Query 013759
Match_columns 437
No_of_seqs 184 out of 804
Neff 7.7
Searched_HMMs 46136
Date Fri Mar 29 07:06:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013759.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013759hhsearch_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 2.5E-92 5.3E-97 714.5 45.2 403 12-418 1-403 (403)
2 TIGR00108 eRF peptide chain re 100.0 7.8E-89 1.7E-93 691.6 45.0 407 9-419 2-408 (409)
3 PRK04011 peptide chain release 100.0 2.7E-88 5.9E-93 688.0 45.5 407 8-418 4-411 (411)
4 COG1503 eRF1 Peptide chain rel 100.0 5E-80 1.1E-84 608.6 31.1 406 9-419 5-410 (411)
5 KOG0688 Peptide chain release 100.0 2.3E-75 5E-80 548.0 21.7 425 8-436 5-429 (431)
6 TIGR00111 pelota probable tran 100.0 1.2E-61 2.6E-66 484.8 28.1 325 29-418 10-351 (351)
7 KOG2869 Meiotic cell division 100.0 8.5E-63 1.8E-67 465.5 13.8 354 18-429 2-379 (379)
8 COG1537 PelA Predicted RNA-bin 100.0 2.2E-52 4.8E-57 403.6 26.1 328 31-419 10-352 (352)
9 PF03465 eRF1_3: eRF1 domain 3 100.0 9.9E-29 2.1E-33 208.2 7.3 113 281-418 1-113 (113)
10 PF03464 eRF1_2: eRF1 domain 2 99.9 9.8E-23 2.1E-27 177.2 12.4 130 144-278 1-133 (133)
11 PF03463 eRF1_1: eRF1 domain 1 99.5 4.1E-15 9E-20 129.0 1.5 110 29-140 11-131 (132)
12 PF10116 Host_attach: Protein 97.3 0.00029 6.2E-09 61.6 4.9 117 145-269 1-135 (138)
13 PRK07714 hypothetical protein; 93.2 0.61 1.3E-05 38.3 8.3 30 298-327 15-44 (100)
14 PRK13602 putative ribosomal pr 93.1 0.59 1.3E-05 36.9 7.7 60 299-402 9-68 (82)
15 PRK13600 putative ribosomal pr 93.0 0.44 9.5E-06 37.8 6.8 57 302-402 14-70 (84)
16 PRK07283 hypothetical protein; 92.9 0.74 1.6E-05 37.6 8.3 31 297-327 14-44 (98)
17 PF08032 SpoU_sub_bind: RNA 2' 92.3 0.25 5.5E-06 37.8 4.6 69 303-417 2-73 (76)
18 PRK06683 hypothetical protein; 91.2 1.3 2.9E-05 34.9 7.6 60 299-402 9-68 (82)
19 TIGR03677 rpl7ae 50S ribosomal 90.7 1.8 3.9E-05 36.6 8.4 74 299-415 24-98 (117)
20 PTZ00106 60S ribosomal protein 90.4 1.8 4E-05 36.0 8.1 39 288-327 13-51 (108)
21 PRK01018 50S ribosomal protein 90.4 2.2 4.8E-05 34.9 8.5 60 299-402 14-74 (99)
22 PRK05583 ribosomal protein L7A 89.8 1.7 3.6E-05 36.0 7.4 31 297-327 13-43 (104)
23 PRK04175 rpl7ae 50S ribosomal 89.6 3.5 7.6E-05 35.1 9.4 61 299-402 28-88 (122)
24 COG1358 RPL8A Ribosomal protei 89.2 1.4 3E-05 37.3 6.5 61 299-402 25-85 (116)
25 PRK13601 putative L7Ae-like ri 88.6 2.3 4.9E-05 33.7 7.0 60 299-402 6-65 (82)
26 PF01248 Ribosomal_L7Ae: Ribos 88.5 3 6.5E-05 33.5 8.0 61 299-402 13-73 (95)
27 PRK09190 hypothetical protein; 86.9 6.2 0.00013 37.2 10.1 33 296-328 106-138 (220)
28 PRK00398 rpoP DNA-directed RNA 85.2 0.46 9.9E-06 33.1 1.2 37 333-375 3-39 (46)
29 TIGR00373 conserved hypothetic 82.2 1.2 2.7E-05 39.7 3.0 45 334-383 110-154 (158)
30 PRK06266 transcription initiat 80.1 1.9 4E-05 39.4 3.5 46 334-384 118-163 (178)
31 PRK03824 hypA hydrogenase nick 76.1 8.8 0.00019 33.3 6.3 11 356-366 106-116 (135)
32 COG1911 RPL30 Ribosomal protei 75.3 43 0.00093 27.2 9.4 71 299-414 17-88 (100)
33 PTZ00222 60S ribosomal protein 75.3 33 0.00071 33.0 10.3 71 301-414 132-202 (263)
34 COG5622 Protein required for a 73.6 1.1 2.4E-05 38.3 0.1 66 197-270 69-134 (139)
35 smart00531 TFIIE Transcription 70.0 3 6.5E-05 36.7 2.0 41 334-376 100-142 (147)
36 smart00834 CxxC_CXXC_SSSS Puta 69.4 7.8 0.00017 25.7 3.6 34 330-366 2-35 (41)
37 COG1592 Rubrerythrin [Energy p 69.1 3.8 8.3E-05 36.8 2.5 24 334-366 135-158 (166)
38 PTZ00365 60S ribosomal protein 66.4 33 0.00071 33.1 8.2 73 300-415 131-203 (266)
39 COG2433 Uncharacterized conser 63.8 18 0.00039 38.8 6.5 32 180-211 149-180 (652)
40 PF09723 Zn-ribbon_8: Zinc rib 62.2 14 0.00029 25.1 3.6 33 330-365 2-34 (42)
41 PRK05452 anaerobic nitric oxid 57.7 72 0.0016 33.7 10.0 39 221-261 304-348 (479)
42 TIGR02605 CxxC_CxxC_SSSS putat 53.4 21 0.00046 25.1 3.6 33 330-365 2-34 (52)
43 TIGR01206 lysW lysine biosynth 52.5 3.3 7.2E-05 30.0 -0.8 12 358-369 23-34 (54)
44 COG2888 Predicted Zn-ribbon RN 51.6 14 0.00031 27.1 2.4 9 333-341 27-35 (61)
45 COG1439 Predicted nucleic acid 50.6 46 0.001 30.2 6.0 27 331-367 137-163 (177)
46 TIGR00354 polC DNA polymerase, 49.9 30 0.00065 39.3 5.6 62 307-389 607-673 (1095)
47 PRK12496 hypothetical protein; 49.4 12 0.00026 33.6 2.2 29 331-367 125-153 (164)
48 PRK14715 DNA polymerase II lar 48.1 18 0.0004 42.3 3.7 62 307-388 656-721 (1627)
49 COG1852 Uncharacterized conser 48.0 21 0.00045 32.8 3.4 36 355-398 109-144 (209)
50 PF07295 DUF1451: Protein of u 46.8 71 0.0015 28.1 6.5 38 322-366 102-139 (146)
51 cd00729 rubredoxin_SM Rubredox 46.5 22 0.00048 23.0 2.5 26 333-366 2-27 (34)
52 PRK12380 hydrogenase nickel in 45.9 17 0.00038 30.4 2.5 25 334-366 71-95 (113)
53 COG1675 TFA1 Transcription ini 44.5 18 0.00039 32.9 2.5 31 355-385 130-160 (176)
54 smart00659 RPOLCX RNA polymera 44.1 23 0.0005 24.4 2.4 27 333-366 2-28 (44)
55 TIGR00100 hypA hydrogenase nic 40.1 24 0.00053 29.6 2.5 35 320-366 61-95 (115)
56 cd00350 rubredoxin_like Rubred 39.7 25 0.00053 22.5 1.9 25 334-366 2-26 (33)
57 PF09538 FYDLN_acid: Protein o 39.7 13 0.00029 30.9 0.8 30 331-368 7-37 (108)
58 PF01155 HypA: Hydrogenase exp 36.0 21 0.00045 29.9 1.5 25 334-366 71-95 (113)
59 COG1066 Sms Predicted ATP-depe 35.7 22 0.00048 36.7 1.8 25 333-367 7-31 (456)
60 PF08271 TF_Zn_Ribbon: TFIIB z 35.1 21 0.00044 24.3 1.0 28 334-366 1-28 (43)
61 TIGR00416 sms DNA repair prote 33.6 20 0.00044 37.6 1.2 25 333-367 7-31 (454)
62 TIGR02098 MJ0042_CXXC MJ0042 f 33.5 36 0.00078 22.2 2.0 32 334-367 3-35 (38)
63 PF04423 Rad50_zn_hook: Rad50 33.2 28 0.0006 24.9 1.5 24 359-382 22-45 (54)
64 PRK14892 putative transcriptio 32.9 77 0.0017 26.0 4.2 61 334-398 22-88 (99)
65 PRK11181 23S rRNA (guanosine-2 32.5 1.5E+02 0.0032 28.3 6.9 70 301-416 3-76 (244)
66 PRK03681 hypA hydrogenase nick 32.4 36 0.00079 28.5 2.3 26 334-366 71-96 (114)
67 PRK11032 hypothetical protein; 31.9 68 0.0015 28.7 4.1 40 320-366 112-151 (160)
68 PRK11823 DNA repair protein Ra 31.7 24 0.00053 36.9 1.4 26 333-368 7-32 (446)
69 COG0566 SpoU rRNA methylases [ 31.6 2.3E+02 0.0051 27.3 8.1 74 300-418 21-95 (260)
70 PRK14864 putative biofilm stre 31.6 60 0.0013 26.9 3.4 42 372-415 62-103 (104)
71 PRK14890 putative Zn-ribbon RN 30.2 23 0.0005 26.1 0.7 32 332-364 24-55 (59)
72 PHA00626 hypothetical protein 29.7 46 0.001 24.2 2.1 29 355-395 21-49 (59)
73 PF13248 zf-ribbon_3: zinc-rib 29.3 17 0.00037 21.9 -0.1 23 334-366 3-25 (26)
74 PRK14873 primosome assembly pr 29.0 62 0.0013 35.8 4.0 15 224-238 295-309 (665)
75 PF11023 DUF2614: Protein of u 28.8 25 0.00055 29.3 0.8 29 333-369 69-97 (114)
76 PRK00564 hypA hydrogenase nick 28.1 34 0.00074 28.8 1.5 25 334-366 72-97 (117)
77 PF10263 SprT-like: SprT-like 28.0 48 0.001 28.9 2.5 36 330-369 120-155 (157)
78 TIGR02300 FYDLN_acid conserved 27.8 32 0.0007 29.4 1.3 29 331-367 7-36 (129)
79 PF13727 CoA_binding_3: CoA-bi 27.7 1E+02 0.0022 26.7 4.7 51 301-394 125-175 (175)
80 cd01675 RNR_III Class III ribo 27.6 55 0.0012 35.4 3.3 22 335-366 520-541 (555)
81 TIGR02487 NrdD anaerobic ribon 27.5 54 0.0012 35.6 3.3 22 335-366 526-547 (579)
82 PRK10864 putative methyltransf 27.1 1.9E+02 0.0042 29.2 6.9 71 300-417 108-182 (346)
83 COG1150 HdrC Heterodisulfide r 27.1 49 0.0011 30.5 2.4 63 302-390 57-119 (195)
84 COG2260 Predicted Zn-ribbon RN 26.9 46 0.001 24.4 1.7 22 335-368 7-28 (59)
85 COG2956 Predicted N-acetylgluc 26.7 33 0.00072 34.3 1.3 23 334-366 355-377 (389)
86 CHL00181 cbbX CbbX; Provisiona 26.1 3.6E+02 0.0079 26.3 8.5 86 224-315 163-249 (287)
87 PF13397 DUF4109: Domain of un 25.9 70 0.0015 26.5 2.8 34 331-366 26-59 (105)
88 cd01121 Sms Sms (bacterial rad 25.9 24 0.00052 36.0 0.2 23 334-366 1-23 (372)
89 PRK08270 anaerobic ribonucleos 25.9 74 0.0016 35.2 3.9 24 335-369 628-651 (656)
90 PF07754 DUF1610: Domain of un 24.0 32 0.0007 20.6 0.4 10 356-365 15-24 (24)
91 PF14803 Nudix_N_2: Nudix N-te 23.9 42 0.0009 21.8 1.0 12 354-365 19-30 (34)
92 PF05265 DUF723: Protein of un 23.9 79 0.0017 23.4 2.5 41 320-364 20-60 (60)
93 PRK05978 hypothetical protein; 23.4 43 0.00092 29.6 1.2 32 334-370 34-65 (148)
94 TIGR00186 rRNA_methyl_3 rRNA m 23.4 2.5E+02 0.0054 26.6 6.6 38 378-417 33-72 (237)
95 PF11608 Limkain-b1: Limkain b 23.1 1.3E+02 0.0028 24.0 3.7 30 376-419 20-49 (90)
96 CHL00174 accD acetyl-CoA carbo 22.9 33 0.00072 33.8 0.5 31 334-369 39-69 (296)
97 PRK13130 H/ACA RNA-protein com 22.8 65 0.0014 23.5 1.9 23 334-368 6-28 (56)
98 PF01976 DUF116: Protein of un 22.8 93 0.002 27.7 3.3 37 356-400 63-99 (158)
99 PF05191 ADK_lid: Adenylate ki 22.6 74 0.0016 20.9 2.0 30 334-367 2-31 (36)
100 COG1545 Predicted nucleic-acid 22.6 59 0.0013 28.3 2.0 23 334-366 30-52 (140)
101 COG2093 DNA-directed RNA polym 22.4 1E+02 0.0022 23.0 2.8 33 356-402 17-50 (64)
102 PF14353 CpXC: CpXC protein 21.9 63 0.0014 27.3 2.0 11 357-367 38-48 (128)
103 PF03833 PolC_DP2: DNA polymer 21.9 30 0.00065 38.7 0.0 33 334-366 656-689 (900)
104 PRK06450 threonine synthase; V 21.5 52 0.0011 33.1 1.6 27 334-369 4-30 (338)
105 TIGR03025 EPS_sugtrans exopoly 21.3 9.1E+02 0.02 24.9 11.0 116 221-412 124-242 (445)
106 PF12172 DUF35_N: Rubredoxin-l 21.0 65 0.0014 20.9 1.5 23 334-366 12-34 (37)
107 TIGR00515 accD acetyl-CoA carb 20.4 41 0.00089 33.1 0.6 31 334-369 27-57 (285)
108 PRK05654 acetyl-CoA carboxylas 20.2 39 0.00085 33.3 0.4 31 334-369 28-58 (292)
109 PF13240 zinc_ribbon_2: zinc-r 20.1 38 0.00081 19.9 0.2 9 358-366 14-22 (23)
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=2.5e-92 Score=714.45 Aligned_cols=403 Identities=37% Similarity=0.638 Sum_probs=382.3
Q ss_pred HHHHHHHHHHHHHHhcCCCcceEEEEcCCCCCHHHHHhhhhhhhhhchhhhhhhhhcccchhHHHHHHHhhhccccCCCc
Q 013759 12 EIWKIKKLIKALEAARGNGTSMISLIMPPRDQVSRVTKMLGDEFGTASNIKSRVNRQSVLGAITSAQQRLKLYNKVPPNG 91 (437)
Q Consensus 12 ~~~~~~k~l~~l~~~~g~~~~~vsly~~~~~d~~~v~nll~~d~~~a~~ir~k~~r~~~~~~~~~~~~~l~l~~~~~~~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 57999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEeceeecCCCceeEEEEEeecCCCceeeeeeccCccchHHHHHhhcCCCcEEEEEEeCCceEEEEEecCeEEEEEEE
Q 013759 92 LVLYTGTIVTDDGKEKKVTIDFEPFRPINASLYLCDNKFHTDALNELLESDDKFGFIVMDGNGTLFGTLSGNTREVLHKF 171 (437)
Q Consensus 92 l~~f~g~~~~~~~~~~~~t~~l~~~~pv~~~k~~~~~~~~l~~L~~a~~~~~~~~vvvvd~~~A~i~~~~g~~~~~~~~i 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 99999999887788899999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EeecCcccCCCCcchHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCcceEEEecChhhHHHhcccccCChhhhcce
Q 013759 172 SVDLPKKHGRGGQSALRFARLRMEKRHNYVRKTAELATQFYINPATSQPNVSGLVLAGSADFKTELSQSDMFDPRLQAKI 251 (437)
Q Consensus 172 ~~~vp~K~~~gG~s~~Rf~r~~ee~~~~f~~~va~~l~~~~~~~~~~~~~~~~liiaGp~~~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 9999999998999999999999999999999999999998753 11236999999999999999998778999999999
Q ss_pred eEEEECCCCCCccHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHccCCCcEEECHHHHHHHHHhCCccEEEeecCCCcee
Q 013759 252 LKVVDVSYGGENGFNQAIELSAESLSNVKFIQEKRLIGKYFEEISQDTGKYVFGADDTLKALDMGAVDTLIVWENLDITR 331 (437)
Q Consensus 252 i~~v~~s~~~~~gl~Evl~~~~~~l~~~~~~~e~~ll~~f~~~~~~~~~~a~yG~~~V~~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 88999999999999999999999999999999999999999999998899999999999999999999999999999999
Q ss_pred EEEEcCCCCcEEEEeeccchhcccCcccCCCccccchhcccccHHHHHHHHHHhcCCEEEEecCCCchhhhhccccccEE
Q 013759 332 YVLKNTVTGEIVIKHLNREQETNQNNFRDSATSAELEVQEKSSLLEWFANEYRRFGCTLEFVTNKSQEGSQFCRGFGGIG 411 (437)
Q Consensus 332 ~~~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~~~~~~~~dvve~Lve~a~~~ga~V~ivs~~~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 VTFKCPNCGYEEEKTVKPEEGD--KSEACPKCGSELEIVEEEDIIEELSELAEESGAKVEIISTDTEEGEQLLKAFGGIA 396 (403)
T ss_pred EEEEcCCCCcceeeeccccccc--ccccCcccCcccccchhhhHHHHHHHHHHHcCCEEEEECCCChhHHHHHHcCCcEE
Confidence 9999999998877777666542 22669999999999889999999999999999999999999999999768999999
Q ss_pred EEeeeec
Q 013759 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 9999996
No 2
>TIGR00108 eRF peptide chain release factor eRF/aRF, subunit 1. Alternative names include eRF1, SUP45, omnipotent suppressor protein 1.
Probab=100.00 E-value=7.8e-89 Score=691.58 Aligned_cols=407 Identities=39% Similarity=0.678 Sum_probs=380.5
Q ss_pred hhhHHHHHHHHHHHHHHhcCCCcceEEEEcCCCCCHHHHHhhhhhhhhhchhhhhhhhhcccchhHHHHHHHhhhccccC
Q 013759 9 KNIEIWKIKKLIKALEAARGNGTSMISLIMPPRDQVSRVTKMLGDEFGTASNIKSRVNRQSVLGAITSAQQRLKLYNKVP 88 (437)
Q Consensus 9 ~~~~~~~~~k~l~~l~~~~g~~~~~vsly~~~~~d~~~v~nll~~d~~~a~~ir~k~~r~~~~~~~~~~~~~l~l~~~~~ 88 (437)
.+.++|+||+.|++|.+++|+||++|||||||++.++++.++|++++.+|+|||||+||++|+++++++++||+++.++|
T Consensus 2 ~~~~~~~~k~~~~~l~~~~g~gt~lisl~ipp~~~i~~~~~~l~~e~~~a~niks~~~r~~v~~ai~~~~~~lk~~~~~p 81 (409)
T TIGR00108 2 SSKNLYEFKRKLQELEKKRGRGTELISLYIPPDRQISDVAKHLREELSQASNIKSKQTRKNVLSAIEAILQRLKLFNKPP 81 (409)
T ss_pred chHHHHHHHHHHHHHHhCcCCCceEEEEEeCCCCcHHHHHHHHHHHHhhhhcccccchhhhHHHHHHHHHHHhhccCCCC
Confidence 35788999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcEEEEeceeecCCCceeEEEEEeecCCCceeeeeeccCccchHHHHHhhcCCCcEEEEEEeCCceEEEEEecCeEEEE
Q 013759 89 PNGLVLYTGTIVTDDGKEKKVTIDFEPFRPINASLYLCDNKFHTDALNELLESDDKFGFIVMDGNGTLFGTLSGNTREVL 168 (437)
Q Consensus 89 ~~Gl~~f~g~~~~~~~~~~~~t~~l~~~~pv~~~k~~~~~~~~l~~L~~a~~~~~~~~vvvvd~~~A~i~~~~g~~~~~~ 168 (437)
+||+++|||.+..+++.+++||++++||.||++++|.||+.||++||.++++++.++++|+||+++|.|+++.|+.++++
T Consensus 82 ~nglv~~~G~v~~~~~~~~~~t~~iep~~pi~~~~y~~d~~f~le~L~e~~~~~~~~g~VvvD~~~A~i~~l~g~~~~~~ 161 (409)
T TIGR00108 82 ENGLVIFCGMVPREGPTEKMETYVIEPPEPIKTYIYHCDSKFYLEPLSEMLEEKDKYGLIVLDRQEATIGLVKGKRITVL 161 (409)
T ss_pred CCcEEEEEeEeccCCCcccEEEEEEeCCCceEEEEEccCChhHHHHHHHHhcCCCCEEEEEEecCCEEEEEEcCCEEEEE
Confidence 99999999999888888899999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEeecCcccCCCCcchHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCcceEEEecChhhHHHhcccccCChhhh
Q 013759 169 HKFSVDLPKKHGRGGQSALRFARLRMEKRHNYVRKTAELATQFYINPATSQPNVSGLVLAGSADFKTELSQSDMFDPRLQ 248 (437)
Q Consensus 169 ~~i~~~vp~K~~~gG~s~~Rf~r~~ee~~~~f~~~va~~l~~~~~~~~~~~~~~~~liiaGp~~~k~~f~~~~~l~~~l~ 248 (437)
+.++.++|+||+.||||+.||+|++++++++||++|++.+.++|.. ..+.++++||||||++++++|.+.++|+++++
T Consensus 162 ~~i~~~vp~K~~~GGqS~~Rf~r~~e~~~~~f~~~Vae~~~~~f~~--~~~~~v~~IIlaGpg~~K~~f~~~~~l~~~l~ 239 (409)
T TIGR00108 162 KKLTSGVPGKHKAGGQSARRFERLRELAAHEFLKKVGEVANEAFLP--NDDVKLKGIILGGPGHTKEEFAEGEYLHHELK 239 (409)
T ss_pred EEEeeeCCCcccCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHhhh--cccccceEEEEeccHHHHHHhhhhhhHHHHhh
Confidence 9999999999998999999999999999999999999999999753 12347999999999999999998778999999
Q ss_pred cceeEEEECCCCCCccHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHccCCCcEEECHHHHHHHHHhCCccEEEeecCCC
Q 013759 249 AKILKVVDVSYGGENGFNQAIELSAESLSNVKFIQEKRLIGKYFEEISQDTGKYVFGADDTLKALDMGAVDTLIVWENLD 328 (437)
Q Consensus 249 ~~vi~~v~~s~~~~~gl~Evl~~~~~~l~~~~~~~e~~ll~~f~~~~~~~~~~a~yG~~~V~~Al~~GaV~tLlV~d~l~ 328 (437)
+++++++++|+++++|++|+++++.++|++.++++|+++|++|++++++++|++|||+++|.+||++|||+||||+|++.
