Query 035914
Match_columns 93
No_of_seqs 106 out of 202
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 07:35:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035914.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035914hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01158 Ribosomal_L36e: Ribos 100.0 4.3E-47 9.4E-52 261.6 6.3 80 7-86 2-98 (98)
2 PTZ00196 60S ribosomal protein 100.0 2.7E-46 5.8E-51 258.0 8.5 80 7-86 2-98 (98)
3 KOG3452 60S ribosomal protein 100.0 1.3E-43 2.7E-48 245.9 8.4 82 7-88 4-102 (102)
4 COG5051 RPL36A Ribosomal prote 100.0 2.6E-29 5.7E-34 172.7 6.5 75 8-82 5-96 (97)
5 PRK14132 riboflavin kinase; Pr 54.4 7.2 0.00016 28.1 1.2 32 10-41 7-38 (126)
6 KOG2659 LisH motif-containing 51.1 24 0.00053 27.8 3.8 66 17-82 78-150 (228)
7 PF10607 CLTH: CTLH/CRA C-term 44.5 60 0.0013 21.8 4.5 43 36-80 40-82 (145)
8 PRK14165 winged helix-turn-hel 41.3 16 0.00036 28.0 1.5 31 11-41 96-126 (217)
9 PF08068 DKCLD: DKCLD (NUC011) 37.0 17 0.00037 23.4 0.8 19 32-50 25-43 (59)
10 PF12169 DNA_pol3_gamma3: DNA 32.3 1.6E+02 0.0034 19.7 5.5 55 28-82 4-60 (143)
11 COG3893 Inactivated superfamil 31.6 38 0.00082 30.8 2.3 34 10-43 584-620 (697)
12 PF01982 CTP-dep_RFKase: Domai 30.4 35 0.00076 24.4 1.6 18 24-41 15-32 (121)
13 COG1329 Transcriptional regula 29.9 45 0.00099 25.3 2.2 32 14-45 98-131 (166)
14 COG1094 Predicted RNA-binding 29.4 68 0.0015 24.8 3.2 52 26-79 67-133 (194)
15 PF13058 DUF3920: Protein of u 26.0 60 0.0013 23.7 2.2 28 34-68 97-124 (126)
16 COG1339 Transcriptional regula 22.8 46 0.001 26.3 1.2 16 26-41 109-124 (214)
17 PF04328 DUF466: Protein of un 22.3 71 0.0015 20.3 1.8 21 23-43 9-29 (65)
18 KOG0396 Uncharacterized conser 20.1 90 0.002 26.6 2.4 37 41-79 196-232 (389)
19 PF12077 DUF3556: Transmembran 20.1 55 0.0012 29.2 1.2 36 9-44 487-522 (574)
20 PF01978 TrmB: Sugar-specific 20.0 59 0.0013 19.4 1.0 17 32-48 2-18 (68)
No 1
>PF01158 Ribosomal_L36e: Ribosomal protein L36e; InterPro: IPR000509 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 [, ]. A number of eukaryotic ribosomal proteins can be grouped on the basis of sequence similarities. The L36E ribosomal family consists of mammalian, Caenorhabditis elegans and Drosophila L36, Candida albicans L39, and yeast YL39 ribosomal proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1B_Q 4A1D_Q 4A19_Q 4A18_Q 3IZS_k 3IZR_k.
