Query 015601
Match_columns 404
No_of_seqs 372 out of 1817
Neff 8.6
Searched_HMMs 46136
Date Fri Mar 29 07:50:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015601.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015601hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2632 Rhomboid family protei 100.0 4.2E-28 9.2E-33 217.5 16.7 207 13-228 5-212 (258)
2 KOG0858 Predicted membrane pro 99.9 1.1E-26 2.4E-31 205.3 15.8 202 14-237 4-210 (239)
3 PRK10907 intramembrane serine 99.9 6.1E-23 1.3E-27 191.4 17.0 172 21-210 92-267 (276)
4 PTZ00101 rhomboid-1 protease; 99.9 5.2E-23 1.1E-27 191.4 16.1 178 21-217 51-244 (278)
5 PF04511 DER1: Der1-like famil 99.9 9.7E-23 2.1E-27 182.8 13.8 183 22-220 1-187 (197)
6 COG5291 Predicted membrane pro 99.9 2.1E-22 4.6E-27 176.7 8.1 170 22-209 19-192 (313)
7 COG0705 Membrane associated se 99.9 2.9E-20 6.2E-25 171.3 17.5 180 22-213 16-211 (228)
8 PF01694 Rhomboid: Rhomboid fa 99.8 4E-19 8.7E-24 151.8 8.2 139 60-214 2-143 (145)
9 KOG2289 Rhomboid family protei 99.7 2.2E-17 4.8E-22 154.8 2.1 137 57-211 112-252 (316)
10 KOG2290 Rhomboid family protei 99.4 2.5E-13 5.5E-18 129.6 3.8 143 61-219 448-591 (652)
11 KOG2890 Predicted membrane pro 99.3 8.8E-12 1.9E-16 114.0 10.5 198 18-219 20-221 (326)
12 PF00627 UBA: UBA/TS-N domain; 99.3 1.9E-12 4.1E-17 83.3 4.2 36 365-400 2-37 (37)
13 KOG4463 Uncharacterized conser 99.3 9.8E-12 2.1E-16 111.0 8.4 181 21-211 10-202 (323)
14 PF08551 DUF1751: Eukaryotic i 99.2 1.8E-11 3.9E-16 96.9 5.0 91 63-155 7-97 (99)
15 smart00165 UBA Ubiquitin assoc 99.1 6.4E-11 1.4E-15 76.3 4.9 35 366-400 2-36 (37)
16 cd00194 UBA Ubiquitin Associat 99.1 9.3E-11 2E-15 76.0 5.0 35 366-400 2-36 (38)
17 TIGR00601 rad23 UV excision re 99.0 6.3E-10 1.4E-14 108.5 8.5 35 366-400 157-191 (378)
18 KOG0011 Nucleotide excision re 98.8 8.3E-09 1.8E-13 95.9 6.6 36 365-400 135-170 (340)
19 KOG2980 Integral membrane prot 98.4 2.4E-07 5.3E-12 85.5 4.1 182 16-211 108-299 (310)
20 KOG0944 Ubiquitin-specific pro 98.3 5E-07 1.1E-11 91.1 4.9 61 344-404 614-675 (763)
21 KOG0418 Ubiquitin-protein liga 97.9 1.1E-06 2.4E-11 75.0 -2.6 37 365-401 162-199 (200)
22 PF14555 UBA_4: UBA-like domai 97.8 4.5E-05 9.7E-10 50.6 4.8 35 366-400 1-36 (43)
23 TIGR00601 rad23 UV excision re 97.6 6.2E-05 1.4E-09 73.7 4.5 39 365-403 337-376 (378)
24 PF02845 CUE: CUE domain; Int 97.4 0.00038 8.2E-09 45.8 4.7 35 366-400 2-38 (42)
25 COG5207 UBP14 Isopeptidase T [ 97.3 0.00024 5.2E-09 70.0 4.3 42 362-403 618-660 (749)
26 KOG0011 Nucleotide excision re 97.2 0.00044 9.5E-09 64.9 4.4 38 366-403 299-337 (340)
27 KOG2561 Adaptor protein NUB1, 96.9 0.00083 1.8E-08 65.3 4.0 36 365-400 303-338 (568)
28 PRK06369 nac nascent polypepti 96.9 0.0019 4.1E-08 51.9 5.4 38 363-400 74-112 (115)
29 smart00546 CUE Domain that may 96.8 0.0027 5.9E-08 41.9 4.8 35 366-400 3-39 (43)
30 TIGR00264 alpha-NAC-related pr 96.7 0.0032 7E-08 50.4 5.0 37 364-400 77-114 (116)
31 COG1308 EGD2 Transcription fac 96.5 0.0073 1.6E-07 48.6 5.8 38 363-400 82-120 (122)
32 PF09288 UBA_3: Fungal ubiquit 96.4 0.0037 7.9E-08 43.0 3.2 26 365-390 9-34 (55)
33 KOG0944 Ubiquitin-specific pro 96.4 0.0053 1.1E-07 62.8 5.6 40 363-402 569-610 (763)
34 COG5207 UBP14 Isopeptidase T [ 96.4 0.0067 1.5E-07 60.1 6.0 38 365-402 558-597 (749)
35 KOG2561 Adaptor protein NUB1, 96.2 0.0064 1.4E-07 59.3 4.9 37 364-400 428-464 (568)
36 KOG0010 Ubiquitin-like protein 95.4 0.019 4.2E-07 57.0 4.7 35 366-400 455-490 (493)
37 COG4008 Predicted metal-bindin 93.8 0.15 3.2E-06 41.1 5.2 35 365-400 114-148 (153)
38 PF06972 DUF1296: Protein of u 93.6 0.16 3.4E-06 35.4 4.4 37 366-402 6-45 (60)
39 PF11626 Rap1_C: TRF2-interact 92.1 0.19 4.1E-06 38.7 3.6 32 369-400 1-32 (87)
40 PF11547 E3_UbLigase_EDD: E3 u 90.8 0.41 8.9E-06 31.7 3.5 38 363-400 7-46 (53)
41 smart00804 TAP_C C-terminal do 89.1 0.83 1.8E-05 32.8 4.4 35 366-400 13-48 (63)
42 PF03943 TAP_C: TAP C-terminal 88.5 0.38 8.2E-06 33.0 2.2 34 367-400 2-36 (51)
43 KOG1071 Mitochondrial translat 87.8 1.2 2.5E-05 42.2 5.6 36 365-400 46-82 (340)
44 PF07499 RuvA_C: RuvA, C-termi 87.5 0.86 1.9E-05 30.6 3.4 25 366-390 4-28 (47)
45 PF07223 DUF1421: Protein of u 84.7 0.86 1.9E-05 44.4 3.2 21 366-386 322-342 (358)
46 PF02954 HTH_8: Bacterial regu 83.6 0.87 1.9E-05 29.6 1.9 24 377-400 5-28 (42)
47 PF08587 UBA_2: Ubiquitin asso 81.5 0.28 6.2E-06 32.5 -1.0 26 366-391 3-29 (46)
48 PF03474 DMA: DMRTA motif; In 79.9 2.7 5.9E-05 26.9 3.1 25 376-400 14-38 (39)
49 PF08938 HBS1_N: HBS1 N-termin 78.3 1.2 2.5E-05 33.6 1.3 27 376-402 42-70 (79)
50 PF11372 DUF3173: Domain of un 77.2 2.6 5.7E-05 29.6 2.7 20 370-389 7-26 (59)
51 KOG2239 Transcription factor c 77.0 8.1 0.00018 34.1 6.2 37 364-400 170-207 (209)
52 PF10152 DUF2360: Predicted co 73.3 30 0.00064 29.4 8.7 29 366-394 116-144 (148)
53 PRK14606 ruvA Holliday junctio 62.1 14 0.0003 32.8 4.6 25 366-390 144-168 (188)
54 PRK14603 ruvA Holliday junctio 60.4 16 0.00035 32.7 4.8 24 366-389 153-176 (197)
55 PRK14602 ruvA Holliday junctio 60.3 15 0.00033 33.0 4.6 24 366-389 156-179 (203)
56 PRK14604 ruvA Holliday junctio 59.9 16 0.00034 32.7 4.6 24 366-389 150-173 (195)
57 PRK14600 ruvA Holliday junctio 59.4 11 0.00024 33.4 3.5 26 366-391 146-171 (186)
58 PRK14601 ruvA Holliday junctio 58.5 11 0.00025 33.2 3.4 25 366-390 143-167 (183)
59 PRK13901 ruvA Holliday junctio 57.9 12 0.00027 33.3 3.6 26 366-391 145-170 (196)
60 TIGR00084 ruvA Holliday juncti 53.5 22 0.00049 31.6 4.5 25 366-390 148-172 (191)
61 COG0632 RuvA Holliday junction 52.5 22 0.00048 31.8 4.3 26 366-391 157-182 (201)
62 KOG1288 Amino acid transporter 52.1 3.4E+02 0.0073 29.3 13.8 88 8-97 313-401 (945)
63 PF10440 WIYLD: Ubiquitin-bind 50.6 25 0.00054 25.3 3.5 23 366-388 12-34 (65)
64 PF09527 ATPase_gene1: Putativ 49.4 82 0.0018 21.5 6.6 39 78-116 8-47 (55)
65 PRK08769 DNA polymerase III su 48.7 31 0.00067 33.4 5.0 35 366-400 175-209 (319)
66 KOG3763 mRNA export factor TAP 47.9 50 0.0011 34.1 6.4 35 366-400 536-571 (585)
67 KOG0943 Predicted ubiquitin-pr 47.2 1.5E+02 0.0033 33.9 10.0 43 360-402 184-229 (3015)
68 COG2103 Predicted sugar phosph 46.4 29 0.00063 32.4 4.1 35 366-400 234-269 (298)
69 PRK07993 DNA polymerase III su 45.2 39 0.00084 32.9 5.1 35 366-400 169-205 (334)
70 PF03765 CRAL_TRIO_N: CRAL/TRI 43.8 32 0.0007 23.4 3.2 28 373-400 25-52 (55)
71 PF03701 UPF0181: Uncharacteri 43.7 27 0.00057 23.7 2.5 20 366-385 17-36 (51)
72 PRK14605 ruvA Holliday junctio 43.0 43 0.00093 29.8 4.6 25 366-390 149-173 (194)
73 PRK05441 murQ N-acetylmuramic 39.6 50 0.0011 31.6 4.8 31 370-400 240-271 (299)
74 KOG1734 Predicted RING-contain 36.4 3.2E+02 0.007 25.6 9.1 40 51-98 89-128 (328)
75 TIGR02230 ATPase_gene1 F0F1-AT 36.0 1.7E+02 0.0038 23.0 6.5 39 78-116 50-89 (100)
76 PRK01905 DNA-binding protein F 35.7 33 0.00071 25.5 2.3 24 377-400 37-60 (77)
77 PF04695 Pex14_N: Peroxisomal 35.1 46 0.001 27.7 3.4 29 365-393 23-51 (136)
78 PRK05114 hypothetical protein; 34.9 43 0.00094 23.3 2.5 20 366-385 17-36 (59)
79 COG3105 Uncharacterized protei 34.1 62 0.0013 26.6 3.8 25 194-218 8-32 (138)
80 cd05007 SIS_Etherase N-acetylm 32.6 34 0.00073 31.9 2.4 31 367-397 224-255 (257)
81 PF05861 PhnI: Bacterial phosp 32.6 60 0.0013 31.5 4.0 33 368-400 44-78 (358)
82 PRK11677 hypothetical protein; 32.1 73 0.0016 26.6 4.0 25 194-218 3-27 (134)
83 COG3140 Uncharacterized protei 31.7 43 0.00093 23.1 2.1 35 366-400 17-55 (60)
84 PF14851 FAM176: FAM176 family 31.3 1.3E+02 0.0029 25.7 5.5 34 79-118 3-36 (153)
85 PF12244 DUF3606: Protein of u 30.5 74 0.0016 22.2 3.3 36 365-400 19-55 (57)
86 TIGR02854 spore_II_GA sigma-E 30.3 4.8E+02 0.01 24.7 11.0 28 78-105 11-38 (288)
87 PRK00430 fis global DNA-bindin 30.2 44 0.00096 26.0 2.3 24 377-400 55-78 (95)
88 PRK00116 ruvA Holliday junctio 29.9 86 0.0019 27.8 4.5 26 366-391 150-175 (192)
89 PLN02250 lipid phosphate phosp 29.6 5.2E+02 0.011 24.9 14.7 24 194-217 223-246 (314)
90 COG5457 Uncharacterized conser 29.2 65 0.0014 23.1 2.8 23 370-392 41-63 (63)
91 TIGR00274 N-acetylmuramic acid 28.8 95 0.0021 29.6 4.8 35 366-400 231-266 (291)
92 PRK12570 N-acetylmuramic acid- 28.8 75 0.0016 30.4 4.1 34 367-400 233-267 (296)
93 PF14898 DUF4491: Domain of un 27.4 1.4E+02 0.0031 23.1 4.5 46 77-123 3-54 (94)
94 PF10979 DUF2786: Protein of u 26.4 98 0.0021 20.2 3.1 23 367-389 5-31 (43)
95 PF08671 SinI: Anti-repressor 25.4 1.2E+02 0.0027 18.2 3.1 22 367-388 7-28 (30)
96 PF13105 DUF3959: Protein of u 25.4 4.6E+02 0.0099 23.1 7.7 11 64-74 87-97 (239)
97 PHA01514 O-antigen conversion 24.9 7.8E+02 0.017 25.4 11.8 22 136-157 318-339 (485)
98 PF09726 Macoilin: Transmembra 24.2 3.8E+02 0.0083 29.0 8.7 15 149-163 102-116 (697)
99 PF03419 Peptidase_U4: Sporula 23.9 6.2E+02 0.013 23.9 10.2 31 78-108 11-41 (293)
100 TIGR00274 N-acetylmuramic acid 23.6 95 0.0021 29.6 3.8 30 369-398 261-291 (291)
101 PRK06090 DNA polymerase III su 23.2 1.4E+02 0.0031 28.8 4.9 33 366-400 170-202 (319)
102 smart00553 SEP Domain present 22.3 62 0.0013 25.2 1.8 15 291-305 74-88 (93)
103 PRK05441 murQ N-acetylmuramic 22.2 1.3E+02 0.0028 28.8 4.4 33 368-400 265-298 (299)
104 COG2103 Predicted sugar phosph 22.2 1.2E+02 0.0026 28.5 3.8 33 367-399 262-295 (298)
105 PF06123 CreD: Inner membrane 22.0 8.4E+02 0.018 24.7 11.3 56 61-125 291-346 (430)
106 KOG4463 Uncharacterized conser 21.7 18 0.00038 33.6 -1.5 24 372-395 281-304 (323)
107 PRK09487 sdhC succinate dehydr 21.6 1.6E+02 0.0034 24.4 4.2 20 65-84 75-96 (129)
108 PF04632 FUSC: Fusaric acid re 21.4 9.7E+02 0.021 25.2 13.6 29 192-220 466-494 (650)
109 PF11848 DUF3368: Domain of un 21.2 1.6E+02 0.0035 19.5 3.5 25 366-390 22-48 (48)
110 PF14474 RTC4: RTC4-like domai 21.2 94 0.002 25.5 2.8 24 366-389 90-114 (124)
111 PF10905 DUF2695: Protein of u 21.1 1.6E+02 0.0035 20.3 3.4 25 367-391 20-44 (53)
112 cd04773 HTH_TioE_rpt2 Second H 20.0 2E+02 0.0043 22.8 4.4 34 367-400 48-83 (108)
No 1
>KOG2632 consensus Rhomboid family proteins [Function unknown]
Probab=99.96 E-value=4.2e-28 Score=217.46 Aligned_cols=207 Identities=44% Similarity=0.724 Sum_probs=184.3
Q ss_pred hhHHHhhccccHHHHHHHHHHHHHHHHHHHhcccccccceeechhhhccCcchhhhhhhhcccCHHHHHHHHHHHHHHHH
Q 015601 13 TRANQWWESIPFFTSAVVIVCGTIYLICLLFGYDSFYEICFLPSAVISRFQVYRFYTSIVFHGSLLHVLFNMLALVPLGS 92 (404)
Q Consensus 13 ~~~~~~~~~~P~vT~~li~~~v~~~~l~~~~~~~~~~~l~~~p~~i~~~~q~WRL~Ts~f~h~~~~hll~n~~~l~~~g~ 92 (404)
.+-.+++...|.+|..++.++.+++++..+... ......|..++.+.|+||++||.|+|.+..|+++||+.++..+.
T Consensus 5 g~~~~~~~~~p~~ts~~~~~~~~i~lv~~~~~i---~~~~~l~~~~l~~~ql~RL~Ty~l~H~s~~hllfnmlaL~~~g~ 81 (258)
T KOG2632|consen 5 GRVGQFWMKIPLLTSIVVVLAILIYLVSFFPGI---VEVLGLPSELLINWQLYRLITYALVHLSLPHLLFNMLALWPLGS 81 (258)
T ss_pred ccCccccccchHHHHHHHHHHHHHHHHhccchh---hhHhcCCHHHhhhHHHHHHHHHHHHhccHHHHHHHHHHHHhchh
Confidence 356678889999999999999999998887443 36677888888999999999999999999999999999999999
Q ss_pred HHHHHhC-cHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccccccccccChhHHHHHHHHHHHhhcCCccceeeEeec
Q 015601 93 ELERIMG-SVRMFYITILLATSNAILHLLIALLVAHIPFYRLQNVMDECAIGFSGVIFSLIVIETSLSGAQSRSVFGLFN 171 (404)
Q Consensus 93 ~lE~~~G-s~~~~~~~l~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~G~sg~i~~l~~~~~~~~p~~~~~~~~~~~ 171 (404)
.+|+.+| +.+++.+..+.+++.++++++++.++. .....++...+|.||+.|+++...+...|.+.+.+++.+.
T Consensus 82 ~fE~~~G~t~~~l~~~~llalf~gIl~ll~~~~~~-----~~d~~~~~~a~G~s~v~Fam~~~~~~~sp~r~~~~fg~~s 156 (258)
T KOG2632|consen 82 QFERTHGTTVRILMFTVLLALFSGILYLLAYHVFL-----LSDLVYVEGAIGFSGVLFAMMAVLEVQSPVRSRSVFGLFS 156 (258)
T ss_pred HHHhhccceehHHHHHHHHHHHHHHHHHHHHHHHh-----hcchhhhcccccccHHHHHHHHHHhhcCcccchhhccccc
Confidence 9999999 999999999999999999999886332 2334446778999999999999988889988888999999
Q ss_pred chhhHHHHHHHHHHHHhccchhHHHHHHHHHHHHHHHHHhhcccCCchhHHHHHhhh
Q 015601 172 IPAKWYPLILLVLFQVLMTNVSLLGHLCGILSGFAYTYGFFNLLMPGTSFYSAIESS 228 (404)
Q Consensus 172 i~~~~~p~~~l~~~~l~~~~~s~~~hl~G~l~G~l~~~~~l~~~~p~~~~~~~~e~~ 228 (404)
||.++.||++++.+.++.++.++++|+||+++|++|.+..+ ++.|..+.++.++..
T Consensus 157 iP~~l~Pw~lLi~~~~lvp~aSFlghl~GllvG~ay~~~~f-~lip~~~~~~~v~~~ 212 (258)
T KOG2632|consen 157 IPIVLAPWALLIATQILVPQASFLGHLCGLLVGYAYAFSSF-GLIPGIRNYRAVTEA 212 (258)
T ss_pred ccHHHHHHHHHHHHHHHccCchHHHHHHHHHHHHHHHHHhh-ccCCcchhHHHhhhh
Confidence 99999999999999999999999999999999999999877 888998888888763
No 2
>KOG0858 consensus Predicted membrane protein [Function unknown]
Probab=99.95 E-value=1.1e-26 Score=205.30 Aligned_cols=202 Identities=21% Similarity=0.326 Sum_probs=170.0
Q ss_pred hHHHhhccccHHHHHHHHHHHHHHHHHHHhcccccccceeechhhhccCcchhhhhhhhcccC-HHHHHHHHHHHHHHHH
Q 015601 14 RANQWWESIPFFTSAVVIVCGTIYLICLLFGYDSFYEICFLPSAVISRFQVYRFYTSIVFHGS-LLHVLFNMLALVPLGS 92 (404)
Q Consensus 14 ~~~~~~~~~P~vT~~li~~~v~~~~l~~~~~~~~~~~l~~~p~~i~~~~q~WRL~Ts~f~h~~-~~hll~n~~~l~~~g~ 92 (404)
.+.+++.++|+|||++.+.|+++.+++.+ +..++.++.++|+.+++++|+||++|+.|..+. .+|+++|++++|.+++
T Consensus 4 ~l~~~~~~iPpVTR~~~~~~v~tt~~~~l-~lIsP~~l~~~p~Lv~kk~QiWRliTs~lyfg~~gf~fl~n~~FlyrY~~ 82 (239)
T KOG0858|consen 4 DLLNFYLQIPPVTRYYTTACVVTTLLVRL-DLISPFQLYLNPELVFKKFQIWRLITSFLYFGPFGFDFLMNLYFLYRYSS 82 (239)
T ss_pred hHHHHHhcCChHHHHHHHHHHHHHHHHhh-cccCchheEecHHHHHhHhHHHHhhhhhheeccccHHHHHHHHHHHHHHH
Confidence 56679999999999999999999999987 677889999999999999999999999999988 5999999999999999
Q ss_pred HHHHHh---CcHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccccccccccChhHHHHHHHHHHHhhcCCccceeeEe
Q 015601 93 ELERIM---GSVRMFYITILLATSNAILHLLIALLVAHIPFYRLQNVMDECAIGFSGVIFSLIVIETSLSGAQSRSVFGL 169 (404)
Q Consensus 93 ~lE~~~---Gs~~~~~~~l~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~G~sg~i~~l~~~~~~~~p~~~~~~~~~ 169 (404)
.||+.. .+.+|++++++++++..+........+ =..+.++++++.|++.+|+.+++++++
T Consensus 83 ~LE~g~f~~rtadf~~mllf~~~l~~~~~~~~~~~f-----------------Lg~~l~~~l~YvWs~~Np~~~v~F~g~ 145 (239)
T KOG0858|consen 83 MLEEGSFRGRTADFLYMLLFGAVLLTLTGLFVYIVF-----------------LGQSLVFMLVYVWSKRNPDVIVSFFGL 145 (239)
T ss_pred HHhcCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHH-----------------HHHHHHHHHHHHHHhhCCCceEEEEEE
Confidence 999875 357889988888887765554322211 123478999999999999999999999
Q ss_pred ecchhhHHHHHHHHHHHHhccchhHHHHHHHHHHHHHHHHHhhcccCCchhH-HHHHhhhccccccccC
Q 015601 170 FNIPAKWYPLILLVLFQVLMTNVSLLGHLCGILSGFAYTYGFFNLLMPGTSF-YSAIESSSLLSTCIRQ 237 (404)
Q Consensus 170 ~~i~~~~~p~~~l~~~~l~~~~~s~~~hl~G~l~G~l~~~~~l~~~~p~~~~-~~~~e~~~~l~~~~~~ 237 (404)
+.++++|+||+++.+..++... + +..+.|+++||+|.+ ++.+.|.... ++.++++.+++++...
