Query 033741
Match_columns 112
No_of_seqs 38 out of 40
Neff 2.7
Searched_HMMs 46136
Date Fri Mar 29 05:46:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033741.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033741hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK13931 stationary phase surv 98.8 5.1E-09 1.1E-13 83.8 4.6 61 2-62 88-186 (261)
2 PRK13933 stationary phase surv 98.8 7.2E-09 1.6E-13 82.8 4.5 61 2-62 88-179 (253)
3 PRK00346 surE 5'(3')-nucleotid 98.8 9.8E-09 2.1E-13 81.8 4.9 61 2-62 83-176 (250)
4 PRK13932 stationary phase surv 98.7 1.1E-08 2.4E-13 82.1 4.7 61 2-62 92-181 (257)
5 PF01975 SurE: Survival protei 98.7 8.6E-09 1.9E-13 78.9 2.9 61 2-62 92-184 (196)
6 TIGR00087 surE 5'/3'-nucleotid 98.7 1.7E-08 3.6E-13 79.8 4.6 61 2-62 87-182 (244)
7 PRK13935 stationary phase surv 98.6 2.8E-08 6E-13 79.7 4.3 61 2-62 87-176 (253)
8 PRK13934 stationary phase surv 98.5 1.3E-07 2.8E-12 76.6 3.9 60 2-63 85-181 (266)
9 COG0496 SurE Predicted acid ph 98.0 9E-06 2E-10 65.9 4.6 61 2-62 84-178 (252)
10 PF03764 EFG_IV: Elongation fa 39.7 25 0.00055 23.8 2.0 30 8-37 71-112 (120)
11 cd03751 proteasome_alpha_type_ 26.4 89 0.0019 23.7 3.3 28 25-52 178-209 (212)
12 cd01684 Tet_like_IV EF-G_domai 26.0 62 0.0013 22.4 2.2 28 9-37 68-107 (115)
13 cd01680 EFG_like_IV Elongation 23.8 60 0.0013 21.6 1.8 29 8-36 67-107 (116)
14 PLN02314 pectinesterase 23.1 80 0.0017 28.6 2.8 41 29-69 219-266 (586)
15 PF03361 Herpes_IE2_3: Herpes 22.4 57 0.0012 25.4 1.6 20 23-42 115-134 (162)
16 PF11884 DUF3404: Domain of un 20.6 1.5E+02 0.0033 24.8 3.8 43 2-44 200-245 (262)
17 PF12252 SidE: Dot/Icm substra 20.4 61 0.0013 32.8 1.7 12 7-19 111-122 (1439)
No 1
>PRK13931 stationary phase survival protein SurE; Provisional
Probab=98.81 E-value=5.1e-09 Score=83.84 Aligned_cols=61 Identities=15% Similarity=0.141 Sum_probs=48.7
Q ss_pred eeEEEecccCCCCcccee------------------------e-c--CCCchhhhhhhhhhhhhhHHHHhhhc-------
Q 033741 2 IFLVIGGINQGLICGHYM------------------------K-K--DESYESEFKDTISVFLPLRNGAIIDI------- 47 (112)
Q Consensus 2 ~~LVISGIN~GsnCG~h~------------------------k-k--~eS~e~DFkdAa~vcLPLInAal~dI------- 47 (112)
+||||||||.|.|+|.++ . + ++..+++|+.|+.++..|+..++..-
T Consensus 88 pDlVvSGIN~G~N~g~~v~ySGTVgAA~Ea~~~GiPsiA~S~~~~~~~~~~~~~~~~a~~~~~~l~~~~l~~~~~~~~~~ 167 (261)
T PRK13931 88 PDLVLSGVNRGNNSAENVLYSGTVGGAMEAALQGLPAIALSQYYGPRNEGLDDPFEAARTHGARVVRKLLEAGPWDDEDY 167 (261)
T ss_pred CCEEEECCccCCCCCcCcccchhHHHHHHHHhcCCCeEEEEeeccCCCccccccHHHHHHHHHHHHHHHHhccCCCCCCC
