Query psy12294
Match_columns 123
No_of_seqs 105 out of 1017
Neff 4.1
Searched_HMMs 46136
Date Fri Aug 16 23:41:57 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12294.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12294hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00070 40S ribosomal protein 100.0 5.1E-41 1.1E-45 273.6 7.6 103 16-118 149-253 (257)
2 TIGR01020 rpsE_arch ribosomal 100.0 1.5E-31 3.3E-36 213.2 6.3 87 17-104 122-210 (212)
3 COG0098 RpsE Ribosomal protein 100.0 1.1E-30 2.4E-35 204.3 5.8 88 17-108 87-176 (181)
4 KOG0877|consensus 100.0 3.6E-31 7.9E-36 210.6 2.8 93 15-107 119-213 (213)
5 PRK04044 rps5p 30S ribosomal p 100.0 1.7E-30 3.7E-35 207.0 6.2 86 18-103 123-210 (211)
6 TIGR01021 rpsE_bact ribosomal 99.9 6.7E-26 1.5E-30 172.8 6.3 77 18-99 66-144 (154)
7 PRK00550 rpsE 30S ribosomal pr 99.9 2E-25 4.2E-30 172.4 5.4 77 22-102 80-158 (168)
8 PF03719 Ribosomal_S5_C: Ribos 99.9 4.9E-25 1.1E-29 150.2 3.4 63 29-92 1-65 (74)
9 CHL00138 rps5 ribosomal protei 99.8 2.5E-20 5.5E-25 141.1 6.8 56 18-73 88-143 (143)
10 KOG2646|consensus 98.1 4.7E-07 1E-11 78.2 0.1 75 16-91 247-323 (396)
11 PRK13186 lpxC UDP-3-O-[3-hydro 63.8 5.4 0.00012 33.7 2.2 17 35-51 23-39 (295)
12 TIGR00325 lpxC UDP-3-0-acyl N- 62.0 5.8 0.00013 33.7 2.1 17 35-51 22-38 (297)
13 PF03331 LpxC: UDP-3-O-acyl N- 57.3 7.3 0.00016 32.6 1.9 16 35-50 22-37 (277)
14 PHA00736 hypothetical protein 57.2 4 8.7E-05 28.4 0.3 13 1-13 52-64 (79)
15 COG0774 LpxC UDP-3-O-acyl-N-ac 49.2 23 0.00049 30.5 3.6 28 23-50 9-38 (300)
16 PRK13187 UDP-3-O-[3-hydroxymyr 47.8 14 0.0003 31.6 2.1 31 21-51 10-49 (304)
17 PRK13188 bifunctional UDP-3-O- 46.7 14 0.0003 33.1 2.1 17 35-51 24-40 (464)
18 PRK14747 cytochrome b6-f compl 39.9 14 0.0003 21.6 0.7 15 1-15 1-15 (29)
19 PF14999 Shadoo: Shadow of pri 38.3 15 0.00033 27.9 0.8 17 32-48 25-41 (131)
20 CHL00009 petN cytochrome b6/f 35.7 21 0.00046 20.8 1.0 15 1-15 1-15 (29)
21 PF03742 PetN: PetN ; InterPr 29.4 26 0.00057 20.4 0.7 14 1-14 1-14 (29)
22 cd01434 EFG_mtEFG1_IV EFG_mtEF 28.5 42 0.00091 23.4 1.8 18 32-49 24-41 (116)
23 PF01989 DUF126: Protein of un 27.6 15 0.00033 25.6 -0.6 39 7-49 4-42 (82)
24 PRK03955 hypothetical protein; 27.5 32 0.0007 25.9 1.1 38 6-47 25-62 (131)
25 cd01684 Tet_like_IV EF-G_domai 27.0 49 0.0011 23.3 1.9 17 33-49 25-41 (115)
26 cd01356 AcnX_swivel Putative A 22.5 48 0.001 24.8 1.2 39 7-49 19-57 (123)
27 PF11267 DUF3067: Protein of u 21.9 58 0.0013 23.7 1.5 25 97-121 31-57 (99)
No 1
>PTZ00070 40S ribosomal protein S2; Provisional
Probab=100.00 E-value=5.1e-41 Score=273.57 Aligned_cols=103 Identities=44% Similarity=0.686 Sum_probs=99.6
Q ss_pred CceecCCCeeeEEEEEEecceEEEeecCCCcceEeeCChhHHHHHhcCCceeeeccCCCCCCcccchhcc--eecccccc
Q psy12294 16 GILFCQHKVLGLIVTGKCGSVQVRLIPAPRGTGIVGAPVPKKLLQMAGIEDCYTSARGSTGTLGNFGECN--TQHETSSY 93 (123)
Q Consensus 16 g~~i~~~~TIph~v~Gk~gs~~V~L~PAp~GtGIVAg~~~r~VlelAGIkDv~tks~Gstnt~~N~~kAT--AL~~~~~~ 93 (123)
|+++++||||||+|+|||||++|+|+|||+|+||||++++|+|||+|||+|||||++|||++++|++||| ||+++|+|
T Consensus 149 ~~~~g~~hTIp~~V~GK~GSv~V~L~PAP~GtGivAg~~vk~VLelAGIkDv~tks~GsTrt~~N~aKATf~AL~~t~~~ 228 (257)
T PTZ00070 149 GNKIGEPHTVPMKVTGKCGSVRVRLVPAPRGTGIVAAPTPKKILEFAGVEDVFTSSRGKTRTRGNFLKATFYALRKTYGF 228 (257)
T ss_pred cccCCCCCCeeeeEEEEeCeEEEEEEeCCCCccEEeCcHHHHHHHHcCccceeeecccCCCChHHHHHHHHHHHHHHhcc
Confidence 3568899999999999999999999999999999999999999999999999999999998888999999 99999999
Q ss_pred cCchhhhhcccccCchHHHHHHHHH
Q psy12294 94 TETQCMQVLVSSHFPISESLNTISE 118 (123)
Q Consensus 94 ~tP~~w~~~~~~~~P~~e~~d~~~~ 118 (123)
+|||+|++..++++|||||+|+|++
T Consensus 229 ~tp~~w~~~~~~~~p~~~~~~~l~~ 253 (257)
T PTZ00070 229 LTPDLWKETELSRSPYDEHSEFLAE 253 (257)
T ss_pred cCHhHccccccCCCchHHHHHHHhh
Confidence 9999999999999999999999976
No 2
>TIGR01020 rpsE_arch ribosomal protein S5(archaeal type)/S2(eukaryote cytosolic type). This model finds eukaryotic ribosomal protein S2 as well as archaeal ribosomal protein S5.
