Query 033291
Match_columns 122
No_of_seqs 166 out of 1082
Neff 7.7
Searched_HMMs 46136
Date Fri Mar 29 12:07:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033291.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033291hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR02227 sigpep_I_bact signal 100.0 1.4E-37 3E-42 220.0 12.7 111 1-112 30-163 (163)
2 KOG0171 Mitochondrial inner me 100.0 3.4E-37 7.4E-42 215.0 9.1 118 1-118 43-165 (176)
3 PRK10861 signal peptidase I; P 100.0 5.4E-33 1.2E-37 214.1 12.7 111 1-112 92-305 (324)
4 KOG1568 Mitochondrial inner me 100.0 1.5E-32 3.2E-37 191.5 9.8 114 1-119 41-159 (174)
5 PRK13838 conjugal transfer pil 99.9 2.4E-26 5.1E-31 164.5 10.8 99 8-107 35-171 (176)
6 PF10502 Peptidase_S26: Signal 99.9 1E-26 2.3E-31 160.6 3.0 86 23-108 21-137 (138)
7 TIGR02771 TraF_Ti conjugative 99.9 2.6E-25 5.6E-30 158.6 9.5 85 22-107 45-168 (171)
8 PRK13884 conjugal transfer pep 99.9 1.4E-24 3.1E-29 155.6 9.8 86 22-107 49-175 (178)
9 TIGR02754 sod_Ni_protease nick 99.9 6.6E-22 1.4E-26 127.0 9.1 83 1-106 8-90 (90)
10 cd06530 S26_SPase_I The S26 Ty 99.8 6.7E-20 1.4E-24 116.2 8.4 76 1-104 10-85 (85)
11 COG4959 TraF Type IV secretory 99.8 5.3E-19 1.2E-23 122.7 5.1 86 23-109 53-169 (173)
12 TIGR02228 sigpep_I_arch signal 99.5 1.6E-13 3.4E-18 96.8 8.7 79 1-105 41-119 (158)
13 COG0681 LepB Signal peptidase 99.2 1.3E-10 2.9E-15 81.1 7.4 97 1-104 41-144 (166)
14 PF00717 Peptidase_S24: Peptid 99.1 5E-10 1.1E-14 67.9 7.4 54 1-60 7-60 (70)
15 cd06462 Peptidase_S24_S26 The 99.0 3.9E-09 8.4E-14 65.6 8.1 74 1-103 10-83 (84)
16 cd06529 S24_LexA-like Peptidas 98.5 1.5E-06 3.2E-11 53.7 8.7 49 1-57 10-58 (81)
17 COG2932 Predicted transcriptio 98.2 1.3E-05 2.8E-10 58.7 8.8 78 1-108 133-210 (214)
18 KOG3342 Signal peptidase I [In 98.1 4E-06 8.7E-11 58.7 4.5 87 1-111 58-149 (180)
19 PRK10276 DNA polymerase V subu 97.9 0.00016 3.5E-09 49.7 9.6 40 1-48 61-101 (139)
20 PRK00215 LexA repressor; Valid 97.9 0.00019 4.1E-09 52.1 9.3 74 1-108 128-202 (205)
21 PRK12423 LexA repressor; Provi 97.8 0.00024 5.2E-09 51.7 9.3 75 1-108 124-199 (202)
22 TIGR00498 lexA SOS regulatory 97.7 0.00047 1E-08 49.7 9.6 76 1-110 121-197 (199)
23 COG1974 LexA SOS-response tran 96.8 0.021 4.6E-07 41.8 9.8 76 3-111 125-200 (201)
24 COG0681 LepB Signal peptidase 89.3 0.53 1.2E-05 32.3 3.4 13 23-35 84-96 (166)
25 PF05257 CHAP: CHAP domain; I 85.4 3.2 6.9E-05 27.3 5.4 39 22-60 61-100 (124)
26 TIGR02594 conserved hypothetic 84.2 7.1 0.00015 26.5 6.7 13 22-34 72-84 (129)
27 cd04712 BAH_DCM_I BAH, or Brom 84.0 11 0.00024 25.6 7.8 83 22-111 4-102 (130)
28 TIGR00008 infA translation ini 77.6 2.8 6.1E-05 25.5 2.6 20 8-30 47-66 (68)
29 COG0361 InfA Translation initi 75.6 3.6 7.8E-05 25.5 2.7 20 8-30 49-68 (75)
30 COG0093 RplN Ribosomal protein 75.3 19 0.0004 24.4 6.2 32 67-99 75-106 (122)
31 PF14085 DUF4265: Domain of un 72.5 24 0.00052 23.4 6.4 48 8-57 10-58 (117)
32 PF01176 eIF-1a: Translation i 69.3 4.2 9.1E-05 24.1 1.9 12 23-34 41-52 (65)
33 cd05793 S1_IF1A S1_IF1A: Trans 68.6 5.1 0.00011 24.8 2.3 10 24-33 39-48 (77)
34 cd04456 S1_IF1A_like S1_IF1A_l 67.5 6.2 0.00013 24.5 2.5 10 24-33 39-48 (78)
35 smart00652 eIF1a eukaryotic tr 66.2 6.1 0.00013 24.8 2.3 10 24-33 44-53 (83)
36 PRK12442 translation initiatio 64.0 9 0.00019 24.5 2.7 20 8-30 49-68 (87)
37 cd04714 BAH_BAHCC1 BAH, or Bro 63.5 11 0.00024 25.1 3.3 27 23-49 3-29 (121)
38 PF01426 BAH: BAH domain; Int 62.6 11 0.00023 24.2 3.1 26 24-49 3-28 (119)
39 smart00002 PLP Myelin proteoli 62.3 1.9 4.2E-05 25.6 -0.5 20 85-104 22-41 (60)
40 PRK04012 translation initiatio 61.7 8.2 0.00018 25.2 2.3 10 24-33 60-69 (100)
41 PF10000 ACT_3: ACT domain; I 61.2 5.1 0.00011 24.5 1.2 16 1-17 14-29 (72)
42 PRK00364 groES co-chaperonin G 55.4 52 0.0011 21.0 8.1 90 5-104 3-94 (95)
43 cd04717 BAH_polybromo BAH, or 53.3 20 0.00042 23.6 3.2 73 23-106 3-83 (121)
44 COG5131 URM1 Ubiquitin-like pr 51.4 20 0.00042 23.1 2.7 30 4-34 57-91 (96)
45 smart00439 BAH Bromo adjacent 51.0 31 0.00067 22.0 3.8 76 24-109 2-85 (120)
46 cd03695 CysN_NodQ_II CysN_NodQ 49.6 53 0.0011 20.0 4.5 34 22-57 25-66 (81)
47 PF06890 Phage_Mu_Gp45: Bacter 48.9 94 0.002 22.0 7.9 41 16-58 67-110 (162)
48 COG3602 Uncharacterized protei 48.5 12 0.00027 25.2 1.5 35 1-36 14-48 (134)
49 PF11132 SplA: Transcriptional 47.3 48 0.001 20.5 3.9 12 3-15 4-15 (75)
50 COG1097 RRP4 RNA-binding prote 46.0 54 0.0012 24.8 4.8 73 1-84 109-195 (239)
51 PF07039 DUF1325: SGF29 tudor- 45.0 96 0.0021 21.0 6.8 56 25-81 1-60 (130)
52 cd04760 BAH_Dnmt1_I BAH, or Br 43.1 68 0.0015 21.7 4.5 79 24-112 4-87 (124)
53 cd04089 eRF3_II eRF3_II: domai 43.1 72 0.0016 19.3 4.4 34 22-57 24-65 (82)
54 PF00238 Ribosomal_L14: Riboso 43.1 19 0.00041 24.3 1.8 31 67-98 75-105 (122)
55 cd05792 S1_eIF1AD_like S1_eIF1 42.7 22 0.00047 22.2 1.9 11 24-34 39-49 (78)
56 KOG4146 Ubiquitin-like protein 41.9 37 0.0008 22.0 2.9 27 8-34 65-96 (101)
57 cd03698 eRF3_II_like eRF3_II_l 41.9 78 0.0017 19.1 4.4 34 22-57 25-66 (83)
58 PF10030 DUF2272: Uncharacteri 41.7 1.3E+02 0.0029 21.7 6.3 39 22-60 92-145 (183)
59 PLN00208 translation initiatio 40.2 26 0.00057 24.4 2.2 10 24-33 71-80 (145)
60 PTZ00329 eukaryotic translatio 39.5 27 0.00059 24.6 2.2 10 24-33 71-80 (155)
61 KOG4226 Adaptor protein NCK/Do 39.5 59 0.0013 25.4 4.2 40 67-106 237-284 (379)
62 PF04319 NifZ: NifZ domain; I 39.2 66 0.0014 19.9 3.7 31 1-32 1-34 (75)
63 PRK10507 bifunctional glutathi 38.7 1.6E+02 0.0035 25.4 7.1 59 21-79 109-177 (619)
64 cd03694 GTPBP_II Domain II of 38.6 83 0.0018 19.3 4.2 37 21-57 24-70 (87)
65 KOG1999 RNA polymerase II tran 38.5 1.3E+02 0.0029 27.3 6.6 35 49-83 461-495 (1024)
66 cd03703 aeIF5B_II aeIF5B_II: T 38.3 44 0.00094 22.2 2.9 14 22-35 25-38 (110)
67 PRK14533 groES co-chaperonin G 36.6 1.1E+02 0.0025 19.4 7.7 84 5-104 3-89 (91)
68 PF11320 DUF3122: Protein of u 36.3 1.4E+02 0.0031 20.5 5.6 45 8-52 10-55 (134)
69 cd04710 BAH_fungalPHD BAH, or 36.3 60 0.0013 22.1 3.5 28 22-49 10-37 (135)
70 cd06555 ASCH_PF0470_like ASC-1 36.1 75 0.0016 21.0 3.8 26 22-48 30-55 (109)
71 cd03697 EFTU_II EFTU_II: Elong 35.8 1E+02 0.0023 18.8 5.5 36 22-57 25-68 (87)
72 PTZ00414 10 kDa heat shock pro 35.2 1.3E+02 0.0028 19.6 7.7 43 3-49 10-52 (100)
73 cd04709 BAH_MTA BAH, or Bromo 34.8 60 0.0013 23.0 3.4 25 86-110 84-108 (164)
74 PRK00809 hypothetical protein; 34.3 42 0.00091 23.2 2.5 28 22-49 33-61 (144)
75 cd04370 BAH BAH, or Bromo Adja 34.2 57 0.0012 20.6 3.1 78 23-110 3-89 (123)
76 TIGR02219 phage_NlpC_fam putat 34.2 69 0.0015 21.5 3.5 13 22-34 75-87 (134)
77 PF01878 EVE: EVE domain; Int 34.2 53 0.0011 22.1 3.0 15 22-36 38-52 (143)
78 COG4127 Uncharacterized conser 33.3 42 0.00092 26.1 2.6 26 22-48 71-96 (318)
79 PF15057 DUF4537: Domain of un 33.0 88 0.0019 20.9 3.9 28 22-49 54-81 (124)
80 PF00278 Orn_DAP_Arg_deC: Pyri 32.2 72 0.0016 20.2 3.3 30 3-35 65-94 (116)
81 PRK04313 30S ribosomal protein 32.1 2.2E+02 0.0049 21.5 7.9 57 23-82 150-229 (237)
82 PLN02289 ribulose-bisphosphate 31.7 45 0.00097 24.0 2.3 28 65-92 95-122 (176)
83 COG4043 Preprotein translocase 31.3 84 0.0018 20.8 3.3 14 20-33 30-43 (111)
84 cd00320 cpn10 Chaperonin 10 Kd 31.1 1.4E+02 0.0031 18.8 6.6 42 5-50 2-43 (93)
85 cd04466 S1_YloQ_GTPase S1_YloQ 30.5 1.1E+02 0.0023 17.4 3.6 13 23-35 37-49 (68)
86 TIGR00523 eIF-1A eukaryotic/ar 30.4 55 0.0012 21.2 2.4 9 24-32 58-66 (99)
87 PRK02268 hypothetical protein; 29.0 59 0.0013 22.6 2.5 28 22-49 34-63 (141)
88 PF12059 DUF3540: Protein of u 28.5 1.3E+02 0.0028 22.0 4.3 27 8-35 20-46 (202)
89 TIGR03673 rpl14p_arch 50S ribo 27.7 2E+02 0.0044 19.6 6.4 32 67-99 85-116 (131)
90 TIGR00739 yajC preprotein tran 26.5 1.7E+02 0.0036 18.2 4.1 30 22-57 36-65 (84)
91 PF11302 DUF3104: Protein of u 26.4 1.6E+02 0.0035 18.2 3.8 30 23-52 5-39 (75)
92 PF09285 Elong-fact-P_C: Elong 26.2 1.4E+02 0.0031 17.3 4.1 29 8-45 28-56 (56)
93 PF00166 Cpn10: Chaperonin 10 26.2 1.7E+02 0.0038 18.3 4.5 88 7-104 4-93 (93)
94 PF01472 PUA: PUA domain; Int 26.1 54 0.0012 19.6 1.7 27 9-35 16-42 (74)
95 COG1188 Ribosome-associated he 26.0 1.4E+02 0.0031 19.5 3.8 41 9-52 33-74 (100)
96 PF15428 Imm14: Immunity prote 25.6 1.2E+02 0.0026 19.8 3.6 22 25-48 1-22 (129)
97 cd04720 BAH_Orc1p_Yeast BAH, o 25.3 1E+02 0.0022 22.0 3.3 74 22-106 51-141 (179)
98 cd05881 Ig1_Necl-2 First (N-te 25.3 1.8E+02 0.004 18.3 4.6 51 43-94 4-55 (95)
99 cd03701 IF2_IF5B_II IF2_IF5B_I 25.2 1.8E+02 0.004 18.3 4.6 36 22-57 25-65 (95)
100 COG0234 GroS Co-chaperonin Gro 25.2 2E+02 0.0043 18.7 6.7 25 5-31 3-27 (96)
101 PF11330 DUF3132: Protein of u 23.5 1.8E+02 0.0039 18.8 3.8 18 27-44 87-104 (124)
102 COG1471 RPS4A Ribosomal protei 22.6 3.5E+02 0.0075 20.5 6.0 58 22-82 151-231 (241)
103 cd03696 selB_II selB_II: this 22.6 1.8E+02 0.004 17.3 4.4 34 22-57 25-66 (83)
104 PF13759 2OG-FeII_Oxy_5: Putat 22.5 1E+02 0.0022 19.3 2.6 24 23-52 69-92 (101)
105 COG2895 CysN GTPases - Sulfate 22.5 3.5E+02 0.0076 22.2 6.0 34 22-57 248-289 (431)
106 PF13550 Phage-tail_3: Putativ 22.5 1.4E+02 0.003 19.9 3.5 26 21-49 137-162 (164)
107 cd03693 EF1_alpha_II EF1_alpha 21.6 2.1E+02 0.0045 17.6 4.5 34 22-57 29-70 (91)
108 cd02792 MopB_CT_Formate-Dh-Na- 21.6 1.5E+02 0.0033 18.8 3.4 26 11-36 36-61 (122)
109 TIGR01067 rplN_bact ribosomal 21.5 64 0.0014 21.7 1.5 31 68-99 76-106 (122)
110 PF00877 NLPC_P60: NlpC/P60 fa 21.1 65 0.0014 20.2 1.5 13 22-34 50-62 (105)
111 cd04713 BAH_plant_3 BAH, or Br 21.1 1.4E+02 0.003 20.5 3.2 78 22-110 19-106 (146)
112 PF02736 Myosin_N: Myosin N-te 21.0 1.1E+02 0.0025 16.2 2.2 26 30-57 4-29 (42)
113 TIGR02390 RNA_pol_rpoA1 DNA-di 20.9 1.3E+02 0.0027 27.0 3.6 35 22-56 406-442 (868)
114 PF13403 Hint_2: Hint domain 20.8 2.7E+02 0.0059 19.0 4.6 77 8-84 5-90 (147)
No 1
>TIGR02227 sigpep_I_bact signal peptidase I, bacterial type. A related model finds a simlar protein in many archaea and a few bacteria, as well as a microsomal (endoplasmic reticulum) protein in eukaryotes.
Probab=100.00 E-value=1.4e-37 Score=220.01 Aligned_cols=111 Identities=36% Similarity=0.591 Sum_probs=98.5
Q ss_pred CccccCCCCCEEEEEeccCCCCCCCCCcEEEEEcCCCCCceeEEEEEEcCCCEEEEecCCC---------C---C-----
Q 033291 1 MLPTINLTGDLVLAERISTRFNKVCPGDVVLVRSPVVPRRIVTKRVIGMEGDRVSYVADPK---------S---S----- 63 (122)
Q Consensus 1 M~Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVv~~~p~~~~~~~iKRV~a~pGd~v~~~~~~~---------~---~----- 63 (122)
|+|||+ +||+|+++|+.+...++++||+|+|+.|...++.++|||+|+|||+|+++++.. . .
T Consensus 30 M~Ptl~-~Gd~vlv~k~~~~~~~~~rGDiVvf~~~~~~~~~~iKRVig~pGd~v~i~~~~l~vNg~~~~~~~~~~~~~~~ 108 (163)
T TIGR02227 30 MEPTLK-EGDRILVNKFAYGTSDPKRGDIVVFKDPDDNKNIYVKRVIGLPGDKVEFRDGKLYINGKKIDEPYLKPNGSLD 108 (163)
T ss_pred cccchh-CCCEEEEEEeEcCCCCCCCCcEEEEecCCCCCceeEEEEEecCCCEEEEECCEEEECCEECcccccccccccc
Confidence 999999 999999999987778999999999999877778999999999999999976411 0 0
Q ss_pred ------CCCceEEeeCCeEEEeeCCCCCCCCCCceecccCCCeeEEEEEEEeCCC
Q 033291 64 ------DKFETVVVPQGHVWIEGDNIYESNDSRKFGAVPYGLIEGRVFLRIWPPK 112 (122)
Q Consensus 64 ------~~~~~~~vp~~~~~v~gdn~~~S~DSR~~G~V~~~~I~Gkv~~~~~p~~ 112 (122)
....+.+||+|+|||+|||+.+|+||||||+|++++|+|||++++||++
T Consensus 109 ~~~~~~~~~~~~~vp~g~~fvlGDnr~~S~DSR~~G~V~~~~I~Gk~~~~~~p~~ 163 (163)
T TIGR02227 109 TSGFNTTDFKPVTVPPGHYFVLGDNRDNSLDSRYFGFVPIDDIIGKVSFVFYPFD 163 (163)
T ss_pred cccccccccCceEECCCCEEEECCCCCCCcccCCcCcCCHHHeEEEEEEEECCCC
Confidence 1124578999999999999999999999999999999999999999985
No 2
>KOG0171 consensus Mitochondrial inner membrane protease, subunit IMP1 [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=3.4e-37 Score=215.04 Aligned_cols=118 Identities=45% Similarity=0.785 Sum_probs=105.9
Q ss_pred CccccCCCCCEEEEEeccCCCCCCCCCcEEEEEcCCCCCceeEEEEEEcCCCEEEEecCCCCCC-----CCceEEeeCCe
Q 033291 1 MLPTINLTGDLVLAERISTRFNKVCPGDVVLVRSPVVPRRIVTKRVIGMEGDRVSYVADPKSSD-----KFETVVVPQGH 75 (122)
Q Consensus 1 M~Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVv~~~p~~~~~~~iKRV~a~pGd~v~~~~~~~~~~-----~~~~~~vp~~~ 75 (122)
|+|||+..||+|+..|+++.++++++||||++..|.++++.++|||+|+|||-+++..++...+ ....+.||+||
T Consensus 43 M~PTl~~~gd~l~aEkls~~f~~~~~gDIVi~~sP~~~~~~~cKRIva~eGD~v~v~~~~~~~n~~~e~~~~~i~VP~Gh 122 (176)
T KOG0171|consen 43 MEPTLHDGGDVLLAEKLSYRFRKPQVGDIVIAKSPPDPKEHICKRIVAMEGDLVEVHDGPLVVNDLVEKFSTPIRVPEGH 122 (176)
T ss_pred cCceecCCCcEEehhhhhHhhcCCCCCCEEEEeCCCCchhhhhheeeccCCceEEEecCCcccchhhhhccceeeccCce
Confidence 9999996677777799999999999999999999999999999999999999998887765322 22457999999
Q ss_pred EEEeeCCCCCCCCCCceecccCCCeeEEEEEEEeCCCCccCCC
Q 033291 76 VWIEGDNIYESNDSRKFGAVPYGLIEGRVFLRIWPPKDFGSLG 118 (122)
Q Consensus 76 ~~v~gdn~~~S~DSR~~G~V~~~~I~Gkv~~~~~p~~~~~~~~ 118 (122)
+||+|||+.+|+|||+|||||...|+||+++++||++++....
T Consensus 123 Vfv~GDN~~nS~DSr~yGplP~glI~gRvv~r~Wp~s~~~~~~ 165 (176)
T KOG0171|consen 123 VFVEGDNRNNSLDSRNYGPLPMGLIQGRVVFRIWPPSRVSGLI 165 (176)
T ss_pred EEEecCCCCCcccccccCCCchhheeeeEEEEecCchhcceee
Confidence 9999999999999999999999999999999999999887653
No 3
>PRK10861 signal peptidase I; Provisional
Probab=100.00 E-value=5.4e-33 Score=214.13 Aligned_cols=111 Identities=33% Similarity=0.548 Sum_probs=96.2
Q ss_pred CccccCCCCCEEEEEeccCCC------------CCCCCCcEEEEEcCCCCCceeEEEEEEcCCCEEEEe--cC-----CC
Q 033291 1 MLPTINLTGDLVLAERISTRF------------NKVCPGDVVLVRSPVVPRRIVTKRVIGMEGDRVSYV--AD-----PK 61 (122)
Q Consensus 1 M~Ptl~~~Gd~vlv~~~~~~~------------~~~~~GDiVv~~~p~~~~~~~iKRV~a~pGd~v~~~--~~-----~~ 61 (122)
|+|||. .||+|+|+|++|.. ++++|||||+|+.|.+++..+||||+|+|||+|+++ ++ +.
T Consensus 92 M~PTL~-~GD~IlVnK~~yg~~~p~~~~~~~~~~~p~RGDIVVF~~P~~~~~~yIKRVIGlPGD~I~~~~~~~~l~iNg~ 170 (324)
T PRK10861 92 MMPTLL-IGDFILVEKFAYGIKDPITQTTLIETGHPKRGDIVVFKYPEDPKLDYIKRVVGLPGDKVTYDPVSKEVTIQPG 170 (324)
T ss_pred CcCccc-CCCEEEEEEeecCccCccccccccccCCCCCCCEEEEecCCCCCCcEEEEeeecCCcEEEEEeCCCEEEEcCc
Confidence 999999 99999999998753 579999999999998888899999999999999996 21 10
Q ss_pred ------------------------C---------------------------------------------C-C--C----
Q 033291 62 ------------------------S---------------------------------------------S-D--K---- 65 (122)
Q Consensus 62 ------------------------~---------------------------------------------~-~--~---- 65 (122)
. . . .