T Consensus 240 ~kvi~~vdvs~gg~~gl~E~l~~~~~~L~~~k~~~E~~lle~F~~ei~~d~G~avyG~~eV~~ALe~GAVetLLV~d~l~ 319 (409)
T TIGR00108 240 KKVISTVDVSYTGEFGIRELIEKSADVLAEVDYMREKKLVQRFLKELIQEDGLACYGEDEVLKALDLGAVETLIVSEDLE 319 (409)
T ss_pred hhEEEEEEcCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcEEeCHHHHHHHHHhCCCcEEEEecccc
Confidence 99988999999999999999999999999999999999999999999998899999999999999999999999999999
Q ss_pred ceeEEEEcCCCCcEEEEeeccchhcccCcccCCCccccchhcccccHHHHHHHHHHhcCCEEEEecCCCchhhhhccccc
Q 013759 329 ITRYVLKNTVTGEIVIKHLNREQETNQNNFRDSATSAELEVQEKSSLLEWFANEYRRFGCTLEFVTNKSQEGSQFCRGFG 408 (437)
Q Consensus 329 ~~~~~~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~~~~~~~~dvve~Lve~a~~~ga~V~ivs~~~e~G~q~L~~~g 408 (437)
..+++|||++|+.. .++.+.+......+.||.||+++++.++.+++++|++.|+++||+|+|||++|++|+||+++||
T Consensus 320 ~~r~~~r~~~~~~~--~~~~~~~~~~~~~~~c~~~~~~~~~~~~~~~ve~L~e~a~~~Ga~V~iiS~~~eeG~ql~~~fG 397 (409)
T TIGR00108 320 YIRVTYKCAECGEV--IEKTVRELKDKKFAICPACGQEMDVVEERDLIEWLSELAENFGAKLEFISTESEEGAQLLTAFG 397 (409)
T ss_pred ceeEEEEcCCCCce--eecccccccccccccCcccCccccchhhhhHHHHHHHHHHHcCCEEEEECCCChhHHHHHHhCC
Confidence 98999999999874 2222222112345689999999998888999999999999999999999999999999779999
Q ss_pred cEEEEeeeecC
Q 013759 409 GIGGILRYQLD 419 (437)
Q Consensus 409 GIaAiLRy~~~ 419 (437)
|||||||||++
T Consensus 398 GIaAiLRy~i~ 408 (409)
T TIGR00108 398 GIGAILRYKPN 408 (409)
T ss_pred CEEEEEecccC
Confidence 99999999986
No 3
>PRK04011 peptide chain release factor 1; Provisional
Probab=100.00 E-value=2.7e-88 Score=688.03 Aligned_cols=407 Identities=35% Similarity=0.613 Sum_probs=385.8
Q ss_pred hhhhHHHHHHHHHHHHHHhcCCCcceEEEEcCCCCCHHHHHhhhhhhhhhchhhhhhhhhcccchhHHHHHHHhhhcccc
Q 013759 8 DKNIEIWKIKKLIKALEAARGNGTSMISLIMPPRDQVSRVTKMLGDEFGTASNIKSRVNRQSVLGAITSAQQRLKLYNKV 87 (437)
Q Consensus 8 ~~~~~~~~~~k~l~~l~~~~g~~~~~vsly~~~~~d~~~v~nll~~d~~~a~~ir~k~~r~~~~~~~~~~~~~l~l~~~~ 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 56799999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCcEEEEeceeecCC-CceeEEEEEeecCCCceeeeeeccCccchHHHHHhhcCCCcEEEEEEeCCceEEEEEecCeEE
Q 013759 88 PPNGLVLYTGTIVTDD-GKEKKVTIDFEPFRPINASLYLCDNKFHTDALNELLESDDKFGFIVMDGNGTLFGTLSGNTRE 166 (437)
Q Consensus 88 ~~~Gl~~f~g~~~~~~-~~~~~~t~~l~~~~pv~~~k~~~~~~~~l~~L~~a~~~~~~~~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 9999999999988765 778899999999999999999899999999999999999999999999999999999999999
Q ss_pred EEEEEEeecCcccCCCCcchHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCcceEEEecChhhHHHhcccccCChh
Q 013759 167 VLHKFSVDLPKKHGRGGQSALRFARLRMEKRHNYVRKTAELATQFYINPATSQPNVSGLVLAGSADFKTELSQSDMFDPR 246 (437)
Q Consensus 167 ~~~~i~~~vp~K~~~gG~s~~Rf~r~~ee~~~~f~~~va~~l~~~~~~~~~~~~~~~~liiaGp~~~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 999999999999998999999999999999999999999999999863 113589999999999999999977789999
Q ss_pred hhcceeEEEECCCCCCccHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHccCCCcEEECHHHHHHHHHhCCccEEEeecC
Q 013759 247 LQAKILKVVDVSYGGENGFNQAIELSAESLSNVKFIQEKRLIGKYFEEISQDTGKYVFGADDTLKALDMGAVDTLIVWEN 326 (437)
Q Consensus 247 l~~~vi~~v~~s~~~~~gl~Evl~~~~~~l~~~~~~~e~~ll~~f~~~~~~~~~~a~yG~~~V~~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 99999999999999999999999999999999999999999999999999988999999999999999999999999999
Q ss_pred CCceeEEEEcCCCCcEEEEeeccchhcccCcccCCCccccchhcccccHHHHHHHHHHhcCCEEEEecCCCchhhhhccc
Q 013759 327 LDITRYVLKNTVTGEIVIKHLNREQETNQNNFRDSATSAELEVQEKSSLLEWFANEYRRFGCTLEFVTNKSQEGSQFCRG 406 (437)
Q Consensus 327 l~~~~~~~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~~~~~~~~dvve~Lve~a~~~ga~V~ivs~~~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 99999999999999887777766653 4456899999999988889999999999999999999999999999996699
Q ss_pred cccEEEEeeeec
Q 013759 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 999999999996
No 4
>COG1503 eRF1 Peptide chain release factor 1 (eRF1) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5e-80 Score=608.63 Aligned_cols=406 Identities=41% Similarity=0.683 Sum_probs=382.7
Q ss_pred hhhHHHHHHHHHHHHHHhcCCCcceEEEEcCCCCCHHHHHhhhhhhhhhchhhhhhhhhcccchhHHHHHHHhhhccccC
Q 013759 9 KNIEIWKIKKLIKALEAARGNGTSMISLIMPPRDQVSRVTKMLGDEFGTASNIKSRVNRQSVLGAITSAQQRLKLYNKVP 88 (437)
Q Consensus 9 ~~~~~~~~~k~l~~l~~~~g~~~~~vsly~~~~~d~~~v~nll~~d~~~a~~ir~k~~r~~~~~~~~~~~~~l~l~~~~~ 88 (437)
...++|+||++|++|.+.+|+||++|||||||+.+++++.|++++++++|+|||||.||++|++++++++++|+++.++|
T Consensus 5 ~~~~~~e~Kk~l~~L~~~rg~gt~lislyIPp~~qisdv~~~lr~e~s~asniksk~tR~~V~~ai~~~~~rLk~~~~~P 84 (411)
T COG1503 5 SMHEMYELKKLLEELKKFRGRGTELISLYIPPDRQISDVVNRLRDEYSTASNIKSKVTRKNVLSAIESAMQRLKDYCKTP 84 (411)
T ss_pred HHHHHHHHHHHHHHHHhhcCCCceEEEEecCCCCchHHHHHHHHhhccchhhhhhcCchHHHHhHHHHHHHHHHhcccCC
Confidence 36899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcEEEEeceeecCCCceeEEEEEeecCCCceeeeeeccCccchHHHHHhhcCCCcEEEEEEeCCceEEEEEecCeEEEE
Q 013759 89 PNGLVLYTGTIVTDDGKEKKVTIDFEPFRPINASLYLCDNKFHTDALNELLESDDKFGFIVMDGNGTLFGTLSGNTREVL 168 (437)
Q Consensus 89 ~~Gl~~f~g~~~~~~~~~~~~t~~l~~~~pv~~~k~~~~~~~~l~~L~~a~~~~~~~~vvvvd~~~A~i~~~~g~~~~~~ 168 (437)
+||+++|+|.+....+...+.+..++||.|++.+.|+|++.||++||.+++.+...|+++++|+.+|.++++.|..++++
T Consensus 85 ~nGlv~f~g~v~~~~~~t~~~~~~~~PP~Pi~~~ly~cDs~F~~e~L~~~l~~~~~ygliv~dr~ea~ig~l~g~r~evl 164 (411)
T COG1503 85 ENGLVLFVGDVLGGGGKTKKVTVVIEPPEPINTFLYRCDSKFYLEPLEEMLEDKDLYGLIVLDRIEATIGLLKGKRIEVL 164 (411)
T ss_pred CCCeEEEEeeeccCCCccceeeecccCCCCcceeeeccccHHHHHHHHHHhhhcccccEEEEecccceeeeeccceeeHh
Confidence 99999999999877677778899999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEeecCcccCCCCcchHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCcceEEEecChhhHHHhcccccCChhhh
Q 013759 169 HKFSVDLPKKHGRGGQSALRFARLRMEKRHNYVRKTAELATQFYINPATSQPNVSGLVLAGSADFKTELSQSDMFDPRLQ 248 (437)
Q Consensus 169 ~~i~~~vp~K~~~gG~s~~Rf~r~~ee~~~~f~~~va~~l~~~~~~~~~~~~~~~~liiaGp~~~k~~f~~~~~l~~~l~ 248 (437)
+.+++.+|+||++||||+.||+|+++++.+.||++|++++.++|.. .+. .++++|+|+||++++++|.+.++|+++++
T Consensus 165 ~~~~s~vpgKh~~Ggqsa~rferl~ee~~h~f~k~vge~A~e~f~~-~~~-~~~kgIilgGp~~tk~ef~e~~yL~~~lk 242 (411)
T COG1503 165 KELTSDVPGKHRAGGQSARRFERLIEEAAHEFYKKVGEAASEAFLP-IAK-KELKGIILGGPGPTKEEFVEGDYLHHELK 242 (411)
T ss_pred hhhcccCcchhhcccchHHHHHHHHHHHHHHHHHHHHHHHHHHhcc-hhh-hhhcceEeeCCcccchhhhcccccchHHH
Confidence 9999999999999999999999999999999999999999999974 222 26899999999999999999999999999
Q ss_pred cceeEEEECCCCCCccHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHccCCCcEEECHHHHHHHHHhCCccEEEeecCCC
Q 013759 249 AKILKVVDVSYGGENGFNQAIELSAESLSNVKFIQEKRLIGKYFEEISQDTGKYVFGADDTLKALDMGAVDTLIVWENLD 328 (437)
Q Consensus 249 ~~vi~~v~~s~~~~~gl~Evl~~~~~~l~~~~~~~e~~ll~~f~~~~~~~~~~a~yG~~~V~~Al~~GaV~tLlV~d~l~ 328 (437)
++++++++++|++++|++|++.++.++|++.++.+|+++|++|++++.+++|+++||.++|++||++|||++|||++++.
T Consensus 243 ~kv~~lvDv~y~~esg~~eli~~A~d~L~~~~~~~eK~l~e~f~~e~~~~~Gla~yG~~~vr~aL~~gaVd~llv~Edl~ 322 (411)
T COG1503 243 KKVLGLVDVSYTGESGLRELIEKAEDALKDVDYVREKKLMEEFFKELAKDSGLAVYGEEEVREALEMGAVDTLLVSEDLE 322 (411)
T ss_pred HHHHhhccccccccccHHHHHHHhHHHHHhhhhhcchhHHHHHHHHhccCcceeecchHHHHHHHHhcccceEEeecccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ceeEEEEcCCCCcEEEEeeccchhcccCcccCCCccccchhcccccHHHHHHHHHHhcCCEEEEecCCCchhhhhccccc
Q 013759 329 ITRYVLKNTVTGEIVIKHLNREQETNQNNFRDSATSAELEVQEKSSLLEWFANEYRRFGCTLEFVTNKSQEGSQFCRGFG 408 (437)
Q Consensus 329 ~~~~~~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~~~~~~~~dvve~Lve~a~~~ga~V~ivs~~~e~G~q~L~~~g 408 (437)
..|+.|+|+.|+........+.. ...+.||.||.++..+...|++|++.+.|++.|++|+|||+++++|.||+++||
T Consensus 323 ~~r~~~~c~~~~~e~~~t~~~~~---~~~~~~~~~~~e~~~v~~~d~vd~l~e~a~~~Ga~ve~is~~~~eg~q~~~afg 399 (411)
T COG1503 323 KERVTYKCPTCGYENLKSKREFE---QKRFRCPECGSEMEEVEVSDLVDELAELAEESGAKVEIISDDTDEGAQLLKAFG 399 (411)
T ss_pred ccceeecCCCcchhhhhcccccc---cccccCccccccccchhhhhHHHHHHHHHHhcCCeEEEecCchHHHHHHHHccc
Confidence 99999999999874222111111 224589999999999999999999999999999999999999999999999999
Q ss_pred cEEEEeeeecC
Q 013759 409 GIGGILRYQLD 419 (437)
Q Consensus 409 GIaAiLRy~~~ 419 (437)
||||||||+++
T Consensus 400 Gi~AiLR~~~~ 410 (411)
T COG1503 400 GLAAILRYRTD 410 (411)
T ss_pred chheeeecccC
Confidence 99999999986
No 5
>KOG0688 consensus Peptide chain release factor 1 (eRF1) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.3e-75 Score=548.00 Aligned_cols=425 Identities=78% Similarity=1.208 Sum_probs=405.3
Q ss_pred hhhhHHHHHHHHHHHHHHhcCCCcceEEEEcCCCCCHHHHHhhhhhhhhhchhhhhhhhhcccchhHHHHHHHhhhcccc
Q 013759 8 DKNIEIWKIKKLIKALEAARGNGTSMISLIMPPRDQVSRVTKMLGDEFGTASNIKSRVNRQSVLGAITSAQQRLKLYNKV 87 (437)
Q Consensus 8 ~~~~~~~~~~k~l~~l~~~~g~~~~~vsly~~~~~d~~~v~nll~~d~~~a~~ir~k~~r~~~~~~~~~~~~~l~l~~~~ 87 (437)
+++.|+|++||+++.|...|||||++|||+|||.+.++++.++|.+++.+|+||||+++|.+|.++++++++||++|.++
T Consensus 5 ~~nveiwkikklik~le~argngtsmisliippkdqisr~skmLadeygtasnikSrVnRlsvl~AitSaq~rLklynkv 84 (431)
T KOG0688|consen 5 DKNVEIWKIKKLIKSLEDARGNGTSMISLIIPPKDQISRVSKMLADEYGTASNIKSRVNRLSVLGAITSAQSRLKLYNKV 84 (431)
T ss_pred hhhhHHHHHHHHHHHHHHhcCCCceeEEEEeCchHHHHHHHHHHHHhhhhhhhhhhhhcchhhhhhhhhhhhhhHHhccC
Confidence 56899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCcEEEEeceeecCCCceeEEEEEeecCCCceeeeeeccCccchHHHHHhhcCCCcEEEEEEeCCceEEEEEecCeEEE
Q 013759 88 PPNGLVLYTGTIVTDDGKEKKVTIDFEPFRPINASLYLCDNKFHTDALNELLESDDKFGFIVMDGNGTLFGTLSGNTREV 167 (437)
Q Consensus 88 ~~~Gl~~f~g~~~~~~~~~~~~t~~l~~~~pv~~~k~~~~~~~~l~~L~~a~~~~~~~~vvvvd~~~A~i~~~~g~~~~~ 167 (437)
|+||+++|||.+.++.|..+.++++++|-.|+....|-|++.||++||.+++....++|++|||..++.|+.+.|+..++
T Consensus 85 Ppnglvly~gti~tedgkekkv~idfepfkpintslyLcdNkfhte~l~~Ll~sd~kfgfivmDg~~tlfgtl~gntrev 164 (431)
T KOG0688|consen 85 PPNGLVLYTGTIVTEDGKEKKVNIDFEPFKPINTSLYLCDNKFHTEALKELLESDNKFGFIVMDGNGTLFGTLQGNTREV 164 (431)
T ss_pred CCCceEEEeeeeEccCCceeeeecccccccccccceEecCCccchHHHHHHHhhcccccEEEEcCCceeEEEeccchHhh
Confidence 99999999999999999999999999999999888888999999999999999999999999999999999999999999
Q ss_pred EEEEEeecCcccCCCCcchHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCcceEEEecChhhHHHhcccccCChhh
Q 013759 168 LHKFSVDLPKKHGRGGQSALRFARLRMEKRHNYVRKTAELATQFYINPATSQPNVSGLVLAGSADFKTELSQSDMFDPRL 247 (437)
Q Consensus 168 ~~~i~~~vp~K~~~gG~s~~Rf~r~~ee~~~~f~~~va~~l~~~~~~~~~~~~~~~~liiaGp~~~k~~f~~~~~l~~~l 247 (437)
+++++.+.|+||++||||+.||.|+|.+..+.|.+++++...+.|.. +...++.+||+||...+|..+.+.+.+++++
T Consensus 165 LhkftVdlPkkhgrggqSalrfarlR~ekRhnYVrkvae~a~q~fi~--~~~~Nv~gLilaGsadfKtelsqSd~fd~rl 242 (431)
T KOG0688|consen 165 LHKFTVDLPKKHGRGGQSALRFARLRMEKRHNYVRKVAELAVQRFIT--NDKPNVAGLILAGSADFKTELSQSDMFDPRL 242 (431)
T ss_pred hheeeecCccccCccchhHHhhhhhhhhhhccceeeecccceeEEec--CCCcceeEEEEecccccccccchhhhcchHH
Confidence 99999999999999999999999999999999999999999999876 5567899999999999999999988999999
Q ss_pred hcceeEEEECCCCCCccHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHccCCCcEEECHHHHHHHHHhCCccEEEeecCC
Q 013759 248 QAKILKVVDVSYGGENGFNQAIELSAESLSNVKFIQEKRLIGKYFEEISQDTGKYVFGADDTLKALDMGAVDTLIVWENL 327 (437)
Q Consensus 248 ~~~vi~~v~~s~~~~~gl~Evl~~~~~~l~~~~~~~e~~ll~~f~~~~~~~~~~a~yG~~~V~~Al~~GaV~tLlV~d~l 327 (437)
+.+++.+++++|||+.|++++++-..++|.+.++.+|++++.+||++++.+.|+.|+|.++++.||++|||+||++.+++
T Consensus 243 qskvi~~vdvsyGGengfnQaIeL~aevlsnvk~vqekkli~~yfdEisqdtgky~Fgv~dTl~aLe~gavetli~~enL 322 (431)
T KOG0688|consen 243 QSKVLKTVDVSYGGENGFNQAIELSAEVLSNVKFVQEKKLIGKYFDEISQDTGKYCFGVEDTLLALEMGAVETLIVWENL 322 (431)
T ss_pred hhhHHhhhcccccchhhHHHHHHHHHhhhhcceeeehhhHHHHHhhhhhcccCcccccHHHHHHHHHcCCeeehhHhhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CceeEEEEcCCCCcEEEEeeccchhcccCcccCCCccccchhcccccHHHHHHHHHHhcCCEEEEecCCCchhhhhcccc
Q 013759 328 DITRYVLKNTVTGEIVIKHLNREQETNQNNFRDSATSAELEVQEKSSLLEWFANEYRRFGCTLEFVTNKSQEGSQFCRGF 407 (437)
Q Consensus 328 ~~~~~~~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~~~~~~~~dvve~Lve~a~~~ga~V~ivs~~~e~G~q~L~~~ 407 (437)
...||+++|. .+...+.++.|.++-+.+.+.....|.++++++..+++||+.+.-+.+||.++||++.+.+|.||.++|
T Consensus 323 d~~ry~~kn~-~~~~~i~~l~~~~e~d~s~~~Dketg~e~elie~~pLlEw~AnnYK~FGa~LE~VTdKSqEgsQFv~Gf 401 (431)
T KOG0688|consen 323 DIIRYELKNS-DGESVIGFLVPDEEKDKSHFTDKETGWEMELIERMPLLEWFANNYKKFGATLEIVTDKSQEGSQFVKGF 401 (431)
T ss_pred hhhhhhhccc-CCccceeeecchhhcccccccccccchhhhHHhhhhHHHHHHHHHhhcCeEEEEecccchhHHHHHhhc
Confidence 9999999998 578888888887764555677788899999999999999999999999999999999999999999999
Q ss_pred ccEEEEeeeecCccCccCcCCCCCCCCCC
Q 013759 408 GGIGGILRYQLDMRSFDEFSDDGEIYDDS 436 (437)
Q Consensus 408 gGIaAiLRy~~~~~~~~~~~~~~~~~~~~ 436 (437)
|||++||||++++..++.++ |++.||+.
