Query psy1800
Match_columns 81
No_of_seqs 101 out of 276
Neff 4.9
Searched_HMMs 46136
Date Fri Aug 16 19:44:21 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1800.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1800hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00036 40S ribosomal protein 100.0 1.1E-30 2.3E-35 195.8 9.5 74 1-74 175-248 (261)
2 PTZ00118 40S ribosomal protein 100.0 1.2E-30 2.6E-35 195.6 9.5 74 1-74 175-248 (262)
3 PTZ00223 40S ribosomal protein 100.0 6.2E-30 1.3E-34 192.7 9.4 74 1-74 172-246 (273)
4 KOG0378|consensus 99.9 2.1E-28 4.6E-33 182.7 5.4 74 1-74 175-248 (263)
5 PRK04313 30S ribosomal protein 99.9 9.5E-26 2.1E-30 167.3 9.2 65 1-66 172-237 (237)
6 COG1471 RPS4A Ribosomal protei 99.9 1.8E-24 4E-29 160.5 9.2 67 1-68 174-241 (241)
7 PF00467 KOW: KOW motif; Inte 97.8 3.6E-05 7.7E-10 40.9 3.7 31 3-36 1-31 (32)
8 smart00739 KOW KOW (Kyprides, 97.7 7E-05 1.5E-09 37.5 3.3 26 1-26 2-27 (28)
9 TIGR01080 rplX_A_E ribosomal p 95.7 0.039 8.4E-07 37.3 5.4 36 2-40 43-78 (114)
10 PRK12281 rplX 50S ribosomal pr 94.7 0.092 2E-06 33.0 4.7 37 1-40 7-43 (76)
11 CHL00141 rpl24 ribosomal prote 94.6 0.099 2.1E-06 33.3 4.7 36 1-39 9-44 (83)
12 PRK00004 rplX 50S ribosomal pr 94.3 0.11 2.5E-06 34.2 4.7 76 1-79 5-103 (105)
13 PRK01191 rpl24p 50S ribosomal 94.3 0.22 4.7E-06 34.1 6.1 34 2-38 47-80 (120)
14 TIGR01079 rplX_bact ribosomal 93.1 0.22 4.8E-06 32.9 4.5 74 1-77 4-101 (104)
15 PF13051 DUF3912: Protein of u 91.5 0.69 1.5E-05 28.6 4.8 50 3-56 5-55 (68)
16 COG2163 RPL14A Ribosomal prote 88.9 1.1 2.3E-05 30.9 4.6 34 1-38 5-38 (125)
17 PTZ00194 60S ribosomal protein 87.6 1.4 3.1E-05 31.0 4.7 51 2-55 48-105 (143)
18 PF01588 tRNA_bind: Putative t 84.1 3.1 6.6E-05 26.3 4.6 22 17-38 2-23 (95)
19 PTZ00065 60S ribosomal protein 83.9 1.5 3.3E-05 30.4 3.3 31 2-36 9-39 (130)
20 PF14001 YdfZ: YdfZ protein 82.4 4.1 8.9E-05 25.2 4.4 40 2-45 11-56 (64)
21 TIGR03784 marine_sortase sorta 81.9 3.7 8E-05 29.1 4.7 47 30-77 111-157 (174)
22 TIGR01076 sortase_fam LPXTG-si 80.3 7.1 0.00015 26.0 5.5 65 8-77 44-112 (136)
23 COG0198 RplX Ribosomal protein 80.0 3.8 8.2E-05 27.4 4.0 26 2-27 6-31 (104)
24 PRK04333 50S ribosomal protein 79.8 2.9 6.3E-05 26.7 3.3 32 1-36 4-35 (84)
25 cd05828 Sortase_D_4 Sortase D 75.0 7.5 0.00016 25.5 4.4 65 7-77 45-109 (127)
26 PTZ00471 60S ribosomal protein 73.0 4.6 0.0001 28.2 3.0 24 1-24 5-28 (134)
27 PRK05609 nusG transcription an 71.3 7.7 0.00017 26.5 3.9 27 1-27 127-153 (181)
28 TIGR00405 L26e_arch ribosomal 70.5 12 0.00026 25.0 4.6 27 1-27 87-113 (145)
29 PRK08559 nusG transcription an 69.3 14 0.0003 25.3 4.8 28 1-28 95-122 (153)
30 cd01723 LSm4 The eukaryotic Sm 69.3 13 0.00028 22.7 4.2 51 15-67 22-73 (76)
31 TIGR00922 nusG transcription t 68.4 8.9 0.00019 26.1 3.7 26 1-26 120-145 (172)
32 PF00181 Ribosomal_L2: Ribosom 64.7 15 0.00033 22.6 3.8 32 17-48 33-65 (77)
33 KOG1708|consensus 63.2 13 0.00029 28.0 3.9 36 1-39 73-108 (236)
34 TIGR03318 YdfZ_fam putative se 61.5 7.5 0.00016 24.1 2.0 40 2-45 12-57 (65)
35 KOG1999|consensus 59.8 21 0.00046 32.1 5.1 27 1-27 460-486 (1024)
36 cd02153 tRNA_bindingDomain The 58.9 24 0.00051 22.0 4.1 20 17-36 2-21 (99)
37 smart00609 VIT Vault protein I 58.5 15 0.00031 24.8 3.2 47 4-53 62-118 (130)
38 cd06166 Sortase_D_5 Sortase D 57.7 41 0.00089 21.9 5.2 65 8-77 45-113 (126)
39 TIGR01955 RfaH transcriptional 56.2 57 0.0012 21.7 6.0 25 1-25 109-133 (159)
40 KOG1999|consensus 54.1 14 0.0003 33.3 3.1 53 2-56 583-636 (1024)
41 cd00004 Sortase Sortases are c 54.0 29 0.00062 22.4 4.0 65 8-78 45-114 (128)
42 cd02800 tRNA_bind_EcMetRS_like 52.8 42 0.00091 21.2 4.5 25 17-41 12-36 (105)
43 PF07290 DUF1449: Protein of u 52.7 21 0.00045 26.1 3.4 30 14-43 136-165 (202)
44 PRK09014 rfaH transcriptional 52.2 24 0.00052 23.8 3.5 25 1-25 110-134 (162)
45 cd05827 Sortase_C_3 Sortase C 52.1 48 0.001 21.7 4.9 65 8-77 47-115 (131)
46 cd01733 LSm10 The eukaryotic S 52.1 51 0.0011 20.3 4.7 47 16-65 31-78 (78)
47 COG0250 NusG Transcription ant 50.1 25 0.00055 25.0 3.5 27 1-27 124-150 (178)
48 TIGR00739 yajC preprotein tran 49.8 50 0.0011 20.8 4.5 40 1-50 38-77 (84)
49 PRK05585 yajC preprotein trans 49.5 73 0.0016 20.9 5.7 40 1-50 53-92 (106)
50 KOG3418|consensus 49.1 22 0.00048 24.9 3.0 23 1-23 5-27 (136)
51 cd02899 PLAT_SR Scavenger rece 49.1 60 0.0013 21.4 5.0 47 18-74 56-108 (109)
52 cd05829 Sortase_E Sortase E (S 49.1 80 0.0017 21.2 6.0 48 30-77 75-124 (144)
53 cd02796 tRNA_bind_bactPheRS tR 49.1 51 0.0011 20.6 4.5 21 17-37 2-22 (103)
54 cd01725 LSm2 The eukaryotic Sm 44.9 46 0.001 20.6 3.7 49 18-67 25-74 (81)
55 PRK09790 hypothetical protein; 44.6 52 0.0011 21.2 3.9 49 11-69 22-75 (91)
56 PF15072 DUF4539: Domain of un 44.4 46 0.001 21.2 3.7 34 18-52 8-41 (86)
57 PF01063 Aminotran_4: Aminotra 44.2 55 0.0012 22.6 4.4 38 31-70 125-162 (231)
58 PRK13922 rod shape-determining 42.7 56 0.0012 23.9 4.4 50 2-55 216-271 (276)
59 cd06165 Sortase_A_1 Sortase A 42.0 73 0.0016 20.6 4.5 65 8-78 44-113 (127)
60 PF01333 Apocytochr_F_C: Apocy 42.0 48 0.001 22.7 3.7 27 17-43 9-35 (118)
61 cd02799 tRNA_bind_EMAP-II_like 41.8 68 0.0015 20.3 4.2 21 17-37 9-29 (105)
62 PF04085 MreC: rod shape-deter 41.3 45 0.00097 22.7 3.5 50 2-55 95-150 (152)
63 PF11717 Tudor-knot: RNA bindi 41.3 68 0.0015 18.2 3.9 37 1-37 1-38 (55)
64 COG0073 ARC1 EMAP domain [Gene 41.1 50 0.0011 21.9 3.6 25 17-41 22-46 (123)
65 COG5164 SPT5 Transcription elo 41.0 22 0.00047 30.0 2.2 27 1-27 140-166 (607)
66 PF00924 MS_channel: Mechanose 40.9 82 0.0018 21.4 4.8 60 1-75 61-121 (206)
67 TIGR01956 NusG_myco NusG famil 40.4 1.1E+02 0.0023 23.5 5.7 26 1-26 206-231 (258)
68 KOG3172|consensus 39.6 72 0.0016 21.8 4.2 44 19-65 30-74 (119)
69 PRK09612 rpl2p 50S ribosomal p 39.4 1E+02 0.0022 23.2 5.4 49 20-77 105-154 (238)
70 cd04716 BAH_plantDCM_I BAH, or 38.5 1.2E+02 0.0026 20.3 5.2 36 1-36 4-40 (122)
71 COG1022 FAA1 Long-chain acyl-C 36.6 22 0.00049 29.9 1.7 59 1-62 451-511 (613)
72 cd04495 BRCA2DBD_OB3 BRCA2DBD_ 36.4 55 0.0012 21.8 3.2 25 18-42 3-28 (100)
73 COG1843 FlgD Flagellar hook ca 36.4 1.6E+02 0.0034 21.9 6.0 47 3-49 95-143 (222)
74 cd01721 Sm_D3 The eukaryotic S 36.3 96 0.0021 18.5 4.8 49 15-66 21-70 (70)
75 PF08806 Sep15_SelM: Sep15/Sel 36.1 63 0.0014 20.1 3.3 25 23-47 34-58 (78)
76 PF01336 tRNA_anti-codon: OB-f 36.1 62 0.0013 18.1 3.1 26 18-43 4-29 (75)
77 CHL00052 rpl2 ribosomal protei 35.8 1.2E+02 0.0026 23.3 5.4 49 20-77 138-187 (273)
78 PF13750 Big_3_3: Bacterial Ig 35.7 1.1E+02 0.0024 21.1 4.8 35 29-64 15-51 (158)
79 KOG3421|consensus 35.7 58 0.0013 22.9 3.3 26 2-27 8-33 (136)
80 TIGR00219 mreC rod shape-deter 35.4 1.1E+02 0.0024 23.1 5.1 40 17-60 236-276 (283)
81 TIGR02222 chap_CsaA export-rel 35.3 73 0.0016 20.6 3.7 26 16-41 9-35 (107)
82 PF01426 BAH: BAH domain; Int 35.1 1.1E+02 0.0024 18.8 5.4 36 1-36 3-42 (119)
83 TIGR01171 rplB_bact ribosomal 34.9 1.3E+02 0.0029 23.1 5.5 49 20-77 138-187 (273)
84 PRK09374 rplB 50S ribosomal pr 33.7 1.5E+02 0.0032 22.8 5.6 49 20-77 140-189 (276)
85 cd04709 BAH_MTA BAH, or Bromo 33.4 1.7E+02 0.0037 20.6 5.5 36 1-36 4-40 (164)
86 cd00449 PLPDE_IV PyridoxaL 5'- 33.1 1.1E+02 0.0024 21.6 4.6 38 31-70 147-184 (256)
87 PF13415 Kelch_3: Galactose ox 31.7 41 0.00088 18.1 1.7 12 4-15 1-12 (49)
88 PRK06606 branched-chain amino 31.5 95 0.0021 23.1 4.2 37 32-70 180-216 (306)
89 TIGR01122 ilvE_I branched-chai 31.3 98 0.0021 22.8 4.2 38 31-70 171-208 (298)
90 PRK13356 aminotransferase; Pro 30.2 1.1E+02 0.0024 22.4 4.3 37 31-69 172-208 (286)
91 TIGR03461 pabC_Proteo aminodeo 29.5 1.2E+02 0.0027 21.7 4.4 37 31-69 157-193 (261)
92 PF01344 Kelch_1: Kelch motif; 29.4 90 0.002 16.1 3.4 13 3-15 10-22 (47)
93 PRK10089 tRNA-binding protein; 28.9 98 0.0021 20.1 3.5 22 16-37 14-36 (112)
94 PRK12400 D-amino acid aminotra 28.1 1.2E+02 0.0025 22.4 4.1 38 29-70 169-206 (290)
95 cd04478 RPA2_DBD_D RPA2_DBD_D: 27.9 1.2E+02 0.0026 18.2 3.6 25 17-42 4-28 (95)
96 PTZ00031 ribosomal protein L2; 27.3 2E+02 0.0044 22.7 5.5 48 20-76 171-219 (317)
97 KOG3401|consensus 27.3 51 0.0011 23.3 2.0 25 3-27 51-76 (145)
98 cd04717 BAH_polybromo BAH, or 27.1 1.8E+02 0.0038 18.7 5.2 29 1-29 4-34 (121)
99 CHL00037 petA cytochrome f 26.7 1.5E+02 0.0033 23.5 4.7 28 17-44 210-238 (320)
100 KOG3384|consensus 26.7 1E+02 0.0023 22.0 3.4 24 24-47 110-133 (154)
101 TIGR00399 metG_C_term methiony 26.5 1.5E+02 0.0033 20.0 4.2 33 16-48 42-74 (137)
102 cd03524 RPA2_OBF_family RPA2_O 26.2 1.1E+02 0.0024 16.1 4.3 27 18-44 3-31 (75)
103 PF08402 TOBE_2: TOBE domain; 26.1 1.2E+02 0.0027 16.6 4.1 55 11-67 13-70 (75)
104 PRK05886 yajC preprotein trans 26.1 2.1E+02 0.0045 19.1 6.1 41 1-51 39-79 (109)
105 cd02798 tRNA_bind_CsaA tRNA-bi 25.1 1.2E+02 0.0027 19.4 3.4 20 17-36 12-32 (107)
106 cd04490 PolII_SU_OBF PolII_SU_ 24.9 1.7E+02 0.0037 17.8 4.4 25 18-43 5-30 (79)
107 PLN02772 guanylate kinase 24.6 1.9E+02 0.004 23.4 4.9 58 2-59 32-97 (398)
108 cd01559 ADCL_like ADCL_like: 4 24.5 1.3E+02 0.0029 21.3 3.8 38 31-70 143-180 (249)
109 PRK06680 D-amino acid aminotra 24.2 1.6E+02 0.0035 21.6 4.3 38 31-70 168-205 (286)
110 PTZ00486 apyrase Superfamily; 23.7 2.7E+02 0.0058 22.4 5.6 45 17-61 133-185 (352)
111 COG5164 SPT5 Transcription elo 23.5 83 0.0018 26.7 2.8 32 1-37 91-122 (607)
112 PRK00122 rimM 16S rRNA-process 23.5 2.5E+02 0.0055 19.2 6.2 32 15-47 115-146 (172)
113 PF12681 Glyoxalase_2: Glyoxal 23.4 1.6E+02 0.0035 17.0 4.0 24 22-45 83-106 (108)
114 COG4014 Uncharacterized protei 23.4 2.3E+02 0.005 18.8 4.7 41 13-56 18-58 (97)
115 TIGR01123 ilvE_II branched-cha 22.9 2.1E+02 0.0045 21.3 4.7 38 32-70 176-215 (313)
116 PRK07650 4-amino-4-deoxychoris 22.2 1.9E+02 0.0041 21.1 4.3 36 33-70 165-200 (283)
117 cd04483 hOBFC1_like hOBFC1_lik 22.2 1.8E+02 0.0038 18.2 3.6 24 18-42 3-26 (92)
118 PRK00528 rpmE 50S ribosomal pr 22.0 1.7E+02 0.0038 17.8 3.5 23 26-49 5-27 (71)
119 cd07247 SgaA_N_like N-terminal 21.8 1.2E+02 0.0026 17.9 2.7 15 32-46 98-112 (114)
120 cd04489 ExoVII_LU_OBF ExoVII_L 21.8 1.1E+02 0.0024 17.5 2.5 25 18-42 5-29 (78)
121 PRK08320 branched-chain amino 21.6 1.8E+02 0.0039 21.2 4.1 38 31-70 170-207 (288)
122 PF08940 DUF1918: Domain of un 20.6 1.8E+02 0.0038 17.6 3.2 31 8-38 9-43 (58)
123 cd04715 BAH_Orc1p_like BAH, or 20.5 3.1E+02 0.0067 19.1 5.3 28 1-28 30-57 (159)
124 PF05610 DUF779: Protein of un 20.4 1.6E+02 0.0036 19.4 3.3 24 25-48 70-93 (95)
125 PTZ00180 60S ribosomal protein 20.2 2.2E+02 0.0047 21.8 4.3 37 16-52 40-77 (260)
126 PF07737 ATLF: Anthrax toxin l 20.0 80 0.0017 23.9 1.9 27 35-62 68-94 (226)
No 1
>PLN00036 40S ribosomal protein S4; Provisional
Probab=99.97 E-value=1.1e-30 Score=195.79 Aligned_cols=74 Identities=59% Similarity=0.937 Sum_probs=72.2
Q ss_pred CCCCcEEEEECCCCcceEEEEEEEEEecCCCcEEEEEcCCCCEEEEeeccEEEEecCCcceEecCCCceeeeee
Q psy1800 1 MFPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKPKRNFVSPRQ 74 (81)
Q Consensus 1 fe~G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp~~kgi~~~~ 74 (81)
||+||+||||||+|+||+|+|.+|+++++++|+||++|++|++|+|+++||||||++++|||+||++|||||++
T Consensus 175 fe~G~l~~vtgG~n~GrvG~I~~i~~~~~~~~iV~i~d~~g~~F~T~~~~vfvIG~~~kp~isLp~~~gi~~~~ 248 (261)
T PLN00036 175 FDVGNLVMVTGGRNRGRVGVIKNREKHKGSFEIIHVKDATGHEFATRLGNVFVIGKGTKPWISLPKGKGIKLSI 248 (261)
T ss_pred cCCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEEEeCCCCeEEEEeeeEEEEccCCCeeEeCcCCCCcccch
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999875
No 2
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=99.97 E-value=1.2e-30 Score=195.59 Aligned_cols=74 Identities=57% Similarity=0.979 Sum_probs=72.2
Q ss_pred CCCCcEEEEECCCCcceEEEEEEEEEecCCCcEEEEEcCCCCEEEEeeccEEEEecCCcceEecCCCceeeeee
Q psy1800 1 MFPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKPKRNFVSPRQ 74 (81)
Q Consensus 1 fe~G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp~~kgi~~~~ 74 (81)
||+||+||||||+|+||+|+|.+++++++++|+||++|++|++|+|+++||||||++++|||+||++||||||+
T Consensus 175 fe~G~l~~vtgG~n~GriG~I~~~~~~~~~~~~V~i~d~~g~~F~T~~~~vfvIG~~~kp~islp~~kgi~~~~ 248 (262)
T PTZ00118 175 FEVGNLVMITGGHNVGRVGTIVSKEKHPGSFDLIHVKDSRGKTFATRLSNVFVIGVGTKPYVSLPRERGIKKDI 248 (262)
T ss_pred cCCCCEEEEECCeeceeEEEEEEEEecCCCCcEEEEEeCCCCeEEEEeeeEEEEccCCCeeEeCcCCCCccccH
Confidence 89999999999999999999999999999999999999999999999999999999899999999999999875
No 3
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=99.96 E-value=6.2e-30 Score=192.66 Aligned_cols=74 Identities=45% Similarity=0.759 Sum_probs=71.7
Q ss_pred CCCCcEEEEECCCCcceEEEEEEEEEecCCCcEEEEEcCCCCEEEEeeccEEEEecC-CcceEecCCCceeeeee
Q psy1800 1 MFPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKG-TKAFCSKPKRNFVSPRQ 74 (81)
Q Consensus 1 fe~G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV~ikd~~g~~F~T~~~nVfvIGk~-~kp~IsLp~~kgi~~~~ 74 (81)
|++||+||||||+|+||+|+|.+|++|++++|+||++|++|++|+|+++||||||++ ++|||+||++||||||+
T Consensus 172 fe~G~l~~vtgG~n~GriG~I~~i~~~~~~~~iv~i~d~~g~~F~T~~~~VfvIG~~~~kp~IsLp~~kgi~~~~ 246 (273)
T PTZ00223 172 NRNGKVVMVTGGANRGRIGEIVSIERHPGAFDIARLKDASGHEFATRAANIFVIGKDMNSVPVTLPKQQGLRINV 246 (273)
T ss_pred cCCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEEEeCCCCeEEEEeeeEEEEeCCCCCcceECcCCCCccccH
Confidence 899999999999999999999999999999999999999999999999999999995 69999999999999975
No 4
>KOG0378|consensus
Probab=99.95 E-value=2.1e-28 Score=182.67 Aligned_cols=74 Identities=59% Similarity=1.029 Sum_probs=72.3
Q ss_pred CCCCcEEEEECCCCcceEEEEEEEEEecCCCcEEEEEcCCCCEEEEeeccEEEEecCCcceEecCCCceeeeee
Q psy1800 1 MFPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKPKRNFVSPRQ 74 (81)
Q Consensus 1 fe~G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp~~kgi~~~~ 74 (81)
|++|++||++||+|+||+|+|.+.|+|+|+||+||++|++|++|+|+++|+|+||+|+|||||||++|||++++
T Consensus 175 f~~~~~~~vtgg~n~gRig~i~~rerh~G~f~vvhvkdt~gnsFatrLsNifvIgkgnKpwisLPkgkgi~~si 248 (263)
T KOG0378|consen 175 FDTGNLCMVTGGANLGRIGVIKNRERHPGSFDVVHVKDTNGNSFATRLSNIFVIGEGNKPWISLPKGKGIALSI 248 (263)
T ss_pred cCccceeeeeccccccccccccccccCCCceEEEEEEecCCcEeeeeeccEEEEecCCCccccCccccCccchh
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999875
No 5
>PRK04313 30S ribosomal protein S4e; Validated
Probab=99.93 E-value=9.5e-26 Score=167.25 Aligned_cols=65 Identities=37% Similarity=0.646 Sum_probs=63.1
Q ss_pred CCCCcEEEEECCCCcceEEEEEEEEEecC-CCcEEEEEcCCCCEEEEeeccEEEEecCCcceEecCC
Q psy1800 1 MFPGNLCMITGGRNLGRVGTVVNRERHPG-SFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKPK 66 (81)
Q Consensus 1 fe~G~~~mVtgG~n~GrvG~I~~ie~~~g-~~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp~ 66 (81)
|++||+||||||+|+||+|+|.+|+++++ ++|+|+++|++|++|+|+++||||||+ ++|+|+||.