T Consensus 171 ~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~E~l~~~~h~i~~~~~~~~~~~~ 250 (324)
T PRK10861 171 CSSGQACENALPVTYSNVEPSDFVQTFSRRNGGEATSGFFQVPLNETKENGIRLSERKETLGDVTHRILTVPGAQDQVGM 250 (324)
T ss_pred cccccccccccccccccccccccccccccccccccccccccccccccccccccceeEEEecCCccceeeecCCccccccc
Confidence 0 0 0 0
Q ss_pred --------CceEEeeCCeEEEeeCCCCCCCCCCceecccCCCeeEEEEEEEeCCC
Q 033291 66 --------FETVVVPQGHVWIEGDNIYESNDSRKFGAVPYGLIEGRVFLRIWPPK 112 (122)
Q Consensus 66 --------~~~~~vp~~~~~v~gdn~~~S~DSR~~G~V~~~~I~Gkv~~~~~p~~ 112 (122)
...++||+|+||++|||+++|+||||||+||+++|+|+|..++|+++
T Consensus 251 ~~~~~~~~~~~~~vp~g~yf~mgdnr~~S~DSRy~G~Vp~~~i~G~a~~i~~s~d 305 (324)
T PRK10861 251 YYQQPGQPLATWVVPPGQYFMMGDNRDNSADSRYWGFVPEANLVGKATAIWMSFE 305 (324)
T ss_pred ccccCCCcCceEEECCCeEEEeCCCCCCCcccCcccccCHHHcEEEEEEEEEEcC
Confidence 13459999999999999999999999999999999999999999886
No 4
>KOG1568 consensus Mitochondrial inner membrane protease, subunit IMP2 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=99.98 E-value=1.5e-32 Score=191.52 Aligned_cols=114 Identities=44% Similarity=0.760 Sum_probs=101.8
Q ss_pred CccccCCC-----CCEEEEEeccCCCCCCCCCcEEEEEcCCCCCceeEEEEEEcCCCEEEEecCCCCCCCCceEEeeCCe
Q 033291 1 MLPTINLT-----GDLVLAERISTRFNKVCPGDVVLVRSPVVPRRIVTKRVIGMEGDRVSYVADPKSSDKFETVVVPQGH 75 (122)
Q Consensus 1 M~Ptl~~~-----Gd~vlv~~~~~~~~~~~~GDiVv~~~p~~~~~~~iKRV~a~pGd~v~~~~~~~~~~~~~~~~vp~~~ 75 (122)
|+|||+|. .|+||++|+......+.+||+|+|.+|.++++.+||||+|++||.+.-. ......+.||+||
T Consensus 41 mqPtlnP~~~~~~~d~Vll~k~~v~n~~~~rGDiVvl~sP~~p~~~~iKRv~alegd~~~t~-----~~k~~~v~vpkgh 115 (174)
T KOG1568|consen 41 MQPTLNPTMNTNEKDTVLLRKWNVKNRKVSRGDIVVLKSPNDPDKVIIKRVAALEGDIMVTE-----DEKEEPVVVPKGH 115 (174)
T ss_pred CCCccCCCcccccccEEEEEeeccccceeccCCEEEEeCCCChhheeeeeeecccccEeccC-----CCCCCceecCCCc
Confidence 88999831 2999999988655669999999999999999999999999999988752 2235789999999
Q ss_pred EEEeeCCCCCCCCCCceecccCCCeeEEEEEEEeCCCCccCCCC
Q 033291 76 VWIEGDNIYESNDSRKFGAVPYGLIEGRVFLRIWPPKDFGSLGR 119 (122)
Q Consensus 76 ~~v~gdn~~~S~DSR~~G~V~~~~I~Gkv~~~~~p~~~~~~~~~ 119 (122)
|||.|||..+|+|||.||||+...|.|||+.++||+.||+++.+
T Consensus 116 cWVegDn~~hs~DSntFGPVS~gli~grai~ilwpP~R~~~~~~ 159 (174)
T KOG1568|consen 116 CWVEGDNQKHSYDSNTFGPVSTGLIVGRAIYILWPPVRWQRLDK 159 (174)
T ss_pred EEEecCCcccccccCccCCcchhheeeeEEEEEcChHHhhhhcc
Confidence 99999999999999999999999999999999999999998864
No 5
>PRK13838 conjugal transfer pilin processing protease TraF; Provisional
Probab=99.94 E-value=2.4e-26 Score=164.53 Aligned_cols=99 Identities=28% Similarity=0.346 Sum_probs=78.9
Q ss_pred CCCEEEEEeccCCCCCCCCCcEEEEEcCCCC-------------------CceeEEEEEEcCCCEEEEec----CCCC--
Q 033291 8 TGDLVLAERISTRFNKVCPGDVVLVRSPVVP-------------------RRIVTKRVIGMEGDRVSYVA----DPKS-- 62 (122)
Q Consensus 8 ~Gd~vlv~~~~~~~~~~~~GDiVv~~~p~~~-------------------~~~~iKRV~a~pGd~v~~~~----~~~~-- 62 (122)
+.+.+.+.++.+..+.+++||+|+|+.|... ...++|||+|+|||+|++.+ |+..
T Consensus 35 ~S~pig~y~~~~~~~~~~rGDiVvf~~P~~~~~~~a~~r~yl~~g~~p~~~~~~iKRViglpGD~V~i~~~v~iNg~~~~ 114 (176)
T PRK13838 35 PSEPLGLWRIEALDRPVAVGDLVFICPPETAAFREARERGYLRRGLCPGGFAPLIKTVAALAGQRVEIGGSVSIDGRPLP 114 (176)
T ss_pred CCCEEEEEEEeccCCCCCCCcEEEEECCchhhhhhhhhcccccccccccCCCceEEEEEEeCCcEEEECCEEEECCEEcc
Confidence 5677888887666678999999999987542 13599999999999999873 1110
Q ss_pred -------------CCCCceEEeeCCeEEEeeCCCCCCCCCCceecccCCCeeEEEEEE
Q 033291 63 -------------SDKFETVVVPQGHVWIEGDNIYESNDSRKFGAVPYGLIEGRVFLR 107 (122)
Q Consensus 63 -------------~~~~~~~~vp~~~~~v~gdn~~~S~DSR~~G~V~~~~I~Gkv~~~ 107 (122)
.......+||+|+|||+|||. +|+||||||+|++++|+|+|..+
T Consensus 115 ~~~~~~~~~~g~~l~~~~~~~vp~g~~fvlgd~~-~S~DSRy~G~V~~~~I~G~a~pi 171 (176)
T PRK13838 115 SSSVRRRDGEGRPLTPFPGGVVPPGHLFLHSSFA-GSYDSRYFGPVPASGLLGLARPV 171 (176)
T ss_pred ccccccccccCCcCCCCCccCcCCCeEEEECCCC-CCCcccccCcccHHHeEEEEEEE
Confidence 001224689999999999985 89999999999999999999863
No 6
>PF10502 Peptidase_S26: Signal peptidase, peptidase S26 ; InterPro: IPR019533 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This entry represents a conserved region found in the S26A family of serine endopeptidases, which function in the processing of newly-synthesised secreted proteins. Peptidase S26 removes the hydrophobic, N-terminal signal peptides as proteins are translocated across membranes. ; PDB: 3S04_B 1KN9_C 1B12_D 3IIQ_B 1T7D_A.
Probab=99.93 E-value=1e-26 Score=160.61 Aligned_cols=86 Identities=31% Similarity=0.402 Sum_probs=32.7
Q ss_pred CCCCCcEEEEEcCCC------------CCceeEEEEEEcCCCEEEEecCCC------------------C-CCCCceEEe
Q 033291 23 KVCPGDVVLVRSPVV------------PRRIVTKRVIGMEGDRVSYVADPK------------------S-SDKFETVVV 71 (122)
Q Consensus 23 ~~~~GDiVv~~~p~~------------~~~~~iKRV~a~pGd~v~~~~~~~------------------~-~~~~~~~~v 71 (122)
.+++||+|+|+.|.. .+..++|||+|+|||+|++++++. . .....+.+|
T Consensus 21 ~~~rGd~V~f~~p~~~~~~~~~~gy~~~~~~~iKrV~a~pGD~V~v~~~~v~iNG~~~~~~~~~d~~g~~l~~~~~~~~v 100 (138)
T PF10502_consen 21 KIERGDLVVFCPPAEVAFFAAERGYLPEGQPLIKRVAAVPGDTVEVTDGGVYINGRPVGEPLATDSDGRPLPQFSGSGTV 100 (138)
T ss_dssp --------------------------------------------------------------------S-T----TEEE-
T ss_pred ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccCCceEe
Confidence 489999999999852 245899999999999999986521 0 111258999
Q ss_pred eCCeEEEeeCCCCCCCCCCceecccCCCeeEEEEEEE
Q 033291 72 PQGHVWIEGDNIYESNDSRKFGAVPYGLIEGRVFLRI 108 (122)
Q Consensus 72 p~~~~~v~gdn~~~S~DSR~~G~V~~~~I~Gkv~~~~ 108 (122)
|+|+|||+|||+.+|+||||||+|++++|+|+|..++
T Consensus 101 p~g~~~v~gd~~~~S~DSRy~G~V~~~~I~g~~~pl~ 137 (138)
T PF10502_consen 101 PEGEYFVLGDNRPNSFDSRYFGPVPRSQIIGKARPLW 137 (138)
T ss_dssp -TTEEEEE-SBTTS--SHHHH--EEGGGEEEEEEEEE
T ss_pred CCCEEEEecCCCCCccccCEecccCHHHEEEEEEEEE
Confidence 9999999999999999999999999999999998843
No 7
>TIGR02771 TraF_Ti conjugative transfer signal peptidase TraF. This protein is found in apparent operons encoding elements of conjugative transfer systems. This family is homologous to a broader family of signal (leader) peptidases such as lepB. This family is present in both Ti-type and I-type conjugative systems.
Probab=99.92 E-value=2.6e-25 Score=158.58 Aligned_cols=85 Identities=35% Similarity=0.470 Sum_probs=70.2
Q ss_pred CCCCCCcEEEEEcCCCCC-------------------ceeEEEEEEcCCCEEEEecCCC-------C-------------
Q 033291 22 NKVCPGDVVLVRSPVVPR-------------------RIVTKRVIGMEGDRVSYVADPK-------S------------- 62 (122)
Q Consensus 22 ~~~~~GDiVv~~~p~~~~-------------------~~~iKRV~a~pGd~v~~~~~~~-------~------------- 62 (122)
..++|||+|+|+.|..+. ..++|||+|+|||+|+++++.. .
T Consensus 45 ~~~~rGDiVvf~~p~~~~~~~~~~rg~l~~g~~p~~~~~~vKRViglpGD~V~i~~~~v~INg~~~~~~~~~~~~~~g~~ 124 (171)
T TIGR02771 45 KPVERGDYVVFCPPDNPQFEEARERGYLREGLCPGGFGPLLKRVLGLPGDRVTVRADVVAINGQLLPYSKPLATDSSGRP 124 (171)
T ss_pred CCCCCCcEEEEeCCCchhhhchhhcCcccccccCcCccceEEEEEEeCCCEEEEECCEEEECCEEcccccccccccCCCc
Confidence 589999999999875321 2799999999999999976411 0
Q ss_pred CCCCceEEeeCCeEEEeeCCCCCCCCCCceecccCCCeeEEEEEE
Q 033291 63 SDKFETVVVPQGHVWIEGDNIYESNDSRKFGAVPYGLIEGRVFLR 107 (122)
Q Consensus 63 ~~~~~~~~vp~~~~~v~gdn~~~S~DSR~~G~V~~~~I~Gkv~~~ 107 (122)
.....+.+||+| ||++|||+++|+||||||+|++++|+|||..+
T Consensus 125 l~~~~~~~vp~g-yf~lgdn~~~S~DSRy~G~V~~~~IiGk~~pl 168 (171)
T TIGR02771 125 LPPFPEGVIPPG-FFVVHDTSPTSFDSRYFGPISREQVIGRVKPL 168 (171)
T ss_pred cccCCCcEECCC-EEEECCCCCCCCcccccceecHHHeEEEEEEe
Confidence 011236899999 99999999999999999999999999999863
No 8
>PRK13884 conjugal transfer peptidase TraF; Provisional
Probab=99.92 E-value=1.4e-24 Score=155.64 Aligned_cols=86 Identities=23% Similarity=0.225 Sum_probs=70.1
Q ss_pred CCCCCCcEEEEEcCCCC-------------------CceeEEEEEEcCCCEEEEecCCC-----C---------------
Q 033291 22 NKVCPGDVVLVRSPVVP-------------------RRIVTKRVIGMEGDRVSYVADPK-----S--------------- 62 (122)
Q Consensus 22 ~~~~~GDiVv~~~p~~~-------------------~~~~iKRV~a~pGd~v~~~~~~~-----~--------------- 62 (122)
..+++||+|+|++|... ...++|||+|+|||+|+++++.. .
T Consensus 49 ~~~~~Gd~V~f~~p~~~~~~~a~~rgyl~~g~~p~~~~~liKRVva~pGD~V~~~~~~l~VNG~~v~~~~~~~~d~~g~~ 128 (178)
T PRK13884 49 APVEKGAYVLFCPPQRGVFDDAKERGYIGAGFCPGGYGYMMKRVLAAKGDAVSVTDDGVRVNGELLPLSKPILADGAGRP 128 (178)
T ss_pred CCCCCCCEEEEeCCchHHHHHHHhCCccccCcCCCCCCceEEEEEeeCCcEEEEECCEEEECCEEccccccccccccCCc
Confidence 47999999999987521 13799999999999999976411 0
Q ss_pred --CCCCceEEeeCCeEEEeeCCCCCCCCCCceecccCCCeeEEEEEE
Q 033291 63 --SDKFETVVVPQGHVWIEGDNIYESNDSRKFGAVPYGLIEGRVFLR 107 (122)
Q Consensus 63 --~~~~~~~~vp~~~~~v~gdn~~~S~DSR~~G~V~~~~I~Gkv~~~ 107 (122)
......++||+|+|||+|||+++|+||||||+|++++|+|++..+
T Consensus 129 l~~~~~~~~~lp~g~~fvlgd~~~~S~DSRYfG~V~~~~I~G~~~Pl 175 (178)
T PRK13884 129 LPRYQANSYTLGESELLLMSDVSATSFDGRYFGPINRSQIKTVIRPV 175 (178)
T ss_pred ccccCCCceEECCCEEEEECCCCCCCCcccccCcccHHHEEEEEEEe
Confidence 001224699999999999999999999999999999999999864
No 9
>TIGR02754 sod_Ni_protease nickel-type superoxide dismutase maturation protease. Members of this protein family are apparent proteases encoded adjacent to the genes for a nickel-type superoxide dismutase. This family belongs to the same larger family (see Pfam model pfam00717) as signal peptidase I, an unusual serine protease suggested to have a Ser/Lys catalytic dyad.
Probab=99.87 E-value=6.6e-22 Score=126.97 Aligned_cols=83 Identities=34% Similarity=0.574 Sum_probs=72.2
Q ss_pred CccccCCCCCEEEEEeccCCCCCCCCCcEEEEEcCCCCCceeEEEEEEcCCCEEEEecCCCCCCCCceEEeeCCeEEEee
Q 033291 1 MLPTINLTGDLVLAERISTRFNKVCPGDVVLVRSPVVPRRIVTKRVIGMEGDRVSYVADPKSSDKFETVVVPQGHVWIEG 80 (122)
Q Consensus 1 M~Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVv~~~p~~~~~~~iKRV~a~pGd~v~~~~~~~~~~~~~~~~vp~~~~~v~g 80 (122)
|+|||+ +||.|+|+++......+++||+|+|+.|..+++.++||++++++ +++|+++
T Consensus 8 M~P~l~-~GD~vlv~~~~~~~~~~~~Gdivv~~~~~~~~~~~vkRv~~~~~----------------------~~~~l~~ 64 (90)
T TIGR02754 8 MSPTLP-PGDRIIVVPWLKIFRVPPIGNVVVVRHPLQPYGLIIKRLAAVDD----------------------NGLFLLG 64 (90)
T ss_pred ccCccC-CCCEEEEEEccccCCCCCCCeEEEEecCCCCcceEEEEeeEEcC----------------------CeEEEeC
Confidence 999999 99999999865434556789999999887667899999998753 4689999
Q ss_pred CCCCCCCCCCceecccCCCeeEEEEE
Q 033291 81 DNIYESNDSRKFGAVPYGLIEGRVFL 106 (122)
Q Consensus 81 dn~~~S~DSR~~G~V~~~~I~Gkv~~ 106 (122)
||+..|.|||++|+|+..+|+|+|+|
T Consensus 65 dN~~~~~d~~~~g~v~~~~I~G~v~~ 90 (90)
T TIGR02754 65 DNPKASTDSRQLGPVPRSLLLGKVLW 90 (90)
T ss_pred CCCCCCCcccccCCCcHHHEEEEEEC
Confidence 99999999999999999999999964
No 10
>cd06530 S26_SPase_I The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3.4.21.89) family members are essential membrane-bound serine proteases that function to cleave the amino-terminal signal peptide extension from proteins that are translocated across biological membranes. The bacterial signal peptidase I, which is the most intensively studied, has two N-terminal transmembrane segments inserted in the plasma membrane and a hydrophilic, C-terminal catalytic region that is located in the periplasmic space. Although the bacterial signal peptidase I is monomeric, signal peptidases of eukaryotic cells commonly function as oligomeric complexes containing two divergent copies of the catalytic monomer. These are the IMP1 and IMP2 signal peptidases of the mitochondrial inner membrane that remove leader peptides from nuclear- and mitochondrial-encoded proteins. Also, two components of the endoplasmic reticulum signal peptidase in mammals (18-kDa and 21-kDa
Probab=99.82 E-value=6.7e-20 Score=116.21 Aligned_cols=76 Identities=46% Similarity=0.691 Sum_probs=68.4
Q ss_pred CccccCCCCCEEEEEeccCCCCCCCCCcEEEEEcCCCCCceeEEEEEEcCCCEEEEecCCCCCCCCceEEeeCCeEEEee
Q 033291 1 MLPTINLTGDLVLAERISTRFNKVCPGDVVLVRSPVVPRRIVTKRVIGMEGDRVSYVADPKSSDKFETVVVPQGHVWIEG 80 (122)
Q Consensus 1 M~Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVv~~~p~~~~~~~iKRV~a~pGd~v~~~~~~~~~~~~~~~~vp~~~~~v~g 80 (122)
|+||+. +||++++++.......+++||+|+|+.+..++..++|||++ ||+.|
T Consensus 10 M~P~i~-~gd~v~v~~~~~~~~~~~~GDiv~~~~~~~~~~~~vkRv~~---------------------------~~~~g 61 (85)
T cd06530 10 MEPTLQ-PGDLVLVNKLSYGFREPKRGDVVVFKSPGDPGKPIIKRVIG---------------------------YFVLG 61 (85)
T ss_pred CcCccc-CCCEEEEEEeecccCCCCCCCEEEEeCCCCCCCEEEEEEEE---------------------------EEEee
Confidence 999998 99999999876433479999999999986556889999988 89999
Q ss_pred CCCCCCCCCCceecccCCCeeEEE
Q 033291 81 DNIYESNDSRKFGAVPYGLIEGRV 104 (122)
Q Consensus 81 dn~~~S~DSR~~G~V~~~~I~Gkv 104 (122)
||..+|.|||+||+++.++|+|++
T Consensus 62 Dn~~ns~d~~~~g~~~~~~i~G~~ 85 (85)
T cd06530 62 DNRNNSLDSRYWGPVPEDDIVGKV 85 (85)
T ss_pred CCCCCCCccCCcCCCcHHHeEEeC
Confidence 999899999999999999999985
No 11
>COG4959 TraF Type IV secretory pathway, protease TraF [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=99.76 E-value=5.3e-19 Score=122.66 Aligned_cols=86 Identities=26% Similarity=0.362 Sum_probs=71.2
Q ss_pred CCCCCcEEEEEcCCC------------CCceeEEEEEEcCCCEEEEecCCC-------------------CCCCCceEEe
Q 033291 23 KVCPGDVVLVRSPVV------------PRRIVTKRVIGMEGDRVSYVADPK-------------------SSDKFETVVV 71 (122)
Q Consensus 23 ~~~~GDiVv~~~p~~------------~~~~~iKRV~a~pGd~v~~~~~~~-------------------~~~~~~~~~v 71 (122)
.+.+||+|++++|.. ...+++|||.|+|||+|++..+.. ...-..+..+
T Consensus 53 Pvt~g~lV~v~pP~~~a~~aA~RGYLp~~~pllK~i~Alpgq~Vci~~~~I~I~G~~v~~sl~~D~~GR~lp~~~gcR~l 132 (173)
T COG4959 53 PVTKGDLVLVCPPQRAAFLAAQRGYLPPYIPLLKRILALPGQHVCITSQGIAIDGKPVAASLPVDRVGRALPRWQGCRYL 132 (173)
T ss_pred CcccCCEEEECCCchHhHhHhhcCccccccHHHHHHhcCCCCcEEEecceEEECCEEeeeeccccccCCcCCcccCCcee
Confidence 469999999999853 356789999999999999876421 1122345559
Q ss_pred eCCeEEEeeCCCCCCCCCCceecccCCCeeEEEEEEEe
Q 033291 72 PQGHVWIEGDNIYESNDSRKFGAVPYGLIEGRVFLRIW 109 (122)
Q Consensus 72 p~~~~~v~gdn~~~S~DSR~~G~V~~~~I~Gkv~~~~~ 109 (122)
-++|+|+|+|..+.|+|||||||||.++|+|.+.. +|
T Consensus 133 ~~~el~lL~~~~~~SfDsRYfGpipas~vig~aRP-vw 169 (173)
T COG4959 133 APSELLLLTDRSSTSFDSRYFGPIPASQVIGVARP-VW 169 (173)
T ss_pred cCCeEEEEeccCCcccccceecccCHHHcceeeee-ee
Confidence 99999999999999999999999999999999987 44
No 12
>TIGR02228 sigpep_I_arch signal peptidase I, archaeal type. This model represents signal peptidase I from most archaea, a subunit of the eukaryotic endoplasmic reticulum signal peptidase I complex, and an apparent signal peptidase I from a small number of bacteria. It is related to but does not overlap in hits with TIGR02227, the bacterial and mitochondrial signal peptidase I.
Probab=99.49 E-value=1.6e-13 Score=96.84 Aligned_cols=79 Identities=34% Similarity=0.430 Sum_probs=64.1
Q ss_pred CccccCCCCCEEEEEeccCCCCCCCCCcEEEEEcCCCCCceeEEEEEEcCCCEEEEecCCCCCCCCceEEeeCCeEEEee
Q 033291 1 MLPTINLTGDLVLAERISTRFNKVCPGDVVLVRSPVVPRRIVTKRVIGMEGDRVSYVADPKSSDKFETVVVPQGHVWIEG 80 (122)
Q Consensus 1 M~Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVv~~~p~~~~~~~iKRV~a~pGd~v~~~~~~~~~~~~~~~~vp~~~~~v~g 80 (122)
|+|||+ +||.+++++.. ..++++||+|+|+.|..+ ..++|||+++.++. .+..|+..|
T Consensus 41 M~Ptl~-~GD~vlv~~~~--~~~~~~GDIVvf~~~~~~-~~iihRVi~v~~~~------------------g~~~~~tkG 98 (158)
T TIGR02228 41 MEPTFN-TGDLILVTGAD--PNDIQVGDVITYKSPGFN-TPVTHRVIEINNSG------------------GELGFITKG 98 (158)
T ss_pred CcCCcc-CCCEEEEEecc--cCCCCCCCEEEEEECCCC-ccEEEEEEEEECCC------------------CcEEEEEEe
Confidence 999999 99999999854 368999999999988543 78999999986431 012377889
Q ss_pred CCCCCCCCCCceecccCCCeeEEEE
Q 033291 81 DNIYESNDSRKFGAVPYGLIEGRVF 105 (122)
Q Consensus 81 dn~~~S~DSR~~G~V~~~~I~Gkv~ 105 (122)
||. .+.| .++|+.++|+|++.
