Query psy6030
Match_columns 118
No_of_seqs 103 out of 249
Neff 5.2
Searched_HMMs 46136
Date Sat Aug 17 00:44:45 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6030.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6030hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3412|consensus 100.0 1.2E-44 2.6E-49 262.7 9.4 109 2-113 3-118 (133)
2 PTZ00197 60S ribosomal protein 100.0 1.4E-43 3.1E-48 262.8 9.4 102 2-114 3-110 (146)
3 PF01778 Ribosomal_L28e: Ribos 100.0 9E-40 1.9E-44 233.8 -0.3 105 6-115 1-111 (117)
4 PLN00040 Protein MAK16 homolog 100.0 4.4E-30 9.5E-35 202.9 8.0 91 1-98 1-98 (233)
5 KOG3064|consensus 99.0 2.2E-10 4.9E-15 92.7 3.0 91 1-98 1-98 (303)
6 COG5129 MAK16 Nuclear protein 98.6 2.3E-08 5E-13 80.2 2.9 90 2-98 1-97 (303)
7 PF01726 LexA_DNA_bind: LexA D 32.2 49 0.0011 21.1 2.4 32 86-117 8-39 (65)
8 PF04316 FlgM: Anti-sigma-28 f 25.3 84 0.0018 19.2 2.5 25 89-113 29-53 (57)
9 PF14990 DUF4516: Domain of un 23.2 16 0.00035 22.6 -1.0 12 97-108 27-38 (47)
10 PF00356 LacI: Bacterial regul 15.8 74 0.0016 19.0 0.8 19 87-105 28-46 (46)
No 1
>KOG3412|consensus
Probab=100.00 E-value=1.2e-44 Score=262.67 Aligned_cols=109 Identities=41% Similarity=0.664 Sum_probs=104.9
Q ss_pred CCcceeeeeeecCceeeeeeC-CCCcccccCCCCCCCcccccccccccceeeEEEeCCCCCcEEEEEecCCC--CCCCCC
Q psy6030 2 VSSHLIWNIVKNNNAYLMKAD-NIKKWFSKEPGNLPNLASFKYSGLIHSKTIHIQPTADNKGFACVTKRATK--KPTADN 78 (118)
Q Consensus 2 mS~dL~W~ivrnnnsFlvK~~-~~~~~FS~EP~NL~n~~S~kysGlan~Kav~V~~~~~~~gv~v~~Kk~k~--kPa~~~ 78 (118)
||+||+|||||||||||+|+. +++++||+||+||.++||||||||+|+|+|||+|+++++||++++|+.+. +|+
T Consensus 3 ~S~~L~W~VIRnNn~FL~k~r~~~k~~FstEpnNL~~vnS~rySGL~nkKtvgV~~aA~~kgvvv~~kk~K~aqkPA--- 79 (133)
T KOG3412|consen 3 TSGHLIWQVIRNNNAFLVKQRGNVKKQFSTEPNNLKNVNSYRYSGLANKKTVGVIPAADKKGVVVVTKKTKGAQKPA--- 79 (133)
T ss_pred cccceeeeeeecCCceeeeeccccccccccCCcccccccccccccccccceeeeeecCCCceEEEEEeccccccCch---
Confidence 899999999999999999976 56899999999999999999999999999999999999999999999998 999
Q ss_pred Ccee----ecchhHHHHHHHhhhhcCCCChhhHHHHHHh
Q psy6030 79 KGFA----CVTKRATKKTLSGHVDIGSARMDARLYIFEM 113 (118)
Q Consensus 79 k~~~----~k~~R~~~~~i~~~v~~~~yRpDL~~~A~~~ 113 (118)
++++ ++++|+++++|++++..++|||||+++|++|
T Consensus 80 k~~~k~~~~k~~r~s~k~la~~i~~nkYR~Dl~~aaiaR 118 (133)
T KOG3412|consen 80 KSVVKSTLKKEPRRSLKSLANQIGDNKYRPDLRKAALAR 118 (133)
T ss_pred hhhhHHHHhcccHHHHHHHHHHhhhcccchHHHHHHHHH
