ring structure that comprises the middle ring of the connector, located between the portal protein (attached to the head) and the gp7 ring (attached to the tail). It is a component of the mature phage and the absence of HK97 gp6 results in defective head-tail joining and the absence of mature phage particles. Although the crystal structure of HK97 gp6 shows an unexpected 13-mer ring, the biological form present in the mature phage is believed to be a dodecamer.
Probab=46.23 E-value=55 Score=23.14 Aligned_cols=64 Identities=16% Similarity=0.166 Sum_probs=47.1
Q ss_pred hhhHhhhccccCCChHHHHHHHHHHHHHHhcCCchhhHHHHHhhcCCCchHHHHHHHHHHHHHHHH
Q psy5629 7 ESHREHLSVLFQLPPEVIQDFCTLTTNYLKDGPNQKLYKSVSKKLSLPSADNVQDSVEGLVYFLLL 72 (203)
Q Consensus 7 ~~hkehL~fL~~~~~~vv~efckiAiefl~~G~n~K~y~~aA~KL~v~~~~~Vq~~Ve~L~~Ll~e 72 (203)
++-|+||.+-..-+.+.+..+..-|.+|+.+..+.......+.-..+ + +.+..||--++.-+-+
T Consensus 3 ~~~K~~Lrid~d~dD~~i~~li~aA~~~i~~~~g~~~~~~~~~~~~~-~-~~~~~Ail~l~~~~Y~ 66 (91)
T cd08054 3 EEAKAHLRIDHDDDDALIELLIDAAEEYIENYTGRDLDEQTADAEEV-P-ALIKLAVLLLVAHLYE 66 (91)
T ss_pred HHHHhHcCCCCCCCHHHHHHHHHHHHHHHHHHhCCchhhcCCccccC-C-HHHHHHHHHHHHHHHh
Confidence 46799999998888999999999999999998877744332222333 4 5777777776665554
No 24
>PF00126 HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family; InterPro: IPR000847 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI [, , , , ]. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3T1B_D 3SZP_A 1O7L_C 1B9N_A 1B9M_A 3FZJ_J 3FXR_B 3FXQ_A 3FXU_A 2IJL_B ....
Probab=45.67 E-value=18 Score=24.48 Aligned_cols=28 Identities=11% Similarity=0.192 Sum_probs=23.0
Q ss_pred chhhHHHHHhhcCCCchHHHHHHHHHHHH
Q psy5629 40 NQKLYKSVSKKLSLPSADNVQDSVEGLVY 68 (203)
Q Consensus 40 n~K~y~~aA~KL~v~~~~~Vq~~Ve~L~~ 68 (203)
....+..||+.|+++. .+|-+.+..|=.
T Consensus 12 ~~gs~~~AA~~l~is~-~~vs~~i~~LE~ 39 (60)
T PF00126_consen 12 ETGSISAAAEELGISQ-SAVSRQIKQLEE 39 (60)
T ss_dssp HHSSHHHHHHHCTSSH-HHHHHHHHHHHH
T ss_pred HhCCHHHHHHHhhccc-hHHHHHHHHHHH
Confidence 3457889999999999 999988877643
No 25
>TIGR01560 put_DNA_pack uncharacterized phage protein (possible DNA packaging). This model describes a small (~ 100 amino acids) protein found in phage and in putative prophage regions of a number of bacterial genomes. Members have been annotated in some cases as a possible DNA packaging protein, but the source of this annotation was not traced during construction of this model.
Probab=44.71 E-value=83 Score=23.13 Aligned_cols=60 Identities=10% Similarity=0.061 Sum_probs=45.1
Q ss_pred hhhHhhhccccCCChHHHHHHHHHHHHHHhcCCchhhHHHHHhhcCCCchHHHHHHHHHHHHHHHH
Q psy5629 7 ESHREHLSVLFQLPPEVIQDFCTLTTNYLKDGPNQKLYKSVSKKLSLPSADNVQDSVEGLVYFLLL 72 (203)
Q Consensus 7 ~~hkehL~fL~~~~~~vv~efckiAiefl~~G~n~K~y~~aA~KL~v~~~~~Vq~~Ve~L~~Ll~e 72 (203)
++-|.||-+=..-+.+.+..+..-|.+|+.++.+.+.+. .. ... ..+..||-.|+.-+-+
T Consensus 3 ~~vK~~LrId~d~dD~li~~~i~aA~~~i~~~ig~~~~~----~~-~~~-~~~~~Avl~lv~~~Ye 62 (91)
T TIGR01560 3 DEVKLSLRIDHDDDDELIKLMIAAAQDYIQSAIGTGVKD----SF-DSK-PLFKLACIKLVAHYYE 62 (91)
T ss_pred HHHHhHhcCCCCccHHHHHHHHHHHHHHHHHHhCCCccc----cc-ccC-HHHHHHHHHHHHHHHH
Confidence 467899988888899999999999999999998776543 12 233 4677777766665554
No 26
>PF14502 HTH_41: Helix-turn-helix domain
Probab=43.99 E-value=29 Score=23.80 Aligned_cols=29 Identities=17% Similarity=0.237 Sum_probs=23.8
Q ss_pred cCCchhhHHHHHhhcCCCchHHHHHHHHHH
Q psy5629 37 DGPNQKLYKSVSKKLSLPSADNVQDSVEGL 66 (203)
Q Consensus 37 ~G~n~K~y~~aA~KL~v~~~~~Vq~~Ve~L 66 (203)
.|+.-+...-.+++++++. -+||+|..-|
T Consensus 2 ~GdRi~tI~e~~~~~~vs~-GtiQ~Alk~L 30 (48)
T PF14502_consen 2 VGDRIPTISEYSEKFGVSR-GTIQNALKFL 30 (48)
T ss_pred CCcccCCHHHHHHHhCcch-hHHHHHHHHH
Confidence 3666677788999999999 9999987654
No 27
>PRK11050 manganese transport regulator MntR; Provisional
Probab=41.24 E-value=46 Score=26.83 Aligned_cols=60 Identities=10% Similarity=0.089 Sum_probs=42.5
Q ss_pred hhhHhhhccccCCChHHHHHHHHHHHH-HHhcCCchhhHHHHHhhcCCCchHHHHHHHHHHHH
Q psy5629 7 ESHREHLSVLFQLPPEVIQDFCTLTTN-YLKDGPNQKLYKSVSKKLSLPSADNVQDSVEGLVY 68 (203)
Q Consensus 7 ~~hkehL~fL~~~~~~vv~efckiAie-fl~~G~n~K~y~~aA~KL~v~~~~~Vq~~Ve~L~~ 68 (203)
++|.+.|.-+..++...+.|=+-..+. ++..+. .....-+|+.++++. .+|-+.+..|-.
T Consensus 17 ~~~~~~~~~~~~~~~~~~~e~~l~~I~~~l~~~~-~~t~~eLA~~l~is~-stVsr~l~~Le~ 77 (152)
T PRK11050 17 EEHVEGFRQVREAHRRELIEDYVELIADLIAEVG-EARQVDIAARLGVSQ-PTVAKMLKRLAR 77 (152)
T ss_pred chhHHHHHHHHHHHhHHHHHHHHHHHHHHHHhcC-CCCHHHHHHHHCCCH-HHHHHHHHHHHH
Confidence 577888887877777655555544444 554432 345679999999999 898888877764
No 28
>PF02627 CMD: Carboxymuconolactone decarboxylase family; InterPro: IPR003779 The catechol and protocatechuate branches of the 3-oxoadipate pathway, which are important for the bacterial degradation of aromatic compounds, converge at the common intermediate 3-oxoadipate enol-lactone. Carboxymuconolactone decarboxylase (CMD) is involved in protocatechuate catabolism. In some bacteria a gene fusion event leads to expression of CMD with a hydrolase involved in the same pathway [].; GO: 0051920 peroxiredoxin activity, 0055114 oxidation-reduction process; PDB: 2GMY_E 2CWQ_C 2QEU_B 1P8C_D 1VKE_C 2OUW_A 2AF7_G 3D7I_A 1ME5_B 1KNC_A ....
Probab=40.83 E-value=67 Score=21.91 Aligned_cols=49 Identities=12% Similarity=0.228 Sum_probs=39.6
Q ss_pred CChHHHHHHHHHHHHHHhcCCc-hhhHHHHHhhcCCCchHHHHHHHHHHHHH
Q psy5629 19 LPPEVIQDFCTLTTNYLKDGPN-QKLYKSVSKKLSLPSADNVQDSVEGLVYF 69 (203)
Q Consensus 19 ~~~~vv~efckiAiefl~~G~n-~K~y~~aA~KL~v~~~~~Vq~~Ve~L~~L 69 (203)
+|+. ..|++.+|+.-.....- .+.....|.+.|++. +.|..++......
T Consensus 21 L~~~-~reli~la~s~~~~~~~c~~~H~~~a~~~G~t~-eei~~~~~~~~~~ 70 (85)
T PF02627_consen 21 LDPK-ERELIALAVSAANGCAYCVKAHARAARKAGVTE-EEIDEAVRWAAPY 70 (85)
T ss_dssp S-HH-HHHHHHHHHHHHTTTHHHHHHHHHHHHHTTTHH-HHHHHHHHHHHHH
T ss_pred CCHH-HHHHHHHHHHHHcCCchHHHHHHHHHHHcCCCH-HHHHHHHHHHHcc
Confidence 5554 89999999999998877 555668899999999 9999888776554
No 29
>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=38.93 E-value=54 Score=24.36 Aligned_cols=34 Identities=15% Similarity=0.050 Sum_probs=29.7
Q ss_pred hHHHHHhhcCCCchHHHHHHHHHHHHHHHHHhhcc
Q psy5629 43 LYKSVSKKLSLPSADNVQDSVEGLVYFLLLATILN 77 (203)
Q Consensus 43 ~y~~aA~KL~v~~~~~Vq~~Ve~L~~Ll~essK~~ 77 (203)
.++.+|++.+++. .+|+..|+++...+.++.+-.
T Consensus 7 li~~ia~~~~~s~-~~v~~vv~~~~~~i~~~L~~g 40 (96)
T TIGR00987 7 MSEYLFDELGLSK-REAKELVELFFEEIRRALENG 40 (96)
T ss_pred HHHHHHHHhCcCH-HHHHHHHHHHHHHHHHHHHcC
Confidence 4678899999999 999999999999999877643
No 30
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=36.97 E-value=50 Score=22.24 Aligned_cols=30 Identities=10% Similarity=0.325 Sum_probs=21.4
Q ss_pred HHHHHhcCCchhhHHHHHhhcCCCchHHHHHHHH
Q psy5629 31 TTNYLKDGPNQKLYKSVSKKLSLPSADNVQDSVE 64 (203)
Q Consensus 31 Aiefl~~G~n~K~y~~aA~KL~v~~~~~Vq~~Ve 64 (203)
.++++.+|+ ....+|+.+||+. -+|.+.+.
T Consensus 15 iI~~~e~g~---s~~~ia~~fgv~~-sTv~~I~K 44 (53)
T PF04218_consen 15 IIKRLEEGE---SKRDIAREFGVSR-STVSTILK 44 (53)
T ss_dssp HHHHHHCTT----HHHHHHHHT--C-CHHHHHHH
T ss_pred HHHHHHcCC---CHHHHHHHhCCCH-HHHHHHHH
Confidence 456778888 4669999999999 88877653
No 31
>PRK00285 ihfA integration host factor subunit alpha; Reviewed
Probab=36.75 E-value=64 Score=23.99 Aligned_cols=34 Identities=18% Similarity=0.076 Sum_probs=29.8
Q ss_pred hHHHHHhhcCCCchHHHHHHHHHHHHHHHHHhhcc
Q psy5629 43 LYKSVSKKLSLPSADNVQDSVEGLVYFLLLATILN 77 (203)
Q Consensus 43 ~y~~aA~KL~v~~~~~Vq~~Ve~L~~Ll~essK~~ 77 (203)
.++.+|++.+++. .+|...|+++...+.++.+-.
T Consensus 8 l~~~ia~~~~~s~-~~v~~vl~~~~~~i~~~L~~g 41 (99)
T PRK00285 8 LAEALFEKVGLSK-REAKELVELFFEEIRDALENG 41 (99)
T ss_pred HHHHHHHHhCcCH-HHHHHHHHHHHHHHHHHHHcC
Confidence 5778999999999 999999999999999877643
No 32
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=36.12 E-value=77 Score=20.28 Aligned_cols=34 Identities=15% Similarity=0.313 Sum_probs=24.4
Q ss_pred HHHHHHHHHhcCCchhhHHHHHhhcCCCchHHHHHHHH
Q psy5629 27 FCTLTTNYLKDGPNQKLYKSVSKKLSLPSADNVQDSVE 64 (203)
Q Consensus 27 fckiAiefl~~G~n~K~y~~aA~KL~v~~~~~Vq~~Ve 64 (203)
|....++-+.++. .+..+|+.+|++. ++|.+.+.
T Consensus 16 ~~~~i~~~~~~~~---s~~~vA~~~~vs~-~TV~ri~~ 49 (52)
T PF13542_consen 16 LEQYILKLLRESR---SFKDVARELGVSW-STVRRIFD 49 (52)
T ss_pred HHHHHHHHHhhcC---CHHHHHHHHCCCH-HHHHHHHH
Confidence 4444555555553 3459999999999 99998765
No 33
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=35.91 E-value=1.2e+02 Score=20.38 Aligned_cols=48 Identities=15% Similarity=0.369 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHHHhcCCc--hhhHHHHHhhcCCCchHHHHHHHHHHHHHHHH
Q psy5629 23 VIQDFCTLTTNYLKDGPN--QKLYKSVSKKLSLPSADNVQDSVEGLVYFLLL 72 (203)
Q Consensus 23 vv~efckiAiefl~~G~n--~K~y~~aA~KL~v~~~~~Vq~~Ve~L~~Ll~e 72 (203)
.+.+.+..-.+.+ +|+. ....+.+++++++++ +.+++-|...+.-|.+
T Consensus 14 ~Ln~~a~~Iw~~~-~g~~t~~ei~~~l~~~y~~~~-~~~~~dv~~fl~~L~~ 63 (68)
T PF05402_consen 14 TLNETAAFIWELL-DGPRTVEEIVDALAEEYDVDP-EEAEEDVEEFLEQLRE 63 (68)
T ss_dssp ---THHHHHHHH---SSS-HHHHHHHHHHHTT--H-HHHHHHHHHHHHHHHH
T ss_pred cccHHHHHHHHHc-cCCCCHHHHHHHHHHHcCCCH-HHHHHHHHHHHHHHHH
Confidence 3455566666666 4433 346889999999999 9999999888877765
No 34
>PF09607 BrkDBD: Brinker DNA-binding domain; InterPro: IPR018586 This DNA-binding domain is the first approx. 100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway []. ; PDB: 2GLO_A.
