Query 030925
Match_columns 169
No_of_seqs 129 out of 1130
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 06:38:50 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030925.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030925hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 CHL00083 rpl12 ribosomal prote 100.0 3.4E-42 7.5E-47 270.1 14.1 130 38-169 2-131 (131)
2 KOG1715 Mitochondrial/chloropl 100.0 4.5E-42 9.8E-47 282.1 15.4 135 34-169 53-187 (187)
3 cd00387 Ribosomal_L7_L12 Ribos 100.0 1.1E-41 2.5E-46 265.6 14.2 127 39-168 1-127 (127)
4 TIGR00855 L12 ribosomal protei 100.0 1.8E-39 4E-44 253.3 13.7 122 40-169 5-126 (126)
5 PRK00157 rplL 50S ribosomal pr 100.0 4.2E-39 9.2E-44 250.4 13.7 122 38-169 2-123 (123)
6 COG0222 RplL Ribosomal protein 100.0 1.3E-38 2.9E-43 247.2 12.3 122 39-169 3-124 (124)
7 PF00542 Ribosomal_L12: Riboso 99.9 5.9E-25 1.3E-29 155.2 5.4 68 101-169 1-68 (68)
8 PRK06771 hypothetical protein; 97.9 1.2E-05 2.6E-10 60.5 3.1 29 111-139 65-93 (93)
9 PF02617 ClpS: ATP-dependent C 89.1 1.1 2.4E-05 31.8 5.1 65 98-163 3-71 (82)
10 PRK00033 clpS ATP-dependent Cl 77.9 17 0.00038 27.5 7.6 72 97-169 23-98 (100)
11 KOG3449 60S acidic ribosomal p 61.6 23 0.00049 27.8 5.1 37 35-74 33-70 (112)
12 PRK13019 clpS ATP-dependent Cl 60.1 52 0.0011 24.6 6.7 72 96-167 16-91 (94)
13 COG0264 Tsf Translation elonga 59.4 9.4 0.0002 34.3 3.0 28 113-140 4-31 (296)
14 PRK12332 tsf elongation factor 58.9 11 0.00024 31.6 3.3 29 115-143 5-33 (198)
15 PF09278 MerR-DNA-bind: MerR, 57.1 17 0.00037 23.9 3.4 22 114-136 3-24 (65)
16 TIGR00116 tsf translation elon 56.9 12 0.00026 33.2 3.3 29 115-143 5-33 (290)
17 PRK10664 transcriptional regul 56.8 5.8 0.00013 28.9 1.1 36 113-148 2-37 (90)
18 PRK09377 tsf elongation factor 55.0 13 0.00029 32.9 3.3 29 115-143 6-34 (290)
19 cd04788 HTH_NolA-AlbR Helix-Tu 54.7 29 0.00063 25.1 4.5 47 112-160 44-90 (96)
20 PRK10753 transcriptional regul 54.3 6.7 0.00015 28.5 1.1 35 113-147 2-36 (90)
21 cd00591 HU_IHF Integration hos 49.2 17 0.00037 25.2 2.5 35 113-147 1-35 (87)
22 PF14520 HHH_5: Helix-hairpin- 48.1 54 0.0012 21.6 4.7 46 116-161 2-60 (60)
23 PF02022 Integrase_Zn: Integra 47.9 25 0.00054 22.5 2.9 27 118-144 12-38 (40)
24 smart00411 BHL bacterial (prok 47.8 17 0.00037 25.4 2.3 36 113-148 2-37 (90)
25 cd04774 HTH_YfmP Helix-Turn-He 45.7 55 0.0012 23.9 4.8 31 112-142 43-73 (96)
26 cd01107 HTH_BmrR Helix-Turn-He 45.1 47 0.001 24.5 4.5 29 112-141 45-73 (108)
27 PF13411 MerR_1: MerR HTH fami 43.6 24 0.00052 23.2 2.4 26 112-138 43-68 (69)
28 PF10925 DUF2680: Protein of u 39.1 53 0.0012 22.6 3.6 26 133-161 21-47 (59)
29 PF10044 Ret_tiss: Retinal tis 39.1 22 0.00047 27.0 1.8 23 116-138 62-88 (95)
30 cd04766 HTH_HspR Helix-Turn-He 38.8 90 0.0019 22.1 5.0 41 112-162 44-84 (91)
31 PRK00285 ihfA integration host 34.9 35 0.00077 24.7 2.3 35 113-147 4-38 (99)
32 TIGR02043 ZntR Zn(II)-responsi 34.8 74 0.0016 24.3 4.2 26 112-138 45-70 (131)
33 PF11363 DUF3164: Protein of u 34.4 56 0.0012 27.3 3.7 83 40-148 35-117 (195)
34 PF11272 DUF3072: Protein of u 33.7 46 0.001 23.2 2.6 19 50-68 38-56 (57)
35 cd04768 HTH_BmrR-like Helix-Tu 33.7 1E+02 0.0022 22.3 4.6 28 112-140 44-71 (96)
36 cd01104 HTH_MlrA-CarA Helix-Tu 33.5 51 0.0011 21.5 2.8 24 113-137 45-68 (68)
37 cd04763 HTH_MlrA-like Helix-Tu 33.4 51 0.0011 21.9 2.8 23 113-136 45-67 (68)
38 cd04782 HTH_BltR Helix-Turn-He 32.3 91 0.002 22.5 4.2 26 113-139 45-70 (97)
39 cd04780 HTH_MerR-like_sg5 Heli 31.5 63 0.0014 23.6 3.2 27 112-138 44-70 (95)
40 cd01105 HTH_GlnR-like Helix-Tu 31.1 64 0.0014 23.0 3.1 26 112-138 45-70 (88)
41 cd04781 HTH_MerR-like_sg6 Heli 28.8 1.7E+02 0.0037 21.8 5.3 26 113-139 44-69 (120)
42 PRK13752 putative transcriptio 27.9 1.1E+02 0.0025 24.0 4.3 25 113-138 52-76 (144)
43 cd01106 HTH_TipAL-Mta Helix-Tu 27.0 1.6E+02 0.0034 21.3 4.7 27 113-140 45-71 (103)
44 cd01109 HTH_YyaN Helix-Turn-He 27.0 78 0.0017 23.3 3.1 26 113-139 45-70 (113)
45 cd01108 HTH_CueR Helix-Turn-He 26.9 1.3E+02 0.0027 22.8 4.3 25 113-138 45-69 (127)
46 PRK10227 DNA-binding transcrip 26.7 1.1E+02 0.0024 23.7 4.0 25 113-138 45-69 (135)
47 PRK05412 putative nucleotide-b 26.5 65 0.0014 26.7 2.7 64 103-167 45-120 (161)
48 cd04777 HTH_MerR-like_sg1 Heli 26.3 83 0.0018 22.9 3.1 25 113-138 43-67 (107)
49 cd04764 HTH_MlrA-like_sg1 Heli 25.1 88 0.0019 20.6 2.8 23 113-136 44-66 (67)
50 PRK00199 ihfB integration host 24.9 36 0.00077 24.4 0.9 35 113-147 2-37 (94)
51 PRK05350 acyl carrier protein; 24.5 96 0.0021 21.6 3.0 26 44-70 32-57 (82)
52 cd04767 HTH_HspR-like_MBC Heli 24.3 1E+02 0.0022 24.0 3.3 33 112-144 43-75 (120)
53 TIGR00517 acyl_carrier acyl ca 24.0 82 0.0018 21.3 2.5 22 49-70 33-54 (77)
54 cd04784 HTH_CadR-PbrR Helix-Tu 23.9 91 0.002 23.4 3.0 25 113-138 45-69 (127)
55 PF04461 DUF520: Protein of un 23.8 53 0.0012 27.1 1.8 64 103-167 45-120 (160)
56 cd04783 HTH_MerR1 Helix-Turn-H 23.7 1.5E+02 0.0033 22.2 4.2 26 113-139 45-70 (126)
57 PF14645 Chibby: Chibby family 23.5 44 0.00096 25.8 1.2 21 1-21 1-21 (116)
58 smart00422 HTH_MERR helix_turn 23.4 1.1E+02 0.0024 19.8 3.0 25 112-137 44-68 (70)
59 PRK08385 nicotinate-nucleotide 22.8 1.1E+02 0.0024 26.9 3.7 43 127-169 190-235 (278)
60 PF00216 Bac_DNA_binding: Bact 22.8 70 0.0015 22.1 2.1 34 113-146 2-35 (90)
61 cd04411 Ribosomal_P1_P2_L12p R 22.3 2.6E+02 0.0056 21.2 5.2 30 36-68 33-62 (105)
62 COG0236 AcpP Acyl carrier prot 22.1 90 0.002 21.6 2.5 22 49-70 35-56 (80)
63 cd02810 DHOD_DHPD_FMN Dihydroo 21.9 1.3E+02 0.0028 25.3 3.8 40 115-166 151-192 (289)
64 PRK15002 redox-sensitivie tran 21.7 1.7E+02 0.0037 23.4 4.3 25 113-138 55-79 (154)
65 CHL00124 acpP acyl carrier pro 21.5 1.4E+02 0.003 20.4 3.3 22 49-70 35-56 (82)
66 COG0789 SoxR Predicted transcr 21.1 1.2E+02 0.0026 22.0 3.1 29 112-141 44-72 (124)
67 PRK09514 zntR zinc-responsive 21.0 1.8E+02 0.0038 22.6 4.2 25 113-138 46-70 (140)
68 cd04787 HTH_HMRTR_unk Helix-Tu 20.8 1.2E+02 0.0025 23.2 3.1 26 113-139 45-70 (133)
69 PF00828 Ribosomal_L18e: Ribos 20.5 94 0.002 23.5 2.5 27 138-168 101-128 (129)
70 TIGR02054 MerD mercuric resist 20.5 1.2E+02 0.0026 23.3 3.1 27 113-140 48-74 (120)
71 cd05833 Ribosomal_P2 Ribosomal 20.4 3.3E+02 0.0072 20.8 5.5 30 37-69 35-64 (109)
72 cd04740 DHOD_1B_like Dihydroor 20.4 1.2E+02 0.0027 25.6 3.4 38 116-165 144-181 (296)
73 TIGR01037 pyrD_sub1_fam dihydr 20.3 1.2E+02 0.0027 25.8 3.4 41 114-166 145-185 (300)
74 PRK13844 recombination protein 20.2 2.5E+02 0.0053 23.9 5.1 45 115-164 11-55 (200)
75 cd04770 HTH_HMRTR Helix-Turn-H 20.1 1.7E+02 0.0037 21.7 3.8 26 113-139 45-70 (123)
No 1
>CHL00083 rpl12 ribosomal protein L12
Probab=100.00 E-value=3.4e-42 Score=270.10 Aligned_cols=130 Identities=39% Similarity=0.595 Sum_probs=112.2
Q ss_pred ChhHHHHHHHHhcCCHHHHHHHHHHHHHHhCCCCCCCCCCCCCCCCCCCCCCCchhhhhhhcceeeEEEeecCcchhHHH
Q 030925 38 TQKLERISDELLDLTKLERYDFATLLGCKLGLDRFGPVVPAFPSSGPAASGSTSAETKAAEKTAFDVKLEKYDQAAKIKI 117 (169)
Q Consensus 38 s~kv~~Ivd~I~~LtLlE~seLv~~leekfgv~~~a~~~~~~~~~~~aa~~~~~~~~~~~EKt~f~V~L~~~~~~kKi~v 117 (169)
|+++++|+|+|++|||+|++||++.|+++|||++.++++++++ +++++++ +.++++.+|||+|||+|++||+++||+|
T Consensus 2 s~k~~~ivd~i~~LTllE~~eLv~~le~~fgv~~~~~~a~~~~-~~~a~~~-~~~~~~~~EKT~F~V~L~~~~~~~Ki~v 79 (131)
T CHL00083 2 STKINEIIEELKSLTLLEAAELVKQIEETFGVDASAPVGGGMM-SAPAAAA-AQAAEEVEEKTEFDVILEEVPADKRIAV 79 (131)
T ss_pred CchHHHHHHHHHhCCHHHHHHHHHHHHHHcCCCccchhhhhhc-cccCccc-ccccchhhhcceeeEEEeecCCcchHHH
Confidence 7899999999999999999999999999999998765432211 1111111 1123457899999999999988999999
Q ss_pred HHHHHHhhCCChhHHHHHHhhcchhhhcCCCHHHHHHHHHHHHHcCcEEEeC
Q 030925 118 IKEVKTFTGLGLKESKDLVEKAPAVIKKGVTKEEADKIVEKLKELNAIVVLE 169 (169)
Q Consensus 118 IK~VR~it~LgLkEAK~lVe~~P~~IKe~vsKeeAE~ik~kLe~aGA~veiE 169 (169)
||+||++|||||+|||+|||++|++||+|++|+|||+||++|+++||+|+|.
