Query 045361
Match_columns 148
No_of_seqs 120 out of 1097
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 12:31:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045361.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045361hhsearch_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 2.9E-42 6.2E-47 264.5 13.1 126 21-148 3-128 (131)
2 KOG1715 Mitochondrial/chloropl 100.0 4.2E-42 9E-47 275.9 14.4 141 7-148 44-184 (187)
3 cd00387 Ribosomal_L7_L12 Ribos 100.0 4.7E-42 1E-46 261.8 13.0 124 22-148 2-125 (127)
4 TIGR00855 L12 ribosomal protei 100.0 6.9E-40 1.5E-44 249.9 12.4 119 22-148 5-123 (126)
5 COG0222 RplL Ribosomal protein 100.0 2.1E-39 4.5E-44 246.0 11.7 118 22-148 4-121 (124)
6 PRK00157 rplL 50S ribosomal pr 100.0 3.5E-39 7.6E-44 245.2 12.6 117 22-148 4-120 (123)
7 PF00542 Ribosomal_L12: Riboso 99.9 2.5E-24 5.4E-29 148.6 5.1 65 83-148 1-65 (68)
8 PRK06771 hypothetical protein; 97.8 1.4E-05 3.1E-10 58.7 3.3 28 94-121 66-93 (93)
9 PF02617 ClpS: ATP-dependent C 74.3 8.3 0.00018 26.6 4.7 65 80-145 3-71 (82)
10 CHL00098 tsf elongation factor 72.9 4.1 8.9E-05 33.5 3.2 29 97-125 2-30 (200)
11 COG0264 Tsf Translation elonga 72.2 4 8.6E-05 35.7 3.1 27 95-121 4-30 (296)
12 PRK12332 tsf elongation factor 69.1 5.7 0.00012 32.5 3.3 29 97-125 5-33 (198)
13 TIGR00116 tsf translation elon 67.6 6 0.00013 34.2 3.3 29 97-125 5-33 (290)
14 PRK09377 tsf elongation factor 67.5 6.1 0.00013 34.2 3.3 29 97-125 6-34 (290)
15 PF02022 Integrase_Zn: Integra 62.4 11 0.00025 23.5 3.0 28 100-127 12-39 (40)
16 PRK10664 transcriptional regul 59.5 5.2 0.00011 28.5 1.2 37 95-131 2-38 (90)
17 cd04788 HTH_NolA-AlbR Helix-Tu 59.2 21 0.00045 25.2 4.3 47 95-143 45-91 (96)
18 PF09278 MerR-DNA-bind: MerR, 58.4 14 0.00031 23.7 3.1 22 96-118 3-24 (65)
19 KOG3449 60S acidic ribosomal p 58.0 32 0.0007 26.2 5.3 31 17-50 33-63 (112)
20 PRK10753 transcriptional regul 55.8 6.3 0.00014 27.9 1.1 36 95-130 2-37 (90)
21 cd04774 HTH_YfmP Helix-Turn-He 53.0 45 0.00096 23.7 5.2 30 95-124 44-73 (96)
22 cd01107 HTH_BmrR Helix-Turn-He 52.7 32 0.0007 24.7 4.5 28 95-123 46-73 (108)
23 PF14520 HHH_5: Helix-hairpin- 50.8 51 0.0011 21.1 4.8 46 98-143 2-60 (60)
24 cd00591 HU_IHF Integration hos 50.5 15 0.00032 24.9 2.3 35 96-130 2-36 (87)
25 smart00411 BHL bacterial (prok 49.7 15 0.00032 25.2 2.2 35 96-130 3-37 (90)
26 PF13411 MerR_1: MerR HTH fami 49.5 19 0.00041 23.1 2.6 25 95-120 44-68 (69)
27 cd04766 HTH_HspR Helix-Turn-He 49.0 54 0.0012 22.7 5.0 39 95-143 45-83 (91)
28 PF10925 DUF2680: Protein of u 48.6 29 0.00062 23.3 3.4 27 114-143 20-47 (59)
29 TIGR02043 ZntR Zn(II)-responsi 40.8 58 0.0013 24.3 4.4 25 95-120 46-70 (131)
30 cd04780 HTH_MerR-like_sg5 Heli 40.3 42 0.00092 23.9 3.4 27 94-120 44-70 (95)
31 PF13565 HTH_32: Homeodomain-l 39.9 58 0.0013 21.3 3.8 35 19-53 32-66 (77)
32 cd04763 HTH_MlrA-like Helix-Tu 39.9 41 0.0009 21.8 3.1 24 95-119 45-68 (68)
33 cd01104 HTH_MlrA-CarA Helix-Tu 39.8 41 0.0009 21.4 3.1 24 95-119 45-68 (68)
34 cd05833 Ribosomal_P2 Ribosomal 39.3 40 0.00087 25.2 3.3 32 17-51 33-64 (109)
35 cd04768 HTH_BmrR-like Helix-Tu 38.3 83 0.0018 22.1 4.7 27 95-122 45-71 (96)
36 PRK05350 acyl carrier protein; 37.9 44 0.00095 22.7 3.1 27 26-53 32-58 (82)
37 cd04782 HTH_BltR Helix-Turn-He 37.1 73 0.0016 22.5 4.2 26 95-121 45-70 (97)
38 cd04781 HTH_MerR-like_sg6 Heli 36.4 1.3E+02 0.0028 21.9 5.6 26 95-121 44-69 (120)
39 PRK00285 ihfA integration host 36.2 31 0.00067 24.4 2.2 35 95-129 4-38 (99)
40 cd00336 Ribosomal_L22 Ribosoma 36.1 51 0.0011 23.6 3.3 30 17-46 9-38 (105)
41 cd01105 HTH_GlnR-like Helix-Tu 34.9 57 0.0012 22.7 3.3 25 95-120 46-70 (88)
42 cd01109 HTH_YyaN Helix-Turn-He 33.2 58 0.0013 23.4 3.3 26 95-121 45-70 (113)
43 PF11272 DUF3072: Protein of u 32.5 53 0.0011 22.3 2.7 19 32-50 38-56 (57)
44 CHL00124 acpP acyl carrier pro 32.5 70 0.0015 21.4 3.4 23 31-53 35-57 (82)
45 PRK13752 putative transcriptio 32.4 94 0.002 23.8 4.4 25 95-120 52-76 (144)
46 cd01108 HTH_CueR Helix-Turn-He 32.2 99 0.0022 22.8 4.4 25 95-120 45-69 (127)
47 TIGR00517 acyl_carrier acyl ca 31.9 62 0.0013 21.4 3.0 23 31-53 33-55 (77)
48 cd04764 HTH_MlrA-like_sg1 Heli 31.7 67 0.0015 20.7 3.1 24 95-119 44-67 (67)
49 cd04777 HTH_MerR-like_sg1 Heli 31.7 64 0.0014 23.0 3.2 25 95-120 43-67 (107)
50 PRK07081 acyl carrier protein; 31.6 60 0.0013 22.5 3.0 23 31-53 31-53 (83)
51 cd04767 HTH_HspR-like_MBC Heli 31.5 72 0.0016 24.2 3.6 31 95-125 44-74 (120)
52 cd01106 HTH_TipAL-Mta Helix-Tu 31.4 1.4E+02 0.003 21.0 5.0 27 95-122 45-71 (103)
53 PF08542 Rep_fac_C: Replicatio 30.1 1.1E+02 0.0024 20.5 4.1 35 19-54 4-38 (89)
54 PF11363 DUF3164: Protein of u 30.0 51 0.0011 26.9 2.7 80 23-130 36-117 (195)
55 smart00422 HTH_MERR helix_turn 29.8 83 0.0018 20.0 3.3 24 95-119 45-68 (70)
56 cd04783 HTH_MerR1 Helix-Turn-H 29.6 1.1E+02 0.0025 22.4 4.4 26 95-121 45-70 (126)
57 TIGR01044 rplV_bact ribosomal 29.6 70 0.0015 23.3 3.2 28 17-44 7-34 (103)
58 PRK05087 D-alanine--poly(phosp 29.5 64 0.0014 22.3 2.8 21 33-53 34-54 (78)
59 PRK05412 putative nucleotide-b 28.8 51 0.0011 26.6 2.5 63 85-148 45-119 (161)
60 PF09999 DUF2240: Uncharacteri 28.8 1.3E+02 0.0027 23.7 4.6 33 22-54 86-123 (144)
61 COG0236 AcpP Acyl carrier prot 28.8 60 0.0013 21.9 2.5 23 31-53 35-57 (80)
62 PRK10227 DNA-binding transcrip 28.6 1E+02 0.0022 23.3 4.1 25 95-120 45-69 (135)
63 cd04784 HTH_CadR-PbrR Helix-Tu 27.3 77 0.0017 23.3 3.1 25 95-120 45-69 (127)
64 PF04461 DUF520: Protein of un 27.1 40 0.00086 27.1 1.6 63 85-148 45-119 (160)
65 COG0789 SoxR Predicted transcr 26.4 91 0.002 22.1 3.3 29 94-123 44-72 (124)
66 PRK15002 redox-sensitivie tran 26.2 1.4E+02 0.003 23.4 4.5 25 95-120 55-79 (154)
67 PRK05828 acyl carrier protein; 25.8 88 0.0019 22.0 3.0 23 31-53 35-57 (84)
68 PRK00199 ihfB integration host 25.7 47 0.001 23.2 1.6 35 96-130 3-38 (94)
69 PF00550 PP-binding: Phosphopa 25.7 1E+02 0.0022 19.2 3.1 23 31-53 27-49 (67)
70 cd04787 HTH_HMRTR_unk Helix-Tu 25.7 92 0.002 23.2 3.3 26 95-121 45-70 (133)
71 PRK12449 acyl carrier protein; 25.6 1.2E+02 0.0026 20.1 3.6 25 29-53 33-57 (80)
72 cd04411 Ribosomal_P1_P2_L12p R 25.4 89 0.0019 23.1 3.1 31 17-50 32-62 (105)
73 TIGR02054 MerD mercuric resist 25.4 95 0.0021 23.3 3.3 27 95-122 48-74 (120)
74 PRK06402 rpl12p 50S ribosomal 25.1 67 0.0015 24.1 2.4 20 19-38 34-53 (106)
75 cd04769 HTH_MerR2 Helix-Turn-H 25.1 1E+02 0.0022 22.4 3.3 28 94-122 43-70 (116)
76 cd04770 HTH_HMRTR Helix-Turn-H 25.0 1.3E+02 0.0028 21.8 3.9 26 95-121 45-70 (123)
77 PF00216 Bac_DNA_binding: Bact 24.9 57 0.0012 22.0 1.9 34 96-129 3-36 (90)
78 PRK07639 acyl carrier protein; 24.8 91 0.002 21.8 2.9 27 26-53 32-58 (86)
79 PRK09514 zntR zinc-responsive 24.6 1.4E+02 0.0031 22.5 4.2 25 95-120 46-70 (140)
80 PF15209 IL31: Interleukin 31 24.6 1.2E+02 0.0026 24.0 3.8 42 9-54 1-43 (137)
81 PRK08172 putative acyl carrier 24.3 81 0.0018 21.9 2.6 21 33-53 36-56 (82)
82 COG3415 Transposase and inacti 24.2 1.6E+02 0.0034 22.9 4.4 38 16-54 62-99 (138)
83 cd01282 HTH_MerR-like_sg3 Heli 24.0 1.1E+02 0.0023 22.2 3.3 25 95-120 44-68 (112)
84 COG4575 ElaB Uncharacterized c 23.9 90 0.0019 23.5 2.9 32 112-143 15-48 (104)
85 PRK09184 acyl carrier protein; 23.9 96 0.0021 22.0 2.9 22 31-52 40-61 (89)
86 TIGR02044 CueR Cu(I)-responsiv 23.8 1.1E+02 0.0023 22.6 3.3 24 95-119 45-68 (127)
87 TIGR02047 CadR-PbrR Cd(II)/Pb( 23.7 1.1E+02 0.0023 22.7 3.3 24 95-119 45-68 (127)
88 PF13592 HTH_33: Winged helix- 23.4 68 0.0015 20.8 1.9 17 38-54 7-23 (60)
89 cd01279 HTH_HspR-like Helix-Tu 23.3 1.2E+02 0.0026 21.5 3.4 30 95-124 45-74 (98)
90 PF10044 Ret_tiss: Retinal tis 23.1 51 0.0011 24.3 1.4 23 97-119 61-87 (95)
91 cd02810 DHOD_DHPD_FMN Dihydroo 22.9 1.2E+02 0.0026 24.9 3.7 39 97-147 151-191 (289)
92 cd04740 DHOD_1B_like Dihydroor 22.8 1E+02 0.0022 25.5 3.4 38 98-147 144-181 (296)
93 TIGR01037 pyrD_sub1_fam dihydr 22.7 1.2E+02 0.0026 25.2 3.7 40 96-147 145-184 (300)
94 cd04790 HTH_Cfa-like_unk Helix 22.4 2E+02 0.0044 22.5 4.8 27 95-122 46-72 (172)
95 PRK06508 acyl carrier protein; 22.3 1.1E+02 0.0023 22.1 2.9 24 30-53 32-55 (93)
96 PF00237 Ribosomal_L22: Riboso 22.3 1.1E+02 0.0024 21.9 3.1 29 17-45 7-35 (105)
97 PRK00565 rplV 50S ribosomal pr 22.2 1.2E+02 0.0026 22.3 3.3 28 17-44 11-38 (112)
98 PRK07117 acyl carrier protein; 22.0 1.1E+02 0.0024 21.2 2.9 22 31-52 35-56 (79)
99 PTZ00373 60S Acidic ribosomal 21.8 1.3E+02 0.0029 22.7 3.5 30 17-49 35-64 (112)
100 PRK13019 clpS ATP-dependent Cl 21.3 3.3E+02 0.0071 19.7 6.8 69 80-148 18-90 (94)
101 PRK00982 acpP acyl carrier pro 21.3 1.3E+02 0.0028 19.8 3.0 22 32-53 34-55 (78)
102 cd04786 HTH_MerR-like_sg7 Heli 21.2 1.3E+02 0.0027 22.7 3.3 26 95-121 45-70 (131)
103 cd04779 HTH_MerR-like_sg4 Heli 20.8 1.3E+02 0.0028 22.9 3.3 27 95-122 44-70 (134)
104 cd04775 HTH_Cfa-like Helix-Tur 20.7 2E+02 0.0043 20.4 4.1 26 95-121 45-70 (102)
105 PF03461 TRCF: TRCF domain; I 20.5 1E+02 0.0022 22.0 2.6 30 24-53 20-50 (101)
106 cd04772 HTH_TioE_rpt1 First He 20.4 1.3E+02 0.0028 21.3 3.1 23 96-120 46-68 (99)
107 PRK07259 dihydroorotate dehydr 20.3 1.3E+02 0.0029 25.0 3.5 40 96-147 145-184 (301)
108 PF07377 DUF1493: Protein of u 20.2 1.4E+02 0.0031 21.7 3.3 26 31-56 37-62 (111)
109 TIGR00987 himA integration hos 20.1 77 0.0017 22.3 1.8 35 96-130 4-38 (96)
