Query 048206
Match_columns 72
No_of_seqs 34 out of 36
Neff 2.7
Searched_HMMs 46136
Date Fri Mar 29 07:24:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/048206.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/048206hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00432 Ribosomal_L18_L5e Ribo 99.0 4.6E-10 1E-14 71.9 4.2 43 29-71 5-47 (103)
2 CHL00139 rpl18 ribosomal prote 98.9 1.3E-09 2.9E-14 72.8 4.1 41 30-71 11-51 (109)
3 PF00861 Ribosomal_L18p: Ribos 98.9 1.7E-09 3.8E-14 71.8 3.7 52 21-72 8-60 (119)
4 TIGR00060 L18_bact ribosomal p 98.8 1E-08 2.2E-13 69.4 5.0 42 29-71 19-60 (114)
5 PRK05593 rplR 50S ribosomal pr 98.6 3.6E-08 7.8E-13 66.5 4.3 36 36-71 25-60 (117)
6 PTZ00032 60S ribosomal protein 97.8 1.9E-05 4.1E-10 59.2 3.4 38 34-71 104-141 (211)
7 PRK08569 rpl18p 50S ribosomal 97.3 0.00039 8.4E-09 51.1 4.4 36 36-71 33-70 (193)
8 COG0256 RplR Ribosomal protein 97.3 0.00035 7.5E-09 48.5 3.6 36 36-71 30-65 (125)
9 PTZ00069 60S ribosomal protein 65.5 8.4 0.00018 30.5 3.4 43 25-67 37-82 (300)
10 cd07881 RHD-n_NFAT N-terminal 33.3 29 0.00063 25.8 1.6 40 29-69 48-95 (175)
11 PF06487 SAP18: Sin3 associate 27.1 47 0.001 22.6 1.7 13 34-46 10-22 (120)
12 PF07533 BRK: BRK domain; Int 25.4 45 0.00097 19.3 1.2 15 48-62 7-21 (46)
13 PF00370 FGGY_N: FGGY family o 25.2 2.2E+02 0.0047 19.6 4.7 29 36-65 1-29 (245)
14 KOG3333 Mitochondrial/chloropl 24.9 1.3E+02 0.0029 22.6 3.8 31 36-67 61-91 (188)
15 cd04093 HBS1_C HBS1_C: this fa 24.6 1.3E+02 0.0029 18.2 3.3 31 31-62 71-101 (107)
16 cd04867 TGS_YchF_C TGS_YchF_C: 24.0 55 0.0012 21.5 1.5 16 38-53 30-45 (83)
17 PF06071 YchF-GTPase_C: Protei 20.9 43 0.00092 22.0 0.6 14 41-54 33-46 (84)
No 1
>cd00432 Ribosomal_L18_L5e Ribosomal L18/L5e: L18 (L5e) is a ribosomal protein found in the central protuberance (CP) of the large subunit. L18 binds 5S rRNA and induces a conformational change that stimulates the binding of L5 to 5S rRNA. Association of 5S rRNA with 23S rRNA depends on the binding of L18 and L5 to 5S rRNA. L18/L5e is generally described as L18 in prokaryotes and archaea, and as L5e (or L5) in eukaryotes. In bacteria, the CP proteins L5, L18, and L25 are required for the ribosome to incorporate 5S rRNA into the large subunit, one of the last steps in ribosome assembly. In archaea, both L18 and L5 bind 5S rRNA; in eukaryotes, only the L18 homolog (L5e) binds 5S rRNA but a homolog to L5 is also identified.
