Query 028962
Match_columns 201
No_of_seqs 93 out of 102
Neff 2.7
Searched_HMMs 46136
Date Fri Mar 29 05:17:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028962.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028962hhsearch_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 1.6E-65 3.4E-70 402.4 13.0 111 73-183 1-111 (111)
2 PRK13612 photosystem II reacti 100.0 2.7E-65 5.8E-70 402.1 13.3 112 71-183 2-113 (113)
3 CHL00128 psbW photosystem II p 100.0 2.4E-65 5.1E-70 402.4 12.8 112 72-183 1-113 (113)
4 TIGR03047 PS_II_psb28 photosys 100.0 7.7E-64 1.7E-68 391.8 11.8 108 75-182 1-109 (109)
5 PF03912 Psb28: Psb28 protein; 100.0 1.9E-63 4.1E-68 389.0 11.0 107 75-181 1-108 (108)
6 PRK13611 photosystem II reacti 100.0 6.7E-62 1.5E-66 378.4 12.9 104 72-181 1-104 (104)
7 PRK13610 photosystem II reacti 100.0 2.1E-60 4.6E-65 374.4 13.0 104 72-176 7-110 (113)
8 PF11497 NADH_Oxid_Nqo15: NADH 83.2 0.79 1.7E-05 37.8 1.9 33 160-192 11-51 (127)
9 TIGR02447 yiiD_Cterm thioester 80.5 4.7 0.0001 31.6 5.3 46 130-175 67-112 (138)
10 PF08722 Tn7_Tnp_TnsA_N: TnsA 78.9 2.5 5.4E-05 30.5 3.1 55 128-182 27-85 (88)
11 PRK13795 hypothetical protein; 64.4 4.8 0.0001 39.4 2.3 22 158-179 431-452 (636)
12 PF04320 DUF469: Protein with 60.1 10 0.00022 30.0 3.0 34 150-184 19-54 (101)
13 TIGR02034 CysN sulfate adenyly 54.5 33 0.00072 31.4 5.8 66 68-133 333-400 (406)
14 cd04095 CysN_NoDQ_III TCysN_No 53.5 20 0.00043 26.3 3.5 36 95-130 58-93 (103)
15 cd04480 RPA1_DBD_A_like RPA1_D 52.6 16 0.00036 26.0 2.9 17 118-134 17-34 (86)
16 cd03705 EF1_alpha_III Domain I 46.1 34 0.00073 24.9 3.7 35 95-129 61-95 (104)
17 PF12132 DUF3587: Protein of u 45.4 16 0.00034 31.9 2.1 25 132-156 56-80 (199)
18 PHA02552 4 head completion pro 44.2 21 0.00046 29.9 2.6 59 123-181 51-135 (151)
19 PF09500 YiiD_Cterm: Putative 42.0 18 0.00038 29.8 1.8 45 130-174 73-117 (144)
20 PF02375 JmjN: jmjN domain; I 41.3 20 0.00044 23.2 1.7 23 158-181 6-28 (34)
21 PF15496 DUF4646: Domain of un 40.2 18 0.00039 28.7 1.6 34 139-174 26-64 (123)
22 cd08815 Death_TNFRSF25_DR3 Dea 39.9 20 0.00042 27.4 1.7 18 152-169 4-21 (77)
23 PRK13794 hypothetical protein; 37.4 24 0.00053 33.6 2.3 22 158-179 435-456 (479)
24 cd01513 Translation_factor_III 35.0 48 0.001 23.5 3.0 35 96-130 60-94 (102)
25 PRK11702 hypothetical protein; 34.8 45 0.00097 26.8 3.0 34 151-184 26-61 (108)
26 PRK05474 xylose isomerase; Pro 33.4 25 0.00054 34.2 1.7 47 143-189 185-234 (437)
27 smart00545 JmjN Small domain f 33.3 22 0.00049 23.9 1.0 24 158-182 8-31 (42)
28 PF14874 PapD-like: Flagellar- 32.6 1.5E+02 0.0032 21.2 5.2 40 97-142 62-101 (102)
29 PF14307 Glyco_tran_WbsX: Glyc 31.1 59 0.0013 29.2 3.5 42 143-186 156-198 (345)
30 PF14524 Wzt_C: Wzt C-terminal 31.0 75 0.0016 23.1 3.5 34 119-157 13-46 (142)
31 TIGR02630 xylose_isom_A xylose 30.5 35 0.00076 33.2 2.1 48 143-190 184-234 (434)
32 PF14810 TGT_C2: Patch-forming 29.8 33 0.00071 25.3 1.4 29 73-101 8-38 (74)
33 cd02967 mauD Methylamine utili 28.9 49 0.0011 23.4 2.2 19 119-137 94-112 (114)
34 PF03799 FtsQ: Cell division p 28.9 38 0.00082 24.1 1.6 15 122-136 8-22 (117)
35 PF03796 DnaB_C: DnaB-like hel 27.7 53 0.0011 27.5 2.5 24 87-110 228-251 (259)
36 PF05549 Allexi_40kDa: Allexiv 27.4 56 0.0012 30.2 2.8 10 41-50 185-194 (271)
37 cd00984 DnaB_C DnaB helicase C 27.3 58 0.0013 26.4 2.6 22 86-107 220-241 (242)
38 PF13088 BNR_2: BNR repeat-lik 26.3 1.4E+02 0.003 24.4 4.6 54 77-136 7-64 (275)
39 PF13535 ATP-grasp_4: ATP-gras 25.0 61 0.0013 24.4 2.2 19 125-143 162-180 (184)
40 TIGR01628 PABP-1234 polyadenyl 23.4 2.4E+02 0.0051 26.5 6.1 78 39-128 64-156 (562)
41 PF03750 DUF310: Protein of un 23.2 52 0.0011 25.7 1.6 15 157-171 93-107 (119)
42 PRK12338 hypothetical protein; 23.2 1.4E+02 0.003 27.6 4.5 43 127-172 227-269 (319)
43 cd02966 TlpA_like_family TlpA- 23.0 1.1E+02 0.0023 20.4 2.9 18 119-136 96-113 (116)
44 COG3171 Uncharacterized protei 22.3 47 0.001 27.4 1.2 22 159-183 47-68 (119)
45 PF14639 YqgF: Holliday-juncti 22.1 1.3E+02 0.0028 24.6 3.7 16 120-135 19-34 (150)
46 PF14259 RRM_6: RNA recognitio 22.0 55 0.0012 21.4 1.3 27 86-112 25-52 (70)
47 PF00989 PAS: PAS fold; Inter 21.9 94 0.002 20.7 2.5 28 120-147 10-37 (113)
48 PRK13189 peroxiredoxin; Provis 21.7 1.8E+02 0.0039 24.7 4.6 18 120-137 125-142 (222)
49 PF08448 PAS_4: PAS fold; Int 21.4 34 0.00074 22.8 0.2 55 122-176 6-63 (110)
50 PRK14681 hypothetical protein; 21.1 1.6E+02 0.0035 24.7 4.2 58 118-180 73-130 (158)
51 PF10126 Nit_Regul_Hom: Unchar 20.6 36 0.00078 27.7 0.2 21 110-131 18-38 (110)
52 PRK05595 replicative DNA helic 20.5 91 0.002 28.8 2.8 25 85-109 407-431 (444)
53 KOG1378 Purple acid phosphatas 20.4 53 0.0011 32.1 1.3 23 152-174 184-207 (452)
54 COG3906 Uncharacterized protei 20.4 93 0.002 25.2 2.5 36 126-163 52-89 (105)
55 PF00703 Glyco_hydro_2: Glycos 20.3 3E+02 0.0064 18.9 6.4 73 87-163 4-80 (110)
56 KOG3697 Adaptor protein SHC an 20.1 62 0.0013 30.7 1.6 20 119-138 290-309 (345)
No 1
>PLN00039 photosystem II reaction center Psb28 protein; Provisional
Probab=100.00 E-value=1.6e-65 Score=402.38 Aligned_cols=111 Identities=74% Similarity=1.172 Sum_probs=107.2
Q ss_pred ceeEeecCCCCCCCCCeeEEeccCCCcceEEEEEcCCcccccCCccCceeeEEEEecCceEEeEeceeeEEcCccceEEE
Q 028962 73 PTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEIGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRIEA 152 (201)
Q Consensus 73 asIQFi~GidEe~iPdVrLTRSrdG~~GtA~F~Fe~Pkal~s~t~~g~ITGMyLIDEEGeI~Tr~V~aKFvNGkP~~IEa 152 (201)
|+||||+||||++||||||||||||++|+|+|+|++|++|+++..+++|||||||||||||+|+|||+|||||||++|||
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 68999999999999999999999999999999999999998864479999999999999999999999999999999999
Q ss_pred EEEeCCchhhHHHHHHHHhhhHhcCCchhhh
