Query 017623
Match_columns 368
No_of_seqs 111 out of 124
Neff 3.3
Searched_HMMs 46136
Date Fri Mar 29 10:15:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/017623.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/017623hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01589 A_thal_3526 uncharac 100.0 3.3E-32 7.2E-37 207.5 6.5 57 55-111 1-57 (57)
2 PF09713 A_thal_3526: Plant pr 100.0 3.6E-31 7.7E-36 200.0 5.7 54 58-111 1-54 (54)
3 KOG3973 Uncharacterized conser 78.6 4.3 9.4E-05 42.1 5.8 58 58-115 141-221 (465)
4 cd01111 HTH_MerD Helix-Turn-He 75.8 30 0.00064 29.1 9.1 38 44-82 33-70 (107)
5 KOG1924 RhoA GTPase effector D 73.5 63 0.0014 37.1 13.2 48 60-116 426-491 (1102)
6 cd04787 HTH_HMRTR_unk Helix-Tu 71.1 46 0.00099 28.7 9.4 69 45-125 34-102 (133)
7 PRK13749 transcriptional regul 69.7 53 0.0012 28.7 9.5 39 44-83 36-74 (121)
8 cd04777 HTH_MerR-like_sg1 Heli 68.5 66 0.0014 26.5 9.7 36 45-81 32-67 (107)
9 PF08145 BOP1NT: BOP1NT (NUC16 65.7 4.1 8.9E-05 40.2 2.1 36 48-88 209-244 (260)
10 PF14775 NYD-SP28_assoc: Sperm 64.6 27 0.00059 27.2 6.0 46 81-130 5-50 (60)
11 cd04781 HTH_MerR-like_sg6 Heli 62.7 94 0.002 26.2 10.6 36 45-81 33-68 (120)
12 TIGR02043 ZntR Zn(II)-responsi 60.7 1E+02 0.0022 26.6 9.5 37 44-81 34-70 (131)
13 PF13565 HTH_32: Homeodomain-l 60.1 28 0.0006 26.4 5.4 39 59-97 37-77 (77)
14 cd04784 HTH_CadR-PbrR Helix-Tu 58.8 1.1E+02 0.0024 25.9 9.8 70 44-125 33-102 (127)
15 TIGR02047 CadR-PbrR Cd(II)/Pb( 58.8 1.2E+02 0.0025 26.1 10.0 72 44-127 33-104 (127)
16 PF04340 DUF484: Protein of un 58.8 5.4 0.00012 36.9 1.5 9 100-108 17-25 (225)
17 TIGR02044 CueR Cu(I)-responsiv 58.8 1.1E+02 0.0025 25.9 9.9 71 44-127 33-104 (127)
18 PF04741 InvH: InvH outer memb 58.3 33 0.00071 31.2 6.2 68 59-126 42-124 (147)
19 PF08986 DUF1889: Domain of un 57.7 13 0.00027 32.7 3.5 35 74-108 67-110 (119)
20 TIGR02051 MerR Hg(II)-responsi 57.5 1.1E+02 0.0024 26.1 9.1 68 44-125 32-99 (124)
21 PRK15002 redox-sensitivie tran 56.3 1.2E+02 0.0027 27.3 9.6 78 44-132 43-120 (154)
22 smart00411 BHL bacterial (prok 55.5 16 0.00034 28.8 3.4 30 70-99 1-30 (90)
23 PF14420 Clr5: Clr5 domain 54.2 53 0.0011 24.6 5.9 36 53-88 3-39 (54)
24 PRK13752 putative transcriptio 52.7 1.4E+02 0.003 26.5 9.2 70 44-127 40-109 (144)
25 COG1725 Predicted transcriptio 50.8 17 0.00037 32.3 3.2 47 54-100 13-62 (125)
26 cd01040 globin Globins are hem 50.4 1E+02 0.0023 24.8 7.6 39 86-125 19-68 (140)
27 cd01110 HTH_SoxR Helix-Turn-He 50.0 1.8E+02 0.0039 25.5 10.2 79 44-133 33-111 (139)
28 PF13720 Acetyltransf_11: Udp 49.5 29 0.00063 28.2 4.2 46 47-92 25-70 (83)
29 PRK14137 recX recombination re 47.0 63 0.0014 30.3 6.5 68 29-101 13-85 (195)
30 cd04789 HTH_Cfa Helix-Turn-Hel 46.7 1.6E+02 0.0035 24.3 8.2 36 44-80 33-68 (102)
31 PF14769 CLAMP: Flagellar C1a 44.8 93 0.002 25.7 6.5 51 48-98 10-73 (101)
32 cd01108 HTH_CueR Helix-Turn-He 43.9 2E+02 0.0044 24.5 9.8 36 44-80 33-68 (127)
33 cd01109 HTH_YyaN Helix-Turn-He 43.4 1.9E+02 0.0041 24.0 8.9 38 44-82 33-70 (113)
34 PF12776 Myb_DNA-bind_3: Myb/S 40.9 60 0.0013 25.5 4.7 43 86-132 26-68 (96)
35 PF00784 MyTH4: MyTH4 domain; 40.2 66 0.0014 26.8 5.1 45 54-98 2-48 (114)
36 PF13411 MerR_1: MerR HTH fami 40.0 44 0.00096 24.7 3.6 37 44-81 32-68 (69)
37 PF10045 DUF2280: Uncharacteri 40.0 1.6E+02 0.0036 25.8 7.4 55 57-111 7-69 (104)
38 PRK10227 DNA-binding transcrip 39.8 2.6E+02 0.0056 24.5 10.0 70 44-126 33-103 (135)
39 PF00216 Bac_DNA_binding: Bact 39.7 30 0.00065 27.0 2.8 27 70-96 1-27 (90)
40 cd04765 HTH_MlrA-like_sg2 Heli 39.6 1.4E+02 0.0029 24.8 6.7 39 44-83 33-72 (99)
41 PRK10963 hypothetical protein; 39.5 57 0.0012 30.7 5.0 20 70-108 3-22 (223)
42 TIGR01950 SoxR redox-sensitive 39.5 2.7E+02 0.0059 24.6 9.6 78 44-132 33-110 (142)
43 cd04763 HTH_MlrA-like Helix-Tu 39.2 72 0.0016 23.9 4.7 35 44-79 33-67 (68)
44 cd04783 HTH_MerR1 Helix-Turn-H 36.8 2.6E+02 0.0057 23.7 8.4 38 44-82 33-70 (126)
45 cd01282 HTH_MerR-like_sg3 Heli 36.6 2.5E+02 0.0055 23.4 9.6 71 44-125 32-104 (112)
46 PF04910 Tcf25: Transcriptiona 35.9 85 0.0019 31.7 5.9 74 54-132 55-130 (360)
47 cd01106 HTH_TipAL-Mta Helix-Tu 35.5 2.5E+02 0.0053 22.9 8.8 63 44-125 33-96 (103)
48 TIGR02054 MerD mercuric resist 35.4 3E+02 0.0065 23.9 8.9 36 44-80 36-71 (120)
49 cd04788 HTH_NolA-AlbR Helix-Tu 35.2 2.3E+02 0.005 23.0 7.4 36 44-80 33-68 (96)
50 TIGR00988 hip integration host 35.2 52 0.0011 26.5 3.5 29 70-98 1-30 (94)
51 PF10632 He_PIG_assoc: He_PIG 34.3 15 0.00033 25.6 0.3 10 322-331 9-18 (29)
52 COG4399 Uncharacterized protei 33.9 64 0.0014 33.6 4.7 64 54-118 84-150 (376)
53 cd04769 HTH_MerR2 Helix-Turn-H 33.2 2.9E+02 0.0063 23.1 10.1 37 46-83 34-70 (116)
54 TIGR00987 himA integration hos 32.5 57 0.0012 26.6 3.4 28 70-97 2-29 (96)
55 smart00352 POU Found in Pit-Oc 32.5 2.5E+02 0.0055 23.2 7.1 64 53-118 8-71 (75)
56 smart00139 MyTH4 Domain in Myo 32.1 1.1E+02 0.0024 27.0 5.4 47 52-98 42-90 (144)
57 PF03979 Sigma70_r1_1: Sigma-7 31.1 64 0.0014 25.8 3.4 48 53-101 4-52 (82)
58 PRK10664 transcriptional regul 30.3 66 0.0014 26.4 3.4 19 70-88 1-19 (90)
59 PRK12461 UDP-N-acetylglucosami 30.2 98 0.0021 29.7 5.1 45 46-90 196-240 (255)
60 PRK14552 C/D box methylation g 29.9 64 0.0014 33.7 4.0 50 46-95 222-272 (414)
61 PRK00199 ihfB integration host 29.7 72 0.0016 25.8 3.6 29 70-98 1-30 (94)
62 COG3415 Transposase and inacti 29.7 1.1E+02 0.0024 27.6 5.0 53 45-101 59-111 (138)
63 PRK00285 ihfA integration host 29.6 67 0.0015 26.2 3.4 29 69-97 2-30 (99)
64 PRK07194 fliG flagellar motor 29.1 2E+02 0.0044 28.7 7.2 70 47-125 166-242 (334)
65 KOG2211 Predicted Golgi transp 28.9 1.5E+02 0.0032 33.6 6.7 76 59-134 329-412 (797)
66 cd01105 HTH_GlnR-like Helix-Tu 28.8 99 0.0022 24.9 4.2 38 45-83 35-72 (88)
67 COG5107 RNA14 Pre-mRNA 3'-end 28.8 1.3E+02 0.0029 32.9 6.1 77 51-130 88-177 (660)
68 PF06413 Neugrin: Neugrin; In 28.4 67 0.0015 31.0 3.6 49 42-95 3-51 (225)
69 PLN02849 beta-glucosidase 28.3 61 0.0013 34.4 3.6 46 63-112 115-171 (503)
70 KOG4721 Serine/threonine prote 28.1 1.9E+02 0.004 32.8 7.2 62 64-132 403-466 (904)
71 cd04764 HTH_MlrA-like_sg1 Heli 28.1 1.2E+02 0.0027 22.5 4.3 35 44-79 32-66 (67)
72 cd04774 HTH_YfmP Helix-Turn-He 27.8 1.7E+02 0.0037 24.0 5.5 37 44-81 32-69 (96)
73 PF13551 HTH_29: Winged helix- 27.6 1.7E+02 0.0037 23.0 5.3 50 50-100 58-111 (112)
74 TIGR01795 CM_mono_cladeE monof 27.5 97 0.0021 25.8 4.0 24 78-101 59-82 (94)
75 cd04790 HTH_Cfa-like_unk Helix 27.4 4.3E+02 0.0093 24.0 8.4 37 44-81 34-70 (172)
76 cd04752 Commd4 COMM_Domain con 27.2 97 0.0021 28.1 4.3 61 61-128 51-111 (174)
77 cd02433 Nodulin-21_like_2 Nodu 27.2 1.1E+02 0.0023 29.5 4.7 55 53-111 83-137 (234)
78 PRK15014 6-phospho-beta-glucos 27.1 80 0.0017 33.2 4.2 38 73-111 113-161 (477)
79 PF05402 PqqD: Coenzyme PQQ sy 27.0 99 0.0021 23.0 3.7 35 61-95 21-56 (68)
80 PLN02814 beta-glucosidase 26.2 77 0.0017 33.6 3.9 45 64-112 114-169 (504)
81 PF13592 HTH_33: Winged helix- 26.2 48 0.001 25.0 1.8 42 55-97 7-48 (60)
82 TIGR00207 fliG flagellar motor 26.2 1.9E+02 0.0042 29.0 6.5 71 48-126 170-246 (338)
83 PLN02998 beta-glucosidase 25.8 74 0.0016 33.7 3.7 45 64-112 119-174 (497)
84 cd04770 HTH_HMRTR Helix-Turn-H 25.4 4E+02 0.0087 22.2 9.7 71 44-126 33-103 (123)
85 cd01104 HTH_MlrA-CarA Helix-Tu 25.3 1.6E+02 0.0034 21.7 4.4 34 45-79 34-67 (68)
86 PF15369 KIAA1328: Uncharacter 25.3 3.2E+02 0.0069 28.3 7.8 73 52-133 4-86 (328)
87 KOG3303 Predicted alpha-helica 24.9 1.6E+02 0.0035 28.3 5.3 46 63-110 76-122 (192)
88 cd04785 HTH_CadR-PbrR-like Hel 24.9 4.4E+02 0.0094 22.4 11.1 71 44-126 33-103 (126)
89 PRK10753 transcriptional regul 24.8 95 0.0021 25.3 3.4 19 70-88 1-19 (90)
90 PF14164 YqzH: YqzH-like prote 24.4 1E+02 0.0022 24.9 3.4 14 56-69 4-17 (64)
91 KOG0871 Class 2 transcription 23.8 6.1E+02 0.013 23.8 9.0 22 114-135 102-130 (156)
92 PF12980 DUF3864: Domain of Un 23.7 21 0.00045 29.7 -0.6 32 81-112 49-80 (82)
93 COG1427 Predicted periplasmic 23.4 1.9E+02 0.0041 28.7 5.8 60 54-116 182-248 (252)
94 PF03399 SAC3_GANP: SAC3/GANP/ 22.6 2.2E+02 0.0049 25.1 5.6 58 58-126 55-123 (204)
95 smart00229 RasGEFN Guanine nuc 22.4 2.1E+02 0.0046 23.5 5.1 64 65-128 35-110 (127)
96 PF11417 Inhibitor_G39P: Loade 22.4 67 0.0015 25.9 2.1 18 70-87 1-18 (71)
97 PRK14135 recX recombination re 22.4 2.8E+02 0.006 26.1 6.5 46 54-100 106-152 (263)
98 cd07313 terB_like_2 tellurium 22.2 2.2E+02 0.0048 22.7 5.1 29 47-77 13-41 (104)
99 PF12295 Symplekin_C: Sympleki 21.9 1.5E+02 0.0033 27.3 4.6 61 67-127 9-86 (183)
100 COG1725 Predicted transcriptio 21.8 1.3E+02 0.0029 26.7 4.0 30 53-82 90-119 (125)
101 PF09763 Sec3_C: Exocyst compl 21.7 2.3E+02 0.0051 30.7 6.6 49 62-110 632-693 (701)
102 PRK09589 celA 6-phospho-beta-g 21.7 1.1E+02 0.0024 32.1 4.0 45 64-112 105-160 (476)
103 COG4359 Uncharacterized conser 21.1 82 0.0018 30.6 2.7 26 67-92 56-81 (220)
104 PF09278 MerR-DNA-bind: MerR, 21.1 3.5E+02 0.0075 19.9 8.1 56 60-126 5-60 (65)
105 PRK05686 fliG flagellar motor 20.9 3E+02 0.0065 27.4 6.7 71 48-126 172-249 (339)
106 PF04358 DsrC: DsrC like prote 20.7 1.8E+02 0.0038 25.2 4.4 34 73-109 25-58 (109)
No 1
>TIGR01589 A_thal_3526 uncharacterized plant-specific domain TIGR01589. This model represents an uncharacterized plant-specific domain 57 residues in length. It is found toward the N-terminus of most proteins that contain it. Examples include at least 10 proteins from Arabidopsis thaliana and at least one from Oryza sativa.
Probab=99.97 E-value=3.3e-32 Score=207.50 Aligned_cols=57 Identities=54% Similarity=0.898 Sum_probs=55.9
Q ss_pred HHHHHHHHHHHHHhhcCHHHHHHHHHHhcCCCCcchHHHHHHHHHHcHHHHHHHHHH
Q 017623 55 IELVQNLIERCLQLYMNRDEVVKTLLTRARIDPGFTTLVWQKLEEENADFFRAYYIR 111 (368)
Q Consensus 55 I~~VQnLIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~VW~kLEeeNpeFFkaYy~R 111 (368)
|++|||||||||++||||+|||++|++||||+|+||++||++||+||||||+|||+|
T Consensus 1 i~~Vq~lIE~Cl~~yMsk~E~v~~L~~~a~I~P~~T~~VW~~LekeN~eFF~aY~~~ 57 (57)
T TIGR01589 1 IDLVQNRIETCIQGYMSKEETVSFLFENAGISPKFTRFVWYLLEKENADFFRCYKTH 57 (57)
T ss_pred CHHHHHHHHHHHHHHCCHHHHHHHHHHHcCCCchhHHHHHHHHHHHHHHHHHHHhcC
Confidence 789999999999999999999999999999999999999999999999999999986
No 2
>PF09713 A_thal_3526: Plant protein 1589 of unknown function (A_thal_3526); InterPro: IPR006476 This plant-specific family of proteins are defined by an uncharacterised region 57 residues in length. It is found toward the N terminus of most proteins that contain it. Examples include at least several proteins from Arabidopsis thaliana (Mouse-ear cress) and Oryza sativa (Rice). The function of the proteins are unknown.
Probab=99.97 E-value=3.6e-31 Score=199.95 Aligned_cols=54 Identities=65% Similarity=1.147 Sum_probs=53.2
Q ss_pred HHHHHHHHHHhhcCHHHHHHHHHHhcCCCCcchHHHHHHHHHHcHHHHHHHHHH
Q 017623 58 VQNLIERCLQLYMNRDEVVKTLLTRARIDPGFTTLVWQKLEEENADFFRAYYIR 111 (368)
Q Consensus 58 VQnLIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~VW~kLEeeNpeFFkaYy~R 111 (368)
||+||||||++||||+|||++|++||||+|.||.+||++||+||||||+|||+|
T Consensus 1 Vq~lIErCl~~yMsk~E~v~~L~~~a~I~P~~T~~VW~~Le~eN~eFF~aY~~r 54 (54)
T PF09713_consen 1 VQNLIERCLQLYMSKEECVRALQKQANIEPVFTSTVWQKLEKENPEFFKAYYTR 54 (54)
T ss_pred CchHHHHHHHHcCCHHHHHHHHHHHcCCChHHHHHHHHHHHHHCHHHHHHhhcC
Confidence 799999999999999999999999999999999999999999999999999987
No 3
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=78.59 E-value=4.3 Score=42.11 Aligned_cols=58 Identities=24% Similarity=0.514 Sum_probs=39.1
Q ss_pred HHHHHH-HHHHhhcCHH-------HHHHHHHHh-----cCCCCc----------chHHHHHHHHHHcHHHHHHHHHHHHH
Q 017623 58 VQNLIE-RCLQLYMNRD-------EVVKTLLTR-----ARIDPG----------FTTLVWQKLEEENADFFRAYYIRLKL 114 (368)
Q Consensus 58 VQnLIE-rCLqlyMsk~-------Evv~~L~~~-----a~I~P~----------fT~~VW~kLEeeNpeFFkaYy~Rl~L 114 (368)
|+.+|+ -|..|.|.|- ...++|.++ +++.|. ++..-|.+||++|.+|=+.||.|+.|
T Consensus 141 v~q~i~~~~~~L~~~k~p~Nin~~~lfe~i~~kl~~ai~kv~p~~~~~PLlKkpl~~a~w~~iE~~~~~~~~ey~~Rr~l 220 (465)
T KOG3973|consen 141 VTQLIDSALRTLNFPKQPGNINEWKLFETIRQKLDGAIKKVSPSQRSHPLLKKPLDEATWPEIEKQCESFSREYYNRRLL 220 (465)
T ss_pred HHHHHHHHHHHcCCCCCCCCchHHHHHHHHHHHHHhHHhcCCHhhcCCchhcCcCChhhHHHHHHHHHHHHHHHHHHHHH
Confidence 556665 6777777652 223333222 345443 45788999999999999999998765
Q ss_pred H
Q 017623 115 K 115 (368)
Q Consensus 115 K 115 (368)
-
T Consensus 221 l 221 (465)
T KOG3973|consen 221 L 221 (465)
T ss_pred H
Confidence 3
No 4
>cd01111 HTH_MerD Helix-Turn-Helix DNA binding domain of the MerD transcription regulator. Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs,
Probab=75.81 E-value=30 Score=29.10 Aligned_cols=38 Identities=5% Similarity=0.088 Sum_probs=31.4
Q ss_pred CCCCCcccHHhHHHHHHHHHHHHHhhcCHHHHHHHHHHh
Q 017623 44 SNDSRKVSRQDIELVQNLIERCLQLYMNRDEVVKTLLTR 82 (368)
Q Consensus 44 ~~~~r~vS~edI~~VQnLIErCLqlyMsk~Evv~~L~~~ 82 (368)
.+..|..+.+|+..++ +|..|.++.|+.+||-+.|...