T Consensus 402 GgiGgiLrY~vd~~~~~~~~-d~~~~~~~ 429 (431)
T KOG0688|consen 402 GGIGGILRYRVDFQGIEYQE-DIEFFDLD 429 (431)
T ss_pred CCcceeEEEEeeeecccccc-CceeeecC
Confidence 99999999999998888888 67777753
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=1.2e-61 Score=484.82 Aligned_cols=325 Identities=21% Similarity=0.358 Sum_probs=282.8
Q ss_pred CCcceEEEEcCCCCCHHHHHhhhhh-hhhhchhhhhhhhhcccchhHHHHHHHhhhcccc------CCCcEEEEeceeec
Q 013759 29 NGTSMISLIMPPRDQVSRVTKMLGD-EFGTASNIKSRVNRQSVLGAITSAQQRLKLYNKV------PPNGLVLYTGTIVT 101 (437)
Q Consensus 29 ~~~~~vsly~~~~~d~~~v~nll~~-d~~~a~~ir~k~~r~~~~~~~~~~~~~l~l~~~~------~~~Gl~~f~g~~~~ 101 (437)
+|.|.|+|.|++.+|+|++||+|+. |.+.|.|+| |++..+.+++.. .+.+++++.+| |.++.++++|.+..
T Consensus 10 ~~~g~v~l~pe~~dDlw~l~nli~~GD~V~~~T~R-kv~~~~~~g~~~-er~~~~l~i~Ve~ief~~~~~~Lri~G~i~~ 87 (351)
T TIGR00111 10 KGGAVIKLLPETLDDLWHLYQIIEKGDVEFAFTKR-RTQDLDKIRSDK-SKDTVKLGIEVESVEFDMKTERLRYKGVIVT 87 (351)
T ss_pred CCcEEEEEEeCChHHHHHHHHhCCCCCEEEEEEEE-EEeccccCCCcc-eEEEEEEEEEEEEEEecCCCCEEEEEEEEec
Confidence 5668999999999999999999999 999999999 787766556544 55556666665 56899999999987
Q ss_pred CC-C---ceeEEEEEeecCCCceeeeeeccCccchHHHHHhhcCC--CcEEEEEEeCCceEEEEEecCeEEEEEEEEeec
Q 013759 102 DD-G---KEKKVTIDFEPFRPINASLYLCDNKFHTDALNELLESD--DKFGFIVMDGNGTLFGTLSGNTREVLHKFSVDL 175 (437)
Q Consensus 102 ~~-~---~~~~~t~~l~~~~pv~~~k~~~~~~~~l~~L~~a~~~~--~~~~vvvvd~~~A~i~~~~g~~~~~~~~i~~~v 175 (437)
++ . .|+|||++|+||+|++++|+ +|+.|++++|++|+++. +.+++|+||+++|.||++.+.+++++++++.++
T Consensus 88 ~~e~~v~~G~~HTl~ie~~~~i~i~K~-~w~~~~le~L~ea~~~~~~~~~~~vv~d~g~A~i~ll~~~~~~~~~~i~~~i 166 (351)
T TIGR00111 88 GPEDDVPVGSYHTLEIKYVYPLSIIKQ-NWKKWQLKRLREAVEISKRPKTAAVVMEEGIAHVGLVRQYSVEEIQKIEYHM 166 (351)
T ss_pred CCcccccccceEEEEEcCCCcEEEEEe-cCCHHHHHHHHHHhccccCCcEEEEEEeCCcEEEEEEcCCEEEEEEEEEEeC
Confidence 65 2 27899999999999999998 89999999999999986 779999999999999999999999999999999
Q ss_pred CcccCCCCcchHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCcceEEEecChhhHHHhccc--ccCChhhhcceeE
Q 013759 176 PKKHGRGGQSALRFARLRMEKRHNYVRKTAELATQFYINPATSQPNVSGLVLAGSADFKTELSQS--DMFDPRLQAKILK 253 (437)
Q Consensus 176 p~K~~~gG~s~~Rf~r~~ee~~~~f~~~va~~l~~~~~~~~~~~~~~~~liiaGp~~~k~~f~~~--~~l~~~l~~~vi~ 253 (437)
|+|++ + +.++++.++||++|++++.+ | .++++||||||||+++.|.++ .++++. ..+.+
T Consensus 167 P~K~~-~--------~~~e~~~~~Ff~~v~~~l~~-~-------~~v~~iIiaGPGf~k~~f~~~l~~~~~~~-~~k~i- 227 (351)
T TIGR00111 167 PGKKR-T--------LKFGELRKEFYKEIAKKLLN-F-------DDLKTIIVAGPGFYKNDFYDFIFERYPEE-ANKAV- 227 (351)
T ss_pred CCCcc-c--------chhHHHHHHHHHHHHHHHhh-h-------cccCEEEEECCHHHHHHHHHHHHHHhhhh-hCCcE-
Confidence 99974 2 22677889999999999854 2 379999999999999999875 222222 23333
Q ss_pred EEECCCCCCccHHHHHHH--HHHHHHhhHHHHHHHHHHHHHHHHccCCCcEEECHHHHHHHHHhCCccEEEeecCCCcee
Q 013759 254 VVDVSYGGENGFNQAIEL--SAESLSNVKFIQEKRLIGKYFEEISQDTGKYVFGADDTLKALDMGAVDTLIVWENLDITR 331 (437)
Q Consensus 254 ~v~~s~~~~~gl~Evl~~--~~~~l~~~~~~~e~~ll~~f~~~~~~~~~~a~yG~~~V~~Al~~GaV~tLlV~d~l~~~~ 331 (437)
+.++|+++++|++|++++ ++++|+++++++|.++|++|+++++++++++|||+++|.+|+++|||+||||+|++
T Consensus 228 i~~~s~g~~~gl~EvL~~~~v~~~l~d~k~~~E~~~l~~f~~~l~kd~~~~~YG~~eV~~Ale~GAVetLLIsD~l---- 303 (351)
T TIGR00111 228 LENCSTGGRAGINEVLKRGLVARILQETRYAKEIMVIDEFLEHLAKDGDKAVYGEDEVVKAAEYGAIEYLLVTDKV---- 303 (351)
T ss_pred EEecCCCchhHHHHHHhChHHHHHHhhhhHHHHHHHHHHHHHHHhcCCCeEEECHHHHHHHHHcCCceEEEEecch----
Confidence 468999999999999997 58999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEcCCCCcEEEEeeccchhcccCcccCCCccccchhcccccHHHHHHHHHHhcCCEEEEecCCCchhhhhccccccEE
Q 013759 332 YVLKNTVTGEIVIKHLNREQETNQNNFRDSATSAELEVQEKSSLLEWFANEYRRFGCTLEFVTNKSQEGSQFCRGFGGIG 411 (437)
Q Consensus 332 ~~~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~~~~~~~~dvve~Lve~a~~~ga~V~ivs~~~e~G~q~L~~~gGIa 411 (437)
+. . | .+ +++|++.|+++||+|.|||++|++|+| |++|||||
T Consensus 304 --~~-~-----------------r-----------------~~-~~~l~~~v~~~gg~V~i~Ss~~e~G~q-L~~lgGia 344 (351)
T TIGR00111 304 --LV-Q-----------------R-----------------EE-IEKLLDSVESMGGKVVILSTEHELGKQ-LDSLGGIA 344 (351)
T ss_pred --hh-h-----------------H-----------------HH-HHHHHHHHHHcCCEEEEEcCCCccHHH-HhhCCCEE
Confidence 21 0 1 11 456999999999999999999999999 89999999
Q ss_pred EEeeeec
Q 013759 412 GILRYQL 418 (437)
Q Consensus 412 AiLRy~~ 418 (437)
||||||+
T Consensus 345 AiLRy~i 351 (351)
T TIGR00111 345 GILRFPI 351 (351)
T ss_pred EEEeccC
Confidence 9999996
No 7
>KOG2869 consensus Meiotic cell division protein Pelota/DOM34 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=8.5e-63 Score=465.45 Aligned_cols=354 Identities=19% Similarity=0.283 Sum_probs=311.3
Q ss_pred HHHHHHHHhcCCCcceEEEEcCCCCCHHHHHhhhhh-hhhhchhhhhhhhhcccchhHHHHHHHhhhcccc------CCC
Q 013759 18 KLIKALEAARGNGTSMISLIMPPRDQVSRVTKMLGD-EFGTASNIKSRVNRQSVLGAITSAQQRLKLYNKV------PPN 90 (437)
Q Consensus 18 k~l~~l~~~~g~~~~~vsly~~~~~d~~~v~nll~~-d~~~a~~ir~k~~r~~~~~~~~~~~~~l~l~~~~------~~~ 90 (437)
|++++-... +|+|.|++.|++.+|||++||+|+. |.+.|+|+| |++....+|...+.+.+++|...+ ...
T Consensus 2 Kli~K~~~r--ng~G~vtmvpEe~eDmw~~ynli~~gD~v~a~T~r-kvq~e~a~G~~~s~rv~~~L~i~VesidfD~~~ 78 (379)
T KOG2869|consen 2 KLIRKDIER--NGSGSVTMVPEESEDLWHLYNLIQVGDSVIASTIR-KVQKEEATGKTKSSRVLLKLKIKVESIDFDTKA 78 (379)
T ss_pred ccchhhhhc--CCCceEEECcCchhHHHHHHhhccCCceeEEEEEE-EeeeccccCcccceEEEEEEEEEEEEeeccccc
Confidence 455565556 8889999999999999999999999 999999999 999988777766677777777666 357
Q ss_pred cEEEEeceeecCCCc---eeEEEEEeecCCCceeeeeeccCccchHHHHHhhcC--CCcEEEEEEeCCceEEEEEecCeE
Q 013759 91 GLVLYTGTIVTDDGK---EKKVTIDFEPFRPINASLYLCDNKFHTDALNELLES--DDKFGFIVMDGNGTLFGTLSGNTR 165 (437)
Q Consensus 91 Gl~~f~g~~~~~~~~---~~~~t~~l~~~~pv~~~k~~~~~~~~l~~L~~a~~~--~~~~~vvvvd~~~A~i~~~~g~~~ 165 (437)
..+++.|++.++|.+ |.|||++|++++|++++|. .|+.+.++.|++|+++ ...+++||+++|-|.||++..+ .
T Consensus 79 ~~L~~KGrti~eNe~Vk~GaYHTidlel~r~FtL~K~-ewds~al~~l~~A~dp~~~ad~aaVvlqEGla~IcLvt~s-~ 156 (379)
T KOG2869|consen 79 CVLRLKGRTIEENEYVKMGAYHTIDLELNRPFTLRKE-EWDSMALKLLKEACDPAPSADVAAVVLQEGLAHICLVTKS-S 156 (379)
T ss_pred cEEEEeeeeeeecccccccceeEEEeccCCceEEEhh-hchHHHHHHHHHhhCcccccceeeeehhcCceeEEEechh-H
Confidence 899999999888765 8899999999999999996 8999999999999997 5779999999999999965544 4
Q ss_pred EEE-EEEEeecCcccCCCCcchHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCcceEEEecChhhHHHhcccccC-
Q 013759 166 EVL-HKFSVDLPKKHGRGGQSALRFARLRMEKRHNYVRKTAELATQFYINPATSQPNVSGLVLAGSADFKTELSQSDMF- 243 (437)
Q Consensus 166 ~~~-~~i~~~vp~K~~~gG~s~~Rf~r~~ee~~~~f~~~va~~l~~~~~~~~~~~~~~~~liiaGp~~~k~~f~~~~~l- 243 (437)
+++ ++++..+|+|++ |+-|+ +++..++||+.|..++.+++++ ..++++|||+|||.++.|.++...
T Consensus 157 tilr~kIe~siPrKr~-~~~s~------~e~~l~kfye~V~qA~~k~v~f-----d~vk~~vvASpgF~~~~~~d~~~q~ 224 (379)
T KOG2869|consen 157 TILRAKIEVSIPRKRK-GDVSQ------HEEGLEKFYENVVQAILKHVNF-----DVVKCVVVASPGFVKDQFMDYLFQQ 224 (379)
T ss_pred HHHHHhhhcccccccC-cchhH------HHHHHHHHHHHHHHHHHHhcCc-----ceEEEEEEcCCchhHHHHHHHHHHH
Confidence 444 899999999954 55666 7899999999999999999987 789999999999999999875221
Q ss_pred ----C----hhhhcceeEEEECCCCCCccHHHHHHH--HHHHHHhhHHHHHHHHHHHHHHHHccCCCcEEECHHHHHHHH
Q 013759 244 ----D----PRLQAKILKVVDVSYGGENGFNQAIEL--SAESLSNVKFIQEKRLIGKYFEEISQDTGKYVFGADDTLKAL 313 (437)
Q Consensus 244 ----~----~~l~~~vi~~v~~s~~~~~gl~Evl~~--~~~~l~~~~~~~e~~ll~~f~~~~~~~~~~a~yG~~~V~~Al 313 (437)
+ -..+.+++ .+++|+|..++++|+|.. ++..|++++++.|.++|++|+.+++++|++||||+++|.+|.
T Consensus 225 A~~~~~k~il~nk~kf~-~~h~ssg~~hslnevL~dp~v~~~l~dtK~~~EvkalddF~~~l~~~~drA~yG~khV~~A~ 303 (379)
T KOG2869|consen 225 AVKLDLKLILENKSKFP-LVHASSGYKHSLNEVLKDPAVASKLQDTKAAKEVKALDDFYVMLSKDPDRACYGPKHVEKAN 303 (379)
T ss_pred HHHhchhhhhhccccee-EEecCCchHHHHHHHhcChHHHHHhhchhhHHHHHHHHHHHHHhccCccccccCHHHHHHHH
Confidence 1 23466776 889999999999999987 889999999999999999999999999999999999999999
Q ss_pred HhCCccEEEeecCCCceeEEEEcCCCCcEEEEeeccchhcccCcccCCCccccchhcccccHHHHHHHHHHhcCCEEEEe
Q 013759 314 DMGAVDTLIVWENLDITRYVLKNTVTGEIVIKHLNREQETNQNNFRDSATSAELEVQEKSSLLEWFANEYRRFGCTLEFV 393 (437)
Q Consensus 314 ~~GaV~tLlV~d~l~~~~~~~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~~~~~~~~dvve~Lve~a~~~ga~V~iv 393 (437)
+.|||+||||+|++ |||+ +.. .|++|.. |++.++..||+|.||
T Consensus 304 e~~AI~tLLitD~l------fr~~-DV~------------tRkkyv~------------------lvesVk~~~gkv~If 346 (379)
T KOG2869|consen 304 EYGAIETLLITDEL------FRSQ-DVA------------TRKKYVR------------------LVESVKENNGKVFIF 346 (379)
T ss_pred hhcchhheehhhhh------cccc-cHH------------HHHHHHH------------------HHHHHHhcCCcEEEE
Confidence 99999999999999 8988 343 2776653 999999999999999
Q ss_pred cCCCchhhhhccccccEEEEeeeecCccCccCcCCC
Q 013759 394 TNKSQEGSQFCRGFGGIGGILRYQLDMRSFDEFSDD 429 (437)
Q Consensus 394 s~~~e~G~q~L~~~gGIaAiLRy~~~~~~~~~~~~~ 429 (437)
|+.|.+|+| |.+++|||||||||+| +|+|.++|
T Consensus 347 ss~H~SGEq-L~qltGiaAiLrfp~p--el~d~e~~ 379 (379)
T KOG2869|consen 347 SSLHVSGEQ-LAQLTGIAAILRFPLP--ELDDSEGD 379 (379)
T ss_pred ehhhccHHH-HHhhcCeeEEEecCCC--ccccccCC
Confidence 999999999 9999999999999999 78877764
No 8
>COG1537 PelA Predicted RNA-binding proteins [General function prediction only]
Probab=100.00 E-value=2.2e-52 Score=403.61 Aligned_cols=328 Identities=23% Similarity=0.327 Sum_probs=275.5
Q ss_pred cceEEEEcCCCCCHHHHHhhhhh-hhhhchhhhhhhhhcccchhHHHHHHHhhhcccc------CCCcEEEEeceeecCC
Q 013759 31 TSMISLIMPPRDQVSRVTKMLGD-EFGTASNIKSRVNRQSVLGAITSAQQRLKLYNKV------PPNGLVLYTGTIVTDD 103 (437)
Q Consensus 31 ~~~vsly~~~~~d~~~v~nll~~-d~~~a~~ir~k~~r~~~~~~~~~~~~~l~l~~~~------~~~Gl~~f~g~~~~~~ 103 (437)
.+.|+|.|++.+|+|+|||.|+. |.+.|.|.| |.++......-...+..+.+..++ .-.+.+++.|.+...+
T Consensus 10 ~g~I~l~pE~lDDLw~L~~Ii~~GD~v~a~T~R-r~~~~d~~r~~~~eri~m~L~IkVe~ieF~~f~nrLRi~G~i~~~~ 88 (352)
T COG1537 10 RGVIKLVPETLDDLWHLYNIIEKGDKVFAKTTR-RDESSDVIRSKKGERIPMTLGIKVEKIEFDKFANRLRIKGPIVEGP 88 (352)
T ss_pred CceEEEecCChHHHHHHHHhcCCCCEEEEEEEE-ecccccccccCcceEEEEEEEEEEEEEEeeecccEEEEEEEEEEcC
Confidence 57999999999999999999999 999998888 444444443333333334454444 2378999999987644
Q ss_pred C---ceeEEEEEeecCCCceeeeeeccCccchHHHHHhhcC--CCcEEEEEEeCCceEEEEEecCeEEEEEEEEeecCcc
Q 013759 104 G---KEKKVTIDFEPFRPINASLYLCDNKFHTDALNELLES--DDKFGFIVMDGNGTLFGTLSGNTREVLHKFSVDLPKK 178 (437)
Q Consensus 104 ~---~~~~~t~~l~~~~pv~~~k~~~~~~~~l~~L~~a~~~--~~~~~vvvvd~~~A~i~~~~g~~~~~~~~i~~~vp~K 178 (437)
. .|+|||++++++.++++.|. .|+.+++++|++|+++ .+.+++|++|.++|.+|++..+++.++.+++...|+|
T Consensus 89 e~~~~G~yHTi~v~~g~~i~I~K~-~W~~~~lerLkeA~~~~~~~~~~~v~~degea~i~iv~~ygi~~~~~i~~~~~gK 167 (352)
T COG1537 89 EEVVKGSYHTINVTIGTEIEIEKE-EWNKDQLERLKEAVEASKRPEVAIVVVDEGEAAIAIVRDYGIIILGKIRSGIPGK 167 (352)
T ss_pred cccccccceEEEeccCceEEEEEc-cCCHHHHHHHHHHhhcccCCceEEEEEecCceEEEEEeccceEEEEEEeccCCCC
Confidence 3 38999999999999999995 5999999999999998 6889999999999999999999999999999999987
Q ss_pred cCCCCcchHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCcceEEEecChhhHHHhcccc-cCChhhhcceeEEEEC
Q 013759 179 HGRGGQSALRFARLRMEKRHNYVRKTAELATQFYINPATSQPNVSGLVLAGSADFKTELSQSD-MFDPRLQAKILKVVDV 257 (437)
Q Consensus 179 ~~~gG~s~~Rf~r~~ee~~~~f~~~va~~l~~~~~~~~~~~~~~~~liiaGp~~~k~~f~~~~-~l~~~l~~~vi~~v~~ 257 (437)
.. +. + +.+ .+||..|++++.+.+ +++.+|||||||+|+.|.++. .-.|.+++ ++ ..++
T Consensus 168 ~~-~~-~-------~~~--~k~~~~i~~~~~~~~--------~~~~iIvaGPGF~k~~~~~~~~~~~p~~~~-~~-~~~~ 226 (352)
T COG1537 168 RE-GD-I-------RAE--RKFFDEIAKALKEYA--------NLDIIIVAGPGFAKEDFYDFLRERYPELAN-IV-IEDT 226 (352)
T ss_pred cc-cc-h-------hhH--HHHHHHHHHHHHHhh--------CCCeEEEeCCchHHHHHHHHHHHhcccccc-eE-EEec
Confidence 43 21 1 112 799999999998864 478899999999999999751 11234444 33 7899
Q ss_pred CCCCCccHHHHHHH--HHHHHHhhHHHHHHHHHHHHHHHHccCCCcEEECHHHHHHHHHhCCccEEEeecCCCceeEEEE
Q 013759 258 SYGGENGFNQAIEL--SAESLSNVKFIQEKRLIGKYFEEISQDTGKYVFGADDTLKALDMGAVDTLIVWENLDITRYVLK 335 (437)
Q Consensus 258 s~~~~~gl~Evl~~--~~~~l~~~~~~~e~~ll~~f~~~~~~~~~~a~yG~~~V~~Al~~GaV~tLlV~d~l~~~~~~~r 335 (437)
|+++.+|++|+|++ +..++.+++.++|.++|++|++.++++++++|||+++|.+|+++|||++|||+|++ ++
T Consensus 227 s~~g~~gi~EvLkr~~v~ki~~e~ria~e~~~~e~fl~~iak~~~~v~YG~~eV~~A~e~GAve~LLv~De~------lr 300 (352)
T COG1537 227 STGGRAGINEVLKRGAVDKILSETRIAEEIELVEEFLERLAKDDDKVAYGLEEVEKAAEYGAVETLLVTDEL------LR 300 (352)
T ss_pred cCcchHHHHHHHhhhhHHhHhhhhHHHHHHHHHHHHHHHHhcCCCceeEcHHHHHHHHhcCcceeEEeehhh------hc
Confidence 99999999999998 67999999999999999999999999889999999999999999999999999999 67
Q ss_pred cCCCCcEEEEeeccchhcccCcccCCCccccchhcccccHHHHHHHHHHhcCCEEEEecCCCchhhhhccccccEEEEee
Q 013759 336 NTVTGEIVIKHLNREQETNQNNFRDSATSAELEVQEKSSLLEWFANEYRRFGCTLEFVTNKSQEGSQFCRGFGGIGGILR 415 (437)
Q Consensus 336 ~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~~~~~~~~dvve~Lve~a~~~ga~V~ivs~~~e~G~q~L~~~gGIaAiLR 415 (437)
.++ .+ ..--++.|++.|+++||+|.|||+.|++|+| |++|||||||||
T Consensus 301 ~~~-~~------------------------------~re~~~~ll~~ve~~ggkV~Ivs~~he~Ge~-Lk~lGGiaaILR 348 (352)
T COG1537 301 SDD-VE------------------------------EREDVEELLEEVESMGGKVVIVSTEHEPGER-LKALGGIAAILR 348 (352)
T ss_pred ccc-hh------------------------------hHHHHHHHHHHHHHcCCeEEEEecCCcchHH-HHhccCeEEEEE
Confidence 651 11 1112567999999999999999999999999 999999999999
Q ss_pred eecC
Q 013759 416 YQLD 419 (437)
Q Consensus 416 y~~~ 419 (437)
||++
T Consensus 349 f~v~ 352 (352)
T COG1537 349 FPVP 352 (352)
T ss_pred ecCC
Confidence 9985
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=99.95 E-value=9.9e-29 Score=208.18 Aligned_cols=113 Identities=39% Similarity=0.690 Sum_probs=95.6
Q ss_pred HHHHHHHHHHHHHHHccCCCcEEECHHHHHHHHHhCCccEEEeecCCCceeEEEEcCCCCcEEEEeeccchhcccCcccC
Q 013759 281 FIQEKRLIGKYFEEISQDTGKYVFGADDTLKALDMGAVDTLIVWENLDITRYVLKNTVTGEIVIKHLNREQETNQNNFRD 360 (437)
Q Consensus 281 ~~~e~~ll~~f~~~~~~~~~~a~yG~~~V~~Al~~GaV~tLlV~d~l~~~~~~~r~~~~~~~~~~~~~~~~~~~r~~~~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 IIKEKKLVEEFFEELAKDPGLAVYGIEEVKKALEMGAVETLLISDDLFRSRDVER----------------------CKC 58 (113)
T ss_dssp HHHHHHHHHHHHHHHHTTCSSEEESHHHHHHHHHTT-EEEEEEEHHHHTESCHHH----------------------HHS
T ss_pred CHHHHHHHHHHHHHHhhCCCcEEECHHHHHHHHHhCCCcEEEEecccccccceec----------------------ccc
Confidence 3689999999999999999999999999999999999999999999954322111 123
Q ss_pred CCccccchhcccccHHHHHHHHHHhcCCEEEEecCCCchhhhhccccccEEEEeeeec
Q 013759 361 SATSAELEVQEKSSLLEWFANEYRRFGCTLEFVTNKSQEGSQFCRGFGGIGGILRYQL 418 (437)
Q Consensus 361 p~~g~~~~~~~~~dvve~Lve~a~~~ga~V~ivs~~~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 78998877654 99999999999999999999999999995599999999999996
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=99.89 E-value=9.8e-23 Score=177.25 Aligned_cols=130 Identities=28% Similarity=0.485 Sum_probs=113.0
Q ss_pred cEEEEEEeCCceEEEEEecCeEEEEEEEEeecCcccCCCCcchHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCcc
Q 013759 144 KFGFIVMDGNGTLFGTLSGNTREVLHKFSVDLPKKHGRGGQSALRFARLRMEKRHNYVRKTAELATQFYINPATSQPNVS 223 (437)
Q Consensus 144 ~~~vvvvd~~~A~i~~~~g~~~~~~~~i~~~vp~K~~~gG~s~~Rf~r~~ee~~~~f~~~va~~l~~~~~~~~~~~~~~~ 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--REKALEKFFKEIAEALKKYFLV---NFDDVK 75 (133)
T ss_dssp EEEEEEEETTEEEEEEEETTEEEEEEEEE-GHCCCSSTTCSHHHHHH--HHHHHHHHHHHHHHHHHHHCCC---HTTTCS
T ss_pred CEEEEEEeCCCEEEEEEcCCEEEEEEEEEecCCCccCCCCcchhhHH--HHHHHHHHHHHHHHHHHHHhhh---cccccc
Confidence 47999999999999999999999999999999999999999999999 9999999999999999999431 136899
Q ss_pred eEEEecChhhHHHhcccccCChhhhc-ceeEEEECCCCCCccHHHHHHH--HHHHHHh
Q 013759 224 GLVLAGSADFKTELSQSDMFDPRLQA-KILKVVDVSYGGENGFNQAIEL--SAESLSN 278 (437)
Q Consensus 224 ~liiaGp~~~k~~f~~~~~l~~~l~~-~vi~~v~~s~~~~~gl~Evl~~--~~~~l~~ 278 (437)
+||||||||+++.|.++.+.+...++ +.+.++++|+++++|++|+|++ ++++|++
T Consensus 76 ~iIiaGPGf~k~~f~~~l~~~~~~~~~~~i~~~~~s~~~~~gl~Evl~~~~v~~~l~d 133 (133)
T PF03464_consen 76 CIIIAGPGFTKEEFYKYLKAEARRKDKKKIVVVDTSSGGESGLNEVLKRPEVQKILKD 133 (133)
T ss_dssp EEEEEESTTHHHHHHHHHHHHHHHHTCCEEEEEE-SSSCHHHHHHHHHSHHHHHHHCT
T ss_pred EEEEECCHHHHHHHHHHHHHhhHhhcCCEEEEEECCCCCHHHHHHHHHhhhHHHHhcC
Confidence 99999999999999987655555555 5555999999999999999998 7777754
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=99.50 E-value=4.1e-15 Score=129.02 Aligned_cols=110 Identities=26% Similarity=0.435 Sum_probs=92.6
Q ss_pred CCcceEEEEcCCCCCHHHHHhhhhh-hhhhchhhhhhhhhc-ccchhHHHHHHHhhhcccc------CCCcEEEEeceee
Q 013759 29 NGTSMISLIMPPRDQVSRVTKMLGD-EFGTASNIKSRVNRQ-SVLGAITSAQQRLKLYNKV------PPNGLVLYTGTIV 100 (437)
Q Consensus 29 ~~~~~vsly~~~~~d~~~v~nll~~-d~~~a~~ir~k~~r~-~~~~~~~~~~~~l~l~~~~------~~~Gl~~f~g~~~ 100 (437)
++.+.|++.++..+|+|++||+|.. |.+.|.+.| |++.. +..+...+.+.++++..++ |.+|+++|+|.+.