T Consensus 172 fe~G~l~~itgG~n~GriG~I~~i~~~~~~~~~~V~i~d~~G~~F~T~~~~vfvIG~-~kp~isl~~ 237 (237)
T PRK04313 172 FEEGNLAIITGGKHVGEIGKIKEIEVTKSSKPNIVTLEDKDGEKFETILDYVFVIGK-EKPVIKLPE 237 (237)
T ss_pred cCCCCEEEEECCeeeeeEEEEEEEEEccCCCCcEEEEEcCCCCEEEEEeeeEEEEcC-CCcceeCCC
Confidence 89999999999999999999999999995 999999999999999999999999999 999999984
No 6
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=99.91 E-value=1.8e-24 Score=160.46 Aligned_cols=67 Identities=40% Similarity=0.657 Sum_probs=65.2
Q ss_pred CCCCcEEEEECCCCcceEEEEEEEEEecC-CCcEEEEEcCCCCEEEEeeccEEEEecCCcceEecCCCc
Q psy1800 1 MFPGNLCMITGGRNLGRVGTVVNRERHPG-SFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKPKRN 68 (81)
Q Consensus 1 fe~G~~~mVtgG~n~GrvG~I~~ie~~~g-~~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp~~k 68 (81)
|++|++|||+||+|+|++|+|.+|+++++ ++|+|+++|.+|+.|+|+++||||||+ ++|+|+||+|+
T Consensus 174 fe~g~~~~vtgG~h~G~~G~I~~I~~~~~~~~~~v~~e~~~g~~F~T~~~yVfvIG~-~k~~i~l~~e~ 241 (241)
T COG1471 174 FEEGALVYVTGGRHVGRVGTIVEIEIQESSKPNLVTVEDEEGNTFQTIKDYVFVIGE-DKPVISLPKEK 241 (241)
T ss_pred cCCCcEEEEECCccccceEEEEEEEEecCCCccEEEEecCCCCceEEeeeEEEEEcC-CCceEeCCCCC
Confidence 79999999999999999999999999996 999999999999999999999999999 99999999985
No 7
>PF00467 KOW: KOW motif; InterPro: IPR005824 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 KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and the bacterial transcription antitermination proteins NusG []. ; PDB: 3BBO_W 2HGJ_X 2HGQ_X 2HGU_X 1NPP_B 1M1G_D 1NPR_A 2XHC_A 2KVQ_G 2JVV_A ....
Probab=97.82 E-value=3.6e-05 Score=40.87 Aligned_cols=31 Identities=26% Similarity=0.427 Sum_probs=26.4
Q ss_pred CCcEEEEECCCCcceEEEEEEEEEecCCCcEEEE
Q psy1800 3 PGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHV 36 (81)
Q Consensus 3 ~G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV~i 36 (81)
+|+.|+|+.|++.|+.|+|.++.++. +.|++
T Consensus 1 ~Gd~V~V~~G~~~G~~G~I~~i~~~~---~~V~v 31 (32)
T PF00467_consen 1 VGDTVKVISGPFKGKIGKIVEIDRSK---VRVTV 31 (32)
T ss_dssp TTSEEEESSSTTTTEEEEEEEEETTT---TEEEE
T ss_pred CCCEEEEeEcCCCCceEEEEEEECCC---CEEEE
Confidence 59999999999999999999998664 45554
No 8
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=97.67 E-value=7e-05 Score=37.46 Aligned_cols=26 Identities=23% Similarity=0.391 Sum_probs=24.1
Q ss_pred CCCCcEEEEECCCCcceEEEEEEEEE
Q psy1800 1 MFPGNLCMITGGRNLGRVGTVVNRER 26 (81)
Q Consensus 1 fe~G~~~mVtgG~n~GrvG~I~~ie~ 26 (81)
|++|+.++|++|.+.|+.|+|.+++.
T Consensus 2 ~~~G~~V~I~~G~~~g~~g~i~~i~~ 27 (28)
T smart00739 2 FEVGDTVRVIAGPFKGKVGKVLEVDG 27 (28)
T ss_pred CCCCCEEEEeECCCCCcEEEEEEEcC
Confidence 68999999999999999999999864
No 9
>TIGR01080 rplX_A_E ribosomal protein L24p/L26e, archaeal/eukaryotic. This model represents the archaeal and eukaryotic branch of the ribosomal protein L24p/L26e family. Bacterial and organellar forms are represented by the related TIGR01079.
Probab=95.66 E-value=0.039 Score=37.33 Aligned_cols=36 Identities=19% Similarity=0.126 Sum_probs=29.3
Q ss_pred CCCcEEEEECCCCcceEEEEEEEEEecCCCcEEEEEcCC
Q psy1800 2 FPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGN 40 (81)
Q Consensus 2 e~G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV~ikd~~ 40 (81)
..|+.+.|++|++-|..|+|.++... .+.|.|+.-+
T Consensus 43 kkGD~V~Vi~Gk~KGk~GkV~~V~~~---~~~V~Vegvn 78 (114)
T TIGR01080 43 RKGDKVRIMRGDFKGHEGKVSKVDLK---RYRIYVEGVT 78 (114)
T ss_pred ecCCEEEEecCCCCCCEEEEEEEEcC---CCEEEEcCeE
Confidence 46999999999999999999999743 3467776544
No 10
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=94.72 E-value=0.092 Score=33.00 Aligned_cols=37 Identities=19% Similarity=0.299 Sum_probs=30.5
Q ss_pred CCCCcEEEEECCCCcceEEEEEEEEEecCCCcEEEEEcCC
Q psy1800 1 MFPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGN 40 (81)
Q Consensus 1 fe~G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV~ikd~~ 40 (81)
+..|+.+.|+.|+.-|+.|+|.++.+. .+.|.+++-+
T Consensus 7 I~kGD~V~Vi~G~dKGK~G~V~~V~~~---~~~V~Vegvn 43 (76)
T PRK12281 7 VKKGDMVKVIAGDDKGKTGKVLAVLPK---KNRVIVEGVK 43 (76)
T ss_pred ccCCCEEEEeEcCCCCcEEEEEEEEcC---CCEEEEcCcE
Confidence 357999999999999999999999764 4467787644
No 11
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=94.61 E-value=0.099 Score=33.33 Aligned_cols=36 Identities=25% Similarity=0.334 Sum_probs=30.0
Q ss_pred CCCCcEEEEECCCCcceEEEEEEEEEecCCCcEEEEEcC
Q psy1800 1 MFPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDG 39 (81)
Q Consensus 1 fe~G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV~ikd~ 39 (81)
+..|+.++|+.|+.-|+.|+|.++.+. .+.|++++-
T Consensus 9 I~~GD~V~Vi~G~dKGK~G~V~~V~~~---~~~V~Vegv 44 (83)
T CHL00141 9 VKIGDTVKIISGSDKGKIGEVLKIIKK---SNKVIVKGI 44 (83)
T ss_pred ccCCCEEEEeEcCCCCcEEEEEEEEcC---CCEEEEcCc
Confidence 357999999999999999999999754 356778654
No 12
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=94.34 E-value=0.11 Score=34.25 Aligned_cols=76 Identities=18% Similarity=0.230 Sum_probs=48.6
Q ss_pred CCCCcEEEEECCCCcceEEEEEEEEEecCCCcEEEEEcCC--------------CC----EEEEeeccEEEEecC-Ccc-
Q psy1800 1 MFPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGN--------------GH----VFATRLNNVFIIGKG-TKA- 60 (81)
Q Consensus 1 fe~G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV~ikd~~--------------g~----~F~T~~~nVfvIGk~-~kp- 60 (81)
+..|+.++|+.|++-|..|+|.++.+. .+.|++++-+ |. +..-..|||+.+-.. .+|
T Consensus 5 i~kGD~V~Vi~G~dKGk~G~V~~V~~~---~~~V~Vegvn~~k~h~k~~~~~~~G~i~~~e~pI~~SnV~lv~p~~~~~~ 81 (105)
T PRK00004 5 IKKGDTVIVIAGKDKGKRGKVLKVLPK---KNKVIVEGVNIVKKHQKPNQENPQGGIIEKEAPIHISNVALVDPKTGKAT 81 (105)
T ss_pred ccCCCEEEEeEcCCCCcEEEEEEEEcC---CCEEEEcCcEEEEEecCCCCCCCCCceEEEECCcCHHHEEEEeCcCCCCe
Confidence 467999999999999999999999654 3456665422 21 112234888888632 333
Q ss_pred eEe--c-CCCceeeeeeeeccc
Q psy1800 61 FCS--K-PKRNFVSPRQTCPTI 79 (81)
Q Consensus 61 ~Is--L-p~~kgi~~~~~~~~~ 79 (81)
-+. + ..++-+|.+.-|-..
T Consensus 82 rv~~~~~~~g~kvRv~k~~g~~ 103 (105)
T PRK00004 82 RVGFKFLEDGKKVRVAKKSGEV 103 (105)
T ss_pred EEEEEEccCCcEEEEEecCCCC
Confidence 222 2 245667777776543
No 13
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=94.27 E-value=0.22 Score=34.10 Aligned_cols=34 Identities=21% Similarity=0.233 Sum_probs=28.0
Q ss_pred CCCcEEEEECCCCcceEEEEEEEEEecCCCcEEEEEc
Q psy1800 2 FPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKD 38 (81)
Q Consensus 2 e~G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV~ikd 38 (81)
..|+.++|+.|+.-|..|+|.++.+. .+.|.|+.
T Consensus 47 kkGD~V~VisG~~KGk~GkV~~V~~~---~~~V~VeG 80 (120)
T PRK01191 47 RKGDTVKVMRGDFKGEEGKVVEVDLK---RGRIYVEG 80 (120)
T ss_pred eCCCEEEEeecCCCCceEEEEEEEcC---CCEEEEeC
Confidence 57999999999999999999999654 34566654
No 14
>TIGR01079 rplX_bact ribosomal protein L24, bacterial/organelle. This model recognizes bacterial and organellar forms of ribosomal protein L24. It excludes eukaryotic and archaeal forms, designated L26 in eukaryotes.
Probab=93.14 E-value=0.22 Score=32.94 Aligned_cols=74 Identities=18% Similarity=0.247 Sum_probs=46.5
Q ss_pred CCCCcEEEEECCCCcceEEEEEEEEEecCCCcEEEEEcC---------------CCCE----EEEeeccEEEEecC-Ccc
Q psy1800 1 MFPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDG---------------NGHV----FATRLNNVFIIGKG-TKA 60 (81)
Q Consensus 1 fe~G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV~ikd~---------------~g~~----F~T~~~nVfvIGk~-~kp 60 (81)
+..|+.+.|+.|+.-|..|+|.++.+.. +.|.+++- .|.. ..-..|||+.+-.. .+|
T Consensus 4 ikkGD~V~Vi~G~dKGK~G~V~~V~~~~---~~V~VegvN~~kkh~k~~~~~~~~g~i~~~e~pI~~SnV~lv~p~~~k~ 80 (104)
T TIGR01079 4 IKKGDTVKVISGKDKGKRGKVLKVLPKT---NKVIVEGVNMVKKHVKPKPTQRSQGGIIEKEAPIHISNVMLFDPKTGKA 80 (104)
T ss_pred ccCCCEEEEeEcCCCCcEEEEEEEEcCC---CEEEECCcEEEEEecCcccCCCCCCceEEEEccCCHHHeEEEcCcCCCC
Confidence 4679999999999999999999996542 34444322 1211 11234888888632 344
Q ss_pred e-Ee---cCCCceeeeeeeec
Q psy1800 61 F-CS---KPKRNFVSPRQTCP 77 (81)
Q Consensus 61 ~-Is---Lp~~kgi~~~~~~~ 77 (81)
. +. +..++-+|.+.-|-
T Consensus 81 ~rv~~~~~~~g~kvRv~k~~g 101 (104)
T TIGR01079 81 TRVGIRFEEDGKKVRVFKKTG 101 (104)
T ss_pred eEEEEEEccCCcEEEEEeccC
Confidence 2 22 33566777776664
No 15
>PF13051 DUF3912: Protein of unknown function (DUF3912)
Probab=91.49 E-value=0.69 Score=28.61 Aligned_cols=50 Identities=24% Similarity=0.434 Sum_probs=38.0
Q ss_pred CCcEEEEECCCCcceEEEEEEEEEecC-CCcEEEEEcCCCCEEEEeeccEEEEec
Q psy1800 3 PGNLCMITGGRNLGRVGTVVNRERHPG-SFDIVHVKDGNGHVFATRLNNVFIIGK 56 (81)
Q Consensus 3 ~G~~~mVtgG~n~GrvG~I~~ie~~~g-~~~iV~ikd~~g~~F~T~~~nVfvIGk 56 (81)
+|..|||-.|.+.-|+|.+++-|.... .|.+|. ++...+--+..+..+|-
T Consensus 5 ~gqkayikdgp~rnrigivk~~e~q~~~~f~ivi----~~q~i~velkdivlvgv 55 (68)
T PF13051_consen 5 VGQKAYIKDGPYRNRIGIVKKNEKQLESHFAIVI----GEQSIDVELKDIVLVGV 55 (68)
T ss_pred cccEeeeccCCccceeEEEecchhhcCCcEEEEE----CCeEEEEEeeeEEEEEe
Confidence 588999999999999999999988866 665553 22456666677777764
No 16
>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]
Probab=88.87 E-value=1.1 Score=30.86 Aligned_cols=34 Identities=21% Similarity=0.346 Sum_probs=28.1
Q ss_pred CCCCcEEEEECCCCcceEEEEEEEEEecCCCcEEEEEc
Q psy1800 1 MFPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKD 38 (81)
Q Consensus 1 fe~G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV~ikd 38 (81)
+++|-.|+++.|+.+|+-.+|..+..+ +.+++-+
T Consensus 5 l~~GrVvvv~~GR~aGkk~VIv~~iDd----~~v~i~g 38 (125)
T COG2163 5 LEVGRVVVVTAGRFAGKKVVIVKIIDD----NFVLITG 38 (125)
T ss_pred ccCCeEEEEecceeCCceEEEEEEccC----CEEEEeC
Confidence 579999999999999999999988654 3555554
No 17
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=87.60 E-value=1.4 Score=30.97 Aligned_cols=51 Identities=25% Similarity=0.384 Sum_probs=35.2
Q ss_pred CCCcEEEEECCCCcceEEEEEEEEEecCCCcEEEEEc-----CCCCEE--EEeeccEEEEe
Q psy1800 2 FPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKD-----GNGHVF--ATRLNNVFIIG 55 (81)
Q Consensus 2 e~G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV~ikd-----~~g~~F--~T~~~nVfvIG 55 (81)
..|+.++|+.|++-|..|+|..+.+.. +.|.|+. .+|..+ --..+||+++-
T Consensus 48 kkGD~V~Vi~Gk~KGk~GkV~~V~~k~---~~ViVEgvn~~Kk~gk~~e~PIh~SNV~iv~ 105 (143)
T PTZ00194 48 RKDDEVMVVRGHHKGREGKVTAVYRKK---WVIHIEKITREKANGEPVQIGIHPSNVIITK 105 (143)
T ss_pred ecCCEEEEecCCCCCCceEEEEEEcCC---CEEEEeCeEEEecCCCEeecCcCchheEEEc
Confidence 469999999999999999999996543 3555543 333322 23346666664
No 18
>PF01588 tRNA_bind: Putative tRNA binding domain; InterPro: IPR002547 This domain is found in prokaryotic methionyl-tRNA synthetases, prokaryotic phenylalanyl tRNA synthetases the yeast GU4 nucleic-binding protein (G4p1 or p42, ARC1) [], human tyrosyl-tRNA synthetase [], and endothelial-monocyte activating polypeptide II. G4p1 binds specifically to tRNA form a complex with methionyl-tRNA synthetases []. In human tyrosyl-tRNA synthetase this domain may direct tRNA to the active site of the enzyme []. This domain may perform a common function in tRNA aminoacylation [].; GO: 0000049 tRNA binding; PDB: 3BU2_C 1PYB_A 2Q2I_A 2Q2H_A 1JJC_B 1EIY_B 1PYS_B 3HFZ_B 3TEH_B 2CWP_A ....
Probab=84.15 E-value=3.1 Score=26.26 Aligned_cols=22 Identities=36% Similarity=0.536 Sum_probs=17.7
Q ss_pred eEEEEEEEEEecCCCcEEEEEc
Q psy1800 17 RVGTVVNRERHPGSFDIVHVKD 38 (81)
Q Consensus 17 rvG~I~~ie~~~g~~~iV~ikd 38 (81)
|+|+|.+.+.||++..+..++=
T Consensus 2 ~vg~I~~~~~hp~sdkL~~~~V 23 (95)
T PF01588_consen 2 RVGKILEVEPHPNSDKLYVLKV 23 (95)
T ss_dssp EEEEEEEEEEETTSSSEEEEEE
T ss_pred EEEEEEEEEECCCCCEEEEEEE
Confidence 6899999999999666665553
No 19
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=83.87 E-value=1.5 Score=30.36 Aligned_cols=31 Identities=32% Similarity=0.518 Sum_probs=27.5
Q ss_pred CCCcEEEEECCCCcceEEEEEEEEEecCCCcEEEE
Q psy1800 2 FPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHV 36 (81)
Q Consensus 2 e~G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV~i 36 (81)
|+|-+|++.-|.+.|+..+|.+|..+ |.|.+
T Consensus 9 EiGRVvli~~Gp~~GKL~vIVDIID~----nRvLV 39 (130)
T PTZ00065 9 EPGRLCLIQYGPDAGKLCFIVDIVTP----TRVLV 39 (130)
T ss_pred eeceEEEEecCCCCCCEEEEEEEEcC----CeEEE
Confidence 78999999999999999999999876 56655
No 20
>PF14001 YdfZ: YdfZ protein
Probab=82.39 E-value=4.1 Score=25.24 Aligned_cols=40 Identities=25% Similarity=0.351 Sum_probs=29.3
Q ss_pred CCCcEEEEECCCCcceEEEEEEEEEe------cCCCcEEEEEcCCCCEEE
Q psy1800 2 FPGNLCMITGGRNLGRVGTVVNRERH------PGSFDIVHVKDGNGHVFA 45 (81)
Q Consensus 2 e~G~~~mVtgG~n~GrvG~I~~ie~~------~g~~~iV~ikd~~g~~F~ 45 (81)
.+|+.+|+-| .|.+|+|+.|.-. -.....|.+++.+| .|+
T Consensus 11 ~~G~rVMiag---tG~~gvikAih~~gl~~eq~rR~kcVel~g~~g-~f~ 56 (64)
T PF14001_consen 11 TTGSRVMIAG---TGATGVIKAIHADGLTAEQIRRAKCVELEGCEG-RFA 56 (64)
T ss_pred CCCCEEEEcC---CCcccEEeeeecCCCCHHHhhhccEEEEeCCCc-eEc
Confidence 5799999977 6788889988544 12456888888776 465
No 21
>TIGR03784 marine_sortase sortase, marine proteobacterial type. Members of this protein family are sortase enzymes, cysteine transpeptidases involved in protein sorting activities. Members of this family tend to be found in proteobacteria, rather than in Gram-positive bacteria where sortases attach proteins to the Gram-positive cell wall or participate in pilin cross-linking. Many species with this sortase appear to contain a signal target sequence, a protein with a Vault protein inter-alpha-trypsin domain (pfam08487) and a von Willebrand factor type A domain (pfam00092), encoded by an adjacent gene. These sortases are designated subfamily 6 according to Comfort and Clubb (2004).
Probab=81.91 E-value=3.7 Score=29.10 Aligned_cols=47 Identities=11% Similarity=0.164 Sum_probs=35.6
Q ss_pred CCcEEEEEcCCCCEEEEeeccEEEEecCCcceEecCCCceeeeeeeec
Q psy1800 30 SFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKPKRNFVSPRQTCP 77 (81)
Q Consensus 30 ~~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp~~kgi~~~~~~~ 77 (81)
.-|.|.+++.+|..+.-+...+.++-. +...+..|.++-.-..+||-
T Consensus 111 ~GD~I~v~~~~g~~~~Y~V~~~~iV~~-~d~~v~~~~~~~~LtLiTC~ 157 (174)
T TIGR03784 111 PGDVIRLQTPDGQWQSYQVTATRVVDE-SETGLDLPADDSQLVLITCY 157 (174)
T ss_pred CCCEEEEEECCCeEEEEEEeEEEEECC-ccceeccCCCCCEEEEEeCC
Confidence 458999999999888888999999988 44455556555555667894
No 22
>TIGR01076 sortase_fam LPXTG-site transpeptidase (sortase) family protein. of an LPXTG motif to the cell wall. It also includes a protein required for correct assembly of an LPXTG-containing fimbrial protein, a set of homologous proteins from Streptococcus pneumoniae, in which LPXTG proteins are common. However, related proteins are found in Bacillus subtilis and Methanobacterium thermoautotrophicum, in which LPXTG-mediated cell wall attachment is not known.