T Consensus 146 ~~f~a~YlPwvll~fs~l~g~~-~-~~dllGi~~GHiy~f--l~~~~p~~~gg~~~l~TP~~l~rl~~~ 210 (239)
T KOG0858|consen 146 ITFKAPYLPWVLLGFSFLFGGS-I-LVDLLGIIVGHIYYF--LDDVYPRDYGGRDLLKTPQFLKRLFAD 210 (239)
T ss_pred ecCccccchHHHHHHHHHhCCc-h-HHHHHhhhhheeEEE--EeeeccCCcCCcCcccCHHHHHHhcCC
Confidence 9999999999988887776543 3 999999999999988 8888877654 7777777766665554
No 3
>PRK10907 intramembrane serine protease GlpG; Provisional
Probab=99.90 E-value=6.1e-23 Score=191.42 Aligned_cols=172 Identities=22% Similarity=0.380 Sum_probs=125.3
Q ss_pred cccHHHHHHHHHHHHHHHHHHHhcccccccceeechhhhccCcchhhhhhhhcccCHHHHHHHHHHHHHHHHHHHHHhCc
Q 015601 21 SIPFFTSAVVIVCGTIYLICLLFGYDSFYEICFLPSAVISRFQVYRFYTSIVFHGSLLHVLFNMLALVPLGSELERIMGS 100 (404)
Q Consensus 21 ~~P~vT~~li~~~v~~~~l~~~~~~~~~~~l~~~p~~i~~~~q~WRL~Ts~f~h~~~~hll~n~~~l~~~g~~lE~~~Gs 100 (404)
+..|+|..++++|+++|++..+.+......+...|......+|+||++|+.|+|.++.|+++||+.+|.+|+.+|+.+|+
T Consensus 92 ~~~p~T~~li~i~i~vf~l~~~~~~~~~~~~l~~~~~~~~~~q~WRl~T~~flH~~~~Hl~fNml~l~~lG~~iE~~~G~ 171 (276)
T PRK10907 92 RAGPLTLGVMIACVVVFILMQILGDQTVMLWLAWPFDPSLKFELWRYFTHALLHFSLLHILFNLLWWWYLGGAVEKRLGS 171 (276)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHhccHHHHHHHhccccccccCCcHHHHhHHHHhCCHHHHHHHHHHHHHHHHHHHHHHCh
Confidence 45669999999999999988765432222233334444567899999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccccccccccChhHHHHHHHHHHHhhcCCccceeeEeecchhhHHH--
Q 015601 101 VRMFYITILLATSNAILHLLIALLVAHIPFYRLQNVMDECAIGFSGVIFSLIVIETSLSGAQSRSVFGLFNIPAKWYP-- 178 (404)
Q Consensus 101 ~~~~~~~l~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~G~sg~i~~l~~~~~~~~p~~~~~~~~~~~i~~~~~p-- 178 (404)
++++.+|++++++++++..++. .....|+||+++|++++........+ ..+ +.+|..++.
T Consensus 172 ~~~l~l~l~s~i~~~~~~~~~~---------------~~~~gGaSGvVygL~g~~~~~~~~~p--~~~-~~lp~~~~~f~ 233 (276)
T PRK10907 172 GKLIVITLISALLSGWVQSKFS---------------GPWFGGLSGVVYALMGYVWLRGERDP--QSG-IYLPRGLIAFA 233 (276)
T ss_pred HHHHHHHHHHHHHHHHHHHHHc---------------cchhhHHHHHHHHHHHHHHHHhcccc--ccc-hhhhHHHHHHH
Confidence 9999999999999988765432 12357999999999986433221111 111 123322222
Q ss_pred --HHHHHHHHHhccchhHHHHHHHHHHHHHHHHH
Q 015601 179 --LILLVLFQVLMTNVSLLGHLCGILSGFAYTYG 210 (404)
Q Consensus 179 --~~~l~~~~l~~~~~s~~~hl~G~l~G~l~~~~ 210 (404)
|+.+.+..++..++++.+|++|+++|+++++.
T Consensus 234 llwl~~g~~~~~g~~Ian~AHlgGli~Gll~g~~ 267 (276)
T PRK10907 234 LLWLVAGYFDLFGMSIANAAHVAGLAVGLAMAFW 267 (276)
T ss_pred HHHHHHHHHHccCcccHHHHHHHHHHHHHHHHHH
Confidence 22222344445678999999999999999884
No 4
>PTZ00101 rhomboid-1 protease; Provisional
Probab=99.90 E-value=5.2e-23 Score=191.36 Aligned_cols=178 Identities=20% Similarity=0.261 Sum_probs=127.6
Q ss_pred cccHHHHHHHHHHHHHHHHHHHhccc--------ccccc-eeechhhhccCcchhhhhhhhcccCHHHHHHHHHHHHHHH
Q 015601 21 SIPFFTSAVVIVCGTIYLICLLFGYD--------SFYEI-CFLPSAVISRFQVYRFYTSIVFHGSLLHVLFNMLALVPLG 91 (404)
Q Consensus 21 ~~P~vT~~li~~~v~~~~l~~~~~~~--------~~~~l-~~~p~~i~~~~q~WRL~Ts~f~h~~~~hll~n~~~l~~~g 91 (404)
++|.+|..++++++++|++....... ....+ +..+..+ .++|+||++|+.|+|.+++|+++||++++.+|
T Consensus 51 ~i~~l~~~Iiii~iivfil~l~~~~~~~l~p~~~~L~~~Ga~~~~~i-~~gq~WRLiT~~FlH~~~~HLl~Nm~~l~~~G 129 (278)
T PTZ00101 51 TWKSFIMAISIIQIIVFIISVSIKPADFLTPSDSLLVTLGANVASRI-KQGEIHRLILPIFLHANIFHTFFNVFFQLRMG 129 (278)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHhcccccCCCCHHHHHHHhCcchhhh-hcCCCHHHHHHHHHccCHHHHHHHHHHHHHHH
Confidence 46889999999999999887663211 11122 3456554 57999999999999999999999999999999
Q ss_pred HHHHHHhCcHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccccccccccChhHHHHHHHHHHHhhcCCccceeeEeec
Q 015601 92 SELERIMGSVRMFYITILLATSNAILHLLIALLVAHIPFYRLQNVMDECAIGFSGVIFSLIVIETSLSGAQSRSVFGLFN 171 (404)
Q Consensus 92 ~~lE~~~Gs~~~~~~~l~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~G~sg~i~~l~~~~~~~~p~~~~~~~~~~~ 171 (404)
..+|+.+|+.|++.+|+++|+.++++..++.. ....+|+||.+||++++.....-..+.. ..
T Consensus 130 ~~lE~~~G~~r~~ilYl~sGi~G~l~s~~~~~--------------~~~svGASgAifGLiGa~~~~lil~w~~----~~ 191 (278)
T PTZ00101 130 FTLEKNYGIVKIIILYFLTGIYGNILSSSVTY--------------CPIKVGASTSGMGLLGIVTSELILLWHV----IR 191 (278)
T ss_pred HHHHHHHChHHHHHHHHHHHHHHHHHHHHHcc--------------CCcEEehhHHHHHHHHHHHHHHHHHHHh----hc
Confidence 99999999999999999999999988765421 2457999999999998764321000000 01
Q ss_pred chhhHHH----HHHH---HHHHHhccchhHHHHHHHHHHHHHHHHHhhcccCC
Q 015601 172 IPAKWYP----LILL---VLFQVLMTNVSLLGHLCGILSGFAYTYGFFNLLMP 217 (404)
Q Consensus 172 i~~~~~p----~~~l---~~~~l~~~~~s~~~hl~G~l~G~l~~~~~l~~~~p 217 (404)
.+.+.+. ++++ +...+..+++++.+|++|+++|+++++.+.+.+..
T Consensus 192 ~~~~~~~~~i~~~li~~~l~~~~~g~~Id~~aHlGG~i~G~llg~~~~~~l~~ 244 (278)
T PTZ00101 192 HRERVVFNIIFFSLISFFYYFTFNGSNIDHVGHLGGLLSGISMGILYNSQMEN 244 (278)
T ss_pred cHHHHHHHHHHHHHHHHHHHHhcCCCCccHHHHHHHHHHHHHHHHHHHhhhhh
Confidence 1111111 1111 11122236789999999999999999987665443
No 5
>PF04511 DER1: Der1-like family; InterPro: IPR007599 The endoplasmic reticulum (ER) of the yeast Saccharomyces cerevisiae (Baker's yeast) contains a proteolytic system able to selectively degrade misfolded lumenal secretory proteins. For examination of the components involved in this degradation process, mutants were isolated. They could be divided into four complementation groups. The mutations led to stabilisation of two different substrates for this process, and the classes were called der for degradation in the ER. DER1 was cloned by complementation of the der1-2 mutation. The DER1 gene codes for a novel, hydrophobic protein that is localized to the ER. Deletion of DER1 abolished degradation of the substrate proteins, suggesting that the function of the Der1 protein may be specifically required for the degradation process associated with the ER []. Interestingly this family seems distantly related to the Rhomboid family of membrane peptidases. This family may also mediate degradation of misfolded proteins.
Probab=99.89 E-value=9.7e-23 Score=182.79 Aligned_cols=183 Identities=30% Similarity=0.425 Sum_probs=148.4
Q ss_pred ccHHHHHHHHHHHHHHHHHHHhcccccccceeechhhhccCcchhhhhhhhcccCH-HHHHHHHHHHHHHHHHHHHHh--
Q 015601 22 IPFFTSAVVIVCGTIYLICLLFGYDSFYEICFLPSAVISRFQVYRFYTSIVFHGSL-LHVLFNMLALVPLGSELERIM-- 98 (404)
Q Consensus 22 ~P~vT~~li~~~v~~~~l~~~~~~~~~~~l~~~p~~i~~~~q~WRL~Ts~f~h~~~-~hll~n~~~l~~~g~~lE~~~-- 98 (404)
+||+||++++.+++++++..+ +..++.++.++++.+++++|+||++|+.|..++. +++++++++++.+++.||+..
T Consensus 1 iPpVTR~~~~~~~~~s~l~~~-~~~~~~~l~~~~~~v~~~~q~WRl~Tsff~~g~~~~~~l~~~~~l~~~s~~LE~~~f~ 79 (197)
T PF04511_consen 1 IPPVTRYWLISTVALSLLVSF-GIISPYYLYFDWELVFKKFQIWRLFTSFFYFGPFSLNFLFNLYFLYQYSSSLEEGHFQ 79 (197)
T ss_pred CChhHHHHHHHHHHHHHHHHC-CCCCHHHeeECcHHHhhhcCceeeEEEEEEEcCCCHHHHHHHHHHHHHhhHhccCCCC
Confidence 599999999999999998876 6567788999999999999999999999998766 899999999999999999983
Q ss_pred C-cHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccccccccccChhHHHHHHHHHHHhhcCCccceeeEeecchhhHH
Q 015601 99 G-SVRMFYITILLATSNAILHLLIALLVAHIPFYRLQNVMDECAIGFSGVIFSLIVIETSLSGAQSRSVFGLFNIPAKWY 177 (404)
Q Consensus 99 G-s~~~~~~~l~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~G~sg~i~~l~~~~~~~~p~~~~~~~~~~~i~~~~~ 177 (404)
+ +.+|+++++++++...++..+..... .+. ..-...+.+++++.|++.+|+.++++++++++|++|+
T Consensus 80 ~~~ady~~~ll~~~~~i~~~~~~~~~~~-----------~~~-~~l~~~l~~~l~Y~wsr~np~~~v~~~g~~~i~a~yl 147 (197)
T PF04511_consen 80 GRSADYLWFLLFGASLILILSLLIGPYF-----------FNI-PFLGSSLSFALTYIWSRKNPNAQVSFFGLFTIKAKYL 147 (197)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHhhccch-----------hHH-HHHHHHHHHHHHHHHHHhCcccceeeEEEEEEChhhH
Confidence 2 26788888877666555554322110 011 1223558899999999999999999999999999999
Q ss_pred HHHHHHHHHHhccchhHHHHHHHHHHHHHHHHHhhcccCCchh
Q 015601 178 PLILLVLFQVLMTNVSLLGHLCGILSGFAYTYGFFNLLMPGTS 220 (404)
Q Consensus 178 p~~~l~~~~l~~~~~s~~~hl~G~l~G~l~~~~~l~~~~p~~~ 220 (404)
||+++++..++. +.+...++.|+++||+|.+ ++...|...
T Consensus 148 P~~~~~~~~l~~-~~~~~~~l~Gi~~Ghly~f--l~~~~p~~~ 187 (197)
T PF04511_consen 148 PWVLLAFSLLFG-GSSPIPDLLGILVGHLYYF--LKDIYPRLP 187 (197)
T ss_pred HHHHHHHHHHhC-CCcHHHHHHHHHHHHHHHH--HHHhccccc
Confidence 999777666655 4467899999999999998 777777654
No 6
>COG5291 Predicted membrane protein [Function unknown]
Probab=99.87 E-value=2.1e-22 Score=176.69 Aligned_cols=170 Identities=16% Similarity=0.306 Sum_probs=132.9
Q ss_pred ccHHHHHHHHHHHHHHHHHHHhcccccccceeechhhhccCcchhhhhhhhcccCH-HHHHHHHHHHHHHHHHHHHHh-C
Q 015601 22 IPFFTSAVVIVCGTIYLICLLFGYDSFYEICFLPSAVISRFQVYRFYTSIVFHGSL-LHVLFNMLALVPLGSELERIM-G 99 (404)
Q Consensus 22 ~P~vT~~li~~~v~~~~l~~~~~~~~~~~l~~~p~~i~~~~q~WRL~Ts~f~h~~~-~hll~n~~~l~~~g~~lE~~~-G 99 (404)
+||+||++.++..++.++..+ +...+..+.++++..+++.|||||+|+.++.++. ++++++++++|.+++.||+-. +
T Consensus 19 IPPITRy~~ll~~a~til~~~-~lvsPwy~ly~~pL~~k~~qiwRlfTs~~~~~~~~~d~~M~vyf~Y~yS~~LE~g~f~ 97 (313)
T COG5291 19 IPPITRYMTLLISAVTILVYV-DLVSPWYSLYYSPLFLKRLQIWRLFTSFLYFGKPTLDMFMHVYFLYRYSRMLEEGCFN 97 (313)
T ss_pred CCcHHHHHHHHHHHHHHHHHH-hhcCccceeeechhHHHHHHHHHHHHHHHhhcCcchhHHHHHHHHHHHHHHHhccccC
Confidence 899999999999999999887 4456666777777888999999999998887765 999999999999999999874 4
Q ss_pred c--HHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccccccccccChhHHHHHHHHHHHhhcCCccceeeEeecchhhHH
Q 015601 100 S--VRMFYITILLATSNAILHLLIALLVAHIPFYRLQNVMDECAIGFSGVIFSLIVIETSLSGAQSRSVFGLFNIPAKWY 177 (404)
Q Consensus 100 s--~~~~~~~l~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~G~sg~i~~l~~~~~~~~p~~~~~~~~~~~i~~~~~ 177 (404)
+ .+|.++++++.+....++.+.. .+++=-++.+.++.+.|+..+++.++.+++++++++||+
T Consensus 98 ~~lv~Y~~yl~~~~l~i~a~s~I~g----------------g~saL~tsf~a~ItY~WS~~N~~~~Iqf~g~i~v~gkYl 161 (313)
T COG5291 98 TSLVEYFWYLLVISLVIFAISNIYG----------------GISALGTSFSATITYIWSKRNPRAIIQFFGFISVPGKYL 161 (313)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHhc----------------chhhhcchhhhheeeeeeecCCceEEEEEEeeecchhhh
Confidence 4 4777777766544333322221 122223456778889999999999999999999999999
Q ss_pred HHHHHHHHHHhccchhHHHHHHHHHHHHHHHH
Q 015601 178 PLILLVLFQVLMTNVSLLGHLCGILSGFAYTY 209 (404)
Q Consensus 178 p~~~l~~~~l~~~~~s~~~hl~G~l~G~l~~~ 209 (404)
|++++.+..+.. ....+..+.|+++|+...+
T Consensus 162 P~Illgfsfl~~-~g~~i~~vlGf~~g~~~h~ 192 (313)
T COG5291 162 PFILLGFSFLSR-RGISIDDVLGFVVGHLFHY 192 (313)
T ss_pred hHHHHHHHHHhc-CCccceeeeeeeecccccc
Confidence 999777665554 3456788899999987655
No 7
>COG0705 Membrane associated serine protease [Amino acid transport and metabolism]
Probab=99.85 E-value=2.9e-20 Score=171.26 Aligned_cols=180 Identities=27% Similarity=0.423 Sum_probs=136.1
Q ss_pred ccHHHHHHHHHHHHHHHHHHHhccccccc-------ceeechhhhccC---cchhhhhhhhcccCHHHHHHHHHHHHHHH
Q 015601 22 IPFFTSAVVIVCGTIYLICLLFGYDSFYE-------ICFLPSAVISRF---QVYRFYTSIVFHGSLLHVLFNMLALVPLG 91 (404)
Q Consensus 22 ~P~vT~~li~~~v~~~~l~~~~~~~~~~~-------l~~~p~~i~~~~---q~WRL~Ts~f~h~~~~hll~n~~~l~~~g 91 (404)
.+++|+.++.+++++++............ ....|....... |+||++|+.|+|.++.|+++||+.++.+|
T Consensus 16 ~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~lit~~FlH~~~~Hll~N~~~l~~fg 95 (228)
T COG0705 16 APPVTLFLILLNILVFLLELVLGWSAIFLLTFLFRLFGLYPLNLLGALARDQLWRLITAIFLHAGFLHLLFNMLALWVFG 95 (228)
T ss_pred cchHHHHHHHHHHHHHHHHHHccchHHHHHHHhhhHHhhcchhhhccccccchHHHHHHHHHHhhHHHHHHHHHHHHHhh
Confidence 58899999999999999888754332222 445565554333 89999999999999999999999999999
Q ss_pred HHHHHHhCcHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccccccccccChhHHHHHHHHHHHhhcCCccceeeEe-e
Q 015601 92 SELERIMGSVRMFYITILLATSNAILHLLIALLVAHIPFYRLQNVMDECAIGFSGVIFSLIVIETSLSGAQSRSVFGL-F 170 (404)
Q Consensus 92 ~~lE~~~Gs~~~~~~~l~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~G~sg~i~~l~~~~~~~~p~~~~~~~~~-~ 170 (404)
..+|+.+|+.+|+.+|+++++++++.+..+... ...+.+|+||.++|++++++...|..+...... +
T Consensus 96 ~~le~~~G~~~f~~~yl~~gl~~~~~~~~~~~~------------~~~~~~GASG~i~gllga~~~~~~~~~~~~~~~~~ 163 (228)
T COG0705 96 SNLERRLGTLRFLLFYLLSGLLAGLAQVLFGPK------------GGAPSLGASGAIFGLLGAYFLLFPFARILLLFLSL 163 (228)
T ss_pred HHHHHHhchhHHHHHHHHHHHHHHHHHHHHccc------------ccCcccchhHHHHHHHHHHHHHccccchhhhhccC
Confidence 999999999999999999999999885554310 025789999999999999999998876655433 3
Q ss_pred cchhhHHHHHHHH--HHHHhcc---chhHHHHHHHHHHHHHHHHHhhc
Q 015601 171 NIPAKWYPLILLV--LFQVLMT---NVSLLGHLCGILSGFAYTYGFFN 213 (404)
Q Consensus 171 ~i~~~~~p~~~l~--~~~l~~~---~~s~~~hl~G~l~G~l~~~~~l~ 213 (404)
+.+...+..+.++ ++..... ++++.+|++|++.|.+++..+.+
T Consensus 164 ~~~~~~~i~~~~~~~~~~~~~~~~~~va~~aHl~G~i~G~l~~~~~~~ 211 (228)
T COG0705 164 PRPALILILIWLLYSLFSGAGSFGPSVAWSAHLGGLIGGLLLAALLSR 211 (228)
T ss_pred chhHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3444433322221 1111111 47799999999999999986544
No 8
>PF01694 Rhomboid: Rhomboid family; InterPro: IPR022764 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of proteins contain serine peptidases belonging to the MEROPS peptidase family S54 (Rhomboid, clan ST). They are integral membrane proteins related to the Drosophila melanogaster (Fruit fly) rhomboid protein P20350 from SWISSPROT. Members of this family are found in archaea, bacteria and eukaryotes. The D. melanogaster rhomboid protease cleaves type-1 transmembrane domains using a catalytic triad composed of serine, histidine and asparagine contributed by different transmembrane domains. It cleaves the transmembrane proteins Spitz, Gurken and Keren within their transmembrane domains to release a soluble TGFalpha-like growth factor. Cleavage occurs in the Golgi, following translocation of the substrates from the endoplasmic reticulum membrane by Star, another transmembrane protein. The growth factors are then able to activate the epidermal growth factor receptor [, ]. Few substrates of mammalian rhomboid homologues have been determined, but rhomboid-like protein 2 (MEROPS S54.002) has been shown to cleave ephrin B3 []. Parasite-encoded rhomboid enzymes are also important for invasion of host cells by Toxoplasma and the malaria parasite. In Saccharomyces cerevisiae (Baker's yeast) the Pcp1 (MDM37) protein (MEROPS S54.007) is a mitochondrial endopeptidase required for the activation of cytochrome c peroxidase and for the processing of the mitochondrial dynamin-like protein Mgm1 [, ]. Mutations in Pcp1 result in cells have fragmented mitochondria, which have very few short tubulues []. This entry represents the 6 transmembrane helix rhomboid domain.; GO: 0004252 serine-type endopeptidase activity, 0016021 integral to membrane; PDB: 3UBB_A 3B45_A 3B44_A 2NRF_A 3TXT_A 2O7L_A 2XTU_A 2IRV_A 2XOW_A 2XTV_A ....