Probab=99.97 E-value=1.5e-31 Score=213.24 Aligned_cols=87 Identities=41% Similarity=0.615 Sum_probs=81.8
Q ss_pred ceecCCCeeeEEEEEEecceEEEeecCCCcceEeeCChhHHHHHhcCCceeeeccCCCCCCcccchhcc--eeccccccc
Q psy12294 17 ILFCQHKVLGLIVTGKCGSVQVRLIPAPRGTGIVGAPVPKKLLQMAGIEDCYTSARGSTGTLGNFGECN--TQHETSSYT 94 (123)
Q Consensus 17 ~~i~~~~TIph~v~Gk~gs~~V~L~PAp~GtGIVAg~~~r~VlelAGIkDv~tks~Gstnt~~N~~kAT--AL~~~~~~~ 94 (123)
+.++++|||||+|+|||||++|.|+|||+|+||+|++++|+|||+|||+||+||++|||++..|++||| ||++++ |+
T Consensus 122 ~~~~~~hTIp~~v~Gk~gs~~V~L~PAP~GtGliag~~~r~ilelAGIkDv~tk~~Gstrn~~N~~kAtf~AL~~~~-~~ 200 (212)
T TIGR01020 122 CGCGRPHSVPFKVTGKCGSVRVRLIPAPRGLGLVAGDVAKKVLRLAGIDDVWTQTRGETRTTVNFAKATFDALKKTY-YV 200 (212)
T ss_pred ccCCCCCcEeEEEEEEEccEEEEEEeCCCCCceecCcHHHHHHHHcCccceeeeccCCCCChhHHHHHHHHHHHhcc-cc
Confidence 456889999999999999999999999999999999999999999999999999999997677999999 999999 99
Q ss_pred Cchhhhhccc
Q psy12294 95 ETQCMQVLVS 104 (123)
Q Consensus 95 tP~~w~~~~~ 104 (123)
+|++|++..+
T Consensus 201 ~~~~~~~~~~ 210 (212)
T TIGR01020 201 TPDLWAEERL 210 (212)
T ss_pred Ccchhccccc
Confidence 9999987654
No 3
>COG0098 RpsE Ribosomal protein S5 [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=1.1e-30 Score=204.31 Aligned_cols=88 Identities=25% Similarity=0.374 Sum_probs=80.3
Q ss_pred ceecCCCeeeEEEEEEecceEEEeecCCCcceEeeCChhHHHHHhcCCceeeeccCCCCCCcccchhcc--eeccccccc
Q psy12294 17 ILFCQHKVLGLIVTGKCGSVQVRLIPAPRGTGIVGAPVPKKLLQMAGIEDCYTSARGSTGTLGNFGECN--TQHETSSYT 94 (123)
Q Consensus 17 ~~i~~~~TIph~v~Gk~gs~~V~L~PAp~GtGIVAg~~~r~VlelAGIkDv~tks~Gstnt~~N~~kAT--AL~~~~~~~ 94 (123)
.++.++|||||+|.||||+++|+|+|||+|||||||+++|+|||+|||+||||||+||+|++ |++||| ||+++ +
T Consensus 87 V~~~~~~Tiph~v~Gk~g~~~V~L~PA~~GtGiiAGg~~r~vlelAGi~Dv~tks~GS~n~~-N~vrAt~~aL~~~---~ 162 (181)
T COG0098 87 VPRGNGHTIPHEVIGKHGAVKVLLKPAPEGTGIIAGGAVRAVLELAGIKDVLAKSLGSRNPI-NVVRATFDALKKL---R 162 (181)
T ss_pred EecCCCceeeeEEEEEECcEEEEEEECCCCceEEeCcHHHHHHHHcCchhhhhhccCCCChh-HHHHHHHHHHHHc---c
Confidence 45678999999999999999999999999999999999999999999999999999988876 999999 99954 6
Q ss_pred CchhhhhcccccCc
Q psy12294 95 ETQCMQVLVSSHFP 108 (123)
Q Consensus 95 tP~~w~~~~~~~~P 108 (123)
+|++|.+.+-...+
T Consensus 163 ~p~~ia~~Rg~~~~ 176 (181)
T COG0098 163 TPEDVAAKRGKKVE 176 (181)
T ss_pred CHHHHHHHcCCcch
Confidence 99999888766544
No 4
>KOG0877|consensus
Probab=99.96 E-value=3.6e-31 Score=210.63 Aligned_cols=93 Identities=55% Similarity=0.803 Sum_probs=90.2
