Query 043519
Match_columns 130
No_of_seqs 195 out of 1138
Neff 7.8
Searched_HMMs 46136
Date Fri Mar 29 05:52:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043519.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043519hhsearch_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 3.3E-38 7.1E-43 225.2 13.6 117 1-124 30-163 (163)
2 PRK10861 signal peptidase I; P 100.0 8.4E-33 1.8E-37 214.9 13.1 117 1-124 92-305 (324)
3 KOG0171 Mitochondrial inner me 100.0 5.6E-33 1.2E-37 195.1 7.0 112 1-129 43-164 (176)
4 PRK13838 conjugal transfer pil 99.9 1.7E-26 3.8E-31 166.6 11.6 112 6-118 34-170 (176)
5 TIGR02771 TraF_Ti conjugative 99.9 3.5E-25 7.6E-30 159.2 10.3 98 21-118 45-167 (171)
6 KOG1568 Mitochondrial inner me 99.9 1.8E-25 4E-30 157.0 8.5 100 1-127 41-155 (174)
7 PF10502 Peptidase_S26: Signal 99.9 2E-26 4.3E-31 160.5 0.5 99 22-120 21-137 (138)
8 PRK13884 conjugal transfer pep 99.9 3.8E-24 8.3E-29 154.7 11.1 98 21-118 49-174 (178)
9 COG4959 TraF Type IV secretory 99.8 2.7E-19 5.8E-24 124.9 4.6 95 23-117 54-166 (173)
10 TIGR02754 sod_Ni_protease nick 99.8 3.1E-18 6.8E-23 110.8 9.2 81 1-117 8-89 (90)
11 cd06530 S26_SPase_I The S26 Ty 99.7 4.5E-16 9.9E-21 99.4 7.9 75 1-116 10-85 (85)
12 TIGR02228 sigpep_I_arch signal 99.3 1.7E-11 3.6E-16 87.3 9.0 79 1-117 41-119 (158)
13 COG0681 LepB Signal peptidase 99.3 6.3E-11 1.4E-15 83.6 9.8 104 1-116 41-144 (166)
14 PF00717 Peptidase_S24: Peptid 99.2 2.6E-11 5.7E-16 74.3 5.6 52 1-64 7-58 (70)
15 cd06462 Peptidase_S24_S26 The 98.5 1.5E-06 3.1E-11 54.3 7.5 52 1-64 10-62 (84)
16 cd06529 S24_LexA-like Peptidas 98.4 1.3E-06 2.9E-11 54.4 6.7 50 1-64 10-59 (81)
17 COG2932 Predicted transcriptio 97.9 4E-05 8.7E-10 56.6 6.2 50 1-63 133-182 (214)
18 PRK10276 DNA polymerase V subu 97.0 0.0025 5.3E-08 44.2 5.6 41 1-55 61-102 (139)
19 KOG3342 Signal peptidase I [In 96.9 0.00067 1.5E-08 48.0 2.2 45 1-55 58-102 (180)
20 PRK12423 LexA repressor; Provi 96.9 0.0058 1.3E-07 44.9 7.1 48 1-63 124-172 (202)
21 PRK00215 LexA repressor; Valid 96.8 0.0069 1.5E-07 44.3 7.0 47 1-62 128-175 (205)
22 TIGR00498 lexA SOS regulatory 96.7 0.01 2.2E-07 43.2 7.2 47 1-62 121-168 (199)
23 COG0681 LepB Signal peptidase 95.5 0.023 5E-07 39.6 4.2 29 45-73 137-165 (166)
24 COG1974 LexA SOS-response tran 89.1 1.8 4E-05 32.0 6.3 46 3-62 125-170 (201)
25 COG1097 RRP4 RNA-binding prote 86.3 1.5 3.2E-05 33.3 4.5 61 1-74 109-194 (239)
26 COG0361 InfA Translation initi 83.0 1.4 3E-05 27.6 2.5 12 23-34 47-58 (75)
27 TIGR00008 infA translation ini 81.8 1.5 3.2E-05 26.9 2.3 12 23-34 45-56 (68)
28 PF05257 CHAP: CHAP domain; I 80.7 5.6 0.00012 26.4 5.1 38 20-64 60-98 (124)
29 PF06890 Phage_Mu_Gp45: Bacter 78.0 16 0.00034 26.1 6.9 39 16-63 68-109 (162)
30 PF11101 DUF2884: Protein of u 73.4 5.2 0.00011 30.0 3.7 25 51-75 17-42 (229)
31 cd05793 S1_IF1A S1_IF1A: Trans 71.2 3.7 7.9E-05 25.6 2.0 12 23-34 39-50 (77)
32 PRK12442 translation initiatio 70.2 5 0.00011 25.8 2.5 12 23-34 47-58 (87)
33 smart00652 eIF1a eukaryotic tr 70.1 4 8.6E-05 25.9 2.0 12 23-34 44-55 (83)
34 PF10000 ACT_3: ACT domain; I 69.8 2.5 5.3E-05 26.1 1.0 15 1-15 14-28 (72)
35 PF01176 eIF-1a: Translation i 68.8 3.4 7.3E-05 24.8 1.4 14 22-35 41-54 (65)
36 cd04456 S1_IF1A_like S1_IF1A_l 67.5 5.3 0.00012 25.0 2.2 12 23-34 39-50 (78)
37 PRK04012 translation initiatio 67.4 4.8 0.0001 26.5 2.1 12 23-34 60-71 (100)
38 TIGR02594 conserved hypothetic 66.2 25 0.00055 23.9 5.6 14 21-34 72-85 (129)
39 PF14085 DUF4265: Domain of un 65.4 36 0.00077 22.7 6.1 46 8-62 11-57 (117)
40 PF04319 NifZ: NifZ domain; I 65.3 13 0.00028 23.2 3.5 30 1-30 1-33 (75)
41 smart00002 PLP Myelin proteoli 63.7 2 4.4E-05 25.6 -0.2 20 97-116 22-41 (60)
42 COG4079 Uncharacterized protei 63.6 19 0.00041 27.7 4.8 31 44-74 248-282 (293)
43 COG3602 Uncharacterized protei 63.3 5 0.00011 27.3 1.5 15 1-15 14-28 (134)
44 cd03695 CysN_NodQ_II CysN_NodQ 62.3 24 0.00052 21.7 4.5 33 21-62 25-65 (81)
45 PRK09919 anti-adapter protein 59.4 11 0.00024 25.4 2.7 22 54-75 39-60 (114)
46 PF02836 Glyco_hydro_2_C: Glyc 53.6 14 0.00029 28.4 2.7 15 60-74 1-15 (298)
47 cd03698 eRF3_II_like eRF3_II_l 53.4 39 0.00084 20.7 4.4 33 21-62 25-65 (83)
48 cd04089 eRF3_II eRF3_II: domai 52.7 40 0.00087 20.6 4.4 33 21-62 24-64 (82)
49 TIGR00523 eIF-1A eukaryotic/ar 51.5 17 0.00037 23.8 2.5 10 23-32 58-67 (99)
50 COG5131 URM1 Ubiquitin-like pr 51.3 20 0.00043 23.2 2.8 31 4-34 57-92 (96)
51 PRK10626 hypothetical protein; 51.3 20 0.00043 27.3 3.2 24 51-75 40-64 (239)
52 PF01479 S4: S4 domain; Inter 49.1 6.7 0.00014 21.5 0.3 15 62-76 23-37 (48)
53 KOG4146 Ubiquitin-like protein 48.7 24 0.00052 23.0 2.8 31 4-34 62-97 (101)
54 PF09285 Elong-fact-P_C: Elong 47.2 58 0.0013 19.1 4.2 25 4-34 25-49 (56)
55 PTZ00329 eukaryotic translatio 46.3 17 0.00037 25.8 2.1 11 23-33 71-81 (155)
56 PLN00208 translation initiatio 45.9 18 0.00038 25.5 2.1 11 23-33 71-81 (145)
57 cd00604 IPT_CGTD IPT domain (d 45.7 31 0.00068 21.5 3.0 23 52-74 9-38 (81)
58 cd05792 S1_eIF1AD_like S1_eIF1 44.9 18 0.00039 22.7 1.8 27 7-34 21-50 (78)
59 PF15057 DUF4537: Domain of un 44.5 16 0.00035 24.8 1.7 12 2-13 53-64 (124)
60 PF11012 DUF2850: Protein of u 44.4 23 0.00049 22.3 2.2 25 57-81 16-40 (79)
61 COG4013 Uncharacterized protei 44.0 28 0.0006 22.3 2.5 12 55-66 36-47 (91)
62 PF06394 Pepsin-I3: Pepsin inh 43.1 20 0.00044 22.4 1.8 15 61-75 24-38 (76)
63 PF13144 SAF_2: SAF-like 41.8 1.1E+02 0.0024 21.8 5.9 52 4-64 122-177 (196)
64 cd04714 BAH_BAHCC1 BAH, or Bro 40.4 46 0.001 22.2 3.4 39 23-72 4-42 (121)
65 PF01426 BAH: BAH domain; Int 38.3 44 0.00094 21.5 3.0 26 23-55 3-28 (119)
66 COG0179 MhpD 2-keto-4-pentenoa 38.1 43 0.00093 25.8 3.3 16 20-35 222-237 (266)
67 TIGR03170 flgA_cterm flagella 37.6 90 0.0019 20.4 4.5 12 23-34 66-77 (122)
68 cd03696 selB_II selB_II: this 35.1 1.1E+02 0.0023 18.6 4.5 33 21-62 25-65 (83)
69 KOG4030 Uncharacterized conser 34.9 48 0.001 23.8 2.9 24 52-78 130-153 (197)
70 cd03693 EF1_alpha_II EF1_alpha 34.3 1.2E+02 0.0025 18.9 4.6 33 21-62 29-69 (91)
71 COG0103 RpsI Ribosomal protein 33.6 51 0.0011 22.7 2.8 29 44-78 11-39 (130)
72 PF00278 Orn_DAP_Arg_deC: Pyri 32.9 72 0.0016 20.4 3.4 31 3-35 65-95 (116)
73 KOG1816 Ubiquitin fusion-degra 32.8 2.4E+02 0.0053 22.3 6.6 40 22-70 145-184 (308)
74 PRK15095 FKBP-type peptidyl-pr 31.6 1.8E+02 0.004 20.3 5.7 17 47-63 108-124 (156)
75 cd06555 ASCH_PF0470_like ASC-1 30.8 1.1E+02 0.0024 20.3 4.0 14 21-34 30-43 (109)
76 PF11320 DUF3122: Protein of u 30.7 1.9E+02 0.004 20.1 5.5 46 7-58 10-55 (134)
77 cd04466 S1_YloQ_GTPase S1_YloQ 30.7 93 0.002 17.9 3.4 13 22-34 37-49 (68)
78 smart00439 BAH Bromo adjacent 30.2 1.1E+02 0.0025 19.4 4.1 26 23-55 2-27 (120)
79 cd05790 S1_Rrp40 S1_Rrp40: Rrp 30.2 45 0.00097 21.2 1.9 14 1-14 46-59 (86)
80 PF08194 DIM: DIM protein; In 29.4 41 0.0009 17.9 1.4 12 63-74 22-33 (36)
81 TIGR02219 phage_NlpC_fam putat 29.1 39 0.00085 22.9 1.7 13 21-33 75-87 (134)
82 COG1126 GlnQ ABC-type polar am 28.8 14 0.00029 28.1 -0.7 43 22-75 24-67 (240)
83 PF01455 HupF_HypC: HupF/HypC 28.3 52 0.0011 19.9 1.9 9 5-13 38-46 (68)
84 PF15428 Imm14: Immunity prote 28.1 1E+02 0.0022 20.4 3.6 22 24-54 1-22 (129)
85 PRK04163 exosome complex RNA-b 27.3 84 0.0018 23.6 3.3 15 1-15 108-122 (235)
86 cd04709 BAH_MTA BAH, or Bromo 27.3 1E+02 0.0022 22.0 3.6 25 23-55 4-28 (164)
87 TIGR02988 YaaA_near_RecF S4 do 27.1 30 0.00064 19.9 0.7 14 62-75 31-44 (59)
88 TIGR00061 L21 ribosomal protei 27.0 88 0.0019 20.5 3.0 22 6-32 14-35 (101)
89 COG4133 CcmA ABC-type transpor 27.0 12 0.00027 27.7 -1.2 58 4-75 9-67 (209)
90 PRK00276 infA translation init 26.3 66 0.0014 19.4 2.2 11 23-33 47-57 (72)
91 TIGR02390 RNA_pol_rpoA1 DNA-di 26.1 89 0.0019 28.2 3.7 37 22-63 407-443 (868)
92 PRK02268 hypothetical protein; 25.8 84 0.0018 21.9 2.8 30 21-55 34-63 (141)
93 cd04717 BAH_polybromo BAH, or 25.7 1.1E+02 0.0023 20.2 3.3 26 23-55 4-29 (121)
94 cd04712 BAH_DCM_I BAH, or Brom 25.6 2.2E+02 0.0048 19.3 7.7 14 22-35 5-18 (130)
95 KOG1535 Predicted fumarylaceto 25.4 94 0.002 23.3 3.1 29 21-63 175-203 (217)
96 PRK05573 rplU 50S ribosomal pr 25.4 1E+02 0.0022 20.2 3.1 10 7-16 16-25 (103)
97 PLN02856 fumarylacetoacetase 25.3 2E+02 0.0043 23.9 5.3 29 4-33 346-374 (424)
98 PF11302 DUF3104: Protein of u 24.9 1.8E+02 0.0039 18.1 4.3 34 22-57 5-38 (75)
99 COG4127 Uncharacterized conser 24.9 70 0.0015 25.2 2.5 26 21-54 71-96 (318)
100 PF13987 YedD: YedD-like prote 24.5 87 0.0019 20.8 2.5 22 50-71 47-68 (111)
101 cd03694 GTPBP_II Domain II of 24.4 1.8E+02 0.0039 17.9 4.4 37 21-62 25-69 (87)
102 PF00829 Ribosomal_L21p: Ribos 23.7 82 0.0018 20.3 2.3 22 6-32 15-36 (96)
103 PF14345 GDYXXLXY: GDYXXLXY pr 23.6 1.1E+02 0.0023 21.0 3.1 33 4-36 16-48 (144)
104 PF01878 EVE: EVE domain; Int 23.4 1.1E+02 0.0024 20.6 3.1 15 21-35 38-52 (143)
105 PF10030 DUF2272: Uncharacteri 23.4 2.3E+02 0.0049 20.6 4.8 46 21-66 92-145 (183)
106 smart00841 Elong-fact-P_C Elon 23.2 1.3E+02 0.0028 17.6 2.9 12 23-34 38-49 (56)
107 PF14415 DUF4424: Domain of un 23.1 76 0.0016 24.3 2.4 19 17-35 6-27 (253)
108 COG4043 Preprotein translocase 22.7 63 0.0014 21.4 1.6 13 20-32 31-43 (111)
109 PF05949 DUF881: Bacterial pro 22.5 1E+02 0.0023 21.4 2.8 23 58-80 72-94 (149)
110 cd04710 BAH_fungalPHD BAH, or 22.3 1.6E+02 0.0035 20.2 3.7 27 22-55 11-37 (135)
111 cd03697 EFTU_II EFTU_II: Elong 22.3 2E+02 0.0043 17.6 5.6 14 21-34 25-38 (87)
112 PF00380 Ribosomal_S9: Ribosom 22.1 71 0.0015 21.6 1.9 26 47-78 5-30 (121)
113 PF11132 SplA: Transcriptional 21.9 76 0.0016 19.7 1.8 13 1-13 1-14 (75)
114 smart00216 VWD von Willebrand 21.8 2.6E+02 0.0057 18.8 4.9 32 48-79 63-97 (162)
115 PF01079 Hint: Hint module; I 21.7 1.4E+02 0.0031 22.2 3.6 15 52-66 69-83 (217)
116 TIGR00074 hypC_hupF hydrogenas 21.3 73 0.0016 19.8 1.7 12 22-33 35-46 (76)
117 PF05382 Amidase_5: Bacterioph 21.2 61 0.0013 22.7 1.4 14 21-34 74-87 (145)
118 PF00877 NLPC_P60: NlpC/P60 fa 21.1 60 0.0013 20.6 1.3 13 21-33 50-62 (105)
119 PF01052 SpoA: Surface present 20.9 1.2E+02 0.0026 18.1 2.6 13 22-34 28-40 (77)
120 COG3250 LacZ Beta-galactosidas 20.6 94 0.002 27.9 2.8 16 59-74 285-300 (808)
121 smart00663 RPOLA_N RNA polymer 20.4 3.1E+02 0.0067 21.5 5.3 37 22-63 198-234 (295)
122 PRK10413 hydrogenase 2 accesso 20.3 79 0.0017 19.9 1.7 12 3-14 41-52 (82)
123 PF06097 DUF945: Bacterial pro 20.3 1.1E+02 0.0024 24.6 2.9 21 56-76 433-457 (460)
124 CHL00010 infA translation init 20.2 1.1E+02 0.0023 18.9 2.3 11 23-33 47-57 (78)
125 PF13759 2OG-FeII_Oxy_5: Putat 20.1 69 0.0015 20.3 1.5 13 22-34 69-81 (101)
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=3.3e-38 Score=225.24 Aligned_cols=117 Identities=24% Similarity=0.329 Sum_probs=103.8
Q ss_pred CccccccCCEEEEEccccCCCCCCCCcEEEEecCCcccccccCCCceEEEEEEEeCCCEEEEeCCEEEECCEEccccccc
Q 043519 1 MLRAYVVTSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEACEGKLIVNGVVRNKDFIL 80 (130)
Q Consensus 1 M~Ptl~~gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~pGD~v~~~~~~l~vng~~~~~~~~~ 80 (130)
|+|||++||+|+++|+.|....+++||+|+|+.|. ..++.++|||+|+|||+|+++++++||||+.++++|..
