Query 020298
Match_columns 328
No_of_seqs 338 out of 1552
Neff 7.9
Searched_HMMs 46136
Date Fri Mar 29 08:37:32 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020298.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020298hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2632 Rhomboid family protei 100.0 5.3E-31 1.1E-35 233.7 17.7 243 31-285 13-258 (258)
2 PTZ00101 rhomboid-1 protease; 99.9 2.1E-24 4.6E-29 197.7 18.7 187 19-221 39-239 (278)
3 PRK10907 intramembrane serine 99.9 9.5E-24 2.1E-28 193.7 16.3 173 31-220 92-268 (276)
4 COG0705 Membrane associated se 99.8 4E-20 8.7E-25 166.5 15.9 178 31-219 15-208 (228)
5 PF01694 Rhomboid: Rhomboid fa 99.8 1.3E-18 2.7E-23 145.4 6.8 135 72-221 2-141 (145)
6 KOG2289 Rhomboid family protei 99.7 4.3E-19 9.3E-24 164.0 0.7 132 71-219 114-251 (316)
7 KOG0858 Predicted membrane pro 99.7 1.8E-16 3.8E-21 139.4 11.7 171 30-221 10-186 (239)
8 PF04511 DER1: Der1-like famil 99.6 1E-14 2.2E-19 128.5 15.0 175 32-221 1-181 (197)
9 KOG2290 Rhomboid family protei 99.4 2.4E-13 5.1E-18 128.5 5.7 133 73-219 448-582 (652)
10 COG5291 Predicted membrane pro 98.9 1.1E-09 2.4E-14 96.5 5.2 168 27-217 14-191 (313)
11 PF08551 DUF1751: Eukaryotic i 98.8 4.4E-09 9.5E-14 82.3 5.0 90 75-165 7-96 (99)
12 KOG2890 Predicted membrane pro 98.8 5.5E-08 1.2E-12 88.5 11.7 185 31-219 23-216 (326)
13 KOG2980 Integral membrane prot 98.4 2.5E-07 5.4E-12 84.5 4.1 172 35-219 117-298 (310)
14 PF00641 zf-RanBP: Zn-finger i 98.1 6.1E-07 1.3E-11 54.4 0.4 29 272-300 2-30 (30)
15 smart00547 ZnF_RBZ Zinc finger 97.8 9.9E-06 2.1E-10 47.3 1.6 25 273-297 1-25 (26)
16 KOG4463 Uncharacterized conser 97.7 1.4E-05 3E-10 71.6 1.7 90 34-128 12-101 (323)
17 KOG4477 RING1 interactor RYBP 94.0 0.037 8.1E-07 47.2 2.3 37 266-302 16-52 (228)
18 KOG4198 RNA-binding Ran Zn-fin 92.2 0.077 1.7E-06 48.8 1.8 32 271-302 137-168 (280)
19 cd00729 rubredoxin_SM Rubredox 90.1 0.13 2.8E-06 31.9 0.7 26 274-299 2-29 (34)
20 cd00350 rubredoxin_like Rubred 89.3 0.17 3.7E-06 31.0 0.9 26 274-299 1-28 (33)
21 COG1592 Rubrerythrin [Energy p 85.5 0.4 8.8E-06 40.9 1.2 26 274-299 134-160 (166)
22 PF13240 zinc_ribbon_2: zinc-r 84.6 0.67 1.4E-05 26.0 1.5 22 276-297 1-22 (23)
23 COG5100 NPL4 Nuclear pore prot 84.5 0.22 4.8E-06 47.7 -0.8 24 275-298 547-570 (571)
24 PF13248 zf-ribbon_3: zinc-rib 82.7 0.86 1.9E-05 26.3 1.4 23 275-297 3-25 (26)
25 COG2093 DNA-directed RNA polym 82.3 0.75 1.6E-05 32.4 1.3 31 275-305 5-35 (64)
26 PRK06393 rpoE DNA-directed RNA 79.8 1.2 2.5E-05 31.7 1.6 27 275-303 6-32 (64)
27 PRK12496 hypothetical protein; 78.4 1.3 2.8E-05 37.8 1.7 23 275-297 128-152 (164)
28 PRK08351 DNA-directed RNA poly 74.1 2.3 5E-05 30.0 1.8 27 276-304 5-31 (61)
29 KOG3476 Microtubule-associated 72.8 0.65 1.4E-05 34.8 -1.3 26 271-300 66-91 (100)
30 PF13597 NRDD: Anaerobic ribon 67.4 2.1 4.6E-05 43.6 0.6 49 274-324 491-544 (546)
31 TIGR02487 NrdD anaerobic ribon 63.6 6.8 0.00015 40.3 3.4 49 274-323 524-577 (579)
32 PRK08271 anaerobic ribonucleos 62.4 7.9 0.00017 40.1 3.6 51 274-325 566-621 (623)
33 PF10235 Cript: Microtubule-as 61.9 4.7 0.0001 30.8 1.4 27 273-303 58-84 (90)
34 PF14206 Cys_rich_CPCC: Cystei 60.6 9.3 0.0002 28.4 2.7 48 275-322 2-55 (78)
35 PF09527 ATPase_gene1: Putativ 60.1 46 0.001 22.5 6.1 40 91-130 9-48 (55)
36 COG3931 Predicted N-formylglut 58.7 8.9 0.00019 34.5 2.8 34 293-327 85-123 (263)
37 PRK11788 tetratricopeptide rep 58.7 5.1 0.00011 38.1 1.4 25 274-298 354-378 (389)
38 KOG4198 RNA-binding Ran Zn-fin 57.2 5.4 0.00012 36.9 1.2 36 268-303 58-93 (280)
39 TIGR02827 RNR_anaer_Bdell anae 56.6 8.6 0.00019 39.5 2.7 48 274-322 532-584 (586)
40 PF12773 DZR: Double zinc ribb 56.4 9.6 0.00021 25.2 2.1 23 273-295 28-50 (50)
41 PF09538 FYDLN_acid: Protein o 54.8 11 0.00023 29.9 2.4 32 275-306 10-45 (108)
42 PF14446 Prok-RING_1: Prokaryo 54.2 7.3 0.00016 26.8 1.2 26 275-300 6-33 (54)
43 PRK07111 anaerobic ribonucleos 52.5 11 0.00024 39.8 2.8 49 274-324 680-733 (735)
44 PRK14704 anaerobic ribonucleos 51.8 13 0.00028 38.6 3.0 51 274-325 559-617 (618)
45 PF12898 Stc1: Stc1 domain; I 51.6 9.9 0.00021 28.6 1.7 40 271-311 34-73 (84)
46 PF06945 DUF1289: Protein of u 48.0 11 0.00024 25.4 1.3 20 279-300 7-26 (51)
47 PF12773 DZR: Double zinc ribb 47.6 12 0.00026 24.7 1.4 23 277-299 1-23 (50)
48 TIGR02300 FYDLN_acid conserved 46.5 16 0.00035 29.6 2.2 27 275-301 10-39 (129)
49 PF04528 Adeno_E4_34: Adenovir 46.3 5.9 0.00013 33.2 -0.3 49 275-327 82-139 (148)
50 cd00730 rubredoxin Rubredoxin; 46.1 13 0.00028 25.1 1.3 9 290-298 36-44 (50)
51 COG1773 Rubredoxin [Energy pro 44.3 11 0.00024 26.0 0.8 10 274-283 3-12 (55)
52 PF12172 DUF35_N: Rubredoxin-l 43.7 8 0.00017 24.0 0.1 24 275-298 12-35 (37)
53 PRK00415 rps27e 30S ribosomal 43.1 12 0.00026 26.2 0.9 25 275-299 12-41 (59)
54 COG4068 Uncharacterized protei 42.7 22 0.00048 24.7 2.1 15 287-301 7-21 (64)
55 COG2051 RPS27A Ribosomal prote 41.9 11 0.00024 26.9 0.6 25 275-299 20-49 (67)
56 PRK08579 anaerobic ribonucleos 41.9 14 0.00029 38.5 1.4 51 272-323 566-621 (625)
57 PF05191 ADK_lid: Adenylate ki 40.9 14 0.0003 23.1 0.8 22 275-296 2-29 (36)
58 COG2995 PqiA Uncharacterized p 40.8 17 0.00036 35.3 1.7 27 271-297 217-244 (418)
59 PF07295 DUF1451: Protein of u 39.7 19 0.00041 30.1 1.7 31 268-298 106-140 (146)
60 KOG4345 NF-kappa B regulator A 39.6 11 0.00023 39.0 0.3 30 275-304 186-215 (774)
61 PRK14526 adenylate kinase; Pro 39.5 33 0.00072 30.3 3.4 40 274-327 122-170 (211)
62 PRK03824 hypA hydrogenase nick 39.3 14 0.00029 30.5 0.8 29 270-298 66-117 (135)
63 COG1066 Sms Predicted ATP-depe 38.2 17 0.00036 35.7 1.4 24 273-296 6-29 (456)
64 PTZ00088 adenylate kinase 1; P 37.7 39 0.00085 30.3 3.6 30 289-327 159-188 (229)
65 PF09723 Zn-ribbon_8: Zinc rib 37.6 23 0.0005 22.7 1.5 26 275-300 6-38 (42)
66 COG5336 Uncharacterized protei 37.1 90 0.002 24.7 5.0 31 207-237 53-83 (116)
67 TIGR03037 anthran_nbaC 3-hydro 36.9 21 0.00045 30.3 1.6 16 281-296 144-159 (159)
68 COG5257 GCD11 Translation init 36.2 25 0.00053 33.6 2.1 26 274-299 57-83 (415)
69 TIGR00416 sms DNA repair prote 35.7 23 0.0005 35.3 1.9 23 274-296 7-29 (454)
70 PF10571 UPF0547: Uncharacteri 35.3 25 0.00055 20.2 1.3 21 276-296 2-22 (26)
71 PRK09263 anaerobic ribonucleos 35.2 34 0.00073 36.2 3.2 51 274-324 641-704 (711)
72 PRK11823 DNA repair protein Ra 34.8 24 0.00053 35.0 2.0 25 273-297 6-30 (446)
73 COG2401 ABC-type ATPase fused 34.6 17 0.00038 35.8 0.8 26 271-297 127-153 (593)
74 PRK05452 anaerobic nitric oxid 34.5 16 0.00035 36.7 0.6 29 271-299 422-469 (479)
75 COG1328 NrdD Oxygen-sensitive 34.3 33 0.00072 36.0 2.9 24 275-298 642-665 (700)
76 PF00301 Rubredoxin: Rubredoxi 34.1 13 0.00029 24.7 0.0 11 270-280 30-40 (47)
77 PF12989 DUF3873: Domain of un 33.7 28 0.00061 25.0 1.6 12 313-324 51-62 (69)
78 COG1110 Reverse gyrase [DNA re 33.5 17 0.00037 39.5 0.7 30 274-303 694-723 (1187)
79 PRK12286 rpmF 50S ribosomal pr 33.4 50 0.0011 22.9 2.8 28 271-299 24-51 (57)
80 PRK12380 hydrogenase nickel in 33.4 23 0.00049 28.2 1.2 29 271-299 67-97 (113)
81 PRK03681 hypA hydrogenase nick 33.0 19 0.00041 28.7 0.7 29 271-299 67-98 (114)
82 TIGR00686 phnA alkylphosphonat 32.9 20 0.00044 28.2 0.8 24 276-299 4-30 (109)
83 PF06946 Phage_holin_5: Phage 32.6 1.2E+02 0.0025 23.4 4.8 11 181-191 31-41 (93)
84 PRK00398 rpoP DNA-directed RNA 31.1 30 0.00066 22.5 1.3 25 275-299 4-32 (46)
85 COG2888 Predicted Zn-ribbon RN 30.6 17 0.00036 25.5 -0.0 21 274-296 38-58 (61)
86 PRK05978 hypothetical protein; 30.2 35 0.00077 28.6 1.9 25 275-299 34-63 (148)
87 TIGR00627 tfb4 transcription f 29.9 40 0.00086 31.4 2.4 30 268-297 249-278 (279)
88 TIGR02230 ATPase_gene1 F0F1-AT 29.5 1.9E+02 0.0041 22.5 5.7 40 90-129 50-89 (100)
89 TIGR00615 recR recombination p 29.1 44 0.00095 29.3 2.4 26 274-301 53-78 (195)
90 PRK10220 hypothetical protein; 28.4 29 0.00064 27.4 1.0 22 276-297 5-29 (111)
91 PF14169 YdjO: Cold-inducible 28.4 37 0.00081 23.8 1.4 27 272-298 16-49 (59)
92 KOG1995 Conserved Zn-finger pr 28.2 45 0.00097 31.8 2.4 37 273-309 217-254 (351)
93 PF09334 tRNA-synt_1g: tRNA sy 27.1 30 0.00065 33.7 1.1 24 275-299 137-160 (391)
94 PRK13130 H/ACA RNA-protein com 26.9 1.3E+02 0.0028 20.9 3.8 24 274-299 5-28 (56)
95 PRK00076 recR recombination pr 26.7 53 0.0011 28.9 2.4 26 274-301 53-78 (196)
96 COG1439 Predicted nucleic acid 26.6 31 0.00066 29.8 0.9 23 275-297 140-162 (177)
97 PRK14559 putative protein seri 26.0 39 0.00086 35.2 1.8 24 276-299 29-52 (645)
98 COG1997 RPL43A Ribosomal prote 25.9 31 0.00067 26.1 0.7 15 269-283 48-62 (89)
99 COG1198 PriA Primosomal protei 25.8 40 0.00086 35.7 1.7 24 273-297 461-484 (730)
100 PF03875 Statherin: Statherin; 25.7 46 0.00099 21.0 1.3 14 315-328 2-15 (42)
101 PF01667 Ribosomal_S27e: Ribos 25.6 33 0.00072 23.7 0.8 22 276-297 9-35 (55)
102 PF08274 PhnA_Zn_Ribbon: PhnA 25.5 40 0.00086 20.2 1.0 21 276-296 4-27 (30)
103 PF02132 RecR: RecR protein; 25.3 15 0.00032 23.5 -1.0 24 274-299 17-40 (41)
104 COG2260 Predicted Zn-ribbon RN 24.6 1.3E+02 0.0028 21.0 3.5 23 275-299 6-28 (59)
105 PF04135 Nop10p: Nucleolar RNA 24.0 76 0.0016 21.7 2.3 44 276-328 7-53 (53)
106 PRK13264 3-hydroxyanthranilate 23.6 33 0.00071 29.6 0.5 21 281-301 150-170 (177)
107 COG1545 Predicted nucleic-acid 23.5 40 0.00086 27.9 1.0 23 275-297 30-52 (140)
108 PF14319 Zn_Tnp_IS91: Transpos 23.1 60 0.0013 25.7 1.9 27 274-300 42-72 (111)
109 PRK00564 hypA hydrogenase nick 23.1 44 0.00095 26.7 1.2 29 271-299 68-99 (117)
110 TIGR02605 CxxC_CxxC_SSSS putat 23.0 49 0.0011 21.9 1.2 30 275-304 6-42 (52)
111 PRK13844 recombination protein 22.5 68 0.0015 28.3 2.3 26 274-301 57-82 (200)
112 PRK14892 putative transcriptio 22.1 44 0.00095 26.0 1.0 29 271-300 18-54 (99)
113 PLN02674 adenylate kinase 21.8 1E+02 0.0023 27.9 3.5 11 317-327 196-206 (244)
114 KOG3474 Molybdopterin converti 21.6 72 0.0016 23.3 1.9 32 289-327 11-42 (84)
115 COG0143 MetG Methionyl-tRNA sy 21.5 51 0.0011 33.8 1.6 25 275-300 143-167 (558)
116 PRK00762 hypA hydrogenase nick 21.5 40 0.00086 27.3 0.6 28 271-299 67-103 (124)
117 PF11672 DUF3268: Protein of u 21.5 1.1E+02 0.0024 23.9 3.1 34 289-325 32-65 (102)
118 COG2176 PolC DNA polymerase II 21.3 71 0.0015 35.6 2.6 33 269-301 909-952 (1444)
119 KOG4443 Putative transcription 21.2 45 0.00098 34.4 1.1 10 272-281 60-69 (694)
120 COG0353 RecR Recombinational D 21.0 72 0.0016 28.0 2.1 26 274-301 54-79 (198)
121 PF11682 DUF3279: Protein of u 20.6 49 0.0011 27.0 1.0 23 274-297 97-119 (128)
122 PF05484 LRV_FeS: LRV protein 20.5 42 0.0009 23.3 0.5 11 317-327 36-46 (57)
123 PRK14715 DNA polymerase II lar 20.4 1E+02 0.0022 34.9 3.5 30 275-306 675-704 (1627)
124 COG4317 Uncharacterized protei 20.4 3E+02 0.0065 20.6 4.9 29 205-235 7-35 (93)
125 cd01675 RNR_III Class III ribo 20.3 63 0.0014 33.1 1.9 23 276-298 520-542 (555)
126 PRK00420 hypothetical protein; 20.2 69 0.0015 25.5 1.7 26 275-300 24-52 (112)
No 1
>KOG2632 consensus Rhomboid family proteins [Function unknown]
Probab=99.97 E-value=5.3e-31 Score=233.75 Aligned_cols=243 Identities=36% Similarity=0.463 Sum_probs=198.6
Q ss_pred CChHHHHHHHHHHHHHHhhhhhhcCchhhhcccccchhhhcccCCcchhccccccCCChhHHHHHHHHHHHHHHHHHhhh
Q 020298 31 WKPPVTAALLATNTLIYLRPAFLDSLVPSIHEVWFNPHLILKYKDLKRFFLSPFYHASESHLFYNMMSLLWKGIQLETSM 110 (328)
Q Consensus 31 ~~P~vt~~li~i~v~v~ll~~~~~~~~~~~~~~~l~p~~i~~~~q~wRL~T~~f~H~~~~Hll~Nm~~L~~~G~~lE~~~ 110 (328)
+.|.+|..++.++.++|+...+. ......+.|..++++.|+||++||+++|.+..|+++||++++..|.++|+.+
T Consensus 13 ~~p~~ts~~~~~~~~i~lv~~~~-----~i~~~~~l~~~~l~~~ql~RL~Ty~l~H~s~~hllfnmlaL~~~g~~fE~~~ 87 (258)
T KOG2632|consen 13 KIPLLTSIVVVLAILIYLVSFFP-----GIVEVLGLPSELLINWQLYRLITYALVHLSLPHLLFNMLALWPLGSQFERTH 87 (258)
T ss_pred cchHHHHHHHHHHHHHHHHhccc-----hhhhHhcCCHHHhhhHHHHHHHHHHHHhccHHHHHHHHHHHHhchhHHHhhc
Confidence 77889999999999999975432 2346677788888899999999999999999999999999999999999999
Q ss_pred C-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccccccccchhHHHHHHHHHHHHhcCCCcc-eeeccc-hhhHHHH
Q 020298 111 G-SNEFAAMVVALLGMSQGITLLLAKSLVLFFDYERAYYSEYAVGFSGVLFAMKVVLNSRSEDYT-NVHGLL-VPARYAA 187 (328)
Q Consensus 111 G-~~~f~~~yl~~~~~~~~l~~ll~~~l~~~~~~~~~~~~~~~~GaSg~ifgl~~~~~~~~~~~~-~~~~i~-i~~~~~~ 187 (328)
| +.+++.++ .+.++.+++.+++.... +......++..++|.||+.||+++....+.+.+. .+++.. ||+++.|
T Consensus 88 G~t~~~l~~~-~llalf~gIl~ll~~~~---~~~~d~~~~~~a~G~s~v~Fam~~~~~~~sp~r~~~~fg~~siP~~l~P 163 (258)
T KOG2632|consen 88 GTTVRILMFT-VLLALFSGILYLLAYHV---FLLSDLVYVEGAIGFSGVLFAMMAVLEVQSPVRSRSVFGLFSIPIVLAP 163 (258)
T ss_pred cceehHHHHH-HHHHHHHHHHHHHHHHH---HhhcchhhhcccccccHHHHHHHHHHhhcCcccchhhcccccccHHHHH
Confidence 9 66665554 56666666666665542 2233344567899999999999999888887665 567765 9999999
Q ss_pred HHHHHHHHhcCCchHHHHHHHHHHHHHHHHHHhccCCCCCcHHHHHHHHHHHhhhhHhhhhhhhccccccCccccccCCC
Q 020298 188 WAELIIIQMFVPGVSFLGHLGGILAGILYLKLKGGYSGSDPLTTIIRGATGVLSWPLRFARYLFRRPRIYGRGTVGGSDT 267 (328)
Q Consensus 188 ~~~l~~~~~~~~~vs~~aHl~G~l~G~ly~~~~~~~~~~~p~~~~~~~~~~~l~~~~~~~~~~~~~~~~~g~g~v~~~~~ 267 (328)
|+.++.+.++.|+.|+++|+||+++|++|.+. .+ +..|..+....++......+++.....+..+..+++.+..+..