No 1
>CHL00083 rpl12 ribosomal protein L12
Probab=100.00 E-value=2.9e-42 Score=264.49 Aligned_cols=126 Identities=54% Similarity=0.782 Sum_probs=106.5
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHHHHHhCCCcccccchhhccCCCCCCCCCCCCcccccccceeEEEecCCCchhHHHH
Q 045361 21 EKIEKLATEISSLTLQEVCNLVDYLQDKLGVSAAAFAPAAAVGVAPGAPGAEAPASVEEEKTEFDVVIDEVPSNARIAVI 100 (148)
Q Consensus 21 ~kv~~ivd~i~~LtllE~~eLv~~le~~fgv~~~~~~p~~~~ga~~~a~~~~~~~~~~~EKt~fdV~L~~~~~~kKi~vI 100 (148)
+++++|+|+|++|||+|++||++.|+++|||++++.+++++++ +++++++. +++..+|||+|||+|++|++++||+||
T Consensus 3 ~k~~~ivd~i~~LTllE~~eLv~~le~~fgv~~~~~~a~~~~~-~~a~~~~~-~~~~~~EKT~F~V~L~~~~~~~Ki~vI 80 (131)
T CHL00083 3 TKINEIIEELKSLTLLEAAELVKQIEETFGVDASAPVGGGMMS-APAAAAAQ-AAEEVEEKTEFDVILEEVPADKRIAVL 80 (131)
T ss_pred chHHHHHHHHHhCCHHHHHHHHHHHHHHcCCCccchhhhhhcc-ccCccccc-ccchhhhcceeeEEEeecCCcchHHHH
Confidence 4899999999999999999999999999999987533322121 11111111 122335999999999999888999999
Q ss_pred HHHHHHcCCCHHHHHHHHhhcChhhhcCCCHHHHHHHHHHHHHcCCcC
Q 045361 101 KAVRTLTNLALKEAKDLIEGLPKKFKEGVSKDDAEAAKKQLEEAGAKF 148 (148)
Q Consensus 101 K~vR~it~LgLkEAK~lVe~~P~~IKe~vsKeeAE~ik~kle~aGA~V 148 (148)
|+||++|||||+|||+|||++|++||+|++|+|||+||++|+++||+|
T Consensus 81 K~vr~it~lgLkeaK~lVe~~P~~ike~v~KeeAe~ik~~le~~Ga~v 128 (131)
T CHL00083 81 KVVRSLTGLGLKEAKELVESLPKTIKEGISKEEAEEAKKQLEEAGAKV 128 (131)
T ss_pred HHHHHHcCCCHHHHHHHHHhCCHHHHhCCCHHHHHHHHHHHHHcCCEE
Confidence 999999999999999999999999999999999999999999999986
No 2
>KOG1715 consensus Mitochondrial/chloroplast ribosomal protein L12 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.2e-42 Score=275.89 Aligned_cols=141 Identities=50% Similarity=0.708 Sum_probs=120.4
Q ss_pred cccccCCCCcCCChHHHHHHHHHHhcCCHHHHHHHHHHHHHHhCCCcccccchhhccCCCCCCCCCCCCcccccccceeE
Q 045361 7 RASHLRPLCAVEAPEKIEKLATEISSLTLQEVCNLVDYLQDKLGVSAAAFAPAAAVGVAPGAPGAEAPASVEEEKTEFDV 86 (148)
Q Consensus 7 ~~~~~~~~~~~~~~~kv~~ivd~i~~LtllE~~eLv~~le~~fgv~~~~~~p~~~~ga~~~a~~~~~~~~~~~EKt~fdV 86 (148)
+..|..+.+....++||.+|+|+|++|||+|++||+++|+++|||+..+++|++++|+++..+ +++.+.++.|+|.|||
T Consensus 44 ~~~~~~~~~~~~~~~KI~~iv~eIssLtLlE~s~L~~~Lk~kl~i~e~~~~~a~~~g~~~~~~-~~a~ee~k~ekt~FdV 122 (187)
T KOG1715|consen 44 RATPLPPIAAVPPPPKISKIVDEISSLTLLETSDLVDLLKKKLNIPELPLAPAAAAGAAAPDA-GGAEEEAKKEKTTFDV 122 (187)
T ss_pred ccCCCCcccccCCCHHHHHHHHHHHhcCHHHHHHHHHHHHHHcCCCcccchhhccccCCCCCc-ccccccchhhcceEEE
Confidence 334555555677788999999999999999999999999999999999887765554333221 2233334457788999
Q ss_pred EEecCCCchhHHHHHHHHHHcCCCHHHHHHHHhhcChhhhcCCCHHHHHHHHHHHHHcCCcC
Q 045361 87 VIDEVPSNARIAVIKAVRTLTNLALKEAKDLIEGLPKKFKEGVSKDDAEAAKKQLEEAGAKF 148 (148)
Q Consensus 87 ~L~~~~~~kKi~vIK~vR~it~LgLkEAK~lVe~~P~~IKe~vsKeeAE~ik~kle~aGA~V 148 (148)
+|++|++..||+|||+||.+|||||+|||+|||++|+.+|+||+|||||+||++|+++||+|
T Consensus 123 kL~~fda~~KIkVIKEVR~~tgL~LkeAKklVE~aP~ilKegvtKeEAEkik~kLea~GakV 184 (187)
T KOG1715|consen 123 KLEKFDASSKIKVIKEVRALTGLGLKEAKKLVEKAPKILKEGVTKEEAEEIKEKLEAAGAKV 184 (187)
T ss_pred EEeecCccchhHHHHHHHHhccccHHHHHHHHHhccHHHHcCCCHHHHHHHHHHHHHcCCeE
Confidence 99999999999999999999999999999999999999999999999999999999999986
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=4.7e-42 Score=261.84 Aligned_cols=124 Identities=56% Similarity=0.752 Sum_probs=105.5
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHHHHHhCCCcccccchhhccCCCCCCCCCCCCcccccccceeEEEecCCCchhHHHHH
Q 045361 22 KIEKLATEISSLTLQEVCNLVDYLQDKLGVSAAAFAPAAAVGVAPGAPGAEAPASVEEEKTEFDVVIDEVPSNARIAVIK 101 (148)
Q Consensus 22 kv~~ivd~i~~LtllE~~eLv~~le~~fgv~~~~~~p~~~~ga~~~a~~~~~~~~~~~EKt~fdV~L~~~~~~kKi~vIK 101 (148)
++++|+|+|++|||+|++||++.|+++|||++.++++++++ ++|+++ .+++...+|||+|||+|++||+++||+|||
T Consensus 2 ~~~~i~d~i~~LtllE~~eLv~~le~~~gv~~~~~~~~~~~-~a~~~~--~~~~~~~~EKt~F~V~L~~~~~~~Ki~vIK 78 (127)
T cd00387 2 KVEEIVEALKELTLLEAAELVKALEEKFGVSASAAAAAAAA-AAPAAA--AAAAAEAEEKTEFDVVLESFGAAKKIAVIK 78 (127)
T ss_pred cHHHHHHHHHhCCHHHHHHHHHHHHHHhCCCcccccccccc-cCcccc--cccccchhhcceEEEEEeeCCchhhHHHHH
Confidence 68999999999999999999999999999998743332222 222221 111112359999999999999889999999
Q ss_pred HHHHHcCCCHHHHHHHHhhcChhhhcCCCHHHHHHHHHHHHHcCCcC
Q 045361 102 AVRTLTNLALKEAKDLIEGLPKKFKEGVSKDDAEAAKKQLEEAGAKF 148 (148)
Q Consensus 102 ~vR~it~LgLkEAK~lVe~~P~~IKe~vsKeeAE~ik~kle~aGA~V 148 (148)
+||++|||||+|||+|||++|++||+|+||+|||+||++|+++||+|
T Consensus 79 ~VR~it~LgLkEAK~lVe~~P~~iKe~vsKeeAE~ik~kLe~aGA~V 125 (127)
T cd00387 79 EVREITGLGLKEAKDLVESAPKVLKEGVSKEEAEEIKKKLEEAGAKV 125 (127)
T ss_pred HHHHHhCCChHHHHHHHHhCcHHHHhCCCHHHHHHHHHHHHHcCCEE
Confidence 99999999999999999999999999999999999999999999986
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=6.9e-40 Score=249.94 Aligned_cols=119 Identities=54% Similarity=0.719 Sum_probs=101.8
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHHHHHhCCCcccccchhhccCCCCCCCCCCCCcccccccceeEEEecCCCchhHHHHH
Q 045361 22 KIEKLATEISSLTLQEVCNLVDYLQDKLGVSAAAFAPAAAVGVAPGAPGAEAPASVEEEKTEFDVVIDEVPSNARIAVIK 101 (148)
Q Consensus 22 kv~~ivd~i~~LtllE~~eLv~~le~~fgv~~~~~~p~~~~ga~~~a~~~~~~~~~~~EKt~fdV~L~~~~~~kKi~vIK 101 (148)
..++|+|+|++|||+|++||++.|+++|||++++. ++++ +++++ .++++ .+|||+|||+|+.++ ++||+|||
T Consensus 5 ~~~~ive~i~~LTllE~~eLv~~lee~fgV~a~a~--~a~~-~a~~~---~~~~~-~eEKt~f~V~L~~~~-~~Ki~vIK 76 (126)
T TIGR00855 5 SKEQIIEALKEMTVLELSELVKALEEKFGVSAAAP--VAAG-AAGAA---AAAAA-AEEKTEFDVILKGAG-DNKIAVIK 76 (126)
T ss_pred cHHHHHHHHHhCCHHHHHHHHHHHHHhcCCCccch--hhhc-ccccc---ccccc-ccccceeeEEEecCC-cchhHHHH
Confidence 35899999999999999999999999999999753 2221 11111 11122 349999999999987 68999999
Q ss_pred HHHHHcCCCHHHHHHHHhhcChhhhcCCCHHHHHHHHHHHHHcCCcC
Q 045361 102 AVRTLTNLALKEAKDLIEGLPKKFKEGVSKDDAEAAKKQLEEAGAKF 148 (148)
Q Consensus 102 ~vR~it~LgLkEAK~lVe~~P~~IKe~vsKeeAE~ik~kle~aGA~V 148 (148)
+||++|||||+|||+|||++|++||+|++|+|||+||++|+++||+|
T Consensus 77 ~vR~itgLgLkEAK~lVe~~P~~ike~vsKeeAe~ik~~Le~aGa~v 123 (126)
T TIGR00855 77 VVREITGLGLKEAKDLVEGAPKVLKEGVSKEEAEELKKKLEEAGAKV 123 (126)
T ss_pred HHHHHcCCcHHHHHHHHHhCcHHHHhCCCHHHHHHHHHHHHHcCCEE
Confidence 99999999999999999999999999999999999999999999986
No 5
>COG0222 RplL Ribosomal protein L7/L12 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.1e-39 Score=245.96 Aligned_cols=118 Identities=54% Similarity=0.756 Sum_probs=102.9
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHHHHHhCCCcccccchhhccCCCCCCCCCCCCcccccccceeEEEecCCCchhHHHHH
Q 045361 22 KIEKLATEISSLTLQEVCNLVDYLQDKLGVSAAAFAPAAAVGVAPGAPGAEAPASVEEEKTEFDVVIDEVPSNARIAVIK 101 (148)
Q Consensus 22 kv~~ivd~i~~LtllE~~eLv~~le~~fgv~~~~~~p~~~~ga~~~a~~~~~~~~~~~EKt~fdV~L~~~~~~kKi~vIK 101 (148)
.+++|+++|++||++|++||++.++++|||++++ |+++++++ + + .+ +..+|||+|||+|++++ ++||+|||
T Consensus 4 ~~e~iie~i~~~svlel~eLvk~~eekfgVsaaa--~va~a~~~-a-~--a~--~aaeEktefdVvL~~~g-~kKI~VIK 74 (124)
T COG0222 4 TKEQIIEALKELTVLELSELVKALEEKFGVTAAA--PVAAAAAG-A-A--AA--EAAEEKTEFDVVLKSAG-GKKIAVIK 74 (124)
T ss_pred cHHHHHHHHHHhhHHHHHHHHHHHHHHhCCccch--hhhhcccc-c-c--cc--ccccccceeEEEecccC-CcchhHHH
Confidence 4689999999999999999999999999999975 44333222 1 1 11 11349999999999996 79999999
Q ss_pred HHHHHcCCCHHHHHHHHhhcChhhhcCCCHHHHHHHHHHHHHcCCcC
Q 045361 102 AVRTLTNLALKEAKDLIEGLPKKFKEGVSKDDAEAAKKQLEEAGAKF 148 (148)
Q Consensus 102 ~vR~it~LgLkEAK~lVe~~P~~IKe~vsKeeAE~ik~kle~aGA~V 148 (148)
+||++|||||||||++||++|++||+|++|+|||+||++|+++||+|
T Consensus 75 ~vR~itGLGLKEAKdlVe~aP~~~KE~v~k~eAe~~kkkleeaGa~V 121 (124)
T COG0222 75 VVRELTGLGLKEAKDLVEGAPKVLKEGVSKEEAEEIKKKLEEAGAKV 121 (124)
T ss_pred HHHHHhcccHHHHHHHHHhCcHHHHccCCHHHHHHHHHHHHHcCCeE
Confidence 99999999999999999999999999999999999999999999986
No 6
>PRK00157 rplL 50S ribosomal protein L7/L12; Reviewed
Probab=100.00 E-value=3.5e-39 Score=245.22 Aligned_cols=117 Identities=56% Similarity=0.771 Sum_probs=102.1
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHHHHHhCCCcccccchhhccCCCCCCCCCCCCcccccccceeEEEecCCCchhHHHHH
Q 045361 22 KIEKLATEISSLTLQEVCNLVDYLQDKLGVSAAAFAPAAAVGVAPGAPGAEAPASVEEEKTEFDVVIDEVPSNARIAVIK 101 (148)
Q Consensus 22 kv~~ivd~i~~LtllE~~eLv~~le~~fgv~~~~~~p~~~~ga~~~a~~~~~~~~~~~EKt~fdV~L~~~~~~kKi~vIK 101 (148)
++++|+|+|++|||+|++||++.|+++|||++++ |++++ ++++ ++ +..+|||+|||+|++|+ ++||+|||
T Consensus 4 ~~~~i~e~i~~LtllE~~eLv~~lee~fgv~a~~--~~~~~---~~~~---~~-~~~eEkt~f~V~L~~~~-~kKi~vIK 73 (123)
T PRK00157 4 TKEQIIEALKEMTVLELSELVKALEEKFGVSAAA--PVAAA---AAAA---AA-AAAEEKTEFDVVLKSAG-DKKIAVIK 73 (123)
T ss_pred cHHHHHHHHHhCCHHHHHHHHHHHHHHcCCCccc--hhccc---cccc---cc-cccccccceeEEEeccc-hhhHHHHH
Confidence 5789999999999999999999999999999875 32221 1111 11 22359999999999994 79999999
Q ss_pred HHHHHcCCCHHHHHHHHhhcChhhhcCCCHHHHHHHHHHHHHcCCcC
Q 045361 102 AVRTLTNLALKEAKDLIEGLPKKFKEGVSKDDAEAAKKQLEEAGAKF 148 (148)
Q Consensus 102 ~vR~it~LgLkEAK~lVe~~P~~IKe~vsKeeAE~ik~kle~aGA~V 148 (148)
+||++|||||+|||+|||++|++||+|++|+|||++|++|+++||+|
T Consensus 74 ~vR~itgLgLkEAK~lVe~~P~~ike~v~keeAe~ik~~Le~aGa~v 120 (123)
T PRK00157 74 AVREITGLGLKEAKDLVEGAPKVVKEGVSKEEAEEIKKKLEEAGAKV 120 (123)
T ss_pred HHHHHhCCCHHHHHHHHHhCCHHHHhCCCHHHHHHHHHHHHHcCCEE
Confidence 99999999999999999999999999999999999999999999986
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=99.90 E-value=2.5e-24 Score=148.64 Aligned_cols=65 Identities=58% Similarity=0.850 Sum_probs=57.3
Q ss_pred ceeEEEecCCCchhHHHHHHHHHHcCCCHHHHHHHHhhcChhhhcCCCHHHHHHHHHHHHHcCCcC
