Query psy1629
Match_columns 77
No_of_seqs 151 out of 1044
Neff 5.8
Searched_HMMs 46136
Date Fri Aug 16 17:35:04 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1629.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1629hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0386 BtuE Glutathione perox 99.9 4.5E-27 9.7E-32 160.4 5.6 51 12-77 86-136 (162)
2 PRK10606 btuE putative glutath 99.9 4.6E-24 1E-28 147.4 6.5 66 12-77 86-155 (183)
3 KOG1651|consensus 99.9 6.5E-24 1.4E-28 146.0 5.0 51 11-77 95-145 (171)
4 PF00255 GSHPx: Glutathione pe 99.4 3.6E-14 7.8E-19 91.5 -0.2 34 4-38 75-108 (108)
5 PTZ00056 glutathione peroxidas 99.0 1.7E-09 3.7E-14 75.0 6.0 55 12-77 100-154 (199)
6 TIGR02540 gpx7 putative glutat 98.7 1.7E-08 3.7E-13 66.3 4.4 45 13-77 85-129 (153)
7 PTZ00256 glutathione peroxidas 98.7 3.7E-08 8.1E-13 67.0 5.3 55 12-77 103-157 (183)
8 PLN02399 phospholipid hydroper 98.6 4.6E-08 9.9E-13 70.2 3.5 50 12-77 161-210 (236)
9 PLN02412 probable glutathione 98.5 4.3E-07 9.2E-12 61.1 5.7 51 11-77 90-140 (167)
10 cd00340 GSH_Peroxidase Glutath 97.8 5.9E-05 1.3E-09 49.4 5.2 49 13-77 84-132 (152)
11 PF02785 Biotin_carb_C: Biotin 50.1 11 0.00024 24.0 1.5 36 6-41 36-72 (107)
12 PLN02172 flavin-containing mon 47.6 13 0.00028 28.8 1.8 35 6-40 279-316 (461)
13 PF12971 NAGLU_N: Alpha-N-acet 41.7 21 0.00046 21.6 1.8 27 16-42 33-67 (86)
14 KOG0072|consensus 40.4 32 0.00068 24.1 2.6 26 16-41 153-178 (182)
15 PF01974 tRNA_int_endo: tRNA i 39.1 13 0.00029 22.1 0.5 15 6-20 17-31 (85)
16 smart00878 Biotin_carb_C Bioti 35.3 36 0.00078 21.5 2.1 25 18-42 49-73 (107)
17 TIGR00324 endA tRNA intron end 34.8 24 0.00053 24.1 1.4 16 6-21 94-109 (170)
18 PRK09297 tRNA-splicing endonuc 30.8 26 0.00057 23.8 1.0 17 6-22 93-109 (169)
19 PF05046 Img2: Mitochondrial l 29.8 39 0.00084 20.6 1.5 23 18-40 63-85 (87)
20 KOG2466|consensus 29.7 30 0.00066 28.3 1.3 17 8-24 111-127 (572)
21 COG4765 Uncharacterized protei 29.3 32 0.00068 23.9 1.2 14 29-42 140-154 (164)
22 PF00380 Ribosomal_S9: Ribosom 28.4 46 0.00099 21.7 1.8 20 6-37 11-30 (121)
23 COG0404 GcvT Glycine cleavage 26.6 40 0.00086 26.0 1.4 24 19-42 55-78 (379)
24 PF15530 Toxin_50: Putative to 26.1 12 0.00026 26.0 -1.3 16 21-36 150-165 (168)
25 cd04157 Arl6 Arl6 subfamily. 25.1 63 0.0014 19.9 2.0 24 17-40 139-162 (162)
26 COG5015 Uncharacterized conser 24.6 86 0.0019 21.1 2.6 34 6-42 25-58 (132)
27 KOG0238|consensus 21.5 74 0.0016 26.4 2.1 37 6-42 368-405 (670)
No 1
>COG0386 BtuE Glutathione peroxidase [Posttranslational modification, protein turnover, chaperones]
Probab=99.94 E-value=4.5e-27 Score=160.37 Aligned_cols=51 Identities=49% Similarity=0.939 Sum_probs=45.5
Q ss_pred CcccceeeeEeEEecCCCCCHHHHHHHhcCCCCCCCCCCcccccccCCCCCCCccccceEEeecCC
Q psy1629 12 NFNPGFQFFHKIQVNGENEHPLYTFLKSSCPPTRDGYRTPVTDLYYRPVRVSDVRWNFEKFLVDHR 77 (77)
Q Consensus 12 ~f~v~Fp~f~Ki~VnG~~ahPLy~~Lk~~~~~~~~~~g~~~~~~~~~~~~~~~I~WNF~KFLVdrd 77 (77)
+|||+||||+||+|||++|||||+||+++++.. .+ ..+|+||||||||||+
T Consensus 86 ~YgVtFp~f~Ki~VnG~~a~PLy~~L~~~~~g~---~~------------~~~IkWNFtKFLvdr~ 136 (162)
T COG0386 86 NYGVTFPMFSKIDVNGKNAHPLYKYLKEQKPGK---LG------------GKDIKWNFTKFLVDRD 136 (162)
T ss_pred ccCceeeeeeEEeecCCCCCcHHHHHHhcCCCC---cc------------CCccceeeEEEEEcCC
Confidence 689999999999999999999999999999732 12 2599999999999996
No 2