T Consensus 11 ~~~~~i~ll~e~~dDlw~L~~li~~gD~v~~~t~R-kv~~~~~~~~~~~~~~v~~~L~i~ve~v~~~~~~~~Lri~G~i~ 89 (132)
T PF03463_consen 11 NGKGLIKLLPEEKDDLWHLYNLIIPGDEVISKTTR-KVQEASNIKGSKTRERVQIALTIKVEKVEFDPENGLLRISGKIV 89 (132)
T ss_dssp HHHHEEEEETTSHHHHHHHHHHEETTTEEEECCHC-HHHHCTCESSHHHHHCEEEEEEEEEEEEEEETTTTEEEEEEEEE
T ss_pred ccCceEEEcccccCCcEEEEEEEECCCEEEEEEEE-eeeecccccCCcceEEEEEEEEEEEEEeEecCCCCEEEEEeEEc
Confidence 4567999999999999999999999 999999999 78443 4455566666666665554 7899999999998
Q ss_pred cCCCc---eeEEEEEeecCCCceeeeeeccCccchHHHHHhhc
Q 013759 101 TDDGK---EKKVTIDFEPFRPINASLYLCDNKFHTDALNELLE 140 (437)
Q Consensus 101 ~~~~~---~~~~t~~l~~~~pv~~~k~~~~~~~~l~~L~~a~~ 140 (437)
.++.+ |+|||++|+||+||+++|+ .|+.++++.|.++++
T Consensus 90 ~~~~~~~~G~~hT~~i~~~~~~ti~K~-~wd~~~~~~l~ea~~ 131 (132)
T PF03463_consen 90 EENEDVKLGKYHTLDIEPGRPFTIIKY-RWDSYFLDRLKEAMD 131 (132)
T ss_dssp EGSCGGGTTSEEEEEEETSSEEEEEEE-EEEHHHHHHHHHHTS
T ss_pred cCCCCCCcceEEEEEEeCCCceEEEEe-cCCHHHHHHHHHHhc
Confidence 87544 8899999999999999998 899999999999876
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=97.33 E-value=0.00029 Score=61.56 Aligned_cols=117 Identities=16% Similarity=0.179 Sum_probs=78.6
Q ss_pred EEEEEEeCCceEEEEEecCeE---EEEEE------------EEeecCcccCCC-Cc--chHHHHHHHHHHHHHHHHHHHH
Q 013759 145 FGFIVMDGNGTLFGTLSGNTR---EVLHK------------FSVDLPKKHGRG-GQ--SALRFARLRMEKRHNYVRKTAE 206 (437)
Q Consensus 145 ~~vvvvd~~~A~i~~~~g~~~---~~~~~------------i~~~vp~K~~~g-G~--s~~Rf~r~~ee~~~~f~~~va~ 206 (437)
.||||.|.+.|.|+...+... ..+.. +..+-|+....+ |. +........++..++|+++|++
T Consensus 1 twVvVaD~~~Ar~f~~~~~~~~~~~~~~~~~~~~~~~~~~dl~~d~~Gr~~~~~g~~~~~~~~~~~~~~~~~~Fa~~vA~ 80 (138)
T PF10116_consen 1 TWVVVADGSRARIFENEGDESEPLLELEELDHPESRLKDRDLVSDRPGRFHDSAGQRGSMEERTDPKEEEEERFAREVAD 80 (138)
T ss_pred CEEEEEecceeEEEEecCCCCCcchhhhhhcccccccchhhhccCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHH
Confidence 379999999999887776643 11111 222344432211 11 2112234577788999999999
Q ss_pred HHHhhhcCCCCCCCCcceEEEecChhhHHHhcccccCChhhhcceeEEEECCCCCCccHHHHH
Q 013759 207 LATQFYINPATSQPNVSGLVLAGSADFKTELSQSDMFDPRLQAKILKVVDVSYGGENGFNQAI 269 (437)
Q Consensus 207 ~l~~~~~~~~~~~~~~~~liiaGp~~~k~~f~~~~~l~~~l~~~vi~~v~~s~~~~~gl~Evl 269 (437)
.|.+.+.. ..++.|||++|..+...+++ .|++.++++|++.++-.... ....|+.
T Consensus 81 ~L~~~~~~-----~~~~~LvlvA~p~~LG~LR~--~L~~~~~~~V~~ei~kDlt~-~~~~ei~ 135 (138)
T PF10116_consen 81 RLEKARRA-----GKFDRLVLVAPPRFLGLLRE--HLSKAVRKRVVGEIDKDLTK-LPADEIE 135 (138)
T ss_pred HHHHHHHh-----CCCCeEEEEECHHHHHHHHH--HhCHHHHHHHHHHHhhhhhc-CCHHHHH
Confidence 99998864 68999999999999999995 78999988887666544443 2444443
No 13
>PRK07714 hypothetical protein; Provisional
Probab=93.22 E-value=0.61 Score=38.26 Aligned_cols=30 Identities=20% Similarity=0.307 Sum_probs=27.4
Q ss_pred CCCcEEECHHHHHHHHHhCCccEEEeecCC
Q 013759 298 DTGKYVFGADDTLKALDMGAVDTLIVWENL 327 (437)
Q Consensus 298 ~~~~a~yG~~~V~~Al~~GaV~tLlV~d~l 327 (437)
..|+.+.|.+.|.+|+..|.+..+|+..|.
T Consensus 15 raGk~v~G~~~v~~al~~g~~~lViiA~D~ 44 (100)
T PRK07714 15 RARKVISGEELVLKEVRSGKAKLVLLSEDA 44 (100)
T ss_pred HhCCeeecHHHHHHHHHhCCceEEEEeCCC
Confidence 358999999999999999999999998876
No 14
>PRK13602 putative ribosomal protein L7Ae-like; Provisional
Probab=93.12 E-value=0.59 Score=36.93 Aligned_cols=60 Identities=27% Similarity=0.329 Sum_probs=49.6
Q ss_pred CCcEEECHHHHHHHHHhCCccEEEeecCCCceeEEEEcCCCCcEEEEeeccchhcccCcccCCCccccchhcccccHHHH
Q 013759 299 TGKYVFGADDTLKALDMGAVDTLIVWENLDITRYVLKNTVTGEIVIKHLNREQETNQNNFRDSATSAELEVQEKSSLLEW 378 (437)
Q Consensus 299 ~~~a~yG~~~V~~Al~~GaV~tLlV~d~l~~~~~~~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~~~~~~~~dvve~ 378 (437)
.|+.+.|.++|++|++.|.+..++|..|.. +++...
T Consensus 9 agkl~~G~~~v~kai~~gkaklViiA~D~~--------------------------------------------~~~~~~ 44 (82)
T PRK13602 9 AKSIVIGTKQTVKALKRGSVKEVVVAEDAD--------------------------------------------PRLTEK 44 (82)
T ss_pred cCCEEEcHHHHHHHHHcCCeeEEEEECCCC--------------------------------------------HHHHHH
Confidence 379999999999999999999999988762 112345
Q ss_pred HHHHHHhcCCEEEEecCCCchhhh
Q 013759 379 FANEYRRFGCTLEFVTNKSQEGSQ 402 (437)
Q Consensus 379 Lve~a~~~ga~V~ivs~~~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 888899999999999987777765
No 15
>PRK13600 putative ribosomal protein L7Ae-like; Provisional
Probab=93.03 E-value=0.44 Score=37.84 Aligned_cols=57 Identities=26% Similarity=0.433 Sum_probs=49.0
Q ss_pred EEECHHHHHHHHHhCCccEEEeecCCCceeEEEEcCCCCcEEEEeeccchhcccCcccCCCccccchhcccccHHHHHHH
Q 013759 302 YVFGADDTLKALDMGAVDTLIVWENLDITRYVLKNTVTGEIVIKHLNREQETNQNNFRDSATSAELEVQEKSSLLEWFAN 381 (437)
Q Consensus 302 a~yG~~~V~~Al~~GaV~tLlV~d~l~~~~~~~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~~~~~~~~dvve~Lve 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 489999999999999999999988772 113556899
Q ss_pred HHHhcCCEEEEecCCCchhhh
Q 013759 382 EYRRFGCTLEFVTNKSQEGSQ 402 (437)
Q Consensus 382 ~a~~~ga~V~ivs~~~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 999999999999998887764
No 16
>PRK07283 hypothetical protein; Provisional
Probab=92.88 E-value=0.74 Score=37.64 Aligned_cols=31 Identities=19% Similarity=0.383 Sum_probs=28.2
Q ss_pred cCCCcEEECHHHHHHHHHhCCccEEEeecCC
Q 013759 297 QDTGKYVFGADDTLKALDMGAVDTLIVWENL 327 (437)
Q Consensus 297 ~~~~~a~yG~~~V~~Al~~GaV~tLlV~d~l 327 (437)
+..|+.+.|.+.|.+|+..|.+..++++.|.
T Consensus 14 ~raGklv~G~~~v~~aik~gk~~lVi~A~Da 44 (98)
T PRK07283 14 QRAGRIISGEELVVKAIQSGQAKLVFLANDA 44 (98)
T ss_pred HHhCCeeEcHHHHHHHHHcCCccEEEEeCCC
Confidence 3458999999999999999999999998886
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=92.26 E-value=0.25 Score=37.84 Aligned_cols=69 Identities=16% Similarity=0.236 Sum_probs=46.2
Q ss_pred EECHHHHHHHHHhCC-ccEEEeecCCCceeEEEEcCCCCcEEEEeeccchhcccCcccCCCccccchhcccccHHHHHHH
Q 013759 303 VFGADDTLKALDMGA-VDTLIVWENLDITRYVLKNTVTGEIVIKHLNREQETNQNNFRDSATSAELEVQEKSSLLEWFAN 381 (437)
Q Consensus 303 ~yG~~~V~~Al~~Ga-V~tLlV~d~l~~~~~~~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~~~~~~~~dvve~Lve 381 (437)
+||...|.+|++.|. +..|+++++.. .+ . +..+++
T Consensus 2 ieG~~~V~eaL~~~~~i~~l~~~~~~~-------~~---~----------------------------------~~~i~~ 37 (76)
T PF08032_consen 2 IEGRHAVEEALKSGPRIKKLFVTEEKA-------DK---R----------------------------------IKEILK 37 (76)
T ss_dssp EESHHHHHHHHHCTGGEEEEEEETT----------C---C----------------------------------THHHHH
T ss_pred EEEHHHHHHHHcCCCCccEEEEEcCcc-------ch---h----------------------------------HHHHHH
Confidence 799999999999986 99999988741 11 0 134889
Q ss_pred HHHhcCCEEEEecCCCchhhhh--ccccccEEEEeeee
Q 013759 382 EYRRFGCTLEFVTNKSQEGSQF--CRGFGGIGGILRYQ 417 (437)
Q Consensus 382 ~a~~~ga~V~ivs~~~e~G~q~--L~~~gGIaAiLRy~ 417 (437)
.+...|..|.+++..-- .++ -....||+|..+-+
T Consensus 38 ~~~~~~i~v~~v~~~~l--~~ls~~~~hQGv~a~v~~~ 73 (76)
T PF08032_consen 38 LAKKKGIPVYEVSKKVL--DKLSDTENHQGVVAVVKPP 73 (76)
T ss_dssp HHHHCT-EEEEE-HHHH--HHCTTTSS-TTEEEEEE--
T ss_pred HHHHcCCeEEEeCHHHH--HHHcCCCCCCeEEEEEeCC
Confidence 99999999999986421 110 13455999988743
No 18
>PRK06683 hypothetical protein; Provisional
Probab=91.23 E-value=1.3 Score=34.94 Aligned_cols=60 Identities=20% Similarity=0.251 Sum_probs=49.5
Q ss_pred CCcEEECHHHHHHHHHhCCccEEEeecCCCceeEEEEcCCCCcEEEEeeccchhcccCcccCCCccccchhcccccHHHH
Q 013759 299 TGKYVFGADDTLKALDMGAVDTLIVWENLDITRYVLKNTVTGEIVIKHLNREQETNQNNFRDSATSAELEVQEKSSLLEW 378 (437)
Q Consensus 299 ~~~a~yG~~~V~~Al~~GaV~tLlV~d~l~~~~~~~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~~~~~~~~dvve~ 378 (437)
.|+.+.|.++|++|++.|.+..++|..|.. +++...
T Consensus 9 agk~v~G~~~v~kaik~gkaklViiA~Da~--------------------------------------------~~~~~~ 44 (82)
T PRK06683 9 AENVVVGHKRTLEAIKNGIVKEVVIAEDAD--------------------------------------------MRLTHV 44 (82)
T ss_pred CCCEEEcHHHHHHHHHcCCeeEEEEECCCC--------------------------------------------HHHHHH
Confidence 589999999999999999999999988762 112345
Q ss_pred HHHHHHhcCCEEEEecCCCchhhh
Q 013759 379 FANEYRRFGCTLEFVTNKSQEGSQ 402 (437)
Q Consensus 379 Lve~a~~~ga~V~ivs~~~e~G~q 402 (437)
+...+...+-.+..+.+..+-|.-
T Consensus 45 i~~~~~~~~Vpv~~~~t~~eLG~A 68 (82)
T PRK06683 45 IIRTALQHNIPITKVESVRKLGKV 68 (82)
T ss_pred HHHHHHhcCCCEEEECCHHHHHHH
Confidence 889999999999999987766654
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=90.67 E-value=1.8 Score=36.64 Aligned_cols=74 Identities=18% Similarity=0.279 Sum_probs=54.3
Q ss_pred CCcEEECHHHHHHHHHhCCccEEEeecCCCceeEEEEcCCCCcEEEEeeccchhcccCcccCCCccccchhcccccHHHH
Q 013759 299 TGKYVFGADDTLKALDMGAVDTLIVWENLDITRYVLKNTVTGEIVIKHLNREQETNQNNFRDSATSAELEVQEKSSLLEW 378 (437)
Q Consensus 299 ~~~a~yG~~~V~~Al~~GaV~tLlV~d~l~~~~~~~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~~~~~~~~dvve~ 378 (437)
.|..+.|.++|.+|++.|.+..++|+.|.. + .++...
T Consensus 24 agkl~~G~~~v~kaikkgka~LVilA~D~s--------~-----------------------------------~~~~~~ 60 (117)
T TIGR03677 24 TGKIKKGTNEVTKAVERGIAKLVVIAEDVE--------P-----------------------------------PEIVAH 60 (117)
T ss_pred cCCEeEcHHHHHHHHHcCCccEEEEeCCCC--------c-----------------------------------HHHHHH
Confidence 589999999999999999999999998872 1 112345
Q ss_pred HHHHHHhcCCEEEEecCCCchhhhhccc-cccEEEEee
Q 013759 379 FANEYRRFGCTLEFVTNKSQEGSQFCRG-FGGIGGILR 415 (437)
Q Consensus 379 Lve~a~~~ga~V~ivs~~~e~G~q~L~~-~gGIaAiLR 415 (437)
+...+...+-.+.++.+..+-|.-+-.. --.+.||+-
T Consensus 61 i~~lc~~~~Ip~~~~~sk~eLG~a~Gk~~~~svvaI~d 98 (117)
T TIGR03677 61 LPALCEEKGIPYVYVKKKEDLGAAAGLEVGAASAAIVD 98 (117)
T ss_pred HHHHHHHcCCCEEEeCCHHHHHHHhCCCCCeEEEEEEc
Confidence 7788888898888888887777652111 133556654
No 20
>PTZ00106 60S ribosomal protein L30; Provisional
Probab=90.38 E-value=1.8 Score=36.03 Aligned_cols=39 Identities=33% Similarity=0.545 Sum_probs=32.0
Q ss_pred HHHHHHHHccCCCcEEECHHHHHHHHHhCCccEEEeecCC
Q 013759 288 IGKYFEEISQDTGKYVFGADDTLKALDMGAVDTLIVWENL 327 (437)
Q Consensus 288 l~~f~~~~~~~~~~a~yG~~~V~~Al~~GaV~tLlV~d~l 327 (437)
++.++....+ .|+.+.|.++|++|++.|.+..++|+.|.
