Query psy4492
Match_columns 96
No_of_seqs 120 out of 1018
Neff 4.4
Searched_HMMs 46136
Date Fri Aug 16 18:28:32 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4492.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4492hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00387 Ribosomal_L7_L12 Ribos 100.0 6E-33 1.3E-37 197.4 9.7 74 21-95 54-127 (127)
2 CHL00083 rpl12 ribosomal prote 100.0 2.9E-31 6.3E-36 190.1 9.8 76 20-96 56-131 (131)
3 KOG1715|consensus 100.0 5.2E-31 1.1E-35 197.9 9.7 76 20-96 112-187 (187)
4 COG0222 RplL Ribosomal protein 100.0 2E-30 4.4E-35 184.4 8.8 73 22-96 52-124 (124)
5 TIGR00855 L12 ribosomal protei 100.0 5E-30 1.1E-34 182.8 9.5 75 20-96 52-126 (126)
6 PRK00157 rplL 50S ribosomal pr 100.0 3.5E-29 7.6E-34 177.8 9.4 75 20-96 49-123 (123)
7 PF00542 Ribosomal_L12: Riboso 99.9 4.5E-26 9.8E-31 146.9 5.7 68 27-96 1-68 (68)
8 PRK06771 hypothetical protein; 98.0 6.8E-06 1.5E-10 56.5 3.5 28 38-66 66-93 (93)
9 PF02617 ClpS: ATP-dependent C 87.2 2.1 4.4E-05 27.5 5.0 69 25-95 4-82 (82)
10 PF09278 MerR-DNA-bind: MerR, 80.5 2.7 5.9E-05 25.1 3.2 22 40-63 3-24 (65)
11 PRK00033 clpS ATP-dependent Cl 74.0 26 0.00056 24.0 7.8 72 23-96 23-98 (100)
12 COG0264 Tsf Translation elonga 72.3 4.4 9.5E-05 33.0 3.2 27 39-66 4-30 (296)
13 CHL00098 tsf elongation factor 70.9 5.5 0.00012 30.3 3.3 29 41-70 2-30 (200)
14 cd04788 HTH_NolA-AlbR Helix-Tu 69.1 12 0.00026 24.5 4.3 46 39-87 45-90 (96)
15 PRK12332 tsf elongation factor 67.3 7.4 0.00016 29.5 3.3 29 41-70 5-33 (198)
16 TIGR00116 tsf translation elon 65.8 7.8 0.00017 31.1 3.4 29 41-70 5-33 (290)
17 PRK09377 tsf elongation factor 64.6 8.4 0.00018 30.9 3.4 27 41-68 6-32 (290)
18 cd01107 HTH_BmrR Helix-Turn-He 61.1 21 0.00046 23.8 4.4 28 39-68 46-73 (108)
19 cd04782 HTH_BltR Helix-Turn-He 60.4 24 0.00051 23.2 4.4 26 39-66 45-70 (97)
20 PRK10753 transcriptional regul 57.0 6.3 0.00014 25.9 1.2 36 39-75 2-37 (90)
21 PRK13019 clpS ATP-dependent Cl 56.9 58 0.0013 22.0 6.8 72 22-94 16-91 (94)
22 PRK10664 transcriptional regul 56.8 6.5 0.00014 25.9 1.2 37 39-76 2-38 (90)
23 PRK13752 putative transcriptio 56.7 24 0.00052 25.1 4.2 25 39-65 52-76 (144)
24 PF06540 GMAP: Galanin message 56.0 6.4 0.00014 25.4 1.1 37 42-80 24-60 (62)
25 cd04768 HTH_BmrR-like Helix-Tu 56.0 33 0.00072 22.4 4.6 27 39-67 45-71 (96)
26 cd00591 HU_IHF Integration hos 55.2 14 0.0003 23.1 2.5 35 40-75 2-36 (87)
27 TIGR02043 ZntR Zn(II)-responsi 52.8 34 0.00074 23.6 4.4 25 39-65 46-70 (131)
28 cd04777 HTH_MerR-like_sg1 Heli 52.5 18 0.00038 24.0 2.8 25 39-65 43-67 (107)
29 cd04784 HTH_CadR-PbrR Helix-Tu 51.4 18 0.0004 24.6 2.8 25 39-65 45-69 (127)
30 cd04783 HTH_MerR1 Helix-Turn-H 50.7 33 0.00073 23.3 4.1 26 39-66 45-70 (126)
31 smart00411 BHL bacterial (prok 50.4 17 0.00037 22.9 2.4 35 40-75 3-37 (90)
32 cd04781 HTH_MerR-like_sg6 Heli 50.2 53 0.0011 22.2 5.0 26 39-66 44-69 (120)
33 cd01109 HTH_YyaN Helix-Turn-He 48.9 22 0.00047 23.7 2.9 26 39-66 45-70 (113)
34 cd04770 HTH_HMRTR Helix-Turn-H 48.3 35 0.00076 22.9 3.8 26 39-66 45-70 (123)
35 COG3797 Uncharacterized protei 47.1 16 0.00034 27.9 2.1 50 35-88 13-62 (178)
36 PRK10227 DNA-binding transcrip 46.6 39 0.00085 23.7 4.0 25 39-65 45-69 (135)
37 PRK15002 redox-sensitivie tran 44.7 46 0.001 24.1 4.2 25 39-65 55-79 (154)
38 TIGR02051 MerR Hg(II)-responsi 43.8 57 0.0012 22.3 4.4 26 39-66 44-69 (124)
39 cd04787 HTH_HMRTR_unk Helix-Tu 43.2 29 0.00063 23.9 2.9 26 39-66 45-70 (133)
40 PRK09514 zntR zinc-responsive 42.7 53 0.0011 23.1 4.1 25 39-65 46-70 (140)
41 PRK13749 transcriptional regul 40.0 35 0.00076 23.9 2.9 28 39-68 48-75 (121)
42 PRK00285 ihfA integration host 39.9 30 0.00065 22.6 2.4 35 39-74 4-38 (99)
43 cd04785 HTH_CadR-PbrR-like Hel 39.1 36 0.00079 23.2 2.8 26 39-66 45-70 (126)
44 PF13411 MerR_1: MerR HTH fami 39.0 30 0.00066 20.4 2.2 25 39-65 44-68 (69)
45 TIGR02044 CueR Cu(I)-responsiv 38.6 38 0.00082 23.1 2.8 24 39-64 45-68 (127)
46 cd01108 HTH_CueR Helix-Turn-He 38.4 38 0.00083 23.2 2.8 25 39-65 45-69 (127)
47 cd01282 HTH_MerR-like_sg3 Heli 37.8 41 0.00089 22.6 2.9 25 39-65 44-68 (112)
48 PF08002 DUF1697: Protein of u 37.7 3.5 7.6E-05 29.1 -2.5 52 26-78 2-55 (137)
49 cd04790 HTH_Cfa-like_unk Helix 37.6 89 0.0019 22.7 4.8 27 39-67 46-72 (172)
50 TIGR02047 CadR-PbrR Cd(II)/Pb( 37.5 40 0.00088 23.2 2.8 25 39-65 45-69 (127)
51 cd01104 HTH_MlrA-CarA Helix-Tu 37.3 40 0.00087 19.8 2.5 24 39-64 45-68 (68)
52 COG0789 SoxR Predicted transcr 37.0 47 0.001 21.8 3.0 28 39-68 45-72 (124)
53 cd04786 HTH_MerR-like_sg7 Heli 36.8 41 0.00088 23.5 2.8 26 39-66 45-70 (131)
54 cd04774 HTH_YfmP Helix-Turn-He 36.2 95 0.0021 20.4 4.4 30 39-69 44-73 (96)
55 cd04769 HTH_MerR2 Helix-Turn-H 35.3 47 0.001 22.3 2.8 27 39-67 44-70 (116)
56 TIGR02054 MerD mercuric resist 34.6 48 0.001 23.1 2.9 27 39-67 48-74 (120)
57 cd01106 HTH_TipAL-Mta Helix-Tu 32.8 1.2E+02 0.0025 19.8 4.4 27 39-67 45-71 (103)
58 cd01110 HTH_SoxR Helix-Turn-He 32.0 57 0.0012 22.9 2.9 26 39-66 45-70 (139)
59 TIGR01950 SoxR redox-sensitive 31.4 60 0.0013 23.0 3.0 26 39-66 45-70 (142)
60 cd04779 HTH_MerR-like_sg4 Heli 30.7 60 0.0013 22.9 2.9 27 39-67 44-70 (134)
61 cd04775 HTH_Cfa-like Helix-Tur 30.7 1.1E+02 0.0023 20.2 4.0 26 39-66 45-70 (102)
62 cd01105 HTH_GlnR-like Helix-Tu 30.5 67 0.0015 20.6 2.9 26 39-66 46-71 (88)
63 PRK05412 putative nucleotide-b 30.0 57 0.0012 24.5 2.7 27 68-94 94-120 (161)
64 PF08671 SinI: Anti-repressor 29.9 93 0.002 17.1 3.0 23 41-65 6-28 (30)
65 PRK00199 ihfB integration host 29.8 57 0.0012 21.1 2.5 35 40-74 3-37 (94)
66 PF14520 HHH_5: Helix-hairpin- 29.7 1.3E+02 0.0027 17.8 4.8 45 42-87 2-59 (60)
67 cd01111 HTH_MerD Helix-Turn-He 29.6 67 0.0015 21.6 2.9 26 39-66 45-70 (107)
68 cd04763 HTH_MlrA-like Helix-Tu 28.6 69 0.0015 19.1 2.6 23 39-63 45-67 (68)
69 cd04766 HTH_HspR Helix-Turn-He 28.1 1.7E+02 0.0036 18.7 4.6 25 39-64 45-69 (91)
70 PF04461 DUF520: Protein of un 27.3 44 0.00095 25.1 1.7 27 68-94 94-120 (160)
71 cd04776 HTH_GnyR Helix-Turn-He 26.7 79 0.0017 21.5 2.8 26 39-66 43-68 (118)
72 COG5275 BRCT domain type II [G 25.7 1.7E+02 0.0036 23.7 4.8 59 24-88 193-251 (276)
73 cd07963 Anticodon_Ia_Cys Antic 25.1 83 0.0018 21.9 2.8 24 71-94 123-146 (156)
74 PRK15348 type III secretion sy 24.9 1.2E+02 0.0025 24.0 3.8 34 61-94 14-47 (249)
75 PF02022 Integrase_Zn: Integra 24.8 1.3E+02 0.0028 17.3 3.1 25 44-69 12-36 (40)
76 PF00216 Bac_DNA_binding: Bact 24.4 71 0.0015 19.9 2.1 34 40-74 3-36 (90)
77 PF00416 Ribosomal_S13: Riboso 23.9 1.7E+02 0.0036 19.7 4.0 46 42-88 12-60 (107)
78 cd04764 HTH_MlrA-like_sg1 Heli 23.7 96 0.0021 18.4 2.5 23 39-63 44-66 (67)
79 PF00828 Ribosomal_L18e: Ribos 23.6 80 0.0017 21.6 2.4 27 65-95 101-128 (129)
80 PRK08385 nicotinate-nucleotide 23.4 1.3E+02 0.0029 23.9 3.9 42 54-95 190-234 (278)
81 cd04789 HTH_Cfa Helix-Turn-Hel 22.5 99 0.0021 20.4 2.6 25 39-65 45-69 (102)
82 KOG4402|consensus 22.5 63 0.0014 23.9 1.8 23 42-64 102-127 (144)
83 cd08494 PBP2_NikA_DppA_OppA_li 22.3 1.7E+02 0.0038 22.9 4.3 43 53-95 297-348 (448)
84 TIGR00987 himA integration hos 22.3 52 0.0011 21.5 1.2 35 40-75 4-38 (96)
85 TIGR00988 hip integration host 22.3 96 0.0021 19.9 2.5 36 40-75 3-38 (94)
86 cd04780 HTH_MerR-like_sg5 Heli 21.6 1.3E+02 0.0029 19.7 3.1 26 39-65 45-70 (95)
87 cd04767 HTH_HspR-like_MBC Heli 21.4 1.2E+02 0.0027 21.3 3.0 32 39-71 44-75 (120)
88 PRK06419 rpl15p 50S ribosomal 21.2 97 0.0021 22.3 2.5 16 80-95 129-144 (148)
89 cd04773 HTH_TioE_rpt2 Second H 20.6 1.3E+02 0.0027 20.1 2.8 26 39-66 45-70 (108)
90 cd08499 PBP2_Ylib_like The sub 20.5 1.9E+02 0.0042 23.0 4.3 42 54-95 301-351 (474)
91 PRK03100 sec-independent trans 20.4 84 0.0018 22.8 2.0 49 33-87 19-67 (136)
92 cd08503 PBP2_NikA_DppA_OppA_li 20.3 2E+02 0.0043 22.9 4.4 42 54-95 305-355 (460)
No 1
>cd00387 Ribosomal_L7_L12 Ribosomal protein L7/L12. Ribosomal protein L7/L12 refers to the large ribosomal subunit proteins L7 and L12, which are identical except that L7 is acetylated at the N terminus. It is a component of the L7/L12 stalk, which is located at the surface of the ribosome. The stalk base consists of a portion of the 23S rRNA and ribosomal proteins L11 and L10. An extended C-terminal helix of L10 provides the binding site for L7/L12. L7/L12 consists of two domains joined by a flexible hinge, with the helical N-terminal domain (NTD) forming pairs of homodimers that bind to the extended helix of L10. It is the only multimeric ribosomal component, with either four or six copies per ribosome that occur as two or three dimers bound to the L10 helix. L7/L12 is the only ribosomal protein that does not interact directly with rRNA, but instead has indirect interactions through L10. The globular C-terminal domains of L7/L12 are highly mobile. They are exposed to the cytoplasm and
Probab=100.00 E-value=6e-33 Score=197.39 Aligned_cols=74 Identities=38% Similarity=0.606 Sum_probs=71.3
Q ss_pred hhhhcceeEEEEeeCCCCCchHHHHHHHHhhcCCCHHHHHHHHhhcChhhhhcCCHHHHHHHHHHHHhCCcEEEe
Q psy4492 21 EKIVQSLFTVKLVKYDDKQKVPLIKEIKGLLEGMNLVQAKKFVESIPAVVKTDVTKEEAEALKASLAKVGGEVSV 95 (96)
Q Consensus 21 ~~~ekt~f~V~L~~~~~~kKi~vIK~VR~i~t~LgLkEAK~lVe~~P~~iKe~v~keeAe~ik~kle~aGa~vei 95 (96)
...|||+|||+|++||+.+||+|||+||++ |||||+|||+|||++|++||+|+||+|||+||++|+++||+|+|
T Consensus 54 ~~~EKt~F~V~L~~~~~~~Ki~vIK~VR~i-t~LgLkEAK~lVe~~P~~iKe~vsKeeAE~ik~kLe~aGA~Vel 127 (127)
T cd00387 54 EAEEKTEFDVVLESFGAAKKIAVIKEVREI-TGLGLKEAKDLVESAPKVLKEGVSKEEAEEIKKKLEEAGAKVEL 127 (127)
T ss_pred chhhcceEEEEEeeCCchhhHHHHHHHHHH-hCCChHHHHHHHHhCcHHHHhCCCHHHHHHHHHHHHHcCCEEeC
Confidence 457899999999999988999999999998 89999999999999999999999999999999999999999986
No 2
>CHL00083 rpl12 ribosomal protein L12
Probab=99.97 E-value=2.9e-31 Score=190.08 Aligned_cols=76 Identities=33% Similarity=0.549 Sum_probs=72.2
Q ss_pred hhhhhcceeEEEEeeCCCCCchHHHHHHHHhhcCCCHHHHHHHHhhcChhhhhcCCHHHHHHHHHHHHhCCcEEEeC
Q psy4492 20 EEKIVQSLFTVKLVKYDDKQKVPLIKEIKGLLEGMNLVQAKKFVESIPAVVKTDVTKEEAEALKASLAKVGGEVSVE 96 (96)
Q Consensus 20 ~~~~ekt~f~V~L~~~~~~kKi~vIK~VR~i~t~LgLkEAK~lVe~~P~~iKe~v~keeAe~ik~kle~aGa~veie 96 (96)
+..+|||+|||+|++|++.+||+|||+||++ |||||+|||+|||++|++||+|+||+|||+||++|+++||+|+|.
