Query 042650
Match_columns 81
No_of_seqs 100 out of 144
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 08:17:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042650.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042650hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4479 Transcription factor e 100.0 1E-36 2.3E-41 191.1 8.6 81 1-81 11-91 (92)
2 PF10163 EnY2: Transcription f 100.0 5E-36 1.1E-40 188.2 9.0 77 1-77 10-86 (86)
3 PF10163 EnY2: Transcription f 87.7 4.2 9.1E-05 25.0 6.4 45 9-55 1-46 (86)
4 PF05008 V-SNARE: Vesicle tran 87.4 4.2 9.2E-05 24.0 6.6 62 9-77 7-68 (79)
5 PF08766 DEK_C: DEK C terminal 83.9 5.2 0.00011 22.4 5.0 51 25-76 3-53 (54)
6 PF06348 DUF1059: Protein of u 78.1 4.1 8.8E-05 23.4 3.3 31 44-74 21-56 (57)
7 PF08328 ASL_C: Adenylosuccina 75.3 7.1 0.00015 25.9 4.2 56 5-70 50-108 (115)
8 cd07347 harmonin_N_like N-term 75.2 16 0.00034 22.6 5.5 59 9-77 7-65 (78)
9 COG1610 Uncharacterized conser 68.9 14 0.00029 25.6 4.6 63 3-69 80-143 (148)
10 PF08429 PLU-1: PLU-1-like pro 68.8 21 0.00046 26.3 6.0 56 13-76 156-211 (335)
11 TIGR02606 antidote_CC2985 puta 67.7 18 0.00038 21.4 4.4 47 2-49 18-68 (69)
12 PF07350 DUF1479: Protein of u 66.4 26 0.00057 27.8 6.3 61 20-80 25-103 (416)
13 PF08411 Exonuc_X-T_C: Exonucl 66.0 18 0.0004 26.6 5.1 55 24-78 214-268 (269)
14 PF05066 HARE-HTH: HB1, ASXL, 63.5 27 0.00058 20.2 4.7 46 27-73 3-53 (72)
15 PF04963 Sigma54_CBD: Sigma-54 63.3 11 0.00025 26.1 3.5 63 7-75 14-79 (194)
16 PF08100 Dimerisation: Dimeris 63.1 13 0.00029 20.9 3.1 38 33-76 13-50 (51)
17 cd05027 S-100B S-100B: S-100B 63.0 32 0.0007 20.9 5.4 50 7-57 29-82 (88)
18 KOG1964 Nuclear pore complex, 62.9 32 0.0007 29.5 6.5 50 18-67 318-387 (800)
19 PF08369 PCP_red: Proto-chloro 61.8 15 0.00032 20.2 3.1 26 25-50 18-43 (45)
20 cd07981 TAF12 TATA Binding Pro 61.6 17 0.00036 21.6 3.5 34 43-78 5-38 (72)
21 PF00486 Trans_reg_C: Transcri 61.4 21 0.00045 20.2 3.9 37 41-78 23-59 (77)
22 PF02037 SAP: SAP domain; Int 61.3 11 0.00024 19.4 2.4 14 63-76 22-35 (35)
23 PF14426 Imm2: Immunity protei 60.3 26 0.00056 20.8 4.0 44 20-72 10-54 (60)
24 PF08775 ParB: ParB family; I 58.9 12 0.00026 24.9 2.8 38 40-77 24-65 (127)
25 PF08542 Rep_fac_C: Replicatio 58.9 35 0.00076 20.1 8.5 62 8-75 6-68 (89)
26 PF02631 RecX: RecX family; I 58.8 28 0.0006 22.0 4.4 24 5-28 5-28 (121)
27 PF03693 RHH_2: Uncharacterise 55.9 12 0.00025 22.9 2.2 51 2-53 21-76 (80)
28 PF14069 SpoVIF: Stage VI spor 55.5 37 0.0008 21.0 4.4 50 25-74 13-62 (79)
29 smart00513 SAP Putative DNA-bi 55.4 21 0.00046 18.1 2.9 15 62-76 21-35 (35)
30 PF13625 Helicase_C_3: Helicas 55.4 27 0.00059 22.4 4.0 34 42-75 54-87 (129)
31 TIGR02366 DHAK_reg probable di 54.7 26 0.00056 22.9 3.9 18 7-24 5-22 (176)
32 PRK02363 DNA-directed RNA poly 53.8 53 0.0012 21.9 5.3 29 28-57 6-34 (129)
33 PRK09462 fur ferric uptake reg 53.8 51 0.0011 21.6 5.2 54 15-68 5-59 (148)
34 PF13026 DUF3887: Protein of u 53.8 57 0.0012 20.9 5.3 45 25-71 5-50 (101)
35 TIGR03499 FlhF flagellar biosy 52.5 74 0.0016 23.2 6.3 69 5-76 111-181 (282)
36 PF11829 DUF3349: Protein of u 52.2 35 0.00077 21.8 4.0 44 5-53 23-66 (96)
37 PF08824 Serine_rich: Serine r 51.6 12 0.00025 26.0 1.9 44 13-66 98-141 (159)
38 PF14766 RPA_interact_N: Repli 51.5 20 0.00043 19.5 2.4 17 22-38 14-30 (42)
39 PF07766 LETM1: LETM1-like pro 51.5 90 0.0019 22.9 6.6 61 12-77 192-253 (268)
40 PF13797 Post_transc_reg: Post 50.7 59 0.0013 20.2 5.4 37 22-58 4-43 (87)
41 TIGR03613 RutR pyrimidine util 50.3 33 0.00072 22.8 3.9 29 24-52 10-38 (202)
42 PRK00117 recX recombination re 50.2 60 0.0013 21.3 5.1 27 10-37 44-70 (157)
43 PF10667 DUF2486: Protein of u 50.1 39 0.00084 25.2 4.5 42 8-52 179-220 (246)
44 PF06744 DUF1215: Protein of u 49.8 63 0.0014 20.7 5.1 56 9-67 26-87 (125)
45 TIGR02395 rpoN_sigma RNA polym 49.1 67 0.0015 25.3 5.9 60 9-74 77-139 (429)
46 PRK14729 miaA tRNA delta(2)-is 49.0 85 0.0018 23.6 6.3 47 6-52 196-247 (300)
47 PRK14828 undecaprenyl pyrophos 48.9 21 0.00046 26.3 3.0 35 4-38 117-169 (256)
48 PF13319 DUF4090: Protein of u 48.9 13 0.00029 23.3 1.6 14 11-24 61-74 (84)
49 TIGR00511 ribulose_e2b2 ribose 47.5 72 0.0016 23.8 5.7 55 23-78 43-97 (301)
50 COG2137 OraA Uncharacterized p 47.5 59 0.0013 22.7 4.9 56 11-70 54-109 (174)
51 COG3343 RpoE DNA-directed RNA 47.4 97 0.0021 22.0 6.0 56 10-75 3-58 (175)
52 PRK10668 DNA-binding transcrip 46.6 42 0.00091 22.5 4.0 27 25-51 14-40 (215)
53 PRK11639 zinc uptake transcrip 46.2 92 0.002 21.1 6.1 60 8-68 7-67 (169)
54 PRK14835 undecaprenyl pyrophos 46.2 31 0.00067 25.8 3.5 49 4-52 136-202 (275)
55 PF00440 TetR_N: Bacterial reg 45.7 34 0.00074 18.1 2.8 24 29-52 3-26 (47)
56 PRK00117 recX recombination re 45.5 67 0.0014 21.1 4.8 29 11-39 28-56 (157)
57 cd08337 DED_c-FLIP_repeat1 Dea 45.2 32 0.0007 21.2 3.0 48 24-75 18-65 (80)
58 COG0735 Fur Fe2+/Zn2+ uptake r 45.1 90 0.002 20.7 5.8 57 11-68 5-62 (145)
59 PRK14135 recX recombination re 44.8 62 0.0013 23.1 4.8 55 12-70 92-147 (263)
60 PF14377 DUF4414: Domain of un 44.5 27 0.00058 22.2 2.6 28 49-76 42-69 (108)
61 TIGR03015 pepcterm_ATPase puta 43.7 1.1E+02 0.0023 21.3 5.8 66 8-73 195-267 (269)
62 PRK09975 DNA-binding transcrip 43.3 47 0.001 22.2 3.9 24 27-50 16-39 (213)
63 PF01715 IPPT: IPP transferase 43.2 89 0.0019 22.6 5.5 66 7-75 163-233 (253)
64 TIGR03384 betaine_BetI transcr 42.8 49 0.0011 21.4 3.8 29 24-52 10-38 (189)
65 PRK05932 RNA polymerase factor 42.1 93 0.002 24.7 5.8 60 9-74 102-164 (455)
66 COG1890 RPS1A Ribosomal protei 42.1 45 0.00097 24.4 3.7 37 25-65 136-172 (214)
67 PF06504 RepC: Replication pro 42.0 23 0.00051 26.8 2.3 51 12-78 207-257 (281)
68 PF06771 Desmo_N: Viral Desmop 41.5 20 0.00044 22.7 1.6 36 42-77 9-44 (86)
69 PLN02152 indole-3-acetate beta 41.4 41 0.00088 26.6 3.7 47 6-52 403-454 (455)
70 cd00280 TRFH Telomeric Repeat 41.3 68 0.0015 23.2 4.5 60 3-78 123-182 (200)
71 PF08513 LisH: LisH; InterPro 40.9 46 0.00099 16.1 4.0 26 8-33 1-26 (27)
72 PF04380 BMFP: Membrane fusoge 40.5 41 0.00089 20.3 2.9 22 57-78 16-39 (79)
73 TIGR02945 SUF_assoc FeS assemb 40.0 11 0.00024 23.1 0.3 47 20-68 49-96 (99)
74 PF02854 MIF4G: MIF4G domain; 39.9 1E+02 0.0022 19.9 5.5 72 4-78 13-85 (209)
75 COG0020 UppS Undecaprenyl pyro 39.9 36 0.00078 25.1 3.0 39 20-58 143-181 (245)
76 PRK15008 HTH-type transcriptio 39.9 60 0.0013 22.0 4.0 28 24-51 20-47 (212)
77 PF05234 UAF_Rrn10: UAF comple 39.6 44 0.00096 22.4 3.1 29 26-54 4-32 (120)
78 TIGR03181 PDH_E1_alph_x pyruva 39.3 1.5E+02 0.0032 22.4 6.3 53 12-68 276-338 (341)
79 PRK12469 RNA polymerase factor 38.9 1.1E+02 0.0023 24.7 5.8 65 9-75 124-191 (481)
80 cd00383 trans_reg_C Effector d 38.6 80 0.0017 18.3 4.1 38 41-79 41-78 (95)
81 PF00298 Ribosomal_L11: Riboso 37.1 91 0.002 18.5 4.2 33 25-59 33-65 (69)
82 COG5559 Uncharacterized conser 37.0 48 0.001 19.8 2.7 21 58-78 9-29 (65)
83 PRK11640 putative transcriptio 36.9 71 0.0015 21.6 4.0 29 24-52 3-31 (191)
84 PF06799 DUF1230: Protein of u 36.8 9.3 0.0002 26.3 -0.4 7 19-25 102-108 (144)
85 PLN02555 limonoid glucosyltran 36.7 22 0.00048 28.3 1.6 54 7-61 416-476 (480)
86 KOG2769 Putative u4/u6 small n 36.2 83 0.0018 25.9 4.7 54 1-63 183-236 (522)
87 PRK00767 transcriptional regul 36.0 71 0.0015 20.9 3.8 27 25-51 12-38 (197)
88 KOG2949 Ketopantoate hydroxyme 35.5 22 0.00047 26.9 1.3 26 19-45 111-136 (306)
89 COG3355 Predicted transcriptio 35.2 87 0.0019 21.0 4.0 30 6-37 92-121 (126)
90 PRK08535 translation initiatio 34.9 1.4E+02 0.0031 22.3 5.6 55 23-78 48-102 (310)
91 PRK14996 TetR family transcrip 34.7 65 0.0014 21.3 3.4 16 9-24 12-27 (192)
92 PRK02260 S-ribosylhomocysteina 34.0 1E+02 0.0022 21.5 4.3 27 19-46 123-154 (158)
93 PF10249 NDUFB10: NADH-ubiquin 33.4 36 0.00079 22.9 2.0 46 9-54 61-108 (128)
94 smart00862 Trans_reg_C Transcr 32.8 93 0.002 17.3 4.5 42 36-78 19-60 (78)
95 cd08051 gp6_gp15_like Head-Tai 32.7 1.2E+02 0.0027 18.8 4.3 20 57-76 42-61 (94)
96 PLN00164 glucosyltransferase; 32.6 64 0.0014 25.5 3.6 52 6-57 417-476 (480)
97 COG1309 AcrR Transcriptional r 32.5 1.1E+02 0.0024 18.5 4.0 28 25-52 15-42 (201)
98 PHA02530 pseT polynucleotide k 31.9 86 0.0019 22.3 3.9 37 43-79 111-147 (300)
99 TIGR03504 FimV_Cterm FimV C-te 31.2 94 0.002 16.8 3.3 32 2-35 10-41 (44)
100 cd03567 VHS_GGA VHS domain fam 31.2 92 0.002 20.8 3.7 31 46-76 84-115 (139)
101 TIGR02499 HrpE_YscL_not type I 31.2 69 0.0015 20.9 3.1 25 7-31 37-61 (166)
102 TIGR00524 eIF-2B_rel eIF-2B al 30.8 2.3E+02 0.005 21.2 6.2 55 23-78 45-100 (303)
103 PLN02210 UDP-glucosyl transfer 30.7 73 0.0016 25.0 3.6 48 6-53 401-454 (456)
104 PF07587 PSD1: Protein of unkn 30.3 54 0.0012 23.9 2.7 29 8-38 52-80 (266)
105 PRK14830 undecaprenyl pyrophos 30.1 82 0.0018 23.2 3.6 17 21-37 150-166 (251)
106 PF08388 GIIM: Group II intron 30.0 99 0.0021 17.7 3.3 33 26-59 3-35 (80)
107 cd08334 DED_Caspase_8_10_repea 29.8 1.4E+02 0.0029 18.2 4.2 50 24-74 20-72 (83)
108 TIGR00174 miaA tRNA isopenteny 29.5 2.2E+02 0.0047 21.3 5.8 48 6-53 194-246 (287)
109 COG5049 XRN1 5'-3' exonuclease 29.4 1E+02 0.0022 26.8 4.4 51 16-66 531-637 (953)
110 PF08776 VASP_tetra: VASP tetr 29.3 82 0.0018 17.2 2.6 18 63-80 22-39 (40)
111 cd05025 S-100A1 S-100A1: S-100 29.2 1.3E+02 0.0028 17.8 5.6 50 7-57 30-83 (92)
112 PRK10307 putative glycosyl tra 29.1 1.1E+02 0.0023 22.6 4.1 36 2-37 355-390 (412)
113 cd06607 STKc_TAO Catalytic dom 29.1 1.4E+02 0.0031 20.8 4.6 57 20-78 236-292 (307)
114 PF14433 SUKH-3: SUKH-3 immuni 29.0 68 0.0015 20.8 2.7 14 11-24 1-14 (142)
115 PF05205 COMPASS-Shg1: COMPASS 28.9 62 0.0013 20.6 2.5 22 14-35 3-24 (106)
116 KOG2235 Uncharacterized conser 28.7 47 0.001 28.3 2.3 26 6-32 116-141 (776)
117 KOG1112 Ribonucleotide reducta 28.7 34 0.00074 28.7 1.5 35 2-39 629-664 (796)
118 PLN02448 UDP-glycosyltransfera 28.7 84 0.0018 24.5 3.6 48 6-53 401-456 (459)
119 KOG1488 Translational represso 28.6 88 0.0019 25.6 3.7 63 12-76 228-290 (503)
120 PRK06654 fliL flagellar basal 27.8 1.4E+02 0.003 21.2 4.2 50 8-78 116-165 (181)
121 PF06971 Put_DNA-bind_N: Putat 27.7 1.1E+02 0.0024 17.1 3.1 33 31-68 17-49 (50)
122 PLN02165 adenylate isopentenyl 27.5 1.9E+02 0.0042 22.2 5.3 48 6-53 184-238 (334)
123 cd07153 Fur_like Ferric uptake 27.3 1.5E+02 0.0033 18.0 4.3 40 28-68 3-42 (116)
124 PRK14135 recX recombination re 27.1 2.1E+02 0.0046 20.3 5.3 58 12-71 75-135 (263)
125 PF05400 FliT: Flagellar prote 26.9 49 0.0011 18.9 1.6 16 2-17 5-20 (84)
126 PRK06995 flhF flagellar biosyn 26.8 3.3E+02 0.0071 22.0 6.6 69 5-76 170-243 (484)
127 cd07977 TFIIE_beta_winged_heli 26.8 1.1E+02 0.0024 18.3 3.2 24 30-53 13-36 (75)
128 PRK05720 mtnA methylthioribose 26.7 2.1E+02 0.0046 22.0 5.4 58 21-79 72-129 (344)
129 PF00406 ADK: Adenylate kinase 26.7 1.3E+02 0.0027 19.2 3.7 15 57-71 52-66 (151)
130 COG1508 RpoN DNA-directed RNA 26.6 2.3E+02 0.0051 22.8 5.8 64 7-75 89-155 (444)
131 cd05030 calgranulins Calgranul 26.5 1.5E+02 0.0033 17.7 5.1 50 7-58 29-83 (88)
132 PF15615 TerB-C: TerB-C domain 25.7 1.6E+02 0.0034 19.5 4.1 48 9-63 77-125 (144)
133 PF01015 Ribosomal_S3Ae: Ribos 25.6 2.2E+02 0.0048 20.1 5.0 40 26-73 135-174 (194)
134 COG1424 BioW Pimeloyl-CoA synt 25.5 88 0.0019 23.0 3.0 32 7-38 73-104 (239)
135 smart00845 GatB_Yqey GatB doma 25.3 2E+02 0.0044 18.8 4.6 47 25-71 91-145 (147)
136 PF10057 DUF2294: Uncharacteri 25.2 1.1E+02 0.0025 19.5 3.3 34 2-36 56-89 (118)
137 TIGR03764 ICE_PFGI_1_parB inte 25.2 2.9E+02 0.0064 20.6 6.0 51 27-77 191-245 (258)
138 cd03561 VHS VHS domain family; 25.1 1.4E+02 0.0029 19.3 3.6 19 58-76 93-111 (133)
139 TIGR01078 arcA arginine deimin 25.0 92 0.002 24.3 3.2 23 31-53 49-71 (405)
140 COG1859 KptA RNA:NAD 2'-phosph 24.7 82 0.0018 22.9 2.7 34 16-52 52-85 (211)
141 PF07569 Hira: TUP1-like enhan 24.5 1.6E+02 0.0034 20.8 4.1 31 3-33 188-218 (219)
142 PF09424 YqeY: Yqey-like prote 24.5 2.2E+02 0.0049 19.0 5.6 55 5-63 78-133 (143)
143 PF13720 Acetyltransf_11: Udp 24.3 1.7E+02 0.0038 17.6 4.9 53 18-77 23-75 (83)
144 TIGR00578 ku70 ATP-dependent D 24.2 1.1E+02 0.0024 25.0 3.6 45 31-77 540-584 (584)
145 PF09784 L31: Mitochondrial ri 24.1 2.1E+02 0.0046 18.6 4.5 46 13-62 23-68 (103)
146 PRK09480 slmA division inhibit 24.1 1.5E+02 0.0032 19.2 3.7 11 41-51 29-39 (194)
147 PRK04057 30S ribosomal protein 24.0 2E+02 0.0043 20.6 4.6 41 25-73 128-168 (203)
148 PF15586 Imm47: Immunity prote 23.8 1.6E+02 0.0036 19.1 3.8 27 6-32 77-106 (116)
149 PRK00091 miaA tRNA delta(2)-is 23.7 3E+02 0.0065 20.6 5.7 48 6-53 198-250 (307)
150 PF06057 VirJ: Bacterial virul 23.6 1.6E+02 0.0035 21.0 4.0 54 20-78 11-64 (192)
151 PLN02534 UDP-glycosyltransfera 23.5 55 0.0012 26.2 1.7 50 6-55 430-487 (491)
152 PLN02848 adenylosuccinate lyas 23.4 3.1E+02 0.0067 21.8 5.9 54 10-70 388-441 (458)
153 PF02697 DUF217: Uncharacteriz 23.4 1.8E+02 0.0038 17.4 5.0 14 41-54 20-33 (71)
154 PRK10829 ribonuclease D; Provi 23.3 2.6E+02 0.0056 21.7 5.4 44 9-53 161-204 (373)
155 COG3514 Uncharacterized protei 23.2 94 0.002 19.9 2.5 19 20-38 74-92 (93)
156 PLN02764 glycosyltransferase f 23.2 1.4E+02 0.0031 23.6 4.0 49 6-54 393-445 (453)
157 PRK13756 tetracycline represso 23.2 1.6E+02 0.0035 20.5 3.9 28 25-52 7-34 (205)
158 PRK01388 arginine deiminase; P 23.1 1.1E+02 0.0023 24.1 3.2 30 23-52 45-77 (406)
159 PRK04309 DNA-directed RNA poly 23.0 1.2E+02 0.0026 23.7 3.5 27 49-75 7-33 (383)
160 COG2115 XylA Xylose isomerase 23.0 2.4E+02 0.0053 22.5 5.1 57 9-74 379-435 (438)
161 COG2901 Fis Factor for inversi 23.0 2.2E+02 0.0048 18.3 4.2 47 22-78 26-72 (98)
162 PF01475 FUR: Ferric uptake re 23.0 1.6E+02 0.0036 18.2 3.6 42 26-68 8-49 (120)
163 PF07830 PP2C_C: Protein serin 22.9 82 0.0018 19.5 2.1 41 19-61 20-60 (81)
164 PF04794 YdjC: YdjC-like prote 22.8 61 0.0013 23.1 1.8 22 56-77 96-117 (261)
165 cd08315 Death_TRAILR_DR4_DR5 D 22.8 2E+02 0.0044 17.9 4.6 45 24-69 47-91 (96)
166 cd03568 VHS_STAM VHS domain fa 22.8 1.5E+02 0.0033 19.7 3.5 17 60-76 93-109 (144)
167 PRK14723 flhF flagellar biosyn 22.7 4E+02 0.0086 23.0 6.7 69 5-76 97-172 (767)
168 cd08776 DED_Caspase-like_repea 22.7 1.7E+02 0.0036 17.6 3.4 48 24-75 17-64 (71)
169 PRK05910 type III secretion sy 22.4 2.3E+02 0.005 23.7 5.1 67 5-79 461-528 (584)
170 TIGR03182 PDH_E1_alph_y pyruva 22.1 3E+02 0.0066 20.4 5.4 41 12-52 263-313 (315)
171 PLN03007 UDP-glucosyltransfera 22.0 1.3E+02 0.0028 23.7 3.5 48 6-53 426-479 (482)
172 PRK09358 adenosine deaminase; 21.9 2E+02 0.0044 21.1 4.4 36 42-77 303-339 (340)
173 cd03399 Band_7_flotillin Band_ 21.8 2E+02 0.0043 18.0 3.9 28 23-51 56-83 (128)
174 PF02205 WH2: WH2 motif; Inte 21.6 69 0.0015 16.1 1.3 14 62-75 2-15 (30)
175 COG1071 AcoA Pyruvate/2-oxoglu 21.5 2.6E+02 0.0057 21.8 5.1 40 13-52 292-341 (358)
176 PF08973 TM1506: Domain of unk 21.5 15 0.00032 24.8 -1.6 49 28-77 77-133 (134)
177 PRK08105 flavodoxin; Provision 21.5 1E+02 0.0023 20.3 2.6 25 3-27 11-35 (149)
178 PF15163 Meiosis_expr: Meiosis 21.3 45 0.00098 20.7 0.7 12 17-28 16-27 (77)
179 PF08006 DUF1700: Protein of u 21.3 1.9E+02 0.0042 19.4 3.9 41 12-52 8-50 (181)
180 PF14689 SPOB_a: Sensor_kinase 21.2 72 0.0016 18.2 1.5 19 18-36 33-51 (62)
181 cd03565 VHS_Tom1 VHS domain fa 21.1 1.6E+02 0.0034 19.5 3.4 27 48-76 88-114 (141)
182 PF11867 DUF3387: Domain of un 20.8 3.4E+02 0.0074 20.3 5.5 23 56-78 260-282 (335)
183 PF12732 YtxH: YtxH-like prote 20.5 1.9E+02 0.0042 16.7 4.5 6 12-17 29-34 (74)
184 PF14428 SCP1201-deam: SCP1.20 20.4 1.5E+02 0.0033 19.7 3.2 55 4-59 43-117 (135)
185 COG4004 Uncharacterized protei 20.4 67 0.0015 20.7 1.4 12 14-25 17-28 (96)
186 PF04376 ATE_N: Arginine-tRNA- 20.4 43 0.00094 20.2 0.5 16 9-24 30-45 (80)
No 1
>KOG4479 consensus Transcription factor e(y)2 [Transcription]
Probab=100.00 E-value=1e-36 Score=191.13 Aligned_cols=81 Identities=52% Similarity=0.888 Sum_probs=78.6
Q ss_pred CccchhHHHHHHHHHHHHHhcChHHHHHHHHHHHHHhhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHHhhhhc
Q 042650 1 MIESGEKERLKELLRERLIECGWRDEMKSLCRAYTRKKGRNNVTVDDLVHVITPKGRASVPDPVKAELLQRIRSFLASTA 80 (81)
Q Consensus 1 LvesGe~erL~~~L~~rL~e~GW~D~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~~VP~~vk~Ell~~Ir~fL~~~~ 80 (81)
+++|||+.+|+++|+.||.||||.|++|.+||++|.++|.+|+|+++|+++|+|+||++|||.||+|||.+||+||.+|+
T Consensus 11 t~~tgdr~~lKeLL~trLvECGW~d~ik~mcrniimEkG~~n~tvdqL~AeitPkaRaLVPd~VKkEll~rirt~L~~~~ 90 (92)
T KOG4479|consen 11 TLRTGDRAALKELLHTRLVECGWHDDIKEMCRNIIMEKGVDNITVDQLAAEITPKARALVPDVVKKELLLRIRTALDKHA 90 (92)
T ss_pred hhhcccHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHhccccccHHHHHHHhCchhhhhchHHHHHHHHHHHHHHHHHHh
Confidence 47899999999999999999999999999999999999999999999999999999999999999999999999999986
Q ss_pred C
Q 042650 81 T 81 (81)
Q Consensus 81 ~ 81 (81)
.
T Consensus 91 ~ 91 (92)
T KOG4479|consen 91 S 91 (92)
T ss_pred c
Confidence 3
No 2
>PF10163 EnY2: Transcription factor e(y)2; InterPro: IPR018783 Enhancer of yellow 2 (EnY2) is a small transcription factor which is combined in a complex with the TAFII40 protein []. This protein is conserved from protozoa to humans.; PDB: 4DHX_C 3FWC_P 3M99_C 3KIK_A 3KJL_C 3FWB_C 3MHS_B 3MHH_B.
Probab=100.00 E-value=5e-36 Score=188.18 Aligned_cols=77 Identities=66% Similarity=1.114 Sum_probs=73.6
Q ss_pred CccchhHHHHHHHHHHHHHhcChHHHHHHHHHHHHHhhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHHhh
Q 042650 1 MIESGEKERLKELLRERLIECGWRDEMKSLCRAYTRKKGRNNVTVDDLVHVITPKGRASVPDPVKAELLQRIRSFLA 77 (81)
Q Consensus 1 LvesGe~erL~~~L~~rL~e~GW~D~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~~VP~~vk~Ell~~Ir~fL~ 77 (81)
|++||||++|+++|+.||.||||+|+||++|+++++++|.+++||++|+++|+|+|+++||++||+||+.+|++||+
T Consensus 10 L~~sGe~~~L~~~L~~rL~e~GW~d~vr~~~re~i~~~g~~~~~~~~l~~~i~P~Ar~~VP~~vk~ell~~Ir~~L~ 86 (86)
T PF10163_consen 10 LVESGEYERLKELLRQRLIECGWRDEVRQLCREIIRERGIDNLTFEDLLEEITPKARAMVPDEVKKELLQRIRAFLD 86 (86)
T ss_dssp HHHCTHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHH-TTTSBHHHHHHHHHHHHHHCS-HHHHHHHHHHHHHHHH
T ss_pred HHHcCcHHHHHHHHHHHHHHCChHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHhC
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999996
No 3
>PF10163 EnY2: Transcription factor e(y)2; InterPro: IPR018783 Enhancer of yellow 2 (EnY2) is a small transcription factor which is combined in a complex with the TAFII40 protein []. This protein is conserved from protozoa to humans.; PDB: 4DHX_C 3FWC_P 3M99_C 3KIK_A 3KJL_C 3FWB_C 3MHS_B 3MHH_B.
Probab=87.67 E-value=4.2 Score=25.03 Aligned_cols=45 Identities=31% Similarity=0.461 Sum_probs=35.0
Q ss_pred HHHHHHHHHHHhcChHHHHHHHHHHHHHhhC-CCCCCHHHHHHhhchh
Q 042650 9 RLKELLRERLIECGWRDEMKSLCRAYTRKKG-RNNVTVDDLVHVITPK 55 (81)
Q Consensus 9 rL~~~L~~rL~e~GW~D~vr~~~re~i~~~g-~~~v~~~~L~~~i~P~ 55 (81)
.|++.++++|.++|=++.++++-+.-+.+.| .+ .+.++..++.-.
T Consensus 1 ~l~~~i~~~L~~sGe~~~L~~~L~~rL~e~GW~d--~vr~~~re~i~~ 46 (86)
T PF10163_consen 1 QLKAQIQQRLVESGEYERLKELLRQRLIECGWRD--EVRQLCREIIRE 46 (86)
T ss_dssp HHHHHHHHHHHHCTHHHHHHHHHHHHHHHTTHHH--HHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHcCcHHHHHHHHHHHHHHCChHH--HHHHHHHHHHHh
Confidence 3789999999999999999999999998887 23 444455544433
No 4
>PF05008 V-SNARE: Vesicle transport v-SNARE protein N-terminus; InterPro: IPR007705 V-SNARE proteins are required for protein traffic between eukaryotic organelles. The v-SNAREs on transport vesicles interact with t-SNAREs on target membranes in order to facilitate this []. This domain is the N-terminal half of the V-Snare proteins. ; GO: 0006886 intracellular protein transport, 0016020 membrane; PDB: 2V8S_V 1VCS_A 3ONL_C 3ONJ_A 2QYW_A.
Probab=87.41 E-value=4.2 Score=23.97 Aligned_cols=62 Identities=21% Similarity=0.335 Sum_probs=42.2
Q ss_pred HHHHHHHHHHHhcChHHHHHHHHHHHHHhhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHHhh
Q 042650 9 RLKELLRERLIECGWRDEMKSLCRAYTRKKGRNNVTVDDLVHVITPKGRASVPDPVKAELLQRIRSFLA 77 (81)
Q Consensus 9 rL~~~L~~rL~e~GW~D~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~~VP~~vk~Ell~~Ir~fL~ 77 (81)
-|...|..-...+| ++=+..++++=..- + ..++++..+.=.++.+ |.+.+..+..+|+.|=.
T Consensus 7 ~i~~~l~~~~~~~~--~~r~~~i~~~e~~l--~--ea~~~l~qMe~E~~~~-p~s~r~~~~~kl~~yr~ 68 (79)
T PF05008_consen 7 EIKSKLERIKNLSG--EQRKSLIREIERDL--D--EAEELLKQMELEVRSL-PPSERNQYKSKLRSYRS 68 (79)
T ss_dssp HHHHHHHHGGGS-C--HHHHHHHHHHHHHH--H--HHHHHHHHHHHHHCTS--HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHhhccCh--HHHHHHHHHHHHHH--H--HHHHHHHHHHHHHHhC-CHHHHHHHHHHHHHHHH
Confidence 34445554445566 56666665543322 2 6788999999999976 99999999999999843
No 5
>PF08766 DEK_C: DEK C terminal domain; InterPro: IPR014876 DEK is a chromatin associated protein that is linked with cancers and autoimmune disease. This domain is found at the C-terminal of DEK and is of clinical importance since it can reverse the characteristic abnormal DNA-mutagen sensitivity in fibroblasts from ataxia-telangiectasia (A-T) patients []. The structure of this domain shows it to be homologous to the E2F/DP transcription factor family []. This domain is also found in chitin synthase proteins like Q8TF96 from SWISSPROT, and in protein phosphatases such as Q6NN85 from SWISSPROT. ; PDB: 1Q1V_A.
Probab=83.93 E-value=5.2 Score=22.42 Aligned_cols=51 Identities=18% Similarity=0.240 Sum_probs=34.4
Q ss_pred HHHHHHHHHHHHhhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHHh
Q 042650 25 DEMKSLCRAYTRKKGRNNVTVDDLVHVITPKGRASVPDPVKAELLQRIRSFL 76 (81)
Q Consensus 25 D~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~~VP~~vk~Ell~~Ir~fL 76 (81)
++++...+++++..+.+++|.-++...+.-+----+. +=|..+=+.|..||
T Consensus 3 ~~i~~~i~~iL~~~dl~~vT~k~vr~~Le~~~~~dL~-~~K~~I~~~I~~~l 53 (54)
T PF08766_consen 3 EEIREAIREILREADLDTVTKKQVREQLEERFGVDLS-SRKKFIKELIDEFL 53 (54)
T ss_dssp HHHHHHHHHHHTTS-GGG--HHHHHHHHHHH-SS--S-HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhCCHhHhhHHHHHHHHHHHHCCCcH-HHHHHHHHHHHHHh
Confidence 6789999999999999999999999998766622222 55555666666665
No 6
>PF06348 DUF1059: Protein of unknown function (DUF1059); InterPro: IPR009409 This entry consists of short hypothetical archaeal and bacterial proteins of unknown function.
