Query 030062
Match_columns 183
No_of_seqs 98 out of 100
Neff 2.8
Searched_HMMs 46136
Date Fri Mar 29 07:55:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030062.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030062hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00039 photosystem II reacti 100.0 3.1E-67 6.6E-72 407.5 13.1 111 73-183 1-111 (111)
2 CHL00128 psbW photosystem II p 100.0 5.2E-67 1.1E-71 407.2 12.9 112 72-183 1-113 (113)
3 PRK13612 photosystem II reacti 100.0 7.5E-67 1.6E-71 406.3 13.4 112 71-183 2-113 (113)
4 TIGR03047 PS_II_psb28 photosys 100.0 2.3E-65 5.1E-70 395.9 11.7 108 75-182 1-109 (109)
5 PF03912 Psb28: Psb28 protein; 100.0 1.2E-64 2.7E-69 391.3 10.7 107 75-181 1-108 (108)
6 PRK13611 photosystem II reacti 100.0 9.9E-63 2.1E-67 378.8 12.8 104 72-181 1-104 (104)
7 PRK13610 photosystem II reacti 100.0 2.3E-61 5E-66 375.6 12.8 104 72-176 7-110 (113)
8 PF08722 Tn7_Tnp_TnsA_N: TnsA 80.5 2.6 5.6E-05 30.0 3.6 54 128-181 27-84 (88)
9 TIGR02447 yiiD_Cterm thioester 78.4 6.3 0.00014 30.5 5.4 44 130-173 67-110 (138)
10 PRK13795 hypothetical protein; 65.6 4.3 9.4E-05 39.2 2.2 22 157-178 430-451 (636)
11 PHA02552 4 head completion pro 58.0 11 0.00023 31.2 2.9 59 123-181 51-135 (151)
12 PF04320 DUF469: Protein with 57.9 13 0.00029 29.0 3.3 31 150-181 19-51 (101)
13 TIGR02034 CysN sulfate adenyly 56.3 30 0.00066 31.2 5.8 66 68-133 333-400 (406)
14 cd04480 RPA1_DBD_A_like RPA1_D 48.9 20 0.00043 25.3 2.8 17 118-134 17-34 (86)
15 cd04095 CysN_NoDQ_III TCysN_No 48.3 27 0.00058 25.3 3.5 36 95-130 58-93 (103)
16 PF12132 DUF3587: Protein of u 47.5 14 0.0003 31.8 2.1 24 132-155 56-79 (199)
17 PF09500 YiiD_Cterm: Putative 45.1 17 0.00036 29.5 2.1 44 130-173 73-116 (144)
18 cd03705 EF1_alpha_III Domain I 43.3 37 0.00079 24.4 3.5 35 95-129 61-95 (104)
19 PF15496 DUF4646: Domain of un 41.4 17 0.00037 28.4 1.6 35 139-174 26-64 (123)
20 cd08815 Death_TNFRSF25_DR3 Dea 40.0 20 0.00043 27.0 1.7 18 152-169 4-21 (77)
21 PRK13794 hypothetical protein; 37.8 24 0.00051 33.3 2.2 23 157-179 434-456 (479)
22 TIGR01628 PABP-1234 polyadenyl 35.7 1.2E+02 0.0027 28.0 6.4 78 39-128 64-156 (562)
23 cd01513 Translation_factor_III 34.0 47 0.001 23.2 2.8 35 96-130 60-94 (102)
24 cd02967 mauD Methylamine utili 33.2 33 0.00071 24.0 1.9 19 119-137 94-112 (114)
25 PF03799 FtsQ: Cell division p 32.1 32 0.00069 24.2 1.7 15 122-136 8-22 (117)
26 PRK11702 hypothetical protein; 30.6 64 0.0014 25.6 3.3 25 157-181 33-58 (108)
27 PF14791 DNA_pol_B_thumb: DNA 30.3 40 0.00088 23.7 1.9 19 164-182 10-28 (64)
28 PF14307 Glyco_tran_WbsX: Glyc 29.7 62 0.0013 28.7 3.4 35 143-179 156-190 (345)
29 PF14874 PapD-like: Flagellar- 28.6 1.9E+02 0.0042 20.3 5.2 39 97-141 62-100 (102)
30 cd00984 DnaB_C DnaB helicase C 27.8 56 0.0012 26.2 2.6 22 86-107 220-241 (242)
31 PF09827 CRISPR_Cas2: CRISPR a 27.8 42 0.0009 23.3 1.6 23 151-173 5-27 (78)
32 PRK12338 hypothetical protein; 27.4 1.1E+02 0.0023 28.0 4.5 43 127-172 227-269 (319)
33 PF03796 DnaB_C: DnaB-like hel 27.2 54 0.0012 27.1 2.5 24 87-110 228-251 (259)
34 PF14810 TGT_C2: Patch-forming 26.6 38 0.00083 24.7 1.3 29 73-101 8-38 (74)
35 PF13535 ATP-grasp_4: ATP-gras 26.5 55 0.0012 24.4 2.2 19 125-143 162-180 (184)
36 PF14524 Wzt_C: Wzt C-terminal 25.5 1E+02 0.0022 22.2 3.3 34 118-156 12-45 (142)
37 cd02966 TlpA_like_family TlpA- 25.4 89 0.0019 20.5 2.8 18 119-136 96-113 (116)
38 PF03750 DUF310: Protein of un 24.8 47 0.001 25.6 1.6 15 157-171 93-107 (119)
39 PF04350 PilO: Pilus assembly 24.8 71 0.0015 23.8 2.5 27 156-182 46-72 (144)
40 COG3171 Uncharacterized protei 24.5 47 0.001 27.0 1.5 20 159-181 47-66 (119)
41 cd05774 Ig_CEACAM_D1 First imm 24.4 2.9E+02 0.0063 20.6 5.7 60 78-140 20-79 (105)
42 PF13088 BNR_2: BNR repeat-lik 24.3 1.7E+02 0.0037 23.5 4.8 54 77-136 7-64 (275)
43 PF08448 PAS_4: PAS fold; Int 23.2 27 0.00059 23.0 -0.0 54 122-175 6-62 (110)
44 PF00989 PAS: PAS fold; Inter 23.2 88 0.0019 20.6 2.5 28 120-147 10-37 (113)
45 PF14259 RRM_6: RNA recognitio 22.3 57 0.0012 21.1 1.4 28 86-113 25-53 (70)
46 PF02375 JmjN: jmjN domain; I 22.0 62 0.0013 20.7 1.5 14 158-171 6-19 (34)
47 PLN02825 amino-acid N-acetyltr 21.7 3.7E+02 0.008 26.1 7.2 60 120-179 405-467 (515)
48 KOG1378 Purple acid phosphatas 21.6 49 0.0011 31.9 1.3 22 153-174 185-207 (452)
49 PRK13189 peroxiredoxin; Provis 21.3 1.7E+02 0.0037 24.5 4.4 18 120-137 125-142 (222)
50 PF14639 YqgF: Holliday-juncti 21.0 1.3E+02 0.0029 24.2 3.6 16 120-135 19-34 (150)
51 PRK05595 replicative DNA helic 20.8 89 0.0019 28.6 2.8 25 85-109 407-431 (444)
52 KOG2792 Putative cytochrome C 20.6 55 0.0012 30.0 1.4 32 103-134 223-255 (280)
53 smart00091 PAS PAS domain. PAS 20.3 1.2E+02 0.0026 15.3 2.2 24 122-145 12-35 (67)
54 cd03014 PRX_Atyp2cys Peroxired 20.3 1E+02 0.0022 22.6 2.6 20 121-140 110-129 (143)
No 1
>PLN00039 photosystem II reaction center Psb28 protein; Provisional
Probab=100.00 E-value=3.1e-67 Score=407.49 Aligned_cols=111 Identities=81% Similarity=1.333 Sum_probs=108.5
Q ss_pred ceeEeecCCCCCCCCCeeEEeccCCCcceEEEEEcCCcccccCCcccceeeEEEEecCceEEeEeceeEEEcCCcceeEE
Q 030062 73 PTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEIGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRIEA 152 (183)
Q Consensus 73 asIQFi~GidEe~iPdVrLtRSrdG~~GtA~F~Fe~p~a~~~~~~~~~ItGMyLiDEEGeI~Tr~V~aKFvnGkp~~iEa 152 (183)
|+||||+||||++||||||||||||++|+|+|+|++|++|++++.+++|||||||||||||+|+|||+|||||||++|||
T Consensus 1 a~IQF~~Gi~E~~vp~VrLtRsrdg~~g~a~f~F~~p~~l~~~~~~~~itgm~liDeEGei~tr~v~~KFvnGkp~~iEa 80 (111)
T PLN00039 1 PSIQFIKGTDETTVPDVRLTRSRDGTNGTAIFVFDQPSVFDSSGELGDITGLYMIDEEGVLQTVDVSAKFVNGKPAGIEA 80 (111)
T ss_pred CcEEEecCCCCCcCCceEEEEccCCCccEEEEEECCchhhccccccCceeeEEEEccCccEEEEecceEEECCCccEEEE
Confidence 68999999999999999999999999999999999999999875689999999999999999999999999999999999
Q ss_pred EEEecCchhHHHHHHHHHhhhhhcCcceecC
Q 030062 153 KYIMRSPREWDRFMRFMERYANQNGLQFVKK 183 (183)
Q Consensus 153 ~y~m~s~~eWdRFMRFMeRYAe~NGL~f~k~ 183 (183)
+|+|+|++|||||||||||||++|||+|+|+
T Consensus 81 ~y~m~s~~~WdRFMRFMeRYA~~ngl~f~k~ 111 (111)
T PLN00039 81 KYVMRSPREWDRFMRFMERYAEENGLGFVKK 111 (111)
T ss_pred EEEECCHHHHHHHHHHHHHHHHhcCCccccC
Confidence 9999999999999999999999999999986
No 2
>CHL00128 psbW photosystem II protein W; Reviewed
Probab=100.00 E-value=5.2e-67 Score=407.23 Aligned_cols=112 Identities=60% Similarity=1.073 Sum_probs=108.9
Q ss_pred eceeEeecCCCCCCCCCeeEEeccCCCcceEEEEEcCCcccccC-CcccceeeEEEEecCceEEeEeceeEEEcCCccee
Q 030062 72 KPTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSS-GEIGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRI 150 (183)
Q Consensus 72 ~asIQFi~GidEe~iPdVrLtRSrdG~~GtA~F~Fe~p~a~~~~-~~~~~ItGMyLiDEEGeI~Tr~V~aKFvnGkp~~i 150 (183)
+|+||||+||||++||||||||||||++|+|+|+|++|++|+++ +.+++|||||||||||||+|+|||+|||||||++|
T Consensus 1 ~a~IQF~~Gi~E~~ip~VrLtRsrdg~~g~a~f~F~~p~al~~~~~~~~~itgm~LiDeEGei~tr~v~~KFvnGkp~~i 80 (113)
T CHL00128 1 MAKIQFIKGIDEEVIPDVRLTRSRDGSTGTATFRFKNPNILDKSTAKQGEITGMYLIDEEGELSTRDVNAKFINGKPQAI 80 (113)
T ss_pred CCeEEEecCCCCCcCCceEEEEccCCCceEEEEEECCchhhhhccccccceeeEEEEccCccEEEEecceEEECCCccEE