T Consensus 13 i~~~Lgla~r-aGKlv~G~~~vlkalk~gkaklViiA~D~ 51 (108)
T PTZ00106 13 INSKLQLVMK-SGKYTLGTKSTLKALRNGKAKLVIISNNC 51 (108)
T ss_pred HHHHHHHHHH-hCCeeecHHHHHHHHHcCCeeEEEEeCCC
Confidence 4445544444 58999999999999999999999998876
No 21
>PRK01018 50S ribosomal protein L30e; Reviewed
Probab=90.36 E-value=2.2 Score=34.92 Aligned_cols=60 Identities=23% Similarity=0.281 Sum_probs=46.9
Q ss_pred CCcEEECHHHHHHHHHhCCccEEEeecCCCceeEEEEcCCCCcEEEEeeccchhcccCcccCCCccccchhcccccHHHH
Q 013759 299 TGKYVFGADDTLKALDMGAVDTLIVWENLDITRYVLKNTVTGEIVIKHLNREQETNQNNFRDSATSAELEVQEKSSLLEW 378 (437)
Q Consensus 299 ~~~a~yG~~~V~~Al~~GaV~tLlV~d~l~~~~~~~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~~~~~~~~dvve~ 378 (437)
.|+.+.|.++|++|++.|.+..++|++|.. ++....
T Consensus 14 agkl~~G~~~v~kai~~gkaklViiA~D~~--------------------------------------------~~~~~~ 49 (99)
T PRK01018 14 TGKVILGSKRTIKAIKLGKAKLVIVASNCP--------------------------------------------KDIKED 49 (99)
T ss_pred cCCEEEcHHHHHHHHHcCCceEEEEeCCCC--------------------------------------------HHHHHH
Confidence 489999999999999999999999988762 112345
Q ss_pred HHHHHHhcCCEEEEe-cCCCchhhh
Q 013759 379 FANEYRRFGCTLEFV-TNKSQEGSQ 402 (437)
Q Consensus 379 Lve~a~~~ga~V~iv-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 778888889888776 466666654
No 22
>PRK05583 ribosomal protein L7Ae family protein; Provisional
Probab=89.78 E-value=1.7 Score=36.02 Aligned_cols=31 Identities=19% Similarity=0.323 Sum_probs=28.1
Q ss_pred cCCCcEEECHHHHHHHHHhCCccEEEeecCC
Q 013759 297 QDTGKYVFGADDTLKALDMGAVDTLIVWENL 327 (437)
Q Consensus 297 ~~~~~a~yG~~~V~~Al~~GaV~tLlV~d~l 327 (437)
+..|+.++|.+.|.+|+..|.+..||+++|.
T Consensus 13 ~rAGklv~G~~~v~~aik~gk~~lVI~A~D~ 43 (104)
T PRK05583 13 KKAGKLLEGYNKCEEAIKKKKVYLIIISNDI 43 (104)
T ss_pred HHhCCeeecHHHHHHHHHcCCceEEEEeCCC
Confidence 3458999999999999999999999998886
No 23
>PRK04175 rpl7ae 50S ribosomal protein L7Ae; Validated
Probab=89.63 E-value=3.5 Score=35.13 Aligned_cols=61 Identities=21% Similarity=0.336 Sum_probs=49.2
Q ss_pred CCcEEECHHHHHHHHHhCCccEEEeecCCCceeEEEEcCCCCcEEEEeeccchhcccCcccCCCccccchhcccccHHHH
Q 013759 299 TGKYVFGADDTLKALDMGAVDTLIVWENLDITRYVLKNTVTGEIVIKHLNREQETNQNNFRDSATSAELEVQEKSSLLEW 378 (437)
Q Consensus 299 ~~~a~yG~~~V~~Al~~GaV~tLlV~d~l~~~~~~~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~~~~~~~~dvve~ 378 (437)
.|..+.|.++|.+|++.|.+..++|+.|.. + .++...
T Consensus 28 agklv~G~~~v~kaikkgkakLVilA~D~s--------~-----------------------------------~~i~~~ 64 (122)
T PRK04175 28 TGKIKKGTNETTKAVERGIAKLVVIAEDVD--------P-----------------------------------EEIVAH 64 (122)
T ss_pred cCCEeEcHHHHHHHHHcCCccEEEEeCCCC--------h-----------------------------------HHHHHH
Confidence 489999999999999999999999998862 1 122345
Q ss_pred HHHHHHhcCCEEEEecCCCchhhh
Q 013759 379 FANEYRRFGCTLEFVTNKSQEGSQ 402 (437)
Q Consensus 379 Lve~a~~~ga~V~ivs~~~e~G~q 402 (437)
+...++..|-.+.++.+..+-|.-
T Consensus 65 ~~~lc~~~~Vp~~~~~tk~eLG~a 88 (122)
T PRK04175 65 LPLLCEEKKIPYVYVPSKKDLGKA 88 (122)
T ss_pred HHHHHHHcCCCEEEECCHHHHHHH
Confidence 788888999998888887777754
No 24
>COG1358 RPL8A Ribosomal protein HS6-type (S12/L30/L7a) [Translation, ribosomal structure and biogenesis]
Probab=89.18 E-value=1.4 Score=37.25 Aligned_cols=61 Identities=18% Similarity=0.337 Sum_probs=50.5
Q ss_pred CCcEEECHHHHHHHHHhCCccEEEeecCCCceeEEEEcCCCCcEEEEeeccchhcccCcccCCCccccchhcccccHHHH
Q 013759 299 TGKYVFGADDTLKALDMGAVDTLIVWENLDITRYVLKNTVTGEIVIKHLNREQETNQNNFRDSATSAELEVQEKSSLLEW 378 (437)
Q Consensus 299 ~~~a~yG~~~V~~Al~~GaV~tLlV~d~l~~~~~~~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~~~~~~~~dvve~ 378 (437)
.+....|.++|.+|++.|....++|++|.. +.+++-.
T Consensus 25 ~~ki~~G~~e~~Kai~~g~a~LVviA~Dv~-------------------------------------------P~~~~~~ 61 (116)
T COG1358 25 AGKLKKGTNEVTKAIERGKAKLVVIAEDVS-------------------------------------------PEELVKH 61 (116)
T ss_pred cCCchhhHHHHHHHHHcCCCcEEEEecCCC-------------------------------------------HHHHHHH
Confidence 478999999999999999999999988872 1234456
Q ss_pred HHHHHHhcCCEEEEecCCCchhhh
Q 013759 379 FANEYRRFGCTLEFVTNKSQEGSQ 402 (437)
Q Consensus 379 Lve~a~~~ga~V~ivs~~~e~G~q 402 (437)
|...+...+.-+.+|.+..+.|.-
T Consensus 62 l~~lc~~~~vpyv~V~sk~~LG~a 85 (116)
T COG1358 62 LPALCEEKNVPYVYVGSKKELGKA 85 (116)
T ss_pred HHHHHHhcCCCEEEeCCHHHHHHH
Confidence 788888999999999998877754
No 25
>PRK13601 putative L7Ae-like ribosomal protein; Provisional
Probab=88.64 E-value=2.3 Score=33.65 Aligned_cols=60 Identities=17% Similarity=0.203 Sum_probs=49.2
Q ss_pred CCcEEECHHHHHHHHHhCCccEEEeecCCCceeEEEEcCCCCcEEEEeeccchhcccCcccCCCccccchhcccccHHHH
Q 013759 299 TGKYVFGADDTLKALDMGAVDTLIVWENLDITRYVLKNTVTGEIVIKHLNREQETNQNNFRDSATSAELEVQEKSSLLEW 378 (437)
Q Consensus 299 ~~~a~yG~~~V~~Al~~GaV~tLlV~d~l~~~~~~~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~~~~~~~~dvve~ 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 378999999999999999999999988762 123445
Q ss_pred HHHHHHhcCCEEEEecCCCchhhh
Q 013759 379 FANEYRRFGCTLEFVTNKSQEGSQ 402 (437)
Q Consensus 379 Lve~a~~~ga~V~ivs~~~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 889999999999888887776654
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=88.49 E-value=3 Score=33.46 Aligned_cols=61 Identities=25% Similarity=0.360 Sum_probs=49.1
Q ss_pred CCcEEECHHHHHHHHHhCCccEEEeecCCCceeEEEEcCCCCcEEEEeeccchhcccCcccCCCccccchhcccccHHHH
Q 013759 299 TGKYVFGADDTLKALDMGAVDTLIVWENLDITRYVLKNTVTGEIVIKHLNREQETNQNNFRDSATSAELEVQEKSSLLEW 378 (437)
Q Consensus 299 ~~~a~yG~~~V~~Al~~GaV~tLlV~d~l~~~~~~~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~~~~~~~~dvve~ 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 378999999999999999999999998862 1 0 11223
Q ss_pred HHHHHHhcCCEEEEecCCCchhhh
Q 013759 379 FANEYRRFGCTLEFVTNKSQEGSQ 402 (437)
Q Consensus 379 Lve~a~~~ga~V~ivs~~~e~G~q 402 (437)
+...+.+.+..+.++++..+-|.-
T Consensus 50 l~~~c~~~~Ip~~~~~s~~eLG~~ 73 (95)
T PF01248_consen 50 LPALCEEKNIPYVFVPSKEELGRA 73 (95)
T ss_dssp HHHHHHHTTEEEEEESHHHHHHHH
T ss_pred chhheeccceeEEEECCHHHHHHH
Confidence 778888999999999987888875
No 27
>PRK09190 hypothetical protein; Provisional
Probab=86.94 E-value=6.2 Score=37.22 Aligned_cols=33 Identities=24% Similarity=0.266 Sum_probs=29.4
Q ss_pred ccCCCcEEECHHHHHHHHHhCCccEEEeecCCC
Q 013759 296 SQDTGKYVFGADDTLKALDMGAVDTLIVWENLD 328 (437)
Q Consensus 296 ~~~~~~a~yG~~~V~~Al~~GaV~tLlV~d~l~ 328 (437)
++..|..+.|.+.|.+|+..|.+..||++.|..
T Consensus 106 ArRAGklVsG~~~V~~alk~gk~~Lvi~A~DaS 138 (220)
T PRK09190 106 ARKAGQVVSGFEKVDAALRSGEAAALIHASDGA 138 (220)
T ss_pred HhhhCCEeecHHHHHHHHHcCCceEEEEeccCC
Confidence 345689999999999999999999999998874
No 28
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=85.16 E-value=0.46 Score=33.06 Aligned_cols=37 Identities=16% Similarity=0.135 Sum_probs=23.2
Q ss_pred EEEcCCCCcEEEEeeccchhcccCcccCCCccccchhcccccH
Q 013759 333 VLKNTVTGEIVIKHLNREQETNQNNFRDSATSAELEVQEKSSL 375 (437)
Q Consensus 333 ~~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~~~~~~~~dv 375 (437)
.++|++||.... +.+. .....||.||.++......++
T Consensus 3 ~y~C~~CG~~~~--~~~~----~~~~~Cp~CG~~~~~~~~~~~ 39 (46)
T PRK00398 3 EYKCARCGREVE--LDEY----GTGVRCPYCGYRILFKERPPV 39 (46)
T ss_pred EEECCCCCCEEE--ECCC----CCceECCCCCCeEEEccCCCc
Confidence 379999997422 2221 226899999998654444443
No 29
>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=82.19 E-value=1.2 Score=39.67 Aligned_cols=45 Identities=16% Similarity=0.109 Sum_probs=31.3
Q ss_pred EEcCCCCcEEEEeeccchhcccCcccCCCccccchhcccccHHHHHHHHH
Q 013759 334 LKNTVTGEIVIKHLNREQETNQNNFRDSATSAELEVQEKSSLLEWFANEY 383 (437)
Q Consensus 334 ~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~~~~~~~~dvve~Lve~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-FTF-NE---AMELNFTCPRCGAMLDYLDNSEAIEKLEEQI 154 (158)
T ss_pred EECCCCCcE-eeH-HH---HHHcCCcCCCCCCEeeeccCHHHHHHHHHHH
Confidence 789988852 211 11 1145799999999998888888887765544
No 30
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=80.13 E-value=1.9 Score=39.35 Aligned_cols=46 Identities=13% Similarity=0.083 Sum_probs=31.4
Q ss_pred EEcCCCCcEEEEeeccchhcccCcccCCCccccchhcccccHHHHHHHHHH
Q 013759 334 LKNTVTGEIVIKHLNREQETNQNNFRDSATSAELEVQEKSSLLEWFANEYR 384 (437)
Q Consensus 334 ~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~~~~~~~~dvve~Lve~a~ 384 (437)
|.|++|+.. ..+.. +-...|.||.||+.|...+..+.+..|=+...
T Consensus 118 Y~Cp~C~~r-ytf~e----A~~~~F~Cp~Cg~~L~~~dn~~~~~~l~~~I~ 163 (178)
T PRK06266 118 FFCPNCHIR-FTFDE----AMEYGFRCPQCGEMLEEYDNSELIKELKEQIK 163 (178)
T ss_pred EECCCCCcE-EeHHH----HhhcCCcCCCCCCCCeecccHHHHHHHHHHHH
Confidence 789999853 22221 11347999999999988887777776655443
No 31
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=76.10 E-value=8.8 Score=33.29 Aligned_cols=11 Identities=0% Similarity=-0.013 Sum_probs=8.5
Q ss_pred CcccCCCcccc
Q 013759 356 NNFRDSATSAE 366 (437)
Q Consensus 356 ~~~~cp~~g~~ 366 (437)
..+.||.||+.
T Consensus 106 ~~~~CP~Cgs~ 116 (135)
T PRK03824 106 AFLKCPKCGSR 116 (135)
T ss_pred cCcCCcCCCCC
Confidence 34679999975
No 32
>COG1911 RPL30 Ribosomal protein L30E [Translation, ribosomal structure and biogenesis]
Probab=75.34 E-value=43 Score=27.24 Aligned_cols=71 Identities=21% Similarity=0.283 Sum_probs=50.2
Q ss_pred CCcEEECHHHHHHHHHhCCccEEEeecCCCceeEEEEcCCCCcEEEEeeccchhcccCcccCCCccccchhcccccHHHH
Q 013759 299 TGKYVFGADDTLKALDMGAVDTLIVWENLDITRYVLKNTVTGEIVIKHLNREQETNQNNFRDSATSAELEVQEKSSLLEW 378 (437)
Q Consensus 299 ~~~a~yG~~~V~~Al~~GaV~tLlV~d~l~~~~~~~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~~~~~~~~dvve~ 378 (437)
+|+++.|.+.+.+++.+|..+.++|..+. | . ++-+.
T Consensus 17 TGkvilG~k~tiK~lk~gkaKliiiAsN~---------P---~--------------------------------~~k~~ 52 (100)
T COG1911 17 TGKVILGSKRTIKSLKLGKAKLIIIASNC---------P---K--------------------------------ELKED 52 (100)
T ss_pred cCCEEEehHHHHHHHHcCCCcEEEEecCC---------C---H--------------------------------HHHHH
Confidence 58999999999999999999999997654 2 1 12234
Q ss_pred HHHHHHhcCCEEEEecCCC-chhhhhccccccEEEEe
Q 013759 379 FANEYRRFGCTLEFVTNKS-QEGSQFCRGFGGIGGIL 414 (437)
Q Consensus 379 Lve~a~~~ga~V~ivs~~~-e~G~q~L~~~gGIaAiL 414 (437)
|--.|+-.+..|.+++..+ |.|.- +...=.||++.
T Consensus 53 ieyYAkLs~ipV~~y~Gt~~eLG~~-cgkpf~v~~la 88 (100)
T COG1911 53 IEYYAKLSDIPVYVYEGTSVELGTV-CGKPFRVAALA 88 (100)
T ss_pred HHHHHHHcCCcEEEecCCceeHHhh-hCCCceEEEEE
Confidence 5566777799999998654 33432 33333466554
No 33
>PTZ00222 60S ribosomal protein L7a; Provisional
Probab=75.29 E-value=33 Score=33.01 Aligned_cols=71 Identities=18% Similarity=0.276 Sum_probs=51.4
Q ss_pred cEEECHHHHHHHHHhCCccEEEeecCCCceeEEEEcCCCCcEEEEeeccchhcccCcccCCCccccchhcccccHHHHHH
Q 013759 301 KYVFGADDTLKALDMGAVDTLIVWENLDITRYVLKNTVTGEIVIKHLNREQETNQNNFRDSATSAELEVQEKSSLLEWFA 380 (437)
Q Consensus 301 ~a~yG~~~V~~Al~~GaV~tLlV~d~l~~~~~~~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~~~~~~~~dvve~Lv 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 4789999999999999999999998872 1 11233577
Q ss_pred HHHHhcCCEEEEecCCCchhhhhccccccEEEEe
Q 013759 381 NEYRRFGCTLEFVTNKSQEGSQFCRGFGGIGGIL 414 (437)
Q Consensus 381 e~a~~~ga~V~ivs~~~e~G~q~L~~~gGIaAiL 414 (437)
..+..+|.-..+|.+..+.|.-+=..-..+.||.
T Consensus 169 aLCrk~~VPY~iVktKaeLG~AIGkKtravVAIt 202 (263)
T PTZ00222 169 NLCRANKIPYAIVKDMARLGDAIGRKTATCVAIT 202 (263)
T ss_pred HHHHhcCCCEEEECCHHHHHHHHCCCCCeEEEEe
Confidence 8888889888888888777754211123455555
No 34
>COG5622 Protein required for attachment to host cells [Cell motility and secretion]
Probab=73.61 E-value=1.1 Score=38.33 Aligned_cols=66 Identities=12% Similarity=0.159 Sum_probs=49.6
Q ss_pred HHHHHHHHHHHHHhhhcCCCCCCCCcceEEEecChhhHHHhcccccCChhhhcceeEEEECCCCCCccHHHHHH
Q 013759 197 RHNYVRKTAELATQFYINPATSQPNVSGLVLAGSADFKTELSQSDMFDPRLQAKILKVVDVSYGGENGFNQAIE 270 (437)
Q Consensus 197 ~~~f~~~va~~l~~~~~~~~~~~~~~~~liiaGp~~~k~~f~~~~~l~~~l~~~vi~~v~~s~~~~~gl~Evl~ 270 (437)
-++|-..+++.|.+.+.. ..++-|||+.+..+...+++ .|++.+++++++.++-...+ +++.++.+
T Consensus 69 ~~~fa~~~a~~l~r~v~~-----g~~~~LvIiAaPrtLG~lRK--~lh~~lk~~~~~EI~Kdlt~-H~v~~iea 134 (139)
T COG5622 69 EDSFAAEIAKELNRSVHG-----GKFKNLVIIAAPRTLGELRK--ELHKGLKEKLTAEIAKDLTG-HPVDEIEA 134 (139)
T ss_pred chhHHHHHHHHHHHHHhh-----cccceeEEEeCchhHHHHHH--HHHHHHHHHHHHHHhhHhhc-CcHHHHHH
Confidence 368999999999998874 68999999988888888886 67888888887666544433 34555433
No 35
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=70.05 E-value=3 Score=36.68 Aligned_cols=41 Identities=15% Similarity=0.137 Sum_probs=23.1
Q ss_pred EEcCCCCcEEEEeeccchh--cccCcccCCCccccchhcccccHH
Q 013759 334 LKNTVTGEIVIKHLNREQE--TNQNNFRDSATSAELEVQEKSSLL 376 (437)
Q Consensus 334 ~r~~~~~~~~~~~~~~~~~--~~r~~~~cp~~g~~~~~~~~~dvv 376 (437)
+.|++|+.. .. ...+.. .....+.||.||+++...+....+
T Consensus 100 Y~Cp~C~~~-y~-~~ea~~~~d~~~~f~Cp~Cg~~l~~~dn~~~~ 142 (147)
T smart00531 100 YKCPNCQSK-YT-FLEANQLLDMDGTFTCPRCGEELEEDDNSEPI 142 (147)
T ss_pred EECcCCCCE-ee-HHHHHHhcCCCCcEECCCCCCEEEEcCchhhH
Confidence 789988853 11 111111 112238999999997655444443
No 36
>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=69.36 E-value=7.8 Score=25.69 Aligned_cols=34 Identities=9% Similarity=0.064 Sum_probs=20.1
Q ss_pred eeEEEEcCCCCcEEEEeeccchhcccCcccCCCcccc
Q 013759 330 TRYVLKNTVTGEIVIKHLNREQETNQNNFRDSATSAE 366 (437)
Q Consensus 330 ~~~~~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~ 366 (437)
+-|.|+|+.||..-.. +.+. .......||.||++
T Consensus 2 p~Y~y~C~~Cg~~fe~-~~~~--~~~~~~~CP~Cg~~ 35 (41)
T smart00834 2 PIYEYRCEDCGHTFEV-LQKI--SDDPLATCPECGGD 35 (41)
T ss_pred CCEEEEcCCCCCEEEE-EEec--CCCCCCCCCCCCCc
Confidence 3466899999973211 1111 11335679999985
No 37
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=69.15 E-value=3.8 Score=36.79 Aligned_cols=24 Identities=13% Similarity=-0.127 Sum_probs=17.7
Q ss_pred EEcCCCCcEEEEeeccchhcccCcccCCCcccc
Q 013759 334 LKNTVTGEIVIKHLNREQETNQNNFRDSATSAE 366 (437)
Q Consensus 334 ~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~ 366 (437)
|+|+-||.... . .....||.||.+
T Consensus 135 ~vC~vCGy~~~---g------e~P~~CPiCga~ 158 (166)
T COG1592 135 WVCPVCGYTHE---G------EAPEVCPICGAP 158 (166)
T ss_pred EEcCCCCCccc---C------CCCCcCCCCCCh
Confidence 89999998532 1 234689999975
No 38
>PTZ00365 60S ribosomal protein L7Ae-like; Provisional
Probab=66.44 E-value=33 Score=33.06 Aligned_cols=73 Identities=11% Similarity=0.161 Sum_probs=52.4
Q ss_pred CcEEECHHHHHHHHHhCCccEEEeecCCCceeEEEEcCCCCcEEEEeeccchhcccCcccCCCccccchhcccccHHHHH
Q 013759 300 GKYVFGADDTLKALDMGAVDTLIVWENLDITRYVLKNTVTGEIVIKHLNREQETNQNNFRDSATSAELEVQEKSSLLEWF 379 (437)
Q Consensus 300 ~~a~yG~~~V~~Al~~GaV~tLlV~d~l~~~~~~~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~~~~~~~~dvve~L 379 (437)
-...||..+|..+++.|.+..+||..|.. + ..++..|
T Consensus 131 ~~vk~Gin~VtklIekkKAkLVIIA~DVs--------P-----------------------------------~t~kk~L 167 (266)
T PTZ00365 131 FMLKYGLNHVTDLVEYKKAKLVVIAHDVD--------P-----------------------------------IELVCFL 167 (266)
T ss_pred hHHHhhhHHHHHHHHhCCccEEEEeCCCC--------H-----------------------------------HHHHHHH
Confidence 34679999999999999999999998872 1 1123345
Q ss_pred HHHHHhcCCEEEEecCCCchhhhhccccccEEEEee
Q 013759 380 ANEYRRFGCTLEFVTNKSQEGSQFCRGFGGIGGILR 415 (437)
Q Consensus 380 ve~a~~~ga~V~ivs~~~e~G~q~L~~~gGIaAiLR 415 (437)
...+..+|.-..++.+..+.|.-+=..--.+.||.-
T Consensus 168 P~LC~k~~VPY~iv~sK~eLG~AIGkktraVVAItd 203 (266)
T PTZ00365 168 PALCRKKEVPYCIIKGKSRLGKLVHQKTAAVVAIDN 203 (266)
T ss_pred HHHHhccCCCEEEECCHHHHHHHhCCCCceEEEecc
Confidence 688889999999999887766541111235666664
No 39
>COG2433 Uncharacterized conserved protein [Function unknown]
Probab=63.81 E-value=18 Score=38.81 Aligned_cols=32 Identities=28% Similarity=0.299 Sum_probs=28.2
Q ss_pred CCCCcchHHHHHHHHHHHHHHHHHHHHHHHhh
Q 013759 180 GRGGQSALRFARLRMEKRHNYVRKTAELATQF 211 (437)
Q Consensus 180 ~~gG~s~~Rf~r~~ee~~~~f~~~va~~l~~~ 211 (437)
+.|||||.||.|..-.++.+-.++|-+.|.+.