T Consensus 164 w~lLi~~~~lvp~aSFlghl~GllvG~ay~~~--~f-~lip~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~ 240 (258)
T KOG2632|consen 164 WALLIATQILVPQASFLGHLCGLLVGYAYAFS--SF-GLIPGIRNYRAVTEAAWSLLRLAPWIQDLGSNSGRGIVFPGLT 240 (258)
T ss_pred HHHHHHHHHHccCchHHHHHHHHHHHHHHHHH--hh-ccCCcchhHHHhhhhhhhhhhcCCcHHHhccccCCceeccCcC
Confidence 99999999999999999999999999999997 44 7888888888888887877777776665555556676666677
Q ss_pred CCCCCCcccCCCCccCCC
Q 020298 268 RRTAPIIWRCPACTFDNS 285 (328)
Q Consensus 268 ~~~~~g~W~c~~C~~~n~ 285 (328)
..+.++.|.|++||++|+
T Consensus 241 ~~~~P~~~~~~~~t~~~~ 258 (258)
T KOG2632|consen 241 GSPFPGPLHCQSGTLDNS 258 (258)
T ss_pred CCCCCCccccCCcccCCC
Confidence 777889999999988874
No 2
>PTZ00101 rhomboid-1 protease; Provisional
Probab=99.93 E-value=2.1e-24 Score=197.65 Aligned_cols=187 Identities=20% Similarity=0.230 Sum_probs=130.4
Q ss_pred hhHHHHHhccCCCChHHHHHHHHHHHHHHhhhhhhcCch---h---hh-cccccchhhhcccCCcchhccccccCCChhH
Q 020298 19 ALHAFNEYHRLPWKPPVTAALLATNTLIYLRPAFLDSLV---P---SI-HEVWFNPHLILKYKDLKRFFLSPFYHASESH 91 (328)
Q Consensus 19 ~~~~~~~~~~~~~~P~vt~~li~i~v~v~ll~~~~~~~~---~---~~-~~~~l~p~~i~~~~q~wRL~T~~f~H~~~~H 91 (328)
.++..++.++.-++|.+|..++++++++|++....+... | .. ...+++|..+ +++|+||++|++|+|.++.|
T Consensus 39 ~i~~ler~Fp~f~i~~l~~~Iiii~iivfil~l~~~~~~~l~p~~~~L~~~Ga~~~~~i-~~gq~WRLiT~~FlH~~~~H 117 (278)
T PTZ00101 39 PIDVLNLIFPHFTWKSFIMAISIIQIIVFIISVSIKPADFLTPSDSLLVTLGANVASRI-KQGEIHRLILPIFLHANIFH 117 (278)
T ss_pred ChHHHHHHcCCccHHHHHHHHHHHHHHHHHHHHHhcccccCCCCHHHHHHHhCcchhhh-hcCCCHHHHHHHHHccCHHH
Confidence 356667777777999999999999999999865533211 1 12 2345677776 57999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhhhChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccccccccchhHHHHHHHHHHHHhcCC
Q 020298 92 LFYNMMSLLWKGIQLETSMGSNEFAAMVVALLGMSQGITLLLAKSLVLFFDYERAYYSEYAVGFSGVLFAMKVVLNSRSE 171 (328)
Q Consensus 92 ll~Nm~~L~~~G~~lE~~~G~~~f~~~yl~~~~~~~~l~~ll~~~l~~~~~~~~~~~~~~~~GaSg~ifgl~~~~~~~~~ 171 (328)
+++||++++.+|..+|+.+|+.|++.+|+ ++|+.+.+. +. .+.. ...++||||++||+++++....-
T Consensus 118 Ll~Nm~~l~~~G~~lE~~~G~~r~~ilYl-~sGi~G~l~---s~----~~~~-----~~~svGASgAifGLiGa~~~~li 184 (278)
T PTZ00101 118 TFFNVFFQLRMGFTLEKNYGIVKIIILYF-LTGIYGNIL---SS----SVTY-----CPIKVGASTSGMGLLGIVTSELI 184 (278)
T ss_pred HHHHHHHHHHHHHHHHHHHChHHHHHHHH-HHHHHHHHH---HH----HHcc-----CCcEEehhHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999995 566665543 11 1221 14589999999999988643210
Q ss_pred CcceeeccchhhHH----HHHHHH---HHHHhcCCchHHHHHHHHHHHHHHHHHHhc
Q 020298 172 DYTNVHGLLVPARY----AAWAEL---IIIQMFVPGVSFLGHLGGILAGILYLKLKG 221 (328)
Q Consensus 172 ~~~~~~~i~i~~~~----~~~~~l---~~~~~~~~~vs~~aHl~G~l~G~ly~~~~~ 221 (328)
... ..+..+.+. ..++.+ .......+++|+.||++|+++|++++....
T Consensus 185 l~w--~~~~~~~~~~~~~i~~~li~~~l~~~~~g~~Id~~aHlGG~i~G~llg~~~~ 239 (278)
T PTZ00101 185 LLW--HVIRHRERVVFNIIFFSLISFFYYFTFNGSNIDHVGHLGGLLSGISMGILYN 239 (278)
T ss_pred HHH--HhhccHHHHHHHHHHHHHHHHHHHHhcCCCCccHHHHHHHHHHHHHHHHHHH
Confidence 000 000001111 111111 112223578999999999999999998643
No 3
>PRK10907 intramembrane serine protease GlpG; Provisional
Probab=99.91 E-value=9.5e-24 Score=193.73 Aligned_cols=173 Identities=18% Similarity=0.310 Sum_probs=120.9
Q ss_pred CChHHHHHHHHHHHHHHhhhhhhcCchhhhcccccchhhhcccCCcchhccccccCCChhHHHHHHHHHHHHHHHHHhhh
Q 020298 31 WKPPVTAALLATNTLIYLRPAFLDSLVPSIHEVWFNPHLILKYKDLKRFFLSPFYHASESHLFYNMMSLLWKGIQLETSM 110 (328)
Q Consensus 31 ~~P~vt~~li~i~v~v~ll~~~~~~~~~~~~~~~l~p~~i~~~~q~wRL~T~~f~H~~~~Hll~Nm~~L~~~G~~lE~~~ 110 (328)
+..|+|..++++|+++|++..+.+. ......+.+ |.....++|+||++|++|+|.|+.|+++||+++|.+|..+|+.+
T Consensus 92 ~~~p~T~~li~i~i~vf~l~~~~~~-~~~~~~l~~-~~~~~~~~q~WRl~T~~flH~~~~Hl~fNml~l~~lG~~iE~~~ 169 (276)
T PRK10907 92 RAGPLTLGVMIACVVVFILMQILGD-QTVMLWLAW-PFDPSLKFELWRYFTHALLHFSLLHILFNLLWWWYLGGAVEKRL 169 (276)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHhcc-HHHHHHHhc-cccccccCCcHHHHhHHHHhCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567999999999999998765433 112223332 33333578999999999999999999999999999999999999
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccccccccchhHHHHHHHHHHHHhcCCCcceeeccchhhHHHH---
Q 020298 111 GSNEFAAMVVALLGMSQGITLLLAKSLVLFFDYERAYYSEYAVGFSGVLFAMKVVLNSRSEDYTNVHGLLVPARYAA--- 187 (328)
Q Consensus 111 G~~~f~~~yl~~~~~~~~l~~ll~~~l~~~~~~~~~~~~~~~~GaSg~ifgl~~~~~~~~~~~~~~~~i~i~~~~~~--- 187 (328)
|+.+++.+|+ ++++.+++. .+.+.. ....|+||+++|++++......... ..++.+|...+.
T Consensus 170 G~~~~l~l~l-~s~i~~~~~-------~~~~~~------~~~gGaSGvVygL~g~~~~~~~~~p-~~~~~lp~~~~~f~l 234 (276)
T PRK10907 170 GSGKLIVITL-ISALLSGWV-------QSKFSG------PWFGGLSGVVYALMGYVWLRGERDP-QSGIYLPRGLIAFAL 234 (276)
T ss_pred ChHHHHHHHH-HHHHHHHHH-------HHHHcc------chhhHHHHHHHHHHHHHHHHhcccc-ccchhhhHHHHHHHH
Confidence 9999999995 455554433 122332 3368999999999987543221111 112223333322
Q ss_pred -HHHHHHHHhcCCchHHHHHHHHHHHHHHHHHHh
Q 020298 188 -WAELIIIQMFVPGVSFLGHLGGILAGILYLKLK 220 (328)
Q Consensus 188 -~~~l~~~~~~~~~vs~~aHl~G~l~G~ly~~~~ 220 (328)
|+.+.....+.+++++.||++|+++|+++++..
T Consensus 235 lwl~~g~~~~~g~~Ian~AHlgGli~Gll~g~~~ 268 (276)
T PRK10907 235 LWLVAGYFDLFGMSIANAAHVAGLAVGLAMAFWD 268 (276)
T ss_pred HHHHHHHHHccCcccHHHHHHHHHHHHHHHHHHh
Confidence 222223444567899999999999999999863
No 4
>COG0705 Membrane associated serine protease [Amino acid transport and metabolism]
Probab=99.84 E-value=4e-20 Score=166.50 Aligned_cols=178 Identities=26% Similarity=0.345 Sum_probs=124.0
Q ss_pred CChHHHHHHHHHHHHHHhhhhhhcCchh-----hhcccccchhhhcccC---CcchhccccccCCChhHHHHHHHHHHHH
Q 020298 31 WKPPVTAALLATNTLIYLRPAFLDSLVP-----SIHEVWFNPHLILKYK---DLKRFFLSPFYHASESHLFYNMMSLLWK 102 (328)
Q Consensus 31 ~~P~vt~~li~i~v~v~ll~~~~~~~~~-----~~~~~~l~p~~i~~~~---q~wRL~T~~f~H~~~~Hll~Nm~~L~~~ 102 (328)
+.|++|..++++|+++++.....+.... ........|....... |+||++|++|+|.|+.|+++||+.+|.+
T Consensus 15 ~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~lit~~FlH~~~~Hll~N~~~l~~f 94 (228)
T COG0705 15 RAPPVTLFLILLNILVFLLELVLGWSAIFLLTFLFRLFGLYPLNLLGALARDQLWRLITAIFLHAGFLHLLFNMLALWVF 94 (228)
T ss_pred ccchHHHHHHHHHHHHHHHHHHccchHHHHHHHhhhHHhhcchhhhccccccchHHHHHHHHHHhhHHHHHHHHHHHHHh
Confidence 4689999999999999998765433210 0112445555443332 8999999999999999999999999999
Q ss_pred HHHHHhhhChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccccccccchhHHHHHHHHHHHHhcCCCcce-eec--c
Q 020298 103 GIQLETSMGSNEFAAMVVALLGMSQGITLLLAKSLVLFFDYERAYYSEYAVGFSGVLFAMKVVLNSRSEDYTN-VHG--L 179 (328)
Q Consensus 103 G~~lE~~~G~~~f~~~yl~~~~~~~~l~~ll~~~l~~~~~~~~~~~~~~~~GaSg~ifgl~~~~~~~~~~~~~-~~~--i 179 (328)
|..+|+.+|+.+|+.+|+ .+++.+++. ...+.... ..+.+||||++||++++.....+.... ... +
T Consensus 95 g~~le~~~G~~~f~~~yl-~~gl~~~~~-------~~~~~~~~---~~~~~GASG~i~gllga~~~~~~~~~~~~~~~~~ 163 (228)
T COG0705 95 GSNLERRLGTLRFLLFYL-LSGLLAGLA-------QVLFGPKG---GAPSLGASGAIFGLLGAYFLLFPFARILLLFLSL 163 (228)
T ss_pred hHHHHHHhchhHHHHHHH-HHHHHHHHH-------HHHHcccc---cCcccchhHHHHHHHHHHHHHccccchhhhhccC
Confidence 999999999999999995 455555543 12233321 147899999999999998876654332 122 3
Q ss_pred chhhHHHHHHHHH--HHHhc-C--CchHHHHHHHHHHHHHHHHHH
Q 020298 180 LVPARYAAWAELI--IIQMF-V--PGVSFLGHLGGILAGILYLKL 219 (328)
Q Consensus 180 ~i~~~~~~~~~l~--~~~~~-~--~~vs~~aHl~G~l~G~ly~~~ 219 (328)
+.+...+..+.++ ++... . +++++.+|++|++.|.+++..
T Consensus 164 ~~~~~~~i~~~~~~~~~~~~~~~~~~va~~aHl~G~i~G~l~~~~ 208 (228)
T COG0705 164 PRPALILILIWLLYSLFSGAGSFGPSVAWSAHLGGLIGGLLLAAL 208 (228)
T ss_pred chhHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHHHHHH
Confidence 3333332222111 12222 1 268999999999999999975
No 5
>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=99.75 E-value=1.3e-18 Score=145.37 Aligned_cols=135 Identities=35% Similarity=0.528 Sum_probs=89.0
Q ss_pred ccCCcchhccccccCCChhHHHHHHHHHHHHHHHHHhhhChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccccccc
Q 020298 72 KYKDLKRFFLSPFYHASESHLFYNMMSLLWKGIQLETSMGSNEFAAMVVALLGMSQGITLLLAKSLVLFFDYERAYYSEY 151 (328)
Q Consensus 72 ~~~q~wRL~T~~f~H~~~~Hll~Nm~~L~~~G~~lE~~~G~~~f~~~yl~~~~~~~~l~~ll~~~l~~~~~~~~~~~~~~ 151 (328)
+++|+||++|++|+|.|+.|+++|++.++.+|..+|+.+|+.++..+|+ .+++.+++...+ +.... ..
T Consensus 2 ~~~~~wrl~T~~f~h~~~~hl~~n~~~l~~~g~~lE~~~G~~~~~~~~l-~~~~~~~l~~~~-------~~~~~----~~ 69 (145)
T PF01694_consen 2 QNGQWWRLFTSPFVHANFLHLLFNLLALWFFGSLLERRLGSRRFLALYL-LSGLLGSLLSLL-------FSPPN----QP 69 (145)
T ss_dssp GCC-TTHHHHGGG--SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHH-------HH-S-------
T ss_pred CCCcchhhhHHHHHccCHHHHHHHHHHHHHhhhhHhhhccchHHHHHHH-HHHHhhhhcccc-------ccccc----cc
Confidence 5799999999999999999999999999999999999999999999995 344444443221 22211 26
Q ss_pred cchhHHHHHHHHHHHHhcCCCc---cee--eccchhhHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHHHHhc
Q 020298 152 AVGFSGVLFAMKVVLNSRSEDY---TNV--HGLLVPARYAAWAELIIIQMFVPGVSFLGHLGGILAGILYLKLKG 221 (328)
Q Consensus 152 ~~GaSg~ifgl~~~~~~~~~~~---~~~--~~i~i~~~~~~~~~l~~~~~~~~~vs~~aHl~G~l~G~ly~~~~~ 221 (328)
.+|+||+++|++++.....+.. ... ..+.++...+++. ......+++++.+|++|+++|++++...+
T Consensus 70 ~~G~Sg~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~hl~G~~~G~~~~~~~~ 141 (145)
T PF01694_consen 70 YVGASGAVFGLLGAFLFLYPQNKKRLRFIYLALVVPIIVLVII---LLLGFIPNISFLGHLGGFLAGLLYGFLIL 141 (145)
T ss_dssp --SSHHHHHHHHHHHHHHHHCCCCCS---HCCCCCCCCCCCHH---HCTSSSSTTTHHHHHHHHHHHHHHHHHHC
T ss_pred cCCCcccchHHHHHHHHHHhhccchhhcchHHHHHHHHHHHHH---HHHHHHHhHHHHHHHHHHHHHHHHHHHHH
Confidence 8999999999998865432211 110 1111111111111 11112788999999999999999998743
No 6
>KOG2289 consensus Rhomboid family proteins [Signal transduction mechanisms]
Probab=99.73 E-value=4.3e-19 Score=164.05 Aligned_cols=132 Identities=27% Similarity=0.348 Sum_probs=97.3
Q ss_pred cccCCcchhccccccCCChhHHHHHHHHHHHHHHHHHhhhChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccccccc
Q 020298 71 LKYKDLKRFFLSPFYHASESHLFYNMMSLLWKGIQLETSMGSNEFAAMVVALLGMSQGITLLLAKSLVLFFDYERAYYSE 150 (328)
Q Consensus 71 ~~~~q~wRL~T~~f~H~~~~Hll~Nm~~L~~~G~~lE~~~G~~~f~~~yl~~~~~~~~l~~ll~~~l~~~~~~~~~~~~~ 150 (328)
.+.+|+||++||+|+|+|+.|+++||+.+..+|..+|..+|..|+..+|+ ++++++++. +.++.. +.
T Consensus 114 ~~r~E~WRllTym~LHaGi~HL~~N~~~ql~iGi~LE~~~G~~RiglIYl-~gg~aGSll-------s~l~d~-----~~ 180 (316)
T KOG2289|consen 114 VHRGELWRLLTYMWLHAGIFHLLLNMLSQLFIGIPLEQVHGFLRIGLIYL-AGGVAGSLL-------SSLFDP-----NS 180 (316)
T ss_pred hhhchhHHHHHHHHHhcCHHHHHHHHHHHHhccccHHhhcCceEEeeehh-hhhhhhHHH-------HHHhcc-----CC
Confidence 35789999999999999999999999999999999999999999999995 577776654 233443 36
Q ss_pred ccchhHHHHHHHHHHHHhcCCCcceeeccchhhHHH------HHHHHHHHHhcCCchHHHHHHHHHHHHHHHHHH
Q 020298 151 YAVGFSGVLFAMKVVLNSRSEDYTNVHGLLVPARYA------AWAELIIIQMFVPGVSFLGHLGGILAGILYLKL 219 (328)
Q Consensus 151 ~~~GaSg~ifgl~~~~~~~~~~~~~~~~i~i~~~~~------~~~~l~~~~~~~~~vs~~aHl~G~l~G~ly~~~ 219 (328)
.++||||++|||+++...+.-.+... ++.+.. .++.+.+.....+.+++++|++|+++|..+++.
T Consensus 181 ~sVGASggvfaLlgA~Ls~l~~Nw~~----m~~~~~~l~~ll~Ii~i~l~~G~~~~~~~~~h~gg~~~G~~~~fi 251 (316)
T KOG2289|consen 181 ISVGASGGVFALLGAHLSNLLTNWTI----MKNKFAALRTLLIIIFINLDLGFAPYVDNFAHIGGLLAGFLLGFV 251 (316)
T ss_pred ceecccHHHHHHHHHHHHHHHhhHHH----hcchHHHHHHHHHHHHHHHhhccccceeccccccccCCCcchhHH
Confidence 69999999999999866543211110 111111 111122233346788889999999999888774
No 7
>KOG0858 consensus Predicted membrane protein [Function unknown]
Probab=99.69 E-value=1.8e-16 Score=139.41 Aligned_cols=171 Identities=24% Similarity=0.328 Sum_probs=119.2
Q ss_pred CCChHHHHHHHHHHHHHHhhhhhhcCchhhhcccccchhhhcccCCcchhccccccCCC-hhHHHHHHHHHHHHHHHHHh
Q 020298 30 PWKPPVTAALLATNTLIYLRPAFLDSLVPSIHEVWFNPHLILKYKDLKRFFLSPFYHAS-ESHLFYNMMSLLWKGIQLET 108 (328)
Q Consensus 30 ~~~P~vt~~li~i~v~v~ll~~~~~~~~~~~~~~~l~p~~i~~~~q~wRL~T~~f~H~~-~~Hll~Nm~~L~~~G~~lE~ 108 (328)
.++|||||+...++++..++..+ + .-+..++.++|+.++++.|+||++|+.+..+. -+|.++||+++|.+++.||+
T Consensus 10 ~~iPpVTR~~~~~~v~tt~~~~l-~--lIsP~~l~~~p~Lv~kk~QiWRliTs~lyfg~~gf~fl~n~~FlyrY~~~LE~ 86 (239)
T KOG0858|consen 10 LQIPPVTRYYTTACVVTTLLVRL-D--LISPFQLYLNPELVFKKFQIWRLITSFLYFGPFGFDFLMNLYFLYRYSSMLEE 86 (239)
T ss_pred hcCChHHHHHHHHHHHHHHHHhh-c--ccCchheEecHHHHHhHhHHHHhhhhhheeccccHHHHHHHHHHHHHHHHHhc
Confidence 68999999999999999987542 2 22356889999999999999999999999877 68999999999999999998
Q ss_pred hh--C-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccccccccchhHHHHHHHHHHHHhcCCCc-ceeec-cchhh
Q 020298 109 SM--G-SNEFAAMVVALLGMSQGITLLLAKSLVLFFDYERAYYSEYAVGFSGVLFAMKVVLNSRSEDY-TNVHG-LLVPA 183 (328)
Q Consensus 109 ~~--G-~~~f~~~yl~~~~~~~~l~~ll~~~l~~~~~~~~~~~~~~~~GaSg~ifgl~~~~~~~~~~~-~~~~~-i~i~~ 183 (328)
-. | +..|+.+. +++++.-.+. +. +. +...+| ++.++.+...+....++. .++++ +.+++
T Consensus 87 g~f~~rtadf~~ml-lf~~~l~~~~----~~----~~------~~~fLg-~~l~~~l~YvWs~~Np~~~v~F~g~~~f~a 150 (239)
T KOG0858|consen 87 GSFRGRTADFLYML-LFGAVLLTLT----GL----FV------YIVFLG-QSLVFMLVYVWSKRNPDVIVSFFGLITFKA 150 (239)
T ss_pred CCCCCchhHHHHHH-HHHHHHHHHH----HH----HH------HHHHHH-HHHHHHHHHHHHhhCCCceEEEEEEecCcc
Confidence 44 2 34555444 3333322111 11 11 011222 233344444444444433 34444 56999
Q ss_pred HHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHHHHhc
Q 020298 184 RYAAWAELIIIQMFVPGVSFLGHLGGILAGILYLKLKG 221 (328)
Q Consensus 184 ~~~~~~~l~~~~~~~~~vs~~aHl~G~l~G~ly~~~~~ 221 (328)
+|+||+++.+..+...+ + +..+-|+++||+|.++..