Q 045361 83 EFDVVIDEVPSNARIAVIKAVRTLTNLALKEAKDLIEGLPKKFKEGVSKDDAEAAKKQLEEAGAKF 148 (148)
Q Consensus 83 ~fdV~L~~~~~~kKi~vIK~vR~it~LgLkEAK~lVe~~P~~IKe~vsKeeAE~ik~kle~aGA~V 148 (148)
+|||+|+++ +++||++||.||++|||||+|||++||++|++|++++++++||+++++|+++||+|
T Consensus 1 ef~V~L~~~-~~~ki~vIK~vR~~tgl~L~eAK~~vd~~p~~ik~~v~keeAe~ik~~Le~aGa~v 65 (68)
T PF00542_consen 1 EFDVVLKSF-GEKKIKVIKEVREITGLGLKEAKKLVDSLPKVIKEGVSKEEAEEIKKKLEAAGAKV 65 (68)
T ss_dssp SEEEEEEE--TTGHHHHHHHHHHHC---HHHHHHHHCTTTEEEEEEE-HHHHHHHHHHHHCCT-EE
T ss_pred CeEEEEeec-ccchHHHHHHHHHHhCCcHHHHHHHHHhCCHHHHcCCCHHHHHHHHHHHHHcCCEE
Confidence 699999999 68999999999999999999999999999999999999999999999999999986
No 8
>PRK06771 hypothetical protein; Provisional
Probab=97.85 E-value=1.4e-05 Score=58.68 Aligned_cols=28 Identities=29% Similarity=0.457 Sum_probs=26.4
Q ss_pred chhHHHHHHHHHHcCCCHHHHHHHHhhc
Q 045361 94 NARIAVIKAVRTLTNLALKEAKDLIEGL 121 (148)
Q Consensus 94 ~kKi~vIK~vR~it~LgLkEAK~lVe~~ 121 (148)
.+|++.||.+|+.||+||+|||++||++
T Consensus 66 Gkki~AIK~~Re~tG~~L~eAK~yVD~L 93 (93)
T PRK06771 66 GQTVTAVKRVREAFGFSLLEAKQYVDKL 93 (93)
T ss_pred CCchHHHHHHHHHcCCCHHHHHHHHhcC
Confidence 4899999999999999999999999975
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=74.34 E-value=8.3 Score=26.60 Aligned_cols=65 Identities=20% Similarity=0.239 Sum_probs=46.5
Q ss_pred cccceeEEEecCCCchhHHHHHHHHHHcCCCHHHHHHHHhhcC----hhhhcCCCHHHHHHHHHHHHHcC
Q 045361 80 EKTEFDVVIDEVPSNARIAVIKAVRTLTNLALKEAKDLIEGLP----KKFKEGVSKDDAEAAKKQLEEAG 145 (148)
Q Consensus 80 EKt~fdV~L~~~~~~kKi~vIK~vR~it~LgLkEAK~lVe~~P----~~IKe~vsKeeAE~ik~kle~aG 145 (148)
+...|.|+|-+=+-..--.||..++...|+...+|..+...+= .+|. .-++++||....+|...|
T Consensus 3 ~~~~~~vvL~NDe~ht~~~Vi~~L~~~~~~s~~~A~~~a~~v~~~G~avv~-~~~~e~ae~~~~~l~~~g 71 (82)
T PF02617_consen 3 EPDMYRVVLWNDEVHTFEQVIDVLRRVFGCSEEQARQIAMEVHREGRAVVG-TGSREEAEEYAEKLQRAG 71 (82)
T ss_dssp S--EEEEEEE--SSSBHHHHHHHHHHHC---HHHHHHHHHHHHHHSEEEEE-EEEHHHHHHHHHHHHHHH
T ss_pred CCCceEEEEEcCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHhHcCCEeee-eCCHHHHHHHHHHHHHHh
Confidence 4467889886544345678999999999999999999877542 4454 458999999999999887
No 10
>CHL00098 tsf elongation factor Ts
Probab=72.88 E-value=4.1 Score=33.47 Aligned_cols=29 Identities=17% Similarity=0.335 Sum_probs=25.2
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHhhcChhh
Q 045361 97 IAVIKAVRTLTNLALKEAKDLIEGLPKKF 125 (148)
Q Consensus 97 i~vIK~vR~it~LgLkEAK~lVe~~P~~I 125 (148)
...||++|+.||.|+.+.|+.++....-+
T Consensus 2 a~~ik~LR~~Tgag~~dck~AL~e~~gd~ 30 (200)
T CHL00098 2 AELVKELRDKTGAGMMDCKKALQEANGDF 30 (200)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHcCCCH
Confidence 46799999999999999999988776555
No 11
>COG0264 Tsf Translation elongation factor Ts [Translation, ribosomal structure and biogenesis]
Probab=72.21 E-value=4 Score=35.74 Aligned_cols=27 Identities=22% Similarity=0.331 Sum_probs=23.8
Q ss_pred hhHHHHHHHHHHcCCCHHHHHHHHhhc
Q 045361 95 ARIAVIKAVRTLTNLALKEAKDLIEGL 121 (148)
Q Consensus 95 kKi~vIK~vR~it~LgLkEAK~lVe~~ 121 (148)
-+...+|++|+.||-|.+++|+.++..
T Consensus 4 ita~~VKeLRe~TgAGMmdCKkAL~E~ 30 (296)
T COG0264 4 ITAALVKELREKTGAGMMDCKKALEEA 30 (296)
T ss_pred ccHHHHHHHHHHhCCcHHHHHHHHHHc
Confidence 357899999999999999999987754
No 12
>PRK12332 tsf elongation factor Ts; Reviewed
Probab=69.14 E-value=5.7 Score=32.53 Aligned_cols=29 Identities=17% Similarity=0.289 Sum_probs=24.9
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHhhcChhh
Q 045361 97 IAVIKAVRTLTNLALKEAKDLIEGLPKKF 125 (148)
Q Consensus 97 i~vIK~vR~it~LgLkEAK~lVe~~P~~I 125 (148)
...||++|+.||.|+.+.|+.+.....-+
T Consensus 5 a~~ik~LR~~tga~~~~ck~AL~~~~gd~ 33 (198)
T PRK12332 5 AKLVKELREKTGAGMMDCKKALEEANGDM 33 (198)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHcCCCH
Confidence 57899999999999999999988766444
No 13
>TIGR00116 tsf translation elongation factor Ts. This protein is found in Bacteria, mitochondria, and chloroplasts.
Probab=67.60 E-value=6 Score=34.24 Aligned_cols=29 Identities=17% Similarity=0.310 Sum_probs=24.6
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHhhcChhh
Q 045361 97 IAVIKAVRTLTNLALKEAKDLIEGLPKKF 125 (148)
Q Consensus 97 i~vIK~vR~it~LgLkEAK~lVe~~P~~I 125 (148)
...||++|+.||.|++++|+.++.+..-+
T Consensus 5 a~~IK~LRe~Tgagm~dCKkAL~e~~gDi 33 (290)
T TIGR00116 5 AQLVKELRERTGAGMMDCKKALTEANGDF 33 (290)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHcCCCH
Confidence 46799999999999999999988765443
No 14
>PRK09377 tsf elongation factor Ts; Provisional
Probab=67.50 E-value=6.1 Score=34.22 Aligned_cols=29 Identities=17% Similarity=0.273 Sum_probs=24.9
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHhhcChhh
Q 045361 97 IAVIKAVRTLTNLALKEAKDLIEGLPKKF 125 (148)
Q Consensus 97 i~vIK~vR~it~LgLkEAK~lVe~~P~~I 125 (148)
...||++|+.||-|+++.|+.++.+..-+
T Consensus 6 ~~~IK~LR~~Tgagm~dCKkAL~e~~gD~ 34 (290)
T PRK09377 6 AALVKELRERTGAGMMDCKKALTEADGDI 34 (290)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHcCCCH
Confidence 57899999999999999999988766443
No 15
>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=62.42 E-value=11 Score=23.46 Aligned_cols=28 Identities=25% Similarity=0.274 Sum_probs=21.5
Q ss_pred HHHHHHHcCCCHHHHHHHHhhcChhhhc
Q 045361 100 IKAVRTLTNLALKEAKDLIEGLPKKFKE 127 (148)
Q Consensus 100 IK~vR~it~LgLkEAK~lVe~~P~~IKe 127 (148)
.|.+|.-.||...+||++|.++|.=-.+
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 5778888999999999999999965433
No 16
>PRK10664 transcriptional regulator HU subunit beta; Provisional
Probab=59.46 E-value=5.2 Score=28.46 Aligned_cols=37 Identities=8% Similarity=0.202 Sum_probs=31.8
Q ss_pred hhHHHHHHHHHHcCCCHHHHHHHHhhcChhhhcCCCH
Q 045361 95 ARIAVIKAVRTLTNLALKEAKDLIEGLPKKFKEGVSK 131 (148)
Q Consensus 95 kKi~vIK~vR~it~LgLkEAK~lVe~~P~~IKe~vsK 131 (148)
.|-.+|+.|.+-+|+.-++++.+||.+=.+|.+.+.+
T Consensus 2 tK~eli~~ia~~~~~s~~~~~~~v~~~~~~i~~~L~~ 38 (90)
T PRK10664 2 NKSQLIDKIAAGADISKAAAGRALDAIIASVTESLKE 38 (90)
T ss_pred CHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHhC
Confidence 3678999999999999999999999988888766544
No 17
>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=59.19 E-value=21 Score=25.25 Aligned_cols=47 Identities=23% Similarity=0.273 Sum_probs=30.0
Q ss_pred hhHHHHHHHHHHcCCCHHHHHHHHhhcChhhhcCCCHHHHHHHHHHHHH
Q 045361 95 ARIAVIKAVRTLTNLALKEAKDLIEGLPKKFKEGVSKDDAEAAKKQLEE 143 (148)
Q Consensus 95 kKi~vIK~vR~it~LgLkEAK~lVe~~P~~IKe~vsKeeAE~ik~kle~ 143 (148)
.++..|+.+|+ +|+.|+|.+.+++.....+++ +-.+..+.+..++++
T Consensus 45 ~~l~~I~~lr~-~G~~l~eI~~~l~~~~~~~~~-~l~~~~~~l~~~i~~ 91 (96)
T cd04788 45 RRLHQIIALRR-LGFSLREIGRALDGPDFDPLE-LLRRQLARLEEQLEL 91 (96)
T ss_pred HHHHHHHHHHH-cCCCHHHHHHHHhCCChhHHH-HHHHHHHHHHHHHHH
Confidence 56777777776 699999999999875532222 233444444444443
No 18
>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=58.42 E-value=14 Score=23.72 Aligned_cols=22 Identities=27% Similarity=0.641 Sum_probs=16.5
Q ss_pred hHHHHHHHHHHcCCCHHHHHHHH
Q 045361 96 RIAVIKAVRTLTNLALKEAKDLI 118 (148)
Q Consensus 96 Ki~vIK~vR~it~LgLkEAK~lV 118 (148)
++..|+..|. +|++|.|-|+++
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 19
>KOG3449 consensus 60S acidic ribosomal protein P2 [Translation, ribosomal structure and biogenesis]
Probab=58.02 E-value=32 Score=26.24 Aligned_cols=31 Identities=19% Similarity=0.251 Sum_probs=22.2
Q ss_pred CCChHHHHHHHHHHhcCCHHHHHHHHHHHHHHhC
Q 045361 17 VEAPEKIEKLATEISSLTLQEVCNLVDYLQDKLG 50 (148)
Q Consensus 17 ~~~~~kv~~ivd~i~~LtllE~~eLv~~le~~fg 50 (148)
...+++++.++.+|+.-|+ .||+..=+++|-
T Consensus 33 E~d~e~i~~visel~GK~i---~ElIA~G~eklA 63 (112)
T KOG3449|consen 33 EIDDERINLVLSELKGKDI---EELIAAGREKLA 63 (112)
T ss_pred ccCHHHHHHHHHHhcCCCH---HHHHHHhHHHHh
Confidence 5556788888888887765 566777777774
No 20
>PRK10753 transcriptional regulator HU subunit alpha; Provisional
Probab=55.83 E-value=6.3 Score=27.90 Aligned_cols=36 Identities=17% Similarity=0.263 Sum_probs=30.9
Q ss_pred hhHHHHHHHHHHcCCCHHHHHHHHhhcChhhhcCCC
Q 045361 95 ARIAVIKAVRTLTNLALKEAKDLIEGLPKKFKEGVS 130 (148)
Q Consensus 95 kKi~vIK~vR~it~LgLkEAK~lVe~~P~~IKe~vs 130 (148)
+|-.+|+.|.+-+++.-++++..|+.+-.+|.+.+.
T Consensus 2 ~K~eli~~ia~~~~~s~~~~~~~v~~~~~~i~~~L~ 37 (90)
T PRK10753 2 NKTQLIDVIADKAELSKTQAKAALESTLAAITESLK 37 (90)
T ss_pred CHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 467899999999999999999999998877766553
No 21
>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=52.95 E-value=45 Score=23.75 Aligned_cols=30 Identities=20% Similarity=0.334 Sum_probs=26.4
Q ss_pred hhHHHHHHHHHHcCCCHHHHHHHHhhcChh
Q 045361 95 ARIAVIKAVRTLTNLALKEAKDLIEGLPKK 124 (148)
Q Consensus 95 kKi~vIK~vR~it~LgLkEAK~lVe~~P~~ 124 (148)
.++..|+.+|+..|++|.+.+.+++..+..
T Consensus 44 ~~l~~I~~L~~~~G~~l~ei~~~l~~~~~~ 73 (96)
T cd04774 44 KRLERILRLREVLGFSLQEVTHFLERPLEP 73 (96)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHhccccc
Confidence 688889999988899999999999887765
No 22
>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=52.74 E-value=32 Score=24.73 Aligned_cols=28 Identities=25% Similarity=0.434 Sum_probs=23.3
Q ss_pred hhHHHHHHHHHHcCCCHHHHHHHHhhcCh
Q 045361 95 ARIAVIKAVRTLTNLALKEAKDLIEGLPK 123 (148)
Q Consensus 95 kKi~vIK~vR~it~LgLkEAK~lVe~~P~ 123 (148)
..+..|+.+|. +|++|.|.+.+++..+.