T Consensus 33 ~~g~R~Y~~~~l~~l~-~I~~lr~~G~~l~~I~~~l~~~ 70 (107)
T cd01111 33 EGGYGLFDDCALQRLR-FVRAAFEAGIGLDELARLCRAL 70 (107)
T ss_pred CCCCeecCHHHHHHHH-HHHHHHHcCCCHHHHHHHHHHH
Confidence 4678899999999987 5566777999999999988643
No 5
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=73.52 E-value=63 Score=37.13 Aligned_cols=48 Identities=25% Similarity=0.483 Sum_probs=29.6
Q ss_pred HHHHHHHHhhcCHHHHHHHHHHhcCCCCcchHHH------------------HHHHHHHcHHHHHHHHHHHHHHH
Q 017623 60 NLIERCLQLYMNRDEVVKTLLTRARIDPGFTTLV------------------WQKLEEENADFFRAYYIRLKLKK 116 (368)
Q Consensus 60 nLIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~V------------------W~kLEeeNpeFFkaYy~Rl~LK~ 116 (368)
.|||.|+... +..+-+++|.|+.-- -++-|++-.||-|.|..-+.-++
T Consensus 426 kLIEecISqI---------vlHr~~~DPdf~yr~~l~id~~~liD~~vdkak~eeseqkA~e~~kk~~ke~ta~q 491 (1102)
T KOG1924|consen 426 KLIEECISQI---------VLHRTGMDPDFKYRFRLDIDLTELIDKMVDKAKAEESEQKAAELEKKFDKELTARQ 491 (1102)
T ss_pred HHHHHHHHHH---------HHhcCCCCCCcchhhcccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHH
Confidence 3677776543 567788888887532 33445566677777765554443
No 6
>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators. Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules, such as, metal ions, drugs, and organic substrates. This subgroup lacks one of the c
Probab=71.05 E-value=46 Score=28.66 Aligned_cols=69 Identities=17% Similarity=0.154 Sum_probs=45.1
Q ss_pred CCCCcccHHhHHHHHHHHHHHHHhhcCHHHHHHHHHHhcCCCCcchHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHH
Q 017623 45 NDSRKVSRQDIELVQNLIERCLQLYMNRDEVVKTLLTRARIDPGFTTLVWQKLEEENADFFRAYYIRLKLKKQILLFNHL 124 (368)
Q Consensus 45 ~~~r~vS~edI~~VQnLIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~VW~kLEeeNpeFFkaYy~Rl~LK~QI~~FN~L 124 (368)
++-|..+.+++..+ .+|.++-.+-|+.+||-+.|.... -...-...++..|++ .+-.|.+||.+...+
T Consensus 34 ~gyR~Y~~~~~~~l-~~I~~lr~~G~sL~eI~~~l~~~~-~~~~~~~~~~~~l~~----------~~~~l~~~i~~l~~~ 101 (133)
T cd04787 34 NGYRLYSEKDLSRL-RFILSARQLGFSLKDIKEILSHAD-QGESPCPMVRRLIEQ----------RLAETERRIKELLKL 101 (133)
T ss_pred CCeeeCCHHHHHHH-HHHHHHHHcCCCHHHHHHHHhhhc-cCCCcHHHHHHHHHH----------HHHHHHHHHHHHHHH
Confidence 56689999999998 588899999999999988775332 222222233333333 234566666666554
Q ss_pred H
Q 017623 125 L 125 (368)
Q Consensus 125 l 125 (368)
+
T Consensus 102 ~ 102 (133)
T cd04787 102 R 102 (133)
T ss_pred H
Confidence 4
No 7
>PRK13749 transcriptional regulator MerD; Provisional
Probab=69.67 E-value=53 Score=28.70 Aligned_cols=39 Identities=3% Similarity=0.054 Sum_probs=34.1
Q ss_pred CCCCCcccHHhHHHHHHHHHHHHHhhcCHHHHHHHHHHhc
Q 017623 44 SNDSRKVSRQDIELVQNLIERCLQLYMNRDEVVKTLLTRA 83 (368)
Q Consensus 44 ~~~~r~vS~edI~~VQnLIErCLqlyMsk~Evv~~L~~~a 83 (368)
.|.-|..+.+++..+ .+|.+|..+-|+.+||-..|.-..
T Consensus 36 ~~gyR~Y~~~~l~rL-~~I~~~r~~G~sL~eI~~ll~l~~ 74 (121)
T PRK13749 36 TGGYGLFDDAALQRL-CFVRAAFEAGIGLDALARLCRALD 74 (121)
T ss_pred CCCCccCCHHHHHHH-HHHHHHHHcCCCHHHHHHHHhhhc
Confidence 467899999999999 589999999999999998886543
No 8
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=68.52 E-value=66 Score=26.49 Aligned_cols=36 Identities=11% Similarity=-0.030 Sum_probs=30.5
Q ss_pred CCCCcccHHhHHHHHHHHHHHHHhhcCHHHHHHHHHH
Q 017623 45 NDSRKVSRQDIELVQNLIERCLQLYMNRDEVVKTLLT 81 (368)
Q Consensus 45 ~~~r~vS~edI~~VQnLIErCLqlyMsk~Evv~~L~~ 81 (368)
++.|..+.+++..++ +|.++-++-|+.+||-+.|..
T Consensus 32 ~g~r~Y~~~~~~~l~-~I~~lr~~G~sL~eI~~~l~~ 67 (107)
T cd04777 32 GGQYFFDEKCQDDLE-FILELKGLGFSLIEIQKIFSY 67 (107)
T ss_pred CCccccCHHHHHHHH-HHHHHHHCCCCHHHHHHHHHh
Confidence 456789999998876 889999999999999987753
No 9
>PF08145 BOP1NT: BOP1NT (NUC169) domain; InterPro: IPR012953 WD-40 repeats (also known as WD or beta-transducin repeats) are short ~40 amino acid motifs, often terminating in a Trp-Asp (W-D) dipeptide. WD40 repeats usually assume a 7-8 bladed beta-propeller fold, but proteins have been found with 4 to 16 repeated units, which also form a circularised beta-propeller structure. WD-repeat proteins are a large family found in all eukaryotes and are implicated in a variety of functions ranging from signal transduction and transcription regulation to cell cycle control and apoptosis. Repeated WD40 motifs act as a site for protein-protein interaction, and proteins containing WD40 repeats are known to serve as platforms for the assembly of protein complexes or mediators of transient interplay among other proteins. The specificity of the proteins is determined by the sequences outside the repeats themselves. Examples of such complexes are G proteins (beta subunit is a beta-propeller), TAFII transcription factor, and E3 ubiquitin ligase [, ]. In Arabidopsis spp., several WD40-containing proteins act as key regulators of plant-specific developmental events. This N-terminal domain is found in BOP1-like WD40 proteins. Bop1 is a nucleolar protein involved in rRNA processing, thereby controlling the cell cycle []. It is required for the maturation of the 25S and 5.8S ribosomal RNAs. It may serve as an essential factor in ribosome formation that coordinates processing of the spacer regions in pre-rRNA. The Pes1-Bop1 complex has several components: BOP1, GRWD1, PES1, ORC6L, and RPL3 and is involved in ribosome biogenesis and altered chromosome segregation. The overexpression of BOP1 increases the percentage of multipolar spindles in human cells. Deregulation of the BOP1 pathway may contribute to colorectal tumourigenesis in humans []. Elevated levels of Bop1 induces Bop1/WDR12 and Bop1/Pes1 subcomplexes and the assembly and integrity of the PeBoW complex is highly sensitive to changes in Bop1 protein levels []. Nop7p-Erb1p-Ytm1p, found in yeast, is potentially the homologous complex of Pes1-Bop1-WDR12 as it is involved in the control of ribosome biogenesis and S phase entry. The integrity of the PeBoW complex is required for ribosome biogenesis and cell proliferation in mammalian cells []. In Giardia, the species specific cytoskeleton protein, beta-giardin, interacts with Bop1 []. ; GO: 0006364 rRNA processing, 0005634 nucleus
Probab=65.68 E-value=4.1 Score=40.16 Aligned_cols=36 Identities=36% Similarity=0.618 Sum_probs=27.6
Q ss_pred CcccHHhHHHHHHHHHHHHHhhcCHHHHHHHHHHhcCCCCc
Q 017623 48 RKVSRQDIELVQNLIERCLQLYMNRDEVVKTLLTRARIDPG 88 (368)
Q Consensus 48 r~vS~edI~~VQnLIErCLqlyMsk~Evv~~L~~~a~I~P~ 88 (368)
|+|- .|=..|+..-||||.|||- =++...+.+|+|.
T Consensus 209 R~Vp-~Y~~~i~ErFeRCLDLYLc----PR~~k~rlnidPe 244 (260)
T PF08145_consen 209 RKVP-AYENFIKERFERCLDLYLC----PRVRKKRLNIDPE 244 (260)
T ss_pred hccc-hHHHHHHHHHHHhhhhhcC----cHhhcccCCCCHH
Confidence 4444 5778899999999999984 4555678888884
No 10
>PF14775 NYD-SP28_assoc: Sperm tail C-terminal domain
Probab=64.64 E-value=27 Score=27.20 Aligned_cols=46 Identities=24% Similarity=0.355 Sum_probs=37.5
Q ss_pred HhcCCCCcchHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 017623 81 TRARIDPGFTTLVWQKLEEENADFFRAYYIRLKLKKQILLFNHLLEHQYH 130 (368)
Q Consensus 81 ~~a~I~P~fT~~VW~kLEeeNpeFFkaYy~Rl~LK~QI~~FN~Lle~Q~~ 130 (368)
+-++|=|.=+.-+|+-|+. |++.|+.-|.=|..|..=+.-|++|..
T Consensus 5 ~~~~vip~~~~~~W~~L~~----~l~rY~~vL~~R~~l~~e~~~L~~qN~ 50 (60)
T PF14775_consen 5 RLANVIPDEKIRLWDALEN----FLKRYNKVLLDRAALIQEKESLEQQNE 50 (60)
T ss_pred HHhhcCChHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567889999999999985 888898888888887777777887764
No 11
>cd04781 HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, an
Probab=62.66 E-value=94 Score=26.21 Aligned_cols=36 Identities=19% Similarity=0.119 Sum_probs=32.1
Q ss_pred CCCCcccHHhHHHHHHHHHHHHHhhcCHHHHHHHHHH
Q 017623 45 NDSRKVSRQDIELVQNLIERCLQLYMNRDEVVKTLLT 81 (368)
Q Consensus 45 ~~~r~vS~edI~~VQnLIErCLqlyMsk~Evv~~L~~ 81 (368)
++.|..+.++|..++ +|..|-.+-|+.+||.+.|..
T Consensus 33 ~gyR~Y~~~~l~~l~-~I~~lr~~G~~L~eI~~~l~~ 68 (120)
T cd04781 33 GLRRQYDPQVLDRLA-LIALGRAAGFSLDEIQAMLSH 68 (120)
T ss_pred CCceecCHHHHHHHH-HHHHHHHcCCCHHHHHHHHhc
Confidence 477899999999997 999999999999999987754
No 12
>TIGR02043 ZntR Zn(II)-responsive transcriptional regulator. This model represents the zinc and cadmium (II) responsive transcriptional activator of the gamma proteobacterial zinc efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-Cys-X(8-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=60.71 E-value=1e+02 Score=26.63 Aligned_cols=37 Identities=19% Similarity=0.235 Sum_probs=31.3
Q ss_pred CCCCCcccHHhHHHHHHHHHHHHHhhcCHHHHHHHHHH
Q 017623 44 SNDSRKVSRQDIELVQNLIERCLQLYMNRDEVVKTLLT 81 (368)
Q Consensus 44 ~~~~r~vS~edI~~VQnLIErCLqlyMsk~Evv~~L~~ 81 (368)
.+.-|..+.+||..++ +|-++-.+-|+.+||...|..
T Consensus 34 ~~gyR~Y~~~~l~~l~-~I~~lr~~G~sl~eI~~~l~~ 70 (131)
T TIGR02043 34 DSGYRLYTDEDQKRLR-FILKAKELGFTLDEIKELLSI 70 (131)
T ss_pred CCCceecCHHHHHHHH-HHHHHHHcCCCHHHHHHHHHh
Confidence 4567899999999987 566789999999999998864
No 13
>PF13565 HTH_32: Homeodomain-like domain
Probab=60.12 E-value=28 Score=26.37 Aligned_cols=39 Identities=15% Similarity=0.095 Sum_probs=26.8
Q ss_pred HHHHHHHHHh-hcCHHHHHHHHHHhcCCCC-cchHHHHHHH
Q 017623 59 QNLIERCLQL-YMNRDEVVKTLLTRARIDP-GFTTLVWQKL 97 (368)
Q Consensus 59 QnLIErCLql-yMsk~Evv~~L~~~a~I~P-~fT~~VW~kL 97 (368)
+.+|+-+... .++.+++...|.++++|.. .=-.+||+-|
T Consensus 37 ~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~~~S~~tv~R~L 77 (77)
T PF13565_consen 37 ERIIALIEEHPRWTPREIAEYLEEEFGISVRVSRSTVYRIL 77 (77)
T ss_pred HHHHHHHHhCCCCCHHHHHHHHHHHhCCCCCccHhHHHHhC
Confidence 3444443333 7999999999999999874 3345677643
No 14
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=58.81 E-value=1.1e+02 Score=25.86 Aligned_cols=70 Identities=24% Similarity=0.273 Sum_probs=47.2
Q ss_pred CCCCCcccHHhHHHHHHHHHHHHHhhcCHHHHHHHHHHhcCCCCcchHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHH
Q 017623 44 SNDSRKVSRQDIELVQNLIERCLQLYMNRDEVVKTLLTRARIDPGFTTLVWQKLEEENADFFRAYYIRLKLKKQILLFNH 123 (368)
Q Consensus 44 ~~~~r~vS~edI~~VQnLIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~VW~kLEeeNpeFFkaYy~Rl~LK~QI~~FN~ 123 (368)
.+.-|..+.+||..++- |.++-.+-|+.+||-+.|... -.+..+..-|..+-++ .+-.|.+||.....
T Consensus 33 ~~gyR~Y~~~~l~~l~~-I~~lr~~G~sL~eI~~~l~~~--~~~~~~~~~~~~~l~~---------~~~~l~~~i~~L~~ 100 (127)
T cd04784 33 ANNYRLYDEEHLERLLF-IRRCRSLDMSLDEIRTLLQLQ--DDPEASCAEVNALIDE---------HLAHVRARIAELQA 100 (127)
T ss_pred CCCCeecCHHHHHHHHH-HHHHHHcCCCHHHHHHHHHhh--hcCCCcHHHHHHHHHH---------HHHHHHHHHHHHHH
Confidence 35678999999999874 788889999999999877532 2344454555443221 33446667776655
Q ss_pred HH
Q 017623 124 LL 125 (368)
Q Consensus 124 Ll 125 (368)
+.
T Consensus 101 ~~ 102 (127)
T cd04784 101 LE 102 (127)
T ss_pred HH
Confidence 44
No 15
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator. This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=58.79 E-value=1.2e+02 Score=26.07 Aligned_cols=72 Identities=21% Similarity=0.281 Sum_probs=47.6
Q ss_pred CCCCCcccHHhHHHHHHHHHHHHHhhcCHHHHHHHHHHhcCCCCcchHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHH
Q 017623 44 SNDSRKVSRQDIELVQNLIERCLQLYMNRDEVVKTLLTRARIDPGFTTLVWQKLEEENADFFRAYYIRLKLKKQILLFNH 123 (368)
Q Consensus 44 ~~~~r~vS~edI~~VQnLIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~VW~kLEeeNpeFFkaYy~Rl~LK~QI~~FN~ 123 (368)
.|+-|..+.++|..++ +|.++-.+.|+.+||-..|.... .+..+..-|.++-++ .+-.|++||.....
T Consensus 33 ~~gyR~Y~~~~l~~l~-~I~~lr~lG~sL~eI~~~l~~~~--~~~~~~~~~~~~l~~---------~~~~l~~~i~~L~~ 100 (127)
T TIGR02047 33 DNNYRVYTVGHVERLA-FIRNCRTLDMSLAEIRQLLRYQD--KPEKSCSDVNALLDE---------HISHVRARIIKLQA 100 (127)
T ss_pred CCCCCcCCHHHHHHHH-HHHHHHHcCCCHHHHHHHHHhhh--CCCCCHHHHHHHHHH---------HHHHHHHHHHHHHH
Confidence 4678899999999987 67778899999999988775322 344444434332222 34456667776665
Q ss_pred HHHH
Q 017623 124 LLEH 127 (368)
Q Consensus 124 Lle~ 127 (368)
+.+.
T Consensus 101 ~~~~ 104 (127)
T TIGR02047 101 LIEQ 104 (127)
T ss_pred HHHH
Confidence 5543
No 16
>PF04340 DUF484: Protein of unknown function, DUF484; InterPro: IPR007435 This family consists of several proteins of uncharacterised function.; PDB: 3E98_B.
Probab=58.79 E-value=5.4 Score=36.93 Aligned_cols=9 Identities=33% Similarity=0.722 Sum_probs=0.0
Q ss_pred HcHHHHHHH
Q 017623 100 ENADFFRAY 108 (368)
Q Consensus 100 eNpeFFkaY 108 (368)
+|||||..|
T Consensus 17 ~~PdFf~~~ 25 (225)
T PF04340_consen 17 QHPDFFERH 25 (225)
T ss_dssp ---------
T ss_pred hCcHHHHhC
Confidence 677777777
No 17
>TIGR02044 CueR Cu(I)-responsive transcriptional regulator. This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue.
Probab=58.75 E-value=1.1e+02 Score=25.94 Aligned_cols=71 Identities=18% Similarity=0.235 Sum_probs=47.6
Q ss_pred CCCCCcccHHhHHHHHHHHHHHHHhhcCHHHHHHHHHHhcCCCCcchHHHHH-HHHHHcHHHHHHHHHHHHHHHHHHHHH
Q 017623 44 SNDSRKVSRQDIELVQNLIERCLQLYMNRDEVVKTLLTRARIDPGFTTLVWQ-KLEEENADFFRAYYIRLKLKKQILLFN 122 (368)
Q Consensus 44 ~~~~r~vS~edI~~VQnLIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~VW~-kLEeeNpeFFkaYy~Rl~LK~QI~~FN 122 (368)
.++.|..+.++|..|+ +|-++-.+-|+.+||-+.|.... ++..+..-|. .|++ .+-.|.++|....
T Consensus 33 ~~gyR~Y~~~~l~~l~-~I~~lr~~G~sL~eI~~~l~~~~--~~~~~~~~~~~~l~~----------~~~~l~~~i~~L~ 99 (127)
T TIGR02044 33 EGGYRTYTQQHLDELR-LISRARQVGFSLEECKELLNLWN--DPNRTSADVKARTLE----------KVAEIERKISELQ 99 (127)
T ss_pred CCCCeecCHHHHHHHH-HHHHHHHCCCCHHHHHHHHHhhc--cCCCCHHHHHHHHHH----------HHHHHHHHHHHHH
Confidence 5678999999999998 88889999999999988775322 2223322222 2322 3455777777666
Q ss_pred HHHHH
Q 017623 123 HLLEH 127 (368)
Q Consensus 123 ~Lle~ 127 (368)
.+.+.
T Consensus 100 ~~~~~ 104 (127)
T TIGR02044 100 SMRDQ 104 (127)
T ss_pred HHHHH
Confidence 65543
No 18
>PF04741 InvH: InvH outer membrane lipoprotein; InterPro: IPR006830 This family represents the Salmonella outer membrane lipoprotein InvH. The molecular function of this protein is unknown, but it is required for the localisation to outer membrane of InvG, which is involved in a type III secretion apparatus mediating host cell invasion [, ].; GO: 0009405 pathogenesis
Probab=58.28 E-value=33 Score=31.21 Aligned_cols=68 Identities=22% Similarity=0.385 Sum_probs=47.7
Q ss_pred HHHHHHHHHhhcCHHHHH--HHHHHh---------cCCCCcchHHHHHHHHHHcHHHHHHH--HHHHHHHHHH--HHHHH
Q 017623 59 QNLIERCLQLYMNRDEVV--KTLLTR---------ARIDPGFTTLVWQKLEEENADFFRAY--YIRLKLKKQI--LLFNH 123 (368)
Q Consensus 59 QnLIErCLqlyMsk~Evv--~~L~~~---------a~I~P~fT~~VW~kLEeeNpeFFkaY--y~Rl~LK~QI--~~FN~ 123 (368)
-+-|.+|..+-+-..+.. ++|.++ -.|.-.+-.--++++.++-..||..+ |+|-+.++|+ .+||+
T Consensus 42 a~sid~c~slpyvps~l~~nktlsn~~s~ns~SknntIsSs~fcEky~q~~~qA~tFFqEHPeYm~s~e~EeqL~~EF~~ 121 (147)
T PF04741_consen 42 ADSIDECMSLPYVPSDLAKNKTLSNQNSDNSASKNNTISSSIFCEKYKQTKEQAFTFFQEHPEYMRSKEDEEQLMAEFKQ 121 (147)
T ss_pred cccHHHHHcCCCCchHHhhcccccccccccccccccchhhHHHHHHHHHHHHHHHHHHHHChHHHhhhHHHHHHHHHHHH
Confidence 356889988876666654 345433 22333333445678889999999998 8999999987 48988
Q ss_pred HHH
Q 017623 124 LLE 126 (368)
Q Consensus 124 Lle 126 (368)
+|-
T Consensus 122 Vl~ 124 (147)
T PF04741_consen 122 VLL 124 (147)
T ss_pred HHc
Confidence 773
No 19
>PF08986 DUF1889: Domain of unknown function (DUF1889); InterPro: IPR015079 This family consist of hypothetical bacterial proteins. ; PDB: 2JN8_A 2ES9_A.
