Query 025591
Match_columns 250
No_of_seqs 197 out of 360
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 07:24:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025591.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025591hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1646 40S ribosomal protein 100.0 1E-114 3E-119 760.7 15.1 235 1-240 1-236 (237)
2 PTZ00028 40S ribosomal protein 100.0 4E-105 8E-110 704.9 21.9 217 1-224 1-217 (218)
3 PF01092 Ribosomal_S6e: Riboso 100.0 6E-64 1.3E-68 413.4 9.8 127 1-129 1-127 (127)
4 PRK04290 30S ribosomal protein 100.0 3.6E-55 7.9E-60 356.0 11.8 112 1-118 4-115 (115)
5 COG2125 RPS6A Ribosomal protei 100.0 8.1E-49 1.7E-53 319.6 10.5 117 1-122 4-120 (120)
6 COG4671 Predicted glycosyl tra 60.3 4.8 0.0001 39.7 1.5 29 40-68 34-63 (400)
7 PF09671 Spore_GerQ: Spore coa 35.0 30 0.00065 27.4 2.1 16 3-18 51-66 (81)
8 PRK00247 putative inner membra 32.6 2E+02 0.0043 28.9 7.7 46 179-224 312-358 (429)
9 PF11208 DUF2992: Protein of u 30.5 1.6E+02 0.0034 25.0 5.8 51 180-230 61-112 (132)
10 PF15232 DUF4585: Domain of un 30.4 54 0.0012 25.6 2.8 37 4-40 10-46 (75)
11 PF01272 GreA_GreB: Transcript 22.4 69 0.0015 23.7 2.0 20 24-43 47-66 (77)
12 PRK05753 nucleoside diphosphat 21.4 1.8E+02 0.004 24.2 4.6 37 3-39 61-111 (137)
13 PTZ00121 MAEBL; Provisional 21.4 49 0.0011 38.4 1.5 61 6-70 670-731 (2084)
14 TIGR01952 nusA_arch NusA famil 21.4 1.6E+02 0.0034 25.1 4.2 52 98-161 23-81 (141)
15 TIGR02728 spore_gerQ spore coa 21.3 70 0.0015 25.4 1.9 16 3-18 49-64 (82)
16 PRK06569 F0F1 ATP synthase sub 20.4 5.7E+02 0.012 22.2 7.7 44 187-230 37-80 (155)
No 1
>KOG1646 consensus 40S ribosomal protein S6 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.4e-114 Score=760.72 Aligned_cols=235 Identities=73% Similarity=1.112 Sum_probs=230.0
Q ss_pred CeEEeecCCCCeeEEEEecChhhhcccccccccceecCcccCCcccCcEEEEccccCCCCCcccCCCCCCceEEEeeeCC
Q 025591 1 MKFNIANPTTGCQKKLEIDDDQKLRAFFDKRISQEVSGDALGEEFKGYVFKIMGGCDKQGFPMKQGVLTPGRVRLLLHRG 80 (250)
Q Consensus 1 MKlnIS~P~tG~qk~iEidde~kl~~f~gKrig~eV~gd~lG~e~kGY~~~ItGGnDkqGFPMkqgVl~~~RvrlLLskG 80 (250)
||||||||+||||++||||||+++++||+|+||+||+||+||+||+||+|+||||||+|||||+|||||++||+|||++|
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 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcccCCCCCCCcceeeeeeceeecCCcceEEEEEEeeccccCCCCCCCCCCCcCCCCchhhhHhhhCCCCccchhhhhh
Q 025591 81 TPCFRGYGRRDGERRRKSVRGCIVSPDLSVLNLVIVKKGEHDLPGLTDTEKPRMRGPKRASKIRKLFNLSKEDDVRKYVN 160 (250)
Q Consensus 81 ~~gyRp~~rr~GERkRKSVRGciV~~~is~LNlvIVkkGek~I~gLTd~~~p~~lgPKRaskIrKlFnLsk~ddv~kyV~ 160 (250)
|||||| ||+||||||||||||||+|+|+||||||++||+|||||||+++|++|||||||+||||||||+||||++||
T Consensus 81 ~scyRp--Rr~GeRkRKSVRGcIV~anlsvLnLvIvKkGekdipGLTdt~~P~rlGPkRaskIrKlfnLskEddvr~~v- 157 (237)
T KOG1646|consen 81 HSCYRP--RRTGERKRKSVRGCIVSANLSVLNLVIVKKGEKDIPGLTDTTVPRRLGPKRASKIRKLFNLSKEDDVRQYV- 157 (237)