Q 028962 153 KYIMRSPREWDRFMRFMERQMVKALLDSHLS 183 (201)
Q Consensus 153 ~y~m~s~~eWdRFMRFMeRYAe~NGLg~~~~ 183 (201)
+|+|+|++|||||||||||||++|||+|..+
T Consensus 81 ~y~m~s~~~WdRFMRFMeRYA~~ngl~f~k~ 111 (111)
T PLN00039 81 KYVMRSPREWDRFMRFMERYAEENGLGFVKK 111 (111)
T ss_pred EEEECCHHHHHHHHHHHHHHHHhcCCccccC
Confidence 9999999999999999999999999999863
No 2
>PRK13612 photosystem II reaction center protein Psb28; Provisional
Probab=100.00 E-value=2.7e-65 Score=402.06 Aligned_cols=112 Identities=52% Similarity=0.859 Sum_probs=107.9
Q ss_pred eeceeEeecCCCCCCCCCeeEEeccCCCcceEEEEEcCCcccccCCccCceeeEEEEecCceEEeEeceeeEEcCccceE
Q 028962 71 VKPTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEIGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRI 150 (201)
Q Consensus 71 ~~asIQFi~GidEe~iPdVrLTRSrdG~~GtA~F~Fe~Pkal~s~t~~g~ITGMyLIDEEGeI~Tr~V~aKFvNGkP~~I 150 (201)
++|+||||+||||++||||||||||||++|+|+|+|++|++|++.. +++|||||||||||||+|+||++|||||||++|
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 KMAAIQFSRGVDEPVVPDIRLTRSRDGRTGQATFYFEQPQALAPET-TGEITGMYMIDEEGEIVTREVKAKFVNGKPSAL 80 (113)
T ss_pred CcceEEEecCCCCCcCCceEEEEccCCCeeEEEEEECCccccCccc-cCceeeEEEEccCccEEEEecceEEECCCccEE
Confidence 4599999999999999999999999999999999999999998854 699999999999999999999999999999999
Q ss_pred EEEEEeCCchhhHHHHHHHHhhhHhcCCchhhh
Q 028962 151 EAKYIMRSPREWDRFMRFMERQMVKALLDSHLS 183 (201)
Q Consensus 151 Ea~y~m~s~~eWdRFMRFMeRYAe~NGLg~~~~ 183 (201)
||+|+|+|++|||||||||||||++|||+|+.+
T Consensus 81 Ea~y~m~s~~~WdRFMRFMeRYA~~ngl~f~~~ 113 (113)
T PRK13612 81 EATYIWKSEQEWDRFMRFMERYAKENGLGFSKS 113 (113)
T ss_pred EEEEEECCHHHHHHHHHHHHHHHHhcCCccccC
Confidence 999999999999999999999999999999864
No 3
>CHL00128 psbW photosystem II protein W; Reviewed
Probab=100.00 E-value=2.4e-65 Score=402.37 Aligned_cols=112 Identities=54% Similarity=0.940 Sum_probs=107.5
Q ss_pred eceeEeecCCCCCCCCCeeEEeccCCCcceEEEEEcCCcccccC-CccCceeeEEEEecCceEEeEeceeeEEcCccceE
Q 028962 72 KPTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSS-GEIGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRI 150 (201)
Q Consensus 72 ~asIQFi~GidEe~iPdVrLTRSrdG~~GtA~F~Fe~Pkal~s~-t~~g~ITGMyLIDEEGeI~Tr~V~aKFvNGkP~~I 150 (201)
+|+||||+||||++||||||||||||++|+|+|+|++|++|+++ ...++|||||||||||||+|+|||+|||||||++|
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 48999999999999999999999999999999999999999875 34699999999999999999999999999999999
Q ss_pred EEEEEeCCchhhHHHHHHHHhhhHhcCCchhhh
Q 028962 151 EAKYIMRSPREWDRFMRFMERQMVKALLDSHLS 183 (201)
Q Consensus 151 Ea~y~m~s~~eWdRFMRFMeRYAe~NGLg~~~~ 183 (201)
||+|+|+|++|||||||||||||++|||+|..+
T Consensus 81 Ea~y~m~s~~~WdRFMRFMeRYA~~ngl~f~~~ 113 (113)
T CHL00128 81 EAIYIMKNPEAWDRFMRFMERYAEDNGLTFTKA 113 (113)
T ss_pred EEEEEECCHHHHHHHHHHHHHHHHhcCCccccC
Confidence 999999999999999999999999999999863
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=7.7e-64 Score=391.81 Aligned_cols=108 Identities=53% Similarity=0.921 Sum_probs=104.1
Q ss_pred eEeecCCCCCCCCCeeEEeccCCCcceEEEEEcCCcccccCC-ccCceeeEEEEecCceEEeEeceeeEEcCccceEEEE
Q 028962 75 IQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSG-EIGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRIEAK 153 (201)
Q Consensus 75 IQFi~GidEe~iPdVrLTRSrdG~~GtA~F~Fe~Pkal~s~t-~~g~ITGMyLIDEEGeI~Tr~V~aKFvNGkP~~IEa~ 153 (201)
||||+||||++||||||||||||++|+|+|+|++|++|++++ .+++|||||||||||||+|+|||+|||||||++|||+
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 899999999999999999999999999999999999998753 3589999999999999999999999999999999999
Q ss_pred EEeCCchhhHHHHHHHHhhhHhcCCchhh
Q 028962 154 YIMRSPREWDRFMRFMERQMVKALLDSHL 182 (201)
Q Consensus 154 y~m~s~~eWdRFMRFMeRYAe~NGLg~~~ 182 (201)
|+|+|++|||||||||||||++|||+|++
T Consensus 81 y~m~s~~~WdRFMRFmeRYA~~ngl~f~~ 109 (109)
T TIGR03047 81 YIMKSEDEWDRFMRFMERYAEANGLGYSK 109 (109)
T ss_pred EEECCHHHHHHHHHHHHHHHHhcCCcccC
Confidence 99999999999999999999999999973
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=1.9e-63 Score=389.03 Aligned_cols=107 Identities=56% Similarity=0.935 Sum_probs=81.5
Q ss_pred eEeecCCCCCCCCCeeEEeccCCCcceEEEEEcCCcccccCCc-cCceeeEEEEecCceEEeEeceeeEEcCccceEEEE
Q 028962 75 IQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGE-IGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRIEAK 153 (201)
Q Consensus 75 IQFi~GidEe~iPdVrLTRSrdG~~GtA~F~Fe~Pkal~s~t~-~g~ITGMyLIDEEGeI~Tr~V~aKFvNGkP~~IEa~ 153 (201)
||||+||||+++|||||||||||++|+|+|+|++|++|++++. .|+|||||||||||||+|+||++|||||||++|||+
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 8999999999999999999999999999999999999987753 579999999999999999999999999999999999
Q ss_pred EEeCCchhhHHHHHHHHhhhHhcCCchh
Q 028962 154 YIMRSPREWDRFMRFMERQMVKALLDSH 181 (201)
Q Consensus 154 y~m~s~~eWdRFMRFMeRYAe~NGLg~~ 181 (201)
|+|+|++|||||||||||||++|||+|+
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 9999999999999999999999999995
No 6
>PRK13611 photosystem II reaction center protein Psb28; Provisional
Probab=100.00 E-value=6.7e-62 Score=378.42 Aligned_cols=104 Identities=39% Similarity=0.668 Sum_probs=100.5
Q ss_pred eceeEeecCCCCCCCCCeeEEeccCCCcceEEEEEcCCcccccCCccCceeeEEEEecCceEEeEeceeeEEcCccceEE
Q 028962 72 KPTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEIGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRIE 151 (201)
Q Consensus 72 ~asIQFi~GidEe~iPdVrLTRSrdG~~GtA~F~Fe~Pkal~s~t~~g~ITGMyLIDEEGeI~Tr~V~aKFvNGkP~~IE 151 (201)
+|+||||+||||+ +|||||||||||++|+|+|+|++|++ .+++|||||||||||||+|+||++|||||||++||
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 4899999999999 99999999999999999999999998 24899999999999999999999999999999999
Q ss_pred EEEEeCCchhhHHHHHHHHhhhHhcCCchh
Q 028962 152 AKYIMRSPREWDRFMRFMERQMVKALLDSH 181 (201)
Q Consensus 152 a~y~m~s~~eWdRFMRFMeRYAe~NGLg~~ 181 (201)
|+|+|+|++|||||||||||||++|||+|.
