Query psy13246
Match_columns 81
No_of_seqs 115 out of 849
Neff 5.2
Searched_HMMs 46136
Date Fri Aug 16 23:51:35 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13246.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13246hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0096 RpsH Ribosomal protein 100.0 9.9E-29 2.1E-33 169.2 7.3 74 1-75 1-80 (132)
2 PTZ00158 40S ribosomal protein 99.9 4.5E-27 9.8E-32 160.3 8.0 75 1-75 1-81 (130)
3 KOG1754|consensus 99.9 7.7E-26 1.7E-30 154.0 7.6 77 1-77 1-83 (130)
4 PLN00146 40S ribosomal protein 99.9 1.5E-25 3.2E-30 152.3 7.9 75 1-75 1-81 (130)
5 PRK04034 rps8p 30S ribosomal p 99.9 8.3E-25 1.8E-29 148.2 7.9 74 1-74 1-80 (130)
6 CHL00042 rps8 ribosomal protei 99.9 1.7E-22 3.7E-27 137.4 7.7 60 3-63 2-61 (132)
7 PRK00136 rpsH 30S ribosomal pr 99.8 6.7E-21 1.4E-25 129.0 7.8 61 2-63 1-61 (130)
8 PF00410 Ribosomal_S8: Ribosom 99.8 2.4E-19 5.2E-24 120.6 8.1 70 5-75 1-86 (129)
9 PF09639 YjcQ: YjcQ protein; 85.6 0.45 9.8E-06 30.0 1.2 25 31-55 24-48 (88)
10 COG1244 Predicted Fe-S oxidore 69.7 7.2 0.00016 31.0 3.8 44 4-48 220-263 (358)
11 PF00919 UPF0004: Uncharacteri 68.1 11 0.00024 24.0 3.9 32 34-69 16-47 (98)
12 COG1695 Predicted transcriptio 66.8 4.1 9E-05 26.6 1.7 39 29-68 42-82 (138)
13 PF13601 HTH_34: Winged helix 60.5 8.9 0.00019 23.5 2.3 22 35-56 32-53 (80)
14 PF13463 HTH_27: Winged helix 55.2 17 0.00037 20.4 2.7 29 34-62 35-63 (68)
15 PF13732 DUF4162: Domain of un 54.2 22 0.00047 21.0 3.2 32 23-55 43-74 (84)
16 PF03551 PadR: Transcriptional 53.0 13 0.00028 21.9 2.0 27 28-54 28-54 (75)
17 PF13412 HTH_24: Winged helix- 50.2 16 0.00034 19.7 1.9 18 31-48 31-48 (48)
18 PF08438 MMR_HSR1_C: GTPase of 49.8 25 0.00054 23.3 3.2 37 8-48 11-47 (109)
19 PF10264 Stork_head: Winged he 48.9 20 0.00044 22.7 2.5 36 11-47 32-67 (80)
20 cd04882 ACT_Bt0572_2 C-termina 48.0 45 0.00098 18.1 3.9 24 21-46 39-62 (65)
21 PF08479 POTRA_2: POTRA domain 47.6 45 0.00097 19.6 3.8 35 29-63 35-71 (76)
22 COG2519 GCD14 tRNA(1-methylade 47.3 45 0.00097 25.4 4.6 41 8-48 175-215 (256)
23 PF01726 LexA_DNA_bind: LexA D 44.4 21 0.00046 21.2 2.0 21 29-49 38-58 (65)
24 PF09012 FeoC: FeoC like trans 44.1 22 0.00048 20.8 2.1 24 31-54 28-51 (69)
25 TIGR03433 padR_acidobact trans 43.6 23 0.00049 22.3 2.2 26 29-54 37-62 (100)
26 PF13541 ChlI: Subunit ChlI of 41.8 17 0.00037 24.2 1.4 26 6-32 96-121 (121)
27 PF13730 HTH_36: Helix-turn-he 41.3 29 0.00062 19.0 2.2 17 31-47 39-55 (55)
28 PF01047 MarR: MarR family; I 40.7 28 0.00062 19.1 2.1 26 32-57 32-57 (59)
29 PHA02943 hypothetical protein; 40.6 24 0.00051 25.4 2.1 21 31-51 38-58 (165)
30 PF02082 Rrf2: Transcriptional 39.0 22 0.00047 21.4 1.5 20 31-50 39-58 (83)
31 cd08788 CARD_NOD2_2_CARD15 Cas 38.4 25 0.00055 22.5 1.8 23 30-52 12-34 (81)
32 PF07006 DUF1310: Protein of u 36.5 32 0.00069 23.2 2.1 16 40-55 56-71 (122)
33 COG1846 MarR Transcriptional r 36.2 40 0.00086 20.2 2.4 32 31-62 50-81 (126)
34 PRK09954 putative kinase; Prov 35.8 75 0.0016 23.7 4.3 29 30-58 30-58 (362)
35 TIGR01889 Staph_reg_Sar staphy 35.7 25 0.00053 22.2 1.4 35 33-68 59-93 (109)
36 PF02813 Retro_M: Retroviral M 34.9 22 0.00047 22.9 1.0 24 28-51 19-42 (86)
37 smart00667 LisH Lissencephaly 33.9 43 0.00093 15.9 1.9 20 31-50 4-23 (34)
38 PF01963 TraB: TraB family; I 33.4 92 0.002 21.8 4.2 39 8-46 214-254 (259)
39 PF09572 RE_XamI: XamI restric 33.1 52 0.0011 25.1 3.0 24 14-48 117-140 (251)
40 smart00347 HTH_MARR helix_turn 33.0 52 0.0011 19.2 2.5 32 31-62 38-69 (101)
41 PF13670 PepSY_2: Peptidase pr 32.6 1.1E+02 0.0025 18.2 4.4 13 34-46 31-43 (83)
42 PF12025 Phage_C: Phage protei 32.3 38 0.00082 20.9 1.8 14 34-47 55-68 (68)
43 PF01022 HTH_5: Bacterial regu 32.0 25 0.00053 19.1 0.9 15 34-48 32-46 (47)
44 PF12802 MarR_2: MarR family; 31.8 44 0.00096 18.3 1.9 24 33-56 37-60 (62)
45 PF12792 CSS-motif: CSS motif 31.7 63 0.0014 21.4 3.0 30 28-57 38-68 (208)
46 COG1522 Lrp Transcriptional re 31.7 62 0.0014 20.9 2.9 25 31-55 36-60 (154)
47 PF09339 HTH_IclR: IclR helix- 31.6 37 0.00081 18.6 1.6 16 33-48 34-49 (52)
48 PF02829 3H: 3H domain; Inter 31.4 71 0.0015 20.7 3.1 41 6-47 48-97 (98)
49 PF05818 TraT: Enterobacterial 31.0 42 0.0009 24.9 2.1 38 32-73 37-78 (215)
50 PF02002 TFIIE_alpha: TFIIE al 31.0 52 0.0011 20.5 2.4 27 31-57 41-67 (105)
51 PRK00111 hypothetical protein; 30.2 43 0.00093 24.1 2.0 19 1-19 1-19 (180)
52 TIGR00537 hemK_rel_arch HemK-r 29.7 1.3E+02 0.0028 20.1 4.3 41 6-46 118-158 (179)
53 TIGR02337 HpaR homoprotocatech 29.0 55 0.0012 20.6 2.2 35 33-68 58-92 (118)
54 PRK14336 (dimethylallyl)adenos 28.7 79 0.0017 24.8 3.5 31 34-68 18-48 (418)
55 COG0325 Predicted enzyme with 28.5 54 0.0012 24.5 2.4 45 1-45 1-49 (228)
56 PF02618 YceG: YceG-like famil 28.5 89 0.0019 23.5 3.6 43 6-50 55-97 (297)
57 PF06819 Arc_PepC: Archaeal Pe 28.2 1.2E+02 0.0026 20.3 3.8 42 8-49 56-106 (110)
58 COG1777 Predicted transcriptio 28.0 63 0.0014 24.1 2.7 28 30-57 41-69 (217)
59 PF08643 DUF1776: Fungal famil 28.0 48 0.001 25.5 2.1 27 21-48 2-31 (299)
60 PRK03573 transcriptional regul 27.6 62 0.0014 20.9 2.4 30 33-62 62-91 (144)
61 PRK14327 (dimethylallyl)adenos 27.3 94 0.002 25.4 3.8 32 34-69 83-114 (509)
62 PRK14340 (dimethylallyl)adenos 27.2 82 0.0018 25.0 3.3 31 34-68 23-53 (445)
63 PF10866 DUF2704: Protein of u 27.2 36 0.00078 24.5 1.2 13 66-78 146-159 (168)
64 TIGR00089 RNA modification enz 27.1 92 0.002 24.2 3.6 31 34-68 16-46 (429)
65 PF02631 RecX: RecX family; I 26.0 63 0.0014 20.6 2.1 22 31-52 8-29 (121)
66 PF03869 Arc: Arc-like DNA bin 25.9 1.2E+02 0.0026 17.1 3.1 37 9-49 14-50 (50)
67 smart00419 HTH_CRP helix_turn_ 25.8 69 0.0015 16.4 2.0 17 32-48 23-39 (48)
68 smart00463 SMR Small MutS-rela 25.5 1.5E+02 0.0033 17.4 5.2 56 4-63 12-77 (80)
69 PF14044 NETI: NETI protein 25.2 49 0.0011 19.9 1.3 14 35-48 11-24 (57)
70 TIGR00373 conserved hypothetic 25.2 1.2E+02 0.0027 20.8 3.6 24 30-54 41-64 (158)
71 PRK14862 rimO ribosomal protei 24.9 1.1E+02 0.0024 24.1 3.7 33 34-70 24-56 (440)
72 PRK09333 30S ribosomal protein 24.5 62 0.0013 22.7 2.0 21 29-49 93-113 (150)
73 PRK11512 DNA-binding transcrip 24.2 68 0.0015 20.9 2.1 35 33-68 70-104 (144)
74 PF08513 LisH: LisH; InterPro 23.9 84 0.0018 15.4 1.9 17 33-49 3-19 (27)
75 COG4451 RbcS Ribulose bisphosp 23.8 67 0.0015 22.1 2.0 26 33-58 23-48 (127)
76 PRK14338 (dimethylallyl)adenos 23.7 1.1E+02 0.0024 24.3 3.5 31 34-68 37-67 (459)
77 PF04566 RNA_pol_Rpb2_4: RNA p 23.5 1.7E+02 0.0037 17.3 3.5 42 33-74 16-60 (63)
78 PRK11920 rirA iron-responsive 23.4 64 0.0014 21.9 1.9 21 31-51 38-58 (153)
79 TIGR02702 SufR_cyano iron-sulf 23.4 1.4E+02 0.003 20.8 3.6 39 30-68 119-158 (203)
80 PF00356 LacI: Bacterial regul 23.2 90 0.0019 17.3 2.2 19 31-49 28-46 (46)
81 TIGR01578 MiaB-like-B MiaB-lik 22.9 1.1E+02 0.0023 24.0 3.2 31 34-68 16-46 (420)
82 PF11061 DUF2862: Protein of u 22.8 68 0.0015 19.6 1.7 30 31-60 14-45 (64)
83 PRK14333 (dimethylallyl)adenos 22.4 1.1E+02 0.0023 24.2 3.2 31 34-68 23-53 (448)
84 PF01454 MAGE: MAGE family; I 22.0 74 0.0016 21.9 2.0 23 32-54 147-169 (195)
85 PRK14334 (dimethylallyl)adenos 21.6 1.2E+02 0.0027 23.7 3.4 31 34-68 17-47 (440)
86 PF14947 HTH_45: Winged helix- 21.5 81 0.0018 18.9 1.9 45 3-48 4-50 (77)
87 PF02205 WH2: WH2 motif; Inte 21.5 82 0.0018 16.2 1.6 16 4-19 2-17 (30)
88 PF07862 Nif11: Nitrogen fixat 21.0 63 0.0014 17.6 1.2 42 1-47 1-42 (49)
89 PRK14328 (dimethylallyl)adenos 21.0 1.3E+02 0.0028 23.6 3.3 31 34-68 18-48 (439)
90 TIGR00247 conserved hypothetic 20.9 95 0.0021 23.8 2.6 26 23-49 40-65 (342)
91 TIGR02944 suf_reg_Xantho FeS a 20.9 73 0.0016 20.5 1.7 20 31-50 39-58 (130)
92 smart00345 HTH_GNTR helix_turn 20.7 98 0.0021 16.3 2.0 18 31-48 34-51 (60)
93 TIGR02719 repress_PhaQ poly-be 20.5 84 0.0018 21.5 2.0 38 30-68 56-95 (138)
94 PRK12338 hypothetical protein; 20.3 1.8E+02 0.0038 22.6 3.9 41 7-48 259-313 (319)
95 PRK14332 (dimethylallyl)adenos 20.2 1.5E+02 0.0032 23.6 3.5 31 34-68 27-57 (449)
96 PF00392 GntR: Bacterial regul 20.2 96 0.0021 17.5 1.9 18 32-49 39-56 (64)
97 cd00861 ProRS_anticodon_short 20.2 1.3E+02 0.0029 17.5 2.7 25 24-48 3-34 (94)
98 TIGR02764 spore_ybaN_pdaB poly 20.1 1.7E+02 0.0037 19.8 3.4 36 11-47 87-122 (191)
99 PRK11014 transcriptional repre 20.1 80 0.0017 20.8 1.8 21 31-51 39-59 (141)
100 PRK14329 (dimethylallyl)adenos 20.1 1.5E+02 0.0032 23.7 3.5 31 34-68 40-70 (467)
101 PF00610 DEP: Domain found in 20.1 72 0.0016 18.4 1.4 21 31-51 38-58 (74)
No 1
>COG0096 RpsH Ribosomal protein S8 [Translation, ribosomal structure and biogenesis]
Probab=99.95 E-value=9.9e-29 Score=169.17 Aligned_cols=74 Identities=34% Similarity=0.375 Sum_probs=70.3
Q ss_pred CCccchHHHHHHHhhhHhhcCCceEEEEechHHHHHHHHHHhhcCccCceEEEcCCccceEEE-----EecCC-Cccccc
Q psy13246 1 MVRVNVLSDALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGKLPEVFVILGIRTTVYCM-----INWSG-IKPNPI 74 (81)
Q Consensus 1 M~~~D~iaD~LtrIrNA~~a~k~~V~~~p~Skl~~~il~IL~~eGYI~~~~~~~~~~~~~i~V-----in~~g-i~pr~~ 74 (81)
|+++|||||||||||||++++|+.|. .|+||++.+||++|++||||++|++++|++++.++| +|.|| |+|+..
T Consensus 1 m~~~DpiAdmltrIrNa~~~~~~~v~-~P~SKl~~~il~vLk~eGYI~~f~~~~~~~~~~~~v~Lky~~n~~~vI~~~~r 79 (132)
T COG0096 1 MMMTDPLADMLTRIRNAERAKKEVVS-MPASKLKGAILKVLKKEGYIKDFEVIDDGRKGKLRVQLKYRINGCGVISPIKR 79 (132)
T ss_pred CccccHHHHHHHHhHhHHHhccceee-cchHHHHHHHHHHHHHcCCcceEEEEeCCcceEEEEEEEeccCCCccccccee
Confidence 88899999999999999999888887 999999999999999999999999999999999999 89999 999876
Q ss_pred e
Q psy13246 75 I 75 (81)
Q Consensus 75 ~ 75 (81)
+
T Consensus 80 V 80 (132)
T COG0096 80 V 80 (132)
T ss_pred c
Confidence 5
No 2
>PTZ00158 40S ribosomal protein S15A; Provisional
Probab=99.94 E-value=4.5e-27 Score=160.34 Aligned_cols=75 Identities=53% Similarity=0.744 Sum_probs=68.9
Q ss_pred CCccchHHHHHHHhhhHhhcCCceEEEEechHHHHHHHHHHhhcCccCceEEEcCCccceEEE-----EecCC-Cccccc
Q psy13246 1 MVRVNVLSDALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGKLPEVFVILGIRTTVYCM-----INWSG-IKPNPI 74 (81)
Q Consensus 1 M~~~D~iaD~LtrIrNA~~a~k~~V~~~p~Skl~~~il~IL~~eGYI~~~~~~~~~~~~~i~V-----in~~g-i~pr~~ 74 (81)
|+.+||||||||+||||++++|++|.++|+||++.+||+||++||||++|++.++++.+.+.| |++|| |+||.-
T Consensus 1 m~~~~~iadmlt~IrNa~~~~~~~V~v~p~Skl~~~il~IL~~eGyI~~~~~~~~~~~~~i~v~l~~rIsk~g~IS~RvY 80 (130)
T PTZ00158 1 MVRMSVLADCLRSIVNAEKQGKRQVLIRPSSKVVVKFLQVMQKHGYIGEFEIVDDHRSGKIVVNLNGRLNKCGVISPRFD 80 (130)
T ss_pred CCcccHHHHHHHhhhhHHhCCCCeEEEeCCcHHHHHHHHHHHHCCcccceEEEecCCEEEEEEEEcCccccCCCCccceE
Confidence 888999999999999999999999984499999999999999999999999988877777766 99999 999875
Q ss_pred e
Q psy13246 75 I 75 (81)
Q Consensus 75 ~ 75 (81)
.