T Consensus 30 M~Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~~~-------~~~~~~iKRVig~pGd~v~i~~~~l~vNg~~~~~~~~~ 102 (163)
T TIGR02227 30 MEPTLKEGDRILVNKFAYGTSDPKRGDIVVFKDPD-------DNKNIYVKRVIGLPGDKVEFRDGKLYINGKKIDEPYLK 102 (163)
T ss_pred cccchhCCCEEEEEEeEcCCCCCCCCcEEEEecCC-------CCCceeEEEEEecCCCEEEEECCEEEECCEECcccccc
Confidence 99999999999999998888899999999999875 35679999999999999999999999999999998765
Q ss_pred cCCC--------CCCCCEEeCCCC---------CCCCCCccccccCCCeeeEEEEEEeeCC
Q 043519 81 EAPF--------YNMTPITVLENS---------NSYDLLVCLDELADHIPSSLDFKYQHHG 124 (130)
Q Consensus 81 ~~~~--------~~~~~~~vp~g~---------~S~DSR~~G~V~~~~I~Gkv~~~~~P~~ 124 (130)
+... ....+++||+|| +|+||||||+|++++|+|||++++||++
T Consensus 103 ~~~~~~~~~~~~~~~~~~~vp~g~~fvlGDnr~~S~DSR~~G~V~~~~I~Gk~~~~~~p~~ 163 (163)
T TIGR02227 103 PNGSLDTSGFNTTDFKPVTVPPGHYFVLGDNRDNSLDSRYFGFVPIDDIIGKVSFVFYPFD 163 (163)
T ss_pred cccccccccccccccCceEECCCCEEEECCCCCCCcccCCcCcCCHHHeEEEEEEEECCCC
Confidence 3211 123467889998 8999999999999999999999999985
No 2
>PRK10861 signal peptidase I; Provisional
Probab=100.00 E-value=8.4e-33 Score=214.92 Aligned_cols=117 Identities=18% Similarity=0.164 Sum_probs=96.4
Q ss_pred CccccccCCEEEEEccccCC------------CCCCCCcEEEEecCCcccccccCCCceEEEEEEEeCCCEEEEe--CCE
Q 043519 1 MLRAYVVTSLRRKGSVTYYF------------REPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEAC--EGK 66 (130)
Q Consensus 1 M~Ptl~~gd~vlv~k~~~~~------------~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~pGD~v~~~--~~~ 66 (130)
|+|||..||+|+|+|++|.+ +.|+|||||+|+.|. +++..+||||||+|||+|+++ +++
T Consensus 92 M~PTL~~GD~IlVnK~~yg~~~p~~~~~~~~~~~p~RGDIVVF~~P~-------~~~~~yIKRVIGlPGD~I~~~~~~~~ 164 (324)
T PRK10861 92 MMPTLLIGDFILVEKFAYGIKDPITQTTLIETGHPKRGDIVVFKYPE-------DPKLDYIKRVVGLPGDKVTYDPVSKE 164 (324)
T ss_pred CcCcccCCCEEEEEEeecCccCccccccccccCCCCCCCEEEEecCC-------CCCCcEEEEeeecCCcEEEEEeCCCE
Confidence 99999999999999999863 579999999999987 457889999999999999997 899
Q ss_pred EEECCEEccccc-----------------cc---------------------------------c-----------CCC-
Q 043519 67 LIVNGVVRNKDF-----------------IL---------------------------------E-----------APF- 84 (130)
Q Consensus 67 l~vng~~~~~~~-----------------~~---------------------------------~-----------~~~- 84 (130)
|||||+.+...+ .. + .+.
T Consensus 165 l~iNg~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~E~l~~~~h~i~~~~~~ 244 (324)
T PRK10861 165 VTIQPGCSSGQACENALPVTYSNVEPSDFVQTFSRRNGGEATSGFFQVPLNETKENGIRLSERKETLGDVTHRILTVPGA 244 (324)
T ss_pred EEEcCccccccccccccccccccccccccccccccccccccccccccccccccccccccceeEEEecCCccceeeecCCc
Confidence 999997421100 00 0 000
Q ss_pred ------------CCCCCEEeCCCC---------CCCCCCccccccCCCeeeEEEEEEeeCC
Q 043519 85 ------------YNMTPITVLENS---------NSYDLLVCLDELADHIPSSLDFKYQHHG 124 (130)
Q Consensus 85 ------------~~~~~~~vp~g~---------~S~DSR~~G~V~~~~I~Gkv~~~~~P~~ 124 (130)
.++.+++||+|+ +|+||||||+||.++|+|+|..++|+++
T Consensus 245 ~~~~~~~~~~~~~~~~~~~vp~g~yf~mgdnr~~S~DSRy~G~Vp~~~i~G~a~~i~~s~d 305 (324)
T PRK10861 245 QDQVGMYYQQPGQPLATWVVPPGQYFMMGDNRDNSADSRYWGFVPEANLVGKATAIWMSFE 305 (324)
T ss_pred ccccccccccCCCcCceEEECCCeEEEeCCCCCCCcccCcccccCHHHcEEEEEEEEEEcC
Confidence 013567999998 8999999999999999999999999986
No 3
>KOG0171 consensus Mitochondrial inner membrane protease, subunit IMP1 [Posttranslational modification, protein turnover, chaperones]
Probab=99.98 E-value=5.6e-33 Score=195.11 Aligned_cols=112 Identities=34% Similarity=0.383 Sum_probs=98.0
Q ss_pred Ccccccc-CCEEEEEccccCCCCCCCCcEEEEecCCcccccccCCCceEEEEEEEeCCCEEEEeCCEEEECCEEcccccc
Q 043519 1 MLRAYVV-TSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEACEGKLIVNGVVRNKDFI 79 (130)
Q Consensus 1 M~Ptl~~-gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~pGD~v~~~~~~l~vng~~~~~~~~ 79 (130)
|+|||++ ||+|++.|++++++.+++||+|++..|. ...+.+||||+|++||-|++.++.+.+|+.. |.+.
T Consensus 43 M~PTl~~~gd~l~aEkls~~f~~~~~gDIVi~~sP~-------~~~~~~cKRIva~eGD~v~v~~~~~~~n~~~--e~~~ 113 (176)
T KOG0171|consen 43 MEPTLHDGGDVLLAEKLSYRFRKPQVGDIVIAKSPP-------DPKEHICKRIVAMEGDLVEVHDGPLVVNDLV--EKFS 113 (176)
T ss_pred cCceecCCCcEEehhhhhHhhcCCCCCCEEEEeCCC-------CchhhhhheeeccCCceEEEecCCcccchhh--hhcc
Confidence 9998886 5666669999999999999999999998 4678899999999999999999988888664 3332
Q ss_pred ccCCCCCCCCEEeCCCC---------CCCCCCccccccCCCeeeEEEEEEeeCCCCCcC
Q 043519 80 LEAPFYNMTPITVLENS---------NSYDLLVCLDELADHIPSSLDFKYQHHGNPSIA 129 (130)
Q Consensus 80 ~~~~~~~~~~~~vp~g~---------~S~DSR~~G~V~~~~I~Gkv~~~~~P~~~~g~~ 129 (130)
.+++||+|| +|+|||+|||||.+.|+||+++++||.+++++.
T Consensus 114 --------~~i~VP~GhVfv~GDN~~nS~DSr~yGplP~glI~gRvv~r~Wp~s~~~~~ 164 (176)
T KOG0171|consen 114 --------TPIRVPEGHVFVEGDNRNNSLDSRNYGPLPMGLIQGRVVFRIWPPSRVSGL 164 (176)
T ss_pred --------ceeeccCceEEEecCCCCCcccccccCCCchhheeeeEEEEecCchhccee
Confidence 367888888 999999999999999999999999999998764
No 4
>PRK13838 conjugal transfer pilin processing protease TraF; Provisional
Probab=99.94 E-value=1.7e-26 Score=166.59 Aligned_cols=112 Identities=16% Similarity=0.041 Sum_probs=86.9
Q ss_pred ccCCEEEEEccccCCCCCCCCcEEEEecCCccc-----cccc-C------CCceEEEEEEEeCCCEEEEeCCEEEECCEE
Q 043519 6 VVTSLRRKGSVTYYFREPFANDILIFKSPPLLQ-----EVGY-T------DDGVYIKGIVAKEGDVVEACEGKLIVNGVV 73 (130)
Q Consensus 6 ~~gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~-----~~~~-~------~~~~~vKRVig~pGD~v~~~~~~l~vng~~ 73 (130)
.+.+.+.+.++.+..+.++|||+|+|+.|...+ +++| . ....++|||+|+|||+|++++ +++|||+.
T Consensus 34 T~S~pig~y~~~~~~~~~~rGDiVvf~~P~~~~~~~a~~r~yl~~g~~p~~~~~~iKRViglpGD~V~i~~-~v~iNg~~ 112 (176)
T PRK13838 34 TPSEPLGLWRIEALDRPVAVGDLVFICPPETAAFREARERGYLRRGLCPGGFAPLIKTVAALAGQRVEIGG-SVSIDGRP 112 (176)
T ss_pred CCCCEEEEEEEeccCCCCCCCcEEEEECCchhhhhhhhhcccccccccccCCCceEEEEEEeCCcEEEECC-EEEECCEE
Confidence 457778888887767889999999999886531 1222 1 124699999999999999985 89999999
Q ss_pred ccccccccCCC--C---CCCCEEeCCCC--------CCCCCCccccccCCCeeeEEEE
Q 043519 74 RNKDFILEAPF--Y---NMTPITVLENS--------NSYDLLVCLDELADHIPSSLDF 118 (130)
Q Consensus 74 ~~~~~~~~~~~--~---~~~~~~vp~g~--------~S~DSR~~G~V~~~~I~Gkv~~ 118 (130)
+.++|...... . .+...+||+|+ +|+||||||+|++++|+|+|.-
T Consensus 113 ~~~~~~~~~~~~g~~l~~~~~~~vp~g~~fvlgd~~~S~DSRy~G~V~~~~I~G~a~p 170 (176)
T PRK13838 113 LPSSSVRRRDGEGRPLTPFPGGVVPPGHLFLHSSFAGSYDSRYFGPVPASGLLGLARP 170 (176)
T ss_pred ccccccccccccCCcCCCCCccCcCCCeEEEECCCCCCCcccccCcccHHHeEEEEEE
Confidence 99987653221 1 12235678887 8999999999999999999963
No 5
>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=3.5e-25 Score=159.20 Aligned_cols=98 Identities=17% Similarity=0.160 Sum_probs=74.5
Q ss_pred CCCCCCcEEEEecCCccc-----cccc-CCC------ceEEEEEEEeCCCEEEEeCCEEEECCEEccccccccCC--C--
Q 043519 21 REPFANDILIFKSPPLLQ-----EVGY-TDD------GVYIKGIVAKEGDVVEACEGKLIVNGVVRNKDFILEAP--F-- 84 (130)
Q Consensus 21 ~~~~rGDiVvf~~p~~~~-----~~~~-~~~------~~~vKRVig~pGD~v~~~~~~l~vng~~~~~~~~~~~~--~-- 84 (130)
+.++|||+|+|+.|.... .++| +.+ ..++|||+|+|||+|+++++.++|||+.+.+.+..... +
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 479999999999886421 1222 122 38999999999999999999999999998876533211 1
Q ss_pred -CCCCCEEeCCCC--------CCCCCCccccccCCCeeeEEEE
Q 043519 85 -YNMTPITVLENS--------NSYDLLVCLDELADHIPSSLDF 118 (130)
Q Consensus 85 -~~~~~~~vp~g~--------~S~DSR~~G~V~~~~I~Gkv~~ 118 (130)
....+.+||+|. +|+||||||+|++++|+|||.-
T Consensus 125 l~~~~~~~vp~gyf~lgdn~~~S~DSRy~G~V~~~~IiGk~~p 167 (171)
T TIGR02771 125 LPPFPEGVIPPGFFVVHDTSPTSFDSRYFGPISREQVIGRVKP 167 (171)
T ss_pred cccCCCcEECCCEEEECCCCCCCCcccccceecHHHeEEEEEE
Confidence 112356666666 8999999999999999999964
No 6
>KOG1568 consensus Mitochondrial inner membrane protease, subunit IMP2 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=99.92 E-value=1.8e-25 Score=156.95 Aligned_cols=100 Identities=22% Similarity=0.152 Sum_probs=85.2
Q ss_pred CccccccC------CEEEEEccccCCCCCCCCcEEEEecCCcccccccCCCceEEEEEEEeCCCEEEEeCCEEEECCEEc
Q 043519 1 MLRAYVVT------SLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEACEGKLIVNGVVR 74 (130)
Q Consensus 1 M~Ptl~~g------d~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~pGD~v~~~~~~l~vng~~~ 74 (130)
|.|||+++ |+||++|+.-.-+.+.|||+|+|.+|. ++++.+||||+|++||++.-.+.
T Consensus 41 mqPtlnP~~~~~~~d~Vll~k~~v~n~~~~rGDiVvl~sP~-------~p~~~~iKRv~alegd~~~t~~~--------- 104 (174)
T KOG1568|consen 41 MQPTLNPTMNTNEKDTVLLRKWNVKNRKVSRGDIVVLKSPN-------DPDKVIIKRVAALEGDIMVTEDE--------- 104 (174)
T ss_pred CCCccCCCcccccccEEEEEeeccccceeccCCEEEEeCCC-------ChhheeeeeeecccccEeccCCC---------
Confidence 88999874 999999987555678999999999998 57899999999999999977321
Q ss_pred cccccccCCCCCCCCEEeCCCC---------CCCCCCccccccCCCeeeEEEEEEeeCCCCC
Q 043519 75 NKDFILEAPFYNMTPITVLENS---------NSYDLLVCLDELADHIPSSLDFKYQHHGNPS 127 (130)
Q Consensus 75 ~~~~~~~~~~~~~~~~~vp~g~---------~S~DSR~~G~V~~~~I~Gkv~~~~~P~~~~g 127 (130)
....+.||+|| .|+|||.||||+...|.|+|++++||+.|++
T Consensus 105 -----------k~~~v~vpkghcWVegDn~~hs~DSntFGPVS~gli~grai~ilwpP~R~~ 155 (174)
T KOG1568|consen 105 -----------KEEPVVVPKGHCWVEGDNQKHSYDSNTFGPVSTGLIVGRAIYILWPPVRWQ 155 (174)
T ss_pred -----------CCCceecCCCcEEEecCCcccccccCccCCcchhheeeeEEEEEcChHHhh
Confidence 12345566666 9999999999999999999999999999875
No 7
>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=99.92 E-value=2e-26 Score=160.55 Aligned_cols=99 Identities=23% Similarity=0.258 Sum_probs=23.0
Q ss_pred CCCCCcEEEEecCCccc----cccc-CCCceEEEEEEEeCCCEEEEeCCEEEECCEEccccccccCCCCC----CCCEEe
Q 043519 22 EPFANDILIFKSPPLLQ----EVGY-TDDGVYIKGIVAKEGDVVEACEGKLIVNGVVRNKDFILEAPFYN----MTPITV 92 (130)
Q Consensus 22 ~~~rGDiVvf~~p~~~~----~~~~-~~~~~~vKRVig~pGD~v~~~~~~l~vng~~~~~~~~~~~~~~~----~~~~~v 92 (130)
.++|||+|+|+.|.... +++| ..+..++|||+|+|||+|+++++.++|||+.+.+.+..+..+.. ..+.+|
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 37999999999997532 3444 45679999999999999999999999999988876654332221 135778
Q ss_pred CCCC---------CCCCCCccccccCCCeeeEEEEEE
Q 043519 93 LENS---------NSYDLLVCLDELADHIPSSLDFKY 120 (130)
Q Consensus 93 p~g~---------~S~DSR~~G~V~~~~I~Gkv~~~~ 120 (130)
|+|+ +|+||||||+|++++|+|+|...+
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 8877 999999999999999999997543
No 8
>PRK13884 conjugal transfer peptidase TraF; Provisional
Probab=99.91 E-value=3.8e-24 Score=154.72 Aligned_cols=98 Identities=20% Similarity=0.233 Sum_probs=74.8
Q ss_pred CCCCCCcEEEEecCCcc-----ccccc------CC-CceEEEEEEEeCCCEEEEeCCEEEECCEEccccc--cccCC---
Q 043519 21 REPFANDILIFKSPPLL-----QEVGY------TD-DGVYIKGIVAKEGDVVEACEGKLIVNGVVRNKDF--ILEAP--- 83 (130)
Q Consensus 21 ~~~~rGDiVvf~~p~~~-----~~~~~------~~-~~~~vKRVig~pGD~v~~~~~~l~vng~~~~~~~--~~~~~--- 83 (130)
..+++||+|+|++|+.. .+++| +. ...++|||+|+|||+|+++++.++|||+.+.+.. ..+..
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 36899999999988742 23343 11 2489999999999999999999999999986543 22211
Q ss_pred --CCCCCCEEeCCCC---------CCCCCCccccccCCCeeeEEEE
Q 043519 84 --FYNMTPITVLENS---------NSYDLLVCLDELADHIPSSLDF 118 (130)
Q Consensus 84 --~~~~~~~~vp~g~---------~S~DSR~~G~V~~~~I~Gkv~~ 118 (130)
.+....++||+|+ +|+||||||+|++++|+|++.-
T Consensus 129 l~~~~~~~~~lp~g~~fvlgd~~~~S~DSRYfG~V~~~~I~G~~~P 174 (178)
T PRK13884 129 LPRYQANSYTLGESELLLMSDVSATSFDGRYFGPINRSQIKTVIRP 174 (178)
T ss_pred ccccCCCceEECCCEEEEECCCCCCCCcccccCcccHHHEEEEEEE
Confidence 1223345788887 8999999999999999999853
No 9
>COG4959 TraF Type IV secretory pathway, protease TraF [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=99.77 E-value=2.7e-19 Score=124.89 Aligned_cols=95 Identities=14% Similarity=0.086 Sum_probs=74.6
Q ss_pred CCCCcEEEEecCCcc----ccccc-CCCceEEEEEEEeCCCEEEEeCCEEEECCEEccccccccCCCCCC----CCEEeC
Q 043519 23 PFANDILIFKSPPLL----QEVGY-TDDGVYIKGIVAKEGDVVEACEGKLIVNGVVRNKDFILEAPFYNM----TPITVL 93 (130)
Q Consensus 23 ~~rGDiVvf~~p~~~----~~~~~-~~~~~~vKRVig~pGD~v~~~~~~l~vng~~~~~~~~~~~~~~~~----~~~~vp 93 (130)
+.+||+|++++|... .++|| +....++|||.|+|||+|++..+.+-|||+.+......+..+..+ ++-.+.