>PRK10606 btuE putative glutathione peroxidase; Provisional
Probab=99.90 E-value=4.6e-24 Score=147.36 Aligned_cols=66 Identities=36% Similarity=0.629 Sum_probs=54.5
Q ss_pred CcccceeeeEeEEecCCCCCHHHHHHHhcCCCCCCCCC----CcccccccCCCCCCCccccceEEeecCC
Q psy1629 12 NFNPGFQFFHKIQVNGENEHPLYTFLKSSCPPTRDGYR----TPVTDLYYRPVRVSDVRWNFEKFLVDHR 77 (77)
Q Consensus 12 ~f~v~Fp~f~Ki~VnG~~ahPLy~~Lk~~~~~~~~~~g----~~~~~~~~~~~~~~~I~WNF~KFLVdrd 77 (77)
+|+++||||+|++|||+++||||+|||+++|....... .....+.|+|...++|+|||+||||||+
T Consensus 86 ~~g~~Fpv~~k~dvnG~~~~pl~~~Lk~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~i~WNF~KFLv~~~ 155 (183)
T PRK10606 86 TWGVTFPMFSKIEVNGEGRHPLYQKLIAAAPTAVAPEESGFYARMVSKGRAPLYPDDILWNFEKFLVGRD 155 (183)
T ss_pred ccCCCceeEEEEccCCCCCCHHHHHHHHhCCCCcCccccchhhhhhccccccccCCcccccCEEEEECCC
Confidence 69999999999999999999999999999985332110 1124456899999999999999999986
No 3
>KOG1651|consensus
Probab=99.89 E-value=6.5e-24 Score=146.04 Aligned_cols=51 Identities=45% Similarity=0.831 Sum_probs=44.4
Q ss_pred CCcccceeeeEeEEecCCCCCHHHHHHHhcCCCCCCCCCCcccccccCCCCCCCccccceEEeecCC
Q psy1629 11 NNFNPGFQFFHKIQVNGENEHPLYTFLKSSCPPTRDGYRTPVTDLYYRPVRVSDVRWNFEKFLVDHR 77 (77)
Q Consensus 11 ~~f~v~Fp~f~Ki~VnG~~ahPLy~~Lk~~~~~~~~~~g~~~~~~~~~~~~~~~I~WNF~KFLVdrd 77 (77)
.+|+++||||+||||||++|||||+|||++++. .+| + +|+|||||||||||
T Consensus 95 ~r~~~~f~if~KidVNG~~~~PlykfLK~~~~~---~lg------------~-~IkWNF~KFLVd~~ 145 (171)
T KOG1651|consen 95 VRYGAEFPIFQKIDVNGDNADPLYKFLKKVKGG---PLG------------D-DIKWNFTKFLVDKD 145 (171)
T ss_pred hccCCCCccEeEEecCCCCCchHHHHHhhcCCC---ccc------------c-cceeeeEEEeECCC
Confidence 356778899999999999999999999999872 333 2 99999999999996
No 4
>PF00255 GSHPx: Glutathione peroxidase; InterPro: IPR000889 Glutathione peroxidase (GSHPx) (1.11.1.9 from EC) is an enzyme that catalyses the reduction of hydroxyperoxides by glutathione [, ]. Its main function is to protect against the damaging effect of endogenously formed hydroxyperoxides. In higher vertebrates, several forms of GSHPx are known, including a ubiquitous cytosolic form (GSHPx-1), a gastrointestinal cytosolic form (GSHPx-GI), a plasma secreted form (GSHPx-P), and an epididymal secretory form (GSHPx-EP). In addition to these characterised forms, the sequence of a protein of unknown function [] has been shown to be evolutionary related to those of GSHPx's. In filarial nematode parasites, the major soluble cuticular protein (gp29) is a secreted GSHPx, which may provide a mechanism of resistance to the immune reaction of the mammalian host by neutralising the products of the oxidative burst of leukocytes []. The Escherichia coli protein btuE, a periplasmic protein involved in vitamin B12 transport, is evolutionarily related to GSHPxs, although the significance of this relationship is unclear. The structure of bovine seleno-glutathione peroxidase has been determined []. The protein belongs to the alpha-beta class, with a 3 layer(aba) sandwich architecture. The catalyic site of GSHPx contains a conserved residue which is either a cysteine or, in many eukaryotic GSHPx, a selenocysteine []. ; GO: 0004602 glutathione peroxidase activity, 0006979 response to oxidative stress, 0055114 oxidation-reduction process; PDB: 3E0U_A 2VUP_A 2RM5_A 2RM6_A 3DWV_B 2P31_B 2R37_B 1GP1_B 2F8A_B 3KIJ_C ....