Confidence 799999999999999997 1 1 11113479999999999999987753
Q ss_pred ---cccccCCCccCC-CcC
Q 033741 48 ---ESIQILTSPLTN-KVC 62 (112)
Q Consensus 48 ---eNI~iPt~p~~n-KGf 62 (112)
=||+||..|... ||+
T Consensus 168 ~~~lNVN~P~~~~~~~~gi 186 (261)
T PRK13931 168 RLFYNVNFPPVPAADVKGI 186 (261)
T ss_pred CeEEEEEeCcCCcccCCce
Confidence 199999988665 888
No 2
>PRK13933 stationary phase survival protein SurE; Provisional
Probab=98.77 E-value=7.2e-09 Score=82.80 Aligned_cols=61 Identities=21% Similarity=0.238 Sum_probs=48.4
Q ss_pred eeEEEecccCCCCcccee-----------------------e-cCCCchhhhhhhhhhhhhhHHHHhhh-cc-----ccc
Q 033741 2 IFLVIGGINQGLICGHYM-----------------------K-KDESYESEFKDTISVFLPLRNGAIID-IE-----SIQ 51 (112)
Q Consensus 2 ~~LVISGIN~GsnCG~h~-----------------------k-k~eS~e~DFkdAa~vcLPLInAal~d-Ie-----NI~ 51 (112)
+||||||||.|.|+|..+ . .+...+.||..|+.++..|++..+.. ++ ||+
T Consensus 88 pDLVvSGIN~G~N~g~dv~ySGTVgAA~ea~~~GiPsiA~S~~~~~~~~~~~~~a~~~~~~lv~~l~~~~~p~~~~lNvN 167 (253)
T PRK13933 88 IDMVISGINKGLNIGNDILYSGTVSAAIEGAIYKVPSIAVSADVKKGKDENYKIAAKYALEVLNILKKEDLKNDVVLNLN 167 (253)
T ss_pred CCEEEECCcCCCCCCcCCccchhHHHHHHHHHcCCCeEEEEeccCCCCcccHHHHHHHHHHHHHHHHhcCCCCCcEEEEe
Confidence 699999999999999997 1 11222347999999999999988764 33 999
Q ss_pred cCCCcc-CCCcC
Q 033741 52 ILTSPL-TNKVC 62 (112)
Q Consensus 52 iPt~p~-~nKGf 62 (112)
||..|. .-||+
T Consensus 168 iP~~~~~~~~g~ 179 (253)
T PRK13933 168 VPFCSEEEIKGI 179 (253)
T ss_pred cCCCchhhcCCe
Confidence 999885 44888
No 3
>PRK00346 surE 5'(3')-nucleotidase/polyphosphatase; Provisional
Probab=98.76 E-value=9.8e-09 Score=81.79 Aligned_cols=61 Identities=20% Similarity=0.180 Sum_probs=48.5
Q ss_pred eeEEEecccCCCCcccee-------------------------ec-CCCchhhhhhhhhhhhhhHHHHhhh-cc-----c
Q 033741 2 IFLVIGGINQGLICGHYM-------------------------KK-DESYESEFKDTISVFLPLRNGAIID-IE-----S 49 (112)
Q Consensus 2 ~~LVISGIN~GsnCG~h~-------------------------kk-~eS~e~DFkdAa~vcLPLInAal~d-Ie-----N 49 (112)
+||||||||.|.|+|..+ .. .....+||+.|+.++..||..++.. ++ |
T Consensus 83 pDlVvSGIN~G~N~g~~v~ySGTVgAA~ea~~~GiPaiA~S~~~~~~~~~~~~~~~a~~~~~~li~~l~~~~~p~~~~lN 162 (250)
T PRK00346 83 PDLVVSGINHGANLGDDVLYSGTVAAAMEGALLGIPAIAVSLAVSEGSRGWRDFETAAKVARELVRKLLEKPLPPGTLLN 162 (250)
T ss_pred CCEEEeCCccCCCCCCCeeccHHHHHHHHHHhcCCCeEEEecccccccCchhhHHHHHHHHHHHHHHHHhcCCCCCcEEE
Confidence 799999999999999998 10 0122247999999999999998875 33 9
Q ss_pred cccCCCc-cCCCcC
Q 033741 50 IQILTSP-LTNKVC 62 (112)
Q Consensus 50 I~iPt~p-~~nKGf 62 (112)