T Consensus 99 DnN-~~~D---~~~v~~~~IiG~v~ 119 (158)
T TIGR02228 99 DNN-PAPD---GEPVPSENVIGKYL 119 (158)
T ss_pred cCC-CCCC---cccCCHHHEEEEEE
Confidence 997 4556 78999999999998
No 13
>COG0681 LepB Signal peptidase I [Intracellular trafficking and secretion]
Probab=99.16 E-value=1.3e-10 Score=81.07 Aligned_cols=97 Identities=35% Similarity=0.458 Sum_probs=74.4
Q ss_pred CccccCCCCCEEEEEeccCCCCCCCCCcEEEEEcCCCCCceeEEEEEEcCCCEEEEecCCCCCCCCceEEeeCCeEEEe-
Q 033291 1 MLPTINLTGDLVLAERISTRFNKVCPGDVVLVRSPVVPRRIVTKRVIGMEGDRVSYVADPKSSDKFETVVVPQGHVWIE- 79 (122)
Q Consensus 1 M~Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVv~~~p~~~~~~~iKRV~a~pGd~v~~~~~~~~~~~~~~~~vp~~~~~v~- 79 (122)
|+|||+ .||+++++|+++....+..++++ ..|......++||+++++||.+.++++.... ...+|++..++.
T Consensus 41 M~Ptl~-~GD~v~v~k~~~~~~~~~~~~~~--~~~~~~~~~~~kr~~~~~GD~i~~~~~~~~~----~~~~~~~~~~~~~ 113 (166)
T COG0681 41 MEPTLN-VGDRVLVKKFSYGFGKLKVPDII--VLPAVVEGDLIKRVIGLRGDIVVFKDDRLYV----VPIIPRVYGLVEK 113 (166)
T ss_pred cccccc-cCCEEEEEeccccccCCccceee--ecCCCCCcceEEEeccCCCCEEEEECCEEEe----ecccCcchhhhhc
Confidence 999999 99999999999988889999998 4444557889999999999999998643211 233455555444
Q ss_pred ------eCCCCCCCCCCceecccCCCeeEEE
Q 033291 80 ------GDNIYESNDSRKFGAVPYGLIEGRV 104 (122)
Q Consensus 80 ------gdn~~~S~DSR~~G~V~~~~I~Gkv 104 (122)
.+....+.+++.++.......+.++
T Consensus 114 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 144 (166)
T COG0681 114 DNGKHLVDVIVNANSSRVFGIITKKDYIKRV 144 (166)
T ss_pred ccccccccccccccCccccccccccccccce
Confidence 4444567788888888888888877
No 14
>PF00717 Peptidase_S24: Peptidase S24-like peptidase classification. ; InterPro: IPR019759 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ].; PDB: 1KCA_H 3BDN_A 1F39_A 1JHH_A 1JHE_B 3JSP_A 1JHF_B 1JHC_A 3JSO_B 1B12_D ....
Probab=99.11 E-value=5e-10 Score=67.94 Aligned_cols=54 Identities=33% Similarity=0.486 Sum_probs=43.1
Q ss_pred CccccCCCCCEEEEEeccCCCCCCCCCcEEEEEcCCCCCceeEEEEEEcCCCEEEEecCC
Q 033291 1 MLPTINLTGDLVLAERISTRFNKVCPGDVVLVRSPVVPRRIVTKRVIGMEGDRVSYVADP 60 (122)
Q Consensus 1 M~Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVv~~~p~~~~~~~iKRV~a~pGd~v~~~~~~ 60 (122)
|+|+|+ +||+|++++.. .++.||+|+|..+... ..++||+.+.+|+.+.+..+.
T Consensus 7 M~P~i~-~Gd~v~v~~~~----~~~~gdivv~~~~~~~-~~~iKrv~~~~~~~~~~~~~n 60 (70)
T PF00717_consen 7 MEPTIK-DGDIVLVDPSS----EPKDGDIVVVKIDGDE-ELYIKRVVGEPGGIILISSNN 60 (70)
T ss_dssp TGGTSS-TTEEEEEEETS-------TTSEEEEEETTEE-SEEEEEEEEETTEEEEE-SST
T ss_pred cccCee-CCCEEEEEEcC----CCccCeEEEEEECCce-eeEEEEEEEeCCCEEEEeccC
Confidence 999999 99999999864 8999999999987431 389999999999999887543
No 15
>cd06462 Peptidase_S24_S26 The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The S26 type I signal peptidase (SPase) family also includes mitochondrial inner membrane protease (IMP)-like members. SPases are essential membrane-bound proteases which function to cleave away the amino-terminal signal peptide from the translocated pre-protein, thus playing a crucial role in the tr
Probab=98.99 E-value=3.9e-09 Score=65.61 Aligned_cols=74 Identities=46% Similarity=0.648 Sum_probs=55.7
Q ss_pred CccccCCCCCEEEEEeccCCCCCCCCCcEEEEEcCCCCCceeEEEEEEcCCCEEEEecCCCCCCCCceEEeeCCeEEEee
Q 033291 1 MLPTINLTGDLVLAERISTRFNKVCPGDVVLVRSPVVPRRIVTKRVIGMEGDRVSYVADPKSSDKFETVVVPQGHVWIEG 80 (122)
Q Consensus 1 M~Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVv~~~p~~~~~~~iKRV~a~pGd~v~~~~~~~~~~~~~~~~vp~~~~~v~g 80 (122)
|+|+|. +||.+++++.. ..++.||+|++..+. +..++||+...++ ++.+++.+
T Consensus 10 M~P~i~-~gd~v~i~~~~---~~~~~G~iv~~~~~~--~~~~ikrl~~~~~---------------------~~~~~l~~ 62 (84)
T cd06462 10 MEPTIP-DGDLVLVDKSS---YEPKRGDIVVFRLPG--GELTVKRVIGLPG---------------------EGHYFLLG 62 (84)
T ss_pred ccCccc-CCCEEEEEecC---CCCcCCEEEEEEcCC--CcEEEEEEEEECC---------------------CCEEEEEC
Confidence 999998 99999999854 249999999999863 4899999998875 24678889
Q ss_pred CCCCCCCCCCceecccCCCeeEE
Q 033291 81 DNIYESNDSRKFGAVPYGLIEGR 103 (122)
Q Consensus 81 dn~~~S~DSR~~G~V~~~~I~Gk 103 (122)
||. ++.+.+..+. ....++|+
T Consensus 63 ~N~-~~~~~~~~~~-~~~~i~g~ 83 (84)
T cd06462 63 DNP-NSPDSRIDGP-PELDIVGV 83 (84)
T ss_pred CCC-CCCcccccCC-CHHHEEEe
Confidence 984 4445544333 55566665
No 16
>cd06529 S24_LexA-like Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The LexA-like proteins contain two-domains: an N-terminal DNA binding domain and a C-terminal domain (CTD) that provides LexA dimerization as well as cleavage activity. They undergo autolysis, cleaving at an Ala-Gly or a Cys-Gly bond, separating the DNA-binding domain from the rest of the
Probab=98.52 E-value=1.5e-06 Score=53.74 Aligned_cols=49 Identities=35% Similarity=0.529 Sum_probs=41.2
Q ss_pred CccccCCCCCEEEEEeccCCCCCCCCCcEEEEEcCCCCCceeEEEEEEcCCCEEEEe
Q 033291 1 MLPTINLTGDLVLAERISTRFNKVCPGDVVLVRSPVVPRRIVTKRVIGMEGDRVSYV 57 (122)
Q Consensus 1 M~Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVv~~~p~~~~~~~iKRV~a~pGd~v~~~ 57 (122)
|+|+++ +||.+++++.. .++.||++++..+ +..++||+...+++.+.+.
T Consensus 10 M~p~i~-~gd~lii~~~~----~~~~g~i~~~~~~---~~~~ikr~~~~~~~~~~L~ 58 (81)
T cd06529 10 MEPTIP-DGDLVLVDPSD----TPRDGDIVVARLD---GELTVKRLQRRGGGRLRLI 58 (81)
T ss_pred cCCccC-CCCEEEEcCCC----CCCCCCEEEEEEC---CEEEEEEEEECCCCcEEEE
Confidence 999998 99999999753 5999999999986 4789999999886655544
No 17
>COG2932 Predicted transcriptional regulator [Transcription]
Probab=98.20 E-value=1.3e-05 Score=58.67 Aligned_cols=78 Identities=23% Similarity=0.177 Sum_probs=52.2
Q ss_pred CccccCCCCCEEEEEeccCCCCCCCCCcEEEEEcCCCCCceeEEEEEEcCCCEEEEecCCCCCCCCceEEeeCCeEEEee
Q 033291 1 MLPTINLTGDLVLAERISTRFNKVCPGDVVLVRSPVVPRRIVTKRVIGMEGDRVSYVADPKSSDKFETVVVPQGHVWIEG 80 (122)
Q Consensus 1 M~Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVv~~~p~~~~~~~iKRV~a~pGd~v~~~~~~~~~~~~~~~~vp~~~~~v~g 80 (122)
|+|+++ +||.++|+.-. +..+||.|++..- .+..+|||+.-.+|-. +.+.+
T Consensus 133 MeP~~~-~Gd~ilVd~~~----~~~~gd~v~v~~~--g~~~~VK~l~~~~~~~----------------------~~l~S 183 (214)
T COG2932 133 MEPTYE-DGDTLLVDPGV----NTRRGDRVYVETD--GGELYVKKLQREPGGL----------------------LRLVS 183 (214)
T ss_pred cccccc-CCCEEEECCCC----ceeeCCEEEEEEe--CCeEEEEEEEEecCCe----------------------EEEEe
Confidence 999999 99999999743 6788896666643 2689999998877654 44667
Q ss_pred CCCCCCCCCCceecccCCCeeEEEEEEE
Q 033291 81 DNIYESNDSRKFGAVPYGLIEGRVFLRI 108 (122)
Q Consensus 81 dn~~~S~DSR~~G~V~~~~I~Gkv~~~~ 108 (122)
+|+...- ...+-.=..=.|+|+|++..
T Consensus 184 ~N~~~~~-~~~~~~~~~v~iIgrVv~~~ 210 (214)
T COG2932 184 LNPDYYP-DEIFSEDDDVEIIGRVVWVS 210 (214)
T ss_pred CCCCCCc-ccccCccceEEEEEEEEEEe
Confidence 7764321 11111111134899998854
No 18
>KOG3342 consensus Signal peptidase I [Intracellular trafficking, secretion, and vesicular transport]
Probab=98.13 E-value=4e-06 Score=58.69 Aligned_cols=87 Identities=24% Similarity=0.268 Sum_probs=60.1
Q ss_pred CccccCCCCCEEEEEeccCCCCCCCCCcEEEEEcCCCCCceeEEEEEEcCCCEEEEecCCCCCCCCceEEeeCCeEEEee
Q 033291 1 MLPTINLTGDLVLAERISTRFNKVCPGDVVLVRSPVVPRRIVTKRVIGMEGDRVSYVADPKSSDKFETVVVPQGHVWIEG 80 (122)
Q Consensus 1 M~Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVv~~~p~~~~~~~iKRV~a~pGd~v~~~~~~~~~~~~~~~~vp~~~~~v~g 80 (122)
|||+++ .||.++..... ....+.||||+|+.+. ..-+++.||+-+-+.+ + .+=.++.-|
T Consensus 58 MePaF~-RGDlLfL~N~~--~~p~~vGdivVf~veg-R~IPiVHRviK~he~~-----~------------~~~~~LTKG 116 (180)
T KOG3342|consen 58 MEPAFH-RGDLLFLTNRN--EDPIRVGDIVVFKVEG-REIPIVHRVIKQHEKS-----N------------GHIKFLTKG 116 (180)
T ss_pred cCcccc-cccEEEEecCC--CCcceeccEEEEEECC-ccCchhHHHHHHhccc-----C------------CcEEEEecC
Confidence 999999 99999987533 2467999999999863 3578899987654320 0 001255667
Q ss_pred CCCCCCCCCCc-----eecccCCCeeEEEEEEEeCC
Q 033291 81 DNIYESNDSRK-----FGAVPYGLIEGRVFLRIWPP 111 (122)
Q Consensus 81 dn~~~S~DSR~-----~G~V~~~~I~Gkv~~~~~p~ 111 (122)
||. ..|-|. .-...+++|+|+|.- +.|.
T Consensus 117 DNN--~~dD~~Ly~~gq~~L~r~~Ivg~~~G-~~Py 149 (180)
T KOG3342|consen 117 DNN--AVDDRGLYAQGQNWLERKDIVGRVRG-YLPY 149 (180)
T ss_pred CCC--cccchhcccccccceeccceeeEEee-cccc
Confidence 884 455553 245888999999976 5553
No 19
>PRK10276 DNA polymerase V subunit UmuD; Provisional
Probab=97.94 E-value=0.00016 Score=49.70 Aligned_cols=40 Identities=23% Similarity=0.422 Sum_probs=32.3
Q ss_pred Cc-cccCCCCCEEEEEeccCCCCCCCCCcEEEEEcCCCCCceeEEEEEE
Q 033291 1 ML-PTINLTGDLVLAERISTRFNKVCPGDVVLVRSPVVPRRIVTKRVIG 48 (122)
Q Consensus 1 M~-Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVv~~~p~~~~~~~iKRV~a 48 (122)
|+ |+|. +||.++|++-. .++.||+|++... ++..+||+.-
T Consensus 61 M~~~~I~-~GD~liVd~~~----~~~~Gdivv~~~~---g~~~vKrl~~ 101 (139)
T PRK10276 61 MIDAGIS-DGDLLIVDSAI----TASHGDIVIAAVD---GEFTVKKLQL 101 (139)
T ss_pred CCCCCCC-CCCEEEEECCC----CCCCCCEEEEEEC---CEEEEEEEEE
Confidence 76 6898 99999999642 5789999999863 5678999864
No 20
>PRK00215 LexA repressor; Validated
Probab=97.85 E-value=0.00019 Score=52.07 Aligned_cols=74 Identities=27% Similarity=0.331 Sum_probs=50.7
Q ss_pred Cc-cccCCCCCEEEEEeccCCCCCCCCCcEEEEEcCCCCCceeEEEEEEcCCCEEEEecCCCCCCCCceEEeeCCeEEEe
Q 033291 1 ML-PTINLTGDLVLAERISTRFNKVCPGDVVLVRSPVVPRRIVTKRVIGMEGDRVSYVADPKSSDKFETVVVPQGHVWIE 79 (122)
Q Consensus 1 M~-Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVv~~~p~~~~~~~iKRV~a~pGd~v~~~~~~~~~~~~~~~~vp~~~~~v~ 79 (122)
|. |++. +||.++|++- ..++.||+|++... ++..+||+.-. + |.+++.
T Consensus 128 M~~~~i~-~Gd~v~v~~~----~~~~~G~ivv~~~~---~~~~vKrl~~~-~----------------------~~~~L~ 176 (205)
T PRK00215 128 MIDAGIL-DGDLVIVRKQ----QTARNGQIVVALID---DEATVKRFRRE-G----------------------GHIRLE 176 (205)
T ss_pred CCCCCcC-CCCEEEEeCC----CCCCCCCEEEEEEC---CEEEEEEEEEe-C----------------------CEEEEE
Confidence 84 7898 9999999973 36789999999875 47899998653 2 345566
Q ss_pred eCCCCCCCCCCceecccCCCeeEEEEEEE
Q 033291 80 GDNIYESNDSRKFGAVPYGLIEGRVFLRI 108 (122)
Q Consensus 80 gdn~~~S~DSR~~G~V~~~~I~Gkv~~~~ 108 (122)
.+|+.. +......= .-.|+|+|+..+
T Consensus 177 s~Np~y--~~~~~~~~-~~~IiG~Vv~~~ 202 (205)
T PRK00215 177 PENPAY--EPIIVDPD-RVTIEGKVVGLI 202 (205)
T ss_pred cCCCCC--CCEEeCCC-cEEEEEEEEEEE
Confidence 676532 22221110 357999998754
No 21
>PRK12423 LexA repressor; Provisional
Probab=97.82 E-value=0.00024 Score=51.75 Aligned_cols=75 Identities=24% Similarity=0.197 Sum_probs=51.2
Q ss_pred Cc-cccCCCCCEEEEEeccCCCCCCCCCcEEEEEcCCCCCceeEEEEEEcCCCEEEEecCCCCCCCCceEEeeCCeEEEe
Q 033291 1 ML-PTINLTGDLVLAERISTRFNKVCPGDVVLVRSPVVPRRIVTKRVIGMEGDRVSYVADPKSSDKFETVVVPQGHVWIE 79 (122)
Q Consensus 1 M~-Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVv~~~p~~~~~~~iKRV~a~pGd~v~~~~~~~~~~~~~~~~vp~~~~~v~ 79 (122)
|. |+|. +||.|+|++- ..++.||+|++... ++..+||+.-. + +.+++.
T Consensus 124 M~~~~i~-~Gd~viv~~~----~~~~~Gdivv~~~~---~~~~vKrl~~~-~----------------------~~~~L~ 172 (202)
T PRK12423 124 MIDDGIL-DGDLVGVHRS----PEARDGQIVVARLD---GEVTIKRLERS-G----------------------DRIRLL 172 (202)
T ss_pred CCCCCcC-CCCEEEEeCC----CcCCCCCEEEEEEC---CEEEEEEEEEe-C----------------------CEEEEE
Confidence 76 7998 9999999973 37889999999863 57889998643 2 235666
Q ss_pred eCCCCCCCCCCceecccCCCeeEEEEEEE
Q 033291 80 GDNIYESNDSRKFGAVPYGLIEGRVFLRI 108 (122)
Q Consensus 80 gdn~~~S~DSR~~G~V~~~~I~Gkv~~~~ 108 (122)
.+|+. ++...+-+-..-.|+|+++..+
T Consensus 173 s~N~~--y~~i~~~~~~~~~I~Gvv~g~~ 199 (202)
T PRK12423 173 PRNPA--YAPIVVAPDQDFAIEGVFCGLI 199 (202)
T ss_pred cCCCC--CCCEEcCCCCcEEEEEEEEEEE
Confidence 77752 2222222222347999998754
No 22
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=97.72 E-value=0.00047 Score=49.73 Aligned_cols=76 Identities=22% Similarity=0.212 Sum_probs=51.7
Q ss_pred Cc-cccCCCCCEEEEEeccCCCCCCCCCcEEEEEcCCCCCceeEEEEEEcCCCEEEEecCCCCCCCCceEEeeCCeEEEe
Q 033291 1 ML-PTINLTGDLVLAERISTRFNKVCPGDVVLVRSPVVPRRIVTKRVIGMEGDRVSYVADPKSSDKFETVVVPQGHVWIE 79 (122)
Q Consensus 1 M~-Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVv~~~p~~~~~~~iKRV~a~pGd~v~~~~~~~~~~~~~~~~vp~~~~~v~ 79 (122)
|. |++. +||.+++++. ..++.||+|++... ++..+||+.-. | +.+++.
T Consensus 121 M~~~~i~-~Gd~v~v~~~----~~~~~G~ivvv~~~---~~~~vKrl~~~-~----------------------~~i~L~ 169 (199)
T TIGR00498 121 MVDAGIC-DGDLLIVRSQ----KDARNGEIVAAMID---GEVTVKRFYKD-G----------------------TKVELK 169 (199)
T ss_pred CCCCCCC-CCCEEEEecC----CCCCCCCEEEEEEC---CEEEEEEEEEE-C----------------------CEEEEE
Confidence 75 5798 9999999964 37899999999972 57899998643 2 345666
Q ss_pred eCCCCCCCCCCceecccCCCeeEEEEEEEeC
Q 033291 80 GDNIYESNDSRKFGAVPYGLIEGRVFLRIWP 110 (122)
Q Consensus 80 gdn~~~S~DSR~~G~V~~~~I~Gkv~~~~~p 110 (122)
.+|+... ...... ..-.|+|+|+..+..
T Consensus 170 s~N~~y~--~i~~~~-~~~~IiG~Vv~~~r~ 197 (199)
T TIGR00498 170 PENPEFD--PIVLNA-EDVTILGKVVGVIRN 197 (199)
T ss_pred cCCCCCc--CCcCCC-CcEEEEEEEEEEEEe
Confidence 7776321 111100 135899999987654
No 23
>COG1974 LexA SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]
Probab=96.83 E-value=0.021 Score=41.85 Aligned_cols=76 Identities=21% Similarity=0.171 Sum_probs=52.9
Q ss_pred cccCCCCCEEEEEeccCCCCCCCCCcEEEEEcCCCCCceeEEEEEEcCCCEEEEecCCCCCCCCceEEeeCCeEEEeeCC
Q 033291 3 PTINLTGDLVLAERISTRFNKVCPGDVVLVRSPVVPRRIVTKRVIGMEGDRVSYVADPKSSDKFETVVVPQGHVWIEGDN 82 (122)
Q Consensus 3 Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVv~~~p~~~~~~~iKRV~a~pGd~v~~~~~~~~~~~~~~~~vp~~~~~v~gdn 82 (122)
+.+. +||+|+|++- .....||||+...+. .+.-+||..-- .+.+++..-|
T Consensus 125 ~gi~-dGDlvvV~~~----~~a~~GdiVvA~i~g--~e~TvKrl~~~-----------------------g~~i~L~p~N 174 (201)
T COG1974 125 AGIL-DGDLVVVDPT----EDAENGDIVVALIDG--EEATVKRLYRD-----------------------GNQILLKPEN 174 (201)
T ss_pred CcCC-CCCEEEEcCC----CCCCCCCEEEEEcCC--CcEEEEEEEEe-----------------------CCEEEEEeCC
Confidence 4555 7999999864 478999999998764 45778887442 2447777777
Q ss_pred CCCCCCCCceecccCCCeeEEEEEEEeCC
Q 033291 83 IYESNDSRKFGAVPYGLIEGRVFLRIWPP 111 (122)
Q Consensus 83 ~~~S~DSR~~G~V~~~~I~Gkv~~~~~p~ 111 (122)
+. +.+..+..- .-.|+|+++..+|+.
T Consensus 175 p~--~~~i~~~~~-~~~I~G~vvgv~r~~ 200 (201)
T COG1974 175 PA--YPPIPVDAD-SVTILGKVVGVIRDI 200 (201)
T ss_pred CC--CCCcccCcc-ceEEEEEEEEEEecC
Confidence 63 233444333 568999999988874
No 24
>COG0681 LepB Signal peptidase I [Intracellular trafficking and secretion]
Probab=89.25 E-value=0.53 Score=32.29 Aligned_cols=13 Identities=23% Similarity=0.371 Sum_probs=11.0
Q ss_pred CCCCCcEEEEEcC
Q 033291 23 KVCPGDVVLVRSP 35 (122)
Q Consensus 23 ~~~~GDiVv~~~p 35 (122)
...+||+|+|+.+
T Consensus 84 ~~~~GD~i~~~~~ 96 (166)
T COG0681 84 IGLRGDIVVFKDD 96 (166)
T ss_pred ccCCCCEEEEECC
Confidence 4679999999983
No 25
>PF05257 CHAP: CHAP domain; InterPro: IPR007921 The CHAP (cysteine, histidine-dependent amidohydrolases/peptidases) domain is a region between 110 and 140 amino acids that is found in proteins from bacteria, bacteriophages, archaea and eukaryotes of the Trypanosomidae family. Many of these proteins are uncharacterised, but it has been proposed that they may function mainly in peptidoglycan hydrolysis. The CHAP domain is found in a wide range of protein architectures; it is commonly associated with bacterial type SH3 domains and with several families of amidase domains. It has been suggested that CHAP domain containing proteins utilise a catalytic cysteine residue in a nucleophilic-attack mechanism [, ]. The CHAP domain contains two invariant residues, a cysteine and a histidine. These residues form part of the putative active site of CHAP domain containing proteins. Secondary structure predictions show that the CHAP domain belongs to the alpha + beta structural class, with the N-terminal half largely containing predicted alpha helices and the C-terminal half principally composed of predicted beta strands [, ]. Some proteins known to contain a CHAP domain are listed below: Bacterial and trypanosomal glutathionylspermidine amidases. A variety of bacterial autolysins. A Nocardia aerocolonigenes putative esterase. Streptococcus pneumoniae choline-binding protein D. Methanosarcina mazei protein MM2478, a putative chloride channel. Several phage-encoded peptidoglycan hydrolases. Cysteine peptidases belonging to MEROPS peptidase family C51 (D-alanyl-glycyl endopeptidase, clan CA). ; PDB: 2LRJ_A 2VPM_B 2VOB_B 2VPS_A 2K3A_A 2IO9_A 2IO8_A 2IOB_A 2IOA_B 2IO7_B ....