Probab=99.40 E-value=3.6e-14 Score=91.55 Aligned_cols=34 Identities=41% Similarity=0.774 Sum_probs=27.5
Q ss_pred ceeeecCCCcccceeeeEeEEecCCCCCHHHHHHH
Q psy1629 4 VRWVRPGNNFNPGFQFFHKIQVNGENEHPLYTFLK 38 (77)
Q Consensus 4 l~~vrpg~~f~v~Fp~f~Ki~VnG~~ahPLy~~Lk 38 (77)
++++++++ |+++||||+||+|||++|||||+|||
T Consensus 75 i~~~~~~~-~~~~F~vf~ki~VnG~~ahPly~~LK 108 (108)
T PF00255_consen 75 IKEFCKEK-FGVTFPVFEKIDVNGPDAHPLYKYLK 108 (108)
T ss_dssp HHHHHCHC-HT-SSEEBS-BBSSSTTB-HHHHHHH
T ss_pred HHHHHHhc-cCCcccceEEEEecCCCCcHHHHHhC
Confidence 45666765 99999999999999999999999997
No 5
>PTZ00056 glutathione peroxidase; Provisional
Probab=98.96 E-value=1.7e-09 Score=74.99 Aligned_cols=55 Identities=42% Similarity=0.820 Sum_probs=43.8
Q ss_pred CcccceeeeEeEEecCCCCCHHHHHHHhcCCCCCCCCCCcccccccCCCCCCCccccceEEeecCC
Q psy1629 12 NFNPGFQFFHKIQVNGENEHPLYTFLKSSCPPTRDGYRTPVTDLYYRPVRVSDVRWNFEKFLVDHR 77 (77)
Q Consensus 12 ~f~v~Fp~f~Ki~VnG~~ahPLy~~Lk~~~~~~~~~~g~~~~~~~~~~~~~~~I~WNF~KFLVdrd 77 (77)
.++++||++.+++|+|+++||+|++|+.+.+...+..+. ...|.|||++||||++
T Consensus 100 ~~~~~fpvl~d~~v~g~~~~~l~~~l~~~~~~~~d~~~~-----------~~~i~~~~~tflID~~ 154 (199)
T PTZ00056 100 KNKIKYNFFEPIEVNGENTHELFKFLKANCDSMHDENGT-----------LKAIGWNFGKFLVNKS 154 (199)
T ss_pred HcCCCceeeeeeeccCCccCHHHHHHHHhCccccccccc-----------CCccCCCCEEEEECCC
Confidence 578899999999999999999999999887632211111 1368899999999986
No 6
>TIGR02540 gpx7 putative glutathione peroxidase Gpx7. This model represents one of several families of known and probable glutathione peroxidases. This family is restricted to animals and designated GPX7.
Probab=98.72 E-value=1.7e-08 Score=66.26 Aligned_cols=45 Identities=36% Similarity=0.749 Sum_probs=39.6
Q ss_pred cccceeeeEeEEecCCCCCHHHHHHHhcCCCCCCCCCCcccccccCCCCCCCccccceEEeecCC
Q psy1629 13 FNPGFQFFHKIQVNGENEHPLYTFLKSSCPPTRDGYRTPVTDLYYRPVRVSDVRWNFEKFLVDHR 77 (77)
Q Consensus 13 f~v~Fp~f~Ki~VnG~~ahPLy~~Lk~~~~~~~~~~g~~~~~~~~~~~~~~~I~WNF~KFLVdrd 77 (77)
++++||++..++|+|+++++.|+|+..... ..++|||++||||++
T Consensus 85 ~~~~fp~~~d~~~~~~~~~~~~~~~~~~~~--------------------~~p~~~~~tflID~~ 129 (153)
T TIGR02540 85 YGVTFPMFSKIKILGSEAEPAFRFLVDSSK--------------------KEPRWNFWKYLVNPE 129 (153)
T ss_pred cCCCCCccceEecCCCCCCcHHHHHHhcCC--------------------CCCCCccEEEEEcCC
Confidence 788999999999999999999999987542 246999999999986
No 7
>PTZ00256 glutathione peroxidase; Provisional
Probab=98.69 E-value=3.7e-08 Score=66.96 Aligned_cols=55 Identities=38% Similarity=0.795 Sum_probs=43.9
Q ss_pred CcccceeeeEeEEecCCCCCHHHHHHHhcCCCCCCCCCCcccccccCCCCCCCccccceEEeecCC
Q psy1629 12 NFNPGFQFFHKIQVNGENEHPLYTFLKSSCPPTRDGYRTPVTDLYYRPVRVSDVRWNFEKFLVDHR 77 (77)
Q Consensus 12 ~f~v~Fp~f~Ki~VnG~~ahPLy~~Lk~~~~~~~~~~g~~~~~~~~~~~~~~~I~WNF~KFLVdrd 77 (77)
.++++||++.+++++|+.+|++|+||+++++...... .....|.|||++||||++
T Consensus 103 ~~~~~fpv~~d~d~~g~~~~~~~~~l~~~~~~~~~~~-----------~~~~~iP~~~~tflID~~ 157 (183)
T PTZ00256 103 KFNVDFPLFQKIEVNGENTHEIYKYLRRNSELFQNNT-----------NEARQIPWNFAKFLIDGQ 157 (183)
T ss_pred hcCCCCCCceEEecCCCCCCHHHHHHHhhCCCCcCcc-----------ccCcccCcceEEEEECCC
Confidence 6789999999999999999999999999876211111 112478999999999986
No 8
>PLN02399 phospholipid hydroperoxide glutathione peroxidase
Probab=98.58 E-value=4.6e-08 Score=70.20 Aligned_cols=50 Identities=44% Similarity=0.820 Sum_probs=42.1
Q ss_pred CcccceeeeEeEEecCCCCCHHHHHHHhcCCCCCCCCCCcccccccCCCCCCCccccceEEeecCC
Q psy1629 12 NFNPGFQFFHKIQVNGENEHPLYTFLKSSCPPTRDGYRTPVTDLYYRPVRVSDVRWNFEKFLVDHR 77 (77)