T Consensus 46 ~~l~~I~~lr~-~G~sl~~i~~l~~~~~~ 73 (108)
T cd01107 46 ERLNRIKYLRD-LGFPLEEIKEILDADND 73 (108)
T ss_pred HHHHHHHHHHH-cCCCHHHHHHHHhcCCH
Confidence 56777777776 89999999999998764
No 23
>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=50.75 E-value=51 Score=21.14 Aligned_cols=46 Identities=22% Similarity=0.289 Sum_probs=31.7
Q ss_pred HHHHHHHHHcCCCHHHHHHHHhhcChhh-------------hcCCCHHHHHHHHHHHHH
Q 045361 98 AVIKAVRTLTNLALKEAKDLIEGLPKKF-------------KEGVSKDDAEAAKKQLEE 143 (148)
Q Consensus 98 ~vIK~vR~it~LgLkEAK~lVe~~P~~I-------------Ke~vsKeeAE~ik~kle~ 143 (148)
.++..+.++.|+|-+-++.|++.--.++ -.|+++..|+.|...+.+
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 4566777778888888888887732222 246888888888877653
No 24
>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=50.55 E-value=15 Score=24.91 Aligned_cols=35 Identities=20% Similarity=0.358 Sum_probs=30.0
Q ss_pred hHHHHHHHHHHcCCCHHHHHHHHhhcChhhhcCCC
Q 045361 96 RIAVIKAVRTLTNLALKEAKDLIEGLPKKFKEGVS 130 (148)
Q Consensus 96 Ki~vIK~vR~it~LgLkEAK~lVe~~P~~IKe~vs 130 (148)
|-.+|+.|.+.+|+.-++++.+++.+-.+|.+.+.
T Consensus 2 K~~l~~~ia~~~~~~~~~v~~vl~~~~~~i~~~L~ 36 (87)
T cd00591 2 KSELIEAIAEKTGLSKKDAEAAVDAFLDVITEALA 36 (87)
T ss_pred HHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHh
Confidence 66899999999999999999999998877765543
No 25
>smart00411 BHL bacterial (prokaryotic) histone like domain.
Probab=49.66 E-value=15 Score=25.15 Aligned_cols=35 Identities=20% Similarity=0.345 Sum_probs=30.7
Q ss_pred hHHHHHHHHHHcCCCHHHHHHHHhhcChhhhcCCC
Q 045361 96 RIAVIKAVRTLTNLALKEAKDLIEGLPKKFKEGVS 130 (148)
Q Consensus 96 Ki~vIK~vR~it~LgLkEAK~lVe~~P~~IKe~vs 130 (148)
|-.+|+.|.+.+++.-++++..++.+-.+|.+.+.
T Consensus 3 k~eli~~ia~~~~~~~~~v~~vl~~l~~~i~~~L~ 37 (90)
T smart00411 3 KSELIDAIAEKAGLSKKDAKAAVDAFLEIITEALK 37 (90)
T ss_pred HHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHh
Confidence 56899999999999999999999999888876553
No 26
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=49.50 E-value=19 Score=23.13 Aligned_cols=25 Identities=32% Similarity=0.558 Sum_probs=20.0
Q ss_pred hhHHHHHHHHHHcCCCHHHHHHHHhh
Q 045361 95 ARIAVIKAVRTLTNLALKEAKDLIEG 120 (148)
Q Consensus 95 kKi~vIK~vR~it~LgLkEAK~lVe~ 120 (148)
..+..|+.+++ .|+.+.+.+++++.
T Consensus 44 ~~l~~i~~l~~-~G~sl~~I~~~l~~ 68 (69)
T PF13411_consen 44 ERLREIKELRK-QGMSLEEIKKLLKQ 68 (69)
T ss_dssp HHHHHHHHHHH-TTTHHHHHHHHH--
T ss_pred HHHHHHHHHHH-CcCCHHHHHHHHcc
Confidence 57788888887 89999999998763
No 27
>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=49.02 E-value=54 Score=22.73 Aligned_cols=39 Identities=18% Similarity=0.348 Sum_probs=29.8
Q ss_pred hhHHHHHHHHHHcCCCHHHHHHHHhhcChhhhcCCCHHHHHHHHHHHHH
Q 045361 95 ARIAVIKAVRTLTNLALKEAKDLIEGLPKKFKEGVSKDDAEAAKKQLEE 143 (148)
Q Consensus 95 kKi~vIK~vR~it~LgLkEAK~lVe~~P~~IKe~vsKeeAE~ik~kle~ 143 (148)
.++..|+.++.-.|++|.+.+.+++ =.++-+.+...|+.
T Consensus 45 ~~l~~i~~L~~d~g~~l~~i~~~l~----------l~~~~~~l~~~l~~ 83 (91)
T cd04766 45 ERLRRIQRLTQELGVNLAGVKRILE----------LEEELAELRAELDE 83 (91)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHH----------HHHHHHHHHHHHHH
Confidence 6778888888889999999999997 34555666666554
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=48.59 E-value=29 Score=23.29 Aligned_cols=27 Identities=26% Similarity=0.607 Sum_probs=21.6
Q ss_pred HHHHHhhcChhhhcC-CCHHHHHHHHHHHHH
Q 045361 114 AKDLIEGLPKKFKEG-VSKDDAEAAKKQLEE 143 (148)
Q Consensus 114 AK~lVe~~P~~IKe~-vsKeeAE~ik~kle~ 143 (148)
-|.+|+. .|+.| +|+|.|+.|++.++.
T Consensus 20 kK~~idk---~Ve~G~iTqeqAd~ik~~id~ 47 (59)
T PF10925_consen 20 KKQIIDK---YVEAGVITQEQADAIKKHIDQ 47 (59)
T ss_pred HHHHHHH---HHHcCCCCHHHHHHHHHHHHH
Confidence 3566664 67777 899999999998875
No 29
>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=40.75 E-value=58 Score=24.32 Aligned_cols=25 Identities=24% Similarity=0.377 Sum_probs=21.1
Q ss_pred hhHHHHHHHHHHcCCCHHHHHHHHhh
Q 045361 95 ARIAVIKAVRTLTNLALKEAKDLIEG 120 (148)
Q Consensus 95 kKi~vIK~vR~it~LgLkEAK~lVe~ 120 (148)
.++..|+.+|+ +|++|+|.+++++.
T Consensus 46 ~~l~~I~~lr~-~G~sl~eI~~~l~~ 70 (131)
T TIGR02043 46 KRLRFILKAKE-LGFTLDEIKELLSI 70 (131)
T ss_pred HHHHHHHHHHH-cCCCHHHHHHHHHh
Confidence 57788888775 79999999999974
No 30
>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=40.29 E-value=42 Score=23.86 Aligned_cols=27 Identities=19% Similarity=0.460 Sum_probs=23.6
Q ss_pred chhHHHHHHHHHHcCCCHHHHHHHHhh
Q 045361 94 NARIAVIKAVRTLTNLALKEAKDLIEG 120 (148)
Q Consensus 94 ~kKi~vIK~vR~it~LgLkEAK~lVe~ 120 (148)
-.++..|+.+|...|++|.+.|.+++.
T Consensus 44 v~~l~~I~~L~~~~G~~l~~I~~~l~~ 70 (95)
T cd04780 44 VERLRLIRALQQEGGLPISQIKEVLDA 70 (95)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 367888888888899999999999986
No 31
>PF13565 HTH_32: Homeodomain-like domain
Probab=39.91 E-value=58 Score=21.26 Aligned_cols=35 Identities=23% Similarity=0.454 Sum_probs=23.5
Q ss_pred ChHHHHHHHHHHhcCCHHHHHHHHHHHHHHhCCCc
Q 045361 19 APEKIEKLATEISSLTLQEVCNLVDYLQDKLGVSA 53 (148)
Q Consensus 19 ~~~kv~~ivd~i~~LtllE~~eLv~~le~~fgv~~ 53 (148)
+++-.+.|++-+.+-...-..+++..|+++||++-
T Consensus 32 ~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~ 66 (77)
T PF13565_consen 32 DPEQRERIIALIEEHPRWTPREIAEYLEEEFGISV 66 (77)
T ss_pred cHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCC
Confidence 34333777777665545555677778999999864
No 32
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=39.88 E-value=41 Score=21.79 Aligned_cols=24 Identities=25% Similarity=0.325 Sum_probs=19.5
Q ss_pred hhHHHHHHHHHHcCCCHHHHHHHHh
Q 045361 95 ARIAVIKAVRTLTNLALKEAKDLIE 119 (148)
Q Consensus 95 kKi~vIK~vR~it~LgLkEAK~lVe 119 (148)
.++..|+.+|+ .|+.|.+.|.++.
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 46777777777 8999999998863
No 33
>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=39.84 E-value=41 Score=21.42 Aligned_cols=24 Identities=21% Similarity=0.397 Sum_probs=17.6
Q ss_pred hhHHHHHHHHHHcCCCHHHHHHHHh
Q 045361 95 ARIAVIKAVRTLTNLALKEAKDLIE 119 (148)
Q Consensus 95 kKi~vIK~vR~it~LgLkEAK~lVe 119 (148)
..+..|+.+++ .|+.|.|.+++++
T Consensus 45 ~~l~~i~~l~~-~g~~l~~i~~~~~ 68 (68)
T cd01104 45 ARLRLIRRLTS-EGVRISQAAALAL 68 (68)
T ss_pred HHHHHHHHHHH-CCCCHHHHHHHhC
Confidence 35555666665 8999999999864
No 34
>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=39.34 E-value=40 Score=25.17 Aligned_cols=32 Identities=22% Similarity=0.284 Sum_probs=23.0
Q ss_pred CCChHHHHHHHHHHhcCCHHHHHHHHHHHHHHhCC
Q 045361 17 VEAPEKIEKLATEISSLTLQEVCNLVDYLQDKLGV 51 (148)
Q Consensus 17 ~~~~~kv~~ivd~i~~LtllE~~eLv~~le~~fgv 51 (148)
...+..+..+++.|..-++ .+|+.....+++-
T Consensus 33 eVe~~~~~lf~~~L~GKdi---~eLIa~g~~kl~s 64 (109)
T cd05833 33 EVDDEKLNKVISELEGKDV---EELIAAGKEKLAS 64 (109)
T ss_pred CccHHHHHHHHHHHcCCCH---HHHHHHhHhhhcC
Confidence 4455677777777777665 7788888888864
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=38.28 E-value=83 Score=22.14 Aligned_cols=27 Identities=22% Similarity=0.319 Sum_probs=22.2
Q ss_pred hhHHHHHHHHHHcCCCHHHHHHHHhhcC
Q 045361 95 ARIAVIKAVRTLTNLALKEAKDLIEGLP 122 (148)
Q Consensus 95 kKi~vIK~vR~it~LgLkEAK~lVe~~P 122 (148)
.++..|+.+|+ .|+.|++.+.+++...
T Consensus 45 ~~l~~I~~lr~-~G~~l~~I~~~l~~~~ 71 (96)
T cd04768 45 YQLQFILFLRE-LGFSLAEIKELLDTEM 71 (96)
T ss_pred HHHHHHHHHHH-cCCCHHHHHHHHhcCc
Confidence 57788888776 6999999999998653
No 36
>PRK05350 acyl carrier protein; Provisional
Probab=37.95 E-value=44 Score=22.73 Aligned_cols=27 Identities=26% Similarity=0.286 Sum_probs=21.2
Q ss_pred HHHHHhcCCHHHHHHHHHHHHHHhCCCc
Q 045361 26 LATEISSLTLQEVCNLVDYLQDKLGVSA 53 (148)
Q Consensus 26 ivd~i~~LtllE~~eLv~~le~~fgv~~ 53 (148)
+.+.+ .+.-+..-+|+-.|+++|||.=
T Consensus 32 l~~dl-g~DSld~veli~~lE~~fgI~i 58 (82)
T PRK05350 32 LYEDL-DLDSIDAVDLVVHLQKLTGKKI 58 (82)
T ss_pred chhhc-CCCHHHHHHHHHHHHHHHCCcc
Confidence 34444 7777888999999999999953
No 37
>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=37.09 E-value=73 Score=22.46 Aligned_cols=26 Identities=23% Similarity=0.473 Sum_probs=20.7
Q ss_pred hhHHHHHHHHHHcCCCHHHHHHHHhhc
Q 045361 95 ARIAVIKAVRTLTNLALKEAKDLIEGL 121 (148)
Q Consensus 95 kKi~vIK~vR~it~LgLkEAK~lVe~~ 121 (148)
.++..|+.+|. +|+.|.|.+++++..
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 46777777775 599999999999753
No 38
>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=36.43 E-value=1.3e+02 Score=21.90 Aligned_cols=26 Identities=23% Similarity=0.371 Sum_probs=21.0
Q ss_pred hhHHHHHHHHHHcCCCHHHHHHHHhhc
Q 045361 95 ARIAVIKAVRTLTNLALKEAKDLIEGL 121 (148)
Q Consensus 95 kKi~vIK~vR~it~LgLkEAK~lVe~~ 121 (148)
.++..|+.+|+ +|++|+|.+.+++..
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 56777777775 699999999999864
No 39
>PRK00285 ihfA integration host factor subunit alpha; Reviewed
Probab=36.19 E-value=31 Score=24.39 Aligned_cols=35 Identities=20% Similarity=0.352 Sum_probs=30.4
Q ss_pred hhHHHHHHHHHHcCCCHHHHHHHHhhcChhhhcCC
Q 045361 95 ARIAVIKAVRTLTNLALKEAKDLIEGLPKKFKEGV 129 (148)
Q Consensus 95 kKi~vIK~vR~it~LgLkEAK~lVe~~P~~IKe~v 129 (148)
.|-.+|+.|.+.+++.-++++..++.+-..|.+.+
T Consensus 4 tk~el~~~ia~~~~~s~~~v~~vl~~~~~~i~~~L 38 (99)
T PRK00285 4 TKADLAEALFEKVGLSKREAKELVELFFEEIRDAL 38 (99)
T ss_pred CHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999999999999988876654
No 40
>cd00336 Ribosomal_L22 Ribosomal protein L22/L17e. L22 (L17 in eukaryotes) is a core protein of the large ribosomal subunit. It is the only ribosomal protein that interacts with all six domains of 23S rRNA, and is one of the proteins important for directing the proper folding and stabilizing the conformation of 23S rRNA. L22 is the largest protein contributor to the surface of the polypeptide exit channel, the tunnel through which the polypeptide product passes. L22 is also one of six proteins located at the putative translocon binding site on the exterior surface of the ribosome.
Probab=36.12 E-value=51 Score=23.63 Aligned_cols=30 Identities=17% Similarity=0.333 Sum_probs=25.4
Q ss_pred CCChHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 045361 17 VEAPEKIEKLATEISSLTLQEVCNLVDYLQ 46 (148)
Q Consensus 17 ~~~~~kv~~ivd~i~~LtllE~~eLv~~le 46 (148)
..|+.|+..+++.|..|++.|+-+..+...
T Consensus 9 ~~S~kK~~~v~~~Irg~~v~~A~~~L~~~~ 38 (105)
T cd00336 9 RISPKKARLVARLIRGMSVDEALAQLEFVP 38 (105)
T ss_pred ccCHHHHHHHHHHHcCCcHHHHHHHHHhCC
Confidence 456789999999999999999888777654
No 41
>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=34.94 E-value=57 Score=22.68 Aligned_cols=25 Identities=24% Similarity=0.351 Sum_probs=21.3
Q ss_pred hhHHHHHHHHHHcCCCHHHHHHHHhh
Q 045361 95 ARIAVIKAVRTLTNLALKEAKDLIEG 120 (148)
Q Consensus 95 kKi~vIK~vR~it~LgLkEAK~lVe~ 120 (148)
.++..|+.+|+ .|+.|.+.++++..