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=2.1e-60 Score=374.44 Aligned_cols=104 Identities=25% Similarity=0.547 Sum_probs=100.6
Q ss_pred eceeEeecCCCCCCCCCeeEEeccCCCcceEEEEEcCCcccccCCccCceeeEEEEecCceEEeEeceeeEEcCccceEE
Q 028962 72 KPTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEIGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRIE 151 (201)
Q Consensus 72 ~asIQFi~GidEe~iPdVrLTRSrdG~~GtA~F~Fe~Pkal~s~t~~g~ITGMyLIDEEGeI~Tr~V~aKFvNGkP~~IE 151 (201)
.|+||||+||||++||||||||||||++|+|+|+|++|++|++. .+++|||||||||||||+|+||++|||||||++||
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 58999999999999999999999999999999999999999885 36999999999999999999999999999999999
Q ss_pred EEEEeCCchhhHHHHHHHHhhhHhc
Q 028962 152 AKYIMRSPREWDRFMRFMERQMVKA 176 (201)
Q Consensus 152 a~y~m~s~~eWdRFMRFMeRYAe~N 176 (201)
|+|+|+|++|||||||||||||++.
T Consensus 86 a~y~m~s~~~WdRFMRFMeRYA~~~ 110 (113)
T PRK13610 86 STYNWNSEEAFERFMRFASRYANSL 110 (113)
T ss_pred EEEEECCHHHHHHHHHHHHHHHHHh
Confidence 9999999999999999999999974
No 8
>PF11497 NADH_Oxid_Nqo15: NADH-quinone oxidoreductase chain 15; InterPro: IPR021093 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This entry represents subunit 15 of NADH-quinone oxidoreductase, also known as Complex I. The nqo15 subunit has probably a role in complex stabilisation, and may be also involved in the storage of iron for iron-sulphur cluster regeneration in the complex [].; PDB: 3M9S_7 3I9V_7 3IAM_H 2FUG_H 3IAS_7 2YBB_7.
Probab=83.24 E-value=0.79 Score=37.80 Aligned_cols=33 Identities=21% Similarity=0.440 Sum_probs=23.4
Q ss_pred hhhHHHHHHHHhhhHhcCCchhhhh--------cccceecc
Q 028962 160 REWDRFMRFMERQMVKALLDSHLSL--------MQKPYALF 192 (201)
Q Consensus 160 ~eWdRFMRFMeRYAe~NGLg~~~~~--------~~~~~~~~ 192 (201)
+.|-..+-+|+-||+++|+.|..-+ |.+||-|=
T Consensus 11 ~aWvell~Wl~eyA~~~g~~fekeaDFPDyIYRMeRPydLP 51 (127)
T PF11497_consen 11 RAWVELLGWLREYAAERGLRFEKEADFPDYIYRMERPYDLP 51 (127)
T ss_dssp HHHHHHHHHHHHHHHHTT-EEEEEEE-HHHHT--SS----S
T ss_pred HHHHHHHHHHHHHHHHcCCceeecccccHHHHhccCcccCC
Confidence 5799999999999999999997654 88898763
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=80.49 E-value=4.7 Score=31.58 Aligned_cols=46 Identities=13% Similarity=0.263 Sum_probs=38.4
Q ss_pred CceEEeEeceeeEEcCccceEEEEEEeCCchhhHHHHHHHHhhhHh
Q 028962 130 EGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMERQMVK 175 (201)
Q Consensus 130 EGeI~Tr~V~aKFvNGkP~~IEa~y~m~s~~eWdRFMRFMeRYAe~ 175 (201)
++.++|.+.+.+|+.---.++.|..+...+++||+|.+=++|-...
T Consensus 67 ~~~~vt~~~~i~yl~P~~~~~~a~~~~~~~~~~~~~~~~l~~~gr~ 112 (138)
T TIGR02447 67 DGDIVIADSHIRYLAPVTGDPVANCEAPDLESWEAFLATLQRGGKA 112 (138)
T ss_pred CCcEEEEEeeeEEcCCcCCCeEEEEEcCCHHHHHHHHHHHHhCCce
Confidence 3589999999999964445699999999999999999988885544
No 10
>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=78.95 E-value=2.5 Score=30.46 Aligned_cols=55 Identities=11% Similarity=0.097 Sum_probs=33.4
Q ss_pred ecCceEEeEeceeeEEcC---ccceEEEEEEeCCch-hhHHHHHHHHhhhHhcCCchhh
Q 028962 128 DEEGTLQSVDVSAKFVNG---RPSRIEAKYIMRSPR-EWDRFMRFMERQMVKALLDSHL 182 (201)
Q Consensus 128 DEEGeI~Tr~V~aKFvNG---kP~~IEa~y~m~s~~-eWdRFMRFMeRYAe~NGLg~~~ 182 (201)
+.....-|.|.=+.+-+| ++..+|+++.-+-.. .+..=.....+|++++|..|+.
T Consensus 27 ~~~~~~yTpDFlv~~~~g~~~~~~~ieVK~~~~l~~~~~~~k~~~~~~y~~~~g~~f~i 85 (88)
T PF08722_consen 27 TGVPIVYTPDFLVTYRDGNGKKPVAIEVKPSSELEKPRTKEKLEIEREYWEEQGIPFRI 85 (88)
T ss_dssp TTEE---EEEEEEEESSS--SSEEEEEE--GGGGGSHHHHHHHHHHHHHHHHCT--EEE
T ss_pred CCCccEEeccEEEEEccCCcceEEEEEEccHHHhcChhHHHHHHHHHHHHHHcCCeEEE
Confidence 555566788888888898 888888888655444 2323334566899999988763
No 11
>PRK13795 hypothetical protein; Provisional
Probab=64.45 E-value=4.8 Score=39.44 Aligned_cols=22 Identities=14% Similarity=0.344 Sum_probs=20.5
Q ss_pred CchhhHHHHHHHHhhhHhcCCc
Q 028962 158 SPREWDRFMRFMERQMVKALLD 179 (201)
Q Consensus 158 s~~eWdRFMRFMeRYAe~NGLg 179 (201)
-|+.|+|+++|+++||+.+|+.
T Consensus 431 ~Pe~~~~~~~~l~~~~~~~g~~ 452 (636)
T PRK13795 431 HPELYEKWEAFLLKWAKRNGLS 452 (636)
T ss_pred CHHHHHHHHHHHHHHHHHcCCC
Confidence 6899999999999999999983
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=60.10 E-value=10 Score=30.00 Aligned_cols=34 Identities=15% Similarity=0.196 Sum_probs=28.0
Q ss_pred EEEEEEe-CCchhhHHHH-HHHHhhhHhcCCchhhhh
Q 028962 150 IEAKYIM-RSPREWDRFM-RFMERQMVKALLDSHLSL 184 (201)
Q Consensus 150 IEa~y~m-~s~~eWdRFM-RFMeRYAe~NGLg~~~~~ 184 (201)
+.|+|.- .++++.|+|+ +|.+ |-++|||.|+-+-
T Consensus 19 v~~~~~~~~~~e~~D~~~D~fId-~Ie~~gL~~~Ggg 54 (101)
T PF04320_consen 19 VSCRFAEGTSEEQIDAFVDAFID-VIEPNGLAFGGGG 54 (101)
T ss_pred EEEEECCCCCHHHHHHHHHHHHH-HHHhCCCEEecCC
Confidence 5666666 6789999999 5777 9999999999865
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=54.48 E-value=33 Score=31.36 Aligned_cols=66 Identities=23% Similarity=0.252 Sum_probs=44.8
Q ss_pred eeceeceeEeecC-CCCCCCCCeeEEeccCCCcceEEEEEcCCcccccCCccCceeeEEEEec-CceE
Q 028962 68 TMAVKPTIQFIQG-TDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEIGDITGFYMIDE-EGTL 133 (201)
Q Consensus 68 ~~~~~asIQFi~G-idEe~iPdVrLTRSrdG~~GtA~F~Fe~Pkal~s~t~~g~ITGMyLIDE-EGeI 133 (201)
+....++|.++.. +|..+--.++-..=+.|..+.|.+.+++|=.++.+++.....++.|+|. +|+.
