Query 047404
Match_columns 291
No_of_seqs 262 out of 1919
Neff 7.7
Searched_HMMs 46136
Date Fri Mar 29 10:46:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047404.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047404hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4463 Uncharacterized conser 100.0 1E-35 2.2E-40 257.7 5.3 290 1-291 1-318 (323)
2 KOG0858 Predicted membrane pro 99.9 6.9E-26 1.5E-30 195.8 15.7 187 11-206 13-210 (239)
3 PF04511 DER1: Der1-like famil 99.9 1.8E-23 3.9E-28 181.0 15.1 184 11-198 2-197 (197)
4 KOG2632 Rhomboid family protei 99.8 7.7E-19 1.7E-23 154.2 16.1 173 11-187 15-195 (258)
5 PRK10907 intramembrane serine 99.8 1.7E-18 3.8E-23 156.5 13.5 163 10-185 93-265 (276)
6 PTZ00101 rhomboid-1 protease; 99.7 5.4E-17 1.2E-21 146.6 12.5 168 8-185 50-235 (278)
7 COG0705 Membrane associated se 99.7 5.1E-16 1.1E-20 137.2 14.5 172 10-186 16-207 (228)
8 COG5291 Predicted membrane pro 99.7 6.5E-17 1.4E-21 139.7 7.8 185 10-204 19-215 (313)
9 PF01694 Rhomboid: Rhomboid fa 99.6 8.6E-16 1.9E-20 125.8 6.3 133 46-187 2-139 (145)
10 PF00627 UBA: UBA/TS-N domain; 99.4 2.4E-13 5.1E-18 85.9 3.9 37 249-285 1-37 (37)
11 cd00194 UBA Ubiquitin Associat 99.3 3.2E-12 6.9E-17 81.1 5.1 38 250-287 1-38 (38)
12 smart00165 UBA Ubiquitin assoc 99.3 3.3E-12 7.2E-17 80.6 4.9 37 250-286 1-37 (37)
13 KOG2289 Rhomboid family protei 99.2 1E-11 2.2E-16 113.6 2.5 136 42-185 111-249 (316)
14 PF08551 DUF1751: Eukaryotic i 98.8 3.2E-09 6.9E-14 81.9 4.7 83 49-131 7-96 (99)
15 TIGR00601 rad23 UV excision re 98.7 1.4E-08 3.1E-13 95.8 4.9 40 249-288 155-194 (378)
16 KOG2890 Predicted membrane pro 98.5 4.5E-07 9.7E-12 81.5 9.3 139 48-186 65-215 (326)
17 KOG0011 Nucleotide excision re 98.3 4.1E-07 8.8E-12 82.7 4.3 41 248-288 133-173 (340)
18 KOG0944 Ubiquitin-specific pro 98.3 4E-07 8.7E-12 89.3 4.2 42 247-288 632-673 (763)
19 KOG2290 Rhomboid family protei 98.3 2.1E-07 4.6E-12 87.6 2.1 128 48-185 449-580 (652)
20 TIGR00601 rad23 UV excision re 98.1 2.3E-06 4.9E-11 81.0 4.6 44 247-290 334-377 (378)
21 PF02845 CUE: CUE domain; Int 97.9 1.6E-05 3.6E-10 51.3 4.1 39 250-288 1-41 (42)
22 PF14555 UBA_4: UBA-like domai 97.8 3.3E-05 7.2E-10 50.1 4.7 40 251-290 1-41 (43)
23 KOG0418 Ubiquitin-protein liga 97.7 3.8E-05 8.3E-10 64.5 4.0 44 245-288 157-200 (200)
24 KOG0011 Nucleotide excision re 97.7 3.4E-05 7.4E-10 70.3 4.0 42 248-289 296-337 (340)
25 COG5207 UBP14 Isopeptidase T [ 97.7 5.5E-05 1.2E-09 72.6 5.3 42 247-288 555-597 (749)
26 smart00546 CUE Domain that may 97.6 0.00017 3.7E-09 46.7 5.0 39 250-288 2-42 (43)
27 KOG0944 Ubiquitin-specific pro 97.5 0.00011 2.5E-09 72.4 5.5 41 248-288 569-610 (763)
28 KOG0010 Ubiquitin-like protein 97.5 0.00016 3.4E-09 69.4 5.1 42 247-288 451-493 (493)
29 KOG2561 Adaptor protein NUB1, 97.4 0.00018 3.8E-09 68.2 4.2 42 247-288 300-341 (568)
30 KOG2561 Adaptor protein NUB1, 97.0 0.00087 1.9E-08 63.6 4.9 43 247-289 426-468 (568)
31 PRK06369 nac nascent polypepti 96.9 0.0022 4.7E-08 50.4 5.3 41 247-287 73-114 (115)
32 COG5207 UBP14 Isopeptidase T [ 96.9 0.00043 9.2E-09 66.6 1.4 42 246-287 617-658 (749)
33 PF09288 UBA_3: Fungal ubiquit 96.7 0.0013 2.7E-08 44.6 2.6 28 248-275 7-34 (55)
34 TIGR00264 alpha-NAC-related pr 96.7 0.003 6.6E-08 49.5 5.0 39 248-286 76-115 (116)
35 COG1308 EGD2 Transcription fac 96.2 0.0097 2.1E-07 47.0 5.1 40 247-286 81-121 (122)
36 PF11547 E3_UbLigase_EDD: E3 u 96.0 0.019 4.2E-07 37.5 4.7 42 246-287 5-48 (53)
37 KOG2980 Integral membrane prot 95.6 0.011 2.4E-07 53.8 3.4 172 13-186 117-297 (310)
38 PF06972 DUF1296: Protein of u 93.9 0.17 3.7E-06 34.8 4.9 37 252-288 7-45 (60)
39 PF11626 Rap1_C: TRF2-interact 93.6 0.094 2E-06 39.2 3.7 35 254-288 1-35 (87)
40 COG4008 Predicted metal-bindin 93.5 0.18 3.9E-06 40.1 5.2 40 247-287 111-150 (153)
41 PF08587 UBA_2: Ubiquitin asso 92.7 0.041 8.8E-07 35.9 0.4 27 250-276 2-29 (46)
42 PF07499 RuvA_C: RuvA, C-termi 92.2 0.099 2.1E-06 34.4 1.8 25 250-274 3-27 (47)
43 smart00804 TAP_C C-terminal do 89.7 0.91 2E-05 31.9 4.9 39 249-287 11-50 (63)
44 PF08938 HBS1_N: HBS1 N-termin 88.8 0.21 4.5E-06 36.7 1.2 27 263-289 45-71 (79)
45 KOG1071 Mitochondrial translat 88.0 0.92 2E-05 41.8 5.0 40 249-288 45-85 (340)
46 PF03474 DMA: DMRTA motif; In 87.6 0.81 1.8E-05 28.9 3.1 24 263-286 16-39 (39)
47 PF02954 HTH_8: Bacterial regu 87.4 0.52 1.1E-05 30.1 2.2 24 262-285 5-28 (42)
48 PF07223 DUF1421: Protein of u 86.4 0.61 1.3E-05 44.0 3.0 27 248-274 319-345 (358)
49 PF03943 TAP_C: TAP C-terminal 81.6 1.6 3.4E-05 29.2 2.6 36 252-287 2-38 (51)
50 PRK14603 ruvA Holliday junctio 80.5 3.6 7.9E-05 35.6 5.2 34 250-283 152-190 (197)
51 TIGR00084 ruvA Holliday juncti 80.4 2.6 5.7E-05 36.2 4.3 26 250-275 147-172 (191)
52 PRK14606 ruvA Holliday junctio 80.4 2.9 6.3E-05 35.9 4.5 26 250-275 143-168 (188)
53 PRK14602 ruvA Holliday junctio 79.9 3.9 8.5E-05 35.5 5.2 25 250-274 155-179 (203)
54 PRK14600 ruvA Holliday junctio 79.7 3.8 8.3E-05 35.1 5.0 33 250-282 145-179 (186)
55 PRK14604 ruvA Holliday junctio 79.5 3.2 6.9E-05 35.9 4.5 25 250-274 149-173 (195)
56 PRK14601 ruvA Holliday junctio 78.5 4.6 9.9E-05 34.6 5.1 33 250-282 142-175 (183)
57 PF11372 DUF3173: Domain of un 76.1 2.9 6.2E-05 28.9 2.6 21 255-275 7-27 (59)
58 KOG2239 Transcription factor c 73.9 4.5 9.7E-05 34.8 3.8 35 250-284 171-206 (209)
59 COG0632 RuvA Holliday junction 73.6 4.5 9.8E-05 35.1 3.8 27 250-276 156-182 (201)
60 PRK13901 ruvA Holliday junctio 72.9 4.1 9E-05 35.2 3.4 26 250-275 144-169 (196)
61 PRK14605 ruvA Holliday junctio 65.5 14 0.00031 31.8 5.2 34 250-283 148-185 (194)
62 KOG0943 Predicted ubiquitin-pr 62.5 16 0.00034 39.9 5.7 46 242-287 181-228 (3015)
63 KOG3450 Huntingtin interacting 58.0 14 0.0003 28.6 3.3 43 245-287 75-118 (119)
64 PRK00116 ruvA Holliday junctio 55.0 19 0.00042 30.8 4.2 34 250-283 149-185 (192)
65 PF10440 WIYLD: Ubiquitin-bind 54.4 18 0.0004 25.5 3.2 24 250-273 11-34 (65)
66 PRK05441 murQ N-acetylmuramic 52.6 23 0.00051 32.6 4.6 31 257-287 242-273 (299)
67 PRK07634 pyrroline-5-carboxyla 51.7 29 0.00063 30.3 5.0 34 251-287 186-219 (245)
68 PRK08769 DNA polymerase III su 51.7 26 0.00057 32.6 4.8 38 250-287 174-211 (319)
69 PF03765 CRAL_TRIO_N: CRAL/TRI 49.0 36 0.00078 22.5 4.0 30 258-287 25-54 (55)
70 PF05861 PhnI: Bacterial phosp 48.5 28 0.0006 32.7 4.4 33 253-285 44-78 (358)
71 PRK07993 DNA polymerase III su 47.7 32 0.00069 32.2 4.8 37 250-286 168-206 (334)
72 PF04695 Pex14_N: Peroxisomal 46.5 24 0.00051 28.6 3.3 31 248-278 21-51 (136)
73 COG2103 Predicted sugar phosph 46.4 35 0.00075 31.1 4.5 37 251-287 234-271 (298)
74 TIGR00274 N-acetylmuramic acid 46.3 34 0.00075 31.4 4.7 34 253-286 233-267 (291)
75 PRK06476 pyrroline-5-carboxyla 45.1 44 0.00095 29.6 5.1 33 250-285 172-204 (258)
76 PF14748 P5CR_dimer: Pyrroline 43.2 61 0.0013 24.9 5.0 35 251-288 25-59 (107)
77 PRK01905 DNA-binding protein F 42.9 24 0.00051 25.5 2.5 24 262-285 37-60 (77)
78 PRK12570 N-acetylmuramic acid- 42.7 40 0.00087 31.0 4.5 26 260-285 242-267 (296)
79 PF11848 DUF3368: Domain of un 40.8 43 0.00092 21.8 3.2 26 250-275 21-48 (48)
80 cd05007 SIS_Etherase N-acetylm 34.5 27 0.00059 31.4 2.0 30 253-282 225-255 (257)
81 PRK00430 fis global DNA-bindin 34.5 36 0.00079 25.7 2.4 24 262-285 55-78 (95)
82 PF04361 DUF494: Protein of un 34.3 48 0.001 27.5 3.3 26 249-274 22-47 (155)
83 PTZ00431 pyrroline carboxylate 32.6 95 0.0021 27.6 5.3 35 251-288 177-211 (260)
84 PRK12491 pyrroline-5-carboxyla 32.0 98 0.0021 27.9 5.3 35 251-288 184-218 (272)
85 KOG3763 mRNA export factor TAP 31.3 1E+02 0.0022 31.1 5.4 41 247-287 532-573 (585)
86 PF12244 DUF3606: Protein of u 30.6 1.4E+02 0.003 20.2 4.6 36 250-285 19-55 (57)
87 PF03672 UPF0154: Uncharacteri 29.5 88 0.0019 22.0 3.4 27 249-275 32-61 (64)
88 PF07848 PaaX: PaaX-like prote 29.5 58 0.0013 23.2 2.7 25 250-274 23-47 (70)
89 PF02536 mTERF: mTERF; InterP 29.4 54 0.0012 30.2 3.2 39 250-288 243-288 (345)
90 PF01988 VIT1: VIT family; In 29.3 56 0.0012 28.4 3.1 38 249-287 81-118 (213)
91 PF01458 UPF0051: Uncharacteri 29.2 53 0.0011 28.7 3.0 27 247-273 201-227 (229)
92 PRK05441 murQ N-acetylmuramic 28.9 77 0.0017 29.1 4.1 32 253-284 265-297 (299)
93 KOG4167 Predicted DNA-binding 28.4 1E+02 0.0022 32.0 5.0 43 247-289 551-602 (907)
94 TIGR00274 N-acetylmuramic acid 27.6 50 0.0011 30.3 2.6 24 260-283 268-291 (291)
95 COG2922 Smg Uncharacterized pr 27.5 93 0.002 25.5 3.7 26 247-272 19-45 (157)
96 KOG4329 DNA-binding protein [G 27.0 1.1E+02 0.0024 29.0 4.7 42 243-284 238-288 (445)
97 KOG1796 Vacuolar protein sorti 26.7 22 0.00049 35.0 0.1 33 256-288 382-414 (609)
98 PF03701 UPF0181: Uncharacteri 26.4 67 0.0014 21.4 2.3 20 251-270 17-36 (51)
99 PRK10923 glnG nitrogen regulat 25.8 52 0.0011 31.8 2.5 24 262-285 429-452 (469)
100 PRK11608 pspF phage shock prot 25.4 55 0.0012 30.4 2.5 24 262-285 286-309 (326)
101 cd02433 Nodulin-21_like_2 Nodu 25.3 61 0.0013 28.8 2.6 38 249-286 99-136 (234)
102 TIGR02974 phageshock_pspF psp 25.3 55 0.0012 30.4 2.5 24 262-285 292-315 (329)
103 PRK15115 response regulator Gl 25.2 55 0.0012 31.4 2.5 24 262-285 398-421 (444)
104 PRK05022 anaerobic nitric oxid 24.6 55 0.0012 32.4 2.5 24 262-285 468-491 (509)
105 COG4241 Predicted membrane pro 24.6 77 0.0017 29.3 3.1 36 250-288 129-164 (314)
106 TIGR01817 nifA Nif-specific re 24.2 58 0.0013 32.4 2.5 24 262-285 490-513 (534)
107 PRK03430 hypothetical protein; 24.0 86 0.0019 26.1 3.1 24 249-272 22-45 (157)
108 COG2103 Predicted sugar phosph 23.8 99 0.0022 28.2 3.6 33 252-284 262-295 (298)
109 PF07553 Lipoprotein_Ltp: Host 23.6 1.1E+02 0.0024 20.1 3.0 23 250-272 21-46 (48)
110 PRK00523 hypothetical protein; 23.0 1.4E+02 0.003 21.5 3.6 26 249-274 40-68 (72)
111 PRK10332 hypothetical protein; 22.9 1.1E+02 0.0024 23.8 3.3 47 6-55 9-55 (107)
112 TIGR01818 ntrC nitrogen regula 22.8 64 0.0014 31.1 2.5 24 262-285 426-449 (463)
113 PRK12570 N-acetylmuramic acid- 22.7 90 0.002 28.7 3.3 31 253-283 261-292 (296)
114 PF03130 HEAT_PBS: PBS lyase H 22.7 1.3E+02 0.0027 16.8 2.8 22 264-287 2-23 (27)
115 cd04773 HTH_TioE_rpt2 Second H 22.6 1.8E+02 0.004 22.2 4.6 33 252-284 48-82 (108)
116 PRK06090 DNA polymerase III su 22.6 1.4E+02 0.003 27.8 4.5 35 250-286 169-203 (319)
117 PF15187 Augurin: Oesophageal 22.3 81 0.0018 24.3 2.4 21 251-271 51-71 (114)
118 PRK03980 flap endonuclease-1; 22.3 1.1E+02 0.0023 28.2 3.7 28 248-275 248-277 (292)
119 TIGR00112 proC pyrroline-5-car 21.6 2E+02 0.0043 25.3 5.3 34 251-287 164-197 (245)
120 PF06755 DUF1219: Protein of u 21.6 1.3E+02 0.0029 23.5 3.5 29 260-288 41-69 (114)
121 TIGR00678 holB DNA polymerase 21.5 98 0.0021 25.8 3.1 32 250-281 157-188 (188)
122 smart00422 HTH_MERR helix_turn 21.1 1.1E+02 0.0024 20.7 2.9 21 252-272 48-68 (70)
123 PRK11361 acetoacetate metaboli 21.1 73 0.0016 30.6 2.5 24 262-285 417-440 (457)
124 TIGR00465 ilvC ketol-acid redu 21.0 1.5E+02 0.0034 27.4 4.5 34 252-288 195-228 (314)
125 smart00733 Mterf Mitochondrial 20.8 73 0.0016 17.3 1.5 14 250-263 18-31 (31)
126 cd01105 HTH_GlnR-like Helix-Tu 20.5 2.4E+02 0.0051 20.6 4.6 35 252-287 49-83 (88)
127 PF13411 MerR_1: MerR HTH fami 20.4 88 0.0019 21.3 2.2 21 253-273 48-68 (69)
128 PF06152 Phage_min_cap2: Phage 20.2 48 0.001 31.4 1.0 41 249-289 45-85 (361)
129 PRK07940 DNA polymerase III su 20.1 1.8E+02 0.004 27.9 4.9 35 251-285 179-214 (394)
No 1
>KOG4463 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=1e-35 Score=257.73 Aligned_cols=290 Identities=67% Similarity=1.089 Sum_probs=235.5
Q ss_pred CCCCCCCCcccchHHHHHHHHHHHHHHHhhhccccccccchHHHhh-hccchhhhhhhcccCChhHHHHHHHHHHHHHHH
Q 047404 1 MNGGPSGFNNAPVTRAFVIACALFTVFFGIQGRFNKLGLSYQDIFQ-NFRLWRLIVSGFAFSSAPELMFGLYLLYYFRVF 79 (291)
Q Consensus 1 ~~~~~~gf~~~PVTk~li~~~~~~sl~~~~~~~~~~l~l~~~~i~~-~~q~WRLlT~~f~h~~~~~ll~n~~~ly~~r~l 79 (291)
|+++|.|+.|.||||..++.+.++++..++...++.+.++++.+++ ++||||++-++|++.+..++++.++.+|++|.+
T Consensus 1 Ms~~p~g~~nmpVTK~~~iT~~~~~vvagI~~~k~~f~l~y~~~l~~y~qywrlL~~qF~~~n~~e~~~~l~I~Y~fR~~ 80 (323)
T KOG4463|consen 1 MSGGPSGFHNMPVTKAFVITSALFTVVAGIQGRKSKFGLSYQDILEKYFQYWRLLMSQFAFSNTPELMFGLYILYYFRVF 80 (323)
T ss_pred CCCCCCcccccchHHHHHHHHHHHHHHHHhhhcccccccchhHHHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHH
Confidence 8999999999999999999999999999988888899999987775 489999999999999999999999999999999
Q ss_pred hhhccchhHHHHHHHHHHHHHHHHHHHHHHhcC--cccccCCChHHHHHHHHHHHHhhcCccceEEEeeeecchh--HHH
Q 047404 80 ERQIGSNKYSVFILFSITVSFLFEVLTLALLKD--PAMKLTSGPYGLIFASFVPFYFDIPVSTRFRVFGVHFSDK--SFI 155 (291)
Q Consensus 80 Er~~Gs~kf~~~~l~~~~~s~ll~~~~~~~~~~--~~~~~~~G~sg~ifal~~~~~~~~P~~~~~~i~g~~~~~k--~~~ 155 (291)
||..||-||+.|+++++.++.++..++..+..+ .+ ....+++|++||.++.|..++|.+..++.++++++|| .+.
T Consensus 81 ERlLGShky~~fiv~s~~~~~l~~~il~~l~~~~~~n-l~~~qp~~liFa~~~~~y~~ip~~~f~r~f~~~f~dkni~~i 159 (323)
T KOG4463|consen 81 ERLLGSHKYSVFIVFSGTVSLLLEVILLSLLKDTTAN-LLTSQPYGLIFASFIPFYLDIPVSTFFRVFGVNFSDKNISFI 159 (323)
T ss_pred HHHhccccceeehhHHHHHHHHHHHHHHHHHHHHHhh-hhhcCCCceeeeeccceEEEecceeEEEeecccccccceeee
Confidence 999999999999999999998887765444321 11 4567778899999999999999998899999999999 677
Q ss_pred HHHHHHHHhcC----------CCchHHHHHHHHHhhHhhcccccCCCCCCccHHHHHHHhhccCCCCCCCCC--------
Q 047404 156 YLAGLQLLISS----------LNRSLLPGMCGILAGSLYRPNFFRIRKAKFPEFITSFFSRLSLPSMGNPPA-------- 217 (291)
Q Consensus 156 ~l~~l~ll~~~----------~~~s~~~~l~Gil~G~ly~~~~~~~~~~~~P~~i~~~~~~~~~p~~~~~~~-------- 217 (291)
++.+.++.-+. ...+....+||++.|++|..+..++.+-++|..+..++++..-|-++....
