Query 013725
Match_columns 437
No_of_seqs 198 out of 794
Neff 7.8
Searched_HMMs 46136
Date Fri Mar 29 06:45:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013725.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013725hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR03676 aRF1/eRF1 peptide ch 100.0 2.1E-99 5E-104 765.1 45.6 403 12-418 1-403 (403)
2 PRK04011 peptide chain release 100.0 2.7E-95 6E-100 738.5 46.7 407 8-418 4-411 (411)
3 TIGR00108 eRF peptide chain re 100.0 4.2E-95 9E-100 736.7 45.1 406 10-419 3-408 (409)
4 COG1503 eRF1 Peptide chain rel 100.0 4.1E-89 8.9E-94 672.2 32.1 405 10-419 6-410 (411)
5 KOG0688 Peptide chain release 100.0 1.2E-89 2.5E-94 643.6 22.6 427 6-436 3-429 (431)
6 TIGR00111 pelota probable tran 100.0 3.4E-55 7.4E-60 437.9 25.9 321 28-418 9-351 (351)
7 COG1537 PelA Predicted RNA-bin 100.0 7E-47 1.5E-51 364.9 23.8 319 32-419 11-352 (352)
8 KOG2869 Meiotic cell division 100.0 3.6E-47 7.7E-52 359.0 15.3 336 28-419 10-371 (379)
9 PF03465 eRF1_3: eRF1 domain 3 100.0 1.6E-29 3.5E-34 212.7 8.1 113 281-418 1-113 (113)
10 PF03464 eRF1_2: eRF1 domain 2 99.9 1.5E-23 3.2E-28 182.2 12.9 129 144-277 1-132 (133)
11 PF03463 eRF1_1: eRF1 domain 1 99.0 9.6E-13 2.1E-17 114.1 -12.5 120 10-140 7-131 (132)
12 PF10116 Host_attach: Protein 97.3 0.00031 6.8E-09 61.2 4.9 109 146-261 2-128 (138)
13 PRK07714 hypothetical protein; 94.4 0.28 6.2E-06 40.2 8.3 75 296-414 13-87 (100)
14 PRK07283 hypothetical protein; 93.9 0.43 9.4E-06 39.0 8.4 34 295-328 12-45 (98)
15 PRK13602 putative ribosomal pr 93.8 0.41 8.8E-06 37.8 7.8 60 299-402 9-68 (82)
16 PRK13600 putative ribosomal pr 93.4 0.37 8E-06 38.2 6.9 57 302-402 14-70 (84)
17 PF08032 SpoU_sub_bind: RNA 2' 92.7 0.28 6E-06 37.6 5.3 69 302-416 1-72 (76)
18 PRK04175 rpl7ae 50S ribosomal 91.4 1.5 3.2E-05 37.4 8.7 62 298-402 27-88 (122)
19 TIGR03677 rpl7ae 50S ribosomal 91.3 1.4 3.1E-05 37.2 8.5 75 298-415 23-98 (117)
20 PRK06683 hypothetical protein; 91.3 1.4 3E-05 34.7 7.8 61 298-402 8-68 (82)
21 PRK01018 50S ribosomal protein 90.9 1.9 4.1E-05 35.3 8.6 60 299-402 14-74 (99)
22 PTZ00106 60S ribosomal protein 90.9 1.6 3.5E-05 36.3 8.2 40 288-328 13-52 (108)
23 PRK05583 ribosomal protein L7A 90.8 1.6 3.4E-05 36.1 8.0 33 296-328 12-44 (104)
24 COG1358 RPL8A Ribosomal protei 90.7 0.84 1.8E-05 38.5 6.4 62 298-402 24-85 (116)
25 PRK09190 hypothetical protein; 90.0 2.8 6E-05 39.5 9.9 42 285-328 97-138 (220)
26 PF01248 Ribosomal_L7Ae: Ribos 88.5 2.9 6.4E-05 33.5 7.9 62 299-403 13-74 (95)
27 PRK13601 putative L7Ae-like ri 88.0 3 6.4E-05 32.9 7.3 60 299-402 6-65 (82)
28 COG1592 Rubrerythrin [Energy p 82.3 1.1 2.3E-05 40.2 2.7 25 333-366 134-158 (166)
29 PRK00398 rpoP DNA-directed RNA 77.9 0.85 1.9E-05 31.6 0.4 31 333-369 3-33 (46)
30 COG2433 Uncharacterized conser 77.6 8.3 0.00018 41.2 7.7 33 179-211 148-180 (652)
31 TIGR00373 conserved hypothetic 76.5 1.9 4.1E-05 38.5 2.3 45 334-383 110-154 (158)
32 PRK06266 transcription initiat 75.8 2.3 5E-05 38.7 2.7 46 333-383 117-162 (178)
33 COG1911 RPL30 Ribosomal protei 74.5 30 0.00066 28.0 8.3 30 298-327 16-45 (100)
34 PTZ00222 60S ribosomal protein 70.3 49 0.0011 31.8 10.2 72 301-415 132-203 (263)
35 smart00834 CxxC_CXXC_SSSS Puta 69.9 4.6 0.0001 26.8 2.5 33 331-366 3-35 (41)
36 PF09723 Zn-ribbon_8: Zinc rib 67.7 7.6 0.00017 26.3 3.2 32 331-365 3-34 (42)
37 cd00729 rubredoxin_SM Rubredox 63.0 8.1 0.00018 25.0 2.5 26 333-366 2-27 (34)
38 smart00531 TFIIE Transcription 62.5 3.9 8.5E-05 35.9 1.2 37 333-370 99-136 (147)
39 PRK03824 hypA hydrogenase nick 61.4 16 0.00035 31.6 4.9 11 332-342 69-79 (135)
40 PTZ00365 60S ribosomal protein 58.0 57 0.0012 31.4 8.2 72 301-415 132-203 (266)
41 PF13248 zf-ribbon_3: zinc-rib 57.5 4.3 9.4E-05 24.5 0.5 23 334-366 3-25 (26)
42 TIGR02605 CxxC_CxxC_SSSS putat 57.2 14 0.00031 26.0 3.2 33 331-366 3-35 (52)
43 PF07295 DUF1451: Protein of u 56.3 9.6 0.00021 33.5 2.6 27 334-366 113-139 (146)
44 COG2051 RPS27A Ribosomal prote 56.1 12 0.00026 28.1 2.6 28 335-367 21-48 (67)
45 PRK05452 anaerobic nitric oxid 56.0 72 0.0016 33.7 9.6 39 221-261 304-348 (479)
46 TIGR00354 polC DNA polymerase, 52.9 17 0.00038 41.0 4.4 62 307-389 607-673 (1095)
47 PRK11032 hypothetical protein; 52.6 12 0.00026 33.4 2.6 36 324-366 116-151 (160)
48 cd00350 rubredoxin_like Rubred 51.9 13 0.00028 23.8 2.0 25 334-366 2-26 (33)
49 PRK14892 putative transcriptio 48.1 26 0.00056 28.7 3.7 62 334-398 22-88 (99)
50 PF13240 zinc_ribbon_2: zinc-r 46.1 9.3 0.0002 22.4 0.6 10 357-366 13-22 (23)
51 PRK14715 DNA polymerase II lar 45.5 18 0.0004 42.2 3.2 63 306-388 655-721 (1627)
52 PRK05978 hypothetical protein; 45.2 11 0.00024 33.2 1.2 31 334-369 34-64 (148)
53 smart00659 RPOLCX RNA polymera 43.8 21 0.00045 24.6 2.1 27 333-366 2-28 (44)
54 PF09538 FYDLN_acid: Protein o 43.5 12 0.00027 31.1 1.2 28 334-368 10-37 (108)
55 PRK12496 hypothetical protein; 43.4 15 0.00033 32.9 1.8 29 331-367 125-153 (164)
56 TIGR01206 lysW lysine biosynth 38.8 5.4 0.00012 28.8 -1.4 7 335-341 4-10 (54)
57 COG2956 Predicted N-acetylgluc 37.5 16 0.00034 36.4 1.1 21 193-213 240-260 (389)
58 COG1212 KdsB CMP-2-keto-3-deox 37.4 50 0.0011 31.3 4.3 54 357-418 20-73 (247)
59 TIGR02098 MJ0042_CXXC MJ0042 f 37.4 18 0.00038 23.7 1.0 32 334-367 3-35 (38)
60 PRK12380 hydrogenase nickel in 36.9 27 0.00058 29.2 2.2 25 334-366 71-95 (113)
61 COG2331 Uncharacterized protei 36.7 12 0.00025 28.9 0.0 60 330-401 9-69 (82)
62 PLN02674 adenylate kinase 36.2 71 0.0015 30.6 5.3 34 221-261 31-64 (244)
63 KOG1859 Leucine-rich repeat pr 36.1 14 0.00031 40.8 0.5 95 297-421 636-734 (1096)
64 TIGR00595 priA primosomal prot 35.8 67 0.0015 34.2 5.6 41 357-398 253-295 (505)
65 PF08271 TF_Zn_Ribbon: TFIIB z 35.6 21 0.00045 24.2 1.1 27 335-366 2-28 (43)
66 PRK08270 anaerobic ribonucleos 35.1 35 0.00077 37.6 3.4 23 335-368 628-650 (656)
67 TIGR00416 sms DNA repair prote 35.1 18 0.00039 38.0 1.1 23 333-365 7-29 (454)
68 PRK11181 23S rRNA (guanosine-2 35.0 1.1E+02 0.0025 29.0 6.6 69 301-415 3-75 (244)
69 PRK11823 DNA repair protein Ra 34.8 18 0.0004 37.8 1.1 23 333-365 7-29 (446)
70 TIGR00100 hypA hydrogenase nic 34.3 31 0.00068 28.9 2.3 35 320-366 61-95 (115)
71 TIGR02487 NrdD anaerobic ribon 34.2 37 0.0008 36.8 3.4 33 318-366 515-547 (579)
72 COG1198 PriA Primosomal protei 33.8 61 0.0013 36.1 5.0 66 331-397 442-516 (730)
73 COG1675 TFA1 Transcription ini 32.4 36 0.00079 30.9 2.5 30 356-385 131-160 (176)
74 COG1110 Reverse gyrase [DNA re 32.3 43 0.00094 38.4 3.5 58 333-402 694-751 (1187)
75 cd01121 Sms Sms (bacterial rad 32.2 17 0.00036 37.1 0.3 10 331-340 12-21 (372)
76 PF04423 Rad50_zn_hook: Rad50 31.8 33 0.00071 24.5 1.7 22 359-380 22-43 (54)
77 COG2260 Predicted Zn-ribbon RN 31.5 31 0.00068 25.2 1.5 23 335-369 7-29 (59)
78 COG0566 SpoU rRNA methylases [ 31.3 2E+02 0.0044 27.7 7.6 73 300-417 21-94 (260)
79 COG1066 Sms Predicted ATP-depe 31.1 25 0.00054 36.2 1.4 24 333-366 7-30 (456)
80 TIGR02300 FYDLN_acid conserved 30.8 28 0.0006 29.7 1.3 28 334-368 10-37 (129)
81 PF13727 CoA_binding_3: CoA-bi 30.7 89 0.0019 27.1 4.8 51 301-394 125-175 (175)
82 COG2888 Predicted Zn-ribbon RN 30.6 38 0.00082 24.9 1.8 10 357-366 27-36 (61)
83 COG5257 GCD11 Translation init 30.3 51 0.0011 33.0 3.2 52 334-394 58-118 (415)
84 PRK14704 anaerobic ribonucleos 30.1 52 0.0011 36.0 3.6 21 335-366 561-581 (618)
85 COG1439 Predicted nucleic acid 29.4 42 0.00091 30.4 2.3 54 304-367 110-163 (177)
86 PF01155 HypA: Hydrogenase exp 29.1 28 0.00061 29.1 1.1 25 334-366 71-95 (113)
87 COG1545 Predicted nucleic-acid 28.6 35 0.00077 29.7 1.7 22 335-366 31-52 (140)
88 PRK09263 anaerobic ribonucleos 28.1 84 0.0018 35.0 4.9 37 318-366 632-668 (711)
89 PRK13130 H/ACA RNA-protein com 27.2 42 0.0009 24.5 1.6 21 335-367 7-27 (56)
90 TIGR00186 rRNA_methyl_3 rRNA m 27.2 1.5E+02 0.0032 28.1 5.8 39 377-417 32-72 (237)
91 PRK10864 putative methyltransf 27.1 1.8E+02 0.004 29.4 6.7 71 300-417 108-182 (346)
92 PF11608 Limkain-b1: Limkain b 26.7 99 0.0021 24.7 3.7 30 376-419 20-49 (90)
93 PRK07111 anaerobic ribonucleos 26.5 63 0.0014 36.2 3.6 21 335-366 682-702 (735)
94 COG5622 Protein required for a 26.1 41 0.00088 29.0 1.5 64 198-269 70-133 (139)
95 PRK03681 hypA hydrogenase nick 25.6 51 0.0011 27.6 2.1 26 334-366 71-96 (114)
96 CHL00174 accD acetyl-CoA carbo 25.1 35 0.00077 33.6 1.2 31 335-370 40-70 (296)
97 COG1150 HdrC Heterodisulfide r 25.1 61 0.0013 29.9 2.6 63 302-390 57-119 (195)
98 PHA00626 hypothetical protein 24.3 55 0.0012 23.8 1.7 31 335-367 2-33 (59)
99 PF10571 UPF0547: Uncharacteri 24.2 38 0.00082 20.5 0.8 10 357-366 14-23 (26)
100 PF12172 DUF35_N: Rubredoxin-l 23.9 48 0.001 21.5 1.3 22 335-366 13-34 (37)
101 PF03833 PolC_DP2: DNA polymer 23.9 26 0.00056 39.2 0.0 12 335-346 657-668 (900)
102 PF11023 DUF2614: Protein of u 23.8 32 0.00069 28.7 0.5 28 334-369 70-97 (114)
103 PF05991 NYN_YacP: YacP-like N 23.4 3E+02 0.0064 24.5 6.8 36 373-409 80-115 (166)
104 PRK00564 hypA hydrogenase nick 23.2 51 0.0011 27.7 1.7 26 334-366 72-97 (117)
105 PF03604 DNA_RNApol_7kD: DNA d 23.1 71 0.0015 20.4 1.9 25 335-366 2-26 (32)
106 PRK08271 anaerobic ribonucleos 22.1 96 0.0021 34.0 3.9 33 318-366 557-589 (623)
107 PRK04023 DNA polymerase II lar 22.1 74 0.0016 36.5 3.0 31 358-388 664-696 (1121)
108 PRK14873 primosome assembly pr 22.0 84 0.0018 34.7 3.5 40 130-169 225-264 (665)
109 PF05191 ADK_lid: Adenylate ki 22.0 66 0.0014 21.1 1.6 30 334-367 2-31 (36)
110 PF14319 Zn_Tnp_IS91: Transpos 21.7 1.3E+02 0.0028 25.0 3.8 43 333-385 42-84 (111)
111 COG3809 Uncharacterized protei 21.7 46 0.00099 25.9 0.9 28 335-366 3-30 (88)
112 PF01976 DUF116: Protein of un 21.7 92 0.002 27.7 3.0 37 357-401 64-100 (158)
113 COG1996 RPC10 DNA-directed RNA 21.5 61 0.0013 22.9 1.5 29 332-366 5-33 (49)
114 cd00730 rubredoxin Rubredoxin; 20.7 78 0.0017 22.4 1.9 12 355-366 32-43 (50)
115 PF13719 zinc_ribbon_5: zinc-r 20.7 70 0.0015 20.9 1.6 31 334-366 3-34 (37)
116 COG2401 ABC-type ATPase fused 20.7 35 0.00077 35.4 0.2 28 332-369 129-156 (593)
117 PRK11788 tetratricopeptide rep 20.7 44 0.00094 33.4 0.9 23 334-366 355-377 (389)
118 COG1867 TRM1 N2,N2-dimethylgua 20.6 90 0.0019 31.8 3.0 48 331-385 238-293 (380)
119 cd01675 RNR_III Class III ribo 20.6 92 0.002 33.6 3.4 22 335-366 520-541 (555)
120 PRK10124 putative UDP-glucose 20.3 1E+03 0.022 25.0 11.8 67 304-414 189-259 (463)
No 1
>TIGR03676 aRF1/eRF1 peptide chain release factor 1, archaeal and eukaryotic forms. Directs the termination of nascent peptide synthesis (translation) in response to the termination codons UAA, UAG and UGA. This model identifies both archaeal (aRF1) and eukaryotic (eRF1) of the protein. Also known as translation termination factor 1.
Probab=100.00 E-value=2.1e-99 Score=765.13 Aligned_cols=403 Identities=38% Similarity=0.644 Sum_probs=384.5
Q ss_pred HHHHHHHHHHHHHccCCCCcceEEEEeCCCCChHHHHhhhhhhhhhhhhhhhhhhhhhhhHhHHHHHHHhhcccccCCCe
Q 013725 12 EIWKIKKLIKALESARGNGTSMISLIMPPRDQISRVTKMLGDEFGTASNIKSRVNRQSVLAAITSAQQRLKLYNKVPPNG 91 (437)
Q Consensus 12 ~~~~~~~~l~~L~~~~g~~t~lvSlyip~~~~~~~v~~~l~~e~~~a~nik~~~~r~~v~~al~~~~~rl~~~~~~~~~G 91 (437)
++|+||++|++|++++|+||+||||||||+++|++|.++|++||++|+|||||.||++|++||+++++||++|.++|+||
T Consensus 1 ~~~~~k~~~~~l~~~~g~gt~lisl~ipp~~~i~~v~~~l~~e~~~a~niks~~~r~~v~~ai~~~~~rlk~~~~~p~nG 80 (403)
T TIGR03676 1 EKYEFKKLLEELKKKKGRGTELISLYIPPDKQISDVVNQLRDEYSQAANIKSKQTRKNVQSAIESIMQRLKLYKKPPENG 80 (403)
T ss_pred CcchHHHHHHHHHhCcCCCceEEEEEeCCCCcHHHHHHHHHHHHhhhhhhhhhhhHHHHHHHHHHHHHHHhccCCCCCCe
Confidence 47999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEeccccCCCCCeeEEEEeecCCCcceeeeeeccCccchHHHHHhhccCCcEEEEEEECCceEEEEEeCCeEEEEeEE
Q 013725 92 LVLYTGTVVTDDGKEKKVTIDFEPFKPINASLYLCDNKFHTEALNELLESDDKFGFIVMDGNGTLFGTLSGNTREVLHKF 171 (437)
Q Consensus 92 l~~fa~~~~~~~G~~~~~tl~i~p~~~v~~~~~~~~~~~~l~~L~~~~~~~~~~~vvvvd~~~A~i~~~~g~~~~~~~~~ 171 (437)
+|+|||.+...+|+.++||++++||+||++++|+||+.||++||.+|++++.++++|+||+++|.||++.|++++++.++
T Consensus 81 lv~f~g~~~~~~~~~~~~t~~iep~~pi~~~~y~cd~~f~lepL~e~l~~~~~~g~VvvD~~~A~i~~l~g~~~e~~~~i 160 (403)
T TIGR03676 81 LVLFAGMVPTGGGTEKMETYVIEPPEPINTYLYRCDSKFYLEPLEEMLEEKDVYGLIVLDRREATIGLLKGKRIEVLKEL 160 (403)
T ss_pred EEEEEeeecCCCCceeEEEEEEeCCCceEEEEecCCChHHHHHHHHHhcCCCCEEEEEEecCceEEEEEcCCEEEEEEEE
Confidence 99999999877788888999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eecCCcccCCCCcchHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCccEEEEecChhcHHHhhhccCCChhhhcce
Q 013725 172 TVDLPKKHGRGGQSALRFARLRMEKRHNYVRKTAELATQFFINPATSQPNVSGLILAGSADFKTELSQSDMFDPRLQAKI 251 (437)
Q Consensus 172 ~~~vp~K~~~gG~s~~Rf~r~~ee~~~~f~~~Vae~l~~~f~~~~~~~~~~~~lilaGp~~~k~~f~~~~~l~~~l~~~v 251 (437)
++++|+||++||||++||+|++++++++||++||+.+.++|++ .+..++++||||||+++|+.|.++++|++++++++
T Consensus 161 ~~~vp~K~~~GGqS~~Rf~R~~e~~~~~f~~~Vae~~~~~f~~--~~~~~v~~lILaGpg~~K~~f~~~~~L~~~l~~kv 238 (403)
T TIGR03676 161 TSGVPGKHRAGGQSARRFERLIEIAAHEFYKRVGEAANEAFLP--LKDKKLKGILIGGPGPTKEEFAEGDYLHHELKKKI 238 (403)
T ss_pred EeeCCCCccCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHhh--cccccccEEEEeCCHHHHHHHhhhhhhhHHHHhhE
Confidence 9999999999999999999999999999999999999999875 33447999999999999999997779999999999
Q ss_pred eEEEeCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcEEEcHHHHHHHHHhCCccEEEeccCccccc
Q 013725 252 LNVVDVSYGGENGFNQAIELSAEILSNVKFIQEKRLIGKYFEEISQDTGKYVFGVDDTLKALELGAVEILIVWENLDINR 331 (437)
Q Consensus 252 i~~v~~s~~~~~gl~E~l~~~~~~l~~~~~~~e~~ll~~f~~~~~~~~g~a~yG~~eV~~Al~~GaV~tLlV~d~l~~~~ 331 (437)
+.++++|+++++|++|++++++++|++.++++|+++|++|++++++++|++|||+++|++||++|||+||||+|++...|
T Consensus 239 i~~vd~s~~~~~Gl~Evl~~~~~~L~~~k~~~E~~lle~f~~el~~d~g~avyG~~eV~~ALe~GAVetLLV~d~l~~~r 318 (403)
T TIGR03676 239 LGLFDVSYTGESGLRELVEKAEDLLKDLELMKEKKLMERFFKELVKDGGLAAYGEEEVRKALEMGAVDTLLISEDLRKIR 318 (403)
T ss_pred EEEEecCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcEEEcHHHHHHHHHhCCCcEEEEEcccccee
Confidence 89999999999999999999999999999999999999999999999899999999999999999999999999999999
Q ss_pred eeeecCCCCceEEEecccccccccCCccCccccchhhhhhhccHHHHHHHHHHhcCCeEEEeCCCCchhhhhhcccccEE
Q 013725 332 YVLKNSATGEIVIKHLNRDQEADQSNFRDAATSAELEVQEKTSLLEWFANEYKQFGCTLEFVTNKSQEGSQFCRGFGGIG 411 (437)
Q Consensus 332 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~~~~~~~~~~v~~l~~~a~~~ga~V~vvs~~~e~G~q~l~~~GGIa 411 (437)
++++|++|+...+.++.+.+... ...||.||.+++++++.++++||+++|+++||+|+|||++|++|.||+++|||||
T Consensus 319 ~~~rc~~c~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~ve~L~e~a~~~Ga~V~~iS~~~eeG~ql~~~fGGIa 396 (403)
T TIGR03676 319 VTFKCPNCGYEEEKTVKPEEGDK--SEACPKCGSELEIVEEEDIIEELSELAEESGAKVEIISTDTEEGEQLLKAFGGIA 396 (403)
T ss_pred EEEEcCCCCcceeeecccccccc--cccCcccCcccccchhhhHHHHHHHHHHHcCCEEEEECCCChhHHHHHHcCCcEE
Confidence 99999999998888877665422 2569999999988888999999999999999999999999999999779999999
Q ss_pred EEeeccc
Q 013725 412 GILRYQL 418 (437)
Q Consensus 412 AiLRy~~ 418 (437)
||||||+
T Consensus 397 AiLRy~i 403 (403)
T TIGR03676 397 AILRYRV 403 (403)
T ss_pred EEEecCC
Confidence 9999986
No 2
>PRK04011 peptide chain release factor 1; Provisional
Probab=100.00 E-value=2.7e-95 Score=738.54 Aligned_cols=407 Identities=36% Similarity=0.624 Sum_probs=387.0
Q ss_pred hhhHHHHHHHHHHHHHHccCCCCcceEEEEeCCCCChHHHHhhhhhhhhhhhhhhhhhhhhhhhHhHHHHHHHhhccccc
Q 013725 8 DKNIEIWKIKKLIKALESARGNGTSMISLIMPPRDQISRVTKMLGDEFGTASNIKSRVNRQSVLAAITSAQQRLKLYNKV 87 (437)
Q Consensus 8 ~~~~~~~~~~~~l~~L~~~~g~~t~lvSlyip~~~~~~~v~~~l~~e~~~a~nik~~~~r~~v~~al~~~~~rl~~~~~~ 87 (437)
+.++++|+||++|++|++++|+||+||||||||+++++++.++|++||++|+|||||++|++|++||+++++||+++.++
T Consensus 4 ~~~~~~~~~k~~~~~l~~~~g~~t~~iSlyip~~~~i~~~~~~l~~e~~~a~nik~~~~r~~v~~ai~~~~~rl~~~~~~ 83 (411)
T PRK04011 4 QSSKEKYEFKKLLEELKKKKGRGTELISLYIPPGRPISDVVNQLRQEYSQASNIKSKTTRKNVQSALESIIQRLKLYKKP 83 (411)
T ss_pred hhHHHHHHHHHHHHHHHhCcCCCceEEEEEECCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCC
Confidence 46799999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCeEEEEeccccCCC-CCeeEEEEeecCCCcceeeeeeccCccchHHHHHhhccCCcEEEEEEECCceEEEEEeCCeEE
Q 013725 88 PPNGLVLYTGTVVTDD-GKEKKVTIDFEPFKPINASLYLCDNKFHTEALNELLESDDKFGFIVMDGNGTLFGTLSGNTRE 166 (437)
Q Consensus 88 ~~~Gl~~fa~~~~~~~-G~~~~~tl~i~p~~~v~~~~~~~~~~~~l~~L~~~~~~~~~~~vvvvd~~~A~i~~~~g~~~~ 166 (437)
|+||+|+|||.+...+ |+.++||++++||.||++++|+||+.||++||.++++...+|++|+||+++|+|+++.+++++
T Consensus 84 p~nGl~~f~g~~~~~~~~~~~~~t~~i~p~~~i~~~~y~~d~~f~le~L~e~~~~~~~~~~VvvD~~~A~i~~l~g~~~~ 163 (411)
T PRK04011 84 PENGLVIFCGAVPIGGPGTEDMETYVIEPPEPVPTFFYRCDSEFHTEPLEDMLEDKEVYGLIVVDRREATIGLLKGKRIE 163 (411)
T ss_pred CCCeEEEEEeecccCCCCCceEEEEEEcCCCccEEEEecCCcHHHHHHHHHHhcCCCCEEEEEEecCceEEEEEeCCEEE
Confidence 9999999999876544 566679999999999999999999999999999999999999999999999999999999999
Q ss_pred EEeEEeecCCcccCCCCcchHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCccEEEEecChhcHHHhhhccCCChh
Q 013725 167 VLHKFTVDLPKKHGRGGQSALRFARLRMEKRHNYVRKTAELATQFFINPATSQPNVSGLILAGSADFKTELSQSDMFDPR 246 (437)
Q Consensus 167 ~~~~~~~~vp~K~~~gG~s~~Rf~r~~ee~~~~f~~~Vae~l~~~f~~~~~~~~~~~~lilaGp~~~k~~f~~~~~l~~~ 246 (437)
++.++++++|+||++||||+.||+|++++++++||++||+.+.++|.+ .++.++++||||||+++|+.|.++++|+++
T Consensus 164 ~~~~i~~~vp~K~~~GG~S~~Rf~r~~e~~~~~f~k~Vae~~~~~f~~--~~~~~v~~IvlaGpg~~K~~f~~~~~L~~~ 241 (411)
T PRK04011 164 VLKELTSFVPGKHRKGGQSARRFERLIEQAAHEFYKRVGEKANEAFLP--LLEGKLKGILIGGPGPTKEEFLEGDYLHYE 241 (411)
T ss_pred EEEEEEeeCCCCccCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHhh--hccccccEEEEECChhHHHHHhhhhhhhHH
Confidence 999999999999999999999999999999999999999999999874 335789999999999999999976799999
Q ss_pred hhcceeEEEeCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcEEEcHHHHHHHHHhCCccEEEeccC
Q 013725 247 LQAKILNVVDVSYGGENGFNQAIELSAEILSNVKFIQEKRLIGKYFEEISQDTGKYVFGVDDTLKALELGAVEILIVWEN 326 (437)
Q Consensus 247 l~~~vi~~v~~s~~~~~gl~E~l~~~~~~l~~~~~~~e~~ll~~f~~~~~~~~g~a~yG~~eV~~Al~~GaV~tLlV~d~ 326 (437)
++++++.++++++++++|++|++++++++|++.++++|+++|++|++++++++|++|||+++|.+||++|||+||||+|+
T Consensus 242 l~~~vv~~~~~s~~~~~Gl~E~l~~~~~~L~~~k~~~e~~lle~f~~~l~~d~g~avyG~~~V~~Ale~GAVetLLV~d~ 321 (411)
T PRK04011 242 LKKKILGLFDVSYTGESGLRELVDKASDLLKEQELVKEKKLMEEFFKELAKDGGLAVYGEEEVRKALEMGAVDTLLISED 321 (411)
T ss_pred HHhheEEEEecCCCCccCHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhcCCCcEEEcHHHHHHHHHcCCceEEEEecc
Confidence 99999899999999999999999999999999999999999999999999988999999999999999999999999999
Q ss_pred ccccceeeecCCCCceEEEecccccccccCCccCccccchhhhhhhccHHHHHHHHHHhcCCeEEEeCCCCchhhhhhcc
Q 013725 327 LDINRYVLKNSATGEIVIKHLNRDQEADQSNFRDAATSAELEVQEKTSLLEWFANEYKQFGCTLEFVTNKSQEGSQFCRG 406 (437)
Q Consensus 327 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~~~~~~~~~~v~~l~~~a~~~ga~V~vvs~~~e~G~q~l~~ 406 (437)
+...|++++|++|+...+.++.+.+. .....||.||.++++++..+++++|++.|+++||+|+|||++|++|.||+++
T Consensus 322 l~~~r~~~~c~~c~~~~~~~~~~~~~--~~~~~c~~~~~~~~~~~~~~~v~~l~e~a~~~g~~v~iis~~~e~G~qL~~~ 399 (411)
T PRK04011 322 LRKDRVTYKCPNCGYEEEKTVKRREE--LPEKTCPKCGSELEIVEEEDIIEELSELAEQSGTKVEVISTDTEEGEQLLKA 399 (411)
T ss_pred ccceeEEEEcCCCCcceeeecccccc--cccccCcccCcccccchhhhHHHHHHHHHHHcCCEEEEECCCChhHHHHHHc
Confidence 99999999999999988888777653 3456899999999888889999999999999999999999999999997799
Q ss_pred cccEEEEeeccc
Q 013725 407 FGGIGGILRYQL 418 (437)
Q Consensus 407 ~GGIaAiLRy~~ 418 (437)
|||||||||||+
T Consensus 400 fGGIaAiLRy~i 411 (411)
T PRK04011 400 FGGIAAILRYKT 411 (411)
T ss_pred CCCEEEEEecCC
Confidence 999999999986
No 3
>TIGR00108 eRF peptide chain release factor eRF/aRF, subunit 1. Alternative names include eRF1, SUP45, omnipotent suppressor protein 1.