Confidence 9987 7899999999999999999999999999999
No 2
>PTZ00197 60S ribosomal protein L28; Provisional
Probab=100.00 E-value=1.4e-43 Score=262.77 Aligned_cols=102 Identities=24% Similarity=0.330 Sum_probs=95.5
Q ss_pred CCcceeeeeeecCceeeeeeCCCCcccccCCCCCCCcccccccccccceeeEEEeCCCCCcEEEEEecCCC--CCCCCCC
Q psy6030 2 VSSHLIWNIVKNNNAYLMKADNIKKWFSKEPGNLPNLASFKYSGLIHSKTIHIQPTADNKGFACVTKRATK--KPTADNK 79 (118)
Q Consensus 2 mS~dL~W~ivrnnnsFlvK~~~~~~~FS~EP~NL~n~~S~kysGlan~Kav~V~~~~~~~gv~v~~Kk~k~--kPa~~~k 79 (118)
-|+||||||||+|||||+|++ |++||+||+||+|+||+|||||+|+|+|||+ + |++||+|++|+.+. +|+ +
T Consensus 3 ~S~dL~W~iVRnnnsFLvKr~--g~~FSrEP~NL~n~nS~KysGL~n~KaVgV~-~-~~kgVvv~tKk~k~~~kPa---k 75 (146)
T PTZ00197 3 HSTDLQWLLVRQNSKFLQKRN--GIRLSSDPFNNNANWTKRHCGFLNTKAAVVK-T-KGDRILVTTKDGSSNNKPK---Q 75 (146)
T ss_pred CchheeeeeeeccceeEEccC--CCcccCCCCccccccccccccccccceEEEE-e-cCCEEEEEEecCCCCCCCc---h
Confidence 389999999999999999998 8899999999999999999999999999999 5 88999999999887 999 8
Q ss_pred cee----ecchhHHHHHHHhhhhcCCCChhhHHHHHHhc
Q psy6030 80 GFA----CVTKRATKKTLSGHVDIGSARMDARLYIFEMG 114 (118)
Q Consensus 80 ~~~----~k~~R~~~~~i~~~v~~~~yRpDL~~~A~~~~ 114 (118)
++. ++|+|++ .|++++.+ |||||+++|++||
T Consensus 76 ~~~~~tlkkg~Rr~--~V~~~v~~--YR~DL~~aAlrRA 110 (146)
T PTZ00197 76 MYKKTVMAAGVRAS--VVSRAVAA--VRPDLASVAFRRA 110 (146)
T ss_pred heeEEeeccCccHH--HHHHHHHh--hCHHHHHHHHHHH
Confidence 876 7899999 59999875 9999999999997
No 3
>PF01778 Ribosomal_L28e: Ribosomal L28e protein family; InterPro: IPR002672 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L28e forms part of the 60S ribosomal subunit []. This family is found in eukaryotes. In rat there are 9 or 10 copies of the L28 gene. The L28 protein contains a possible internal duplication of 9 residues [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1D_O 4A1B_O 4A18_O 4A19_O 3IZR_b.
Probab=100.00 E-value=9e-40 Score=233.80 Aligned_cols=105 Identities=40% Similarity=0.665 Sum_probs=83.7
Q ss_pred eeeeeeecCceeeeeeCCCCcccccCCCCCCCcccccccccccceeeEEEeCCCCCcEEEEEecCCC--CCCCCCCcee-
Q psy6030 6 LIWNIVKNNNAYLMKADNIKKWFSKEPGNLPNLASFKYSGLIHSKTIHIQPTADNKGFACVTKRATK--KPTADNKGFA- 82 (118)
Q Consensus 6 L~W~ivrnnnsFlvK~~~~~~~FS~EP~NL~n~~S~kysGlan~Kav~V~~~~~~~gv~v~~Kk~k~--kPa~~~k~~~- 82 (118)
|||||||+|||||+|+++++.+||+||+||+|+||++||||||+|+|||+|++ +++|+|++|+.+. +|+ +++.