Probab=99.00 E-value=4.6e-10 Score=71.86 Aligned_cols=43 Identities=19% Similarity=-0.054 Sum_probs=39.5
Q ss_pred hhhcccceeEEEeeeccceEEEEEeeccceEEEEEeccccccC
Q 048206 29 TNMYMRPFLFNVFFSKKFVHAKVMHRSISKVISVATTNVDDSY 71 (72)
Q Consensus 29 t~~ymrPf~L~vffSkk~V~A~ViHr~Ts~VvavAsT~sKdlr 71 (72)
...+++++-|.||+||++|+|||||..+++|+++|||++++++
T Consensus 5 ~~~~~~~~RL~v~~Sn~~i~aqvi~~~~~~vl~sast~e~~~~ 47 (103)
T cd00432 5 RLGTQERPRLVVRKSNKHIYAQIIDDSGDKTLVSASTLELAIK 47 (103)
T ss_pred ecCcCCCCEEEEEEeCCEEEEEEEEeCcCeEEEEEecCchhhc
Confidence 3346689999999999999999999999999999999999986
No 2
>CHL00139 rpl18 ribosomal protein L18; Validated
Probab=98.92 E-value=1.3e-09 Score=72.75 Aligned_cols=41 Identities=24% Similarity=0.295 Sum_probs=38.0
Q ss_pred hhcccceeEEEeeeccceEEEEEeeccceEEEEEeccccccC
Q 048206 30 NMYMRPFLFNVFFSKKFVHAKVMHRSISKVISVATTNVDDSY 71 (72)
Q Consensus 30 ~~ymrPf~L~vffSkk~V~A~ViHr~Ts~VvavAsT~sKdlr 71 (72)
....+|. |.||+||++|+|||||.++++|+|+|||++||++
T Consensus 11 g~~~rpR-L~V~rSnkhiyaQvidd~~g~tlasaST~ek~~~ 51 (109)
T CHL00139 11 GTAERPR-LSVFRSNKHIYAQIIDDTNGKTLVACSTLEPDVK 51 (109)
T ss_pred CCCCCCE-EEEEEeCCeEEEEEEECCCCCEEEEEecCchhhh
Confidence 4577886 9999999999999999999999999999999986
No 3
>PF00861 Ribosomal_L18p: Ribosomal L18p/L5e family; InterPro: IPR005484 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 includes L18 from bacteria and L5 from eukaryotes. The ribosomal 5S RNA is the only known rRNA species to bind a ribosomal protein before its assembly into the ribosomal subunits []. In eukaryotes, the 5S rRNA molecule binds one protein species, a 34kDa protein which has been implicated in the intracellular transport of 5 S rRNA, while in bacteria it binds two or three different protein species []. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_M 4A1C_M 4A1A_M 4A17_M 3IZR_Q 3O58_E 1S1I_E 3IZS_Q 3O5H_E 1KQS_M ....
Probab=98.88 E-value=1.7e-09 Score=71.78 Aligned_cols=52 Identities=21% Similarity=0.142 Sum_probs=43.6
Q ss_pred CcccHHHhhhhcc-cceeEEEeeeccceEEEEEeeccceEEEEEeccccccCC
Q 048206 21 NRKSWKQRTNMYM-RPFLFNVFFSKKFVHAKVMHRSISKVISVATTNVDDSYE 72 (72)
Q Consensus 21 ~~~sfkqrt~~ym-rPf~L~vffSkk~V~A~ViHr~Ts~VvavAsT~sKdlr~ 72 (72)
++....|+..++. ..+-|.||+||++|+|||||..++.++++|||.++||++
T Consensus 8 ~r~~~~r~~~~~~~~~~RL~V~~Snk~i~aQii~~~~~~~l~~aSt~~~~l~~ 60 (119)
T PF00861_consen 8 RRKLRIRRKIKGTAERPRLVVFRSNKHIYAQIIDDSKGGTLASASTLSKELKK 60 (119)
T ss_dssp HHHHHHHHHHHHTTSSEEEEEEEESSEEEEEEEECTTTEEEEEEEEETTTGGG
T ss_pred HHHHHHHHHHhcCCCCCEEEEEeccCeEEEEEEeeCCCCeEEEEEecchhhhh
Confidence 4445555555554 459999999999999999999999999999999999973
No 4
>TIGR00060 L18_bact ribosomal protein L18, bacterial type. The archaeal and eukaryotic type rpL18 is not detectable under this model.