Confidence 48999999999999999999999999999999999999999986 46899999999999999999999999999999999
Q ss_pred EEEEEecCchhHHHHHHHHHhhhhhcCcceecC
Q 030062 151 EAKYIMRSPREWDRFMRFMERYANQNGLQFVKK 183 (183)
Q Consensus 151 Ea~y~m~s~~eWdRFMRFMeRYAe~NGL~f~k~ 183 (183)
||+|+|+|++|||||||||||||++|||+|+|+
T Consensus 81 Ea~y~m~s~~~WdRFMRFMeRYA~~ngl~f~~~ 113 (113)
T CHL00128 81 EAIYIMKNPEAWDRFMRFMERYAEDNGLTFTKA 113 (113)
T ss_pred EEEEEECCHHHHHHHHHHHHHHHHhcCCccccC
Confidence 999999999999999999999999999999986
No 3
>PRK13612 photosystem II reaction center protein Psb28; Provisional
Probab=100.00 E-value=7.5e-67 Score=406.32 Aligned_cols=112 Identities=56% Similarity=0.986 Sum_probs=108.8
Q ss_pred eeceeEeecCCCCCCCCCeeEEeccCCCcceEEEEEcCCcccccCCcccceeeEEEEecCceEEeEeceeEEEcCCccee
Q 030062 71 VKPTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEIGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRI 150 (183)
Q Consensus 71 ~~asIQFi~GidEe~iPdVrLtRSrdG~~GtA~F~Fe~p~a~~~~~~~~~ItGMyLiDEEGeI~Tr~V~aKFvnGkp~~i 150 (183)
++|+||||+||||++||||||||||||++|+|+|+|++|++|++. .+++|||||||||||||+|+||++|||||||++|
T Consensus 2 ~~a~IQF~~Gi~E~~ip~VrLtRsrdg~~g~a~f~F~~p~al~~~-~~~~itgm~LiDeEGei~tr~v~~KFvnGkp~~i 80 (113)
T PRK13612 2 KMAAIQFSRGVDEPVVPDIRLTRSRDGRTGQATFYFEQPQALAPE-TTGEITGMYMIDEEGEIVTREVKAKFVNGKPSAL 80 (113)
T ss_pred CcceEEEecCCCCCcCCceEEEEccCCCeeEEEEEECCccccCcc-ccCceeeEEEEccCccEEEEecceEEECCCccEE
Confidence 459999999999999999999999999999999999999999984 5899999999999999999999999999999999
Q ss_pred EEEEEecCchhHHHHHHHHHhhhhhcCcceecC
Q 030062 151 EAKYIMRSPREWDRFMRFMERYANQNGLQFVKK 183 (183)
Q Consensus 151 Ea~y~m~s~~eWdRFMRFMeRYAe~NGL~f~k~ 183 (183)
||+|+|+|++|||||||||||||++|||+|+|+
T Consensus 81 Ea~y~m~s~~~WdRFMRFMeRYA~~ngl~f~~~ 113 (113)
T PRK13612 81 EATYIWKSEQEWDRFMRFMERYAKENGLGFSKS 113 (113)
T ss_pred EEEEEECCHHHHHHHHHHHHHHHHhcCCccccC
Confidence 999999999999999999999999999999986
No 4
>TIGR03047 PS_II_psb28 photosystem II reaction center protein Psb28. Members of this protein family are the Psb28 protein of photosystem II. Two different protein families, apparently without homology between them, have been designated PsbW. Cyanobacterial proteins previously designated PsbW are members of the family described here. However, while members of the plant PsbW family are not found (so far) in Cyanobacteria, members of the present family do occur in plants. We therefore support the alternative designation that has emerged for this protein family, Psp28, rather than PsbW.
Probab=100.00 E-value=2.3e-65 Score=395.95 Aligned_cols=108 Identities=57% Similarity=1.048 Sum_probs=105.5
Q ss_pred eEeecCCCCCCCCCeeEEeccCCCcceEEEEEcCCcccccCC-cccceeeEEEEecCceEEeEeceeEEEcCCcceeEEE
Q 030062 75 IQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSG-EIGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRIEAK 153 (183)
Q Consensus 75 IQFi~GidEe~iPdVrLtRSrdG~~GtA~F~Fe~p~a~~~~~-~~~~ItGMyLiDEEGeI~Tr~V~aKFvnGkp~~iEa~ 153 (183)
||||+||||++||||||||||||++|+|+|+|++|++|++++ .+++|||||||||||||+|+|||+|||||||++|||+
T Consensus 1 IQF~~Gi~E~~ip~VrLtRsrdg~~g~a~f~F~~p~al~~~~~~~~~itGm~LiDeEGei~tr~v~~KFvnGkp~~iEa~ 80 (109)
T TIGR03047 1 IQFFRGIDEEVIPDVRLTRSRDGGTGTALFRFENPKALDKFNSDTGEITGMYLIDEEGEIVTREVKAKFVNGKPKALEAV 80 (109)
T ss_pred CccccCCCCCcCCceEEEEccCCCceEEEEEECCchhhhhccccccceeeEEEEccCccEEEEecceEEECCCccEEEEE
Confidence 899999999999999999999999999999999999999874 5789999999999999999999999999999999999
Q ss_pred EEecCchhHHHHHHHHHhhhhhcCcceec
Q 030062 154 YIMRSPREWDRFMRFMERYANQNGLQFVK 182 (183)
Q Consensus 154 y~m~s~~eWdRFMRFMeRYAe~NGL~f~k 182 (183)
|+|+|++|||||||||||||++|||+|+|
T Consensus 81 y~m~s~~~WdRFMRFmeRYA~~ngl~f~~ 109 (109)
T TIGR03047 81 YIMKSEDEWDRFMRFMERYAEANGLGYSK 109 (109)
T ss_pred EEECCHHHHHHHHHHHHHHHHhcCCcccC
Confidence 99999999999999999999999999986
No 5
>PF03912 Psb28: Psb28 protein; InterPro: IPR005610 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. This family represents the low molecular weight transmembrane protein Psb28 (PsbW) found in PSII, where it is a subunit of the oxygen-evolving complex. Psb28 appears to have several roles, including guiding PSII biogenesis and assembly, stabilising dimeric PSII [], and facilitating PSII repair after photo-inhibition []. There appears to be two classes of Psb28, class 1 being found predominantly in algae and cyanobacteria, and class 2 being found predominantly in plants. This entry represents class 1 Psb28.; GO: 0015979 photosynthesis, 0009523 photosystem II, 0009654 oxygen evolving complex, 0016020 membrane; PDB: 2KVO_A.
Probab=100.00 E-value=1.2e-64 Score=391.33 Aligned_cols=107 Identities=61% Similarity=1.063 Sum_probs=82.0
Q ss_pred eEeecCCCCCCCCCeeEEeccCCCcceEEEEEcCCcccccCC-cccceeeEEEEecCceEEeEeceeEEEcCCcceeEEE
Q 030062 75 IQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSG-EIGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRIEAK 153 (183)
Q Consensus 75 IQFi~GidEe~iPdVrLtRSrdG~~GtA~F~Fe~p~a~~~~~-~~~~ItGMyLiDEEGeI~Tr~V~aKFvnGkp~~iEa~ 153 (183)
||||+||||+++|||||||||||++|+|+|+|++|++|++++ ++++|||||||||||||+|+||++|||||||++|||+
T Consensus 1 IQF~~Gi~E~~~pdVrLtRsrdg~~g~a~f~F~~p~al~~~~~~~~~itgm~liDeEGei~t~~v~~kFvnG~p~~iEa~ 80 (108)
T PF03912_consen 1 IQFIKGIDEEVVPDVRLTRSRDGGTGTATFYFENPKALEKFSSDKGEITGMYLIDEEGEISTRDVNAKFVNGKPQAIEAT 80 (108)
T ss_dssp EESSSS-------EEEEEE-TTS-SEEEEEEEES-GGGTSS-GG--G---EEEE-SS-EEEE--EEEEEETTEEEEEEEE
T ss_pred CccccCCCCccCCCeEEEEccCCCceEEEEEECCCcccccccccccccceEEEEccCccEEEEecceEEECCceEEEEEE
Confidence 899999999999999999999999999999999999999986 4689999999999999999999999999999999999
Q ss_pred EEecCchhHHHHHHHHHhhhhhcCccee
Q 030062 154 YIMRSPREWDRFMRFMERYANQNGLQFV 181 (183)
Q Consensus 154 y~m~s~~eWdRFMRFMeRYAe~NGL~f~ 181 (183)
|+|+|++|||||||||||||++|||+|+
T Consensus 81 y~m~s~~~WdRFMRFMeRYA~~Ngl~f~ 108 (108)
T PF03912_consen 81 YIMKSEEEWDRFMRFMERYAEANGLGFS 108 (108)
T ss_dssp EEE-SSHHHHHHHHHHHHHHHH--SSS-
T ss_pred EEECCHHHHHHHHHHHHHHHHhcCCccC
Confidence 9999999999999999999999999996
No 6
>PRK13611 photosystem II reaction center protein Psb28; Provisional
Probab=100.00 E-value=9.9e-63 Score=378.84 Aligned_cols=104 Identities=40% Similarity=0.723 Sum_probs=100.7
Q ss_pred eceeEeecCCCCCCCCCeeEEeccCCCcceEEEEEcCCcccccCCcccceeeEEEEecCceEEeEeceeEEEcCCcceeE
Q 030062 72 KPTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEIGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRIE 151 (183)
Q Consensus 72 ~asIQFi~GidEe~iPdVrLtRSrdG~~GtA~F~Fe~p~a~~~~~~~~~ItGMyLiDEEGeI~Tr~V~aKFvnGkp~~iE 151 (183)
+|+||||+||||+ +|||||||||||++|+|+|+|++|++ .+++|||||||||||||+|+||++|||||||++||
T Consensus 1 ma~IQF~~Gi~E~-~p~VrLtRsrdg~~g~a~f~F~~~~~-----~~~~itgm~liDeEGei~tr~v~~KFvnGkp~~iE 74 (104)
T PRK13611 1 MASIEFSPGIPEV-PTQVRLLKSKTGKRGSAIFRFEDLKS-----DTQNILGMRMIDEEGELTTRNIKAKFLNGEFKALE 74 (104)
T ss_pred CCeEEEecCCCCC-CCceEEEEccCCCccEEEEEEcCCcc-----cccceeeEEEEccCCcEEEEecceEEECCCccEEE
Confidence 3899999999999 99999999999999999999999998 35899999999999999999999999999999999
Q ss_pred EEEEecCchhHHHHHHHHHhhhhhcCccee
Q 030062 152 AKYIMRSPREWDRFMRFMERYANQNGLQFV 181 (183)
Q Consensus 152 a~y~m~s~~eWdRFMRFMeRYAe~NGL~f~ 181 (183)
|+|+|+|++|||||||||||||++|||+|.
