Query gi|254780715|ref|YP_003065128.1| 50S ribosomal protein L19 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 141 No_of_seqs 113 out of 921 Neff 4.8 Searched_HMMs 39220 Date Tue May 31 14:55:08 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780715.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 PRK05338 rplS 50S ribosomal pr 100.0 0 0 313.0 11.5 112 1-117 1-112 (112) 2 CHL00084 rpl19 ribosomal prote 100.0 1.4E-45 0 308.7 10.9 112 2-118 6-117 (117) 3 pfam01245 Ribosomal_L19 Riboso 100.0 7E-45 0 304.0 11.6 113 1-118 1-113 (113) 4 COG0335 RplS Ribosomal protein 100.0 1E-43 0 296.4 8.8 112 1-117 1-114 (115) 5 KOG1698 consensus 100.0 5E-33 1.3E-37 229.0 10.2 124 2-126 75-198 (201) 6 TIGR01024 rplS_bact ribosomal 99.9 2.4E-26 6E-31 186.9 7.8 113 1-117 1-115 (116) 7 PRK01191 rpl24p 50S ribosomal 79.1 5.7 0.00014 20.6 8.4 76 16-101 40-117 (119) 8 pfam03888 MucB_RseB MucB/RseB 75.6 6.2 0.00016 20.3 4.7 52 41-95 36-87 (314) 9 PRK09455 rseB periplasmic nega 69.3 9.9 0.00025 19.0 4.7 51 42-95 21-71 (302) 10 pfam02211 NHase_beta Nitrile h 57.8 12 0.00031 18.5 3.2 39 19-58 128-170 (220) 11 pfam02765 Telo_bind Telomeric 54.2 19 0.00047 17.3 3.8 49 19-76 64-113 (141) 12 cd04497 hPOT1_OB1_like hPOT1_O 51.8 20 0.00051 17.1 4.9 50 18-75 63-112 (138) 13 cd05791 S1_CSL4 S1_CSL4: CSL4, 49.5 18 0.00045 17.5 2.9 34 25-63 5-38 (92) 14 COG1566 EmrA Multidrug resista 49.2 22 0.00057 16.8 5.3 62 15-80 250-320 (352) 15 COG2139 RPL21A Ribosomal prote 46.6 24 0.00062 16.6 3.5 38 21-60 30-72 (98) 16 pfam02014 Reeler Reeler domain 45.8 25 0.00064 16.5 4.5 32 23-59 29-60 (127) 17 TIGR02579 cas_csx3 CRISPR-asso 44.8 9.4 0.00024 19.2 0.9 15 18-32 76-90 (90) 18 TIGR00998 8a0101 efflux pump m 44.6 26 0.00067 16.4 3.4 40 14-57 285-324 (379) 19 pfam10447 EXOSC1 Exosome compo 40.4 20 0.0005 17.2 2.0 34 25-63 3-36 (72) 20 COG1499 NMD3 NMD protein affec 39.8 18 0.00045 17.4 1.7 14 20-33 243-256 (355) 21 cd05706 S1_Rrp5_repeat_sc10 S1 38.8 31 0.00078 15.9 2.8 30 16-45 40-69 (73) 22 PRK03999 translation initiatio 38.2 33 0.00084 15.8 3.8 53 21-81 8-62 (129) 23 TIGR01955 RfaH transcriptional 36.9 19 0.0005 17.2 1.5 60 2-70 89-149 (162) 24 cd03451 FkbR2 FkbR2 is a Strep 36.4 35 0.00089 15.6 2.8 18 23-40 91-108 (146) 25 cd05707 S1_Rrp5_repeat_sc11 S1 36.2 30 0.00077 16.0 2.4 29 17-45 38-66 (68) 26 cd03454 YdeM YdeM is a Bacillu 35.6 36 0.00092 15.5 3.0 17 23-39 88-104 (140) 27 KOG3416 consensus 35.1 20 0.00051 17.1 1.4 23 23-53 61-83 (134) 28 cd05697 S1_Rrp5_repeat_hs5 S1_ 32.5 40 0.001 15.2 3.1 23 23-45 44-66 (69) 29 pfam08948 DUF1859 Domain of un 32.4 41 0.001 15.2 4.7 66 21-90 30-102 (126) 30 pfam09430 DUF2012 Protein of u 32.2 19 0.00048 17.3 0.9 49 59-110 25-77 (113) 31 PRK00006 fabZ (3R)-hydroxymyri 32.0 41 0.001 15.1 4.5 28 24-52 104-131 (149) 32 cd03452 MaoC_C MaoC_C The C-t 31.8 41 0.0011 15.1 2.9 16 23-38 88-103 (142) 33 TIGR00922 nusG transcription t 30.5 44 0.0011 15.0 3.6 29 20-55 136-164 (193) 34 pfam05641 Agenet Agenet domain 30.5 44 0.0011 15.0 4.8 38 24-67 1-38 (68) 35 COG0361 InfA Translation initi 30.0 36 0.00091 15.5 2.0 24 21-44 44-67 (75) 36 cd04460 S1_RpoE S1_RpoE: RpoE, 28.6 47 0.0012 14.8 3.8 42 19-61 49-90 (99) 37 PRK10476 multidrug resistance 28.3 48 0.0012 14.7 4.3 58 17-79 254-325 (348) 38 cd04455 S1_NusA S1_NusA: N-uti 28.1 48 0.0012 14.7 3.1 23 19-41 34-58 (67) 39 cd01288 FabZ FabZ is a 17kD be 28.0 48 0.0012 14.7 4.4 27 24-51 88-114 (131) 40 PRK10559 p-hydroxybenzoic acid 27.8 48 0.0012 14.7 4.9 56 16-78 197-267 (310) 41 PRK08190 bifunctional enoyl-Co 27.6 49 0.0012 14.7 4.4 36 23-58 95-131 (465) 42 pfam06940 DUF1287 Domain of un 27.0 50 0.0013 14.6 4.3 49 22-78 105-153 (164) 43 TIGR00008 infA translation ini 26.9 47 0.0012 14.8 2.1 26 20-45 41-66 (69) 44 COG0231 Efp Translation elonga 26.4 51 0.0013 14.5 4.0 52 22-81 7-59 (131) 45 cd05685 S1_Tex S1_Tex: The C-t 26.2 52 0.0013 14.5 3.1 25 21-45 42-66 (68) 46 TIGR02346 chap_CCT_theta T-com 25.8 53 0.0013 14.5 3.3 56 2-59 170-229 (554) 47 TIGR02303 HpaG-C-term 4-hydrox 24.7 55 0.0014 14.3 2.2 18 17-34 219-236 (249) 48 TIGR01652 ATPase-Plipid phosph 24.4 32 0.00083 15.8 0.9 12 23-34 202-213 (1249) 49 TIGR01511 ATPase-IB1_Cu copper 23.7 24 0.0006 16.6 0.1 31 18-55 88-118 (545) 50 TIGR03630 arch_S17P archaeal r 23.4 58 0.0015 14.2 2.7 21 43-66 26-46 (102) 51 TIGR02278 PaaN-DH phenylacetic 23.4 58 0.0015 14.2 2.9 28 21-48 631-658 (690) 52 TIGR01073 pcrA ATP-dependent D 23.1 59 0.0015 14.1 2.4 44 39-84 765-810 (811) 53 pfam07653 SH3_2 Variant SH3 do 23.0 60 0.0015 14.1 2.4 15 22-36 16-30 (53) 54 PRK13198 ureB urease subunit b 23.0 60 0.0015 14.1 2.6 41 17-58 87-132 (158) 55 PRK09014 rfaH transcriptional 22.4 61 0.0016 14.0 4.7 25 24-55 110-134 (162) 56 cd05708 S1_Rrp5_repeat_sc12 S1 22.0 62 0.0016 14.0 3.0 22 23-44 47-68 (77) 57 PRK03598 hypothetical protein; 21.8 63 0.0016 14.0 3.9 45 19-71 249-293 (331) 58 cd06201 SiR_like2 Cytochrome p 21.8 63 0.0016 14.0 2.9 56 19-78 79-143 (289) 59 PRK13980 NAD synthetase; Provi 21.7 15 0.00038 17.9 -1.2 41 