Probab=80.26 E-value=7.1 Score=26.00 Aligned_cols=65 Identities=12% Similarity=0.088 Sum_probs=43.7
Q ss_pred EEECCCCcce----EEEEEEEEEecCCCcEEEEEcCCCCEEEEeeccEEEEecCCcceEecCCCceeeeeeeec
Q psy1800 8 MITGGRNLGR----VGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKPKRNFVSPRQTCP 77 (81)
Q Consensus 8 mVtgG~n~Gr----vG~I~~ie~~~g~~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp~~kgi~~~~~~~ 77 (81)
+|+.|+|.++ ...+.+. ..-+.|.+++.+ ..|.-....+.++-+.+-+++..+.++..-..+||-
T Consensus 44 ~vIaGH~~~~~~~~F~~L~~l----~~GD~i~v~~~~-~~~~Y~V~~~~~v~~~d~~~l~~~~~~~~LtLiTC~ 112 (136)
T TIGR01076 44 IVITGHRGLPTATMFTNLDKL----KKGDMLYLHVGN-EVLTYQVTSTKIVEPTDTEVLLIQHGKDYLTLITCT 112 (136)
T ss_pred EEEEecCCCCCCCccCCHHHC----CCCCEEEEEECC-cEEEEEEEEEEEECcCcceeEeccCCCCEEEEEEeC
Confidence 4556666433 2233332 244688999876 579999999999998666677666666666678894
No 23
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=79.95 E-value=3.8 Score=27.38 Aligned_cols=26 Identities=19% Similarity=0.381 Sum_probs=23.1
Q ss_pred CCCcEEEEECCCCcceEEEEEEEEEe
Q psy1800 2 FPGNLCMITGGRNLGRVGTVVNRERH 27 (81)
Q Consensus 2 e~G~~~mVtgG~n~GrvG~I~~ie~~ 27 (81)
..|+.++|+.|++-|.-|+|.++...
T Consensus 6 rkGD~V~Vi~GkdKGk~GkVl~v~~k 31 (104)
T COG0198 6 KKGDTVKVIAGKDKGKEGKVLKVLPK 31 (104)
T ss_pred ecCCEEEEEecCCCCcceEEEEEecC
Confidence 46999999999999999999998644
No 24
>PRK04333 50S ribosomal protein L14e; Validated
Probab=79.82 E-value=2.9 Score=26.70 Aligned_cols=32 Identities=31% Similarity=0.523 Sum_probs=27.0
Q ss_pred CCCCcEEEEECCCCcceEEEEEEEEEecCCCcEEEE
Q psy1800 1 MFPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHV 36 (81)
Q Consensus 1 fe~G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV~i 36 (81)
+++|.+|++.-|+..|+..+|.++... +.|.+
T Consensus 4 v~~GrvV~~~~Grd~gk~~vIv~i~d~----~~vlV 35 (84)
T PRK04333 4 IEVGRVCVKTAGREAGRKCVIVDIIDK----NFVLV 35 (84)
T ss_pred ccccEEEEEeccCCCCCEEEEEEEecC----CEEEE
Confidence 578999999999999999999998543 56666
No 25
>cd05828 Sortase_D_4 Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at the cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Class D sortases are further classified into subfamilies 4 and 5. This group contains a subset of Class D sortases belonging to subfamily-4. These sortases recognize a unique sorting signal (LPXTA) and they constitute a specialized sorting pathway found in bacilli. Their substrates are predicted to be predominantly enzymes such as 5'-nucleotidases, glycosyl hydrolase, and subtilase.
Probab=75.03 E-value=7.5 Score=25.53 Aligned_cols=65 Identities=15% Similarity=0.206 Sum_probs=44.4
Q ss_pred EEEECCCCcceEEEEEEEEEecCCCcEEEEEcCCCCEEEEeeccEEEEecCCcceEecCCCceeeeeeeec
Q psy1800 7 CMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKPKRNFVSPRQTCP 77 (81)
Q Consensus 7 ~mVtgG~n~GrvG~I~~ie~~~g~~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp~~kgi~~~~~~~ 77 (81)
-+|+-|+|....+.+.+.+ .-+.|.+.+. +..|+-....+.++-+.+.. +-.+.++..-...||-
T Consensus 45 n~vIaGH~~~~F~~L~~l~----~Gd~i~v~~~-~~~~~Y~V~~~~~v~~~~~~-~~~~~~~~~LtLiTC~ 109 (127)
T cd05828 45 NIVIAGHRDTHFRFLGELE----PGDIITLQTL-GGTYTYRVTSTRIVDADDTS-VLAPSDDPTLTLITCY 109 (127)
T ss_pred cEEEEEeCchhhhChhcCC----CCCEEEEEEC-CEEEEEEEeeEEEECccccE-EccCCCCCEEEEEeCC
Confidence 3456677765555555543 3478999998 78899999999999874443 3335556666778895
No 26
>PTZ00471 60S ribosomal protein L27; Provisional
Probab=73.00 E-value=4.6 Score=28.20 Aligned_cols=24 Identities=33% Similarity=0.710 Sum_probs=21.0
Q ss_pred CCCCcEEEEECCCCcceEEEEEEE
Q psy1800 1 MFPGNLCMITGGRNLGRVGTVVNR 24 (81)
Q Consensus 1 fe~G~~~mVtgG~n~GrvG~I~~i 24 (81)
|.+|.+|+|..|+.+|+-.+|..-
T Consensus 5 ~kpgkVVivL~GR~AGkKaVivk~ 28 (134)
T PTZ00471 5 LKPGKVVIVTSGRYAGRKAVIVQN 28 (134)
T ss_pred ccCCEEEEEEccccCCcEEEEEee
Confidence 578999999999999998887664
No 27
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=71.35 E-value=7.7 Score=26.52 Aligned_cols=27 Identities=19% Similarity=0.175 Sum_probs=24.2
Q ss_pred CCCCcEEEEECCCCcceEEEEEEEEEe
Q psy1800 1 MFPGNLCMITGGRNLGRVGTVVNRERH 27 (81)
Q Consensus 1 fe~G~~~mVtgG~n~GrvG~I~~ie~~ 27 (81)
|++|+.+-|++|.=.|..|.|.++.++
T Consensus 127 ~~~Gd~VrI~~GPf~G~~g~v~~i~~~ 153 (181)
T PRK05609 127 FEVGEMVRVIDGPFADFNGTVEEVDYE 153 (181)
T ss_pred CCCCCEEEEeccCCCCCEEEEEEEeCC
Confidence 578999999999999999999998643
No 28
>TIGR00405 L26e_arch ribosomal protein L24p/L26e, archaeal. This protein contains a KOW domain, shared by bacterial NusG and the L24p/L26e family of ribosomal proteins. Although called archaeal NusG in several publications, it is the only close homolog of eukaryotic L26e in archaeal genomes, shares an operon with L11 in many genomes, and has been sequenced from purified ribosomes. It is here designated as a ribosomal protein for these reasons.
Probab=70.53 E-value=12 Score=24.99 Aligned_cols=27 Identities=19% Similarity=0.320 Sum_probs=24.6
Q ss_pred CCCCcEEEEECCCCcceEEEEEEEEEe
Q psy1800 1 MFPGNLCMITGGRNLGRVGTVVNRERH 27 (81)
Q Consensus 1 fe~G~~~mVtgG~n~GrvG~I~~ie~~ 27 (81)
|++|+.+-|+.|.=.|..|+|.+++.+
T Consensus 87 ~~~Gd~V~I~~GPf~G~~g~v~~~d~~ 113 (145)
T TIGR00405 87 IKKGDIVEIISGPFKGERAKVIRVDES 113 (145)
T ss_pred cCCCCEEEEeecCCCCCeEEEEEEcCC
Confidence 578999999999999999999999763
No 29
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=69.34 E-value=14 Score=25.31 Aligned_cols=28 Identities=18% Similarity=0.293 Sum_probs=25.4
Q ss_pred CCCCcEEEEECCCCcceEEEEEEEEEec
Q psy1800 1 MFPGNLCMITGGRNLGRVGTVVNRERHP 28 (81)
Q Consensus 1 fe~G~~~mVtgG~n~GrvG~I~~ie~~~ 28 (81)
|++|+.+-|+.|.-.|..|+|.++..+.
T Consensus 95 ~~~G~~V~I~~Gpf~g~~g~V~~vd~~k 122 (153)
T PRK08559 95 IKEGDIVELIAGPFKGEKARVVRVDESK 122 (153)
T ss_pred CCCCCEEEEeccCCCCceEEEEEEcCCC
Confidence 6799999999999999999999997653
No 30
>cd01723 LSm4 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=69.33 E-value=13 Score=22.70 Aligned_cols=51 Identities=20% Similarity=0.300 Sum_probs=34.4
Q ss_pred cceEEEEEEEEEecC-CCcEEEEEcCCCCEEEEeeccEEEEecCCcceEecCCC
Q psy1800 15 LGRVGTVVNRERHPG-SFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKPKR 67 (81)
Q Consensus 15 ~GrvG~I~~ie~~~g-~~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp~~ 67 (81)
.=-.|++...+.++. .=+=+...+.+|+.| ..++.+|+=|+ .=-+|++|..
T Consensus 22 ~~~~G~L~~~D~~mNi~L~~~~~~~~~g~~~-~~~~~v~IRG~-~I~~i~~p~~ 73 (76)
T cd01723 22 ETYNGHLVNCDNWMNIHLREVICTSKDGDKF-WKMPECYIRGN-TIKYLRVPDE 73 (76)
T ss_pred CEEEEEEEEEcCCCceEEEeEEEECCCCcEe-eeCCcEEEeCC-EEEEEEcCHH
Confidence 345799999988876 222244556777654 45688999887 5566788764
No 31
>TIGR00922 nusG transcription termination/antitermination factor NusG. Archaeal proteins once termed NusG share the KOW domain but are actually a ribosomal protein corresponding to L24p in bacterial and L26e in eukaryotes (TIGR00405).
Probab=68.41 E-value=8.9 Score=26.11 Aligned_cols=26 Identities=19% Similarity=0.166 Sum_probs=23.7
Q ss_pred CCCCcEEEEECCCCcceEEEEEEEEE
Q psy1800 1 MFPGNLCMITGGRNLGRVGTVVNRER 26 (81)
Q Consensus 1 fe~G~~~mVtgG~n~GrvG~I~~ie~ 26 (81)
|++|+.+-|+.|.=.|..|+|.++.+
T Consensus 120 ~~~G~~V~I~~Gpf~G~~g~v~~~~~ 145 (172)
T TIGR00922 120 FEVGEQVRVNDGPFANFTGTVEEVDY 145 (172)
T ss_pred CCCCCEEEEeecCCCCcEEEEEEEcC
Confidence 56899999999999999999999864
No 32
>PF00181 Ribosomal_L2: Ribosomal Proteins L2, RNA binding domain; InterPro: IPR022666 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 L2 is one of the proteins from the large ribosomal subunit. This entry represents the best conserved region located in the C-terminal section of these proteins.In Escherichia coli, L2 is known to bind to the 23S rRNA and to have peptidyltransferase activity. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, ], groups: Eubacterial L2. Algal and plant chloroplast L2. Cyanelle L2. Archaebacterial L2. Plant L2. Slime mold L2. Marchantia polymorpha mitochondrial L2. Paramecium tetraurelia mitochondrial L2. Fission yeast K5, K37 and KD4. Yeast YL6. Vertebrate L8. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1YIT_A 1Q7Y_C 1YJN_A 3CPW_A 3I56_A 1VQ9_A 1M1K_C 3CC7_A 1YIJ_A 1K9M_C ....
Probab=64.68 E-value=15 Score=22.58 Aligned_cols=32 Identities=28% Similarity=0.217 Sum_probs=26.1
Q ss_pred eEEEEEEEEEecC-CCcEEEEEcCCCCEEEEee
Q psy1800 17 RVGTVVNRERHPG-SFDIVHVKDGNGHVFATRL 48 (81)
Q Consensus 17 rvG~I~~ie~~~g-~~~iV~ikd~~g~~F~T~~ 48 (81)
..|+|.+|+-.|+ +..+..|+..+|+.+-.+.
T Consensus 33 ~~g~V~~i~~DP~Rsa~iAlV~~~~g~~~yiiA 65 (77)
T PF00181_consen 33 IKGIVIDIEYDPNRSAPIALVKYEDGEKRYIIA 65 (77)
T ss_dssp EEEEEEEEEEETTTSSEEEEEEETTSEEEEEEE
T ss_pred CcEEEEEEEecCCcCccEEEEEecCCcEEEEEe
Confidence 4699999999998 9999999988877664333
No 33
>KOG1708|consensus
Probab=63.22 E-value=13 Score=28.03 Aligned_cols=36 Identities=31% Similarity=0.410 Sum_probs=29.1
Q ss_pred CCCCcEEEEECCCCcceEEEEEEEEEecCCCcEEEEEcC
Q psy1800 1 MFPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDG 39 (81)
Q Consensus 1 fe~G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV~ikd~ 39 (81)
|-.|+.+=|.-|+.-|+.|.+..+.+|. |-|.+++-
T Consensus 73 ff~GDtVeVlvGkDkGkqG~Vtqv~r~~---s~VvV~gl 108 (236)
T KOG1708|consen 73 FFFGDTVEVLVGKDKGKQGEVTQVIRHR---SWVVVKGL 108 (236)
T ss_pred EecCCEEEEEecccCCccceEEEEeecC---ceEEEccc
Confidence 4579999999999999999999998873 44556553
No 34
>TIGR03318 YdfZ_fam putative selenium-binding protein YdfZ. This small protein has a very limited distribution, being found so far only among some gamma-Proteobacteria. The member from Escherichia coli was shown to bind selenium in the absence of a working SelD-dependent selenium incorporation system. Note that while the E. coli member contains a single Cys residue, a likely selenium binding site, some other members of this protein family contain two Cys residues or none.
Probab=61.52 E-value=7.5 Score=24.13 Aligned_cols=40 Identities=23% Similarity=0.314 Sum_probs=27.5
Q ss_pred CCCcEEEEECCCCcceEEEEEEEEEe------cCCCcEEEEEcCCCCEEE
Q psy1800 2 FPGNLCMITGGRNLGRVGTVVNRERH------PGSFDIVHVKDGNGHVFA 45 (81)
Q Consensus 2 e~G~~~mVtgG~n~GrvG~I~~ie~~------~g~~~iV~ikd~~g~~F~ 45 (81)
.+|+.+||.| .|++|+|+.|.-. -.....|.++-.+| .|.
T Consensus 12 t~G~rVMia~---tG~tgvikaIh~dglt~~Q~rR~k~Vel~g~e~-~f~ 57 (65)
T TIGR03318 12 TTGSRVMIAG---TGHTGVIKAIHTEGLTAEQARREKCVELEGCEE-RFA 57 (65)
T ss_pred CCCcEEEEec---CCccceeehhhhCCCCHHHhhhccEEEEecccc-eec
Confidence 4799999987 6788889988532 12445777776554 454
No 35
>KOG1999|consensus
Probab=59.81 E-value=21 Score=32.09 Aligned_cols=27 Identities=33% Similarity=0.511 Sum_probs=25.7
Q ss_pred CCCCcEEEEECCCCcceEEEEEEEEEe
Q psy1800 1 MFPGNLCMITGGRNLGRVGTVVNRERH 27 (81)
Q Consensus 1 fe~G~~~mVtgG~n~GrvG~I~~ie~~ 27 (81)
|++|+.|=|+-|++-|..|.|..++.+
T Consensus 460 F~~GDhVKVi~G~~eG~tGlVvrVe~~ 486 (1024)
T KOG1999|consen 460 FEPGDHVKVIAGRYEGDTGLVVRVEQG 486 (1024)
T ss_pred ccCCCeEEEEeccccCCcceEEEEeCC
Confidence 899999999999999999999999875
No 36
>cd02153 tRNA_bindingDomain The tRNA binding domain is also known as the Myf domain in literature. This domain is found in a diverse collection of tRNA binding proteins, including prokaryotic phenylalanyl tRNA synthetases (PheRS), methionyl-tRNA synthetases (MetRS), human tyrosyl-tRNA synthetase(hTyrRS), Saccharomyces cerevisiae Arc1p, Thermus thermophilus CsaA, Aquifex aeolicus Trbp111, human p43 and human EMAP-II. PheRS, MetRS and hTyrRS aminoacylate their cognate tRNAs. Arc1p is a transactivator of yeast methionyl-tRNA and glutamyl-tRNA synthetases. The molecular chaperones Trbp111 and CsaA also contain this domain. CsaA has export related activities; Trbp111 is structure-specific recognizing the L-shape of the tRNA fold. This domain has general tRNA binding properties. In a subset of this family this domain has the added capability of a cytokine. For example the p43 component of the Human aminoacyl-tRNA synthetase complex is cleaved to release EMAP-II cytokine. EMAP-II has multi
Probab=58.89 E-value=24 Score=21.97 Aligned_cols=20 Identities=35% Similarity=0.615 Sum_probs=15.4
Q ss_pred eEEEEEEEEEecCCCcEEEE
Q psy1800 17 RVGTVVNRERHPGSFDIVHV 36 (81)
Q Consensus 17 rvG~I~~ie~~~g~~~iV~i 36 (81)
++|+|.+.+.||.+..+..+
T Consensus 2 ~vg~I~~~~~~p~~~kL~~~ 21 (99)
T cd02153 2 RVGKIVEAEPHPNADKLYVL 21 (99)
T ss_pred EEEEEEEEEECCCCCCCEEE
Confidence 68999999999986544433
No 37
>smart00609 VIT Vault protein Inter-alpha-Trypsin domain.
Probab=58.54 E-value=15 Score=24.83 Aligned_cols=47 Identities=23% Similarity=0.379 Sum_probs=32.3
Q ss_pred CcEEEEECCCCcceEEEEEEEEEe---------cC-CCcEEEEEcCCCCEEEEeeccEEE
Q psy1800 4 GNLCMITGGRNLGRVGTVVNRERH---------PG-SFDIVHVKDGNGHVFATRLNNVFI 53 (81)
Q Consensus 4 G~~~mVtgG~n~GrvG~I~~ie~~---------~g-~~~iV~ikd~~g~~F~T~~~nVfv 53 (81)
.+++|.+||+. ..|.|++.++. .| ...++.=.+.+.+.|.+.. |+-.
T Consensus 62 ~~~~~~i~~r~--i~g~vkeK~~Ar~~Ye~A~~~G~~a~L~eq~~~~~~~F~~~V-NIpp 118 (130)
T smart00609 62 SNFAMTIDGKT--YVGEIKEKEVAQKQYEKAVSQGKTAGLVRASGRSMEQFTVSV-NVAP 118 (130)
T ss_pred EeEEEEECCEE--EEEEEeeHHHHHHHHHHHHHcCCCeEEEEecCCccCcEEEEE-EeCC
Confidence 35778889998 48999998754 34 4444443334448899999 8654
No 38
>cd06166 Sortase_D_5 Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at the cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Class D sortases are further classified into subfamilies 4 and 5. This group contains a subset of Class D sortases belonging to subfamily-5, represented by Clostridium perfringens CPE2315. Subfamily-5 sortases recognize a nonstandard sorting signal (LAXTG) and have replaced Sortase A in some gram-postive bacteria. They may play a housekeeping role in the cell.
Probab=57.75 E-value=41 Score=21.94 Aligned_cols=65 Identities=12% Similarity=0.190 Sum_probs=40.1
Q ss_pred EEECCCCcceEE----EEEEEEEecCCCcEEEEEcCCCCEEEEeeccEEEEecCCcceEecCCCceeeeeeeec
Q psy1800 8 MITGGRNLGRVG----TVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKPKRNFVSPRQTCP 77 (81)
Q Consensus 8 mVtgG~n~GrvG----~I~~ie~~~g~~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp~~kgi~~~~~~~ 77 (81)
+|+-|+|..+-| .+.+. ..-+.|.+.|. +..|+-....+.++-..+...+.-..++-.-...||-
T Consensus 45 ~viaGH~~~~~~~~F~~L~~l----~~Gd~v~v~~~-~~~~~Y~V~~~~~v~~~~~~~~~~~~~~~~LtLiTC~ 113 (126)
T cd06166 45 FAIAGHRSYTYGRIFNRLDEV----EKGDEIKVTTK-NGTYKYKITSIFVVEPTDTDVLNQDKSKKEITLITCT 113 (126)
T ss_pred EEEEeCcCCCCCcccCChHHC----CCCCEEEEEEC-CEEEEEEEEEEEEECCCcceEeccCCCCcEEEEEEcC
Confidence 455666665333 22222 24578999987 5689999999999987554444322214444566885
No 39
>TIGR01955 RfaH transcriptional activator RfaH. This model represents the transcriptional activator protein, RfaH. This protein is most closely related to the transcriptional termination/antitermination protein NusG (TIGR00922) and contains the KOW motif (pfam00467). This protein appears to be limited to the gamma proteobacteria. In E. coli, this gene appears to control the expression of haemolysin, sex factor and lipopolysaccharide genes.
Probab=56.20 E-value=57 Score=21.68 Aligned_cols=25 Identities=20% Similarity=0.287 Sum_probs=23.2
Q ss_pred CCCCcEEEEECCCCcceEEEEEEEE
Q psy1800 1 MFPGNLCMITGGRNLGRVGTVVNRE 25 (81)
Q Consensus 1 fe~G~~~mVtgG~n~GrvG~I~~ie 25 (81)
|++|+.+.|++|.-.|..|.|.++.
T Consensus 109 ~~~G~~V~V~~GPf~g~~g~v~~~~ 133 (159)
T TIGR01955 109 PYKGDKVRITDGAFAGFEAIFLEPD 133 (159)
T ss_pred CCCCCEEEEeccCCCCcEEEEEEEC
Confidence 5789999999999999999999985
No 40
>KOG1999|consensus
Probab=54.11 E-value=14 Score=33.25 Aligned_cols=53 Identities=25% Similarity=0.322 Sum_probs=41.9
Q ss_pred CCCcEEEEECCCCcceEEEEEEEEEecC-CCcEEEEEcCCCCEEEEeeccEEEEec
Q psy1800 2 FPGNLCMITGGRNLGRVGTVVNRERHPG-SFDIVHVKDGNGHVFATRLNNVFIIGK 56 (81)
Q Consensus 2 e~G~~~mVtgG~n~GrvG~I~~ie~~~g-~~~iV~ikd~~g~~F~T~~~nVfvIGk 56 (81)
+.++++-+++|.|.||-|.|.+|-+..= ..+.-++ .++-.|.++.+|+..+|.