Q Consensus 12 ~f~v~Fp~f~Ki~VnG~~ahPLy~~Lk~~~~~~~~~~g~~~~~~~~~~~~~~~I~WNF~KFLVdrd 77 (77)
.|+++||++.+.+++|+.++|+|++|+.+.+. ..| ..|.||+++||||++
T Consensus 161 ~~g~~fPvl~~~D~~G~~~~~~y~~l~~~~~~---~~g-------------~~i~~~PttfLIDk~ 210 (236)
T PLN02399 161 RFKAEFPIFDKVDVNGPSTAPVYQFLKSNAGG---FLG-------------DLIKWNFEKFLVDKN 210 (236)
T ss_pred hcCCCCccccccCCCcchhhHHHHHHHHhcCC---ccC-------------CccccCceEEEECCC
Confidence 58899999999999999999999999877641 112 268999999999986
No 9
>PLN02412 probable glutathione peroxidase
Probab=98.47 E-value=4.3e-07 Score=61.06 Aligned_cols=51 Identities=39% Similarity=0.818 Sum_probs=42.4
Q ss_pred CCcccceeeeEeEEecCCCCCHHHHHHHhcCCCCCCCCCCcccccccCCCCCCCccccceEEeecCC
Q psy1629 11 NNFNPGFQFFHKIQVNGENEHPLYTFLKSSCPPTRDGYRTPVTDLYYRPVRVSDVRWNFEKFLVDHR 77 (77)
Q Consensus 11 ~~f~v~Fp~f~Ki~VnG~~ahPLy~~Lk~~~~~~~~~~g~~~~~~~~~~~~~~~I~WNF~KFLVdrd 77 (77)
..++++||++.+++++|..++++|.+|+..... ..+ ..|.||+++||||++
T Consensus 90 ~~~~~~fpvl~~~d~~g~~~~~~~~~~~~~~~~---~~~-------------~~v~~~p~tflId~~ 140 (167)
T PLN02412 90 TRFKAEFPIFDKVDVNGKNTAPLYKYLKAEKGG---LFG-------------DAIKWNFTKFLVSKE 140 (167)
T ss_pred HccCCCCceEeEEeeCCCCCCHHHHHHHhhCCC---CCC-------------CCcCCCCeeEEECCC
Confidence 467899999999999999999999999987531 111 368999999999986
No 10
>cd00340 GSH_Peroxidase Glutathione (GSH) peroxidase family; tetrameric selenoenzymes that catalyze the reduction of a variety of hydroperoxides including lipid peroxidases, using GSH as a specific electron donor substrate. GSH peroxidase contains one selenocysteine residue per subunit, which is involved in catalysis. Different isoenzymes are known in mammals,which are involved in protection against reactive oxygen species, redox regulation of many metabolic processes, peroxinitrite scavenging, and modulation of inflammatory processes.
Probab=97.79 E-value=5.9e-05 Score=49.43 Aligned_cols=49 Identities=51% Similarity=0.984 Sum_probs=40.9
Q ss_pred cccceeeeEeEEecCCCCCHHHHHHHhcCCCCCCCCCCcccccccCCCCCCCccccceEEeecCC
Q psy1629 13 FNPGFQFFHKIQVNGENEHPLYTFLKSSCPPTRDGYRTPVTDLYYRPVRVSDVRWNFEKFLVDHR 77 (77)
Q Consensus 13 f~v~Fp~f~Ki~VnG~~ahPLy~~Lk~~~~~~~~~~g~~~~~~~~~~~~~~~I~WNF~KFLVdrd 77 (77)
++.+||++...+++|..+++.|.++....|.. . ...+.||++.||||++
T Consensus 84 ~~~~fp~~~d~d~~~~~~~~~~~~~~~~~p~~---~-------------~~~~~~~~ttflId~~ 132 (152)
T cd00340 84 YGVTFPMFAKIDVNGENAHPLYKYLKEEAPGL---L-------------GKDIKWNFTKFLVDRD 132 (152)
T ss_pred cCCCceeeeeEeccCCCCChHHHHHHhcCCCC---C-------------CCccccccEEEEECCC
Confidence 67899999888999999999999988887621 0 1378999999999986
No 11
>PF02785 Biotin_carb_C: Biotin carboxylase C-terminal domain; InterPro: IPR005482 Acetyl-CoA carboxylase is found in all animals, plants, and bacteria and catalyzes the first committed step in fatty acid synthesis. It is a multicomponent enzyme containing a biotin carboxylase activity, a biotin carboxyl carrier protein, and a carboxyltransferase functionality. The "B-domain" extends from the main body of the subunit where it folds into two alpha-helical regions and three strands of beta-sheet. Following the excursion into the B-domain, the polypeptide chain folds back into the body of the protein where it forms an eight-stranded antiparallel beta-sheet. In addition to this major secondary structural element, the C-terminal domain also contains a smaller three-stranded antiparallel beta-sheet and seven alpha-helices []. ; GO: 0016874 ligase activity; PDB: 1W96_B 1W93_A 3VA7_A 2GPW_A 2W70_A 3G8D_A 1DV2_A 2VR1_B 2J9G_B 1DV1_A ....