T Consensus 160 ~~~G~a~sh~~NkredksaveWk~~i~f~~~gLi~~~~~~~~~agi~~~~~~~~~~~f~d~~~~p~~~~~~~PVSyfisq 239 (323)
T KOG4463|consen 160 YLAGVALSHSSNKREDKSAVEWKRSIFFGICGLIAGSLYRLNIAGIRKAKFPEFVASFFDRLSFPSFGNSPPPVSYFISQ 239 (323)
T ss_pred cccchhhhcCcccccccccceeecccccccchhhhhhHhhcccccccccccHHHHHhhhccccCCCCCCCCCchhhhccc
Confidence 77777666543 345677889999999999988777777788999999998887665544322
Q ss_pred -CCCCCcCCCCCCccccccccCCCCCCCCCCCCCHHHHHH-HHcCCCCHHHHHHHHHHhCCCHHH---HHHHHHhcCCC
Q 047404 218 -APSRNVLGSIPSHAGRQAESNYPLPVPSTIEPPEDSIAM-LVSMGFDRNSARQALVQARNDINA---ATNILLEAQPH 291 (291)
Q Consensus 218 -~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~v~~-l~~mGf~~~~~~~aL~~~~~~~~~---A~~~l~~~~~~ 291 (291)
.|.|.+.+.+....+|...++++.+.+.+.++++|.+.. .++||++.+.++.+|-...||.+. +++.+++-|.|
T Consensus 240 ~pPTR~nv~~~A~at~~~aaas~~~~~~~s~~p~g~t~~SGp~S~~l~g~S~rp~l~~~r~dd~~gad~t~r~l~~Q~l 318 (323)
T KOG4463|consen 240 APPTRNNVGTIAPATGRRAAASQPAPLPSSVEPSGETITSGPVSMGLDGNSARPALVHARNDDNAGADATNRLLEAQSL 318 (323)
T ss_pred CCcchhhhhhccccccchhhhcCCCCCccccCCCCcccCCCccccccCCCcCCcccccccccccccccccchhhhhhhH
Confidence 233433332222234545555555555666777888887 999999999999999999888887 77788887765
No 2
>KOG0858 consensus Predicted membrane protein [Function unknown]
Probab=99.94 E-value=6.9e-26 Score=195.80 Aligned_cols=187 Identities=22% Similarity=0.396 Sum_probs=146.7
Q ss_pred cchHHHHHHHHHHHHHHHhhhcccc-ccccchHHHhhhccchhhhhhhcccCC-hhHHHHHHHHHHHH-HHHhhhccchh
Q 047404 11 APVTRAFVIACALFTVFFGIQGRFN-KLGLSYQDIFQNFRLWRLIVSGFAFSS-APELMFGLYLLYYF-RVFERQIGSNK 87 (291)
Q Consensus 11 ~PVTk~li~~~~~~sl~~~~~~~~~-~l~l~~~~i~~~~q~WRLlT~~f~h~~-~~~ll~n~~~ly~~-r~lEr~~Gs~k 87 (291)
|||||++.++|+++++++.+.-..+ +++++++.+++++|+||++|+.++++. ..|.++||+++|++ +.||+-.-.+|
T Consensus 13 PpVTR~~~~~~v~tt~~~~l~lIsP~~l~~~p~Lv~kk~QiWRliTs~lyfg~~gf~fl~n~~FlyrY~~~LE~g~f~~r 92 (239)
T KOG0858|consen 13 PPVTRYYTTACVVTTLLVRLDLISPFQLYLNPELVFKKFQIWRLITSFLYFGPFGFDFLMNLYFLYRYSSMLEEGSFRGR 92 (239)
T ss_pred ChHHHHHHHHHHHHHHHHhhcccCchheEecHHHHHhHhHHHHhhhhhheeccccHHHHHHHHHHHHHHHHHhcCCCCCc
Confidence 9999999999999999987654444 788999999999999999999999988 45999999999997 88999666667
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCcccccCCChHHHHHHHHHHHHhhcCccceEEEeeeecchhHHHH-HHHHHHHhcC
Q 047404 88 YSVFILFSITVSFLFEVLTLALLKDPAMKLTSGPYGLIFASFVPFYFDIPVSTRFRVFGVHFSDKSFIY-LAGLQLLISS 166 (291)
Q Consensus 88 f~~~~l~~~~~s~ll~~~~~~~~~~~~~~~~~G~sg~ifal~~~~~~~~P~~~~~~i~g~~~~~k~~~~-l~~l~ll~~~ 166 (291)
.++|+.+..+.+.++.+. .++. ..+.-..++++++.|.|++.+|...+-.+.+++++++++|| +++++++..+
T Consensus 93 tadf~~mllf~~~l~~~~--~~~~----~~~fLg~~l~~~l~YvWs~~Np~~~v~F~g~~~f~a~YlPwvll~fs~l~g~ 166 (239)
T KOG0858|consen 93 TADFLYMLLFGAVLLTLT--GLFV----YIVFLGQSLVFMLVYVWSKRNPDVIVSFFGLITFKAPYLPWVLLGFSFLFGG 166 (239)
T ss_pred hhHHHHHHHHHHHHHHHH--HHHH----HHHHHHHHHHHHHHHHHHhhCCCceEEEEEEecCccccchHHHHHHHHHhCC
Confidence 777776655555444322 1111 11222247899999999999999875444559999999999 5578887742
Q ss_pred CCchHHHHHHHHHhhHhhc--ccccCC----C-CCCccHHHHHHHhh
Q 047404 167 LNRSLLPGMCGILAGSLYR--PNFFRI----R-KAKFPEFITSFFSR 206 (291)
Q Consensus 167 ~~~s~~~~l~Gil~G~ly~--~~~~~~----~-~~~~P~~i~~~~~~ 206 (291)
. .+.++.|+++||+|. .++.+. + .+++|.|++++++.
T Consensus 167 --~-~~~dllGi~~GHiy~fl~~~~p~~~gg~~~l~TP~~l~rl~~~ 210 (239)
T KOG0858|consen 167 --S-ILVDLLGIIVGHIYYFLDDVYPRDYGGRDLLKTPQFLKRLFAD 210 (239)
T ss_pred --c-hHHHHHhhhhheeEEEEeeeccCCcCCcCcccCHHHHHHhcCC
Confidence 3 499999999999998 455543 3 38999999999976
No 3
>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=99.91 E-value=1.8e-23 Score=181.04 Aligned_cols=184 Identities=23% Similarity=0.398 Sum_probs=136.9
Q ss_pred cchHHHHHHHHHHHHHHHhhhccc-cccccchHHHhhhccchhhhhhhcccCChh-HHHHHHHHHHHH-HHHhhhccchh
Q 047404 11 APVTRAFVIACALFTVFFGIQGRF-NKLGLSYQDIFQNFRLWRLIVSGFAFSSAP-ELMFGLYLLYYF-RVFERQIGSNK 87 (291)
Q Consensus 11 ~PVTk~li~~~~~~sl~~~~~~~~-~~l~l~~~~i~~~~q~WRLlT~~f~h~~~~-~ll~n~~~ly~~-r~lEr~~Gs~k 87 (291)
|||||++++.+++++++....-.. .++.++++.+++++|+||++|+.|++++.+ +++++++++|++ +.+|+....+|
T Consensus 2 PpVTR~~~~~~~~~s~l~~~~~~~~~~l~~~~~~v~~~~q~WRl~Tsff~~g~~~~~~l~~~~~l~~~s~~LE~~~f~~~ 81 (197)
T PF04511_consen 2 PPVTRYWLISTVALSLLVSFGIISPYYLYFDWELVFKKFQIWRLFTSFFYFGPFSLNFLFNLYFLYQYSSSLEEGHFQGR 81 (197)
T ss_pred ChhHHHHHHHHHHHHHHHHCCCCCHHHeeECcHHHhhhcCceeeEEEEEEEcCCCHHHHHHHHHHHHHhhHhccCCCCCC
Confidence 899999999999999987654332 267789999999999999999999998886 999999999997 78999866677
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCcccccCCChHHHHHHHHHHHHhhcCccceEEEe-eeecchhHHHHH-HHHHHHhc
Q 047404 88 YSVFILFSITVSFLFEVLTLALLKDPAMKLTSGPYGLIFASFVPFYFDIPVSTRFRVF-GVHFSDKSFIYL-AGLQLLIS 165 (291)
Q Consensus 88 f~~~~l~~~~~s~ll~~~~~~~~~~~~~~~~~G~sg~ifal~~~~~~~~P~~~~~~i~-g~~~~~k~~~~l-~~l~ll~~ 165 (291)
.++|+.+..+++.++..+.. +........+.-..++.++++|.|++.+|+.++ +++ +++++++++||+ +++.+++.
T Consensus 82 ~ady~~~ll~~~~~i~~~~~-~~~~~~~~~~~l~~~l~~~l~Y~wsr~np~~~v-~~~g~~~i~a~ylP~~~~~~~~l~~ 159 (197)
T PF04511_consen 82 SADYLWFLLFGASLILILSL-LIGPYFFNIPFLGSSLSFALTYIWSRKNPNAQV-SFFGLFTIKAKYLPWVLLAFSLLFG 159 (197)
T ss_pred HHHHHHHHHHHHHHHHHHHH-hhccchhHHHHHHHHHHHHHHHHHHHhCcccce-eeEEEEEEChhhHHHHHHHHHHHhC
Confidence 77776665554444332211 111000011233457999999999999998874 555 489999999995 46667664
Q ss_pred CCCchHHHHHHHHHhhHhhc--ccccCC----CC-CCccH
Q 047404 166 SLNRSLLPGMCGILAGSLYR--PNFFRI----RK-AKFPE 198 (291)
Q Consensus 166 ~~~~s~~~~l~Gil~G~ly~--~~~~~~----~~-~~~P~ 198 (291)
+ .+.+.++.|+++||+|+ .+++|. ++ +++|.
T Consensus 160 ~--~~~~~~l~Gi~~Ghly~fl~~~~p~~~~G~~~l~tP~ 197 (197)
T PF04511_consen 160 G--SSPIPDLLGILVGHLYYFLKDIYPRLPGGKDLLKTPQ 197 (197)
T ss_pred C--CcHHHHHHHHHHHHHHHHHHHhcccccCCCccCCCcC
Confidence 2 47889999999999998 455553 33 66763
No 4
>KOG2632 consensus Rhomboid family proteins [Function unknown]
Probab=99.81 E-value=7.7e-19 Score=154.17 Aligned_cols=173 Identities=23% Similarity=0.340 Sum_probs=136.1
Q ss_pred cchHHHHHHHHHHHHHHHhhhccccccccchHHHhhhccchhhhhhhcccCChhHHHHHHHHHHHH-HHHhhhcc-chhH
Q 047404 11 APVTRAFVIACALFTVFFGIQGRFNKLGLSYQDIFQNFRLWRLIVSGFAFSSAPELMFGLYLLYYF-RVFERQIG-SNKY 88 (291)
Q Consensus 11 ~PVTk~li~~~~~~sl~~~~~~~~~~l~l~~~~i~~~~q~WRLlT~~f~h~~~~~ll~n~~~ly~~-r~lEr~~G-s~kf 88 (291)
|+.|.+++..|.++.+........ .....+..+.+++|+||++|+.++|.+..|++|||+.++.. ..+||..| +.++
T Consensus 15 p~~ts~~~~~~~~i~lv~~~~~i~-~~~~l~~~~l~~~ql~RL~Ty~l~H~s~~hllfnmlaL~~~g~~fE~~~G~t~~~ 93 (258)
T KOG2632|consen 15 PLLTSIVVVLAILIYLVSFFPGIV-EVLGLPSELLINWQLYRLITYALVHLSLPHLLFNMLALWPLGSQFERTHGTTVRI 93 (258)
T ss_pred hHHHHHHHHHHHHHHHHhccchhh-hHhcCCHHHhhhHHHHHHHHHHHHhccHHHHHHHHHHHHhchhHHHhhccceehH
Confidence 668999999888888875443332 33455567888999999999999999999999999998886 78999999 7888
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhc-Cccc--ccCCChHHHHHHHHHHHHhhcCccceEEEee-eecchhHHHHHH--HHHH
Q 047404 89 SVFILFSITVSFLFEVLTLALLK-DPAM--KLTSGPYGLIFASFVPFYFDIPVSTRFRVFG-VHFSDKSFIYLA--GLQL 162 (291)
Q Consensus 89 ~~~~l~~~~~s~ll~~~~~~~~~-~~~~--~~~~G~sg~ifal~~~~~~~~P~~~~~~i~g-~~~~~k~~~~l~--~l~l 162 (291)
+.|.....+.+.++.+++...+. .+.. ..+.|.+++.||++..-....|... ..++| +.++.+..+|+. +.++
T Consensus 94 l~~~~llalf~gIl~ll~~~~~~~~d~~~~~~a~G~s~v~Fam~~~~~~~sp~r~-~~~fg~~siP~~l~Pw~lLi~~~~ 172 (258)
T KOG2632|consen 94 LMFTVLLALFSGILYLLAYHVFLLSDLVYVEGAIGFSGVLFAMMAVLEVQSPVRS-RSVFGLFSIPIVLAPWALLIATQI 172 (258)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcchhhhcccccccHHHHHHHHHHhhcCcccc-hhhcccccccHHHHHHHHHHHHHH
Confidence 88888888899988877665222 2221 6789999999999998776666543 24556 557888888743 5556
Q ss_pred HhcCCCchHHHHHHHHHhhHhhccc
Q 047404 163 LISSLNRSLLPGMCGILAGSLYRPN 187 (291)
Q Consensus 163 l~~~~~~s~~~~l~Gil~G~ly~~~ 187 (291)
+. ++.|+++|+||+++|+.|.+.
T Consensus 173 lv--p~aSFlghl~GllvG~ay~~~ 195 (258)
T KOG2632|consen 173 LV--PQASFLGHLCGLLVGYAYAFS 195 (258)
T ss_pred Hc--cCchHHHHHHHHHHHHHHHHH
Confidence 55 579999999999999999974
No 5
>PRK10907 intramembrane serine protease GlpG; Provisional
Probab=99.78 E-value=1.7e-18 Score=156.45 Aligned_cols=163 Identities=21% Similarity=0.343 Sum_probs=114.6
Q ss_pred ccchHHHHHHHHHHHHHHHhhhcccc-ccccchH-HHhhhccchhhhhhhcccCChhHHHHHHHHHHHH-HHHhhhccch
Q 047404 10 NAPVTRAFVIACALFTVFFGIQGRFN-KLGLSYQ-DIFQNFRLWRLIVSGFAFSSAPELMFGLYLLYYF-RVFERQIGSN 86 (291)
Q Consensus 10 ~~PVTk~li~~~~~~sl~~~~~~~~~-~l~l~~~-~i~~~~q~WRLlT~~f~h~~~~~ll~n~~~ly~~-r~lEr~~Gs~ 86 (291)
..|+|..++++|++++++..+..... ...+.++ ...+++|+||++|+.|.|.+..|+++||+.+|.+ +.+|+.+|++
T Consensus 93 ~~p~T~~li~i~i~vf~l~~~~~~~~~~~~l~~~~~~~~~~q~WRl~T~~flH~~~~Hl~fNml~l~~lG~~iE~~~G~~ 172 (276)
T PRK10907 93 AGPLTLGVMIACVVVFILMQILGDQTVMLWLAWPFDPSLKFELWRYFTHALLHFSLLHILFNLLWWWYLGGAVEKRLGSG 172 (276)
T ss_pred CCCHHHHHHHHHHHHHHHHHHhccHHHHHHHhccccccccCCcHHHHhHHHHhCCHHHHHHHHHHHHHHHHHHHHHHChH
Confidence 47899999999999998865433211 1112222 3345789999999999999999999999999986 8999999999
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHhcCcccccCCChHHHHHHHHHHHHh---hcCccceEEEeeeecchhHHHHHHH---H
Q 047404 87 KYSVFILFSITVSFLFEVLTLALLKDPAMKLTSGPYGLIFASFVPFYF---DIPVSTRFRVFGVHFSDKSFIYLAG---L 160 (291)
Q Consensus 87 kf~~~~l~~~~~s~ll~~~~~~~~~~~~~~~~~G~sg~ifal~~~~~~---~~P~~~~~~i~g~~~~~k~~~~l~~---l 160 (291)
|++.+++++++++++++... .+ ....|.||+++|++.+... ..|.. ++.++...+.++++ +
T Consensus 173 ~~l~l~l~s~i~~~~~~~~~----~~---~~~gGaSGvVygL~g~~~~~~~~~p~~------~~~lp~~~~~f~llwl~~ 239 (276)
T PRK10907 173 KLIVITLISALLSGWVQSKF----SG---PWFGGLSGVVYALMGYVWLRGERDPQS------GIYLPRGLIAFALLWLVA 239 (276)
T ss_pred HHHHHHHHHHHHHHHHHHHH----cc---chhhHHHHHHHHHHHHHHHHhcccccc------chhhhHHHHHHHHHHHHH
Confidence 99999999999999886532 22 2367999999999975432 12221 12222222222111 1
Q ss_pred HHH-hcCCCchHHHHHHHHHhhHhhc
Q 047404 161 QLL-ISSLNRSLLPGMCGILAGSLYR 185 (291)
Q Consensus 161 ~ll-~~~~~~s~~~~l~Gil~G~ly~ 185 (291)
.+. ..+.+.+..+|++|+++|.+..
T Consensus 240 g~~~~~g~~Ian~AHlgGli~Gll~g 265 (276)
T PRK10907 240 GYFDLFGMSIANAAHVAGLAVGLAMA 265 (276)
T ss_pred HHHHccCcccHHHHHHHHHHHHHHHH
Confidence 111 1234588999999999999965
No 6
>PTZ00101 rhomboid-1 protease; Provisional
Probab=99.72 E-value=5.4e-17 Score=146.57 Aligned_cols=168 Identities=11% Similarity=0.122 Sum_probs=112.5
Q ss_pred CcccchHHHHHHHHHHHHHHHhhhccc----c------ccccchHHHhhhccchhhhhhhcccCChhHHHHHHHHHHHH-
Q 047404 8 FNNAPVTRAFVIACALFTVFFGIQGRF----N------KLGLSYQDIFQNFRLWRLIVSGFAFSSAPELMFGLYLLYYF- 76 (291)
Q Consensus 8 f~~~PVTk~li~~~~~~sl~~~~~~~~----~------~l~l~~~~i~~~~q~WRLlT~~f~h~~~~~ll~n~~~ly~~- 76 (291)
|+-+-+|+.++++.++++++....+.. + ++....+..+.++|+||++|+.|.|.++.|+++||+.+|.+
T Consensus 50 f~i~~l~~~Iiii~iivfil~l~~~~~~~l~p~~~~L~~~Ga~~~~~i~~gq~WRLiT~~FlH~~~~HLl~Nm~~l~~~G 129 (278)
T PTZ00101 50 FTWKSFIMAISIIQIIVFIISVSIKPADFLTPSDSLLVTLGANVASRIKQGEIHRLILPIFLHANIFHTFFNVFFQLRMG 129 (278)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHhcccccCCCCHHHHHHHhCcchhhhhcCCCHHHHHHHHHccCHHHHHHHHHHHHHHH
Confidence 444668889999988887764321110 1 12122234446899999999999999999999999999986
Q ss_pred HHHhhhccchhHHHHHHHHHHHHHHHHHHHHHHhcCcccccCCChHHHHHHHHHHHHhhcCccceEEEeeeecchhHHH-
Q 047404 77 RVFERQIGSNKYSVFILFSITVSFLFEVLTLALLKDPAMKLTSGPYGLIFASFVPFYFDIPVSTRFRVFGVHFSDKSFI- 155 (291)
Q Consensus 77 r~lEr~~Gs~kf~~~~l~~~~~s~ll~~~~~~~~~~~~~~~~~G~sg~ifal~~~~~~~~P~~~~~~i~g~~~~~k~~~- 155 (291)
+.+||.+|+.||...|++++++++++.... . +. ....|+||.+||++..+..+.=.. +. ..+.+.+.+.
T Consensus 130 ~~lE~~~G~~r~~ilYl~sGi~G~l~s~~~----~-~~-~~svGASgAifGLiGa~~~~lil~--w~--~~~~~~~~~~~ 199 (278)
T PTZ00101 130 FTLEKNYGIVKIIILYFLTGIYGNILSSSV----T-YC-PIKVGASTSGMGLLGIVTSELILL--WH--VIRHRERVVFN 199 (278)
T ss_pred HHHHHHHChHHHHHHHHHHHHHHHHHHHHH----c-cC-CcEEehhHHHHHHHHHHHHHHHHH--HH--hhccHHHHHHH
Confidence 789999999999999999999999876532 1 12 457899999999998764321000 00 0111222211
Q ss_pred --HHHH--HHHH--hcCCCchHHHHHHHHHhhHhhc
Q 047404 156 --YLAG--LQLL--ISSLNRSLLPGMCGILAGSLYR 185 (291)
Q Consensus 156 --~l~~--l~ll--~~~~~~s~~~~l~Gil~G~ly~ 185 (291)
.+++ +.+. ..+++.+..+|++|+++|.+..
T Consensus 200 ~i~~~li~~~l~~~~~g~~Id~~aHlGG~i~G~llg 235 (278)
T PTZ00101 200 IIFFSLISFFYYFTFNGSNIDHVGHLGGLLSGISMG 235 (278)
T ss_pred HHHHHHHHHHHHHhcCCCCccHHHHHHHHHHHHHHH
Confidence 1111 1111 1245688999999999998865
No 7
>COG0705 Membrane associated serine protease [Amino acid transport and metabolism]
Probab=99.69 E-value=5.1e-16 Score=137.24 Aligned_cols=172 Identities=21% Similarity=0.321 Sum_probs=121.7
Q ss_pred ccchHHHHHHHHHHHHHHHhhhcccc---------ccccchHHHhhhc---cchhhhhhhcccCChhHHHHHHHHHHHH-
Q 047404 10 NAPVTRAFVIACALFTVFFGIQGRFN---------KLGLSYQDIFQNF---RLWRLIVSGFAFSSAPELMFGLYLLYYF- 76 (291)
Q Consensus 10 ~~PVTk~li~~~~~~sl~~~~~~~~~---------~l~l~~~~i~~~~---q~WRLlT~~f~h~~~~~ll~n~~~ly~~- 76 (291)
.+++|+.++.+|+++++......... ...+.+....... |+||++|+.|.|.++.|+++||+.+|.+
T Consensus 16 ~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~lit~~FlH~~~~Hll~N~~~l~~fg 95 (228)
T COG0705 16 APPVTLFLILLNILVFLLELVLGWSAIFLLTFLFRLFGLYPLNLLGALARDQLWRLITAIFLHAGFLHLLFNMLALWVFG 95 (228)
T ss_pred cchHHHHHHHHHHHHHHHHHHccchHHHHHHHhhhHHhhcchhhhccccccchHHHHHHHHHHhhHHHHHHHHHHHHHhh
Confidence 38899999999999888754322211 0122222222222 8999999999999999999999999987
Q ss_pred HHHhhhccchhHHHHHHHHHHHHHHHHHHHHHHhcCcccccCCChHHHHHHHHHHHHhhcCccceEEEee--eecchhHH
Q 047404 77 RVFERQIGSNKYSVFILFSITVSFLFEVLTLALLKDPAMKLTSGPYGLIFASFVPFYFDIPVSTRFRVFG--VHFSDKSF 154 (291)
Q Consensus 77 r~lEr~~Gs~kf~~~~l~~~~~s~ll~~~~~~~~~~~~~~~~~G~sg~ifal~~~~~~~~P~~~~~~i~g--~~~~~k~~ 154 (291)
+.+||.+|+.||..+++.+++++++.+... ...+.....|+||.+|+++.++....|.... .... ++.....+
T Consensus 96 ~~le~~~G~~~f~~~yl~~gl~~~~~~~~~----~~~~~~~~~GASG~i~gllga~~~~~~~~~~-~~~~~~~~~~~~~~ 170 (228)
T COG0705 96 SNLERRLGTLRFLLFYLLSGLLAGLAQVLF----GPKGGAPSLGASGAIFGLLGAYFLLFPFARI-LLLFLSLPRPALIL 170 (228)
T ss_pred HHHHHHhchhHHHHHHHHHHHHHHHHHHHH----cccccCcccchhHHHHHHHHHHHHHccccch-hhhhccCchhHHHH
Confidence 689999999999999999999998875432 2111146899999999999999998887542 1111 22232333
Q ss_pred HHH-HHHHHHhcCC----CchHHHHHHHHHhhHhhcc
Q 047404 155 IYL-AGLQLLISSL----NRSLLPGMCGILAGSLYRP 186 (291)
Q Consensus 155 ~~l-~~l~ll~~~~----~~s~~~~l~Gil~G~ly~~ 186 (291)
..+ +..+++.... ..++.+|++|+++|.+|..