Probab=78.10 E-value=4.1 Score=23.42 Aligned_cols=31 Identities=19% Similarity=0.514 Sum_probs=24.7
Q ss_pred CHHHHHHhhchhhhcc-----CCHHHHHHHHHHHHH
Q 042650 44 TVDDLVHVITPKGRAS-----VPDPVKAELLQRIRS 74 (81)
Q Consensus 44 ~~~~L~~~i~P~Ar~~-----VP~~vk~Ell~~Ir~ 74 (81)
|-++|++.+..+|+.. +|+++...+-+.|++
T Consensus 21 tedEll~~~~~Ha~~~Hg~~~~~~el~~~ir~~I~~ 56 (57)
T PF06348_consen 21 TEDELLEAVVEHAREVHGMTEIPEELREKIRSAIKD 56 (57)
T ss_pred CHHHHHHHHHHHHHHhcCCccCCHHHHHHHHHHhhc
Confidence 7888999888888876 788888777777764
No 7
>PF08328 ASL_C: Adenylosuccinate lyase C-terminal; InterPro: IPR013539 This domain is found at the C terminus of adenylosuccinate lyase(ASL; PurB in Escherichia coli). It has been identified in bacteria, eukaryotes and archaea and is found together with the lyase domain IPR000362 from INTERPRO. ASL catalyses the cleavage of succinylaminoimidazole carboxamide ribotide to aminoimidazole carboxamide ribotide and fumarate and the cleavage of adenylosuccinate to adenylate and fumarate []. ; GO: 0004018 N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity, 0006188 IMP biosynthetic process; PDB: 2HVG_A 2QGA_C 2PTS_A 2PTR_A 2PTQ_B 3BHG_A 3GZH_A.
Probab=75.33 E-value=7.1 Score=25.92 Aligned_cols=56 Identities=30% Similarity=0.465 Sum_probs=34.8
Q ss_pred hhHHHHHHHHHHHHHhcCh---HHHHHHHHHHHHHhhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHH
Q 042650 5 GEKERLKELLRERLIECGW---RDEMKSLCRAYTRKKGRNNVTVDDLVHVITPKGRASVPDPVKAELLQ 70 (81)
Q Consensus 5 Ge~erL~~~L~~rL~e~GW---~D~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~~VP~~vk~Ell~ 70 (81)
.+|+-|.+-++.-|.-.|- ++.+|++.| | ..+|-+++.+-|.--. ||+++|.+|+.
T Consensus 50 ~nWeVlaEpIQTvmRr~g~~~pYE~LK~lTR------g-~~it~~~l~~fI~~L~---ip~~~k~~L~~ 108 (115)
T PF08328_consen 50 ENWEVLAEPIQTVMRRYGIPNPYEKLKELTR------G-KKITKEDLREFIESLD---IPEEAKARLLA 108 (115)
T ss_dssp T-GGGGHHHHHHHHHHTT-SSHHHHHHHHHT------T-S---HHHHHHHHHTSS---S-HHHHHHHHH
T ss_pred HCHHHHHHHHHHHHHHcCCCCHHHHHHHHHc------C-CCCCHHHHHHHHHhCC---CCHHHHHHHHh
Confidence 3566677777777777665 566766664 4 3667777777775444 99999999875
No 8
>cd07347 harmonin_N_like N-terminal protein-binding module of harmonin and similar domains. This domain is found in harmonin, and similar proteins such as delphilin, and whirlin. These are postsynaptic density-95/discs-large/ZO-1 (PDZ) domain-containing scaffold proteins. Harmonin and whirlin are organizers of the Usher protein network of the inner ear and the retina, delphilin is found at the cerebellar parallel fiber-Purkinje cell synapses. This harmonin_N_like domain is found in either one or two copies. Harmonin contains a single copy, which is found at its N-terminus and binds specifically to a short internal peptide fragment of the cadherin 23 cytoplasmic domain; cadherin 23 is a component of the Usher protein network. Whirlin contains two copies of the harmonin_N_like domain; the first of these has been assayed for interaction with the cytoplasmic domain of cadherin 23 and no interaction could be detected.
Probab=75.20 E-value=16 Score=22.56 Aligned_cols=59 Identities=24% Similarity=0.423 Sum_probs=44.2
Q ss_pred HHHHHHHHHHHhcChHHHHHHHHHHHHHhhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHHhh
Q 042650 9 RLKELLRERLIECGWRDEMKSLCRAYTRKKGRNNVTVDDLVHVITPKGRASVPDPVKAELLQRIRSFLA 77 (81)
Q Consensus 9 rL~~~L~~rL~e~GW~D~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~~VP~~vk~Ell~~Ir~fL~ 77 (81)
.+.+.++.-|.+.- ++.+-...+++-..+ |+++|+..+ ..+++..-|..|+..||.++-
T Consensus 7 ~f~~q~~~LL~~~E-r~~~~~~L~~Y~~~~-----~Vd~LV~~L----~~vLdtPaK~~Ll~~iR~lIp 65 (78)
T cd07347 7 EFSQQVDHLLTDAE-REQVTRALERYHQER-----NVDDLVRDL----YLVLDTPAKLPLLQFLRQVIP 65 (78)
T ss_pred HHHHHHHHHCCHHH-HHHHHHHHHHHHhcC-----CHHHHHHHH----HHHcCcHhHHHHHHHHHHHcC
Confidence 45566666665544 667777776665432 899999999 568899999999999999874
No 9
>COG1610 Uncharacterized conserved protein [Function unknown]
Probab=68.91 E-value=14 Score=25.64 Aligned_cols=63 Identities=22% Similarity=0.345 Sum_probs=50.6
Q ss_pred cchhHHHHHHHHHHHHHhcChHHHHHHHHHHHHHhhCCCC-CCHHHHHHhhchhhhccCCHHHHHHHH
Q 042650 3 ESGEKERLKELLRERLIECGWRDEMKSLCRAYTRKKGRNN-VTVDDLVHVITPKGRASVPDPVKAELL 69 (81)
Q Consensus 3 esGe~erL~~~L~~rL~e~GW~D~vr~~~re~i~~~g~~~-v~~~~L~~~i~P~Ar~~VP~~vk~Ell 69 (81)
|.+|-..|..+|-++|.+ ++|+..|.+.|.+-|... -..-.+-..+.|+.....+-....-+.
T Consensus 80 E~~Ei~Ii~~ylP~qLsd----~e~~~~v~~aIae~Gas~~~dMGkvM~al~~k~~GkaD~~~vs~~V 143 (148)
T COG1610 80 ERAEIAIIEEYLPQQLSE----DELRALVDAAIAEVGASSMKDMGKVMKALKPKVAGKADGGRVSKLV 143 (148)
T ss_pred HHhHHHHHHHhCcccCCH----HHHHHHHHHHHHHHHHhhHHHHHHHHHHHhHHhcccCcHHHHHHHH
Confidence 568889999999999997 899999999998887443 256678888999998888876555443
No 10
>PF08429 PLU-1: PLU-1-like protein; InterPro: IPR013637 This domain is found in the central region of lysine-specific demethylases, which are nuclear proteins that may have a role in DNA-binding and transcription, and are associated with malignant cancer phenotypes []. The domain is also found in various other Jumonji/ARID domain-containing proteins (see IPR013129 from INTERPRO, IPR001606 from INTERPRO). ; GO: 0016706 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors, 0055114 oxidation-reduction process
Probab=68.82 E-value=21 Score=26.31 Aligned_cols=56 Identities=23% Similarity=0.490 Sum_probs=37.1
Q ss_pred HHHHHHHhcChHHHHHHHHHHHHHhhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHHh
Q 042650 13 LLRERLIECGWRDEMKSLCRAYTRKKGRNNVTVDDLVHVITPKGRASVPDPVKAELLQRIRSFL 76 (81)
Q Consensus 13 ~L~~rL~e~GW~D~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~~VP~~vk~Ell~~Ir~fL 76 (81)
.|+.++..+.|.++++.... +.+.+|++++-.-|. .|....| .--.+.+..++..+
T Consensus 156 ~L~~~l~~~~W~~~~~~~~~------~~~~~tL~~l~~Ll~-~g~~l~~-~~~~~~~~~L~~~l 211 (335)
T PF08429_consen 156 QLRRRLEQLEWLEEAREILS------DPDRLTLDELRELLD-EGERLGI-PSDEKLMAELQELL 211 (335)
T ss_pred HHHHHHHHHHHHHHHHHHhc------cccCCcHHHHHHHHH-hhhcCCC-ccchHHHHHHHHHH
Confidence 46677788899999987663 223579988877776 8888877 33333444444433
No 11
>TIGR02606 antidote_CC2985 putative addiction module antidote protein, CC2985 family. This bacterial protein family has a very similar seed alignment to that of Pfam model pfam03693 but is a more stringent model with higher cutoff scores. Proteins that score above the trusted cutoff to this model almost invariably are found adjacent to a ParE family protein (pfam05016), where ParE is the killing partner of an addiction module for plasmid stabilization. Members of this family, therefore, are putative addiction module antidote proteins. Some are encoded on plasmids or in prophage regions, but others appear chromosomal. A genome may contain several identical copies, such as the four in Magnetococcus sp. MC-1. This family is named for one member, CC2985 of Caulobacter crescentus CB15.
Probab=67.66 E-value=18 Score=21.43 Aligned_cols=47 Identities=15% Similarity=0.181 Sum_probs=27.9
Q ss_pred ccchhHH----HHHHHHHHHHHhcChHHHHHHHHHHHHHhhCCCCCCHHHHH
Q 042650 2 IESGEKE----RLKELLRERLIECGWRDEMKSLCRAYTRKKGRNNVTVDDLV 49 (81)
Q Consensus 2 vesGe~e----rL~~~L~~rL~e~GW~D~vr~~~re~i~~~g~~~v~~~~L~ 49 (81)
|+||.|. -+++.|+.--..+.|.+.+|....+-+.. |....++++++
T Consensus 18 V~sG~Y~s~SEVir~aLR~le~~e~~~~~Lr~~i~~g~~s-g~~~~~~d~~~ 68 (69)
T TIGR02606 18 VQSGRYGSASEVVRAALRLLEERETKLQALRDAIEEGEQS-GEAGRSLDDFL 68 (69)
T ss_pred HHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC-CCCCCCHHHHh
Confidence 5677764 44555554445567777777777655543 43344676654
No 12
>PF07350 DUF1479: Protein of unknown function (DUF1479); InterPro: IPR010856 This family consists of several hypothetical Enterobacterial proteins, of around 420 residues in length. Members of this family are often known as YbiU. The function of this family is unknown.; PDB: 2CSG_A 2DBI_A 2DBN_A.
Probab=66.39 E-value=26 Score=27.81 Aligned_cols=61 Identities=18% Similarity=0.324 Sum_probs=40.6
Q ss_pred hcChHHHHHHHHHHH--HHhhC---CCCCCHHHHHHh-hchh------------hhccCCHHHHHHHHHHHHHHhhhhc
Q 042650 20 ECGWRDEMKSLCRAY--TRKKG---RNNVTVDDLVHV-ITPK------------GRASVPDPVKAELLQRIRSFLASTA 80 (81)
Q Consensus 20 e~GW~D~vr~~~re~--i~~~g---~~~v~~~~L~~~-i~P~------------Ar~~VP~~vk~Ell~~Ir~fL~~~~ 80 (81)
...|..-++.+-+++ |.+.| +..++|.+|.+- +.+. -|+.||.+.-....+.|++|+..+.
T Consensus 25 ~~sw~rll~~l~~~~~~i~~~G~~~IP~i~f~di~~~~~~~~~~~~ir~rG~~VIR~Vvp~~ea~~w~~e~~~Y~~~n~ 103 (416)
T PF07350_consen 25 FASWERLLEALEREIEEIAAKGSSIIPEIDFADIENGGVSEEFLAEIRRRGCVVIRGVVPREEALAWKQELKEYLKANP 103 (416)
T ss_dssp HHHHHHHHHHHHHHHHHHHHCT--SS-EEEHHHHHCT---HHHHHHHHHHSEEEECTSS-HHHHHHHHHHHHHHHHHT-
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCCCceeeHHHHhCCCCCHHHHHHHHhcCEEEEeCCCCHHHHHHHHHHHHHHHHhCc
Confidence 446777777765543 56666 455688888765 2221 2678999999999999999998753
No 13
>PF08411 Exonuc_X-T_C: Exonuclease C-terminal; InterPro: IPR013620 This bacterial domain is found at the C terminus of exodeoxyribonuclease I/Exonuclease I (IPR013520 from INTERPRO), which is a single-strand specific DNA nuclease affecting recombination and expression pathways. The exonuclease I protein in Escherichia coli is associated with DNA deoxyribophosphodiesterase (dRPase) []. ; GO: 0008852 exodeoxyribonuclease I activity, 0006281 DNA repair; PDB: 2QXF_A 3C94_A 3HL8_A 3C95_A 1FXX_A 3HP9_A.
Probab=66.03 E-value=18 Score=26.56 Aligned_cols=55 Identities=15% Similarity=0.233 Sum_probs=39.9
Q ss_pred HHHHHHHHHHHHHhhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHHhhh
Q 042650 24 RDEMKSLCRAYTRKKGRNNVTVDDLVHVITPKGRASVPDPVKAELLQRIRSFLAS 78 (81)
Q Consensus 24 ~D~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~~VP~~vk~Ell~~Ir~fL~~ 78 (81)
+.+++.+|++.+...+....|+++..++|.--+..--.+.-+..||..+.+|.++
T Consensus 214 ~~~W~~~~~~rL~~~~~~~~tl~~~~~~i~~L~~~~~~~~~~~~lL~~L~~Y~~~ 268 (269)
T PF08411_consen 214 QQRWQEYCQQRLTDPDGGWLTLEEYFQEIEELRAEYDDDEEKQALLEALEDYAES 268 (269)
T ss_dssp HHHHHHHHHHHS-HHH-----HHHHHHHHHHHHHHTTT-HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHccCCccchHHHHHHHHHHHHHHhhccCCHHHHHHHHHHHHHHhc
Confidence 4667788888886655567899999999988888766667899999999999864
No 14
>PF05066 HARE-HTH: HB1, ASXL, restriction endonuclease HTH domain; InterPro: IPR007759 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. The delta protein is a dispensable subunit of Bacillus subtilis RNA polymerase (RNAP) that has major effects on the biochemical properties of the purified enzyme. In the presence of delta, RNAP displays an increased specificity of transcription, a decreased affinity for nucleic acids, and an increased efficiency of RNA synthesis because of enhanced recycling []. The delta protein, contains two distinct regions, an N-terminal domain and a glutamate and aspartate residue-rich C-terminal region [].; GO: 0003677 DNA binding, 0006351 transcription, DNA-dependent; PDB: 2KRC_A.
Probab=63.53 E-value=27 Score=20.20 Aligned_cols=46 Identities=20% Similarity=0.327 Sum_probs=30.3
Q ss_pred HHHHHHHHHHhhCCCCCCHHHHHHhhchhhhcc----CCHHHH-HHHHHHHH
Q 042650 27 MKSLCRAYTRKKGRNNVTVDDLVHVITPKGRAS----VPDPVK-AELLQRIR 73 (81)
Q Consensus 27 vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~~----VP~~vk-~Ell~~Ir 73 (81)
+.+.|.+++++.| ..+++.+|+++|.-...-. -|.... ..|...|+
T Consensus 3 ~~eaa~~vL~~~~-~pm~~~eI~~~i~~~~~~~~~~k~p~~~i~a~ly~~~~ 53 (72)
T PF05066_consen 3 FKEAAYEVLEEAG-RPMTFKEIWEEIQERGLYKKSGKTPEATIAAQLYTDIK 53 (72)
T ss_dssp HHHHHHHHHHHH--S-EEHHHHHHHHHHHHTS---GGGGGHHHH-HHHHHHH
T ss_pred HHHHHHHHHHhcC-CCcCHHHHHHHHHHhCCCCcccCCHHHHHHHHHHHHcc
Confidence 4678899999998 7889999999997655433 443333 36666665
No 15
>PF04963 Sigma54_CBD: Sigma-54 factor, core binding domain; InterPro: IPR007046 This domain makes a direct interaction with the core RNA polymerase, to form an enhancer dependent holoenzyme []. The centre of this domain contains a very weak similarity to a helix-turn-helix motif, which may represent a DNA binding domain.; GO: 0003677 DNA binding, 0006352 transcription initiation, DNA-dependent; PDB: 2K9L_A 2K9M_A.
Probab=63.32 E-value=11 Score=26.14 Aligned_cols=63 Identities=17% Similarity=0.248 Sum_probs=42.5
Q ss_pred HHHHHHHHHHHHHhcChHHHHHHHHHHHH---HhhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHH
Q 042650 7 KERLKELLRERLIECGWRDEMKSLCRAYT---RKKGRNNVTVDDLVHVITPKGRASVPDPVKAELLQRIRSF 75 (81)
Q Consensus 7 ~erL~~~L~~rL~e~GW~D~vr~~~re~i---~~~g~~~v~~~~L~~~i~P~Ar~~VP~~vk~Ell~~Ir~f 75 (81)
.+-|.+.|..+|.-+...+..+..|.-+| ..+|-=..+.+++..... |+.+--.+++..|+.|
T Consensus 14 ~~sL~e~L~~Ql~~~~l~~~~~~ia~~lI~~LD~~GyL~~~~~eia~~l~------~~~~~v~~~l~~lQ~l 79 (194)
T PF04963_consen 14 EESLYEHLLEQLNLSPLSEEEREIAEYLIDNLDDDGYLTESLEEIAEELG------VSEEEVEKALELLQSL 79 (194)
T ss_dssp -----HHHHHHHHHH---TCCHHHHHHHCCCBTTTSTCSS-HHHHHHHCT------S-HHHHHHHHHHHHTT
T ss_pred ccCHHHHHHHHHcCcccCHHHHHHHHHHHHcCCCCCccCCCHHHHHHHhC------CCHHHHHHHHHHHHcC
Confidence 45678899999998888888888888776 456766679999988774 8888888888888763
No 16
>PF08100 Dimerisation: Dimerisation domain; InterPro: IPR012967 This domain is found at the N terminus of a variety of plant O-methyltransferases. It has been shown to mediate dimerisation of these proteins [].; GO: 0008168 methyltransferase activity, 0046983 protein dimerization activity; PDB: 1ZGJ_A 1ZG3_A 1ZHF_A 1ZGA_A 2QYO_A 1KYW_A 1KYZ_A 3REO_D 1FPX_A 1FP2_A ....
Probab=63.08 E-value=13 Score=20.91 Aligned_cols=38 Identities=16% Similarity=0.384 Sum_probs=26.5
Q ss_pred HHHHhhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHHh
Q 042650 33 AYTRKKGRNNVTVDDLVHVITPKGRASVPDPVKAELLQRIRSFL 76 (81)
Q Consensus 33 e~i~~~g~~~v~~~~L~~~i~P~Ar~~VP~~vk~Ell~~Ir~fL 76 (81)
++|.+.|...+|..+|++.+-+ . ...+-..+.||-.||
T Consensus 13 dii~~~g~~~ls~~eia~~l~~-----~-~p~~~~~L~RimR~L 50 (51)
T PF08100_consen 13 DIIHNAGGGPLSLSEIAARLPT-----S-NPSAPPMLDRIMRLL 50 (51)
T ss_dssp HHHHHHTTS-BEHHHHHHTSTC-----T--TTHHHHHHHHHHHH
T ss_pred HHHHHcCCCCCCHHHHHHHcCC-----C-CcchHHHHHHHHHHh
Confidence 5666666567899999999853 2 233567889988887
No 17
>cd05027 S-100B S-100B: S-100B domain found in proteins similar to S100B. S100B is a calcium-binding protein belonging to a large S100 vertebrate-specific protein family within the EF-hand superfamily of calcium-binding proteins. Note that the S-100 hierarchy, to which this S-100B group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100B is most abundant in glial cells of the central nervous system, predominately in astrocytes. S100B is involved in signal transduction via the inhibition of protein phoshorylation, regulation of enzyme activity and by affecting the calcium homeostasis. Upon calcium binding the S100B homodimer changes conformation to expose a hydrophobic cleft, which represents the interaction site of S100B with its more than 20 known target proteins. These target proteins include several cellular architecture proteins such as tubulin and GFAP; S100B can inhibit polymerization of these oligomeric molecules. Furthermore, S100B i
Probab=63.01 E-value=32 Score=20.95 Aligned_cols=50 Identities=14% Similarity=0.242 Sum_probs=33.2
Q ss_pred HHHHHHHHHHHHHhcC---h-HHHHHHHHHHHHHhhCCCCCCHHHHHHhhchhhh
Q 042650 7 KERLKELLRERLIECG---W-RDEMKSLCRAYTRKKGRNNVTVDDLVHVITPKGR 57 (81)
Q Consensus 7 ~erL~~~L~~rL~e~G---W-~D~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar 57 (81)
.+.|+.+|+..|..-+ + .++|..+.++. ...|...++|++.+.-+...|.
T Consensus 29 ~~eL~~ll~~~~~~~lg~~~~~~~v~~~i~~~-D~n~dG~v~f~eF~~li~~~~~ 82 (88)
T cd05027 29 KSELKELINNELSHFLEEIKEQEVVDKVMETL-DSDGDGECDFQEFMAFVAMVTT 82 (88)
T ss_pred HHHHHHHHHHHhHHHhcCCCCHHHHHHHHHHh-CCCCCCcCcHHHHHHHHHHHHH
Confidence 4667777776443332 3 35588888765 4445578999999888876654
No 18
>KOG1964 consensus Nuclear pore complex, rNup107 component (sc Nup84) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=62.86 E-value=32 Score=29.48 Aligned_cols=50 Identities=14% Similarity=0.312 Sum_probs=39.8
Q ss_pred HHhcChHHHHHHHHHHHHHhh--------------------CCCCCCHHHHHHhhchhhhccCCHHHHHH
Q 042650 18 LIECGWRDEMKSLCRAYTRKK--------------------GRNNVTVDDLVHVITPKGRASVPDPVKAE 67 (81)
Q Consensus 18 L~e~GW~D~vr~~~re~i~~~--------------------g~~~v~~~~L~~~i~P~Ar~~VP~~vk~E 67 (81)
|.-+||.|.|=.+.+..+..+ +..+.|.+.+++++.-.+-+.||++...-
T Consensus 318 l~~s~Wed~vWAy~n~~v~~~ie~~l~~a~~~~tq~~p~~~~~~~lT~e~ifeEL~~~~~a~v~~ea~~~ 387 (800)
T KOG1964|consen 318 LLKSGWEDKVWAYLNSMVQARIEAYLGAAPLNETQETPSDLFNGPLTSELIFEELRNEADARVEEEAQHP 387 (800)
T ss_pred HHhcchHHHHHHHHHHHHHHHHHHHHhhccccccCCChhhhcCCcCcHHHHHHHHHHHhhhcchhhhhch
Confidence 345799999999998877543 23456999999999999999999976554
No 19
>PF08369 PCP_red: Proto-chlorophyllide reductase 57 kD subunit; InterPro: IPR013580 This domain is found in bacteria and plant chloroplast proteins. It often appears at the C-terminal of nitrogenase component 1 type oxidoreductases (IPR000510 from INTERPRO) and sometimes independently in bacterial proteins such as the proto-chlorophyllide reductase subunit B of the cyanobacterium Synechocystis. This domain is also associated with chlorophyllide reductase subunit Z, converts chlorophylls (Chl) into bacteriochlorophylls (BChl) by reducing ring B of the tetrapyrrole.; GO: 0016491 oxidoreductase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process, 0055114 oxidation-reduction process; PDB: 2KRU_A 2L09_A.
Probab=61.79 E-value=15 Score=20.16 Aligned_cols=26 Identities=19% Similarity=0.498 Sum_probs=19.2
Q ss_pred HHHHHHHHHHHHhhCCCCCCHHHHHH
Q 042650 25 DEMKSLCRAYTRKKGRNNVTVDDLVH 50 (81)
Q Consensus 25 D~vr~~~re~i~~~g~~~v~~~~L~~ 50 (81)
..+|..+-...+++|.+.||.+.+.+
T Consensus 18 ~~~r~~~E~~Ar~~G~~~IT~e~v~~ 43 (45)
T PF08369_consen 18 KKLRDAAEKYARERGYDEITVEVVDA 43 (45)
T ss_dssp HHHHHHHHHHHHHCT-SEE-HHHHHH
T ss_pred HHHHHHHHHHHHHcCCCeECHHHHHh
Confidence 56777777788889999999987764
No 20
>cd07981 TAF12 TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of the seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs function such as serving as activator-bind
Probab=61.61 E-value=17 Score=21.56 Aligned_cols=34 Identities=21% Similarity=0.390 Sum_probs=29.5
Q ss_pred CCHHHHHHhhchhhhccCCHHHHHHHHHHHHHHhhh
Q 042650 43 VTVDDLVHVITPKGRASVPDPVKAELLQRIRSFLAS 78 (81)
Q Consensus 43 v~~~~L~~~i~P~Ar~~VP~~vk~Ell~~Ir~fL~~ 78 (81)
-++.+|+..+-|. ..|.+++...|....-+|+++
T Consensus 5 ~~l~~lv~~id~~--~~~~~da~~~l~~~~e~fv~~ 38 (72)
T cd07981 5 RKLQELLKEIDPR--EQLDPDVEELLLEIADDFVDD 38 (72)
T ss_pred HHHHHHHHhhCCC--CCcCHHHHHHHHHHHHHHHHH
Confidence 3678899999886 779999999999999999875
No 21
>PF00486 Trans_reg_C: Transcriptional regulatory protein, C terminal; InterPro: IPR001867 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. This entry represents a domain that is almost always found associated with the response regulator receiver domain (see IPR001789 from INTERPRO). It may play a role in DNA binding [].; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0000160 two-component signal transduction system (phosphorelay), 0006355 regulation of transcription, DNA-dependent; PDB: 2K4J_A 2JPB_A 1ODD_A 1OPC_A 1KGS_A 2PMU_E 2JZY_A 1GXP_B 1QQI_A 2Z33_A ....
Probab=61.37 E-value=21 Score=20.15 Aligned_cols=37 Identities=19% Similarity=0.265 Sum_probs=33.7
Q ss_pred CCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHHhhh
Q 042650 41 NNVTVDDLVHVITPKGRASVPDPVKAELLQRIRSFLAS 78 (81)
Q Consensus 41 ~~v~~~~L~~~i~P~Ar~~VP~~vk~Ell~~Ir~fL~~ 78 (81)
..+|.++|++.|-|..- .+++..-.-.+.++|..|..
T Consensus 23 ~~vs~~~l~~~~w~~~~-~~~~~~l~~~I~rLR~kL~~ 59 (77)
T PF00486_consen 23 RVVSREELIEALWGDEE-DVSDNSLDVHISRLRKKLED 59 (77)
T ss_dssp SEEEHHHHHHHHTSSSS-TTCTHHHHHHHHHHHHHHHS
T ss_pred CCCCHHHhCChhhhccc-ccchhhHHHHHHHHHHHHhh
Confidence 67899999999999888 88889999999999999976
No 22
>PF02037 SAP: SAP domain; InterPro: IPR003034 The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA binding domain found in diverse nuclear proteins involved in chromosomal organisation [], including in apoptosis []. In yeast, SAP is found in the most distal N-terminal region of E3 SUMO-protein ligase SIZ1, where it is involved in nuclear localization [].; GO: 0003676 nucleic acid binding; PDB: 2RNN_A 1JEQ_A 2KW9_A 2KVU_A 2DO1_A 1ZBU_B 1ZBH_A 2DO5_A 2RNO_A 1H1J_S ....
Probab=61.31 E-value=11 Score=19.41 Aligned_cols=14 Identities=43% Similarity=0.684 Sum_probs=10.2
Q ss_pred HHHHHHHHHHHHHh
Q 042650 63 PVKAELLQRIRSFL 76 (81)
Q Consensus 63 ~vk~Ell~~Ir~fL 76 (81)
-.|.+|++||.+|+
T Consensus 22 G~K~~Li~Rl~~~l 35 (35)
T PF02037_consen 22 GKKAELIERLKEHL 35 (35)
T ss_dssp SSHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHhC
Confidence 34778888888775
No 23
>PF14426 Imm2: Immunity protein Imm2
Probab=60.26 E-value=26 Score=20.80 Aligned_cols=44 Identities=20% Similarity=0.457 Sum_probs=30.3
Q ss_pred hcChHHHHHH-HHHHHHHhhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHH
Q 042650 20 ECGWRDEMKS-LCRAYTRKKGRNNVTVDDLVHVITPKGRASVPDPVKAELLQRI 72 (81)
Q Consensus 20 e~GW~D~vr~-~~re~i~~~g~~~v~~~~L~~~i~P~Ar~~VP~~vk~Ell~~I 72 (81)
--||..++-+ .|+.+|...- .+..+++|++.| |++--.+++.-.
T Consensus 10 sgg~~pd~v~~~h~~~I~~~l-~~~~l~~Ll~~i--------p~eEae~l~~D~ 54 (60)
T PF14426_consen 10 SGGWHPDVVEMFHRNWIHKLL-SEIPLNNLLDDI--------PSEEAEELRHDM 54 (60)
T ss_pred HccCChHHHHHHHHHHHHHHH-HhCCHHHHHhhC--------CHHHHHHHHHHH
Confidence 3489877766 9999987653 456899999876 655555554433
No 24
>PF08775 ParB: ParB family; InterPro: IPR014884 ParB is a component of the par system which mediates accurate DNA partition during cell division. It recognises A-box and B-box DNA motifs. ParB forms an asymmetric dimer with 2 extended helix-turn-helix (HTH) motifs that bind to A-boxes. The HTH motifs emanate from a beta sheet coiled coil DNA binding module []. Both DNA binding elements are free to rotate around a flexible linker, this enables them to bind to complex arrays of A- and B-box elements on adjacent DNA arms of the looped partition site []. ; PDB: 1ZX4_A 2NTZ_B.
Probab=58.94 E-value=12 Score=24.94 Aligned_cols=38 Identities=29% Similarity=0.496 Sum_probs=28.8
Q ss_pred CCCCCHHHHHHhhchhhhc----cCCHHHHHHHHHHHHHHhh
Q 042650 40 RNNVTVDDLVHVITPKGRA----SVPDPVKAELLQRIRSFLA 77 (81)
Q Consensus 40 ~~~v~~~~L~~~i~P~Ar~----~VP~~vk~Ell~~Ir~fL~ 77 (81)
..+++++++++.|...-.. .=|+++|+.+|..|++.+.
T Consensus 24 ~~~~~l~~~i~~v~~~~~~~~~~~~~de~K~~Il~~ik~~~~ 65 (127)
T PF08775_consen 24 KNKVSLDELIDNVRSEIENIDDELSPDEVKKKILKLIKAELK 65 (127)
T ss_dssp T-HHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHH
T ss_pred hcCCCHHHHHHHHHHHHHhhccccChHHHHHHHHHHHHHHHH
Confidence 3566888888888775444 4478999999999999885
No 25
>PF08542 Rep_fac_C: Replication factor C C-terminal domain; InterPro: IPR013748 Replication factor C (RFC) is a multimeric AAA+ protein complex that loads the DNA polymerase processivity clamp PCNA (Proliferating Cell Nuclear Antigen) onto DNA using ATP to drive the reaction []. PCNA functions at multiple levels in directing DNA metabolic pathways []. When bound to DNA, PCNA organises various proteins involved in DNA replication, DNA repair, DNA modification, and chromatin modelling. Replication factor C consists of five subunits in a spiral arrangement: Rfc1, Rfc2, Rfc3, Rfc4, and Rfc5 subunits. Rfc1 and Rfc2 load the PCNA sliding clamp onto DNA, while Rfc3 binds ATP and also acts as a checkpoint sensor. The RFC complex contains four ATP sites (sites A, B, C, and D) located at subunit interfaces. In each ATP site, an arginine residue from one subunit is located near the gamma-phosphate of ATP bound in the adjacent subunit. These arginine residues act as "arginine fingers" that can potentially perform two functions: sensing that ATP is bound and catalyzing ATP hydrolysis []. This entry represents the core domain found in Rfc1-5.; GO: 0003689 DNA clamp loader activity, 0005524 ATP binding, 0006260 DNA replication, 0005663 DNA replication factor C complex; PDB: 1SXJ_B 2CHG_B 2CHV_F 2CHQ_C 1IQP_A.
Probab=58.90 E-value=35 Score=20.07 Aligned_cols=62 Identities=23% Similarity=0.301 Sum_probs=44.1
Q ss_pred HHHHHHHHHHHHhcChHHHHHHHHHHHHHhhCCCCCCHHHHHHhhchhhhc-cCCHHHHHHHHHHHHHH
Q 042650 8 ERLKELLRERLIECGWRDEMKSLCRAYTRKKGRNNVTVDDLVHVITPKGRA-SVPDPVKAELLQRIRSF 75 (81)
Q Consensus 8 erL~~~L~~rL~e~GW~D~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~-~VP~~vk~Ell~~Ir~f 75 (81)
+.+.+.+..-+. |=.++++..+.+.+.+ | .+..+++..+...... -+|+..|.+++..+-.+
T Consensus 6 ~~i~~i~~~~~~--~~~~~~~~~~~~l~~~-G---~s~~~Il~~l~~~l~~~~~~~~~k~~i~~~la~~ 68 (89)
T PF08542_consen 6 EVIEEILESCLN--GDFKEARKKLYELLVE-G---YSASDILKQLHEVLVESDIPDSQKAEILKILAEI 68 (89)
T ss_dssp HHHHHHHHHHHH--TCHHHHHHHHHHHHHT-T-----HHHHHHHHHHHHHTSTSSHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHh--CCHHHHHHHHHHHHHc-C---CCHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHH
Confidence 345555555544 3456688888888875 4 5899999999998888 55899999999887654
No 26
>PF02631 RecX: RecX family; InterPro: IPR003783 RecX is a putative bacterial regulatory protein []. The gene encoding RecX is found downstream of recA, and it is suggested that the RecX protein might be regulator of RecA activity by interaction with the RecA protein or filament [].; GO: 0006282 regulation of DNA repair; PDB: 3DFG_A 3D5L_B 3C1D_B 3E3V_A.