Probab=100.00 E-value=4.3e-47 Score=261.63 Aligned_cols=80 Identities=59% Similarity=0.818 Sum_probs=74.7
Q ss_pred CccceeeecCCC-----------------CCcchhHHHHHHHHhhccchhhHHHHhhhhccchhhHhHHHHHhhchhHHH
Q 035914 7 NTGLFVGLSKGK-----------------TSKGVDFERNVIREVAGFASYKKGINKLLKVGKDKRTLKVAKKKLGAHKRA 69 (93)
Q Consensus 7 ~~g~avGlnkg~-----------------~tk~~kfvr~vIrEV~GfaPYEkr~mELlk~skdKrALKf~KKRlGth~RA 69 (93)
++|||||||||| +|+|++||||||+|||||||||+|+||||++|+||+||||+|||||||+||
T Consensus 2 ~~~iavGlnkGh~vtk~~~~~r~s~~kg~~tk~~kfvr~vIrEv~GfaPYEkr~mELlkv~kdKrAlKf~KKRlGth~RA 81 (98)
T PF01158_consen 2 RYGIAVGLNKGHKVTKNVSKPRPSRRKGRLTKRTKFVRDVIREVCGFAPYEKRAMELLKVSKDKRALKFAKKRLGTHIRA 81 (98)
T ss_dssp -TTSTTSSS-S-----TTS---STTS-SHHCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHCCHHHHHHHHHHHHCHHHHH
T ss_pred CCceeeeCCCCcccCCCCCCCCcccccCccchhHHHHHHHHHHhcCCChHHHHHHHHHhcchhHHHHHHHHHHhhhhHHH
Confidence 589999999976 689999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhc
Q 035914 70 KMKREEMSNVLRWTRAT 86 (93)
Q Consensus 70 KrK~eel~~vl~~~Rk~ 86 (93)
|+|+|||+|||++||++
T Consensus 82 KrKrEel~~vl~~~rk~ 98 (98)
T PF01158_consen 82 KRKREELSNVLAAMRKA 98 (98)
T ss_dssp HHHHHHHHHHHHHHHH-
T ss_pred HHHHHHHHHHHHHHhcC
Confidence 99999999999999985
No 2
>PTZ00196 60S ribosomal protein L36; Provisional
Probab=100.00 E-value=2.7e-46 Score=258.01 Aligned_cols=80 Identities=55% Similarity=0.834 Sum_probs=77.1
Q ss_pred CccceeeecCCC-----------------CCcchhHHHHHHHHhhccchhhHHHHhhhhccchhhHhHHHHHhhchhHHH
Q 035914 7 NTGLFVGLSKGK-----------------TSKGVDFERNVIREVAGFASYKKGINKLLKVGKDKRTLKVAKKKLGAHKRA 69 (93)
Q Consensus 7 ~~g~avGlnkg~-----------------~tk~~kfvr~vIrEV~GfaPYEkr~mELlk~skdKrALKf~KKRlGth~RA 69 (93)
++|||||||||| +|||++||||||+|||||||||+|+||||++|+||+||||+|+|||||+||
T Consensus 2 ~~g~avGlnKGh~vtk~~~~~r~s~rkg~~tkr~~fVr~vIrEV~GfaPYErr~mELLkv~kdKrAlKfaKkRlGth~Ra 81 (98)
T PTZ00196 2 RTGIAVGLNKGHIVTKRARKPSPSKRKGLLSKRKRLVKDVIREVCGFSPYERRMIELLKVGKDKRALKYAKKRLGTHKRA 81 (98)
T ss_pred CCceeeecCCCcccCcCCCCCCcccccCCCCchhHHHHHHHHHHhcccHHHHHHHHHHHhcchHHHHHHHHHHhhhHHHH
Confidence 589999999965 699999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhc
Q 035914 70 KMKREEMSNVLRWTRAT 86 (93)
Q Consensus 70 KrK~eel~~vl~~~Rk~ 86 (93)
|+|+|||+|||++||+.