Q ss_pred cCceecCCCeeeEEEEEEecceEEEeecCCCcceEeeCChhHHHHHhcCCceeeeccCCCCCCcccchhcc--eeccccc
Q psy12294 15 SGILFCQHKVLGLIVTGKCGSVQVRLIPAPRGTGIVGAPVPKKLLQMAGIEDCYTSARGSTGTLGNFGECN--TQHETSS 92 (123)
Q Consensus 15 ~g~~i~~~~TIph~v~Gk~gs~~V~L~PAp~GtGIVAg~~~r~VlelAGIkDv~tks~Gstnt~~N~~kAT--AL~~~~~ 92 (123)
-||+|++|||+||+++|+||++.|+|.|||||||||+++++|++|+||||+||+++++|||++++|++||+ |+.++|+
T Consensus 119 w~~~~g~pHt~~~kvtg~~~svlv~l~papRgtGivs~p~~kkll~mAGi~d~~t~~~G~t~tl~n~~ka~~~a~~~ty~ 198 (213)
T KOG0877|consen 119 WGNKIGKPHTVPCKVTGDCGSVLVRLIPAPRGTGIVSAPVPKKLLMMAGIDDCYTSARGCTATLGNFAKATFDAISKTYS 198 (213)
T ss_pred cccccCCCccccCcccccCCcceEEEeecCCCCceeeccccHHHHHhccccccchhhcccchhhccHHHHHHHHHHhhhh
Confidence 35999999999999999999999999999999999999999999999999999999999999999999999 9999999
Q ss_pred ccCchhhhhcccccC
Q psy12294 93 YTETQCMQVLVSSHF 107 (123)
Q Consensus 93 ~~tP~~w~~~~~~~~ 107 (123)
|+|||+|++++++++
T Consensus 199 ~ltp~~w~e~~~~~~ 213 (213)
T KOG0877|consen 199 YLTPDLWKETVFTKS 213 (213)
T ss_pred hhChhhccccccccC
Confidence 999999999998764
No 5
>PRK04044 rps5p 30S ribosomal protein S5P; Reviewed
Probab=99.96 E-value=1.7e-30 Score=206.97 Aligned_cols=86 Identities=36% Similarity=0.470 Sum_probs=80.6
Q ss_pred eecCCCeeeEEEEEEecceEEEeecCCCcceEeeCChhHHHHHhcCCceeeeccCCCCCCcccchhcc--eecccccccC
Q psy12294 18 LFCQHKVLGLIVTGKCGSVQVRLIPAPRGTGIVGAPVPKKLLQMAGIEDCYTSARGSTGTLGNFGECN--TQHETSSYTE 95 (123)
Q Consensus 18 ~i~~~~TIph~v~Gk~gs~~V~L~PAp~GtGIVAg~~~r~VlelAGIkDv~tks~Gstnt~~N~~kAT--AL~~~~~~~t 95 (123)
...++|||||+|+|||||++|.|+|||+|+||+|++.+|+|||+|||+||++|++|||++..|++||| ||++++++++
T Consensus 123 ~~~~~~TI~h~v~gk~gs~~V~l~Pap~GtGiiag~~vr~vlelaGIkDv~aK~~Gstrn~~N~vkAt~~AL~~~~~~~~ 202 (211)
T PRK04044 123 GCGEPHSVPFKVTGKAGSVEVTLKPAPRGLGLVAGDVAKKVLELAGIKDVWTRTFGETRTTVNFAKATFNALKNTYKVRT 202 (211)
T ss_pred cCCCCCcCCeEEEEEEccEEEEEEECCCCCeEEECcHHHHHHHHcCcceEEEEccCCCCChhHHHHHHHHHHHHHHcccC
Confidence 35678999999999999999999999999999999999999999999999999999985566999999 9999999999
Q ss_pred chhhhhcc
Q psy12294 96 TQCMQVLV 103 (123)
Q Consensus 96 P~~w~~~~ 103 (123)
|++|.+..
T Consensus 203 p~~~~~~~ 210 (211)
T PRK04044 203 PPDWAEKR 210 (211)
T ss_pred HHHHHhhc
Confidence 99998753
No 6
>TIGR01021 rpsE_bact ribosomal protein S5, bacterial/organelle type. This model finds chloroplast ribosomal protein S5 as well as bacterial ribosomal protein S5. A candidate mitochondrial form (Saccharomyces cerevisiae YBR251W and its homolog) differs substantially and is not included in this model.