T Consensus 151 ~YlPwvll~fs~l~g~~-~-~~dllGi~~GHiy~fl~~ 186 (239)
T KOG0858|consen 151 PYLPWVLLGFSFLFGGS-I-LVDLLGIIVGHIYYFLDD 186 (239)
T ss_pred ccchHHHHHHHHHhCCc-h-HHHHHhhhhheeEEEEee
Confidence 99999988776665444 3 889999999999988644
No 8
>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=99.62 E-value=1e-14 Score=128.54 Aligned_cols=175 Identities=25% Similarity=0.374 Sum_probs=119.6
Q ss_pred ChHHHHHHHHHHHHHHhhhhhhcCchhhhcccccchhhhcccCCcchhccccccCCCh-hHHHHHHHHHHHHHHHHHhhh
Q 020298 32 KPPVTAALLATNTLIYLRPAFLDSLVPSIHEVWFNPHLILKYKDLKRFFLSPFYHASE-SHLFYNMMSLLWKGIQLETSM 110 (328)
Q Consensus 32 ~P~vt~~li~i~v~v~ll~~~~~~~~~~~~~~~l~p~~i~~~~q~wRL~T~~f~H~~~-~Hll~Nm~~L~~~G~~lE~~~ 110 (328)
+|||||.+++..+++.++..+ + .....++.++++.++++.|+||++|+.|..++. .++++|++.++..++.+|+..
T Consensus 1 iPpVTR~~~~~~~~~s~l~~~-~--~~~~~~l~~~~~~v~~~~q~WRl~Tsff~~g~~~~~~l~~~~~l~~~s~~LE~~~ 77 (197)
T PF04511_consen 1 IPPVTRYWLISTVALSLLVSF-G--IISPYYLYFDWELVFKKFQIWRLFTSFFYFGPFSLNFLFNLYFLYQYSSSLEEGH 77 (197)
T ss_pred CChhHHHHHHHHHHHHHHHHC-C--CCCHHHeeECcHHHhhhcCceeeEEEEEEEcCCCHHHHHHHHHHHHHhhHhccCC
Confidence 599999999999999987543 2 123456779999998889999999999987665 699999999999999999973
Q ss_pred --Ch-HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccccccccchhHHHHHHHHHHHHhcCCC-cceeec-cchhhHH
Q 020298 111 --GS-NEFAAMVVALLGMSQGITLLLAKSLVLFFDYERAYYSEYAVGFSGVLFAMKVVLNSRSED-YTNVHG-LLVPARY 185 (328)
Q Consensus 111 --G~-~~f~~~yl~~~~~~~~l~~ll~~~l~~~~~~~~~~~~~~~~GaSg~ifgl~~~~~~~~~~-~~~~~~-i~i~~~~ 185 (328)
++ ..|+.+.+ +++. +..+++. + .... ..+.... .++..+++...+....|+ ..++++ +++|+++
T Consensus 78 f~~~~ady~~~ll-~~~~---~i~~~~~-~---~~~~--~~~~~~l-~~~l~~~l~Y~wsr~np~~~v~~~g~~~i~a~y 146 (197)
T PF04511_consen 78 FQGRSADYLWFLL-FGAS---LILILSL-L---IGPY--FFNIPFL-GSSLSFALTYIWSRKNPNAQVSFFGLFTIKAKY 146 (197)
T ss_pred CCCCHHHHHHHHH-HHHH---HHHHHHH-h---hccc--hhHHHHH-HHHHHHHHHHHHHHhCcccceeeEEEEEEChhh
Confidence 22 45554432 2222 1111111 1 1100 0011122 244555665556655554 334555 5799999
Q ss_pred HHHHHHHHHHhcCCchHHHHHHHHHHHHHHHHHHhc
Q 020298 186 AAWAELIIIQMFVPGVSFLGHLGGILAGILYLKLKG 221 (328)
Q Consensus 186 ~~~~~l~~~~~~~~~vs~~aHl~G~l~G~ly~~~~~ 221 (328)
+||+.+++..+..+ .+...++.|+++||+|.++..
T Consensus 147 lP~~~~~~~~l~~~-~~~~~~l~Gi~~Ghly~fl~~ 181 (197)
T PF04511_consen 147 LPWVLLAFSLLFGG-SSPIPDLLGILVGHLYYFLKD 181 (197)
T ss_pred HHHHHHHHHHHhCC-CcHHHHHHHHHHHHHHHHHHH
Confidence 99998776666654 356799999999999999854
No 9
>KOG2290 consensus Rhomboid family proteins [Signal transduction mechanisms]
Probab=99.40 E-value=2.4e-13 Score=128.51 Aligned_cols=133 Identities=22% Similarity=0.236 Sum_probs=97.4
Q ss_pred cCCcchhccccccCCChhHHHHHHHHHHHHHHHHHhhhChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccccccccc
Q 020298 73 YKDLKRFFLSPFYHASESHLFYNMMSLLWKGIQLETSMGSNEFAAMVVALLGMSQGITLLLAKSLVLFFDYERAYYSEYA 152 (328)
Q Consensus 73 ~~q~wRL~T~~f~H~~~~Hll~Nm~~L~~~G~~lE~~~G~~~f~~~yl~~~~~~~~l~~ll~~~l~~~~~~~~~~~~~~~ 152 (328)
..|.|||.|+.|+|+++.|++..+.+.+.+-+.+|+..|+.|...+|+ ++|+.|.+. +.+|-. | .+.
T Consensus 448 PdQfYRL~~SLFlHagviH~~vSi~FQm~vmrdlEkL~g~~riAIiy~-~SGitGNLA-------SAIFlp---Y--~~e 514 (652)
T KOG2290|consen 448 PDQFYRLWLSLFLHAGVIHLLVSICFQMTVMRDLEKLAGWHRIAIIYF-LSGITGNLA-------SAIFLP---Y--RAE 514 (652)
T ss_pred hhHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHhhcchhhheeee-cccccccch-------heeeec---c--ccc
Confidence 579999999999999999999999999999999999999999999994 677776543 112322 1 568
Q ss_pred chhHHHHHHHHHHHHhcCCCcceeeccchh--hHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHHHH
Q 020298 153 VGFSGVLFAMKVVLNSRSEDYTNVHGLLVP--ARYAAWAELIIIQMFVPGVSFLGHLGGILAGILYLKL 219 (328)
Q Consensus 153 ~GaSg~ifgl~~~~~~~~~~~~~~~~i~i~--~~~~~~~~l~~~~~~~~~vs~~aHl~G~l~G~ly~~~ 219 (328)
+|.||+-||+++.+..+.-+.+.+.--+-. .+.++ ..+++...+.|.+++++|+.|.+.|++..+.
T Consensus 515 VgPa~sQ~Gila~l~vEl~qs~~il~~~w~a~~~Lia-~~L~L~iGliPWiDN~aHlfG~i~GLl~s~~ 582 (652)
T KOG2290|consen 515 VGPAGSQFGILACLFVELFQSWQILERPWRAFFHLIA-TLLVLCIGLIPWIDNWAHLFGTIFGLLTSII 582 (652)
T ss_pred cCCcccccchHHHHHHHHHhhhHhhhhHHHHHHHHHH-HHHHHHhccccchhhHHHHHHHHHHHHHHHH
Confidence 999999999998876643222211110100 11111 1223334678999999999999999998764
No 10
>COG5291 Predicted membrane protein [Function unknown]
Probab=98.93 E-value=1.1e-09 Score=96.46 Aligned_cols=168 Identities=16% Similarity=0.209 Sum_probs=97.7
Q ss_pred ccCCCChHHHHHHHHHHHHHHhhhhhhcCchhhhcccccchhhhcccCCcchhccccccCCC-hhHHHHHHHHHHHHHHH
Q 020298 27 HRLPWKPPVTAALLATNTLIYLRPAFLDSLVPSIHEVWFNPHLILKYKDLKRFFLSPFYHAS-ESHLFYNMMSLLWKGIQ 105 (328)
Q Consensus 27 ~~~~~~P~vt~~li~i~v~v~ll~~~~~~~~~~~~~~~l~p~~i~~~~q~wRL~T~~f~H~~-~~Hll~Nm~~L~~~G~~ 105 (328)
.+..++||+|+.+..+..++-++.. .+... .++..+.....++.-|+||++|+..+.++ -+..++|++++|...++
T Consensus 14 g~~~~IPPITRy~~ll~~a~til~~-~~lvs--Pwy~ly~~pL~~k~~qiwRlfTs~~~~~~~~~d~~M~vyf~Y~yS~~ 90 (313)
T COG5291 14 GQMLRIPPITRYMTLLISAVTILVY-VDLVS--PWYSLYYSPLFLKRLQIWRLFTSFLYFGKPTLDMFMHVYFLYRYSRM 90 (313)
T ss_pred cccccCCcHHHHHHHHHHHHHHHHH-HhhcC--ccceeeechhHHHHHHHHHHHHHHHhhcCcchhHHHHHHHHHHHHHH
Confidence 3555799999999988888887633 23222 23344444556678899999998887766 57999999999999999
Q ss_pred HHhh-hChH--HHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccccccccchhHHHHHHHHHHHHh-----cCCCcceee
Q 020298 106 LETS-MGSN--EFAAMVVALLGMSQGITLLLAKSLVLFFDYERAYYSEYAVGFSGVLFAMKVVLNS-----RSEDYTNVH 177 (328)
Q Consensus 106 lE~~-~G~~--~f~~~yl~~~~~~~~l~~ll~~~l~~~~~~~~~~~~~~~~GaSg~ifgl~~~~~~-----~~~~~~~~~ 177 (328)
||+- +++. ++..+. ..+.+ .+. - +. ...-|.|..--++.+...+ +......++
T Consensus 91 LE~g~f~~~lv~Y~~yl-~~~~l--~i~-a--------~s-------~I~gg~saL~tsf~a~ItY~WS~~N~~~~Iqf~ 151 (313)
T COG5291 91 LEEGCFNTSLVEYFWYL-LVISL--VIF-A--------IS-------NIYGGISALGTSFSATITYIWSKRNPRAIIQFF 151 (313)
T ss_pred HhccccCccHHHHHHHH-HHHHH--HHH-H--------HH-------HHhcchhhhcchhhhheeeeeeecCCceEEEEE
Confidence 9983 3433 443322 11111 110 0 00 0111222222223233222 112222344
Q ss_pred -ccchhhHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHH
Q 020298 178 -GLLVPARYAAWAELIIIQMFVPGVSFLGHLGGILAGILYL 217 (328)
Q Consensus 178 -~i~i~~~~~~~~~l~~~~~~~~~vs~~aHl~G~l~G~ly~ 217 (328)
.++++.||+|++.+.+..+...+ ...-.+-|+.+|++.-
T Consensus 152 g~i~v~gkYlP~Illgfsfl~~~g-~~i~~vlGf~~g~~~h 191 (313)
T COG5291 152 GFISVPGKYLPFILLGFSFLSRRG-ISIDDVLGFVVGHLFH 191 (313)
T ss_pred EeeecchhhhhHHHHHHHHHhcCC-ccceeeeeeeeccccc
Confidence 45799999999877665544322 3344566777776543
No 11
>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=98.83 E-value=4.4e-09 Score=82.28 Aligned_cols=90 Identities=22% Similarity=0.343 Sum_probs=69.2
Q ss_pred CcchhccccccCCChhHHHHHHHHHHHHHHHHHhhhChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccccccccch
Q 020298 75 DLKRFFLSPFYHASESHLFYNMMSLLWKGIQLETSMGSNEFAAMVVALLGMSQGITLLLAKSLVLFFDYERAYYSEYAVG 154 (328)
Q Consensus 75 q~wRL~T~~f~H~~~~Hll~Nm~~L~~~G~~lE~~~G~~~f~~~yl~~~~~~~~l~~ll~~~l~~~~~~~~~~~~~~~~G 154 (328)
.+|+++|+.|++.++..+++|.+.++..|+.+|+.||+++++.++++ ..+.+++...+...+.+....+..+...+.-|
T Consensus 7 ~pWtl~T~~fve~~i~~~l~~~~~l~~~g~~lE~~WGs~E~lkFi~v-v~~~tnl~~~~~~~~~y~i~~~~~~l~~~i~G 85 (99)
T PF08551_consen 7 YPWTLFTAGFVETNIIGLLFSLLTLFYGGRYLEPIWGSREFLKFILV-VNVITNLLTFLLYLLLYAITGNESYLFVPISG 85 (99)
T ss_pred ehHHHHHHHHHHhHHHHHHHHHHHHHHhhHHHHHhcChHHHHHHHHH-HHHHhHHHHHHHHHHHHHHhCCCceeEEEecC
Confidence 79999999999999999999999999999999999999999988754 44444444455555555555444432366778
Q ss_pred hHHHHHHHHHH
Q 020298 155 FSGVLFAMKVV 165 (328)
Q Consensus 155 aSg~ifgl~~~ 165 (328)
..|.+.|++++
T Consensus 86 ~~~~~~g~lVa 96 (99)
T PF08551_consen 86 FMGVLAGFLVA 96 (99)
T ss_pred cHHhHhheEEE
Confidence 88888777654
No 12
>KOG2890 consensus Predicted membrane protein [Function unknown]
Probab=98.80 E-value=5.5e-08 Score=88.52 Aligned_cols=185 Identities=16% Similarity=0.130 Sum_probs=112.6
Q ss_pred CChHHHHHHHHHHHHHHhhhhhhcCchh-hhcccccchhhhcccCCcchhccccccCCChhHHHHHHHHHHHHHHHHHhh
Q 020298 31 WKPPVTAALLATNTLIYLRPAFLDSLVP-SIHEVWFNPHLILKYKDLKRFFLSPFYHASESHLFYNMMSLLWKGIQLETS 109 (328)
Q Consensus 31 ~~P~vt~~li~i~v~v~ll~~~~~~~~~-~~~~~~l~p~~i~~~~q~wRL~T~~f~H~~~~Hll~Nm~~L~~~G~~lE~~ 109 (328)
+.-++.+.|..+.+..|+.......... ..-.+.+.|..++ ...|+++|+.|+-.+.+..+.|...+...|+.+|+.
T Consensus 23 n~~vvvs~ic~~tlf~yi~sf~~~t~~l~~~p~y~lvp~~~~--~~~WtliTs~fie~~vw~V~~sv~~L~v~G~~lEp~ 100 (326)
T KOG2890|consen 23 NLEVVVSAICVLTLFGYILSFGNFTILLATLPGYQLVPNALF--FFPWTLITSGFIELNVWDVLVSVLTLSVGGKFLEPN 100 (326)
T ss_pred hchhHHHHHHHHHHHHHHHHHHHhHHHHHhccccccCCcchh--hhhHHHHhcchhhhhHHHHHHHHHheeecceeeccC
Confidence 4455566666666667765432111110 0112234443332 479999999999999999999999999999999999
Q ss_pred hChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccccccccchhHHHHHHHHHHHHhcCCCcceeeccc---hhhHHH
Q 020298 110 MGSNEFAAMVVALLGMSQGITLLLAKSLVLFFDYERAYYSEYAVGFSGVLFAMKVVLNSRSEDYTNVHGLL---VPARYA 186 (328)
Q Consensus 110 ~G~~~f~~~yl~~~~~~~~l~~ll~~~l~~~~~~~~~~~~~~~~GaSg~ifgl~~~~~~~~~~~~~~~~i~---i~~~~~ 186 (328)
||+.+++.+|.+.-+..+ +..++...+.+.+....-+...+..|..|.+-|+++++....|+... .-.+ +..+.+
T Consensus 101 Wg~~e~lkff~ivn~~~~-l~v~v~~~l~Y~it~n~v~L~~~i~G~~gilaGilVa~kQllpd~~i-l~~~~~r~~~~~l 178 (326)
T KOG2890|consen 101 WGSLELLKFFAIVNGSTT-LVVLVPALLLYMITDNHVYLYIPIHGTTGILAGILVAWKQLLPDTII-LELKSGRFLYAHL 178 (326)
T ss_pred CCCHHHHHHHHHhhchhH-HHHHHHHHHHHHHhcCceEEEEEeccchHHHHHHHHHHHHHcCceeE-EeccchhhhhhhC
Confidence 999999998854333332 22333344444444433333356899999999999998887776532 2222 222224
Q ss_pred HHHHHHHHH-----hcCCchHHHHHHHHHHHHHHHHHH
Q 020298 187 AWAELIIIQ-----MFVPGVSFLGHLGGILAGILYLKL 219 (328)
Q Consensus 187 ~~~~l~~~~-----~~~~~vs~~aHl~G~l~G~ly~~~ 219 (328)
|+..+++.. .+....++..-..|..+++.|-.+
T Consensus 179 P~~~l~~~~il~i~~f~~f~~l~s~~~g~~~sWtYLRf 216 (326)
T KOG2890|consen 179 PLLVLFLSLILSIITFLVFASLPSITFGVLVSWTYLRF 216 (326)
T ss_pred CHHHHHHHHHHHHHHHHHhhhhHHHHHhhhhhhhhhee
Confidence 444332211 122233455556677777776644
No 13
>KOG2980 consensus Integral membrane protease of the rhomboid family involved in different forms of regulated intramembrane proteolysis [Signal transduction mechanisms]
Probab=98.39 E-value=2.5e-07 Score=84.51 Aligned_cols=172 Identities=22% Similarity=0.206 Sum_probs=107.9
Q ss_pred HHHHHHHHHHHHHhhhhhhcCchhhhcccccchhhhcccCCcchhccccccCCChhHHHHHHHHHHHHHH-HHHhhhChH
Q 020298 35 VTAALLATNTLIYLRPAFLDSLVPSIHEVWFNPHLILKYKDLKRFFLSPFYHASESHLFYNMMSLLWKGI-QLETSMGSN 113 (328)
Q Consensus 35 vt~~li~i~v~v~ll~~~~~~~~~~~~~~~l~p~~i~~~~q~wRL~T~~f~H~~~~Hll~Nm~~L~~~G~-~lE~~~G~~ 113 (328)
+...++++|+++|.++....-..-...++...+. . .--.|.++++.|.|-+.+|+..||+.+..+.. .+-...|..
T Consensus 117 ~v~~ll~~n~~vf~lWrv~~~~~~~~~~mls~~~--~-~t~~w~i~~s~Fsh~~a~h~g~~~~~~~~y~~~a~~~~~~~~ 193 (310)
T KOG2980|consen 117 VVFGLLIANAFVFTLWRVPQKQFTMIPWMLSRNA--Y-KTGCWKIILSTFSHYSALHLGPNMLVLKSYLAGALKGSLGFS 193 (310)
T ss_pred chhHHHHHHHHHHHHHHhcchhhhhhhHHhhccc--c-cccceeEEeehhcchhHhhhcHHHHHHHHHhcccccCCcchh
Confidence 8889999999999987654321111122222232 1 23467799999999999999999999888877 677778888
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhc-ccccccccccchhHHHHHHHHHHHHhcCCCcceee--ccchhhHH-HHHH
Q 020298 114 EFAAMVVALLGMSQGITLLLAKSLVLFFD-YERAYYSEYAVGFSGVLFAMKVVLNSRSEDYTNVH--GLLVPARY-AAWA 189 (328)
Q Consensus 114 ~f~~~yl~~~~~~~~l~~ll~~~l~~~~~-~~~~~~~~~~~GaSg~ifgl~~~~~~~~~~~~~~~--~i~i~~~~-~~~~ 189 (328)
.+.++|+. .+.- +.. +. ..+ -+... ..+.+||||+++++++..+...|+....+ .+++|.-+ +++-
T Consensus 194 ~~~AlylS-a~~~-~~~------i~-~~~~v~~~~-~gp~LGAsGav~ai~a~~~~lfP~~~~~i~f~~~v~~ga~~~~~ 263 (310)
T KOG2980|consen 194 SFFALYLS-AGVK-GLF------IS-VKDKVPTSW-AGPSLGASGAVYAILALDCTLFPKTTLYILFVFPVPAGAGLAFK 263 (310)
T ss_pred hcccceec-cccc-cce------eE-eeccccccc-cccccccchHHHHHHHHHhhcCcCcceeEEEeecccccchhHHH
Confidence 88888841 1111 110 00 011 01111 26789999999999999988888655432 23344422 1211
Q ss_pred HHHHHH-----hcCCchHHHHHHHHHHHHHHHHHH
Q 020298 190 ELIIIQ-----MFVPGVSFLGHLGGILAGILYLKL 219 (328)
Q Consensus 190 ~l~~~~-----~~~~~vs~~aHl~G~l~G~ly~~~ 219 (328)
.+.... +.....++.+|++|-+.|..++..