|+||..+ ...||+
T Consensus 163 vN~P~~~~~~~~g~ 176 (250)
T PRK00346 163 VNVPDLPPEEIKGI 176 (250)
T ss_pred EEeCCCCcccCCCE
Confidence 9999976 455887
No 4
>PRK13932 stationary phase survival protein SurE; Provisional
Probab=98.74 E-value=1.1e-08 Score=82.11 Aligned_cols=61 Identities=16% Similarity=0.153 Sum_probs=47.9
Q ss_pred eeEEEecccCCCCcccee-------------ecC---------CCchhhhhhhhhhhhhhHHHHhhh-cc-----ccccC
Q 033741 2 IFLVIGGINQGLICGHYM-------------KKD---------ESYESEFKDTISVFLPLRNGAIID-IE-----SIQIL 53 (112)
Q Consensus 2 ~~LVISGIN~GsnCG~h~-------------kk~---------eS~e~DFkdAa~vcLPLInAal~d-Ie-----NI~iP 53 (112)
+||||||||.|.|||..+ ..| ....+||..|+.++..|+...+.. ++ ||+||
T Consensus 92 pDLVvSGIN~G~N~G~dv~ySGTVgAA~Ea~~~GiPsIA~S~~~~~~~~~~~aa~~~~~l~~~l~~~~~p~~~~LNVN~P 171 (257)
T PRK13932 92 PDLIVSGINYGSNTATNTLYSGTVAAALEGAIQGIPSLAFSLTTYENADFTYAGKFARKLARKVLREGLPPDTILSVNIP 171 (257)
T ss_pred CCEEEECCcCCCCCCcCEecchhHHHHHHHHHcCCCeEEEEcccCCcCCHHHHHHHHHHHHHHHHhcCCCCCcEEEEEeC
Confidence 699999999999999998 011 112248999999999999987654 33 99999
Q ss_pred CCccC-CCcC
Q 033741 54 TSPLT-NKVC 62 (112)
Q Consensus 54 t~p~~-nKGf 62 (112)
..|.. .||+
T Consensus 172 ~~~~~~~~gi 181 (257)
T PRK13932 172 NVPESDIQGV 181 (257)
T ss_pred CCCccccCCE
Confidence 98744 5888
No 5
>PF01975 SurE: Survival protein SurE; InterPro: IPR002828 This entry represents a SurE-like structural domain with a 3-layer alpha/bete/alpha topology that bears some topological similarity to the N-terminal domain of the glutaminase/asparaginase family. This domain is found in the stationary phase survival protein SurE, a metal ion-dependent phosphatase found in eubacteria, archaea and eukaryotes. In Escherichia coli, SurE also has activity as a nucleotidase and exopolyphosphatase, and may be involved in the stress response []. E. coli cells with mutations in the surE gene survive poorly in stationary phase []. The structure of SurE homologues have been determined from Thermotoga maritima [] and the archaea Pyrobaculum aerophilum []. The T. maritima SurE homologue has phosphatase activity that is inhibited by vanadate or tungstate, both of which bind adjacent to the divalent metal ion. This domain is found in acid phosphatases (3.1.3.2 from EC), 5'-nucleotidases (3.1.3.5 from EC), 3'-nucleotidases (3.1.3.6 from EC) and exopolyphosphatases (3.6.1.11 from EC).; GO: 0016787 hydrolase activity; PDB: 1L5X_B 2V4O_D 2V4N_A 2WQK_B 2E6G_G 2E69_D 2E6C_C 2E6B_D 2E6E_A 2E6H_A ....