T Consensus 80 IK~vr~it~lgLkeaK~lVe~~P~~ike~v~KeeAe~ik~~le~~Ga~v~lk 131 (131)
T CHL00083 80 LKVVRSLTGLGLKEAKELVESLPKTIKEGISKEEAEEAKKQLEEAGAKVIIK 131 (131)
T ss_pred HHHHHHHcCCCHHHHHHHHHhCCHHHHhCCCHHHHHHHHHHHHHcCCEEEeC
Confidence 9999999999999999999999999999999999999999999999999983
No 2
>KOG1715 consensus Mitochondrial/chloroplast ribosomal protein L12 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.5e-42 Score=282.08 Aligned_cols=135 Identities=47% Similarity=0.651 Sum_probs=116.9
Q ss_pred cccCChhHHHHHHHHhcCCHHHHHHHHHHHHHHhCCCCCCCCCCCCCCCCCCCCCCCchhhhhhhcceeeEEEeecCcch
Q 030925 34 TESRTQKLERISDELLDLTKLERYDFATLLGCKLGLDRFGPVVPAFPSSGPAASGSTSAETKAAEKTAFDVKLEKYDQAA 113 (169)
Q Consensus 34 ~~~~s~kv~~Ivd~I~~LtLlE~seLv~~leekfgv~~~a~~~~~~~~~~~aa~~~~~~~~~~~EKt~f~V~L~~~~~~k 113 (169)
+...++||.+|+|+|++|||+|.+||+++|+++|||+..+.++++++.+++.. +++..++.++|+|.|||+|++||+..
T Consensus 53 ~~~~~~KI~~iv~eIssLtLlE~s~L~~~Lk~kl~i~e~~~~~a~~~g~~~~~-~~~a~ee~k~ekt~FdVkL~~fda~~ 131 (187)
T KOG1715|consen 53 AVPPPPKISKIVDEISSLTLLETSDLVDLLKKKLNIPELPLAPAAAAGAAAPD-AGGAEEEAKKEKTTFDVKLEKFDASS 131 (187)
T ss_pred ccCCCHHHHHHHHHHHhcCHHHHHHHHHHHHHHcCCCcccchhhccccCCCCC-cccccccchhhcceEEEEEeecCccc
Confidence 37789999999999999999999999999999999998865443222212111 12224566778888999999999999
Q ss_pred hHHHHHHHHHhhCCChhHHHHHHhhcchhhhcCCCHHHHHHHHHHHHHcCcEEEeC
Q 030925 114 KIKIIKEVKTFTGLGLKESKDLVEKAPAVIKKGVTKEEADKIVEKLKELNAIVVLE 169 (169)
Q Consensus 114 Ki~vIK~VR~it~LgLkEAK~lVe~~P~~IKe~vsKeeAE~ik~kLe~aGA~veiE 169 (169)
||+|||+||.+|||||+|||+|||++|+.+|+|++|||||+||++|+++||+|+||
T Consensus 132 KIkVIKEVR~~tgL~LkeAKklVE~aP~ilKegvtKeEAEkik~kLea~GakV~le 187 (187)
T KOG1715|consen 132 KIKVIKEVRALTGLGLKEAKKLVEKAPKILKEGVTKEEAEEIKEKLEAAGAKVVLE 187 (187)
T ss_pred hhHHHHHHHHhccccHHHHHHHHHhccHHHHcCCCHHHHHHHHHHHHHcCCeEeeC
Confidence 99999999999999999999999999999999999999999999999999999997
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=1.1e-41 Score=265.58 Aligned_cols=127 Identities=48% Similarity=0.662 Sum_probs=107.9
Q ss_pred hhHHHHHHHHhcCCHHHHHHHHHHHHHHhCCCCCCCCCCCCCCCCCCCCCCCchhhhhhhcceeeEEEeecCcchhHHHH
Q 030925 39 QKLERISDELLDLTKLERYDFATLLGCKLGLDRFGPVVPAFPSSGPAASGSTSAETKAAEKTAFDVKLEKYDQAAKIKII 118 (169)
Q Consensus 39 ~kv~~Ivd~I~~LtLlE~seLv~~leekfgv~~~a~~~~~~~~~~~aa~~~~~~~~~~~EKt~f~V~L~~~~~~kKi~vI 118 (169)
+++++|+|+|++|||+|++||++.|+++|||++.+++++++ +++|+++ ..++++.+|||+|||+|++||+++||+||
T Consensus 1 ~~~~~i~d~i~~LtllE~~eLv~~le~~~gv~~~~~~~~~~-~~a~~~~--~~~~~~~~EKt~F~V~L~~~~~~~Ki~vI 77 (127)
T cd00387 1 LKVEEIVEALKELTLLEAAELVKALEEKFGVSASAAAAAAA-AAAPAAA--AAAAAEAEEKTEFDVVLESFGAAKKIAVI 77 (127)
T ss_pred CcHHHHHHHHHhCCHHHHHHHHHHHHHHhCCCccccccccc-ccCcccc--cccccchhhcceEEEEEeeCCchhhHHHH
Confidence 36899999999999999999999999999999763222111 1112211 11223367999999999999988999999
Q ss_pred HHHHHhhCCChhHHHHHHhhcchhhhcCCCHHHHHHHHHHHHHcCcEEEe
Q 030925 119 KEVKTFTGLGLKESKDLVEKAPAVIKKGVTKEEADKIVEKLKELNAIVVL 168 (169)
Q Consensus 119 K~VR~it~LgLkEAK~lVe~~P~~IKe~vsKeeAE~ik~kLe~aGA~vei 168 (169)
|+||++|||||+|||+|||++|++||+|+||+|||+||++|+++||+|+|
T Consensus 78 K~VR~it~LgLkEAK~lVe~~P~~iKe~vsKeeAE~ik~kLe~aGA~Vel 127 (127)
T cd00387 78 KEVREITGLGLKEAKDLVESAPKVLKEGVSKEEAEEIKKKLEEAGAKVEL 127 (127)
T ss_pred HHHHHHhCCChHHHHHHHHhCcHHHHhCCCHHHHHHHHHHHHHcCCEEeC
Confidence 99999999999999999999999999999999999999999999999986
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=1.8e-39 Score=253.32 Aligned_cols=122 Identities=43% Similarity=0.596 Sum_probs=106.2
Q ss_pred hHHHHHHHHhcCCHHHHHHHHHHHHHHhCCCCCCCCCCCCCCCCCCCCCCCchhhhhhhcceeeEEEeecCcchhHHHHH
Q 030925 40 KLERISDELLDLTKLERYDFATLLGCKLGLDRFGPVVPAFPSSGPAASGSTSAETKAAEKTAFDVKLEKYDQAAKIKIIK 119 (169)
Q Consensus 40 kv~~Ivd~I~~LtLlE~seLv~~leekfgv~~~a~~~~~~~~~~~aa~~~~~~~~~~~EKt~f~V~L~~~~~~kKi~vIK 119 (169)
+.++|+|+|++|||+|++||++.|+++|||++.++++++. + +++ + ++++.+|||+|||+|+.++ ++||+|||
T Consensus 5 ~~~~ive~i~~LTllE~~eLv~~lee~fgV~a~a~~a~~~--a--~~~-~--~~~~~eEKt~f~V~L~~~~-~~Ki~vIK 76 (126)
T TIGR00855 5 SKEQIIEALKEMTVLELSELVKALEEKFGVSAAAPVAAGA--A--GAA-A--AAAAAEEKTEFDVILKGAG-DNKIAVIK 76 (126)
T ss_pred cHHHHHHHHHhCCHHHHHHHHHHHHHhcCCCccchhhhcc--c--ccc-c--ccccccccceeeEEEecCC-cchhHHHH
Confidence 4689999999999999999999999999999876543211 1 111 1 1234679999999999886 68999999
Q ss_pred HHHHhhCCChhHHHHHHhhcchhhhcCCCHHHHHHHHHHHHHcCcEEEeC
Q 030925 120 EVKTFTGLGLKESKDLVEKAPAVIKKGVTKEEADKIVEKLKELNAIVVLE 169 (169)
Q Consensus 120 ~VR~it~LgLkEAK~lVe~~P~~IKe~vsKeeAE~ik~kLe~aGA~veiE 169 (169)
+||++|||||+|||+|||++|++||+|++|+|||++|++|+++||+|+|.