45-86 26-66 (264) 60 TIGR01700 PNPH purine nucleosi 21.6 55 0.0014 14.3 1.7 13 21-33 97-109 (259) 61 cd05790 S1_Rrp40 S1_Rrp40: Rrp 21.6 64 0.0016 13.9 2.9 34 17-54 43-76 (86) 62 pfam11302 DUF3104 Protein of u 21.5 64 0.0016 13.9 4.8 51 22-72 4-58 (75) 63 PRK12442 translation initiatio 21.3 64 0.0016 13.9 2.0 10 25-34 48-57 (87) 64 pfam12148 DUF3590 Protein of u 21.1 46 0.0012 14.8 1.2 16 23-38 65-80 (85) 65 cd05688 S1_RPS1_repeat_ec3 S1_ 21.1 65 0.0017 13.9 2.9 23 23-45 44-66 (68) 66 TIGR03516 ppisom_GldI peptidyl 20.8 66 0.0017 13.8 4.5 69 24-92 86-174 (177) 67 pfam07154 DUF1392 Protein of u 20.6 67 0.0017 13.8 3.3 34 18-54 82-115 (150) 68 KOG3901 consensus 20.5 31 0.00078 15.9 0.2 27 92-118 56-83 (109) No 1 >PRK05338 rplS 50S ribosomal protein L19; Provisional Probab=100.00 E-value=0 Score=313.00 Aligned_cols=112 Identities=62% Similarity=1.065 Sum_probs=110.1 Q ss_pred CCHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCCCCEEEEEEECCCCCCEEEEEC Q ss_conf 93589997999999760279897378998999999835887740123453543136666433886300356130289991 Q gi|254780715|r 1 MNIIDELDHEEMVRIESKRSLPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGINKNFTVRKISYGEGMNRLFPL 80 (141) Q Consensus 1 Mnli~~le~~~~~~~~~k~~~P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~~stftvRki~~g~GVE~~fpl 80 (141) ||+|+.+|++++ ++++|+|+|||||+|+++|.||+|+|+|.|+|+||+++++|+++||||||+++|+|||++||| T Consensus 1 ~~ii~~ve~~~~-----k~~iP~f~~GDtV~V~~~i~EG~KeRiQ~feGvvI~~~~~G~~~tftvRki~~GvGVEr~fpl 75 (112) T PRK05338 1 MNLIKEIEAEQL-----RKDIPEFRPGDTVRVHVKVVEGNKERIQAFEGVVIARRGRGLNETFTVRKISYGVGVERTFPL 75 (112) T ss_pred CCHHHHHHHHHH-----CCCCCCCCCCCEEEEEEEEEECCCEEEEEEEEEEEEEECCCCCCEEEEEEEECCCCEEEEEEC T ss_conf 966999999872-----446998599999999999996896388756899999737887623889996058758999977 Q ss_pred CCCCEEEEEEEECCHHHHHHHHHHCCCCCCEEEHHHH Q ss_conf 0786101222000204678768750888410220120 Q gi|254780715|r 81 YSPMIQDITVIRRGKVRRSKLYYLQDLRGKAARIKEN 117 (141) Q Consensus 81 ~SP~i~~Iev~r~gkvRrakLyYLR~~~gk~arik~~ 117 (141) |||+|++|||+++|+|||||||||||+.||+|||+|+ T Consensus 76 ~SP~i~~iev~~~gkvRRaKLyYLR~~~GK~arike~ 112 (112) T PRK05338 76 HSPRIDSIEVVRRGKVRRAKLYYLRELSGKAARIKER 112 (112) T ss_pred CCCCCCEEEEEEECCCHHHHHHHHHCCCCCHHEECCC T ss_conf 7997467999980530234444350375602345359 No 2 >CHL00084 rpl19 ribosomal protein L19 Probab=100.00 E-value=1.4e-45 Score=308.68 Aligned_cols=112 Identities=46% Similarity=0.778 Sum_probs=108.3 Q ss_pred CHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCCCCEEEEEEECCCCCCEEEEECC Q ss_conf 35899979999997602798973789989999998358877401234535431366664338863003561302899910 Q gi|254780715|r 2 NIIDELDHEEMVRIESKRSLPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGINKNFTVRKISYGEGMNRLFPLY 81 (141) Q Consensus 2 nli~~le~~~~~~~~~k~~~P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~~stftvRki~~g~GVE~~fpl~ 81 (141) |+|+.+|++++ +.++|+|+|||||+|+++|.||+|+|+|.|+|+||+++++|+++|||||++++|+|||++|||| T Consensus 6 ~li~~ie~~~~-----k~~~p~f~~GDtV~V~~~i~EG~keRiQ~FeGvVIa~~~~G~~~tfTVRki~~GvGVEr~fpl~ 80 (117) T CHL00084 6 QLVKEIESEFL-----KTDLPEIRVGDTVKVGVLIQEGNKERVQAYEGTVIAKKNSGINTTITVRRVFQGIGVERVFLLH 80 (117) T ss_pred HHHHHHHHHHC-----CCCCCCCCCCCEEEEEEEEEECCEEEEEEEEEEEEEEECCCCCCEEEEEEECCCCCEEEEEECC T ss_conf 99999999871-----1359983999999999999848906987888999997089998449999842787589999857 Q ss_pred CCCEEEEEEEECCHHHHHHHHHHCCCCCCEEEHHHHC Q ss_conf 7861012220002046787687508884102201200 Q gi|254780715|r 82 SPMIQDITVIRRGKVRRSKLYYLQDLRGKAARIKENT 118 (141) Q Consensus 82 SP~i~~Iev~r~gkvRrakLyYLR~~~gk~arik~~~ 118 (141) ||+|++|||+++|+|||||||||||+.||+|||+|++ T Consensus 81 SP~i~~IeV~r~gkVRRAKLYYLR~~~GKaaRikekf 117 (117) T CHL00084 81 SPKIASIEVLRHSKVRRAKLYYLRNRVGKATRLKQKF 117 (117) T ss_pred CCCCCEEEEEEECCCHHHHHHHHCCCCCHHHHCCCCC T ss_conf 9984689999705421355564512756345114359 No 3 >pfam01245 Ribosomal_L19 Ribosomal protein L19. Probab=100.00 E-value=7e-45 Score=304.02 Aligned_cols=113 Identities=62% Similarity=1.014 Sum_probs=110.5 Q ss_pred CCHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCCCCEEEEEEECCCCCCEEEEEC Q ss_conf 93589997999999760279897378998999999835887740123453543136666433886300356130289991 Q gi|254780715|r 1 MNIIDELDHEEMVRIESKRSLPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGINKNFTVRKISYGEGMNRLFPL 80 (141) Q Consensus 1 Mnli~~le~~~~~~~~~k~~~P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~~stftvRki~~g~GVE~~fpl 80 (141) ||+|+.+|++++ ++++|+|+|||||+|+++|.||+|+|+|.|+|+||+++++|+++||||||+++|+|||++||| T Consensus 1 ~~~i~~~e~~~~-----k~~ip~f~~GDtv~V~~~i~Eg~k~RiQ~FeGvvI~~~~~G~~~tftvRki~~g~GVEr~fpl 75 (113) T pfam01245 1 MNLIKEIEAEQL-----KKDLPEFRVGDTVRVHVKIKEGNKERIQVFEGVVIARRGRGLNSTFTVRKISQGVGVERVFPL 75 (113) T ss_pred CCHHHHHHHHHH-----CCCCCCCCCCCEEEEEEEEEECCEEEEEEEEEEEEEEECCCCCEEEEEEEECCCCCEEEEEEC T ss_conf 967999999874-----245998499999999999984881688899999999957887416999983168758999987 Q ss_pred CCCCEEEEEEEECCHHHHHHHHHHCCCCCCEEEHHHHC Q ss_conf 07861012220002046787687508884102201200 Q gi|254780715|r 81 YSPMIQDITVIRRGKVRRSKLYYLQDLRGKAARIKENT 118 (141) Q Consensus 81 ~SP~i~~Iev~r~gkvRrakLyYLR~~~gk~arik~~~ 118 (141) |||+|++|||+++|||||||||||||+.