Query 037146
Match_columns 185
No_of_seqs 152 out of 1142
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 09:07:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037146.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037146hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1715 Mitochondrial/chloropl 100.0 3.9E-44 8.4E-49 297.9 15.2 139 39-185 49-187 (187)
2 CHL00083 rpl12 ribosomal prote 100.0 5.4E-42 1.2E-46 272.4 14.2 131 46-185 1-131 (131)
3 cd00387 Ribosomal_L7_L12 Ribos 100.0 6.4E-42 1.4E-46 270.5 13.9 127 48-184 1-127 (127)
4 TIGR00855 L12 ribosomal protei 100.0 8.9E-40 1.9E-44 258.3 13.7 123 48-185 4-126 (126)
5 PRK00157 rplL 50S ribosomal pr 100.0 3.2E-39 6.9E-44 254.2 13.9 122 47-185 2-123 (123)
6 COG0222 RplL Ribosomal protein 100.0 3.7E-39 8E-44 253.2 12.6 122 48-185 3-124 (124)
7 PF00542 Ribosomal_L12: Riboso 99.9 4.5E-25 9.8E-30 157.7 5.7 68 117-185 1-68 (68)
8 PRK06771 hypothetical protein; 97.9 7.2E-06 1.6E-10 62.5 3.1 28 128-155 66-93 (93)
9 PF02617 ClpS: ATP-dependent C 88.6 1.4 3E-05 31.8 5.3 69 115-184 4-82 (82)
10 PRK00033 clpS ATP-dependent Cl 73.4 39 0.00084 25.9 8.5 70 115-185 25-98 (100)
11 COG0264 Tsf Translation elonga 64.8 6.5 0.00014 35.7 3.1 28 129-156 4-31 (296)
12 PRK09377 tsf elongation factor 60.0 9.1 0.0002 34.4 3.1 29 131-159 6-34 (290)
13 cd04788 HTH_NolA-AlbR Helix-Tu 58.3 22 0.00047 26.2 4.4 29 128-157 44-72 (96)
14 PF02022 Integrase_Zn: Integra 57.0 14 0.00031 24.0 2.8 28 134-161 12-39 (40)
15 PF09278 MerR-DNA-bind: MerR, 54.5 17 0.00036 24.3 3.1 22 130-152 3-24 (65)
16 PRK10664 transcriptional regul 54.5 6.3 0.00014 29.1 1.0 36 129-164 2-37 (90)
17 PRK10753 transcriptional regul 52.7 6.9 0.00015 28.8 1.0 35 129-163 2-36 (90)
18 PF14520 HHH_5: Helix-hairpin- 50.5 53 0.0012 21.9 5.0 46 132-177 2-60 (60)
19 cd04774 HTH_YfmP Helix-Turn-He 50.4 43 0.00092 24.8 4.9 31 128-158 43-73 (96)
20 cd01107 HTH_BmrR Helix-Turn-He 47.2 37 0.00081 25.4 4.2 29 128-157 45-73 (108)
21 cd04766 HTH_HspR Helix-Turn-He 45.8 59 0.0013 23.5 5.0 41 128-178 44-84 (91)
22 PF13411 MerR_1: MerR HTH fami 45.3 21 0.00046 23.8 2.4 26 128-154 43-68 (69)
23 PF10925 DUF2680: Protein of u 45.2 31 0.00067 24.1 3.2 26 149-177 21-47 (59)
24 PRK13019 clpS ATP-dependent Cl 44.8 1.2E+02 0.0026 22.9 6.6 69 114-183 18-91 (94)
25 cd00591 HU_IHF Integration hos 44.7 19 0.0004 25.4 2.1 34 130-163 2-35 (87)
26 smart00411 BHL bacterial (prok 43.2 19 0.00042 25.5 2.0 36 129-164 2-37 (90)
27 cd01104 HTH_MlrA-CarA Helix-Tu 37.0 42 0.00092 22.3 2.9 24 129-153 45-68 (68)
28 cd04768 HTH_BmrR-like Helix-Tu 36.8 76 0.0016 23.3 4.4 28 128-156 44-71 (96)
29 cd04781 HTH_MerR-like_sg6 Heli 35.4 1.1E+02 0.0025 23.1 5.4 27 128-155 43-69 (120)
30 TIGR02043 ZntR Zn(II)-responsi 34.6 70 0.0015 24.9 4.1 26 128-154 45-70 (131)
31 cd04763 HTH_MlrA-like Helix-Tu 34.3 50 0.0011 22.3 2.9 24 129-153 45-68 (68)
32 cd04780 HTH_MerR-like_sg5 Heli 33.7 55 0.0012 24.2 3.2 27 128-154 44-70 (95)
33 cd01105 HTH_GlnR-like Helix-Tu 32.6 59 0.0013 23.5 3.2 26 128-154 45-70 (88)
34 cd04782 HTH_BltR Helix-Turn-He 31.8 93 0.002 22.8 4.2 26 129-155 45-70 (97)
35 PRK00285 ihfA integration host 30.7 39 0.00085 24.8 2.0 35 129-163 4-38 (99)
36 PRK05350 acyl carrier protein; 29.9 68 0.0015 22.7 3.1 26 54-80 33-58 (82)
37 PF11272 DUF3072: Protein of u 29.8 59 0.0013 23.0 2.7 19 59-77 38-56 (57)
38 PRK13752 putative transcriptio 29.6 93 0.002 24.8 4.1 25 129-154 52-76 (144)
39 PF11363 DUF3164: Protein of u 29.3 82 0.0018 26.7 3.9 82 50-164 36-117 (195)
40 cd01109 HTH_YyaN Helix-Turn-He 29.2 67 0.0014 24.0 3.1 26 129-155 45-70 (113)
41 PF09999 DUF2240: Uncharacteri 29.2 94 0.002 25.4 4.1 33 48-80 85-122 (144)
42 cd01106 HTH_TipAL-Mta Helix-Tu 28.2 1.5E+02 0.0032 21.8 4.7 27 129-156 45-71 (103)
43 cd04777 HTH_MerR-like_sg1 Heli 27.5 76 0.0017 23.5 3.1 25 129-154 43-67 (107)
44 COG3797 Uncharacterized protei 27.5 51 0.0011 28.1 2.4 50 125-178 13-63 (178)
45 KOG3449 60S acidic ribosomal p 27.3 1.8E+02 0.0038 23.2 5.2 29 45-76 34-62 (112)
46 cd02810 DHOD_DHPD_FMN Dihydroo 27.3 95 0.0021 26.5 4.1 40 131-182 151-192 (289)
47 cd04764 HTH_MlrA-like_sg1 Heli 27.1 78 0.0017 21.2 2.9 24 129-153 44-67 (67)
48 PRK10227 DNA-binding transcrip 26.7 1E+02 0.0022 24.2 3.9 25 129-154 45-69 (135)
49 TIGR01037 pyrD_sub1_fam dihydr 25.3 92 0.002 27.0 3.7 42 129-182 144-185 (300)
50 CHL00124 acpP acyl carrier pro 25.2 1.1E+02 0.0023 21.4 3.4 24 58-81 35-58 (82)
51 smart00422 HTH_MERR helix_turn 25.1 99 0.0022 20.4 3.1 25 128-153 44-68 (70)
52 PRK05412 putative nucleotide-b 25.0 71 0.0015 26.8 2.8 64 119-183 45-120 (161)
53 cd08494 PBP2_NikA_DppA_OppA_li 25.0 1.2E+02 0.0026 27.0 4.4 44 142-185 297-349 (448)
54 cd04784 HTH_CadR-PbrR Helix-Tu 25.0 83 0.0018 24.0 3.0 25 129-154 45-69 (127)
55 cd04767 HTH_HspR-like_MBC Heli 24.9 97 0.0021 24.4 3.4 32 128-159 43-74 (120)
56 TIGR00517 acyl_carrier acyl ca 24.7 94 0.002 21.4 3.0 23 58-80 33-55 (77)
57 PF04461 DUF520: Protein of un 24.5 54 0.0012 27.4 2.0 64 119-183 45-120 (160)
58 PRK00199 ihfB integration host 24.0 38 0.00082 24.7 0.9 34 130-163 3-37 (94)
59 cd04740 DHOD_1B_like Dihydroor 23.7 1E+02 0.0022 26.5 3.7 39 131-181 143-181 (296)
60 cd08499 PBP2_Ylib_like The sub 23.7 1.3E+02 0.0028 27.2 4.4 44 142-185 300-352 (474)
61 PRK07081 acyl carrier protein; 23.3 99 0.0021 22.2 3.0 23 58-80 31-53 (83)
62 cd01108 HTH_CueR Helix-Turn-He 22.8 1E+02 0.0022 23.7 3.1 26 128-154 44-69 (127)
63 PF08542 Rep_fac_C: Replicatio 22.6 1.3E+02 0.0029 20.9 3.5 36 45-81 3-38 (89)
64 cd08503 PBP2_NikA_DppA_OppA_li 22.6 1.3E+02 0.0028 27.2 4.2 44 142-185 304-356 (460)
65 TIGR02054 MerD mercuric resist 22.5 1E+02 0.0023 24.0 3.1 26 129-155 48-73 (120)
66 PRK07259 dihydroorotate dehydr 22.2 98 0.0021 26.8 3.3 41 129-181 144-184 (301)
67 cd04787 HTH_HMRTR_unk Helix-Tu 22.1 1.1E+02 0.0023 23.8 3.1 27 128-155 44-70 (133)
68 PRK15002 redox-sensitivie tran 21.5 1.6E+02 0.0035 23.9 4.1 25 129-154 55-79 (154)
69 COG4575 ElaB Uncharacterized c 21.4 1E+02 0.0022 24.2 2.9 33 146-178 15-49 (104)
70 PF00216 Bac_DNA_binding: Bact 21.4 40 0.00087 23.7 0.6 32 130-161 3-34 (90)
71 cd01282 HTH_MerR-like_sg3 Heli 21.3 1.2E+02 0.0025 22.9 3.1 25 129-154 44-68 (112)
72 PRK05087 D-alanine--poly(phosp 21.2 1.1E+02 0.0024 22.0 2.8 21 60-80 34-54 (78)
73 cd04770 HTH_HMRTR Helix-Turn-H 21.1 1.5E+02 0.0033 22.3 3.8 26 129-155 45-70 (123)
74 PRK09514 zntR zinc-responsive 21.1 1.6E+02 0.0036 23.1 4.1 25 129-154 46-70 (140)
75 TIGR02044 CueR Cu(I)-responsiv 21.0 1.2E+02 0.0025 23.3 3.1 25 128-153 44-68 (127)
76 cd04769 HTH_MerR2 Helix-Turn-H 20.9 1.2E+02 0.0026 22.9 3.1 27 128-155 43-69 (116)
77 cd08497 PBP2_NikA_DppA_OppA_li 20.7 1.7E+02 0.0038 26.8 4.7 43 143-185 318-380 (491)
78 TIGR02047 CadR-PbrR Cd(II)/Pb( 20.7 1.2E+02 0.0026 23.4 3.1 24 129-153 45-68 (127)
79 COG0236 AcpP Acyl carrier prot 20.7 1E+02 0.0022 21.7 2.5 23 58-80 35-57 (80)
80 cd02932 OYE_YqiM_FMN Old yello 20.5 1.3E+02 0.0028 26.7 3.7 41 131-181 208-256 (336)
81 cd04783 HTH_MerR1 Helix-Turn-H 20.5 1.2E+02 0.0026 23.1 3.1 26 129-155 45-70 (126)
82 PF00550 PP-binding: Phosphopa 20.5 1.4E+02 0.003 19.4 3.1 24 58-81 27-50 (67)
83 TIGR00426 competence protein C 20.4 2E+02 0.0043 19.5 3.9 40 136-175 17-67 (69)
84 COG0789 SoxR Predicted transcr 20.4 1.3E+02 0.0027 22.3 3.1 28 128-156 44-71 (124)
85 cd05833 Ribosomal_P2 Ribosomal 20.0 2.6E+02 0.0056 21.7 4.8 31 45-78 34-64 (109)
No 1
>KOG1715 consensus Mitochondrial/chloroplast ribosomal protein L12 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.9e-44 Score=297.87 Aligned_cols=139 Identities=48% Similarity=0.703 Sum_probs=118.0
Q ss_pred cCCCCCCCChhHHHHHHHHhcCCHHHHHHHHHHHHHHhCCCCCcchhcccCCCCccccccccCCCCCCCcccccccccee
Q 037146 39 YCTPSQEPSEKVASIVDEISCLSLVEVMDLADVVRNKLGIKEMPNMCVMMPGMGFSVKGATARGGTGTGKAEEKVEKTVF 118 (185)
Q Consensus 39 ~~~~~~~~s~KV~~Ivd~I~~LtLlE~~eLv~~leekfgv~~~~~~~~~~p~~~~~~~~~~aa~~a~~~~~e~~~EKt~f 118 (185)
+....+++++||.+|+|+|++|||+|++||++.|+++|||+..+.++++ +..+ ++ +++.++.++++.|||.|
T Consensus 49 ~~~~~~~~~~KI~~iv~eIssLtLlE~s~L~~~Lk~kl~i~e~~~~~a~----~~g~-~~---~~~~~a~ee~k~ekt~F 120 (187)
T KOG1715|consen 49 PPIAAVPPPPKISKIVDEISSLTLLETSDLVDLLKKKLNIPELPLAPAA----AAGA-AA---PDAGGAEEEAKKEKTTF 120 (187)
T ss_pred CcccccCCCHHHHHHHHHHHhcCHHHHHHHHHHHHHHcCCCcccchhhc----cccC-CC---CCcccccccchhhcceE
Confidence 3333468999999999999999999999999999999999998754321 1111 11 11122334556788889
Q ss_pred EEEEecCCcchhHHHHHHHHhhcCCChhHHHHHHhhcchhhhcCCCHHHHHHHHHHHHHcCCEEEeC
Q 037146 119 DLKLAGYGAEAKLKVIKEVRGFTGLGLKESKELVEKVPTLLKRGVTKDEADKIVAKLKEVGAQVSME 185 (185)
Q Consensus 119 ~V~L~~~~a~kKi~vIK~VR~it~LgLkEAK~lVe~~P~~IKe~vsKeeAe~ik~kle~aGA~VelE 185 (185)
||+|++||+.+||+|||+||.+|||||+|||+|||++|+++|+|++|||||+||++|+++||+|+||
T Consensus 121 dVkL~~fda~~KIkVIKEVR~~tgL~LkeAKklVE~aP~ilKegvtKeEAEkik~kLea~GakV~le 187 (187)
T KOG1715|consen 121 DVKLEKFDASSKIKVIKEVRALTGLGLKEAKKLVEKAPKILKEGVTKEEAEEIKEKLEAAGAKVVLE 187 (187)
T ss_pred EEEEeecCccchhHHHHHHHHhccccHHHHHHHHHhccHHHHcCCCHHHHHHHHHHHHHcCCeEeeC
Confidence 9999999999999999999999999999999999999999999999999999999999999999997
No 2
>CHL00083 rpl12 ribosomal protein L12
Probab=100.00 E-value=5.4e-42 Score=272.38 Aligned_cols=131 Identities=36% Similarity=0.557 Sum_probs=110.7
Q ss_pred CChhHHHHHHHHhcCCHHHHHHHHHHHHHHhCCCCCcchhcccCCCCccccccccCCCCCCCccccccccceeEEEEecC
Q 037146 46 PSEKVASIVDEISCLSLVEVMDLADVVRNKLGIKEMPNMCVMMPGMGFSVKGATARGGTGTGKAEEKVEKTVFDLKLAGY 125 (185)
Q Consensus 46 ~s~KV~~Ivd~I~~LtLlE~~eLv~~leekfgv~~~~~~~~~~p~~~~~~~~~~aa~~a~~~~~e~~~EKt~f~V~L~~~ 125 (185)
.|+++++|+|+|++|||+|++||++.|+++|||++.++.+. +++ +++ ++ ++++++++.+|||+|||+|++|
T Consensus 1 ~s~k~~~ivd~i~~LTllE~~eLv~~le~~fgv~~~~~~a~----~~~--~~~-a~--~~~~~~~~~~EKT~F~V~L~~~ 71 (131)
T CHL00083 1 MSTKINEIIEELKSLTLLEAAELVKQIEETFGVDASAPVGG----GMM--SAP-AA--AAAQAAEEVEEKTEFDVILEEV 71 (131)
T ss_pred CCchHHHHHHHHHhCCHHHHHHHHHHHHHHcCCCccchhhh----hhc--ccc-Cc--ccccccchhhhcceeeEEEeec
Confidence 37899999999999999999999999999999998753211 110 000 11 1112234568999999999999
Q ss_pred CcchhHHHHHHHHhhcCCChhHHHHHHhhcchhhhcCCCHHHHHHHHHHHHHcCCEEEeC
Q 037146 126 GAEAKLKVIKEVRGFTGLGLKESKELVEKVPTLLKRGVTKDEADKIVAKLKEVGAQVSME 185 (185)
Q Consensus 126 ~a~kKi~vIK~VR~it~LgLkEAK~lVe~~P~~IKe~vsKeeAe~ik~kle~aGA~VelE 185 (185)
|+++||+|||+||++|||||+|||+|||++|++||+|++|+|||+||++|+++||+|+|.