Probab=57.74 E-value=13 Score=32.68 Aligned_cols=35 Identities=29% Similarity=0.549 Sum_probs=22.8
Q ss_pred HHHHHHHHhcCCCCcchHHH--HHHH-------HHHcHHHHHHH
Q 017623 74 EVVKTLLTRARIDPGFTTLV--WQKL-------EEENADFFRAY 108 (368)
Q Consensus 74 Evv~~L~~~a~I~P~fT~~V--W~kL-------EeeNpeFFkaY 108 (368)
+-|.+--+|-|-+|+||..| |.+- --.|||||..|
T Consensus 67 ~dv~aRg~qeGWn~gFT~k~agwaeki~sG~rivIKnPEyFs~Y 110 (119)
T PF08986_consen 67 ADVTARGEQEGWNPGFTEKVAGWAEKIASGERIVIKNPEYFSSY 110 (119)
T ss_dssp HHHHHHHHHCT--HHHHHHHHHHHHHHHCT-----SSGGGS-HH
T ss_pred HHHHHhcccccCChhHHHHHHHHHHHHhcCCeeeecChHHHHHH
Confidence 34445667899999999987 5432 24799999999
No 20
>TIGR02051 MerR Hg(II)-responsive transcriptional regulator. This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=57.46 E-value=1.1e+02 Score=26.10 Aligned_cols=68 Identities=10% Similarity=0.067 Sum_probs=45.5
Q ss_pred CCCCCcccHHhHHHHHHHHHHHHHhhcCHHHHHHHHHHhcCCCCcchHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHH
Q 017623 44 SNDSRKVSRQDIELVQNLIERCLQLYMNRDEVVKTLLTRARIDPGFTTLVWQKLEEENADFFRAYYIRLKLKKQILLFNH 123 (368)
Q Consensus 44 ~~~~r~vS~edI~~VQnLIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~VW~kLEeeNpeFFkaYy~Rl~LK~QI~~FN~ 123 (368)
.+.-|..+.++|..++ +|-..-.+.|+.+||-+.|..... .+..-|..+-+ ..+-.|++||.....
T Consensus 32 ~~g~R~Y~~~~l~~l~-~I~~l~~~G~sl~eI~~~l~~~~~----~~~~~~~~~l~---------~~~~~l~~~i~~L~~ 97 (124)
T TIGR02051 32 EGGYRRYPEETVKRLR-FIKRAQELGFSLEEIGGLLGLVDG----THCREMYELAS---------RKLKSVQAKMADLLR 97 (124)
T ss_pred CCCCEeECHHHHHHHH-HHHHHHHCCCCHHHHHHHHhcccC----CCHHHHHHHHH---------HHHHHHHHHHHHHHH
Confidence 4567889999999996 888899999999999998854332 11222222211 233456777777665
Q ss_pred HH
Q 017623 124 LL 125 (368)
Q Consensus 124 Ll 125 (368)
+.
T Consensus 98 ~~ 99 (124)
T TIGR02051 98 IE 99 (124)
T ss_pred HH
Confidence 54
No 21
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=56.27 E-value=1.2e+02 Score=27.33 Aligned_cols=78 Identities=14% Similarity=0.229 Sum_probs=51.5
Q ss_pred CCCCCcccHHhHHHHHHHHHHHHHhhcCHHHHHHHHHHhcCCCCcchHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHH
Q 017623 44 SNDSRKVSRQDIELVQNLIERCLQLYMNRDEVVKTLLTRARIDPGFTTLVWQKLEEENADFFRAYYIRLKLKKQILLFNH 123 (368)
Q Consensus 44 ~~~~r~vS~edI~~VQnLIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~VW~kLEeeNpeFFkaYy~Rl~LK~QI~~FN~ 123 (368)
.+..|..+.++|..+ .+|.+|-.+-|+.+||-+.|..... .+..+...|..+-++ .+..|.+||.....
T Consensus 43 ~~g~R~Y~~~~i~~L-~~I~~lr~lG~sL~eIk~ll~~~~~-~~~~~~~~~~~ll~~---------k~~~l~~~I~~L~~ 111 (154)
T PRK15002 43 SGNQRRYKRDVLRYV-AIIKIAQRIGIPLATIGEAFGVLPE-GHTLSAKEWKQLSSQ---------WREELDRRIHTLVA 111 (154)
T ss_pred CCCCEEECHHHHHHH-HHHHHHHHcCCCHHHHHHHHHHhhc-CCCCCHHHHHHHHHH---------HHHHHHHHHHHHHH
Confidence 345699999999988 5899999999999999887753211 122223334443322 34578888888877
Q ss_pred HHHHHHhhh
Q 017623 124 LLEHQYHLM 132 (368)
Q Consensus 124 Lle~Q~~lm 132 (368)
+++.=.+++
T Consensus 112 ~~~~L~~~i 120 (154)
T PRK15002 112 LRDELDGCI 120 (154)
T ss_pred HHHHHHHHH
Confidence 765544444
No 22
>smart00411 BHL bacterial (prokaryotic) histone like domain.
Probab=55.51 E-value=16 Score=28.81 Aligned_cols=30 Identities=13% Similarity=0.231 Sum_probs=23.4
Q ss_pred cCHHHHHHHHHHhcCCCCcchHHHHHHHHH
Q 017623 70 MNRDEVVKTLLTRARIDPGFTTLVWQKLEE 99 (368)
Q Consensus 70 Msk~Evv~~L~~~a~I~P~fT~~VW~kLEe 99 (368)
||++|+++.|.++.++...-...|++.|.+
T Consensus 1 mtk~eli~~ia~~~~~~~~~v~~vl~~l~~ 30 (90)
T smart00411 1 MTKSELIDAIAEKAGLSKKDAKAAVDAFLE 30 (90)
T ss_pred CCHHHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 899999999999988876666666655443
No 23
>PF14420 Clr5: Clr5 domain
Probab=54.15 E-value=53 Score=24.65 Aligned_cols=36 Identities=19% Similarity=0.184 Sum_probs=28.8
Q ss_pred HhHHHHHHHHHHHH-HhhcCHHHHHHHHHHhcCCCCc
Q 017623 53 QDIELVQNLIERCL-QLYMNRDEVVKTLLTRARIDPG 88 (368)
Q Consensus 53 edI~~VQnLIErCL-qlyMsk~Evv~~L~~~a~I~P~ 88 (368)
++-...+..|+++- ...++.+||++.|.+++|..+.
T Consensus 3 ~~We~~K~~I~~LY~~e~~tl~~v~~~M~~~~~F~at 39 (54)
T PF14420_consen 3 EDWEPHKEEIERLYIDENKTLEEVMEIMKEEHGFKAT 39 (54)
T ss_pred chHHHHHHHHHHHHHhCCCcHHHHHHHHHHHhCCCcC
Confidence 45666777886544 6788999999999999988876
No 24
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=52.67 E-value=1.4e+02 Score=26.50 Aligned_cols=70 Identities=13% Similarity=0.129 Sum_probs=45.7
Q ss_pred CCCCCcccHHhHHHHHHHHHHHHHhhcCHHHHHHHHHHhcCCCCcchHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHH
Q 017623 44 SNDSRKVSRQDIELVQNLIERCLQLYMNRDEVVKTLLTRARIDPGFTTLVWQKLEEENADFFRAYYIRLKLKKQILLFNH 123 (368)
Q Consensus 44 ~~~~r~vS~edI~~VQnLIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~VW~kLEeeNpeFFkaYy~Rl~LK~QI~~FN~ 123 (368)
.|.-|-.+.++|..++ +|-++..+-|+.+||-+.|....+ . +...|..|-+ ..+-.|++||.....
T Consensus 40 ~~gyR~Y~~~~l~rl~-~I~~lr~~G~sL~eI~~ll~~~~~---~-~~~~~~~ll~---------~k~~~l~~~i~~L~~ 105 (144)
T PRK13752 40 YGSIRRYGEADVTRVR-FVKSAQRLGFSLDEIAELLRLEDG---T-HCEEASSLAE---------HKLKDVREKMADLAR 105 (144)
T ss_pred CCCCeecCHHHHHHHH-HHHHHHHcCCCHHHHHHHHhccCC---C-CHHHHHHHHH---------HHHHHHHHHHHHHHH
Confidence 4567899999999987 678899999999999987753221 1 1122222221 133557777777666
Q ss_pred HHHH
Q 017623 124 LLEH 127 (368)
Q Consensus 124 Lle~ 127 (368)
+...
T Consensus 106 ~~~~ 109 (144)
T PRK13752 106 MEAV 109 (144)
T ss_pred HHHH
Confidence 5543
No 25
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=50.82 E-value=17 Score=32.25 Aligned_cols=47 Identities=17% Similarity=0.261 Sum_probs=41.9
Q ss_pred hHHHHHHHHHHHHHhhcCHHH---HHHHHHHhcCCCCcchHHHHHHHHHH
Q 017623 54 DIELVQNLIERCLQLYMNRDE---VVKTLLTRARIDPGFTTLVWQKLEEE 100 (368)
Q Consensus 54 dI~~VQnLIErCLqlyMsk~E---vv~~L~~~a~I~P~fT~~VW~kLEee 100 (368)
|.+.++.+++.|+.--+...| -|+.|..+.+|.|..+.-++++||++
T Consensus 13 Y~QI~~qIk~~I~~g~l~pGdkLPSvRelA~~~~VNpnTv~raY~eLE~e 62 (125)
T COG1725 13 YEQIANQIKEQIASGELKPGDKLPSVRELAKDLGVNPNTVQRAYQELERE 62 (125)
T ss_pred HHHHHHHHHHHHHhCCcCCCCCCCcHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 667788888999998888777 48999999999999999999999976
No 26
>cd01040 globin Globins are heme proteins, which bind and transport oxygen. This family summarizes a diverse set of homologous protein domains, including: (1) tetrameric vertebrate hemoglobins, which are the major protein component of erythrocytes and transport oxygen in the bloodstream, (2) microorganismal flavohemoglobins, which are linked to C-terminal FAD-dependend reductase domains, (3) homodimeric bacterial hemoglobins, such as from Vitreoscilla, (4) plant leghemoglobins (symbiotic hemoglobins, involved in nitrogen metabolism in plant rhizomes), (5) plant non-symbiotic hexacoordinate globins and hexacoordinate globins from bacteria and animals, such as neuroglobin, (6) invertebrate hemoglobins, which may occur in tandem-repeat arrangements, and (7) monomeric myoglobins found in animal muscle tissue.
Probab=50.35 E-value=1e+02 Score=24.80 Aligned_cols=39 Identities=18% Similarity=0.213 Sum_probs=25.9
Q ss_pred CCcchHHHHHHHHHHcHHHHHHHHHHH-----------HHHHHHHHHHHHH
Q 017623 86 DPGFTTLVWQKLEEENADFFRAYYIRL-----------KLKKQILLFNHLL 125 (368)
Q Consensus 86 ~P~fT~~VW~kLEeeNpeFFkaYy~Rl-----------~LK~QI~~FN~Ll 125 (368)
...+...+|.+|-+++|++ +.|+.+. .++.|..+|=..|
T Consensus 19 ~~~~g~~~f~~lf~~~P~~-~~~F~~~~~~~~~~~~~~~~~~~~~~~~~~l 68 (140)
T cd01040 19 REEIGLEFYERLFKAHPET-RALFSRFGGLSAALKGSPKFKAHGKRVLNAL 68 (140)
T ss_pred HHhHHHHHHHHHHHHChhH-HHHhHHhCCchHhHccCHHHHHHHHHHHHHH
Confidence 3445566888999999988 4555554 6777766554444
No 27
>cd01110 HTH_SoxR Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator. Helix-turn-helix (HTH) transcriptional regulator SoxR. The global regulator, SoxR, up-regulates gene expression of another transcription activator, SoxS, which directly stimulates the oxidative stress regulon genes in E. coli. The soxRS response renders the bacterial cell resistant to superoxide-generating agents, macrophage-generated nitric oxide, organic solvents, and antibiotics. The SoxR proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the unusually long spacer between the -35 and -10 promoter elements. They also harbor a regulatory C-terminal domain containing an iron-sulfur center.
Probab=50.04 E-value=1.8e+02 Score=25.52 Aligned_cols=79 Identities=19% Similarity=0.274 Sum_probs=53.3
Q ss_pred CCCCCcccHHhHHHHHHHHHHHHHhhcCHHHHHHHHHHhcCCCCcchHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHH
Q 017623 44 SNDSRKVSRQDIELVQNLIERCLQLYMNRDEVVKTLLTRARIDPGFTTLVWQKLEEENADFFRAYYIRLKLKKQILLFNH 123 (368)
Q Consensus 44 ~~~~r~vS~edI~~VQnLIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~VW~kLEeeNpeFFkaYy~Rl~LK~QI~~FN~ 123 (368)
.+..|..+.+|+..++ +|..+..+-|+.+||-+.|.... -...-+...|.++.++. +-.|++||.....
T Consensus 33 ~~g~R~Y~~~dl~~l~-~I~~lr~~G~sl~eI~~~l~~~~-~~~~~~~~~~~~~l~~~---------~~~l~~~i~~L~~ 101 (139)
T cd01110 33 AGNQRRYPRDVLRRIA-FIKVAQRLGLSLAEIAEALATLP-EDRTPTKADWERLSRAW---------RDRLDERIAELQQ 101 (139)
T ss_pred CCCCeEECHHHHHHHH-HHHHHHHcCCCHHHHHHHHHHhc-cCCCCCHHHHHHHHHHH---------HHHHHHHHHHHHH
Confidence 3567889999999987 55677889999999998875322 12223445565554332 3458888888887
Q ss_pred HHHHHHhhhc
Q 017623 124 LLEHQYHLMK 133 (368)
Q Consensus 124 Lle~Q~~lm~ 133 (368)
+...=.+++.
T Consensus 102 ~~~~L~~~i~ 111 (139)
T cd01110 102 LRDQLDGCIG 111 (139)
T ss_pred HHHHHHHHHh
Confidence 7755444443
No 28
>PF13720 Acetyltransf_11: Udp N-acetylglucosamine O-acyltransferase; Domain 2; PDB: 3I3A_A 3I3X_A 3HSQ_B 2JF2_A 1LXA_A 2AQ9_A 2QIV_X 2QIA_A 2JF3_A 4EQY_F ....
Probab=49.52 E-value=29 Score=28.18 Aligned_cols=46 Identities=13% Similarity=0.192 Sum_probs=35.5
Q ss_pred CCcccHHhHHHHHHHHHHHHHhhcCHHHHHHHHHHhcCCCCcchHH
Q 017623 47 SRKVSRQDIELVQNLIERCLQLYMNRDEVVKTLLTRARIDPGFTTL 92 (368)
Q Consensus 47 ~r~vS~edI~~VQnLIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~ 92 (368)
++.+|.++|..++.....-+...++.+|.++.|.+...=.|.+...
T Consensus 25 R~Gfs~~~i~~l~~ayr~l~~~~~~~~~a~~~l~~~~~~~~~v~~~ 70 (83)
T PF13720_consen 25 RRGFSKEEISALRRAYRILFRSGLTLEEALEELEEEYPDSPEVREI 70 (83)
T ss_dssp HTTS-HHHHHHHHHHHHHHHTSSS-HHHHHHHHHHHTTSCHHHHHH
T ss_pred HcCCCHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHhccCCHHHHHH
Confidence 3569999999999998888888889999999998866656666554
No 29
>PRK14137 recX recombination regulator RecX; Provisional
Probab=46.97 E-value=63 Score=30.29 Aligned_cols=68 Identities=21% Similarity=0.230 Sum_probs=49.8
Q ss_pred CCCCCCCCCCCccccCCCC-CcccHHhHHHHHHHHHHHHHh----hcCHHHHHHHHHHhcCCCCcchHHHHHHHHHHc
Q 017623 29 TTEAPLADSGSISASSNDS-RKVSRQDIELVQNLIERCLQL----YMNRDEVVKTLLTRARIDPGFTTLVWQKLEEEN 101 (368)
Q Consensus 29 ~~~~~~~~~~s~~~~~~~~-r~vS~edI~~VQnLIErCLql----yMsk~Evv~~L~~~a~I~P~fT~~VW~kLEeeN 101 (368)
...+|.+|+++.- .... +.++.+ +.-+.+..+||.+ -.|..|+-+.|.++ ++++.+-..|..+|++.+
T Consensus 13 ~~~~~~~~~~~~~--~~~~~~~~~~~--e~~~~~~~~Al~~Ls~R~rS~~ELr~KL~~k-g~~~e~Ie~vI~rL~e~g 85 (195)
T PRK14137 13 EGEAPGTDTEGPV--RPERRTPPTPD--EAREALLAYAFRALAARAMTAAELRAKLERR-SEDEALVTEVLERVQELG 85 (195)
T ss_pred cCCCCCCcCCCCc--cccccCCCCHH--HHHHHHHHHHHHHHhcchhhHHHHHHHHHhc-CCCHHHHHHHHHHHHHcC
Confidence 4456666666652 1122 224555 4556888999988 88999999999755 799999999999999875
No 30
>cd04789 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator. Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=46.73 E-value=1.6e+02 Score=24.30 Aligned_cols=36 Identities=19% Similarity=0.192 Sum_probs=31.4
Q ss_pred CCCCCcccHHhHHHHHHHHHHHHHhhcCHHHHHHHHH
Q 017623 44 SNDSRKVSRQDIELVQNLIERCLQLYMNRDEVVKTLL 80 (368)
Q Consensus 44 ~~~~r~vS~edI~~VQnLIErCLqlyMsk~Evv~~L~ 80 (368)
.++.|..+.+||..++ +|.++-.+-|+.+||...|.
T Consensus 33 ~~g~R~Y~~~~l~~l~-~I~~l~~~G~~l~ei~~~l~ 68 (102)
T cd04789 33 ANGYRLYPDSDLQRLL-LIQQLQAGGLSLKECLACLQ 68 (102)
T ss_pred CCCCeeCCHHHHHHHH-HHHHHHHCCCCHHHHHHHHc
Confidence 3677899999999999 89889999999999887663
No 31
>PF14769 CLAMP: Flagellar C1a complex subunit C1a-32
Probab=44.82 E-value=93 Score=25.72 Aligned_cols=51 Identities=14% Similarity=0.156 Sum_probs=37.0
Q ss_pred CcccHHhH----HHHHHHHHHHHHhhcCHHHHHHHHHHh-cCCCC--------cchHHHHHHHH
Q 017623 48 RKVSRQDI----ELVQNLIERCLQLYMNRDEVVKTLLTR-ARIDP--------GFTTLVWQKLE 98 (368)
Q Consensus 48 r~vS~edI----~~VQnLIErCLqlyMsk~Evv~~L~~~-a~I~P--------~fT~~VW~kLE 98 (368)
+.+|++.+ ..++.|.+.|+...|+.+|+++.|.+. .++.. .|+..-.+.+-
T Consensus 10 ~~fs~~q~s~~~~i~~~ll~~~i~~~~~~~~~~~~fk~~l~~~sv~rpp~~~~iFs~~~~~~i~ 73 (101)
T PF14769_consen 10 QGFSWEQTSAFLSILKELLEKNIEKGMSLEDSFKYFKELLLRHSVQRPPFSIGIFSVDQVKAII 73 (101)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHHHHHhccCCCCcccCcCCHHHHHHHH
Confidence 45565544 457788888999999999999988765 23333 38877777766
No 32
>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements
Probab=43.92 E-value=2e+02 Score=24.48 Aligned_cols=36 Identities=28% Similarity=0.388 Sum_probs=30.8
Q ss_pred CCCCCcccHHhHHHHHHHHHHHHHhhcCHHHHHHHHH
Q 017623 44 SNDSRKVSRQDIELVQNLIERCLQLYMNRDEVVKTLL 80 (368)
Q Consensus 44 ~~~~r~vS~edI~~VQnLIErCLqlyMsk~Evv~~L~ 80 (368)
.+..|..+.+|+..++ +|-.+-.+.|+.+||-..|.