T Consensus 75 a~y~m~s~~~wdRFMRFmeRYA~~Ngl~f~ 104 (104)
T PRK13611 75 VIYDMETEAEWDRFLRFMERFSAANQMGMA 104 (104)
T ss_pred EEEEECCHHHHHHHHHHHHHHHHhcCCccC
Confidence 999999999999999999999999999983
No 7
>PRK13610 photosystem II reaction center protein Psb28; Provisional
Probab=100.00 E-value=2.3e-61 Score=375.64 Aligned_cols=104 Identities=28% Similarity=0.601 Sum_probs=101.1
Q ss_pred eceeEeecCCCCCCCCCeeEEeccCCCcceEEEEEcCCcccccCCcccceeeEEEEecCceEEeEeceeEEEcCCcceeE
Q 030062 72 KPTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEIGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRIE 151 (183)
Q Consensus 72 ~asIQFi~GidEe~iPdVrLtRSrdG~~GtA~F~Fe~p~a~~~~~~~~~ItGMyLiDEEGeI~Tr~V~aKFvnGkp~~iE 151 (183)
.|+||||+||||++||||||||||||++|+|+|+|++|++|++. .+++|||||||||||||+|+||++|||||||++||
T Consensus 7 ~a~IQF~~Gi~E~~vp~VrLtRsrdG~tG~A~f~F~~p~~l~~~-~~~~ItGM~LiDeEGei~tr~v~aKFvnGkp~~iE 85 (113)
T PRK13610 7 NVAIQFVKGENEKDQPEIRLFRNLDGKKGKAVYKFYKPKTITLT-NYKSVQRMFLIDSEGVLSTKKIDLSISEDHVKEVK 85 (113)
T ss_pred CcEEEEecCCCCCcCCceEEEEccCCCccEEEEEECCchhcccc-cccceeeeEEEccCceEEEEeeeEEEEcCCccEEE
Confidence 58999999999999999999999999999999999999999984 58999999999999999999999999999999999
Q ss_pred EEEEecCchhHHHHHHHHHhhhhhc
Q 030062 152 AKYIMRSPREWDRFMRFMERYANQN 176 (183)
Q Consensus 152 a~y~m~s~~eWdRFMRFMeRYAe~N 176 (183)
|+|+|+|++|||||||||||||++.
T Consensus 86 a~y~m~s~~~WdRFMRFMeRYA~~~ 110 (113)
T PRK13610 86 STYNWNSEEAFERFMRFASRYANSL 110 (113)
T ss_pred EEEEECCHHHHHHHHHHHHHHHHHh
Confidence 9999999999999999999999974
No 8
>PF08722 Tn7_Tnp_TnsA_N: TnsA endonuclease N terminal; InterPro: IPR014833 The Tn7 transposase is composed of proteins TnsA and TnsB. DNA breakage at the 5'-end of the transposon is carried out by TnsA, and breakage and joining at the 3'-end is carried out by TnsB. The N-terminal domain of TnsA is catalytic. ; PDB: 1F1Z_B 1T0F_B.
Probab=80.50 E-value=2.6 Score=30.03 Aligned_cols=54 Identities=17% Similarity=0.265 Sum_probs=33.2
Q ss_pred ecCceEEeEeceeEEEcC---CcceeEEEEEecCch-hHHHHHHHHHhhhhhcCccee
Q 030062 128 DEEGTLQSVDVSAKFVNG---RPSRIEAKYIMRSPR-EWDRFMRFMERYANQNGLQFV 181 (183)
Q Consensus 128 DEEGeI~Tr~V~aKFvnG---kp~~iEa~y~m~s~~-eWdRFMRFMeRYAe~NGL~f~ 181 (183)
+.....-|.|.=+.+-+| ++..+|+++.-+-.. .+..=.....+|++++|..|.
T Consensus 27 ~~~~~~yTpDFlv~~~~g~~~~~~~ieVK~~~~l~~~~~~~k~~~~~~y~~~~g~~f~ 84 (88)
T PF08722_consen 27 TGVPIVYTPDFLVTYRDGNGKKPVAIEVKPSSELEKPRTKEKLEIEREYWEEQGIPFR 84 (88)
T ss_dssp TTEE---EEEEEEEESSS--SSEEEEEE--GGGGGSHHHHHHHHHHHHHHHHCT--EE
T ss_pred CCCccEEeccEEEEEccCCcceEEEEEEccHHHhcChhHHHHHHHHHHHHHHcCCeEE
Confidence 445566788888888898 888899888654444 333334556789999999884
No 9
>TIGR02447 yiiD_Cterm thioesterase domain, putative. This family consists of a broadly distributed uncharacterized domain found often as a standalone protein. The member from Shewanella oneidensis, PDB|1T82_A (Forouhar, et al., unpublished) is described from crystallography work as a putative thioesterase. About half of the members of this family are fused to an Acetyltransf_1 domain (PFAM model pfam00583). The function of this protein is unknown.
Probab=78.38 E-value=6.3 Score=30.51 Aligned_cols=44 Identities=14% Similarity=0.299 Sum_probs=36.9
Q ss_pred CceEEeEeceeEEEcCCcceeEEEEEecCchhHHHHHHHHHhhh
Q 030062 130 EGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMERYA 173 (183)
Q Consensus 130 EGeI~Tr~V~aKFvnGkp~~iEa~y~m~s~~eWdRFMRFMeRYA 173 (183)
++..+|.+.+..|+.---.++.|......+++||+|.+=++|..
T Consensus 67 ~~~~vt~~~~i~yl~P~~~~~~a~~~~~~~~~~~~~~~~l~~~g 110 (138)
T TIGR02447 67 DGDIVIADSHIRYLAPVTGDPVANCEAPDLESWEAFLATLQRGG 110 (138)
T ss_pred CCcEEEEEeeeEEcCCcCCCeEEEEEcCCHHHHHHHHHHHHhCC
Confidence 35899999999999644446999999999999999998877753
No 10
>PRK13795 hypothetical protein; Provisional
Probab=65.62 E-value=4.3 Score=39.25 Aligned_cols=22 Identities=27% Similarity=0.700 Sum_probs=20.4
Q ss_pred cCchhHHHHHHHHHhhhhhcCc
Q 030062 157 RSPREWDRFMRFMERYANQNGL 178 (183)
Q Consensus 157 ~s~~eWdRFMRFMeRYAe~NGL 178 (183)
.-|+.|+++++|+++||+.+|+
T Consensus 430 ~~Pe~~~~~~~~l~~~~~~~g~ 451 (636)
T PRK13795 430 LHPELYEKWEAFLLKWAKRNGL 451 (636)
T ss_pred HCHHHHHHHHHHHHHHHHHcCC
Confidence 3689999999999999999998
No 11
>PHA02552 4 head completion protein; Provisional
Probab=57.95 E-value=11 Score=31.18 Aligned_cols=59 Identities=20% Similarity=0.246 Sum_probs=39.4
Q ss_pred eEEEEec-CceE--EeEeceeEEEcCCcceeEEEEEecCc----------hhHHHHH-------------HHHHhhhhhc
Q 030062 123 GFYMIDE-EGTL--QSVDVSAKFVNGRPSRIEAKYIMRSP----------REWDRFM-------------RFMERYANQN 176 (183)
Q Consensus 123 GMyLiDE-EGeI--~Tr~V~aKFvnGkp~~iEa~y~m~s~----------~eWdRFM-------------RFMeRYAe~N 176 (183)
.+.-+|. +|.. =+-|.=+++.+|++.-||.++.-+.. ..|.||| .-..+||+++
T Consensus 51 ~I~Y~~~~~Gk~r~Y~PDFLV~~~dG~~~lvEVKp~~~~~~p~~~~~~~~~~~~~~~~~~~~w~~~~~K~~Aa~~~a~~~ 130 (151)
T PHA02552 51 VIPYFSNADGKRRRYFMDFYVKVDNGQKFLIEVKPKKETQPPKKPAKMTTAAKKRFINEVYTWSVNTDKWKAARALCEKK 130 (151)
T ss_pred EEEEEecCCCCeeeEcCcEEEEEeCCCEEEEEEccHHHccCcccccccchhhhhhhhhhhhhHHHHHHHHHHHHHHHHHc
Confidence 4433553 4643 34566688889988888888775544 2366666 3467888999
Q ss_pred Cccee
Q 030062 177 GLQFV 181 (183)
Q Consensus 177 GL~f~ 181 (183)
|..|.
T Consensus 131 Gw~F~ 135 (151)
T PHA02552 131 GWKFK 135 (151)
T ss_pred CCEEE
Confidence 99984
No 12
>PF04320 DUF469: Protein with unknown function (DUF469); InterPro: IPR007416 This entry represents a family of uncharacterised proteins which are predicted to function as phosphotransferases.
Probab=57.90 E-value=13 Score=28.97 Aligned_cols=31 Identities=26% Similarity=0.555 Sum_probs=25.0
Q ss_pred eEEEEEe-cCchhHHHHH-HHHHhhhhhcCccee
Q 030062 150 IEAKYIM-RSPREWDRFM-RFMERYANQNGLQFV 181 (183)
Q Consensus 150 iEa~y~m-~s~~eWdRFM-RFMeRYAe~NGL~f~ 181 (183)
+.|+|.- .++++.|+|+ +|.+ |-++|||.|.