T Consensus 77 ~vR~itgLgLkEAK~lVe~~P~~ike~vsKeeAe~ik~~Le~aGa~veik 126 (126)
T TIGR00855 77 VVREITGLGLKEAKDLVEGAPKVLKEGVSKEEAEELKKKLEEAGAKVEVK 126 (126)
T ss_pred HHHHHcCCcHHHHHHHHHhCcHHHHhCCCHHHHHHHHHHHHHcCCEEEeC
Confidence 99999999999999999999999999999999999999999999999983
No 5
>PRK00157 rplL 50S ribosomal protein L7/L12; Reviewed
Probab=100.00 E-value=4.2e-39 Score=250.39 Aligned_cols=122 Identities=47% Similarity=0.621 Sum_probs=107.3
Q ss_pred ChhHHHHHHHHhcCCHHHHHHHHHHHHHHhCCCCCCCCCCCCCCCCCCCCCCCchhhhhhhcceeeEEEeecCcchhHHH
Q 030925 38 TQKLERISDELLDLTKLERYDFATLLGCKLGLDRFGPVVPAFPSSGPAASGSTSAETKAAEKTAFDVKLEKYDQAAKIKI 117 (169)
Q Consensus 38 s~kv~~Ivd~I~~LtLlE~seLv~~leekfgv~~~a~~~~~~~~~~~aa~~~~~~~~~~~EKt~f~V~L~~~~~~kKi~v 117 (169)
+-++++|+|+|++|||+|++||++.|+++|||++.++++++ ++++ .++..+|||+|||+|++| +++||+|
T Consensus 2 ~~~~~~i~e~i~~LtllE~~eLv~~lee~fgv~a~~~~~~~-----~~~~----~~~~~eEkt~f~V~L~~~-~~kKi~v 71 (123)
T PRK00157 2 ALTKEQIIEALKEMTVLELSELVKALEEKFGVSAAAPVAAA-----AAAA----AAAAAEEKTEFDVVLKSA-GDKKIAV 71 (123)
T ss_pred CccHHHHHHHHHhCCHHHHHHHHHHHHHHcCCCccchhccc-----cccc----cccccccccceeEEEecc-chhhHHH
Confidence 34689999999999999999999999999999987653221 1111 123467999999999999 5799999
Q ss_pred HHHHHHhhCCChhHHHHHHhhcchhhhcCCCHHHHHHHHHHHHHcCcEEEeC
Q 030925 118 IKEVKTFTGLGLKESKDLVEKAPAVIKKGVTKEEADKIVEKLKELNAIVVLE 169 (169)
Q Consensus 118 IK~VR~it~LgLkEAK~lVe~~P~~IKe~vsKeeAE~ik~kLe~aGA~veiE 169 (169)
||+||++|||||+|||+|||++|++||+|++|+|||++|++|+++||+|+|.
T Consensus 72 IK~vR~itgLgLkEAK~lVe~~P~~ike~v~keeAe~ik~~Le~aGa~velk 123 (123)
T PRK00157 72 IKAVREITGLGLKEAKDLVEGAPKVVKEGVSKEEAEEIKKKLEEAGAKVELK 123 (123)
T ss_pred HHHHHHHhCCCHHHHHHHHHhCCHHHHhCCCHHHHHHHHHHHHHcCCEEeeC
Confidence 9999999999999999999999999999999999999999999999999984
No 6
>COG0222 RplL Ribosomal protein L7/L12 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.3e-38 Score=247.23 Aligned_cols=122 Identities=48% Similarity=0.626 Sum_probs=107.5
Q ss_pred hhHHHHHHHHhcCCHHHHHHHHHHHHHHhCCCCCCCCCCCCCCCCCCCCCCCchhhhhhhcceeeEEEeecCcchhHHHH
Q 030925 39 QKLERISDELLDLTKLERYDFATLLGCKLGLDRFGPVVPAFPSSGPAASGSTSAETKAAEKTAFDVKLEKYDQAAKIKII 118 (169)
Q Consensus 39 ~kv~~Ivd~I~~LtLlE~seLv~~leekfgv~~~a~~~~~~~~~~~aa~~~~~~~~~~~EKt~f~V~L~~~~~~kKi~vI 118 (169)
..+++|++.|++||++|+++|++.++++|||++.+|++.++ ++ ++ .++..+|||+|||+|.++ +++||+||
T Consensus 3 ~~~e~iie~i~~~svlel~eLvk~~eekfgVsaaa~va~a~--~~--a~----a~~aaeEktefdVvL~~~-g~kKI~VI 73 (124)
T COG0222 3 LTKEQIIEALKELTVLELSELVKALEEKFGVTAAAPVAAAA--AG--AA----AAEAAEEKTEFDVVLKSA-GGKKIAVI 73 (124)
T ss_pred CcHHHHHHHHHHhhHHHHHHHHHHHHHHhCCccchhhhhcc--cc--cc----ccccccccceeEEEeccc-CCcchhHH
Confidence 35789999999999999999999999999999887744321 11 11 123367999999999999 58999999
Q ss_pred HHHHHhhCCChhHHHHHHhhcchhhhcCCCHHHHHHHHHHHHHcCcEEEeC
Q 030925 119 KEVKTFTGLGLKESKDLVEKAPAVIKKGVTKEEADKIVEKLKELNAIVVLE 169 (169)
Q Consensus 119 K~VR~it~LgLkEAK~lVe~~P~~IKe~vsKeeAE~ik~kLe~aGA~veiE 169 (169)
|+||++|||||||||++||++|++||+|++|+|||++|++|+++||+|++.
T Consensus 74 K~vR~itGLGLKEAKdlVe~aP~~~KE~v~k~eAe~~kkkleeaGa~V~~k 124 (124)
T COG0222 74 KVVRELTGLGLKEAKDLVEGAPKVLKEGVSKEEAEEIKKKLEEAGAKVELK 124 (124)
T ss_pred HHHHHHhcccHHHHHHHHHhCcHHHHccCCHHHHHHHHHHHHHcCCeEeeC
Confidence 999999999999999999999999999999999999999999999999984
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=5.9e-25 Score=155.18 Aligned_cols=68 Identities=54% Similarity=0.800 Sum_probs=60.3
Q ss_pred eeeEEEeecCcchhHHHHHHHHHhhCCChhHHHHHHhhcchhhhcCCCHHHHHHHHHHHHHcCcEEEeC
Q 030925 101 AFDVKLEKYDQAAKIKIIKEVKTFTGLGLKESKDLVEKAPAVIKKGVTKEEADKIVEKLKELNAIVVLE 169 (169)
Q Consensus 101 ~f~V~L~~~~~~kKi~vIK~VR~it~LgLkEAK~lVe~~P~~IKe~vsKeeAE~ik~kLe~aGA~veiE 169 (169)
+|||+|+++ +++||++||.||++|||||+|||++||++|++|+++++++|||+++++|+++||+|+|+
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 699999999 78999999999999999999999999999999999999999999999999999999985
No 8
>PRK06771 hypothetical protein; Provisional
Probab=97.85 E-value=1.2e-05 Score=60.54 Aligned_cols=29 Identities=28% Similarity=0.466 Sum_probs=27.1
Q ss_pred cchhHHHHHHHHHhhCCChhHHHHHHhhc
Q 030925 111 QAAKIKIIKEVKTFTGLGLKESKDLVEKA 139 (169)
Q Consensus 111 ~~kKi~vIK~VR~it~LgLkEAK~lVe~~ 139 (169)
..+||+.||.+|+.||+||+|||++||++
T Consensus 65 ~Gkki~AIK~~Re~tG~~L~eAK~yVD~L 93 (93)
T PRK06771 65 EGQTVTAVKRVREAFGFSLLEAKQYVDKL 93 (93)
T ss_pred cCCchHHHHHHHHHcCCCHHHHHHHHhcC
Confidence 36999999999999999999999999975
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=89.10 E-value=1.1 Score=31.82 Aligned_cols=65 Identities=20% Similarity=0.288 Sum_probs=48.2
Q ss_pred hcceeeEEEeecCcchhHHHHHHHHHhhCCChhHHHHHHhhcc----hhhhcCCCHHHHHHHHHHHHHcC
Q 030925 98 EKTAFDVKLEKYDQAAKIKIIKEVKTFTGLGLKESKDLVEKAP----AVIKKGVTKEEADKIVEKLKELN 163 (169)
Q Consensus 98 EKt~f~V~L~~~~~~kKi~vIK~VR~it~LgLkEAK~lVe~~P----~~IKe~vsKeeAE~ik~kLe~aG 163 (169)
+...|.|+|-+-+-..--.||..++...|+...+|.++...+- .+|.. -++++||....+|...|
T Consensus 3 ~~~~~~vvL~NDe~ht~~~Vi~~L~~~~~~s~~~A~~~a~~v~~~G~avv~~-~~~e~ae~~~~~l~~~g 71 (82)
T PF02617_consen 3 EPDMYRVVLWNDEVHTFEQVIDVLRRVFGCSEEQARQIAMEVHREGRAVVGT-GSREEAEEYAEKLQRAG 71 (82)
T ss_dssp S--EEEEEEE--SSSBHHHHHHHHHHHC---HHHHHHHHHHHHHHSEEEEEE-EEHHHHHHHHHHHHHHH
T ss_pred CCCceEEEEEcCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHhHcCCEeeee-CCHHHHHHHHHHHHHHh
Confidence 4567899997655556779999999999999999999887553 35544 59999999999999998
No 10
>PRK00033 clpS ATP-dependent Clp protease adaptor protein ClpS; Reviewed
Probab=77.87 E-value=17 Score=27.46 Aligned_cols=72 Identities=17% Similarity=0.264 Sum_probs=56.9
Q ss_pred hhcceeeEEEeecCcchhHHHHHHHHHhhCCChhHHHHHHhhcch----hhhcCCCHHHHHHHHHHHHHcCcEEEeC
Q 030925 97 AEKTAFDVKLEKYDQAAKIKIIKEVKTFTGLGLKESKDLVEKAPA----VIKKGVTKEEADKIVEKLKELNAIVVLE 169 (169)
Q Consensus 97 ~EKt~f~V~L~~~~~~kKi~vIK~VR~it~LgLkEAK~lVe~~P~----~IKe~vsKeeAE~ik~kLe~aGA~veiE 169 (169)
+....|.|+|-+-|-...==||..++.+.|++..+|.++.-.+=. ++.. -++|.||-...+|...|-.+.||
T Consensus 23 ~~~~~y~ViL~NDd~ntmd~Vv~vL~~vf~~s~~~A~~iml~vH~~G~avv~~-~~~e~AE~~~~~l~~~~L~~~ie 98 (100)
T PRK00033 23 KPPPMYKVLLHNDDYTPMEFVVYVLQKFFGYDRERATQIMLEVHNEGKAVVGV-CTREVAETKVEQVHQHGLLCTME 98 (100)
T ss_pred CCCCceEEEEEcCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHhcCCcEEEEE-EcHHHHHHHHHHHHcCCCeEEEe
Confidence 344569999977554455579999999999999999988765422 3443 49999999999999999988886
No 11
>KOG3449 consensus 60S acidic ribosomal protein P2 [Translation, ribosomal structure and biogenesis]
Probab=61.59 E-value=23 Score=27.80 Aligned_cols=37 Identities=16% Similarity=0.116 Sum_probs=24.2
Q ss_pred ccCChhHHHHHHHHhcCCHHHHHHHHHHHHHHh-CCCCCCC
Q 030925 35 ESRTQKLERISDELLDLTKLERYDFATLLGCKL-GLDRFGP 74 (169)
Q Consensus 35 ~~~s~kv~~Ivd~I~~LtLlE~seLv~~leekf-gv~~~a~ 74 (169)
....++++.++.+|+.-|+- ||+..=+++| .||..++
T Consensus 33 E~d~e~i~~visel~GK~i~---ElIA~G~eklAsvpsGGa 70 (112)
T KOG3449|consen 33 EIDDERINLVLSELKGKDIE---ELIAAGREKLASVPSGGA 70 (112)
T ss_pred ccCHHHHHHHHHHhcCCCHH---HHHHHhHHHHhcCCCCCc