T ss_pred cccccc--ccccccccccccceeecccceeeeeeEeccCcccCCCccccccccccCchhhHHHHHHhCCCccccceeeE-
Confidence 999999 99999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhcccccccCC-ccccccCCcccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHhhhhhh
Q 025591 161 TYRRTFTTKTG-KKVSKAPKIQRLVTPLTLQRKRARIAEKKQRIAKAKAEAAEYQKLLATRLKEQRERRSESLAKKRSRL 239 (250)
Q Consensus 161 ~vrr~l~~k~g-k~~~KaPKIQrLvTp~~lqrk~~~~a~kk~~~~k~keea~eY~klla~r~ke~k~~~~~~~~r~~~s~ 239 (250)
||+|++ ++| +|+||||||||||||.+||||++++|+|++++.+++|+||||++||++|++|+++++.+..+++++|+
T Consensus 158 -ir~~~~-~~~~k~~tkaPKIqrlvtp~~lqrk~~~~alkk~~~~k~re~aaey~kLLakr~kE~k~kr~e~~~rr~ss~ 235 (237)
T KOG1646|consen 158 -IRRPLT-KEGKKPKTKAPKIQRLVTPRRLQRKRQRIALKKKQIKKNREEAAEYAKLLAKRLKEAKEKRFEVKRRRASSL 235 (237)
T ss_pred -Eecccc-ccCCCccccCcchhhccchHHHHhhhhHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence 999999 566 99999999999999999999999999999999999999999999999999999999988777777775
Q ss_pred c
Q 025591 240 S 240 (250)
Q Consensus 240 ~ 240 (250)
+
T Consensus 236 ~ 236 (237)
T KOG1646|consen 236 R 236 (237)
T ss_pred c
Confidence 4
No 2
>PTZ00028 40S ribosomal protein S6e; Provisional
Probab=100.00 E-value=3.9e-105 Score=704.90 Aligned_cols=217 Identities=66% Similarity=1.023 Sum_probs=213.1
Q ss_pred CeEEeecCCCCeeEEEEecChhhhcccccccccceecCcccCCcccCcEEEEccccCCCCCcccCCCCCCceEEEeeeCC
Q 025591 1 MKFNIANPTTGCQKKLEIDDDQKLRAFFDKRISQEVSGDALGEEFKGYVFKIMGGCDKQGFPMKQGVLTPGRVRLLLHRG 80 (250)
Q Consensus 1 MKlnIS~P~tG~qk~iEidde~kl~~f~gKrig~eV~gd~lG~e~kGY~~~ItGGnDkqGFPMkqgVl~~~RvrlLLskG 80 (250)
||||||||+||+||+||||||++++.|||++||+||||++||+||+||+|+||||||+|||||+|||+|++||+|||++|
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 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcccCCCCCCCcceeeeeeceeecCCcceEEEEEEeeccccCCCCCCCCCCCcCCCCchhhhHhhhCCCCccchhhhhh
Q 025591 81 TPCFRGYGRRDGERRRKSVRGCIVSPDLSVLNLVIVKKGEHDLPGLTDTEKPRMRGPKRASKIRKLFNLSKEDDVRKYVN 160 (250)
Q Consensus 81 ~~gyRp~~rr~GERkRKSVRGciV~~~is~LNlvIVkkGek~I~gLTd~~~p~~lgPKRaskIrKlFnLsk~ddv~kyV~ 160 (250)
|+|||| +++||||||||||||||+||||||++||++||++||||||+++|++|||||||+|||||||||+|||++||
T Consensus 81 ~~gyrp--rr~GeRkRKsVRGciVs~dis~lNlvIvk~Ge~~i~gLtd~~~prrlgPkraskirklfnlsk~ddvrk~v- 157 (218)
T PTZ00028 81 MKCYRP--RRTGEMKRKSVRGCIVGHDLSVLNLVLVKKGPQEIPGLTDGERPRRLGPKRASKIRKLFNLSKSDDVRKFV- 157 (218)
T ss_pred CCCCCc--CCCCcceeeeeeeeeecCCceEEEEEEEecCCccChhhccCcCCccCCCcchhhhHHHhCCCccCChhhce-
Confidence 999999 99999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhcccccccCCccccccCCcccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025591 161 TYRRTFTTKTGKKVSKAPKIQRLVTPLTLQRKRARIAEKKQRIAKAKAEAAEYQKLLATRLKEQ 224 (250)
Q Consensus 161 ~vrr~l~~k~gk~~~KaPKIQrLvTp~~lqrk~~~~a~kk~~~~k~keea~eY~klla~r~ke~ 224 (250)
||+++ +||..+|||||||||||.+||||++++++|+++.++++++++||++||++|++|.