||+||++|+. T Consensus 76 ~SP~i~~IeV~r~~kvRRakLyYLR~~~GK~arike~~ 113 (113) T pfam01245 76 HSPRIDSIEVVRRGKVRRAKLYYLRDLSGKAARIKEKR 113 (113) T ss_pred CCCCCCEEEEEECCCHHHHHHHHHHCCCCHHHEECCCC T ss_conf 79974679999716401455553512756134221259 No 4 >COG0335 RplS Ribosomal protein L19 [Translation, ribosomal structure and biogenesis] Probab=100.00 E-value=1e-43 Score=296.44 Aligned_cols=112 Identities=63% Similarity=1.083 Sum_probs=108.9 Q ss_pred CC--HHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCCCCEEEEEEECCCCCCEEEE Q ss_conf 93--5899979999997602798973789989999998358877401234535431366664338863003561302899 Q gi|254780715|r 1 MN--IIDELDHEEMVRIESKRSLPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGINKNFTVRKISYGEGMNRLF 78 (141) Q Consensus 1 Mn--li~~le~~~~~~~~~k~~~P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~~stftvRki~~g~GVE~~f 78 (141) || +|+++|++|+ ++++|+|+|||||+|+++|.||+|+|+|.|+|+||+++|+|+++|||||++++|+|||++| T Consensus 1 m~~~~i~~le~~q~-----~~~iP~f~~GDtvrv~vki~Eg~keR~Q~FeGvVia~r~~G~~~tftvRkis~G~GVEr~F 75 (115) T COG0335 1 MNIPIIQQLEQEQI-----KKDIPSFRPGDTVRVHVKIVEGSKERVQAFEGVVIARRGRGISETFTVRKISYGVGVERVF 75 (115) T ss_pred CCCHHHHHHHHHHH-----HHCCCCCCCCCEEEEEEEEEECCCEEEEEEEEEEEEECCCCCCCEEEEEEEECCCEEEEEE T ss_conf 97279999999988-----8508989999889999999868807876255899998799865118999840584088997 Q ss_pred ECCCCCEEEEEEEECCHHHHHHHHHHCCCCCCEEEHHHH Q ss_conf 910786101222000204678768750888410220120 Q gi|254780715|r 79 PLYSPMIQDITVIRRGKVRRSKLYYLQDLRGKAARIKEN 117 (141) Q Consensus 79 pl~SP~i~~Iev~r~gkvRrakLyYLR~~~gk~arik~~ 117 (141) |+|||+|++|||+++|+||||||||||++.||+|||+++ T Consensus 76 p~~SP~Ie~IeV~rrGkVRRAKLYYLR~~~GKaArIke~ 114 (115) T COG0335 76 PLHSPLIESIEVVRRGKVRRAKLYYLRERRGKAARIKEK 114 (115) T ss_pred ECCCCCEEEEEEEECCCEEEEEEEEEECCCCCCEEEEEC T ss_conf 258984507999961826144467641355521056533 No 5 >KOG1698 consensus Probab=100.00 E-value=5e-33 Score=229.03 Aligned_cols=124 Identities=31% Similarity=0.618 Sum_probs=117.3 Q ss_pred CHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCCCCEEEEEEECCCCCCEEEEECC Q ss_conf 35899979999997602798973789989999998358877401234535431366664338863003561302899910 Q gi|254780715|r 2 NIIDELDHEEMVRIESKRSLPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGINKNFTVRKISYGEGMNRLFPLY 81 (141) Q Consensus 2 nli~~le~~~~~~~~~k~~~P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~~stftvRki~~g~GVE~~fpl~ 81 (141) .+++.||+++|+..+...++|+|++||+|+|++...+ ++.++..|.|+||++++.|+++||+|||++.|+|||.+|||| T Consensus 75 ~~~e~Ldr~a~~~rr~~r~iPe~~~G~Iv~V~s~~p~-~k~k~s~f~Gi~I~R~~~Gl~atf~LRnvIagvGVEi~~pLY 153 (201) T KOG1698 75 RIMEILDRQAVLERRKVRDIPEFKVGSIVRVTSEDPE-NKRKVSRFKGICIRRRNAGLNATFLLRNVIAGVGVEIVFPLY 153 (201) T ss_pred HHHHHHCHHHHHHHHHCCCCCCCCCCCEEEEEECCCC-CCCCEEEEEEEEEEECCCCCCCEEEEEEHHHCCEEEEEEECC T ss_conf 8987637688999985456876214558999962776-677424689999972346876267720033074059998636 Q ss_pred CCCEEEEEEEECCHHHHHHHHHHCCCCCCEEEHHHHCCCCCCCCC Q ss_conf 786101222000204678768750888410220120012123654 Q gi|254780715|r 82 SPMIQDITVIRRGKVRRSKLYYLQDLRGKAARIKENTGKRAKALN 126 (141) Q Consensus 82 SP~i~~Iev~r~gkvRrakLyYLR~~~gk~arik~~~~~~~~~~~ 126 (141) ||+|++|+|++..|+|||+||||||..+.+++++..|.+...... T Consensus 154 sP~IkeI~Vlk~~k~rra~LyYLRd~lp~lstfd~~m~~~~~~~~ 198 (201) T KOG1698 154 SPNIKEIKVLKLEKRRRAKLYYLRDALPELSTFDANMRPKKEENG 198 (201) T ss_pred CCCEEEEEEECHHHCCCCCHHHHHCCCCCCCCHHHCCCCCCCCCC T ss_conf 997147898433241112013222244445834423532235578 No 6 >TIGR01024 rplS_bact ribosomal protein L19; InterPro: IPR001857 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 of 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 L19 is one of the proteins from the large ribosomal subunit , . In Escherichia coli, L19 is known to be located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site. It belongs to a family of ribosomal proteins, including L19 from bacteria and the chloroplasts of red algae. L19 is a protein of 120 to 130 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome. Probab=99.93 E-value=2.4e-26 Score=186.94 Aligned_cols=113 Identities=61% Similarity=0.999 Sum_probs=107.3 Q ss_pred CCHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCCCCEEEEEEE-CCCCCCEEEEE Q ss_conf 93589997999999760279897378998999999835887740123453543136666433886300-35613028999 Q gi|254780715|r 1 MNIIDELDHEEMVRIESKRSLPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGINKNFTVRKI-SYGEGMNRLFP 79 (141) Q Consensus 1 Mnli~~le~~~~~~~~~k~~~P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~~stftvRki-~~g~GVE~~fp 79 (141) +++++.++.++. .+.++|+|++||+++|++++.||.++|+|.|+|+||+.+++|++.||++|++ ++|+|+|+.