Probab=99.78 E-value=4e-19 Score=151.84 Aligned_cols=139 Identities=32% Similarity=0.484 Sum_probs=102.0
Q ss_pred ccCcchhhhhhhhcccCHHHHHHHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccccccc
Q 015601 60 SRFQVYRFYTSIVFHGSLLHVLFNMLALVPLGSELERIMGSVRMFYITILLATSNAILHLLIALLVAHIPFYRLQNVMDE 139 (404)
Q Consensus 60 ~~~q~WRL~Ts~f~h~~~~hll~n~~~l~~~g~~lE~~~Gs~~~~~~~l~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~ 139 (404)
+++|+||++|+.|+|.|+.|+++|++.++.++..+|+.+|+.+++.+++++++.++++.+++... ..
T Consensus 2 ~~~~~wrl~T~~f~h~~~~hl~~n~~~l~~~g~~lE~~~G~~~~~~~~l~~~~~~~l~~~~~~~~-------------~~ 68 (145)
T PF01694_consen 2 QNGQWWRLFTSPFVHANFLHLLFNLLALWFFGSLLERRLGSRRFLALYLLSGLLGSLLSLLFSPP-------------NQ 68 (145)
T ss_dssp GCC-TTHHHHGGG--SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-S---------------
T ss_pred CCCcchhhhHHHHHccCHHHHHHHHHHHHHhhhhHhhhccchHHHHHHHHHHHhhhhcccccccc-------------cc
Confidence 57899999999999999999999999999999999999999999999999999998887765531 11
Q ss_pred cccChhHHHHHHHHHHHhhcCCccceeeE---eecchhhHHHHHHHHHHHHhccchhHHHHHHHHHHHHHHHHHhhcc
Q 015601 140 CAIGFSGVIFSLIVIETSLSGAQSRSVFG---LFNIPAKWYPLILLVLFQVLMTNVSLLGHLCGILSGFAYTYGFFNL 214 (404)
Q Consensus 140 ~~~G~sg~i~~l~~~~~~~~p~~~~~~~~---~~~i~~~~~p~~~l~~~~l~~~~~s~~~hl~G~l~G~l~~~~~l~~ 214 (404)
+..|+||.+++++.++....+..+..... .+.+...++++.+.. ...++.++.+|++|+++|+++++.+.++
T Consensus 69 ~~~G~Sg~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~hl~G~~~G~~~~~~~~~~ 143 (145)
T PF01694_consen 69 PYVGASGAVFGLLGAFLFLYPQNKKRLRFIYLALVVPIIVLVIILLL---GFIPNISFLGHLGGFLAGLLYGFLILRR 143 (145)
T ss_dssp ---SSHHHHHHHHHHHHHHHHCCCCCS---HCCCCCCCCCCCHHHCT---SSSSTTTHHHHHHHHHHHHHHHHHHCH-
T ss_pred ccCCCcccchHHHHHHHHHHhhccchhhcchHHHHHHHHHHHHHHHH---HHHHhHHHHHHHHHHHHHHHHHHHHHHc
Confidence 67999999999999988887765433221 112222222222111 1157789999999999999999987653
No 9
>KOG2289 consensus Rhomboid family proteins [Signal transduction mechanisms]
Probab=99.66 E-value=2.2e-17 Score=154.84 Aligned_cols=137 Identities=22% Similarity=0.387 Sum_probs=103.8
Q ss_pred hhhccCcchhhhhhhhcccCHHHHHHHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccccc
Q 015601 57 AVISRFQVYRFYTSIVFHGSLLHVLFNMLALVPLGSELERIMGSVRMFYITILLATSNAILHLLIALLVAHIPFYRLQNV 136 (404)
Q Consensus 57 ~i~~~~q~WRL~Ts~f~h~~~~hll~n~~~l~~~g~~lE~~~Gs~~~~~~~l~~~~~~~l~~~l~~~~~~~~~~~~~~~~ 136 (404)
...+++|+||++||+|+|.+++|+++|++.+..+|..||..+|..|+..+|+++++.++++.+++..
T Consensus 112 ~~~~r~E~WRllTym~LHaGi~HL~~N~~~ql~iGi~LE~~~G~~RiglIYl~gg~aGSlls~l~d~------------- 178 (316)
T KOG2289|consen 112 KPVHRGELWRLLTYMWLHAGIFHLLLNMLSQLFIGIPLEQVHGFLRIGLIYLAGGVAGSLLSSLFDP------------- 178 (316)
T ss_pred ChhhhchhHHHHHHHHHhcCHHHHHHHHHHHHhccccHHhhcCceEEeeehhhhhhhhHHHHHHhcc-------------
Confidence 4456899999999999999999999999999999999999999999999999999999999887642
Q ss_pred ccccccChhHHHHHHHHHHHhhcCCccceeeEeecchhh-HHHHHHHHHHHH---hccchhHHHHHHHHHHHHHHHHHh
Q 015601 137 MDECAIGFSGVIFSLIVIETSLSGAQSRSVFGLFNIPAK-WYPLILLVLFQV---LMTNVSLLGHLCGILSGFAYTYGF 211 (404)
Q Consensus 137 ~~~~~~G~sg~i~~l~~~~~~~~p~~~~~~~~~~~i~~~-~~p~~~l~~~~l---~~~~~s~~~hl~G~l~G~l~~~~~ 211 (404)
+..++|+||.+||+++++....-..+.. + .=+.. ....++++++.+ +.+..++++|++|++.|..+++..
T Consensus 179 -~~~sVGASggvfaLlgA~Ls~l~~Nw~~-m---~~~~~~l~~ll~Ii~i~l~~G~~~~~~~~~h~gg~~~G~~~~fil 252 (316)
T KOG2289|consen 179 -NSISVGASGGVFALLGAHLSNLLTNWTI-M---KNKFAALRTLLIIIFINLDLGFAPYVDNFAHIGGLLAGFLLGFVL 252 (316)
T ss_pred -CCceecccHHHHHHHHHHHHHHHhhHHH-h---cchHHHHHHHHHHHHHHHhhccccceeccccccccCCCcchhHHh
Confidence 5668999999999998876433222111 1 10111 111221212222 235678899999999999999853
No 10
>KOG2290 consensus Rhomboid family proteins [Signal transduction mechanisms]
Probab=99.37 E-value=2.5e-13 Score=129.55 Aligned_cols=143 Identities=17% Similarity=0.255 Sum_probs=104.5
Q ss_pred cCcchhhhhhhhcccCHHHHHHHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccccccccc
Q 015601 61 RFQVYRFYTSIVFHGSLLHVLFNMLALVPLGSELERIMGSVRMFYITILLATSNAILHLLIALLVAHIPFYRLQNVMDEC 140 (404)
Q Consensus 61 ~~q~WRL~Ts~f~h~~~~hll~n~~~l~~~g~~lE~~~Gs~~~~~~~l~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~ 140 (404)
..|+|||+|+.|+|.+.+|++..+.+.+.+.+.+|+..|+.|.+.+|+++|+.+++.+.++. + +.+
T Consensus 448 PdQfYRL~~SLFlHagviH~~vSi~FQm~vmrdlEkL~g~~riAIiy~~SGitGNLASAIFl---------p-----Y~~ 513 (652)
T KOG2290|consen 448 PDQFYRLWLSLFLHAGVIHLLVSICFQMTVMRDLEKLAGWHRIAIIYFLSGITGNLASAIFL---------P-----YRA 513 (652)
T ss_pred hhHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHhhcchhhheeeecccccccchheeee---------c-----ccc
Confidence 46999999999999999999999999999999999999999999999999999999865422 1 456
Q ss_pred ccChhHHHHHHHHHHHhhcCCccceeeEe-ecchhhHHHHHHHHHHHHhccchhHHHHHHHHHHHHHHHHHhhcccCCch
Q 015601 141 AIGFSGVIFSLIVIETSLSGAQSRSVFGL-FNIPAKWYPLILLVLFQVLMTNVSLLGHLCGILSGFAYTYGFFNLLMPGT 219 (404)
Q Consensus 141 ~~G~sg~i~~l~~~~~~~~p~~~~~~~~~-~~i~~~~~p~~~l~~~~l~~~~~s~~~hl~G~l~G~l~~~~~l~~~~p~~ 219 (404)
.+|++|.-+|++.......-+.+ .++-- +..-.+++..++++.+ -+.|+++.++|+.|.+.|++..+.++.++.-..
T Consensus 514 eVgPa~sQ~Gila~l~vEl~qs~-~il~~~w~a~~~Lia~~L~L~i-GliPWiDN~aHlfG~i~GLl~s~~~~PYi~Fg~ 591 (652)
T KOG2290|consen 514 EVGPAGSQFGILACLFVELFQSW-QILERPWRAFFHLIATLLVLCI-GLIPWIDNWAHLFGTIFGLLTSIIFLPYIDFGD 591 (652)
T ss_pred ccCCcccccchHHHHHHHHHhhh-HhhhhHHHHHHHHHHHHHHHHh-ccccchhhHHHHHHHHHHHHHHHHhhccccccc
Confidence 78999988888765433222111 11100 0000112222222222 455899999999999999999998777666444
No 11
>KOG2890 consensus Predicted membrane protein [Function unknown]
Probab=99.32 E-value=8.8e-12 Score=113.96 Aligned_cols=198 Identities=17% Similarity=0.169 Sum_probs=130.9
Q ss_pred hhccccHHHHHHHHHHHHHHHHHHHhccc---ccccceeechhhhccCcchhhhhhhhcccCHHHHHHHHHHHHHHHHHH
Q 015601 18 WWESIPFFTSAVVIVCGTIYLICLLFGYD---SFYEICFLPSAVISRFQVYRFYTSIVFHGSLLHVLFNMLALVPLGSEL 94 (404)
Q Consensus 18 ~~~~~P~vT~~li~~~v~~~~l~~~~~~~---~~~~l~~~p~~i~~~~q~WRL~Ts~f~h~~~~hll~n~~~l~~~g~~l 94 (404)
...+.-.+.+.|+.+.+..++........ ....+.+.|..++ ..+|+++|+.|+..+.+..++|++.+...|+.+
T Consensus 20 ~l~n~~vvvs~ic~~tlf~yi~sf~~~t~~l~~~p~y~lvp~~~~--~~~WtliTs~fie~~vw~V~~sv~~L~v~G~~l 97 (326)
T KOG2890|consen 20 LLLNLEVVVSAICVLTLFGYILSFGNFTILLATLPGYQLVPNALF--FFPWTLITSGFIELNVWDVLVSVLTLSVGGKFL 97 (326)
T ss_pred HhhhchhHHHHHHHHHHHHHHHHHHHhHHHHHhccccccCCcchh--hhhHHHHhcchhhhhHHHHHHHHHheeecceee
Confidence 34444445566665666666555431110 0111223333322 469999999999999999999999999999999
Q ss_pred HHHhCcHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccccccccccChhHHHHHHHHHHHhhcCCccceeeEeecchh
Q 015601 95 ERIMGSVRMFYITILLATSNAILHLLIALLVAHIPFYRLQNVMDECAIGFSGVIFSLIVIETSLSGAQSRSVFGLFNIPA 174 (404)
Q Consensus 95 E~~~Gs~~~~~~~l~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~G~sg~i~~l~~~~~~~~p~~~~~~~~~~~i~~ 174 (404)
|+.||+.+++.++.+.....+++..+.+.+.++ ++....+...+..|..|++.|+++++.+..|+..+.....-.+..
T Consensus 98 Ep~Wg~~e~lkff~ivn~~~~l~v~v~~~l~Y~--it~n~v~L~~~i~G~~gilaGilVa~kQllpd~~il~~~~~r~~~ 175 (326)
T KOG2890|consen 98 EPNWGSLELLKFFAIVNGSTTLVVLVPALLLYM--ITDNHVYLYIPIHGTTGILAGILVAWKQLLPDTIILELKSGRFLY 175 (326)
T ss_pred ccCCCCHHHHHHHHHhhchhHHHHHHHHHHHHH--HhcCceEEEEEeccchHHHHHHHHHHHHHcCceeEEeccchhhhh
Confidence 999999999999988877766665555444433 233344456678999999999999999999987543332223333
Q ss_pred hHHHHHHHHHHHHhc-cchhHHHHHHHHHHHHHHHHHhhcccCCch
Q 015601 175 KWYPLILLVLFQVLM-TNVSLLGHLCGILSGFAYTYGFFNLLMPGT 219 (404)
Q Consensus 175 ~~~p~~~l~~~~l~~-~~~s~~~hl~G~l~G~l~~~~~l~~~~p~~ 219 (404)
+.+|+.++++..++. -.......+.-+.+|...+|.|+++..+..
T Consensus 176 ~~lP~~~l~~~~il~i~~f~~f~~l~s~~~g~~~sWtYLRfyq~h~ 221 (326)
T KOG2890|consen 176 AHLPLLVLFLSLILSIITFLVFASLPSITFGVLVSWTYLRFYQRHP 221 (326)
T ss_pred hhCCHHHHHHHHHHHHHHHHHhhhhHHHHHhhhhhhhhheecccCC
Confidence 446655443332221 122345666777788888888888777554
No 12
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=99.32 E-value=1.9e-12 Score=83.26 Aligned_cols=36 Identities=39% Similarity=0.690 Sum_probs=33.7
Q ss_pred CHHHHHHHHhcCCCHHHHHHHHHHcCCCHHHHHHhh
Q 015601 365 SDEEIQKLVSMGFDKTQVEVALAAADGDLNVAVEIL 400 (404)
Q Consensus 365 ~~~~i~~l~~mg~~~~~~~~al~~~~~~~~~a~~~l 400 (404)
++++|++|++|||++++|++||++++||+|+|++||
T Consensus 2 ~~~~v~~L~~mGf~~~~~~~AL~~~~~nve~A~~~L 37 (37)
T PF00627_consen 2 DEEKVQQLMEMGFSREQAREALRACNGNVERAVDWL 37 (37)
T ss_dssp HHHHHHHHHHHTS-HHHHHHHHHHTTTSHHHHHHHH
T ss_pred CHHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHhC
Confidence 478999999999999999999999999999999997
No 13
>KOG4463 consensus Uncharacterized conserved protein [Function unknown]
Probab=99.28 E-value=9.8e-12 Score=110.99 Aligned_cols=181 Identities=18% Similarity=0.231 Sum_probs=120.8
Q ss_pred cccHHHHHHHHHHHHHHHHHHHhcccccccceeechhhhccCcchhhhhhhhcccCHHHHHHHHHHHHHHHHHHHHHhCc
Q 015601 21 SIPFFTSAVVIVCGTIYLICLLFGYDSFYEICFLPSAVISRFQVYRFYTSIVFHGSLLHVLFNMLALVPLGSELERIMGS 100 (404)
Q Consensus 21 ~~P~vT~~li~~~v~~~~l~~~~~~~~~~~l~~~p~~i~~~~q~WRL~Ts~f~h~~~~hll~n~~~l~~~g~~lE~~~Gs 100 (404)
++| |||.+++.+.++.++..+.+......+.+.+.. ..++|+|||+.+.|+..+--.+++.++.+|++ +.+||..|+
T Consensus 10 nmp-VTK~~~iT~~~~~vvagI~~~k~~f~l~y~~~l-~~y~qywrlL~~qF~~~n~~e~~~~l~I~Y~f-R~~ERlLGS 86 (323)
T KOG4463|consen 10 NMP-VTKAFVITSALFTVVAGIQGRKSKFGLSYQDIL-EKYFQYWRLLMSQFAFSNTPELMFGLYILYYF-RVFERLLGS 86 (323)
T ss_pred ccc-hHHHHHHHHHHHHHHHHhhhcccccccchhHHH-HHHHHHHHHHHHHHHhcCChHHHHHHHHHHHH-HHHHHHhcc
Confidence 445 999999988888887777666555555554432 34689999999999999999999999999998 999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccccccccccChhHHHHHHHHHHHhhcCCccceeeEeecchhhHHHHH
Q 015601 101 VRMFYITILLATSNAILHLLIALLVAHIPFYRLQNVMDECAIGFSGVIFSLIVIETSLSGAQSRSVFGLFNIPAKWYPLI 180 (404)
Q Consensus 101 ~~~~~~~l~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~G~sg~i~~l~~~~~~~~p~~~~~~~~~~~i~~~~~p~~ 180 (404)
-||+.+++.++..+.++...+..+... +.. +...++..|++|+.++-+....|.......+.+++..|..-++
T Consensus 87 hky~~fiv~s~~~~~l~~~il~~l~~~--~~~-----nl~~~qp~~liFa~~~~~y~~ip~~~f~r~f~~~f~dkni~~i 159 (323)
T KOG4463|consen 87 HKYSVFIVFSGTVSLLLEVILLSLLKD--TTA-----NLLTSQPYGLIFASFIPFYLDIPVSTFFRVFGVNFSDKNISFI 159 (323)
T ss_pred ccceeehhHHHHHHHHHHHHHHHHHHH--HHh-----hhhhcCCCceeeeeccceEEEecceeEEEeecccccccceeee
Confidence 999999999988888777666554432 111 3445677778898887665555543221112234444422221
Q ss_pred HHHHHHHh-cc-----------chhHHHHHHHHHHHHHHHHHh
Q 015601 181 LLVLFQVL-MT-----------NVSLLGHLCGILSGFAYTYGF 211 (404)
Q Consensus 181 ~l~~~~l~-~~-----------~~s~~~hl~G~l~G~l~~~~~ 211 (404)
.+.-..+. .+ ..+..--++|++.|++|-...
T Consensus 160 ~~~G~a~sh~~NkredksaveWk~~i~f~~~gLi~~~~~~~~~ 202 (323)
T KOG4463|consen 160 YLAGVALSHSSNKREDKSAVEWKRSIFFGICGLIAGSLYRLNI 202 (323)
T ss_pred cccchhhhcCcccccccccceeecccccccchhhhhhHhhccc
Confidence 11111111 11 123345678999999887653
No 14
>PF08551 DUF1751: Eukaryotic integral membrane protein (DUF1751); InterPro: IPR013861 This entry is found in eukaryotic integral membrane proteins. Q12239 from SWISSPROT, a Saccharomyces cerevisiae (Baker's yeast) protein, has been shown to localise COP II vesicles [].
Probab=99.20 E-value=1.8e-11 Score=96.86 Aligned_cols=91 Identities=22% Similarity=0.330 Sum_probs=77.6
Q ss_pred cchhhhhhhhcccCHHHHHHHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccccccccccc
Q 015601 63 QVYRFYTSIVFHGSLLHVLFNMLALVPLGSELERIMGSVRMFYITILLATSNAILHLLIALLVAHIPFYRLQNVMDECAI 142 (404)
Q Consensus 63 q~WRL~Ts~f~h~~~~hll~n~~~l~~~g~~lE~~~Gs~~~~~~~l~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~ 142 (404)
.+|+++|+.|++.+++.+++|.+.++..|+.+|+.||+++++.++++.+++++++..+...+.+. ...+..+...+..