T Consensus 54 vt~g~lV~v~pP~~~a~~aA~RGYLp~~~pllK~i~Alpgq~Vci~~~~I~I~G~~v~~sl~~D~~GR~lp~~~gcR~l~ 133 (173)
T COG4959 54 VTKGDLVLVCPPQRAAFLAAQRGYLPPYIPLLKRILALPGQHVCITSQGIAIDGKPVAASLPVDRVGRALPRWQGCRYLA 133 (173)
T ss_pred cccCCEEEECCCchHhHhHhhcCccccccHHHHHHhcCCCCcEEEecceEEECCEEeeeeccccccCCcCCcccCCceec
Confidence 499999999999863 34777 668899999999999999999999999999987654444333221 111233
Q ss_pred CCC---------CCCCCCccccccCCCeeeEEE
Q 043519 94 ENS---------NSYDLLVCLDELADHIPSSLD 117 (130)
Q Consensus 94 ~g~---------~S~DSR~~G~V~~~~I~Gkv~ 117 (130)
+++ .||||||||+||.++|+|.+.
T Consensus 134 ~~el~lL~~~~~~SfDsRYfGpipas~vig~aR 166 (173)
T COG4959 134 PSELLLLTDRSSTSFDSRYFGPIPASQVIGVAR 166 (173)
T ss_pred CCeEEEEeccCCcccccceecccCHHHcceeee
Confidence 333 899999999999999999985
No 10
>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=99.77 E-value=3.1e-18 Score=110.76 Aligned_cols=81 Identities=15% Similarity=0.053 Sum_probs=65.9
Q ss_pred CccccccCCEEEEEccccCCCCCCCCcEEEEecCCcccccccCCCceEEEEEEEeCCCEEEEeCCEEEECCEEccccccc
Q 043519 1 MLRAYVVTSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEACEGKLIVNGVVRNKDFIL 80 (130)
Q Consensus 1 M~Ptl~~gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~pGD~v~~~~~~l~vng~~~~~~~~~ 80 (130)
|+|||++||+|+++++......+++||+|+|+.|. .++..++||+++++++.+.+
T Consensus 8 M~P~l~~GD~vlv~~~~~~~~~~~~Gdivv~~~~~-------~~~~~~vkRv~~~~~~~~~l------------------ 62 (90)
T TIGR02754 8 MSPTLPPGDRIIVVPWLKIFRVPPIGNVVVVRHPL-------QPYGLIIKRLAAVDDNGLFL------------------ 62 (90)
T ss_pred ccCccCCCCEEEEEEccccCCCCCCCeEEEEecCC-------CCcceEEEEeeEEcCCeEEE------------------
Confidence 99999999999999865444556789999999875 24689999999997654433
Q ss_pred cCCCCCCCCEEeCCCC-CCCCCCccccccCCCeeeEEE
Q 043519 81 EAPFYNMTPITVLENS-NSYDLLVCLDELADHIPSSLD 117 (130)
Q Consensus 81 ~~~~~~~~~~~vp~g~-~S~DSR~~G~V~~~~I~Gkv~ 117 (130)
..+|. .|.|||++|+|+..+|+|+|+
T Consensus 63 -----------~~dN~~~~~d~~~~g~v~~~~I~G~v~ 89 (90)
T TIGR02754 63 -----------LGDNPKASTDSRQLGPVPRSLLLGKVL 89 (90)
T ss_pred -----------eCCCCCCCCcccccCCCcHHHEEEEEE
Confidence 23333 689999999999999999985
No 11
>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=99.66 E-value=4.5e-16 Score=99.39 Aligned_cols=75 Identities=27% Similarity=0.305 Sum_probs=62.8
Q ss_pred CccccccCCEEEEEccccCCCCCCCCcEEEEecCCcccccccCCCceEEEEEEEeCCCEEEEeCCEEEECCEEccccccc
Q 043519 1 MLRAYVVTSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEACEGKLIVNGVVRNKDFIL 80 (130)
Q Consensus 1 M~Ptl~~gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~pGD~v~~~~~~l~vng~~~~~~~~~ 80 (130)
|+||++.||+|++++....+..+++||+|+|+.+. ..+..++|||++
T Consensus 10 M~P~i~~gd~v~v~~~~~~~~~~~~GDiv~~~~~~-------~~~~~~vkRv~~-------------------------- 56 (85)
T cd06530 10 MEPTLQPGDLVLVNKLSYGFREPKRGDVVVFKSPG-------DPGKPIIKRVIG-------------------------- 56 (85)
T ss_pred CcCcccCCCEEEEEEeecccCCCCCCCEEEEeCCC-------CCCCEEEEEEEE--------------------------
Confidence 99999999999999876544579999999999975 236899999999
Q ss_pred cCCCCCCCCEEeCCCC-CCCCCCccccccCCCeeeEE
Q 043519 81 EAPFYNMTPITVLENS-NSYDLLVCLDELADHIPSSL 116 (130)
Q Consensus 81 ~~~~~~~~~~~vp~g~-~S~DSR~~G~V~~~~I~Gkv 116 (130)
.++.+++. +|.|||+||+++.++|+|++
T Consensus 57 --------~~~~gDn~~ns~d~~~~g~~~~~~i~G~~ 85 (85)
T cd06530 57 --------YFVLGDNRNNSLDSRYWGPVPEDDIVGKV 85 (85)
T ss_pred --------EEEeeCCCCCCCccCCcCCCcHHHeEEeC
Confidence 12345554 89999999999999999985
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=99.31 E-value=1.7e-11 Score=87.26 Aligned_cols=79 Identities=14% Similarity=0.104 Sum_probs=58.5
Q ss_pred CccccccCCEEEEEccccCCCCCCCCcEEEEecCCcccccccCCCceEEEEEEEeCCCEEEEeCCEEEECCEEccccccc
Q 043519 1 MLRAYVVTSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEACEGKLIVNGVVRNKDFIL 80 (130)
Q Consensus 1 M~Ptl~~gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~pGD~v~~~~~~l~vng~~~~~~~~~ 80 (130)
|+|||++||++++++.. ..++++||+|+|+.|. ..+.++|||+++.++ ++ +. .
T Consensus 41 M~Ptl~~GD~vlv~~~~--~~~~~~GDIVvf~~~~--------~~~~iihRVi~v~~~-----~g------~~---~--- 93 (158)
T TIGR02228 41 MEPTFNTGDLILVTGAD--PNDIQVGDVITYKSPG--------FNTPVTHRVIEINNS-----GG------EL---G--- 93 (158)
T ss_pred CcCCccCCCEEEEEecc--cCCCCCCCEEEEEECC--------CCccEEEEEEEEECC-----CC------cE---E---
Confidence 99999999999999854 3589999999999875 237899999998643 11 10 0
Q ss_pred cCCCCCCCCEEeCCCCCCCCCCccccccCCCeeeEEE
Q 043519 81 EAPFYNMTPITVLENSNSYDLLVCLDELADHIPSSLD 117 (130)
Q Consensus 81 ~~~~~~~~~~~vp~g~~S~DSR~~G~V~~~~I~Gkv~ 117 (130)
-++-+++..+.| .++|+.++|+|++.
T Consensus 94 --------~~tkGDnN~~~D---~~~v~~~~IiG~v~ 119 (158)
T TIGR02228 94 --------FITKGDNNPAPD---GEPVPSENVIGKYL 119 (158)
T ss_pred --------EEEEecCCCCCC---cccCCHHHEEEEEE
Confidence 112233334445 68999999999997
No 13
>COG0681 LepB Signal peptidase I [Intracellular trafficking and secretion]
Probab=99.26 E-value=6.3e-11 Score=83.59 Aligned_cols=104 Identities=18% Similarity=0.115 Sum_probs=72.5
Q ss_pred CccccccCCEEEEEccccCCCCCCCCcEEEEecCCcccccccCCCceEEEEEEEeCCCEEEEeCCEEEECCEEccccccc
Q 043519 1 MLRAYVVTSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEACEGKLIVNGVVRNKDFIL 80 (130)
Q Consensus 1 M~Ptl~~gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~pGD~v~~~~~~l~vng~~~~~~~~~ 80 (130)
|+|||+.||+|+++|++|....+..++++.+ |. .....++||+++++||++.++++.+++ +..+.+.+..
T Consensus 41 M~Ptl~~GD~v~v~k~~~~~~~~~~~~~~~~--~~-------~~~~~~~kr~~~~~GD~i~~~~~~~~~-~~~~~~~~~~ 110 (166)
T COG0681 41 MEPTLNVGDRVLVKKFSYGFGKLKVPDIIVL--PA-------VVEGDLIKRVIGLRGDIVVFKDDRLYV-VPIIPRVYGL 110 (166)
T ss_pred cccccccCCEEEEEeccccccCCccceeeec--CC-------CCCcceEEEeccCCCCEEEEECCEEEe-ecccCcchhh
Confidence 9999999999999999999888999999832 22 357899999999999999999999998 3333332211
Q ss_pred cCCCCCCCCEEeCCCCCCCCCCccccccCCCeeeEE
Q 043519 81 EAPFYNMTPITVLENSNSYDLLVCLDELADHIPSSL 116 (130)
Q Consensus 81 ~~~~~~~~~~~vp~g~~S~DSR~~G~V~~~~I~Gkv 116 (130)
... ............+.+++.++.......+.++
T Consensus 111 ~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 144 (166)
T COG0681 111 VEK--DNGKHLVDVIVNANSSRVFGIITKKDYIKRV 144 (166)
T ss_pred hhc--ccccccccccccccCccccccccccccccce
Confidence 100 0000011111166777777776666666666
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=99.22 E-value=2.6e-11 Score=74.31 Aligned_cols=52 Identities=23% Similarity=0.346 Sum_probs=42.3
Q ss_pred CccccccCCEEEEEccccCCCCCCCCcEEEEecCCcccccccCCCceEEEEEEEeCCCEEEEeC
Q 043519 1 MLRAYVVTSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEACE 64 (130)
Q Consensus 1 M~Ptl~~gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~pGD~v~~~~ 64 (130)
|+|+|++||+|++++.. .++.||+|+|..+. ....++||+++.+|+.+.+..
T Consensus 7 M~P~i~~Gd~v~v~~~~----~~~~gdivv~~~~~--------~~~~~iKrv~~~~~~~~~~~~ 58 (70)
T PF00717_consen 7 MEPTIKDGDIVLVDPSS----EPKDGDIVVVKIDG--------DEELYIKRVVGEPGGIILISS 58 (70)
T ss_dssp TGGTSSTTEEEEEEETS-------TTSEEEEEETT--------EESEEEEEEEEETTEEEEE-S
T ss_pred cccCeeCCCEEEEEEcC----CCccCeEEEEEECC--------ceeeEEEEEEEeCCCEEEEec
Confidence 99999999999999764 78999999999864 124999999999999999864
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=98.45 E-value=1.5e-06 Score=54.34 Aligned_cols=52 Identities=19% Similarity=0.217 Sum_probs=42.9
Q ss_pred CccccccCCEEEEEccccCCCCCCCCcEEEEecCCcccccccCCCceEEEEEEEeCC-CEEEEeC
Q 043519 1 MLRAYVVTSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEG-DVVEACE 64 (130)
Q Consensus 1 M~Ptl~~gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~pG-D~v~~~~ 64 (130)
|+|++.+||+|++++.. ..++.||++++..+ .+..++||+...++ +.+.+..
T Consensus 10 M~P~i~~gd~v~i~~~~---~~~~~G~iv~~~~~---------~~~~~ikrl~~~~~~~~~~l~~ 62 (84)
T cd06462 10 MEPTIPDGDLVLVDKSS---YEPKRGDIVVFRLP---------GGELTVKRVIGLPGEGHYFLLG 62 (84)
T ss_pred ccCcccCCCEEEEEecC---CCCcCCEEEEEEcC---------CCcEEEEEEEEECCCCEEEEEC
Confidence 99999999999999753 14899999999985 24899999999997 6665543
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=98.42 E-value=1.3e-06 Score=54.43 Aligned_cols=50 Identities=14% Similarity=0.137 Sum_probs=42.7
Q ss_pred CccccccCCEEEEEccccCCCCCCCCcEEEEecCCcccccccCCCceEEEEEEEeCCCEEEEeC
Q 043519 1 MLRAYVVTSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEACE 64 (130)
Q Consensus 1 M~Ptl~~gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~pGD~v~~~~ 64 (130)
|+|++++||.|++++.. .++.||++++..+ +..++||+...+++.+.+..
T Consensus 10 M~p~i~~gd~lii~~~~----~~~~g~i~~~~~~----------~~~~ikr~~~~~~~~~~L~s 59 (81)
T cd06529 10 MEPTIPDGDLVLVDPSD----TPRDGDIVVARLD----------GELTVKRLQRRGGGRLRLIS 59 (81)
T ss_pred cCCccCCCCEEEEcCCC----CCCCCCEEEEEEC----------CEEEEEEEEECCCCcEEEEe
Confidence 99999999999998753 4899999999984 37899999999977776653
No 17
>COG2932 Predicted transcriptional regulator [Transcription]
Probab=97.88 E-value=4e-05 Score=56.64 Aligned_cols=50 Identities=12% Similarity=0.146 Sum_probs=41.6
Q ss_pred CccccccCCEEEEEccccCCCCCCCCcEEEEecCCcccccccCCCceEEEEEEEeCCCEEEEe
Q 043519 1 MLRAYVVTSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEAC 63 (130)
Q Consensus 1 M~Ptl~~gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~pGD~v~~~ 63 (130)
|+|++++||.++|+.-. +..+||.|++..- .+..+|||+.-.+|-.+.+.
T Consensus 133 MeP~~~~Gd~ilVd~~~----~~~~gd~v~v~~~---------g~~~~VK~l~~~~~~~~~l~ 182 (214)
T COG2932 133 MEPTYEDGDTLLVDPGV----NTRRGDRVYVETD---------GGELYVKKLQREPGGLLRLV 182 (214)
T ss_pred ccccccCCCEEEECCCC----ceeeCCEEEEEEe---------CCeEEEEEEEEecCCeEEEE
Confidence 99999999999998643 5678997777653 46899999999999988664
No 18
>PRK10276 DNA polymerase V subunit UmuD; Provisional
Probab=96.96 E-value=0.0025 Score=44.16 Aligned_cols=41 Identities=20% Similarity=0.159 Sum_probs=32.9
Q ss_pred Cc-cccccCCEEEEEccccCCCCCCCCcEEEEecCCcccccccCCCceEEEEEEEe
Q 043519 1 ML-RAYVVTSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAK 55 (130)
Q Consensus 1 M~-Ptl~~gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~ 55 (130)
|. |+|..||+|++++-. .++.||+|++.. .+...+||+.-.
T Consensus 61 M~~~~I~~GD~liVd~~~----~~~~Gdivv~~~----------~g~~~vKrl~~~ 102 (139)
T PRK10276 61 MIDAGISDGDLLIVDSAI----TASHGDIVIAAV----------DGEFTVKKLQLR 102 (139)
T ss_pred CCCCCCCCCCEEEEECCC----CCCCCCEEEEEE----------CCEEEEEEEEEC
Confidence 86 689999999998642 578999999875 356889998753
No 19
>KOG3342 consensus Signal peptidase I [Intracellular trafficking, secretion, and vesicular transport]
Probab=96.89 E-value=0.00067 Score=47.95 Aligned_cols=45 Identities=16% Similarity=0.109 Sum_probs=34.8
Q ss_pred CccccccCCEEEEEccccCCCCCCCCcEEEEecCCcccccccCCCceEEEEEEEe
Q 043519 1 MLRAYVVTSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAK 55 (130)
Q Consensus 1 M~Ptl~~gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~ 55 (130)
|+|..+.||.++..... -...+.||+|+|+.+. ...+.+-||+-+
T Consensus 58 MePaF~RGDlLfL~N~~--~~p~~vGdivVf~veg--------R~IPiVHRviK~ 102 (180)
T KOG3342|consen 58 MEPAFHRGDLLFLTNRN--EDPIRVGDIVVFKVEG--------REIPIVHRVIKQ 102 (180)
T ss_pred cCcccccccEEEEecCC--CCcceeccEEEEEECC--------ccCchhHHHHHH
Confidence 99999999999986422 2346899999999975 456777777754
No 20
>PRK12423 LexA repressor; Provisional
Probab=96.86 E-value=0.0058 Score=44.89 Aligned_cols=48 Identities=21% Similarity=0.223 Sum_probs=36.8
Q ss_pred Cc-cccccCCEEEEEccccCCCCCCCCcEEEEecCCcccccccCCCceEEEEEEEeCCCEEEEe
Q 043519 1 ML-RAYVVTSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEAC 63 (130)
Q Consensus 1 M~-Ptl~~gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~pGD~v~~~ 63 (130)
|. |+|.+||+|+|++- ..++.||+|++.. .+...+||+.-. ++.+.+.