|| T Consensus 1 ~~~~~~~~~~~~----~~~~~p~~~~gd~~~~~~~~~~g~~~~~~~~~g~~~~~~~~g~~~~~~~~~~g~~g~g~~~~f~ 76 (116) T TIGR01024 1 SNLIKELEQENQ----LKKDLPDFRPGDTVRVGVKIVEGGKERLQAFEGVVIARRGGGIGETFTVRKIGSYGVGVERIFP 76 (116) T ss_pred CHHHHHHHHHHH----HCCCCCCCCCCCEEEEEEEEEECCCCEEEECCCEEEEECCCCCCCEEEEEECCCCCCCCCEEEE T ss_conf 903655444331----0012333457851468888740774100110314786417876512466422666666200100 Q ss_pred CCCCCEEEEEEEECCHHHHHHHHHHCCCCCC-EEEHHHH Q ss_conf 1078610122200020467876875088841-0220120 Q gi|254780715|r 80 LYSPMIQDITVIRRGKVRRSKLYYLQDLRGK-AARIKEN 117 (141) Q Consensus 80 l~SP~i~~Iev~r~gkvRrakLyYLR~~~gk-~arik~~ 117 (141) +|||.+.+|++++.|++++|+|||||++.|+ ++++++. T Consensus 77 ~~~p~~~~~~~~~~g~~~~~~~~y~~~~~g~~~~~~~~~ 115 (116) T TIGR01024 77 LHSPNIESIEVVRRGKVRRAKLYYLRERRGKAAAKIKER 115 (116) T ss_pred CCCCCCCEEEHHHCCCHHHHHHHHHHCCCCHHHHHHHHC T ss_conf 136531000000003201233222220243012232104 No 7 >PRK01191 rpl24p 50S ribosomal protein L24P; Validated Probab=79.09 E-value=5.7 Score=20.56 Aligned_cols=76 Identities=21% Similarity=0.210 Sum_probs=46.3 Q ss_pred HHCCCCCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCCCCEEEEEEE--CCCCCCEEEEECCCCCEEEEEEEEC Q ss_conf 60279897378998999999835887740123453543136666433886300--3561302899910786101222000 Q gi|254780715|r 16 ESKRSLPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGINKNFTVRKI--SYGEGMNRLFPLYSPMIQDITVIRR 93 (141) Q Consensus 16 ~~k~~~P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~~stftvRki--~~g~GVE~~fpl~SP~i~~Iev~r~ 93 (141) +..+++| ++.||+|.|.- -..|+ -+|-|+.+...-. .+.|-.+ .---|-+.-+|+|..++.=.++.-. T Consensus 40 y~~Rs~~-IrkgD~V~V~r---G~~kG----~~GkV~~V~~k~~--~V~VEgv~~~K~~G~~v~~pIhpSnvvItkL~l~ 109 (119) T PRK01191 40 YGIRSLP-VRKGDTVKVMR---GDFKG----EEGKVVEVDLKRY--RIYVEGVTIKKADGTEVPYPIHPSNVMITKLDLS 109 (119) T ss_pred HCCCCCC-EECCCEEEEEE---CCCCC----CCCEEEEEECCCC--EEEEEEEEEECCCCCEEEEEECCCCEEEEECCCC T ss_conf 4887443-54699999955---27789----6231899973688--9999436998479987864225631799974668 Q ss_pred CHHHHHHH Q ss_conf 20467876 Q gi|254780715|r 94 GKVRRSKL 101 (141) Q Consensus 94 gkvRrakL 101 (141) -+.|.++| T Consensus 110 Dk~R~~~L 117 (119) T PRK01191 110 DERRFKIL 117 (119) T ss_pred CHHHHHHH T ss_conf 87899874 No 8 >pfam03888 MucB_RseB MucB/RseB family. Members of this family are regulators of the anti-sigma E protein RseD. Probab=75.64 E-value=6.2 Score=20.31 Aligned_cols=52 Identities=21% Similarity=0.289 Sum_probs=43.1 Q ss_pred CCCCEEEEEEEEEECCCCCCCEEEEEEECCCCCCEEEEECCCCCEEEEEEEECCH Q ss_conf 7740123453543136666433886300356130289991078610122200020 Q gi|254780715|r 41 KSRIQAYEGVCIARSGRGINKNFTVRKISYGEGMNRLFPLYSPMIQDITVIRRGK 95 (141) Q Consensus 41 k~R~Q~F~GvvI~~~~~G~~stftvRki~~g~GVE~~fpl~SP~i~~Iev~r~gk 95 (141) -.+.+.|+|+.+-.++..+.+.=.+..+.+|.-.|+...|..|..+ |+|++. T Consensus 36 A~~~lnY~G~fvy~~~~~i~s~ri~H~~~~g~e~erL~~LdG~~rE---iiR~~d 87 (314) T pfam03888 36 ASQQLSYEGSFVYERNGSFSSLRYRHARQDGKSYAQLLQLDGPQQE---VVRRDN 87 (314) T ss_pred HHHHCCEEEEEEEEECCEEEEEEEEEEECCCEEEEEEEECCCCHHE---EEEECC T ss_conf 8875774799999919902159999995599699999954998002---899699 No 9 >PRK09455 rseB periplasmic negative regulator of sigmaE; Provisional Probab=69.29 E-value=9.9 Score=19.02 Aligned_cols=51 Identities=25% Similarity=0.271 Sum_probs=41.4 Q ss_pred CCCEEEEEEEEEECCCCCCCEEEEEEECCCCCCEEEEECCCCCEEEEEEEECCH Q ss_conf 740123453543136666433886300356130289991078610122200020 Q gi|254780715|r 42 SRIQAYEGVCIARSGRGINKNFTVRKISYGEGMNRLFPLYSPMIQDITVIRRGK 95 (141) Q Consensus 42 ~R~Q~F~GvvI~~~~~G~~stftvRki~~g~GVE~~fpl~SP~i~~Iev~r~gk 95 (141) .+.+.|+|+.+..++..+.+.=.+.-+.+|.-+|+.-.|..|..+ |+|++. T Consensus 21 ~~~lnY~G~fv~~~~~~i~s~ri~H~~~~~~e~erL~~LdG~~rE---viR~~d 71 (302) T PRK09455 21 SQSLNYELSFISINKQGIESLRYRHARLDNKPLAQLLQLDGPRRE---VIQRGN 71 (302) T ss_pred HHHCCEEEEEEEEECCEEEEEEEEEEECCCEEEEEEEECCCCCEE---EEEECC T ss_conf 874781599999939925689999996599699998835998417---999599 No 10 >pfam02211 NHase_beta Nitrile hydratase beta subunit. Nitrile hydratases EC:4.2.1.84 are unusual metalloenzymes that catalyse the hydration of nitriles to their corresponding amides. They are used as biocatalysts in acrylamide production, one of the few commercial scale bioprocesses, as well as in environmental remediation for the removal of nitriles from waste streams. Nitrile hydratases are composed of two subunits, alpha and beta, and they contain one iron atom per alpha beta unit. Probab=57.80 E-value=12 Score=18.47 Aligned_cols=39 Identities=23% Similarity=0.517 Sum_probs=27.4 Q ss_pred CCCCCCCCCCEEEEEEEEECCCCCCCEEE----EEEEEEECCCC Q ss_conf 79897378998999999835887740123----45354313666 Q gi|254780715|r 19 RSLPKFSPGDTLCVKTIITEGDKSRIQAY----EGVCIARSGRG 58 (141) Q Consensus 19 ~~~P~f~~GD~v~V~~~i~eg~k~R~Q~F----~GvvI~~~~~G 58 (141) ..-|.|.+||.|+|.- .....-+|+..| .|++++.++.- T Consensus 128 ~~~p~F~vGd~Vrv~~-~~~~gHtRlP~Y~rgk~G~I~~~~G~~ 170 (220) T pfam02211 128 DAPPRFAVGDRVRTRN-INPNGHTRLPRYVRGKTGTIVRVHGAH 170 (220) T ss_pred CCCCCCCCCCEEEEEE-CCCCCCCCCHHHHCCCEEEEEEEECCC T ss_conf 9999779999899822-799975235367678745899884687 No 11 >pfam02765 Telo_bind Telomeric single stranded DNA binding POT1/CDC13. This domain binds single stranded telomeric DNA and adopts an OB fold. It includes the proteins POT1 and CDC13 which have been shown to regulate telomere length, replication and capping. Probab=54.22 E-value=19 Score=17.32 Aligned_cols=49 Identities=18% Similarity=0.285 Sum_probs=30.0 Q ss_pred CCCCCCC-CCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCCCCEEEEEEECCCCCCEE Q ss_conf 7989737-899899999983588774012345354313666643388630035613028 Q gi|254780715|r 19 RSLPKFS-PGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGINKNFTVRKISYGEGMNR 76 (141) Q Consensus 19 ~~~P~f~-~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~~stftvRki~~g~GVE~ 76 (141) ..