T Consensus 82 K~Kreel~~vl~~~rkk 98 (98)
T PTZ00196 82 KAKRDEIQEALRAQRKK 98 (98)
T ss_pred HHHHHHHHHHHHHHhcC
Confidence 99999999999999973
No 3
>KOG3452 consensus 60S ribosomal protein L36 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.3e-43 Score=245.93 Aligned_cols=82 Identities=60% Similarity=0.822 Sum_probs=78.5
Q ss_pred CccceeeecCCC-----------------CCcchhHHHHHHHHhhccchhhHHHHhhhhccchhhHhHHHHHhhchhHHH
Q 035914 7 NTGLFVGLSKGK-----------------TSKGVDFERNVIREVAGFASYKKGINKLLKVGKDKRTLKVAKKKLGAHKRA 69 (93)
Q Consensus 7 ~~g~avGlnkg~-----------------~tk~~kfvr~vIrEV~GfaPYEkr~mELlk~skdKrALKf~KKRlGth~RA 69 (93)
.+|++||||||+ +|+|++||+|+|+|||||||||+++||||++|+||+|+||+|+|||||+||
T Consensus 4 ~~~~~vglnkgh~~tk~~~~pr~s~~kg~~sk~tkfvr~lirEv~G~aPyErr~meLlkvskdkrA~K~lKkRlGth~RA 83 (102)
T KOG3452|consen 4 CYGLAVGLNKGHKVTKRVSKPRQSRRKGETSKRTKFVRDLIREVAGFAPYERRAMELLKVSKDKRALKLLKKRLGTHKRA 83 (102)
T ss_pred ccceeecccccchhhcccCCCCcCccccchhhhHHHHHHHHHHHhCCChHHHHHHHHHHHcccHHHHHHHHHHhhHHHHH
Confidence 379999999965 799999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhcCC
Q 035914 70 KMKREEMSNVLRWTRATGG 88 (93)
Q Consensus 70 KrK~eel~~vl~~~Rk~~~ 88 (93)
|+|+|||+|||++||++++
T Consensus 84 k~KrEELsnvl~~~rk~~~ 102 (102)
T KOG3452|consen 84 KRKREELSNVLAAMRKAHA 102 (102)
T ss_pred HHHHHHHHHHHHHHHhccC
Confidence 9999999999999999863
No 4
>COG5051 RPL36A Ribosomal protein L36E [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=2.6e-29 Score=172.71 Aligned_cols=75 Identities=45% Similarity=0.769 Sum_probs=71.8
Q ss_pred ccceeeecCC-----------------CCCcchhHHHHHHHHhhccchhhHHHHhhhhccchhhHhHHHHHhhchhHHHH
Q 035914 8 TGLFVGLSKG-----------------KTSKGVDFERNVIREVAGFASYKKGINKLLKVGKDKRTLKVAKKKLGAHKRAK 70 (93)
Q Consensus 8 ~g~avGlnkg-----------------~~tk~~kfvr~vIrEV~GfaPYEkr~mELlk~skdKrALKf~KKRlGth~RAK 70 (93)
.|++||||+| .+|+|+.||+++++|++||+|||+++||||++|.|++|.|++|||||||+||+
T Consensus 5 ~g~~~glNkgKkvt~r~p~~rps~kkgq~s~Rt~fvrsivrEiaGlsPyErr~i~Lirns~~krArKlakKRLGs~kRAk 84 (97)
T COG5051 5 PGLVVGLNKGKKVTKRQPPERPSRKKGQLSKRTEFVRSIVREIAGLSPYERRVIELIRNSQDKRARKLAKKRLGSLKRAK 84 (97)
T ss_pred cchhhhhcccceeeeccCCCCcchhhhccccHHHHHHHHHHHHccCCHHHHHHHHHHHhcccHHHHHHHHHHhhhHHHHH
Confidence 5899999994 48999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHH
Q 035914 71 MKREEMSNVLRW 82 (93)
Q Consensus 71 rK~eel~~vl~~ 82 (93)
.|.|||.++|++
T Consensus 85 aKvEel~~~i~~ 96 (97)