T Consensus 1 L~W~iir~~~~Fl~K~~~~~~~fs~ep~NL~~~~s~kysgLan~k~v~V~~~~-~g~v~l~~K~~~~~~~P~---k~~~~ 76 (117)
T PF01778_consen 1 LQWEIIRNNNCFLVKRNGIGKTFSREPGNLTNLNSFKYSGLANSKAVGVRPAP-NGGVVLVTKKPKRANKPA---KSWEK 76 (117)
T ss_dssp HHHHHHTTT-TTEEEET--TEEEE--TT-SSSB-STTT-TTTSS--EECCCEG-GGECCCEEE-----TTTT-----EEE
T ss_pred CEEEEecCcceEEEEeCCCCCcccCCCCcccccccccccccccceeEEEEECC-CCcEEEEEccccccCCCc---ceeEE
Confidence 79999999999999998778999999999999999999999999999999985 5689999999977 999 8877
Q ss_pred ---ecchhHHHHHHHhhhhcCCCChhhHHHHHHhcc
Q psy6030 83 ---CVTKRATKKTLSGHVDIGSARMDARLYIFEMGL 115 (118)
Q Consensus 83 ---~k~~R~~~~~i~~~v~~~~yRpDL~~~A~~~~~ 115 (118)
++|+|+++++|++.+.. +|||||+++|++|+-
T Consensus 77 ~~l~k~~r~a~~~I~~~~~~-~yr~dL~~~a~~R~s 111 (117)
T PF01778_consen 77 VTLSKNSRKALKSIKKQLAK-KYRPDLRKAALRRAS 111 (117)
T ss_dssp EEESSCHHHHHHHHHHHTSS-THHHHHCCHHHHHHH
T ss_pred EecCccHHHHHHHHHHHHHh-cCCHHHHHHHHHHHH
Confidence 67999999999999997 799999999999974
No 4
>PLN00040 Protein MAK16 homolog; Provisional
Probab=99.96 E-value=4.4e-30 Score=202.87 Aligned_cols=91 Identities=19% Similarity=0.318 Sum_probs=85.7
Q ss_pred CCCcceeeeeeecCce-eeeeeCCCCcccccCCCCCCCcccccccccccceeeEEEeCCCCCcEEEEEecCCC--CCCCC
Q psy6030 1 MVSSHLIWNIVKNNNA-YLMKADNIKKWFSKEPGNLPNLASFKYSGLIHSKTIHIQPTADNKGFACVTKRATK--KPTAD 77 (118)
Q Consensus 1 mmS~dL~W~ivrnnns-FlvK~~~~~~~FS~EP~NL~n~~S~kysGlan~Kav~V~~~~~~~gv~v~~Kk~k~--kPa~~ 77 (118)
|||+||+|+|||++|| |++|+. +.+||+||+||+|+||++||||||++++||.++ +++|+|++|+.+. +|+
T Consensus 1 m~SddLiW~IIr~~~csF~vK~~--~~~Fcrnp~NltglcsrkycgLANsKyatV~~~--~G~v~L~~Kt~erah~Pa-- 74 (233)
T PLN00040 1 MQHDEVIWQVINHNHCSFKAKID--TGNFCRNKYNVTGLCNRSSCPLANSRYATIREE--DGRFYLYMKTIERAHMPN-- 74 (233)
T ss_pred CCccchhhhhhcCcceeEEEccC--CCcccCCCCcccccccccccccccceeeEEEEc--CCEEEEEEecccccCCcc--
Confidence 8999999999999999 788877 889999999999999999999999999999996 5779999999998 999
Q ss_pred CCcee----ecchhHHHHHHHhhhh
Q psy6030 78 NKGFA----CVTKRATKKTLSGHVD 98 (118)
Q Consensus 78 ~k~~~----~k~~R~~~~~i~~~v~ 98 (118)
+++. ++|+|+++++|.+.+.
T Consensus 75 -k~w~kv~Lskn~rkalk~I~~~L~ 98 (233)
T PLN00040 75 -KLWEKVKLSRNYEKALEQIDKHLA 98 (233)
T ss_pred -cceEEEecCCCHHHHHHHHHHHHh
Confidence 9887 7899999999999887
No 5
>KOG3064|consensus
Probab=98.99 E-value=2.2e-10 Score=92.67 Aligned_cols=91 Identities=15% Similarity=0.238 Sum_probs=80.4
Q ss_pred CCCcceeeeeeecCcee-eeeeCCCCcccccCCCCCCCcccccccccccceeeEEEeCCCCCcEEEEEecCCC--CCCCC
Q psy6030 1 MVSSHLIWNIVKNNNAY-LMKADNIKKWFSKEPGNLPNLASFKYSGLIHSKTIHIQPTADNKGFACVTKRATK--KPTAD 77 (118)
Q Consensus 1 mmS~dL~W~ivrnnnsF-lvK~~~~~~~FS~EP~NL~n~~S~kysGlan~Kav~V~~~~~~~gv~v~~Kk~k~--kPa~~ 77 (118)
|||+|.+|++|.+++|- .+|.. +.+|++..+|||+++....|.|||++...|... ++-+.|.+|.... -|.