T Consensus 264 ~i~~~~~a~~~l~~~~~n~~Ah~~gsl~Gv~va~~ 298 (310)
T KOG2980|consen 264 AIAAYDFAGLILGWGFFNHAAHLSGSLFGVVVATY 298 (310)
T ss_pred HHHHhhhcceeeccccchhHhhhcchHHHHHHHHH
Confidence 111111 112344677999999999998754
No 14
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=98.13 E-value=6.1e-07 Score=54.37 Aligned_cols=29 Identities=45% Similarity=0.980 Sum_probs=23.5
Q ss_pred CCcccCCCCccCCCCCCccccccCCCCCC
Q 020298 272 PIIWRCPACTFDNSGWLSICEMCGTSRSG 300 (328)
Q Consensus 272 ~g~W~c~~C~~~n~~~~~~c~~cg~~~~~ 300 (328)
.|.|.|+.|++.|.++...|.+|+++|++
T Consensus 2 ~g~W~C~~C~~~N~~~~~~C~~C~~~rp~ 30 (30)
T PF00641_consen 2 EGDWKCPSCTFMNPASRSKCVACGAPRPG 30 (30)
T ss_dssp SSSEEETTTTEEEESSSSB-TTT--BTTB
T ss_pred CcCccCCCCcCCchHHhhhhhCcCCCCcC
Confidence 45799999999999999999999999874
No 15
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=97.81 E-value=9.9e-06 Score=47.26 Aligned_cols=25 Identities=48% Similarity=0.891 Sum_probs=23.3
Q ss_pred CcccCCCCccCCCCCCccccccCCC
Q 020298 273 IIWRCPACTFDNSGWLSICEMCGTS 297 (328)
Q Consensus 273 g~W~c~~C~~~n~~~~~~c~~cg~~ 297 (328)
|.|.|+.|+++|.++...|++|+++
T Consensus 1 g~W~C~~C~~~N~~~~~~C~~C~~p 25 (26)
T smart00547 1 GDWECPACTFLNFASRSKCFACGAP 25 (26)
T ss_pred CcccCCCCCCcChhhhccccccCCc
Confidence 4699999999999999999999986
No 16
>KOG4463 consensus Uncharacterized conserved protein [Function unknown]
Probab=97.71 E-value=1.4e-05 Score=71.58 Aligned_cols=90 Identities=22% Similarity=0.364 Sum_probs=62.9
Q ss_pred HHHHHHHHHHHHHHhhhhhhcCchhhhcccccchhhhcccCCcchhccccccCCChhHHHHHHHHHHHHHHHHHhhhChH
Q 020298 34 PVTAALLATNTLIYLRPAFLDSLVPSIHEVWFNPHLILKYKDLKRFFLSPFYHASESHLFYNMMSLLWKGIQLETSMGSN 113 (328)
Q Consensus 34 ~vt~~li~i~v~v~ll~~~~~~~~~~~~~~~l~p~~i~~~~q~wRL~T~~f~H~~~~Hll~Nm~~L~~~G~~lE~~~G~~ 113 (328)
|||+..++...++.+...+... .....+.+.+... ++.|+||++.+-|+..+-..+++-++.+|.+ +.+|+.+|+-
T Consensus 12 pVTK~~~iT~~~~~vvagI~~~--k~~f~l~y~~~l~-~y~qywrlL~~qF~~~n~~e~~~~l~I~Y~f-R~~ERlLGSh 87 (323)
T KOG4463|consen 12 PVTKAFVITSALFTVVAGIQGR--KSKFGLSYQDILE-KYFQYWRLLMSQFAFSNTPELMFGLYILYYF-RVFERLLGSH 87 (323)
T ss_pred chHHHHHHHHHHHHHHHHhhhc--ccccccchhHHHH-HHHHHHHHHHHHHHhcCChHHHHHHHHHHHH-HHHHHHhccc
Confidence 6888887777666664332211 1112233444332 4589999999999999999999999988877 8999999999
Q ss_pred HHHHHHHHHHHHHHH
Q 020298 114 EFAAMVVALLGMSQG 128 (328)
Q Consensus 114 ~f~~~yl~~~~~~~~ 128 (328)
||..+.+ +++..+.
T Consensus 88 ky~~fiv-~s~~~~~ 101 (323)
T KOG4463|consen 88 KYSVFIV-FSGTVSL 101 (323)
T ss_pred cceeehh-HHHHHHH
Confidence 9987653 3444443
No 17
>KOG4477 consensus RING1 interactor RYBP and related Zn-finger-containing proteins [Transcription]
Probab=93.95 E-value=0.037 Score=47.19 Aligned_cols=37 Identities=24% Similarity=0.523 Sum_probs=29.7
Q ss_pred CCCCCCCCcccCCCCccCCCCCCccccccCCCCCCCC
Q 020298 266 DTRRTAPIIWRCPACTFDNSGWLSICEMCGTSRSGND 302 (328)
Q Consensus 266 ~~~~~~~g~W~c~~C~~~n~~~~~~c~~cg~~~~~~~ 302 (328)
.-.....|-|-|+.|||.|++..-.|-||++....+.
T Consensus 16 akp~~Deg~WdCsvCTFrNsAeAfkC~vCdvRKGTST 52 (228)
T KOG4477|consen 16 AKPNDDEGKWDCSVCTFRNSAEAFKCFVCDVRKGTST 52 (228)
T ss_pred CCCccccCceeeeeeeecchhhhhheeeecccccccc
Confidence 3344456679999999999998899999999876543
No 18
>KOG4198 consensus RNA-binding Ran Zn-finger protein and related proteins [General function prediction only]
Probab=92.22 E-value=0.077 Score=48.83 Aligned_cols=32 Identities=34% Similarity=0.691 Sum_probs=28.7
Q ss_pred CCCcccCCCCccCCCCCCccccccCCCCCCCC
Q 020298 271 APIIWRCPACTFDNSGWLSICEMCGTSRSGND 302 (328)
Q Consensus 271 ~~g~W~c~~C~~~n~~~~~~c~~cg~~~~~~~ 302 (328)
.+|-|.|+.|+|+|-+.-..|-.||..|.-++
T Consensus 137 ~~GDW~Cp~C~fhNfarn~~C~rC~~~r~~~a 168 (280)
T KOG4198|consen 137 RSGDWECPGCNFHNFARNSECFRCGAKRPLAA 168 (280)
T ss_pred cccCcccCCCCceeccccchhhhcCCcCcccc
Confidence 56779999999999999999999999998644
No 19
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=90.09 E-value=0.13 Score=31.88 Aligned_cols=26 Identities=27% Similarity=0.954 Sum_probs=20.0
Q ss_pred cccCCCCccCC--CCCCccccccCCCCC
Q 020298 274 IWRCPACTFDN--SGWLSICEMCGTSRS 299 (328)
Q Consensus 274 ~W~c~~C~~~n--~~~~~~c~~cg~~~~ 299 (328)
.|.|..|.|.- ....++|++||.+.+
T Consensus 2 ~~~C~~CG~i~~g~~~p~~CP~Cg~~~~ 29 (34)
T cd00729 2 VWVCPVCGYIHEGEEAPEKCPICGAPKE 29 (34)
T ss_pred eEECCCCCCEeECCcCCCcCcCCCCchH
Confidence 49999998883 224679999998743
No 20
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=89.30 E-value=0.17 Score=31.02 Aligned_cols=26 Identities=23% Similarity=0.743 Sum_probs=20.0
Q ss_pred cccCCCCccCCC--CCCccccccCCCCC
Q 020298 274 IWRCPACTFDNS--GWLSICEMCGTSRS 299 (328)
Q Consensus 274 ~W~c~~C~~~n~--~~~~~c~~cg~~~~ 299 (328)
.|.|..|.|.-. .....|+.||.+++
T Consensus 1 ~~~C~~CGy~y~~~~~~~~CP~Cg~~~~ 28 (33)
T cd00350 1 KYVCPVCGYIYDGEEAPWVCPVCGAPKD 28 (33)
T ss_pred CEECCCCCCEECCCcCCCcCcCCCCcHH
Confidence 499999988832 24678999998754
No 21
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=85.47 E-value=0.4 Score=40.86 Aligned_cols=26 Identities=27% Similarity=1.072 Sum_probs=21.6
Q ss_pred cccCCCCccCC-CCCCccccccCCCCC
Q 020298 274 IWRCPACTFDN-SGWLSICEMCGTSRS 299 (328)
Q Consensus 274 ~W~c~~C~~~n-~~~~~~c~~cg~~~~ 299 (328)
.|.|..|.|.- ...+.+|+.||.+.+
T Consensus 134 ~~vC~vCGy~~~ge~P~~CPiCga~k~ 160 (166)
T COG1592 134 VWVCPVCGYTHEGEAPEVCPICGAPKE 160 (166)
T ss_pred EEEcCCCCCcccCCCCCcCCCCCChHH
Confidence 79999999984 366789999998754
No 22
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=84.64 E-value=0.67 Score=26.02 Aligned_cols=22 Identities=32% Similarity=0.755 Sum_probs=19.3
Q ss_pred cCCCCccCCCCCCccccccCCC
Q 020298 276 RCPACTFDNSGWLSICEMCGTS 297 (328)
Q Consensus 276 ~c~~C~~~n~~~~~~c~~cg~~ 297 (328)
.|+.|...++.....|+.||.+
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCGTP 22 (23)
T ss_pred CCcccCCCCCCcCcchhhhCCc
Confidence 4899999998888899999975
No 23
>COG5100 NPL4 Nuclear pore protein [Nuclear structure]
Probab=84.54 E-value=0.22 Score=47.69 Aligned_cols=24 Identities=46% Similarity=1.078 Sum_probs=22.8
Q ss_pred ccCCCCccCCCCCCccccccCCCC
Q 020298 275 WRCPACTFDNSGWLSICEMCGTSR 298 (328)
Q Consensus 275 W~c~~C~~~n~~~~~~c~~cg~~~ 298 (328)
|.|+.||+.|+...-.||||..+|
T Consensus 547 we~~~~~~i~~~~~~t~~m~~~~~ 570 (571)
T COG5100 547 WECKMCTFINEKNSCTCEMCNSTR 570 (571)
T ss_pred HHHHHHHHhcccCceEEEeecccC
Confidence 999999999999999999999876
No 24
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=82.69 E-value=0.86 Score=26.28 Aligned_cols=23 Identities=26% Similarity=0.635 Sum_probs=20.4
Q ss_pred ccCCCCccCCCCCCccccccCCC
Q 020298 275 WRCPACTFDNSGWLSICEMCGTS 297 (328)
Q Consensus 275 W~c~~C~~~n~~~~~~c~~cg~~ 297 (328)
..|+.|...++++...|+.||.+
T Consensus 3 ~~Cp~Cg~~~~~~~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGAEIDPDAKFCPNCGAK 25 (26)
T ss_pred CCCcccCCcCCcccccChhhCCC
Confidence 57999999999989999999975
No 25
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=82.25 E-value=0.75 Score=32.37 Aligned_cols=31 Identities=19% Similarity=0.425 Sum_probs=24.8
Q ss_pred ccCCCCccCCCCCCccccccCCCCCCCCCCc
Q 020298 275 WRCPACTFDNSGWLSICEMCGTSRSGNDLSS 305 (328)
Q Consensus 275 W~c~~C~~~n~~~~~~c~~cg~~~~~~~~~~ 305 (328)
-.|..|.+.-.....+|+.||++....-|+-
T Consensus 5 kAC~~Ck~l~~~d~e~CP~Cgs~~~te~W~G 35 (64)
T COG2093 5 KACKNCKRLTPEDTEICPVCGSTDLTEEWFG 35 (64)
T ss_pred HHHhhccccCCCCCccCCCCCCcccchhhcc
Confidence 4699999998888889999999976555543
No 26
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=79.85 E-value=1.2 Score=31.74 Aligned_cols=27 Identities=15% Similarity=0.446 Sum_probs=20.2
Q ss_pred ccCCCCccCCCCCCccccccCCCCCCCCC
Q 020298 275 WRCPACTFDNSGWLSICEMCGTSRSGNDL 303 (328)
Q Consensus 275 W~c~~C~~~n~~~~~~c~~cg~~~~~~~~ 303 (328)
=.|..|++.... +.|+.||.....+.|
T Consensus 6 ~AC~~C~~i~~~--~~Cp~Cgs~~~S~~w 32 (64)
T PRK06393 6 RACKKCKRLTPE--KTCPVHGDEKTTTEW 32 (64)
T ss_pred hhHhhCCcccCC--CcCCCCCCCcCCcCc
Confidence 358999999854 699999997544444
No 27
>PRK12496 hypothetical protein; Provisional
Probab=78.42 E-value=1.3 Score=37.84 Aligned_cols=23 Identities=26% Similarity=0.746 Sum_probs=18.5
Q ss_pred ccCCCCc--cCCCCCCccccccCCC
Q 020298 275 WRCPACT--FDNSGWLSICEMCGTS 297 (328)
Q Consensus 275 W~c~~C~--~~n~~~~~~c~~cg~~ 297 (328)
.+|+.|. |+.....+.||+||.+
T Consensus 128 ~~C~gC~~~~~~~~~~~~C~~CG~~ 152 (164)
T PRK12496 128 KVCKGCKKKYPEDYPDDVCEICGSP 152 (164)
T ss_pred EECCCCCccccCCCCCCcCCCCCCh
Confidence 5699996 7665556899999976
No 28
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=74.07 E-value=2.3 Score=30.00 Aligned_cols=27 Identities=19% Similarity=0.647 Sum_probs=20.5
Q ss_pred cCCCCccCCCCCCccccccCCCCCCCCCC
Q 020298 276 RCPACTFDNSGWLSICEMCGTSRSGNDLS 304 (328)
Q Consensus 276 ~c~~C~~~n~~~~~~c~~cg~~~~~~~~~ 304 (328)
.|..|++.... +.|+.||.....+.|+
T Consensus 5 AC~~C~~i~~~--~~CP~Cgs~~~T~~W~ 31 (61)
T PRK08351 5 ACRHCHYITTE--DRCPVCGSRDLSDEWF 31 (61)
T ss_pred hhhhCCcccCC--CcCCCCcCCccccccc
Confidence 69999999854 5899999977444443
No 29
>KOG3476 consensus Microtubule-associated protein CRIPT [Cytoskeleton]
Probab=72.84 E-value=0.65 Score=34.79 Aligned_cols=26 Identities=31% Similarity=0.811 Sum_probs=20.4
Q ss_pred CCCcccCCCCccCCCCCCccccccCCCCCC
Q 020298 271 APIIWRCPACTFDNSGWLSICEMCGTSRSG 300 (328)
Q Consensus 271 ~~g~W~c~~C~~~n~~~~~~c~~cg~~~~~ 300 (328)
++|...|+.|-|.- .+|+|||..-.|
T Consensus 66 Q~GshYC~tCAY~K----giCAMCGKki~n 91 (100)
T KOG3476|consen 66 QPGSHYCQTCAYKK----GICAMCGKKILN 91 (100)
T ss_pred CCcchhHhHhhhhh----hHHHHhhhHhhc
Confidence 56678899998865 789999976554
No 30
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=67.44 E-value=2.1 Score=43.63 Aligned_cols=49 Identities=22% Similarity=0.398 Sum_probs=15.1
Q ss_pred cccCCCCccCCCCCCccccccCCCCCC-----CCCCcccccCCCCCChHHHHHHHh
Q 020298 274 IWRCPACTFDNSGWLSICEMCGTSRSG-----NDLSSDQLSRHSNIPLEELRHRRI 324 (328)
Q Consensus 274 ~W~c~~C~~~n~~~~~~c~~cg~~~~~-----~~~~~~~~~~~~~~~~~~~r~~~~ 324 (328)
.-.|..|.|.... .+.|+.||.+.-+ -++=+ +-+++|+-+++|++.|+-
T Consensus 491 ~~~C~~CG~~~~~-~~~CP~CGs~~~~~~~Rv~GYl~-~v~~~n~gK~~E~~~R~~ 544 (546)
T PF13597_consen 491 IDICPDCGYIGGE-GDKCPKCGSENIEVYSRVTGYLR-PVSRWNKGKQAEFKDRVK 544 (546)
T ss_dssp EEEETTT---S---EEE-CCC----EEEEB-SSSS-B-TTS---------------
T ss_pred cccccCCCcCCCC-CCCCCCCCCcccceEEEeecccc-CccccCHHHHHHHHHhcc
Confidence 4789999999887 8999999998432 12211 344577888999998864
No 31
>TIGR02487 NrdD anaerobic ribonucleoside-triphosphate reductase. This model represents the oxygen-sensitive (anaerobic, class III) ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centered radical, a C-terminal zinc binding site, and a set of conserved active site cysteines and asparagines. This enzyme requires an activating component, NrdG, a radical-SAM domain containing enzyme (TIGR02491). Together the two form an alpha-2/beta-2 heterodimer.
Probab=63.62 E-value=6.8 Score=40.28 Aligned_cols=49 Identities=16% Similarity=0.410 Sum_probs=33.5
Q ss_pred cccCCCCccCCCCCCccccccCCCCCCC-----CCCcccccCCCCCChHHHHHHH
Q 020298 274 IWRCPACTFDNSGWLSICEMCGTSRSGN-----DLSSDQLSRHSNIPLEELRHRR 323 (328)
Q Consensus 274 ~W~c~~C~~~n~~~~~~c~~cg~~~~~~-----~~~~~~~~~~~~~~~~~~r~~~ 323 (328)
.-.|..|.|......+.|+.||....+. ++=+ +..++|+-++.|++.|.
T Consensus 524 ~~~C~~CG~~g~~~~~~CP~Cgs~~~~~~~Rv~GYl~-~v~~~n~gK~~E~~~R~ 577 (579)
T TIGR02487 524 VDVCEDCGYTGEGLNDKCPKCGSHDIEVISRITGYLG-PVENWNDGKQAEFKDRK 577 (579)
T ss_pred CccCCCCCCCCCCCCCcCcCCCCccceehhhhhhhhc-cccccccccHHHHHHHh
Confidence 4789999996655457999999753221 1111 34467788899998886
No 32
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=62.36 E-value=7.9 Score=40.12 Aligned_cols=51 Identities=20% Similarity=0.352 Sum_probs=34.4
Q ss_pred cccCCCCccCCCCCCccccccCCCCCCC-----CCCcccccCCCCCChHHHHHHHhh
Q 020298 274 IWRCPACTFDNSGWLSICEMCGTSRSGN-----DLSSDQLSRHSNIPLEELRHRRIE 325 (328)
Q Consensus 274 ~W~c~~C~~~n~~~~~~c~~cg~~~~~~-----~~~~~~~~~~~~~~~~~~r~~~~~ 325 (328)
.-.|..|.|......+.|+.||....+. ++= ++-+++|+-+++|+++|--.
T Consensus 566 ~~iC~~CG~~~~g~~~~CP~CGs~~~ev~~RV~GYl-~~v~~wN~gK~~E~~~R~~~ 621 (623)
T PRK08271 566 ITICNDCHHIDKRTGKRCPICGSENIDYYTRVIGYL-KRVSAFSKVRQKEYPRRHYH 621 (623)
T ss_pred CccCCCCCCcCCCCCcCCcCCCCcchhHHHHHhhhh-cCccccccccHHHHHHHhhc
Confidence 4789999998555578999999754321 111 11245677889999988643
No 33
>PF10235 Cript: Microtubule-associated protein CRIPT; InterPro: IPR019367 The CRIPT protein is a cytoskeletal protein involved in microtubule production. This C-terminal domain is essential for binding to the PDZ3 domain of the SAP90 protein, one of a super-family of PDZ-containing proteins that play an important role in coupling the membrane ion channels with their signalling partners [].
Probab=61.86 E-value=4.7 Score=30.76 Aligned_cols=27 Identities=26% Similarity=0.641 Sum_probs=20.6
Q ss_pred CcccCCCCccCCCCCCccccccCCCCCCCCC
Q 020298 273 IIWRCPACTFDNSGWLSICEMCGTSRSGNDL 303 (328)
Q Consensus 273 g~W~c~~C~~~n~~~~~~c~~cg~~~~~~~~ 303 (328)
|.-.||.|-|.. .+|.|||..-.|...
T Consensus 58 g~~YCq~CAYkk----GiCamCGKki~dtk~ 84 (90)
T PF10235_consen 58 GAKYCQTCAYKK----GICAMCGKKILDTKN 84 (90)
T ss_pred CCccChhhhccc----CcccccCCeeccccc
Confidence 446688888876 689999998776544
No 34
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=60.61 E-value=9.3 Score=28.38 Aligned_cols=48 Identities=25% Similarity=0.574 Sum_probs=28.7
Q ss_pred ccCCCCccC---CCCC--CccccccCCCCCCCCCCccccc-CCCCCChHHHHHH
Q 020298 275 WRCPACTFD---NSGW--LSICEMCGTSRSGNDLSSDQLS-RHSNIPLEELRHR 322 (328)
Q Consensus 275 W~c~~C~~~---n~~~--~~~c~~cg~~~~~~~~~~~~~~-~~~~~~~~~~r~~ 322 (328)
.+|+-|.|. ..+. .++|++|+=.--+......... +.|.+|+.|-|..