T COG5051 85 AKVEELTSVIQS 96 (97)
T ss_pred HHHHHHHHHHhc
Confidence 999999999974
No 5
>PRK14132 riboflavin kinase; Provisional
Probab=54.43 E-value=7.2 Score=28.09 Aligned_cols=32 Identities=22% Similarity=0.379 Sum_probs=21.7
Q ss_pred ceeeecCCCCCcchhHHHHHHHHhhccchhhH
Q 035914 10 LFVGLSKGKTSKGVDFERNVIREVAGFASYKK 41 (93)
Q Consensus 10 ~avGlnkg~~tk~~kfvr~vIrEV~GfaPYEk 41 (93)
+.-||-.|.-==.....++-++|.+||.||.=
T Consensus 7 VvSGlGEG~yyvsl~~Y~~qf~~~LGf~PyPG 38 (126)
T PRK14132 7 VVSGLGEGAYFLSLPPYKEKFKEKLGFTPYEG 38 (126)
T ss_pred EecccccceEEEeCHHHHHHHHHHhCCcCCCC
Confidence 34466666522223457888999999999973
No 6
>KOG2659 consensus LisH motif-containing protein [Cytoskeleton]
Probab=51.13 E-value=24 Score=27.77 Aligned_cols=66 Identities=20% Similarity=0.298 Sum_probs=47.1
Q ss_pred CCCCcchhHHHHHHHHhhccch------hhHHHHhhhhccchhhHhHHHHHhhchhH-HHHHHHHHHHHHHHH
Q 035914 17 GKTSKGVDFERNVIREVAGFAS------YKKGINKLLKVGKDKRTLKVAKKKLGAHK-RAKMKREEMSNVLRW 82 (93)
Q Consensus 17 g~~tk~~kfvr~vIrEV~GfaP------YEkr~mELlk~skdKrALKf~KKRlGth~-RAKrK~eel~~vl~~ 82 (93)
|.+..-..++.++-.|+..-.+ -..+.+|||+.++-..|++|++-+|--.- ..-.+.++|..++..
T Consensus 78 G~Ie~Aie~in~l~PeiLd~n~~l~F~Lq~q~lIEliR~~~~eeal~F~q~~LA~~a~e~~~~~~elE~~l~l 150 (228)
T KOG2659|consen 78 GQIEEAIEKVNQLNPEILDTNRELFFHLQQLHLIELIREGKTEEALEFAQTKLAPFAEENPKKMEELERTLAL 150 (228)
T ss_pred ccHHHHHHHHHHhChHHHccchhHHHHHHHHHHHHHHHhhhHHHHHHHHHHHccccccccHHHHHHHHHHHHH
Confidence 4444445566677777766555 35699999999999999999999984332 223678888877754
No 7
>PF10607 CLTH: CTLH/CRA C-terminal to LisH motif domain; InterPro: IPR019589 This entry represents the CRA (or CT11-RanBPM) domain, which is a protein-protein interaction domain present in crown eukaryotes (plants, animals, fungi) and which is found in Ran-binding proteins such as Ran-binding protein 9 (RanBP9 or RanBPM) and RanBP10. RanBPM is a scaffolding protein important in regulating cellular function in both the immune system and the nervous system, and may act as an adapter protein to couple membrane receptors to intracellular signaling pathways. This domain is at the C terminus of the proteins and is the binding domain for the CRA motif, which is comprised of approximately 100 amino acids at the C-terminal of RanBPM. It was found to be important for the interaction of RanBPM with fragile X mental retardation protein (FMRP), but its functional significance has yet to be determined [].