T Consensus 33 ~~g~R~Y~~~~~~~l~-~I~~lr~~G~sL~eI~~~l~ 68 (127)
T cd01108 33 DNGYRVYNQRDIEELR-FIRRARDLGFSLEEIRELLA 68 (127)
T ss_pred CCCceecCHHHHHHHH-HHHHHHHcCCCHHHHHHHHH
Confidence 4677899999999987 57788899999999998775
No 33
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=43.43 E-value=1.9e+02 Score=23.98 Aligned_cols=38 Identities=18% Similarity=0.246 Sum_probs=31.2
Q ss_pred CCCCCcccHHhHHHHHHHHHHHHHhhcCHHHHHHHHHHh
Q 017623 44 SNDSRKVSRQDIELVQNLIERCLQLYMNRDEVVKTLLTR 82 (368)
Q Consensus 44 ~~~~r~vS~edI~~VQnLIErCLqlyMsk~Evv~~L~~~ 82 (368)
.+.-|..+.++|..++ +|-.+-.+-|+.+||-..|...
T Consensus 33 ~~gyR~Y~~~~l~~l~-~I~~lr~~G~sL~eI~~~l~~~ 70 (113)
T cd01109 33 ENGIRDFTEEDLEWLE-FIKCLRNTGMSIKDIKEYAELR 70 (113)
T ss_pred CCCCccCCHHHHHHHH-HHHHHHHcCCCHHHHHHHHHHH
Confidence 4567899999999986 6667778999999999888654
No 34
>PF12776 Myb_DNA-bind_3: Myb/SANT-like DNA-binding domain; InterPro: IPR024752 This domain, found in a range of uncharacterised proteins, may be related to Myb/SANT-like DNA binding domains.
Probab=40.89 E-value=60 Score=25.47 Aligned_cols=43 Identities=23% Similarity=0.425 Sum_probs=34.1
Q ss_pred CCcchHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 017623 86 DPGFTTLVWQKLEEENADFFRAYYIRLKLKKQILLFNHLLEHQYHLM 132 (368)
Q Consensus 86 ~P~fT~~VW~kLEeeNpeFFkaYy~Rl~LK~QI~~FN~Lle~Q~~lm 132 (368)
...|+...|+.+.++=.++|...+.+-.||.++. .|++++.+.
T Consensus 26 ~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~----~lk~~y~~~ 68 (96)
T PF12776_consen 26 NGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWK----TLKKDYRIW 68 (96)
T ss_pred CCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHH----HHHHHHHHH
Confidence 5699999999999998889999999888888843 334555544
No 35
>PF00784 MyTH4: MyTH4 domain; InterPro: IPR000857 The microtubule-based kinesin motors and actin-based myosin motors generate movements required for intracellular trafficking, cell division, and muscle contraction. In general, these proteins consist of a motor domain that generates movement and a tail region that varies widely from class to class and is thought to mediate many of the regulatory or cargo binding functions specific to each class of motor []. The Myosin Tail Homology 4 (MyTH4) domain has been identified as a conserved domain in the tail domains of several different unconventional myosins [] and a plant kinesin-like protein [], but has more recently been found in several non-motor proteins []. Although the function is not yet fully understood, there is an evidence that the MyTH4 domain of Myosin-X (Myo10) binds to microtubules and thus could provide a link between an actin-based motor protein and the microtubule cytoskeleton []. The MyTH4 domain is found in one or two copies associated with other domains, such as myosin head, kinesin motor, FERM, PH, SH3 and IQ. The domain is predicted to be largely alpha-helical, interrupted by three or four turns. The MyTH4 domain contains four highly conserved regions designated MGD (consensus sequence L(K/R)(F/Y)MGDhP, LRDE (consensus LRDEhYCQhhKQHxxxN), RGW (consensus RGWxLh), and ELEA (RxxPPSxhELEA), where h indicates a hydrophobic residue and x is any residue [].; GO: 0005856 cytoskeleton; PDB: 3AU5_A 3AU4_A 3PZD_A 3PVL_A.
Probab=40.20 E-value=66 Score=26.82 Aligned_cols=45 Identities=29% Similarity=0.471 Sum_probs=36.9
Q ss_pred hHHHHHHHHHHHHHhhcCHHHHHHHHHHhcCCCCc--chHHHHHHHH
Q 017623 54 DIELVQNLIERCLQLYMNRDEVVKTLLTRARIDPG--FTTLVWQKLE 98 (368)
Q Consensus 54 dI~~VQnLIErCLqlyMsk~Evv~~L~~~a~I~P~--fT~~VW~kLE 98 (368)
.++++|++|+.|+..--=++|+.-.|-||-.=.|. .....|+-|-
T Consensus 2 ~~~l~~~Il~~~l~~~~LrDEiy~QliKQtt~np~~~s~~r~W~Ll~ 48 (114)
T PF00784_consen 2 EIDLIQNILQKGLENPELRDEIYCQLIKQTTNNPSPDSCIRGWQLLA 48 (114)
T ss_dssp HHHHHHHHHHHHHH-CCHHHHHHHHHHHHTSS-SSCHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcchhhHHHHHHHHHHHHHCCCchhhHHHHHHHHH
Confidence 46889999999999999999999999999766664 5568999886
No 36
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=40.03 E-value=44 Score=24.69 Aligned_cols=37 Identities=27% Similarity=0.272 Sum_probs=29.0
Q ss_pred CCCCCcccHHhHHHHHHHHHHHHHhhcCHHHHHHHHHH
Q 017623 44 SNDSRKVSRQDIELVQNLIERCLQLYMNRDEVVKTLLT 81 (368)
Q Consensus 44 ~~~~r~vS~edI~~VQnLIErCLqlyMsk~Evv~~L~~ 81 (368)
.+..|..+.+||..+. .|.++....|+.+||-+.|..
T Consensus 32 ~~g~r~y~~~dv~~l~-~i~~l~~~G~sl~~I~~~l~~ 68 (69)
T PF13411_consen 32 ENGYRYYSEEDVERLR-EIKELRKQGMSLEEIKKLLKQ 68 (69)
T ss_dssp TTSSEEE-HHHHHHHH-HHHHHHHTTTHHHHHHHHH--
T ss_pred cCceeeccHHHHHHHH-HHHHHHHCcCCHHHHHHHHcc
Confidence 4555889999999987 577888899999999998864
No 37
>PF10045 DUF2280: Uncharacterized conserved protein (DUF2280); InterPro: IPR018738 This entry is represented by Burkholderia phage Bups phi1, Orf2.36. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=40.01 E-value=1.6e+02 Score=25.78 Aligned_cols=55 Identities=22% Similarity=0.208 Sum_probs=46.3
Q ss_pred HHHHHHHHHHHhhcCHHHHHHHHHHhcCCC--------CcchHHHHHHHHHHcHHHHHHHHHH
Q 017623 57 LVQNLIERCLQLYMNRDEVVKTLLTRARID--------PGFTTLVWQKLEEENADFFRAYYIR 111 (368)
Q Consensus 57 ~VQnLIErCLqlyMsk~Evv~~L~~~a~I~--------P~fT~~VW~kLEeeNpeFFkaYy~R 111 (368)
-|+--|=+-|--|.+..||++++.+.+||+ -.=|...=+.|-++-.+.|+....+
T Consensus 7 ~vK~FIVQ~LAcfdTPs~v~~aVk~eFgi~vsrQqve~yDPTK~aG~~Ls~k~~~lF~~TR~~ 69 (104)
T PF10045_consen 7 EVKAFIVQSLACFDTPSEVAEAVKEEFGIDVSRQQVESYDPTKRAGRDLSKKWVDLFEETRKR 69 (104)
T ss_pred HHHHHHHHHHHhhCCHHHHHHHHHHHhCCccCHHHHHHcCchHHHHHHHHHHHHHHHHHHHHH
Confidence 467788888999999999999999999987 3457788889999999999876544
No 38
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=39.77 E-value=2.6e+02 Score=24.48 Aligned_cols=70 Identities=16% Similarity=0.160 Sum_probs=46.6
Q ss_pred CCCCCcccHHhHHHHHHHHHHHHHhhcCHHHHHHHHHHhcCCCCcchHHHHHH-HHHHcHHHHHHHHHHHHHHHHHHHHH
Q 017623 44 SNDSRKVSRQDIELVQNLIERCLQLYMNRDEVVKTLLTRARIDPGFTTLVWQK-LEEENADFFRAYYIRLKLKKQILLFN 122 (368)
Q Consensus 44 ~~~~r~vS~edI~~VQnLIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~VW~k-LEeeNpeFFkaYy~Rl~LK~QI~~FN 122 (368)
.|.-|-.+.+|+..++ +|.+|-++-|+.+||-+.|.-. -++..+..-|.+ |++ ..-.|.+||....
T Consensus 33 ~~gyR~Y~~~~l~~l~-~I~~lr~~G~sl~eI~~~l~~~--~~~~~~~~~~~~~l~~----------~~~~l~~~i~~L~ 99 (135)
T PRK10227 33 ENGYRTYTQQHLNELT-LLRQARQVGFNLEESGELVNLF--NDPQRHSADVKRRTLE----------KVAEIERHIEELQ 99 (135)
T ss_pred CCCcccCCHHHHHHHH-HHHHHHHCCCCHHHHHHHHHhh--ccCCCCHHHHHHHHHH----------HHHHHHHHHHHHH
Confidence 5677899999999987 6788889999999987766422 123444333322 222 2445777777666
Q ss_pred HHHH
Q 017623 123 HLLE 126 (368)
Q Consensus 123 ~Lle 126 (368)
.+.+
T Consensus 100 ~~~~ 103 (135)
T PRK10227 100 SMRD 103 (135)
T ss_pred HHHH
Confidence 6554
No 39
>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=39.72 E-value=30 Score=27.02 Aligned_cols=27 Identities=15% Similarity=0.277 Sum_probs=19.9
Q ss_pred cCHHHHHHHHHHhcCCCCcchHHHHHH
Q 017623 70 MNRDEVVKTLLTRARIDPGFTTLVWQK 96 (368)
Q Consensus 70 Msk~Evv~~L~~~a~I~P~fT~~VW~k 96 (368)
||++|+++.+.++.++...-...|...
T Consensus 1 Mtk~eli~~ia~~~~~s~~~v~~vl~~ 27 (90)
T PF00216_consen 1 MTKKELIKRIAEKTGLSKKDVEAVLDA 27 (90)
T ss_dssp EBHHHHHHHHHHHHTSSHHHHHHHHHH
T ss_pred CCHHHHHHHHHHhcCCCHHHHHHHHHH
Confidence 899999999998887765554444443
No 40
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=39.58 E-value=1.4e+02 Score=24.83 Aligned_cols=39 Identities=18% Similarity=0.191 Sum_probs=30.8
Q ss_pred CCCCCcccHHhHHHHHHHHHHHH-HhhcCHHHHHHHHHHhc
Q 017623 44 SNDSRKVSRQDIELVQNLIERCL-QLYMNRDEVVKTLLTRA 83 (368)
Q Consensus 44 ~~~~r~vS~edI~~VQnLIErCL-qlyMsk~Evv~~L~~~a 83 (368)
.++.|..|.+||..++. |.+|| ..-|+.++|.+.|....
T Consensus 33 ~~g~R~Yt~~di~~l~~-I~~llr~~G~~l~~i~~~l~~~~ 72 (99)
T cd04765 33 AGGRRYYRPKDVELLLL-IKHLLYEKGYTIEGAKQALKEDG 72 (99)
T ss_pred CCCCeeeCHHHHHHHHH-HHHHHHHCCCCHHHHHHHHHhcc
Confidence 45678899999998774 44566 57999999999887654
No 41
>PRK10963 hypothetical protein; Provisional
Probab=39.55 E-value=57 Score=30.65 Aligned_cols=20 Identities=40% Similarity=0.632 Sum_probs=15.0
Q ss_pred cCHHHHHHHHHHhcCCCCcchHHHHHHHHHHcHHHHHHH
Q 017623 70 MNRDEVVKTLLTRARIDPGFTTLVWQKLEEENADFFRAY 108 (368)
Q Consensus 70 Msk~Evv~~L~~~a~I~P~fT~~VW~kLEeeNpeFFkaY 108 (368)
|+-++|+.+|. +|||||..+
T Consensus 3 l~~~~V~~yL~-------------------~~PdFf~~h 22 (223)
T PRK10963 3 LDDRAVVDYLL-------------------QNPDFFIRN 22 (223)
T ss_pred CCHHHHHHHHH-------------------HCchHHhhC
Confidence 66777777775 778888776
No 42
>TIGR01950 SoxR redox-sensitive transcriptional activator SoxR. SoxR is a MerR-family homodimeric transcription factor with a 2Fe-2S cluster in each monomer. The motif CIGCGCxxxxxC is conserved. Oxidation of the iron-sulfur cluster activates SoxR. The physiological role in E. coli is response to oxidative stress. It is activated by superoxide, singlet oxygen, nitric oxide (NO), and hydrogen peroxide. In E. coli, SoxR increases expression of transcription factor SoxS; different downstream targets may exist in other species.
Probab=39.53 E-value=2.7e+02 Score=24.63 Aligned_cols=78 Identities=18% Similarity=0.206 Sum_probs=49.5
Q ss_pred CCCCCcccHHhHHHHHHHHHHHHHhhcCHHHHHHHHHHhcCCCCcchHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHH
Q 017623 44 SNDSRKVSRQDIELVQNLIERCLQLYMNRDEVVKTLLTRARIDPGFTTLVWQKLEEENADFFRAYYIRLKLKKQILLFNH 123 (368)
Q Consensus 44 ~~~~r~vS~edI~~VQnLIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~VW~kLEeeNpeFFkaYy~Rl~LK~QI~~FN~ 123 (368)
.++.|..+.+||..++ +|.++-.+-|+.+||...|..-. =....+..-|..+-++ .+-.|.+||...+.
T Consensus 33 ~~g~R~Y~~~di~~l~-~I~~lr~~G~sL~eI~~~l~~~~-~~~~~~~~~~~~~l~~---------~~~~l~~ki~~L~~ 101 (142)
T TIGR01950 33 SGNQRRYKRDVLRRVA-VIKAAQRVGIPLATIGEALAVLP-EGRTPTADDWARLSSQ---------WREELDERIDQLNA 101 (142)
T ss_pred CCCCEEECHHHHHHHH-HHHHHHHcCCCHHHHHHHHHhcc-cCCCCCHHHHHHHHHH---------HHHHHHHHHHHHHH
Confidence 3456899999999987 48888999999999999885321 1111222333333222 34567778877776
Q ss_pred HHHHHHhhh
Q 017623 124 LLEHQYHLM 132 (368)
Q Consensus 124 Lle~Q~~lm 132 (368)
+...=.+++
T Consensus 102 ~~~~L~~~~ 110 (142)
T TIGR01950 102 LRDQLDGCI 110 (142)
T ss_pred HHHHHHHHH
Confidence 654433333
No 43
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=39.23 E-value=72 Score=23.94 Aligned_cols=35 Identities=23% Similarity=0.294 Sum_probs=29.4
Q ss_pred CCCCCcccHHhHHHHHHHHHHHHHhhcCHHHHHHHH
Q 017623 44 SNDSRKVSRQDIELVQNLIERCLQLYMNRDEVVKTL 79 (368)
Q Consensus 44 ~~~~r~vS~edI~~VQnLIErCLqlyMsk~Evv~~L 79 (368)
.+..|..+.+||..++. |-+.++.-|+.+||.+.|
T Consensus 33 ~~g~R~yt~~di~~l~~-i~~l~~~g~~l~~i~~~l 67 (68)
T cd04763 33 DGGHRLFNDADIDRILE-IKRWIDNGVQVSKVKKLL 67 (68)
T ss_pred CCCCcccCHHHHHHHHH-HHHHHHcCCCHHHHHHHh
Confidence 45668899999999875 777788999999998866
No 44
>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=36.83 E-value=2.6e+02 Score=23.67 Aligned_cols=38 Identities=18% Similarity=0.309 Sum_probs=32.1
Q ss_pred CCCCCcccHHhHHHHHHHHHHHHHhhcCHHHHHHHHHHh
Q 017623 44 SNDSRKVSRQDIELVQNLIERCLQLYMNRDEVVKTLLTR 82 (368)
Q Consensus 44 ~~~~r~vS~edI~~VQnLIErCLqlyMsk~Evv~~L~~~ 82 (368)
.+.-|..+.+||..++ +|-.+-.+-|+.+||...|...
T Consensus 33 ~~gyR~Y~~~~l~~l~-~I~~lr~~G~sL~eI~~~l~~~ 70 (126)
T cd04783 33 EGGYRRYPEETVTRLR-FIKRAQELGFTLDEIAELLELD 70 (126)
T ss_pred CCCCeecCHHHHHHHH-HHHHHHHcCCCHHHHHHHHhcc
Confidence 4567889999999996 7888999999999999888543
No 45
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=36.62 E-value=2.5e+02 Score=23.45 Aligned_cols=71 Identities=15% Similarity=0.104 Sum_probs=45.1
Q ss_pred CCCCCcccHHhHHHHHHHHHHHHHhhcCHHHHHHHHHHhcCCC-C-cchHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHH
Q 017623 44 SNDSRKVSRQDIELVQNLIERCLQLYMNRDEVVKTLLTRARID-P-GFTTLVWQKLEEENADFFRAYYIRLKLKKQILLF 121 (368)
Q Consensus 44 ~~~~r~vS~edI~~VQnLIErCLqlyMsk~Evv~~L~~~a~I~-P-~fT~~VW~kLEeeNpeFFkaYy~Rl~LK~QI~~F 121 (368)
.++.|..+.+||..++ +|-+|-.+-|+.+||-..|.....-+ + .-...+++.|++ .+-.|.+||...
T Consensus 32 ~~g~R~Y~~~~~~~l~-~I~~lr~~G~sl~eI~~~l~~~~~~~~~~~~~~~~~~~l~~----------~~~~l~~~i~~L 100 (112)
T cd01282 32 ANGYRDYDEAAVDRVR-QIRRLLAAGLTLEEIREFLPCLRGGEPTFRPCPDLLAVLRR----------ELARIDRQIADL 100 (112)
T ss_pred CCCCeecCHHHHHHHH-HHHHHHHcCCCHHHHHHHHHHhhCCCccCCccHHHHHHHHH----------HHHHHHHHHHHH
Confidence 4577899999999987 56677789999999998875432211 1 112233333433 234567777766
Q ss_pred HHHH
Q 017623 122 NHLL 125 (368)
Q Consensus 122 N~Ll 125 (368)
....
T Consensus 101 ~~~~ 104 (112)
T cd01282 101 TRSR 104 (112)
T ss_pred HHHH
Confidence 6544
No 46
>PF04910 Tcf25: Transcriptional repressor TCF25; InterPro: IPR006994 This entry appears to represent a novel family of basic helix-loop-helix (bHLH) proteins that control differentiation and development of a variety of organs [, ]. Human Nulp1 (Q2MK75 from SWISSPROT) is a basic helix-loop-helix protein expressed broadly during early embryonic organogenesis. Over expression of human Nulp1 in COS-7 cells inhibits the transcriptional activity of serum response factor (SRF), suggesting that Nulp1 may act as a novel bHLH transcriptional repressor in the SRF signalling pathway to mediate cellular functions [].