T Consensus 171 i~~~~~~~~~~~~~~~~~~va~~aHl~G~i~G~l~~~ 207 (228)
T COG0705 171 ILIWLLYSLFSGAGSFGPSVAWSAHLGGLIGGLLLAA 207 (228)
T ss_pred HHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHHHHH
Confidence 322 2344444221 4779999999999999884
No 8
>COG5291 Predicted membrane protein [Function unknown]
Probab=99.68 E-value=6.5e-17 Score=139.73 Aligned_cols=185 Identities=14% Similarity=0.261 Sum_probs=126.7
Q ss_pred ccchHHHHHHHHHHHHHHHhhhcccc-ccccchHHHhhhccchhhhhhhcccCChh-HHHHHHHHHHHH-HHHhhh-ccc
Q 047404 10 NAPVTRAFVIACALFTVFFGIQGRFN-KLGLSYQDIFQNFRLWRLIVSGFAFSSAP-ELMFGLYLLYYF-RVFERQ-IGS 85 (291)
Q Consensus 10 ~~PVTk~li~~~~~~sl~~~~~~~~~-~l~l~~~~i~~~~q~WRLlT~~f~h~~~~-~ll~n~~~ly~~-r~lEr~-~Gs 85 (291)
-|||||.+.....+++++....-..+ ++.+.++..+++.|+||++|+.+++++.. +.+++++++|.. |.|||- +++
T Consensus 19 IPPITRy~~ll~~a~til~~~~lvsPwy~ly~~pL~~k~~qiwRlfTs~~~~~~~~~d~~M~vyf~Y~yS~~LE~g~f~~ 98 (313)
T COG5291 19 IPPITRYMTLLISAVTILVYVDLVSPWYSLYYSPLFLKRLQIWRLFTSFLYFGKPTLDMFMHVYFLYRYSRMLEEGCFNT 98 (313)
T ss_pred CCcHHHHHHHHHHHHHHHHHHhhcCccceeeechhHHHHHHHHHHHHHHHhhcCcchhHHHHHHHHHHHHHHHhccccCc
Confidence 49999999999999998865444445 55666788999999999999999999876 999999999997 889994 344
Q ss_pred h--hHHHHHHHHHHHHHHHHHHHHHHhcCcccccCCChHHHHHHHHHHHHhhcCccceEEEeeeecchhHHHHH-HHHHH
Q 047404 86 N--KYSVFILFSITVSFLFEVLTLALLKDPAMKLTSGPYGLIFASFVPFYFDIPVSTRFRVFGVHFSDKSFIYL-AGLQL 162 (291)
Q Consensus 86 ~--kf~~~~l~~~~~s~ll~~~~~~~~~~~~~~~~~G~sg~ifal~~~~~~~~P~~~~~~i~g~~~~~k~~~~l-~~l~l 162 (291)
. +|+.|++++. .++.-+ .....++ ++--++..-++-|.|++++|+..+..+.++++..|++|++ +++.+
T Consensus 99 ~lv~Y~~yl~~~~---l~i~a~-s~I~gg~----saL~tsf~a~ItY~WS~~N~~~~Iqf~g~i~v~gkYlP~Illgfsf 170 (313)
T COG5291 99 SLVEYFWYLLVIS---LVIFAI-SNIYGGI----SALGTSFSATITYIWSKRNPRAIIQFFGFISVPGKYLPFILLGFSF 170 (313)
T ss_pred cHHHHHHHHHHHH---HHHHHH-HHHhcch----hhhcchhhhheeeeeeecCCceEEEEEEeeecchhhhhHHHHHHHH
Confidence 3 5555554332 222111 1111111 1222356667789999999998765555699999999995 57777
Q ss_pred HhcCCCchHHHHHHHHHhhHhhc--ccccCC--CC-CCccHHHHHHH
Q 047404 163 LISSLNRSLLPGMCGILAGSLYR--PNFFRI--RK-AKFPEFITSFF 204 (291)
Q Consensus 163 l~~~~~~s~~~~l~Gil~G~ly~--~~~~~~--~~-~~~P~~i~~~~ 204 (291)
+.. .+-.+..+.|+++||+.. .++.+. ++ ..+|-|+.+++
T Consensus 171 l~~--~g~~i~~vlGf~~g~~~h~~g~I~~mi~r~~~~t~~~~~~~~ 215 (313)
T COG5291 171 LSR--RGISIDDVLGFVVGHLFHYFGDIYPMIGRDILSTPCWVKKLF 215 (313)
T ss_pred Hhc--CCccceeeeeeeeccccccccchhhhhhcccCCCcccccccc
Confidence 653 345677889999998865 344432 12 33455554443
No 9
>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=99.61 E-value=8.6e-16 Score=125.80 Aligned_cols=133 Identities=29% Similarity=0.463 Sum_probs=93.5
Q ss_pred hhccchhhhhhhcccCChhHHHHHHHHHHHH-HHHhhhccchhHHHHHHHHHHHHHHHHHHHHHHhcCcccccCCChHHH
Q 047404 46 QNFRLWRLIVSGFAFSSAPELMFGLYLLYYF-RVFERQIGSNKYSVFILFSITVSFLFEVLTLALLKDPAMKLTSGPYGL 124 (291)
Q Consensus 46 ~~~q~WRLlT~~f~h~~~~~ll~n~~~ly~~-r~lEr~~Gs~kf~~~~l~~~~~s~ll~~~~~~~~~~~~~~~~~G~sg~ 124 (291)
+++|+||++|+.|.|.|..|+++|++.++.+ +.+||.+|++|+...++.+++.+++....... .. ....|+|+.
T Consensus 2 ~~~~~wrl~T~~f~h~~~~hl~~n~~~l~~~g~~lE~~~G~~~~~~~~l~~~~~~~l~~~~~~~----~~-~~~~G~Sg~ 76 (145)
T PF01694_consen 2 QNGQWWRLFTSPFVHANFLHLLFNLLALWFFGSLLERRLGSRRFLALYLLSGLLGSLLSLLFSP----PN-QPYVGASGA 76 (145)
T ss_dssp GCC-TTHHHHGGG--SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----S------SSHHH
T ss_pred CCCcchhhhHHHHHccCHHHHHHHHHHHHHhhhhHhhhccchHHHHHHHHHHHhhhhccccccc----cc-cccCCCccc
Confidence 6789999999999999999999999999987 78999999999999999999999887654321 11 257999999
Q ss_pred HHHHHHHHHhhcCccce-EEE--eeeecchhHHHHHHHHHHHh-cCCCchHHHHHHHHHhhHhhccc
Q 047404 125 IFASFVPFYFDIPVSTR-FRV--FGVHFSDKSFIYLAGLQLLI-SSLNRSLLPGMCGILAGSLYRPN 187 (291)
Q Consensus 125 ifal~~~~~~~~P~~~~-~~i--~g~~~~~k~~~~l~~l~ll~-~~~~~s~~~~l~Gil~G~ly~~~ 187 (291)
+++++..+....|.... ... ....+.... +.+.+.. ..+..+..+|++|+++|.+|...
T Consensus 77 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~hl~G~~~G~~~~~~ 139 (145)
T PF01694_consen 77 VFGLLGAFLFLYPQNKKRLRFIYLALVVPIIV----LVIILLLGFIPNISFLGHLGGFLAGLLYGFL 139 (145)
T ss_dssp HHHHHHHHHHHHHCCCCCS---HCCCCCCCCC----CCHHHCTSSSSTTTHHHHHHHHHHHHHHHHH
T ss_pred chHHHHHHHHHHhhccchhhcchHHHHHHHHH----HHHHHHHHHHHhHHHHHHHHHHHHHHHHHHH
Confidence 99999999888776532 111 001111111 1112221 14678999999999999998743
No 10
>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=99.40 E-value=2.4e-13 Score=85.92 Aligned_cols=37 Identities=32% Similarity=0.556 Sum_probs=34.3
Q ss_pred CCHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHHHHH
Q 047404 249 PPEDSIAMLVSMGFDRNSARQALVQARNDINAATNIL 285 (291)
Q Consensus 249 ~~~~~v~~l~~mGf~~~~~~~aL~~~~~~~~~A~~~l 285 (291)
.++++|++|++|||++++|++||++++||+|+|++||
T Consensus 1 i~~~~v~~L~~mGf~~~~~~~AL~~~~~nve~A~~~L 37 (37)
T PF00627_consen 1 IDEEKVQQLMEMGFSREQAREALRACNGNVERAVDWL 37 (37)
T ss_dssp SHHHHHHHHHHHTS-HHHHHHHHHHTTTSHHHHHHHH
T ss_pred CCHHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHhC
Confidence 3689999999999999999999999999999999997
No 11
>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=99.31 E-value=3.2e-12 Score=81.15 Aligned_cols=38 Identities=39% Similarity=0.649 Sum_probs=36.0
Q ss_pred CHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHHHHHHh
Q 047404 250 PEDSIAMLVSMGFDRNSARQALVQARNDINAATNILLE 287 (291)
Q Consensus 250 ~~~~v~~l~~mGf~~~~~~~aL~~~~~~~~~A~~~l~~ 287 (291)
++++|++|++|||++++|++||++++||+++|++||++
T Consensus 1 ~~~~v~~L~~mGf~~~~~~~AL~~~~~d~~~A~~~L~~ 38 (38)
T cd00194 1 DEEKLEQLLEMGFSREEARKALRATNNNVERAVEWLLE 38 (38)
T ss_pred CHHHHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHHhC
Confidence 47899999999999999999999999999999999984
No 12
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=99.31 E-value=3.3e-12 Score=80.58 Aligned_cols=37 Identities=38% Similarity=0.581 Sum_probs=35.3
Q ss_pred CHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHHHHHH
Q 047404 250 PEDSIAMLVSMGFDRNSARQALVQARNDINAATNILL 286 (291)
Q Consensus 250 ~~~~v~~l~~mGf~~~~~~~aL~~~~~~~~~A~~~l~ 286 (291)
++++|++|++|||++++|++||++++||+++|++||+
T Consensus 1 ~~~~v~~L~~mGf~~~~a~~aL~~~~~d~~~A~~~L~ 37 (37)
T smart00165 1 DEEKIDQLLEMGFSREEALKALRAANGNVERAAEYLL 37 (37)
T ss_pred CHHHHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHHC
Confidence 4789999999999999999999999999999999986
No 13
>KOG2289 consensus Rhomboid family proteins [Signal transduction mechanisms]
Probab=99.17 E-value=1e-11 Score=113.57 Aligned_cols=136 Identities=17% Similarity=0.263 Sum_probs=92.9
Q ss_pred HHHhhhccchhhhhhhcccCChhHHHHHHHHHHHH-HHHhhhccchhHHHHHHHHHHHHHHHHHHHHHHhcCcccccCCC
Q 047404 42 QDIFQNFRLWRLIVSGFAFSSAPELMFGLYLLYYF-RVFERQIGSNKYSVFILFSITVSFLFEVLTLALLKDPAMKLTSG 120 (291)
Q Consensus 42 ~~i~~~~q~WRLlT~~f~h~~~~~ll~n~~~ly~~-r~lEr~~Gs~kf~~~~l~~~~~s~ll~~~~~~~~~~~~~~~~~G 120 (291)
..+.+++|+||++|+.+.|.+..|+.+||+.+-.. -.+|+..|..|+...|+++++.+++++.+ .+++ ....|
T Consensus 111 ~~~~~r~E~WRllTym~LHaGi~HL~~N~~~ql~iGi~LE~~~G~~RiglIYl~gg~aGSlls~l-----~d~~-~~sVG 184 (316)
T KOG2289|consen 111 YKPVHRGELWRLLTYMWLHAGIFHLLLNMLSQLFIGIPLEQVHGFLRIGLIYLAGGVAGSLLSSL-----FDPN-SISVG 184 (316)
T ss_pred cChhhhchhHHHHHHHHHhcCHHHHHHHHHHHHhccccHHhhcCceEEeeehhhhhhhhHHHHHH-----hccC-Cceec
Confidence 35667899999999999999999999999876555 57999999999999999999999998664 2344 56899
Q ss_pred hHHHHHHHHHHHHhhcCccceEEEeeeecchh-HHHHHHHHHHHhc-CCCchHHHHHHHHHhhHhhc
Q 047404 121 PYGLIFASFVPFYFDIPVSTRFRVFGVHFSDK-SFIYLAGLQLLIS-SLNRSLLPGMCGILAGSLYR 185 (291)
Q Consensus 121 ~sg~ifal~~~~~~~~P~~~~~~i~g~~~~~k-~~~~l~~l~ll~~-~~~~s~~~~l~Gil~G~ly~ 185 (291)
+||.+||++..+..++=.+ +....=+..+. .+..++++.+-++ -+.....+|++|...|..+.
T Consensus 185 ASggvfaLlgA~Ls~l~~N--w~~m~~~~~~l~~ll~Ii~i~l~~G~~~~~~~~~h~gg~~~G~~~~ 249 (316)
T KOG2289|consen 185 ASGGVFALLGAHLSNLLTN--WTIMKNKFAALRTLLIIIFINLDLGFAPYVDNFAHIGGLLAGFLLG 249 (316)
T ss_pred ccHHHHHHHHHHHHHHHhh--HHHhcchHHHHHHHHHHHHHHHhhccccceeccccccccCCCcchh
Confidence 9999999998876543222 11111011111 1111223344332 22344566777777776654
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=98.85 E-value=3.2e-09 Score=81.85 Aligned_cols=83 Identities=28% Similarity=0.426 Sum_probs=65.2
Q ss_pred cchhhhhhhcccCChhHHHHHHHHHHH-HHHHhhhccchhHHHHHHHHHHHHHHHHHHHHHH----hcCccc--ccCCCh
Q 047404 49 RLWRLIVSGFAFSSAPELMFGLYLLYY-FRVFERQIGSNKYSVFILFSITVSFLFEVLTLAL----LKDPAM--KLTSGP 121 (291)
Q Consensus 49 q~WRLlT~~f~h~~~~~ll~n~~~ly~-~r~lEr~~Gs~kf~~~~l~~~~~s~ll~~~~~~~----~~~~~~--~~~~G~ 121 (291)
.+|+++|+.|++.++..++++.+.++. +|.+||.||+++++.|+.+..++++++..+.... ..+.++ ..-.|.
T Consensus 7 ~pWtl~T~~fve~~i~~~l~~~~~l~~~g~~lE~~WGs~E~lkFi~vv~~~tnl~~~~~~~~~y~i~~~~~~l~~~i~G~ 86 (99)
T PF08551_consen 7 YPWTLFTAGFVETNIIGLLFSLLTLFYGGRYLEPIWGSREFLKFILVVNVITNLLTFLLYLLLYAITGNESYLFVPISGF 86 (99)
T ss_pred ehHHHHHHHHHHhHHHHHHHHHHHHHHhhHHHHHhcChHHHHHHHHHHHHHhHHHHHHHHHHHHHHhCCCceeEEEecCc
Confidence 689999999999999999999987665 5999999999999999999888888775543322 223331 445777
Q ss_pred HHHHHHHHHH
Q 047404 122 YGLIFASFVP 131 (291)
Q Consensus 122 sg~ifal~~~ 131 (291)
++++.|+++.
T Consensus 87 ~~~~~g~lVa 96 (99)
T PF08551_consen 87 MGVLAGFLVA 96 (99)
T ss_pred HHhHhheEEE
Confidence 7887777654
No 15
>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=98.70 E-value=1.4e-08 Score=95.79 Aligned_cols=40 Identities=30% Similarity=0.469 Sum_probs=37.8
Q ss_pred CCHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHHHHHHhc
Q 047404 249 PPEDSIAMLVSMGFDRNSARQALVQARNDINAATNILLEA 288 (291)
Q Consensus 249 ~~~~~v~~l~~mGf~~~~~~~aL~~~~~~~~~A~~~l~~~ 288 (291)
..|+.|++||+|||+|++|++|||++.||.|||+|||+++
T Consensus 155 ~~e~~I~~i~eMGf~R~qV~~ALRAafNNPdRAVEYL~tG 194 (378)
T TIGR00601 155 ERETTIEEIMEMGYEREEVERALRAAFNNPDRAVEYLLTG 194 (378)
T ss_pred HHHHHHHHHHHhCCCHHHHHHHHHHHhCCHHHHHHHHHhC
Confidence 4588999999999999999999999999999999999975
No 16
>KOG2890 consensus Predicted membrane protein [Function unknown]
Probab=98.53 E-value=4.5e-07 Score=81.55 Aligned_cols=139 Identities=19% Similarity=0.202 Sum_probs=94.3
Q ss_pred ccchhhhhhhcccCChhHHHHHHHHHHHH-HHHhhhccchhHHHHHHHHHHHHHHH----HHHHHHHhcCccc--ccCCC
Q 047404 48 FRLWRLIVSGFAFSSAPELMFGLYLLYYF-RVFERQIGSNKYSVFILFSITVSFLF----EVLTLALLKDPAM--KLTSG 120 (291)
Q Consensus 48 ~q~WRLlT~~f~h~~~~~ll~n~~~ly~~-r~lEr~~Gs~kf~~~~l~~~~~s~ll----~~~~~~~~~~~~~--~~~~G 120 (291)
+.+|+++|+.|+-.+.++++.+...+-.+ +.+|+.||+.+++.|+.+.-...++. .++.+.++.+..+ ..-.|
T Consensus 65 ~~~WtliTs~fie~~vw~V~~sv~~L~v~G~~lEp~Wg~~e~lkff~ivn~~~~l~v~v~~~l~Y~it~n~v~L~~~i~G 144 (326)
T KOG2890|consen 65 FFPWTLITSGFIELNVWDVLVSVLTLSVGGKFLEPNWGSLELLKFFAIVNGSTTLVVLVPALLLYMITDNHVYLYIPIHG 144 (326)
T ss_pred hhhHHHHhcchhhhhHHHHHHHHHheeecceeeccCCCCHHHHHHHHHhhchhHHHHHHHHHHHHHHhcCceEEEEEecc
Confidence 58999999999999999999999887765 78999999999999886544333332 2222333333322 33789
Q ss_pred hHHHHHHHHHHHHhhcCccceEEEeeeecchhHHHHHH-----HHHHHhcCCCchHHHHHHHHHhhHhhcc
Q 047404 121 PYGLIFASFVPFYFDIPVSTRFRVFGVHFSDKSFIYLA-----GLQLLISSLNRSLLPGMCGILAGSLYRP 186 (291)
Q Consensus 121 ~sg~ifal~~~~~~~~P~~~~~~i~g~~~~~k~~~~l~-----~l~ll~~~~~~s~~~~l~Gil~G~ly~~ 186 (291)
..|++.++++.|.+..|+..+...---+++.+-+|.++ ++++.......++..-..|..+++.|..