Probab=98.70 E-value=8.6e-09 Score=78.94 Aligned_cols=61 Identities=23% Similarity=0.296 Sum_probs=43.9
Q ss_pred eeEEEecccCCCCcccee-------------------------ecCCCchhhhhhhhhhhhhhHHHHhhh-cc-----cc
Q 033741 2 IFLVIGGINQGLICGHYM-------------------------KKDESYESEFKDTISVFLPLRNGAIID-IE-----SI 50 (112)
Q Consensus 2 ~~LVISGIN~GsnCG~h~-------------------------kk~eS~e~DFkdAa~vcLPLInAal~d-Ie-----NI 50 (112)
+||||||||.|.|+|..+ ...+..+.||+.|+.+...||...+.. ++ ||
T Consensus 92 pDLViSGiN~G~N~g~~v~~SGTVgAA~ea~~~GipaIA~S~~~~~~~~~~~~~~aa~~~~~~i~~~~~~~~~~~~~lNV 171 (196)
T PF01975_consen 92 PDLVISGINHGANLGTDVLYSGTVGAAMEAALRGIPAIAVSLDSDSESKDPDFETAARFAVKLIEKLLKNPLPPGVVLNV 171 (196)
T ss_dssp -SEEEEEEEES---GGGGGG-HHHHHHHHHHHTTSEEEEEEEESSST-SSCHHHHHHHHHHHHHHHHHHSGSSTTSEEEE
T ss_pred CCEEEECCCCCccCCcCcccccHHHHHHHHHHcCCCeEEEeccccCCCcHHHHHHHHHHHHHHHHHHhhcCCCCCcEEEE
Confidence 799999999999999997 222334568999999999999999954 32 99
Q ss_pred ccCCCc-cCCCcC
Q 033741 51 QILTSP-LTNKVC 62 (112)
Q Consensus 51 ~iPt~p-~~nKGf 62 (112)
+||..+ ..-||+
T Consensus 172 N~P~~~~~~~~g~ 184 (196)
T PF01975_consen 172 NFPSVPCEEIKGI 184 (196)
T ss_dssp EEESS-GGG-SEE
T ss_pred EcCCCCcccCCCE
Confidence 999976 444676
No 6
>TIGR00087 surE 5'/3'-nucleotidase SurE. E. coli SurE is Recommended cutoffs are 15 for homology, 40 for probable orthology, and 200 for orthology with full-length homology.
Probab=98.70 E-value=1.7e-08 Score=79.84 Aligned_cols=61 Identities=21% Similarity=0.200 Sum_probs=48.6
Q ss_pred eeEEEecccCCCCcccee-----------------------e---cCC--CchhhhhhhhhhhhhhHHHHhhh-cc----
Q 033741 2 IFLVIGGINQGLICGHYM-----------------------K---KDE--SYESEFKDTISVFLPLRNGAIID-IE---- 48 (112)
Q Consensus 2 ~~LVISGIN~GsnCG~h~-----------------------k---k~e--S~e~DFkdAa~vcLPLInAal~d-Ie---- 48 (112)
+||||||||.|.|+|..+ - .++ +..+||+.|+.++..|+..++.. ++
T Consensus 87 pDLVvSGiN~G~N~g~~v~ySGTVgAA~ea~~~GipaiA~S~~~~~~~~~~~~~~~~~aa~~~~~li~~l~~~~~p~~~~ 166 (244)
T TIGR00087 87 PDLVISGINAGENLGTDVTYSGTVGAAMEAAIHGVPAIAISLQIFNGYKNSSPLDFDIAAKVTNAIVKNLLKNGLPGGDL 166 (244)
T ss_pred CCeEEeccccCCCCCccEecchhHHHHHHHHHcCCCeEEEEecccCcccccccccHHHHHHHHHHHHHHHHhcCCCCCcE
Confidence 699999999999999987 1 111 22457999999999999988865 33
Q ss_pred -ccccCCCcc-CCCcC
Q 033741 49 -SIQILTSPL-TNKVC 62 (112)
Q Consensus 49 -NI~iPt~p~-~nKGf 62 (112)
||+||..|. ..||+
T Consensus 167 lNVN~P~~~~~~~~g~ 182 (244)
T TIGR00087 167 LNVNVPLVPSIQNTGI 182 (244)
T ss_pred EEEEeCCCCcccCCCE
Confidence 999999884 56887
No 7
>PRK13935 stationary phase survival protein SurE; Provisional
Probab=98.65 E-value=2.8e-08 Score=79.69 Aligned_cols=61 Identities=21% Similarity=0.268 Sum_probs=47.5