T Consensus 124 M~~~~i~~Gd~viv~~~----~~~~~Gdivv~~~----------~~~~~vKrl~~~-~~~~~L~ 172 (202)
T PRK12423 124 MIDDGILDGDLVGVHRS----PEARDGQIVVARL----------DGEVTIKRLERS-GDRIRLL 172 (202)
T ss_pred CCCCCcCCCCEEEEeCC----CcCCCCCEEEEEE----------CCEEEEEEEEEe-CCEEEEE
Confidence 86 79999999999863 3678999999986 356899998755 3445443
No 21
>PRK00215 LexA repressor; Validated
Probab=96.77 E-value=0.0069 Score=44.26 Aligned_cols=47 Identities=13% Similarity=0.113 Sum_probs=36.0
Q ss_pred Cc-cccccCCEEEEEccccCCCCCCCCcEEEEecCCcccccccCCCceEEEEEEEeCCCEEEE
Q 043519 1 ML-RAYVVTSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEA 62 (130)
Q Consensus 1 M~-Ptl~~gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~pGD~v~~ 62 (130)
|. |++.+||+|+|++- ..++.||+|++... +..++||+.-. ++.+.+
T Consensus 128 M~~~~i~~Gd~v~v~~~----~~~~~G~ivv~~~~----------~~~~vKrl~~~-~~~~~L 175 (205)
T PRK00215 128 MIDAGILDGDLVIVRKQ----QTARNGQIVVALID----------DEATVKRFRRE-GGHIRL 175 (205)
T ss_pred CCCCCcCCCCEEEEeCC----CCCCCCCEEEEEEC----------CEEEEEEEEEe-CCEEEE
Confidence 84 79999999999863 25789999999873 47899999865 334444
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=96.67 E-value=0.01 Score=43.17 Aligned_cols=47 Identities=21% Similarity=0.183 Sum_probs=36.3
Q ss_pred Cc-cccccCCEEEEEccccCCCCCCCCcEEEEecCCcccccccCCCceEEEEEEEeCCCEEEE
Q 043519 1 ML-RAYVVTSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEA 62 (130)
Q Consensus 1 M~-Ptl~~gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~pGD~v~~ 62 (130)
|. |++.+||+|++++. ..++.||+|++.. .+...+||+.-. |+.+.+
T Consensus 121 M~~~~i~~Gd~v~v~~~----~~~~~G~ivvv~~----------~~~~~vKrl~~~-~~~i~L 168 (199)
T TIGR00498 121 MVDAGICDGDLLIVRSQ----KDARNGEIVAAMI----------DGEVTVKRFYKD-GTKVEL 168 (199)
T ss_pred CCCCCCCCCCEEEEecC----CCCCCCCEEEEEE----------CCEEEEEEEEEE-CCEEEE
Confidence 75 68999999999864 3688999999987 357899998754 444444
No 23
>COG0681 LepB Signal peptidase I [Intracellular trafficking and secretion]
Probab=95.54 E-value=0.023 Score=39.62 Aligned_cols=29 Identities=28% Similarity=0.415 Sum_probs=24.2
Q ss_pred CceEEEEEEEeCCCEEEEeCCEEEECCEE
Q 043519 45 DGVYIKGIVAKEGDVVEACEGKLIVNGVV 73 (130)
Q Consensus 45 ~~~~vKRVig~pGD~v~~~~~~l~vng~~ 73 (130)
...++||++++|||.+...+..+++||++
T Consensus 137 ~~~~~~~~~~~~gd~~~~~~~~~~~~g~~ 165 (166)
T COG0681 137 KKDYIKRVIGLPGDNILYTDDDLPINGKP 165 (166)
T ss_pred ccccccceEEeeccceeeccCceeecCCC
Confidence 46799999999999999986448888764
No 24
>COG1974 LexA SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]
Probab=89.08 E-value=1.8 Score=31.97 Aligned_cols=46 Identities=11% Similarity=0.119 Sum_probs=31.7
Q ss_pred cccccCCEEEEEccccCCCCCCCCcEEEEecCCcccccccCCCceEEEEEEEeCCCEEEE
Q 043519 3 RAYVVTSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEA 62 (130)
Q Consensus 3 Ptl~~gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~pGD~v~~ 62 (130)
+.+.+||+|+|++- .....||+|+.... ..+.-+||..-- |+.+.+
T Consensus 125 ~gi~dGDlvvV~~~----~~a~~GdiVvA~i~---------g~e~TvKrl~~~-g~~i~L 170 (201)
T COG1974 125 AGILDGDLVVVDPT----EDAENGDIVVALID---------GEEATVKRLYRD-GNQILL 170 (201)
T ss_pred CcCCCCCEEEEcCC----CCCCCCCEEEEEcC---------CCcEEEEEEEEe-CCEEEE
Confidence 55678999999863 36788999998874 355788887643 444433
No 25
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=86.29 E-value=1.5 Score=33.29 Aligned_cols=61 Identities=15% Similarity=0.193 Sum_probs=38.4
Q ss_pred CccccccCCEEEEEcccc-------------CCCCCCCCcEEEEecCCcccccccCCCceEEEEEEEeCCCEE-------
Q 043519 1 MLRAYVVTSLRRKGSVTY-------------YFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVV------- 60 (130)
Q Consensus 1 M~Ptl~~gd~vlv~k~~~-------------~~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~pGD~v------- 60 (130)
|.|.|+.||.|++.-... .++.++.|-+|-..+.. +-|+++--|--+
T Consensus 109 ~r~~l~vGD~v~AkV~~vd~~~~~~L~~k~~~~GkL~~G~iv~i~p~k-------------VpRvig~~~sm~~~l~~~~ 175 (239)
T COG1097 109 LRPFLNVGDLVYAKVVDVDRDGEVELTLKDEGLGKLKNGQIVKIPPSK-------------VPRVIGKKGSMLNMLKEKT 175 (239)
T ss_pred cccccccCCEEEEEEEEccCCCceEEEeecCCCccccCCEEEEEchhh-------------cceEecCCCcHHHHhhhhc
Confidence 789999999998763221 23567777777776532 333443333222
Q ss_pred -----EEeCCEEEECCEEc
Q 043519 61 -----EACEGKLIVNGVVR 74 (130)
Q Consensus 61 -----~~~~~~l~vng~~~ 74 (130)
.=.||.+||+++..
T Consensus 176 ~~~I~VG~NG~IWV~~~~~ 194 (239)
T COG1097 176 GCEIIVGQNGRIWVDGENE 194 (239)
T ss_pred CeEEEEecCCEEEecCCCc
Confidence 22589999999865
No 26
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=82.98 E-value=1.4 Score=27.57 Aligned_cols=12 Identities=8% Similarity=0.338 Sum_probs=6.5
Q ss_pred CCCCcEEEEecC
Q 043519 23 PFANDILIFKSP 34 (130)
Q Consensus 23 ~~rGDiVvf~~p 34 (130)
+..||+|++...
T Consensus 47 I~~GD~V~Ve~~ 58 (75)
T COG0361 47 ILPGDVVLVELS 58 (75)
T ss_pred eCCCCEEEEEec
Confidence 345666665553
No 27
>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=81.79 E-value=1.5 Score=26.90 Aligned_cols=12 Identities=8% Similarity=0.058 Sum_probs=7.3
Q ss_pred CCCCcEEEEecC
Q 043519 23 PFANDILIFKSP 34 (130)
Q Consensus 23 ~~rGDiVvf~~p 34 (130)
+..||.|.+...
T Consensus 45 I~~GD~V~Ve~s 56 (68)
T TIGR00008 45 ILPGDKVKVELS 56 (68)
T ss_pred ECCCCEEEEEEC
Confidence 456666666654
No 28
>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=80.67 E-value=5.6 Score=26.40 Aligned_cols=38 Identities=16% Similarity=0.198 Sum_probs=23.6
Q ss_pred CCCCCCCcEEEEecCCcccccccCCCceEEEEEEEe-CCCEEEEeC
Q 043519 20 FREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAK-EGDVVEACE 64 (130)
Q Consensus 20 ~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~-pGD~v~~~~ 64 (130)
...|+.||||+|.... ...--.+--|.++ .+++|.+.+
T Consensus 60 ~~~P~~Gdivv~~~~~-------~~~~GHVaIV~~v~~~~~i~v~e 98 (124)
T PF05257_consen 60 GSTPQPGDIVVWDSGS-------GGGYGHVAIVESVNDGGTITVIE 98 (124)
T ss_dssp CS---TTEEEEEEECT-------TTTT-EEEEEEEE-TTSEEEEEE
T ss_pred CcccccceEEEeccCC-------CCCCCeEEEEEEECCCCEEEEEE
Confidence 3579999999996221 1333466678888 888988754
No 29
>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=78.01 E-value=16 Score=26.13 Aligned_cols=39 Identities=10% Similarity=0.183 Sum_probs=28.6
Q ss_pred cccCCCCCCCCcEEEEecCCcccccccCCCceEEEE---EEEeCCCEEEEe
Q 043519 16 VTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKG---IVAKEGDVVEAC 63 (130)
Q Consensus 16 ~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKR---Vig~pGD~v~~~ 63 (130)
-.|+.+.++.|++++|..- ....++|| +|.+.++++++.
T Consensus 68 ~~yR~~~L~~GEvalY~~~---------G~~I~L~~~G~ii~~~~~~~~v~ 109 (162)
T PF06890_consen 68 RRYRPKGLKPGEVALYDDE---------GQKIHLKRDGRIIEVTCKTVTVN 109 (162)
T ss_pred ccccccCCCCCcEEEEcCC---------CCEEEEEecceEEeccCceEEEe
Confidence 3466677899999999863 34566665 777788888775
No 30
>PF11101 DUF2884: Protein of unknown function (DUF2884); InterPro: IPR021307 Some members in this bacterial family of proteins are annotated as YggN which currently has no known function.
Probab=73.37 E-value=5.2 Score=30.01 Aligned_cols=25 Identities=24% Similarity=0.472 Sum_probs=20.8
Q ss_pred EEEEeCCCEEEE-eCCEEEECCEEcc
Q 043519 51 GIVAKEGDVVEA-CEGKLIVNGVVRN 75 (130)
Q Consensus 51 RVig~pGD~v~~-~~~~l~vng~~~~ 75 (130)
+|++..|+.+.| .+|.|||||+.+.
T Consensus 17 ~v~~~~~~~~~I~~~g~L~i~G~~v~ 42 (229)
T PF11101_consen 17 EVVQASGEKLRIDPDGNLFINGKKVS 42 (229)
T ss_pred EEEeCCCceEEEcCCCcEEECCEEcc
Confidence 367788889999 6799999999864
No 31
>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=71.18 E-value=3.7 Score=25.65 Aligned_cols=12 Identities=17% Similarity=0.088 Sum_probs=8.3
Q ss_pred CCCCcEEEEecC
Q 043519 23 PFANDILIFKSP 34 (130)
Q Consensus 23 ~~rGDiVvf~~p 34 (130)
+.+||+|++...
T Consensus 39 I~~GD~V~Ve~~ 50 (77)
T cd05793 39 INEGDIVLVAPW 50 (77)
T ss_pred EcCCCEEEEEec
Confidence 577777777654
No 32
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=70.20 E-value=5 Score=25.76 Aligned_cols=12 Identities=17% Similarity=0.202 Sum_probs=5.9
Q ss_pred CCCCcEEEEecC
Q 043519 23 PFANDILIFKSP 34 (130)
Q Consensus 23 ~~rGDiVvf~~p 34 (130)
+..||.|.+...
T Consensus 47 Il~GD~V~VE~s 58 (87)
T PRK12442 47 ILAGDRVTLELS 58 (87)
T ss_pred ecCCCEEEEEEC
Confidence 344555555543
No 33
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=70.05 E-value=4 Score=25.85 Aligned_cols=12 Identities=17% Similarity=0.094 Sum_probs=8.5
Q ss_pred CCCCcEEEEecC
Q 043519 23 PFANDILIFKSP 34 (130)
Q Consensus 23 ~~rGDiVvf~~p 34 (130)
+++||+|++...
T Consensus 44 I~~GD~VlVe~~ 55 (83)
T smart00652 44 IRRGDIVLVDPW 55 (83)
T ss_pred EcCCCEEEEEec
Confidence 577888777653
No 34
>PF10000 ACT_3: ACT domain; InterPro: IPR018717 This domain has no known function.; PDB: 1ZVP_C.
Probab=69.82 E-value=2.5 Score=26.12 Aligned_cols=15 Identities=7% Similarity=-0.301 Sum_probs=10.9
Q ss_pred CccccccCCEEEEEc
Q 043519 1 MLRAYVVTSLRRKGS 15 (130)
Q Consensus 1 M~Ptl~~gd~vlv~k 15 (130)
|.|.|++|++|++.-
T Consensus 14 m~P~L~~~~yVF~t~ 28 (72)
T PF10000_consen 14 MSPELNPGEYVFCTV 28 (72)
T ss_dssp -EEEE-SS-EEEEEE
T ss_pred CCcEeCCCCEEEEEe
Confidence 899999999999974
No 35
>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=68.75 E-value=3.4 Score=24.76 Aligned_cols=14 Identities=14% Similarity=0.231 Sum_probs=8.7
Q ss_pred CCCCCcEEEEecCC
Q 043519 22 EPFANDILIFKSPP 35 (130)
Q Consensus 22 ~~~rGDiVvf~~p~ 35 (130)
.+++||+|++...+
T Consensus 41 wI~~GD~V~V~~~~ 54 (65)
T PF01176_consen 41 WIKRGDFVLVEPSP 54 (65)
T ss_dssp ---TTEEEEEEEST
T ss_pred ecCCCCEEEEEecc
Confidence 47889999888643
No 36
>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=67.53 E-value=5.3 Score=24.99 Aligned_cols=12 Identities=25% Similarity=0.169 Sum_probs=8.4
Q ss_pred CCCCcEEEEecC
Q 043519 23 PFANDILIFKSP 34 (130)
Q Consensus 23 ~~rGDiVvf~~p 34 (130)
+++||+|++...
T Consensus 39 I~~GD~VlV~~~ 50 (78)
T cd04456 39 IKRGDFLIVDPI 50 (78)
T ss_pred EcCCCEEEEEec
Confidence 577777777654
No 37
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=67.43 E-value=4.8 Score=26.46 Aligned_cols=12 Identities=17% Similarity=0.094 Sum_probs=8.1
Q ss_pred CCCCcEEEEecC
Q 043519 23 PFANDILIFKSP 34 (130)
Q Consensus 23 ~~rGDiVvf~~p 34 (130)
+.+||+|++...
T Consensus 60 I~~GD~VlVe~~ 71 (100)
T PRK04012 60 IREGDVVIVAPW 71 (100)
T ss_pred ecCCCEEEEEec
Confidence 567777777653
No 38
>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=66.20 E-value=25 Score=23.94 Aligned_cols=14 Identities=14% Similarity=0.116 Sum_probs=11.6
Q ss_pred CCCCCCcEEEEecC
Q 043519 21 REPFANDILIFKSP 34 (130)
Q Consensus 21 ~~~~rGDiVvf~~p 34 (130)
.+|+.||+|+|+..
T Consensus 72 ~~p~~GDiv~f~~~ 85 (129)
T TIGR02594 72 SKPAYGCIAVKRRG 85 (129)
T ss_pred CCCCccEEEEEECC
Confidence 46899999999753
No 39
>PF14085 DUF4265: Domain of unknown function (DUF4265)
Probab=65.38 E-value=36 Score=22.71 Aligned_cols=46 Identities=9% Similarity=0.255 Sum_probs=29.1
Q ss_pred CCEEEEEccccCCCCCCCCcEEEEecCCcccccccCCCceEEEEEEEeCCC-EEEE
Q 043519 8 TSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGD-VVEA 62 (130)
Q Consensus 8 gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~pGD-~v~~ 62 (130)
.|...+.........+..||+|.+.... +.+.+.+++--.|. |+++
T Consensus 11 ~~~y~l~n~Pf~a~glA~gDvV~~~~~~---------g~~~~~~~v~~sGnsTiRv 57 (117)
T PF14085_consen 11 DDTYRLDNIPFFAYGLALGDVVRAEPDD---------GELWFQKVVESSGNSTIRV 57 (117)
T ss_pred CCEEEEEecccccCCCCCCCEEEEEeCC---------CeEEEEEEEecCCCEEEEE
Confidence 3444454455555689999999999853 55555555554554 5554
No 40
>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=65.32 E-value=13 Score=23.24 Aligned_cols=30 Identities=10% Similarity=-0.051 Sum_probs=21.3
Q ss_pred CccccccCCEEEEEccccCCCC---CCCCcEEE
Q 043519 1 MLRAYVVTSLRRKGSVTYYFRE---PFANDILI 30 (130)
Q Consensus 1 M~Ptl~~gd~vlv~k~~~~~~~---~~rGDiVv 30 (130)
|+|.++.||.|.+.+..+...+ ...|++++
T Consensus 1 ~~p~f~~G~~V~a~~~irNDGt~Pg~~~g~lLv 33 (75)
T PF04319_consen 1 MPPRFEWGDKVRARKDIRNDGTFPGKEIGELLV 33 (75)
T ss_pred CCCccCCCCEEEEEEEeEcCCCCCCCCCCCEEE
Confidence 8999999999999876544332 34555555
No 41
>smart00002 PLP Myelin proteolipid protein (PLP or lipophilin).
Probab=63.72 E-value=2 Score=25.65 Aligned_cols=20 Identities=10% Similarity=-0.152 Sum_probs=17.2
Q ss_pred CCCCCCccccccCCCeeeEE
Q 043519 97 NSYDLLVCLDELADHIPSSL 116 (130)
Q Consensus 97 ~S~DSR~~G~V~~~~I~Gkv 116 (130)
-+.|-|.||.+|-.+.-||+
T Consensus 22 lC~D~RQyGilpwna~pgK~ 41 (60)
T smart00002 22 LCVDARQYGILPWNAFPGKV 41 (60)
T ss_pred EEeechhcceeecCCCCCch
Confidence 47899999999988888876
No 42
>COG4079 Uncharacterized protein conserved in archaea [Function unknown]
Probab=63.62 E-value=19 Score=27.71 Aligned_cols=31 Identities=16% Similarity=0.235 Sum_probs=24.9
Q ss_pred CCceEEEEEEE----eCCCEEEEeCCEEEECCEEc
Q 043519 44 DDGVYIKGIVA----KEGDVVEACEGKLIVNGVVR 74 (130)
Q Consensus 44 ~~~~~vKRVig----~pGD~v~~~~~~l~vng~~~ 74 (130)
++...+++|-+ .|||.|.++||.+.|+|+.+
T Consensus 248 Pg~~v~m~v~~~g~~~pGd~vvv~dg~mki~G~d~ 282 (293)
T COG4079 248 PGEEVVMAVEGNGEVEPGDRVVVKDGVMKIDGKDL 282 (293)
T ss_pred CCceEEEEEccCCccCCCCEEEEecCceEeccccc
Confidence 45666777665 48999999999999999864
No 43
>COG3602 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=63.29 E-value=5 Score=27.26 Aligned_cols=15 Identities=7% Similarity=-0.212 Sum_probs=13.6
Q ss_pred CccccccCCEEEEEc
Q 043519 1 MLRAYVVTSLRRKGS 15 (130)
Q Consensus 1 M~Ptl~~gd~vlv~k 15 (130)
|.|.|.+||+|++.-
T Consensus 14 mtPeL~~G~yVfcT~ 28 (134)
T COG3602 14 MTPELLDGDYVFCTV 28 (134)
T ss_pred cCccccCCceEEEEe
Confidence 899999999999864
No 44
>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=62.31 E-value=24 Score=21.73 Aligned_cols=33 Identities=18% Similarity=0.155 Sum_probs=24.0
Q ss_pred CCCCCCcEEEEecCCcccccccCCCceEEEEEE--------EeCCCEEEE
Q 043519 21 REPFANDILIFKSPPLLQEVGYTDDGVYIKGIV--------AKEGDVVEA 62 (130)
Q Consensus 21 ~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVi--------g~pGD~v~~ 62 (130)
..++.||-|.+.+.. ...-||.+- |.|||.|.+
T Consensus 25 G~v~~Gd~v~~~P~~---------~~~~V~si~~~~~~~~~a~aGd~v~l 65 (81)
T cd03695 25 GSIRVGDEVVVLPSG---------KTSRVKSIETFDGELDEAGAGESVTL 65 (81)
T ss_pred ceEECCCEEEEcCCC---------CeEEEEEEEECCcEeCEEcCCCEEEE
Confidence 468899999988643 345566665 888988877
No 45
>PRK09919 anti-adapter protein IraM; Provisional
Probab=59.42 E-value=11 Score=25.43 Aligned_cols=22 Identities=9% Similarity=0.241 Sum_probs=19.4
Q ss_pred EeCCCEEEEeCCEEEECCEEcc
Q 043519 54 AKEGDVVEACEGKLIVNGVVRN 75 (130)
Q Consensus 54 g~pGD~v~~~~~~l~vng~~~~ 75 (130)
=.|||.+...+..+.||+++..