T Consensus 583 ~~kD~Vkvi~Gp~~g~~G~v~~i~r~~~F~h~r~~~--En~Gv~vck~k~~~~~g~ 636 (1024)
T KOG1999|consen 583 RVKDTVKVIGGPSKGREGEVLHIYRPFVFLHSRKNL--ENGGVFVCKEKNLILAGG 636 (1024)
T ss_pred cccceEEEecCCCCCccCccceeecceeeeeehhhc--ccCCeEEEecCCceeccc
Confidence 4689999999999999999999976422 3333334 455689999999999986
No 41
>cd00004 Sortase Sortases are cysteine transpeptidases, found in gram-positive bacteria, that anchor surface proteins to peptidoglycans of the bacterial cell wall envelope. They do so by catalyzing a transpeptidation reaction in which the surface protein substrate is cleaved at a conserved cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. The different classes are called Sortase A or SrtA (subfamily 1), B or SrtB (subfamily 2), C or SrtC (subfamily3), D or SrtD (subfamilies 4 and 5), and E or SrtE. In two different sortase subfamilies, the N-terminus either functions as both a signal peptide for secretion and a stop-transfer signal for membrane anchoring, or it contains a signal peptide only and the C-terminus serves as a membrane anchor. Most gram-positive bacteria contain more than one s
Probab=53.99 E-value=29 Score=22.43 Aligned_cols=65 Identities=17% Similarity=0.348 Sum_probs=42.0
Q ss_pred EEECCCCcce----EEEEEEEEEecCCCcEEEEEcCCCCEEEEeeccEEEEecCCc-ceEecCCCceeeeeeeecc
Q psy1800 8 MITGGRNLGR----VGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTK-AFCSKPKRNFVSPRQTCPT 78 (81)
Q Consensus 8 mVtgG~n~Gr----vG~I~~ie~~~g~~~iV~ikd~~g~~F~T~~~nVfvIGk~~k-p~IsLp~~kgi~~~~~~~~ 78 (81)
+|+-|+|.+. ...+.+.+ .-+.|.+.|. +..++-....+.++-+ +. ..+..+.++-.-...||-.
T Consensus 45 ~viaGH~~~~~~~~F~~L~~l~----~Gd~v~v~~~-~~~~~Y~V~~~~~v~~-~~~~~~~~~~~~~~LtLiTC~~ 114 (128)
T cd00004 45 TVIAGHRGGDSGTVFSDLDNLK----KGDKIYLTDG-GKTYVYKVTSILTVTP-TDVVVVNPPTGDPILTLITCTP 114 (128)
T ss_pred EEEEeeeCCCCCcccCCHHHCC----CCCEEEEEEC-CEEEEEEEEEEEEECC-CceEEeccCCCCCEEEEEEcCC
Confidence 4555677654 33333332 3478999987 6788888888999876 44 3444555656667778853
No 42
>cd02800 tRNA_bind_EcMetRS_like tRNA-binding-domain-containing Escherichia coli methionyl-tRNA synthetase (EcMetRS)-like proteins. This family includes EcMetRS and Aquifex aeolicus Trbp111 (AaTrbp111). This domain has general tRNA binding properties. MetRS aminoacylates methionine transfer RNAs (tRNAmet). AaTrbp111 is structure-specific molecular chaperone recognizing the L-shape of the tRNA fold. AaTrbp111 plays a role in nuclear trafficking of tRNAs. The functional unit of EcMetRs and AaTrbp111 is a homodimer, this domain acts as the dimerization domain.
Probab=52.80 E-value=42 Score=21.24 Aligned_cols=25 Identities=36% Similarity=0.518 Sum_probs=18.3
Q ss_pred eEEEEEEEEEecCCCcEEEEEcCCC
Q psy1800 17 RVGTVVNRERHPGSFDIVHVKDGNG 41 (81)
Q Consensus 17 rvG~I~~ie~~~g~~~iV~ikd~~g 41 (81)
|+|+|.+.+.||.+..+..++=..|
T Consensus 12 ~vg~I~~~~~~p~a~kL~~~~vd~G 36 (105)
T cd02800 12 RVGKVLEAERVEGSDKLLKLTVDLG 36 (105)
T ss_pred EEEEEEEEEecCCCCcceEEEEEeC
Confidence 7899999999998766655433334
No 43
>PF07290 DUF1449: Protein of unknown function (DUF1449); InterPro: IPR010840 This family consists of several bacterial proteins of around 210 residues in length. The function of this family is unknown.
Probab=52.70 E-value=21 Score=26.10 Aligned_cols=30 Identities=37% Similarity=0.454 Sum_probs=24.6
Q ss_pred CcceEEEEEEEEEecCCCcEEEEEcCCCCE
Q psy1800 14 NLGRVGTVVNRERHPGSFDIVHVKDGNGHV 43 (81)
Q Consensus 14 n~GrvG~I~~ie~~~g~~~iV~ikd~~g~~ 43 (81)
=.||+|+|+.-.-.+|++.-+.++|..|+.
T Consensus 136 LiGr~a~Vt~g~a~~g~~aqa~V~D~~Gq~ 165 (202)
T PF07290_consen 136 LIGRVATVTSGTARQGSPAQARVKDQFGQL 165 (202)
T ss_pred cCcceEEEEecccCCCCceEEEEEecCCCE
Confidence 368999998866667888999999998874
No 44
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=52.21 E-value=24 Score=23.83 Aligned_cols=25 Identities=24% Similarity=0.286 Sum_probs=23.0
Q ss_pred CCCCcEEEEECCCCcceEEEEEEEE
Q psy1800 1 MFPGNLCMITGGRNLGRVGTVVNRE 25 (81)
Q Consensus 1 fe~G~~~mVtgG~n~GrvG~I~~ie 25 (81)
|++|+.+.|+.|.=.|..|.|.++.
T Consensus 110 ~~~G~~V~I~~Gp~~g~eg~v~~~~ 134 (162)
T PRK09014 110 PKPGDKVIITEGAFEGLQAIYTEPD 134 (162)
T ss_pred CCCCCEEEEecCCCCCcEEEEEEeC
Confidence 5789999999999999999999885
No 45
>cd05827 Sortase_C_3 Sortase C (SrtC) or subfamily-3 sortases are membrane cysteine transpeptidases found in Gram-positive bacteria that anchor surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at a conserved cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Sortase C cleaves surface proteins at the LPXTG motif between Thr and Gly and catalyzes the formation of an amide bond between the carboxyl group of Thr and the amino group of cell-wall cross bridges. It is a narrow-range enzyme required for anchoring a few substrates. It plays a role in Streptococcus pneumoniae pathogenesis and is required in the assembly of pili on the surface of Corynebacterium diphtheriae. Sortase C is
Probab=52.14 E-value=48 Score=21.67 Aligned_cols=65 Identities=8% Similarity=-0.032 Sum_probs=41.3
Q ss_pred EEECCCCcce----EEEEEEEEEecCCCcEEEEEcCCCCEEEEeeccEEEEecCCcceEecCCCceeeeeeeec
Q psy1800 8 MITGGRNLGR----VGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKPKRNFVSPRQTCP 77 (81)
Q Consensus 8 mVtgG~n~Gr----vG~I~~ie~~~g~~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp~~kgi~~~~~~~ 77 (81)
+|+-|+|..+ .+.+.+.+ ..+.|.+++.++ .|.-....++++-..+.+++..++++-+-...||-
T Consensus 47 ~viaGH~~~~~~~~F~~L~~l~----~gd~i~l~t~~~-~~~Y~V~~~~~v~~~d~~~~~~~~~~~~LTL~TC~ 115 (131)
T cd05827 47 SVITGHRGLPNAKLFTDLDKLK----KGDKFYIHVLGE-TLAYQVDQIEVVLPDDTDKLKIVPGKDLVTLLTCT 115 (131)
T ss_pred EEEEeCCCCCCCcccCCHHHCC----CCCEEEEEECCe-EEEEEEEEEEEECcccceEeccCCCCcEEEEEEcC
Confidence 4556677532 23333332 336788887664 78888888888876454555566665566777885
No 46
>cd01733 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm10 is an SmD1-like protein which is thought to bind U7 snRNA along with LSm11 and five other Sm subunits to form a 7-member ring structure. LSm10 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.
Probab=52.13 E-value=51 Score=20.33 Aligned_cols=47 Identities=15% Similarity=0.370 Sum_probs=29.8
Q ss_pred ceEEEEEEEEEecC-CCcEEEEEcCCCCEEEEeeccEEEEecCCcceEecC
Q psy1800 16 GRVGTVVNRERHPG-SFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKP 65 (81)
Q Consensus 16 GrvG~I~~ie~~~g-~~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp 65 (81)
=-.|++.+.+.++. .=+=+.+.+.+|..+ .++.+|+=|. +=-+|.||
T Consensus 31 ~~~G~L~~vD~~MNl~L~~~~~~~~~~~~~--~~~~v~IRG~-nI~yI~lP 78 (78)
T cd01733 31 TVTGRIASVDAFMNIRLAKVTIIDRNGKQV--QVEEIMVTGR-NIRYVHIP 78 (78)
T ss_pred EEEEEEEEEcCCceeEEEEEEEEcCCCcee--ECCcEEEECC-EEEEEEcC
Confidence 35688888887765 222233445555433 6789999886 55567776
No 47
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=50.11 E-value=25 Score=25.04 Aligned_cols=27 Identities=22% Similarity=0.314 Sum_probs=24.7
Q ss_pred CCCCcEEEEECCCCcceEEEEEEEEEe
Q psy1800 1 MFPGNLCMITGGRNLGRVGTVVNRERH 27 (81)
Q Consensus 1 fe~G~~~mVtgG~n~GrvG~I~~ie~~ 27 (81)
|++|+.+-|+.|.=.|..|+|.+++..
T Consensus 124 ~e~Gd~VrI~~GpFa~f~g~V~evd~e 150 (178)
T COG0250 124 FEPGDVVRIIDGPFAGFKAKVEEVDEE 150 (178)
T ss_pred CCCCCEEEEeccCCCCccEEEEEEcCc
Confidence 789999999999999999999999643
No 48
>TIGR00739 yajC preprotein translocase, YajC subunit. While this protein is part of the preprotein translocase in Escherichia coli, it is not essential for viability or protein secretion. The N-terminus region contains a predicted membrane-spanning region followed by a region consisting almost entirely of residues with charged (acidic, basic, or zwitterionic) side chains. This small protein is about 100 residues in length, and is restricted to bacteria; however, this protein is absent from some lineages, including spirochetes and Mycoplasmas.
Probab=49.80 E-value=50 Score=20.76 Aligned_cols=40 Identities=20% Similarity=0.297 Sum_probs=28.3
Q ss_pred CCCCcEEEEECCCCcceEEEEEEEEEecCCCcEEEEEcCCCCEEEEeecc
Q psy1800 1 MFPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNN 50 (81)
Q Consensus 1 fe~G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV~ikd~~g~~F~T~~~n 50 (81)
+++|+-++-+|| -+|+|.++.. +.+.++.+.| ..-|...+
T Consensus 38 L~~Gd~VvT~gG----i~G~V~~i~d-----~~v~vei~~g-~~i~~~r~ 77 (84)
T TIGR00739 38 LKKGDKVLTIGG----IIGTVTKIAE-----NTIVIELNDN-TEITFSKN 77 (84)
T ss_pred CCCCCEEEECCC----eEEEEEEEeC-----CEEEEEECCC-eEEEEEhH
Confidence 468888888875 6899999863 5678887765 34554443
No 49
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=49.53 E-value=73 Score=20.91 Aligned_cols=40 Identities=18% Similarity=0.283 Sum_probs=30.1
Q ss_pred CCCCcEEEEECCCCcceEEEEEEEEEecCCCcEEEEEcCCCCEEEEeecc
Q psy1800 1 MFPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNN 50 (81)
Q Consensus 1 fe~G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV~ikd~~g~~F~T~~~n 50 (81)
+++|+-++-+|| -+|+|.++.. +.|.++-++| ..-|+..+
T Consensus 53 Lk~Gd~VvT~gG----i~G~Vv~i~~-----~~v~lei~~g-~~i~~~r~ 92 (106)
T PRK05585 53 LAKGDEVVTNGG----IIGKVTKVSE-----DFVIIELNDD-TEIKIQKS 92 (106)
T ss_pred cCCCCEEEECCC----eEEEEEEEeC-----CEEEEEECCC-eEEEEEhH
Confidence 467888888875 6899999853 6888887665 56666665
No 50
>KOG3418|consensus
Probab=49.14 E-value=22 Score=24.91 Aligned_cols=23 Identities=26% Similarity=0.658 Sum_probs=19.9
Q ss_pred CCCCcEEEEECCCCcceEEEEEE
Q psy1800 1 MFPGNLCMITGGRNLGRVGTVVN 23 (81)
Q Consensus 1 fe~G~~~mVtgG~n~GrvG~I~~ 23 (81)
|.+|..+++..|+++|+-.+|..
T Consensus 5 lkPgkvv~v~sG~yAg~KaVivk 27 (136)
T KOG3418|consen 5 LKPGKVVLVLSGRYAGKKAVIVK 27 (136)
T ss_pred ccCCcEEEeecccccCccEEEEe
Confidence 57899999999999998777654
No 51
>cd02899 PLAT_SR Scavenger receptor protein. A subfamily of PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2) domain. It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates. This subfamily contains Toxoplasma gondii Scavenger protein TgSR1.
Probab=49.12 E-value=60 Score=21.38 Aligned_cols=47 Identities=21% Similarity=0.253 Sum_probs=32.2
Q ss_pred EEEEEEEEEe-----cC-CCcEEEEEcCCCCEEEEeeccEEEEecCCcceEecCCCceeeeee
Q psy1800 18 VGTVVNRERH-----PG-SFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKPKRNFVSPRQ 74 (81)
Q Consensus 18 vG~I~~ie~~-----~g-~~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp~~kgi~~~~ 74 (81)
+|.|..|+.. ++ --+-|.|+|.+|+. |.|...+ |+.-|-++-|+++.
T Consensus 56 LG~l~~i~l~n~g~~~~Wf~~~V~V~~~~g~~------~~Fpc~r----Wla~~~~~~v~~~~ 108 (109)
T cd02899 56 VGDINAIILSNTALNDPWYCDYVRIKSEDGKV------FAFNVKR----WIGYPYEQSVEVSL 108 (109)
T ss_pred cCceEEEEEECCCCCCCceeeEEEEECCCCCE------EEEEcce----eeCCchhceEEEec
Confidence 3445555544 23 23578888866654 4599888 99999999998764
No 52
>cd05829 Sortase_E Sortase E (SrtE) is a membrane transpeptidase found in gram-positive bacteria that cleaves surface proteins at a cell sorting motif and catalyzes a transpeptidation reaction in which the surface protein substrate is covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. The function of Sortase E is unknown. In two different sortase families, the N-terminus either functions as both a signal peptide for secretion and a stop-transfer signal for membrane anchoring, or it contains a signal peptide only and the C-terminus serves as a membrane anchor. Most gram-positive bacteria contain more than one sortase and it is thought that the different sortases anchor different surface protein classes. The sortase domain is a modified beta-barrel flanked by two (SrtA) or three (SrtB) short alpha-helices.
Probab=49.08 E-value=80 Score=21.22 Aligned_cols=48 Identities=19% Similarity=0.093 Sum_probs=35.3
Q ss_pred CCcEEEEEcCCCCEEEEeeccEEEEecCCcce--EecCCCceeeeeeeec
Q psy1800 30 SFDIVHVKDGNGHVFATRLNNVFIIGKGTKAF--CSKPKRNFVSPRQTCP 77 (81)
Q Consensus 30 ~~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~--IsLp~~kgi~~~~~~~ 77 (81)
.-|.|.|++.+|+.|.-+...+.++-+.+-|. +-.+.++.--..+||-
T Consensus 75 ~GD~I~v~~~~g~~~~Y~V~~~~~v~~~~~~~~~~~~~~~~~~LtLiTC~ 124 (144)
T cd05829 75 KGDKVEVTRADGQTATFRVDRVEVYPKDAFPTDAVYGDTGPPRLRLITCG 124 (144)
T ss_pred CCCEEEEEECCCCEEEEEEeEEEEECcccCChhheecCCCCCEEEEEEeC
Confidence 45899999999999999999999998743232 2234566666778995
No 53
>cd02796 tRNA_bind_bactPheRS tRNA-binding-domain-containing prokaryotic phenylalanly tRNA synthetase (PheRS) beta chain. PheRS aminoacylate phenylalanine transfer RNAs (tRNAphe). PheRSs belong structurally to class II aminoacyl tRNA synthetases (aaRSs) but, as they aminoacylate the 2'OH of the terminal ribose of tRNA they belong functionally to class 1 aaRSs. This domain has general tRNA binding properties and is believed to direct tRNAphe to the active site of the enzyme.
Probab=49.07 E-value=51 Score=20.61 Aligned_cols=21 Identities=33% Similarity=0.442 Sum_probs=16.3
Q ss_pred eEEEEEEEEEecCCCcEEEEE
Q psy1800 17 RVGTVVNRERHPGSFDIVHVK 37 (81)
Q Consensus 17 rvG~I~~ie~~~g~~~iV~ik 37 (81)
++|.|.+.+.||.+..+..++
T Consensus 2 ~vg~I~~~~~hp~~~kL~~~~ 22 (103)
T cd02796 2 VVGKVLEVEPHPNADKLNVCK 22 (103)
T ss_pred EEEEEEEEEecCCCCceEEEE
Confidence 589999999999865555543
No 54
>cd01725 LSm2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm2 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=44.88 E-value=46 Score=20.56 Aligned_cols=49 Identities=18% Similarity=0.258 Sum_probs=30.8
Q ss_pred EEEEEEEEEecC-CCcEEEEEcCCCCEEEEeeccEEEEecCCcceEecCCC
Q psy1800 18 VGTVVNRERHPG-SFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKPKR 67 (81)
Q Consensus 18 vG~I~~ie~~~g-~~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp~~ 67 (81)
.|++.+.+.++. .=+=+.+.+.++......++.+|+=|. .=-+|.+|..
T Consensus 25 ~G~L~~vD~~MNi~L~n~~~~~~~~~~~~~~~~~v~IRG~-~I~~I~lp~~ 74 (81)
T cd01725 25 RGTLHSVDQYLNIKLTNISVTDPEKYPHMLSVKNCFIRGS-VVRYVQLPAD 74 (81)
T ss_pred EEEEEEECCCcccEEEEEEEEcCCCcccccccCeEEEECC-EEEEEEeChh
Confidence 788888887765 212223334444333445588999886 5567888865
No 55
>PRK09790 hypothetical protein; Reviewed
Probab=44.61 E-value=52 Score=21.21 Aligned_cols=49 Identities=24% Similarity=0.451 Sum_probs=30.1
Q ss_pred CCCCcceEEEEEEEEEecCCCcEEEEEcCCCCEEEEeecc-----EEEEecCCcceEecCCCce
Q psy1800 11 GGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNN-----VFIIGKGTKAFCSKPKRNF 69 (81)
Q Consensus 11 gG~n~GrvG~I~~ie~~~g~~~iV~ikd~~g~~F~T~~~n-----VfvIGk~~kp~IsLp~~kg 69 (81)
-|+|.| -+.+-|-..-.|.+|-+....|+ |.|..+- +.-||+ .||.+|-
T Consensus 22 egk~ig---yviktenketpftvvdidg~sgn-~ktl~eg~~kmclv~ig~------nlpaekk 75 (91)
T PRK09790 22 EGKRIG---YVIKTENKETPFTVVDIDGPSGN-VKTLDEGVKKMCLVHIGK------NLPAEKK 75 (91)
T ss_pred cCcEEE---EEEEecCCCCCeEEEeccCCCCc-eeEhhhccceEEEEEecC------CCCcccc
Confidence 355544 44444544557888887667776 8887553 344677 5777664
No 56
>PF15072 DUF4539: Domain of unknown function (DUF4539)
Probab=44.41 E-value=46 Score=21.18 Aligned_cols=34 Identities=21% Similarity=0.152 Sum_probs=25.5
Q ss_pred EEEEEEEEEecCCCcEEEEEcCCCCEEEEeeccEE
Q psy1800 18 VGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVF 52 (81)
Q Consensus 18 vG~I~~ie~~~g~~~iV~ikd~~g~~F~T~~~nVf 52 (81)
++.|+++... +....|.++|..|+.-.|+-.-|+
T Consensus 8 ~v~Iks~~~~-~~D~~v~l~DpTG~i~~tiH~~v~ 41 (86)
T PF15072_consen 8 VVIIKSIVPS-SEDAFVVLKDPTGEIRGTIHRKVL 41 (86)
T ss_pred EEEEEEeecc-CCCeEEEEECCCCcEEEEEeHHHH
Confidence 4566666554 347799999999999898876655
No 57
>PF01063 Aminotran_4: Aminotransferase class IV; InterPro: IPR001544 Aminotransferases share certain mechanistic features with other pyridoxal-phosphate dependent enzymes, such as the covalent binding of the pyridoxal-phosphate group to a lysine residue. On the basis of sequence similarity, these various enzymes can be grouped [] into subfamilies. One of these, called class-IV, currently consists of proteins of about 270 to 415 amino-acid residues that share a few regions of sequence similarity. Surprisingly, the best conserved region does not include the lysine residue to which the pyridoxal-phosphate group is known to be attached, in ilvE, but is located some 40 residues at the C terminus side of the pyridoxal-phosphate-lysine. The D-amino acid transferases (D-AAT), which are among the members of this entry, are required by bacteria to catalyse the synthesis of D-glutamic acid and D-alanine, which are essential constituents of bacterial cell wall and are the building block for other D-amino acids. Despite the difference in the structure of the substrates, D-AATs and L-ATTs have strong similarity [, ]. ; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 1EKV_A 2HGX_A 1EKP_A 1KTA_B 1KT8_B 2A1H_B 2HDK_A 2HGW_B 1EKF_B 2HG8_A ....