Probab=98.79 E-value=1e-08 Score=69.37 Aligned_cols=42 Identities=31% Similarity=0.304 Sum_probs=39.3
Q ss_pred hhhcccceeEEEeeeccceEEEEEeeccceEEEEEeccccccC
Q 048206 29 TNMYMRPFLFNVFFSKKFVHAKVMHRSISKVISVATTNVDDSY 71 (72)
Q Consensus 29 t~~ymrPf~L~vffSkk~V~A~ViHr~Ts~VvavAsT~sKdlr 71 (72)
|.+|.+| -|.||+||++++||||+..+++|+|+|||++|+++
T Consensus 19 t~~~~rp-RL~V~rSnk~iyaQiIdd~~~~tlasaST~ek~~~ 60 (114)
T TIGR00060 19 TGEANRP-RLVVFRSNRHIYAQVIDDSKSEVLASASTLEKKLK 60 (114)
T ss_pred CCCCCCc-EEEEEEeCCeEEEEEEECCCCEEEEEEecchhhhc
Confidence 6677899 99999999999999999999999999999999974
No 5
>PRK05593 rplR 50S ribosomal protein L18; Reviewed
Probab=98.65 E-value=3.6e-08 Score=66.45 Aligned_cols=36 Identities=25% Similarity=0.259 Sum_probs=34.1
Q ss_pred eeEEEeeeccceEEEEEeeccceEEEEEeccccccC
Q 048206 36 FLFNVFFSKKFVHAKVMHRSISKVISVATTNVDDSY 71 (72)
Q Consensus 36 f~L~vffSkk~V~A~ViHr~Ts~VvavAsT~sKdlr 71 (72)
.-|.||+||++|+|||||..+++|+++|||++++++
T Consensus 25 pRL~V~~SnkhiyAQvidd~~~~tl~saST~e~~~k 60 (117)
T PRK05593 25 PRLSVFRSNRHIYAQVIDDVKGKTLASASTLEKDVR 60 (117)
T ss_pred CEEEEEEeCCeEEEEEEECCCCEEEEEEecCcHhHh
Confidence 469999999999999999999999999999999985
No 6
>PTZ00032 60S ribosomal protein L18; Provisional
Probab=97.81 E-value=1.9e-05 Score=59.15 Aligned_cols=38 Identities=13% Similarity=0.072 Sum_probs=35.2
Q ss_pred cceeEEEeeeccceEEEEEeeccceEEEEEeccccccC
Q 048206 34 RPFLFNVFFSKKFVHAKVMHRSISKVISVATTNVDDSY 71 (72)
Q Consensus 34 rPf~L~vffSkk~V~A~ViHr~Ts~VvavAsT~sKdlr 71 (72)
|=.-|-||.||+.++||||+-.+++++|+|||.++|++
T Consensus 104 rrPRLsV~RSnkHIYAQIIDD~~~~TLasaSTlek~l~ 141 (211)
T PTZ00032 104 RRPRLTLKNTNNQMYATIVDDYTRHVLCFSCTNFKYLS 141 (211)
T ss_pred CcceEEEEecCCeEEEEEEECCCCCEEEEecCCCHHHH
Confidence 34579999999999999999999999999999999985
No 7
>PRK08569 rpl18p 50S ribosomal protein L18P; Reviewed
Probab=97.30 E-value=0.00039 Score=51.08 Aligned_cols=36 Identities=17% Similarity=0.120 Sum_probs=32.9
Q ss_pred eeEEEeeeccceEEEEE--eeccceEEEEEeccccccC
Q 048206 36 FLFNVFFSKKFVHAKVM--HRSISKVISVATTNVDDSY 71 (72)
Q Consensus 36 f~L~vffSkk~V~A~Vi--Hr~Ts~VvavAsT~sKdlr 71 (72)
+-|-|++||+.|.|||| .-..++|+|+|+|.+++++
T Consensus 33 pRLvV~rSNkhIyaQiI~~dd~gd~tLaSAsS~el~~~ 70 (193)
T PRK08569 33 PRLVVRKTNKHVIAQIVKYDPKGDRTLASAHSRELAKY 70 (193)
T ss_pred CEEEEEEeCCeEEEEEEEccCCCCEEEEEEecCchhhc
Confidence 46889999999999999 8899999999999998864
No 8
>COG0256 RplR Ribosomal protein L18 [Translation, ribosomal structure and biogenesis]
Probab=97.26 E-value=0.00035 Score=48.46 Aligned_cols=36 Identities=14% Similarity=0.073 Sum_probs=34.0
Q ss_pred eeEEEeeeccceEEEEEeeccceEEEEEeccccccC
Q 048206 36 FLFNVFFSKKFVHAKVMHRSISKVISVATTNVDDSY 71 (72)
Q Consensus 36 f~L~vffSkk~V~A~ViHr~Ts~VvavAsT~sKdlr 71 (72)
--|-||.||+.|.||||--..+.++++|||-++||+
T Consensus 30 pRL~V~rSnkhi~aQiId~~~~~tla~aSt~~~~l~ 65 (125)
T COG0256 30 PRLVVRRSNRHIYAQIIDDVKGGTLASASTLSKELR 65 (125)
