Query psy17954
Match_columns 143
No_of_seqs 166 out of 333
Neff 4.2
Searched_HMMs 46136
Date Fri Aug 16 18:37:33 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17954.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17954hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1646|consensus 100.0 1.8E-71 3.9E-76 452.3 4.9 136 1-143 1-189 (237)
2 PTZ00028 40S ribosomal protein 100.0 8.1E-69 1.8E-73 437.8 8.3 133 1-143 1-186 (218)
3 PF01092 Ribosomal_S6e: Riboso 100.0 1.5E-35 3.3E-40 225.8 5.5 89 1-90 1-99 (127)
4 PRK04290 30S ribosomal protein 100.0 5.7E-33 1.2E-37 208.8 5.8 88 1-92 4-100 (115)
5 COG2125 RPS6A Ribosomal protei 99.9 1.2E-26 2.7E-31 175.3 5.9 86 1-89 4-98 (120)
6 COG4671 Predicted glycosyl tra 50.1 8.8 0.00019 34.8 1.4 27 40-66 34-61 (400)
7 PF01272 GreA_GreB: Transcript 46.3 14 0.00031 25.0 1.6 28 16-44 40-67 (77)
8 PF09671 Spore_GerQ: Spore coa 42.7 21 0.00047 25.8 2.1 16 3-18 51-66 (81)
9 PF15232 DUF4585: Domain of un 36.1 44 0.00095 23.9 2.9 35 5-39 11-45 (75)
10 PF04360 Serglycin: Serglycin 29.7 48 0.001 26.5 2.4 45 54-98 19-91 (150)
11 TIGR02728 spore_gerQ spore coa 28.2 48 0.001 24.1 2.0 16 3-18 49-64 (82)
12 COG0782 Uncharacterized conser 28.1 42 0.00091 26.0 1.8 28 16-44 113-140 (151)
13 cd04459 Rho_CSD Rho_CSD: Rho p 25.0 1E+02 0.0022 21.2 3.1 46 49-104 4-51 (68)
14 PF07497 Rho_RNA_bind: Rho ter 24.1 46 0.00099 23.6 1.3 43 58-109 13-57 (78)
No 1
>KOG1646|consensus
Probab=100.00 E-value=1.8e-71 Score=452.26 Aligned_cols=136 Identities=79% Similarity=1.236 Sum_probs=133.9
Q ss_pred CeEEeecCCCCeeEEEEecCcccccccccccccceecCCccCCcccccEEEEcCccCCCCcccccC--------------
Q psy17954 1 MKLNISYPATGCQKLVEIADEHKLRVFYDKRMGMEVPADSIGDEWKGYIVRISGGNDKQGFPMKQG-------------- 66 (143)
Q Consensus 1 MKlnIS~P~tG~qk~ievdde~~l~~f~gKrig~ev~g~~lG~e~kGY~~~ItGGnDkqGFPMkqG-------------- 66 (143)
||||||||+||||++|||||+++|+.||+|+||+||+||+||+||+||+|+||||||+|||||+||
T Consensus 1 mkln~s~p~~g~qk~~Eidde~klR~fydKrm~qev~~d~lGeE~kGyv~~I~GGndkQGFPMkqGvLt~~RvrlLL~kg 80 (237)
T KOG1646|consen 1 MKLNISYPATGCQKLFEIDDERKLRTFYDKRMGQEVAGDALGEEFKGYVFRITGGNDKQGFPMKQGVLTPGRVRLLLSKG 80 (237)
T ss_pred CcccccccccccceeeeechHHHHHHHHHHhhhhhhccchhchhhceEEEEEcCCccccCCcccccccccchhhhhhhcC
Confidence 999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ---------------------------------------CCCCCcccCCCCcCCCcchhhhhcccCCCcCCCceeeEEee
Q psy17954 67 ---------------------------------------EIPGLTDTTIPRRLGPKRASKIRKLFNLSKEDDVRQYVIKR 107 (143)
Q Consensus 67 ---------------------------------------dIpGltd~~vPr~lgpKRaskIRKLf~lsk~ddv~~yvvrr 107 (143)