Q ss_pred eeEEEecccCCCCcccee-------------ecC-----CC----chhhhhhhhhhhhhhHHHHhhh-cc-----ccccC
Q 033741 2 IFLVIGGINQGLICGHYM-------------KKD-----ES----YESEFKDTISVFLPLRNGAIID-IE-----SIQIL 53 (112)
Q Consensus 2 ~~LVISGIN~GsnCG~h~-------------kk~-----eS----~e~DFkdAa~vcLPLInAal~d-Ie-----NI~iP 53 (112)
+||||||||.|.|||..+ ..| -| ...||+.|+.++..|+...+.. ++ ||+||
T Consensus 87 pDLVvSGIN~G~N~g~~v~ySGTVgAA~ea~~~GiPaiA~S~~~~~~~~~~~aa~~~~~l~~~l~~~~~p~~~~LNVN~P 166 (253)
T PRK13935 87 VDLVISGINRGPNLGTDVLYSGTVSGALEGAMMGVPSIAISSADFENPDYETAARFLLNFLEEFDFSLLPPFTALNINVP 166 (253)
T ss_pred CCEEEeCCccCCCCCcCCcccHhHHHHHHHHhcCCCeEEEEcccCCccCHHHHHHHHHHHHHHHHhcCCCCCcEEEEEeC
Confidence 699999999999999997 111 11 1248999999999999987665 33 99999
Q ss_pred CCcc-CCCcC
Q 033741 54 TSPL-TNKVC 62 (112)
Q Consensus 54 t~p~-~nKGf 62 (112)
..|. ..||+
T Consensus 167 ~~~~~~~~gi 176 (253)
T PRK13935 167 SVPYGEIKGW 176 (253)
T ss_pred cCChhhcCCe
Confidence 9874 34787
No 8
>PRK13934 stationary phase survival protein SurE; Provisional
Probab=98.47 E-value=1.3e-07 Score=76.60 Aligned_cols=60 Identities=17% Similarity=0.095 Sum_probs=39.7
Q ss_pred eeEEEecccCCCCccce-e-----------------------e--cC-CCch---hhhhhhhhhhhhhHHHHhhh-----
Q 033741 2 IFLVIGGINQGLICGHY-M-----------------------K--KD-ESYE---SEFKDTISVFLPLRNGAIID----- 46 (112)
Q Consensus 2 ~~LVISGIN~GsnCG~h-~-----------------------k--k~-eS~e---~DFkdAa~vcLPLInAal~d----- 46 (112)
+||||||||.|.|||+. + - +. ++.+ .+|..++.+...|+...+..
T Consensus 85 pDLViSGIN~G~NlG~d~v~ySGTVgAA~Ea~~~GIPsIAvS~~~~~~~~~~~~~~~~~~a~~~~~~lv~~l~~~~~p~~ 164 (266)
T PRK13934 85 YDLVLSGINLGDNTSLQVILSSGTLGAAFQAALLGIPAVAYSAYVDDWEELLEDGEALEIMKAVVRATAEYVLKRGMPKG 164 (266)
T ss_pred CCeEEecCccCCCCCcCcccccHhHHHHHHHHhcCCCEEEEecccCCcccccccchhHHHHHHHHHHHHHHHHhcCCCCC
Confidence 79999999999999998 4 1 10 1111 13666666655555554432
Q ss_pred --ccccccCCCccCCCcCC
Q 033741 47 --IESIQILTSPLTNKVCP 63 (112)
Q Consensus 47 --IeNI~iPt~p~~nKGf~ 63 (112)
+=||+||..|. ||+.
T Consensus 165 ~~~LNVN~P~~~~--~gi~ 181 (266)
T PRK13934 165 VDVISVNFPRRLR--RGVK 181 (266)
T ss_pred CcEEEEecCCCCC--CCCc
Confidence 12999999987 7773
No 9
>COG0496 SurE Predicted acid phosphatase [General function prediction only]
Probab=97.98 E-value=9e-06 Score=65.90 Aligned_cols=61 Identities=20% Similarity=0.149 Sum_probs=47.4
Q ss_pred eeEEEecccCCCCcccee-------------------------ec--CCCchhhhhhhhhhhhhhHHHHhhhcc------
Q 033741 2 IFLVIGGINQGLICGHYM-------------------------KK--DESYESEFKDTISVFLPLRNGAIIDIE------ 48 (112)
Q Consensus 2 ~~LVISGIN~GsnCG~h~-------------------------kk--~eS~e~DFkdAa~vcLPLInAal~dIe------ 48 (112)
+||||||||.|.|=|-.+ .+ ...+.-||.-|+.++.-|+...+....