T Consensus 56 ~~~~EKT~F~V~L~~~~~~~Ki~vIK~vr~i-t~lgLkeaK~lVe~~P~~ike~v~KeeAe~ik~~le~~Ga~v~lk 131 (131)
T CHL00083 56 EEVEEKTEFDVILEEVPADKRIAVLKVVRSL-TGLGLKEAKELVESLPKTIKEGISKEEAEEAKKQLEEAGAKVIIK 131 (131)
T ss_pred chhhhcceeeEEEeecCCcchHHHHHHHHHH-cCCCHHHHHHHHHhCCHHHHhCCCHHHHHHHHHHHHHcCCEEEeC
Confidence 4568899999999999777999999999998 899999999999999999999999999999999999999999973
No 3
>KOG1715|consensus
Probab=99.97 E-value=5.2e-31 Score=197.92 Aligned_cols=76 Identities=45% Similarity=0.685 Sum_probs=71.6
Q ss_pred hhhhhcceeEEEEeeCCCCCchHHHHHHHHhhcCCCHHHHHHHHhhcChhhhhcCCHHHHHHHHHHHHhCCcEEEeC
Q psy4492 20 EEKIVQSLFTVKLVKYDDKQKVPLIKEIKGLLEGMNLVQAKKFVESIPAVVKTDVTKEEAEALKASLAKVGGEVSVE 96 (96)
Q Consensus 20 ~~~~ekt~f~V~L~~~~~~kKi~vIK~VR~i~t~LgLkEAK~lVe~~P~~iKe~v~keeAe~ik~kle~aGa~veie 96 (96)
+.+.|+|.|||+|++|++.+||+|||+||.+ |||||+|||+|||++|+.+|+|++|||||+|+++|+++||+|.||
T Consensus 112 e~k~ekt~FdVkL~~fda~~KIkVIKEVR~~-tgL~LkeAKklVE~aP~ilKegvtKeEAEkik~kLea~GakV~le 187 (187)
T KOG1715|consen 112 EAKKEKTTFDVKLEKFDASSKIKVIKEVRAL-TGLGLKEAKKLVEKAPKILKEGVTKEEAEEIKEKLEAAGAKVVLE 187 (187)
T ss_pred cchhhcceEEEEEeecCccchhHHHHHHHHh-ccccHHHHHHHHHhccHHHHcCCCHHHHHHHHHHHHHcCCeEeeC
Confidence 4455567899999999999999999999987 999999999999999999999999999999999999999999987
No 4
>COG0222 RplL Ribosomal protein L7/L12 [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=2e-30 Score=184.42 Aligned_cols=73 Identities=36% Similarity=0.547 Sum_probs=69.9
Q ss_pred hhhcceeEEEEeeCCCCCchHHHHHHHHhhcCCCHHHHHHHHhhcChhhhhcCCHHHHHHHHHHHHhCCcEEEeC
Q psy4492 22 KIVQSLFTVKLVKYDDKQKVPLIKEIKGLLEGMNLVQAKKFVESIPAVVKTDVTKEEAEALKASLAKVGGEVSVE 96 (96)
Q Consensus 22 ~~ekt~f~V~L~~~~~~kKi~vIK~VR~i~t~LgLkEAK~lVe~~P~~iKe~v~keeAe~ik~kle~aGa~veie 96 (96)
.+|||+|||+|+++++ +||+|||.||++ |||||||||+|||++|++||+|++|+|||+||++|+++||+|++.
T Consensus 52 aeEktefdVvL~~~g~-kKI~VIK~vR~i-tGLGLKEAKdlVe~aP~~~KE~v~k~eAe~~kkkleeaGa~V~~k 124 (124)
T COG0222 52 AEEKTEFDVVLKSAGG-KKIAVIKVVREL-TGLGLKEAKDLVEGAPKVLKEGVSKEEAEEIKKKLEEAGAKVELK 124 (124)
T ss_pred ccccceeEEEecccCC-cchhHHHHHHHH-hcccHHHHHHHHHhCcHHHHccCCHHHHHHHHHHHHHcCCeEeeC
Confidence 6789999999999975 999999999998 899999999999999999999999999999999999999999974
No 5
>TIGR00855 L12 ribosomal protein L7/L12. THis model resembles Pfam model pfam00542 but matches the full length of prokaryotic and organellar proteins rather than just the C-terminus.
Probab=99.96 E-value=5e-30 Score=182.81 Aligned_cols=75 Identities=37% Similarity=0.550 Sum_probs=70.6
Q ss_pred hhhhhcceeEEEEeeCCCCCchHHHHHHHHhhcCCCHHHHHHHHhhcChhhhhcCCHHHHHHHHHHHHhCCcEEEeC
Q psy4492 20 EEKIVQSLFTVKLVKYDDKQKVPLIKEIKGLLEGMNLVQAKKFVESIPAVVKTDVTKEEAEALKASLAKVGGEVSVE 96 (96)
Q Consensus 20 ~~~~ekt~f~V~L~~~~~~kKi~vIK~VR~i~t~LgLkEAK~lVe~~P~~iKe~v~keeAe~ik~kle~aGa~veie 96 (96)
+..+|||+|||+|+++++ +||+|||+||++ |||||+|||+|||++|++||+|+||+|||++|++|+++||+|+|.
T Consensus 52 ~~~eEKt~f~V~L~~~~~-~Ki~vIK~vR~i-tgLgLkEAK~lVe~~P~~ike~vsKeeAe~ik~~Le~aGa~veik 126 (126)
T TIGR00855 52 AAAEEKTEFDVILKGAGD-NKIAVIKVVREI-TGLGLKEAKDLVEGAPKVLKEGVSKEEAEELKKKLEEAGAKVEVK 126 (126)
T ss_pred ccccccceeeEEEecCCc-chhHHHHHHHHH-cCCcHHHHHHHHHhCcHHHHhCCCHHHHHHHHHHHHHcCCEEEeC
Confidence 345789999999999885 799999999998 899999999999999999999999999999999999999999973
No 6
>PRK00157 rplL 50S ribosomal protein L7/L12; Reviewed
Probab=99.96 E-value=3.5e-29 Score=177.85 Aligned_cols=75 Identities=35% Similarity=0.545 Sum_probs=70.7
Q ss_pred hhhhhcceeEEEEeeCCCCCchHHHHHHHHhhcCCCHHHHHHHHhhcChhhhhcCCHHHHHHHHHHHHhCCcEEEeC
Q psy4492 20 EEKIVQSLFTVKLVKYDDKQKVPLIKEIKGLLEGMNLVQAKKFVESIPAVVKTDVTKEEAEALKASLAKVGGEVSVE 96 (96)
Q Consensus 20 ~~~~ekt~f~V~L~~~~~~kKi~vIK~VR~i~t~LgLkEAK~lVe~~P~~iKe~v~keeAe~ik~kle~aGa~veie 96 (96)
+..+|||+|||+|++|+ .+||+|||+||++ |||||+|||+|||++|++||+|+||+|||++|++|+++||+|+|.
T Consensus 49 ~~~eEkt~f~V~L~~~~-~kKi~vIK~vR~i-tgLgLkEAK~lVe~~P~~ike~v~keeAe~ik~~Le~aGa~velk 123 (123)
T PRK00157 49 AAAEEKTEFDVVLKSAG-DKKIAVIKAVREI-TGLGLKEAKDLVEGAPKVVKEGVSKEEAEEIKKKLEEAGAKVELK 123 (123)
T ss_pred cccccccceeEEEeccc-hhhHHHHHHHHHH-hCCCHHHHHHHHHhCCHHHHhCCCHHHHHHHHHHHHHcCCEEeeC
Confidence 34578999999999996 4999999999998 899999999999999999999999999999999999999999973
No 7
>PF00542 Ribosomal_L12: Ribosomal protein L7/L12 C-terminal domain; InterPro: IPR013823 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents the C-terminal domain of the large subunit ribosomal proteins, known as the L7/L12 family. L7/L12 is present in each 50S subunit in four copies organised as two dimers. The L8 protein complex consisting of two dimers of L7/L12 and L10 in Escherichia coli ribosomes is assembled on the conserved region of 23 S rRNA termed the GTPase-associated domain []. The L7/L12 dimer probably interacts with EF-Tu. L7 and L12 only differ in a single post translational modification of the addition of an acetyl group to the N terminus of L7.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1DD4_B 1DD3_A 1RQU_B 2GYA_5 2GYC_5 1RQS_A 1RQV_A 1CTF_A 2XUX_L.
Probab=99.93 E-value=4.5e-26 Score=146.92 Aligned_cols=68 Identities=40% Similarity=0.688 Sum_probs=59.4
Q ss_pred eeEEEEeeCCCCCchHHHHHHHHhhcCCCHHHHHHHHhhcChhhhhcCCHHHHHHHHHHHHhCCcEEEeC
Q psy4492 27 LFTVKLVKYDDKQKVPLIKEIKGLLEGMNLVQAKKFVESIPAVVKTDVTKEEAEALKASLAKVGGEVSVE 96 (96)
Q Consensus 27 ~f~V~L~~~~~~kKi~vIK~VR~i~t~LgLkEAK~lVe~~P~~iKe~v~keeAe~ik~kle~aGa~veie 96 (96)
+|||+|+++ ..+||++||.||++ |||||+|||++||++|++|++++++++|++++++|+++||+|+|+
T Consensus 1 ef~V~L~~~-~~~ki~vIK~vR~~-tgl~L~eAK~~vd~~p~~ik~~v~keeAe~ik~~Le~aGa~v~l~ 68 (68)
T PF00542_consen 1 EFDVVLKSF-GEKKIKVIKEVREI-TGLGLKEAKKLVDSLPKVIKEGVSKEEAEEIKKKLEAAGAKVELK 68 (68)
T ss_dssp SEEEEEEE--TTGHHHHHHHHHHH-C---HHHHHHHHCTTTEEEEEEE-HHHHHHHHHHHHCCT-EEEEE
T ss_pred CeEEEEeec-ccchHHHHHHHHHH-hCCcHHHHHHHHHhCCHHHHcCCCHHHHHHHHHHHHHcCCEEEeC
Confidence 599999999 56999999999998 899999999999999999999999999999999999999999984
No 8
>PRK06771 hypothetical protein; Provisional
Probab=97.99 E-value=6.8e-06 Score=56.49 Aligned_cols=28 Identities=29% Similarity=0.577 Sum_probs=26.2
Q ss_pred CCchHHHHHHHHhhcCCCHHHHHHHHhhc
Q psy4492 38 KQKVPLIKEIKGLLEGMNLVQAKKFVESI 66 (96)
Q Consensus 38 ~kKi~vIK~VR~i~t~LgLkEAK~lVe~~ 66 (96)
.+|+..||.+|+. ||+||+|||++||++
T Consensus 66 Gkki~AIK~~Re~-tG~~L~eAK~yVD~L 93 (93)
T PRK06771 66 GQTVTAVKRVREA-FGFSLLEAKQYVDKL 93 (93)
T ss_pred CCchHHHHHHHHH-cCCCHHHHHHHHhcC
Confidence 4899999999998 999999999999985
No 9
>PF02617 ClpS: ATP-dependent Clp protease adaptor protein ClpS; InterPro: IPR003769 In the bacterial cytosol, ATP-dependent protein degradation is performed by several different chaperone-protease pairs, including ClpAP. ClpS directly influences the ClpAP machine by binding to the N-terminal domain of the chaperone ClpA. The degradation of ClpAP substrates, both SsrA-tagged proteins and ClpA itself, is specifically inhibited by ClpS. ClpS modifies ClpA substrate specificity, potentially redirecting degradation by ClpAP toward aggregated proteins []. ClpS is a small alpha/beta protein that consists of three alpha-helices connected to three antiparallel beta-strands []. The protein has a globular shape, with a curved layer of three antiparallel alpha-helices over a twisted antiparallel beta-sheet. Dimerization of ClpS may occur through its N-terminal domain. This short extended N-terminal region in ClpS is followed by the central seven-residue beta-strand, which is flanked by two other beta-strands in a small beta-sheet. ; GO: 0030163 protein catabolic process; PDB: 3O2O_B 1MBU_D 3O2B_C 2WA9_D 3O1F_A 2W9R_A 1MG9_A 1MBX_C 2WA8_C 1R6O_D ....