|||||||+++|++|||||||+||||||||+||||++||||+
T Consensus 81 ~scyRpRr~GeRkRKSVRGcIV~anlsvLnLvIvKkGekdipGLTdt~~P~rlGPkRaskIrKlfnLskEddvr~~vir~ 160 (237)
T KOG1646|consen 81 HSCYRPRRTGERKRKSVRGCIVSANLSVLNLVIVKKGEKDIPGLTDTTVPRRLGPKRASKIRKLFNLSKEDDVRQYVIRR 160 (237)
T ss_pred ccccccccccccccccccceeecccceeeeeeEeccCcccCCCccccccccccCchhhHHHHHHhCCCccccceeeEEec
Confidence 99999999999999999999999999999999999999999
Q ss_pred cCCCCCCCCCCccccccccCCCcccccCcccccccC
Q psy17954 108 TLPPKPAKEGKKKVRKLYKAPKIQRLITPVTLQVSG 143 (143)
Q Consensus 108 ~~~~~~~k~gkk~~~~~~kapKIqrlvtp~~lq~k~ 143 (143)
++ +++|+| |+||||||||||||.+||||+
T Consensus 161 ~~----~~~~~k---~~tkaPKIqrlvtp~~lqrk~ 189 (237)
T KOG1646|consen 161 PL----TKEGKK---PKTKAPKIQRLVTPRRLQRKR 189 (237)
T ss_pred cc----cccCCC---ccccCcchhhccchHHHHhhh
Confidence 99 589999 999999999999999999985
No 2
>PTZ00028 40S ribosomal protein S6e; Provisional
Probab=100.00 E-value=8.1e-69 Score=437.77 Aligned_cols=133 Identities=71% Similarity=1.101 Sum_probs=129.5
Q ss_pred CeEEeecCCCCeeEEEEecCcccccccccccccceecCCccCCcccccEEEEcCccCCCCcccccC--------------
Q psy17954 1 MKLNISYPATGCQKLVEIADEHKLRVFYDKRMGMEVPADSIGDEWKGYIVRISGGNDKQGFPMKQG-------------- 66 (143)
Q Consensus 1 MKlnIS~P~tG~qk~ievdde~~l~~f~gKrig~ev~g~~lG~e~kGY~~~ItGGnDkqGFPMkqG-------------- 66 (143)
||||||||+||+||+||||||++|+.|||++||+||+|++||+||+||+|+||||||+|||||+||
T Consensus 1 MKlnIsdP~tG~qk~iEidde~~l~~f~gkrIG~EVdg~~lG~e~kGY~lkITGGsDkqGfPMkqgV~~~~RvrlLL~kG 80 (218)
T PTZ00028 1 MKLNIANPFTGLQKCIEIDDEKKLLPFFEKRIGAEVPGDSLGDEFKGYIFKISGGNDKQGFPMMQGVLTNNRVRLLFRKG 80 (218)
T ss_pred CeEEEecCCCCeeEEEEecCHHHhhhhhcccccceecccccCcccCCcEEEEecccCCCCcccCCCccCCceEEEEecCC
Confidence 999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ---------------------------------------CCCCCcccCCCCcCCCcchhhhhcccCCCcCCCceeeEEee
Q psy17954 67 ---------------------------------------EIPGLTDTTIPRRLGPKRASKIRKLFNLSKEDDVRQYVIKR 107 (143)
Q Consensus 67 ---------------------------------------dIpGltd~~vPr~lgpKRaskIRKLf~lsk~ddv~~yvvrr 107 (143)
+||||||+++|++|||||||+|||||||||+|||++|||||
T Consensus 81 ~~gyrprr~GeRkRKsVRGciVs~dis~lNlvIvk~Ge~~i~gLtd~~~prrlgPkraskirklfnlsk~ddvrk~virr 160 (218)
T PTZ00028 81 MKCYRPRRTGEMKRKSVRGCIVGHDLSVLNLVLVKKGPQEIPGLTDGERPRRLGPKRASKIRKLFNLSKSDDVRKFVVRR 160 (218)
T ss_pred CCCCCcCCCCcceeeeeeeeeecCCceEEEEEEEecCCccChhhccCcCCccCCCcchhhhHHHhCCCccCChhhceecc
Confidence 89999999999999999999999999999999999999999
Q ss_pred cCCCCCCCCCCccccccccCCCcccccCcccccccC
Q psy17954 108 TLPPKPAKEGKKKVRKLYKAPKIQRLITPVTLQVSG 143 (143)
Q Consensus 108 ~~~~~~~k~gkk~~~~~~kapKIqrlvtp~~lq~k~ 143 (143)