T Consensus 158 -irr~~---~gkk~~KapKIQRLiTp~~lqrKr~~~~~k~~r~~~~k~~~~ey~kll~~~~~e~ 217 (218)
T PTZ00028 158 -VRRKI---EGKNKTKAPKIQRLVTPQRLQRKRRYRKTLKKKVLQSREEAKEYQKLLEEYKNEK 217 (218)
T ss_pred -ecccc---CCCCCCcCCceeecCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 99999 5766699999999999999999999999999999999999999999999998774
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=6e-64 Score=413.36 Aligned_cols=127 Identities=69% Similarity=1.127 Sum_probs=102.2
Q ss_pred CeEEeecCCCCeeEEEEecChhhhcccccccccceecCcccCCcccCcEEEEccccCCCCCcccCCCCCCceEEEeeeCC
Q 025591 1 MKFNIANPTTGCQKKLEIDDDQKLRAFFDKRISQEVSGDALGEEFKGYVFKIMGGCDKQGFPMKQGVLTPGRVRLLLHRG 80 (250)
Q Consensus 1 MKlnIS~P~tG~qk~iEidde~kl~~f~gKrig~eV~gd~lG~e~kGY~~~ItGGnDkqGFPMkqgVl~~~RvrlLLskG 80 (250)
||||||||+||+||+|||||+.++++||||+||+||+|++||+||+||+|+||||||+|||||+|||++++||++||++|
T Consensus 1 mKl~isdP~tG~~~~iei~~~~~~~~f~gkrig~evdg~~lG~e~~Gy~~kItGGsD~~GfPMr~~v~~~~rvr~Ll~~G 80 (127)
T PF01092_consen 1 MKLNISDPKTGKQKQIEIDDERALRPFYGKRIGDEVDGDILGEELKGYKLKITGGSDKQGFPMRQGVLGPGRVRLLLSKG 80 (127)
T ss_dssp -EEEEEETTTTEEEEEE--SHHHHCCCTT-BTT-EEETCCGTTTSSS-EEEEEEEEECCC-BB-TT---SSEEEEEE-TT
T ss_pred CEEEEEcCCCCEEEEEEeCchHHhhHhhhcchheeEeeeecCccccccEEEEecccCCCCceeecCCCCcceEEEEEeCC
Confidence 99999999999999999999999989999999999999999999999999999999999999999999999999999999
Q ss_pred CCcccCCCCCCCcceeeeeeceeecCCcceEEEEEEeeccccCCCCCCC
Q 025591 81 TPCFRGYGRRDGERRRKSVRGCIVSPDLSVLNLVIVKKGEHDLPGLTDT 129 (250)
Q Consensus 81 ~~gyRp~~rr~GERkRKSVRGciV~~~is~LNlvIVkkGek~I~gLTd~ 129 (250)
++|||| +++||||||||||||||+||||||++||++||++||||||+
T Consensus 81 ~~gyrp--~r~GeRrRKsVRG~~is~di~qiN~~Iv~~G~k~i~glt~~ 127 (127)
T PF01092_consen 81 GPGYRP--RRKGERRRKSVRGNIISADISQINLVIVKKGEKPIPGLTDT 127 (127)
T ss_dssp BTTB----SSTT--EEEEEE-SC--TTEEEEEEEEEE--SS--HHHHT-
T ss_pred Cccccc--CcCCeEeeeeeeccEecCCeeeEEEEEEEecCccCccccCC
Confidence 999999 99999999999999999999999999999999999999996
No 4
>PRK04290 30S ribosomal protein S6e; Validated
Probab=100.00 E-value=3.6e-55 Score=356.00 Aligned_cols=112 Identities=42% Similarity=0.745 Sum_probs=108.4
