Query 040088
Match_columns 131
No_of_seqs 112 out of 241
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 05:00:00 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040088.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040088hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3412 60S ribosomal protein 100.0 7.5E-40 1.6E-44 247.4 7.9 110 1-130 1-115 (133)
2 PTZ00197 60S ribosomal protein 100.0 2.7E-38 5.9E-43 243.0 9.7 104 3-130 2-106 (146)
3 PF01778 Ribosomal_L28e: Ribos 100.0 2.9E-33 6.4E-38 205.2 -1.5 103 8-130 1-106 (117)
4 PLN00040 Protein MAK16 homolog 99.9 7.3E-24 1.6E-28 173.1 8.2 95 4-118 2-98 (233)
5 KOG3064 RNA-binding nuclear pr 94.7 0.017 3.7E-07 49.4 1.9 94 4-118 2-98 (303)
6 COG5129 MAK16 Nuclear protein 91.7 0.093 2E-06 44.5 1.5 93 4-117 1-96 (303)
7 PF14990 DUF4516: Domain of un 31.3 11 0.00024 24.5 -0.7 12 117-128 27-38 (47)
8 PF04316 FlgM: Anti-sigma-28 f 14.9 99 0.0021 19.7 1.2 22 110-131 30-51 (57)
9 COG0187 GyrB Type IIA topoisom 14.8 4.9E+02 0.011 25.0 6.1 38 7-44 39-114 (635)
10 PRK04330 hypothetical protein; 14.6 1.6E+02 0.0034 21.4 2.3 30 100-129 25-54 (88)
No 1
>KOG3412 consensus 60S ribosomal protein L28 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=7.5e-40 Score=247.44 Aligned_cols=110 Identities=40% Similarity=0.684 Sum_probs=103.5
Q ss_pred CCCCCccceEEEEecCceeEEeecCC-C---ccCcCccceeeeeeecccccccccceeceeecCcccccccceEEEEe-C
Q 040088 1 MATVGGQLIWEIVKKNNCFLVKEFGR-G---SASAHAVITCSVYKFGGRKIECSTFVFGRFCGNRGKKIKLKTVTIQP-G 75 (131)
Q Consensus 1 m~~~S~dL~W~iVrnnnsFLvK~~g~-~---s~s~~NL~n~~s~KysG~~~~~~~~~~~~l~~~~~~~~~~KaV~V~~-~ 75 (131)
|+ ||+||+|||||||||||+|+.+. + |.||.||.+++||+||| ||| +|||||+| +
T Consensus 1 ma-~S~~L~W~VIRnNn~FL~k~r~~~k~~FstEpnNL~~vnS~rySG------------L~n-------kKtvgV~~aA 60 (133)
T KOG3412|consen 1 MA-TSGHLIWQVIRNNNAFLVKQRGNVKKQFSTEPNNLKNVNSYRYSG------------LAN-------KKTVGVIPAA 60 (133)
T ss_pred CC-cccceeeeeeecCCceeeeeccccccccccCCccccccccccccc------------ccc-------cceeeeeecC
Confidence 66 89999999999999999998743 3 66789999999999999 999 99999999 6
Q ss_pred CCCeEEEEEeccCCCCCCcceeeeeeeccchhHHHHHHHHHhcCCCCChhhhhhh
Q 040088 76 KDQVVVLATTKTKKQNKPIALLHKSVMKHEIHRMAKVIANRVGDNYYQPDLKNAV 130 (131)
Q Consensus 76 ~~~gVvl~tkk~k~~~kPak~~~~~~~k~~~Rr~~k~I~~~v~~n~YRpDL~~aA 130 (131)