T Consensus 72 ~~~~Ki~vIK~vr~it~lgLkeaK~lVe~~P~~ike~v~KeeAe~ik~~le~~Ga~v~lk 131 (131)
T CHL00083 72 PADKRIAVLKVVRSLTGLGLKEAKELVESLPKTIKEGISKEEAEEAKKQLEEAGAKVIIK 131 (131)
T ss_pred CCcchHHHHHHHHHHcCCCHHHHHHHHHhCCHHHHhCCCHHHHHHHHHHHHHcCCEEEeC
Confidence 889999999999999999999999999999999999999999999999999999999984
No 3
>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=6.4e-42 Score=270.50 Aligned_cols=127 Identities=43% Similarity=0.661 Sum_probs=107.0
Q ss_pred hhHHHHHHHHhcCCHHHHHHHHHHHHHHhCCCCCcchhcccCCCCccccccccCCCCCCCccccccccceeEEEEecCCc
Q 037146 48 EKVASIVDEISCLSLVEVMDLADVVRNKLGIKEMPNMCVMMPGMGFSVKGATARGGTGTGKAEEKVEKTVFDLKLAGYGA 127 (185)
Q Consensus 48 ~KV~~Ivd~I~~LtLlE~~eLv~~leekfgv~~~~~~~~~~p~~~~~~~~~~aa~~a~~~~~e~~~EKt~f~V~L~~~~a 127 (185)
.++++|+|+|++|||+|++||++.|+++|||++.++.+. + ++++++ ++++++++++|||+|||+|++||+
T Consensus 1 ~~~~~i~d~i~~LtllE~~eLv~~le~~~gv~~~~~~~~----~---~~~a~~---~~~~~~~~~~EKt~F~V~L~~~~~ 70 (127)
T cd00387 1 LKVEEIVEALKELTLLEAAELVKALEEKFGVSASAAAAA----A---AAAAPA---AAAAAAAEAEEKTEFDVVLESFGA 70 (127)
T ss_pred CcHHHHHHHHHhCCHHHHHHHHHHHHHHhCCCccccccc----c---cccCcc---cccccccchhhcceEEEEEeeCCc
Confidence 368999999999999999999999999999998632110 0 111111 111122235799999999999998
Q ss_pred chhHHHHHHHHhhcCCChhHHHHHHhhcchhhhcCCCHHHHHHHHHHHHHcCCEEEe
Q 037146 128 EAKLKVIKEVRGFTGLGLKESKELVEKVPTLLKRGVTKDEADKIVAKLKEVGAQVSM 184 (185)
Q Consensus 128 ~kKi~vIK~VR~it~LgLkEAK~lVe~~P~~IKe~vsKeeAe~ik~kle~aGA~Vel 184 (185)
++||+|||+||++|||||+|||+|||++|++||+|+||+|||+||++|+++||+|+|
T Consensus 71 ~~Ki~vIK~VR~it~LgLkEAK~lVe~~P~~iKe~vsKeeAE~ik~kLe~aGA~Vel 127 (127)
T cd00387 71 AKKIAVIKEVREITGLGLKEAKDLVESAPKVLKEGVSKEEAEEIKKKLEEAGAKVEL 127 (127)
T ss_pred hhhHHHHHHHHHHhCCChHHHHHHHHhCcHHHHhCCCHHHHHHHHHHHHHcCCEEeC
Confidence 899999999999999999999999999999999999999999999999999999986
No 4
>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=100.00 E-value=8.9e-40 Score=258.25 Aligned_cols=123 Identities=38% Similarity=0.632 Sum_probs=105.3
Q ss_pred hhHHHHHHHHhcCCHHHHHHHHHHHHHHhCCCCCcchhcccCCCCccccccccCCCCCCCccccccccceeEEEEecCCc
Q 037146 48 EKVASIVDEISCLSLVEVMDLADVVRNKLGIKEMPNMCVMMPGMGFSVKGATARGGTGTGKAEEKVEKTVFDLKLAGYGA 127 (185)
Q Consensus 48 ~KV~~Ivd~I~~LtLlE~~eLv~~leekfgv~~~~~~~~~~p~~~~~~~~~~aa~~a~~~~~e~~~EKt~f~V~L~~~~a 127 (185)
-+.++|+|+|++|||+|++||++.|+++|||++.++++ ++ ++ +++ + +++..+|||+|||+|+.++
T Consensus 4 ~~~~~ive~i~~LTllE~~eLv~~lee~fgV~a~a~~a-----~~----~a-~~~-~---~~~~~eEKt~f~V~L~~~~- 68 (126)
T TIGR00855 4 LSKEQIIEALKEMTVLELSELVKALEEKFGVSAAAPVA-----AG----AA-GAA-A---AAAAAEEKTEFDVILKGAG- 68 (126)
T ss_pred ccHHHHHHHHHhCCHHHHHHHHHHHHHhcCCCccchhh-----hc----cc-ccc-c---ccccccccceeeEEEecCC-
Confidence 34689999999999999999999999999999875321 11 11 011 1 1233579999999999887
Q ss_pred chhHHHHHHHHhhcCCChhHHHHHHhhcchhhhcCCCHHHHHHHHHHHHHcCCEEEeC
Q 037146 128 EAKLKVIKEVRGFTGLGLKESKELVEKVPTLLKRGVTKDEADKIVAKLKEVGAQVSME 185 (185)
Q Consensus 128 ~kKi~vIK~VR~it~LgLkEAK~lVe~~P~~IKe~vsKeeAe~ik~kle~aGA~VelE 185 (185)
++||+|||+||++|||||+|||+|||++|++||+|++|+|||+||++|+++||+|+|.
T Consensus 69 ~~Ki~vIK~vR~itgLgLkEAK~lVe~~P~~ike~vsKeeAe~ik~~Le~aGa~veik 126 (126)
T TIGR00855 69 DNKIAVIKVVREITGLGLKEAKDLVEGAPKVLKEGVSKEEAEELKKKLEEAGAKVEVK 126 (126)
T ss_pred cchhHHHHHHHHHcCCcHHHHHHHHHhCcHHHHhCCCHHHHHHHHHHHHHcCCEEEeC
Confidence 6899999999999999999999999999999999999999999999999999999983
No 5
>PRK00157 rplL 50S ribosomal protein L7/L12; Reviewed
Probab=100.00 E-value=3.2e-39 Score=254.23 Aligned_cols=122 Identities=36% Similarity=0.593 Sum_probs=106.0
Q ss_pred ChhHHHHHHHHhcCCHHHHHHHHHHHHHHhCCCCCcchhcccCCCCccccccccCCCCCCCccccccccceeEEEEecCC
Q 037146 47 SEKVASIVDEISCLSLVEVMDLADVVRNKLGIKEMPNMCVMMPGMGFSVKGATARGGTGTGKAEEKVEKTVFDLKLAGYG 126 (185)
Q Consensus 47 s~KV~~Ivd~I~~LtLlE~~eLv~~leekfgv~~~~~~~~~~p~~~~~~~~~~aa~~a~~~~~e~~~EKt~f~V~L~~~~ 126 (185)
+-++++|+|+|++|||+|++||++.|+++|||++.++++. + ++ ++ +++..+|||+|||+|++|
T Consensus 2 ~~~~~~i~e~i~~LtllE~~eLv~~lee~fgv~a~~~~~~----~-----~~--~~-----~~~~~eEkt~f~V~L~~~- 64 (123)
T PRK00157 2 ALTKEQIIEALKEMTVLELSELVKALEEKFGVSAAAPVAA----A-----AA--AA-----AAAAAEEKTEFDVVLKSA- 64 (123)
T ss_pred CccHHHHHHHHHhCCHHHHHHHHHHHHHHcCCCccchhcc----c-----cc--cc-----cccccccccceeEEEecc-
Confidence 4568999999999999999999999999999998753210 0 01 11 122357999999999999
Q ss_pred cchhHHHHHHHHhhcCCChhHHHHHHhhcchhhhcCCCHHHHHHHHHHHHHcCCEEEeC
Q 037146 127 AEAKLKVIKEVRGFTGLGLKESKELVEKVPTLLKRGVTKDEADKIVAKLKEVGAQVSME 185 (185)
Q Consensus 127 a~kKi~vIK~VR~it~LgLkEAK~lVe~~P~~IKe~vsKeeAe~ik~kle~aGA~VelE 185 (185)
+++||+|||+||++|||||+|||+|||++|++||+|++|+|||++|++|+++||+|+|.
T Consensus 65 ~~kKi~vIK~vR~itgLgLkEAK~lVe~~P~~ike~v~keeAe~ik~~Le~aGa~velk 123 (123)
T PRK00157 65 GDKKIAVIKAVREITGLGLKEAKDLVEGAPKVVKEGVSKEEAEEIKKKLEEAGAKVELK 123 (123)
T ss_pred chhhHHHHHHHHHHhCCCHHHHHHHHHhCCHHHHhCCCHHHHHHHHHHHHHcCCEEeeC
Confidence 47999999999999999999999999999999999999999999999999999999984
No 6
>COG0222 RplL Ribosomal protein L7/L12 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.7e-39 Score=253.24 Aligned_cols=122 Identities=39% Similarity=0.614 Sum_probs=105.8
Q ss_pred hhHHHHHHHHhcCCHHHHHHHHHHHHHHhCCCCCcchhcccCCCCccccccccCCCCCCCccccccccceeEEEEecCCc
Q 037146 48 EKVASIVDEISCLSLVEVMDLADVVRNKLGIKEMPNMCVMMPGMGFSVKGATARGGTGTGKAEEKVEKTVFDLKLAGYGA 127 (185)
Q Consensus 48 ~KV~~Ivd~I~~LtLlE~~eLv~~leekfgv~~~~~~~~~~p~~~~~~~~~~aa~~a~~~~~e~~~EKt~f~V~L~~~~a 127 (185)
-..++|+++|++||++|+++|++.++++|||+++++++. + ++ ++ ++.+..+|||+|||+|.+++
T Consensus 3 ~~~e~iie~i~~~svlel~eLvk~~eekfgVsaaa~va~----a-----~~--~a----~a~~aaeEktefdVvL~~~g- 66 (124)
T COG0222 3 LTKEQIIEALKELTVLELSELVKALEEKFGVTAAAPVAA----A-----AA--GA----AAAEAAEEKTEFDVVLKSAG- 66 (124)
T ss_pred CcHHHHHHHHHHhhHHHHHHHHHHHHHHhCCccchhhhh----c-----cc--cc----cccccccccceeEEEecccC-
Confidence 357899999999999999999999999999998754321 0 01 10 11122578999999999995
Q ss_pred chhHHHHHHHHhhcCCChhHHHHHHhhcchhhhcCCCHHHHHHHHHHHHHcCCEEEeC
Q 037146 128 EAKLKVIKEVRGFTGLGLKESKELVEKVPTLLKRGVTKDEADKIVAKLKEVGAQVSME 185 (185)
Q Consensus 128 ~kKi~vIK~VR~it~LgLkEAK~lVe~~P~~IKe~vsKeeAe~ik~kle~aGA~VelE 185 (185)
++||+|||+||++|||||||||++||++|++||+|++|+|||+||++|+++||+|++.