Confidence 44567788888888877654 5666666666 5665444
No 12
>PRK13019 clpS ATP-dependent Clp protease adaptor; Reviewed
Probab=60.11 E-value=52 Score=24.60 Aligned_cols=72 Identities=13% Similarity=0.083 Sum_probs=54.3
Q ss_pred hhhcceeeEEEeecCcchhHHHH-HHHHHhhCCChhHHHHHHhhcch---hhhcCCCHHHHHHHHHHHHHcCcEEE
Q 030925 96 AAEKTAFDVKLEKYDQAAKIKII-KEVKTFTGLGLKESKDLVEKAPA---VIKKGVTKEEADKIVEKLKELNAIVV 167 (169)
Q Consensus 96 ~~EKt~f~V~L~~~~~~kKi~vI-K~VR~it~LgLkEAK~lVe~~P~---~IKe~vsKeeAE~ik~kLe~aGA~ve 167 (169)
......|.|+|-+-|-.--==|| ..++.+.+++..+|..+.-.+=. -|----++|.||-...+|...|.++|
T Consensus 16 ~~~p~~ykViL~NDd~~t~dfVi~~vl~~vf~~s~~~A~~iml~vH~~G~avv~~~~~E~AE~~~~~l~~~glt~e 91 (94)
T PRK13019 16 LERYPLYKVIVLNDDFNTFEHVVNCLLKAIPGMSEDRAWRLMITAHKEGSAVVWVGPLEQAELYHQQLTDAGLTMA 91 (94)
T ss_pred ccCCCceEEEEEcCCCCCHHHHHHHHHHHhcCCCHHHHHHHHHHHhcCCcEEEEEecHHHHHHHHHHHHHcccccC
Confidence 34556799999875544455688 67788899999999998765432 22222599999999999999998765
No 13
>COG0264 Tsf Translation elongation factor Ts [Translation, ribosomal structure and biogenesis]
Probab=59.39 E-value=9.4 Score=34.30 Aligned_cols=28 Identities=29% Similarity=0.491 Sum_probs=24.0
Q ss_pred hhHHHHHHHHHhhCCChhHHHHHHhhcc
Q 030925 113 AKIKIIKEVKTFTGLGLKESKDLVEKAP 140 (169)
Q Consensus 113 kKi~vIK~VR~it~LgLkEAK~lVe~~P 140 (169)
-+.+.+|++|+.||-|..+.|+.++..-
T Consensus 4 ita~~VKeLRe~TgAGMmdCKkAL~E~~ 31 (296)
T COG0264 4 ITAALVKELREKTGAGMMDCKKALEEAN 31 (296)
T ss_pred ccHHHHHHHHHHhCCcHHHHHHHHHHcC
Confidence 4568999999999999999999876543
No 14
>PRK12332 tsf elongation factor Ts; Reviewed
Probab=58.86 E-value=11 Score=31.58 Aligned_cols=29 Identities=31% Similarity=0.525 Sum_probs=25.5
Q ss_pred HHHHHHHHHhhCCChhHHHHHHhhcchhh
Q 030925 115 IKIIKEVKTFTGLGLKESKDLVEKAPAVI 143 (169)
Q Consensus 115 i~vIK~VR~it~LgLkEAK~lVe~~P~~I 143 (169)
...||++|+.||.|+.+.|+.++.....+
T Consensus 5 a~~ik~LR~~tga~~~~ck~AL~~~~gd~ 33 (198)
T PRK12332 5 AKLVKELREKTGAGMMDCKKALEEANGDM 33 (198)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHcCCCH
Confidence 47899999999999999999988776655
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=57.11 E-value=17 Score=23.92 Aligned_cols=22 Identities=23% Similarity=0.688 Sum_probs=16.1
Q ss_pred hHHHHHHHHHhhCCChhHHHHHH
Q 030925 114 KIKIIKEVKTFTGLGLKESKDLV 136 (169)
Q Consensus 114 Ki~vIK~VR~it~LgLkEAK~lV 136 (169)
++..|+..|. .|++|.|-|+++
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 4566776664 799999999999
No 16
>TIGR00116 tsf translation elongation factor Ts. This protein is found in Bacteria, mitochondria, and chloroplasts.
Probab=56.87 E-value=12 Score=33.21 Aligned_cols=29 Identities=24% Similarity=0.447 Sum_probs=25.3
Q ss_pred HHHHHHHHHhhCCChhHHHHHHhhcchhh
Q 030925 115 IKIIKEVKTFTGLGLKESKDLVEKAPAVI 143 (169)
Q Consensus 115 i~vIK~VR~it~LgLkEAK~lVe~~P~~I 143 (169)
.+.||++|+.||-|+.+.|+..+.....+
T Consensus 5 a~~IK~LRe~Tgagm~dCKkAL~e~~gDi 33 (290)
T TIGR00116 5 AQLVKELRERTGAGMMDCKKALTEANGDF 33 (290)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHcCCCH
Confidence 36799999999999999999988777655
No 17
>PRK10664 transcriptional regulator HU subunit beta; Provisional
Probab=56.81 E-value=5.8 Score=28.90 Aligned_cols=36 Identities=8% Similarity=0.168 Sum_probs=30.9
Q ss_pred hhHHHHHHHHHhhCCChhHHHHHHhhcchhhhcCCC
Q 030925 113 AKIKIIKEVKTFTGLGLKESKDLVEKAPAVIKKGVT 148 (169)
Q Consensus 113 kKi~vIK~VR~it~LgLkEAK~lVe~~P~~IKe~vs 148 (169)
+|-.+|+.|.+-+|+.-++++.+||.+=..|.+.+.
T Consensus 2 tK~eli~~ia~~~~~s~~~~~~~v~~~~~~i~~~L~ 37 (90)
T PRK10664 2 NKSQLIDKIAAGADISKAAAGRALDAIIASVTESLK 37 (90)
T ss_pred CHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHh
Confidence 466899999999999999999999998888776544
No 18
>PRK09377 tsf elongation factor Ts; Provisional
Probab=55.00 E-value=13 Score=32.90 Aligned_cols=29 Identities=28% Similarity=0.462 Sum_probs=25.4
Q ss_pred HHHHHHHHHhhCCChhHHHHHHhhcchhh
Q 030925 115 IKIIKEVKTFTGLGLKESKDLVEKAPAVI 143 (169)
Q Consensus 115 i~vIK~VR~it~LgLkEAK~lVe~~P~~I 143 (169)
.+.||++|+.||-|+.+.|+..+.....+
T Consensus 6 ~~~IK~LR~~Tgagm~dCKkAL~e~~gD~ 34 (290)
T PRK09377 6 AALVKELRERTGAGMMDCKKALTEADGDI 34 (290)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHcCCCH
Confidence 47899999999999999999988776655
No 19
>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=54.71 E-value=29 Score=25.14 Aligned_cols=47 Identities=13% Similarity=0.247 Sum_probs=29.6
Q ss_pred chhHHHHHHHHHhhCCChhHHHHHHhhcchhhhcCCCHHHHHHHHHHHH
Q 030925 112 AAKIKIIKEVKTFTGLGLKESKDLVEKAPAVIKKGVTKEEADKIVEKLK 160 (169)
Q Consensus 112 ~kKi~vIK~VR~it~LgLkEAK~lVe~~P~~IKe~vsKeeAE~ik~kLe 160 (169)
=.++..|+..|+ +|++|+|.+.+++.....+++ +=.+..+.+..+++
T Consensus 44 l~~l~~I~~lr~-~G~~l~eI~~~l~~~~~~~~~-~l~~~~~~l~~~i~ 90 (96)
T cd04788 44 IRRLHQIIALRR-LGFSLREIGRALDGPDFDPLE-LLRRQLARLEEQLE 90 (96)
T ss_pred HHHHHHHHHHHH-cCCCHHHHHHHHhCCChhHHH-HHHHHHHHHHHHHH
Confidence 356777777775 699999999999876532222 22334444444444
No 20
>PRK10753 transcriptional regulator HU subunit alpha; Provisional
Probab=54.26 E-value=6.7 Score=28.47 Aligned_cols=35 Identities=20% Similarity=0.279 Sum_probs=30.2
Q ss_pred hhHHHHHHHHHhhCCChhHHHHHHhhcchhhhcCC
Q 030925 113 AKIKIIKEVKTFTGLGLKESKDLVEKAPAVIKKGV 147 (169)
Q Consensus 113 kKi~vIK~VR~it~LgLkEAK~lVe~~P~~IKe~v 147 (169)
+|-.+|+.|.+-+++.-++++..|+.+-.+|.+.+
T Consensus 2 ~K~eli~~ia~~~~~s~~~~~~~v~~~~~~i~~~L 36 (90)
T PRK10753 2 NKTQLIDVIADKAELSKTQAKAALESTLAAITESL 36 (90)
T ss_pred CHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999999999999877776654
No 21
>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=49.23 E-value=17 Score=25.21 Aligned_cols=35 Identities=26% Similarity=0.386 Sum_probs=30.0
Q ss_pred hhHHHHHHHHHhhCCChhHHHHHHhhcchhhhcCC
Q 030925 113 AKIKIIKEVKTFTGLGLKESKDLVEKAPAVIKKGV 147 (169)
Q Consensus 113 kKi~vIK~VR~it~LgLkEAK~lVe~~P~~IKe~v 147 (169)
+|-.+|+.|.+.+|+.-++++..++.+-..|.+.+
T Consensus 1 ~K~~l~~~ia~~~~~~~~~v~~vl~~~~~~i~~~L 35 (87)
T cd00591 1 TKSELIEAIAEKTGLSKKDAEAAVDAFLDVITEAL 35 (87)
T ss_pred CHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 36689999999999999999999999887776654
No 22
>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=48.10 E-value=54 Score=21.57 Aligned_cols=46 Identities=24% Similarity=0.486 Sum_probs=31.4
Q ss_pred HHHHHHHHhhCCChhHHHHHHhhcchhh-------------hcCCCHHHHHHHHHHHHH
Q 030925 116 KIIKEVKTFTGLGLKESKDLVEKAPAVI-------------KKGVTKEEADKIVEKLKE 161 (169)
Q Consensus 116 ~vIK~VR~it~LgLkEAK~lVe~~P~~I-------------Ke~vsKeeAE~ik~kLe~ 161 (169)
.++..+.++.|+|-+-++.|++.--.++ ..|+++..|+.|...+.+
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 4566777778888888888877622222 146788888888877653
No 23
>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=47.88 E-value=25 Score=22.50 Aligned_cols=27 Identities=19% Similarity=0.295 Sum_probs=20.6
Q ss_pred HHHHHHhhCCChhHHHHHHhhcchhhh
Q 030925 118 IKEVKTFTGLGLKESKDLVEKAPAVIK 144 (169)
Q Consensus 118 IK~VR~it~LgLkEAK~lVe~~P~~IK 144 (169)
.|.+|.-.|+...+||++|.+.|.=-.