T Consensus 19 v~~~~~~~~~~e~~D~~~D~fId-~Ie~~gL~~~ 51 (101)
T PF04320_consen 19 VSCRFAEGTSEEQIDAFVDAFID-VIEPNGLAFG 51 (101)
T ss_pred EEEEECCCCCHHHHHHHHHHHHH-HHHhCCCEEe
Confidence 5566666 6789999999 5777 9999999985
No 13
>TIGR02034 CysN sulfate adenylyltransferase, large subunit. Homologous to this E.coli activation pathway are nodPQH gene products found among members of the Rhizobiaceae family. These gene products have been shown to exhibit ATP sulfurase and APS kinase activity, yet are involved in Nod factor sulfation, and sulfation of other macromolecules. With members of the Rhizobiaceae family, nodQ often appears as a fusion of cysN (large subunit of ATP sulfurase) and cysC (APS kinase).
Probab=56.34 E-value=30 Score=31.24 Aligned_cols=66 Identities=23% Similarity=0.252 Sum_probs=45.4
Q ss_pred eeceeceeEeecC-CCCCCCCCeeEEeccCCCcceEEEEEcCCcccccCCcccceeeEEEEec-CceE
Q 030062 68 TMAVKPTIQFIQG-TDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEIGDITGFYMIDE-EGTL 133 (183)
Q Consensus 68 ~~~~~asIQFi~G-idEe~iPdVrLtRSrdG~~GtA~F~Fe~p~a~~~~~~~~~ItGMyLiDE-EGeI 133 (183)
+..+.++|.++.. +|..+--.++-..-+.|..+.|.|.+++|=.++.+++.....++.|+|. +|+.
T Consensus 333 t~~~~~~i~~i~~~~d~~t~~~~~~~~l~~~~~~~v~l~~~~p~~~~~~~~~~~lGr~~l~d~~~~~t 400 (406)
T TIGR02034 333 TRKVRASVAAIKHKVDVNTLEKGAAKSLELNEIGRVNLSLDEPIAFDPYAENRTTGAFILIDRLSNRT 400 (406)
T ss_pred CCEEEEEEEEEEEEecCCCCcccCCcccCCCCEEEEEEEECCeeccCcccCCCcceeEEEEECCCCCe
Confidence 4456677877754 2332211122222347899999999999999998877889999999994 5554
No 14
>cd04480 RPA1_DBD_A_like RPA1_DBD_A_like: A subgroup of uncharacterized plant OB folds with similarity to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of RPA is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change.
Probab=48.94 E-value=20 Score=25.25 Aligned_cols=17 Identities=24% Similarity=0.587 Sum_probs=13.9
Q ss_pred ccceeeEEEEecCc-eEE
Q 030062 118 IGDITGFYMIDEEG-TLQ 134 (183)
Q Consensus 118 ~~~ItGMyLiDEEG-eI~ 134 (183)
.+....|.|+||+| .|.
T Consensus 17 ~~~~~~miL~De~G~~I~ 34 (86)
T cd04480 17 SGESLEMVLVDEKGNRIH 34 (86)
T ss_pred CCcEEEEEEEcCCCCEEE
Confidence 56788999999999 444
No 15
>cd04095 CysN_NoDQ_III TCysN_NoDQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN and a smaller subunit CysD and CysN. ATPS produces adenosine-5'-phosphosulfate (APS) from ATP and sulfate, coupled with GTP hydrolysis. In the subsequent reaction APS is phosphorylated by an APS kinase (CysC), to produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS) for use in amino acid (aa) biosynthesis. The Rhizobiaceae group (alpha-proteobacteria) appears to carry out the same chemistry for the sufation of a nodulation factor. In Rhizobium meliloti, a the hererodimeric complex comprised of NodP and NodQ appears to possess both ATPS and APS kinase activities. The N and C termini of NodQ correspond to CysN and CysC, respectively. Other eubacteria, Archaea, and eukaryotes use a different ATP sulfurylase, which s
Probab=48.34 E-value=27 Score=25.26 Aligned_cols=36 Identities=28% Similarity=0.324 Sum_probs=30.6
Q ss_pred cCCCcceEEEEEcCCcccccCCcccceeeEEEEecC
Q 030062 95 RDGSNGMAIFSFSEPSVFDSSGEIGDITGFYMIDEE 130 (183)
Q Consensus 95 rdG~~GtA~F~Fe~p~a~~~~~~~~~ItGMyLiDEE 130 (183)
+.|..+.+.|.+++|=.+|...+......+.|+|.+
T Consensus 58 ~~n~~a~v~i~~~~pi~~d~~~~~~~~GrfiliD~~ 93 (103)
T cd04095 58 ELNDIGRVELSLSKPLAFDPYRENRATGSFILIDRL 93 (103)
T ss_pred CCCCeEEEEEEeCCccEecchhhCCCcceEEEEECC
Confidence 458899999999999999988767778889999963
No 16
>PF12132 DUF3587: Protein of unknown function (DUF3587); InterPro: IPR021982 This entry is represented by Hyposoter fugitivus ichnovirus, Gp7; it is a family of uncharacterised viral proteins.
Probab=47.52 E-value=14 Score=31.80 Aligned_cols=24 Identities=29% Similarity=0.620 Sum_probs=20.4
Q ss_pred eEEeEeceeEEEcCCcceeEEEEE
Q 030062 132 TLQSVDVSAKFVNGRPSRIEAKYI 155 (183)
Q Consensus 132 eI~Tr~V~aKFvnGkp~~iEa~y~ 155 (183)
.++|+...++|+|||+-.||=.|.
T Consensus 56 ~lSt~~~~ttF~NGK~L~IeYnfD 79 (199)
T PF12132_consen 56 RLSTHKITTTFLNGKPLEIEYNFD 79 (199)
T ss_pred hcccceEEEEEECCcEEEEEEecC
Confidence 378999999999999887777665
No 17
>PF09500 YiiD_Cterm: Putative thioesterase (yiiD_Cterm); InterPro: IPR012660 This entry consists of a broadly distributed uncharacterised domain found often as a standalone protein. The member from is described from crystallography work as a putative thioesterase. About half of the members of this family are fused to an N-terminal acetyltransferase domain (IPR000182 from INTERPRO). The function of these proteins are unknown. ; PDB: 1T82_C.
Probab=45.09 E-value=17 Score=29.50 Aligned_cols=44 Identities=18% Similarity=0.524 Sum_probs=21.6
Q ss_pred CceEEeEeceeEEEcCCcceeEEEEEecCchhHHHHHHHHHhhh
Q 030062 130 EGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMERYA 173 (183)
Q Consensus 130 EGeI~Tr~V~aKFvnGkp~~iEa~y~m~s~~eWdRFMRFMeRYA 173 (183)
+|.|+..+.+.++..==...+.|.-.+..+++|++|.+=..|..
T Consensus 73 ~~~IVi~~~~i~Y~~Pv~~d~~A~~~~~~~~~~~~~~~~l~~~g 116 (144)
T PF09500_consen 73 NGDIVIADSNIRYLKPVTGDFTARCSLPEPEDWERFLQTLARGG 116 (144)
T ss_dssp --EEEEEEEEEEE-S---S--EEEEE-------S---GGGGCTS
T ss_pred CCcEEEEeCceEEcCCCCCCcEEEEeccccchhHHHHHHHHcCC
Confidence 49999999999998665566889999999999999987666544
No 18
>cd03705 EF1_alpha_III Domain III of EF-1. Eukaryotic elongation factor 1 (EF-1) is responsible for the GTP-dependent binding of aminoacyl-tRNAs to ribosomes. EF-1 is composed of four subunits: the alpha chain, which binds GTP and aminoacyl-tRNAs, the gamma chain that probably plays a role in anchoring the complex to other cellular components and the beta and delta (or beta') chains. This family is the alpha subunit, and represents the counterpart of bacterial EF-Tu for the archaea (aEF-1 alpha) and eukaryotes (eEF-1 alpha).
Probab=43.31 E-value=37 Score=24.37 Aligned_cols=35 Identities=17% Similarity=0.263 Sum_probs=30.1
Q ss_pred cCCCcceEEEEEcCCcccccCCcccceeeEEEEec
Q 030062 95 RDGSNGMAIFSFSEPSVFDSSGEIGDITGFYMIDE 129 (183)
Q Consensus 95 rdG~~GtA~F~Fe~p~a~~~~~~~~~ItGMyLiDE 129 (183)
.-|..+.+.+.+.+|=.+|...+......+.|+|+
T Consensus 61 ~~n~~a~v~l~~~~pi~~e~~~~~~~lgrf~lrd~ 95 (104)
T cd03705 61 KSGDAAIVKIVPQKPLVVETFSEYPPLGRFAVRDM 95 (104)
T ss_pred CCCCEEEEEEEECCeeEEEEcccCCCccCEEEEeC
Confidence 45889999999999999998876778888999995
No 19
>PF15496 DUF4646: Domain of unknown function (DUF4646)
Probab=41.44 E-value=17 Score=28.45 Aligned_cols=35 Identities=26% Similarity=0.357 Sum_probs=24.7
Q ss_pred eeEEEcCCcce----eEEEEEecCchhHHHHHHHHHhhhh
Q 030062 139 SAKFVNGRPSR----IEAKYIMRSPREWDRFMRFMERYAN 174 (183)
Q Consensus 139 ~aKFvnGkp~~----iEa~y~m~s~~eWdRFMRFMeRYAe 174 (183)
+.++.+|=|.. .-+.|.+ +++||-||+..+..=|.