Probab=35.94 E-value=85 Score=31.68 Aligned_cols=74 Identities=20% Similarity=0.292 Sum_probs=41.6
Q ss_pred hHHHHHHHHHHHHHhhcCHHHHHHHHHHhc--CCCCcchHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 017623 54 DIELVQNLIERCLQLYMNRDEVVKTLLTRA--RIDPGFTTLVWQKLEEENADFFRAYYIRLKLKKQILLFNHLLEHQYHL 131 (368)
Q Consensus 54 dI~~VQnLIErCLqlyMsk~Evv~~L~~~a--~I~P~fT~~VW~kLEeeNpeFFkaYy~Rl~LK~QI~~FN~Lle~Q~~l 131 (368)
|...-..||||||--+ +-+....+... +..-+-..+-|. ..||+.||.|-+..+..-.+=-.+..-+|-=+=|
T Consensus 55 d~~~A~~lleRALf~~---e~~~~~~F~~~~~~~~~g~~rL~~~--~~eNR~fflal~r~i~~L~~RG~~rTAlE~~KlL 129 (360)
T PF04910_consen 55 DHAQANDLLERALFAF---ERAFHPSFSPFRSNLTSGNCRLDYR--RPENRQFFLALFRYIQSLGRRGCWRTALEWCKLL 129 (360)
T ss_pred CHHHHHHHHHHHHHHH---HHHHHHHhhhhhcccccCccccCCc--cccchHHHHHHHHHHHHHHhcCcHHHHHHHHHHH
Confidence 6677788999999877 33444444221 111122222222 3589999999877776655444444444433333
Q ss_pred h
Q 017623 132 M 132 (368)
Q Consensus 132 m 132 (368)
.
T Consensus 130 l 130 (360)
T PF04910_consen 130 L 130 (360)
T ss_pred H
Confidence 3
No 47
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=35.50 E-value=2.5e+02 Score=22.95 Aligned_cols=63 Identities=19% Similarity=0.249 Sum_probs=42.4
Q ss_pred CCCCCcccHHhHHHHHHHHHHHHHhhcCHHHHHHHHHHhcCCCCcchHHHHHHHHHHcHHHHHHH-HHHHHHHHHHHHHH
Q 017623 44 SNDSRKVSRQDIELVQNLIERCLQLYMNRDEVVKTLLTRARIDPGFTTLVWQKLEEENADFFRAY-YIRLKLKKQILLFN 122 (368)
Q Consensus 44 ~~~~r~vS~edI~~VQnLIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~VW~kLEeeNpeFFkaY-y~Rl~LK~QI~~FN 122 (368)
.+..|..+.+||..++.+. .|-...|+.+|+-+.|.... .++-..+ ..+-.|++||.+.+
T Consensus 33 ~~g~R~y~~~di~~l~~i~-~lr~~g~~l~~i~~~~~~~~------------------~~~~~~l~~~~~~l~~~i~~l~ 93 (103)
T cd01106 33 ENGYRLYTEEDLERLQQIL-FLKELGFSLKEIKELLKDPS------------------EDLLEALREQKELLEEKKERLD 93 (103)
T ss_pred CCCceeeCHHHHHHHHHHH-HHHHcCCCHHHHHHHHHcCc------------------HHHHHHHHHHHHHHHHHHHHHH
Confidence 3467889999999988654 57778999999988774221 2222222 23455778888777
Q ss_pred HHH
Q 017623 123 HLL 125 (368)
Q Consensus 123 ~Ll 125 (368)
..+
T Consensus 94 ~~~ 96 (103)
T cd01106 94 KLI 96 (103)
T ss_pred HHH
Confidence 655
No 48
>TIGR02054 MerD mercuric resistence transcriptional repressor protein MerD. This model represents a transcriptional repressor protein of the MerR family (pfam00376) whose expression is regulated by the mercury-sensitive transcriptional activator, MerR. MerD has been shown to repress the transcription of the mer operon.
Probab=35.39 E-value=3e+02 Score=23.92 Aligned_cols=36 Identities=3% Similarity=0.110 Sum_probs=31.3
Q ss_pred CCCCCcccHHhHHHHHHHHHHHHHhhcCHHHHHHHHH
Q 017623 44 SNDSRKVSRQDIELVQNLIERCLQLYMNRDEVVKTLL 80 (368)
Q Consensus 44 ~~~~r~vS~edI~~VQnLIErCLqlyMsk~Evv~~L~ 80 (368)
.+.-|..+.++|..++ +|.+|-..-|+.+||-..|.
T Consensus 36 ~~gyR~Y~~~~l~rL~-~I~~lr~~G~~L~eI~~ll~ 71 (120)
T TIGR02054 36 TSGYGIFDDASLQRLR-FVRAAFEAGIGLGELARLCR 71 (120)
T ss_pred CCCCeeCCHHHHHHHH-HHHHHHHcCCCHHHHHHHHH
Confidence 4677899999999987 78899999999999988764
No 49
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=35.23 E-value=2.3e+02 Score=23.05 Aligned_cols=36 Identities=22% Similarity=0.192 Sum_probs=30.3
Q ss_pred CCCCCcccHHhHHHHHHHHHHHHHhhcCHHHHHHHHH
Q 017623 44 SNDSRKVSRQDIELVQNLIERCLQLYMNRDEVVKTLL 80 (368)
Q Consensus 44 ~~~~r~vS~edI~~VQnLIErCLqlyMsk~Evv~~L~ 80 (368)
.+..|..+.+|+..++ .|-++.++-|+.+||-+.|.
T Consensus 33 ~~gyR~Y~~~~l~~l~-~I~~lr~~G~~l~eI~~~l~ 68 (96)
T cd04788 33 EGGHRLYDRADIRRLH-QIIALRRLGFSLREIGRALD 68 (96)
T ss_pred CCCceeeCHHHHHHHH-HHHHHHHcCCCHHHHHHHHh
Confidence 4567889999999987 56678899999999999874
No 50
>TIGR00988 hip integration host factor, beta subunit. This protein forms a site-specific DNA-binding heterodimer with the homologous integration host factor alpha subunit. It is closely related to the DNA-binding protein HU.
Probab=35.22 E-value=52 Score=26.48 Aligned_cols=29 Identities=10% Similarity=0.193 Sum_probs=21.3
Q ss_pred cCHHHHHHHHHHh-cCCCCcchHHHHHHHH
Q 017623 70 MNRDEVVKTLLTR-ARIDPGFTTLVWQKLE 98 (368)
Q Consensus 70 Msk~Evv~~L~~~-a~I~P~fT~~VW~kLE 98 (368)
|||+|+++.+.++ .++.+.-...|++.+.
T Consensus 1 m~k~eli~~i~~~~~~~s~~~v~~vv~~~~ 30 (94)
T TIGR00988 1 MTKSELIERIATQQSHLPAKDVEDAVKTML 30 (94)
T ss_pred CCHHHHHHHHHHHcCCCCHHHHHHHHHHHH
Confidence 8999999999875 4677766666665543
No 51
>PF10632 He_PIG_assoc: He_PIG associated, NEW1 domain of bacterial glycohydrolase; InterPro: IPR019599 This domain has been named NEW1 but its actual function is not known. It is found on proteins which are bacterial galactosidases []. The domain is associated with IPR008009 from INTERPRO, a putative Ig-containing domain.
Probab=34.35 E-value=15 Score=25.55 Aligned_cols=10 Identities=70% Similarity=1.381 Sum_probs=9.5
Q ss_pred CCCCCCCCCC
Q 017623 322 LGNYPGSPFL 331 (368)
Q Consensus 322 L~nY~gSPFL 331 (368)
.|+|+|+|||
T Consensus 9 ~G~rPg~pfl 18 (29)
T PF10632_consen 9 FGARPGSPFL 18 (29)
T ss_pred EcccCCCcEE
Confidence 7999999998
No 52
>COG4399 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.90 E-value=64 Score=33.64 Aligned_cols=64 Identities=23% Similarity=0.166 Sum_probs=45.3
Q ss_pred hHHHHHHHHHHHHHhhcCHHHHHHH-HHHh--cCCCCcchHHHHHHHHHHcHHHHHHHHHHHHHHHHH
Q 017623 54 DIELVQNLIERCLQLYMNRDEVVKT-LLTR--ARIDPGFTTLVWQKLEEENADFFRAYYIRLKLKKQI 118 (368)
Q Consensus 54 dI~~VQnLIErCLqlyMsk~Evv~~-L~~~--a~I~P~fT~~VW~kLEeeNpeFFkaYy~Rl~LK~QI 118 (368)
--+.|..+|++-||+.|.++-..+. |..+ ++++-..-.-+-+.|++++.|+|..|..+ .++++|
T Consensus 84 ~~~rv~~~i~~~lqk~lk~~~t~k~~l~~~~~~d~e~~~i~~~~~~l~~~l~e~f~e~qsn-~i~e~I 150 (376)
T COG4399 84 FQERVTEAIDQLLQKLLKSEVTDKEQLHQQIFADIEKDLIGNSERWLEKELAEKFTEAQSN-TIFELI 150 (376)
T ss_pred HHHHHHHHHHHHHHHHHHhhcchHHHHHHHHHhhHHHHHHHhhHHHHHHHHHHHHHHHHhh-HHHHhc
Confidence 3456999999999999988766443 3333 45555556666788999999999998543 345544
No 53
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=33.20 E-value=2.9e+02 Score=23.12 Aligned_cols=37 Identities=19% Similarity=0.226 Sum_probs=30.4
Q ss_pred CCCcccHHhHHHHHHHHHHHHHhhcCHHHHHHHHHHhc
Q 017623 46 DSRKVSRQDIELVQNLIERCLQLYMNRDEVVKTLLTRA 83 (368)
Q Consensus 46 ~~r~vS~edI~~VQnLIErCLqlyMsk~Evv~~L~~~a 83 (368)
+-|..+.+|+..++ .|-+|-.+.|+.+||-..|....
T Consensus 34 ~yR~Y~~~d~~~l~-~I~~lr~~G~sl~eI~~~l~~~~ 70 (116)
T cd04769 34 NYRVYDAQHVECLR-FIKEARQLGFTLAELKAIFAGHE 70 (116)
T ss_pred CceeeCHHHHHHHH-HHHHHHHcCCCHHHHHHHHhccc
Confidence 45889999999986 67788899999999998775443
No 54
>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=32.53 E-value=57 Score=26.62 Aligned_cols=28 Identities=7% Similarity=0.120 Sum_probs=21.6
Q ss_pred cCHHHHHHHHHHhcCCCCcchHHHHHHH
Q 017623 70 MNRDEVVKTLLTRARIDPGFTTLVWQKL 97 (368)
Q Consensus 70 Msk~Evv~~L~~~a~I~P~fT~~VW~kL 97 (368)
||++|+++.|.++.++...-...|.+.+
T Consensus 2 mtk~eli~~ia~~~~~s~~~v~~vv~~~ 29 (96)
T TIGR00987 2 LTKAEMSEYLFDELGLSKREAKELVELF 29 (96)
T ss_pred CCHHHHHHHHHHHhCcCHHHHHHHHHHH
Confidence 8999999999999887766665555443
No 55
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=32.46 E-value=2.5e+02 Score=23.19 Aligned_cols=64 Identities=14% Similarity=0.123 Sum_probs=51.4
Q ss_pred HhHHHHHHHHHHHHHhhcCHHHHHHHHHHhcCCCCcchHHHHHHHHHHcHHHHHHHHHHHHHHHHH
Q 017623 53 QDIELVQNLIERCLQLYMNRDEVVKTLLTRARIDPGFTTLVWQKLEEENADFFRAYYIRLKLKKQI 118 (368)
Q Consensus 53 edI~~VQnLIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~VW~kLEeeNpeFFkaYy~Rl~LK~QI 118 (368)
|-=.+.+.++++=+.+.||+.|+.+.|-...|. .++..--.++|+-+=.|=.+|.++--|++=|
T Consensus 8 ele~~~~~lk~~R~~lGLTQ~dvA~~lg~~~g~--i~SQstISR~Es~~ls~~n~~kl~p~l~~wl 71 (75)
T smart00352 8 ELEAFAKTFKQRRIKLGFTQADVGLALGALYGP--DFSQTTICRFEALQLSFKNMCKLKPLLEKWL 71 (75)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHhcccccC--cCCHHHHHHHHhcCccHHHHHHHHHHHHHHH
Confidence 334567788899999999999999999877776 7888888889998888877777776666543
No 56
>smart00139 MyTH4 Domain in Myosin and Kinesin Tails. Domain present twice in myosin-VIIa, and also present in 3 other myosins.
Probab=32.12 E-value=1.1e+02 Score=27.03 Aligned_cols=47 Identities=23% Similarity=0.323 Sum_probs=38.2
Q ss_pred HHhHHHHHHHHHHHHHhhcCHHHHHHHHHHhcCCCC--cchHHHHHHHH
Q 017623 52 RQDIELVQNLIERCLQLYMNRDEVVKTLLTRARIDP--GFTTLVWQKLE 98 (368)
Q Consensus 52 ~edI~~VQnLIErCLqlyMsk~Evv~~L~~~a~I~P--~fT~~VW~kLE 98 (368)
+..++++|++|+.|+..=-=++|+.-.|-||-.=.| .-..-.|+-|-
T Consensus 42 ~~~~~l~~~i~~~~~~~~~LrDEiy~QLiKQtt~Np~~~s~~rgW~Ll~ 90 (144)
T smart00139 42 DSHLDLVQFILQKGLAHPELRDEIYCQLIKQLTDNPSRQSEERGWELLY 90 (144)
T ss_pred chHHHHHHHHHHHHhccHHHHHHHHHHHHHHHhCCCCchHHHHHHHHHH
Confidence 567899999999999988889999988988854444 45567888875
No 57
>PF03979 Sigma70_r1_1: Sigma-70 factor, region 1.1; InterPro: IPR007127 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. This entry represents Region 1.1 which modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase [, ]. Region 1.1 is also involved in promoter binding.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2K6X_A.
Probab=31.13 E-value=64 Score=25.80 Aligned_cols=48 Identities=29% Similarity=0.447 Sum_probs=32.4
Q ss_pred HhHHHHHHHHHHH-HHhhcCHHHHHHHHHHhcCCCCcchHHHHHHHHHHc
Q 017623 53 QDIELVQNLIERC-LQLYMNRDEVVKTLLTRARIDPGFTTLVWQKLEEEN 101 (368)
Q Consensus 53 edI~~VQnLIErC-LqlyMsk~Evv~~L~~~a~I~P~fT~~VW~kLEeeN 101 (368)
.+...|+.||++- =+-|+|.+||.++|. ...+.|.--.-|...|++.+
T Consensus 4 ~~~~~i~~Li~~gK~~G~lT~~eI~~~L~-~~~~~~e~id~i~~~L~~~g 52 (82)
T PF03979_consen 4 QYEEAIKKLIEKGKKKGYLTYDEINDALP-EDDLDPEQIDEIYDTLEDEG 52 (82)
T ss_dssp HHHHHHHHHHHHHHHHSS-BHHHHHHH-S--S---HHHHHHHHHHHHTT-
T ss_pred hhHHHHHHHHHHHhhcCcCCHHHHHHHcC-ccCCCHHHHHHHHHHHHHCC
Confidence 4667889999865 478999999999997 55588877777777777654
No 58
>PRK10664 transcriptional regulator HU subunit beta; Provisional
Probab=30.27 E-value=66 Score=26.35 Aligned_cols=19 Identities=21% Similarity=0.461 Sum_probs=15.8
Q ss_pred cCHHHHHHHHHHhcCCCCc
Q 017623 70 MNRDEVVKTLLTRARIDPG 88 (368)
Q Consensus 70 Msk~Evv~~L~~~a~I~P~ 88 (368)
|||.|+|+.|.++.++...
T Consensus 1 MtK~eli~~ia~~~~~s~~ 19 (90)
T PRK10664 1 MNKSQLIDKIAAGADISKA 19 (90)
T ss_pred CCHHHHHHHHHHHhCCCHH
Confidence 8999999999988776554
No 59
>PRK12461 UDP-N-acetylglucosamine acyltransferase; Provisional
Probab=30.17 E-value=98 Score=29.72 Aligned_cols=45 Identities=13% Similarity=0.108 Sum_probs=37.6
Q ss_pred CCCcccHHhHHHHHHHHHHHHHhhcCHHHHHHHHHHhcCCCCcch
Q 017623 46 DSRKVSRQDIELVQNLIERCLQLYMNRDEVVKTLLTRARIDPGFT 90 (368)
Q Consensus 46 ~~r~vS~edI~~VQnLIErCLqlyMsk~Evv~~L~~~a~I~P~fT 90 (368)
.++.++.+.|+.++......++.-++.+|.++.|.++..-.|.+-
T Consensus 196 ~r~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 240 (255)
T PRK12461 196 RRRGFSSRAIRALKRAYKIIYRSGLSVQQAVAELELQQFESPEVE 240 (255)
T ss_pred hhcCCCHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHhccCCHHHH
Confidence 455699999999999999889999999999999988776566543
No 60
>PRK14552 C/D box methylation guide ribonucleoprotein complex aNOP56 subunit; Provisional
Probab=29.90 E-value=64 Score=33.66 Aligned_cols=50 Identities=30% Similarity=0.417 Sum_probs=42.0
Q ss_pred CCCcccHHhHHHHHHHHHHHHHhhcCHHHHHHHHHHhcC-CCCcchHHHHH
Q 017623 46 DSRKVSRQDIELVQNLIERCLQLYMNRDEVVKTLLTRAR-IDPGFTTLVWQ 95 (368)
Q Consensus 46 ~~r~vS~edI~~VQnLIErCLqlyMsk~Evv~~L~~~a~-I~P~fT~~VW~ 95 (368)
.+..+|..|+..|+++|++.+.++=.++++.++|..++. |.|.+|.+|=.
T Consensus 222 ~G~~lse~dl~~I~~~a~~I~~L~e~R~~L~~yI~~~M~~iAPNLtaLVG~ 272 (414)
T PRK14552 222 MGADLSEFDLEAIKKLANEILDLYKLREELEDYLETVMKEVAPNLTALVGP 272 (414)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccHHHHHHhh
Confidence 345588899999999999999999999999999998854 57877777544
No 61
>PRK00199 ihfB integration host factor subunit beta; Reviewed
Probab=29.74 E-value=72 Score=25.76 Aligned_cols=29 Identities=14% Similarity=0.250 Sum_probs=20.2
Q ss_pred cCHHHHHHHHHHh-cCCCCcchHHHHHHHH
Q 017623 70 MNRDEVVKTLLTR-ARIDPGFTTLVWQKLE 98 (368)
Q Consensus 70 Msk~Evv~~L~~~-a~I~P~fT~~VW~kLE 98 (368)
|||.|+|+.|.++ .++...-...|++.+.
T Consensus 1 mtk~eli~~ia~~~~~~s~~~~~~vv~~~~ 30 (94)
T PRK00199 1 MTKSELIERLAARNPHLSAKDVENAVKEIL 30 (94)
T ss_pred CCHHHHHHHHHHHcCCCCHHHHHHHHHHHH
Confidence 8999999999864 5666666555555443
No 62
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=29.72 E-value=1.1e+02 Score=27.58 Aligned_cols=53 Identities=25% Similarity=0.216 Sum_probs=41.4
Q ss_pred CCCCcccHHhHHHHHHHHHHHHHhhcCHHHHHHHHHHhcCCCCcchHHHHHHHHHHc
Q 017623 45 NDSRKVSRQDIELVQNLIERCLQLYMNRDEVVKTLLTRARIDPGFTTLVWQKLEEEN 101 (368)
Q Consensus 45 ~~~r~vS~edI~~VQnLIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~VW~kLEeeN 101 (368)
+-.++++.+.++. |+|+|=+.+.+..|++..|..+++|.=+-. .||..|.+.-
T Consensus 59 GrP~kl~~~q~~~---l~e~~~~k~wTl~~~~~~l~~e~gv~y~~~-~v~~~l~~~G 111 (138)
T COG3415 59 GRPRKLSEEQLEI---LLERLREKDWTLKELVEELGLEFGVWYHAS-AVRRLLHELG 111 (138)
T ss_pred CCCcccCHHHHHH---HHHHHhcccchHHHHHHHHhhhcCeEEeHH-HHHHHHHHcC
Confidence 3445677665554 778888888999999999999999986655 8999888753
No 63
>PRK00285 ihfA integration host factor subunit alpha; Reviewed
Probab=29.60 E-value=67 Score=26.20 Aligned_cols=29 Identities=3% Similarity=0.168 Sum_probs=21.3
Q ss_pred hcCHHHHHHHHHHhcCCCCcchHHHHHHH
Q 017623 69 YMNRDEVVKTLLTRARIDPGFTTLVWQKL 97 (368)
Q Consensus 69 yMsk~Evv~~L~~~a~I~P~fT~~VW~kL 97 (368)
.||++|+++.+.++.++...-...||+.|
T Consensus 2 tmtk~el~~~ia~~~~~s~~~v~~vl~~~ 30 (99)
T PRK00285 2 TLTKADLAEALFEKVGLSKREAKELVELF 30 (99)
T ss_pred CcCHHHHHHHHHHHhCcCHHHHHHHHHHH
Confidence 48999999999988877655555555443
No 64
>PRK07194 fliG flagellar motor switch protein G; Reviewed
Probab=29.09 E-value=2e+02 Score=28.74 Aligned_cols=70 Identities=19% Similarity=0.326 Sum_probs=48.6
Q ss_pred CCcccHHhHHHHHHHHHHHHHhhcCH-------HHHHHHHHHhcCCCCcchHHHHHHHHHHcHHHHHHHHHHHHHHHHHH
Q 017623 47 SRKVSRQDIELVQNLIERCLQLYMNR-------DEVVKTLLTRARIDPGFTTLVWQKLEEENADFFRAYYIRLKLKKQIL 119 (368)
Q Consensus 47 ~r~vS~edI~~VQnLIErCLqlyMsk-------~Evv~~L~~~a~I~P~fT~~VW~kLEeeNpeFFkaYy~Rl~LK~QI~ 119 (368)
-+.|+.+.++.|-..+++|+..+.+. .+.+..+.++.. . .- ..+|..|++.+|++... +|+.+=
T Consensus 166 l~~Vs~e~~~~V~e~l~~~~~~~~~~~~~~~~G~~~aa~ILn~l~-~-~~-~~il~~L~~~dp~~a~~------Ir~~mF 236 (334)
T PRK07194 166 LDDVDRDVVDELDELIERCLAVLSEQSHTKVIGVKQAADIINRFP-G-DR-QQLMEMLKEHDEEVVNE------IEDNMY 236 (334)
T ss_pred cCCCCHHHHHHHHHHHHHHHHhhhhcccccCCCHHHHHHHHHhCc-h-hH-HHHHHHHHhhCHHHHHH------HHHhcC
Confidence 36789999999988899999865432 345555666654 2 22 58999999999998765 444455
Q ss_pred HHHHHH
Q 017623 120 LFNHLL 125 (368)
Q Consensus 120 ~FN~Ll 125 (368)
.|-.|.