Q ss_pred CeEEeecCCCCeeEEEEecChhhhcccccccccceecCcccCCcccCcEEEEccccCCCCCcccCCCCCCceEEEeeeCC
Q 025591 1 MKFNIANPTTGCQKKLEIDDDQKLRAFFDKRISQEVSGDALGEEFKGYVFKIMGGCDKQGFPMKQGVLTPGRVRLLLHRG 80 (250)
Q Consensus 1 MKlnIS~P~tG~qk~iEidde~kl~~f~gKrig~eV~gd~lG~e~kGY~~~ItGGnDkqGFPMkqgVl~~~RvrlLLskG 80 (250)
||||||||+||+||+|||||+.. ..|||++|||||||++||+ +||+|+||||||+|||||+|||++++|++|||++|
T Consensus 4 ~Kl~IsdP~tG~~~~~ei~~~~~-~~f~gkriG~evdg~~lG~--~Gy~l~ItGGsDk~GfPM~~~v~~~~r~rlLl~~g 80 (115)
T PRK04290 4 FKVVVSDPKTGKAYQIEIDGAEA-NRLIGKKIGDEIDGSIVGL--DGYKLKITGGSDKSGFPMRPDVPGPVRRRILLSGG 80 (115)
T ss_pred eEEEEEcCCCCeEEEEEeCcHHH-hhhhccccccEEccceeCC--CCeEEEEecccCCCCccccCCccCCceEEEEecCC
Confidence 89999999999999999999984 5599999999999999997 79999999999999999999999999999999999
Q ss_pred CCcccCCCCCCCcceeeeeeceeecCCcceEEEEEEee
Q 025591 81 TPCFRGYGRRDGERRRKSVRGCIVSPDLSVLNLVIVKK 118 (250)
Q Consensus 81 ~~gyRp~~rr~GERkRKSVRGciV~~~is~LNlvIVkk 118 (250)
+|||| +++||||||||||||||+||+|||++||++
T Consensus 81 -~gyrp--~r~GeRrRKsVRG~~vs~di~qiN~~iv~~ 115 (115)
T PRK04290 81 -PGFRP--KEKGERRRKTVRGNTISDDIVQINAKVVEY 115 (115)
T ss_pred -CCCCc--CCCCcEEEEEEEccEEcCCeeEEEEEEEcC
Confidence 89999 999999999999999999999999999974
No 5
>COG2125 RPS6A Ribosomal protein S6E (S10) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=8.1e-49 Score=319.60 Aligned_cols=117 Identities=50% Similarity=0.843 Sum_probs=112.5
Q ss_pred CeEEeecCCCCeeEEEEecChhhhcccccccccceecCcccCCcccCcEEEEccccCCCCCcccCCCCCCceEEEeeeCC
Q 025591 1 MKFNIANPTTGCQKKLEIDDDQKLRAFFDKRISQEVSGDALGEEFKGYVFKIMGGCDKQGFPMKQGVLTPGRVRLLLHRG 80 (250)
Q Consensus 1 MKlnIS~P~tG~qk~iEidde~kl~~f~gKrig~eV~gd~lG~e~kGY~~~ItGGnDkqGFPMkqgVl~~~RvrlLLskG 80 (250)
|||+||||.||.||++||+++. ++.|+|++||+||||.++|++|. |+|+||||||++||||++||++++|+++|||+
T Consensus 4 ~kvvisdp~~G~~~~~ei~~~~-a~~ligkkIGd~~dG~~vg~~~~-yk~kItGGsD~~GfPMr~dv~g~~r~riLls~- 80 (120)
T COG2125 4 FKVVISDPKTGRAYQFEIDEAR-ARRLIGKKIGDEVDGVIVGLEFE-YKLKITGGSDKDGFPMRPDVPGPRRVRILLSG- 80 (120)