T Consensus 145 ~~gilaGilVa~kQllpd~~il~~~~~r~~~~~lP~~~l~~~~il~i~~f~~f~~l~s~~~g~~~sWtYLR 215 (326)
T KOG2890|consen 145 TTGILAGILVAWKQLLPDTIILELKSGRFLYAHLPLLVLFLSLILSIITFLVFASLPSITFGVLVSWTYLR 215 (326)
T ss_pred chHHHHHHHHHHHHHcCceeEEeccchhhhhhhCCHHHHHHHHHHHHHHHHHhhhhHHHHHhhhhhhhhhe
Confidence 99999999999999999986544322333333344321 2222211122556666789999999983
No 17
>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]
Probab=98.35 E-value=4.1e-07 Score=82.67 Aligned_cols=41 Identities=29% Similarity=0.462 Sum_probs=38.5
Q ss_pred CCCHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHHHHHHhc
Q 047404 248 EPPEDSIAMLVSMGFDRNSARQALVQARNDINAATNILLEA 288 (291)
Q Consensus 248 ~~~~~~v~~l~~mGf~~~~~~~aL~~~~~~~~~A~~~l~~~ 288 (291)
...++.|+++|+|||+|+++++||+++-||.|||+|||+++
T Consensus 133 ~~~e~~V~~Im~MGy~re~V~~AlRAafNNPeRAVEYLl~G 173 (340)
T KOG0011|consen 133 SEYEQTVQQIMEMGYDREEVERALRAAFNNPERAVEYLLNG 173 (340)
T ss_pred chhHHHHHHHHHhCccHHHHHHHHHHhhCChhhhHHHHhcC
Confidence 36789999999999999999999999999999999999874
No 18
>KOG0944 consensus Ubiquitin-specific protease UBP14 [Posttranslational modification, protein turnover, chaperones]
Probab=98.33 E-value=4e-07 Score=89.29 Aligned_cols=42 Identities=38% Similarity=0.557 Sum_probs=39.9
Q ss_pred CCCCHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHHHHHHhc
Q 047404 247 IEPPEDSIAMLVSMGFDRNSARQALVQARNDINAATNILLEA 288 (291)
Q Consensus 247 ~~~~~~~v~~l~~mGf~~~~~~~aL~~~~~~~~~A~~~l~~~ 288 (291)
.+++++.|+.+++|||++++|++||+++|||||||+||+|++
T Consensus 632 ~~~~e~~v~si~smGf~~~qa~~aL~~~n~nveravDWif~h 673 (763)
T KOG0944|consen 632 REVDEESVASIVSMGFSRNQAIKALKATNNNVERAVDWIFSH 673 (763)
T ss_pred CCCChhHheeeeeecCcHHHHHHHHHhcCccHHHHHHHHHhc
Confidence 368999999999999999999999999999999999999975
No 19
>KOG2290 consensus Rhomboid family proteins [Signal transduction mechanisms]
Probab=98.33 E-value=2.1e-07 Score=87.59 Aligned_cols=128 Identities=18% Similarity=0.274 Sum_probs=89.5
Q ss_pred ccchhhhhhhcccCChhHHHHHHHHHHH-HHHHhhhccchhHHHHHHHHHHHHHHHHHHHHHHhcCcccccCCChHHHHH
Q 047404 48 FRLWRLIVSGFAFSSAPELMFGLYLLYY-FRVFERQIGSNKYSVFILFSITVSFLFEVLTLALLKDPAMKLTSGPYGLIF 126 (291)
Q Consensus 48 ~q~WRLlT~~f~h~~~~~ll~n~~~ly~-~r~lEr~~Gs~kf~~~~l~~~~~s~ll~~~~~~~~~~~~~~~~~G~sg~if 126 (291)
.|.+||.|+.|.|.+..|++..+.+=++ .|.+|...|+.|.+..|+.+++.+++.+-+.+ | |....||+|..|
T Consensus 449 dQfYRL~~SLFlHagviH~~vSi~FQm~vmrdlEkL~g~~riAIiy~~SGitGNLASAIFl-----p-Y~~eVgPa~sQ~ 522 (652)
T KOG2290|consen 449 DQFYRLWLSLFLHAGVIHLLVSICFQMTVMRDLEKLAGWHRIAIIYFLSGITGNLASAIFL-----P-YRAEVGPAGSQF 522 (652)
T ss_pred hHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHhhcchhhheeeecccccccchheeee-----c-cccccCCccccc
Confidence 4889999999999999999999977444 59999999999999999999999998754321 1 144577777777
Q ss_pred HHHHHHHhhcCccceEEEeeeecchhHHHHHHHHHHHh---cCCCchHHHHHHHHHhhHhhc
Q 047404 127 ASFVPFYFDIPVSTRFRVFGVHFSDKSFIYLAGLQLLI---SSLNRSLLPGMCGILAGSLYR 185 (291)
Q Consensus 127 al~~~~~~~~P~~~~~~i~g~~~~~k~~~~l~~l~ll~---~~~~~s~~~~l~Gil~G~ly~ 185 (291)
+++.....+.=.. .+++ .=+.+.+.-+++..|++ .-|.+..++|+.|.+.|++-.
T Consensus 523 Gila~l~vEl~qs--~~il--~~~w~a~~~Lia~~L~L~iGliPWiDN~aHlfG~i~GLl~s 580 (652)
T KOG2290|consen 523 GILACLFVELFQS--WQIL--ERPWRAFFHLIATLLVLCIGLIPWIDNWAHLFGTIFGLLTS 580 (652)
T ss_pred chHHHHHHHHHhh--hHhh--hhHHHHHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHH
Confidence 7776555433211 1111 11333443333332222 136688899999999998855
No 20
>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=98.14 E-value=2.3e-06 Score=80.98 Aligned_cols=44 Identities=27% Similarity=0.367 Sum_probs=40.7
Q ss_pred CCCCHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHHHHHHhcCC
Q 047404 247 IEPPEDSIAMLVSMGFDRNSARQALVQARNDINAATNILLEAQP 290 (291)
Q Consensus 247 ~~~~~~~v~~l~~mGf~~~~~~~aL~~~~~~~~~A~~~l~~~~~ 290 (291)
.+.+.|+|++|++|||+|+.|++|..+|+.|.|.|+||||++..
T Consensus 334 T~eE~~AIeRL~~LGF~r~~viqaY~ACdKNEelAAn~Lf~~~~ 377 (378)
T TIGR00601 334 TPEEKEAIERLCALGFDRGLVIQAYFACDKNEELAANYLLSQNF 377 (378)
T ss_pred CHHHHHHHHHHHHcCCCHHHHHHHHHhcCCcHHHHHHHHHhhcC
Confidence 45678999999999999999999999999999999999998754
No 21
>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=97.91 E-value=1.6e-05 Score=51.29 Aligned_cols=39 Identities=31% Similarity=0.443 Sum_probs=34.7
Q ss_pred CHHHHHHHHcC--CCCHHHHHHHHHHhCCCHHHHHHHHHhc
Q 047404 250 PEDSIAMLVSM--GFDRNSARQALVQARNDINAATNILLEA 288 (291)
Q Consensus 250 ~~~~v~~l~~m--Gf~~~~~~~aL~~~~~~~~~A~~~l~~~ 288 (291)
.++.|++|.+| .++++.++++|++++||+|+|++.|++.
T Consensus 1 ~~~~v~~L~~mFP~~~~~~I~~~L~~~~~~ve~ai~~LL~~ 41 (42)
T PF02845_consen 1 REEMVQQLQEMFPDLDREVIEAVLQANNGDVEAAIDALLEM 41 (42)
T ss_dssp CHHHHHHHHHHSSSS-HHHHHHHHHHTTTTHHHHHHHHHHH
T ss_pred CHHHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence 37899999999 5689999999999999999999999975
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=97.84 E-value=3.3e-05 Score=50.12 Aligned_cols=40 Identities=30% Similarity=0.373 Sum_probs=33.9
Q ss_pred HHHHHHHHc-CCCCHHHHHHHHHHhCCCHHHHHHHHHhcCC
Q 047404 251 EDSIAMLVS-MGFDRNSARQALVQARNDINAATNILLEAQP 290 (291)
Q Consensus 251 ~~~v~~l~~-mGf~~~~~~~aL~~~~~~~~~A~~~l~~~~~ 290 (291)
+|+|+++++ .|-+++.|++-|+++|||+|+|++..+++++
T Consensus 1 ~e~i~~F~~iTg~~~~~A~~~L~~~~wdle~Av~~y~~~~~ 41 (43)
T PF14555_consen 1 DEKIAQFMSITGADEDVAIQYLEANNWDLEAAVNAYFDDGE 41 (43)
T ss_dssp HHHHHHHHHHH-SSHHHHHHHHHHTTT-HHHHHHHHHHSS-
T ss_pred CHHHHHHHHHHCcCHHHHHHHHHHcCCCHHHHHHHHHhCCC
Confidence 578999888 6999999999999999999999999988654
No 23
>KOG0418 consensus Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.70 E-value=3.8e-05 Score=64.52 Aligned_cols=44 Identities=23% Similarity=0.241 Sum_probs=39.6
Q ss_pred CCCCCCHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHHHHHHhc
Q 047404 245 STIEPPEDSIAMLVSMGFDRNSARQALVQARNDINAATNILLEA 288 (291)
Q Consensus 245 ~~~~~~~~~v~~l~~mGf~~~~~~~aL~~~~~~~~~A~~~l~~~ 288 (291)
+....+..+|+.|.+|||+|++++.+|+..++|+++|++.++++
T Consensus 157 ~~~~~~~~~v~~l~~mGf~~~~~i~~L~~~~w~~~~a~~~~~s~ 200 (200)
T KOG0418|consen 157 PDDPWDKKKVDSLIEMGFSELEAILVLSGSDWNLADATEQLLSG 200 (200)
T ss_pred CCCchhHHHHHHHHHhcccHHHHHHHhhccccchhhhhHhhccC
Confidence 34456789999999999999999999999999999999998863
No 24
>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]
Probab=97.70 E-value=3.4e-05 Score=70.33 Aligned_cols=42 Identities=26% Similarity=0.347 Sum_probs=39.0
Q ss_pred CCCHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHHHHHHhcC
Q 047404 248 EPPEDSIAMLVSMGFDRNSARQALVQARNDINAATNILLEAQ 289 (291)
Q Consensus 248 ~~~~~~v~~l~~mGf~~~~~~~aL~~~~~~~~~A~~~l~~~~ 289 (291)
+.+.|+|+.|.+|||+|.-+++|.-+|+.|.|.|+||||++.
T Consensus 296 pee~eAIeRL~alGF~ralViqayfACdKNEelAAN~Ll~~~ 337 (340)
T KOG0011|consen 296 PEEKEAIERLEALGFPRALVIQAYFACDKNEELAANYLLSHS 337 (340)
T ss_pred HHHHHHHHHHHHhCCcHHHHHHHHHhcCccHHHHHHHHHhhc
Confidence 356889999999999999999999999999999999999863
No 25
>COG5207 UBP14 Isopeptidase T [Posttranslational modification, protein turnover, chaperones]
Probab=97.68 E-value=5.5e-05 Score=72.55 Aligned_cols=42 Identities=33% Similarity=0.423 Sum_probs=38.3
Q ss_pred CCCCHHHHHHHHcCCCCHHHHHHHHHHhCC-CHHHHHHHHHhc
Q 047404 247 IEPPEDSIAMLVSMGFDRNSARQALVQARN-DINAATNILLEA 288 (291)
Q Consensus 247 ~~~~~~~v~~l~~mGf~~~~~~~aL~~~~~-~~~~A~~~l~~~ 288 (291)
..+++..|+||++|||+.++|.+||-.++| |.|.|+||||++
T Consensus 555 ~t~Nqs~I~qL~~mGfp~~~~~rAL~~tgNqDaEsAMNWLFqH 597 (749)
T COG5207 555 FTDNQSLIRQLVDMGFPEEDAARALGITGNQDAESAMNWLFQH 597 (749)
T ss_pred cCchHHHHHHHHHcCCCHHHHHHHHhhccCcchHHHHHHHHhh
Confidence 556788999999999999999999999955 999999999974
No 26
>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=97.58 E-value=0.00017 Score=46.68 Aligned_cols=39 Identities=23% Similarity=0.385 Sum_probs=34.9
Q ss_pred CHHHHHHHHcC--CCCHHHHHHHHHHhCCCHHHHHHHHHhc
Q 047404 250 PEDSIAMLVSM--GFDRNSARQALVQARNDINAATNILLEA 288 (291)
Q Consensus 250 ~~~~v~~l~~m--Gf~~~~~~~aL~~~~~~~~~A~~~l~~~ 288 (291)
.++.+++|.+| ..+++.++++|++++||+|.|++.|++.
T Consensus 2 ~~~~v~~L~~mFP~l~~~~I~~~L~~~~g~ve~~i~~LL~~ 42 (43)
T smart00546 2 NDEALHDLKDMFPNLDEEVIKAVLEANNGNVEATINNLLEG 42 (43)
T ss_pred hHHHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence 47889999999 3379999999999999999999999875
No 27
>KOG0944 consensus Ubiquitin-specific protease UBP14 [Posttranslational modification, protein turnover, chaperones]
Probab=97.55 E-value=0.00011 Score=72.44 Aligned_cols=41 Identities=34% Similarity=0.497 Sum_probs=37.8
Q ss_pred CCCHHHHHHHHcCCCCHHHHHHHHHHh-CCCHHHHHHHHHhc
Q 047404 248 EPPEDSIAMLVSMGFDRNSARQALVQA-RNDINAATNILLEA 288 (291)
Q Consensus 248 ~~~~~~v~~l~~mGf~~~~~~~aL~~~-~~~~~~A~~~l~~~ 288 (291)
..++..|.||++|||++++|++||-.+ |.|.|.|.|||+++
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 367889999999999999999999999 78999999999874
No 28
>KOG0010 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones; General function prediction only]
Probab=97.46 E-value=0.00016 Score=69.36 Aligned_cols=42 Identities=40% Similarity=0.483 Sum_probs=37.8
Q ss_pred CCCCHHHHHHHHcCCC-CHHHHHHHHHHhCCCHHHHHHHHHhc
Q 047404 247 IEPPEDSIAMLVSMGF-DRNSARQALVQARNDINAATNILLEA 288 (291)
Q Consensus 247 ~~~~~~~v~~l~~mGf-~~~~~~~aL~~~~~~~~~A~~~l~~~ 288 (291)
.+..+..++||-+||| ||++..+||++++||+++|+|.|+.+
T Consensus 451 e~r~q~QLeQL~~MGF~nre~nlqAL~atgGdi~aAverll~s 493 (493)
T KOG0010|consen 451 EERYQTQLEQLNDMGFLDREANLQALRATGGDINAAVERLLGS 493 (493)
T ss_pred hHHHHHHHHHHHhcCCccHHHHHHHHHHhcCcHHHHHHHHhcC
Confidence 3456778999999999 89999999999999999999999853
No 29
>KOG2561 consensus Adaptor protein NUB1, contains UBA domain [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=97.37 E-value=0.00018 Score=68.16 Aligned_cols=42 Identities=29% Similarity=0.631 Sum_probs=38.9
Q ss_pred CCCCHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHHHHHHhc
Q 047404 247 IEPPEDSIAMLVSMGFDRNSARQALVQARNDINAATNILLEA 288 (291)
Q Consensus 247 ~~~~~~~v~~l~~mGf~~~~~~~aL~~~~~~~~~A~~~l~~~ 288 (291)
...+++++..+++|||.+.+||.||+.|+|||+.|++++.+.
T Consensus 300 lki~d~~lsllv~mGfeesdaRlaLRsc~g~Vd~AvqfI~er 341 (568)
T KOG2561|consen 300 LKINDETLSLLVGMGFEESDARLALRSCNGDVDSAVQFIIER 341 (568)
T ss_pred eeccchHHHHHHHcCCCchHHHHHHHhccccHHHHHHHHHHH
Confidence 456889999999999999999999999999999999999874
No 30
>KOG2561 consensus Adaptor protein NUB1, contains UBA domain [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=97.02 E-value=0.00087 Score=63.60 Aligned_cols=43 Identities=35% Similarity=0.409 Sum_probs=39.2
Q ss_pred CCCCHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHHHHHHhcC
Q 047404 247 IEPPEDSIAMLVSMGFDRNSARQALVQARNDINAATNILLEAQ 289 (291)
Q Consensus 247 ~~~~~~~v~~l~~mGf~~~~~~~aL~~~~~~~~~A~~~l~~~~ 289 (291)
.+++++++++|+.|||++..|+.||+..+||++.|...|..+-
T Consensus 426 ~~vd~~~la~Lv~mGF~e~~A~~ALe~~gnn~~~a~~~L~~s~ 468 (568)
T KOG2561|consen 426 EQVDGISLAELVSMGFEEGKARSALEAGGNNEDTAQRLLSASV 468 (568)
T ss_pred cccchhhHHHHHHhccccchHHHHHHhcCCcHHHHHHHHHHhC
Confidence 4468999999999999999999999999999999999987653
No 31
>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed
Probab=96.88 E-value=0.0022 Score=50.41 Aligned_cols=41 Identities=32% Similarity=0.484 Sum_probs=36.9
Q ss_pred CCCCHHHHHHHHc-CCCCHHHHHHHHHHhCCCHHHHHHHHHh
Q 047404 247 IEPPEDSIAMLVS-MGFDRNSARQALVQARNDINAATNILLE 287 (291)
Q Consensus 247 ~~~~~~~v~~l~~-mGf~~~~~~~aL~~~~~~~~~A~~~l~~ 287 (291)
...+++.|+.+++ -|-++++|++||..||||+-.|+-+|-+
T Consensus 73 ~~i~~edI~lv~~q~gvs~~~A~~AL~~~~gDl~~AI~~L~~ 114 (115)
T PRK06369 73 VEIPEEDIELVAEQTGVSEEEARKALEEANGDLAEAILKLSS 114 (115)
T ss_pred CCCCHHHHHHHHHHHCcCHHHHHHHHHHcCCcHHHHHHHHhc
Confidence 4678999999998 6999999999999999999999987754
No 32
>COG5207 UBP14 Isopeptidase T [Posttranslational modification, protein turnover, chaperones]
Probab=96.86 E-value=0.00043 Score=66.65 Aligned_cols=42 Identities=21% Similarity=0.257 Sum_probs=39.5
Q ss_pred CCCCCHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHHHHHHh
Q 047404 246 TIEPPEDSIAMLVSMGFDRNSARQALVQARNDINAATNILLE 287 (291)
Q Consensus 246 ~~~~~~~~v~~l~~mGf~~~~~~~aL~~~~~~~~~A~~~l~~ 287 (291)
+.+++|++++.|.||||+.+.||+||...|+|++|+++|.++
T Consensus 617 DkeVdE~~~~Slle~Gln~n~~Rkal~~~n~d~~r~V~w~~N 658 (749)
T COG5207 617 DKEVDESKARSLLENGLNPNLCRKALMDMNTDSKRRVVWCIN 658 (749)
T ss_pred cccccHHHHHHHHHcCCCHHHHHHHHHHccCCchheEEEEEe
Confidence 347899999999999999999999999999999999999887
No 33
>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=96.74 E-value=0.0013 Score=44.65 Aligned_cols=28 Identities=21% Similarity=0.374 Sum_probs=22.1
Q ss_pred CCCHHHHHHHHcCCCCHHHHHHHHHHhC
Q 047404 248 EPPEDSIAMLVSMGFDRNSARQALVQAR 275 (291)
Q Consensus 248 ~~~~~~v~~l~~mGf~~~~~~~aL~~~~ 275 (291)
-.+.+.|+++++|||+++++++||++-|
T Consensus 7 Gi~~~lVd~F~~mGF~~dkVvevlrrlg 34 (55)
T PF09288_consen 7 GIDKDLVDQFENMGFERDKVVEVLRRLG 34 (55)
T ss_dssp --SHHHHHHHHHHT--HHHHHHHHHHS-
T ss_pred CCCHHHHHHHHHcCCcHHHHHHHHHHhC
Confidence 3578999999999999999999999874
No 34
>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=96.72 E-value=0.003 Score=49.51 Aligned_cols=39 Identities=28% Similarity=0.383 Sum_probs=35.8
Q ss_pred CCCHHHHHHHHc-CCCCHHHHHHHHHHhCCCHHHHHHHHH
Q 047404 248 EPPEDSIAMLVS-MGFDRNSARQALVQARNDINAATNILL 286 (291)
Q Consensus 248 ~~~~~~v~~l~~-mGf~~~~~~~aL~~~~~~~~~A~~~l~ 286 (291)
+.+++.|+.+++ -|-++++|++||.+||||+-.|+-+|-
T Consensus 76 ~i~~eDI~lV~eq~gvs~e~A~~AL~~~~gDl~~AI~~L~ 115 (116)
T TIGR00264 76 EITEDDIELVMKQCNVSKEEARRALEECGGDLAEAIMKLE 115 (116)
T ss_pred CCCHHHHHHHHHHhCcCHHHHHHHHHHcCCCHHHHHHHhh
Confidence 589999999988 699999999999999999999998764
No 35
>COG1308 EGD2 Transcription factor homologous to NACalpha-BTF3 [Transcription]
Probab=96.23 E-value=0.0097 Score=46.98 Aligned_cols=40 Identities=28% Similarity=0.374 Sum_probs=35.5
Q ss_pred CCCCHHHHHHHHc-CCCCHHHHHHHHHHhCCCHHHHHHHHH
Q 047404 247 IEPPEDSIAMLVS-MGFDRNSARQALVQARNDINAATNILL 286 (291)
Q Consensus 247 ~~~~~~~v~~l~~-mGf~~~~~~~aL~~~~~~~~~A~~~l~ 286 (291)
...++|.|+-.++ -|-||++|++||..+|||+-.|+--|.
T Consensus 81 ~~i~eeDIkLV~eQa~VsreeA~kAL~e~~GDlaeAIm~L~ 121 (122)
T COG1308 81 SDISEEDIKLVMEQAGVSREEAIKALEEAGGDLAEAIMKLT 121 (122)
T ss_pred CCCCHHHHHHHHHHhCCCHHHHHHHHHHcCCcHHHHHHHhc
Confidence 3578999999888 799999999999999999999987663
No 36
>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=95.97 E-value=0.019 Score=37.55 Aligned_cols=42 Identities=33% Similarity=0.351 Sum_probs=33.8
Q ss_pred CCCCCHHHHHHHHc--CCCCHHHHHHHHHHhCCCHHHHHHHHHh
Q 047404 246 TIEPPEDSIAMLVS--MGFDRNSARQALVQARNDINAATNILLE 287 (291)
Q Consensus 246 ~~~~~~~~v~~l~~--mGf~~~~~~~aL~~~~~~~~~A~~~l~~ 287 (291)
...++||.|++-.. -|=+|+-+++-|+++|=|++.|+|-|++
T Consensus 5 a~~vPedlI~q~q~VLqgksR~vIirELqrTnLdVN~AvNNlLs 48 (53)
T PF11547_consen 5 ASQVPEDLINQAQVVLQGKSRNVIIRELQRTNLDVNLAVNNLLS 48 (53)
T ss_dssp GGGS-HHHHHHHHHHSTTS-HHHHHHHHHHTTT-HHHHHHHHHH
T ss_pred cccCCHHHHHHHHHHHcCCcHHHHHHHHHHhcccHHHHHHHHhc
Confidence 34567888888655 6999999999999999999999999886
No 37
>KOG2980 consensus Integral membrane protease of the rhomboid family involved in different forms of regulated intramembrane proteolysis [Signal transduction mechanisms]
Probab=95.59 E-value=0.011 Score=53.77 Aligned_cols=172 Identities=15% Similarity=0.158 Sum_probs=96.1
Q ss_pred hHHHHHHHHHHHHHHHhhhccccccccch-HHHhhhccchhhhhhhcccCChhHHHHHHHHHHHH--HHHhhhccchhHH
Q 047404 13 VTRAFVIACALFTVFFGIQGRFNKLGLSY-QDIFQNFRLWRLIVSGFAFSSAPELMFGLYLLYYF--RVFERQIGSNKYS 89 (291)
Q Consensus 13 VTk~li~~~~~~sl~~~~~~~~~~l~l~~-~~i~~~~q~WRLlT~~f~h~~~~~ll~n~~~ly~~--r~lEr~~Gs~kf~ 89 (291)
+...++++++.++.+......+....... .......-.|.++++.|.|-+..|+-.||+.++.+ ..+-...|...+-
T Consensus 117 ~v~~ll~~n~~vf~lWrv~~~~~~~~~~mls~~~~~t~~w~i~~s~Fsh~~a~h~g~~~~~~~~y~~~a~~~~~~~~~~~ 196 (310)
T KOG2980|consen 117 VVFGLLIANAFVFTLWRVPQKQFTMIPWMLSRNAYKTGCWKIILSTFSHYSALHLGPNMLVLKSYLAGALKGSLGFSSFF 196 (310)
T ss_pred chhHHHHHHHHHHHHHHhcchhhhhhhHHhhcccccccceeEEeehhcchhHhhhcHHHHHHHHHhcccccCCcchhhcc
Confidence 55567777777777654432211110000 11122345788999999999999988888766654 3555555555444
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCcccccCCChHHHHHHHHHHHHhhcCccceEEEeeeecchhH-HHH--HHHHHHH---
Q 047404 90 VFILFSITVSFLFEVLTLALLKDPAMKLTSGPYGLIFASFVPFYFDIPVSTRFRVFGVHFSDKS-FIY--LAGLQLL--- 163 (291)
Q Consensus 90 ~~~l~~~~~s~ll~~~~~~~~~~~~~~~~~G~sg~ifal~~~~~~~~P~~~~~~i~g~~~~~k~-~~~--l~~l~ll--- 163 (291)
.+++.+...+..+... ...... ......|++|.++++....+...|.++.+.++-.+++.-. +++ ++...+.