++ +||| ++|||||||||||.+||||+
T Consensus 161 ~~------~gkk----~~KapKIQRLiTp~~lqrKr 186 (218)
T PTZ00028 161 KI------EGKN----KTKAPKIQRLVTPQRLQRKR 186 (218)
T ss_pred cc------CCCC----CCcCCceeecCCHHHHHHHH
Confidence 99 5766 49999999999999999984
No 3
>PF01092 Ribosomal_S6e: Ribosomal protein S6e; InterPro: IPR001377 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 and archaeal ribosomal proteins have been grouped on the basis of sequence similarities. Ribosomal protein S6 is the major substrate of protein kinases in eukaryotic ribosomes [] and may play an important role in controlling cell growth and proliferation through the selective translation of particular classes of mRNA.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2XZM_Y 2XZN_Y 3U5C_G 3U5G_G 3J16_C.
Probab=100.00 E-value=1.5e-35 Score=225.81 Aligned_cols=89 Identities=54% Similarity=0.862 Sum_probs=66.2
Q ss_pred CeEEeecCCCCeeEEEEecCcccccccccccccceecCCccCCcccccEEEEcCccCCCCcccccCCCCCCccc------
Q psy17954 1 MKLNISYPATGCQKLVEIADEHKLRVFYDKRMGMEVPADSIGDEWKGYIVRISGGNDKQGFPMKQGEIPGLTDT------ 74 (143)
Q Consensus 1 MKlnIS~P~tG~qk~ievdde~~l~~f~gKrig~ev~g~~lG~e~kGY~~~ItGGnDkqGFPMkqGdIpGltd~------ 74 (143)
||||||||+||+||+|||+|++++++||||+||+||+|++||+||+||+|+||||||+|||||+| +|+|....
T Consensus 1 mKl~isdP~tG~~~~iei~~~~~~~~f~gkrig~evdg~~lG~e~~Gy~~kItGGsD~~GfPMr~-~v~~~~rvr~Ll~~ 79 (127)
T PF01092_consen 1 MKLNISDPKTGKQKQIEIDDERALRPFYGKRIGDEVDGDILGEELKGYKLKITGGSDKQGFPMRQ-GVLGPGRVRLLLSK 79 (127)
T ss_dssp -EEEEEETTTTEEEEEE--SHHHHCCCTT-BTT-EEETCCGTTTSSS-EEEEEEEEECCC-BB-T-T---SSEEEEEE-T
T ss_pred CEEEEEcCCCCEEEEEEeCchHHhhHhhhcchheeEeeeecCccccccEEEEecccCCCCceeec-CCCCcceEEEEEeC
Confidence 99999999999999999999999999999999999999999999999999999999999999999 88885331
Q ss_pred ----CCCCcCCCcchhhhhc
Q psy17954 75 ----TIPRRLGPKRASKIRK 90 (143)
Q Consensus 75 ----~vPr~lgpKRaskIRK 90 (143)
..|++.|.+|...+|-
T Consensus 80 G~~gyrp~r~GeRrRKsVRG 99 (127)
T PF01092_consen 80 GGPGYRPRRKGERRRKSVRG 99 (127)
T ss_dssp TBTTB--SSTT--EEEEEE-
T ss_pred CCcccccCcCCeEeeeeeec
Confidence 3477777777666665
No 4
>PRK04290 30S ribosomal protein S6e; Validated
Probab=99.97 E-value=5.7e-33 Score=208.78 Aligned_cols=88 Identities=33% Similarity=0.613 Sum_probs=77.5
Q ss_pred CeEEeecCCCCeeEEEEecCcccccccccccccceecCCccCCcccccEEEEcCccCCCCcccccCCCCCCccc------
Q psy17954 1 MKLNISYPATGCQKLVEIADEHKLRVFYDKRMGMEVPADSIGDEWKGYIVRISGGNDKQGFPMKQGEIPGLTDT------ 74 (143)
Q Consensus 1 MKlnIS~P~tG~qk~ievdde~~l~~f~gKrig~ev~g~~lG~e~kGY~~~ItGGnDkqGFPMkqGdIpGltd~------ 74 (143)
||||||||+||+||+|||+|+.+++ |||++||+||+|++||+ +||+|+||||||+|||||+| +|+|....