T ss_pred cEEEEeccCcceeeeeeechhh-hhhhhhheeccccCCcEeccccc-EEEEEeCCcCCCCCcccCCCCCcceEEEEecc-
Confidence 7999999999999999999765 89999999999999999999865 99999999999999999999999999999997
Q ss_pred CCcccCCCCCCCcceeeeeeceeecCCcceEEEEEEeecccc
Q 025591 81 TPCFRGYGRRDGERRRKSVRGCIVSPDLSVLNLVIVKKGEHD 122 (250)
Q Consensus 81 ~~gyRp~~rr~GERkRKSVRGciV~~~is~LNlvIVkkGek~ 122 (250)
++|||| +++|||||||||||||++||+|||++||++|+++
T Consensus 81 ~~GyrP--~~~GeRrRKtVRG~~Is~dI~QiN~~Iv~~ge~~ 120 (120)
T COG2125 81 GPGYRP--RRKGERKRKTVRGNIISPDIVQINLVIVEYGEKP 120 (120)
T ss_pred CCCcCC--CCCCceeeeeecccccchhheeeEEEEEecCCCC
Confidence 689999 9999999999999999999999999999999874
No 6
>COG4671 Predicted glycosyl transferase [General function prediction only]
Probab=60.33 E-value=4.8 Score=39.73 Aligned_cols=29 Identities=41% Similarity=0.697 Sum_probs=22.7
Q ss_pred ccCCcccCc-EEEEccccCCCCCcccCCCC
Q 025591 40 ALGEEFKGY-VFKIMGGCDKQGFPMKQGVL 68 (250)
Q Consensus 40 ~lG~e~kGY-~~~ItGGnDkqGFPMkqgVl 68 (250)
+|.+++.|+ ++-||||..-+||||.+||-
T Consensus 34 aLv~d~~~~~Il~IsG~~~~~~F~~~~gVd 63 (400)
T COG4671 34 ALVEDYLGFDILIISGGPPAGGFPGPAGVD 63 (400)
T ss_pred HHhhcccCceEEEEeCCCccCCCCCcccCc
Confidence 344444454 78899999999999999985
No 7
>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=35.00 E-value=30 Score=27.37 Aligned_cols=16 Identities=31% Similarity=0.428 Sum_probs=14.0
Q ss_pred EEeecCCCCeeEEEEe
Q 025591 3 FNIANPTTGCQKKLEI 18 (250)
Q Consensus 3 lnIS~P~tG~qk~iEi 18 (250)
+.||||.||..+++-+
T Consensus 51 iiisDp~tg~ryLllm 66 (81)
T PF09671_consen 51 IIISDPKTGKRYLLLM 66 (81)
T ss_pred EEEeCCCCCcEEEEEE
Confidence 6899999999998764
No 8
>PRK00247 putative inner membrane protein translocase component YidC; Validated
Probab=32.59 E-value=2e+02 Score=28.93 Aligned_cols=46 Identities=22% Similarity=0.294 Sum_probs=27.8
Q ss_pred CcccCcchHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025591 179 KIQRLVTPLTLQRKRARIA-EKKQRIAKAKAEAAEYQKLLATRLKEQ 224 (250)
Q Consensus 179 KIQrLvTp~~lqrk~~~~a-~kk~~~~k~keea~eY~klla~r~ke~ 224 (250)
-.+-||+|..+..=+..++ +|+.+++..+++.++-..+-++|.+..