Probab=44.18 E-value=55 Score=22.57 Aligned_cols=38 Identities=18% Similarity=0.298 Sum_probs=28.7
Q ss_pred CcEEEEEcCCCCEEEEeeccEEEEecCCcceEecCCCcee
Q psy1800 31 FDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKPKRNFV 70 (81)
Q Consensus 31 ~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp~~kgi 70 (81)
++-+.+-|.+|+.-++-.+|+|++= +.-+++=|.+.|+
T Consensus 125 ~de~ll~d~~G~v~E~~~sNif~~~--~~~~~TP~~~~gi 162 (231)
T PF01063_consen 125 ADEALLLDEDGNVTEGSTSNIFFVK--DGTLYTPPLDSGI 162 (231)
T ss_dssp SSEEEEEETTSBEEEESSSEEEEEE--TTEEEEESGSSSS
T ss_pred cchhheecCCCCcCCCCCccccccc--CCEEEcCChhhhh
Confidence 3445677899999999999999983 3337777777655
No 58
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=42.71 E-value=56 Score=23.92 Aligned_cols=50 Identities=34% Similarity=0.436 Sum_probs=33.4
Q ss_pred CCCcEEEEECCCCc----c-eEEEEEEEEEecC-CCcEEEEEcCCCCEEEEeeccEEEEe
Q psy1800 2 FPGNLCMITGGRNL----G-RVGTVVNRERHPG-SFDIVHVKDGNGHVFATRLNNVFIIG 55 (81)
Q Consensus 2 e~G~~~mVtgG~n~----G-rvG~I~~ie~~~g-~~~iV~ikd~~g~~F~T~~~nVfvIG 55 (81)
++|+.+ +|.|-.- | .||+|.+++..+. .+-.+.++-... -..++||+||=
T Consensus 216 ~~GD~V-vTSGl~g~fP~Gi~VG~V~~v~~~~~~~~~~~~v~p~~d---~~~l~~V~Vi~ 271 (276)
T PRK13922 216 KVGDLV-VTSGLGGIFPAGLPVGKVTSVERDDYGLFKTVYVKPAAD---LDRLRYVLVVK 271 (276)
T ss_pred CCCCEE-EECCCCCcCCCCCEEEEEEEEEeCCCCCeeEEEEEECcc---cCCCcEEEEEe
Confidence 456664 4444421 1 4899999987766 577888876442 56789999984
No 59
>cd06165 Sortase_A_1 Sortase A (SrtA) or subfamily-1 sortases are cysteine transpeptidases found in gram-positive bacteria that anchor surface proteins to peptidoglycans of the bacterial cell wall envelope. They do so by catalyzing a transpeptidation reaction in which the surface protein substrate is cleaved at a conserved cell wall sorting signal (usually a pentapeptide motif), and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. This group contains a subset of Class A (subfamily-1) sortases, excluding SrtA from Staphylococcus aureus. Sortase A cleaves between threonine and glycine of the LPXTG motif in a wide range of protein substrates. It affects the ability of a pathogen to establish successful infection. Sortase A contains an N-terminal region that functions as both a signal peptide for secretion and a stop-tra
Probab=42.00 E-value=73 Score=20.60 Aligned_cols=65 Identities=12% Similarity=0.156 Sum_probs=41.1
Q ss_pred EEECCCCcc----eEEEEEEEEEecCCCcEEEEEcCCCCEEEEeeccEEEEecCCcceEecCCC-ceeeeeeeecc
Q psy1800 8 MITGGRNLG----RVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKPKR-NFVSPRQTCPT 78 (81)
Q Consensus 8 mVtgG~n~G----rvG~I~~ie~~~g~~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp~~-kgi~~~~~~~~ 78 (81)
+|+-|+|.+ ..+.+.+.+ .-+.|.+++.+ ..|.-.....+++-..+-..+. |.. +-.-...||-.
T Consensus 44 ~vIaGH~~~~~~~~F~~L~~l~----~Gd~I~l~~~~-~~~~Y~V~~~~~v~~~~~~~~~-~~~~~~~ltLiTC~p 113 (127)
T cd06165 44 YALAGHNMRNKGVLFSPLYKVK----VGDKIYLTDKD-NVYEYKVTSKKIVDPTRVDVID-DVPGKKLITLITCDD 113 (127)
T ss_pred EEEEcccCCCCCcccCCHHHCc----CCCEEEEEECC-EEEEEEEeeEEEECcccceeec-cCCCCCEEEEEecCC
Confidence 566677776 344555544 34788999865 5899999999999874443432 322 33445568853
No 60
>PF01333 Apocytochr_F_C: Apocytochrome F, C-terminal; InterPro: IPR002325 The cytochrome b6f integral membrane protein complex transfers electrons between the two reaction centre complexes of oxygenic photosynthetic membranes, and participates in formation of the transmembrane electrochemical proton gradient by also transferring protons from the stromal to the internal lumen compartment []. The cytochrome b6f complex contains four polypeptides: cytochrome f (285 aa); cytochrome b6 (215 aa); Rieske iron-sulphur protein (179 aa); and subunit IV (160 aa) []. In its structure and functions, the cytochrome b6f complex bears extensive analogy to the cytochrome bc1 complex of mitochondria and photosynthetic purple bacteria; cytochrome f (cyt f) plays a role analogous to that of cytochrome c1, in spite of their different structures [].; GO: 0005506 iron ion binding, 0009055 electron carrier activity, 0020037 heme binding, 0015979 photosynthesis, 0031361 integral to thylakoid membrane; PDB: 2E75_C 2E74_C 1VF5_P 2D2C_P 2E76_C 1TU2_B 2ZT9_C 1E2V_A 1CFM_A 1E2W_B ....
Probab=41.98 E-value=48 Score=22.75 Aligned_cols=27 Identities=19% Similarity=0.254 Sum_probs=20.6
Q ss_pred eEEEEEEEEEecCCCcEEEEEcCCCCE
Q psy1800 17 RVGTVVNRERHPGSFDIVHVKDGNGHV 43 (81)
Q Consensus 17 rvG~I~~ie~~~g~~~iV~ikd~~g~~ 43 (81)
.-|+|.+|.+....-..|+|+.++|+.
T Consensus 9 ~~G~I~~I~~~ekgg~~vtI~~~dG~~ 35 (118)
T PF01333_consen 9 AAGTITKITRKEKGGYEVTIETSDGET 35 (118)
T ss_dssp SSEEEEEEEEETTSEEEEEEETTTSEE
T ss_pred CCeEEEEEEEcCCCCEEEEEECCCCCE
Confidence 458899999887655567789999854
No 61
>cd02799 tRNA_bind_EMAP-II_like tRNA-binding-domain-containing EMAP2-like proteins. This family contains a diverse fraction of tRNA binding proteins, including Caenorhabditis elegans methionyl-tRNA synthetase (CeMetRS), human tyrosyl- tRNA synthetase (hTyrRS), Saccharomyces cerevisiae Arc1p, human p43 and EMAP2. CeMetRS and hTyrRS aminoacylate their cognate tRNAs. Arc1p is a transactivator of yeast methionyl-tRNA and glutamyl-tRNA synthetases. This domain has general tRNA binding properties. In a subset of this family this domain has the added capability of a cytokine. For example the p43 component of the Human aminoacyl-tRNA synthetase complex is cleaved to release EMAP-II cytokine. EMAP-II has multiple activities during apoptosis, angiogenesis and inflammation and participates in malignant transformation. A EMAP-II-like cytokine also is released from hTyrRS upon cleavage. The active cytokine heptapeptide locates to this domain.
Probab=41.78 E-value=68 Score=20.30 Aligned_cols=21 Identities=24% Similarity=0.499 Sum_probs=16.1
Q ss_pred eEEEEEEEEEecCCCcEEEEE
Q psy1800 17 RVGTVVNRERHPGSFDIVHVK 37 (81)
Q Consensus 17 rvG~I~~ie~~~g~~~iV~ik 37 (81)
++|.|.+.+.||.+..+..++
T Consensus 9 ~vg~I~~~~~~p~s~kL~~l~ 29 (105)
T cd02799 9 RVGKILKVRKHPDADSLYVEE 29 (105)
T ss_pred EEEEEEEEEecCCCCccEEEE
Confidence 589999999999865554443
No 62
>PF04085 MreC: rod shape-determining protein MreC; InterPro: IPR007221 MreC (murein formation C) is involved in the rod shape determination in Escherichia coli, and more generally in cell shape determination of bacteria whether or not they are rod-shaped.; GO: 0008360 regulation of cell shape; PDB: 2J5U_B 2QF4_B 2QF5_A.
Probab=41.34 E-value=45 Score=22.67 Aligned_cols=50 Identities=34% Similarity=0.434 Sum_probs=29.8
Q ss_pred CCCcEEEEECCCCc----c-eEEEEEEEEEecC-CCcEEEEEcCCCCEEEEeeccEEEEe
Q psy1800 2 FPGNLCMITGGRNL----G-RVGTVVNRERHPG-SFDIVHVKDGNGHVFATRLNNVFIIG 55 (81)
Q Consensus 2 e~G~~~mVtgG~n~----G-rvG~I~~ie~~~g-~~~iV~ikd~~g~~F~T~~~nVfvIG 55 (81)
++|+.++-. |-.. | .+|+|.+++..+. .+-.+.++=+.. ...++||+|+-
T Consensus 95 ~~GD~V~TS-G~~~~fP~Gi~VG~V~~v~~~~~~~~~~~~v~p~~d---~~~l~~V~Vi~ 150 (152)
T PF04085_consen 95 KKGDIVVTS-GLGGIFPPGIPVGTVSSVEPDKSGLFKEVYVKPAVD---FSRLEYVFVIK 150 (152)
T ss_dssp -TT-EEEEE--TTSSS-CCEEEEEEEEEECTTTCCCEEEEEEESS-----TT--EEEEEE
T ss_pred CCCCEEEEC-CCCCcCCCCCEEEEEEEEEeCCCCcEEEEEEEECCC---cCcCcEEEEEe
Confidence 456665543 3221 1 4899999998877 778888875442 34568898875
No 63
>PF11717 Tudor-knot: RNA binding activity-knot of a chromodomain ; PDB: 2EKO_A 2RO0_A 2RNZ_A 1WGS_A 3E9G_A 3E9F_A 2K3X_A 2K3Y_A 2EFI_A 2F5K_F ....
Probab=41.32 E-value=68 Score=18.21 Aligned_cols=37 Identities=11% Similarity=0.038 Sum_probs=28.0
Q ss_pred CCCCcEEEEECCCCcceEEEEEEEEEecC-CCcEEEEE
Q psy1800 1 MFPGNLCMITGGRNLGRVGTVVNRERHPG-SFDIVHVK 37 (81)
Q Consensus 1 fe~G~~~mVtgG~n~GrvG~I~~ie~~~g-~~~iV~ik 37 (81)
|++|..+++.-+.+.-.-++|.+++..++ ..=.||-.
T Consensus 1 ~~vG~~v~~~~~~~~~y~A~I~~~r~~~~~~~YyVHY~ 38 (55)
T PF11717_consen 1 FEVGEKVLCKYKDGQWYEAKILDIREKNGEPEYYVHYQ 38 (55)
T ss_dssp --TTEEEEEEETTTEEEEEEEEEEEECTTCEEEEEEET
T ss_pred CCcCCEEEEEECCCcEEEEEEEEEEecCCCEEEEEEcC
Confidence 68999999999999999999999988665 33345554
No 64
>COG0073 ARC1 EMAP domain [General function prediction only]
Probab=41.06 E-value=50 Score=21.86 Aligned_cols=25 Identities=40% Similarity=0.589 Sum_probs=17.8
Q ss_pred eEEEEEEEEEecCCCcEEEEEcCCC
Q psy1800 17 RVGTVVNRERHPGSFDIVHVKDGNG 41 (81)
Q Consensus 17 rvG~I~~ie~~~g~~~iV~ikd~~g 41 (81)
++|+|.+.++||.+..+..++=.-|
T Consensus 22 ~vg~V~~~~~~p~adkL~~~~Vd~G 46 (123)
T COG0073 22 RVGKVVEAEPHPNADKLLVLKVDLG 46 (123)
T ss_pred EEEEEEEeEECCCCCeeEEEEEEcC
Confidence 6899999999999655444443333
No 65
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=41.05 E-value=22 Score=30.03 Aligned_cols=27 Identities=22% Similarity=0.479 Sum_probs=24.9
Q ss_pred CCCCcEEEEECCCCcceEEEEEEEEEe
Q psy1800 1 MFPGNLCMITGGRNLGRVGTVVNRERH 27 (81)
Q Consensus 1 fe~G~~~mVtgG~n~GrvG~I~~ie~~ 27 (81)
|+.|+++-|+-|.+.+++|.|..|+..
T Consensus 140 f~~gD~vkVI~g~~~~d~g~V~rI~~~ 166 (607)
T COG5164 140 FYKGDLVKVIEGGEMVDIGTVPRIDGE 166 (607)
T ss_pred cccCCeEEEeccccccccceEEEecCc
Confidence 789999999999999999999999754
No 66
>PF00924 MS_channel: Mechanosensitive ion channel; InterPro: IPR006685 Mechanosensitive (MS) channels provide protection against hypo-osmotic shock, responding both to stretching of the cell membrane and to membrane depolarisation. They are present in the membranes of organisms from the three domains of life: bacteria, archaea, and eukarya []. There are two families of MS channels: large-conductance MS channels (MscL) and small-conductance MS channels (MscS or YGGB). The pressure threshold for MscS opening is 50% that of MscL []. The MscS family is much larger and more variable in size and sequence than the MscL family. Much of the diversity in MscS proteins occurs in the size of the transmembrane regions, which ranges from three to eleven transmembrane helices, although the three C-terminal helices are conserved. This family contains sequences form the MscS family of proteins. MscS folds as a homo-heptamer with a cylindrical shape, and can be divided into transmembrane and extramembrane regions: an N-terminal periplasmic region, a transmembrane region, and a C-terminal cytoplasmic region (middle and C-terminal domains). The transmembrane region forms a channel through the membrane that opens into a chamber enclosed by the extramembrane portion, the latter connecting to the cytoplasm through distinct portals [].; GO: 0055085 transmembrane transport, 0016020 membrane; PDB: 2OAU_E 2VV5_F.
Probab=40.93 E-value=82 Score=21.41 Aligned_cols=60 Identities=13% Similarity=0.148 Sum_probs=32.0
Q ss_pred CCCCcEEEEECCCCcceEEEEEEEEEecCCCcEEEEEcCCCCEEEEeeccEEEEecCCcceEecCC-Cceeeeeee
Q psy1800 1 MFPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKPK-RNFVSPRQT 75 (81)
Q Consensus 1 fe~G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp~-~kgi~~~~~ 75 (81)
|++|+++-+- |..|+|.+|... -..+++.+|+. -++-...|. +++.+.+.+ ....+....
T Consensus 61 f~vGD~I~i~-----~~~G~V~~I~l~-----~t~l~~~~g~~-v~IPNs~l~----~~~i~N~s~~~~~~~~~v~ 121 (206)
T PF00924_consen 61 FKVGDRIEIG-----GVEGRVEEIGLR-----STRLRTWDGEI-VIIPNSKLI----SSPIVNYSRSSPYRRVVVE 121 (206)
T ss_dssp S-TT-EEESS-----S-EEEEEEE-SS-----EEEEEETTS-E-EEEEHHHHH----CS-EEETTT-SSEEEEEEE
T ss_pred ccCCCEEEEE-----EeehHHHhcCcc-----eeeeecCCCCE-EEEEchhee----eEEEEEeeccCCceeeeee
Confidence 6788886665 788899988532 45667777653 333333332 556666666 455544443
No 67
>TIGR01956 NusG_myco NusG family protein. This model represents a family of Mycoplasma proteins orthologous to the bacterial transcription termination/antitermination factor NusG. These sequences from Mycoplasma are notably diverged (long branches in a Neighbor-joining phylogenetic tree) from the bacterial species. And although NusA and ribosomal protein S10 (NusE) appear to be present, NusB may be absent in Mycoplasmas calling into question whether these species have a functional Nus system including this family as a member.
Probab=40.42 E-value=1.1e+02 Score=23.51 Aligned_cols=26 Identities=27% Similarity=0.392 Sum_probs=24.2
Q ss_pred CCCCcEEEEECCCCcceEEEEEEEEE
Q psy1800 1 MFPGNLCMITGGRNLGRVGTVVNRER 26 (81)
Q Consensus 1 fe~G~~~mVtgG~n~GrvG~I~~ie~ 26 (81)
|++|+.+-|+.|.=.|..|+|.++..
T Consensus 206 f~vGd~VrI~dGPF~GfeG~I~eid~ 231 (258)
T TIGR01956 206 FRVGNFVKIVDGPFKGIVGKIKKIDQ 231 (258)
T ss_pred CCCCCEEEEEecCCCCcEEEEEEEeC
Confidence 67999999999999999999999964
No 68
>KOG3172|consensus
Probab=39.62 E-value=72 Score=21.81 Aligned_cols=44 Identities=25% Similarity=0.468 Sum_probs=27.0
Q ss_pred EEEEEEEEecC-CCcEEEEEcCCCCEEEEeeccEEEEecCCcceEecC
Q psy1800 19 GTVVNRERHPG-SFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKP 65 (81)
Q Consensus 19 G~I~~ie~~~g-~~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp 65 (81)
|++.|-|..+. .-+-|++.-.+|. .+.+++||+=|+ .=-++-||
T Consensus 30 GkliEaeDnmNcql~di~vT~~dg~--vs~le~V~IRGS-~IRFlvlP 74 (119)
T KOG3172|consen 30 GKLIEAEDNMNCQLRDITVTARDGR--VSQLEQVFIRGS-KIRFLVLP 74 (119)
T ss_pred eeeEEeccccccEEEEEEEEccCCc--ceeeeeEEEecC-eEEEEECc
Confidence 66777776665 3333334445554 688999999886 43344454
No 69
>PRK09612 rpl2p 50S ribosomal protein L2P; Validated
Probab=39.39 E-value=1e+02 Score=23.24 Aligned_cols=49 Identities=22% Similarity=0.411 Sum_probs=31.4
Q ss_pred EEEEEEEecC-CCcEEEEEcCCCCEEEEeeccEEEEecCCcceEecCCCceeeeeeeec
Q psy1800 20 TVVNRERHPG-SFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKPKRNFVSPRQTCP 77 (81)
Q Consensus 20 ~I~~ie~~~g-~~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp~~kgi~~~~~~~ 77 (81)
.|.+||..|+ .-.++ -+.|. |++++.. +++.-.|.||.++=.+++..|-
T Consensus 105 ~I~NIE~~pG~Ggkl~---RSAGt-~A~Ii~k-----~~~~~~vkLPSGe~r~i~~~c~ 154 (238)
T PRK09612 105 PVCNIESRPGDGGKFA---RSSGT-YALVVGH-----EGDKVIVQLPSGKIKELNPRCR 154 (238)
T ss_pred EEEEEEecCCCCcceE---EcCCC-eEEEEEe-----cCCEEEEECCCCCeEEECCcCe
Confidence 4667777777 33333 24553 6655432 2255678999999888888884
No 70
>cd04716 BAH_plantDCM_I BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5)-methyltransferases (DCM) from plants. 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=38.47 E-value=1.2e+02 Score=20.25 Aligned_cols=36 Identities=8% Similarity=0.027 Sum_probs=22.7
Q ss_pred CCCCcEEEEECCCC-cceEEEEEEEEEecCCCcEEEE
Q psy1800 1 MFPGNLCMITGGRN-LGRVGTVVNRERHPGSFDIVHV 36 (81)
Q Consensus 1 fe~G~~~mVtgG~n-~GrvG~I~~ie~~~g~~~iV~i 36 (81)
|+.|+-|+|..+.+ -=.+|+|.++.........+++
T Consensus 4 ~~lgD~V~v~~~~~~~~yi~rI~~i~e~~~g~~~~~v 40 (122)
T cd04716 4 YNLGDDAYVQGGEGEEPFICKITEFFEGTDGKTYFTA 40 (122)
T ss_pred EEcCCEEEEECCCCCCCEEEEEEEEEEcCCCceEEEE
Confidence 46789999998853 1138888888755333334443
No 71
>COG1022 FAA1 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]
Probab=36.59 E-value=22 Score=29.94 Aligned_cols=59 Identities=14% Similarity=0.188 Sum_probs=41.2
Q ss_pred CCCCcEEEEECCCCcceEEEEEEEEEecCCCcEE--EEEcCCCCEEEEeeccEEEEecCCcceE
Q psy1800 1 MFPGNLCMITGGRNLGRVGTVVNRERHPGSFDIV--HVKDGNGHVFATRLNNVFIIGKGTKAFC 62 (81)
Q Consensus 1 fe~G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV--~ikd~~g~~F~T~~~nVfvIGk~~kp~I 62 (81)
|..|++..+..+.++=.+|+.+++.+.....+|- -||+.- ......++++|+|. +++.+
T Consensus 451 f~TGDlg~~d~~g~L~i~gRkK~~i~l~~GknIaP~~IE~~l--~~~~~I~qi~vvg~-~k~~~ 511 (613)
T COG1022 451 FRTGDLGELDEDGYLVITGRKKELIKLSNGKNIAPEPIESKL--AKSPLIEQICVVGD-DKKFL 511 (613)
T ss_pred cccCceeEEcCCCcEEEeecccceEECCCCcccChHHHHHHH--hcCCCeeEEEEEec-CCcce
Confidence 6788898888888888888888887776533332 234322 24677899999996 65543
No 72
>cd04495 BRCA2DBD_OB3 BRCA2DBD_OB3: A subfamily of OB folds corresponding to the third OB fold (OB3) of the 800-amino acid C-terminal ssDNA binding domain (DBD) of BRCA2 (breast cancer susceptibility gene 2) protein, called BRCA2DBD. BRCA2 participates in homologous recombination-mediated repair of double-strand DNA breaks. It stimulates the displacement of Replication protein A (RPA), the most abundant eukaryotic ssDNA binding protein. It also facilitates filament formation. Mutations that map throughout the BRCA2 protein are associated with breast cancer susceptibility. BRCA2 is a large nuclear protein and its most conserved region is the C-terminal BRCA2DBD. BRCA2DBD binds ssDNA in vitro, and is composed of five structural domains, three of which are OB folds (OB1, OB2, and OB3). BRCA2DBD OB2 and OB3 are arranged in tandem, and their mode of binding can be considered qualitatively similar to two OB folds of RPA1, DBD-A and DBD-B (the major DBDs of RPA).