Probab=44.53 E-value=60 Score=21.78 Aligned_cols=43 Identities=21% Similarity=0.254 Sum_probs=29.9
Q ss_pred cchhhHHHHhhhhccchhhHhHHHHHhhchhHHHHHHHHHHHHHH
Q 035914 36 FASYKKGINKLLKVGKDKRTLKVAKKKLGAHKRAKMKREEMSNVL 80 (93)
Q Consensus 36 faPYEkr~mELlk~skdKrALKf~KKRlGth~RAKrK~eel~~vl 80 (93)
|.=+-.+.+||++.++-..|+.|+++.+ ++- .....+++..++
T Consensus 40 f~L~~q~fiell~~~~~~~Ai~y~r~~l-~~~-~~~~~~~l~~~~ 82 (145)
T PF10607_consen 40 FELRCQQFIELLREGDIMEAIEYARKHL-SPF-NDEFLEELKKLM 82 (145)
T ss_pred HHHHHHHHHHHHHHHhHHHHHHHHHHHh-hhh-HHHHHHHHHHHH
Confidence 4445668899999999999999999988 422 223444554444
No 8
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=41.34 E-value=16 Score=28.04 Aligned_cols=31 Identities=26% Similarity=0.328 Sum_probs=20.8
Q ss_pred eeeecCCCCCcchhHHHHHHHHhhccchhhH
Q 035914 11 FVGLSKGKTSKGVDFERNVIREVAGFASYKK 41 (93)
Q Consensus 11 avGlnkg~~tk~~kfvr~vIrEV~GfaPYEk 41 (93)
.-||-.|.-==.....++-++|.+||.||.=
T Consensus 96 ~sGlGeG~~y~~~~~Y~~~f~~~lGf~PypG 126 (217)
T PRK14165 96 VKGLGEGKYYINIKGYKIQFEEKLGFIPYPG 126 (217)
T ss_pred hhccCCccEEEeCHHHHHHHHHHhCCcCCCC
Confidence 4455555522223456888999999999974
No 9
>PF08068 DKCLD: DKCLD (NUC011) domain; InterPro: IPR012960 This is an N-terminal domain of dyskerin-like proteins, which is often associated with the TruB N-terminal(IPR002501 from INTERPRO) and PUA(IPR002478 from INTERPRO) domains [].; PDB: 3ZV0_D 3UAI_A 3U28_A 2AUS_C 2RFK_A 3LWV_A 3HJY_A 3HAX_A 3LWO_A 3HAY_A ....
Probab=37.05 E-value=17 Score=23.36 Aligned_cols=19 Identities=26% Similarity=0.434 Sum_probs=13.5
Q ss_pred HhhccchhhHHHHhhhhcc
Q 035914 32 EVAGFASYKKGINKLLKVG 50 (93)
Q Consensus 32 EV~GfaPYEkr~mELlk~s 50 (93)
.-+|..|++|-+-|+|+.|
T Consensus 25 ~~~G~~P~~R~i~~~i~~G 43 (59)
T PF08068_consen 25 PPYGCSPLKRPIEEYIKYG 43 (59)
T ss_dssp TTSS--GGGS-HHHHHHTE
T ss_pred cccCcCcccCCHHHHHhCC
Confidence 4589999999999999854
No 10
>PF12169 DNA_pol3_gamma3: DNA polymerase III subunits gamma and tau domain III; InterPro: IPR022754 This domain is found in bacteria and eukaryotes, and is approximately 110 amino acids in length. It is found in association with PF00004 from PFAM. This domain is also present in the tau subunit before it undergoes cleavage. Domains I-III are shared between the tau and the gamma subunits, while most of the DnaB-binding Domain IV and all of the alpha-interacting Domain V are unique to tau. ; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G.
Probab=32.30 E-value=1.6e+02 Score=19.69 Aligned_cols=55 Identities=18% Similarity=0.256 Sum_probs=37.0
Q ss_pred HHHHHhhccchhhH--HHHhhhhccchhhHhHHHHHhhchhHHHHHHHHHHHHHHHH
Q 035914 28 NVIREVAGFASYKK--GINKLLKVGKDKRTLKVAKKKLGAHKRAKMKREEMSNVLRW 82 (93)
Q Consensus 28 ~vIrEV~GfaPYEk--r~mELlk~skdKrALKf~KKRlGth~RAKrK~eel~~vl~~ 82 (93)
+-|+++.|..|.|. .+++.|-.++-..++.++.+=+-.-+-...=.++|.+.++.