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 3445677777754 2332221122222347899999999999999988877789999999994 5554
No 14
>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=53.54 E-value=20 Score=26.27 Aligned_cols=36 Identities=28% Similarity=0.324 Sum_probs=30.6
Q ss_pred cCCCcceEEEEEcCCcccccCCccCceeeEEEEecC
Q 028962 95 RDGSNGMAIFSFSEPSVFDSSGEIGDITGFYMIDEE 130 (201)
Q Consensus 95 rdG~~GtA~F~Fe~Pkal~s~t~~g~ITGMyLIDEE 130 (201)
+.|..+.+.+.+++|=.++.+.+......+.|||.+
T Consensus 58 ~~n~~a~v~i~~~~pi~~d~~~~~~~~GrfiliD~~ 93 (103)
T cd04095 58 ELNDIGRVELSLSKPLAFDPYRENRATGSFILIDRL 93 (103)
T ss_pred CCCCeEEEEEEeCCccEecchhhCCCcceEEEEECC
Confidence 458899999999999999988776777889999963
No 15
>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=52.58 E-value=16 Score=26.02 Aligned_cols=17 Identities=24% Similarity=0.587 Sum_probs=13.8
Q ss_pred cCceeeEEEEecCc-eEE
Q 028962 118 IGDITGFYMIDEEG-TLQ 134 (201)
Q Consensus 118 ~g~ITGMyLIDEEG-eI~ 134 (201)
.+....|.|+||+| .|.
T Consensus 17 ~~~~~~miL~De~G~~I~ 34 (86)
T cd04480 17 SGESLEMVLVDEKGNRIH 34 (86)
T ss_pred CCcEEEEEEEcCCCCEEE
Confidence 47888999999999 443
No 16
>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=46.13 E-value=34 Score=24.85 Aligned_cols=35 Identities=17% Similarity=0.263 Sum_probs=30.2
Q ss_pred cCCCcceEEEEEcCCcccccCCccCceeeEEEEec
Q 028962 95 RDGSNGMAIFSFSEPSVFDSSGEIGDITGFYMIDE 129 (201)
Q Consensus 95 rdG~~GtA~F~Fe~Pkal~s~t~~g~ITGMyLIDE 129 (201)
+-|..+.+.+.+++|=.++++.+......+.|+|+
T Consensus 61 ~~n~~a~v~l~~~~pi~~e~~~~~~~lgrf~lrd~ 95 (104)
T cd03705 61 KSGDAAIVKIVPQKPLVVETFSEYPPLGRFAVRDM 95 (104)
T ss_pred CCCCEEEEEEEECCeeEEEEcccCCCccCEEEEeC
Confidence 45889999999999998998876778888999995
No 17
>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=45.43 E-value=16 Score=31.90 Aligned_cols=25 Identities=28% Similarity=0.563 Sum_probs=20.9
Q ss_pred eEEeEeceeeEEcCccceEEEEEEe
Q 028962 132 TLQSVDVSAKFVNGRPSRIEAKYIM 156 (201)
Q Consensus 132 eI~Tr~V~aKFvNGkP~~IEa~y~m 156 (201)
.++|+...++|+|||+-.||=.|.=
T Consensus 56 ~lSt~~~~ttF~NGK~L~IeYnfDp 80 (199)
T PF12132_consen 56 RLSTHKITTTFLNGKPLEIEYNFDP 80 (199)
T ss_pred hcccceEEEEEECCcEEEEEEecCC
Confidence 3789999999999999888776653
No 18
>PHA02552 4 head completion protein; Provisional
Probab=44.19 E-value=21 Score=29.87 Aligned_cols=59 Identities=19% Similarity=0.118 Sum_probs=39.4
Q ss_pred eEEEEe-cCceEE--eEeceeeEEcCccceEEEEEEeCCch----------hhHHHH-------------HHHHhhhHhc
Q 028962 123 GFYMID-EEGTLQ--SVDVSAKFVNGRPSRIEAKYIMRSPR----------EWDRFM-------------RFMERQMVKA 176 (201)
Q Consensus 123 GMyLID-EEGeI~--Tr~V~aKFvNGkP~~IEa~y~m~s~~----------eWdRFM-------------RFMeRYAe~N 176 (201)
.+.-+| .+|... +-|.=+++.+|++.-||.+..-+..+ .|.||| .-..+||+++
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 333355 346433 45666888889888888887765542 366666 3467888999
Q ss_pred CCchh
Q 028962 177 LLDSH 181 (201)
Q Consensus 177 GLg~~ 181 (201)
|..|.
T Consensus 131 Gw~F~ 135 (151)
T PHA02552 131 GWKFK 135 (151)
T ss_pred CCEEE
Confidence 99885
No 19
>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=42.05 E-value=18 Score=29.76 Aligned_cols=45 Identities=18% Similarity=0.491 Sum_probs=21.5
Q ss_pred CceEEeEeceeeEEcCccceEEEEEEeCCchhhHHHHHHHHhhhH
Q 028962 130 EGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMERQMV 174 (201)
Q Consensus 130 EGeI~Tr~V~aKFvNGkP~~IEa~y~m~s~~eWdRFMRFMeRYAe 174 (201)
+|.|+..+.+.++..==...+.|+-.+..+++|++|.+=..|..+
T Consensus 73 ~~~IVi~~~~i~Y~~Pv~~d~~A~~~~~~~~~~~~~~~~l~~~gr 117 (144)
T PF09500_consen 73 NGDIVIADSNIRYLKPVTGDFTARCSLPEPEDWERFLQTLARGGR 117 (144)
T ss_dssp --EEEEEEEEEEE-S---S--EEEEE-------S---GGGGCTS-
T ss_pred CCcEEEEeCceEEcCCCCCCcEEEEeccccchhHHHHHHHHcCCc
Confidence 499999999999986555668889999999999998876665443
No 20
>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=41.26 E-value=20 Score=23.23 Aligned_cols=23 Identities=4% Similarity=0.088 Sum_probs=15.7
Q ss_pred CchhhHHHHHHHHhhhHhcCCchh
Q 028962 158 SPREWDRFMRFMERQMVKALLDSH 181 (201)
Q Consensus 158 s~~eWdRFMRFMeRYAe~NGLg~~ 181 (201)
+.+||.-|+.|+++ -+..|..||
T Consensus 6 t~eEF~dp~~yi~~-i~~~g~~~G 28 (34)
T PF02375_consen 6 TMEEFKDPIKYISS-IEPEGEKYG 28 (34)
T ss_dssp -HHHHS-HHHHHHH-HHHTTGGGS
T ss_pred CHHHHhCHHHHHHH-HHHHHHHCC
Confidence 67899999999998 444565554
No 21
>PF15496 DUF4646: Domain of unknown function (DUF4646)
Probab=40.22 E-value=18 Score=28.67 Aligned_cols=34 Identities=24% Similarity=0.430 Sum_probs=24.3
Q ss_pred eeeEEcCccc-----eEEEEEEeCCchhhHHHHHHHHhhhH
Q 028962 139 SAKFVNGRPS-----RIEAKYIMRSPREWDRFMRFMERQMV 174 (201)
Q Consensus 139 ~aKFvNGkP~-----~IEa~y~m~s~~eWdRFMRFMeRYAe 174 (201)
+.++.+|=|. -+ +.|.+ +++||-||+..+..=|.
T Consensus 26 s~~l~~gFp~~~~P~~l-~~~DV-s~eDW~~F~~dl~~aa~ 64 (123)
T PF15496_consen 26 SDSLSSGFPYLYPPPPL-ASHDV-SEEDWTRFLNDLSEAAS 64 (123)
T ss_pred CCccccCCCCcCCCchh-hhcCC-CHHHHHHHHHHHHHHHh
Confidence 4445566443 45 78888 89999999999887543
No 22
>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=39.93 E-value=20 Score=27.36 Aligned_cols=18 Identities=28% Similarity=0.534 Sum_probs=14.4
Q ss_pred EEEEeCCchhhHHHHHHH
Q 028962 152 AKYIMRSPREWDRFMRFM 169 (201)
Q Consensus 152 a~y~m~s~~eWdRFMRFM 169 (201)
+.++.-..+.|++|||.+
T Consensus 4 ~v~D~VP~~~wk~F~R~L 21 (77)
T cd08815 4 AVMDAVPARRWKEFVRTL 21 (77)
T ss_pred eeeccCChHHHHHHHHHc
Confidence 455666789999999986
No 23
>PRK13794 hypothetical protein; Provisional
Probab=37.42 E-value=24 Score=33.57 Aligned_cols=22 Identities=23% Similarity=0.495 Sum_probs=20.1
Q ss_pred CchhhHHHHHHHHhhhHhcCCc
Q 028962 158 SPREWDRFMRFMERQMVKALLD 179 (201)
Q Consensus 158 s~~eWdRFMRFMeRYAe~NGLg 179 (201)
-|+.|++|.+|.++||+.+|+.