Probab=85.37 E-value=3.2 Score=27.34 Aligned_cols=39 Identities=18% Similarity=0.192 Sum_probs=25.9
Q ss_pred CCCCCCcEEEEEcCCCCCceeEEEEEEc-CCCEEEEecCC
Q 033291 22 NKVCPGDVVLVRSPVVPRRIVTKRVIGM-EGDRVSYVADP 60 (122)
Q Consensus 22 ~~~~~GDiVv~~~p~~~~~~~iKRV~a~-pGd~v~~~~~~ 60 (122)
..|+.||||+|.......--.+.=|.+. .+++|.+.+..
T Consensus 61 ~~P~~Gdivv~~~~~~~~~GHVaIV~~v~~~~~i~v~e~N 100 (124)
T PF05257_consen 61 STPQPGDIVVWDSGSGGGYGHVAIVESVNDGGTITVIEQN 100 (124)
T ss_dssp S---TTEEEEEEECTTTTT-EEEEEEEE-TTSEEEEEECS
T ss_pred cccccceEEEeccCCCCCCCeEEEEEEECCCCEEEEEECC
Confidence 5899999999963333344578888888 88899887543
No 26
>TIGR02594 conserved hypothetical protein TIGR02594. Members of this protein family known so far are restricted to the bacteria, and for the most to the proteobacteria. The function is unknown.
Probab=84.21 E-value=7.1 Score=26.48 Aligned_cols=13 Identities=23% Similarity=0.281 Sum_probs=11.1
Q ss_pred CCCCCCcEEEEEc
Q 033291 22 NKVCPGDVVLVRS 34 (122)
Q Consensus 22 ~~~~~GDiVv~~~ 34 (122)
..++.||||+|+.
T Consensus 72 ~~p~~GDiv~f~~ 84 (129)
T TIGR02594 72 SKPAYGCIAVKRR 84 (129)
T ss_pred CCCCccEEEEEEC
Confidence 4689999999985
No 27
>cd04712 BAH_DCM_I BAH, or Bromo Adjacent Homology domain, as present in DNA (Cytosine-5)-methyltransferases (DCM) 1. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=83.99 E-value=11 Score=25.58 Aligned_cols=83 Identities=13% Similarity=0.039 Sum_probs=43.6
Q ss_pred CCCCCCcEEEEEcCCCC----------CceeEEEEEEcCCC---EEEEecC--CCCCCC-CceEEeeCCeEEEeeCCCCC
Q 033291 22 NKVCPGDVVLVRSPVVP----------RRIVTKRVIGMEGD---RVSYVAD--PKSSDK-FETVVVPQGHVWIEGDNIYE 85 (122)
Q Consensus 22 ~~~~~GDiVv~~~p~~~----------~~~~iKRV~a~pGd---~v~~~~~--~~~~~~-~~~~~vp~~~~~v~gdn~~~ 85 (122)
..++.||+|+++.++.. ...+|-||..+--+ .-.+... -...+. ... .-.+.++|+.......
T Consensus 4 ~~i~vGD~V~v~~d~~~~~~~~~~~~~~~~~i~~V~~~~e~~~g~~~~h~~W~yrp~eTv~g~-~~~~~ElFLSd~c~~~ 82 (130)
T cd04712 4 LTIRVGDVVSVERDDADSTTKWNDDHRWLPLVQFVEYMKKGSDGSKMFHGRWLYRGCDTVLGN-YANERELFLTNECTCL 82 (130)
T ss_pred CEEeCCCEEEEcCCCCCccccccccccccceEEEEEEeeecCCCceEEEEEEEEcchhccccc-cCCCceEEEecccccc
Confidence 35778999999876543 24577777665332 1111100 000000 111 4556778775333222
Q ss_pred CCCCCceecccCCCeeEEEEEEEeCC
Q 033291 86 SNDSRKFGAVPYGLIEGRVFLRIWPP 111 (122)
Q Consensus 86 S~DSR~~G~V~~~~I~Gkv~~~~~p~ 111 (122)
+.++. .+.|+||+..-+.+.
T Consensus 83 ~~~~~------~~~I~~k~~V~~~~~ 102 (130)
T cd04712 83 ELDLL------STEIKGVHKVDWSGT 102 (130)
T ss_pred ccccc------cceeEEEEEEEEecC
Confidence 22222 569999998876654
No 28
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=77.59 E-value=2.8 Score=25.50 Aligned_cols=20 Identities=25% Similarity=0.320 Sum_probs=10.1
Q ss_pred CCCEEEEEeccCCCCCCCCCcEE
Q 033291 8 TGDLVLAERISTRFNKVCPGDVV 30 (122)
Q Consensus 8 ~Gd~vlv~~~~~~~~~~~~GDiV 30 (122)
.||.|.|....| ++.+|+||
T Consensus 47 ~GD~V~Ve~spy---d~tkgrIi 66 (68)
T TIGR00008 47 PGDKVKVELSPY---DLTRGRIT 66 (68)
T ss_pred CCCEEEEEECcc---cCCcEeEE
Confidence 455555554443 35555554
No 29
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=75.58 E-value=3.6 Score=25.53 Aligned_cols=20 Identities=35% Similarity=0.547 Sum_probs=10.6
Q ss_pred CCCEEEEEeccCCCCCCCCCcEE
Q 033291 8 TGDLVLAERISTRFNKVCPGDVV 30 (122)
Q Consensus 8 ~Gd~vlv~~~~~~~~~~~~GDiV 30 (122)
.||.|+|..+.| .+.+|||+
T Consensus 49 ~GD~V~Ve~~~~---d~~kg~I~ 68 (75)
T COG0361 49 PGDVVLVELSPY---DLTKGRIV 68 (75)
T ss_pred CCCEEEEEeccc---ccccccEE
Confidence 456666555443 35555554
No 30
>COG0093 RplN Ribosomal protein L14 [Translation, ribosomal structure and biogenesis]
Probab=75.32 E-value=19 Score=24.37 Aligned_cols=32 Identities=22% Similarity=0.250 Sum_probs=22.0
Q ss_pred ceEEeeCCeEEEeeCCCCCCCCCCceecccCCC
Q 033291 67 ETVVVPQGHVWIEGDNIYESNDSRKFGAVPYGL 99 (122)
Q Consensus 67 ~~~~vp~~~~~v~gdn~~~S~DSR~~G~V~~~~ 99 (122)
..+..-+|.+.++.++ ..-.-+|-||||.++.
T Consensus 75 s~i~FddNA~Viin~~-g~P~GtrI~GPVaREl 106 (122)
T COG0093 75 SYIKFDDNAAVIINPD-GEPRGTRIFGPVAREL 106 (122)
T ss_pred CEEEeCCceEEEECCC-CCcccceEecchhHHH
Confidence 3445555666666555 4778899999998763
No 31
>PF14085 DUF4265: Domain of unknown function (DUF4265)
Probab=72.49 E-value=24 Score=23.35 Aligned_cols=48 Identities=15% Similarity=0.141 Sum_probs=31.4
Q ss_pred CCCEEEEEeccCCCCCCCCCcEEEEEcCCCCCceeEEEEEEcC-CCEEEEe
Q 033291 8 TGDLVLAERISTRFNKVCPGDVVLVRSPVVPRRIVTKRVIGME-GDRVSYV 57 (122)
Q Consensus 8 ~Gd~vlv~~~~~~~~~~~~GDiVv~~~p~~~~~~~iKRV~a~p-Gd~v~~~ 57 (122)
.+|...+.....-...+..||+|.++... +.+.+.+++.-. .-++++.
T Consensus 10 ~~~~y~l~n~Pf~a~glA~gDvV~~~~~~--g~~~~~~~v~~sGnsTiRv~ 58 (117)
T PF14085_consen 10 GDDTYRLDNIPFFAYGLALGDVVRAEPDD--GELWFQKVVESSGNSTIRVI 58 (117)
T ss_pred CCCEEEEEecccccCCCCCCCEEEEEeCC--CeEEEEEEEecCCCEEEEEE
Confidence 35666666666556789999999999864 455555444444 4455553
No 32
>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.
Probab=69.25 E-value=4.2 Score=24.14 Aligned_cols=12 Identities=42% Similarity=0.526 Sum_probs=6.3
Q ss_pred CCCCCcEEEEEc
Q 033291 23 KVCPGDVVLVRS 34 (122)
Q Consensus 23 ~~~~GDiVv~~~ 34 (122)
-+++||+|+...
T Consensus 41 wI~~GD~V~V~~ 52 (65)
T PF01176_consen 41 WIKRGDFVLVEP 52 (65)
T ss_dssp ---TTEEEEEEE
T ss_pred ecCCCCEEEEEe
Confidence 367777777764
No 33
>cd05793 S1_IF1A S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A in archaea, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=68.58 E-value=5.1 Score=24.79 Aligned_cols=10 Identities=50% Similarity=0.846 Sum_probs=5.6
Q ss_pred CCCCcEEEEE
Q 033291 24 VCPGDVVLVR 33 (122)
Q Consensus 24 ~~~GDiVv~~ 33 (122)
+++||+|+..
T Consensus 39 I~~GD~V~Ve 48 (77)
T cd05793 39 INEGDIVLVA 48 (77)
T ss_pred EcCCCEEEEE
Confidence 4555655554
No 34
>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=67.51 E-value=6.2 Score=24.49 Aligned_cols=10 Identities=30% Similarity=0.617 Sum_probs=5.6
Q ss_pred CCCCcEEEEE
Q 033291 24 VCPGDVVLVR 33 (122)
Q Consensus 24 ~~~GDiVv~~ 33 (122)
+++||+|++.
T Consensus 39 I~~GD~VlV~ 48 (78)
T cd04456 39 IKRGDFLIVD 48 (78)
T ss_pred EcCCCEEEEE
Confidence 4555555554
No 35
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=66.24 E-value=6.1 Score=24.81 Aligned_cols=10 Identities=50% Similarity=0.830 Sum_probs=6.1
Q ss_pred CCCCcEEEEE
Q 033291 24 VCPGDVVLVR 33 (122)
Q Consensus 24 ~~~GDiVv~~ 33 (122)
+++||+|++.
T Consensus 44 I~~GD~VlVe 53 (83)
T smart00652 44 IRRGDIVLVD 53 (83)
T ss_pred EcCCCEEEEE
Confidence 5566666665
No 36
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=64.02 E-value=9 Score=24.45 Aligned_cols=20 Identities=25% Similarity=0.287 Sum_probs=11.6
Q ss_pred CCCEEEEEeccCCCCCCCCCcEE
Q 033291 8 TGDLVLAERISTRFNKVCPGDVV 30 (122)
Q Consensus 8 ~Gd~vlv~~~~~~~~~~~~GDiV 30 (122)
.||.|.|.-..| ++.+|+|+
T Consensus 49 ~GD~V~VE~spY---DltkGRIi 68 (87)
T PRK12442 49 AGDRVTLELSPY---DLTKGRIN 68 (87)
T ss_pred CCCEEEEEECcc---cCCceeEE
Confidence 466666665544 45666654
No 37
>cd04714 BAH_BAHCC1 BAH, or Bromo Adjacent Homology domain, as present in mammalian BAHCC1 and similar proteins. BAHCC1 stands for BAH domain and coiled-coil containing 1. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=63.47 E-value=11 Score=25.07 Aligned_cols=27 Identities=30% Similarity=0.401 Sum_probs=21.0
Q ss_pred CCCCCcEEEEEcCCCCCceeEEEEEEc
Q 033291 23 KVCPGDVVLVRSPVVPRRIVTKRVIGM 49 (122)
Q Consensus 23 ~~~~GDiVv~~~p~~~~~~~iKRV~a~ 49 (122)
.++.||.|.++.+..+...+|.||..+
T Consensus 3 ~~~vGD~V~v~~~~~~~~pyIgrI~~i 29 (121)
T cd04714 3 IIRVGDCVLFKSPGRPSLPYVARIESL 29 (121)
T ss_pred EEEcCCEEEEeCCCCCCCCEEEEEEEE
Confidence 367899999998765567889998664
No 38
>PF01426 BAH: BAH domain; InterPro: IPR001025 The BAH (bromo-adjacent homology) family contains proteins such as eukaryotic DNA (cytosine-5) methyltransferases IPR001525 from INTERPRO, the origin recognition complex 1 (Orc1) proteins, as well as several proteins involved in transcriptional regulation. The BAH domain appears to act as a protein-protein interaction module specialised in gene silencing, as suggested for example by its interaction within yeast Orc1p with the silent information regulator Sir1p. The BAH module might therefore play an important role by linking DNA methylation, replication and transcriptional regulation [].; GO: 0003677 DNA binding; PDB: 4DA4_A 3PT6_B 3AV6_A 3AV5_A 3AV4_A 3PT9_A 3SWR_A 3PTA_A 1M4Z_A 1ZBX_A ....
Probab=62.56 E-value=11 Score=24.22 Aligned_cols=26 Identities=23% Similarity=0.258 Sum_probs=20.4
Q ss_pred CCCCcEEEEEcCCCCCceeEEEEEEc
Q 033291 24 VCPGDVVLVRSPVVPRRIVTKRVIGM 49 (122)
Q Consensus 24 ~~~GDiVv~~~p~~~~~~~iKRV~a~ 49 (122)
++.||.|.+..+.......|.||..+
T Consensus 3 ~~vGD~V~v~~~~~~~~~~v~~I~~i 28 (119)
T PF01426_consen 3 YKVGDFVYVKPDDPPEPPYVARIEEI 28 (119)
T ss_dssp EETTSEEEEECTSTTSEEEEEEEEEE
T ss_pred EeCCCEEEEeCCCCCCCCEEEEEEEE
Confidence 56789998888765677888888766
No 39
>smart00002 PLP Myelin proteolipid protein (PLP or lipophilin).
Probab=62.27 E-value=1.9 Score=25.58 Aligned_cols=20 Identities=30% Similarity=0.732 Sum_probs=16.9
Q ss_pred CCCCCCceecccCCCeeEEE
Q 033291 85 ESNDSRKFGAVPYGLIEGRV 104 (122)
Q Consensus 85 ~S~DSR~~G~V~~~~I~Gkv 104 (122)
-+.|-|.||.||-+..-|||
T Consensus 22 lC~D~RQyGilpwna~pgK~ 41 (60)
T smart00002 22 LCVDARQYGILPWNAFPGKV 41 (60)
T ss_pred EEeechhcceeecCCCCCch
Confidence 47899999999988877775
No 40
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=61.71 E-value=8.2 Score=25.18 Aligned_cols=10 Identities=50% Similarity=0.803 Sum_probs=5.2
Q ss_pred CCCCcEEEEE
Q 033291 24 VCPGDVVLVR 33 (122)
Q Consensus 24 ~~~GDiVv~~ 33 (122)
+.+||+|++.
T Consensus 60 I~~GD~VlVe 69 (100)
T PRK04012 60 IREGDVVIVA 69 (100)
T ss_pred ecCCCEEEEE
Confidence 4455555554
No 41
>PF10000 ACT_3: ACT domain; InterPro: IPR018717 This domain has no known function.; PDB: 1ZVP_C.
Probab=61.22 E-value=5.1 Score=24.51 Aligned_cols=16 Identities=31% Similarity=0.561 Sum_probs=10.8
Q ss_pred CccccCCCCCEEEEEec
Q 033291 1 MLPTINLTGDLVLAERI 17 (122)
Q Consensus 1 M~Ptl~~~Gd~vlv~~~ 17 (122)
|+|.|+ +|++||+.--
T Consensus 14 m~P~L~-~~~yVF~t~~ 29 (72)
T PF10000_consen 14 MSPELN-PGEYVFCTVP 29 (72)
T ss_dssp -EEEE--SS-EEEEEE-
T ss_pred CCcEeC-CCCEEEEEec
Confidence 899999 9999998753
No 42
>PRK00364 groES co-chaperonin GroES; Reviewed
Probab=55.37 E-value=52 Score=20.98 Aligned_cols=90 Identities=19% Similarity=0.168 Sum_probs=45.9
Q ss_pred cCCCCCEEEEEeccCCCCCCCCCcEEEEEcCCCCCceeEEEEEEcCCCEEEEecCCCCCCCCceEEeeCCeEEEeeCCC-
Q 033291 5 INLTGDLVLAERISTRFNKVCPGDVVLVRSPVVPRRIVTKRVIGMEGDRVSYVADPKSSDKFETVVVPQGHVWIEGDNI- 83 (122)
Q Consensus 5 l~~~Gd~vlv~~~~~~~~~~~~GDiVv~~~p~~~~~~~iKRV~a~pGd~v~~~~~~~~~~~~~~~~vp~~~~~v~gdn~- 83 (122)
|+|-||+|+|.+... .+-..|-|++=.. .........|+|+.-.... . ++ ...+..|..|..-+..+..
T Consensus 3 i~Pl~drVLV~~~~~--e~~T~gGI~Lp~~--a~~k~~~G~VvaVG~G~~~-~-~G----~~~~~~vk~GD~Vlf~~~~g 72 (95)
T PRK00364 3 LKPLGDRVLVKRLEE--EEKTAGGIVLPDS--AKEKPQEGEVVAVGPGRRL-D-NG----ERVPLDVKVGDKVLFGKYAG 72 (95)
T ss_pred ceEcCCEEEEEEccc--CccccceEEcCcc--ccCCcceEEEEEECCCeEC-C-CC----CEeecccCCCCEEEEcCCCC
Confidence 556799999998642 3455676666322 2245566777777432111 0 00 0112233344433333332
Q ss_pred -CCCCCCCceecccCCCeeEEE
Q 033291 84 -YESNDSRKFGAVPYGLIEGRV 104 (122)
Q Consensus 84 -~~S~DSR~~G~V~~~~I~Gkv 104 (122)
.--+|...|=.++.++|+|++
T Consensus 73 ~ev~~~~~~y~iv~~~DIlavi 94 (95)
T PRK00364 73 TEVKIDGEEYLILRESDILAIV 94 (95)
T ss_pred eEEEECCEEEEEEEHHHEEEEe
Confidence 112355556667777777764
No 43
>cd04717 BAH_polybromo BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human polybromo protein (BAF180) is a component of the SWI/SNF chromatin-remodeling complex PBAF. It is thought that polybromo participates in transcriptional regulation. Saccharomyces cerevisiae RSC1 and RSC2 are part of the 15-subunit nucleosome remodeling RSC complex. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=53.29 E-value=20 Score=23.63 Aligned_cols=73 Identities=22% Similarity=0.302 Sum_probs=39.7
Q ss_pred CCCCCcEEEEEcCCCCCceeEEEEEEc---C-CCEEEEecC----CCCCCCCceEEeeCCeEEEeeCCCCCCCCCCceec
Q 033291 23 KVCPGDVVLVRSPVVPRRIVTKRVIGM---E-GDRVSYVAD----PKSSDKFETVVVPQGHVWIEGDNIYESNDSRKFGA 94 (122)
Q Consensus 23 ~~~~GDiVv~~~p~~~~~~~iKRV~a~---p-Gd~v~~~~~----~~~~~~~~~~~vp~~~~~v~gdn~~~S~DSR~~G~ 94 (122)
.++.||.|.+..+..+....|.||..+ + |+ ..+... +...........-++|+|+.+ .+-.
T Consensus 3 ~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~-~~~~~~Wf~rP~et~~~~~~~~~~~Evfls~----------~~d~ 71 (121)
T cd04717 3 QYRVGDCVYVANPEDPSKPIIFRIERLWKDEDGE-KFFFGCWFYRPEETFHEPTRKFYKNEVFKSP----------LYET 71 (121)
T ss_pred EEECCCEEEEeCCCCCCCCEEEEEeEEEECCCCC-EEEEEEEEeChHHccCCCccccccCceEEcC----------cccc
Confidence 357899999988765566777777554 2 22 111110 000000111223456666642 3445
Q ss_pred ccCCCeeEEEEE
Q 033291 95 VPYGLIEGRVFL 106 (122)
Q Consensus 95 V~~~~I~Gkv~~ 106 (122)
+|.+.|+||+..
T Consensus 72 ~~~~~I~~kc~V 83 (121)
T cd04717 72 VPVEEIVGKCAV 83 (121)
T ss_pred ccHHHhcCeeEE
Confidence 888899999854
No 44
>COG5131 URM1 Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=51.39 E-value=20 Score=23.11 Aligned_cols=30 Identities=17% Similarity=0.331 Sum_probs=18.5
Q ss_pred ccCCCCCEEEEEeccCCC-----CCCCCCcEEEEEc
Q 033291 4 TINLTGDLVLAERISTRF-----NKVCPGDVVLVRS 34 (122)
Q Consensus 4 tl~~~Gd~vlv~~~~~~~-----~~~~~GDiVv~~~ 34 (122)
+|. +|=.++++...+.. ..++.||+|+|-+
T Consensus 57 ~lr-pGiI~LINd~DWeLleke~y~ledgDiIvfis 91 (96)
T COG5131 57 ELR-PGIICLINDMDWELLEKERYPLEDGDIIVFIS 91 (96)
T ss_pred CCc-ccEEEEEcCccHhhhhcccccCCCCCEEEEEe
Confidence 455 56677777655421 3567777777764
No 45
>smart00439 BAH Bromo adjacent homology domain.
Probab=50.97 E-value=31 Score=21.97 Aligned_cols=76 Identities=16% Similarity=0.226 Sum_probs=38.4
Q ss_pred CCCCcEEEEEcCCCCCceeEEEEEEc---CCCE-EEEecC----CCCCCCCceEEeeCCeEEEeeCCCCCCCCCCceecc
Q 033291 24 VCPGDVVLVRSPVVPRRIVTKRVIGM---EGDR-VSYVAD----PKSSDKFETVVVPQGHVWIEGDNIYESNDSRKFGAV 95 (122)
Q Consensus 24 ~~~GDiVv~~~p~~~~~~~iKRV~a~---pGd~-v~~~~~----~~~~~~~~~~~vp~~~~~v~gdn~~~S~DSR~~G~V 95 (122)
++.||.|.+..+.......+.||..+ +++. +.+... +............++++|.... +--+
T Consensus 2 ~~vgd~V~v~~~~~~~~~~i~~I~~i~~~~~~~~~~~~v~Wf~rp~e~~~~~~~~~~~~Elf~s~~----------~~~i 71 (120)
T smart00439 2 IRVGDFVLVEPDDADEPYYIGRIEEIFETKKNSEKMVRVRWFYRPEETVLEKAALFDKNEVFLSDE----------YDTV 71 (120)
T ss_pred cccCCEEEEeCCCCCCCCEEEEEEEEEECCCCCEEEEEEEEEEChhhccccccccCCCcceEEEcc----------CccC
Confidence 45677777776643344566665544 2222 222211 0000001111234677775432 1258
Q ss_pred cCCCeeEEEEEEEe
Q 033291 96 PYGLIEGRVFLRIW 109 (122)
Q Consensus 96 ~~~~I~Gkv~~~~~ 109 (122)
+.+.|+||+.....