T Consensus 4 e~V~~~lG~v~~~~i~~l~~ai~~~d~~~~l~~~~~l~~~G~d~~~~l~~L~~~~R~ 60 (143)
T PF12169_consen 4 EDVREILGLVDEEQIFELLDAILEGDAAEALELLNELLEQGKDPKQFLDDLIEYLRD 60 (143)
T ss_dssp HHHHHHHTHTSTHHHHHHHHHHHTT-HHHHHHHHHHHHHCT--HHHHHHHHHHHHHH
T ss_pred HHHHHHHCCCCHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 56899999999997 56666767888889988887554444445555555555443
No 11
>COG3893 Inactivated superfamily I helicase [DNA replication, recombination, and repair]
Probab=31.58 E-value=38 Score=30.79 Aligned_cols=34 Identities=24% Similarity=0.359 Sum_probs=28.0
Q ss_pred ceeeecCCCC---CcchhHHHHHHHHhhccchhhHHH
Q 035914 10 LFVGLSKGKT---SKGVDFERNVIREVAGFASYKKGI 43 (93)
Q Consensus 10 ~avGlnkg~~---tk~~kfvr~vIrEV~GfaPYEkr~ 43 (93)
+.||+|.|.. |-.--|...-+|--.|+.|||+|+
T Consensus 584 Vi~glNEg~wP~~~~nd~FlSr~mr~~lgL~pperR~ 620 (697)
T COG3893 584 VIVGLNEGVWPSKTPNDLFLSRPMRKSLGLPPPERRI 620 (697)
T ss_pred EEecCCcccCCCCCccchhhchHHHHhcCCCChHHHh
Confidence 6789999874 445568888889999999999986
No 12
>PF01982 CTP-dep_RFKase: Domain of unknown function DUF120; InterPro: IPR023602 Riboflavin is converted into catalytically active cofactors (FAD and FMN) by the actions of riboflavin kinase (2.7.1.26 from EC), which converts it into FMN, and FAD synthetase (2.7.7.2 from EC), which adenylates FMN to FAD. Eukaryotes usually have two separate enzymes, while most prokaryotes have a single bifunctional protein that can carry out both catalyses, although exceptions occur in both cases. While eukaryotic monofunctional riboflavin kinase is orthologous to the bifunctional prokaryotic enzyme [], the monofunctional FAD synthetase differs from its prokaryotic counterpart, and is instead related to the PAPS-reductase family []. The bacterial FAD synthetase that is part of the bifunctional enzyme has remote similarity to nucleotidyl transferases and, hence, it may be involved in the adenylylation reaction of FAD synthetases []. This entry represents a CTP-dependent riboflavin kinase domain, found primarily in archaea, that catalyses the phosphorylation of riboflavin to form flavin mononucleotide in riboflavin biosynthesis. Its structure resembles a RIFT barrel, structurally similar to but topologically distinct from bacterial and eukaryotic examples []. The N-terminal is a winged helix-turn-helix DNA-binding domain, and the C-terminal half is most similar in sequence to a group of cradle-loop barrels.; GO: 0016773 phosphotransferase activity, alcohol group as acceptor; PDB: 2VBV_A 2VBU_A 2VBS_A 2VBT_A 2P3M_A 2OYN_A 3CTA_A.