Probab=58.83 E-value=28 Score=22.02 Aligned_cols=24 Identities=33% Similarity=0.439 Sum_probs=15.3
Q ss_pred hhHHHHHHHHHHHHHhcChHHHHH
Q 042650 5 GEKERLKELLRERLIECGWRDEMK 28 (81)
Q Consensus 5 Ge~erL~~~L~~rL~e~GW~D~vr 28 (81)
|--+..-+..-.+|.++||.|+-+
T Consensus 5 g~~~e~I~~vi~~l~~~gyidD~~ 28 (121)
T PF02631_consen 5 GFSEEAIEEVIDRLKELGYIDDER 28 (121)
T ss_dssp T--HHHHHHHHHHHHHTTSS-HHH
T ss_pred CCCHHHHHHHHHHHHHcCCCCHHH
Confidence 334445566678899999998865
No 27
>PF03693 RHH_2: Uncharacterised protein family (UPF0156); InterPro: IPR022789 This family of proteins are about 80 amino acids in length and their function is unknown. The proteins contain a conserved GRY motif. This family appears to be related to ribbon-helix-helix DNA-binding proteins. ; PDB: 3KXE_C.
Probab=55.90 E-value=12 Score=22.95 Aligned_cols=51 Identities=18% Similarity=0.233 Sum_probs=24.3
Q ss_pred ccchhHHHHHHHHHHHHHh----cChHHHHHHHHHHHHHhhC-CCCCCHHHHHHhhc
Q 042650 2 IESGEKERLKELLRERLIE----CGWRDEMKSLCRAYTRKKG-RNNVTVDDLVHVIT 53 (81)
Q Consensus 2 vesGe~erL~~~L~~rL~e----~GW~D~vr~~~re~i~~~g-~~~v~~~~L~~~i~ 53 (81)
|+||.|.--++.++.-|.- ..+...+|....+-+. .| ....+++++++...
T Consensus 21 V~sG~Y~s~SEvvR~aLRlle~~e~~~~~Lr~~l~~g~~-sG~~~~~~~~~~~~~~~ 76 (80)
T PF03693_consen 21 VASGRYSSASEVVREALRLLEEREAKLEALREALQEGLE-SGESEPFDMDDILARAR 76 (80)
T ss_dssp HCTTS-SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-T-EESS--HHHHHHHCC
T ss_pred HHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-CCCCCCCCHHHHHHHHH
Confidence 6788887666666554431 1233334443333322 24 33467778777654
No 28
>PF14069 SpoVIF: Stage VI sporulation protein F
Probab=55.53 E-value=37 Score=20.98 Aligned_cols=50 Identities=12% Similarity=0.257 Sum_probs=35.6
Q ss_pred HHHHHHHHHHHHhhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHH
Q 042650 25 DEMKSLCRAYTRKKGRNNVTVDDLVHVITPKGRASVPDPVKAELLQRIRS 74 (81)
Q Consensus 25 D~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~~VP~~vk~Ell~~Ir~ 74 (81)
++|..+|...=.+.=-+.-++-+|+..|.-.|..-||++.-.+|.+.|.+
T Consensus 13 ~~i~kLA~sv~~adlqdE~~vR~lIk~vs~~an~~Vs~~~ed~IV~~I~~ 62 (79)
T PF14069_consen 13 EDIFKLANSVQKADLQDEKKVRQLIKQVSQIANKPVSKEQEDQIVQAIIN 62 (79)
T ss_pred HHHHHHHHhcchhhcccHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHh
Confidence 56666665433322123447888999999999999999988888877754
No 29
>smart00513 SAP Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation.
Probab=55.44 E-value=21 Score=18.08 Aligned_cols=15 Identities=40% Similarity=0.490 Sum_probs=11.0
Q ss_pred HHHHHHHHHHHHHHh
Q 042650 62 DPVKAELLQRIRSFL 76 (81)
Q Consensus 62 ~~vk~Ell~~Ir~fL 76 (81)
.-.|.+|..+|.+|+
T Consensus 21 ~G~K~~Lv~Rl~~~~ 35 (35)
T smart00513 21 SGTKAELVDRLLEAL 35 (35)
T ss_pred CCCHHHHHHHHHHhC
Confidence 456888888888774
No 30
>PF13625 Helicase_C_3: Helicase conserved C-terminal domain
Probab=55.39 E-value=27 Score=22.45 Aligned_cols=34 Identities=12% Similarity=0.409 Sum_probs=28.7
Q ss_pred CCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHH
Q 042650 42 NVTVDDLVHVITPKGRASVPDPVKAELLQRIRSF 75 (81)
Q Consensus 42 ~v~~~~L~~~i~P~Ar~~VP~~vk~Ell~~Ir~f 75 (81)
..+.+++++.+.-.++.-||+.|+..|.+-.+.|
T Consensus 54 G~~~e~i~~~L~~~S~~~lP~~v~~~i~~w~~~~ 87 (129)
T PF13625_consen 54 GLTAEEIIEFLERYSKNPLPQNVEQSIEDWARRY 87 (129)
T ss_pred CCCHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhc
Confidence 5699999999999999999999998776655543
No 31
>TIGR02366 DHAK_reg probable dihydroxyacetone kinase regulator. The seed alignment for this family was built from a set of closely related uncharacterized proteins associated with operons for the type of bacterial dihydroxyacetone kinase that transfers PEP-derived phosphate from a phosphoprotein, as in phosphotransferase system transport, rather than from ATP. Members have a TetR transcriptional regulator domain (pfam00440) at the N-terminus and sequence homology throughout.
Probab=54.67 E-value=26 Score=22.87 Aligned_cols=18 Identities=6% Similarity=0.268 Sum_probs=11.5
Q ss_pred HHHHHHHHHHHHHhcChH
Q 042650 7 KERLKELLRERLIECGWR 24 (81)
Q Consensus 7 ~erL~~~L~~rL~e~GW~ 24 (81)
+++|.+-+-+-|.+-|+.
T Consensus 5 k~~I~~a~~~Ll~~k~~~ 22 (176)
T TIGR02366 5 KKKIAKAFKDLMEVQAFS 22 (176)
T ss_pred HHHHHHHHHHHHHHCCCc
Confidence 456666666667776754
No 32
>PRK02363 DNA-directed RNA polymerase subunit delta; Reviewed
Probab=53.85 E-value=53 Score=21.90 Aligned_cols=29 Identities=17% Similarity=0.120 Sum_probs=23.4
Q ss_pred HHHHHHHHHhhCCCCCCHHHHHHhhchhhh
Q 042650 28 KSLCRAYTRKKGRNNVTVDDLVHVITPKGR 57 (81)
Q Consensus 28 r~~~re~i~~~g~~~v~~~~L~~~i~P~Ar 57 (81)
=..|.++++++| ..++|.+|+.+|.....
T Consensus 6 idvAy~iL~~~~-~~m~f~dL~~ev~~~~~ 34 (129)
T PRK02363 6 IEVAYEILKEKK-EPMSFYDLVNEIQKYLG 34 (129)
T ss_pred HHHHHHHHHHcC-CcccHHHHHHHHHHHhC
Confidence 357889998886 78999999999966544
No 33
>PRK09462 fur ferric uptake regulator; Provisional
Probab=53.81 E-value=51 Score=21.61 Aligned_cols=54 Identities=15% Similarity=0.129 Sum_probs=37.5
Q ss_pred HHHHHhcChH-HHHHHHHHHHHHhhCCCCCCHHHHHHhhchhhhccCCHHHHHHH
Q 042650 15 RERLIECGWR-DEMKSLCRAYTRKKGRNNVTVDDLVHVITPKGRASVPDPVKAEL 68 (81)
Q Consensus 15 ~~rL~e~GW~-D~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~~VP~~vk~El 68 (81)
.+.|.+.|.+ ..-|...-+++.+.....+|.++|++.+....-.+=+..|++-|
T Consensus 5 ~~~l~~~glr~T~qR~~Il~~l~~~~~~h~sa~eI~~~l~~~~~~i~~aTVYR~L 59 (148)
T PRK09462 5 NTALKKAGLKVTLPRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVL 59 (148)
T ss_pred HHHHHHcCCCCCHHHHHHHHHHHhCCCCCCCHHHHHHHHHhhCCCCCHHHHHHHH
Confidence 3455666764 66677777888765446899999999997776554456666544
No 34
>PF13026 DUF3887: Protein of unknown function (DUF3887)
Probab=53.77 E-value=57 Score=20.93 Aligned_cols=45 Identities=9% Similarity=0.067 Sum_probs=31.8
Q ss_pred HHHHHHHHHHHHhhCCCCCCHHHHHHhhchhhhccCC-HHHHHHHHHH
Q 042650 25 DEMKSLCRAYTRKKGRNNVTVDDLVHVITPKGRASVP-DPVKAELLQR 71 (81)
Q Consensus 25 D~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~~VP-~~vk~Ell~~ 71 (81)
++|++.|.+.|.--+ .-.|+.+.+...++-.+.+| +.++..+-.-
T Consensus 5 Ekv~~~Aeevi~~~N--~~dy~~v~~~~d~~mk~aL~~e~~~~~~~~~ 50 (101)
T PF13026_consen 5 EKVKQKAEEVIDLLN--EKDYDKVHEKYDEKMKNALTAEELKEKWGPV 50 (101)
T ss_pred HHHHHHHHHHHHHHh--HhhHHHHHHHHhHHHHHhcCHHHHHHHHHHH
Confidence 678888888876532 33788899888888888888 4445544433
No 35
>TIGR03499 FlhF flagellar biosynthetic protein FlhF.
Probab=52.48 E-value=74 Score=23.20 Aligned_cols=69 Identities=19% Similarity=0.217 Sum_probs=37.6
Q ss_pred hhHHHHHHHHHHHHHhcChH--HHHHHHHHHHHHhhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHHh
Q 042650 5 GEKERLKELLRERLIECGWR--DEMKSLCRAYTRKKGRNNVTVDDLVHVITPKGRASVPDPVKAELLQRIRSFL 76 (81)
Q Consensus 5 Ge~erL~~~L~~rL~e~GW~--D~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~~VP~~vk~Ell~~Ir~fL 76 (81)
.|+..|+.+|...+....|. +.......+.+.+.|++.--.++|++++... .=++.+...+...|...|
T Consensus 111 ~e~~~lk~~l~~~~~~~~~~~~~~~l~~l~~~L~~~gv~~~la~~L~~~l~~~---~~~~~~~~~~~~~l~~~l 181 (282)
T TIGR03499 111 KELEALRELLERLLAGLAWLQRDPEGAKLLERLLRAGVSPELARELLEKLPER---ADAEDAWRWLREALEKML 181 (282)
T ss_pred HHHHHHHHHHHHHHHhhhhcccCHHHHHHHHHHHHCCCCHHHHHHHHHHhhcc---CCHHHHHHHHHHHHHHHh
Confidence 46777888887777665552 2222334455666676655566666665431 112334444555554444
No 36
>PF11829 DUF3349: Protein of unknown function (DUF3349); InterPro: IPR021784 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 99 to 124 amino acids in length. ; PDB: 2KVC_A 3OL3_B 3OL4_A 2LKY_A.
Probab=52.16 E-value=35 Score=21.83 Aligned_cols=44 Identities=27% Similarity=0.306 Sum_probs=30.4
Q ss_pred hhHHHHHHHHHHHHHhcChHHHHHHHHHHHHHhhCCCCCCHHHHHHhhc
Q 042650 5 GEKERLKELLRERLIECGWRDEMKSLCRAYTRKKGRNNVTVDDLVHVIT 53 (81)
Q Consensus 5 Ge~erL~~~L~~rL~e~GW~D~vr~~~re~i~~~g~~~v~~~~L~~~i~ 53 (81)
.+|--|-.+|+.+|.+ |+|++.+.+.+...+. .++-.++-..|+
T Consensus 23 ~Dy~PLlALL~r~Ltd----~ev~~Va~~L~~~~~~-~~~~~dI~~~I~ 66 (96)
T PF11829_consen 23 TDYVPLLALLRRRLTD----DEVAEVAAELAARGDP-PVDRIDIGVAIT 66 (96)
T ss_dssp HHHHHHHHHHTTTS-H----HHHHHHHHHHHHHTSS--BSCCHHHHHHH
T ss_pred CccHHHHHHhcccCCH----HHHHHHHHHHHhcCCC-CCCHHHHHHHHH
Confidence 4778889999999997 8999999988876543 234444444443
No 37
>PF08824 Serine_rich: Serine rich protein interaction domain; InterPro: IPR014928 This is a serine rich protein that is found in the docking protein p130(cas) (Crk-associated substrate). The protein folds into a four helix bundle which is associated with protein-protein interactions []. ; PDB: 2L81_A 1Z23_A.
Probab=51.63 E-value=12 Score=26.04 Aligned_cols=44 Identities=27% Similarity=0.468 Sum_probs=24.6
Q ss_pred HHHHHHHhcChHHHHHHHHHHHHHhhCCCCCCHHHHHHhhchhhhccCCHHHHH
Q 042650 13 LLRERLIECGWRDEMKSLCRAYTRKKGRNNVTVDDLVHVITPKGRASVPDPVKA 66 (81)
Q Consensus 13 ~L~~rL~e~GW~D~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~~VP~~vk~ 66 (81)
...+-|..|||-= ..+++. +..+ ..-.+|.++.-- ..||+++|+
T Consensus 98 ~~~q~Ld~~~Wsl--~~La~~--k~~~-~~DdLDrfVmva-----R~vpdD~kq 141 (159)
T PF08824_consen 98 QTSQALDSCNWSL--DVLARD--KPQN-KPDDLDRFVMVA-----RTVPDDAKQ 141 (159)
T ss_dssp HHHHHHHHTTTSH--HHHTT----SS--TCHHHHHHHHHH-----CCHHHHHHH
T ss_pred HHHHHHHcCCCCH--HHHhcC--CCCC-CcchHHHHHHHH-----HhchHHHHH
Confidence 3456899999953 344544 1111 111455555443 789999975
No 38
>PF14766 RPA_interact_N: Replication protein A interacting N-terminal
Probab=51.51 E-value=20 Score=19.53 Aligned_cols=17 Identities=18% Similarity=0.685 Sum_probs=14.9
Q ss_pred ChHHHHHHHHHHHHHhh
Q 042650 22 GWRDEMKSLCRAYTRKK 38 (81)
Q Consensus 22 GW~D~vr~~~re~i~~~ 38 (81)
-|.|.+|+-|.+-+++.
T Consensus 14 ~WKe~lR~rC~~R~r~~ 30 (42)
T PF14766_consen 14 PWKETLRERCLERVRES 30 (42)
T ss_pred cHHHHHHHHHHHHHHHH
Confidence 59999999999999754
No 39
>PF07766 LETM1: LETM1-like protein; InterPro: IPR011685 This is a group of mainly hypothetical eukaryotic proteins. Putative features found in LETM1, such as a transmembrane domain and a CK2 and PKC phosphorylation site [], are relatively conserved throughout the family. Deletion of LETM1 is thought to be involved in the development of Wolf-Hirschhorn syndrome in humans []. A member of this family, P91927 from SWISSPROT, is known to be expressed in the mitochondria of Drosophila melanogaster [], suggesting that this may be a group of mitochondrial proteins.; PDB: 3SKQ_A.
Probab=51.47 E-value=90 Score=22.86 Aligned_cols=61 Identities=23% Similarity=0.287 Sum_probs=37.8
Q ss_pred HHHHHHHHhcChHHHHHHHHHHHHHhhCCCCCCHHHHHHhhchhhhccCCHH-HHHHHHHHHHHHhh
Q 042650 12 ELLRERLIECGWRDEMKSLCRAYTRKKGRNNVTVDDLVHVITPKGRASVPDP-VKAELLQRIRSFLA 77 (81)
Q Consensus 12 ~~L~~rL~e~GW~D~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~~VP~~-vk~Ell~~Ir~fL~ 77 (81)
.+|+.||. .+...++..=+.+.++ |+++.|.++|...-.- |++-|.. -..++......+|+
T Consensus 192 ~~lr~rL~--~~~~~l~~dD~~i~~e-Gv~~Ls~~EL~~Ac~~--RGl~~~~~s~~~lr~~L~~WL~ 253 (268)
T PF07766_consen 192 SLLRRRLR--KRLRYLKQDDRLIKRE-GVDSLSEEELQDACYE--RGLRSTGLSEEELREWLKQWLQ 253 (268)
T ss_dssp HHHHHHHH--HHHHHHHHHHHHHHHH--GGGS-HHHHHHHHHH--TT---TT--HHHHHHHHHHHHH
T ss_pred HHHHHHHH--HHHHHHHHHHHHHHHh-ccccCCHHHHHHHHHH--hCCCcCCCCHHHHHHHHHHHHH
Confidence 34566666 4666677777777776 9999999999987754 4454433 34666677777765
No 40
>PF13797 Post_transc_reg: Post-transcriptional regulator
Probab=50.65 E-value=59 Score=20.17 Aligned_cols=37 Identities=24% Similarity=0.391 Sum_probs=30.0
Q ss_pred ChHHHHHHHHHHHHH---hhCCCCCCHHHHHHhhchhhhc
Q 042650 22 GWRDEMKSLCRAYTR---KKGRNNVTVDDLVHVITPKGRA 58 (81)
Q Consensus 22 GW~D~vr~~~re~i~---~~g~~~v~~~~L~~~i~P~Ar~ 58 (81)
.|+++|+-.|...++ .-|.++||.++|-+-++-+...
T Consensus 4 ~~~~~v~p~l~sK~eEf~~lGY~~vt~~dlw~yl~~~~WK 43 (87)
T PF13797_consen 4 EWREQVEPALQSKAEEFHLLGYESVTEEDLWSYLTEKKWK 43 (87)
T ss_pred HHHHHHHHHHHHHHHHHHHhCcCcCCHHHHHHHHHHHHhc
Confidence 688999998886654 3589999999999999876544
No 41
>TIGR03613 RutR pyrimidine utilization regulatory protein R. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the TetR family of transcriptional regulators defined by the N-teminal model pfam00440 and the C-terminal model pfam08362 (YcdC-like protein, C-terminal region).
Probab=50.35 E-value=33 Score=22.77 Aligned_cols=29 Identities=10% Similarity=0.185 Sum_probs=19.6
Q ss_pred HHHHHHHHHHHHHhhCCCCCCHHHHHHhh
Q 042650 24 RDEMKSLCRAYTRKKGRNNVTVDDLVHVI 52 (81)
Q Consensus 24 ~D~vr~~~re~i~~~g~~~v~~~~L~~~i 52 (81)
++.+-+.+.+.+.++|.+++|+.+|.+..
T Consensus 10 r~~Il~aA~~lf~e~G~~~~s~~~IA~~a 38 (202)
T TIGR03613 10 RKAILSAALDTFSRFGFHGTSLEQIAELA 38 (202)
T ss_pred HHHHHHHHHHHHHHhCcccCCHHHHHHHh
Confidence 44556667777777777777777776543
No 42
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=50.20 E-value=60 Score=21.34 Aligned_cols=27 Identities=26% Similarity=0.426 Sum_probs=16.4
Q ss_pred HHHHHHHHHHhcChHHHHHHHHHHHHHh
Q 042650 10 LKELLRERLIECGWRDEMKSLCRAYTRK 37 (81)
Q Consensus 10 L~~~L~~rL~e~GW~D~vr~~~re~i~~ 37 (81)
.-+..-.+|.++||.|+- ..|...++.
T Consensus 44 ~i~~vl~~l~~~~~ldD~-~~a~~~~~~ 70 (157)
T PRK00117 44 VIEAVLDRLKEEGLLDDE-RFAESFVRS 70 (157)
T ss_pred HHHHHHHHHHHcCCCCHH-HHHHHHHHH
Confidence 334444677888888875 555555533
No 43
>PF10667 DUF2486: Protein of unknown function (DUF2486); InterPro: IPR018924 This family is made up of members from various Burkholderia spp. The function is unknown.
Probab=50.07 E-value=39 Score=25.20 Aligned_cols=42 Identities=19% Similarity=0.275 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHhcChHHHHHHHHHHHHHhhCCCCCCHHHHHHhh
Q 042650 8 ERLKELLRERLIECGWRDEMKSLCRAYTRKKGRNNVTVDDLVHVI 52 (81)
Q Consensus 8 erL~~~L~~rL~e~GW~D~vr~~~re~i~~~g~~~v~~~~L~~~i 52 (81)
+||+.-+...|. .-|++=|...||+.+.++ ...=+++|..+|
T Consensus 179 eRl~~r~~~~l~-gegr~~IEarCR~al~~h--~~~Lv~qitrev 220 (246)
T PF10667_consen 179 ERLRGRVANYLT-GEGRGLIEARCRDALQEH--TAWLVGQITREV 220 (246)
T ss_pred HHHHHHHHHHHc-cccHHHHHHHHHHHHHHH--HHHHHHHHHHHH
Confidence 566666666665 479999999999999876 223344444443
No 44
>PF06744 DUF1215: Protein of unknown function (DUF1215); InterPro: IPR010623 This domain represents a conserved region situated towards the C-terminal end of several hypothetical bacterial proteins of unknown function. A few members resemble the ImcF protein, which has been proposed [] to be involved in Vibrio cholerae cell surface reorganisation that results in increased adherence to epithelial cells line and increased conjugation frequency.
Probab=49.77 E-value=63 Score=20.72 Aligned_cols=56 Identities=16% Similarity=0.296 Sum_probs=38.4
Q ss_pred HHHHHHHHHHHhcChHHHHHHHHHHHHHhh------CCCCCCHHHHHHhhchhhhccCCHHHHHH
Q 042650 9 RLKELLRERLIECGWRDEMKSLCRAYTRKK------GRNNVTVDDLVHVITPKGRASVPDPVKAE 67 (81)
Q Consensus 9 rL~~~L~~rL~e~GW~D~vr~~~re~i~~~------g~~~v~~~~L~~~i~P~Ar~~VP~~vk~E 67 (81)
.+..--+..|. ..|.++|-..|++.|..+ ....++++|+-+-.-|. ..+..=+.+.
T Consensus 26 ~~~~~a~~~ln-~~w~~~V~~~~~~~i~gRYPF~~~s~~dv~l~Df~~fF~p~--G~ld~F~~~~ 87 (125)
T PF06744_consen 26 LVLQGARSYLN-KAWQAEVYPFCRQAIAGRYPFDPDSSRDVSLADFARFFGPG--GVLDQFFNQY 87 (125)
T ss_pred HHHHHHHHHHH-HHHHHHHHHHHHHHhcCCCCCCCCCcccCCHHHHHHHhcCC--CcHHHHHHHH
Confidence 33344444444 489999999999999654 34668999999988887 4454444433
No 45
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
Probab=49.11 E-value=67 Score=25.29 Aligned_cols=60 Identities=15% Similarity=0.203 Sum_probs=47.3
Q ss_pred HHHHHHHHHHHhcChHHHHHHHHHHHHHh---hCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHH
Q 042650 9 RLKELLRERLIECGWRDEMKSLCRAYTRK---KGRNNVTVDDLVHVITPKGRASVPDPVKAELLQRIRS 74 (81)
Q Consensus 9 rL~~~L~~rL~e~GW~D~vr~~~re~i~~---~g~~~v~~~~L~~~i~P~Ar~~VP~~vk~Ell~~Ir~ 74 (81)
-|.+.|..+|.-..+.+..+.+|..+|.. +|-=..+++++...+ -++.+...+++..|+.
T Consensus 77 sL~e~L~~Ql~~~~~~~~~~~ia~~iI~~LD~~GyL~~~~~eia~~l------~~~~~~ve~~l~~iq~ 139 (429)
T TIGR02395 77 SLFEHLLEQLDLQLFTERDRKIALYIIDNLDEDGYLEIDLEEIADEL------EVSEEEVEKVLELIQR 139 (429)
T ss_pred CHHHHHHHHHhccCCCHHHHHHHHHHHHhCCCCCCCCCCHHHHHHHc------CCCHHHHHHHHHHHhc
Confidence 46789999999999999999999998855 454445888888776 2677777788887775
No 46
>PRK14729 miaA tRNA delta(2)-isopentenylpyrophosphate transferase; Provisional
Probab=49.01 E-value=85 Score=23.64 Aligned_cols=47 Identities=21% Similarity=0.310 Sum_probs=27.0
Q ss_pred hHHHHHHHHHHH---HHhcChHHHHHHHHHHHHH-hh-CCCCCCHHHHHHhh
Q 042650 6 EKERLKELLRER---LIECGWRDEMKSLCRAYTR-KK-GRNNVTVDDLVHVI 52 (81)
Q Consensus 6 e~erL~~~L~~r---L~e~GW~D~vr~~~re~i~-~~-g~~~v~~~~L~~~i 52 (81)
+++.|.+-+.+| ..+.||.|+|+.+...-.. .. ....+-|-+++..+
T Consensus 196 ~r~~L~~rI~~Rv~~Ml~~GlieEv~~l~~~~~~~~~~~~~aIGYkE~~~yl 247 (300)
T PRK14729 196 PMEEMKSRIISRVNNMIDCGLLSEIKSLLGKGYNENTPAFKGIGYREFLLWK 247 (300)
T ss_pred CHHHHHHHHHHHHHHHHHCCHHHHHHHHHhcCCCCCCCcceeEcHHHHHHHH
Confidence 445555555444 2467999999988752110 00 12345577777766
No 47
>PRK14828 undecaprenyl pyrophosphate synthase; Provisional
Probab=48.88 E-value=21 Score=26.32 Aligned_cols=35 Identities=26% Similarity=0.299 Sum_probs=26.1
Q ss_pred chhHHHHHHHHHHHHHh------------------cChHHHHHHHHHHHHHhh
Q 042650 4 SGEKERLKELLRERLIE------------------CGWRDEMKSLCRAYTRKK 38 (81)
Q Consensus 4 sGe~erL~~~L~~rL~e------------------~GW~D~vr~~~re~i~~~ 38 (81)
.|+.+.|-+-+++.+.+ .|+++++-+.++.++++.
T Consensus 117 iG~~~~lp~~~~~~~~~~e~~T~~~~~~~Lnia~~Yggr~EI~~A~~~~~~~~ 169 (256)
T PRK14828 117 VGSLDLLPAPSANRLKEAEEATVGNDGIKVNVAVGYGGRQEIVDAVRSLLTEH 169 (256)
T ss_pred ECChhhCCHHHHHHHHHHHHhhcCCCCcEEEEEecCCCHHHHHHHHHHHHHHH
Confidence 46667776776666654 599999999999888653
No 48
>PF13319 DUF4090: Protein of unknown function (DUF4090)
Probab=48.87 E-value=13 Score=23.29 Aligned_cols=14 Identities=50% Similarity=1.080 Sum_probs=12.3
Q ss_pred HHHHHHHHHhcChH
Q 042650 11 KELLRERLIECGWR 24 (81)
Q Consensus 11 ~~~L~~rL~e~GW~ 24 (81)
.+.|+++|.+.||.
T Consensus 61 q~~Lnq~L~~Ag~~ 74 (84)
T PF13319_consen 61 QEELNQRLIDAGWE 74 (84)
T ss_pred HHHHHHHHHHcCcc
Confidence 57899999999995
No 49
>TIGR00511 ribulose_e2b2 ribose-1,5-bisphosphate isomerase, e2b2 family. The delineation of this family was based originally, in part, on a discussion and neighbor-joining phylogenetic study by Kyrpides and Woese of archaeal and other proteins homologous to the alpha, beta, and delta subunits of eukaryotic initiation factor 2B (eIF-2B), a five-subunit molecule that catalyzes GTP recycling for eIF-2. Recently, Sato, et al. assigned the function ribulose-1,5 bisphosphate isomerase.
Probab=47.50 E-value=72 Score=23.80 Aligned_cols=55 Identities=13% Similarity=0.293 Sum_probs=39.1
Q ss_pred hHHHHHHHHHHHHHhhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHHhhh
Q 042650 23 WRDEMKSLCRAYTRKKGRNNVTVDDLVHVITPKGRASVPDPVKAELLQRIRSFLAS 78 (81)
Q Consensus 23 W~D~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~~VP~~vk~Ell~~Ir~fL~~ 78 (81)
..+.++..+....+.+ ...+++...+..+....+..=+++.|+.++..+.+|++.
T Consensus 43 ~~~~l~~~~~~L~~ar-Pt~v~l~nai~~~~~~i~~~~~~~~k~~l~~~~~~~~~e 97 (301)
T TIGR00511 43 FRAEMREAANILISTR-PTAVSLPNAVRYVLKYMSGEDVETLRETVIERADAFINQ 97 (301)
T ss_pred HHHHHHHHHHHHHHcC-CchhhHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHH
Confidence 4456777776655554 466777777777766555544578999999999999865
No 50
>COG2137 OraA Uncharacterized protein conserved in bacteria [General function prediction only]
Probab=47.46 E-value=59 Score=22.71 Aligned_cols=56 Identities=29% Similarity=0.466 Sum_probs=36.2
Q ss_pred HHHHHHHHHhcChHHHHHHHHHHHHHhhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHH
Q 042650 11 KELLRERLIECGWRDEMKSLCRAYTRKKGRNNVTVDDLVHVITPKGRASVPDPVKAELLQ 70 (81)
Q Consensus 11 ~~~L~~rL~e~GW~D~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~~VP~~vk~Ell~ 70 (81)
=+..=.+|.+.||-|+-+ .|...++.+....-..-.|-.++.-++ |++++..+.|.
T Consensus 54 Ie~Vi~~l~~~~~ldD~~-fAe~~i~~r~~~g~G~~rl~qeL~qkG---i~~~~Ie~aL~ 109 (174)
T COG2137 54 IEEVIDRLAEEGYLDDTR-FAEAYIRSRSRKGKGPARLKQELKQKG---IDDEIIEEALE 109 (174)
T ss_pred HHHHHHHHHHcCcccHHH-HHHHHHHHHHhcccChHHHHHHHHHcC---CCHHHHHHHHh
Confidence 344556889999999976 555666655333245666666665554 77777666665
No 51
>COG3343 RpoE DNA-directed RNA polymerase, delta subunit [Transcription]
Probab=47.41 E-value=97 Score=22.00 Aligned_cols=56 Identities=25% Similarity=0.342 Sum_probs=35.8
Q ss_pred HHHHHHHHHHhcChHHHHHHHHHHHHHhhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHH
Q 042650 10 LKELLRERLIECGWRDEMKSLCRAYTRKKGRNNVTVDDLVHVITPKGRASVPDPVKAELLQRIRSF 75 (81)
Q Consensus 10 L~~~L~~rL~e~GW~D~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~~VP~~vk~Ell~~Ir~f 75 (81)
|+.+..+.+.+- .+=..|+.++..+|- .++|++|+.+|.-. -.--+.++-.+|-.|
T Consensus 3 l~~~~~qe~~el----s~IevA~~ile~~~~-~~~F~dii~EI~~~-----~~~s~~ei~~~i~~F 58 (175)
T COG3343 3 LKVLMGQELSEL----SLIEVAHAILEEKKK-PFNFSDIINEIQKL-----LGVSKEEIRSRIGQF 58 (175)
T ss_pred hHHHHHHHHHHH----HHHHHHHHHHHHcCC-CccHHHHHHHHHHH-----hCcCHHHHHHHHHHH
Confidence 555666666653 344568888888884 79999999999332 222344555555444
No 52
>PRK10668 DNA-binding transcriptional repressor AcrR; Provisional
Probab=46.58 E-value=42 Score=22.54 Aligned_cols=27 Identities=7% Similarity=0.197 Sum_probs=15.3
Q ss_pred HHHHHHHHHHHHhhCCCCCCHHHHHHh
Q 042650 25 DEMKSLCRAYTRKKGRNNVTVDDLVHV 51 (81)
Q Consensus 25 D~vr~~~re~i~~~g~~~v~~~~L~~~ 51 (81)
++|-+.+.+.+.++|.+.+|+++|.++
T Consensus 14 ~~Il~AA~~lf~e~G~~~~t~~~Ia~~ 40 (215)
T PRK10668 14 QHILDAALRLFSQQGVSATSLADIAKA 40 (215)
T ss_pred HHHHHHHHHHHHHcCcccCCHHHHHHH
Confidence 344445555666666666666665544
No 53
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=46.19 E-value=92 Score=21.12 Aligned_cols=60 Identities=12% Similarity=0.093 Sum_probs=43.2
Q ss_pred HHHHHHHHHHHHhcChH-HHHHHHHHHHHHhhCCCCCCHHHHHHhhchhhhccCCHHHHHHH
Q 042650 8 ERLKELLRERLIECGWR-DEMKSLCRAYTRKKGRNNVTVDDLVHVITPKGRASVPDPVKAEL 68 (81)
Q Consensus 8 erL~~~L~~rL~e~GW~-D~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~~VP~~vk~El 68 (81)
+.+.+.+.+.|...|.+ ..-|...-+++.+.+ ..+|.++|++.+....-..=...|++-|
T Consensus 7 ~~~~~~~~~~L~~~GlR~T~qR~~IL~~l~~~~-~hlSa~eI~~~L~~~~~~is~aTVYRtL 67 (169)
T PRK11639 7 QELLAQAEKLCAQRNVRLTPQRLEVLRLMSLQP-GAISAYDLLDLLREAEPQAKPPTVYRAL 67 (169)
T ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcC-CCCCHHHHHHHHHhhCCCCCcchHHHHH
Confidence 45566677778888885 677777778887654 6899999999997776544445565544
No 54
>PRK14835 undecaprenyl pyrophosphate synthase; Provisional
Probab=46.18 E-value=31 Score=25.81 Aligned_cols=49 Identities=12% Similarity=0.205 Sum_probs=33.8
Q ss_pred chhHHHHHHHHHHHHH------------------hcChHHHHHHHHHHHHHhhCCCCCCHHHHHHhh
Q 042650 4 SGEKERLKELLRERLI------------------ECGWRDEMKSLCRAYTRKKGRNNVTVDDLVHVI 52 (81)
Q Consensus 4 sGe~erL~~~L~~rL~------------------e~GW~D~vr~~~re~i~~~g~~~v~~~~L~~~i 52 (81)
.|+.+.|-+.++..+. -.|+++++-..++.+++......++.+++.+++
T Consensus 136 iGd~~~Lp~~l~~~i~~~e~~T~~~~~~~Lnia~~Yggr~EI~~A~k~i~~~~~~g~~~~~~i~~~~ 202 (275)
T PRK14835 136 IGRHDGFPPKVLEALEELEERTEGHEGMLLNIAVGYGGREEIVDAVKSLLLEAAATGKSPEEVAAEL 202 (275)
T ss_pred ecChhhCCHHHHHHHHHHHHHhcCCCCeEEEEEeccCCHHHHHHHHHHHHHHHHcCCCChHHhcccC
Confidence 3777777777766664 359999999999999876433455666654444
No 55
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=45.71 E-value=34 Score=18.07 Aligned_cols=24 Identities=17% Similarity=0.243 Sum_probs=19.2
Q ss_pred HHHHHHHHhhCCCCCCHHHHHHhh
Q 042650 29 SLCRAYTRKKGRNNVTVDDLVHVI 52 (81)
Q Consensus 29 ~~~re~i~~~g~~~v~~~~L~~~i 52 (81)
+.+.+.+.+.|...+|++++.++.