Probab=50.12 E-value=11 Score=23.96 Aligned_cols=36 Identities=19% Similarity=0.323 Sum_probs=27.3
Q ss_pred eeecCCCcccce-eeeEeEEecCCCCCHHHHHHHhcC
Q psy1629 6 WVRPGNNFNPGF-QFFHKIQVNGENEHPLYTFLKSSC 41 (77)
Q Consensus 6 ~vrpg~~f~v~F-p~f~Ki~VnG~~ahPLy~~Lk~~~ 41 (77)
+|++|..-.+.| ||.+|+-|.|++-....+-|..+.
T Consensus 36 ~~~~G~~v~~~yDsmiaKliv~g~~R~~Ai~~l~~AL 72 (107)
T PF02785_consen 36 GVYSGYEVSPYYDSMIAKLIVHGPDREEAIARLRRAL 72 (107)
T ss_dssp SESTTCEE-SSSSSEEEEEEEEESSHHHHHHHHHHHH
T ss_pred cCccccccCCCchhhhhhheeeccchHHHHHHHHhhc
Confidence 467777777788 999999999999777666665543
No 12
>PLN02172 flavin-containing monooxygenase FMO GS-OX
Probab=47.60 E-value=13 Score=28.83 Aligned_cols=35 Identities=14% Similarity=0.382 Sum_probs=28.5
Q ss_pred eeecCCCcccceeeeEe---EEecCCCCCHHHHHHHhc
Q psy1629 6 WVRPGNNFNPGFQFFHK---IQVNGENEHPLYTFLKSS 40 (77)
Q Consensus 6 ~vrpg~~f~v~Fp~f~K---i~VnG~~ahPLy~~Lk~~ 40 (77)
.|=.|-||..+||+++. +.|++..-+|||+.+-.-
T Consensus 279 ~Ii~~TGy~~~~pfL~~~~~i~v~~~~v~~Ly~~~f~~ 316 (461)
T PLN02172 279 TIVHCTGYKYHFPFLETNGYMRIDENRVEPLYKHVFPP 316 (461)
T ss_pred EEEECCcCCccccccCcccceeeCCCcchhhHHhhcCC
Confidence 45567899999999975 677888889999988764
No 13
>PF12971 NAGLU_N: Alpha-N-acetylglucosaminidase (NAGLU) N-terminal domain; InterPro: IPR024240 Alpha-N-acetylglucosaminidase, is a lysosomal enzyme required for the stepwise degradation of heparan sulphate []. Mutations on the alpha-N-acetylglucosaminidase (NAGLU) gene can lead to Mucopolysaccharidosis type IIIB (MPS IIIB; or Sanfilippo syndrome type B) characterised by neurological dysfunction but relatively mild somatic manifestations []. The structure shows that the enzyme is composed of three domains. This entry represents the N-terminal domain of Alpha-N-acetylglucosaminidase which has an alpha-beta fold [].; PDB: 4A4A_A 2VC9_A 2VCC_A 2VCB_A 2VCA_A.
Probab=41.70 E-value=21 Score=21.55 Aligned_cols=27 Identities=30% Similarity=0.461 Sum_probs=20.8
Q ss_pred ceeeeE----eEEecCCCC----CHHHHHHHhcCC
Q psy1629 16 GFQFFH----KIQVNGENE----HPLYTFLKSSCP 42 (77)
Q Consensus 16 ~Fp~f~----Ki~VnG~~a----hPLy~~Lk~~~~ 42 (77)
.|.+-. ||.|.|.+. .=|+.|||..|.
T Consensus 33 ~F~l~~~~~gki~I~G~s~vala~Gl~~YLk~~c~ 67 (86)
T PF12971_consen 33 VFELSSADNGKIVIRGNSGVALASGLNWYLKYYCH 67 (86)
T ss_dssp EEEEEE-SSS-EEEEESSHHHHHHHHHHHHHHHS-
T ss_pred EEEEEeCCCCeEEEEeCCHHHHHHHHHHHHHHHhC
Confidence 477776 999999986 568999999995
No 14
>KOG0072|consensus
Probab=40.38 E-value=32 Score=24.14 Aligned_cols=26 Identities=23% Similarity=0.360 Sum_probs=23.6
Q ss_pred ceeeeEeEEecCCCCCHHHHHHHhcC
Q psy1629 16 GFQFFHKIQVNGENEHPLYTFLKSSC 41 (77)
Q Consensus 16 ~Fp~f~Ki~VnG~~ahPLy~~Lk~~~ 41 (77)
.+.|++-+.|+|+.-.|.|.||.+..