T Consensus 312 ~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~k~~~k~~~~~~~~~~ 358 (429)
T PRK00247 312 RLRMIITPWRAPELHAENAEIKKTRTAEKNEAKARKKEIAQKRRAAE 358 (429)
T ss_pred cccccCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4566999987766555544 455555555666665555555554443
No 9
>PF11208 DUF2992: Protein of unknown function (DUF2992); InterPro: IPR016787 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=30.45 E-value=1.6e+02 Score=24.99 Aligned_cols=51 Identities=22% Similarity=0.268 Sum_probs=26.6
Q ss_pred cccCcchHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHhHH
Q 025591 180 IQRLVTPLTLQRKRARIAEKK-QRIAKAKAEAAEYQKLLATRLKEQRERRSE 230 (250)
Q Consensus 180 IQrLvTp~~lqrk~~~~a~kk-~~~~k~keea~eY~klla~r~ke~k~~~~~ 230 (250)
...-+.|-+|||.-..-..+. -.|+....-..+|......|....++++.+
T Consensus 61 ~~~~~NPKR~qR~a~ke~~~~g~~TkAQ~ALk~q~E~~K~~rk~~~k~~re~ 112 (132)
T PF11208_consen 61 KEKKINPKRLQREAKKEMKKKGISTKAQQALKLQREQRKKERKKRSKEQREA 112 (132)
T ss_pred cccCCChhHHHHHHHHhhhccCCChHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455678888887544332221 124444444555555555555555555433
No 10
>PF15232 DUF4585: Domain of unknown function (DUF4585)
Probab=30.38 E-value=54 Score=25.64 Aligned_cols=37 Identities=19% Similarity=0.228 Sum_probs=31.1
Q ss_pred EeecCCCCeeEEEEecChhhhcccccccccceecCcc
Q 025591 4 NIANPTTGCQKKLEIDDDQKLRAFFDKRISQEVSGDA 40 (250)
Q Consensus 4 nIS~P~tG~qk~iEidde~kl~~f~gKrig~eV~gd~ 40 (250)
++-||.||.-+.+|+--.-+++.||+=.-|+=|+..+
T Consensus 10 vL~DP~SG~Yy~vd~P~Qp~~k~lfDPETGqYVeV~i 46 (75)
T PF15232_consen 10 VLQDPESGQYYVVDAPVQPKTKTLFDPETGQYVEVLI 46 (75)
T ss_pred EeecCCCCCEEEEecCCCcceeeeecCCCCcEEEEeC
Confidence 3459999999999998877899999998888777643
No 11
>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=22.39 E-value=69 Score=23.70 Aligned_cols=20 Identities=25% Similarity=0.401 Sum_probs=13.7
Q ss_pred hcccccccccceecCcccCC
Q 025591 24 LRAFFDKRISQEVSGDALGE 43 (250)
Q Consensus 24 l~~f~gKrig~eV~gd~lG~ 43 (250)
...++|++.||+|+-.+-+-
T Consensus 47 G~ALlG~~~Gd~v~~~~~~g 66 (77)
T PF01272_consen 47 GKALLGKKVGDEVEVELPGG 66 (77)
T ss_dssp HHHHTT-BTT-EEEEEETTB
T ss_pred HHHhcCCCCCCEEEEEeCCc
Confidence 45689999999998876653
No 12
>PRK05753 nucleoside diphosphate kinase regulator; Provisional
Probab=21.45 E-value=1.8e+02 Score=24.19 Aligned_cols=37 Identities=8% Similarity=0.111 Sum_probs=21.6
Q ss_pred EEeecCCCCeeEEEEecChhhh--------------cccccccccceecCc
Q 025591 3 FNIANPTTGCQKKLEIDDDQKL--------------RAFFDKRISQEVSGD 39 (250)
Q Consensus 3 lnIS~P~tG~qk~iEidde~kl--------------~~f~gKrig~eV~gd 39 (250)
+.+.|-.+|....+.|-+...+ ..++|++.||+|.-.