T Consensus 435 ~Pe~~~~w~~~l~~~~~~~g~~ 456 (479)
T PRK13794 435 YPELWEKWENFLKAWAKKHGLS 456 (479)
T ss_pred CHHHHHHHHHHHHHHHHhcCCC
Confidence 5789999999999999999995
No 24
>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=35.01 E-value=48 Score=23.50 Aligned_cols=35 Identities=17% Similarity=0.311 Sum_probs=26.2
Q ss_pred CCCcceEEEEEcCCcccccCCccCceeeEEEEecC
Q 028962 96 DGSNGMAIFSFSEPSVFDSSGEIGDITGFYMIDEE 130 (201)
Q Consensus 96 dG~~GtA~F~Fe~Pkal~s~t~~g~ITGMyLIDEE 130 (201)
.|..+.+.+.|++|-.++.+.+......+.|+|.-
T Consensus 60 ~~~~a~v~l~~~~pi~~e~~~~~~~~grfilr~~~ 94 (102)
T cd01513 60 SGERGIVEVELQKPVALETFSENQEGGRFALRDGG 94 (102)
T ss_pred CCCEEEEEEEECCceEEEEhhhCCCcccEEEEeCC
Confidence 48999999999999988877655555555565553
No 25
>PRK11702 hypothetical protein; Provisional
Probab=34.79 E-value=45 Score=26.84 Aligned_cols=34 Identities=15% Similarity=0.064 Sum_probs=25.3
Q ss_pred EEEEEe-CCchhhHHHH-HHHHhhhHhcCCchhhhh
Q 028962 151 EAKYIM-RSPREWDRFM-RFMERQMVKALLDSHLSL 184 (201)
Q Consensus 151 Ea~y~m-~s~~eWdRFM-RFMeRYAe~NGLg~~~~~ 184 (201)
.++|.- .++++-|.|+ +|.+.+-++|||.|+-+-
T Consensus 26 ~~~~~~~~~~e~~D~~vD~fIde~Ie~ngL~f~G~G 61 (108)
T PRK11702 26 NWRFPEGTSEEQIDATVDAFIDEVIEPNGLAFDGSG 61 (108)
T ss_pred EEEECCCCCHHHHHHHHHHHHHHHHhcCCceecCCc
Confidence 334433 4567788888 577889999999999875
No 26
>PRK05474 xylose isomerase; Provisional
Probab=33.43 E-value=25 Score=34.15 Aligned_cols=47 Identities=19% Similarity=0.205 Sum_probs=39.1
Q ss_pred EcCccceEEEEEEeCCchhhHHHHHHHH---hhhHhcCCchhhhhcccce
Q 028962 143 VNGRPSRIEAKYIMRSPREWDRFMRFME---RQMVKALLDSHLSLMQKPY 189 (201)
Q Consensus 143 vNGkP~~IEa~y~m~s~~eWdRFMRFMe---RYAe~NGLg~~~~~~~~~~ 189 (201)
++|+-+|-|..+..+=..+||++-||+. .|+.+.|...+-.+--||+
T Consensus 185 ~WgGREGye~~~ntD~~~e~d~~~~~l~~v~dYa~~iGf~~~f~IEPKP~ 234 (437)
T PRK05474 185 FWGGREGYETLLNTDLKREREQLARFLQMVVDYKHKIGFKGTFLIEPKPQ 234 (437)
T ss_pred ECCCcccccchhhcCHHHHHHHHHHHHHHHHHHhhhcCCCceEEeccCCC
Confidence 6999999999999999999999888854 4777777766777777775
No 27
>smart00545 JmjN Small domain found in the jumonji family of transcription factors. To date, this domain always co-occurs with the JmjC domain (although the reverse is not true).
Probab=33.29 E-value=22 Score=23.90 Aligned_cols=24 Identities=4% Similarity=0.088 Sum_probs=18.8
Q ss_pred CchhhHHHHHHHHhhhHhcCCchhh
Q 028962 158 SPREWDRFMRFMERQMVKALLDSHL 182 (201)
Q Consensus 158 s~~eWdRFMRFMeRYAe~NGLg~~~ 182 (201)
+.+||+.|+.|++.+.. .|..||-
T Consensus 8 t~eEF~Dp~~yi~~i~~-~~~~yGi 31 (42)
T smart00545 8 TMEEFKDPLAYISKIRP-QAEKYGI 31 (42)
T ss_pred CHHHHHCHHHHHHHHHH-HHhhCCE
Confidence 67899999999998766 4766653
No 28
>PF14874 PapD-like: Flagellar-associated PapD-like
Probab=32.61 E-value=1.5e+02 Score=21.17 Aligned_cols=40 Identities=28% Similarity=0.379 Sum_probs=31.8
Q ss_pred CCcceEEEEEcCCcccccCCccCceeeEEEEecCceEEeEeceeeE
Q 028962 97 GSNGMAIFSFSEPSVFDSSGEIGDITGFYMIDEEGTLQSVDVSAKF 142 (201)
Q Consensus 97 G~~GtA~F~Fe~Pkal~s~t~~g~ITGMyLIDEEGeI~Tr~V~aKF 142 (201)
|.+......|.-++ ..|++.+...|.-||....-+|+|+-
T Consensus 62 G~~~~~~V~~~~~~------~~g~~~~~l~i~~e~~~~~i~v~a~~ 101 (102)
T PF14874_consen 62 GESVELEVTFSPTK------PLGDYEGSLVITTEGGSFEIPVKAEV 101 (102)
T ss_pred CCEEEEEEEEEeCC------CCceEEEEEEEEECCeEEEEEEEEEE
Confidence 77788888887443 24788888899999999999998873
No 29
>PF14307 Glyco_tran_WbsX: Glycosyltransferase WbsX
Probab=31.12 E-value=59 Score=29.17 Aligned_cols=42 Identities=17% Similarity=0.146 Sum_probs=31.9
Q ss_pred EcCccceEEEEEEeCCchhhHHHHHHHHhhhHhcCCc-hhhhhcc
Q 028962 143 VNGRPSRIEAKYIMRSPREWDRFMRFMERQMVKALLD-SHLSLMQ 186 (201)
Q Consensus 143 vNGkP~~IEa~y~m~s~~eWdRFMRFMeRYAe~NGLg-~~~~~~~ 186 (201)
|||||- =.+|.-..-.+-.++|..+.+.|.++|++ .+.-+.+
T Consensus 156 VdGKPv--~~Iy~p~~~pd~~~~~~~wr~~a~~~G~~giyii~~~ 198 (345)
T PF14307_consen 156 VDGKPV--FLIYRPGDIPDIKEMIERWREEAKEAGLPGIYIIAVQ 198 (345)
T ss_pred ECCEEE--EEEECcccccCHHHHHHHHHHHHHHcCCCceEEEEEe
Confidence 678874 55666677788999999999999999987 4443333
No 30
>PF14524 Wzt_C: Wzt C-terminal domain; PDB: 2R5O_B.
Probab=31.04 E-value=75 Score=23.12 Aligned_cols=34 Identities=32% Similarity=0.572 Sum_probs=25.3
Q ss_pred CceeeEEEEecCceEEeEeceeeEEcCccceEEEEEEeC
Q 028962 119 GDITGFYMIDEEGTLQSVDVSAKFVNGRPSRIEAKYIMR 157 (201)
Q Consensus 119 g~ITGMyLIDEEGeI~Tr~V~aKFvNGkP~~IEa~y~m~ 157 (201)
..|+...++|++|+.... |..|.+-.|+..|...