Probab=35.32 E-value=71 Score=22.72 Aligned_cols=35 Identities=17% Similarity=0.320 Sum_probs=25.3
Q ss_pred HHHHHHHHHHhcCCchh-hHHHHHhhcCCCchHHHHH
Q psy5629 26 DFCTLTTNYLKDGPNQK-LYKSVSKKLSLPSADNVQD 61 (203)
Q Consensus 26 efckiAiefl~~G~n~K-~y~~aA~KL~v~~~~~Vq~ 61 (203)
+|=--+++|-.+..|-+ -|..||+|+||+. -.|+.
T Consensus 9 ~FKL~Vv~~a~~~~nc~~~~RAaarkf~V~r-~~Vr~ 44 (58)
T PF09607_consen 9 EFKLKVVEYAEKDNNCKGNQRAAARKFNVSR-RQVRK 44 (58)
T ss_dssp HHHHHHHHHHHH-TTTTT-HHHHHHHTTS-H-HHHHH
T ss_pred HHHHHHHHHHHHccchhhhHHHHHHHhCccH-HHHHH
Confidence 45556888888777765 6889999999999 77764
No 35
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=35.07 E-value=51 Score=21.57 Aligned_cols=37 Identities=19% Similarity=0.289 Sum_probs=29.6
Q ss_pred HHHHHhcCCchhhHHHHHhhcCCCchHHHHHHHHHHHH
Q psy5629 31 TTNYLKDGPNQKLYKSVSKKLSLPSADNVQDSVEGLVY 68 (203)
Q Consensus 31 Aiefl~~G~n~K~y~~aA~KL~v~~~~~Vq~~Ve~L~~ 68 (203)
-++++...+.+-....+|+.+|++. -++.+.+..|..
T Consensus 8 iL~~l~~~~~~~t~~eia~~~gl~~-stv~r~L~tL~~ 44 (52)
T PF09339_consen 8 ILEALAESGGPLTLSEIARALGLPK-STVHRLLQTLVE 44 (52)
T ss_dssp HHHCHHCTBSCEEHHHHHHHHTS-H-HHHHHHHHHHHH
T ss_pred HHHHHHcCCCCCCHHHHHHHHCcCH-HHHHHHHHHHHH
Confidence 4677888877777889999999999 899888887754
No 36
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=34.89 E-value=34 Score=23.31 Aligned_cols=41 Identities=17% Similarity=0.242 Sum_probs=29.2
Q ss_pred HHHHhcCCchhhHHHHHhhcCCCchHHHHHHHHHHHHHHHHHh
Q psy5629 32 TNYLKDGPNQKLYKSVSKKLSLPSADNVQDSVEGLVYFLLLAT 74 (203)
Q Consensus 32 iefl~~G~n~K~y~~aA~KL~v~~~~~Vq~~Ve~L~~Ll~ess 74 (203)
+++|.+ .+.-.+.-+|+++|++. -+|++.+.-|-.+|.+..
T Consensus 11 l~~L~~-~~~~~~~ela~~l~~S~-rti~~~i~~L~~~f~~~~ 51 (59)
T PF08280_consen 11 LELLLK-NKWITLKELAKKLNISE-RTIKNDINELNEFFPENI 51 (59)
T ss_dssp HHHHHH-HTSBBHHHHHHHCTS-H-HHHHHHHHHHHTT--TCC
T ss_pred HHHHHc-CCCCcHHHHHHHHCCCH-HHHHHHHHHHHHHhhhhc
Confidence 455655 44446779999999999 999999998877766543
No 37
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=34.29 E-value=44 Score=21.62 Aligned_cols=26 Identities=19% Similarity=0.466 Sum_probs=19.6
Q ss_pred chhhHHHHHhhcCCCchHHHHHHHHHH
Q psy5629 40 NQKLYKSVSKKLSLPSADNVQDSVEGL 66 (203)
Q Consensus 40 n~K~y~~aA~KL~v~~~~~Vq~~Ve~L 66 (203)
....|..+|+.+|+++ .+|.+-+..|
T Consensus 16 ~r~s~~~la~~lglS~-~~v~~Ri~rL 41 (42)
T PF13404_consen 16 GRRSYAELAEELGLSE-STVRRRIRRL 41 (42)
T ss_dssp TTS-HHHHHHHHTS-H-HHHHHHHHHH
T ss_pred CCccHHHHHHHHCcCH-HHHHHHHHHh
Confidence 3456999999999999 9998877654
No 38
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=34.09 E-value=77 Score=20.12 Aligned_cols=25 Identities=12% Similarity=0.250 Sum_probs=21.3
Q ss_pred hHHHHHhhcCCCchHHHHHHHHHHHH
Q psy5629 43 LYKSVSKKLSLPSADNVQDSVEGLVY 68 (203)
Q Consensus 43 ~y~~aA~KL~v~~~~~Vq~~Ve~L~~ 68 (203)
.-..+|+.+|++. .+|.+++..|..
T Consensus 22 s~~~la~~~~vs~-~tv~~~l~~L~~ 46 (60)
T smart00345 22 SERELAAQLGVSR-TTVREALSRLEA 46 (60)
T ss_pred CHHHHHHHHCCCH-HHHHHHHHHHHH
Confidence 4568899999999 999999988764
No 39
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=33.98 E-value=95 Score=27.23 Aligned_cols=49 Identities=16% Similarity=0.207 Sum_probs=38.4
Q ss_pred hhhccccCCChHHHHHHHHHHHHHHhcCCchhhHHHHHhhcCCCchHHHHHHHHHHHH
Q psy5629 11 EHLSVLFQLPPEVIQDFCTLTTNYLKDGPNQKLYKSVSKKLSLPSADNVQDSVEGLVY 68 (203)
Q Consensus 11 ehL~fL~~~~~~vv~efckiAiefl~~G~n~K~y~~aA~KL~v~~~~~Vq~~Ve~L~~ 68 (203)
.-|.++.+.+..-+.-|..++- .+.|..||++|+++. .+|-+.+.-|=.
T Consensus 21 ~~~~~~~~m~l~~L~~f~av~e--------~gs~s~AA~~L~isQ-pavS~~I~~LE~ 69 (317)
T PRK11482 21 QIFRTLRNIDLNLLTIFEAVYV--------HKGIVNAAKILNLTP-SAISQSIQKLRV 69 (317)
T ss_pred HHhhcccccchhHHHHHHHHHH--------cCCHHHHHHHhCCCh-HHHHHHHHHHHH
Confidence 3467788888887777777664 667899999999999 888888776643
No 40
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=33.88 E-value=1.2e+02 Score=18.74 Aligned_cols=32 Identities=16% Similarity=0.406 Sum_probs=24.3
Q ss_pred HHHHhcCCchhhHHHHHhhcCCCchHHHHHHHHHHH
Q psy5629 32 TNYLKDGPNQKLYKSVSKKLSLPSADNVQDSVEGLV 67 (203)
Q Consensus 32 iefl~~G~n~K~y~~aA~KL~v~~~~~Vq~~Ve~L~ 67 (203)
+.++..| ..+..+|+.+|++. .+|...+..+.
T Consensus 12 ~~~~~~g---~s~~eia~~l~is~-~tv~~~~~~~~ 43 (58)
T smart00421 12 LRLLAEG---LTNKEIAERLGISE-KTVKTHLSNIM 43 (58)
T ss_pred HHHHHcC---CCHHHHHHHHCCCH-HHHHHHHHHHH
Confidence 3444555 36679999999999 99988887664
No 41
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=33.65 E-value=48 Score=23.58 Aligned_cols=30 Identities=13% Similarity=0.300 Sum_probs=20.6
Q ss_pred HHHHHhcCCchhhHHHHHhhcCCCchHHHHH
Q psy5629 31 TTNYLKDGPNQKLYKSVSKKLSLPSADNVQD 61 (203)
Q Consensus 31 Aiefl~~G~n~K~y~~aA~KL~v~~~~~Vq~ 61 (203)
|++.-........+.-+|++|||++ .+|..
T Consensus 12 A~e~y~~~~g~i~lkdIA~~Lgvs~-~tIr~ 41 (60)
T PF10668_consen 12 AFEIYKESNGKIKLKDIAEKLGVSE-STIRK 41 (60)
T ss_pred HHHHHHHhCCCccHHHHHHHHCCCH-HHHHH
Confidence 4444444444455678999999999 88763
No 42
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=32.90 E-value=82 Score=22.17 Aligned_cols=36 Identities=14% Similarity=0.237 Sum_probs=29.2
Q ss_pred HHHHHhcCCchhhHHHHHhhcCCCchHHHHHHHHHHH
Q psy5629 31 TTNYLKDGPNQKLYKSVSKKLSLPSADNVQDSVEGLV 67 (203)
Q Consensus 31 Aiefl~~G~n~K~y~~aA~KL~v~~~~~Vq~~Ve~L~ 67 (203)
-+++|...+.+-....+|+.+|++. .+|.+.+..|.
T Consensus 10 Il~~l~~~~~~~t~~~ia~~l~i~~-~tv~r~l~~L~ 45 (91)
T smart00346 10 VLRALAEEPGGLTLAELAERLGLSK-STAHRLLNTLQ 45 (91)
T ss_pred HHHHHHhCCCCcCHHHHHHHhCCCH-HHHHHHHHHHH
Confidence 4677777655677889999999999 89888887775
No 43
>PF05135 Phage_connect_1: Phage gp6-like head-tail connector protein; InterPro: IPR021146 The members of this family contain a conserved QLRG motif. This family of phage proteins are largely uncharacterised, although Q97HW6 from SWISSPROT and Q9XJA2 from SWISSPROT suggest a role in DNA packaging.; PDB: 2KBZ_A 3JVO_M.
Probab=32.48 E-value=1.2e+02 Score=21.86 Aligned_cols=61 Identities=11% Similarity=0.048 Sum_probs=42.1
Q ss_pred hhhHhhhccccCCChHHHHHHHHHHHHHHhcCCchhhHHHHHhhcCCCchHHHHHHHHHHHHHHH
Q psy5629 7 ESHREHLSVLFQLPPEVIQDFCTLTTNYLKDGPNQKLYKSVSKKLSLPSADNVQDSVEGLVYFLL 71 (203)
Q Consensus 7 ~~hkehL~fL~~~~~~vv~efckiAiefl~~G~n~K~y~~aA~KL~v~~~~~Vq~~Ve~L~~Ll~ 71 (203)
++-|.||.+=..-+.+.+..+...|.+|+.+-.+.+. -.....--+ ..+..+|..++.-+-
T Consensus 7 e~vK~~Lrid~d~dD~~l~~li~~A~~~i~~~~~~~~---~~~~~~~~~-~~~~~av~~l~~~~y 67 (101)
T PF05135_consen 7 EEVKQHLRIDDDDDDDLLELLIDAAEEYIENYTGRSF---DFPDDDEIP-PLFKLAVLLLVAHYY 67 (101)
T ss_dssp HHCHHHCTTTTTTTHHHHHHHHHHHHHHHHCCCT-ST---TTTSGCGS--HHHHHHHHHHHHHHH
T ss_pred HHHHHHcCCCCCccHHHHHHHHHHHHHHHHHHhhhhh---cccccccCC-HHHHHHHHHHHHHHH
Confidence 5779999998888899999999999999999888654 011112223 456666666555443
No 44
>PF05678 VQ: VQ motif; InterPro: IPR008889 This short motif is found in a variety of plant proteins. These proteins vary greatly in length and are mostly composed of low complexity regions. They all conserve a short motif FXhVQChTG, where X is any amino acid and h is a hydrophobic amino acid. The function of this motif is uncertain, however one protein in this family has been found to bind the SigA sigma factor Q9LDH1 from SWISSPROT. It would seem plausible that this motif is needed for this activity and that this whole family might be involved in modulating plastid sigma factors.
Probab=32.15 E-value=49 Score=20.56 Aligned_cols=17 Identities=18% Similarity=0.157 Sum_probs=15.9
Q ss_pred eeecChhHHHHHHHHHH
Q psy5629 155 DLEMDVRSVLNITQILE 171 (203)
Q Consensus 155 ~LqTDp~~L~hl~~~LE 171 (203)
+++|||++-.-|.|.|-
T Consensus 7 vi~~d~~~Fr~lVQ~LT 23 (31)
T PF05678_consen 7 VIHTDPSNFRALVQRLT 23 (31)
T ss_pred EEEeCHHHHHHHHHHhH
Confidence 89999999999999985
No 45
>PF13518 HTH_28: Helix-turn-helix domain
Probab=31.99 E-value=81 Score=19.89 Aligned_cols=29 Identities=7% Similarity=0.280 Sum_probs=20.9
Q ss_pred HHHHhcCCchhhHHHHHhhcCCCchHHHHHHHH
Q psy5629 32 TNYLKDGPNQKLYKSVSKKLSLPSADNVQDSVE 64 (203)
Q Consensus 32 iefl~~G~n~K~y~~aA~KL~v~~~~~Vq~~Ve 64 (203)
++.+.+|- .+..+|+++||+. .+|.+-+.
T Consensus 6 v~~~~~g~---s~~~~a~~~gis~-~tv~~w~~ 34 (52)
T PF13518_consen 6 VELYLEGE---SVREIAREFGISR-STVYRWIK 34 (52)
T ss_pred HHHHHcCC---CHHHHHHHHCCCH-hHHHHHHH
Confidence 44444664 5668999999999 88876553
No 46
>cd05030 calgranulins Calgranulins: S-100 domain found in proteins belonging to the Calgranulin subgroup of the S100 family of EF-hand calcium-modulated proteins, including S100A8, S100A9, and S100A12 . Note that the S-100 hierarchy, to which this Calgranulin group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. These proteins are expressed mainly in granulocytes, and are involved in inflammation, allergy, and neuritogenesis, as well as in host-parasite response. Calgranulins are modulated not only by calcium, but also by other metals such as zinc and copper. Structural data suggested that calgranulins may exist in multiple structural forms, homodimers, as well as hetero-oligomers. For example, the S100A8/S100A9 complex called calprotectin plays important roles in the regulation of inflammatory processes, wound repair, and regulating zinc-dependent enzymes as well as microbial growth.