+++||+++++++|.+++|++++.++++++++|+++++|++++.+++|||||+++|
T Consensus 61 ~~kgvvv~~kk~K~aqkPAk~~~k~~~~k~~r~s~k~la~~i~~nkYR~Dl~~aa 115 (133)
T KOG3412|consen 61 DKKGVVVVTKKTKGAQKPAKSVVKSTLKKEPRRSLKSLANQIGDNKYRPDLRKAA 115 (133)
T ss_pred CCceEEEEEeccccccCchhhhhHHHHhcccHHHHHHHHHHhhhcccchHHHHHH
Confidence 7789999999999999999999999999999999999999999999999999987
No 2
>PTZ00197 60S ribosomal protein L28; Provisional
Probab=100.00 E-value=2.7e-38 Score=243.04 Aligned_cols=104 Identities=25% Similarity=0.384 Sum_probs=99.0
Q ss_pred CCCccceEEEEecCceeEEeecCCC-ccCcCccceeeeeeecccccccccceeceeecCcccccccceEEEEeCCCCeEE
Q 040088 3 TVGGQLIWEIVKKNNCFLVKEFGRG-SASAHAVITCSVYKFGGRKIECSTFVFGRFCGNRGKKIKLKTVTIQPGKDQVVV 81 (131)
Q Consensus 3 ~~S~dL~W~iVrnnnsFLvK~~g~~-s~s~~NL~n~~s~KysG~~~~~~~~~~~~l~~~~~~~~~~KaV~V~~~~~~gVv 81 (131)
+.|+||||||||+|||||+|++|.. |.||+||+|+||||||| |+| .|+|||+ ++++||+
T Consensus 2 ~~S~dL~W~iVRnnnsFLvKr~g~~FSrEP~NL~n~nS~KysG------------L~n-------~KaVgV~-~~~kgVv 61 (146)
T PTZ00197 2 THSTDLQWLLVRQNSKFLQKRNGIRLSSDPFNNNANWTKRHCG------------FLN-------TKAAVVK-TKGDRIL 61 (146)
T ss_pred CCchheeeeeeeccceeEEccCCCcccCCCCcccccccccccc------------ccc-------cceEEEE-ecCCEEE
Confidence 3799999999999999999998776 88999999999999999 999 9999999 7999999
Q ss_pred EEEeccCCCCCCcceeeeeeeccchhHHHHHHHHHhcCCCCChhhhhhh
Q 040088 82 LATTKTKKQNKPIALLHKSVMKHEIHRMAKVIANRVGDNYYQPDLKNAV 130 (131)
Q Consensus 82 l~tkk~k~~~kPak~~~~~~~k~~~Rr~~k~I~~~v~~n~YRpDL~~aA 130 (131)
|+|++.+++++|++++.+++|++|+|++ .|++++.+ |||||+++|
T Consensus 62 v~tKk~k~~~kPak~~~~~tlkkg~Rr~--~V~~~v~~--YR~DL~~aA 106 (146)
T PTZ00197 62 VTTKDGSSNNKPKQMYKKTVMAAGVRAS--VVSRAVAA--VRPDLASVA 106 (146)
T ss_pred EEEecCCCCCCCchheeEEeeccCccHH--HHHHHHHh--hCHHHHHHH
Confidence 9999999999999999999999999999 59999876 999999988
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=99.97 E-value=2.9e-33 Score=205.22 Aligned_cols=103 Identities=34% Similarity=0.617 Sum_probs=82.5
Q ss_pred ceEEEEecCceeEEeecC--CC-ccCcCccceeeeeeecccccccccceeceeecCcccccccceEEEEeCCCCeEEEEE
Q 040088 8 LIWEIVKKNNCFLVKEFG--RG-SASAHAVITCSVYKFGGRKIECSTFVFGRFCGNRGKKIKLKTVTIQPGKDQVVVLAT 84 (131)
Q Consensus 8 L~W~iVrnnnsFLvK~~g--~~-s~s~~NL~n~~s~KysG~~~~~~~~~~~~l~~~~~~~~~~KaV~V~~~~~~gVvl~t 84 (131)