T Consensus 39 L~pG~~i~~~~~gvliNdk~~p 60 (114)
T PRK09919 39 LPPGSIITPVKSGVLLNDKPYP 60 (114)
T ss_pred eCCCCEEEEcCCeEEECCcEeE
Confidence 4699999999999999999754
No 46
>PF02836 Glyco_hydro_2_C: Glycosyl hydrolases family 2, TIM barrel domain; InterPro: IPR006103 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Glycoside hydrolase family 2 GH2 from CAZY comprises enzymes with several known activities; beta-galactosidase (3.2.1.23 from EC); beta-mannosidase (3.2.1.25 from EC); beta-glucuronidase (3.2.1.31 from EC). These enzymes contain a conserved glutamic acid residue which has been shown [], in Escherichia coli lacZ (P00722 from SWISSPROT), to be the general acid/base catalyst in the active site of the enzyme. Beta-galactosidase from E. coli has a TIM-barrel-like core surrounded by four other largely beta domains [].; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0005975 carbohydrate metabolic process; PDB: 3CMG_A 3FN9_C 1YQ2_A 3K4D_B 3LPG_B 3LPF_A 3K4A_B 3K46_B 3GM8_A 3DEC_A ....
Probab=53.63 E-value=14 Score=28.36 Aligned_cols=15 Identities=33% Similarity=0.448 Sum_probs=13.5
Q ss_pred EEEeCCEEEECCEEc
Q 043519 60 VEACEGKLIVNGVVR 74 (130)
Q Consensus 60 v~~~~~~l~vng~~~ 74 (130)
|+++++.+++||+++
T Consensus 1 vev~~~~~~lNGk~~ 15 (298)
T PF02836_consen 1 VEVKDGGFYLNGKPI 15 (298)
T ss_dssp EEEETTEEEETTEEE
T ss_pred CEEECCEEEECCEEE
Confidence 689999999999975
No 47
>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=53.41 E-value=39 Score=20.72 Aligned_cols=33 Identities=24% Similarity=0.280 Sum_probs=22.8
Q ss_pred CCCCCCcEEEEecCCcccccccCCCceEEEEEE--------EeCCCEEEE
Q 043519 21 REPFANDILIFKSPPLLQEVGYTDDGVYIKGIV--------AKEGDVVEA 62 (130)
Q Consensus 21 ~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVi--------g~pGD~v~~ 62 (130)
+.++.||-|.+.+.. ...-||.+- |.+||.|.+
T Consensus 25 G~i~~Gd~v~i~P~~---------~~~~V~si~~~~~~~~~a~aGd~v~~ 65 (83)
T cd03698 25 GSIQKGDTLLVMPSK---------ESVEVKSIYVDDEEVDYAVAGENVRL 65 (83)
T ss_pred eEEeCCCEEEEeCCC---------cEEEEEEEEECCeECCEECCCCEEEE
Confidence 467888888887642 345566655 788888876
No 48
>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=52.68 E-value=40 Score=20.62 Aligned_cols=33 Identities=21% Similarity=0.187 Sum_probs=22.9
Q ss_pred CCCCCCcEEEEecCCcccccccCCCceEEEEEE--------EeCCCEEEE
Q 043519 21 REPFANDILIFKSPPLLQEVGYTDDGVYIKGIV--------AKEGDVVEA 62 (130)
Q Consensus 21 ~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVi--------g~pGD~v~~ 62 (130)
..++.||-|.+.+.. ...-||.+- |.+||.+.+
T Consensus 24 G~i~~G~~v~i~P~~---------~~~~V~si~~~~~~~~~a~aGd~v~l 64 (82)
T cd04089 24 GTIKKGDKLLVMPNK---------TQVEVLSIYNEDVEVRYARPGENVRL 64 (82)
T ss_pred eEEecCCEEEEeCCC---------cEEEEEEEEECCEECCEECCCCEEEE
Confidence 467889988887642 345566665 777887776
No 49
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=51.45 E-value=17 Score=23.82 Aligned_cols=10 Identities=30% Similarity=0.385 Sum_probs=7.4
Q ss_pred CCCCcEEEEe
Q 043519 23 PFANDILIFK 32 (130)
Q Consensus 23 ~~rGDiVvf~ 32 (130)
+.+||+|++.
T Consensus 58 I~~GD~VlVs 67 (99)
T TIGR00523 58 IREGDVVIVK 67 (99)
T ss_pred ecCCCEEEEE
Confidence 6778888873
No 50
>COG5131 URM1 Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=51.32 E-value=20 Score=23.21 Aligned_cols=31 Identities=13% Similarity=0.098 Sum_probs=22.2
Q ss_pred ccccCCEEEEEccccCC-----CCCCCCcEEEEecC
Q 043519 4 AYVVTSLRRKGSVTYYF-----REPFANDILIFKSP 34 (130)
Q Consensus 4 tl~~gd~vlv~k~~~~~-----~~~~rGDiVvf~~p 34 (130)
+|.+|=.++++...+.. ..++.||+|+|-+.
T Consensus 57 ~lrpGiI~LINd~DWeLleke~y~ledgDiIvfist 92 (96)
T COG5131 57 ELRPGIICLINDMDWELLEKERYPLEDGDIIVFIST 92 (96)
T ss_pred CCcccEEEEEcCccHhhhhcccccCCCCCEEEEEec
Confidence 57788888888755432 34688999999764
No 51
>PRK10626 hypothetical protein; Provisional
Probab=51.32 E-value=20 Score=27.30 Aligned_cols=24 Identities=21% Similarity=0.447 Sum_probs=18.1
Q ss_pred EEEEeCCCEEEEe-CCEEEECCEEcc
Q 043519 51 GIVAKEGDVVEAC-EGKLIVNGVVRN 75 (130)
Q Consensus 51 RVig~pGD~v~~~-~~~l~vng~~~~ 75 (130)
.|++..|+ +.|. +|.|||||+.+.
T Consensus 40 ~V~~~sg~-l~I~~dg~L~inGk~v~ 64 (239)
T PRK10626 40 QVVGASGN-LVISPDGNVMRNGKQLS 64 (239)
T ss_pred EEEecCCc-eEEcCCCCEEECCEEec
Confidence 36777887 6665 579999999864
No 52
>PF01479 S4: S4 domain; InterPro: IPR002942 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 [, ]. The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterised, small proteins that may be involved in translation regulation []. The S4 domain probably mediates binding to RNA.; GO: 0003723 RNA binding; PDB: 3BBU_A 1DM9_B 2K6P_A 3U5G_E 3U5C_E 3IZB_D 2XZM_D 2XZN_D 3O30_E 3O2Z_E ....
Probab=49.13 E-value=6.7 Score=21.49 Aligned_cols=15 Identities=33% Similarity=0.488 Sum_probs=12.3
Q ss_pred EeCCEEEECCEEccc
Q 043519 62 ACEGKLIVNGVVRNK 76 (130)
Q Consensus 62 ~~~~~l~vng~~~~~ 76 (130)
+++|.++|||+.+..
T Consensus 23 I~~g~V~VNg~~v~~ 37 (48)
T PF01479_consen 23 IKQGRVKVNGKVVKD 37 (48)
T ss_dssp HHTTTEEETTEEESS
T ss_pred cCCCEEEECCEEEcC
Confidence 357899999999863
No 53
>KOG4146 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=48.72 E-value=24 Score=23.01 Aligned_cols=31 Identities=10% Similarity=0.034 Sum_probs=21.3
Q ss_pred ccccCCEEEEEccccCC-----CCCCCCcEEEEecC
Q 043519 4 AYVVTSLRRKGSVTYYF-----REPFANDILIFKSP 34 (130)
Q Consensus 4 tl~~gd~vlv~k~~~~~-----~~~~rGDiVvf~~p 34 (130)
++.+|=.++++...+.. ..++.||.|+|-+.
T Consensus 62 svrpGii~lINd~DWEllekedy~ledgD~ivfiST 97 (101)
T KOG4146|consen 62 SVRPGIIVLINDMDWELLEKEDYPLEDGDHIVFIST 97 (101)
T ss_pred cCcCcEEEEEeccchhhhcccccCcccCCEEEEEEe
Confidence 56677788887655321 35788999988764
No 54
>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=47.18 E-value=58 Score=19.06 Aligned_cols=25 Identities=4% Similarity=-0.156 Sum_probs=14.3
Q ss_pred ccccCCEEEEEccccCCCCCCCCcEEEEecC
Q 043519 4 AYVVTSLRRKGSVTYYFREPFANDILIFKSP 34 (130)
Q Consensus 4 tl~~gd~vlv~k~~~~~~~~~rGDiVvf~~p 34 (130)
+|..|-.|.|..+ ++.||.|.++..
T Consensus 25 ~letG~~i~VP~F------I~~Gd~I~VdT~ 49 (56)
T PF09285_consen 25 TLETGAEIQVPLF------IEEGDKIKVDTR 49 (56)
T ss_dssp EETTS-EEEEETT--------TT-EEEEETT
T ss_pred EEcCCCEEEccce------ecCCCEEEEECC
Confidence 3556666666543 678999999874
No 55
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=46.26 E-value=17 Score=25.82 Aligned_cols=11 Identities=18% Similarity=0.193 Sum_probs=5.2
Q ss_pred CCCCcEEEEec
Q 043519 23 PFANDILIFKS 33 (130)
Q Consensus 23 ~~rGDiVvf~~ 33 (130)
+.+||+|++..
T Consensus 71 I~~GD~VlVel 81 (155)
T PTZ00329 71 INIGDIILVSL 81 (155)
T ss_pred ecCCCEEEEec
Confidence 34455555443
No 56
>PLN00208 translation initiation factor (eIF); Provisional
Probab=45.93 E-value=18 Score=25.50 Aligned_cols=11 Identities=27% Similarity=0.277 Sum_probs=5.5
Q ss_pred CCCCcEEEEec
Q 043519 23 PFANDILIFKS 33 (130)
Q Consensus 23 ~~rGDiVvf~~ 33 (130)
+.+||+|++..
T Consensus 71 I~~GD~VlVel 81 (145)
T PLN00208 71 IAAGDIILVGL 81 (145)
T ss_pred ecCCCEEEEEc
Confidence 44555555543
No 57
>cd00604 IPT_CGTD IPT domain (domain D) of cyclodextrin glycosyltransferase (CGTase) and similar enzymes. These enzymes are involved in the enzymatic hydrolysis of alpha-1,4 linkages of starch polymers and belong to the glycosyl hydrolase family 13. Most consist of three domains (A,B,C) but CGTase is more complex and has two additional domains (D,E). The function of the IPT/D domain is unknown.
Probab=45.71 E-value=31 Score=21.49 Aligned_cols=23 Identities=22% Similarity=0.478 Sum_probs=18.2
Q ss_pred EEEeCCCEEEEe-------CCEEEECCEEc
Q 043519 52 IVAKEGDVVEAC-------EGKLIVNGVVR 74 (130)
Q Consensus 52 Vig~pGD~v~~~-------~~~l~vng~~~ 74 (130)
-.|.||++|.|. .+.+++++...
T Consensus 9 ~~g~pG~~VtI~G~gFg~~~~~V~~g~~~a 38 (81)
T cd00604 9 VMGKPGNTVTISGEGFGSTGGTVYFGGTAA 38 (81)
T ss_pred CCCCCCCEEEEEEECCCCCccEEEECCEEE
Confidence 457899999996 57899988764
No 58
>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=44.94 E-value=18 Score=22.68 Aligned_cols=27 Identities=15% Similarity=0.031 Sum_probs=16.8
Q ss_pred cCCEEEEEccccCCCC---CCCCcEEEEecC
Q 043519 7 VTSLRRKGSVTYYFRE---PFANDILIFKSP 34 (130)
Q Consensus 7 ~gd~vlv~k~~~~~~~---~~rGDiVvf~~p 34 (130)
+|...++.- .-+|+. +++||+|++.+-
T Consensus 21 dG~~~l~~i-P~KfRk~iWIkrGd~VlV~p~ 50 (78)
T cd05792 21 NGSRYLVSM-PTKFRKNIWIKRGDFVLVEPI 50 (78)
T ss_pred CCCEEEEEe-chhhcccEEEEeCCEEEEEec
Confidence 566666652 223333 689999999764
No 59
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=44.46 E-value=16 Score=24.75 Aligned_cols=12 Identities=8% Similarity=-0.161 Sum_probs=6.0
Q ss_pred ccccccCCEEEE
Q 043519 2 LRAYVVTSLRRK 13 (130)
Q Consensus 2 ~Ptl~~gd~vlv 13 (130)
.+.|+.||.||+
T Consensus 53 ~~~L~~GD~VLA 64 (124)
T PF15057_consen 53 RHSLQVGDKVLA 64 (124)
T ss_pred cCcCCCCCEEEE
Confidence 444555555554
No 60
>PF11012 DUF2850: Protein of unknown function (DUF2850); InterPro: IPR021271 This family of proteins with unknown function appear to be restricted to Vibrionaceae.
Probab=44.38 E-value=23 Score=22.32 Aligned_cols=25 Identities=16% Similarity=0.262 Sum_probs=19.2
Q ss_pred CCEEEEeCCEEEECCEEcccccccc
Q 043519 57 GDVVEACEGKLIVNGVVRNKDFILE 81 (130)
Q Consensus 57 GD~v~~~~~~l~vng~~~~~~~~~~ 81 (130)
=|++++....+++||+.++..|..+
T Consensus 16 ~e~~~l~~~GV~~ngrlV~T~F~fD 40 (79)
T PF11012_consen 16 AEEFTLNESGVFRNGRLVATSFEFD 40 (79)
T ss_pred ccEEEECCCcEEECCCEEeeEEEEC
Confidence 4677788888899998888776554
No 61
>COG4013 Uncharacterized protein conserved in archaea [Function unknown]
Probab=44.01 E-value=28 Score=22.28 Aligned_cols=12 Identities=33% Similarity=0.393 Sum_probs=6.3
Q ss_pred eCCCEEEEeCCE
Q 043519 55 KEGDVVEACEGK 66 (130)
Q Consensus 55 ~pGD~v~~~~~~ 66 (130)
+||..|..++|.
T Consensus 36 IpG~vv~~n~g~ 47 (91)
T COG4013 36 IPGRVVHYNDGL 47 (91)
T ss_pred eccEEEEeeccE
Confidence 455555555554
No 62
>PF06394 Pepsin-I3: Pepsin inhibitor-3-like repeated domain; InterPro: IPR010480 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. The members of this group of proteins belong to MEROPS inhibitor family I33, clan IR; the nematode aspartyl protease inhibitors or Aspins. They are restricted to parasitic nematode species. Structural features common to the nematode Aspins include the presence of a signal peptide sequence and the conservation of all four cysteine residues in the mature protein. The Y[V.A]RDLT sequence motif has been suggested as being of crucial functional importance in several filarial nematode inhibitors [], this sequence is not conserved in Tco-API-1 from Trichostrongylus colubriformis (Black scour worm) and it has been demonstrated that Tco-API-1, is not an Aspin as it does not inhibit porcine pepsin []. Related inhibitors from Onchocerca volvulus, Ov33 [] and Ascaris suum (Pig roundworm), PI-3 [] inhibit the in vitro activity of aspartyl proteases such as pepsin and cathepsin E (MEROPS peptidase family A1). Aspin may facilitate the safe passage of the eggs of Ascaris through the host stomach without digestion by pepsin [, ]. The other parasitic nematodes known to express homologous proteins do not pass through the stomach of their hosts []. Several proteins in the family are potent allergens in mammals. The three-dimensional structures of pepsin inhibitor-3 (PI-3) from A. suum and of the complex between PI-3 and porcine pepsin at 1. 75 A and 2.45 A resolution, respectively, have revealed the mechanism of aspartic protease inhibition. PI-3 has a new fold consisting of two identical domains, each comprising an antiparallel beta-sheet flanked by an alpha-helix. In the enzyme-inhibitor complex, the N-terminal beta-strand of PI-3 pairs with one strand of the 'active site flap' (residues 70-82) of pepsin, thus forming an eight-stranded beta-sheet that spans the two proteins. PI-3 has a novel mode of inhibition, using its N-terminal residues to occupy and therefore block the first three binding pockets in pepsin for substrate residues C-terminal to the scissile bond (S1'-S3') [].; PDB: 1F32_A 1F34_B.
Probab=43.12 E-value=20 Score=22.38 Aligned_cols=15 Identities=33% Similarity=0.319 Sum_probs=12.0
Q ss_pred EEeCCEEEECCEEcc
Q 043519 61 EACEGKLIVNGVVRN 75 (130)
Q Consensus 61 ~~~~~~l~vng~~~~ 75 (130)
.+.+++|||||..+.