Probab=31.89 E-value=77 Score=23.08 Aligned_cols=31 Identities=6% Similarity=0.147 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHHHHHHh-h----ccCChhhhhhhhh
Q psy5629 58 NVQDSVEGLVYFLLLAT-I----LNISEYDFCNTLY 88 (203)
Q Consensus 58 ~Vq~~Ve~L~~Ll~ess-K----~~ise~dF~dsl~ 88 (203)
.+++||.+|+..+-+.+ | -.|+..+|+..+.
T Consensus 2 ~~e~~i~~~~~~f~~y~~~~~~~~~Is~~El~~ll~ 37 (88)
T cd05030 2 ELEKAIETIINVFHQYSVRKGHPDTLYKKEFKQLVE 37 (88)
T ss_pred hHHHHHHHHHHHHHHHhccCCCcccCCHHHHHHHHH
Confidence 47899999999999855 3 5899999998775
No 47
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=31.86 E-value=1.2e+02 Score=20.04 Aligned_cols=43 Identities=14% Similarity=0.173 Sum_probs=35.4
Q ss_pred HHHHHHHhcCCchhhHHHHHhhcCCCchHHHHHHHHHHHHHHHHHhh
Q psy5629 29 TLTTNYLKDGPNQKLYKSVSKKLSLPSADNVQDSVEGLVYFLLLATI 75 (203)
Q Consensus 29 kiAiefl~~G~n~K~y~~aA~KL~v~~~~~Vq~~Ve~L~~Ll~essK 75 (203)
=+++-|++.|.... -+|..+||+. .+|.+.+.....+|.+..+
T Consensus 10 ll~L~~LR~~~~~~---~La~~FgIs~-stvsri~~~~~~~L~~~l~ 52 (53)
T PF13613_consen 10 LLTLMYLRLNLTFQ---DLAYRFGISQ-STVSRIFHEWIPLLYQVLK 52 (53)
T ss_pred HHHHHHHHcCCcHh---HHhhheeecH-HHHHHHHHHHHHHHHHhcC
Confidence 35677888887644 8999999999 9999999999988877544
No 48
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=31.67 E-value=55 Score=20.83 Aligned_cols=29 Identities=17% Similarity=0.354 Sum_probs=18.6
Q ss_pred HHHHHhcCCchhhHHHHHhhcCCCchHHHHHHH
Q psy5629 31 TTNYLKDGPNQKLYKSVSKKLSLPSADNVQDSV 63 (203)
Q Consensus 31 Aiefl~~G~n~K~y~~aA~KL~v~~~~~Vq~~V 63 (203)
++..+..|-+. ..+|+.||++. .+|.+-+
T Consensus 10 ii~l~~~G~s~---~~ia~~lgvs~-~Tv~~w~ 38 (50)
T PF13384_consen 10 IIRLLREGWSI---REIAKRLGVSR-STVYRWI 38 (50)
T ss_dssp HHHHHHHT--H---HHHHHHHTS-H-HHHHHHH
T ss_pred HHHHHHCCCCH---HHHHHHHCcCH-HHHHHHH
Confidence 34444455444 49999999999 8887654
No 49
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=31.50 E-value=95 Score=19.45 Aligned_cols=34 Identities=18% Similarity=0.235 Sum_probs=25.0
Q ss_pred HHHHhcCCchhhHHHHHhhcCCCchHHHHHHHHHHHH
Q psy5629 32 TNYLKDGPNQKLYKSVSKKLSLPSADNVQDSVEGLVY 68 (203)
Q Consensus 32 iefl~~G~n~K~y~~aA~KL~v~~~~~Vq~~Ve~L~~ 68 (203)
++++.++ +-....+|+.++++. .+|.+.+.-|..
T Consensus 3 l~~l~~~--~~~~~~i~~~l~is~-~~v~~~l~~L~~ 36 (66)
T smart00418 3 LKLLAEG--ELCVCELAEILGLSQ-STVSHHLKKLRE 36 (66)
T ss_pred HHHhhcC--CccHHHHHHHHCCCH-HHHHHHHHHHHH
Confidence 3455533 345678999999999 899988887764
No 50
>smart00411 BHL bacterial (prokaryotic) histone like domain.
Probab=31.05 E-value=88 Score=22.39 Aligned_cols=33 Identities=15% Similarity=0.270 Sum_probs=28.8
Q ss_pred hHHHHHhhcCCCchHHHHHHHHHHHHHHHHHhhc
Q psy5629 43 LYKSVSKKLSLPSADNVQDSVEGLVYFLLLATIL 76 (203)
Q Consensus 43 ~y~~aA~KL~v~~~~~Vq~~Ve~L~~Ll~essK~ 76 (203)
.+..+|++.+++. .+|...++++...+.++..-
T Consensus 6 li~~ia~~~~~~~-~~v~~vl~~l~~~i~~~L~~ 38 (90)
T smart00411 6 LIDAIAEKAGLSK-KDAKAAVDAFLEIITEALKK 38 (90)
T ss_pred HHHHHHHHhCCCH-HHHHHHHHHHHHHHHHHHhC
Confidence 4668899999999 99999999999999887664
No 51
>PF12244 DUF3606: Protein of unknown function (DUF3606); InterPro: IPR022037 This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=31.00 E-value=37 Score=23.51 Aligned_cols=22 Identities=9% Similarity=0.383 Sum_probs=18.6
Q ss_pred HHHHHhhcCCCchHHHHHHHHHH
Q psy5629 44 YKSVSKKLSLPSADNVQDSVEGL 66 (203)
Q Consensus 44 y~~aA~KL~v~~~~~Vq~~Ve~L 66 (203)
..--|++|||+. +.+..||...
T Consensus 23 v~ywa~~~gvt~-~~L~~AV~~v 44 (57)
T PF12244_consen 23 VRYWAKRFGVTE-EQLREAVRAV 44 (57)
T ss_pred HHHHHHHHCcCH-HHHHHHHHHH
Confidence 446789999999 9999999864
No 52
>PRK10753 transcriptional regulator HU subunit alpha; Provisional
Probab=30.66 E-value=95 Score=22.99 Aligned_cols=33 Identities=12% Similarity=0.130 Sum_probs=29.0
Q ss_pred hHHHHHhhcCCCchHHHHHHHHHHHHHHHHHhhc
Q psy5629 43 LYKSVSKKLSLPSADNVQDSVEGLVYFLLLATIL 76 (203)
Q Consensus 43 ~y~~aA~KL~v~~~~~Vq~~Ve~L~~Ll~essK~ 76 (203)
..+.+|++.+++. .+++..|+++...+.++.+-
T Consensus 6 li~~ia~~~~~s~-~~~~~~v~~~~~~i~~~L~~ 38 (90)
T PRK10753 6 LIDVIADKAELSK-TQAKAALESTLAAITESLKE 38 (90)
T ss_pred HHHHHHHHhCCCH-HHHHHHHHHHHHHHHHHHHc
Confidence 4668899999999 99999999999999998763
No 53
>PF14908 DUF4496: Domain of unknown function (DUF4496)
Probab=30.66 E-value=85 Score=24.68 Aligned_cols=38 Identities=18% Similarity=0.183 Sum_probs=32.6
Q ss_pred cCCchhh-HHHHHhhcCCCchHHHHHHHHHHHHHHHHHhh
Q psy5629 37 DGPNQKL-YKSVSKKLSLPSADNVQDSVEGLVYFLLLATI 75 (203)
Q Consensus 37 ~G~n~K~-y~~aA~KL~v~~~~~Vq~~Ve~L~~Ll~essK 75 (203)
+++..+. |..+|...+++. |.|+.||+.++..+.++.+
T Consensus 77 ~~~~~~~n~~~ia~~~~~~k-d~v~~~l~~~~~~l~~~l~ 115 (140)
T PF14908_consen 77 HIPVVQLNYSEIAASCGFSK-DVVEACLREIFQALGDALR 115 (140)
T ss_pred CCceeccCHHHHHHHcCCCH-HHHHHHHHHHHHHHHHHHh
Confidence 3444443 889999999999 9999999999999999887
No 54
>smart00005 DEATH DEATH domain, found in proteins involved in cell death (apoptosis). Alpha-helical domain present in a variety of proteins with apoptotic functions. Some (but not all) of these domains form homotypic and heterotypic dimers.
Probab=30.61 E-value=83 Score=22.23 Aligned_cols=29 Identities=21% Similarity=0.353 Sum_probs=20.6
Q ss_pred HHHHhcCCchhhHHHHHhhcCCCchHHHHH
Q psy5629 32 TNYLKDGPNQKLYKSVSKKLSLPSADNVQD 61 (203)
Q Consensus 32 iefl~~G~n~K~y~~aA~KL~v~~~~~Vq~ 61 (203)
+.++.+++-.+.+...|++||++. ..|..
T Consensus 8 ~~~l~~~~~g~~W~~la~~Lg~~~-~~i~~ 36 (88)
T smart00005 8 LAKLLDHPLGLDWRELARKLGLSE-ADIDQ 36 (88)
T ss_pred HHHHHcCccchHHHHHHHHcCCCH-HHHHH
Confidence 344555545567999999999987 66544
No 55
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=30.23 E-value=49 Score=21.62 Aligned_cols=23 Identities=22% Similarity=0.410 Sum_probs=19.7
Q ss_pred CchhhHHHHHhhcCCCchHHHHHH
Q psy5629 39 PNQKLYKSVSKKLSLPSADNVQDS 62 (203)
Q Consensus 39 ~n~K~y~~aA~KL~v~~~~~Vq~~ 62 (203)
|+...+..+|..+|++. ..|+.=
T Consensus 25 p~~~~~~~la~~l~l~~-~~V~~W 47 (57)
T PF00046_consen 25 PSKEEREELAKELGLTE-RQVKNW 47 (57)
T ss_dssp CHHHHHHHHHHHHTSSH-HHHHHH
T ss_pred ccccccccccccccccc-cccccC
Confidence 66778999999999999 988753
No 56
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=30.09 E-value=1.4e+02 Score=18.53 Aligned_cols=31 Identities=16% Similarity=0.362 Sum_probs=22.9
Q ss_pred HHHHhcCCchhhHHHHHhhcCCCchHHHHHHHHHH
Q psy5629 32 TNYLKDGPNQKLYKSVSKKLSLPSADNVQDSVEGL 66 (203)
Q Consensus 32 iefl~~G~n~K~y~~aA~KL~v~~~~~Vq~~Ve~L 66 (203)
+.++..|- .+..+|+.+|+++ .+|...+..+
T Consensus 9 ~~~~~~~~---s~~eia~~l~~s~-~tv~~~~~~~ 39 (57)
T cd06170 9 LRLLAEGK---TNKEIADILGISE-KTVKTHLRNI 39 (57)
T ss_pred HHHHHcCC---CHHHHHHHHCCCH-HHHHHHHHHH
Confidence 34444553 5679999999999 8888887754
No 57
>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=29.76 E-value=99 Score=19.88 Aligned_cols=34 Identities=21% Similarity=0.363 Sum_probs=26.0
Q ss_pred HHHHHhcCCchhhHHHHHhhcCCCchHHHHHHHHHHH
Q psy5629 31 TTNYLKDGPNQKLYKSVSKKLSLPSADNVQDSVEGLV 67 (203)
Q Consensus 31 Aiefl~~G~n~K~y~~aA~KL~v~~~~~Vq~~Ve~L~ 67 (203)
-+.++..++ -....+|+.++++. .+|.+.+..|.
T Consensus 12 il~~l~~~~--~~~~ei~~~~~i~~-~~i~~~l~~L~ 45 (78)
T cd00090 12 ILRLLLEGP--LTVSELAERLGLSQ-STVSRHLKKLE 45 (78)
T ss_pred HHHHHHHCC--cCHHHHHHHHCcCH-hHHHHHHHHHH
Confidence 456666666 44678999999999 88888887764
No 58
>PF13624 SurA_N_3: SurA N-terminal domain; PDB: 3NRK_A.
Probab=29.67 E-value=88 Score=24.30 Aligned_cols=53 Identities=25% Similarity=0.352 Sum_probs=27.8
Q ss_pred CchhhHHHHHhhcCC--CchHHHHHHHHHHHHHHHHHhhccCChhhhhhhhhhcCCCCh
Q psy5629 39 PNQKLYKSVSKKLSL--PSADNVQDSVEGLVYFLLLATILNISEYDFCNTLYHMGFTQD 95 (203)
Q Consensus 39 ~n~K~y~~aA~KL~v--~~~~~Vq~~Ve~L~~Ll~essK~~ise~dF~dsl~~l~F~ee 95 (203)
.+.+....+|+++|+ +. +.|+..+..+-..-. .. ..++..|...+...|++++
T Consensus 84 I~~~ll~q~A~~~gi~vsd-~ev~~~i~~~~~f~~-~g--~~~~~~f~~~L~~~g~t~~ 138 (154)
T PF13624_consen 84 IDQKLLLQEAKKLGISVSD-AEVDDAIKQIPAFQE-NG--KFDKEAFEEFLKQQGMTEE 138 (154)
T ss_dssp HHHHHHHHHHHHTT----H-HHHHHHHHH--HHHH-H------HHHHHHHHH-------
T ss_pred HHHHHHHHHHHHcCCCCCH-HHHHHHHHHHHHHHH-CC--CCCHHHHHHHHHHhhcccc
Confidence 446777889999876 45 778888777543222 22 2478889988888888876
No 59
>PF04792 LcrV: V antigen (LcrV) protein; InterPro: IPR005413 The type III secretion system of Gram-negative bacteria is used to transport virulence factors from the pathogen directly into the host cell [] and is only triggered when the bacterium comes into close contact with the host. Effector proteins secreted by the type III system do not possess a secretion signal, and are considered unique because of this. Yersinia spp. secrete effector proteins called YopB and YopD that facilitate the spread of other translocated proteins through the type III needle and the host cell cytoplasm []. In turn, the transcription of these moieties is thought to be regulated by another gene, lcrV, found on the Yops virulon that encodes the entire type III system []. The product of this gene, LcrV protein, also regulates the secretion of YopD through the type III translocon [], and itself acts as a protective "V" antigen for Yersinia pestis, the causative agent of plague []. Recently, a homologue of the Y. pestis LcrV protein (PcrV) was found in Pseudomonas aeruginosa, an opportunistic pathogen. In vivo studies using mice found that immunisation with the protein protected burned animals from infection by P. aeruginosa, and enhanced survival. In addition, it is speculated that PcrV determines the size of the needle pore for type III secreted effectors [].; GO: 0009405 pathogenesis, 0005576 extracellular region; PDB: 1R6F_A.