T Consensus 46 ~~l~~I~~Lr~-~G~sl~~i~~~l~~ 70 (88)
T cd01105 46 DRLLVIKELLD-EGFTLAAAVEKLRR 70 (88)
T ss_pred HHHHHHHHHHH-CCCCHHHHHHHHHH
Confidence 57778888877 89999999999974
No 42
>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=33.21 E-value=58 Score=23.40 Aligned_cols=26 Identities=27% Similarity=0.422 Sum_probs=21.0
Q ss_pred hhHHHHHHHHHHcCCCHHHHHHHHhhc
Q 045361 95 ARIAVIKAVRTLTNLALKEAKDLIEGL 121 (148)
Q Consensus 95 kKi~vIK~vR~it~LgLkEAK~lVe~~ 121 (148)
.++..|+.+|+ +|++|+|.+++++..
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 46777777775 799999999998753
No 43
>PF11272 DUF3072: Protein of unknown function (DUF3072); InterPro: IPR021425 This bacterial family of proteins has no known function.
Probab=32.53 E-value=53 Score=22.31 Aligned_cols=19 Identities=37% Similarity=0.448 Sum_probs=17.5
Q ss_pred cCCHHHHHHHHHHHHHHhC
Q 045361 32 SLTLQEVCNLVDYLQDKLG 50 (148)
Q Consensus 32 ~LtllE~~eLv~~le~~fg 50 (148)
.||-.|++++++.|+.+.|
T Consensus 38 ~LtkaeAs~rId~L~~~~g 56 (57)
T PF11272_consen 38 DLTKAEASERIDELQAQTG 56 (57)
T ss_pred cccHHHHHHHHHHHHHHhC
Confidence 6999999999999999876
No 44
>CHL00124 acpP acyl carrier protein; Validated
Probab=32.45 E-value=70 Score=21.40 Aligned_cols=23 Identities=17% Similarity=0.257 Sum_probs=18.5
Q ss_pred hcCCHHHHHHHHHHHHHHhCCCc
Q 045361 31 SSLTLQEVCNLVDYLQDKLGVSA 53 (148)
Q Consensus 31 ~~LtllE~~eLv~~le~~fgv~~ 53 (148)
..+.-+...+|+-.|+++|||.-
T Consensus 35 lg~DSl~~~eli~~le~~f~i~i 57 (82)
T CHL00124 35 LGADSLDVVELVMAIEEKFDIEI 57 (82)
T ss_pred cCCcHHHHHHHHHHHHHHHCCcc
Confidence 45666778899999999999854
No 45
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=32.43 E-value=94 Score=23.84 Aligned_cols=25 Identities=20% Similarity=0.392 Sum_probs=20.2
Q ss_pred hhHHHHHHHHHHcCCCHHHHHHHHhh
Q 045361 95 ARIAVIKAVRTLTNLALKEAKDLIEG 120 (148)
Q Consensus 95 kKi~vIK~vR~it~LgLkEAK~lVe~ 120 (148)
.++..|+..| -+|++|+|-+++++.
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 5677777776 579999999999974
No 46
>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements
Probab=32.24 E-value=99 Score=22.81 Aligned_cols=25 Identities=20% Similarity=0.422 Sum_probs=20.9
Q ss_pred hhHHHHHHHHHHcCCCHHHHHHHHhh
Q 045361 95 ARIAVIKAVRTLTNLALKEAKDLIEG 120 (148)
Q Consensus 95 kKi~vIK~vR~it~LgLkEAK~lVe~ 120 (148)
.++..|+.+|. +|++|+|-+.+++.
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 57788888874 89999999999973
No 47
>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=31.90 E-value=62 Score=21.40 Aligned_cols=23 Identities=13% Similarity=0.196 Sum_probs=18.6
Q ss_pred hcCCHHHHHHHHHHHHHHhCCCc
Q 045361 31 SSLTLQEVCNLVDYLQDKLGVSA 53 (148)
Q Consensus 31 ~~LtllE~~eLv~~le~~fgv~~ 53 (148)
..+.=+...+|+-.||++|||.-
T Consensus 33 lglDSl~~veli~~lE~~f~i~i 55 (77)
T TIGR00517 33 LGADSLDTVELVMALEEEFDIEI 55 (77)
T ss_pred cCCcHHHHHHHHHHHHHHHCCCC
Confidence 35666778899999999999854
No 48
>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=31.74 E-value=67 Score=20.65 Aligned_cols=24 Identities=25% Similarity=0.454 Sum_probs=19.1
Q ss_pred hhHHHHHHHHHHcCCCHHHHHHHHh
Q 045361 95 ARIAVIKAVRTLTNLALKEAKDLIE 119 (148)
Q Consensus 95 kKi~vIK~vR~it~LgLkEAK~lVe 119 (148)
..+..|+.+++ .|+.|.|.+.++.
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 46777777777 8999999998763
No 49
>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=31.72 E-value=64 Score=22.96 Aligned_cols=25 Identities=12% Similarity=0.222 Sum_probs=20.8
Q ss_pred hhHHHHHHHHHHcCCCHHHHHHHHhh
Q 045361 95 ARIAVIKAVRTLTNLALKEAKDLIEG 120 (148)
Q Consensus 95 kKi~vIK~vR~it~LgLkEAK~lVe~ 120 (148)
.++..|+.+|+ +|++|+|-+++++.
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 50
>PRK07081 acyl carrier protein; Provisional
Probab=31.60 E-value=60 Score=22.46 Aligned_cols=23 Identities=13% Similarity=0.245 Sum_probs=19.9
Q ss_pred hcCCHHHHHHHHHHHHHHhCCCc
Q 045361 31 SSLTLQEVCNLVDYLQDKLGVSA 53 (148)
Q Consensus 31 ~~LtllE~~eLv~~le~~fgv~~ 53 (148)
..+.-+.+.+|+-.||++|||.=
T Consensus 31 lGlDSl~~v~li~~lE~~f~I~i 53 (83)
T PRK07081 31 AGLSSLATVQLMLAIEDAFDIEI 53 (83)
T ss_pred cCCCHHHHHHHHHHHHHHhCCcC
Confidence 35888999999999999999853
No 51
>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=31.52 E-value=72 Score=24.18 Aligned_cols=31 Identities=19% Similarity=0.231 Sum_probs=25.5
Q ss_pred hhHHHHHHHHHHcCCCHHHHHHHHhhcChhh
Q 045361 95 ARIAVIKAVRTLTNLALKEAKDLIEGLPKKF 125 (148)
Q Consensus 95 kKi~vIK~vR~it~LgLkEAK~lVe~~P~~I 125 (148)
..++.|+.+|+-.|+.|.+.+.+++-.|.-.
T Consensus 44 ~rL~~I~~L~~e~G~~l~eI~~~L~l~~~~~ 74 (120)
T cd04767 44 KRLRFIKKLINEKGLNIAGVKQILSMYPCWS 74 (120)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHhCcccc
Confidence 5677777777778999999999999888653
No 52
>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=31.42 E-value=1.4e+02 Score=21.03 Aligned_cols=27 Identities=26% Similarity=0.422 Sum_probs=21.8
Q ss_pred hhHHHHHHHHHHcCCCHHHHHHHHhhcC
Q 045361 95 ARIAVIKAVRTLTNLALKEAKDLIEGLP 122 (148)
Q Consensus 95 kKi~vIK~vR~it~LgLkEAK~lVe~~P 122 (148)
..+..|+.+|. .|++|.+.+.+++...
T Consensus 45 ~~l~~i~~lr~-~g~~l~~i~~~~~~~~ 71 (103)
T cd01106 45 ERLQQILFLKE-LGFSLKEIKELLKDPS 71 (103)
T ss_pred HHHHHHHHHHH-cCCCHHHHHHHHHcCc
Confidence 46677777776 6999999999998764
No 53
>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=30.14 E-value=1.1e+02 Score=20.55 Aligned_cols=35 Identities=26% Similarity=0.245 Sum_probs=29.1
Q ss_pred ChHHHHHHHHHHhcCCHHHHHHHHHHHHHHhCCCcc
Q 045361 19 APEKIEKLATEISSLTLQEVCNLVDYLQDKLGVSAA 54 (148)
Q Consensus 19 ~~~kv~~ivd~i~~LtllE~~eLv~~le~~fgv~~~ 54 (148)
.|+.+++|++.+.+=++.++...+..|-.. |++..
T Consensus 4 ~~~~i~~i~~~~~~~~~~~~~~~~~~l~~~-G~s~~ 38 (89)
T PF08542_consen 4 PPEVIEEILESCLNGDFKEARKKLYELLVE-GYSAS 38 (89)
T ss_dssp -HHHHHHHHHHHHHTCHHHHHHHHHHHHHT-T--HH
T ss_pred CHHHHHHHHHHHHhCCHHHHHHHHHHHHHc-CCCHH
Confidence 467899999999999999999999999888 98764
No 54
>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=30.01 E-value=51 Score=26.92 Aligned_cols=80 Identities=16% Similarity=0.327 Sum_probs=47.6
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHHHHHhCCCcccccchhhccCCCCCCCCCCCCcccccccceeEEEecCCCchhHHHHHH
Q 045361 23 IEKLATEISSLTLQEVCNLVDYLQDKLGVSAAAFAPAAAVGVAPGAPGAEAPASVEEEKTEFDVVIDEVPSNARIAVIKA 102 (148)
Q Consensus 23 v~~ivd~i~~LtllE~~eLv~~le~~fgv~~~~~~p~~~~ga~~~a~~~~~~~~~~~EKt~fdV~L~~~~~~kKi~vIK~ 102 (148)
+.+.+...+.-+.-++..+++++.+.+|+.-.. ..=++.|.+||+..||.+ .
T Consensus 36 l~~~l~~fK~~~f~d~~af~~l~~e~Yg~k~gg--------------------------~kGn~Tl~sfDG~~kV~i--~ 87 (195)
T PF11363_consen 36 LSEQLAEFKAHTFEDIEAFIELSAEEYGVKLGG--------------------------KKGNVTLTSFDGRYKVTI--A 87 (195)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCC--------------------------CcCcEEEEEeCCCEEEEE--E
Confidence 344455555666778888888888888883310 011456667776544433 3
Q ss_pred HHHH--cCCCHHHHHHHHhhcChhhhcCCC
Q 045361 103 VRTL--TNLALKEAKDLIEGLPKKFKEGVS 130 (148)
Q Consensus 103 vR~i--t~LgLkEAK~lVe~~P~~IKe~vs 130 (148)
+++. .+=.|.-||.+|+.|=.-.-+|.+
T Consensus 88 ~~~~~~Fde~l~~Ak~lIde~l~~w~~g~~ 117 (195)
T PF11363_consen 88 VQDRISFDERLQAAKALIDECLNEWAKGAD 117 (195)
T ss_pred ecccCCcChHHHHHHHHHHHHHHHHhcCCC
Confidence 3332 355577778888776555555543
No 55
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=29.81 E-value=83 Score=19.97 Aligned_cols=24 Identities=33% Similarity=0.618 Sum_probs=20.2
Q ss_pred hhHHHHHHHHHHcCCCHHHHHHHHh
Q 045361 95 ARIAVIKAVRTLTNLALKEAKDLIE 119 (148)
Q Consensus 95 kKi~vIK~vR~it~LgLkEAK~lVe 119 (148)
..+..|+.+|+ .|+++.+.+.+++
T Consensus 45 ~~l~~i~~lr~-~g~~~~~i~~~l~ 68 (70)
T smart00422 45 ERLRFIKRLKE-LGFSLEEIKELLE 68 (70)
T ss_pred HHHHHHHHHHH-cCCCHHHHHHHHh
Confidence 57788888887 8999999998876
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=29.65 E-value=1.1e+02 Score=22.37 Aligned_cols=26 Identities=27% Similarity=0.373 Sum_probs=20.1
Q ss_pred hhHHHHHHHHHHcCCCHHHHHHHHhhc
Q 045361 95 ARIAVIKAVRTLTNLALKEAKDLIEGL 121 (148)
Q Consensus 95 kKi~vIK~vR~it~LgLkEAK~lVe~~ 121 (148)
.++..|+.+|+ +|++|+|-|++++..
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 46666666663 799999999999854
No 57
>TIGR01044 rplV_bact ribosomal protein L22, bacterial type. This model decribes bacterial and chloroplast ribosomal protein L22.
Probab=29.64 E-value=70 Score=23.30 Aligned_cols=28 Identities=14% Similarity=0.287 Sum_probs=24.4
Q ss_pred CCChHHHHHHHHHHhcCCHHHHHHHHHH
Q 045361 17 VEAPEKIEKLATEISSLTLQEVCNLVDY 44 (148)
Q Consensus 17 ~~~~~kv~~ivd~i~~LtllE~~eLv~~ 44 (148)
..||.|+..+++.|..|++.|+-.....
T Consensus 7 r~SpkK~~~va~~IrG~~v~~A~~~L~f 34 (103)
T TIGR01044 7 RISPRKARLVADLIRGKSVSQALDILRF 34 (103)
T ss_pred ccCHHHHHHHHHHHcCCcHHHHHHHHhh
Confidence 4577899999999999999999887774
No 58
>PRK05087 D-alanine--poly(phosphoribitol) ligase subunit 2; Validated
Probab=29.49 E-value=64 Score=22.32 Aligned_cols=21 Identities=14% Similarity=0.276 Sum_probs=18.0
Q ss_pred CCHHHHHHHHHHHHHHhCCCc
Q 045361 33 LTLQEVCNLVDYLQDKLGVSA 53 (148)
Q Consensus 33 LtllE~~eLv~~le~~fgv~~ 53 (148)
|.-+.+-+|+-.||++|||.=
T Consensus 34 lDSl~~veli~~lE~~fgi~i 54 (78)
T PRK05087 34 LDSMGTVELLVELENRFDIEV 54 (78)
T ss_pred cchHHHHHHHHHHHHHhCCcc
Confidence 667788899999999999953
No 59
>PRK05412 putative nucleotide-binding protein; Reviewed
Probab=28.81 E-value=51 Score=26.58 Aligned_cols=63 Identities=16% Similarity=0.297 Sum_probs=40.8
Q ss_pred eEEEecCCCchhHHHH-HHHHHH---cCCCHHHHHH-HHh-------hcChhhhcCCCHHHHHHHHHHHHHcCCcC
Q 045361 85 DVVIDEVPSNARIAVI-KAVRTL---TNLALKEAKD-LIE-------GLPKKFKEGVSKDDAEAAKKQLEEAGAKF 148 (148)
Q Consensus 85 dV~L~~~~~~kKi~vI-K~vR~i---t~LgLkEAK~-lVe-------~~P~~IKe~vsKeeAE~ik~kle~aGA~V 148 (148)
.++|..-+ +.|+.-+ -.++.- -|++++--.- -.+ .....|++|++++.|.+|.+.+++.+-+|
T Consensus 45 ~i~l~a~~-d~kl~~v~diL~~kl~KR~i~~k~ld~~~~e~~sG~~vrq~i~lk~GI~~e~AKkIvK~IKd~klKV 119 (161)
T PRK05412 45 EITLTAES-DFQLKQVKDILRSKLIKRGIDLKALDYGKVEKASGKTVKQEVKLKQGIDQELAKKIVKLIKDSKLKV 119 (161)
T ss_pred EEEEEeCC-HHHHHHHHHHHHHHHHHcCCCHHHcCCCCccccCCCEEEEEEehhhccCHHHHHHHHHHHHhcCCce
Confidence 57777654 6676654 444432 2666652221 111 12357899999999999999999988765
No 60
>PF09999 DUF2240: Uncharacterized protein conserved in archaea (DUF2240); InterPro: IPR018716 This family of various hypothetical archaeal proteins has no known function.