T Consensus 3 ~aa~~l~~~~G~~~~s~~~Ia~~~ 26 (47)
T PF00440_consen 3 EAALELFAEKGYEAVSIRDIARRA 26 (47)
T ss_dssp HHHHHHHHHHHTTTSSHHHHHHHH
T ss_pred HHHHHHHHHhCHHhCCHHHHHHHH
Confidence 346677788899999999998765
No 56
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=45.49 E-value=67 Score=21.12 Aligned_cols=29 Identities=21% Similarity=0.381 Sum_probs=14.8
Q ss_pred HHHHHHHHHhcChHHHHHHHHHHHHHhhC
Q 042650 11 KELLRERLIECGWRDEMKSLCRAYTRKKG 39 (81)
Q Consensus 11 ~~~L~~rL~e~GW~D~vr~~~re~i~~~g 39 (81)
...|+++|.+-|.-+++-+.+-+.+.+.|
T Consensus 28 ~~el~~kL~~kg~~~~~i~~vl~~l~~~~ 56 (157)
T PRK00117 28 RAELRRKLAAKGFSEEVIEAVLDRLKEEG 56 (157)
T ss_pred HHHHHHHHHhcCCCHHHHHHHHHHHHHcC
Confidence 34455555555555555555555554444
No 57
>cd08337 DED_c-FLIP_repeat1 Death Effector Domain, repeat 1, of cellular FLICE-Inhibitory Protein. Death Effector Domain (DED), repeat 1, similar to that found in FLICE-inhibitory protein (c-FLIP/CASH, also known as Casper/iFLICE/FLAME-1/CLARP/MRIT/usurpin). c-FLIP is a catalytically inactive homolog of the initator procaspases-8 and -10. It negatively influences apoptotic signaling by interfering with the efficient formation of the Death Inducing Signalling Complex (DISC). At low levels, c-FLIP has been shown to enhance apoptotic signaling by allosterically activating caspase-8. As a modulator of the initiator caspases, c-FLIP regulates life and death in various types of cells and tissues. All members contain two N-terminal DEDs and a C-terminal pseudo-caspase domain. DEDs comprise a subfamily of the Death Domain (DD) superfamily. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association
Probab=45.22 E-value=32 Score=21.25 Aligned_cols=48 Identities=25% Similarity=0.399 Sum_probs=36.0
Q ss_pred HHHHHHHHHHHHHhhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHH
Q 042650 24 RDEMKSLCRAYTRKKGRNNVTVDDLVHVITPKGRASVPDPVKAELLQRIRSF 75 (81)
Q Consensus 24 ~D~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~~VP~~vk~Ell~~Ir~f 75 (81)
.+-++=+|+..+..+... ++.+++..+. .+++++.+.-.|++-+|+.|
T Consensus 18 ~e~L~FLC~D~ip~~~~e--~~~~l~~~L~--e~~~L~~~~L~ELLy~i~R~ 65 (80)
T cd08337 18 DELLLFLCRDAAPDCTTA--QLRDLLRALN--ERGKLTLAALAELLYRVKRF 65 (80)
T ss_pred HHHHHHHcccccccccch--hHHHHHHHHH--HcCCCCHHHHHHHHHHHhHH
Confidence 455667788888766444 4558887764 47788888999999999876
No 58
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=45.11 E-value=90 Score=20.70 Aligned_cols=57 Identities=19% Similarity=0.192 Sum_probs=42.8
Q ss_pred HHHHHHHHHhcChH-HHHHHHHHHHHHhhCCCCCCHHHHHHhhchhhhccCCHHHHHHH
Q 042650 11 KELLRERLIECGWR-DEMKSLCRAYTRKKGRNNVTVDDLVHVITPKGRASVPDPVKAEL 68 (81)
Q Consensus 11 ~~~L~~rL~e~GW~-D~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~~VP~~vk~El 68 (81)
...+..+|.+-|++ ..=|...-+++.+.+ +.+|.++|+..+....-.+=|..|++-|
T Consensus 5 ~~~~~~~lk~~glr~T~qR~~vl~~L~~~~-~~~sAeei~~~l~~~~p~islaTVYr~L 62 (145)
T COG0735 5 LEDAIERLKEAGLRLTPQRLAVLELLLEAD-GHLSAEELYEELREEGPGISLATVYRTL 62 (145)
T ss_pred HHHHHHHHHHcCCCcCHHHHHHHHHHHhcC-CCCCHHHHHHHHHHhCCCCCHhHHHHHH
Confidence 34566788888884 556666777777664 4499999999998877777788888765
No 59
>PRK14135 recX recombination regulator RecX; Provisional
Probab=44.80 E-value=62 Score=23.11 Aligned_cols=55 Identities=18% Similarity=0.253 Sum_probs=28.9
Q ss_pred HHHHHHHHhcChHHHHHHHHHHHHHhhC-CCCCCHHHHHHhhchhhhccCCHHHHHHHHH
Q 042650 12 ELLRERLIECGWRDEMKSLCRAYTRKKG-RNNVTVDDLVHVITPKGRASVPDPVKAELLQ 70 (81)
Q Consensus 12 ~~L~~rL~e~GW~D~vr~~~re~i~~~g-~~~v~~~~L~~~i~P~Ar~~VP~~vk~Ell~ 70 (81)
+..-.+|.+.||.|+ ...|+..++..- ...-+...|..++..+ -||+++..+.+.
T Consensus 92 e~vl~~l~~~~~ldD-~~~a~~~~~~~~~~~~~g~~~I~~kL~~k---Gi~~~~Ie~~l~ 147 (263)
T PRK14135 92 SEVIDKLKEEKYIDD-KEYAESYVRTNINTGDKGPRVIKQKLLQK---GIEDEIIEEALS 147 (263)
T ss_pred HHHHHHHHHcCCCCH-HHHHHHHHHHHHhccccchHHHHHHHHHc---CCCHHHHHHHHH
Confidence 344467888898888 666666665431 0112444444444332 244444444444
No 60
>PF14377 DUF4414: Domain of unknown function (DUF4414)
Probab=44.48 E-value=27 Score=22.18 Aligned_cols=28 Identities=25% Similarity=0.306 Sum_probs=23.3
Q ss_pred HHhhchhhhccCCHHHHHHHHHHHHHHh
Q 042650 49 VHVITPKGRASVPDPVKAELLQRIRSFL 76 (81)
Q Consensus 49 ~~~i~P~Ar~~VP~~vk~Ell~~Ir~fL 76 (81)
-..|-|.-.+.+|++++.|++..-+..-
T Consensus 42 ~~~I~pefL~ALP~diR~EVl~qe~~~~ 69 (108)
T PF14377_consen 42 PSQIDPEFLAALPPDIREEVLAQERRER 69 (108)
T ss_pred ccccCHHHHHhCCHHHHHHHHHHHHHHH
Confidence 4567788889999999999999887654
No 61
>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily. Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.
Probab=43.67 E-value=1.1e+02 Score=21.26 Aligned_cols=66 Identities=18% Similarity=0.207 Sum_probs=38.5
Q ss_pred HHHHHHHHHHHHhcChHHH--HH-HHHHHHHHhhCCCCCCHHHHHHhhchhh----hccCCHHHHHHHHHHHH
Q 042650 8 ERLKELLRERLIECGWRDE--MK-SLCRAYTRKKGRNNVTVDDLVHVITPKG----RASVPDPVKAELLQRIR 73 (81)
Q Consensus 8 erL~~~L~~rL~e~GW~D~--vr-~~~re~i~~~g~~~v~~~~L~~~i~P~A----r~~VP~~vk~Ell~~Ir 73 (81)
+.+.+++..+|..+|+.+. +. ..+..+.+..|...-.+..+...+.-.| ...|..++-.+.+..|+
T Consensus 195 ~e~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~~~~a~~~~~~~i~~~~v~~~~~~~~ 267 (269)
T TIGR03015 195 EETREYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGIPRLINILCDRLLLSAFLEEKREIGGEEVREVIAEID 267 (269)
T ss_pred HHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCcccHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhh
Confidence 5677888888888887422 22 3333333333433445666666664443 55677777777766664
No 62
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=43.27 E-value=47 Score=22.19 Aligned_cols=24 Identities=21% Similarity=0.279 Sum_probs=11.1
Q ss_pred HHHHHHHHHHhhCCCCCCHHHHHH
Q 042650 27 MKSLCRAYTRKKGRNNVTVDDLVH 50 (81)
Q Consensus 27 vr~~~re~i~~~g~~~v~~~~L~~ 50 (81)
+-+.+.+.+.++|.+.+|++++.+
T Consensus 16 Il~aa~~lf~~~G~~~~ti~~Ia~ 39 (213)
T PRK09975 16 LIETAIAQFALRGVSNTTLNDIAD 39 (213)
T ss_pred HHHHHHHHHHHcCcccCCHHHHHH
Confidence 333444444445554555444443
No 63
>PF01715 IPPT: IPP transferase; InterPro: IPR002627 tRNA isopentenyltransferases 2.5.1.8 from EC also known as tRNA delta(2)-isopentenylpyrophosphate transferases or IPP transferases. These enzymes modify both cytoplasmic and mitochondrial tRNAs at A(37) to give isopentenyl A(37) [].; GO: 0005524 ATP binding, 0008033 tRNA processing; PDB: 2ZXU_A 3FOZ_A 2ZM5_B 3D3Q_A 3EXA_B 2QGN_A 3A8T_A 3EPK_B 3EPH_A 3EPJ_A ....
Probab=43.22 E-value=89 Score=22.65 Aligned_cols=66 Identities=14% Similarity=0.259 Sum_probs=36.8
Q ss_pred HHHHHHHHHHHH---HhcChHHHHHHHHHHHHHhh--CCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHH
Q 042650 7 KERLKELLRERL---IECGWRDEMKSLCRAYTRKK--GRNNVTVDDLVHVITPKGRASVPDPVKAELLQRIRSF 75 (81)
Q Consensus 7 ~erL~~~L~~rL---~e~GW~D~vr~~~re~i~~~--g~~~v~~~~L~~~i~P~Ar~~VP~~vk~Ell~~Ir~f 75 (81)
++.|.+-+..|. .+.||.|+|+.+........ ....+-|.++++.+.- ..--++....+....|.|
T Consensus 163 r~~L~~RI~~Rvd~Ml~~GlleEv~~L~~~~~~~~~~~~~aIGYkE~~~~l~g---~~~~~e~~e~i~~~Trqy 233 (253)
T PF01715_consen 163 REELYERINKRVDEMLEQGLLEEVRALLERGLPPDLPAMQAIGYKEFIDYLEG---EISLEEAIERIKTNTRQY 233 (253)
T ss_dssp HHHHHHHHHHHHHHHHHTTHHHHHHHHHHTTGGTTSCGGGSTTHHHHHHHHTT---SSCHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHhHHHHHHHHHHHcCCCCcchhceeeehHHHHHhhcC---CCCHHHHHHHHHHHHHHH
Confidence 444444444443 34699999999887653221 1345678888777744 111334444444444444
No 64
>TIGR03384 betaine_BetI transcriptional repressor BetI. BetI is a DNA-binding transcriptional repressor of the bet (betaine) regulon. In sequence, it is related to TetR (pfam00440). Choline, through BetI, induces the expression of the betaine biosynthesis genes betA and betB by derepression. The choline porter gene betT is also part of this regulon in Escherichia coli. Note that a different transcriptional regulator, ArcA, controls the expression of bet regulon genes in response to oxygen, as BetA is an oxygen-dependent enzyme.
Probab=42.77 E-value=49 Score=21.44 Aligned_cols=29 Identities=17% Similarity=0.248 Sum_probs=19.9
Q ss_pred HHHHHHHHHHHHHhhCCCCCCHHHHHHhh
Q 042650 24 RDEMKSLCRAYTRKKGRNNVTVDDLVHVI 52 (81)
Q Consensus 24 ~D~vr~~~re~i~~~g~~~v~~~~L~~~i 52 (81)
++.+-+.|.+.+.++|..++|++++.++.
T Consensus 10 r~~Il~aA~~lf~~~G~~~~s~~~IA~~a 38 (189)
T TIGR03384 10 RAELIDATIESIGERGSLDVTIAQIARRA 38 (189)
T ss_pred HHHHHHHHHHHHHhcCcccCCHHHHHHHh
Confidence 35566667777777777777777776543
No 65
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=42.15 E-value=93 Score=24.71 Aligned_cols=60 Identities=15% Similarity=0.238 Sum_probs=47.3
Q ss_pred HHHHHHHHHHHhcChHHHHHHHHHHHHHh---hCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHH
Q 042650 9 RLKELLRERLIECGWRDEMKSLCRAYTRK---KGRNNVTVDDLVHVITPKGRASVPDPVKAELLQRIRS 74 (81)
Q Consensus 9 rL~~~L~~rL~e~GW~D~vr~~~re~i~~---~g~~~v~~~~L~~~i~P~Ar~~VP~~vk~Ell~~Ir~ 74 (81)
-|.+.|..+|..+.+.+..+.+|..+|.. +|-=..+++++.... -++.+.-..++..|+.
T Consensus 102 sL~e~L~~Ql~~~~l~~~~~~ia~~iI~~LD~~GyL~~~~~eia~~l------~~~~~~v~~~l~~lQ~ 164 (455)
T PRK05932 102 SLQDHLLEQIELTPFSETDRAIATYIIDALDDEGYLTEDLEEIAESL------GVELDEVEAVLKRIQS 164 (455)
T ss_pred CHHHHHHHHHcccCCCHHHHHHHHHHHHhCCCCCCCCCCHHHHHHHc------CCCHHHHHHHHHHHhc
Confidence 68899999999999999999999988854 454445888887776 2677777777777766
No 66
>COG1890 RPS1A Ribosomal protein S3AE [Translation, ribosomal structure and biogenesis]
Probab=42.10 E-value=45 Score=24.38 Aligned_cols=37 Identities=11% Similarity=0.371 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHHhhCCCCCCHHHHHHhhchhhhccCCHHHH
Q 042650 25 DEMKSLCRAYTRKKGRNNVTVDDLVHVITPKGRASVPDPVK 65 (81)
Q Consensus 25 D~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~~VP~~vk 65 (81)
-.+|+.-.++|.+.+ ...+|++++.++.| +.++.++.
T Consensus 136 ~aIRk~M~eii~~~a-~e~~f~~fv~~li~---g~i~~~I~ 172 (214)
T COG1890 136 RAIRKIMFEIIEEKA-SELTFEEFVQELIP---GRIAAEIE 172 (214)
T ss_pred HHHHHHHHHHHHHHh-ccCCHHHHHHHHhh---hhHHHHHH
Confidence 356777778888776 56799999998877 44444443
No 67
>PF06504 RepC: Replication protein C (RepC); InterPro: IPR010522 This family consists of several bacterial replication protein C (RepC) sequences.
Probab=42.00 E-value=23 Score=26.80 Aligned_cols=51 Identities=33% Similarity=0.522 Sum_probs=36.4
Q ss_pred HHHHHHHHhcChHHHHHHHHHHHHHhhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHHhhh
Q 042650 12 ELLRERLIECGWRDEMKSLCRAYTRKKGRNNVTVDDLVHVITPKGRASVPDPVKAELLQRIRSFLAS 78 (81)
Q Consensus 12 ~~L~~rL~e~GW~D~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~~VP~~vk~Ell~~Ir~fL~~ 78 (81)
.+|+++| |||.+--+ ...|++|.|...|=|.+ .=|+.+|+ =.++||.+|..
T Consensus 207 rllH~rL--c~wi~pGk-----------s~~v~LDTL~~~VW~~~--a~~~~~Rk-RR~~lR~AL~E 257 (281)
T PF06504_consen 207 RLLHQRL--CGWIDPGK-----------SRPVGLDTLCSYVWGDE--ASGSAMRK-RRQRLRKALAE 257 (281)
T ss_pred HHHHHHH--HcCCCCCc-----------CCccchhhhhhhcCCCC--CChHHHHH-HHHHHHHHHHH
Confidence 4566666 57766433 35789999999999977 34555554 44889999865
No 68
>PF06771 Desmo_N: Viral Desmoplakin N-terminus; InterPro: IPR009615 This entry represents the N terminus of viral desmoplakin. Desmoplakin is a component of mature desmosomes, which are the main adhesive junctions in epithelia and cardiac muscle. Desmoplakin is also essential for the maturation of adherens junctions []. Note that many family members are hypothetical.
Probab=41.49 E-value=20 Score=22.66 Aligned_cols=36 Identities=25% Similarity=0.409 Sum_probs=29.2
Q ss_pred CCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHHhh
Q 042650 42 NVTVDDLVHVITPKGRASVPDPVKAELLQRIRSFLA 77 (81)
Q Consensus 42 ~v~~~~L~~~i~P~Ar~~VP~~vk~Ell~~Ir~fL~ 77 (81)
.-||..|+.-|.-+....--.+-+.+.+++||..+-
T Consensus 9 ~~TV~nLl~TIns~s~~~k~~~~~~d~~~rIr~II~ 44 (86)
T PF06771_consen 9 PHTVHNLLKTINSMSQRCKTQSSTEDFLRRIRSIIL 44 (86)
T ss_pred HHHHHHHHHHHHHHhHHhhccccchhHHHHHHHHHh
Confidence 336889999998888777777888899999998774
No 69
>PLN02152 indole-3-acetate beta-glucosyltransferase
Probab=41.40 E-value=41 Score=26.59 Aligned_cols=47 Identities=19% Similarity=0.314 Sum_probs=32.7
Q ss_pred hHHHHHHHHHHHHHhcC--hHHHH---HHHHHHHHHhhCCCCCCHHHHHHhh
Q 042650 6 EKERLKELLRERLIECG--WRDEM---KSLCRAYTRKKGRNNVTVDDLVHVI 52 (81)
Q Consensus 6 e~erL~~~L~~rL~e~G--W~D~v---r~~~re~i~~~g~~~v~~~~L~~~i 52 (81)
+.+.|.+.+++-+.+.| .+.++ +..+++.+...|....++++++++|
T Consensus 403 ~~e~l~~av~~vm~~~~~~~r~~a~~~~~~~~~a~~~ggsS~~nl~~li~~i 454 (455)
T PLN02152 403 ERGEIRRCLEAVMEEKSVELRESAEKWKRLAIEAGGEGGSSDKNVEAFVKTL 454 (455)
T ss_pred cHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHh
Confidence 57788888888886544 44444 6666666666676666888888776
No 70
>cd00280 TRFH Telomeric Repeat binding Factor or TTAGGG Repeat binding Factor, central (dimerization) domain Homology; TRFH. Telomeres are protein/DNA complexes that make up the physical ends of eukaryotic linear chromosomes and are essential for chromosome stability, protecting the chromosome ends from degradation and end-to-end fusion. Proteins TRF1, TRF2 and Taz1 bind telomeric DNA and are also involved in recruiting interacting proteins, TIN2, and Rap1, to the telomeres. It has also been demonstrated that PARP1 associates with TRF2 and is capable of poly(ADP-ribosyl)ation of TRF2, which affects binding of TRF2 to telomeric DNA. TRF1, TRF2 and Taz1 proteins contain three functional domains: an N-terminal acidic domain, a central TRF-specific/dimerization domain, and a C-terminal DNA binding domain with a single Myb-like repeat. Homodimerization, a prerequisite to DNA binding, results in the juxtaposition of two Myb DNA binding domains.
Probab=41.30 E-value=68 Score=23.24 Aligned_cols=60 Identities=15% Similarity=0.243 Sum_probs=29.5
Q ss_pred cchhHHHHHHHHHHHHHhcChHHHHHHHHHHHHHhhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHHhhh
Q 042650 3 ESGEKERLKELLRERLIECGWRDEMKSLCRAYTRKKGRNNVTVDDLVHVITPKGRASVPDPVKAELLQRIRSFLAS 78 (81)
Q Consensus 3 esGe~erL~~~L~~rL~e~GW~D~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~~VP~~vk~Ell~~Ir~fL~~ 78 (81)
++|+++.=.+.|..-..+.|=... |..--.+|++++. +...+-.-....++++|..|++.
T Consensus 123 ~~g~Fk~A~eiLkr~~~d~~~~~~-r~kL~~II~~Kd~---------------~h~~lqnFSy~~~~~ki~~~ve~ 182 (200)
T cd00280 123 ENGEFKKAEEVLKRLFSDPESQKL-RMKLLMIIREKDP---------------AHPVLQNFSYSHFMQKMKSYVEL 182 (200)
T ss_pred hcCchHHHHHHHHHHhcCCCchhH-HHHHHHHHHcccc---------------ccHHHHhccHHHHHHHHHHHHHH
Confidence 455555544444444444444333 4444445554431 12223334566777777777754
No 71
>PF08513 LisH: LisH; InterPro: IPR013720 The LisH motif is found in a large number of eukaryotic proteins, from metazoa, fungi and plants that have a wide range of functions. The recently solved structure of the LisH domain in the N-terminal region of LIS1 depicted it as a novel dimerization motif, and that other structural elements are likely to play an important role in dimerisation [, , ]. The LisH (lis homology) domain mediates protein dimerisation and tetramerisation. The LisH domain is found in Sif2, a component of the Set3 complex which is responsible for repressing meiotic genes. It has been shown that the LisH domain helps mediate interaction with components of the Set3 complex []. ; PDB: 2XTE_L 2XTC_B 2XTD_A 1UUJ_B.
Probab=40.85 E-value=46 Score=16.09 Aligned_cols=26 Identities=27% Similarity=0.643 Sum_probs=20.4
Q ss_pred HHHHHHHHHHHHhcChHHHHHHHHHH
Q 042650 8 ERLKELLRERLIECGWRDEMKSLCRA 33 (81)
Q Consensus 8 erL~~~L~~rL~e~GW~D~vr~~~re 33 (81)
+.|..++..=|.++|-.+--+..++|
T Consensus 1 ~~Ln~lI~~YL~~~Gy~~tA~~f~~E 26 (27)
T PF08513_consen 1 EELNQLIYDYLVENGYKETAKAFAKE 26 (27)
T ss_dssp HHHHHHHHHHHHHCT-HHHHHHHHHH
T ss_pred CHHHHHHHHHHHHCCcHHHHHHHHhc
Confidence 46788889999999999888877765
No 72
>PF04380 BMFP: Membrane fusogenic activity; InterPro: IPR007475 BMFP consists of two structural domains, a coiled-coil C-terminal domain via which the protein self-associates as a trimer, and an N-terminal domain disordered at neutral pH but adopting an amphipathic alpha-helical structure in the presence of phospholipid vesicles, high ionic strength, acidic pH or SDS. BMFP interacts with phospholipid vesicles though the predicted amphipathic alpha-helix induced in the N-terminal half of the protein and promotes aggregation and fusion of vesicles in vitro.
Probab=40.52 E-value=41 Score=20.35 Aligned_cols=22 Identities=27% Similarity=0.433 Sum_probs=11.9
Q ss_pred hccCC--HHHHHHHHHHHHHHhhh
Q 042650 57 RASVP--DPVKAELLQRIRSFLAS 78 (81)
Q Consensus 57 r~~VP--~~vk~Ell~~Ir~fL~~ 78 (81)
.+.+| ...+.|+-..||+-+++
T Consensus 16 ~~~~~~~~~~~~e~e~~~r~~l~~ 39 (79)
T PF04380_consen 16 SEALPAAQGPREEIEKNIRARLQS 39 (79)
T ss_pred HHHHHhhhhhHHHHHHHHHHHHHH
Confidence 44444 55666666666555543
No 73
>TIGR02945 SUF_assoc FeS assembly SUF system protein. Members of this family belong to the broader Pfam family pfam01883, or Domain of Unknown Function DUF59. Many members of DUF59 are candidate ring hydroxylating complex subunits. However, members of the narrower family defined here all are found in genomes that carry the FeS assembly SUF system. For 70 % of these species, the member of this protein family is found as part of the SUF locus, usually immediately downstream of the sufS gene.
Probab=39.95 E-value=11 Score=23.12 Aligned_cols=47 Identities=21% Similarity=0.268 Sum_probs=30.2
Q ss_pred hcChHHHHHHHHHHHHHh-hCCCCCCHHHHHHhhchhhhccCCHHHHHHH
Q 042650 20 ECGWRDEMKSLCRAYTRK-KGRNNVTVDDLVHVITPKGRASVPDPVKAEL 68 (81)
Q Consensus 20 e~GW~D~vr~~~re~i~~-~g~~~v~~~~L~~~i~P~Ar~~VP~~vk~El 68 (81)
-|++.+.+++.+++.+.. .|..++++. +..-.|-.-+++.++.|.+|
T Consensus 49 ~~~~~~~l~~~i~~al~~l~gv~~v~v~--i~~~~~~~~~~~~~~~~~~~ 96 (99)
T TIGR02945 49 NCPVAGSMPGEVENAVRAVPGVGSVTVE--LVWDPPWTPERMSEEARLEL 96 (99)
T ss_pred CCChHHHHHHHHHHHHHhCCCCceEEEE--EEeeCCCChHHCCHHHHHHc
Confidence 367889999999998876 365555432 12333555566677776654
No 74
>PF02854 MIF4G: MIF4G domain; InterPro: IPR003890 This entry represents an MIF4G-like domain. MIF4G domains share a common structure but can differ in sequence. This entry is designated "type 3", and is found in nuclear cap-binding proteins, eIF4G, and UPF2. The MIF4G domain is a structural motif with an ARM (Armadillo) repeat-type fold, consisting of a 2-layer alpha/alpha right-handed superhelix. Proteins usually contain two or more structurally similar MIF4G domains connected by unstructured linkers. MIF4G domains are found in several proteins involved in RNA metabolism, including eIF4G (eukaryotic initiation factor 4-gamma), eIF-2b (translation initiation factor), UPF2 (regulator of nonsense transcripts 2), and nuclear cap-binding proteins (CBP80, CBC1, NCBP1), although the sequence identity between them may be low []. The nuclear cap-binding complex (CBC) is a heterodimer. Human CBC consists of a large CBP80 subunit and a small CBP20 subunit, the latter being critical for cap binding. CBP80 contains three MIF4G domains connected with long linkers, while CBP20 has an RNP (ribonucleoprotein)-type domain that associates with domains 2 and 3 of CBP80 []. The complex binds to 5'-cap of eukaryotic RNA polymerase II transcripts, such as mRNA and U snRNA. The binding is important for several mRNA nuclear maturation steps and for nonsense-mediated decay. It is also essential for nuclear export of U snRNAs in metazoans []. Eukaryotic translation initiation factor 4 gamma (eIF4G) plays a critical role in protein expression, and is at the centre of a complex regulatory network. Together with the cap-binding protein eIF4E, it recruits the small ribosomal subunit to the 5'-end of mRNA and promotes the assembly of a functional translation initiation complex, which scans along the mRNA to the translation start codon. The activity of eIF4G in translation initiation could be regulated through intra- and inter-protein interactions involving the ARM repeats []. In eIF4G, the MIF4G domain binds eIF4A, eIF3, RNA and DNA. Nonsense-mediated mRNA decay (NMD) in eukaryotes involves UPF1, UPF2 and UPF3 to accelerate the decay rate of two unique classes of transcripts: (1) nonsense mRNAs that arise through errors in gene expression, and (2) naturally occurring transcripts that lack coding errors but have built-in features that target them for accelerated decay (error-free mRNAs). NMD can trigger decay during any round of translation and can target CBC-bound or eIF-4E-bound transcripts []. UPF2 contains MIF4G domains, while UPF3 contains an RNP domain []. ; GO: 0005515 protein binding, 0016070 RNA metabolic process; PDB: 3FEY_A 3FEX_A 1H6K_C 1H2V_C 1H2U_A 1H2T_C 1N54_A 1N52_A 1HU3_A 3RK6_A ....
Probab=39.92 E-value=1e+02 Score=19.93 Aligned_cols=72 Identities=13% Similarity=0.115 Sum_probs=46.1
Q ss_pred chhHHHHHHHHHHHHHhcChHH-HHHHHHHHHHHhhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHHhhh
Q 042650 4 SGEKERLKELLRERLIECGWRD-EMKSLCRAYTRKKGRNNVTVDDLVHVITPKGRASVPDPVKAELLQRIRSFLAS 78 (81)
Q Consensus 4 sGe~erL~~~L~~rL~e~GW~D-~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~~VP~~vk~Ell~~Ir~fL~~ 78 (81)
.++.+.+.+.|..-...+ .. .+...++-++. .-....++-.+++.+.-.-....|..+...++.++...+..
T Consensus 13 ~~n~~~~~~~l~~~~~~~--~~~~~~~i~~~i~~-~a~~~~~~~~~~a~l~~~l~~~~~~~f~~~ll~~~~~~f~~ 85 (209)
T PF02854_consen 13 PSNFESIIDELIKLNWSD--DPETLKEIVKLIFE-KAVEEPNFSPLYARLCAALNSRFPSEFRSLLLNRCQEEFEE 85 (209)
T ss_dssp STTHHHHHHHHHHHHHHS--CHHHHHHHHHHHHH-HHHHSGGGHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHhhc--cHHHHHHHHHHHhh-hhhcCchHHHHHHHHHHHHhccchhhHHHHHHHHHHHHHHH
Confidence 456666666665555544 22 34444444443 22234477788888888888888888888888888776654
No 75
>COG0020 UppS Undecaprenyl pyrophosphate synthase [Lipid metabolism]
Probab=39.89 E-value=36 Score=25.06 Aligned_cols=39 Identities=15% Similarity=0.214 Sum_probs=28.0
Q ss_pred hcChHHHHHHHHHHHHHhhCCCCCCHHHHHHhhchhhhc
Q 042650 20 ECGWRDEMKSLCRAYTRKKGRNNVTVDDLVHVITPKGRA 58 (81)
Q Consensus 20 e~GW~D~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~ 58 (81)
-.|+++++-+.+|.++..--...++.+++-+++..+-..
T Consensus 143 nYGGR~eI~~avr~ia~~v~~g~l~~~~I~e~~i~~~L~ 181 (245)
T COG0020 143 NYGGRDEIVDAVRKIAEDVAAGKLSPEDIDEELISSHLY 181 (245)
T ss_pred CCCCHHHHHHHHHHHHHHHHcCCCChHHcCHHHHHHhhc
Confidence 359999999999999977644456666666666554433
No 76
>PRK15008 HTH-type transcriptional regulator RutR; Provisional
Probab=39.88 E-value=60 Score=22.04 Aligned_cols=28 Identities=7% Similarity=0.143 Sum_probs=14.6
Q ss_pred HHHHHHHHHHHHHhhCCCCCCHHHHHHh
Q 042650 24 RDEMKSLCRAYTRKKGRNNVTVDDLVHV 51 (81)
Q Consensus 24 ~D~vr~~~re~i~~~g~~~v~~~~L~~~ 51 (81)
++.+-+.+.+.+.++|.+++|+++|.+.
T Consensus 20 r~~IL~AA~~lf~e~Gy~~~s~~dIA~~ 47 (212)
T PRK15008 20 KKAILSAALDTFSQFGFHGTRLEQIAEL 47 (212)
T ss_pred HHHHHHHHHHHHHHhCcccCCHHHHHHH
Confidence 3444455555555555555555555443
No 77
>PF05234 UAF_Rrn10: UAF complex subunit Rrn10; InterPro: IPR022793 The protein Rrn10 has been identified as a component of the Upstream Activating Factor (UAF), an RNA polymerase I (pol I) specific transcription stimulatory factor [].