Probab=29.57 E-value=1e+02 Score=28.77 Aligned_cols=67 Identities=18% Similarity=0.264 Sum_probs=46.4
Q ss_pred CCCchHHHHHHHHHHHHHHHHHhhccCChhhhhhhhhh-c-C--CCChhHHHHHHHHHH---HHHHHhHHHHhhhhhh
Q psy5629 52 SLPSADNVQDSVEGLVYFLLLATILNISEYDFCNTLYH-M-G--FTQDDKCEKILYEFY---TQEKYNLYRTLISEYI 122 (203)
Q Consensus 52 ~v~~~~~Vq~~Ve~L~~Ll~essK~~ise~dF~dsl~~-l-~--F~ee~~~~~vL~q~y---~~~r~~I~r~iLs~~~ 122 (203)
||.. ..+++|+++|=.++=...+..-+-.||...+.. + | |.|+ +..++.... .++|+++ |.-|.++.
T Consensus 88 g~~~-~q~~~Gi~~lk~~le~~~~t~wtlrdfl~~~~ssLt~DR~Ddd--Vi~~~~~~m~~~d~kR~~l-kdeL~eLT 161 (323)
T PF04792_consen 88 GHPD-SQIKNGIEALKGFLESQPKTQWTLRDFLAVSHSSLTGDRIDDD--VIFAFNEVMVFHDEKRKEL-KDELAELT 161 (323)
T ss_dssp -----HHHHHHHHHHHHHHHHSS-SEEEHHHHHHHHHHHHSTT---HH--HHHHHHHHHHTT--HHHHH-HHHHHHHH
T ss_pred CCcc-hhHHHHHHHHHHHHhcCCcCcccHHHHHHHHHHhhccccccHH--HHHHHHHHHhhhHHHHHHH-HHHHHHHH
Confidence 7888 999999999999999888888888899876655 3 4 7777 777776544 5678888 88777774
No 60
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=29.31 E-value=88 Score=20.72 Aligned_cols=35 Identities=14% Similarity=0.284 Sum_probs=27.3
Q ss_pred HHHHHhcCCchhhHHHHHhhcCCCchHHHHHHHHHHHHH
Q psy5629 31 TTNYLKDGPNQKLYKSVSKKLSLPSADNVQDSVEGLVYF 69 (203)
Q Consensus 31 Aiefl~~G~n~K~y~~aA~KL~v~~~~~Vq~~Ve~L~~L 69 (203)
.+.++..|-+.+ .+|+.+|+++ .+|..-...++.-
T Consensus 11 vl~~l~~G~~~~---eIA~~l~is~-~tV~~~~~~i~~K 45 (58)
T PF00196_consen 11 VLRLLAQGMSNK---EIAEELGISE-KTVKSHRRRIMKK 45 (58)
T ss_dssp HHHHHHTTS-HH---HHHHHHTSHH-HHHHHHHHHHHHH
T ss_pred HHHHHHhcCCcc---hhHHhcCcch-hhHHHHHHHHHHH
Confidence 467788887777 8999999999 9998877776653
No 61
>PF05942 PaREP1: Archaeal PaREP1/PaREP8 family; InterPro: IPR010268 This family consists of several archaeal PaREP1 proteins, the function of the family is unknown.; PDB: 2Q00_A 2JPU_A.
Probab=28.85 E-value=1.3e+02 Score=23.08 Aligned_cols=39 Identities=13% Similarity=0.130 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHHhcCCchhhHHHHHhhcCCCchHHHHHHHHHHHHHH
Q psy5629 24 IQDFCTLTTNYLKDGPNQKLYKSVSKKLSLPSADNVQDSVEGLVYFL 70 (203)
Q Consensus 24 v~efckiAiefl~~G~n~K~y~~aA~KL~v~~~~~Vq~~Ve~L~~Ll 70 (203)
...+.+.|.+||.+| .+..||+|+ . -++..+|.+|+...
T Consensus 6 a~~~l~~A~e~L~~G----~~rqAaeK~---~-~A~~~~ikaLa~~~ 44 (115)
T PF05942_consen 6 AEKELEEADELLEKG----DLRQAAEKA---F-KAVEAAIKALAVKN 44 (115)
T ss_dssp HHHHHHHHHHHHHTT-----HHHHHHHH---H-HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcC----CHHHHHHHH---H-HHHHHHHHHHHHHh
Confidence 356789999999999 455677776 4 55666666666553
No 62
>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B.
Probab=28.28 E-value=1e+02 Score=20.84 Aligned_cols=35 Identities=14% Similarity=0.320 Sum_probs=26.5
Q ss_pred HHHHhcCCchhhHHHHHhhcCCCchHHHHHHHHHHHHHH
Q psy5629 32 TNYLKDGPNQKLYKSVSKKLSLPSADNVQDSVEGLVYFL 70 (203)
Q Consensus 32 iefl~~G~n~K~y~~aA~KL~v~~~~~Vq~~Ve~L~~Ll 70 (203)
.-|+.+|-|.+ .+|++|++-. .+|..=++-+-.++
T Consensus 6 ~~yl~~~~n~~---~tA~~L~iHr-NTl~yRl~ki~~l~ 40 (59)
T PF13556_consen 6 RAYLENNGNIS---KTARALHIHR-NTLRYRLKKIEELL 40 (59)
T ss_dssp HHHHHTTT-HH---HHHHHHTS-H-HHHHHHHHHHHHHH
T ss_pred HHHHHcCCCHH---HHHHHHCCCH-HHHHHHHHHHHHHH
Confidence 45888888877 8999999999 99888777766554
No 63
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=27.92 E-value=1.7e+02 Score=23.22 Aligned_cols=45 Identities=22% Similarity=0.449 Sum_probs=34.5
Q ss_pred ccCCChHHHHHHHHHHHHHHhcCCchhhHHHHHhhcCCCchHHHHHHHHHHHH
Q psy5629 16 LFQLPPEVIQDFCTLTTNYLKDGPNQKLYKSVSKKLSLPSADNVQDSVEGLVY 68 (203)
Q Consensus 16 L~~~~~~vv~efckiAiefl~~G~n~K~y~~aA~KL~v~~~~~Vq~~Ve~L~~ 68 (203)
+..++++ =.+|.+ .|+.+..|-| ..|+.|||+. .+|.+=.+.|+.
T Consensus 31 ~~~L~~E-~~~Fi~---~Fi~~rGnlK---e~e~~lgiSY-PTvR~rLd~ii~ 75 (113)
T PF09862_consen 31 FARLSPE-QLEFIK---LFIKNRGNLK---EMEKELGISY-PTVRNRLDKIIE 75 (113)
T ss_pred hhcCCHH-HHHHHH---HHHHhcCCHH---HHHHHHCCCc-HHHHHHHHHHHH
Confidence 4455555 345544 7999999998 8999999999 999987777654
No 64
>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=27.59 E-value=1.2e+02 Score=19.19 Aligned_cols=35 Identities=26% Similarity=0.451 Sum_probs=24.5
Q ss_pred HHHHHhcCCchhhHHHHHhhcCCCchHHHHHHHHHHH
Q psy5629 31 TTNYLKDGPNQKLYKSVSKKLSLPSADNVQDSVEGLV 67 (203)
Q Consensus 31 Aiefl~~G~n~K~y~~aA~KL~v~~~~~Vq~~Ve~L~ 67 (203)
-+.+|.+.|. -.-..+|+++|++. .+|...+.-|.
T Consensus 8 Il~~l~~~~~-~t~~ela~~~~is~-~tv~~~l~~L~ 42 (48)
T PF13412_consen 8 ILNYLRENPR-ITQKELAEKLGISR-STVNRYLKKLE 42 (48)
T ss_dssp HHHHHHHCTT-S-HHHHHHHHTS-H-HHHHHHHHHHH
T ss_pred HHHHHHHcCC-CCHHHHHHHhCCCH-HHHHHHHHHHH
Confidence 3567777554 33558999999999 99988877654
No 65
>PHA02591 hypothetical protein; Provisional
Probab=27.13 E-value=1.2e+02 Score=22.97 Aligned_cols=35 Identities=17% Similarity=0.321 Sum_probs=30.2
Q ss_pred HHHHHHHHHHhcCCchhhHHHHHhhcCCCchHHHHHHHH
Q psy5629 26 DFCTLTTNYLKDGPNQKLYKSVSKKLSLPSADNVQDSVE 64 (203)
Q Consensus 26 efckiAiefl~~G~n~K~y~~aA~KL~v~~~~~Vq~~Ve 64 (203)
+...+|-+....|-.+. .+|+.||++. ++|.+.+.
T Consensus 47 d~~~vA~eL~eqGlSqe---qIA~~LGVsq-etVrKYL~ 81 (83)
T PHA02591 47 DLISVTHELARKGFTVE---KIASLLGVSV-RKVRRYLE 81 (83)
T ss_pred hHHHHHHHHHHcCCCHH---HHHHHhCCCH-HHHHHHHh
Confidence 45688999999998887 8999999999 99988764
No 66
>cd08794 Death_IRAK1 Death domain of Interleukin 1 Receptor Associated Kinase-1. Death Domain (DD) of Interleukin-1 Receptor-Associated Kinase 1 (IRAK1). IRAKs are essential components of innate immunity and inflammation in mammals and other vertebrates. They are involved in signal transduction pathways involving IL-1 and IL-18 receptors, Toll-like receptors, nuclear factor-kappaB (NF-kB), and mitogen-activated protein kinases (MAPKs). IRAKs contain an N-terminal DD domain and a C-terminal kinase domain. IRAK1 is an active kinase and also plays adaptor functions. It binds to the MyD88-IRAK4 complex via its DD, which facilitates its phosphorylation by IRAK4, activating it for further auto-phosphorylation. Hyper-phosphorylated IRAK1 forms a cytosolic complex with TRAF6, leading to the activation of NF-kB and MAPK pathways. IRAK1 is involved in autoimmunity and may be associated with lupus pathogenesis. DDs are protein-protein interaction domains found in a variety of domain architectures.
Probab=27.08 E-value=47 Score=25.29 Aligned_cols=16 Identities=44% Similarity=1.086 Sum_probs=14.7
Q ss_pred cccCCChHHHHHHHHH
Q psy5629 15 VLFQLPPEVIQDFCTL 30 (203)
Q Consensus 15 fL~~~~~~vv~efcki 30 (203)
||-++++.|..+||+.
T Consensus 2 ~Ly~lP~~vm~~fc~~ 17 (84)
T cd08794 2 FLYELPPSVMWRFCLV 17 (84)
T ss_pred ccccCCHHHHHHHHHH
Confidence 7889999999999985
No 67
>PF10410 DnaB_bind: DnaB-helicase binding domain of primase; InterPro: IPR019475 This entry represents the C-terminal region three-helical domain of DNA primase []. Primases synthesise short RNA strands on single-stranded DNA templates, thereby generating the hybrid duplexes required for the initiation of synthesis by DNA polymerases. Primases are recruited to single-stranded DNA by helicases - this domain binds DnaB-helicase []. It is associated with the Toprim domain IPR006171 from INTERPRO, which is the central catalytic core. ; GO: 0016779 nucleotidyltransferase activity; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A.
Probab=27.06 E-value=1.4e+02 Score=19.51 Aligned_cols=38 Identities=13% Similarity=0.248 Sum_probs=27.1
Q ss_pred ChHHHHHHHHHHHHHHhcCCchhh----HHHHHhhcCCCchHH
Q psy5629 20 PPEVIQDFCTLTTNYLKDGPNQKL----YKSVSKKLSLPSADN 58 (203)
Q Consensus 20 ~~~vv~efckiAiefl~~G~n~K~----y~~aA~KL~v~~~~~ 58 (203)
+++.-.+|.+-+..+|..=+++-. .+.+|+++|++. ++
T Consensus 17 ~~egk~~~~~~~~~~i~~i~~~i~r~~y~~~la~~~~i~~-~~ 58 (59)
T PF10410_consen 17 TPEGKAEAVREAAPLIAQIPDPIERELYIRELAERLGISE-DA 58 (59)
T ss_dssp SHHHHHHHHHHHHHHHTT--SHHHHHHHHHHHHHHCT-SS-TT
T ss_pred CHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHhCcCc-cc
Confidence 556778888999999988877553 448899999998 64
No 68
>KOG0869|consensus
Probab=26.89 E-value=2.3e+02 Score=24.12 Aligned_cols=39 Identities=23% Similarity=0.352 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHHHHH-HHh-------hccCChhhhhhhhhhcCCCCh
Q psy5629 57 DNVQDSVEGLVYFLL-LAT-------ILNISEYDFCNTLYHMGFTQD 95 (203)
Q Consensus 57 ~~Vq~~Ve~L~~Ll~-ess-------K~~ise~dF~dsl~~l~F~ee 95 (203)
|+||.||--.+.+++ |++ |-.|+..|..-.+..|||++=
T Consensus 58 E~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~tLGFe~Y 104 (168)
T KOG0869|consen 58 ETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMSTLGFENY 104 (168)
T ss_pred HHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHHHcCcHhH
Confidence 899999977666665 443 368999999999999999976
No 69
>PF13730 HTH_36: Helix-turn-helix domain
Probab=26.44 E-value=1.8e+02 Score=18.68 Aligned_cols=25 Identities=20% Similarity=0.294 Sum_probs=22.1
Q ss_pred hHHHHHhhcCCCchHHHHHHHHHHHH
Q psy5629 43 LYKSVSKKLSLPSADNVQDSVEGLVY 68 (203)
Q Consensus 43 ~y~~aA~KL~v~~~~~Vq~~Ve~L~~ 68 (203)
.++.+|+.+|++. .+|++++..|..
T Consensus 27 S~~~la~~~g~s~-~Tv~~~i~~L~~ 51 (55)
T PF13730_consen 27 SQETLAKDLGVSR-RTVQRAIKELEE 51 (55)
T ss_pred CHHHHHHHHCcCH-HHHHHHHHHHHH
Confidence 5789999999999 999999988753
No 70
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=26.14 E-value=1e+02 Score=25.04 Aligned_cols=27 Identities=15% Similarity=0.130 Sum_probs=23.0
Q ss_pred hhHHHHHhhcCCCchHHHHHHHHHHHHH
Q psy5629 42 KLYKSVSKKLSLPSADNVQDSVEGLVYF 69 (203)
Q Consensus 42 K~y~~aA~KL~v~~~~~Vq~~Ve~L~~L 69 (203)
..-+.+|+.||.+. -+|++++.-|+..