T Consensus 81 ~ 81 (130)
T PTZ00158 81 V 81 (130)
T ss_pred C
Confidence 4
No 3
>KOG1754|consensus
Probab=99.93 E-value=7.7e-26 Score=153.99 Aligned_cols=77 Identities=62% Similarity=0.839 Sum_probs=73.7
Q ss_pred CCccchHHHHHHHhhhHhhcCCceEEEEechHHHHHHHHHHhhcCccCceEEEcCCccceEEE-----EecCC-Cccccc
Q psy13246 1 MVRVNVLSDALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGKLPEVFVILGIRTTVYCM-----INWSG-IKPNPI 74 (81)
Q Consensus 1 M~~~D~iaD~LtrIrNA~~a~k~~V~~~p~Skl~~~il~IL~~eGYI~~~~~~~~~~~~~i~V-----in~~g-i~pr~~ 74 (81)
|+.+|.+||+|+.|+||.++||.||.+.|+||...+||.+|++||||++|++++|++.|++.| +|+|| |+|||-
T Consensus 1 m~~~~vLaDalksinNA~krGK~qvlirp~Skvii~FL~vmmkhGyIg~fei~ddhragkivv~L~gRlNkcg~Isprfd 80 (130)
T KOG1754|consen 1 MVRMNVLADALKSINNAEKRGKRQVLIRPSSKVIIRFLTVMMKHGYIGEFEIIDDHRAGKIVVNLTGRLNKCGVISPRFD 80 (130)
T ss_pred CchHHHHHHHHHHhhhHHhcCCceEEecccHHHHHHHHHHHHHcCcccceEEecCCccceEEEecccccccccccccccc
Confidence 778999999999999999999999999999999999999999999999999999999999988 99999 999997
Q ss_pred eee
Q psy13246 75 ITL 77 (81)
Q Consensus 75 ~~~ 77 (81)
+-+
T Consensus 81 V~l 83 (130)
T KOG1754|consen 81 VKL 83 (130)
T ss_pred ccc
Confidence 643
No 4
>PLN00146 40S ribosomal protein S15a; Provisional
Probab=99.92 E-value=1.5e-25 Score=152.32 Aligned_cols=75 Identities=55% Similarity=0.746 Sum_probs=68.4
Q ss_pred CCccchHHHHHHHhhhHhhcCCceEEEEechHHHHHHHHHHhhcCccCceEEEcCCccceEEE-----EecCC-Cccccc
Q psy13246 1 MVRVNVLSDALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGKLPEVFVILGIRTTVYCM-----INWSG-IKPNPI 74 (81)
Q Consensus 1 M~~~D~iaD~LtrIrNA~~a~k~~V~~~p~Skl~~~il~IL~~eGYI~~~~~~~~~~~~~i~V-----in~~g-i~pr~~ 74 (81)
|+.+||||||||+||||++++|++|.++|+||++.+|+++|++||||++|+..++++.+.+.| ||+|+ |+||.-
T Consensus 1 m~~~~~iad~lt~IrNa~~a~~~~v~~~p~Skl~~~il~iL~~eGyI~~~~~~~~~~~~~i~v~Lk~~i~~~~~IS~Rvy 80 (130)
T PLN00146 1 MVRRSVLNDALKTMYNAEKRGKRQVLIRPSSKVVIKFLKVMQKHGYIGEFEVVDDHRSGKIVVELNGRLNKCGVISPRFD 80 (130)
T ss_pred CCCcChHHHHHHHhHhHHHcCCCeEEEEcChHHHHHHHHHHHHCCCCcceEEEecCCcceEEEEEcccccCCcEEEcCEe
Confidence 888999999999999999999999975799999999999999999999999887776667766 89999 999875
Q ss_pred e
Q psy13246 75 I 75 (81)
Q Consensus 75 ~ 75 (81)
.
T Consensus 81 ~ 81 (130)
T PLN00146 81 V 81 (130)
T ss_pred c
Confidence 4
No 5
>PRK04034 rps8p 30S ribosomal protein S8P; Reviewed
Probab=99.91 E-value=8.3e-25 Score=148.17 Aligned_cols=74 Identities=41% Similarity=0.525 Sum_probs=66.7
Q ss_pred CCccchHHHHHHHhhhHhhcCCceEEEEechHHHHHHHHHHhhcCccCceEEEcCCccceEEE-----EecCC-Cccccc
Q psy13246 1 MVRVNVLSDALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGKLPEVFVILGIRTTVYCM-----INWSG-IKPNPI 74 (81)
Q Consensus 1 M~~~D~iaD~LtrIrNA~~a~k~~V~~~p~Skl~~~il~IL~~eGYI~~~~~~~~~~~~~i~V-----in~~g-i~pr~~ 74 (81)
|+++||||||||+||||++|++++|..+|+||++.+||++|++||||++|++.++++.+.+.| +|+|. ||||.-
T Consensus 1 m~~~d~iad~lt~IrNa~~a~~~~v~~~p~Sk~~~~il~iL~~eGyI~~~~~~~~~~~~~~~v~Lk~~~~~~~~IkPRvy 80 (130)
T PRK04034 1 MVLLDPLANALSTIKNAEMVGKKEVIIKPASKLIGNVLRVMQDEGYIGEFEYIDDGRAGKFKVELLGRINKCGAIKPRYP 80 (130)
T ss_pred CCcccHHHHHHHHhHhHHHcCCceEEEEcccHHHHHHHHHHHHCCCceEEEEEcCCCccceEEEECCccCCCCcCCCCeE
Confidence 777899999999999999999999866999999999999999999999999887776666666 78899 999764
No 6
>CHL00042 rps8 ribosomal protein S8
Probab=99.88 E-value=1.7e-22 Score=137.38 Aligned_cols=60 Identities=17% Similarity=0.243 Sum_probs=55.5
Q ss_pred ccchHHHHHHHhhhHhhcCCceEEEEechHHHHHHHHHHhhcCccCceEEEcCCccceEEE
Q psy13246 3 RVNVLSDALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGKLPEVFVILGIRTTVYCM 63 (81)
Q Consensus 3 ~~D~iaD~LtrIrNA~~a~k~~V~~~p~Skl~~~il~IL~~eGYI~~~~~~~~~~~~~i~V 63 (81)
++||||||||+||||++++|.+|. +|+||++.+||++|++||||++|++.++++.+.+.|
T Consensus 2 ~~d~iad~lt~IrNa~~a~~~~v~-ip~Skl~~~il~iL~~eGyI~~~~~~~~~~~~~i~v 61 (132)
T CHL00042 2 GNDTIADMLTRIRNANMVKKGTVR-IPATNITENIVKILLREGFIENVREHRENNKYFLVL 61 (132)
T ss_pred CcchHHHHHHHhHHHHHCCCCEEE-EeccHHHHHHHHHHHHCCcccceEEEecCCeeEEEE
Confidence 489999999999999999999998 799999999999999999999999887777767665
No 7
>PRK00136 rpsH 30S ribosomal protein S8; Validated
Probab=99.84 E-value=6.7e-21 Score=128.96 Aligned_cols=61 Identities=20% Similarity=0.243 Sum_probs=55.3
Q ss_pred CccchHHHHHHHhhhHhhcCCceEEEEechHHHHHHHHHHhhcCccCceEEEcCCccceEEE
Q psy13246 2 VRVNVLSDALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGKLPEVFVILGIRTTVYCM 63 (81)
Q Consensus 2 ~~~D~iaD~LtrIrNA~~a~k~~V~~~p~Skl~~~il~IL~~eGYI~~~~~~~~~~~~~i~V 63 (81)
+++||||||||+||||+++||.+|. +|+||++.+||++|++||||++|+..++++.++++|
T Consensus 1 m~~d~i~d~lt~IrNa~~~~~~~v~-ip~sk~~~~il~iL~~eGyI~~~~~~~~~~~~~~~v 61 (130)
T PRK00136 1 SMTDPIADMLTRIRNAQMAKHETVS-MPASKLKVAIAEILKEEGYIKDYEVEEDGKQGILRI 61 (130)
T ss_pred CCcChHHHHHHHHHHHHHcCCCeEE-ecccHHHHHHHHHHHHCCcccceEEEecCCcceEEE
Confidence 1489999999999999999999998 999999999999999999999999887666566666
No 8
>PF00410 Ribosomal_S8: Ribosomal protein S8; InterPro: IPR000630 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 S8 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S8 is known to bind directly to 16S ribosomal RNA. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [], groups eubacterial, algal and plant chloroplast, cyanelle, archaebacterial and Marchantia polymorpha mitochondrial S8; mammalian and plant S15A; and yeast S22 (S24) ribosomal proteins.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1S1H_H 3O30_O 3O2Z_O 3IZB_H 3U5G_W 3U5C_W 3OTO_H 1AN7_A 2HGR_K 3BBN_H ....
Probab=99.80 E-value=2.4e-19 Score=120.60 Aligned_cols=70 Identities=27% Similarity=0.320 Sum_probs=61.4
Q ss_pred chHHHHHHHhhhHhhcCCceEEEEechHHHHHHHHHHhhcCccCceEEEcCCcc-ceEEE--------------EecCC-
Q psy13246 5 NVLSDALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGKLPEVFVILGIRT-TVYCM--------------INWSG- 68 (81)
Q Consensus 5 D~iaD~LtrIrNA~~a~k~~V~~~p~Skl~~~il~IL~~eGYI~~~~~~~~~~~-~~i~V--------------in~~g- 68 (81)
|||||+|++||||++++|++|. +|+|+++.++|++|++||||++|++.+++++ +.+.| |+.|.
T Consensus 1 D~lad~l~~I~Na~~~~~~~v~-ip~sk~~~~il~iL~~eGyI~~f~~~~~~~~~~~i~I~Lky~~~~~~~i~~i~~iSk 79 (129)
T PF00410_consen 1 DPLADLLTRIRNASRARKRFVI-IPYSKLNLSILKILKKEGYISGFEIIDDNRNGKRIWIELKYRRNGKPVIKKIKRISK 79 (129)
T ss_dssp SHHHHHHHHHHHHHHTTCSEEE-EEHCHHHHHHHHHHHHTTSEEEEEEEESSSSEEEEEEEESBCSSSSBSSSEEEESSB
T ss_pred CcHHHHHHHhHHHHHCCCCEEE-ecccHHHHHHHHHHhhccccceeEeeccCCCceEEEEEEccccccchhhhhhhcccC
Confidence 9999999999999999999998 7999999999999999999999999888875 45666 55666
Q ss_pred Cccccce
Q psy13246 69 IKPNPII 75 (81)
Q Consensus 69 i~pr~~~ 75 (81)
..+|+-+
T Consensus 80 p~~r~y~ 86 (129)
T PF00410_consen 80 PGRRVYI 86 (129)
T ss_dssp TTCCCEE
T ss_pred CCcceec
Confidence 6666544
No 9
>PF09639 YjcQ: YjcQ protein; InterPro: IPR018597 YjcQ is a protein of approx. 100 residues containing four alpha helices and three beta strands. It is found in bacteria and also in the Lactococcus phage Tuc2009. In bacteria it appears to be under the regulation of SigD RNA polymerase which is responsible for the expression of many genes encoding cell-surface proteins related to flagellar assembly, motility, chemotaxis and autolysis in the late exponential growth phase. The exact function of YjcQ is unknown []. However, it is thought to be the major head protein in viruses [] and is found in prophage in bacteria. ; PDB: 2HGC_A.
Probab=85.59 E-value=0.45 Score=29.95 Aligned_cols=25 Identities=16% Similarity=0.177 Sum_probs=19.3
Q ss_pred hHHHHHHHHHHhhcCccCceEEEcC
Q psy13246 31 SKVIVKFLTVMMKHGKLPEVFVILG 55 (81)
Q Consensus 31 Skl~~~il~IL~~eGYI~~~~~~~~ 55 (81)
+..-..+++-|+++|||+|+.+..+
T Consensus 24 ~~~~~~il~~L~d~GyI~G~~~~~~ 48 (88)
T PF09639_consen 24 DSYWSDILRMLQDEGYIKGVSVVRY 48 (88)
T ss_dssp HHHHHHHHHHHHHHTSEE--EESSS
T ss_pred HHHHHHHHHHHHHCCCccceEEEec
Confidence 4666789999999999999988765
No 10
>COG1244 Predicted Fe-S oxidoreductase [General function prediction only]
Probab=69.68 E-value=7.2 Score=30.99 Aligned_cols=44 Identities=20% Similarity=0.309 Sum_probs=39.6
Q ss_pred cchHHHHHHHhhhHhhcCCceEEEEechHHHHHHHHHHhhcCccC
Q psy13246 4 VNVLSDALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGKLP 48 (81)
Q Consensus 4 ~D~iaD~LtrIrNA~~a~k~~V~~~p~Skl~~~il~IL~~eGYI~ 48 (81)
-+.|.|++..|+ |...+-..+.+.|++=-+..+.+-|++.|-=.