Probab=36.45 E-value=55 Score=21.83 Aligned_cols=25 Identities=28% Similarity=0.365 Sum_probs=21.6
Q ss_pred EEEEEEEEEec-CCCcEEEEEcCCCC
Q psy1800 18 VGTVVNRERHP-GSFDIVHVKDGNGH 42 (81)
Q Consensus 18 vG~I~~ie~~~-g~~~iV~ikd~~g~ 42 (81)
+|.|..+.+.+ |.+..|++-|.+-+
T Consensus 3 VGvVvsV~~~~~g~~~~vYLaDe~~n 28 (100)
T cd04495 3 VGVVISVGKPIEGKFPAVYLADECLN 28 (100)
T ss_pred eEEEEEEcccccCccceEEEecCCcC
Confidence 79999999888 79999999987743
No 73
>COG1843 FlgD Flagellar hook capping protein [Cell motility and secretion]
Probab=36.39 E-value=1.6e+02 Score=21.87 Aligned_cols=47 Identities=28% Similarity=0.209 Sum_probs=37.2
Q ss_pred CCcEEEEECCCCcceEEEEEEEEEecC--CCcEEEEEcCCCCEEEEeec
Q psy1800 3 PGNLCMITGGRNLGRVGTVVNRERHPG--SFDIVHVKDGNGHVFATRLN 49 (81)
Q Consensus 3 ~G~~~mVtgG~n~GrvG~I~~ie~~~g--~~~iV~ikd~~g~~F~T~~~ 49 (81)
.|..+|+.+++..+..|.+.-...-+. ..-.+++.|.+|....|...
T Consensus 95 IGk~V~v~~~~~~~~~~~~~~~~~~~~~~~~v~~~I~d~~g~vv~t~~~ 143 (222)
T COG1843 95 IGKTVMVADGKVTLVDGTVKFVVTLPQAANNVGIEITDGNGVVVRTIDL 143 (222)
T ss_pred cCcEEEeecCceeeeeeeEEEEEEcccccccceEEEEecCCCEEEeccc
Confidence 588999999999997777877777765 55678888999988776543
No 74
>cd01721 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D3 heterodimerizes with subunit B and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=36.35 E-value=96 Score=18.49 Aligned_cols=49 Identities=24% Similarity=0.373 Sum_probs=31.4
Q ss_pred cceEEEEEEEEEecC-CCcEEEEEcCCCCEEEEeeccEEEEecCCcceEecCC
Q psy1800 15 LGRVGTVVNRERHPG-SFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKPK 66 (81)
Q Consensus 15 ~GrvG~I~~ie~~~g-~~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp~ 66 (81)
.=-.|++...+.++. .=+=+...+.+|+. ..++.+|+=|. +=-+|.||.
T Consensus 21 ~~~~G~L~~~D~~MNl~L~~~~~~~~~g~~--~~~~~v~IRG~-nI~~v~lPd 70 (70)
T cd01721 21 EVYRGKLIEAEDNMNCQLKDVTVTARDGRV--SQLEQVYIRGS-KIRFFILPD 70 (70)
T ss_pred cEEEEEEEEEcCCceeEEEEEEEECCCCcE--eEcCcEEEeCC-EEEEEEeCC
Confidence 334788888887765 22223344567763 45689999776 555677774
No 75
>PF08806 Sep15_SelM: Sep15/SelM redox domain; InterPro: IPR014912 Sep15 and SelM are eukaryotic selenoproteins that have a thioredoxin-like domain and a surface accessible active site redox motif []. This suggests that they function as thiol-disulphide isomerases involved in disulphide bond formation in the endoplasmic reticulum []. ; PDB: 2A4H_A 2A2P_A.
Probab=36.15 E-value=63 Score=20.08 Aligned_cols=25 Identities=16% Similarity=0.167 Sum_probs=14.1
Q ss_pred EEEEecCCCcEEEEEcCCCCEEEEe
Q psy1800 23 NRERHPGSFDIVHVKDGNGHVFATR 47 (81)
Q Consensus 23 ~ie~~~g~~~iV~ikd~~g~~F~T~ 47 (81)
+++..+|++..+++.|.+|+.-+++
T Consensus 34 ~vk~i~G~~P~L~l~d~~g~~~E~i 58 (78)
T PF08806_consen 34 EVKYIPGAPPELVLLDEDGEEVERI 58 (78)
T ss_dssp EEEEESS---EEEEE-SSS--SEEE
T ss_pred EEEEeCCCCCEEEEEcCCCCEEEEE
Confidence 3455688889999999999876664
No 76
>PF01336 tRNA_anti-codon: OB-fold nucleic acid binding domain; InterPro: IPR004365 The OB-fold (oligonucleotide/oligosaccharide-binding fold) is found in all three kingdoms and its common architecture presents a binding face that has adapted to bind different ligands. The OB-fold is a five/six-stranded closed beta-barrel formed by 70-80 amino acid residues. The strands are connected by loops of varying length which form the functional appendages of the protein. The majority of OB-fold proteins use the same face for ligand binding or as an active site. Different OB-fold proteins use this 'fold-related binding face' to, variously, bind oligosaccharides, oligonucleotides, proteins, metal ions and catalytic substrates. This entry contains OB-fold domains that bind to nucleic acids []. It includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl-tRNA synthetases (See IPR004364 from INTERPRO). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule 6.1.1 from EC. This domain is found in RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family [, ]. This domain is also found at the C terminus of bacterial DNA polymerase III alpha chain.; GO: 0003676 nucleic acid binding; PDB: 1BBU_A 1KRS_A 1BBW_A 1KRT_A 1EQR_B 1IL2_B 1C0A_A 3KFU_A 1EOV_A 1ASY_A ....
Probab=36.07 E-value=62 Score=18.05 Aligned_cols=26 Identities=27% Similarity=0.509 Sum_probs=21.1
Q ss_pred EEEEEEEEEecCCCcEEEEEcCCCCE
Q psy1800 18 VGTVVNRERHPGSFDIVHVKDGNGHV 43 (81)
Q Consensus 18 vG~I~~ie~~~g~~~iV~ikd~~g~~ 43 (81)
.|.|.++++..++.-.+.|.|..|..
T Consensus 4 ~G~V~~~~~~~~~~~~~~l~D~tg~i 29 (75)
T PF01336_consen 4 EGRVTSIRRSGGKIVFFTLEDGTGSI 29 (75)
T ss_dssp EEEEEEEEEEETTEEEEEEEETTEEE
T ss_pred EEEEEEEEcCCCCEEEEEEEECCccE
Confidence 58888888666788899999988754
No 77
>CHL00052 rpl2 ribosomal protein L2
Probab=35.84 E-value=1.2e+02 Score=23.30 Aligned_cols=49 Identities=20% Similarity=0.314 Sum_probs=30.4
Q ss_pred EEEEEEEecC-CCcEEEEEcCCCCEEEEeeccEEEEecCCcceEecCCCceeeeeeeec
Q psy1800 20 TVVNRERHPG-SFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKPKRNFVSPRQTCP 77 (81)
Q Consensus 20 ~I~~ie~~~g-~~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp~~kgi~~~~~~~ 77 (81)
.|.+||..|+ .-.++ -++|. |++++.. +++.-.|.||.++=.+++..|-
T Consensus 138 ~I~NIE~~pg~Ggk~~---RsAGt-~A~ii~k-----~~~~~~vkLPSGe~r~v~~~c~ 187 (273)
T CHL00052 138 AIHNIEITPGKGGQLA---RAAGA-VAKLIAK-----EGKSATLKLPSGEVRLISKNCS 187 (273)
T ss_pred EEEEEEecCCCCceEE---EecCC-eEEEEEe-----cCCEEEEECCCCCeEEECCcCe
Confidence 3556676666 32222 24553 5654432 2356678999999888898885
No 78
>PF13750 Big_3_3: Bacterial Ig-like domain (group 3)
Probab=35.73 E-value=1.1e+02 Score=21.12 Aligned_cols=35 Identities=23% Similarity=0.388 Sum_probs=26.2
Q ss_pred CCCcEEE--EEcCCCCEEEEeeccEEEEecCCcceEec
Q psy1800 29 GSFDIVH--VKDGNGHVFATRLNNVFIIGKGTKAFCSK 64 (81)
Q Consensus 29 g~~~iV~--ikd~~g~~F~T~~~nVfvIGk~~kp~IsL 64 (81)
|++++.. ..|..|+.-++....-|.|-+ ..|.|++
T Consensus 15 G~Y~l~~~~a~D~agN~~~~~~~~~~~iD~-T~Ptisi 51 (158)
T PF13750_consen 15 GSYTLTVVTATDAAGNTSTSTVSETFTIDN-TPPTISI 51 (158)
T ss_pred ccEEEEEEEEEecCCCEEEEEEeeEEEEcC-CCCEEEE
Confidence 4555555 689999977666665677876 9999999
No 79
>KOG3421|consensus
Probab=35.67 E-value=58 Score=22.86 Aligned_cols=26 Identities=15% Similarity=0.331 Sum_probs=24.2
Q ss_pred CCCcEEEEECCCCcceEEEEEEEEEe
Q psy1800 2 FPGNLCMITGGRNLGRVGTVVNRERH 27 (81)
Q Consensus 2 e~G~~~mVtgG~n~GrvG~I~~ie~~ 27 (81)
|+|..+++.-|...|+.-.|.++..+
T Consensus 8 eVGrva~v~~G~~~GkL~AIVdviDq 33 (136)
T KOG3421|consen 8 EVGRVALVSFGPDAGKLVAIVDVIDQ 33 (136)
T ss_pred hcceEEEEEecCCCceEEEEEEeecc
Confidence 78999999999999999999998766
No 80
>TIGR00219 mreC rod shape-determining protein MreC. MreC (murein formation C) is involved in the rod shape determination in E. coli, and more generally in cell shape determination of bacteria whether or not they are rod-shaped. Cells defective in MreC are round. Species with MreC include many of the Proteobacteria, Gram-positives, and spirochetes.
Probab=35.39 E-value=1.1e+02 Score=23.09 Aligned_cols=40 Identities=20% Similarity=0.240 Sum_probs=30.2
Q ss_pred eEEEEEEEEEecC-CCcEEEEEcCCCCEEEEeeccEEEEecCCcc
Q psy1800 17 RVGTVVNRERHPG-SFDIVHVKDGNGHVFATRLNNVFIIGKGTKA 60 (81)
Q Consensus 17 rvG~I~~ie~~~g-~~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp 60 (81)
.||+|.+++..+. .+-.+.++=+.. -..+++|+|+-+ +-|
T Consensus 236 ~VG~V~~v~~~~~~~~~~v~v~P~ad---~~~l~~V~Vi~~-~~~ 276 (283)
T TIGR00219 236 PIGVVTSVHIDSYNSLLVIEVKPAAV---LDRLRYVLLVWN-DVP 276 (283)
T ss_pred EEEEEEEEEeCCCCceEEEEEEECCC---cccceEEEEEeC-CCC
Confidence 4899999998765 777888875442 467899999976 444
No 81
>TIGR02222 chap_CsaA export-related chaperone CsaA. This model describes Bacillus subtilis CsaA, an export-related chaperone that interacts with the Sec system, and related proteins from a number of other bacteria and archaea. The crystal structure is known for the homodimer from Thermus thermophilus.
Probab=35.26 E-value=73 Score=20.63 Aligned_cols=26 Identities=27% Similarity=0.281 Sum_probs=18.2
Q ss_pred ceEEEEEEEEEecCCCc-EEEEEcCCC
Q psy1800 16 GRVGTVVNRERHPGSFD-IVHVKDGNG 41 (81)
Q Consensus 16 GrvG~I~~ie~~~g~~~-iV~ikd~~g 41 (81)
=|+|.|.+.+.|+.+.. +..++=..|
T Consensus 9 lrvg~I~~~~~~p~a~k~L~~l~vd~G 35 (107)
T TIGR02222 9 LRVGRIVRAEPFPEARKPAYKLWVDFG 35 (107)
T ss_pred heeEEEEEEeecCCcccceeEEEEEec
Confidence 37899999999998764 544443333
No 82
>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=35.07 E-value=1.1e+02 Score=18.81 Aligned_cols=36 Identities=11% Similarity=0.086 Sum_probs=27.0
Q ss_pred CCCCcEEEEECCC--CcceEEEEEEEEEecCCC--cEEEE
Q psy1800 1 MFPGNLCMITGGR--NLGRVGTVVNRERHPGSF--DIVHV 36 (81)
Q Consensus 1 fe~G~~~mVtgG~--n~GrvG~I~~ie~~~g~~--~iV~i 36 (81)
|.+|+.+|+-.+. .-=.+|.|.+|....... -.+++
T Consensus 3 ~~vGD~V~v~~~~~~~~~~v~~I~~i~~~~~~~~~~~~~v 42 (119)
T PF01426_consen 3 YKVGDFVYVKPDDPPEPPYVARIEEIWEDKDGNKEKMVKV 42 (119)
T ss_dssp EETTSEEEEECTSTTSEEEEEEEEEEEEETTTSEEEEEEE
T ss_pred EeCCCEEEEeCCCCCCCCEEEEEEEEEcCCCCCEEEEEEE
Confidence 4679999999988 778899999997665533 34444
No 83
>TIGR01171 rplB_bact ribosomal protein L2, bacterial/organellar. This model distinguishes bacterial and organellar ribosomal protein L2 from its counterparts in the archaea nad in the eukaryotic cytosol. Plant mitochondrial examples tend to have long, variable inserts.
Probab=34.90 E-value=1.3e+02 Score=23.06 Aligned_cols=49 Identities=24% Similarity=0.279 Sum_probs=31.5
Q ss_pred EEEEEEEecCC-CcEEEEEcCCCCEEEEeeccEEEEecCCcceEecCCCceeeeeeeec
Q psy1800 20 TVVNRERHPGS-FDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKPKRNFVSPRQTCP 77 (81)
Q Consensus 20 ~I~~ie~~~g~-~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp~~kgi~~~~~~~ 77 (81)
.|.+||..|+. -.++ -++| .|++++.. +++.-.+.||.++=.+++..|.
T Consensus 138 ~I~NIE~~pg~Ggkl~---RsAG-t~A~ii~k-----~~~~~~vkLPSGe~r~i~~~c~ 187 (273)
T TIGR01171 138 TVHNIELKPGKGGQLA---RSAG-TSAQILAK-----EGGYVTLRLPSGEMRMVLKECR 187 (273)
T ss_pred EEEEEEecCCCCceEE---EecC-CeEEEEEe-----cCCEEEEECCCCCeEEECCcCe
Confidence 35677777773 2222 2555 36655432 2355677999999999999985
No 84
>PRK09374 rplB 50S ribosomal protein L2; Validated
Probab=33.74 E-value=1.5e+02 Score=22.84 Aligned_cols=49 Identities=24% Similarity=0.280 Sum_probs=31.1
Q ss_pred EEEEEEEecC-CCcEEEEEcCCCCEEEEeeccEEEEecCCcceEecCCCceeeeeeeec
Q psy1800 20 TVVNRERHPG-SFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKPKRNFVSPRQTCP 77 (81)
Q Consensus 20 ~I~~ie~~~g-~~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp~~kgi~~~~~~~ 77 (81)
.|.+||..|+ .-.++ -++| .|++++.. +++.-.|.||.++=..++..|.
T Consensus 140 ~I~NIE~~pG~Ggkl~---RsAG-t~A~ii~k-----~~~~~~vkLPSGe~r~i~~~c~ 189 (276)
T PRK09374 140 TVHNIELKPGKGGQLA---RSAG-TSAQLVAK-----EGKYATLRLPSGEVRKVLAECR 189 (276)
T ss_pred EEEEEEecCCCCceeE---eecC-CeEEEEEe-----cCCEEEEECCCCCeEEEccccc
Confidence 4566777776 32232 2455 36654432 2356678999999989899985
No 85
>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=33.44 E-value=1.7e+02 Score=20.59 Aligned_cols=36 Identities=8% Similarity=0.027 Sum_probs=25.3
Q ss_pred CCCCcEEEEECCCC-cceEEEEEEEEEecCCCcEEEE
Q psy1800 1 MFPGNLCMITGGRN-LGRVGTVVNRERHPGSFDIVHV 36 (81)
Q Consensus 1 fe~G~~~mVtgG~n-~GrvG~I~~ie~~~g~~~iV~i 36 (81)
+.+|+.|++--..+ -.-||+|.++...+...-.+.+
T Consensus 4 yrvGD~Vy~~~~~~~Py~I~rI~e~~~~~~~~~~vkV 40 (164)
T cd04709 4 YRVGDYVYFESSPNNPYLIRRIEELNKTARGHVEAKV 40 (164)
T ss_pred EecCCEEEEECCCCCCCEEEEEEEEEeCCCCCEEEEE
Confidence 46899999986655 3789999999766543333444
No 86
>cd00449 PLPDE_IV PyridoxaL 5'-Phosphate Dependent Enzymes class IV (PLPDE_IV). This D-amino acid superfamily, one of five classes of PLPDE, consists of branched-chain amino acid aminotransferases (BCAT), D-amino acid transferases (DAAT), and 4-amino-4-deoxychorismate lyases (ADCL). BCAT catalyzes the reversible transamination reaction between the L-branched-chain amino and alpha-keto acids. DAAT catalyzes the synthesis of D-glutamic acid and D-alanine, and ADCL converts 4-amino-4-deoxychorismate to p-aminobenzoate and pyruvate. Except for a few enzymes, i. e., Escherichia coli and Salmonella BCATs, which are homohexamers arranged as a double trimer, the class IV PLPDEs are homodimers. Homodimer formation is required for catalytic activity.
Probab=33.15 E-value=1.1e+02 Score=21.58 Aligned_cols=38 Identities=26% Similarity=0.319 Sum_probs=27.6
Q ss_pred CcEEEEEcCCCCEEEEeeccEEEEecCCcceEecCCCcee
Q psy1800 31 FDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKPKRNFV 70 (81)
Q Consensus 31 ~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp~~kgi 70 (81)
++-+.+-|.+|+.=++-.+|+|++=. .-|++-|.+.|+
T Consensus 147 ~de~llld~~g~v~E~s~sNlf~~~~--~~l~TP~~~~g~ 184 (256)
T cd00449 147 ADEALLLDDNGYVTEGSASNVFIVKD--GELVTPPLDGGI 184 (256)
T ss_pred CCEEEEECCCCcEEEcCceEEEEEEC--CEEEeCCCCCCc
Confidence 34556668889999999999999842 346676666554
No 87
>PF13415 Kelch_3: Galactose oxidase, central domain
Probab=31.75 E-value=41 Score=18.11 Aligned_cols=12 Identities=33% Similarity=0.476 Sum_probs=10.5
Q ss_pred CcEEEEECCCCc
Q psy1800 4 GNLCMITGGRNL 15 (81)
Q Consensus 4 G~~~mVtgG~n~ 15 (81)
|+..+|.||.+.
T Consensus 1 g~~~~vfGG~~~ 12 (49)
T PF13415_consen 1 GNKLYVFGGYDD 12 (49)
T ss_pred CCEEEEECCcCC
Confidence 688999999985
No 88
>PRK06606 branched-chain amino acid aminotransferase; Validated
Probab=31.51 E-value=95 Score=23.06 Aligned_cols=37 Identities=22% Similarity=0.275 Sum_probs=26.5
Q ss_pred cEEEEEcCCCCEEEEeeccEEEEecCCcceEecCCCcee
Q psy1800 32 DIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKPKRNFV 70 (81)
Q Consensus 32 ~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp~~kgi 70 (81)
+-+.+-|.+|+.=++-.+|+|++= +.-+++-|...|+
T Consensus 180 de~l~l~~~g~v~E~~~sNlf~v~--~~~l~TP~~~~gi 216 (306)
T PRK06606 180 DEALLLDVEGYVSEGSGENIFIVR--DGVLYTPPLTSSI 216 (306)
T ss_pred CEEEEECCCCCEEEcCceEEEEEE--CCEEECCCCcCCc
Confidence 445556899999999999999983 3346665555544
No 89
>TIGR01122 ilvE_I branched-chain amino acid aminotransferase, group I. Among the class IV aminotransferases are two phylogenetically separable groups of branched-chain amino acid aminotransferase (IlvE). The last common ancestor of the two lineages appears also to have given rise to a family of D-amino acid aminotransferases (DAAT). This model represents the IlvE family more strongly similar to the DAAT family.
Probab=31.32 E-value=98 Score=22.79 Aligned_cols=38 Identities=21% Similarity=0.318 Sum_probs=27.3
Q ss_pred CcEEEEEcCCCCEEEEeeccEEEEecCCcceEecCCCcee
Q psy1800 31 FDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKPKRNFV 70 (81)
Q Consensus 31 ~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp~~kgi 70 (81)
++-+.+-|.+|+.=++-.+|+|++-. + -+++-|.+.|+
T Consensus 171 ~de~l~ld~~g~v~E~s~sNlf~v~~-~-~l~TP~~~~~~ 208 (298)
T TIGR01122 171 YDEAILLDVEGYVAEGSGENIFIVKD-G-VLFTPPVTSSI 208 (298)
T ss_pred CCEEEEECCCCCEEECCceEEEEEEC-C-EEECCCCCCCc
Confidence 45555668899999999999999953 3 46665555443
No 90
>PRK13356 aminotransferase; Provisional
Probab=30.22 E-value=1.1e+02 Score=22.42 Aligned_cols=37 Identities=27% Similarity=0.285 Sum_probs=26.4
Q ss_pred CcEEEEEcCCCCEEEEeeccEEEEecCCcceEecCCCce
Q psy1800 31 FDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKPKRNF 69 (81)
Q Consensus 31 ~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp~~kg 69 (81)
++-+.+-|.+|+.=++-.+|+|++-+ + -+++-|.+.|
T Consensus 172 ~deal~ld~~G~v~E~~~sNlf~v~~-~-~l~TP~~~~~ 208 (286)
T PRK13356 172 FDNALVLDMLGNVAETATSNVFMVKD-G-VVFTPVPNGT 208 (286)
T ss_pred CCEEEEECCCCCEEEcCceEEEEEEC-C-EEEcCCCCCC
Confidence 45556668999999999999999943 3 3555554444
No 91
>TIGR03461 pabC_Proteo aminodeoxychorismate lyase. Members of this protein family are aminodeoxychorismate lyase (ADC lyase), EC 4.1.3.38, the PabC protein of PABA biosynthesis. PABA (para-aminobenzoate) is a precursor of folate, needed for de novo purine biosynthesis. This enzyme is a pyridoxal-phosphate-binding protein in the class IV aminotransferase family (pfam01063).