T Consensus 197 AlylSa~~~~~~i~~~-~~v~~~-~~gp~LGAsGav~ai~a~~~~lfP~~~~~i~f~~~v~~ga~~~~~~i~~~~~a~~~ 274 (310)
T KOG2980|consen 197 ALYLSAGVKGLFISVK-DKVPTS-WAGPSLGASGAVYAILALDCTLFPKTTLYILFVFPVPAGAGLAFKAIAAYDFAGLI 274 (310)
T ss_pred cceeccccccceeEee-cccccc-ccccccccchHHHHHHHHHhhcCcCcceeEEEeecccccchhHHHHHHHhhhccee
Confidence 4444333333322110 100000 1145689999999999999999998875555544444421 111 1111111
Q ss_pred hcCCCchHHHHHHHHHhhHhhcc
Q 047404 164 ISSLNRSLLPGMCGILAGSLYRP 186 (291)
Q Consensus 164 ~~~~~~s~~~~l~Gil~G~ly~~ 186 (291)
+.-+.....+|++|-+.|..|..
T Consensus 275 l~~~~~n~~Ah~~gsl~Gv~va~ 297 (310)
T KOG2980|consen 275 LGWGFFNHAAHLSGSLFGVVVAT 297 (310)
T ss_pred eccccchhHhhhcchHHHHHHHH
Confidence 11122334488888888888763
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=93.85 E-value=0.17 Score=34.77 Aligned_cols=37 Identities=19% Similarity=0.259 Sum_probs=30.1
Q ss_pred HHHHHHHc-CC-CCHHHHHHHHHHhCCCHHHHHHHHHhc
Q 047404 252 DSIAMLVS-MG-FDRNSARQALVQARNDINAATNILLEA 288 (291)
Q Consensus 252 ~~v~~l~~-mG-f~~~~~~~aL~~~~~~~~~A~~~l~~~ 288 (291)
.-||.+.| -| .+++++-..|+.||.|.+.|++.|++.
T Consensus 7 k~VQ~iKEiv~~hse~eIya~L~ecnMDpnea~qrLL~q 45 (60)
T PF06972_consen 7 KTVQSIKEIVGCHSEEEIYAMLKECNMDPNEAVQRLLSQ 45 (60)
T ss_pred HHHHHHHHHhcCCCHHHHHHHHHHhCCCHHHHHHHHHhc
Confidence 34555555 23 699999999999999999999999974
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=93.59 E-value=0.094 Score=39.24 Aligned_cols=35 Identities=23% Similarity=0.336 Sum_probs=29.9
Q ss_pred HHHHHcCCCCHHHHHHHHHHhCCCHHHHHHHHHhc
Q 047404 254 IAMLVSMGFDRNSARQALVQARNDINAATNILLEA 288 (291)
Q Consensus 254 v~~l~~mGf~~~~~~~aL~~~~~~~~~A~~~l~~~ 288 (291)
|+.+.+.|++++.+.+||.+|.+|++.|..++++.
T Consensus 1 i~~~~~~g~~~~~v~~aL~~tSgd~~~a~~~vl~~ 35 (87)
T PF11626_consen 1 IKHYEELGYSREFVTHALYATSGDPELARRFVLNF 35 (87)
T ss_dssp -HHHHHHTB-HHHHHHHHHHTTTBHHHHHHHHHHC
T ss_pred CchHHHhCCCHHHHHHHHHHhCCCHHHHHHHHHHH
Confidence 45678899999999999999999999999987764
No 40
>COG4008 Predicted metal-binding transcription factor [Transcription]
Probab=93.53 E-value=0.18 Score=40.06 Aligned_cols=40 Identities=33% Similarity=0.442 Sum_probs=36.0
Q ss_pred CCCCHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHHHHHHh
Q 047404 247 IEPPEDSIAMLVSMGFDRNSARQALVQARNDINAATNILLE 287 (291)
Q Consensus 247 ~~~~~~~v~~l~~mGf~~~~~~~aL~~~~~~~~~A~~~l~~ 287 (291)
.+++.|.|+-+.+-|.+.++|++||..+| |+-+|+++|..
T Consensus 111 s~~~~e~v~v~a~a~v~~eeAr~aleeag-Dl~~A~k~l~~ 150 (153)
T COG4008 111 SEPPVEEVEVLADAFVTPEEAREALEEAG-DLRTAMKILRM 150 (153)
T ss_pred CCCcHHHHHHHHHhcCCHHHHHHHHHHcC-CHHHHHHHHHH
Confidence 45678999999999999999999999997 99999998754
No 41
>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=92.68 E-value=0.041 Score=35.94 Aligned_cols=27 Identities=30% Similarity=0.528 Sum_probs=18.8
Q ss_pred CHHHHHHHHc-CCCCHHHHHHHHHHhCC
Q 047404 250 PEDSIAMLVS-MGFDRNSARQALVQARN 276 (291)
Q Consensus 250 ~~~~v~~l~~-mGf~~~~~~~aL~~~~~ 276 (291)
+++.|..|.. |||+|+++..||++...
T Consensus 2 de~vv~~Ls~tMGY~kdeI~eaL~~~~~ 29 (46)
T PF08587_consen 2 DEDVVSKLSKTMGYDKDEIYEALESSEP 29 (46)
T ss_dssp -HCCHHHHHCTT---HHHHHHHCCSSS-
T ss_pred cHHHHHHHHHHhCCCHHHHHHHHHcCCC
Confidence 5677888877 99999999999988543
No 42
>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=92.21 E-value=0.099 Score=34.38 Aligned_cols=25 Identities=28% Similarity=0.601 Sum_probs=22.1
Q ss_pred CHHHHHHHHcCCCCHHHHHHHHHHh
Q 047404 250 PEDSIAMLVSMGFDRNSARQALVQA 274 (291)
Q Consensus 250 ~~~~v~~l~~mGf~~~~~~~aL~~~ 274 (291)
.+|.++.|+++||++.++.+|+++.
T Consensus 3 ~~d~~~AL~~LGy~~~e~~~av~~~ 27 (47)
T PF07499_consen 3 LEDALEALISLGYSKAEAQKAVSKL 27 (47)
T ss_dssp HHHHHHHHHHTTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHh
Confidence 4788999999999999999999988
No 43
>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=89.74 E-value=0.91 Score=31.87 Aligned_cols=39 Identities=13% Similarity=0.207 Sum_probs=30.7
Q ss_pred CCHHHHHHHHc-CCCCHHHHHHHHHHhCCCHHHHHHHHHh
Q 047404 249 PPEDSIAMLVS-MGFDRNSARQALVQARNDINAATNILLE 287 (291)
Q Consensus 249 ~~~~~v~~l~~-mGf~~~~~~~aL~~~~~~~~~A~~~l~~ 287 (291)
..++.|.++.+ -|-..+=++++|..+|||.++|+.-..+
T Consensus 11 ~q~~~v~~~~~~Tgmn~~~s~~cLe~~~Wd~~~Al~~F~~ 50 (63)
T smart00804 11 EQQEMVQAFSAQTGMNAEYSQMCLEDNNWDYERALKNFTE 50 (63)
T ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 34555555554 5899999999999999999999986544
No 44
>PF08938 HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This domain is found in various eukaryotic HBS1-like proteins. ; PDB: 1UFZ_A 3IZQ_1.
Probab=88.83 E-value=0.21 Score=36.66 Aligned_cols=27 Identities=22% Similarity=0.229 Sum_probs=23.3
Q ss_pred CHHHHHHHHHHhCCCHHHHHHHHHhcC
Q 047404 263 DRNSARQALVQARNDINAATNILLEAQ 289 (291)
Q Consensus 263 ~~~~~~~aL~~~~~~~~~A~~~l~~~~ 289 (291)
++.+.++||-.++.|+++|+++|+++.
T Consensus 45 ~e~~i~eal~~~~fDvekAl~~Ll~~~ 71 (79)
T PF08938_consen 45 PEEQIKEALWHYYFDVEKALDYLLSKF 71 (79)
T ss_dssp -CCHHHHHHHHTTT-CCHHHHHHHHCC
T ss_pred CHHHHHHHHHHHcCCHHHHHHHHHHhc
Confidence 888999999999999999999999864
No 45
>KOG1071 consensus Mitochondrial translation elongation factor EF-Tsmt, catalyzes nucleotide exchange on EF-Tumt [Translation, ribosomal structure and biogenesis]
Probab=88.00 E-value=0.92 Score=41.77 Aligned_cols=40 Identities=18% Similarity=0.195 Sum_probs=35.9
Q ss_pred CCHHHHHHHHc-CCCCHHHHHHHHHHhCCCHHHHHHHHHhc
Q 047404 249 PPEDSIAMLVS-MGFDRNSARQALVQARNDINAATNILLEA 288 (291)
Q Consensus 249 ~~~~~v~~l~~-mGf~~~~~~~aL~~~~~~~~~A~~~l~~~ 288 (291)
...+.|.+|-+ -|++-..|++||..||||+..|-+||-+.
T Consensus 45 ~~~allk~LR~kTgas~~ncKkALee~~gDl~~A~~~L~k~ 85 (340)
T KOG1071|consen 45 SSKALLKKLREKTGASMVNCKKALEECGGDLVLAEEWLHKK 85 (340)
T ss_pred ccHHHHHHHHHHcCCcHHHHHHHHHHhCCcHHHHHHHHHHH
Confidence 46788999887 79999999999999999999999999653
No 46
>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=87.58 E-value=0.81 Score=28.86 Aligned_cols=24 Identities=21% Similarity=0.270 Sum_probs=20.6
Q ss_pred CHHHHHHHHHHhCCCHHHHHHHHH
Q 047404 263 DRNSARQALVQARNDINAATNILL 286 (291)
Q Consensus 263 ~~~~~~~aL~~~~~~~~~A~~~l~ 286 (291)
.|+.-...|+.||||+-+|+|.++
T Consensus 16 kr~~Le~iL~~C~GDvv~AIE~~l 39 (39)
T PF03474_consen 16 KRSVLELILQRCNGDVVQAIEQFL 39 (39)
T ss_pred ChHHHHHHHHHcCCcHHHHHHHhC
Confidence 567788899999999999999753
No 47
>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=87.39 E-value=0.52 Score=30.05 Aligned_cols=24 Identities=29% Similarity=0.548 Sum_probs=20.0
Q ss_pred CCHHHHHHHHHHhCCCHHHHHHHH
Q 047404 262 FDRNSARQALVQARNDINAATNIL 285 (291)
Q Consensus 262 f~~~~~~~aL~~~~~~~~~A~~~l 285 (291)
|+++-.++||..++||+.+|++.|
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 457788999999999999999875
No 48
>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=86.45 E-value=0.61 Score=43.96 Aligned_cols=27 Identities=33% Similarity=0.589 Sum_probs=22.4
Q ss_pred CCCHHHHHHHHcCCCCHHHHHHHHHHh
Q 047404 248 EPPEDSIAMLVSMGFDRNSARQALVQA 274 (291)
Q Consensus 248 ~~~~~~v~~l~~mGf~~~~~~~aL~~~ 274 (291)
.+-+|-||+++.|||.||.++...++.
T Consensus 319 ~p~ddvidKv~~MGf~rDqV~a~v~rl 345 (358)
T PF07223_consen 319 HPYDDVIDKVASMGFRRDQVRATVRRL 345 (358)
T ss_pred CcHHHHHHHHHHcCCcHHHHHHHHHHH
Confidence 346899999999999999998766554
No 49
>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=81.58 E-value=1.6 Score=29.23 Aligned_cols=36 Identities=14% Similarity=0.192 Sum_probs=26.4
Q ss_pred HHHHHHHc-CCCCHHHHHHHHHHhCCCHHHHHHHHHh
Q 047404 252 DSIAMLVS-MGFDRNSARQALVQARNDINAATNILLE 287 (291)
Q Consensus 252 ~~v~~l~~-mGf~~~~~~~aL~~~~~~~~~A~~~l~~ 287 (291)
|-|.++.. -|-+.+=+.++|..++||.++|+.-..+
T Consensus 2 ~mv~~~s~~Tgmn~~~s~~CL~~n~Wd~~~A~~~F~~ 38 (51)
T PF03943_consen 2 EMVQQFSQQTGMNLEWSQKCLEENNWDYERALQNFEE 38 (51)
T ss_dssp HHHHHHHHHCSS-CCHHHHHHHHTTT-CCHHHHHHHH
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 34455544 5788889999999999999999986554
No 50
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=80.52 E-value=3.6 Score=35.57 Aligned_cols=34 Identities=18% Similarity=0.406 Sum_probs=27.5
Q ss_pred CHHHHHHHHcCCCCHHHHHHHHHHh-----CCCHHHHHH
Q 047404 250 PEDSIAMLVSMGFDRNSARQALVQA-----RNDINAATN 283 (291)
Q Consensus 250 ~~~~v~~l~~mGf~~~~~~~aL~~~-----~~~~~~A~~ 283 (291)
.+|.++.|+++||++++|.+|+++. +.|+|..+.
T Consensus 152 ~~ea~~AL~~LGy~~~ea~~al~~i~~~~~~~~~e~lir 190 (197)
T PRK14603 152 AEDAVLALLALGFREAQVRSVVAELLAQNPEASAQTLIR 190 (197)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCHHHHHH
Confidence 4789999999999999999999986 235555443
No 51
>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=80.41 E-value=2.6 Score=36.24 Aligned_cols=26 Identities=27% Similarity=0.498 Sum_probs=23.5
Q ss_pred CHHHHHHHHcCCCCHHHHHHHHHHhC
Q 047404 250 PEDSIAMLVSMGFDRNSARQALVQAR 275 (291)
Q Consensus 250 ~~~~v~~l~~mGf~~~~~~~aL~~~~ 275 (291)
.+|.++.|.++||++++|.+|+.+..
T Consensus 147 ~~e~~~aL~~LGy~~~e~~~ai~~~~ 172 (191)
T TIGR00084 147 RDELFEALVSLGYKPQEIQQALKKIK 172 (191)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHh
Confidence 47899999999999999999999873
No 52
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=80.36 E-value=2.9 Score=35.93 Aligned_cols=26 Identities=31% Similarity=0.512 Sum_probs=23.8
Q ss_pred CHHHHHHHHcCCCCHHHHHHHHHHhC
Q 047404 250 PEDSIAMLVSMGFDRNSARQALVQAR 275 (291)
Q Consensus 250 ~~~~v~~l~~mGf~~~~~~~aL~~~~ 275 (291)
.+|.++.|+++||++++|++|+++..
T Consensus 143 ~~e~~~AL~~LGy~~~ea~~av~~~~ 168 (188)
T PRK14606 143 YHESLEALVSLGYPEKQAREAVKHVY 168 (188)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHh
Confidence 47899999999999999999999883
No 53
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=79.89 E-value=3.9 Score=35.54 Aligned_cols=25 Identities=28% Similarity=0.485 Sum_probs=23.4
Q ss_pred CHHHHHHHHcCCCCHHHHHHHHHHh
Q 047404 250 PEDSIAMLVSMGFDRNSARQALVQA 274 (291)
Q Consensus 250 ~~~~v~~l~~mGf~~~~~~~aL~~~ 274 (291)
.+|.++.|+++||++.+|.+|+.+.
T Consensus 155 ~~ea~~AL~~LGy~~~ea~~av~~~ 179 (203)
T PRK14602 155 FRDALAGLANLGYGEEEARPVLKEV 179 (203)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 4789999999999999999999988
No 54
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=79.74 E-value=3.8 Score=35.13 Aligned_cols=33 Identities=21% Similarity=0.475 Sum_probs=27.0
Q ss_pred CHHHHHHHHcCCCCHHHHHHHHHHhCC--CHHHHH
Q 047404 250 PEDSIAMLVSMGFDRNSARQALVQARN--DINAAT 282 (291)
Q Consensus 250 ~~~~v~~l~~mGf~~~~~~~aL~~~~~--~~~~A~ 282 (291)
.+|.++.|+++||++++|++|+++... |+|..+
T Consensus 145 ~~e~~~aL~~LGy~~~ea~~al~~v~~~~~~eeli 179 (186)
T PRK14600 145 NDDALAALISLGYEKTKAFNAIQKIKPNLSTQDII 179 (186)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhhcCCCHHHHH
Confidence 478999999999999999999998743 455443
No 55
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=79.46 E-value=3.2 Score=35.88 Aligned_cols=25 Identities=20% Similarity=0.403 Sum_probs=23.2
Q ss_pred CHHHHHHHHcCCCCHHHHHHHHHHh
Q 047404 250 PEDSIAMLVSMGFDRNSARQALVQA 274 (291)
Q Consensus 250 ~~~~v~~l~~mGf~~~~~~~aL~~~ 274 (291)
.+|.++.|+++||++++|.+|+.+.
T Consensus 149 ~~e~~~aL~~LGy~~~ea~~ai~~i 173 (195)
T PRK14604 149 DRELSEILISLGYSAAEAAAAIAAL 173 (195)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 4789999999999999999999887
No 56
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=78.49 E-value=4.6 Score=34.56 Aligned_cols=33 Identities=15% Similarity=0.389 Sum_probs=26.8
Q ss_pred CHHHHHHHHcCCCCHHHHHHHHHHhC-CCHHHHH
Q 047404 250 PEDSIAMLVSMGFDRNSARQALVQAR-NDINAAT 282 (291)
Q Consensus 250 ~~~~v~~l~~mGf~~~~~~~aL~~~~-~~~~~A~ 282 (291)
.+|.++.|+++||++.+|++|+++.. .|+|..+
T Consensus 142 ~~ea~~AL~~LGy~~~ea~~a~~~~~~~~~eeli 175 (183)
T PRK14601 142 KSEALAALLTLGFKQEKIIKVLASCQSTGTSELI 175 (183)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhcccCCHHHHH
Confidence 47899999999999999999999873 3455433
No 57
>PF11372 DUF3173: Domain of unknown function (DUF3173); InterPro: IPR021512 This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=76.13 E-value=2.9 Score=28.94 Aligned_cols=21 Identities=33% Similarity=0.626 Sum_probs=18.3
Q ss_pred HHHHcCCCCHHHHHHHHHHhC
Q 047404 255 AMLVSMGFDRNSARQALVQAR 275 (291)
Q Consensus 255 ~~l~~mGf~~~~~~~aL~~~~ 275 (291)
+.|++|||++.+|++-++++.
T Consensus 7 ~dLi~lGf~~~tA~~IIrqAK 27 (59)
T PF11372_consen 7 KDLIELGFSESTARDIIRQAK 27 (59)
T ss_pred HHHHHcCCCHHHHHHHHHHHH
Confidence 568999999999999988873
No 58
>KOG2239 consensus Transcription factor containing NAC and TS-N domains [Transcription]
Probab=73.87 E-value=4.5 Score=34.80 Aligned_cols=35 Identities=29% Similarity=0.305 Sum_probs=28.2
Q ss_pred CHHHHHHHHc-CCCCHHHHHHHHHHhCCCHHHHHHH
Q 047404 250 PEDSIAMLVS-MGFDRNSARQALVQARNDINAATNI 284 (291)
Q Consensus 250 ~~~~v~~l~~-mGf~~~~~~~aL~~~~~~~~~A~~~ 284 (291)
+++.|+..+. .+-+|.+|++||+.++||+-.|+=-
T Consensus 171 e~kDIeLVmsQanvSR~kAVkALk~~~~DiVnAIM~ 206 (209)
T KOG2239|consen 171 EAKDIELVMSQANVSRAKAVKALKNNNNDIVNAIME 206 (209)
T ss_pred chhhHHHHHHHhhhhHHHHHHHHHhccchHHHHHHH
Confidence 4455666665 6899999999999999999888743
No 59
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=73.57 E-value=4.5 Score=35.12 Aligned_cols=27 Identities=19% Similarity=0.476 Sum_probs=22.9
Q ss_pred CHHHHHHHHcCCCCHHHHHHHHHHhCC
Q 047404 250 PEDSIAMLVSMGFDRNSARQALVQARN 276 (291)
Q Consensus 250 ~~~~v~~l~~mGf~~~~~~~aL~~~~~ 276 (291)
.++.++.|+++||+++++++|+++..-
T Consensus 156 ~~~~v~AL~~LGy~~~e~~~av~~v~~ 182 (201)
T COG0632 156 LEEAVEALVALGYKEKEIKKAVKKVLK 182 (201)
T ss_pred hhHHHHHHHHcCCCHHHHHHHHHHHHh
Confidence 345599999999999999999988753
No 60
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=72.88 E-value=4.1 Score=35.22 Aligned_cols=26 Identities=27% Similarity=0.387 Sum_probs=23.5
Q ss_pred CHHHHHHHHcCCCCHHHHHHHHHHhC
Q 047404 250 PEDSIAMLVSMGFDRNSARQALVQAR 275 (291)
Q Consensus 250 ~~~~v~~l~~mGf~~~~~~~aL~~~~ 275 (291)
.+|.++.|+++||++++|.+|++..-
T Consensus 144 ~~ea~~AL~~LGy~~~ea~~al~~v~ 169 (196)
T PRK13901 144 FKELEQSIVNMGFDRKLVNSAIKEIM 169 (196)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHh
Confidence 47899999999999999999998873
No 61
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=65.52 E-value=14 Score=31.79 Aligned_cols=34 Identities=18% Similarity=0.324 Sum_probs=27.6
Q ss_pred CHHHHHHHHcCCCCHHHHHHHHHHhC----CCHHHHHH
Q 047404 250 PEDSIAMLVSMGFDRNSARQALVQAR----NDINAATN 283 (291)
Q Consensus 250 ~~~~v~~l~~mGf~~~~~~~aL~~~~----~~~~~A~~ 283 (291)
.+|.+..|.++||++++|.+|+.+.. .|++..+.