Probab=99.92 E-value=6.7e-26 Score=172.79 Aligned_cols=77 Identities=22% Similarity=0.380 Sum_probs=70.9
Q ss_pred eecCCCeeeEEEEEEecceEEEeecCCCcceEeeCChhHHHHHhcCCceeeeccCCCCCCcccchhcc--eecccccccC
Q psy12294 18 LFCQHKVLGLIVTGKCGSVQVRLIPAPRGTGIVGAPVPKKLLQMAGIEDCYTSARGSTGTLGNFGECN--TQHETSSYTE 95 (123)
Q Consensus 18 ~i~~~~TIph~v~Gk~gs~~V~L~PAp~GtGIVAg~~~r~VlelAGIkDv~tks~Gstnt~~N~~kAT--AL~~~~~~~t 95 (123)
++.++ ||||+++|||||++|.|+|||+|+||+|++.+|+|||+|||+||++|++||+|++ |++||| ||++++ |
T Consensus 66 ~~~~~-Ti~~~v~gk~gs~~V~l~Pap~G~Gi~a~~~~~~il~laGI~Dv~~k~~Gs~n~~-n~vkAt~~aL~~~~---s 140 (154)
T TIGR01021 66 PLTKG-TIPHEVIGVSGAAKVLLKPASPGTGVIAGGAVRAILELAGVKDILAKSLGSNNPI-NVVRATFDALLKLK---S 140 (154)
T ss_pred ecCCC-ccceEEEEEECcEEEEEEECCCCCceEeCcHHHHHHHHcCcceEEEEccCCCChH-HHHHHHHHHHHcCC---C
Confidence 34555 9999999999999999999999999999999999999999999999999999887 999999 999976 6
Q ss_pred chhh
Q psy12294 96 TQCM 99 (123)
Q Consensus 96 P~~w 99 (123)
|+..
T Consensus 141 ~~~i 144 (154)
T TIGR01021 141 PEDV 144 (154)
T ss_pred HHHH
Confidence 6654
No 7
>PRK00550 rpsE 30S ribosomal protein S5; Validated
Probab=99.91 E-value=2e-25 Score=172.36 Aligned_cols=77 Identities=23% Similarity=0.398 Sum_probs=71.5
Q ss_pred CCeeeEEEEEEecceEEEeecCCCcceEeeCChhHHHHHhcCCceeeeccCCCCCCcccchhcc--eecccccccCchhh
Q psy12294 22 HKVLGLIVTGKCGSVQVRLIPAPRGTGIVGAPVPKKLLQMAGIEDCYTSARGSTGTLGNFGECN--TQHETSSYTETQCM 99 (123)
Q Consensus 22 ~~TIph~v~Gk~gs~~V~L~PAp~GtGIVAg~~~r~VlelAGIkDv~tks~Gstnt~~N~~kAT--AL~~~~~~~tP~~w 99 (123)
+|||||++.|||||++|.|+|||+|+||+|++.+|+|||+|||+||++|++||+|++ |++||| ||++++ ||+..
T Consensus 80 ~~Ti~~~v~gk~gs~kV~l~Pap~G~Gl~a~~~i~~il~laGI~dv~~k~~Gs~n~~-n~vkA~~~aL~~~~---s~~~i 155 (168)
T PRK00550 80 GGTIPHEVIGKFGAAKVLLKPASEGTGVIAGGAVRAVLELAGVKDVLAKSLGSNNPI-NVVRATFDALKQLR---SPEEV 155 (168)
T ss_pred CCccceeEEEEEceEEEEEEeCCCCCceEeChHHHHHHHHcCccceeeeccCCCChH-HHHHHHHHHHHhCC---CHHHH
Confidence 899999999999999999999999999999999999999999999999999999876 999999 999987 77654
Q ss_pred hhc
Q psy12294 100 QVL 102 (123)
Q Consensus 100 ~~~ 102 (123)
.+.
T Consensus 156 a~~ 158 (168)
T PRK00550 156 AAK 158 (168)
T ss_pred HHH
Confidence 443
No 8
>PF03719 Ribosomal_S5_C: Ribosomal protein S5, C-terminal domain; InterPro: IPR005324 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 is a family of proteins related to the 30S ribosomal protein S5P from Sulfolobus acidocaldarius (O05641 from SWISSPROT). Ribosomal protein S5 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S5 is known to be important in the assembly and function of the 30S ribosomal subunit. Mutations in S5 have been shown to increase translational error frequencies.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2XZN_E 2XZM_E 2WDK_E 3KNJ_E 3HUY_E 2B9M_E 2Y18_E 1XMQ_E 1IBM_E 3TVF_H ....