T Consensus 7 ~pWtl~T~~fve~~i~~~l~~~~~l~~~g~~lE~~WGs~E~lkFi~vv~~~tnl~~~~~~~~~y~--i~~~~~~l~~~i~ 84 (99)
T PF08551_consen 7 YPWTLFTAGFVETNIIGLLFSLLTLFYGGRYLEPIWGSREFLKFILVVNVITNLLTFLLYLLLYA--ITGNESYLFVPIS 84 (99)
T ss_pred ehHHHHHHHHHHhHHHHHHHHHHHHHHhhHHHHHhcChHHHHHHHHHHHHHhHHHHHHHHHHHHH--HhCCCceeEEEec
Confidence 69999999999999999999999999999999999999999999999999999988877766543 2333333457788
Q ss_pred ChhHHHHHHHHHH
Q 015601 143 GFSGVIFSLIVIE 155 (404)
Q Consensus 143 G~sg~i~~l~~~~ 155 (404)
|..|++.|+++++
T Consensus 85 G~~~~~~g~lVa~ 97 (99)
T PF08551_consen 85 GFMGVLAGFLVAF 97 (99)
T ss_pred CcHHhHhheEEEE
Confidence 9999998887654
No 15
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=99.15 E-value=6.4e-11 Score=76.27 Aligned_cols=35 Identities=40% Similarity=0.666 Sum_probs=33.9
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHcCCCHHHHHHhh
Q 015601 366 DEEIQKLVSMGFDKTQVEVALAAADGDLNVAVEIL 400 (404)
Q Consensus 366 ~~~i~~l~~mg~~~~~~~~al~~~~~~~~~a~~~l 400 (404)
+++|++|++|||++++|++||++++||+++|++||
T Consensus 2 ~~~v~~L~~mGf~~~~a~~aL~~~~~d~~~A~~~L 36 (37)
T smart00165 2 EEKIDQLLEMGFSREEALKALRAANGNVERAAEYL 36 (37)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHH
Confidence 68899999999999999999999999999999997
No 16
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=99.13 E-value=9.3e-11 Score=76.00 Aligned_cols=35 Identities=34% Similarity=0.638 Sum_probs=34.0
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHcCCCHHHHHHhh
Q 015601 366 DEEIQKLVSMGFDKTQVEVALAAADGDLNVAVEIL 400 (404)
Q Consensus 366 ~~~i~~l~~mg~~~~~~~~al~~~~~~~~~a~~~l 400 (404)
+++|++|++|||++++|++||++++||+++|++||
T Consensus 2 ~~~v~~L~~mGf~~~~~~~AL~~~~~d~~~A~~~L 36 (38)
T cd00194 2 EEKLEQLLEMGFSREEARKALRATNNNVERAVEWL 36 (38)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHH
Confidence 67899999999999999999999999999999998
No 17
>TIGR00601 rad23 UV excision repair protein Rad23. All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.03 E-value=6.3e-10 Score=108.47 Aligned_cols=35 Identities=37% Similarity=0.584 Sum_probs=34.6
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHcCCCHHHHHHhh
Q 015601 366 DEEIQKLVSMGFDKTQVEVALAAADGDLNVAVEIL 400 (404)
Q Consensus 366 ~~~i~~l~~mg~~~~~~~~al~~~~~~~~~a~~~l 400 (404)
|+.|++||+|||+|++|++|||+++||+|||||||
T Consensus 157 e~~I~~i~eMGf~R~qV~~ALRAafNNPdRAVEYL 191 (378)
T TIGR00601 157 ETTIEEIMEMGYEREEVERALRAAFNNPDRAVEYL 191 (378)
T ss_pred HHHHHHHHHhCCCHHHHHHHHHHHhCCHHHHHHHH
Confidence 88999999999999999999999999999999999
No 18
>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]
Probab=98.80 E-value=8.3e-09 Score=95.85 Aligned_cols=36 Identities=39% Similarity=0.577 Sum_probs=35.1
Q ss_pred CHHHHHHHHhcCCCHHHHHHHHHHcCCCHHHHHHhh
Q 015601 365 SDEEIQKLVSMGFDKTQVEVALAAADGDLNVAVEIL 400 (404)
Q Consensus 365 ~~~~i~~l~~mg~~~~~~~~al~~~~~~~~~a~~~l 400 (404)
.++.|++||+||++|+++++|||+++||+|||||||
T Consensus 135 ~e~~V~~Im~MGy~re~V~~AlRAafNNPeRAVEYL 170 (340)
T KOG0011|consen 135 YEQTVQQIMEMGYDREEVERALRAAFNNPERAVEYL 170 (340)
T ss_pred hHHHHHHHHHhCccHHHHHHHHHHhhCChhhhHHHH
Confidence 488999999999999999999999999999999999
No 19
>KOG2980 consensus Integral membrane protease of the rhomboid family involved in different forms of regulated intramembrane proteolysis [Signal transduction mechanisms]
Probab=98.39 E-value=2.4e-07 Score=85.50 Aligned_cols=182 Identities=15% Similarity=0.233 Sum_probs=121.7
Q ss_pred HHhhccccHHHHHHHHHHHHHHHHHHHhcccccccceeechhh---hccCcchhhhhhhhcccCHHHHHHHHHHHHHHHH
Q 015601 16 NQWWESIPFFTSAVVIVCGTIYLICLLFGYDSFYEICFLPSAV---ISRFQVYRFYTSIVFHGSLLHVLFNMLALVPLGS 92 (404)
Q Consensus 16 ~~~~~~~P~vT~~li~~~v~~~~l~~~~~~~~~~~l~~~p~~i---~~~~q~WRL~Ts~f~h~~~~hll~n~~~l~~~g~ 92 (404)
+.|.+..|.+...++++++++|.+..+.... ....+..+ ..+.-.|.++++.|.|-+.+|+-.|++.+..+..
T Consensus 108 k~w~~~~~g~v~~ll~~n~~vf~lWrv~~~~----~~~~~~mls~~~~~t~~w~i~~s~Fsh~~a~h~g~~~~~~~~y~~ 183 (310)
T KOG2980|consen 108 KHWISGANGVVFGLLIANAFVFTLWRVPQKQ----FTMIPWMLSRNAYKTGCWKIILSTFSHYSALHLGPNMLVLKSYLA 183 (310)
T ss_pred HHHhhcCCcchhHHHHHHHHHHHHHHhcchh----hhhhhHHhhcccccccceeEEeehhcchhHhhhcHHHHHHHHHhc
Confidence 4556666778888899999999888874321 11122111 1234578899999999999999999998888766
Q ss_pred -HHHHHhCcHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccccccccccChhHHHHHHHHHHHhhcCCccceeeEeec
Q 015601 93 -ELERIMGSVRMFYITILLATSNAILHLLIALLVAHIPFYRLQNVMDECAIGFSGVIFSLIVIETSLSGAQSRSVFGLFN 171 (404)
Q Consensus 93 -~lE~~~Gs~~~~~~~l~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~G~sg~i~~l~~~~~~~~p~~~~~~~~~~~ 171 (404)
.+-...|...+..+|+..+..+..+... .........+.+|+||.+++++.+.+.++|+....+++.++
T Consensus 184 ~a~~~~~~~~~~~AlylSa~~~~~~i~~~----------~~v~~~~~gp~LGAsGav~ai~a~~~~lfP~~~~~i~f~~~ 253 (310)
T KOG2980|consen 184 GALKGSLGFSSFFALYLSAGVKGLFISVK----------DKVPTSWAGPSLGASGAVYAILALDCTLFPKTTLYILFVFP 253 (310)
T ss_pred ccccCCcchhhcccceeccccccceeEee----------ccccccccccccccchHHHHHHHHHhhcCcCcceeEEEeec
Confidence 5666667777777776443333332110 11122335678999999999999999999988877777777
Q ss_pred chhhHH-HHHHHHHHH---Hh--ccchhHHHHHHHHHHHHHHHHHh
Q 015601 172 IPAKWY-PLILLVLFQ---VL--MTNVSLLGHLCGILSGFAYTYGF 211 (404)
Q Consensus 172 i~~~~~-p~~~l~~~~---l~--~~~~s~~~hl~G~l~G~l~~~~~ 211 (404)
++.-+. ++-++.... +. ....++.+|++|-+.|.+++...
T Consensus 254 v~~ga~~~~~~i~~~~~a~~~l~~~~~n~~Ah~~gsl~Gv~va~~~ 299 (310)
T KOG2980|consen 254 VPAGAGLAFKAIAAYDFAGLILGWGFFNHAAHLSGSLFGVVVATYL 299 (310)
T ss_pred ccccchhHHHHHHHhhhcceeeccccchhHhhhcchHHHHHHHHHH
Confidence 776433 222121111 11 13346679999999999988854
No 20
>KOG0944 consensus Ubiquitin-specific protease UBP14 [Posttranslational modification, protein turnover, chaperones]
Probab=98.33 E-value=5e-07 Score=91.09 Aligned_cols=61 Identities=26% Similarity=0.421 Sum_probs=48.7
Q ss_pred CCCCCCcccCCCCCCCCCCCCCHHHHHHHHhcCCCHHHHHHHHHHcCCCHHHHHHhh-hcCC
Q 015601 344 PALGTAVAVDRVPAGQQGAVVSDEEIQKLVSMGFDKTQVEVALAAADGDLNVAVEIL-SQQG 404 (404)
Q Consensus 344 ~~~~~~~~~~~~~~~~~~~~~~~~~i~~l~~mg~~~~~~~~al~~~~~~~~~a~~~l-~~~~ 404 (404)
+.+++|...+...+...+..++++.+..+++|||++.||++||+++|||+|||+||+ +|.|
T Consensus 614 pd~~~p~vvp~~~~~a~~~~~~e~~v~si~smGf~~~qa~~aL~~~n~nveravDWif~h~d 675 (763)
T KOG0944|consen 614 PDIDDPFVVPGNSPKADAREVDEESVASIVSMGFSRNQAIKALKATNNNVERAVDWIFSHMD 675 (763)
T ss_pred cccCCceecCCCCCccccCCCChhHheeeeeecCcHHHHHHHHHhcCccHHHHHHHHHhccc
Confidence 334455555555554444467899999999999999999999999999999999999 8754
No 21
>KOG0418 consensus Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.87 E-value=1.1e-06 Score=75.03 Aligned_cols=37 Identities=30% Similarity=0.495 Sum_probs=34.9
Q ss_pred CHHHHHHHHhcCCCHHHHHHHHHHcCCCHHHHHHhh-h
Q 015601 365 SDEEIQKLVSMGFDKTQVEVALAAADGDLNVAVEIL-S 401 (404)
Q Consensus 365 ~~~~i~~l~~mg~~~~~~~~al~~~~~~~~~a~~~l-~ 401 (404)
+..+|++|.+|||+|++++.+|+..+||.++|.|.| +
T Consensus 162 ~~~~v~~l~~mGf~~~~~i~~L~~~~w~~~~a~~~~~s 199 (200)
T KOG0418|consen 162 DKKKVDSLIEMGFSELEAILVLSGSDWNLADATEQLLS 199 (200)
T ss_pred hHHHHHHHHHhcccHHHHHHHhhccccchhhhhHhhcc
Confidence 478999999999999999999999999999999988 5
No 22
>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A.
Probab=97.80 E-value=4.5e-05 Score=50.55 Aligned_cols=35 Identities=34% Similarity=0.433 Sum_probs=30.5
Q ss_pred HHHHHHHHhc-CCCHHHHHHHHHHcCCCHHHHHHhh
Q 015601 366 DEEIQKLVSM-GFDKTQVEVALAAADGDLNVAVEIL 400 (404)
Q Consensus 366 ~~~i~~l~~m-g~~~~~~~~al~~~~~~~~~a~~~l 400 (404)
+++|+++++. |.++++|++-|++++||+|+||+.-
T Consensus 1 ~e~i~~F~~iTg~~~~~A~~~L~~~~wdle~Av~~y 36 (43)
T PF14555_consen 1 DEKIAQFMSITGADEDVAIQYLEANNWDLEAAVNAY 36 (43)
T ss_dssp HHHHHHHHHHH-SSHHHHHHHHHHTTT-HHHHHHHH
T ss_pred CHHHHHHHHHHCcCHHHHHHHHHHcCCCHHHHHHHH
Confidence 5789999886 9999999999999999999999987
No 23
>TIGR00601 rad23 UV excision repair protein Rad23. All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.60 E-value=6.2e-05 Score=73.75 Aligned_cols=39 Identities=36% Similarity=0.506 Sum_probs=36.3
Q ss_pred CHHHHHHHHhcCCCHHHHHHHHHHcCCCHHHHHHhh-hcC
Q 015601 365 SDEEIQKLVSMGFDKTQVEVALAAADGDLNVAVEIL-SQQ 403 (404)
Q Consensus 365 ~~~~i~~l~~mg~~~~~~~~al~~~~~~~~~a~~~l-~~~ 403 (404)
+.+.|++|++|||+|+.|++|-.+|+.|.|.|++|| +|.
T Consensus 337 E~~AIeRL~~LGF~r~~viqaY~ACdKNEelAAn~Lf~~~ 376 (378)
T TIGR00601 337 EKEAIERLCALGFDRGLVIQAYFACDKNEELAANYLLSQN 376 (378)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhcCCcHHHHHHHHHhhc
Confidence 467999999999999999999999999999999999 653
No 24
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=97.38 E-value=0.00038 Score=45.83 Aligned_cols=35 Identities=34% Similarity=0.639 Sum_probs=32.5
Q ss_pred HHHHHHHHhc--CCCHHHHHHHHHHcCCCHHHHHHhh
Q 015601 366 DEEIQKLVSM--GFDKTQVEVALAAADGDLNVAVEIL 400 (404)
Q Consensus 366 ~~~i~~l~~m--g~~~~~~~~al~~~~~~~~~a~~~l 400 (404)
+++|++|.+| .++++..+++|++++||+|+|++.|
T Consensus 2 ~~~v~~L~~mFP~~~~~~I~~~L~~~~~~ve~ai~~L 38 (42)
T PF02845_consen 2 EEMVQQLQEMFPDLDREVIEAVLQANNGDVEAAIDAL 38 (42)
T ss_dssp HHHHHHHHHHSSSS-HHHHHHHHHHTTTTHHHHHHHH
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence 6789999999 8999999999999999999999998
No 25
>COG5207 UBP14 Isopeptidase T [Posttranslational modification, protein turnover, chaperones]
Probab=97.29 E-value=0.00024 Score=69.98 Aligned_cols=42 Identities=17% Similarity=0.205 Sum_probs=39.1
Q ss_pred CCCCHHHHHHHHhcCCCHHHHHHHHHHcCCCHHHHHHhh-hcC
Q 015601 362 AVVSDEEIQKLVSMGFDKTQVEVALAAADGDLNVAVEIL-SQQ 403 (404)
Q Consensus 362 ~~~~~~~i~~l~~mg~~~~~~~~al~~~~~~~~~a~~~l-~~~ 403 (404)
..++|++++.|.+|||+..++|+||-..++|.+|+|+|. ++.
T Consensus 618 keVdE~~~~Slle~Gln~n~~Rkal~~~n~d~~r~V~w~~N~~ 660 (749)
T COG5207 618 KEVDESKARSLLENGLNPNLCRKALMDMNTDSKRRVVWCINDD 660 (749)
T ss_pred ccccHHHHHHHHHcCCCHHHHHHHHHHccCCchheEEEEEeCC
Confidence 367899999999999999999999999999999999999 754
No 26
>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]
Probab=97.17 E-value=0.00044 Score=64.88 Aligned_cols=38 Identities=32% Similarity=0.451 Sum_probs=35.9
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHcCCCHHHHHHhh-hcC
Q 015601 366 DEEIQKLVSMGFDKTQVEVALAAADGDLNVAVEIL-SQQ 403 (404)
Q Consensus 366 ~~~i~~l~~mg~~~~~~~~al~~~~~~~~~a~~~l-~~~ 403 (404)
.+.|++|++|||+|..|++|--+|+.|.|.|++|| +|.
T Consensus 299 ~eAIeRL~alGF~ralViqayfACdKNEelAAN~Ll~~~ 337 (340)
T KOG0011|consen 299 KEAIERLEALGFPRALVIQAYFACDKNEELAANYLLSHS 337 (340)
T ss_pred HHHHHHHHHhCCcHHHHHHHHHhcCccHHHHHHHHHhhc
Confidence 67899999999999999999999999999999999 763
No 27
>KOG2561 consensus Adaptor protein NUB1, contains UBA domain [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=96.93 E-value=0.00083 Score=65.32 Aligned_cols=36 Identities=36% Similarity=0.736 Sum_probs=34.4
Q ss_pred CHHHHHHHHhcCCCHHHHHHHHHHcCCCHHHHHHhh
Q 015601 365 SDEEIQKLVSMGFDKTQVEVALAAADGDLNVAVEIL 400 (404)
Q Consensus 365 ~~~~i~~l~~mg~~~~~~~~al~~~~~~~~~a~~~l 400 (404)
++++...+|+|||.+.+|+.|||.|+||+|.||.|+
T Consensus 303 ~d~~lsllv~mGfeesdaRlaLRsc~g~Vd~AvqfI 338 (568)
T KOG2561|consen 303 NDETLSLLVGMGFEESDARLALRSCNGDVDSAVQFI 338 (568)
T ss_pred cchHHHHHHHcCCCchHHHHHHHhccccHHHHHHHH
Confidence 478899999999999999999999999999999998
No 28
>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed
Probab=96.92 E-value=0.0019 Score=51.85 Aligned_cols=38 Identities=29% Similarity=0.464 Sum_probs=35.2
Q ss_pred CCCHHHHHHHHhc-CCCHHHHHHHHHHcCCCHHHHHHhh
Q 015601 363 VVSDEEIQKLVSM-GFDKTQVEVALAAADGDLNVAVEIL 400 (404)
Q Consensus 363 ~~~~~~i~~l~~m-g~~~~~~~~al~~~~~~~~~a~~~l 400 (404)
..+++.|+.+++- |.++++|++||++|+||+-.|+-+|
T Consensus 74 ~i~~edI~lv~~q~gvs~~~A~~AL~~~~gDl~~AI~~L 112 (115)
T PRK06369 74 EIPEEDIELVAEQTGVSEEEARKALEEANGDLAEAILKL 112 (115)
T ss_pred CCCHHHHHHHHHHHCcCHHHHHHHHHHcCCcHHHHHHHH
Confidence 4579999999885 9999999999999999999999998
No 29
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=96.83 E-value=0.0027 Score=41.93 Aligned_cols=35 Identities=26% Similarity=0.542 Sum_probs=32.8
Q ss_pred HHHHHHHHhc--CCCHHHHHHHHHHcCCCHHHHHHhh
Q 015601 366 DEEIQKLVSM--GFDKTQVEVALAAADGDLNVAVEIL 400 (404)
Q Consensus 366 ~~~i~~l~~m--g~~~~~~~~al~~~~~~~~~a~~~l 400 (404)
++.+++|.+| ..++++++++|++++||+|.|++.|
T Consensus 3 ~~~v~~L~~mFP~l~~~~I~~~L~~~~g~ve~~i~~L 39 (43)
T smart00546 3 DEALHDLKDMFPNLDEEVIKAVLEANNGNVEATINNL 39 (43)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence 5789999999 7899999999999999999999988
No 30
>TIGR00264 alpha-NAC-related protein. This hypothetical protein is found so far only in the Archaea. Its C-terminal domain of about 40 amino acids is homologous to the C-termini of the nascent polypeptide-associated complex alpha chain (alpha-NAC) and its yeast ortholog Egd2p and to the huntingtin-interacting protein HYPK. It shows weaker similarity, possibly through shared structural constraints rather than through homology, with the amino-terminal domain of elongation factor Ts. Alpha-NAC plays a role in preventing nascent polypeptides from binding inappropriately to membrane-targeting apparatus during translation, but is also active as a transcription regulator.