T Consensus 148 ~~e~~~aL~~LGy~~~~a~~ai~~~~~~~~~~~~~~ir 185 (194)
T PRK14605 148 NSDILATLTALGYSSSEAAKAISSLGDNGDLPLEERIK 185 (194)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhhccCCCCHHHHHH
Confidence 47899999999999999999999884 25555544
No 62
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=62.54 E-value=16 Score=39.89 Aligned_cols=46 Identities=28% Similarity=0.307 Sum_probs=38.5
Q ss_pred CCCCCCCCCHHHHHHHHc--CCCCHHHHHHHHHHhCCCHHHHHHHHHh
Q 047404 242 PVPSTIEPPEDSIAMLVS--MGFDRNSARQALVQARNDINAATNILLE 287 (291)
Q Consensus 242 ~~~~~~~~~~~~v~~l~~--mGf~~~~~~~aL~~~~~~~~~A~~~l~~ 287 (291)
|.-|...++||-|.+... -|=+|+-+++-|+++|=||+.|+|-|++
T Consensus 181 PriPAsniPEELInnaQqVLQGKSRdVIIRELQRTgLdVNeAVNNLLS 228 (3015)
T KOG0943|consen 181 PRIPASNIPEELINNAQQVLQGKSRDVIIRELQRTGLDVNEAVNNLLS 228 (3015)
T ss_pred CcCCcccCcHHHHHHHHHHHhCCchhHHHHHHHHhCCcHHHHHHhhhc
Confidence 344566778988876544 6999999999999999999999999986
No 63
>KOG3450 consensus Huntingtin interacting protein HYPK [General function prediction only]
Probab=58.02 E-value=14 Score=28.60 Aligned_cols=43 Identities=12% Similarity=0.307 Sum_probs=37.3
Q ss_pred CCCCCCHHHHHHHHc-CCCCHHHHHHHHHHhCCCHHHHHHHHHh
Q 047404 245 STIEPPEDSIAMLVS-MGFDRNSARQALVQARNDINAATNILLE 287 (291)
Q Consensus 245 ~~~~~~~~~v~~l~~-mGf~~~~~~~aL~~~~~~~~~A~~~l~~ 287 (291)
+......|.++-+|. |-.++..|++-|+.++||+-.|+.-|++
T Consensus 75 akV~IkkeDlelImnELei~k~~aer~LrE~~Gdvv~Alral~s 118 (119)
T KOG3450|consen 75 AKVTIKKEDLELIMNELEISKAAAERSLREHMGDVVEALRALTS 118 (119)
T ss_pred cccccCHHHHHHHHHHHHHHHHHHHHHHHHhcccHHHHHHHHhc
Confidence 556778888888774 8889999999999999999999988765
No 64
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=54.99 E-value=19 Score=30.84 Aligned_cols=34 Identities=18% Similarity=0.418 Sum_probs=28.0
Q ss_pred CHHHHHHHHcCCCCHHHHHHHHHHhCC---CHHHHHH
Q 047404 250 PEDSIAMLVSMGFDRNSARQALVQARN---DINAATN 283 (291)
Q Consensus 250 ~~~~v~~l~~mGf~~~~~~~aL~~~~~---~~~~A~~ 283 (291)
.+|.++.|.++||++++|.+|+++.+. |+|..+.
T Consensus 149 ~~ev~~aL~~LG~~~~~a~~~~~~~~~~~~~~~~~i~ 185 (192)
T PRK00116 149 LEEAVSALVALGYKPKEASKAVAKILKEAASVEELIR 185 (192)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHhccCCCHHHHHH
Confidence 478999999999999999999998853 5665443
No 65
>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=54.36 E-value=18 Score=25.48 Aligned_cols=24 Identities=17% Similarity=0.445 Sum_probs=20.3
Q ss_pred CHHHHHHHHcCCCCHHHHHHHHHH
Q 047404 250 PEDSIAMLVSMGFDRNSARQALVQ 273 (291)
Q Consensus 250 ~~~~v~~l~~mGf~~~~~~~aL~~ 273 (291)
-+.+++.+..|||++++++..|++
T Consensus 11 ~daA~dam~~lG~~~~~v~~vl~~ 34 (65)
T PF10440_consen 11 IDAALDAMRQLGFSKKQVRPVLKN 34 (65)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHH
Confidence 467888899999999999888765
No 66
>PRK05441 murQ N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=52.57 E-value=23 Score=32.56 Aligned_cols=31 Identities=26% Similarity=0.403 Sum_probs=21.7
Q ss_pred HHc-CCCCHHHHHHHHHHhCCCHHHHHHHHHh
Q 047404 257 LVS-MGFDRNSARQALVQARNDINAATNILLE 287 (291)
Q Consensus 257 l~~-mGf~~~~~~~aL~~~~~~~~~A~~~l~~ 287 (291)
+++ .|-++++|+++|.+++|++-.|+-.++.
T Consensus 242 ~~~~~~~~~~~a~~~l~~~~~~vk~a~~~~~~ 273 (299)
T PRK05441 242 VMEATGVSREEAEAALEAADGSVKLAIVMILT 273 (299)
T ss_pred HHHHHCcCHHHHHHHHHHhCCCcHHHHHHHHh
Confidence 444 5778888888888888777777665443
No 67
>PRK07634 pyrroline-5-carboxylate reductase; Reviewed
Probab=51.72 E-value=29 Score=30.31 Aligned_cols=34 Identities=26% Similarity=0.431 Sum_probs=26.1
Q ss_pred HHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHHHHHHh
Q 047404 251 EDSIAMLVSMGFDRNSARQALVQARNDINAATNILLE 287 (291)
Q Consensus 251 ~~~v~~l~~mGf~~~~~~~aL~~~~~~~~~A~~~l~~ 287 (291)
+.-++..+++|+++++|++.+..+ +..+++.+.+
T Consensus 186 ~a~~~~~~~~Gl~~~~a~~~~~~~---~~g~~~~~~~ 219 (245)
T PRK07634 186 ESLIEATKSYGVDEETAKHLVIQM---ISGSASMLEQ 219 (245)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHH---HHHHHHHHhC
Confidence 566777889999999999999887 4555555543
No 68
>PRK08769 DNA polymerase III subunit delta'; Validated
Probab=51.65 E-value=26 Score=32.61 Aligned_cols=38 Identities=29% Similarity=0.390 Sum_probs=32.8
Q ss_pred CHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHHHHHHh
Q 047404 250 PEDSIAMLVSMGFDRNSARQALVQARNDINAATNILLE 287 (291)
Q Consensus 250 ~~~~v~~l~~mGf~~~~~~~aL~~~~~~~~~A~~~l~~ 287 (291)
.++..+-|.+-|.+++++..+++.++|++.+|.+++-+
T Consensus 174 ~~~~~~~L~~~~~~~~~a~~~~~l~~G~p~~A~~~~~~ 211 (319)
T PRK08769 174 AHEALAWLLAQGVSERAAQEALDAARGHPGLAAQWLRE 211 (319)
T ss_pred HHHHHHHHHHcCCChHHHHHHHHHcCCCHHHHHHHhcC
Confidence 46777788888999999999999999999999987643
No 69
>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=49.04 E-value=36 Score=22.50 Aligned_cols=30 Identities=20% Similarity=0.148 Sum_probs=23.3
Q ss_pred HcCCCCHHHHHHHHHHhCCCHHHHHHHHHh
Q 047404 258 VSMGFDRNSARQALVQARNDINAATNILLE 287 (291)
Q Consensus 258 ~~mGf~~~~~~~aL~~~~~~~~~A~~~l~~ 287 (291)
.....+..-..+=|++.++|++.|.+.|-+
T Consensus 25 ~~~~~~d~~llRFLRARkf~v~~A~~mL~~ 54 (55)
T PF03765_consen 25 EKEDHDDNFLLRFLRARKFDVEKAFKMLKK 54 (55)
T ss_dssp HTSS-SHHHHHHHHHHTTT-HHHHHHHHHH
T ss_pred ccCCCCHHHHHHHHHHccCCHHHHHHHHHh
Confidence 334568889999999999999999998753
No 70
>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=48.49 E-value=28 Score=32.73 Aligned_cols=33 Identities=33% Similarity=0.448 Sum_probs=27.0
Q ss_pred HHHHHHcCC--CCHHHHHHHHHHhCCCHHHHHHHH
Q 047404 253 SIAMLVSMG--FDRNSARQALVQARNDINAATNIL 285 (291)
Q Consensus 253 ~v~~l~~mG--f~~~~~~~aL~~~~~~~~~A~~~l 285 (291)
.|++.|+=| |+++-|..|++++.||+.+|+=.|
T Consensus 44 avdrVMsEgsLYdp~LAAlAiKQa~GD~~EAiFLL 78 (358)
T PF05861_consen 44 AVDRVMSEGSLYDPELAALAIKQARGDLIEAIFLL 78 (358)
T ss_pred HHHHHhccccccCHHHHHHHHHHhcCCHHHHHHHH
Confidence 355566555 899999999999999999999654
No 71
>PRK07993 DNA polymerase III subunit delta'; Validated
Probab=47.67 E-value=32 Score=32.22 Aligned_cols=37 Identities=22% Similarity=0.197 Sum_probs=29.4
Q ss_pred CHHHH-HHHHcC-CCCHHHHHHHHHHhCCCHHHHHHHHH
Q 047404 250 PEDSI-AMLVSM-GFDRNSARQALVQARNDINAATNILL 286 (291)
Q Consensus 250 ~~~~v-~~l~~m-Gf~~~~~~~aL~~~~~~~~~A~~~l~ 286 (291)
++|.+ +-|.+- |.+.+++..+++.++|++.+|.+++-
T Consensus 168 ~~~~~~~~L~~~~~~~~~~a~~~~~la~G~~~~Al~l~~ 206 (334)
T PRK07993 168 PEQYALTWLSREVTMSQDALLAALRLSAGAPGAALALLQ 206 (334)
T ss_pred CHHHHHHHHHHccCCCHHHHHHHHHHcCCCHHHHHHHhc
Confidence 34444 457664 89999999999999999999998763
No 72
>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=46.51 E-value=24 Score=28.55 Aligned_cols=31 Identities=32% Similarity=0.377 Sum_probs=24.0
Q ss_pred CCCHHHHHHHHcCCCCHHHHHHHHHHhCCCH
Q 047404 248 EPPEDSIAMLVSMGFDRNSARQALVQARNDI 278 (291)
Q Consensus 248 ~~~~~~v~~l~~mGf~~~~~~~aL~~~~~~~ 278 (291)
.+.++|++-|.+-|.+.+|+.+||++++++.
T Consensus 21 sp~~~k~~FL~sKGLt~~EI~~al~~a~~~~ 51 (136)
T PF04695_consen 21 SPLEKKIAFLESKGLTEEEIDEALGRAGSPP 51 (136)
T ss_dssp S-HHHHHHHHHHCT--HHHHHHHHHHHT--S
T ss_pred CCHHHHHHHHHcCCCCHHHHHHHHHhcCCcc
Confidence 3468999999999999999999999998766
No 73
>COG2103 Predicted sugar phosphate isomerase [General function prediction only]
Probab=46.37 E-value=35 Score=31.06 Aligned_cols=37 Identities=19% Similarity=0.363 Sum_probs=25.1
Q ss_pred HHHHHHHHc-CCCCHHHHHHHHHHhCCCHHHHHHHHHh
Q 047404 251 EDSIAMLVS-MGFDRNSARQALVQARNDINAATNILLE 287 (291)
Q Consensus 251 ~~~v~~l~~-mGf~~~~~~~aL~~~~~~~~~A~~~l~~ 287 (291)
+.+++-+++ -|-++++|.++|.++++++-.|+=+++.
T Consensus 234 dRa~RIv~~aT~~~~~~A~~~L~~~~~~vK~AIvm~~~ 271 (298)
T COG2103 234 DRAVRIVMEATGCSAEEAEALLEEAGGNVKLAIVMLLT 271 (298)
T ss_pred HHHHHHHHHHhCCCHHHHHHHHHHcCCccHhHHHHHHh
Confidence 334444555 5778888888888888887777765543
No 74
>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=46.32 E-value=34 Score=31.36 Aligned_cols=34 Identities=18% Similarity=0.362 Sum_probs=22.9
Q ss_pred HHHHHHc-CCCCHHHHHHHHHHhCCCHHHHHHHHH
Q 047404 253 SIAMLVS-MGFDRNSARQALVQARNDINAATNILL 286 (291)
Q Consensus 253 ~v~~l~~-mGf~~~~~~~aL~~~~~~~~~A~~~l~ 286 (291)
+++.+++ .|-++++|+++|.+++|++-.|+-.++
T Consensus 233 a~~i~~~~~~~~~~~a~~~l~~~~~~vk~Ai~~~~ 267 (291)
T TIGR00274 233 AVRIVRQATDCNKELAEQTLLAADQNVKLAIVMIL 267 (291)
T ss_pred HHHHHHHHhCcCHHHHHHHHHHhCCCcHHHHHHHH
Confidence 3333444 677888888888888877777776543
No 75
>PRK06476 pyrroline-5-carboxylate reductase; Reviewed
Probab=45.14 E-value=44 Score=29.64 Aligned_cols=33 Identities=21% Similarity=0.219 Sum_probs=25.7
Q ss_pred CHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHHHHH
Q 047404 250 PEDSIAMLVSMGFDRNSARQALVQARNDINAATNIL 285 (291)
Q Consensus 250 ~~~~v~~l~~mGf~~~~~~~aL~~~~~~~~~A~~~l 285 (291)
-++.++-.+++|+|++++++.+..+ +.-+++.+
T Consensus 172 ~~~~~~~~~~~Gl~~~~a~~~~~~~---~~G~~~l~ 204 (258)
T PRK06476 172 LETATGWLEEQGLKRQKARAYLAPL---FASLAQDA 204 (258)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHH---HHHHHHHH
Confidence 3667777888999999999999877 55566653
No 76
>PF14748 P5CR_dimer: Pyrroline-5-carboxylate reductase dimerisation; PDB: 2RCY_D 3TRI_A 2IZZ_B 2GR9_B 2GRA_B 2GER_C 1YQG_A 2AG8_A 3GT0_A 2AMF_E ....
Probab=43.20 E-value=61 Score=24.89 Aligned_cols=35 Identities=29% Similarity=0.375 Sum_probs=23.8
Q ss_pred HHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHHHHHHhc
Q 047404 251 EDSIAMLVSMGFDRNSARQALVQARNDINAATNILLEA 288 (291)
Q Consensus 251 ~~~v~~l~~mGf~~~~~~~aL~~~~~~~~~A~~~l~~~ 288 (291)
|.-++-.+.+|+++++|++...++ +.-+++.+.++
T Consensus 25 eal~~a~v~~Gl~~~~A~~lv~~t---~~G~a~ll~~~ 59 (107)
T PF14748_consen 25 EALADAAVAQGLPREEARKLVAQT---FIGAAKLLEES 59 (107)
T ss_dssp HHHHHHHHHTT--HHHHHHHHHHH---HHHHHHHHHHC
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHH---HHHHHHHHHcc
Confidence 445666778999999999988777 55666665543
No 77
>PRK01905 DNA-binding protein Fis; Provisional
Probab=42.87 E-value=24 Score=25.48 Aligned_cols=24 Identities=17% Similarity=0.181 Sum_probs=21.0
Q ss_pred CCHHHHHHHHHHhCCCHHHHHHHH
Q 047404 262 FDRNSARQALVQARNDINAATNIL 285 (291)
Q Consensus 262 f~~~~~~~aL~~~~~~~~~A~~~l 285 (291)
|+++..+++|..+++|..+|++.|
T Consensus 37 ~E~~~i~~aL~~~~gn~s~aAr~L 60 (77)
T PRK01905 37 VEKPLLEVVMEQAGGNQSLAAEYL 60 (77)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHH
Confidence 468889999999999999998865
No 78
>PRK12570 N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=42.71 E-value=40 Score=31.00 Aligned_cols=26 Identities=23% Similarity=0.440 Sum_probs=16.8
Q ss_pred CCCCHHHHHHHHHHhCCCHHHHHHHH
Q 047404 260 MGFDRNSARQALVQARNDINAATNIL 285 (291)
Q Consensus 260 mGf~~~~~~~aL~~~~~~~~~A~~~l 285 (291)
.|-++++|.++|.++++++-.|+-.+
T Consensus 242 ~~~~~~~a~~~l~~~~~~vk~ai~~~ 267 (296)
T PRK12570 242 TGCSEDEAKELLKESDNDVKLAILMI 267 (296)
T ss_pred HCcCHHHHHHHHHHhCCccHHHHHHH
Confidence 56677777777777666666665543
No 79
>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=40.81 E-value=43 Score=21.82 Aligned_cols=26 Identities=19% Similarity=0.216 Sum_probs=21.6
Q ss_pred CHHHHHHHHcCCC--CHHHHHHHHHHhC
Q 047404 250 PEDSIAMLVSMGF--DRNSARQALVQAR 275 (291)
Q Consensus 250 ~~~~v~~l~~mGf--~~~~~~~aL~~~~ 275 (291)
-++.+++|.+-|| +++...++|+.++
T Consensus 21 ~~~~l~~l~~~g~~is~~l~~~~L~~~g 48 (48)
T PF11848_consen 21 VKPLLDRLQQAGFRISPKLIEEILRRAG 48 (48)
T ss_pred HHHHHHHHHHcCcccCHHHHHHHHHHcC
Confidence 3667899999998 8999999998764
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=34.53 E-value=27 Score=31.35 Aligned_cols=30 Identities=33% Similarity=0.522 Sum_probs=24.5
Q ss_pred HHHHHHc-CCCCHHHHHHHHHHhCCCHHHHH
Q 047404 253 SIAMLVS-MGFDRNSARQALVQARNDINAAT 282 (291)
Q Consensus 253 ~v~~l~~-mGf~~~~~~~aL~~~~~~~~~A~ 282 (291)
+++.+++ .|-++++|+++|.++++++-.|+
T Consensus 225 a~~i~~~~~~~~~~~a~~~l~~~~~~~k~a~ 255 (257)
T cd05007 225 AIRIVMEATGVSRDEAEAALEQAGGDVKTAI 255 (257)
T ss_pred HHHHHHHHHCcCHHHHHHHHHHhCCCceeee
Confidence 4444555 78999999999999999998775
No 81
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=34.52 E-value=36 Score=25.72 Aligned_cols=24 Identities=13% Similarity=0.124 Sum_probs=21.3
Q ss_pred CCHHHHHHHHHHhCCCHHHHHHHH
Q 047404 262 FDRNSARQALVQARNDINAATNIL 285 (291)
Q Consensus 262 f~~~~~~~aL~~~~~~~~~A~~~l 285 (291)
|+++-.++||..++||..+|++.|
T Consensus 55 ~Er~~i~~aL~~~~gn~s~AAr~L 78 (95)
T PRK00430 55 VEAPLLDMVMQYTRGNQTRAALML 78 (95)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHh
Confidence 568889999999999999999865
No 82
>PF04361 DUF494: Protein of unknown function (DUF494); InterPro: IPR007456 Members of this family of uncharacterised proteins are often named Smg.
Probab=34.34 E-value=48 Score=27.54 Aligned_cols=26 Identities=23% Similarity=0.288 Sum_probs=20.5
Q ss_pred CCHHHHHHHHcCCCCHHHHHHHHHHh
Q 047404 249 PPEDSIAMLVSMGFDRNSARQALVQA 274 (291)
Q Consensus 249 ~~~~~v~~l~~mGf~~~~~~~aL~~~ 274 (291)
..++--++|.+.||+.+++.+||.=-
T Consensus 22 d~~~L~~~L~~aGF~~~eI~~Al~WL 47 (155)
T PF04361_consen 22 DQDDLTRELSAAGFEDEEINKALDWL 47 (155)
T ss_pred CHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 34566677999999999999988643
No 83
>PTZ00431 pyrroline carboxylate reductase; Provisional
Probab=32.57 E-value=95 Score=27.63 Aligned_cols=35 Identities=20% Similarity=0.343 Sum_probs=25.5
Q ss_pred HHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHHHHHHhc
Q 047404 251 EDSIAMLVSMGFDRNSARQALVQARNDINAATNILLEA 288 (291)
Q Consensus 251 ~~~v~~l~~mGf~~~~~~~aL~~~~~~~~~A~~~l~~~ 288 (291)
|.-++-.+++|++|++|++-..++ +.-+++.|.++
T Consensus 177 ~al~~~~v~~Gl~~~~a~~l~~~~---~~G~a~ll~~~ 211 (260)
T PTZ00431 177 ESLIDAGVKNGLNRDVSKNLVLQT---ILGSVHMVKAS 211 (260)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHH---HHHHHHHHHhc
Confidence 556666777999999999887776 55566655554
No 84
>PRK12491 pyrroline-5-carboxylate reductase; Reviewed
Probab=31.95 E-value=98 Score=27.91 Aligned_cols=35 Identities=26% Similarity=0.281 Sum_probs=24.6
Q ss_pred HHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHHHHHHhc
Q 047404 251 EDSIAMLVSMGFDRNSARQALVQARNDINAATNILLEA 288 (291)
Q Consensus 251 ~~~v~~l~~mGf~~~~~~~aL~~~~~~~~~A~~~l~~~ 288 (291)
|.-++-.++||+++++|++...++ +.-+++.|.++
T Consensus 184 eal~~a~v~~Gl~~~~A~~l~~~t---~~G~a~ll~~~ 218 (272)
T PRK12491 184 EAMADAAVLGGMPRKQAYKFAAQA---VLGSAKMVLET 218 (272)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHH---HHHHHHHHHhc
Confidence 556666778999999999887776 44455555444
No 85
>KOG3763 consensus mRNA export factor TAP/MEX67 [RNA processing and modification]
Probab=31.33 E-value=1e+02 Score=31.06 Aligned_cols=41 Identities=15% Similarity=0.303 Sum_probs=33.7
Q ss_pred CCCCHHHHHHHHc-CCCCHHHHHHHHHHhCCCHHHHHHHHHh
Q 047404 247 IEPPEDSIAMLVS-MGFDRNSARQALVQARNDINAATNILLE 287 (291)
Q Consensus 247 ~~~~~~~v~~l~~-mGf~~~~~~~aL~~~~~~~~~A~~~l~~ 287 (291)
..+.+|++..+.+ -|-.-+=+..++.++|||-|+|..-..+
T Consensus 532 ~~~~~e~l~~~~~~tGln~~~s~~c~e~~nWdy~~A~k~F~~ 573 (585)
T KOG3763|consen 532 VDVTDEKLLKFQEETGLNSEWSTMCLEQNNWDYERALKLFIE 573 (585)
T ss_pred cchHHHHHHHHHHHhcCChHHHHHHHHHccCCHHHHHHHHHH
Confidence 3345778877776 6999999999999999999999986554
No 86
>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=30.59 E-value=1.4e+02 Score=20.23 Aligned_cols=36 Identities=17% Similarity=0.198 Sum_probs=28.8
Q ss_pred CHHHHHHHHc-CCCCHHHHHHHHHHhCCCHHHHHHHH
Q 047404 250 PEDSIAMLVS-MGFDRNSARQALVQARNDINAATNIL 285 (291)
Q Consensus 250 ~~~~v~~l~~-mGf~~~~~~~aL~~~~~~~~~A~~~l 285 (291)
++..|+-.+. .|-++++.++|.++.|++.+.--++|
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 4556777666 79999999999999999987665554
No 87
>PF03672 UPF0154: Uncharacterised protein family (UPF0154); InterPro: IPR005359 The proteins in this entry are functionally uncharacterised.