T Consensus 2 ~~CPCCg~~Tl~~~~~~~ydIC~VC~WEdD~~q~~~pd~~~G~N~~SL~eAr~n 55 (78)
T PF14206_consen 2 YPCPCCGYYTLEERGEGTYDICPVCFWEDDGVQLRDPDYYGGANHMSLNEAREN 55 (78)
T ss_pred ccCCCCCcEEeccCCCcCceECCCCCcccCCccccCCcccCCCCHHHHHHHHHH
Confidence 368888554 4444 8899999854333222332223 4458888887764
No 35
>PF09527 ATPase_gene1: Putative F0F1-ATPase subunit (ATPase_gene1)
Probab=60.08 E-value=46 Score=22.47 Aligned_cols=40 Identities=18% Similarity=0.370 Sum_probs=28.4
Q ss_pred HHHHHHHHHHHHHHHHHhhhChHHHHHHHHHHHHHHHHHH
Q 020298 91 HLFYNMMSLLWKGIQLETSMGSNEFAAMVVALLGMSQGIT 130 (328)
Q Consensus 91 Hll~Nm~~L~~~G~~lE~~~G~~~f~~~yl~~~~~~~~l~ 130 (328)
.+..+++.-+.+|..+++.+++.....+...+.|+.+++.
T Consensus 9 ~~~~~i~~g~~~G~~lD~~~~t~p~~~~~g~llG~~~g~~ 48 (55)
T PF09527_consen 9 TMAAPILVGFFLGYWLDKWFGTSPWFTLIGLLLGIAAGFY 48 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHH
Confidence 5677888889999999999999555554434555555544
No 36
>COG3931 Predicted N-formylglutamate amidohydrolase [Amino acid transport and metabolism]
Probab=58.70 E-value=8.9 Score=34.49 Aligned_cols=34 Identities=32% Similarity=0.513 Sum_probs=23.8
Q ss_pred ccCCCCCCCC----CCcccccCCC-CCChHHHHHHHhhhc
Q 020298 293 MCGTSRSGND----LSSDQLSRHS-NIPLEELRHRRIERF 327 (328)
Q Consensus 293 ~cg~~~~~~~----~~~~~~~~~~-~~~~~~~r~~~~~~~ 327 (328)
-|+++.++.. .|+.-..-+| ++ -||+|++|+++|
T Consensus 85 DcNRp~d~p~lip~~Se~~~VPgN~~l-s~~ER~~R~~~~ 123 (263)
T COG3931 85 DCNRPEDAPDLIPQLSEGTVVPGNHPL-SEEERRARIDRF 123 (263)
T ss_pred cCCCCCCcchhhhccccceeccCCCCC-CHHHHHHHHHHH
Confidence 3777777643 3444444778 88 578899999987
No 37
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=58.66 E-value=5.1 Score=38.07 Aligned_cols=25 Identities=24% Similarity=0.587 Sum_probs=22.8
Q ss_pred cccCCCCccCCCCCCccccccCCCC
Q 020298 274 IWRCPACTFDNSGWLSICEMCGTSR 298 (328)
Q Consensus 274 ~W~c~~C~~~n~~~~~~c~~cg~~~ 298 (328)
.|.|++|.+......+.||.||+-.
T Consensus 354 ~~~c~~cg~~~~~~~~~c~~c~~~~ 378 (389)
T PRK11788 354 RYRCRNCGFTARTLYWHCPSCKAWE 378 (389)
T ss_pred CEECCCCCCCCccceeECcCCCCcc
Confidence 3999999999999999999999863
No 38
>KOG4198 consensus RNA-binding Ran Zn-finger protein and related proteins [General function prediction only]
Probab=57.22 E-value=5.4 Score=36.91 Aligned_cols=36 Identities=36% Similarity=0.694 Sum_probs=29.8
Q ss_pred CCCCCCcccCCCCccCCCCCCccccccCCCCCCCCC
Q 020298 268 RRTAPIIWRCPACTFDNSGWLSICEMCGTSRSGNDL 303 (328)
Q Consensus 268 ~~~~~g~W~c~~C~~~n~~~~~~c~~cg~~~~~~~~ 303 (328)
....+|.|.|..|+.+|......|++|+-+......
T Consensus 58 ~~~~pgdw~c~~c~~~n~arr~~c~~c~~s~~~~~~ 93 (280)
T KOG4198|consen 58 DPPRPGDWNCPLCGFHNSARRLLCFRCGFSKVPLDS 93 (280)
T ss_pred CCCCCcccccCccchhhHHHhhhcceecccCCCccc
Confidence 344566799999999999999999999998876444
No 39
>TIGR02827 RNR_anaer_Bdell anaerobic ribonucleoside-triphosphate reductase. Members of this family belong to the class III anaerobic ribonucleoside-triphosphate reductases (RNR). These glycine-radical-containing enzymes are oxygen-sensitive and operate under anaerobic conditions. The genes for this family are pair with genes for an acitivating protein that creates a glycine radical. Members of this family, though related, fall outside the scope of TIGR02487, a functionally equivalent protein set; no genome has members in both familes. Identification as RNR is supported by gene pairing with the activating protein, lack of other anaerobic RNR, and presence of an upstream regulatory element strongly conserved upstream of most RNR operons.
Probab=56.61 E-value=8.6 Score=39.53 Aligned_cols=48 Identities=23% Similarity=0.355 Sum_probs=31.6
Q ss_pred cccCCCCccCCCCCCccccccCCCCCCC-----CCCcccccCCCCCChHHHHHH
Q 020298 274 IWRCPACTFDNSGWLSICEMCGTSRSGN-----DLSSDQLSRHSNIPLEELRHR 322 (328)
Q Consensus 274 ~W~c~~C~~~n~~~~~~c~~cg~~~~~~-----~~~~~~~~~~~~~~~~~~r~~ 322 (328)
.-.|..|.|......+.|+.||....+. ++= ++-+++|+-+++|+++|
T Consensus 532 ~siC~~CGy~~g~~~~~CP~CGs~~~ev~sRv~GYl-~~v~~wN~gK~~E~~~R 584 (586)
T TIGR02827 532 ITICNDCHHIDKRTLHRCPVCGSANIDYGTRVIGYL-KRVSAFSKERQIEAARR 584 (586)
T ss_pred CeecCCCCCcCCCcCCcCcCCCCccceEEEeeccee-cCccccccccHHhhhcc
Confidence 4789999996554568999999643221 111 23345677788888876
No 40
>PF12773 DZR: Double zinc ribbon
Probab=56.43 E-value=9.6 Score=25.22 Aligned_cols=23 Identities=30% Similarity=0.661 Sum_probs=17.7
Q ss_pred CcccCCCCccCCCCCCccccccC
Q 020298 273 IIWRCPACTFDNSGWLSICEMCG 295 (328)
Q Consensus 273 g~W~c~~C~~~n~~~~~~c~~cg 295 (328)
..+.|+.|...|++....|+.||
T Consensus 28 ~~~~C~~Cg~~~~~~~~fC~~CG 50 (50)
T PF12773_consen 28 SKKICPNCGAENPPNAKFCPNCG 50 (50)
T ss_pred CCCCCcCCcCCCcCCcCccCccc
Confidence 35778888888887777888776
No 41
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=54.84 E-value=11 Score=29.90 Aligned_cols=32 Identities=31% Similarity=0.629 Sum_probs=23.4
Q ss_pred ccCCCC---ccCCCCCCccccccCCCCCCC-CCCcc
Q 020298 275 WRCPAC---TFDNSGWLSICEMCGTSRSGN-DLSSD 306 (328)
Q Consensus 275 W~c~~C---~~~n~~~~~~c~~cg~~~~~~-~~~~~ 306 (328)
..|+.| -|+......+|+.||+..... ...++
T Consensus 10 R~Cp~CG~kFYDLnk~PivCP~CG~~~~~~~~~k~r 45 (108)
T PF09538_consen 10 RTCPSCGAKFYDLNKDPIVCPKCGTEFPPEPPLKSR 45 (108)
T ss_pred ccCCCCcchhccCCCCCccCCCCCCccCcccccccc
Confidence 789999 466444678899999998877 44333
No 42
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=54.21 E-value=7.3 Score=26.75 Aligned_cols=26 Identities=23% Similarity=0.718 Sum_probs=19.7
Q ss_pred ccCCCCccC--CCCCCccccccCCCCCC
Q 020298 275 WRCPACTFD--NSGWLSICEMCGTSRSG 300 (328)
Q Consensus 275 W~c~~C~~~--n~~~~~~c~~cg~~~~~ 300 (328)
-+|+.|.-. ++.+-.+|++||.++.-
T Consensus 6 ~~C~~Cg~~~~~~dDiVvCp~CgapyHR 33 (54)
T PF14446_consen 6 CKCPVCGKKFKDGDDIVVCPECGAPYHR 33 (54)
T ss_pred ccChhhCCcccCCCCEEECCCCCCcccH
Confidence 468888544 46777889999999874
No 43
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=52.53 E-value=11 Score=39.83 Aligned_cols=49 Identities=24% Similarity=0.444 Sum_probs=33.8
Q ss_pred cccCCCCccCCCCCCccccccCCCCCC-----CCCCcccccCCCCCChHHHHHHHh
Q 020298 274 IWRCPACTFDNSGWLSICEMCGTSRSG-----NDLSSDQLSRHSNIPLEELRHRRI 324 (328)
Q Consensus 274 ~W~c~~C~~~n~~~~~~c~~cg~~~~~-----~~~~~~~~~~~~~~~~~~~r~~~~ 324 (328)
.-.|..|.|.... ...|+.||....+ -++= ++.+++|+-++.|++.|.-
T Consensus 680 ~~~C~~CG~~~~~-~~~CP~CG~~~~~~~~Ri~GYl-~~v~~wn~gK~~E~~~R~~ 733 (735)
T PRK07111 680 VDRCPVCGYLGVI-EDKCPKCGSTNIQRIRRITGYL-GTLDRFNSAKKAERRDRVK 733 (735)
T ss_pred CeecCCCCCCCCc-CccCcCCCCccceeeehhhhhc-cchhhcccccHHHHHHHhc
Confidence 4789999997765 5899999973211 1111 3445678888999988853
No 44
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=51.75 E-value=13 Score=38.61 Aligned_cols=51 Identities=18% Similarity=0.362 Sum_probs=33.5
Q ss_pred cccCCCCccCCCCCCccccccCCCCCC--C------CCCcccccCCCCCChHHHHHHHhh
Q 020298 274 IWRCPACTFDNSGWLSICEMCGTSRSG--N------DLSSDQLSRHSNIPLEELRHRRIE 325 (328)
Q Consensus 274 ~W~c~~C~~~n~~~~~~c~~cg~~~~~--~------~~~~~~~~~~~~~~~~~~r~~~~~ 325 (328)
.-.|..|.|.- .....|+.||...++ + ++=.++.+++|+-+++|++.|-..
T Consensus 559 ~~~C~~CGy~g-~~~~~CP~CG~~d~~~~~v~~Ri~GYl~~pv~~wN~gK~~E~~~R~~h 617 (618)
T PRK14704 559 VDRCKCCSYHG-VIGNECPSCGNEDEANIERIRRITGYLVGDMSKWNSAKRSEEMDRVKH 617 (618)
T ss_pred CeecCCCCCCC-CcCccCcCCCCCCcchhHHHHHHHhHhcCchhhcCcccHHHHHHHhcc
Confidence 47899999943 345899999976421 1 111123446788889999888643
No 45
>PF12898 Stc1: Stc1 domain; InterPro: IPR024630 The domain contains 8 conserved cysteines that may bind to zinc. In S. pombe, proteins containing the domain act as protein linkers, which link the chromatin modifying CLRC complex to RNAi by tethering it to the RITS complex. This domain has a slightly different arrangement of its CxxC pairs from the LIM domain, hence it is not part of that family []. The tandem zinc-finger structure could mediate protein-protein interactions.
Probab=51.58 E-value=9.9 Score=28.58 Aligned_cols=40 Identities=25% Similarity=0.396 Sum_probs=31.7
Q ss_pred CCCcccCCCCccCCCCCCccccccCCCCCCCCCCcccccCC
Q 020298 271 APIIWRCPACTFDNSGWLSICEMCGTSRSGNDLSSDQLSRH 311 (328)
Q Consensus 271 ~~g~W~c~~C~~~n~~~~~~c~~cg~~~~~~~~~~~~~~~~ 311 (328)
..+.-.|..|+-. +..-..|++|+...+-|.||..|...+
T Consensus 34 ~~~~i~C~~ct~~-q~~El~C~~C~~~k~ld~FSK~QR~~~ 73 (84)
T PF12898_consen 34 ANSGIRCRECTGG-QVVELTCSPCGKTKPLDEFSKNQRRKP 73 (84)
T ss_pred CCCCCCCccCCCC-CcCcCEeccCCCCcCHHHHhHHhhcCC
Confidence 3445789999977 455678999999999999998877644
No 46
>PF06945 DUF1289: Protein of unknown function (DUF1289); InterPro: IPR010710 This family consists of a number of hypothetical bacterial proteins. The aligned region spans around 56 residues and contains 4 highly conserved cysteine residues towards the N terminus. The function of this family is unknown.
Probab=47.96 E-value=11 Score=25.44 Aligned_cols=20 Identities=30% Similarity=0.742 Sum_probs=14.4
Q ss_pred CCccCCCCCCccccccCCCCCC
Q 020298 279 ACTFDNSGWLSICEMCGTSRSG 300 (328)
Q Consensus 279 ~C~~~n~~~~~~c~~cg~~~~~ 300 (328)
.|.+|.. .++|..|+++...
T Consensus 7 vC~~d~~--~~~C~GC~RT~dE 26 (51)
T PF06945_consen 7 VCKLDPS--DGVCRGCGRTLDE 26 (51)
T ss_pred ccccCCC--CCccCCCCCcHHH
Confidence 4666653 4899999998653
No 47
>PF12773 DZR: Double zinc ribbon
Probab=47.57 E-value=12 Score=24.72 Aligned_cols=23 Identities=35% Similarity=0.778 Sum_probs=11.8
Q ss_pred CCCCccCCCCCCccccccCCCCC
Q 020298 277 CPACTFDNSGWLSICEMCGTSRS 299 (328)
Q Consensus 277 c~~C~~~n~~~~~~c~~cg~~~~ 299 (328)
|+.|...|+.....|+-||++-.
T Consensus 1 Cp~Cg~~~~~~~~fC~~CG~~l~ 23 (50)
T PF12773_consen 1 CPHCGTPNPDDAKFCPHCGTPLP 23 (50)
T ss_pred CCCcCCcCCccccCChhhcCChh
Confidence 44555555555555555555433
No 48
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=46.48 E-value=16 Score=29.63 Aligned_cols=27 Identities=15% Similarity=0.263 Sum_probs=21.3
Q ss_pred ccCCCC---ccCCCCCCccccccCCCCCCC
Q 020298 275 WRCPAC---TFDNSGWLSICEMCGTSRSGN 301 (328)
Q Consensus 275 W~c~~C---~~~n~~~~~~c~~cg~~~~~~ 301 (328)
+.|+.| -|+......+|+.||......
T Consensus 10 r~Cp~cg~kFYDLnk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 10 RICPNTGSKFYDLNRRPAVSPYTGEQFPPE 39 (129)
T ss_pred ccCCCcCccccccCCCCccCCCcCCccCcc
Confidence 678888 466445789999999997765
No 49
>PF04528 Adeno_E4_34: Adenovirus early E4 34 kDa protein conserved region; InterPro: IPR007615 Adenoviruses E4 is essential for DNA replication and late protein synthesis []. The adenovirus, early region 4 open reading frame 3 (E4 ORF3) protein is required for viral DNA replication during the interferon (IFN)-induced antiviral state []. The E4 ORF3 protein reorganises the promyelocytic leukemia (PML) protein nuclear bodies. These normally punctate structures are reorganised by E4 ORF3 into tracks that eventually surround viral replication centres. PML rearrangement is an evolutionarily conserved function of E4 ORF3 []. The product of adenovirus early region 4 (E4), open reading frame 6, is E4 34k. It modulates viral late gene expression, DNA replication, apoptosis, double strand break repair, and transformation through multiple interactions with components in infected and transformed cells [, ]. Conservation of several cysteine and histidine residues among E4 34k sequences suggests the presence of a zinc binding domain, which is important for its function []. This entry is a conserved region found in the Adenovirus E4 34 kDa protein.
Probab=46.30 E-value=5.9 Score=33.16 Aligned_cols=49 Identities=16% Similarity=0.209 Sum_probs=26.2
Q ss_pred ccCCCCccCCCCCCcccc---------ccCCCCCCCCCCcccccCCCCCChHHHHHHHhhhc
Q 020298 275 WRCPACTFDNSGWLSICE---------MCGTSRSGNDLSSDQLSRHSNIPLEELRHRRIERF 327 (328)
Q Consensus 275 W~c~~C~~~n~~~~~~c~---------~cg~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~ 327 (328)
=.|..|.-.++.+...|. |+.--.+++.-++...+ -.+||.|||-|+|+
T Consensus 82 L~C~~C~~~se~~~r~CA~RtR~ll~r~~~~l~~~~~~~~~~~~----s~~E~~RQr~Lr~~ 139 (148)
T PF04528_consen 82 LCCRSCADLSEISVRCCARRTRRLLRRMLRALDKRTRVPRPLRR----SRTERRRQRLLRRL 139 (148)
T ss_pred EEeCcCCChhHHHHHHHHHHHHHHHHHHHHHhhcCCCCCccCCc----cchHHHHHHHHHHH
Confidence 468888766666666665 22222222221111111 23799999988864
No 50
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=46.06 E-value=13 Score=25.14 Aligned_cols=9 Identities=33% Similarity=1.387 Sum_probs=5.9
Q ss_pred cccccCCCC
Q 020298 290 ICEMCGTSR 298 (328)
Q Consensus 290 ~c~~cg~~~ 298 (328)
+|+.||.+.
T Consensus 36 ~CP~C~a~K 44 (50)
T cd00730 36 VCPVCGAGK 44 (50)
T ss_pred CCCCCCCcH
Confidence 577777654
No 51
>COG1773 Rubredoxin [Energy production and conversion]
Probab=44.29 E-value=11 Score=26.01 Aligned_cols=10 Identities=40% Similarity=1.368 Sum_probs=6.0
Q ss_pred cccCCCCccC
Q 020298 274 IWRCPACTFD 283 (328)
Q Consensus 274 ~W~c~~C~~~ 283 (328)
.|+|+.|-|.
T Consensus 3 ~~~C~~CG~v 12 (55)
T COG1773 3 RWRCSVCGYV 12 (55)
T ss_pred ceEecCCceE
Confidence 3777777443
No 52
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=43.68 E-value=8 Score=24.02 Aligned_cols=24 Identities=25% Similarity=0.548 Sum_probs=13.4
Q ss_pred ccCCCCccCCCCCCccccccCCCC
Q 020298 275 WRCPACTFDNSGWLSICEMCGTSR 298 (328)
Q Consensus 275 W~c~~C~~~n~~~~~~c~~cg~~~ 298 (328)
=+|..|....-+..++|+.|+...
T Consensus 12 ~rC~~Cg~~~~pPr~~Cp~C~s~~ 35 (37)
T PF12172_consen 12 QRCRDCGRVQFPPRPVCPHCGSDE 35 (37)
T ss_dssp EE-TTT--EEES--SEETTTT---
T ss_pred EEcCCCCCEecCCCcCCCCcCccc
Confidence 478888888777789999998654
No 53
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=43.12 E-value=12 Score=26.19 Aligned_cols=25 Identities=28% Similarity=0.844 Sum_probs=18.4
Q ss_pred ccCCCCc-----cCCCCCCccccccCCCCC
Q 020298 275 WRCPACT-----FDNSGWLSICEMCGTSRS 299 (328)
Q Consensus 275 W~c~~C~-----~~n~~~~~~c~~cg~~~~ 299 (328)
=+|+.|. |++..+...|..||++=.
T Consensus 12 VkCp~C~n~q~vFsha~t~V~C~~Cg~~L~ 41 (59)
T PRK00415 12 VKCPDCGNEQVVFSHASTVVRCLVCGKTLA 41 (59)
T ss_pred EECCCCCCeEEEEecCCcEEECcccCCCcc
Confidence 5788884 445667777999998743
No 54
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=42.72 E-value=22 Score=24.73 Aligned_cols=15 Identities=20% Similarity=0.441 Sum_probs=11.6
Q ss_pred CCccccccCCCCCCC
Q 020298 287 WLSICEMCGTSRSGN 301 (328)
Q Consensus 287 ~~~~c~~cg~~~~~~ 301 (328)
.+..|.+||++-+.|
T Consensus 7 PH~HC~VCg~aIp~d 21 (64)
T COG4068 7 PHRHCVVCGKAIPPD 21 (64)
T ss_pred CCccccccCCcCCCc
Confidence 356799999997744
No 55
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=41.95 E-value=11 Score=26.90 Aligned_cols=25 Identities=32% Similarity=0.926 Sum_probs=19.4
Q ss_pred ccCCCC-----ccCCCCCCccccccCCCCC
Q 020298 275 WRCPAC-----TFDNSGWLSICEMCGTSRS 299 (328)
Q Consensus 275 W~c~~C-----~~~n~~~~~~c~~cg~~~~ 299 (328)
=+|+.| .|++.++...|..||+.=.