T Consensus 26 s~~l~~gFp~~~~P~~l~~~DV-s~eDW~~F~~dl~~aa~ 64 (123)
T PF15496_consen 26 SDSLSSGFPYLYPPPPLASHDV-SEEDWTRFLNDLSEAAS 64 (123)
T ss_pred CCccccCCCCcCCCchhhhcCC-CHHHHHHHHHHHHHHHh
Confidence 44456664441 3378888 89999999999877543
No 20
>cd08815 Death_TNFRSF25_DR3 Death domain of Tumor Necrosis Factor Receptor superfamily 25. Death Domain (DD) found in Tumor Necrosis Factor (TNF) receptor superfamily 25 (TNFRSF25), also known as TRAMP (TNF receptor-related apoptosis-mediating protein), LARD, APO-3, WSL-1, or DR3 (Death Receptor-3). TNFRSF25 is primarily expressed in T cells, is activated by binding to its ligand TL1A, and plays an important role in T-cell function. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=39.98 E-value=20 Score=26.97 Aligned_cols=18 Identities=28% Similarity=0.534 Sum_probs=13.9
Q ss_pred EEEEecCchhHHHHHHHH
Q 030062 152 AKYIMRSPREWDRFMRFM 169 (183)
Q Consensus 152 a~y~m~s~~eWdRFMRFM 169 (183)
+.+..-..+.|++|||.+
T Consensus 4 ~v~D~VP~~~wk~F~R~L 21 (77)
T cd08815 4 AVMDAVPARRWKEFVRTL 21 (77)
T ss_pred eeeccCChHHHHHHHHHc
Confidence 445556788999999985
No 21
>PRK13794 hypothetical protein; Provisional
Probab=37.80 E-value=24 Score=33.25 Aligned_cols=23 Identities=26% Similarity=0.817 Sum_probs=19.8
Q ss_pred cCchhHHHHHHHHHhhhhhcCcc
Q 030062 157 RSPREWDRFMRFMERYANQNGLQ 179 (183)
Q Consensus 157 ~s~~eWdRFMRFMeRYAe~NGL~ 179 (183)
.-|+.|++|.+|.++||+.+|+.
T Consensus 434 ~~Pe~~~~w~~~l~~~~~~~g~~ 456 (479)
T PRK13794 434 EYPELWEKWENFLKAWAKKHGLS 456 (479)
T ss_pred HCHHHHHHHHHHHHHHHHhcCCC
Confidence 35889999999999999998883
No 22
>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.
Probab=35.69 E-value=1.2e+02 Score=27.98 Aligned_cols=78 Identities=18% Similarity=0.345 Sum_probs=47.5
Q ss_pred CCCcCCeeeeecCCCCCccccCCccccceeeceeceeEeecCCCCC--------------CCCCeeEEeccCC-CcceEE
Q 030062 39 QSPFNGQSVHMPRMRLSPVTRNSKVSGPITMAVKPTIQFIQGTDEL--------------TVPDVKLTKSRDG-SNGMAI 103 (183)
Q Consensus 39 ~s~f~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~asIQFi~GidEe--------------~iPdVrLtRSrdG-~~GtA~ 103 (183)
+..++|..+.+-..+.....+.+. ..--|+++++++ .|-.|++.+..+| +.|.|.
T Consensus 64 ~~~i~gk~i~i~~s~~~~~~~~~~----------~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~~g~skg~af 133 (562)
T TIGR01628 64 FKRLGGKPIRIMWSQRDPSLRRSG----------VGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGF 133 (562)
T ss_pred CCEECCeeEEeecccccccccccC----------CCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecCCCCcccEEE
Confidence 356889988875332211111111 112488888865 3556888888877 789999
Q ss_pred EEEcCCcccccCCcccceeeEEEEe
Q 030062 104 FSFSEPSVFDSSGEIGDITGFYMID 128 (183)
Q Consensus 104 F~Fe~p~a~~~~~~~~~ItGMyLiD 128 (183)
..|++.+.-+. -.....|+.+-|
T Consensus 134 V~F~~~e~A~~--Ai~~lng~~~~~ 156 (562)
T TIGR01628 134 VHFEKEESAKA--AIQKVNGMLLND 156 (562)
T ss_pred EEECCHHHHHH--HHHHhcccEecC
Confidence 99999875432 133456666644
No 23
>cd01513 Translation_factor_III Domain III of Elongation factor (EF) Tu (EF-TU) and EF-G. Elongation factors (EF) EF-Tu and EF-G participate in the elongation phase during protein biosynthesis on the ribosome. Their functional cycles depend on GTP binding and its hydrolysis. The EF-Tu complexed with GTP and aminoacyl-tRNA delivers tRNA to the ribosome, whereas EF-G stimulates translocation, a process in which tRNA and mRNA movements occur in the ribosome. Experimental data showed that: (1) intrinsic GTPase activity of EF-G is influenced by excision of its domain III; (2) that EF-G lacking domain III has a 1,000-fold decreased GTPase activity on the ribosome and, a slightly decreased affinity for GTP; and (3) EF-G lacking domain III does not stimulate translocation, despite the physical presence of domain IV which is also very important for translocation. These findings indicate an essential contribution of domain III to activation of GTP hydrolysis. Domains III and V of EF-G have the s
Probab=33.98 E-value=47 Score=23.23 Aligned_cols=35 Identities=17% Similarity=0.311 Sum_probs=26.1
Q ss_pred CCCcceEEEEEcCCcccccCCcccceeeEEEEecC
Q 030062 96 DGSNGMAIFSFSEPSVFDSSGEIGDITGFYMIDEE 130 (183)
Q Consensus 96 dG~~GtA~F~Fe~p~a~~~~~~~~~ItGMyLiDEE 130 (183)
-|..+.+.+.|++|-.++.+.+......+.|+|.-
T Consensus 60 ~~~~a~v~l~~~~pi~~e~~~~~~~~grfilr~~~ 94 (102)
T cd01513 60 SGERGIVEVELQKPVALETFSENQEGGRFALRDGG 94 (102)
T ss_pred CCCEEEEEEEECCceEEEEhhhCCCcccEEEEeCC
Confidence 48999999999999988876555555555565553
No 24
>cd02967 mauD Methylamine utilization (mau) D family; mauD protein is the translation product of the mauD gene found in methylotrophic bacteria, which are able to use methylamine as a sole carbon source and a nitrogen source. mauD is an essential accessory protein for the biosynthesis of methylamine dehydrogenase (MADH), the enzyme that catalyzes the oxidation of methylamine and other primary amines. MADH possesses an alpha2beta2 subunit structure; the alpha subunit is also referred to as the large subunit. Each beta (small) subunit contains a tryptophan tryptophylquinone (TTQ) prosthetic group. Accessory proteins are essential for the proper transport of MADH to the periplasm, TTQ synthesis and the formation of several structural disulfide bonds. Bacterial mutants containing an insertion on the mauD gene were unable to grow on methylamine as a sole carbon source, were found to lack the MADH small subunit and had decreased amounts of the MADH large subunit.
Probab=33.23 E-value=33 Score=24.04 Aligned_cols=19 Identities=16% Similarity=0.335 Sum_probs=15.9
Q ss_pred cceeeEEEEecCceEEeEe
Q 030062 119 GDITGFYMIDEEGTLQSVD 137 (183)
Q Consensus 119 ~~ItGMyLiDEEGeI~Tr~ 137 (183)
..+-.+|+||.+|+|.-+.
T Consensus 94 ~~~P~~~vid~~G~v~~~~ 112 (114)
T cd02967 94 SKLPYAVLLDEAGVIAAKG 112 (114)
T ss_pred CCcCeEEEECCCCeEEecc
Confidence 4578899999999998764
No 25
>PF03799 FtsQ: Cell division protein FtsQ; InterPro: IPR005548 FtsQ is one of several cell division proteins. FtsQ interacts with other Fts proteins, reviewed in []. The precise function of FtsQ is unknown.; PDB: 2VH1_B 2VH2_B 2ALJ_A 1YR1_A.
Probab=32.10 E-value=32 Score=24.22 Aligned_cols=15 Identities=33% Similarity=0.838 Sum_probs=12.6
Q ss_pred eeEEEEecCceEEeE
Q 030062 122 TGFYMIDEEGTLQSV 136 (183)
Q Consensus 122 tGMyLiDEEGeI~Tr 136 (183)
.+.|+||++|++-..
T Consensus 8 ~~~~lvd~~G~v~~~ 22 (117)
T PF03799_consen 8 GGYYLVDENGVVFEP 22 (117)
T ss_dssp TEEEEEETTS-EECC
T ss_pred CceEEECCCCeEEec
Confidence 578999999999887
No 26
>PRK11702 hypothetical protein; Provisional
Probab=30.60 E-value=64 Score=25.61 Aligned_cols=25 Identities=28% Similarity=0.460 Sum_probs=20.3
Q ss_pred cCchhHHHHH-HHHHhhhhhcCccee
Q 030062 157 RSPREWDRFM-RFMERYANQNGLQFV 181 (183)
Q Consensus 157 ~s~~eWdRFM-RFMeRYAe~NGL~f~ 181 (183)
.++++-|.|+ +|.+.|-++|||.|-
T Consensus 33 ~~~e~~D~~vD~fIde~Ie~ngL~f~ 58 (108)
T PRK11702 33 TSEEQIDATVDAFIDEVIEPNGLAFD 58 (108)
T ss_pred CCHHHHHHHHHHHHHHHHhcCCceec
Confidence 4567788888 577889999999984
No 27
>PF14791 DNA_pol_B_thumb: DNA polymerase beta thumb ; PDB: 1HUZ_A 3K75_D 1HUO_A 2BPC_A 1RPL_A 1NOM_A 1ZQX_A 1ZQU_A 1ZQZ_A 1ZQV_A ....
Probab=30.30 E-value=40 Score=23.75 Aligned_cols=19 Identities=26% Similarity=0.641 Sum_probs=15.9
Q ss_pred HHHHHHHhhhhhcCcceec
Q 030062 164 RFMRFMERYANQNGLQFVK 182 (183)
Q Consensus 164 RFMRFMeRYAe~NGL~f~k 182 (183)
-|-|.|.+||.+.||.++.