T Consensus 237 ~FedL~ 242 (334)
T PRK07194 237 DFFILS 242 (334)
T ss_pred CHHHHh
Confidence 555443
No 65
>KOG2211 consensus Predicted Golgi transport complex 1 protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=28.94 E-value=1.5e+02 Score=33.57 Aligned_cols=76 Identities=20% Similarity=0.232 Sum_probs=44.7
Q ss_pred HHHHHHHHHhhcCHH------HHHHHHHH-hcCCCCcchHHHHHHHHHHcHHHHHHHHHHHHHHH-HHHHHHHHHHHHHh
Q 017623 59 QNLIERCLQLYMNRD------EVVKTLLT-RARIDPGFTTLVWQKLEEENADFFRAYYIRLKLKK-QILLFNHLLEHQYH 130 (368)
Q Consensus 59 QnLIErCLqlyMsk~------Evv~~L~~-~a~I~P~fT~~VW~kLEeeNpeFFkaYy~Rl~LK~-QI~~FN~Lle~Q~~ 130 (368)
-||-+-|.|--|=++ +.+..+++ --++++.++..+|++|++.=.-=|+.-+.--.||+ +..-+-+||.--..
T Consensus 329 d~lf~~c~qv~hlq~vl~kkrDh~~l~~e~sk~gd~cI~~rfw~~l~qal~sqfd~a~~~~fltq~f~~gypKLl~~a~g 408 (797)
T KOG2211|consen 329 DNLFVDCIQVAHLQEVLKKKRDHAELSQEMSKNGDKCIPERFWKKLEQALHSQFDDALLGDFLTQNFMTGYPKLLQTADG 408 (797)
T ss_pred HHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHhccchhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhchHHHHHHHHh
Confidence 466677766554322 12333322 25799999999999999876555554443344443 33455567765555
Q ss_pred hhcC
Q 017623 131 LMKY 134 (368)
Q Consensus 131 lm~~ 134 (368)
|.+.
T Consensus 409 L~kR 412 (797)
T KOG2211|consen 409 LTKR 412 (797)
T ss_pred HHHH
Confidence 5543
No 66
>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=28.82 E-value=99 Score=24.86 Aligned_cols=38 Identities=24% Similarity=0.264 Sum_probs=31.3
Q ss_pred CCCCcccHHhHHHHHHHHHHHHHhhcCHHHHHHHHHHhc
Q 017623 45 NDSRKVSRQDIELVQNLIERCLQLYMNRDEVVKTLLTRA 83 (368)
Q Consensus 45 ~~~r~vS~edI~~VQnLIErCLqlyMsk~Evv~~L~~~a 83 (368)
|..|..+.+||..++ .|-+|....|+.+||.+.|..+.
T Consensus 35 ~g~R~Ys~~dv~~l~-~I~~Lr~~G~sl~~i~~~l~~~~ 72 (88)
T cd01105 35 GGQRKYSLADVDRLL-VIKELLDEGFTLAAAVEKLRRRR 72 (88)
T ss_pred CCceecCHHHHHHHH-HHHHHHHCCCCHHHHHHHHHHcc
Confidence 467899999999876 46678889999999999986443
No 67
>COG5107 RNA14 Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]
Probab=28.78 E-value=1.3e+02 Score=32.95 Aligned_cols=77 Identities=21% Similarity=0.256 Sum_probs=57.3
Q ss_pred cHHhHHHHHHHHHHHHHhhcCHHHHHHHHHHhcCCCCcchHH-------HHHHHH------HHcHHHHHHHHHHHHHHHH
Q 017623 51 SRQDIELVQNLIERCLQLYMNRDEVVKTLLTRARIDPGFTTL-------VWQKLE------EENADFFRAYYIRLKLKKQ 117 (368)
Q Consensus 51 S~edI~~VQnLIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~-------VW~kLE------eeNpeFFkaYy~Rl~LK~Q 117 (368)
-+.|-+.|..|.-|||..-++.+=-+.+|..--+|.|.+|-- +++-.- -+-..|...| +-.++|
T Consensus 88 A~~df~svE~lf~rCL~k~l~ldLW~lYl~YIRr~n~~~tGq~r~~i~~ayefv~~~~~~e~~s~~~W~ey---~~fle~ 164 (660)
T COG5107 88 ARKDFRSVESLFGRCLKKSLNLDLWMLYLEYIRRVNNLITGQKRFKIYEAYEFVLGCAIFEPQSENYWDEY---GLFLEY 164 (660)
T ss_pred hhhhHHHHHHHHHHHHhhhccHhHHHHHHHHHHhhCcccccchhhhhHHHHHHHHhcccccccccchHHHH---HHHHHh
Confidence 357889999999999999999999999999888899887741 111111 1445566666 457889
Q ss_pred HHHHHHHHHHHHh
Q 017623 118 ILLFNHLLEHQYH 130 (368)
Q Consensus 118 I~~FN~Lle~Q~~ 130 (368)
|..||+.=+||+-
T Consensus 165 ~~~~~kwEeQqri 177 (660)
T COG5107 165 IEELGKWEEQQRI 177 (660)
T ss_pred ccccccHHHHHHH
Confidence 9999998777753
No 68
>PF06413 Neugrin: Neugrin; InterPro: IPR010487 This family contains mouse and human neugrin proteins. Neugrin and m-neugrin are mainly expressed in neurons in the nervous system, and are thought to play an important role in the process of neuronal differentiation []. Homologues of neugrin are found in fungi suggesting they have a alternative role or more than one function.
Probab=28.43 E-value=67 Score=30.95 Aligned_cols=49 Identities=18% Similarity=0.272 Sum_probs=36.4
Q ss_pred ccCCCCCcccHHhHHHHHHHHHHHHHhhcCHHHHHHHHHHhcCCCCcchHHHHH
Q 017623 42 ASSNDSRKVSRQDIELVQNLIERCLQLYMNRDEVVKTLLTRARIDPGFTTLVWQ 95 (368)
Q Consensus 42 ~~~~~~r~vS~edI~~VQnLIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~VW~ 95 (368)
++.+-.|++||+.++.|+.|=+ -.-.+=.+..|.+.++|.|....-|.+
T Consensus 3 ~~~~p~k~Ls~~~~~~ir~L~~-----~~p~~~t~~~Lae~F~vspe~irrILk 51 (225)
T PF06413_consen 3 PPGNPPKKLSREAMEQIRYLHK-----EDPEEWTVERLAESFKVSPEAIRRILK 51 (225)
T ss_pred CCCCCCCCCCHHHHHHHHHHHH-----hCccccCHHHHHhhCCCCHHHHHHHHh
Confidence 3567789999999999876643 222222688899999999998776643
No 69
>PLN02849 beta-glucosidase
Probab=28.30 E-value=61 Score=34.35 Aligned_cols=46 Identities=28% Similarity=0.398 Sum_probs=30.3
Q ss_pred HHHHHhhcCHHHHHHHHHHhcCCCCcchHHHH---HHHH--------HHcHHHHHHHHHHH
Q 017623 63 ERCLQLYMNRDEVVKTLLTRARIDPGFTTLVW---QKLE--------EENADFFRAYYIRL 112 (368)
Q Consensus 63 ErCLqlyMsk~Evv~~L~~~a~I~P~fT~~VW---~kLE--------eeNpeFFkaYy~Rl 112 (368)
++=|++| +++|++| ..+||+|.+|..=| +.|+ ++..++|..|-..+
T Consensus 115 ~~gl~fY---~~lid~l-~~~GI~P~VTL~H~dlP~~L~~~yGGW~nr~~v~~F~~YA~~~ 171 (503)
T PLN02849 115 PKGLQFY---KNFIQEL-VKHGIEPHVTLFHYDHPQYLEDDYGGWINRRIIKDFTAYADVC 171 (503)
T ss_pred HHHHHHH---HHHHHHH-HHcCCeEEEeecCCCCcHHHHHhcCCcCCchHHHHHHHHHHHH
Confidence 3446666 5667766 47889999998766 2344 35567888884433
No 70
>KOG4721 consensus Serine/threonine protein kinase, contains leucine zipper domain [Signal transduction mechanisms]
Probab=28.12 E-value=1.9e+02 Score=32.84 Aligned_cols=62 Identities=23% Similarity=0.347 Sum_probs=40.7
Q ss_pred HHHHhhcCHHHHHHHHHHhcCCCCcchHHHHHHHHHHcHHHHH--HHHHHHHHHHHHHHHHHHHHHHHhhh
Q 017623 64 RCLQLYMNRDEVVKTLLTRARIDPGFTTLVWQKLEEENADFFR--AYYIRLKLKKQILLFNHLLEHQYHLM 132 (368)
Q Consensus 64 rCLqlyMsk~Evv~~L~~~a~I~P~fT~~VW~kLEeeNpeFFk--aYy~Rl~LK~QI~~FN~Lle~Q~~lm 132 (368)
+|+..| .+|+|+-=.++.+---.|...-=.|||+.|.=||+ +-+++|+||+. .|+|.-..|.
T Consensus 403 t~ih~~--eeelirrR~eelrHa~DIR~~YE~KLertN~ly~eLs~cm~qLelkEk-----ElaerEq~l~ 466 (904)
T KOG4721|consen 403 TCIHRL--EEELIRRRREELRHALDIREHYERKLERTNNLYMELSACMLQLELKEK-----ELAEREQALE 466 (904)
T ss_pred chHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHH
Confidence 566655 55665544444443445666667899999999998 45778888886 5666554443
No 71
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=28.06 E-value=1.2e+02 Score=22.51 Aligned_cols=35 Identities=29% Similarity=0.413 Sum_probs=29.4
Q ss_pred CCCCCcccHHhHHHHHHHHHHHHHhhcCHHHHHHHH
Q 017623 44 SNDSRKVSRQDIELVQNLIERCLQLYMNRDEVVKTL 79 (368)
Q Consensus 44 ~~~~r~vS~edI~~VQnLIErCLqlyMsk~Evv~~L 79 (368)
.+..|..+.+||..++. |-+..+..|+.+||.+.|
T Consensus 32 ~~g~R~y~~~~l~~l~~-i~~l~~~g~~l~~i~~~l 66 (67)
T cd04764 32 ENGRRYYTDEDIELLKK-IKTLLEKGLSIKEIKEIL 66 (67)
T ss_pred CCCceeeCHHHHHHHHH-HHHHHHCCCCHHHHHHHh
Confidence 55678899999998876 667788999999998866
No 72
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=27.77 E-value=1.7e+02 Score=24.02 Aligned_cols=37 Identities=24% Similarity=0.214 Sum_probs=30.3
Q ss_pred CCCCCcccHHhHHHHHHHHHHHHH-hhcCHHHHHHHHHH
Q 017623 44 SNDSRKVSRQDIELVQNLIERCLQ-LYMNRDEVVKTLLT 81 (368)
Q Consensus 44 ~~~~r~vS~edI~~VQnLIErCLq-lyMsk~Evv~~L~~ 81 (368)
.+..|..+.+||..++ +|-+|.. +-|+.+|+...|..
T Consensus 32 ~~g~R~Y~~~dv~~l~-~I~~L~~~~G~~l~ei~~~l~~ 69 (96)
T cd04774 32 EGRYRLYSEEDLKRLE-RILRLREVLGFSLQEVTHFLER 69 (96)
T ss_pred CCCCEEECHHHHHHHH-HHHHHHHHcCCCHHHHHHHHhc
Confidence 4567899999999887 5667777 89999999888854
No 73
>PF13551 HTH_29: Winged helix-turn helix
Probab=27.56 E-value=1.7e+02 Score=23.00 Aligned_cols=50 Identities=14% Similarity=0.101 Sum_probs=34.9
Q ss_pred ccHHhHHHHHHHHHHHHH---hhcCHHHHHHHH-HHhcCCCCcchHHHHHHHHHH
Q 017623 50 VSRQDIELVQNLIERCLQ---LYMNRDEVVKTL-LTRARIDPGFTTLVWQKLEEE 100 (368)
Q Consensus 50 vS~edI~~VQnLIErCLq---lyMsk~Evv~~L-~~~a~I~P~fT~~VW~kLEee 100 (368)
++.+.+..|..++++=-. ...+.+++.+.| .++.+|.+.. .+||+-|.+.
T Consensus 58 l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~-~ti~r~L~~~ 111 (112)
T PF13551_consen 58 LSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSP-STIRRILKRA 111 (112)
T ss_pred CCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCH-HHHHHHHHHC
Confidence 788888875555543211 247889999988 7777777765 6788888764
No 74
>TIGR01795 CM_mono_cladeE monofunctional chorismate mutase, alpha proteobacterial type. The alpha proteobacterial members are trusted because the pathways of CM are evident and there is only one plausible CM in the genome. In S. coelicolor, however, there is another aparrent monofunctional CM.
Probab=27.45 E-value=97 Score=25.83 Aligned_cols=24 Identities=25% Similarity=0.304 Sum_probs=19.7
Q ss_pred HHHHhcCCCCcchHHHHHHHHHHc
Q 017623 78 TLLTRARIDPGFTTLVWQKLEEEN 101 (368)
Q Consensus 78 ~L~~~a~I~P~fT~~VW~kLEeeN 101 (368)
.+.++.|++|.|...+|+.+-++.
T Consensus 59 ~~a~~~gl~p~~~e~i~~~i~~es 82 (94)
T TIGR01795 59 RLAIDAGLDPEFAEKFLNFIVTEV 82 (94)
T ss_pred HHHHHCCCCHHHHHHHHHHHHHHH
Confidence 355788999999999999887764
No 75
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domain
Probab=27.36 E-value=4.3e+02 Score=23.98 Aligned_cols=37 Identities=14% Similarity=0.145 Sum_probs=31.6
Q ss_pred CCCCCcccHHhHHHHHHHHHHHHHhhcCHHHHHHHHHH
Q 017623 44 SNDSRKVSRQDIELVQNLIERCLQLYMNRDEVVKTLLT 81 (368)
Q Consensus 44 ~~~~r~vS~edI~~VQnLIErCLqlyMsk~Evv~~L~~ 81 (368)
.++-|..+.+|+..+ .+|-.+-.+-|+.+||-..|..
T Consensus 34 ~~gyR~Y~~~dl~rL-~~I~~lr~~G~sL~eI~~ll~~ 70 (172)
T cd04790 34 ESNYRLYGERDLERL-EQICAYRSAGVSLEDIRSLLQQ 70 (172)
T ss_pred CCCCccCCHHHHHHH-HHHHHHHHcCCCHHHHHHHHhc
Confidence 467789999999999 6788888899999998887753
No 76
>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=27.20 E-value=97 Score=28.15 Aligned_cols=61 Identities=11% Similarity=0.208 Sum_probs=40.4
Q ss_pred HHHHHHHhhcCHHHHHHHHHHhcCCCCcchHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 017623 61 LIERCLQLYMNRDEVVKTLLTRARIDPGFTTLVWQKLEEENADFFRAYYIRLKLKKQILLFNHLLEHQ 128 (368)
Q Consensus 61 LIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~VW~kLEeeNpeFFkaYy~Rl~LK~QI~~FN~Lle~Q 128 (368)
+++.+..+.++.+++...|+ +.|+....+..+|+...+.-+ .+|-.++++..++|+|..-.
T Consensus 51 iL~~A~k~n~~~~~l~~eL~-~lglp~e~~~~l~~~~~~~~~------~l~~~l~~~~l~~~~L~d~~ 111 (174)
T cd04752 51 ILSSAAKYNVDGESLSSELQ-QLGLPKEHATSLCRSYEEKQS------KLQESLRANSLRLSRLESVD 111 (174)
T ss_pred HHHHHHHcCCCHHHHHHHHH-HcCCCHHHHHHHHHHHHHHHH------HHHHHHHhcCCCCCcccccc
Confidence 34566667788888888884 558999888888875443222 25556677766777765433
No 77
>cd02433 Nodulin-21_like_2 Nodulin-21 and CCC1-related protein family. Nodulin-21_like_2: This is a family of proteins closely related to nodulin-21, a plant nodule-specific protein that may be involved in symbiotic nitrogen fixation. This family is also related to CCC1, a yeast vacuole transmembrane protein that functions as an iron and manganese transporter.
Probab=27.18 E-value=1.1e+02 Score=29.48 Aligned_cols=55 Identities=11% Similarity=0.024 Sum_probs=39.7
Q ss_pred HhHHHHHHHHHHHHHhhcCHHHHHHHHHHhcCCCCcchHHHHHHHHHHcHHHHHHHHHH
Q 017623 53 QDIELVQNLIERCLQLYMNRDEVVKTLLTRARIDPGFTTLVWQKLEEENADFFRAYYIR 111 (368)
Q Consensus 53 edI~~VQnLIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~VW~kLEeeNpeFFkaYy~R 111 (368)
..++.-+..|+.|.+ .-++|+++.++++ |+.+.--..|=++|.+ |+++|.....+
T Consensus 83 ~~~~re~~~i~~~p~--~e~~el~~iy~~~-G~~~~~a~~~~~~l~~-~~~~~~~~~~~ 137 (234)
T cd02433 83 ASIPDERRELRKHPL--EEAAELALIYRAK-GLDEEEAKRVASQLMN-DPEQALDTLAR 137 (234)
T ss_pred HHHHHHHHHhhhCcH--HHHHHHHHHHHHc-CCCHHHHHHHHHHHHh-CcchhHHHHHH
Confidence 345566677777776 4578888877554 9999999999999975 68887555443
No 78
>PRK15014 6-phospho-beta-glucosidase BglA; Provisional
Probab=27.10 E-value=80 Score=33.20 Aligned_cols=38 Identities=24% Similarity=0.369 Sum_probs=24.3
Q ss_pred HHHHHHHHHhcCCCCcchHHHHHH---HH--------HHcHHHHHHHHHH
Q 017623 73 DEVVKTLLTRARIDPGFTTLVWQK---LE--------EENADFFRAYYIR 111 (368)
Q Consensus 73 ~Evv~~L~~~a~I~P~fT~~VW~k---LE--------eeNpeFFkaYy~R 111 (368)
+++|++| .++||+|.+|..=|.- |+ ++..+.|..|-..