T Consensus 153 ~~~Iv~tSA~kg~Gld~~~DWL~~~l 178 (182)
T KOG0072|consen 153 IWQIVKTSAVKGEGLDPAMDWLQRPL 178 (182)
T ss_pred eeEEEeeccccccCCcHHHHHHHHHH
Confidence 48899999999999999999998754
No 15
>PF01974 tRNA_int_endo: tRNA intron endonuclease, catalytic C-terminal domain; InterPro: IPR006677 This entry represents a 3-layer alpha/beta/alpha domain found as the catalytic domain at the C-terminal in homotetrameric tRNA-intron endonucleases [], and as domains 2 and 4 (C-terminal) in the homodimeric enzymes []. tRNA-intron endonucleases (3.1.27.9 from EC) remove tRNA introns by cleaving pre-tRNA at the 5'- and 3'-splice sites to release the intron. The products are an intron and two tRNA half-molecules bearing 2',3' cyclic phosphate and 5'-hydroxyl termini []. These enzymes recognise a pseudosymmetric substrate in which 2 bulged loops of 3 bases are separated by a stem of 4 bp []. Although homotetrameric enzymes contain four active sites, only two participate in the cleavage, and should therefore, be considered as a dimer of dimers.; GO: 0000213 tRNA-intron endonuclease activity, 0006388 tRNA splicing, via endonucleolytic cleavage and ligation; PDB: 3IEY_B 3IF0_X 2CV8_A 3P1Z_B 3AJV_B 2GJW_D 1R0V_A 3P1Y_C 1R11_B 1RLV_A ....
Probab=39.08 E-value=13 Score=22.10 Aligned_cols=15 Identities=33% Similarity=0.682 Sum_probs=13.8
Q ss_pred eeecCCCcccceeee
Q psy1629 6 WVRPGNNFNPGFQFF 20 (77)
Q Consensus 6 ~vrpg~~f~v~Fp~f 20 (77)
+|+||-+||.+|-+.
T Consensus 17 ~v~~G~kfG~df~vY 31 (85)
T PF01974_consen 17 VVKPGIKFGCDFLVY 31 (85)
T ss_dssp EEEEEGGGTSSEEEE
T ss_pred EECccCcCCceEEEE
Confidence 689999999999987
No 16
>smart00878 Biotin_carb_C Biotin carboxylase C-terminal domain. Biotin carboxylase is a component of the acetyl-CoA carboxylase multi-component enzyme which catalyses the first committed step in fatty acid synthesis in animals, plants and bacteria. Most of the active site residues reported in reference are in this C-terminal domain.
Probab=35.34 E-value=36 Score=21.52 Aligned_cols=25 Identities=20% Similarity=0.303 Sum_probs=20.3
Q ss_pred eeeEeEEecCCCCCHHHHHHHhcCC
Q psy1629 18 QFFHKIQVNGENEHPLYTFLKSSCP 42 (77)
Q Consensus 18 p~f~Ki~VnG~~ahPLy~~Lk~~~~ 42 (77)
||++|+-|-|++-.-..+-|.....
T Consensus 49 smlAKliv~g~~R~~A~~rl~~aL~ 73 (107)
T smart00878 49 SMIAKLIVHGETREEAIARLRRALD 73 (107)
T ss_pred hhceEEEEEcCCHHHHHHHHHHHHH
Confidence 8999999999998887776666543
No 17
>TIGR00324 endA tRNA intron endonuclease. The enzyme catalyses the endonucleolytic cleavage of pre tRNA at the 5' and 3' splice sites to release the intron and produces two half tRNA molecules bearing 5' hydroxyl and 2', 3'-cyclic phosphate termini. The genes are homologous in Eucarya and Archea. The two yeast genes have been functionally studied (PubMed:97344075) and are two subunits of a heterotetramer enzyme in yeast the other two subunits of which have no known homologs.
Probab=34.81 E-value=24 Score=24.05 Aligned_cols=16 Identities=25% Similarity=0.661 Sum_probs=13.8
Q ss_pred eeecCCCcccceeeeE
Q psy1629 6 WVRPGNNFNPGFQFFH 21 (77)
Q Consensus 6 ~vrpg~~f~v~Fp~f~ 21 (77)
+|+||-+||.+|-+..