T Consensus 67 ~kKI~VIK~vR~itGLGLKEAKdlVe~aP~~~KE~v~k~eAe~~kkkleeaGa~V~~k 124 (124)
T COG0222 67 GKKIAVIKVVRELTGLGLKEAKDLVEGAPKVLKEGVSKEEAEEIKKKLEEAGAKVELK 124 (124)
T ss_pred CcchhHHHHHHHHhcccHHHHHHHHHhCcHHHHccCCHHHHHHHHHHHHHcCCeEeeC
Confidence 7999999999999999999999999999999999999999999999999999999984
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=99.91 E-value=4.5e-25 Score=157.74 Aligned_cols=68 Identities=51% Similarity=0.853 Sum_probs=60.2
Q ss_pred eeEEEEecCCcchhHHHHHHHHhhcCCChhHHHHHHhhcchhhhcCCCHHHHHHHHHHHHHcCCEEEeC
Q 037146 117 VFDLKLAGYGAEAKLKVIKEVRGFTGLGLKESKELVEKVPTLLKRGVTKDEADKIVAKLKEVGAQVSME 185 (185)
Q Consensus 117 ~f~V~L~~~~a~kKi~vIK~VR~it~LgLkEAK~lVe~~P~~IKe~vsKeeAe~ik~kle~aGA~VelE 185 (185)
+|||+|+++ +++||++||.||++|||||+|||++||++|.+|++|++++|||+++++|+++||+|+|+
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-GEKKIKVIKEVREITGLGLKEAKKLVDSLPKVIKEGVSKEEAEEIKKKLEAAGAKVELK 68 (68)
T ss_dssp SEEEEEEE--TTGHHHHHHHHHHHC---HHHHHHHHCTTTEEEEEEE-HHHHHHHHHHHHCCT-EEEEE
T ss_pred CeEEEEeec-ccchHHHHHHHHHHhCCcHHHHHHHHHhCCHHHHcCCCHHHHHHHHHHHHHcCCEEEeC
Confidence 599999999 68999999999999999999999999999999999999999999999999999999985
No 8
>PRK06771 hypothetical protein; Provisional
Probab=97.93 E-value=7.2e-06 Score=62.49 Aligned_cols=28 Identities=32% Similarity=0.503 Sum_probs=26.6
Q ss_pred chhHHHHHHHHhhcCCChhHHHHHHhhc
Q 037146 128 EAKLKVIKEVRGFTGLGLKESKELVEKV 155 (185)
Q Consensus 128 ~kKi~vIK~VR~it~LgLkEAK~lVe~~ 155 (185)
.+||+.||.+|+.||+||+|||++||++
T Consensus 66 Gkki~AIK~~Re~tG~~L~eAK~yVD~L 93 (93)
T PRK06771 66 GQTVTAVKRVREAFGFSLLEAKQYVDKL 93 (93)
T ss_pred CCchHHHHHHHHHcCCCHHHHHHHHhcC
Confidence 5999999999999999999999999974
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=88.57 E-value=1.4 Score=31.77 Aligned_cols=69 Identities=16% Similarity=0.294 Sum_probs=49.9
Q ss_pred cceeEEEEecCCcchhHHHHHHHHhhcCCChhHHHHHHhhcc----hhhhcCCCHHHHHHHHHHHHHcC------CEEEe
Q 037146 115 KTVFDLKLAGYGAEAKLKVIKEVRGFTGLGLKESKELVEKVP----TLLKRGVTKDEADKIVAKLKEVG------AQVSM 184 (185)
Q Consensus 115 Kt~f~V~L~~~~a~kKi~vIK~VR~it~LgLkEAK~lVe~~P----~~IKe~vsKeeAe~ik~kle~aG------A~Vel 184 (185)
...|.|+|=+-+-..--.||..++.+.|+...+|..+...+= .+|.. -++++||....+|...| -+++|
T Consensus 4 ~~~~~vvL~NDe~ht~~~Vi~~L~~~~~~s~~~A~~~a~~v~~~G~avv~~-~~~e~ae~~~~~l~~~g~~~~~PL~~ti 82 (82)
T PF02617_consen 4 PDMYRVVLWNDEVHTFEQVIDVLRRVFGCSEEQARQIAMEVHREGRAVVGT-GSREEAEEYAEKLQRAGRDSGHPLRATI 82 (82)
T ss_dssp --EEEEEEE--SSSBHHHHHHHHHHHC---HHHHHHHHHHHHHHSEEEEEE-EEHHHHHHHHHHHHHHHHHTT---EEEE
T ss_pred CCceEEEEEcCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHhHcCCEeeee-CCHHHHHHHHHHHHHHhhccCCCeEEeC
Confidence 456899997655556779999999999999999999877542 45655 58999999999999999 66654
No 10
>PRK00033 clpS ATP-dependent Clp protease adaptor protein ClpS; Reviewed
Probab=73.42 E-value=39 Score=25.94 Aligned_cols=70 Identities=16% Similarity=0.248 Sum_probs=55.8
Q ss_pred cceeEEEEecCCcchhHHHHHHHHhhcCCChhHHHHHHhhcc----hhhhcCCCHHHHHHHHHHHHHcCCEEEeC
Q 037146 115 KTVFDLKLAGYGAEAKLKVIKEVRGFTGLGLKESKELVEKVP----TLLKRGVTKDEADKIVAKLKEVGAQVSME 185 (185)
Q Consensus 115 Kt~f~V~L~~~~a~kKi~vIK~VR~it~LgLkEAK~lVe~~P----~~IKe~vsKeeAe~ik~kle~aGA~VelE 185 (185)
..-|.|+|-+-|-..-==||..++.+.|++..+|.++.-.+= .++.. -++|.||....+|...|-.+.||
T Consensus 25 ~~~y~ViL~NDd~ntmd~Vv~vL~~vf~~s~~~A~~iml~vH~~G~avv~~-~~~e~AE~~~~~l~~~~L~~~ie 98 (100)
T PRK00033 25 PPMYKVLLHNDDYTPMEFVVYVLQKFFGYDRERATQIMLEVHNEGKAVVGV-CTREVAETKVEQVHQHGLLCTME 98 (100)
T ss_pred CCceEEEEEcCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHhcCCcEEEEE-EcHHHHHHHHHHHHcCCCeEEEe
Confidence 345999997654344557999999999999999998876542 34444 49999999999999999988886
No 11
>COG0264 Tsf Translation elongation factor Ts [Translation, ribosomal structure and biogenesis]
Probab=64.82 E-value=6.5 Score=35.74 Aligned_cols=28 Identities=29% Similarity=0.471 Sum_probs=23.9
Q ss_pred hhHHHHHHHHhhcCCChhHHHHHHhhcc
Q 037146 129 AKLKVIKEVRGFTGLGLKESKELVEKVP 156 (185)
Q Consensus 129 kKi~vIK~VR~it~LgLkEAK~lVe~~P 156 (185)
-+.+.+|++|+.||-|.++.|+.++.+-
T Consensus 4 ita~~VKeLRe~TgAGMmdCKkAL~E~~ 31 (296)
T COG0264 4 ITAALVKELREKTGAGMMDCKKALEEAN 31 (296)
T ss_pred ccHHHHHHHHHHhCCcHHHHHHHHHHcC
Confidence 3568999999999999999999876543
No 12
>PRK09377 tsf elongation factor Ts; Provisional
Probab=60.02 E-value=9.1 Score=34.43 Aligned_cols=29 Identities=24% Similarity=0.398 Sum_probs=25.4
Q ss_pred HHHHHHHHhhcCCChhHHHHHHhhcchhh
Q 037146 131 LKVIKEVRGFTGLGLKESKELVEKVPTLL 159 (185)
Q Consensus 131 i~vIK~VR~it~LgLkEAK~lVe~~P~~I 159 (185)
.+.||++|+.||-|+++.|+.++.+..-+
T Consensus 6 ~~~IK~LR~~Tgagm~dCKkAL~e~~gD~ 34 (290)
T PRK09377 6 AALVKELRERTGAGMMDCKKALTEADGDI 34 (290)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHcCCCH
Confidence 47899999999999999999988776555
No 13
>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=58.33 E-value=22 Score=26.21 Aligned_cols=29 Identities=21% Similarity=0.265 Sum_probs=23.3
Q ss_pred chhHHHHHHHHhhcCCChhHHHHHHhhcch
Q 037146 128 EAKLKVIKEVRGFTGLGLKESKELVEKVPT 157 (185)
Q Consensus 128 ~kKi~vIK~VR~it~LgLkEAK~lVe~~P~ 157 (185)
-.++..|+.+|+ +|+.|+|.+.+++....
T Consensus 44 l~~l~~I~~lr~-~G~~l~eI~~~l~~~~~ 72 (96)
T cd04788 44 IRRLHQIIALRR-LGFSLREIGRALDGPDF 72 (96)
T ss_pred HHHHHHHHHHHH-cCCCHHHHHHHHhCCCh
Confidence 367777888776 69999999999987543
No 14
>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=57.02 E-value=14 Score=23.96 Aligned_cols=28 Identities=21% Similarity=0.323 Sum_probs=21.3
Q ss_pred HHHHHhhcCCChhHHHHHHhhcchhhhc
Q 037146 134 IKEVRGFTGLGLKESKELVEKVPTLLKR 161 (185)
Q Consensus 134 IK~VR~it~LgLkEAK~lVe~~P~~IKe 161 (185)
.|.+|.-.|+...+||++|.++|.=-.+
T Consensus 12 ~~~L~~~f~ip~~vAk~IV~~C~~Cq~~ 39 (40)
T PF02022_consen 12 AKALRHKFGIPRLVAKQIVNQCPKCQQK 39 (40)
T ss_dssp HHHHHHHHT--HHHHHHHHHHSCCHHST
T ss_pred HHHHHHHHccCHHHHHHHHHHCHHHhhC
Confidence 5678888899999999999999964433
No 15
>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=54.54 E-value=17 Score=24.31 Aligned_cols=22 Identities=36% Similarity=0.726 Sum_probs=16.4
Q ss_pred hHHHHHHHHhhcCCChhHHHHHH
Q 037146 130 KLKVIKEVRGFTGLGLKESKELV 152 (185)
Q Consensus 130 Ki~vIK~VR~it~LgLkEAK~lV 152 (185)
++..|+..|+ .|++|.|-|+++
T Consensus 3 rL~~I~~~r~-lGfsL~eI~~~l 24 (65)
T PF09278_consen 3 RLQFIRRLRE-LGFSLEEIRELL 24 (65)
T ss_dssp HHHHHHHHHH-TT--HHHHHHHH
T ss_pred HHHHHHHHHH-cCCCHHHHHHHH
Confidence 5667777775 799999999999
No 16
>PRK10664 transcriptional regulator HU subunit beta; Provisional
Probab=54.45 E-value=6.3 Score=29.14 Aligned_cols=36 Identities=6% Similarity=0.149 Sum_probs=30.2
Q ss_pred hhHHHHHHHHhhcCCChhHHHHHHhhcchhhhcCCC
Q 037146 129 AKLKVIKEVRGFTGLGLKESKELVEKVPTLLKRGVT 164 (185)
Q Consensus 129 kKi~vIK~VR~it~LgLkEAK~lVe~~P~~IKe~vs 164 (185)
.|-.+|+.|.+-+|+.-++++.+||..=.+|.+.+.
T Consensus 2 tK~eli~~ia~~~~~s~~~~~~~v~~~~~~i~~~L~ 37 (90)
T PRK10664 2 NKSQLIDKIAAGADISKAAAGRALDAIIASVTESLK 37 (90)
T ss_pred CHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHh
Confidence 366899999999999999999999998777765443
No 17
>PRK10753 transcriptional regulator HU subunit alpha; Provisional
Probab=52.71 E-value=6.9 Score=28.82 Aligned_cols=35 Identities=14% Similarity=0.210 Sum_probs=29.6
Q ss_pred hhHHHHHHHHhhcCCChhHHHHHHhhcchhhhcCC
Q 037146 129 AKLKVIKEVRGFTGLGLKESKELVEKVPTLLKRGV 163 (185)
Q Consensus 129 kKi~vIK~VR~it~LgLkEAK~lVe~~P~~IKe~v 163 (185)
+|-.+|+.|.+-+++.-++++..|+.+-.+|.+.+
T Consensus 2 ~K~eli~~ia~~~~~s~~~~~~~v~~~~~~i~~~L 36 (90)
T PRK10753 2 NKTQLIDVIADKAELSKTQAKAALESTLAAITESL 36 (90)
T ss_pred CHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999999999999877665544
No 18
>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=50.54 E-value=53 Score=21.92 Aligned_cols=46 Identities=26% Similarity=0.450 Sum_probs=31.7
Q ss_pred HHHHHHHhhcCCChhHHHHHHhhcchhhh-------------cCCCHHHHHHHHHHHHH
Q 037146 132 KVIKEVRGFTGLGLKESKELVEKVPTLLK-------------RGVTKDEADKIVAKLKE 177 (185)
Q Consensus 132 ~vIK~VR~it~LgLkEAK~lVe~~P~~IK-------------e~vsKeeAe~ik~kle~ 177 (185)
.++..+.++.|+|-+-++.|++.--.++. .|+++.-|+.|...+.+
T Consensus 2 ~~~~~L~~I~Gig~~~a~~L~~~G~~t~~~l~~a~~~~L~~i~Gig~~~a~~i~~~~~~ 60 (60)
T PF14520_consen 2 GVFDDLLSIPGIGPKRAEKLYEAGIKTLEDLANADPEELAEIPGIGEKTAEKIIEAARE 60 (60)
T ss_dssp HHHHHHHTSTTCHHHHHHHHHHTTCSSHHHHHTSHHHHHHTSTTSSHHHHHHHHHHHHH
T ss_pred HHHHhhccCCCCCHHHHHHHHhcCCCcHHHHHcCCHHHHhcCCCCCHHHHHHHHHHHhC
Confidence 45667777888888888888877333232 46788888888777653
No 19
>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=50.36 E-value=43 Score=24.82 Aligned_cols=31 Identities=23% Similarity=0.332 Sum_probs=27.2
Q ss_pred chhHHHHHHHHhhcCCChhHHHHHHhhcchh
Q 037146 128 EAKLKVIKEVRGFTGLGLKESKELVEKVPTL 158 (185)
Q Consensus 128 ~kKi~vIK~VR~it~LgLkEAK~lVe~~P~~ 158 (185)
-.++..|+.+|+..|++|.+.+.+++..+..