T Consensus 84 pDLVvSGIN~G~Nlg~dv~ySGTVaaA~Ea~~~GipsIA~S~~~~~~~~~~~~~~e~A~~~~~~lv~~l~~~p~~~~~ll 163 (252)
T COG0496 84 PDLVVSGINAGANLGDDVIYSGTVAAAMEAALLGIPAIAISLAYREAFGKQDVDFETAAKVARALVEALLANPLPPDTLL 163 (252)
T ss_pred CCEEEeCccCCCccccceeeeehHHHHHHHHHcCccceeeeehhccccccccccHHHHHHHHHHHHHHHHhCCCCCCcEE
Confidence 799999999999999876 11 111223899999999999999999833
Q ss_pred ccccCCC-ccCCCcC
Q 033741 49 SIQILTS-PLTNKVC 62 (112)
Q Consensus 49 NI~iPt~-p~~nKGf 62 (112)
||+||.. +...||.
T Consensus 164 NVNiP~~~~~~~~gi 178 (252)
T COG0496 164 NVNIPNLPLEEIKGI 178 (252)
T ss_pred EEeCCCCCccccCcE
Confidence 9999984 4456666
No 10
>PF03764 EFG_IV: Elongation factor G, domain IV; InterPro: IPR005517 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. Elongation factor EF2 (EF-G) is a G-protein. It brings about the translocation of peptidyl-tRNA and mRNA through a ratchet-like mechanism: the binding of GTP-EF2 to the ribosome causes a counter-clockwise rotation in the small ribosomal subunit; the hydrolysis of GTP to GDP by EF2 and the subsequent release of EF2 causes a clockwise rotation of the small subunit back to the starting position [, ]. This twisting action destabilises tRNA-ribosome interactions, freeing the tRNA to translocate along the ribosome upon GTP-hydrolysis by EF2. EF2 binding also affects the entry and exit channel openings for the mRNA, widening it when bound to enable the mRNA to translocate along the ribosome. EF2 has five domains. This entry represents domain IV found in EF2 (or EF-G) of both prokaryotes and eukaryotes. The EF2-GTP-ribosome complex undergoes extensive structural rearrangement for tRNA-mRNA movement to occur. Domain IV, which extends from the 'body' of the EF2 molecule much like a lever arm, appears to be essential for the structural transition to take place. More information about these proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005525 GTP binding; PDB: 3J0E_H 1FNM_A 3IZP_E 2OM7_L 1KTV_A 2J7K_A 2BM1_A 2BM0_A 2BV3_A 1ZM3_E ....
Probab=39.70 E-value=25 Score=23.77 Aligned_cols=30 Identities=17% Similarity=0.383 Sum_probs=23.5
Q ss_pred cccCCCCcccee------------ecCCCchhhhhhhhhhhh
Q 033741 8 GINQGLICGHYM------------KKDESYESEFKDTISVFL 37 (112)
Q Consensus 8 GIN~GsnCG~h~------------kk~eS~e~DFkdAa~vcL 37 (112)
..+.|--|||.| -...|++..|..|+.-|+
T Consensus 71 a~~~Gpl~g~pv~~v~v~l~~~~~~~~~s~~~a~~~aa~~a~ 112 (120)
T PF03764_consen 71 ALSSGPLCGYPVTDVKVTLTDGEYHEVDSSPGAFRAAARRAF 112 (120)
T ss_dssp HHCSSTTTSSEB-SEEEEEEEEEC-TTTBSHHHHHHHHHHHH
T ss_pred eecccccCCCceEEEEEEEEEeeecCCcCCHHHHHHHHHHHH
Confidence 456788899998 235799999999998775
No 11
>cd03751 proteasome_alpha_type_3 proteasome_alpha_type_3. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.