T Consensus 13 ~~I~~v~i~~~~g~~~~~-----~~~ge~~~i~i~~~~~ 46 (142)
T PF14524_consen 13 ARITSVRILDSDGEPTSS-----FESGEPIRIRIDYEVN 46 (142)
T ss_dssp EEEEEEEEEETTEES-SS-----EETTSEEEEEEEEEES
T ss_pred EEEEEEEEEeCCCCEeeE-----EeCCCEEEEEEEEEEC
Confidence 589999999999976543 6677777777777663
No 31
>TIGR02630 xylose_isom_A xylose isomerase. Members of this family are the enzyme xylose isomerase (5.3.1.5), which interconverts D-xylose and D-xylulose.
Probab=30.50 E-value=35 Score=33.19 Aligned_cols=48 Identities=21% Similarity=0.225 Sum_probs=39.2
Q ss_pred EcCccceEEEEEEeCCchhhHHHHHHHH---hhhHhcCCchhhhhccccee
Q 028962 143 VNGRPSRIEAKYIMRSPREWDRFMRFME---RQMVKALLDSHLSLMQKPYA 190 (201)
Q Consensus 143 vNGkP~~IEa~y~m~s~~eWdRFMRFMe---RYAe~NGLg~~~~~~~~~~~ 190 (201)
++|+-+|-|..+..+-..+||++-||+. .|+.+.|..-+-.+--||+-
T Consensus 184 ~WgGREGye~~lntD~~~e~d~~~~~l~~~~dYa~~iGf~~~f~IEPKP~E 234 (434)
T TIGR02630 184 FWGGREGYETLLNTDMKRELDHLARFLHMAVDYAKKIGFKGQFLIEPKPKE 234 (434)
T ss_pred ECCCccccccccccCHHHHHHHHHHHHHHHHHHhhhcCCCceEEeccCCCC
Confidence 6999999999999999999998888876 57777666667777777763
No 32
>PF14810 TGT_C2: Patch-forming domain C2 of tRNA-guanine transglycosylase; PDB: 1J2B_A 1IT8_A 1IT7_B 1IQ8_A.
Probab=29.78 E-value=33 Score=25.34 Aligned_cols=29 Identities=24% Similarity=0.489 Sum_probs=19.1
Q ss_pred ceeEeecCCCCCCCCC-eeEEec-cCCCcce
Q 028962 73 PTIQFIQGTDELTVPD-VKLTKS-RDGSNGM 101 (201)
Q Consensus 73 asIQFi~GidEe~iPd-VrLTRS-rdG~~Gt 101 (201)
|.-||=.|..+..+|| +.+.+| +.|..+.
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 4555443
No 33
>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=28.91 E-value=49 Score=23.42 Aligned_cols=19 Identities=16% Similarity=0.335 Sum_probs=16.0
Q ss_pred CceeeEEEEecCceEEeEe
Q 028962 119 GDITGFYMIDEEGTLQSVD 137 (201)
Q Consensus 119 g~ITGMyLIDEEGeI~Tr~ 137 (201)
..+-.+|+||.+|+|.-+.
T Consensus 94 ~~~P~~~vid~~G~v~~~~ 112 (114)
T cd02967 94 SKLPYAVLLDEAGVIAAKG 112 (114)
T ss_pred CCcCeEEEECCCCeEEecc
Confidence 4678899999999998764
No 34
>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=28.91 E-value=38 Score=24.12 Aligned_cols=15 Identities=33% Similarity=0.838 Sum_probs=12.6
Q ss_pred eeEEEEecCceEEeE
Q 028962 122 TGFYMIDEEGTLQSV 136 (201)
Q Consensus 122 TGMyLIDEEGeI~Tr 136 (201)
.+.++||++|++-..
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 578999999999888
No 35
>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=27.73 E-value=53 Score=27.47 Aligned_cols=24 Identities=21% Similarity=0.519 Sum_probs=18.8
Q ss_pred CCeeEEeccCCCcceEEEEEcCCc
Q 028962 87 PDVKLTKSRDGSNGMAIFSFSEPS 110 (201)
Q Consensus 87 PdVrLTRSrdG~~GtA~F~Fe~Pk 110 (201)
-++.+.++|+|.+|++.+.|+...
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 468999999999999999998654
No 36
>PF05549 Allexi_40kDa: Allexivirus 40kDa protein; InterPro: IPR008398 This family of sequences contains the 40 kDa polypeptides from garlic viruses (Allexiviruses), which do not resemble any other plant virus gene products reported so far []. Rod-shaped flexuous viruses have been isolated from garlic plants, Allium sativum. Infection by this virus creates typical mosaic symptoms. The core-like sequence of a zinc finger protein preceded by a cluster of basic amino acid residues shows similarities to the corresponding 12K proteins of the potexviruses and carlaviruses []. Viral epidemics by allexiviruses are also known to be caused by aphids and eriophyid mites (Aceria tulipae) carrying Potyviruses, Carlaviruses, and Allexiviruses [].
Probab=27.44 E-value=56 Score=30.17 Aligned_cols=10 Identities=50% Similarity=1.059 Sum_probs=9.1
Q ss_pred CcCCeeeeec
Q 028962 41 PFNGQSVHMP 50 (201)
Q Consensus 41 ~f~g~~~~~~ 50 (201)
-|+|+++++|
T Consensus 185 ~fnG~~l~iP 194 (271)
T PF05549_consen 185 EFNGSSLRIP 194 (271)
T ss_pred EECCEeeecc
Confidence 4999999998
No 37
>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=27.32 E-value=58 Score=26.40 Aligned_cols=22 Identities=23% Similarity=0.617 Sum_probs=19.7
Q ss_pred CCCeeEEeccCCCcceEEEEEc
Q 028962 86 VPDVKLTKSRDGSNGMAIFSFS 107 (201)
Q Consensus 86 iPdVrLTRSrdG~~GtA~F~Fe 107 (201)
.-.|.+.++|.|.+|.+.+.|+
T Consensus 220 ~~~l~v~KnR~G~~g~~~l~~~ 241 (242)
T cd00984 220 IAEIIVAKNRNGPTGTVELRFD 241 (242)
T ss_pred ceEEEEECCCCCCCeeEEEEee
Confidence 4578899999999999999996
No 38
>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=26.26 E-value=1.4e+02 Score=24.37 Aligned_cols=54 Identities=24% Similarity=0.358 Sum_probs=34.3
Q ss_pred eecCCCCCCCCCeeEEec--cCCCcceEEEEEcCCcccccCC--ccCceeeEEEEecCceEEeE
Q 028962 77 FIQGTDELTVPDVKLTKS--RDGSNGMAIFSFSEPSVFDSSG--EIGDITGFYMIDEEGTLQSV 136 (201)
Q Consensus 77 Fi~GidEe~iPdVrLTRS--rdG~~GtA~F~Fe~Pkal~s~t--~~g~ITGMyLIDEEGeI~Tr 136 (201)
|..|-+|. -+||.+.|| +||+. +...|..+.... ....-....+.|..|+|..-
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 44488888 899999999 88766 344444442221 12233456677888888765
No 39
>PF13535 ATP-grasp_4: ATP-grasp domain; PDB: 3VMM_A 3LN6_A 3LN7_B 2PN1_A 4DIM_A.
Probab=25.05 E-value=61 Score=24.44 Aligned_cols=19 Identities=21% Similarity=0.704 Sum_probs=15.5
Q ss_pred EEEecCceEEeEeceeeEE
Q 028962 125 YMIDEEGTLQSVDVSAKFV 143 (201)
Q Consensus 125 yLIDEEGeI~Tr~V~aKFv 143 (201)
+++|++|++..-|+|.++-
T Consensus 162 ~~~~~~g~~~~iEiN~R~~ 180 (184)
T PF13535_consen 162 FIVDPDGELYFIEINPRFG 180 (184)
T ss_dssp EEEETCCEEEEEEEESS--
T ss_pred EEEeCCCCEEEEEECccCC
Confidence 5889999999999999763
No 40
>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=23.39 E-value=2.4e+02 Score=26.47 Aligned_cols=78 Identities=19% Similarity=0.382 Sum_probs=47.3
Q ss_pred CCCcCCeeeeecCCCCCccccCCccccceeeceeceeEeecCCCCC--------------CCCCeeEEeccCC-CcceEE
Q 028962 39 QSPFNGQSVHMPRMRLSPVTRNSKVSGPITMAVKPTIQFIQGTDEL--------------TVPDVKLTKSRDG-SNGMAI 103 (201)
Q Consensus 39 ~s~f~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~asIQFi~GidEe--------------~iPdVrLTRSrdG-~~GtA~ 103 (201)
+..++|..+.+-..+.....+.+ . ..--|+.+++++ .|-.|++.+..+| +.|.|.