Probab=100.00 E-value=4.2e-95 Score=736.72 Aligned_cols=406 Identities=41% Similarity=0.688 Sum_probs=380.1
Q ss_pred hHHHHHHHHHHHHHHccCCCCcceEEEEeCCCCChHHHHhhhhhhhhhhhhhhhhhhhhhhhHhHHHHHHHhhcccccCC
Q 013725 10 NIEIWKIKKLIKALESARGNGTSMISLIMPPRDQISRVTKMLGDEFGTASNIKSRVNRQSVLAAITSAQQRLKLYNKVPP 89 (437)
Q Consensus 10 ~~~~~~~~~~l~~L~~~~g~~t~lvSlyip~~~~~~~v~~~l~~e~~~a~nik~~~~r~~v~~al~~~~~rl~~~~~~~~ 89 (437)
+.++|++|+.|++|++++|+||+||||||||+++|+++.++|++||++|+|||||.||++|++||+++++||++++++|+
T Consensus 3 ~~~~~~~k~~~~~l~~~~g~gt~lisl~ipp~~~i~~~~~~l~~e~~~a~niks~~~r~~v~~ai~~~~~~lk~~~~~p~ 82 (409)
T TIGR00108 3 SKNLYEFKRKLQELEKKRGRGTELISLYIPPDRQISDVAKHLREELSQASNIKSKQTRKNVLSAIEAILQRLKLFNKPPE 82 (409)
T ss_pred hHHHHHHHHHHHHHHhCcCCCceEEEEEeCCCCcHHHHHHHHHHHHhhhhcccccchhhhHHHHHHHHHHHhhccCCCCC
Confidence 57889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CeEEEEeccccCCCCCeeEEEEeecCCCcceeeeeeccCccchHHHHHhhccCCcEEEEEEECCceEEEEEeCCeEEEEe
Q 013725 90 NGLVLYTGTVVTDDGKEKKVTIDFEPFKPINASLYLCDNKFHTEALNELLESDDKFGFIVMDGNGTLFGTLSGNTREVLH 169 (437)
Q Consensus 90 ~Gl~~fa~~~~~~~G~~~~~tl~i~p~~~v~~~~~~~~~~~~l~~L~~~~~~~~~~~vvvvd~~~A~i~~~~g~~~~~~~ 169 (437)
||+++|||.+....|..++||++++||.||++++|.||+.||++||.+|++++.+|++|+||+++|.||++.|++++++.
T Consensus 83 nglv~~~G~v~~~~~~~~~~t~~iep~~pi~~~~y~~d~~f~le~L~e~~~~~~~~g~VvvD~~~A~i~~l~g~~~~~~~ 162 (409)
T TIGR00108 83 NGLVIFCGMVPREGPTEKMETYVIEPPEPIKTYIYHCDSKFYLEPLSEMLEEKDKYGLIVLDRQEATIGLVKGKRITVLK 162 (409)
T ss_pred CcEEEEEeEeccCCCcccEEEEEEeCCCceEEEEEccCChhHHHHHHHHhcCCCCEEEEEEecCCEEEEEEcCCEEEEEE
Confidence 99999999876555555669999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEeecCCcccCCCCcchHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCccEEEEecChhcHHHhhhccCCChhhhc
Q 013725 170 KFTVDLPKKHGRGGQSALRFARLRMEKRHNYVRKTAELATQFFINPATSQPNVSGLILAGSADFKTELSQSDMFDPRLQA 249 (437)
Q Consensus 170 ~~~~~vp~K~~~gG~s~~Rf~r~~ee~~~~f~~~Vae~l~~~f~~~~~~~~~~~~lilaGp~~~k~~f~~~~~l~~~l~~ 249 (437)
.+++++|+||++||||+.||+|++++++++||++||+.+.++|++ .+..++++||||||+++|++|.++++|++++++
T Consensus 163 ~i~~~vp~K~~~GGqS~~Rf~r~~e~~~~~f~~~Vae~~~~~f~~--~~~~~v~~IIlaGpg~~K~~f~~~~~l~~~l~~ 240 (409)
T TIGR00108 163 KLTSGVPGKHKAGGQSARRFERLRELAAHEFLKKVGEVANEAFLP--NDDVKLKGIILGGPGHTKEEFAEGEYLHHELKK 240 (409)
T ss_pred EEeeeCCCcccCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHhhh--cccccceEEEEeccHHHHHHhhhhhhHHHHhhh
Confidence 999999999999999999999999999999999999999999975 444589999999999999999987799999999
Q ss_pred ceeEEEeCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcEEEcHHHHHHHHHhCCccEEEeccCccc
Q 013725 250 KILNVVDVSYGGENGFNQAIELSAEILSNVKFIQEKRLIGKYFEEISQDTGKYVFGVDDTLKALELGAVEILIVWENLDI 329 (437)
Q Consensus 250 ~vi~~v~~s~~~~~gl~E~l~~~~~~l~~~~~~~e~~ll~~f~~~~~~~~g~a~yG~~eV~~Al~~GaV~tLlV~d~l~~ 329 (437)
+++.++++|++|++|++|++++++++|++.++.+|+++|++|++++++++|++|||+++|.+||++|||+||||+|++..
T Consensus 241 kvi~~vdvs~gg~~gl~E~l~~~~~~L~~~k~~~E~~lle~F~~ei~~d~G~avyG~~eV~~ALe~GAVetLLV~d~l~~ 320 (409)
T TIGR00108 241 KVISTVDVSYTGEFGIRELIEKSADVLAEVDYMREKKLVQRFLKELIQEDGLACYGEDEVLKALDLGAVETLIVSEDLEY 320 (409)
T ss_pred hEEEEEEcCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcEEeCHHHHHHHHHhCCCcEEEEeccccc
Confidence 98888999999999999999999999999999999999999999999988999999999999999999999999999999
Q ss_pred cceeeecCCCCceEEEecccccccccCCccCccccchhhhhhhccHHHHHHHHHHhcCCeEEEeCCCCchhhhhhccccc
Q 013725 330 NRYVLKNSATGEIVIKHLNRDQEADQSNFRDAATSAELEVQEKTSLLEWFANEYKQFGCTLEFVTNKSQEGSQFCRGFGG 409 (437)
Q Consensus 330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~~~~~~~~~~v~~l~~~a~~~ga~V~vvs~~~e~G~q~l~~~GG 409 (437)
.|++++|++|++. .++.+.+........||.||.++++.++.++++||++.|+++||+|+|||++|++|.||+++|||
T Consensus 321 ~r~~~r~~~~~~~--~~~~~~~~~~~~~~~c~~~~~~~~~~~~~~~ve~L~e~a~~~Ga~V~iiS~~~eeG~ql~~~fGG 398 (409)
T TIGR00108 321 IRVTYKCAECGEV--IEKTVRELKDKKFAICPACGQEMDVVEERDLIEWLSELAENFGAKLEFISTESEEGAQLLTAFGG 398 (409)
T ss_pred eeEEEEcCCCCce--eecccccccccccccCcccCccccchhhhhHHHHHHHHHHHcCCEEEEECCCChhHHHHHHhCCC
Confidence 9999999999974 23333322223456899999999888888999999999999999999999999999998899999
Q ss_pred EEEEeecccC
Q 013725 410 IGGILRYQLD 419 (437)
Q Consensus 410 IaAiLRy~~~ 419 (437)
||||||||++
T Consensus 399 IaAiLRy~i~ 408 (409)
T TIGR00108 399 IGAILRYKPN 408 (409)
T ss_pred EEEEEecccC
Confidence 9999999986
No 4
>COG1503 eRF1 Peptide chain release factor 1 (eRF1) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.1e-89 Score=672.20 Aligned_cols=405 Identities=42% Similarity=0.688 Sum_probs=383.3
Q ss_pred hHHHHHHHHHHHHHHccCCCCcceEEEEeCCCCChHHHHhhhhhhhhhhhhhhhhhhhhhhhHhHHHHHHHhhcccccCC
Q 013725 10 NIEIWKIKKLIKALESARGNGTSMISLIMPPRDQISRVTKMLGDEFGTASNIKSRVNRQSVLAAITSAQQRLKLYNKVPP 89 (437)
Q Consensus 10 ~~~~~~~~~~l~~L~~~~g~~t~lvSlyip~~~~~~~v~~~l~~e~~~a~nik~~~~r~~v~~al~~~~~rl~~~~~~~~ 89 (437)
.+++|+||++|++|.+++|+||++|||||||++||++|.++|+++|++|+|||||.||++|++||++++++|+.+.++|.
T Consensus 6 ~~~~~e~Kk~l~~L~~~rg~gt~lislyIPp~~qisdv~~~lr~e~s~asniksk~tR~~V~~ai~~~~~rLk~~~~~P~ 85 (411)
T COG1503 6 MHEMYELKKLLEELKKFRGRGTELISLYIPPDRQISDVVNRLRDEYSTASNIKSKVTRKNVLSAIESAMQRLKDYCKTPE 85 (411)
T ss_pred HHHHHHHHHHHHHHHhhcCCCceEEEEecCCCCchHHHHHHHHhhccchhhhhhcCchHHHHhHHHHHHHHHHhcccCCC
Confidence 69999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CeEEEEeccccCCCCCeeEEEEeecCCCcceeeeeeccCccchHHHHHhhccCCcEEEEEEECCceEEEEEeCCeEEEEe
Q 013725 90 NGLVLYTGTVVTDDGKEKKVTIDFEPFKPINASLYLCDNKFHTEALNELLESDDKFGFIVMDGNGTLFGTLSGNTREVLH 169 (437)
Q Consensus 90 ~Gl~~fa~~~~~~~G~~~~~tl~i~p~~~v~~~~~~~~~~~~l~~L~~~~~~~~~~~vvvvd~~~A~i~~~~g~~~~~~~ 169 (437)
||+++|+|.+....|...+.+..++||.|++.++|+|++.||++||.+++.+...|+++++|+.+|+++++.|.++++++
T Consensus 86 nGlv~f~g~v~~~~~~t~~~~~~~~PP~Pi~~~ly~cDs~F~~e~L~~~l~~~~~ygliv~dr~ea~ig~l~g~r~evl~ 165 (411)
T COG1503 86 NGLVLFVGDVLGGGGKTKKVTVVIEPPEPINTFLYRCDSKFYLEPLEEMLEDKDLYGLIVLDRIEATIGLLKGKRIEVLK 165 (411)
T ss_pred CCeEEEEeeeccCCCccceeeecccCCCCcceeeeccccHHHHHHHHHHhhhcccccEEEEecccceeeeeccceeeHhh
Confidence 99999999998666667778888999999999999999999999999999999999999999999999999999999999
Q ss_pred EEeecCCcccCCCCcchHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCccEEEEecChhcHHHhhhccCCChhhhc
Q 013725 170 KFTVDLPKKHGRGGQSALRFARLRMEKRHNYVRKTAELATQFFINPATSQPNVSGLILAGSADFKTELSQSDMFDPRLQA 249 (437)
Q Consensus 170 ~~~~~vp~K~~~gG~s~~Rf~r~~ee~~~~f~~~Vae~l~~~f~~~~~~~~~~~~lilaGp~~~k~~f~~~~~l~~~l~~ 249 (437)
.+++.+|+||++||||++||+|+++++.|.||++|++.+.++|++ ....++++|+|+||+++|++|.+.+||+++|++
T Consensus 166 ~~~s~vpgKh~~Ggqsa~rferl~ee~~h~f~k~vge~A~e~f~~--~~~~~~kgIilgGp~~tk~ef~e~~yL~~~lk~ 243 (411)
T COG1503 166 ELTSDVPGKHRAGGQSARRFERLIEEAAHEFYKKVGEAASEAFLP--IAKKELKGIILGGPGPTKEEFVEGDYLHHELKK 243 (411)
T ss_pred hhcccCcchhhcccchHHHHHHHHHHHHHHHHHHHHHHHHHHhcc--hhhhhhcceEeeCCcccchhhhcccccchHHHH
Confidence 999999999999999999999999999999999999999999985 333379999999999999999999999999999
Q ss_pred ceeEEEeCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcEEEcHHHHHHHHHhCCccEEEeccCccc
Q 013725 250 KILNVVDVSYGGENGFNQAIELSAEILSNVKFIQEKRLIGKYFEEISQDTGKYVFGVDDTLKALELGAVEILIVWENLDI 329 (437)
Q Consensus 250 ~vi~~v~~s~~~~~gl~E~l~~~~~~l~~~~~~~e~~ll~~f~~~~~~~~g~a~yG~~eV~~Al~~GaV~tLlV~d~l~~ 329 (437)
+++++||++|++++|++|++.++.++|++.++.+|+++|++|++++.+++|+++||.++|++||++|||++|||++++..
T Consensus 244 kv~~lvDv~y~~esg~~eli~~A~d~L~~~~~~~eK~l~e~f~~e~~~~~Gla~yG~~~vr~aL~~gaVd~llv~Edl~~ 323 (411)
T COG1503 244 KVLGLVDVSYTGESGLRELIEKAEDALKDVDYVREKKLMEEFFKELAKDSGLAVYGEEEVREALEMGAVDTLLVSEDLEK 323 (411)
T ss_pred HHHhhccccccccccHHHHHHHhHHHHHhhhhhcchhHHHHHHHHhccCcceeecchHHHHHHHHhcccceEEeeccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cceeeecCCCCceEEEecccccccccCCccCccccchhhhhhhccHHHHHHHHHHhcCCeEEEeCCCCchhhhhhccccc
Q 013725 330 NRYVLKNSATGEIVIKHLNRDQEADQSNFRDAATSAELEVQEKTSLLEWFANEYKQFGCTLEFVTNKSQEGSQFCRGFGG 409 (437)
Q Consensus 330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~~~~~~~~~~v~~l~~~a~~~ga~V~vvs~~~e~G~q~l~~~GG 409 (437)
.|++++|+.|+....++..+.. ...+.||.||.++..+...++++++++.|++.|++|+|||+++++|.||+++|||
T Consensus 324 ~r~~~~c~~~~~e~~~t~~~~~---~~~~~~~~~~~e~~~v~~~d~vd~l~e~a~~~Ga~ve~is~~~~eg~q~~~afgG 400 (411)
T COG1503 324 ERVTYKCPTCGYENLKSKREFE---QKRFRCPECGSEMEEVEVSDLVDELAELAEESGAKVEIISDDTDEGAQLLKAFGG 400 (411)
T ss_pred cceeecCCCcchhhhhcccccc---cccccCccccccccchhhhhHHHHHHHHHHhcCCeEEEecCchHHHHHHHHcccc
Confidence 9999999999974332221111 1134899999999999999999999999999999999999999999999999999
Q ss_pred EEEEeecccC
Q 013725 410 IGGILRYQLD 419 (437)
Q Consensus 410 IaAiLRy~~~ 419 (437)
|||||||+++
T Consensus 401 i~AiLR~~~~ 410 (411)
T COG1503 401 LAAILRYRTD 410 (411)
T ss_pred hheeeecccC
Confidence 9999999986
No 5
>KOG0688 consensus Peptide chain release factor 1 (eRF1) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.2e-89 Score=643.56 Aligned_cols=427 Identities=80% Similarity=1.203 Sum_probs=408.7
Q ss_pred chhhhHHHHHHHHHHHHHHccCCCCcceEEEEeCCCCChHHHHhhhhhhhhhhhhhhhhhhhhhhhHhHHHHHHHhhccc
Q 013725 6 ETDKNIEIWKIKKLIKALESARGNGTSMISLIMPPRDQISRVTKMLGDEFGTASNIKSRVNRQSVLAAITSAQQRLKLYN 85 (437)
Q Consensus 6 ~~~~~~~~~~~~~~l~~L~~~~g~~t~lvSlyip~~~~~~~v~~~l~~e~~~a~nik~~~~r~~v~~al~~~~~rl~~~~ 85 (437)
+.++++|+|++|++|+.|+.+||+||++|||+|||.++++++.+||.+||+||+|||||++|++|.+||+++++||++|+
T Consensus 3 ~~~~nveiwkikklik~le~argngtsmisliippkdqisr~skmLadeygtasnikSrVnRlsvl~AitSaq~rLklyn 82 (431)
T KOG0688|consen 3 EADKNVEIWKIKKLIKSLEDARGNGTSMISLIIPPKDQISRVSKMLADEYGTASNIKSRVNRLSVLGAITSAQSRLKLYN 82 (431)
T ss_pred chhhhhHHHHHHHHHHHHHHhcCCCceeEEEEeCchHHHHHHHHHHHHhhhhhhhhhhhhcchhhhhhhhhhhhhhHHhc
Confidence 34689999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCeEEEEeccccCCCCCeeEEEEeecCCCcceeeeeeccCccchHHHHHhhccCCcEEEEEEECCceEEEEEeCCeE
Q 013725 86 KVPPNGLVLYTGTVVTDDGKEKKVTIDFEPFKPINASLYLCDNKFHTEALNELLESDDKFGFIVMDGNGTLFGTLSGNTR 165 (437)
Q Consensus 86 ~~~~~Gl~~fa~~~~~~~G~~~~~tl~i~p~~~v~~~~~~~~~~~~l~~L~~~~~~~~~~~vvvvd~~~A~i~~~~g~~~ 165 (437)
++|+||+++|||.+...+|+.++++++++|..||....|.|++.||++||.+++....++|+++||..++.|+++.|+..
T Consensus 83 kvPpnglvly~gti~tedgkekkv~idfepfkpintslyLcdNkfhte~l~~Ll~sd~kfgfivmDg~~tlfgtl~gntr 162 (431)
T KOG0688|consen 83 KVPPNGLVLYTGTIVTEDGKEKKVNIDFEPFKPINTSLYLCDNKFHTEALKELLESDNKFGFIVMDGNGTLFGTLQGNTR 162 (431)
T ss_pred cCCCCceEEEeeeeEccCCceeeeecccccccccccceEecCCccchHHHHHHHhhcccccEEEEcCCceeEEEeccchH
Confidence 99999999999999988999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEeEEeecCCcccCCCCcchHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCccEEEEecChhcHHHhhhccCCCh
Q 013725 166 EVLHKFTVDLPKKHGRGGQSALRFARLRMEKRHNYVRKTAELATQFFINPATSQPNVSGLILAGSADFKTELSQSDMFDP 245 (437)
Q Consensus 166 ~~~~~~~~~vp~K~~~gG~s~~Rf~r~~ee~~~~f~~~Vae~l~~~f~~~~~~~~~~~~lilaGp~~~k~~f~~~~~l~~ 245 (437)
++++.+..++|+||++||||+.||.|+|.+..|.|.++||+.+.+.|+. .+..++.+||+||.+.+|.++.+++.+++
T Consensus 163 evLhkftVdlPkkhgrggqSalrfarlR~ekRhnYVrkvae~a~q~fi~--~~~~Nv~gLilaGsadfKtelsqSd~fd~ 240 (431)
T KOG0688|consen 163 EVLHKFTVDLPKKHGRGGQSALRFARLRMEKRHNYVRKVAELAVQRFIT--NDKPNVAGLILAGSADFKTELSQSDMFDP 240 (431)
T ss_pred hhhheeeecCccccCccchhHHhhhhhhhhhhccceeeecccceeEEec--CCCcceeEEEEecccccccccchhhhcch
Confidence 9999999999999999999999999999999999999999999999997 77899999999999999999999999999
Q ss_pred hhhcceeEEEeCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcEEEcHHHHHHHHHhCCccEEEecc
Q 013725 246 RLQAKILNVVDVSYGGENGFNQAIELSAEILSNVKFIQEKRLIGKYFEEISQDTGKYVFGVDDTLKALELGAVEILIVWE 325 (437)
Q Consensus 246 ~l~~~vi~~v~~s~~~~~gl~E~l~~~~~~l~~~~~~~e~~ll~~f~~~~~~~~g~a~yG~~eV~~Al~~GaV~tLlV~d 325 (437)
||+.+++.+|+++|||+.|++|+|+.++++|+++++.+|++++.+||+++..++|+.|||..+++.||++|||+||+|++
T Consensus 241 rlqskvi~~vdvsyGGengfnQaIeL~aevlsnvk~vqekkli~~yfdEisqdtgky~Fgv~dTl~aLe~gavetli~~e 320 (431)
T KOG0688|consen 241 RLQSKVLKTVDVSYGGENGFNQAIELSAEVLSNVKFVQEKKLIGKYFDEISQDTGKYCFGVEDTLLALEMGAVETLIVWE 320 (431)
T ss_pred HHhhhHHhhhcccccchhhHHHHHHHHHhhhhcceeeehhhHHHHHhhhhhcccCcccccHHHHHHHHHcCCeeehhHhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CccccceeeecCCCCceEEEecccccccccCCccCccccchhhhhhhccHHHHHHHHHHhcCCeEEEeCCCCchhhhhhc
Q 013725 326 NLDINRYVLKNSATGEIVIKHLNRDQEADQSNFRDAATSAELEVQEKTSLLEWFANEYKQFGCTLEFVTNKSQEGSQFCR 405 (437)
Q Consensus 326 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~~~~~~~~~~v~~l~~~a~~~ga~V~vvs~~~e~G~q~l~ 405 (437)
++...||+++|.. |+..+.++.|+++.+++.+.+...|-+|+++++.++++|+.++++.+||-++||++.+.+|.||++
T Consensus 321 nLd~~ry~~kn~~-~~~~i~~l~~~~e~d~s~~~Dketg~e~elie~~pLlEw~AnnYK~FGa~LE~VTdKSqEgsQFv~ 399 (431)
T KOG0688|consen 321 NLDIIRYELKNSD-GESVIGFLVPDEEKDKSHFTDKETGWEMELIERMPLLEWFANNYKKFGATLEIVTDKSQEGSQFVK 399 (431)
T ss_pred hhhhhhhhhcccC-CccceeeecchhhcccccccccccchhhhHHhhhhHHHHHHHHHhhcCeEEEEecccchhHHHHHh
Confidence 9999999999985 677888888777655666777888999999999999999999999999999999999999999999
Q ss_pred ccccEEEEeecccCcccccccCCCCCCCCCC
Q 013725 406 GFGGIGGILRYQLDIRSYDELSDDGGVYEDS 436 (437)
Q Consensus 406 ~~GGIaAiLRy~~~~~~~~~~~~~~~~~~~~ 436 (437)
+||||||||||+++++.++.++ ++++|+++
T Consensus 400 GfGgiGgiLrY~vd~~~~~~~~-d~~~~~~~ 429 (431)
T KOG0688|consen 400 GFGGIGGILRYRVDFQGIEYQE-DIEFFDLD 429 (431)
T ss_pred hcCCcceeEEEEeeeecccccc-CceeeecC
Confidence 9999999999999999888776 55666654
No 6
>TIGR00111 pelota probable translation factor pelota. This model describes the Drosophila protein Pelota, the budding yeast protein DOM34 which it can replace, and a set of closely related archaeal proteins. Members contain a proposed RNA binding motif. The meiotic defect in pelota mutants may be a complex result of a protein translation defect, as suggested in yeast by ribosomal protein RPS30A being a multicopy suppressor and by an altered polyribosome profile in DOM34 mutants rescued by RPS30A. This family is homologous to a family of peptide chain release factors. Pelota is proposed to act in protein translation.