Probab=26.41 E-value=89 Score=23.70 Aligned_cols=28 Identities=7% Similarity=0.073 Sum_probs=22.3
Q ss_pred chhhhhhhhhhhhhhHHHHhhhcc----cccc
Q 033741 25 YESEFKDTISVFLPLRNGAIIDIE----SIQI 52 (112)
Q Consensus 25 ~e~DFkdAa~vcLPLInAal~dIe----NI~i 52 (112)
.+=++.+|...++=.++.++.+.+ ||||
T Consensus 178 ~dms~eeai~l~~~~L~~~~~~~~~~~~~iei 209 (212)
T cd03751 178 SELTCREAVKEAAKIIYIVHDEIKDKAFELEL 209 (212)
T ss_pred CCCCHHHHHHHHHHHHHHHhhccCCCCccEEE
Confidence 345678899999999999999664 7775
No 12
>cd01684 Tet_like_IV EF-G_domain IV_RPP domain is a part of bacterial ribosomal protected proteins (RPP) family. RPPs such as tetracycline resistance proteins Tet(M) and Tet(O) mediate tetracycline resistance in both gram-positive and -negative species. Tetracyclines inhibit the accommodation of aminoacyl-tRNA into ribosomal A site and therefore prevent the addition of new amino acids to the growing polypeptide. RPPs Tet(M) confer tetracycline resistance by releasing tetracycline from the ribosome and thereby freeing the ribosome from inhibitory effects of the drug, such that aa-tRNA can bind to the A site and protein synthesis can continue.
Probab=25.96 E-value=62 Score=22.38 Aligned_cols=28 Identities=25% Similarity=0.430 Sum_probs=21.8
Q ss_pred ccCCCCcccee------------ecCCCchhhhhhhhhhhh
Q 033741 9 INQGLICGHYM------------KKDESYESEFKDTISVFL 37 (112)
Q Consensus 9 IN~GsnCG~h~------------kk~eS~e~DFkdAa~vcL 37 (112)
...|-. ||.+ -.+.|++-+|+.|+.-|+
T Consensus 68 l~~G~l-G~pv~dv~V~l~~~~~h~~~ss~~af~~Aa~~a~ 107 (115)
T cd01684 68 LQQGLY-GWEVTDCKVTLTYGRYHSPVSTAADFRELTPRVL 107 (115)
T ss_pred HhcCCC-CCCEeeEEEEEEEeeecCCCCCHHHHHHHHHHHH
Confidence 456777 8886 455799999999999873
No 13
>cd01680 EFG_like_IV Elongation Factor G-like domain IV. This family includes the translational elongation factor termed EF-2 (for Archaea and Eukarya) and EF-G (for Bacteria), ribosomal protection proteins that mediate tetracycline resistance and, an evolutionarily conserved U5 snRNP-specific protein (U5-116kD). In complex with GTP, EF-G/EF-2 promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site of the small subunit of ribosome and the mRNA is shifted one codon relative to the ribosome. It has been shown that EF-G/EF-2_IV domain mimics the shape of anticodon arm of the tRNA in the structurally homologous ternary complex of Petra, EF-Tu (another transcriptional elongation factor) and GTP analog. The tip portion of this domain is found in a position that overlaps the anticodon arm of the A-site tRNA, implying that EF-G/EF-2 displaces the A-site tRNA to the P-site by physical interaction with the anticodon arm.
Probab=23.79 E-value=60 Score=21.62 Aligned_cols=29 Identities=17% Similarity=0.226 Sum_probs=20.6
Q ss_pred cccCCCCcccee------------ecCCCchhhhhhhhhhh
Q 033741 8 GINQGLICGHYM------------KKDESYESEFKDTISVF 36 (112)
Q Consensus 8 GIN~GsnCG~h~------------kk~eS~e~DFkdAa~vc 36 (112)
..+.|--|||.| -.+.|.+..|+.|+.-|
T Consensus 67 a~~~Gpl~g~pv~~v~v~l~~~~~~~~~~~~~~~~~aa~~a 107 (116)
T cd01680 67 ACASGPLTGYPLTDVRVTVLDVPYHEGVSTEAGFRAAAGRA 107 (116)
T ss_pred HHhcCcccCCceeeEEEEEEEEEecCCCCCHHHHHHHHHHH
Confidence 457888999998 23356777887777655
No 14
>PLN02314 pectinesterase
Probab=23.05 E-value=80 Score=28.58 Aligned_cols=41 Identities=17% Similarity=0.050 Sum_probs=27.7
Q ss_pred hhhhhhhhhhhHHHHhhhccccccCC-CccCC------CcCCChhhhh
Q 033741 29 FKDTISVFLPLRNGAIIDIESIQILT-SPLTN------KVCPSKGTIS 69 (112)
Q Consensus 29 FkdAa~vcLPLInAal~dIeNI~iPt-~p~~n------KGf~~W~aVs 69 (112)
...-.+-+|.|++.....+.+.++|. ..+.. .|||+|-...