T Consensus 43 ~tvdelae~lnr~r-Stv~rsl~~L~~~ 69 (126)
T COG3355 43 LTVDELAEILNRSR-STVYRSLQNLLEA 69 (126)
T ss_pred cCHHHHHHHHCccH-HHHHHHHHHHHHc
Confidence 33479999999999 9999999988763
No 71
>KOG0275|consensus
Probab=25.20 E-value=1.9e+02 Score=27.84 Aligned_cols=99 Identities=21% Similarity=0.321 Sum_probs=62.8
Q ss_pred HHHHHHHHHHhcCCchhhHHHHHhhcCCCchHHHHHHHHHHHHHHHHHhhccCChhhhhhhhhhcCCCChhHHHHHHHHH
Q psy5629 26 DFCTLTTNYLKDGPNQKLYKSVSKKLSLPSADNVQDSVEGLVYFLLLATILNISEYDFCNTLYHMGFTQDDKCEKILYEF 105 (203)
Q Consensus 26 efckiAiefl~~G~n~K~y~~aA~KL~v~~~~~Vq~~Ve~L~~Ll~essK~~ise~dF~dsl~~l~F~ee~~~~~vL~q~ 105 (203)
+.+|+-..|+....-.+.++.+-+.-+|+- ++|. +|+|.+.=... . .=......+..+.+|+. | |..+
T Consensus 9 dVIrli~QflKE~~L~rtl~tLQeEt~VSL-NTVD-Svd~Fv~dI~s-G----~WD~VL~~vqsLKLP~k-k----L~dL 76 (508)
T KOG0275|consen 9 DVIRLIEQFLKENSLHRTLQTLQEETNVSL-NTVD-SVDGFVNDINS-G----HWDTVLKTVQSLKLPDK-K----LIDL 76 (508)
T ss_pred hHHHHHHHHHhhhhHHHHHHHHHHhhccce-eech-hHHHHHHhccc-C----chHHHHHHHHhccCchh-H----HHHH
Confidence 567888889988887888999999999998 7775 45554432111 0 01223334566888876 2 3555
Q ss_pred HHHHHHhHHHHhhhhhhheecccccccccCceEEEE
Q psy5629 106 YTQEKYNLYRTLISEYISVVATRSHLNQCEPKFTIR 141 (203)
Q Consensus 106 y~~~r~~I~r~iLs~~~vqiASRsl~~q~~P~vtmk 141 (203)
|++---++ - -|.++ -+-|++.+|..|++.||
T Consensus 77 YEqivlEl-i-ELREL---~tAR~~lRQTdpM~~lK 107 (508)
T KOG0275|consen 77 YEQIVLEL-I-ELREL---GTARSLLRQTDPMIMLK 107 (508)
T ss_pred HHHHHHHH-H-HHHhh---hHHHHHHhccCceehhh
Confidence 65544433 0 01111 25699999999999876
No 72
>cd07979 TAF9 TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Human TAF9 has a paralogue gene (TAF9L) whi
Probab=25.07 E-value=1.2e+02 Score=23.94 Aligned_cols=51 Identities=22% Similarity=0.370 Sum_probs=42.3
Q ss_pred cCCChHHHHHHHHHHHHHHhcC-CchhhHHHHHhhcCCCchHHHHHHHHHHHH
Q psy5629 17 FQLPPEVIQDFCTLTTNYLKDG-PNQKLYKSVSKKLSLPSADNVQDSVEGLVY 68 (203)
Q Consensus 17 ~~~~~~vv~efckiAiefl~~G-~n~K~y~~aA~KL~v~~~~~Vq~~Ve~L~~ 68 (203)
.++++.|+..+..+|.+|...= ...+.|..-|.+=.|+. ++|+=|+...+.
T Consensus 17 ~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~-eDV~lAi~~r~~ 68 (117)
T cd07979 17 TEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDA-DDVKLAIQSRVD 68 (117)
T ss_pred CccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCH-HHHHHHHHHHhc
Confidence 4788999999999999998875 55677889999999999 999888776554
No 73
>cd08306 Death_FADD Fas-associated Death Domain protein-protein interaction domain. Death domain (DD) found in FAS-associated via death domain (FADD). FADD is a component of the death-inducing signaling complex (DISC) and serves as an adaptor in the signaling pathway of death receptor proteins. It modulates apoptosis as well as non-apoptotic processes such as cell cycle progression, survival, innate immune signaling, and hematopoiesis. FADD contains an N-terminal DED and a C-terminal DD. Its DD interacts with the DD of the activated death receptor, FAS, and its DED recruits the initiator caspases, caspase-8 and -10, to the DISC complex via a homotypic interaction with the N-terminal DED of the caspase. 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 associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain),
Probab=25.04 E-value=82 Score=23.21 Aligned_cols=31 Identities=10% Similarity=0.292 Sum_probs=23.1
Q ss_pred HHHHHhcCCchhhHHHHHhhcCCCchHHHHHHH
Q psy5629 31 TTNYLKDGPNQKLYKSVSKKLSLPSADNVQDSV 63 (203)
Q Consensus 31 Aiefl~~G~n~K~y~~aA~KL~v~~~~~Vq~~V 63 (203)
+++++.+... +.+...|++||++. .+|++..
T Consensus 4 ~f~~i~~~lG-~~Wk~laR~LGlse-~~Id~i~ 34 (86)
T cd08306 4 AFDVICENVG-RDWRKLARKLGLSE-TKIESIE 34 (86)
T ss_pred HHHHHHHHHh-hhHHHHHHHcCCCH-HHHHHHH
Confidence 5666766655 45889999999998 7777554
No 74
>PF09312 SurA_N: SurA N-terminal domain; InterPro: IPR015391 The correct folding of outer membrane proteins in Gram negative bacteria is facilitated by the survival protein SurA []. This entry represents the domain found at the N terminus of the chaperone SurA. It is a helical domain of unknown function. The C terminus of the SurA protein folds back and forms part of this domain also but is not included in the current alignment. ; PDB: 3RGC_B 2PV3_B 1M5Y_A.
Probab=24.93 E-value=1.5e+02 Score=22.76 Aligned_cols=49 Identities=18% Similarity=0.350 Sum_probs=33.3
Q ss_pred chhhHHHHHhhcCC--CchHHHHHHHHHHHHHHHHHhhccCChhhhhhhhhhcCCCCh
Q psy5629 40 NQKLYKSVSKKLSL--PSADNVQDSVEGLVYFLLLATILNISEYDFCNTLYHMGFTQD 95 (203)
Q Consensus 40 n~K~y~~aA~KL~v--~~~~~Vq~~Ve~L~~Ll~essK~~ise~dF~dsl~~l~F~ee 95 (203)
+.+.-...|+++|+ +. +.|.++++.++ .+.++|..+|...+..-|.+-+
T Consensus 52 ~e~L~~q~ak~~gI~vsd-~evd~~i~~ia------~~n~ls~~ql~~~L~~~G~s~~ 102 (118)
T PF09312_consen 52 DEKLQLQEAKRLGIKVSD-EEVDEAIANIA------KQNNLSVEQLRQQLEQQGISYE 102 (118)
T ss_dssp HHHHHHHHHHHCT----H-HHHHHHHHHHH------HHTT--HHHHHHHCHHCT--HH
T ss_pred HHHHHHHHHHHcCCCCCH-HHHHHHHHHHH------HHcCCCHHHHHHHHHHcCCCHH
Confidence 45556678888865 56 77888887754 6778899999999999888755
No 75
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=24.77 E-value=1.6e+02 Score=25.33 Aligned_cols=40 Identities=13% Similarity=0.151 Sum_probs=29.8
Q ss_pred CCChHHHHHHHHHHHHHHhcCCchhhHHHHHhhcCCCchHHHHHHHHHH
Q psy5629 18 QLPPEVIQDFCTLTTNYLKDGPNQKLYKSVSKKLSLPSADNVQDSVEGL 66 (203)
Q Consensus 18 ~~~~~vv~efckiAiefl~~G~n~K~y~~aA~KL~v~~~~~Vq~~Ve~L 66 (203)
+++..-+.-|+-+|- ...+.+||++|+++. .+|-+++..|
T Consensus 3 ~~~l~~L~~f~av~~--------~gS~s~AAe~L~isq-savS~~Ik~L 42 (309)
T PRK11013 3 AVSLRHIEIFHAVMT--------AGSLTEAARLLHTSQ-PTVSRELARF 42 (309)
T ss_pred CccHHHHHHHHHHHH--------hCcHHHHHHHHCCCc-HHHHHHHHHH
Confidence 345555555665553 567889999999999 9998888776
No 76
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=24.61 E-value=3.6e+02 Score=21.36 Aligned_cols=83 Identities=7% Similarity=0.056 Sum_probs=56.6
Q ss_pred CChHHHHHHHHHHHHHHhcCCchh--hHHHHHhhcCCCchHHHHHHHHHHHH-----------HHHHHh-hccCChhhhh
Q psy5629 19 LPPEVIQDFCTLTTNYLKDGPNQK--LYKSVSKKLSLPSADNVQDSVEGLVY-----------FLLLAT-ILNISEYDFC 84 (203)
Q Consensus 19 ~~~~vv~efckiAiefl~~G~n~K--~y~~aA~KL~v~~~~~Vq~~Ve~L~~-----------Ll~ess-K~~ise~dF~ 84 (203)
++.+.+..--+.|+.||...+-+. +.+.+.+| |+++ +.|+.+++-|.. -+..+. .-+-+..-..
T Consensus 5 ~~~~~~~~a~~~al~~L~~r~~s~~el~~kL~~k-g~~~-~~i~~vl~~l~~~~~ldD~~~a~~~~~~~~~~~~g~~~I~ 82 (157)
T PRK00117 5 ARRRMYASARARALRLLARREHSRAELRRKLAAK-GFSE-EVIEAVLDRLKEEGLLDDERFAESFVRSRARKGYGPRRIR 82 (157)
T ss_pred ccccHHHHHHHHHHHHHccchhHHHHHHHHHHhc-CCCH-HHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhCCchHHHHH
Confidence 445667777889999999986554 35555554 9999 999999987754 222221 2345667777
Q ss_pred hhhhhcCCCChhHHHHHHHHH
Q psy5629 85 NTLYHMGFTQDDKCEKILYEF 105 (203)
Q Consensus 85 dsl~~l~F~ee~~~~~vL~q~ 105 (203)
..|..-||+.+ ..+-.++-
T Consensus 83 ~~L~~kGi~~~--~I~~~l~~ 101 (157)
T PRK00117 83 QELRQKGVDRE--IIEEALAE 101 (157)
T ss_pred HHHHHcCCCHH--HHHHHHHH
Confidence 77888889877 55544443
No 77
>PF03333 PapB: Adhesin biosynthesis transcription regulatory protein; InterPro: IPR004356 P pili, or fimbriae, are ~68A in diameter and 1 micron in length, the bulk of which is a fibre composed of the main structural protein PapA []. At its tip, the pilus is terminated by a fibrillum consisting of repeating units of the PapE protein. This, in turn, is topped by the adhesins, PapF and PapG, both of which are needed for receptor binding. The tip fibrillum is anchored to the main PapA fibre by the PapK pilus-adaptor protein. PapH, an outer membrane protein, then anchors the entire rod in the bacterial envelope []. A cytoplasmic chaperone (PapD) assists in assembling the monomers of the macromolecule in the membrane. All of the functional pap genes are arranged in a cluster (operon) on the Escherichia coli genome. It is believed that selective pressure exerted by the host's urinal and intestinal tract isoreceptors forced the spread of this operon to other strains via lateral transfer []. PapB, encoded within the cluster, acts as a transcriptional regulator of the functional pap genes and is located in the bacterial cytoplasm []. Its mechanism involves differential binding to separate sites in the cluster, suggesting that this protein is both an activator and repressor of pilus-adhesion transcription. The protein shares similarity with other E. coli fimbrial- adhesion transcription regulators, such as AfaA, DaaA and FanB. ; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 3M8J_A.
Probab=24.45 E-value=1.2e+02 Score=23.28 Aligned_cols=52 Identities=17% Similarity=0.317 Sum_probs=28.4
Q ss_pred HhhhccccCCChHHHHHHHHHHHHHHhcCCchhhHHHHHhhcCCCchHHHHHHHHH
Q psy5629 10 REHLSVLFQLPPEVIQDFCTLTTNYLKDGPNQKLYKSVSKKLSLPSADNVQDSVEG 65 (203)
Q Consensus 10 kehL~fL~~~~~~vv~efckiAiefl~~G~n~K~y~~aA~KL~v~~~~~Vq~~Ve~ 65 (203)
.+|+.+|-++++=--.+...-=-|||+.|-+.| -|+++.||.. ...-.++.-
T Consensus 25 ~e~F~lLl~ls~IrS~kiI~AL~dyLV~G~srk---eac~~~gV~~-syfs~~L~r 76 (91)
T PF03333_consen 25 EEHFWLLLELSSIRSEKIIAALRDYLVDGLSRK---EACERHGVNQ-SYFSRALNR 76 (91)
T ss_dssp HHHHHHHHHHS----HHHHHHHHHHHTT---HH---HHHHHTT--H-HHHHHHHHH
T ss_pred HHHHHHHHHHCCCCcHHHHHHHHHHHHcCCcHH---HHHHHhCCCH-HHHHHHHHH
Confidence 456666665555444455555568999999888 8889999987 554444433
No 78
>PF00216 Bac_DNA_binding: Bacterial DNA-binding protein; InterPro: IPR000119 Bacteria synthesise a set of small, usually basic proteins of about 90 residues that bind DNA and are known as histone-like proteins [, ]. Examples include the HU protein in Escherichia coli is a dimer of closely related alpha and beta chains and in other bacteria can be a dimer of identical chains. HU-type proteins have been found in a variety of eubacteria, cyanobacteria and archaebacteria, and are also encoded in the chloroplast genome of some algae []. The integration host factor (IHF), a dimer of closely related chains which seem to function in genetic recombination as well as in translational and transcriptional control [] is found in enterobacteria and viral proteins include the African Swine fever virus protein A104R (or LMW5-AR) []. The exact function of these proteins is not yet clear but they are capable of wrapping DNA and stabilising it from denaturation under extreme environmental conditions. The structure is known for one of these proteins []. The protein exists as a dimer and two "beta-arms" function as the non-specific binding site for bacterial DNA. ; GO: 0003677 DNA binding; PDB: 3C4I_B 2O97_A 1MUL_A 1P78_A 1P51_C 1P71_B 2HT0_A 1OWG_A 2IIF_A 1OUZ_A ....