|+|||||+|||||+|+++ .. +.||+||+|+|||+|+| |+| .|+|||+|.++++|+|++
T Consensus 1 L~W~iir~~~~Fl~K~~~~~~~fs~ep~NL~~~~s~kysg------------Lan-------~k~v~V~~~~~g~v~l~~ 61 (117)
T PF01778_consen 1 LQWEIIRNNNCFLVKRNGIGKTFSREPGNLTNLNSFKYSG------------LAN-------SKAVGVRPAPNGGVVLVT 61 (117)
T ss_dssp HHHHHHTTT-TTEEEET--TEEEE--TT-SSSB-STTT-T------------TTS-------S--EECCCEGGGECCCEE
T ss_pred CEEEEecCcceEEEEeCCCCCcccCCCCcccccccccccc------------ccc-------ceeEEEEECCCCcEEEEE
Confidence 799999999999999994 33 77899999999999999 999 999999997678999999
Q ss_pred eccCCCCCCcceeeeeeeccchhHHHHHHHHHhcCCCCChhhhhhh
Q 040088 85 TKTKKQNKPIALLHKSVMKHEIHRMAKVIANRVGDNYYQPDLKNAV 130 (131)
Q Consensus 85 kk~k~~~kPak~~~~~~~k~~~Rr~~k~I~~~v~~n~YRpDL~~aA 130 (131)
|+.+..++|++++.++++++++|++++.|++.+.. +|||||+.+|
T Consensus 62 K~~~~~~~P~k~~~~~~l~k~~r~a~~~I~~~~~~-~yr~dL~~~a 106 (117)
T PF01778_consen 62 KKPKRANKPAKSWEKVTLSKNSRKALKSIKKQLAK-KYRPDLRKAA 106 (117)
T ss_dssp E-----TTTT--EEEEEESSCHHHHHHHHHHHTSS-THHHHHCCHH
T ss_pred ccccccCCCcceeEEEecCccHHHHHHHHHHHHHh-cCCHHHHHHH
Confidence 99999999999999999999999999999999998 8999999887
No 4
>PLN00040 Protein MAK16 homolog; Provisional
Probab=99.90 E-value=7.3e-24 Score=173.14 Aligned_cols=95 Identities=16% Similarity=0.232 Sum_probs=88.9
Q ss_pred CCccceEEEEecCce-eEEeecCCC-ccCcCccceeeeeeecccccccccceeceeecCcccccccceEEEEeCCCCeEE
Q 040088 4 VGGQLIWEIVKKNNC-FLVKEFGRG-SASAHAVITCSVYKFGGRKIECSTFVFGRFCGNRGKKIKLKTVTIQPGKDQVVV 81 (131)
Q Consensus 4 ~S~dL~W~iVrnnns-FLvK~~g~~-s~s~~NL~n~~s~KysG~~~~~~~~~~~~l~~~~~~~~~~KaV~V~~~~~~gVv 81 (131)
||+||+|+|||+||| |++|+.+.. +.+|+||+|+||++|+| |+| ++++||.|. +++|+
T Consensus 2 ~SddLiW~IIr~~~csF~vK~~~~~Fcrnp~Nltglcsrkycg------------LAN-------sKyatV~~~-~G~v~ 61 (233)
T PLN00040 2 QHDEVIWQVINHNHCSFKAKIDTGNFCRNKYNVTGLCNRSSCP------------LAN-------SRYATIREE-DGRFY 61 (233)
T ss_pred CccchhhhhhcCcceeEEEccCCCcccCCCCcccccccccccc------------ccc-------ceeeEEEEc-CCEEE
Confidence 799999999999999 889877554 66789999999999999 999 999999996 78899
Q ss_pred EEEeccCCCCCCcceeeeeeeccchhHHHHHHHHHhc
Q 040088 82 LATTKTKKQNKPIALLHKSVMKHEIHRMAKVIANRVG 118 (131)
Q Consensus 82 l~tkk~k~~~kPak~~~~~~~k~~~Rr~~k~I~~~v~ 118 (131)
|++|+.+.+++|+++..++++++++|++++.|.+.+.