T Consensus 113 ~~lid~l-~~~GI~P~vTL~H~dlP~~L~~~yGGW~n~~~~~~F~~Ya~~ 161 (477)
T PRK15014 113 DDMFDEL-LKYNIEPVITLSHFEMPLHLVQQYGSWTNRKVVDFFVRFAEV 161 (477)
T ss_pred HHHHHHH-HHcCCEEEEEeeCCCCCHHHHHhcCCCCChHHHHHHHHHHHH
Confidence 4556655 4678999999854432 43 4556778888433
No 79
>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=27.04 E-value=99 Score=22.96 Aligned_cols=35 Identities=23% Similarity=0.175 Sum_probs=21.4
Q ss_pred HHHHHHHhhcCHHHHHHHHHHhcCCCCc-chHHHHH
Q 017623 61 LIERCLQLYMNRDEVVKTLLTRARIDPG-FTTLVWQ 95 (368)
Q Consensus 61 LIErCLqlyMsk~Evv~~L~~~a~I~P~-fT~~VW~ 95 (368)
.|=+++..-.|.+|+++.|.++++++|. ...-|.+
T Consensus 21 ~Iw~~~~g~~t~~ei~~~l~~~y~~~~~~~~~dv~~ 56 (68)
T PF05402_consen 21 FIWELLDGPRTVEEIVDALAEEYDVDPEEAEEDVEE 56 (68)
T ss_dssp HHHHH--SSS-HHHHHHHHHHHTT--HHHHHHHHHH
T ss_pred HHHHHccCCCCHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 3433336778999999999999999987 3333433
No 80
>PLN02814 beta-glucosidase
Probab=26.24 E-value=77 Score=33.63 Aligned_cols=45 Identities=27% Similarity=0.385 Sum_probs=29.7
Q ss_pred HHHHhhcCHHHHHHHHHHhcCCCCcchHHHH---HHHH--------HHcHHHHHHHHHHH
Q 017623 64 RCLQLYMNRDEVVKTLLTRARIDPGFTTLVW---QKLE--------EENADFFRAYYIRL 112 (368)
Q Consensus 64 rCLqlyMsk~Evv~~L~~~a~I~P~fT~~VW---~kLE--------eeNpeFFkaYy~Rl 112 (368)
+=|++| +++|+.| ..+||+|.+|..=| +.|+ ++..++|..|-..+
T Consensus 114 ~Gl~fY---~~lId~l-~~~GI~P~VTL~H~dlP~~L~~~yGGW~n~~~i~~F~~YA~~~ 169 (504)
T PLN02814 114 KGLLFY---KNLIKEL-RSHGIEPHVTLYHYDLPQSLEDEYGGWINRKIIEDFTAFADVC 169 (504)
T ss_pred HHHHHH---HHHHHHH-HHcCCceEEEecCCCCCHHHHHhcCCcCChhHHHHHHHHHHHH
Confidence 444454 5556655 46889999998776 2344 46678898885444
No 81
>PF13592 HTH_33: Winged helix-turn helix
Probab=26.20 E-value=48 Score=24.97 Aligned_cols=42 Identities=14% Similarity=0.048 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHHHhhcCHHHHHHHHHHhcCCCCcchHHHHHHH
Q 017623 55 IELVQNLIERCLQLYMNRDEVVKTLLTRARIDPGFTTLVWQKL 97 (368)
Q Consensus 55 I~~VQnLIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~VW~kL 97 (368)
...|+.+|++++.--++..-|-+.| ++.|+...-...+=.+-
T Consensus 7 ~~~i~~~I~~~fgv~ys~~~v~~lL-~r~G~s~~kp~~~~~k~ 48 (60)
T PF13592_consen 7 LKEIAAYIEEEFGVKYSPSGVYRLL-KRLGFSYQKPRPRPPKA 48 (60)
T ss_pred HHHHHHHHHHHHCCEEcHHHHHHHH-HHcCCccccCCCCcccC
Confidence 5678889999999999888877755 68888777766653333
No 82
>TIGR00207 fliG flagellar motor switch protein FliG. The fliG protein along with fliM and fliN interact to form the switch complex of the bacterial flagellar motor located at the base of the basal body. This complex interacts with chemotaxis proteins (eg CHEY). In addition the complex interacts with other components of the motor that determine the direction of flagellar rotation. The model contains putative members of the fliG family at scores of less than 100 from Agrobacterium radiobacter and Sinorhizobium meliloti as well as fliG-like genes from treponema pallidum and Borrelia burgdorferi. That is why the suggested cutoff is set at 20 but was set at 100 to construct the family.
Probab=26.16 E-value=1.9e+02 Score=28.98 Aligned_cols=71 Identities=17% Similarity=0.312 Sum_probs=50.4
Q ss_pred CcccHHhHHHHHHHHHHHHHhhcCHH------HHHHHHHHhcCCCCcchHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHH
Q 017623 48 RKVSRQDIELVQNLIERCLQLYMNRD------EVVKTLLTRARIDPGFTTLVWQKLEEENADFFRAYYIRLKLKKQILLF 121 (368)
Q Consensus 48 r~vS~edI~~VQnLIErCLqlyMsk~------Evv~~L~~~a~I~P~fT~~VW~kLEeeNpeFFkaYy~Rl~LK~QI~~F 121 (368)
+.|+.+-++.|-..+++|+..+-++. +.+..+.++ ++..-...|...|++.+|++.+. +|+.+=.|
T Consensus 170 ~~vs~~~i~~ie~~L~~~~~~~~~~~~~~gG~~~~a~ILN~--~~~~~~~~il~~L~~~dp~la~~------Ir~~mF~F 241 (338)
T TIGR00207 170 GRTSPEVVAEVERVLEGKLDSLNSDYTKMGGVRAVAEIINL--MDRKTEKTIITSLEEFDPELAEE------IKKEMFVF 241 (338)
T ss_pred CCCCHHHHHHHHHHHHHHHHhhccccccCChHHHHHHHHHh--CCchHHHHHHHHHHHhCHHHHHH------HHHHccCH
Confidence 57888899999999999998765421 223333332 34555568999999999999874 67777777
Q ss_pred HHHHH
Q 017623 122 NHLLE 126 (368)
Q Consensus 122 N~Lle 126 (368)
-.|+.
T Consensus 242 edl~~ 246 (338)
T TIGR00207 242 EDIVD 246 (338)
T ss_pred HHHhc
Confidence 77764
No 83
>PLN02998 beta-glucosidase
Probab=25.81 E-value=74 Score=33.68 Aligned_cols=45 Identities=29% Similarity=0.377 Sum_probs=29.9
Q ss_pred HHHHhhcCHHHHHHHHHHhcCCCCcchHHHH---HHH--------HHHcHHHHHHHHHHH
Q 017623 64 RCLQLYMNRDEVVKTLLTRARIDPGFTTLVW---QKL--------EEENADFFRAYYIRL 112 (368)
Q Consensus 64 rCLqlyMsk~Evv~~L~~~a~I~P~fT~~VW---~kL--------EeeNpeFFkaYy~Rl 112 (368)
+=|++| +++|++| ...||+|.+|..=| +.| -++..++|..|-..+
T Consensus 119 ~gl~~Y---~~lid~L-~~~GIeP~VTL~H~dlP~~L~~~yGGW~n~~~v~~F~~YA~~~ 174 (497)
T PLN02998 119 KGLQYY---NNLIDEL-ITHGIQPHVTLHHFDLPQALEDEYGGWLSQEIVRDFTAYADTC 174 (497)
T ss_pred HHHHHH---HHHHHHH-HHcCCceEEEecCCCCCHHHHHhhCCcCCchHHHHHHHHHHHH
Confidence 445555 5666666 47889999998766 233 346678888884433
No 84
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=25.39 E-value=4e+02 Score=22.22 Aligned_cols=71 Identities=17% Similarity=0.173 Sum_probs=45.3
Q ss_pred CCCCCcccHHhHHHHHHHHHHHHHhhcCHHHHHHHHHHhcCCCCcchHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHH
Q 017623 44 SNDSRKVSRQDIELVQNLIERCLQLYMNRDEVVKTLLTRARIDPGFTTLVWQKLEEENADFFRAYYIRLKLKKQILLFNH 123 (368)
Q Consensus 44 ~~~~r~vS~edI~~VQnLIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~VW~kLEeeNpeFFkaYy~Rl~LK~QI~~FN~ 123 (368)
.+.-|..+.++|..++ +|-.+-.+-|+.+||-..|.... ....+..-|.. +++. .+-.|.+||.....
T Consensus 33 ~~gyR~Y~~~~i~~l~-~I~~lr~~G~sl~eI~~~l~~~~--~~~~~~~~~~~-------~l~~--~~~~l~~~i~~l~~ 100 (123)
T cd04770 33 ENGYRLYGEADLARLR-FIRRAQALGFSLAEIRELLSLRD--DGAAPCAEVRA-------LLEE--KLAEVEAKIAELQA 100 (123)
T ss_pred CCCCccCCHHHHHHHH-HHHHHHHCCCCHHHHHHHHHhhh--cCCCCHHHHHH-------HHHH--HHHHHHHHHHHHHH
Confidence 4567899999999985 67778999999999998885432 12223322222 2221 23446777776655
Q ss_pred HHH
Q 017623 124 LLE 126 (368)
Q Consensus 124 Lle 126 (368)
+.+
T Consensus 101 ~~~ 103 (123)
T cd04770 101 LRA 103 (123)
T ss_pred HHH
Confidence 543
No 85
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=25.35 E-value=1.6e+02 Score=21.69 Aligned_cols=34 Identities=12% Similarity=0.077 Sum_probs=26.9
Q ss_pred CCCCcccHHhHHHHHHHHHHHHHhhcCHHHHHHHH
Q 017623 45 NDSRKVSRQDIELVQNLIERCLQLYMNRDEVVKTL 79 (368)
Q Consensus 45 ~~~r~vS~edI~~VQnLIErCLqlyMsk~Evv~~L 79 (368)
++.|.++.+||..++.+ -.+...-|+.+|+.+.|
T Consensus 34 ~~~r~yt~~~v~~l~~i-~~l~~~g~~l~~i~~~~ 67 (68)
T cd01104 34 GGHRLYSEADVARLRLI-RRLTSEGVRISQAAALA 67 (68)
T ss_pred CCCeecCHHHHHHHHHH-HHHHHCCCCHHHHHHHh
Confidence 46689999999988754 44566899999998865
No 86
>PF15369 KIAA1328: Uncharacterised protein KIAA1328
Probab=25.31 E-value=3.2e+02 Score=28.27 Aligned_cols=73 Identities=21% Similarity=0.179 Sum_probs=47.6
Q ss_pred HHhHHHHHHHHHHHHHhhcCHHHHHHHHHHhcCCCCcchHHHHHHHHHHcHHHHH----------HHHHHHHHHHHHHHH
Q 017623 52 RQDIELVQNLIERCLQLYMNRDEVVKTLLTRARIDPGFTTLVWQKLEEENADFFR----------AYYIRLKLKKQILLF 121 (368)
Q Consensus 52 ~edI~~VQnLIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~VW~kLEeeNpeFFk----------aYy~Rl~LK~QI~~F 121 (368)
.+|-+.|.|||+.--..-=-|++++.-|..+ -.--+.-.++||++|.=.-+ .----|.|-+|
T Consensus 4 ~~dk~ri~~li~~la~~~~~~e~~~~~~~~~----~~~~e~~~~~l~~~~~~~~~~~~~~~~qyrecqell~lyq~---- 75 (328)
T PF15369_consen 4 PEDKRRIANLIKELARVSEEKEVTEERLKAE----QESFEKKIRQLEEQNELIIKEREDLQQQYRECQELLSLYQK---- 75 (328)
T ss_pred hhHHHHHHHHHHHHHHhhhHHHHHHHHHHHH----HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHH----
Confidence 4788999999998777777777777766533 22223345678888764333 33334556666
Q ss_pred HHHHHHHHhhhc
Q 017623 122 NHLLEHQYHLMK 133 (368)
Q Consensus 122 N~Lle~Q~~lm~ 133 (368)
+|.++|..|..
T Consensus 76 -ylseqq~kl~~ 86 (328)
T PF15369_consen 76 -YLSEQQEKLTM 86 (328)
T ss_pred -HHHHHHHHHhc
Confidence 77788887744
No 87
>KOG3303 consensus Predicted alpha-helical protein, potentially involved in replication/repair [Replication, recombination and repair]
Probab=24.87 E-value=1.6e+02 Score=28.32 Aligned_cols=46 Identities=22% Similarity=0.381 Sum_probs=34.6
Q ss_pred HHHHHhhc-CHHHHHHHHHHhcCCCCcchHHHHHHHHHHcHHHHHHHHH
Q 017623 63 ERCLQLYM-NRDEVVKTLLTRARIDPGFTTLVWQKLEEENADFFRAYYI 110 (368)
Q Consensus 63 ErCLqlyM-sk~Evv~~L~~~a~I~P~fT~~VW~kLEeeNpeFFkaYy~ 110 (368)
+|||--|- .+.+.++.+.=..| -..-+.+=..|-.+-.|||+.|..
T Consensus 76 kRClmAY~~~R~~~lr~~~W~~g--~~lps~i~~sls~~E~eyf~~Ys~ 122 (192)
T KOG3303|consen 76 KRCLMAYVYLRLARLRDLAWSYG--LDLPSSIRFSLSHEEEEYFKNYSN 122 (192)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcC--CCccHHHHHhhhHHHHHHHHHHHH
Confidence 79999885 46788888876666 444455556688889999999954
No 88
>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators. Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=24.85 E-value=4.4e+02 Score=22.45 Aligned_cols=71 Identities=14% Similarity=0.152 Sum_probs=47.3
Q ss_pred CCCCCcccHHhHHHHHHHHHHHHHhhcCHHHHHHHHHHhcCCCCcchHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHH
Q 017623 44 SNDSRKVSRQDIELVQNLIERCLQLYMNRDEVVKTLLTRARIDPGFTTLVWQKLEEENADFFRAYYIRLKLKKQILLFNH 123 (368)
Q Consensus 44 ~~~~r~vS~edI~~VQnLIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~VW~kLEeeNpeFFkaYy~Rl~LK~QI~~FN~ 123 (368)
.+..|..+.++|..++ +|-++-..-|+.+||-+.|.... .+..+...|..+-++ .+-.|.++|.+...
T Consensus 33 ~~g~R~Y~~~~l~~l~-~I~~lr~~G~sL~eI~~~l~~~~--~~~~~~~~~~~~l~~---------~~~~l~~~i~~L~~ 100 (126)
T cd04785 33 AGGYRLYGAAHVERLR-FIRRARDLGFSLEEIRALLALSD--RPDRSCAEADAIARA---------HLADVRARIADLRR 100 (126)
T ss_pred CCCccccCHHHHHHHH-HHHHHHHCCCCHHHHHHHHhhhh--cCCCCHHHHHHHHHH---------HHHHHHHHHHHHHH
Confidence 4577899999999987 56778889999999998875332 344444444333221 34557777777666
Q ss_pred HHH
Q 017623 124 LLE 126 (368)
Q Consensus 124 Lle 126 (368)
+..
T Consensus 101 ~~~ 103 (126)
T cd04785 101 LEA 103 (126)
T ss_pred HHH
Confidence 543
No 89
>PRK10753 transcriptional regulator HU subunit alpha; Provisional
Probab=24.79 E-value=95 Score=25.31 Aligned_cols=19 Identities=16% Similarity=0.468 Sum_probs=15.3
Q ss_pred cCHHHHHHHHHHhcCCCCc
Q 017623 70 MNRDEVVKTLLTRARIDPG 88 (368)
Q Consensus 70 Msk~Evv~~L~~~a~I~P~ 88 (368)
|||.|+|+.|.++.++...
T Consensus 1 M~K~eli~~ia~~~~~s~~ 19 (90)
T PRK10753 1 MNKTQLIDVIADKAELSKT 19 (90)
T ss_pred CCHHHHHHHHHHHhCCCHH
Confidence 8999999999888766544
No 90
>PF14164 YqzH: YqzH-like protein
Probab=24.45 E-value=1e+02 Score=24.92 Aligned_cols=14 Identities=36% Similarity=0.914 Sum_probs=12.5
Q ss_pred HHHHHHHHHHHHhh
Q 017623 56 ELVQNLIERCLQLY 69 (368)
Q Consensus 56 ~~VQnLIErCLqly 69 (368)
++++.+|-+||+.|
T Consensus 4 k~I~Kmi~~~l~QY 17 (64)
T PF14164_consen 4 KLIEKMIINCLRQY 17 (64)
T ss_pred HHHHHHHHHHHHHh
Confidence 56888999999999
No 91
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=23.82 E-value=6.1e+02 Score=23.79 Aligned_cols=22 Identities=23% Similarity=0.329 Sum_probs=17.6
Q ss_pred HHHHHHHHHH-------HHHHHHhhhcCC
Q 017623 114 LKKQILLFNH-------LLEHQYHLMKYP 135 (368)
Q Consensus 114 LK~QI~~FN~-------Lle~Q~~lm~~~ 135 (368)
..+++.+|+. |+++|.+|....
T Consensus 102 ~~~kssk~e~~Gi~eEEL~~qQqeLf~~A 130 (156)
T KOG0871|consen 102 RRRKSSKFEKSGIPEEELLRQQQELFAKA 130 (156)
T ss_pred hhhhhhhHHhcCCCHHHHHHHHHHHHHHH
Confidence 6678889984 899999987654
No 92
>PF12980 DUF3864: Domain of Unknown Function with PDB structure (DUF3864); InterPro: IPR024335 This entry represents a functionally uncharacterised domain found in bacterial sequences. The structure of one of the sequences, A6LGL1 from SWISSPROT from Parabacteroides distasonis atcc 8503, has been determined.; PDB: 3LM3_A.
Probab=23.74 E-value=21 Score=29.73 Aligned_cols=32 Identities=25% Similarity=0.528 Sum_probs=21.6
Q ss_pred HhcCCCCcchHHHHHHHHHHcHHHHHHHHHHH
Q 017623 81 TRARIDPGFTTLVWQKLEEENADFFRAYYIRL 112 (368)
Q Consensus 81 ~~a~I~P~fT~~VW~kLEeeNpeFFkaYy~Rl 112 (368)
+|.+..|.=+-.+.++|++++.+|-++||-.|
T Consensus 49 nqkglrpqd~pvll~~l~~~~q~li~kyyp~l 80 (82)
T PF12980_consen 49 NQKGLRPQDKPVLLSELSQEDQDLIRKYYPEL 80 (82)
T ss_dssp -TT--SGGGS-B-GGGS-HHHHHHHHHH-GGG
T ss_pred hhccCCCcCcchHHHHHhHHHHHHHHHHhHHh
Confidence 46677788788889999999999999999754
No 93
>COG1427 Predicted periplasmic solute-binding protein [General function prediction only]
Probab=23.41 E-value=1.9e+02 Score=28.66 Aligned_cols=60 Identities=15% Similarity=0.165 Sum_probs=44.3
Q ss_pred hHHHHHHHHHHHHHhhcCHHHHHHHHHHhcCCCCcchHHHHHHHH-------HHcHHHHHHHHHHHHHHH
Q 017623 54 DIELVQNLIERCLQLYMNRDEVVKTLLTRARIDPGFTTLVWQKLE-------EENADFFRAYYIRLKLKK 116 (368)
Q Consensus 54 dI~~VQnLIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~VW~kLE-------eeNpeFFkaYy~Rl~LK~ 116 (368)
+-+.++..+++--.++ +||++.++++.||...+-+--+..+. +++-++|..|+.+..+|.
T Consensus 182 ~~~~~~~~~~~~~~~~---~ei~~~~a~~lglp~~~~~eYy~~~~Y~l~~e~~~~l~~f~~~~~~~~~~~ 248 (252)
T COG1427 182 YKRALLEFEETKAKFP---AEILKEAAKRLGLPRSDVEEYYTNIRYSLGTEEQRGLERFYEYLGALRLKA 248 (252)
T ss_pred hhhhHHHHHHHHHhhh---HHHHHHHHHHcCCCHHHHHHHHHHheeecCHHHHHHHHHHHHHHhhhhhcc
Confidence 4455666666666666 99999999999999887766655553 667788888877776653
No 94
>PF03399 SAC3_GANP: SAC3/GANP/Nin1/mts3/eIF-3 p25 family; InterPro: IPR005062 This large family includes diverse proteins involved in large complexes [, , ]. The alignment contains one highly conserved negatively charged residue and one highly conserved positively charged residue that are probably important for the function of these proteins. The family includes the yeast nuclear export factor Sac3 [], and mammalian GANP/MCM3-associated proteins, which facilitate the nuclear localisation of MCM3, a protein that associates with chromatin in the G1 phase of the cell-cycle. The 26S protease (or 26S proteasome) is responsible for degrading ubiquitin conjugates. It consists of 19S regulatory complexes associated with the ends of 20S proteasomes. The 19S regulatory complex is composed of about 20 different polypeptides and confers ATP-dependence and substrate specificity to the 26S enzyme. The conserved region occurs at the C-terminal of the Nin1-like regulatory subunit [, , ]. This family includes several eukaryotic translation initiation factor 3 subunit 11 (eIF-3 p25) proteins. Eukaryotic initiation factor 3 (eIF3) is a multisubunit complex that is required for binding of mRNA to 40 S ribosomal subunits, stabilisation of ternary complex binding to 40 S subunits, and dissociation of 40 and 60 S subunits [].; PDB: 3T5V_D.