T Consensus 220 ~eAI~D~i~Si~-~~~~~~d~iSinptnVqKgTlvE~lw~~g~YR 263 (358)
T COG1244 220 KEAIEDVISSIV-AAKPGTDTISINPTNVQKGTLVEKLWRRGLYR 263 (358)
T ss_pred HHHHHHHHHHHH-HhccCCCeEEecccccchhhHHHHHHHcCCCC
Confidence 378999999999 99999999999999999999999999998543
No 11
>PF00919 UPF0004: Uncharacterized protein family UPF0004; InterPro: IPR013848 The methylthiotransferase (MTTase) or miaB-like family is named after the (dimethylallyl)adenosine tRNA MTTase miaB protein, which catalyses a C-H to C-S bond conversion in the methylthiolation of tRNA. A related bacterial enzyme rimO performs a similar methylthiolation, but on a protein substrate. RimO acts on the ribosomal protein S12 and forms a separate MTTase subfamily. The miaB-subfamily includes mammalian CDK5 regulatory subunit-associated proteins and similar proteins in other eukaryotes. Two other subfamilies, yqeV and CDKAL1, are named after a Bacillus subtilis and a human protein, respectively. While yqeV-like proteins are found in bacteria, CDKAL1 subfamily members occur in eukaryotes and in archaebacteria. The likely MTTases from these 4 subfamilies contain an N-terminal MTTase domain, a central radical generating fold and a C-terminal TRAM domain (see PDOC50926 from PROSITEDOC). The core forms a radical SAM fold (or AdoMet radical), containing a cysteine motif CxxxCxxC that binds a [4Fe-4S] cluster [, , ]. A reducing equivalent from the [4Fe-4S]+ cluster is used to cleave S-adenosylmethionine (SAM) to generate methionine and a 5'-deoxyadenosyl radical. The latter is thought to produce a reactive substrate radical that is amenable to sulphur insertion [, ]. The N-terminal MTTase domain contains 3 cysteines that bind a second [4Fe-4S] cluster, in addition to the radical-generating [4Fe-4S] cluster, which could be involved in the thiolation reaction. The C-terminal TRAM domain is not shared with other radical SAM proteins outside the MTTase family. The TRAM domain can bind to RNA substrate and seems to be important for substrate recognition. The tertiary structure of the central radical SAM fold has six beta/alpha motifs resembling a three-quarter TIM barrel core (see PDOC00155 from PROSITEDOC) []. The N-terminal MTTase domain might form an additional [beta/alpha]2 TIM barrel unit []. ; GO: 0003824 catalytic activity, 0051539 4 iron, 4 sulfur cluster binding, 0009451 RNA modification
Probab=68.10 E-value=11 Score=24.03 Aligned_cols=32 Identities=9% Similarity=0.096 Sum_probs=22.8
Q ss_pred HHHHHHHHhhcCccCceEEEcCCccceEEEEecCCC
Q psy13246 34 IVKFLTVMMKHGKLPEVFVILGIRTTVYCMINWSGI 69 (81)
Q Consensus 34 ~~~il~IL~~eGYI~~~~~~~~~~~~~i~Vin~~gi 69 (81)
.+.+...|.+.|| +.+++...-.+.|||-|++
T Consensus 16 se~i~~~l~~~G~----~~~~~~e~AD~iiiNTC~V 47 (98)
T PF00919_consen 16 SERIASILQAAGY----EIVDDPEEADVIIINTCTV 47 (98)
T ss_pred HHHHHHHHHhcCC----eeecccccCCEEEEEcCCC
Confidence 4568888999988 5555544455667999983
No 12
>COG1695 Predicted transcriptional regulators [Transcription]
Probab=66.76 E-value=4.1 Score=26.64 Aligned_cols=39 Identities=21% Similarity=0.267 Sum_probs=27.5
Q ss_pred echHHHHHHHHHHhhcCccCceEEEcCC-c-cceEEEEecCC
Q psy13246 29 PCSKVIVKFLTVMMKHGKLPEVFVILGI-R-TTVYCMINWSG 68 (81)
Q Consensus 29 p~Skl~~~il~IL~~eGYI~~~~~~~~~-~-~~~i~Vin~~g 68 (81)
|.--..--+|+-|+++|||.......++ + .+.++ ++.+|
T Consensus 42 ~s~gtiYp~L~~Le~~Gli~~~~~~~~~g~~rk~Y~-lTe~G 82 (138)
T COG1695 42 PSPGTIYPLLKRLEKEGLIESRWEESGGGPPRKYYR-LTEKG 82 (138)
T ss_pred CCCCcHHHHHHHHHHCCCeEEEecccCCCCCceEEE-ECHHH
Confidence 5556677899999999999998765544 2 23334 77776
No 13
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=60.53 E-value=8.9 Score=23.53 Aligned_cols=22 Identities=18% Similarity=0.077 Sum_probs=16.7
Q ss_pred HHHHHHHhhcCccCceEEEcCC
Q psy13246 35 VKFLTVMMKHGKLPEVFVILGI 56 (81)
Q Consensus 35 ~~il~IL~~eGYI~~~~~~~~~ 56 (81)
..-++.|.++|||+..+...++
T Consensus 32 s~hL~~Le~~GyV~~~k~~~~~ 53 (80)
T PF13601_consen 32 SKHLKKLEEAGYVEVEKEFEGR 53 (80)
T ss_dssp HHHHHHHHHTTSEEEEEE-SSS
T ss_pred HHHHHHHHHCCCEEEEEeccCC
Confidence 4568999999999987766554
No 14
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=55.20 E-value=17 Score=20.38 Aligned_cols=29 Identities=10% Similarity=0.140 Sum_probs=20.9
Q ss_pred HHHHHHHHhhcCccCceEEEcCCccceEE
Q psy13246 34 IVKFLTVMMKHGKLPEVFVILGIRTTVYC 62 (81)
Q Consensus 34 ~~~il~IL~~eGYI~~~~~~~~~~~~~i~ 62 (81)
....++-|.+.|||+...-..|++...++
T Consensus 35 vs~~i~~L~~~glv~~~~~~~d~R~~~~~ 63 (68)
T PF13463_consen 35 VSRIIKKLEEKGLVEKERDPHDKRSKRYR 63 (68)
T ss_dssp HHHHHHHHHHTTSEEEEEESSCTTSEEEE
T ss_pred HHHHHHHHHHCCCEEecCCCCcCCeeEEE
Confidence 34788999999999776655566654444
No 15
>PF13732 DUF4162: Domain of unknown function (DUF4162)
Probab=54.23 E-value=22 Score=20.97 Aligned_cols=32 Identities=6% Similarity=-0.008 Sum_probs=25.0
Q ss_pred ceEEEEechHHHHHHHHHHhhcCccCceEEEcC
Q psy13246 23 RQVLIRPCSKVIVKFLTVMMKHGKLPEVFVILG 55 (81)
Q Consensus 23 ~~V~~~p~Skl~~~il~IL~~eGYI~~~~~~~~ 55 (81)
-.+. +.-.....++|+.|.++|+|.+|+....
T Consensus 43 ~~i~-l~~~~~~~~ll~~l~~~g~I~~f~~~~P 74 (84)
T PF13732_consen 43 LRIK-LEDEETANELLQELIEKGIIRSFEEEEP 74 (84)
T ss_pred EEEE-ECCcccHHHHHHHHHhCCCeeEEEEcCC
Confidence 3454 4455677999999999999999988654
No 16
>PF03551 PadR: Transcriptional regulator PadR-like family; InterPro: IPR005149 Phenolic acids, also called substituted hydroxycinnamic acids, are abundant in the plant kingdom because they are involved in the structure of plant cell walls and are present in some vacuoles. In plant-soil ecosystems they are released as free acids by hemicellulases produced by several fungi and bacteria. Of these weak acids, the most abundant are p-coumaric, ferulic, and caffeic acids, considered to be natural toxins that inhibit the growth of microorganisms, especially at low pHs. In spite of this chemical stress, some bacteria can use phenolic acids as a sole source of carbon. For other microorganisms, these compounds induce a specific response by which the organism adapts to its environment. The ubiquitous lactic acid bacterium Lactobacillus plantarum exhibits an inducible phenolic acid decarboxylase (PAD) activity which converts these substrates into less-toxic vinyl phenol derivatives. PadR acts as a repressor of padA gene expression in the phenolic acid stress response [].; PDB: 1XMA_B 2ESH_A 2DQL_B 3L9F_C 3ELK_B 4EJO_B 3L7W_A 3HHH_A 1YG2_A 3F8B_A ....
Probab=53.01 E-value=13 Score=21.95 Aligned_cols=27 Identities=7% Similarity=0.039 Sum_probs=22.8
Q ss_pred EechHHHHHHHHHHhhcCccCceEEEc
Q psy13246 28 RPCSKVIVKFLTVMMKHGKLPEVFVIL 54 (81)
Q Consensus 28 ~p~Skl~~~il~IL~~eGYI~~~~~~~ 54 (81)
.+.....-..|+-|.++|+|......+
T Consensus 28 ~i~~g~lY~~L~~Le~~gli~~~~~~~ 54 (75)
T PF03551_consen 28 KISPGSLYPALKRLEEEGLIESRWEEE 54 (75)
T ss_dssp ETTHHHHHHHHHHHHHTTSEEEEEEEE
T ss_pred ccChhHHHHHHHHHHhCCCEEEeeecc
Confidence 456777889999999999999998764
No 17
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=50.18 E-value=16 Score=19.65 Aligned_cols=18 Identities=11% Similarity=0.379 Sum_probs=14.2
Q ss_pred hHHHHHHHHHHhhcCccC
Q psy13246 31 SKVIVKFLTVMMKHGKLP 48 (81)
Q Consensus 31 Skl~~~il~IL~~eGYI~ 48 (81)
.......++-|.++|||+
T Consensus 31 ~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 31 RSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHHHCcCcC
Confidence 455677889999999984
No 18
>PF08438 MMR_HSR1_C: GTPase of unknown function C-terminal; InterPro: IPR013646 This domain is found at the C terminus of IPR002917 from INTERPRO in archaeal and eukaryotic GTP-binding proteins. ; PDB: 1WXQ_A.
Probab=49.82 E-value=25 Score=23.34 Aligned_cols=37 Identities=16% Similarity=0.187 Sum_probs=23.0
Q ss_pred HHHHHHhhhHhhcCCceEEEEechHHHHHHHHHHhhcCccC
Q psy13246 8 SDALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGKLP 48 (81)
Q Consensus 8 aD~LtrIrNA~~a~k~~V~~~p~Skl~~~il~IL~~eGYI~ 48 (81)
.+-+.+|+... ....+ +|+|-..+-.|+-+.+.|||+
T Consensus 11 ~~ni~kl~~~~--~~~~v--Vp~SA~aEl~Lr~a~k~g~I~ 47 (109)
T PF08438_consen 11 DENIEKLKEKY--PDEPV--VPTSAAAELALRKAAKAGLID 47 (109)
T ss_dssp HHHHHHHHHHH--TT-EE--EEE-HHHHHHHHS-SSS----
T ss_pred HhHHHHHHHhC--CCCce--eeccHHHHHHHHHHHHCCCEE
Confidence 35567777755 23333 799999999999999999998
No 19
>PF10264 Stork_head: Winged helix Storkhead-box1 domain; InterPro: IPR019391 In humans the Storkhead-box protein controls polyploidization of extravillus trophoblast and is implicated in pre-eclampsia []. This entry represents the conserved N-terminal winged-helix domain, which is likely to bind DNA.
Probab=48.86 E-value=20 Score=22.72 Aligned_cols=36 Identities=14% Similarity=0.285 Sum_probs=32.1
Q ss_pred HHHhhhHhhcCCceEEEEechHHHHHHHHHHhhcCcc
Q psy13246 11 LKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGKL 47 (81)
Q Consensus 11 LtrIrNA~~a~k~~V~~~p~Skl~~~il~IL~~eGYI 47 (81)
+.+|+++.......+. .|+..+....|--|.+||.|
T Consensus 32 ~E~l~~~L~~~yp~i~-~Ps~e~l~~~L~~Li~erkI 67 (80)
T PF10264_consen 32 QETLREHLRKHYPGIA-IPSQEVLYNTLGTLIKERKI 67 (80)
T ss_pred HHHHHHHHHHhCCCCC-CCCHHHHHHHHHHHHHcCce
Confidence 5578888888888887 89999999999999999877
No 20
>cd04882 ACT_Bt0572_2 C-terminal ACT domain of a novel protein composed of just two ACT domains. Included in this CD is the C-terminal ACT domain of a novel protein composed of just two ACT domains, as seen in the yet uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related proteins. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=47.96 E-value=45 Score=18.08 Aligned_cols=24 Identities=25% Similarity=0.361 Sum_probs=16.5
Q ss_pred CCceEEEEechHHHHHHHHHHhhcCc
Q psy13246 21 GKRQVLIRPCSKVIVKFLTVMMKHGK 46 (81)
Q Consensus 21 ~k~~V~~~p~Skl~~~il~IL~~eGY 46 (81)
+...+. +.... ...+++.|++.||
T Consensus 39 ~~~~v~-~~ve~-~~~~~~~L~~~G~ 62 (65)
T cd04882 39 GKALLI-FRTED-IEKAIEVLQERGV 62 (65)
T ss_pred CeEEEE-EEeCC-HHHHHHHHHHCCc
Confidence 344554 44444 7788899999887
No 21
>PF08479 POTRA_2: POTRA domain, ShlB-type; InterPro: IPR013686 The POTRA domain (for polypeptide-transport-associated domain) is found towards the N terminus of ShlB family proteins (IPR005565 from INTERPRO). ShlB is important in the secretion and activation of the haemolysin ShlA. It has been postulated that the POTRA domain has a chaperone-like function over ShlA; it may fold back into the C-terminal beta-barrel channel []. ; PDB: 2X8X_X 2QDZ_A 3NJT_A 3MC8_A 3MC9_B.
Probab=47.62 E-value=45 Score=19.63 Aligned_cols=35 Identities=6% Similarity=0.030 Sum_probs=23.8
Q ss_pred echHHHHHHHHHHhhcCccCceEEEcCC--ccceEEE
Q psy13246 29 PCSKVIVKFLTVMMKHGKLPEVFVILGI--RTTVYCM 63 (81)
Q Consensus 29 p~Skl~~~il~IL~~eGYI~~~~~~~~~--~~~~i~V 63 (81)
-...+..++-+.+.++||+-..-.+.+. ..|.+++
T Consensus 35 ~l~~~~~~l~~~y~~~GY~~s~v~~p~q~i~~G~l~i 71 (76)
T PF08479_consen 35 DLQQLADALTNYYREKGYITSRVYLPPQDISDGVLTI 71 (76)
T ss_dssp HHHHHHHHHHHHHHHTT-TT-EEEEEEEEETTSEEEE
T ss_pred HHHHHHHHHHHHHHHcCceEEEEEeCCeecCCCEEEE
Confidence 4467888899999999999887655543 4566654
No 22
>COG2519 GCD14 tRNA(1-methyladenosine) methyltransferase and related methyltransferases [Translation, ribosomal structure and biogenesis]
Probab=47.35 E-value=45 Score=25.39 Aligned_cols=41 Identities=20% Similarity=0.290 Sum_probs=36.0
Q ss_pred HHHHHHhhhHhhcCCceEEEEechHHHHHHHHHHhhcCccC
Q psy13246 8 SDALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGKLP 48 (81)
Q Consensus 8 aD~LtrIrNA~~a~k~~V~~~p~Skl~~~il~IL~~eGYI~ 48 (81)
.+++-.+.++.+.|-.-+...|+.....+.++.|.+.||..
T Consensus 175 W~~le~~~~~Lkpgg~~~~y~P~veQv~kt~~~l~~~g~~~ 215 (256)
T COG2519 175 WNVLEHVSDALKPGGVVVVYSPTVEQVEKTVEALRERGFVD 215 (256)
T ss_pred HHHHHHHHHHhCCCcEEEEEcCCHHHHHHHHHHHHhcCccc
Confidence 36788888888888888888999999999999999999875
No 23
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=44.38 E-value=21 Score=21.23 Aligned_cols=21 Identities=10% Similarity=0.325 Sum_probs=17.6
Q ss_pred echHHHHHHHHHHhhcCccCc
Q psy13246 29 PCSKVIVKFLTVMMKHGKLPE 49 (81)
Q Consensus 29 p~Skl~~~il~IL~~eGYI~~ 49 (81)
.++.....-|+.|.+.|||..
T Consensus 38 ~S~~tv~~~L~~Le~kG~I~r 58 (65)
T PF01726_consen 38 KSTSTVQRHLKALERKGYIRR 58 (65)
T ss_dssp SSHHHHHHHHHHHHHTTSEEE
T ss_pred CChHHHHHHHHHHHHCcCccC
Confidence 357788899999999999963
No 24
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=44.10 E-value=22 Score=20.79 Aligned_cols=24 Identities=13% Similarity=0.270 Sum_probs=19.4
Q ss_pred hHHHHHHHHHHhhcCccCceEEEc
Q psy13246 31 SKVIVKFLTVMMKHGKLPEVFVIL 54 (81)
Q Consensus 31 Skl~~~il~IL~~eGYI~~~~~~~ 54 (81)
....+.+|+.|.+.|||+......