Probab=99.91 E-value=4.9e-25 Score=150.18 Aligned_cols=63 Identities=40% Similarity=0.670 Sum_probs=60.2
Q ss_pred EEEEecceEEEeecCCCcceEeeCChhHHHHHhcCCceeeeccCCCCCCcccchhcc--eeccccc
Q psy12294 29 VTGKCGSVQVRLIPAPRGTGIVGAPVPKKLLQMAGIEDCYTSARGSTGTLGNFGECN--TQHETSS 92 (123)
Q Consensus 29 v~Gk~gs~~V~L~PAp~GtGIVAg~~~r~VlelAGIkDv~tks~Gstnt~~N~~kAT--AL~~~~~ 92 (123)
|+||||+++|.|+|||+|+||+|++.+|+|||+|||+||++|++||+|++ |++||| ||+++++
T Consensus 1 V~gk~g~~~V~l~Pap~G~Gl~a~~~vr~il~laGI~Dv~~K~~Gs~n~~-n~v~A~~~aL~~~~s 65 (74)
T PF03719_consen 1 VTGKFGATKVFLKPAPPGTGLVAGGAVRAILELAGIKDVYAKSRGSRNPI-NVVKATFKALKNQRS 65 (74)
T ss_dssp EEEEETTEEEEEEESCTTSCEESSHHHHHHHHHTTESSEEEEEESBSSHH-HHHHHHHHHHHTSCS
T ss_pred CEEEEeeEEEEEEeCCCCcceeechhHHHHHHhcccccEEeeccCCCChh-hHHHHHHHHHHhcCC
Confidence 78999999999999999999999999999999999999999999988765 999999 9999983
No 9
>CHL00138 rps5 ribosomal protein S5; Validated
Probab=99.82 E-value=2.5e-20 Score=141.10 Aligned_cols=56 Identities=23% Similarity=0.446 Sum_probs=53.8
Q ss_pred eecCCCeeeEEEEEEecceEEEeecCCCcceEeeCChhHHHHHhcCCceeeeccCC
Q psy12294 18 LFCQHKVLGLIVTGKCGSVQVRLIPAPRGTGIVGAPVPKKLLQMAGIEDCYTSARG 73 (123)
Q Consensus 18 ~i~~~~TIph~v~Gk~gs~~V~L~PAp~GtGIVAg~~~r~VlelAGIkDv~tks~G 73 (123)
++.++|||||+|+|||||++|.|+|||+|+||+|++.+|+|||+|||+||++|++|
T Consensus 88 ~~~~~~TI~~~v~gk~gs~~V~l~Pap~G~Gi~a~~~i~~vlelaGI~Dv~aK~~G 143 (143)
T CHL00138 88 PLTKSNSIPHNITGIFGAAKVILRPSAPGSGVIAGGSVRIVLELAGIKNILAKQLG 143 (143)
T ss_pred EcCCCCeEeeEEEEEEeeEEEEEEECCCCCcEEECcHHHHHHHHcCcceeEeeecC
Confidence 45688999999999999999999999999999999999999999999999999987
No 10
>KOG2646|consensus
Probab=98.14 E-value=4.7e-07 Score=78.17 Aligned_cols=75 Identities=19% Similarity=0.261 Sum_probs=69.3
Q ss_pred CceecCCCeeeEEEEEEecceEEEeecCCCcceEeeCChhHHHHHhcCCceeeeccCCCCCCcccchhcc--eecccc
Q psy12294 16 GILFCQHKVLGLIVTGKCGSVQVRLIPAPRGTGIVGAPVPKKLLQMAGIEDCYTSARGSTGTLGNFGECN--TQHETS 91 (123)
Q Consensus 16 g~~i~~~~TIph~v~Gk~gs~~V~L~PAp~GtGIVAg~~~r~VlelAGIkDv~tks~Gstnt~~N~~kAT--AL~~~~ 91 (123)
++.--+.+||-+++.-+|-.+++.|+-+|+|-|+-..+...+|++.+||+|++.|..||.|-+ |+++|+ ||.++.
T Consensus 247 ~ieRyE~rTiygDi~~r~~~~~l~mk~rp~GfGLrcn~il~kIC~~~GIKDis~kv~GsrN~m-~i~k~~~e~l~~qe 323 (396)
T KOG2646|consen 247 YIERYERRTIYGDIDDRFHEVRLDMKSRPDGFGLRCNPILIKICECAGIKDISGKVKGSRNEM-NITKAAFEALALQE 323 (396)
T ss_pred ccccccCccccccchhhhhhhhhhhhhCCCcccccccHHHHHHHHHhccccccceeeccchHH-HHHHHHHHHHhhhh
Confidence 366677899999999999999999999999999999999999999999999999999999866 999999 877765
No 11
>PRK13186 lpxC UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed
Probab=63.81 E-value=5.4 Score=33.73 Aligned_cols=17 Identities=53% Similarity=0.694 Sum_probs=14.1
Q ss_pred ceEEEeecCCCcceEee
Q psy12294 35 SVQVRLIPAPRGTGIVG 51 (123)
Q Consensus 35 s~~V~L~PAp~GtGIVA 51 (123)
.++|.++|||.|+||+=
T Consensus 23 ~v~v~~~PA~~~tGI~F 39 (295)
T PRK13186 23 KVTLTLRPAPANTGIVF 39 (295)
T ss_pred EEEEEEEcCCCCCEEEE
Confidence 35678999999999874
No 12
>TIGR00325 lpxC UDP-3-0-acyl N-acetylglucosamine deacetylase. UDP-3-O-(R-3-hydroxymyristoyl)-GlcNAc deacetylase from E. coli, LpxC, was previously designated EnvA. This enzyme is involved in lipid-A precursor biosynthesis. It is essential for cell viability.