Probab=100.00 E-value=3.4e-55 Score=437.86 Aligned_cols=321 Identities=21% Similarity=0.337 Sum_probs=264.2
Q ss_pred CCCcceEEEEeCCCCChHHHHhhhh-hhhhhhhhhhhhhhhhhhhHhHHHHHHHhhcc--------------cccCCCeE
Q 013725 28 GNGTSMISLIMPPRDQISRVTKMLG-DEFGTASNIKSRVNRQSVLAAITSAQQRLKLY--------------NKVPPNGL 92 (437)
Q Consensus 28 g~~t~lvSlyip~~~~~~~v~~~l~-~e~~~a~nik~~~~r~~v~~al~~~~~rl~~~--------------~~~~~~Gl 92 (437)
.+|.+.|+|.+...+|+|+++|.+. .+...+...|. +......++-. +|...+ +.++.+|+
T Consensus 9 ~~~~g~v~l~pe~~dDlw~l~nli~~GD~V~~~T~Rk-v~~~~~~g~~~---er~~~~l~i~Ve~ief~~~~~~Lri~G~ 84 (351)
T TIGR00111 9 NKGGAVIKLLPETLDDLWHLYQIIEKGDVEFAFTKRR-TQDLDKIRSDK---SKDTVKLGIEVESVEFDMKTERLRYKGV 84 (351)
T ss_pred CCCcEEEEEEeCChHHHHHHHHhCCCCCEEEEEEEEE-EeccccCCCcc---eEEEEEEEEEEEEEEecCCCCEEEEEEE
Confidence 4455789999999999999999998 65555554442 32222122211 333211 34556777
Q ss_pred EEEeccccCCCCCeeEEEEeecCCCcceeeeeeccCccchHHHHHhhccC--CcEEEEEEECCceEEEEEeCCeEEEEeE
Q 013725 93 VLYTGTVVTDDGKEKKVTIDFEPFKPINASLYLCDNKFHTEALNELLESD--DKFGFIVMDGNGTLFGTLSGNTREVLHK 170 (437)
Q Consensus 93 ~~fa~~~~~~~G~~~~~tl~i~p~~~v~~~~~~~~~~~~l~~L~~~~~~~--~~~~vvvvd~~~A~i~~~~g~~~~~~~~ 170 (437)
++..++.....|+| ||++++||+|++++|+ ||+.|++++|++|++.. +.+++|+||+++|.||++++++++++.+
T Consensus 85 i~~~~e~~v~~G~~--HTl~ie~~~~i~i~K~-~w~~~~le~L~ea~~~~~~~~~~~vv~d~g~A~i~ll~~~~~~~~~~ 161 (351)
T TIGR00111 85 IVTGPEDDVPVGSY--HTLEIKYVYPLSIIKQ-NWKKWQLKRLREAVEISKRPKTAAVVMEEGIAHVGLVRQYSVEEIQK 161 (351)
T ss_pred EecCCcccccccce--EEEEEcCCCcEEEEEe-cCCHHHHHHHHHHhccccCCcEEEEEEeCCcEEEEEEcCCEEEEEEE
Confidence 76654222245888 9999999999999998 79999999999999987 7799999999999999999999999999
Q ss_pred EeecCCcccCCCCcchHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCccEEEEecChhcHHHhhhccCCChhhh--
Q 013725 171 FTVDLPKKHGRGGQSALRFARLRMEKRHNYVRKTAELATQFFINPATSQPNVSGLILAGSADFKTELSQSDMFDPRLQ-- 248 (437)
Q Consensus 171 ~~~~vp~K~~~gG~s~~Rf~r~~ee~~~~f~~~Vae~l~~~f~~~~~~~~~~~~lilaGp~~~k~~f~~~~~l~~~l~-- 248 (437)
+++++|+||+ + +.++++.++||++|++++.+ +.++++||||||||+|+.|.++ +..++.
T Consensus 162 i~~~iP~K~~-~--------~~~e~~~~~Ff~~v~~~l~~--------~~~v~~iIiaGPGf~k~~f~~~--l~~~~~~~ 222 (351)
T TIGR00111 162 IEYHMPGKKR-T--------LKFGELRKEFYKEIAKKLLN--------FDDLKTIIVAGPGFYKNDFYDF--IFERYPEE 222 (351)
T ss_pred EEEeCCCCcc-c--------chhHHHHHHHHHHHHHHHhh--------hcccCEEEEECCHHHHHHHHHH--HHHHhhhh
Confidence 9999999974 2 23577889999999999854 2479999999999999999965 443332
Q ss_pred -cceeEEEeCCCCCcccHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHhccCCCcEEEcHHHHHHHHHhCCccEEEecc
Q 013725 249 -AKILNVVDVSYGGENGFNQAIELS--AEILSNVKFIQEKRLIGKYFEEISQDTGKYVFGVDDTLKALELGAVEILIVWE 325 (437)
Q Consensus 249 -~~vi~~v~~s~~~~~gl~E~l~~~--~~~l~~~~~~~e~~ll~~f~~~~~~~~g~a~yG~~eV~~Al~~GaV~tLlV~d 325 (437)
.+. .+.++|+++++|++|+|+++ +++|++.++++|.++|++|+++++++++++|||+++|.+|+++|||+||||+|
T Consensus 223 ~~k~-ii~~~s~g~~~gl~EvL~~~~v~~~l~d~k~~~E~~~l~~f~~~l~kd~~~~~YG~~eV~~Ale~GAVetLLIsD 301 (351)
T TIGR00111 223 ANKA-VLENCSTGGRAGINEVLKRGLVARILQETRYAKEIMVIDEFLEHLAKDGDKAVYGEDEVVKAAEYGAIEYLLVTD 301 (351)
T ss_pred hCCc-EEEecCCCchhHHHHHHhChHHHHHHhhhhHHHHHHHHHHHHHHHhcCCCeEEECHHHHHHHHHcCCceEEEEec
Confidence 222 24689999999999999986 69999999999999999999999999999999999999999999999999999
Q ss_pred CccccceeeecCCCCceEEEecccccccccCCccCccccchhhhhhhccHHHHHHHHHHhcCCeEEEeCCCCchhhhhhc
Q 013725 326 NLDINRYVLKNSATGEIVIKHLNRDQEADQSNFRDAATSAELEVQEKTSLLEWFANEYKQFGCTLEFVTNKSQEGSQFCR 405 (437)
Q Consensus 326 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~~~~~~~~~~v~~l~~~a~~~ga~V~vvs~~~e~G~q~l~ 405 (437)
++...| .+ +++|++.|+++||+|.|||++|++|+| |+
T Consensus 302 ~l~~~r---------------------------------~~---------~~~l~~~v~~~gg~V~i~Ss~~e~G~q-L~ 338 (351)
T TIGR00111 302 KVLVQR---------------------------------EE---------IEKLLDSVESMGGKVVILSTEHELGKQ-LD 338 (351)
T ss_pred chhhhH---------------------------------HH---------HHHHHHHHHHcCCEEEEEcCCCccHHH-Hh
Confidence 995110 11 578999999999999999999999999 89
Q ss_pred ccccEEEEeeccc
Q 013725 406 GFGGIGGILRYQL 418 (437)
Q Consensus 406 ~~GGIaAiLRy~~ 418 (437)
+|||||||||||+
T Consensus 339 ~lgGiaAiLRy~i 351 (351)
T TIGR00111 339 SLGGIAGILRFPI 351 (351)
T ss_pred hCCCEEEEEeccC
Confidence 9999999999996
No 7
>COG1537 PelA Predicted RNA-binding proteins [General function prediction only]
Probab=100.00 E-value=7e-47 Score=364.94 Aligned_cols=319 Identities=24% Similarity=0.366 Sum_probs=261.4
Q ss_pred ceEEEEeCCCCChHHHHhhhh-hhhhhhhhhhhhhhhhhhhHhHHHHH-HHh--------------hcccccCCCeEEEE
Q 013725 32 SMISLIMPPRDQISRVTKMLG-DEFGTASNIKSRVNRQSVLAAITSAQ-QRL--------------KLYNKVPPNGLVLY 95 (437)
Q Consensus 32 ~lvSlyip~~~~~~~v~~~l~-~e~~~a~nik~~~~r~~v~~al~~~~-~rl--------------~~~~~~~~~Gl~~f 95 (437)
+.++|.+..-+|+|++++-++ .+...|..-+. .++.. .+.+.. +|+ ++.++++..|.++.
T Consensus 11 g~I~l~pE~lDDLw~L~~Ii~~GD~v~a~T~Rr-~~~~d---~~r~~~~eri~m~L~IkVe~ieF~~f~nrLRi~G~i~~ 86 (352)
T COG1537 11 GVIKLVPETLDDLWHLYNIIEKGDKVFAKTTRR-DESSD---VIRSKKGERIPMTLGIKVEKIEFDKFANRLRIKGPIVE 86 (352)
T ss_pred ceEEEecCChHHHHHHHHhcCCCCEEEEEEEEe-ccccc---ccccCcceEEEEEEEEEEEEEEeeecccEEEEEEEEEE
Confidence 478998888889999999888 44333322220 01111 111111 222 13467888999999
Q ss_pred eccccCCCCCeeEEEEeecCCCcceeeeeeccCccchHHHHHhhcc--CCcEEEEEEECCceEEEEEeCCeEEEEeEEee
Q 013725 96 TGTVVTDDGKEKKVTIDFEPFKPINASLYLCDNKFHTEALNELLES--DDKFGFIVMDGNGTLFGTLSGNTREVLHKFTV 173 (437)
Q Consensus 96 a~~~~~~~G~~~~~tl~i~p~~~v~~~~~~~~~~~~l~~L~~~~~~--~~~~~vvvvd~~~A~i~~~~g~~~~~~~~~~~ 173 (437)
+..... .|+| ||++++++.++++.|. .|+.++++.|+++++. .+.+++|+||.++|.||+++.+++..+.++..
T Consensus 87 ~~e~~~-~G~y--HTi~v~~g~~i~I~K~-~W~~~~lerLkeA~~~~~~~~~~~v~~degea~i~iv~~ygi~~~~~i~~ 162 (352)
T COG1537 87 GPEEVV-KGSY--HTINVTIGTEIEIEKE-EWNKDQLERLKEAVEASKRPEVAIVVVDEGEAAIAIVRDYGIIILGKIRS 162 (352)
T ss_pred cCcccc-cccc--eEEEeccCceEEEEEc-cCCHHHHHHHHHHhhcccCCceEEEEEecCceEEEEEeccceEEEEEEec
Confidence 987654 6888 9999999999999996 4999999999999998 57899999999999999999999999999999
Q ss_pred cCCcccCCCCcchHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCccEEEEecChhcHHHhhhccCCCh---hhhcc
Q 013725 174 DLPKKHGRGGQSALRFARLRMEKRHNYVRKTAELATQFFINPATSQPNVSGLILAGSADFKTELSQSDMFDP---RLQAK 250 (437)
Q Consensus 174 ~vp~K~~~gG~s~~Rf~r~~ee~~~~f~~~Vae~l~~~f~~~~~~~~~~~~lilaGp~~~k~~f~~~~~l~~---~l~~~ 250 (437)
..|+|.. +. + +.+ .+||..|++.+.+.+ +++.+|||||||+|+.|+++ +.. .++.
T Consensus 163 ~~~gK~~-~~-~-------~~~--~k~~~~i~~~~~~~~--------~~~~iIvaGPGF~k~~~~~~--~~~~~p~~~~- 220 (352)
T COG1537 163 GIPGKRE-GD-I-------RAE--RKFFDEIAKALKEYA--------NLDIIIVAGPGFAKEDFYDF--LRERYPELAN- 220 (352)
T ss_pred cCCCCcc-cc-h-------hhH--HHHHHHHHHHHHHhh--------CCCeEEEeCCchHHHHHHHH--HHHhcccccc-
Confidence 9998832 21 1 112 789999999998872 68899999999999999964 432 3333
Q ss_pred eeEEEeCCCCCcccHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHhccCCCcEEEcHHHHHHHHHhCCccEEEeccCcc
Q 013725 251 ILNVVDVSYGGENGFNQAIELSA--EILSNVKFIQEKRLIGKYFEEISQDTGKYVFGVDDTLKALELGAVEILIVWENLD 328 (437)
Q Consensus 251 vi~~v~~s~~~~~gl~E~l~~~~--~~l~~~~~~~e~~ll~~f~~~~~~~~g~a~yG~~eV~~Al~~GaV~tLlV~d~l~ 328 (437)
+.+.++|.+|.+|++|+|++.. .++++.++++|.++|++|++.++++++++|||+++|.+|+++|||++|||+|++.
T Consensus 221 -~~~~~~s~~g~~gi~EvLkr~~v~ki~~e~ria~e~~~~e~fl~~iak~~~~v~YG~~eV~~A~e~GAve~LLv~De~l 299 (352)
T COG1537 221 -IVIEDTSTGGRAGINEVLKRGAVDKILSETRIAEEIELVEEFLERLAKDDDKVAYGLEEVEKAAEYGAVETLLVTDELL 299 (352)
T ss_pred -eEEEeccCcchHHHHHHHhhhhHHhHhhhhHHHHHHHHHHHHHHHHhcCCCceeEcHHHHHHHHhcCcceeEEeehhhh
Confidence 4779999999999999999964 8999999999999999999999999899999999999999999999999999997
Q ss_pred ccceeeecCCCCceEEEecccccccccCCccCccccchhhhhhhccHHHHHHHHHHhcCCeEEEeCCCCchhhhhhcccc
Q 013725 329 INRYVLKNSATGEIVIKHLNRDQEADQSNFRDAATSAELEVQEKTSLLEWFANEYKQFGCTLEFVTNKSQEGSQFCRGFG 408 (437)
Q Consensus 329 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~~~~~~~~~~v~~l~~~a~~~ga~V~vvs~~~e~G~q~l~~~G 408 (437)
+.++. +...-++.|++.++++||+|.|||+.|+.|+| |++||
T Consensus 300 ------r~~~~-------------------------------~~re~~~~ll~~ve~~ggkV~Ivs~~he~Ge~-Lk~lG 341 (352)
T COG1537 300 ------RSDDV-------------------------------EEREDVEELLEEVESMGGKVVIVSTEHEPGER-LKALG 341 (352)
T ss_pred ------cccch-------------------------------hhHHHHHHHHHHHHHcCCeEEEEecCCcchHH-HHhcc
Confidence 43311 11122589999999999999999999999999 99999
Q ss_pred cEEEEeecccC
Q 013725 409 GIGGILRYQLD 419 (437)
Q Consensus 409 GIaAiLRy~~~ 419 (437)
|||||||||++
T Consensus 342 GiaaILRf~v~ 352 (352)
T COG1537 342 GIAAILRFPVP 352 (352)
T ss_pred CeEEEEEecCC
Confidence 99999999985
No 8
>KOG2869 consensus Meiotic cell division protein Pelota/DOM34 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.6e-47 Score=358.97 Aligned_cols=336 Identities=18% Similarity=0.259 Sum_probs=278.7
Q ss_pred CCCcceEEEEeCCCCChHHHHhhhh-hhhhhhhhhhhhhhhhhhhHhHHHHHHHhhcc------------cccCCCeEEE
Q 013725 28 GNGTSMISLIMPPRDQISRVTKMLG-DEFGTASNIKSRVNRQSVLAAITSAQQRLKLY------------NKVPPNGLVL 94 (437)
Q Consensus 28 g~~t~lvSlyip~~~~~~~v~~~l~-~e~~~a~nik~~~~r~~v~~al~~~~~rl~~~------------~~~~~~Gl~~ 94 (437)
-+|++.|++.....+++|+++|.+. .+-..|+.++ |+......|.-.+.+.++++. ..++..|+.+
T Consensus 10 rng~G~vtmvpEe~eDmw~~ynli~~gD~v~a~T~r-kvq~e~a~G~~~s~rv~~~L~i~VesidfD~~~~~L~~KGrti 88 (379)
T KOG2869|consen 10 RNGSGSVTMVPEESEDLWHLYNLIQVGDSVIASTIR-KVQKEEATGKTKSSRVLLKLKIKVESIDFDTKACVLRLKGRTI 88 (379)
T ss_pred cCCCceEEECcCchhHHHHHHhhccCCceeEEEEEE-EeeeccccCcccceEEEEEEEEEEEEeeccccccEEEEeeeee
Confidence 4566799999999999999999998 5566666665 333332223222222222221 1245688888
Q ss_pred EeccccCCCCCeeEEEEeecCCCcceeeeeeccCccchHHHHHhhccC--CcEEEEEEECCceEEEEEeCCeEEEEeEEe
Q 013725 95 YTGTVVTDDGKEKKVTIDFEPFKPINASLYLCDNKFHTEALNELLESD--DKFGFIVMDGNGTLFGTLSGNTREVLHKFT 172 (437)
Q Consensus 95 fa~~~~~~~G~~~~~tl~i~p~~~v~~~~~~~~~~~~l~~L~~~~~~~--~~~~vvvvd~~~A~i~~~~g~~~~~~~~~~ 172 (437)
..+..+ ..|.| ||++++|++|+++.|. .|+.+.++.|++|+++. ..+++|++++|-|.||+++...+...++++
T Consensus 89 ~eNe~V-k~GaY--HTidlel~r~FtL~K~-ewds~al~~l~~A~dp~~~ad~aaVvlqEGla~IcLvt~s~tilr~kIe 164 (379)
T KOG2869|consen 89 EENEYV-KMGAY--HTIDLELNRPFTLRKE-EWDSMALKLLKEACDPAPSADVAAVVLQEGLAHICLVTKSSTILRAKIE 164 (379)
T ss_pred eecccc-cccce--eEEEeccCCceEEEhh-hchHHHHHHHHHhhCcccccceeeeehhcCceeEEEechhHHHHHHhhh
Confidence 887665 57999 9999999999999997 79999999999999986 458899999999999999998887788999
Q ss_pred ecCCcccCCCCcchHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCccEEEEecChhcHHHhhhccCC-----C--h
Q 013725 173 VDLPKKHGRGGQSALRFARLRMEKRHNYVRKTAELATQFFINPATSQPNVSGLILAGSADFKTELSQSDMF-----D--P 245 (437)
Q Consensus 173 ~~vp~K~~~gG~s~~Rf~r~~ee~~~~f~~~Vae~l~~~f~~~~~~~~~~~~lilaGp~~~k~~f~~~~~l-----~--~ 245 (437)
..+|+|+ +|+-|+ .++..++||..|..++.++ +++..++++|||+|||.++.|.++... + +
T Consensus 165 ~siPrKr-~~~~s~------~e~~l~kfye~V~qA~~k~-----v~fd~vk~~vvASpgF~~~~~~d~~~q~A~~~~~k~ 232 (379)
T KOG2869|consen 165 VSIPRKR-KGDVSQ------HEEGLEKFYENVVQAILKH-----VNFDVVKCVVVASPGFVKDQFMDYLFQQAVKLDLKL 232 (379)
T ss_pred ccccccc-CcchhH------HHHHHHHHHHHHHHHHHHh-----cCcceEEEEEEcCCchhHHHHHHHHHHHHHHhchhh
Confidence 9999994 465666 6899999999999999999 668899999999999999999875211 1 1
Q ss_pred --hhhcceeEEEeCCCCCcccHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHhccCCCcEEEcHHHHHHHHHhCCccEE
Q 013725 246 --RLQAKILNVVDVSYGGENGFNQAIELSA--EILSNVKFIQEKRLIGKYFEEISQDTGKYVFGVDDTLKALELGAVEIL 321 (437)
Q Consensus 246 --~l~~~vi~~v~~s~~~~~gl~E~l~~~~--~~l~~~~~~~e~~ll~~f~~~~~~~~g~a~yG~~eV~~Al~~GaV~tL 321 (437)
..+.|+ ..++.|+|..++++|+|..+. ..|++++++.|.++|++|+..+++++.+||||+++|..|.+.||++||
T Consensus 233 il~nk~kf-~~~h~ssg~~hslnevL~dp~v~~~l~dtK~~~EvkalddF~~~l~~~~drA~yG~khV~~A~e~~AI~tL 311 (379)
T KOG2869|consen 233 ILENKSKF-PLVHASSGYKHSLNEVLKDPAVASKLQDTKAAKEVKALDDFYVMLSKDPDRACYGPKHVEKANEYGAIETL 311 (379)
T ss_pred hhhcccce-eEEecCCchHHHHHHHhcChHHHHHhhchhhHHHHHHHHHHHHHhccCccccccCHHHHHHHHhhcchhhe
Confidence 123344 678999999999999999965 899999999999999999999999999999999999999999999999
Q ss_pred EeccCccccceeeecCCCCceEEEecccccccccCCccCccccchhhhhhhccHHHHHHHHHHhcCCeEEEeCCCCchhh
Q 013725 322 IVWENLDINRYVLKNSATGEIVIKHLNRDQEADQSNFRDAATSAELEVQEKTSLLEWFANEYKQFGCTLEFVTNKSQEGS 401 (437)
Q Consensus 322 lV~d~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~~~~~~~~~~v~~l~~~a~~~ga~V~vvs~~~e~G~ 401 (437)
||+|+++ ||.+.. .+++ +..|++.++.+||+|.|+|+.|.+|+
T Consensus 312 LitD~lf------r~~DV~----------------------tRkk---------yv~lvesVk~~~gkv~Ifss~H~SGE 354 (379)
T KOG2869|consen 312 LITDELF------RSQDVA----------------------TRKK---------YVRLVESVKENNGKVFIFSSLHVSGE 354 (379)
T ss_pred ehhhhhc------ccccHH----------------------HHHH---------HHHHHHHHHhcCCcEEEEehhhccHH
Confidence 9999998 766321 1233 46899999999999999999999999
Q ss_pred hhhcccccEEEEeecccC
Q 013725 402 QFCRGFGGIGGILRYQLD 419 (437)
Q Consensus 402 q~l~~~GGIaAiLRy~~~ 419 (437)
| |..++|||||||||++
T Consensus 355 q-L~qltGiaAiLrfp~p 371 (379)
T KOG2869|consen 355 Q-LAQLTGIAAILRFPLP 371 (379)
T ss_pred H-HHhhcCeeEEEecCCC
Confidence 9 9999999999999998
No 9
>PF03465 eRF1_3: eRF1 domain 3; InterPro: IPR005142 This domain is found in the release factor eRF1 which terminates protein biosynthesis by recognizing stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known []. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site []. This domain is also found in other proteins which may also be involved in translation termination but this awaits experimental verification.; PDB: 3OBY_A 3E1Y_D 1DT9_A 2KTU_A 2KTV_A 3IR9_A 3E20_H 3OBW_A 3AGJ_F 3MCA_B ....
Probab=99.96 E-value=1.6e-29 Score=212.72 Aligned_cols=113 Identities=40% Similarity=0.687 Sum_probs=96.7
Q ss_pred HHHHHHHHHHHHHHhccCCCcEEEcHHHHHHHHHhCCccEEEeccCccccceeeecCCCCceEEEecccccccccCCccC
Q 013725 281 FIQEKRLIGKYFEEISQDTGKYVFGVDDTLKALELGAVEILIVWENLDINRYVLKNSATGEIVIKHLNRDQEADQSNFRD 360 (437)
Q Consensus 281 ~~~e~~ll~~f~~~~~~~~g~a~yG~~eV~~Al~~GaV~tLlV~d~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~c 360 (437)
+++|+++|++|++++.+++++++||+++|.+|+++|||+||||+|++...+...+|+ |
T Consensus 1 ~~~E~~~ve~f~~~l~k~~~~~~yG~~eV~~Al~~GaV~~LlI~d~l~~~~~~~r~~----------------------~ 58 (113)
T PF03465_consen 1 IIKEKKLVEEFFEELAKDPGLAVYGIEEVKKALEMGAVETLLISDDLFRSRDVERCK----------------------C 58 (113)
T ss_dssp HHHHHHHHHHHHHHHHTTCSSEEESHHHHHHHHHTT-EEEEEEEHHHHTESCHHHHH----------------------S
T ss_pred CHHHHHHHHHHHHHHhhCCCcEEECHHHHHHHHHhCCCcEEEEecccccccceeccc----------------------c
Confidence 468999999999999999999999999999999999999999999998655433332 3
Q ss_pred ccccchhhhhhhccHHHHHHHHHHhcCCeEEEeCCCCchhhhhhcccccEEEEeeccc
Q 013725 361 AATSAELEVQEKTSLLEWFANEYKQFGCTLEFVTNKSQEGSQFCRGFGGIGGILRYQL 418 (437)
Q Consensus 361 p~~~~~~~~~~~~~~v~~l~~~a~~~ga~V~vvs~~~e~G~q~l~~~GGIaAiLRy~~ 418 (437)
|.||.+++.++ ++++|++.|+++||+|+|||++|++|+||+++|||||||||||+
T Consensus 59 ~~~~~~~~~~~---~i~~l~~~a~~~g~~v~iis~~~e~G~~L~~~~gGIaaiLRy~i 113 (113)
T PF03465_consen 59 PECGGELEVVE---LIEELIELAEQSGAKVEIISSEHEEGEQLLKGFGGIAAILRYPI 113 (113)
T ss_dssp TTTHSEEEEEE---HHHHHHHHHHHTTSEEEEE-TTSHHHHHHHHCTTTEEEEESS--
T ss_pred ccccchhhhHH---HHHHHHHHHHHcCCEEEEEcCCCccHHHHHhcCCcEEEEEeccC
Confidence 67887765433 99999999999999999999999999996699999999999996
No 10
>PF03464 eRF1_2: eRF1 domain 2; InterPro: IPR005141 This domain is found in the release factor eRF1 which terminates protein biosynthesis by recognizing stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known []. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site []. This domain is also found in other proteins which may also be involved in translation termination ; PDB: 3AGK_A 2VGN_A 2VGM_A 3J16_A 3IZQ 3IR9_A 3OBW_A 3MCA_B 2QI2_A 3E1Y_D ....