T Consensus 28 ~~~ve~mL~~l~~kG~I~~~~~~~ 51 (69)
T PF09012_consen 28 PEAVEAMLEQLIRKGYIRKVDMSS 51 (69)
T ss_dssp HHHHHHHHHHHHCCTSCEEEEEE-
T ss_pred HHHHHHHHHHHHHCCcEEEecCCC
Confidence 467889999999999999776544
No 25
>TIGR03433 padR_acidobact transcriptional regulator, Acidobacterial, PadR-family. Members of this protein family are putative transcriptional regulators of the PadR family, as found in species of the Acidobacteria. This family of proteins has expanded greatly in this lineage, and where it regularly is found in the vicinity of a putative transporter protein
Probab=43.62 E-value=23 Score=22.27 Aligned_cols=26 Identities=8% Similarity=-0.027 Sum_probs=20.2
Q ss_pred echHHHHHHHHHHhhcCccCceEEEc
Q psy13246 29 PCSKVIVKFLTVMMKHGKLPEVFVIL 54 (81)
Q Consensus 29 p~Skl~~~il~IL~~eGYI~~~~~~~ 54 (81)
+.....-.+|+-|+++|||......+
T Consensus 37 i~~gtlY~~L~rLe~~GlI~~~~~~~ 62 (100)
T TIGR03433 37 VEEGSLYPALHRLERRGWIAAEWGES 62 (100)
T ss_pred cCCCcHHHHHHHHHHCCCeEEEeeec
Confidence 33456788999999999999975444
No 26
>PF13541 ChlI: Subunit ChlI of Mg-chelatase
Probab=41.82 E-value=17 Score=24.21 Aligned_cols=26 Identities=27% Similarity=0.360 Sum_probs=22.1
Q ss_pred hHHHHHHHhhhHhhcCCceEEEEechH
Q psy13246 6 VLSDALKSINNAEKRGKRQVLIRPCSK 32 (81)
Q Consensus 6 ~iaD~LtrIrNA~~a~k~~V~~~p~Sk 32 (81)
|+..++.++..|.+.|.+.+. +|..+
T Consensus 96 ~v~~~~~~~~~A~~~G~~~vi-vP~~N 121 (121)
T PF13541_consen 96 PVPGILPRIIEAKKLGFKRVI-VPKAN 121 (121)
T ss_pred ecCcHHHHHHHHHHCCCCEEE-eCCCC
Confidence 667889999999999999997 89764
No 27
>PF13730 HTH_36: Helix-turn-helix domain
Probab=41.32 E-value=29 Score=18.95 Aligned_cols=17 Identities=6% Similarity=0.304 Sum_probs=13.9
Q ss_pred hHHHHHHHHHHhhcCcc
Q psy13246 31 SKVIVKFLTVMMKHGKL 47 (81)
Q Consensus 31 Skl~~~il~IL~~eGYI 47 (81)
-+...+.++.|++.|||
T Consensus 39 ~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 39 RRTVQRAIKELEEKGLI 55 (55)
T ss_pred HHHHHHHHHHHHHCcCC
Confidence 45677888999999997
No 28
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=40.66 E-value=28 Score=19.09 Aligned_cols=26 Identities=12% Similarity=0.097 Sum_probs=19.5
Q ss_pred HHHHHHHHHHhhcCccCceEEEcCCc
Q psy13246 32 KVIVKFLTVMMKHGKLPEVFVILGIR 57 (81)
Q Consensus 32 kl~~~il~IL~~eGYI~~~~~~~~~~ 57 (81)
...-.+++-|++.|||..-.--+|.|
T Consensus 32 ~~~t~~i~~L~~~g~I~r~~~~~D~R 57 (59)
T PF01047_consen 32 STVTRIIKRLEKKGLIERERDPDDRR 57 (59)
T ss_dssp HHHHHHHHHHHHTTSEEEEEETTETT
T ss_pred hHHHHHHHHHHHCCCEEeccCCCCCC
Confidence 34567889999999999876655554
No 29
>PHA02943 hypothetical protein; Provisional
Probab=40.56 E-value=24 Score=25.35 Aligned_cols=21 Identities=19% Similarity=0.143 Sum_probs=17.8
Q ss_pred hHHHHHHHHHHhhcCccCceE
Q psy13246 31 SKVIVKFLTVMMKHGKLPEVF 51 (81)
Q Consensus 31 Skl~~~il~IL~~eGYI~~~~ 51 (81)
......+|.+|.+||+|+..+
T Consensus 38 ~~qa~~~LyvLErEG~VkrV~ 58 (165)
T PHA02943 38 HSMARNALYQLAKEGMVLKVE 58 (165)
T ss_pred HHHHHHHHHHHHHcCceEEEe
Confidence 456788999999999999855
No 30
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=39.05 E-value=22 Score=21.43 Aligned_cols=20 Identities=20% Similarity=0.277 Sum_probs=16.9
Q ss_pred hHHHHHHHHHHhhcCccCce
Q psy13246 31 SKVIVKFLTVMMKHGKLPEV 50 (81)
Q Consensus 31 Skl~~~il~IL~~eGYI~~~ 50 (81)
-.....+++.|+++|||+..
T Consensus 39 ~~~l~kil~~L~~~Gli~s~ 58 (83)
T PF02082_consen 39 PSYLRKILQKLKKAGLIESS 58 (83)
T ss_dssp HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHHHhhCCeeEec
Confidence 45678999999999999755
No 31
>cd08788 CARD_NOD2_2_CARD15 Caspase activation and recruitment domain of NOD2, repeat 2. Caspase activation and recruitment domain (CARD) similar to that found in human NOD2 (CARD15), repeat 2. NOD2 is a member of the Nod-like receptor (NLR) family, which plays a central role in the innate immune response. NLRs typically contain an N-terminal effector domain, a central nucleotide-binding domain and a C-terminal ligand-binding region of several leucine-rich repeats (LRRs). In NOD2, as well as NOD1, the N-terminal effector domain is a CARD. NOD2 contains two N-terminal CARD repeats. Mutations in NOD2 have been associated with Crohns disease and Blau syndrome. Nod2-CARDs have been shown to interact with the CARD domain of the downstream effector RICK (RIP2, CARDIAK), a serine/threonine kinase. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are pr
Probab=38.35 E-value=25 Score=22.46 Aligned_cols=23 Identities=9% Similarity=0.095 Sum_probs=19.6
Q ss_pred chHHHHHHHHHHhhcCccCceEE
Q psy13246 30 CSKVIVKFLTVMMKHGKLPEVFV 52 (81)
Q Consensus 30 ~Skl~~~il~IL~~eGYI~~~~~ 52 (81)
.+..+..+|+.|++.|++..||-
T Consensus 12 l~~~V~~~Ld~ll~~G~is~~Ec 34 (81)
T cd08788 12 LQHHVDGALELLLTRGFFSSYDC 34 (81)
T ss_pred HHHHHHHHHHHHHHcCCccHhhc
Confidence 34568899999999999999874
No 32
>PF07006 DUF1310: Protein of unknown function (DUF1310); InterPro: IPR010738 This family consists of several hypothetical proteins of around 125 residues in length. Members of this family seem to be specific to Listeria and Streptococcus species. The function of this family is unknown.
Probab=36.50 E-value=32 Score=23.20 Aligned_cols=16 Identities=13% Similarity=0.177 Sum_probs=12.2
Q ss_pred HHhhcCccCceEEEcC
Q psy13246 40 VMMKHGKLPEVFVILG 55 (81)
Q Consensus 40 IL~~eGYI~~~~~~~~ 55 (81)
.|-+||.|++|++-++
T Consensus 56 AlT~~G~IksY~Id~~ 71 (122)
T PF07006_consen 56 ALTEEGKIKSYEIDKD 71 (122)
T ss_pred hhccCCeeEEEEEccc
Confidence 4567999999997543
No 33
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=36.24 E-value=40 Score=20.20 Aligned_cols=32 Identities=9% Similarity=0.114 Sum_probs=23.2
Q ss_pred hHHHHHHHHHHhhcCccCceEEEcCCccceEE
Q psy13246 31 SKVIVKFLTVMMKHGKLPEVFVILGIRTTVYC 62 (81)
Q Consensus 31 Skl~~~il~IL~~eGYI~~~~~~~~~~~~~i~ 62 (81)
....-..++-|.+.|||....--+|.+...+.
T Consensus 50 ~~~vt~~l~~Le~~glv~r~~~~~DrR~~~l~ 81 (126)
T COG1846 50 RSTVTRLLKRLEDKGLIERLRDPEDRRAVLVR 81 (126)
T ss_pred HHHHHHHHHHHHHCCCeeecCCccccceeeEE
Confidence 34566789999999999988766665544443
No 34
>PRK09954 putative kinase; Provisional
Probab=35.85 E-value=75 Score=23.74 Aligned_cols=29 Identities=14% Similarity=0.217 Sum_probs=22.2
Q ss_pred chHHHHHHHHHHhhcCccCceEEEcCCcc
Q psy13246 30 CSKVIVKFLTVMMKHGKLPEVFVILGIRT 58 (81)
Q Consensus 30 ~Skl~~~il~IL~~eGYI~~~~~~~~~~~ 58 (81)
+...+...++-|+++|||++|.+.-+...
T Consensus 30 s~~~v~~~i~~L~~~g~i~~~~~~l~~~~ 58 (362)
T PRK09954 30 SRSRVAAHIMDLMRKGRIKGKGYILTEQE 58 (362)
T ss_pred CHHHHHHHHHHHHHCCCcCCcEEEEcCCc
Confidence 35667788999999999999886554444
No 35
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=35.73 E-value=25 Score=22.23 Aligned_cols=35 Identities=23% Similarity=0.215 Sum_probs=24.5
Q ss_pred HHHHHHHHHhhcCccCceEEEcCCccceEEEEecCC
Q psy13246 33 VIVKFLTVMMKHGKLPEVFVILGIRTTVYCMINWSG 68 (81)
Q Consensus 33 l~~~il~IL~~eGYI~~~~~~~~~~~~~i~Vin~~g 68 (81)
..-.+++-|.+.|||....-.+|+|.-.+. ++..|
T Consensus 59 tvs~~i~~Le~kg~I~r~~~~~D~R~~~i~-lT~~G 93 (109)
T TIGR01889 59 ALVKIIKKLSKKGYLSKERSEDDERKVIIS-INKEQ 93 (109)
T ss_pred HHHHHHHHHHHCCCEeccCCcccCCeEEEE-ECHHH
Confidence 445678999999999988766676654443 44444
No 36
>PF02813 Retro_M: Retroviral M domain; InterPro: IPR004028 The Gag polyprotein directs the assembly and release of virus particles from infected cells. The Gag polyprotein has three domains required for activity: an N-terminal membrane-binding (M) domain that directs Gag to the plasma membrane, an interaction (I) domain involved in Gag aggregation, and a late assembly (L) domain that mediates the budding process []. During viral maturation, the Gag polyprotein is then cleaved into major structural proteins by the viral protease, yielding the matrix, capsid, nucleoprotein, and some smaller peptides. In Rous sarcoma virus (RSV), the M domain consists of the first 85 residues of the matrix protein. However, unlike other Gag polyproteins, the M domain of RSV Gag is not myristylated, but retains full activity [].This domain forms an alpha helical bundle structure []. This entry represents the M domain of the Gag polyprotein found in avian retroviruses. This entry also identifies Gag polyproteins from several avian endogenous retroviruses, which arise when one or more copies of the retroviral genome becomes integrated into the host genome [].; PDB: 1A6S_A.
Probab=34.90 E-value=22 Score=22.95 Aligned_cols=24 Identities=29% Similarity=0.386 Sum_probs=18.8
Q ss_pred EechHHHHHHHHHHhhcCccCceE
Q psy13246 28 RPCSKVIVKFLTVMMKHGKLPEVF 51 (81)
Q Consensus 28 ~p~Skl~~~il~IL~~eGYI~~~~ 51 (81)
-|++|-+.++|..|++||.+.+-.
T Consensus 19 sps~Kei~a~Ls~L~~Eg~L~sPs 42 (86)
T PF02813_consen 19 SPSKKEIGAMLSLLQKEGLLTSPS 42 (86)
T ss_dssp SS-SSHHHHHHHTGGGTT-TT-GG
T ss_pred CCcHHHHHHHHHHHHHccCcCChh
Confidence 478999999999999999998764
No 37
>smart00667 LisH Lissencephaly type-1-like homology motif. Alpha-helical motif present in Lis1, treacle, Nopp140, some katanin p60 subunits, muskelin, tonneau, LEUNIG and numerous WD40 repeat-containing proteins. It is suggested that LisH motifs contribute to the regulation of microtubule dynamics, either by mediating dimerisation, or else by binding cytoplasmic dynein heavy chain or microtubules directly.
Probab=33.90 E-value=43 Score=15.90 Aligned_cols=20 Identities=15% Similarity=0.215 Sum_probs=15.9
Q ss_pred hHHHHHHHHHHhhcCccCce
Q psy13246 31 SKVIVKFLTVMMKHGKLPEV 50 (81)
Q Consensus 31 Skl~~~il~IL~~eGYI~~~ 50 (81)
+.+..-|++-|.++||-...
T Consensus 4 ~~l~~lI~~yL~~~g~~~ta 23 (34)
T smart00667 4 SELNRLILEYLLRNGYEETA 23 (34)
T ss_pred HHHHHHHHHHHHHcCHHHHH
Confidence 45677899999999997654
No 38
>PF01963 TraB: TraB family; InterPro: IPR002816 In prokaryotes, for example Enterococcus faecalis (Streptococcus faecalis), the conjugative transfer of certain plasmids is controlled by peptide pheromones []. Plasmid free recipient cells secret plasmid specific oligopeptides, termed sex pheromones. They induce bacterial clumping and specifically activate the conjugative transfer of the corresponding plasmid. Once recipient cells acquire the plasmid they start to produce a pheromone inhibitor to block the activity of the pheromone and to prevent plasmid containing cells from clumping; they also become donor cells able to transfer the plasmid to plasmid free recipient cells. Examples of such plasmid-pheromone systems are bacteriocin plasmid pPD1 [], haemolysin/bacteriocin plasmid, pAD1 [], tetracycline-resistance plasmid, pCF10 [], and the haemolysin/bacteriocin plasmid, pOB1 []. TraB in combination with another factor contributes to pheromone shutdown in cells that have acquired a plasmid. It exact function has not yet been determined [, ]. This entry also contains plant and mammalian proteins, suggesting that these Trab-related proteins may have a somewhat wider or different function in eukaryotes.
Probab=33.42 E-value=92 Score=21.78 Aligned_cols=39 Identities=15% Similarity=0.161 Sum_probs=30.0
Q ss_pred HHHHHHhhhHhhcCCceEEEEechHHH--HHHHHHHhhcCc
Q psy13246 8 SDALKSINNAEKRGKRQVLIRPCSKVI--VKFLTVMMKHGK 46 (81)
Q Consensus 8 aD~LtrIrNA~~a~k~~V~~~p~Skl~--~~il~IL~~eGY 46 (81)
.++..+|..+...++..+.++.+.=+. ..+++.|+++||
T Consensus 214 ~~~~~~i~~~l~~~~~~fvvVGa~HL~G~~gvl~lLr~~Gy 254 (259)
T PF01963_consen 214 RRWAEKIEELLKEGGTVFVVVGAGHLPGEDGVLDLLRKKGY 254 (259)
T ss_pred HHHHHHHHHHHhcCCCEEEEEcchhccchhhHHHHHHhCCc
Confidence 356777777777775666678888775 579999999998
No 39
>PF09572 RE_XamI: XamI restriction endonuclease; InterPro: IPR019072 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry includes the XamI restriction endonuclease which recognises GTCGAC but cleavage site unknown. ; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system
Probab=33.08 E-value=52 Score=25.06 Aligned_cols=24 Identities=21% Similarity=0.187 Sum_probs=20.0
Q ss_pred hhhHhhcCCceEEEEechHHHHHHHHHHhhcCccC
Q psy13246 14 INNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGKLP 48 (81)
Q Consensus 14 IrNA~~a~k~~V~~~p~Skl~~~il~IL~~eGYI~ 48 (81)
+|||+.++ .-..|.+.|...||-+
T Consensus 117 iRnaqErR-----------Qe~~i~~~L~~~GYt~ 140 (251)
T PF09572_consen 117 IRNAQERR-----------QEAAIAEWLEARGYTK 140 (251)
T ss_pred HHhHHHHH-----------HHHHHHHHHHhcCceE
Confidence 99999996 4566788899999975
No 40
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=33.02 E-value=52 Score=19.16 Aligned_cols=32 Identities=13% Similarity=0.170 Sum_probs=21.3
Q ss_pred hHHHHHHHHHHhhcCccCceEEEcCCccceEE
Q psy13246 31 SKVIVKFLTVMMKHGKLPEVFVILGIRTTVYC 62 (81)
Q Consensus 31 Skl~~~il~IL~~eGYI~~~~~~~~~~~~~i~ 62 (81)
.......++-|.+.|||..++...+++...+.
T Consensus 38 ~~~i~~~l~~L~~~g~v~~~~~~~~~r~~~~~ 69 (101)
T smart00347 38 PSTVTRVLDRLEKKGLIRRLPSPEDRRSVLVS 69 (101)
T ss_pred chhHHHHHHHHHHCCCeEecCCCCCCCeEEEE
Confidence 34466899999999999877543333433343
No 41
>PF13670 PepSY_2: Peptidase propeptide and YPEB domain This Prosite motif covers only the active site. This is family M4 in the peptidase classification.
Probab=32.58 E-value=1.1e+02 Score=18.22 Aligned_cols=13 Identities=15% Similarity=0.209 Sum_probs=11.9
Q ss_pred HHHHHHHHhhcCc
Q psy13246 34 IVKFLTVMMKHGK 46 (81)
Q Consensus 34 ~~~il~IL~~eGY 46 (81)
...+...|+++||
T Consensus 31 ~~~~~~~l~~~G~ 43 (83)
T PF13670_consen 31 IEQAVAKLEAQGY 43 (83)
T ss_pred HHHHHHHHHhcCC
Confidence 7889999999998
No 42
>PF12025 Phage_C: Phage protein C; InterPro: IPR016407 This family of phage proteins is functionally uncharacterised. Proteins in this family are typically between 68 to 86 amino acids in length.; GO: 0019073 viral DNA genome packaging
Probab=32.35 E-value=38 Score=20.88 Aligned_cols=14 Identities=21% Similarity=0.408 Sum_probs=11.7
Q ss_pred HHHHHHHHhhcCcc
Q psy13246 34 IVKFLTVMMKHGKL 47 (81)
Q Consensus 34 ~~~il~IL~~eGYI 47 (81)
+.+++++|++.||.