Probab=87.16 E-value=2.1 Score=27.52 Aligned_cols=69 Identities=23% Similarity=0.300 Sum_probs=49.4
Q ss_pred cceeEEEEeeCCCCCchHHHHHHHHhhcCCCHHHHHHHHhhcC----hhhhhcCCHHHHHHHHHHHHhCC------cEEE
Q psy4492 25 QSLFTVKLVKYDDKQKVPLIKEIKGLLEGMNLVQAKKFVESIP----AVVKTDVTKEEAEALKASLAKVG------GEVS 94 (96)
Q Consensus 25 kt~f~V~L~~~~~~kKi~vIK~VR~i~t~LgLkEAK~lVe~~P----~~iKe~v~keeAe~ik~kle~aG------a~ve 94 (96)
...|.|+|=+-+-..--.||..++.+ .|++..+|..+...+- .+|.. -++++|+.....|...| -.++
T Consensus 4 ~~~~~vvL~NDe~ht~~~Vi~~L~~~-~~~s~~~A~~~a~~v~~~G~avv~~-~~~e~ae~~~~~l~~~g~~~~~PL~~t 81 (82)
T PF02617_consen 4 PDMYRVVLWNDEVHTFEQVIDVLRRV-FGCSEEQARQIAMEVHREGRAVVGT-GSREEAEEYAEKLQRAGRDSGHPLRAT 81 (82)
T ss_dssp --EEEEEEE--SSSBHHHHHHHHHHH-C---HHHHHHHHHHHHHHSEEEEEE-EEHHHHHHHHHHHHHHHHHTT---EEE
T ss_pred CCceEEEEEcCCCCCHHHHHHHHHHH-HCCCHHHHHHHHHHHhHcCCEeeee-CCHHHHHHHHHHHHHHhhccCCCeEEe
Confidence 46789999776555677999999998 4999999998877553 45544 59999999999999998 6655
Q ss_pred e
Q psy4492 95 V 95 (96)
Q Consensus 95 i 95 (96)
|
T Consensus 82 i 82 (82)
T PF02617_consen 82 I 82 (82)
T ss_dssp E
T ss_pred C
Confidence 4
No 10
>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=80.49 E-value=2.7 Score=25.15 Aligned_cols=22 Identities=18% Similarity=0.635 Sum_probs=18.2
Q ss_pred chHHHHHHHHhhcCCCHHHHHHHH
Q psy4492 40 KVPLIKEIKGLLEGMNLVQAKKFV 63 (96)
Q Consensus 40 Ki~vIK~VR~i~t~LgLkEAK~lV 63 (96)
++..|+..|.+ |++|.|-++++
T Consensus 3 rL~~I~~~r~l--GfsL~eI~~~l 24 (65)
T PF09278_consen 3 RLQFIRRLREL--GFSLEEIRELL 24 (65)
T ss_dssp HHHHHHHHHHT--T--HHHHHHHH
T ss_pred HHHHHHHHHHc--CCCHHHHHHHH
Confidence 57889999995 99999999999
No 11
>PRK00033 clpS ATP-dependent Clp protease adaptor protein ClpS; Reviewed
Probab=73.98 E-value=26 Score=24.04 Aligned_cols=72 Identities=19% Similarity=0.210 Sum_probs=57.3
Q ss_pred hhcceeEEEEeeCCCCCchHHHHHHHHhhcCCCHHHHHHHHhhcC----hhhhhcCCHHHHHHHHHHHHhCCcEEEeC
Q psy4492 23 IVQSLFTVKLVKYDDKQKVPLIKEIKGLLEGMNLVQAKKFVESIP----AVVKTDVTKEEAEALKASLAKVGGEVSVE 96 (96)
Q Consensus 23 ~ekt~f~V~L~~~~~~kKi~vIK~VR~i~t~LgLkEAK~lVe~~P----~~iKe~v~keeAe~ik~kle~aGa~veie 96 (96)
+....|.|+|-+-+-...==||..++.++ +++..+|-++...+- .++.. -++|.||-...++...|-.+.||
T Consensus 23 ~~~~~y~ViL~NDd~ntmd~Vv~vL~~vf-~~s~~~A~~iml~vH~~G~avv~~-~~~e~AE~~~~~l~~~~L~~~ie 98 (100)
T PRK00033 23 KPPPMYKVLLHNDDYTPMEFVVYVLQKFF-GYDRERATQIMLEVHNEGKAVVGV-CTREVAETKVEQVHQHGLLCTME 98 (100)
T ss_pred CCCCceEEEEEcCCCCCHHHHHHHHHHHH-CCCHHHHHHHHHHHhcCCcEEEEE-EcHHHHHHHHHHHHcCCCeEEEe
Confidence 33456999998766545667999999995 999999998876553 33443 49999999999999999988875
No 12
>COG0264 Tsf Translation elongation factor Ts [Translation, ribosomal structure and biogenesis]
Probab=72.34 E-value=4.4 Score=33.00 Aligned_cols=27 Identities=26% Similarity=0.446 Sum_probs=23.2
Q ss_pred CchHHHHHHHHhhcCCCHHHHHHHHhhc
Q psy4492 39 QKVPLIKEIKGLLEGMNLVQAKKFVESI 66 (96)
Q Consensus 39 kKi~vIK~VR~i~t~LgLkEAK~lVe~~ 66 (96)
-+.+.+|++|+. ||-|++++|+.++-.
T Consensus 4 ita~~VKeLRe~-TgAGMmdCKkAL~E~ 30 (296)
T COG0264 4 ITAALVKELREK-TGAGMMDCKKALEEA 30 (296)
T ss_pred ccHHHHHHHHHH-hCCcHHHHHHHHHHc
Confidence 356899999997 999999999987655
No 13
>CHL00098 tsf elongation factor Ts
Probab=70.94 E-value=5.5 Score=30.35 Aligned_cols=29 Identities=21% Similarity=0.378 Sum_probs=24.0
Q ss_pred hHHHHHHHHhhcCCCHHHHHHHHhhcChhh
Q psy4492 41 VPLIKEIKGLLEGMNLVQAKKFVESIPAVV 70 (96)
Q Consensus 41 i~vIK~VR~i~t~LgLkEAK~lVe~~P~~i 70 (96)
...||.+|+. ||.|+++.|+.++....-+
T Consensus 2 a~~ik~LR~~-Tgag~~dck~AL~e~~gd~ 30 (200)
T CHL00098 2 AELVKELRDK-TGAGMMDCKKALQEANGDF 30 (200)
T ss_pred HHHHHHHHHH-HCCCHHHHHHHHHHcCCCH
Confidence 4689999997 9999999999887766433
No 14
>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=69.14 E-value=12 Score=24.53 Aligned_cols=46 Identities=13% Similarity=0.221 Sum_probs=30.7
Q ss_pred CchHHHHHHHHhhcCCCHHHHHHHHhhcChhhhhcCCHHHHHHHHHHHH
Q psy4492 39 QKVPLIKEIKGLLEGMNLVQAKKFVESIPAVVKTDVTKEEAEALKASLA 87 (96)
Q Consensus 39 kKi~vIK~VR~i~t~LgLkEAK~lVe~~P~~iKe~v~keeAe~ik~kle 87 (96)
.++..|+.+|+. |++|.|.+.+++.....+++ +-.+..+.+..+++
T Consensus 45 ~~l~~I~~lr~~--G~~l~eI~~~l~~~~~~~~~-~l~~~~~~l~~~i~ 90 (96)
T cd04788 45 RRLHQIIALRRL--GFSLREIGRALDGPDFDPLE-LLRRQLARLEEQLE 90 (96)
T ss_pred HHHHHHHHHHHc--CCCHHHHHHHHhCCChhHHH-HHHHHHHHHHHHHH
Confidence 578889999984 99999999999876532222 23344444444443
No 15
>PRK12332 tsf elongation factor Ts; Reviewed
Probab=67.30 E-value=7.4 Score=29.53 Aligned_cols=29 Identities=24% Similarity=0.406 Sum_probs=24.3
Q ss_pred hHHHHHHHHhhcCCCHHHHHHHHhhcChhh
Q psy4492 41 VPLIKEIKGLLEGMNLVQAKKFVESIPAVV 70 (96)
Q Consensus 41 i~vIK~VR~i~t~LgLkEAK~lVe~~P~~i 70 (96)
...||.+|+- ||.|+++.|+.+.....-+
T Consensus 5 a~~ik~LR~~-tga~~~~ck~AL~~~~gd~ 33 (198)
T PRK12332 5 AKLVKELREK-TGAGMMDCKKALEEANGDM 33 (198)
T ss_pred HHHHHHHHHH-HCCCHHHHHHHHHHcCCCH
Confidence 4789999997 9999999999887766433
No 16
>TIGR00116 tsf translation elongation factor Ts. This protein is found in Bacteria, mitochondria, and chloroplasts.
Probab=65.83 E-value=7.8 Score=31.11 Aligned_cols=29 Identities=21% Similarity=0.350 Sum_probs=24.0
Q ss_pred hHHHHHHHHhhcCCCHHHHHHHHhhcChhh
Q psy4492 41 VPLIKEIKGLLEGMNLVQAKKFVESIPAVV 70 (96)
Q Consensus 41 i~vIK~VR~i~t~LgLkEAK~lVe~~P~~i 70 (96)
...||++|+. ||.|+++.|+.++....-+
T Consensus 5 a~~IK~LRe~-Tgagm~dCKkAL~e~~gDi 33 (290)
T TIGR00116 5 AQLVKELRER-TGAGMMDCKKALTEANGDF 33 (290)
T ss_pred HHHHHHHHHH-HCCCHHHHHHHHHHcCCCH
Confidence 3679999997 9999999999888765433
No 17
>PRK09377 tsf elongation factor Ts; Provisional
Probab=64.65 E-value=8.4 Score=30.90 Aligned_cols=27 Identities=22% Similarity=0.418 Sum_probs=23.6
Q ss_pred hHHHHHHHHhhcCCCHHHHHHHHhhcCh
Q psy4492 41 VPLIKEIKGLLEGMNLVQAKKFVESIPA 68 (96)
Q Consensus 41 i~vIK~VR~i~t~LgLkEAK~lVe~~P~ 68 (96)
...||++|+. ||.|+++.|+.++....
T Consensus 6 ~~~IK~LR~~-Tgagm~dCKkAL~e~~g 32 (290)
T PRK09377 6 AALVKELRER-TGAGMMDCKKALTEADG 32 (290)
T ss_pred HHHHHHHHHH-HCCCHHHHHHHHHHcCC
Confidence 4789999997 99999999999887654
No 18
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares 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=61.10 E-value=21 Score=23.76 Aligned_cols=28 Identities=21% Similarity=0.400 Sum_probs=24.2
Q ss_pred CchHHHHHHHHhhcCCCHHHHHHHHhhcCh
Q psy4492 39 QKVPLIKEIKGLLEGMNLVQAKKFVESIPA 68 (96)
Q Consensus 39 kKi~vIK~VR~i~t~LgLkEAK~lVe~~P~ 68 (96)
..+..|+.+|.. |++|.+.+.+++..+.
T Consensus 46 ~~l~~I~~lr~~--G~sl~~i~~l~~~~~~ 73 (108)
T cd01107 46 ERLNRIKYLRDL--GFPLEEIKEILDADND 73 (108)
T ss_pred HHHHHHHHHHHc--CCCHHHHHHHHhcCCH
Confidence 578889999984 9999999999988764
No 19
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators 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 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=60.41 E-value=24 Score=23.16 Aligned_cols=26 Identities=23% Similarity=0.519 Sum_probs=22.4
Q ss_pred CchHHHHHHHHhhcCCCHHHHHHHHhhc
Q psy4492 39 QKVPLIKEIKGLLEGMNLVQAKKFVESI 66 (96)
Q Consensus 39 kKi~vIK~VR~i~t~LgLkEAK~lVe~~ 66 (96)
..+..|+.+|.. |+.|.|-+.+++..
T Consensus 45 ~~l~~I~~lr~~--G~~l~eI~~~l~~~ 70 (97)
T cd04782 45 EQLDIILLLKEL--GISLKEIKDYLDNR 70 (97)
T ss_pred HHHHHHHHHHHc--CCCHHHHHHHHhcC
Confidence 478899999984 99999999998753
No 20
>PRK10753 transcriptional regulator HU subunit alpha; Provisional
Probab=57.00 E-value=6.3 Score=25.86 Aligned_cols=36 Identities=28% Similarity=0.289 Sum_probs=30.2
Q ss_pred CchHHHHHHHHhhcCCCHHHHHHHHhhcChhhhhcCC
Q psy4492 39 QKVPLIKEIKGLLEGMNLVQAKKFVESIPAVVKTDVT 75 (96)
Q Consensus 39 kKi~vIK~VR~i~t~LgLkEAK~lVe~~P~~iKe~v~ 75 (96)
+|-.+|+.|.+- +++.-++++..|+.+-..|.+.+.
T Consensus 2 ~K~eli~~ia~~-~~~s~~~~~~~v~~~~~~i~~~L~ 37 (90)
T PRK10753 2 NKTQLIDVIADK-AELSKTQAKAALESTLAAITESLK 37 (90)
T ss_pred CHHHHHHHHHHH-hCCCHHHHHHHHHHHHHHHHHHHH
Confidence 467899999986 799999999999999877766553
No 21
>PRK13019 clpS ATP-dependent Clp protease adaptor; Reviewed
Probab=56.90 E-value=58 Score=21.99 Aligned_cols=72 Identities=18% Similarity=0.134 Sum_probs=54.5
Q ss_pred hhhcceeEEEEeeCCCCCchHHH-HHHHHhhcCCCHHHHHHHHhhcC---hhhhhcCCHHHHHHHHHHHHhCCcEEE
Q psy4492 22 KIVQSLFTVKLVKYDDKQKVPLI-KEIKGLLEGMNLVQAKKFVESIP---AVVKTDVTKEEAEALKASLAKVGGEVS 94 (96)
Q Consensus 22 ~~ekt~f~V~L~~~~~~kKi~vI-K~VR~i~t~LgLkEAK~lVe~~P---~~iKe~v~keeAe~ik~kle~aGa~ve 94 (96)
......|.|+|-+-|-..-==|| ..++.+ .+++..+|-.+.-.+- +-+=---++|.||-...+|...|.+++
T Consensus 16 ~~~p~~ykViL~NDd~~t~dfVi~~vl~~v-f~~s~~~A~~iml~vH~~G~avv~~~~~E~AE~~~~~l~~~glt~e 91 (94)
T PRK13019 16 LERYPLYKVIVLNDDFNTFEHVVNCLLKAI-PGMSEDRAWRLMITAHKEGSAVVWVGPLEQAELYHQQLTDAGLTMA 91 (94)
T ss_pred ccCCCceEEEEEcCCCCCHHHHHHHHHHHh-cCCCHHHHHHHHHHHhcCCcEEEEEecHHHHHHHHHHHHHcccccC
Confidence 34456899999876654555788 577777 7999999999877654 222233599999999999999998765
No 22
>PRK10664 transcriptional regulator HU subunit beta; Provisional
Probab=56.85 E-value=6.5 Score=25.92 Aligned_cols=37 Identities=22% Similarity=0.276 Sum_probs=30.8
Q ss_pred CchHHHHHHHHhhcCCCHHHHHHHHhhcChhhhhcCCH
Q psy4492 39 QKVPLIKEIKGLLEGMNLVQAKKFVESIPAVVKTDVTK 76 (96)
Q Consensus 39 kKi~vIK~VR~i~t~LgLkEAK~lVe~~P~~iKe~v~k 76 (96)
+|-.+|+.|.+- +++.-++++.+||++=..|.+.+..