Probab=28.81 E-value=1.3e+02 Score=23.72 Aligned_cols=33 Identities=27% Similarity=0.460 Sum_probs=27.8
Q ss_pred HHHHHHHHHhc---CCHHHHHHHHHHHHHHhC--CCcc
Q 045361 22 KIEKLATEISS---LTLQEVCNLVDYLQDKLG--VSAA 54 (148)
Q Consensus 22 kv~~ivd~i~~---LtllE~~eLv~~le~~fg--v~~~ 54 (148)
-.++|+|.|.. ++-.|+-..++.++++|| |+.-
T Consensus 86 ~fe~ild~ia~~~g~~~~evv~~in~~q~~~~~~l~~e 123 (144)
T PF09999_consen 86 PFERILDYIAAKTGIEKQEVVAEINELQEELGGLLDPE 123 (144)
T ss_pred HHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhccCCHH
Confidence 46788888866 999999999999999999 7643
No 61
>COG0236 AcpP Acyl carrier protein [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]
Probab=28.77 E-value=60 Score=21.93 Aligned_cols=23 Identities=22% Similarity=0.391 Sum_probs=19.2
Q ss_pred hcCCHHHHHHHHHHHHHHhCCCc
Q 045361 31 SSLTLQEVCNLVDYLQDKLGVSA 53 (148)
Q Consensus 31 ~~LtllE~~eLv~~le~~fgv~~ 53 (148)
..+.-+.+.+|+-.||++|||.-
T Consensus 35 lg~DSld~veLi~~lE~~f~i~i 57 (80)
T COG0236 35 LGLDSLDLVELVMALEEEFGIEI 57 (80)
T ss_pred cCccHHHHHHHHHHHHHHHCCcC
Confidence 45666788999999999999854
No 62
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=28.64 E-value=1e+02 Score=23.30 Aligned_cols=25 Identities=16% Similarity=0.436 Sum_probs=19.4
Q ss_pred hhHHHHHHHHHHcCCCHHHHHHHHhh
Q 045361 95 ARIAVIKAVRTLTNLALKEAKDLIEG 120 (148)
Q Consensus 95 kKi~vIK~vR~it~LgLkEAK~lVe~ 120 (148)
.++..|+.+|. +|++|+|.|++++.
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 46666666664 69999999999974
No 63
>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=27.32 E-value=77 Score=23.25 Aligned_cols=25 Identities=24% Similarity=0.502 Sum_probs=19.2
Q ss_pred hhHHHHHHHHHHcCCCHHHHHHHHhh
Q 045361 95 ARIAVIKAVRTLTNLALKEAKDLIEG 120 (148)
Q Consensus 95 kKi~vIK~vR~it~LgLkEAK~lVe~ 120 (148)
.++..|+.+|+ +|++|.|.|++++.
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 45666666664 59999999999974
No 64
>PF04461 DUF520: Protein of unknown function (DUF520); InterPro: IPR007551 This entry represents the UPF0234 family of uncharacterised proteins.; PDB: 1IN0_A.
Probab=27.14 E-value=40 Score=27.15 Aligned_cols=63 Identities=21% Similarity=0.305 Sum_probs=33.0
Q ss_pred eEEEecCCCchhHHHHHH-HHHH-c--CCCHHHHHHH-Hhh-------cChhhhcCCCHHHHHHHHHHHHHcCCcC
Q 045361 85 DVVIDEVPSNARIAVIKA-VRTL-T--NLALKEAKDL-IEG-------LPKKFKEGVSKDDAEAAKKQLEEAGAKF 148 (148)
Q Consensus 85 dV~L~~~~~~kKi~vIK~-vR~i-t--~LgLkEAK~l-Ve~-------~P~~IKe~vsKeeAE~ik~kle~aGA~V 148 (148)
.++|..-+ +.|+.-+.. ++.- . |+.++=-.-- .+. ....|++|+++|.|.+|.+.+++.+-+|
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~klKV 119 (160)
T PF04461_consen 45 TITLTAED-EFKLKQVKDILRSKLIKRGIDLKALDFGKIESASGGTVRQVIKLKQGIDQDTAKKIVKLIKDSKLKV 119 (160)
T ss_dssp EEEEEESS-HHHHHHHHHHHHHHHHHTT--GGGEE--SS-EEETTEEEEEEEE--S--HHHHHHHHHHHHHH--SE
T ss_pred EEEEEeCC-HHHHHHHHHHHHHHHHHcCCCHHHcCCCCCccccCCEEEEEEEeecccCHHHHHHHHHHHHhcCCce
Confidence 77887755 666655444 3432 1 5655421111 111 1246899999999999999999987664
No 65
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=26.37 E-value=91 Score=22.11 Aligned_cols=29 Identities=28% Similarity=0.410 Sum_probs=22.3
Q ss_pred chhHHHHHHHHHHcCCCHHHHHHHHhhcCh
Q 045361 94 NARIAVIKAVRTLTNLALKEAKDLIEGLPK 123 (148)
Q Consensus 94 ~kKi~vIK~vR~it~LgLkEAK~lVe~~P~ 123 (148)
-..+.+|+..| .+|++|++-|++++....
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 35666666666 689999999999987653
No 66
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=26.23 E-value=1.4e+02 Score=23.35 Aligned_cols=25 Identities=16% Similarity=0.227 Sum_probs=20.2
Q ss_pred hhHHHHHHHHHHcCCCHHHHHHHHhh
Q 045361 95 ARIAVIKAVRTLTNLALKEAKDLIEG 120 (148)
Q Consensus 95 kKi~vIK~vR~it~LgLkEAK~lVe~ 120 (148)
.++..|+.+|+ +|++|.|-+++++.
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 56677777774 79999999999975
No 67
>PRK05828 acyl carrier protein; Validated
Probab=25.83 E-value=88 Score=21.98 Aligned_cols=23 Identities=4% Similarity=0.196 Sum_probs=20.0
Q ss_pred hcCCHHHHHHHHHHHHHHhCCCc
Q 045361 31 SSLTLQEVCNLVDYLQDKLGVSA 53 (148)
Q Consensus 31 ~~LtllE~~eLv~~le~~fgv~~ 53 (148)
..+.-+..-+|+-.||++|||.=
T Consensus 35 Lg~DSLd~velv~~lE~~f~I~i 57 (84)
T PRK05828 35 LKIDSLDMFSIIVSLESEFNIEF 57 (84)
T ss_pred cCCCHHHHHHHHHHHHHHHCCCc
Confidence 67788899999999999999853
No 68
>PRK00199 ihfB integration host factor subunit beta; Reviewed
Probab=25.70 E-value=47 Score=23.20 Aligned_cols=35 Identities=9% Similarity=0.322 Sum_probs=29.2
Q ss_pred hHHHHHHHHH-HcCCCHHHHHHHHhhcChhhhcCCC
Q 045361 96 RIAVIKAVRT-LTNLALKEAKDLIEGLPKKFKEGVS 130 (148)
Q Consensus 96 Ki~vIK~vR~-it~LgLkEAK~lVe~~P~~IKe~vs 130 (148)
|-.+|+.|.+ .++++-++++.+|+.+-..|.+.+.
T Consensus 3 k~eli~~ia~~~~~~s~~~~~~vv~~~~~~i~~~L~ 38 (94)
T PRK00199 3 KSELIERLAARNPHLSAKDVENAVKEILEEMSDALA 38 (94)
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 5688999987 4799999999999999888776553
No 69
>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=25.69 E-value=1e+02 Score=19.25 Aligned_cols=23 Identities=22% Similarity=0.393 Sum_probs=19.1
Q ss_pred hcCCHHHHHHHHHHHHHHhCCCc
Q 045361 31 SSLTLQEVCNLVDYLQDKLGVSA 53 (148)
Q Consensus 31 ~~LtllE~~eLv~~le~~fgv~~ 53 (148)
..++-+.+.+|+..|+++||+.-
T Consensus 27 lG~DSl~~~~l~~~l~~~~g~~i 49 (67)
T PF00550_consen 27 LGLDSLDAIELVSELEEEFGIKI 49 (67)
T ss_dssp TTSSHHHHHHHHHHHHHHHTSST
T ss_pred hCCchHHHHHHHHHHHHHHcCCC
Confidence 45677888999999999999854
No 70
>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=25.68 E-value=92 Score=23.17 Aligned_cols=26 Identities=23% Similarity=0.466 Sum_probs=20.8
Q ss_pred hhHHHHHHHHHHcCCCHHHHHHHHhhc
Q 045361 95 ARIAVIKAVRTLTNLALKEAKDLIEGL 121 (148)
Q Consensus 95 kKi~vIK~vR~it~LgLkEAK~lVe~~ 121 (148)
..+..|+.+|+ +|++|+|-|++++..
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 56677777764 899999999999853
No 71
>PRK12449 acyl carrier protein; Provisional
Probab=25.58 E-value=1.2e+02 Score=20.11 Aligned_cols=25 Identities=8% Similarity=0.206 Sum_probs=20.1
Q ss_pred HHhcCCHHHHHHHHHHHHHHhCCCc
Q 045361 29 EISSLTLQEVCNLVDYLQDKLGVSA 53 (148)
Q Consensus 29 ~i~~LtllE~~eLv~~le~~fgv~~ 53 (148)
.-..+.-+...+|+-.+|++|||.-
T Consensus 33 ~dlg~DSl~~~~li~~lE~~f~i~i 57 (80)
T PRK12449 33 DDLAVDSIELVEFIINVEDEFHIAI 57 (80)
T ss_pred HHcCCcHHHHHHHHHHHHHHhCCCC
Confidence 4456677788999999999999954
No 72
>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=25.41 E-value=89 Score=23.13 Aligned_cols=31 Identities=6% Similarity=0.228 Sum_probs=21.8
Q ss_pred CCChHHHHHHHHHHhcCCHHHHHHHHHHHHHHhC
Q 045361 17 VEAPEKIEKLATEISSLTLQEVCNLVDYLQDKLG 50 (148)
Q Consensus 17 ~~~~~kv~~ivd~i~~LtllE~~eLv~~le~~fg 50 (148)
...+.++..+++.|...++ .+|+.....+++
T Consensus 32 eVe~~~~~~~~~aLaGk~V---~eli~~g~~kl~ 62 (105)
T cd04411 32 EIEPERVKLFLSALNGKNI---DEVISKGKELMS 62 (105)
T ss_pred CcCHHHHHHHHHHHcCCCH---HHHHHHHHhhcc
Confidence 3445677777787777765 667777878875
No 73
>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=25.39 E-value=95 Score=23.28 Aligned_cols=27 Identities=22% Similarity=0.345 Sum_probs=20.8
Q ss_pred hhHHHHHHHHHHcCCCHHHHHHHHhhcC
Q 045361 95 ARIAVIKAVRTLTNLALKEAKDLIEGLP 122 (148)
Q Consensus 95 kKi~vIK~vR~it~LgLkEAK~lVe~~P 122 (148)
.++..|+..|. +|++|.|.+.++.-..
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 46666666665 8999999999987543
No 74
>PRK06402 rpl12p 50S ribosomal protein L12P; Reviewed
Probab=25.13 E-value=67 Score=24.08 Aligned_cols=20 Identities=10% Similarity=0.410 Sum_probs=10.7
Q ss_pred ChHHHHHHHHHHhcCCHHHH
Q 045361 19 APEKIEKLATEISSLTLQEV 38 (148)
Q Consensus 19 ~~~kv~~ivd~i~~LtllE~ 38 (148)
.+.++..+++.|...++-|+
T Consensus 34 ee~~~k~~v~aL~GkdIeEl 53 (106)
T PRK06402 34 DEARVKALVAALEDVNIEEA 53 (106)
T ss_pred cHHHHHHHHHHHcCCCHHHH
Confidence 33455566666666555443
No 75
>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=25.10 E-value=1e+02 Score=22.36 Aligned_cols=28 Identities=25% Similarity=0.341 Sum_probs=23.0
Q ss_pred chhHHHHHHHHHHcCCCHHHHHHHHhhcC
Q 045361 94 NARIAVIKAVRTLTNLALKEAKDLIEGLP 122 (148)
Q Consensus 94 ~kKi~vIK~vR~it~LgLkEAK~lVe~~P 122 (148)
-.++..|+.+|+ +|++|+|-+.+++...
T Consensus 43 ~~~l~~I~~lr~-~G~sl~eI~~~l~~~~ 70 (116)
T cd04769 43 VECLRFIKEARQ-LGFTLAELKAIFAGHE 70 (116)
T ss_pred HHHHHHHHHHHH-cCCCHHHHHHHHhccc
Confidence 367888888886 8999999999997643
No 76
>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=24.98 E-value=1.3e+02 Score=21.75 Aligned_cols=26 Identities=23% Similarity=0.390 Sum_probs=20.3
Q ss_pred hhHHHHHHHHHHcCCCHHHHHHHHhhc
Q 045361 95 ARIAVIKAVRTLTNLALKEAKDLIEGL 121 (148)
Q Consensus 95 kKi~vIK~vR~it~LgLkEAK~lVe~~ 121 (148)
..+..|+.+| -+|++|+|.|.+++..
T Consensus 45 ~~l~~I~~lr-~~G~sl~eI~~~l~~~ 70 (123)
T cd04770 45 ARLRFIRRAQ-ALGFSLAEIRELLSLR 70 (123)
T ss_pred HHHHHHHHHH-HCCCCHHHHHHHHHhh
Confidence 4666777776 3599999999999854
No 77
>PF00216 Bac_DNA_binding: Bacterial DNA-binding protein; InterPro: IPR000119 Bacteria synthesise a set of small, usually basic proteins of about 90 residues that bind DNA and are known as histone-like proteins [, ]. Examples include the HU protein in Escherichia coli is a dimer of closely related alpha and beta chains and in other bacteria can be a dimer of identical chains. HU-type proteins have been found in a variety of eubacteria, cyanobacteria and archaebacteria, and are also encoded in the chloroplast genome of some algae []. The integration host factor (IHF), a dimer of closely related chains which seem to function in genetic recombination as well as in translational and transcriptional control [] is found in enterobacteria and viral proteins include the African Swine fever virus protein A104R (or LMW5-AR) []. The exact function of these proteins is not yet clear but they are capable of wrapping DNA and stabilising it from denaturation under extreme environmental conditions. The structure is known for one of these proteins []. The protein exists as a dimer and two "beta-arms" function as the non-specific binding site for bacterial DNA. ; GO: 0003677 DNA binding; PDB: 3C4I_B 2O97_A 1MUL_A 1P78_A 1P51_C 1P71_B 2HT0_A 1OWG_A 2IIF_A 1OUZ_A ....