T Consensus 72 ~~~~I~~kc~V~~~ 85 (120)
T smart00439 72 PLSDIIGKCNVLSK 85 (120)
T ss_pred ChHHeeeEEEEEEc
Confidence 99999999987543
No 46
>cd03695 CysN_NodQ_II CysN_NodQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN and a smaller subunit CysD and CysN. ATPS produces adenosine-5'-phosphosulfate (APS) from ATP and sulfate, coupled with GTP hydrolysis. In the subsequent reaction APS is phosphorylated by an APS kinase (CysC), to produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS) for use in amino acid (aa) biosynthesis. The Rhizobiaceae group (alpha-proteobacteria) appears to carry out the same chemistry for the sufation of a nodulation factor. In Rhizobium meliloti, a the hererodimeric complex comprised of NodP and NodQ appears to possess both ATPS and APS kinase activities. The N and C termini of NodQ correspond to CysN and CysC, respectively. Other eubacteria, Archaea, and eukaryotes use a different ATP sulfurylase, which sho
Probab=49.59 E-value=53 Score=19.99 Aligned_cols=34 Identities=21% Similarity=0.257 Sum_probs=26.1
Q ss_pred CCCCCCcEEEEEcCCCCCceeEEEEE--------EcCCCEEEEe
Q 033291 22 NKVCPGDVVLVRSPVVPRRIVTKRVI--------GMEGDRVSYV 57 (122)
Q Consensus 22 ~~~~~GDiVv~~~p~~~~~~~iKRV~--------a~pGd~v~~~ 57 (122)
+.++.||-|.+.+.. ...-+|.+- |.+||.+.+.
T Consensus 25 G~v~~Gd~v~~~P~~--~~~~V~si~~~~~~~~~a~aGd~v~l~ 66 (81)
T cd03695 25 GSIRVGDEVVVLPSG--KTSRVKSIETFDGELDEAGAGESVTLT 66 (81)
T ss_pred ceEECCCEEEEcCCC--CeEEEEEEEECCcEeCEEcCCCEEEEE
Confidence 688999999998642 356677776 8889988875
No 47
>PF06890 Phage_Mu_Gp45: Bacteriophage Mu Gp45 protein; InterPro: IPR014462 This entry is represented by the Bacteriophage Mu, Gp45. The characteristics of the protein distribution suggest prophage matches.
Probab=48.95 E-value=94 Score=22.00 Aligned_cols=41 Identities=27% Similarity=0.319 Sum_probs=30.0
Q ss_pred eccCCCCCCCCCcEEEEEcCCCCCceeEEE---EEEcCCCEEEEec
Q 033291 16 RISTRFNKVCPGDVVLVRSPVVPRRIVTKR---VIGMEGDRVSYVA 58 (122)
Q Consensus 16 ~~~~~~~~~~~GDiVv~~~p~~~~~~~iKR---V~a~pGd~v~~~~ 58 (122)
.-.|+.+.++.|++++|... ....++|| ++.+.++++.+..
T Consensus 67 d~~yR~~~L~~GEvalY~~~--G~~I~L~~~G~ii~~~~~~~~v~a 110 (162)
T PF06890_consen 67 DRRYRPKGLKPGEVALYDDE--GQKIHLKRDGRIIEVTCKTVTVNA 110 (162)
T ss_pred CccccccCCCCCcEEEEcCC--CCEEEEEecceEEeccCceEEEec
Confidence 33455667999999999964 24566765 7778889888874
No 48
>COG3602 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=48.53 E-value=12 Score=25.22 Aligned_cols=35 Identities=17% Similarity=0.201 Sum_probs=20.6
Q ss_pred CccccCCCCCEEEEEeccCCCCCCCCCcEEEEEcCC
Q 033291 1 MLPTINLTGDLVLAERISTRFNKVCPGDVVLVRSPV 36 (122)
Q Consensus 1 M~Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVv~~~p~ 36 (122)
|+|-|. +||+|++.--.--.....---+-.|+-++
T Consensus 14 mtPeL~-~G~yVfcT~~~ga~~~~~lePla~FRE~E 48 (134)
T COG3602 14 MTPELL-DGDYVFCTVAPGALQPKNLEPLATFRERE 48 (134)
T ss_pred cCcccc-CCceEEEEecCCcCCCcCCChHhhhcccc
Confidence 899999 99999975432111122233355666543
No 49
>PF11132 SplA: Transcriptional regulator protein (SplA); InterPro: IPR022608 The SplA protein functions in trans as a negative regulator of the level of splB-lacZ expression in the developing forespore [].
Probab=47.33 E-value=48 Score=20.45 Aligned_cols=12 Identities=25% Similarity=0.432 Sum_probs=7.2
Q ss_pred cccCCCCCEEEEE
Q 033291 3 PTINLTGDLVLAE 15 (122)
Q Consensus 3 Ptl~~~Gd~vlv~ 15 (122)
..++ .||.|+|-
T Consensus 4 ~~~~-~GD~VyVi 15 (75)
T PF11132_consen 4 KPYH-AGDIVYVI 15 (75)
T ss_pred cccC-CCCEEEEE
Confidence 4555 66666654
No 50
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=45.96 E-value=54 Score=24.79 Aligned_cols=73 Identities=27% Similarity=0.547 Sum_probs=39.1
Q ss_pred CccccCCCCCEEEEEeccC-------------CCCCCCCCcEEEEEcCCCCCceeEEEEEEcCCCEEEEecCCCCCCCCc
Q 033291 1 MLPTINLTGDLVLAERIST-------------RFNKVCPGDVVLVRSPVVPRRIVTKRVIGMEGDRVSYVADPKSSDKFE 67 (122)
Q Consensus 1 M~Ptl~~~Gd~vlv~~~~~-------------~~~~~~~GDiVv~~~p~~~~~~~iKRV~a~pGd~v~~~~~~~~~~~~~ 67 (122)
|.|.|+ .||.|...-... .++.++.|-+|-+.+- .+-|+++--|--+..-. .....
T Consensus 109 ~r~~l~-vGD~v~AkV~~vd~~~~~~L~~k~~~~GkL~~G~iv~i~p~------kVpRvig~~~sm~~~l~----~~~~~ 177 (239)
T COG1097 109 LRPFLN-VGDLVYAKVVDVDRDGEVELTLKDEGLGKLKNGQIVKIPPS------KVPRVIGKKGSMLNMLK----EKTGC 177 (239)
T ss_pred cccccc-cCCEEEEEEEEccCCCceEEEeecCCCccccCCEEEEEchh------hcceEecCCCcHHHHhh----hhcCe
Confidence 677887 788887533221 2356666666666532 34556555444332110 01122
Q ss_pred eEEee-CCeEEEeeCCCC
Q 033291 68 TVVVP-QGHVWIEGDNIY 84 (122)
Q Consensus 68 ~~~vp-~~~~~v~gdn~~ 84 (122)
.+.|. .|.+||-+.|..
T Consensus 178 ~I~VG~NG~IWV~~~~~~ 195 (239)
T COG1097 178 EIIVGQNGRIWVDGENES 195 (239)
T ss_pred EEEEecCCEEEecCCCcc
Confidence 33343 478899988863
No 51
>PF07039 DUF1325: SGF29 tudor-like domain; InterPro: IPR010750 SAGA-associated factor 29 is involved in transcriptional regulation, probably through association with histone acetyltransferase (HAT) complexes like the TFTC-HAT or STAGA complexes. It also may be involved in MYC-mediated oncogenic transformation. It is a component of the ATAC complex, which is a complex with histone acetyltransferase activity on histones H3 and H4 []. This entry represents a domain found in yeast and human SAGA-associated factor 29 proteins that is related to the tudor domain. ; PDB: 3MP6_A 3MP1_A 3MP8_A 3MET_B 3ME9_A 3MEU_B 3MEA_A 3MEV_B 3LX7_A 3MEW_A.
Probab=45.01 E-value=96 Score=20.98 Aligned_cols=56 Identities=11% Similarity=0.084 Sum_probs=38.5
Q ss_pred CCCcEEEEEcC--CCCCceeEEEEEEcCCCE--EEEecCCCCCCCCceEEeeCCeEEEeeC
Q 033291 25 CPGDVVLVRSP--VVPRRIVTKRVIGMEGDR--VSYVADPKSSDKFETVVVPQGHVWIEGD 81 (122)
Q Consensus 25 ~~GDiVv~~~p--~~~~~~~iKRV~a~pGd~--v~~~~~~~~~~~~~~~~vp~~~~~v~gd 81 (122)
+.||-|+++.+ ...+..++-+|+..-++. .++.+..... ....++++..++..|-.
T Consensus 1 q~G~~VAak~~~~~~~~~WIla~Vv~~~~~~~rYeV~D~d~~~-~~~~~~~~~~~iIPLP~ 60 (130)
T PF07039_consen 1 QPGDQVAAKVKQGNEEEEWILAEVVKYNSDGNRYEVEDPDPEE-EKKRYKLSRKQIIPLPK 60 (130)
T ss_dssp -TT-EEEEEECTTTTTCEEEEEEEEEEETTTTEEEEEETTTCT-TTEEEEEEGGGEEEE-S
T ss_pred CCCCEEEEEcCCCCCCCCEEEEEEEEEeCCCCEEEEecCCCCC-CCceEEeCHHHEEECCC
Confidence 47999999876 344678899999887775 6665432211 33589999999998877
No 52
>cd04760 BAH_Dnmt1_I BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=43.13 E-value=68 Score=21.72 Aligned_cols=79 Identities=18% Similarity=0.120 Sum_probs=39.9
Q ss_pred CCCCcEEEEEcCCCCCceeEEEEEEcCCCE-----EEEecCCCCCCCCceEEeeCCeEEEeeCCCCCCCCCCceecccCC
Q 033291 24 VCPGDVVLVRSPVVPRRIVTKRVIGMEGDR-----VSYVADPKSSDKFETVVVPQGHVWIEGDNIYESNDSRKFGAVPYG 98 (122)
Q Consensus 24 ~~~GDiVv~~~p~~~~~~~iKRV~a~pGd~-----v~~~~~~~~~~~~~~~~vp~~~~~v~gdn~~~S~DSR~~G~V~~~ 98 (122)
+..||-|.++++......+|-||..+--+. +..+-=-...+....-+-.+-++|+. +..--.+.+
T Consensus 4 i~vGD~V~v~~~~~~~p~~I~rV~~mfe~~~g~k~~h~rWf~Rg~dTVlG~~~~~kEvFls----------d~c~d~~l~ 73 (124)
T cd04760 4 LEAGDCVSVKPDDPTKPLYIARVTYMWKDSIGGKMFHAHWFCRGSDTVLGETSDPLELFLV----------DECEDMALS 73 (124)
T ss_pred EecCCEEEEecCCCCCCcEEEEEhhheecCCCCcEEEEEEEEECCcccccccCCCcEEEee----------cccCCcchH
Confidence 567888888865444556888886553332 11000000000000001222334443 333446777
Q ss_pred CeeEEEEEEEeCCC
Q 033291 99 LIEGRVFLRIWPPK 112 (122)
Q Consensus 99 ~I~Gkv~~~~~p~~ 112 (122)
.|.||+...+-+++
T Consensus 74 ~I~~Kv~V~~~~p~ 87 (124)
T cd04760 74 SIHGKVNVIYKAPS 87 (124)
T ss_pred HheeeeEEEEeCCC
Confidence 99999998877665
No 53
>cd04089 eRF3_II eRF3_II: domain II of the eukaryotic class II release factor (eRF3). In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribsome. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM is a non-pathogenic prion-li
Probab=43.08 E-value=72 Score=19.28 Aligned_cols=34 Identities=18% Similarity=0.264 Sum_probs=25.7
Q ss_pred CCCCCCcEEEEEcCCCCCceeEEEEE--------EcCCCEEEEe
Q 033291 22 NKVCPGDVVLVRSPVVPRRIVTKRVI--------GMEGDRVSYV 57 (122)
Q Consensus 22 ~~~~~GDiVv~~~p~~~~~~~iKRV~--------a~pGd~v~~~ 57 (122)
+.++.||-|.+.+.. ...-+|.+- |.+||.+.+.
T Consensus 24 G~i~~G~~v~i~P~~--~~~~V~si~~~~~~~~~a~aGd~v~l~ 65 (82)
T cd04089 24 GTIKKGDKLLVMPNK--TQVEVLSIYNEDVEVRYARPGENVRLR 65 (82)
T ss_pred eEEecCCEEEEeCCC--cEEEEEEEEECCEECCEECCCCEEEEE
Confidence 678999999888542 356677776 7888888875
No 54
>PF00238 Ribosomal_L14: Ribosomal protein L14p/L23e; InterPro: IPR000218 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 L14 is one of the proteins from the large ribosomal subunit. In eubacteria, L14 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins, which have been grouped on the basis of sequence similarities []. Based on amino-acid sequence homology, it is predicted that ribosomal protein L14 is a member of a recently identified family of structurally related RNA-binding proteins []. L14 is a protein of 119 to 137 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3IZR_M 4A1C_J 4A1E_J 4A1A_J 4A17_J 1VSP_I 3D5D_O 1VSA_I 3MRZ_K 3F1F_O ....
Probab=43.06 E-value=19 Score=24.25 Aligned_cols=31 Identities=19% Similarity=0.239 Sum_probs=24.3
Q ss_pred ceEEeeCCeEEEeeCCCCCCCCCCceecccCC
Q 033291 67 ETVVVPQGHVWIEGDNIYESNDSRKFGAVPYG 98 (122)
Q Consensus 67 ~~~~vp~~~~~v~gdn~~~S~DSR~~G~V~~~ 98 (122)
......+|.+-++.++. ....+|-+||||.+
T Consensus 75 ~~i~F~~Na~VLln~~~-~p~GtrI~Gpv~~e 105 (122)
T PF00238_consen 75 SFIKFDDNAVVLLNKKG-NPLGTRIFGPVPRE 105 (122)
T ss_dssp EEEEESSEEEEEEETTS-SBSSSSBCSEEEHH
T ss_pred cEEEeCCccEEEEcCCC-CEeeeEEEeeehHH
Confidence 34556677788888775 79999999999864
No 55
>cd05792 S1_eIF1AD_like S1_eIF1AD_like: eukaryotic translation initiation factor 1A domain containing protein (eIF1AD)-like, S1-like RNA-binding domain. eIF1AD is also known as MGC11102 protein. Little is known about the function of eIF1AD. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins, including translation initiation factor IF1A (also referred to as eIF1A in eukaryotes). eIF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors.
Probab=42.72 E-value=22 Score=22.15 Aligned_cols=11 Identities=45% Similarity=0.679 Sum_probs=8.2
Q ss_pred CCCCcEEEEEc
Q 033291 24 VCPGDVVLVRS 34 (122)
Q Consensus 24 ~~~GDiVv~~~ 34 (122)
+++||+|+..+
T Consensus 39 IkrGd~VlV~p 49 (78)
T cd05792 39 IKRGDFVLVEP 49 (78)
T ss_pred EEeCCEEEEEe
Confidence 67888887764
No 56
>KOG4146 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=41.93 E-value=37 Score=22.02 Aligned_cols=27 Identities=22% Similarity=0.230 Sum_probs=13.4
Q ss_pred CCCEEEEEeccCC-----CCCCCCCcEEEEEc
Q 033291 8 TGDLVLAERISTR-----FNKVCPGDVVLVRS 34 (122)
Q Consensus 8 ~Gd~vlv~~~~~~-----~~~~~~GDiVv~~~ 34 (122)
+|-.++++...+. ...++.||.|+|-+
T Consensus 65 pGii~lINd~DWEllekedy~ledgD~ivfiS 96 (101)
T KOG4146|consen 65 PGIIVLINDMDWELLEKEDYPLEDGDHIVFIS 96 (101)
T ss_pred CcEEEEEeccchhhhcccccCcccCCEEEEEE
Confidence 4555555554431 12456666666653
No 57
>cd03698 eRF3_II_like eRF3_II_like: domain similar to domain II of the eukaryotic class II release factor (eRF3). In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribsome. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM
Probab=41.88 E-value=78 Score=19.13 Aligned_cols=34 Identities=21% Similarity=0.379 Sum_probs=25.3
Q ss_pred CCCCCCcEEEEEcCCCCCceeEEEEE--------EcCCCEEEEe
Q 033291 22 NKVCPGDVVLVRSPVVPRRIVTKRVI--------GMEGDRVSYV 57 (122)
Q Consensus 22 ~~~~~GDiVv~~~p~~~~~~~iKRV~--------a~pGd~v~~~ 57 (122)
+.++.||-|.+.+.. ...-||.+. |.+||.+.+.
T Consensus 25 G~i~~Gd~v~i~P~~--~~~~V~si~~~~~~~~~a~aGd~v~~~ 66 (83)
T cd03698 25 GSIQKGDTLLVMPSK--ESVEVKSIYVDDEEVDYAVAGENVRLK 66 (83)
T ss_pred eEEeCCCEEEEeCCC--cEEEEEEEEECCeECCEECCCCEEEEE
Confidence 678899999887542 345677766 8889988875
No 58
>PF10030 DUF2272: Uncharacterized protein conserved in bacteria (DUF2272); InterPro: IPR019262 This is a domain of unknown function found in proteins of unknown function.
Probab=41.74 E-value=1.3e+02 Score=21.68 Aligned_cols=39 Identities=18% Similarity=0.217 Sum_probs=25.6
Q ss_pred CCCCCCcEEEEEcCCC------------CCceeEEEEEE---cCCCEEEEecCC
Q 033291 22 NKVCPGDVVLVRSPVV------------PRRIVTKRVIG---MEGDRVSYVADP 60 (122)
Q Consensus 22 ~~~~~GDiVv~~~p~~------------~~~~~iKRV~a---~pGd~v~~~~~~ 60 (122)
..|+.||+|.+..... .-...+--|++ ..|+++....+.
T Consensus 92 y~P~~GDlIc~~R~~~~~~~~~~~~~~~~~~~HcdIVVa~~~~d~~~v~~IGGN 145 (183)
T PF10030_consen 92 YKPRPGDLICYDRGRSKTYDFASLPTSGGFPSHCDIVVAVNVVDGRTVTTIGGN 145 (183)
T ss_pred CCCCCCCEEEecCCCCcccchhhhccCCCCCCceeEEEeeccCCCCEEEEEcCc
Confidence 4789999999875431 12346667777 666777766543
No 59
>PLN00208 translation initiation factor (eIF); Provisional
Probab=40.16 E-value=26 Score=24.42 Aligned_cols=10 Identities=40% Similarity=0.926 Sum_probs=5.4
Q ss_pred CCCCcEEEEE
Q 033291 24 VCPGDVVLVR 33 (122)
Q Consensus 24 ~~~GDiVv~~ 33 (122)
+++||+|++.
T Consensus 71 I~~GD~VlVe 80 (145)
T PLN00208 71 IAAGDIILVG 80 (145)
T ss_pred ecCCCEEEEE
Confidence 4555555554
No 60
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=39.50 E-value=27 Score=24.63 Aligned_cols=10 Identities=40% Similarity=0.780 Sum_probs=4.8
Q ss_pred CCCCcEEEEE
Q 033291 24 VCPGDVVLVR 33 (122)
Q Consensus 24 ~~~GDiVv~~ 33 (122)
+..||+|++.
T Consensus 71 I~~GD~VlVe 80 (155)
T PTZ00329 71 INIGDIILVS 80 (155)
T ss_pred ecCCCEEEEe
Confidence 4445555544
No 61
>KOG4226 consensus Adaptor protein NCK/Dock, contains SH2 and SH3 domains [Signal transduction mechanisms]
Probab=39.46 E-value=59 Score=25.43 Aligned_cols=40 Identities=23% Similarity=0.275 Sum_probs=29.8
Q ss_pred ceEEeeCCeEEEeeCCCCC---CCCCC-----ceecccCCCeeEEEEE
Q 033291 67 ETVVVPQGHVWIEGDNIYE---SNDSR-----KFGAVPYGLIEGRVFL 106 (122)
Q Consensus 67 ~~~~vp~~~~~v~gdn~~~---S~DSR-----~~G~V~~~~I~Gkv~~ 106 (122)
....||.+++-|+.|+... +-+|- +-||.+..+..|+-|+
T Consensus 237 ~vGLVPrNYv~vl~d~~~ts~~~~~s~~pq~sgn~p~~sg~~ag~~WY 284 (379)
T KOG4226|consen 237 QVGLVPRNYVVVLSDGPSTSKALHPSHAPQISGNGPSSSGRFAGRPWY 284 (379)
T ss_pred ccceeecceEEEeccCccccccCCccccccccCCCCCccccccCCcce
Confidence 4578999999999999844 23441 3588888888887766
No 62
>PF04319 NifZ: NifZ domain; InterPro: IPR007415 NifZ is a short protein is found in the nif (nitrogen fixation) operon. It is required for the maturation of the nitrogenase MoFe protein. In the absence of NifZ, only one of the two P-clusters of the MoFe protein is matured to the ultimate [8Fe-7S] structure. The other P-cluster site in the protein contains a [4Fe-4S] cluster pair, suggesting that NifZ is specifically required for the formation of the second P-cluster [, , ].; GO: 0009399 nitrogen fixation
Probab=39.24 E-value=66 Score=19.90 Aligned_cols=31 Identities=26% Similarity=0.309 Sum_probs=21.0
Q ss_pred CccccCCCCCEEEEEeccCC---CCCCCCCcEEEE
Q 033291 1 MLPTINLTGDLVLAERISTR---FNKVCPGDVVLV 32 (122)
Q Consensus 1 M~Ptl~~~Gd~vlv~~~~~~---~~~~~~GDiVv~ 32 (122)
|.|.++ -||.|.+.+-... +.....|++.+-
T Consensus 1 ~~p~f~-~G~~V~a~~~irNDGt~Pg~~~g~lLv~ 34 (75)
T PF04319_consen 1 MPPRFE-WGDKVRARKDIRNDGTFPGKEIGELLVR 34 (75)
T ss_pred CCCccC-CCCEEEEEEEeEcCCCCCCCCCCCEEEc
Confidence 899998 8999998875432 233455555553
No 63
>PRK10507 bifunctional glutathionylspermidine amidase/glutathionylspermidine synthetase; Provisional
Probab=38.68 E-value=1.6e+02 Score=25.37 Aligned_cols=59 Identities=10% Similarity=0.053 Sum_probs=38.1
Q ss_pred CCCCCCCcEEEEEcC-CCCCceeEEEEEEcCCCEEEEecCCCC---------CCCCceEEeeCCeEEEe
Q 033291 21 FNKVCPGDVVLVRSP-VVPRRIVTKRVIGMEGDRVSYVADPKS---------SDKFETVVVPQGHVWIE 79 (122)
Q Consensus 21 ~~~~~~GDiVv~~~p-~~~~~~~iKRV~a~pGd~v~~~~~~~~---------~~~~~~~~vp~~~~~v~ 79 (122)
...|+.||++++... +...-=.|.=|+.+-.+.|.|..+... .......+.-.|.|++.
T Consensus 109 ~~~P~~gdLlI~~~~~~~~p~GHVAVVt~V~~~~V~iaeQN~~~~~w~~~~~~sR~l~l~~~~g~~~i~ 177 (619)
T PRK10507 109 PRAPEAGALLIWDKGGEFKDTGHVAIITQLHGNKVRIAEQNVIHSPLPQGQQWTRELEMVVENGCYTLK 177 (619)
T ss_pred CCCCCCCcEEEeCCCCCCCCCceEEEEEEEcCCeEEEEeccccccCCCCCCCeeeEEEEEEeCCEEEEE
Confidence 368999999999943 211233677778888899999765321 11123344467888876
No 64
>cd03694 GTPBP_II Domain II of the GP-1 family of GTPase. This group includes proteins similar to GTPBP1 and GTPBP2. GTPB1 is structurally, related to elongation factor 1 alpha, a key component of protein biosynthesis machinery. Immunohistochemical analyses on mouse tissues revealed that GTPBP1 is expressed in some neurons and smooth muscle cells of various organs as well as macrophages. Immunofluorescence analyses revealed that GTPBP1 is localized exclusively in cytoplasm and shows a diffuse granular network forming a gradient from the nucleus to the periphery of the cells in smooth muscle cell lines and macrophages. No significant difference was observed in the immune response to protein antigen between mutant mice and wild-type mice, suggesting normal function of antigen-presenting cells of the mutant mice. The absence of an eminent phenotype in GTPBP1-deficient mice may be due to functional compensation by GTPBP2, which is similar to GTPBP1 in structure and tissue distribution.