Probab=61.99 E-value=5.8 Score=33.65 Aligned_cols=17 Identities=41% Similarity=0.534 Sum_probs=14.4
Q ss_pred ceEEEeecCCCcceEee
Q psy12294 35 SVQVRLIPAPRGTGIVG 51 (123)
Q Consensus 35 s~~V~L~PAp~GtGIVA 51 (123)
.++|.++|||.++||+=
T Consensus 22 ~v~ltl~PA~~~tGI~F 38 (297)
T TIGR00325 22 KVTLTLRPAAANTGVVF 38 (297)
T ss_pred EEEEEEEcCCCCCcEEE
Confidence 46779999999999874
No 13
>PF03331 LpxC: UDP-3-O-acyl N-acetylglycosamine deacetylase; InterPro: IPR004463 UDP-3-O-N-acetylglucosamine deacetylases are zinc-dependent metalloamidases that catalyse the second and committed step in the biosynthesis of lipid A. Lipid A anchors lipopolysaccharide (the major constituent of the outer membrane) into the membrane in Gram negative bacteria. LpxC shows no homology to mammalian metalloamidases and is essential for cell viability, making it an important target for the development of novel antibacterial compounds []. The structure of UDP-3-O-N-acetylglucosamine deacetylase (LpxC) from Aquifex aeolicus has a two-layer alpha/beta structure similar to that of the second domain of ribosomal protein S5, only in LpxC there is a duplication giving two structural repeats of this fold, each repeat being elaborated with additional structures forming the active site. LpxC contains a zinc-binding motif, which resides at the base of an active site cleft and adjacent to a hydrophobic tunnel occupied by a fatty acid []. This tunnel accounts for the specificity of LpxC toward substrates and inhibitors bearing appropriately positioned 3-O-fatty acid substituents []. This entry represents the UDP-3-O-N-acetylglucosamine deacetylase family of proteins.; GO: 0008759 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase activity, 0009245 lipid A biosynthetic process; PDB: 2VES_C 3U1Y_A 3P3E_A 3UHM_A 1XXE_A 2IER_A 1YH8_B 2GO4_A 2O3Z_B 2GO3_B ....
Probab=57.34 E-value=7.3 Score=32.62 Aligned_cols=16 Identities=56% Similarity=0.852 Sum_probs=11.0
Q ss_pred ceEEEeecCCCcceEe
Q psy12294 35 SVQVRLIPAPRGTGIV 50 (123)
Q Consensus 35 s~~V~L~PAp~GtGIV 50 (123)
.++|.++|||.++||+
T Consensus 22 ~v~l~l~PA~~~~Gi~ 37 (277)
T PF03331_consen 22 PVTLTLRPAPANTGIV 37 (277)
T ss_dssp EEEEEEEE--TT-EEE
T ss_pred EEEEEEEECCCCCCEE
Confidence 4677999999999987
No 14
>PHA00736 hypothetical protein
Probab=57.25 E-value=4 Score=28.39 Aligned_cols=13 Identities=62% Similarity=1.352 Sum_probs=10.8
Q ss_pred CchhhHhhhhhhh
Q psy12294 1 MDFLQLFWGHLMV 13 (123)
Q Consensus 1 ~~~~~~~~~~~~~ 13 (123)
||||-+|||.-..
T Consensus 52 mdflplfwgi~vi 64 (79)
T PHA00736 52 MDFLPLFWGITVI 64 (79)
T ss_pred HHHHHHHHHHHHH
Confidence 7999999997543
No 15
>COG0774 LpxC UDP-3-O-acyl-N-acetylglucosamine deacetylase [Cell envelope biogenesis, outer membrane]
Probab=49.22 E-value=23 Score=30.46 Aligned_cols=28 Identities=39% Similarity=0.627 Sum_probs=19.5
Q ss_pred CeeeEEEEEEecc--eEEEeecCCCcceEe
Q psy12294 23 KVLGLIVTGKCGS--VQVRLIPAPRGTGIV 50 (123)
Q Consensus 23 ~TIph~v~Gk~gs--~~V~L~PAp~GtGIV 50 (123)
++|-+.=.|-|.. +.+.|.||+.|||||
T Consensus 9 ~~v~~~GVGlHsG~~v~ltl~Pa~a~tGIv 38 (300)
T COG0774 9 RIVSLTGVGLHSGKKVTLTLRPAPANTGIV 38 (300)
T ss_pred cceEEEEEEeccCcEEEEEEEecCCCCeEE
Confidence 3444444555554 556889999999998
No 16
>PRK13187 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed
Probab=47.79 E-value=14 Score=31.57 Aligned_cols=31 Identities=32% Similarity=0.385 Sum_probs=20.2
Q ss_pred CCCeeeEEE----EEEec--ceEEEeecCCCcc---eEee
Q psy12294 21 QHKVLGLIV----TGKCG--SVQVRLIPAPRGT---GIVG 51 (123)
Q Consensus 21 ~~~TIph~v----~Gk~g--s~~V~L~PAp~Gt---GIVA 51 (123)
+.+||-..| .|=|. .+.|.++|||.++ ||+=
T Consensus 10 ~Q~Tl~~~v~~~GiGLHSG~~v~vtl~PA~~~t~~~GIvF 49 (304)
T PRK13187 10 SQGTLARPLTIDGHGLHTGRRVGVRILPARPEDGVTGIVF 49 (304)
T ss_pred ccccccceEEEEEEEecCCcEEEEEEEcCCCCCCCccEEE
Confidence 345554443 23343 4667899999999 9874
No 17