T Consensus 219 ~~eLtSNaLAIi~~l~~~~~~~~~~~~~~l~~~~~~~~~~~p~w~~~~ 266 (586)
T PLN02314 219 STEFTSNSLAIVSKILGILSDLGIPIHRRLLSFHHDLSSGFPSWVNIG 266 (586)
T ss_pred HHHHHHHHHHHHhhhccccccccccccccccccccccccCCCcccccc
Confidence 34446788999999777777776663 23322 5999996544
No 15
>PF03361 Herpes_IE2_3: Herpes virus intermediate/early protein 2/3; InterPro: IPR005028 This domain of unknown function is found in the intermediate/early proteins of the Herpes virus. Many of these proteins play a role in transcriptional regulation.; GO: 0006355 regulation of transcription, DNA-dependent
Probab=22.42 E-value=57 Score=25.36 Aligned_cols=20 Identities=20% Similarity=0.368 Sum_probs=16.6
Q ss_pred CCchhhhhhhhhhhhhhHHH
Q 033741 23 ESYESEFKDTISVFLPLRNG 42 (112)
Q Consensus 23 eS~e~DFkdAa~vcLPLInA 42 (112)
.-..-||=+|+.+|+||+.-
T Consensus 115 AATp~Dfl~A~~lC~~~~~k 134 (162)
T PF03361_consen 115 AATPKDFLGAAKLCLPLAQK 134 (162)
T ss_pred CCCcHHHHHHHHHHHHHHHh
Confidence 34567999999999999864
No 16
>PF11884 DUF3404: Domain of unknown function (DUF3404); InterPro: IPR021821 This domain is functionally uncharacterised. This domain is found in bacteria. This presumed domain is about 260 amino acids in length. This domain is found associated with PF02518 from PFAM, PF00512 from PFAM.
Probab=20.62 E-value=1.5e+02 Score=24.76 Aligned_cols=43 Identities=19% Similarity=0.006 Sum_probs=36.2
Q ss_pred eeEEEecccCCCCcccee---ecCCCchhhhhhhhhhhhhhHHHHh
Q 033741 2 IFLVIGGINQGLICGHYM---KKDESYESEFKDTISVFLPLRNGAI 44 (112)
Q Consensus 2 ~~LVISGIN~GsnCG~h~---kk~eS~e~DFkdAa~vcLPLInAal 44 (112)
+.|-++.++.|++|.+.. |=++...++.-.-.-++|-++|..+
T Consensus 200 ~~l~l~~~~~~~sC~~r~gNlCw~~~~~s~l~~~~~i~L~~~~i~l 245 (262)
T PF11884_consen 200 AGLTLSLRSAGNSCFVRYGNLCWSEEDHSHLLRISMIALVLANILL 245 (262)
T ss_pred cCceEecccCCCcccceecceeeccCCchhHHHHHHHHHHHHHHHH
Confidence 356789999999999985 8888888898888888998888765
No 17
>PF12252 SidE: Dot/Icm substrate protein; InterPro: IPR021014 This entry represents bacterial proteins that are typically between 397 and 1543 amino acids in length including SidE protein in the Dot/Icm pathway of Legionella pneumophila bacteria. There is little literature describing the family.
Probab=20.42 E-value=61 Score=32.77 Aligned_cols=12 Identities=50% Similarity=1.187 Sum_probs=10.4
Q ss_pred ecccCCCCcccee
Q 033741 7 GGINQGLICGHYM 19 (112)
Q Consensus 7 SGIN~GsnCG~h~ 19 (112)
+|.|||. |||-+
T Consensus 111 ~~ln~gl-cgywv 122 (1439)
T PF12252_consen 111 PGLNMGL-CGYWV 122 (1439)
T ss_pred CCcCccc-hhhhh
Confidence 6899985 99987
Done!