T Consensus 24 ~V~~nklyvng~~~R 38 (76)
T PF06394_consen 24 VVQNNKLYVNGKYAR 38 (76)
T ss_dssp EEETTEEEETTCEEE
T ss_pred EEECCEEEECCEeec
Confidence 457899999998753
No 63
>PF13144 SAF_2: SAF-like
Probab=41.81 E-value=1.1e+02 Score=21.78 Aligned_cols=52 Identities=8% Similarity=-0.116 Sum_probs=27.1
Q ss_pred ccccCCEEEEEccccCCCCCCCCcEEEEecCCcccccccCCCceEEEEEE----EeCCCEEEEeC
Q 043519 4 AYVVTSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIV----AKEGDVVEACE 64 (130)
Q Consensus 4 tl~~gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVi----g~pGD~v~~~~ 64 (130)
+|..|+.+.-+.+. ...-+++||.|....-. .+-.+--... |--||+|.++|
T Consensus 122 ~i~~G~~i~~~~l~-~~~~V~~G~~V~v~~~~--------g~i~i~~~g~Al~~G~~G~~I~V~N 177 (196)
T PF13144_consen 122 NIRAGQPITPSDLE-PPPLVKRGDIVTVIARS--------GGISISTEGKALEDGALGDTIRVKN 177 (196)
T ss_pred EcCCCCEeeecccc-cceecCCCCEEEEEEEe--------CCEEEEEEEEEccCCCCCCEEEEEE
Confidence 34556666555442 12346778877776532 2222222222 34577777765
No 64
>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=40.39 E-value=46 Score=22.22 Aligned_cols=39 Identities=28% Similarity=0.316 Sum_probs=26.2
Q ss_pred CCCCcEEEEecCCcccccccCCCceEEEEEEEeCCCEEEEeCCEEEECCE
Q 043519 23 PFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEACEGKLIVNGV 72 (130)
Q Consensus 23 ~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~pGD~v~~~~~~l~vng~ 72 (130)
++.||.|.++++. .....+|-||.-+= +-.+|..++++.
T Consensus 4 ~~vGD~V~v~~~~-------~~~~pyIgrI~~i~----e~~~g~~~~~v~ 42 (121)
T cd04714 4 IRVGDCVLFKSPG-------RPSLPYVARIESLW----EDPEGNMVVRVK 42 (121)
T ss_pred EEcCCEEEEeCCC-------CCCCCEEEEEEEEE----EcCCCCEEEEEE
Confidence 4679999999875 23668899996651 113355666655
No 65
>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=38.31 E-value=44 Score=21.47 Aligned_cols=26 Identities=15% Similarity=0.148 Sum_probs=19.3
Q ss_pred CCCCcEEEEecCCcccccccCCCceEEEEEEEe
Q 043519 23 PFANDILIFKSPPLLQEVGYTDDGVYIKGIVAK 55 (130)
Q Consensus 23 ~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~ 55 (130)
++.||.|.+.++. .....+|.||..+
T Consensus 3 ~~vGD~V~v~~~~-------~~~~~~v~~I~~i 28 (119)
T PF01426_consen 3 YKVGDFVYVKPDD-------PPEPPYVARIEEI 28 (119)
T ss_dssp EETTSEEEEECTS-------TTSEEEEEEEEEE
T ss_pred EeCCCEEEEeCCC-------CCCCCEEEEEEEE
Confidence 3568888888765 3567888888877
No 66
>COG0179 MhpD 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=38.12 E-value=43 Score=25.83 Aligned_cols=16 Identities=19% Similarity=0.403 Sum_probs=10.5
Q ss_pred CCCCCCCcEEEEecCC
Q 043519 20 FREPFANDILIFKSPP 35 (130)
Q Consensus 20 ~~~~~rGDiVvf~~p~ 35 (130)
+.+++.||||.==.|.
T Consensus 222 ~~tL~pGDvI~TGTP~ 237 (266)
T COG0179 222 FMTLEPGDVILTGTPS 237 (266)
T ss_pred CcccCCCCEEEeCCCC
Confidence 3467777777766654
No 67
>TIGR03170 flgA_cterm flagella basal body P-ring formation protein FlgA. This model describes a conserved C-terminal region of the flagellar basal body P-ring formation protein FlgA. This sequence region contains a SAF domain, now described by Pfam model pfam08666.
Probab=37.58 E-value=90 Score=20.44 Aligned_cols=12 Identities=8% Similarity=-0.047 Sum_probs=7.2
Q ss_pred CCCCcEEEEecC
Q 043519 23 PFANDILIFKSP 34 (130)
Q Consensus 23 ~~rGDiVvf~~p 34 (130)
+++||.|.....
T Consensus 66 V~~G~~V~i~~~ 77 (122)
T TIGR03170 66 VKRGDTVTVIAR 77 (122)
T ss_pred EcCCCEEEEEEe
Confidence 466666666553
No 68
>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=35.13 E-value=1.1e+02 Score=18.62 Aligned_cols=33 Identities=21% Similarity=0.180 Sum_probs=21.2
Q ss_pred CCCCCCcEEEEecCCcccccccCCCceEEEEEE--------EeCCCEEEE
Q 043519 21 REPFANDILIFKSPPLLQEVGYTDDGVYIKGIV--------AKEGDVVEA 62 (130)
Q Consensus 21 ~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVi--------g~pGD~v~~ 62 (130)
..++.||-|.+.+.. ...-||.+- |.|||.|.+
T Consensus 25 G~i~~g~~v~~~p~~---------~~~~V~sI~~~~~~~~~a~aGd~v~i 65 (83)
T cd03696 25 GSVKVGDKVEILPLG---------EETRVRSIQVHGKDVEEAKAGDRVAL 65 (83)
T ss_pred cEEeCCCEEEECCCC---------ceEEEEEEEECCcCcCEEcCCCEEEE
Confidence 457788888877642 234445444 677888776
No 69
>KOG4030 consensus Uncharacterized conserved protein, contains SPRY domain [Function unknown]
Probab=34.87 E-value=48 Score=23.85 Aligned_cols=24 Identities=29% Similarity=0.300 Sum_probs=15.5
Q ss_pred EEEeCCCEEEEeCCEEEECCEEccccc
Q 043519 52 IVAKEGDVVEACEGKLIVNGVVRNKDF 78 (130)
Q Consensus 52 Vig~pGD~v~~~~~~l~vng~~~~~~~ 78 (130)
|+|+.=|.|+. .+|+||+.+..++
T Consensus 130 vVGvayDHVEL---nfY~NGKn~e~p~ 153 (197)
T KOG4030|consen 130 VVGVAYDHVEL---NFYVNGKNVEDPI 153 (197)
T ss_pred EEEEEeeeEEE---EEEEcCceecccc
Confidence 44444445544 5899999876654
No 70
>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=34.32 E-value=1.2e+02 Score=18.91 Aligned_cols=33 Identities=18% Similarity=0.066 Sum_probs=22.4
Q ss_pred CCCCCCcEEEEecCCcccccccCCCceEEEEEE--------EeCCCEEEE
Q 043519 21 REPFANDILIFKSPPLLQEVGYTDDGVYIKGIV--------AKEGDVVEA 62 (130)
Q Consensus 21 ~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVi--------g~pGD~v~~ 62 (130)
+.++.||-|.+-+.. ...-||.|- |.+||.|.+
T Consensus 29 G~i~~gd~v~i~P~~---------~~~~V~sI~~~~~~~~~a~aG~~v~i 69 (91)
T cd03693 29 GVLKPGMVVTFAPAG---------VTGEVKSVEMHHEPLEEALPGDNVGF 69 (91)
T ss_pred ceeecCCEEEECCCC---------cEEEEEEEEECCcCcCEECCCCEEEE
Confidence 467889988887642 334555554 778888876
No 71
>COG0103 RpsI Ribosomal protein S9 [Translation, ribosomal structure and biogenesis]
Probab=33.56 E-value=51 Score=22.75 Aligned_cols=29 Identities=24% Similarity=0.299 Sum_probs=23.9
Q ss_pred CCceEEEEEEEeCCCEEEEeCCEEEECCEEccccc
Q 043519 44 DDGVYIKGIVAKEGDVVEACEGKLIVNGVVRNKDF 78 (130)
Q Consensus 44 ~~~~~vKRVig~pGD~v~~~~~~l~vng~~~~~~~ 78 (130)
..+.-+-||.-.|| .|++.|||+++++-|
T Consensus 11 kRK~AvArv~l~~g------~G~i~vNg~~~e~yf 39 (130)
T COG0103 11 KRKSAVARVRLVPG------KGKITVNGRPLELYF 39 (130)
T ss_pred cccceEEEEEEEcC------CcEEEECCcCHHHhc
Confidence 46788899998888 689999999987644
No 72
>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=32.89 E-value=72 Score=20.43 Aligned_cols=31 Identities=13% Similarity=0.083 Sum_probs=19.5
Q ss_pred cccccCCEEEEEccccCCCCCCCCcEEEEecCC
Q 043519 3 RAYVVTSLRRKGSVTYYFREPFANDILIFKSPP 35 (130)
Q Consensus 3 Ptl~~gd~vlv~k~~~~~~~~~rGDiVvf~~p~ 35 (130)
||-..+|++.-.... ..+++.||+++|..-.
T Consensus 65 ptC~~~D~i~~~~~l--P~~l~~GD~l~f~~~G 95 (116)
T PF00278_consen 65 PTCDSGDVIARDVML--PKELEVGDWLVFENMG 95 (116)
T ss_dssp SSSSTTSEEEEEEEE--ESTTTTT-EEEESS-S
T ss_pred CCcCCCceEeeeccC--CCCCCCCCEEEEecCc
Confidence 566678887643221 1278999999998754
No 73
>KOG1816 consensus Ubiquitin fusion-degradation protein [Posttranslational modification, protein turnover, chaperones]
Probab=32.82 E-value=2.4e+02 Score=22.28 Aligned_cols=40 Identities=18% Similarity=0.228 Sum_probs=27.1
Q ss_pred CCCCCcEEEEecCCcccccccCCCceEEEEEEEeCCCEEEEeCCEEEEC
Q 043519 22 EPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEACEGKLIVN 70 (130)
Q Consensus 22 ~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~pGD~v~~~~~~l~vn 70 (130)
.+..||++.... +...+.++=+-..|...|.|.+--+-|+
T Consensus 145 cLT~gDvi~i~Y---------n~k~y~i~V~e~kPa~aVsIiEtD~~VD 184 (308)
T KOG1816|consen 145 CLTTGDVILINY---------NEKTYELKVVETKPANAVSIIETDLNVD 184 (308)
T ss_pred ccccCCEEEEec---------CCeEEEEEEEEecCCceeEEEEcceeec
Confidence 355666666655 3456778888889988888865544444
No 74
>PRK15095 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=31.57 E-value=1.8e+02 Score=20.29 Aligned_cols=17 Identities=18% Similarity=0.040 Sum_probs=9.1
Q ss_pred eEEEEEEEeCCCEEEEe
Q 043519 47 VYIKGIVAKEGDVVEAC 63 (130)
Q Consensus 47 ~~vKRVig~pGD~v~~~ 63 (130)
.+.-||+.+-+++|.+.
T Consensus 108 ~~~~~V~~i~~~~v~vD 124 (156)
T PRK15095 108 EMPGVIREINGDSITVD 124 (156)
T ss_pred EEEEEEEEEcCCEEEEE
Confidence 34445555555555554
No 75
>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=30.83 E-value=1.1e+02 Score=20.32 Aligned_cols=14 Identities=14% Similarity=0.287 Sum_probs=11.5
Q ss_pred CCCCCCcEEEEecC
Q 043519 21 REPFANDILIFKSP 34 (130)
Q Consensus 21 ~~~~rGDiVvf~~p 34 (130)
+.++.||.++|..-
T Consensus 30 ~~ikvGD~I~f~~~ 43 (109)
T cd06555 30 QQIKVGDKILFNDL 43 (109)
T ss_pred hcCCCCCEEEEEEc
Confidence 36899999999864
No 76
>PF11320 DUF3122: Protein of unknown function (DUF3122); InterPro: IPR021469 This family of proteins with unknown function appear to be restricted to Cyanobacteria.
Probab=30.75 E-value=1.9e+02 Score=20.10 Aligned_cols=46 Identities=9% Similarity=-0.003 Sum_probs=31.8
Q ss_pred cCCEEEEEccccCCCCCCCCcEEEEecCCcccccccCCCceEEEEEEEeCCC
Q 043519 7 VTSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGD 58 (130)
Q Consensus 7 ~gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~pGD 58 (130)
+|..+.=++-+.+...-+.=.+|+|+.... +....+.=|+||-||.
T Consensus 10 pgq~~yrS~qsLrD~~g~sWQvV~fkr~~~------~~~~~i~LRLVGfPG~ 55 (134)
T PF11320_consen 10 PGQVLYRSRQSLRDQDGNSWQVVLFKRIKP------GQVKPINLRLVGFPGS 55 (134)
T ss_pred CCcEEEEeeeeecCCCCCceEEEEEEecCC------CCCCceEEEEeeCCCc
Confidence 455555555544444556778899987652 2467899999999997
No 77
>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=30.74 E-value=93 Score=17.86 Aligned_cols=13 Identities=23% Similarity=0.381 Sum_probs=9.0
Q ss_pred CCCCCcEEEEecC
Q 043519 22 EPFANDILIFKSP 34 (130)
Q Consensus 22 ~~~rGDiVvf~~p 34 (130)
.|..||.|.+..+
T Consensus 37 ~~~VGD~V~~~~~ 49 (68)
T cd04466 37 PPAVGDRVEFEPE 49 (68)
T ss_pred CCCCCcEEEEEEC
Confidence 3677888887653
No 78
>smart00439 BAH Bromo adjacent homology domain.
Probab=30.25 E-value=1.1e+02 Score=19.40 Aligned_cols=26 Identities=19% Similarity=0.262 Sum_probs=15.4
Q ss_pred CCCCcEEEEecCCcccccccCCCceEEEEEEEe
Q 043519 23 PFANDILIFKSPPLLQEVGYTDDGVYIKGIVAK 55 (130)
Q Consensus 23 ~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~ 55 (130)
++.||.|.+.++. .....++-||..+
T Consensus 2 ~~vgd~V~v~~~~-------~~~~~~i~~I~~i 27 (120)
T smart00439 2 IRVGDFVLVEPDD-------ADEPYYIGRIEEI 27 (120)
T ss_pred cccCCEEEEeCCC-------CCCCCEEEEEEEE
Confidence 4567777777654 1234566666554
No 79
>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=30.25 E-value=45 Score=21.21 Aligned_cols=14 Identities=14% Similarity=-0.145 Sum_probs=10.8
Q ss_pred CccccccCCEEEEE
Q 043519 1 MLRAYVVTSLRRKG 14 (130)
Q Consensus 1 M~Ptl~~gd~vlv~ 14 (130)
|.|.|+.||.|++.
T Consensus 46 ~rp~L~~GDlV~Ar 59 (86)
T cd05790 46 NRPNLNVGDLVYAR 59 (86)
T ss_pred ccccCCCCCEEEEE
Confidence 46788888888775
No 80
>PF08194 DIM: DIM protein; InterPro: IPR013172 Drosophila immune-induced molecules (DIMs) are short proteins induced during the immune response of Drosophila []. This entry includes DIMs 1 to 4 and DIM23.
Probab=29.39 E-value=41 Score=17.93 Aligned_cols=12 Identities=33% Similarity=0.601 Sum_probs=9.4
Q ss_pred eCCEEEECCEEc
Q 043519 63 CEGKLIVNGVVR 74 (130)
Q Consensus 63 ~~~~l~vng~~~ 74 (130)
+.|+|+|||+-+
T Consensus 22 ~pG~ViING~C~ 33 (36)
T PF08194_consen 22 TPGNVIINGKCI 33 (36)
T ss_pred CCCeEEECceee
Confidence 468899999854
No 81
>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=29.10 E-value=39 Score=22.91 Aligned_cols=13 Identities=23% Similarity=0.498 Sum_probs=11.1
Q ss_pred CCCCCCcEEEEec
Q 043519 21 REPFANDILIFKS 33 (130)
Q Consensus 21 ~~~~rGDiVvf~~ 33 (130)
.++++||+|.|..
T Consensus 75 ~~~qpGDlvff~~ 87 (134)
T TIGR02219 75 DAAQPGDVLVFRW 87 (134)
T ss_pred hcCCCCCEEEEee
Confidence 3689999999985
No 82
>COG1126 GlnQ ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]
Probab=28.79 E-value=14 Score=28.12 Aligned_cols=43 Identities=14% Similarity=0.203 Sum_probs=30.1
Q ss_pred CCCCCcEEEEecCCcccccccCCCceEEEEEE-EeCCCEEEEeCCEEEECCEEcc
Q 043519 22 EPFANDILIFKSPPLLQEVGYTDDGVYIKGIV-AKEGDVVEACEGKLIVNGVVRN 75 (130)
Q Consensus 22 ~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVi-g~pGD~v~~~~~~l~vng~~~~ 75 (130)
++++|++|++.-|. ..++.-+=|++ ++. .++.|.++|+|+.+.
T Consensus 24 ~v~~Gevv~iiGpS-------GSGKSTlLRclN~LE----~~~~G~I~i~g~~~~ 67 (240)
T COG1126 24 SVEKGEVVVIIGPS-------GSGKSTLLRCLNGLE----EPDSGSITVDGEDVG 67 (240)
T ss_pred eEcCCCEEEEECCC-------CCCHHHHHHHHHCCc----CCCCceEEECCEecc
Confidence 57899999999886 34554444443 443 467899999997653
No 83
>PF01455 HupF_HypC: HupF/HypC family; InterPro: IPR001109 The large subunit of [NiFe]-hydrogenase, as well as other nickel metalloenzymes, is synthesised as a precursor devoid of the metalloenzyme active site. This precursor then undergoes a complex post-translational maturation process that requires a number of accessory proteins. The hydrogenase expression/formation proteins (HupF/HypC) form a family of small proteins that are hydrogenase precursor-specific chaperones required for this maturation process []. They are believed to keep the hydrogenase precursor in a conformation accessible for metal incorporation [, ].; PDB: 3D3R_A 2Z1C_C 2OT2_A.