T Consensus 61 V~~~~~~~~~~~~~~iVg~~Ead~~~~~ISi~SPlG~ALlG~~~Gd~v~v~ 111 (137)
T PRK05753 61 VRFRDLSSGEERVRTLVYPADADDSEGQLSVLAPVGAALLGLSVGQSIDWP 111 (137)
T ss_pred EEEEECCCCCEEEEEEEChhHcCccCCcCcccCHHHHHHcCCCCCCEEEEE
Confidence 3444555666655554333222 347888888888754
No 13
>PTZ00121 MAEBL; Provisional
Probab=21.43 E-value=49 Score=38.37 Aligned_cols=61 Identities=23% Similarity=0.311 Sum_probs=33.8
Q ss_pred ecCCCCeeEEEE-ecChhhhcccccccccceecCcccCCcccCcEEEEccccCCCCCcccCCCCCC
Q 025591 6 ANPTTGCQKKLE-IDDDQKLRAFFDKRISQEVSGDALGEEFKGYVFKIMGGCDKQGFPMKQGVLTP 70 (250)
Q Consensus 6 S~P~tG~qk~iE-idde~kl~~f~gKrig~eV~gd~lG~e~kGY~~~ItGGnDkqGFPMkqgVl~~ 70 (250)
|+|.=|....++ +++.. -.-.|.-..-.||....|+-- -.+.+.|. -|+.||.|.+|.|++
T Consensus 670 SCPNYGK~i~v~~l~~~~-~d~~~n~~fLNEI~tG~Lnk~-~~~~vEip--~~kSG~AM~~G~l~~ 731 (2084)
T PTZ00121 670 SCPNYGKAIIVENLEGEE-EDKNFNLEFLNEIHTGYLGKI-FIKDVEIP--YDKSGIAMHHGFLAS 731 (2084)
T ss_pred CCCCCCceEEEecccccc-cchhhhHHHHHHHHhhhcccc-cccceeec--ccchhhHHhcCCccc
Confidence 556666666665 44332 112333344455666566642 23445543 578888888888765
No 14
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.
Probab=21.37 E-value=1.6e+02 Score=25.08 Aligned_cols=52 Identities=17% Similarity=0.400 Sum_probs=35.8
Q ss_pred eeeceeecCCcceEEEEEEeeccccCCCCCCCCCCCcCCC--CchhhhHhhhCC-----CCccchhhhhhh
Q 025591 98 SVRGCIVSPDLSVLNLVIVKKGEHDLPGLTDTEKPRMRGP--KRASKIRKLFNL-----SKEDDVRKYVNT 161 (250)
Q Consensus 98 SVRGciV~~~is~LNlvIVkkGek~I~gLTd~~~p~~lgP--KRaskIrKlFnL-----sk~ddv~kyV~~ 161 (250)
+++-|++|++- -=+.||+.| .+..+.|+ .|..+|+.|+|- .-.+|..+||.+
T Consensus 23 ~~~dc~~d~~~--riifvV~~g----------~vG~~IG~~G~rIk~i~el~gekIdVVeys~D~~~fI~N 81 (141)
T TIGR01952 23 TVVDCLIDDRN--RVVFVVKEG----------EMGAAIGKGGENVKRLEELIGKSIELIEYSENLEEFVAN 81 (141)
T ss_pred ceEEEEecCCc--EEEEEEcCC----------CccccCCCCchHHHHHHHhcCCeeEEEEcCCCHHHHHHH
Confidence 57889999986 334566766 35566776 677778777772 223888999844
No 15
>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=21.33 E-value=70 Score=25.38 Aligned_cols=16 Identities=25% Similarity=0.457 Sum_probs=13.8
Q ss_pred EEeecCCCCeeEEEEe
Q 025591 3 FNIANPTTGCQKKLEI 18 (250)
Q Consensus 3 lnIS~P~tG~qk~iEi 18 (250)
+.||||.||.-+++-+
T Consensus 49 iiisdp~tg~RyLl~m 64 (82)
T TIGR02728 49 IVISDPQSGMRYLLLM 64 (82)
T ss_pred EEEcCCCCCcEEEeeE
Confidence 6899999999998754
No 16
>PRK06569 F0F1 ATP synthase subunit B'; Validated
Probab=20.43 E-value=5.7e+02 Score=22.20 Aligned_cols=44 Identities=7% Similarity=0.160 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHH
Q 025591 187 LTLQRKRARIAEKKQRIAKAKAEAAEYQKLLATRLKEQRERRSE 230 (250)
Q Consensus 187 ~~lqrk~~~~a~kk~~~~k~keea~eY~klla~r~ke~k~~~~~ 230 (250)
.+|.-+...|+-.....+..++++++..+-..+.+.+++.+.++
T Consensus 37 ~iLe~R~~~I~~~L~~Ae~~k~eAe~l~a~ye~~L~~Ar~eA~~ 80 (155)
T PRK06569 37 EIFNNRQTNIQDNITQADTLTIEVEKLNKYYNEEIDKTNTEIDR 80 (155)
T ss_pred HHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45667777888777778888887766555555555555555444
Done!