T Consensus 4 ~Kl~IsdP~tG~~~~~ei~~~~~~~-f~gkriG~evdg~~lG~--~Gy~l~ItGGsDk~GfPM~~-~v~~~~r~rlLl~~ 79 (115)
T PRK04290 4 FKVVVSDPKTGKAYQIEIDGAEANR-LIGKKIGDEIDGSIVGL--DGYKLKITGGSDKSGFPMRP-DVPGPVRRRILLSG 79 (115)
T ss_pred eEEEEEcCCCCeEEEEEeCcHHHhh-hhccccccEEccceeCC--CCeEEEEecccCCCCccccC-CccCCceEEEEecC
Confidence 8999999999999999999999865 99999999999999999 59999999999999999999 88885443
Q ss_pred ---CCCCcCCCcchhhhhccc
Q psy17954 75 ---TIPRRLGPKRASKIRKLF 92 (143)
Q Consensus 75 ---~vPr~lgpKRaskIRKLf 92 (143)
..|++.|.+|...+|=..
T Consensus 80 g~gyrp~r~GeRrRKsVRG~~ 100 (115)
T PRK04290 80 GPGFRPKEKGERRRKTVRGNT 100 (115)
T ss_pred CCCCCcCCCCcEEEEEEEccE
Confidence 337778888776666544
No 5
>COG2125 RPS6A Ribosomal protein S6E (S10) [Translation, ribosomal structure and biogenesis]
Probab=99.93 E-value=1.2e-26 Score=175.30 Aligned_cols=86 Identities=37% Similarity=0.674 Sum_probs=73.7
Q ss_pred CeEEeecCCCCeeEEEEecCcccccccccccccceecCCccCCcccccEEEEcCccCCCCcccccCCCCCCccc------
Q psy17954 1 MKLNISYPATGCQKLVEIADEHKLRVFYDKRMGMEVPADSIGDEWKGYIVRISGGNDKQGFPMKQGEIPGLTDT------ 74 (143)
Q Consensus 1 MKlnIS~P~tG~qk~ievdde~~l~~f~gKrig~ev~g~~lG~e~kGY~~~ItGGnDkqGFPMkqGdIpGltd~------ 74 (143)
||++||||++|.|+++||+++.+ +.|+|++||+||||.++|++|. |+|+||||||++||||++ |+||....