Probab=39.62 E-value=44 Score=22.36 Aligned_cols=29 Identities=14% Similarity=0.297 Sum_probs=24.6
Q ss_pred HHHHHHHHHHHhhCCCCCCHHHHHHhhch
Q 042650 26 EMKSLCRAYTRKKGRNNVTVDDLVHVITP 54 (81)
Q Consensus 26 ~vr~~~re~i~~~g~~~v~~~~L~~~i~P 54 (81)
.|...|.+.|++.|...++-++++++-.+
T Consensus 4 nvyeacsdLI~~~g~~~vsaDEvL~~k~~ 32 (120)
T PF05234_consen 4 NVYEACSDLIKEFGTHVVSADEVLAEKID 32 (120)
T ss_pred cHHHHHHHHHHhcCCcccCHHHHHHHhcC
Confidence 58899999999998778999999986544
No 78
>TIGR03181 PDH_E1_alph_x pyruvate dehydrogenase E1 component, alpha subunit. Members of this protein family are the alpha subunit of the E1 component of pyruvate dehydrogenase (PDH). This model represents one branch of a larger family that E1-alpha proteins from 2-oxoisovalerate dehydrogenase, acetoin dehydrogenase, another PDH clade, etc.
Probab=39.32 E-value=1.5e+02 Score=22.39 Aligned_cols=53 Identities=17% Similarity=0.202 Sum_probs=34.5
Q ss_pred HHHHHHHHhcChH-----HHHHHHHHHHHHh-----hCCCCCCHHHHHHhhchhhhccCCHHHHHHH
Q 042650 12 ELLRERLIECGWR-----DEMKSLCRAYTRK-----KGRNNVTVDDLVHVITPKGRASVPDPVKAEL 68 (81)
Q Consensus 12 ~~L~~rL~e~GW~-----D~vr~~~re~i~~-----~g~~~v~~~~L~~~i~P~Ar~~VP~~vk~El 68 (81)
..++++|.+.||. +.+++.+++.+.+ .....++.++++..|... .|+.++.++
T Consensus 276 ~~~~~~L~~~g~~~~~e~~~i~~~~~~~v~~a~~~a~~~p~P~~~~~~~~vy~~----~~~~~~~~~ 338 (341)
T TIGR03181 276 LRLRKYLERKGLWDEEQEEALEEEAEAEVAEAVAEALALPPPPVDDIFDHVYAE----LPPELEEQR 338 (341)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHhhcccC----CCHHHHHHH
Confidence 4577888888862 2233333333321 245778999999999763 888887765
No 79
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=38.94 E-value=1.1e+02 Score=24.73 Aligned_cols=65 Identities=15% Similarity=0.202 Sum_probs=49.7
Q ss_pred HHHHHHHHHHHhcChHHHHHHHHHHHHHh---hCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHH
Q 042650 9 RLKELLRERLIECGWRDEMKSLCRAYTRK---KGRNNVTVDDLVHVITPKGRASVPDPVKAELLQRIRSF 75 (81)
Q Consensus 9 rL~~~L~~rL~e~GW~D~vr~~~re~i~~---~g~~~v~~~~L~~~i~P~Ar~~VP~~vk~Ell~~Ir~f 75 (81)
-|.+.|..+|.-+.+-+..+..|..+|.. +|-=..+++++.+...+.. -++.+.-..++..|+.|
T Consensus 124 sL~~~L~~Ql~~~~~~~~~~~ia~~lI~~LD~~GyL~~~~~eia~~~~~~l--~~~~~~ve~vL~~iQ~l 191 (481)
T PRK12469 124 TLHEHLHDALRLYFLTERDREIARTIIDALDDDGYLRQDLSELAEAADPEL--GLSEQELEVALRLVQSL 191 (481)
T ss_pred CHHHHHHHHHhccCCCHHHHHHHHHHHhhCCCCCCCCCCHHHHHhcccccc--CCCHHHHHHHHHHHhcC
Confidence 58889999999999999999999988854 4544468888887732111 37888888888888774
No 80
>cd00383 trans_reg_C Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and a response regulator. The former autophosphorylates in a histidine residue on detecting an external stimulus. The phosphate is then transferred to an invariant aspartate residue in a highly conserved receiver domain of the response regulator. Phosphorylation activates a variable effector domain of the response regulator, which triggers the cellular response. The C-terminal effector domain contains DNA and RNA polymerase binding sites. Several dimers or monomers bind head to tail to small tandem repeats upstream of the genes. The RNA polymerase binding sites interact with the alpha or sigma subunite of RNA polymerase.
Probab=38.64 E-value=80 Score=18.28 Aligned_cols=38 Identities=16% Similarity=0.211 Sum_probs=30.7
Q ss_pred CCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHHhhhh
Q 042650 41 NNVTVDDLVHVITPKGRASVPDPVKAELLQRIRSFLAST 79 (81)
Q Consensus 41 ~~v~~~~L~~~i~P~Ar~~VP~~vk~Ell~~Ir~fL~~~ 79 (81)
..+|.++|++.+-|..- .+++..-.-.+.+||..|...
T Consensus 41 ~~vs~~~l~~~lw~~~~-~~~~~~l~~~I~rLRkkl~~~ 78 (95)
T cd00383 41 RVLSREQLLEAVWGDDY-DVDDRTVDVHISRLRKKLEDD 78 (95)
T ss_pred CcCCHHHHHHHhcCCCC-CCCcccHHHHHHHHHHHhccC
Confidence 68899999999987554 356777888899999998753
No 81
>PF00298 Ribosomal_L11: Ribosomal protein L11, RNA binding domain; InterPro: IPR020783 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 L11 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L11 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, ], groups bacteria, plant chloroplast, red algal chloroplast, cyanelle and archaeabacterial L11; and mammalian, plant and yeast L12 (YL15). L11 is a protein of 140 to 165 amino-acid residues. In E. coli, the C-terminal half of L11 has been shown [] to be in an extended and loosely folded conformation and is likely to be buried within the ribosomal structure.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 1VQN_I 2OTJ_I 3G6E_I 3CME_I 1YIJ_I 1YI2_I 3G4S_I 3CMA_I 3I55_I 1VQ7_I ....
Probab=37.09 E-value=91 Score=18.47 Aligned_cols=33 Identities=12% Similarity=0.234 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHHhhCCCCCCHHHHHHhhchhhhcc
Q 042650 25 DEMKSLCRAYTRKKGRNNVTVDDLVHVITPKGRAS 59 (81)
Q Consensus 25 D~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~~ 59 (81)
++|.+.|+... .+..+.+++..+..|.-.|+.|
T Consensus 33 ~~i~eIAk~K~--~d~~~~~l~~~~k~v~Gta~Sm 65 (69)
T PF00298_consen 33 KQIYEIAKIKQ--KDLNAKSLESAVKSVIGTARSM 65 (69)
T ss_dssp HHHHHHHHHHT--TTSSSSSHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHhh--cccccCCHHHHHHHHHHHHhcC
Confidence 56666775543 3557889999999999888875
No 82
>COG5559 Uncharacterized conserved small protein [Function unknown]
Probab=37.01 E-value=48 Score=19.83 Aligned_cols=21 Identities=33% Similarity=0.539 Sum_probs=16.3
Q ss_pred ccCCHHHHHHHHHHHHHHhhh
Q 042650 58 ASVPDPVKAELLQRIRSFLAS 78 (81)
Q Consensus 58 ~~VP~~vk~Ell~~Ir~fL~~ 78 (81)
.-+||+.|.|++.-|.-.++.
T Consensus 9 qkLPDdLKrEvldY~EfLlek 29 (65)
T COG5559 9 QKLPDDLKREVLDYIEFLLEK 29 (65)
T ss_pred HHCcHHHHHHHHHHHHHHHHH
Confidence 357999999999988655543
No 83
>PRK11640 putative transcriptional regulator; Provisional
Probab=36.94 E-value=71 Score=21.65 Aligned_cols=29 Identities=17% Similarity=0.286 Sum_probs=23.1
Q ss_pred HHHHHHHHHHHHHhhCCCCCCHHHHHHhh
Q 042650 24 RDEMKSLCRAYTRKKGRNNVTVDDLVHVI 52 (81)
Q Consensus 24 ~D~vr~~~re~i~~~g~~~v~~~~L~~~i 52 (81)
++.|=..+.+.+.++|...+++++|.++.
T Consensus 3 r~~il~~A~~lf~~~Gy~~tsi~~I~~~a 31 (191)
T PRK11640 3 REDVLGEALKLLEQQGLANTTLEMLAERV 31 (191)
T ss_pred HHHHHHHHHHHHHHhCcccCCHHHHHHHh
Confidence 45666778888888898888999887765
No 84
>PF06799 DUF1230: Protein of unknown function (DUF1230); InterPro: IPR009631 This family represents Ycf36, which is found in plants, encoded in the genomes of algal chloroplasts and in cyanobacteria. As the family is exclusively found in phototrophic organisms it may play a role in photosynthesis.
Probab=36.84 E-value=9.3 Score=26.27 Aligned_cols=7 Identities=57% Similarity=1.175 Sum_probs=6.2
Q ss_pred HhcChHH
Q 042650 19 IECGWRD 25 (81)
Q Consensus 19 ~e~GW~D 25 (81)
.|+||+|
T Consensus 102 EESGWYD 108 (144)
T PF06799_consen 102 EESGWYD 108 (144)
T ss_pred cccCccC
Confidence 5899999
No 85
>PLN02555 limonoid glucosyltransferase
Probab=36.73 E-value=22 Score=28.26 Aligned_cols=54 Identities=20% Similarity=0.223 Sum_probs=35.0
Q ss_pred HHHHHHHHHHHHHhcChHHHHH-------HHHHHHHHhhCCCCCCHHHHHHhhchhhhccCC
Q 042650 7 KERLKELLRERLIECGWRDEMK-------SLCRAYTRKKGRNNVTVDDLVHVITPKGRASVP 61 (81)
Q Consensus 7 ~erL~~~L~~rL~e~GW~D~vr-------~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~~VP 61 (81)
.+.|...+++-+.+..+ +++| +.|++.+.+.|+..-+++++++++...+.+.|.
T Consensus 416 ~~~v~~~v~~vm~~~~g-~~~r~ra~~l~~~a~~A~~egGSS~~~l~~~v~~i~~~~~~~~~ 476 (480)
T PLN02555 416 REEVAECLLEATVGEKA-AELKQNALKWKEEAEAAVAEGGSSDRNFQEFVDKLVRKSVEIVD 476 (480)
T ss_pred HHHHHHHHHHHhcCchH-HHHHHHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHhccceecc
Confidence 56666666666642111 3344 445555666677778999999999888766654
No 86
>KOG2769 consensus Putative u4/u6 small nuclear ribonucleoprotein [RNA processing and modification]
Probab=36.19 E-value=83 Score=25.88 Aligned_cols=54 Identities=22% Similarity=0.308 Sum_probs=38.8
Q ss_pred CccchhHHHHHHHHHHHHHhcChHHHHHHHHHHHHHhhCCCCCCHHHHHHhhchhhhccCCHH
Q 042650 1 MIESGEKERLKELLRERLIECGWRDEMKSLCRAYTRKKGRNNVTVDDLVHVITPKGRASVPDP 63 (81)
Q Consensus 1 LvesGe~erL~~~L~~rL~e~GW~D~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~~VP~~ 63 (81)
|.+||.+.++.+-.+.. -|-+.+..-..+.++.-|+. --..++.|.|+ +-||+.
T Consensus 183 f~e~gkf~~~an~~r~~----a~le~Lq~eis~~a~k~gI~---~~~~la~~~p~--~~iP~i 236 (522)
T KOG2769|consen 183 FHESGKFIKLANRHRYK----AQLERLQNEISQAARKTGIS---TATKLALIAPK--DDIPAI 236 (522)
T ss_pred ecccchHHHHHHHHHHH----HHHHHHHHHHHHHHHhcCCc---hhhhhhhccCC--CCCchh
Confidence 56899999998876532 34556666666666766643 37788899998 888874
No 87
>PRK00767 transcriptional regulator BetI; Validated
Probab=36.00 E-value=71 Score=20.88 Aligned_cols=27 Identities=7% Similarity=0.081 Sum_probs=16.2
Q ss_pred HHHHHHHHHHHHhhCCCCCCHHHHHHh
Q 042650 25 DEMKSLCRAYTRKKGRNNVTVDDLVHV 51 (81)
Q Consensus 25 D~vr~~~re~i~~~g~~~v~~~~L~~~ 51 (81)
+.+=+.|.+.+.++|...+|+++|.++
T Consensus 12 ~~Il~aA~~lf~~~G~~~~s~~~Ia~~ 38 (197)
T PRK00767 12 QQLIDATLRAIGEVGLLDATIAQIARR 38 (197)
T ss_pred HHHHHHHHHHHHHcCcccCCHHHHHHH
Confidence 344455666666666666666666554
No 88
>KOG2949 consensus Ketopantoate hydroxymethyltransferase [Coenzyme transport and metabolism]
Probab=35.55 E-value=22 Score=26.89 Aligned_cols=26 Identities=27% Similarity=0.571 Sum_probs=19.3
Q ss_pred HhcChHHHHHHHHHHHHHhhCCCCCCH
Q 042650 19 IECGWRDEMKSLCRAYTRKKGRNNVTV 45 (81)
Q Consensus 19 ~e~GW~D~vr~~~re~i~~~g~~~v~~ 45 (81)
.||||-|-+++.++ +++..|.+.|.+
T Consensus 111 yeS~~sda~knAv~-vmk~~g~~~vK~ 136 (306)
T KOG2949|consen 111 YESSWSDAVKNAVR-VMKEGGMDAVKL 136 (306)
T ss_pred ccccHHHHHHHHHH-HHHhcCCceEEE
Confidence 58999999998876 666666665543
No 89
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=35.16 E-value=87 Score=20.96 Aligned_cols=30 Identities=33% Similarity=0.630 Sum_probs=25.5
Q ss_pred hHHHHHHHHHHHHHhcChHHHHHHHHHHHHHh
Q 042650 6 EKERLKELLRERLIECGWRDEMKSLCRAYTRK 37 (81)
Q Consensus 6 e~erL~~~L~~rL~e~GW~D~vr~~~re~i~~ 37 (81)
+++++++.+...|.+ |++++++...+....
T Consensus 92 ~~ee~k~~i~~~l~~--w~~~~~~~i~~~~~~ 121 (126)
T COG3355 92 DPEEIKKKILKDLDE--WYDKMKQLIEEFEKK 121 (126)
T ss_pred CHHHHHHHHHHHHHH--HHHHHHHHHHHHhcc
Confidence 678999999999995 999999998876643
No 90
>PRK08535 translation initiation factor IF-2B subunit delta; Provisional
Probab=34.90 E-value=1.4e+02 Score=22.28 Aligned_cols=55 Identities=13% Similarity=0.304 Sum_probs=38.8
Q ss_pred hHHHHHHHHHHHHHhhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHHhhh
Q 042650 23 WRDEMKSLCRAYTRKKGRNNVTVDDLVHVITPKGRASVPDPVKAELLQRIRSFLAS 78 (81)
Q Consensus 23 W~D~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~~VP~~vk~Ell~~Ir~fL~~ 78 (81)
..+.++..++...+.+ ...+++...+..|.......=.++.|+.+++.|..|++.
T Consensus 48 l~~~l~~~~~~L~~ar-Pt~v~l~nair~v~~~~~~~~~~~~k~~l~e~~~~~~~e 102 (310)
T PRK08535 48 FKAEMRAAANILISTR-PTAVSLPNAVRYVMRYYSGETVEEARESVIERAEEFIES 102 (310)
T ss_pred HHHHHHHHHHHHHHcC-CchhhHHHHHHHHHHhhccCCHHHHHHHHHHHHHHHHHH
Confidence 4456777777665554 467788877777765433333478999999999999864
No 91
>PRK14996 TetR family transcriptional regulator; Provisional
Probab=34.67 E-value=65 Score=21.29 Aligned_cols=16 Identities=6% Similarity=0.063 Sum_probs=7.1
Q ss_pred HHHHHHHHHHHhcChH
Q 042650 9 RLKELLRERLIECGWR 24 (81)
Q Consensus 9 rL~~~L~~rL~e~GW~ 24 (81)
+|-+--.+-+.+.|+.
T Consensus 12 ~Il~aA~~lf~e~G~~ 27 (192)
T PRK14996 12 VILQAAMRVALAEGFA 27 (192)
T ss_pred HHHHHHHHHHHhcChh
Confidence 3333334444455554
No 92
>PRK02260 S-ribosylhomocysteinase; Provisional
Probab=34.04 E-value=1e+02 Score=21.48 Aligned_cols=27 Identities=19% Similarity=0.300 Sum_probs=17.9
Q ss_pred HhcChHH-----HHHHHHHHHHHhhCCCCCCHH
Q 042650 19 IECGWRD-----EMKSLCRAYTRKKGRNNVTVD 46 (81)
Q Consensus 19 ~e~GW~D-----~vr~~~re~i~~~g~~~v~~~ 46 (81)
.+|||+- ..+..|+.++.+ +....+++
T Consensus 123 ~~CGny~~hsL~~Ak~~a~~~L~~-~~~~~~~~ 154 (158)
T PRK02260 123 YQCGNYKDHSLEGAKEIARKILDQ-GISVNPNE 154 (158)
T ss_pred hcCCChhhCCHHHHHHHHHHHHHh-hcccCchh
Confidence 6899985 467888888865 33333443
No 93
>PF10249 NDUFB10: NADH-ubiquinone oxidoreductase subunit 10; InterPro: IPR019377 NADH-ubiquinone oxidoreductase subunit 10 of (NDUFB10) is a member of a family of conserved proteins of up to 180 residues. It is one of the 41 protein subunits within the hydrophobic fraction of the NADH:ubiquinone oxidoreductase (complex I), a multiprotein complex located in the inner mitochondrial membrane whose main function is the transport of electrons from NADH to ubiquinone, which is accompanied by translocation of protons from the mitochondrial matrix to the intermembrane space. NDUFB10 is encoded in the nucleus.
Probab=33.45 E-value=36 Score=22.91 Aligned_cols=46 Identities=20% Similarity=0.248 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHhcChHHHHH--HHHHHHHHhhCCCCCCHHHHHHhhch
Q 042650 9 RLKELLRERLIECGWRDEMK--SLCRAYTRKKGRNNVTVDDLVHVITP 54 (81)
Q Consensus 9 rL~~~L~~rL~e~GW~D~vr--~~~re~i~~~g~~~v~~~~L~~~i~P 54 (81)
.|-+.|++||..|-+++.+- +.|+.++..-.-...+|..=+.++-+
T Consensus 61 EIlkILReRl~~C~~~EG~nh~qnC~~l~~qy~ea~~~y~~kYgdlg~ 108 (128)
T PF10249_consen 61 EILKILRERLEACYRREGVNHYQNCRKLVEQYEEAAKNYFIKYGDLGA 108 (128)
T ss_pred HHHHHHHHHHHHHHHHHCcCHhhhhHHHHHHHHHHHHHHHHHHHhcCc
Confidence 36678999999999998765 46888775532223355555555533
No 94
>smart00862 Trans_reg_C Transcriptional regulatory protein, C terminal. This domain is almost always found associated with the response regulator receiver domain. It may play a role in DNA binding.
Probab=32.80 E-value=93 Score=17.27 Aligned_cols=42 Identities=21% Similarity=0.315 Sum_probs=32.3
Q ss_pred HhhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHHhhh
Q 042650 36 RKKGRNNVTVDDLVHVITPKGRASVPDPVKAELLQRIRSFLAS 78 (81)
Q Consensus 36 ~~~g~~~v~~~~L~~~i~P~Ar~~VP~~vk~Ell~~Ir~fL~~ 78 (81)
...| ..++.++|.+.+-|..-...+...-.-.+.++|..|..
T Consensus 19 ~~~~-~~vs~~~l~~~lw~~~~~~~~~~~l~~~i~~LR~~l~~ 60 (78)
T smart00862 19 RNPG-RVVSREELLEAVWGDDDDDVDDNTLDVHISRLRKKLED 60 (78)
T ss_pred hCCC-CccCHHHHHHHHcCCCCCCCccchHHHHHHHHHHHHhc
Confidence 3344 47899999999988643356677888899999999865
No 95
>cd08051 gp6_gp15_like Head-Tail Connector Proteins gp6 and gp15, and similar proteins. Members of this family include the proteins gp6 and gp15 from bacteriophage HK97 and SPP1, respectively. They are critical in the assembly of the connector, a specialized structure that serves as an interface for head and tail attachment, as well as a point at which DNA exits the head during infection by the bacteriophage. They form dodecameric ring structures that comprise the middle ring of the connector, located between the portal protein (attached to the head) and the gp7/gp16 ring (attached to the tail). They are components of the mature phage and the absence or mutation of HK97 gp6 or SPP1 gp15, respectively, result in defective head-tail joining and the absence of mature phage particles. The genome maps of HK97 and SPP1 show that genes encoding gp6 and gp15 are in the same relative position on the genome, located adjacent to the major capsid protein (MCP) gene and in between head and tail gene
Probab=32.67 E-value=1.2e+02 Score=18.78 Aligned_cols=20 Identities=25% Similarity=0.537 Sum_probs=17.3
Q ss_pred hccCCHHHHHHHHHHHHHHh
Q 042650 57 RASVPDPVKAELLQRIRSFL 76 (81)
Q Consensus 57 r~~VP~~vk~Ell~~Ir~fL 76 (81)
-..+|+.||.-++.-|.-|-
T Consensus 42 ~~~lp~~vk~A~l~li~~~y 61 (94)
T cd08051 42 AADIPAAVKGAVLKVFQFYF 61 (94)
T ss_pred ccCCCHHHHHHHHHHHHHHH
Confidence 56899999999999988774
No 96
>PLN00164 glucosyltransferase; Provisional
Probab=32.63 E-value=64 Score=25.49 Aligned_cols=52 Identities=21% Similarity=0.257 Sum_probs=32.1
Q ss_pred hHHHHHHHHHHHHHhcC--------hHHHHHHHHHHHHHhhCCCCCCHHHHHHhhchhhh
Q 042650 6 EKERLKELLRERLIECG--------WRDEMKSLCRAYTRKKGRNNVTVDDLVHVITPKGR 57 (81)
Q Consensus 6 e~erL~~~L~~rL~e~G--------W~D~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar 57 (81)
+.+.|...+++-+.+.+ -..++++.+++.+.+.|+..-+++++++++.+.|-
T Consensus 417 ~~e~l~~av~~vm~~~~~~~~~~r~~a~~~~~~~~~a~~~gGSS~~~l~~~v~~~~~~~~ 476 (480)
T PLN00164 417 EAAELERAVRSLMGGGEEEGRKAREKAAEMKAACRKAVEEGGSSYAALQRLAREIRHGAV 476 (480)
T ss_pred cHHHHHHHHHHHhcCCchhHHHHHHHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHhccC
Confidence 46777777777665322 12333444444455556666689999999877654
No 97
>COG1309 AcrR Transcriptional regulator [Transcription]
Probab=32.53 E-value=1.1e+02 Score=18.47 Aligned_cols=28 Identities=18% Similarity=0.268 Sum_probs=20.4
Q ss_pred HHHHHHHHHHHHhhCCCCCCHHHHHHhh
Q 042650 25 DEMKSLCRAYTRKKGRNNVTVDDLVHVI 52 (81)
Q Consensus 25 D~vr~~~re~i~~~g~~~v~~~~L~~~i 52 (81)
.++-..+.+.+..+|.+++|+.+|.++.
T Consensus 15 ~~ii~aa~~l~~~~G~~~~t~~~Ia~~a 42 (201)
T COG1309 15 ERILDAALRLFAEKGYAATTVDEIAKAA 42 (201)
T ss_pred HHHHHHHHHHHHHcCcCCCCHHHHHHHh
Confidence 4455566666666888888888888876
No 98
>PHA02530 pseT polynucleotide kinase; Provisional
Probab=31.86 E-value=86 Score=22.34 Aligned_cols=37 Identities=22% Similarity=0.481 Sum_probs=31.5
Q ss_pred CCHHHHHHhhchhhhccCCHHHHHHHHHHHHHHhhhh
Q 042650 43 VTVDDLVHVITPKGRASVPDPVKAELLQRIRSFLAST 79 (81)
Q Consensus 43 v~~~~L~~~i~P~Ar~~VP~~vk~Ell~~Ir~fL~~~ 79 (81)
.+.+.+.+.+.-.+...+|+++-+.+..++..|...+
T Consensus 111 ~~~e~~~~R~~~R~~~~~~~~~i~~~~~~~~~~~~~~ 147 (300)
T PHA02530 111 VPVEELVKRNRKRGERAVPEDVLRSMFKQMKEYRGLV 147 (300)
T ss_pred CCHHHHHHHHHccCcCCCCHHHHHHHHHHHHHhcCCC
Confidence 3678899999888778899999999999999997653
No 99
>TIGR03504 FimV_Cterm FimV C-terminal domain. This protein is found at the extreme C-terminus of FimV from Pseudomonas aeruginosa, and of TspA of Neisseria meningitidis. Disruption of the former blocks twitching motility from type IV pili; Semmler, et al. suggest a role in peptidoglycan layer remodelling required by type IV fimbrial systems.
Probab=31.19 E-value=94 Score=16.83 Aligned_cols=32 Identities=34% Similarity=0.445 Sum_probs=17.1
Q ss_pred ccchhHHHHHHHHHHHHHhcChHHHHHHHHHHHH
Q 042650 2 IESGEKERLKELLRERLIECGWRDEMKSLCRAYT 35 (81)
Q Consensus 2 vesGe~erL~~~L~~rL~e~GW~D~vr~~~re~i 35 (81)
++.|+++.=+++|.+-+. .| ....+..++..+
T Consensus 10 ie~Gd~e~Ar~lL~evl~-~~-~~~q~~eA~~LL 41 (44)
T TIGR03504 10 IEMGDLEGARELLEEVIE-EG-DEAQRQEARALL 41 (44)
T ss_pred HHcCChHHHHHHHHHHHH-cC-CHHHHHHHHHHH
Confidence 456666666666666652 22 244555555444
No 100
>cd03567 VHS_GGA VHS domain family, GGA subfamily; GGA (Golgi-localized, Gamma-ear-containing, Arf-binding) comprise a subfamily of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins. The VHS domain has a superhelical structure similar to the structure of the ARM (Armadillo) repeats and is present at the N-termini of proteins. GGA proteins have a multidomain structure consisting of an N-terminal VHS domain linked by a short proline-rich linker to a GAT (GGA and TOM) domain, which is followed by a long flexible linker to the C-terminal appendage, GAE (gamma-adaptin ear) domain. The VHS domain of GGA proteins binds to the acidic-cluster dileucine (DxxLL) motif found on the cytoplasmic tails of cargo proteins trafficked between the trans-Golgi network and the endosomal system.
Probab=31.18 E-value=92 Score=20.77 Aligned_cols=31 Identities=19% Similarity=0.495 Sum_probs=23.4
Q ss_pred HHHHHhhchhhh-ccCCHHHHHHHHHHHHHHh
Q 042650 46 DDLVHVITPKGR-ASVPDPVKAELLQRIRSFL 76 (81)
Q Consensus 46 ~~L~~~i~P~Ar-~~VP~~vk~Ell~~Ir~fL 76 (81)
++|+.-+.|+.. ...|..||+.++.-|+++=
T Consensus 84 ~el~kl~~~k~~~~~~~~~Vk~kil~li~~W~ 115 (139)
T cd03567 84 NELIKLVSPKYLGSRTSEKVKTKIIELLYSWT 115 (139)
T ss_pred HHHHHHhccccCCCCCCHHHHHHHHHHHHHHH
Confidence 467777766553 4678999999999998763
No 101
>TIGR02499 HrpE_YscL_not type III secretion apparatus protein, HrpE/YscL family. This model is related to Pfam model pfam06188, but is broader. pfam06188 describes HrpE-like proteins, components of bacterial type III secretion systems primarily in bacteria that infect plants. This model includes also the homologous proteins of animal pathogens, such as YscL of Yersinia pestis. This model excludes the related protein FliH of the bacterial flagellar apparatus (see pfam02108)
Probab=31.17 E-value=69 Score=20.89 Aligned_cols=25 Identities=24% Similarity=0.324 Sum_probs=12.2
Q ss_pred HHHHHHHHHHHHHhcChHHHHHHHH
Q 042650 7 KERLKELLRERLIECGWRDEMKSLC 31 (81)
Q Consensus 7 ~erL~~~L~~rL~e~GW~D~vr~~~ 31 (81)
++++++.-...=.+.||.+-...+.
T Consensus 37 ~e~~~~~g~~~G~~~g~~e~~~~~~ 61 (166)
T TIGR02499 37 AEASRQLGYEQGLEQFWQEAAAQLA 61 (166)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444444445556655444443
No 102
>TIGR00524 eIF-2B_rel eIF-2B alpha/beta/delta-related uncharacterized proteins. This model, eIF-2B_rel, describes half of a superfamily, where the other half consists of eukaryotic translation initiation factor 2B (eIF-2B) subunits alpha, beta, and delta. It is unclear whether the eIF-2B_rel set is monophyletic, or whether they are all more closely related to each other than to any eIF-2B subunit because the eIF-2B clade is highly derived. Members of this branch of the family are all uncharacterized with respect to function and are found in the Archaea, Bacteria, and Eukarya, although a number are described as putative translation intiation factor components. Proteins found by eIF-2B_rel include at least three clades, including a set of uncharacterized eukaryotic proteins, a set found in some but not all Archaea, and a set universal so far among the Archaea and closely related to several uncharacterized bacterial proteins.
Probab=30.78 E-value=2.3e+02 Score=21.22 Aligned_cols=55 Identities=7% Similarity=0.155 Sum_probs=37.6
Q ss_pred hHHHHHHHHHHHHHhhCCCCCCHHHHHHhhchhhhccCC-HHHHHHHHHHHHHHhhh
Q 042650 23 WRDEMKSLCRAYTRKKGRNNVTVDDLVHVITPKGRASVP-DPVKAELLQRIRSFLAS 78 (81)
Q Consensus 23 W~D~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~~VP-~~vk~Ell~~Ir~fL~~ 78 (81)
..+.++..+......+ ...+++...+..+....+...+ ++.|+.++..+..|++.
T Consensus 45 ~~~~l~~~~~~L~~~R-Pt~v~l~na~~~~~~~i~~~~~~~~~k~~l~~~~~~~~~e 100 (303)
T TIGR00524 45 FKEDLEKAADFLLSTR-PTAVNLFWALERVLNSAENGESVEEAKESLLREAIEIIEE 100 (303)
T ss_pred HHHHHHHHHHHHHHhC-CchhhHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHH
Confidence 4466777766554544 4667888777777655443333 67889999999999864
No 103
>PLN02210 UDP-glucosyl transferase
Probab=30.74 E-value=73 Score=25.01 Aligned_cols=48 Identities=17% Similarity=0.172 Sum_probs=32.1
Q ss_pred hHHHHHHHHHHHHHhcC---hHHH---HHHHHHHHHHhhCCCCCCHHHHHHhhc
Q 042650 6 EKERLKELLRERLIECG---WRDE---MKSLCRAYTRKKGRNNVTVDDLVHVIT 53 (81)
Q Consensus 6 e~erL~~~L~~rL~e~G---W~D~---vr~~~re~i~~~g~~~v~~~~L~~~i~ 53 (81)
+.+.|.+.++.-+.+.. ++.+ +++.+++.+.+.|+...|++.++++|.
T Consensus 401 ~~~~l~~av~~~m~~~~g~~~r~~a~~l~~~a~~Av~~gGSS~~~l~~~v~~~~ 454 (456)
T PLN02210 401 KVEEVERCIEAVTEGPAAADIRRRAAELKHVARLALAPGGSSARNLDLFISDIT 454 (456)
T ss_pred CHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHh
Confidence 56778888877775432 4433 445566666666777778899988874
No 104
>PF07587 PSD1: Protein of unknown function (DUF1553); InterPro: IPR022655 The function is not known. It is found associated with IPR011444 from INTERPRO It is also found associated with the Planctomycete cytochrome C domain IPR011429 from INTERPRO.
Probab=30.27 E-value=54 Score=23.86 Aligned_cols=29 Identities=28% Similarity=0.605 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHHhcChHHHHHHHHHHHHHhh
Q 042650 8 ERLKELLRERLIECGWRDEMKSLCRAYTRKK 38 (81)
Q Consensus 8 erL~~~L~~rL~e~GW~D~vr~~~re~i~~~ 38 (81)
..|-+.|-..+++.|| ++|.+.|.|+.++
T Consensus 52 PeLLd~La~~F~~~g~--dlK~L~R~I~~S~ 80 (266)
T PF07587_consen 52 PELLDWLAAEFVEHGW--DLKHLIRLIVTSR 80 (266)
T ss_pred HHHHHHHHHHHHHcCC--CHHHHHHHHHccH
Confidence 3678999999999999 6999999998553
No 105
>PRK14830 undecaprenyl pyrophosphate synthase; Provisional
Probab=30.14 E-value=82 Score=23.18 Aligned_cols=17 Identities=24% Similarity=0.348 Sum_probs=14.4
Q ss_pred cChHHHHHHHHHHHHHh
Q 042650 21 CGWRDEMKSLCRAYTRK 37 (81)
Q Consensus 21 ~GW~D~vr~~~re~i~~ 37 (81)
.|+++++-+.++.++++
T Consensus 150 YggR~EI~~A~~~~~~~ 166 (251)
T PRK14830 150 YGGRAEIVSAVKEIAKD 166 (251)
T ss_pred CCCHHHHHHHHHHHHHH
Confidence 58999999999988764
No 106
>PF08388 GIIM: Group II intron, maturase-specific domain; InterPro: IPR013597 This region is found mainly in various bacterial and archaeal species, but a few members of this family are expressed by fungal and chlamydomonal species. It has been implicated in the binding of intron RNA during reverse transcription and splicing [].
Probab=30.00 E-value=99 Score=17.72 Aligned_cols=33 Identities=15% Similarity=0.330 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHhhCCCCCCHHHHHHhhchhhhcc
Q 042650 26 EMKSLCRAYTRKKGRNNVTVDDLVHVITPKGRAS 59 (81)
Q Consensus 26 ~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~~ 59 (81)
.+++.+++++.. ...+.+++++++++-|.-++.