T Consensus 55 ~~sllDiLkeRglL 68 (68)
T PF12025_consen 55 KKSLLDILKERGLL 68 (68)
T ss_pred hHHHHHHHHHccCC
Confidence 46889999999984
No 43
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=32.02 E-value=25 Score=19.06 Aligned_cols=15 Identities=13% Similarity=0.275 Sum_probs=11.6
Q ss_pred HHHHHHHHhhcCccC
Q psy13246 34 IVKFLTVMMKHGKLP 48 (81)
Q Consensus 34 ~~~il~IL~~eGYI~ 48 (81)
...=|+.|.+.|+|+
T Consensus 32 vs~hL~~L~~~glV~ 46 (47)
T PF01022_consen 32 VSHHLKKLREAGLVE 46 (47)
T ss_dssp HHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHCcCee
Confidence 445688899999985
No 44
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=31.82 E-value=44 Score=18.31 Aligned_cols=24 Identities=8% Similarity=-0.009 Sum_probs=16.8
Q ss_pred HHHHHHHHHhhcCccCceEEEcCC
Q psy13246 33 VIVKFLTVMMKHGKLPEVFVILGI 56 (81)
Q Consensus 33 l~~~il~IL~~eGYI~~~~~~~~~ 56 (81)
..-.+++-|.+.|||..-.--+|+
T Consensus 37 ~vs~~v~~L~~~Glv~r~~~~~D~ 60 (62)
T PF12802_consen 37 TVSRIVKRLEKKGLVERERDPGDR 60 (62)
T ss_dssp HHHHHHHHHHHTTSEEEEE-SSST
T ss_pred HHHHHHHHHHHCCCEEEeCCCCCC
Confidence 456788999999999766443343
No 45
>PF12792 CSS-motif: CSS motif domain associated with EAL ; InterPro: IPR024744 This domain, with its characteristic highly conserved CSS sequence motif, is found N-terminal to the EAL domain (PF00563 from PFAM), found in many putative cyclic diguanylate phosphodiesterases.
Probab=31.71 E-value=63 Score=21.39 Aligned_cols=30 Identities=13% Similarity=0.345 Sum_probs=26.8
Q ss_pred EechHH-HHHHHHHHhhcCccCceEEEcCCc
Q psy13246 28 RPCSKV-IVKFLTVMMKHGKLPEVFVILGIR 57 (81)
Q Consensus 28 ~p~Skl-~~~il~IL~~eGYI~~~~~~~~~~ 57 (81)
.|||+. ...+-++....-||++..+++++.
T Consensus 38 ~~Cs~~~~~~Lr~~~~~~~~ir~i~~~~~g~ 68 (208)
T PF12792_consen 38 QPCSPAHLNALRQIVARSPYIRDIGLVRNGR 68 (208)
T ss_pred CCCCHHHHHHHHHHHHhchhhhheeEEeCCe
Confidence 799999 899999999999999999887663
No 46
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=31.68 E-value=62 Score=20.91 Aligned_cols=25 Identities=8% Similarity=0.248 Sum_probs=20.6
Q ss_pred hHHHHHHHHHHhhcCccCceEEEcC
Q psy13246 31 SKVIVKFLTVMMKHGKLPEVFVILG 55 (81)
Q Consensus 31 Skl~~~il~IL~~eGYI~~~~~~~~ 55 (81)
...+.+-++-|+++|.|++|...-+
T Consensus 36 ~~~v~~Ri~~L~~~GiI~~~~~~v~ 60 (154)
T COG1522 36 PSTVLRRIKRLEEEGVIKGYTAVLD 60 (154)
T ss_pred HHHHHHHHHHHHHCCceeeEEEEEC
Confidence 4567788899999999999986554
No 47
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=31.55 E-value=37 Score=18.61 Aligned_cols=16 Identities=13% Similarity=0.451 Sum_probs=13.8
Q ss_pred HHHHHHHHHhhcCccC
Q psy13246 33 VIVKFLTVMMKHGKLP 48 (81)
Q Consensus 33 l~~~il~IL~~eGYI~ 48 (81)
....+++-|.++||+.
T Consensus 34 tv~r~L~tL~~~g~v~ 49 (52)
T PF09339_consen 34 TVHRLLQTLVEEGYVE 49 (52)
T ss_dssp HHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHCcCee
Confidence 5678999999999985
No 48
>PF02829 3H: 3H domain; InterPro: IPR004173 The 3H domain is named after its three highly conserved histidine residues. The 3H domain appears to be a small molecule-binding domain, based on its occurrence with other domains []. Several proteins carrying this domain are transcriptional regulators from the biotin repressor family. The transcription regulator TM1602 from Thermotoga maritima is a DNA-binding protein thought to belong to a family of de novo NAD synthesis pathway regulators. TM1602 has an N-terminal DNA-binding domain and a C-terminal 3H regulatory domain. The N-terminal domain appears to bind to the NAD promoter region and repress the de novo NAD biosynthesis operon, while the C-terminal 3H domain may bind to nicotinamide, nicotinic acid, or other substrate/products []. The 3H domain has a 2-layer alpha/beta sandwich fold.; GO: 0005488 binding; PDB: 1J5Y_A.
Probab=31.41 E-value=71 Score=20.67 Aligned_cols=41 Identities=12% Similarity=0.199 Sum_probs=26.7
Q ss_pred hHHHHHHHhhhHhhc---------CCceEEEEechHHHHHHHHHHhhcCcc
Q psy13246 6 VLSDALKSINNAEKR---------GKRQVLIRPCSKVIVKFLTVMMKHGKL 47 (81)
Q Consensus 6 ~iaD~LtrIrNA~~a---------~k~~V~~~p~Skl~~~il~IL~~eGYI 47 (81)
-+..++.++++.... .-.++. .|.-.....|.+.|+++||+
T Consensus 48 Dv~~Fi~~l~~~~~~~Ls~LT~GvH~HtI~-a~~~e~l~~I~~~L~~~G~L 97 (98)
T PF02829_consen 48 DVDKFIEKLEKSKAKPLSSLTGGVHYHTIE-APDEEDLDKIEEALKKKGFL 97 (98)
T ss_dssp HHHHHHHHHHH--S--STTGGGGEEEEEEE-ESSHHHHHHHHHHHHHTT-B
T ss_pred HHHHHHHHHhccCCcchHHhcCCEeeEEEE-ECCHHHHHHHHHHHHHCCCc
Confidence 345566666655322 224555 78888999999999999995
No 49
>PF05818 TraT: Enterobacterial TraT complement resistance protein; InterPro: IPR008874 The traT gene is one of the F factor transfer genes and encodes an outer membrane protein which is involved in interactions between Escherichia coli and its surroundings []. The protein plays a role in preventing unproductive conjugation between bacteria carrying like plasmids.; GO: 0046999 regulation of conjugation, 0019867 outer membrane
Probab=31.01 E-value=42 Score=24.88 Aligned_cols=38 Identities=16% Similarity=0.378 Sum_probs=29.1
Q ss_pred HHHHHHHHHHhhcCccCceEEEcCCccceEEE---EecCC-Ccccc
Q psy13246 32 KVIVKFLTVMMKHGKLPEVFVILGIRTTVYCM---INWSG-IKPNP 73 (81)
Q Consensus 32 kl~~~il~IL~~eGYI~~~~~~~~~~~~~i~V---in~~g-i~pr~ 73 (81)
.+..+|-.-|+.+| |+++++...-.+-+ +-.|| ..|+-
T Consensus 37 ~l~~~i~~~L~~kG----Y~vv~~P~~A~Y~lq~NVL~~~k~~~~~ 78 (215)
T PF05818_consen 37 NLESQIISALQAKG----YQVVDDPDEAHYWLQANVLYVGKMDPNA 78 (215)
T ss_pred chHHHHHHHHHHCC----CEEecChhhCeEEEEeeehhccCCChhH
Confidence 68889999999999 68988765555545 55899 88774
No 50
>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024550 The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation, together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits, TFIIE-alpha and TFIIE-beta, and joins the preinitiation complex after RNA polymerase II and TFIIF []. This entry represents a helix-turn-helix (HTH) domain found in eukaryotic TFIIE-alpha []. It is also found in proteins from archaebacteria that are presumed to be TFIIE-alpha subunits [], the transcriptional regulator SarR, and also DNA-directed RNA polymerase III subunit Rpc3.; PDB: 1VD4_A 1Q1H_A.
Probab=31.01 E-value=52 Score=20.55 Aligned_cols=27 Identities=19% Similarity=0.057 Sum_probs=18.5
Q ss_pred hHHHHHHHHHHhhcCccCceEEEcCCc
Q psy13246 31 SKVIVKFLTVMMKHGKLPEVFVILGIR 57 (81)
Q Consensus 31 Skl~~~il~IL~~eGYI~~~~~~~~~~ 57 (81)
++-...+|..|.++|+|......++++
T Consensus 41 ~~~vRkiL~~L~~~~lv~~~~~~d~~~ 67 (105)
T PF02002_consen 41 PKEVRKILYKLYEDGLVSYRRRKDDER 67 (105)
T ss_dssp HHHHHHHHHHHHHHSS-EEEEE-----
T ss_pred HHHHHHHHHHHHHCCCeEEEEEEcCCC
Confidence 688899999999999997776655444
No 51
>PRK00111 hypothetical protein; Provisional
Probab=30.20 E-value=43 Score=24.10 Aligned_cols=19 Identities=16% Similarity=0.263 Sum_probs=16.2
Q ss_pred CCccchHHHHHHHhhhHhh
Q psy13246 1 MVRVNVLSDALKSINNAEK 19 (81)
Q Consensus 1 M~~~D~iaD~LtrIrNA~~ 19 (81)
|.+.||++++|.++|--.+
T Consensus 1 ~~~~~~~~~~~~~~~~~~~ 19 (180)
T PRK00111 1 MTMTDPIEQAFERIRAEAM 19 (180)
T ss_pred CCcccHHHHHHHHHHHHHh
Confidence 6678999999999996665
No 52
>TIGR00537 hemK_rel_arch HemK-related putative methylase. The gene hemK from E. coli was found to contribute to heme biosynthesis and originally suggested to be protoporphyrinogen oxidase (Medline 95189105). Functional analysis of the nearest homolog in Saccharomyces cerevisiae, YNL063w, finds it is not protoporphyrinogen oxidase and sequence analysis suggests that HemK homologs have S-adenosyl-methionine-dependent methyltransferase activity (Medline 99237242). Homologs are found, usually in a single copy, in nearly all completed genomes, but varying somewhat in apparent domain architecture. This model represents an archaeal and eukaryotic protein family that lacks an N-terminal domain found in HemK and its eubacterial homologs. It is found in a single copy in the first six completed archaeal and eukaryotic genomes.
Probab=29.74 E-value=1.3e+02 Score=20.06 Aligned_cols=41 Identities=20% Similarity=0.191 Sum_probs=29.5
Q ss_pred hHHHHHHHhhhHhhcCCceEEEEechHHHHHHHHHHhhcCc
Q psy13246 6 VLSDALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGK 46 (81)
Q Consensus 6 ~iaD~LtrIrNA~~a~k~~V~~~p~Skl~~~il~IL~~eGY 46 (81)
.+.++|..+....+-|-.-+...+...-..++++.|++.||
T Consensus 118 ~~~~~l~~~~~~Lk~gG~~~~~~~~~~~~~~~~~~l~~~gf 158 (179)
T TIGR00537 118 VIDRFLDELPEILKEGGRVQLIQSSLNGEPDTFDKLDERGF 158 (179)
T ss_pred HHHHHHHhHHHhhCCCCEEEEEEeccCChHHHHHHHHhCCC
Confidence 35677888888777766666534444447899999999987
No 53
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=28.98 E-value=55 Score=20.58 Aligned_cols=35 Identities=11% Similarity=0.143 Sum_probs=23.8
Q ss_pred HHHHHHHHHhhcCccCceEEEcCCccceEEEEecCC
Q psy13246 33 VIVKFLTVMMKHGKLPEVFVILGIRTTVYCMINWSG 68 (81)
Q Consensus 33 l~~~il~IL~~eGYI~~~~~~~~~~~~~i~Vin~~g 68 (81)
..-.+++-|.++|||....--+|.+...+. ++.-|
T Consensus 58 tvs~~l~~Le~~GlI~r~~~~~D~R~~~v~-LT~~G 92 (118)
T TIGR02337 58 SLTGILARLERDGLVTRLKASNDQRRVYIS-LTPKG 92 (118)
T ss_pred hHHHHHHHHHHCCCEEeccCCCCCCeeEEE-ECHhH
Confidence 467889999999999987655555544443 44333
No 54
>PRK14336 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=28.69 E-value=79 Score=24.76 Aligned_cols=31 Identities=6% Similarity=-0.062 Sum_probs=21.3
Q ss_pred HHHHHHHHhhcCccCceEEEcCCccceEEEEecCC
Q psy13246 34 IVKFLTVMMKHGKLPEVFVILGIRTTVYCMINWSG 68 (81)
Q Consensus 34 ~~~il~IL~~eGYI~~~~~~~~~~~~~i~Vin~~g 68 (81)
.+.+...|.++|| +.+++...-.+.|||-|+
T Consensus 18 se~~~~~l~~~G~----~~~~~~~~AD~viiNTC~ 48 (418)
T PRK14336 18 SERLGRLFELWGY----SLADKAEDAELVLVNSCV 48 (418)
T ss_pred HHHHHHHHHHCcC----EECCCcccCCEEEEeccc
Confidence 3567888889886 444443334566799998
No 55
>COG0325 Predicted enzyme with a TIM-barrel fold [General function prediction only]
Probab=28.50 E-value=54 Score=24.55 Aligned_cols=45 Identities=22% Similarity=0.262 Sum_probs=32.3
Q ss_pred CCccchHHHHHHHhhhHhhc-CC--ceEEEEechHHH-HHHHHHHhhcC
Q psy13246 1 MVRVNVLSDALKSINNAEKR-GK--RQVLIRPCSKVI-VKFLTVMMKHG 45 (81)
Q Consensus 1 M~~~D~iaD~LtrIrNA~~a-~k--~~V~~~p~Skl~-~~il~IL~~eG 45 (81)
|.+.+.+....++|+.|..+ |+ ..|.+++.||.. .+-.+.+.+.|
T Consensus 1 ~~i~~nl~~v~~~I~~a~~~a~R~~~~V~LvAVSK~~~~~~I~~~~~aG 49 (228)
T COG0325 1 MDIKENLAAVRERIAAAAERAGRNPGSVTLVAVSKTVPAEDIREAYEAG 49 (228)
T ss_pred CcHHHHHHHHHHHHHHHHHHcCCCCCcEEEEEEeCCCCHHHHHHHHHcC
Confidence 55678899999999988764 33 379999999975 34445555555
No 56
>PF02618 YceG: YceG-like family; InterPro: IPR003770 This uncharacterised protein family, found in three of four microbial genomes, virtually always once per genome, includes YceG from Escherichia coli. Proteins in this family are typically between 332 and 389 amino acids in length. This protein is encoded next to PabC, 4-amino-4-deoxychorismate lyase, in Escherichia coli and numerous other proteobacteria, but that proximity is not conserved in other lineages. Numerous members of this family have been misannotated as aminodeoxychorismate lyase, apparently because of promiximty to PabC. The structure of Swiss:P28306 was solved by X-ray crystallography. This group represents an uncharacterised protein family UPF0755.; PDB: 2R1F_B.