T ss_pred cEEEEEEeCCcEEEEEEEcCCCceEEEEEcchHHHH
Confidence 368999999999999999999999999999999986
No 9
>PTZ00069 60S ribosomal protein L5; Provisional
Probab=65.54 E-value=8.4 Score=30.51 Aligned_cols=43 Identities=21% Similarity=0.317 Sum_probs=31.4
Q ss_pred HHHhhhhcccc-eeEEEeeeccceEEEEEeec-c-ceEEEEEeccc
Q 048206 25 WKQRTNMYMRP-FLFNVFFSKKFVHAKVMHRS-I-SKVISVATTNV 67 (72)
Q Consensus 25 fkqrt~~ymrP-f~L~vffSkk~V~A~ViHr~-T-s~VvavAsT~s 67 (72)
-.|..++|=-| |-|-|-|||+.|-|||+..- . -.|+|+|+|.+
T Consensus 37 i~q~knKynspK~RlVVR~TN~~ii~Qiv~~~~~GD~vl~sA~S~e 82 (300)
T PTZ00069 37 ILQDKNKYNSPKYRLVVRITNKDIICQIVYATIVGDKVLAAAYSHE 82 (300)
T ss_pred HHccccccCCCCceEEEEEECCcEEEEEEEeecCCCEEEEEeehhh
Confidence 34444555555 67899999999999999753 3 37888888754
No 10
>cd07881 RHD-n_NFAT N-terminal sub-domain of the Rel homology domain (RHD) of nuclear factor of activated T-cells (NFAT) proteins. Proteins containing the Rel homology domain (RHD) are metazoan transcription factors. The RHD is composed of two structural sub-domains; this model characterizes the N-terminal RHD sub-domain of the NFAT family of transcription factors. NFAT transcription complexes are a target of calcineurin, a calcium dependent phosphatase, and activate genes that are mainly involved in cell-cell interaction. Upon de-phosphorylation of the nuclear localization signal, NFAT enters the nucleus and acts as a transcription factor; its export from the nucleus is triggered by phosphorylation via export kinases. NFATs play important roles in mediating the immune response, and are found in T cells, B Cells, NK cells, mast cells, and monocytes. NFATs are also found in various non-hematopoietic cell types, where they play roles in development.
Probab=33.27 E-value=29 Score=25.83 Aligned_cols=40 Identities=20% Similarity=0.431 Sum_probs=26.8
Q ss_pred hhhcc--cceeEEEeeecc---ceEEE---EEeeccceEEEEEeccccc
Q 048206 29 TNMYM--RPFLFNVFFSKK---FVHAK---VMHRSISKVISVATTNVDD 69 (72)
Q Consensus 29 t~~ym--rPf~L~vffSkk---~V~A~---ViHr~Ts~VvavAsT~sKd 69 (72)
+.-|+ +|-.|.||+.+. +|.-- -+||+||+.|+.+ ++|++
T Consensus 48 L~Gy~e~kp~~LQvFigt~d~r~~~PH~FYQ~hritGk~v~T~-~~E~~ 95 (175)
T cd07881 48 LHGYMENKPLTLQMFIGTADDRYLRPHAFYQVHRITGKTVATA-SQEII 95 (175)
T ss_pred EEeecCCcceEEEEEEecCCCcccCCccceEEEEEEcCCCccc-ceeEe
Confidence 45687 599999999884 33221 3699999988544 34443
No 11
>PF06487 SAP18: Sin3 associated polypeptide p18 (SAP18); InterPro: IPR010516 This family consists of several eukaryotic Sin3 associated polypeptide p18 (SAP18) sequences. SAP18 is known to be a component of the Sin3-containing complex, which is responsible for the repression of transcription via the modification of histone polypeptides []. SAP18 is also present in the ASAP complex which is thought to be involved in the regulation of splicing during the execution of programmed cell death [].; PDB: 2HDE_A 4A90_A 4A6Q_A 4A8X_C.