T Consensus 3 ~~~~kik~~~~~-~~~~~~~~~~i~~LN~~lrGW 35 (80)
T PF08388_consen 3 RFRRKIKEITRR-RNRGKSLEELIKKLNPILRGW 35 (80)
T ss_pred HHHHHHHHHHhC-CCCCCCHHHHHHHHHHHHHHH
Confidence 456667777732 235679999999999987764
No 107
>cd08334 DED_Caspase_8_10_repeat2 Death effector domain, repeat 2, of initator caspases 8 and 10. Death Effector Domain (DED) found in caspase-8 and caspase-10, repeat 2. Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. Initiator caspases are the first to be activated following death- or inflammation-inducing signals. Caspase-8 and -10 are the initiators of death receptor mediated apoptosis, and they play partially redundant roles. Together with FADD and the pseudo-caspase c-FLIP, they form the death-inducing signaling complex (DISC), whose formation is triggered by the activation of type 1 tumor necrosis factor (TNF) receptors such as Fas, TNF receptor 1, and TRAIL receptor. Caspase-8 and -10 also play important functions in cell adhesion and motility. They contain two N-terminal DED domains and a C-terminal caspase domain. DEDs comprise a subfamily of the Death Domain (DD) superfamily. DDs are protein-protein interaction domains foun
Probab=29.77 E-value=1.4e+02 Score=18.23 Aligned_cols=50 Identities=16% Similarity=0.148 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHHHhhCCCCC-CHHHHHHhhchhhhccCCH--HHHHHHHHHHHH
Q 042650 24 RDEMKSLCRAYTRKKGRNNV-TVDDLVHVITPKGRASVPD--PVKAELLQRIRS 74 (81)
Q Consensus 24 ~D~vr~~~re~i~~~g~~~v-~~~~L~~~i~P~Ar~~VP~--~vk~Ell~~Ir~ 74 (81)
.+.++=+|++.|-++..+++ |+-+++.++.-.+. +=|+ ..-.+++.+||.
T Consensus 20 l~~lKFLc~d~ip~~kle~~~s~ldlf~~Lek~~~-l~~~nl~~L~elL~~ir~ 72 (83)
T cd08334 20 LDKLKFLLSSKLPRSKLEDNKTLLDVFVEMEKQGL-LGEDNLDELKRILKSLDK 72 (83)
T ss_pred HHHHHHHhHhhcchhhhhccCCHHHHHHHHHHcCC-CCCccHHHHHHHHHHHHH
Confidence 35677788888865544444 78888888865433 2244 336666666643
No 108
>TIGR00174 miaA tRNA isopentenyltransferase (miaA). Catalyzes the first step in the modification of an adenosine near the anticodon to 2-methylthio-N6-isopentyladenosine.
Probab=29.47 E-value=2.2e+02 Score=21.31 Aligned_cols=48 Identities=19% Similarity=0.378 Sum_probs=28.4
Q ss_pred hHHHHHHHHHHH---HHhcChHHHHHHHHHHHHH-hh-CCCCCCHHHHHHhhc
Q 042650 6 EKERLKELLRER---LIECGWRDEMKSLCRAYTR-KK-GRNNVTVDDLVHVIT 53 (81)
Q Consensus 6 e~erL~~~L~~r---L~e~GW~D~vr~~~re~i~-~~-g~~~v~~~~L~~~i~ 53 (81)
+++.|.+-+..| ..+.||.|+|+.+-..... .. ....+-|.++++.+.
T Consensus 194 dr~~L~~rI~~Rv~~Mi~~Gl~eEv~~l~~~~~~~~~~~~~aIGYkE~~~~l~ 246 (287)
T TIGR00174 194 SREPLHQRIEQRVHDMLESGLLAEVKALYAQYDLCDLPSIQAIGYKEFLLYLE 246 (287)
T ss_pred CHHHHHHHHHHHHHHHHHCCHHHHHHHHHhccCCcCCchhhhccHHHHHHHHc
Confidence 445555555444 3457999999988643211 11 134557778877764
No 109
>COG5049 XRN1 5'-3' exonuclease [DNA replication, recombination, and repair / Cell division and chromosome partitioning / Translation]
Probab=29.38 E-value=1e+02 Score=26.84 Aligned_cols=51 Identities=18% Similarity=0.467 Sum_probs=40.2
Q ss_pred HHHHhcChHH---------------HHHHHHHHHHHhh-----------------------------------------C
Q 042650 16 ERLIECGWRD---------------EMKSLCRAYTRKK-----------------------------------------G 39 (81)
Q Consensus 16 ~rL~e~GW~D---------------~vr~~~re~i~~~-----------------------------------------g 39 (81)
-+|.+-||++ +||++|+.++.-- |
T Consensus 531 v~l~~~g~~erYY~~K~~~t~~~~E~irdm~k~YVeGL~WVL~YYY~GC~SW~WyYpyHyAP~aaD~~k~~~~dIkFe~g 610 (953)
T COG5049 531 VNLRFPGWKERYYTSKLHFTTDSEEKIRDMAKEYVEGLQWVLSYYYRGCPSWDWYYPYHYAPLAADLSKLSDNDIKFELG 610 (953)
T ss_pred hhhcccchhhhhhhhhcCCCcCCHHHHHHHHHHHhhhhhhhhhhhhcCCCCcccccccccchhhhhhhhcccceeeecCC
Confidence 4678889998 8999999998541 2
Q ss_pred CCCCCHHHHHHhhchhhhccCCHHHHH
Q 042650 40 RNNVTVDDLVHVITPKGRASVPDPVKA 66 (81)
Q Consensus 40 ~~~v~~~~L~~~i~P~Ar~~VP~~vk~ 66 (81)
-.-.-|++|.+.+-+..+++||+-.+.
T Consensus 611 ~PF~P~EQLm~VLPa~Sk~~vP~~fr~ 637 (953)
T COG5049 611 TPFRPFEQLMAVLPARSKNLVPEGFRP 637 (953)
T ss_pred CCCCcHHHHHhhcchhhcCcCchhhhh
Confidence 222378999999999999999987653
No 110
>PF08776 VASP_tetra: VASP tetramerisation domain; InterPro: IPR014885 Vasodilator-stimulated phosphoprotein (VASP) is an actin cytoskeletal regulatory protein. This region corresponds to the tetramerisation domain which forms a right handed alpha helical coiled coil structure []. ; PDB: 1USE_A 1USD_A.
Probab=29.25 E-value=82 Score=17.22 Aligned_cols=18 Identities=33% Similarity=0.503 Sum_probs=12.3
Q ss_pred HHHHHHHHHHHHHhhhhc
Q 042650 63 PVKAELLQRIRSFLASTA 80 (81)
Q Consensus 63 ~vk~Ell~~Ir~fL~~~~ 80 (81)
.+|+|++.-|+..|...+
T Consensus 22 K~K~EIIeA~~~eL~r~~ 39 (40)
T PF08776_consen 22 KVKEEIIEAIRQELSRRS 39 (40)
T ss_dssp HHHHHHHHHHHHHHHHH-
T ss_pred HHHHHHHHHHHHHHhccC
Confidence 567788888877776543
No 111
>cd05025 S-100A1 S-100A1: S-100A1 domain found in proteins similar to S100A1. S100A1 is a calcium-binding protein belonging to a large S100 vertebrate-specific protein family within the EF-hand superfamily of calcium-binding proteins. Note that the S-100 hierarchy, to which this S-100A1 group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. As is the case with many other members of S100 protein family, S100A1 is implicated in intracellular and extracellular regulatory activities, including interaction with myosin-associated twitchin kinase, actin-capping protein CapZ, sinapsin I, and tubulin. Structural data suggests that S100A1 proteins exist within cells as antiparallel homodimers, while heterodimers with S100A4 and S100B also has been reported. Upon binding calcium S100A1 changes conformation to expose a hydrophobic cleft which is the interaction site of S100A1 with its more that 20 known target proteins.
Probab=29.20 E-value=1.3e+02 Score=17.83 Aligned_cols=50 Identities=20% Similarity=0.373 Sum_probs=29.2
Q ss_pred HHHHHHHHHHHHHh-cCh---HHHHHHHHHHHHHhhCCCCCCHHHHHHhhchhhh
Q 042650 7 KERLKELLRERLIE-CGW---RDEMKSLCRAYTRKKGRNNVTVDDLVHVITPKGR 57 (81)
Q Consensus 7 ~erL~~~L~~rL~e-~GW---~D~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar 57 (81)
.+.|+.+|+..+-. .|. .++++.+.++. ...+...++|++.+.-+.+.|-
T Consensus 30 ~~El~~~l~~~lg~~~~~~~s~~~v~~i~~~~-D~d~~G~I~f~eF~~l~~~~~~ 83 (92)
T cd05025 30 KKELKDLLQTELSDFLDAQKDADAVDKIMKEL-DENGDGEVDFQEFVVLVAALTV 83 (92)
T ss_pred HHHHHHHHHHHHHHHccCCCCHHHHHHHHHHH-CCCCCCcCcHHHHHHHHHHHHH
Confidence 45566666554422 222 24455555542 3334457999999988887764
No 112
>PRK10307 putative glycosyl transferase; Provisional
Probab=29.12 E-value=1.1e+02 Score=22.63 Aligned_cols=36 Identities=17% Similarity=0.273 Sum_probs=24.9
Q ss_pred ccchhHHHHHHHHHHHHHhcChHHHHHHHHHHHHHh
Q 042650 2 IESGEKERLKELLRERLIECGWRDEMKSLCRAYTRK 37 (81)
Q Consensus 2 vesGe~erL~~~L~~rL~e~GW~D~vr~~~re~i~~ 37 (81)
++.|+-+.|.+.|..-+..-..+.++.+.+++.+.+
T Consensus 355 ~~~~d~~~la~~i~~l~~~~~~~~~~~~~a~~~~~~ 390 (412)
T PRK10307 355 VEPESVEALVAAIAALARQALLRPKLGTVAREYAER 390 (412)
T ss_pred eCCCCHHHHHHHHHHHHhCHHHHHHHHHHHHHHHHH
Confidence 456778888888876655556667777777776653
No 113
>cd06607 STKc_TAO Catalytic domain of the Protein Serine/Threonine Kinase, Thousand-and-one amino acids proteins. Serine/threonine kinases (STKs), thousand-and-one amino acids (TAO) subfamily, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The TAO subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. TAO proteins possess mitogen-activated protein kinase (MAPK) kinase kinase (MAPKKK or MAP3K or MKKK) activity. They activate the MAPKs, p38 and c-Jun N-terminal kinase (JNK), by phosphorylating and activating the respective MAP/ERK kinases (MEKs, also known as MKKs or MAPKKs), MEK3/MEK6 and MKK4/MKK7. MAPK signaling cascades are important in mediating cellular responses to extracellular signals. Vertebrates contain three TAO subfamily
Probab=29.10 E-value=1.4e+02 Score=20.76 Aligned_cols=57 Identities=16% Similarity=0.283 Sum_probs=42.9
Q ss_pred hcChHHHHHHHHHHHHHhhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHHhhh
Q 042650 20 ECGWRDEMKSLCRAYTRKKGRNNVTVDDLVHVITPKGRASVPDPVKAELLQRIRSFLAS 78 (81)
Q Consensus 20 e~GW~D~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~~VP~~vk~Ell~~Ir~fL~~ 78 (81)
..+|-++++...+..+...-..-+++.+++.+ |--...-|.+...+++.+.++++..
T Consensus 236 ~~~~~~~~~~li~~~l~~~p~~Rp~~~~il~~--~~~~~~~~~~~~~~~~~~~~~~~~~ 292 (307)
T cd06607 236 SNDWSDYFRNFVDSCLQKIPQDRPSSEELLKH--RFVLRERPPTVIIDLIQRTKDAVRE 292 (307)
T ss_pred chhhCHHHHHHHHHHhcCChhhCcCHHHHhcC--hhhcccCCcHHHHHHHHHHHHHhhh
Confidence 34688888888888886443345689999874 6666677888889999999888754
No 114
>PF14433 SUKH-3: SUKH-3 immunity protein
Probab=28.98 E-value=68 Score=20.79 Aligned_cols=14 Identities=43% Similarity=0.634 Sum_probs=11.6
Q ss_pred HHHHHHHHHhcChH
Q 042650 11 KELLRERLIECGWR 24 (81)
Q Consensus 11 ~~~L~~rL~e~GW~ 24 (81)
++.+.+.|...||.
T Consensus 1 ~~~v~~~L~~aGW~ 14 (142)
T PF14433_consen 1 KEKVIELLRAAGWY 14 (142)
T ss_pred CHHHHHHHHHcCCC
Confidence 35678899999999
No 115
>PF05205 COMPASS-Shg1: COMPASS (Complex proteins associated with Set1p) component shg1
Probab=28.95 E-value=62 Score=20.58 Aligned_cols=22 Identities=27% Similarity=0.345 Sum_probs=13.4
Q ss_pred HHHHHHhcChHHHHHHHHHHHH
Q 042650 14 LRERLIECGWRDEMKSLCRAYT 35 (81)
Q Consensus 14 L~~rL~e~GW~D~vr~~~re~i 35 (81)
|-..+...|=.|++|..|-+-.
T Consensus 3 Lv~~fKk~G~FD~lRk~~l~~~ 24 (106)
T PF05205_consen 3 LVEEFKKQGHFDKLRKECLADF 24 (106)
T ss_pred HHHHHHhCCChHHHHHHHHHhc
Confidence 3445566677777776665544
No 116
>KOG2235 consensus Uncharacterized conserved protein [Function unknown]
Probab=28.74 E-value=47 Score=28.26 Aligned_cols=26 Identities=27% Similarity=0.388 Sum_probs=19.8
Q ss_pred hHHHHHHHHHHHHHhcChHHHHHHHHH
Q 042650 6 EKERLKELLRERLIECGWRDEMKSLCR 32 (81)
Q Consensus 6 e~erL~~~L~~rL~e~GW~D~vr~~~r 32 (81)
=+++|.+.++.+|.|||=. -+-.+|+
T Consensus 116 Y~d~iaeEinekLqE~gqv-tiaeLak 141 (776)
T KOG2235|consen 116 YVDRIAEEINEKLQEQGQV-TIAELAK 141 (776)
T ss_pred HHHHHHHHHHHHHHHhcch-HHHHHHH
Confidence 3789999999999999954 2445554
No 117
>KOG1112 consensus Ribonucleotide reductase, alpha subunit [Nucleotide transport and metabolism]
Probab=28.71 E-value=34 Score=28.69 Aligned_cols=35 Identities=37% Similarity=0.585 Sum_probs=28.1
Q ss_pred ccchhHHHHHHHHHHHHHhcC-hHHHHHHHHHHHHHhhC
Q 042650 2 IESGEKERLKELLRERLIECG-WRDEMKSLCRAYTRKKG 39 (81)
Q Consensus 2 vesGe~erL~~~L~~rL~e~G-W~D~vr~~~re~i~~~g 39 (81)
|-|||.......|-.-|.+-| |.|++++.. |..+|
T Consensus 629 vlsGeFqiVN~hll~DLv~~glW~~~mKn~l---I~~nG 664 (796)
T KOG1112|consen 629 VLSGEFQIVNPHLLKDLVELGLWDDEMKNKL---IANNG 664 (796)
T ss_pred ecccceEEEcHHHHHHHHHhccCCHHHHHHH---HhcCC
Confidence 458999888999988999988 999999764 45555
No 118
>PLN02448 UDP-glycosyltransferase family protein
Probab=28.67 E-value=84 Score=24.48 Aligned_cols=48 Identities=21% Similarity=0.416 Sum_probs=31.8
Q ss_pred hHHHHHHHHHHHHHhc-----Ch---HHHHHHHHHHHHHhhCCCCCCHHHHHHhhc
Q 042650 6 EKERLKELLRERLIEC-----GW---RDEMKSLCRAYTRKKGRNNVTVDDLVHVIT 53 (81)
Q Consensus 6 e~erL~~~L~~rL~e~-----GW---~D~vr~~~re~i~~~g~~~v~~~~L~~~i~ 53 (81)
..+.|.+.+++-|.+- +. ..++++.+++.+.+.|+..-|++++++.+.
T Consensus 401 ~~~~l~~av~~vl~~~~~~~~~~r~~a~~~~~~~~~a~~~gGss~~~l~~~v~~~~ 456 (459)
T PLN02448 401 GREEIAELVKRFMDLESEEGKEMRRRAKELQEICRGAIAKGGSSDTNLDAFIRDIS 456 (459)
T ss_pred cHHHHHHHHHHHhcCCchhHHHHHHHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHh
Confidence 4677888888777532 12 334455566666666766778888888775
No 119
>KOG1488 consensus Translational repressor Pumilio/PUF3 and related RNA-binding proteins (Puf superfamily) [Translation, ribosomal structure and biogenesis]
Probab=28.55 E-value=88 Score=25.57 Aligned_cols=63 Identities=14% Similarity=0.202 Sum_probs=49.5
Q ss_pred HHHHHHHHhcChHHHHHHHHHHHHHhhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHHh
Q 042650 12 ELLRERLIECGWRDEMKSLCRAYTRKKGRNNVTVDDLVHVITPKGRASVPDPVKAELLQRIRSFL 76 (81)
Q Consensus 12 ~~L~~rL~e~GW~D~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~~VP~~vk~Ell~~Ir~fL 76 (81)
+.+-++..|+|=.|+-+.+. ..+.. ++-.++++.--=.|.++|.+.|+.+...+|+..+...+
T Consensus 228 NyvIQkffE~gt~~q~~~l~-~~~~g-~v~~Lsld~ygCRVIQkale~id~~~~~~Li~ELd~~v 290 (503)
T KOG1488|consen 228 NYVIQKFFEHGTEDQRNLLH-SQIKG-HVLELSLDMYGCRVIQKALEKVDVSLQIQLIDELDGHL 290 (503)
T ss_pred CchhhhhhccCCHHHHHHHH-HHHHh-hhhhhhcccccchhHHHHHHhcCHHHHHHHHHHHHhhH
Confidence 45567788999999944444 44432 36778999999999999999999999999999886554
No 120
>PRK06654 fliL flagellar basal body-associated protein FliL; Reviewed
Probab=27.77 E-value=1.4e+02 Score=21.24 Aligned_cols=50 Identities=30% Similarity=0.433 Sum_probs=34.9
Q ss_pred HHHHHHHHHHHHhcChHHHHHHHHHHHHHhhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHHhhh
Q 042650 8 ERLKELLRERLIECGWRDEMKSLCRAYTRKKGRNNVTVDDLVHVITPKGRASVPDPVKAELLQRIRSFLAS 78 (81)
Q Consensus 8 erL~~~L~~rL~e~GW~D~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~~VP~~vk~Ell~~Ir~fL~~ 78 (81)
+.+++.|..|.- +||+....++.++ ++++|- =++..|.||+.+|...|.+
T Consensus 116 ~~l~~EL~~r~p------qIRD~Ii~~LssK-----t~~eL~----------Gk~~LKeEI~~rIN~iL~~ 165 (181)
T PRK06654 116 KNILNELGRRKV------RLKDIIREYFSQK-----TGQELK----------NESQIKAEIKARINSILRN 165 (181)
T ss_pred HHHHHHHHhccH------HHHHHHHHHHHhC-----CHHHHc----------CHHHHHHHHHHHHHHhcCC
Confidence 345555655544 5777777777654 677775 2378999999999998864
No 121
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=27.66 E-value=1.1e+02 Score=17.08 Aligned_cols=33 Identities=18% Similarity=0.388 Sum_probs=22.3
Q ss_pred HHHHHHhhCCCCCCHHHHHHhhchhhhccCCHHHHHHH
Q 042650 31 CRAYTRKKGRNNVTVDDLVHVITPKGRASVPDPVKAEL 68 (81)
Q Consensus 31 ~re~i~~~g~~~v~~~~L~~~i~P~Ar~~VP~~vk~El 68 (81)
+-+.+.+.|.+.++-.+|-+.+ ..=|..|++++
T Consensus 17 ~L~~l~~~G~~~vSS~~La~~~-----gi~~~qVRKDl 49 (50)
T PF06971_consen 17 YLEQLKEEGVERVSSQELAEAL-----GITPAQVRKDL 49 (50)
T ss_dssp HHHHHHHTT-SEE-HHHHHHHH-----TS-HHHHHHHH
T ss_pred HHHHHHHcCCeeECHHHHHHHH-----CCCHHHhcccC
Confidence 4456777899999999988776 66667777665
No 122
>PLN02165 adenylate isopentenyltransferase
Probab=27.51 E-value=1.9e+02 Score=22.21 Aligned_cols=48 Identities=17% Similarity=0.260 Sum_probs=28.9
Q ss_pred hHHHHHHHHHHHH---HhcChHHHHHHHHHHHHHh----hCCCCCCHHHHHHhhc
Q 042650 6 EKERLKELLRERL---IECGWRDEMKSLCRAYTRK----KGRNNVTVDDLVHVIT 53 (81)
Q Consensus 6 e~erL~~~L~~rL---~e~GW~D~vr~~~re~i~~----~g~~~v~~~~L~~~i~ 53 (81)
+++.|.+-+..|. .+.||.|+|+.+....... .....+-|-++...+.
T Consensus 184 dr~~L~~RI~~Rvd~Ml~~GlldEv~~L~~~~~~~~~~~~~~qaIGYkE~~~yL~ 238 (334)
T PLN02165 184 SEPVLFEYLSKRVDEMMDSGMFEELAEFYDPVKSGSEPLGIRKAIGVPEFDRYFK 238 (334)
T ss_pred CHHHHHHHHHHHHHHHHHCCHHHHHHHHHHccCCcccCCCceeEEcHHHHHHHHH
Confidence 3444455454442 4589999999887532211 1134456888888875
No 123
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=27.26 E-value=1.5e+02 Score=18.03 Aligned_cols=40 Identities=13% Similarity=0.133 Sum_probs=26.0
Q ss_pred HHHHHHHHHhhCCCCCCHHHHHHhhchhhhccCCHHHHHHH
Q 042650 28 KSLCRAYTRKKGRNNVTVDDLVHVITPKGRASVPDPVKAEL 68 (81)
Q Consensus 28 r~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~~VP~~vk~El 68 (81)
|...-+.+.+.+ ..+|.++|++.+..+.-..=+..|++-|
T Consensus 3 R~~Il~~l~~~~-~~~sa~ei~~~l~~~~~~i~~~TVYR~L 42 (116)
T cd07153 3 RLAILEVLLESD-GHLTAEEIYERLRKKGPSISLATVYRTL 42 (116)
T ss_pred HHHHHHHHHhCC-CCCCHHHHHHHHHhcCCCCCHHHHHHHH
Confidence 344555666553 5789999999997765555555555543
No 124
>PRK14135 recX recombination regulator RecX; Provisional
Probab=27.13 E-value=2.1e+02 Score=20.29 Aligned_cols=58 Identities=16% Similarity=0.177 Sum_probs=29.5
Q ss_pred HHHHHHHHhcChHHHHHHHHHHHHHhhCCCCCCHHHHHHhhchhh---hccCCHHHHHHHHHH
Q 042650 12 ELLRERLIECGWRDEMKSLCRAYTRKKGRNNVTVDDLVHVITPKG---RASVPDPVKAELLQR 71 (81)
Q Consensus 12 ~~L~~rL~e~GW~D~vr~~~re~i~~~g~~~v~~~~L~~~i~P~A---r~~VP~~vk~Ell~~ 71 (81)
..|+++|..-|.-+++=+.+-+.+.+.|. ++=........-.- ...-|..++.+|.++
T Consensus 75 ~el~~kL~~kg~~~~~Ie~vl~~l~~~~~--ldD~~~a~~~~~~~~~~~~~g~~~I~~kL~~k 135 (263)
T PRK14135 75 KEVRDYLKKHEISEEIISEVIDKLKEEKY--IDDKEYAESYVRTNINTGDKGPRVIKQKLLQK 135 (263)
T ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHcCC--CCHHHHHHHHHHHHHhccccchHHHHHHHHHc
Confidence 55666666666666666666666665552 22233333222221 123555666666553
No 125
>PF05400 FliT: Flagellar protein FliT; InterPro: IPR008622 This entry represents the bacterial flagellar FliT family of dual-function proteins. Together with FlgN, FliT has been proposed to act as a substrate-specific export chaperone, facilitating the incorporation of the enterobacterial hook-associated axial proteins (HAPs) FlgK/FlgL and FliD into the growing flagellum []. FliT has also been shown to act as a transcriptional regulator in Salmonella typhimurium [].; GO: 0019861 flagellum; PDB: 3A7M_A 3H3M_B 3NKZ_C 2G42_A 2FZT_B.
Probab=26.92 E-value=49 Score=18.95 Aligned_cols=16 Identities=56% Similarity=0.802 Sum_probs=11.4
Q ss_pred ccchhHHHHHHHHHHH
Q 042650 2 IESGEKERLKELLRER 17 (81)
Q Consensus 2 vesGe~erL~~~L~~r 17 (81)
.+.|+|+.+..++..|
T Consensus 5 a~~~dWe~l~~l~~~R 20 (84)
T PF05400_consen 5 AEAGDWEELEELLDER 20 (84)
T ss_dssp HHCT-HHHHHHHHHHH
T ss_pred HhhCcHHHHHHHHHHH
Confidence 4678999998888554
No 126
>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated
Probab=26.81 E-value=3.3e+02 Score=22.04 Aligned_cols=69 Identities=17% Similarity=0.185 Sum_probs=42.7
Q ss_pred hhHHHHHHHHHHHHHhcChH-----HHHHHHHHHHHHhhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHHh
Q 042650 5 GEKERLKELLRERLIECGWR-----DEMKSLCRAYTRKKGRNNVTVDDLVHVITPKGRASVPDPVKAELLQRIRSFL 76 (81)
Q Consensus 5 Ge~erL~~~L~~rL~e~GW~-----D~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~~VP~~vk~Ell~~Ir~fL 76 (81)
.|...+++.|..++..--|. +.+.....+.+-+.|+..-..++|++.+... .-++.++.-+...|...+
T Consensus 170 ~El~~lr~~l~~~~~~l~~~~~~~~~p~~~~l~~~Ll~~dv~~~la~~l~~~l~~~---~~~~~~~~~l~~~l~~~l 243 (484)
T PRK06995 170 QELRSLRGMLEEQLASLAWGERQRRDPVRAALLKHLLAAGFSAQLVRMLVDNLPEG---DDAEAALDWVQSALAKNL 243 (484)
T ss_pred HHHHHHHHHHHHHHHHHhccccccccHHHHHHHHHHHHCCCCHHHHHHHHHHHHhh---hchhHHHHHHHHHHHHHH
Confidence 35677888888888776663 3445555666777788777778888877433 233444544444444443
No 127
>cd07977 TFIIE_beta_winged_helix TFIIE_beta_winged_helix domain, located at the central core region of TFIIE beta, with double-stranded DNA binding activity. Transcription Factor IIE (TFIIE) beta winged-helix (or forkhead) domain is located at the central core region of TFIIE beta. The winged-helix is a form of helix-turn-helix (HTH) domain which typically binds DNA with the 3rd helix. The winged-helix domain is distinguished by the presence of a C-terminal beta-strand hairpin unit (the wing) that packs against the cleft of the tri-helical core. Although most winged-helix domains are multi-member families, TFIIE beta winged-helix domain is typically found as a single orthologous group. TFIIE is one of the six eukaryotic general transcription factors (TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH) that are required for transcription initiation of protein-coding genes. TFIIE is a heterotetramer consisting of two copies each of alpha and beta subunits. TFIIE beta contains several functional
Probab=26.76 E-value=1.1e+02 Score=18.34 Aligned_cols=24 Identities=17% Similarity=0.451 Sum_probs=19.4
Q ss_pred HHHHHHHhhCCCCCCHHHHHHhhc
Q 042650 30 LCRAYTRKKGRNNVTVDDLVHVIT 53 (81)
Q Consensus 30 ~~re~i~~~g~~~v~~~~L~~~i~ 53 (81)
.+=+.+++++...++|++|+++.-
T Consensus 13 ~aV~ymK~r~~~Plt~~EIl~~ls 36 (75)
T cd07977 13 KIVDYMKKRHQHPLTLDEILDYLS 36 (75)
T ss_pred HHHHHHHhcCCCCccHHHHHHHHh
Confidence 455788888756799999999984
No 128
>PRK05720 mtnA methylthioribose-1-phosphate isomerase; Reviewed
Probab=26.73 E-value=2.1e+02 Score=21.97 Aligned_cols=58 Identities=7% Similarity=-0.058 Sum_probs=40.2
Q ss_pred cChHHHHHHHHHHHHHhhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHHhhhh
Q 042650 21 CGWRDEMKSLCRAYTRKKGRNNVTVDDLVHVITPKGRASVPDPVKAELLQRIRSFLAST 79 (81)
Q Consensus 21 ~GW~D~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~~VP~~vk~Ell~~Ir~fL~~~ 79 (81)
.+|.+.++..+....+.+ ...+|+-.-+..+.......=++++|..++..+..|++..
T Consensus 72 ~~~~~~l~~~~~~L~~~R-PtavnL~~ai~~~~~~i~~~~~~~~~~~l~~~a~~~~~e~ 129 (344)
T PRK05720 72 EEFLKKLEEAAAYLAASR-PTAVNLFWALDRMREVLAPLPGAERKAALEEEAIEIHEED 129 (344)
T ss_pred HHHHHHHHHHHHHHHHhC-CCHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHH
Confidence 357788887776655555 4667777777666554433235789999999999998653
No 129
>PF00406 ADK: Adenylate kinase; InterPro: IPR000850 Adenylate kinases (ADK) are phosphotransferases that catalyse the reversible reaction AMP + MgATP = ADP + MgADP an essential reaction for many processes in living cells. Two ADK isozymes have been identified in mammalian cells. These specifically bind AMP and favour binding to ATP over other nucleotide triphosphates (AK1 is cytosolic and AK2 is located in the mitochondria). A third ADK has been identified in bovine heart and human cells [], this is a mitochondrial GTP:AMP phosphotransferase, also specific for the phosphorylation of AMP, but can only use GTP or ITP as a substrate []. ADK has also been identified in different bacterial species and in yeast []. Two further enzymes are known to be related to the ADK family, i.e. yeast uridine monophosphokinase and slime mold UMP-CMP kinase. Within the ADK family there are several conserved regions, including the ATP-binding domains. One of the most conserved areas includes an Arg residue, whose modification inactivates the enzyme, together with an Asp that resides in the catalytic cleft of the enzyme and participates in a salt bridge.; GO: 0005524 ATP binding, 0019205 nucleobase-containing compound kinase activity, 0006139 nucleobase-containing compound metabolic process; PDB: 1ZD8_A 3TLX_D 1TEV_A 1ZAK_B 3CM0_A 3ADK_A 1ZIP_A 1ZIO_A 1ZIN_A 3NDP_A ....
Probab=26.70 E-value=1.3e+02 Score=19.24 Aligned_cols=15 Identities=40% Similarity=0.554 Sum_probs=8.3
Q ss_pred hccCCHHHHHHHHHH
Q 042650 57 RASVPDPVKAELLQR 71 (81)
Q Consensus 57 r~~VP~~vk~Ell~~ 71 (81)
-.+||+++--+++..
T Consensus 52 g~~vp~~~v~~ll~~ 66 (151)
T PF00406_consen 52 GELVPDELVIELLKE 66 (151)
T ss_dssp TSS--HHHHHHHHHH
T ss_pred hccchHHHHHHHHHH
Confidence 357888886666543
No 130
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=26.64 E-value=2.3e+02 Score=22.81 Aligned_cols=64 Identities=19% Similarity=0.279 Sum_probs=47.1
Q ss_pred HHHHHHHHHHHHHhcChHHHHHHHHHHHHHhh---CCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHH
Q 042650 7 KERLKELLRERLIECGWRDEMKSLCRAYTRKK---GRNNVTVDDLVHVITPKGRASVPDPVKAELLQRIRSF 75 (81)
Q Consensus 7 ~erL~~~L~~rL~e~GW~D~vr~~~re~i~~~---g~~~v~~~~L~~~i~P~Ar~~VP~~vk~Ell~~Ir~f 75 (81)
..-|++.|..++...--.+.-+.+|..+|..- |-=..|++++.+..-| |-.+....++.+|+.|
T Consensus 89 ~~tL~e~L~~Ql~~~~~s~~e~~Ia~~lI~~Ldd~GYl~~~le~~~~~l~~-----~~~~eve~vl~~iQ~l 155 (444)
T COG1508 89 TKTLSEYLLEQLRLLPLSDTERAIATYLIDALDDEGYLTESLEEIAELLGS-----VDEEEVEKVLARIQSL 155 (444)
T ss_pred ccCHHHHHHHHHhhcCCChHHHHHHHHHHhhcCcCCCcccCHHHHHHhccc-----ccHHHHHHHHHHHhcC
Confidence 34688999999999888889999999888654 4334577777666655 5567777777777654
No 131
>cd05030 calgranulins Calgranulins: S-100 domain found in proteins belonging to the Calgranulin subgroup of the S100 family of EF-hand calcium-modulated proteins, including S100A8, S100A9, and S100A12 . Note that the S-100 hierarchy, to which this Calgranulin group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. These proteins are expressed mainly in granulocytes, and are involved in inflammation, allergy, and neuritogenesis, as well as in host-parasite response. Calgranulins are modulated not only by calcium, but also by other metals such as zinc and copper. Structural data suggested that calgranulins may exist in multiple structural forms, homodimers, as well as hetero-oligomers. For example, the S100A8/S100A9 complex called calprotectin plays important roles in the regulation of inflammatory processes, wound repair, and regulating zinc-dependent enzymes as well as microbial growth.