Probab=29.50 E-value=1.2e+02 Score=21.66 Aligned_cols=37 Identities=19% Similarity=0.157 Sum_probs=25.8
Q ss_pred CcEEEEEcCCCCEEEEeeccEEEEecCCcceEecCCCce
Q psy1800 31 FDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKPKRNF 69 (81)
Q Consensus 31 ~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp~~kg 69 (81)
++-+.+-|.+|+.=++-.+|+|++-. .-|++-|...|
T Consensus 157 ~de~llln~~g~v~E~s~sNif~~~~--~~l~TP~~~~~ 193 (261)
T TIGR03461 157 ADEALVLDTDGNVVECTAANIFWRKG--NQVFTPDLSYC 193 (261)
T ss_pred CCEEEEECCCCCEEEeccEEEEEEEC--CEEECCCcccc
Confidence 34455668899999999999999843 34665444443
No 92
>PF01344 Kelch_1: Kelch motif; InterPro: IPR006652 Kelch is a 50-residue motif, named after the Drosophila mutant in which it was first identified []. This sequence motif represents one beta-sheet blade, and several of these repeats can associate to form a beta-propeller. For instance, the motif appears 6 times in Drosophila egg-chamber regulatory protein, creating a 6-bladed beta-propeller. The motif is also found in mouse protein MIPP [] and in a number of poxviruses. In addition, kelch repeats have been recognised in alpha- and beta-scruin [, ], and in galactose oxidase from the fungus Dactylium dendroides [, ]. The structure of galactose oxidase reveals that the repeated sequence corresponds to a 4-stranded anti-parallel beta-sheet motif that forms the repeat unit in a super-barrel structural fold []. The known functions of kelch-containing proteins are diverse: scruin is an actin cross-linking protein; galactose oxidase catalyses the oxidation of the hydroxyl group at the C6 position in D-galactose; neuraminidase hydrolyses sialic acid residues from glycoproteins; and kelch may have a cytoskeletal function, as it is localised to the actin-rich ring canals that connect the 15 nurse cells to the developing oocyte in Drosophila []. Nevertheless, based on the location of the kelch pattern in the catalytic unit in galactose oxidase, functionally important residues have been predicted in glyoxal oxidase []. This entry represents a type of kelch sequence motif that comprises one beta-sheet blade.; GO: 0005515 protein binding; PDB: 2XN4_A 2WOZ_A 3II7_A 4ASC_A 1U6D_X 1ZGK_A 2FLU_X 2VPJ_A 2DYH_A 1X2R_A ....
Probab=29.43 E-value=90 Score=16.08 Aligned_cols=13 Identities=31% Similarity=0.434 Sum_probs=10.7
Q ss_pred CCcEEEEECCCCc
Q psy1800 3 PGNLCMITGGRNL 15 (81)
Q Consensus 3 ~G~~~mVtgG~n~ 15 (81)
.++..||+||.+.
T Consensus 10 ~~~~iyv~GG~~~ 22 (47)
T PF01344_consen 10 VGNKIYVIGGYDG 22 (47)
T ss_dssp ETTEEEEEEEBES
T ss_pred ECCEEEEEeeecc
Confidence 3678899999887
No 93
>PRK10089 tRNA-binding protein; Provisional
Probab=28.88 E-value=98 Score=20.09 Aligned_cols=22 Identities=32% Similarity=0.342 Sum_probs=16.9
Q ss_pred ceEEEEEEEEEecCCCcE-EEEE
Q psy1800 16 GRVGTVVNRERHPGSFDI-VHVK 37 (81)
Q Consensus 16 GrvG~I~~ie~~~g~~~i-V~ik 37 (81)
-|+|.|.+.+.|+.+..+ ..++
T Consensus 14 lrvg~I~~~~~~p~a~kL~~~l~ 36 (112)
T PRK10089 14 IRVGTIVEAEPFPEARKPAYKLW 36 (112)
T ss_pred eeeEEEEEEEEcCCcCcceEEEE
Confidence 478999999999987666 4443
No 94
>PRK12400 D-amino acid aminotransferase; Reviewed
Probab=28.13 E-value=1.2e+02 Score=22.41 Aligned_cols=38 Identities=24% Similarity=0.469 Sum_probs=26.5
Q ss_pred CCCcEEEEEcCCCCEEEEeeccEEEEecCCcceEecCCCcee
Q psy1800 29 GSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKPKRNFV 70 (81)
Q Consensus 29 g~~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp~~kgi 70 (81)
+.++.+.+ | +|+.=++-.+|+|++=. .-|++=|...|+
T Consensus 169 g~deaL~l-~-~g~v~E~t~sNif~v~~--~~l~TPpl~~g~ 206 (290)
T PRK12400 169 GCKEALFV-R-NGTVTEGSHSNFFLIKN--GTLYTHPANHLI 206 (290)
T ss_pred CCCEEEEE-c-CCEEEEcCceEEEEEEC--CEEEeCCCCCCc
Confidence 34566666 6 78999999999999843 336665555544
No 95
>cd04478 RPA2_DBD_D RPA2_DBD_D: A subfamily of OB folds corresponding to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle dependent manner in response to DNA dam
Probab=27.86 E-value=1.2e+02 Score=18.22 Aligned_cols=25 Identities=32% Similarity=0.413 Sum_probs=18.7
Q ss_pred eEEEEEEEEEecCCCcEEEEEcCCCC
Q psy1800 17 RVGTVVNRERHPGSFDIVHVKDGNGH 42 (81)
Q Consensus 17 rvG~I~~ie~~~g~~~iV~ikd~~g~ 42 (81)
-+|.|.+++.. +++-..+|.|..|.
T Consensus 4 ~vG~V~~~~~~-~~~~~~tL~D~TG~ 28 (95)
T cd04478 4 LVGVVRNVEEQ-STNITYTIDDGTGT 28 (95)
T ss_pred EEEEEEeeeEc-ccEEEEEEECCCCc
Confidence 47889998865 45567888887774
No 96
>PTZ00031 ribosomal protein L2; Provisional
Probab=27.32 E-value=2e+02 Score=22.70 Aligned_cols=48 Identities=23% Similarity=0.269 Sum_probs=0.0
Q ss_pred EEEEEEEecC-CCcEEEEEcCCCCEEEEeeccEEEEecCCcceEecCCCceeeeeeee
Q psy1800 20 TVVNRERHPG-SFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKPKRNFVSPRQTC 76 (81)
Q Consensus 20 ~I~~ie~~~g-~~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp~~kgi~~~~~~ 76 (81)
.|.+||..|| .-.++ -+.|. |++++.. .++.-.|.||.++=..++..|
T Consensus 171 ~IhNIE~~pG~Ggkl~---RSAGt-~A~Ii~k-----~~~~~~VkLPSGe~r~i~~~C 219 (317)
T PTZ00031 171 IVHNVEMRPGAGGQII---RAGGT-YATVVSK-----DEQFATLKLKSTEIRKFPLDC 219 (317)
T ss_pred EEEEEEecCCCCceEE---EecCC-eEEEEEc-----cCCEEEEECCCCCEEEECccC
No 97
>KOG3401|consensus
Probab=27.31 E-value=51 Score=23.34 Aligned_cols=25 Identities=20% Similarity=0.316 Sum_probs=21.4
Q ss_pred CCcEEEEECCCCcc-eEEEEEEEEEe
Q psy1800 3 PGNLCMITGGRNLG-RVGTVVNRERH 27 (81)
Q Consensus 3 ~G~~~mVtgG~n~G-rvG~I~~ie~~ 27 (81)
.++.+-|.+|+..| .+|++.++-+.
T Consensus 51 ~ddev~v~rg~~kG~q~G~v~~vyrK 76 (145)
T KOG3401|consen 51 KDDEVQVVRGHFKGFQIGKVSQVYRK 76 (145)
T ss_pred eccEEEEEeccccccccceehhhhhh
Confidence 46788999999999 99999988654
No 98
>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=27.13 E-value=1.8e+02 Score=18.69 Aligned_cols=29 Identities=3% Similarity=-0.055 Sum_probs=21.8
Q ss_pred CCCCcEEEEECCC--CcceEEEEEEEEEecC
Q psy1800 1 MFPGNLCMITGGR--NLGRVGTVVNRERHPG 29 (81)
Q Consensus 1 fe~G~~~mVtgG~--n~GrvG~I~~ie~~~g 29 (81)
+.+|+.|+|.... .--.+|+|.++-..+.
T Consensus 4 ~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~ 34 (121)
T cd04717 4 YRVGDCVYVANPEDPSKPIIFRIERLWKDED 34 (121)
T ss_pred EECCCEEEEeCCCCCCCCEEEEEeEEEECCC
Confidence 4689999998654 4566999999877653
No 99
>CHL00037 petA cytochrome f
Probab=26.74 E-value=1.5e+02 Score=23.49 Aligned_cols=28 Identities=21% Similarity=0.353 Sum_probs=18.8
Q ss_pred eEEEEEEEEEecC-CCcEEEEEcCCCCEE
Q psy1800 17 RVGTVVNRERHPG-SFDIVHVKDGNGHVF 44 (81)
Q Consensus 17 rvG~I~~ie~~~g-~~~iV~ikd~~g~~F 44 (81)
.-|+|.+|.+... .+.+...+.++|+..
T Consensus 210 ~~G~I~~I~~~ekGg~~vti~~t~~G~~v 238 (320)
T CHL00037 210 AAGIVSKILRKEKGGYEITIVDTSDGRQV 238 (320)
T ss_pred cCcEEEEEEEcCCCcEEEEEEecCCCCEE
Confidence 3688999988765 444444477888643
No 100
>KOG3384|consensus
Probab=26.69 E-value=1e+02 Score=21.96 Aligned_cols=24 Identities=17% Similarity=0.167 Sum_probs=18.8
Q ss_pred EEEecCCCcEEEEEcCCCCEEEEe
Q psy1800 24 RERHPGSFDIVHVKDGNGHVFATR 47 (81)
Q Consensus 24 ie~~~g~~~iV~ikd~~g~~F~T~ 47 (81)
|+-..|+++.+.+.|++|+.-+++
T Consensus 110 vkyVrg~~P~l~llDadgk~kE~l 133 (154)
T KOG3384|consen 110 VKYVRGSDPVLKLLDADGKHKESL 133 (154)
T ss_pred EEEecCCCCeeEeecCCCCcccee
Confidence 444478999999999999876654
No 101
>TIGR00399 metG_C_term methionyl-tRNA synthetase C-terminal region/beta chain. The methionyl-tRNA synthetase (metG) is a class I amino acyl-tRNA ligase. This model describes a region of the methionyl-tRNA synthetase that is present at the C-terminus of MetG in some species (E. coli, B. subtilis, Thermotoga maritima, Methanobacterium thermoautotrophicum), and as a separate beta chain in Aquifex aeolicus. It is absent in a number of other species (e.g. Mycoplasma genitalium, Mycobacterium tuberculosis), while Pyrococcus horikoshii has both a full length MetG and a second protein homologous to the beta chain only. Proteins hit by this model should called methionyl-tRNA synthetase beta chain if and only if the model metG hits a separate protein not also hit by this model.
Probab=26.54 E-value=1.5e+02 Score=20.01 Aligned_cols=33 Identities=24% Similarity=0.227 Sum_probs=20.8
Q ss_pred ceEEEEEEEEEecCCCcEEEEEcCCCCEEEEee
Q psy1800 16 GRVGTVVNRERHPGSFDIVHVKDGNGHVFATRL 48 (81)
Q Consensus 16 GrvG~I~~ie~~~g~~~iV~ikd~~g~~F~T~~ 48 (81)
-++|.|.+.+.||.+..+..++=..|....++.
T Consensus 42 i~Vg~I~eve~hp~adkL~v~~Vd~G~~~~qIv 74 (137)
T TIGR00399 42 LRVGKILKAERVEKSDKLLKLKLDLGDEKRQIV 74 (137)
T ss_pred eEEEEEEEEeecCCCCcceEEEEEeCCceEEEE
Confidence 368999999999986666544333333334443
No 102
>cd03524 RPA2_OBF_family RPA2_OBF_family: A family of oligonucleotide binding (OB) folds with similarity to the OB fold of the single strand (ss) DNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA contains six OB folds, which are involved in ssDNA binding and in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. This family also includes OB folds similar to those found in Escherichia coli SSB, the wedge domain of E. coli RecG (a branched-DNA-specific helicase), E. coli ssDNA specific exodeoxyribonuclease VII large subunit, Pyroco
Probab=26.15 E-value=1.1e+02 Score=16.11 Aligned_cols=27 Identities=37% Similarity=0.511 Sum_probs=18.9
Q ss_pred EEEEEEEEEec--CCCcEEEEEcCCCCEE
Q psy1800 18 VGTVVNRERHP--GSFDIVHVKDGNGHVF 44 (81)
Q Consensus 18 vG~I~~ie~~~--g~~~iV~ikd~~g~~F 44 (81)
.|.|.++.... .....+.|.|..|..+
T Consensus 3 ~g~v~~~~~~~~~~~~~~~~l~D~~~~~i 31 (75)
T cd03524 3 VGIVVAVEEIRTEGKVLIFTLTDGTGGTI 31 (75)
T ss_pred EEEEEeecccccCCeEEEEEEEcCCCCEE
Confidence 57788887665 4678888998773333
No 103
>PF08402 TOBE_2: TOBE domain; InterPro: IPR013611 The TOBE domain [] (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner. Probably involved in the recognition of small ligands such as molybdenum (e.g. P46930 from SWISSPROT) and sulphate (P16676 from SWISSPROT). Found in ABC transporters immediately after the ATPase domain. A strong RPE motif is found at the presumed N terminus of the domain. ; GO: 0005215 transporter activity, 0005524 ATP binding, 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0006810 transport, 0043190 ATP-binding cassette (ABC) transporter complex; PDB: 1Q12_A 1Q1B_C 2AWN_D 3RLF_B 3PUX_B 2R6G_B 3PUV_B 1Q1E_A 3PV0_B 2AWO_A ....
Probab=26.11 E-value=1.2e+02 Score=16.62 Aligned_cols=55 Identities=27% Similarity=0.219 Sum_probs=32.9
Q ss_pred CCCCcceEEEEEEEEEecCCCcEEEEEcCCCCEEEEeeccEE---EEecCCcceEecCCC
Q psy1800 11 GGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVF---IIGKGTKAFCSKPKR 67 (81)
Q Consensus 11 gG~n~GrvG~I~~ie~~~g~~~iV~ikd~~g~~F~T~~~nVf---vIGk~~kp~IsLp~~ 67 (81)
.+.| +.-|+|.+++ ..|+...++++-.++........+-- ..-.|++-+++++.+
T Consensus 13 ~~~~-~~~g~V~~~~-~~G~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~G~~v~l~~~~~ 70 (75)
T PF08402_consen 13 EGEN-RLPGTVVSVE-FLGSETRYTVRLEGGEELVVRVPNSQRDSPLEPGDEVRLSWDPD 70 (75)
T ss_dssp STTT-EEEEEEEEEE-EESSEEEEEEEETTSSEEEEEEESSG-TTT--TTSEEEEEEEGG
T ss_pred CCCC-eEEEEEEEEE-ECCCEEEEEEEECCCCEEEEEecCccccCCCCCCCEEEEEECcc
Confidence 4456 8889999987 45888888888777766444333321 111234445555544
No 104
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=26.06 E-value=2.1e+02 Score=19.10 Aligned_cols=41 Identities=27% Similarity=0.328 Sum_probs=29.7
Q ss_pred CCCCcEEEEECCCCcceEEEEEEEEEecCCCcEEEEEcCCCCEEEEeeccE
Q psy1800 1 MFPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNV 51 (81)
Q Consensus 1 fe~G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV~ikd~~g~~F~T~~~nV 51 (81)
+++|+-++-+|| -+|+|.+|. .+.|.++-+.| ..-|+..+-
T Consensus 39 Lk~GD~VvT~gG----i~G~V~~I~-----d~~v~leia~g-v~i~~~r~A 79 (109)
T PRK05886 39 LQPGDRVHTTSG----LQATIVGIT-----DDTVDLEIAPG-VVTTWMKLA 79 (109)
T ss_pred cCCCCEEEECCC----eEEEEEEEe-----CCEEEEEECCC-eEEEEEhhh
Confidence 467888888775 689999986 36888886665 556666553
No 105
>cd02798 tRNA_bind_CsaA tRNA-binding-domain-containing CsaA-like proteins. CsaA is a molecular chaperone with export related activities. CsaA has a putative tRNA binding activity. The functional unit of CsaA is a homodimer and this domain acts as a dimerization domain.
Probab=25.10 E-value=1.2e+02 Score=19.40 Aligned_cols=20 Identities=35% Similarity=0.504 Sum_probs=15.5
Q ss_pred eEEEEEEEEEecCC-CcEEEE
Q psy1800 17 RVGTVVNRERHPGS-FDIVHV 36 (81)
Q Consensus 17 rvG~I~~ie~~~g~-~~iV~i 36 (81)
++|.|.+.+.|+.+ ..+..+
T Consensus 12 ~vG~V~~~~~~p~a~~kL~~~ 32 (107)
T cd02798 12 RVGTIVEVEDFPEARKPAYKL 32 (107)
T ss_pred EEEEEEEEEECCCcccceEEE
Confidence 68999999999887 555444
No 106
>cd04490 PolII_SU_OBF PolII_SU_OBF: A subfamily of OB folds corresponding to the OB fold found in Pyrococcus abyssi DNA polymerase II (PolII) small subunit. PolII is a family D DNA polymerase, having a 3-prime to 5-prime exonuclease activity. P. abyssi PolII is heterodimeric. The large subunit appears to be the polymerase, and the small subunit may be the exonuclease. The small subunit contains a calcineurin-like phosphatase superfamily domain C-terminal to this OB-fold domain.
Probab=24.93 E-value=1.7e+02 Score=17.76 Aligned_cols=25 Identities=28% Similarity=0.510 Sum_probs=18.1
Q ss_pred EEEEEEEEEec-CCCcEEEEEcCCCCE
Q psy1800 18 VGTVVNRERHP-GSFDIVHVKDGNGHV 43 (81)
Q Consensus 18 vG~I~~ie~~~-g~~~iV~ikd~~g~~ 43 (81)
.|.|.++..+. |++ ++.++|..|..
T Consensus 5 ~GiI~~v~~TK~g~~-~~~leD~~G~~ 30 (79)
T cd04490 5 IGMVNDVRSTKNGHR-IVELEDTTGRI 30 (79)
T ss_pred EEEEeEEEEcCCCCE-EEEEECCCCEE
Confidence 57777777333 355 99999999864
No 107
>PLN02772 guanylate kinase
Probab=24.56 E-value=1.9e+02 Score=23.44 Aligned_cols=58 Identities=17% Similarity=0.248 Sum_probs=32.3
Q ss_pred CCCcEEEEECCCCcce-EEEEEEE-EEecCCCcEEEEE-----cCCCCEEEEe-eccEEEEecCCc
Q psy1800 2 FPGNLCMITGGRNLGR-VGTVVNR-ERHPGSFDIVHVK-----DGNGHVFATR-LNNVFIIGKGTK 59 (81)
Q Consensus 2 e~G~~~mVtgG~n~Gr-vG~I~~i-e~~~g~~~iV~ik-----d~~g~~F~T~-~~nVfvIGk~~k 59 (81)
..|+..||+||+|-+. .--...| +.....-.+-.+. -.+|+++..+ .+.+.||+++..
T Consensus 32 ~igdk~yv~GG~~d~~~~~~~v~i~D~~t~~W~~P~V~G~~P~~r~GhSa~v~~~~rilv~~~~~~ 97 (398)
T PLN02772 32 TIGDKTYVIGGNHEGNTLSIGVQILDKITNNWVSPIVLGTGPKPCKGYSAVVLNKDRILVIKKGSA 97 (398)
T ss_pred EECCEEEEEcccCCCccccceEEEEECCCCcEecccccCCCCCCCCcceEEEECCceEEEEeCCCC
Confidence 3588999999999863 2222222 2111110111111 1457777777 588999987543
No 108
>cd01559 ADCL_like ADCL_like: 4-Amino-4-deoxychorismate lyase: is a member of the fold-type IV of PLP dependent enzymes that converts 4-amino-4-deoxychorismate (ADC) to p-aminobenzoate and pyruvate. Based on the information available from the crystal structure, most members of this subgroup are likely to function as dimers. The enzyme from E.Coli, the structure of which is available, is a homodimer that is folded into a small and a larger domain. The coenzyme pyridoxal 5; -phosphate resides at the interface of the two domains that is linked by a flexible loop. Members of this subgroup are found in Eukaryotes and bacteria.