T Consensus 12 ~~~L~~~f~ip~~vAk~IV~~C~~Cq~ 38 (40)
T PF02022_consen 12 AKALRHKFGIPRLVAKQIVNQCPKCQQ 38 (40)
T ss_dssp HHHHHHHHT--HHHHHHHHHHSCCHHS
T ss_pred HHHHHHHHccCHHHHHHHHHHCHHHhh
Confidence 467788889999999999999997443
No 24
>smart00411 BHL bacterial (prokaryotic) histone like domain.
Probab=47.77 E-value=17 Score=25.40 Aligned_cols=36 Identities=22% Similarity=0.371 Sum_probs=31.0
Q ss_pred hhHHHHHHHHHhhCCChhHHHHHHhhcchhhhcCCC
Q 030925 113 AKIKIIKEVKTFTGLGLKESKDLVEKAPAVIKKGVT 148 (169)
Q Consensus 113 kKi~vIK~VR~it~LgLkEAK~lVe~~P~~IKe~vs 148 (169)
+|-.+|+.|.+.+|+.-++++..++.+...|.+.+.
T Consensus 2 tk~eli~~ia~~~~~~~~~v~~vl~~l~~~i~~~L~ 37 (90)
T smart00411 2 TKSELIDAIAEKAGLSKKDAKAAVDAFLEIITEALK 37 (90)
T ss_pred CHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHh
Confidence 356889999999999999999999999888876543
No 25
>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=45.69 E-value=55 Score=23.89 Aligned_cols=31 Identities=16% Similarity=0.347 Sum_probs=26.9
Q ss_pred chhHHHHHHHHHhhCCChhHHHHHHhhcchh
Q 030925 112 AAKIKIIKEVKTFTGLGLKESKDLVEKAPAV 142 (169)
Q Consensus 112 ~kKi~vIK~VR~it~LgLkEAK~lVe~~P~~ 142 (169)
-.++..|+.+|+..|++|.+.+.+++..+..
T Consensus 43 v~~l~~I~~L~~~~G~~l~ei~~~l~~~~~~ 73 (96)
T cd04774 43 LKRLERILRLREVLGFSLQEVTHFLERPLEP 73 (96)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHhccccc
Confidence 3788899999988899999999999887765
No 26
>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=45.14 E-value=47 Score=24.46 Aligned_cols=29 Identities=21% Similarity=0.412 Sum_probs=23.4
Q ss_pred chhHHHHHHHHHhhCCChhHHHHHHhhcch
Q 030925 112 AAKIKIIKEVKTFTGLGLKESKDLVEKAPA 141 (169)
Q Consensus 112 ~kKi~vIK~VR~it~LgLkEAK~lVe~~P~ 141 (169)
-..+..|+..|. +|++|.|.+.+++..+.
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 356777777776 89999999999988764
No 27
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=43.56 E-value=24 Score=23.21 Aligned_cols=26 Identities=31% Similarity=0.641 Sum_probs=20.7
Q ss_pred chhHHHHHHHHHhhCCChhHHHHHHhh
Q 030925 112 AAKIKIIKEVKTFTGLGLKESKDLVEK 138 (169)
Q Consensus 112 ~kKi~vIK~VR~it~LgLkEAK~lVe~ 138 (169)
=..+..|+.+++ .|+++.+.+++++.
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 467888888888 99999999998763
No 28
>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=39.10 E-value=53 Score=22.58 Aligned_cols=26 Identities=27% Similarity=0.640 Sum_probs=20.5
Q ss_pred HHHHhhcchhhhcC-CCHHHHHHHHHHHHH
Q 030925 133 KDLVEKAPAVIKKG-VTKEEADKIVEKLKE 161 (169)
Q Consensus 133 K~lVe~~P~~IKe~-vsKeeAE~ik~kLe~ 161 (169)
|++|+ +.++.| +|+|.|+.|++.++.
T Consensus 21 K~~id---k~Ve~G~iTqeqAd~ik~~id~ 47 (59)
T PF10925_consen 21 KQIID---KYVEAGVITQEQADAIKKHIDQ 47 (59)
T ss_pred HHHHH---HHHHcCCCCHHHHHHHHHHHHH
Confidence 45555 457777 899999999998875
No 29
>PF10044 Ret_tiss: Retinal tissue protein; InterPro: IPR018737 Rtp is a family of proteins of approximately 112 amino acids in length which is conserved from nematodes to humans. The proposed tertiary structure is of almost entirely alpha helix interrupted only by loops located at proline residues. Three sites in the protein sequence reveal two types of possible post-translation modification. A serine residue, at position 41, is a candidate for protein kinase C phosphorylation. Glycine residues at position 69 and 91 are probable sites for acetylation by covalent amide linkage of myristate via N-myristoyl transferase. Rtp is differentially expressed in the trout retina between parr and smolt developmental stages (smoltification). It is likely to be a house-keeping protein [].
Probab=39.05 E-value=22 Score=26.96 Aligned_cols=23 Identities=30% Similarity=0.648 Sum_probs=16.1
Q ss_pred HHHHHHHHh----hCCChhHHHHHHhh
Q 030925 116 KIIKEVKTF----TGLGLKESKDLVEK 138 (169)
Q Consensus 116 ~vIK~VR~i----t~LgLkEAK~lVe~ 138 (169)
.++..||++ -.|||.|||++--+
T Consensus 62 ~L~~~Ik~L~~~aYqLGl~EaKEmtRG 88 (95)
T PF10044_consen 62 QLIEKIKKLQDEAYQLGLEEAKEMTRG 88 (95)
T ss_pred HHHHHHHHHHHHHHHHhHHHHHHHHhh
Confidence 455555544 68999999998543
No 30
>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=38.82 E-value=90 Score=22.14 Aligned_cols=41 Identities=24% Similarity=0.409 Sum_probs=30.0
Q ss_pred chhHHHHHHHHHhhCCChhHHHHHHhhcchhhhcCCCHHHHHHHHHHHHHc
Q 030925 112 AAKIKIIKEVKTFTGLGLKESKDLVEKAPAVIKKGVTKEEADKIVEKLKEL 162 (169)
Q Consensus 112 ~kKi~vIK~VR~it~LgLkEAK~lVe~~P~~IKe~vsKeeAE~ik~kLe~a 162 (169)
=.++..|+.++.-.|+++.+.+.+++ =.++-+.+...|+..
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 36788888888889999999999997 334555555555543
No 31
>PRK00285 ihfA integration host factor subunit alpha; Reviewed
Probab=34.87 E-value=35 Score=24.70 Aligned_cols=35 Identities=26% Similarity=0.329 Sum_probs=30.5
Q ss_pred hhHHHHHHHHHhhCCChhHHHHHHhhcchhhhcCC
Q 030925 113 AKIKIIKEVKTFTGLGLKESKDLVEKAPAVIKKGV 147 (169)
Q Consensus 113 kKi~vIK~VR~it~LgLkEAK~lVe~~P~~IKe~v 147 (169)
+|-.+|+.|.+.+++.-++++..++.+-..|.+.+
T Consensus 4 tk~el~~~ia~~~~~s~~~v~~vl~~~~~~i~~~L 38 (99)
T PRK00285 4 TKADLAEALFEKVGLSKREAKELVELFFEEIRDAL 38 (99)
T ss_pred CHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 46689999999999999999999999988887654
No 32
>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=34.81 E-value=74 Score=24.34 Aligned_cols=26 Identities=27% Similarity=0.478 Sum_probs=21.2
Q ss_pred chhHHHHHHHHHhhCCChhHHHHHHhh
Q 030925 112 AAKIKIIKEVKTFTGLGLKESKDLVEK 138 (169)
Q Consensus 112 ~kKi~vIK~VR~it~LgLkEAK~lVe~ 138 (169)
-.++..|+.+|+ .|++|+|.+++++.
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 367777777775 79999999999974
No 33
>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=34.42 E-value=56 Score=27.35 Aligned_cols=83 Identities=20% Similarity=0.186 Sum_probs=53.2
Q ss_pred hHHHHHHHHhcCCHHHHHHHHHHHHHHhCCCCCCCCCCCCCCCCCCCCCCCchhhhhhhcceeeEEEeecCcchhHHHHH
Q 030925 40 KLERISDELLDLTKLERYDFATLLGCKLGLDRFGPVVPAFPSSGPAASGSTSAETKAAEKTAFDVKLEKYDQAAKIKIIK 119 (169)
Q Consensus 40 kv~~Ivd~I~~LtLlE~seLv~~leekfgv~~~a~~~~~~~~~~~aa~~~~~~~~~~~EKt~f~V~L~~~~~~kKi~vIK 119 (169)
.+.+.+...+.-+.-++..+++++.+.||+...+ ..-++.|++||+..||.+--
T Consensus 35 ~l~~~l~~fK~~~f~d~~af~~l~~e~Yg~k~gg--------------------------~kGn~Tl~sfDG~~kV~i~~ 88 (195)
T PF11363_consen 35 ELSEQLAEFKAHTFEDIEAFIELSAEEYGVKLGG--------------------------KKGNVTLTSFDGRYKVTIAV 88 (195)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCC--------------------------CcCcEEEEEeCCCEEEEEEe
Confidence 3455566666777888999999999999985210 11245677887666654432
Q ss_pred HHHHhhCCChhHHHHHHhhcchhhhcCCC
Q 030925 120 EVKTFTGLGLKESKDLVEKAPAVIKKGVT 148 (169)
Q Consensus 120 ~VR~it~LgLkEAK~lVe~~P~~IKe~vs 148 (169)
.-+--.+=.|.-||++|+.+=...-+|..
T Consensus 89 ~~~~~Fde~l~~Ak~lIde~l~~w~~g~~ 117 (195)
T PF11363_consen 89 QDRISFDERLQAAKALIDECLNEWAKGAD 117 (195)
T ss_pred cccCCcChHHHHHHHHHHHHHHHHhcCCC
Confidence 22222455678888888877666666643
No 34
>PF11272 DUF3072: Protein of unknown function (DUF3072); InterPro: IPR021425 This bacterial family of proteins has no known function.
Probab=33.75 E-value=46 Score=23.21 Aligned_cols=19 Identities=37% Similarity=0.361 Sum_probs=17.6
Q ss_pred cCCHHHHHHHHHHHHHHhC
Q 030925 50 DLTKLERYDFATLLGCKLG 68 (169)
Q Consensus 50 ~LtLlE~seLv~~leekfg 68 (169)
.||-.|++++++.|+.+.|
T Consensus 38 ~LtkaeAs~rId~L~~~~g 56 (57)
T PF11272_consen 38 DLTKAEASERIDELQAQTG 56 (57)
T ss_pred cccHHHHHHHHHHHHHHhC
Confidence 7999999999999999876
No 35
>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=33.66 E-value=1e+02 Score=22.29 Aligned_cols=28 Identities=21% Similarity=0.370 Sum_probs=22.4
Q ss_pred chhHHHHHHHHHhhCCChhHHHHHHhhcc
Q 030925 112 AAKIKIIKEVKTFTGLGLKESKDLVEKAP 140 (169)
Q Consensus 112 ~kKi~vIK~VR~it~LgLkEAK~lVe~~P 140 (169)
-.++..|+.+|+ .|++|++.+++++...