Probab=30.38 E-value=35 Score=24.38 Aligned_cols=18 Identities=33% Similarity=0.397 Sum_probs=11.8
Q ss_pred hHHHHHHHHhhccchhhH
Q 035914 24 DFERNVIREVAGFASYKK 41 (93)
Q Consensus 24 kfvr~vIrEV~GfaPYEk 41 (93)
...++-++|.+||.||.=
T Consensus 15 ~~Y~~qf~~~LGf~PyPG 32 (121)
T PF01982_consen 15 PGYRRQFREKLGFEPYPG 32 (121)
T ss_dssp HHHHHHHHHHCSS---SS
T ss_pred HHHHHHHHHHhCCCCCCC
Confidence 346788999999999963
No 13
>COG1329 Transcriptional regulators, similar to M. xanthus CarD [Transcription]
Probab=29.87 E-value=45 Score=25.28 Aligned_cols=32 Identities=13% Similarity=0.188 Sum_probs=25.8
Q ss_pred ecCCCCCcchhHHHHHHHHh--hccchhhHHHHh
Q 035914 14 LSKGKTSKGVDFERNVIREV--AGFASYKKGINK 45 (93)
Q Consensus 14 lnkg~~tk~~kfvr~vIrEV--~GfaPYEkr~mE 45 (93)
||.|.+..-..+|||+-|-. -+++++||++++
T Consensus 98 lksGdi~~~AevvrdL~r~~~qr~l~~~Er~ll~ 131 (166)
T COG1329 98 LKSGDIIDIAEVVRDLYRRDKQRELSYSERRLLE 131 (166)
T ss_pred hccCChhHHHHHHHHHHHhhcccCCChHHHHHHH
Confidence 34477888888999998765 599999999875
No 14
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=29.42 E-value=68 Score=24.78 Aligned_cols=52 Identities=29% Similarity=0.479 Sum_probs=40.6
Q ss_pred HHHHHHHh-hccchhhHHHHhhhh-------------ccchhhHhHHHHHhh-chhHHHHHHHHHHHHH
Q 035914 26 ERNVIREV-AGFASYKKGINKLLK-------------VGKDKRTLKVAKKKL-GAHKRAKMKREEMSNV 79 (93)
Q Consensus 26 vr~vIrEV-~GfaPYEkr~mELlk-------------~skdKrALKf~KKRl-Gth~RAKrK~eel~~v 79 (93)
++|+|+-+ -||.|=+ ++-||. ++....++.=+|-|+ |..-++++=.|+|+++
T Consensus 67 a~d~VkAIgrGF~pe~--A~~LL~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~ 133 (194)
T COG1094 67 ARDVVKAIGRGFPPEK--ALKLLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGV 133 (194)
T ss_pred HHHHHHHHhcCCCHHH--HHHHhcCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCC
Confidence 57888887 7999864 555555 355677788888887 9999999999999864
No 15
>PF13058 DUF3920: Protein of unknown function (DUF3920)
Probab=25.96 E-value=60 Score=23.69 Aligned_cols=28 Identities=29% Similarity=0.354 Sum_probs=22.3
Q ss_pred hccchhhHHHHhhhhccchhhHhHHHHHhhchhHH
Q 035914 34 AGFASYKKGINKLLKVGKDKRTLKVAKKKLGAHKR 68 (93)
Q Consensus 34 ~GfaPYEkr~mELlk~skdKrALKf~KKRlGth~R 68 (93)
.|-.|||.|.||- | |..|+-..|-..+|
T Consensus 97 vg~e~yEeR~ie~-----D--Ar~FAe~kl~ey~~ 124 (126)
T PF13058_consen 97 VGKEPYEERWIEK-----D--ARAFAERKLDEYKR 124 (126)
T ss_pred eccchHHHHHHHH-----H--HHHHHHHHHHHHhc
Confidence 7899999999974 5 88999887765543
No 16
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=22.83 E-value=46 Score=26.25 Aligned_cols=16 Identities=38% Similarity=0.563 Sum_probs=13.9
Q ss_pred HHHHHHHhhccchhhH
Q 035914 26 ERNVIREVAGFASYKK 41 (93)
Q Consensus 26 vr~vIrEV~GfaPYEk 41 (93)
-+..++|..||.||.-
T Consensus 109 Y~~qf~ekLGf~PyPG 124 (214)
T COG1339 109 YRRQFREKLGFDPYPG 124 (214)
T ss_pred HHHHHHHHhCCCCCCC
Confidence 4788999999999973
No 17
>PF04328 DUF466: Protein of unknown function (DUF466); InterPro: IPR007423 This is a small bacterial protein of unknown function.