Probab=24.53 E-value=1.3e+02 Score=21.34 Aligned_cols=38 Identities=16% Similarity=0.172 Sum_probs=27.4
Q ss_pred CcEEEEEcCCCCEEEEeeccEEEEecCCcceEecCCCcee
Q psy1800 31 FDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKPKRNFV 70 (81)
Q Consensus 31 ~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp~~kgi 70 (81)
++-+.+-|.+|+.-++-.+|+|++=. + -|++-|...|+
T Consensus 143 ~de~l~l~~~g~v~E~~~~Nif~~~~-~-~~~TP~~~~g~ 180 (249)
T cd01559 143 ADEALFLDTDGRVIEGTASNLFFVKD-G-ELVTPSLDRGG 180 (249)
T ss_pred CCEEEEEcCCCCEEEecceEEEEEEC-C-EEECCCcccCc
Confidence 44555668899999999999999853 3 36665555554
No 109
>PRK06680 D-amino acid aminotransferase; Reviewed
Probab=24.18 E-value=1.6e+02 Score=21.59 Aligned_cols=38 Identities=24% Similarity=0.431 Sum_probs=26.7
Q ss_pred CcEEEEEcCCCCEEEEeeccEEEEecCCcceEecCCCcee
Q psy1800 31 FDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKPKRNFV 70 (81)
Q Consensus 31 ~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp~~kgi 70 (81)
++-+.+-| +|+.=++-.+|+|++-+ +.-|++-|...|+
T Consensus 168 ~dd~l~ld-~g~v~E~~~sN~f~~~~-~~~l~TP~~~~~i 205 (286)
T PRK06680 168 AQEAWMVD-DGFVTEGASSNAWIVTK-DGKLVTRPADNFI 205 (286)
T ss_pred CCEEEEec-CCEEEEcCcEEEEEEEE-CCEEEeCCCCCCC
Confidence 44455668 89888999999999933 2347776666554
No 110
>PTZ00486 apyrase Superfamily; Provisional
Probab=23.67 E-value=2.7e+02 Score=22.37 Aligned_cols=45 Identities=27% Similarity=0.425 Sum_probs=33.5
Q ss_pred eEEEEEEEEEecC-CCcEEEEEcCCCC-------EEEEeeccEEEEecCCcce
Q psy1800 17 RVGTVVNRERHPG-SFDIVHVKDGNGH-------VFATRLNNVFIIGKGTKAF 61 (81)
Q Consensus 17 rvG~I~~ie~~~g-~~~iV~ikd~~g~-------~F~T~~~nVfvIGk~~kp~ 61 (81)
|.|.|-+|..... ..+-|.|-|.+|+ +.+|..+..+-+|.--+.|
T Consensus 133 rTGiVy~i~~~~~~~~PwvIL~dGdG~~~kGfK~EWaTVKd~~LyVGs~Gkew 185 (352)
T PTZ00486 133 RTGIVYEIDIDKKKAYPRHILSDGNGNSDKGMKIEWATVYDDKLYVGSIGKEF 185 (352)
T ss_pred CceEEEEEEcCCCcEeeEEEEecCCCCCCCCcceeeEEEECCEEEEeccccee
Confidence 5688988864333 6778899999884 4789999999998544433
No 111
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=23.46 E-value=83 Score=26.71 Aligned_cols=32 Identities=28% Similarity=0.413 Sum_probs=25.3
Q ss_pred CCCCcEEEEECCCCcceEEEEEEEEEecCCCcEEEEE
Q psy1800 1 MFPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVK 37 (81)
Q Consensus 1 fe~G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV~ik 37 (81)
|++|+-.=|..|...|++|++.+.. .+|.+|+
T Consensus 91 fqpgD~~Evl~Geqrg~~gVV~~~~-----~~I~tm~ 122 (607)
T COG5164 91 FQPGDALEVLRGEQRGRVGVVPRQK-----EMIETMT 122 (607)
T ss_pred cCCCCeeeeecceecccceeecccc-----cceeeee
Confidence 7899999999999999999986432 2455555
No 112
>PRK00122 rimM 16S rRNA-processing protein RimM; Provisional
Probab=23.45 E-value=2.5e+02 Score=19.23 Aligned_cols=32 Identities=16% Similarity=0.113 Sum_probs=22.7
Q ss_pred cceEEEEEEEEEecCCCcEEEEEcCCCCEEEEe
Q psy1800 15 LGRVGTVVNRERHPGSFDIVHVKDGNGHVFATR 47 (81)
Q Consensus 15 ~GrvG~I~~ie~~~g~~~iV~ikd~~g~~F~T~ 47 (81)
-+.+|+|.++... ++.++..+++.+++++.-.
T Consensus 115 g~~lG~V~~v~~~-~a~dll~I~~~~~~e~liP 146 (172)
T PRK00122 115 GEELGKVTDILET-GANDVLVVLKDKKEERLIP 146 (172)
T ss_pred CcEEEEEEEEccC-CCceEEEEECCCCCEEEEe
Confidence 3679999999754 5668888876666655433
No 113
>PF12681 Glyoxalase_2: Glyoxalase-like domain; PDB: 3G12_B 1JIF_B 1JIE_B 1QTO_A 3OXH_A 2PJS_A 2RBB_A 3SK1_B 3SK2_B 3RRI_A ....
Probab=23.43 E-value=1.6e+02 Score=17.03 Aligned_cols=24 Identities=13% Similarity=0.111 Sum_probs=14.2
Q ss_pred EEEEEecCCCcEEEEEcCCCCEEE
Q psy1800 22 VNRERHPGSFDIVHVKDGNGHVFA 45 (81)
Q Consensus 22 ~~ie~~~g~~~iV~ikd~~g~~F~ 45 (81)
...+..+.......++|.+|+.++
T Consensus 83 ~~~~~~~~g~~~~~~~DPdG~~ie 106 (108)
T PF12681_consen 83 TEPRDDPWGQRSFYFIDPDGNRIE 106 (108)
T ss_dssp EEEEEETTSEEEEEEE-TTS-EEE
T ss_pred eCCEEcCCCeEEEEEECCCCCEEE
Confidence 344444444468889999999875
No 114
>COG4014 Uncharacterized protein conserved in archaea [Function unknown]
Probab=23.42 E-value=2.3e+02 Score=18.77 Aligned_cols=41 Identities=22% Similarity=0.233 Sum_probs=26.0
Q ss_pred CCcceEEEEEEEEEecCCCcEEEEEcCCCCEEEEeeccEEEEec
Q psy1800 13 RNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGK 56 (81)
Q Consensus 13 ~n~GrvG~I~~ie~~~g~~~iV~ikd~~g~~F~T~~~nVfvIGk 56 (81)
-|+|.+|+|..|.+..-..-=|.+.+.+ .--+..|+=++-|
T Consensus 18 vnTgTvgrV~dIkkdEdG~~WV~Ldstd---LwYre~~le~vdK 58 (97)
T COG4014 18 VNTGTVGRVVDIKKDEDGDIWVVLDSTD---LWYREHYLEVVDK 58 (97)
T ss_pred eecCceeeEEEEEeecCCceEEEEecCC---ceecccceeeecc
Confidence 3788889998887654433345554333 4566777777654
No 115
>TIGR01123 ilvE_II branched-chain amino acid aminotransferase, group II. Among the class IV aminotransferases are two phylogenetically separable groups of branched-chain amino acid aminotransferase (IlvE). The last common ancestor of the two lineages appears also to have given rise to a family of D-amino acid aminotransferases (DAAT). This model represents the IlvE family less similar to the DAAT family.
Probab=22.94 E-value=2.1e+02 Score=21.32 Aligned_cols=38 Identities=21% Similarity=0.207 Sum_probs=25.5
Q ss_pred cEEEEEcCCCC--EEEEeeccEEEEecCCcceEecCCCcee
Q psy1800 32 DIVHVKDGNGH--VFATRLNNVFIIGKGTKAFCSKPKRNFV 70 (81)
Q Consensus 32 ~iV~ikd~~g~--~F~T~~~nVfvIGk~~kp~IsLp~~kgi 70 (81)
+-+.+-|.+|+ .=++-.+|+|++=+ +.-+++-|...|+
T Consensus 176 deal~ld~~g~g~v~E~~~sNlf~v~~-~g~l~Tp~l~~~~ 215 (313)
T TIGR01123 176 DQVVYLDPVEHTYIEEVGAMNFFFITG-DGELVTPPLSGSI 215 (313)
T ss_pred CEEEEEeCCCCeEEEEcCcEeEEEEEc-CCEEEeCCCCCCC
Confidence 33444488877 88999999999953 2246676665443
No 116
>PRK07650 4-amino-4-deoxychorismate lyase; Provisional
Probab=22.23 E-value=1.9e+02 Score=21.11 Aligned_cols=36 Identities=11% Similarity=0.036 Sum_probs=25.9
Q ss_pred EEEEEcCCCCEEEEeeccEEEEecCCcceEecCCCcee
Q psy1800 33 IVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKPKRNFV 70 (81)
Q Consensus 33 iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp~~kgi 70 (81)
-+.+-|.+|+.=++-.+|+|++= +.-|++=|.+.|+
T Consensus 165 e~llln~~G~v~E~s~sNif~v~--~g~l~TP~l~~g~ 200 (283)
T PRK07650 165 EGIFLTEEGYVAEGIVSNLFWVK--GDIVYTPSLETGI 200 (283)
T ss_pred eEEEECCCCeEEEcCceEEEEEE--CCEEEcCCCcCCC
Confidence 34466899999999999999994 3346665555444
No 117
>cd04483 hOBFC1_like hOBFC1_like: A subfamily of OB folds similar to that found in human OB fold containing protein 1 (hOBFC1). Members of this group belong to the Replication protein A subunit 2 (RPA2) family of OB folds. RPA is a nuclear ssDNA binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The OB fold domain of RPA2 has dual roles in ssDNA binding and trimerization.
Probab=22.20 E-value=1.8e+02 Score=18.25 Aligned_cols=24 Identities=42% Similarity=0.654 Sum_probs=19.6
Q ss_pred EEEEEEEEEecCCCcEEEEEcCCCC
Q psy1800 18 VGTVVNRERHPGSFDIVHVKDGNGH 42 (81)
Q Consensus 18 vG~I~~ie~~~g~~~iV~ikd~~g~ 42 (81)
+|.|.+++..+ .+-...|.|..|.
T Consensus 3 vG~V~sv~~~~-~~~~~tLdDgTG~ 26 (92)
T cd04483 3 LGTVVSRRERE-TFYSFGVDDGTGV 26 (92)
T ss_pred EEEEEEEEecC-CeEEEEEecCCce
Confidence 78999997655 6788899999985
No 118
>PRK00528 rpmE 50S ribosomal protein L31; Reviewed
Probab=22.04 E-value=1.7e+02 Score=17.85 Aligned_cols=23 Identities=26% Similarity=0.297 Sum_probs=15.1
Q ss_pred EecCCCcEEEEEcCCCCEEEEeec
Q psy1800 26 RHPGSFDIVHVKDGNGHVFATRLN 49 (81)
Q Consensus 26 ~~~g~~~iV~ikd~~g~~F~T~~~ 49 (81)
.||-...++. .=.+|++|.|.+-
T Consensus 5 IHP~y~~v~~-~~~~g~~f~~~ST 27 (71)
T PRK00528 5 IHPDYHPIKV-VMTDGTEYETRST 27 (71)
T ss_pred CCCCCEEEEE-EEeCCCEEEEEEc
Confidence 3776544433 3468999999863
No 119
>cd07247 SgaA_N_like N-terminal domain of Streptomyces griseus SgaA (suppression of growth disturbance caused by A-factor at a high concentration under high osmolality during early growth phase), and similar domains. SgaA suppresses the growth disturbances caused by high osmolarity and a high concentration of A-factor, a microbial hormone, during the early growth phase in Streptomyces griseus. A-factor (2-isocapryloyl-3R-hydroxymethyl-gamma-butyrolactone) controls morphological differentiation and secondary metabolism in Streptomyces griseus. It is a chemical signaling molecule that at a very low concentration acts as a switch for yellow pigment production, aerial mycelium formation, streptomycin production, and streptomycin resistance. The structure and amino acid sequence of SgaA are closely related to a group of antibiotics resistance proteins, including bleomycin resistance protein, mitomycin resistance protein, and fosfomycin resistance proteins. SgaA might also function as a strep
Probab=21.80 E-value=1.2e+02 Score=17.93 Aligned_cols=15 Identities=27% Similarity=0.399 Sum_probs=11.2
Q ss_pred cEEEEEcCCCCEEEE
Q psy1800 32 DIVHVKDGNGHVFAT 46 (81)
Q Consensus 32 ~iV~ikd~~g~~F~T 46 (81)
....++|.+|+.|+-
T Consensus 98 ~~~~~~DPdG~~~~l 112 (114)
T cd07247 98 RFAVFADPEGAVFGL 112 (114)
T ss_pred EEEEEECCCCCEEEe
Confidence 467788888887763
No 120
>cd04489 ExoVII_LU_OBF ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit. E. coli ExoVII is composed of two non-identical subunits. E. coli ExoVII is a single-strand-specific exonuclease which degrades ssDNA from both 3-prime and 5-prime ends. ExoVII plays a role in methyl-directed mismatch repair in vivo. ExoVII may also guard the genome from mutagenesis by removing excess ssDNA, since the build up of ssDNA would lead to SOS induction and PolIV-dependent mutagenesis.
Probab=21.79 E-value=1.1e+02 Score=17.54 Aligned_cols=25 Identities=20% Similarity=0.278 Sum_probs=17.3
Q ss_pred EEEEEEEEEecCCCcEEEEEcCCCC
Q psy1800 18 VGTVVNRERHPGSFDIVHVKDGNGH 42 (81)
Q Consensus 18 vG~I~~ie~~~g~~~iV~ikd~~g~ 42 (81)
.|.|.+++.+.+..-.++++|..|.
T Consensus 5 ~g~v~~i~~tk~g~~~~~L~D~~~~ 29 (78)
T cd04489 5 EGEISNLKRPSSGHLYFTLKDEDAS 29 (78)
T ss_pred EEEEecCEECCCcEEEEEEEeCCeE
Confidence 4777777764334678888887764
No 121
>PRK08320 branched-chain amino acid aminotransferase; Reviewed
Probab=21.56 E-value=1.8e+02 Score=21.22 Aligned_cols=38 Identities=18% Similarity=0.232 Sum_probs=27.5
Q ss_pred CcEEEEEcCCCCEEEEeeccEEEEecCCcceEecCCCcee
Q psy1800 31 FDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKPKRNFV 70 (81)
Q Consensus 31 ~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp~~kgi 70 (81)
++-+.+-|.+|+.=++-.+|+|++=. .-|++-|...|+
T Consensus 170 ~de~L~ld~~g~v~E~s~sNlf~~~~--~~l~TP~~~~~~ 207 (288)
T PRK08320 170 VDEAIMLNDEGYVAEGTGDNIFIVKN--GKLITPPTYAGA 207 (288)
T ss_pred CCEEEEECCCCeEEEcCcEEEEEEEC--CEEECCCCcCCC
Confidence 45566778899999999999998842 346665555554
No 122
>PF08940 DUF1918: Domain of unknown function (DUF1918); InterPro: IPR015035 This domain is found in various hypothetical bacterial proteins, and has no known function. ; PDB: 2A7Y_A.
Probab=20.59 E-value=1.8e+02 Score=17.61 Aligned_cols=31 Identities=29% Similarity=0.503 Sum_probs=18.3
Q ss_pred EEECCCCcc---eEEEEEEEEEecC-CCcEEEEEc
Q psy1800 8 MITGGRNLG---RVGTVVNRERHPG-SFDIVHVKD 38 (81)
Q Consensus 8 mVtgG~n~G---rvG~I~~ie~~~g-~~~iV~ikd 38 (81)
+++.|+++| |.|.|.++.-..| -+=+|...|
T Consensus 9 lvv~g~~vg~~~r~GeIveV~g~dG~PPY~VRw~D 43 (58)
T PF08940_consen 9 LVVHGRTVGQPDRHGEIVEVRGPDGSPPYLVRWDD 43 (58)
T ss_dssp EEES-TTTS--EEEEEEEE-S-SSS-S-EEEEETT
T ss_pred EEEcCCcCCCCCcEeEEEEEECCCCCCCEEEEecC
Confidence 566777776 6788888776667 455666643
No 123
>cd04715 BAH_Orc1p_like BAH, or Bromo Adjacent Homology domain, as present in the Schizosaccharomyces pombe homolog of Saccharomyces cerevisiae Orc1p and similar proteins. Orc1 is part of the Yeast Sir1-origin recognition complex, the Orc1p BAH doman functions in epigenetic silencing. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=20.50 E-value=3.1e+02 Score=19.13 Aligned_cols=28 Identities=7% Similarity=0.057 Sum_probs=23.7
Q ss_pred CCCCcEEEEECCCCcceEEEEEEEEEec
Q psy1800 1 MFPGNLCMITGGRNLGRVGTVVNRERHP 28 (81)
Q Consensus 1 fe~G~~~mVtgG~n~GrvG~I~~ie~~~ 28 (81)
+.+|+-|+|-.+.+--.||+|.+|-...
T Consensus 30 y~lGD~Vlv~s~~~~~yIgkI~~iwe~~ 57 (159)
T cd04715 30 YRLYDDVYVHNGDSEPYIGKIIKIYETA 57 (159)
T ss_pred EeCCCEEEEeCCCCCCEEEEEEEEEEcC
Confidence 4679999999888878899999997664
No 124
>PF05610 DUF779: Protein of unknown function (DUF779); InterPro: IPR008497 This family consists of several bacterial proteins of unknown function.
Probab=20.43 E-value=1.6e+02 Score=19.38 Aligned_cols=24 Identities=25% Similarity=0.295 Sum_probs=15.4
Q ss_pred EEecCCCcEEEEEcCCCCEEEEee
Q psy1800 25 ERHPGSFDIVHVKDGNGHVFATRL 48 (81)
Q Consensus 25 e~~~g~~~iV~ikd~~g~~F~T~~ 48 (81)
+..||.-..-.++...|..|.|++
T Consensus 70 DVv~GrG~~FSLE~~~G~rF~~rs 93 (95)
T PF05610_consen 70 DVVPGRGGGFSLEAPEGKRFLTRS 93 (95)
T ss_pred EEEecCCCeeeccCCCCcEEEEee
Confidence 444554456667777777777765
No 125
>PTZ00180 60S ribosomal protein L8; Provisional
Probab=20.18 E-value=2.2e+02 Score=21.85 Aligned_cols=37 Identities=16% Similarity=0.139 Sum_probs=25.2
Q ss_pred ceEEEEEEEEEecC-CCcEEEEEcCCCCEEEEeeccEE
Q psy1800 16 GRVGTVVNRERHPG-SFDIVHVKDGNGHVFATRLNNVF 52 (81)
Q Consensus 16 GrvG~I~~ie~~~g-~~~iV~ikd~~g~~F~T~~~nVf 52 (81)
+..|+|..||-.|+ +-.+..|+-.++..|.-...|+.
T Consensus 40 ~~~g~V~~IeyDPnRsA~IAlv~~~d~~~~~g~~~YIl 77 (260)
T PTZ00180 40 YIRGVVKDIEHDPGRGAPLARVEFRDPYKYKRVKELMV 77 (260)
T ss_pred CcCEEEEEEEECCCCCceEEEEEecCCccccCceEEEE
Confidence 34599999999898 77888787677654422333443
No 126
>PF07737 ATLF: Anthrax toxin lethal factor, N- and C-terminal domain; InterPro: IPR014781 Anthrax toxin is a plasmid-encoded toxin complex produced by the Gram-positive, spore-forming bacteria, Bacillus anthracis. The toxin consists of three non-toxic proteins: the protective antigen (PA), the lethal factor (LF) and the edema factor (EF) []. These component proteins self-assemble at the surface of host cell receptors, yielding a series of toxic complexes that can produce shock-like symptoms and death. Anthrax toxin is one of a large group of Bacillus and Clostridium exotoxins referred to as binary toxins, forming independent enzymatic (A moiety) and binding (B moiety) components. The LF and EF proteins are the enzymes (A moiety) that act on cytosolic substrates, while PA is a multi-functional protein (B moiety) that binds to cell surface receptors, mediates the assembly and internalisation of the complexes, and delivers them to the host cell endosome []. Once PA is attached to the host receptor [], it must then be cleaved by a host cell surface (furin family) protease before it is able to bind EF and LF. The cleavage of the N terminus of PA enables the C-terminal fragment to self-associate into a ring-shaped heptameric complex (prepore) that can bind LF or EF competitively. The PA-LF/EF complex is then internalised by endocytosis, and delivered to the endosome, where PA forms a pore in the endosomal membrane in order to translocate LF and EF to the cytosol. LF is a Zn-dependent metalloprotease that cleaves and inactivates mitogen-activated protein (MAP) kinases, kills macrophages, and causes death of the host by inhibiting cell proliferation [, ]. EF is a calcium-and calmodulin-dependent adenylyl cyclase that can cause edema (fluid-filled swelling) when associated with PA. EF is not toxic by itself, and is required for the survival of germinated Bacillus spores within macrophages at the early stages of infection. EF dramatically elevates the level of host intracellular cAMP, a ubiquitous messenger that integrates many processes of the cell; increases in cAMP can interfere with host intracellular signalling []. This entry represents the N- and C-terminal domains found in both lethal factor and edema factor proteins of anthrax toxin.; GO: 0003824 catalytic activity, 0046872 metal ion binding, 0009405 pathogenesis, 0005576 extracellular region; PDB: 1PWV_B 1PWW_A 1PWQ_B 1PWP_B 1J7N_A 1JKY_A 2L0R_A 1PWU_A 4DV8_A 1YQY_A ....
Probab=20.02 E-value=80 Score=23.90 Aligned_cols=27 Identities=22% Similarity=0.341 Sum_probs=22.7
Q ss_pred EEEcCCCCEEEEeeccEEEEecCCcceE
Q psy1800 35 HVKDGNGHVFATRLNNVFIIGKGTKAFC 62 (81)
Q Consensus 35 ~ikd~~g~~F~T~~~nVfvIGk~~kp~I 62 (81)
.++|++|+.+.-..-+||-+|. ..|..
T Consensus 68 ~i~d~~G~~v~l~~~fVf~~~g-~~p~l 94 (226)
T PF07737_consen 68 NIKDSEGKEVSLDSHFVFSKGG-KEPIL 94 (226)
T ss_dssp CCCCTTSSEEEGGGCSEEEESS-SSGEE
T ss_pred eeecCCCceeeccceEEEecCC-CCceE
Confidence 3679999999999999999985 77654
Done!