T Consensus 10 ~fnr~lR~~A~~~g~~L~~ 28 (64)
T PF14791_consen 10 EFNRDLRQYAKKKGMKLSE 28 (64)
T ss_dssp HHHHHHHHHHHHTTEEEES
T ss_pred HHHHHHHHHHHHcCCeeCc
Confidence 4777888999999998875
No 28
>PF14307 Glyco_tran_WbsX: Glycosyltransferase WbsX
Probab=29.67 E-value=62 Score=28.69 Aligned_cols=35 Identities=20% Similarity=0.312 Sum_probs=28.3
Q ss_pred EcCCcceeEEEEEecCchhHHHHHHHHHhhhhhcCcc
Q 030062 143 VNGRPSRIEAKYIMRSPREWDRFMRFMERYANQNGLQ 179 (183)
Q Consensus 143 vnGkp~~iEa~y~m~s~~eWdRFMRFMeRYAe~NGL~ 179 (183)
||||| |=.+|.-..-.+-.++|..+.+.|.++|++
T Consensus 156 VdGKP--v~~Iy~p~~~pd~~~~~~~wr~~a~~~G~~ 190 (345)
T PF14307_consen 156 VDGKP--VFLIYRPGDIPDIKEMIERWREEAKEAGLP 190 (345)
T ss_pred ECCEE--EEEEECcccccCHHHHHHHHHHHHHHcCCC
Confidence 67877 355666666678899999999999999986
No 29
>PF14874 PapD-like: Flagellar-associated PapD-like
Probab=28.55 E-value=1.9e+02 Score=20.31 Aligned_cols=39 Identities=28% Similarity=0.388 Sum_probs=31.2
Q ss_pred CCcceEEEEEcCCcccccCCcccceeeEEEEecCceEEeEeceeE
Q 030062 97 GSNGMAIFSFSEPSVFDSSGEIGDITGFYMIDEEGTLQSVDVSAK 141 (183)
Q Consensus 97 G~~GtA~F~Fe~p~a~~~~~~~~~ItGMyLiDEEGeI~Tr~V~aK 141 (183)
|.+......|.-++ ..|++.+...|.-||....-+|+|+
T Consensus 62 G~~~~~~V~~~~~~------~~g~~~~~l~i~~e~~~~~i~v~a~ 100 (102)
T PF14874_consen 62 GESVELEVTFSPTK------PLGDYEGSLVITTEGGSFEIPVKAE 100 (102)
T ss_pred CCEEEEEEEEEeCC------CCceEEEEEEEEECCeEEEEEEEEE
Confidence 77788888887443 3577888888999999999888887
No 30
>cd00984 DnaB_C DnaB helicase C terminal domain. The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.
Probab=27.84 E-value=56 Score=26.16 Aligned_cols=22 Identities=23% Similarity=0.617 Sum_probs=19.7
Q ss_pred CCCeeEEeccCCCcceEEEEEc
Q 030062 86 VPDVKLTKSRDGSNGMAIFSFS 107 (183)
Q Consensus 86 iPdVrLtRSrdG~~GtA~F~Fe 107 (183)
.-.|.+.++|.|.+|.+.+.|+
T Consensus 220 ~~~l~v~KnR~G~~g~~~l~~~ 241 (242)
T cd00984 220 IAEIIVAKNRNGPTGTVELRFD 241 (242)
T ss_pred ceEEEEECCCCCCCeeEEEEee
Confidence 4578899999999999999996
No 31
>PF09827 CRISPR_Cas2: CRISPR associated protein Cas2; InterPro: IPR019199 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. Members of this family of bacterial proteins comprise various hypothetical proteins, as well as CRISPR (clustered regularly interspaced short palindromic repeats) associated proteins, conferring resistance to infection by certain bacteriophages. ; PDB: 3EXC_X 2I0X_A 3OQ2_B 3UI3_A 1ZPW_X 2I8E_A 2IVY_A.
Probab=27.82 E-value=42 Score=23.27 Aligned_cols=23 Identities=9% Similarity=0.341 Sum_probs=20.9
Q ss_pred EEEEEecCchhHHHHHHHHHhhh
Q 030062 151 EAKYIMRSPREWDRFMRFMERYA 173 (183)
Q Consensus 151 Ea~y~m~s~~eWdRFMRFMeRYA 173 (183)
=..|.+..+....++.+++++|+
T Consensus 5 lv~YDi~~~k~~~kv~k~L~~~g 27 (78)
T PF09827_consen 5 LVAYDISDNKRRNKVRKILKSYG 27 (78)
T ss_dssp EEEEEEHSHHHHHHHHHHHHHTT
T ss_pred EEEEECCCcHHHHHHHHHHHHhC
Confidence 35799999999999999999998
No 32
>PRK12338 hypothetical protein; Provisional
Probab=27.37 E-value=1.1e+02 Score=28.00 Aligned_cols=43 Identities=16% Similarity=0.328 Sum_probs=33.5
Q ss_pred EecCceEEeEeceeEEEcCCcceeEEEEEecCchhHHHHHHHHHhh
Q 030062 127 IDEEGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMERY 172 (183)
Q Consensus 127 iDEEGeI~Tr~V~aKFvnGkp~~iEa~y~m~s~~eWdRFMRFMeRY 172 (183)
+|--|.| .||. -=|.|.++-|.+...++|.+++++||.=|+.+
T Consensus 227 vd~Gg~v--~dV~-h~iyG~~~~i~~~l~i~s~~dv~~Fi~~~~~~ 269 (319)
T PRK12338 227 KRHGGRI--TDIS-YPIPGFKDPLKREVNVSDPDEAEKFIKRLNEN 269 (319)
T ss_pred ecCCCEE--EEec-ccCCCCCceeEEEEccCCHHHHHHHHHHHhhC
Confidence 3444444 4555 66789888999999999999999999877654
No 33
>PF03796 DnaB_C: DnaB-like helicase C terminal domain; InterPro: IPR007694 The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis. ; GO: 0003678 DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication; PDB: 1Q57_E 1E0K_D 1E0J_B 1CR2_A 1CR4_A 1CR1_A 1CR0_A 1MI8_A 2R6D_B 2R6C_C ....
Probab=27.23 E-value=54 Score=27.06 Aligned_cols=24 Identities=21% Similarity=0.519 Sum_probs=18.7
Q ss_pred CCeeEEeccCCCcceEEEEEcCCc
Q 030062 87 PDVKLTKSRDGSNGMAIFSFSEPS 110 (183)
Q Consensus 87 PdVrLtRSrdG~~GtA~F~Fe~p~ 110 (183)
-++.+.++|+|.+|++.+.|+...
T Consensus 228 ~~l~v~KnR~G~~g~v~~~f~~~~ 251 (259)
T PF03796_consen 228 AELIVAKNRNGPTGTVPLRFNPET 251 (259)
T ss_dssp EEEEEEEESSS--EEEEEEEETTT
T ss_pred EEEEEEecCCCCCceEEEEEECCC
Confidence 368999999999999999997643
No 34
>PF14810 TGT_C2: Patch-forming domain C2 of tRNA-guanine transglycosylase; PDB: 1J2B_A 1IT8_A 1IT7_B 1IQ8_A.
Probab=26.63 E-value=38 Score=24.67 Aligned_cols=29 Identities=24% Similarity=0.489 Sum_probs=19.0
Q ss_pred ceeEeecCCCCCCCCC-eeEEec-cCCCcce
Q 030062 73 PTIQFIQGTDELTVPD-VKLTKS-RDGSNGM 101 (183)
Q Consensus 73 asIQFi~GidEe~iPd-VrLtRS-rdG~~Gt 101 (183)
|.-||=.|..+..+|| +.+.+| +.|.-+.
T Consensus 8 AdYQFG~gag~~lf~d~~~i~~s~~t~riR~ 38 (74)
T PF14810_consen 8 ADYQFGRGAGDALFPDDIEIQRSKKTGRIRQ 38 (74)
T ss_dssp HHHHT-TTGGGGTTT---EEEE--SSS-EEE
T ss_pred HHHHcCcChHHHhcccCcEEEEeccCCceEE
Confidence 6779999999998998 999999 4454443
No 35
>PF13535 ATP-grasp_4: ATP-grasp domain; PDB: 3VMM_A 3LN6_A 3LN7_B 2PN1_A 4DIM_A.
Probab=26.50 E-value=55 Score=24.38 Aligned_cols=19 Identities=21% Similarity=0.704 Sum_probs=15.4
Q ss_pred EEEecCceEEeEeceeEEE
Q 030062 125 YMIDEEGTLQSVDVSAKFV 143 (183)
Q Consensus 125 yLiDEEGeI~Tr~V~aKFv 143 (183)
+++|++|++..-|+|.++-
T Consensus 162 ~~~~~~g~~~~iEiN~R~~ 180 (184)
T PF13535_consen 162 FIVDPDGELYFIEINPRFG 180 (184)
T ss_dssp EEEETCCEEEEEEEESS--
T ss_pred EEEeCCCCEEEEEECccCC
Confidence 5779999999999999763
No 36
>PF14524 Wzt_C: Wzt C-terminal domain; PDB: 2R5O_B.
Probab=25.52 E-value=1e+02 Score=22.17 Aligned_cols=34 Identities=32% Similarity=0.543 Sum_probs=25.3
Q ss_pred ccceeeEEEEecCceEEeEeceeEEEcCCcceeEEEEEe
Q 030062 118 IGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRIEAKYIM 156 (183)
Q Consensus 118 ~~~ItGMyLiDEEGeI~Tr~V~aKFvnGkp~~iEa~y~m 156 (183)
...|+...++|++|+.... |..|.+-.|+..|..
T Consensus 12 ~~~I~~v~i~~~~g~~~~~-----~~~ge~~~i~i~~~~ 45 (142)
T PF14524_consen 12 EARITSVRILDSDGEPTSS-----FESGEPIRIRIDYEV 45 (142)
T ss_dssp SEEEEEEEEEETTEES-SS-----EETTSEEEEEEEEEE
T ss_pred CEEEEEEEEEeCCCCEeeE-----EeCCCEEEEEEEEEE
Confidence 4589999999999976543 777777777777765
No 37
>cd02966 TlpA_like_family TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a CXXC motif located in the periplasm. The TRX domains of this family contain an insert, approximately 25 residues in length, which correspond to an extra alpha helix and a beta strand when compared with TRX. TlpA catalyzes an essential reaction in the biogenesis of cytochrome aa3, while ResA and DsbE are essential proteins in cytochrome c maturation. Also included in this family are proteins containing a TlpA-like TRX domain with domain architectures similar to E. coli DipZ protein, and the N-terminal TRX domain of PilB protein from Neisseria which acts as a disulfide reductase that can recylce methionine sulfoxide reductases.
Probab=25.41 E-value=89 Score=20.52 Aligned_cols=18 Identities=17% Similarity=0.523 Sum_probs=14.2
Q ss_pred cceeeEEEEecCceEEeE
Q 030062 119 GDITGFYMIDEEGTLQSV 136 (183)
Q Consensus 119 ~~ItGMyLiDEEGeI~Tr 136 (183)
..+-.++++|++|+|.-+
T Consensus 96 ~~~P~~~l~d~~g~v~~~ 113 (116)
T cd02966 96 RGLPTTFLIDRDGRIRAR 113 (116)
T ss_pred CccceEEEECCCCcEEEE
Confidence 367788999999988643
No 38
>PF03750 DUF310: Protein of unknown function (DUF310); InterPro: IPR010149 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. This entry represents the C-terminal domain of a minor family of CRISPR-associated proteins. These proteins are found adjacent to a characteristic short, palindromic repeat cluster termed CRISPR, a probable mobile DNA element.