Probab=24.13 E-value=1.3e+02 Score=21.37 Aligned_cols=32 Identities=22% Similarity=0.296 Sum_probs=27.2
Q ss_pred hHHHHHhhcCCCchHHHHHHHHHHHHHHHHHhh
Q psy5629 43 LYKSVSKKLSLPSADNVQDSVEGLVYFLLLATI 75 (203)
Q Consensus 43 ~y~~aA~KL~v~~~~~Vq~~Ve~L~~Ll~essK 75 (203)
....+|++.+++. .+|...++++...+.+..+
T Consensus 6 li~~ia~~~~~s~-~~v~~vl~~~~~~i~~~L~ 37 (90)
T PF00216_consen 6 LIKRIAEKTGLSK-KDVEAVLDALFDVIKEALK 37 (90)
T ss_dssp HHHHHHHHHTSSH-HHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHhcCCCH-HHHHHHHHHHHHHHHHHHh
Confidence 4668889999999 9999999999998888654
No 79
>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=24.00 E-value=1.6e+02 Score=20.77 Aligned_cols=35 Identities=23% Similarity=0.433 Sum_probs=24.1
Q ss_pred HHHHh-cCCchhhHHHHHhhcCCCchHHHHHHHHHHH
Q psy5629 32 TNYLK-DGPNQKLYKSVSKKLSLPSADNVQDSVEGLV 67 (203)
Q Consensus 32 iefl~-~G~n~K~y~~aA~KL~v~~~~~Vq~~Ve~L~ 67 (203)
.+|+. +|-.| .+.-+|+.+|+.+-.+|++-+.+|-
T Consensus 16 ~~~~~~~G~~P-t~rEIa~~~g~~S~~tv~~~L~~Le 51 (65)
T PF01726_consen 16 REYIEENGYPP-TVREIAEALGLKSTSTVQRHLKALE 51 (65)
T ss_dssp HHHHHHHSS----HHHHHHHHTSSSHHHHHHHHHHHH
T ss_pred HHHHHHcCCCC-CHHHHHHHhCCCChHHHHHHHHHHH
Confidence 35555 45444 6788999999983299999998875
No 80
>cd08311 Death_p75NR Death domain of p75 Neurotophin Receptor. Death Domain (DD) found in p75 neurotrophin receptor (p75NTR, NGFR, TNFRSF16). p75NTR binds members of the neurotrophin (NT) family including nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF), and NT3, among others. It contains an NT-binding extracellular region that bears four cysteine-rich repeats, a transmembrane domain, and an intracellular DD. p75NTR plays roles in the immune, vascular, and nervous systems, and has been shown to promote cell death or survival, and to induce neurite outgrowth or collapse depending on its ligands and co-receptors. In general, 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 associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptor
Probab=23.85 E-value=83 Score=23.06 Aligned_cols=27 Identities=11% Similarity=0.260 Sum_probs=20.5
Q ss_pred hcCCchhhHHHHHhhcCCCchHHHHHHH
Q psy5629 36 KDGPNQKLYKSVSKKLSLPSADNVQDSV 63 (203)
Q Consensus 36 ~~G~n~K~y~~aA~KL~v~~~~~Vq~~V 63 (203)
..|.--+-|...|++||++. +.|++--
T Consensus 10 ~~~nlG~dW~~LA~~LG~~~-~~I~~i~ 36 (77)
T cd08311 10 ESGRPGRDWRSLAGELGYED-EAIDTFG 36 (77)
T ss_pred hCCCCccCHHHHHHHcCCCH-HHHHHHH
Confidence 33433566999999999999 8887654
No 81
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=23.76 E-value=92 Score=19.98 Aligned_cols=23 Identities=22% Similarity=0.323 Sum_probs=20.1
Q ss_pred CchhhHHHHHhhcCCCchHHHHHH
Q psy5629 39 PNQKLYKSVSKKLSLPSADNVQDS 62 (203)
Q Consensus 39 ~n~K~y~~aA~KL~v~~~~~Vq~~ 62 (203)
|+......+|..+|++. ..|+.=
T Consensus 25 P~~~~~~~la~~~~l~~-~qV~~W 47 (59)
T cd00086 25 PSREEREELAKELGLTE-RQVKIW 47 (59)
T ss_pred CCHHHHHHHHHHHCcCH-HHHHHH
Confidence 77778999999999999 988764
No 82
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=23.56 E-value=2.5e+02 Score=19.25 Aligned_cols=42 Identities=12% Similarity=0.201 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHHhcCCchhhHHHHHhhcCCCchHHHHHHHHHHH
Q psy5629 24 IQDFCTLTTNYLKDGPNQKLYKSVSKKLSLPSADNVQDSVEGLV 67 (203)
Q Consensus 24 v~efckiAiefl~~G~n~K~y~~aA~KL~v~~~~~Vq~~Ve~L~ 67 (203)
..+..+.-.+... +..+-.-..+|+.|||++ .+|-..+.-|.
T Consensus 6 ~e~YL~~Iy~l~~-~~~~v~~~~iA~~L~vs~-~tvt~ml~~L~ 47 (60)
T PF01325_consen 6 EEDYLKAIYELSE-EGGPVRTKDIAERLGVSP-PTVTEMLKRLA 47 (60)
T ss_dssp HHHHHHHHHHHHH-CTSSBBHHHHHHHHTS-H-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHc-CCCCccHHHHHHHHCCCh-HHHHHHHHHHH
Confidence 4455554444444 445555679999999999 88888877654
No 83
>PRK10664 transcriptional regulator HU subunit beta; Provisional
Probab=23.30 E-value=1.5e+02 Score=22.04 Aligned_cols=33 Identities=3% Similarity=0.073 Sum_probs=28.9
Q ss_pred hHHHHHhhcCCCchHHHHHHHHHHHHHHHHHhhc
Q psy5629 43 LYKSVSKKLSLPSADNVQDSVEGLVYFLLLATIL 76 (203)
Q Consensus 43 ~y~~aA~KL~v~~~~~Vq~~Ve~L~~Ll~essK~ 76 (203)
....+|++.|++. .++...|+++...+.++.+-
T Consensus 6 li~~ia~~~~~s~-~~~~~~v~~~~~~i~~~L~~ 38 (90)
T PRK10664 6 LIDKIAAGADISK-AAAGRALDAIIASVTESLKE 38 (90)
T ss_pred HHHHHHHHhCCCH-HHHHHHHHHHHHHHHHHHhC
Confidence 4668899999999 99999999999999987763
No 84
>PRK10086 DNA-binding transcriptional regulator DsdC; Provisional
Probab=23.27 E-value=1.6e+02 Score=25.48 Aligned_cols=45 Identities=16% Similarity=0.205 Sum_probs=34.0
Q ss_pred cccCCChHHHHHHHHHHHHHHhcCCchhhHHHHHhhcCCCchHHHHHHHHHHHH
Q psy5629 15 VLFQLPPEVIQDFCTLTTNYLKDGPNQKLYKSVSKKLSLPSADNVQDSVEGLVY 68 (203)
Q Consensus 15 fL~~~~~~vv~efckiAiefl~~G~n~K~y~~aA~KL~v~~~~~Vq~~Ve~L~~ 68 (203)
++.+.+..-+.-|+.+|- +..+..||+.|+++. .+|-+.+..|=.
T Consensus 10 ~~~~~~l~~L~~f~~va~--------~gs~s~AA~~L~iSQ-pavS~~I~~LE~ 54 (311)
T PRK10086 10 LLNGWQLSKLHTFEVAAR--------HQSFALAADELSLTP-SAVSHRINQLEE 54 (311)
T ss_pred hhcCCcHHHHHHHHHHHH--------cCCHHHHHHHHCCCH-HHHHHHHHHHHH
Confidence 455666666666666654 567889999999999 999888877743
No 85
>PF08440 Poty_PP: Potyviridae polyprotein; InterPro: IPR013648 This domain is found in polyproteins of the viral Potyviridae taxon. ; GO: 0003968 RNA-directed RNA polymerase activity, 0005198 structural molecule activity, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0018144 RNA-protein covalent cross-linking
Probab=23.23 E-value=2.1e+02 Score=26.01 Aligned_cols=73 Identities=14% Similarity=0.098 Sum_probs=49.0
Q ss_pred hhhhhhhhhcCCCChhHHHHHHHHHHHHHHHhHHHHhhhhhhheecccccccccCceEEEEEeecCCCcccccceeecCh
Q psy5629 81 YDFCNTLYHMGFTQDDKCEKILYEFYTQEKYNLYRTLISEYISVVATRSHLNQCEPKFTIRLHLENPDEQEKQIDLEMDV 160 (203)
Q Consensus 81 ~dF~dsl~~l~F~ee~~~~~vL~q~y~~~r~~I~r~iLs~~~vqiASRsl~~q~~P~vtmkL~l~~~~~~~~~~~LqTDp 160 (203)
.+-+--+..=|+||. .-.-||+.+.++|... +...+..-..+ +. -..|+|||
T Consensus 103 ~~vrIPF~~~dipe~--l~e~lw~~v~~~k~d~------------~f~r~~s~~a~-------------ki-AytLsTd~ 154 (274)
T PF08440_consen 103 DDVRIPFYVKDIPEK--LYEKLWEAVQKYKPDA------------GFGRISSVNAC-------------KI-AYTLSTDP 154 (274)
T ss_pred CCCeeceeeCCCCHH--HHHHHHHHHHHhCCcc------------cccccccCCcC-------------eE-EEEcccCh
Confidence 333334455688888 8899999999988877 11111111111 12 24789999
Q ss_pred hHHHHHHHHHHHHHHHhhhhh
Q psy5629 161 RSVLNITQILEEALSHAKLNQ 181 (203)
Q Consensus 161 ~~L~hl~~~LE~AL~e~kT~h 181 (203)
.++-.-+..++..|.+-++-+
T Consensus 155 ~sI~rTi~iId~Li~~e~~K~ 175 (274)
T PF08440_consen 155 HSIPRTIAIIDHLIEEERQKQ 175 (274)
T ss_pred HHHhHHHHHHHHHHHHHHHHH
Confidence 999999999999998866544
No 86
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=23.20 E-value=2.8e+02 Score=23.51 Aligned_cols=63 Identities=21% Similarity=0.237 Sum_probs=46.6
Q ss_pred hccccCCChHHHHHHHHHHHHHHhcCCchhh----HHHHHhhcCCCchHHHHHHHHHHHHHHHHHhhccC
Q psy5629 13 LSVLFQLPPEVIQDFCTLTTNYLKDGPNQKL----YKSVSKKLSLPSADNVQDSVEGLVYFLLLATILNI 78 (203)
Q Consensus 13 L~fL~~~~~~vv~efckiAiefl~~G~n~K~----y~~aA~KL~v~~~~~Vq~~Ve~L~~Ll~essK~~i 78 (203)
..-+.+++++-.+.|.+..-+.++.||.+++ |....-|.|-..++.+. +.|+-+++|++|-+|
T Consensus 92 ~ee~eeLs~deke~~~~sl~dL~~d~PkT~vA~~rfKk~~~K~g~~v~~~~~---dIlVdv~SEt~kK~i 158 (158)
T PF10083_consen 92 IEEDEELSPDEKEQFKESLPDLTKDTPKTKVAATRFKKILSKAGSIVGDAIR---DILVDVASETAKKSI 158 (158)
T ss_pred HHHhhcCCHHHHHHHHhhhHHHhhcCCccHHHHHHHHHHHHHHhHHHHHHHH---HHHHHHHHHHHHhhC
Confidence 3457788999899999999999999998874 66666666666544443 456788889888543
No 87
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=23.16 E-value=1.7e+02 Score=25.02 Aligned_cols=39 Identities=10% Similarity=0.134 Sum_probs=28.7
Q ss_pred ChHHHHHHHHHHHHHHhcCCchhhHHHHHhhcCCCchHHHHHHHHHHH
Q psy5629 20 PPEVIQDFCTLTTNYLKDGPNQKLYKSVSKKLSLPSADNVQDSVEGLV 67 (203)
Q Consensus 20 ~~~vv~efckiAiefl~~G~n~K~y~~aA~KL~v~~~~~Vq~~Ve~L~ 67 (203)
+..-+.-|+.+|- ...|..||++|+++. .+|-+.+..|=
T Consensus 5 ~l~~L~~F~~v~e--------~gs~s~AA~~L~isq-pavS~~I~~LE 43 (296)
T PRK11062 5 NYNHLYYFWMVCK--------EGSVVGAAEALFLTP-QTITGQIKALE 43 (296)
T ss_pred CHHHHHHHHHHHh--------cCCHHHHHHHhCCCh-HHHHHHHHHHH
Confidence 3344555555543 567889999999999 99999888773
No 88
>TIGR00122 birA_repr_reg BirA biotin operon repressor domain. This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.