+|... +||++.++- -++|.|.|-..+..+.+-.++|.|= .++.|..- T Consensus 64 e~LP~v~~~GDIi~l~r-------~~v~~~~~~~~~~~~~~~~ss~a~f--~g~~~~~~ 113 (141) T pfam02765 64 EDLPNVQSAGDIIRLHR-------VKVKLYNGKPQGVARDKNNSSWAIF--SGDLGAPF 113 (141) T ss_pred HHCCCCCCCCCEEEEEE-------EEEEEECCEEEEEECCCCCEEEEEE--CCCCCCCC T ss_conf 78998677798999977-------8999998967898727884057997--18899986 No 12 >cd04497 hPOT1_OB1_like hPOT1_OB1_like: A subfamily of OB folds similar to the first OB fold (OB1) of human protection of telomeres 1 protein (hPOT1), the single OB fold of the N-terminal domain of Schizosaccharomyces pombe POT1 (SpPOT1), and the first OB fold of the N-terminal domain of the alpha subunit (OB1Nalpha) of Oxytricha nova telomere end binding protein (OnTEBP). POT1 proteins recognize single-stranded (ss) 3-prime ends of the telomere. A 3-prime ss overhang is conserved in ciliated protozoa, yeast, and mammals. SpPOT1 is essential for telomere maintenance. It binds specifically to the ss G-rich telomeric sequence (GGTTAC) of S. pombe. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. Deletion of the S. pombe pot1+ gene results in a rapid loss of telomere sequences, chromosome mis-segregation and chromosome circularization. hPOT1 is implicated in telomere length regulation. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB Probab=51.82 E-value=20 Score=17.08 Aligned_cols=50 Identities=24% Similarity=0.309 Sum_probs=32.1 Q ss_pred CCCCCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCCCCEEEEEEECCCCCCE Q ss_conf 2798973789989999998358877401234535431366664338863003561302 Q gi|254780715|r 18 KRSLPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGINKNFTVRKISYGEGMN 75 (141) Q Consensus 18 k~~~P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~~stftvRki~~g~GVE 75 (141) ...+|..++||+|.++-- ++|.|.|-..+..+. -.++|.|=+-..+.+.+ T Consensus 63 ~~~LP~v~~GDiIll~~~-------~v~~~~~~~~~~~~~-~~sswavF~g~~~~~~~ 112 (138) T cd04497 63 EESLPIVKVGDIILLRRV-------KIQSYNGKPQGISND-RGSSWAVFRGDDGVVPI 112 (138) T ss_pred HHHCCCCCCCCEEEEEEE-------EEEEECCEEEEEECC-CCEEEEEECCCCCCCCC T ss_conf 656989999989999888-------999988907999778-84169998588899868 No 13 >cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure". Probab=49.48 E-value=18 Score=17.47 Aligned_cols=34 Identities=12% Similarity=0.180 Sum_probs=14.7 Q ss_pred CCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCCCCEE Q ss_conf 789989999998358877401234535431366664338 Q gi|254780715|r 25 SPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGINKNF 63 (141) Q Consensus 25 ~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~~stf 63 (141) ++||+|...+. .-+ .|.-.--++++.++.+..+| T Consensus 5 ~vGdiV~~rVt--rv~---~~~a~v~Il~v~~~~l~~~f 38 (92) T cd05791 5 KVGSIVIARVT--RIN---PRFAKVDILCVGGRPLKESF 38 (92) T ss_pred CCCCEEEEEEE--EEC---CCEEEEEEEEECCEECCCEE T ss_conf 89999999999--971---13789999999999837625 No 14 >COG1566 EmrA Multidrug resistance efflux pump [Defense mechanisms] Probab=49.19 E-value=22 Score=16.82 Aligned_cols=62 Identities=15% Similarity=0.097 Sum_probs=44.4 Q ss_pred HHHCCCCCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCC-C--------CCCEEEEEEECCCCCCEEEEEC Q ss_conf 7602798973789989999998358877401234535431366-6--------6433886300356130289991 Q gi|254780715|r 15 IESKRSLPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGR-G--------INKNFTVRKISYGEGMNRLFPL 80 (141) Q Consensus 15 ~~~k~~~P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~-G--------~~stftvRki~~g~GVE~~fpl 80 (141) .++..++..+++|+-+.|++....++ ..|+|++-++... | .++|+..=++++.+.|...|.= T Consensus 250 nFkETqL~~~r~Gq~a~I~~da~~~~----~~~~G~v~~i~~~tg~~fsllp~~natgN~tkvvQRvPVrI~ld~ 320 (352) T COG1566 250 NFKETQLARVRPGQPAEITLDAYPGN----GVVEGIVEGIAPATGSAFSLLPAQNATGNWTKVVQRVPVRIELDP 320 (352) T ss_pred EEEEEECCCCCCCCEEEEEEECCCCC----EEEEEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEEEEEEECC T ss_conf 20011347445897089999737984----589999987447865300157874678888999976658999667 No 15 >COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis] Probab=46.60 E-value=24 Score=16.57 Aligned_cols=38 Identities=26% Similarity=0.477 Sum_probs=26.8 Q ss_pred CCCCCCCCEEEEEEEEEC----CC-CCCCEEEEEEEEEECCCCCC Q ss_conf 897378998999999835----88-77401234535431366664 Q gi|254780715|r 21 LPKFSPGDTLCVKTIITE----GD-KSRIQAYEGVCIARSGRGIN 60 (141) Q Consensus 21 ~P~f~~GD~v~V~~~i~e----g~-k~R~Q~F~GvvI~~~~~G~~ 60 (141) +-+|.+||.|.+ .|+. |. -.|.|-..|+|+..