T Consensus 2 tK~eli~~ia~~-~~~s~~~~~~~v~~~~~~i~~~L~~ 38 (90)
T PRK10664 2 NKSQLIDKIAAG-ADISKAAAGRALDAIIASVTESLKE 38 (90)
T ss_pred CHHHHHHHHHHH-hCCCHHHHHHHHHHHHHHHHHHHhC
Confidence 366899999987 7999999999999998887765543
No 23
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=56.68 E-value=24 Score=25.14 Aligned_cols=25 Identities=20% Similarity=0.420 Sum_probs=22.1
Q ss_pred CchHHHHHHHHhhcCCCHHHHHHHHhh
Q psy4492 39 QKVPLIKEIKGLLEGMNLVQAKKFVES 65 (96)
Q Consensus 39 kKi~vIK~VR~i~t~LgLkEAK~lVe~ 65 (96)
.++..|+..|.+ |++|.|-+.+++.
T Consensus 52 ~rl~~I~~lr~~--G~sL~eI~~ll~~ 76 (144)
T PRK13752 52 TRVRFVKSAQRL--GFSLDEIAELLRL 76 (144)
T ss_pred HHHHHHHHHHHc--CCCHHHHHHHHhc
Confidence 688899999984 9999999999974
No 24
>PF06540 GMAP: Galanin message associated peptide (GMAP); InterPro: IPR013068 Galanin is a peptide hormone that controls various biological activities []. Galanin-like immuno-reactivity has been found in the central and peripheral nervous systems of mammals, with high concentrations demonstrated in discrete regions of the central nervous system, including the median eminence, hypothalamus, arcuate nucleus, septum, neuro-intermediate lobe of the pituitary, and the spinal cord. Its localisation within neurosecretory granules suggests that galanin may function as a neurotransmitter, and it has been shown to coexist with a variety of other peptide and amine neurotransmitters within individual neurons []. Although the precise physiological role of galanin is uncertain, it has a number of pharmacological properties: it stimulates food intake, when injected into the third ventricle of rats; it increases levels of plasma growth hormone and prolactin, and decreases dopamine levels in the median eminence []; and infusion into humans results in hyperglycemia and glucose intolerance, and inhibits pancreatic release of insulin, somatostatin and pancreatic peptide. Galanin also modulates smooth muscle contractility within the gastro-intestinal and genito-urinary tracts, all such activities suggesting that the hormone may play an important role in the nervous modulation of endocrine and smooth muscle function []. This domain represents the galanin message-associated peptide (GMAP) domain which is found C-terminal to the galanin domain in the preprogalanin precursor protein. GMAP sequences in different species show a high degree of homology, but the biological function of the GMAP peptide is not known [].
Probab=56.01 E-value=6.4 Score=25.40 Aligned_cols=37 Identities=19% Similarity=0.428 Sum_probs=28.2
Q ss_pred HHHHHHHHhhcCCCHHHHHHHHhhcChhhhhcCCHHHHH
Q psy4492 42 PLIKEIKGLLEGMNLVQAKKFVESIPAVVKTDVTKEEAE 80 (96)
Q Consensus 42 ~vIK~VR~i~t~LgLkEAK~lVe~~P~~iKe~v~keeAe 80 (96)
+|++.|-+.+|-|-|||+-.| +++|-.. ..+|-|+.+
T Consensus 24 nivrTiiEFLtfLhLKEaGAL-d~Lp~lp-~a~SsEd~~ 60 (62)
T PF06540_consen 24 NIVRTIIEFLTFLHLKEAGAL-DNLPDLP-SAASSEDTE 60 (62)
T ss_pred HHHHHHHHHHHHHHHHHhcch-hccCCCc-cccCHHhhc
Confidence 788888888899999999766 8888433 335666654
No 25
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They 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 HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. 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=55.97 E-value=33 Score=22.40 Aligned_cols=27 Identities=19% Similarity=0.390 Sum_probs=23.4
Q ss_pred CchHHHHHHHHhhcCCCHHHHHHHHhhcC
Q psy4492 39 QKVPLIKEIKGLLEGMNLVQAKKFVESIP 67 (96)
Q Consensus 39 kKi~vIK~VR~i~t~LgLkEAK~lVe~~P 67 (96)
.++..|+.+|.. |+.|.+.+.+++...
T Consensus 45 ~~l~~I~~lr~~--G~~l~~I~~~l~~~~ 71 (96)
T cd04768 45 YQLQFILFLREL--GFSLAEIKELLDTEM 71 (96)
T ss_pred HHHHHHHHHHHc--CCCHHHHHHHHhcCc
Confidence 578899999984 999999999998754
No 26
>cd00591 HU_IHF Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and higher-order nucleoprotein complex assembly. The dimer subunits associate to form a compact globular core from which two beta ribbon arms (one from each subunit) protrude. The beta arms track and bind the DNA minor groove. Despite sequence and structural similarity, IHF and HU can be distinguished by their different DNA substrate preferences.
Probab=55.20 E-value=14 Score=23.14 Aligned_cols=35 Identities=23% Similarity=0.325 Sum_probs=29.8
Q ss_pred chHHHHHHHHhhcCCCHHHHHHHHhhcChhhhhcCC
Q psy4492 40 KVPLIKEIKGLLEGMNLVQAKKFVESIPAVVKTDVT 75 (96)
Q Consensus 40 Ki~vIK~VR~i~t~LgLkEAK~lVe~~P~~iKe~v~ 75 (96)
|-.+|+.|..- +++.-++++.+++.+-..|.+.+.
T Consensus 2 K~~l~~~ia~~-~~~~~~~v~~vl~~~~~~i~~~L~ 36 (87)
T cd00591 2 KSELIEAIAEK-TGLSKKDAEAAVDAFLDVITEALA 36 (87)
T ss_pred HHHHHHHHHHH-hCcCHHHHHHHHHHHHHHHHHHHh
Confidence 56899999987 799999999999999887776553
No 27
>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=52.82 E-value=34 Score=23.65 Aligned_cols=25 Identities=24% Similarity=0.442 Sum_probs=22.1
Q ss_pred CchHHHHHHHHhhcCCCHHHHHHHHhh
Q psy4492 39 QKVPLIKEIKGLLEGMNLVQAKKFVES 65 (96)
Q Consensus 39 kKi~vIK~VR~i~t~LgLkEAK~lVe~ 65 (96)
.++..|+.+|.+ |++|.|.+.+++.
T Consensus 46 ~~l~~I~~lr~~--G~sl~eI~~~l~~ 70 (131)
T TIGR02043 46 KRLRFILKAKEL--GFTLDEIKELLSI 70 (131)
T ss_pred HHHHHHHHHHHc--CCCHHHHHHHHHh
Confidence 678899999984 9999999999974
No 28
>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=52.54 E-value=18 Score=23.97 Aligned_cols=25 Identities=32% Similarity=0.640 Sum_probs=22.4
Q ss_pred CchHHHHHHHHhhcCCCHHHHHHHHhh
Q psy4492 39 QKVPLIKEIKGLLEGMNLVQAKKFVES 65 (96)
Q Consensus 39 kKi~vIK~VR~i~t~LgLkEAK~lVe~ 65 (96)
.++..|+.+|++ |++|.|-+.+++.
T Consensus 43 ~~l~~I~~lr~~--G~sL~eI~~~l~~ 67 (107)
T cd04777 43 DDLEFILELKGL--GFSLIEIQKIFSY 67 (107)
T ss_pred HHHHHHHHHHHC--CCCHHHHHHHHHh
Confidence 678999999995 9999999999974
No 29
>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=51.35 E-value=18 Score=24.60 Aligned_cols=25 Identities=16% Similarity=0.434 Sum_probs=21.6
Q ss_pred CchHHHHHHHHhhcCCCHHHHHHHHhh
Q psy4492 39 QKVPLIKEIKGLLEGMNLVQAKKFVES 65 (96)
Q Consensus 39 kKi~vIK~VR~i~t~LgLkEAK~lVe~ 65 (96)
.++..|+..|.+ |++|.|.|.+++.
T Consensus 45 ~~l~~I~~lr~~--G~sL~eI~~~l~~ 69 (127)
T cd04784 45 ERLLFIRRCRSL--DMSLDEIRTLLQL 69 (127)
T ss_pred HHHHHHHHHHHc--CCCHHHHHHHHHh
Confidence 567888999985 9999999999974
No 30
>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=50.70 E-value=33 Score=23.31 Aligned_cols=26 Identities=23% Similarity=0.387 Sum_probs=22.5
Q ss_pred CchHHHHHHHHhhcCCCHHHHHHHHhhc
Q psy4492 39 QKVPLIKEIKGLLEGMNLVQAKKFVESI 66 (96)
Q Consensus 39 kKi~vIK~VR~i~t~LgLkEAK~lVe~~ 66 (96)
.++..|+.+|.+ |++|.|-|.+++..
T Consensus 45 ~~l~~I~~lr~~--G~sL~eI~~~l~~~ 70 (126)
T cd04783 45 TRLRFIKRAQEL--GFTLDEIAELLELD 70 (126)
T ss_pred HHHHHHHHHHHc--CCCHHHHHHHHhcc
Confidence 578889999984 99999999999754
No 31
>smart00411 BHL bacterial (prokaryotic) histone like domain.
Probab=50.44 E-value=17 Score=22.89 Aligned_cols=35 Identities=23% Similarity=0.334 Sum_probs=30.3
Q ss_pred chHHHHHHHHhhcCCCHHHHHHHHhhcChhhhhcCC
Q psy4492 40 KVPLIKEIKGLLEGMNLVQAKKFVESIPAVVKTDVT 75 (96)
Q Consensus 40 Ki~vIK~VR~i~t~LgLkEAK~lVe~~P~~iKe~v~ 75 (96)
|-.+|+.|.+- +++.-++++..++.+...|.+.+.
T Consensus 3 k~eli~~ia~~-~~~~~~~v~~vl~~l~~~i~~~L~ 37 (90)
T smart00411 3 KSELIDAIAEK-AGLSKKDAKAAVDAFLEIITEALK 37 (90)
T ss_pred HHHHHHHHHHH-hCCCHHHHHHHHHHHHHHHHHHHh
Confidence 56899999987 899999999999999988877654
No 32
>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=50.17 E-value=53 Score=22.18 Aligned_cols=26 Identities=15% Similarity=0.256 Sum_probs=22.7
Q ss_pred CchHHHHHHHHhhcCCCHHHHHHHHhhc
Q psy4492 39 QKVPLIKEIKGLLEGMNLVQAKKFVESI 66 (96)
Q Consensus 39 kKi~vIK~VR~i~t~LgLkEAK~lVe~~ 66 (96)
.++..|+.+|.+ |++|.|.+.+++..
T Consensus 44 ~~l~~I~~lr~~--G~~L~eI~~~l~~~ 69 (120)
T cd04781 44 DRLALIALGRAA--GFSLDEIQAMLSHD 69 (120)
T ss_pred HHHHHHHHHHHc--CCCHHHHHHHHhcc
Confidence 578899999984 99999999999864
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=48.85 E-value=22 Score=23.72 Aligned_cols=26 Identities=23% Similarity=0.411 Sum_probs=22.2
Q ss_pred CchHHHHHHHHhhcCCCHHHHHHHHhhc
Q psy4492 39 QKVPLIKEIKGLLEGMNLVQAKKFVESI 66 (96)
Q Consensus 39 kKi~vIK~VR~i~t~LgLkEAK~lVe~~ 66 (96)
.++..|+.+|.+ |++|.|.+.+++..
T Consensus 45 ~~l~~I~~lr~~--G~sL~eI~~~l~~~ 70 (113)
T cd01109 45 EWLEFIKCLRNT--GMSIKDIKEYAELR 70 (113)
T ss_pred HHHHHHHHHHHc--CCCHHHHHHHHHHH
Confidence 578889999984 99999999998753
No 34
>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=48.29 E-value=35 Score=22.89 Aligned_cols=26 Identities=15% Similarity=0.452 Sum_probs=22.4
Q ss_pred CchHHHHHHHHhhcCCCHHHHHHHHhhc
Q psy4492 39 QKVPLIKEIKGLLEGMNLVQAKKFVESI 66 (96)
Q Consensus 39 kKi~vIK~VR~i~t~LgLkEAK~lVe~~ 66 (96)
..+..|+.+|.+ |++|.|.+.+++..
T Consensus 45 ~~l~~I~~lr~~--G~sl~eI~~~l~~~ 70 (123)
T cd04770 45 ARLRFIRRAQAL--GFSLAEIRELLSLR 70 (123)
T ss_pred HHHHHHHHHHHC--CCCHHHHHHHHHhh
Confidence 577889999984 99999999999764
No 35
>COG3797 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=47.08 E-value=16 Score=27.91 Aligned_cols=50 Identities=18% Similarity=0.342 Sum_probs=38.4
Q ss_pred CCCCCchHHHHHHHHhhcCCCHHHHHHHHhhcChhhhhcCCHHHHHHHHHHHHh
Q psy4492 35 YDDKQKVPLIKEIKGLLEGMNLVQAKKFVESIPAVVKTDVTKEEAEALKASLAK 88 (96)
Q Consensus 35 ~~~~kKi~vIK~VR~i~t~LgLkEAK~lVe~~P~~iKe~v~keeAe~ik~kle~ 88 (96)
+|+.+| =+...+|..+|+||+...+-+|.|-.-++-.+.+ +.++..+||+
T Consensus 13 VGgg~k-V~MAdLka~~~dlGf~~v~T~iaSGNlvf~s~~~---~~el~~klE~ 62 (178)
T COG3797 13 VGGGRK-VVMADLKAALTDLGFANVRTYIASGNLVFESEAG---AAELEAKLEA 62 (178)
T ss_pred ecCCce-EeHHHHHHHHHHcCcchhhHhhhcCCEEEEcCCC---hHHHHHHHHH
Confidence 455445 4668899888999999999999999877777666 5566666665
No 36
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=46.63 E-value=39 Score=23.71 Aligned_cols=25 Identities=20% Similarity=0.519 Sum_probs=21.4
Q ss_pred CchHHHHHHHHhhcCCCHHHHHHHHhh
Q psy4492 39 QKVPLIKEIKGLLEGMNLVQAKKFVES 65 (96)
Q Consensus 39 kKi~vIK~VR~i~t~LgLkEAK~lVe~ 65 (96)
.++..|+..|.+ |++|.|.+++++.