T Consensus 43 v~~l~~I~~L~~~~G~~l~ei~~~l~~~~~~ 73 (96)
T cd04774 43 LKRLERILRLREVLGFSLQEVTHFLERPLEP 73 (96)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHhccccc
Confidence 4788999999998999999999999877664
No 20
>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=47.20 E-value=37 Score=25.39 Aligned_cols=29 Identities=31% Similarity=0.420 Sum_probs=23.9
Q ss_pred chhHHHHHHHHhhcCCChhHHHHHHhhcch
Q 037146 128 EAKLKVIKEVRGFTGLGLKESKELVEKVPT 157 (185)
Q Consensus 128 ~kKi~vIK~VR~it~LgLkEAK~lVe~~P~ 157 (185)
-..+..|+.+|. +|++|.|.+.+++..+.
T Consensus 45 i~~l~~I~~lr~-~G~sl~~i~~l~~~~~~ 73 (108)
T cd01107 45 LERLNRIKYLRD-LGFPLEEIKEILDADND 73 (108)
T ss_pred HHHHHHHHHHHH-cCCCHHHHHHHHhcCCH
Confidence 367778888876 89999999999988663
No 21
>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=45.77 E-value=59 Score=23.46 Aligned_cols=41 Identities=24% Similarity=0.396 Sum_probs=31.4
Q ss_pred chhHHHHHHHHhhcCCChhHHHHHHhhcchhhhcCCCHHHHHHHHHHHHHc
Q 037146 128 EAKLKVIKEVRGFTGLGLKESKELVEKVPTLLKRGVTKDEADKIVAKLKEV 178 (185)
Q Consensus 128 ~kKi~vIK~VR~it~LgLkEAK~lVe~~P~~IKe~vsKeeAe~ik~kle~a 178 (185)
=.++..|+.++.-.|++|.+.+.+++ =.++-+.+...|+..
T Consensus 44 v~~l~~i~~L~~d~g~~l~~i~~~l~----------l~~~~~~l~~~l~~l 84 (91)
T cd04766 44 IERLRRIQRLTQELGVNLAGVKRILE----------LEEELAELRAELDEL 84 (91)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHH----------HHHHHHHHHHHHHHH
Confidence 47888888888889999999999997 345556666666543
No 22
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=45.29 E-value=21 Score=23.81 Aligned_cols=26 Identities=38% Similarity=0.661 Sum_probs=21.2
Q ss_pred chhHHHHHHHHhhcCCChhHHHHHHhh
Q 037146 128 EAKLKVIKEVRGFTGLGLKESKELVEK 154 (185)
Q Consensus 128 ~kKi~vIK~VR~it~LgLkEAK~lVe~ 154 (185)
-..+..|+.+++ .|+.+.|.+++++.
T Consensus 43 v~~l~~i~~l~~-~G~sl~~I~~~l~~ 68 (69)
T PF13411_consen 43 VERLREIKELRK-QGMSLEEIKKLLKQ 68 (69)
T ss_dssp HHHHHHHHHHHH-TTTHHHHHHHHH--
T ss_pred HHHHHHHHHHHH-CcCCHHHHHHHHcc
Confidence 468888888888 99999999998763
No 23
>PF10925 DUF2680: Protein of unknown function (DUF2680); InterPro: IPR024485 Members in this family of proteins are annotated as YckD however currently no function is known.
Probab=45.17 E-value=31 Score=24.08 Aligned_cols=26 Identities=27% Similarity=0.659 Sum_probs=20.9
Q ss_pred HHHHhhcchhhhcC-CCHHHHHHHHHHHHH
Q 037146 149 KELVEKVPTLLKRG-VTKDEADKIVAKLKE 177 (185)
Q Consensus 149 K~lVe~~P~~IKe~-vsKeeAe~ik~kle~ 177 (185)
|++|+. -|+.| +|+|.|+.|++.++.
T Consensus 21 K~~idk---~Ve~G~iTqeqAd~ik~~id~ 47 (59)
T PF10925_consen 21 KQIIDK---YVEAGVITQEQADAIKKHIDQ 47 (59)
T ss_pred HHHHHH---HHHcCCCCHHHHHHHHHHHHH
Confidence 566664 47777 899999999998875
No 24
>PRK13019 clpS ATP-dependent Clp protease adaptor; Reviewed
Probab=44.78 E-value=1.2e+02 Score=22.94 Aligned_cols=69 Identities=9% Similarity=0.125 Sum_probs=52.1
Q ss_pred ccceeEEEEecCCcchhHHHH-HHHHhhcCCChhHHHHHHhhcc----hhhhcCCCHHHHHHHHHHHHHcCCEEE
Q 037146 114 EKTVFDLKLAGYGAEAKLKVI-KEVRGFTGLGLKESKELVEKVP----TLLKRGVTKDEADKIVAKLKEVGAQVS 183 (185)
Q Consensus 114 EKt~f~V~L~~~~a~kKi~vI-K~VR~it~LgLkEAK~lVe~~P----~~IKe~vsKeeAe~ik~kle~aGA~Ve 183 (185)
....|.|+|-+-|-.--==|| ..++.+.+++..+|..+.-.+= .++. --++|.||-...+|...|.++|
T Consensus 18 ~p~~ykViL~NDd~~t~dfVi~~vl~~vf~~s~~~A~~iml~vH~~G~avv~-~~~~E~AE~~~~~l~~~glt~e 91 (94)
T PRK13019 18 RYPLYKVIVLNDDFNTFEHVVNCLLKAIPGMSEDRAWRLMITAHKEGSAVVW-VGPLEQAELYHQQLTDAGLTMA 91 (94)
T ss_pred CCCceEEEEEcCCCCCHHHHHHHHHHHhcCCCHHHHHHHHHHHhcCCcEEEE-EecHHHHHHHHHHHHHcccccC
Confidence 445699999765433444688 5777889999999999876542 2222 2689999999999999998775
No 25
>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=44.73 E-value=19 Score=25.37 Aligned_cols=34 Identities=21% Similarity=0.364 Sum_probs=29.0
Q ss_pred hHHHHHHHHhhcCCChhHHHHHHhhcchhhhcCC
Q 037146 130 KLKVIKEVRGFTGLGLKESKELVEKVPTLLKRGV 163 (185)
Q Consensus 130 Ki~vIK~VR~it~LgLkEAK~lVe~~P~~IKe~v 163 (185)
|-.+|+.|.+.+|+.-++++.+++.+-.+|++.+
T Consensus 2 K~~l~~~ia~~~~~~~~~v~~vl~~~~~~i~~~L 35 (87)
T cd00591 2 KSELIEAIAEKTGLSKKDAEAAVDAFLDVITEAL 35 (87)
T ss_pred HHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 6689999999999999999999998877666543
No 26
>smart00411 BHL bacterial (prokaryotic) histone like domain.
Probab=43.22 E-value=19 Score=25.53 Aligned_cols=36 Identities=19% Similarity=0.353 Sum_probs=30.4
Q ss_pred hhHHHHHHHHhhcCCChhHHHHHHhhcchhhhcCCC
Q 037146 129 AKLKVIKEVRGFTGLGLKESKELVEKVPTLLKRGVT 164 (185)
Q Consensus 129 kKi~vIK~VR~it~LgLkEAK~lVe~~P~~IKe~vs 164 (185)
+|-.+|+.|.+.+|+.-++++..++.+-.+|.+.+.
T Consensus 2 tk~eli~~ia~~~~~~~~~v~~vl~~l~~~i~~~L~ 37 (90)
T smart00411 2 TKSELIDAIAEKAGLSKKDAKAAVDAFLEIITEALK 37 (90)
T ss_pred CHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHh
Confidence 356899999999999999999999998887766443
No 27
>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=36.98 E-value=42 Score=22.26 Aligned_cols=24 Identities=21% Similarity=0.509 Sum_probs=18.2
Q ss_pred hhHHHHHHHHhhcCCChhHHHHHHh
Q 037146 129 AKLKVIKEVRGFTGLGLKESKELVE 153 (185)
Q Consensus 129 kKi~vIK~VR~it~LgLkEAK~lVe 153 (185)
..+..|+.+++ .|+.|.|.+++++
T Consensus 45 ~~l~~i~~l~~-~g~~l~~i~~~~~ 68 (68)
T cd01104 45 ARLRLIRRLTS-EGVRISQAAALAL 68 (68)
T ss_pred HHHHHHHHHHH-CCCCHHHHHHHhC
Confidence 45666666665 8999999999864
No 28
>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=36.79 E-value=76 Score=23.26 Aligned_cols=28 Identities=32% Similarity=0.358 Sum_probs=22.9
Q ss_pred chhHHHHHHHHhhcCCChhHHHHHHhhcc
Q 037146 128 EAKLKVIKEVRGFTGLGLKESKELVEKVP 156 (185)
Q Consensus 128 ~kKi~vIK~VR~it~LgLkEAK~lVe~~P 156 (185)
-.++..|+.+|+ .|+.|+|.+++++...
T Consensus 44 l~~l~~I~~lr~-~G~~l~~I~~~l~~~~ 71 (96)
T cd04768 44 LYQLQFILFLRE-LGFSLAEIKELLDTEM 71 (96)
T ss_pred HHHHHHHHHHHH-cCCCHHHHHHHHhcCc
Confidence 367888888876 5999999999998653
No 29
>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=35.43 E-value=1.1e+02 Score=23.12 Aligned_cols=27 Identities=22% Similarity=0.342 Sum_probs=21.7
Q ss_pred chhHHHHHHHHhhcCCChhHHHHHHhhc
Q 037146 128 EAKLKVIKEVRGFTGLGLKESKELVEKV 155 (185)
Q Consensus 128 ~kKi~vIK~VR~it~LgLkEAK~lVe~~ 155 (185)
-.++..|+.+|+ +|++|+|.+++++..
T Consensus 43 l~~l~~I~~lr~-~G~~L~eI~~~l~~~ 69 (120)
T cd04781 43 LDRLALIALGRA-AGFSLDEIQAMLSHD 69 (120)
T ss_pred HHHHHHHHHHHH-cCCCHHHHHHHHhcc
Confidence 367777777776 699999999999864
No 30
>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=34.55 E-value=70 Score=24.85 Aligned_cols=26 Identities=31% Similarity=0.502 Sum_probs=21.9
Q ss_pred chhHHHHHHHHhhcCCChhHHHHHHhh
Q 037146 128 EAKLKVIKEVRGFTGLGLKESKELVEK 154 (185)
Q Consensus 128 ~kKi~vIK~VR~it~LgLkEAK~lVe~ 154 (185)
-.++..|+.+|+ .|++|+|.+++++.
T Consensus 45 l~~l~~I~~lr~-~G~sl~eI~~~l~~ 70 (131)
T TIGR02043 45 QKRLRFILKAKE-LGFTLDEIKELLSI 70 (131)
T ss_pred HHHHHHHHHHHH-cCCCHHHHHHHHHh
Confidence 367888888875 79999999999974
No 31
>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=34.31 E-value=50 Score=22.29 Aligned_cols=24 Identities=21% Similarity=0.339 Sum_probs=20.0
Q ss_pred hhHHHHHHHHhhcCCChhHHHHHHh
Q 037146 129 AKLKVIKEVRGFTGLGLKESKELVE 153 (185)
Q Consensus 129 kKi~vIK~VR~it~LgLkEAK~lVe 153 (185)
..+..|+.+++ .|+.|.|.|.++.
T Consensus 45 ~~l~~i~~l~~-~g~~l~~i~~~l~ 68 (68)
T cd04763 45 DRILEIKRWID-NGVQVSKVKKLLS 68 (68)
T ss_pred HHHHHHHHHHH-cCCCHHHHHHHhC
Confidence 57777888887 9999999998863
No 32
>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=33.65 E-value=55 Score=24.24 Aligned_cols=27 Identities=22% Similarity=0.468 Sum_probs=24.1
Q ss_pred chhHHHHHHHHhhcCCChhHHHHHHhh
Q 037146 128 EAKLKVIKEVRGFTGLGLKESKELVEK 154 (185)
Q Consensus 128 ~kKi~vIK~VR~it~LgLkEAK~lVe~ 154 (185)
-.++..|+.+|...|++|.+.|.+++.
T Consensus 44 v~~l~~I~~L~~~~G~~l~~I~~~l~~ 70 (95)
T cd04780 44 VERLRLIRALQQEGGLPISQIKEVLDA 70 (95)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 478888888888899999999999986
No 33
>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=32.62 E-value=59 Score=23.54 Aligned_cols=26 Identities=31% Similarity=0.425 Sum_probs=22.3
Q ss_pred chhHHHHHHHHhhcCCChhHHHHHHhh
Q 037146 128 EAKLKVIKEVRGFTGLGLKESKELVEK 154 (185)
Q Consensus 128 ~kKi~vIK~VR~it~LgLkEAK~lVe~ 154 (185)
=.++..|+.+|+ .|+.|++++++++.
T Consensus 45 v~~l~~I~~Lr~-~G~sl~~i~~~l~~ 70 (88)
T cd01105 45 VDRLLVIKELLD-EGFTLAAAVEKLRR 70 (88)
T ss_pred HHHHHHHHHHHH-CCCCHHHHHHHHHH
Confidence 367888888887 99999999999973
No 34
>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=31.84 E-value=93 Score=22.82 Aligned_cols=26 Identities=27% Similarity=0.496 Sum_probs=21.0
Q ss_pred hhHHHHHHHHhhcCCChhHHHHHHhhc
Q 037146 129 AKLKVIKEVRGFTGLGLKESKELVEKV 155 (185)
Q Consensus 129 kKi~vIK~VR~it~LgLkEAK~lVe~~ 155 (185)
..+..|+.+|. +|+.|.|.+++++..