Probab=22.29 E-value=71 Score=20.31 Aligned_cols=21 Identities=19% Similarity=0.150 Sum_probs=17.5
Q ss_pred hhHHHHHHHHhhccchhhHHH
Q 035914 23 VDFERNVIREVAGFASYKKGI 43 (93)
Q Consensus 23 ~kfvr~vIrEV~GfaPYEkr~ 43 (93)
.+-++..+++++|..-||+=+
T Consensus 9 ~~~~~~~~r~l~G~~~Ye~Yv 29 (65)
T PF04328_consen 9 WRRVRWYARLLVGEPDYERYV 29 (65)
T ss_pred HHHHHHHHHHhcCcHHHHHHH
Confidence 456789999999999999744
No 18
>KOG0396 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.12 E-value=90 Score=26.64 Aligned_cols=37 Identities=19% Similarity=0.334 Sum_probs=26.8
Q ss_pred HHHHhhhhccchhhHhHHHHHhhchhHHHHHHHHHHHHH
Q 035914 41 KGINKLLKVGKDKRTLKVAKKKLGAHKRAKMKREEMSNV 79 (93)
Q Consensus 41 kr~mELlk~skdKrALKf~KKRlGth~RAKrK~eel~~v 79 (93)
...+||+++.+-..|.-|++|-+++-- +.=-++|.-.
T Consensus 196 QefIELi~~~~~~~Ai~~akk~f~~~~--~~~~~~Lk~a 232 (389)
T KOG0396|consen 196 QEFIELIKVDNYDKAIAFAKKHFAPWA--KSHKSDLKLA 232 (389)
T ss_pred HHHHHHHHhccHHHHHHHHHHHHhhhh--hhhHHHHHHH
Confidence 357899999999999999999776643 2333444433
No 19
>PF12077 DUF3556: Transmembrane protein of unknown function (DUF3556); InterPro: IPR021941 This family of transmembrane proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 576 to 592 amino acids in length.
Probab=20.07 E-value=55 Score=29.20 Aligned_cols=36 Identities=11% Similarity=0.105 Sum_probs=25.7
Q ss_pred cceeeecCCCCCcchhHHHHHHHHhhccchhhHHHH
Q 035914 9 GLFVGLSKGKTSKGVDFERNVIREVAGFASYKKGIN 44 (93)
Q Consensus 9 g~avGlnkg~~tk~~kfvr~vIrEV~GfaPYEkr~m 44 (93)
+.++|.|=|-=.=|....=..+++-|||+|=|-+++
T Consensus 487 ~~~iGwNFGDGHLHnE~lIaAvQ~rC~FePGE~rvv 522 (574)
T PF12077_consen 487 NTAIGWNFGDGHLHNEQLIAAVQRRCGFEPGEVRVV 522 (574)
T ss_pred cceeeecccCcccccHHHHHHHHHHcCCCCCeEEEE
Confidence 468999984333344445667889999999997654
No 20
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=20.04 E-value=59 Score=19.45 Aligned_cols=17 Identities=24% Similarity=0.282 Sum_probs=14.4
Q ss_pred HhhccchhhHHHHhhhh
Q 035914 32 EVAGFASYKKGINKLLK 48 (93)
Q Consensus 32 EV~GfaPYEkr~mELlk 48 (93)
+..||+.+|.+++..|-
T Consensus 2 ~~~gLs~~E~~vy~~Ll 18 (68)
T PF01978_consen 2 EVLGLSENEAKVYLALL 18 (68)
T ss_dssp HHHCHHHHHHHHHHHHH
T ss_pred CcCCcCHHHHHHHHHHH
Confidence 37899999999997765
Done!