T Consensus 94 ~vk~G~kFG~dF~vY~ 109 (170)
T TIGR00324 94 VVKTGFKFGADFRLYE 109 (170)
T ss_pred EecCCcccCceEEEEC
Confidence 7999999999996654
No 18
>PRK09297 tRNA-splicing endonuclease subunit alpha; Reviewed
Probab=30.81 E-value=26 Score=23.82 Aligned_cols=17 Identities=18% Similarity=0.626 Sum_probs=14.7
Q ss_pred eeecCCCcccceeeeEe
Q psy1629 6 WVRPGNNFNPGFQFFHK 22 (77)
Q Consensus 6 ~vrpg~~f~v~Fp~f~K 22 (77)
+|+||-+||.+|-+..+
T Consensus 93 ~vk~G~kfG~df~vY~~ 109 (169)
T PRK09297 93 IVKSGLKYGSDFRVYER 109 (169)
T ss_pred ccCCCCcCCeeEEEECC
Confidence 68999999999988754
No 19
>PF05046 Img2: Mitochondrial large subunit ribosomal protein (Img2); InterPro: IPR007740 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family of proteins has been identified as part of the mitochondrial large ribosomal subunit in Saccharomyces cerevisiae [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome
Probab=29.78 E-value=39 Score=20.59 Aligned_cols=23 Identities=13% Similarity=0.355 Sum_probs=20.4
Q ss_pred eeeEeEEecCCCCCHHHHHHHhc
Q psy1629 18 QFFHKIQVNGENEHPLYTFLKSS 40 (77)
Q Consensus 18 p~f~Ki~VnG~~ahPLy~~Lk~~ 40 (77)
++..+|.|+|+....+=+||.+.
T Consensus 63 ~~~g~i~IkG~~~~~Vk~wL~~~ 85 (87)
T PF05046_consen 63 ELTGHIEIKGDHVEEVKKWLLEK 85 (87)
T ss_pred ecCCEEEEcCccHHHHHHHHHHC
Confidence 67789999999999999999765
No 20
>KOG2466|consensus
Probab=29.73 E-value=30 Score=28.25 Aligned_cols=17 Identities=24% Similarity=0.704 Sum_probs=14.6
Q ss_pred ecCCCcccceeeeEeEE
Q psy1629 8 RPGNNFNPGFQFFHKIQ 24 (77)
Q Consensus 8 rpg~~f~v~Fp~f~Ki~ 24 (77)
|||..|.+.||+.++..
T Consensus 111 ~~G~~yhIsFpv~sR~s 127 (572)
T KOG2466|consen 111 RPGSDYHISFPVLSRSS 127 (572)
T ss_pred CCCcccccceeeeeeee
Confidence 89999999999988754
No 21
>COG4765 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.35 E-value=32 Score=23.91 Aligned_cols=14 Identities=43% Similarity=0.809 Sum_probs=11.2
Q ss_pred CCCHHHH-HHHhcCC
Q psy1629 29 NEHPLYT-FLKSSCP 42 (77)
Q Consensus 29 ~ahPLy~-~Lk~~~~ 42 (77)
=+||+|. |||.+..
T Consensus 140 ~EHPIYdvwlk~Ckq 154 (164)
T COG4765 140 VEHPIYDVWLKDCKQ 154 (164)
T ss_pred ccchHHHHHHHHhhh
Confidence 4699998 8888764
No 22
>PF00380 Ribosomal_S9: Ribosomal protein S9/S16; InterPro: IPR000754 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S9 is one of the proteins from the small ribosomal subunit. It belongs to the S9P family of ribosomal proteins which, on the basis of sequence similarities [, ], groups bacterial; algal chloroplast; cyanelle and archaeal S9 proteins; and mammalian; plant; and yeast mitochondrial ribosomal S9 proteins. These proteins adopt a beta-alpha-beta fold similar to that found in numerous RNA/DNA-binding proteins, as well as in kinases from the GHMP kinase family [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2V46_I 3T1H_I 3MR8_I 3F1G_I 3D5C_I 3D5A_I 2WDG_I 3MS0_I 2WDM_I 2J02_I ....