T Consensus 62 L~~Kt~erah~Pak~w~kv~Lskn~rkalk~I~~~L~ 98 (233)
T PLN00040 62 LYMKTIERAHMPNKLWEKVKLSRNYEKALEQIDKHLA 98 (233)
T ss_pred EEEecccccCCcccceEEEecCCCHHHHHHHHHHHHh
Confidence 9999999999999999999999999999999999876
No 5
>KOG3064 consensus RNA-binding nuclear protein (MAK16) containing a distinct C4 Zn-finger [RNA processing and modification]
Probab=94.73 E-value=0.017 Score=49.36 Aligned_cols=94 Identities=13% Similarity=0.236 Sum_probs=73.1
Q ss_pred CCccceEEEEecCce-eEEeecCCCccCc--CccceeeeeeecccccccccceeceeecCcccccccceEEEEeCCCCeE
Q 040088 4 VGGQLIWEIVKKNNC-FLVKEFGRGSASA--HAVITCSVYKFGGRKIECSTFVFGRFCGNRGKKIKLKTVTIQPGKDQVV 80 (131)
Q Consensus 4 ~S~dL~W~iVrnnns-FLvK~~g~~s~s~--~NL~n~~s~KysG~~~~~~~~~~~~l~~~~~~~~~~KaV~V~~~~~~gV 80 (131)
||++.+|++|.++.| |-+|-.+ .+|=. .|||++-...-.- |+| .+--+|.. +++.+
T Consensus 2 q~DeviW~vin~~~CS~k~kte~-~~fCRNeyNvTGLCnR~SCP------------LAN-------SrYATVre-~~g~~ 60 (303)
T KOG3064|consen 2 QSDEVIWQVINKSFCSYKIKTET-QTFCRNEYNVTGLCNRSSCP------------LAN-------SRYATVRE-ENGVL 60 (303)
T ss_pred cchHHHHHHhchhhcceeeeccc-cchhccccccceeeccccCc------------Ccc-------ccceeEee-cCCEE
Confidence 799999999976665 4455432 35544 5999988877777 999 88888885 55666
Q ss_pred EEEEeccCCCCCCcceeeeeeeccchhHHHHHHHHHhc
Q 040088 81 VLATTKTKKQNKPIALLHKSVMKHEIHRMAKVIANRVG 118 (131)
Q Consensus 81 vl~tkk~k~~~kPak~~~~~~~k~~~Rr~~k~I~~~v~ 118 (131)
-|-.|..-.+.-|.++..++-++++.-+++..|-..+-
T Consensus 61 yLymKt~ERaH~P~klwErikLSkNyekALeQIde~Ll 98 (303)
T KOG3064|consen 61 YLYMKTIERAHMPRKLWERIKLSKNYEKALEQIDEQLL 98 (303)
T ss_pred EEEEechhhhcCcHHHHHHHhcchhHHHHHHHHHHHHh
Confidence 77777777889999999999999999898888876543
No 6
>COG5129 MAK16 Nuclear protein with HMG-like acidic region [General function prediction only]
Probab=91.68 E-value=0.093 Score=44.53 Aligned_cols=93 Identities=13% Similarity=0.231 Sum_probs=73.0
Q ss_pred CCccceEEEEecCce-eEEeecCCCccCc--CccceeeeeeecccccccccceeceeecCcccccccceEEEEeCCCCeE
Q 040088 4 VGGQLIWEIVKKNNC-FLVKEFGRGSASA--HAVITCSVYKFGGRKIECSTFVFGRFCGNRGKKIKLKTVTIQPGKDQVV 80 (131)
Q Consensus 4 ~S~dL~W~iVrnnns-FLvK~~g~~s~s~--~NL~n~~s~KysG~~~~~~~~~~~~l~~~~~~~~~~KaV~V~~~~~~gV 80 (131)
||+..+|+++-.|-| |-+|-.++ .|-+ .|++++-..--.- |+| .+-.+|.+ +++.+
T Consensus 1 msDE~~Wqv~g~~fCS~rik~e~q-nfCRNeyNVTGLC~RqSCP------------LAN-------SrYATVr~-dngkL 59 (303)
T COG5129 1 MSDESLWQVSGENFCSFRIKTEEQ-NFCRNEYNVTGLCDRQSCP------------LAN-------SRYATVRA-DNGKL 59 (303)
T ss_pred CchhHHHHHccccccceeeecchh-hhhhcccccceeeccccCc------------Ccc-------CcceEEEe-cCCEE
Confidence 689999998877766 44665433 3333 6999887766666 999 88888885 66788
Q ss_pred EEEEeccCCCCCCcceeeeeeeccchhHHHHHHHHHh
Q 040088 81 VLATTKTKKQNKPIALLHKSVMKHEIHRMAKVIANRV 117 (131)