Probab=27.07 E-value=47 Score=22.61 Aligned_cols=13 Identities=38% Similarity=0.782 Sum_probs=9.1
Q ss_pred cceeEEEeeeccc
Q 048206 34 RPFLFNVFFSKKF 46 (72)
Q Consensus 34 rPf~L~vffSkk~ 46 (72)
=||+|.||..+.-
T Consensus 10 cPfLLRvF~~~g~ 22 (120)
T PF06487_consen 10 CPFLLRVFYRNGR 22 (120)
T ss_dssp --EEEEEEESSSS
T ss_pred CCeEEEEEEecCC
Confidence 4999999987654
No 12
>PF07533 BRK: BRK domain; InterPro: IPR006576 BRK is a domain of unknown function found only in the metazoa and in association with CHROMO domain (IPR000953 from INTERPRO) and DEAD/DEAH box helicase domain (IPR011545 from INTERPRO).; GO: 0005515 protein binding, 0016817 hydrolase activity, acting on acid anhydrides; PDB: 2DL6_A 2CKA_A 2V0F_A 2V0E_A 2CKC_A.
Probab=25.44 E-value=45 Score=19.32 Aligned_cols=15 Identities=20% Similarity=0.313 Sum_probs=10.5
Q ss_pred EEEEEeeccceEEEE
Q 048206 48 HAKVMHRSISKVISV 62 (72)
Q Consensus 48 ~A~ViHr~Ts~Vvav 62 (72)
+-.|||+.||+++.-
T Consensus 7 rV~Vi~~~tGk~l~G 21 (46)
T PF07533_consen 7 RVPVINRKTGKRLTG 21 (46)
T ss_dssp B--EEETTTTEEE-C
T ss_pred eeEeEECCCCCCccc
Confidence 457999999999864
No 13
>PF00370 FGGY_N: FGGY family of carbohydrate kinases, N-terminal domain; InterPro: IPR018484 It has been shown [] that four different type of carbohydrate kinases seem to be evolutionary related. These enzymes include L-fucolokinase (2.7.1.51 from EC) (gene fucK); gluconokinase (2.7.1.12 from EC) (gene gntK); glycerol kinase (2.7.1.30 from EC) (gene glpK); xylulokinase (2.7.1.17 from EC) (gene xylB); and L-xylulose kinase (2.7.1.53 from EC) (gene lyxK). These enzymes are proteins of from 480 to 520 amino acid residues. This entry represents the N-terminal domain of these proteins. It adopts a ribonuclease H-like fold and is structurally related to the C-terminal domain [, ].; GO: 0016773 phosphotransferase activity, alcohol group as acceptor, 0005975 carbohydrate metabolic process; PDB: 3G25_D 3GE1_D 2NLX_A 2ITM_A 2ZF5_Y 3L0Q_B 3GG4_B 3I8B_A 3H3O_C 3FLC_X ....
Probab=25.15 E-value=2.2e+02 Score=19.56 Aligned_cols=29 Identities=14% Similarity=0.271 Sum_probs=25.8
Q ss_pred eeEEEeeeccceEEEEEeeccceEEEEEec
Q 048206 36 FLFNVFFSKKFVHAKVMHRSISKVISVATT 65 (72)
Q Consensus 36 f~L~vffSkk~V~A~ViHr~Ts~VvavAsT 65 (72)
|+|=|.+..-.+.|.++. .++++++.++.
T Consensus 1 y~lgiDiGTts~K~~l~d-~~g~iv~~~~~ 29 (245)
T PF00370_consen 1 YYLGIDIGTTSVKAVLFD-EDGKIVASASR 29 (245)
T ss_dssp EEEEEEECSSEEEEEEEE-TTSCEEEEEEE
T ss_pred CEEEEEEcccceEEEEEe-CCCCEEEEEEE
Confidence 678899999999999999 99999988763
No 14
>KOG3333 consensus Mitochondrial/chloroplast ribosomal protein L18 [Translation, ribosomal structure and biogenesis]
Probab=24.85 E-value=1.3e+02 Score=22.60 Aligned_cols=31 Identities=26% Similarity=0.270 Sum_probs=24.3
Q ss_pred eeEEEeeeccceEEEEEeeccceEEEEEeccc
Q 048206 36 FLFNVFFSKKFVHAKVMHRSISKVISVATTNV 67 (72)
Q Consensus 36 f~L~vffSkk~V~A~ViHr~Ts~VvavAsT~s 67 (72)
+-|.|-=++.+|.+-|.|--.+.||+ |||-|
T Consensus 61 h~lev~~~~~hveg~v~H~~~gvvvS-AST~E 91 (188)
T KOG3333|consen 61 HRLEVIRTQHHVEGLVEHQNGGVVVS-ASTRE 91 (188)
T ss_pred eEEEEeecccceeeeeeEecCCEEEE-ecccc
Confidence 45788889999999999988776665 55544
No 15
>cd04093 HBS1_C HBS1_C: this family represents the C-terminal domain of Hsp70 subfamily B suppressor 1 (HBS1) which is homologous to the domain III of EF-1alpha. This group contains proteins similar to yeast Hbs1, a G protein known to be important for efficient growth and protein synthesis under conditions of limiting translation initiation and, to associate with Dom34. It has been speculated that yeast Hbs1 and Dom34 proteins may function as part of a complex with a role in gene expression.