Probab=24.77 E-value=47 Score=25.61 Aligned_cols=15 Identities=27% Similarity=0.875 Sum_probs=13.4
Q ss_pred cCchhHHHHHHHHHh
Q 030062 157 RSPREWDRFMRFMER 171 (183)
Q Consensus 157 ~s~~eWdRFMRFMeR 171 (183)
++.+++++|++|||-
T Consensus 93 ~~~~~f~~F~~~fEA 107 (119)
T PF03750_consen 93 KDKKDFERFCKFFEA 107 (119)
T ss_pred CCHHHHHHHHHHHHH
Confidence 788999999999984
No 39
>PF04350 PilO: Pilus assembly protein, PilO; PDB: 2RJZ_B.
Probab=24.75 E-value=71 Score=23.77 Aligned_cols=27 Identities=15% Similarity=0.378 Sum_probs=22.1
Q ss_pred ecCchhHHHHHHHHHhhhhhcCcceec
Q 030062 156 MRSPREWDRFMRFMERYANQNGLQFVK 182 (183)
Q Consensus 156 m~s~~eWdRFMRFMeRYAe~NGL~f~k 182 (183)
+-.+.++..|+.-+++.|+++|+.+.+
T Consensus 46 lP~~~~~~~ll~~l~~~A~~~gv~l~~ 72 (144)
T PF04350_consen 46 LPAEEEIPSLLEDLNRLAKKSGVKLTS 72 (144)
T ss_dssp TTGGGHHHHHHHHHHHHHHHTT-EEEE
T ss_pred CCCchhHHHHHHHHHHHHHHCCCeEEE
Confidence 345778999999999999999998753
No 40
>COG3171 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.47 E-value=47 Score=27.05 Aligned_cols=20 Identities=35% Similarity=0.557 Sum_probs=13.3
Q ss_pred chhHHHHHHHHHhhhhhcCccee
Q 030062 159 PREWDRFMRFMERYANQNGLQFV 181 (183)
Q Consensus 159 ~~eWdRFMRFMeRYAe~NGL~f~ 181 (183)
++..||||-+. -+.|||.|-
T Consensus 47 dea~drFidev---I~~Ngl~~~ 66 (119)
T COG3171 47 DEAVDRFIDEV---IAPNGLAFA 66 (119)
T ss_pred HHHHHHHHHHH---HccCceeEc
Confidence 45566666555 459999984
No 41
>cd05774 Ig_CEACAM_D1 First immunoglobulin (Ig)-like domain of carcinoembryonic antigen (CEA) related cell adhesion molecule (CEACAM). IG_CEACAM_D1: immunoglobulin (Ig)-like domain 1 in carcinoembryonic antigen (CEA) related cell adhesion molecule (CEACAM) protein subfamily. The CEA family is a group of anchored or secreted glycoproteins, expressed by epithelial cells, leukocytes, endothelial cells and placenta. The CEA family is divided into the CEACAM and pregnancy-specific glycoprotein (PSG) subfamilies. This group represents the CEACAM subfamily. CEACAM1 has many important cellular functions, it is a cell adhesion molecule, and a signaling molecule that regulates the growth of tumor cells, it is an angiogenic factor, and is a receptor for bacterial and viral pathogens, including mouse hepatitis virus (MHV). In mice, four isoforms of CEACAM1 generated by alternative splicing have either two [D1, D4] or four [D1-D4] Ig-like domains on the cell surface. This family corresponds to the D
Probab=24.42 E-value=2.9e+02 Score=20.64 Aligned_cols=60 Identities=18% Similarity=0.089 Sum_probs=40.8
Q ss_pred ecCCCCCCCCCeeEEeccCCCcceEEEEEcCCcccccCCcccceeeEEEEecCceEEeEecee
Q 030062 78 IQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEIGDITGFYMIDEEGTLQSVDVSA 140 (183)
Q Consensus 78 i~GidEe~iPdVrLtRSrdG~~GtA~F~Fe~p~a~~~~~~~~~ItGMyLiDEEGeI~Tr~V~a 140 (183)
+.|.+|+ +-+++-.|+.....+.+++.|....-- ........|=..+.+.|.|..++|..
T Consensus 20 v~~~p~~-~~~~~W~kg~~~~~~~~I~~y~~~~~~--~~~gp~~~gR~~~~~ngSL~I~~v~~ 79 (105)
T cd05774 20 VHNLPEN-LLAYAWYKGKTVSPNFLIASYIISTNS--STPGPAYSGRETIYPNGSLLIQNVTQ 79 (105)
T ss_pred ecCCCCC-ceEEEEEcCCCCCCCEEEEEEECCCcc--cccCcccCCcEEEeCCCcEEEecCCc
Confidence 4566665 667888887777778888888877321 11123566777788888888877753
No 42
>PF13088 BNR_2: BNR repeat-like domain; PDB: 2F11_A 2F0Z_A 1VCU_B 2F25_B 1SO7_A 2F29_A 1SNT_A 2F13_A 2F28_A 2F27_A ....
Probab=24.27 E-value=1.7e+02 Score=23.54 Aligned_cols=54 Identities=24% Similarity=0.358 Sum_probs=34.2
Q ss_pred eecCCCCCCCCCeeEEec--cCCCcceEEEEEcCCcccccCC--cccceeeEEEEecCceEEeE
Q 030062 77 FIQGTDELTVPDVKLTKS--RDGSNGMAIFSFSEPSVFDSSG--EIGDITGFYMIDEEGTLQSV 136 (183)
Q Consensus 77 Fi~GidEe~iPdVrLtRS--rdG~~GtA~F~Fe~p~a~~~~~--~~~~ItGMyLiDEEGeI~Tr 136 (183)
|..|-+|. -+||.+.|| +||+. +...|..+.... ....-....+.|..|+|..-
T Consensus 7 ~~~~~~~~-~~d~~i~~S~s~D~G~-----tWs~~~~v~~~~~~~~~~~~p~~~~~~~g~l~l~ 64 (275)
T PF13088_consen 7 WEGGSDEG-AIDIVIRRSRSTDGGK-----TWSEPRIVADGPKPGRRYGNPSLVVDPDGRLWLF 64 (275)
T ss_dssp EEESSCSC-CEEEEEEEECCCCCTT-----EEEEEEEEETSTBTTCEEEEEEEEEETTSEEEEE
T ss_pred EECCcccC-CCCEEEEEEEeeCCCC-----eeCCCEEEeeccccCCcccCcEEEEeCCCCEEEE
Confidence 34488888 899999999 88765 344444433221 12334455667888888765
No 43
>PF08448 PAS_4: PAS fold; InterPro: IPR013656 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []. The PAS fold appears in archaea, eubacteria and eukarya. ; PDB: 3K3D_A 3K3C_B 3KX0_X 3FC7_B 3LUQ_D 3MXQ_A 3BWL_C 3FG8_A.
Probab=23.23 E-value=27 Score=23.02 Aligned_cols=54 Identities=17% Similarity=0.369 Sum_probs=35.3
Q ss_pred eeEEEEecCceEEeEeceeEEEcCCcce-eEEE--EEecCchhHHHHHHHHHhhhhh
Q 030062 122 TGFYMIDEEGTLQSVDVSAKFVNGRPSR-IEAK--YIMRSPREWDRFMRFMERYANQ 175 (183)
Q Consensus 122 tGMyLiDEEGeI~Tr~V~aKFvnGkp~~-iEa~--y~m~s~~eWdRFMRFMeRYAe~ 175 (183)
.+++++|.+|.|...+-.+.=..|.+.. +... ..+-.++.++.|.+.+++=++.
T Consensus 6 ~~i~v~D~~~~i~~~N~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~ 62 (110)
T PF08448_consen 6 DGIFVIDPDGRIVYANQAAAELFGVSPEELIGRSLFDLLPPEDREEFQAALRRALAG 62 (110)
T ss_dssp SEEEEEETTSBEEEE-HHHHHHHTSTHHHHTTSBHHHHSCCGCHHHHHHHHHHHHHH
T ss_pred ceeEEECCCCEEEEEHHHHHHHhCCCHHHHhhccchhccccchhhhhHHHHHHhhcc
Confidence 5789999999998776665544443332 1111 1355677899999999886554
No 44
>PF00989 PAS: PAS fold; InterPro: IPR013767 PAS domains are involved in many signalling proteins where they are used as a signal sensor domain []. PAS domains appear in archaea, bacteria and eukaryotes. Several PAS-domain proteins are known to detect their signal by way of an associated cofactor. Haeme, flavin, and a 4-hydroxycinnamyl chromophore are used in different proteins. The PAS domain was named after three proteins that it occurs in: Per- period circadian protein Arnt- Ah receptor nuclear translocator protein Sim- single-minded protein. PAS domains are often associated with PAC domains IPR001610 from INTERPRO. It appears that these domains are directly linked, and that together they form the conserved 3D PAS fold. The division between the PAS and PAC domains is caused by major differences in sequences in the region connecting these two motifs []. In human PAS kinase, this region has been shown to be very flexible, and adopts different conformations depending on the bound ligand []. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels [].; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 2GJ3_A 4F3L_B 1XFN_A 1OTD_A 2PYR_A 1KOU_A 1XFQ_A 2ZOI_A 2ZOH_A 1OTA_A ....
Probab=23.20 E-value=88 Score=20.63 Aligned_cols=28 Identities=29% Similarity=0.498 Sum_probs=20.6
Q ss_pred ceeeEEEEecCceEEeEeceeEEEcCCc
Q 030062 120 DITGFYMIDEEGTLQSVDVSAKFVNGRP 147 (183)
Q Consensus 120 ~ItGMyLiDEEGeI~Tr~V~aKFvnGkp 147 (183)
...|++++|.+|.|.-.+-.+.=+.|.+
T Consensus 10 ~~~~i~~~d~~g~I~~~N~a~~~l~g~~ 37 (113)
T PF00989_consen 10 SPDGIFVIDEDGRILYVNQAAEELLGYS 37 (113)
T ss_dssp SSSEEEEEETTSBEEEECHHHHHHHSS-
T ss_pred CCceEEEEeCcCeEEEECHHHHHHHccC
Confidence 3579999999999988776665555533
No 45
>PF14259 RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....