+++... T Consensus 30 l~ey~~Gd~V~I--~IdpSv~kGmPh~rf~G~TG~Vvg~~g~ay~ 72 (98) T COG2139 30 LQEYKVGDKVHI--DIDPSVHKGMPHPRFQGKTGTVVGVRGRAYK 72 (98) T ss_pred HHHCCCCCEEEE--EECCCCCCCCCCCCCCCCCEEEEECCCCEEE T ss_conf 876079987999--8476202698775304763079841487799 No 16 >pfam02014 Reeler Reeler domain. Probab=45.77 E-value=25 Score=16.49 Aligned_cols=32 Identities=16% Similarity=0.297 Sum_probs=22.9 Q ss_pred CCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCC Q ss_conf 7378998999999835887740123453543136666 Q gi|254780715|r 23 KFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGI 59 (141) Q Consensus 23 ~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~ 59 (141) .+.||+.+.|++.-.. ...|.|..|.-++.+. T Consensus 29 ~y~pG~~~~Vtl~~~~-----~~~F~GFllqAr~~~~ 60 (127) T pfam02014 29 SYVPGQTYTVTISKSS-----GDTFRGFLLQARNGDP 60 (127) T ss_pred EECCCCEEEEEEECCC-----CCCCCEEEEEEECCCC T ss_conf 7889998999996689-----9871589999973889 No 17 >TIGR02579 cas_csx3 CRISPR-associated protein, Csx3 family; InterPro: IPR013409 This entry is encoded in CRISPR-associated (cas) gene clusters, near CRISPR repeats, in the genomes of several different thermophiles: Archaeoglobus fulgidus (archaeal), Aquifex aeolicus (Aquificae), Dictyoglomus thermophilum (Dictyoglomi), and a thermophilic Synechococcus (Cyanobacteria). It is not yet assigned to a specific CRISPR/cas subtype (hence the x designation csx3).. Probab=44.80 E-value=9.4 Score=19.18 Aligned_cols=15 Identities=20% Similarity=0.328 Sum_probs=11.3 Q ss_pred CCCCCCCCCCCEEEE Q ss_conf 279897378998999 Q gi|254780715|r 18 KRSLPKFSPGDTLCV 32 (141) Q Consensus 18 k~~~P~f~~GD~v~V 32 (141) ....|++|+||++.+ T Consensus 76 ~SH~Pe~r~GdVi~~ 90 (90) T TIGR02579 76 SSHSPELRVGDVIDW 90 (90) T ss_pred EECCCCCCCCCEECC T ss_conf 514899987743429 No 18 >TIGR00998 8a0101 efflux pump membrane protein; InterPro: IPR005694 emrA and emrB confer resistance to carbonylcyanide m-chlorophenylhydrazone, nalidixic acid, and a number of other toxic compounds. EmrB encodes a highly hydrophobic 56.2-kDa peptide, with 14 potential alpha-helices to span the inner membrane. EmrA encodes a putative 42.7-kDa peptide containing a single hydrophobic domain and a large C-terminal hydrophilic domain.; GO: 0015238 drug transporter activity, 0006855 multidrug transport, 0009276 1-2nm peptidoglycan-based cell wall. Probab=44.60 E-value=26 Score=16.38 Aligned_cols=40 Identities=15% Similarity=0.171 Sum_probs=33.3 Q ss_pred HHHHCCCCCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCC Q ss_conf 97602798973789989999998358877401234535431366 Q gi|254780715|r 14 RIESKRSLPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGR 57 (141) Q Consensus 14 ~~~~k~~~P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~ 57 (141) ..++-.++...|+|.-+.|+.-...+++ .|+|.|-.+... T Consensus 285 ANFkETqL~~vR~G~~v~i~~DlYg~dv----~F~GkV~gi~~G 324 (379) T TIGR00998 285 ANFKETQLKNVRIGQPVTIRSDLYGSDV----VFEGKVTGISMG 324 (379) T ss_pred EEEECCCCCCCCCCCCEEEEEEECCCCC----EEEEEEEECCCC T ss_conf 7520132057457872589985438980----797488422663 No 19 >pfam10447 EXOSC1 Exosome component EXOSC1/CSL4. This family of proteins are components of the exosome 3'-5' exoribonuclease complex. The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions. Probab=40.36 E-value=20 Score=17.16 Aligned_cols=34 Identities=15% Similarity=0.224 Sum_probs=15.1 Q ss_pred CCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCCCCEE Q ss_conf 789989999998358877401234535431366664338 Q gi|254780715|r 25 SPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGINKNF 63 (141) Q Consensus 25 ~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~~stf 63 (141) .+||+|...+.-. +. +.-..-+++..+..+..+| T Consensus 3 ~vGdiV~arVtrv--~~---~~a~~~Il~v~~~~l~~~f 36 (72) T pfam10447 3 KVGDIVLARVTRV--TP---RQAYCEILAVGGTALKETF 36 (72) T ss_pred CCCCEEEEEEEEE--CH---HEEEEEEEEECCEECCCCE T ss_conf 8999999999997--50---1579999999999878855 No 20 >COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis] Probab=39.84 E-value=18 Score=17.44 Aligned_cols=14 Identities=43% Similarity=1.058 Sum_probs=11.5 Q ss_pred CCCCCCCCCEEEEE Q ss_conf 98973789989999 Q gi|254780715|r 20 SLPKFSPGDTLCVK 33 (141) Q Consensus 20 ~~P~f~~GD~v~V~ 33 (141) -+|+|++||+|.+. T Consensus 243 rip~~~~gDiV~~~ 256 (355) T COG1499 243 RIPEFRPGDIVSVR 256 (355) T ss_pred ECCCCCCCCEEEEC T ss_conf 87887988789977 No 21 >cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea. Probab=38.79 E-value=31 Score=15.94 Aligned_cols=30 Identities=17% Similarity=0.122 Sum_probs=19.5 Q ss_pred HHCCCCCCCCCCCEEEEEEEEECCCCCCCE Q ss_conf 602798973789989999998358877401 Q gi|254780715|r 16 ESKRSLPKFSPGDTLCVKTIITEGDKSRIQ 45 (141) Q Consensus 16 ~~k~~~P~f~~GD~v~V~~~i~eg~k~R~Q 45 (141) +.+.....|++||.|+|.+.-.+-++.|++ T Consensus 40 ~~~~~~~~~~~g~~V~v~Vl~VD~~~krI~ 69 (73) T cd05706 40 YSEALPYKFKKNDIVRACVLSVDVPNKKIA 69 (73) T ss_pred CCCCCHHHCCCCCEEEEEEEEEECCCCEEE T ss_conf 013817516899999999999988899898 No 22 >PRK03999 translation initiation factor IF-5A; Provisional Probab=38.21 E-value=33 Score=15.76 Aligned_cols=53 Identities=17% Similarity=0.344 Sum_probs=38.2 Q ss_pred CCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCC-CC-CCEEEEEEECCCCCCEEEEECC Q ss_conf 8973789989999998358877401234535431366-66-4338863003561302899910 Q gi|254780715|r 21 LPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGR-GI-NKNFTVRKISYGEGMNRLFPLY 81 (141) Q Consensus 21 ~P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~-G~-~stftvRki~~g~GVE~~fpl~ 81 (141) .