T Consensus 149 g~GGwSq~RY~R~vh~av~~~~reIee~L~~a 180 (652)
T COG2433 149 GPGGWSQNRYRRRVHGAVKRVVREIEEKLDEA 180 (652)
T ss_pred CCCCccHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 45899999999999999999999999988764
No 40
>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=62.16 E-value=14 Score=25.13 Aligned_cols=33 Identities=9% Similarity=0.061 Sum_probs=20.0
Q ss_pred eeEEEEcCCCCcEEEEeeccchhcccCcccCCCccc
Q 013759 330 TRYVLKNTVTGEIVIKHLNREQETNQNNFRDSATSA 365 (437)
Q Consensus 330 ~~~~~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~ 365 (437)
|-|.|+|++||..-.. +.+- .+.....||.||+
T Consensus 2 P~Yey~C~~Cg~~fe~-~~~~--~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 2 PIYEYRCEECGHEFEV-LQSI--SEDDPVPCPECGS 34 (42)
T ss_pred CCEEEEeCCCCCEEEE-EEEc--CCCCCCcCCCCCC
Confidence 3466899999953211 1111 1134578999998
No 41
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=57.68 E-value=72 Score=33.74 Aligned_cols=39 Identities=18% Similarity=0.190 Sum_probs=22.1
Q ss_pred CcceEEEecChhhH------HHhcccccCChhhhcceeEEEECCCCC
Q 013759 221 NVSGLVLAGSADFK------TELSQSDMFDPRLQAKILKVVDVSYGG 261 (437)
Q Consensus 221 ~~~~liiaGp~~~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 36899999987322 233322 123346778776665 3444
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=53.41 E-value=21 Score=25.09 Aligned_cols=33 Identities=9% Similarity=0.012 Sum_probs=19.1
Q ss_pred eeEEEEcCCCCcEEEEeeccchhcccCcccCCCccc
Q 013759 330 TRYVLKNTVTGEIVIKHLNREQETNQNNFRDSATSA 365 (437)
Q Consensus 330 ~~~~~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~ 365 (437)
+-|.|+|.+||..-... .+.. +.....||.||.
T Consensus 2 P~Yey~C~~Cg~~fe~~-~~~~--~~~~~~CP~Cg~ 34 (52)
T TIGR02605 2 PIYEYRCTACGHRFEVL-QKMS--DDPLATCPECGG 34 (52)
T ss_pred CCEEEEeCCCCCEeEEE-EecC--CCCCCCCCCCCC
Confidence 34668999998632211 1111 123457999997
No 43
>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=52.47 E-value=3.3 Score=29.97 Aligned_cols=12 Identities=42% Similarity=0.332 Sum_probs=6.7
Q ss_pred ccCCCccccchh
Q 013759 358 FRDSATSAELEV 369 (437)
Q Consensus 358 ~~cp~~g~~~~~ 369 (437)
..||.||..+++
T Consensus 23 V~Cp~CGaeleV 34 (54)
T TIGR01206 23 VICDECGAELEV 34 (54)
T ss_pred EeCCCCCCEEEE
Confidence 456666655443
No 44
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=51.60 E-value=14 Score=27.14 Aligned_cols=9 Identities=22% Similarity=0.206 Sum_probs=4.9
Q ss_pred EEEcCCCCc
Q 013759 333 VLKNTVTGE 341 (437)
Q Consensus 333 ~~r~~~~~~ 341 (437)
.|-|++||+
T Consensus 27 ~F~CPnCGe 35 (61)
T COG2888 27 KFPCPNCGE 35 (61)
T ss_pred EeeCCCCCc
Confidence 355555554
No 45
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=50.63 E-value=46 Score=30.21 Aligned_cols=27 Identities=11% Similarity=-0.006 Sum_probs=18.5
Q ss_pred eEEEEcCCCCcEEEEeeccchhcccCcccCCCccccc
Q 013759 331 RYVLKNTVTGEIVIKHLNREQETNQNNFRDSATSAEL 367 (437)
Q Consensus 331 ~~~~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~~ 367 (437)
.|.+||..|... +. .....||.||+++
T Consensus 137 ~w~~rC~GC~~~--f~--------~~~~~Cp~CG~~~ 163 (177)
T COG1439 137 KWRLRCHGCKRI--FP--------EPKDFCPICGSPL 163 (177)
T ss_pred eeeEEEecCcee--cC--------CCCCcCCCCCCce
Confidence 456789988763 21 2356899999984
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=49.87 E-value=30 Score=39.25 Aligned_cols=62 Identities=15% Similarity=0.153 Sum_probs=37.8
Q ss_pred HHHHHHHHhC-CccEEEeecCCCceeEEEEcCCCCcEEEEeeccchhcccCcccCCCccccchhc----ccccHHHHHHH
Q 013759 307 DDTLKALDMG-AVDTLIVWENLDITRYVLKNTVTGEIVIKHLNREQETNQNNFRDSATSAELEVQ----EKSSLLEWFAN 381 (437)
Q Consensus 307 ~~V~~Al~~G-aV~tLlV~d~l~~~~~~~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~~~~~----~~~dvve~Lve 381 (437)
..+.+|.+.| .++. =| .. .+|++||.. .-...||.||+..... ...|+-+.+-.
T Consensus 607 R~i~~A~~~g~~i~v-ev--~~------RKCPkCG~y------------Tlk~rCP~CG~~Te~~~pc~~~i~l~~~~~~ 665 (1095)
T TIGR00354 607 RDIKNAINYTKEIEV-EI--AI------RKCPQCGKE------------SFWLKCPVCGELTEQLYYGKRKVDLRELYEE 665 (1095)
T ss_pred hhHHHHhccCCeeEE-EE--EE------EECCCCCcc------------cccccCCCCCCccccccceeEEecHHHHHHH
Confidence 4588899888 4322 11 11 689999974 2357899999874221 14566665555
Q ss_pred HHHhcCCE
Q 013759 382 EYRRFGCT 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
>PRK12496 hypothetical protein; Provisional
Probab=49.35 E-value=12 Score=33.58 Aligned_cols=29 Identities=3% Similarity=-0.137 Sum_probs=18.2
Q ss_pred eEEEEcCCCCcEEEEeeccchhcccCcccCCCccccc
Q 013759 331 RYVLKNTVTGEIVIKHLNREQETNQNNFRDSATSAEL 367 (437)
Q Consensus 331 ~~~~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~~ 367 (437)
.|.++|+.|+.. | +. +.....||.||.++
T Consensus 125 ~w~~~C~gC~~~---~--~~---~~~~~~C~~CG~~~ 153 (164)
T PRK12496 125 KWRKVCKGCKKK---Y--PE---DYPDDVCEICGSPV 153 (164)
T ss_pred eeeEECCCCCcc---c--cC---CCCCCcCCCCCChh
Confidence 355789999863 1 00 02235699999874
No 48
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=48.10 E-value=18 Score=42.28 Aligned_cols=62 Identities=10% Similarity=0.078 Sum_probs=39.6
Q ss_pred HHHHHHHHhCCccEEEeecCCCceeEEEEcCCCCcEEEEeeccchhcccCcccCCCccccchhc----ccccHHHHHHHH
Q 013759 307 DDTLKALDMGAVDTLIVWENLDITRYVLKNTVTGEIVIKHLNREQETNQNNFRDSATSAELEVQ----EKSSLLEWFANE 382 (437)
Q Consensus 307 ~~V~~Al~~GaV~tLlV~d~l~~~~~~~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~~~~~----~~~dvve~Lve~ 382 (437)
..+.+|++.|.++.+=|.. ++|++||.. .-...||.||...+.. ...++-+.+-..
T Consensus 656 R~i~~A~~~g~~~~vei~~--------~~Cp~Cg~~------------~~~~~Cp~CG~~~~~~~~~~~~i~~~~~~~~A 715 (1627)
T PRK14715 656 RLINKAVEENKTDDIEIAF--------FKCPKCGKV------------GLYHVCPFCGTRVELKPYARREIPPKDYWYAA 715 (1627)
T ss_pred hhHHHHhhcCCcceEEEEe--------eeCCCCCCc------------cccccCcccCCcccCCCccceecCHHHHHHHH
Confidence 4688999999987555532 689999974 2356899999752221 144555555444
Q ss_pred HHhcCC
Q 013759 383 YRRFGC 388 (437)
Q Consensus 383 a~~~ga 388 (437)
.+.-|-
T Consensus 716 ~~~v~~ 721 (1627)
T PRK14715 716 LENLKI 721 (1627)
T ss_pred HHHhCC
Confidence 444444
No 49
>COG1852 Uncharacterized conserved protein [Function unknown]
Probab=48.00 E-value=21 Score=32.81 Aligned_cols=36 Identities=8% Similarity=0.104 Sum_probs=30.1
Q ss_pred cCcccCCCccccchhcccccHHHHHHHHHHhcCCEEEEecCCCc
Q 013759 355 QNNFRDSATSAELEVQEKSSLLEWFANEYRRFGCTLEFVTNKSQ 398 (437)
Q Consensus 355 r~~~~cp~~g~~~~~~~~~dvve~Lve~a~~~ga~V~ivs~~~e 398 (437)
+.-+.|-.||.- ++-++++.|++.|-+|.|+|+.+-
T Consensus 109 ~~G~~Ck~CgkC--------vi~ei~e~ae~~gykvfIvpGgs~ 144 (209)
T COG1852 109 PTGYECKKCGKC--------VIGEIKEIAEKYGYKVFIVPGGSF 144 (209)
T ss_pred cccceecccCCe--------ehHHHHHHHHHhCcEEEEecChHH
Confidence 557889999976 345799999999999999998773
No 50
>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=46.82 E-value=71 Score=28.12 Aligned_cols=38 Identities=8% Similarity=-0.204 Sum_probs=24.3
Q ss_pred EeecCCCceeEEEEcCCCCcEEEEeeccchhcccCcccCCCcccc
Q 013759 322 IVWENLDITRYVLKNTVTGEIVIKHLNREQETNQNNFRDSATSAE 366 (437)
Q Consensus 322 lV~d~l~~~~~~~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~ 366 (437)
.-+-+...+|. ++|.+||....+. .| ..-..||.||+.
T Consensus 102 Y~sGE~~g~G~-l~C~~Cg~~~~~~-~~-----~~l~~Cp~C~~~ 139 (146)
T PF07295_consen 102 YHSGEVVGPGT-LVCENCGHEVELT-HP-----ERLPPCPKCGHT 139 (146)
T ss_pred eecCcEecCce-EecccCCCEEEec-CC-----CcCCCCCCCCCC
Confidence 33445555565 7999999864432 22 224689999975
No 51
>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=46.52 E-value=22 Score=22.97 Aligned_cols=26 Identities=19% Similarity=0.050 Sum_probs=17.5
Q ss_pred EEEcCCCCcEEEEeeccchhcccCcccCCCcccc
Q 013759 333 VLKNTVTGEIVIKHLNREQETNQNNFRDSATSAE 366 (437)
Q Consensus 333 ~~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~ 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 389999997421 10 224689999975
No 52
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=45.95 E-value=17 Score=30.41 Aligned_cols=25 Identities=12% Similarity=0.024 Sum_probs=16.9
Q ss_pred EEcCCCCcEEEEeeccchhcccCcccCCCcccc
Q 013759 334 LKNTVTGEIVIKHLNREQETNQNNFRDSATSAE 366 (437)
Q Consensus 334 ~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~ 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 79999996311 1 1345679999975
No 53
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=44.51 E-value=18 Score=32.87 Aligned_cols=31 Identities=19% Similarity=0.221 Sum_probs=23.7
Q ss_pred cCcccCCCccccchhcccccHHHHHHHHHHh
Q 013759 355 QNNFRDSATSAELEVQEKSSLLEWFANEYRR 385 (437)
Q Consensus 355 r~~~~cp~~g~~~~~~~~~dvve~Lve~a~~ 385 (437)
...+.||.||+.++..+....+.+|-+...+
T Consensus 130 ~~~F~Cp~Cg~~L~~~d~s~~i~~l~~~i~~ 160 (176)
T COG1675 130 ELGFTCPKCGEDLEEYDSSEEIEELESELDE 160 (176)
T ss_pred HhCCCCCCCCchhhhccchHHHHHHHHHHHH
Confidence 4468999999998888877777777665543
No 54
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=44.08 E-value=23 Score=24.42 Aligned_cols=27 Identities=7% Similarity=0.010 Sum_probs=18.3
Q ss_pred EEEcCCCCcEEEEeeccchhcccCcccCCCcccc
Q 013759 333 VLKNTVTGEIVIKHLNREQETNQNNFRDSATSAE 366 (437)
Q Consensus 333 ~~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~ 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 378999997422 22 1446789999987
No 55
>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=40.15 E-value=24 Score=29.61 Aligned_cols=35 Identities=11% Similarity=-0.042 Sum_probs=21.4
Q ss_pred EEEeecCCCceeEEEEcCCCCcEEEEeeccchhcccCcccCCCcccc
Q 013759 320 TLIVWENLDITRYVLKNTVTGEIVIKHLNREQETNQNNFRDSATSAE 366 (437)
Q Consensus 320 tLlV~d~l~~~~~~~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~ 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 55554433 2379999996411 1 1235789999976
No 56
>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=39.73 E-value=25 Score=22.49 Aligned_cols=25 Identities=16% Similarity=0.130 Sum_probs=17.2
Q ss_pred EEcCCCCcEEEEeeccchhcccCcccCCCcccc
Q 013759 334 LKNTVTGEIVIKHLNREQETNQNNFRDSATSAE 366 (437)
Q Consensus 334 ~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~ 366 (437)
|+|..||... .+ ....+.||.||..
T Consensus 2 ~~C~~CGy~y----~~----~~~~~~CP~Cg~~ 26 (33)
T cd00350 2 YVCPVCGYIY----DG----EEAPWVCPVCGAP 26 (33)
T ss_pred EECCCCCCEE----CC----CcCCCcCcCCCCc
Confidence 6899899741 11 1346899999975
No 57
>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=39.72 E-value=13 Score=30.94 Aligned_cols=30 Identities=13% Similarity=0.015 Sum_probs=19.6
Q ss_pred eEEEEcCCCCcEEEEe-eccchhcccCcccCCCccccch
Q 013759 331 RYVLKNTVTGEIVIKH-LNREQETNQNNFRDSATSAELE 368 (437)
Q Consensus 331 ~~~~r~~~~~~~~~~~-~~~~~~~~r~~~~cp~~g~~~~ 368 (437)
|....|++||.. |+ |. +....||+||....
T Consensus 7 GtKR~Cp~CG~k--FYDLn------k~PivCP~CG~~~~ 37 (108)
T PF09538_consen 7 GTKRTCPSCGAK--FYDLN------KDPIVCPKCGTEFP 37 (108)
T ss_pred CCcccCCCCcch--hccCC------CCCccCCCCCCccC
Confidence 344579999863 22 32 55578999998743
No 58
>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=35.98 E-value=21 Score=29.88 Aligned_cols=25 Identities=8% Similarity=0.108 Sum_probs=15.7
Q ss_pred EEcCCCCcEEEEeeccchhcccCcccCCCcccc
Q 013759 334 LKNTVTGEIVIKHLNREQETNQNNFRDSATSAE 366 (437)
Q Consensus 334 ~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~ 366 (437)
++|.+|+... .+. ...+.||.||+.
T Consensus 71 ~~C~~Cg~~~----~~~----~~~~~CP~Cgs~ 95 (113)
T PF01155_consen 71 ARCRDCGHEF----EPD----EFDFSCPRCGSP 95 (113)
T ss_dssp EEETTTS-EE----ECH----HCCHH-SSSSSS
T ss_pred EECCCCCCEE----ecC----CCCCCCcCCcCC
Confidence 7999999741 111 334789999986
No 59
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=35.70 E-value=22 Score=36.66 Aligned_cols=25 Identities=12% Similarity=-0.175 Sum_probs=17.4
Q ss_pred EEEcCCCCcEEEEeeccchhcccCcccCCCccccc
Q 013759 333 VLKNTVTGEIVIKHLNREQETNQNNFRDSATSAEL 367 (437)
Q Consensus 333 ~~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~~ 367 (437)
.|.|++||.... +=.-.||.||..-
T Consensus 7 ~f~C~~CG~~s~----------KW~GkCp~Cg~Wn 31 (456)
T COG1066 7 AFVCQECGYVSP----------KWLGKCPACGAWN 31 (456)
T ss_pred EEEcccCCCCCc----------cccccCCCCCCcc
Confidence 489999998421 1133799999863
No 60
>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=35.08 E-value=21 Score=24.25 Aligned_cols=28 Identities=11% Similarity=0.087 Sum_probs=16.0
Q ss_pred EEcCCCCcEEEEeeccchhcccCcccCCCcccc
Q 013759 334 LKNTVTGEIVIKHLNREQETNQNNFRDSATSAE 366 (437)
Q Consensus 334 ~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~ 366 (437)
++|+.|+...+ ...+ .+..+.|+.||.-
T Consensus 1 m~Cp~Cg~~~~-~~D~----~~g~~vC~~CG~V 28 (43)
T PF08271_consen 1 MKCPNCGSKEI-VFDP----ERGELVCPNCGLV 28 (43)
T ss_dssp ESBTTTSSSEE-EEET----TTTEEEETTT-BB
T ss_pred CCCcCCcCCce-EEcC----CCCeEECCCCCCE
Confidence 36777776431 1221 2567789999864
No 61
>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=33.60 E-value=20 Score=37.63 Aligned_cols=25 Identities=12% Similarity=-0.215 Sum_probs=18.3
Q ss_pred EEEcCCCCcEEEEeeccchhcccCcccCCCccccc
Q 013759 333 VLKNTVTGEIVIKHLNREQETNQNNFRDSATSAEL 367 (437)
Q Consensus 333 ~~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~~ 367 (437)
.|+|.+||.... +-.+.||.||.+-
T Consensus 7 ~y~C~~Cg~~~~----------~~~g~Cp~C~~w~ 31 (454)
T TIGR00416 7 KFVCQHCGADSP----------KWQGKCPACHAWN 31 (454)
T ss_pred eEECCcCCCCCc----------cccEECcCCCCcc
Confidence 489999998421 3356899999873
No 62
>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=33.46 E-value=36 Score=22.17 Aligned_cols=32 Identities=9% Similarity=-0.053 Sum_probs=19.0
Q ss_pred EEcCCCCcEEEEeeccchhc-ccCcccCCCccccc
Q 013759 334 LKNTVTGEIVIKHLNREQET-NQNNFRDSATSAEL 367 (437)
Q Consensus 334 ~r~~~~~~~~~~~~~~~~~~-~r~~~~cp~~g~~~ 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 578888863 333433321 13357899999764
No 63
>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=33.23 E-value=28 Score=24.86 Aligned_cols=24 Identities=13% Similarity=0.228 Sum_probs=12.6
Q ss_pred cCCCccccchhcccccHHHHHHHH
Q 013759 359 RDSATSAELEVQEKSSLLEWFANE 382 (437)
Q Consensus 359 ~cp~~g~~~~~~~~~dvve~Lve~ 382 (437)
.||.||.++..-....++..+-..