Probab=99.90 E-value=1.5e-23 Score=182.17 Aligned_cols=129 Identities=31% Similarity=0.509 Sum_probs=113.9
Q ss_pred cEEEEEEECCceEEEEEeCCeEEEEeEEeecCCcccCCCCcchHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCcc
Q 013725 144 KFGFIVMDGNGTLFGTLSGNTREVLHKFTVDLPKKHGRGGQSALRFARLRMEKRHNYVRKTAELATQFFINPATSQPNVS 223 (437)
Q Consensus 144 ~~~vvvvd~~~A~i~~~~g~~~~~~~~~~~~vp~K~~~gG~s~~Rf~r~~ee~~~~f~~~Vae~l~~~f~~~~~~~~~~~ 223 (437)
.+++|+||+++|.||++++++++++.+++.++|+||..||||+.||+ |+++.++||++|++.+.++|+ .++.+++
T Consensus 1 ~v~~v~id~g~A~i~~l~~~~~~~~~~i~~~ip~K~~~Gg~s~~rf~--r~~~~~~f~~~i~~~l~~~f~---~~~~~~~ 75 (133)
T PF03464_consen 1 KVGIVVIDEGEANICLLRGYGTEILQRIESNIPGKHKKGGQSQRRFE--REKALEKFFKEIAEALKKYFL---VNFDDVK 75 (133)
T ss_dssp EEEEEEEETTEEEEEEEETTEEEEEEEEE-GHCCCSSTTCSHHHHHH--HHHHHHHHHHHHHHHHHHHCC---CHTTTCS
T ss_pred CEEEEEEeCCCEEEEEEcCCEEEEEEEEEecCCCccCCCCcchhhHH--HHHHHHHHHHHHHHHHHHHhh---hcccccc
Confidence 47899999999999999999999999999999999999999999999 899999999999999999976 3467999
Q ss_pred EEEEecChhcHHHhhhccCCChhhhc-ceeEEEeCCCCCcccHHHHHHH--HHHHHH
Q 013725 224 GLILAGSADFKTELSQSDMFDPRLQA-KILNVVDVSYGGENGFNQAIEL--SAEILS 277 (437)
Q Consensus 224 ~lilaGp~~~k~~f~~~~~l~~~l~~-~vi~~v~~s~~~~~gl~E~l~~--~~~~l~ 277 (437)
+|||||||++|+.|.++.+.+...++ +.+.++++|+++++|++|+|++ ++++|+
T Consensus 76 ~iIiaGPGf~k~~f~~~l~~~~~~~~~~~i~~~~~s~~~~~gl~Evl~~~~v~~~l~ 132 (133)
T PF03464_consen 76 CIIIAGPGFTKEEFYKYLKAEARRKDKKKIVVVDTSSGGESGLNEVLKRPEVQKILK 132 (133)
T ss_dssp EEEEEESTTHHHHHHHHHHHHHHHHTCCEEEEEE-SSSCHHHHHHHHHSHHHHHHHC
T ss_pred EEEEECCHHHHHHHHHHHHHhhHhhcCCEEEEEECCCCCHHHHHHHHHhhhHHHHhc
Confidence 99999999999999987655555555 5568999999999999999999 446554
No 11
>PF03463 eRF1_1: eRF1 domain 1; InterPro: IPR005140 This domain is found in the release factor eRF1 which terminates protein biosynthesis by recognizing stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known []. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site []. This domain is also found in other proteins for which the precise molecular function is unknown. Many of them are from Archaebacteria. These proteins may also be involved in translation termination but this awaits experimental verification.; PDB: 2VGN_A 2VGM_A 3J16_A 3IZQ 3AGK_A 3AGJ_B 3OBW_A 3E1Y_D 1DT9_A 2LLX_A ....
Probab=98.97 E-value=9.6e-13 Score=114.09 Aligned_cols=120 Identities=33% Similarity=0.476 Sum_probs=98.9
Q ss_pred hHHHHHHHHHHHHHHccCCCCcceEEEEeCCCCChHHHHhhhhhhhhhhhhhhhhhhhhhhhHhHHHHHHHhhcccccCC
Q 013725 10 NIEIWKIKKLIKALESARGNGTSMISLIMPPRDQISRVTKMLGDEFGTASNIKSRVNRQSVLAAITSAQQRLKLYNKVPP 89 (437)
Q Consensus 10 ~~~~~~~~~~l~~L~~~~g~~t~lvSlyip~~~~~~~v~~~l~~e~~~a~nik~~~~r~~v~~al~~~~~rl~~~~~~~~ 89 (437)
+++ |+.+..|+-+....++.|.+.+||.|++..++...+.+ .+ ++|++++.++..++.+|....+++++ .|.
T Consensus 7 ~~~-~~~~~~i~ll~e~~dDlw~L~~li~~gD~v~~~t~Rkv-~~---~~~~~~~~~~~~v~~~L~i~ve~v~~---~~~ 78 (132)
T PF03463_consen 7 DIE-KNGKGLIKLLPEEKDDLWHLYNLIIPGDEVISKTTRKV-QE---ASNIKGSKTRERVQIALTIKVEKVEF---DPE 78 (132)
T ss_dssp CHC-HHHHHEEEEETTSHHHHHHHHHHEETTTEEEECCHCHH-HH---CTCESSHHHHHCEEEEEEEEEEEEEE---ETT
T ss_pred hhc-cccCceEEEcccccCCcEEEEEEEECCCEEEEEEEEee-ee---cccccCCcceEEEEEEEEEEEEEeEe---cCC
Confidence 455 88888888888888899999999999998888888877 43 66888889999999988887777776 577
Q ss_pred CeEEEEeccccCC-----CCCeeEEEEeecCCCcceeeeeeccCccchHHHHHhhc
Q 013725 90 NGLVLYTGTVVTD-----DGKEKKVTIDFEPFKPINASLYLCDNKFHTEALNELLE 140 (437)
Q Consensus 90 ~Gl~~fa~~~~~~-----~G~~~~~tl~i~p~~~v~~~~~~~~~~~~l~~L~~~~~ 140 (437)
+|++.|+|.+... .|+| ||++++|++||+++|| +|+.++++.|.++++
T Consensus 79 ~~~Lri~G~i~~~~~~~~~G~~--hT~~i~~~~~~ti~K~-~wd~~~~~~l~ea~~ 131 (132)
T PF03463_consen 79 NGLLRISGKIVEENEDVKLGKY--HTLDIEPGRPFTIIKY-RWDSYFLDRLKEAMD 131 (132)
T ss_dssp TTEEEEEEEEEEGSCGGGTTSE--EEEEEETSSEEEEEEE-EEEHHHHHHHHHHTS
T ss_pred CCEEEEEeEEccCCCCCCcceE--EEEEEeCCCceEEEEe-cCCHHHHHHHHHHhc
Confidence 7777777776533 4788 9999999999999998 688888888888765
No 12
>PF10116 Host_attach: Protein required for attachment to host cells; InterPro: IPR019291 Members of this family of bacterial proteins are required for the attachment of the bacterium to host cells [, ].
Probab=97.31 E-value=0.00031 Score=61.24 Aligned_cols=109 Identities=17% Similarity=0.222 Sum_probs=75.9
Q ss_pred EEEEEECCceEEEEEeCCeE---EEEe------------EEeecCCcccCCC-Cc--chHHHHHHHHHHHHHHHHHHHHH
Q 013725 146 GFIVMDGNGTLFGTLSGNTR---EVLH------------KFTVDLPKKHGRG-GQ--SALRFARLRMEKRHNYVRKTAEL 207 (437)
Q Consensus 146 ~vvvvd~~~A~i~~~~g~~~---~~~~------------~~~~~vp~K~~~g-G~--s~~Rf~r~~ee~~~~f~~~Vae~ 207 (437)
+|||.|.+.|.|+...+... ..+. .+..+-||....+ |+ +........++..++|+++||+.
T Consensus 2 wVvVaD~~~Ar~f~~~~~~~~~~~~~~~~~~~~~~~~~~dl~~d~~Gr~~~~~g~~~~~~~~~~~~~~~~~~Fa~~vA~~ 81 (138)
T PF10116_consen 2 WVVVADGSRARIFENEGDESEPLLELEELDHPESRLKDRDLVSDRPGRFHDSAGQRGSMEERTDPKEEEEERFAREVADR 81 (138)
T ss_pred EEEEEecceeEEEEecCCCCCcchhhhhhcccccccchhhhccCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHH
Confidence 68999999999998877643 2122 1233444432221 11 22222345677789999999999
Q ss_pred HHHhhcCCCCCCCCccEEEEecChhcHHHhhhccCCChhhhcceeEEEeCCCCC
Q 013725 208 ATQFFINPATSQPNVSGLILAGSADFKTELSQSDMFDPRLQAKILNVVDVSYGG 261 (437)
Q Consensus 208 l~~~f~~~~~~~~~~~~lilaGp~~~k~~f~~~~~l~~~l~~~vi~~v~~s~~~ 261 (437)
|.+... ...++.|||++|..+...++ ..|++.++++|++.++-+...
T Consensus 82 L~~~~~-----~~~~~~LvlvA~p~~LG~LR--~~L~~~~~~~V~~ei~kDlt~ 128 (138)
T PF10116_consen 82 LEKARR-----AGKFDRLVLVAPPRFLGLLR--EHLSKAVRKRVVGEIDKDLTK 128 (138)
T ss_pred HHHHHH-----hCCCCeEEEEECHHHHHHHH--HHhCHHHHHHHHHHHhhhhhc
Confidence 999854 56899999999999999999 569999988886666655543
No 13
>PRK07714 hypothetical protein; Provisional
Probab=94.38 E-value=0.28 Score=40.17 Aligned_cols=75 Identities=16% Similarity=0.269 Sum_probs=51.1
Q ss_pred ccCCCcEEEcHHHHHHHHHhCCccEEEeccCccccceeeecCCCCceEEEecccccccccCCccCccccchhhhhhhccH
Q 013725 296 SQDTGKYVFGVDDTLKALELGAVEILIVWENLDINRYVLKNSATGEIVIKHLNRDQEADQSNFRDAATSAELEVQEKTSL 375 (437)
Q Consensus 296 ~~~~g~a~yG~~eV~~Al~~GaV~tLlV~d~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~~~~~~~~~~ 375 (437)
++..|+.++|.+.|.+|++.|.+..+|++.|.... .
T Consensus 13 a~raGk~v~G~~~v~~al~~g~~~lViiA~D~s~~--------------------------------------------~ 48 (100)
T PRK07714 13 ANRARKVISGEELVLKEVRSGKAKLVLLSEDASVN--------------------------------------------T 48 (100)
T ss_pred HHHhCCeeecHHHHHHHHHhCCceEEEEeCCCCHH--------------------------------------------H
Confidence 44458999999999999999999999998776411 1
Q ss_pred HHHHHHHHHhcCCeEEEeCCCCchhhhhhcccccEEEEe
Q 013725 376 LEWFANEYKQFGCTLEFVTNKSQEGSQFCRGFGGIGGIL 414 (437)
Q Consensus 376 v~~l~~~a~~~ga~V~vvs~~~e~G~q~l~~~GGIaAiL 414 (437)
...+...|...+..+..+.+..+-|.-+=+.+-.++||+
T Consensus 49 ~~ki~~~~~~~~vp~~~~~sk~eLG~a~Gk~~~~~vai~ 87 (100)
T PRK07714 49 TKKITDKCTYYNVPMRKVENRQQLGHAIGKDERVVVAVL 87 (100)
T ss_pred HHHHHHHHHhcCCCEEEeCCHHHHHHHhCCCcceEEEEe
Confidence 245566677777777777666666654322233355553
No 14
>PRK07283 hypothetical protein; Provisional
Probab=93.88 E-value=0.43 Score=38.96 Aligned_cols=34 Identities=18% Similarity=0.418 Sum_probs=29.3
Q ss_pred hccCCCcEEEcHHHHHHHHHhCCccEEEeccCcc
Q 013725 295 ISQDTGKYVFGVDDTLKALELGAVEILIVWENLD 328 (437)
Q Consensus 295 ~~~~~g~a~yG~~eV~~Al~~GaV~tLlV~d~l~ 328 (437)
+++..|+.+.|.+.|.+|++.|.+..++++.|..
T Consensus 12 lA~raGklv~G~~~v~~aik~gk~~lVi~A~Das 45 (98)
T PRK07283 12 LAQRAGRIISGEELVVKAIQSGQAKLVFLANDAG 45 (98)
T ss_pred HHHHhCCeeEcHHHHHHHHHcCCccEEEEeCCCC
Confidence 3445689999999999999999999999987764
No 15
>PRK13602 putative ribosomal protein L7Ae-like; Provisional
Probab=93.79 E-value=0.41 Score=37.78 Aligned_cols=60 Identities=27% Similarity=0.321 Sum_probs=49.8
Q ss_pred CCcEEEcHHHHHHHHHhCCccEEEeccCccccceeeecCCCCceEEEecccccccccCCccCccccchhhhhhhccHHHH
Q 013725 299 TGKYVFGVDDTLKALELGAVEILIVWENLDINRYVLKNSATGEIVIKHLNRDQEADQSNFRDAATSAELEVQEKTSLLEW 378 (437)
Q Consensus 299 ~g~a~yG~~eV~~Al~~GaV~tLlV~d~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~~~~~~~~~~v~~ 378 (437)
.|+.+.|.++|++|++.|.+..++|..|.. + +....
T Consensus 9 agkl~~G~~~v~kai~~gkaklViiA~D~~------------~--------------------------------~~~~~ 44 (82)
T PRK13602 9 AKSIVIGTKQTVKALKRGSVKEVVVAEDAD------------P--------------------------------RLTEK 44 (82)
T ss_pred cCCEEEcHHHHHHHHHcCCeeEEEEECCCC------------H--------------------------------HHHHH
Confidence 378999999999999999999999987654 0 12357
Q ss_pred HHHHHHhcCCeEEEeCCCCchhhh
Q 013725 379 FANEYKQFGCTLEFVTNKSQEGSQ 402 (437)
Q Consensus 379 l~~~a~~~ga~V~vvs~~~e~G~q 402 (437)
+...+...+-.+..+.+..+-|..
T Consensus 45 i~~~c~~~~Vp~~~~~s~~eLG~a 68 (82)
T PRK13602 45 VEALANEKGVPVSKVDSMKKLGKA 68 (82)
T ss_pred HHHHHHHcCCCEEEECCHHHHHHH
Confidence 788999999999999988777766
No 16
>PRK13600 putative ribosomal protein L7Ae-like; Provisional
Probab=93.42 E-value=0.37 Score=38.21 Aligned_cols=57 Identities=28% Similarity=0.447 Sum_probs=49.0
Q ss_pred EEEcHHHHHHHHHhCCccEEEeccCccccceeeecCCCCceEEEecccccccccCCccCccccchhhhhhhccHHHHHHH
Q 013725 302 YVFGVDDTLKALELGAVEILIVWENLDINRYVLKNSATGEIVIKHLNRDQEADQSNFRDAATSAELEVQEKTSLLEWFAN 381 (437)
Q Consensus 302 a~yG~~eV~~Al~~GaV~tLlV~d~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~~~~~~~~~~v~~l~~ 381 (437)
.++|.++|.+|++.|.+..++|..|.. ..++..|..
T Consensus 14 ~vvG~kqt~Kai~kg~~~~v~iA~Da~--------------------------------------------~~vv~~l~~ 49 (84)
T PRK13600 14 FVVGLKETLKALKKDQVTSLIIAEDVE--------------------------------------------VYLMTRVLS 49 (84)
T ss_pred ceeeHHHHHHHHhcCCceEEEEeCCCC--------------------------------------------HHHHHHHHH
Confidence 489999999999999999999987764 112568889
Q ss_pred HHHhcCCeEEEeCCCCchhhh
Q 013725 382 EYKQFGCTLEFVTNKSQEGSQ 402 (437)
Q Consensus 382 ~a~~~ga~V~vvs~~~e~G~q 402 (437)
.|++.|-.+.+|++..+-|.-
T Consensus 50 lceek~Ip~v~V~s~~~LGkA 70 (84)
T PRK13600 50 QINQKNIPVSFFKSKHALGKH 70 (84)
T ss_pred HHHHcCCCEEEECCHHHHHHH
Confidence 999999999999998887765
No 17
>PF08032 SpoU_sub_bind: RNA 2'-O ribose methyltransferase substrate binding; InterPro: IPR013123 Most cellular RNAs undergo a number of post-transcriptional nucleoside modifications. While the biological role of many of these modifications is unknown, some have been shown to be necessary for cell growth or for resistance to antibiotics [, ]. One of the most common modifications is 2'O-ribose methylation catalysed by the RNA 2'O-ribose methyltransferases, a large enzyme family that transfer a methyl group from S-adenosyl-L-methionine (AdoMet) to the 2'-OH group of the backbone ribose []. This entry represents a substrate-binding domain found in a variety of bacterial and mitochondrial RNA 2'-O ribose methyltransferases. These include the bacterial enzyme RlmB, which specifically methylates the conserved nucleotide guanosine 2251 in 23S RNA, and PET56, which specifically methylates the equivalent guanosine in mitochondrial 21S RNA [, ]. This domain forms a four-stranded mixed beta sheet similar to that found in other RNA binding enzymes []. It shows considerable conformational flexibility which is thought to be important for its ability to bind RNA.; GO: 0008168 methyltransferase activity; PDB: 1GZ0_D 1IPA_A.
Probab=92.75 E-value=0.28 Score=37.60 Aligned_cols=69 Identities=17% Similarity=0.219 Sum_probs=47.0
Q ss_pred EEEcHHHHHHHHHhCC-ccEEEeccCccccceeeecCCCCceEEEecccccccccCCccCccccchhhhhhhccHHHHHH
Q 013725 302 YVFGVDDTLKALELGA-VEILIVWENLDINRYVLKNSATGEIVIKHLNRDQEADQSNFRDAATSAELEVQEKTSLLEWFA 380 (437)
Q Consensus 302 a~yG~~eV~~Al~~Ga-V~tLlV~d~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~~~~~~~~~~v~~l~ 380 (437)
.+||...|.+||+.|. +..|+++++.. .+ . +..++
T Consensus 1 lieG~~~V~eaL~~~~~i~~l~~~~~~~-------~~----------------------------~---------~~~i~ 36 (76)
T PF08032_consen 1 LIEGRHAVEEALKSGPRIKKLFVTEEKA-------DK----------------------------R---------IKEIL 36 (76)
T ss_dssp EEESHHHHHHHHHCTGGEEEEEEETT----------C----------------------------C---------THHHH
T ss_pred CEEEHHHHHHHHcCCCCccEEEEEcCcc-------ch----------------------------h---------HHHHH
Confidence 3799999999999987 99999988732 11 1 25778
Q ss_pred HHHHhcCCeEEEeCCCCchhhhh--hcccccEEEEeec
Q 013725 381 NEYKQFGCTLEFVTNKSQEGSQF--CRGFGGIGGILRY 416 (437)
Q Consensus 381 ~~a~~~ga~V~vvs~~~e~G~q~--l~~~GGIaAiLRy 416 (437)
+.+...|..|.+++..-- .++ -....||+|..+-
T Consensus 37 ~~~~~~~i~v~~v~~~~l--~~ls~~~~hQGv~a~v~~ 72 (76)
T PF08032_consen 37 KLAKKKGIPVYEVSKKVL--DKLSDTENHQGVVAVVKP 72 (76)
T ss_dssp HHHHHCT-EEEEE-HHHH--HHCTTTSS-TTEEEEEE-
T ss_pred HHHHHcCCeEEEeCHHHH--HHHcCCCCCCeEEEEEeC
Confidence 999999999999986321 111 2445699998763
No 18
>PRK04175 rpl7ae 50S ribosomal protein L7Ae; Validated
Probab=91.39 E-value=1.5 Score=37.38 Aligned_cols=62 Identities=24% Similarity=0.392 Sum_probs=49.2
Q ss_pred CCCcEEEcHHHHHHHHHhCCccEEEeccCccccceeeecCCCCceEEEecccccccccCCccCccccchhhhhhhccHHH
Q 013725 298 DTGKYVFGVDDTLKALELGAVEILIVWENLDINRYVLKNSATGEIVIKHLNRDQEADQSNFRDAATSAELEVQEKTSLLE 377 (437)
Q Consensus 298 ~~g~a~yG~~eV~~Al~~GaV~tLlV~d~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~~~~~~~~~~v~ 377 (437)
.+|..+.|.++|.+|++.|.+..++|+.|.. + .++..
T Consensus 27 ragklv~G~~~v~kaikkgkakLVilA~D~s--------~-----------------------------------~~i~~ 63 (122)
T PRK04175 27 DTGKIKKGTNETTKAVERGIAKLVVIAEDVD--------P-----------------------------------EEIVA 63 (122)
T ss_pred HcCCEeEcHHHHHHHHHcCCccEEEEeCCCC--------h-----------------------------------HHHHH
Confidence 3588999999999999999999999988764 1 01135
Q ss_pred HHHHHHHhcCCeEEEeCCCCchhhh
Q 013725 378 WFANEYKQFGCTLEFVTNKSQEGSQ 402 (437)
Q Consensus 378 ~l~~~a~~~ga~V~vvs~~~e~G~q 402 (437)
.+...|+..|-.+.++.+..+-|..
T Consensus 64 ~~~~lc~~~~Vp~~~~~tk~eLG~a 88 (122)
T PRK04175 64 HLPLLCEEKKIPYVYVPSKKDLGKA 88 (122)
T ss_pred HHHHHHHHcCCCEEEECCHHHHHHH
Confidence 6778888888888888887777765
No 19
>TIGR03677 rpl7ae 50S ribosomal protein L7Ae. Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, box H/ACA, box C/D and box C'/D' sRNAs. Interacts with protein L15e.
Probab=91.32 E-value=1.4 Score=37.16 Aligned_cols=75 Identities=19% Similarity=0.341 Sum_probs=54.2
Q ss_pred CCCcEEEcHHHHHHHHHhCCccEEEeccCccccceeeecCCCCceEEEecccccccccCCccCccccchhhhhhhccHHH
Q 013725 298 DTGKYVFGVDDTLKALELGAVEILIVWENLDINRYVLKNSATGEIVIKHLNRDQEADQSNFRDAATSAELEVQEKTSLLE 377 (437)
Q Consensus 298 ~~g~a~yG~~eV~~Al~~GaV~tLlV~d~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~~~~~~~~~~v~ 377 (437)
.+|..+.|.++|.+|++.|.+..++|+.|.. + .+...
T Consensus 23 ragkl~~G~~~v~kaikkgka~LVilA~D~s--------~-----------------------------------~~~~~ 59 (117)
T TIGR03677 23 ETGKIKKGTNEVTKAVERGIAKLVVIAEDVE--------P-----------------------------------PEIVA 59 (117)
T ss_pred HcCCEeEcHHHHHHHHHcCCccEEEEeCCCC--------c-----------------------------------HHHHH
Confidence 4588999999999999999999999988764 1 01135
Q ss_pred HHHHHHHhcCCeEEEeCCCCchhhhhhccc-ccEEEEee
Q 013725 378 WFANEYKQFGCTLEFVTNKSQEGSQFCRGF-GGIGGILR 415 (437)
Q Consensus 378 ~l~~~a~~~ga~V~vvs~~~e~G~q~l~~~-GGIaAiLR 415 (437)
.+...|+..+-.+.++.+..+-|..+-+.. =.+.||+-
T Consensus 60 ~i~~lc~~~~Ip~~~~~sk~eLG~a~Gk~~~~svvaI~d 98 (117)
T TIGR03677 60 HLPALCEEKGIPYVYVKKKEDLGAAAGLEVGAASAAIVD 98 (117)
T ss_pred HHHHHHHHcCCCEEEeCCHHHHHHHhCCCCCeEEEEEEc
Confidence 667888888888888888777776522211 23555554
No 20
>PRK06683 hypothetical protein; Provisional
Probab=91.26 E-value=1.4 Score=34.75 Aligned_cols=61 Identities=21% Similarity=0.253 Sum_probs=49.9
Q ss_pred CCCcEEEcHHHHHHHHHhCCccEEEeccCccccceeeecCCCCceEEEecccccccccCCccCccccchhhhhhhccHHH
Q 013725 298 DTGKYVFGVDDTLKALELGAVEILIVWENLDINRYVLKNSATGEIVIKHLNRDQEADQSNFRDAATSAELEVQEKTSLLE 377 (437)
Q Consensus 298 ~~g~a~yG~~eV~~Al~~GaV~tLlV~d~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~~~~~~~~~~v~ 377 (437)
..|+.+.|.+.|++|++.|.+..++|..|.. +++..
T Consensus 8 ~agk~v~G~~~v~kaik~gkaklViiA~Da~--------------------------------------------~~~~~ 43 (82)
T PRK06683 8 NAENVVVGHKRTLEAIKNGIVKEVVIAEDAD--------------------------------------------MRLTH 43 (82)
T ss_pred hCCCEEEcHHHHHHHHHcCCeeEEEEECCCC--------------------------------------------HHHHH
Confidence 3588999999999999999999999987654 11235
Q ss_pred HHHHHHHhcCCeEEEeCCCCchhhh
Q 013725 378 WFANEYKQFGCTLEFVTNKSQEGSQ 402 (437)
Q Consensus 378 ~l~~~a~~~ga~V~vvs~~~e~G~q 402 (437)
.+.+.+..++-.+..+.+..+-|.-
T Consensus 44 ~i~~~~~~~~Vpv~~~~t~~eLG~A 68 (82)
T PRK06683 44 VIIRTALQHNIPITKVESVRKLGKV 68 (82)
T ss_pred HHHHHHHhcCCCEEEECCHHHHHHH
Confidence 7789999999999999987776654
No 21
>PRK01018 50S ribosomal protein L30e; Reviewed
Probab=90.94 E-value=1.9 Score=35.27 Aligned_cols=60 Identities=27% Similarity=0.300 Sum_probs=46.8
Q ss_pred CCcEEEcHHHHHHHHHhCCccEEEeccCccccceeeecCCCCceEEEecccccccccCCccCccccchhhhhhhccHHHH
Q 013725 299 TGKYVFGVDDTLKALELGAVEILIVWENLDINRYVLKNSATGEIVIKHLNRDQEADQSNFRDAATSAELEVQEKTSLLEW 378 (437)
Q Consensus 299 ~g~a~yG~~eV~~Al~~GaV~tLlV~d~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~~~~~~~~~~v~~ 378 (437)
.|..+.|.++|++|++.|.+..++|++|... +....