T Consensus 45 ~~l~~I~~lr~-~G~~l~eI~~~l~~~ 70 (97)
T cd04782 45 EQLDIILLLKE-LGISLKEIKDYLDNR 70 (97)
T ss_pred HHHHHHHHHHH-cCCCHHHHHHHHhcC
Confidence 57777777775 599999999999753
No 35
>PRK00285 ihfA integration host factor subunit alpha; Reviewed
Probab=30.73 E-value=39 Score=24.83 Aligned_cols=35 Identities=26% Similarity=0.313 Sum_probs=30.0
Q ss_pred hhHHHHHHHHhhcCCChhHHHHHHhhcchhhhcCC
Q 037146 129 AKLKVIKEVRGFTGLGLKESKELVEKVPTLLKRGV 163 (185)
Q Consensus 129 kKi~vIK~VR~it~LgLkEAK~lVe~~P~~IKe~v 163 (185)
.|-.+|+.|.+.+++.-++++..|+.+-..|.+.+
T Consensus 4 tk~el~~~ia~~~~~s~~~v~~vl~~~~~~i~~~L 38 (99)
T PRK00285 4 TKADLAEALFEKVGLSKREAKELVELFFEEIRDAL 38 (99)
T ss_pred CHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 46689999999999999999999999887776544
No 36
>PRK05350 acyl carrier protein; Provisional
Probab=29.90 E-value=68 Score=22.66 Aligned_cols=26 Identities=19% Similarity=0.301 Sum_probs=21.3
Q ss_pred HHHHhcCCHHHHHHHHHHHHHHhCCCC
Q 037146 54 VDEISCLSLVEVMDLADVVRNKLGIKE 80 (185)
Q Consensus 54 vd~I~~LtLlE~~eLv~~leekfgv~~ 80 (185)
.+.+ ++.=+...+|+-.|+++|||.-
T Consensus 33 ~~dl-g~DSld~veli~~lE~~fgI~i 58 (82)
T PRK05350 33 YEDL-DLDSIDAVDLVVHLQKLTGKKI 58 (82)
T ss_pred hhhc-CCCHHHHHHHHHHHHHHHCCcc
Confidence 3443 7788889999999999999964
No 37
>PF11272 DUF3072: Protein of unknown function (DUF3072); InterPro: IPR021425 This bacterial family of proteins has no known function.
Probab=29.82 E-value=59 Score=22.95 Aligned_cols=19 Identities=21% Similarity=0.263 Sum_probs=17.4
Q ss_pred cCCHHHHHHHHHHHHHHhC
Q 037146 59 CLSLVEVMDLADVVRNKLG 77 (185)
Q Consensus 59 ~LtLlE~~eLv~~leekfg 77 (185)
.||-.|++++++.|+.+.|
T Consensus 38 ~LtkaeAs~rId~L~~~~g 56 (57)
T PF11272_consen 38 DLTKAEASERIDELQAQTG 56 (57)
T ss_pred cccHHHHHHHHHHHHHHhC
Confidence 6999999999999999876
No 38
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=29.56 E-value=93 Score=24.82 Aligned_cols=25 Identities=24% Similarity=0.456 Sum_probs=20.4
Q ss_pred hhHHHHHHHHhhcCCChhHHHHHHhh
Q 037146 129 AKLKVIKEVRGFTGLGLKESKELVEK 154 (185)
Q Consensus 129 kKi~vIK~VR~it~LgLkEAK~lVe~ 154 (185)
.++..|+..| -+|++|+|.+++++.
T Consensus 52 ~rl~~I~~lr-~~G~sL~eI~~ll~~ 76 (144)
T PRK13752 52 TRVRFVKSAQ-RLGFSLDEIAELLRL 76 (144)
T ss_pred HHHHHHHHHH-HcCCCHHHHHHHHhc
Confidence 6777777777 579999999999974
No 39
>PF11363 DUF3164: Protein of unknown function (DUF3164); InterPro: IPR021505 This entry is represented by Bacteriophage B3, Orf6. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=29.26 E-value=82 Score=26.74 Aligned_cols=82 Identities=12% Similarity=0.210 Sum_probs=49.5
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHHHHHhCCCCCcchhcccCCCCccccccccCCCCCCCccccccccceeEEEEecCCcch
Q 037146 50 VASIVDEISCLSLVEVMDLADVVRNKLGIKEMPNMCVMMPGMGFSVKGATARGGTGTGKAEEKVEKTVFDLKLAGYGAEA 129 (185)
Q Consensus 50 V~~Ivd~I~~LtLlE~~eLv~~leekfgv~~~~~~~~~~p~~~~~~~~~~aa~~a~~~~~e~~~EKt~f~V~L~~~~a~k 129 (185)
+.+.+.+.+.-+.-++..+++++.+.+|+..- + +.=+|+|++||+..
T Consensus 36 l~~~l~~fK~~~f~d~~af~~l~~e~Yg~k~g----------------g-----------------~kGn~Tl~sfDG~~ 82 (195)
T PF11363_consen 36 LSEQLAEFKAHTFEDIEAFIELSAEEYGVKLG----------------G-----------------KKGNVTLTSFDGRY 82 (195)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcC----------------C-----------------CcCcEEEEEeCCCE
Confidence 34444555556677888888899999988421 0 01255677887655
Q ss_pred hHHHHHHHHhhcCCChhHHHHHHhhcchhhhcCCC
Q 037146 130 KLKVIKEVRGFTGLGLKESKELVEKVPTLLKRGVT 164 (185)
Q Consensus 130 Ki~vIK~VR~it~LgLkEAK~lVe~~P~~IKe~vs 164 (185)
||.+--.-+--.+=.|.-||++|+.+=...-+|..
T Consensus 83 kV~i~~~~~~~Fde~l~~Ak~lIde~l~~w~~g~~ 117 (195)
T PF11363_consen 83 KVTIAVQDRISFDERLQAAKALIDECLNEWAKGAD 117 (195)
T ss_pred EEEEEecccCCcChHHHHHHHHHHHHHHHHhcCCC
Confidence 54432222222355678888888877666666643
No 40
>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=29.23 E-value=67 Score=24.05 Aligned_cols=26 Identities=38% Similarity=0.495 Sum_probs=21.4
Q ss_pred hhHHHHHHHHhhcCCChhHHHHHHhhc
Q 037146 129 AKLKVIKEVRGFTGLGLKESKELVEKV 155 (185)
Q Consensus 129 kKi~vIK~VR~it~LgLkEAK~lVe~~ 155 (185)
.++..|+.+|+ .|++|+|.+++++..
T Consensus 45 ~~l~~I~~lr~-~G~sL~eI~~~l~~~ 70 (113)
T cd01109 45 EWLEFIKCLRN-TGMSIKDIKEYAELR 70 (113)
T ss_pred HHHHHHHHHHH-cCCCHHHHHHHHHHH
Confidence 57777888775 799999999999753
No 41
>PF09999 DUF2240: Uncharacterized protein conserved in archaea (DUF2240); InterPro: IPR018716 This family of various hypothetical archaeal proteins has no known function.
Probab=29.16 E-value=94 Score=25.41 Aligned_cols=33 Identities=21% Similarity=0.391 Sum_probs=27.9
Q ss_pred hhHHHHHHHHhc---CCHHHHHHHHHHHHHHhC--CCC
Q 037146 48 EKVASIVDEISC---LSLVEVMDLADVVRNKLG--IKE 80 (185)
Q Consensus 48 ~KV~~Ivd~I~~---LtLlE~~eLv~~leekfg--v~~ 80 (185)
+-.++|+|.|.. ++-.|+-..++.++++|| |+.
T Consensus 85 ~~fe~ild~ia~~~g~~~~evv~~in~~q~~~~~~l~~ 122 (144)
T PF09999_consen 85 DPFERILDYIAAKTGIEKQEVVAEINELQEELGGLLDP 122 (144)
T ss_pred cHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhccCCH
Confidence 347888888866 899999999999999999 764
No 42
>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=28.19 E-value=1.5e+02 Score=21.81 Aligned_cols=27 Identities=33% Similarity=0.470 Sum_probs=22.3
Q ss_pred hhHHHHHHHHhhcCCChhHHHHHHhhcc
Q 037146 129 AKLKVIKEVRGFTGLGLKESKELVEKVP 156 (185)
Q Consensus 129 kKi~vIK~VR~it~LgLkEAK~lVe~~P 156 (185)
..+..|+.+|. .|++|.+.+.+++...
T Consensus 45 ~~l~~i~~lr~-~g~~l~~i~~~~~~~~ 71 (103)
T cd01106 45 ERLQQILFLKE-LGFSLKEIKELLKDPS 71 (103)
T ss_pred HHHHHHHHHHH-cCCCHHHHHHHHHcCc
Confidence 56777777776 6999999999998764
No 43
>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=27.55 E-value=76 Score=23.50 Aligned_cols=25 Identities=28% Similarity=0.497 Sum_probs=20.8
Q ss_pred hhHHHHHHHHhhcCCChhHHHHHHhh
Q 037146 129 AKLKVIKEVRGFTGLGLKESKELVEK 154 (185)
Q Consensus 129 kKi~vIK~VR~it~LgLkEAK~lVe~ 154 (185)
.++..|+.+|+ +|++|+|-+++++.
T Consensus 43 ~~l~~I~~lr~-~G~sL~eI~~~l~~ 67 (107)
T cd04777 43 DDLEFILELKG-LGFSLIEIQKIFSY 67 (107)
T ss_pred HHHHHHHHHHH-CCCCHHHHHHHHHh
Confidence 57777777776 69999999999974
No 44
>COG3797 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.50 E-value=51 Score=28.08 Aligned_cols=50 Identities=20% Similarity=0.335 Sum_probs=36.6
Q ss_pred CCcchhHHHHHHHHhh-cCCChhHHHHHHhhcchhhhcCCCHHHHHHHHHHHHHc
Q 037146 125 YGAEAKLKVIKEVRGF-TGLGLKESKELVEKVPTLLKRGVTKDEADKIVAKLKEV 178 (185)
Q Consensus 125 ~~a~kKi~vIK~VR~i-t~LgLkEAK~lVe~~P~~IKe~vsKeeAe~ik~kle~a 178 (185)
+++.+| =+..++|.. |+||+..++-+|.+---++-.+.+ +.++.++||++
T Consensus 13 VGgg~k-V~MAdLka~~~dlGf~~v~T~iaSGNlvf~s~~~---~~el~~klE~a 63 (178)
T COG3797 13 VGGGRK-VVMADLKAALTDLGFANVRTYIASGNLVFESEAG---AAELEAKLEAA 63 (178)
T ss_pred ecCCce-EeHHHHHHHHHHcCcchhhHhhhcCCEEEEcCCC---hHHHHHHHHHH
Confidence 343333 456778876 899999999999998777776666 55677777754
No 45
>KOG3449 consensus 60S acidic ribosomal protein P2 [Translation, ribosomal structure and biogenesis]
Probab=27.32 E-value=1.8e+02 Score=23.18 Aligned_cols=29 Identities=21% Similarity=0.328 Sum_probs=21.1
Q ss_pred CCChhHHHHHHHHhcCCHHHHHHHHHHHHHHh
Q 037146 45 EPSEKVASIVDEISCLSLVEVMDLADVVRNKL 76 (185)
Q Consensus 45 ~~s~KV~~Ivd~I~~LtLlE~~eLv~~leekf 76 (185)
...++++.++.+|..-|+ .||+..=+++|
T Consensus 34 ~d~e~i~~visel~GK~i---~ElIA~G~ekl 62 (112)
T KOG3449|consen 34 IDDERINLVLSELKGKDI---EELIAAGREKL 62 (112)
T ss_pred cCHHHHHHHHHHhcCCCH---HHHHHHhHHHH
Confidence 456788888888888876 45666666666
No 46
>cd02810 DHOD_DHPD_FMN Dihydroorotate dehydrogenase (DHOD) and Dihydropyrimidine dehydrogenase (DHPD) FMN-binding domain. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences and cellular location. Members of class 1 are cytosolic enzymes and multimers while class 2 enzymes are membrane associated and monomeric. The class 1 enzymes can be further divided into subtypes 1A and 1B which are homodimers and heterotetrameric proteins, respectively. DHPD catalyzes the first step in pyrimidine degradation: the NADPH-dependent reduction of uracil and thymine to the corresponding 5,6-dihydropyrimidines. DHPD contains two FAD, two FMN and eight [4Fe-4S] clusters, arranged in two electron transfer chains that pass its homodimeric interface twice. Two of
Probab=27.25 E-value=95 Score=26.53 Aligned_cols=40 Identities=18% Similarity=0.289 Sum_probs=30.4
Q ss_pred HHHHHHHHhhcCCChhHHHHHHhhcchhhhc--CCCHHHHHHHHHHHHHcCCEE
Q 037146 131 LKVIKEVRGFTGLGLKESKELVEKVPTLLKR--GVTKDEADKIVAKLKEVGAQV 182 (185)
Q Consensus 131 i~vIK~VR~it~LgLkEAK~lVe~~P~~IKe--~vsKeeAe~ik~kle~aGA~V 182 (185)
..+++.||+.+ +.|-.+|- +++.+|..++.+.++++|+..
T Consensus 151 ~eiv~~vr~~~------------~~pv~vKl~~~~~~~~~~~~a~~l~~~Gad~ 192 (289)
T cd02810 151 ANLLKAVKAAV------------DIPLLVKLSPYFDLEDIVELAKAAERAGADG 192 (289)
T ss_pred HHHHHHHHHcc------------CCCEEEEeCCCCCHHHHHHHHHHHHHcCCCE
Confidence 46777777654 36777773 467779999999999999874
No 47
>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=27.10 E-value=78 Score=21.18 Aligned_cols=24 Identities=42% Similarity=0.563 Sum_probs=19.6
Q ss_pred hhHHHHHHHHhhcCCChhHHHHHHh
Q 037146 129 AKLKVIKEVRGFTGLGLKESKELVE 153 (185)
Q Consensus 129 kKi~vIK~VR~it~LgLkEAK~lVe 153 (185)
..+..|+.+++ .|+.|.|.+.+++
T Consensus 44 ~~l~~i~~l~~-~g~~l~~i~~~l~ 67 (67)
T cd04764 44 ELLKKIKTLLE-KGLSIKEIKEILN 67 (67)
T ss_pred HHHHHHHHHHH-CCCCHHHHHHHhC
Confidence 57777888877 8999999998763
No 48
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=26.73 E-value=1e+02 Score=24.25 Aligned_cols=25 Identities=36% Similarity=0.620 Sum_probs=19.9
Q ss_pred hhHHHHHHHHhhcCCChhHHHHHHhh
Q 037146 129 AKLKVIKEVRGFTGLGLKESKELVEK 154 (185)
Q Consensus 129 kKi~vIK~VR~it~LgLkEAK~lVe~ 154 (185)
..+..|+..|. +|++|+|.|++++.