T Consensus 64 ~~~i~gk~i~i~~s~~~~~~~~~---~-------~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~~g~skg~af 133 (562)
T TIGR01628 64 FKRLGGKPIRIMWSQRDPSLRRS---G-------VGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGF 133 (562)
T ss_pred CCEECCeeEEeeccccccccccc---C-------CCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecCCCCcccEEE
Confidence 35588998887533221111111 1 112478888765 3556888888877 789999
Q ss_pred EEEcCCcccccCCccCceeeEEEEe
Q 028962 104 FSFSEPSVFDSSGEIGDITGFYMID 128 (201)
Q Consensus 104 F~Fe~Pkal~s~t~~g~ITGMyLID 128 (201)
..|++.+.-+.- .....|+.+.|
T Consensus 134 V~F~~~e~A~~A--i~~lng~~~~~ 156 (562)
T TIGR01628 134 VHFEKEESAKAA--IQKVNGMLLND 156 (562)
T ss_pred EEECCHHHHHHH--HHHhcccEecC
Confidence 999998754321 23556666644
No 41
>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=23.18 E-value=52 Score=25.69 Aligned_cols=15 Identities=27% Similarity=0.875 Sum_probs=13.5
Q ss_pred CCchhhHHHHHHHHh
Q 028962 157 RSPREWDRFMRFMER 171 (201)
Q Consensus 157 ~s~~eWdRFMRFMeR 171 (201)
++.+++++|++|||-
T Consensus 93 ~~~~~f~~F~~~fEA 107 (119)
T PF03750_consen 93 KDKKDFERFCKFFEA 107 (119)
T ss_pred CCHHHHHHHHHHHHH
Confidence 788999999999985
No 42
>PRK12338 hypothetical protein; Provisional
Probab=23.16 E-value=1.4e+02 Score=27.61 Aligned_cols=43 Identities=16% Similarity=0.344 Sum_probs=33.5
Q ss_pred EecCceEEeEeceeeEEcCccceEEEEEEeCCchhhHHHHHHHHhh
Q 028962 127 IDEEGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMERQ 172 (201)
Q Consensus 127 IDEEGeI~Tr~V~aKFvNGkP~~IEa~y~m~s~~eWdRFMRFMeRY 172 (201)
+|--|.| .||. -=|.|.++-|.+...++|.+++++||.=|+.+
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 4555544 3555 66788888999999999999999999877654
No 43
>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=22.99 E-value=1.1e+02 Score=20.37 Aligned_cols=18 Identities=17% Similarity=0.523 Sum_probs=14.4
Q ss_pred CceeeEEEEecCceEEeE
Q 028962 119 GDITGFYMIDEEGTLQSV 136 (201)
Q Consensus 119 g~ITGMyLIDEEGeI~Tr 136 (201)
..+-.++++|++|+|.-+
T Consensus 96 ~~~P~~~l~d~~g~v~~~ 113 (116)
T cd02966 96 RGLPTTFLIDRDGRIRAR 113 (116)
T ss_pred CccceEEEECCCCcEEEE
Confidence 467788999999988643
No 44
>COG3171 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.29 E-value=47 Score=27.41 Aligned_cols=22 Identities=23% Similarity=0.132 Sum_probs=15.5
Q ss_pred chhhHHHHHHHHhhhHhcCCchhhh
Q 028962 159 PREWDRFMRFMERQMVKALLDSHLS 183 (201)
Q Consensus 159 ~~eWdRFMRFMeRYAe~NGLg~~~~ 183 (201)
++..||||.+. -+.|||.|.-+
T Consensus 47 dea~drFidev---I~~Ngl~~~G~ 68 (119)
T COG3171 47 DEAVDRFIDEV---IAPNGLAFAGS 68 (119)
T ss_pred HHHHHHHHHHH---HccCceeEcCC
Confidence 44556655554 45999999988
No 45
>PF14639 YqgF: Holliday-junction resolvase-like of SPT6 ; PDB: 3PSI_A 3PSF_A.
Probab=22.07 E-value=1.3e+02 Score=24.61 Aligned_cols=16 Identities=25% Similarity=0.368 Sum_probs=10.1
Q ss_pred ceeeEEEEecCceEEe
Q 028962 120 DITGFYMIDEEGTLQS 135 (201)
Q Consensus 120 ~ITGMyLIDEEGeI~T 135 (201)
+-+-..++|++|++.-
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 4555789999999864
No 46
>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=21.99 E-value=55 Score=21.40 Aligned_cols=27 Identities=37% Similarity=0.584 Sum_probs=22.5
Q ss_pred CCCeeEEeccCCC-cceEEEEEcCCccc
Q 028962 86 VPDVKLTKSRDGS-NGMAIFSFSEPSVF 112 (201)
Q Consensus 86 iPdVrLTRSrdG~-~GtA~F~Fe~Pkal 112 (201)
|.+|++.++++|. +|.|...|.+++..
T Consensus 25 v~~v~~~~~~~~~~~~~a~v~f~~~~~a 52 (70)
T PF14259_consen 25 VEKVRLIKNKDGQSRGFAFVEFSSEEDA 52 (70)
T ss_dssp EEEEEEEESTTSSEEEEEEEEESSHHHH
T ss_pred cceEEEEeeeccccCCEEEEEeCCHHHH
Confidence 6799999998754 79999999988754
No 47
>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=21.90 E-value=94 Score=20.72 Aligned_cols=28 Identities=29% Similarity=0.498 Sum_probs=21.2
Q ss_pred ceeeEEEEecCceEEeEeceeeEEcCcc
Q 028962 120 DITGFYMIDEEGTLQSVDVSAKFVNGRP 147 (201)
Q Consensus 120 ~ITGMyLIDEEGeI~Tr~V~aKFvNGkP 147 (201)
-..|++++|.+|.|.-.+-.+.=+.|-+
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 3469999999999998877666555543
No 48
>PRK13189 peroxiredoxin; Provisional
Probab=21.72 E-value=1.8e+02 Score=24.68 Aligned_cols=18 Identities=17% Similarity=0.575 Sum_probs=14.1
Q ss_pred ceeeEEEEecCceEEeEe
Q 028962 120 DITGFYMIDEEGTLQSVD 137 (201)
Q Consensus 120 ~ITGMyLIDEEGeI~Tr~ 137 (201)
.+-+.|+||.+|.|...-
T Consensus 125 ~~r~tfIID~~G~Ir~~~ 142 (222)
T PRK13189 125 TVRAVFIIDPKGIIRAIL 142 (222)
T ss_pred ceeEEEEECCCCeEEEEE
Confidence 466789999999887554
No 49
>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=21.37 E-value=34 Score=22.79 Aligned_cols=55 Identities=16% Similarity=0.404 Sum_probs=36.8
Q ss_pred eeEEEEecCceEEeEeceeeEEcCccce-EEEE--EEeCCchhhHHHHHHHHhhhHhc
Q 028962 122 TGFYMIDEEGTLQSVDVSAKFVNGRPSR-IEAK--YIMRSPREWDRFMRFMERQMVKA 176 (201)
Q Consensus 122 TGMyLIDEEGeI~Tr~V~aKFvNGkP~~-IEa~--y~m~s~~eWdRFMRFMeRYAe~N 176 (201)
.+++++|.+|.|...+..+.=..|.+.. +... .++-.++++++|.+.+++=++..