Probab=28.46 E-value=89 Score=23.47 Aligned_cols=43 Identities=9% Similarity=0.149 Sum_probs=28.1
Q ss_pred hHHHHHHHhhhHhhcCCceEEEEechHHHHHHHHHHhhcCccCce
Q psy13246 6 VLSDALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGKLPEV 50 (81)
Q Consensus 6 ~iaD~LtrIrNA~~a~k~~V~~~p~Skl~~~il~IL~~eGYI~~~ 50 (81)
...+++..|.++.... ..|. +|--....+|++.|.+.|.+..-
T Consensus 55 S~~eil~~L~~g~~~~-~~vT-IpEG~t~~~i~~~l~~~~~~~~~ 97 (297)
T PF02618_consen 55 SYKEILSILTSGKVAQ-VRVT-IPEGFTLEQIAQRLAEKGGISKE 97 (297)
T ss_dssp -HHHHHHHHHH------EEEE-E-TT--HHHHHHHHHCSTTEE--
T ss_pred CHHHHHHHHHhcccce-eEEE-ecCCCcHHHHHHHHHhccCCCHH
Confidence 5678899998887775 4787 89999999999999999998543
No 57
>PF06819 Arc_PepC: Archaeal Peptidase A24 C-terminal Domain; InterPro: IPR009639 This region is of unknown function found at the C terminus of some archael proteins that have multiple transmembrane domains and are predicted to be aspartic peptidases belonging to the MEROPS peptidase subfamily A24A (type 4 prepilin peptidase 1.
Probab=28.24 E-value=1.2e+02 Score=20.31 Aligned_cols=42 Identities=24% Similarity=0.264 Sum_probs=31.5
Q ss_pred HHHHHHhhhHhhcCCceE-----EEEe----chHHHHHHHHHHhhcCccCc
Q psy13246 8 SDALKSINNAEKRGKRQV-----LIRP----CSKVIVKFLTVMMKHGKLPE 49 (81)
Q Consensus 8 aD~LtrIrNA~~a~k~~V-----~~~p----~Skl~~~il~IL~~eGYI~~ 49 (81)
+|++.|++.|...+.-.. .+.| .|+--.+.|+-|.+||=|++
T Consensus 56 ~~~~~r~k~~l~~~~~~~l~g~~i~~~~~EGLs~E~IE~Lk~Lv~eGKi~n 106 (110)
T PF06819_consen 56 SSFFKRFKFALKTEDGSALTGEKIISTDAEGLSKEDIEKLKKLVEEGKIEN 106 (110)
T ss_pred ccHHHHHHHHHHhcccccccCCeEEeccccCCCHHHHHHHHHHHHcCCCcc
Confidence 678888888887765433 2244 37788899999999998875
No 58
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=28.04 E-value=63 Score=24.13 Aligned_cols=28 Identities=21% Similarity=0.306 Sum_probs=22.3
Q ss_pred chHHHHHHHHHHhhcCccCc-eEEEcCCc
Q psy13246 30 CSKVIVKFLTVMMKHGKLPE-VFVILGIR 57 (81)
Q Consensus 30 ~Skl~~~il~IL~~eGYI~~-~~~~~~~~ 57 (81)
++|.+.+=|++|.++|.+++ |+.+.-|+
T Consensus 41 sqkAVl~HL~~LE~AGlveS~ie~~~Rg~ 69 (217)
T COG1777 41 SQKAVLKHLRILERAGLVESRIEKIPRGR 69 (217)
T ss_pred CHHHHHHHHHHHHHcCCchhhccccccCC
Confidence 46788888999999999999 56555544
No 59
>PF08643 DUF1776: Fungal family of unknown function (DUF1776); InterPro: IPR013952 This is a fungal protein of unknown function. One of the proteins P32792 from SWISSPROT has been localised to the mitochondria [].
Probab=27.99 E-value=48 Score=25.54 Aligned_cols=27 Identities=15% Similarity=0.180 Sum_probs=22.1
Q ss_pred CCceEEEE---echHHHHHHHHHHhhcCccC
Q psy13246 21 GKRQVLIR---PCSKVIVKFLTVMMKHGKLP 48 (81)
Q Consensus 21 ~k~~V~~~---p~Skl~~~il~IL~~eGYI~ 48 (81)
+++-|+ + |...+++.++-=|++.|||=
T Consensus 2 R~evVv-I~Gs~~~PltR~la~DLeRRGFIV 31 (299)
T PF08643_consen 2 RKEVVV-IAGSPHDPLTRSLALDLERRGFIV 31 (299)
T ss_pred ceeEEE-EECCCCCccHHHHHHHHhhCCeEE
Confidence 344454 5 88999999999999999995
No 60
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=27.60 E-value=62 Score=20.95 Aligned_cols=30 Identities=13% Similarity=0.112 Sum_probs=21.8
Q ss_pred HHHHHHHHHhhcCccCceEEEcCCccceEE
Q psy13246 33 VIVKFLTVMMKHGKLPEVFVILGIRTTVYC 62 (81)
Q Consensus 33 l~~~il~IL~~eGYI~~~~~~~~~~~~~i~ 62 (81)
..-.+++-|.+.|||....--+|.|...+.
T Consensus 62 tvt~~v~~Le~~GlV~r~~~~~DrR~~~l~ 91 (144)
T PRK03573 62 SLVRTLDQLEEKGLISRQTCASDRRAKRIK 91 (144)
T ss_pred hHHHHHHHHHHCCCEeeecCCCCcCeeeeE
Confidence 345789999999999987655566654444
No 61
>PRK14327 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=27.28 E-value=94 Score=25.37 Aligned_cols=32 Identities=9% Similarity=-0.043 Sum_probs=22.2
Q ss_pred HHHHHHHHhhcCccCceEEEcCCccceEEEEecCCC
Q psy13246 34 IVKFLTVMMKHGKLPEVFVILGIRTTVYCMINWSGI 69 (81)
Q Consensus 34 ~~~il~IL~~eGYI~~~~~~~~~~~~~i~Vin~~gi 69 (81)
.+.++.+|.+.|| +.+++...-.+.|||-|.+
T Consensus 83 se~~~~~L~~~Gy----~~~~~~~~ADviiiNTC~V 114 (509)
T PRK14327 83 TEVMAGIFEALGY----EPTDDTEDADVILLNTCAI 114 (509)
T ss_pred HHHHHHHHHHCcC----EECCCcCCCCEEEEECCCC
Confidence 4678889999987 4444433345667999984
No 62
>PRK14340 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=27.17 E-value=82 Score=24.97 Aligned_cols=31 Identities=6% Similarity=0.018 Sum_probs=21.5
Q ss_pred HHHHHHHHhhcCccCceEEEcCCccceEEEEecCC
Q psy13246 34 IVKFLTVMMKHGKLPEVFVILGIRTTVYCMINWSG 68 (81)
Q Consensus 34 ~~~il~IL~~eGYI~~~~~~~~~~~~~i~Vin~~g 68 (81)
.+.++..|.++|| +.+++.....+.|||-|+
T Consensus 23 se~~~~~l~~~G~----~~~~~~~~ADviiiNTC~ 53 (445)
T PRK14340 23 SEIITALLQDEGY----VPAASEEDADIVLLNTCA 53 (445)
T ss_pred HHHHHHHHHHCcC----EECCCcccCCEEEEEeee
Confidence 3567888888886 455544444566799998
No 63
>PF10866 DUF2704: Protein of unknown function (DUF2704); InterPro: IPR022594 This group of viral proteins has no known function.
Probab=27.16 E-value=36 Score=24.46 Aligned_cols=13 Identities=46% Similarity=0.628 Sum_probs=10.2
Q ss_pred cCC-Cccccceeee
Q psy13246 66 WSG-IKPNPIITLV 78 (81)
Q Consensus 66 ~~g-i~pr~~~~~~ 78 (81)
-+| |||+||..-.
T Consensus 146 ~~~yikpnciv~tf 159 (168)
T PF10866_consen 146 SAGYIKPNCIVLTF 159 (168)
T ss_pred ccCccCCCeEEEee
Confidence 578 9999997643
No 64
>TIGR00089 RNA modification enzyme, MiaB family. This subfamily is aparrently a part of a larger superfamily of enzymes utilizing both a 4Fe4S cluster and S-adenosyl methionine (SAM) to initiate radical reactions. MiaB acts on a particular isoprenylated Adenine base of certain tRNAs causing thiolation at an aromatic carbon, and probably also transferring a methyl grouyp from SAM to the thiol. The particular substrate of the three other clades is unknown but may be very closely related.
Probab=27.12 E-value=92 Score=24.16 Aligned_cols=31 Identities=13% Similarity=-0.027 Sum_probs=21.8
Q ss_pred HHHHHHHHhhcCccCceEEEcCCccceEEEEecCC
Q psy13246 34 IVKFLTVMMKHGKLPEVFVILGIRTTVYCMINWSG 68 (81)
Q Consensus 34 ~~~il~IL~~eGYI~~~~~~~~~~~~~i~Vin~~g 68 (81)
.+.+...|.+.|| +.+++.....+.+||-|+
T Consensus 16 s~~~~~~l~~~g~----~~~~~~~~aD~v~intC~ 46 (429)
T TIGR00089 16 SEIMAGLLKEAGY----EVTDDPEEADVIIINTCA 46 (429)
T ss_pred HHHHHHHHHHCcC----EECCCcccCCEEEEecce
Confidence 3567888888887 555544444666799888
No 65
>PF02631 RecX: RecX family; InterPro: IPR003783 RecX is a putative bacterial regulatory protein []. The gene encoding RecX is found downstream of recA, and it is suggested that the RecX protein might be regulator of RecA activity by interaction with the RecA protein or filament [].; GO: 0006282 regulation of DNA repair; PDB: 3DFG_A 3D5L_B 3C1D_B 3E3V_A.
Probab=25.98 E-value=63 Score=20.58 Aligned_cols=22 Identities=9% Similarity=0.146 Sum_probs=17.6
Q ss_pred hHHHHHHHHHHhhcCccCceEE
Q psy13246 31 SKVIVKFLTVMMKHGKLPEVFV 52 (81)
Q Consensus 31 Skl~~~il~IL~~eGYI~~~~~ 52 (81)
......++.-|++.|||.+..+
T Consensus 8 ~e~I~~vi~~l~~~gyidD~~y 29 (121)
T PF02631_consen 8 EEAIEEVIDRLKELGYIDDERY 29 (121)
T ss_dssp HHHHHHHHHHHHHTTSS-HHHH
T ss_pred HHHHHHHHHHHHHcCCCCHHHH
Confidence 5578899999999999998653
No 66
>PF03869 Arc: Arc-like DNA binding domain; InterPro: IPR005569 Arc repressor act by the cooperative binding of two Arc repressor dimers to a 21-base-pair operator site. Each Arc dimer uses an antiparallel beta-sheet to recognise bases in the major groove [].; GO: 0003677 DNA binding; PDB: 3QOQ_D 1MNT_B 1QTG_B 1BDV_A 1PAR_C 1BDT_C 1ARR_B 1MYL_F 1MYK_A 1NLA_B ....
Probab=25.90 E-value=1.2e+02 Score=17.06 Aligned_cols=37 Identities=11% Similarity=0.325 Sum_probs=27.5
Q ss_pred HHHHHhhhHhhcCCceEEEEechHHHHHHHHHHhhcCccCc
Q psy13246 9 DALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGKLPE 49 (81)
Q Consensus 9 D~LtrIrNA~~a~k~~V~~~p~Skl~~~il~IL~~eGYI~~ 49 (81)
++..+|+.......+++- +-+...+-+-|.+||=|.+
T Consensus 14 ~l~~~lk~~A~~~gRS~N----sEIv~~L~~~l~~e~~i~~ 50 (50)
T PF03869_consen 14 ELKEKLKERAEENGRSMN----SEIVQRLEEALKKEGRIQA 50 (50)
T ss_dssp HHHHHHHHHHHHTTS-HH----HHHHHHHHHHHHHCTSSCT
T ss_pred HHHHHHHHHHHHhCCChH----HHHHHHHHHHHhccccCCC
Confidence 667788888888777775 6677777788888987753
No 67
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=25.83 E-value=69 Score=16.40 Aligned_cols=17 Identities=18% Similarity=0.354 Sum_probs=14.3
Q ss_pred HHHHHHHHHHhhcCccC
Q psy13246 32 KVIVKFLTVMMKHGKLP 48 (81)
Q Consensus 32 kl~~~il~IL~~eGYI~ 48 (81)
......++.|.++||+.
T Consensus 23 ~tv~~~l~~L~~~g~l~ 39 (48)
T smart00419 23 ETVSRTLKRLEKEGLIS 39 (48)
T ss_pred HHHHHHHHHHHHCCCEE
Confidence 44678899999999996
No 68
>smart00463 SMR Small MutS-related domain.
Probab=25.55 E-value=1.5e+02 Score=17.35 Aligned_cols=56 Identities=18% Similarity=0.079 Sum_probs=32.9
Q ss_pred cchHHHHHHHhhhHhhcCC-ceEEEEe---------chHHHHHHHHHHhhcCccCceEEEcCCccceEEE
Q psy13246 4 VNVLSDALKSINNAEKRGK-RQVLIRP---------CSKVIVKFLTVMMKHGKLPEVFVILGIRTTVYCM 63 (81)
Q Consensus 4 ~D~iaD~LtrIrNA~~a~k-~~V~~~p---------~Skl~~~il~IL~~eGYI~~~~~~~~~~~~~i~V 63 (81)
.+.+.-+-..|.++...+. +.+.++. .++++..+.+.+..+||- ..++++.|.+.|
T Consensus 12 ~eA~~~l~~~l~~~~~~~~~~~~~II~G~G~~s~~g~~~i~~~l~~~l~~~~~~----~~~~~~~G~~~v 77 (80)
T smart00463 12 EEALTALDKFLNNARLKGLEQKLVIITGKGKHSLGGKSGVKPALKEHLRVESFR----FAEEGNSGVLVV 77 (80)
T ss_pred HHHHHHHHHHHHHHHHcCCCceEEEEEcccCCCccchhhHHHHHHhchhhcccc----cCCCCCCeEEEE
Confidence 3455555667777777777 6676432 356677777777655554 333344455543
No 69
>PF14044 NETI: NETI protein
Probab=25.18 E-value=49 Score=19.88 Aligned_cols=14 Identities=36% Similarity=0.541 Sum_probs=8.9
Q ss_pred HHHHHHHhhcCccC
Q psy13246 35 VKFLTVMMKHGKLP 48 (81)
Q Consensus 35 ~~il~IL~~eGYI~ 48 (81)
.+-|.-|++|||..
T Consensus 11 ~~CL~RM~~eGY~P 24 (57)
T PF14044_consen 11 SDCLARMKKEGYMP 24 (57)
T ss_pred HHHHHHHHHcCCCc
Confidence 34566667777765
No 70
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=25.16 E-value=1.2e+02 Score=20.76 Aligned_cols=24 Identities=13% Similarity=-0.105 Sum_probs=19.8
Q ss_pred chHHHHHHHHHHhhcCccCceEEEc
Q psy13246 30 CSKVIVKFLTVMMKHGKLPEVFVIL 54 (81)
Q Consensus 30 ~Skl~~~il~IL~~eGYI~~~~~~~ 54 (81)
..+....+|..|.+.|++. |+...
T Consensus 41 ~~~~VRk~L~~L~e~~Lv~-~~r~r 64 (158)
T TIGR00373 41 KLNEVRKALYALYDAGLAD-YKRRK 64 (158)
T ss_pred CHHHHHHHHHHHHHCCCce-eeeee
Confidence 4688899999999999999 65443
No 71
>PRK14862 rimO ribosomal protein S12 methylthiotransferase; Provisional
Probab=24.87 E-value=1.1e+02 Score=24.08 Aligned_cols=33 Identities=15% Similarity=0.135 Sum_probs=22.2
Q ss_pred HHHHHHHHhhcCccCceEEEcCCccceEEEEecCCCc
Q psy13246 34 IVKFLTVMMKHGKLPEVFVILGIRTTVYCMINWSGIK 70 (81)
Q Consensus 34 ~~~il~IL~~eGYI~~~~~~~~~~~~~i~Vin~~gi~ 70 (81)
.+.++..|.++|| +.+++...-.+.|||-|++.
T Consensus 24 se~~~~~l~~~G~----~~~~~~~~aD~ivinTC~v~ 56 (440)
T PRK14862 24 SERILTQLRAEGY----EISPSYDGADLVIVNTCGFI 56 (440)
T ss_pred HHHHHHHHHHCcC----EECCCcccCCEEEEeccccc
Confidence 4678888999887 44444333456679999943
No 72
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=24.54 E-value=62 Score=22.75 Aligned_cols=21 Identities=24% Similarity=0.335 Sum_probs=17.9
Q ss_pred echHHHHHHHHHHhhcCccCc
Q psy13246 29 PCSKVIVKFLTVMMKHGKLPE 49 (81)
Q Consensus 29 p~Skl~~~il~IL~~eGYI~~ 49 (81)
-+.++.+.+|+.|++.|||+.