Probab=22.61 E-value=2.2e+02 Score=25.10 Aligned_cols=58 Identities=24% Similarity=0.379 Sum_probs=34.0
Q ss_pred HHHHHHHHHHhhcCH------HHHHHHHHHhcCCCCcchHHHHHHH----HHHcHHHHHHHHHHHHH-HHHHHHHHHHHH
Q 017623 58 VQNLIERCLQLYMNR------DEVVKTLLTRARIDPGFTTLVWQKL----EEENADFFRAYYIRLKL-KKQILLFNHLLE 126 (368)
Q Consensus 58 VQnLIErCLqlyMsk------~Evv~~L~~~a~I~P~fT~~VW~kL----EeeNpeFFkaYy~Rl~L-K~QI~~FN~Lle 126 (368)
+-.+.|+|..+++-- .+|+..|.+ .+..+ ..+|..-|.+|++-..| .+++..|+..++
T Consensus 55 ~i~v~E~~ar~~i~~~d~~qf~~c~~~L~~-----------lY~~~~~~~~~~~~~ef~~y~lL~~l~~~~~~~~~~~l~ 123 (204)
T PF03399_consen 55 AIKVYERIARFAIESGDLEQFNQCLSQLKE-----------LYDDLRDLPPSPNEAEFIAYYLLYLLCQNNIPDFHMELE 123 (204)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHT---TTHHHHHHHHHHHTT-T---THHHHHHT
T ss_pred HHHHHHHHHHHHhhcCCHHHHHHHHHHHHH-----------HHHhhccCCCCCCHHHHHHHHHHHHHHcccchHHHHHHH
Confidence 666778777777632 234444432 22333 46788889999887777 677788887653
No 95
>smart00229 RasGEFN Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif. A subset of guanine nucleotide exchange factor for Ras-like small GTPases appear to possess this domain N-terminal to the RasGef (Cdc25-like) domain. The recent crystal structureof Sos shows that this domain is alpha-helical and plays a "purely structural role" (Nature 394, 337-343).
Probab=22.40 E-value=2.1e+02 Score=23.53 Aligned_cols=64 Identities=19% Similarity=0.272 Sum_probs=35.8
Q ss_pred HHHhhcCHHHHHHHHHHhcCCCCcc------------hHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 017623 65 CLQLYMNRDEVVKTLLTRARIDPGF------------TTLVWQKLEEENADFFRAYYIRLKLKKQILLFNHLLEHQ 128 (368)
Q Consensus 65 CLqlyMsk~Evv~~L~~~a~I~P~f------------T~~VW~kLEeeNpeFFkaYy~Rl~LK~QI~~FN~Lle~Q 128 (368)
+...+++-.|++..|..+++..|.. ...|-+-|..==..||..|.....|++++..|-..+++.
T Consensus 35 tyr~F~tp~~ll~~L~~rf~~~~~~~~~~~~~~~~~~~~rv~~~l~~Wv~~~~~dF~~~~~l~~~l~~f~~~~~~~ 110 (127)
T smart00229 35 TYRSFITTQELLQLLLYRYNAIPPESWVERKVNPLRVKNRVLNILRHWVENYWQDFEDDPKLILRLLEFLDLVDQE 110 (127)
T ss_pred HhhhhCCHHHHHHHHHHHhCCCCcHHHHHHHhhHHHHHHHHHHHHHHHHHHCCcccccCHHHHHHHHHHHHHHhhC
Confidence 4567889999999999998876654 222222222211223333444445666666666555433
No 96
>PF11417 Inhibitor_G39P: Loader and inhibitor of phage G40P; InterPro: IPR024424 G39P inhibits the initiation of DNA replication by blocking G40P replicative helicase. G39P has a bipartite stricture consisting of a folded N-terminal domain and an unfolded C-terminal domain. The C-terminal is essential for helicase interaction [].; PDB: 1NO1_B.
Probab=22.39 E-value=67 Score=25.86 Aligned_cols=18 Identities=28% Similarity=0.316 Sum_probs=10.3
Q ss_pred cCHHHHHHHHHHhcCCCC
Q 017623 70 MNRDEVVKTLLTRARIDP 87 (368)
Q Consensus 70 Msk~Evv~~L~~~a~I~P 87 (368)
|+|+|+++-|..-...=|
T Consensus 1 Mtk~E~~~ll~~I~~aYP 18 (71)
T PF11417_consen 1 MTKEETAKLLKLIKAAYP 18 (71)
T ss_dssp --HHHHHHHHHHHHHHST
T ss_pred CCHHHHHHHHHHHHHHCC
Confidence 899999997654433333
No 97
>PRK14135 recX recombination regulator RecX; Provisional
Probab=22.36 E-value=2.8e+02 Score=26.13 Aligned_cols=46 Identities=15% Similarity=0.200 Sum_probs=36.0
Q ss_pred hHHHHHHHHHHHHHh-hcCHHHHHHHHHHhcCCCCcchHHHHHHHHHH
Q 017623 54 DIELVQNLIERCLQL-YMNRDEVVKTLLTRARIDPGFTTLVWQKLEEE 100 (368)
Q Consensus 54 dI~~VQnLIErCLql-yMsk~Evv~~L~~~a~I~P~fT~~VW~kLEee 100 (368)
|.++++..+..++.. ...+.++...|. +.||.+.+...|+..|+++
T Consensus 106 D~~~a~~~~~~~~~~~~~g~~~I~~kL~-~kGi~~~~Ie~~l~~l~~~ 152 (263)
T PRK14135 106 DKEYAESYVRTNINTGDKGPRVIKQKLL-QKGIEDEIIEEALSEYTEE 152 (263)
T ss_pred HHHHHHHHHHHHHhccccchHHHHHHHH-HcCCCHHHHHHHHHhCChh
Confidence 567778888777764 468889999996 5699999999999888543
No 98
>cd07313 terB_like_2 tellurium resistance terB-like protein, subgroup 2. This family includes several uncharacterized bacterial proteins. Protein sequence homology analysis shows they are similar to tellurium resistance protein terB, but the function of this family is unknown.
Probab=22.21 E-value=2.2e+02 Score=22.66 Aligned_cols=29 Identities=7% Similarity=0.274 Sum_probs=22.9
Q ss_pred CCcccHHhHHHHHHHHHHHHHhhcCHHHHHH
Q 017623 47 SRKVSRQDIELVQNLIERCLQLYMNRDEVVK 77 (368)
Q Consensus 47 ~r~vS~edI~~VQnLIErCLqlyMsk~Evv~ 77 (368)
..+|+.++++.+.+++.+.+. ++.+|.-.
T Consensus 13 DG~v~~~E~~~i~~~l~~~~~--l~~~~~~~ 41 (104)
T cd07313 13 DGEYDEEERAAIDRLLAERFG--LDAEEAAE 41 (104)
T ss_pred cCCCCHHHHHHHHHHHHHHhC--cCHHHHHH
Confidence 367999999999999999864 56666644
No 99
>PF12295 Symplekin_C: Symplekin tight junction protein C terminal; InterPro: IPR022075 This domain family is found in eukaryotes, and is approximately 180 amino acids in length. There is a single completely conserved residue P that may be functionally important. Symplekn has been localized, by light and electron microscopy, to the plaque associated with the cytoplasmic face of the tight junction-containing zone (zonula occludens) of polar epithelial cells and of Sertoli cells of testis. However, both the mRNA and the protein can also be detected in a wide range of cell types that do not form tight junctions. Careful analyses have revealed that the protein occurs in all these diverse cells in the nucleoplasm, and only in those cells forming tight junctions is it recruited, partly but specifically, to the plaque structure of the zonula occludens.
Probab=21.94 E-value=1.5e+02 Score=27.33 Aligned_cols=61 Identities=20% Similarity=0.222 Sum_probs=49.4
Q ss_pred HhhcCHHHHHHHHHHhcCC-CCcchHHHHHHHHH-----------HcHHHHHHHHHH-----HHHHHHHHHHHHHHHH
Q 017623 67 QLYMNRDEVVKTLLTRARI-DPGFTTLVWQKLEE-----------ENADFFRAYYIR-----LKLKKQILLFNHLLEH 127 (368)
Q Consensus 67 qlyMsk~Evv~~L~~~a~I-~P~fT~~VW~kLEe-----------eNpeFFkaYy~R-----l~LK~QI~~FN~Lle~ 127 (368)
.-+++|+|++..|=+--+. .+..-..++++|-+ ...|.+-+|+.- ..+|+.|...|..++.
T Consensus 9 l~~L~k~ev~~~LP~li~~~~~~~~k~~~~rll~~~~~~~~~~~ltp~ElLv~lH~id~~~~~~~k~~~~a~~~Cf~~ 86 (183)
T PF12295_consen 9 LGGLDKDEVISLLPKLISLEPPKVVKEVFNRLLQAPSSSTGESPLTPSELLVALHNIDPEKDVPLKKIIEALDLCFSM 86 (183)
T ss_pred ccCCCHHHHHHHhHHHHHcCCHHHHHHHHHHHhcCCCCCCCCCCCCHHHHHHHHHhCCccccccHHHHHHHHHHHHcc
Confidence 3578999999988777777 77777888888877 267899999886 8999999999888754
No 100
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=21.82 E-value=1.3e+02 Score=26.74 Aligned_cols=30 Identities=20% Similarity=0.233 Sum_probs=25.2
Q ss_pred HhHHHHHHHHHHHHHhhcCHHHHHHHHHHh
Q 017623 53 QDIELVQNLIERCLQLYMNRDEVVKTLLTR 82 (368)
Q Consensus 53 edI~~VQnLIErCLqlyMsk~Evv~~L~~~ 82 (368)
.-...++++|+.|..+.+|++|+.+.|.+-
T Consensus 90 ~~~~~l~~~I~~~~~~G~s~eei~~~~~~~ 119 (125)
T COG1725 90 LAEEELEEFIEEAKALGLSLEEILELLKEI 119 (125)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 345678999999999999999999987643
No 101
>PF09763 Sec3_C: Exocyst complex component Sec3; InterPro: IPR019160 The exocyst complex is composed of 8 subunits: Exoc1, Exoc2, Exoc3, Exoc4, Exoc5, Exoc6, Exoc7 and Exoc8. This entry represents the subunit Exoc1 (Sec3). Sec3 binds to the C-terminal cytoplasmic domain of GLYT1 (glycine transporter protein 1). Sec3 is the exocyst component that is closest to the plasma membrane docking site and it serves as a spatial landmark in the plasma membrane for incoming secretory vesicles. Sec3 is recruited to the sites of polarised membrane growth through its interaction with Rho1p, a small GTP-binding protein.
Probab=21.75 E-value=2.3e+02 Score=30.74 Aligned_cols=49 Identities=14% Similarity=0.358 Sum_probs=31.8
Q ss_pred HHHHHHhhcCHH------HHHHHHHHhc-------CCCCcchHHHHHHHHHHcHHHHHHHHH
Q 017623 62 IERCLQLYMNRD------EVVKTLLTRA-------RIDPGFTTLVWQKLEEENADFFRAYYI 110 (368)
Q Consensus 62 IErCLqlyMsk~------Evv~~L~~~a-------~I~P~fT~~VW~kLEeeNpeFFkaYy~ 110 (368)
..++|..|-+|+ ..-+-+.||+ ..+...-..||+.+|++--+.|+.|+.
T Consensus 632 l~kvl~~y~~kev~k~i~~l~krveKHf~~~~~~~~~~~~Ll~~vW~~~q~~~i~~~~~l~~ 693 (701)
T PF09763_consen 632 LKKVLKSYPSKEVRKGIEALYKRVEKHFSRDADDPSFEEDLLQVVWSAMQEEFIRQYERLET 693 (701)
T ss_pred HHHHHHhCChHHHHHHHHHHHHHHHHHcCCccccccchhhHHHHHHHHHHHHHHHHHHHHHH
Confidence 345555664332 2334456777 678888899999999886555555543
No 102
>PRK09589 celA 6-phospho-beta-glucosidase; Reviewed
Probab=21.69 E-value=1.1e+02 Score=32.10 Aligned_cols=45 Identities=24% Similarity=0.397 Sum_probs=29.6
Q ss_pred HHHHhhcCHHHHHHHHHHhcCCCCcchHHHHH---HHH--------HHcHHHHHHHHHHH
Q 017623 64 RCLQLYMNRDEVVKTLLTRARIDPGFTTLVWQ---KLE--------EENADFFRAYYIRL 112 (368)
Q Consensus 64 rCLqlyMsk~Evv~~L~~~a~I~P~fT~~VW~---kLE--------eeNpeFFkaYy~Rl 112 (368)
+=|.+| +++|+.| .++||+|.+|..=|. .|+ ++..++|..|-..+
T Consensus 105 ~gl~~Y---~~lid~L-~~~GI~P~VTL~H~dlP~~L~~~yGGW~n~~~i~~F~~YA~~~ 160 (476)
T PRK09589 105 EGLQFY---DDLFDEC-LKQGIEPVVTLSHFEMPYHLVTEYGGWRNRKLIDFFVRFAEVV 160 (476)
T ss_pred HHHHHH---HHHHHHH-HHcCCEEEEEecCCCCCHHHHHhcCCcCChHHHHHHHHHHHHH
Confidence 335555 4556655 367899999987664 454 34567899885444
No 103
>COG4359 Uncharacterized conserved protein [Function unknown]
Probab=21.15 E-value=82 Score=30.63 Aligned_cols=26 Identities=31% Similarity=0.640 Sum_probs=22.2
Q ss_pred HhhcCHHHHHHHHHHhcCCCCcchHH
Q 017623 67 QLYMNRDEVVKTLLTRARIDPGFTTL 92 (368)
Q Consensus 67 qlyMsk~Evv~~L~~~a~I~P~fT~~ 92 (368)
..+.+.+||.+.|.+.++|+|.|-..
T Consensus 56 ~i~~s~~Eile~llk~i~Idp~fKef 81 (220)
T COG4359 56 SIHSSLEEILEFLLKDIKIDPGFKEF 81 (220)
T ss_pred hcCCCHHHHHHHHHhhcccCccHHHH
Confidence 45678899999999999999998654
No 104
>PF09278 MerR-DNA-bind: MerR, DNA binding; InterPro: IPR015358 This entry represents a family of DNA-binding domains that are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold []. ; PDB: 3QAO_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q09_A 1Q08_B 1Q0A_B 1Q07_A ....
Probab=21.05 E-value=3.5e+02 Score=19.90 Aligned_cols=56 Identities=20% Similarity=0.124 Sum_probs=38.3
Q ss_pred HHHHHHHHhhcCHHHHHHHHHHhcCCCCcchHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHH
Q 017623 60 NLIERCLQLYMNRDEVVKTLLTRARIDPGFTTLVWQKLEEENADFFRAYYIRLKLKKQILLFNHLLE 126 (368)
Q Consensus 60 nLIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~VW~kLEeeNpeFFkaYy~Rl~LK~QI~~FN~Lle 126 (368)
++|.+|=.+-||.+||-+.|.-..+ +.-+..-|..+-++ .+-.+.+||....++.+
T Consensus 5 ~~I~~~r~lGfsL~eI~~~l~l~~~--~~~~~~~~~~~l~~---------~~~~i~~~i~~L~~~~~ 60 (65)
T PF09278_consen 5 QFIRRLRELGFSLEEIRELLELYDQ--GDPPCADRRALLEE---------KLEEIEEQIAELQALRA 60 (65)
T ss_dssp HHHHHHHHTT--HHHHHHHHHHCCS--HCHHHHHHHHHHHH---------HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHcCCCHHHHHHHHhccCC--CCCCHHHHHHHHHH---------HHHHHHHHHHHHHHHHH
Confidence 4789999999999999998854343 77777777755443 34457777777766543
No 105
>PRK05686 fliG flagellar motor switch protein G; Validated
Probab=20.93 E-value=3e+02 Score=27.43 Aligned_cols=71 Identities=23% Similarity=0.413 Sum_probs=51.1
Q ss_pred CcccHHhHHHHHHHHHHHHHhhc-CH------HHHHHHHHHhcCCCCcchHHHHHHHHHHcHHHHHHHHHHHHHHHHHHH
Q 017623 48 RKVSRQDIELVQNLIERCLQLYM-NR------DEVVKTLLTRARIDPGFTTLVWQKLEEENADFFRAYYIRLKLKKQILL 120 (368)
Q Consensus 48 r~vS~edI~~VQnLIErCLqlyM-sk------~Evv~~L~~~a~I~P~fT~~VW~kLEeeNpeFFkaYy~Rl~LK~QI~~ 120 (368)
..|+.+-++.|-..+++||.... .+ -+.|-.+.+ ++++.-...|...|++.+|++.+ ++|+.+=.
T Consensus 172 ~~v~~~~~~~i~~~L~~~l~~~~~~~~~~~~g~~~~a~Iln--~~~~~~~~~il~~L~~~d~~~a~------~Ir~~mF~ 243 (339)
T PRK05686 172 EGVSPEALKEVEEVLEKKLSSMANADRTKMGGVKTVAEILN--NLDRQTEKTILESLEEEDPELAE------KIKDLMFV 243 (339)
T ss_pred CCCCHHHHHHHHHHHHHHHhhcccccccccCcHHHHHHHHh--cCCchHHHHHHHHHHhhCHHHHH------HHHHHhcC
Confidence 46788888888889999997622 11 122323322 35666677899999999999997 47788888
Q ss_pred HHHHHH
Q 017623 121 FNHLLE 126 (368)
Q Consensus 121 FN~Lle 126 (368)
|-.|+.
T Consensus 244 Fedl~~ 249 (339)
T PRK05686 244 FEDLVD 249 (339)
T ss_pred HHHHhc
Confidence 888764
No 106
>PF04358 DsrC: DsrC like protein; InterPro: IPR007453 DsrC (P45573 from SWISSPROT) has been observed to co-purify with Desulphovibrio vulgaris dissimilatory sulphite reductase []. However, DsrC appears to be only loosely associated to the sulphite reductase, which suggests that it may not be an integral part of the dissimilatory sulphite reductase. Many proteins in this entry are found in organisms such as Escherichia coli and Haemophilus influenzae which do not contain dissimilatory sulphite reductases but can synthesise assimilatory sirohaem sulphite and nitrite reductases. It is speculated that DsrC may be involved in the assembly, folding or stabilisation of sirohaem proteins []. The strictly conserved cysteine in the C terminus suggests that DsrC may have a catalytic function in the metabolism of sulphur compounds []. Also included in this entry is TusE, a partner to TusBCD in a sulphur relay system for 2-thiouridine biosynthesis, a tRNA base modification process. Many proteins in this entry are annotated as the third (gamma) subunit of dissimilatory sulphite reductase ; PDB: 2V4J_F 2A5W_C 1SAU_A 1JI8_A 1YX3_A.
Probab=20.70 E-value=1.8e+02 Score=25.19 Aligned_cols=34 Identities=24% Similarity=0.495 Sum_probs=24.5
Q ss_pred HHHHHHHHHhcCCCCcchHHHHHHHHHHcHHHHHHHH
Q 017623 73 DEVVKTLLTRARIDPGFTTLVWQKLEEENADFFRAYY 109 (368)
Q Consensus 73 ~Evv~~L~~~a~I~P~fT~~VW~kLEeeNpeFFkaYy 109 (368)
+|+.++|.++-||+ +|..-|+-+.- =++||+.|.
T Consensus 25 eevA~~lA~~egI~--Ltd~HW~vI~f-lR~~y~~~~ 58 (109)
T PF04358_consen 25 EEVAEALAKEEGIE--LTDEHWEVIRF-LRDYYQEYG 58 (109)
T ss_dssp HHHHHHHHHCTT-S----HHHHHHHHH-HHHHHHHHS
T ss_pred HHHHHHHHHHcCCC--CCHHHHHHHHH-HHHHHHHHC
Confidence 68999999999999 99999987753 345666664
Done!