T Consensus 6 ~~i~v~D~~~~i~~~N~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 (110)
T PF08448_consen 6 DGIFVIDPDGRIVYANQAAAELFGVSPEELIGRSLFDLLPPEDREEFQAALRRALAGG 63 (110)
T ss_dssp SEEEEEETTSBEEEE-HHHHHHHTSTHHHHTTSBHHHHSCCGCHHHHHHHHHHHHHHT
T ss_pred ceeEEECCCCEEEEEHHHHHHHhCCCHHHHhhccchhccccchhhhhHHHHHHhhccC
Confidence 5789999999998877665544454322 1110 13567779999999999876664
No 50
>PRK14681 hypothetical protein; Provisional
Probab=21.11 E-value=1.6e+02 Score=24.69 Aligned_cols=58 Identities=12% Similarity=0.061 Sum_probs=42.6
Q ss_pred cCceeeEEEEecCceEEeEeceeeEEcCccceEEEEEEeCCchhhHHHHHHHHhhhHhcCCch
Q 028962 118 IGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMERQMVKALLDS 180 (201)
Q Consensus 118 ~g~ITGMyLIDEEGeI~Tr~V~aKFvNGkP~~IEa~y~m~s~~eWdRFMRFMeRYAe~NGLg~ 180 (201)
.||| .+.+.|++|+|+-.||+.+=-.+--.+.|+. +..-..|.+|=.+.|..+|+..+
T Consensus 73 ~GEI-DIIa~d~~~~LVFVEVKtR~~~~~g~p~eaV----t~~Kqrrl~raA~~yL~~~~~~~ 130 (158)
T PRK14681 73 YGEL-DIVALNPEYTIVFVEVKTRRSMHYGYPQEAV----TAAKQHNLRKAACDWLLERRNRV 130 (158)
T ss_pred CCcE-EEEEEcCCceEEEEEEEeccCCCCCChHHcC----CHHHHHHHHHHHHHHHHhCCCCC
Confidence 4677 4667787789999999987432211234442 78899999999999999988654
No 51
>PF10126 Nit_Regul_Hom: Uncharacterized protein, homolog of nitrogen regulatory protein PII; InterPro: IPR019296 This family consists of various hypothetical archaeal proteins. It includes a putative nitrogen regulatory protein PII homolog.
Probab=20.62 E-value=36 Score=27.69 Aligned_cols=21 Identities=38% Similarity=0.760 Sum_probs=16.1
Q ss_pred cccccCCccCceeeEEEEecCc
Q 028962 110 SVFDSSGEIGDITGFYMIDEEG 131 (201)
Q Consensus 110 kal~s~t~~g~ITGMyLIDEEG 131 (201)
+|++.-++ +.|||+||.+=-|
T Consensus 18 KaINaLte-~GITGFyl~eYkG 38 (110)
T PF10126_consen 18 KAINALTE-GGITGFYLHEYKG 38 (110)
T ss_pred HHHHHHHh-cCccEEEeEeecC
Confidence 34566664 8999999998776
No 52
>PRK05595 replicative DNA helicase; Provisional
Probab=20.50 E-value=91 Score=28.84 Aligned_cols=25 Identities=20% Similarity=0.449 Sum_probs=21.7
Q ss_pred CCCCeeEEeccCCCcceEEEEEcCC
Q 028962 85 TVPDVKLTKSRDGSNGMAIFSFSEP 109 (201)
Q Consensus 85 ~iPdVrLTRSrdG~~GtA~F~Fe~P 109 (201)
.+.++.+.++|+|.+|++.+.|+..
T Consensus 407 ~~~e~iv~K~R~G~~g~~~~~~~~~ 431 (444)
T PRK05595 407 NVAECIIAKQRNGPTGTVKLAWLGQ 431 (444)
T ss_pred CceEEEEEccCCCCCceEEEEEecC
Confidence 3678999999999999999999653
No 53
>KOG1378 consensus Purple acid phosphatase [Carbohydrate transport and metabolism]
Probab=20.45 E-value=53 Score=32.07 Aligned_cols=23 Identities=30% Similarity=0.485 Sum_probs=19.2
Q ss_pred EEEEeCCc-hhhHHHHHHHHhhhH
Q 028962 152 AKYIMRSP-REWDRFMRFMERQMV 174 (201)
Q Consensus 152 a~y~m~s~-~eWdRFMRFMeRYAe 174 (201)
-.|.+.-+ .-||-||||+|.-|.
T Consensus 184 lsYa~~~~n~~wD~f~r~vEp~As 207 (452)
T KOG1378|consen 184 LSYAMGYSNWQWDEFGRQVEPIAS 207 (452)
T ss_pred hhhcCCCCccchHHHHhhhhhhhc
Confidence 35777777 699999999999775
No 54
>COG3906 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.36 E-value=93 Score=25.20 Aligned_cols=36 Identities=19% Similarity=0.328 Sum_probs=25.0
Q ss_pred EEecCceEEeEeceeeEE-cC-ccceEEEEEEeCCchhhH
Q 028962 126 MIDEEGTLQSVDVSAKFV-NG-RPSRIEAKYIMRSPREWD 163 (201)
Q Consensus 126 LIDEEGeI~Tr~V~aKFv-NG-kP~~IEa~y~m~s~~eWd 163 (201)
++||.|+|..- ...|. |+ +-+|.+....++++++||
T Consensus 52 e~~e~~eiei~--a~~~~~d~dG~eg~~~l~p~etdeEWd 89 (105)
T COG3906 52 EEDEDGEIEIF--AYSFTPDEDGTEGDLQLVPIETDEEWD 89 (105)
T ss_pred cccCCCcEEEE--EeecCcccccccCceeeecccchHHHH
Confidence 45777777653 34455 32 456677788999999999
No 55
>PF00703 Glyco_hydro_2: Glycosyl hydrolases family 2; InterPro: IPR006102 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Glycoside hydrolase family 2 GH2 from CAZY comprises enzymes with several known activities: beta-galactosidase (3.2.1.23 from EC); beta-mannosidase (3.2.1.25 from EC); beta-glucuronidase (3.2.1.31 from EC). These enzymes contain a conserved glutamic acid residue which has been shown [], in Escherichia coli lacZ (P00722 from SWISSPROT), to be the general acid/base catalyst in the active site of the enzyme. This entry describes the immunoglobulin-like beta-sandwich domain [].; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0005975 carbohydrate metabolic process; PDB: 3FN9_C 3DEC_A 3OB8_A 3OBA_A 3CMG_A 3GM8_A 3HN3_E 1BHG_A 2VZU_A 2X09_A ....
Probab=20.33 E-value=3e+02 Score=18.86 Aligned_cols=73 Identities=19% Similarity=0.243 Sum_probs=38.7
Q ss_pred CCeeEEeccCC-CcceEEEEEcCCcccccC-CccCceeeEEEEecCceEEeEeceeeEEcCccce--EEEEEEeCCchhh
Q 028962 87 PDVKLTKSRDG-SNGMAIFSFSEPSVFDSS-GEIGDITGFYMIDEEGTLQSVDVSAKFVNGRPSR--IEAKYIMRSPREW 162 (201)
Q Consensus 87 PdVrLTRSrdG-~~GtA~F~Fe~Pkal~s~-t~~g~ITGMyLIDEEGeI~Tr~V~aKFvNGkP~~--IEa~y~m~s~~eW 162 (201)
-||.++=..+. +++.+.+.. ++-+.. ....--=...+.|.+|..... ....+....+.. +...+.++++.-|
T Consensus 4 ~dv~v~~~~~~~~~~~v~v~~---~~~~~~~~~~~~~v~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~i~~~~lW 79 (110)
T PF00703_consen 4 EDVFVTPDLDDDDSAKVSVEV---EVRNESNKPLDVTVRVRLFDPEGKKVVT-QSPVVSLSAPGQARITLTIEIPNPKLW 79 (110)
T ss_dssp EEEEEEEEEETTSEEEEEEEE---EEEEESSSSCEEEEEEEEEETTSEEEEE-EEEEEEECCCCEEEEEEEEEEESS-BB
T ss_pred EEEEEEEEEcCCCEEEEEEEE---EEEeCCCCcEEEEEEEEEECCCCCEEEE-eeeEEEecCCceeEEEEEEEcCCCCCc
Confidence 35666666655 444444444 111111 111122235788888888777 444444443333 4468999999988
Q ss_pred H
Q 028962 163 D 163 (201)
Q Consensus 163 d 163 (201)
.
T Consensus 80 ~ 80 (110)
T PF00703_consen 80 S 80 (110)
T ss_dssp E
T ss_pred C
Confidence 5
No 56
>KOG3697 consensus Adaptor protein SHC and related proteins [Signal transduction mechanisms]
Probab=20.08 E-value=62 Score=30.68 Aligned_cols=20 Identities=25% Similarity=0.529 Sum_probs=16.7
Q ss_pred CceeeEEEEecCceEEeEec
Q 028962 119 GDITGFYMIDEEGTLQSVDV 138 (201)
Q Consensus 119 g~ITGMyLIDEEGeI~Tr~V 138 (201)
|+-..++|+|.||.+.|+|-
T Consensus 290 ~~~khlllvdpegvvrtkd~ 309 (345)
T KOG3697|consen 290 GQPKHLLLVDPEGVVRTKDR 309 (345)
T ss_pred CCcceEEEECCccceecccc
Confidence 45667899999999999874
Done!