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 367777777776 6999999999998754
No 36
>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=33.54 E-value=51 Score=21.53 Aligned_cols=24 Identities=17% Similarity=0.522 Sum_probs=17.1
Q ss_pred hhHHHHHHHHHhhCCChhHHHHHHh
Q 030925 113 AKIKIIKEVKTFTGLGLKESKDLVE 137 (169)
Q Consensus 113 kKi~vIK~VR~it~LgLkEAK~lVe 137 (169)
..+..|+.+++ .|+.|.|.+++++
T Consensus 45 ~~l~~i~~l~~-~g~~l~~i~~~~~ 68 (68)
T cd01104 45 ARLRLIRRLTS-EGVRISQAAALAL 68 (68)
T ss_pred HHHHHHHHHHH-CCCCHHHHHHHhC
Confidence 34555555554 8999999999863
No 37
>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=33.44 E-value=51 Score=21.89 Aligned_cols=23 Identities=26% Similarity=0.349 Sum_probs=18.9
Q ss_pred hhHHHHHHHHHhhCCChhHHHHHH
Q 030925 113 AKIKIIKEVKTFTGLGLKESKDLV 136 (169)
Q Consensus 113 kKi~vIK~VR~it~LgLkEAK~lV 136 (169)
.++..|+.+|+ .|+.|.+.|+++
T Consensus 45 ~~l~~i~~l~~-~g~~l~~i~~~l 67 (68)
T cd04763 45 DRILEIKRWID-NGVQVSKVKKLL 67 (68)
T ss_pred HHHHHHHHHHH-cCCCHHHHHHHh
Confidence 56777777777 999999999886
No 38
>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=32.33 E-value=91 Score=22.53 Aligned_cols=26 Identities=35% Similarity=0.551 Sum_probs=20.5
Q ss_pred hhHHHHHHHHHhhCCChhHHHHHHhhc
Q 030925 113 AKIKIIKEVKTFTGLGLKESKDLVEKA 139 (169)
Q Consensus 113 kKi~vIK~VR~it~LgLkEAK~lVe~~ 139 (169)
..+..|+.+|. .|++|.|.+++++..
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 56777777765 599999999999753
No 39
>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=31.52 E-value=63 Score=23.56 Aligned_cols=27 Identities=15% Similarity=0.491 Sum_probs=23.7
Q ss_pred chhHHHHHHHHHhhCCChhHHHHHHhh
Q 030925 112 AAKIKIIKEVKTFTGLGLKESKDLVEK 138 (169)
Q Consensus 112 ~kKi~vIK~VR~it~LgLkEAK~lVe~ 138 (169)
-.++..|+.+|...|++|.+.|.+++.
T Consensus 44 v~~l~~I~~L~~~~G~~l~~I~~~l~~ 70 (95)
T cd04780 44 VERLRLIRALQQEGGLPISQIKEVLDA 70 (95)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 478888888888889999999999986
No 40
>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=31.11 E-value=64 Score=22.99 Aligned_cols=26 Identities=19% Similarity=0.420 Sum_probs=21.7
Q ss_pred chhHHHHHHHHHhhCCChhHHHHHHhh
Q 030925 112 AAKIKIIKEVKTFTGLGLKESKDLVEK 138 (169)
Q Consensus 112 ~kKi~vIK~VR~it~LgLkEAK~lVe~ 138 (169)
=.++..|+.+|+ .|+.|.+.+++++.
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 367778888877 89999999999973
No 41
>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=28.83 E-value=1.7e+02 Score=21.81 Aligned_cols=26 Identities=15% Similarity=0.394 Sum_probs=20.7
Q ss_pred hhHHHHHHHHHhhCCChhHHHHHHhhc
Q 030925 113 AKIKIIKEVKTFTGLGLKESKDLVEKA 139 (169)
Q Consensus 113 kKi~vIK~VR~it~LgLkEAK~lVe~~ 139 (169)
.++..|+..|+ .|++|+|.+++++..
T Consensus 44 ~~l~~I~~lr~-~G~~L~eI~~~l~~~ 69 (120)
T cd04781 44 DRLALIALGRA-AGFSLDEIQAMLSHD 69 (120)
T ss_pred HHHHHHHHHHH-cCCCHHHHHHHHhcc
Confidence 56667766665 699999999999864
No 42
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=27.85 E-value=1.1e+02 Score=23.99 Aligned_cols=25 Identities=20% Similarity=0.473 Sum_probs=19.7
Q ss_pred hhHHHHHHHHHhhCCChhHHHHHHhh
Q 030925 113 AKIKIIKEVKTFTGLGLKESKDLVEK 138 (169)
Q Consensus 113 kKi~vIK~VR~it~LgLkEAK~lVe~ 138 (169)
.++..|+..| -+|++|.|-+++++.
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 5666666666 479999999999974
No 43
>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=27.04 E-value=1.6e+02 Score=21.29 Aligned_cols=27 Identities=30% Similarity=0.480 Sum_probs=21.9
Q ss_pred hhHHHHHHHHHhhCCChhHHHHHHhhcc
Q 030925 113 AKIKIIKEVKTFTGLGLKESKDLVEKAP 140 (169)
Q Consensus 113 kKi~vIK~VR~it~LgLkEAK~lVe~~P 140 (169)
..+..|+.+|. .|++|.+.+.+++...
T Consensus 45 ~~l~~i~~lr~-~g~~l~~i~~~~~~~~ 71 (103)
T cd01106 45 ERLQQILFLKE-LGFSLKEIKELLKDPS 71 (103)
T ss_pred HHHHHHHHHHH-cCCCHHHHHHHHHcCc
Confidence 56667777776 6999999999998764
No 44
>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=26.98 E-value=78 Score=23.33 Aligned_cols=26 Identities=27% Similarity=0.473 Sum_probs=20.7
Q ss_pred hhHHHHHHHHHhhCCChhHHHHHHhhc
Q 030925 113 AKIKIIKEVKTFTGLGLKESKDLVEKA 139 (169)
Q Consensus 113 kKi~vIK~VR~it~LgLkEAK~lVe~~ 139 (169)
.++..|+..|+ .|++|+|.+++++..
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 56777777775 799999999998753
No 45
>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=26.87 E-value=1.3e+02 Score=22.82 Aligned_cols=25 Identities=20% Similarity=0.553 Sum_probs=20.6
Q ss_pred hhHHHHHHHHHhhCCChhHHHHHHhh
Q 030925 113 AKIKIIKEVKTFTGLGLKESKDLVEK 138 (169)
Q Consensus 113 kKi~vIK~VR~it~LgLkEAK~lVe~ 138 (169)
.++..|+..|. +|++|+|-+++++.
T Consensus 45 ~~l~~I~~lr~-~G~sL~eI~~~l~~ 69 (127)
T cd01108 45 EELRFIRRARD-LGFSLEEIRELLAL 69 (127)
T ss_pred HHHHHHHHHHH-cCCCHHHHHHHHHH
Confidence 57777777774 89999999999873
No 46
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=26.69 E-value=1.1e+02 Score=23.72 Aligned_cols=25 Identities=24% Similarity=0.593 Sum_probs=19.3
Q ss_pred hhHHHHHHHHHhhCCChhHHHHHHhh
Q 030925 113 AKIKIIKEVKTFTGLGLKESKDLVEK 138 (169)
Q Consensus 113 kKi~vIK~VR~it~LgLkEAK~lVe~ 138 (169)
.++..|+..|. +|++|+|.|++++.
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 56666666654 69999999999874
No 47
>PRK05412 putative nucleotide-binding protein; Reviewed
Probab=26.51 E-value=65 Score=26.69 Aligned_cols=64 Identities=28% Similarity=0.377 Sum_probs=41.5
Q ss_pred eEEEeecCcchhHHHHH-HHHHh---hCCChhHHHH-HHh-------hcchhhhcCCCHHHHHHHHHHHHHcCcEEE
Q 030925 103 DVKLEKYDQAAKIKIIK-EVKTF---TGLGLKESKD-LVE-------KAPAVIKKGVTKEEADKIVEKLKELNAIVV 167 (169)
Q Consensus 103 ~V~L~~~~~~kKi~vIK-~VR~i---t~LgLkEAK~-lVe-------~~P~~IKe~vsKeeAE~ik~kLe~aGA~ve 167 (169)
.++|..- ++.|+.-++ .++.- -|++++--.- -++ .-...|++|++++.|.+|.+.+.+.+-+|.
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 EITLTAE-SDFQLKQVKDILRSKLIKRGIDLKALDYGKVEKASGKTVKQEVKLKQGIDQELAKKIVKLIKDSKLKVQ 120 (161)
T ss_pred EEEEEeC-CHHHHHHHHHHHHHHHHHcCCCHHHcCCCCccccCCCEEEEEEehhhccCHHHHHHHHHHHHhcCCcee
Confidence 4677765 467776544 44422 3566542211 111 123479999999999999999999998874
No 48
>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=26.30 E-value=83 Score=22.95 Aligned_cols=25 Identities=24% Similarity=0.388 Sum_probs=20.3
Q ss_pred hhHHHHHHHHHhhCCChhHHHHHHhh
Q 030925 113 AKIKIIKEVKTFTGLGLKESKDLVEK 138 (169)
Q Consensus 113 kKi~vIK~VR~it~LgLkEAK~lVe~ 138 (169)
.++..|+..|+ +|++|+|-+++++.
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 56777777775 69999999999974
No 49
>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=25.08 E-value=88 Score=20.61 Aligned_cols=23 Identities=35% Similarity=0.550 Sum_probs=18.4
Q ss_pred hhHHHHHHHHHhhCCChhHHHHHH
Q 030925 113 AKIKIIKEVKTFTGLGLKESKDLV 136 (169)
Q Consensus 113 kKi~vIK~VR~it~LgLkEAK~lV 136 (169)
..+..|+.+++ .|+.|.|.+.++
T Consensus 44 ~~l~~i~~l~~-~g~~l~~i~~~l 66 (67)
T cd04764 44 ELLKKIKTLLE-KGLSIKEIKEIL 66 (67)
T ss_pred HHHHHHHHHHH-CCCCHHHHHHHh
Confidence 56677777776 899999999876
No 50
>PRK00199 ihfB integration host factor subunit beta; Reviewed
Probab=24.87 E-value=36 Score=24.45 Aligned_cols=35 Identities=14% Similarity=0.246 Sum_probs=28.9
Q ss_pred hhHHHHHHHHHh-hCCChhHHHHHHhhcchhhhcCC
Q 030925 113 AKIKIIKEVKTF-TGLGLKESKDLVEKAPAVIKKGV 147 (169)
Q Consensus 113 kKi~vIK~VR~i-t~LgLkEAK~lVe~~P~~IKe~v 147 (169)
+|-.+|+.|.+. ++++-++++..|+.+-..|.+.+
T Consensus 2 tk~eli~~ia~~~~~~s~~~~~~vv~~~~~~i~~~L 37 (94)
T PRK00199 2 TKSELIERLAARNPHLSAKDVENAVKEILEEMSDAL 37 (94)
T ss_pred CHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHH
Confidence 356788999874 79999999999999988887654
No 51
>PRK05350 acyl carrier protein; Provisional
Probab=24.53 E-value=96 Score=21.56 Aligned_cols=26 Identities=23% Similarity=0.381 Sum_probs=21.4
Q ss_pred HHHHHhcCCHHHHHHHHHHHHHHhCCC
Q 030925 44 ISDELLDLTKLERYDFATLLGCKLGLD 70 (169)
Q Consensus 44 Ivd~I~~LtLlE~seLv~~leekfgv~ 70 (169)
+.+.+ ++.=+...+|+-.|+++|||.