Q Consensus 81 vl~tkk~k~~~kPak~~~~~~~k~~~Rr~~k~I~~~v 117 (131)
-|-+|.+-...-|+++..++.++++.-++++.|-..+
T Consensus 60 yLymKtpERaH~P~klwerIkLSkNY~kAL~QIde~L 96 (303)
T COG5129 60 YLYMKTPERAHVPRKLWERIKLSKNYEKALKQIDESL 96 (303)
T ss_pred EEEecChhhccCcHHHHHHHHhhhhHHHHHHHHHHHH
Confidence 8888988899999999999999999988888886543
No 7
>PF14990 DUF4516: Domain of unknown function (DUF4516)
Probab=31.34 E-value=11 Score=24.48 Aligned_cols=12 Identities=50% Similarity=0.736 Sum_probs=9.0
Q ss_pred hcCCCCChhhhh
Q 040088 117 VGDNYYQPDLKN 128 (131)
Q Consensus 117 v~~n~YRpDL~~ 128 (131)
+-.++|||||.-
T Consensus 27 vVH~~ykPdlti 38 (47)
T PF14990_consen 27 VVHNIYKPDLTI 38 (47)
T ss_pred HHHHHhCccCCC
Confidence 345789999974
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=14.87 E-value=99 Score=19.67 Aligned_cols=22 Identities=18% Similarity=0.289 Sum_probs=13.7
Q ss_pred HHHHHHHhcCCCCChhhhhhhC
Q 040088 110 AKVIANRVGDNYYQPDLKNAVE 131 (131)
Q Consensus 110 ~k~I~~~v~~n~YRpDL~~aA~ 131 (131)
...|+..+..+.|..|....|+
T Consensus 30 V~~ik~~I~~G~Y~vd~~~iA~ 51 (57)
T PF04316_consen 30 VAEIKAAIASGTYKVDAEKIAE 51 (57)
T ss_dssp HHHHHHHHHTT-----HHHHHH
T ss_pred HHHHHHHHHcCCCCCCHHHHHH
Confidence 5569999999999999988774
No 9
>COG0187 GyrB Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), B subunit [DNA replication, recombination, and repair]
Probab=14.79 E-value=4.9e+02 Score=25.03 Aligned_cols=38 Identities=32% Similarity=0.690 Sum_probs=25.4
Q ss_pred cceEEEEec-------------------CceeEEeecCCC-ccCcC----------cccee--------eeeeecc
Q 040088 7 QLIWEIVKK-------------------NNCFLVKEFGRG-SASAH----------AVITC--------SVYKFGG 44 (131)
Q Consensus 7 dL~W~iVrn-------------------nnsFLvK~~g~~-s~s~~----------NL~n~--------~s~KysG 44 (131)
+|+||||=| .|+--|.-+|+| +.+.| =++.+ .+||+||
T Consensus 39 Hlv~EVvDNsiDEalaG~~~~I~V~l~~d~sisV~DnGRGIPvdiH~~~~~~~vEvI~T~LHAGGKFd~~~YkvSG 114 (635)
T COG0187 39 HLVWEVVDNSIDEALAGYADRIDVTLHEDGSISVEDNGRGIPVDIHPKEKVSAVEVIFTVLHAGGKFDNDSYKVSG 114 (635)
T ss_pred eeEeEeeechHhHHhhCcCcEEEEEEcCCCeEEEEECCCCCccccCCCCCCCceEEEEEeeccCcccCCCccEeec
Confidence 789998864 466667778877 54433 23334 4899998
No 10
>PRK04330 hypothetical protein; Provisional
Probab=14.65 E-value=1.6e+02 Score=21.43 Aligned_cols=30 Identities=17% Similarity=0.214 Sum_probs=25.7
Q ss_pred eeeccchhHHHHHHHHHhcCCCCChhhhhh
Q 040088 100 SVMKHEIHRMAKVIANRVGDNYYQPDLKNA 129 (131)
Q Consensus 100 ~~~k~~~Rr~~k~I~~~v~~n~YRpDL~~a 129 (131)
+++..+.||++......+...++-|+++.|
T Consensus 25 ~sVPRNIRraa~ea~~~L~~e~~~~~vRaA 54 (88)
T PRK04330 25 TSVPRNIRRAATEAKEILLNEEESPGVRAA 54 (88)
T ss_pred CCCChHHHHHHHHHHHHHhCcCcchhHHHH
Confidence 455679999999999999888999999876
Done!