T Consensus 45 ~~l~~I~~lr~~--G~sl~eI~~~l~~ 69 (135)
T PRK10227 45 NELTLLRQARQV--GFNLEESGELVNL 69 (135)
T ss_pred HHHHHHHHHHHC--CCCHHHHHHHHHh
Confidence 578888888884 9999999999874
No 37
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=44.68 E-value=46 Score=24.10 Aligned_cols=25 Identities=20% Similarity=0.275 Sum_probs=22.2
Q ss_pred CchHHHHHHHHhhcCCCHHHHHHHHhh
Q psy4492 39 QKVPLIKEIKGLLEGMNLVQAKKFVES 65 (96)
Q Consensus 39 kKi~vIK~VR~i~t~LgLkEAK~lVe~ 65 (96)
..+..|+..|.+ |++|.|-+.+++.
T Consensus 55 ~~L~~I~~lr~l--G~sL~eIk~ll~~ 79 (154)
T PRK15002 55 RYVAIIKIAQRI--GIPLATIGEAFGV 79 (154)
T ss_pred HHHHHHHHHHHc--CCCHHHHHHHHHH
Confidence 678899999984 9999999999975
No 38
>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=43.83 E-value=57 Score=22.27 Aligned_cols=26 Identities=19% Similarity=0.418 Sum_probs=22.2
Q ss_pred CchHHHHHHHHhhcCCCHHHHHHHHhhc
Q psy4492 39 QKVPLIKEIKGLLEGMNLVQAKKFVESI 66 (96)
Q Consensus 39 kKi~vIK~VR~i~t~LgLkEAK~lVe~~ 66 (96)
.++..|+.+|.+ |++|.|.|.+++..
T Consensus 44 ~~l~~I~~l~~~--G~sl~eI~~~l~~~ 69 (124)
T TIGR02051 44 KRLRFIKRAQEL--GFSLEEIGGLLGLV 69 (124)
T ss_pred HHHHHHHHHHHC--CCCHHHHHHHHhcc
Confidence 578888888884 99999999999754
No 39
>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=43.23 E-value=29 Score=23.95 Aligned_cols=26 Identities=19% Similarity=0.395 Sum_probs=22.6
Q ss_pred CchHHHHHHHHhhcCCCHHHHHHHHhhc
Q psy4492 39 QKVPLIKEIKGLLEGMNLVQAKKFVESI 66 (96)
Q Consensus 39 kKi~vIK~VR~i~t~LgLkEAK~lVe~~ 66 (96)
..+..|+..|.+ |++|+|-+.+++..
T Consensus 45 ~~l~~I~~lr~~--G~sL~eI~~~l~~~ 70 (133)
T cd04787 45 SRLRFILSARQL--GFSLKDIKEILSHA 70 (133)
T ss_pred HHHHHHHHHHHc--CCCHHHHHHHHhhh
Confidence 678899999984 99999999999854
No 40
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=42.70 E-value=53 Score=23.05 Aligned_cols=25 Identities=24% Similarity=0.515 Sum_probs=21.8
Q ss_pred CchHHHHHHHHhhcCCCHHHHHHHHhh
Q psy4492 39 QKVPLIKEIKGLLEGMNLVQAKKFVES 65 (96)
Q Consensus 39 kKi~vIK~VR~i~t~LgLkEAK~lVe~ 65 (96)
.++..|+.+|.. |++|.|.+.+++.
T Consensus 46 ~~l~~I~~lr~~--G~sL~eI~~~l~~ 70 (140)
T PRK09514 46 QRLRFIRRAKQL--GFTLEEIRELLSI 70 (140)
T ss_pred HHHHHHHHHHHc--CCCHHHHHHHHHh
Confidence 578889999984 9999999999974
No 41
>PRK13749 transcriptional regulator MerD; Provisional
Probab=39.99 E-value=35 Score=23.92 Aligned_cols=28 Identities=14% Similarity=0.303 Sum_probs=23.3
Q ss_pred CchHHHHHHHHhhcCCCHHHHHHHHhhcCh
Q psy4492 39 QKVPLIKEIKGLLEGMNLVQAKKFVESIPA 68 (96)
Q Consensus 39 kKi~vIK~VR~i~t~LgLkEAK~lVe~~P~ 68 (96)
.++..|+..|.+ |++|.|.+.+++-.+.
T Consensus 48 ~rL~~I~~~r~~--G~sL~eI~~ll~l~~~ 75 (121)
T PRK13749 48 QRLCFVRAAFEA--GIGLDALARLCRALDA 75 (121)
T ss_pred HHHHHHHHHHHc--CCCHHHHHHHHhhhcC
Confidence 567788888884 9999999999987654
No 42
>PRK00285 ihfA integration host factor subunit alpha; Reviewed
Probab=39.94 E-value=30 Score=22.63 Aligned_cols=35 Identities=20% Similarity=0.248 Sum_probs=30.2
Q ss_pred CchHHHHHHHHhhcCCCHHHHHHHHhhcChhhhhcC
Q psy4492 39 QKVPLIKEIKGLLEGMNLVQAKKFVESIPAVVKTDV 74 (96)
Q Consensus 39 kKi~vIK~VR~i~t~LgLkEAK~lVe~~P~~iKe~v 74 (96)
+|-.+|+.|.+- ++++-.+++..++.+-..|.+.+
T Consensus 4 tk~el~~~ia~~-~~~s~~~v~~vl~~~~~~i~~~L 38 (99)
T PRK00285 4 TKADLAEALFEK-VGLSKREAKELVELFFEEIRDAL 38 (99)
T ss_pred CHHHHHHHHHHH-hCcCHHHHHHHHHHHHHHHHHHH
Confidence 466899999987 79999999999999988887655
No 43
>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=39.11 E-value=36 Score=23.24 Aligned_cols=26 Identities=15% Similarity=0.446 Sum_probs=21.8
Q ss_pred CchHHHHHHHHhhcCCCHHHHHHHHhhc
Q psy4492 39 QKVPLIKEIKGLLEGMNLVQAKKFVESI 66 (96)
Q Consensus 39 kKi~vIK~VR~i~t~LgLkEAK~lVe~~ 66 (96)
..+..|+..|.+ |++|.|.|.+++..
T Consensus 45 ~~l~~I~~lr~~--G~sL~eI~~~l~~~ 70 (126)
T cd04785 45 ERLRFIRRARDL--GFSLEEIRALLALS 70 (126)
T ss_pred HHHHHHHHHHHC--CCCHHHHHHHHhhh
Confidence 578888888874 99999999999743
No 44
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=38.96 E-value=30 Score=20.44 Aligned_cols=25 Identities=32% Similarity=0.611 Sum_probs=19.2
Q ss_pred CchHHHHHHHHhhcCCCHHHHHHHHhh
Q psy4492 39 QKVPLIKEIKGLLEGMNLVQAKKFVES 65 (96)
Q Consensus 39 kKi~vIK~VR~i~t~LgLkEAK~lVe~ 65 (96)
..+..|+.++. .|++|.+.++++..
T Consensus 44 ~~l~~i~~l~~--~G~sl~~I~~~l~~ 68 (69)
T PF13411_consen 44 ERLREIKELRK--QGMSLEEIKKLLKQ 68 (69)
T ss_dssp HHHHHHHHHHH--TTTHHHHHHHHH--
T ss_pred HHHHHHHHHHH--CcCCHHHHHHHHcc
Confidence 57778888888 39999999998753
No 45
>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=38.56 E-value=38 Score=23.14 Aligned_cols=24 Identities=21% Similarity=0.511 Sum_probs=21.1
Q ss_pred CchHHHHHHHHhhcCCCHHHHHHHHh
Q psy4492 39 QKVPLIKEIKGLLEGMNLVQAKKFVE 64 (96)
Q Consensus 39 kKi~vIK~VR~i~t~LgLkEAK~lVe 64 (96)
..+..|+..|.+ |++|.|.+.+++
T Consensus 45 ~~l~~I~~lr~~--G~sL~eI~~~l~ 68 (127)
T TIGR02044 45 DELRLISRARQV--GFSLEECKELLN 68 (127)
T ss_pred HHHHHHHHHHHC--CCCHHHHHHHHH
Confidence 578889999984 999999999987
No 46
>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=38.45 E-value=38 Score=23.16 Aligned_cols=25 Identities=16% Similarity=0.489 Sum_probs=21.9
Q ss_pred CchHHHHHHHHhhcCCCHHHHHHHHhh
Q psy4492 39 QKVPLIKEIKGLLEGMNLVQAKKFVES 65 (96)
Q Consensus 39 kKi~vIK~VR~i~t~LgLkEAK~lVe~ 65 (96)
.++..|+.+|.+ |++|+|-+.+++.
T Consensus 45 ~~l~~I~~lr~~--G~sL~eI~~~l~~ 69 (127)
T cd01108 45 EELRFIRRARDL--GFSLEEIRELLAL 69 (127)
T ss_pred HHHHHHHHHHHc--CCCHHHHHHHHHH
Confidence 588899999984 9999999999874
No 47
>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=37.77 E-value=41 Score=22.56 Aligned_cols=25 Identities=20% Similarity=0.492 Sum_probs=21.4
Q ss_pred CchHHHHHHHHhhcCCCHHHHHHHHhh
Q psy4492 39 QKVPLIKEIKGLLEGMNLVQAKKFVES 65 (96)
Q Consensus 39 kKi~vIK~VR~i~t~LgLkEAK~lVe~ 65 (96)
..+..|+.+|.. |++|.|.+.+++.
T Consensus 44 ~~l~~I~~lr~~--G~sl~eI~~~l~~ 68 (112)
T cd01282 44 DRVRQIRRLLAA--GLTLEEIREFLPC 68 (112)
T ss_pred HHHHHHHHHHHc--CCCHHHHHHHHHH
Confidence 578888888884 9999999999875
No 48
>PF08002 DUF1697: Protein of unknown function (DUF1697); InterPro: IPR012545 This family contains many hypothetical bacterial proteins.; PDB: 2HIY_B.
Probab=37.69 E-value=3.5 Score=29.14 Aligned_cols=52 Identities=19% Similarity=0.365 Sum_probs=34.6
Q ss_pred ceeEEEEee--CCCCCchHHHHHHHHhhcCCCHHHHHHHHhhcChhhhhcCCHHH
Q psy4492 26 SLFTVKLVK--YDDKQKVPLIKEIKGLLEGMNLVQAKKFVESIPAVVKTDVTKEE 78 (96)
Q Consensus 26 t~f~V~L~~--~~~~kKi~vIK~VR~i~t~LgLkEAK~lVe~~P~~iKe~v~kee 78 (96)
+.|-..|.+ +|..+||+ -+++|++++++|+.+.+-++.|=..++....+.++
T Consensus 2 ~~yiaLLRGINVGG~nki~-MaeLr~~l~~~Gf~~V~Tyi~SGNvvf~~~~~~~~ 55 (137)
T PF08002_consen 2 TTYIALLRGINVGGKNKIK-MAELREALEDLGFTNVRTYIQSGNVVFESDRDPAE 55 (137)
T ss_dssp EEEEEEESS-SBTTBS----HHHHHHHHHHCT-EEEEEETTTTEEEEEESS-HHH
T ss_pred ceEEEEEcceecCCCCccc-HHHHHHHHHHcCCCCceEEEeeCCEEEecCCChHH
Confidence 356667766 46557787 68888888999999999999888777774444443
No 49
>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=37.57 E-value=89 Score=22.68 Aligned_cols=27 Identities=11% Similarity=0.274 Sum_probs=23.4
Q ss_pred CchHHHHHHHHhhcCCCHHHHHHHHhhcC
Q psy4492 39 QKVPLIKEIKGLLEGMNLVQAKKFVESIP 67 (96)
Q Consensus 39 kKi~vIK~VR~i~t~LgLkEAK~lVe~~P 67 (96)
.++..|+.+|.+ |++|.|.+.+++...
T Consensus 46 ~rL~~I~~lr~~--G~sL~eI~~ll~~~~ 72 (172)
T cd04790 46 ERLEQICAYRSA--GVSLEDIRSLLQQPG 72 (172)
T ss_pred HHHHHHHHHHHc--CCCHHHHHHHHhcCC
Confidence 678899999984 999999999998654
No 50
>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=37.48 E-value=40 Score=23.15 Aligned_cols=25 Identities=16% Similarity=0.499 Sum_probs=21.6
Q ss_pred CchHHHHHHHHhhcCCCHHHHHHHHhh
Q psy4492 39 QKVPLIKEIKGLLEGMNLVQAKKFVES 65 (96)
Q Consensus 39 kKi~vIK~VR~i~t~LgLkEAK~lVe~ 65 (96)
.++..|+..|.+ |++|.|-|.+++.