Probab=96.68 E-value=0.0032 Score=50.39 Aligned_cols=37 Identities=24% Similarity=0.439 Sum_probs=34.3
Q ss_pred CCHHHHHHHHhc-CCCHHHHHHHHHHcCCCHHHHHHhh
Q 015601 364 VSDEEIQKLVSM-GFDKTQVEVALAAADGDLNVAVEIL 400 (404)
Q Consensus 364 ~~~~~i~~l~~m-g~~~~~~~~al~~~~~~~~~a~~~l 400 (404)
.+++.|+.+++- |.++++|++||++|+||+-.|+-+|
T Consensus 77 i~~eDI~lV~eq~gvs~e~A~~AL~~~~gDl~~AI~~L 114 (116)
T TIGR00264 77 ITEDDIELVMKQCNVSKEEARRALEECGGDLAEAIMKL 114 (116)
T ss_pred CCHHHHHHHHHHhCcCHHHHHHHHHHcCCCHHHHHHHh
Confidence 578999999885 9999999999999999999999887
No 31
>COG1308 EGD2 Transcription factor homologous to NACalpha-BTF3 [Transcription]
Probab=96.49 E-value=0.0073 Score=48.65 Aligned_cols=38 Identities=32% Similarity=0.457 Sum_probs=34.1
Q ss_pred CCCHHHHHHHHhc-CCCHHHHHHHHHHcCCCHHHHHHhh
Q 015601 363 VVSDEEIQKLVSM-GFDKTQVEVALAAADGDLNVAVEIL 400 (404)
Q Consensus 363 ~~~~~~i~~l~~m-g~~~~~~~~al~~~~~~~~~a~~~l 400 (404)
..+++.|+..++- |.+|++|++||+++|||+-.|+--|
T Consensus 82 ~i~eeDIkLV~eQa~VsreeA~kAL~e~~GDlaeAIm~L 120 (122)
T COG1308 82 DISEEDIKLVMEQAGVSREEAIKALEEAGGDLAEAIMKL 120 (122)
T ss_pred CCCHHHHHHHHHHhCCCHHHHHHHHHHcCCcHHHHHHHh
Confidence 3579999999885 9999999999999999999998766
No 32
>PF09288 UBA_3: Fungal ubiquitin-associated domain ; InterPro: IPR015368 This C-terminal domain is found in ubiquitin binding proteins, it adopts a structure consisting of a three alpha-helix bundle. This domain is predominantly found in fungi []. ; PDB: 1TTE_A.
Probab=96.41 E-value=0.0037 Score=43.02 Aligned_cols=26 Identities=19% Similarity=0.432 Sum_probs=21.6
Q ss_pred CHHHHHHHHhcCCCHHHHHHHHHHcC
Q 015601 365 SDEEIQKLVSMGFDKTQVEVALAAAD 390 (404)
Q Consensus 365 ~~~~i~~l~~mg~~~~~~~~al~~~~ 390 (404)
+.+.|+++++|||+++++++||+.-+
T Consensus 9 ~~~lVd~F~~mGF~~dkVvevlrrlg 34 (55)
T PF09288_consen 9 DKDLVDQFENMGFERDKVVEVLRRLG 34 (55)
T ss_dssp SHHHHHHHHHHT--HHHHHHHHHHS-
T ss_pred CHHHHHHHHHcCCcHHHHHHHHHHhC
Confidence 57899999999999999999999865
No 33
>KOG0944 consensus Ubiquitin-specific protease UBP14 [Posttranslational modification, protein turnover, chaperones]
Probab=96.39 E-value=0.0053 Score=62.80 Aligned_cols=40 Identities=25% Similarity=0.331 Sum_probs=36.1
Q ss_pred CCCHHHHHHHHhcCCCHHHHHHHHHHc-CCCHHHHHHhh-hc
Q 015601 363 VVSDEEIQKLVSMGFDKTQVEVALAAA-DGDLNVAVEIL-SQ 402 (404)
Q Consensus 363 ~~~~~~i~~l~~mg~~~~~~~~al~~~-~~~~~~a~~~l-~~ 402 (404)
..++..|.+|++|||.++.+++||-.+ |.+.|.|.+|| .|
T Consensus 569 ~~d~s~i~qL~~MGFp~eac~rAly~tgN~~aEaA~NWl~~H 610 (763)
T KOG0944|consen 569 AADRSVISQLVEMGFPEEACRRALYYTGNSGAEAASNWLMEH 610 (763)
T ss_pred chhHHHHHHHHHcCCCHHHHHHHHhhhcCccHHHHHHHHHHh
Confidence 346889999999999999999999999 77899999999 54
No 34
>COG5207 UBP14 Isopeptidase T [Posttranslational modification, protein turnover, chaperones]
Probab=96.37 E-value=0.0067 Score=60.11 Aligned_cols=38 Identities=29% Similarity=0.444 Sum_probs=34.9
Q ss_pred CHHHHHHHHhcCCCHHHHHHHHHHcCC-CHHHHHHhh-hc
Q 015601 365 SDEEIQKLVSMGFDKTQVEVALAAADG-DLNVAVEIL-SQ 402 (404)
Q Consensus 365 ~~~~i~~l~~mg~~~~~~~~al~~~~~-~~~~a~~~l-~~ 402 (404)
.+..|+||++|||+++.+.+||-.++| |.|.|++|| .|
T Consensus 558 Nqs~I~qL~~mGfp~~~~~rAL~~tgNqDaEsAMNWLFqH 597 (749)
T COG5207 558 NQSLIRQLVDMGFPEEDAARALGITGNQDAESAMNWLFQH 597 (749)
T ss_pred hHHHHHHHHHcCCCHHHHHHHHhhccCcchHHHHHHHHhh
Confidence 467899999999999999999999988 999999999 44
No 35
>KOG2561 consensus Adaptor protein NUB1, contains UBA domain [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=96.22 E-value=0.0064 Score=59.34 Aligned_cols=37 Identities=32% Similarity=0.506 Sum_probs=35.5
Q ss_pred CCHHHHHHHHhcCCCHHHHHHHHHHcCCCHHHHHHhh
Q 015601 364 VSDEEIQKLVSMGFDKTQVEVALAAADGDLNVAVEIL 400 (404)
Q Consensus 364 ~~~~~i~~l~~mg~~~~~~~~al~~~~~~~~~a~~~l 400 (404)
+++.+|.+|+.|||++..|+.||+..+||.+.|.+.|
T Consensus 428 vd~~~la~Lv~mGF~e~~A~~ALe~~gnn~~~a~~~L 464 (568)
T KOG2561|consen 428 VDGISLAELVSMGFEEGKARSALEAGGNNEDTAQRLL 464 (568)
T ss_pred cchhhHHHHHHhccccchHHHHHHhcCCcHHHHHHHH
Confidence 4688999999999999999999999999999999998
No 36
>KOG0010 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones; General function prediction only]
Probab=95.41 E-value=0.019 Score=56.98 Aligned_cols=35 Identities=43% Similarity=0.640 Sum_probs=32.4
Q ss_pred HHHHHHHHhcCC-CHHHHHHHHHHcCCCHHHHHHhh
Q 015601 366 DEEIQKLVSMGF-DKTQVEVALAAADGDLNVAVEIL 400 (404)
Q Consensus 366 ~~~i~~l~~mg~-~~~~~~~al~~~~~~~~~a~~~l 400 (404)
+...++|-+||| +|++..+||++++||+++|||.|
T Consensus 455 q~QLeQL~~MGF~nre~nlqAL~atgGdi~aAverl 490 (493)
T KOG0010|consen 455 QTQLEQLNDMGFLDREANLQALRATGGDINAAVERL 490 (493)
T ss_pred HHHHHHHHhcCCccHHHHHHHHHHhcCcHHHHHHHH
Confidence 457899999998 89999999999999999999988
No 37
>COG4008 Predicted metal-binding transcription factor [Transcription]
Probab=93.77 E-value=0.15 Score=41.12 Aligned_cols=35 Identities=31% Similarity=0.357 Sum_probs=33.1
Q ss_pred CHHHHHHHHhcCCCHHHHHHHHHHcCCCHHHHHHhh
Q 015601 365 SDEEIQKLVSMGFDKTQVEVALAAADGDLNVAVEIL 400 (404)
Q Consensus 365 ~~~~i~~l~~mg~~~~~~~~al~~~~~~~~~a~~~l 400 (404)
+.+.++-+++-+.++|+|++||..+| |+-+|++.|
T Consensus 114 ~~e~v~v~a~a~v~~eeAr~aleeag-Dl~~A~k~l 148 (153)
T COG4008 114 PVEEVEVLADAFVTPEEAREALEEAG-DLRTAMKIL 148 (153)
T ss_pred cHHHHHHHHHhcCCHHHHHHHHHHcC-CHHHHHHHH
Confidence 57889999999999999999999997 999999998
No 38
>PF06972 DUF1296: Protein of unknown function (DUF1296); InterPro: IPR009719 This family represents a conserved region approximately 60 residues long within a number of plant proteins of unknown function.
Probab=93.57 E-value=0.16 Score=35.43 Aligned_cols=37 Identities=27% Similarity=0.372 Sum_probs=31.8
Q ss_pred HHHHHHHHhc-C-CCHHHHHHHHHHcCCCHHHHHHhh-hc
Q 015601 366 DEEIQKLVSM-G-FDKTQVEVALAAADGDLNVAVEIL-SQ 402 (404)
Q Consensus 366 ~~~i~~l~~m-g-~~~~~~~~al~~~~~~~~~a~~~l-~~ 402 (404)
...||.|.|. | .++++.-.+|+.||.|++.|++-| +|
T Consensus 6 rk~VQ~iKEiv~~hse~eIya~L~ecnMDpnea~qrLL~q 45 (60)
T PF06972_consen 6 RKTVQSIKEIVGCHSEEEIYAMLKECNMDPNEAVQRLLSQ 45 (60)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHhCCCHHHHHHHHHhc
Confidence 4567888775 4 599999999999999999999999 75
No 39
>PF11626 Rap1_C: TRF2-interacting telomeric protein/Rap1 - C terminal domain; InterPro: IPR021661 This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres []. The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C-terminal domain []. ; PDB: 3K6G_C 3CZ6_A 3OWT_A.
Probab=92.11 E-value=0.19 Score=38.67 Aligned_cols=32 Identities=28% Similarity=0.456 Sum_probs=28.0
Q ss_pred HHHHHhcCCCHHHHHHHHHHcCCCHHHHHHhh
Q 015601 369 IQKLVSMGFDKTQVEVALAAADGDLNVAVEIL 400 (404)
Q Consensus 369 i~~l~~mg~~~~~~~~al~~~~~~~~~a~~~l 400 (404)
|+.+.+.|++++.+.+||.+|.+|++.|..|+
T Consensus 1 i~~~~~~g~~~~~v~~aL~~tSgd~~~a~~~v 32 (87)
T PF11626_consen 1 IKHYEELGYSREFVTHALYATSGDPELARRFV 32 (87)
T ss_dssp -HHHHHHTB-HHHHHHHHHHTTTBHHHHHHHH
T ss_pred CchHHHhCCCHHHHHHHHHHhCCCHHHHHHHH
Confidence 56688999999999999999999999999966
No 40
>PF11547 E3_UbLigase_EDD: E3 ubiquitin ligase EDD; InterPro: IPR024725 EDD, the ER ubiquitin ligase from the HECT ligases, contains an N-terminal ubiquitin-associated (UBA) domain which binds ubiquitin. Ubiquitin is recognised by helices alpha-1 and -3 in in the UBA domain. EDD is involved in DNA damage repair pathways and binds to mono-ubiquitinated proteins [].; GO: 0043130 ubiquitin binding; PDB: 2QHO_H.
Probab=90.83 E-value=0.41 Score=31.73 Aligned_cols=38 Identities=24% Similarity=0.281 Sum_probs=31.1
Q ss_pred CCCHHHHHHHHh--cCCCHHHHHHHHHHcCCCHHHHHHhh
Q 015601 363 VVSDEEIQKLVS--MGFDKTQVEVALAAADGDLNVAVEIL 400 (404)
Q Consensus 363 ~~~~~~i~~l~~--mg~~~~~~~~al~~~~~~~~~a~~~l 400 (404)
.++|+.|++... -|=+|+-.++-|+.+|=|++.||+-|
T Consensus 7 ~vPedlI~q~q~VLqgksR~vIirELqrTnLdVN~AvNNl 46 (53)
T PF11547_consen 7 QVPEDLINQAQVVLQGKSRNVIIRELQRTNLDVNLAVNNL 46 (53)
T ss_dssp GS-HHHHHHHHHHSTTS-HHHHHHHHHHTTT-HHHHHHHH
T ss_pred cCCHHHHHHHHHHHcCCcHHHHHHHHHHhcccHHHHHHHH
Confidence 456899998755 59999999999999999999999988
No 41
>smart00804 TAP_C C-terminal domain of vertebrate Tap protein. The vertebrate Tap protein is a member of the NXF family of shuttling transport receptors for the nuclear export of mRNA. Its most C-terminal domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate shuttling. This domain forms a compact four-helix fold related to that of a UBA domain.
Probab=89.12 E-value=0.83 Score=32.76 Aligned_cols=35 Identities=17% Similarity=0.289 Sum_probs=29.3
Q ss_pred HHHHHHHHh-cCCCHHHHHHHHHHcCCCHHHHHHhh
Q 015601 366 DEEIQKLVS-MGFDKTQVEVALAAADGDLNVAVEIL 400 (404)
Q Consensus 366 ~~~i~~l~~-mg~~~~~~~~al~~~~~~~~~a~~~l 400 (404)
++.|.++.. -|-+.+=++++|+.++||.++|+.-.
T Consensus 13 ~~~v~~~~~~Tgmn~~~s~~cLe~~~Wd~~~Al~~F 48 (63)
T smart00804 13 QEMVQAFSAQTGMNAEYSQMCLEDNNWDYERALKNF 48 (63)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence 566766644 49999999999999999999998754
No 42
>PF03943 TAP_C: TAP C-terminal domain; InterPro: IPR005637 This entry contains the NXF family of shuttling transport receptors for nuclear export of mRNA, which include: vertebrate mRNA export factor TAP or nuclear RNA export factor 1 (NXF1). Caenorhabditis elegans nuclear RNA export factor 1 (nxf-1). yeast mRNA export factor MEX67. Members of the NXF family have a modular structure. A nuclear localization sequence and a noncanonical RNA recognition motif (RRM) (see PDOC00030 from PROSITEDOC) followed by four LRR repeats are located in its N-terminal half. The C-terminal half contains a NTF2 domain (see PDOC50177 from PROSITEDOC) followed by a second domain, TAP-C. The TAP-C domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate nuclear shuttling [,]. The Tap-C domain is made of four alpha helices packed against each other. The arrangement of helices 1, 2 and 3 is similar to that seen in a UBA fold. and is joined to the next module by flexible 12-residue Pro-rich linker [, ].; GO: 0051028 mRNA transport, 0005634 nucleus; PDB: 1OAI_A 1GO5_A 2KHH_A 2JP7_A.
Probab=88.50 E-value=0.38 Score=32.96 Aligned_cols=34 Identities=18% Similarity=0.248 Sum_probs=26.5
Q ss_pred HHHHHHHh-cCCCHHHHHHHHHHcCCCHHHHHHhh
Q 015601 367 EEIQKLVS-MGFDKTQVEVALAAADGDLNVAVEIL 400 (404)
Q Consensus 367 ~~i~~l~~-mg~~~~~~~~al~~~~~~~~~a~~~l 400 (404)
+.|.++.. -|-+.+-+.+.|..++||.++|+.-.
T Consensus 2 ~mv~~~s~~Tgmn~~~s~~CL~~n~Wd~~~A~~~F 36 (51)
T PF03943_consen 2 EMVQQFSQQTGMNLEWSQKCLEENNWDYERALQNF 36 (51)
T ss_dssp HHHHHHHHHCSS-CCHHHHHHHHTTT-CCHHHHHH
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence 55666644 48999999999999999999999765
No 43
>KOG1071 consensus Mitochondrial translation elongation factor EF-Tsmt, catalyzes nucleotide exchange on EF-Tumt [Translation, ribosomal structure and biogenesis]
Probab=87.81 E-value=1.2 Score=42.24 Aligned_cols=36 Identities=33% Similarity=0.378 Sum_probs=33.1
Q ss_pred CHHHHHHHH-hcCCCHHHHHHHHHHcCCCHHHHHHhh
Q 015601 365 SDEEIQKLV-SMGFDKTQVEVALAAADGDLNVAVEIL 400 (404)
Q Consensus 365 ~~~~i~~l~-~mg~~~~~~~~al~~~~~~~~~a~~~l 400 (404)
+.+.|++|. +-|++-..+++||..||||++.|.+||
T Consensus 46 ~~allk~LR~kTgas~~ncKkALee~~gDl~~A~~~L 82 (340)
T KOG1071|consen 46 SKALLKKLREKTGASMVNCKKALEECGGDLVLAEEWL 82 (340)
T ss_pred cHHHHHHHHHHcCCcHHHHHHHHHHhCCcHHHHHHHH
Confidence 478899995 469999999999999999999999999
No 44
>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB []. Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1HJP_A 1CUK_A 1C7Y_A 1IXS_A 1IXR_B 1BVS_E 2ZTC_A 2ZTD_B 2H5X_A.
Probab=87.50 E-value=0.86 Score=30.55 Aligned_cols=25 Identities=20% Similarity=0.522 Sum_probs=21.7
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHcC
Q 015601 366 DEEIQKLVSMGFDKTQVEVALAAAD 390 (404)
Q Consensus 366 ~~~i~~l~~mg~~~~~~~~al~~~~ 390 (404)
+|.++-|+.+||++.++.+|++...
T Consensus 4 ~d~~~AL~~LGy~~~e~~~av~~~~ 28 (47)
T PF07499_consen 4 EDALEALISLGYSKAEAQKAVSKLL 28 (47)
T ss_dssp HHHHHHHHHTTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHhh
Confidence 6789999999999999999999873
No 45
>PF07223 DUF1421: Protein of unknown function (DUF1421); InterPro: IPR010820 This family represents a conserved region approximately 350 residues long within a number of plant proteins of unknown function.
Probab=84.70 E-value=0.86 Score=44.35 Aligned_cols=21 Identities=43% Similarity=0.746 Sum_probs=18.9
Q ss_pred HHHHHHHHhcCCCHHHHHHHH
Q 015601 366 DEEIQKLVSMGFDKTQVEVAL 386 (404)
Q Consensus 366 ~~~i~~l~~mg~~~~~~~~al 386 (404)
+|.|++++.|||.||+|+...
T Consensus 322 ddvidKv~~MGf~rDqV~a~v 342 (358)
T PF07223_consen 322 DDVIDKVASMGFRRDQVRATV 342 (358)
T ss_pred HHHHHHHHHcCCcHHHHHHHH
Confidence 799999999999999998643
No 46
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=83.59 E-value=0.87 Score=29.65 Aligned_cols=24 Identities=29% Similarity=0.545 Sum_probs=20.3
Q ss_pred CCHHHHHHHHHHcCCCHHHHHHhh
Q 015601 377 FDKTQVEVALAAADGDLNVAVEIL 400 (404)
Q Consensus 377 ~~~~~~~~al~~~~~~~~~a~~~l 400 (404)
|+++-.++||+.++||..+|++.|
T Consensus 5 ~E~~~i~~aL~~~~gn~~~aA~~L 28 (42)
T PF02954_consen 5 FEKQLIRQALERCGGNVSKAARLL 28 (42)
T ss_dssp HHHHHHHHHHHHTTT-HHHHHHHH
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHH
Confidence 456778899999999999999998
No 47
>PF08587 UBA_2: Ubiquitin associated domain (UBA) ; InterPro: IPR013896 This is a UBA (ubiquitin associated) protein []. Ubiquitin is involved in intracellular proteolysis. ; GO: 0004674 protein serine/threonine kinase activity; PDB: 3H4J_B.
Probab=81.50 E-value=0.28 Score=32.46 Aligned_cols=26 Identities=31% Similarity=0.611 Sum_probs=17.5
Q ss_pred HHHHHHH-HhcCCCHHHHHHHHHHcCC
Q 015601 366 DEEIQKL-VSMGFDKTQVEVALAAADG 391 (404)
Q Consensus 366 ~~~i~~l-~~mg~~~~~~~~al~~~~~ 391 (404)
++.|..| ..|||+||++..||+....
T Consensus 3 e~vv~~Ls~tMGY~kdeI~eaL~~~~~ 29 (46)
T PF08587_consen 3 EDVVSKLSKTMGYDKDEIYEALESSEP 29 (46)
T ss_dssp HCCHHHHHCTT---HHHHHHHCCSSS-
T ss_pred HHHHHHHHHHhCCCHHHHHHHHHcCCC
Confidence 4557777 4599999999999998643
No 48
>PF03474 DMA: DMRTA motif; InterPro: IPR005173 This region is found to the C terminus of the DM DNA-binding domain IPR001275 from INTERPRO []. DM-domain proteins with this motif are known as DMRTA proteins. The function of this region is unknown.
Probab=79.94 E-value=2.7 Score=26.88 Aligned_cols=25 Identities=24% Similarity=0.403 Sum_probs=20.8
Q ss_pred CCCHHHHHHHHHHcCCCHHHHHHhh
Q 015601 376 GFDKTQVEVALAAADGDLNVAVEIL 400 (404)
Q Consensus 376 g~~~~~~~~al~~~~~~~~~a~~~l 400 (404)
.-.++.-...|+.|+||+-+|+|.+
T Consensus 14 ~~kr~~Le~iL~~C~GDvv~AIE~~ 38 (39)
T PF03474_consen 14 HQKRSVLELILQRCNGDVVQAIEQF 38 (39)
T ss_pred CCChHHHHHHHHHcCCcHHHHHHHh
Confidence 3456777889999999999999964
No 49
>PF08938 HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This domain is found in various eukaryotic HBS1-like proteins. ; PDB: 1UFZ_A 3IZQ_1.