Probab=28.44 E-value=46 Score=21.70 Aligned_cols=20 Identities=45% Similarity=1.193 Sum_probs=16.1
Q ss_pred eeecCCCcccceeeeEeEEecCCCCCHHHHHH
Q psy1629 6 WVRPGNNFNPGFQFFHKIQVNGENEHPLYTFL 37 (77)
Q Consensus 6 ~vrpg~~f~v~Fp~f~Ki~VnG~~ahPLy~~L 37 (77)
++.||+ .+|.|||. |++.|+
T Consensus 11 ~l~~G~---------G~i~INg~---~l~~yf 30 (121)
T PF00380_consen 11 WLKPGS---------GKIRINGK---PLEEYF 30 (121)
T ss_dssp EEEESS---------SEEEETTS---EHHHHS
T ss_pred EEEeCc---------eEEEECCE---EHHHhc
Confidence 567775 58999998 788887
No 23
>COG0404 GcvT Glycine cleavage system T protein (aminomethyltransferase) [Amino acid transport and metabolism]
Probab=26.59 E-value=40 Score=25.97 Aligned_cols=24 Identities=17% Similarity=0.256 Sum_probs=20.9
Q ss_pred eeEeEEecCCCCCHHHHHHHhcCC
Q psy1629 19 FFHKIQVNGENEHPLYTFLKSSCP 42 (77)
Q Consensus 19 ~f~Ki~VnG~~ahPLy~~Lk~~~~ 42 (77)
-|.|++|.|++|..+-++|..+.-
T Consensus 55 hmgk~~V~GpdA~~~L~~l~~ndv 78 (379)
T COG0404 55 HMGKVEVSGPDAAAFLQRLLTNDV 78 (379)
T ss_pred CceEEEEECCCHHHHHHHHccccc
Confidence 478999999999999999987653
No 24
>PF15530 Toxin_50: Putative toxin 50
Probab=26.11 E-value=12 Score=26.00 Aligned_cols=16 Identities=25% Similarity=0.764 Sum_probs=14.3
Q ss_pred EeEEecCCCCCHHHHH
Q psy1629 21 HKIQVNGENEHPLYTF 36 (77)
Q Consensus 21 ~Ki~VnG~~ahPLy~~ 36 (77)
+|+||||.....+|.|
T Consensus 150 ~~vdiNGs~ttE~y~y 165 (168)
T PF15530_consen 150 EKVDINGSSTTEIYHY 165 (168)
T ss_pred ccccccCCccceEEec
Confidence 8899999999988876
No 25
>cd04157 Arl6 Arl6 subfamily. Arl6 (Arf-like 6) forms a subfamily of the Arf family of small GTPases. Arl6 expression is limited to the brain and kidney in adult mice, but it is expressed in the neural plate and somites during embryogenesis, suggesting a possible role for Arl6 in early development. Arl6 is also believed to have a role in cilia or flagella function. Several proteins have been identified that bind Arl6, including Arl6 interacting protein (Arl6ip), and SEC61beta, a subunit of the heterotrimeric conducting channel SEC61p. Based on Arl6 binding to these effectors, Arl6 is also proposed to play a role in protein transport, membrane trafficking, or cell signaling during hematopoietic maturation. At least three specific homozygous Arl6 mutations in humans have been found to cause Bardet-Biedl syndrome, a disorder characterized by obesity, retinopathy, polydactyly, renal and cardiac malformations, learning disabilities, and hypogenitalism. Older literature suggests that A
Probab=25.14 E-value=63 Score=19.86 Aligned_cols=24 Identities=17% Similarity=0.335 Sum_probs=18.0
Q ss_pred eeeeEeEEecCCCCCHHHHHHHhc
Q psy1629 17 FQFFHKIQVNGENEHPLYTFLKSS 40 (77)
Q Consensus 17 Fp~f~Ki~VnG~~ahPLy~~Lk~~ 40 (77)
+++|+-...+|.+-..+++||.+|
T Consensus 139 ~~~~~~Sa~~g~gv~~~~~~l~~~ 162 (162)
T cd04157 139 WHIFASNALTGEGLDEGVQWLQAQ 162 (162)
T ss_pred EEEEEeeCCCCCchHHHHHHHhcC
Confidence 456777777888888888888553
No 26
>COG5015 Uncharacterized conserved protein [Function unknown]
Probab=24.62 E-value=86 Score=21.06 Aligned_cols=34 Identities=29% Similarity=0.348 Sum_probs=28.7
Q ss_pred eeecCCCcccceeeeEeEEecCCCCCHHHHHHHhcCC
Q psy1629 6 WVRPGNNFNPGFQFFHKIQVNGENEHPLYTFLKSSCP 42 (77)
Q Consensus 6 ~vrpg~~f~v~Fp~f~Ki~VnG~~ahPLy~~Lk~~~~ 42 (77)
-||| |++-|-.=+|+-.=-++.-|+|+.+|....
T Consensus 25 rvRp---fq~~f~~g~KlYfcTantK~~yKqik~np~ 58 (132)
T COG5015 25 RVRP---FQVMFVEGEKLYFCTANTKPYYKQIKKNPE 58 (132)
T ss_pred ceee---ccceeeeCCEEEEEeCCChHHHHHHhhCCC
Confidence 3677 777788888999889999999999998864
No 27
>KOG0238|consensus
Probab=21.47 E-value=74 Score=26.42 Aligned_cols=37 Identities=22% Similarity=0.318 Sum_probs=32.1
Q ss_pred eeecCCCcccce-eeeEeEEecCCCCCHHHHHHHhcCC
Q psy1629 6 WVRPGNNFNPGF-QFFHKIQVNGENEHPLYTFLKSSCP 42 (77)
Q Consensus 6 ~vrpg~~f~v~F-p~f~Ki~VnG~~ahPLy~~Lk~~~~ 42 (77)
.||+|+.-.+.+ ||.+|+.|-|++....-.-|+.+..
T Consensus 368 gV~~g~~vs~~YDpmiaKlvvwg~dR~~Al~kl~~aL~ 405 (670)
T KOG0238|consen 368 GVRSGDEVSIHYDPMIAKLVVWGKDREEALNKLKDALD 405 (670)
T ss_pred CcccCCcccccccchheeeeEecCCHHHHHHHHHHHHh
Confidence 588999888988 9999999999999888888877654
Done!