Probab=23.06 E-value=1.4e+02 Score=20.35 Aligned_cols=32 Identities=19% Similarity=0.296 Sum_probs=25.1
Q ss_pred HHHhcCCchhhHHHHHhhcCCCchHHHHHHHHHHH
Q psy5629 33 NYLKDGPNQKLYKSVSKKLSLPSADNVQDSVEGLV 67 (203)
Q Consensus 33 efl~~G~n~K~y~~aA~KL~v~~~~~Vq~~Ve~L~ 67 (203)
+.+.+|+- ....+|+.+|++. .+|.+.+..|-
T Consensus 7 ~~L~~~~~--~~~eLa~~l~vS~-~tv~~~l~~L~ 38 (69)
T TIGR00122 7 ALLADNPF--SGEKLGEALGMSR-TAVNKHIQTLR 38 (69)
T ss_pred HHHHcCCc--CHHHHHHHHCCCH-HHHHHHHHHHH
Confidence 34666643 3789999999999 99999988874
No 89
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=22.92 E-value=1.4e+02 Score=21.32 Aligned_cols=46 Identities=9% Similarity=0.226 Sum_probs=26.3
Q ss_pred CCChHHHHHHHHHHHHHHhcC-CchhhHHHHHhhcCCCchHHHHHHHH
Q psy5629 18 QLPPEVIQDFCTLTTNYLKDG-PNQKLYKSVSKKLSLPSADNVQDSVE 64 (203)
Q Consensus 18 ~~~~~vv~efckiAiefl~~G-~n~K~y~~aA~KL~v~~~~~Vq~~Ve 64 (203)
...+..+..|..++.+|+.+= .....|...|.+-.+.. .+|..|.+
T Consensus 23 ~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~-~Dv~~Al~ 69 (77)
T smart00576 23 SFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNL-GDVVLALE 69 (77)
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCH-HHHHHHHH
Confidence 445556666777777776654 33344555555555555 55555543
No 90
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=22.79 E-value=1.1e+02 Score=21.12 Aligned_cols=32 Identities=16% Similarity=0.421 Sum_probs=19.3
Q ss_pred HHHhcCCchhhHHHHHhhcCCCchHHHHHHHHHH
Q psy5629 33 NYLKDGPNQKLYKSVSKKLSLPSADNVQDSVEGL 66 (203)
Q Consensus 33 efl~~G~n~K~y~~aA~KL~v~~~~~Vq~~Ve~L 66 (203)
+||..+... ...-+|+.+++++ ++|+..++-|
T Consensus 7 ~~l~~~~~~-S~~eLa~~~~~s~-~~ve~mL~~l 38 (69)
T PF09012_consen 7 DYLRERGRV-SLAELAREFGISP-EAVEAMLEQL 38 (69)
T ss_dssp HHHHHS-SE-EHHHHHHHTT--H-HHHHHHHHHH
T ss_pred HHHHHcCCc-CHHHHHHHHCcCH-HHHHHHHHHH
Confidence 556555433 3568999999999 7776665544
No 91
>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=22.68 E-value=1.6e+02 Score=20.86 Aligned_cols=32 Identities=16% Similarity=0.312 Sum_probs=26.4
Q ss_pred hHHHHHhhcCCCchHHHHHHHHHHHHHHHHHhh
Q psy5629 43 LYKSVSKKLSLPSADNVQDSVEGLVYFLLLATI 75 (203)
Q Consensus 43 ~y~~aA~KL~v~~~~~Vq~~Ve~L~~Ll~essK 75 (203)
....+|++.+++. .+|...++++...+.++..
T Consensus 5 l~~~ia~~~~~~~-~~v~~vl~~~~~~i~~~L~ 36 (87)
T cd00591 5 LIEAIAEKTGLSK-KDAEAAVDAFLDVITEALA 36 (87)
T ss_pred HHHHHHHHhCcCH-HHHHHHHHHHHHHHHHHHh
Confidence 4567888999999 8999999998888887655
No 92
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=22.39 E-value=1.8e+02 Score=18.52 Aligned_cols=25 Identities=8% Similarity=0.221 Sum_probs=18.8
Q ss_pred CchhhHHHHHhhcCCCchHHHHHHHH
Q psy5629 39 PNQKLYKSVSKKLSLPSADNVQDSVE 64 (203)
Q Consensus 39 ~n~K~y~~aA~KL~v~~~~~Vq~~Ve 64 (203)
-....|.-+|+.+|++. .+|.+-..
T Consensus 18 ~~~~t~~eIa~~lg~s~-~~V~~~~~ 42 (50)
T PF04545_consen 18 FEGLTLEEIAERLGISR-STVRRILK 42 (50)
T ss_dssp TST-SHHHHHHHHTSCH-HHHHHHHH
T ss_pred cCCCCHHHHHHHHCCcH-HHHHHHHH
Confidence 34455889999999999 88876543
No 93
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=22.27 E-value=2.6e+02 Score=19.59 Aligned_cols=42 Identities=14% Similarity=0.083 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHHHhcCCchhhHHHHHhhcCCCchHHHHHHHHH
Q psy5629 23 VIQDFCTLTTNYLKDGPNQKLYKSVSKKLSLPSADNVQDSVEG 65 (203)
Q Consensus 23 vv~efckiAiefl~~G~n~K~y~~aA~KL~v~~~~~Vq~~Ve~ 65 (203)
....+.+.++--+.+.-+.-.++..|+.++++. +.|+..+-.
T Consensus 6 l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~~-~~vE~~i~~ 47 (88)
T smart00088 6 LQRKIRLTNLLQLSEPYSSISLSDLAKLLGLSV-PEVEKLVSK 47 (88)
T ss_pred HHHHHHHHHHHHHhHHhceeeHHHHHHHhCcCH-HHHHHHHHH
Confidence 445555666555555445556889999999999 765554433
No 94
>smart00753 PAM PCI/PINT associated module.
Probab=22.27 E-value=2.6e+02 Score=19.59 Aligned_cols=42 Identities=14% Similarity=0.083 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHHHhcCCchhhHHHHHhhcCCCchHHHHHHHHH
Q psy5629 23 VIQDFCTLTTNYLKDGPNQKLYKSVSKKLSLPSADNVQDSVEG 65 (203)
Q Consensus 23 vv~efckiAiefl~~G~n~K~y~~aA~KL~v~~~~~Vq~~Ve~ 65 (203)
....+.+.++--+.+.-+.-.++..|+.++++. +.|+..+-.
T Consensus 6 l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~~-~~vE~~i~~ 47 (88)
T smart00753 6 LQRKIRLTNLLQLSEPYSSISLSDLAKLLGLSV-PEVEKLVSK 47 (88)
T ss_pred HHHHHHHHHHHHHhHHhceeeHHHHHHHhCcCH-HHHHHHHHH
Confidence 445555666555555445556889999999999 765554433
No 95
>PF05589 DUF768: Protein of unknown function (DUF768); InterPro: IPR008486 This family consists of several uncharacterised hypothetical proteins from Rhizobium loti (Mesorhizobium loti).
Probab=21.97 E-value=1.3e+02 Score=21.61 Aligned_cols=30 Identities=13% Similarity=0.227 Sum_probs=23.1
Q ss_pred hHHHHHhhcCCCchHHHHHHHHHHHHHHHHH
Q psy5629 43 LYKSVSKKLSLPSADNVQDSVEGLVYFLLLA 73 (203)
Q Consensus 43 ~y~~aA~KL~v~~~~~Vq~~Ve~L~~Ll~es 73 (203)
.+-..|+++|++. +.++.-|..+.-+..++
T Consensus 34 kl~adA~a~Gi~~-~ei~eEvg~i~e~I~~a 63 (64)
T PF05589_consen 34 KLFADAEAAGIPR-EEIEEEVGSIYEAILDA 63 (64)
T ss_pred HHHHHHHHcCCCH-HHHHHHhccHHHHHHhh
Confidence 3457889999999 88998888777666543
No 96
>KOG0478|consensus
Probab=21.84 E-value=1.2e+02 Score=31.40 Aligned_cols=88 Identities=15% Similarity=0.125 Sum_probs=65.3
Q ss_pred CeeecchhhHhhhccccCCChHHHHHHHHHHHHHHhcCCc---hh---hHHHHHhhcCCCchHHHHHHHHHHHHHHHHHh
Q psy5629 1 MIINLNESHREHLSVLFQLPPEVIQDFCTLTTNYLKDGPN---QK---LYKSVSKKLSLPSADNVQDSVEGLVYFLLLAT 74 (203)
Q Consensus 1 mll~Ls~~hkehL~fL~~~~~~vv~efckiAiefl~~G~n---~K---~y~~aA~KL~v~~~~~Vq~~Ve~L~~Ll~ess 74 (203)
||+.|++-|.++. +...+....|.|+.+++-+=|.--++ +. .|--+....-+.. ..++.-.+++..++...+
T Consensus 695 sLiRlsEahak~r-~s~~ve~~dV~eA~~l~R~aL~~~a~d~~tg~vd~~~l~tg~s~~~~-~~~~~~~~ai~~~l~~~~ 772 (804)
T KOG0478|consen 695 SLIRLSEAHAKMR-LSNRVEEIDVEEAVRLLREALKQSATDPATGKVDMDILATGNSVVSR-KKVEILGGAILKMLKDES 772 (804)
T ss_pred HHHHHHHHHHHhh-cccccchhhHHHHHHHHHHHhcccCCCCCCCceeehhhhhcccccch-HHHHHHHHHHHHHhHHHH
Confidence 4778888888765 77888888899998888777766543 22 1334444455556 889999999999999778
Q ss_pred hccCChhhhhhhhhhc
Q psy5629 75 ILNISEYDFCNTLYHM 90 (203)
Q Consensus 75 K~~ise~dF~dsl~~l 90 (203)
...+.+..|.+.+..+
T Consensus 773 ~~~~~~~~~~~al~~l 788 (804)
T KOG0478|consen 773 QKGIEEEMFLEALEEL 788 (804)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 8888888888766655
No 97
>PF11248 DUF3046: Protein of unknown function (DUF3046); InterPro: IPR021408 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=21.78 E-value=73 Score=22.93 Aligned_cols=34 Identities=12% Similarity=0.453 Sum_probs=29.8
Q ss_pred HHHHHHH-HHHHHHHhcCCchh-hHHHHHhhcCCCc
Q psy5629 22 EVIQDFC-TLTTNYLKDGPNQK-LYKSVSKKLSLPS 55 (203)
Q Consensus 22 ~vv~efc-kiAiefl~~G~n~K-~y~~aA~KL~v~~ 55 (203)
-|+.+++ +.|-+-|..|..+| ++..++.-+.||.
T Consensus 26 hvL~~LGgrT~~eAL~~G~dpr~VW~AlC~~~dVP~ 61 (63)
T PF11248_consen 26 HVLSELGGRTAAEALEAGVDPRDVWRALCDAFDVPE 61 (63)
T ss_pred cchhhcCCcCHHHHHHcCCCHHHHHHHHHHHcCCCC
Confidence 3788888 89999999998888 5999999999986
No 98
>PF01486 K-box: K-box region; InterPro: IPR002487 MADS genes in plants encode key developmental regulators of vegetative and reproductive development. The majority of the plant MADS proteins share a stereotypical MIKC structure. It comprises (from N- to C-terminal) an N-terminal domain, which is, however, present only in a minority of proteins; a MADS domain (see PDOC00302 from PROSITEDOC, IPR002100 from INTERPRO), which is the major determinant of DNA-binding but which also performs dimerisation and accessory factor binding functions; a weakly conserved intervening (I) domain, which constitutes a key molecular determinant for the selective formation of DNA-binding dimers; a keratin-like (K-box) domain, which promotes protein dimerisation; and a C-terminal (C) domain, which is involved in transcriptional activation or in the formation of ternary or quaternary protein complexes. The 80-amino acid K-box domain was originally identified as a region with low but significant similarity to a region of keratin, which is part of the coiled-coil sequence constituting the central rod-shaped domain of keratin [, , ]. The K-box protein-protein interaction domain which mediates heterodimerization of MIKC-type MADS proteins contains several heptad repeats in which the first and the fourth positions are occupied by hydrophobic amino acids suggesting that the K-box domain forms three amphipathic alpha-helices referred to as K1, K2, and K3 [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=21.61 E-value=1.2e+02 Score=22.72 Aligned_cols=38 Identities=16% Similarity=0.284 Sum_probs=30.9
Q ss_pred ecChhHHHHHHHHHHHHHHHhhhhh-hhhHhhhhhhhhh
Q psy5629 157 EMDVRSVLNITQILEEALSHAKLNQ-RKMSRRKQLSQTK 194 (203)
Q Consensus 157 qTDp~~L~hl~~~LE~AL~e~kT~h-RrI~R~~~~~~~~ 194 (203)
.+++..|..|=+.||.||..+++.. +.+...+..-+.|
T Consensus 45 ~Ls~~eL~~LE~~Le~aL~~VR~rK~~~l~~~i~~l~~k 83 (100)
T PF01486_consen 45 SLSLKELQQLEQQLESALKRVRSRKDQLLMEQIEELKKK 83 (100)
T ss_pred ccchHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHH
Confidence 5789999999999999999999998 7776655544443
No 99
>PF06784 UPF0240: Uncharacterised protein family (UPF0240); InterPro: IPR009622 This is a group of proteins of unknown function.
Probab=21.20 E-value=95 Score=26.32 Aligned_cols=35 Identities=9% Similarity=0.207 Sum_probs=26.6
Q ss_pred HHHHHHHHhcC-Cchhh--HHHHHhhcCCCchHHHHHHH
Q psy5629 28 CTLTTNYLKDG-PNQKL--YKSVSKKLSLPSADNVQDSV 63 (203)
Q Consensus 28 ckiAiefl~~G-~n~K~--y~~aA~KL~v~~~~~Vq~~V 63 (203)
.+-|++||.++ .++.. -+.+|+.++++. +.|.+..
T Consensus 120 l~qal~lL~~Hq~~P~~WtaekIA~eY~L~~-~dv~~iL 157 (179)
T PF06784_consen 120 LRQALELLNNHQLDPETWTAEKIAQEYKLDE-KDVKNIL 157 (179)
T ss_pred HHHHHHHHHHhccCccccCHHHHHHHhCCCH-HHHHHHH
Confidence 35689999988 44544 568999999999 8777643
No 100
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=21.12 E-value=3.3e+02 Score=22.60 Aligned_cols=72 Identities=17% Similarity=0.203 Sum_probs=41.1
Q ss_pred hHHHHHhhc----CCCchHHHHHHHHHHHHHHHHHhh-ccCChhhhhhhhhhcCCCChhHHHHHHHHHHHHHHHhHHHHh
Q psy5629 43 LYKSVSKKL----SLPSADNVQDSVEGLVYFLLLATI-LNISEYDFCNTLYHMGFTQDDKCEKILYEFYTQEKYNLYRTL 117 (203)
Q Consensus 43 ~y~~aA~KL----~v~~~~~Vq~~Ve~L~~Ll~essK-~~ise~dF~dsl~~l~F~ee~~~~~vL~q~y~~~r~~I~r~i 117 (203)
.|....+-+ ++++ .+|++.=...+.+=.++.. +...+.||-. .++|++++ .-+-+.+.-.+.|+.| ..+
T Consensus 78 ~y~~t~~~l~~~~~~~~-~avr~~h~q~~~lA~~al~~~p~~~R~~s~--~T~~vs~~--~~~ki~~~i~~fRk~i-~~i 151 (171)
T PF14394_consen 78 KYVQTDKSLTTSSEIPS-EAVRSYHKQMLELAQEALDRVPPEERDFSG--LTMSVSRE--DYEKIKKEIREFRKKI-IAI 151 (171)
T ss_pred cEEEecceeeCCCCCcH-HHHHHHHHHHHHHHHHHHHhCCccccceee--eEEEeCHH--HHHHHHHHHHHHHHHH-HHH
Confidence 344444444 3334 4444444444444455444 5566666653 56788877 6666677777778888 555
Q ss_pred hhh
Q psy5629 118 ISE 120 (203)
Q Consensus 118 Ls~ 120 (203)
.++
T Consensus 152 ~~~ 154 (171)
T PF14394_consen 152 AEE 154 (171)
T ss_pred Hhc
Confidence 444
No 101
>PF14842 FliG_N: FliG N-terminal domain; PDB: 3HJL_A 3AJC_A 3USY_B.