Probab=78.26 E-value=1.2 Score=33.61 Aligned_cols=27 Identities=26% Similarity=0.162 Sum_probs=22.4
Q ss_pred CC-CHHHHHHHHHHcCCCHHHHHHhh-hc
Q 015601 376 GF-DKTQVEVALAAADGDLNVAVEIL-SQ 402 (404)
Q Consensus 376 g~-~~~~~~~al~~~~~~~~~a~~~l-~~ 402 (404)
.. ++.+.+.||-.++.|+++|++|| ++
T Consensus 42 ~~~~e~~i~eal~~~~fDvekAl~~Ll~~ 70 (79)
T PF08938_consen 42 YVPPEEQIKEALWHYYFDVEKALDYLLSK 70 (79)
T ss_dssp CC--CCHHHHHHHHTTT-CCHHHHHHHHC
T ss_pred cCCCHHHHHHHHHHHcCCHHHHHHHHHHh
Confidence 35 88999999999999999999999 54
No 50
>PF11372 DUF3173: Domain of unknown function (DUF3173); InterPro: IPR021512 This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=77.19 E-value=2.6 Score=29.64 Aligned_cols=20 Identities=20% Similarity=0.502 Sum_probs=18.2
Q ss_pred HHHHhcCCCHHHHHHHHHHc
Q 015601 370 QKLVSMGFDKTQVEVALAAA 389 (404)
Q Consensus 370 ~~l~~mg~~~~~~~~al~~~ 389 (404)
+.|++|||++.+|++-++++
T Consensus 7 ~dLi~lGf~~~tA~~IIrqA 26 (59)
T PF11372_consen 7 KDLIELGFSESTARDIIRQA 26 (59)
T ss_pred HHHHHcCCCHHHHHHHHHHH
Confidence 67999999999999999876
No 51
>KOG2239 consensus Transcription factor containing NAC and TS-N domains [Transcription]
Probab=77.03 E-value=8.1 Score=34.06 Aligned_cols=37 Identities=22% Similarity=0.304 Sum_probs=30.6
Q ss_pred CCHHHHHHHHhc-CCCHHHHHHHHHHcCCCHHHHHHhh
Q 015601 364 VSDEEIQKLVSM-GFDKTQVEVALAAADGDLNVAVEIL 400 (404)
Q Consensus 364 ~~~~~i~~l~~m-g~~~~~~~~al~~~~~~~~~a~~~l 400 (404)
..++.|+.++.. +.+|.+|++||++++||+=.|+=-|
T Consensus 170 ve~kDIeLVmsQanvSR~kAVkALk~~~~DiVnAIM~L 207 (209)
T KOG2239|consen 170 VEAKDIELVMSQANVSRAKAVKALKNNNNDIVNAIMEL 207 (209)
T ss_pred CchhhHHHHHHHhhhhHHHHHHHHHhccchHHHHHHHh
Confidence 446778887664 8999999999999999998887544
No 52
>PF10152 DUF2360: Predicted coiled-coil domain-containing protein (DUF2360); InterPro: IPR019309 This entry represents a component of the WASH complex. The WASH complex is present at the surface of endosomes and recruits and activates the Arp2/3 complex to induce actin polymerisation. The WASH complex plays a key role in the fission of tubules that serve as transport intermediates during endosome sorting []. The WASH complex's subunit structure: F-actin-capping protein subunit alpha (CAPZA1, CAPZA2 or CAPZA3), F-actin-capping protein subunit beta (CAPZB), WASH (WASH1, WASH2P, WASH3P, WASH4P, WASH5P or WASH6P), FAM21 (FAM21A, FAM21B or FAM21C), KIAA1033, KIAA0196 (strumpellin) and CCDC53.
Probab=73.25 E-value=30 Score=29.41 Aligned_cols=29 Identities=21% Similarity=0.259 Sum_probs=24.8
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHcCCCHH
Q 015601 366 DEEIQKLVSMGFDKTQVEVALAAADGDLN 394 (404)
Q Consensus 366 ~~~i~~l~~mg~~~~~~~~al~~~~~~~~ 394 (404)
=++=-+|+.||..++.++.-+++.|=|++
T Consensus 116 y~kYfKMl~~GvP~~aVk~KM~~eGlDp~ 144 (148)
T PF10152_consen 116 YAKYFKMLKMGVPREAVKQKMQAEGLDPS 144 (148)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHcCCCHH
Confidence 35666788999999999999999988775
No 53
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=62.14 E-value=14 Score=32.82 Aligned_cols=25 Identities=28% Similarity=0.462 Sum_probs=23.0
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHcC
Q 015601 366 DEEIQKLVSMGFDKTQVEVALAAAD 390 (404)
Q Consensus 366 ~~~i~~l~~mg~~~~~~~~al~~~~ 390 (404)
+|.++.|+.+||++++|.+|+++..
T Consensus 144 ~e~~~AL~~LGy~~~ea~~av~~~~ 168 (188)
T PRK14606 144 HESLEALVSLGYPEKQAREAVKHVY 168 (188)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHh
Confidence 6789999999999999999999884
No 54
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=60.40 E-value=16 Score=32.67 Aligned_cols=24 Identities=25% Similarity=0.555 Sum_probs=22.4
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHc
Q 015601 366 DEEIQKLVSMGFDKTQVEVALAAA 389 (404)
Q Consensus 366 ~~~i~~l~~mg~~~~~~~~al~~~ 389 (404)
+|.++.|+.+||++++|.+|+++.
T Consensus 153 ~ea~~AL~~LGy~~~ea~~al~~i 176 (197)
T PRK14603 153 EDAVLALLALGFREAQVRSVVAEL 176 (197)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHH
Confidence 678999999999999999999986
No 55
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=60.27 E-value=15 Score=32.98 Aligned_cols=24 Identities=13% Similarity=0.401 Sum_probs=22.7
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHc
Q 015601 366 DEEIQKLVSMGFDKTQVEVALAAA 389 (404)
Q Consensus 366 ~~~i~~l~~mg~~~~~~~~al~~~ 389 (404)
+|.++.|+.+||++.+|.+|+++.
T Consensus 156 ~ea~~AL~~LGy~~~ea~~av~~~ 179 (203)
T PRK14602 156 RDALAGLANLGYGEEEARPVLKEV 179 (203)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHH
Confidence 688999999999999999999987
No 56
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=59.88 E-value=16 Score=32.65 Aligned_cols=24 Identities=29% Similarity=0.466 Sum_probs=22.4
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHc
Q 015601 366 DEEIQKLVSMGFDKTQVEVALAAA 389 (404)
Q Consensus 366 ~~~i~~l~~mg~~~~~~~~al~~~ 389 (404)
+|.++.|+.+||++++|.+|+++.
T Consensus 150 ~e~~~aL~~LGy~~~ea~~ai~~i 173 (195)
T PRK14604 150 RELSEILISLGYSAAEAAAAIAAL 173 (195)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHH
Confidence 678999999999999999999887
No 57
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=59.35 E-value=11 Score=33.40 Aligned_cols=26 Identities=27% Similarity=0.514 Sum_probs=23.5
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHcCC
Q 015601 366 DEEIQKLVSMGFDKTQVEVALAAADG 391 (404)
Q Consensus 366 ~~~i~~l~~mg~~~~~~~~al~~~~~ 391 (404)
+|.++.|+.+||++.+|++|+++...
T Consensus 146 ~e~~~aL~~LGy~~~ea~~al~~v~~ 171 (186)
T PRK14600 146 DDALAALISLGYEKTKAFNAIQKIKP 171 (186)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHhhc
Confidence 68899999999999999999998753
No 58
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=58.54 E-value=11 Score=33.18 Aligned_cols=25 Identities=24% Similarity=0.549 Sum_probs=23.1
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHcC
Q 015601 366 DEEIQKLVSMGFDKTQVEVALAAAD 390 (404)
Q Consensus 366 ~~~i~~l~~mg~~~~~~~~al~~~~ 390 (404)
+|.++.|+.+||++.+|++|+++..
T Consensus 143 ~ea~~AL~~LGy~~~ea~~a~~~~~ 167 (183)
T PRK14601 143 SEALAALLTLGFKQEKIIKVLASCQ 167 (183)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHhcc
Confidence 6889999999999999999999873
No 59
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=57.93 E-value=12 Score=33.32 Aligned_cols=26 Identities=35% Similarity=0.414 Sum_probs=23.4
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHcCC
Q 015601 366 DEEIQKLVSMGFDKTQVEVALAAADG 391 (404)
Q Consensus 366 ~~~i~~l~~mg~~~~~~~~al~~~~~ 391 (404)
+|.++.|+.+||++.+|.+|+++.-.
T Consensus 145 ~ea~~AL~~LGy~~~ea~~al~~v~~ 170 (196)
T PRK13901 145 KELEQSIVNMGFDRKLVNSAIKEIML 170 (196)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHhc
Confidence 68899999999999999999988744
No 60
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=53.48 E-value=22 Score=31.55 Aligned_cols=25 Identities=32% Similarity=0.562 Sum_probs=22.8
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHcC
Q 015601 366 DEEIQKLVSMGFDKTQVEVALAAAD 390 (404)
Q Consensus 366 ~~~i~~l~~mg~~~~~~~~al~~~~ 390 (404)
++.++.|+.+||++++|.+|+++..
T Consensus 148 ~e~~~aL~~LGy~~~e~~~ai~~~~ 172 (191)
T TIGR00084 148 DELFEALVSLGYKPQEIQQALKKIK 172 (191)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHh
Confidence 6788999999999999999999874
No 61
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=52.49 E-value=22 Score=31.84 Aligned_cols=26 Identities=19% Similarity=0.491 Sum_probs=22.6
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHcCC
Q 015601 366 DEEIQKLVSMGFDKTQVEVALAAADG 391 (404)
Q Consensus 366 ~~~i~~l~~mg~~~~~~~~al~~~~~ 391 (404)
++.++.|+.+||++.|+++|+++..-
T Consensus 157 ~~~v~AL~~LGy~~~e~~~av~~v~~ 182 (201)
T COG0632 157 EEAVEALVALGYKEKEIKKAVKKVLK 182 (201)
T ss_pred hHHHHHHHHcCCCHHHHHHHHHHHHh
Confidence 45599999999999999999988764
No 62
>KOG1288 consensus Amino acid transporters [Amino acid transport and metabolism]
Probab=52.07 E-value=3.4e+02 Score=29.33 Aligned_cols=88 Identities=16% Similarity=0.079 Sum_probs=53.9
Q ss_pred ccccchhHHHhhccccHHHHHHHHHHHHHHHHHHHhcc-cccccceeechhhhccCcchhhhhhhhcccCHHHHHHHHHH
Q 015601 8 EAGLSTRANQWWESIPFFTSAVVIVCGTIYLICLLFGY-DSFYEICFLPSAVISRFQVYRFYTSIVFHGSLLHVLFNMLA 86 (404)
Q Consensus 8 ~~~~~~~~~~~~~~~P~vT~~li~~~v~~~~l~~~~~~-~~~~~l~~~p~~i~~~~q~WRL~Ts~f~h~~~~hll~n~~~ 86 (404)
-+.|+-++++=-+++|..|..-++.++++|++..+.-. .....+....+.+++.-..|+.|+-.=+.. ..+.-.|..
T Consensus 313 GAnMSgELk~PSkSIP~GTl~ava~Tf~~Yvl~~flm~~t~~r~~Lq~dy~v~~~isl~p~fi~iGi~s--ttlfss~s~ 390 (945)
T KOG1288|consen 313 GANMSGELKAPSKSIPKGTLSAVAFTFFVYVLVIFLMGCTVPRTLLQNDYDVMMHISLHPPFILIGILS--TTLFSSMSG 390 (945)
T ss_pred CCCcCccccCccccCCccchHHHHHHHHHHHHHHHHhccCcchHHhhhchhheeeccccchHHHHHHHH--HHHHHHHHH
Confidence 35666677777788999999999999999988776422 223344445555666667787776532221 123333444
Q ss_pred HHHHHHHHHHH
Q 015601 87 LVPLGSELERI 97 (404)
Q Consensus 87 l~~~g~~lE~~ 97 (404)
+.--++.||..
T Consensus 391 liGasrvL~al 401 (945)
T KOG1288|consen 391 LIGASRVLEAL 401 (945)
T ss_pred HhhHHHHHHHH
Confidence 44455566643
No 63
>PF10440 WIYLD: Ubiquitin-binding WIYLD domain; InterPro: IPR018848 This entry represents a presumed domain which has been predicted to contain three alpha helices. It was named the WIYLD domain based on the pattern of the ost conserved residues []. This domain appears to be specific to plant SET-domain proteins. ; GO: 0018024 histone-lysine N-methyltransferase activity
Probab=50.55 E-value=25 Score=25.34 Aligned_cols=23 Identities=30% Similarity=0.541 Sum_probs=19.3
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHH
Q 015601 366 DEEIQKLVSMGFDKTQVEVALAA 388 (404)
Q Consensus 366 ~~~i~~l~~mg~~~~~~~~al~~ 388 (404)
+..++.+..|||++++++..|+.
T Consensus 12 daA~dam~~lG~~~~~v~~vl~~ 34 (65)
T PF10440_consen 12 DAALDAMRQLGFSKKQVRPVLKN 34 (65)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHH
Confidence 56788899999999999887764
No 64
>PF09527 ATPase_gene1: Putative F0F1-ATPase subunit (ATPase_gene1)
Probab=49.39 E-value=82 Score=21.48 Aligned_cols=39 Identities=21% Similarity=0.257 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHhCcHHH-HHHHHHHHHHHHH
Q 015601 78 LHVLFNMLALVPLGSELERIMGSVRM-FYITILLATSNAI 116 (404)
Q Consensus 78 ~hll~n~~~l~~~g~~lE~~~Gs~~~-~~~~l~~~~~~~l 116 (404)
..++.+++.-+..|..+++.+++... ....++.|+.+++
T Consensus 8 ~~~~~~i~~g~~~G~~lD~~~~t~p~~~~~g~llG~~~g~ 47 (55)
T PF09527_consen 8 FTMAAPILVGFFLGYWLDKWFGTSPWFTLIGLLLGIAAGF 47 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHH
Confidence 56788888889999999999999443 3444455554444
No 65
>PRK08769 DNA polymerase III subunit delta'; Validated
Probab=48.71 E-value=31 Score=33.36 Aligned_cols=35 Identities=29% Similarity=0.390 Sum_probs=31.8
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHcCCCHHHHHHhh
Q 015601 366 DEEIQKLVSMGFDKTQVEVALAAADGDLNVAVEIL 400 (404)
Q Consensus 366 ~~~i~~l~~mg~~~~~~~~al~~~~~~~~~a~~~l 400 (404)
++.++-|.+-|.+++++..+++.++|++.+|.+++
T Consensus 175 ~~~~~~L~~~~~~~~~a~~~~~l~~G~p~~A~~~~ 209 (319)
T PRK08769 175 HEALAWLLAQGVSERAAQEALDAARGHPGLAAQWL 209 (319)
T ss_pred HHHHHHHHHcCCChHHHHHHHHHcCCCHHHHHHHh
Confidence 56677788889999999999999999999999998
No 66
>KOG3763 consensus mRNA export factor TAP/MEX67 [RNA processing and modification]
Probab=47.88 E-value=50 Score=34.12 Aligned_cols=35 Identities=20% Similarity=0.369 Sum_probs=30.7
Q ss_pred HHHHHHHHh-cCCCHHHHHHHHHHcCCCHHHHHHhh
Q 015601 366 DEEIQKLVS-MGFDKTQVEVALAAADGDLNVAVEIL 400 (404)
Q Consensus 366 ~~~i~~l~~-mg~~~~~~~~al~~~~~~~~~a~~~l 400 (404)
+|+|.++.+ -|-..+=+...|+.++||.|+|..-.
T Consensus 536 ~e~l~~~~~~tGln~~~s~~c~e~~nWdy~~A~k~F 571 (585)
T KOG3763|consen 536 DEKLLKFQEETGLNSEWSTMCLEQNNWDYERALKLF 571 (585)
T ss_pred HHHHHHHHHHhcCChHHHHHHHHHccCCHHHHHHHH
Confidence 788888854 59999999999999999999998654
No 67
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=47.16 E-value=1.5e+02 Score=33.87 Aligned_cols=43 Identities=26% Similarity=0.263 Sum_probs=35.8
Q ss_pred CCCCCCHHHHHHH--HhcCCCHHHHHHHHHHcCCCHHHHHHhh-hc
Q 015601 360 QGAVVSDEEIQKL--VSMGFDKTQVEVALAAADGDLNVAVEIL-SQ 402 (404)
Q Consensus 360 ~~~~~~~~~i~~l--~~mg~~~~~~~~al~~~~~~~~~a~~~l-~~ 402 (404)
+++..+||.|++. |=-|=+|+-.++-|+.+|=|++.||+-| +.
T Consensus 184 PAsniPEELInnaQqVLQGKSRdVIIRELQRTgLdVNeAVNNLLSR 229 (3015)
T KOG0943|consen 184 PASNIPEELINNAQQVLQGKSRDVIIRELQRTGLDVNEAVNNLLSR 229 (3015)
T ss_pred CcccCcHHHHHHHHHHHhCCchhHHHHHHHHhCCcHHHHHHhhhcc
Confidence 3345578988875 4469999999999999999999999998 53
No 68
>COG2103 Predicted sugar phosphate isomerase [General function prediction only]
Probab=46.36 E-value=29 Score=32.38 Aligned_cols=35 Identities=23% Similarity=0.481 Sum_probs=26.7
Q ss_pred HHHHHHHHhc-CCCHHHHHHHHHHcCCCHHHHHHhh
Q 015601 366 DEEIQKLVSM-GFDKTQVEVALAAADGDLNVAVEIL 400 (404)
Q Consensus 366 ~~~i~~l~~m-g~~~~~~~~al~~~~~~~~~a~~~l 400 (404)
++.++-+++. |.++|+|.++|+++++++..|+=.+
T Consensus 234 dRa~RIv~~aT~~~~~~A~~~L~~~~~~vK~AIvm~ 269 (298)
T COG2103 234 DRAVRIVMEATGCSAEEAEALLEEAGGNVKLAIVML 269 (298)
T ss_pred HHHHHHHHHHhCCCHHHHHHHHHHcCCccHhHHHHH
Confidence 4445555554 8999999999999999988887554
No 69
>PRK07993 DNA polymerase III subunit delta'; Validated
Probab=45.19 E-value=39 Score=32.92 Aligned_cols=35 Identities=17% Similarity=0.197 Sum_probs=29.3
Q ss_pred HHHH-HHHHhc-CCCHHHHHHHHHHcCCCHHHHHHhh
Q 015601 366 DEEI-QKLVSM-GFDKTQVEVALAAADGDLNVAVEIL 400 (404)
Q Consensus 366 ~~~i-~~l~~m-g~~~~~~~~al~~~~~~~~~a~~~l 400 (404)
++.+ +-|.+- |.+++++..+++.++|++.+|.+++
T Consensus 169 ~~~~~~~L~~~~~~~~~~a~~~~~la~G~~~~Al~l~ 205 (334)
T PRK07993 169 EQYALTWLSREVTMSQDALLAALRLSAGAPGAALALL 205 (334)
T ss_pred HHHHHHHHHHccCCCHHHHHHHHHHcCCCHHHHHHHh
Confidence 4444 457665 8999999999999999999999998
No 70
>PF03765 CRAL_TRIO_N: CRAL/TRIO, N-terminal domain; InterPro: IPR008273 This entry defines the N-terminal of various retinaldehyde/retinal-binding proteins that may be functional components of the visual cycle. Cellular retinaldehyde-binding protein (CRALBP) carries 11-cis-retinol or 11-cis-retinaldehyde as endogenous ligands and may function as a substrate carrier protein that modulates interaction of these retinoids with visual cycle enzymes []. The multidomain protein Trio binds the LAR transmembrane tyrosine phosphatase, contains a protein kinase domain, and has separate rac-specific and rho-specific guanine nucleotide exchange factor domains []. Trio is a multifunctional protein that integrates and amplifies signals involved in coordinating actin remodeling, which is necessary for cell migration and growth. Other members of the family are transfer proteins that include, guanine nucleotide exchange factor that may function as an effector of RAC1, phosphatidylinositol/phosphatidylcholine transfer protein that is required for the transport of secretory proteins from the golgi complex and alpha-tocopherol transfer protein that enhances the transfer of the ligand between separate membranes.; PDB: 1OIZ_A 1R5L_A 1OIP_A 3HX3_A 3HY5_A 1AUA_A 3Q8G_A 3B7Q_B 3B7Z_A 3B7N_A ....
Probab=43.80 E-value=32 Score=23.43 Aligned_cols=28 Identities=21% Similarity=0.126 Sum_probs=22.2
Q ss_pred HhcCCCHHHHHHHHHHcCCCHHHHHHhh
Q 015601 373 VSMGFDKTQVEVALAAADGDLNVAVEIL 400 (404)
Q Consensus 373 ~~mg~~~~~~~~al~~~~~~~~~a~~~l 400 (404)
.....++....+=|++..||++.|.+.|
T Consensus 25 ~~~~~~d~~llRFLRARkf~v~~A~~mL 52 (55)
T PF03765_consen 25 EKEDHDDNFLLRFLRARKFDVEKAFKML 52 (55)
T ss_dssp HTSS-SHHHHHHHHHHTTT-HHHHHHHH
T ss_pred ccCCCCHHHHHHHHHHccCCHHHHHHHH
Confidence 3445678889999999999999999987
No 71
>PF03701 UPF0181: Uncharacterised protein family (UPF0181); InterPro: IPR005371 This family contains small proteins of about 50 amino acids of unknown function. The family includes YoaH P76260 from SWISSPROT.