>PRK13188 bifunctional UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase/(3R)-hydroxymyristoyl-[acyl-carrier-protein] dehydratase; Reviewed
Probab=46.70 E-value=14 Score=33.07 Aligned_cols=17 Identities=29% Similarity=0.462 Sum_probs=14.4
Q ss_pred ceEEEeecCCCcceEee
Q psy12294 35 SVQVRLIPAPRGTGIVG 51 (123)
Q Consensus 35 s~~V~L~PAp~GtGIVA 51 (123)
.++|.++|||.++||+=
T Consensus 24 ~~~~~~~Pa~~~~Gi~F 40 (464)
T PRK13188 24 EVTITFKPAPENHGYKF 40 (464)
T ss_pred EEEEEEEcCCCCCcEEE
Confidence 46779999999999874
No 18
>PRK14747 cytochrome b6-f complex subunit PetN; Provisional
Probab=39.92 E-value=14 Score=21.61 Aligned_cols=15 Identities=40% Similarity=0.609 Sum_probs=13.4
Q ss_pred CchhhHhhhhhhhhc
Q psy12294 1 MDFLQLFWGHLMVTS 15 (123)
Q Consensus 1 ~~~~~~~~~~~~~~~ 15 (123)
||.+.+.|.-+|+.-
T Consensus 1 mdivsl~Waalm~~F 15 (29)
T PRK14747 1 MDILTLGWVSVLVLF 15 (29)
T ss_pred CceehhHHHHHHHHH
Confidence 899999999999864
No 19
>PF14999 Shadoo: Shadow of prion protein, neuroprotective
Probab=38.29 E-value=15 Score=27.90 Aligned_cols=17 Identities=47% Similarity=0.733 Sum_probs=14.6
Q ss_pred EecceEEEeecCCCcce
Q psy12294 32 KCGSVQVRLIPAPRGTG 48 (123)
Q Consensus 32 k~gs~~V~L~PAp~GtG 48 (123)
-.|+++|+++||||-.|
T Consensus 25 srgasRvrvr~apRY~G 41 (131)
T PF14999_consen 25 SRGASRVRVRPAPRYGG 41 (131)
T ss_pred cCCcceeeeccccccCc
Confidence 35899999999999874
No 20
>CHL00009 petN cytochrome b6/f complex subunit VIII
Probab=35.71 E-value=21 Score=20.81 Aligned_cols=15 Identities=47% Similarity=0.811 Sum_probs=13.5
Q ss_pred CchhhHhhhhhhhhc
Q psy12294 1 MDFLQLFWGHLMVTS 15 (123)
Q Consensus 1 ~~~~~~~~~~~~~~~ 15 (123)
||.+.+.|.-+||.-
T Consensus 1 mdiv~~gWaalmv~f 15 (29)
T CHL00009 1 MDIVSLAWAALMVVF 15 (29)
T ss_pred CchhhhHHHHHHHHh
Confidence 899999999999864
No 21
>PF03742 PetN: PetN ; InterPro: IPR005497 PetN is a small hydrophobic protein, crucial for cytochrome b6-f complex assembly and/or stability. It is found in bacteria and plants. Cytochrome b6-f complex is composed of 4 large subunits: cytochrome b6, subunit IV (17 kDa polypeptide, petD), cytochrome f and the Rieske protein, as well as 4 small subunits: petG, petL, petM and petN. The complex functions as a dimer. The cytochrome b6-f complex mediates electron transfer between photosystem II (PSII) and photosystem I (PSI) [].; GO: 0045158 electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II activity, 0017004 cytochrome complex assembly, 0009512 cytochrome b6f complex; PDB: 2ZT9_H 2D2C_H 2E76_H 1VF5_U 2E75_H 2E74_H.
Probab=29.43 E-value=26 Score=20.43 Aligned_cols=14 Identities=50% Similarity=0.866 Sum_probs=11.4
Q ss_pred CchhhHhhhhhhhh
Q psy12294 1 MDFLQLFWGHLMVT 14 (123)
Q Consensus 1 ~~~~~~~~~~~~~~ 14 (123)
||.+++.|.-+|+.
T Consensus 1 mdiv~lgWaal~~~ 14 (29)
T PF03742_consen 1 MDIVSLGWAALMVV 14 (29)
T ss_dssp -HHHCHHHHHHHHH
T ss_pred CcchhhhHHHHHHH
Confidence 89999999998874
No 22
>cd01434 EFG_mtEFG1_IV EFG_mtEFG1_IV: domains similar to domain IV of the bacterial translational elongation factor (EF) EF-G. Included in this group is a domain of mitochondrial Elongation factor G1 (mtEFG1) proteins homologous to domain IV of EF-G. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. In bacteria this translocation step is catalyzed by EF-G_GTP, which is hydrolyzed to provi
Probab=28.48 E-value=42 Score=23.37 Aligned_cols=18 Identities=39% Similarity=0.851 Sum_probs=16.0
Q ss_pred EecceEEEeecCCCcceE
Q psy12294 32 KCGSVQVRLIPAPRGTGI 49 (123)
Q Consensus 32 k~gs~~V~L~PAp~GtGI 49 (123)
.++.+.+.|.|+++|.|+
T Consensus 24 ~~a~v~l~v~P~~~g~g~ 41 (116)
T cd01434 24 QYGHVVLEIEPLPRGSGF 41 (116)
T ss_pred eEEEEEEEEEECCCCCCC
Confidence 588899999999999887
No 23
>PF01989 DUF126: Protein of unknown function DUF126; InterPro: IPR002840 These archaebacterial proteins have no known function.; PDB: 2HI6_A.