T Consensus 14 agkl~~G~~~v~kai~~gkaklViiA~D~~~--------------------------------------------~~~~~ 49 (99)
T PRK01018 14 TGKVILGSKRTIKAIKLGKAKLVIVASNCPK--------------------------------------------DIKED 49 (99)
T ss_pred cCCEEEcHHHHHHHHHcCCceEEEEeCCCCH--------------------------------------------HHHHH
Confidence 4889999999999999999999999877530 11356
Q ss_pred HHHHHHhcCCeEEEe-CCCCchhhh
Q 013725 379 FANEYKQFGCTLEFV-TNKSQEGSQ 402 (437)
Q Consensus 379 l~~~a~~~ga~V~vv-s~~~e~G~q 402 (437)
+...|...+..+..+ .+..+-|..
T Consensus 50 i~~~c~~~~Ip~~~~~~tk~eLG~a 74 (99)
T PRK01018 50 IEYYAKLSGIPVYEYEGSSVELGTL 74 (99)
T ss_pred HHHHHHHcCCCEEEECCCHHHHHHH
Confidence 678888888888666 476677765
No 22
>PTZ00106 60S ribosomal protein L30; Provisional
Probab=90.89 E-value=1.6 Score=36.31 Aligned_cols=40 Identities=33% Similarity=0.521 Sum_probs=31.9
Q ss_pred HHHHHHHhccCCCcEEEcHHHHHHHHHhCCccEEEeccCcc
Q 013725 288 IGKYFEEISQDTGKYVFGVDDTLKALELGAVEILIVWENLD 328 (437)
Q Consensus 288 l~~f~~~~~~~~g~a~yG~~eV~~Al~~GaV~tLlV~d~l~ 328 (437)
++.++.. +...|+.+.|.+.|++|++.|.+..++|+.|..
T Consensus 13 i~~~Lgl-a~raGKlv~G~~~vlkalk~gkaklViiA~D~~ 52 (108)
T PTZ00106 13 INSKLQL-VMKSGKYTLGTKSTLKALRNGKAKLVIISNNCP 52 (108)
T ss_pred HHHHHHH-HHHhCCeeecHHHHHHHHHcCCeeEEEEeCCCC
Confidence 4444443 334599999999999999999999999987764
No 23
>PRK05583 ribosomal protein L7Ae family protein; Provisional
Probab=90.77 E-value=1.6 Score=36.11 Aligned_cols=33 Identities=18% Similarity=0.377 Sum_probs=28.8
Q ss_pred ccCCCcEEEcHHHHHHHHHhCCccEEEeccCcc
Q 013725 296 SQDTGKYVFGVDDTLKALELGAVEILIVWENLD 328 (437)
Q Consensus 296 ~~~~g~a~yG~~eV~~Al~~GaV~tLlV~d~l~ 328 (437)
++..|+.++|.+.|.+|++.|.+..||+++|..
T Consensus 12 A~rAGklv~G~~~v~~aik~gk~~lVI~A~D~s 44 (104)
T PRK05583 12 TKKAGKLLEGYNKCEEAIKKKKVYLIIISNDIS 44 (104)
T ss_pred HHHhCCeeecHHHHHHHHHcCCceEEEEeCCCC
Confidence 445689999999999999999999999987764
No 24
>COG1358 RPL8A Ribosomal protein HS6-type (S12/L30/L7a) [Translation, ribosomal structure and biogenesis]
Probab=90.73 E-value=0.84 Score=38.50 Aligned_cols=62 Identities=19% Similarity=0.364 Sum_probs=50.8
Q ss_pred CCCcEEEcHHHHHHHHHhCCccEEEeccCccccceeeecCCCCceEEEecccccccccCCccCccccchhhhhhhccHHH
Q 013725 298 DTGKYVFGVDDTLKALELGAVEILIVWENLDINRYVLKNSATGEIVIKHLNRDQEADQSNFRDAATSAELEVQEKTSLLE 377 (437)
Q Consensus 298 ~~g~a~yG~~eV~~Al~~GaV~tLlV~d~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~~~~~~~~~~v~ 377 (437)
..+...+|.++|.+|++.|.+..++|++|.. +.+++.
T Consensus 24 ~~~ki~~G~~e~~Kai~~g~a~LVviA~Dv~-------------------------------------------P~~~~~ 60 (116)
T COG1358 24 RAGKLKKGTNEVTKAIERGKAKLVVIAEDVS-------------------------------------------PEELVK 60 (116)
T ss_pred hcCCchhhHHHHHHHHHcCCCcEEEEecCCC-------------------------------------------HHHHHH
Confidence 3478999999999999999999999987764 122345
Q ss_pred HHHHHHHhcCCeEEEeCCCCchhhh
Q 013725 378 WFANEYKQFGCTLEFVTNKSQEGSQ 402 (437)
Q Consensus 378 ~l~~~a~~~ga~V~vvs~~~e~G~q 402 (437)
.|-..+...+..+.+|.+..+-|..
T Consensus 61 ~l~~lc~~~~vpyv~V~sk~~LG~a 85 (116)
T COG1358 61 HLPALCEEKNVPYVYVGSKKELGKA 85 (116)
T ss_pred HHHHHHHhcCCCEEEeCCHHHHHHH
Confidence 7778888999999999998877764
No 25
>PRK09190 hypothetical protein; Provisional
Probab=90.02 E-value=2.8 Score=39.50 Aligned_cols=42 Identities=21% Similarity=0.305 Sum_probs=33.6
Q ss_pred HHHHHHHHHHhccCCCcEEEcHHHHHHHHHhCCccEEEeccCcc
Q 013725 285 KRLIGKYFEEISQDTGKYVFGVDDTLKALELGAVEILIVWENLD 328 (437)
Q Consensus 285 ~~ll~~f~~~~~~~~g~a~yG~~eV~~Al~~GaV~tLlV~d~l~ 328 (437)
+++++-+ .+++..|..++|.+.|.+|++.|.+..||++.|..
T Consensus 97 ~ril~lL--GLArRAGklVsG~~~V~~alk~gk~~Lvi~A~DaS 138 (220)
T PRK09190 97 RRALDAL--GLARKAGQVVSGFEKVDAALRSGEAAALIHASDGA 138 (220)
T ss_pred HHHHHHH--HHHhhhCCEeecHHHHHHHHHcCCceEEEEeccCC
Confidence 4455444 34555699999999999999999999999988875
No 26
>PF01248 Ribosomal_L7Ae: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; InterPro: IPR004038 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 [, ]. This family includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, ribosomal protein L30 from eukaryotes and archaebacteria, Gadd45 and MyD118 [].; PDB: 2CZW_A 3V7E_B 2QEX_F 1YJ9_F 1VQ8_F 1YJN_F 3I56_F 1VQ6_F 2OTJ_F 1YIJ_F ....
Probab=88.48 E-value=2.9 Score=33.49 Aligned_cols=62 Identities=24% Similarity=0.410 Sum_probs=49.7
Q ss_pred CCcEEEcHHHHHHHHHhCCccEEEeccCccccceeeecCCCCceEEEecccccccccCCccCccccchhhhhhhccHHHH
Q 013725 299 TGKYVFGVDDTLKALELGAVEILIVWENLDINRYVLKNSATGEIVIKHLNRDQEADQSNFRDAATSAELEVQEKTSLLEW 378 (437)
Q Consensus 299 ~g~a~yG~~eV~~Al~~GaV~tLlV~d~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~~~~~~~~~~v~~ 378 (437)
.++.++|..+|.++++.|.+..++++.|.. + . .....
T Consensus 13 ~~~lv~G~~~v~k~l~~~~~~lvilA~d~~--------~----------------------------~-------~~~~~ 49 (95)
T PF01248_consen 13 AGRLVKGIKEVLKALKKGKAKLVILAEDCS--------P----------------------------D-------SIKKH 49 (95)
T ss_dssp HSEEEESHHHHHHHHHTTCESEEEEETTSS--------S----------------------------G-------HHHHH
T ss_pred cCCEEEchHHHHHHHHcCCCcEEEEcCCCC--------h----------------------------h-------hhccc
Confidence 378999999999999999999999987764 1 0 00124
Q ss_pred HHHHHHhcCCeEEEeCCCCchhhhh
Q 013725 379 FANEYKQFGCTLEFVTNKSQEGSQF 403 (437)
Q Consensus 379 l~~~a~~~ga~V~vvs~~~e~G~q~ 403 (437)
+...+.+.+..+.++++..+-|..+
T Consensus 50 l~~~c~~~~Ip~~~~~s~~eLG~~~ 74 (95)
T PF01248_consen 50 LPALCEEKNIPYVFVPSKEELGRAC 74 (95)
T ss_dssp HHHHHHHTTEEEEEESHHHHHHHHT
T ss_pred chhheeccceeEEEECCHHHHHHHH
Confidence 7788889999999999878888763
No 27
>PRK13601 putative L7Ae-like ribosomal protein; Provisional
Probab=87.98 E-value=3 Score=32.92 Aligned_cols=60 Identities=15% Similarity=0.191 Sum_probs=49.0
Q ss_pred CCcEEEcHHHHHHHHHhCCccEEEeccCccccceeeecCCCCceEEEecccccccccCCccCccccchhhhhhhccHHHH
Q 013725 299 TGKYVFGVDDTLKALELGAVEILIVWENLDINRYVLKNSATGEIVIKHLNRDQEADQSNFRDAATSAELEVQEKTSLLEW 378 (437)
Q Consensus 299 ~g~a~yG~~eV~~Al~~GaV~tLlV~d~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~~~~~~~~~~v~~ 378 (437)
.|+.+.|.++|++|++.|.+..++|..|.. +++...
T Consensus 6 ~GKlv~G~~~vlkaIk~gkakLViiA~Da~--------------------------------------------~~~~k~ 41 (82)
T PRK13601 6 PSKRVVGAKQTLKAITNCNVLQVYIAKDAE--------------------------------------------EHVTKK 41 (82)
T ss_pred CccEEEchHHHHHHHHcCCeeEEEEeCCCC--------------------------------------------HHHHHH
Confidence 378999999999999999999999987653 112467
Q ss_pred HHHHHHhcCCeEEEeCCCCchhhh
Q 013725 379 FANEYKQFGCTLEFVTNKSQEGSQ 402 (437)
Q Consensus 379 l~~~a~~~ga~V~vvs~~~e~G~q 402 (437)
+.+.+..++-.+.++.+..+-|.-
T Consensus 42 i~~~c~~~~Vpv~~~~t~~eLG~A 65 (82)
T PRK13601 42 IKELCEEKSIKIVYIDTMKELGVM 65 (82)
T ss_pred HHHHHHhCCCCEEEeCCHHHHHHH
Confidence 788999999999888887777765
No 28
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=82.34 E-value=1.1 Score=40.21 Aligned_cols=25 Identities=12% Similarity=-0.104 Sum_probs=17.8
Q ss_pred eeecCCCCceEEEecccccccccCCccCccccch
Q 013725 333 VLKNSATGEIVIKHLNRDQEADQSNFRDAATSAE 366 (437)
Q Consensus 333 ~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~ 366 (437)
+|+|+-||+... ......||.||.+
T Consensus 134 ~~vC~vCGy~~~---------ge~P~~CPiCga~ 158 (166)
T COG1592 134 VWVCPVCGYTHE---------GEAPEVCPICGAP 158 (166)
T ss_pred EEEcCCCCCccc---------CCCCCcCCCCCCh
Confidence 489999998432 1224689999965
No 29
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=77.95 E-value=0.85 Score=31.62 Aligned_cols=31 Identities=13% Similarity=0.013 Sum_probs=19.7
Q ss_pred eeecCCCCceEEEecccccccccCCccCccccchhhh
Q 013725 333 VLKNSATGEIVIKHLNRDQEADQSNFRDAATSAELEV 369 (437)
Q Consensus 333 ~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~~~~ 369 (437)
.++|++||....+ .+. .....||.||.++..
T Consensus 3 ~y~C~~CG~~~~~--~~~----~~~~~Cp~CG~~~~~ 33 (46)
T PRK00398 3 EYKCARCGREVEL--DEY----GTGVRCPYCGYRILF 33 (46)
T ss_pred EEECCCCCCEEEE--CCC----CCceECCCCCCeEEE
Confidence 3599999974321 111 126789999988543
No 30
>COG2433 Uncharacterized conserved protein [Function unknown]
Probab=77.58 E-value=8.3 Score=41.18 Aligned_cols=33 Identities=27% Similarity=0.271 Sum_probs=28.1
Q ss_pred cCCCCcchHHHHHHHHHHHHHHHHHHHHHHHHh
Q 013725 179 HGRGGQSALRFARLRMEKRHNYVRKTAELATQF 211 (437)
Q Consensus 179 ~~~gG~s~~Rf~r~~ee~~~~f~~~Vae~l~~~ 211 (437)
.++|||||.||.|..-.++.+-.++|-+.+.+.
T Consensus 148 ~g~GGwSq~RY~R~vh~av~~~~reIee~L~~a 180 (652)
T COG2433 148 LGPGGWSQNRYRRRVHGAVKRVVREIEEKLDEA 180 (652)
T ss_pred CCCCCccHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 456899999999999888888888888888765
No 31
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=76.52 E-value=1.9 Score=38.47 Aligned_cols=45 Identities=13% Similarity=0.100 Sum_probs=29.1
Q ss_pred eecCCCCceEEEecccccccccCCccCccccchhhhhhhccHHHHHHHHH
Q 013725 334 LKNSATGEIVIKHLNRDQEADQSNFRDAATSAELEVQEKTSLLEWFANEY 383 (437)
Q Consensus 334 ~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~~~~~~~~~~v~~l~~~a 383 (437)
+.||+|+.. ..+. + +-...+.||.||+.++..+...++..|-+..
T Consensus 110 Y~Cp~c~~r-~tf~--e--A~~~~F~Cp~Cg~~L~~~dn~~~i~~l~~~i 154 (158)
T TIGR00373 110 FICPNMCVR-FTFN--E--AMELNFTCPRCGAMLDYLDNSEAIEKLEEQI 154 (158)
T ss_pred EECCCCCcE-eeHH--H--HHHcCCcCCCCCCEeeeccCHHHHHHHHHHH
Confidence 489999741 1111 1 1134689999999987777777776665443
No 32
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=75.82 E-value=2.3 Score=38.72 Aligned_cols=46 Identities=13% Similarity=0.081 Sum_probs=28.8
Q ss_pred eeecCCCCceEEEecccccccccCCccCccccchhhhhhhccHHHHHHHHH
Q 013725 333 VLKNSATGEIVIKHLNRDQEADQSNFRDAATSAELEVQEKTSLLEWFANEY 383 (437)
Q Consensus 333 ~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~~~~~~~~~~v~~l~~~a 383 (437)
-+.||+|+. .+.+.. +-...+.||.||+.+...+..+.+..|-+..
T Consensus 117 ~Y~Cp~C~~-rytf~e----A~~~~F~Cp~Cg~~L~~~dn~~~~~~l~~~I 162 (178)
T PRK06266 117 FFFCPNCHI-RFTFDE----AMEYGFRCPQCGEMLEEYDNSELIKELKEQI 162 (178)
T ss_pred EEECCCCCc-EEeHHH----HhhcCCcCCCCCCCCeecccHHHHHHHHHHH
Confidence 358999974 221111 1234789999999987766666665554433
No 33
>COG1911 RPL30 Ribosomal protein L30E [Translation, ribosomal structure and biogenesis]
Probab=74.47 E-value=30 Score=28.05 Aligned_cols=30 Identities=37% Similarity=0.672 Sum_probs=26.8
Q ss_pred CCCcEEEcHHHHHHHHHhCCccEEEeccCc
Q 013725 298 DTGKYVFGVDDTLKALELGAVEILIVWENL 327 (437)
Q Consensus 298 ~~g~a~yG~~eV~~Al~~GaV~tLlV~d~l 327 (437)
.+|.++.|.+.+.+++.+|....++|..+.
T Consensus 16 kTGkvilG~k~tiK~lk~gkaKliiiAsN~ 45 (100)
T COG1911 16 KTGKVILGSKRTIKSLKLGKAKLIIIASNC 45 (100)
T ss_pred hcCCEEEehHHHHHHHHcCCCcEEEEecCC
Confidence 468999999999999999999999997643
No 34
>PTZ00222 60S ribosomal protein L7a; Provisional
Probab=70.33 E-value=49 Score=31.81 Aligned_cols=72 Identities=18% Similarity=0.302 Sum_probs=53.2
Q ss_pred cEEEcHHHHHHHHHhCCccEEEeccCccccceeeecCCCCceEEEecccccccccCCccCccccchhhhhhhccHHHHHH
Q 013725 301 KYVFGVDDTLKALELGAVEILIVWENLDINRYVLKNSATGEIVIKHLNRDQEADQSNFRDAATSAELEVQEKTSLLEWFA 380 (437)
Q Consensus 301 ~a~yG~~eV~~Al~~GaV~tLlV~d~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~~~~~~~~~~v~~l~ 380 (437)
..++|..+|..+++.|.+..+||..|.. + ..++.+|.
T Consensus 132 ~LvsG~n~VtkaIekkKAkLVIIA~DVs--------P-----------------------------------ie~vk~Lp 168 (263)
T PTZ00222 132 AVVTGLQEVTRAIEKKQARMVVIANNVD--------P-----------------------------------VELVLWMP 168 (263)
T ss_pred eeccCHHHHHHHHHcCCceEEEEeCCCC--------H-----------------------------------HHHHHHHH
Confidence 3779999999999999999999988764 1 11235678
Q ss_pred HHHHhcCCeEEEeCCCCchhhhhhcccccEEEEee
Q 013725 381 NEYKQFGCTLEFVTNKSQEGSQFCRGFGGIGGILR 415 (437)
Q Consensus 381 ~~a~~~ga~V~vvs~~~e~G~q~l~~~GGIaAiLR 415 (437)
..|..+|.-..+|.+..+-|.-+=+.--.+.||.-
T Consensus 169 aLCrk~~VPY~iVktKaeLG~AIGkKtravVAItD 203 (263)
T PTZ00222 169 NLCRANKIPYAIVKDMARLGDAIGRKTATCVAITD 203 (263)
T ss_pred HHHHhcCCCEEEECCHHHHHHHHCCCCCeEEEEee
Confidence 88999999999999888877652111234556653
No 35
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS 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=69.90 E-value=4.6 Score=26.78 Aligned_cols=33 Identities=9% Similarity=0.057 Sum_probs=19.5
Q ss_pred ceeeecCCCCceEEEecccccccccCCccCccccch
Q 013725 331 RYVLKNSATGEIVIKHLNRDQEADQSNFRDAATSAE 366 (437)
Q Consensus 331 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~ 366 (437)
.+.++|+.||..-... ... .......||.||.+
T Consensus 3 ~Y~y~C~~Cg~~fe~~-~~~--~~~~~~~CP~Cg~~ 35 (41)
T smart00834 3 IYEYRCEDCGHTFEVL-QKI--SDDPLATCPECGGD 35 (41)
T ss_pred CEEEEcCCCCCEEEEE-Eec--CCCCCCCCCCCCCc
Confidence 4567999999732211 111 11235679999985
No 36
>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=67.67 E-value=7.6 Score=26.33 Aligned_cols=32 Identities=6% Similarity=0.008 Sum_probs=19.4
Q ss_pred ceeeecCCCCceEEEecccccccccCCccCccccc
Q 013725 331 RYVLKNSATGEIVIKHLNRDQEADQSNFRDAATSA 365 (437)
Q Consensus 331 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~ 365 (437)
.|.++|++||..-... .+. .+.....||.||.
T Consensus 3 ~Yey~C~~Cg~~fe~~-~~~--~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 3 IYEYRCEECGHEFEVL-QSI--SEDDPVPCPECGS 34 (42)
T ss_pred CEEEEeCCCCCEEEEE-EEc--CCCCCCcCCCCCC
Confidence 4567999999532221 111 1134568999998
No 37
>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=63.04 E-value=8.1 Score=24.99 Aligned_cols=26 Identities=15% Similarity=0.028 Sum_probs=17.2
Q ss_pred eeecCCCCceEEEecccccccccCCccCccccch
Q 013725 333 VLKNSATGEIVIKHLNRDQEADQSNFRDAATSAE 366 (437)
Q Consensus 333 ~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~ 366 (437)
.|+|..||+... .. .....||.||..
T Consensus 2 ~~~C~~CG~i~~---g~-----~~p~~CP~Cg~~ 27 (34)
T cd00729 2 VWVCPVCGYIHE---GE-----EAPEKCPICGAP 27 (34)
T ss_pred eEECCCCCCEeE---CC-----cCCCcCcCCCCc
Confidence 479999997421 11 123589999975
No 38
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=62.49 E-value=3.9 Score=35.92 Aligned_cols=37 Identities=22% Similarity=0.195 Sum_probs=19.7
Q ss_pred eeecCCCCceEEEecccccccc-cCCccCccccchhhhh
Q 013725 333 VLKNSATGEIVIKHLNRDQEAD-QSNFRDAATSAELEVQ 370 (437)
Q Consensus 333 ~~~~~~~~~~~~~~~~~~~~~~-~~~~~cp~~~~~~~~~ 370 (437)
.+.||+|+.. +.+..-....+ .+.+.||.||..+...
T Consensus 99 ~Y~Cp~C~~~-y~~~ea~~~~d~~~~f~Cp~Cg~~l~~~ 136 (147)
T smart00531 99 YYKCPNCQSK-YTFLEANQLLDMDGTFTCPRCGEELEED 136 (147)
T ss_pred EEECcCCCCE-eeHHHHHHhcCCCCcEECCCCCCEEEEc
Confidence 3589999852 11111100001 2238899999886543
No 39
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=61.42 E-value=16 Score=31.61 Aligned_cols=11 Identities=36% Similarity=0.317 Sum_probs=8.5
Q ss_pred eeeecCCCCce
Q 013725 332 YVLKNSATGEI 342 (437)
Q Consensus 332 ~~~~~~~~~~~ 342 (437)
..|+|++||..
T Consensus 69 ~~~~C~~CG~~ 79 (135)
T PRK03824 69 AVLKCRNCGNE 79 (135)
T ss_pred eEEECCCCCCE
Confidence 34799999963
No 40
>PTZ00365 60S ribosomal protein L7Ae-like; Provisional
Probab=57.97 E-value=57 Score=31.43 Aligned_cols=72 Identities=11% Similarity=0.220 Sum_probs=53.1
Q ss_pred cEEEcHHHHHHHHHhCCccEEEeccCccccceeeecCCCCceEEEecccccccccCCccCccccchhhhhhhccHHHHHH
Q 013725 301 KYVFGVDDTLKALELGAVEILIVWENLDINRYVLKNSATGEIVIKHLNRDQEADQSNFRDAATSAELEVQEKTSLLEWFA 380 (437)
Q Consensus 301 ~a~yG~~eV~~Al~~GaV~tLlV~d~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~~~~~~~~~~v~~l~ 380 (437)
...||+.+|..+++.|.+..+||..|.. | ..++.+|.
T Consensus 132 ~vk~Gin~VtklIekkKAkLVIIA~DVs--------P-----------------------------------~t~kk~LP 168 (266)
T PTZ00365 132 MLKYGLNHVTDLVEYKKAKLVVIAHDVD--------P-----------------------------------IELVCFLP 168 (266)
T ss_pred HHHhhhHHHHHHHHhCCccEEEEeCCCC--------H-----------------------------------HHHHHHHH
Confidence 4669999999999999999999988764 1 11234667
Q ss_pred HHHHhcCCeEEEeCCCCchhhhhhcccccEEEEee
Q 013725 381 NEYKQFGCTLEFVTNKSQEGSQFCRGFGGIGGILR 415 (437)
Q Consensus 381 ~~a~~~ga~V~vvs~~~e~G~q~l~~~GGIaAiLR 415 (437)
..|..+|.-..++.+..+-|.-+=+..-.+.||.-
T Consensus 169 ~LC~k~~VPY~iv~sK~eLG~AIGkktraVVAItd 203 (266)
T PTZ00365 169 ALCRKKEVPYCIIKGKSRLGKLVHQKTAAVVAIDN 203 (266)
T ss_pred HHHhccCCCEEEECCHHHHHHHhCCCCceEEEecc
Confidence 88999999999999887777642111235666664
No 41
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=57.50 E-value=4.3 Score=24.47 Aligned_cols=23 Identities=13% Similarity=0.043 Sum_probs=15.4
Q ss_pred eecCCCCceEEEecccccccccCCccCccccch
Q 013725 334 LKNSATGEIVIKHLNRDQEADQSNFRDAATSAE 366 (437)
Q Consensus 334 ~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~ 366 (437)
..|++||... ..+...||.||.+
T Consensus 3 ~~Cp~Cg~~~----------~~~~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGAEI----------DPDAKFCPNCGAK 25 (26)
T ss_pred CCCcccCCcC----------CcccccChhhCCC
Confidence 3799998621 1335679999975
No 42
>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=57.15 E-value=14 Score=25.96 Aligned_cols=33 Identities=15% Similarity=0.087 Sum_probs=19.0
Q ss_pred ceeeecCCCCceEEEecccccccccCCccCccccch
Q 013725 331 RYVLKNSATGEIVIKHLNRDQEADQSNFRDAATSAE 366 (437)
Q Consensus 331 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~ 366 (437)
.|.++|++||..-... .+.. ......||.||..