T Consensus 4 ~kvvisdp~~G~~~~~ei~~~~a-~~ligkkIGd~~dG~~vg~~~~-yk~kItGGsD~~GfPMr~-dv~g~~r~riLls~ 80 (120)
T COG2125 4 FKVVISDPKTGRAYQFEIDEARA-RRLIGKKIGDEVDGVIVGLEFE-YKLKITGGSDKDGFPMRP-DVPGPRRVRILLSG 80 (120)
T ss_pred cEEEEeccCcceeeeeeechhhh-hhhhhheeccccCCcEeccccc-EEEEEeCCcCCCCCcccC-CCCCcceEEEEecc
Confidence 79999999999999999997776 8899999999999999999965 999999999999999999 99996443
Q ss_pred ---CCCCcCCCcchhhhh
Q psy17954 75 ---TIPRRLGPKRASKIR 89 (143)
Q Consensus 75 ---~vPr~lgpKRaskIR 89 (143)
..|++.|.+|...+|
T Consensus 81 ~~GyrP~~~GeRrRKtVR 98 (120)
T COG2125 81 GPGYRPRRKGERKRKTVR 98 (120)
T ss_pred CCCcCCCCCCceeeeeec
Confidence 335666665544444
No 6
>COG4671 Predicted glycosyl transferase [General function prediction only]
Probab=50.07 E-value=8.8 Score=34.83 Aligned_cols=27 Identities=37% Similarity=0.778 Sum_probs=20.9
Q ss_pred ccCCccccc-EEEEcCccCCCCcccccC
Q psy17954 40 SIGDEWKGY-IVRISGGNDKQGFPMKQG 66 (143)
Q Consensus 40 ~lG~e~kGY-~~~ItGGnDkqGFPMkqG 66 (143)
+|.+++-|+ ++-||||..-+||||.+|
T Consensus 34 aLv~d~~~~~Il~IsG~~~~~~F~~~~g 61 (400)
T COG4671 34 ALVEDYLGFDILIISGGPPAGGFPGPAG 61 (400)
T ss_pred HHhhcccCceEEEEeCCCccCCCCCccc
Confidence 344444444 788999999999999988
No 7
>PF01272 GreA_GreB: Transcription elongation factor, GreA/GreB, C-term; InterPro: IPR001437 Bacterial proteins greA and greB are necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites. Arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked DNA/RNA/ polymerase ternary complexes. Cleavage of the nascent transcript by cleavage factors, such as greA or greB, allows the resumption of elongation from the new 3' terminus [, ]. Escherichia coli GreA and GreB are sequence homologues and have homologues in every known bacterial genome []. GreA induces cleavage two or three nucleotides behind the terminus and can only prevent the formation of arrested complexes while greB releases longer sequences up to eighteen nucleotides in length and can rescue preexisting arrested complexes. These functional differences correlate with a distinctive structural feature, the distribution of positively charged residues on one face of the N-terminal coiled coil. Remarkably, despite close functional similarity, the prokaryotic Gre factors have no sequence or structural similarity with eukaryotic TFIIS. ; GO: 0003677 DNA binding, 0032784 regulation of transcription elongation, DNA-dependent; PDB: 2P4V_E 2ETN_B 3BMB_B 2PN0_D 1GRJ_A 2EUL_C 3AOH_Y 3AOI_X 2F23_A.
Probab=46.25 E-value=14 Score=24.99 Aligned_cols=28 Identities=25% Similarity=0.417 Sum_probs=16.8
Q ss_pred EEecCcccccccccccccceecCCccCCc
Q psy17954 16 VEIADEHKLRVFYDKRMGMEVPADSIGDE 44 (143)
Q Consensus 16 ievdde~~l~~f~gKrig~ev~g~~lG~e 44 (143)
|-++.+-. .+++|++.|++|...+-+-+
T Consensus 40 IS~~SPLG-~ALlG~~~Gd~v~~~~~~g~ 67 (77)
T PF01272_consen 40 ISIDSPLG-KALLGKKVGDEVEVELPGGE 67 (77)
T ss_dssp EETTSHHH-HHHTT-BTT-EEEEEETTBE
T ss_pred EEecCHHH-HHhcCCCCCCEEEEEeCCce
Confidence 44444433 46899999999987765544
No 8
>PF09671 Spore_GerQ: Spore coat protein (Spore_GerQ); InterPro: IPR014099 Members of this protein family are the spore coat protein GerQ of endospore-forming Firmicutes (low GC Gram-positive bacteria). This protein is cross-linked by a spore coat-associated transglutaminase.
Probab=42.69 E-value=21 Score=25.80 Aligned_cols=16 Identities=38% Similarity=0.455 Sum_probs=13.9
Q ss_pred EEeecCCCCeeEEEEe
Q psy17954 3 LNISYPATGCQKLVEI 18 (143)
Q Consensus 3 lnIS~P~tG~qk~iev 18 (143)
+.||||+||..+++-+
T Consensus 51 iiisDp~tg~ryLllm 66 (81)
T PF09671_consen 51 IIISDPKTGKRYLLLM 66 (81)
T ss_pred EEEeCCCCCcEEEEEE
Confidence 6799999999998754
No 9
>PF15232 DUF4585: Domain of unknown function (DUF4585)
Probab=36.05 E-value=44 Score=23.89 Aligned_cols=35 Identities=20% Similarity=0.309 Sum_probs=30.0
Q ss_pred eecCCCCeeEEEEecCcccccccccccccceecCC
Q psy17954 5 ISYPATGCQKLVEIADEHKLRVFYDKRMGMEVPAD 39 (143)
Q Consensus 5 IS~P~tG~qk~ievdde~~l~~f~gKrig~ev~g~ 39 (143)
+-||.||.-+.+|+--.-+++.||+=.-|+-|+..