T Consensus 45 ~~l~~I~~lr~-~G~sl~eI~~~l~~ 69 (135)
T PRK10227 45 NELTLLRQARQ-VGFNLEESGELVNL 69 (135)
T ss_pred HHHHHHHHHHH-CCCCHHHHHHHHHh
Confidence 56677777665 69999999999974
No 49
>TIGR01037 pyrD_sub1_fam dihydroorotate dehydrogenase (subfamily 1) family protein. This family includes subfamily 1 dihydroorotate dehydrogenases while excluding the closely related subfamily 2 (TIGR01036). This family also includes a number of uncharacterized proteins and a domain of dihydropyrimidine dehydrogenase. The uncharacterized proteins might all be dihydroorotate dehydrogenase.
Probab=25.25 E-value=92 Score=26.95 Aligned_cols=42 Identities=26% Similarity=0.325 Sum_probs=32.7
Q ss_pred hhHHHHHHHHhhcCCChhHHHHHHhhcchhhhcCCCHHHHHHHHHHHHHcCCEE
Q 037146 129 AKLKVIKEVRGFTGLGLKESKELVEKVPTLLKRGVTKDEADKIVAKLKEVGAQV 182 (185)
Q Consensus 129 kKi~vIK~VR~it~LgLkEAK~lVe~~P~~IKe~vsKeeAe~ik~kle~aGA~V 182 (185)
.-..+++.||+.+ ..|-.+|=..+-+|..++.+.++++|+..
T Consensus 144 ~~~eiv~~vr~~~------------~~pv~vKi~~~~~~~~~~a~~l~~~G~d~ 185 (300)
T TIGR01037 144 LSADVVKAVKDKT------------DVPVFAKLSPNVTDITEIAKAAEEAGADG 185 (300)
T ss_pred HHHHHHHHHHHhc------------CCCEEEECCCChhhHHHHHHHHHHcCCCE
Confidence 3457777777654 35888887777889999999999999864
No 50
>CHL00124 acpP acyl carrier protein; Validated
Probab=25.19 E-value=1.1e+02 Score=21.36 Aligned_cols=24 Identities=17% Similarity=0.228 Sum_probs=19.8
Q ss_pred hcCCHHHHHHHHHHHHHHhCCCCC
Q 037146 58 SCLSLVEVMDLADVVRNKLGIKEM 81 (185)
Q Consensus 58 ~~LtLlE~~eLv~~leekfgv~~~ 81 (185)
.++.=+...+|+-.|+++|||.-.
T Consensus 35 lg~DSl~~~eli~~le~~f~i~i~ 58 (82)
T CHL00124 35 LGADSLDVVELVMAIEEKFDIEIP 58 (82)
T ss_pred cCCcHHHHHHHHHHHHHHHCCccC
Confidence 466777889999999999999643
No 51
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=25.09 E-value=99 Score=20.41 Aligned_cols=25 Identities=40% Similarity=0.652 Sum_probs=21.0
Q ss_pred chhHHHHHHHHhhcCCChhHHHHHHh
Q 037146 128 EAKLKVIKEVRGFTGLGLKESKELVE 153 (185)
Q Consensus 128 ~kKi~vIK~VR~it~LgLkEAK~lVe 153 (185)
-..+..|+.+|+ .|+++.+.+.+++
T Consensus 44 l~~l~~i~~lr~-~g~~~~~i~~~l~ 68 (70)
T smart00422 44 LERLRFIKRLKE-LGFSLEEIKELLE 68 (70)
T ss_pred HHHHHHHHHHHH-cCCCHHHHHHHHh
Confidence 367888888887 9999999998876
No 52
>PRK05412 putative nucleotide-binding protein; Reviewed
Probab=25.04 E-value=71 Score=26.81 Aligned_cols=64 Identities=31% Similarity=0.421 Sum_probs=41.9
Q ss_pred EEEEecCCcchhHHHHH-HHHhh---cCCChhHHHH-HHhh-------cchhhhcCCCHHHHHHHHHHHHHcCCEEE
Q 037146 119 DLKLAGYGAEAKLKVIK-EVRGF---TGLGLKESKE-LVEK-------VPTLLKRGVTKDEADKIVAKLKEVGAQVS 183 (185)
Q Consensus 119 ~V~L~~~~a~kKi~vIK-~VR~i---t~LgLkEAK~-lVe~-------~P~~IKe~vsKeeAe~ik~kle~aGA~Ve 183 (185)
.|+|.+-+ +.|+.-++ .++.- -|+.++--.- -++. -...||+|++++.|.+|.+.+.+.+-+|.
T Consensus 45 ~i~l~a~~-d~kl~~v~diL~~kl~KR~i~~k~ld~~~~e~~sG~~vrq~i~lk~GI~~e~AKkIvK~IKd~klKVq 120 (161)
T PRK05412 45 EITLTAES-DFQLKQVKDILRSKLIKRGIDLKALDYGKVEKASGKTVKQEVKLKQGIDQELAKKIVKLIKDSKLKVQ 120 (161)
T ss_pred EEEEEeCC-HHHHHHHHHHHHHHHHHcCCCHHHcCCCCccccCCCEEEEEEehhhccCHHHHHHHHHHHHhcCCcee
Confidence 46777654 67776544 34432 3666552211 1111 23579999999999999999999998874
No 53
>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=24.97 E-value=1.2e+02 Score=27.00 Aligned_cols=44 Identities=20% Similarity=0.311 Sum_probs=31.8
Q ss_pred CCChhHHHHHHhhcch------hh---hcCCCHHHHHHHHHHHHHcCCEEEeC
Q 037146 142 GLGLKESKELVEKVPT------LL---KRGVTKDEADKIVAKLKEVGAQVSME 185 (185)
Q Consensus 142 ~LgLkEAK~lVe~~P~------~I---Ke~vsKeeAe~ik~kle~aGA~VelE 185 (185)
..++++||++++.+-. .| .....+.-|+.|+..|+++|-+|+++
T Consensus 297 ~~d~~kA~~lL~~aG~~~g~~l~l~~~~~~~~~~~a~~i~~~l~~~GI~v~i~ 349 (448)
T cd08494 297 PYDPDKARQLLAEAGAAYGLTLTLTLPPLPYARRIGEIIASQLAEVGITVKIE 349 (448)
T ss_pred CCCHHHHHHHHHHcCCCCCeEEEEEecCCcchhHHHHHHHHHHHhcCcEEEEE
Confidence 4577888888877531 11 12235788999999999999999873
No 54
>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=24.96 E-value=83 Score=24.01 Aligned_cols=25 Identities=24% Similarity=0.444 Sum_probs=19.5
Q ss_pred hhHHHHHHHHhhcCCChhHHHHHHhh
Q 037146 129 AKLKVIKEVRGFTGLGLKESKELVEK 154 (185)
Q Consensus 129 kKi~vIK~VR~it~LgLkEAK~lVe~ 154 (185)
.++..|+.+|+ +|++|+|.|++++.
T Consensus 45 ~~l~~I~~lr~-~G~sL~eI~~~l~~ 69 (127)
T cd04784 45 ERLLFIRRCRS-LDMSLDEIRTLLQL 69 (127)
T ss_pred HHHHHHHHHHH-cCCCHHHHHHHHHh
Confidence 56666666664 59999999999974
No 55
>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=24.85 E-value=97 Score=24.42 Aligned_cols=32 Identities=22% Similarity=0.353 Sum_probs=26.4
Q ss_pred chhHHHHHHHHhhcCCChhHHHHHHhhcchhh
Q 037146 128 EAKLKVIKEVRGFTGLGLKESKELVEKVPTLL 159 (185)
Q Consensus 128 ~kKi~vIK~VR~it~LgLkEAK~lVe~~P~~I 159 (185)
-..++.|+.+|+-.|+.|.+.+.+++-.|...
T Consensus 43 v~rL~~I~~L~~e~G~~l~eI~~~L~l~~~~~ 74 (120)
T cd04767 43 LKRLRFIKKLINEKGLNIAGVKQILSMYPCWS 74 (120)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHhCcccc
Confidence 36777777777779999999999999888653
No 56
>TIGR00517 acyl_carrier acyl carrier protein. S (Ser) at position 37 in the seed alignment, in the motif DSLD, is the phosphopantetheine attachment site.
Probab=24.68 E-value=94 Score=21.36 Aligned_cols=23 Identities=9% Similarity=0.176 Sum_probs=19.4
Q ss_pred hcCCHHHHHHHHHHHHHHhCCCC
Q 037146 58 SCLSLVEVMDLADVVRNKLGIKE 80 (185)
Q Consensus 58 ~~LtLlE~~eLv~~leekfgv~~ 80 (185)
..+.=+...+|+-.||++|||.-
T Consensus 33 lglDSl~~veli~~lE~~f~i~i 55 (77)
T TIGR00517 33 LGADSLDTVELVMALEEEFDIEI 55 (77)
T ss_pred cCCcHHHHHHHHHHHHHHHCCCC
Confidence 45677788999999999999964
No 57
>PF04461 DUF520: Protein of unknown function (DUF520); InterPro: IPR007551 This entry represents the UPF0234 family of uncharacterised proteins.; PDB: 1IN0_A.
Probab=24.53 E-value=54 Score=27.44 Aligned_cols=64 Identities=33% Similarity=0.441 Sum_probs=35.0
Q ss_pred EEEEecCCcchhHHHHHHH-Hhh---cCCChhHHHHH-Hhhc-------chhhhcCCCHHHHHHHHHHHHHcCCEEE
Q 037146 119 DLKLAGYGAEAKLKVIKEV-RGF---TGLGLKESKEL-VEKV-------PTLLKRGVTKDEADKIVAKLKEVGAQVS 183 (185)
Q Consensus 119 ~V~L~~~~a~kKi~vIK~V-R~i---t~LgLkEAK~l-Ve~~-------P~~IKe~vsKeeAe~ik~kle~aGA~Ve 183 (185)
.++|.+-+ +.|+.-+..| +.- -|+.++--.-- .|.+ ...||+|++++.|.+|.+.+.+.+-+|.
T Consensus 45 ~i~l~a~~-e~kl~~v~diL~~kl~KR~i~~k~ld~~k~e~asg~~vrq~i~lk~GI~~d~AKkIvK~IKd~klKVq 120 (160)
T PF04461_consen 45 TITLTAED-EFKLKQVKDILRSKLIKRGIDLKALDFGKIESASGGTVRQVIKLKQGIDQDTAKKIVKLIKDSKLKVQ 120 (160)
T ss_dssp EEEEEESS-HHHHHHHHHHHHHHHHHTT--GGGEE--SS-EEETTEEEEEEEE--S--HHHHHHHHHHHHHH--SEE
T ss_pred EEEEEeCC-HHHHHHHHHHHHHHHHHcCCCHHHcCCCCCccccCCEEEEEEEeecccCHHHHHHHHHHHHhcCCcee
Confidence 77888755 6776655443 332 26665522221 1221 3478999999999999999999988774
No 58
>PRK00199 ihfB integration host factor subunit beta; Reviewed
Probab=24.01 E-value=38 Score=24.69 Aligned_cols=34 Identities=15% Similarity=0.243 Sum_probs=28.1
Q ss_pred hHHHHHHHHh-hcCCChhHHHHHHhhcchhhhcCC
Q 037146 130 KLKVIKEVRG-FTGLGLKESKELVEKVPTLLKRGV 163 (185)
Q Consensus 130 Ki~vIK~VR~-it~LgLkEAK~lVe~~P~~IKe~v 163 (185)
|-.+|+.|.+ .++++-++++.+|+.+-..|.+.+
T Consensus 3 k~eli~~ia~~~~~~s~~~~~~vv~~~~~~i~~~L 37 (94)
T PRK00199 3 KSELIERLAARNPHLSAKDVENAVKEILEEMSDAL 37 (94)
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHH
Confidence 5678999987 489999999999999887776644
No 59
>cd04740 DHOD_1B_like Dihydroorotate dehydrogenase (DHOD) class 1B FMN-binding domain. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences and cellular location. Members of class 1 are cytosolic enzymes and multimers while class 2 enzymes are membrane associated and monomeric. The class 1 enzymes can be further divided into subtypes 1A and 1B which are homodimers and heterotetrameric proteins, respectively.
Probab=23.74 E-value=1e+02 Score=26.51 Aligned_cols=39 Identities=26% Similarity=0.382 Sum_probs=30.4
Q ss_pred HHHHHHHHhhcCCChhHHHHHHhhcchhhhcCCCHHHHHHHHHHHHHcCCE
Q 037146 131 LKVIKEVRGFTGLGLKESKELVEKVPTLLKRGVTKDEADKIVAKLKEVGAQ 181 (185)
Q Consensus 131 i~vIK~VR~it~LgLkEAK~lVe~~P~~IKe~vsKeeAe~ik~kle~aGA~ 181 (185)
..+++.||+.+ ..|..+|=+...+|..++.+.++++|+.