Probab=27.60 E-value=15 Score=25.64 Aligned_cols=39 Identities=18% Similarity=0.505 Sum_probs=22.4
Q ss_pred hhhhhhhhcCceecCCCeeeEEEEEEecceEEEeecCCCcceE
Q psy12294 7 FWGHLMVTSGILFCQHKVLGLIVTGKCGSVQVRLIPAPRGTGI 49 (123)
Q Consensus 7 ~~~~~~~~~g~~i~~~~TIph~v~Gk~gs~~V~L~PAp~GtGI 49 (123)
|||-+.-..|.-+-+. |+..|++=+-+|++.|..||+-.
T Consensus 4 f~ggvDp~tG~ii~~~----H~l~G~si~gkILv~p~~kGSt~ 42 (82)
T PF01989_consen 4 FWGGVDPETGVIIDKG----HPLEGQSIAGKILVFPSGKGSTV 42 (82)
T ss_dssp TTS-B-TTT-BB-S------SSSTT-B-TTSEEEES--S--SS
T ss_pred ccccccCCceEEEecC----CCcCCCcccCeEEEecCCCCccH
Confidence 7998888888877654 55678888999999999999865
No 24
>PRK03955 hypothetical protein; Reviewed
Probab=27.47 E-value=32 Score=25.92 Aligned_cols=38 Identities=18% Similarity=0.313 Sum_probs=31.1
Q ss_pred HhhhhhhhhcCceecCCCeeeEEEEEEecceEEEeecCCCcc
Q psy12294 6 LFWGHLMVTSGILFCQHKVLGLIVTGKCGSVQVRLIPAPRGT 47 (123)
Q Consensus 6 ~~~~~~~~~~g~~i~~~~TIph~v~Gk~gs~~V~L~PAp~Gt 47 (123)
-|||-.....|.-+.+. |+..|++=+-+|++.|..+|+
T Consensus 25 Sf~ggvd~~tG~iid~~----h~l~G~si~gkIlv~p~~kGS 62 (131)
T PRK03955 25 SFLGGVDPETGIVIDKE----HDLYGESIKGKILVFPHGKGS 62 (131)
T ss_pred cccccccCCCCEEEecC----CCcCCCccCCEEEEEeCCCcc
Confidence 47888887777766543 778899999999999999988
No 25
>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=26.98 E-value=49 Score=23.32 Aligned_cols=17 Identities=41% Similarity=0.886 Sum_probs=15.0
Q ss_pred ecceEEEeecCCCcceE
Q psy12294 33 CGSVQVRLIPAPRGTGI 49 (123)
Q Consensus 33 ~gs~~V~L~PAp~GtGI 49 (123)
++.+.+.|.|.++|.|+
T Consensus 25 ~a~v~l~veP~~~g~g~ 41 (115)
T cd01684 25 WATVGLRVEPLPRGSGL 41 (115)
T ss_pred EEEEEEEEEECCCCCCc
Confidence 88899999999999765
No 26
>cd01356 AcnX_swivel Putative Aconitase X swivel domain. It is predicted by comparative genomic analysis. The proteins are mainly found in archaea and proteobacteria. They are distantly related to Aconitase family of proteins by sequence similarity and seconary structure prediction. The functions have not yet been experimentally characterized. Thus, the prediction should be treated with caution.
Probab=22.53 E-value=48 Score=24.77 Aligned_cols=39 Identities=21% Similarity=0.433 Sum_probs=31.3
Q ss_pred hhhhhhhhcCceecCCCeeeEEEEEEecceEEEeecCCCcceE
Q psy12294 7 FWGHLMVTSGILFCQHKVLGLIVTGKCGSVQVRLIPAPRGTGI 49 (123)
Q Consensus 7 ~~~~~~~~~g~~i~~~~TIph~v~Gk~gs~~V~L~PAp~GtGI 49 (123)
|||-..-..|.-+.+ .|+..|++=+-+|++.|..||+-.
T Consensus 19 F~GgvDp~tG~iid~----~H~l~G~si~gkILv~p~~kGSt~ 57 (123)
T cd01356 19 FWGGVDPETGKVIDP----HHPLYGESIAGKVLVLPGGKGSTV 57 (123)
T ss_pred eeeccccCCCeEeeC----CCCcCCCcccceEEEecCCCCcch
Confidence 788888888876654 456688888999999999999754
No 27
>PF11267 DUF3067: Protein of unknown function (DUF3067); InterPro: IPR021420 This family of proteins has no known function. ; PDB: 2LJW_A.
Probab=21.88 E-value=58 Score=23.72 Aligned_cols=25 Identities=24% Similarity=0.440 Sum_probs=18.2
Q ss_pred hhhhhcccccCchHH--HHHHHHHHhh
Q psy12294 97 QCMQVLVSSHFPISE--SLNTISEILE 121 (123)
Q Consensus 97 ~~w~~~~~~~~P~~e--~~d~~~~~~~ 121 (123)
-||+-......|+.| |-.||..|.|
T Consensus 31 VMW~yLeQ~SFPltE~eY~~hL~~va~ 57 (99)
T PF11267_consen 31 VMWKYLEQRSFPLTEEEYLEHLDAVAE 57 (99)
T ss_dssp EEEEETTSTT-SS-HHHHHHHHHHHHH
T ss_pred EehhhccCCCcCCCHHHHHHHHHHHHH
Confidence 368888888999877 8888887765
Done!