Probab=24.89 E-value=57 Score=22.03 Aligned_cols=34 Identities=24% Similarity=0.384 Sum_probs=28.5
Q ss_pred hHHHHHHHHHHcCCCHHHHHHHHhhcChhhhcCC
Q 045361 96 RIAVIKAVRTLTNLALKEAKDLIEGLPKKFKEGV 129 (148)
Q Consensus 96 Ki~vIK~vR~it~LgLkEAK~lVe~~P~~IKe~v 129 (148)
|-.+|+.|.+.+++.-++++..++.+=.+|.+.+
T Consensus 3 k~eli~~ia~~~~~s~~~v~~vl~~~~~~i~~~L 36 (90)
T PF00216_consen 3 KKELIKRIAEKTGLSKKDVEAVLDALFDVIKEAL 36 (90)
T ss_dssp HHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHH
Confidence 5689999999999999999999998776666543
No 78
>PRK07639 acyl carrier protein; Provisional
Probab=24.79 E-value=91 Score=21.78 Aligned_cols=27 Identities=11% Similarity=0.272 Sum_probs=21.3
Q ss_pred HHHHHhcCCHHHHHHHHHHHHHHhCCCc
Q 045361 26 LATEISSLTLQEVCNLVDYLQDKLGVSA 53 (148)
Q Consensus 26 ivd~i~~LtllE~~eLv~~le~~fgv~~ 53 (148)
+.+.+ .|.-+.+-+|+-.||++|||.-
T Consensus 32 l~edL-~lDSld~velv~~lE~~fgi~i 58 (86)
T PRK07639 32 LNEDL-YIDSVMMLQLIVYIEMDVKLCV 58 (86)
T ss_pred ccccc-CCChHHHHHHHHHHHHHHCCcc
Confidence 44443 6778889999999999999853
No 79
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=24.57 E-value=1.4e+02 Score=22.53 Aligned_cols=25 Identities=20% Similarity=0.445 Sum_probs=20.1
Q ss_pred hhHHHHHHHHHHcCCCHHHHHHHHhh
Q 045361 95 ARIAVIKAVRTLTNLALKEAKDLIEG 120 (148)
Q Consensus 95 kKi~vIK~vR~it~LgLkEAK~lVe~ 120 (148)
.++..|+.+|+ +|++|+|.+++++.
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 46777777765 69999999999974
No 80
>PF15209 IL31: Interleukin 31
Probab=24.57 E-value=1.2e+02 Score=23.96 Aligned_cols=42 Identities=29% Similarity=0.520 Sum_probs=29.5
Q ss_pred cccCCCCcCCChHHHHHHHHHHhcCCHHHHHHHHH-HHHHHhCCCcc
Q 045361 9 SHLRPLCAVEAPEKIEKLATEISSLTLQEVCNLVD-YLQDKLGVSAA 54 (148)
Q Consensus 9 ~~~~~~~~~~~~~kv~~ivd~i~~LtllE~~eLv~-~le~~fgv~~~ 54 (148)
+|..|+....++..+..|+++|..++- .|.+ .-++..||+..
T Consensus 1 sh~~~~~~~~p~~d~kkIi~eLq~~Sk----~Lledy~~kE~Gvp~~ 43 (137)
T PF15209_consen 1 SHMLPIHAPIPKSDIKKIIEELQALSK----KLLEDYKEKEKGVPES 43 (137)
T ss_pred CCcCCCCCCCChHHHHHHHHHHHHHHH----HHHHHHHHhhcCCCcc
Confidence 588887777777789999998887763 3333 33555888765
No 81
>PRK08172 putative acyl carrier protein IacP; Validated
Probab=24.28 E-value=81 Score=21.87 Aligned_cols=21 Identities=14% Similarity=0.230 Sum_probs=17.9
Q ss_pred CCHHHHHHHHHHHHHHhCCCc
Q 045361 33 LTLQEVCNLVDYLQDKLGVSA 53 (148)
Q Consensus 33 LtllE~~eLv~~le~~fgv~~ 53 (148)
+.-+..-+|+-.||++|||.=
T Consensus 36 ~DSld~v~lv~~lEe~F~I~i 56 (82)
T PRK08172 36 ADSLDLIDIVFGLSEEFDISC 56 (82)
T ss_pred CCHHHHHHHHHHHHHHHCCCc
Confidence 666788899999999999953
No 82
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=24.16 E-value=1.6e+02 Score=22.95 Aligned_cols=38 Identities=21% Similarity=0.169 Sum_probs=30.5
Q ss_pred cCCChHHHHHHHHHHhcCCHHHHHHHHHHHHHHhCCCcc
Q 045361 16 AVEAPEKIEKLATEISSLTLQEVCNLVDYLQDKLGVSAA 54 (148)
Q Consensus 16 ~~~~~~kv~~ivd~i~~LtllE~~eLv~~le~~fgv~~~ 54 (148)
+..+.+.++.|++.+..-. ..+.+++..|+.+|||.=.
T Consensus 62 ~kl~~~q~~~l~e~~~~k~-wTl~~~~~~l~~e~gv~y~ 99 (138)
T COG3415 62 RKLSEEQLEILLERLREKD-WTLKELVEELGLEFGVWYH 99 (138)
T ss_pred cccCHHHHHHHHHHHhccc-chHHHHHHHHhhhcCeEEe
Confidence 3445567888888888877 8899999999999999643
No 83
>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=24.03 E-value=1.1e+02 Score=22.21 Aligned_cols=25 Identities=20% Similarity=0.441 Sum_probs=19.5
Q ss_pred hhHHHHHHHHHHcCCCHHHHHHHHhh
Q 045361 95 ARIAVIKAVRTLTNLALKEAKDLIEG 120 (148)
Q Consensus 95 kKi~vIK~vR~it~LgLkEAK~lVe~ 120 (148)
..+..|+.+|+ +|++|.|.|.+++.
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 46666666664 79999999999874
No 84
>COG4575 ElaB Uncharacterized conserved protein [Function unknown]
Probab=23.93 E-value=90 Score=23.54 Aligned_cols=32 Identities=25% Similarity=0.463 Sum_probs=25.3
Q ss_pred HHHHHHHhhcChhhhcC--CCHHHHHHHHHHHHH
Q 045361 112 KEAKDLIEGLPKKFKEG--VSKDDAEAAKKQLEE 143 (148)
Q Consensus 112 kEAK~lVe~~P~~IKe~--vsKeeAE~ik~kle~ 143 (148)
-|-+.|++++-.+++.. .+++|+++++.+++.
T Consensus 15 ~el~~L~d~lEevL~ssg~~a~~e~~~lR~r~~~ 48 (104)
T COG4575 15 AELQELLDTLEEVLKSSGSLAGDEAEELRSKAES 48 (104)
T ss_pred HHHHHHHHHHHHHHHhcccchhhHHHHHHHHHHH
Confidence 45667788888888765 788999999998875
No 85
>PRK09184 acyl carrier protein; Provisional
Probab=23.86 E-value=96 Score=22.00 Aligned_cols=22 Identities=9% Similarity=0.220 Sum_probs=17.7
Q ss_pred hcCCHHHHHHHHHHHHHHhCCC
Q 045361 31 SSLTLQEVCNLVDYLQDKLGVS 52 (148)
Q Consensus 31 ~~LtllE~~eLv~~le~~fgv~ 52 (148)
.+|.-+.+-+|+-.||++||+.
T Consensus 40 LglDSld~velv~~lE~~fgi~ 61 (89)
T PRK09184 40 LGLDSIDILEIALVISKRYGFQ 61 (89)
T ss_pred CCCcHHHHHHHHHHHHHHHCCc
Confidence 3566678889999999999984
No 86
>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=23.83 E-value=1.1e+02 Score=22.61 Aligned_cols=24 Identities=25% Similarity=0.517 Sum_probs=19.5
Q ss_pred hhHHHHHHHHHHcCCCHHHHHHHHh
Q 045361 95 ARIAVIKAVRTLTNLALKEAKDLIE 119 (148)
Q Consensus 95 kKi~vIK~vR~it~LgLkEAK~lVe 119 (148)
.++..|+.+| -+|++|+|.+++++
T Consensus 45 ~~l~~I~~lr-~~G~sL~eI~~~l~ 68 (127)
T TIGR02044 45 DELRLISRAR-QVGFSLEECKELLN 68 (127)
T ss_pred HHHHHHHHHH-HCCCCHHHHHHHHH
Confidence 5667777766 48999999999997
No 87
>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=23.70 E-value=1.1e+02 Score=22.74 Aligned_cols=24 Identities=33% Similarity=0.634 Sum_probs=20.0
Q ss_pred hhHHHHHHHHHHcCCCHHHHHHHHh
Q 045361 95 ARIAVIKAVRTLTNLALKEAKDLIE 119 (148)
Q Consensus 95 kKi~vIK~vR~it~LgLkEAK~lVe 119 (148)
.++..|+.+|+ +|++|.|-|.+++
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 56777777764 8999999999987
No 88
>PF13592 HTH_33: Winged helix-turn helix
Probab=23.40 E-value=68 Score=20.76 Aligned_cols=17 Identities=18% Similarity=0.583 Sum_probs=14.2
Q ss_pred HHHHHHHHHHHhCCCcc
Q 045361 38 VCNLVDYLQDKLGVSAA 54 (148)
Q Consensus 38 ~~eLv~~le~~fgv~~~ 54 (148)
+.++...|+++|||.-+
T Consensus 7 ~~~i~~~I~~~fgv~ys 23 (60)
T PF13592_consen 7 LKEIAAYIEEEFGVKYS 23 (60)
T ss_pred HHHHHHHHHHHHCCEEc
Confidence 56888999999999754
No 89
>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator HspR and related proteins, 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 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=23.33 E-value=1.2e+02 Score=21.48 Aligned_cols=30 Identities=17% Similarity=0.228 Sum_probs=24.2
Q ss_pred hhHHHHHHHHHHcCCCHHHHHHHHhhcChh
Q 045361 95 ARIAVIKAVRTLTNLALKEAKDLIEGLPKK 124 (148)
Q Consensus 95 kKi~vIK~vR~it~LgLkEAK~lVe~~P~~ 124 (148)
..+..|+.+++-.|++|.+.+.+++...+.
T Consensus 45 ~~l~~I~~L~~~~G~~l~~i~~~l~l~~~~ 74 (98)
T cd01279 45 ELLRQVQRLSQDEGFNLAGIKRIIELYPQV 74 (98)
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHhhhHH
Confidence 567777777777899999999999876543
No 90
>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=23.13 E-value=51 Score=24.30 Aligned_cols=23 Identities=30% Similarity=0.515 Sum_probs=16.5
Q ss_pred HHHHHHHHHH----cCCCHHHHHHHHh
Q 045361 97 IAVIKAVRTL----TNLALKEAKDLIE 119 (148)
Q Consensus 97 i~vIK~vR~i----t~LgLkEAK~lVe 119 (148)
-.++..||++ ..|||.|||++--
T Consensus 61 ~~L~~~Ik~L~~~aYqLGl~EaKEmtR 87 (95)
T PF10044_consen 61 DQLIEKIKKLQDEAYQLGLEEAKEMTR 87 (95)
T ss_pred HHHHHHHHHHHHHHHHHhHHHHHHHHh
Confidence 3555566653 5899999999854
No 91
>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=22.86 E-value=1.2e+02 Score=24.89 Aligned_cols=39 Identities=28% Similarity=0.315 Sum_probs=29.2
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHhhcChhhhc--CCCHHHHHHHHHHHHHcCCc
Q 045361 97 IAVIKAVRTLTNLALKEAKDLIEGLPKKFKE--GVSKDDAEAAKKQLEEAGAK 147 (148)
Q Consensus 97 i~vIK~vR~it~LgLkEAK~lVe~~P~~IKe--~vsKeeAE~ik~kle~aGA~ 147 (148)
..+++.||+.+ +.|..+|- +++.++..++-+.++++|+.
T Consensus 151 ~eiv~~vr~~~------------~~pv~vKl~~~~~~~~~~~~a~~l~~~Gad 191 (289)
T cd02810 151 ANLLKAVKAAV------------DIPLLVKLSPYFDLEDIVELAKAAERAGAD 191 (289)
T ss_pred HHHHHHHHHcc------------CCCEEEEeCCCCCHHHHHHHHHHHHHcCCC
Confidence 35677777654 36877774 46777999999999999974
No 92
>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=22.76 E-value=1e+02 Score=25.47 Aligned_cols=38 Identities=32% Similarity=0.378 Sum_probs=29.0
Q ss_pred HHHHHHHHHcCCCHHHHHHHHhhcChhhhcCCCHHHHHHHHHHHHHcCCc
Q 045361 98 AVIKAVRTLTNLALKEAKDLIEGLPKKFKEGVSKDDAEAAKKQLEEAGAK 147 (148)
Q Consensus 98 ~vIK~vR~it~LgLkEAK~lVe~~P~~IKe~vsKeeAE~ik~kle~aGA~ 147 (148)
.+++.||+.+ ..|..+|=+...++..++-+.++++|+.
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 4788888777777888999999999974
No 93
>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=22.75 E-value=1.2e+02 Score=25.21 Aligned_cols=40 Identities=35% Similarity=0.345 Sum_probs=30.7
Q ss_pred hHHHHHHHHHHcCCCHHHHHHHHhhcChhhhcCCCHHHHHHHHHHHHHcCCc
Q 045361 96 RIAVIKAVRTLTNLALKEAKDLIEGLPKKFKEGVSKDDAEAAKKQLEEAGAK 147 (148)
Q Consensus 96 Ki~vIK~vR~it~LgLkEAK~lVe~~P~~IKe~vsKeeAE~ik~kle~aGA~ 147 (148)
-..+++.||+.+ ..|..+|=..+-++..++.+.++++|+.
T Consensus 145 ~~eiv~~vr~~~------------~~pv~vKi~~~~~~~~~~a~~l~~~G~d 184 (300)
T TIGR01037 145 SADVVKAVKDKT------------DVPVFAKLSPNVTDITEIAKAAEEAGAD 184 (300)
T ss_pred HHHHHHHHHHhc------------CCCEEEECCCChhhHHHHHHHHHHcCCC
Confidence 356677776643 3688888777778899999999999974
No 94
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domain
Probab=22.40 E-value=2e+02 Score=22.48 Aligned_cols=27 Identities=22% Similarity=0.402 Sum_probs=21.7
Q ss_pred hhHHHHHHHHHHcCCCHHHHHHHHhhcC
Q 045361 95 ARIAVIKAVRTLTNLALKEAKDLIEGLP 122 (148)
Q Consensus 95 kKi~vIK~vR~it~LgLkEAK~lVe~~P 122 (148)
.++..|+.+|+ +|++|.|.+.+++...