T Consensus 143 ~eiv~~vr~~~------------~~Pv~vKl~~~~~~~~~~a~~~~~~G~d 181 (296)
T cd04740 143 AEIVKAVKKAT------------DVPVIVKLTPNVTDIVEIARAAEEAGAD 181 (296)
T ss_pred HHHHHHHHhcc------------CCCEEEEeCCCchhHHHHHHHHHHcCCC
Confidence 35677777554 4688888777777899999999999986
No 60
>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=23.72 E-value=1.3e+02 Score=27.22 Aligned_cols=44 Identities=20% Similarity=0.235 Sum_probs=31.1
Q ss_pred CCChhHHHHHHhhcchh----h----hc-CCCHHHHHHHHHHHHHcCCEEEeC
Q 037146 142 GLGLKESKELVEKVPTL----L----KR-GVTKDEADKIVAKLKEVGAQVSME 185 (185)
Q Consensus 142 ~LgLkEAK~lVe~~P~~----I----Ke-~vsKeeAe~ik~kle~aGA~VelE 185 (185)
..++.+||++++.+-.. | -. ......|+.+++.|+++|-+|+++
T Consensus 300 ~~d~~~A~~lL~eaG~~~~~~l~l~~~~~~~~~~~a~~i~~~l~~~GI~v~i~ 352 (474)
T cd08499 300 EYDPEKAKELLAEAGYPDGFETTLWTNDNRERIKIAEFIQQQLAQIGIDVEIE 352 (474)
T ss_pred CCCHHHHHHHHHHcCCCCCceEEEEecCCCchhHHHHHHHHHHHHcCceEEEE
Confidence 45778888888765321 1 11 134678999999999999999873
No 61
>PRK07081 acyl carrier protein; Provisional
Probab=23.31 E-value=99 Score=22.24 Aligned_cols=23 Identities=17% Similarity=0.245 Sum_probs=20.4
Q ss_pred hcCCHHHHHHHHHHHHHHhCCCC
Q 037146 58 SCLSLVEVMDLADVVRNKLGIKE 80 (185)
Q Consensus 58 ~~LtLlE~~eLv~~leekfgv~~ 80 (185)
.++.=+.+.+|+-.||++|||.-
T Consensus 31 lGlDSl~~v~li~~lE~~f~I~i 53 (83)
T PRK07081 31 AGLSSLATVQLMLAIEDAFDIEI 53 (83)
T ss_pred cCCCHHHHHHHHHHHHHHhCCcC
Confidence 46888999999999999999964
No 62
>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=22.79 E-value=1e+02 Score=23.68 Aligned_cols=26 Identities=31% Similarity=0.539 Sum_probs=21.6
Q ss_pred chhHHHHHHHHhhcCCChhHHHHHHhh
Q 037146 128 EAKLKVIKEVRGFTGLGLKESKELVEK 154 (185)
Q Consensus 128 ~kKi~vIK~VR~it~LgLkEAK~lVe~ 154 (185)
-.++..|+.+|. +|++|+|-+.+++.
T Consensus 44 ~~~l~~I~~lr~-~G~sL~eI~~~l~~ 69 (127)
T cd01108 44 IEELRFIRRARD-LGFSLEEIRELLAL 69 (127)
T ss_pred HHHHHHHHHHHH-cCCCHHHHHHHHHH
Confidence 367888888875 89999999999973
No 63
>PF08542 Rep_fac_C: Replication factor C C-terminal domain; InterPro: IPR013748 Replication factor C (RFC) is a multimeric AAA+ protein complex that loads the DNA polymerase processivity clamp PCNA (Proliferating Cell Nuclear Antigen) onto DNA using ATP to drive the reaction []. PCNA functions at multiple levels in directing DNA metabolic pathways []. When bound to DNA, PCNA organises various proteins involved in DNA replication, DNA repair, DNA modification, and chromatin modelling. Replication factor C consists of five subunits in a spiral arrangement: Rfc1, Rfc2, Rfc3, Rfc4, and Rfc5 subunits. Rfc1 and Rfc2 load the PCNA sliding clamp onto DNA, while Rfc3 binds ATP and also acts as a checkpoint sensor. The RFC complex contains four ATP sites (sites A, B, C, and D) located at subunit interfaces. In each ATP site, an arginine residue from one subunit is located near the gamma-phosphate of ATP bound in the adjacent subunit. These arginine residues act as "arginine fingers" that can potentially perform two functions: sensing that ATP is bound and catalyzing ATP hydrolysis []. This entry represents the core domain found in Rfc1-5.; GO: 0003689 DNA clamp loader activity, 0005524 ATP binding, 0006260 DNA replication, 0005663 DNA replication factor C complex; PDB: 1SXJ_B 2CHG_B 2CHV_F 2CHQ_C 1IQP_A.
Probab=22.60 E-value=1.3e+02 Score=20.94 Aligned_cols=36 Identities=14% Similarity=0.099 Sum_probs=28.9
Q ss_pred CCChhHHHHHHHHhcCCHHHHHHHHHHHHHHhCCCCC
Q 037146 45 EPSEKVASIVDEISCLSLVEVMDLADVVRNKLGIKEM 81 (185)
Q Consensus 45 ~~s~KV~~Ivd~I~~LtLlE~~eLv~~leekfgv~~~ 81 (185)
++...|++|++.+.+=++.++...+..|-.. |++..
T Consensus 3 p~~~~i~~i~~~~~~~~~~~~~~~~~~l~~~-G~s~~ 38 (89)
T PF08542_consen 3 PPPEVIEEILESCLNGDFKEARKKLYELLVE-GYSAS 38 (89)
T ss_dssp --HHHHHHHHHHHHHTCHHHHHHHHHHHHHT-T--HH
T ss_pred CCHHHHHHHHHHHHhCCHHHHHHHHHHHHHc-CCCHH
Confidence 4567799999999999999999999999888 98754
No 64
>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=22.58 E-value=1.3e+02 Score=27.15 Aligned_cols=44 Identities=11% Similarity=0.132 Sum_probs=31.2
Q ss_pred CCChhHHHHHHhhcch-----h--hhcC--CCHHHHHHHHHHHHHcCCEEEeC
Q 037146 142 GLGLKESKELVEKVPT-----L--LKRG--VTKDEADKIVAKLKEVGAQVSME 185 (185)
Q Consensus 142 ~LgLkEAK~lVe~~P~-----~--IKe~--vsKeeAe~ik~kle~aGA~VelE 185 (185)
.-.++.||++++.+-. + ...+ ....-|+.++..|+++|-+|+++
T Consensus 304 ~~d~~~A~~lL~eaG~~~~~l~l~~~~~~~~~~~~a~~i~~~l~~~Gi~v~i~ 356 (460)
T cd08503 304 EYDPDKAKALLAEAGLPDLEVELVTSDAAPGAVDAAVLFAEQAAQAGININVK 356 (460)
T ss_pred CCCHHHHHHHHHHcCCCCceEEEEecCCCccHHHHHHHHHHHHHhhCCEEEEE
Confidence 4567778887776531 1 1222 46778999999999999998873
No 65
>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=22.51 E-value=1e+02 Score=24.01 Aligned_cols=26 Identities=23% Similarity=0.488 Sum_probs=20.7
Q ss_pred hhHHHHHHHHhhcCCChhHHHHHHhhc
Q 037146 129 AKLKVIKEVRGFTGLGLKESKELVEKV 155 (185)
Q Consensus 129 kKi~vIK~VR~it~LgLkEAK~lVe~~ 155 (185)
.++..|+..|. +|++|+|.+.+++-.
T Consensus 48 ~rL~~I~~lr~-~G~~L~eI~~ll~~~ 73 (120)
T TIGR02054 48 QRLRFVRAAFE-AGIGLGELARLCRAL 73 (120)
T ss_pred HHHHHHHHHHH-cCCCHHHHHHHHHhh
Confidence 56677777665 899999999998754
No 66
>PRK07259 dihydroorotate dehydrogenase 1B; Reviewed
Probab=22.17 E-value=98 Score=26.84 Aligned_cols=41 Identities=27% Similarity=0.387 Sum_probs=32.3
Q ss_pred hhHHHHHHHHhhcCCChhHHHHHHhhcchhhhcCCCHHHHHHHHHHHHHcCCE
Q 037146 129 AKLKVIKEVRGFTGLGLKESKELVEKVPTLLKRGVTKDEADKIVAKLKEVGAQ 181 (185)
Q Consensus 129 kKi~vIK~VR~it~LgLkEAK~lVe~~P~~IKe~vsKeeAe~ik~kle~aGA~ 181 (185)
.=..+|+.||+.+ ..|-.+|=+.+-+|..++.+.|+++|+.
T Consensus 144 ~~~eiv~~vr~~~------------~~pv~vKl~~~~~~~~~~a~~l~~~G~d 184 (301)
T PRK07259 144 LAYEVVKAVKEVV------------KVPVIVKLTPNVTDIVEIAKAAEEAGAD 184 (301)
T ss_pred HHHHHHHHHHHhc------------CCCEEEEcCCCchhHHHHHHHHHHcCCC
Confidence 4457777777654 4688888777778999999999999986
No 67
>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=22.05 E-value=1.1e+02 Score=23.77 Aligned_cols=27 Identities=30% Similarity=0.517 Sum_probs=21.6
Q ss_pred chhHHHHHHHHhhcCCChhHHHHHHhhc
Q 037146 128 EAKLKVIKEVRGFTGLGLKESKELVEKV 155 (185)
Q Consensus 128 ~kKi~vIK~VR~it~LgLkEAK~lVe~~ 155 (185)
-..+..|+..|+ +|++|+|-|++++..
T Consensus 44 ~~~l~~I~~lr~-~G~sL~eI~~~l~~~ 70 (133)
T cd04787 44 LSRLRFILSARQ-LGFSLKDIKEILSHA 70 (133)
T ss_pred HHHHHHHHHHHH-cCCCHHHHHHHHhhh
Confidence 367777777774 899999999999853
No 68
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=21.48 E-value=1.6e+02 Score=23.92 Aligned_cols=25 Identities=20% Similarity=0.198 Sum_probs=20.2
Q ss_pred hhHHHHHHHHhhcCCChhHHHHHHhh
Q 037146 129 AKLKVIKEVRGFTGLGLKESKELVEK 154 (185)
Q Consensus 129 kKi~vIK~VR~it~LgLkEAK~lVe~ 154 (185)
..+..|+..|+ +|++|.|-|++++.
T Consensus 55 ~~L~~I~~lr~-lG~sL~eIk~ll~~ 79 (154)
T PRK15002 55 RYVAIIKIAQR-IGIPLATIGEAFGV 79 (154)
T ss_pred HHHHHHHHHHH-cCCCHHHHHHHHHH
Confidence 56677777764 89999999999974
No 69
>COG4575 ElaB Uncharacterized conserved protein [Function unknown]
Probab=21.42 E-value=1e+02 Score=24.15 Aligned_cols=33 Identities=27% Similarity=0.471 Sum_probs=25.9
Q ss_pred hHHHHHHhhcchhhhcC--CCHHHHHHHHHHHHHc
Q 037146 146 KESKELVEKVPTLLKRG--VTKDEADKIVAKLKEV 178 (185)
Q Consensus 146 kEAK~lVe~~P~~IKe~--vsKeeAe~ik~kle~a 178 (185)
-|-+.|++++-.+++.. .+++|+++|+.+++.+
T Consensus 15 ~el~~L~d~lEevL~ssg~~a~~e~~~lR~r~~~~ 49 (104)
T COG4575 15 AELQELLDTLEEVLKSSGSLAGDEAEELRSKAESA 49 (104)
T ss_pred HHHHHHHHHHHHHHHhcccchhhHHHHHHHHHHHH
Confidence 45567888888888765 7789999999988753
No 70
>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=21.36 E-value=40 Score=23.72 Aligned_cols=32 Identities=25% Similarity=0.415 Sum_probs=26.7
Q ss_pred hHHHHHHHHhhcCCChhHHHHHHhhcchhhhc
Q 037146 130 KLKVIKEVRGFTGLGLKESKELVEKVPTLLKR 161 (185)
Q Consensus 130 Ki~vIK~VR~it~LgLkEAK~lVe~~P~~IKe 161 (185)
|-.+|+.|.+-+++.-++++..++.+=.+|.+
T Consensus 3 k~eli~~ia~~~~~s~~~v~~vl~~~~~~i~~ 34 (90)
T PF00216_consen 3 KKELIKRIAEKTGLSKKDVEAVLDALFDVIKE 34 (90)
T ss_dssp HHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHH
Confidence 56899999999999999999999887655544
No 71
>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=21.28 E-value=1.2e+02 Score=22.92 Aligned_cols=25 Identities=24% Similarity=0.488 Sum_probs=20.1
Q ss_pred hhHHHHHHHHhhcCCChhHHHHHHhh
Q 037146 129 AKLKVIKEVRGFTGLGLKESKELVEK 154 (185)
Q Consensus 129 kKi~vIK~VR~it~LgLkEAK~lVe~ 154 (185)
..+..|+.+|+ +|++|.|.|.+++.
T Consensus 44 ~~l~~I~~lr~-~G~sl~eI~~~l~~ 68 (112)
T cd01282 44 DRVRQIRRLLA-AGLTLEEIREFLPC 68 (112)
T ss_pred HHHHHHHHHHH-cCCCHHHHHHHHHH
Confidence 56677777764 89999999999874
No 72
>PRK05087 D-alanine--poly(phosphoribitol) ligase subunit 2; Validated
Probab=21.24 E-value=1.1e+02 Score=22.04 Aligned_cols=21 Identities=19% Similarity=0.313 Sum_probs=18.3
Q ss_pred CCHHHHHHHHHHHHHHhCCCC
Q 037146 60 LSLVEVMDLADVVRNKLGIKE 80 (185)
Q Consensus 60 LtLlE~~eLv~~leekfgv~~ 80 (185)
|.-+.+-+|+-.||++|||.-
T Consensus 34 lDSl~~veli~~lE~~fgi~i 54 (78)
T PRK05087 34 LDSMGTVELLVELENRFDIEV 54 (78)
T ss_pred cchHHHHHHHHHHHHHhCCcc
Confidence 667788999999999999964
No 73
>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=21.14 E-value=1.5e+02 Score=22.27 Aligned_cols=26 Identities=31% Similarity=0.544 Sum_probs=20.5
Q ss_pred hhHHHHHHHHhhcCCChhHHHHHHhhc
Q 037146 129 AKLKVIKEVRGFTGLGLKESKELVEKV 155 (185)
Q Consensus 129 kKi~vIK~VR~it~LgLkEAK~lVe~~ 155 (185)
..+..|+.+|+ +|++|+|.|++++..