Probab=24.64 E-value=1.3e+02 Score=18.24 Aligned_cols=31 Identities=23% Similarity=0.300 Sum_probs=22.6
Q ss_pred hcccceeEEEeeeccceEEEEEeeccceEEEE
Q 048206 31 MYMRPFLFNVFFSKKFVHAKVMHRSISKVISV 62 (72)
Q Consensus 31 ~ymrPf~L~vffSkk~V~A~ViHr~Ts~Vvav 62 (72)
...+|.|+|-|-.+...-.=++ |-++++||+
T Consensus 71 ~~~~pi~~e~~~~~~~~Grfil-r~~~~Tva~ 101 (107)
T cd04093 71 ELERPIPLELFKDNKELGRVVL-RRDGETIAA 101 (107)
T ss_pred EECCeEEEEEcccCCCcceEEE-EcCCCEEEE
Confidence 3578999998876665555555 888888876
No 16
>cd04867 TGS_YchF_C TGS_YchF_C: This subfamily represents TGS domain-containing YchF GTP-binding protein, a universally conserved GTPase whose function is unknown. The N-terminal domain of the YchF protein belongs to the Obg-like family of GTPases, and some members of the family contain a C-terminal TGS domain. TGS is a small domain of about 50 amino acid residues with a predominantly beta-sheet structure. There is no direct information on the function of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role.
Probab=24.01 E-value=55 Score=21.52 Aligned_cols=16 Identities=38% Similarity=0.617 Sum_probs=13.0
Q ss_pred EEEeeeccceEEEEEe
Q 048206 38 FNVFFSKKFVHAKVMH 53 (72)
Q Consensus 38 L~vffSkk~V~A~ViH 53 (72)
+--.|.+.||+|.||+
T Consensus 30 IHsDfekgFIrAeVi~ 45 (83)
T cd04867 30 IHTDFEKGFIRAEVMK 45 (83)
T ss_pred cccccccCcEEEEEEc
Confidence 3446889999999997
No 17
>PF06071 YchF-GTPase_C: Protein of unknown function (DUF933); InterPro: IPR013029 This domain is found at the C terminus of family of conserved hypothetical proteins found in both prokaryotes and eukaryotes. While the function of these proteins is not known, the crystal structure of P44681 from SWISSPROT from Haemophilus influenzae has been determined []. This protein consists of three domains: an N-terminal domain which has a mononucleotide binding fold typical for the P-loop NTPases, a central domain which forms an alpha-helical coiled coil, and this C-terminal domain which is composed of a six-stranded half-barrel curved around an alpha helix. The central domain and this domain are topologically similar to RNA-binding proteins, while the N-terminal region contains the features typical of GTP-dependent molecular switches. The purified protein was capable of binding both double-stranded nucleic acid and GTP. It was suggested, therefore, that this protein might be part of a nucleoprotein complex and could function as a GTP-dependent translation factor.; PDB: 1NI3_A 1JAL_A 2DWQ_B 2DBY_A 2OHF_A.
Probab=20.91 E-value=43 Score=21.95 Aligned_cols=14 Identities=36% Similarity=0.548 Sum_probs=11.5
Q ss_pred eeeccceEEEEEee
Q 048206 41 FFSKKFVHAKVMHR 54 (72)
Q Consensus 41 ffSkk~V~A~ViHr 54 (72)
.|.+.||+|.||+-
T Consensus 33 DfekgFI~Aevi~~ 46 (84)
T PF06071_consen 33 DFEKGFIRAEVISY 46 (84)
T ss_dssp HHHHHEEEEEEEEH
T ss_pred HHHhhceEEEEEcH
Confidence 36789999999974
Done!