T Consensus 45 ~~l~~I~~lr~l--G~sL~eI~~~l~~ 69 (127)
T TIGR02047 45 ERLAFIRNCRTL--DMSLAEIRQLLRY 69 (127)
T ss_pred HHHHHHHHHHHc--CCCHHHHHHHHHh
Confidence 578899999984 9999999999873
No 51
>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=37.29 E-value=40 Score=19.83 Aligned_cols=24 Identities=25% Similarity=0.491 Sum_probs=17.4
Q ss_pred CchHHHHHHHHhhcCCCHHHHHHHHh
Q psy4492 39 QKVPLIKEIKGLLEGMNLVQAKKFVE 64 (96)
Q Consensus 39 kKi~vIK~VR~i~t~LgLkEAK~lVe 64 (96)
..+..|+.++. .|+.|.+.+++++
T Consensus 45 ~~l~~i~~l~~--~g~~l~~i~~~~~ 68 (68)
T cd01104 45 ARLRLIRRLTS--EGVRISQAAALAL 68 (68)
T ss_pred HHHHHHHHHHH--CCCCHHHHHHHhC
Confidence 35556666666 3999999998863
No 52
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=36.96 E-value=47 Score=21.82 Aligned_cols=28 Identities=21% Similarity=0.495 Sum_probs=22.7
Q ss_pred CchHHHHHHHHhhcCCCHHHHHHHHhhcCh
Q psy4492 39 QKVPLIKEIKGLLEGMNLVQAKKFVESIPA 68 (96)
Q Consensus 39 kKi~vIK~VR~i~t~LgLkEAK~lVe~~P~ 68 (96)
..+.+|+..|. .|++|.+-|++++....
T Consensus 45 ~~l~~I~~~r~--~G~~L~~I~~~l~~~~~ 72 (124)
T COG0789 45 ELLQIIKTLRE--LGFSLAEIKELLDLLSA 72 (124)
T ss_pred HHHHHHHHHHH--cCCCHHHHHHHHhcccc
Confidence 56777888886 49999999999987753
No 53
>cd04786 HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine 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, and organic su
Probab=36.83 E-value=41 Score=23.51 Aligned_cols=26 Identities=12% Similarity=0.238 Sum_probs=22.6
Q ss_pred CchHHHHHHHHhhcCCCHHHHHHHHhhc
Q psy4492 39 QKVPLIKEIKGLLEGMNLVQAKKFVESI 66 (96)
Q Consensus 39 kKi~vIK~VR~i~t~LgLkEAK~lVe~~ 66 (96)
.++.+|+.+|.+ |++|.|.+.++...
T Consensus 45 ~~l~~I~~lr~~--GfsL~eI~~ll~~~ 70 (131)
T cd04786 45 WVLEIISSAQQA--GFSLDEIRQLLPAD 70 (131)
T ss_pred HHHHHHHHHHHc--CCCHHHHHHHHhcc
Confidence 678899999984 99999999999753
No 54
>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=36.17 E-value=95 Score=20.39 Aligned_cols=30 Identities=17% Similarity=0.323 Sum_probs=24.3
Q ss_pred CchHHHHHHHHhhcCCCHHHHHHHHhhcChh
Q psy4492 39 QKVPLIKEIKGLLEGMNLVQAKKFVESIPAV 69 (96)
Q Consensus 39 kKi~vIK~VR~i~t~LgLkEAK~lVe~~P~~ 69 (96)
.++..|+.+|+- .|++|.+.+.+++..+..
T Consensus 44 ~~l~~I~~L~~~-~G~~l~ei~~~l~~~~~~ 73 (96)
T cd04774 44 KRLERILRLREV-LGFSLQEVTHFLERPLEP 73 (96)
T ss_pred HHHHHHHHHHHH-cCCCHHHHHHHHhccccc
Confidence 577788888873 399999999999887765
No 55
>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=35.26 E-value=47 Score=22.32 Aligned_cols=27 Identities=26% Similarity=0.401 Sum_probs=23.5
Q ss_pred CchHHHHHHHHhhcCCCHHHHHHHHhhcC
Q psy4492 39 QKVPLIKEIKGLLEGMNLVQAKKFVESIP 67 (96)
Q Consensus 39 kKi~vIK~VR~i~t~LgLkEAK~lVe~~P 67 (96)
.++..|+.+|.+ |++|.|-+.+++...
T Consensus 44 ~~l~~I~~lr~~--G~sl~eI~~~l~~~~ 70 (116)
T cd04769 44 ECLRFIKEARQL--GFTLAELKAIFAGHE 70 (116)
T ss_pred HHHHHHHHHHHc--CCCHHHHHHHHhccc
Confidence 688999999995 999999999987653
No 56
>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=34.64 E-value=48 Score=23.09 Aligned_cols=27 Identities=11% Similarity=0.330 Sum_probs=22.6
Q ss_pred CchHHHHHHHHhhcCCCHHHHHHHHhhcC
Q psy4492 39 QKVPLIKEIKGLLEGMNLVQAKKFVESIP 67 (96)
Q Consensus 39 kKi~vIK~VR~i~t~LgLkEAK~lVe~~P 67 (96)
.++..|+..|.+ |++|.+.+.++.-..
T Consensus 48 ~rL~~I~~lr~~--G~~L~eI~~ll~~~~ 74 (120)
T TIGR02054 48 QRLRFVRAAFEA--GIGLGELARLCRALD 74 (120)
T ss_pred HHHHHHHHHHHc--CCCHHHHHHHHHhhc
Confidence 578889999984 999999999987543
No 57
>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=32.85 E-value=1.2e+02 Score=19.79 Aligned_cols=27 Identities=22% Similarity=0.391 Sum_probs=22.7
Q ss_pred CchHHHHHHHHhhcCCCHHHHHHHHhhcC
Q psy4492 39 QKVPLIKEIKGLLEGMNLVQAKKFVESIP 67 (96)
Q Consensus 39 kKi~vIK~VR~i~t~LgLkEAK~lVe~~P 67 (96)
..+..|+.+|.. |++|.+.+.+++...
T Consensus 45 ~~l~~i~~lr~~--g~~l~~i~~~~~~~~ 71 (103)
T cd01106 45 ERLQQILFLKEL--GFSLKEIKELLKDPS 71 (103)
T ss_pred HHHHHHHHHHHc--CCCHHHHHHHHHcCc
Confidence 567778888884 999999999998765
No 58
>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=31.97 E-value=57 Score=22.88 Aligned_cols=26 Identities=19% Similarity=0.494 Sum_probs=22.2
Q ss_pred CchHHHHHHHHhhcCCCHHHHHHHHhhc
Q psy4492 39 QKVPLIKEIKGLLEGMNLVQAKKFVESI 66 (96)
Q Consensus 39 kKi~vIK~VR~i~t~LgLkEAK~lVe~~ 66 (96)
.++..|+.+|.. |++|.|.+.++..+
T Consensus 45 ~~l~~I~~lr~~--G~sl~eI~~~l~~~ 70 (139)
T cd01110 45 RRIAFIKVAQRL--GLSLAEIAEALATL 70 (139)
T ss_pred HHHHHHHHHHHc--CCCHHHHHHHHHHh
Confidence 678889999884 99999999998753
No 59
>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=31.44 E-value=60 Score=23.02 Aligned_cols=26 Identities=19% Similarity=0.402 Sum_probs=22.6
Q ss_pred CchHHHHHHHHhhcCCCHHHHHHHHhhc
Q psy4492 39 QKVPLIKEIKGLLEGMNLVQAKKFVESI 66 (96)
Q Consensus 39 kKi~vIK~VR~i~t~LgLkEAK~lVe~~ 66 (96)
.++..|+..|+. |++|.+-+.++..+
T Consensus 45 ~~l~~I~~lr~~--G~sL~eI~~~l~~~ 70 (142)
T TIGR01950 45 RRVAVIKAAQRV--GIPLATIGEALAVL 70 (142)
T ss_pred HHHHHHHHHHHc--CCCHHHHHHHHHhc
Confidence 678899999984 99999999999754
No 60
>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). 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=30.70 E-value=60 Score=22.91 Aligned_cols=27 Identities=26% Similarity=0.533 Sum_probs=23.5
Q ss_pred CchHHHHHHHHhhcCCCHHHHHHHHhhcC
Q psy4492 39 QKVPLIKEIKGLLEGMNLVQAKKFVESIP 67 (96)
Q Consensus 39 kKi~vIK~VR~i~t~LgLkEAK~lVe~~P 67 (96)
.++..|+..|+. |++|.|.+++++..-
T Consensus 44 ~~l~~I~~lr~~--G~sL~eI~~~l~~~~ 70 (134)
T cd04779 44 DRLQLIEHLKGQ--RLSLAEIKDQLEEVQ 70 (134)
T ss_pred HHHHHHHHHHHC--CCCHHHHHHHHHhhc
Confidence 688999999984 999999999998654
No 61
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, 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 dissimil
Probab=30.67 E-value=1.1e+02 Score=20.16 Aligned_cols=26 Identities=12% Similarity=0.124 Sum_probs=21.6
Q ss_pred CchHHHHHHHHhhcCCCHHHHHHHHhhc
Q psy4492 39 QKVPLIKEIKGLLEGMNLVQAKKFVESI 66 (96)
Q Consensus 39 kKi~vIK~VR~i~t~LgLkEAK~lVe~~ 66 (96)
..+..|+..|+. |++|.|.+.++..-
T Consensus 45 ~~l~~I~~l~~~--G~~l~ei~~~~~~~ 70 (102)
T cd04775 45 SRLEKIVFLQAG--GLPLEEIAGCLAQP 70 (102)
T ss_pred HHHHHHHHHHHC--CCCHHHHHHHHcCC
Confidence 577888888884 99999999998753
No 62
>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=30.48 E-value=67 Score=20.63 Aligned_cols=26 Identities=27% Similarity=0.397 Sum_probs=21.6
Q ss_pred CchHHHHHHHHhhcCCCHHHHHHHHhhc
Q psy4492 39 QKVPLIKEIKGLLEGMNLVQAKKFVESI 66 (96)
Q Consensus 39 kKi~vIK~VR~i~t~LgLkEAK~lVe~~ 66 (96)
..+..|+.+|+ .|+.|.+.+.++...
T Consensus 46 ~~l~~I~~Lr~--~G~sl~~i~~~l~~~ 71 (88)
T cd01105 46 DRLLVIKELLD--EGFTLAAAVEKLRRR 71 (88)
T ss_pred HHHHHHHHHHH--CCCCHHHHHHHHHHc
Confidence 57788888888 399999999999743
No 63
>PRK05412 putative nucleotide-binding protein; Reviewed
Probab=29.98 E-value=57 Score=24.50 Aligned_cols=27 Identities=15% Similarity=0.149 Sum_probs=24.4
Q ss_pred hhhhhcCCHHHHHHHHHHHHhCCcEEE
Q psy4492 68 AVVKTDVTKEEAEALKASLAKVGGEVS 94 (96)
Q Consensus 68 ~~iKe~v~keeAe~ik~kle~aGa~ve 94 (96)
..|++|++++.|.+|.+.+.+.+-+|.
T Consensus 94 i~lk~GI~~e~AKkIvK~IKd~klKVq 120 (161)
T PRK05412 94 VKLKQGIDQELAKKIVKLIKDSKLKVQ 120 (161)
T ss_pred EehhhccCHHHHHHHHHHHHhcCCcee
Confidence 468999999999999999999988764
No 64
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=29.86 E-value=93 Score=17.10 Aligned_cols=23 Identities=39% Similarity=0.550 Sum_probs=16.5
Q ss_pred hHHHHHHHHhhcCCCHHHHHHHHhh
Q psy4492 41 VPLIKEIKGLLEGMNLVQAKKFVES 65 (96)
Q Consensus 41 i~vIK~VR~i~t~LgLkEAK~lVe~ 65 (96)
+.+|++-|+. ||+..|-+.|.+.
T Consensus 6 ~~Li~eA~~~--Gls~eeir~FL~~ 28 (30)
T PF08671_consen 6 VELIKEAKES--GLSKEEIREFLEF 28 (30)
T ss_dssp HHHHHHHHHT--T--HHHHHHHHHH
T ss_pred HHHHHHHHHc--CCCHHHHHHHHHh
Confidence 5678888884 8998888888764
No 65
>PRK00199 ihfB integration host factor subunit beta; Reviewed
Probab=29.78 E-value=57 Score=21.06 Aligned_cols=35 Identities=14% Similarity=0.158 Sum_probs=28.3
Q ss_pred chHHHHHHHHhhcCCCHHHHHHHHhhcChhhhhcC
Q psy4492 40 KVPLIKEIKGLLEGMNLVQAKKFVESIPAVVKTDV 74 (96)
Q Consensus 40 Ki~vIK~VR~i~t~LgLkEAK~lVe~~P~~iKe~v 74 (96)
|-.+|+.|.+-.++++-.+++..|+.+-..|.+.+
T Consensus 3 k~eli~~ia~~~~~~s~~~~~~vv~~~~~~i~~~L 37 (94)
T PRK00199 3 KSELIERLAARNPHLSAKDVENAVKEILEEMSDAL 37 (94)
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHH
Confidence 56788988753268999999999999988887765
No 66
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=29.72 E-value=1.3e+02 Score=17.82 Aligned_cols=45 Identities=13% Similarity=0.245 Sum_probs=29.2
Q ss_pred HHHHHHHHhhcCCCHHHHHHHHhhcChhhh-------------hcCCHHHHHHHHHHHH
Q psy4492 42 PLIKEIKGLLEGMNLVQAKKFVESIPAVVK-------------TDVTKEEAEALKASLA 87 (96)
Q Consensus 42 ~vIK~VR~i~t~LgLkEAK~lVe~~P~~iK-------------e~v~keeAe~ik~kle 87 (96)
.++..+.+| +|+|-+-+..|++.--.++. .|+++..|+.|...+.
T Consensus 2 ~~~~~L~~I-~Gig~~~a~~L~~~G~~t~~~l~~a~~~~L~~i~Gig~~~a~~i~~~~~ 59 (60)
T PF14520_consen 2 GVFDDLLSI-PGIGPKRAEKLYEAGIKTLEDLANADPEELAEIPGIGEKTAEKIIEAAR 59 (60)
T ss_dssp HHHHHHHTS-TTCHHHHHHHHHHTTCSSHHHHHTSHHHHHHTSTTSSHHHHHHHHHHHH
T ss_pred HHHHhhccC-CCCCHHHHHHHHhcCCCcHHHHHcCCHHHHhcCCCCCHHHHHHHHHHHh
Confidence 456667776 78888888888776222221 3677777777777664
No 67
>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=29.58 E-value=67 Score=21.58 Aligned_cols=26 Identities=12% Similarity=0.356 Sum_probs=22.0
Q ss_pred CchHHHHHHHHhhcCCCHHHHHHHHhhc
Q psy4492 39 QKVPLIKEIKGLLEGMNLVQAKKFVESI 66 (96)
Q Consensus 39 kKi~vIK~VR~i~t~LgLkEAK~lVe~~ 66 (96)
.++..|+..|.. |++|.+-+.+++..