-+|+.|..+.+ +|..+++.-|. .++-|+ |- -..+.+++++.|-=.|.+||-. T Consensus 8 ~~dlK~G~~i~i-----dg~pckVve~~---~sKpGKHG~Akvr~~~~~i~tG~k~e~~~~~~ 62 (129) T PRK03999 8 VGELKEGSYVVI-----DGEPCRIVEIS---KSKPGKHGSAKARIVAIGIFDGQKRSLVAPVD 62 (129) T ss_pred HHHCCCCCEEEE-----CCEEEEEEEEE---EECCCCCCCEEEEEEEEECCCCCEEEEEECCC T ss_conf 899268999999-----99859999988---86499985369999999646797899988798 No 23 >TIGR01955 RfaH transcriptional activator RfaH; InterPro: IPR010215 This entry represents the transcriptional activator protein, RfaH . This protein is most closely related to the transcriptional termination/antitermination protein NusG (IPR001062 from INTERPRO) and contains the KOW motif (IPR005824 from INTERPRO) . This protein appears to be limited to the proteobacteria. In Escherichia coli, this gene appears to control the expression of haemolysin, sex factor and lipopolysaccharide genes.; GO: 0003711 transcription elongation regulator activity, 0006355 regulation of transcription DNA-dependent. Probab=36.90 E-value=19 Score=17.19 Aligned_cols=60 Identities=18% Similarity=0.375 Sum_probs=34.8 Q ss_pred CHHHHHHHHHHHHHHHCCCCCC-CCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCCCCEEEEEEECC Q ss_conf 3589997999999760279897-37899899999983588774012345354313666643388630035 Q gi|254780715|r 2 NIIDELDHEEMVRIESKRSLPK-FSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGINKNFTVRKISY 70 (141) Q Consensus 2 nli~~le~~~~~~~~~k~~~P~-f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~~stftvRki~~ 70 (141) ++|++|...+..........|. |..||.|.+ .+|.=. -||||=. ...|-.-+..|=|+++ T Consensus 89 ~~I~~l~~~~~~~~~~~~~~P~~~~~G~~V~i----~~G~fa---g~EAIF~--~~dG~~R~~~Llnm~~ 149 (162) T TIGR01955 89 DLIHQLRQKELEASVPAKKTPLLFKKGDKVRI----TDGSFA---GLEAIFL--EPDGEKRSVLLLNMIG 149 (162) T ss_pred HHHHHHHHCCCCCCCCHHHCCCCCCCCCEEEE----EECCCC---CCCEEEE--CCCCCHHHHHHHHHHC T ss_conf 89898640343225583135657789887998----628713---6003540--7884247766546636 No 24 >cd03451 FkbR2 FkbR2 is a Streptomyces hygroscopicus protein with a hot dog fold that belongs to a conserved family of proteins found in prokaryotes and archaea but not in eukaryotes. FkbR2 has sequence similarity to (R)-specific enoyl-CoA hydratase, the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. The function of FkbR2 is unknown. Probab=36.40 E-value=35 Score=15.58 Aligned_cols=18 Identities=22% Similarity=0.254 Sum_probs=14.3 Q ss_pred CCCCCCEEEEEEEEECCC Q ss_conf 737899899999983588 Q gi|254780715|r 23 KFSPGDTLCVKTIITEGD 40 (141) Q Consensus 23 ~f~~GD~v~V~~~i~eg~ 40 (141) ..++||||.+...|.+-. T Consensus 91 PV~~GDtl~~~~eV~~~r 108 (146) T cd03451 91 PVFHGDTLYAESEVLSKR 108 (146) T ss_pred CCCCCCEEEEEEEEEEEE T ss_conf 776999999999999987 No 25 >cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea. Probab=36.19 E-value=30 Score=15.99 Aligned_cols=29 Identities=24% Similarity=0.294 Sum_probs=20.1 Q ss_pred HCCCCCCCCCCCEEEEEEEEECCCCCCCE Q ss_conf 02798973789989999998358877401 Q gi|254780715|r 17 SKRSLPKFSPGDTLCVKTIITEGDKSRIQ 45 (141) Q Consensus 17 ~k~~~P~f~~GD~v~V~~~i~eg~k~R~Q 45 (141) -+..-..|.+|++|++.+.-.+-.+.|++ T Consensus 38 Vkd~~~~f~vGq~V~~kV~~iD~~~~ri~ 66 (68) T cd05707 38 LKDWKKRFKVGQLVKGKIVSIDPDNGRIE 66 (68) T ss_pred HCCHHHHCCCCCEEEEEEEEEECCCCEEE T ss_conf 64998917999999999999828758673 No 26 >cd03454 YdeM YdeM is a Bacillus subtilis protein that belongs to a family of prokaryotic proteins of unkown function. YdeM has sequence similarity to the hot-dog fold of (R)-specific enoyl-CoA hydratase. Other enzymes with this fold include the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. Probab=35.65 E-value=36 Score=15.50 Aligned_cols=17 Identities=35% Similarity=0.591 Sum_probs=14.0 Q ss_pred CCCCCCEEEEEEEEECC Q ss_conf 73789989999998358 Q gi|254780715|r 23 KFSPGDTLCVKTIITEG 39 (141) Q Consensus 23 ~f~~GD~v~V~~~i~eg 39 (141) ..++||||.+...|.+- T Consensus 88 PV~~GDTi~~~~eV~~~ 104 (140) T cd03454 88 PVRPGDTLSVEVEVLDK 104 (140) T ss_pred CCCCCCEEEEEEEEEEE T ss_conf 87689999999999993 No 27 >KOG3416 consensus Probab=35.07 E-value=20 Score=17.09 Aligned_cols=23 Identities=22% Similarity=0.642 Sum_probs=13.5 Q ss_pred CCCCCCEEEEEEEEECCCCCCCEEEEEEEEE Q ss_conf 7378998999999835887740123453543 Q gi|254780715|r 23 KFSPGDTLCVKTIITEGDKSRIQAYEGVCIA 53 (141) Q Consensus 23 ~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~ 53 (141) -|.|||+|+.+ +.=.+.|+| |+- T Consensus 61 ~~~PGDIirLt-------~Gy~Si~qg-~Lt 83 (134) T KOG3416 61 LIQPGDIIRLT-------GGYASIFQG-CLT 83 (134) T ss_pred CCCCCCEEEEC-------CCCHHHHCC-CEE T ss_conf 45886689963-------630434038-569 No 28 >cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea. Probab=32.52 E-value=40 Score=15.18 Aligned_cols=23 Identities=26% Similarity=0.534 Sum_probs=17.1 Q ss_pred CCCCCCEEEEEEEEECCCCCCCE Q ss_conf 73789989999998358877401 Q gi|254780715|r 23 KFSPGDTLCVKTIITEGDKSRIQ 45 (141) Q Consensus 23 ~f~~GD~v~V~~~i~eg~k~R~Q 45 (141) .