Probab=26.48 E-value=1.5e+02 Score=17.69 Aligned_cols=50 Identities=12% Similarity=0.289 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHHHhcCh-----HHHHHHHHHHHHHhhCCCCCCHHHHHHhhchhhhc
Q 042650 7 KERLKELLRERLIECGW-----RDEMKSLCRAYTRKKGRNNVTVDDLVHVITPKGRA 58 (81)
Q Consensus 7 ~erL~~~L~~rL~e~GW-----~D~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~ 58 (81)
++.|+.+|...+-+ .. .+++..+.++. ...+...++|++.+..+.+.|.+
T Consensus 29 ~~El~~ll~~~~g~-~~t~~~~~~~v~~i~~~~-D~d~dG~I~f~eF~~~~~~~~~~ 83 (88)
T cd05030 29 KKEFKQLVEKELPN-FLKKEKNQKAIDKIFEDL-DTNQDGQLSFEEFLVLVIKVGVA 83 (88)
T ss_pred HHHHHHHHHHHhhH-hhccCCCHHHHHHHHHHc-CCCCCCcCcHHHHHHHHHHHHHH
Confidence 45666666654422 12 24455544432 22334579999999888877643
No 132
>PF15615 TerB-C: TerB-C domain
Probab=25.75 E-value=1.6e+02 Score=19.52 Aligned_cols=48 Identities=27% Similarity=0.460 Sum_probs=33.3
Q ss_pred HHHHHHHHHHHhcCh-HHHHHHHHHHHHHhhCCCCCCHHHHHHhhchhhhccCCHH
Q 042650 9 RLKELLRERLIECGW-RDEMKSLCRAYTRKKGRNNVTVDDLVHVITPKGRASVPDP 63 (81)
Q Consensus 9 rL~~~L~~rL~e~GW-~D~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~~VP~~ 63 (81)
.=..+|+.-|..-.| ++++..+|++ . .+-++-+++.|=-.|-+.+-+.
T Consensus 77 ~~~~lL~~Ll~~~~w~r~e~~~~a~~----~---glm~~~~ie~INE~afd~~gd~ 125 (144)
T PF15615_consen 77 EHSALLRALLSRESWSREELEDIARD----H---GLMPDGAIESINEKAFDYFGDP 125 (144)
T ss_pred HHHHHHHHHHhCCCccHHHHHHHHHH----c---CCCHHHHHHHHHHHHHHhcCCe
Confidence 345677777888899 9999999976 2 3456777777766665555443
No 133
>PF01015 Ribosomal_S3Ae: Ribosomal S3Ae family; InterPro: IPR001593 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 [, ]. A number of eukaryotic and archaebacterial ribosomal proteins can be grouped on the basis of sequence similarities. One of these families consists of proteins that have from 220 to 250 amino acids and represents Rps1 (eukaryotic) and Rps3Ae (archaeal and eukaryotic).; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2XZN_4 2XZM_4 3U5C_B 3U5G_B.
Probab=25.60 E-value=2.2e+02 Score=20.11 Aligned_cols=40 Identities=10% Similarity=0.321 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHhhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHH
Q 042650 26 EMKSLCRAYTRKKGRNNVTVDDLVHVITPKGRASVPDPVKAELLQRIR 73 (81)
Q Consensus 26 ~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~~VP~~vk~Ell~~Ir 73 (81)
.+|....+++.+.. .+.++++++..+ +|+++-+||..+.+
T Consensus 135 ~IRk~m~~ii~~~~-~~~~~~e~V~~l-------i~~~i~~eI~k~~k 174 (194)
T PF01015_consen 135 AIRKKMVEIITEEA-SELDLKELVKKL-------IPGSIGKEIEKACK 174 (194)
T ss_dssp HHHHHHHHHHHHHC-CTSHHHHHHHHH-------CTTHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHh-ccCcHHHHHHHH-------ccchHHHHHHHHhc
Confidence 56777778888775 677999999766 57777777766543
No 134
>COG1424 BioW Pimeloyl-CoA synthetase [Coenzyme metabolism]
Probab=25.46 E-value=88 Score=23.04 Aligned_cols=32 Identities=19% Similarity=0.171 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHHHhcChHHHHHHHHHHHHHhh
Q 042650 7 KERLKELLRERLIECGWRDEMKSLCRAYTRKK 38 (81)
Q Consensus 7 ~erL~~~L~~rL~e~GW~D~vr~~~re~i~~~ 38 (81)
.+.=++..+..|.+||-.++|-+.+-++|.+-
T Consensus 73 ~Ee~re~a~~ll~~eGv~e~vi~ka~e~i~k~ 104 (239)
T COG1424 73 PEEARENAQKLLQEEGVTEQVINKAYEIIKKG 104 (239)
T ss_pred HHHHHHHHHHHHHhcCCcHHHHHHHHHhhccC
Confidence 34456788899999999999999999999763
No 135
>smart00845 GatB_Yqey GatB domain. This domain is found in GatB and proteins related to bacterial Yqey. It is about 140 amino acid residues long. This domain is found at the C terminus of GatB which transamidates Glu-tRNA to Gln-tRNA. The function of this domain is uncertain. It does however suggest that Yqey and its relatives have a role in tRNA metabolism.
Probab=25.35 E-value=2e+02 Score=18.82 Aligned_cols=47 Identities=15% Similarity=0.200 Sum_probs=29.2
Q ss_pred HHHHHHHHHHHHhhC--------CCCCCHHHHHHhhchhhhccCCHHHHHHHHHH
Q 042650 25 DEMKSLCRAYTRKKG--------RNNVTVDDLVHVITPKGRASVPDPVKAELLQR 71 (81)
Q Consensus 25 D~vr~~~re~i~~~g--------~~~v~~~~L~~~i~P~Ar~~VP~~vk~Ell~~ 71 (81)
++++.+|.+++.+.+ ...-.+.-|+..+....+..+...+-.+++.+
T Consensus 91 ~el~~~v~~vi~~~~~~v~~~~~g~~k~~~~l~G~vMk~~~G~ad~~~v~~~l~~ 145 (147)
T smart00845 91 GELEAIVDEVIAENPKAVEDYRAGKKKALGFLVGQVMKATRGKADPKLVNELLKE 145 (147)
T ss_pred HHHHHHHHHHHHHCHHHHHHHHCCHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHH
Confidence 467788877776542 01113566677777777777777666666553
No 136
>PF10057 DUF2294: Uncharacterized conserved protein (DUF2294); InterPro: IPR018745 This domain of unknown function is found in a family of hypothetical bacterial proteins with no known function. It is also found at the C terminus of proteins provisionally annotated as response regulators.
Probab=25.23 E-value=1.1e+02 Score=19.47 Aligned_cols=34 Identities=26% Similarity=0.326 Sum_probs=26.6
Q ss_pred ccchhHHHHHHHHHHHHHhcChHHHHHHHHHHHHH
Q 042650 2 IESGEKERLKELLRERLIECGWRDEMKSLCRAYTR 36 (81)
Q Consensus 2 vesGe~erL~~~L~~rL~e~GW~D~vr~~~re~i~ 36 (81)
+++.+...+-...|..|.+++ .++++.+..+++.
T Consensus 56 ~~~~~g~~lv~~~R~~l~~~~-~~~l~~~ie~i~g 89 (118)
T PF10057_consen 56 AETEEGRELVKQVRTSLIESL-KPELKEMIEEILG 89 (118)
T ss_pred HhCcchHHHHHHHHHHHHHHH-HHHHHHHHHHHhC
Confidence 455556667778899999999 8889988887773
No 137
>TIGR03764 ICE_PFGI_1_parB integrating conjugative element, PFGI_1 class, ParB family protein. Members of this protein family carry the ParB-type nuclease domain and are found in integrating conjugative elements (ICE) in the same class as PFGI-1 of Pseudomonas fluorescens Pf-5.
Probab=25.18 E-value=2.9e+02 Score=20.61 Aligned_cols=51 Identities=8% Similarity=0.175 Sum_probs=39.6
Q ss_pred HHHHHHHHHHhhCC-CCCCHHHHHHhhchh---hhccCCHHHHHHHHHHHHHHhh
Q 042650 27 MKSLCRAYTRKKGR-NNVTVDDLVHVITPK---GRASVPDPVKAELLQRIRSFLA 77 (81)
Q Consensus 27 vr~~~re~i~~~g~-~~v~~~~L~~~i~P~---Ar~~VP~~vk~Ell~~Ir~fL~ 77 (81)
++..|..++..... ..+.|++++..+.-. +-...|+.++.||+.++-.-|.
T Consensus 191 L~~~a~~~w~~~~~~~~~~f~~~f~~~~~~~d~~~~~~~~~~~deli~~~~~~l~ 245 (258)
T TIGR03764 191 LRKAAEKIWNRYSSGVEVDFEEVFQEVLARFDDPEEFSLERFRDELIGEMAKALG 245 (258)
T ss_pred HHHHHHHHHHHHccccCCCHHHHHHHHHHhcCCcccCCHHHHHHHHHHHHHHHcC
Confidence 56667777776653 347999999998765 5578899999999999987664
No 138
>cd03561 VHS VHS domain family; The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It has a superhelical structure similar to that of the ARM (Armadillo) repeats and is present at the N-termini of proteins involved in intracellular membrane trafficking. There are four general groups of VHS domain containing proteins based on their association with other domains. The first group consists of proteins of the STAM/EAST/Hbp family which has the domain composition VHS-SH3-ITAM. The second consists of proteins with a FYVE domain C-terminal to VHS. The third consists of GGA proteins with a domain composition VHS-GAT (GGA and TOM)-GAE (gamma-adaptin ear) domain. The fourth consists of proteins with a VHS domain alone or with domains other than those mentioned above. In GGA proteins, VHS domains are involved in cargo recognition in trans-Golgi, thereby having a general me
Probab=25.11 E-value=1.4e+02 Score=19.30 Aligned_cols=19 Identities=16% Similarity=0.200 Sum_probs=16.2
Q ss_pred ccCCHHHHHHHHHHHHHHh
Q 042650 58 ASVPDPVKAELLQRIRSFL 76 (81)
Q Consensus 58 ~~VP~~vk~Ell~~Ir~fL 76 (81)
..+|..||+.++.-|.++=
T Consensus 93 ~~~~~~Vk~kil~ll~~W~ 111 (133)
T cd03561 93 PKYDPKVREKALELILAWS 111 (133)
T ss_pred CCCCHHHHHHHHHHHHHHH
Confidence 4799999999999988764
No 139
>TIGR01078 arcA arginine deiminase. Arginine deiminase is the first enzyme of the arginine deiminase pathway of arginine degradation.
Probab=24.96 E-value=92 Score=24.34 Aligned_cols=23 Identities=17% Similarity=0.209 Sum_probs=19.2
Q ss_pred HHHHHHhhCCCCCCHHHHHHhhc
Q 042650 31 CRAYTRKKGRNNVTVDDLVHVIT 53 (81)
Q Consensus 31 ~re~i~~~g~~~v~~~~L~~~i~ 53 (81)
-.++++++|+..+-+++|+++..
T Consensus 49 f~~~Lr~~GveV~~l~dll~e~l 71 (405)
T TIGR01078 49 FANTLRDNGIEVLYLEDLLAETL 71 (405)
T ss_pred HHHHHHHCCCEEEEhHHHHHHHh
Confidence 44678889999999999999883
No 140
>COG1859 KptA RNA:NAD 2'-phosphotransferase [Translation, ribosomal structure and biogenesis]
Probab=24.75 E-value=82 Score=22.93 Aligned_cols=34 Identities=38% Similarity=0.508 Sum_probs=23.0
Q ss_pred HHHHhcChHHHHHHHHHHHHHhhCCCCCCHHHHHHhh
Q 042650 16 ERLIECGWRDEMKSLCRAYTRKKGRNNVTVDDLVHVI 52 (81)
Q Consensus 16 ~rL~e~GW~D~vr~~~re~i~~~g~~~v~~~~L~~~i 52 (81)
-+|-++||.| ++.++. .++..| .-++.+-|..-+
T Consensus 52 l~lD~~Gwa~-i~~l~~-~~~k~~-~~~~~~~l~~iV 85 (211)
T COG1859 52 LRLDEEGWAD-IDELLE-GLRKAG-RWLTRELLLAVV 85 (211)
T ss_pred eeeccccchh-HHHHHH-HHHhhc-cCCCHHHHHHHH
Confidence 3678999999 777764 455544 456777766655
No 141
>PF07569 Hira: TUP1-like enhancer of split; InterPro: IPR011494 The Hira proteins are found in a range of eukaryotes and are implicated in the assembly of repressive chromatin. These proteins also contain IPR001680 from INTERPRO.; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=24.47 E-value=1.6e+02 Score=20.81 Aligned_cols=31 Identities=23% Similarity=0.383 Sum_probs=25.0
Q ss_pred cchhHHHHHHHHHHHHHhcChHHHHHHHHHH
Q 042650 3 ESGEKERLKELLRERLIECGWRDEMKSLCRA 33 (81)
Q Consensus 3 esGe~erL~~~L~~rL~e~GW~D~vr~~~re 33 (81)
+..||...--..-.+|-+.|=.+++++.|++
T Consensus 188 s~~Ey~~wl~~Y~k~L~~~g~~~rlrel~~~ 218 (219)
T PF07569_consen 188 SPDEYRHWLLMYVKRLAEEGSEERLRELCDD 218 (219)
T ss_pred CHHHHHHHHHHHHHHHHhCchHHHHHHHHhh
Confidence 4566777777778899999999999999875
No 142
>PF09424 YqeY: Yqey-like protein; InterPro: IPR019004 Putative protein of unknown function; the authentic protein is detected in highly purified mitochondria in high-throughput studies; YOR215C is not an essential gene. ; PDB: 1NG6_A.
Probab=24.46 E-value=2.2e+02 Score=18.97 Aligned_cols=55 Identities=18% Similarity=0.300 Sum_probs=34.9
Q ss_pred hhHHHHHHHHHHHHHhcChHHHHHHHHHHHHHhhCCCC-CCHHHHHHhhchhhhccCCHH
Q 042650 5 GEKERLKELLRERLIECGWRDEMKSLCRAYTRKKGRNN-VTVDDLVHVITPKGRASVPDP 63 (81)
Q Consensus 5 Ge~erL~~~L~~rL~e~GW~D~vr~~~re~i~~~g~~~-v~~~~L~~~i~P~Ar~~VP~~ 63 (81)
-|.+.|..+|-..|.+ ++++..+.+.|.+.|... -+.-.+...+.|+..+-+--.
T Consensus 78 ~Ei~iL~~yLP~~lse----eEi~~~v~~~i~e~ga~~~k~mG~vMk~l~~~~~G~~Dgk 133 (143)
T PF09424_consen 78 AEIEILEEYLPKQLSE----EEIEAIVEEAIAELGASSMKDMGKVMKALMAKLKGRADGK 133 (143)
T ss_dssp HHHHHHGGGS-----H----HHHHHHHHHHHHHTT--BGGGHHHHHHHHHHHHTTTS-HH
T ss_pred HHHHHHHHhCcCCCCH----HHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHcCCcccHH
Confidence 3456677888888886 789999999988877543 378888888888766555433
No 143
>PF13720 Acetyltransf_11: Udp N-acetylglucosamine O-acyltransferase; Domain 2; PDB: 3I3A_A 3I3X_A 3HSQ_B 2JF2_A 1LXA_A 2AQ9_A 2QIV_X 2QIA_A 2JF3_A 4EQY_F ....
Probab=24.29 E-value=1.7e+02 Score=17.64 Aligned_cols=53 Identities=19% Similarity=0.207 Sum_probs=27.2
Q ss_pred HHhcChHHHHHHHHHHHHHhhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHHhh
Q 042650 18 LIECGWRDEMKSLCRAYTRKKGRNNVTVDDLVHVITPKGRASVPDPVKAELLQRIRSFLA 77 (81)
Q Consensus 18 L~e~GW~D~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~~VP~~vk~Ell~~Ir~fL~ 77 (81)
|.-.||.++-....+...+--=..+.++++-++++....-. ......|-+|+.
T Consensus 23 LrR~Gfs~~~i~~l~~ayr~l~~~~~~~~~a~~~l~~~~~~-------~~~v~~~~~Fi~ 75 (83)
T PF13720_consen 23 LRRRGFSKEEISALRRAYRILFRSGLTLEEALEELEEEYPD-------SPEVREIVDFIR 75 (83)
T ss_dssp HHHTTS-HHHHHHHHHHHHHHHTSSS-HHHHHHHHHHHTTS-------CHHHHHHHHHHH
T ss_pred HHHcCCCHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHhccC-------CHHHHHHHHHHH
Confidence 44567766655544444322111346899988888553322 333455666665
No 144
>TIGR00578 ku70 ATP-dependent DNA helicase ii, 70 kDa subunit (ku70). Proteins in this family are involved in non-homologous end joining, a process used for the repair of double stranded DNA breaks. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Cutoff does not detect the putative ku70 homologs in yeast.
Probab=24.24 E-value=1.1e+02 Score=25.02 Aligned_cols=45 Identities=22% Similarity=0.234 Sum_probs=33.7
Q ss_pred HHHHHHhhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHHhh
Q 042650 31 CRAYTRKKGRNNVTVDDLVHVITPKGRASVPDPVKAELLQRIRSFLA 77 (81)
Q Consensus 31 ~re~i~~~g~~~v~~~~L~~~i~P~Ar~~VP~~vk~Ell~~Ir~fL~ 77 (81)
++..+++.+..+.|+.+|=+-+.-+... ...-|.+|+.+|.+|++
T Consensus 540 ~~~~~~~~~l~kltv~~Lk~~l~~~g~~--~~~kKadLi~~i~~~~~ 584 (584)
T TIGR00578 540 LREHAKKGTLGKLTVSVLKDFCRAYGLR--SGSKKQELLDALTKHFK 584 (584)
T ss_pred HHHHHHcCChhhccHHHHHHHHHHcCCC--ccccHHHHHHHHHHHhC
Confidence 3445555667889999999988777544 34468899999999974
No 145
>PF09784 L31: Mitochondrial ribosomal protein L31; InterPro: IPR016340 This group represents a predicted mitochondrial ribosomal protein L31, fungal type [, ].
Probab=24.15 E-value=2.1e+02 Score=18.62 Aligned_cols=46 Identities=24% Similarity=0.271 Sum_probs=33.1
Q ss_pred HHHHHHHhcChHHHHHHHHHHHHHhhCCCCCCHHHHHHhhchhhhccCCH
Q 042650 13 LLRERLIECGWRDEMKSLCRAYTRKKGRNNVTVDDLVHVITPKGRASVPD 62 (81)
Q Consensus 13 ~L~~rL~e~GW~D~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~~VP~ 62 (81)
-++.||.. .|+|=+...+.+...|..-..++.+..+ .|+-.+|.|-
T Consensus 23 r~R~Rlr~---VD~vi~~l~~al~~~~~~~~~~~~~~~~-~P~E~eM~pk 68 (103)
T PF09784_consen 23 RQRKRLRA---VDSVIDTLYEALKKKGKQCKALERLKFE-FPKESEMSPK 68 (103)
T ss_pred HHHHHHHH---HHHHHHHHHHHHHHcCCcHHHHHHHHHh-CCChhhcCcc
Confidence 35566654 5777777777777777766678888887 5777777774
No 146
>PRK09480 slmA division inhibitor protein; Provisional
Probab=24.08 E-value=1.5e+02 Score=19.23 Aligned_cols=11 Identities=18% Similarity=0.253 Sum_probs=5.6
Q ss_pred CCCCHHHHHHh
Q 042650 41 NNVTVDDLVHV 51 (81)
Q Consensus 41 ~~v~~~~L~~~ 51 (81)
.++|+++|.++
T Consensus 29 ~~~ti~~Ia~~ 39 (194)
T PRK09480 29 ERITTAKLAAR 39 (194)
T ss_pred CccCHHHHHHH
Confidence 55555555443
No 147
>PRK04057 30S ribosomal protein S3Ae; Validated
Probab=24.04 E-value=2e+02 Score=20.61 Aligned_cols=41 Identities=15% Similarity=0.360 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHhhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHH
Q 042650 25 DEMKSLCRAYTRKKGRNNVTVDDLVHVITPKGRASVPDPVKAELLQRIR 73 (81)
Q Consensus 25 D~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~~VP~~vk~Ell~~Ir 73 (81)
-.+|....+++.+.. .+.++++++..+ +|+.+-+||....+
T Consensus 128 ~~IRk~m~~~i~~~~-~~~~~~e~V~~~-------i~g~i~~eI~~~~k 168 (203)
T PRK04057 128 HAIRKIMEEIIEEKA-SELTFEEFVQEI-------VFGKLASEIYKEAK 168 (203)
T ss_pred HHHHHHHHHHHHHHH-hcCCHHHHHHHH-------ccchHHHHHHHhhh
Confidence 456777777777664 577999999766 55666666665544
No 148
>PF15586 Imm47: Immunity protein 47
Probab=23.77 E-value=1.6e+02 Score=19.08 Aligned_cols=27 Identities=19% Similarity=0.558 Sum_probs=20.3
Q ss_pred hHHHHHHHHHHHHHhcC---hHHHHHHHHH
Q 042650 6 EKERLKELLRERLIECG---WRDEMKSLCR 32 (81)
Q Consensus 6 e~erL~~~L~~rL~e~G---W~D~vr~~~r 32 (81)
++++|++.|+.-+..|. |.+-.++++|
T Consensus 77 d~~~I~~~i~~~i~~c~~~~W~~~~~kLsr 106 (116)
T PF15586_consen 77 DYDEIKKTIERIIESCEGDDWDEIAEKLSR 106 (116)
T ss_pred CHHHHHHHHHHHHHHccCCCHHHHHHHHHH
Confidence 67888888888888876 7766666654
No 149
>PRK00091 miaA tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed
Probab=23.74 E-value=3e+02 Score=20.60 Aligned_cols=48 Identities=19% Similarity=0.311 Sum_probs=27.0
Q ss_pred hHHHHHHHHHHHH---HhcChHHHHHHHHHHHHH-hh-CCCCCCHHHHHHhhc
Q 042650 6 EKERLKELLRERL---IECGWRDEMKSLCRAYTR-KK-GRNNVTVDDLVHVIT 53 (81)
Q Consensus 6 e~erL~~~L~~rL---~e~GW~D~vr~~~re~i~-~~-g~~~v~~~~L~~~i~ 53 (81)
+++.|.+-+..|. .+.||.|+|+.+...-.. .. -...+-|.++++.+.
T Consensus 198 dr~~L~~rI~~Rv~~Ml~~Gl~eEv~~l~~~~~~~~~~~~~aIGykE~~~yl~ 250 (307)
T PRK00091 198 DREELYERINQRVDQMLEQGLLEEVRALLARGYLPDLPAMRAIGYKELLAYLD 250 (307)
T ss_pred CHHHHHHHHHHHHHHHHHCcHHHHHHHHHHcCCCCCCccceeecHHHHHHHHc
Confidence 4455555555443 457999999998753111 11 123445666666553
No 150
>PF06057 VirJ: Bacterial virulence protein (VirJ); InterPro: IPR010333 This entry contains several bacterial VirJ virulence proteins. VirJ is thought to be involved in the type IV secretion system. It is thought that the substrate proteins localised to the periplasm may associate with the pilus in a manner that is mediated by VirJ, and suggest a two-step process for type IV secretion in Agrobacterium [].
Probab=23.57 E-value=1.6e+02 Score=21.00 Aligned_cols=54 Identities=31% Similarity=0.453 Sum_probs=41.0
Q ss_pred hcChHHHHHHHHHHHHHhhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHHhhh
Q 042650 20 ECGWRDEMKSLCRAYTRKKGRNNVTVDDLVHVITPKGRASVPDPVKAELLQRIRSFLAS 78 (81)
Q Consensus 20 e~GW~D~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~~VP~~vk~Ell~~Ir~fL~~ 78 (81)
+-||++--+..|. .+.++|+..+-++.+-=-. ...=|+++-.+|-.-|+.|...
T Consensus 11 DgGw~~~d~~~a~-~l~~~G~~VvGvdsl~Yfw----~~rtP~~~a~Dl~~~i~~y~~~ 64 (192)
T PF06057_consen 11 DGGWRDLDKQIAE-ALAKQGVPVVGVDSLRYFW----SERTPEQTAADLARIIRHYRAR 64 (192)
T ss_pred CCCchhhhHHHHH-HHHHCCCeEEEechHHHHh----hhCCHHHHHHHHHHHHHHHHHH
Confidence 3599976666665 5677898888777776555 4666899999999999988764
No 151
>PLN02534 UDP-glycosyltransferase
Probab=23.52 E-value=55 Score=26.17 Aligned_cols=50 Identities=14% Similarity=0.286 Sum_probs=33.0
Q ss_pred hHHHHHHHHHHHHH---hcC-----hHHHHHHHHHHHHHhhCCCCCCHHHHHHhhchh
Q 042650 6 EKERLKELLRERLI---ECG-----WRDEMKSLCRAYTRKKGRNNVTVDDLVHVITPK 55 (81)
Q Consensus 6 e~erL~~~L~~rL~---e~G-----W~D~vr~~~re~i~~~g~~~v~~~~L~~~i~P~ 55 (81)
..+.|...++.-+. |.| -..++++.|++.+.+.|+...|+++++++|..+
T Consensus 430 ~~eev~~~v~~~m~~~~eeg~~~R~rA~elk~~a~~Av~~GGSS~~nl~~fv~~i~~~ 487 (491)
T PLN02534 430 KKDEVEKAVKTLMDDGGEEGERRRRRAQELGVMARKAMELGGSSHINLSILIQDVLKQ 487 (491)
T ss_pred CHHHHHHHHHHHhccccccHHHHHHHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHHH
Confidence 46777777766664 222 233455566666676677778999999988643
No 152
>PLN02848 adenylosuccinate lyase
Probab=23.39 E-value=3.1e+02 Score=21.82 Aligned_cols=54 Identities=19% Similarity=0.328 Sum_probs=31.7
Q ss_pred HHHHHHHHHHhcChHHHHHHHHHHHHHhhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHH
Q 042650 10 LKELLRERLIECGWRDEMKSLCRAYTRKKGRNNVTVDDLVHVITPKGRASVPDPVKAELLQ 70 (81)
Q Consensus 10 L~~~L~~rL~e~GW~D~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~~VP~~vk~Ell~ 70 (81)
+.+.+...|.+.| +++-.+..++....+.+..-++.++++.+ .+|++++.+|+.
T Consensus 388 ~sE~~~~~l~~~G-~~~A~e~v~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~l~~ 441 (458)
T PLN02848 388 LAEPIQTVMRRYG-VPEPYEKLKELTRGRAVTKESMREFIEGL------ELPEEAKDQLLK 441 (458)
T ss_pred HHHHHHHHHHHhC-hHHHHHHHHHHHHHccCCHHHHHHHHHHc------CCCHHHHHHHHh
Confidence 5556666666666 45555555555554433333444444443 399999988874
No 153
>PF02697 DUF217: Uncharacterized ACR, COG1753; InterPro: IPR003847 This entry is represented by Natrialba phage PhiCh1, Orf96. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=23.39 E-value=1.8e+02 Score=17.42 Aligned_cols=14 Identities=7% Similarity=0.311 Sum_probs=12.2
Q ss_pred CCCCHHHHHHhhch
Q 042650 41 NNVTVDDLVHVITP 54 (81)
Q Consensus 41 ~~v~~~~L~~~i~P 54 (81)
++-||++++..++|
T Consensus 20 ~~eSFSdvI~rli~ 33 (71)
T PF02697_consen 20 EDESFSDVIERLIE 33 (71)
T ss_pred CCCCHHHHHHHHHh
Confidence 45599999999999
No 154
>PRK10829 ribonuclease D; Provisional
Probab=23.29 E-value=2.6e+02 Score=21.66 Aligned_cols=44 Identities=16% Similarity=0.311 Sum_probs=33.3
Q ss_pred HHHHHHHHHHHhcChHHHHHHHHHHHHHhhCCCCCCHHHHHHhhc
Q 042650 9 RLKELLRERLIECGWRDEMKSLCRAYTRKKGRNNVTVDDLVHVIT 53 (81)
Q Consensus 9 rL~~~L~~rL~e~GW~D~vr~~~re~i~~~g~~~v~~~~L~~~i~ 53 (81)
.|.+.|..+|.+.|+.+-+.+-|..+...+ ....+.++.+..|.
T Consensus 161 ~l~~~L~~~L~~~g~~~w~~ee~~~l~~~~-~~~~~~~~~~~~ik 204 (373)
T PRK10829 161 PIAAKLMAETEAAGWLPAALDECRLLCQRR-QEVLAPEEAYRDIT 204 (373)
T ss_pred HHHHHHHHHHHHcCcHHHHHHHHHHHHhcc-ccCCChHHHHHHhc
Confidence 356788999999999999999998776543 23456677777774
No 155
>COG3514 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.22 E-value=94 Score=19.93 Aligned_cols=19 Identities=21% Similarity=0.564 Sum_probs=15.6
Q ss_pred hcChHHHHHHHHHHHHHhh
Q 042650 20 ECGWRDEMKSLCRAYTRKK 38 (81)
Q Consensus 20 e~GW~D~vr~~~re~i~~~ 38 (81)
.-||.+.|-..-|+++...
T Consensus 74 GkGwQtRiN~aLR~~~~~~ 92 (93)
T COG3514 74 GKGWQTRINAALRQYMAAH 92 (93)
T ss_pred CccHHHHHHHHHHHHHHhc
Confidence 3589999999999888764
No 156
>PLN02764 glycosyltransferase family protein
Probab=23.18 E-value=1.4e+02 Score=23.63 Aligned_cols=49 Identities=16% Similarity=0.177 Sum_probs=28.9
Q ss_pred hHHHHHHHHHHHHHhcC-hHHHHHHHH---HHHHHhhCCCCCCHHHHHHhhch
Q 042650 6 EKERLKELLRERLIECG-WRDEMKSLC---RAYTRKKGRNNVTVDDLVHVITP 54 (81)
Q Consensus 6 e~erL~~~L~~rL~e~G-W~D~vr~~~---re~i~~~g~~~v~~~~L~~~i~P 54 (81)
+.+.|.+.+++-+...+ =..++|..+ |+.+++.|+...++++|++++.-
T Consensus 393 ~~e~i~~av~~vm~~~~~~g~~~r~~a~~~~~~~~~~GSS~~~l~~lv~~~~~ 445 (453)
T PLN02764 393 SKESLRDAINSVMKRDSEIGNLVKKNHTKWRETLASPGLLTGYVDNFIESLQD 445 (453)
T ss_pred CHHHHHHHHHHHhcCCchhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Confidence 56778888876664332 022333333 34455667766788888887743
No 157
>PRK13756 tetracycline repressor protein TetR; Provisional
Probab=23.17 E-value=1.6e+02 Score=20.45 Aligned_cols=28 Identities=11% Similarity=0.181 Sum_probs=14.9
Q ss_pred HHHHHHHHHHHHhhCCCCCCHHHHHHhh
Q 042650 25 DEMKSLCRAYTRKKGRNNVTVDDLVHVI 52 (81)
Q Consensus 25 D~vr~~~re~i~~~g~~~v~~~~L~~~i 52 (81)
+.|=..+.+.+.+.|.+.+|+.+|.+++
T Consensus 7 e~Il~aA~~l~~e~G~~~lsmr~lA~~l 34 (205)
T PRK13756 7 EKVIDSALELLNEVGIEGLTTRKLAQKL 34 (205)
T ss_pred HHHHHHHHHHHHHcCcccCCHHHHHHHh
Confidence 3444455555555555555555555443
No 158
>PRK01388 arginine deiminase; Provisional
Probab=23.09 E-value=1.1e+02 Score=24.07 Aligned_cols=30 Identities=17% Similarity=0.368 Sum_probs=22.3
Q ss_pred hHHHHHH---HHHHHHHhhCCCCCCHHHHHHhh
Q 042650 23 WRDEMKS---LCRAYTRKKGRNNVTVDDLVHVI 52 (81)
Q Consensus 23 W~D~vr~---~~re~i~~~g~~~v~~~~L~~~i 52 (81)
|.++.++ .-.++++++|+..+-+++|+++.
T Consensus 45 ~l~~aq~EHd~f~~~Lr~~GveV~~l~dll~e~ 77 (406)
T PRK01388 45 WVERAQKEHDAFAQTLRDRGVEVLYLEDLLAET 77 (406)
T ss_pred CHHHHHHHHHHHHHHHHHCCCEEEEhHHHHHHH
Confidence 5554443 34467888999999999999988
No 159
>PRK04309 DNA-directed RNA polymerase subunit A''; Validated
Probab=23.03 E-value=1.2e+02 Score=23.74 Aligned_cols=27 Identities=15% Similarity=0.260 Sum_probs=19.8
Q ss_pred HHhhchhhhccCCHHHHHHHHHHHHHH
Q 042650 49 VHVITPKGRASVPDPVKAELLQRIRSF 75 (81)
Q Consensus 49 ~~~i~P~Ar~~VP~~vk~Ell~~Ir~f 75 (81)
+++..-.+...+|+.+++|+..++..+
T Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 33 (383)
T PRK04309 7 LEEKLEDASLELPQKLKEELREKLEER 33 (383)
T ss_pred HHHHHHhhcccCCHHHHHHHHHHHHHc
Confidence 444445556669999999999988764
No 160
>COG2115 XylA Xylose isomerase [Carbohydrate transport and metabolism]
Probab=22.99 E-value=2.4e+02 Score=22.46 Aligned_cols=57 Identities=18% Similarity=0.354 Sum_probs=42.0
Q ss_pred HHHHHHHHHHHhcChHHHHHHHHHHHHHhhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHH
Q 042650 9 RLKELLRERLIECGWRDEMKSLCRAYTRKKGRNNVTVDDLVHVITPKGRASVPDPVKAELLQRIRS 74 (81)
Q Consensus 9 rL~~~L~~rL~e~GW~D~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~~VP~~vk~Ell~~Ir~ 74 (81)
.|++.+..|-. ||...+- +++++ | ..|+++|.+.+..+-.+-.|++=++|.+..|-+
T Consensus 379 ~l~~~i~eRYa--~~~~~~g---q~il~--G--~~~le~la~~~~~~~~~~~~~Sg~qE~len~vN 435 (438)
T COG2115 379 VLSKPIAERYA--GWNSELG---QQILN--G--KTSLEELAAYALEHDLNPEHQSGRQEYLENLVN 435 (438)
T ss_pred hhhHHHHHHhh--ccchHHH---HHHHc--C--cCCHHHHHHHHHhcCCCCCCCccHHHHHHHHHh
Confidence 34455555554 7876554 44553 4 569999999999999999999999999887643
No 161
>COG2901 Fis Factor for inversion stimulation Fis, transcriptional activator [Transcription / DNA replication, recombination, and repair]
Probab=22.99 E-value=2.2e+02 Score=18.34 Aligned_cols=47 Identities=21% Similarity=0.336 Sum_probs=31.9
Q ss_pred ChHHHHHHHHHHHHHhhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHHhhh
Q 042650 22 GWRDEMKSLCRAYTRKKGRNNVTVDDLVHVITPKGRASVPDPVKAELLQRIRSFLAS 78 (81)
Q Consensus 22 GW~D~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~~VP~~vk~Ell~~Ir~fL~~ 78 (81)
--+|.|++.-+.+++.-+ .-.+.+||+.|. .+|-+=|+..|-++-..