T Consensus 45 ~~l~~I~~lr~~--G~~l~~I~~~l~~~ 70 (107)
T cd01111 45 QRLRFVRAAFEA--GIGLDELARLCRAL 70 (107)
T ss_pred HHHHHHHHHHHc--CCCHHHHHHHHHHH
Confidence 578888888884 99999999998754
No 68
>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=28.63 E-value=69 Score=19.14 Aligned_cols=23 Identities=22% Similarity=0.404 Sum_probs=18.2
Q ss_pred CchHHHHHHHHhhcCCCHHHHHHHH
Q psy4492 39 QKVPLIKEIKGLLEGMNLVQAKKFV 63 (96)
Q Consensus 39 kKi~vIK~VR~i~t~LgLkEAK~lV 63 (96)
..+..|+.+|+ .|+.|.+.+.++
T Consensus 45 ~~l~~i~~l~~--~g~~l~~i~~~l 67 (68)
T cd04763 45 DRILEIKRWID--NGVQVSKVKKLL 67 (68)
T ss_pred HHHHHHHHHHH--cCCCHHHHHHHh
Confidence 46677777777 399999999876
No 69
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. 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 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=28.11 E-value=1.7e+02 Score=18.68 Aligned_cols=25 Identities=24% Similarity=0.438 Sum_probs=19.5
Q ss_pred CchHHHHHHHHhhcCCCHHHHHHHHh
Q psy4492 39 QKVPLIKEIKGLLEGMNLVQAKKFVE 64 (96)
Q Consensus 39 kKi~vIK~VR~i~t~LgLkEAK~lVe 64 (96)
.++..|+.++.- .|++|.+.+.+++
T Consensus 45 ~~l~~i~~L~~d-~g~~l~~i~~~l~ 69 (91)
T cd04766 45 ERLRRIQRLTQE-LGVNLAGVKRILE 69 (91)
T ss_pred HHHHHHHHHHHH-cCCCHHHHHHHHH
Confidence 566677777663 4999999999987
No 70
>PF04461 DUF520: Protein of unknown function (DUF520); InterPro: IPR007551 This entry represents the UPF0234 family of uncharacterised proteins.; PDB: 1IN0_A.
Probab=27.32 E-value=44 Score=25.06 Aligned_cols=27 Identities=11% Similarity=0.160 Sum_probs=18.5
Q ss_pred hhhhhcCCHHHHHHHHHHHHhCCcEEE
Q psy4492 68 AVVKTDVTKEEAEALKASLAKVGGEVS 94 (96)
Q Consensus 68 ~~iKe~v~keeAe~ik~kle~aGa~ve 94 (96)
..|++|++.+.|.+|.+.+.+.+-+|.
T Consensus 94 i~lk~GI~~d~AKkIvK~IKd~klKVq 120 (160)
T PF04461_consen 94 IKLKQGIDQDTAKKIVKLIKDSKLKVQ 120 (160)
T ss_dssp EEE--S--HHHHHHHHHHHHHH--SEE
T ss_pred EEeecccCHHHHHHHHHHHHhcCCcee
Confidence 468999999999999999999887764
No 71
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. 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 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=26.68 E-value=79 Score=21.51 Aligned_cols=26 Identities=23% Similarity=0.404 Sum_probs=22.2
Q ss_pred CchHHHHHHHHhhcCCCHHHHHHHHhhc
Q psy4492 39 QKVPLIKEIKGLLEGMNLVQAKKFVESI 66 (96)
Q Consensus 39 kKi~vIK~VR~i~t~LgLkEAK~lVe~~ 66 (96)
..+..|+..|.. |++|.+.+.+++..
T Consensus 43 ~~l~~I~~lr~~--G~~L~~I~~~l~~~ 68 (118)
T cd04776 43 ARLKLILRGKRL--GFSLEEIRELLDLY 68 (118)
T ss_pred HHHHHHHHHHHC--CCCHHHHHHHHHhh
Confidence 577888889984 99999999999864
No 72
>COG5275 BRCT domain type II [General function prediction only]
Probab=25.69 E-value=1.7e+02 Score=23.68 Aligned_cols=59 Identities=17% Similarity=0.175 Sum_probs=42.4
Q ss_pred hcceeEEEEeeCCCCCchHHHHHHHHhhcCCCHHHHHHHHhhcChhhhhcCCHHHHHHHHHHHHh
Q psy4492 24 VQSLFTVKLVKYDDKQKVPLIKEIKGLLEGMNLVQAKKFVESIPAVVKTDVTKEEAEALKASLAK 88 (96)
Q Consensus 24 ekt~f~V~L~~~~~~kKi~vIK~VR~i~t~LgLkEAK~lVe~~P~~iKe~v~keeAe~ik~kle~ 88 (96)
-+|.|-|-=.+.|+ +|+.-||.++ | ..++=-+-+-|+-.+|.-.- .-++||+...+++.
T Consensus 193 skTtflvlGdnaGP-~K~ekiKqlk-I-kaidEegf~~LI~~~pa~gg---~gaaaeka~~K~e~ 251 (276)
T COG5275 193 SKTTFLVLGDNAGP-SKMEKIKQLK-I-KAIDEEGFDSLIKDTPAAGG---GGAAAEKATEKAES 251 (276)
T ss_pred cceeEEEecCCCCh-HHHHHHHHhC-C-ccccHHHHHHHHhcCcccCC---chHHHHHHHHHHHh
Confidence 46887654467776 8999999988 3 45666666689999996554 55777777777654
No 73
>cd07963 Anticodon_Ia_Cys Anticodon-binding domain of cysteinyl tRNA synthetases. This domain is found in cysteinyl tRNA synthetases (CysRS), which belong to the class Ia aminoacyl tRNA synthetases. It lies C-terminal to the catalytic core domain, and recognizes and specifically binds to the tRNA anticodon. CysRS catalyzes the transfer of cysteine to the 3'-end of its tRNA.
Probab=25.10 E-value=83 Score=21.86 Aligned_cols=24 Identities=21% Similarity=0.234 Sum_probs=19.7
Q ss_pred hhcCCHHHHHHHHHHHHhCCcEEE
Q psy4492 71 KTDVTKEEAEALKASLAKVGGEVS 94 (96)
Q Consensus 71 Ke~v~keeAe~ik~kle~aGa~ve 94 (96)
+.+=.-+.|+.|+..|.+.|-.|+
T Consensus 123 R~~Kdf~~AD~IRd~L~~~Gi~i~ 146 (156)
T cd07963 123 RKAKDWAEADRIRDELAAQGIILE 146 (156)
T ss_pred HHhcCHHHHHHHHHHHHHCCcEEE
Confidence 344467889999999999998875
No 74
>PRK15348 type III secretion system lipoprotein SsaJ; Provisional
Probab=24.86 E-value=1.2e+02 Score=23.99 Aligned_cols=34 Identities=15% Similarity=0.152 Sum_probs=26.8
Q ss_pred HHHhhcChhhhhcCCHHHHHHHHHHHHhCCcEEE
Q psy4492 61 KFVESIPAVVKTDVTKEEAEALKASLAKVGGEVS 94 (96)
Q Consensus 61 ~lVe~~P~~iKe~v~keeAe~ik~kle~aGa~ve 94 (96)
-++-.|-..|-.|++.+||.++...|.+.|-..+
T Consensus 14 ~~l~gC~~~LysgL~~~dA~~I~a~L~~~gI~y~ 47 (249)
T PRK15348 14 FFLTACDVDLYRSLPEDEANQMLALLMQHHIDAE 47 (249)
T ss_pred HHHhcCChHHHcCCCHHHHHHHHHHHHHcCCCce
Confidence 4556677788889999999999999988876653
No 75
>PF02022 Integrase_Zn: Integrase Zinc binding domain The structure of the N-terminal zinc binding domain.; InterPro: IPR003308 Retroviral integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains: an N-terminal zinc binding domain, a central catalytic core and a C-terminal DNA-binding domain [, ]. Often found as part of the POL polyprotein.; GO: 0008270 zinc ion binding; PDB: 1E0E_A 3F9K_F 1E27_C 1K6Y_B 1WJD_A 1WJB_A 1WJF_A 1WJE_B 3HPG_B 3HPH_C ....
Probab=24.80 E-value=1.3e+02 Score=17.33 Aligned_cols=25 Identities=24% Similarity=0.420 Sum_probs=17.1
Q ss_pred HHHHHHhhcCCCHHHHHHHHhhcChh
Q psy4492 44 IKEIKGLLEGMNLVQAKKFVESIPAV 69 (96)
Q Consensus 44 IK~VR~i~t~LgLkEAK~lVe~~P~~ 69 (96)
.+.+|.-. ||....||++|.+.|.=
T Consensus 12 ~~~L~~~f-~ip~~vAk~IV~~C~~C 36 (40)
T PF02022_consen 12 AKALRHKF-GIPRLVAKQIVNQCPKC 36 (40)
T ss_dssp HHHHHHHH-T--HHHHHHHHHHSCCH
T ss_pred HHHHHHHH-ccCHHHHHHHHHHCHHH
Confidence 35566332 89999999999999853
No 76
>PF00216 Bac_DNA_binding: Bacterial DNA-binding protein; InterPro: IPR000119 Bacteria synthesise a set of small, usually basic proteins of about 90 residues that bind DNA and are known as histone-like proteins [, ]. Examples include the HU protein in Escherichia coli is a dimer of closely related alpha and beta chains and in other bacteria can be a dimer of identical chains. HU-type proteins have been found in a variety of eubacteria, cyanobacteria and archaebacteria, and are also encoded in the chloroplast genome of some algae []. The integration host factor (IHF), a dimer of closely related chains which seem to function in genetic recombination as well as in translational and transcriptional control [] is found in enterobacteria and viral proteins include the African Swine fever virus protein A104R (or LMW5-AR) []. The exact function of these proteins is not yet clear but they are capable of wrapping DNA and stabilising it from denaturation under extreme environmental conditions. The structure is known for one of these proteins []. The protein exists as a dimer and two "beta-arms" function as the non-specific binding site for bacterial DNA. ; GO: 0003677 DNA binding; PDB: 3C4I_B 2O97_A 1MUL_A 1P78_A 1P51_C 1P71_B 2HT0_A 1OWG_A 2IIF_A 1OUZ_A ....
Probab=24.43 E-value=71 Score=19.87 Aligned_cols=34 Identities=24% Similarity=0.364 Sum_probs=27.7
Q ss_pred chHHHHHHHHhhcCCCHHHHHHHHhhcChhhhhcC
Q psy4492 40 KVPLIKEIKGLLEGMNLVQAKKFVESIPAVVKTDV 74 (96)
Q Consensus 40 Ki~vIK~VR~i~t~LgLkEAK~lVe~~P~~iKe~v 74 (96)
|-.+|+.|..- +++.-.+++..++.+=..|.+.+
T Consensus 3 k~eli~~ia~~-~~~s~~~v~~vl~~~~~~i~~~L 36 (90)
T PF00216_consen 3 KKELIKRIAEK-TGLSKKDVEAVLDALFDVIKEAL 36 (90)
T ss_dssp HHHHHHHHHHH-HTSSHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHh-cCCCHHHHHHHHHHHHHHHHHHH
Confidence 55889999986 79999999999998877666543
No 77
>PF00416 Ribosomal_S13: Ribosomal protein S13/S18; InterPro: IPR001892 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S13 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S13 is known to be involved in binding fMet-tRNA and, hence, in the initiation of translation. It is a basic protein of 115 to 177 amino-acid residues that contains thee helices and a beta-hairpin in the core of the protein, forming a helix-two turns-helix (H2TH) motif, and a non-globular C-terminal extension. This family of ribosomal proteins is present in prokaryotes, eukaryotes and archaea [, ].; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3BBN_M 2QBB_M 3I1M_M 3OFP_M 3OFX_M 3OFO_M 1VS5_M 3OAQ_M 2QAL_M 3J18_M ....
Probab=23.88 E-value=1.7e+02 Score=19.67 Aligned_cols=46 Identities=20% Similarity=0.403 Sum_probs=38.4
Q ss_pred HHHHHHHHhhcCCCHHHHHHHHhhc---ChhhhhcCCHHHHHHHHHHHHh
Q psy4492 42 PLIKEIKGLLEGMNLVQAKKFVESI---PAVVKTDVTKEEAEALKASLAK 88 (96)
Q Consensus 42 ~vIK~VR~i~t~LgLkEAK~lVe~~---P~~iKe~v~keeAe~ik~kle~ 88 (96)
.|.-.+..| -|+|..-|+.+...+ |..--..++.++-+.|.+.|+.
T Consensus 12 ~i~~aLt~I-yGIG~~~A~~Ic~~lgi~~~~~~~~Ls~~~i~~l~~~i~~ 60 (107)
T PF00416_consen 12 PIYIALTKI-YGIGRRKAKQICKKLGINPNKKVGDLSDEQIDKLRKIIEK 60 (107)
T ss_dssp BHHHHHTTS-TTBCHHHHHHHHHHTTS-SSSBTTTSTHHHHHHHHHHHHT
T ss_pred chHhHHhhh-hccCHHHHHHHHHHcCCChhhhcccCCHHHHHHHHHHHHH
Confidence 678888898 799999999999877 5455557999999999988875
No 78
>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=23.67 E-value=96 Score=18.38 Aligned_cols=23 Identities=17% Similarity=0.384 Sum_probs=18.0
Q ss_pred CchHHHHHHHHhhcCCCHHHHHHHH
Q psy4492 39 QKVPLIKEIKGLLEGMNLVQAKKFV 63 (96)
Q Consensus 39 kKi~vIK~VR~i~t~LgLkEAK~lV 63 (96)
..+..|+.++. .|+.|.+.+.++
T Consensus 44 ~~l~~i~~l~~--~g~~l~~i~~~l 66 (67)
T cd04764 44 ELLKKIKTLLE--KGLSIKEIKEIL 66 (67)
T ss_pred HHHHHHHHHHH--CCCCHHHHHHHh
Confidence 46677777777 399999998875
No 79
>PF00828 Ribosomal_L18e: Ribosomal protein L18e/L15; InterPro: IPR021131 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents both L15 and L18e ribosomal proteins, which share a common structure consisting mainly of parallel beta sheets (beta-alpha-beta units) with a core of three turns of irregular (beta-beta-alpha)n superhelix [, ].; PDB: 3O58_Y 1S1I_V 3O5H_Y 3IZS_O 3IZR_R 2OTL_L 1M1K_M 3G6E_L 1VQ9_L 1YIT_L ....