T Consensus 3 ~Yey~C~~Cg~~fe~~-~~~~--~~~~~~CP~Cg~~ 35 (52)
T TIGR02605 3 IYEYRCTACGHRFEVL-QKMS--DDPLATCPECGGE 35 (52)
T ss_pred CEEEEeCCCCCEeEEE-EecC--CCCCCCCCCCCCC
Confidence 4567999998632211 1111 1234579999973
No 43
>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=56.28 E-value=9.6 Score=33.52 Aligned_cols=27 Identities=11% Similarity=-0.059 Sum_probs=18.7
Q ss_pred eecCCCCceEEEecccccccccCCccCccccch
Q 013725 334 LKNSATGEIVIKHLNRDQEADQSNFRDAATSAE 366 (437)
Q Consensus 334 ~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~ 366 (437)
++|.+||+...++ .|.. -+.||.||..
T Consensus 113 l~C~~Cg~~~~~~-~~~~-----l~~Cp~C~~~ 139 (146)
T PF07295_consen 113 LVCENCGHEVELT-HPER-----LPPCPKCGHT 139 (146)
T ss_pred EecccCCCEEEec-CCCc-----CCCCCCCCCC
Confidence 5899999865443 2221 4689999976
No 44
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=56.11 E-value=12 Score=28.08 Aligned_cols=28 Identities=11% Similarity=0.035 Sum_probs=20.3
Q ss_pred ecCCCCceEEEecccccccccCCccCccccchh
Q 013725 335 KNSATGEIVIKHLNRDQEADQSNFRDAATSAEL 367 (437)
Q Consensus 335 ~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~~ 367 (437)
+|++|+..++.+-.+ +....|+.||..+
T Consensus 21 kCpdC~N~q~vFsha-----st~V~C~~CG~~l 48 (67)
T COG2051 21 KCPDCGNEQVVFSHA-----STVVTCLICGTTL 48 (67)
T ss_pred ECCCCCCEEEEeccC-----ceEEEecccccEE
Confidence 899999877766332 2356799999763
No 45
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=56.01 E-value=72 Score=33.73 Aligned_cols=39 Identities=18% Similarity=0.200 Sum_probs=21.7
Q ss_pred CccEEEEecChhcHH------HhhhccCCChhhhcceeEEEeCCCCC
Q 013725 221 NVSGLILAGSADFKT------ELSQSDMFDPRLQAKILNVVDVSYGG 261 (437)
Q Consensus 221 ~~~~lilaGp~~~k~------~f~~~~~l~~~l~~~vi~~v~~s~~~ 261 (437)
+.++||++.|..... .|.+. .....++.|.++.+. ||+.
T Consensus 304 ~ad~vilGspT~~~~~~p~~~~fl~~-l~~~~l~gK~~~vFG-Sygw 348 (479)
T PRK05452 304 RSKGVLVGSSTMNNVMMPKIAGLLEE-ITGLRFRNKRASAFG-SHGW 348 (479)
T ss_pred hCCEEEEECCccCCcchHHHHHHHHH-hhccCcCCCEEEEEE-CCCc
Confidence 368999998874322 23321 123346777756665 4543
No 46
>TIGR00354 polC DNA polymerase, archaeal type II, large subunit. This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.
Probab=52.95 E-value=17 Score=40.95 Aligned_cols=62 Identities=18% Similarity=0.205 Sum_probs=36.3
Q ss_pred HHHHHHHHhC-CccEEEeccCccccceeeecCCCCceEEEecccccccccCCccCccccchhhhh----hhccHHHHHHH
Q 013725 307 DDTLKALELG-AVEILIVWENLDINRYVLKNSATGEIVIKHLNRDQEADQSNFRDAATSAELEVQ----EKTSLLEWFAN 381 (437)
Q Consensus 307 ~eV~~Al~~G-aV~tLlV~d~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~~~~~----~~~~~v~~l~~ 381 (437)
..+.+|.+.| .++.=+ .. .+||+||..+. ...||.||...+.. ...++-+.+-+
T Consensus 607 R~i~~A~~~g~~i~vev---~~------RKCPkCG~yTl------------k~rCP~CG~~Te~~~pc~~~i~l~~~~~~ 665 (1095)
T TIGR00354 607 RDIKNAINYTKEIEVEI---AI------RKCPQCGKESF------------WLKCPVCGELTEQLYYGKRKVDLRELYEE 665 (1095)
T ss_pred hhHHHHhccCCeeEEEE---EE------EECCCCCcccc------------cccCCCCCCccccccceeEEecHHHHHHH
Confidence 4688899888 432211 11 28999996322 56899999773221 13455555555
Q ss_pred HHHhcCCe
Q 013725 382 EYKQFGCT 389 (437)
Q Consensus 382 ~a~~~ga~ 389 (437)
..++-|-.
T Consensus 666 A~~~lg~~ 673 (1095)
T TIGR00354 666 AIANLGEY 673 (1095)
T ss_pred HHHHhCCC
Confidence 55555543
No 47
>PRK11032 hypothetical protein; Provisional
Probab=52.56 E-value=12 Score=33.42 Aligned_cols=36 Identities=3% Similarity=-0.291 Sum_probs=21.7
Q ss_pred ccCccccceeeecCCCCceEEEecccccccccCCccCccccch
Q 013725 324 WENLDINRYVLKNSATGEIVIKHLNRDQEADQSNFRDAATSAE 366 (437)
Q Consensus 324 ~d~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~ 366 (437)
+-+....+. ++|.+||+...++ .|.. -+.||.||..
T Consensus 116 sGEvvg~G~-LvC~~Cg~~~~~~-~p~~-----i~pCp~C~~~ 151 (160)
T PRK11032 116 SGEVVGLGN-LVCEKCHHHLAFY-TPEV-----LPLCPKCGHD 151 (160)
T ss_pred cceeeecce-EEecCCCCEEEec-CCCc-----CCCCCCCCCC
Confidence 333333343 4899999855432 2221 4679999976
No 48
>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=51.93 E-value=13 Score=23.75 Aligned_cols=25 Identities=12% Similarity=0.132 Sum_probs=16.7
Q ss_pred eecCCCCceEEEecccccccccCCccCccccch
Q 013725 334 LKNSATGEIVIKHLNRDQEADQSNFRDAATSAE 366 (437)
Q Consensus 334 ~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~ 366 (437)
|+|+.||+.. .+. .....||.||..
T Consensus 2 ~~C~~CGy~y----~~~----~~~~~CP~Cg~~ 26 (33)
T cd00350 2 YVCPVCGYIY----DGE----EAPWVCPVCGAP 26 (33)
T ss_pred EECCCCCCEE----CCC----cCCCcCcCCCCc
Confidence 6899999732 111 235689999975
No 49
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=48.13 E-value=26 Score=28.70 Aligned_cols=62 Identities=10% Similarity=0.111 Sum_probs=39.6
Q ss_pred eecCCCCceEEEecccccccccCCccCccccchh-----hhhhhccHHHHHHHHHHhcCCeEEEeCCCCc
Q 013725 334 LKNSATGEIVIKHLNRDQEADQSNFRDAATSAEL-----EVQEKTSLLEWFANEYKQFGCTLEFVTNKSQ 398 (437)
Q Consensus 334 ~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~~-----~~~~~~~~v~~l~~~a~~~ga~V~vvs~~~e 398 (437)
+.||+||+..+ ...-. .......||.||-.. .+.+..|+....++.+.+.-..+.+.....+
T Consensus 22 f~CP~Cge~~v-~v~~~--k~~~h~~C~~CG~y~~~~V~~l~epIDVY~~wiD~~~eg~i~~~~~~~~~~ 88 (99)
T PRK14892 22 FECPRCGKVSI-SVKIK--KNIAIITCGNCGLYTEFEVPSVYDEVDVYNKFIDLYLEGKIEIKERKNEET 88 (99)
T ss_pred eECCCCCCeEe-eeecC--CCcceEECCCCCCccCEECCccccchhhHHHHHHHHHhcCCCccccCcccc
Confidence 38999995322 10000 012356799999442 1235689999999999988888777765443
No 50
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=46.08 E-value=9.3 Score=22.42 Aligned_cols=10 Identities=0% Similarity=-0.330 Sum_probs=7.2
Q ss_pred CccCccccch
Q 013725 357 NFRDAATSAE 366 (437)
Q Consensus 357 ~~~cp~~~~~ 366 (437)
...||.||.+
T Consensus 13 ~~fC~~CG~~ 22 (23)
T PF13240_consen 13 AKFCPNCGTP 22 (23)
T ss_pred CcchhhhCCc
Confidence 4568888865
No 51
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=45.46 E-value=18 Score=42.20 Aligned_cols=63 Identities=11% Similarity=0.103 Sum_probs=38.4
Q ss_pred HHHHHHHHHhCCccEEEeccCccccceeeecCCCCceEEEecccccccccCCccCccccchhhhh----hhccHHHHHHH
Q 013725 306 VDDTLKALELGAVEILIVWENLDINRYVLKNSATGEIVIKHLNRDQEADQSNFRDAATSAELEVQ----EKTSLLEWFAN 381 (437)
Q Consensus 306 ~~eV~~Al~~GaV~tLlV~d~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~~~~~----~~~~~v~~l~~ 381 (437)
...+.+|.+.|.++.+=|.. .+||+||.... ...||.||...+.. ...++-+.+-.
T Consensus 655 ~R~i~~A~~~g~~~~vei~~--------~~Cp~Cg~~~~------------~~~Cp~CG~~~~~~~~~~~~i~~~~~~~~ 714 (1627)
T PRK14715 655 VRLINKAVEENKTDDIEIAF--------FKCPKCGKVGL------------YHVCPFCGTRVELKPYARREIPPKDYWYA 714 (1627)
T ss_pred hhhHHHHhhcCCcceEEEEe--------eeCCCCCCccc------------cccCcccCCcccCCCccceecCHHHHHHH
Confidence 35688999999886554432 28999996322 46899999663321 12444444444
Q ss_pred HHHhcCC
Q 013725 382 EYKQFGC 388 (437)
Q Consensus 382 ~a~~~ga 388 (437)
+.++-|-
T Consensus 715 A~~~v~~ 721 (1627)
T PRK14715 715 ALENLKI 721 (1627)
T ss_pred HHHHhCC
Confidence 4444443
No 52
>PRK05978 hypothetical protein; Provisional
Probab=45.18 E-value=11 Score=33.16 Aligned_cols=31 Identities=16% Similarity=-0.038 Sum_probs=20.6
Q ss_pred eecCCCCceEEEecccccccccCCccCccccchhhh
Q 013725 334 LKNSATGEIVIKHLNRDQEADQSNFRDAATSAELEV 369 (437)
Q Consensus 334 ~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~~~~ 369 (437)
.+||+||+...+. . --+-...||.||.+++.
T Consensus 34 grCP~CG~G~LF~-g----~Lkv~~~C~~CG~~~~~ 64 (148)
T PRK05978 34 GRCPACGEGKLFR-A----FLKPVDHCAACGEDFTH 64 (148)
T ss_pred CcCCCCCCCcccc-c----ccccCCCccccCCcccc
Confidence 4899999754421 0 01335789999999765
No 53
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=43.77 E-value=21 Score=24.59 Aligned_cols=27 Identities=7% Similarity=0.021 Sum_probs=17.9
Q ss_pred eeecCCCCceEEEecccccccccCCccCccccch
Q 013725 333 VLKNSATGEIVIKHLNRDQEADQSNFRDAATSAE 366 (437)
Q Consensus 333 ~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~ 366 (437)
.++|.+||.... +. ......||.||.+
T Consensus 2 ~Y~C~~Cg~~~~--~~-----~~~~irC~~CG~r 28 (44)
T smart00659 2 IYICGECGRENE--IK-----SKDVVRCRECGYR 28 (44)
T ss_pred EEECCCCCCEee--cC-----CCCceECCCCCce
Confidence 368999987432 11 1235789999977
No 54
>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=43.53 E-value=12 Score=31.09 Aligned_cols=28 Identities=7% Similarity=0.023 Sum_probs=18.1
Q ss_pred eecCCCCceEEEecccccccccCCccCccccchhh
Q 013725 334 LKNSATGEIVIKHLNRDQEADQSNFRDAATSAELE 368 (437)
Q Consensus 334 ~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~~~ 368 (437)
..|++||.. || . -++....||+||..+.
T Consensus 10 R~Cp~CG~k--FY-D----Lnk~PivCP~CG~~~~ 37 (108)
T PF09538_consen 10 RTCPSCGAK--FY-D----LNKDPIVCPKCGTEFP 37 (108)
T ss_pred ccCCCCcch--hc-c----CCCCCccCCCCCCccC
Confidence 379999862 22 1 0244567999998864
No 55
>PRK12496 hypothetical protein; Provisional
Probab=43.43 E-value=15 Score=32.92 Aligned_cols=29 Identities=3% Similarity=-0.063 Sum_probs=17.8
Q ss_pred ceeeecCCCCceEEEecccccccccCCccCccccchh
Q 013725 331 RYVLKNSATGEIVIKHLNRDQEADQSNFRDAATSAEL 367 (437)
Q Consensus 331 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~~ 367 (437)
+|.++|+.|+.. | . . ......||.||.++
T Consensus 125 ~w~~~C~gC~~~---~-~-~---~~~~~~C~~CG~~~ 153 (164)
T PRK12496 125 KWRKVCKGCKKK---Y-P-E---DYPDDVCEICGSPV 153 (164)
T ss_pred eeeEECCCCCcc---c-c-C---CCCCCcCCCCCChh
Confidence 345689999851 1 0 0 11235699999884
No 56
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=38.80 E-value=5.4 Score=28.81 Aligned_cols=7 Identities=14% Similarity=0.269 Sum_probs=5.3
Q ss_pred ecCCCCc
Q 013725 335 KNSATGE 341 (437)
Q Consensus 335 ~~~~~~~ 341 (437)
.||.||.
T Consensus 4 ~CP~CG~ 10 (54)
T TIGR01206 4 ECPDCGA 10 (54)
T ss_pred CCCCCCC
Confidence 6888876
No 57
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=37.52 E-value=16 Score=36.43 Aligned_cols=21 Identities=14% Similarity=0.381 Sum_probs=16.5
Q ss_pred HHHHHHHHHHHHHHHHHHhhc
Q 013725 193 RMEKRHNYVRKTAELATQFFI 213 (437)
Q Consensus 193 ~ee~~~~f~~~Vae~l~~~f~ 213 (437)
+.++=..|+-.|.+.+..++.
T Consensus 240 v~eQn~~yl~evl~~L~~~Y~ 260 (389)
T COG2956 240 VLEQNPEYLSEVLEMLYECYA 260 (389)
T ss_pred HHHhChHHHHHHHHHHHHHHH
Confidence 555667799999999988874
No 58
>COG1212 KdsB CMP-2-keto-3-deoxyoctulosonic acid synthetase [Cell envelope biogenesis, outer membrane]
Probab=37.42 E-value=50 Score=31.30 Aligned_cols=54 Identities=11% Similarity=0.085 Sum_probs=40.1
Q ss_pred CccCccccchhhhhhhccHHHHHHHHHHhcCCeEEEeCCCCchhhhhhcccccEEEEeeccc
Q 013725 357 NFRDAATSAELEVQEKTSLLEWFANEYKQFGCTLEFVTNKSQEGSQFCRGFGGIGGILRYQL 418 (437)
Q Consensus 357 ~~~cp~~~~~~~~~~~~~~v~~l~~~a~~~ga~V~vvs~~~e~G~q~l~~~GGIaAiLRy~~ 418 (437)
...|.-+|++| +.+..+.|.+.|++=.+|.++++.=..-.++|||-+.+-|=..
T Consensus 20 KPLadI~Gkpm--------I~rV~e~a~~s~~~rvvVATDde~I~~av~~~G~~avmT~~~h 73 (247)
T COG1212 20 KPLADIGGKPM--------IVRVAERALKSGADRVVVATDDERIAEAVQAFGGEAVMTSKDH 73 (247)
T ss_pred CchhhhCCchH--------HHHHHHHHHHcCCCeEEEEcCCHHHHHHHHHhCCEEEecCCCC
Confidence 34445566665 5788999999998888888777776666889988888876543
No 59
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=37.38 E-value=18 Score=23.66 Aligned_cols=32 Identities=6% Similarity=-0.026 Sum_probs=18.6
Q ss_pred eecCCCCceEEEeccccccc-ccCCccCccccchh
Q 013725 334 LKNSATGEIVIKHLNRDQEA-DQSNFRDAATSAEL 367 (437)
Q Consensus 334 ~~~~~~~~~~~~~~~~~~~~-~~~~~~cp~~~~~~ 367 (437)
+.||+|+.. +.+.+.... ......||.||..+
T Consensus 3 ~~CP~C~~~--~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCPNCKTS--FRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred EECCCCCCE--EEeCHHHcCCCCCEEECCCCCCEE
Confidence 479999863 223332222 12357899998764
No 60
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=36.90 E-value=27 Score=29.23 Aligned_cols=25 Identities=12% Similarity=0.031 Sum_probs=15.9
Q ss_pred eecCCCCceEEEecccccccccCCccCccccch
Q 013725 334 LKNSATGEIVIKHLNRDQEADQSNFRDAATSAE 366 (437)
Q Consensus 334 ~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~ 366 (437)
++|++||.... . ......||.||..
T Consensus 71 ~~C~~Cg~~~~--~------~~~~~~CP~Cgs~ 95 (113)
T PRK12380 71 AWCWDCSQVVE--I------HQHDAQCPHCHGE 95 (113)
T ss_pred EEcccCCCEEe--c------CCcCccCcCCCCC
Confidence 59999985321 1 1123569999965
No 61
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.72 E-value=12 Score=28.94 Aligned_cols=60 Identities=17% Similarity=0.127 Sum_probs=31.6
Q ss_pred cceeeecCCCCceEEEecccccccccCCccCccccchhhhhhhccHHHHHHH-HHHhcCCeEEEeCCCCchhh
Q 013725 330 NRYVLKNSATGEIVIKHLNRDQEADQSNFRDAATSAELEVQEKTSLLEWFAN-EYKQFGCTLEFVTNKSQEGS 401 (437)
Q Consensus 330 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~~~~~~~~~~v~~l~~-~a~~~ga~V~vvs~~~e~G~ 401 (437)
+-+.++|.+||+.-.+ + +...+.....||.||.++. .++. -...+-+.=+.|.+.-.+|.
T Consensus 9 PtY~Y~c~~cg~~~dv-v--q~~~ddplt~ce~c~a~~k---------k~l~~vgi~fKGSGfYvtDsRksg~ 69 (82)
T COG2331 9 PTYSYECTECGNRFDV-V--QAMTDDPLTTCEECGARLK---------KLLNAVGIVFKGSGFYVTDSRKSGK 69 (82)
T ss_pred cceEEeecccchHHHH-H--HhcccCccccChhhChHHH---------HhhccceEEEecceEEEecccccCC
Confidence 4456799999862100 0 0011233567999998852 3333 33355555555555444443
No 62
>PLN02674 adenylate kinase
Probab=36.18 E-value=71 Score=30.57 Aligned_cols=34 Identities=9% Similarity=0.120 Sum_probs=22.2
Q ss_pred CccEEEEecChhcHHHhhhccCCChhhhcceeEEEeCCCCC
Q 013725 221 NVSGLILAGSADFKTELSQSDMFDPRLQAKILNVVDVSYGG 261 (437)
Q Consensus 221 ~~~~lilaGp~~~k~~f~~~~~l~~~l~~~vi~~v~~s~~~ 261 (437)
..+.+|+|+||-=|..... .|.++. +..++|.|.
T Consensus 31 ~~~i~l~G~PGsGKgT~a~------~La~~~-~~~his~Gd 64 (244)
T PLN02674 31 DKRLILIGPPGSGKGTQSP------IIKDEY-CLCHLATGD 64 (244)
T ss_pred CceEEEECCCCCCHHHHHH------HHHHHc-CCcEEchhH
Confidence 4567788888877877763 455554 556776653
No 63
>KOG1859 consensus Leucine-rich repeat proteins [General function prediction only]
Probab=36.11 E-value=14 Score=40.77 Aligned_cols=95 Identities=14% Similarity=0.144 Sum_probs=60.4
Q ss_pred cCCCcEEEcHHHHHHHHHhCCccEEEeccCccccce-eeecCCCCceEEEeccccccc---ccCCccCccccchhhhhhh
Q 013725 297 QDTGKYVFGVDDTLKALELGAVEILIVWENLDINRY-VLKNSATGEIVIKHLNRDQEA---DQSNFRDAATSAELEVQEK 372 (437)
Q Consensus 297 ~~~g~a~yG~~eV~~Al~~GaV~tLlV~d~l~~~~~-~~~~~~~~~~~~~~~~~~~~~---~~~~~~cp~~~~~~~~~~~ 372 (437)
+|..-+||-.+.++--..+-+-+.+...+++...|. +++|-+||.. +.++|.. ...+..||.|.+...
T Consensus 636 ~D~~ss~~e~en~ls~~~~~~~eq~~~~rdL~~~r~~i~~C~~cgt~----F~~eqp~kg~~~kelr~pd~~k~~t---- 707 (1096)
T KOG1859|consen 636 SDKQSSCSEVENYLSEELESNLEQILLQRDLTENRISIYRCVNCGTQ----FLIEQPEKGSKIKELRCPDSRKVYT---- 707 (1096)
T ss_pred ccccchhhhhhhcccHhhhhhHhhhhhhhhhhccccceeeecccccc----ccccCcccccchhhhcCcchhhccc----
Confidence 343346777777666666667777777787776665 5699999852 2333332 244678999876521
Q ss_pred ccHHHHHHHHHHhcCCeEEEeCCCCchhhhhhcccccEEEEeecccCcc
Q 013725 373 TSLLEWFANEYKQFGCTLEFVTNKSQEGSQFCRGFGGIGGILRYQLDIR 421 (437)
Q Consensus 373 ~~~v~~l~~~a~~~ga~V~vvs~~~e~G~q~l~~~GGIaAiLRy~~~~~ 421 (437)
+ .|-+..| -++..|||+|+-|+..+++
T Consensus 708 ---------------~--~v~~~~~-----s~~~~~~v~a~~rl~p~~~ 734 (1096)
T KOG1859|consen 708 ---------------T--NVTSGLH-----SLKPSGGVNAEPRLSPKMI 734 (1096)
T ss_pred ---------------c--ccccccc-----ccCCccceecccccCcchh
Confidence 0 1222222 1688999999999977654
No 64
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=35.77 E-value=67 Score=34.20 Aligned_cols=41 Identities=12% Similarity=0.054 Sum_probs=21.9
Q ss_pred CccCccccchhhhhhhccHHHHHHHHHHhc--CCeEEEeCCCCc
Q 013725 357 NFRDAATSAELEVQEKTSLLEWFANEYKQF--GCTLEFVTNKSQ 398 (437)
Q Consensus 357 ~~~cp~~~~~~~~~~~~~~v~~l~~~a~~~--ga~V~vvs~~~e 398 (437)
...||.||... +....-=++.+.+...+. ++.|..+..++.
T Consensus 253 ~~~Cp~C~s~~-l~~~g~Gte~~~e~l~~~fp~~~v~~~d~d~~ 295 (505)
T TIGR00595 253 PKTCPQCGSED-LVYKGYGTEQVEEELAKLFPGARIARIDSDTT 295 (505)
T ss_pred CCCCCCCCCCe-eEeecccHHHHHHHHHhhCCCCcEEEEecccc
Confidence 45799998751 111111123444444443 678888776654
No 65
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 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 a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=35.58 E-value=21 Score=24.21 Aligned_cols=27 Identities=11% Similarity=0.104 Sum_probs=15.5
Q ss_pred ecCCCCceEEEecccccccccCCccCccccch
Q 013725 335 KNSATGEIVIKHLNRDQEADQSNFRDAATSAE 366 (437)
Q Consensus 335 ~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~ 366 (437)
+||+||...+ ...+ ..+...|+.||.-
T Consensus 2 ~Cp~Cg~~~~-~~D~----~~g~~vC~~CG~V 28 (43)
T PF08271_consen 2 KCPNCGSKEI-VFDP----ERGELVCPNCGLV 28 (43)
T ss_dssp SBTTTSSSEE-EEET----TTTEEEETTT-BB
T ss_pred CCcCCcCCce-EEcC----CCCeEECCCCCCE
Confidence 6888886542 2221 2446689999854
No 66
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=35.08 E-value=35 Score=37.56 Aligned_cols=23 Identities=13% Similarity=-0.036 Sum_probs=16.0
Q ss_pred ecCCCCceEEEecccccccccCCccCccccchhh
Q 013725 335 KNSATGEIVIKHLNRDQEADQSNFRDAATSAELE 368 (437)
Q Consensus 335 ~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~~~ 368 (437)
+|+.||... .....||.||.+++
T Consensus 628 ~C~~CG~~~-----------g~~~~CP~CG~~~~ 650 (656)
T PRK08270 628 ICPKHGYLS-----------GEHEFCPKCGEETE 650 (656)
T ss_pred ccCCCCCcC-----------CCCCCCcCCcCccc
Confidence 799998621 12468999997743
No 67
>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=35.08 E-value=18 Score=37.96 Aligned_cols=23 Identities=13% Similarity=-0.106 Sum_probs=15.0
Q ss_pred eeecCCCCceEEEecccccccccCCccCccccc
Q 013725 333 VLKNSATGEIVIKHLNRDQEADQSNFRDAATSA 365 (437)
Q Consensus 333 ~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~ 365 (437)
.|+|.+||+... +-..+||.|+.
T Consensus 7 ~y~C~~Cg~~~~----------~~~g~Cp~C~~ 29 (454)
T TIGR00416 7 KFVCQHCGADSP----------KWQGKCPACHA 29 (454)
T ss_pred eEECCcCCCCCc----------cccEECcCCCC
Confidence 468999987321 11457999973
No 68
>PRK11181 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional
Probab=35.05 E-value=1.1e+02 Score=29.04 Aligned_cols=69 Identities=14% Similarity=0.202 Sum_probs=45.8
Q ss_pred cEEEcHHHHHHHHHh-C-CccEEEeccCccccceeeecCCCCceEEEecccccccccCCccCccccchhhhhhhccHHHH
Q 013725 301 KYVFGVDDTLKALEL-G-AVEILIVWENLDINRYVLKNSATGEIVIKHLNRDQEADQSNFRDAATSAELEVQEKTSLLEW 378 (437)
Q Consensus 301 ~a~yG~~eV~~Al~~-G-aV~tLlV~d~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~~~~~~~~~~v~~ 378 (437)
...||...|.+||+. + .+.+|++..+.. + .+ ...