T Consensus 22 ~CPlC~r~l~~e~~~~li~~~~~~ 45 (54)
T PF04423_consen 22 CCPLCGRPLDEEHRQELIKKYKSE 45 (54)
T ss_dssp E-TTT--EE-HHHHHHHHHHHHHH
T ss_pred cCCCCCCCCCHHHHHHHHHHHHHH
Confidence 899999998765555555554433
No 64
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=32.88 E-value=77 Score=25.97 Aligned_cols=61 Identities=11% Similarity=0.123 Sum_probs=39.6
Q ss_pred EEcCCCCcEEEE-eeccchhcccCcccCCCcccc-----chhcccccHHHHHHHHHHhcCCEEEEecCCCc
Q 013759 334 LKNTVTGEIVIK-HLNREQETNQNNFRDSATSAE-----LEVQEKSSLLEWFANEYRRFGCTLEFVTNKSQ 398 (437)
Q Consensus 334 ~r~~~~~~~~~~-~~~~~~~~~r~~~~cp~~g~~-----~~~~~~~dvve~Lve~a~~~ga~V~ivs~~~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 FECPRCGKVSISVKIKK----NIAIITCGNCGLYTEFEVPSVYDEVDVYNKFIDLYLEGKIEIKERKNEET 88 (99)
T ss_pred eECCCCCCeEeeeecCC----CcceEECCCCCCccCEECCccccchhhHHHHHHHHHhcCCCccccCcccc
Confidence 799999953220 0000 1235689999953 23345778999999999988777777665443
No 65
>PRK11181 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional
Probab=32.46 E-value=1.5e+02 Score=28.27 Aligned_cols=70 Identities=13% Similarity=0.149 Sum_probs=46.4
Q ss_pred cEEECHHHHHHHHHh-C-CccEEEeecCCCceeEEEEcCCCCcEEEEeeccchhcccCcccCCCccccchhcccccHHHH
Q 013759 301 KYVFGADDTLKALDM-G-AVDTLIVWENLDITRYVLKNTVTGEIVIKHLNREQETNQNNFRDSATSAELEVQEKSSLLEW 378 (437)
Q Consensus 301 ~a~yG~~~V~~Al~~-G-aV~tLlV~d~l~~~~~~~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~~~~~~~~dvve~ 378 (437)
...||...|.+|++. + .+.+|++..+.. .. ...+
T Consensus 3 ~~i~G~~~v~eal~~~~~~~~~l~~~~~~~-----------~~---------------------------------~~~~ 38 (244)
T PRK11181 3 EIIYGIHAVQALLERAPERFIEVFVLKGRE-----------DK---------------------------------RLLP 38 (244)
T ss_pred cEEEehHHHHHHHhCCCCceeEEEEECCCc-----------ch---------------------------------HHHH
Confidence 467999999999986 3 678888865431 00 0134
Q ss_pred HHHHHHhcCCEEEEecCCCchhhhh--ccccccEEEEeee
Q 013759 379 FANEYRRFGCTLEFVTNKSQEGSQF--CRGFGGIGGILRY 416 (437)
Q Consensus 379 Lve~a~~~ga~V~ivs~~~e~G~q~--L~~~gGIaAiLRy 416 (437)
++..+...|..+.+++...- .++ -....||+|+.+-
T Consensus 39 ~~~~~~~~~i~~~~v~~~~l--~~ls~~~~~qGv~a~~~~ 76 (244)
T PRK11181 39 LINELEAQGIVIQLANRQTL--DEKAEGAVHQGIIARVKP 76 (244)
T ss_pred HHHHHHHcCCcEEEeCHHHH--hhhhcCCCCceEEEEEec
Confidence 66777778889988875321 121 1347899999873
No 66
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=32.38 E-value=36 Score=28.52 Aligned_cols=26 Identities=15% Similarity=-0.014 Sum_probs=16.5
Q ss_pred EEcCCCCcEEEEeeccchhcccCcccCCCcccc
Q 013759 334 LKNTVTGEIVIKHLNREQETNQNNFRDSATSAE 366 (437)
Q Consensus 334 ~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~ 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 79999996311 00 1223679999975
No 67
>PRK11032 hypothetical protein; Provisional
Probab=31.86 E-value=68 Score=28.68 Aligned_cols=40 Identities=3% Similarity=-0.291 Sum_probs=25.3
Q ss_pred EEEeecCCCceeEEEEcCCCCcEEEEeeccchhcccCcccCCCcccc
Q 013759 320 TLIVWENLDITRYVLKNTVTGEIVIKHLNREQETNQNNFRDSATSAE 366 (437)
Q Consensus 320 tLlV~d~l~~~~~~~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~ 366 (437)
-+..+-+...+|. ++|.+||....+. .| ..-..||.||+.
T Consensus 112 g~Y~sGEvvg~G~-LvC~~Cg~~~~~~-~p-----~~i~pCp~C~~~ 151 (160)
T PRK11032 112 GVYHSGEVVGLGN-LVCEKCHHHLAFY-TP-----EVLPLCPKCGHD 151 (160)
T ss_pred Ceeecceeeecce-EEecCCCCEEEec-CC-----CcCCCCCCCCCC
Confidence 3444555556665 7999999754332 22 223579999975
No 68
>PRK11823 DNA repair protein RadA; Provisional
Probab=31.66 E-value=24 Score=36.94 Aligned_cols=26 Identities=12% Similarity=-0.240 Sum_probs=18.4
Q ss_pred EEEcCCCCcEEEEeeccchhcccCcccCCCccccch
Q 013759 333 VLKNTVTGEIVIKHLNREQETNQNNFRDSATSAELE 368 (437)
Q Consensus 333 ~~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~~~ 368 (437)
.|+|++||.... +-.+.||.||..--
T Consensus 7 ~y~C~~Cg~~~~----------~~~g~Cp~C~~w~t 32 (446)
T PRK11823 7 AYVCQECGAESP----------KWLGRCPECGAWNT 32 (446)
T ss_pred eEECCcCCCCCc----------ccCeeCcCCCCccc
Confidence 489999998421 23568999998633
No 69
>COG0566 SpoU rRNA methylases [Translation, ribosomal structure and biogenesis]
Probab=31.59 E-value=2.3e+02 Score=27.28 Aligned_cols=74 Identities=16% Similarity=0.124 Sum_probs=52.6
Q ss_pred CcEEECHHHHHHHHHhC-CccEEEeecCCCceeEEEEcCCCCcEEEEeeccchhcccCcccCCCccccchhcccccHHHH
Q 013759 300 GKYVFGADDTLKALDMG-AVDTLIVWENLDITRYVLKNTVTGEIVIKHLNREQETNQNNFRDSATSAELEVQEKSSLLEW 378 (437)
Q Consensus 300 ~~a~yG~~~V~~Al~~G-aV~tLlV~d~l~~~~~~~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~~~~~~~~dvve~ 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 46889999999999999 899999887651 1 0 234
Q ss_pred HHHHHHhcCCEEEEecCCCchhhhhccccccEEEEeeeec
Q 013759 379 FANEYRRFGCTLEFVTNKSQEGSQFCRGFGGIGGILRYQL 418 (437)
Q Consensus 379 Lve~a~~~ga~V~ivs~~~e~G~q~L~~~gGIaAiLRy~~ 418 (437)
+...+...|..+..++...-.-----..+.||+|...-+-
T Consensus 56 ~~~~~~~~~~~~~~v~~~~l~~~~~~~~hqGi~a~~~~~~ 95 (260)
T COG0566 56 LLALAAAKGIPVYVVSEAILDKLSGTENHQGIVAVVKKRR 95 (260)
T ss_pred HHHHHHhcCCeEEEECHHHHHHHhCCCCCCeEEEEEeccc
Confidence 7888888999999998753211000135788999886443
No 70
>PRK14864 putative biofilm stress and motility protein A; Provisional
Probab=31.56 E-value=60 Score=26.87 Aligned_cols=42 Identities=5% Similarity=-0.074 Sum_probs=31.8
Q ss_pred cccHHHHHHHHHHhcCCEEEEecCCCchhhhhccccccEEEEee
Q 013759 372 KSSLLEWFANEYRRFGCTLEFVTNKSQEGSQFCRGFGGIGGILR 415 (437)
Q Consensus 372 ~~dvve~Lve~a~~~ga~V~ivs~~~e~G~q~L~~~gGIaAiLR 415 (437)
..|+..+|-++|.+.||+-+.|-..++.+.. ..+-|-|-|+|
T Consensus 62 p~d~~~~La~KAda~GA~yYrIi~~~e~~~~--~~~~atA~iYk 103 (104)
T PRK14864 62 PDDAEREIQAKANAAGADYYVIVMVDETVVP--GQWYSQAILYR 103 (104)
T ss_pred HHHHHHHHHHHHHHcCCCEEEEEEccccCCC--CeEEEEEEEec
Confidence 5678889999999999998877665654333 45677888876
No 71
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=30.16 E-value=23 Score=26.06 Aligned_cols=32 Identities=13% Similarity=0.181 Sum_probs=17.4
Q ss_pred EEEEcCCCCcEEEEeeccchhcccCcccCCCcc
Q 013759 332 YVLKNTVTGEIVIKHLNREQETNQNNFRDSATS 364 (437)
Q Consensus 332 ~~~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g 364 (437)
+.|.|++||+..+.--.. .-.....|.||.||
T Consensus 24 ~~F~CPnCG~~~I~RC~~-CRk~~~~Y~CP~CG 55 (59)
T PRK14890 24 VKFLCPNCGEVIIYRCEK-CRKQSNPYTCPKCG 55 (59)
T ss_pred CEeeCCCCCCeeEeechh-HHhcCCceECCCCC
Confidence 458899998742211000 00012368999998
No 72
>PHA00626 hypothetical protein
Probab=29.75 E-value=46 Score=24.20 Aligned_cols=29 Identities=10% Similarity=-0.023 Sum_probs=19.8
Q ss_pred cCcccCCCccccchhcccccHHHHHHHHHHhcCCEEEEecC
Q 013759 355 QNNFRDSATSAELEVQEKSSLLEWFANEYRRFGCTLEFVTN 395 (437)
Q Consensus 355 r~~~~cp~~g~~~~~~~~~dvve~Lve~a~~~ga~V~ivs~ 395 (437)
+..|.||.||=. ....|....++-+||.-
T Consensus 21 snrYkCkdCGY~------------ft~~~~~~~~~~~~~~~ 49 (59)
T PHA00626 21 SDDYVCCDCGYN------------DSKDAFGERGKNEFVRI 49 (59)
T ss_pred CcceEcCCCCCe------------echhhhhhccccceEEe
Confidence 567999999976 34555655666666653
No 73
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=29.29 E-value=17 Score=21.87 Aligned_cols=23 Identities=9% Similarity=0.001 Sum_probs=13.8
Q ss_pred EEcCCCCcEEEEeeccchhcccCcccCCCcccc
Q 013759 334 LKNTVTGEIVIKHLNREQETNQNNFRDSATSAE 366 (437)
Q Consensus 334 ~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~ 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 3577787621 1234468888865
No 74
>PRK14873 primosome assembly protein PriA; Provisional
Probab=28.99 E-value=62 Score=35.80 Aligned_cols=15 Identities=20% Similarity=0.333 Sum_probs=10.7
Q ss_pred eEEEecChhhHHHhc
Q 013759 224 GLVLAGSADFKTELS 238 (437)
Q Consensus 224 ~liiaGp~~~k~~f~ 238 (437)
.||++|.....+.++
T Consensus 295 ~lvLgSaTPSles~~ 309 (665)
T PRK14873 295 ALLIGGHARTAEAQA 309 (665)
T ss_pred cEEEECCCCCHHHHH
Confidence 577788777777664
No 75
>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=28.76 E-value=25 Score=29.33 Aligned_cols=29 Identities=10% Similarity=-0.055 Sum_probs=19.0
Q ss_pred EEEcCCCCcEEEEeeccchhcccCcccCCCccccchh
Q 013759 333 VLKNTVTGEIVIKHLNREQETNQNNFRDSATSAELEV 369 (437)
Q Consensus 333 ~~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~~~~ 369 (437)
..+||+|+..+- -+ .+...|+.|+.++..
T Consensus 69 ~V~CP~C~K~TK-mL-------Gr~D~CM~C~~pLTL 97 (114)
T PF11023_consen 69 QVECPNCGKQTK-ML-------GRVDACMHCKEPLTL 97 (114)
T ss_pred eeECCCCCChHh-hh-------chhhccCcCCCcCcc
Confidence 368999996311 11 234689999998643
No 76
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=28.14 E-value=34 Score=28.84 Aligned_cols=25 Identities=8% Similarity=0.141 Sum_probs=15.8
Q ss_pred EEcCCCCcEEEEeeccchhcccCcc-cCCCcccc
Q 013759 334 LKNTVTGEIVIKHLNREQETNQNNF-RDSATSAE 366 (437)
Q Consensus 334 ~r~~~~~~~~~~~~~~~~~~~r~~~-~cp~~g~~ 366 (437)
++|.+|+... +. ....+ .||.||+.
T Consensus 72 ~~C~~Cg~~~-----~~---~~~~~~~CP~Cgs~ 97 (117)
T PRK00564 72 LECKDCSHVF-----KP---NALDYGVCEKCHSK 97 (117)
T ss_pred EEhhhCCCcc-----cc---CCccCCcCcCCCCC
Confidence 7999999631 10 02234 49999975
No 77
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=28.00 E-value=48 Score=28.90 Aligned_cols=36 Identities=19% Similarity=0.349 Sum_probs=22.3
Q ss_pred eeEEEEcCCCCcEEEEeeccchhcccCcccCCCccccchh
Q 013759 330 TRYVLKNTVTGEIVIKHLNREQETNQNNFRDSATSAELEV 369 (437)
Q Consensus 330 ~~~~~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~~~~ 369 (437)
..+.|+|+.|+.....+. . .....+.|+.||+.+..
T Consensus 120 ~~~~~~C~~C~~~~~r~~-~---~~~~~~~C~~C~~~l~~ 155 (157)
T PF10263_consen 120 KKYVYRCPSCGREYKRHR-R---SKRKRYRCGRCGGPLVQ 155 (157)
T ss_pred cceEEEcCCCCCEeeeec-c---cchhhEECCCCCCEEEE
Confidence 356789988986422110 0 01346789999988653
No 78
>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=27.83 E-value=32 Score=29.40 Aligned_cols=29 Identities=17% Similarity=-0.014 Sum_probs=19.1
Q ss_pred eEEEEcCCCCcEEEEe-eccchhcccCcccCCCccccc
Q 013759 331 RYVLKNTVTGEIVIKH-LNREQETNQNNFRDSATSAEL 367 (437)
Q Consensus 331 ~~~~r~~~~~~~~~~~-~~~~~~~~r~~~~cp~~g~~~ 367 (437)
|....|++||.. |+ | ++....||+||...
T Consensus 7 GtKr~Cp~cg~k--FYDL------nk~p~vcP~cg~~~ 36 (129)
T TIGR02300 7 GTKRICPNTGSK--FYDL------NRRPAVSPYTGEQF 36 (129)
T ss_pred CccccCCCcCcc--cccc------CCCCccCCCcCCcc
Confidence 334569999863 22 2 25567899999863
No 79
>PF13727 CoA_binding_3: CoA-binding domain; PDB: 3NKL_B.
Probab=27.75 E-value=1e+02 Score=26.67 Aligned_cols=51 Identities=14% Similarity=0.175 Sum_probs=33.0
Q ss_pred cEEECHHHHHHHHHhCCccEEEeecCCCceeEEEEcCCCCcEEEEeeccchhcccCcccCCCccccchhcccccHHHHHH
Q 013759 301 KYVFGADDTLKALDMGAVDTLIVWENLDITRYVLKNTVTGEIVIKHLNREQETNQNNFRDSATSAELEVQEKSSLLEWFA 380 (437)
Q Consensus 301 ~a~yG~~~V~~Al~~GaV~tLlV~d~l~~~~~~~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~~~~~~~~dvve~Lv 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 4445579999999999999999975541 011245699
Q ss_pred HHHHhcCCEEEEec
Q 013759 381 NEYRRFGCTLEFVT 394 (437)
Q Consensus 381 e~a~~~ga~V~ivs 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 80
>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=27.58 E-value=55 Score=35.36 Aligned_cols=22 Identities=18% Similarity=0.155 Sum_probs=15.7
Q ss_pred EcCCCCcEEEEeeccchhcccCcccCCCcccc
Q 013759 335 KNTVTGEIVIKHLNREQETNQNNFRDSATSAE 366 (437)
Q Consensus 335 r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~ 366 (437)
+|.+||... ....+.||.||..
T Consensus 520 ~C~~CG~~~----------~~~~~~CP~CGs~ 541 (555)
T cd01675 520 ICNDCGYIG----------EGEGFKCPKCGSE 541 (555)
T ss_pred cCCCCCCCC----------cCCCCCCcCCCCc
Confidence 798898731 1346899999965
No 81
>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=27.48 E-value=54 Score=35.59 Aligned_cols=22 Identities=9% Similarity=-0.201 Sum_probs=14.7
Q ss_pred EcCCCCcEEEEeeccchhcccCcccCCCcccc
Q 013759 335 KNTVTGEIVIKHLNREQETNQNNFRDSATSAE 366 (437)
Q Consensus 335 r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~ 366 (437)
+|.+||..+. ...+.||.||..
T Consensus 526 ~C~~CG~~g~----------~~~~~CP~Cgs~ 547 (579)
T TIGR02487 526 VCEDCGYTGE----------GLNDKCPKCGSH 547 (579)
T ss_pred cCCCCCCCCC----------CCCCcCcCCCCc
Confidence 6888886311 223689999964
No 82
>PRK10864 putative methyltransferase; Provisional
Probab=27.14 E-value=1.9e+02 Score=29.22 Aligned_cols=71 Identities=8% Similarity=0.081 Sum_probs=47.1
Q ss_pred CcEEECHHHHHHHHHh--CCccEEEeecCCCceeEEEEcCCCCcEEEEeeccchhcccCcccCCCccccchhcccccHHH
Q 013759 300 GKYVFGADDTLKALDM--GAVDTLIVWENLDITRYVLKNTVTGEIVIKHLNREQETNQNNFRDSATSAELEVQEKSSLLE 377 (437)
Q Consensus 300 ~~a~yG~~~V~~Al~~--GaV~tLlV~d~l~~~~~~~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~~~~~~~~dvve 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 4678999999999986 4588888865431 0 0 12
Q ss_pred HHHHHHHhcCCEEEEecCCCchhhhh--ccccccEEEEeeee
Q 013759 378 WFANEYRRFGCTLEFVTNKSQEGSQF--CRGFGGIGGILRYQ 417 (437)
Q Consensus 378 ~Lve~a~~~ga~V~ivs~~~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 356666667888888875321 121 24578999999754
No 83
>COG1150 HdrC Heterodisulfide reductase, subunit C [Energy production and conversion]
Probab=27.08 E-value=49 Score=30.50 Aligned_cols=63 Identities=13% Similarity=0.075 Sum_probs=44.6
Q ss_pred EEECHHHHHHHHHhCCccEEEeecCCCceeEEEEcCCCCcEEEEeeccchhcccCcccCCCccccchhcccccHHHHHHH
Q 013759 302 YVFGADDTLKALDMGAVDTLIVWENLDITRYVLKNTVTGEIVIKHLNREQETNQNNFRDSATSAELEVQEKSSLLEWFAN 381 (437)
Q Consensus 302 a~yG~~~V~~Al~~GaV~tLlV~d~l~~~~~~~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~~~~~~~~dvve~Lve 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 TDYSPRKIIRKARLGLVDLILSSESL------WACVTCYT--------------CTERCPRGV------KIVEVVKALRN 110 (195)
T ss_pred CCCCHHHHHHHHHcccHHHHhcCCcc------eeeeechh--------------hhhhCCCCC------CHHHHHHHHHH
Confidence 45999999999999999955556666 99987752 134677644 34556666667
Q ss_pred HHHhcCCEE
Q 013759 382 EYRRFGCTL 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 777766644
No 84
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=26.91 E-value=46 Score=24.42 Aligned_cols=22 Identities=9% Similarity=0.040 Sum_probs=14.9
Q ss_pred EcCCCCcEEEEeeccchhcccCcccCCCccccch
Q 013759 335 KNTVTGEIVIKHLNREQETNQNNFRDSATSAELE 368 (437)
Q Consensus 335 r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~~~ 368 (437)
+|++|+.=+ -+..||.||+...
T Consensus 7 kC~~cg~YT------------Lke~Cp~CG~~t~ 28 (59)
T COG2260 7 KCPKCGRYT------------LKEKCPVCGGDTK 28 (59)
T ss_pred cCcCCCcee------------ecccCCCCCCccc
Confidence 688887521 1357999998744
No 85
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=26.68 E-value=33 Score=34.30 Aligned_cols=23 Identities=9% Similarity=-0.088 Sum_probs=17.4
Q ss_pred EEcCCCCcEEEEeeccchhcccCcccCCCcccc
Q 013759 334 LKNTVTGEIVIKHLNREQETNQNNFRDSATSAE 366 (437)
Q Consensus 334 ~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~ 366 (437)
+||.+||...+ .--|.||.|...
T Consensus 355 YRC~~CGF~a~----------~l~W~CPsC~~W 377 (389)
T COG2956 355 YRCQNCGFTAH----------TLYWHCPSCRAW 377 (389)
T ss_pred ceecccCCcce----------eeeeeCCCcccc
Confidence 69999998532 225799999875
No 86
>CHL00181 cbbX CbbX; Provisional
Probab=26.06 E-value=3.6e+02 Score=26.30 Aligned_cols=86 Identities=17% Similarity=0.206 Sum_probs=43.0
Q ss_pred eEEEecChhhHHHhcccccCChhhhcceeEEEECCCCCCccHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHccCCCcEE
Q 013759 224 GLVLAGSADFKTELSQSDMFDPRLQAKILKVVDVSYGGENGFNQAIELSAESLSNVKFIQEKRLIGKYFEEISQDTGKYV 303 (437)
Q Consensus 224 ~liiaGp~~~k~~f~~~~~l~~~l~~~vi~~v~~s~~~~~gl~Evl~~~~~~l~~~~~~~e~~ll~~f~~~~~~~~~~a~ 303 (437)
.||++|.....+.|. .++|.+++++-..+..+.-. ..|+.+-+...+++....-..+..+.+...+.+....-.