T Consensus 93 ~sg~iiR~~LqqLE~~glVek 113 (150)
T PRK09333 93 GSGSIIRKILQQLEKAGLVEK 113 (150)
T ss_pred CccHHHHHHHHHHHHCCCeee
Confidence 345679999999999999984
No 73
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=24.15 E-value=68 Score=20.93 Aligned_cols=35 Identities=14% Similarity=0.140 Sum_probs=23.5
Q ss_pred HHHHHHHHHhhcCccCceEEEcCCccceEEEEecCC
Q psy13246 33 VIVKFLTVMMKHGKLPEVFVILGIRTTVYCMINWSG 68 (81)
Q Consensus 33 l~~~il~IL~~eGYI~~~~~~~~~~~~~i~Vin~~g 68 (81)
..-.+++-|.+.|||..-.--+|.+...+. +.+-|
T Consensus 70 tvsr~l~~Le~~GlI~R~~~~~DrR~~~l~-LT~~G 104 (144)
T PRK11512 70 ALTRMLDRLVCKGWVERLPNPNDKRGVLVK-LTTSG 104 (144)
T ss_pred HHHHHHHHHHHCCCEEeccCcccCCeeEeE-EChhH
Confidence 455678999999999877555566554444 44444
No 74
>PF08513 LisH: LisH; InterPro: IPR013720 The LisH motif is found in a large number of eukaryotic proteins, from metazoa, fungi and plants that have a wide range of functions. The recently solved structure of the LisH domain in the N-terminal region of LIS1 depicted it as a novel dimerization motif, and that other structural elements are likely to play an important role in dimerisation [, , ]. The LisH (lis homology) domain mediates protein dimerisation and tetramerisation. The LisH domain is found in Sif2, a component of the Set3 complex which is responsible for repressing meiotic genes. It has been shown that the LisH domain helps mediate interaction with components of the Set3 complex []. ; PDB: 2XTE_L 2XTC_B 2XTD_A 1UUJ_B.
Probab=23.87 E-value=84 Score=15.45 Aligned_cols=17 Identities=6% Similarity=0.079 Sum_probs=12.2
Q ss_pred HHHHHHHHHhhcCccCc
Q psy13246 33 VIVKFLTVMMKHGKLPE 49 (81)
Q Consensus 33 l~~~il~IL~~eGYI~~ 49 (81)
+..-|.+-|+++||.+.
T Consensus 3 Ln~lI~~YL~~~Gy~~t 19 (27)
T PF08513_consen 3 LNQLIYDYLVENGYKET 19 (27)
T ss_dssp HHHHHHHHHHHCT-HHH
T ss_pred HHHHHHHHHHHCCcHHH
Confidence 44568899999999753
No 75
>COG4451 RbcS Ribulose bisphosphate carboxylase small subunit [Energy production and conversion]
Probab=23.78 E-value=67 Score=22.14 Aligned_cols=26 Identities=15% Similarity=0.100 Sum_probs=21.1
Q ss_pred HHHHHHHHHhhcCccCceEEEcCCcc
Q psy13246 33 VIVKFLTVMMKHGKLPEVFVILGIRT 58 (81)
Q Consensus 33 l~~~il~IL~~eGYI~~~~~~~~~~~ 58 (81)
-..+=++.|..+||+-++|.+|+.+.
T Consensus 23 qi~~QVrylL~QGykigvE~~d~rrp 48 (127)
T COG4451 23 QIAEQVRYLLSQGYKIGVEYVDDRRP 48 (127)
T ss_pred HHHHHHHHHHhCCcccceeecccCCc
Confidence 45566788999999999999987653
No 76
>PRK14338 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=23.74 E-value=1.1e+02 Score=24.27 Aligned_cols=31 Identities=6% Similarity=-0.021 Sum_probs=21.2
Q ss_pred HHHHHHHHhhcCccCceEEEcCCccceEEEEecCC
Q psy13246 34 IVKFLTVMMKHGKLPEVFVILGIRTTVYCMINWSG 68 (81)
Q Consensus 34 ~~~il~IL~~eGYI~~~~~~~~~~~~~i~Vin~~g 68 (81)
.+.+...|.+.|| +.+++...-.+.|||-|+
T Consensus 37 se~~~~~l~~~G~----~~~~~~~~AD~~iiNTC~ 67 (459)
T PRK14338 37 SERLEAALQGVGY----SPAERPEDADFIVLNSCS 67 (459)
T ss_pred HHHHHHHHHHCcC----EECCCcccCCEEEEeccc
Confidence 4678888999886 444433334566799998
No 77
>PF04566 RNA_pol_Rpb2_4: RNA polymerase Rpb2, domain 4; InterPro: IPR007646 RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). Domain 4, is also known as the external 2 domain [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3S17_B 1I6H_B 4A3B_B 3K1F_B 4A3I_B 1TWA_B 3S14_B 3S15_B 2NVX_B 3M3Y_B ....
Probab=23.53 E-value=1.7e+02 Score=17.26 Aligned_cols=42 Identities=21% Similarity=0.306 Sum_probs=27.1
Q ss_pred HHHHHHHHHhhcCccCce-EEEcCCccceEEEEecCC--Cccccc
Q psy13246 33 VIVKFLTVMMKHGKLPEV-FVILGIRTTVYCMINWSG--IKPNPI 74 (81)
Q Consensus 33 l~~~il~IL~~eGYI~~~-~~~~~~~~~~i~Vin~~g--i~pr~~ 74 (81)
--.+-++-|.++|.|..+ .+.-+...+.+.|-.+.| .+|=++
T Consensus 16 ~l~~~lr~~RR~g~i~~~vsi~~~~~~~ei~I~tD~GR~~RPL~v 60 (63)
T PF04566_consen 16 ELVKTLRNLRRSGKISKEVSIVYDIREKEIRINTDAGRLCRPLFV 60 (63)
T ss_dssp HHHHHHHHHHHTTSS-TTSEEEEETTTTEEEEE-SSCEEEEEEEE
T ss_pred HHHHHHHHHhhccCCcceeEEEEeccCCEEEEEccCCcccceeEE
Confidence 345667888999998876 344455556777666999 777544
No 78
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=23.40 E-value=64 Score=21.90 Aligned_cols=21 Identities=19% Similarity=0.290 Sum_probs=17.9
Q ss_pred hHHHHHHHHHHhhcCccCceE
Q psy13246 31 SKVIVKFLTVMMKHGKLPEVF 51 (81)
Q Consensus 31 Skl~~~il~IL~~eGYI~~~~ 51 (81)
-+...+|+..|.+.|+|.+.+
T Consensus 38 ~~~L~kIl~~L~~aGlv~S~r 58 (153)
T PRK11920 38 ELFLFKILQPLVEAGLVETVR 58 (153)
T ss_pred HHHHHHHHHHHHHCCCEEeec
Confidence 467789999999999998764
No 79
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=23.37 E-value=1.4e+02 Score=20.79 Aligned_cols=39 Identities=8% Similarity=0.171 Sum_probs=25.3
Q ss_pred chHHHHHHHHHHhhcCccCceEEEcCCccceEEE-EecCC
Q psy13246 30 CSKVIVKFLTVMMKHGKLPEVFVILGIRTTVYCM-INWSG 68 (81)
Q Consensus 30 ~Skl~~~il~IL~~eGYI~~~~~~~~~~~~~i~V-in~~g 68 (81)
...-...++++|-++||-.+.+-.+++..+.+.+ .+.|-
T Consensus 119 ~~~~~~~l~~~~~~~Gy~~~~~~~~~~~~~~~~l~~~~CP 158 (203)
T TIGR02702 119 LAERLAQLVALRQQEGFMAEVHPVSDEQKEAFILTEYNCA 158 (203)
T ss_pred HHHHHHHHHHHHHhCCCeEEEEecCCCCCCeEEEEeCCCc
Confidence 3456788899999999998886444333333433 45553
No 80
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=23.22 E-value=90 Score=17.32 Aligned_cols=19 Identities=16% Similarity=0.216 Sum_probs=15.7
Q ss_pred hHHHHHHHHHHhhcCccCc
Q psy13246 31 SKVIVKFLTVMMKHGKLPE 49 (81)
Q Consensus 31 Skl~~~il~IL~~eGYI~~ 49 (81)
....+.|+++..+-||..+
T Consensus 28 ~~tr~rI~~~a~~lgY~pN 46 (46)
T PF00356_consen 28 EETRERILEAAEELGYRPN 46 (46)
T ss_dssp HHHHHHHHHHHHHHTB-SS
T ss_pred HHHHHHHHHHHHHHCCCCC
Confidence 6788999999999999754
No 81
>TIGR01578 MiaB-like-B MiaB-like tRNA modifying enzyme, archaeal-type. This clade is a member of a subfamily (TIGR00089) and spans the archaea and eukaryotes. The only archaeal miaB-like genes are in this clade, while eukaryotes have sequences described by this model as well as ones falling within the scope of the MiaB equivalog model.
Probab=22.87 E-value=1.1e+02 Score=23.98 Aligned_cols=31 Identities=6% Similarity=0.009 Sum_probs=21.1
Q ss_pred HHHHHHHHhhcCccCceEEEcCCccceEEEEecCC
Q psy13246 34 IVKFLTVMMKHGKLPEVFVILGIRTTVYCMINWSG 68 (81)
Q Consensus 34 ~~~il~IL~~eGYI~~~~~~~~~~~~~i~Vin~~g 68 (81)
...+...|.++|| +++++.....+.|||-|+
T Consensus 16 s~~~~~~l~~~G~----~~~~~~~~ADviiinTC~ 46 (420)
T TIGR01578 16 SEIMKNSLAAYGH----ELVNNAEEADLAILNTCT 46 (420)
T ss_pred HHHHHHHHHHCCC----EECCCcccCCEEEEEeee
Confidence 4568889999998 344433334566799998
No 82
>PF11061 DUF2862: Protein of unknown function (DUF2862); InterPro: IPR021291 This family of proteins has no known function.
Probab=22.82 E-value=68 Score=19.57 Aligned_cols=30 Identities=13% Similarity=0.146 Sum_probs=24.3
Q ss_pred hHHHHHHHHHHhh--cCccCceEEEcCCccce
Q psy13246 31 SKVIVKFLTVMMK--HGKLPEVFVILGIRTTV 60 (81)
Q Consensus 31 Skl~~~il~IL~~--eGYI~~~~~~~~~~~~~ 60 (81)
.++-.++++-|.+ .|-|.+|+.+|...-|.
T Consensus 14 DRi~~~l~~~l~~~~~g~I~~fKmtDG~giG~ 45 (64)
T PF11061_consen 14 DRIPKELVDKLGKNPIGTIKGFKMTDGSGIGV 45 (64)
T ss_pred hhccHHHHHHhccCCcEEEEEEEEecCCcEEE
Confidence 5667889999999 99999999988665443
No 83
>PRK14333 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=22.41 E-value=1.1e+02 Score=24.17 Aligned_cols=31 Identities=6% Similarity=-0.090 Sum_probs=21.1
Q ss_pred HHHHHHHHhhcCccCceEEEcCCccceEEEEecCC
Q psy13246 34 IVKFLTVMMKHGKLPEVFVILGIRTTVYCMINWSG 68 (81)
Q Consensus 34 ~~~il~IL~~eGYI~~~~~~~~~~~~~i~Vin~~g 68 (81)
.+.+...|.++|| +.+++...-.+.|||-|+
T Consensus 23 s~~~~~~l~~~G~----~~~~~~~~ADiiiiNTC~ 53 (448)
T PRK14333 23 SERMAGILEDMGY----QWAEDELQADLVLYNTCT 53 (448)
T ss_pred HHHHHHHHHHCcC----EECCCcccCCEEEEEeee
Confidence 3567888889886 444444334566799998
No 84
>PF01454 MAGE: MAGE family; InterPro: IPR002190 The first mammalian members of the MAGE (melanoma-associated antigen) gene family were originally described as completely silent in normal adult tissues, with the exception of male germ cells and, for some of them, placenta. By contrast, these genes were expressed in various kinds of tumors. However, other members of the family were recently found to be expressed in normal cells, indicating that the family is larger and more disparate than initially expected. MAGE-like genes have also been identified in non-mammalian species, including Drosophila melanogaster (Fruit fly) and Danio rerio (Zebrafish). Although no MAGE homologous sequences have been identified in Caenorhabditis elegans, Saccharomyces cerevisiae (Baker's yeast) or Schizosaccharomyces pombe (Fission yeast), MAGE sequences have been found in several vegetal species, including Arabidopsis thaliana (Mouse-ear cress) []. The only region of homology shared by all of the members of the family is a stretch of about 200 amino acids which has been named the MAGE conserved domain. The MAGE conserved domain is usually located close to the C-terminal, although it can also be found in a more central position in some proteins. The MAGE conserved domain is generally present as a single copy but it is duplicated in some proteins. It has been proposed that the MAGE conserved domain of MAGE-D proteins might interact with p75 neurotrophin or related receptors [].; PDB: 3NW0_B 2WA0_A 1I4F_C.
Probab=22.01 E-value=74 Score=21.89 Aligned_cols=23 Identities=17% Similarity=0.154 Sum_probs=15.0
Q ss_pred HHHHHHHHHHhhcCccCceEEEc
Q psy13246 32 KVIVKFLTVMMKHGKLPEVFVIL 54 (81)
Q Consensus 32 kl~~~il~IL~~eGYI~~~~~~~ 54 (81)
....-+++-|.++||+..++.+.
T Consensus 147 ~~~~~i~~~~vkq~YL~~~k~~~ 169 (195)
T PF01454_consen 147 DIKKLILKEFVKQGYLVRYKQVP 169 (195)
T ss_dssp -HHHHHHCHHHHCTSE-EEE---
T ss_pred CHHHHHHHHHHHhcCHHheeecC
Confidence 55566669999999998887443
No 85
>PRK14334 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=21.59 E-value=1.2e+02 Score=23.74 Aligned_cols=31 Identities=6% Similarity=0.131 Sum_probs=20.7
Q ss_pred HHHHHHHHhhcCccCceEEEcCCccceEEEEecCC
Q psy13246 34 IVKFLTVMMKHGKLPEVFVILGIRTTVYCMINWSG 68 (81)
Q Consensus 34 ~~~il~IL~~eGYI~~~~~~~~~~~~~i~Vin~~g 68 (81)
.+.+...|.+.|| +.+++...-.+.|||-|+
T Consensus 17 s~~~~~~l~~~G~----~~~~~~~~ADi~iiNTC~ 47 (440)
T PRK14334 17 THLVESELVSLGA----EIVDSVDEADFVLVNTCA 47 (440)
T ss_pred HHHHHHHHHHCcC----EECCCcccCCEEEEeccc
Confidence 3567788888886 444443334566789888
No 86
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=21.54 E-value=81 Score=18.85 Aligned_cols=45 Identities=18% Similarity=0.382 Sum_probs=27.5
Q ss_pred ccchHHHHHHHhhhHhhcCCceEE--EEechHHHHHHHHHHhhcCccC
Q psy13246 3 RVNVLSDALKSINNAEKRGKRQVL--IRPCSKVIVKFLTVMMKHGKLP 48 (81)
Q Consensus 3 ~~D~iaD~LtrIrNA~~a~k~~V~--~~p~Skl~~~il~IL~~eGYI~ 48 (81)
..|.+.|.|..+.++... ..++. .-=..+.....++.|.++|+|+
T Consensus 4 ~~~Ii~~IL~~l~~~~~~-~t~i~~~~~L~~~~~~~yL~~L~~~gLI~ 50 (77)
T PF14947_consen 4 RLEIIFDILKILSKGGAK-KTEIMYKANLNYSTLKKYLKELEEKGLIK 50 (77)
T ss_dssp TTHHHHHHHHHH-TT-B--HHHHHTTST--HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHHHcCCCC-HHHHHHHhCcCHHHHHHHHHHHHHCcCee
Confidence 358899999998644332 22221 0012456678999999999994
No 87
>PF02205 WH2: WH2 motif; InterPro: IPR003124 The WH2 (WASP-Homology 2, or Wiskott-Aldrich homology 2) domain is an ~18 amino acids actin-binding motif. This domain was first recognised as an essential element for the regulation of the cytoskeleton by the mammalian Wiskott-Aldrich syndrome protein (WASP) family. WH2 proteins occur in eukaryotes from yeast to mammals, in insect viruses, and in some bacteria. The WH2 domain is found as a modular part of larger proteins; it can be associated with the WH1 or EVH1 domain and with the CRIB domain, and the WH2 domain can occur as a tandem repeat. The WH2 domain binds actin monomers and can facilitate the assembly of actin monomers into newly forming actin filaments [, ]. ; GO: 0005515 protein binding; PDB: 2D1K_C 3M1F_V 2A41_C 2A3Z_C 2VCP_E 2A40_F 3P8C_D 3M3N_W.