T Consensus 46 ~rL~~I~~lr~-~G~sL~eI~~ll~~~~ 72 (172)
T cd04790 46 ERLEQICAYRS-AGVSLEDIRSLLQQPG 72 (172)
T ss_pred HHHHHHHHHHH-cCCCHHHHHHHHhcCC
Confidence 57777777764 7999999999998654
No 95
>PRK06508 acyl carrier protein; Provisional
Probab=22.33 E-value=1.1e+02 Score=22.07 Aligned_cols=24 Identities=8% Similarity=0.155 Sum_probs=18.6
Q ss_pred HhcCCHHHHHHHHHHHHHHhCCCc
Q 045361 30 ISSLTLQEVCNLVDYLQDKLGVSA 53 (148)
Q Consensus 30 i~~LtllE~~eLv~~le~~fgv~~ 53 (148)
..++.-+...+|+-.||++|||.=
T Consensus 32 dL~~DSLd~veli~~lE~eFgI~i 55 (93)
T PRK06508 32 DLGIDSLDFLDIVFAIDKAFGIKL 55 (93)
T ss_pred ccCCCHHHHHHHHHHHHHHHCCcc
Confidence 345556778899999999999853
No 96
>PF00237 Ribosomal_L22: Ribosomal protein L22p/L17e; InterPro: IPR001063 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L22 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L22 is known to bind 23S rRNA. It belongs to a family of ribosomal proteins which includes: bacterial L22; algal and plant chloroplast L22 (in legumes L22 is encoded in the nucleus instead of the chloroplast); cyanelle L22; archaebacterial L22; mammalian L17; plant L17 and yeast YL17.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3CD6_R 1Q7Y_S 1VQ6_R 1YI2_R 1QVF_Q 3CCR_R 3CCU_R 3CCL_R 1YJ9_R 3CCQ_R ....
Probab=22.27 E-value=1.1e+02 Score=21.89 Aligned_cols=29 Identities=17% Similarity=0.405 Sum_probs=22.6
Q ss_pred CCChHHHHHHHHHHhcCCHHHHHHHHHHH
Q 045361 17 VEAPEKIEKLATEISSLTLQEVCNLVDYL 45 (148)
Q Consensus 17 ~~~~~kv~~ivd~i~~LtllE~~eLv~~l 45 (148)
..|+.|...+++.|..|++.|+-...+.+
T Consensus 7 ~~S~kk~~~v~~~Irg~~v~~A~~~L~~~ 35 (105)
T PF00237_consen 7 RISPKKLREVARLIRGMSVDEAIAQLKFV 35 (105)
T ss_dssp SS-HHHHHHHHHHHTTSBHHHHHHHHHHH
T ss_pred cCCHHHHHHHHHHHcCCCHHHHHHHHHhC
Confidence 45678999999999999999976555543
No 97
>PRK00565 rplV 50S ribosomal protein L22; Reviewed
Probab=22.17 E-value=1.2e+02 Score=22.34 Aligned_cols=28 Identities=18% Similarity=0.300 Sum_probs=23.4
Q ss_pred CCChHHHHHHHHHHhcCCHHHHHHHHHH
Q 045361 17 VEAPEKIEKLATEISSLTLQEVCNLVDY 44 (148)
Q Consensus 17 ~~~~~kv~~ivd~i~~LtllE~~eLv~~ 44 (148)
..||.|+..+++.|..|++.|+-.....
T Consensus 11 ~~SpkK~~~v~~~IrG~~v~~A~~~L~~ 38 (112)
T PRK00565 11 RVSPRKARLVADLIRGKKVEEALAILKF 38 (112)
T ss_pred ccCHHHHHHHHHHHcCCcHHHHHHHHHH
Confidence 4577899999999999999998766553
No 98
>PRK07117 acyl carrier protein; Validated
Probab=22.02 E-value=1.1e+02 Score=21.19 Aligned_cols=22 Identities=9% Similarity=0.078 Sum_probs=19.9
Q ss_pred hcCCHHHHHHHHHHHHHHhCCC
Q 045361 31 SSLTLQEVCNLVDYLQDKLGVS 52 (148)
Q Consensus 31 ~~LtllE~~eLv~~le~~fgv~ 52 (148)
.++.-+...+|+-.++++|||.
T Consensus 35 Lg~DSlD~veiv~~led~f~i~ 56 (79)
T PRK07117 35 LGANSMDRAEIVIMTLESLSLK 56 (79)
T ss_pred cCCChHHHHHHHHHHHHHHCCc
Confidence 7788899999999999999984
No 99
>PTZ00373 60S Acidic ribosomal protein P2; Provisional
Probab=21.80 E-value=1.3e+02 Score=22.68 Aligned_cols=30 Identities=13% Similarity=0.111 Sum_probs=19.4
Q ss_pred CCChHHHHHHHHHHhcCCHHHHHHHHHHHHHHh
Q 045361 17 VEAPEKIEKLATEISSLTLQEVCNLVDYLQDKL 49 (148)
Q Consensus 17 ~~~~~kv~~ivd~i~~LtllE~~eLv~~le~~f 49 (148)
...+.++..+++.|..-++ .||+..=.++|
T Consensus 35 eVd~~~~~l~~~~L~GKdI---~ELIa~G~~kl 64 (112)
T PTZ00373 35 DVEDDVLDNFFKSLEGKTP---HELIAAGMKKL 64 (112)
T ss_pred CccHHHHHHHHHHHcCCCH---HHHHHHhHHHH
Confidence 4455677778888777666 45565555555
No 100
>PRK13019 clpS ATP-dependent Clp protease adaptor; Reviewed
Probab=21.32 E-value=3.3e+02 Score=19.74 Aligned_cols=69 Identities=16% Similarity=0.116 Sum_probs=51.3
Q ss_pred cccceeEEEecCCCchhHHHH-HHHHHHcCCCHHHHHHHHhhcC---hhhhcCCCHHHHHHHHHHHHHcCCcC
Q 045361 80 EKTEFDVVIDEVPSNARIAVI-KAVRTLTNLALKEAKDLIEGLP---KKFKEGVSKDDAEAAKKQLEEAGAKF 148 (148)
Q Consensus 80 EKt~fdV~L~~~~~~kKi~vI-K~vR~it~LgLkEAK~lVe~~P---~~IKe~vsKeeAE~ik~kle~aGA~V 148 (148)
....|.|+|-+=|-.--==|| ..++.+.+++..+|..+.-.+= +-|=---++|.||-...++...|.++
T Consensus 18 ~p~~ykViL~NDd~~t~dfVi~~vl~~vf~~s~~~A~~iml~vH~~G~avv~~~~~E~AE~~~~~l~~~glt~ 90 (94)
T PRK13019 18 RYPLYKVIVLNDDFNTFEHVVNCLLKAIPGMSEDRAWRLMITAHKEGSAVVWVGPLEQAELYHQQLTDAGLTM 90 (94)
T ss_pred CCCceEEEEEcCCCCCHHHHHHHHHHHhcCCCHHHHHHHHHHHhcCCcEEEEEecHHHHHHHHHHHHHccccc
Confidence 446799999764433344688 6777889999999999876542 33333368999999999999999764
No 101
>PRK00982 acpP acyl carrier protein; Provisional
Probab=21.29 E-value=1.3e+02 Score=19.76 Aligned_cols=22 Identities=18% Similarity=0.335 Sum_probs=17.9
Q ss_pred cCCHHHHHHHHHHHHHHhCCCc
Q 045361 32 SLTLQEVCNLVDYLQDKLGVSA 53 (148)
Q Consensus 32 ~LtllE~~eLv~~le~~fgv~~ 53 (148)
.+.=+...+|+..|+++||+.-
T Consensus 34 glDSl~~~~li~~le~~f~i~i 55 (78)
T PRK00982 34 GADSLDTVELVMALEEEFGIEI 55 (78)
T ss_pred CCCHHHHHHHHHHHHHHHCCCc
Confidence 5666778899999999999853
No 102
>cd04786 HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic su
Probab=21.24 E-value=1.3e+02 Score=22.72 Aligned_cols=26 Identities=15% Similarity=0.321 Sum_probs=20.8
Q ss_pred hhHHHHHHHHHHcCCCHHHHHHHHhhc
Q 045361 95 ARIAVIKAVRTLTNLALKEAKDLIEGL 121 (148)
Q Consensus 95 kKi~vIK~vR~it~LgLkEAK~lVe~~ 121 (148)
.++..|+.+|. +|++|.|.|.++...
T Consensus 45 ~~l~~I~~lr~-~GfsL~eI~~ll~~~ 70 (131)
T cd04786 45 WVLEIISSAQQ-AGFSLDEIRQLLPAD 70 (131)
T ss_pred HHHHHHHHHHH-cCCCHHHHHHHHhcc
Confidence 56777777765 799999999999753
No 103
>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=20.82 E-value=1.3e+02 Score=22.88 Aligned_cols=27 Identities=30% Similarity=0.518 Sum_probs=22.7
Q ss_pred hhHHHHHHHHHHcCCCHHHHHHHHhhcC
Q 045361 95 ARIAVIKAVRTLTNLALKEAKDLIEGLP 122 (148)
Q Consensus 95 kKi~vIK~vR~it~LgLkEAK~lVe~~P 122 (148)
.++..|+.+|+ .|+.|.|.|++++..-
T Consensus 44 ~~l~~I~~lr~-~G~sL~eI~~~l~~~~ 70 (134)
T cd04779 44 DRLQLIEHLKG-QRLSLAEIKDQLEEVQ 70 (134)
T ss_pred HHHHHHHHHHH-CCCCHHHHHHHHHhhc
Confidence 67888888874 8999999999998654
No 104
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil
Probab=20.69 E-value=2e+02 Score=20.41 Aligned_cols=26 Identities=19% Similarity=0.259 Sum_probs=20.2
Q ss_pred hhHHHHHHHHHHcCCCHHHHHHHHhhc
Q 045361 95 ARIAVIKAVRTLTNLALKEAKDLIEGL 121 (148)
Q Consensus 95 kKi~vIK~vR~it~LgLkEAK~lVe~~ 121 (148)
.++..|+.+|+ +|++|.|.+.++..-
T Consensus 45 ~~l~~I~~l~~-~G~~l~ei~~~~~~~ 70 (102)
T cd04775 45 SRLEKIVFLQA-GGLPLEEIAGCLAQP 70 (102)
T ss_pred HHHHHHHHHHH-CCCCHHHHHHHHcCC
Confidence 46677777765 699999999998753
No 105
>PF03461 TRCF: TRCF domain; InterPro: IPR005118 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli. A lesion in the template strand blocks the RNA polymerase complex (RNAP). The RNAP-DNA-RNA complex is specifically recognised by the transcription-repair-coupling factor (TRCF) which releases RNAP and the truncated transcript.; GO: 0003684 damaged DNA binding, 0004386 helicase activity, 0005524 ATP binding, 0006281 DNA repair; PDB: 2QSR_A 2EYQ_A.
Probab=20.52 E-value=1e+02 Score=22.04 Aligned_cols=30 Identities=23% Similarity=0.282 Sum_probs=21.2
Q ss_pred HHHHHHHhcCC-HHHHHHHHHHHHHHhCCCc
Q 045361 24 EKLATEISSLT-LQEVCNLVDYLQDKLGVSA 53 (148)
Q Consensus 24 ~~ivd~i~~Lt-llE~~eLv~~le~~fgv~~ 53 (148)
-++-..|.+.. .-|+.+|...|+++||-..
T Consensus 20 l~~Yrrl~~~~~~~el~~l~~El~DRFG~~P 50 (101)
T PF03461_consen 20 LELYRRLASAESEEELEDLREELIDRFGPLP 50 (101)
T ss_dssp HHHHHHHHC--SHHHHHHHHHHHHHHH-S--
T ss_pred HHHHHHHhhCCCHHHHHHHHHHHHHHcCCCc
Confidence 34677777765 8899999999999999654
No 106
>cd04772 HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.
Probab=20.38 E-value=1.3e+02 Score=21.35 Aligned_cols=23 Identities=9% Similarity=0.252 Sum_probs=16.5
Q ss_pred hHHHHHHHHHHcCCCHHHHHHHHhh
Q 045361 96 RIAVIKAVRTLTNLALKEAKDLIEG 120 (148)
Q Consensus 96 Ki~vIK~vR~it~LgLkEAK~lVe~ 120 (148)
.+..|+.+| .|+||.+.++++..
T Consensus 46 ~l~~I~~l~--~g~~l~~i~~~~~~ 68 (99)
T cd04772 46 ALRAYRALL--PGYGYRVAQRIMRA 68 (99)
T ss_pred HHHHHHHHh--hCCCHHHHHHHHHH
Confidence 444455444 69999999988875
No 107
>PRK07259 dihydroorotate dehydrogenase 1B; Reviewed
Probab=20.25 E-value=1.3e+02 Score=24.99 Aligned_cols=40 Identities=33% Similarity=0.348 Sum_probs=30.7
Q ss_pred hHHHHHHHHHHcCCCHHHHHHHHhhcChhhhcCCCHHHHHHHHHHHHHcCCc
Q 045361 96 RIAVIKAVRTLTNLALKEAKDLIEGLPKKFKEGVSKDDAEAAKKQLEEAGAK 147 (148)
Q Consensus 96 Ki~vIK~vR~it~LgLkEAK~lVe~~P~~IKe~vsKeeAE~ik~kle~aGA~ 147 (148)
=..+++.||+.+ ..|..+|=+.+-++..++-+.++++|+.
T Consensus 145 ~~eiv~~vr~~~------------~~pv~vKl~~~~~~~~~~a~~l~~~G~d 184 (301)
T PRK07259 145 AYEVVKAVKEVV------------KVPVIVKLTPNVTDIVEIAKAAEEAGAD 184 (301)
T ss_pred HHHHHHHHHHhc------------CCCEEEEcCCCchhHHHHHHHHHHcCCC
Confidence 456677777654 4688888777778888999999999973
No 108
>PF07377 DUF1493: Protein of unknown function (DUF1493); InterPro: IPR010862 This family consists of several bacterial proteins of around 115 residues in length. Members of this family are largely found in Salmonella and Yersinia species and several have been described as being putative cytoplasmic proteins. The function of this family is unknown.
Probab=20.22 E-value=1.4e+02 Score=21.65 Aligned_cols=26 Identities=15% Similarity=0.293 Sum_probs=23.0
Q ss_pred hcCCHHHHHHHHHHHHHHhCCCcccc
Q 045361 31 SSLTLQEVCNLVDYLQDKLGVSAAAF 56 (148)
Q Consensus 31 ~~LtllE~~eLv~~le~~fgv~~~~~ 56 (148)
..++--++.+|...+.++|||+...+
T Consensus 37 L~~~~dda~elm~~f~~~F~Vd~~~f 62 (111)
T PF07377_consen 37 LGLDGDDAEELMEDFFERFNVDLSDF 62 (111)
T ss_pred cCCCHHHHHHHHHHHHHHhCCCcCcc
Confidence 67889999999999999999987653
No 109
>TIGR00987 himA integration host factor, alpha subunit. This protein forms a site-specific DNA-binding heterodimer with the integration host factor beta subunit. It is closely related to the DNA-binding protein HU.
Probab=20.12 E-value=77 Score=22.30 Aligned_cols=35 Identities=17% Similarity=0.256 Sum_probs=29.6
Q ss_pred hHHHHHHHHHHcCCCHHHHHHHHhhcChhhhcCCC
Q 045361 96 RIAVIKAVRTLTNLALKEAKDLIEGLPKKFKEGVS 130 (148)
Q Consensus 96 Ki~vIK~vR~it~LgLkEAK~lVe~~P~~IKe~vs 130 (148)
|-.+|+.|.+.+++.-++++..++.+-.+|.+.+.
T Consensus 4 k~eli~~ia~~~~~s~~~v~~vv~~~~~~i~~~L~ 38 (96)
T TIGR00987 4 KAEMSEYLFDELGLSKREAKELVELFFEEIRRALE 38 (96)
T ss_pred HHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 56889999999999999999999998877766543
Done!