T Consensus 11 L~DP~SG~Yy~vd~P~Qp~~k~lfDPETGqYVeV~ 45 (75)
T PF15232_consen 11 LQDPESGQYYVVDAPVQPKTKTLFDPETGQYVEVL 45 (75)
T ss_pred eecCCCCCEEEEecCCCcceeeeecCCCCcEEEEe
Confidence 45999999999999888889999998888877653
No 10
>PF04360 Serglycin: Serglycin ; InterPro: IPR007455 Serglycin is the most prevalent proteoglycan produced in haemopoietic cells. Serglycin is a proteinase resistant secretory granule proteoglycan [].
Probab=29.71 E-value=48 Score=26.50 Aligned_cols=45 Identities=24% Similarity=0.527 Sum_probs=27.1
Q ss_pred CccCCCCcccccC------------------------CC-CCCcccCCCCcCC---CcchhhhhcccCCCcCC
Q psy17954 54 GGNDKQGFPMKQG------------------------EI-PGLTDTTIPRRLG---PKRASKIRKLFNLSKED 98 (143)
Q Consensus 54 GGnDkqGFPMkqG------------------------dI-pGltd~~vPr~lg---pKRaskIRKLf~lsk~d 98 (143)
-++.-||+||+.+ |+ ||-.+...|.+-- -.|....-..|-||.++
T Consensus 19 l~ssvqG~P~rrArYqWVrC~PDsnsANCieEKGP~FdL~pGesnrI~pp~tdp~~~~~~q~l~d~fPlSed~ 91 (150)
T PF04360_consen 19 LDSSVQGAPARRARYQWVRCNPDSNSANCIEEKGPLFDLLPGESNRILPPRTDPFPMTRSQNLNDIFPLSEDY 91 (150)
T ss_pred hccccccCcchhcceeEEecCCCCCCCccccccCCceecCCCccccCCCCcCCccchhcccchhhcCcccccc
Confidence 3555689999866 44 7766665554333 23444555667776644
No 11
>TIGR02728 spore_gerQ spore coat protein GerQ. Members of this protein family are the spore coat protein GerQ of endospore-forming Firmicutes (low GC Gram-positive bacteria). This protein is cross-linked by a spore coat-associated transglutaminase.
Probab=28.24 E-value=48 Score=24.07 Aligned_cols=16 Identities=31% Similarity=0.490 Sum_probs=13.7
Q ss_pred EEeecCCCCeeEEEEe
Q psy17954 3 LNISYPATGCQKLVEI 18 (143)
Q Consensus 3 lnIS~P~tG~qk~iev 18 (143)
+.||||.||..+++-+
T Consensus 49 iiisdp~tg~RyLl~m 64 (82)
T TIGR02728 49 IVISDPQSGMRYLLLM 64 (82)
T ss_pred EEEcCCCCCcEEEeeE
Confidence 6799999999998754
No 12
>COG0782 Uncharacterized conserved protein, YhbC family [Function unknown]
Probab=28.13 E-value=42 Score=26.05 Aligned_cols=28 Identities=21% Similarity=0.423 Sum_probs=18.9
Q ss_pred EEecCcccccccccccccceecCCccCCc
Q psy17954 16 VEIADEHKLRVFYDKRMGMEVPADSIGDE 44 (143)
Q Consensus 16 ievdde~~l~~f~gKrig~ev~g~~lG~e 44 (143)
|.++.+.. +.|+|++.||+|.-..-|-+
T Consensus 113 IS~~SPig-~aLlGk~vGd~v~v~~p~g~ 140 (151)
T COG0782 113 ISVDSPLG-RALLGKKVGDTVEVNTPGGE 140 (151)
T ss_pred eeccCHHH-HHHhCCCCCCEEEEecCCce
Confidence 44444444 67999999999987655443
No 13
>cd04459 Rho_CSD Rho_CSD: Rho protein cold-shock domain (CSD). Rho protein is a transcription termination factor in most bacteria. In bacteria, there are two distinct mechanisms for mRNA transcription termination. In intrinsic termination, RNA polymerase and nascent mRNA are released from DNA template by an mRNA stem loop structure, which resembles the transcription termination mechanism used by eukaryotic pol III. The second mechanism is mediated by Rho factor. Rho factor terminates transcription by using energy from ATP hydrolysis to forcibly dissociate the transcripts from RNA polymerase. Rho protein contains an N-terminal S1-like domain, which binds single-stranded RNA. Rho has a C-terminal ATPase domain which hydrolyzes ATP to provide energy to strip RNA polymerase and mRNA from the DNA template. Rho functions as a homohexamer.