Probab=21.52 E-value=82 Score=16.16 Aligned_cols=16 Identities=25% Similarity=0.156 Sum_probs=12.2
Q ss_pred cchHHHHHHHhhhHhh
Q psy13246 4 VNVLSDALKSINNAEK 19 (81)
Q Consensus 4 ~D~iaD~LtrIrNA~~ 19 (81)
.|.-+++|..||++..
T Consensus 2 ~~~R~~LL~~Ir~G~k 17 (30)
T PF02205_consen 2 GDGRSALLSQIRKGSK 17 (30)
T ss_dssp STTHHHHHHHHHHH--
T ss_pred CCcHHHHHHHHHHccc
Confidence 3677899999999954
No 88
>PF07862 Nif11: Nitrogen fixation protein of unknown function; InterPro: IPR012903 This domain is found in the cyanobacteria, and the nitrogen-fixing proteobacterium Azotobacter vinelandii and may be involved in nitrogen fixation, but no role has been assigned [].
Probab=21.04 E-value=63 Score=17.63 Aligned_cols=42 Identities=14% Similarity=0.257 Sum_probs=26.6
Q ss_pred CCccchHHHHHHHhhhHhhcCCceEEEEechHHHHHHHHHHhhcCcc
Q psy13246 1 MVRVNVLSDALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGKL 47 (81)
Q Consensus 1 M~~~D~iaD~LtrIrNA~~a~k~~V~~~p~Skl~~~il~IL~~eGYI 47 (81)
|+ .+-+..+|.++++-..- +.++. .+ +-..+++.+-+++||-
T Consensus 1 MS-~~~l~~Fl~~~~~d~~l-~~~l~--~~-~~~~e~~~lA~~~Gy~ 42 (49)
T PF07862_consen 1 MS-IESLKAFLEKVKSDPEL-REQLK--AC-QNPEEVVALAREAGYD 42 (49)
T ss_pred CC-HHHHHHHHHHHhcCHHH-HHHHH--hc-CCHHHHHHHHHHcCCC
Confidence 55 46677888888754444 22222 12 2567888899999983
No 89
>PRK14328 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=20.97 E-value=1.3e+02 Score=23.61 Aligned_cols=31 Identities=10% Similarity=-0.080 Sum_probs=21.6
Q ss_pred HHHHHHHHhhcCccCceEEEcCCccceEEEEecCC
Q psy13246 34 IVKFLTVMMKHGKLPEVFVILGIRTTVYCMINWSG 68 (81)
Q Consensus 34 ~~~il~IL~~eGYI~~~~~~~~~~~~~i~Vin~~g 68 (81)
.+.+...|.++|| +++++.....+.|||-|+
T Consensus 18 s~~~~~~l~~~G~----~~~~~~~~ADv~iiNTC~ 48 (439)
T PRK14328 18 SEKLAGMLKSMGY----ERTENREEADIIIFNTCC 48 (439)
T ss_pred HHHHHHHHHHCcC----EECCCcCcCCEEEEeccc
Confidence 3567888888886 455544445666799998
No 90
>TIGR00247 conserved hypothetical protein, YceG family. This uncharacterized protein family, found in three of four microbial genomes, virtually always once per genome, includes YceG from Escherichia coli. This protein is encoded next to PabC, 4-amino-4-deoxychorismate lyase, in E. coli and numerous other proteobacteria, but that proximity is not conserved in other lineages. Numerous members of this family have been misannotated as aminodeoxychorismate lyase, apparently because of promiximty to PabC.
Probab=20.95 E-value=95 Score=23.79 Aligned_cols=26 Identities=8% Similarity=-0.038 Sum_probs=23.0
Q ss_pred ceEEEEechHHHHHHHHHHhhcCccCc
Q psy13246 23 RQVLIRPCSKVIVKFLTVMMKHGKLPE 49 (81)
Q Consensus 23 ~~V~~~p~Skl~~~il~IL~~eGYI~~ 49 (81)
..|. +|..--..+|++.|+++|.|++
T Consensus 40 v~v~-Ip~G~s~~~Ia~~L~~~GvI~s 65 (342)
T TIGR00247 40 YEFN-IEKGTGVSKIAKELKKQKLIKS 65 (342)
T ss_pred EEEE-ECCCCCHHHHHHHHHHCCCCCC
Confidence 3455 8999999999999999999997
No 91
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=20.93 E-value=73 Score=20.46 Aligned_cols=20 Identities=15% Similarity=0.215 Sum_probs=17.3
Q ss_pred hHHHHHHHHHHhhcCccCce
Q psy13246 31 SKVIVKFLTVMMKHGKLPEV 50 (81)
Q Consensus 31 Skl~~~il~IL~~eGYI~~~ 50 (81)
-.....+++.|.+.|||..+
T Consensus 39 ~~~v~~~l~~L~~~Gli~~~ 58 (130)
T TIGR02944 39 APTVSKILKQLSLAGIVTSK 58 (130)
T ss_pred HHHHHHHHHHHHHCCcEEec
Confidence 46788999999999999775
No 92
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=20.73 E-value=98 Score=16.31 Aligned_cols=18 Identities=11% Similarity=0.193 Sum_probs=14.5
Q ss_pred hHHHHHHHHHHhhcCccC
Q psy13246 31 SKVIVKFLTVMMKHGKLP 48 (81)
Q Consensus 31 Skl~~~il~IL~~eGYI~ 48 (81)
.......++-|.++|+|.
T Consensus 34 ~~tv~~~l~~L~~~g~i~ 51 (60)
T smart00345 34 RTTVREALSRLEAEGLVQ 51 (60)
T ss_pred HHHHHHHHHHHHHCCCEE
Confidence 356677899999999985
No 93
>TIGR02719 repress_PhaQ poly-beta-hydroxybutyrate-responsive repressor. Members of this family are transcriptional regulatory proteins found in the vicinity of poly-beta-hydroxybutyrate (PHB) operons in several species of Bacillus. This protein appears to have repressor activity modulated by PHB itself. This protein belongs to the larger PadR family (see pfam03551).
Probab=20.51 E-value=84 Score=21.51 Aligned_cols=38 Identities=11% Similarity=0.118 Sum_probs=25.0
Q ss_pred chHHHHHHHHHHhhcCccCceEEEcC-Ccc-ceEEEEecCC
Q psy13246 30 CSKVIVKFLTVMMKHGKLPEVFVILG-IRT-TVYCMINWSG 68 (81)
Q Consensus 30 ~Skl~~~il~IL~~eGYI~~~~~~~~-~~~-~~i~Vin~~g 68 (81)
.....--+|+-|.++|||..+....+ ++. +.++ |+..|
T Consensus 56 ~~GtLYp~L~RLE~~GlI~~~~~~~~~gp~RK~Y~-LTe~G 95 (138)
T TIGR02719 56 DQGNVYRTLRKLEKDNLISSQWDTSAEGPAKRIYS-LTDAG 95 (138)
T ss_pred CcChHHHHHHHHHHCCCEEEEeeecCCCCCcEEEE-ECHHH
Confidence 34567788999999999998765443 332 3344 55555
No 94
>PRK12338 hypothetical protein; Provisional
Probab=20.28 E-value=1.8e+02 Score=22.60 Aligned_cols=41 Identities=15% Similarity=0.249 Sum_probs=29.7
Q ss_pred HHHHHHHhhhHhh--------------cCCceEEEEechHHHHHHHHHHhhcCccC
Q psy13246 7 LSDALKSINNAEK--------------RGKRQVLIRPCSKVIVKFLTVMMKHGKLP 48 (81)
Q Consensus 7 iaD~LtrIrNA~~--------------a~k~~V~~~p~Skl~~~il~IL~~eGYI~ 48 (81)
+.+++.+|++... .....+. .|.-.....|.+-|+++||+-
T Consensus 259 v~~Fi~~~~~~~~~~~~~~~L~~lT~gvH~Hti~-a~~~e~l~~i~~~L~~~G~L~ 313 (319)
T PRK12338 259 AEKFIKRLNENPKKKEDLKRLYSLSNNVHSHRIC-APDEESLNRIIEELEEEGLLY 313 (319)
T ss_pred HHHHHHHHhhCCccccchhhHHHHhCCeeEEEEE-eCCHHHHHHHHHHHHHCCccc
Confidence 5566777766552 2234554 788889999999999999974
No 95
>PRK14332 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=20.24 E-value=1.5e+02 Score=23.63 Aligned_cols=31 Identities=6% Similarity=-0.143 Sum_probs=20.9
Q ss_pred HHHHHHHHhhcCccCceEEEcCCccceEEEEecCC
Q psy13246 34 IVKFLTVMMKHGKLPEVFVILGIRTTVYCMINWSG 68 (81)
Q Consensus 34 ~~~il~IL~~eGYI~~~~~~~~~~~~~i~Vin~~g 68 (81)
.+.++..|.+.|| +.+++.....+.|||-|+
T Consensus 27 se~~~~~l~~~G~----~~~~~~~~ADvviiNTC~ 57 (449)
T PRK14332 27 SGIVSSLMRDAEY----STSNDPENSDIIFLNTCA 57 (449)
T ss_pred HHHHHHHHHHCcC----EECCCcccCCEEEEEccC
Confidence 4567888999988 343333334566799998
No 96
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=20.18 E-value=96 Score=17.51 Aligned_cols=18 Identities=11% Similarity=0.185 Sum_probs=14.5
Q ss_pred HHHHHHHHHHhhcCccCc
Q psy13246 32 KVIVKFLTVMMKHGKLPE 49 (81)
Q Consensus 32 kl~~~il~IL~~eGYI~~ 49 (81)
....+.++.|.++|+|..
T Consensus 39 ~tvr~al~~L~~~g~i~~ 56 (64)
T PF00392_consen 39 TTVREALRRLEAEGLIER 56 (64)
T ss_dssp HHHHHHHHHHHHTTSEEE
T ss_pred cHHHHHHHHHHHCCcEEE
Confidence 456778999999999853
No 97
>cd00861 ProRS_anticodon_short ProRS Prolyl-anticodon binding domain, short version found predominantly in bacteria. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only.
Probab=20.18 E-value=1.3e+02 Score=17.51 Aligned_cols=25 Identities=20% Similarity=0.223 Sum_probs=15.2
Q ss_pred eEEEEechH-------HHHHHHHHHhhcCccC
Q psy13246 24 QVLIRPCSK-------VIVKFLTVMMKHGKLP 48 (81)
Q Consensus 24 ~V~~~p~Sk-------l~~~il~IL~~eGYI~ 48 (81)
+|.++|.+. ...++++.|.+.||--
T Consensus 3 qv~i~p~~~~~~~~~~~a~~la~~Lr~~g~~v 34 (94)
T cd00861 3 DVVIIPMNMKDEVQQELAEKLYAELQAAGVDV 34 (94)
T ss_pred EEEEEEcCCCcHHHHHHHHHHHHHHHHCCCEE
Confidence 344566543 5667777777777644
No 98
>TIGR02764 spore_ybaN_pdaB polysaccharide deacetylase family sporulation protein PdaB. This model describes the YbaN protein family, also called PdaB and SpoVIE, of Gram-positive bacteria. Although ybaN null mutants have only a mild sporulation defect, ybaN/ytrI double mutants show drastically reducted sporulation efficiencies. This synthetic defect suggests the role of this sigmaE-controlled gene in sporulation had been masked by functional redundancy. Members of this family are homologous to a characterized polysaccharide deacetylase; the exact function this protein family is unknown.
Probab=20.09 E-value=1.7e+02 Score=19.77 Aligned_cols=36 Identities=11% Similarity=0.032 Sum_probs=25.9
Q ss_pred HHHhhhHhhcCCceEEEEechHHHHHHHHHHhhcCcc
Q psy13246 11 LKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGKL 47 (81)
Q Consensus 11 LtrIrNA~~a~k~~V~~~p~Skl~~~il~IL~~eGYI 47 (81)
...|+++.-..-+... .|+-.....+++++.+.||.
T Consensus 87 ~~~l~~~~g~~~~~fr-~P~G~~~~~~~~~l~~~G~~ 122 (191)
T TIGR02764 87 QEIIEKLTGKKPTLFR-PPSGAFNKAVLKAAESLGYT 122 (191)
T ss_pred HHHHHHHhCCCCCEEE-CCCcCCCHHHHHHHHHcCCe
Confidence 3445544433334454 89999999999999999997
No 99
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=20.08 E-value=80 Score=20.77 Aligned_cols=21 Identities=19% Similarity=0.325 Sum_probs=17.0
Q ss_pred hHHHHHHHHHHhhcCccCceE
Q psy13246 31 SKVIVKFLTVMMKHGKLPEVF 51 (81)
Q Consensus 31 Skl~~~il~IL~~eGYI~~~~ 51 (81)
-...++++..|.++|||....
T Consensus 39 ~~~vrk~l~~L~~~Glv~s~~ 59 (141)
T PRK11014 39 RNHMVKIINQLSRAGYVTAVR 59 (141)
T ss_pred HHHHHHHHHHHHhCCEEEEec
Confidence 356788999999999997653
No 100
>PRK14329 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=20.08 E-value=1.5e+02 Score=23.66 Aligned_cols=31 Identities=6% Similarity=0.037 Sum_probs=21.5
Q ss_pred HHHHHHHHhhcCccCceEEEcCCccceEEEEecCC
Q psy13246 34 IVKFLTVMMKHGKLPEVFVILGIRTTVYCMINWSG 68 (81)
Q Consensus 34 ~~~il~IL~~eGYI~~~~~~~~~~~~~i~Vin~~g 68 (81)
.+.++..|.++|| ++.++.....+.|||-|+
T Consensus 40 se~~~~~l~~~G~----~~~~~~~~ADiviiNTC~ 70 (467)
T PRK14329 40 SEIVASILQMAGY----NTTENLEEADLVLVNTCS 70 (467)
T ss_pred HHHHHHHHHHCcC----EECCCcccCCEEEEeCcc
Confidence 4678889999987 344433334566799998
No 101
>PF00610 DEP: Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP); InterPro: IPR000591 This entry represents the DEP (Dishevelled, Egl-10 and Pleckstrin) domain, a globular domain of about 80 residues that is found in over 50 proteins involved in G-protein signalling pathways. It was named after the three proteins it was initially found in: Dishevelled (Dsh and Dvl), which play a key role in the transduction of the Wg/Wnt signal from the cell surface to the nucleus; it is a segment polarity protein required to establish coherent arrays of polarized cells and segments in embryos, and plays a role in wingless signalling. Egl-10, which regulates G-protein signalling in the central nervous system. Pleckstrin, the major substrate of protein kinase C in platelets; Pleckstrin contains two PH domains flanking the DEP domain. Mammalian regulators of G-protein signalling also contain these domains, and regulate signal transduction by increasing the GTPase activity of G-protein alpha subunits, thereby driving them into their inactive GDP-bound form. It has been proposed that the DEP domain could play a selective role in targeting DEP domain-containing proteins to specific subcellular membranous sites, perhaps even to specific G protein-coupled signaling pathways [, ]. Nuclear magnetic resonance spectroscopy has revealed that the DEP domain comprises a three-helix bundle, a beta-hairpin 'arm' composed of two beta-strands and two short beta-strands in the C-terminal region [].; GO: 0035556 intracellular signal transduction; PDB: 1UHW_A 1V3F_A 2YSR_A 2CSO_A 1W4M_A 2PBI_C 1O7F_A 2BYV_E 1FSH_A 3ML6_D ....
Probab=20.05 E-value=72 Score=18.40 Aligned_cols=21 Identities=19% Similarity=0.281 Sum_probs=16.5
Q ss_pred hHHHHHHHHHHhhcCccCceE
Q psy13246 31 SKVIVKFLTVMMKHGKLPEVF 51 (81)
Q Consensus 31 Skl~~~il~IL~~eGYI~~~~ 51 (81)
-.--..+++.|.++|||....
T Consensus 38 r~eA~~l~q~Ll~~g~i~~v~ 58 (74)
T PF00610_consen 38 REEAVQLGQELLDHGFIEHVS 58 (74)
T ss_dssp HHHHHHHHHHHHHCTSEEESS
T ss_pred HHHHHHHHHHHHHCCCEEECC
Confidence 345678899999999998653
Done!