T Consensus 3 ~~i~G~~~v~eal~~~~~~~~~l~~~~~~~-----------~------------------------~~---------~~~ 38 (244)
T PRK11181 3 EIIYGIHAVQALLERAPERFIEVFVLKGRE-----------D------------------------KR---------LLP 38 (244)
T ss_pred cEEEehHHHHHHHhCCCCceeEEEEECCCc-----------c------------------------hH---------HHH
Confidence 368999999999986 3 678888864331 0 00 235
Q ss_pred HHHHHHhcCCeEEEeCCCCchhhhhh--cccccEEEEee
Q 013725 379 FANEYKQFGCTLEFVTNKSQEGSQFC--RGFGGIGGILR 415 (437)
Q Consensus 379 l~~~a~~~ga~V~vvs~~~e~G~q~l--~~~GGIaAiLR 415 (437)
++..+...|..+..++...- .++. ....||.|+.+
T Consensus 39 ~~~~~~~~~i~~~~v~~~~l--~~ls~~~~~qGv~a~~~ 75 (244)
T PRK11181 39 LINELEAQGIVIQLANRQTL--DEKAEGAVHQGIIARVK 75 (244)
T ss_pred HHHHHHHcCCcEEEeCHHHH--hhhhcCCCCceEEEEEe
Confidence 56777778888888875321 1211 34789999986
No 69
>PRK11823 DNA repair protein RadA; Provisional
Probab=34.83 E-value=18 Score=37.81 Aligned_cols=23 Identities=13% Similarity=-0.132 Sum_probs=13.7
Q ss_pred eeecCCCCceEEEecccccccccCCccCccccc
Q 013725 333 VLKNSATGEIVIKHLNRDQEADQSNFRDAATSA 365 (437)
Q Consensus 333 ~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~ 365 (437)
.|+|.+||+... +=..+||.|+.
T Consensus 7 ~y~C~~Cg~~~~----------~~~g~Cp~C~~ 29 (446)
T PRK11823 7 AYVCQECGAESP----------KWLGRCPECGA 29 (446)
T ss_pred eEECCcCCCCCc----------ccCeeCcCCCC
Confidence 357888886321 11357888863
No 70
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=34.27 E-value=31 Score=28.89 Aligned_cols=35 Identities=11% Similarity=-0.035 Sum_probs=20.5
Q ss_pred EEEeccCccccceeeecCCCCceEEEecccccccccCCccCccccch
Q 013725 320 ILIVWENLDINRYVLKNSATGEIVIKHLNRDQEADQSNFRDAATSAE 366 (437)
Q Consensus 320 tLlV~d~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~ 366 (437)
+|.|..-. ...+|++||.... . ......||.||..
T Consensus 61 ~L~I~~~p----~~~~C~~Cg~~~~--~------~~~~~~CP~Cgs~ 95 (115)
T TIGR00100 61 KLNIEDEP----VECECEDCSEEVS--P------EIDLYRCPKCHGI 95 (115)
T ss_pred EEEEEeeC----cEEEcccCCCEEe--c------CCcCccCcCCcCC
Confidence 55554332 2359999986321 0 0124679999976
No 71
>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=34.15 E-value=37 Score=36.84 Aligned_cols=33 Identities=9% Similarity=-0.059 Sum_probs=19.7
Q ss_pred ccEEEeccCccccceeeecCCCCceEEEecccccccccCCccCccccch
Q 013725 318 VEILIVWENLDINRYVLKNSATGEIVIKHLNRDQEADQSNFRDAATSAE 366 (437)
Q Consensus 318 V~tLlV~d~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~ 366 (437)
+.-.=+.-.+. +|.+||.... .....||.||..
T Consensus 515 i~Y~~~n~~~~------~C~~CG~~g~----------~~~~~CP~Cgs~ 547 (579)
T TIGR02487 515 IGYFGINPPVD------VCEDCGYTGE----------GLNDKCPKCGSH 547 (579)
T ss_pred CceEEeccCCc------cCCCCCCCCC----------CCCCcCcCCCCc
Confidence 44444444444 8999986221 112579999965
No 72
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=33.78 E-value=61 Score=36.12 Aligned_cols=66 Identities=12% Similarity=0.134 Sum_probs=0.0
Q ss_pred ceeeecCCCCceEEEecccccc-------cccCCccCccccchhhhhhhccHHHHHHHHHHhc--CCeEEEeCCCC
Q 013725 331 RYVLKNSATGEIVIKHLNRDQE-------ADQSNFRDAATSAELEVQEKTSLLEWFANEYKQF--GCTLEFVTNKS 397 (437)
Q Consensus 331 ~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~cp~~~~~~~~~~~~~~v~~l~~~a~~~--ga~V~vvs~~~ 397 (437)
+++..||+|+-.=..+-..... ..+....||.||.+ .+.....=.+.+-+..... ++.|..++.++
T Consensus 442 g~v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~-~L~~~G~GterieeeL~~~FP~~rv~r~d~Dt 516 (730)
T COG1198 442 GYIAECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSE-HLRAVGPGTERIEEELKRLFPGARIIRIDSDT 516 (730)
T ss_pred CCcccCCCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCCC-eeEEecccHHHHHHHHHHHCCCCcEEEEcccc
No 73
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=32.36 E-value=36 Score=30.88 Aligned_cols=30 Identities=17% Similarity=0.234 Sum_probs=21.1
Q ss_pred CCccCccccchhhhhhhccHHHHHHHHHHh
Q 013725 356 SNFRDAATSAELEVQEKTSLLEWFANEYKQ 385 (437)
Q Consensus 356 ~~~~cp~~~~~~~~~~~~~~v~~l~~~a~~ 385 (437)
..+.||.||..++..+....+..|-+...+
T Consensus 131 ~~F~Cp~Cg~~L~~~d~s~~i~~l~~~i~~ 160 (176)
T COG1675 131 LGFTCPKCGEDLEEYDSSEEIEELESELDE 160 (176)
T ss_pred hCCCCCCCCchhhhccchHHHHHHHHHHHH
Confidence 357899999998776666666666555543
No 74
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=32.26 E-value=43 Score=38.38 Aligned_cols=58 Identities=17% Similarity=0.202 Sum_probs=34.1
Q ss_pred eeecCCCCceEEEecccccccccCCccCccccchhhhhhhccHHHHHHHHHHhcCCeEEEeCCCCchhhh
Q 013725 333 VLKNSATGEIVIKHLNRDQEADQSNFRDAATSAELEVQEKTSLLEWFANEYKQFGCTLEFVTNKSQEGSQ 402 (437)
Q Consensus 333 ~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~~~~~~~~~~v~~l~~~a~~~ga~V~vvs~~~e~G~q 402 (437)
.+||.+||+..+ .....||.||... +......++.|=+.|.+.+ +|.|=++.-.+|+.
T Consensus 694 IKrC~dcg~q~~----------~~~~~cP~Cgs~~-v~d~~~~ve~lRelA~EvD-eVlIgTDPDtEGEK 751 (1187)
T COG1110 694 IKRCRDCGEQFV----------DSEDKCPRCGSRN-VEDKTETVEALRELALEVD-EILIGTDPDTEGEK 751 (1187)
T ss_pred HHHHhhcCceec----------cccccCCCCCCcc-ccccHHHHHHHHHHHhhcC-EEEEcCCCCCccch
Confidence 357999987322 1134799999863 2344555666666665432 34444555566764
No 75
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=32.23 E-value=17 Score=37.14 Aligned_cols=10 Identities=20% Similarity=0.405 Sum_probs=4.8
Q ss_pred ceeeecCCCC
Q 013725 331 RYVLKNSATG 340 (437)
Q Consensus 331 ~~~~~~~~~~ 340 (437)
++.|+||+|+
T Consensus 12 ~~~g~cp~c~ 21 (372)
T cd01121 12 KWLGKCPECG 21 (372)
T ss_pred CccEECcCCC
Confidence 3444555554
No 76
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=31.80 E-value=33 Score=24.45 Aligned_cols=22 Identities=9% Similarity=0.176 Sum_probs=10.7
Q ss_pred cCccccchhhhhhhccHHHHHH
Q 013725 359 RDAATSAELEVQEKTSLLEWFA 380 (437)
Q Consensus 359 ~cp~~~~~~~~~~~~~~v~~l~ 380 (437)
.||.|+.++..-....++..+-
T Consensus 22 ~CPlC~r~l~~e~~~~li~~~~ 43 (54)
T PF04423_consen 22 CCPLCGRPLDEEHRQELIKKYK 43 (54)
T ss_dssp E-TTT--EE-HHHHHHHHHHHH
T ss_pred cCCCCCCCCCHHHHHHHHHHHH
Confidence 7999999875544444444443
No 77
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=31.48 E-value=31 Score=25.23 Aligned_cols=23 Identities=17% Similarity=0.211 Sum_probs=15.3
Q ss_pred ecCCCCceEEEecccccccccCCccCccccchhhh
Q 013725 335 KNSATGEIVIKHLNRDQEADQSNFRDAATSAELEV 369 (437)
Q Consensus 335 ~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~~~~ 369 (437)
+|++||.=+ + ...||.||+...+
T Consensus 7 kC~~cg~YT---L---------ke~Cp~CG~~t~~ 29 (59)
T COG2260 7 KCPKCGRYT---L---------KEKCPVCGGDTKV 29 (59)
T ss_pred cCcCCCcee---e---------cccCCCCCCcccc
Confidence 788888521 2 2469999988543
No 78
>COG0566 SpoU rRNA methylases [Translation, ribosomal structure and biogenesis]
Probab=31.26 E-value=2e+02 Score=27.67 Aligned_cols=73 Identities=16% Similarity=0.124 Sum_probs=51.1
Q ss_pred CcEEEcHHHHHHHHHhC-CccEEEeccCccccceeeecCCCCceEEEecccccccccCCccCccccchhhhhhhccHHHH
Q 013725 300 GKYVFGVDDTLKALELG-AVEILIVWENLDINRYVLKNSATGEIVIKHLNRDQEADQSNFRDAATSAELEVQEKTSLLEW 378 (437)
Q Consensus 300 g~a~yG~~eV~~Al~~G-aV~tLlV~d~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~~~~~~~~~~v~~ 378 (437)
...+||...|.+|++.+ .+..+++.++.. + . ...
T Consensus 21 ~~~~~G~~~v~~al~~~~~i~~i~~~~~~~--------~----------------------------~---------~~~ 55 (260)
T COG0566 21 EFLIEGEHAVLEALASGPKIVRILVTEGRL--------P----------------------------R---------FEE 55 (260)
T ss_pred cEEEeeHHHHHHHHhcCCCceEEEEecccc--------h----------------------------h---------HHH
Confidence 35789999999999999 888998876543 0 0 246
Q ss_pred HHHHHHhcCCeEEEeCCCCchhhhhhcccccEEEEeecc
Q 013725 379 FANEYKQFGCTLEFVTNKSQEGSQFCRGFGGIGGILRYQ 417 (437)
Q Consensus 379 l~~~a~~~ga~V~vvs~~~e~G~q~l~~~GGIaAiLRy~ 417 (437)
+...+...|..+..++...-.-----..+.||+|...-+
T Consensus 56 ~~~~~~~~~~~~~~v~~~~l~~~~~~~~hqGi~a~~~~~ 94 (260)
T COG0566 56 LLALAAAKGIPVYVVSEAILDKLSGTENHQGIVAVVKKR 94 (260)
T ss_pred HHHHHHhcCCeEEEECHHHHHHHhCCCCCCeEEEEEecc
Confidence 677888889999988864321100013477899888544
No 79
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=31.13 E-value=25 Score=36.24 Aligned_cols=24 Identities=17% Similarity=-0.051 Sum_probs=16.0
Q ss_pred eeecCCCCceEEEecccccccccCCccCccccch
Q 013725 333 VLKNSATGEIVIKHLNRDQEADQSNFRDAATSAE 366 (437)
Q Consensus 333 ~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~ 366 (437)
.|.|++||+...++ ...||.||.=
T Consensus 7 ~f~C~~CG~~s~KW----------~GkCp~Cg~W 30 (456)
T COG1066 7 AFVCQECGYVSPKW----------LGKCPACGAW 30 (456)
T ss_pred EEEcccCCCCCccc----------cccCCCCCCc
Confidence 46899999743221 3579999843
No 80
>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=30.76 E-value=28 Score=29.74 Aligned_cols=28 Identities=11% Similarity=-0.001 Sum_probs=18.1
Q ss_pred eecCCCCceEEEecccccccccCCccCccccchhh
Q 013725 334 LKNSATGEIVIKHLNRDQEADQSNFRDAATSAELE 368 (437)
Q Consensus 334 ~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~~~ 368 (437)
..|++||.. +| . -++....||+||..+.
T Consensus 10 r~Cp~cg~k--FY-D----Lnk~p~vcP~cg~~~~ 37 (129)
T TIGR02300 10 RICPNTGSK--FY-D----LNRRPAVSPYTGEQFP 37 (129)
T ss_pred ccCCCcCcc--cc-c----cCCCCccCCCcCCccC
Confidence 379999862 22 1 1244678999998753
No 81
>PF13727 CoA_binding_3: CoA-binding domain; PDB: 3NKL_B.
Probab=30.68 E-value=89 Score=27.08 Aligned_cols=51 Identities=12% Similarity=0.169 Sum_probs=33.2
Q ss_pred cEEEcHHHHHHHHHhCCccEEEeccCccccceeeecCCCCceEEEecccccccccCCccCccccchhhhhhhccHHHHHH
Q 013725 301 KYVFGVDDTLKALELGAVEILIVWENLDINRYVLKNSATGEIVIKHLNRDQEADQSNFRDAATSAELEVQEKTSLLEWFA 380 (437)
Q Consensus 301 ~a~yG~~eV~~Al~~GaV~tLlV~d~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~~~~~~~~~~v~~l~ 380 (437)
......++..+.++.+.|+.++|+-+.. ..+-+..++
T Consensus 125 ~~lg~~~~l~~~~~~~~id~v~ial~~~-------------------------------------------~~~~i~~ii 161 (175)
T PF13727_consen 125 PVLGDLDDLPELVREHDIDEVIIALPWS-------------------------------------------EEEQIKRII 161 (175)
T ss_dssp EEE--GGGHHHHHHHHT--EEEE--TTS--------------------------------------------HHHHHHHH
T ss_pred eeEcCHHHHHHHHHhCCCCEEEEEcCcc-------------------------------------------CHHHHHHHH
Confidence 3445689999999999999999975443 011247889
Q ss_pred HHHHhcCCeEEEeC
Q 013725 381 NEYKQFGCTLEFVT 394 (437)
Q Consensus 381 ~~a~~~ga~V~vvs 394 (437)
+.+.+.|.+|.+||
T Consensus 162 ~~~~~~~v~v~~vP 175 (175)
T PF13727_consen 162 EELENHGVRVRVVP 175 (175)
T ss_dssp HHHHTTT-EEEE--
T ss_pred HHHHhCCCEEEEeC
Confidence 99999999999986
No 82
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=30.65 E-value=38 Score=24.91 Aligned_cols=10 Identities=10% Similarity=0.059 Sum_probs=5.1
Q ss_pred CccCccccch
Q 013725 357 NFRDAATSAE 366 (437)
Q Consensus 357 ~~~cp~~~~~ 366 (437)
.+.||.||+.
T Consensus 27 ~F~CPnCGe~ 36 (61)
T COG2888 27 KFPCPNCGEV 36 (61)
T ss_pred EeeCCCCCce
Confidence 3455555533
No 83
>COG5257 GCD11 Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]
Probab=30.25 E-value=51 Score=33.04 Aligned_cols=52 Identities=12% Similarity=0.037 Sum_probs=30.1
Q ss_pred eecCCCCceEEEecccccccccCCccCccccchhhhhhhc---------cHHHHHHHHHHhcCCeEEEeC
Q 013725 334 LKNSATGEIVIKHLNRDQEADQSNFRDAATSAELEVQEKT---------SLLEWFANEYKQFGCTLEFVT 394 (437)
Q Consensus 334 ~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~~~~~~~~---------~~v~~l~~~a~~~ga~V~vvs 394 (437)
++|++|....- -.....||.||.+.+.+... -++.-++.-|.-++|-+.+|.
T Consensus 58 ~kC~~c~~~~~---------y~~~~~C~~cg~~~~l~R~VSfVDaPGHe~LMATMLsGAAlMDgAlLvIa 118 (415)
T COG5257 58 YKCPECYRPEC---------YTTEPKCPNCGAETELVRRVSFVDAPGHETLMATMLSGAALMDGALLVIA 118 (415)
T ss_pred EeCCCCCCCcc---------cccCCCCCCCCCCccEEEEEEEeeCCchHHHHHHHhcchhhhcceEEEEe
Confidence 59999974211 12356799999886554432 244445555555555555554
No 84
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=30.06 E-value=52 Score=36.00 Aligned_cols=21 Identities=5% Similarity=-0.099 Sum_probs=14.7
Q ss_pred ecCCCCceEEEecccccccccCCccCccccch
Q 013725 335 KNSATGEIVIKHLNRDQEADQSNFRDAATSAE 366 (437)
Q Consensus 335 ~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~ 366 (437)
+|+.||.... -...||.||..
T Consensus 561 ~C~~CGy~g~-----------~~~~CP~CG~~ 581 (618)
T PRK14704 561 RCKCCSYHGV-----------IGNECPSCGNE 581 (618)
T ss_pred ecCCCCCCCC-----------cCccCcCCCCC
Confidence 7999986321 12679999955
No 85
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=29.35 E-value=42 Score=30.43 Aligned_cols=54 Identities=13% Similarity=0.092 Sum_probs=29.7
Q ss_pred EcHHHHHHHHHhCCccEEEeccCccccceeeecCCCCceEEEecccccccccCCccCccccchh
Q 013725 304 FGVDDTLKALELGAVEILIVWENLDINRYVLKNSATGEIVIKHLNRDQEADQSNFRDAATSAEL 367 (437)
Q Consensus 304 yG~~eV~~Al~~GaV~tLlV~d~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~~ 367 (437)
|.+..|...|..+-..-.+=..-.....+.++|..|+. ++. .....||.||+++
T Consensus 110 ysvQNVa~~Lgi~~~~~~~~~~I~~v~~w~~rC~GC~~--~f~--------~~~~~Cp~CG~~~ 163 (177)
T COG1439 110 YSVQNVALQLGLNVRSISYKGKIKKVRKWRLRCHGCKR--IFP--------EPKDFCPICGSPL 163 (177)
T ss_pred hHHHHHHHHhCceEEeeeccCccceEeeeeEEEecCce--ecC--------CCCCcCCCCCCce
Confidence 77888777665433221111101112245669999974 111 1246799999884
No 86
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=29.13 E-value=28 Score=29.06 Aligned_cols=25 Identities=12% Similarity=0.105 Sum_probs=14.9
Q ss_pred eecCCCCceEEEecccccccccCCccCccccch
Q 013725 334 LKNSATGEIVIKHLNRDQEADQSNFRDAATSAE 366 (437)
Q Consensus 334 ~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~ 366 (437)
.+|.+||..-. . ......||.||..
T Consensus 71 ~~C~~Cg~~~~--~------~~~~~~CP~Cgs~ 95 (113)
T PF01155_consen 71 ARCRDCGHEFE--P------DEFDFSCPRCGSP 95 (113)
T ss_dssp EEETTTS-EEE--C------HHCCHH-SSSSSS
T ss_pred EECCCCCCEEe--c------CCCCCCCcCCcCC
Confidence 59999996321 1 1223679999977
No 87
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=28.60 E-value=35 Score=29.67 Aligned_cols=22 Identities=14% Similarity=0.143 Sum_probs=15.9
Q ss_pred ecCCCCceEEEecccccccccCCccCccccch
Q 013725 335 KNSATGEIVIKHLNRDQEADQSNFRDAATSAE 366 (437)
Q Consensus 335 ~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~ 366 (437)
+|++||... . +....||.|+.+
T Consensus 31 kC~~CG~v~---~-------PPr~~Cp~C~~~ 52 (140)
T COG1545 31 KCKKCGRVY---F-------PPRAYCPKCGSE 52 (140)
T ss_pred EcCCCCeEE---c-------CCcccCCCCCCC
Confidence 899999632 2 234579999977
No 88
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=28.13 E-value=84 Score=35.04 Aligned_cols=37 Identities=14% Similarity=-0.009 Sum_probs=22.1
Q ss_pred ccEEEeccCccccceeeecCCCCceEEEecccccccccCCccCccccch
Q 013725 318 VEILIVWENLDINRYVLKNSATGEIVIKHLNRDQEADQSNFRDAATSAE 366 (437)
Q Consensus 318 V~tLlV~d~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~ 366 (437)
+--.=|+-.+. +|+.||+.+.+.. ......||.||..
T Consensus 632 i~Y~~in~~~~------~C~~CG~~Ge~~~------~~~~~~CP~CG~~ 668 (711)
T PRK09263 632 VGYLGTNTPID------ECYECGFTGEFEC------TEKGFTCPKCGNH 668 (711)
T ss_pred CCeEEeCCCCc------ccCCCCCCccccC------CCCCCcCcCCCCC
Confidence 55555555555 8999997432211 0112679999954
No 89
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=27.22 E-value=42 Score=24.47 Aligned_cols=21 Identities=14% Similarity=0.017 Sum_probs=14.8
Q ss_pred ecCCCCceEEEecccccccccCCccCccccchh
Q 013725 335 KNSATGEIVIKHLNRDQEADQSNFRDAATSAEL 367 (437)
Q Consensus 335 ~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~~ 367 (437)
+|++||.-. | ...||.||...
T Consensus 7 ~C~~CgvYT---L---------k~~CP~CG~~t 27 (56)
T PRK13130 7 KCPKCGVYT---L---------KEICPVCGGKT 27 (56)
T ss_pred ECCCCCCEE---c---------cccCcCCCCCC
Confidence 799998522 2 34699999874
No 90
>TIGR00186 rRNA_methyl_3 rRNA methylase, putative, group 3. this is part of the trmH (spoU) family of rRNA methylases
Probab=27.19 E-value=1.5e+02 Score=28.14 Aligned_cols=39 Identities=15% Similarity=0.191 Sum_probs=25.6
Q ss_pred HHHHHHHHhcCCeEEEeCCCCchhhhhh--cccccEEEEeecc
Q 013725 377 EWFANEYKQFGCTLEFVTNKSQEGSQFC--RGFGGIGGILRYQ 417 (437)
Q Consensus 377 ~~l~~~a~~~ga~V~vvs~~~e~G~q~l--~~~GGIaAiLRy~ 417 (437)
..++..+.+.+..+..++..- =.++. ....||.|+.+.+
T Consensus 32 ~~~~~~~~~~~~~~~~v~~~~--l~~l~~~~~~qGv~a~~~~~ 72 (237)
T TIGR00186 32 KKLIQLAKKQGINIQLVDRQK--LDQLTKGGNHQGIAAKVKPI 72 (237)
T ss_pred HHHHHHHHHcCCcEEEeCHHH--HHHHhCCCCCCeEEEEEecC
Confidence 356777788889999997532 11211 2367999999854
No 91
>PRK10864 putative methyltransferase; Provisional
Probab=27.06 E-value=1.8e+02 Score=29.35 Aligned_cols=71 Identities=8% Similarity=0.071 Sum_probs=46.4
Q ss_pred CcEEEcHHHHHHHHHh--CCccEEEeccCccccceeeecCCCCceEEEecccccccccCCccCccccchhhhhhhccHHH
Q 013725 300 GKYVFGVDDTLKALEL--GAVEILIVWENLDINRYVLKNSATGEIVIKHLNRDQEADQSNFRDAATSAELEVQEKTSLLE 377 (437)
Q Consensus 300 g~a~yG~~eV~~Al~~--GaV~tLlV~d~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~~~~~~~~~~v~ 377 (437)
...+||...|.+|++. ..|..|++.++.. + . ..
T Consensus 108 ~~~I~G~~aV~ealk~~~~~i~~l~~~~~~~--------~----------------------------~---------~~ 142 (346)
T PRK10864 108 ETRVYGENACQALFQSRPEAIVRAWFIQSVT--------P----------------------------R---------FK 142 (346)
T ss_pred CcEEEEHHHHHHHHhCCCCceeEEEEecCcc--------H----------------------------H---------HH
Confidence 4578999999999986 4678888865421 0 0 13
Q ss_pred HHHHHHHhcCCeEEEeCCCCchhhhh--hcccccEEEEeecc
Q 013725 378 WFANEYKQFGCTLEFVTNKSQEGSQF--CRGFGGIGGILRYQ 417 (437)
Q Consensus 378 ~l~~~a~~~ga~V~vvs~~~e~G~q~--l~~~GGIaAiLRy~ 417 (437)
+++..+...+..+.+|+..-- .++ ....+||+|+.+-+
T Consensus 143 ~il~~~~~~~~~v~~V~~~~l--~kls~~~~hqGV~A~v~~~ 182 (346)
T PRK10864 143 EALRWMAANRKAYHVVDEAEL--TKASGTEHHGGVCFLIKKR 182 (346)
T ss_pred HHHHHHHHcCCcEEEeCHHHH--HHHhCCCCCCeEEEEEeCC
Confidence 455656667778888875321 221 13478999998743
No 92
>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.
Probab=26.71 E-value=99 Score=24.67 Aligned_cols=30 Identities=17% Similarity=0.169 Sum_probs=20.0
Q ss_pred HHHHHHHHHhcCCeEEEeCCCCchhhhhhcccccEEEEeecccC
Q 013725 376 LEWFANEYKQFGCTLEFVTNKSQEGSQFCRGFGGIGGILRYQLD 419 (437)
Q Consensus 376 v~~l~~~a~~~ga~V~vvs~~~e~G~q~l~~~GGIaAiLRy~~~ 419 (437)
--.|-+.+.+.||+|.-|+.. -|||||+-.
T Consensus 20 ~~RL~qLsdNCGGkVl~v~~~--------------tAilrF~~~ 49 (90)
T PF11608_consen 20 KNRLRQLSDNCGGKVLSVSGG--------------TAILRFPNQ 49 (90)
T ss_dssp HHHHHHHHHTTT--EEE--TT---------------EEEEESSH
T ss_pred HHHHHHHhhccCCEEEEEeCC--------------EEEEEeCCH
Confidence 457778899999999998753 388999865
No 93
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=26.48 E-value=63 Score=36.16 Aligned_cols=21 Identities=5% Similarity=0.039 Sum_probs=14.7
Q ss_pred ecCCCCceEEEecccccccccCCccCccccch
Q 013725 335 KNSATGEIVIKHLNRDQEADQSNFRDAATSAE 366 (437)
Q Consensus 335 ~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~ 366 (437)
+|+.||.... ....||.||..