T Consensus 26 plRdsV~~~L~~Y~~~L~--G~~v~~lY~mVL--------~evE~PLL~~vM~~~~g 72 (98)
T COG2901 26 PLRDSVKQALKNYFADLN--GQDVNDLYEMVL--------AEVEQPLLDMVMQYTRG 72 (98)
T ss_pred cHHHHHHHHHHHHHHHcC--CCChhhHHHHHH--------HHHHhHHHHHHHHHhcc
Confidence 457889999999988654 447788887654 35556666666665543
No 162
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=22.96 E-value=1.6e+02 Score=18.18 Aligned_cols=42 Identities=12% Similarity=0.138 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHhhCCCCCCHHHHHHhhchhhhccCCHHHHHHH
Q 042650 26 EMKSLCRAYTRKKGRNNVTVDDLVHVITPKGRASVPDPVKAEL 68 (81)
Q Consensus 26 ~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~~VP~~vk~El 68 (81)
.-|...-+.+.+.+. .+|.++|++.+.++...+=+..|++-|
T Consensus 8 ~~R~~Il~~l~~~~~-~~ta~ei~~~l~~~~~~is~~TVYR~L 49 (120)
T PF01475_consen 8 PQRLAILELLKESPE-HLTAEEIYDKLRKKGPRISLATVYRTL 49 (120)
T ss_dssp HHHHHHHHHHHHHSS-SEEHHHHHHHHHHTTTT--HHHHHHHH
T ss_pred HHHHHHHHHHHcCCC-CCCHHHHHHHhhhccCCcCHHHHHHHH
Confidence 345666677777764 899999999998766555455566544
No 163
>PF07830 PP2C_C: Protein serine/threonine phosphatase 2C, C-terminal domain; InterPro: IPR012911 Protein phosphatase 2C (PP2C) is involved in regulating cellular responses to stress in various eukaryotes. It consists of two domains: an N-terminal catalytic domain and a C-terminal domain characteristic of mammalian PP2Cs. This domain consists of three antiparallel alpha helices, one of which packs against two corresponding alpha-helices of the N-terminal domain. The C-terminal domain does not seem to play a role in catalysis, but it may provide protein substrate specificity due to the cleft that is created between it and the catalytic domain []. ; GO: 0000287 magnesium ion binding, 0004721 phosphoprotein phosphatase activity, 0030145 manganese ion binding; PDB: 2P8E_A 3FXL_A 3FXO_A 1A6Q_A 3FXK_A 3FXM_A 3FXJ_A.
Probab=22.95 E-value=82 Score=19.49 Aligned_cols=41 Identities=17% Similarity=0.199 Sum_probs=18.7
Q ss_pred HhcChHHHHHHHHHHHHHhhCCCCCCHHHHHHhhchhhhccCC
Q 042650 19 IECGWRDEMKSLCRAYTRKKGRNNVTVDDLVHVITPKGRASVP 61 (81)
Q Consensus 19 ~e~GW~D~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~~VP 61 (81)
.|-.|...+.+.+++++++.+ ...+.+|+.-+.--|.+-+|
T Consensus 20 ~E~eLd~~l~~rv~ei~~~~~--~~~~~~l~~V~~~L~~e~ip 60 (81)
T PF07830_consen 20 KEAELDKYLEQRVEEIIEKSS--EEENPDLVYVMRTLASEDIP 60 (81)
T ss_dssp HHHHHHHHHHHHHHHHT------------HHHHHHHHHHTT-S
T ss_pred HHHHHHHHHHHHHHHHHHHhc--ccCCCCHHHHHHHHHhccCC
Confidence 345677888889999997743 22344444333334444444
No 164
>PF04794 YdjC: YdjC-like protein; InterPro: IPR006879 This entry contains ChbG (YdjC), which is is an uncharacterised protein encoded by the chb (N,N'-diacetylchitobiose, also called [GlcNAc]2) or cel operon, which encodes enzymes involved in growth on an N,N'-diacetylchitobiose carbon source [, ]. The entry also contains HpnK, which is a protein associated with hopanoid biosynthesis.; PDB: 2E67_C 2I5I_B.
Probab=22.83 E-value=61 Score=23.15 Aligned_cols=22 Identities=32% Similarity=0.344 Sum_probs=17.7
Q ss_pred hhccCCHHHHHHHHHHHHHHhh
Q 042650 56 GRASVPDPVKAELLQRIRSFLA 77 (81)
Q Consensus 56 Ar~~VP~~vk~Ell~~Ir~fL~ 77 (81)
.+..-+++|..|+-.||..|++
T Consensus 96 ~~~~~~~ev~~E~~AQi~~f~~ 117 (261)
T PF04794_consen 96 LRRADYEEVERELRAQIERFLD 117 (261)
T ss_dssp CCC--HHHHHHHHHHHHHHHHC
T ss_pred hccCCHHHHHHHHHHHHHHHHH
Confidence 3566789999999999999986
No 165
>cd08315 Death_TRAILR_DR4_DR5 Death domain of Tumor necrosis factor-Related Apoptosis-Inducing Ligand Receptors. Death Domain (DD) found in Tumor necrosis factor-Related Apoptosis-Inducing Ligand (TRAIL) Receptors. In mammals, this family includes TRAILR1 (also called DR4 or TNFRSF10A) and TRAILR2 (also called DR5, TNFRSF10B, or KILLER). They function as receptors for the cytokine TRAIL and are involved in apoptosis signaling pathways. TRAIL preferentially induces apoptosis in cancer cells while exhibiting little toxicity in normal cells. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=22.81 E-value=2e+02 Score=17.86 Aligned_cols=45 Identities=18% Similarity=0.434 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHHHhhCCCCCCHHHHHHhhchhhhccCCHHHHHHHH
Q 042650 24 RDEMKSLCRAYTRKKGRNNVTVDDLVHVITPKGRASVPDPVKAELL 69 (81)
Q Consensus 24 ~D~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~~VP~~vk~Ell 69 (81)
.+++.++-+..-+..| .+.|++.|++.+.-.....+-+.|...++
T Consensus 47 ~eq~~qmL~~W~~~~G-~~At~~~L~~aL~~~~~~~~Ae~I~~~l~ 91 (96)
T cd08315 47 REQLYQMLLTWVNKTG-RKASVNTLLDALEAIGLRLAKESIQDELI 91 (96)
T ss_pred HHHHHHHHHHHHHhhC-CCcHHHHHHHHHHHcccccHHHHHHHHHH
Confidence 6666666665556566 46799999999987777777777755543
No 166
>cd03568 VHS_STAM VHS domain family, STAM subfamily; members include STAM (Signal Transducing Adaptor Molecule), EAST (EGFR-associated protein with SH3 and TAM domains) and Hbp (Hrs-binding protein). Collectively, they are referred to as STAM. All STAMs have at their N-termini a VHS domain, which is involved in cytokine-mediated intracellular signal transduction and has a superhelical structure similar to the structure of ARM (Armadillo) repeats, followed by a SH3 (Src homology 3) domain, a well-established protein-protein interaction domain. At the C-termini of most vertebrate STAMS, an ITAM (Immunoreceptor Tyrosine-based Activation) motif is present, which mediates the binding of HRS (hepatocyte growth factor-regulated tyrosine kinase substrate) in endocytic and exocytic machineries.
Probab=22.76 E-value=1.5e+02 Score=19.75 Aligned_cols=17 Identities=24% Similarity=0.382 Sum_probs=14.9
Q ss_pred CCHHHHHHHHHHHHHHh
Q 042650 60 VPDPVKAELLQRIRSFL 76 (81)
Q Consensus 60 VP~~vk~Ell~~Ir~fL 76 (81)
.|..||+.++.-|+++=
T Consensus 93 ~~~~Vk~kil~li~~W~ 109 (144)
T cd03568 93 VHPTVKEKLREVVKQWA 109 (144)
T ss_pred CCHHHHHHHHHHHHHHH
Confidence 89999999999998763
No 167
>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional
Probab=22.70 E-value=4e+02 Score=22.99 Aligned_cols=69 Identities=13% Similarity=0.139 Sum_probs=43.1
Q ss_pred hhHHHHHHHHHHHHHhc--ChH-----HHHHHHHHHHHHhhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHHh
Q 042650 5 GEKERLKELLRERLIEC--GWR-----DEMKSLCRAYTRKKGRNNVTVDDLVHVITPKGRASVPDPVKAELLQRIRSFL 76 (81)
Q Consensus 5 Ge~erL~~~L~~rL~e~--GW~-----D~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~~VP~~vk~Ell~~Ir~fL 76 (81)
.|...++++|.+++..- .|. +.+.....+.+-+.|++.....+|++++... .-|+.+++-+.+.|..++
T Consensus 97 ~El~~lk~~L~~~l~~~~~~~~~~~~~~~~~~~l~~~Ll~~dv~~~la~~l~~~l~~~---~~~~~~~~~l~~~L~~~l 172 (767)
T PRK14723 97 GELQSMRGMLERQLAGLLWAAGEVAGRDPLRASLFRWLLGAGFSGQLARALLERLPVG---YDRPAAMAWIRNELATHL 172 (767)
T ss_pred HHHHHHHHHHHHHHHHHhhhccccccChHHHHHHHHHHHHCCCCHHHHHHHHHHHHhc---CCHHHHHHHHHHHHHHHh
Confidence 46677888887777664 333 4555556677777888877788888887332 234455555555554443
No 168
>cd08776 DED_Caspase-like_repeat1 Death effector domain, repeat 1, of initator caspase-like proteins. Death Effector Domain (DED), first repeat, found in initator caspase-like proteins, like caspase-8 and -10 and c-FLIP. Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. Initiator caspases are the first to be activated following death- or inflammation-inducing signals. Caspase-8 and -10 are the initiators of death receptor mediated apoptosis. Together with FADD and the pseudo-caspase c-FLIP, they form the death-inducing signaling complex (DISC), whose formation is triggered by the activation of type 1 tumor necrosis factor (TNF) receptors such as Fas, TNF receptor 1, and TRAIL receptor. Caspase-8 and -10 also play important functions in cell adhesion and motility. c-FLIP is a catalytically inactive homolog of the initator procaspases-8 and -10. It negatively influences apoptotic signaling by interfering with the efficient formation of DI
Probab=22.65 E-value=1.7e+02 Score=17.60 Aligned_cols=48 Identities=17% Similarity=0.169 Sum_probs=33.8
Q ss_pred HHHHHHHHHHHHHhhCCCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHH
Q 042650 24 RDEMKSLCRAYTRKKGRNNVTVDDLVHVITPKGRASVPDPVKAELLQRIRSF 75 (81)
Q Consensus 24 ~D~vr~~~re~i~~~g~~~v~~~~L~~~i~P~Ar~~VP~~vk~Ell~~Ir~f 75 (81)
.+.++=+|+..|-++..+ +.-+++..+ +-+++++...-.|++.+|+-+
T Consensus 17 ~~~lkFLC~d~ip~~~le--~~~~lf~~L--~e~~~L~~~fL~ElL~~I~R~ 64 (71)
T cd08776 17 REVLLFLLNVFIPQPTLA--QLIGALRAL--KEEGRLTLPLLAECLYRAGRR 64 (71)
T ss_pred HHHHHHHcccccccccch--hHHHHHHHH--HHcCCCCHHHHHHHHHHhCHH
Confidence 456777888888654333 366777765 346777889999999998653
No 169
>PRK05910 type III secretion system protein; Validated
Probab=22.38 E-value=2.3e+02 Score=23.68 Aligned_cols=67 Identities=18% Similarity=0.273 Sum_probs=43.8
Q ss_pred hhHHHHHHHHHHHHHhcChHHHHHHHHHHHHHhhC-CCCCCHHHHHHhhchhhhccCCHHHHHHHHHHHHHHhhhh
Q 042650 5 GEKERLKELLRERLIECGWRDEMKSLCRAYTRKKG-RNNVTVDDLVHVITPKGRASVPDPVKAELLQRIRSFLAST 79 (81)
Q Consensus 5 Ge~erL~~~L~~rL~e~GW~D~vr~~~re~i~~~g-~~~v~~~~L~~~i~P~Ar~~VP~~vk~Ell~~Ir~fL~~~ 79 (81)
.|-+.|-+..|++|. |+.|..+....| ...++++.=++...-.+..-++++.-+.+++++++.+++.
T Consensus 461 kd~~~LtE~VR~~L~--------r~I~~~~~~~~g~L~vitL~p~~E~~l~~si~~L~P~~~~~li~~v~~~~~~~ 528 (584)
T PRK05910 461 KSSEELVEKVRKYLG--------KQIGRSLWNRQDTLEVITIDSHVEQFIRDSYSKSNPDMNEKVVAQVKSLLERS 528 (584)
T ss_pred CCHHHHHHHHHHHHH--------HHHHHHhhCCCCeEEEEEeCHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHH
Confidence 455667777777776 577777765444 3334444444444444444488889999999999887653
No 170
>TIGR03182 PDH_E1_alph_y pyruvate dehydrogenase E1 component, alpha subunit. Members of this protein family are the alpha subunit of the E1 component of pyruvate dehydrogenase (PDH). This model represents one branch of a larger family that E1-alpha proteins from 2-oxoisovalerate dehydrogenase, acetoin dehydrogenase, another PDH clade, etc.
Probab=22.10 E-value=3e+02 Score=20.42 Aligned_cols=41 Identities=24% Similarity=0.349 Sum_probs=22.0
Q ss_pred HHHHHHHHhcC---------hHHHHHHHHHHHHH-hhCCCCCCHHHHHHhh
Q 042650 12 ELLRERLIECG---------WRDEMKSLCRAYTR-KKGRNNVTVDDLVHVI 52 (81)
Q Consensus 12 ~~L~~rL~e~G---------W~D~vr~~~re~i~-~~g~~~v~~~~L~~~i 52 (81)
..++++|.+.| |.+++++...+..+ ......++.+++++.|
T Consensus 263 ~~~~~~L~~~g~~~~~~~~~~~~~~~~~v~~a~~~a~~~p~p~~~~~~~~v 313 (315)
T TIGR03182 263 EKLKARLIEQGIASEEELKEIDKEVRAEVEEAVEFAENSPEPPVEELYTDV 313 (315)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHhhc
Confidence 47788898888 33333333333222 1223455666666654
No 171
>PLN03007 UDP-glucosyltransferase family protein
Probab=21.98 E-value=1.3e+02 Score=23.68 Aligned_cols=48 Identities=13% Similarity=0.295 Sum_probs=32.3
Q ss_pred hHHHHHHHHHHHHHhc---ChHHH---HHHHHHHHHHhhCCCCCCHHHHHHhhc
Q 042650 6 EKERLKELLRERLIEC---GWRDE---MKSLCRAYTRKKGRNNVTVDDLVHVIT 53 (81)
Q Consensus 6 e~erL~~~L~~rL~e~---GW~D~---vr~~~re~i~~~g~~~v~~~~L~~~i~ 53 (81)
+.+.|.+.++.-+.+. .++++ +++.+++.+.+.|+..-+++++++.+.
T Consensus 426 ~~~~l~~av~~~m~~~~~~~~r~~a~~~~~~a~~a~~~gGsS~~~l~~~v~~~~ 479 (482)
T PLN03007 426 SREKVEKAVREVIVGEEAEERRLRAKKLAEMAKAAVEEGGSSFNDLNKFMEELN 479 (482)
T ss_pred cHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHH
Confidence 5677888887777554 45444 445566666666766678888888775
No 172
>PRK09358 adenosine deaminase; Provisional
Probab=21.91 E-value=2e+02 Score=21.07 Aligned_cols=36 Identities=25% Similarity=0.380 Sum_probs=24.8
Q ss_pred CCCHHHHHHhhc-hhhhccCCHHHHHHHHHHHHHHhh
Q 042650 42 NVTVDDLVHVIT-PKGRASVPDPVKAELLQRIRSFLA 77 (81)
Q Consensus 42 ~v~~~~L~~~i~-P~Ar~~VP~~vk~Ell~~Ir~fL~ 77 (81)
+++.+++..-.. ...-...|++.|++++.+|.+++.
T Consensus 303 ~l~~~el~~l~~nai~~sf~~~~~k~~l~~~~~~~~~ 339 (340)
T PRK09358 303 GLSDEDLAQLARNALEAAFLSEEEKAALLAEVDAWLA 339 (340)
T ss_pred CCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHhc
Confidence 456666554322 233457899999999999998764
No 173
>cd03399 Band_7_flotillin Band_7_flotillin: a subgroup of the band 7 domain of flotillin (reggie) like proteins. This subgroup contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin. These two proteins are lipid raft-associated. Individual proteins of this band 7 domain family may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. Microdomains formed from flotillin proteins may in addition be dynamic units with their own regulatory functions. Flotillins have been implicated in signal transduction, vesicle trafficking, cytoskeleton rearrangement and, interact with a variety of proteins. Flotillins may play a role in the progression of prion disease, in the pathogenesis of neurodegenerative diseases such as Parkinson's and Alzheimer's disease and, in cancer invasion and metastasis.
Probab=21.77 E-value=2e+02 Score=17.96 Aligned_cols=28 Identities=14% Similarity=0.178 Sum_probs=18.0
Q ss_pred hHHHHHHHHHHHHHhhCCCCCCHHHHHHh
Q 042650 23 WRDEMKSLCRAYTRKKGRNNVTVDDLVHV 51 (81)
Q Consensus 23 W~D~vr~~~re~i~~~g~~~v~~~~L~~~ 51 (81)
....++..++..++.- +.+.++++|+..
T Consensus 56 ~~~~l~~~~~~~lR~~-ig~~tl~el~~~ 83 (128)
T cd03399 56 IEELVKEVLEGHLRAV-VGTMTVEEIYED 83 (128)
T ss_pred HHHHHHHHHHHHHHHH-HHhCCHHHHHHh
Confidence 4555555555555543 357799999985
No 174
>PF02205 WH2: WH2 motif; InterPro: IPR003124 The WH2 (WASP-Homology 2, or Wiskott-Aldrich homology 2) domain is an ~18 amino acids actin-binding motif. This domain was first recognised as an essential element for the regulation of the cytoskeleton by the mammalian Wiskott-Aldrich syndrome protein (WASP) family. WH2 proteins occur in eukaryotes from yeast to mammals, in insect viruses, and in some bacteria. The WH2 domain is found as a modular part of larger proteins; it can be associated with the WH1 or EVH1 domain and with the CRIB domain, and the WH2 domain can occur as a tandem repeat. The WH2 domain binds actin monomers and can facilitate the assembly of actin monomers into newly forming actin filaments [, ]. ; GO: 0005515 protein binding; PDB: 2D1K_C 3M1F_V 2A41_C 2A3Z_C 2VCP_E 2A40_F 3P8C_D 3M3N_W.
Probab=21.62 E-value=69 Score=16.09 Aligned_cols=14 Identities=29% Similarity=0.316 Sum_probs=10.7
Q ss_pred HHHHHHHHHHHHHH
Q 042650 62 DPVKAELLQRIRSF 75 (81)
Q Consensus 62 ~~vk~Ell~~Ir~f 75 (81)
..-+..||..|+.+
T Consensus 2 ~~~R~~LL~~Ir~G 15 (30)
T PF02205_consen 2 GDGRSALLSQIRKG 15 (30)
T ss_dssp STTHHHHHHHHHHH
T ss_pred CCcHHHHHHHHHHc
Confidence 34467889999988
No 175
>COG1071 AcoA Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, alpha subunit [Energy production and conversion]
Probab=21.54 E-value=2.6e+02 Score=21.82 Aligned_cols=40 Identities=23% Similarity=0.296 Sum_probs=25.4
Q ss_pred HHHHHHHhcC-----hHHHHHHHHHHHHHh-----hCCCCCCHHHHHHhh
Q 042650 13 LLRERLIECG-----WRDEMKSLCRAYTRK-----KGRNNVTVDDLVHVI 52 (81)
Q Consensus 13 ~L~~rL~e~G-----W~D~vr~~~re~i~~-----~g~~~v~~~~L~~~i 52 (81)
.|+..|.+-| |.+++++.|++++++ .....++.+++++.|
T Consensus 292 r~~~~L~~~g~~see~~~~i~~e~~~~V~ea~e~a~~~p~P~~~~~~~~V 341 (358)
T COG1071 292 RLRKYLIEAGILSEEELEAIEAEAKAEVDEAVEFAEASPYPDVSELFEDV 341 (358)
T ss_pred HHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHHHhCCCCChhHhhhcc
Confidence 4566666666 566677777777764 233456677776666
No 176
>PF08973 TM1506: Domain of unknown function (DUF1893); InterPro: IPR015067 This family consist of hypothetical bacterial proteins. ; PDB: 1VK9_A.
Probab=21.52 E-value=15 Score=24.83 Aligned_cols=49 Identities=18% Similarity=0.209 Sum_probs=27.0
Q ss_pred HHHHHHHHHhhCCCCCCHHHHHHhhchhh--------hccCCHHHHHHHHHHHHHHhh
Q 042650 28 KSLCRAYTRKKGRNNVTVDDLVHVITPKG--------RASVPDPVKAELLQRIRSFLA 77 (81)
Q Consensus 28 r~~~re~i~~~g~~~v~~~~L~~~i~P~A--------r~~VP~~vk~Ell~~Ir~fL~ 77 (81)
.+.|.+.+++.|+ .++|++++..|.-+. .-...-+--+|+...|++|+.
T Consensus 77 S~~Al~~L~~~gI-~v~y~~~Vp~I~NR~~tg~CP~E~~v~~~~d~ee~~~~i~~~~~ 133 (134)
T PF08973_consen 77 SEPALDLLEEAGI-KVSYDELVPYIINRDGTGMCPMETLVLEVEDPEEAYELIEEFIK 133 (134)
T ss_dssp EHHHHHHHHHTT---EEEEEEESS-B-SSSSSB-HHHHHHHT---HHHHHHHH-----
T ss_pred hHHHHHHHHHcCC-ceeHhhhhhhhccCCCCCCCcHHHHHHccCCHHHHHHHHHhhcC
Confidence 3568888999886 579999888887432 333334556788888888875
No 177
>PRK08105 flavodoxin; Provisional
Probab=21.49 E-value=1e+02 Score=20.28 Aligned_cols=25 Identities=16% Similarity=0.060 Sum_probs=20.9
Q ss_pred cchhHHHHHHHHHHHHHhcChHHHH
Q 042650 3 ESGEKERLKELLRERLIECGWRDEM 27 (81)
Q Consensus 3 esGe~erL~~~L~~rL~e~GW~D~v 27 (81)
++|+.+.+.+.|...|.+.|-.-.+
T Consensus 11 ~tGnte~~A~~l~~~l~~~g~~~~~ 35 (149)
T PRK08105 11 VYGNALLVAEEAEAILTAQGHEVTL 35 (149)
T ss_pred CchHHHHHHHHHHHHHHhCCCceEE
Confidence 6899999999999999888865443
No 178
>PF15163 Meiosis_expr: Meiosis-expressed
Probab=21.27 E-value=45 Score=20.68 Aligned_cols=12 Identities=42% Similarity=0.955 Sum_probs=10.1
Q ss_pred HHHhcChHHHHH
Q 042650 17 RLIECGWRDEMK 28 (81)
Q Consensus 17 rL~e~GW~D~vr 28 (81)
|+...||+|++.
T Consensus 16 RfQ~AGyRDe~E 27 (77)
T PF15163_consen 16 RFQQAGYRDEIE 27 (77)
T ss_pred HHHHcccccHHH
Confidence 677789999986
No 179
>PF08006 DUF1700: Protein of unknown function (DUF1700); InterPro: IPR012963 This family contains many hypothetical bacterial proteins and two putative membrane proteins (Q6GFD0 from SWISSPROT and Q6G806 from SWISSPROT).
Probab=21.25 E-value=1.9e+02 Score=19.41 Aligned_cols=41 Identities=15% Similarity=0.263 Sum_probs=26.8
Q ss_pred HHHHHHHHhcC--hHHHHHHHHHHHHHhhCCCCCCHHHHHHhh
Q 042650 12 ELLRERLIECG--WRDEMKSLCRAYTRKKGRNNVTVDDLVHVI 52 (81)
Q Consensus 12 ~~L~~rL~e~G--W~D~vr~~~re~i~~~g~~~v~~~~L~~~i 52 (81)
+.|+..|.... =++++-+..+|.+.+.+.+..|-+++++++
T Consensus 8 ~~L~~~L~~lp~~e~~e~l~~Y~e~f~d~~~~G~sEeeii~~L 50 (181)
T PF08006_consen 8 NELEKYLKKLPEEEREEILEYYEEYFDDAGEEGKSEEEIIAEL 50 (181)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhCCCCHHHHHHHc
Confidence 34444444222 356667777888887776667888888887
No 180
>PF14689 SPOB_a: Sensor_kinase_SpoOB-type, alpha-helical domain; PDB: 1F51_C 2FTK_B 1IXM_B.
Probab=21.21 E-value=72 Score=18.20 Aligned_cols=19 Identities=21% Similarity=0.407 Sum_probs=10.7
Q ss_pred HHhcChHHHHHHHHHHHHH
Q 042650 18 LIECGWRDEMKSLCRAYTR 36 (81)
Q Consensus 18 L~e~GW~D~vr~~~re~i~ 36 (81)
|.+.|=.|++++++.++..
T Consensus 33 llqlg~~~~a~eYi~~~~~ 51 (62)
T PF14689_consen 33 LLQLGKYEEAKEYIKELSK 51 (62)
T ss_dssp HHHTT-HHHHHHHHHHHHH
T ss_pred HHHCCCHHHHHHHHHHHHH
Confidence 4555666666666665554
No 181
>cd03565 VHS_Tom1 VHS domain family, Tom1 subfamily; The VHS domain is an essential part of Tom1 (Target of myb1 - retroviral oncogene) protein. The VHS domain has a superhelical structure similar to the structure of the ARM repeats and is present at the very N-termini of proteins. It is a right-handed superhelix of eight alpha helices. The VHS domain has been found in a number of proteins, some of which have been implicated in intracellular trafficking and sorting. The VHS domain of the Tom1 protein is essential for the negative regulation of Interleukin-1 and Tumor Necrosis Factor-induced signaling pathways.
Probab=21.06 E-value=1.6e+02 Score=19.49 Aligned_cols=27 Identities=33% Similarity=0.586 Sum_probs=19.4
Q ss_pred HHHhhchhhhccCCHHHHHHHHHHHHHHh
Q 042650 48 LVHVITPKGRASVPDPVKAELLQRIRSFL 76 (81)
Q Consensus 48 L~~~i~P~Ar~~VP~~vk~Ell~~Ir~fL 76 (81)
|+.-+.|+ ...|..||+.++.-|+++=
T Consensus 88 L~~~i~~~--~~~~~~Vk~kil~li~~W~ 114 (141)
T cd03565 88 LVKLINPK--NNPPTIVQEKVLALIQAWA 114 (141)
T ss_pred HHHHHccc--CCCcHHHHHHHHHHHHHHH
Confidence 55555443 3478899999999988764
No 182
>PF11867 DUF3387: Domain of unknown function (DUF3387); InterPro: IPR021810 This domain is functionally uncharacterised. This domain is found in bacteria and archaea. This presumed domain is typically between 255 to 340 amino acids in length. This domain is found associated with PF04851 from PFAM, PF04313 from PFAM.
Probab=20.75 E-value=3.4e+02 Score=20.28 Aligned_cols=23 Identities=17% Similarity=0.164 Sum_probs=11.7
Q ss_pred hhccCCHHHHHHHHHHHHHHhhh
Q 042650 56 GRASVPDPVKAELLQRIRSFLAS 78 (81)
Q Consensus 56 Ar~~VP~~vk~Ell~~Ir~fL~~ 78 (81)
+....+++.-.++-..|-+.|..
T Consensus 260 ~~~~~~~e~l~~la~el~~~lk~ 282 (335)
T PF11867_consen 260 AVEEMGDEELKELAKELTETLKE 282 (335)
T ss_pred ccccccHHHHHHHHHHHHHHhcc
Confidence 34455555555555555554443
No 183
>PF12732 YtxH: YtxH-like protein; InterPro: IPR024623 This family of uncharacterised proteins is found in bacteria. Proteins in this family are typically between 100 and 143 amino acids in length. The N-terminal region is the most conserved.
Probab=20.52 E-value=1.9e+02 Score=16.74 Aligned_cols=6 Identities=33% Similarity=0.756 Sum_probs=2.2
Q ss_pred HHHHHH
Q 042650 12 ELLRER 17 (81)
Q Consensus 12 ~~L~~r 17 (81)
+.|...
T Consensus 29 ~~l~~~ 34 (74)
T PF12732_consen 29 EKLKDK 34 (74)
T ss_pred HHHHHH
Confidence 333333
No 184
>PF14428 SCP1201-deam: SCP1.201-like deaminase
Probab=20.45 E-value=1.5e+02 Score=19.72 Aligned_cols=55 Identities=24% Similarity=0.396 Sum_probs=41.8
Q ss_pred chhHHHHHHHHHHHHHhcC------hHHHHHHHHHHHHHhhCCCCC----C----------HHHHHHhhchhhhcc
Q 042650 4 SGEKERLKELLRERLIECG------WRDEMKSLCRAYTRKKGRNNV----T----------VDDLVHVITPKGRAS 59 (81)
Q Consensus 4 sGe~erL~~~L~~rL~e~G------W~D~vr~~~re~i~~~g~~~v----~----------~~~L~~~i~P~Ar~~ 59 (81)
|| .+.....+...|.+.| +.+.|...+-..++..|..+. | -++++..|.|+...|
T Consensus 43 Sg-~d~~~~~~~~~l~~~~~~~~~~~~~HVE~k~Aa~Mr~~g~~~a~vvIN~n~pC~~~~gC~~~l~~iLP~GstL 117 (135)
T PF14428_consen 43 SG-RDEPAAAVNAFLPELGPPGPPTAASHVEGKAAAWMRRNGIKHATVVINPNGPCGGRDGCDQLLPAILPEGSTL 117 (135)
T ss_pred cC-CCchHHHHHHHhhhcCCCCCccchhhhhHHHHHHHHHcCCeEEEEEEeCCCCCCCccCHHHHHHHhCCCCCEE
Confidence 77 7778888888999999 888888888878877663221 3 788888888876543
No 185
>COG4004 Uncharacterized protein conserved in archaea [Function unknown]
Probab=20.42 E-value=67 Score=20.70 Aligned_cols=12 Identities=33% Similarity=0.625 Sum_probs=8.6
Q ss_pred HHHHHHhcChHH
Q 042650 14 LRERLIECGWRD 25 (81)
Q Consensus 14 L~~rL~e~GW~D 25 (81)
|.+.|.||||.=
T Consensus 17 i~~~l~e~g~~v 28 (96)
T COG4004 17 IMRGLSELGWTV 28 (96)
T ss_pred HHHHHHHhCeeE
Confidence 456678999963
No 186
>PF04376 ATE_N: Arginine-tRNA-protein transferase, N terminus; InterPro: IPR007471 Arginine-tRNA-protein transferase catalyses the post-translational conjugation of arginine to the N terminus of a protein. In eukaryotes, this functions as part of the N terminus rule pathway of protein degradation by conjugating a destabilising amino acid to the N-terminal aspartate or glutamate of a protein, targeting the protein for ubiquitin-dependent proteolysis. N-terminal cysteine is sometimes modified []. In Saccharomyces cerevisiae, Cys20, 23, 94 and/or 95 are thought to be important for activity []. Of these, only Cys 94 appears to be completely conserved in this family. This entry represents the N-terminal region of the enzyme arginine-tRNA-protein transferase, found in both eukaryotic and prokaryotic enzymes.; GO: 0004057 arginyltransferase activity, 0016598 protein arginylation
Probab=20.35 E-value=43 Score=20.22 Aligned_cols=16 Identities=25% Similarity=0.422 Sum_probs=12.9
Q ss_pred HHHHHHHHHHHhcChH
Q 042650 9 RLKELLRERLIECGWR 24 (81)
Q Consensus 9 rL~~~L~~rL~e~GW~ 24 (81)
.+...+.+.|.+-||+
T Consensus 30 ~~~~~~y~~Ll~~G~R 45 (80)
T PF04376_consen 30 SLSPEDYQQLLDRGFR 45 (80)
T ss_pred cCCHHHHHHHHHhCCc
Confidence 4556788899999997
Done!