T Consensus 45 ~~l~~I~~lr~-~G~sl~eI~~~l~~~ 70 (123)
T cd04770 45 ARLRFIRRAQA-LGFSLAEIRELLSLR 70 (123)
T ss_pred HHHHHHHHHHH-CCCCHHHHHHHHHhh
Confidence 56677777764 599999999999754
No 74
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=21.10 E-value=1.6e+02 Score=23.11 Aligned_cols=25 Identities=28% Similarity=0.555 Sum_probs=20.6
Q ss_pred hhHHHHHHHHhhcCCChhHHHHHHhh
Q 037146 129 AKLKVIKEVRGFTGLGLKESKELVEK 154 (185)
Q Consensus 129 kKi~vIK~VR~it~LgLkEAK~lVe~ 154 (185)
.++..|+.+|+ +|++|+|.+++++.
T Consensus 46 ~~l~~I~~lr~-~G~sL~eI~~~l~~ 70 (140)
T PRK09514 46 QRLRFIRRAKQ-LGFTLEEIRELLSI 70 (140)
T ss_pred HHHHHHHHHHH-cCCCHHHHHHHHHh
Confidence 57777777775 69999999999974
No 75
>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=21.03 E-value=1.2e+02 Score=23.31 Aligned_cols=25 Identities=36% Similarity=0.597 Sum_probs=20.2
Q ss_pred chhHHHHHHHHhhcCCChhHHHHHHh
Q 037146 128 EAKLKVIKEVRGFTGLGLKESKELVE 153 (185)
Q Consensus 128 ~kKi~vIK~VR~it~LgLkEAK~lVe 153 (185)
-..+..|+..| -+|++|+|.+++++
T Consensus 44 l~~l~~I~~lr-~~G~sL~eI~~~l~ 68 (127)
T TIGR02044 44 LDELRLISRAR-QVGFSLEECKELLN 68 (127)
T ss_pred HHHHHHHHHHH-HCCCCHHHHHHHHH
Confidence 35677777776 38999999999997
No 76
>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=20.89 E-value=1.2e+02 Score=22.88 Aligned_cols=27 Identities=33% Similarity=0.384 Sum_probs=23.1
Q ss_pred chhHHHHHHHHhhcCCChhHHHHHHhhc
Q 037146 128 EAKLKVIKEVRGFTGLGLKESKELVEKV 155 (185)
Q Consensus 128 ~kKi~vIK~VR~it~LgLkEAK~lVe~~ 155 (185)
-.++..|+.+|+ +|++|+|-|.+++..
T Consensus 43 ~~~l~~I~~lr~-~G~sl~eI~~~l~~~ 69 (116)
T cd04769 43 VECLRFIKEARQ-LGFTLAELKAIFAGH 69 (116)
T ss_pred HHHHHHHHHHHH-cCCCHHHHHHHHhcc
Confidence 478888888886 899999999999764
No 77
>cd08497 PBP2_NikA_DppA_OppA_like_14 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=20.74 E-value=1.7e+02 Score=26.80 Aligned_cols=43 Identities=19% Similarity=0.254 Sum_probs=33.2
Q ss_pred CChhHHHHHHhhcchhhh--------------------cCCCHHHHHHHHHHHHHcCCEEEeC
Q 037146 143 LGLKESKELVEKVPTLLK--------------------RGVTKDEADKIVAKLKEVGAQVSME 185 (185)
Q Consensus 143 LgLkEAK~lVe~~P~~IK--------------------e~vsKeeAe~ik~kle~aGA~VelE 185 (185)
.++..||+|++.+-.... .+..+.-|+.++..|+++|-+|+++
T Consensus 318 ~d~~kAk~lL~~aG~~~~~g~~~~~~~G~~l~l~~~~~~~~~~~~a~~i~~~l~~iGi~v~i~ 380 (491)
T cd08497 318 FNLRKALELLAEAGWTVRGGDILVNADGEPLSFEILLDSPTFERVLLPYVRNLKKLGIDASLR 380 (491)
T ss_pred CCHHHHHHHHHHcCCccCCCCEEECCCCCEEEEEEEeCCCcHHHHHHHHHHHHHhcCceEEEe
Confidence 579999999998754311 1235677999999999999999874
No 78
>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=20.72 E-value=1.2e+02 Score=23.41 Aligned_cols=24 Identities=25% Similarity=0.495 Sum_probs=20.3
Q ss_pred hhHHHHHHHHhhcCCChhHHHHHHh
Q 037146 129 AKLKVIKEVRGFTGLGLKESKELVE 153 (185)
Q Consensus 129 kKi~vIK~VR~it~LgLkEAK~lVe 153 (185)
.++..|+..|+ +|++|+|-|++++
T Consensus 45 ~~l~~I~~lr~-lG~sL~eI~~~l~ 68 (127)
T TIGR02047 45 ERLAFIRNCRT-LDMSLAEIRQLLR 68 (127)
T ss_pred HHHHHHHHHHH-cCCCHHHHHHHHH
Confidence 57777777774 8999999999987
No 79
>COG0236 AcpP Acyl carrier protein [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]
Probab=20.67 E-value=1e+02 Score=21.65 Aligned_cols=23 Identities=17% Similarity=0.371 Sum_probs=19.3
Q ss_pred hcCCHHHHHHHHHHHHHHhCCCC
Q 037146 58 SCLSLVEVMDLADVVRNKLGIKE 80 (185)
Q Consensus 58 ~~LtLlE~~eLv~~leekfgv~~ 80 (185)
..+.=+.+.+|+-.||++||+.-
T Consensus 35 lg~DSld~veLi~~lE~~f~i~i 57 (80)
T COG0236 35 LGLDSLDLVELVMALEEEFGIEI 57 (80)
T ss_pred cCccHHHHHHHHHHHHHHHCCcC
Confidence 45666788999999999999964
No 80
>cd02932 OYE_YqiM_FMN Old yellow enzyme (OYE) YqjM-like FMN binding domain. YqjM is involved in the oxidative stress response of Bacillus subtilis. Like the other OYE members, each monomer of YqjM contains FMN as a non-covalently bound cofactor and uses NADPH as a reducing agent. The YqjM enzyme exists as a homotetramer that is assembled as a dimer of catalytically dependent dimers, while other OYE members exist only as monomers or dimers. Moreover, the protein displays a shared active site architecture where an arginine finger at the COOH terminus of one monomer extends into the active site of the adjacent monomer and is directly involved in substrate recognition. Another remarkable difference in the binding of the ligand in YqjM is represented by the contribution of the NH2-terminal tyrosine instead of a COOH-terminal tyrosine in OYE and its homologs.
Probab=20.49 E-value=1.3e+02 Score=26.71 Aligned_cols=41 Identities=24% Similarity=0.429 Sum_probs=29.9
Q ss_pred HHHHHHHHhhcCCChhHHHHHHhhcchhhh--------cCCCHHHHHHHHHHHHHcCCE
Q 037146 131 LKVIKEVRGFTGLGLKESKELVEKVPTLLK--------RGVTKDEADKIVAKLKEVGAQ 181 (185)
Q Consensus 131 i~vIK~VR~it~LgLkEAK~lVe~~P~~IK--------e~vsKeeAe~ik~kle~aGA~ 181 (185)
+.||+.||+.+|= ..|-.|| .|.+.+|+.++.+.|++.|..
T Consensus 208 ~eiv~aIR~~vG~----------d~~v~vri~~~~~~~~g~~~~e~~~ia~~Le~~gvd 256 (336)
T cd02932 208 LEVVDAVRAVWPE----------DKPLFVRISATDWVEGGWDLEDSVELAKALKELGVD 256 (336)
T ss_pred HHHHHHHHHHcCC----------CceEEEEEcccccCCCCCCHHHHHHHHHHHHHcCCC
Confidence 6889999987641 1233333 677899999999999998853
No 81
>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=20.47 E-value=1.2e+02 Score=23.14 Aligned_cols=26 Identities=35% Similarity=0.496 Sum_probs=20.5
Q ss_pred hhHHHHHHHHhhcCCChhHHHHHHhhc
Q 037146 129 AKLKVIKEVRGFTGLGLKESKELVEKV 155 (185)
Q Consensus 129 kKi~vIK~VR~it~LgLkEAK~lVe~~ 155 (185)
.++..|+.+|. +|++|+|.|++++..
T Consensus 45 ~~l~~I~~lr~-~G~sL~eI~~~l~~~ 70 (126)
T cd04783 45 TRLRFIKRAQE-LGFTLDEIAELLELD 70 (126)
T ss_pred HHHHHHHHHHH-cCCCHHHHHHHHhcc
Confidence 56667777664 899999999999854
No 82
>PF00550 PP-binding: Phosphopantetheine attachment site; InterPro: IPR006163 Phosphopantetheine (or pantetheine 4' phosphate) is the prosthetic group of acyl carrier proteins (ACP) in some multienzyme complexes where it serves as a 'swinging arm' for the attachment of activated fatty acid and amino-acid groups []. The amino-terminal region of the ACP proteins is well defined and consists of alpha four helices arranged in a right-handed bundle held together by interhelical hydrophobic interactions. The Asp-Ser-Leu (DSL)motif is conserved in all of the ACP sequences, and the 4'-PP prosthetic group is covalently linked via a phosphodiester bond to the serine residue. The DSL sequence is present at the amino terminus of helix II, a domain of the protein referred to as the recognition helix and which is responsible for the interaction of ACPs with the enzymes of type II fatty acid synthesis [].; GO: 0048037 cofactor binding; PDB: 3EJB_E 3EJE_G 1L0I_A 2FHS_C 3EJD_E 2FAE_B 2FAD_B 2FAC_B 2K94_A 1ACP_A ....
Probab=20.47 E-value=1.4e+02 Score=19.36 Aligned_cols=24 Identities=21% Similarity=0.360 Sum_probs=19.5
Q ss_pred hcCCHHHHHHHHHHHHHHhCCCCC
Q 037146 58 SCLSLVEVMDLADVVRNKLGIKEM 81 (185)
Q Consensus 58 ~~LtLlE~~eLv~~leekfgv~~~ 81 (185)
..++-+.+.+|+..|+++||+.-.
T Consensus 27 lG~DSl~~~~l~~~l~~~~g~~i~ 50 (67)
T PF00550_consen 27 LGLDSLDAIELVSELEEEFGIKIP 50 (67)
T ss_dssp TTSSHHHHHHHHHHHHHHHTSSTT
T ss_pred hCCchHHHHHHHHHHHHHHcCCCC
Confidence 456677889999999999998644
No 83
>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region. Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model.
Probab=20.45 E-value=2e+02 Score=19.53 Aligned_cols=40 Identities=25% Similarity=0.405 Sum_probs=27.8
Q ss_pred HHHh-hcCCChhHHHHHHhhcc--------hhh--hcCCCHHHHHHHHHHH
Q 037146 136 EVRG-FTGLGLKESKELVEKVP--------TLL--KRGVTKDEADKIVAKL 175 (185)
Q Consensus 136 ~VR~-it~LgLkEAK~lVe~~P--------~~I--Ke~vsKeeAe~ik~kl 175 (185)
++.. +.|+|.+.|+.+++.-+ .-+ -.|++++-|+.|+..+
T Consensus 17 ~L~~~ipgig~~~a~~Il~~R~~~g~~~s~~dL~~v~gi~~~~~~~i~~~~ 67 (69)
T TIGR00426 17 ELQRAMNGVGLKKAEAIVSYREEYGPFKTVEDLKQVPGIGNSLVEKNLAVI 67 (69)
T ss_pred HHHhHCCCCCHHHHHHHHHHHHHcCCcCCHHHHHcCCCCCHHHHHHHHhhc
Confidence 5555 67888888888888732 112 2478888888887654
No 84
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=20.43 E-value=1.3e+02 Score=22.26 Aligned_cols=28 Identities=36% Similarity=0.500 Sum_probs=22.2
Q ss_pred chhHHHHHHHHhhcCCChhHHHHHHhhcc
Q 037146 128 EAKLKVIKEVRGFTGLGLKESKELVEKVP 156 (185)
Q Consensus 128 ~kKi~vIK~VR~it~LgLkEAK~lVe~~P 156 (185)
-..+.+|+..| .+|+.|++-|++++...
T Consensus 44 l~~l~~I~~~r-~~G~~L~~I~~~l~~~~ 71 (124)
T COG0789 44 LELLQIIKTLR-ELGFSLAEIKELLDLLS 71 (124)
T ss_pred HHHHHHHHHHH-HcCCCHHHHHHHHhccc
Confidence 45666777666 68999999999998765
No 85
>cd05833 Ribosomal_P2 Ribosomal protein P2. This subfamily represents the eukaryotic large ribosomal protein P2. Eukaryotic P1 and P2 are functionally equivalent to the bacterial protein L7/L12, but are not homologous to L7/L12. P2 is located in the L12 stalk, with proteins P1, P0, L11, and 28S rRNA. P1 and P2 are the only proteins in the ribosome to occur as multimers, always appearing as sets of heterodimers. Recent data indicate that eukaryotes have four copies (two heterodimers), while most archaeal species contain six copies of L12p (three homodimers). Bacteria may have four or six copies of L7/L12 (two or three homodimers) depending on the species. Experiments using S. cerevisiae P1 and P2 indicate that P1 proteins are positioned more internally with limited reactivity in the C-terminal domains, while P2 proteins seem to be more externally located and are more likely to interact with other cellular components. In lower eukaryotes, P1 and P2 are further subdivided into P1A, P1B, P2
Probab=20.05 E-value=2.6e+02 Score=21.70 Aligned_cols=31 Identities=19% Similarity=0.299 Sum_probs=22.7
Q ss_pred CCChhHHHHHHHHhcCCHHHHHHHHHHHHHHhCC
Q 037146 45 EPSEKVASIVDEISCLSLVEVMDLADVVRNKLGI 78 (185)
Q Consensus 45 ~~s~KV~~Ivd~I~~LtLlE~~eLv~~leekfgv 78 (185)
....++.-+++.|..-++ .+|+.....+++-
T Consensus 34 Ve~~~~~lf~~~L~GKdi---~eLIa~g~~kl~s 64 (109)
T cd05833 34 VDDEKLNKVISELEGKDV---EELIAAGKEKLAS 64 (109)
T ss_pred ccHHHHHHHHHHHcCCCH---HHHHHHhHhhhcC
Confidence 455677788888887665 6778888888764
Done!