Probab=38.60 E-value=83 Score=19.32 Aligned_cols=37 Identities=19% Similarity=0.192 Sum_probs=25.8
Q ss_pred CCCCCCCcEEEEEcCCCC--CceeEEEEE--------EcCCCEEEEe
Q 033291 21 FNKVCPGDVVLVRSPVVP--RRIVTKRVI--------GMEGDRVSYV 57 (122)
Q Consensus 21 ~~~~~~GDiVv~~~p~~~--~~~~iKRV~--------a~pGd~v~~~ 57 (122)
.+.++.||-+.+.+..+. ...-||.+- |.+||.+.+.
T Consensus 24 ~G~v~~g~~v~~~P~~~g~~~~~~V~sI~~~~~~~~~a~aGd~v~l~ 70 (87)
T cd03694 24 KGVIRLGDTLLLGPDQDGSFRPVTVKSIHRNRSPVRVVRAGQSASLA 70 (87)
T ss_pred cCEEeCCCEEEECCCCCCCEeEEEEEEEEECCeECCEECCCCEEEEE
Confidence 367899999998764211 245666665 7888888875
No 65
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=38.53 E-value=1.3e+02 Score=27.35 Aligned_cols=35 Identities=31% Similarity=0.277 Sum_probs=20.6
Q ss_pred cCCCEEEEecCCCCCCCCceEEeeCCeEEEeeCCC
Q 033291 49 MEGDRVSYVADPKSSDKFETVVVPQGHVWIEGDNI 83 (122)
Q Consensus 49 ~pGd~v~~~~~~~~~~~~~~~~vp~~~~~v~gdn~ 83 (122)
.|||+|.+..+.......--..|-++.++++.|-.
T Consensus 461 ~~GDhVKVi~G~~eG~tGlVvrVe~~~vi~~Sd~t 495 (1024)
T KOG1999|consen 461 EPGDHVKVIAGRYEGDTGLVVRVEQGDVILLSDLT 495 (1024)
T ss_pred cCCCeEEEEeccccCCcceEEEEeCCeEEEEecCc
Confidence 35555555444333444455677778888877764
No 66
>cd03703 aeIF5B_II aeIF5B_II: This family represents the domain II of archeal and eukaryotic aeIF5B. aeIF5B is a homologue of prokaryotic Initiation Factor 2 (IF2). Disruption of the eIF5B gene (FUN12) in yeast causes a severe slow-growth phenotype, associated with a defect in translation. eIF5B has a function analogous to prokaryotic IF2 in mediating the joining of joining of 60S subunits. The eIF5B consists of three N-terminal domains (I, II, II) connected by a long helix to domain IV. Domain I is a G domain, domain II and IV are beta-barrels and domain III has a novel alpha-beta-alpha sandwich fold. The G domain and the beta-barrel domain II display a similar structure and arrangement to the homologous domains of EF1A, eEF1A and aeIF2gamma.
Probab=38.26 E-value=44 Score=22.19 Aligned_cols=14 Identities=21% Similarity=0.361 Sum_probs=11.5
Q ss_pred CCCCCCcEEEEEcC
Q 033291 22 NKVCPGDVVLVRSP 35 (122)
Q Consensus 22 ~~~~~GDiVv~~~p 35 (122)
+.++.||.|++...
T Consensus 25 GtL~~GD~Iv~g~~ 38 (110)
T cd03703 25 GTLREGDTIVVCGL 38 (110)
T ss_pred CeEecCCEEEEccC
Confidence 67899999999754
No 67
>PRK14533 groES co-chaperonin GroES; Provisional
Probab=36.60 E-value=1.1e+02 Score=19.40 Aligned_cols=84 Identities=18% Similarity=0.171 Sum_probs=45.5
Q ss_pred cCCCCCEEEEEeccCCCCCCCCCcEEEEEcCCCCCceeEEEEEEcC-CCEEEEecCCCCCCCCceEEeeCCeEEEeeCCC
Q 033291 5 INLTGDLVLAERISTRFNKVCPGDVVLVRSPVVPRRIVTKRVIGME-GDRVSYVADPKSSDKFETVVVPQGHVWIEGDNI 83 (122)
Q Consensus 5 l~~~Gd~vlv~~~~~~~~~~~~GDiVv~~~p~~~~~~~iKRV~a~p-Gd~v~~~~~~~~~~~~~~~~vp~~~~~v~gdn~ 83 (122)
|.|-||+|+|.+... ..-..|-|++=... ........|+|+. |.. ..+..|..|..-+.++..
T Consensus 3 i~Pl~DRVLVk~~~~--e~~T~gGI~Lp~~a--~ek~~~G~VvavG~g~~------------~~~~~Vk~GD~Vl~~~y~ 66 (91)
T PRK14533 3 VIPLGERLLIKPIKE--EKKTEGGIVLPDSA--KEKPMKAEVVAVGKLDD------------EEDFDIKVGDKVIFSKYA 66 (91)
T ss_pred ceEcCCEEEEEEccc--cceecccEEecccc--cCCcceEEEEEECCCCc------------cccccccCCCEEEEccCC
Confidence 455799999988642 34556777664332 2345566776664 221 112334444444444433
Q ss_pred C--CCCCCCceecccCCCeeEEE
Q 033291 84 Y--ESNDSRKFGAVPYGLIEGRV 104 (122)
Q Consensus 84 ~--~S~DSR~~G~V~~~~I~Gkv 104 (122)
- --+|...|=.++.++|+|++
T Consensus 67 g~ev~~~~~~y~iv~e~DILa~i 89 (91)
T PRK14533 67 GTEIKIDDEDYIIIDVNDILAKI 89 (91)
T ss_pred CeEEEECCEEEEEEEhHhEEEEe
Confidence 1 12455556667777777764
No 68
>PF11320 DUF3122: Protein of unknown function (DUF3122); InterPro: IPR021469 This family of proteins with unknown function appear to be restricted to Cyanobacteria.
Probab=36.30 E-value=1.4e+02 Score=20.49 Aligned_cols=45 Identities=22% Similarity=0.292 Sum_probs=32.5
Q ss_pred CCCEEEEEeccCCCCCCCCCcEEEEEcCCC-CCceeEEEEEEcCCC
Q 033291 8 TGDLVLAERISTRFNKVCPGDVVLVRSPVV-PRRIVTKRVIGMEGD 52 (122)
Q Consensus 8 ~Gd~vlv~~~~~~~~~~~~GDiVv~~~p~~-~~~~~iKRV~a~pGd 52 (122)
+|..+.=++-+.+...-+.-.+|+|+.... ....+.=|++|-||.
T Consensus 10 pgq~~yrS~qsLrD~~g~sWQvV~fkr~~~~~~~~i~LRLVGfPG~ 55 (134)
T PF11320_consen 10 PGQVLYRSRQSLRDQDGNSWQVVLFKRIKPGQVKPINLRLVGFPGS 55 (134)
T ss_pred CCcEEEEeeeeecCCCCCceEEEEEEecCCCCCCceEEEEeeCCCc
Confidence 455555555444556678889999997543 356788999999998
No 69
>cd04710 BAH_fungalPHD BAH, or Bromo Adjacent Homology domain, as present in fungal proteins containing PHD domains. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=36.28 E-value=60 Score=22.13 Aligned_cols=28 Identities=11% Similarity=0.088 Sum_probs=21.6
Q ss_pred CCCCCCcEEEEEcCCCCCceeEEEEEEc
Q 033291 22 NKVCPGDVVLVRSPVVPRRIVTKRVIGM 49 (122)
Q Consensus 22 ~~~~~GDiVv~~~p~~~~~~~iKRV~a~ 49 (122)
..++.||-|.+.+......++|.||..+
T Consensus 10 ~~~~vgD~Vyv~~~~~~ePyyIgrI~e~ 37 (135)
T cd04710 10 ELLKVNDHIYMSSEPPGEPYYIGRIMEF 37 (135)
T ss_pred eEEeCCCEEEEecCCCCCCCEEEEEEEE
Confidence 4688999999997544456789999774
No 70
>cd06555 ASCH_PF0470_like ASC-1 homology domain, subfamily similar to Pyrococcus furiosus Pf0470. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation.
Probab=36.15 E-value=75 Score=20.98 Aligned_cols=26 Identities=15% Similarity=0.256 Sum_probs=17.2
Q ss_pred CCCCCCcEEEEEcCCCCCceeEEEEEE
Q 033291 22 NKVCPGDVVLVRSPVVPRRIVTKRVIG 48 (122)
Q Consensus 22 ~~~~~GDiVv~~~p~~~~~~~iKRV~a 48 (122)
+.++.||.++|..-.+ +..+.-+|+.
T Consensus 30 ~~ikvGD~I~f~~~~~-~~~l~v~V~~ 55 (109)
T cd06555 30 QQIKVGDKILFNDLDT-GQQLLVKVVD 55 (109)
T ss_pred hcCCCCCEEEEEEcCC-CcEEEEEEEE
Confidence 5799999999986432 3445555544
No 71
>cd03697 EFTU_II EFTU_II: Elongation factor Tu domain II. Elongation factors Tu (EF-Tu) are three-domain GTPases with an essential function in the elongation phase of mRNA translation. The GTPase center of EF-Tu is in the N-terminal domain (domain I), also known as the catalytic or G-domain. The G-domain is composed of about 200 amino acid residues, arranged into a predominantly parallel six-stranded beta-sheet core surrounded by seven a-helices. Non-catalytic domains II and III are beta-barrels of seven and six, respectively, antiparallel beta-strands that share an extended interface. Either non-catalytic domain is composed of about 100 amino acid residues. EF-Tu proteins exist in two principal conformations: in a compact one, EF-Tu*GTP, with tight interfaces between all three domains and a high affinity for aminoacyl-tRNA, and in an open one, EF-Tu*GDP, with essentially no G-domain-domain II interactions and a low affinity for aminoacyl-tRNA. EF-Tu has approximately a 100-fold higher
Probab=35.82 E-value=1e+02 Score=18.77 Aligned_cols=36 Identities=17% Similarity=0.147 Sum_probs=24.0
Q ss_pred CCCCCCcEEEEEcCCCCCceeEEEEE--------EcCCCEEEEe
Q 033291 22 NKVCPGDVVLVRSPVVPRRIVTKRVI--------GMEGDRVSYV 57 (122)
Q Consensus 22 ~~~~~GDiVv~~~p~~~~~~~iKRV~--------a~pGd~v~~~ 57 (122)
+.++.||-|.+.++......-||.+- |.|||.+.+.
T Consensus 25 G~v~~gd~v~~~p~~~~~~~~V~si~~~~~~~~~a~~G~~v~l~ 68 (87)
T cd03697 25 GTIKVGDEVEIVGFGETLKTTVTGIEMFRKTLDEAEAGDNVGVL 68 (87)
T ss_pred CCCccCCEEEEeCCCCCceEEEEEEEECCcCCCEECCCCEEEEE
Confidence 68899999988754222334455543 6688888876
No 72
>PTZ00414 10 kDa heat shock protein; Provisional
Probab=35.25 E-value=1.3e+02 Score=19.61 Aligned_cols=43 Identities=16% Similarity=0.250 Sum_probs=25.4
Q ss_pred cccCCCCCEEEEEeccCCCCCCCCCcEEEEEcCCCCCceeEEEEEEc
Q 033291 3 PTINLTGDLVLAERISTRFNKVCPGDVVLVRSPVVPRRIVTKRVIGM 49 (122)
Q Consensus 3 Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVv~~~p~~~~~~~iKRV~a~ 49 (122)
+.|+|-||+|+|.+... .+-..|-|++=... ..+.....|+|+
T Consensus 10 ~~ikPL~dRVLVk~~~~--e~kT~gGIiLP~sa--kekp~~g~VvAV 52 (100)
T PTZ00414 10 KKLQPLGQRVLVKRTLA--AKQTKAGVLIPEQV--AGKVNEGTVVAV 52 (100)
T ss_pred ccceecCCEEEEEEccc--ccccccCEEccccc--ccCCceeEEEEE
Confidence 34666799999988642 34556776663322 233445556655
No 73
>cd04709 BAH_MTA BAH, or Bromo Adjacent Homology domain, as present in MTA1 and similar proteins. The Metastasis-associated protein MTA1 is part of the NURD (nucleosome remodeling and deacetylating) complex and plays a role in cellular transformation and metastasis. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=34.81 E-value=60 Score=22.99 Aligned_cols=25 Identities=20% Similarity=0.228 Sum_probs=19.5
Q ss_pred CCCCCceecccCCCeeEEEEEEEeC
Q 033291 86 SNDSRKFGAVPYGLIEGRVFLRIWP 110 (122)
Q Consensus 86 S~DSR~~G~V~~~~I~Gkv~~~~~p 110 (122)
-+=|++.-.+|.+.|.||.......
T Consensus 84 LF~S~~~d~~p~~~IrGKC~V~~~~ 108 (164)
T cd04709 84 LFLSRQVETLPATHIRGKCSVTLLN 108 (164)
T ss_pred eEEecccccccHHHeeeeEEEEEeh
Confidence 4556678889999999999876543
No 74
>PRK00809 hypothetical protein; Provisional
Probab=34.29 E-value=42 Score=23.16 Aligned_cols=28 Identities=21% Similarity=0.468 Sum_probs=17.8
Q ss_pred CCCCCCcEEEEEcCC-CCCceeEEEEEEc
Q 033291 22 NKVCPGDVVLVRSPV-VPRRIVTKRVIGM 49 (122)
Q Consensus 22 ~~~~~GDiVv~~~p~-~~~~~~iKRV~a~ 49 (122)
+.++.||.++|.++. ..+....+.++|+
T Consensus 33 r~Mk~GD~v~fYhs~~~~~~~~~~~ivgi 61 (144)
T PRK00809 33 EKVKPGDKLIIYVSQEYGAERLPGKIVGI 61 (144)
T ss_pred hhCCCCCEEEEEECCccCCCCCCceEEEE
Confidence 359999999999885 1122233455554
No 75
>cd04370 BAH BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in mammalian DNA methyltransferases and the MTA1 subunits of histone deacetylase complexes. A BAH domain is also found in Yeast Sir3p and in the origin receptor complex protein 1 (Orc1p), where it was found to interact with the N-terminal lobe of the silence information regulator 1 protein (Sir1p), confirming the initial hypothesis that BAH plays a role in protein-protein interactions.
Probab=34.22 E-value=57 Score=20.60 Aligned_cols=78 Identities=14% Similarity=0.134 Sum_probs=41.4
Q ss_pred CCCCCcEEEEEcCCC--CCceeEEEEEEcCCC---EEEEecC----CCCCCCCceEEeeCCeEEEeeCCCCCCCCCCcee
Q 033291 23 KVCPGDVVLVRSPVV--PRRIVTKRVIGMEGD---RVSYVAD----PKSSDKFETVVVPQGHVWIEGDNIYESNDSRKFG 93 (122)
Q Consensus 23 ~~~~GDiVv~~~p~~--~~~~~iKRV~a~pGd---~v~~~~~----~~~~~~~~~~~vp~~~~~v~gdn~~~S~DSR~~G 93 (122)
.++.||.|++..+.. ....+|.||..+--+ ...+... +............++++|+..+ .-
T Consensus 3 ~y~vgd~V~v~~~~~~~~~~~~i~~I~~i~~~~~~~~~~~v~wf~rp~e~~~~~~~~~~~~Elf~s~~----------~~ 72 (123)
T cd04370 3 TYEVGDSVYVEPDDSIKSDPPYIARIEELWEDTNGSKQVKVRWFYRPEETPKGLSPFALRRELFLSDH----------LD 72 (123)
T ss_pred EEecCCEEEEecCCcCCCCCCEEEEEeeeeECCCCCEEEEEEEEEchhHhccccccccccceeEEecC----------cc
Confidence 356788888876643 345777777665322 1222110 0000000111345567776432 22
Q ss_pred cccCCCeeEEEEEEEeC
Q 033291 94 AVPYGLIEGRVFLRIWP 110 (122)
Q Consensus 94 ~V~~~~I~Gkv~~~~~p 110 (122)
-++.+.|.|++.....+
T Consensus 73 ~i~v~~I~gkc~V~~~~ 89 (123)
T cd04370 73 EIPVESIIGKCKVLFVS 89 (123)
T ss_pred ccCHHHhccccEEEech
Confidence 58888999999876654
No 76
>TIGR02219 phage_NlpC_fam putative phage cell wall peptidase, NlpC/P60 family. Members of this family show sequence similarity to members of the NlpC/P60 family described by Pfam model pfam00877 and by Anantharaman and Aravind (PubMed:12620121). The NlpC/P60 family includes a number of characterized bacterial cell wall hydrolases. Members of this related family are all found in prophage regions of bacterial genomes.
Probab=34.21 E-value=69 Score=21.50 Aligned_cols=13 Identities=38% Similarity=0.690 Sum_probs=11.1
Q ss_pred CCCCCCcEEEEEc
Q 033291 22 NKVCPGDVVLVRS 34 (122)
Q Consensus 22 ~~~~~GDiVv~~~ 34 (122)
.++++||+|.|+.
T Consensus 75 ~~~qpGDlvff~~ 87 (134)
T TIGR02219 75 DAAQPGDVLVFRW 87 (134)
T ss_pred hcCCCCCEEEEee
Confidence 4689999999984
No 77
>PF01878 EVE: EVE domain; InterPro: IPR002740 The EVE domain is part of the wider PUA domain superfamily. The function of this domain is not known but, given the structural similarities to PUA, is likely to involve RNA binding []. ; PDB: 2G2X_B 2AR1_A 3EOP_A 2EVE_A 2HD9_A 2ZBN_A 1WMM_A 2P5D_A 2GBS_A 1ZCE_A.
Probab=34.18 E-value=53 Score=22.06 Aligned_cols=15 Identities=27% Similarity=0.465 Sum_probs=10.2
Q ss_pred CCCCCCcEEEEEcCC
Q 033291 22 NKVCPGDVVLVRSPV 36 (122)
Q Consensus 22 ~~~~~GDiVv~~~p~ 36 (122)
+.++.||.|+|.++.
T Consensus 38 ~~mk~GD~vifY~s~ 52 (143)
T PF01878_consen 38 KRMKPGDKVIFYHSG 52 (143)
T ss_dssp HC--TT-EEEEEETS
T ss_pred hcCCCCCEEEEEEcC
Confidence 479999999999875
No 78
>COG4127 Uncharacterized conserved protein [Function unknown]
Probab=33.27 E-value=42 Score=26.14 Aligned_cols=26 Identities=27% Similarity=0.396 Sum_probs=21.5
Q ss_pred CCCCCCcEEEEEcCCCCCceeEEEEEE
Q 033291 22 NKVCPGDVVLVRSPVVPRRIVTKRVIG 48 (122)
Q Consensus 22 ~~~~~GDiVv~~~p~~~~~~~iKRV~a 48 (122)
.++++||+|+...+.. ++++|.+|.+
T Consensus 71 neI~KGDlvi~y~k~~-r~y~IGkVts 96 (318)
T COG4127 71 NEIQKGDLVITYSKSN-RTYLIGKVTS 96 (318)
T ss_pred HHhccCcEEEeecccC-ceEEEEEecC
Confidence 4799999999988744 7889999865
No 79
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=32.97 E-value=88 Score=20.91 Aligned_cols=28 Identities=25% Similarity=0.093 Sum_probs=19.9
Q ss_pred CCCCCCcEEEEEcCCCCCceeEEEEEEc
Q 033291 22 NKVCPGDVVLVRSPVVPRRIVTKRVIGM 49 (122)
Q Consensus 22 ~~~~~GDiVv~~~p~~~~~~~iKRV~a~ 49 (122)
..++.||-|+..++.....+.=..|++.
T Consensus 54 ~~L~~GD~VLA~~~~~~~~Y~Pg~V~~~ 81 (124)
T PF15057_consen 54 HSLQVGDKVLAPWEPDDCRYGPGTVIAG 81 (124)
T ss_pred CcCCCCCEEEEecCcCCCEEeCEEEEEC
Confidence 5788999999887755445454778754
No 80
>PF00278 Orn_DAP_Arg_deC: Pyridoxal-dependent decarboxylase, C-terminal sheet domain; InterPro: IPR022643 These enzymes are collectively known as group IV decarboxylases []. Pyridoxal-dependent decarboxylases acting on ornithine, lysine, arginine and related substrates can be classified into two different families on the basis of sequence similarities [, ]. Members of this family while most probably evolutionary related, do not share extensive regions of sequence similarities. The proteins contain a conserved lysine residue which is known, in mouse ODC [], to be the site of attachment of the pyridoxal-phosphate group. The proteins also contain a stretch of three consecutive glycine residues and has been proposed to be part of a substrate- binding region []. This entry represents the C-terminal region of the Orn/DAP/Arg decarboxylases.; GO: 0003824 catalytic activity; PDB: 1TWI_B 1TUF_A 3MT1_A 3N2B_C 2O0T_A 1HKW_A 1HKV_A 3VAB_A 3N2O_A 7ODC_A ....
Probab=32.24 E-value=72 Score=20.22 Aligned_cols=30 Identities=20% Similarity=0.387 Sum_probs=17.9
Q ss_pred cccCCCCCEEEEEeccCCCCCCCCCcEEEEEcC
Q 033291 3 PTINLTGDLVLAERISTRFNKVCPGDVVLVRSP 35 (122)
Q Consensus 3 Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVv~~~p 35 (122)
||-. .+|.+.-.... ..+++.||+++|..-
T Consensus 65 ptC~-~~D~i~~~~~l--P~~l~~GD~l~f~~~ 94 (116)
T PF00278_consen 65 PTCD-SGDVIARDVML--PKELEVGDWLVFENM 94 (116)
T ss_dssp SSSS-TTSEEEEEEEE--ESTTTTT-EEEESS-
T ss_pred CCcC-CCceEeeeccC--CCCCCCCCEEEEecC
Confidence 4554 67777643322 137899999999853
No 81
>PRK04313 30S ribosomal protein S4e; Validated
Probab=32.07 E-value=2.2e+02 Score=21.46 Aligned_cols=57 Identities=16% Similarity=0.169 Sum_probs=33.2
Q ss_pred CCCCCcEEEEEcCCCCCceeEEEEEEcCCCEEEEecCCC-----------------------CCCCCceEEeeCCeEEEe
Q 033291 23 KVCPGDVVLVRSPVVPRRIVTKRVIGMEGDRVSYVADPK-----------------------SSDKFETVVVPQGHVWIE 79 (122)
Q Consensus 23 ~~~~GDiVv~~~p~~~~~~~iKRV~a~pGd~v~~~~~~~-----------------------~~~~~~~~~vp~~~~~v~ 79 (122)
.++.||-|++..|++ .++.-+---+|..+.+..+.. .......+.-..+++||.