T Consensus 20 VkCpdC~N~q~vFshast~V~C~~CG~~l~ 49 (67)
T COG2051 20 VKCPDCGNEQVVFSHASTVVTCLICGTTLA 49 (67)
T ss_pred EECCCCCCEEEEeccCceEEEecccccEEE
Confidence 578888 5777777788999998643
No 56
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=41.90 E-value=14 Score=38.47 Aligned_cols=51 Identities=22% Similarity=0.411 Sum_probs=33.3
Q ss_pred CCcccCCCCccCCCCCCccccccCCCCCC-----CCCCcccccCCCCCChHHHHHHH
Q 020298 272 PIIWRCPACTFDNSGWLSICEMCGTSRSG-----NDLSSDQLSRHSNIPLEELRHRR 323 (328)
Q Consensus 272 ~g~W~c~~C~~~n~~~~~~c~~cg~~~~~-----~~~~~~~~~~~~~~~~~~~r~~~ 323 (328)
+..-.|..|.|.-....+.|+.||....+ -++= ++-+++|+-+++|++.|+
T Consensus 566 p~~~~C~~CG~~~~g~~~~CP~CGs~~~~v~~Rv~GYl-~~v~~wN~gK~~E~~~R~ 621 (625)
T PRK08579 566 PAITVCNKCGRSTTGLYTRCPRCGSEDVEVWSRIIGYY-RPLKNWNPYRKKEFWLRK 621 (625)
T ss_pred CCCccCCCCCCccCCCCCcCcCCCCchhHHHHHHHhhh-ccccccccccHHHHHHHh
Confidence 34588999998534446899999975321 1111 133467778888888775
No 57
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=40.87 E-value=14 Score=23.11 Aligned_cols=22 Identities=32% Similarity=0.928 Sum_probs=13.4
Q ss_pred ccCCCC--ccC---C-CCCCccccccCC
Q 020298 275 WRCPAC--TFD---N-SGWLSICEMCGT 296 (328)
Q Consensus 275 W~c~~C--~~~---n-~~~~~~c~~cg~ 296 (328)
|.|+.| +|+ | +....+|+.||.
T Consensus 2 r~C~~Cg~~Yh~~~~pP~~~~~Cd~cg~ 29 (36)
T PF05191_consen 2 RICPKCGRIYHIEFNPPKVEGVCDNCGG 29 (36)
T ss_dssp EEETTTTEEEETTTB--SSTTBCTTTTE
T ss_pred cCcCCCCCccccccCCCCCCCccCCCCC
Confidence 567777 222 3 234467999987
No 58
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=40.80 E-value=17 Score=35.32 Aligned_cols=27 Identities=19% Similarity=0.423 Sum_probs=22.2
Q ss_pred CCCcccCCCCccCCCC-CCccccccCCC
Q 020298 271 APIIWRCPACTFDNSG-WLSICEMCGTS 297 (328)
Q Consensus 271 ~~g~W~c~~C~~~n~~-~~~~c~~cg~~ 297 (328)
..+.-.|..|+|.+.. ....|..||++
T Consensus 217 ~~~~~~C~~C~~~~~~~~~~~CpRC~~~ 244 (418)
T COG2995 217 REGLRSCLCCHYILPHDAEPRCPRCGSK 244 (418)
T ss_pred cccceecccccccCCHhhCCCCCCCCCh
Confidence 3345689999999876 78899999987
No 59
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=39.74 E-value=19 Score=30.11 Aligned_cols=31 Identities=23% Similarity=0.567 Sum_probs=22.7
Q ss_pred CCCCCCcccCCCCccC----CCCCCccccccCCCC
Q 020298 268 RRTAPIIWRCPACTFD----NSGWLSICEMCGTSR 298 (328)
Q Consensus 268 ~~~~~g~W~c~~C~~~----n~~~~~~c~~cg~~~ 298 (328)
...++|.-.|..|.+. ....-+.|+.||..+
T Consensus 106 E~~g~G~l~C~~Cg~~~~~~~~~~l~~Cp~C~~~~ 140 (146)
T PF07295_consen 106 EVVGPGTLVCENCGHEVELTHPERLPPCPKCGHTE 140 (146)
T ss_pred cEecCceEecccCCCEEEecCCCcCCCCCCCCCCe
Confidence 3446788999999654 445567799999764
No 60
>KOG4345 consensus NF-kappa B regulator AP20/Cezanne [Signal transduction mechanisms]
Probab=39.60 E-value=11 Score=39.02 Aligned_cols=30 Identities=10% Similarity=-0.042 Sum_probs=27.4
Q ss_pred ccCCCCccCCCCCCccccccCCCCCCCCCC
Q 020298 275 WRCPACTFDNSGWLSICEMCGTSRSGNDLS 304 (328)
Q Consensus 275 W~c~~C~~~n~~~~~~c~~cg~~~~~~~~~ 304 (328)
|.|..|+|.|.+-++.|-+||+.++.+..-
T Consensus 186 W~~lik~ass~pr~~r~~~~~~~~~~e~s~ 215 (774)
T KOG4345|consen 186 WTELIKLASSEPRMHRSGNGGTGGGVEISE 215 (774)
T ss_pred HHHHHHhhcccchhhhcccCCCCCCccccc
Confidence 999999999999999999999999976553
No 61
>PRK14526 adenylate kinase; Provisional
Probab=39.49 E-value=33 Score=30.34 Aligned_cols=40 Identities=25% Similarity=0.608 Sum_probs=22.3
Q ss_pred cccCCCCc--cC----CCCCCccccccCCC---CCCCCCCcccccCCCCCChHHHHHHHhhhc
Q 020298 274 IWRCPACT--FD----NSGWLSICEMCGTS---RSGNDLSSDQLSRHSNIPLEELRHRRIERF 327 (328)
Q Consensus 274 ~W~c~~C~--~~----n~~~~~~c~~cg~~---~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~ 327 (328)
.+.|+.|. |+ .++...+|+.|+.. |.|| .||.=++||+.|
T Consensus 122 R~~~~~~g~~y~~~~~pp~~~~~~~~~~~~l~~R~DD--------------~~e~i~~Rl~~y 170 (211)
T PRK14526 122 RRICKSCNNIFNIYTLPTKEKGICDVCKGDLYQRKDD--------------KEESLKTRLQEY 170 (211)
T ss_pred CCcccccCCccccccCCCCccCcCCCCCCeeeccCCC--------------CHHHHHHHHHHH
Confidence 37777773 22 23344568888743 2222 356667777655
No 62
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=39.31 E-value=14 Score=30.48 Aligned_cols=29 Identities=21% Similarity=0.473 Sum_probs=20.1
Q ss_pred CCCCcccCCCCccCCCC-----------------------CCccccccCCCC
Q 020298 270 TAPIIWRCPACTFDNSG-----------------------WLSICEMCGTSR 298 (328)
Q Consensus 270 ~~~g~W~c~~C~~~n~~-----------------------~~~~c~~cg~~~ 298 (328)
..+..|.|..|.+.-.. ....|+.||...
T Consensus 66 ~~p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~ 117 (135)
T PRK03824 66 EEEAVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRD 117 (135)
T ss_pred ecceEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCC
Confidence 34567999999866322 234599999764
No 63
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=38.20 E-value=17 Score=35.71 Aligned_cols=24 Identities=29% Similarity=0.969 Sum_probs=21.8
Q ss_pred CcccCCCCccCCCCCCccccccCC
Q 020298 273 IIWRCPACTFDNSGWLSICEMCGT 296 (328)
Q Consensus 273 g~W~c~~C~~~n~~~~~~c~~cg~ 296 (328)
..|.|+.|.|......-.|+-||.
T Consensus 6 t~f~C~~CG~~s~KW~GkCp~Cg~ 29 (456)
T COG1066 6 TAFVCQECGYVSPKWLGKCPACGA 29 (456)
T ss_pred cEEEcccCCCCCccccccCCCCCC
Confidence 459999999999999999999994
No 64
>PTZ00088 adenylate kinase 1; Provisional
Probab=37.69 E-value=39 Score=30.31 Aligned_cols=30 Identities=27% Similarity=0.548 Sum_probs=16.3
Q ss_pred ccccccCCCCCCCCCCcccccCCCCCChHHHHHHHhhhc
Q 020298 289 SICEMCGTSRSGNDLSSDQLSRHSNIPLEELRHRRIERF 327 (328)
Q Consensus 289 ~~c~~cg~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~ 327 (328)
..|+.||.... +....+ ..||.-++|++.|
T Consensus 159 ~~c~~~~~~~~--------l~~R~D-D~~e~i~~Rl~~Y 188 (229)
T PTZ00088 159 ADCEGCKGNPK--------LQKRSD-DTEEIVAHRLNTY 188 (229)
T ss_pred CcccccCCccc--------ccCCCC-CCHHHHHHHHHHH
Confidence 47999986311 111121 1466667787765
No 65
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=37.62 E-value=23 Score=22.73 Aligned_cols=26 Identities=23% Similarity=0.659 Sum_probs=16.4
Q ss_pred ccCCCCccC-------CCCCCccccccCCCCCC
Q 020298 275 WRCPACTFD-------NSGWLSICEMCGTSRSG 300 (328)
Q Consensus 275 W~c~~C~~~-------n~~~~~~c~~cg~~~~~ 300 (328)
.+|+.|... .+.....|+.||.....
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~ 38 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSISEDDPVPCPECGSTEVR 38 (42)
T ss_pred EEeCCCCCEEEEEEEcCCCCCCcCCCCCCCceE
Confidence 467777521 22456789999985443
No 66
>COG5336 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.14 E-value=90 Score=24.73 Aligned_cols=31 Identities=26% Similarity=0.302 Sum_probs=22.5
Q ss_pred HHHHHHHHHHHHHhccCCCCCcHHHHHHHHH
Q 020298 207 LGGILAGILYLKLKGGYSGSDPLTTIIRGAT 237 (328)
Q Consensus 207 l~G~l~G~ly~~~~~~~~~~~p~~~~~~~~~ 237 (328)
++|+++|..++++..++-+..|+--++..+.
T Consensus 53 IsGilVGa~iG~llD~~agTsPwglIv~lll 83 (116)
T COG5336 53 ISGILVGAGIGWLLDKFAGTSPWGLIVFLLL 83 (116)
T ss_pred HHHHHHHHHHHHHHHHhcCCCcHHHHHHHHH
Confidence 5688888888888777777778766554433
No 67
>TIGR03037 anthran_nbaC 3-hydroxyanthranilate 3,4-dioxygenase. Members of this protein family, from both bacteria and eukaryotes, are the enzyme 3-hydroxyanthranilate 3,4-dioxygenase. This enzyme acts on the tryptophan metabolite 3-hydroxyanthranilate and produces 2-amino-3-carboxymuconate semialdehyde, which can rearrange spontaneously to quinolinic acid and feed into nicotinamide biosynthesis, or undergo further enzymatic degradation.
Probab=36.94 E-value=21 Score=30.28 Aligned_cols=16 Identities=25% Similarity=0.542 Sum_probs=11.6
Q ss_pred ccCCCCCCccccccCC
Q 020298 281 TFDNSGWLSICEMCGT 296 (328)
Q Consensus 281 ~~~n~~~~~~c~~cg~ 296 (328)
.|.++.....|..||+
T Consensus 144 ~f~~~~~~rtC~~Cg~ 159 (159)
T TIGR03037 144 HFYSNEDARTCKNCGH 159 (159)
T ss_pred HHhCChhhccCCccCC
Confidence 4556667788999985
No 68
>COG5257 GCD11 Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]
Probab=36.24 E-value=25 Score=33.56 Aligned_cols=26 Identities=27% Similarity=0.648 Sum_probs=21.1
Q ss_pred cccCCCCccC-CCCCCccccccCCCCC
Q 020298 274 IWRCPACTFD-NSGWLSICEMCGTSRS 299 (328)
Q Consensus 274 ~W~c~~C~~~-n~~~~~~c~~cg~~~~ 299 (328)
.|+|+.|.+- +....+.|+.||..-+
T Consensus 57 i~kC~~c~~~~~y~~~~~C~~cg~~~~ 83 (415)
T COG5257 57 IYKCPECYRPECYTTEPKCPNCGAETE 83 (415)
T ss_pred eEeCCCCCCCcccccCCCCCCCCCCcc
Confidence 5999999874 5677889999998754
No 69
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=35.68 E-value=23 Score=35.29 Aligned_cols=23 Identities=26% Similarity=0.795 Sum_probs=20.8
Q ss_pred cccCCCCccCCCCCCccccccCC
Q 020298 274 IWRCPACTFDNSGWLSICEMCGT 296 (328)
Q Consensus 274 ~W~c~~C~~~n~~~~~~c~~cg~ 296 (328)
.|.|+.|.|......-.|+-|+.
T Consensus 7 ~y~C~~Cg~~~~~~~g~Cp~C~~ 29 (454)
T TIGR00416 7 KFVCQHCGADSPKWQGKCPACHA 29 (454)
T ss_pred eEECCcCCCCCccccEECcCCCC
Confidence 59999999999998999999975
No 70
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=35.34 E-value=25 Score=20.25 Aligned_cols=21 Identities=29% Similarity=0.787 Sum_probs=14.0
Q ss_pred cCCCCccCCCCCCccccccCC
Q 020298 276 RCPACTFDNSGWLSICEMCGT 296 (328)
Q Consensus 276 ~c~~C~~~n~~~~~~c~~cg~ 296 (328)
.|+.|.-.=+.+...|+.||-
T Consensus 2 ~CP~C~~~V~~~~~~Cp~CG~ 22 (26)
T PF10571_consen 2 TCPECGAEVPESAKFCPHCGY 22 (26)
T ss_pred cCCCCcCCchhhcCcCCCCCC
Confidence 466666665556677888874
No 71
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=35.23 E-value=34 Score=36.17 Aligned_cols=51 Identities=22% Similarity=0.298 Sum_probs=30.1
Q ss_pred cccCCCCccCCCC----CCccccccCCCCCC--------CCCCcccccC-CCCCChHHHHHHHh
Q 020298 274 IWRCPACTFDNSG----WLSICEMCGTSRSG--------NDLSSDQLSR-HSNIPLEELRHRRI 324 (328)
Q Consensus 274 ~W~c~~C~~~n~~----~~~~c~~cg~~~~~--------~~~~~~~~~~-~~~~~~~~~r~~~~ 324 (328)
.-.|..|.|...- ..+.|+.||....+ -++=..+..+ +|+-+++|++.|..
T Consensus 641 ~~~C~~CG~~Ge~~~~~~~~~CP~CG~~~~~~~~v~~Ri~GYl~~~~~r~~N~gK~~E~~~R~~ 704 (711)
T PRK09263 641 IDECYECGFTGEFECTEKGFTCPKCGNHDPKTVSVTRRTCGYLGNPDARPFNHGRQEEIKRRVK 704 (711)
T ss_pred CcccCCCCCCccccCCCCCCcCcCCCCCCCcceeEEEeeccccCCcccccCccccHHHHHHHHH
Confidence 4789999984211 12689999965311 1111122222 67778999998864
No 72
>PRK11823 DNA repair protein RadA; Provisional
Probab=34.84 E-value=24 Score=34.99 Aligned_cols=25 Identities=28% Similarity=0.848 Sum_probs=21.4
Q ss_pred CcccCCCCccCCCCCCccccccCCC
Q 020298 273 IIWRCPACTFDNSGWLSICEMCGTS 297 (328)
Q Consensus 273 g~W~c~~C~~~n~~~~~~c~~cg~~ 297 (328)
-.|.|+.|.|......-.|+.|+.-
T Consensus 6 ~~y~C~~Cg~~~~~~~g~Cp~C~~w 30 (446)
T PRK11823 6 TAYVCQECGAESPKWLGRCPECGAW 30 (446)
T ss_pred CeEECCcCCCCCcccCeeCcCCCCc
Confidence 3599999999999989999999753
No 73
>COG2401 ABC-type ATPase fused to a predicted acetyltransferase domain [General function prediction only]
Probab=34.57 E-value=17 Score=35.84 Aligned_cols=26 Identities=27% Similarity=0.740 Sum_probs=18.8
Q ss_pred CCCcccCCCCccC-CCCCCccccccCCC
Q 020298 271 APIIWRCPACTFD-NSGWLSICEMCGTS 297 (328)
Q Consensus 271 ~~g~W~c~~C~~~-n~~~~~~c~~cg~~ 297 (328)
.-..|+|..|.-. ..-.++.| .||++
T Consensus 127 ~va~w~c~~cg~~iean~kp~c-~cg~~ 153 (593)
T COG2401 127 KVALWRCEKCGTIIEANTKPEC-KCGSH 153 (593)
T ss_pred eEEEEecchhchhhhhcCCccc-CCCCc
Confidence 3346999999544 44456799 99994
No 74
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=34.53 E-value=16 Score=36.66 Aligned_cols=29 Identities=14% Similarity=0.329 Sum_probs=20.5
Q ss_pred CCCcccCCCCccCCCC-------------------CCccccccCCCCC
Q 020298 271 APIIWRCPACTFDNSG-------------------WLSICEMCGTSRS 299 (328)
Q Consensus 271 ~~g~W~c~~C~~~n~~-------------------~~~~c~~cg~~~~ 299 (328)
....|+|+.|.|.=.+ ..-+|+.||.+..
T Consensus 422 ~~~~~~c~~c~~~yd~~~g~~~~~~~~gt~~~~lp~~~~cp~c~~~k~ 469 (479)
T PRK05452 422 LGPRMQCSVCQWIYDPAKGEPMQDVAPGTPWSEVPDNFLCPECSLGKD 469 (479)
T ss_pred CCCeEEECCCCeEECCCCCCcccCCCCCCChhhCCCCCcCcCCCCcHH
Confidence 4556999999776332 1237999998865
No 75
>COG1328 NrdD Oxygen-sensitive ribonucleoside-triphosphate reductase [Nucleotide transport and metabolism]
Probab=34.30 E-value=33 Score=36.05 Aligned_cols=24 Identities=25% Similarity=0.739 Sum_probs=18.8
Q ss_pred ccCCCCccCCCCCCccccccCCCC
Q 020298 275 WRCPACTFDNSGWLSICEMCGTSR 298 (328)
Q Consensus 275 W~c~~C~~~n~~~~~~c~~cg~~~ 298 (328)
-.|..|.|+-......|+.||..+
T Consensus 642 ~~C~~cg~~~~~~~~~Cp~CG~~d 665 (700)
T COG1328 642 SVCNRCGYSGEGLRTRCPKCGSED 665 (700)
T ss_pred eeeccCCcccccccccCCCCCCcc
Confidence 569999998665555699999776
No 76
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=34.11 E-value=13 Score=24.68 Aligned_cols=11 Identities=45% Similarity=1.262 Sum_probs=3.6
Q ss_pred CCCCcccCCCC
Q 020298 270 TAPIIWRCPAC 280 (328)
Q Consensus 270 ~~~g~W~c~~C 280 (328)
.-+..|.|+.|
T Consensus 30 ~Lp~~w~CP~C 40 (47)
T PF00301_consen 30 DLPDDWVCPVC 40 (47)
T ss_dssp GS-TT-B-TTT
T ss_pred HCCCCCcCcCC
Confidence 33444555554
No 77
>PF12989 DUF3873: Domain of unknown function, B. Theta Gene description (DUF3873); InterPro: IPR024356 This entry represents a family of uncharacterised proteins found primarily in Bacteroides species. The Bacteroides thetaiotaomicron gene appears to be upregulated in the presence of host or other bacterial species compared to growth in pure culture [, ].
Probab=33.73 E-value=28 Score=25.04 Aligned_cols=12 Identities=42% Similarity=0.304 Sum_probs=10.6
Q ss_pred CCChHHHHHHHh
Q 020298 313 NIPLEELRHRRI 324 (328)
Q Consensus 313 ~~~~~~~r~~~~ 324 (328)
.+++||+|++|=
T Consensus 51 ~~tLeEcRr~rd 62 (69)
T PF12989_consen 51 APTLEECRRLRD 62 (69)
T ss_pred hccHHHHHHHHH
Confidence 789999999983
No 78
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=33.51 E-value=17 Score=39.51 Aligned_cols=30 Identities=23% Similarity=0.443 Sum_probs=25.1
Q ss_pred cccCCCCccCCCCCCccccccCCCCCCCCC
Q 020298 274 IWRCPACTFDNSGWLSICEMCGTSRSGNDL 303 (328)
Q Consensus 274 ~W~c~~C~~~n~~~~~~c~~cg~~~~~~~~ 303 (328)
.|+|..|.+.-..+.+.|+.||+...+|+-
T Consensus 694 IKrC~dcg~q~~~~~~~cP~Cgs~~v~d~~ 723 (1187)
T COG1110 694 IKRCRDCGEQFVDSEDKCPRCGSRNVEDKT 723 (1187)
T ss_pred HHHHhhcCceeccccccCCCCCCccccccH
Confidence 399999999987778899999998776543
No 79
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=33.45 E-value=50 Score=22.87 Aligned_cols=28 Identities=29% Similarity=0.665 Sum_probs=20.3
Q ss_pred CCCcccCCCCccCCCCCCccccccCCCCC
Q 020298 271 APIIWRCPACTFDNSGWLSICEMCGTSRS 299 (328)
Q Consensus 271 ~~g~W~c~~C~~~n~~~~~~c~~cg~~~~ 299 (328)
.+..-.|+.|.-.-.+ .++|..||..++
T Consensus 24 ~~~l~~C~~CG~~~~~-H~vC~~CG~Y~g 51 (57)
T PRK12286 24 APGLVECPNCGEPKLP-HRVCPSCGYYKG 51 (57)
T ss_pred CCcceECCCCCCccCC-eEECCCCCcCCC
Confidence 4455778888766555 688999997654
No 80
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=33.36 E-value=23 Score=28.17 Aligned_cols=29 Identities=21% Similarity=0.259 Sum_probs=20.2
Q ss_pred CCCcccCCCCccCCCC--CCccccccCCCCC
Q 020298 271 APIIWRCPACTFDNSG--WLSICEMCGTSRS 299 (328)
Q Consensus 271 ~~g~W~c~~C~~~n~~--~~~~c~~cg~~~~ 299 (328)
.+...+|..|...-.. ....|+.||++..