T Consensus 32 l~~dl-g~DSld~veli~~lE~~fgI~ 57 (82)
T PRK05350 32 LYEDL-DLDSIDAVDLVVHLQKLTGKK 57 (82)
T ss_pred chhhc-CCCHHHHHHHHHHHHHHHCCc
Confidence 33444 788889999999999999997
No 52
>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=24.29 E-value=1e+02 Score=24.01 Aligned_cols=33 Identities=18% Similarity=0.314 Sum_probs=26.5
Q ss_pred chhHHHHHHHHHhhCCChhHHHHHHhhcchhhh
Q 030925 112 AAKIKIIKEVKTFTGLGLKESKDLVEKAPAVIK 144 (169)
Q Consensus 112 ~kKi~vIK~VR~it~LgLkEAK~lVe~~P~~IK 144 (169)
=..++.|+.+|+-.|++|.+.+.+++-.|...-
T Consensus 43 v~rL~~I~~L~~e~G~~l~eI~~~L~l~~~~~~ 75 (120)
T cd04767 43 LKRLRFIKKLINEKGLNIAGVKQILSMYPCWSI 75 (120)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHhCccccc
Confidence 366777777777789999999999999887543
No 53
>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=23.98 E-value=82 Score=21.35 Aligned_cols=22 Identities=14% Similarity=0.311 Sum_probs=19.2
Q ss_pred hcCCHHHHHHHHHHHHHHhCCC
Q 030925 49 LDLTKLERYDFATLLGCKLGLD 70 (169)
Q Consensus 49 ~~LtLlE~seLv~~leekfgv~ 70 (169)
..+.=+...+|+-.|+++|||.
T Consensus 33 lglDSl~~veli~~lE~~f~i~ 54 (77)
T TIGR00517 33 LGADSLDTVELVMALEEEFDIE 54 (77)
T ss_pred cCCcHHHHHHHHHHHHHHHCCC
Confidence 3677788899999999999997
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=23.90 E-value=91 Score=23.44 Aligned_cols=25 Identities=16% Similarity=0.429 Sum_probs=18.8
Q ss_pred hhHHHHHHHHHhhCCChhHHHHHHhh
Q 030925 113 AKIKIIKEVKTFTGLGLKESKDLVEK 138 (169)
Q Consensus 113 kKi~vIK~VR~it~LgLkEAK~lVe~ 138 (169)
.++..|+..|. +|++|+|.|++++.
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 45566666653 59999999999974
No 55
>PF04461 DUF520: Protein of unknown function (DUF520); InterPro: IPR007551 This entry represents the UPF0234 family of uncharacterised proteins.; PDB: 1IN0_A.
Probab=23.83 E-value=53 Score=27.14 Aligned_cols=64 Identities=28% Similarity=0.405 Sum_probs=34.7
Q ss_pred eEEEeecCcchhHHHHHHH-HHh---hCCChhHHHHH-Hhhc-------chhhhcCCCHHHHHHHHHHHHHcCcEEE
Q 030925 103 DVKLEKYDQAAKIKIIKEV-KTF---TGLGLKESKDL-VEKA-------PAVIKKGVTKEEADKIVEKLKELNAIVV 167 (169)
Q Consensus 103 ~V~L~~~~~~kKi~vIK~V-R~i---t~LgLkEAK~l-Ve~~-------P~~IKe~vsKeeAE~ik~kLe~aGA~ve 167 (169)
.++|..-+ +.|+.-+..| +.- -|+.++--.-- .+.+ ...|++|+++|.|.+|.+.+.+.+-+|.
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 77887754 6776555443 432 36665532222 1221 2368999999999999999999988764
No 56
>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=23.74 E-value=1.5e+02 Score=22.24 Aligned_cols=26 Identities=27% Similarity=0.523 Sum_probs=19.8
Q ss_pred hhHHHHHHHHHhhCCChhHHHHHHhhc
Q 030925 113 AKIKIIKEVKTFTGLGLKESKDLVEKA 139 (169)
Q Consensus 113 kKi~vIK~VR~it~LgLkEAK~lVe~~ 139 (169)
.++..|+.+|. .|++|+|-|++++..
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 55666666653 799999999999854
No 57
>PF14645 Chibby: Chibby family
Probab=23.54 E-value=44 Score=25.79 Aligned_cols=21 Identities=14% Similarity=0.025 Sum_probs=16.2
Q ss_pred CCcccccCCCCccccccccch
Q 030925 1 MHSVTIKFPRLGRVFTTLKVT 21 (169)
Q Consensus 1 ~~~~~~~~~~~~~~~~~l~~~ 21 (169)
||+|..+|+|=.+..||..+-
T Consensus 1 Mp~F~~~fspk~~p~rr~~s~ 21 (116)
T PF14645_consen 1 MPLFSRKFSPKKPPLRRSSSL 21 (116)
T ss_pred CCCccCCCCCCCCCCchhhcc
Confidence 999999999966666665443
No 58
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=23.41 E-value=1.1e+02 Score=19.84 Aligned_cols=25 Identities=36% Similarity=0.674 Sum_probs=20.4
Q ss_pred chhHHHHHHHHHhhCCChhHHHHHHh
Q 030925 112 AAKIKIIKEVKTFTGLGLKESKDLVE 137 (169)
Q Consensus 112 ~kKi~vIK~VR~it~LgLkEAK~lVe 137 (169)
-..+..|+.+|+ .|+++.+.+.+++
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 367778888877 8999999998875
No 59
>PRK08385 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=22.85 E-value=1.1e+02 Score=26.95 Aligned_cols=43 Identities=21% Similarity=0.317 Sum_probs=35.3
Q ss_pred CChhHHHHHHhhcch-hhhcCCCHHHHHHHHHHHHHcC--cEEEeC
Q 030925 127 LGLKESKDLVEKAPA-VIKKGVTKEEADKIVEKLKELN--AIVVLE 169 (169)
Q Consensus 127 LgLkEAK~lVe~~P~-~IKe~vsKeeAE~ik~kLe~aG--A~veiE 169 (169)
=+|.|+++.++.-+. +..++++.++..++.+.+.+.| .++.||
T Consensus 190 ~~leea~~a~~agaDiI~LDn~~~e~l~~~v~~l~~~~~~~~~~le 235 (278)
T PRK08385 190 ESLEDALKAAKAGADIIMLDNMTPEEIREVIEALKREGLRERVKIE 235 (278)
T ss_pred CCHHHHHHHHHcCcCEEEECCCCHHHHHHHHHHHHhcCcCCCEEEE
Confidence 479999999997666 4489999999999999998876 456554
No 60
>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=22.80 E-value=70 Score=22.10 Aligned_cols=34 Identities=29% Similarity=0.420 Sum_probs=28.0
Q ss_pred hhHHHHHHHHHhhCCChhHHHHHHhhcchhhhcC
Q 030925 113 AKIKIIKEVKTFTGLGLKESKDLVEKAPAVIKKG 146 (169)
Q Consensus 113 kKi~vIK~VR~it~LgLkEAK~lVe~~P~~IKe~ 146 (169)
+|-.+|+.|.+-+++.-++++..++.+=..|.+.
T Consensus 2 tk~eli~~ia~~~~~s~~~v~~vl~~~~~~i~~~ 35 (90)
T PF00216_consen 2 TKKELIKRIAEKTGLSKKDVEAVLDALFDVIKEA 35 (90)
T ss_dssp BHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHH
Confidence 3568899999999999999999999876666554
No 61
>cd04411 Ribosomal_P1_P2_L12p Ribosomal protein P1, P2, and L12p. Ribosomal proteins P1 and P2 are the eukaryotic proteins that are functionally equivalent to bacterial L7/L12. L12p is the archaeal homolog. Unlike other ribosomal proteins, the archaeal L12p and eukaryotic P1 and P2 do not share sequence similarity with their bacterial counterparts. They are part of the ribosomal stalk (called the L7/L12 stalk in bacteria), along with 28S rRNA and the proteins L11 and P0 in eukaryotes (23S rRNA, L11, and L10e in archaea). In bacterial ribosomes, L7/L12 homodimers bind the extended C-terminal helix of L10 to anchor the L7/L12 molecules to the ribosome. Eukaryotic P1/P2 heterodimers and archaeal L12p homodimers are believed to bind the L10 equivalent proteins, eukaryotic P0 and archaeal L10e, in a similar fashion. P1 and P2 (L12p, L7/L12) are the only proteins in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain
Probab=22.32 E-value=2.6e+02 Score=21.22 Aligned_cols=30 Identities=3% Similarity=-0.087 Sum_probs=20.6
Q ss_pred cCChhHHHHHHHHhcCCHHHHHHHHHHHHHHhC
Q 030925 36 SRTQKLERISDELLDLTKLERYDFATLLGCKLG 68 (169)
Q Consensus 36 ~~s~kv~~Ivd~I~~LtLlE~seLv~~leekfg 68 (169)
....++..+++.|.+.++ .+|+.....+++
T Consensus 33 Ve~~~~~~~~~aLaGk~V---~eli~~g~~kl~ 62 (105)
T cd04411 33 IEPERVKLFLSALNGKNI---DEVISKGKELMS 62 (105)
T ss_pred cCHHHHHHHHHHHcCCCH---HHHHHHHHhhcc
Confidence 344567777777777765 566777777774
No 62
>COG0236 AcpP Acyl carrier protein [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]
Probab=22.10 E-value=90 Score=21.59 Aligned_cols=22 Identities=23% Similarity=0.457 Sum_probs=19.2
Q ss_pred hcCCHHHHHHHHHHHHHHhCCC
Q 030925 49 LDLTKLERYDFATLLGCKLGLD 70 (169)
Q Consensus 49 ~~LtLlE~seLv~~leekfgv~ 70 (169)
..+.=+.+.+|+-.|+++||+.
T Consensus 35 lg~DSld~veLi~~lE~~f~i~ 56 (80)
T COG0236 35 LGLDSLDLVELVMALEEEFGIE 56 (80)
T ss_pred cCccHHHHHHHHHHHHHHHCCc
Confidence 4666778999999999999997
No 63
>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=21.90 E-value=1.3e+02 Score=25.28 Aligned_cols=40 Identities=18% Similarity=0.187 Sum_probs=29.9
Q ss_pred HHHHHHHHHhhCCChhHHHHHHhhcchhhhc--CCCHHHHHHHHHHHHHcCcEE
Q 030925 115 IKIIKEVKTFTGLGLKESKDLVEKAPAVIKK--GVTKEEADKIVEKLKELNAIV 166 (169)
Q Consensus 115 i~vIK~VR~it~LgLkEAK~lVe~~P~~IKe--~vsKeeAE~ik~kLe~aGA~v 166 (169)
..+++.||+.+ +.|-.+|- +.+.++..++.+.++++|+..