T Consensus 150 ~~k~~Dtv~i~l~~~---kI~~~i~fe~G~l~~itgG~n~GriG~I~~i~~~~~~~~~~V~i~d~~G~~F~T~~~~vfvI 226 (237)
T PRK04313 150 DYKTGDSLLISLPEQ---EIVDHIPFEEGNLAIITGGKHVGEIGKIKEIEVTKSSKPNIVTLEDKDGEKFETILDYVFVI 226 (237)
T ss_pred ccccCCEEEEECCCC---ceeEEEecCCCCEEEEECCeeeeeEEEEEEEEEccCCCCcEEEEEcCCCCEEEEEeeeEEEE
Confidence 677888888887643 344444445555555443311 011123467777889999
Q ss_pred eCC
Q 033291 80 GDN 82 (122)
Q Consensus 80 gdn 82 (122)
|.+
T Consensus 227 G~~ 229 (237)
T PRK04313 227 GKE 229 (237)
T ss_pred cCC
Confidence 964
No 82
>PLN02289 ribulose-bisphosphate carboxylase small chain
Probab=31.75 E-value=45 Score=24.00 Aligned_cols=28 Identities=18% Similarity=0.159 Sum_probs=22.3
Q ss_pred CCceEEeeCCeEEEeeCCCCCCCCCCce
Q 033291 65 KFETVVVPQGHVWIEGDNIYESNDSRKF 92 (122)
Q Consensus 65 ~~~~~~vp~~~~~v~gdn~~~S~DSR~~ 92 (122)
.+-+++.++|.++....+....+|.|||
T Consensus 95 pclEf~~~~~~~~r~~~~s~~yyD~rYW 122 (176)
T PLN02289 95 PCLEFELEHGFVYREHHRSPGYYDGRYW 122 (176)
T ss_pred eeeeeccCCceeEecCCCCCCcccCcee
Confidence 3566777888888888777788999997
No 83
>COG4043 Preprotein translocase subunit Sec61beta [Intracellular trafficking, secretion, and vesicular transport]
Probab=31.29 E-value=84 Score=20.75 Aligned_cols=14 Identities=21% Similarity=0.598 Sum_probs=12.0
Q ss_pred CCCCCCCCcEEEEE
Q 033291 20 RFNKVCPGDVVLVR 33 (122)
Q Consensus 20 ~~~~~~~GDiVv~~ 33 (122)
..+.+++||.|+|.
T Consensus 30 krr~ik~GD~IiF~ 43 (111)
T COG4043 30 KRRQIKPGDKIIFN 43 (111)
T ss_pred hhcCCCCCCEEEEc
Confidence 34689999999998
No 84
>cd00320 cpn10 Chaperonin 10 Kd subunit (cpn10 or GroES); Cpn10 cooperates with chaperonin 60 (cpn60 or GroEL), an ATPase, to assist the folding and assembly of proteins and is found in eubacterial cytosol, as well as in the matrix of mitochondria and chloroplasts. It forms heptameric rings with a dome-like structure, forming a lid to the large cavity of the tetradecameric cpn60 cylinder and thereby tightly regulating release and binding of proteins to the cpn60 surface.
Probab=31.07 E-value=1.4e+02 Score=18.85 Aligned_cols=42 Identities=26% Similarity=0.419 Sum_probs=26.3
Q ss_pred cCCCCCEEEEEeccCCCCCCCCCcEEEEEcCCCCCceeEEEEEEcC
Q 033291 5 INLTGDLVLAERISTRFNKVCPGDVVLVRSPVVPRRIVTKRVIGME 50 (122)
Q Consensus 5 l~~~Gd~vlv~~~~~~~~~~~~GDiVv~~~p~~~~~~~iKRV~a~p 50 (122)
|.|-||+|+|.+... .+-..|-|++=.. .........|+|+.
T Consensus 2 i~Pl~DrVLV~~~~~--e~~T~~GI~Lp~~--~~~k~~~g~VvAVG 43 (93)
T cd00320 2 IKPLGDRVLVKRIEA--EEKTKGGIILPDS--AKEKPQEGKVVAVG 43 (93)
T ss_pred ceecCCEEEEEEccc--cceecceEEeCCC--cCCCceEEEEEEEC
Confidence 345689999998642 3455666665332 22456777787774
No 85
>cd04466 S1_YloQ_GTPase S1_YloQ_GTPase: YloQ GTase family (also known as YjeQ and CpgA), S1-like RNA-binding domain. Proteins in the YloQ GTase family bind the ribosome and have GTPase activity. The precise role of this family is unknown. The protein structure is composed of three domains: an N-terminal S1 domain, a central GTPase domain, and a C-terminal zinc finger domain. This N-terminal S1 domain binds ssRNA. The central GTPase domain contains nucleotide-binding signature motifs: G1 (walker A), G3 (walker B) and G4 motifs. Experiments show that the bacterial YloQ and YjeQ proteins have low intrinsic GTPase activity. The C-terminal zinc-finger domain has structural similarity to a portion of the DNA-repair protein Rad51. This suggests a possible role for this GTPase as a regulator of translation, perhaps as a translation initiation factor. This family is classified based on the N-terminal S1 domain.
Probab=30.55 E-value=1.1e+02 Score=17.43 Aligned_cols=13 Identities=23% Similarity=0.171 Sum_probs=9.5
Q ss_pred CCCCCcEEEEEcC
Q 033291 23 KVCPGDVVLVRSP 35 (122)
Q Consensus 23 ~~~~GDiVv~~~p 35 (122)
.+..||.|++..+
T Consensus 37 ~~~VGD~V~~~~~ 49 (68)
T cd04466 37 PPAVGDRVEFEPE 49 (68)
T ss_pred CCCCCcEEEEEEC
Confidence 4678888888754
No 86
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=30.43 E-value=55 Score=21.21 Aligned_cols=9 Identities=56% Similarity=0.914 Sum_probs=5.9
Q ss_pred CCCCcEEEE
Q 033291 24 VCPGDVVLV 32 (122)
Q Consensus 24 ~~~GDiVv~ 32 (122)
+++||+|++
T Consensus 58 I~~GD~VlV 66 (99)
T TIGR00523 58 IREGDVVIV 66 (99)
T ss_pred ecCCCEEEE
Confidence 566666666
No 87
>PRK02268 hypothetical protein; Provisional
Probab=28.99 E-value=59 Score=22.55 Aligned_cols=28 Identities=18% Similarity=0.310 Sum_probs=18.7
Q ss_pred CCCCCCcEEEEEcCCC--CCceeEEEEEEc
Q 033291 22 NKVCPGDVVLVRSPVV--PRRIVTKRVIGM 49 (122)
Q Consensus 22 ~~~~~GDiVv~~~p~~--~~~~~iKRV~a~ 49 (122)
+.++.||.|+|.+|.. .+...++.++|+
T Consensus 34 ~RmkpGD~ivyYsp~~~~~~~~~~qaftAi 63 (141)
T PRK02268 34 RRMKPGDWIIYYSPKTTFGGKDKLQAFTAI 63 (141)
T ss_pred hcCCCCCEEEEEeceEecCCCcccceEEEE
Confidence 4679999999988742 234455555554
No 88
>PF12059 DUF3540: Protein of unknown function (DUF3540); InterPro: IPR021927 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 212 to 238 amino acids in length. This protein has a conserved SCL sequence motif.
Probab=28.54 E-value=1.3e+02 Score=22.01 Aligned_cols=27 Identities=30% Similarity=0.362 Sum_probs=20.2
Q ss_pred CCCEEEEEeccCCCCCCCCCcEEEEEcC
Q 033291 8 TGDLVLAERISTRFNKVCPGDVVLVRSP 35 (122)
Q Consensus 8 ~Gd~vlv~~~~~~~~~~~~GDiVv~~~p 35 (122)
+|. +-+.+-..+.-.|..||.|++..+
T Consensus 20 ~G~-~~arrAaSCLl~P~~GD~VLv~~~ 46 (202)
T PF12059_consen 20 DGE-WRARRAASCLLEPAVGDTVLVSGV 46 (202)
T ss_pred CCE-EEEEeccccccCCCCCCEEEEeec
Confidence 344 666666667779999999999664
No 89
>TIGR03673 rpl14p_arch 50S ribosomal protein L14P. Part of the 50S ribosomal subunit. Forms a cluster with proteins L3 and L24e, part of which may contact the 16S rRNA in 2 intersubunit bridges.
Probab=27.69 E-value=2e+02 Score=19.62 Aligned_cols=32 Identities=19% Similarity=0.091 Sum_probs=24.9
Q ss_pred ceEEeeCCeEEEeeCCCCCCCCCCceecccCCC
Q 033291 67 ETVVVPQGHVWIEGDNIYESNDSRKFGAVPYGL 99 (122)
Q Consensus 67 ~~~~vp~~~~~v~gdn~~~S~DSR~~G~V~~~~ 99 (122)
..+..-+|.+-++.++. +-.-+|-||||+++.
T Consensus 85 s~i~FddNa~VLin~~~-~P~GTRI~GpV~rEl 116 (131)
T TIGR03673 85 TRVKFEDNAVVIVTPDG-EPKGTEIKGPVAREA 116 (131)
T ss_pred cEEEeCCcEEEEECCCC-CEeeeEEEccchHHH
Confidence 45666777777777665 678899999999876
No 90
>TIGR00739 yajC preprotein translocase, YajC subunit. While this protein is part of the preprotein translocase in Escherichia coli, it is not essential for viability or protein secretion. The N-terminus region contains a predicted membrane-spanning region followed by a region consisting almost entirely of residues with charged (acidic, basic, or zwitterionic) side chains. This small protein is about 100 residues in length, and is restricted to bacteria; however, this protein is absent from some lineages, including spirochetes and Mycoplasmas.
Probab=26.49 E-value=1.7e+02 Score=18.25 Aligned_cols=30 Identities=17% Similarity=0.180 Sum_probs=23.5
Q ss_pred CCCCCCcEEEEEcCCCCCceeEEEEEEcCCCEEEEe
Q 033291 22 NKVCPGDVVLVRSPVVPRRIVTKRVIGMEGDRVSYV 57 (122)
Q Consensus 22 ~~~~~GDiVv~~~p~~~~~~~iKRV~a~pGd~v~~~ 57 (122)
.++++||-|+... =+..+|+.+.+|++.+.
T Consensus 36 ~~L~~Gd~VvT~g------Gi~G~V~~i~d~~v~ve 65 (84)
T TIGR00739 36 ESLKKGDKVLTIG------GIIGTVTKIAENTIVIE 65 (84)
T ss_pred HhCCCCCEEEECC------CeEEEEEEEeCCEEEEE
Confidence 4789999999873 27788888888887765
No 91
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=26.41 E-value=1.6e+02 Score=18.22 Aligned_cols=30 Identities=33% Similarity=0.448 Sum_probs=18.1
Q ss_pred CCCCCcEEEEEcCC-----CCCceeEEEEEEcCCC
Q 033291 23 KVCPGDVVLVRSPV-----VPRRIVTKRVIGMEGD 52 (122)
Q Consensus 23 ~~~~GDiVv~~~p~-----~~~~~~iKRV~a~pGd 52 (122)
.++.||.|+++... ..+...+..|+...|.
T Consensus 5 ~Vk~Gd~ViV~~~~~~~~~~~~dWWmg~Vi~~~gg 39 (75)
T PF11302_consen 5 SVKPGDTVIVQDEQEVGQKQDKDWWMGQVIHCEGG 39 (75)
T ss_pred ccCCCCEEEEecCccccccCCCCcEEEEEEEEecc
Confidence 56778888887653 1235566666555443
No 92
>PF09285 Elong-fact-P_C: Elongation factor P, C-terminal; InterPro: IPR015365 These nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology []. ; GO: 0043043 peptide biosynthetic process, 0005737 cytoplasm; PDB: 1YBY_A 3OYY_B 1UEB_B 3HUW_V 3HUY_V 3A5Z_H.
Probab=26.22 E-value=1.4e+02 Score=17.28 Aligned_cols=29 Identities=21% Similarity=0.200 Sum_probs=15.9
Q ss_pred CCCEEEEEeccCCCCCCCCCcEEEEEcCCCCCceeEEE
Q 033291 8 TGDLVLAERISTRFNKVCPGDVVLVRSPVVPRRIVTKR 45 (122)
Q Consensus 8 ~Gd~vlv~~~~~~~~~~~~GDiVv~~~p~~~~~~~iKR 45 (122)
.|-.+.|.. -++.||.|.+... ...++.|
T Consensus 28 tG~~i~VP~------FI~~Gd~I~VdT~---~g~Yv~R 56 (56)
T PF09285_consen 28 TGAEIQVPL------FIEEGDKIKVDTR---DGSYVER 56 (56)
T ss_dssp TS-EEEEET------T--TT-EEEEETT---TTEEEEE
T ss_pred CCCEEEccc------eecCCCEEEEECC---CCeEeCC
Confidence 566666654 3778999999864 3455555
No 93
>PF00166 Cpn10: Chaperonin 10 Kd subunit; InterPro: IPR020818 The chaperonins are `helper' molecules required for correct folding and subsequent assembly of some proteins []. These are required for normal cell growth [], and are stress-induced, acting to stabilise or protect disassembled polypeptides under heat-shock conditions. Type I chaperonins present in eubacteria, mitochondria and chloroplasts require the concerted action of 2 proteins, chaperonin 60 (cpn60) and chaperonin 10 (cpn10) []. The 10 kDa chaperonin (cpn10 - or groES in bacteria) exists as a ring-shaped oligomer of between six to eight identical subunits, while the 60 kDa chaperonin (cpn60 - or groEL in bacteria) forms a structure comprising 2 stacked rings, each ring containing 7 identical subunits []. These ring structures assemble by self-stimulation in the presence of Mg2+-ATP. The central cavity of the cylindrical cpn60 tetradecamer provides as isolated environment for protein folding whilst cpn-10 binds to cpn-60 and synchronizes the release of the folded protein in an Mg2+-ATP dependent manner []. The binding of cpn10 to cpn60 inhibits the weak ATPase activity of cpn60. Escherichia coli GroES has also been shown to bind ATP cooperatively, and with an affinity comparable to that of GroEL []. Each GroEL subunit contains three structurally distinct domains: an apical, an intermediate and an equatorial domain. The apical domain contains the binding sites for both GroES and the unfolded protein substrate. The equatorial domain contains the ATP-binding site and most of the oligomeric contacts. The intermediate domain links the apical and equatorial domains and transfers allosteric information between them. The GroEL oligomer is a tetradecamer, cylindrically shaped, that is organised in two heptameric rings stacked back to back. Each GroEL ring contains a central cavity, known as the `Anfinsen cage', that provides an isolated environment for protein folding. The identical 10 kDa subunits of GroES form a dome-like heptameric oligomer in solution. ATP binding to GroES may be important in charging the seven subunits of the interacting GroEL ring with ATP, to facilitate cooperative ATP binding and hydrolysis for substrate protein release.; GO: 0006457 protein folding, 0005737 cytoplasm; PDB: 1PF9_Q 1AON_P 1SX4_T 1SVT_R 2C7D_P 1PCQ_O 2C7C_Q 1GRU_Q 1WNR_F 1P3H_I ....
Probab=26.18 E-value=1.7e+02 Score=18.29 Aligned_cols=88 Identities=17% Similarity=0.123 Sum_probs=46.6
Q ss_pred CCCCEEEEEeccCCCCCCCCCcEEEEEcCCCCCceeEEEEEEcCCCEEEEecCCCCCCCCceEEeeCCeEEEeeCCCC--
Q 033291 7 LTGDLVLAERISTRFNKVCPGDVVLVRSPVVPRRIVTKRVIGMEGDRVSYVADPKSSDKFETVVVPQGHVWIEGDNIY-- 84 (122)
Q Consensus 7 ~~Gd~vlv~~~~~~~~~~~~GDiVv~~~p~~~~~~~iKRV~a~pGd~v~~~~~~~~~~~~~~~~vp~~~~~v~gdn~~-- 84 (122)
|-||+|++.+... ..-..|-|++=.. ........+|+|+.-.... .++. .-+..|..|..-+..+...
T Consensus 4 Pl~drVLV~~~~~--e~~T~~GiiLp~~--~~~~~~~G~VvaVG~G~~~-~~g~-----~~~~~vk~GD~Vl~~~~~g~~ 73 (93)
T PF00166_consen 4 PLGDRVLVKKIEA--EEKTASGIILPES--AKEKPNQGKVVAVGPGRYN-ENGE-----EVPMDVKVGDKVLFPKYAGTE 73 (93)
T ss_dssp ESTTEEEEEECSC--TCTCTTSCCE-CC--SSSSEEEEEEEEE-SEEET-TTSS-----EEETSS-TTSEEEEETTTSEE
T ss_pred ecCCEEEEEEccc--cceecceEEeccc--cccccceeEEEEcCCcccc-CCCc-----EeeeeeeeccEEeccccCceE
Confidence 4589999998632 4566777776632 2245677788887542222 1000 0112233344444444331
Q ss_pred CCCCCCceecccCCCeeEEE
Q 033291 85 ESNDSRKFGAVPYGLIEGRV 104 (122)
Q Consensus 85 ~S~DSR~~G~V~~~~I~Gkv 104 (122)
-.+|...|=.++.++|+|++
T Consensus 74 v~~~~~~~~~~~~~dIlavi 93 (93)
T PF00166_consen 74 VKFDGEKYLIVREDDILAVI 93 (93)
T ss_dssp EEETTEEEEEEEGGGEEEEE
T ss_pred EEECCEEEEEEEHHHeEEEC
Confidence 13466667778888887763
No 94
>PF01472 PUA: PUA domain; InterPro: IPR002478 The PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain was named after the proteins in which it was first found []. PUA is a highly conserved RNA-binding motif found in a wide range of archaeal, bacterial and eukaryotic proteins, including enzymes that catalyse tRNA and rRNA post-transcriptional modifications, proteins involved in ribosome biogenesis and translation, as well as in enzymes involved in proline biosynthesis [, ]. The structures of several PUA-RNA complexes reveal a common RNA recognition surface, but also some versatility in the way in which the motif binds to RNA []. PUA motifs are involved in dyskeratosis congenita and cancer, pointing to links between RNA metabolism and human diseases [].; GO: 0003723 RNA binding; PDB: 1ZE2_A 1ZE1_A 1R3E_A 2AB4_A 3R90_D 2J5T_A 2J5V_B 1Q7H_A 2APO_A 2RFK_A ....
Probab=26.07 E-value=54 Score=19.55 Aligned_cols=27 Identities=19% Similarity=0.191 Sum_probs=15.3
Q ss_pred CCEEEEEeccCCCCCCCCCcEEEEEcC
Q 033291 9 GDLVLAERISTRFNKVCPGDVVLVRSP 35 (122)
Q Consensus 9 Gd~vlv~~~~~~~~~~~~GDiVv~~~p 35 (122)
|--++..-......++++||+|.+..+
T Consensus 16 Ga~L~~~GV~~~~~~f~~gd~V~i~~~ 42 (74)
T PF01472_consen 16 GASLFAPGVVEVDGDFRKGDEVAIVDE 42 (74)
T ss_dssp TSEEEGGGEEEEETT--TTSEEEEEET
T ss_pred CCCcchHHhEECCCCcCCCCEEEEEcC
Confidence 444443222222367999999999986
No 95
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=25.98 E-value=1.4e+02 Score=19.46 Aligned_cols=41 Identities=20% Similarity=0.265 Sum_probs=27.4
Q ss_pred CCEEEEEeccC-CCCCCCCCcEEEEEcCCCCCceeEEEEEEcCCC
Q 033291 9 GDLVLAERIST-RFNKVCPGDVVLVRSPVVPRRIVTKRVIGMEGD 52 (122)
Q Consensus 9 Gd~vlv~~~~~-~~~~~~~GDiVv~~~p~~~~~~~iKRV~a~pGd 52 (122)
+..|-+|.-.. -...++.||++.+... +..+.=+|.+++..
T Consensus 33 ~GrV~vNG~~aKpS~~VK~GD~l~i~~~---~~~~~v~Vl~~~~~ 74 (100)
T COG1188 33 GGRVKVNGQRAKPSKEVKVGDILTIRFG---NKEFTVKVLALGEQ 74 (100)
T ss_pred CCeEEECCEEcccccccCCCCEEEEEeC---CcEEEEEEEecccc
Confidence 44454443221 2357999999999975 56677788888764
No 96
>PF15428 Imm14: Immunity protein 14
Probab=25.64 E-value=1.2e+02 Score=19.85 Aligned_cols=22 Identities=32% Similarity=0.450 Sum_probs=16.5
Q ss_pred CCCcEEEEEcCCCCCceeEEEEEE
Q 033291 25 CPGDVVLVRSPVVPRRIVTKRVIG 48 (122)
Q Consensus 25 ~~GDiVv~~~p~~~~~~~iKRV~a 48 (122)
+.|||..+..+ .+.+...||++
T Consensus 1 K~GDIF~ipL~--~~~y~~G~Vi~ 22 (129)
T PF15428_consen 1 KPGDIFCIPLD--DGKYGFGRVIG 22 (129)
T ss_pred CCceEEEEEcC--CCCEEEEEEEe
Confidence 46888888865 36778888883
No 97
>cd04720 BAH_Orc1p_Yeast BAH, or Bromo Adjacent Homology domain, as present in Orc1p, which again is part of the Saccharomyces cerevisiae Sir1-origin recognition complex, and as present in Sir3p. The Orc1p BAH doman functions in epigenetic silencing. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=25.34 E-value=1e+02 Score=22.00 Aligned_cols=74 Identities=9% Similarity=0.182 Sum_probs=42.1
Q ss_pred CCCCCCcEEEEEcCCCCCceeEEEEEEc----CCCEEEEecC------CCCCCCC----c---eEEeeCCeEEEeeCCCC
Q 033291 22 NKVCPGDVVLVRSPVVPRRIVTKRVIGM----EGDRVSYVAD------PKSSDKF----E---TVVVPQGHVWIEGDNIY 84 (122)
Q Consensus 22 ~~~~~GDiVv~~~p~~~~~~~iKRV~a~----pGd~v~~~~~------~~~~~~~----~---~~~vp~~~~~v~gdn~~ 84 (122)
..++.||.|+++.+.. +...+..|..+ .++.+.+... ....... . .-.+.++++|+...
T Consensus 51 ~~~~vGD~Vlik~~~~-~~~~V~iI~ei~~~~~~~~v~i~v~Wy~r~~Ei~~~~~~~~~~~~~~~~~~~nElflT~~--- 126 (179)
T cd04720 51 LELSVGDTILVKDDVA-NSPSVYLIHEIRLNTLNNEVELWVMWFLRWFEINPARYYKQFDPEFRSESNKNELYLTAE--- 126 (179)
T ss_pred eEEeCCCEEEEeCCCC-CCCEEEEEEEEEeCCCCCEEEEEEEEcCCHHHcccccccccccchhcccCCCceEEEecc---
Confidence 4689999999998754 55556555443 2233443321 0000000 0 01345788887532
Q ss_pred CCCCCCceecccCCCeeEEEEE
Q 033291 85 ESNDSRKFGAVPYGLIEGRVFL 106 (122)
Q Consensus 85 ~S~DSR~~G~V~~~~I~Gkv~~ 106 (122)
+-.|+...|+|++..
T Consensus 127 -------~d~i~l~~Ii~k~~V 141 (179)
T cd04720 127 -------LSEIKLKDIIDKANV 141 (179)
T ss_pred -------cceEEhhheeeeEEE
Confidence 335899999999854
No 98
>cd05881 Ig1_Necl-2 First (N-terminal) immunoglobulin (Ig)-like domain of nectin-like molecule 2 (also known as cell adhesion molecule 1 (CADM1)). Ig1_Necl-2: domain similar to the N-terminal immunoglobulin (Ig)-like domain of nectin-like molecule-2, Necl-2 (also known as cell adhesion molecule 1 (CADM1), SynCAM1, IGSF4A, Tslc1, sgIGSF, and RA175). Nectin-like molecules have similar domain structures to those of nectins. At least five nectin-like molecules have been identified (Necl-1 - Necl-5). They all have an extracellular region containing three Ig-like domains, a transmembrane region, and a cytoplasmic region. The N-terminal Ig-like domain of the extracellular region, belongs to the V-type subfamily of Ig domains, is essential to cell-cell adhesion, and plays a part in the interaction with the envelope glycoprotein D of various viruses. Necl-2 has Ca(2+)-independent homophilic and heterophilic cell-cell adhesion activity. Necl-2 is expressed in a wide variety of tissues, and is a
Probab=25.28 E-value=1.8e+02 Score=18.30 Aligned_cols=51 Identities=20% Similarity=0.069 Sum_probs=25.9
Q ss_pred EEEEEEcCCCEEEEecCCCCCCCCceEEeeCC-eEEEeeCCCCCCCCCCceec
Q 033291 43 TKRVIGMEGDRVSYVADPKSSDKFETVVVPQG-HVWIEGDNIYESNDSRKFGA 94 (122)
Q Consensus 43 iKRV~a~pGd~v~~~~~~~~~~~~~~~~vp~~-~~~v~gdn~~~S~DSR~~G~ 94 (122)
..-|.+.+|+++.+.-.........-.-...| .....+++. .+.|+|+.+.