T Consensus 682 ~C~~CG~~~~-----------~~~~CP~CG~~ 702 (735)
T PRK07111 682 RCPVCGYLGV-----------IEDKCPKCGST 702 (735)
T ss_pred ecCCCCCCCC-----------cCccCcCCCCc
Confidence 7999996321 13679999953
No 94
>COG5622 Protein required for attachment to host cells [Cell motility and secretion]
Probab=26.06 E-value=41 Score=28.96 Aligned_cols=64 Identities=11% Similarity=0.155 Sum_probs=47.4
Q ss_pred HHHHHHHHHHHHHhhcCCCCCCCCccEEEEecChhcHHHhhhccCCChhhhcceeEEEeCCCCCcccHHHHH
Q 013725 198 HNYVRKTAELATQFFINPATSQPNVSGLILAGSADFKTELSQSDMFDPRLQAKILNVVDVSYGGENGFNQAI 269 (437)
Q Consensus 198 ~~f~~~Vae~l~~~f~~~~~~~~~~~~lilaGp~~~k~~f~~~~~l~~~l~~~vi~~v~~s~~~~~gl~E~l 269 (437)
++|...+++.+.+... ...++-|||+-+..+.-.+++ .|++.|++++++.++-...+. ++.++.
T Consensus 70 ~~fa~~~a~~l~r~v~-----~g~~~~LvIiAaPrtLG~lRK--~lh~~lk~~~~~EI~Kdlt~H-~v~~ie 133 (139)
T COG5622 70 DSFAAEIAKELNRSVH-----GGKFKNLVIIAAPRTLGELRK--ELHKGLKEKLTAEIAKDLTGH-PVDEIE 133 (139)
T ss_pred hhHHHHHHHHHHHHHh-----hcccceeEEEeCchhHHHHHH--HHHHHHHHHHHHHHhhHhhcC-cHHHHH
Confidence 6899999999998865 367888888888888888885 578889988876666555443 344443
No 95
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=25.58 E-value=51 Score=27.59 Aligned_cols=26 Identities=15% Similarity=-0.017 Sum_probs=15.8
Q ss_pred eecCCCCceEEEecccccccccCCccCccccch
Q 013725 334 LKNSATGEIVIKHLNRDQEADQSNFRDAATSAE 366 (437)
Q Consensus 334 ~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~ 366 (437)
++|.+||.... .. ......||.||..
T Consensus 71 ~~C~~Cg~~~~--~~-----~~~~~~CP~Cgs~ 96 (114)
T PRK03681 71 CWCETCQQYVT--LL-----TQRVRRCPQCHGD 96 (114)
T ss_pred EEcccCCCeee--cC-----CccCCcCcCcCCC
Confidence 59999996321 00 0112569999966
No 96
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=25.12 E-value=35 Score=33.60 Aligned_cols=31 Identities=3% Similarity=-0.192 Sum_probs=19.1
Q ss_pred ecCCCCceEEEecccccccccCCccCccccchhhhh
Q 013725 335 KNSATGEIVIKHLNRDQEADQSNFRDAATSAELEVQ 370 (437)
Q Consensus 335 ~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~~~~~ 370 (437)
+|+.|+... +... -..+...||.||.-+.+.
T Consensus 40 kc~~C~~~~--~~~~---l~~~~~vcp~c~~h~rlt 70 (296)
T CHL00174 40 QCENCYGLN--YKKF---LKSKMNICEQCGYHLKMS 70 (296)
T ss_pred ECCCccchh--hHHH---HHHcCCCCCCCCCCcCCC
Confidence 899998621 1110 023456899999876543
No 97
>COG1150 HdrC Heterodisulfide reductase, subunit C [Energy production and conversion]
Probab=25.08 E-value=61 Score=29.86 Aligned_cols=63 Identities=13% Similarity=0.035 Sum_probs=44.1
Q ss_pred EEEcHHHHHHHHHhCCccEEEeccCccccceeeecCCCCceEEEecccccccccCCccCccccchhhhhhhccHHHHHHH
Q 013725 302 YVFGVDDTLKALELGAVEILIVWENLDINRYVLKNSATGEIVIKHLNRDQEADQSNFRDAATSAELEVQEKTSLLEWFAN 381 (437)
Q Consensus 302 a~yG~~eV~~Al~~GaV~tLlV~d~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~~~~~~~~~~v~~l~~ 381 (437)
..|+...+.+-+..|-++ +++.++.. |.|..|.. =..+||..- ...+++-.|-+
T Consensus 57 t~y~pR~ii~~~~~g~~d-~il~~~~l-----W~C~tCyt--------------C~eRCPr~v------~i~~vv~~lR~ 110 (195)
T COG1150 57 TDYSPRKIIRKARLGLVD-LILSSESL-----WACVTCYT--------------CTERCPRGV------KIVEVVKALRN 110 (195)
T ss_pred CCCCHHHHHHHHHcccHH-HHhcCCcc-----eeeeechh--------------hhhhCCCCC------CHHHHHHHHHH
Confidence 469999999999999999 44444443 89988842 145788843 33556667777
Q ss_pred HHHhcCCeE
Q 013725 382 EYKQFGCTL 390 (437)
Q Consensus 382 ~a~~~ga~V 390 (437)
.|.+.|-..
T Consensus 111 ~a~k~G~~~ 119 (195)
T COG1150 111 IAVKEGLIE 119 (195)
T ss_pred HHHHhcccc
Confidence 777777654
No 98
>PHA00626 hypothetical protein
Probab=24.32 E-value=55 Score=23.80 Aligned_cols=31 Identities=6% Similarity=-0.018 Sum_probs=17.1
Q ss_pred ecCCCCceEEEecccccccc-cCCccCccccchh
Q 013725 335 KNSATGEIVIKHLNRDQEAD-QSNFRDAATSAEL 367 (437)
Q Consensus 335 ~~~~~~~~~~~~~~~~~~~~-~~~~~cp~~~~~~ 367 (437)
.||+||...+. .... -.. +....||.||-.+
T Consensus 2 ~CP~CGS~~Iv-rcg~-cr~~snrYkCkdCGY~f 33 (59)
T PHA00626 2 SCPKCGSGNIA-KEKT-MRGWSDDYVCCDCGYND 33 (59)
T ss_pred CCCCCCCceee-eece-ecccCcceEcCCCCCee
Confidence 58888864332 1000 011 3467899999663
No 99
>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=24.24 E-value=38 Score=20.53 Aligned_cols=10 Identities=0% Similarity=-0.333 Sum_probs=7.2
Q ss_pred CccCccccch
Q 013725 357 NFRDAATSAE 366 (437)
Q Consensus 357 ~~~cp~~~~~ 366 (437)
...||.||-.
T Consensus 14 ~~~Cp~CG~~ 23 (26)
T PF10571_consen 14 AKFCPHCGYD 23 (26)
T ss_pred cCcCCCCCCC
Confidence 4568888865
No 100
>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=23.88 E-value=48 Score=21.52 Aligned_cols=22 Identities=5% Similarity=0.066 Sum_probs=10.9
Q ss_pred ecCCCCceEEEecccccccccCCccCccccch
Q 013725 335 KNSATGEIVIKHLNRDQEADQSNFRDAATSAE 366 (437)
Q Consensus 335 ~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~ 366 (437)
+|.+||.... +....||.|+..
T Consensus 13 rC~~Cg~~~~----------pPr~~Cp~C~s~ 34 (37)
T PF12172_consen 13 RCRDCGRVQF----------PPRPVCPHCGSD 34 (37)
T ss_dssp E-TTT--EEE----------S--SEETTTT--
T ss_pred EcCCCCCEec----------CCCcCCCCcCcc
Confidence 8999986332 234679999865
No 101
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=23.87 E-value=26 Score=39.15 Aligned_cols=12 Identities=8% Similarity=0.158 Sum_probs=0.0
Q ss_pred ecCCCCceEEEe
Q 013725 335 KNSATGEIVIKH 346 (437)
Q Consensus 335 ~~~~~~~~~~~~ 346 (437)
+|++||..+...
T Consensus 657 ~Cp~Cg~~t~~~ 668 (900)
T PF03833_consen 657 RCPKCGKETFYN 668 (900)
T ss_dssp ------------
T ss_pred cCcccCCcchhh
Confidence 677777654433
No 102
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=23.85 E-value=32 Score=28.69 Aligned_cols=28 Identities=11% Similarity=0.006 Sum_probs=17.8
Q ss_pred eecCCCCceEEEecccccccccCCccCccccchhhh
Q 013725 334 LKNSATGEIVIKHLNRDQEADQSNFRDAATSAELEV 369 (437)
Q Consensus 334 ~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~~~~ 369 (437)
.+||+|+..+- .+. ....|+.|+.++..
T Consensus 70 V~CP~C~K~TK-mLG-------r~D~CM~C~~pLTL 97 (114)
T PF11023_consen 70 VECPNCGKQTK-MLG-------RVDACMHCKEPLTL 97 (114)
T ss_pred eECCCCCChHh-hhc-------hhhccCcCCCcCcc
Confidence 48999986221 111 13579999988643
No 103
>PF05991 NYN_YacP: YacP-like NYN domain; InterPro: IPR010298 This family consists of several hypothetical bacterial proteins as well as some uncharacterised sequences from Arabidopsis thaliana. The function of this family is unknown.
Probab=23.36 E-value=3e+02 Score=24.51 Aligned_cols=36 Identities=22% Similarity=0.283 Sum_probs=23.7
Q ss_pred ccHHHHHHHHHHhcCCeEEEeCCCCchhhhhhccccc
Q 013725 373 TSLLEWFANEYKQFGCTLEFVTNKSQEGSQFCRGFGG 409 (437)
Q Consensus 373 ~~~v~~l~~~a~~~ga~V~vvs~~~e~G~q~l~~~GG 409 (437)
+++|+.++......+.+|.||++++..-.. ..+.|.
T Consensus 80 D~~Ie~~v~~~~~~~~~v~VVTSD~~iq~~-~~~~GA 115 (166)
T PF05991_consen 80 DDYIERLVRELKNRPRQVTVVTSDREIQRA-ARGRGA 115 (166)
T ss_pred HHHHHHHHHHhccCCCeEEEEeCCHHHHHH-HhhCCC
Confidence 344556666655556799999999876554 555554
No 104
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=23.21 E-value=51 Score=27.72 Aligned_cols=26 Identities=8% Similarity=-0.073 Sum_probs=15.3
Q ss_pred eecCCCCceEEEecccccccccCCccCccccch
Q 013725 334 LKNSATGEIVIKHLNRDQEADQSNFRDAATSAE 366 (437)
Q Consensus 334 ~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~ 366 (437)
.+|.+||.... +. ......||.||..
T Consensus 72 ~~C~~Cg~~~~--~~-----~~~~~~CP~Cgs~ 97 (117)
T PRK00564 72 LECKDCSHVFK--PN-----ALDYGVCEKCHSK 97 (117)
T ss_pred EEhhhCCCccc--cC-----CccCCcCcCCCCC
Confidence 59999985210 00 0112359999976
No 105
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=23.07 E-value=71 Score=20.41 Aligned_cols=25 Identities=16% Similarity=0.077 Sum_probs=14.5
Q ss_pred ecCCCCceEEEecccccccccCCccCccccch
Q 013725 335 KNSATGEIVIKHLNRDQEADQSNFRDAATSAE 366 (437)
Q Consensus 335 ~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~ 366 (437)
.|.+||.... +. .....+||.||.+
T Consensus 2 ~C~~Cg~~~~--~~-----~~~~irC~~CG~R 26 (32)
T PF03604_consen 2 ICGECGAEVE--LK-----PGDPIRCPECGHR 26 (32)
T ss_dssp BESSSSSSE---BS-----TSSTSSBSSSS-S
T ss_pred CCCcCCCeeE--cC-----CCCcEECCcCCCe
Confidence 5777876432 11 1235689999976
No 106
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=22.13 E-value=96 Score=33.98 Aligned_cols=33 Identities=9% Similarity=0.024 Sum_probs=20.5
Q ss_pred ccEEEeccCccccceeeecCCCCceEEEecccccccccCCccCccccch
Q 013725 318 VEILIVWENLDINRYVLKNSATGEIVIKHLNRDQEADQSNFRDAATSAE 366 (437)
Q Consensus 318 V~tLlV~d~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~ 366 (437)
+.-.=++-.+. +|+.||... ......||.||..
T Consensus 557 i~Yf~in~~~~------iC~~CG~~~----------~g~~~~CP~CGs~ 589 (623)
T PRK08271 557 CNYFAFNVKIT------ICNDCHHID----------KRTGKRCPICGSE 589 (623)
T ss_pred CceEEeCCCCc------cCCCCCCcC----------CCCCcCCcCCCCc
Confidence 44444455555 899999731 1125689999954
No 107
>PRK04023 DNA polymerase II large subunit; Validated
Probab=22.08 E-value=74 Score=36.47 Aligned_cols=31 Identities=16% Similarity=0.112 Sum_probs=15.2
Q ss_pred ccCccccchhhhh--hhccHHHHHHHHHHhcCC
Q 013725 358 FRDAATSAELEVQ--EKTSLLEWFANEYKQFGC 388 (437)
Q Consensus 358 ~~cp~~~~~~~~~--~~~~~v~~l~~~a~~~ga 388 (437)
..||.||.+.... ...++-+.+-+..++-|-
T Consensus 664 y~CPKCG~El~~~s~~~i~l~~~~~~A~~~lg~ 696 (1121)
T PRK04023 664 DECEKCGREPTPYSKRKIDLKELYDRALENLGE 696 (1121)
T ss_pred CcCCCCCCCCCccceEEecHHHHHHHHHHHhCC
Confidence 4577777663322 124455444444445444
No 108
>PRK14873 primosome assembly protein PriA; Provisional
Probab=22.01 E-value=84 Score=34.74 Aligned_cols=40 Identities=8% Similarity=0.023 Sum_probs=22.5
Q ss_pred cchHHHHHhhccCCcEEEEEEECCceEEEEEeCCeEEEEe
Q 013725 130 FHTEALNELLESDDKFGFIVMDGNGTLFGTLSGNTREVLH 169 (437)
Q Consensus 130 ~~l~~L~~~~~~~~~~~vvvvd~~~A~i~~~~g~~~~~~~ 169 (437)
-.-+.+..+..-..--.-|||-...|.|.=+..-+..++.
T Consensus 225 ~~~~R~~~w~~~~~G~~~IViGtRSAvFaP~~~LgLIIvd 264 (665)
T PRK14873 225 GPADRYRRWLAVLRGQARVVVGTRSAVFAPVEDLGLVAIW 264 (665)
T ss_pred CHHHHHHHHHHHhCCCCcEEEEcceeEEeccCCCCEEEEE
Confidence 3445555544433233356777778888777665555443
No 109
>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=22.01 E-value=66 Score=21.08 Aligned_cols=30 Identities=17% Similarity=0.025 Sum_probs=17.6
Q ss_pred eecCCCCceEEEecccccccccCCccCccccchh
Q 013725 334 LKNSATGEIVIKHLNRDQEADQSNFRDAATSAEL 367 (437)
Q Consensus 334 ~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~~ 367 (437)
+.|+.||..=.....|. +....|..||+++
T Consensus 2 r~C~~Cg~~Yh~~~~pP----~~~~~Cd~cg~~L 31 (36)
T PF05191_consen 2 RICPKCGRIYHIEFNPP----KVEGVCDNCGGEL 31 (36)
T ss_dssp EEETTTTEEEETTTB------SSTTBCTTTTEBE
T ss_pred cCcCCCCCccccccCCC----CCCCccCCCCCee
Confidence 37888986332222221 3356799999874
No 110
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=21.75 E-value=1.3e+02 Score=25.03 Aligned_cols=43 Identities=12% Similarity=0.004 Sum_probs=24.9
Q ss_pred eeecCCCCceEEEecccccccccCCccCccccchhhhhhhccHHHHHHHHHHh
Q 013725 333 VLKNSATGEIVIKHLNRDQEADQSNFRDAATSAELEVQEKTSLLEWFANEYKQ 385 (437)
Q Consensus 333 ~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~~~~~~~~~~v~~l~~~a~~ 385 (437)
.++|++||...+.+.+= + .-.||.||... .+.-++...+....
T Consensus 42 ~~~C~~Cg~~~~~~~SC-----k-~R~CP~C~~~~----~~~W~~~~~~~ll~ 84 (111)
T PF14319_consen 42 RYRCEDCGHEKIVYNSC-----K-NRHCPSCQAKA----TEQWIEKQREDLLP 84 (111)
T ss_pred eeecCCCCceEEecCcc-----c-CcCCCCCCChH----HHHHHHHHHhhCCC
Confidence 35899999866543221 1 23799999772 33444444444444
No 111
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.72 E-value=46 Score=25.90 Aligned_cols=28 Identities=4% Similarity=-0.175 Sum_probs=15.0
Q ss_pred ecCCCCceEEEecccccccccCCccCccccch
Q 013725 335 KNSATGEIVIKHLNRDQEADQSNFRDAATSAE 366 (437)
Q Consensus 335 ~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~ 366 (437)
.||+|+-.-+ +.+-....-.-||.|++-
T Consensus 3 lCP~C~v~l~----~~~rs~vEiD~CPrCrGV 30 (88)
T COG3809 3 LCPICGVELV----MSVRSGVEIDYCPRCRGV 30 (88)
T ss_pred ccCcCCceee----eeeecCceeeeCCccccE
Confidence 6899975321 111001223469999865
No 112
>PF01976 DUF116: Protein of unknown function DUF116; InterPro: IPR002829 These archaeal and bacterial proteins have no known function. Members of this family contain seven conserved cysteines and may also be an integral membrane protein.
Probab=21.68 E-value=92 Score=27.72 Aligned_cols=37 Identities=5% Similarity=0.032 Sum_probs=28.9
Q ss_pred CccCccccchhhhhhhccHHHHHHHHHHhcCCeEEEeCCCCchhh
Q 013725 357 NFRDAATSAELEVQEKTSLLEWFANEYKQFGCTLEFVTNKSQEGS 401 (437)
Q Consensus 357 ~~~cp~~~~~~~~~~~~~~v~~l~~~a~~~ga~V~vvs~~~e~G~ 401 (437)
-..|..||.-- +-.|.+.+++.|-+|.++++.+-.-+
T Consensus 64 g~~C~~Cg~C~--------Ig~l~~lae~~g~~v~i~~Ggt~ar~ 100 (158)
T PF01976_consen 64 GYNCKRCGKCD--------IGDLKKLAEKYGYKVYIATGGTLARK 100 (158)
T ss_pred CCcCCCCCCCc--------hhHHHHHHHHcCCEEEEEcChHHHHH
Confidence 34677887542 46899999999999999999875543
No 113
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=21.51 E-value=61 Score=22.91 Aligned_cols=29 Identities=14% Similarity=0.118 Sum_probs=17.4
Q ss_pred eeeecCCCCceEEEecccccccccCCccCccccch
Q 013725 332 YVLKNSATGEIVIKHLNRDQEADQSNFRDAATSAE 366 (437)
Q Consensus 332 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~ 366 (437)
..++|..||.... .+..-...+||.||.+
T Consensus 5 ~~Y~C~~Cg~~~~------~~~~~~~irCp~Cg~r 33 (49)
T COG1996 5 MEYKCARCGREVE------LDQETRGIRCPYCGSR 33 (49)
T ss_pred EEEEhhhcCCeee------hhhccCceeCCCCCcE
Confidence 3468999986321 0001234689999977
No 114
>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=20.72 E-value=78 Score=22.43 Aligned_cols=12 Identities=8% Similarity=0.080 Sum_probs=9.2
Q ss_pred cCCccCccccch
Q 013725 355 QSNFRDAATSAE 366 (437)
Q Consensus 355 ~~~~~cp~~~~~ 366 (437)
+....||.||..
T Consensus 32 p~~w~CP~C~a~ 43 (50)
T cd00730 32 PDDWVCPVCGAG 43 (50)
T ss_pred CCCCCCCCCCCc
Confidence 446799999965
No 115
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=20.69 E-value=70 Score=20.93 Aligned_cols=31 Identities=6% Similarity=-0.027 Sum_probs=17.5
Q ss_pred eecCCCCceEEEeccccccc-ccCCccCccccch
Q 013725 334 LKNSATGEIVIKHLNRDQEA-DQSNFRDAATSAE 366 (437)
Q Consensus 334 ~~~~~~~~~~~~~~~~~~~~-~~~~~~cp~~~~~ 366 (437)
..||+|+.. +-+.+.+.+ .....+||.|+..
T Consensus 3 i~CP~C~~~--f~v~~~~l~~~~~~vrC~~C~~~ 34 (37)
T PF13719_consen 3 ITCPNCQTR--FRVPDDKLPAGGRKVRCPKCGHV 34 (37)
T ss_pred EECCCCCce--EEcCHHHcccCCcEEECCCCCcE
Confidence 378888752 223333332 2336789998865
No 116
>COG2401 ABC-type ATPase fused to a predicted acetyltransferase domain [General function prediction only]
Probab=20.68 E-value=35 Score=35.38 Aligned_cols=28 Identities=7% Similarity=0.150 Sum_probs=17.3
Q ss_pred eeeecCCCCceEEEecccccccccCCccCccccchhhh
Q 013725 332 YVLKNSATGEIVIKHLNRDQEADQSNFRDAATSAELEV 369 (437)
Q Consensus 332 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~~~~ 369 (437)
..|+|+.||..-. ....+.| .||..+++
T Consensus 129 a~w~c~~cg~~ie---------an~kp~c-~cg~~~~~ 156 (593)
T COG2401 129 ALWRCEKCGTIIE---------ANTKPEC-KCGSHVHI 156 (593)
T ss_pred EEEecchhchhhh---------hcCCccc-CCCCceEE
Confidence 3489999996221 1224568 88876544
No 117
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=20.68 E-value=44 Score=33.43 Aligned_cols=23 Identities=9% Similarity=-0.051 Sum_probs=15.6
Q ss_pred eecCCCCceEEEecccccccccCCccCccccch
Q 013725 334 LKNSATGEIVIKHLNRDQEADQSNFRDAATSAE 366 (437)
Q Consensus 334 ~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~ 366 (437)
|.|..||.... .=...||.|+.-
T Consensus 355 ~~c~~cg~~~~----------~~~~~c~~c~~~ 377 (389)
T PRK11788 355 YRCRNCGFTAR----------TLYWHCPSCKAW 377 (389)
T ss_pred EECCCCCCCCc----------cceeECcCCCCc
Confidence 58999997321 114689999854
No 118
>COG1867 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=20.64 E-value=90 Score=31.75 Aligned_cols=48 Identities=17% Similarity=0.208 Sum_probs=25.5
Q ss_pred ceeeecCCCCceEEEecccccccccCCccCccccch------hhhh--hhccHHHHHHHHHHh
Q 013725 331 RYVLKNSATGEIVIKHLNRDQEADQSNFRDAATSAE------LEVQ--EKTSLLEWFANEYKQ 385 (437)
Q Consensus 331 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~------~~~~--~~~~~v~~l~~~a~~ 385 (437)
++++.|+.||+.. ... ......||.||+. +++- ....+++.+++.+++
T Consensus 238 g~~~~c~~cg~~~-~~~------~~~~~~c~~Cg~~~~~~GPlW~GpL~d~~f~e~~l~~~~~ 293 (380)
T COG1867 238 GYIYHCSRCGEIV-GSF------REVDEKCPHCGGKVHLAGPLWLGPLHDEEFIEEMLEIAEG 293 (380)
T ss_pred CcEEEccccccee-ccc------ccccccCCcccccceeccCcccCcccCHHHHHHHHHHhhc
Confidence 4456788887311 000 1235679999944 3321 225566677666643
No 119
>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=20.63 E-value=92 Score=33.63 Aligned_cols=22 Identities=18% Similarity=0.134 Sum_probs=15.2
Q ss_pred ecCCCCceEEEecccccccccCCccCccccch
Q 013725 335 KNSATGEIVIKHLNRDQEADQSNFRDAATSAE 366 (437)
Q Consensus 335 ~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~ 366 (437)
+|.+||.... .....||.||.+
T Consensus 520 ~C~~CG~~~~----------~~~~~CP~CGs~ 541 (555)
T cd01675 520 ICNDCGYIGE----------GEGFKCPKCGSE 541 (555)
T ss_pred cCCCCCCCCc----------CCCCCCcCCCCc
Confidence 7999986221 124689999965
No 120
>PRK10124 putative UDP-glucose lipid carrier transferase; Provisional
Probab=20.29 E-value=1e+03 Score=24.96 Aligned_cols=67 Identities=9% Similarity=0.181 Sum_probs=46.2
Q ss_pred Ec-HHHHHHHHHhCCccEEEeccCccccceeeecCCCCceEEEecccccccccCCccCccccchhhhhhhccHHHHHHHH
Q 013725 304 FG-VDDTLKALELGAVEILIVWENLDINRYVLKNSATGEIVIKHLNRDQEADQSNFRDAATSAELEVQEKTSLLEWFANE 382 (437)
Q Consensus 304 yG-~~eV~~Al~~GaV~tLlV~d~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~cp~~~~~~~~~~~~~~v~~l~~~ 382 (437)
+| .+++.+.++...|+.++|+-+.. .. .+ +.++++.
T Consensus 189 lG~~~dL~~~v~~~~IdeViIAip~~-----------~~-----------------------~~---------l~ell~~ 225 (463)
T PRK10124 189 AGNLQQLVEDAKAGKIHNVYIAMSMC-----------DG-----------------------AR---------VKKLVRQ 225 (463)
T ss_pred CCCHHHHHHHHHhCCCCEEEEeCCCc-----------ch-----------------------HH---------HHHHHHH
Confidence 44 47788899999999999975332 00 01 4688999
Q ss_pred HHhcCCeEEEeCCCCch---hhhhhcccccEEEEe
Q 013725 383 YKQFGCTLEFVTNKSQE---GSQFCRGFGGIGGIL 414 (437)
Q Consensus 383 a~~~ga~V~vvs~~~e~---G~q~l~~~GGIaAiL 414 (437)
+...|.+|.++|+-.+- ... +..+||+-.+-
T Consensus 226 ~~~~~v~V~ivP~l~~~~~~~~~-~~~~~~~p~~~ 259 (463)
T PRK10124 226 LADTTCSVLLIPDVFTFNILHSR-LEEMNGVPVVP 259 (463)
T ss_pred HHHcCCeEEEecchhhccccccc-hhhcCCeeEEE
Confidence 99999999999975421 122 56677766553
Done!