Probab=28.27 E-value=52 Score=19.90 Aligned_cols=9 Identities=11% Similarity=-0.215 Sum_probs=3.6
Q ss_pred cccCCEEEE
Q 043519 5 YVVTSLRRK 13 (130)
Q Consensus 5 l~~gd~vlv 13 (130)
.+.||+|++
T Consensus 38 v~~Gd~VLV 46 (68)
T PF01455_consen 38 VKVGDYVLV 46 (68)
T ss_dssp B-TT-EEEE
T ss_pred CCCCCEEEE
Confidence 445555554
No 84
>PF15428 Imm14: Immunity protein 14
Probab=28.08 E-value=1e+02 Score=20.39 Aligned_cols=22 Identities=14% Similarity=0.135 Sum_probs=16.8
Q ss_pred CCCcEEEEecCCcccccccCCCceEEEEEEE
Q 043519 24 FANDILIFKSPPLLQEVGYTDDGVYIKGIVA 54 (130)
Q Consensus 24 ~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig 54 (130)
+.|||..+..+ .+.+...||++
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 46898888875 46788888884
No 85
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=27.32 E-value=84 Score=23.56 Aligned_cols=15 Identities=0% Similarity=-0.144 Sum_probs=10.4
Q ss_pred CccccccCCEEEEEc
Q 043519 1 MLRAYVVTSLRRKGS 15 (130)
Q Consensus 1 M~Ptl~~gd~vlv~k 15 (130)
|.+.|+.||.|.+.-
T Consensus 108 ~~~~~~~GDlV~akV 122 (235)
T PRK04163 108 LRKYLDIGDYIIAKV 122 (235)
T ss_pred hHhhCCCCCEEEEEE
Confidence 456677788887653
No 86
>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=27.28 E-value=1e+02 Score=21.97 Aligned_cols=25 Identities=24% Similarity=0.336 Sum_probs=19.1
Q ss_pred CCCCcEEEEecCCcccccccCCCceEEEEEEEe
Q 043519 23 PFANDILIFKSPPLLQEVGYTDDGVYIKGIVAK 55 (130)
Q Consensus 23 ~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~ 55 (130)
++.||-|.|.++. ...++|.||.-+
T Consensus 4 yrvGD~Vy~~~~~--------~~Py~I~rI~e~ 28 (164)
T cd04709 4 YRVGDYVYFESSP--------NNPYLIRRIEEL 28 (164)
T ss_pred EecCCEEEEECCC--------CCCCEEEEEEEE
Confidence 4679999999864 334789999876
No 87
>TIGR02988 YaaA_near_RecF S4 domain protein YaaA. This small protein has a single S4 domain (pfam01479), as do bacterial ribosomal protein S4, some pseudouridine synthases, tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein family are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members of this family that are not near recF are found instead near dnaA and/or dnaN, the usual neighbors of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage.
Probab=27.12 E-value=30 Score=19.87 Aligned_cols=14 Identities=36% Similarity=0.574 Sum_probs=11.5
Q ss_pred EeCCEEEECCEEcc
Q 043519 62 ACEGKLIVNGVVRN 75 (130)
Q Consensus 62 ~~~~~l~vng~~~~ 75 (130)
+++|.++|||+.+.
T Consensus 31 i~~G~V~VNg~~~~ 44 (59)
T TIGR02988 31 LQENEVLVNGELEN 44 (59)
T ss_pred HHcCCEEECCEEcc
Confidence 36899999999873
No 88
>TIGR00061 L21 ribosomal protein L21. Eubacterial and chloroplast.
Probab=26.98 E-value=88 Score=20.49 Aligned_cols=22 Identities=14% Similarity=0.080 Sum_probs=11.4
Q ss_pred ccCCEEEEEccccCCCCCCCCcEEEEe
Q 043519 6 VVTSLRRKGSVTYYFREPFANDILIFK 32 (130)
Q Consensus 6 ~~gd~vlv~k~~~~~~~~~rGDiVvf~ 32 (130)
..||.+.++++. .+.||-|.|.
T Consensus 14 ~~Gd~i~Ve~l~-----~~~G~~i~l~ 35 (101)
T TIGR00061 14 EEGQTVRIEKLD-----AAPGDTVEFD 35 (101)
T ss_pred eCCCEEEEcccC-----CCCCCEEEEE
Confidence 356666666542 2345555544
No 89
>COG4133 CcmA ABC-type transport system involved in cytochrome c biogenesis, ATPase component [Posttranslational modification, protein turnover, chaperones]
Probab=26.95 E-value=12 Score=27.73 Aligned_cols=58 Identities=10% Similarity=0.082 Sum_probs=39.9
Q ss_pred ccccCCEEEEEccccCCCCCCCCcEEEEecCCcccccccCCCceEEEEEE-EeCCCEEEEeCCEEEECCEEcc
Q 043519 4 AYVVTSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIV-AKEGDVVEACEGKLIVNGVVRN 75 (130)
Q Consensus 4 tl~~gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVi-g~pGD~v~~~~~~l~vng~~~~ 75 (130)
+.+.|++.+...+++ .+..|+++++.-|. ..++.-+=|++ |+ .+-..|+|+.||+.+.
T Consensus 9 ~~~R~e~~lf~~L~f---~l~~Ge~~~i~G~N-------G~GKTtLLRilaGL----l~p~~G~v~~~~~~i~ 67 (209)
T COG4133 9 SCERGERTLFSDLSF---TLNAGEALQITGPN-------GAGKTTLLRILAGL----LRPDAGEVYWQGEPIQ 67 (209)
T ss_pred hhccCcceeecceeE---EEcCCCEEEEECCC-------CCcHHHHHHHHHcc----cCCCCCeEEecCCCCc
Confidence 345688888887775 46789999998875 34555444544 44 3456789999987654
No 90
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=26.33 E-value=66 Score=19.43 Aligned_cols=11 Identities=9% Similarity=0.096 Sum_probs=9.8
Q ss_pred CCCCcEEEEec
Q 043519 23 PFANDILIFKS 33 (130)
Q Consensus 23 ~~rGDiVvf~~ 33 (130)
|..||+|.|..
T Consensus 47 i~vGD~V~ve~ 57 (72)
T PRK00276 47 ILPGDKVTVEL 57 (72)
T ss_pred cCCCCEEEEEE
Confidence 78899999995
No 91
>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=26.11 E-value=89 Score=28.21 Aligned_cols=37 Identities=16% Similarity=0.250 Sum_probs=26.7
Q ss_pred CCCCCcEEEEecCCcccccccCCCceEEEEEEEeCCCEEEEe
Q 043519 22 EPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEAC 63 (130)
Q Consensus 22 ~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~pGD~v~~~ 63 (130)
.+..||+|+|.-.+++. .-...--||.-+||.|+++.
T Consensus 407 hl~dgd~vl~NRqPsLH-----r~si~a~~~~v~~~~t~r~n 443 (868)
T TIGR02390 407 HLIDGDIVLFNRQPSLH-----RMSMMGHKVKVLPGKTFRLN 443 (868)
T ss_pred ehhcCccceeccCCccc-----cccceeEEEEEecCceEeec
Confidence 46789999998766442 23355667777899999884
No 92
>PRK02268 hypothetical protein; Provisional
Probab=25.82 E-value=84 Score=21.94 Aligned_cols=30 Identities=20% Similarity=0.195 Sum_probs=19.7
Q ss_pred CCCCCCcEEEEecCCcccccccCCCceEEEEEEEe
Q 043519 21 REPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAK 55 (130)
Q Consensus 21 ~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~ 55 (130)
+.++.||.|+|.+|... -.++..+..++|+
T Consensus 34 ~RmkpGD~ivyYsp~~~-----~~~~~~~qaftAi 63 (141)
T PRK02268 34 RRMKPGDWIIYYSPKTT-----FGGKDKLQAFTAI 63 (141)
T ss_pred hcCCCCCEEEEEeceEe-----cCCCcccceEEEE
Confidence 45799999999988642 1344455555554
No 93
>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=25.66 E-value=1.1e+02 Score=20.18 Aligned_cols=26 Identities=15% Similarity=0.027 Sum_probs=18.1
Q ss_pred CCCCcEEEEecCCcccccccCCCceEEEEEEEe
Q 043519 23 PFANDILIFKSPPLLQEVGYTDDGVYIKGIVAK 55 (130)
Q Consensus 23 ~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~ 55 (130)
++.||.|.+.++. .+...+|-||..+
T Consensus 4 ~~vGD~V~v~~~~-------~~~~~~i~~I~~i 29 (121)
T cd04717 4 YRVGDCVYVANPE-------DPSKPIIFRIERL 29 (121)
T ss_pred EECCCEEEEeCCC-------CCCCCEEEEEeEE
Confidence 4679999998875 2356777777654
No 94
>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=25.58 E-value=2.2e+02 Score=19.28 Aligned_cols=14 Identities=7% Similarity=0.052 Sum_probs=11.2
Q ss_pred CCCCCcEEEEecCC
Q 043519 22 EPFANDILIFKSPP 35 (130)
Q Consensus 22 ~~~rGDiVvf~~p~ 35 (130)
.++.||+|.+++++
T Consensus 5 ~i~vGD~V~v~~d~ 18 (130)
T cd04712 5 TIRVGDVVSVERDD 18 (130)
T ss_pred EEeCCCEEEEcCCC
Confidence 46789999998875
No 95
>KOG1535 consensus Predicted fumarylacetoacetate hydralase [General function prediction only]
Probab=25.44 E-value=94 Score=23.27 Aligned_cols=29 Identities=21% Similarity=0.289 Sum_probs=19.3
Q ss_pred CCCCCCcEEEEecCCcccccccCCCceEEEEEEEeCCCEEEEe
Q 043519 21 REPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEAC 63 (130)
Q Consensus 21 ~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~pGD~v~~~ 63 (130)
..+..||+|+=-.|+ +.--+| |||.++..
T Consensus 175 ~tL~~GDvILTGTP~---------GVg~v~-----~Gd~i~~e 203 (217)
T KOG1535|consen 175 MTLEPGDVILTGTPE---------GVGEVK-----PGDVIQCE 203 (217)
T ss_pred eeecCCCEEEecCCC---------cccccc-----CCCEEEec
Confidence 356779988888775 222233 88888764
No 96
>PRK05573 rplU 50S ribosomal protein L21; Validated
Probab=25.40 E-value=1e+02 Score=20.21 Aligned_cols=10 Identities=0% Similarity=-0.031 Sum_probs=5.3
Q ss_pred cCCEEEEEcc
Q 043519 7 VTSLRRKGSV 16 (130)
Q Consensus 7 ~gd~vlv~k~ 16 (130)
.||.+.++++
T Consensus 16 ~Gd~i~v~~l 25 (103)
T PRK05573 16 EGDVIKVEKL 25 (103)
T ss_pred CCCEEEEccc
Confidence 4555555544
No 97
>PLN02856 fumarylacetoacetase
Probab=25.28 E-value=2e+02 Score=23.88 Aligned_cols=29 Identities=10% Similarity=-0.049 Sum_probs=13.9
Q ss_pred ccccCCEEEEEccccCCCCCCCCcEEEEec
Q 043519 4 AYVVTSLRRKGSVTYYFREPFANDILIFKS 33 (130)
Q Consensus 4 tl~~gd~vlv~k~~~~~~~~~rGDiVvf~~ 33 (130)
||++||++.---.+ .....+.|+.+....
T Consensus 346 tL~pGDLi~TGTps-G~~~~~~G~llElt~ 374 (424)
T PLN02856 346 NLRPGDLLGSGTIS-GPEPGSLGCLLELTW 374 (424)
T ss_pred ecCCCCEEEeCCCC-CCccCCCCCEEEEEe
Confidence 45566666543222 122345566665543
No 98
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=24.94 E-value=1.8e+02 Score=18.10 Aligned_cols=34 Identities=15% Similarity=0.248 Sum_probs=16.6
Q ss_pred CCCCCcEEEEecCCcccccccCCCceEEEEEEEeCC
Q 043519 22 EPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEG 57 (130)
Q Consensus 22 ~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~pG 57 (130)
.++.||.|+++......+. ......+.-|+-..|
T Consensus 5 ~Vk~Gd~ViV~~~~~~~~~--~~~dWWmg~Vi~~~g 38 (75)
T PF11302_consen 5 SVKPGDTVIVQDEQEVGQK--QDKDWWMGQVIHCEG 38 (75)
T ss_pred ccCCCCEEEEecCcccccc--CCCCcEEEEEEEEec
Confidence 4567777777765422111 233455555554433
No 99
>COG4127 Uncharacterized conserved protein [Function unknown]
Probab=24.87 E-value=70 Score=25.16 Aligned_cols=26 Identities=19% Similarity=0.199 Sum_probs=20.6
Q ss_pred CCCCCCcEEEEecCCcccccccCCCceEEEEEEE
Q 043519 21 REPFANDILIFKSPPLLQEVGYTDDGVYIKGIVA 54 (130)
Q Consensus 21 ~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig 54 (130)
.+++.||.|+...+. ..+++|.+|.+
T Consensus 71 neI~KGDlvi~y~k~--------~r~y~IGkVts 96 (318)
T COG4127 71 NEIQKGDLVITYSKS--------NRTYLIGKVTS 96 (318)
T ss_pred HHhccCcEEEeeccc--------CceEEEEEecC
Confidence 468999999998875 57788887765
No 100
>PF13987 YedD: YedD-like protein
Probab=24.55 E-value=87 Score=20.79 Aligned_cols=22 Identities=18% Similarity=0.252 Sum_probs=14.5
Q ss_pred EEEEEeCCCEEEEeCCEEEECC
Q 043519 50 KGIVAKEGDVVEACEGKLIVNG 71 (130)
Q Consensus 50 KRVig~pGD~v~~~~~~l~vng 71 (130)
-||||+||-.....+.-.-|+-
T Consensus 47 QRVia~PGKL~~~~~d~yNVt~ 68 (111)
T PF13987_consen 47 QRVIAKPGKLMLRDDDLYNVTR 68 (111)
T ss_pred heeeecccceeeecCCEEEecc
Confidence 4788888877766655444443
No 101
>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=24.40 E-value=1.8e+02 Score=17.88 Aligned_cols=37 Identities=16% Similarity=0.066 Sum_probs=21.8
Q ss_pred CCCCCCcEEEEecCCcccccccCCCceEEEEEE--------EeCCCEEEE
Q 043519 21 REPFANDILIFKSPPLLQEVGYTDDGVYIKGIV--------AKEGDVVEA 62 (130)
Q Consensus 21 ~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVi--------g~pGD~v~~ 62 (130)
..++.||-+.+.+.... .....-||.|- |.|||.+.+
T Consensus 25 G~v~~g~~v~~~P~~~g-----~~~~~~V~sI~~~~~~~~~a~aGd~v~l 69 (87)
T cd03694 25 GVIRLGDTLLLGPDQDG-----SFRPVTVKSIHRNRSPVRVVRAGQSASL 69 (87)
T ss_pred CEEeCCCEEEECCCCCC-----CEeEEEEEEEEECCeECCEECCCCEEEE
Confidence 46788888888764200 00134455554 777887776
No 102
>PF00829 Ribosomal_L21p: Ribosomal prokaryotic L21 protein; InterPro: IPR001787 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 L21 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L21 is known to bind to the 23S rRNA in the presence of L20. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities, groups: Bacterial L21. Marchantia polymorpha chloroplast L21. Cyanelle L21. Plant chloroplast L21 (nuclear-encoded). Bacterial L21 is a protein of about 100 amino-acid residues, the mature form of the spinach chloroplast L21 has 200 residues.; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2XG0_V 2X9S_V 2XG2_V 3UZ1_2 2Y19_V 2WDL_V 3V23_V 2WRO_V 2WRL_V 2Y11_V ....
Probab=23.73 E-value=82 Score=20.33 Aligned_cols=22 Identities=5% Similarity=-0.059 Sum_probs=12.8
Q ss_pred ccCCEEEEEccccCCCCCCCCcEEEEe
Q 043519 6 VVTSLRRKGSVTYYFREPFANDILIFK 32 (130)
Q Consensus 6 ~~gd~vlv~k~~~~~~~~~rGDiVvf~ 32 (130)
..||.+.++++. ...||-|.|+
T Consensus 15 ~~gd~i~v~~l~-----~~~G~~i~l~ 36 (96)
T PF00829_consen 15 EEGDVIDVERLD-----AEVGDKIELD 36 (96)
T ss_dssp SSSEEEEEESTS-----SSTTSEEEET
T ss_pred eCCCEEEECCcC-----cCCCCEEEEE
Confidence 456777776652 3456666554
No 103
>PF14345 GDYXXLXY: GDYXXLXY protein
Probab=23.64 E-value=1.1e+02 Score=20.95 Aligned_cols=33 Identities=6% Similarity=-0.098 Sum_probs=25.4
Q ss_pred ccccCCEEEEEccccCCCCCCCCcEEEEecCCc
Q 043519 4 AYVVTSLRRKGSVTYYFREPFANDILIFKSPPL 36 (130)
Q Consensus 4 tl~~gd~vlv~k~~~~~~~~~rGDiVvf~~p~~ 36 (130)
++..|.-|++.--.+..+.+-+||.|.++...+
T Consensus 16 ~l~~G~~v~L~~~PvDPRdllrGdYv~L~Y~i~ 48 (144)
T PF14345_consen 16 ILAQGKEVTLKTAPVDPRDLLRGDYVALNYDIS 48 (144)
T ss_pred HHhCCCEEEEEecccCcccccccceEEEEcccc
Confidence 467788888776556667889999999998653
No 104
>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=23.37 E-value=1.1e+02 Score=20.60 Aligned_cols=15 Identities=20% Similarity=0.224 Sum_probs=9.9
Q ss_pred CCCCCCcEEEEecCC
Q 043519 21 REPFANDILIFKSPP 35 (130)
Q Consensus 21 ~~~~rGDiVvf~~p~ 35 (130)
+.++.||.|+|..+.
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 478999999999864
No 105
>PF10030 DUF2272: Uncharacterized protein conserved in bacteria (DUF2272); InterPro: IPR019262 This is a domain of unknown function found in proteins of unknown function.
Probab=23.37 E-value=2.3e+02 Score=20.65 Aligned_cols=46 Identities=15% Similarity=0.133 Sum_probs=28.6
Q ss_pred CCCCCCcEEEEecCCccc----c-cccCCCceEEEEEEE---eCCCEEEEeCCE
Q 043519 21 REPFANDILIFKSPPLLQ----E-VGYTDDGVYIKGIVA---KEGDVVEACEGK 66 (130)
Q Consensus 21 ~~~~rGDiVvf~~p~~~~----~-~~~~~~~~~vKRVig---~pGD~v~~~~~~ 66 (130)
..|+.||+|.+....... . .........+--|++ ..|++|++-+|.