T Consensus 4 ~~nvtv~~G~ta~L~C~v~~~~~~~v~w~~~~~~~i~~~~~~-~~~d~Rf~~~ 55 (95)
T cd05881 4 TEDVTVVEGEVAIISCRVKNNDDSVIQLLNPNRQTIYFRDVR-PLKDSRFQLV 55 (95)
T ss_pred cCceEEcCCCcEEEEEEEccCCccEEEEEecCCcEEEecCcc-ccCCcCEEEE
Confidence 35577888998887532111100111111233 333355555 5689998744
No 99
>cd03701 IF2_IF5B_II IF2_IF5B_II: This family represents the domain II of prokaryotic Initiation Factor 2 (IF2) and its archeal and eukaryotic homologue aeIF5B. IF2, the largest initiation factor is an essential GTP binding protein. In E. coli three natural forms of IF2 exist in the cell, IF2alpha, IF2beta1, and IF2beta2. Disruption of the eIF5B gene (FUN12) in yeast causes a severe slow-growth phenotype, associated with a defect in translation. eIF5B has a function analogous to prokaryotic IF2 in mediating the joining of the 60S ribosomal subunit. The eIF5B consists of three N-terminal domains (I, II, II) connected by a long helix to domain IV. Domain I is a G domain, domain II and IV are beta-barrels and domain III has a novel alpha-beta-alpha sandwich fold. The G domain and the beta-barrel domain II display a similar structure and arrangement to the homologous domains in EF1A, eEF1A and aeIF2gamma.
Probab=25.24 E-value=1.8e+02 Score=18.27 Aligned_cols=36 Identities=14% Similarity=0.151 Sum_probs=21.3
Q ss_pred CCCCCCcEEEEEcCCCCCceeEE----EE-EEcCCCEEEEe
Q 033291 22 NKVCPGDVVLVRSPVVPRRIVTK----RV-IGMEGDRVSYV 57 (122)
Q Consensus 22 ~~~~~GDiVv~~~p~~~~~~~iK----RV-~a~pGd~v~~~ 57 (122)
+.++.||.++.......-..++. ++ .|.|++-|.+.
T Consensus 25 GtL~~Gd~iv~G~~~GkVr~~~d~~g~~v~~a~Ps~~v~i~ 65 (95)
T cd03701 25 GTLKKGDVIVAGGTYGKIRTMVDENGKALLEAGPSTPVEIL 65 (95)
T ss_pred CeEecCCEEEECCccceEEEEECCCCCCccccCCCCCEEEe
Confidence 68999999999754322112222 22 56677766654
No 100
>COG0234 GroS Co-chaperonin GroES (HSP10) [Posttranslational modification, protein turnover, chaperones]
Probab=25.18 E-value=2e+02 Score=18.66 Aligned_cols=25 Identities=36% Similarity=0.591 Sum_probs=14.7
Q ss_pred cCCCCCEEEEEeccCCCCCCCCCcEEE
Q 033291 5 INLTGDLVLAERISTRFNKVCPGDVVL 31 (122)
Q Consensus 5 l~~~Gd~vlv~~~~~~~~~~~~GDiVv 31 (122)
|+|-||+|+|.+.-. .+-..|-||+
T Consensus 3 ikPL~DRVlVk~~e~--EekT~gGIvl 27 (96)
T COG0234 3 IKPLGDRVLVKRVEE--EEKTAGGIVL 27 (96)
T ss_pred ceecCCEEEEEEchh--hccccCcEEe
Confidence 445689999988642 2333444444
No 101
>PF11330 DUF3132: Protein of unknown function (DUF3132); InterPro: IPR021479 This entry is represented by the Citrus psorosis virus, 54kDa protein; it is a family of uncharacterised viral proteins.
Probab=23.52 E-value=1.8e+02 Score=18.82 Aligned_cols=18 Identities=28% Similarity=0.399 Sum_probs=6.9
Q ss_pred CcEEEEEcCCCCCceeEE
Q 033291 27 GDVVLVRSPVVPRRIVTK 44 (122)
Q Consensus 27 GDiVv~~~p~~~~~~~iK 44 (122)
|++|++-+..+.+..+||
T Consensus 87 gevvmildsrdegrmwik 104 (124)
T PF11330_consen 87 GEVVMILDSRDEGRMWIK 104 (124)
T ss_pred CcEEEEEeccccCceeee
Confidence 444444333333333333
No 102
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=22.64 E-value=3.5e+02 Score=20.53 Aligned_cols=58 Identities=17% Similarity=0.243 Sum_probs=36.1
Q ss_pred CCCCCCcEEEEEcCCCCCceeEEEEEEcCCCEEEEecCCC-----------------------CCCCCceEEeeCCeEEE
Q 033291 22 NKVCPGDVVLVRSPVVPRRIVTKRVIGMEGDRVSYVADPK-----------------------SSDKFETVVVPQGHVWI 78 (122)
Q Consensus 22 ~~~~~GDiVv~~~p~~~~~~~iKRV~a~pGd~v~~~~~~~-----------------------~~~~~~~~~vp~~~~~v 78 (122)
..++.||.|++..|+ +.++..+---+|-.+.+..+.. .......+.--.+++||
T Consensus 151 ~~~k~~Dtv~i~lp~---~~I~~~i~fe~g~~~~vtgG~h~G~~G~I~~I~~~~~~~~~~v~~e~~~g~~F~T~~~yVfv 227 (241)
T COG1471 151 DNYKTGDTVKISLPE---QKIVEHIKFEEGALVYVTGGRHVGRVGTIVEIEIQESSKPNLVTVEDEEGNTFQTIKDYVFV 227 (241)
T ss_pred CccccccEEEEeCCC---hhheeEeccCCCcEEEEECCccccceEEEEEEEEecCCCccEEEEecCCCCceEEeeeEEEE
Confidence 578999999999884 3455555555666555554311 01112355566678899
Q ss_pred eeCC
Q 033291 79 EGDN 82 (122)
Q Consensus 79 ~gdn 82 (122)
.|..
T Consensus 228 IG~~ 231 (241)
T COG1471 228 IGED 231 (241)
T ss_pred EcCC
Confidence 8874
No 103
>cd03696 selB_II selB_II: this subfamily represents the domain of elongation factor SelB, homologous to domain II of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3' or 5' non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation.
Probab=22.61 E-value=1.8e+02 Score=17.34 Aligned_cols=34 Identities=24% Similarity=0.242 Sum_probs=24.1
Q ss_pred CCCCCCcEEEEEcCCCCCceeEEEEE--------EcCCCEEEEe
Q 033291 22 NKVCPGDVVLVRSPVVPRRIVTKRVI--------GMEGDRVSYV 57 (122)
Q Consensus 22 ~~~~~GDiVv~~~p~~~~~~~iKRV~--------a~pGd~v~~~ 57 (122)
+.++.||-+.+.+.. ...-||.+- |.+||.+.+.
T Consensus 25 G~i~~g~~v~~~p~~--~~~~V~sI~~~~~~~~~a~aGd~v~i~ 66 (83)
T cd03696 25 GSVKVGDKVEILPLG--EETRVRSIQVHGKDVEEAKAGDRVALN 66 (83)
T ss_pred cEEeCCCEEEECCCC--ceEEEEEEEECCcCcCEEcCCCEEEEE
Confidence 678889888887532 345566665 7788888876
No 104
>PF13759 2OG-FeII_Oxy_5: Putative 2OG-Fe(II) oxygenase; PDB: 3BVC_B 2RG4_A.
Probab=22.54 E-value=1e+02 Score=19.29 Aligned_cols=24 Identities=29% Similarity=0.237 Sum_probs=10.7
Q ss_pred CCCCCcEEEEEcCCCCCceeEEEEEEcCCC
Q 033291 23 KVCPGDVVLVRSPVVPRRIVTKRVIGMEGD 52 (122)
Q Consensus 23 ~~~~GDiVv~~~p~~~~~~~iKRV~a~pGd 52 (122)
+++.||+|+|.. .+.-+|..-.+|
T Consensus 69 ~p~~G~lvlFPs------~l~H~v~p~~~~ 92 (101)
T PF13759_consen 69 EPEEGDLVLFPS------WLWHGVPPNNSD 92 (101)
T ss_dssp ---TTEEEEEET------TSEEEE----SS
T ss_pred CCCCCEEEEeCC------CCEEeccCcCCC
Confidence 577888888874 244455444443
No 105
>COG2895 CysN GTPases - Sulfate adenylate transferase subunit 1 [Inorganic ion transport and metabolism]
Probab=22.49 E-value=3.5e+02 Score=22.18 Aligned_cols=34 Identities=29% Similarity=0.438 Sum_probs=22.9
Q ss_pred CCCCCCcEEEEEcCCCCCceeEEEEEEc--------CCCEEEEe
Q 033291 22 NKVCPGDVVLVRSPVVPRRIVTKRVIGM--------EGDRVSYV 57 (122)
Q Consensus 22 ~~~~~GDiVv~~~p~~~~~~~iKRV~a~--------pGd~v~~~ 57 (122)
+.++.||-|++-+. ....-+|||+.- +|+.|++.
T Consensus 248 G~v~~Gd~vvvlPs--G~~s~V~~Ivt~dg~~~~A~aG~aVtl~ 289 (431)
T COG2895 248 GSVKVGDEVVVLPS--GKTSRVKRIVTFDGELAQASAGEAVTLV 289 (431)
T ss_pred cceecCCeEEEccC--CCeeeEEEEeccCCchhhccCCceEEEE
Confidence 57899997766643 246778998754 55666554
No 106
>PF13550 Phage-tail_3: Putative phage tail protein
Probab=22.46 E-value=1.4e+02 Score=19.93 Aligned_cols=26 Identities=23% Similarity=0.293 Sum_probs=19.0
Q ss_pred CCCCCCCcEEEEEcCCCCCceeEEEEEEc
Q 033291 21 FNKVCPGDVVLVRSPVVPRRIVTKRVIGM 49 (122)
Q Consensus 21 ~~~~~~GDiVv~~~p~~~~~~~iKRV~a~ 49 (122)
.-.++.||+|.+.++ .....-||.++
T Consensus 137 ~~~l~pGDvi~l~~~---~~~~~~RI~~i 162 (164)
T PF13550_consen 137 GLALEPGDVIALSDD---GRDMRFRITEI 162 (164)
T ss_pred hccCCCCCEEEEEeC---CCceEEEEEEE
Confidence 347899999999987 44566677654
No 107
>cd03693 EF1_alpha_II EF1_alpha_II: this family represents the domain II of elongation factor 1-alpha (EF-1a) that is found in archaea and all eukaryotic lineages. EF-1A is very abundant in the cytosol, where it is involved in the GTP-dependent binding of aminoacyl-tRNAs to the A site of the ribosomes in the second step of translation from mRNAs to proteins. Both domain II of EF1A and domain IV of IF2/eIF5B have been implicated in recognition of the 3'-ends of tRNA. More than 61% of eukaryotic elongation factor 1A (eEF-1A) in cells is estimated to be associated with actin cytoskeleton. The binding of eEF1A to actin is a noncanonical function that may link two distinct cellular processes, cytoskeleton organization and gene expression.
Probab=21.60 E-value=2.1e+02 Score=17.58 Aligned_cols=34 Identities=26% Similarity=0.271 Sum_probs=25.3
Q ss_pred CCCCCCcEEEEEcCCCCCceeEEEEE--------EcCCCEEEEe
Q 033291 22 NKVCPGDVVLVRSPVVPRRIVTKRVI--------GMEGDRVSYV 57 (122)
Q Consensus 22 ~~~~~GDiVv~~~p~~~~~~~iKRV~--------a~pGd~v~~~ 57 (122)
+.++.||-|.+-+.. ...-||.+- |.+||.+.+.
T Consensus 29 G~i~~gd~v~i~P~~--~~~~V~sI~~~~~~~~~a~aG~~v~i~ 70 (91)
T cd03693 29 GVLKPGMVVTFAPAG--VTGEVKSVEMHHEPLEEALPGDNVGFN 70 (91)
T ss_pred ceeecCCEEEECCCC--cEEEEEEEEECCcCcCEECCCCEEEEE
Confidence 678999998887542 345666666 7889988876
No 108
>cd02792 MopB_CT_Formate-Dh-Na-like Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the major electron donor to the nitrate respiratory chain. Also included in this CD is the Desulfovibrio gigas tungsten formate dehydrogenase, DgW-FDH. In contrast to Fdh-N, which is a functional heterotrimer, DgW-FDH is a heterodimer. The DgW-FDH complex is composed of a large subunit carrying the W active site and one [4Fe-4S] center, and a small subunit that harbors a series of three [4Fe-4S] clusters as well as a putative vacant binding site for a fourth cluster. The smaller subunit is not included in this alignment. This CD (MopB_CT_Formate-Dh-Na-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=21.59 E-value=1.5e+02 Score=18.82 Aligned_cols=26 Identities=27% Similarity=0.227 Sum_probs=16.4
Q ss_pred EEEEEeccCCCCCCCCCcEEEEEcCC
Q 033291 11 LVLAERISTRFNKVCPGDVVLVRSPV 36 (122)
Q Consensus 11 ~vlv~~~~~~~~~~~~GDiVv~~~p~ 36 (122)
.+.++.-......++.||.|.+..+.
T Consensus 36 ~v~i~p~dA~~lgi~~Gd~V~v~s~~ 61 (122)
T cd02792 36 FVEISPELAAERGIKNGDMVWVSSPR 61 (122)
T ss_pred EEEECHHHHHHcCCCCCCEEEEEcCC
Confidence 45555433334578888888888764
No 109
>TIGR01067 rplN_bact ribosomal protein L14, bacterial/organelle. This model distinguishes bacterial and most organellar examples of ribosomal protein L14 from all archaeal and eukaryotic forms.
Probab=21.55 E-value=64 Score=21.74 Aligned_cols=31 Identities=23% Similarity=0.289 Sum_probs=22.8
Q ss_pred eEEeeCCeEEEeeCCCCCCCCCCceecccCCC
Q 033291 68 TVVVPQGHVWIEGDNIYESNDSRKFGAVPYGL 99 (122)
Q Consensus 68 ~~~vp~~~~~v~gdn~~~S~DSR~~G~V~~~~ 99 (122)
.+...+|.+-++.++. +-.-+|-||||+++.
T Consensus 76 ~i~F~~Na~VLin~~~-~p~GTrI~Gpv~~el 106 (122)
T TIGR01067 76 YIRFDDNACVLINKNK-EPRGTRIFGPVAREL 106 (122)
T ss_pred EEECCCceEEEECCCC-CEeeeEEEccchHHH
Confidence 4455667776776554 678899999999775
No 110
>PF00877 NLPC_P60: NlpC/P60 family; InterPro: IPR000064 The Escherichia coli NLPC/Listeria P60 domain occurs at the C terminus of a number of different bacterial and viral proteins. The viral proteins are either described as tail assembly proteins or Gp19. In bacteria, the proteins are variously described as being putative tail component of prophage, invasin, invasion associated protein, putative lipoprotein, cell wall hydrolase, or putative endopeptidase. The E. coli NLPC/Listeria P60 domain is contained within the boundaries of the cysteine peptidase domain that defines the MEROPS peptidase family C40 (clan C-). A type example being dipeptidyl-peptidase VI from Bacillus sphaericus and gamma-glutamyl-diamino acid-endopeptidase precursor from Lactococcus lactis 3.4.19.11 from EC. This group also contains proteins classified as non-peptidase homologues in that they either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity of peptidases in the C40 family. ; PDB: 3PVQ_B 3GT2_A 3NPF_B 2K1G_A 3I86_A 3S0Q_A 2XIV_A 3PBC_A 3NE0_A 3M1U_B ....
Probab=21.12 E-value=65 Score=20.21 Aligned_cols=13 Identities=23% Similarity=0.782 Sum_probs=11.0
Q ss_pred CCCCCCcEEEEEc
Q 033291 22 NKVCPGDVVLVRS 34 (122)
Q Consensus 22 ~~~~~GDiVv~~~ 34 (122)
.++++||++.|..
T Consensus 50 ~~~~pGDlif~~~ 62 (105)
T PF00877_consen 50 SELQPGDLIFFKG 62 (105)
T ss_dssp GG-TTTEEEEEEG
T ss_pred hcCCcccEEEEeC
Confidence 5799999999997
No 111
>cd04713 BAH_plant_3 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=21.09 E-value=1.4e+02 Score=20.49 Aligned_cols=78 Identities=13% Similarity=0.020 Sum_probs=41.1
Q ss_pred CCCCCCcEEEEEcCCCCCceeEEEEEEc---CCCEEEEecC------CCCCCCCc-eEEeeCCeEEEeeCCCCCCCCCCc
Q 033291 22 NKVCPGDVVLVRSPVVPRRIVTKRVIGM---EGDRVSYVAD------PKSSDKFE-TVVVPQGHVWIEGDNIYESNDSRK 91 (122)
Q Consensus 22 ~~~~~GDiVv~~~p~~~~~~~iKRV~a~---pGd~v~~~~~------~~~~~~~~-~~~vp~~~~~v~gdn~~~S~DSR~ 91 (122)
..++.||.|++.++.. ...+|.+|..+ ......+... ........ ...-.++++|.. ++
T Consensus 19 ~~y~vgD~Vlv~~~~~-~~pyI~~I~~i~~~~~~~~~v~V~WFyRpeEi~~~~~~~~~~~~~~ElF~S-~~--------- 87 (146)
T cd04713 19 NKYRLEDCVLLVPEDD-QKPYIAIIKDIYKQEEGSLKLEVQWLYRPEEIEKKKGGNWKAEDPRELFYS-FH--------- 87 (146)
T ss_pred EEEECCCEEEEeCCCC-CCCEEEEEEEEEEcCCCCEEEEEEeeECHHHhccccccccccCCCCeEEEe-CC---------
Confidence 4688999999997644 45555565544 2222222211 00000000 011124566654 22
Q ss_pred eecccCCCeeEEEEEEEeC
Q 033291 92 FGAVPYGLIEGRVFLRIWP 110 (122)
Q Consensus 92 ~G~V~~~~I~Gkv~~~~~p 110 (122)
.=.++.+.|+||+.....|
T Consensus 88 ~d~~~~~~I~gkc~V~~~~ 106 (146)
T cd04713 88 RDEVPAESVLHPCKVAFVP 106 (146)
T ss_pred CCcCCHHHCcceeEEEECC
Confidence 2348899999999876655
No 112
>PF02736 Myosin_N: Myosin N-terminal SH3-like domain; InterPro: IPR004009 This domain has an SH3-like fold. It is found at the N terminus of many but not all myosins. The function of this domain is unknown.; GO: 0003774 motor activity, 0005524 ATP binding, 0016459 myosin complex; PDB: 2EC6_A 2W4H_M 1O1E_P 1O1D_D 1O18_A 1O1C_P 1O1B_D 1O1F_A 2W4A_M 2W4G_M ....
Probab=21.04 E-value=1.1e+02 Score=16.22 Aligned_cols=26 Identities=35% Similarity=0.512 Sum_probs=20.0
Q ss_pred EEEEcCCCCCceeEEEEEEcCCCEEEEe
Q 033291 30 VLVRSPVVPRRIVTKRVIGMEGDRVSYV 57 (122)
Q Consensus 30 Vv~~~p~~~~~~~iKRV~a~pGd~v~~~ 57 (122)
|-+.++ ...++..+|+...|+.+.+.
T Consensus 4 vWvpD~--~egfv~g~I~~~~g~~vtV~ 29 (42)
T PF02736_consen 4 VWVPDP--KEGFVKGEIIEEEGDKVTVK 29 (42)
T ss_dssp EEEEES--SSSEEEEEEEEEESSEEEEE
T ss_pred EEEeCC--cccEEEEEEEEEcCCEEEEE
Confidence 444444 35788899999999999986
No 113
>TIGR02390 RNA_pol_rpoA1 DNA-directed RNA polymerase subunit A'. This family consists of the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.
Probab=20.88 E-value=1.3e+02 Score=27.05 Aligned_cols=35 Identities=17% Similarity=0.292 Sum_probs=26.1
Q ss_pred CCCCCCcEEEEEcCCC--CCceeEEEEEEcCCCEEEE
Q 033291 22 NKVCPGDVVLVRSPVV--PRRIVTKRVIGMEGDRVSY 56 (122)
Q Consensus 22 ~~~~~GDiVv~~~p~~--~~~~~iKRV~a~pGd~v~~ 56 (122)
+.+..||+|+|+.... .-...--||.-+||.++.+
T Consensus 406 rhl~dgd~vl~NRqPsLHr~si~a~~~~v~~~~t~r~ 442 (868)
T TIGR02390 406 RHLIDGDIVLFNRQPSLHRMSMMGHKVKVLPGKTFRL 442 (868)
T ss_pred EehhcCccceeccCCccccccceeEEEEEecCceEee
Confidence 3688999999985432 2345668888899999886
No 114
>PF13403 Hint_2: Hint domain
Probab=20.77 E-value=2.7e+02 Score=18.99 Aligned_cols=77 Identities=17% Similarity=0.108 Sum_probs=38.7
Q ss_pred CCCEEEEEeccCCCCCCCCCcEEEEEcCCCCCceeEEE-EE-----EcCC--CEEEEecCCCC-CCCCceEEeeCCeEEE
Q 033291 8 TGDLVLAERISTRFNKVCPGDVVLVRSPVVPRRIVTKR-VI-----GMEG--DRVSYVADPKS-SDKFETVVVPQGHVWI 78 (122)
Q Consensus 8 ~Gd~vlv~~~~~~~~~~~~GDiVv~~~p~~~~~~~iKR-V~-----a~pG--d~v~~~~~~~~-~~~~~~~~vp~~~~~v 78 (122)
.|..|....-.....+++.||.|+=.+.....-..+.| .+ ..+. .-|.|..+... ........|+++|-++
T Consensus 5 ~GT~I~T~~G~~~Ve~L~~GD~V~T~dgg~~~V~wig~~~~~~~~~~~~~~~~pvri~a~alG~g~P~~dl~vsp~hrvl 84 (147)
T PF13403_consen 5 AGTLIETPDGPRPVEDLRPGDRVLTRDGGFQPVRWIGRRTVSPADLPAPPRLAPVRIPAGALGNGRPSRDLLVSPQHRVL 84 (147)
T ss_pred CCCEEecCCcCeEeeccCCCCEEEecCCCEEEEEEEEEEEecccccCcCCCcceEEEECCccCCCCCCcCeEECccccee
Confidence 45555544433234579999999888643222223332 22 1122 22334433221 1224567777777777
Q ss_pred eeCCCC
Q 033291 79 EGDNIY 84 (122)
Q Consensus 79 ~gdn~~ 84 (122)
+.+...
T Consensus 85 ~~~~~~ 90 (147)
T PF13403_consen 85 LRGPRA 90 (147)
T ss_pred ecchhh
Confidence 776543
Done!