Probab=21.09 E-value=2.3e+02 Score=21.56 Aligned_cols=59 Identities=17% Similarity=0.205 Sum_probs=31.7
Q ss_pred HHHhhcCCCchHHHHHHHHHHHHHHHHHhhccCChhhhhhhhhhcCCCChhHHHHHHHHHH
Q psy5629 46 SVSKKLSLPSADNVQDSVEGLVYFLLLATILNISEYDFCNTLYHMGFTQDDKCEKILYEFY 106 (203)
Q Consensus 46 ~aA~KL~v~~~~~Vq~~Ve~L~~Ll~essK~~ise~dF~dsl~~l~F~ee~~~~~vL~q~y 106 (203)
.+|+-=+|++ +.+...++--........-......||-..++.-.|+++ +...+|.++.
T Consensus 41 ~ma~l~~v~~-~~~~~Vl~EF~~~~~~~~~~~~gg~~~~~~lL~~alg~~-~a~~il~~~~ 99 (108)
T PF14842_consen 41 EMAKLGSVSP-EEVEEVLEEFYDEIRAQGGIVSGGRDFARRLLEKALGEE-KAKEILDRLE 99 (108)
T ss_dssp HHHT-----H-HHHHHHHHHHHHHHHHTT---S-HHHHHHH-HHHHS----HHHHH-----
T ss_pred HHHccCCCCH-HHHHHHHHHHHHHHHHccccccChHHHHHHHHHHHCCHH-HHHHHHHHHh
Confidence 3444447888 999998888888777777788888999999998888887 4555554444
No 102
>PF00632 HECT: HECT-domain (ubiquitin-transferase); InterPro: IPR000569 The name HECT comes from 'Homologous to the E6-AP Carboxyl Terminus' []. Proteins containing this domain at the C terminus include ubiquitin-protein ligase, which regulates ubiquitination of CDC25. Ubiquitin-protein ligase accepts ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester, and then directly transfers the ubiquitin to targeted substrates. A cysteine residue is required for ubiquitin-thiolester formation. Human thyroid receptor interacting protein 12, which also contains this domain, is a component of an ATP-dependent multisubunit protein that interacts with the ligand binding domain of the thyroid hormone receptor. It could be an E3 ubiquitin-protein ligase. Human ubiquitin-protein ligase E3A interacts with the E6 protein of the cancer-associated Human papillomavirus type 16 and Human papillomavirus type 18. The E6/E6-AP complex binds to and targets the P53 tumour-suppressor protein for ubiquitin-mediated proteolysis.; GO: 0016881 acid-amino acid ligase activity, 0006464 protein modification process, 0005622 intracellular; PDB: 3TUG_A 1ZVD_A 1C4Z_C 1D5F_B 1ND7_A 2XBB_A 2XBF_A 3PT3_A 3G1N_B 3H1D_A ....
Probab=20.96 E-value=5.7e+02 Score=22.36 Aligned_cols=152 Identities=17% Similarity=0.232 Sum_probs=82.0
Q ss_pred CCChHHHHHHHHHHHHHHhcCCchhhHHHHHhhc--CCCchHHHHH-HHHHHHHHHHHHhhcc-CChhhhhhhhhhc-CC
Q psy5629 18 QLPPEVIQDFCTLTTNYLKDGPNQKLYKSVSKKL--SLPSADNVQD-SVEGLVYFLLLATILN-ISEYDFCNTLYHM-GF 92 (203)
Q Consensus 18 ~~~~~vv~efckiAiefl~~G~n~K~y~~aA~KL--~v~~~~~Vq~-~Ve~L~~Ll~essK~~-ise~dF~dsl~~l-~F 92 (203)
.|+.+.+.++++.+++|...+.-.+-++...+=+ -++. ..+.- ..+-|..++ |..-. ++-.+++.....- |+
T Consensus 142 ~Vt~~N~~eyv~~~~~~~l~~~~~~~~~~~r~Gf~~vi~~-~~l~~f~~~eL~~l~--~G~~~~i~~~~l~~~~~~~~g~ 218 (317)
T PF00632_consen 142 PVTNENKEEYVRLLAQYRLNESVKKQLEAFRKGFYSVIPL-ELLSLFSPEELERLL--CGSPEPIDVEDLKSNTRYEGGY 218 (317)
T ss_dssp B-TTTTHHHHHHHHHHHHHTTTTHHHHHHHHHHHHHHSSH-HHHTTSSHHHHHHHH--HCBSS---HHHHHHTEEEESSS
T ss_pred ccchhhhhHHHHhhhhhhcccccchhHHHHhcchhhcchh-HHHHcCCHHHHHHHh--cCccccCCHHHHHhcccchhcc
Confidence 3777889999999999888774444343332222 0111 11110 012222222 22334 8888888877765 88
Q ss_pred CChhHHHHHHHHHHHH-HHHhHHHHhhhhhhheecccccc----cccCceEEEEEeecCCCc-----cc--ccceeecCh
Q psy5629 93 TQDDKCEKILYEFYTQ-EKYNLYRTLISEYISVVATRSHL----NQCEPKFTIRLHLENPDE-----QE--KQIDLEMDV 160 (203)
Q Consensus 93 ~ee~~~~~vL~q~y~~-~r~~I~r~iLs~~~vqiASRsl~----~q~~P~vtmkL~l~~~~~-----~~--~~~~LqTDp 160 (203)
++++...+.||+...+ ...+. +..|.-.. |+..+- ....|.+++...-..+.+ +. ..+.|- +|
T Consensus 219 ~~~~~~i~~fw~vl~~~s~~~~-~~fL~F~T---G~~~lP~~G~~~l~~~i~i~~~~~~~~~~LP~a~TCf~~L~LP-~Y 293 (317)
T PF00632_consen 219 TESSPVIQWFWEVLEEFSQEER-RKFLRFVT---GSSRLPPGGFSNLNPKITIQFSDDSPDDRLPTAHTCFNTLKLP-RY 293 (317)
T ss_dssp -TTSHHHHHHHHHHHHS-HHHH-HHHHHHHH---SSSSB-TTGGGGGE-EEEEEEESC-STTS--EEEGGGTEEEEE-E-
T ss_pred ccccceeeEEeeeeccCCHHHh-heeEEEec---CCCCCCccccccccceeEEeecCCCccccCceecCcCCEEECC-CC
Confidence 8777799999999866 33444 55554442 111111 123377777665542121 11 123444 69
Q ss_pred hHHHHHHHHHHHHHHHh
Q psy5629 161 RSVLNITQILEEALSHA 177 (203)
Q Consensus 161 ~~L~hl~~~LE~AL~e~ 177 (203)
++-..|.+.|..|+.+.
T Consensus 294 ss~e~l~~kL~~Ai~~~ 310 (317)
T PF00632_consen 294 SSKEILREKLLYAIENG 310 (317)
T ss_dssp SSHHHHHHHHHHHHHHT
T ss_pred CCHHHHHHHHHHHHHcC
Confidence 99999999999999876
No 103
>PF00531 Death: Death domain; InterPro: IPR000488 The death domain (DD) is a homotypic protein interaction module composed of a bundle of six alpha-helices. DD is related in sequence and structure to the death effector domain (DED, see IPR001875 from INTERPRO) and the caspase recruitment domain (CARD, see IPR001315 from INTERPRO), which work in similar pathways and show similar interaction properties []. DD bind each other forming oligomers. Mammals have numerous and diverse DD-containing proteins []. Within these proteins, the DD domains can be found in combination with other domains, including: CARDs, DEDs, ankyrin repeats (IPR002110 from INTERPRO), caspase-like folds, kinase domains, leucine zippers (IPR002158 from INTERPRO), leucine-rich repeats (LRR) (IPR001611 from INTERPRO), TIR domains (IPR000157 from INTERPRO), and ZU5 domains (IPR000906 from INTERPRO) []. Some DD-containing proteins are involved in the regulation of apoptosis and inflammation through their activation of caspases and NF-kappaB, which typically involves interactions with TNF (tumour necrosis factor) cytokine receptors [, ]. In humans, eight of the over 30 known TNF receptors contain DD in their cytoplasmic tails; several of these TNF receptors use caspase activation as a signalling mechanism. The DD mediates self-association of these receptors, thus giving the signal to downstream events that lead to apoptosis. Other DD-containing proteins, such as ankyrin, MyD88 and pelle, are probably not directly involved in cell death signalling. DD-containing proteins also have links to innate immunity, communicating with Toll family receptors through bipartite adapter proteins such as MyD88 [].; GO: 0005515 protein binding, 0007165 signal transduction; PDB: 3OQ9_L 3EZQ_F 1E41_A 1E3Y_A 2GF5_A 2OF5_L 3EWV_E 3G5B_A 3MOP_L 2A9I_A ....
Probab=20.86 E-value=90 Score=21.55 Aligned_cols=27 Identities=19% Similarity=0.292 Sum_probs=18.7
Q ss_pred cCCchhhHHHHHhhcCCCchHHHHHHHH
Q psy5629 37 DGPNQKLYKSVSKKLSLPSADNVQDSVE 64 (203)
Q Consensus 37 ~G~n~K~y~~aA~KL~v~~~~~Vq~~Ve 64 (203)
.....+.|...|++||++. ..|+..-.
T Consensus 8 ~~~~~~~Wk~La~~Lg~~~-~~i~~i~~ 34 (83)
T PF00531_consen 8 AEDLGSDWKRLARKLGLSE-SEIENIEE 34 (83)
T ss_dssp HHSHSTCHHHHHHHTTS-H-HHHHHHHH
T ss_pred hhcchhhHHHHHHHhCcCH-HHHHHHHH
Confidence 3344566889999999998 77766543
No 104
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=20.54 E-value=1.7e+02 Score=24.23 Aligned_cols=47 Identities=19% Similarity=0.130 Sum_probs=32.3
Q ss_pred HHHHHHHHHHHHHHhcCCchh-hHHHHHhhc--CCCchHHHHHHHHHHHHH
Q psy5629 22 EVIQDFCTLTTNYLKDGPNQK-LYKSVSKKL--SLPSADNVQDSVEGLVYF 69 (203)
Q Consensus 22 ~vv~efckiAiefl~~G~n~K-~y~~aA~KL--~v~~~~~Vq~~Ve~L~~L 69 (203)
+.+.++-..|+.=|..=.+-+ -+..+|+++ +++. +.|+++++.|..+
T Consensus 19 ~~~~~W~~~~ir~l~~l~~~~~d~~~iak~l~p~is~-~ev~~sL~~L~~~ 68 (171)
T PF14394_consen 19 EYYSSWYHPAIRELLPLMPFAPDPEWIAKRLRPKISA-EEVRDSLEFLEKL 68 (171)
T ss_pred HHHhhhHHHHHHHHhhcCCCCCCHHHHHHHhcCCCCH-HHHHHHHHHHHHC
Confidence 344444455554444443333 678999999 9999 9999999877654
No 105
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
Probab=20.27 E-value=2e+02 Score=27.51 Aligned_cols=27 Identities=19% Similarity=0.459 Sum_probs=23.2
Q ss_pred hhHHHHHhhcCCCchHHHHHHHHHHHHH
Q psy5629 42 KLYKSVSKKLSLPSADNVQDSVEGLVYF 69 (203)
Q Consensus 42 K~y~~aA~KL~v~~~~~Vq~~Ve~L~~L 69 (203)
+.|..+|++++++. +.|+.+++-|-.|
T Consensus 183 ~~~~~i~~~l~is~-~~v~~~~~~I~~L 209 (429)
T TIGR02395 183 KDFRRLAKKLGLSE-EELKEALDLIKSL 209 (429)
T ss_pred ccHHHHHHHHCcCH-HHHHHHHHHHhCC
Confidence 46889999999999 9999999877654
No 106
>PRK14135 recX recombination regulator RecX; Provisional
Probab=20.11 E-value=5.7e+02 Score=22.01 Aligned_cols=77 Identities=10% Similarity=0.084 Sum_probs=50.4
Q ss_pred HHHHHHHHHHhcCCchh--hHHHHHhhcCCCchHHHHHHHHHHHH-----------HHHHH--hhccCChhhhhhhhhhc
Q psy5629 26 DFCTLTTNYLKDGPNQK--LYKSVSKKLSLPSADNVQDSVEGLVY-----------FLLLA--TILNISEYDFCNTLYHM 90 (203)
Q Consensus 26 efckiAiefl~~G~n~K--~y~~aA~KL~v~~~~~Vq~~Ve~L~~-----------Ll~es--sK~~ise~dF~dsl~~l 90 (203)
.--..|+.||...+.+. +++.+.+| |+++ +.|+.+++-|.. -++.+ .+-.-+......-|..-
T Consensus 58 ~a~~~Al~~L~~r~~s~~el~~kL~~k-g~~~-~~Ie~vl~~l~~~~~ldD~~~a~~~~~~~~~~~~~g~~~I~~kL~~k 135 (263)
T PRK14135 58 KGKNLALYYLSYQMRTEKEVRDYLKKH-EISE-EIISEVIDKLKEEKYIDDKEYAESYVRTNINTGDKGPRVIKQKLLQK 135 (263)
T ss_pred HHHHHHHHHhhhccccHHHHHHHHHHC-CCCH-HHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhccccchHHHHHHHHHc
Confidence 33457899999987766 34444444 9999 999999986632 22221 11234677777888888
Q ss_pred CCCChhHHHHHHHHHH
Q psy5629 91 GFTQDDKCEKILYEFY 106 (203)
Q Consensus 91 ~F~ee~~~~~vL~q~y 106 (203)
||+++ ..+-.++.+
T Consensus 136 Gi~~~--~Ie~~l~~l 149 (263)
T PRK14135 136 GIEDE--IIEEALSEY 149 (263)
T ss_pred CCCHH--HHHHHHHhC
Confidence 99988 655544433
Done!