Probab=43.72 E-value=27 Score=23.68 Aligned_cols=20 Identities=25% Similarity=0.348 Sum_probs=17.7
Q ss_pred HHHHHHHHhcCCCHHHHHHH
Q 015601 366 DEEIQKLVSMGFDKTQVEVA 385 (404)
Q Consensus 366 ~~~i~~l~~mg~~~~~~~~a 385 (404)
-|+|++||+-|.+..+|++-
T Consensus 17 vE~Iq~LMaqGmSsgEAI~~ 36 (51)
T PF03701_consen 17 VERIQELMAQGMSSGEAIAI 36 (51)
T ss_pred HHHHHHHHHhcccHHHHHHH
Confidence 57899999999999999874
No 72
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=42.98 E-value=43 Score=29.85 Aligned_cols=25 Identities=12% Similarity=0.419 Sum_probs=23.1
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHcC
Q 015601 366 DEEIQKLVSMGFDKTQVEVALAAAD 390 (404)
Q Consensus 366 ~~~i~~l~~mg~~~~~~~~al~~~~ 390 (404)
+|.+..|..+||++.+|.+|+++..
T Consensus 149 ~e~~~aL~~LGy~~~~a~~ai~~~~ 173 (194)
T PRK14605 149 SDILATLTALGYSSSEAAKAISSLG 173 (194)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHhh
Confidence 6789999999999999999999885
No 73
>PRK05441 murQ N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=39.62 E-value=50 Score=31.60 Aligned_cols=31 Identities=29% Similarity=0.581 Sum_probs=24.3
Q ss_pred HHHHh-cCCCHHHHHHHHHHcCCCHHHHHHhh
Q 015601 370 QKLVS-MGFDKTQVEVALAAADGDLNVAVEIL 400 (404)
Q Consensus 370 ~~l~~-mg~~~~~~~~al~~~~~~~~~a~~~l 400 (404)
.-+++ .|.++++|+++|.+++|++..|+-.+
T Consensus 240 ~i~~~~~~~~~~~a~~~l~~~~~~vk~a~~~~ 271 (299)
T PRK05441 240 RIVMEATGVSREEAEAALEAADGSVKLAIVMI 271 (299)
T ss_pred HHHHHHHCcCHHHHHHHHHHhCCCcHHHHHHH
Confidence 33443 48999999999999999888888765
No 74
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=36.41 E-value=3.2e+02 Score=25.64 Aligned_cols=40 Identities=20% Similarity=0.303 Sum_probs=26.4
Q ss_pred ceeechhhhccCcchhhhhhhhcccCHHHHHHHHHHHHHHHHHHHHHh
Q 015601 51 ICFLPSAVISRFQVYRFYTSIVFHGSLLHVLFNMLALVPLGSELERIM 98 (404)
Q Consensus 51 l~~~p~~i~~~~q~WRL~Ts~f~h~~~~hll~n~~~l~~~g~~lE~~~ 98 (404)
..+.|..+.-+.||||++.. -++|..+..+...+.+-+-+
T Consensus 89 m~~iPlyf~~~~~w~rfl~~--------WlmF~~~tafi~~ka~rkp~ 128 (328)
T KOG1734|consen 89 MLFIPLYFFLYMQWYRFLFC--------WLMFCGFTAFITLKALRKPI 128 (328)
T ss_pred HHHhhhhhhhhHHHHHHHHH--------HHHHHHHHHHHHHHHHhccc
Confidence 45667777777899998754 45566666666656666554
No 75
>TIGR02230 ATPase_gene1 F0F1-ATPase subunit, putative. This model represents a protein found encoded in F1F0-ATPase operons in several genomes, including Methanosarcina barkeri (archaeal) and Chlorobium tepidum (bacterial). It is a small protein (about 100 amino acids) with long hydrophic stretches and is presumed to be a subunit of the enzyme.
Probab=35.95 E-value=1.7e+02 Score=23.03 Aligned_cols=39 Identities=18% Similarity=0.075 Sum_probs=27.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHhCcHHH-HHHHHHHHHHHHH
Q 015601 78 LHVLFNMLALVPLGSELERIMGSVRM-FYITILLATSNAI 116 (404)
Q Consensus 78 ~hll~n~~~l~~~g~~lE~~~Gs~~~-~~~~l~~~~~~~l 116 (404)
++++.-++.-+.+|..|.+.+++... ...+++.|++.++
T Consensus 50 ~~~v~pil~G~~lG~WLD~~~~t~~~~tl~~lllGv~~G~ 89 (100)
T TIGR02230 50 WSVAIPTLLGVAVGIWLDRHYPSPFSWTLTMLIVGVVIGC 89 (100)
T ss_pred HHHHHHHHHHHHHHHHHHhhcCCCcHHHHHHHHHHHHHHH
Confidence 68888888889999999999987443 3333444444333
No 76
>PRK01905 DNA-binding protein Fis; Provisional
Probab=35.65 E-value=33 Score=25.50 Aligned_cols=24 Identities=33% Similarity=0.526 Sum_probs=21.7
Q ss_pred CCHHHHHHHHHHcCCCHHHHHHhh
Q 015601 377 FDKTQVEVALAAADGDLNVAVEIL 400 (404)
Q Consensus 377 ~~~~~~~~al~~~~~~~~~a~~~l 400 (404)
++++..+++|+.++||..+|++.|
T Consensus 37 ~E~~~i~~aL~~~~gn~s~aAr~L 60 (77)
T PRK01905 37 VEKPLLEVVMEQAGGNQSLAAEYL 60 (77)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHH
Confidence 467789999999999999999988
No 77
>PF04695 Pex14_N: Peroxisomal membrane anchor protein (Pex14p) conserved region; InterPro: IPR006785 This conserved region defines a group of peroxisomal membrane anchor proteins which bind the PTS1 (peroxisomal targeting signal) receptor and are required for the import of PTS1-containing proteins into peroxisomes. Loss of functional Pex14p results in defects in both the PTS1 and PTS2-dependent import pathways. Deletion analysis of this conserved region implicates it in selective peroxisome degradation. In the majority of members this region is situated at the N terminus of the protein [, ].; GO: 0005777 peroxisome, 0016020 membrane; PDB: 2W85_A 2W84_A 3FF5_B.
Probab=35.08 E-value=46 Score=27.74 Aligned_cols=29 Identities=24% Similarity=0.322 Sum_probs=23.3
Q ss_pred CHHHHHHHHhcCCCHHHHHHHHHHcCCCH
Q 015601 365 SDEEIQKLVSMGFDKTQVEVALAAADGDL 393 (404)
Q Consensus 365 ~~~~i~~l~~mg~~~~~~~~al~~~~~~~ 393 (404)
.++||+=|..-|.++|+..+||+.++.+.
T Consensus 23 ~~~k~~FL~sKGLt~~EI~~al~~a~~~~ 51 (136)
T PF04695_consen 23 LEKKIAFLESKGLTEEEIDEALGRAGSPP 51 (136)
T ss_dssp HHHHHHHHHHCT--HHHHHHHHHHHT--S
T ss_pred HHHHHHHHHcCCCCHHHHHHHHHhcCCcc
Confidence 48999999999999999999999998776
No 78
>PRK05114 hypothetical protein; Provisional
Probab=34.92 E-value=43 Score=23.33 Aligned_cols=20 Identities=25% Similarity=0.341 Sum_probs=17.6
Q ss_pred HHHHHHHHhcCCCHHHHHHH
Q 015601 366 DEEIQKLVSMGFDKTQVEVA 385 (404)
Q Consensus 366 ~~~i~~l~~mg~~~~~~~~a 385 (404)
-|+|++||+-|.+-.+|++-
T Consensus 17 VErIq~LMaqGmSsgEAI~~ 36 (59)
T PRK05114 17 VERIQELMAQGMSSGEAIAL 36 (59)
T ss_pred HHHHHHHHHccccHHHHHHH
Confidence 57899999999999998863
No 79
>COG3105 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.15 E-value=62 Score=26.63 Aligned_cols=25 Identities=16% Similarity=0.012 Sum_probs=14.7
Q ss_pred HHHHHHHHHHHHHHHHHhhcccCCc
Q 015601 194 LLGHLCGILSGFAYTYGFFNLLMPG 218 (404)
Q Consensus 194 ~~~hl~G~l~G~l~~~~~l~~~~p~ 218 (404)
|..-+.|+++|.++++.+.|...+.
T Consensus 8 W~~a~igLvvGi~IG~li~Rlt~~~ 32 (138)
T COG3105 8 WEYALIGLVVGIIIGALIARLTNRK 32 (138)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcchh
Confidence 4555666666666666655544433
No 80
>cd05007 SIS_Etherase N-acetylmuramic acid 6-phosphate etherase. Members of this family contain the SIS (Sugar ISomerase) domain. The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. The bacterial cell wall sugar N-acetylmuramic acid carries a unique D-lactyl ether substituent at the C3 position. The etherase catalyzes the cleavage of the lactyl ether bond of N-acetylmuramic acid 6-phosphate.
Probab=32.60 E-value=34 Score=31.94 Aligned_cols=31 Identities=29% Similarity=0.542 Sum_probs=24.9
Q ss_pred HHHHHHHh-cCCCHHHHHHHHHHcCCCHHHHH
Q 015601 367 EEIQKLVS-MGFDKTQVEVALAAADGDLNVAV 397 (404)
Q Consensus 367 ~~i~~l~~-mg~~~~~~~~al~~~~~~~~~a~ 397 (404)
+.+.-+++ .|.++++|+++|.++++++..|+
T Consensus 224 ra~~i~~~~~~~~~~~a~~~l~~~~~~~k~a~ 255 (257)
T cd05007 224 RAIRIVMEATGVSRDEAEAALEQAGGDVKTAI 255 (257)
T ss_pred HHHHHHHHHHCcCHHHHHHHHHHhCCCceeee
Confidence 34444544 59999999999999999998886
No 81
>PF05861 PhnI: Bacterial phosphonate metabolism protein (PhnI); InterPro: IPR008773 This family consists of several proteobacterial phosphonate metabolism protein (PhnI) sequences. Bacteria that use phosphonates as a phosphorus source must be able to break the stable carbon-phosphorus bond. In Escherichia coli phosphonates are broken down by a C-P lyase that has a broad substrate specificity. The genes for phosphonate uptake and degradation in E. coli are organised in an operon of 14 genes, named phnC to phnP. Three gene products (PhnC, PhnD and PhnE) comprise a binding protein-dependent phosphonate transporter, which also transports phosphate, phosphite, and certain phosphate esters such as phosphoserine; two gene products (PhnF and PhnO) may have a role in gene regulation; and nine gene products (PhnG, PhnH, PhnI, PhnJ, PhnK, PhnL, PhnM, PhnN, and PhnP) probably comprise a membrane-associated C-P lyase enzyme complex [].; GO: 0015716 phosphonate transport
Probab=32.59 E-value=60 Score=31.47 Aligned_cols=33 Identities=30% Similarity=0.526 Sum_probs=28.4
Q ss_pred HHHHHHhcC--CCHHHHHHHHHHcCCCHHHHHHhh
Q 015601 368 EIQKLVSMG--FDKTQVEVALAAADGDLNVAVEIL 400 (404)
Q Consensus 368 ~i~~l~~mg--~~~~~~~~al~~~~~~~~~a~~~l 400 (404)
.|+++|.=| |+++.|-.|++++.||+..|+=+|
T Consensus 44 avdrVMsEgsLYdp~LAAlAiKQa~GD~~EAiFLL 78 (358)
T PF05861_consen 44 AVDRVMSEGSLYDPELAALAIKQARGDLIEAIFLL 78 (358)
T ss_pred HHHHHhccccccCHHHHHHHHHHhcCCHHHHHHHH
Confidence 456666666 899999999999999999999776
No 82
>PRK11677 hypothetical protein; Provisional
Probab=32.14 E-value=73 Score=26.57 Aligned_cols=25 Identities=12% Similarity=-0.033 Sum_probs=14.0
Q ss_pred HHHHHHHHHHHHHHHHHhhcccCCc
Q 015601 194 LLGHLCGILSGFAYTYGFFNLLMPG 218 (404)
Q Consensus 194 ~~~hl~G~l~G~l~~~~~l~~~~p~ 218 (404)
|+.-+.|+++|.++|+...+...+.
T Consensus 3 W~~a~i~livG~iiG~~~~R~~~~~ 27 (134)
T PRK11677 3 WEYALIGLVVGIIIGAVAMRFGNRK 27 (134)
T ss_pred HHHHHHHHHHHHHHHHHHHhhccch
Confidence 3444566666666666655544443
No 83
>COG3140 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.74 E-value=43 Score=23.07 Aligned_cols=35 Identities=23% Similarity=0.233 Sum_probs=25.6
Q ss_pred HHHHHHHHhcCCCHHHHHH----HHHHcCCCHHHHHHhh
Q 015601 366 DEEIQKLVSMGFDKTQVEV----ALAAADGDLNVAVEIL 400 (404)
Q Consensus 366 ~~~i~~l~~mg~~~~~~~~----al~~~~~~~~~a~~~l 400 (404)
-|+|++||+-|.+-.+|++ .||+.--+.++++...
T Consensus 17 VE~Iq~lMaeGmSsGEAIa~VA~elRe~hk~~~~~~~~f 55 (60)
T COG3140 17 VERIQELMAEGMSSGEAIALVAQELRENHKGENRIVARF 55 (60)
T ss_pred HHHHHHHHHccccchhHHHHHHHHHHHHhcccccccccc
Confidence 5789999999999888775 5666665555555443
No 84
>PF14851 FAM176: FAM176 family
Probab=31.30 E-value=1.3e+02 Score=25.65 Aligned_cols=34 Identities=18% Similarity=0.135 Sum_probs=20.7
Q ss_pred HHHHHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHH
Q 015601 79 HVLFNMLALVPLGSELERIMGSVRMFYITILLATSNAILH 118 (404)
Q Consensus 79 hll~n~~~l~~~g~~lE~~~Gs~~~~~~~l~~~~~~~l~~ 118 (404)
-++-|.+..|.+-+ ....-+.+||++||+.+++.
T Consensus 3 ~llSnsLaaya~I~------~~PE~~aLYFv~gVC~GLlL 36 (153)
T PF14851_consen 3 ELLSNSLAAYAHIR------DNPERFALYFVSGVCAGLLL 36 (153)
T ss_pred hHHHHHHHHHHHHH------hChHHHHHHHHHHHHHHHHH
Confidence 35566666665543 34445667888877766653
No 85
>PF12244 DUF3606: Protein of unknown function (DUF3606); InterPro: IPR022037 This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=30.54 E-value=74 Score=22.16 Aligned_cols=36 Identities=17% Similarity=0.193 Sum_probs=30.1
Q ss_pred CHHHHHHHH-hcCCCHHHHHHHHHHcCCCHHHHHHhh
Q 015601 365 SDEEIQKLV-SMGFDKTQVEVALAAADGDLNVAVEIL 400 (404)
Q Consensus 365 ~~~~i~~l~-~mg~~~~~~~~al~~~~~~~~~a~~~l 400 (404)
++..|+-.+ ..|.++++.++|-++.|++.+.--+||
T Consensus 19 e~~ev~ywa~~~gvt~~~L~~AV~~vG~~~~~V~~~L 55 (57)
T PF12244_consen 19 EPYEVRYWAKRFGVTEEQLREAVRAVGNSRAAVRAYL 55 (57)
T ss_pred CHHHHHHHHHHHCcCHHHHHHHHHHHCcCHHHHHHHH
Confidence 356677775 469999999999999999998877777
No 86
>TIGR02854 spore_II_GA sigma-E processing peptidase SpoIIGA. Members of this protein family are the stage II sporulation protein SpoIIGA. This protein acts as an activating protease for Sigma-E, one of several specialized sigma factors of the sporulation process in Bacillus subtilis and related endospore-forming bacteria.
Probab=30.26 E-value=4.8e+02 Score=24.71 Aligned_cols=28 Identities=11% Similarity=0.198 Sum_probs=22.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHhCcHHHHH
Q 015601 78 LHVLFNMLALVPLGSELERIMGSVRMFY 105 (404)
Q Consensus 78 ~hll~n~~~l~~~g~~lE~~~Gs~~~~~ 105 (404)
..+++|.+.|+..++.+-+....+|.+.
T Consensus 11 ~Nf~~d~~LL~~t~~~lk~~~~~~Rll~ 38 (288)
T TIGR02854 11 ENFIIDYFLLYLTARTLKDKVSQWRLLL 38 (288)
T ss_pred HHHHHHHHHHHHHHHHhhccchHHHHHH
Confidence 5789999999999998888776666553
No 87
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=30.16 E-value=44 Score=26.02 Aligned_cols=24 Identities=13% Similarity=0.275 Sum_probs=21.9
Q ss_pred CCHHHHHHHHHHcCCCHHHHHHhh
Q 015601 377 FDKTQVEVALAAADGDLNVAVEIL 400 (404)
Q Consensus 377 ~~~~~~~~al~~~~~~~~~a~~~l 400 (404)
++++..+++|+.++||..+|++.|
T Consensus 55 ~Er~~i~~aL~~~~gn~s~AAr~L 78 (95)
T PRK00430 55 VEAPLLDMVMQYTRGNQTRAALML 78 (95)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHh
Confidence 567788999999999999999998
No 88
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=29.93 E-value=86 Score=27.79 Aligned_cols=26 Identities=23% Similarity=0.422 Sum_probs=23.6
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHcCC
Q 015601 366 DEEIQKLVSMGFDKTQVEVALAAADG 391 (404)
Q Consensus 366 ~~~i~~l~~mg~~~~~~~~al~~~~~ 391 (404)
++.++.|+++||++.+|.+|+++...
T Consensus 150 ~ev~~aL~~LG~~~~~a~~~~~~~~~ 175 (192)
T PRK00116 150 EEAVSALVALGYKPKEASKAVAKILK 175 (192)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHhc
Confidence 67899999999999999999999864
No 89
>PLN02250 lipid phosphate phosphatase
Probab=29.59 E-value=5.2e+02 Score=24.92 Aligned_cols=24 Identities=17% Similarity=0.263 Sum_probs=14.7
Q ss_pred HHHHHHHHHHHHHHHHHhhcccCC
Q 015601 194 LLGHLCGILSGFAYTYGFFNLLMP 217 (404)
Q Consensus 194 ~~~hl~G~l~G~l~~~~~l~~~~p 217 (404)
+..-++|.+.|.++++...+...|
T Consensus 223 ~sDVlaG~lIG~~~A~~~y~~~fp 246 (314)
T PLN02250 223 WQDVFAGALIGLTVASFCYLQFFP 246 (314)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcC
Confidence 455567777777777654444444
No 90
>COG5457 Uncharacterized conserved small protein [Function unknown]
Probab=29.18 E-value=65 Score=23.09 Aligned_cols=23 Identities=17% Similarity=0.241 Sum_probs=19.1
Q ss_pred HHHHhcCCCHHHHHHHHHHcCCC
Q 015601 370 QKLVSMGFDKTQVEVALAAADGD 392 (404)
Q Consensus 370 ~~l~~mg~~~~~~~~al~~~~~~ 392 (404)
.+|.|.|.+|.++.....+.+|+
T Consensus 41 ~~L~DiGisR~d~~~e~~k~fw~ 63 (63)
T COG5457 41 HLLSDIGISRADIEAEAAKPFWR 63 (63)
T ss_pred HHHHHcCCCHHHHHHHHHHhhcC
Confidence 56788999999999988877664
No 91
>TIGR00274 N-acetylmuramic acid 6-phosphate etherase. This protein, MurQ, is involved in recycling components of the bacterial murein sacculus turned over during cell growth. The cell wall metabolite anhydro-N-acetylmuramic acid (anhMurNAc) is converted by a kinase, AnmK, to MurNAc-phosphate, then converted to N-acetylglucosamine-phosphate by this etherase, called MurQ. This family of proteins is similar to the C-terminal half of a number of vertebrate glucokinase regulator proteins and contains a Prosite pattern which is shared by this group of proteins in a region of local similarity.