T Consensus 1 Mq~DeviW~vin~~~CS~k~kte--~~~fCRNeyNvTGLCnR~SCPLANSrYATVre~--~g~~yLymKt~ERaH~P~-- 74 (303)
T KOG3064|consen 1 MQSDEVIWQVINKSFCSYKIKTE--TQTFCRNEYNVTGLCNRSSCPLANSRYATVREE--NGVLYLYMKTIERAHMPR-- 74 (303)
T ss_pred CcchHHHHHHhchhhcceeeecc--ccchhccccccceeeccccCcCccccceeEeec--CCEEEEEEechhhhcCcH--
Confidence 99999999999888875 46655 789999999999999999999999999999974 5668899999987 999
Q ss_pred CCcee----ecchhHHHHHHHhhhh
Q psy6030 78 NKGFA----CVTKRATKKTLSGHVD 98 (118)
Q Consensus 78 ~k~~~----~k~~R~~~~~i~~~v~ 98 (118)
+.+. +++.-+++..|...+-
T Consensus 75 -klwErikLSkNyekALeQIde~Ll 98 (303)
T KOG3064|consen 75 -KLWERIKLSKNYEKALEQIDEQLL 98 (303)
T ss_pred -HHHHHHhcchhHHHHHHHHHHHHh
Confidence 9987 7899999999987664
No 6
>COG5129 MAK16 Nuclear protein with HMG-like acidic region [General function prediction only]
Probab=98.61 E-value=2.3e-08 Score=80.22 Aligned_cols=90 Identities=17% Similarity=0.263 Sum_probs=79.8
Q ss_pred CCcceeeeeeecCceee-eeeCCCCcccccCCCCCCCcccccccccccceeeEEEeCCCCCcEEEEEecCCC--CCCCCC
Q psy6030 2 VSSHLIWNIVKNNNAYL-MKADNIKKWFSKEPGNLPNLASFKYSGLIHSKTIHIQPTADNKGFACVTKRATK--KPTADN 78 (118)
Q Consensus 2 mS~dL~W~ivrnnnsFl-vK~~~~~~~FS~EP~NL~n~~S~kysGlan~Kav~V~~~~~~~gv~v~~Kk~k~--kPa~~~ 78 (118)
||++.+|+++-.++|-. +|.. ++.|++..+|+|+++....|.|+|++...|.. +|+.+.|.+|.+.. -|+
T Consensus 1 msDE~~Wqv~g~~fCS~rik~e--~qnfCRNeyNVTGLC~RqSCPLANSrYATVr~--dngkLyLymKtpERaH~P~--- 73 (303)
T COG5129 1 MSDESLWQVSGENFCSFRIKTE--EQNFCRNEYNVTGLCDRQSCPLANSRYATVRA--DNGKLYLYMKTPERAHVPR--- 73 (303)
T ss_pred CchhHHHHHccccccceeeecc--hhhhhhcccccceeeccccCcCccCcceEEEe--cCCEEEEEecChhhccCcH---
Confidence 89999999999998865 5555 88999999999999999999999999999986 57789999999987 999
Q ss_pred Ccee----ecchhHHHHHHHhhhh
Q psy6030 79 KGFA----CVTKRATKKTLSGHVD 98 (118)
Q Consensus 79 k~~~----~k~~R~~~~~i~~~v~ 98 (118)
+.+. +++.-+++++|...+-
T Consensus 74 klwerIkLSkNY~kAL~QIde~Ll 97 (303)
T COG5129 74 KLWERIKLSKNYEKALKQIDESLL 97 (303)
T ss_pred HHHHHHHhhhhHHHHHHHHHHHHh
Confidence 9887 7889999999987653
No 7
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=32.23 E-value=49 Score=21.08 Aligned_cols=32 Identities=13% Similarity=0.105 Sum_probs=25.3
Q ss_pred hhHHHHHHHhhhhcCCCChhhHHHHHHhcccc
Q psy6030 86 KRATKKTLSGHVDIGSARMDARLYIFEMGLMS 117 (118)
Q Consensus 86 ~R~~~~~i~~~v~~~~yRpDL~~~A~~~~~~~ 117 (118)
-++++..|...+..++|=|-.++.|-+.|+.|
T Consensus 8 Q~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S 39 (65)
T PF01726_consen 8 QKEVLEFIREYIEENGYPPTVREIAEALGLKS 39 (65)
T ss_dssp HHHHHHHHHHHHHHHSS---HHHHHHHHTSSS