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 468999999987654210 0 000113356667888 777888887664
No 106
>smart00841 Elong-fact-P_C Elongation factor P, C-terminal. 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 PUBMED:15210970.
Probab=23.21 E-value=1.3e+02 Score=17.55 Aligned_cols=12 Identities=8% Similarity=-0.020 Sum_probs=8.6
Q ss_pred CCCCcEEEEecC
Q 043519 23 PFANDILIFKSP 34 (130)
Q Consensus 23 ~~rGDiVvf~~p 34 (130)
++.||.|.++..
T Consensus 38 I~~Gd~I~V~T~ 49 (56)
T smart00841 38 INEGDKIKVDTR 49 (56)
T ss_pred ccCCCEEEEECC
Confidence 567888777764
No 107
>PF14415 DUF4424: Domain of unknown function (DUF4424)
Probab=23.08 E-value=76 Score=24.28 Aligned_cols=19 Identities=37% Similarity=0.787 Sum_probs=14.9
Q ss_pred ccCCCCCCCCcE---EEEecCC
Q 043519 17 TYYFREPFANDI---LIFKSPP 35 (130)
Q Consensus 17 ~~~~~~~~rGDi---Vvf~~p~ 35 (130)
.|.|..+...|+ |.|..|+
T Consensus 6 ~Y~F~N~t~~dv~~~VaFPlP~ 27 (253)
T PF14415_consen 6 RYVFRNPTDQDVTVTVAFPLPD 27 (253)
T ss_pred EEEEeCCCCCcEEEEEEEeCCC
Confidence 467778888885 9999885
No 108
>COG4043 Preprotein translocase subunit Sec61beta [Intracellular trafficking, secretion, and vesicular transport]
Probab=22.67 E-value=63 Score=21.45 Aligned_cols=13 Identities=31% Similarity=0.391 Sum_probs=10.9
Q ss_pred CCCCCCCcEEEEe
Q 043519 20 FREPFANDILIFK 32 (130)
Q Consensus 20 ~~~~~rGDiVvf~ 32 (130)
.+.+++||.|+|.
T Consensus 31 rr~ik~GD~IiF~ 43 (111)
T COG4043 31 RRQIKPGDKIIFN 43 (111)
T ss_pred hcCCCCCCEEEEc
Confidence 3578999999996
No 109
>PF05949 DUF881: Bacterial protein of unknown function (DUF881); InterPro: IPR010273 This family consists of a series of hypothetical bacterial proteins. One of the family members Q45543 from SWISSPROT from Bacillus subtilis is thought to be involved in cell division and sporulation [].; PDB: 3GMG_B.
Probab=22.52 E-value=1e+02 Score=21.39 Aligned_cols=23 Identities=17% Similarity=0.505 Sum_probs=16.3
Q ss_pred CEEEEeCCEEEECCEEccccccc
Q 043519 58 DVVEACEGKLIVNGVVRNKDFIL 80 (130)
Q Consensus 58 D~v~~~~~~l~vng~~~~~~~~~ 80 (130)
-.|++.++.+.|||+++..+|..
T Consensus 72 S~Ir~~g~~i~Vng~~i~~Py~I 94 (149)
T PF05949_consen 72 SAIRCAGGTILVNGRPISPPYVI 94 (149)
T ss_dssp --EEEETTEEEETTEEE-SSEEE
T ss_pred EEEEEeCCEEEECCEEccCCEEE
Confidence 34566689999999999888744
No 110
>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=22.28 E-value=1.6e+02 Score=20.20 Aligned_cols=27 Identities=26% Similarity=0.289 Sum_probs=20.6
Q ss_pred CCCCCcEEEEecCCcccccccCCCceEEEEEEEe
Q 043519 22 EPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAK 55 (130)
Q Consensus 22 ~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~ 55 (130)
.++.||-|.+.+.. ....++|.||...
T Consensus 11 ~~~vgD~Vyv~~~~-------~~ePyyIgrI~e~ 37 (135)
T cd04710 11 LLKVNDHIYMSSEP-------PGEPYYIGRIMEF 37 (135)
T ss_pred EEeCCCEEEEecCC-------CCCCCEEEEEEEE
Confidence 46889999999864 2456789999874
No 111
>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=22.27 E-value=2e+02 Score=17.61 Aligned_cols=14 Identities=7% Similarity=-0.223 Sum_probs=10.9
Q ss_pred CCCCCCcEEEEecC
Q 043519 21 REPFANDILIFKSP 34 (130)
Q Consensus 21 ~~~~rGDiVvf~~p 34 (130)
..++.||-|.+.++
T Consensus 25 G~v~~gd~v~~~p~ 38 (87)
T cd03697 25 GTIKVGDEVEIVGF 38 (87)
T ss_pred CCCccCCEEEEeCC
Confidence 56889999988764
No 112
>PF00380 Ribosomal_S9: Ribosomal protein S9/S16; InterPro: IPR000754 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 S9 is one of the proteins from the small ribosomal subunit. It belongs to the S9P family of ribosomal proteins which, on the basis of sequence similarities [, ], groups bacterial; algal chloroplast; cyanelle and archaeal S9 proteins; and mammalian; plant; and yeast mitochondrial ribosomal S9 proteins. These proteins adopt a beta-alpha-beta fold similar to that found in numerous RNA/DNA-binding proteins, as well as in kinases from the GHMP kinase family [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2V46_I 3T1H_I 3MR8_I 3F1G_I 3D5C_I 3D5A_I 2WDG_I 3MS0_I 2WDM_I 2J02_I ....
Probab=22.06 E-value=71 Score=21.62 Aligned_cols=26 Identities=31% Similarity=0.431 Sum_probs=18.9
Q ss_pred eEEEEEEEeCCCEEEEeCCEEEECCEEccccc
Q 043519 47 VYIKGIVAKEGDVVEACEGKLIVNGVVRNKDF 78 (130)
Q Consensus 47 ~~vKRVig~pGD~v~~~~~~l~vng~~~~~~~ 78 (130)
.-+-||.-.|| +|.+.|||+++.+-|
T Consensus 5 ~a~A~v~l~~G------~G~i~INg~~l~~yf 30 (121)
T PF00380_consen 5 TAIARVWLKPG------SGKIRINGKPLEEYF 30 (121)
T ss_dssp TEEEEEEEEES------SSEEEETTSEHHHHS
T ss_pred eEEEEEEEEeC------ceEEEECCEEHHHhc
Confidence 44556666666 589999999986644
No 113
>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=21.88 E-value=76 Score=19.72 Aligned_cols=13 Identities=15% Similarity=0.153 Sum_probs=9.6
Q ss_pred Cc-cccccCCEEEE
Q 043519 1 ML-RAYVVTSLRRK 13 (130)
Q Consensus 1 M~-Ptl~~gd~vlv 13 (130)
|. .+++.||.|+|
T Consensus 1 M~~~~~~~GD~VyV 14 (75)
T PF11132_consen 1 MDMKPYHAGDIVYV 14 (75)
T ss_pred CCccccCCCCEEEE
Confidence 44 67788888877
No 114
>smart00216 VWD von Willebrand factor (vWF) type D domain. Von Willebrand factor contains several type D domains: D1 and D2 are present within the N-terminal propeptide whereas the remaining D domains are required for multimerisation.
Probab=21.81 E-value=2.6e+02 Score=18.85 Aligned_cols=32 Identities=28% Similarity=0.385 Sum_probs=22.0
Q ss_pred EEEE-EEEeCCCEEEEe--CCEEEECCEEcccccc
Q 043519 48 YIKG-IVAKEGDVVEAC--EGKLIVNGVVRNKDFI 79 (130)
Q Consensus 48 ~vKR-Vig~pGD~v~~~--~~~l~vng~~~~~~~~ 79 (130)
..|. .+-+.++.|.+. +..+.+||+.+.-++.
T Consensus 63 ~~~~v~v~~~~~~i~~~~~~~~v~vng~~v~~p~~ 97 (162)
T smart00216 63 CLKSVKVELNGDEIELKDDNGTVTVNGQQVSLPYK 97 (162)
T ss_pred EEEEEEEEECCEEEEEEeCCCEEEECCEEeeCCcC
Confidence 3444 456667778887 5799999997655543
No 115
>PF01079 Hint: Hint module; InterPro: IPR001767 This domain identifies a group of cysteine peptidases correspond to MEROPS peptidase family C46 (clan CH). The type example is the Hedgehog protein from Drosophila melanogaster (Fruit fly). These are involved in intracellular signalling required for a variety of patterning events during development. The hedgehog family of proteins self process by a cysteine-dependent mechanism, which is a one-time autolytic cleavage. It is differentiated from a typical peptidase reaction by the fact that the newly-formed carboxyl group is esterified with cholesterol, rather than being left free. The three-dimensional structure of the autolytic domain of the hedgehog protein of D. melanogaster shows that it is formed from two divergent copies of a module that also occurs in inteins, called a Hint domain [,].; GO: 0008233 peptidase activity, 0006508 proteolysis; PDB: 3K7H_B 3K7I_B 3K7G_B 1AT0_A 3MXW_A 3M1N_B 3HO5_H 2WFR_A 2WFQ_A 2WG3_B ....
Probab=21.70 E-value=1.4e+02 Score=22.19 Aligned_cols=15 Identities=13% Similarity=0.277 Sum_probs=6.7
Q ss_pred EEEeCCCEEEEeCCE
Q 043519 52 IVAKEGDVVEACEGK 66 (130)
Q Consensus 52 Vig~pGD~v~~~~~~ 66 (130)
|--..|.++.++..+
T Consensus 69 i~te~g~~l~LTp~H 83 (217)
T PF01079_consen 69 IETEDGRSLTLTPNH 83 (217)
T ss_dssp EEETTS-EEEE-TT-
T ss_pred EEcCCCCeEEecCCc
Confidence 444455666666544
No 116
>TIGR00074 hypC_hupF hydrogenase assembly chaperone HypC/HupF. An additional proposed function is to shuttle the iron atom that has been liganded at the HypC/HypD complex to the precursor of the large hydrogenase (HycE) subunit. PubMed:12441107.
Probab=21.32 E-value=73 Score=19.78 Aligned_cols=12 Identities=17% Similarity=0.205 Sum_probs=7.1
Q ss_pred CCCCCcEEEEec
Q 043519 22 EPFANDILIFKS 33 (130)
Q Consensus 22 ~~~rGDiVvf~~ 33 (130)
+++.||+|+...
T Consensus 35 ~~~vGD~VLVH~ 46 (76)
T TIGR00074 35 EVKVGDYVLVHV 46 (76)
T ss_pred CCCCCCEEEEec
Confidence 355666666654
No 117
>PF05382 Amidase_5: Bacteriophage peptidoglycan hydrolase ; InterPro: IPR008044 This entry is represented by Bacteriophage SFi21, lysin (Cell wall hydrolase; 3.5.1.28 from EC). At least one of proteins in this entry, the Pal protein from the pneumococcal bacteriophage Dp-1 (O03979 from SWISSPROT) has been shown to be an N-acetylmuramoyl-L-alanine amidase []. According to the known modular structure of this and other peptidoglycan hydrolases from the pneumococcal system, the active site should reside within this domain while a C-terminal domain binds to the choline residues of the cell wall teichoic acids [, ].
Probab=21.21 E-value=61 Score=22.70 Aligned_cols=14 Identities=21% Similarity=0.247 Sum_probs=11.5
Q ss_pred CCCCCCcEEEEecC
Q 043519 21 REPFANDILIFKSP 34 (130)
Q Consensus 21 ~~~~rGDiVvf~~p 34 (130)
..+++|||+++...
T Consensus 74 ~~~q~GDI~I~g~~ 87 (145)
T PF05382_consen 74 WNLQRGDIFIWGRR 87 (145)
T ss_pred ccccCCCEEEEcCC
Confidence 36899999998664
No 118
>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=21.14 E-value=60 Score=20.58 Aligned_cols=13 Identities=31% Similarity=0.542 Sum_probs=10.8
Q ss_pred CCCCCCcEEEEec
Q 043519 21 REPFANDILIFKS 33 (130)
Q Consensus 21 ~~~~rGDiVvf~~ 33 (130)
.++++||++.|..
T Consensus 50 ~~~~pGDlif~~~ 62 (105)
T PF00877_consen 50 SELQPGDLIFFKG 62 (105)
T ss_dssp GG-TTTEEEEEEG
T ss_pred hcCCcccEEEEeC
Confidence 4689999999998
No 119
>PF01052 SpoA: Surface presentation of antigens (SPOA); InterPro: IPR001543 Proteins in this group are involved in a secretory pathway responsible for the surface presentation of invasion plasmid antigen needed for the entry of Salmonella and other species into mammalian cells [, ].They could play a role in preserving the translocation competence of the IPA antigens and are required for secretion of the three IPA proteins []. The C-terminal region of flagellar motor switch proteins FliN and FliM is also included in this entry. ; PDB: 3UEP_A 1O9Y_B 1YAB_A.
Probab=20.92 E-value=1.2e+02 Score=18.13 Aligned_cols=13 Identities=15% Similarity=0.360 Sum_probs=8.1
Q ss_pred CCCCCcEEEEecC
Q 043519 22 EPFANDILIFKSP 34 (130)
Q Consensus 22 ~~~rGDiVvf~~p 34 (130)
+++.||++.+..+
T Consensus 28 ~L~~Gdvi~l~~~ 40 (77)
T PF01052_consen 28 NLKVGDVIPLDKP 40 (77)
T ss_dssp C--TT-EEEECCE
T ss_pred cCCCCCEEEeCCC
Confidence 5788888888876
No 120
>COG3250 LacZ Beta-galactosidase/beta-glucuronidase [Carbohydrate transport and metabolism]
Probab=20.64 E-value=94 Score=27.90 Aligned_cols=16 Identities=38% Similarity=0.530 Sum_probs=14.1
Q ss_pred EEEEeCCEEEECCEEc
Q 043519 59 VVEACEGKLIVNGVVR 74 (130)
Q Consensus 59 ~v~~~~~~l~vng~~~ 74 (130)
+|+++++.++|||+++
T Consensus 285 ~iei~~~~~~iNGkpv 300 (808)
T COG3250 285 TVEIKDGLLLINGKPV 300 (808)
T ss_pred EEEEECCeEEECCeEE
Confidence 6788899999999986
No 121
>smart00663 RPOLA_N RNA polymerase I subunit A N-terminus.
Probab=20.38 E-value=3.1e+02 Score=21.49 Aligned_cols=37 Identities=16% Similarity=0.349 Sum_probs=26.5
Q ss_pred CCCCCcEEEEecCCcccccccCCCceEEEEEEEeCCCEEEEe
Q 043519 22 EPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEAC 63 (130)
Q Consensus 22 ~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~pGD~v~~~ 63 (130)
.+..||+|+|.-..++. ......-|+.-++|.|+.+.
T Consensus 198 ~l~dgd~Vl~NRqPsLH-----r~si~a~~v~v~~~~tir~n 234 (295)
T smart00663 198 HVIDGDVVLFNRQPTLH-----RMSIQAHRVRVLEGKTIRLN 234 (295)
T ss_pred ehhcCCEEEEecCCccc-----cccceeEEEEEecCceEEec
Confidence 56789999998766543 23355667777788888884
No 122
>PRK10413 hydrogenase 2 accessory protein HypG; Provisional
Probab=20.29 E-value=79 Score=19.93 Aligned_cols=12 Identities=8% Similarity=-0.180 Sum_probs=7.4
Q ss_pred cccccCCEEEEE
Q 043519 3 RAYVVTSLRRKG 14 (130)
Q Consensus 3 Ptl~~gd~vlv~ 14 (130)
|..+.||+|++.
T Consensus 41 ~~~~vGDyVLVH 52 (82)
T PRK10413 41 PADLLGQWVLVH 52 (82)
T ss_pred cccccCCEEEEe
Confidence 345567777764
No 123
>PF06097 DUF945: Bacterial protein of unknown function (DUF945); InterPro: IPR010352 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=20.29 E-value=1.1e+02 Score=24.63 Aligned_cols=21 Identities=29% Similarity=0.330 Sum_probs=16.5
Q ss_pred CCCEEEE----eCCEEEECCEEccc
Q 043519 56 EGDVVEA----CEGKLIVNGVVRNK 76 (130)
Q Consensus 56 pGD~v~~----~~~~l~vng~~~~~ 76 (130)
.|+.+.. ++|++.+||++++.
T Consensus 433 ~~~~~~~~~~~~~g~l~lNG~~ipl 457 (460)
T PF06097_consen 433 DGDNYVLELQLKNGQLTLNGQPIPL 457 (460)
T ss_pred cCCEEEEEEEEECCEEEECCeECch
Confidence 6776654 69999999998764
No 124
>CHL00010 infA translation initiation factor 1
Probab=20.18 E-value=1.1e+02 Score=18.89 Aligned_cols=11 Identities=9% Similarity=0.042 Sum_probs=9.5
Q ss_pred CCCCcEEEEec
Q 043519 23 PFANDILIFKS 33 (130)
Q Consensus 23 ~~rGDiVvf~~ 33 (130)
|..||.|.|..
T Consensus 47 ~~vGD~V~ve~ 57 (78)
T CHL00010 47 ILPGDRVKVEL 57 (78)
T ss_pred cCCCCEEEEEE
Confidence 67899999995
No 125
>PF13759 2OG-FeII_Oxy_5: Putative 2OG-Fe(II) oxygenase; PDB: 3BVC_B 2RG4_A.
Probab=20.09 E-value=69 Score=20.28 Aligned_cols=13 Identities=38% Similarity=0.600 Sum_probs=8.8
Q ss_pred CCCCCcEEEEecC
Q 043519 22 EPFANDILIFKSP 34 (130)
Q Consensus 22 ~~~rGDiVvf~~p 34 (130)
+|+.||+|+|.+-
T Consensus 69 ~p~~G~lvlFPs~ 81 (101)
T PF13759_consen 69 EPEEGDLVLFPSW 81 (101)
T ss_dssp ---TTEEEEEETT
T ss_pred CCCCCEEEEeCCC
Confidence 5899999999863
Done!