Probab=22.30 E-value=57 Score=21.09 Aligned_cols=28 Identities=36% Similarity=0.570 Sum_probs=22.8
Q ss_pred CCCeeEEeccCCC-cceEEEEEcCCcccc
Q 030062 86 VPDVKLTKSRDGS-NGMAIFSFSEPSVFD 113 (183)
Q Consensus 86 iPdVrLtRSrdG~-~GtA~F~Fe~p~a~~ 113 (183)
|.+|++.++++|. +|.|...|.+++...
T Consensus 25 v~~v~~~~~~~~~~~~~a~v~f~~~~~a~ 53 (70)
T PF14259_consen 25 VEKVRLIKNKDGQSRGFAFVEFSSEEDAK 53 (70)
T ss_dssp EEEEEEEESTTSSEEEEEEEEESSHHHHH
T ss_pred cceEEEEeeeccccCCEEEEEeCCHHHHH
Confidence 6789999998754 799999999887543
No 46
>PF02375 JmjN: jmjN domain; InterPro: IPR003349 Jumonji protein is required for neural tube formation in mice [].There is evidence of domain swapping within the jumonji family of transcription factors []. This domain is often associated with JmjC (see IPR003347 from INTERPRO).; PDB: 2XML_A 2W2I_C 3DXT_A 3DXU_A 2OX0_B 2OQ6_B 2WWJ_A 2Q8D_A 3PDQ_A 2YBK_A ....
Probab=22.00 E-value=62 Score=20.67 Aligned_cols=14 Identities=7% Similarity=0.380 Sum_probs=10.1
Q ss_pred CchhHHHHHHHHHh
Q 030062 158 SPREWDRFMRFMER 171 (183)
Q Consensus 158 s~~eWdRFMRFMeR 171 (183)
+.+||.-|+.|+++
T Consensus 6 t~eEF~dp~~yi~~ 19 (34)
T PF02375_consen 6 TMEEFKDPIKYISS 19 (34)
T ss_dssp -HHHHS-HHHHHHH
T ss_pred CHHHHhCHHHHHHH
Confidence 57889988888877
No 47
>PLN02825 amino-acid N-acetyltransferase
Probab=21.71 E-value=3.7e+02 Score=26.08 Aligned_cols=60 Identities=18% Similarity=0.404 Sum_probs=36.2
Q ss_pred ceeeEEEEecCceEEeEeceeEEEcCCcceeEEEEEe---cCchhHHHHHHHHHhhhhhcCcc
Q 030062 120 DITGFYMIDEEGTLQSVDVSAKFVNGRPSRIEAKYIM---RSPREWDRFMRFMERYANQNGLQ 179 (183)
Q Consensus 120 ~ItGMyLiDEEGeI~Tr~V~aKFvnGkp~~iEa~y~m---~s~~eWdRFMRFMeRYAe~NGL~ 179 (183)
+|..+|+++++|+|.--=.=..|...+--.|.|.|+- +..--=.+.|.+++++|+++|+.
T Consensus 405 ei~~f~V~e~Dg~IVG~aal~~~~~~~~aEI~~laV~P~yRGkGiG~~LL~~le~~Ar~~G~~ 467 (515)
T PLN02825 405 ALDSFVVVEREGSIIACAALFPFFEEKCGEVAAIAVSPECRGQGQGDKLLDYIEKKAASLGLE 467 (515)
T ss_pred cCCcEEEEEECCEEEEEEEEEeecCCCcEEEEEEEECHHHcCCCHHHHHHHHHHHHHHHCCCC
Confidence 5677888988898764321111221111226666652 12222267999999999999975
No 48
>KOG1378 consensus Purple acid phosphatase [Carbohydrate transport and metabolism]
Probab=21.59 E-value=49 Score=31.90 Aligned_cols=22 Identities=36% Similarity=0.619 Sum_probs=18.9
Q ss_pred EEEecCc-hhHHHHHHHHHhhhh
Q 030062 153 KYIMRSP-REWDRFMRFMERYAN 174 (183)
Q Consensus 153 ~y~m~s~-~eWdRFMRFMeRYAe 174 (183)
.|.+.-+ .-||-||||+|.-|.
T Consensus 185 sYa~~~~n~~wD~f~r~vEp~As 207 (452)
T KOG1378|consen 185 SYAMGYSNWQWDEFGRQVEPIAS 207 (452)
T ss_pred hhcCCCCccchHHHHhhhhhhhc
Confidence 5778777 699999999999875
No 49
>PRK13189 peroxiredoxin; Provisional
Probab=21.34 E-value=1.7e+02 Score=24.47 Aligned_cols=18 Identities=17% Similarity=0.575 Sum_probs=14.0
Q ss_pred ceeeEEEEecCceEEeEe
Q 030062 120 DITGFYMIDEEGTLQSVD 137 (183)
Q Consensus 120 ~ItGMyLiDEEGeI~Tr~ 137 (183)
.+-+.|+||.+|.|...-
T Consensus 125 ~~r~tfIID~~G~Ir~~~ 142 (222)
T PRK13189 125 TVRAVFIIDPKGIIRAIL 142 (222)
T ss_pred ceeEEEEECCCCeEEEEE
Confidence 466789999999887554
No 50
>PF14639 YqgF: Holliday-junction resolvase-like of SPT6 ; PDB: 3PSI_A 3PSF_A.
Probab=20.98 E-value=1.3e+02 Score=24.16 Aligned_cols=16 Identities=25% Similarity=0.368 Sum_probs=10.0
Q ss_pred ceeeEEEEecCceEEe
Q 030062 120 DITGFYMIDEEGTLQS 135 (183)
Q Consensus 120 ~ItGMyLiDEEGeI~T 135 (183)
+-+-..++|++|++.-
T Consensus 19 ~~~~~v~ld~~G~v~d 34 (150)
T PF14639_consen 19 DAVFCVVLDENGEVLD 34 (150)
T ss_dssp S-EEEEEE-TTS-EEE
T ss_pred CCEEEEEECCCCcEEE
Confidence 4455789999999864
No 51
>PRK05595 replicative DNA helicase; Provisional
Probab=20.83 E-value=89 Score=28.55 Aligned_cols=25 Identities=20% Similarity=0.449 Sum_probs=21.7
Q ss_pred CCCCeeEEeccCCCcceEEEEEcCC
Q 030062 85 TVPDVKLTKSRDGSNGMAIFSFSEP 109 (183)
Q Consensus 85 ~iPdVrLtRSrdG~~GtA~F~Fe~p 109 (183)
-+.++.+.++|+|.+|++.+.|+..
T Consensus 407 ~~~e~iv~K~R~G~~g~~~~~~~~~ 431 (444)
T PRK05595 407 NVAECIIAKQRNGPTGTVKLAWLGQ 431 (444)
T ss_pred CceEEEEEccCCCCCceEEEEEecC
Confidence 3678999999999999999999643
No 52
>KOG2792 consensus Putative cytochrome C oxidase assembly protein [Energy production and conversion]
Probab=20.60 E-value=55 Score=29.96 Aligned_cols=32 Identities=28% Similarity=0.328 Sum_probs=20.4
Q ss_pred EEEEcC-CcccccCCcccceeeEEEEecCceEE
Q 030062 103 IFSFSE-PSVFDSSGEIGDITGFYMIDEEGTLQ 134 (183)
Q Consensus 103 ~F~Fe~-p~a~~~~~~~~~ItGMyLiDEEGeI~ 134 (183)
-.+|.. |+-.+..=-..----|||||.||+++
T Consensus 223 RVYfs~gp~d~~~DYlVDHSi~mYLidPeg~Fv 255 (280)
T KOG2792|consen 223 RVYFSTGPKDEDQDYLVDHSIFMYLIDPEGEFV 255 (280)
T ss_pred EEeeccCCCCCCCCeeeeeeEEEEEECCCccee
Confidence 478888 77543321122234699999999875
No 53
>smart00091 PAS PAS domain. PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels ([1]; Ponting & Aravind, in press).
Probab=20.34 E-value=1.2e+02 Score=15.27 Aligned_cols=24 Identities=21% Similarity=0.475 Sum_probs=15.9
Q ss_pred eeEEEEecCceEEeEeceeEEEcC
Q 030062 122 TGFYMIDEEGTLQSVDVSAKFVNG 145 (183)
Q Consensus 122 tGMyLiDEEGeI~Tr~V~aKFvnG 145 (183)
.+++++|.+|.+...+-...-+.|
T Consensus 12 ~~~~~~~~~~~~~~~~~~~~~~~~ 35 (67)
T smart00091 12 DGIFVLDLDGRILYANPAAEELLG 35 (67)
T ss_pred ceEEEEcCCCeEEEECHHHHHHhC
Confidence 578899999988765444433334
No 54
>cd03014 PRX_Atyp2cys Peroxiredoxin (PRX) family, Atypical 2-cys PRX subfamily; composed of PRXs containing peroxidatic and resolving cysteines, similar to the homodimeric thiol specific antioxidant (TSA) protein also known as TRX-dependent thiol peroxidase (Tpx). Tpx is a bacterial periplasmic peroxidase which differs from other PRXs in that it shows substrate specificity toward alkyl hydroperoxides over hydrogen peroxide. As with all other PRXs, the peroxidatic cysteine (N-terminal) of Tpx is oxidized into a sulfenic acid intermediate upon reaction with peroxides. Tpx is able to resolve this intermediate by forming an intramolecular disulfide bond with a conserved C-terminal cysteine (the resolving cysteine), which can then be reduced by thioredoxin. This differs from the typical 2-cys PRX which resolves the oxidized cysteine by forming an intermolecular disulfide bond with the resolving cysteine from the other subunit of the homodimer. Atypical 2-cys PRX homodimers have a loop-based
Probab=20.31 E-value=1e+02 Score=22.62 Aligned_cols=20 Identities=25% Similarity=0.524 Sum_probs=16.3
Q ss_pred eeeEEEEecCceEEeEecee
Q 030062 121 ITGFYMIDEEGTLQSVDVSA 140 (183)
Q Consensus 121 ItGMyLiDEEGeI~Tr~V~a 140 (183)
+.+.|+||++|.|.-..+..
T Consensus 110 ~~~~~iid~~G~I~~~~~~~ 129 (143)
T cd03014 110 ARAVFVIDENGKVIYVELVP 129 (143)
T ss_pred ceEEEEEcCCCeEEEEEECC
Confidence 45789999999998887654
Done!