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCC
Confidence 46789999999999999999999999988864
No 8
>PF04316 FlgM: Anti-sigma-28 factor, FlgM; InterPro: IPR007412 FlgM binds and inhibits the activity of the transcription factor sigma 28. Inhibition of sigma 28 prevents the expression of genes from flagellar transcriptional class 3, which include genes for the filament and chemotaxis. Correctly assembled basal body-hook structures export FlgM, relieving inhibition of sigma 28 and allowing expression of class 3 genes. NMR studies show that free FlgM is mostly unfolded, which may facilitate its export. The C-terminal half of FlgM adopts a tertiary structure when it binds to sigma 28. All mutations in FlgM that prevent sigma 28 inhibition affect the C-terminal domain and is the region thought to constitute the binding domain. A minimal binding domain has been identified between Glu 64 and Arg 88 in Salmonella typhimurium (P26477 from SWISSPROT).The N-terminal portion remains unstructured and may be necessary for recognition by the export machinery [].; GO: 0045892 negative regulation of transcription, DNA-dependent, 0019861 flagellum; PDB: 1RP3_B 1SC5_B.
Probab=25.25 E-value=84 Score=19.23 Aligned_cols=25 Identities=16% Similarity=0.231 Sum_probs=15.8
Q ss_pred HHHHHHhhhhcCCCChhhHHHHHHh
Q psy6030 89 TKKTLSGHVDIGSARMDARLYIFEM 113 (118)
Q Consensus 89 ~~~~i~~~v~~~~yRpDL~~~A~~~ 113 (118)
-...|+..+..+.|.+|....|-++
T Consensus 29 kV~~ik~~I~~G~Y~vd~~~iA~~m 53 (57)
T PF04316_consen 29 KVAEIKAAIASGTYKVDAEKIAEKM 53 (57)
T ss_dssp HHHHHHHHHHTT-----HHHHHHHH
T ss_pred HHHHHHHHHHcCCCCCCHHHHHHHH
Confidence 3677999999999999998877553
No 9
>PF14990 DUF4516: Domain of unknown function (DUF4516)
Probab=23.18 E-value=16 Score=22.56 Aligned_cols=12 Identities=17% Similarity=0.033 Sum_probs=8.8
Q ss_pred hhcCCCChhhHH
Q psy6030 97 VDIGSARMDARL 108 (118)
Q Consensus 97 v~~~~yRpDL~~ 108 (118)
+-.+.|||||+-
T Consensus 27 vVH~~ykPdlti 38 (47)
T PF14990_consen 27 VVHNIYKPDLTI 38 (47)
T ss_pred HHHHHhCccCCC
Confidence 345689999974
No 10
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=15.76 E-value=74 Score=18.97 Aligned_cols=19 Identities=11% Similarity=0.074 Sum_probs=11.7
Q ss_pred hHHHHHHHhhhhcCCCChh
Q psy6030 87 RATKKTLSGHVDIGSARMD 105 (118)
Q Consensus 87 R~~~~~i~~~v~~~~yRpD 105 (118)
..+.+.|...+.+-+|+|+
T Consensus 28 ~~tr~rI~~~a~~lgY~pN 46 (46)
T PF00356_consen 28 EETRERILEAAEELGYRPN 46 (46)
T ss_dssp HHHHHHHHHHHHHHTB-SS
T ss_pred HHHHHHHHHHHHHHCCCCC
Confidence 3455566676766678875
Done!