T Consensus 67 vp~~~~C~~Cg~~~~~~~~~~~CP~Cgs~~~ 97 (113)
T PRK12380 67 KPAQAWCWDCSQVVEIHQHDAQCPHCHGERL 97 (113)
T ss_pred eCcEEEcccCCCEEecCCcCccCcCCCCCCc
Confidence 5566999999765322 3445999997744
No 81
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=32.99 E-value=19 Score=28.67 Aligned_cols=29 Identities=14% Similarity=0.232 Sum_probs=20.1
Q ss_pred CCCcccCCCCccCCCCC---CccccccCCCCC
Q 020298 271 APIIWRCPACTFDNSGW---LSICEMCGTSRS 299 (328)
Q Consensus 271 ~~g~W~c~~C~~~n~~~---~~~c~~cg~~~~ 299 (328)
.++..+|..|...-... ...|+.||+...
T Consensus 67 ~p~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~~~ 98 (114)
T PRK03681 67 QEAECWCETCQQYVTLLTQRVRRCPQCHGDML 98 (114)
T ss_pred eCcEEEcccCCCeeecCCccCCcCcCcCCCCc
Confidence 55679999997663322 245999997753
No 82
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=32.92 E-value=20 Score=28.21 Aligned_cols=24 Identities=29% Similarity=0.646 Sum_probs=15.5
Q ss_pred cCCCCccCC---CCCCccccccCCCCC
Q 020298 276 RCPACTFDN---SGWLSICEMCGTSRS 299 (328)
Q Consensus 276 ~c~~C~~~n---~~~~~~c~~cg~~~~ 299 (328)
.|+.|...+ ....-+|++|+-.-.
T Consensus 4 ~CP~C~seytY~dg~~~iCpeC~~EW~ 30 (109)
T TIGR00686 4 PCPKCNSEYTYHDGTQLICPSCLYEWN 30 (109)
T ss_pred cCCcCCCcceEecCCeeECcccccccc
Confidence 588884442 233688999986543
No 83
>PF06946 Phage_holin_5: Phage holin; InterPro: IPR009708 This entry represents the Bacteriophage A118, holin protein. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This protein family represent one of a large number of mutually dissimilar families of phage holins. It is thought that the temporal precision of holin-mediated lysis may occur through the build-up of a holin oligomer which causes the lysis [].
Probab=32.57 E-value=1.2e+02 Score=23.35 Aligned_cols=11 Identities=18% Similarity=0.531 Sum_probs=7.1
Q ss_pred hhhHHHHHHHH
Q 020298 181 VPARYAAWAEL 191 (328)
Q Consensus 181 i~~~~~~~~~l 191 (328)
+|.||+|++..
T Consensus 31 v~~K~iPlIs~ 41 (93)
T PF06946_consen 31 VPNKWIPLISV 41 (93)
T ss_pred CCcchhhHHHH
Confidence 56777776643
No 84
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=31.10 E-value=30 Score=22.51 Aligned_cols=25 Identities=24% Similarity=0.553 Sum_probs=16.2
Q ss_pred ccCCCCccCC----CCCCccccccCCCCC
Q 020298 275 WRCPACTFDN----SGWLSICEMCGTSRS 299 (328)
Q Consensus 275 W~c~~C~~~n----~~~~~~c~~cg~~~~ 299 (328)
.+|+.|.-.. ......|+.||.+-.
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCGYRIL 32 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCCCeEE
Confidence 5788885542 222567999997643
No 85
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=30.60 E-value=17 Score=25.49 Aligned_cols=21 Identities=33% Similarity=0.779 Sum_probs=15.6
Q ss_pred cccCCCCccCCCCCCccccccCC
Q 020298 274 IWRCPACTFDNSGWLSICEMCGT 296 (328)
Q Consensus 274 ~W~c~~C~~~n~~~~~~c~~cg~ 296 (328)
.|+|+.|.-.+.+ -+|+.||=
T Consensus 38 I~Rc~~CRk~g~~--Y~Cp~CGF 58 (61)
T COG2888 38 IYRCAKCRKLGNP--YRCPKCGF 58 (61)
T ss_pred eehhhhHHHcCCc--eECCCcCc
Confidence 5888888776543 67988883
No 86
>PRK05978 hypothetical protein; Provisional
Probab=30.24 E-value=35 Score=28.56 Aligned_cols=25 Identities=32% Similarity=0.655 Sum_probs=18.6
Q ss_pred ccCCCCccCCC-----CCCccccccCCCCC
Q 020298 275 WRCPACTFDNS-----GWLSICEMCGTSRS 299 (328)
Q Consensus 275 W~c~~C~~~n~-----~~~~~c~~cg~~~~ 299 (328)
=+|+.|.-..- ...+.|+.||...+
T Consensus 34 grCP~CG~G~LF~g~Lkv~~~C~~CG~~~~ 63 (148)
T PRK05978 34 GRCPACGEGKLFRAFLKPVDHCAACGEDFT 63 (148)
T ss_pred CcCCCCCCCcccccccccCCCccccCCccc
Confidence 68999964432 35688999999866
No 87
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=29.85 E-value=40 Score=31.35 Aligned_cols=30 Identities=23% Similarity=0.537 Sum_probs=24.2
Q ss_pred CCCCCCcccCCCCccCCCCCCccccccCCC
Q 020298 268 RRTAPIIWRCPACTFDNSGWLSICEMCGTS 297 (328)
Q Consensus 268 ~~~~~g~W~c~~C~~~n~~~~~~c~~cg~~ 297 (328)
.+....+|.|+.|.-.-+.-++.|..||+.
T Consensus 249 ~k~v~~GyvCs~Clsi~C~~p~~C~~Cgt~ 278 (279)
T TIGR00627 249 HQLVSIGFVCSVCLSVLCQYTPICKTCKTA 278 (279)
T ss_pred CccccceEECCCccCCcCCCCCCCCCCCCC
Confidence 344666799999998877667899999974
No 88
>TIGR02230 ATPase_gene1 F0F1-ATPase subunit, putative. This model represents a protein found encoded in F1F0-ATPase operons in several genomes, including Methanosarcina barkeri (archaeal) and Chlorobium tepidum (bacterial). It is a small protein (about 100 amino acids) with long hydrophic stretches and is presumed to be a subunit of the enzyme.
Probab=29.53 E-value=1.9e+02 Score=22.53 Aligned_cols=40 Identities=15% Similarity=0.079 Sum_probs=26.9
Q ss_pred hHHHHHHHHHHHHHHHHHhhhChHHHHHHHHHHHHHHHHH
Q 020298 90 SHLFYNMMSLLWKGIQLETSMGSNEFAAMVVALLGMSQGI 129 (328)
Q Consensus 90 ~Hll~Nm~~L~~~G~~lE~~~G~~~f~~~yl~~~~~~~~l 129 (328)
++++.-.+.-.++|..|.+.+++...+.+-+++.|+..++
T Consensus 50 ~~~v~pil~G~~lG~WLD~~~~t~~~~tl~~lllGv~~G~ 89 (100)
T TIGR02230 50 WSVAIPTLLGVAVGIWLDRHYPSPFSWTLTMLIVGVVIGC 89 (100)
T ss_pred HHHHHHHHHHHHHHHHHHhhcCCCcHHHHHHHHHHHHHHH
Confidence 4667777788889999999998754444333445555444
No 89
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=29.09 E-value=44 Score=29.35 Aligned_cols=26 Identities=23% Similarity=0.716 Sum_probs=20.7
Q ss_pred cccCCCCccCCCCCCccccccCCCCCCC
Q 020298 274 IWRCPACTFDNSGWLSICEMCGTSRSGN 301 (328)
Q Consensus 274 ~W~c~~C~~~n~~~~~~c~~cg~~~~~~ 301 (328)
.-.|+.|....+ .+.|+.|.-++.|+
T Consensus 53 i~~C~~C~~lse--~~~C~IC~d~~Rd~ 78 (195)
T TIGR00615 53 LRTCSVCGAISD--QEVCNICSDERRDN 78 (195)
T ss_pred CCcCCCCCCCCC--CCcCCCCCCCCCCC
Confidence 478999976654 47899999998875
No 90
>PRK10220 hypothetical protein; Provisional
Probab=28.44 E-value=29 Score=27.37 Aligned_cols=22 Identities=27% Similarity=0.795 Sum_probs=13.9
Q ss_pred cCCCCccCC---CCCCccccccCCC
Q 020298 276 RCPACTFDN---SGWLSICEMCGTS 297 (328)
Q Consensus 276 ~c~~C~~~n---~~~~~~c~~cg~~ 297 (328)
.|+.|...+ ....-+|++|+--
T Consensus 5 ~CP~C~seytY~d~~~~vCpeC~hE 29 (111)
T PRK10220 5 HCPKCNSEYTYEDNGMYICPECAHE 29 (111)
T ss_pred cCCCCCCcceEcCCCeEECCcccCc
Confidence 588884442 2335778888854
No 91
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=28.42 E-value=37 Score=23.76 Aligned_cols=27 Identities=26% Similarity=0.752 Sum_probs=18.0
Q ss_pred CCcccCCC--Ccc---CC--CCCCccccccCCCC
Q 020298 272 PIIWRCPA--CTF---DN--SGWLSICEMCGTSR 298 (328)
Q Consensus 272 ~g~W~c~~--C~~---~n--~~~~~~c~~cg~~~ 298 (328)
...|.|+. |.- +| ....++|+.|+++=
T Consensus 16 t~VW~Ct~e~C~gWmR~nFs~~~~p~CPlC~s~M 49 (59)
T PF14169_consen 16 TKVWECTSEDCNGWMRDNFSFEEEPVCPLCKSPM 49 (59)
T ss_pred eeeEEeCCCCCCcccccccccCCCccCCCcCCcc
Confidence 34699998 732 23 23458899999863
No 92
>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]
Probab=28.20 E-value=45 Score=31.85 Aligned_cols=37 Identities=27% Similarity=0.637 Sum_probs=29.9
Q ss_pred CcccCC-CCccCCCCCCccccccCCCCCCCCCCccccc
Q 020298 273 IIWRCP-ACTFDNSGWLSICEMCGTSRSGNDLSSDQLS 309 (328)
Q Consensus 273 g~W~c~-~C~~~n~~~~~~c~~cg~~~~~~~~~~~~~~ 309 (328)
+-|.|. .|.=.|-....-|..|..++.....++...+
T Consensus 217 ~Dw~c~~~c~N~nfa~r~~cnrck~~Kp~~~~~~gg~~ 254 (351)
T KOG1995|consen 217 GDWDCPPSCGNRNFAWREECNRCKAPKPERSLPSGGGP 254 (351)
T ss_pred ccccccccccccccccccccccccCCCcccccCCCCCC
Confidence 349999 9999999889999999999997755444444
No 93
>PF09334 tRNA-synt_1g: tRNA synthetases class I (M); InterPro: IPR015413 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This domain is found in methionyl and leucyl tRNA synthetases. ; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 2D5B_A 1A8H_A 1WOY_A 2D54_A 4DLP_A 2CT8_B 2CSX_A 1MED_A 1PFU_A 1PFW_A ....
Probab=27.14 E-value=30 Score=33.74 Aligned_cols=24 Identities=33% Similarity=0.685 Sum_probs=17.7
Q ss_pred ccCCCCccCCCCCCccccccCCCCC
Q 020298 275 WRCPACTFDNSGWLSICEMCGTSRS 299 (328)
Q Consensus 275 W~c~~C~~~n~~~~~~c~~cg~~~~ 299 (328)
=.|+.|.++... .+.||.||.+-+
T Consensus 137 g~CP~C~~~~a~-g~~Ce~cG~~~~ 160 (391)
T PF09334_consen 137 GTCPYCGSDKAR-GDQCENCGRPLE 160 (391)
T ss_dssp CEETTT--SSCT-TTEETTTSSBEE
T ss_pred ccccCcCccccC-CCcccCCCCCcc
Confidence 578999988765 488999998766
No 94
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=26.86 E-value=1.3e+02 Score=20.86 Aligned_cols=24 Identities=33% Similarity=0.855 Sum_probs=16.6
Q ss_pred cccCCCCccCCCCCCccccccCCCCC
Q 020298 274 IWRCPACTFDNSGWLSICEMCGTSRS 299 (328)
Q Consensus 274 ~W~c~~C~~~n~~~~~~c~~cg~~~~ 299 (328)
+=.|+.|.-..- ..+|+.||.+-.
T Consensus 5 mr~C~~CgvYTL--k~~CP~CG~~t~ 28 (56)
T PRK13130 5 IRKCPKCGVYTL--KEICPVCGGKTK 28 (56)
T ss_pred ceECCCCCCEEc--cccCcCCCCCCC
Confidence 457888843332 688999998744
No 95
>PRK00076 recR recombination protein RecR; Reviewed
Probab=26.75 E-value=53 Score=28.88 Aligned_cols=26 Identities=27% Similarity=0.631 Sum_probs=20.5
Q ss_pred cccCCCCccCCCCCCccccccCCCCCCC
Q 020298 274 IWRCPACTFDNSGWLSICEMCGTSRSGN 301 (328)
Q Consensus 274 ~W~c~~C~~~n~~~~~~c~~cg~~~~~~ 301 (328)
.-.|+.|....+. +.|+.|.-+..|+
T Consensus 53 i~~C~~C~~lse~--~~C~IC~d~~Rd~ 78 (196)
T PRK00076 53 IKHCSVCGNLTEQ--DPCEICSDPRRDQ 78 (196)
T ss_pred CCcCCCCCCcCCC--CcCCCCCCCCCCC
Confidence 4789999776544 8899999887764
No 96
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=26.62 E-value=31 Score=29.78 Aligned_cols=23 Identities=26% Similarity=0.637 Sum_probs=17.7
Q ss_pred ccCCCCccCCCCCCccccccCCC
Q 020298 275 WRCPACTFDNSGWLSICEMCGTS 297 (328)
Q Consensus 275 W~c~~C~~~n~~~~~~c~~cg~~ 297 (328)
-+|..|-=.=+...+.|+.||.+
T Consensus 140 ~rC~GC~~~f~~~~~~Cp~CG~~ 162 (177)
T COG1439 140 LRCHGCKRIFPEPKDFCPICGSP 162 (177)
T ss_pred EEEecCceecCCCCCcCCCCCCc
Confidence 57888854433668999999987
No 97
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=25.95 E-value=39 Score=35.24 Aligned_cols=24 Identities=25% Similarity=0.592 Sum_probs=21.6
Q ss_pred cCCCCccCCCCCCccccccCCCCC
Q 020298 276 RCPACTFDNSGWLSICEMCGTSRS 299 (328)
Q Consensus 276 ~c~~C~~~n~~~~~~c~~cg~~~~ 299 (328)
.|+.|...|.++...|+-||..=.
T Consensus 29 ~Cp~CG~~~~~~~~fC~~CG~~~~ 52 (645)
T PRK14559 29 PCPQCGTEVPVDEAHCPNCGAETG 52 (645)
T ss_pred cCCCCCCCCCcccccccccCCccc
Confidence 699999999999999999998754
No 98
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=25.85 E-value=31 Score=26.13 Aligned_cols=15 Identities=40% Similarity=0.928 Sum_probs=9.2
Q ss_pred CCCCCcccCCCCccC
Q 020298 269 RTAPIIWRCPACTFD 283 (328)
Q Consensus 269 ~~~~g~W~c~~C~~~ 283 (328)
+.+.|.|.|..|.+.
T Consensus 48 R~a~GIW~C~kCg~~ 62 (89)
T COG1997 48 RIATGIWKCRKCGAK 62 (89)
T ss_pred eeccCeEEcCCCCCe
Confidence 345666777777554
No 99
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=25.81 E-value=40 Score=35.72 Aligned_cols=24 Identities=25% Similarity=0.610 Sum_probs=18.1
Q ss_pred CcccCCCCccCCCCCCccccccCCC
Q 020298 273 IIWRCPACTFDNSGWLSICEMCGTS 297 (328)
Q Consensus 273 g~W~c~~C~~~n~~~~~~c~~cg~~ 297 (328)
+.=.|.+|.+. ++....|+-||+.
T Consensus 461 ~~L~CH~Cg~~-~~~p~~Cp~Cgs~ 484 (730)
T COG1198 461 GQLRCHYCGYQ-EPIPQSCPECGSE 484 (730)
T ss_pred CeeEeCCCCCC-CCCCCCCCCCCCC
Confidence 34678888777 5557889999887
No 100
>PF03875 Statherin: Statherin; InterPro: IPR005575 Statherin functions biologically to inhibit the nucleation and growth of calcium phosphate minerals. The N terminus of statherin is highly charged, the glutamic acids of which have been shown to be important in the recognition hydroxyapatite [].
Probab=25.74 E-value=46 Score=20.97 Aligned_cols=14 Identities=43% Similarity=0.387 Sum_probs=11.3
Q ss_pred ChHHHHHHHhhhcC
Q 020298 315 PLEELRHRRIERFG 328 (328)
Q Consensus 315 ~~~~~r~~~~~~~~ 328 (328)
|-||-=.|||+||+
T Consensus 2 sseekflrrl~r~~ 15 (42)
T PF03875_consen 2 SSEEKFLRRLGRFF 15 (42)
T ss_pred chHHHHHHHHHhhc
Confidence 45788889999985
No 101
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=25.59 E-value=33 Score=23.66 Aligned_cols=22 Identities=36% Similarity=1.038 Sum_probs=13.0
Q ss_pred cCCCC-----ccCCCCCCccccccCCC
Q 020298 276 RCPAC-----TFDNSGWLSICEMCGTS 297 (328)
Q Consensus 276 ~c~~C-----~~~n~~~~~~c~~cg~~ 297 (328)
+|+.| .|++......|..||+.
T Consensus 9 kCp~C~~~q~vFSha~t~V~C~~Cg~~ 35 (55)
T PF01667_consen 9 KCPGCYNIQTVFSHAQTVVKCVVCGTV 35 (55)
T ss_dssp E-TTT-SEEEEETT-SS-EE-SSSTSE
T ss_pred ECCCCCCeeEEEecCCeEEEcccCCCE
Confidence 57777 35566666779999985
No 102
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=25.53 E-value=40 Score=20.19 Aligned_cols=21 Identities=38% Similarity=1.017 Sum_probs=8.6
Q ss_pred cCCCCccCC---CCCCccccccCC
Q 020298 276 RCPACTFDN---SGWLSICEMCGT 296 (328)
Q Consensus 276 ~c~~C~~~n---~~~~~~c~~cg~ 296 (328)
+|..|.-++ ....-+|+.|+-
T Consensus 4 ~Cp~C~se~~y~D~~~~vCp~C~~ 27 (30)
T PF08274_consen 4 KCPLCGSEYTYEDGELLVCPECGH 27 (30)
T ss_dssp --TTT-----EE-SSSEEETTTTE
T ss_pred CCCCCCCcceeccCCEEeCCcccc
Confidence 466664442 234566777763
No 103
>PF02132 RecR: RecR protein; InterPro: IPR023628 The bacterial protein RecR seems to play a role in a recombinational process of DNA repair []. It may act with RecF and RecO. RecR's structure consists of a N-terminal helix-hairpin-helix (HhH) motif, followed by a Cys4 zinc-finger motif, a Toprim domain and a Walker B motif []. This entry represents the C4-type zinc finger.; PDB: 1VDD_D 2V1C_B.
Probab=25.32 E-value=15 Score=23.54 Aligned_cols=24 Identities=25% Similarity=0.560 Sum_probs=13.1
Q ss_pred cccCCCCccCCCCCCccccccCCCCC
Q 020298 274 IWRCPACTFDNSGWLSICEMCGTSRS 299 (328)
Q Consensus 274 ~W~c~~C~~~n~~~~~~c~~cg~~~~ 299 (328)
.-.|+.|..... .+.|++|..++.