Probab=29.52 E-value=88 Score=22.01 Aligned_cols=27 Identities=19% Similarity=0.266 Sum_probs=18.6
Q ss_pred CCHHHHHHHHc-CCC--CHHHHHHHHHHhC
Q 047404 249 PPEDSIAMLVS-MGF--DRNSARQALVQAR 275 (291)
Q Consensus 249 ~~~~~v~~l~~-mGf--~~~~~~~aL~~~~ 275 (291)
.+|+.|+.+.. ||- |+.++.+.++.-+
T Consensus 32 ine~mir~M~~QMG~kpSekqi~Q~m~~mk 61 (64)
T PF03672_consen 32 INEKMIRAMMMQMGRKPSEKQIKQMMRSMK 61 (64)
T ss_pred CCHHHHHHHHHHhCCCccHHHHHHHHHHHH
Confidence 56788877654 887 6677777776543
No 88
>PF07848 PaaX: PaaX-like protein; InterPro: IPR012906 This entry describes the N-terminal region of proteins that are similar to, and nclude, the product of the paaX gene of Escherichia coli (P76086 from SWISSPROT). PaaX is a transcriptional regulator that is always found in association with operons believed to be involved in the degradation of phenylacetic acid []. The gene product has been shown to bind to the promoter sites and repress their transcription []. ; PDB: 3KFW_X 3L09_B.
Probab=29.52 E-value=58 Score=23.16 Aligned_cols=25 Identities=24% Similarity=0.397 Sum_probs=19.4
Q ss_pred CHHHHHHHHcCCCCHHHHHHHHHHh
Q 047404 250 PEDSIAMLVSMGFDRNSARQALVQA 274 (291)
Q Consensus 250 ~~~~v~~l~~mGf~~~~~~~aL~~~ 274 (291)
..+-|+-+.++|+++..+|.||.+.
T Consensus 23 ~~~Li~ll~~~Gv~e~avR~alsRl 47 (70)
T PF07848_consen 23 VASLIRLLAAFGVSESAVRTALSRL 47 (70)
T ss_dssp HHHHHHHHCCTT--HHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCChHHHHHHHHHH
Confidence 3567788888999999999999876
No 89
>PF02536 mTERF: mTERF; InterPro: IPR003690 This family currently contains one sequence of known function human mitochondrial transcription termination factor (mTERF), a multizipper protein but binds to DNA as a monomer, with evidence pointing to intramolecular leucine zipper interactions []. The precursors contain a mitochondrial targeting sequence, and the mature mTERF exhibits three leucine zippers, of which one is bipartite, and two widely spaced basic domains. Both basic domains and the three leucine zipper motifs are necessary for DNA binding. The leucine zippers are not implicated in a dimerisation role as in other leucine zippers []. The rest of the family consists of hypothetical proteins none of which have any functional information.; PDB: 3M66_A 3OPG_A 3MVA_O 3MVB_O 3N7Q_A 3N6S_A.
Probab=29.41 E-value=54 Score=30.22 Aligned_cols=39 Identities=15% Similarity=0.290 Sum_probs=26.9
Q ss_pred CHHHHHHHHcCCCCHHHHHHHHHHhC----CC---HHHHHHHHHhc
Q 047404 250 PEDSIAMLVSMGFDRNSARQALVQAR----ND---INAATNILLEA 288 (291)
Q Consensus 250 ~~~~v~~l~~mGf~~~~~~~aL~~~~----~~---~~~A~~~l~~~ 288 (291)
-+++++.|.++||+++++.+.+.++- -+ +..-++||.+.
T Consensus 243 l~~~i~~L~~lG~s~~ei~~mv~~~P~iL~~s~e~l~~k~~fl~~~ 288 (345)
T PF02536_consen 243 LKPKIEFLQSLGFSEEEIAKMVRRFPQILSYSIEKLKPKFEFLVKE 288 (345)
T ss_dssp HHHHHHHHHTTT--HHHHHHHHHHSGGGGGS-HHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHhcCcHHHHHHHHHhCcchhhcchhhhhHHHHHHHHH
Confidence 36788899999999999999998872 33 44455666653
No 90
>PF01988 VIT1: VIT family; InterPro: IPR008217 Proteins containing this entry have no known function and are predicted to be integral membrane proteins. They include the Ccc1 protein from Saccharomyces cerevisiae (Baker's yeast) (P47818 from SWISSPROT) that may have a role in regulating calcium levels [].
Probab=29.32 E-value=56 Score=28.36 Aligned_cols=38 Identities=13% Similarity=0.301 Sum_probs=30.1
Q ss_pred CCHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHHHHHHh
Q 047404 249 PPEDSIAMLVSMGFDRNSARQALVQARNDINAATNILLE 287 (291)
Q Consensus 249 ~~~~~v~~l~~mGf~~~~~~~aL~~~~~~~~~A~~~l~~ 287 (291)
..+|-++.+.+.|++++++++..+....|.|. +|....
T Consensus 81 e~~el~~iy~~~Gl~~~~a~~i~~~l~~~~~~-~~~m~~ 118 (213)
T PF01988_consen 81 EKEELVEIYRAKGLSEEDAEEIAEELSKDKDA-LDFMMR 118 (213)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHhCchH-HHHHHh
Confidence 44677788889999999999998887777777 776543
No 91
>PF01458 UPF0051: Uncharacterized protein family (UPF0051); InterPro: IPR000825 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] []. FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins [, ]. It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly []. The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA []. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA [], acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins []. Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen []. This entry represents SufB and SufD proteins that form part of the SufBCD complex in the SUF system. No specific functions have been assigned to these proteins.; GO: 0016226 iron-sulfur cluster assembly; PDB: 1VH4_B 2ZU0_A 4DN7_A.
Probab=29.24 E-value=53 Score=28.73 Aligned_cols=27 Identities=26% Similarity=0.402 Sum_probs=21.1
Q ss_pred CCCCHHHHHHHHcCCCCHHHHHHHHHH
Q 047404 247 IEPPEDSIAMLVSMGFDRNSARQALVQ 273 (291)
Q Consensus 247 ~~~~~~~v~~l~~mGf~~~~~~~aL~~ 273 (291)
-+.|||++=-|++.|+++++|++-|.+
T Consensus 201 G~idee~LFYL~SRGl~~~eA~~Liv~ 227 (229)
T PF01458_consen 201 GQIDEEQLFYLMSRGLSEEEARKLIVK 227 (229)
T ss_dssp EES-HHHHHHHHCTT--HHHHHHHHHH
T ss_pred ecCCHHHHHHHHHcCCCHHHHHHHHHh
Confidence 367999999999999999999998754
No 92
>PRK05441 murQ N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=28.89 E-value=77 Score=29.12 Aligned_cols=32 Identities=19% Similarity=0.268 Sum_probs=25.3
Q ss_pred HHHHHHc-CCCCHHHHHHHHHHhCCCHHHHHHH
Q 047404 253 SIAMLVS-MGFDRNSARQALVQARNDINAATNI 284 (291)
Q Consensus 253 ~v~~l~~-mGf~~~~~~~aL~~~~~~~~~A~~~ 284 (291)
++.-++. .|.+.++|++.|.+++|++.+|++-
T Consensus 265 k~a~~~~~~~~~~~~a~~~l~~~~g~~~~~~~~ 297 (299)
T PRK05441 265 KLAIVMILTGLDAAEAKALLARHGGFLRKALAE 297 (299)
T ss_pred HHHHHHHHhCCCHHHHHHHHHHcCCCHHHHHhh
Confidence 3344443 4789999999999999999999864
No 93
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=28.37 E-value=1e+02 Score=32.00 Aligned_cols=43 Identities=21% Similarity=0.370 Sum_probs=34.8
Q ss_pred CCCCHHHHHHHHc------C---CCCHHHHHHHHHHhCCCHHHHHHHHHhcC
Q 047404 247 IEPPEDSIAMLVS------M---GFDRNSARQALVQARNDINAATNILLEAQ 289 (291)
Q Consensus 247 ~~~~~~~v~~l~~------m---Gf~~~~~~~aL~~~~~~~~~A~~~l~~~~ 289 (291)
..+++|.|..|.. | |=+.|-|...|..+.|||+.|+|.|+-..
T Consensus 551 i~~~q~rvt~l~nlaCSsa~PggGtN~ElALH~L~EakGnv~vAlE~LLlr~ 602 (907)
T KOG4167|consen 551 IHDLQQRVTNLLNLACSSALPGGGTNSELALHSLFEAKGNVMVALEMLLLRK 602 (907)
T ss_pred ccccHHHHHHHHHHHhhhcCCCCCccHHHHHHHHHHhcccHHHHHHHHHhcC
Confidence 3556777777654 2 77899999999999999999999987543
No 94
>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=27.56 E-value=50 Score=30.28 Aligned_cols=24 Identities=13% Similarity=0.083 Sum_probs=21.5
Q ss_pred CCCCHHHHHHHHHHhCCCHHHHHH
Q 047404 260 MGFDRNSARQALVQARNDINAATN 283 (291)
Q Consensus 260 mGf~~~~~~~aL~~~~~~~~~A~~ 283 (291)
-|++.++|++.|.+++|++.+|+|
T Consensus 268 ~~~~~~~a~~~l~~~~g~~~~~l~ 291 (291)
T TIGR00274 268 STLSASEAKVLLDRHGGFLRQALD 291 (291)
T ss_pred hCCCHHHHHHHHHHcCCcHHHhhC
Confidence 479999999999999999999875
No 95
>COG2922 Smg Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.45 E-value=93 Score=25.52 Aligned_cols=26 Identities=35% Similarity=0.532 Sum_probs=20.4
Q ss_pred CCCCHHHHHH-HHcCCCCHHHHHHHHH
Q 047404 247 IEPPEDSIAM-LVSMGFDRNSARQALV 272 (291)
Q Consensus 247 ~~~~~~~v~~-l~~mGf~~~~~~~aL~ 272 (291)
.++|+|++++ |.+-||+|++.-.||.
T Consensus 19 l~vd~d~L~~~L~~aGF~~~dI~naL~ 45 (157)
T COG2922 19 LPVDQDSLENDLEDAGFDREDIYNALM 45 (157)
T ss_pred CCcCHHHHHhHHHHcCCCHHHHHHHHH
Confidence 3467777776 6779999999888875
No 96
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=27.03 E-value=1.1e+02 Score=29.04 Aligned_cols=42 Identities=19% Similarity=0.210 Sum_probs=31.6
Q ss_pred CCCCCCCCHHHHHHHHcCCCCHHHHHHHHH---------HhCCCHHHHHHH
Q 047404 243 VPSTIEPPEDSIAMLVSMGFDRNSARQALV---------QARNDINAATNI 284 (291)
Q Consensus 243 ~~~~~~~~~~~v~~l~~mGf~~~~~~~aL~---------~~~~~~~~A~~~ 284 (291)
....+..+|+++=.|+..+|+.++|.+-|+ .++|+.+.+-++
T Consensus 238 ~gt~vkDnEqAL~~LvkcnfDteeAlrr~rfnvk~~rd~l~~wsEeEcr~F 288 (445)
T KOG4329|consen 238 EGTEVKDNEQALYELVKCNFDTEEALRRLRFNVKTVRDDLSGWSEEECRNF 288 (445)
T ss_pred ccccccccHHHHHHHHHcCCcHHHHHHhcCCcceecccccccCCHHHHHHH
Confidence 334567789999999999999998887765 346777776664
No 97
>KOG1796 consensus Vacuolar protein sorting-associated protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=26.68 E-value=22 Score=34.98 Aligned_cols=33 Identities=24% Similarity=0.474 Sum_probs=30.7
Q ss_pred HHHcCCCCHHHHHHHHHHhCCCHHHHHHHHHhc
Q 047404 256 MLVSMGFDRNSARQALVQARNDINAATNILLEA 288 (291)
Q Consensus 256 ~l~~mGf~~~~~~~aL~~~~~~~~~A~~~l~~~ 288 (291)
++.+-||.++++++||.++++..-.|..|||++
T Consensus 382 ~~Q~w~f~~d~c~~~l~~~~~q~k~~~s~lfd~ 414 (609)
T KOG1796|consen 382 RLQEWGFSMDDCRKALLACQGQLKKAASWLFDN 414 (609)
T ss_pred ccccccccccchhHHHHhhhhhhccchhhhhcc
Confidence 577899999999999999999999999999975
No 98
>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=26.40 E-value=67 Score=21.44 Aligned_cols=20 Identities=20% Similarity=0.272 Sum_probs=17.0
Q ss_pred HHHHHHHHcCCCCHHHHHHH
Q 047404 251 EDSIAMLVSMGFDRNSARQA 270 (291)
Q Consensus 251 ~~~v~~l~~mGf~~~~~~~a 270 (291)
-|+|++||+-|-+..+|++-
T Consensus 17 vE~Iq~LMaqGmSsgEAI~~ 36 (51)
T PF03701_consen 17 VERIQELMAQGMSSGEAIAI 36 (51)
T ss_pred HHHHHHHHHhcccHHHHHHH
Confidence 57899999999998888764
No 99
>PRK10923 glnG nitrogen regulation protein NR(I); Provisional
Probab=25.76 E-value=52 Score=31.84 Aligned_cols=24 Identities=21% Similarity=0.329 Sum_probs=21.6
Q ss_pred CCHHHHHHHHHHhCCCHHHHHHHH
Q 047404 262 FDRNSARQALVQARNDINAATNIL 285 (291)
Q Consensus 262 f~~~~~~~aL~~~~~~~~~A~~~l 285 (291)
++|+..++||++++||..+|++.|
T Consensus 429 ~E~~~i~~aL~~~~gn~~~aA~~L 452 (469)
T PRK10923 429 LERTLLTTALRHTQGHKQEAARLL 452 (469)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHh
Confidence 578889999999999999999875
No 100
>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional
Probab=25.36 E-value=55 Score=30.37 Aligned_cols=24 Identities=21% Similarity=0.320 Sum_probs=22.0
Q ss_pred CCHHHHHHHHHHhCCCHHHHHHHH
Q 047404 262 FDRNSARQALVQARNDINAATNIL 285 (291)
Q Consensus 262 f~~~~~~~aL~~~~~~~~~A~~~l 285 (291)
++++...+||+.++||..+|++.|
T Consensus 286 ~Er~~I~~aL~~~~gn~~~aA~~L 309 (326)
T PRK11608 286 QEKELLQRSLQQAKFNQKRAAELL 309 (326)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHh
Confidence 778889999999999999999875
No 101
>cd02433 Nodulin-21_like_2 Nodulin-21 and CCC1-related protein family. Nodulin-21_like_2: This is a family of proteins closely related to nodulin-21, a plant nodule-specific protein that may be involved in symbiotic nitrogen fixation. This family is also related to CCC1, a yeast vacuole transmembrane protein that functions as an iron and manganese transporter.
Probab=25.34 E-value=61 Score=28.78 Aligned_cols=38 Identities=21% Similarity=0.263 Sum_probs=30.6
Q ss_pred CCHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHHHHHH
Q 047404 249 PPEDSIAMLVSMGFDRNSARQALVQARNDINAATNILL 286 (291)
Q Consensus 249 ~~~~~v~~l~~mGf~~~~~~~aL~~~~~~~~~A~~~l~ 286 (291)
+.+|-++.+.+-|++++++++.-+.-..|.|.++|...
T Consensus 99 e~~el~~iy~~~G~~~~~a~~~~~~l~~~~~~~~~~~~ 136 (234)
T cd02433 99 EAAELALIYRAKGLDEEEAKRVASQLMNDPEQALDTLA 136 (234)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHhCcchhHHHHH
Confidence 45777888888999999999998888777777777544
No 102
>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF. Members of this protein family are PspF, the sigma-54-dependent transcriptional activator of the phage shock protein (psp) operon, in Escherichia coli and numerous other species. The psp operon is induced by a number of stress conditions, including heat shock, ethanol, and filamentous phage infection. Changed com_name to adhere to TIGR role notes conventions. 09/15/06 - DMH
Probab=25.29 E-value=55 Score=30.45 Aligned_cols=24 Identities=25% Similarity=0.378 Sum_probs=22.3
Q ss_pred CCHHHHHHHHHHhCCCHHHHHHHH
Q 047404 262 FDRNSARQALVQARNDINAATNIL 285 (291)
Q Consensus 262 f~~~~~~~aL~~~~~~~~~A~~~l 285 (291)
|.++..++||++++||..+|++.|
T Consensus 292 ~E~~~I~~aL~~~~gn~~~aA~~L 315 (329)
T TIGR02974 292 YEIELLQQALAEAQFNQRKAAELL 315 (329)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHh
Confidence 789999999999999999999875
No 103
>PRK15115 response regulator GlrR; Provisional
Probab=25.20 E-value=55 Score=31.38 Aligned_cols=24 Identities=21% Similarity=0.378 Sum_probs=21.7
Q ss_pred CCHHHHHHHHHHhCCCHHHHHHHH
Q 047404 262 FDRNSARQALVQARNDINAATNIL 285 (291)
Q Consensus 262 f~~~~~~~aL~~~~~~~~~A~~~l 285 (291)
+.++..++||+.++||..+|++.|
T Consensus 398 ~E~~~i~~al~~~~gn~~~aA~~L 421 (444)
T PRK15115 398 FELNYLRKLLQITKGNVTHAARMA 421 (444)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHh
Confidence 578889999999999999999875
No 104
>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional
Probab=24.63 E-value=55 Score=32.38 Aligned_cols=24 Identities=42% Similarity=0.516 Sum_probs=22.0
Q ss_pred CCHHHHHHHHHHhCCCHHHHHHHH
Q 047404 262 FDRNSARQALVQARNDINAATNIL 285 (291)
Q Consensus 262 f~~~~~~~aL~~~~~~~~~A~~~l 285 (291)
++|+..++||++++||..+|++.|
T Consensus 468 ~Er~~I~~aL~~~~gn~~~aA~~L 491 (509)
T PRK05022 468 FQRQLIRQALAQHQGNWAAAARAL 491 (509)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHh
Confidence 678899999999999999999875
No 105
>COG4241 Predicted membrane protein [Function unknown]
Probab=24.57 E-value=77 Score=29.30 Aligned_cols=36 Identities=28% Similarity=0.362 Sum_probs=28.1
Q ss_pred CHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHHHHHHhc
Q 047404 250 PEDSIAMLVSMGFDRNSARQALVQARNDINAATNILLEA 288 (291)
Q Consensus 250 ~~~~v~~l~~mGf~~~~~~~aL~~~~~~~~~A~~~l~~~ 288 (291)
-++.+.++. -+-++|.++-.+++||+|+|++.|.++
T Consensus 129 v~~a~~~~R---qsl~~a~~~~i~~G~~~~~~l~iLees 164 (314)
T COG4241 129 VDDAVVYLR---QSLNAAIKMAIAAGNNVDDALKILEES 164 (314)
T ss_pred cHHHHHHHH---hhhHHHHHHHHHccCChHHHHHHHHHH
Confidence 355565554 357889999999999999999988775
No 106
>TIGR01817 nifA Nif-specific regulatory protein. This model represents NifA, a DNA-binding regulatory protein for nitrogen fixation. The model produces scores between the trusted and noise cutoffs for a well-described NifA homolog in Aquifex aeolicus (which lacks nitrogenase), for transcriptional activators of alternative nitrogenases (VFe or FeFe instead of MoFe), and truncated forms.
Probab=24.17 E-value=58 Score=32.37 Aligned_cols=24 Identities=29% Similarity=0.156 Sum_probs=22.1
Q ss_pred CCHHHHHHHHHHhCCCHHHHHHHH
Q 047404 262 FDRNSARQALVQARNDINAATNIL 285 (291)
Q Consensus 262 f~~~~~~~aL~~~~~~~~~A~~~l 285 (291)
++|+..++||+.++||..+|++.|
T Consensus 490 ~Er~~i~~aL~~~~gn~~~aA~~L 513 (534)
T TIGR01817 490 SERERLIAALEQAGWVQAKAARLL 513 (534)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHH
Confidence 688899999999999999999875
No 107
>PRK03430 hypothetical protein; Validated
Probab=24.04 E-value=86 Score=26.13 Aligned_cols=24 Identities=25% Similarity=0.340 Sum_probs=19.8
Q ss_pred CCHHHHHHHHcCCCCHHHHHHHHH
Q 047404 249 PPEDSIAMLVSMGFDRNSARQALV 272 (291)
Q Consensus 249 ~~~~~v~~l~~mGf~~~~~~~aL~ 272 (291)
+.++--++|.+-||+++++.+||.
T Consensus 22 d~~~L~~~L~~aGF~~~eI~~AL~ 45 (157)
T PRK03430 22 DQDKLEDDLTDAGFHREDIYNALL 45 (157)
T ss_pred CHHHHHHHHHHcCCCHHHHHHHHH
Confidence 356667789999999999999875
No 108
>COG2103 Predicted sugar phosphate isomerase [General function prediction only]
Probab=23.80 E-value=99 Score=28.20 Aligned_cols=33 Identities=18% Similarity=0.241 Sum_probs=26.8
Q ss_pred HHHHHHHc-CCCCHHHHHHHHHHhCCCHHHHHHH
Q 047404 252 DSIAMLVS-MGFDRNSARQALVQARNDINAATNI 284 (291)
Q Consensus 252 ~~v~~l~~-mGf~~~~~~~aL~~~~~~~~~A~~~ 284 (291)
-|+.-+|- -|.+.++|++.|.+++|++.+|++.