Probab=24.98 E-value=1e+02 Score=21.16 Aligned_cols=46 Identities=33% Similarity=0.522 Sum_probs=30.3
Q ss_pred EEEEcCccCCCCcccccC--CCCCCcccCCCCcCCCcchhhhhcccCCCcCCCceeeE
Q psy17954 49 IVRISGGNDKQGFPMKQG--EIPGLTDTTIPRRLGPKRASKIRKLFNLSKEDDVRQYV 104 (143)
Q Consensus 49 ~~~ItGGnDkqGFPMkqG--dIpGltd~~vPr~lgpKRaskIRKLf~lsk~ddv~~yv 104 (143)
+|.|+.. .-||--..+ =.|+..|..|| ++-||+ |+|-..|-|.-.|
T Consensus 4 iLdi~~~--g~GFLR~~~~~y~~~~~DvyVs-------~~~Irr-~~LR~GD~V~G~v 51 (68)
T cd04459 4 VLEILPD--GFGFLRSSGYNYLPGPDDIYVS-------PSQIRR-FNLRTGDTVVGQI 51 (68)
T ss_pred EEEEcCC--CceEEecCCcCCCCCCCCEEEC-------HHHHHH-hCCCCCCEEEEEE
Confidence 3444432 355544332 26889999998 456776 8999998776655
No 14
>PF07497 Rho_RNA_bind: Rho termination factor, RNA-binding domain; InterPro: IPR011113 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers [].; GO: 0003723 RNA binding, 0006353 transcription termination, DNA-dependent; PDB: 1A8V_B 1PVO_A 1PV4_D 3ICE_A 1XPU_C 1XPO_D 1XPR_F 2A8V_B 2HT1_B 1A63_A ....
Probab=24.10 E-value=46 Score=23.61 Aligned_cols=43 Identities=28% Similarity=0.380 Sum_probs=23.9
Q ss_pred CCCccccc--CCCCCCcccCCCCcCCCcchhhhhcccCCCcCCCceeeEEeecC
Q psy17954 58 KQGFPMKQ--GEIPGLTDTTIPRRLGPKRASKIRKLFNLSKEDDVRQYVIKRTL 109 (143)
Q Consensus 58 kqGFPMkq--GdIpGltd~~vPr~lgpKRaskIRKLf~lsk~ddv~~yvvrr~~ 109 (143)
.-||--.. |=.||..|..||. +-||+ |+|-..|-|.-.| |.|-
T Consensus 13 GyGFLR~~~~~y~~~~~DvYVs~-------~qIrr-f~LR~GD~V~G~v-r~p~ 57 (78)
T PF07497_consen 13 GYGFLRSPDNNYLPSPDDVYVSP-------SQIRR-FGLRTGDLVEGQV-RPPR 57 (78)
T ss_dssp S-EEEE-GGGTTS-STTSEEE-C-------CCCCC-TT--TTEEEEEEE-E--S
T ss_pred CcEEeECCCcCCCCCCCCEEECH-------HHHHH-cCCCCCCEEEEEE-eCCC
Confidence 34565444 4578899999984 45655 8998888776666 5443
Done!