T Consensus 17 i~~C~~C~nlse--~~~C~IC~d~~R 40 (41)
T PF02132_consen 17 IKFCSICGNLSE--EDPCEICSDPKR 40 (41)
T ss_dssp -EE-SSS--EES--SSS-HHHH-TTS
T ss_pred CCccCCCCCcCC--CCcCcCCCCCCC
Confidence 357888876654 378999987754
No 104
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=24.60 E-value=1.3e+02 Score=21.04 Aligned_cols=23 Identities=26% Similarity=0.704 Sum_probs=14.9
Q ss_pred ccCCCCccCCCCCCccccccCCCCC
Q 020298 275 WRCPACTFDNSGWLSICEMCGTSRS 299 (328)
Q Consensus 275 W~c~~C~~~n~~~~~~c~~cg~~~~ 299 (328)
-.|..|.--.- .+.|+.||..-.
T Consensus 6 rkC~~cg~YTL--ke~Cp~CG~~t~ 28 (59)
T COG2260 6 RKCPKCGRYTL--KEKCPVCGGDTK 28 (59)
T ss_pred hcCcCCCceee--cccCCCCCCccc
Confidence 46777743321 379999998654
No 105
>PF04135 Nop10p: Nucleolar RNA-binding protein, Nop10p family; InterPro: IPR007264 H/ACA ribonucleoprotein particles (RNPs) are a family of RNA pseudouridine synthases that specify modification sites through guide RNAs. More than 100 mammalian H/ACA RNAs form an equal number of ribonucleoproteins (RNPs) by associating with the same four core proteins: Cbf5, Gar1, Nhp2 and Nop10. The function of these H/ACA RNPs is essential for biogenesis of the ribosome, splicing of precursor mRNAs (pre-mRNAs), maintenance of telomeres and probably for additional cellular processes []. Recent crystal structures of archaeal H/ACA protein complexes show how the same four proteins accommodate >100 distinct but related H/ACA RNAs []. The complex contains a stable core composed of Cbf5 and Nop10, to which Gar1 and Nhp2 subsequently bind, the complex interacts with snoRNAs []. In eukaryotes Nop10 is a nucleolar protein that is specifically associated with H/ACA snoRNAs. It is essential for normal 18S rRNA production and rRNA pseudouridylation by the ribonucleoprotein particles containing H/ACA snoRNAs (H/ACA snoRNPs). Nop10 is probably necessary for the stability of these RNPs [].; PDB: 2RFK_B 3LWR_B 2HVY_C 3HAX_C 3MQK_B 3LWO_B 3LWV_B 3HAY_C 3HJY_B 2EY4_E ....
Probab=23.97 E-value=76 Score=21.72 Aligned_cols=44 Identities=27% Similarity=0.605 Sum_probs=23.2
Q ss_pred cCCCCc-cCCCCCCccccccCCCCCCCCCCccccc-CCC-CCChHHHHHHHhhhcC
Q 020298 276 RCPACT-FDNSGWLSICEMCGTSRSGNDLSSDQLS-RHS-NIPLEELRHRRIERFG 328 (328)
Q Consensus 276 ~c~~C~-~~n~~~~~~c~~cg~~~~~~~~~~~~~~-~~~-~~~~~~~r~~~~~~~~ 328 (328)
.|..|. |.- .+.|+.||.+-.. .|+ +=| |=+--+-|+.-=+|||
T Consensus 7 ~c~~~~~YTL---k~~cp~cG~~T~~------ahPaRFSPdDky~~yRi~lKkrfg 53 (53)
T PF04135_consen 7 KCPGCRVYTL---KDKCPPCGGPTES------AHPARFSPDDKYSKYRIALKKRFG 53 (53)
T ss_dssp ECTTTCEEES---SSBBTTTSSBSEE------SSSSSS-TTTTTCHHHHHHHHHH-
T ss_pred cCCCCCcEeC---CCccCCCCCCCcC------CcCCCCCCCCccHHHHHHHHhhcC
Confidence 356663 333 3789999987432 122 223 3334456666666765
No 106
>PRK13264 3-hydroxyanthranilate 3,4-dioxygenase; Provisional
Probab=23.61 E-value=33 Score=29.65 Aligned_cols=21 Identities=38% Similarity=0.711 Sum_probs=15.8
Q ss_pred ccCCCCCCccccccCCCCCCC
Q 020298 281 TFDNSGWLSICEMCGTSRSGN 301 (328)
Q Consensus 281 ~~~n~~~~~~c~~cg~~~~~~ 301 (328)
.|.++.....|..||+--...
T Consensus 150 ~f~~~~e~rtC~~CG~v~~~~ 170 (177)
T PRK13264 150 AFYASEELRTCDNCGTVHPGK 170 (177)
T ss_pred HHhcCHhhccCCcCCcccCcc
Confidence 455666788899999986654
No 107
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=23.48 E-value=40 Score=27.87 Aligned_cols=23 Identities=22% Similarity=0.447 Sum_probs=21.0
Q ss_pred ccCCCCccCCCCCCccccccCCC
Q 020298 275 WRCPACTFDNSGWLSICEMCGTS 297 (328)
Q Consensus 275 W~c~~C~~~n~~~~~~c~~cg~~ 297 (328)
-+|..|-.---|....|+.|++.
T Consensus 30 ~kC~~CG~v~~PPr~~Cp~C~~~ 52 (140)
T COG1545 30 TKCKKCGRVYFPPRAYCPKCGSE 52 (140)
T ss_pred EEcCCCCeEEcCCcccCCCCCCC
Confidence 79999988888888999999998
No 108
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=23.13 E-value=60 Score=25.68 Aligned_cols=27 Identities=26% Similarity=0.570 Sum_probs=20.4
Q ss_pred cccCCCCccC----CCCCCccccccCCCCCC
Q 020298 274 IWRCPACTFD----NSGWLSICEMCGTSRSG 300 (328)
Q Consensus 274 ~W~c~~C~~~----n~~~~~~c~~cg~~~~~ 300 (328)
.|.|..|... |+=....|+.||..+..
T Consensus 42 ~~~C~~Cg~~~~~~~SCk~R~CP~C~~~~~~ 72 (111)
T PF14319_consen 42 RYRCEDCGHEKIVYNSCKNRHCPSCQAKATE 72 (111)
T ss_pred eeecCCCCceEEecCcccCcCCCCCCChHHH
Confidence 4999999877 44344589999988664
No 109
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=23.08 E-value=44 Score=26.70 Aligned_cols=29 Identities=17% Similarity=0.444 Sum_probs=19.8
Q ss_pred CCCcccCCCCccCCCC---CCccccccCCCCC
Q 020298 271 APIIWRCPACTFDNSG---WLSICEMCGTSRS 299 (328)
Q Consensus 271 ~~g~W~c~~C~~~n~~---~~~~c~~cg~~~~ 299 (328)
.+...+|..|...-+. ....|+.||++..
T Consensus 68 vp~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~~~ 99 (117)
T PRK00564 68 EKVELECKDCSHVFKPNALDYGVCEKCHSKNV 99 (117)
T ss_pred cCCEEEhhhCCCccccCCccCCcCcCCCCCce
Confidence 4556999999755332 2335999998754
No 110
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=23.03 E-value=49 Score=21.93 Aligned_cols=30 Identities=33% Similarity=0.690 Sum_probs=17.0
Q ss_pred ccCCCCccC-------CCCCCccccccCCCCCCCCCC
Q 020298 275 WRCPACTFD-------NSGWLSICEMCGTSRSGNDLS 304 (328)
Q Consensus 275 W~c~~C~~~-------n~~~~~~c~~cg~~~~~~~~~ 304 (328)
.+|..|... .......|+.||.......+|
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~r~~s 42 (52)
T TIGR02605 6 YRCTACGHRFEVLQKMSDDPLATCPECGGEKLRRLLS 42 (52)
T ss_pred EEeCCCCCEeEEEEecCCCCCCCCCCCCCCceeEEec
Confidence 457777541 112345799999854433333
No 111
>PRK13844 recombination protein RecR; Provisional
Probab=22.54 E-value=68 Score=28.27 Aligned_cols=26 Identities=19% Similarity=0.661 Sum_probs=20.2
Q ss_pred cccCCCCccCCCCCCccccccCCCCCCC
Q 020298 274 IWRCPACTFDNSGWLSICEMCGTSRSGN 301 (328)
Q Consensus 274 ~W~c~~C~~~n~~~~~~c~~cg~~~~~~ 301 (328)
.-.|+.|....+. +.|+.|.-++.|+
T Consensus 57 i~~C~~C~~lte~--~~C~IC~d~~Rd~ 82 (200)
T PRK13844 57 IKKCVYCQALTED--DVCNICSNTNRDD 82 (200)
T ss_pred CCcCCCCCCCCCC--CCCCCCCCCCCCC
Confidence 4789999766544 7899999887764
No 112
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=22.10 E-value=44 Score=26.00 Aligned_cols=29 Identities=31% Similarity=0.557 Sum_probs=20.7
Q ss_pred CCCcccCCCCccCCCC--------CCccccccCCCCCC
Q 020298 271 APIIWRCPACTFDNSG--------WLSICEMCGTSRSG 300 (328)
Q Consensus 271 ~~g~W~c~~C~~~n~~--------~~~~c~~cg~~~~~ 300 (328)
.+..-.|+.|.- ..- .+.+|..||..+.-
T Consensus 18 lpt~f~CP~Cge-~~v~v~~~k~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 18 LPKIFECPRCGK-VSISVKIKKNIAIITCGNCGLYTEF 54 (99)
T ss_pred CCcEeECCCCCC-eEeeeecCCCcceEECCCCCCccCE
Confidence 344688999982 222 37789999998774
No 113
>PLN02674 adenylate kinase
Probab=21.77 E-value=1e+02 Score=27.94 Aligned_cols=11 Identities=27% Similarity=0.531 Sum_probs=6.9
Q ss_pred HHHHHHHhhhc
Q 020298 317 EELRHRRIERF 327 (328)
Q Consensus 317 ~~~r~~~~~~~ 327 (328)
||.=++||+-|
T Consensus 196 ~e~i~~RL~~Y 206 (244)
T PLN02674 196 AAVLKSRLEAF 206 (244)
T ss_pred HHHHHHHHHHH
Confidence 56666677654
No 114
>KOG3474 consensus Molybdopterin converting factor, small subunit [Energy production and conversion]
Probab=21.63 E-value=72 Score=23.27 Aligned_cols=32 Identities=25% Similarity=0.477 Sum_probs=24.6
Q ss_pred ccccccCCCCCCCCCCcccccCCCCCChHHHHHHHhhhc
Q 020298 289 SICEMCGTSRSGNDLSSDQLSRHSNIPLEELRHRRIERF 327 (328)
Q Consensus 289 ~~c~~cg~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~ 327 (328)
..||..|.+.+.-.|++. -+.||+|..-+|.|
T Consensus 11 ~A~eLtG~~d~ai~~Pe~-------s~~ee~~deil~kf 42 (84)
T KOG3474|consen 11 EACELTGKPDEAIDFPEE-------SDTEECLDEILEKF 42 (84)
T ss_pred hhHHhcCCchhhccCCCC-------CCHHHHHHHHHHhC
Confidence 469999999888778766 45778877777765
No 115
>COG0143 MetG Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=21.53 E-value=51 Score=33.76 Aligned_cols=25 Identities=28% Similarity=0.639 Sum_probs=18.3
Q ss_pred ccCCCCccCCCCCCccccccCCCCCC
Q 020298 275 WRCPACTFDNSGWLSICEMCGTSRSG 300 (328)
Q Consensus 275 W~c~~C~~~n~~~~~~c~~cg~~~~~ 300 (328)
=.|+.|.+.... -|.||.||.....
T Consensus 143 g~cp~cg~~~ar-GD~Ce~Cg~~~~P 167 (558)
T COG0143 143 GTCPKCGGEDAR-GDQCENCGRTLDP 167 (558)
T ss_pred ccCCCcCccccC-cchhhhccCcCCc
Confidence 567777777655 4789999988764
No 116
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=21.49 E-value=40 Score=27.27 Aligned_cols=28 Identities=25% Similarity=0.773 Sum_probs=18.8
Q ss_pred CCCcccCCCCccCCC----C-----CCccccccCCCCC
Q 020298 271 APIIWRCPACTFDNS----G-----WLSICEMCGTSRS 299 (328)
Q Consensus 271 ~~g~W~c~~C~~~n~----~-----~~~~c~~cg~~~~ 299 (328)
.+...+| .|...-. + ....|+.||....
T Consensus 67 vp~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~~ 103 (124)
T PRK00762 67 IPVEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKRA 103 (124)
T ss_pred cCeeEEe-eCcCcccccccchhccccCCcCcCCCCCCC
Confidence 5567999 9976621 1 1246999997764
No 117
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=21.48 E-value=1.1e+02 Score=23.92 Aligned_cols=34 Identities=18% Similarity=0.222 Sum_probs=19.5
Q ss_pred ccccccCCCCCCCCCCcccccCCCCCChHHHHHHHhh
Q 020298 289 SICEMCGTSRSGNDLSSDQLSRHSNIPLEELRHRRIE 325 (328)
Q Consensus 289 ~~c~~cg~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~ 325 (328)
-+|+-|+-.-.-+..+.. ++| -+--+|+|++|.+
T Consensus 32 y~C~~C~AyVG~H~~t~~--PlG-tLAd~~lR~~R~~ 65 (102)
T PF11672_consen 32 YVCTPCDAYVGCHPGTDI--PLG-TLADAELRRARKA 65 (102)
T ss_pred EECCCCCceeeeeCCCCC--cCc-ccCCHHHHHHHHH
Confidence 345556655555554433 222 2557889988865
No 118
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=21.28 E-value=71 Score=35.62 Aligned_cols=33 Identities=27% Similarity=0.688 Sum_probs=21.2
Q ss_pred CCCCCcccCCCCccC---CCCC--------CccccccCCCCCCC
Q 020298 269 RTAPIIWRCPACTFD---NSGW--------LSICEMCGTSRSGN 301 (328)
Q Consensus 269 ~~~~g~W~c~~C~~~---n~~~--------~~~c~~cg~~~~~~ 301 (328)
++-+-...|+.|.|. +..+ --.|+.||++-..|
T Consensus 909 NPL~PHY~Cp~Cky~Ef~~d~svgsGfDLpdK~CPkCg~pl~kD 952 (1444)
T COG2176 909 NPLPPHYLCPECKYSEFIDDGSVGSGFDLPDKDCPKCGTPLKKD 952 (1444)
T ss_pred CCCCccccCCCCceeeeecCCCcCCCCCCCCCCCCcCCCccccC
Confidence 333445999999775 3221 22399999996643
No 119
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=21.17 E-value=45 Score=34.44 Aligned_cols=10 Identities=50% Similarity=1.391 Sum_probs=7.4
Q ss_pred CCcccCCCCc
Q 020298 272 PIIWRCPACT 281 (328)
Q Consensus 272 ~g~W~c~~C~ 281 (328)
.+.|+|..|+
T Consensus 60 ~~gWrC~~cr 69 (694)
T KOG4443|consen 60 SGGWRCPSCR 69 (694)
T ss_pred cCCcccCCce
Confidence 3459999985
No 120
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=21.03 E-value=72 Score=27.99 Aligned_cols=26 Identities=19% Similarity=0.574 Sum_probs=20.0
Q ss_pred cccCCCCccCCCCCCccccccCCCCCCC
Q 020298 274 IWRCPACTFDNSGWLSICEMCGTSRSGN 301 (328)
Q Consensus 274 ~W~c~~C~~~n~~~~~~c~~cg~~~~~~ 301 (328)
.-.|+.|.-.... +.|+.|.-++.|.
T Consensus 54 i~~C~~C~~~te~--d~C~ICsd~~Rd~ 79 (198)
T COG0353 54 IKHCSVCGNLTES--DPCDICSDESRDK 79 (198)
T ss_pred CccccccCCcCCC--CcCcCcCCcccCC
Confidence 4789999655443 7999999888775
No 121
>PF11682 DUF3279: Protein of unknown function (DUF3279); InterPro: IPR021696 This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.
Probab=20.60 E-value=49 Score=26.98 Aligned_cols=23 Identities=35% Similarity=0.868 Sum_probs=18.5
Q ss_pred cccCCCCccCCCCCCccccccCCC
Q 020298 274 IWRCPACTFDNSGWLSICEMCGTS 297 (328)
Q Consensus 274 ~W~c~~C~~~n~~~~~~c~~cg~~ 297 (328)
.|.|.+|.-+=.. .-.|+.|++-
T Consensus 97 ~W~Cv~C~~~Y~G-eK~C~~C~tG 119 (128)
T PF11682_consen 97 DWHCVMCGNHYHG-EKYCPKCGTG 119 (128)
T ss_pred eEEEecCCCccCc-CEecCCCCCc
Confidence 4999999877655 5789999873
No 122
>PF05484 LRV_FeS: LRV protein FeS4 cluster; InterPro: IPR008665 This iron sulphur cluster is found at the N terminus of some proteins containing leucine-repeat variant (LRV) repeats (IPR004830 from INTERPRO). These proteins have a two-domain structure, composed of a small N-terminal domain containing a cluster of four Cys residues that houses the 4Fe:4S cluster, and a larger C-terminal domain containing the LRV repeats []. Biochemical studies revealed that the 4Fe:4S cluster is sensitive to oxygen, but does not appear to have reversible redox activity.; PDB: 1LRV_A.
Probab=20.54 E-value=42 Score=23.34 Aligned_cols=11 Identities=45% Similarity=0.830 Sum_probs=7.5
Q ss_pred HHHHHHHhhhc
Q 020298 317 EELRHRRIERF 327 (328)
Q Consensus 317 ~~~r~~~~~~~ 327 (328)
-.-+.|||+||
T Consensus 36 ~dryaRrIdRF 46 (57)
T PF05484_consen 36 QDRYARRIDRF 46 (57)
T ss_dssp SSS-HHHHHHH
T ss_pred hhhHHHHHHHH
Confidence 34478899998
No 123
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=20.40 E-value=1e+02 Score=34.87 Aligned_cols=30 Identities=23% Similarity=0.659 Sum_probs=22.5
Q ss_pred ccCCCCccCCCCCCccccccCCCCCCCCCCcc
Q 020298 275 WRCPACTFDNSGWLSICEMCGTSRSGNDLSSD 306 (328)
Q Consensus 275 W~c~~C~~~n~~~~~~c~~cg~~~~~~~~~~~ 306 (328)
-+|+.|.... ....|+.||+..+....+.+
T Consensus 675 ~~Cp~Cg~~~--~~~~Cp~CG~~~~~~~~~~~ 704 (1627)
T PRK14715 675 FKCPKCGKVG--LYHVCPFCGTRVELKPYARR 704 (1627)
T ss_pred eeCCCCCCcc--ccccCcccCCcccCCCccce
Confidence 7899997653 35889999999776555443
No 124
>COG4317 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.35 E-value=3e+02 Score=20.62 Aligned_cols=29 Identities=28% Similarity=0.461 Sum_probs=17.4
Q ss_pred HHHHHHHHHHHHHHHhccCCCCCcHHHHHHH
Q 020298 205 GHLGGILAGILYLKLKGGYSGSDPLTTIIRG 235 (328)
Q Consensus 205 aHl~G~l~G~ly~~~~~~~~~~~p~~~~~~~ 235 (328)
+-..|+++|++|+++ ..+...|+.-.+..
T Consensus 7 slgAGllVGiiyaLl--~vrsPAPP~iAlvG 35 (93)
T COG4317 7 SLGAGLLVGIIYALL--KVRSPAPPAIALVG 35 (93)
T ss_pred HHhhhHHHHHHHHHH--hCCCCCCcHHHHHH
Confidence 345689999999987 33344444433333
No 125
>cd01675 RNR_III Class III ribonucleotide reductase. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit w
Probab=20.34 E-value=63 Score=33.12 Aligned_cols=23 Identities=26% Similarity=0.614 Sum_probs=18.8
Q ss_pred cCCCCccCCCCCCccccccCCCC
Q 020298 276 RCPACTFDNSGWLSICEMCGTSR 298 (328)
Q Consensus 276 ~c~~C~~~n~~~~~~c~~cg~~~ 298 (328)
.|..|.|......+.|+.||...
T Consensus 520 ~C~~CG~~~~~~~~~CP~CGs~~ 542 (555)
T cd01675 520 ICNDCGYIGEGEGFKCPKCGSED 542 (555)
T ss_pred cCCCCCCCCcCCCCCCcCCCCcC
Confidence 89999997755578999999753
No 126
>PRK00420 hypothetical protein; Validated
Probab=20.20 E-value=69 Score=25.50 Aligned_cols=26 Identities=19% Similarity=0.394 Sum_probs=19.1
Q ss_pred ccCCCCccCC---CCCCccccccCCCCCC
Q 020298 275 WRCPACTFDN---SGWLSICEMCGTSRSG 300 (328)
Q Consensus 275 W~c~~C~~~n---~~~~~~c~~cg~~~~~ 300 (328)
-.|+.|.+.. ......|+.||.....
T Consensus 24 ~~CP~Cg~pLf~lk~g~~~Cp~Cg~~~~v 52 (112)
T PRK00420 24 KHCPVCGLPLFELKDGEVVCPVHGKVYIV 52 (112)
T ss_pred CCCCCCCCcceecCCCceECCCCCCeeee
Confidence 5799997652 3456789999996553
Done!