T Consensus 262 vK~AIvm~~~~~~a~~A~~~L~~~~g~lr~Al~~ 295 (298)
T COG2103 262 VKLAIVMLLTGLSAEEAKRLLERAGGFLRQALSE 295 (298)
T ss_pred cHhHHHHHHhCCCHHHHHHHHHHccChHHHHHhh
Confidence 35555555 4789999999999999999999874
No 109
>PF07553 Lipoprotein_Ltp: Host cell surface-exposed lipoprotein; InterPro: IPR011434 This domain is found as 1-3 copies in a small family of proteins of unknown function.
Probab=23.64 E-value=1.1e+02 Score=20.09 Aligned_cols=23 Identities=26% Similarity=0.290 Sum_probs=17.9
Q ss_pred CHHHHHHHHcC---CCCHHHHHHHHH
Q 047404 250 PEDSIAMLVSM---GFDRNSARQALV 272 (291)
Q Consensus 250 ~~~~v~~l~~m---Gf~~~~~~~aL~ 272 (291)
.++-.+||++= ||+.++|.-|+.
T Consensus 21 k~~l~~QL~se~ge~Ft~e~A~YAv~ 46 (48)
T PF07553_consen 21 KQGLYDQLTSEYGEGFTEEEAQYAVD 46 (48)
T ss_pred HHHHHHHHHhhcccCCCHHHHHHHHH
Confidence 46677888875 899999888764
No 110
>PRK00523 hypothetical protein; Provisional
Probab=23.05 E-value=1.4e+02 Score=21.50 Aligned_cols=26 Identities=19% Similarity=0.263 Sum_probs=16.9
Q ss_pred CCHHHHHHHHc-CCC--CHHHHHHHHHHh
Q 047404 249 PPEDSIAMLVS-MGF--DRNSARQALVQA 274 (291)
Q Consensus 249 ~~~~~v~~l~~-mGf--~~~~~~~aL~~~ 274 (291)
.+||.|+.++. ||- |+.++++.++.-
T Consensus 40 ine~mir~M~~QMGqKPSekki~Q~m~~m 68 (72)
T PRK00523 40 ITENMIRAMYMQMGRKPSESQIKQVMRSV 68 (72)
T ss_pred CCHHHHHHHHHHhCCCccHHHHHHHHHHH
Confidence 46777776544 886 566667766654
No 111
>PRK10332 hypothetical protein; Provisional
Probab=22.94 E-value=1.1e+02 Score=23.85 Aligned_cols=47 Identities=28% Similarity=0.342 Sum_probs=23.3
Q ss_pred CCCcccchHHHHHHHHHHHHHHHhhhccccccccchHHHhhhccchhhhh
Q 047404 6 SGFNNAPVTRAFVIACALFTVFFGIQGRFNKLGLSYQDIFQNFRLWRLIV 55 (291)
Q Consensus 6 ~gf~~~PVTk~li~~~~~~sl~~~~~~~~~~l~l~~~~i~~~~q~WRLlT 55 (291)
+||.-+=|--++.+.++++. .+.++.+.+.-.+...+++.|.||+.=
T Consensus 9 ~GFsL~EvlvAm~i~~i~~~---al~~~~p~L~~~F~~~wQqRQaWrla~ 55 (107)
T PRK10332 9 RGFSLPEVLLAMVLMVMIVT---ALSGYQRTLMNSFASRNQYRQLWRHAW 55 (107)
T ss_pred CCccHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45544444334333333222 222333344445556677788999743
No 112
>TIGR01818 ntrC nitrogen regulation protein NR(I). This model represents NtrC, a DNA-binding response regulator that is phosphorylated by NtrB and interacts with sigma-54. NtrC usually controls the expression of glutamine synthase, GlnA, and may be called GlnL, GlnG, etc.
Probab=22.75 E-value=64 Score=31.07 Aligned_cols=24 Identities=29% Similarity=0.427 Sum_probs=21.7
Q ss_pred CCHHHHHHHHHHhCCCHHHHHHHH
Q 047404 262 FDRNSARQALVQARNDINAATNIL 285 (291)
Q Consensus 262 f~~~~~~~aL~~~~~~~~~A~~~l 285 (291)
++++...+||+.++||..+|++.|
T Consensus 426 ~E~~~i~~al~~~~gn~~~aA~~L 449 (463)
T TIGR01818 426 FERPLLEAALQHTRGHKQEAAALL 449 (463)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHh
Confidence 578889999999999999999875
No 113
>PRK12570 N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=22.70 E-value=90 Score=28.67 Aligned_cols=31 Identities=32% Similarity=0.430 Sum_probs=25.3
Q ss_pred HHHHHHc-CCCCHHHHHHHHHHhCCCHHHHHH
Q 047404 253 SIAMLVS-MGFDRNSARQALVQARNDINAATN 283 (291)
Q Consensus 253 ~v~~l~~-mGf~~~~~~~aL~~~~~~~~~A~~ 283 (291)
++.-||. .|.+.++|++.|.+++|++..|++
T Consensus 261 k~ai~~~~~~~~~~~a~~~l~~~~~~~~~~l~ 292 (296)
T PRK12570 261 KLAILMILTGMDVEQARAALSHADGFLRKAIE 292 (296)
T ss_pred HHHHHHHHhCCCHHHHHHHHHHcCChHHHHHH
Confidence 3444543 479999999999999999999986
No 114
>PF03130 HEAT_PBS: PBS lyase HEAT-like repeat; InterPro: IPR004155 These proteins contain a short bi-helical repeat that is related to HEAT. Cyanobacteria and red algae harvest light energy using macromolecular complexes known as phycobilisomes (PBS), peripherally attached to the photosynthetic membrane. The major components of PBS are the phycobiliproteins. These heterodimeric proteins are covalently attached to phycobilins: open-chain tetrapyrrole chromophores, which function as the photosynthetic light-harvesting pigments. Phycobiliproteins differ in sequence and in the nature and number of attached phycobilins to each of their subunits. These proteins include the lyase enzymes that specifically attach particular phycobilins to apophycobiliprotein subunits. The most comprehensively studied of these is the CpcE/Flyase P31967 from SWISSPROT, P31968 from SWISSPROT, which attaches phycocyanobilin (PCB) to the alpha subunit of apophycocyanin []. Similarly, MpeU/V attaches phycoerythrobilin to phycoerythrin II, while CpeY/Z is thought to be involved in phycoerythrobilin (PEB) attachment to phycoerythrin (PE) I (PEs I and II differ in sequence and in the number of attached molecules of PEB: PE I has five, PE II has six) []. All the reactions of the above lyases involve an apoprotein cysteine SH addition to a terminal delta 3,3'-double bond. Such a reaction is not possible in the case of phycoviolobilin (PVB), the phycobilin of alpha-phycoerythrocyanin (alpha-PEC). It is thought that in this case, PCB, not PVB, is first added to apo-alpha-PEC, and is then isomerized to PVB. The addition reaction has been shown to occur in the presence of either of the components of alpha-PEC-PVB lyase PecE or PecF (or both). The isomerisation reaction occurs only when both PecE and PecF components are present, i.e. the PecE/F phycobiliprotein lyase is also a phycobilin isomerase []. Another member of this family is the NblB protein, whose similarity to the phycobiliprotein lyases was previously noted []. This constitutively expressed protein is not known to have any lyase activity. It is thought to be involved in the coordination of PBS degradation with environmental nutrient limitation. It has been suggested that the similarity of NblB to the phycobiliprotein lyases is due to the ability to bind tetrapyrrole phycobilins via the common repeated motif [].; PDB: 1TE4_A.
Probab=22.68 E-value=1.3e+02 Score=16.82 Aligned_cols=22 Identities=36% Similarity=0.374 Sum_probs=13.6
Q ss_pred HHHHHHHHHHhCCCHHHHHHHHHh
Q 047404 264 RNSARQALVQARNDINAATNILLE 287 (291)
Q Consensus 264 ~~~~~~aL~~~~~~~~~A~~~l~~ 287 (291)
|..|..||-+-++ ++|++.|.+
T Consensus 2 R~~Aa~aLg~igd--~~ai~~L~~ 23 (27)
T PF03130_consen 2 RRAAARALGQIGD--PRAIPALIE 23 (27)
T ss_dssp HHHHHHHHGGG-S--HHHHHHHHH
T ss_pred HHHHHHHHHHcCC--HHHHHHHHH
Confidence 4566777766654 677776654
No 115
>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=22.63 E-value=1.8e+02 Score=22.16 Aligned_cols=33 Identities=15% Similarity=0.098 Sum_probs=23.6
Q ss_pred HHHHHHHcCCCCHHHHHHHHHHh--CCCHHHHHHH
Q 047404 252 DSIAMLVSMGFDRNSARQALVQA--RNDINAATNI 284 (291)
Q Consensus 252 ~~v~~l~~mGf~~~~~~~aL~~~--~~~~~~A~~~ 284 (291)
..|..|.++||+-+++++.|... +++.+...+.
T Consensus 48 ~~I~~lr~~G~~l~~I~~~l~~~~~~~~~~~~~~~ 82 (108)
T cd04773 48 RLIHLLRRGGYLLEQIATVVEQLRHAGGTEALAAA 82 (108)
T ss_pred HHHHHHHHCCCCHHHHHHHHHHhhcCCCHHHHHHH
Confidence 45677888999999999999865 2445544443
No 116
>PRK06090 DNA polymerase III subunit delta'; Validated
Probab=22.57 E-value=1.4e+02 Score=27.83 Aligned_cols=35 Identities=11% Similarity=0.078 Sum_probs=28.3
Q ss_pred CHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHHHHHH
Q 047404 250 PEDSIAMLVSMGFDRNSARQALVQARNDINAATNILL 286 (291)
Q Consensus 250 ~~~~v~~l~~mGf~~~~~~~aL~~~~~~~~~A~~~l~ 286 (291)
+++..+-|.+.|.+ ++..+++.++|++.+|.+++-
T Consensus 169 ~~~~~~~L~~~~~~--~~~~~l~l~~G~p~~A~~~~~ 203 (319)
T PRK06090 169 TAQAMQWLKGQGIT--VPAYALKLNMGSPLKTLAMMK 203 (319)
T ss_pred HHHHHHHHHHcCCc--hHHHHHHHcCCCHHHHHHHhC
Confidence 46667788888887 456889999999999998764
No 117
>PF15187 Augurin: Oesophageal cancer-related gene 4
Probab=22.33 E-value=81 Score=24.29 Aligned_cols=21 Identities=24% Similarity=0.395 Sum_probs=16.5
Q ss_pred HHHHHHHHcCCCCHHHHHHHH
Q 047404 251 EDSIAMLVSMGFDRNSARQAL 271 (291)
Q Consensus 251 ~~~v~~l~~mGf~~~~~~~aL 271 (291)
++=++|.+-||||+.+-..-|
T Consensus 51 QQW~qQFlYmGFDEak~E~Dl 71 (114)
T PF15187_consen 51 QQWYQQFLYMGFDEAKFEDDL 71 (114)
T ss_pred HHHHHHHHHhcchHHHhhhhH
Confidence 677999999999987655443
No 118
>PRK03980 flap endonuclease-1; Provisional
Probab=22.29 E-value=1.1e+02 Score=28.16 Aligned_cols=28 Identities=29% Similarity=0.483 Sum_probs=21.7
Q ss_pred CCCHHHHHH-HH-cCCCCHHHHHHHHHHhC
Q 047404 248 EPPEDSIAM-LV-SMGFDRNSARQALVQAR 275 (291)
Q Consensus 248 ~~~~~~v~~-l~-~mGf~~~~~~~aL~~~~ 275 (291)
.++.|.+.+ |+ +.||+++++++++.+-.
T Consensus 248 ~pd~~~l~~fl~~e~~f~~~rv~~~~~~l~ 277 (292)
T PRK03980 248 EPDKEGIIEFLVEEHDFSEERVKKALERLE 277 (292)
T ss_pred CCCHHHHHHHHhccCCCCHHHHHHHHHHHH
Confidence 466777766 44 69999999999988763
No 119
>TIGR00112 proC pyrroline-5-carboxylate reductase. This enzyme catalyzes the final step in proline biosynthesis. Among the four paralogs in Bacillus subtilis (proG, proH, proI, and comER), ComER is the most divergent and does not prevent proline auxotrophy from mutation of the other three. It is excluded from the seed and scores between the trusted and noise cutoffs.
Probab=21.65 E-value=2e+02 Score=25.34 Aligned_cols=34 Identities=26% Similarity=0.272 Sum_probs=23.6
Q ss_pred HHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHHHHHHh
Q 047404 251 EDSIAMLVSMGFDRNSARQALVQARNDINAATNILLE 287 (291)
Q Consensus 251 ~~~v~~l~~mGf~~~~~~~aL~~~~~~~~~A~~~l~~ 287 (291)
|.-++-.+++|+++++|++...++ +.-+++.+.+
T Consensus 164 ~al~~~~v~~Gl~~~~A~~lv~~~---~~G~a~l~~~ 197 (245)
T TIGR00112 164 EALADAGVKQGLPRELALELAAQT---VKGAAKLLEE 197 (245)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHH---HHHHHHHHHh
Confidence 556667778999999998887766 4445555443
No 120
>PF06755 DUF1219: Protein of unknown function (DUF1219); InterPro: IPR009610 This family consists of several hypothetical proteins which seem to be specific to the enterobacteria Escherichia coli and Shigella flexneri. Family members are often known as YeeV proteins and are around 125 residues in length. The function of this family is unknown.
Probab=21.61 E-value=1.3e+02 Score=23.46 Aligned_cols=29 Identities=24% Similarity=0.255 Sum_probs=21.3
Q ss_pred CCCCHHHHHHHHHHhCCCHHHHHHHHHhc
Q 047404 260 MGFDRNSARQALVQARNDINAATNILLEA 288 (291)
Q Consensus 260 mGf~~~~~~~aL~~~~~~~~~A~~~l~~~ 288 (291)
-.|+.+.+++....+|=.+-.|+|+|.+.
T Consensus 41 T~f~de~vI~~hidaGIs~~~AVN~LVeK 69 (114)
T PF06755_consen 41 TPFSDETVIQEHIDAGISPADAVNFLVEK 69 (114)
T ss_pred CccchHHHHHHHHHhCCCHHHHHHHHHHH
Confidence 34677777777777777777788877664
No 121
>TIGR00678 holB DNA polymerase III, delta' subunit. At position 126-127 of the seed alignment, this family lacks the HM motif of gamma/tau; at 132 it has a near-invariant A vs. an invariant F in gamma/tau.
Probab=21.53 E-value=98 Score=25.76 Aligned_cols=32 Identities=25% Similarity=0.274 Sum_probs=25.4
Q ss_pred CHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHH
Q 047404 250 PEDSIAMLVSMGFDRNSARQALVQARNDINAA 281 (291)
Q Consensus 250 ~~~~v~~l~~mGf~~~~~~~aL~~~~~~~~~A 281 (291)
.+|..+-|...|.+++++...+..++||+.+|
T Consensus 157 ~~~~~~~l~~~gi~~~~~~~i~~~~~g~~r~~ 188 (188)
T TIGR00678 157 EEALLQWLIRQGISEEAAELLLALAGGSPGAA 188 (188)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHcCCCcccC
Confidence 34556667777999999999999999998765
No 122
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=21.11 E-value=1.1e+02 Score=20.72 Aligned_cols=21 Identities=24% Similarity=0.344 Sum_probs=17.1
Q ss_pred HHHHHHHcCCCCHHHHHHHHH
Q 047404 252 DSIAMLVSMGFDRNSARQALV 272 (291)
Q Consensus 252 ~~v~~l~~mGf~~~~~~~aL~ 272 (291)
+.+..|.++|++-++++++|.
T Consensus 48 ~~i~~lr~~g~~~~~i~~~l~ 68 (70)
T smart00422 48 RFIKRLKELGFSLEEIKELLE 68 (70)
T ss_pred HHHHHHHHcCCCHHHHHHHHh
Confidence 456778889999999998875
No 123
>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional
Probab=21.06 E-value=73 Score=30.56 Aligned_cols=24 Identities=13% Similarity=0.184 Sum_probs=21.5
Q ss_pred CCHHHHHHHHHHhCCCHHHHHHHH
Q 047404 262 FDRNSARQALVQARNDINAATNIL 285 (291)
Q Consensus 262 f~~~~~~~aL~~~~~~~~~A~~~l 285 (291)
++++..++||++++||..+|++.|
T Consensus 417 ~E~~~i~~al~~~~gn~~~aA~~L 440 (457)
T PRK11361 417 VEKRIIMEVLEQQEGNRTRTALML 440 (457)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHH
Confidence 578889999999999999999875
No 124
>TIGR00465 ilvC ketol-acid reductoisomerase. This is the second enzyme in the parallel isoleucine-valine biosynthetic pathway
Probab=21.02 E-value=1.5e+02 Score=27.38 Aligned_cols=34 Identities=18% Similarity=0.319 Sum_probs=23.8
Q ss_pred HHHHHHHcCCCCHHHHHHHHHHhCCCHHHHHHHHHhc
Q 047404 252 DSIAMLVSMGFDRNSARQALVQARNDINAATNILLEA 288 (291)
Q Consensus 252 ~~v~~l~~mGf~~~~~~~aL~~~~~~~~~A~~~l~~~ 288 (291)
.-++.|+++|++++.|.+--.++ +.-+++.+.++
T Consensus 195 ~~~ealv~~G~~~e~A~~~~~~~---~~g~~~l~~e~ 228 (314)
T TIGR00465 195 AGFDTLVEAGYQPELAYFETVHE---LKLIVDLIYEG 228 (314)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHH---HHHHHHHHHHh
Confidence 35688899999999887654444 55666666543
No 125
>smart00733 Mterf Mitochondrial termination factor repeats. Human mitochondrial termination factor is a DNA-binding protein that acts as a transcription termination factor. Six repeats occur in human mTERF, that also are present in numerous plant proteins.
Probab=20.76 E-value=73 Score=17.28 Aligned_cols=14 Identities=21% Similarity=0.534 Sum_probs=10.6
Q ss_pred CHHHHHHHHcCCCC
Q 047404 250 PEDSIAMLVSMGFD 263 (291)
Q Consensus 250 ~~~~v~~l~~mGf~ 263 (291)
-+++++-|.+|||+
T Consensus 18 l~~~~~~l~~~g~~ 31 (31)
T smart00733 18 LKPKVEFLKELGFS 31 (31)
T ss_pred hhHHHHHHHHcCCC
Confidence 35578888889985
No 126
>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. 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. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=20.46 E-value=2.4e+02 Score=20.62 Aligned_cols=35 Identities=23% Similarity=0.210 Sum_probs=26.3
Q ss_pred HHHHHHHcCCCCHHHHHHHHHHhCCCHHHHHHHHHh
Q 047404 252 DSIAMLVSMGFDRNSARQALVQARNDINAATNILLE 287 (291)
Q Consensus 252 ~~v~~l~~mGf~~~~~~~aL~~~~~~~~~A~~~l~~ 287 (291)
..|..|.+.|++-+++++.+. ..++.+..+.-|..
T Consensus 49 ~~I~~Lr~~G~sl~~i~~~l~-~~~~~~~~~~~~~~ 83 (88)
T cd01105 49 LVIKELLDEGFTLAAAVEKLR-RRRVQAEVRRRLMK 83 (88)
T ss_pred HHHHHHHHCCCCHHHHHHHHH-HccCHHHHHHHHHH
Confidence 457788899999999999986 44566666665554
No 127
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=20.44 E-value=88 Score=21.29 Aligned_cols=21 Identities=24% Similarity=0.283 Sum_probs=15.4
Q ss_pred HHHHHHcCCCCHHHHHHHHHH
Q 047404 253 SIAMLVSMGFDRNSARQALVQ 273 (291)
Q Consensus 253 ~v~~l~~mGf~~~~~~~aL~~ 273 (291)
.|..|.+.|++-+++++.|++
T Consensus 48 ~i~~l~~~G~sl~~I~~~l~~ 68 (69)
T PF13411_consen 48 EIKELRKQGMSLEEIKKLLKQ 68 (69)
T ss_dssp HHHHHHHTTTHHHHHHHHH--
T ss_pred HHHHHHHCcCCHHHHHHHHcc
Confidence 455677789999999998864
No 128
>PF06152 Phage_min_cap2: Phage minor capsid protein 2; InterPro: IPR009319 This entry is represented by Bacteriophage A118, Gp4, the minor capsid protein. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; GO: 0005198 structural molecule activity, 0019028 viral capsid
Probab=20.23 E-value=48 Score=31.43 Aligned_cols=41 Identities=12% Similarity=0.140 Sum_probs=35.6
Q ss_pred CCHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHHHHHHhcC
Q 047404 249 PPEDSIAMLVSMGFDRNSARQALVQARNDINAATNILLEAQ 289 (291)
Q Consensus 249 ~~~~~v~~l~~mGf~~~~~~~aL~~~~~~~~~A~~~l~~~~ 289 (291)
..+=.+++|.+||...+++++-+.+..+..+..++.++++.
T Consensus 45 ~~~WQ~~kL~~lg~~~~~i~k~I~~~~~~s~~~i~~~i~~a 85 (361)
T PF06152_consen 45 TADWQIEKLQELGMLNKEIKKIIAKYLGISEEEIRELIENA 85 (361)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34567999999999999999999999999999999888754
No 129
>PRK07940 DNA polymerase III subunit delta'; Validated
Probab=20.12 E-value=1.8e+02 Score=27.85 Aligned_cols=35 Identities=29% Similarity=0.374 Sum_probs=27.8
Q ss_pred HHHHHHHH-cCCCCHHHHHHHHHHhCCCHHHHHHHH
Q 047404 251 EDSIAMLV-SMGFDRNSARQALVQARNDINAATNIL 285 (291)
Q Consensus 251 ~~~v~~l~-~mGf~~~~~~~aL~~~~~~~~~A~~~l 285 (291)
++..+.|. ..|.+++++..+.+.++|++.+|.+++
T Consensus 179 ~~i~~~L~~~~~~~~~~a~~la~~s~G~~~~A~~l~ 214 (394)
T PRK07940 179 EAVAEVLVRRDGVDPETARRAARASQGHIGRARRLA 214 (394)
T ss_pred HHHHHHHHHhcCCCHHHHHHHHHHcCCCHHHHHHHh
Confidence 44455564 469999999999999999999998775
Done!