Probab=23.62 E-value=80 Score=21.57 Aligned_cols=27 Identities=30% Similarity=0.521 Sum_probs=17.4
Q ss_pred hcChhhhh-cCCHHHHHHHHHHHHhCCcEEEe
Q psy4492 65 SIPAVVKT-DVTKEEAEALKASLAKVGGEVSV 95 (96)
Q Consensus 65 ~~P~~iKe-~v~keeAe~ik~kle~aGa~vei 95 (96)
+.|-+|+- .+|+ ..+++++++|++|++
T Consensus 101 ~~~l~I~a~~~S~----~A~ekIe~aGG~v~~ 128 (129)
T PF00828_consen 101 TKPLTIKAHRFSK----SAKEKIEAAGGEVVT 128 (129)
T ss_dssp SSSEEEEESEETH----HHHHHHHHTSEEEEE
T ss_pred ccceEEEEEecCH----HHHHHHHHcCCEEEe
Confidence 44544443 3443 567788999999875
No 80
>PRK08385 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=23.40 E-value=1.3e+02 Score=23.85 Aligned_cols=42 Identities=21% Similarity=0.272 Sum_probs=33.8
Q ss_pred CCHHHHHHHHhhcCh-hhhhcCCHHHHHHHHHHHHhCC--cEEEe
Q psy4492 54 MNLVQAKKFVESIPA-VVKTDVTKEEAEALKASLAKVG--GEVSV 95 (96)
Q Consensus 54 LgLkEAK~lVe~~P~-~iKe~v~keeAe~ik~kle~aG--a~vei 95 (96)
=+|.|+++.++.-+. ++.+|++.++..++.+.+...| -.+.|
T Consensus 190 ~~leea~~a~~agaDiI~LDn~~~e~l~~~v~~l~~~~~~~~~~l 234 (278)
T PRK08385 190 ESLEDALKAAKAGADIIMLDNMTPEEIREVIEALKREGLRERVKI 234 (278)
T ss_pred CCHHHHHHHHHcCcCEEEECCCCHHHHHHHHHHHHhcCcCCCEEE
Confidence 378999999997664 4589999999999999998876 44544
No 81
>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=22.47 E-value=99 Score=20.38 Aligned_cols=25 Identities=20% Similarity=0.426 Sum_probs=20.7
Q ss_pred CchHHHHHHHHhhcCCCHHHHHHHHhh
Q psy4492 39 QKVPLIKEIKGLLEGMNLVQAKKFVES 65 (96)
Q Consensus 39 kKi~vIK~VR~i~t~LgLkEAK~lVe~ 65 (96)
..+..|+..|.. |+.|.|.+.+++.
T Consensus 45 ~~l~~I~~l~~~--G~~l~ei~~~l~~ 69 (102)
T cd04789 45 QRLLLIQQLQAG--GLSLKECLACLQG 69 (102)
T ss_pred HHHHHHHHHHHC--CCCHHHHHHHHcC
Confidence 467788888884 9999999998864
No 82
>KOG4402|consensus
Probab=22.46 E-value=63 Score=23.86 Aligned_cols=23 Identities=22% Similarity=0.439 Sum_probs=16.1
Q ss_pred HHHHHHHHh---hcCCCHHHHHHHHh
Q psy4492 42 PLIKEIKGL---LEGMNLVQAKKFVE 64 (96)
Q Consensus 42 ~vIK~VR~i---~t~LgLkEAK~lVe 64 (96)
.+++.||.+ +=.|||.||.++--
T Consensus 102 dl~~kIr~iqn~vYqLGl~EaremtR 127 (144)
T KOG4402|consen 102 DLAKKIRNIQNSVYQLGLEEAREMTR 127 (144)
T ss_pred HHHHHHHHHHHHHHHHhhHHHHHHhh
Confidence 467777765 12489999988754
No 83
>cd08494 PBP2_NikA_DppA_OppA_like_6 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most si
Probab=22.33 E-value=1.7e+02 Score=22.91 Aligned_cols=43 Identities=19% Similarity=0.257 Sum_probs=30.2
Q ss_pred CCCHHHHHHHHhhcCh------hh---hhcCCHHHHHHHHHHHHhCCcEEEe
Q psy4492 53 GMNLVQAKKFVESIPA------VV---KTDVTKEEAEALKASLAKVGGEVSV 95 (96)
Q Consensus 53 ~LgLkEAK~lVe~~P~------~i---Ke~v~keeAe~ik~kle~aGa~vei 95 (96)
..++..||++++.+-. .| .....+.-|+.|+..|+.+|-+|++
T Consensus 297 ~~d~~kA~~lL~~aG~~~g~~l~l~~~~~~~~~~~a~~i~~~l~~~GI~v~i 348 (448)
T cd08494 297 PYDPDKARQLLAEAGAAYGLTLTLTLPPLPYARRIGEIIASQLAEVGITVKI 348 (448)
T ss_pred CCCHHHHHHHHHHcCCCCCeEEEEEecCCcchhHHHHHHHHHHHhcCcEEEE
Confidence 3567888888876521 11 1123567899999999999998876
No 84
>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=22.30 E-value=52 Score=21.46 Aligned_cols=35 Identities=17% Similarity=0.194 Sum_probs=28.5
Q ss_pred chHHHHHHHHhhcCCCHHHHHHHHhhcChhhhhcCC
Q psy4492 40 KVPLIKEIKGLLEGMNLVQAKKFVESIPAVVKTDVT 75 (96)
Q Consensus 40 Ki~vIK~VR~i~t~LgLkEAK~lVe~~P~~iKe~v~ 75 (96)
|-.+|+.|.+- +++.-.+++..++.+-..|.+.+.
T Consensus 4 k~eli~~ia~~-~~~s~~~v~~vv~~~~~~i~~~L~ 38 (96)
T TIGR00987 4 KAEMSEYLFDE-LGLSKREAKELVELFFEEIRRALE 38 (96)
T ss_pred HHHHHHHHHHH-hCcCHHHHHHHHHHHHHHHHHHHH
Confidence 55789999986 799999999999988877766543
No 85
>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=22.26 E-value=96 Score=19.88 Aligned_cols=36 Identities=14% Similarity=0.168 Sum_probs=28.3
Q ss_pred chHHHHHHHHhhcCCCHHHHHHHHhhcChhhhhcCC
Q psy4492 40 KVPLIKEIKGLLEGMNLVQAKKFVESIPAVVKTDVT 75 (96)
Q Consensus 40 Ki~vIK~VR~i~t~LgLkEAK~lVe~~P~~iKe~v~ 75 (96)
|-.+|+.|.+-.+++.-++++..++.+-..|.+.+.
T Consensus 3 k~eli~~i~~~~~~~s~~~v~~vv~~~~~~i~~~L~ 38 (94)
T TIGR00988 3 KSELIERIATQQSHLPAKDVEDAVKTMLEHMASALA 38 (94)
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 557899998632689999999999998877766553
No 86
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), 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=21.64 E-value=1.3e+02 Score=19.70 Aligned_cols=26 Identities=19% Similarity=0.488 Sum_probs=21.1
Q ss_pred CchHHHHHHHHhhcCCCHHHHHHHHhh
Q psy4492 39 QKVPLIKEIKGLLEGMNLVQAKKFVES 65 (96)
Q Consensus 39 kKi~vIK~VR~i~t~LgLkEAK~lVe~ 65 (96)
.++..|+.+|.- .|++|.+.+.+++.
T Consensus 45 ~~l~~I~~L~~~-~G~~l~~I~~~l~~ 70 (95)
T cd04780 45 ERLRLIRALQQE-GGLPISQIKEVLDA 70 (95)
T ss_pred HHHHHHHHHHHH-cCCCHHHHHHHHHh
Confidence 577777777753 39999999999986
No 87
>cd04767 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators. Putative helix-turn-helix (HTH) transcription regulator HspR-like proteins. Unlike the characterized HspR, these proteins have a C-terminal domain with putative metal binding cysteines (MBC). Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. 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 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 spe
Probab=21.38 E-value=1.2e+02 Score=21.26 Aligned_cols=32 Identities=19% Similarity=0.399 Sum_probs=23.1
Q ss_pred CchHHHHHHHHhhcCCCHHHHHHHHhhcChhhh
Q psy4492 39 QKVPLIKEIKGLLEGMNLVQAKKFVESIPAVVK 71 (96)
Q Consensus 39 kKi~vIK~VR~i~t~LgLkEAK~lVe~~P~~iK 71 (96)
..+..|+.+|.- .|++|.+.+.+++-+|...-
T Consensus 44 ~rL~~I~~L~~e-~G~~l~eI~~~L~l~~~~~~ 75 (120)
T cd04767 44 KRLRFIKKLINE-KGLNIAGVKQILSMYPCWSI 75 (120)
T ss_pred HHHHHHHHHHHH-cCCCHHHHHHHHHhCccccc
Confidence 455556666552 49999999999999886543
No 88
>PRK06419 rpl15p 50S ribosomal protein L15P; Reviewed
Probab=21.23 E-value=97 Score=22.35 Aligned_cols=16 Identities=31% Similarity=0.491 Sum_probs=13.1
Q ss_pred HHHHHHHHhCCcEEEe
Q psy4492 80 EALKASLAKVGGEVSV 95 (96)
Q Consensus 80 e~ik~kle~aGa~vei 95 (96)
+..++++|++|++|++
T Consensus 129 ~~A~ekIe~aGG~v~l 144 (148)
T PRK06419 129 EKAIEKIEAAGGEVVL 144 (148)
T ss_pred HHHHHHHHHcCCEEEE
Confidence 4567789999999976
No 89
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. 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. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=20.57 E-value=1.3e+02 Score=20.08 Aligned_cols=26 Identities=27% Similarity=0.313 Sum_probs=21.7
Q ss_pred CchHHHHHHHHhhcCCCHHHHHHHHhhc
Q psy4492 39 QKVPLIKEIKGLLEGMNLVQAKKFVESI 66 (96)
Q Consensus 39 kKi~vIK~VR~i~t~LgLkEAK~lVe~~ 66 (96)
..+..|+.+|.. |++|.+.+.+++..
T Consensus 45 ~~l~~I~~lr~~--G~~l~~I~~~l~~~ 70 (108)
T cd04773 45 RDARLIHLLRRG--GYLLEQIATVVEQL 70 (108)
T ss_pred HHHHHHHHHHHC--CCCHHHHHHHHHHh
Confidence 567788888873 99999999999864
No 90
>cd08499 PBP2_Ylib_like The substrate-binding component of an uncharacterized ABC-type peptide import system Ylib contains the type 2 periplasmic binding fold. This family represents the periplasmic substrate-binding component of an uncharacterized ATP-binding cassette (ABC)-type peptide transport system YliB. Although the ligand specificity of Ylib protein is not known, it shares significant sequence similarity to the ABC-type dipeptide and oligopeptide binding proteins. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling
Probab=20.55 E-value=1.9e+02 Score=23.00 Aligned_cols=42 Identities=19% Similarity=0.232 Sum_probs=29.0
Q ss_pred CCHHHHHHHHhhcChh----h----hh-cCCHHHHHHHHHHHHhCCcEEEe
Q psy4492 54 MNLVQAKKFVESIPAV----V----KT-DVTKEEAEALKASLAKVGGEVSV 95 (96)
Q Consensus 54 LgLkEAK~lVe~~P~~----i----Ke-~v~keeAe~ik~kle~aGa~vei 95 (96)
.++..||+|++.+... | -. .....-|+.++..|+++|-+|++
T Consensus 301 ~d~~~A~~lL~eaG~~~~~~l~l~~~~~~~~~~~a~~i~~~l~~~GI~v~i 351 (474)
T cd08499 301 YDPEKAKELLAEAGYPDGFETTLWTNDNRERIKIAEFIQQQLAQIGIDVEI 351 (474)
T ss_pred CCHHHHHHHHHHcCCCCCceEEEEecCCCchhHHHHHHHHHHHHcCceEEE
Confidence 4677788887754321 1 11 13467799999999999998876
No 91
>PRK03100 sec-independent translocase; Provisional
Probab=20.42 E-value=84 Score=22.82 Aligned_cols=49 Identities=18% Similarity=0.291 Sum_probs=34.4
Q ss_pred eeCCCCCchHHHHHHHHhhcCCCHHHHHHHHhhcChhhhhcCCHHHHHHHHHHHH
Q psy4492 33 VKYDDKQKVPLIKEIKGLLEGMNLVQAKKFVESIPAVVKTDVTKEEAEALKASLA 87 (96)
Q Consensus 33 ~~~~~~kKi~vIK~VR~i~t~LgLkEAK~lVe~~P~~iKe~v~keeAe~ik~kle 87 (96)
.=||+ +| +=..+|.+ |-.+++.|+++..+-..+++.+. .|-+++++.|.
T Consensus 19 vv~GP-kr--LP~~~r~l--G~~vr~~R~~~~~~~~~~~~elg-~e~~dlrk~l~ 67 (136)
T PRK03100 19 VILGP-ER--LPGAIRWT--ARALRQARDYASGATSQLREELG-PEFDDLRKPLG 67 (136)
T ss_pred hhcCc-hH--HHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHh-hhHHHHHHHHH
Confidence 34666 33 33456664 66789999999999999988776 55667766554
No 92
>cd08503 PBP2_NikA_DppA_OppA_like_17 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=20.35 E-value=2e+02 Score=22.88 Aligned_cols=42 Identities=14% Similarity=0.141 Sum_probs=28.9
Q ss_pred CCHHHHHHHHhhcC-----hhh--hhc--CCHHHHHHHHHHHHhCCcEEEe
Q psy4492 54 MNLVQAKKFVESIP-----AVV--KTD--VTKEEAEALKASLAKVGGEVSV 95 (96)
Q Consensus 54 LgLkEAK~lVe~~P-----~~i--Ke~--v~keeAe~ik~kle~aGa~vei 95 (96)
.++..||++++.+. -.| ..+ ....-|+.++..|+.+|-+|++
T Consensus 305 ~d~~~A~~lL~eaG~~~~~l~l~~~~~~~~~~~~a~~i~~~l~~~Gi~v~i 355 (460)
T cd08503 305 YDPDKAKALLAEAGLPDLEVELVTSDAAPGAVDAAVLFAEQAAQAGININV 355 (460)
T ss_pred CCHHHHHHHHHHcCCCCceEEEEecCCCccHHHHHHHHHHHHHhhCCEEEE
Confidence 45677777776552 111 122 4577899999999999988876
Done!