Probab=28.83 E-value=95 Score=29.57 Aligned_cols=35 Identities=20% Similarity=0.331 Sum_probs=25.4
Q ss_pred HHHHHHHHh-cCCCHHHHHHHHHHcCCCHHHHHHhh
Q 015601 366 DEEIQKLVS-MGFDKTQVEVALAAADGDLNVAVEIL 400 (404)
Q Consensus 366 ~~~i~~l~~-mg~~~~~~~~al~~~~~~~~~a~~~l 400 (404)
++.+.-+++ .|-++++|+++|.+++|++..|+-.+
T Consensus 231 ~Ra~~i~~~~~~~~~~~a~~~l~~~~~~vk~Ai~~~ 266 (291)
T TIGR00274 231 ARAVRIVRQATDCNKELAEQTLLAADQNVKLAIVMI 266 (291)
T ss_pred HHHHHHHHHHhCcCHHHHHHHHHHhCCCcHHHHHHH
Confidence 334444444 58888889999999888888887654
No 92
>PRK12570 N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=28.80 E-value=75 Score=30.36 Aligned_cols=34 Identities=15% Similarity=0.395 Sum_probs=24.0
Q ss_pred HHHHHHHh-cCCCHHHHHHHHHHcCCCHHHHHHhh
Q 015601 367 EEIQKLVS-MGFDKTQVEVALAAADGDLNVAVEIL 400 (404)
Q Consensus 367 ~~i~~l~~-mg~~~~~~~~al~~~~~~~~~a~~~l 400 (404)
+.+..+++ .|.++++|.++|.++++++..|+-.+
T Consensus 233 Ra~~i~~~~~~~~~~~a~~~l~~~~~~vk~ai~~~ 267 (296)
T PRK12570 233 RAVRIVMQATGCSEDEAKELLKESDNDVKLAILMI 267 (296)
T ss_pred HHHHHHHHHHCcCHHHHHHHHHHhCCccHHHHHHH
Confidence 33333433 48888888888888888888877654
No 93
>PF14898 DUF4491: Domain of unknown function (DUF4491)
Probab=27.44 E-value=1.4e+02 Score=23.14 Aligned_cols=46 Identities=17% Similarity=0.348 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHHHHHH------HHHHHhCcHHHHHHHHHHHHHHHHHHHHHHH
Q 015601 77 LLHVLFNMLALVPLGS------ELERIMGSVRMFYITILLATSNAILHLLIAL 123 (404)
Q Consensus 77 ~~hll~n~~~l~~~g~------~lE~~~Gs~~~~~~~l~~~~~~~l~~~l~~~ 123 (404)
+..+++.+..+...|- ..|..+|+ |...++++.|+.+.+.++.+..
T Consensus 3 ~~Giiigi~tFliIG~fHpiVIk~EYyfg~-~~W~~FL~~Gi~~~~~Sl~~~~ 54 (94)
T PF14898_consen 3 FTGIIIGIATFLIIGLFHPIVIKGEYYFGT-RIWPIFLLAGIACIIASLFVSN 54 (94)
T ss_pred hhhHHHHHHHHHHHHccCeEEEEEEEecCC-CcHHHHHHHHHHHHHHHHHHcc
Confidence 3345555555555543 24666777 5677777787777776665543
No 94
>PF10979 DUF2786: Protein of unknown function (DUF2786); InterPro: IPR024498 This domain is found in proteins that have no known function.
Probab=26.40 E-value=98 Score=20.24 Aligned_cols=23 Identities=43% Similarity=0.673 Sum_probs=17.8
Q ss_pred HHHHHHHhc----CCCHHHHHHHHHHc
Q 015601 367 EEIQKLVSM----GFDKTQVEVALAAA 389 (404)
Q Consensus 367 ~~i~~l~~m----g~~~~~~~~al~~~ 389 (404)
++|+.|..+ |.++++|..|++.+
T Consensus 5 ~kI~kLLalA~~~~~~~~EA~~A~~kA 31 (43)
T PF10979_consen 5 EKIRKLLALAESTGSNEHEAEAALAKA 31 (43)
T ss_pred HHHHHHHHHhhCCCCCHHHHHHHHHHH
Confidence 678888765 57788898888765
No 95
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=25.42 E-value=1.2e+02 Score=18.16 Aligned_cols=22 Identities=23% Similarity=0.279 Sum_probs=15.8
Q ss_pred HHHHHHHhcCCCHHHHHHHHHH
Q 015601 367 EEIQKLVSMGFDKTQVEVALAA 388 (404)
Q Consensus 367 ~~i~~l~~mg~~~~~~~~al~~ 388 (404)
+-|+.-++||.+.+++++=|+.
T Consensus 7 ~Li~eA~~~Gls~eeir~FL~~ 28 (30)
T PF08671_consen 7 ELIKEAKESGLSKEEIREFLEF 28 (30)
T ss_dssp HHHHHHHHTT--HHHHHHHHHH
T ss_pred HHHHHHHHcCCCHHHHHHHHHh
Confidence 3567778999999999987764
No 96
>PF13105 DUF3959: Protein of unknown function (DUF3959)
Probab=25.36 E-value=4.6e+02 Score=23.14 Aligned_cols=11 Identities=27% Similarity=0.322 Sum_probs=6.1
Q ss_pred chhhhhhhhcc
Q 015601 64 VYRFYTSIVFH 74 (404)
Q Consensus 64 ~WRL~Ts~f~h 74 (404)
+.|+-||.+..
T Consensus 87 ~frfrtyglt~ 97 (239)
T PF13105_consen 87 LFRFRTYGLTL 97 (239)
T ss_pred HHHHHHHHHHH
Confidence 45666665443
No 97
>PHA01514 O-antigen conversion protein C
Probab=24.89 E-value=7.8e+02 Score=25.38 Aligned_cols=22 Identities=18% Similarity=0.226 Sum_probs=16.1
Q ss_pred cccccccChhHHHHHHHHHHHh
Q 015601 136 VMDECAIGFSGVIFSLIVIETS 157 (404)
Q Consensus 136 ~~~~~~~G~sg~i~~l~~~~~~ 157 (404)
......+|++|.++.+......
T Consensus 318 ~~PRvligfg~~m~~~~~~~~~ 339 (485)
T PHA01514 318 YAPRVLIGMGGFMFFCCLCVFY 339 (485)
T ss_pred ccceeeeehHHHHHHHHHHHHH
Confidence 4456789999998887765544
No 98
>PF09726 Macoilin: Transmembrane protein; InterPro: IPR019130 This entry represents the multi-pass transmembrane protein Macoilin, which is highly conserved in eukaryotes. ; GO: 0016021 integral to membrane
Probab=24.18 E-value=3.8e+02 Score=29.02 Aligned_cols=15 Identities=0% Similarity=-0.248 Sum_probs=7.5
Q ss_pred HHHHHHHHhhcCCcc
Q 015601 149 FSLIVIETSLSGAQS 163 (404)
Q Consensus 149 ~~l~~~~~~~~p~~~ 163 (404)
+|-.|+|..+.....
T Consensus 102 ~~~~~v~~~~~~~~~ 116 (697)
T PF09726_consen 102 AASTYVWVQYVWHTD 116 (697)
T ss_pred HHhHHHHHHHhhhcc
Confidence 344455665555443
No 99
>PF03419 Peptidase_U4: Sporulation factor SpoIIGA This family belongs to family U4 of the peptidase classification.; InterPro: IPR005081 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. The peptidases families associated with clan U- have an unknown catalytic mechanism as the protein fold of the active site domain and the active site residues have not been reported. This group of peptidases belong to the MEROPS peptidase family U4 (SpoIIGA peptidase family, clan U-). Sporulation in bacteria such as Bacillus subtilis involves the formation of a polar septum, which divides the sporangium into a mother cell and a forespore. The sigma E factor, which is encoded within the spoIIG operon, is a cell-specific regulatory protein that directs gene transcription in the mother cell. Sigma E is synthesised as an inactive proprotein pro-sigma E, which is converted to the mature factor by the putative processing enzyme SpoIIGA []. ; GO: 0004190 aspartic-type endopeptidase activity, 0006508 proteolysis, 0030436 asexual sporulation
Probab=23.87 E-value=6.2e+02 Score=23.87 Aligned_cols=31 Identities=16% Similarity=0.174 Sum_probs=23.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHhCcHHHHHHHH
Q 015601 78 LHVLFNMLALVPLGSELERIMGSVRMFYITI 108 (404)
Q Consensus 78 ~hll~n~~~l~~~g~~lE~~~Gs~~~~~~~l 108 (404)
..+++|.+.|+..++.+-+....+|.+.--+
T Consensus 11 ~N~~md~~lL~~t~~~~~~~~~~~Rll~~A~ 41 (293)
T PF03419_consen 11 VNFLMDYFLLWLTARLLKRRASRWRLLLGAA 41 (293)
T ss_pred HHHHHHHHHHHHHHHHhcCCCcHHHHHHHHH
Confidence 5788899999999888887777777654333
No 100
>TIGR00274 N-acetylmuramic acid 6-phosphate etherase. This protein, MurQ, is involved in recycling components of the bacterial murein sacculus turned over during cell growth. The cell wall metabolite anhydro-N-acetylmuramic acid (anhMurNAc) is converted by a kinase, AnmK, to MurNAc-phosphate, then converted to N-acetylglucosamine-phosphate by this etherase, called MurQ. This family of proteins is similar to the C-terminal half of a number of vertebrate glucokinase regulator proteins and contains a Prosite pattern which is shared by this group of proteins in a region of local similarity.
Probab=23.63 E-value=95 Score=29.58 Aligned_cols=30 Identities=17% Similarity=0.253 Sum_probs=24.5
Q ss_pred HHHHHh-cCCCHHHHHHHHHHcCCCHHHHHH
Q 015601 369 IQKLVS-MGFDKTQVEVALAAADGDLNVAVE 398 (404)
Q Consensus 369 i~~l~~-mg~~~~~~~~al~~~~~~~~~a~~ 398 (404)
+.-||. -|++.++|++.|.+++|++.+|+|
T Consensus 261 ~Ai~~~~~~~~~~~a~~~l~~~~g~~~~~l~ 291 (291)
T TIGR00274 261 LAIVMILSTLSASEAKVLLDRHGGFLRQALD 291 (291)
T ss_pred HHHHHHHhCCCHHHHHHHHHHcCCcHHHhhC
Confidence 334433 379999999999999999999975
No 101
>PRK06090 DNA polymerase III subunit delta'; Validated
Probab=23.18 E-value=1.4e+02 Score=28.80 Aligned_cols=33 Identities=18% Similarity=0.177 Sum_probs=27.9
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHcCCCHHHHHHhh
Q 015601 366 DEEIQKLVSMGFDKTQVEVALAAADGDLNVAVEIL 400 (404)
Q Consensus 366 ~~~i~~l~~mg~~~~~~~~al~~~~~~~~~a~~~l 400 (404)
++.++-|.+.|.+ ++..+|+.++|++.+|.+++
T Consensus 170 ~~~~~~L~~~~~~--~~~~~l~l~~G~p~~A~~~~ 202 (319)
T PRK06090 170 AQAMQWLKGQGIT--VPAYALKLNMGSPLKTLAMM 202 (319)
T ss_pred HHHHHHHHHcCCc--hHHHHHHHcCCCHHHHHHHh
Confidence 5666778888887 45689999999999999998
No 102
>smart00553 SEP Domain present in Saccharomyces cerevisiae Shp1, Drosophila melanogaster eyes closed gene (eyc), and vertebrate p47.
Probab=22.29 E-value=62 Score=25.16 Aligned_cols=15 Identities=33% Similarity=0.614 Sum_probs=12.4
Q ss_pred CCCCCCCccccCCCC
Q 015601 291 SRFPGRGRTLSSSQS 305 (404)
Q Consensus 291 ~~~~g~g~~lg~~~~ 305 (404)
..|.|.|++||+...
T Consensus 74 ~~F~G~G~~LGs~~p 88 (93)
T smart00553 74 KPFSGSGQKLGSPGP 88 (93)
T ss_pred cCCccCCccCCCCCC
Confidence 469999999998743
No 103
>PRK05441 murQ N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=22.22 E-value=1.3e+02 Score=28.80 Aligned_cols=33 Identities=24% Similarity=0.339 Sum_probs=26.4
Q ss_pred HHHHHHh-cCCCHHHHHHHHHHcCCCHHHHHHhh
Q 015601 368 EIQKLVS-MGFDKTQVEVALAAADGDLNVAVEIL 400 (404)
Q Consensus 368 ~i~~l~~-mg~~~~~~~~al~~~~~~~~~a~~~l 400 (404)
|+.-|+. .|.+.++|++.|.+++|++.+|++-+
T Consensus 265 k~a~~~~~~~~~~~~a~~~l~~~~g~~~~~~~~~ 298 (299)
T PRK05441 265 KLAIVMILTGLDAAEAKALLARHGGFLRKALAEL 298 (299)
T ss_pred HHHHHHHHhCCCHHHHHHHHHHcCCCHHHHHhhc
Confidence 3444444 37999999999999999999998753
No 104
>COG2103 Predicted sugar phosphate isomerase [General function prediction only]
Probab=22.22 E-value=1.2e+02 Score=28.50 Aligned_cols=33 Identities=18% Similarity=0.252 Sum_probs=27.9
Q ss_pred HHHHHHHhc-CCCHHHHHHHHHHcCCCHHHHHHh
Q 015601 367 EEIQKLVSM-GFDKTQVEVALAAADGDLNVAVEI 399 (404)
Q Consensus 367 ~~i~~l~~m-g~~~~~~~~al~~~~~~~~~a~~~ 399 (404)
-|+.-+|-+ |.+.++|++.|..++|++.+|++.
T Consensus 262 vK~AIvm~~~~~~a~~A~~~L~~~~g~lr~Al~~ 295 (298)
T COG2103 262 VKLAIVMLLTGLSAEEAKRLLERAGGFLRQALSE 295 (298)
T ss_pred cHhHHHHHHhCCCHHHHHHHHHHccChHHHHHhh
Confidence 356666665 799999999999999999999875
No 105
>PF06123 CreD: Inner membrane protein CreD; InterPro: IPR010364 This family consists of several bacterial CreD or Cet inner membrane proteins. Dominant mutations of the cet gene of Escherichia coli result in tolerance to colicin E2 and increased amounts of an inner membrane protein with a Mr of 42,000. The cet gene is shown to be in the same operon as the phoM gene, which is required in a phoR background for expression of the structural gene for alkaline phosphatase, phoA. Although the Cet protein is not required for phoA expression, it has been suggested that the Cet protein has an enhancing effect on the transcription of phoA [].
Probab=22.02 E-value=8.4e+02 Score=24.71 Aligned_cols=56 Identities=14% Similarity=0.038 Sum_probs=31.6
Q ss_pred cCcchhhhhhhhcccCHHHHHHHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHHHHHHHHH
Q 015601 61 RFQVYRFYTSIVFHGSLLHVLFNMLALVPLGSELERIMGSVRMFYITILLATSNAILHLLIALLV 125 (404)
Q Consensus 61 ~~q~WRL~Ts~f~h~~~~hll~n~~~l~~~g~~lE~~~Gs~~~~~~~l~~~~~~~l~~~l~~~~~ 125 (404)
+.+..|-+-|.++ |=++.+..+ -.+|-.-+.+--..=|++.|+.-.++|+++-.+.
T Consensus 291 Y~~~~Ra~KYgiL--------FI~LTF~~f-flfE~~~~~~iHpiQY~LVGlAl~lFYlLLLSlS 346 (430)
T PF06123_consen 291 YQKSERAVKYGIL--------FIGLTFLAF-FLFELLSKLRIHPIQYLLVGLALVLFYLLLLSLS 346 (430)
T ss_pred HHHHHHHHHHHHH--------HHHHHHHHH-HHHHHHhcCcccHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455666666443 223333333 3567666655556667777777777777665543
No 106
>KOG4463 consensus Uncharacterized conserved protein [Function unknown]
Probab=21.70 E-value=18 Score=33.57 Aligned_cols=24 Identities=42% Similarity=0.446 Sum_probs=15.8
Q ss_pred HHhcCCCHHHHHHHHHHcCCCHHH
Q 015601 372 LVSMGFDKTQVEVALAAADGDLNV 395 (404)
Q Consensus 372 l~~mg~~~~~~~~al~~~~~~~~~ 395 (404)
.++||++...++.+|-..-||.+.
T Consensus 281 p~S~~l~g~S~rp~l~~~r~dd~~ 304 (323)
T KOG4463|consen 281 PVSMGLDGNSARPALVHARNDDNA 304 (323)
T ss_pred ccccccCCCcCCcccccccccccc
Confidence 566777777777777666666553
No 107
>PRK09487 sdhC succinate dehydrogenase cytochrome b556 large membrane subunit; Provisional
Probab=21.63 E-value=1.6e+02 Score=24.35 Aligned_cols=20 Identities=20% Similarity=0.610 Sum_probs=10.2
Q ss_pred hhhhhhhhcc--cCHHHHHHHH
Q 015601 65 YRFYTSIVFH--GSLLHVLFNM 84 (404)
Q Consensus 65 WRL~Ts~f~h--~~~~hll~n~ 84 (404)
|-+..+.+.| .++=|++.++
T Consensus 75 ~~~~~al~yH~~nGIRHL~wD~ 96 (129)
T PRK09487 75 WGILTALAYHVVVGIRHLLMDF 96 (129)
T ss_pred HHHHHHHHHHHHhhHHHHHHHc
Confidence 3334444555 3455666665
No 108
>PF04632 FUSC: Fusaric acid resistance protein family; InterPro: IPR006726 This entry represents the p-hydroxybenzoic acid efflux pump subunit AaeB (pHBA efflux pump protein B) whose substrates are p-hydroxybenzoic acid (pHBA), 6-hydroxy-2-naphthoic and 2-hydroxycinnamate. It could function as a metabolic relief valve, allowing to eliminate certain compounds when they accumulate to high levels in the cell []. This family also includes fusaric acid resistance proteins [], which are likely to be membrane transporter proteins, and uncharacterised transporter YdhK.; GO: 0006810 transport, 0005886 plasma membrane
Probab=21.44 E-value=9.7e+02 Score=25.24 Aligned_cols=29 Identities=24% Similarity=0.347 Sum_probs=19.6
Q ss_pred hhHHHHHHHHHHHHHHHHHhhcccCCchh
Q 015601 192 VSLLGHLCGILSGFAYTYGFFNLLMPGTS 220 (404)
Q Consensus 192 ~s~~~hl~G~l~G~l~~~~~l~~~~p~~~ 220 (404)
..+.....|++.|.++++..++.+.|...
T Consensus 466 ~~f~n~~la~l~G~~~a~l~~~li~p~~~ 494 (650)
T PF04632_consen 466 ATFLNRALAILLGIVIAALVFRLIRPFSP 494 (650)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCCCh
Confidence 34677778888888877776666655443
No 109
>PF11848 DUF3368: Domain of unknown function (DUF3368); InterPro: IPR021799 This domain is functionally uncharacterised. This domain is found in bacteria and archaea. This presumed domain is about 50 amino acids in length.
Probab=21.22 E-value=1.6e+02 Score=19.52 Aligned_cols=25 Identities=24% Similarity=0.360 Sum_probs=20.2
Q ss_pred HHHHHHHHhcCC--CHHHHHHHHHHcC
Q 015601 366 DEEIQKLVSMGF--DKTQVEVALAAAD 390 (404)
Q Consensus 366 ~~~i~~l~~mg~--~~~~~~~al~~~~ 390 (404)
.+.+++|.+-|| +++...++|+.++
T Consensus 22 ~~~l~~l~~~g~~is~~l~~~~L~~~g 48 (48)
T PF11848_consen 22 KPLLDRLQQAGFRISPKLIEEILRRAG 48 (48)
T ss_pred HHHHHHHHHcCcccCHHHHHHHHHHcC
Confidence 567888988996 8888888888764
No 110
>PF14474 RTC4: RTC4-like domain
Probab=21.16 E-value=94 Score=25.50 Aligned_cols=24 Identities=17% Similarity=0.347 Sum_probs=18.7
Q ss_pred HHHHHHH-HhcCCCHHHHHHHHHHc
Q 015601 366 DEEIQKL-VSMGFDKTQVEVALAAA 389 (404)
Q Consensus 366 ~~~i~~l-~~mg~~~~~~~~al~~~ 389 (404)
|-.+..+ .|||.++++|++-|+.+
T Consensus 90 El~~~LI~EDm~v~~~~A~~il~eS 114 (124)
T PF14474_consen 90 ELAVRLIMEDMGVDDEEARQILEES 114 (124)
T ss_pred HHHHHHHHHHhCCCHHHHHHHHHHH
Confidence 4444444 47999999999999987
No 111
>PF10905 DUF2695: Protein of unknown function (DUF2695); InterPro: IPR024248 This bacterial family of proteins has no known function.
Probab=21.05 E-value=1.6e+02 Score=20.27 Aligned_cols=25 Identities=24% Similarity=0.036 Sum_probs=21.4
Q ss_pred HHHHHHHhcCCCHHHHHHHHHHcCC
Q 015601 367 EEIQKLVSMGFDKTQVEVALAAADG 391 (404)
Q Consensus 367 ~~i~~l~~mg~~~~~~~~al~~~~~ 391 (404)
-..+-|.+|+++.+++...|++.+|
T Consensus 20 ~t~~fl~~~~~~~~~vl~~l~~nGg 44 (53)
T PF10905_consen 20 LTRQFLRQRQLDWEDVLEWLRENGG 44 (53)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHcCC
Confidence 3556688999999999999999886
No 112
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=20.02 E-value=2e+02 Score=22.75 Aligned_cols=34 Identities=18% Similarity=0.188 Sum_probs=25.3
Q ss_pred HHHHHHHhcCCCHHHHHHHHHHc--CCCHHHHHHhh
Q 015601 367 EEIQKLVSMGFDKTQVEVALAAA--DGDLNVAVEIL 400 (404)
Q Consensus 367 ~~i~~l~~mg~~~~~~~~al~~~--~~~~~~a~~~l 400 (404)
..|..|.++||+-+++++.|... +++.+...+.|
T Consensus 48 ~~I~~lr~~G~~l~~I~~~l~~~~~~~~~~~~~~~l 83 (108)
T cd04773 48 RLIHLLRRGGYLLEQIATVVEQLRHAGGTEALAAAL 83 (108)
T ss_pred HHHHHHHHCCCCHHHHHHHHHHhhcCCCHHHHHHHH
Confidence 46777889999999999999864 24455555555
Done!