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 36776663 467789999999999999874
No 64
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=21.73 E-value=1.7e+02 Score=23.41 Aligned_cols=25 Identities=20% Similarity=0.226 Sum_probs=19.4
Q ss_pred hhHHHHHHHHHhhCCChhHHHHHHhh
Q 030925 113 AKIKIIKEVKTFTGLGLKESKDLVEK 138 (169)
Q Consensus 113 kKi~vIK~VR~it~LgLkEAK~lVe~ 138 (169)
.++..|+..|. +|++|.|-|++++.
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 55666666664 89999999999974
No 65
>CHL00124 acpP acyl carrier protein; Validated
Probab=21.54 E-value=1.4e+02 Score=20.45 Aligned_cols=22 Identities=14% Similarity=0.295 Sum_probs=19.3
Q ss_pred hcCCHHHHHHHHHHHHHHhCCC
Q 030925 49 LDLTKLERYDFATLLGCKLGLD 70 (169)
Q Consensus 49 ~~LtLlE~seLv~~leekfgv~ 70 (169)
.++.=+...+|+-.|+++|||.
T Consensus 35 lg~DSl~~~eli~~le~~f~i~ 56 (82)
T CHL00124 35 LGADSLDVVELVMAIEEKFDIE 56 (82)
T ss_pred cCCcHHHHHHHHHHHHHHHCCc
Confidence 4677788899999999999996
No 66
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=21.12 E-value=1.2e+02 Score=22.05 Aligned_cols=29 Identities=31% Similarity=0.457 Sum_probs=21.8
Q ss_pred chhHHHHHHHHHhhCCChhHHHHHHhhcch
Q 030925 112 AAKIKIIKEVKTFTGLGLKESKDLVEKAPA 141 (169)
Q Consensus 112 ~kKi~vIK~VR~it~LgLkEAK~lVe~~P~ 141 (169)
-..+.+|+..| -+|++|++-|++++....
T Consensus 44 l~~l~~I~~~r-~~G~~L~~I~~~l~~~~~ 72 (124)
T COG0789 44 LELLQIIKTLR-ELGFSLAEIKELLDLLSA 72 (124)
T ss_pred HHHHHHHHHHH-HcCCCHHHHHHHHhcccc
Confidence 35566666555 589999999999987653
No 67
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=21.00 E-value=1.8e+02 Score=22.59 Aligned_cols=25 Identities=24% Similarity=0.559 Sum_probs=19.9
Q ss_pred hhHHHHHHHHHhhCCChhHHHHHHhh
Q 030925 113 AKIKIIKEVKTFTGLGLKESKDLVEK 138 (169)
Q Consensus 113 kKi~vIK~VR~it~LgLkEAK~lVe~ 138 (169)
.++..|+..|+ +|++|+|.+++++.
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 56777777665 69999999999974
No 68
>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=20.82 E-value=1.2e+02 Score=23.18 Aligned_cols=26 Identities=23% Similarity=0.574 Sum_probs=20.5
Q ss_pred hhHHHHHHHHHhhCCChhHHHHHHhhc
Q 030925 113 AKIKIIKEVKTFTGLGLKESKDLVEKA 139 (169)
Q Consensus 113 kKi~vIK~VR~it~LgLkEAK~lVe~~ 139 (169)
..+..|+..|+ +|++|+|-|++++..
T Consensus 45 ~~l~~I~~lr~-~G~sL~eI~~~l~~~ 70 (133)
T cd04787 45 SRLRFILSARQ-LGFSLKDIKEILSHA 70 (133)
T ss_pred HHHHHHHHHHH-cCCCHHHHHHHHhhh
Confidence 56666666664 899999999999853
No 69
>PF00828 Ribosomal_L18e: Ribosomal protein L18e/L15; InterPro: IPR021131 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents both L15 and L18e ribosomal proteins, which share a common structure consisting mainly of parallel beta sheets (beta-alpha-beta units) with a core of three turns of irregular (beta-beta-alpha)n superhelix [, ].; PDB: 3O58_Y 1S1I_V 3O5H_Y 3IZS_O 3IZR_R 2OTL_L 1M1K_M 3G6E_L 1VQ9_L 1YIT_L ....
Probab=20.49 E-value=94 Score=23.54 Aligned_cols=27 Identities=30% Similarity=0.342 Sum_probs=17.8
Q ss_pred hcchhhhc-CCCHHHHHHHHHHHHHcCcEEEe
Q 030925 138 KAPAVIKK-GVTKEEADKIVEKLKELNAIVVL 168 (169)
Q Consensus 138 ~~P~~IKe-~vsKeeAE~ik~kLe~aGA~vei 168 (169)
+.|-+|+- ..|+ ..++++|++|++|++
T Consensus 101 ~~~l~I~a~~~S~----~A~ekIe~aGG~v~~ 128 (129)
T PF00828_consen 101 TKPLTIKAHRFSK----SAKEKIEAAGGEVVT 128 (129)
T ss_dssp SSSEEEEESEETH----HHHHHHHHTSEEEEE
T ss_pred ccceEEEEEecCH----HHHHHHHHcCCEEEe
Confidence 45555543 2443 567788999999875
No 70
>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=20.48 E-value=1.2e+02 Score=23.30 Aligned_cols=27 Identities=19% Similarity=0.420 Sum_probs=20.5
Q ss_pred hhHHHHHHHHHhhCCChhHHHHHHhhcc
Q 030925 113 AKIKIIKEVKTFTGLGLKESKDLVEKAP 140 (169)
Q Consensus 113 kKi~vIK~VR~it~LgLkEAK~lVe~~P 140 (169)
.++..|+..|. +|++|.|.+.++.-..
T Consensus 48 ~rL~~I~~lr~-~G~~L~eI~~ll~~~~ 74 (120)
T TIGR02054 48 QRLRFVRAAFE-AGIGLGELARLCRALD 74 (120)
T ss_pred HHHHHHHHHHH-cCCCHHHHHHHHHhhc
Confidence 56666666665 8999999999987543
No 71
>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=20.44 E-value=3.3e+02 Score=20.78 Aligned_cols=30 Identities=20% Similarity=0.144 Sum_probs=20.7
Q ss_pred CChhHHHHHHHHhcCCHHHHHHHHHHHHHHhCC
Q 030925 37 RTQKLERISDELLDLTKLERYDFATLLGCKLGL 69 (169)
Q Consensus 37 ~s~kv~~Ivd~I~~LtLlE~seLv~~leekfgv 69 (169)
.+..+..+++.|..-++ .+|+.....+++-
T Consensus 35 e~~~~~lf~~~L~GKdi---~eLIa~g~~kl~s 64 (109)
T cd05833 35 DDEKLNKVISELEGKDV---EELIAAGKEKLAS 64 (109)
T ss_pred cHHHHHHHHHHHcCCCH---HHHHHHhHhhhcC
Confidence 44566677777777655 6778888888754
No 72
>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=20.42 E-value=1.2e+02 Score=25.63 Aligned_cols=38 Identities=26% Similarity=0.313 Sum_probs=29.3
Q ss_pred HHHHHHHHhhCCChhHHHHHHhhcchhhhcCCCHHHHHHHHHHHHHcCcE
Q 030925 116 KIIKEVKTFTGLGLKESKDLVEKAPAVIKKGVTKEEADKIVEKLKELNAI 165 (169)
Q Consensus 116 ~vIK~VR~it~LgLkEAK~lVe~~P~~IKe~vsKeeAE~ik~kLe~aGA~ 165 (169)
.+++.||+.+ ..|-.+|=+...++..++.+.++++|+.
T Consensus 144 eiv~~vr~~~------------~~Pv~vKl~~~~~~~~~~a~~~~~~G~d 181 (296)
T cd04740 144 EIVKAVKKAT------------DVPVIVKLTPNVTDIVEIARAAEEAGAD 181 (296)
T ss_pred HHHHHHHhcc------------CCCEEEEeCCCchhHHHHHHHHHHcCCC
Confidence 5666666544 4688888776777899999999999986
No 73
>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=20.32 E-value=1.2e+02 Score=25.76 Aligned_cols=41 Identities=22% Similarity=0.222 Sum_probs=31.4
Q ss_pred hHHHHHHHHHhhCCChhHHHHHHhhcchhhhcCCCHHHHHHHHHHHHHcCcEE
Q 030925 114 KIKIIKEVKTFTGLGLKESKDLVEKAPAVIKKGVTKEEADKIVEKLKELNAIV 166 (169)
Q Consensus 114 Ki~vIK~VR~it~LgLkEAK~lVe~~P~~IKe~vsKeeAE~ik~kLe~aGA~v 166 (169)
-..+++.||+.+ ..|-.+|=..+-++..++.+.++++|+..
T Consensus 145 ~~eiv~~vr~~~------------~~pv~vKi~~~~~~~~~~a~~l~~~G~d~ 185 (300)
T TIGR01037 145 SADVVKAVKDKT------------DVPVFAKLSPNVTDITEIAKAAEEAGADG 185 (300)
T ss_pred HHHHHHHHHHhc------------CCCEEEECCCChhhHHHHHHHHHHcCCCE
Confidence 356777777543 36888887767789999999999999874
No 74
>PRK13844 recombination protein RecR; Provisional
Probab=20.18 E-value=2.5e+02 Score=23.91 Aligned_cols=45 Identities=22% Similarity=0.317 Sum_probs=36.7
Q ss_pred HHHHHHHHHhhCCChhHHHHHHhhcchhhhcCCCHHHHHHHHHHHHHcCc
Q 030925 115 IKIIKEVKTFTGLGLKESKDLVEKAPAVIKKGVTKEEADKIVEKLKELNA 164 (169)
Q Consensus 115 i~vIK~VR~it~LgLkEAK~lVe~~P~~IKe~vsKeeAE~ik~kLe~aGA 164 (169)
-++|..++.++|.|-|.|..|+-. .++ .++++++.+...|.++--
T Consensus 11 ~~LI~~l~~LPGIG~KsA~Rla~~---lL~--~~~~~~~~la~~i~~~~~ 55 (200)
T PRK13844 11 SAVIESLRKLPTIGKKSSQRLALY---LLD--KSPETAIAIANSLLDATA 55 (200)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHH---HHc--CCHHHHHHHHHHHHHHHH
Confidence 478999999999999999999753 343 589999999998887643
No 75
>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=20.13 E-value=1.7e+02 Score=21.66 Aligned_cols=26 Identities=23% Similarity=0.548 Sum_probs=19.8
Q ss_pred hhHHHHHHHHHhhCCChhHHHHHHhhc
Q 030925 113 AKIKIIKEVKTFTGLGLKESKDLVEKA 139 (169)
Q Consensus 113 kKi~vIK~VR~it~LgLkEAK~lVe~~ 139 (169)
..+..|+.+|+ +|++|+|.|++++..
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 55666666653 699999999999754
Done!