T Consensus 163 ~vI~ag~~~~~~~~~---~~np~L~sR~~~~i~F~~~t---~~el~~I~~~~l~~~~~~l~~~~~~~L~~~i~~~~~~~~ 236 (287)
T CHL00181 163 VVIFAGYKDRMDKFY---ESNPGLSSRIANHVDFPDYT---PEELLQIAKIMLEEQQYQLTPEAEKALLDYIKKRMEQPL 236 (287)
T ss_pred EEEEeCCcHHHHHHH---hcCHHHHHhCCceEEcCCcC---HHHHHHHHHHHHHHhcCCCChhHHHHHHHHHHHhCCCCC
Confidence 566777665556666 35678888764345554433 334433333333332222222334444444443223345
Q ss_pred EC-HHHHHHHHHh
Q 013759 304 FG-ADDTLKALDM 315 (437)
Q Consensus 304 yG-~~~V~~Al~~ 315 (437)
+| -.+|.+.++.
T Consensus 237 ~GNaR~vrn~ve~ 249 (287)
T CHL00181 237 FANARSVRNALDR 249 (287)
T ss_pred CccHHHHHHHHHH
Confidence 77 5666666543
No 87
>PF13397 DUF4109: Domain of unknown function (DUF4109)
Probab=25.91 E-value=70 Score=26.49 Aligned_cols=34 Identities=12% Similarity=-0.010 Sum_probs=19.7
Q ss_pred eEEEEcCCCCcEEEEeeccchhcccCcccCCCcccc
Q 013759 331 RYVLKNTVTGEIVIKHLNREQETNQNNFRDSATSAE 366 (437)
Q Consensus 331 ~~~~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~ 366 (437)
.+.|.|++ |......++-+.+ ....|.||.||.+
T Consensus 26 ~v~Y~C~~-Gh~~~v~Fa~eAe-vP~~WeC~~cG~~ 59 (105)
T PF13397_consen 26 RVSYWCPN-GHETEVPFAAEAE-VPATWECPRCGLP 59 (105)
T ss_pred EEEEECCC-CCEEeccccccCC-CCCceeCCCCCCc
Confidence 45688984 5433322222211 2667999999976
No 88
>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=25.87 E-value=24 Score=36.05 Aligned_cols=23 Identities=4% Similarity=-0.225 Sum_probs=14.9
Q ss_pred EEcCCCCcEEEEeeccchhcccCcccCCCcccc
Q 013759 334 LKNTVTGEIVIKHLNREQETNQNNFRDSATSAE 366 (437)
Q Consensus 334 ~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~ 366 (437)
|+|++||.... +-...||.||..
T Consensus 1 ~~c~~cg~~~~----------~~~g~cp~c~~w 23 (372)
T cd01121 1 YVCSECGYVSP----------KWLGKCPECGEW 23 (372)
T ss_pred CCCCCCCCCCC----------CccEECcCCCCc
Confidence 46888887411 224578888876
No 89
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=25.87 E-value=74 Score=35.16 Aligned_cols=24 Identities=17% Similarity=0.027 Sum_probs=17.0
Q ss_pred EcCCCCcEEEEeeccchhcccCcccCCCccccchh
Q 013759 335 KNTVTGEIVIKHLNREQETNQNNFRDSATSAELEV 369 (437)
Q Consensus 335 r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~~~~ 369 (437)
+|+.||.. ....+.||.||.++++
T Consensus 628 ~C~~CG~~-----------~g~~~~CP~CG~~~~v 651 (656)
T PRK08270 628 ICPKHGYL-----------SGEHEFCPKCGEETEV 651 (656)
T ss_pred ccCCCCCc-----------CCCCCCCcCCcCccce
Confidence 68888863 1335899999977544
No 90
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=23.96 E-value=32 Score=20.55 Aligned_cols=10 Identities=10% Similarity=-0.081 Sum_probs=7.8
Q ss_pred CcccCCCccc
Q 013759 356 NNFRDSATSA 365 (437)
Q Consensus 356 ~~~~cp~~g~ 365 (437)
..|.||.||.
T Consensus 15 v~f~CPnCG~ 24 (24)
T PF07754_consen 15 VPFPCPNCGF 24 (24)
T ss_pred ceEeCCCCCC
Confidence 3689999983
No 91
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=23.92 E-value=42 Score=21.81 Aligned_cols=12 Identities=8% Similarity=0.061 Sum_probs=8.3
Q ss_pred ccCcccCCCccc
Q 013759 354 NQNNFRDSATSA 365 (437)
Q Consensus 354 ~r~~~~cp~~g~ 365 (437)
+|..+.||.||.
T Consensus 19 ~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 19 DRERLVCPACGF 30 (34)
T ss_dssp SS-EEEETTTTE
T ss_pred CccceECCCCCC
Confidence 377788888874
No 92
>PF05265 DUF723: Protein of unknown function (DUF723); InterPro: IPR007929 This family contains several uncharacterised proteins from Neisseria meningitidis. These proteins may have a role in DNA binding.
Probab=23.87 E-value=79 Score=23.39 Aligned_cols=41 Identities=5% Similarity=0.058 Sum_probs=22.5
Q ss_pred EEEeecCCCceeEEEEcCCCCcEEEEeeccchhcccCcccCCCcc
Q 013759 320 TLIVWENLDITRYVLKNTVTGEIVIKHLNREQETNQNNFRDSATS 364 (437)
Q Consensus 320 tLlV~d~l~~~~~~~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g 364 (437)
+|+--.+...+ ++++||-.|. ++.++-+...++++-||.||
T Consensus 20 slvef~g~~~P-vtI~CP~HG~---~~~s~~~~~~~sk~GCP~Cg 60 (60)
T PF05265_consen 20 SLVEFSGVATP-VTIRCPKHGN---FTCSTFNSFIKSKHGCPECG 60 (60)
T ss_pred eEEEEeCCCCc-eEEECCCCCc---EEeccHHhhhhhccCCCCCC
Confidence 44444444333 3478986554 33444433235667899996
No 93
>PRK05978 hypothetical protein; Provisional
Probab=23.40 E-value=43 Score=29.58 Aligned_cols=32 Identities=9% Similarity=-0.077 Sum_probs=20.1
Q ss_pred EEcCCCCcEEEEeeccchhcccCcccCCCccccchhc
Q 013759 334 LKNTVTGEIVIKHLNREQETNQNNFRDSATSAELEVQ 370 (437)
Q Consensus 334 ~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~~~~~ 370 (437)
.|||+||+-..+. .- -.-...||.||.+++..
T Consensus 34 grCP~CG~G~LF~-g~----Lkv~~~C~~CG~~~~~~ 65 (148)
T PRK05978 34 GRCPACGEGKLFR-AF----LKPVDHCAACGEDFTHH 65 (148)
T ss_pred CcCCCCCCCcccc-cc----cccCCCccccCCccccC
Confidence 5899999754321 00 02245899999886653
No 94
>TIGR00186 rRNA_methyl_3 rRNA methylase, putative, group 3. this is part of the trmH (spoU) family of rRNA methylases
Probab=23.36 E-value=2.5e+02 Score=26.56 Aligned_cols=38 Identities=13% Similarity=0.216 Sum_probs=25.3
Q ss_pred HHHHHHHhcCCEEEEecCCCchhhhhc--cccccEEEEeeee
Q 013759 378 WFANEYRRFGCTLEFVTNKSQEGSQFC--RGFGGIGGILRYQ 417 (437)
Q Consensus 378 ~Lve~a~~~ga~V~ivs~~~e~G~q~L--~~~gGIaAiLRy~ 417 (437)
.++..+.+.+..+..++..-- .++. ....||.|..+.+
T Consensus 33 ~~~~~~~~~~~~~~~v~~~~l--~~l~~~~~~qGv~a~~~~~ 72 (237)
T TIGR00186 33 KLIQLAKKQGINIQLVDRQKL--DQLTKGGNHQGIAAKVKPI 72 (237)
T ss_pred HHHHHHHHcCCcEEEeCHHHH--HHHhCCCCCCeEEEEEecC
Confidence 367778888999999985321 1211 2367999999854
No 95
>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=23.13 E-value=1.3e+02 Score=24.04 Aligned_cols=30 Identities=17% Similarity=0.155 Sum_probs=19.0
Q ss_pred HHHHHHHHHhcCCEEEEecCCCchhhhhccccccEEEEeeeecC
Q 013759 376 LEWFANEYRRFGCTLEFVTNKSQEGSQFCRGFGGIGGILRYQLD 419 (437)
Q Consensus 376 ve~Lve~a~~~ga~V~ivs~~~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 345778888999999988753 378898764
No 96
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=22.87 E-value=33 Score=33.84 Aligned_cols=31 Identities=3% Similarity=-0.203 Sum_probs=19.5
Q ss_pred EEcCCCCcEEEEeeccchhcccCcccCCCccccchh
Q 013759 334 LKNTVTGEIVIKHLNREQETNQNNFRDSATSAELEV 369 (437)
Q Consensus 334 ~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~~~~ 369 (437)
.+|++|+... +.... .+..+.||.||.-+..
T Consensus 39 ~kc~~C~~~~--~~~~l---~~~~~vcp~c~~h~rl 69 (296)
T CHL00174 39 VQCENCYGLN--YKKFL---KSKMNICEQCGYHLKM 69 (296)
T ss_pred eECCCccchh--hHHHH---HHcCCCCCCCCCCcCC
Confidence 4899998641 11111 1456899999986544
No 97
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=22.82 E-value=65 Score=23.50 Aligned_cols=23 Identities=9% Similarity=-0.122 Sum_probs=16.0
Q ss_pred EEcCCCCcEEEEeeccchhcccCcccCCCccccch
Q 013759 334 LKNTVTGEIVIKHLNREQETNQNNFRDSATSAELE 368 (437)
Q Consensus 334 ~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~~~ 368 (437)
-+|++||.-+ -+..||.||+.+.
T Consensus 6 r~C~~CgvYT------------Lk~~CP~CG~~t~ 28 (56)
T PRK13130 6 RKCPKCGVYT------------LKEICPVCGGKTK 28 (56)
T ss_pred eECCCCCCEE------------ccccCcCCCCCCC
Confidence 3688888631 2568999998754
No 98
>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=22.80 E-value=93 Score=27.71 Aligned_cols=37 Identities=5% Similarity=0.059 Sum_probs=28.8
Q ss_pred CcccCCCccccchhcccccHHHHHHHHHHhcCCEEEEecCCCchh
Q 013759 356 NNFRDSATSAELEVQEKSSLLEWFANEYRRFGCTLEFVTNKSQEG 400 (437)
Q Consensus 356 ~~~~cp~~g~~~~~~~~~dvve~Lve~a~~~ga~V~ivs~~~e~G 400 (437)
.-+.|..||.-. +..|.+.+++.|-+|.|+++.+-.-
T Consensus 63 ~g~~C~~Cg~C~--------Ig~l~~lae~~g~~v~i~~Ggt~ar 99 (158)
T PF01976_consen 63 DGYNCKRCGKCD--------IGDLKKLAEKYGYKVYIATGGTLAR 99 (158)
T ss_pred CCCcCCCCCCCc--------hhHHHHHHHHcCCEEEEEcChHHHH
Confidence 346788888542 4568999999999999999987543
No 99
>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=22.63 E-value=74 Score=20.88 Aligned_cols=30 Identities=17% Similarity=0.005 Sum_probs=17.8
Q ss_pred EEcCCCCcEEEEeeccchhcccCcccCCCccccc
Q 013759 334 LKNTVTGEIVIKHLNREQETNQNNFRDSATSAEL 367 (437)
Q Consensus 334 ~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~~ 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 46788886433222321 3456899999875
No 100
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=22.56 E-value=59 Score=28.32 Aligned_cols=23 Identities=13% Similarity=0.068 Sum_probs=17.0
Q ss_pred EEcCCCCcEEEEeeccchhcccCcccCCCcccc
Q 013759 334 LKNTVTGEIVIKHLNREQETNQNNFRDSATSAE 366 (437)
Q Consensus 334 ~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~ 366 (437)
.+|++||.... .....||.||.+
T Consensus 30 ~kC~~CG~v~~----------PPr~~Cp~C~~~ 52 (140)
T COG1545 30 TKCKKCGRVYF----------PPRAYCPKCGSE 52 (140)
T ss_pred EEcCCCCeEEc----------CCcccCCCCCCC
Confidence 48999997422 345689999987
No 101
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=22.42 E-value=1e+02 Score=22.98 Aligned_cols=33 Identities=3% Similarity=-0.049 Sum_probs=19.2
Q ss_pred CcccCCCccccchhcccccHHHHHHHHHHhcCCEEEEecCCC-chhhh
Q 013759 356 NNFRDSATSAELEVQEKSSLLEWFANEYRRFGCTLEFVTNKS-QEGSQ 402 (437)
Q Consensus 356 ~~~~cp~~g~~~~~~~~~dvve~Lve~a~~~ga~V~ivs~~~-e~G~q 402 (437)
....||.||+. +..++=.|=|.|+.++. +-..+
T Consensus 17 d~e~CP~Cgs~--------------~~te~W~G~~iIidpe~SeIAkr 50 (64)
T COG2093 17 DTEICPVCGST--------------DLTEEWFGLLIIIDPEKSEIAKR 50 (64)
T ss_pred CCccCCCCCCc--------------ccchhhccEEEEEcCcHHHHHHH
Confidence 34579999986 33344556666665443 44433
No 102
>PF14353 CpXC: CpXC protein
Probab=21.91 E-value=63 Score=27.35 Aligned_cols=11 Identities=9% Similarity=0.253 Sum_probs=8.2
Q ss_pred cccCCCccccc
Q 013759 357 NFRDSATSAEL 367 (437)
Q Consensus 357 ~~~cp~~g~~~ 367 (437)
.+.||.||...
T Consensus 38 ~~~CP~Cg~~~ 48 (128)
T PF14353_consen 38 SFTCPSCGHKF 48 (128)
T ss_pred EEECCCCCCce
Confidence 46889998763
No 103
>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=21.88 E-value=30 Score=38.72 Aligned_cols=33 Identities=9% Similarity=0.016 Sum_probs=0.0
Q ss_pred EEcCCCCcEEEEeeccchhcc-cCcccCCCcccc
Q 013759 334 LKNTVTGEIVIKHLNREQETN-QNNFRDSATSAE 366 (437)
Q Consensus 334 ~r~~~~~~~~~~~~~~~~~~~-r~~~~cp~~g~~ 366 (437)
.+|++||..++...=|.|... ...|.||.||..
T Consensus 656 r~Cp~Cg~~t~~~~Cp~CG~~T~~~~~Cp~C~~~ 689 (900)
T PF03833_consen 656 RRCPKCGKETFYNRCPECGSHTEPVYVCPDCGIE 689 (900)
T ss_dssp ----------------------------------
T ss_pred ccCcccCCcchhhcCcccCCccccceeccccccc
Confidence 578888876655555555421 234566666644
No 104
>PRK06450 threonine synthase; Validated
Probab=21.49 E-value=52 Score=33.08 Aligned_cols=27 Identities=11% Similarity=0.041 Sum_probs=18.5
Q ss_pred EEcCCCCcEEEEeeccchhcccCcccCCCccccchh
Q 013759 334 LKNTVTGEIVIKHLNREQETNQNNFRDSATSAELEV 369 (437)
Q Consensus 334 ~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~~~~ 369 (437)
++|..||..- .+ ...+.||.||+.+++
T Consensus 4 ~~C~~Cg~~~----~~-----~~~~~C~~cg~~l~~ 30 (338)
T PRK06450 4 EVCMKCGKER----ES-----IYEIRCKKCGGPFEI 30 (338)
T ss_pred eEECCcCCcC----CC-----cccccCCcCCCEeEE
Confidence 6899999631 11 124789999998765
No 105
>TIGR03025 EPS_sugtrans exopolysaccharide biosynthesis polyprenyl glycosylphosphotransferase. Certain closely related transferase enzymes such as Sinorhizobium ExoY and Lactococcus EpsD lack the N-terminal domain and are not found by this model.
Probab=21.25 E-value=9.1e+02 Score=24.88 Aligned_cols=116 Identities=20% Similarity=0.272 Sum_probs=68.2
Q ss_pred CcceEEEecChhhHHHhcccccCChhhhcceeEEEECCCCCCccHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHccCCC
Q 013759 221 NVSGLVLAGSADFKTELSQSDMFDPRLQAKILKVVDVSYGGENGFNQAIELSAESLSNVKFIQEKRLIGKYFEEISQDTG 300 (437)
Q Consensus 221 ~~~~liiaGp~~~k~~f~~~~~l~~~l~~~vi~~v~~s~~~~~gl~Evl~~~~~~l~~~~~~~e~~ll~~f~~~~~~~~~ 300 (437)
..+.++|.|.+.....+.+...-++...=+++|.++-+... + ..+ .+
T Consensus 124 ~~~rvLIvGag~~a~~l~~~L~~~~~~g~~vvG~idd~~~~--~----------------------------~~i---~g 170 (445)
T TIGR03025 124 NLRRVLIVGTGEAARELAAALSRNPDLGYRVVGFVDDRPSD--R----------------------------VEV---AG 170 (445)
T ss_pred CCCcEEEEECCHHHHHHHHHHhhCccCCeEEEEEEeCCccc--c----------------------------ccc---CC
Confidence 34568888888877777653212233333567777532110 0 001 12
Q ss_pred cEEE-CHHHHHHHHHhCCccEEEeecCCCceeEEEEcCCCCcEEEEeeccchhcccCcccCCCccccchhcccccHHHHH
Q 013759 301 KYVF-GADDTLKALDMGAVDTLIVWENLDITRYVLKNTVTGEIVIKHLNREQETNQNNFRDSATSAELEVQEKSSLLEWF 379 (437)
Q Consensus 301 ~a~y-G~~~V~~Al~~GaV~tLlV~d~l~~~~~~~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~~~~~~~~dvve~L 379 (437)
.-++ +.++..+.++...|+.++|+.... . .+-..++
T Consensus 171 ~pVlg~~~~l~~~i~~~~id~ViIa~p~~-----------~--------------------------------~~~~~~l 207 (445)
T TIGR03025 171 LPVLGKLDDLVELVRAHRVDEVIIALPLS-----------E--------------------------------EARILEL 207 (445)
T ss_pred CcccCCHHHHHHHHHhCCCCEEEEecCcc-----------c--------------------------------HHHHHHH
Confidence 2234 467788889999999999974331 0 0113458
Q ss_pred HHHHHhcCCEEEEecCCCc--hhhhhccccccEEE
Q 013759 380 ANEYRRFGCTLEFVTNKSQ--EGSQFCRGFGGIGG 412 (437)
Q Consensus 380 ve~a~~~ga~V~ivs~~~e--~G~q~L~~~gGIaA 412 (437)
++.+...|.+|.++|+-.+ .|..-+..++|+-.
T Consensus 208 l~~~~~~gv~V~~vP~~~e~~~~~~~~~~i~~v~~ 242 (445)
T TIGR03025 208 LLQLRDLGVDVRLVPDLFEFLLGRLRIEELGGVPL 242 (445)
T ss_pred HHHHHhcCCEEEEeCchhhhccCCcceEEECCEEE
Confidence 8999999999999997543 12221556666653
No 106
>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=21.00 E-value=65 Score=20.90 Aligned_cols=23 Identities=4% Similarity=-0.015 Sum_probs=11.5
Q ss_pred EEcCCCCcEEEEeeccchhcccCcccCCCcccc
Q 013759 334 LKNTVTGEIVIKHLNREQETNQNNFRDSATSAE 366 (437)
Q Consensus 334 ~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~ 366 (437)
-+|.+||.... .....||.||+.
T Consensus 12 ~rC~~Cg~~~~----------pPr~~Cp~C~s~ 34 (37)
T PF12172_consen 12 QRCRDCGRVQF----------PPRPVCPHCGSD 34 (37)
T ss_dssp EE-TTT--EEE----------S--SEETTTT--
T ss_pred EEcCCCCCEec----------CCCcCCCCcCcc
Confidence 38999987422 335789999864
No 107
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=20.36 E-value=41 Score=33.06 Aligned_cols=31 Identities=10% Similarity=0.052 Sum_probs=19.5
Q ss_pred EEcCCCCcEEEEeeccchhcccCcccCCCccccchh
Q 013759 334 LKNTVTGEIVIKHLNREQETNQNNFRDSATSAELEV 369 (437)
Q Consensus 334 ~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~~~~ 369 (437)
.+|+.|+... +.... .+..+.||.||.-+..
T Consensus 27 ~~c~~c~~~~--~~~~l---~~~~~vc~~c~~h~rl 57 (285)
T TIGR00515 27 TKCPKCGQVL--YTKEL---ERNLEVCPKCDHHMRM 57 (285)
T ss_pred eECCCCcchh--hHHHH---HhhCCCCCCCCCcCcC
Confidence 4899998741 11111 1446899999986554
No 108
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=20.23 E-value=39 Score=33.32 Aligned_cols=31 Identities=10% Similarity=0.013 Sum_probs=19.4
Q ss_pred EEcCCCCcEEEEeeccchhcccCcccCCCccccchh
Q 013759 334 LKNTVTGEIVIKHLNREQETNQNNFRDSATSAELEV 369 (437)
Q Consensus 334 ~r~~~~~~~~~~~~~~~~~~~r~~~~cp~~g~~~~~ 369 (437)
.+|+.|+.. .+.... .+..+.||.||.-+..
T Consensus 28 ~~c~~c~~~--~~~~~l---~~~~~vc~~c~~h~rl 58 (292)
T PRK05654 28 TKCPSCGQV--LYRKEL---EANLNVCPKCGHHMRI 58 (292)
T ss_pred eECCCccch--hhHHHH---HhcCCCCCCCCCCeeC
Confidence 489999863 111111 1445799999987554
No 109
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=20.12 E-value=38 Score=19.88 Aligned_cols=9 Identities=0% Similarity=-0.352 Sum_probs=6.2
Q ss_pred ccCCCcccc
Q 013759 358 FRDSATSAE 366 (437)
Q Consensus 358 ~~cp~~g~~ 366 (437)
--||.||.+
T Consensus 14 ~fC~~CG~~ 22 (23)
T PF13240_consen 14 KFCPNCGTP 22 (23)
T ss_pred cchhhhCCc
Confidence 348888865
Done!