|++||.|++.+.-.+-++.|+. T Consensus 44 ~fk~G~~Vk~rVl~vD~~~~ri~ 66 (69) T cd05697 44 KFKPGLKVKCRVLSVEPERKRLV 66 (69) T ss_pred CCCCCCEEEEEEEEEECCCCEEE T ss_conf 08999999999999948879988 No 29 >pfam08948 DUF1859 Domain of unknown function (DUF1859). This domain has no known function. It is predominantly found in the N-terminus of bacteriophage spike proteins. Probab=32.38 E-value=41 Score=15.17 Aligned_cols=66 Identities=20% Similarity=0.323 Sum_probs=45.8 Q ss_pred CCCCCCCCEEEEEEEEECCCCCCCEEEEEE-EEEECCCCCCCEEEEE------EECCCCCCEEEEECCCCCEEEEEE Q ss_conf 897378998999999835887740123453-5431366664338863------003561302899910786101222 Q gi|254780715|r 21 LPKFSPGDTLCVKTIITEGDKSRIQAYEGV-CIARSGRGINKNFTVR------KISYGEGMNRLFPLYSPMIQDITV 90 (141) Q Consensus 21 ~P~f~~GD~v~V~~~i~eg~k~R~Q~F~Gv-vI~~~~~G~~stftvR------ki~~g~GVE~~fpl~SP~i~~Iev 90 (141) .-+--+|.+|++.++... -+|-|.|+ ||-+.++..+-.|++- +|-.-.|-.--|||-||...+.-+ T Consensus 30 ~~eaiaG~~V~~DL~~~~----~T~~~sGVQ~~YID~~e~~G~~~i~v~eTGQRIt~~AG~QGYfPlL~~~~~KFv~ 102 (126) T pfam08948 30 YFDAVAGENVKYDLTYLA----DTQGFTGVQCIYIDNAENDGAFEIDVEETGQRIKCPAGKQGYFPLLVPGRAKFVA 102 (126) T ss_pred HHHHCCCCEEEEEEEEEE----CCCCCCEEEEEEEECCCCCCCEEEECCCCCCEEECCCCCCCCCEEECCCHHHHHH T ss_conf 534348955999999972----2587030589998652356857996222684887457785322466066655544 No 30 >pfam09430 DUF2012 Protein of unknown function (DUF2012). This is a eukaryotic family of uncharacterized proteins. Probab=32.18 E-value=19 Score=17.25 Aligned_cols=49 Identities=22% Similarity=0.331 Sum_probs=36.1 Q ss_pred CCCEEEEEEECCCCCCEEEEECCCCCE----EEEEEEECCHHHHHHHHHHCCCCCC Q ss_conf 643388630035613028999107861----0122200020467876875088841 Q gi|254780715|r 59 INKNFTVRKISYGEGMNRLFPLYSPMI----QDITVIRRGKVRRSKLYYLQDLRGK 110 (141) Q Consensus 59 ~~stftvRki~~g~GVE~~fpl~SP~i----~~Iev~r~gkvRrakLyYLR~~~gk 110 (141) .+.||+++|+-.|.- ...++||.. -.|+|...|+.|.-+++|.....+. T Consensus 25 ~dGsF~f~nVp~Gsy---~ldv~~~~~~F~pvRVdV~~~g~~~~~~~~~~~~~~~~ 77 (113) T pfam09430 25 RDGSFVFHNVPAGSY---LLEVESPGYRFEPVRVDVSAKGKVRAVQLNIVETYEVN 77 (113) T ss_pred CCCEEEECCCCCEEE---EEEEECCCCEECCEEEEEECCCCCCCEEEEECCCCCCC T ss_conf 687799738998338---99984698280578999946986464687732354576 No 31 >PRK00006 fabZ (3R)-hydroxymyristoyl-ACP dehydratase; Reviewed Probab=32.00 E-value=41 Score=15.13 Aligned_cols=28 Identities=25% Similarity=0.494 Sum_probs=18.9 Q ss_pred CCCCCEEEEEEEEECCCCCCCEEEEEEEE Q ss_conf 37899899999983588774012345354 Q gi|254780715|r 24 FSPGDTLCVKTIITEGDKSRIQAYEGVCI 52 (141) Q Consensus 24 f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI 52 (141) ..|||++.++.++.. .+...-.|.|.+- T Consensus 104 V~PGd~l~i~~~l~~-~~~~~~~~~~~a~ 131 (149) T PRK00006 104 VVPGDQLILEVEFLK-KRRGIGKFKGVAK 131 (149) T ss_pred CCCCCEEEEEEEEEE-EECCEEEEEEEEE T ss_conf 799999999999999-6589999999999 No 32 >cd03452 MaoC_C MaoC_C The C-terminal hot dog fold of the MaoC (monoamine oxidase C) dehydratase regulatory protein. Orthologs of MaoC include PaaZ [Escherichia coli] and PaaN [Pseudomonas putida], which are putative ring-opening enzymes involved in phenylacetic acid degradation. The C-terminal domain of MaoC has sequence similarity to (R)-specific enoyl-CoA hydratase,Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. MaoC also has an N-terminal PutA domain like that found in the E. coli PutA proline dehydrogenase and other members of the aldehyde dehydrogenase family. Probab=31.84 E-value=41 Score=15.11 Aligned_cols=16 Identities=31% Similarity=0.480 Sum_probs=13.3 Q ss_pred CCCCCCEEEEEEEEEC Q ss_conf 7378998999999835 Q gi|254780715|r 23 KFSPGDTLCVKTIITE 38 (141) Q Consensus 23 ~f~~GD~v~V~~~i~e 38 (141) ..++||||.+.+.|.+ T Consensus 88 PV~~GDTi~~~~~V~e 103 (142) T cd03452 88 PVYPGDTIQVRLTCKR 103 (142) T ss_pred CCCCCCEEEEEEEEEE T ss_conf 9899999999999999 No 33 >TIGR00922 nusG transcription termination/antitermination factor NusG; InterPro: IPR001062 Bacterial transcription antitermination protein, nusG, is a component of the transcription complex and interacts with the termination factor Rho and RNA polymerase , . NusG is a bacterial transcriptional elongation factor involved in transcription termination and anti-termination .; GO: 0003711 transcription elongation regulator activity, 0006355 regulation of transcription DNA-dependent. Probab=30.49 E-value=44 Score=14.97 Aligned_cols=29 Identities=17% Similarity=0.338 Sum_probs=22.3 Q ss_pred CCCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEEC Q ss_conf 989737899899999983588774012345354313 Q gi|254780715|r 20 SLPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARS 55 (141) Q Consensus 20 ~~P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~ 55 (141) .--+|-+|+.|+| .+| -.+.|.|.|..+. T Consensus 136 ~~~~fE~Ge~Vrv----~dG---PF~~F~G~Veev~ 164 (193) T TIGR00922 136 VKIDFEVGEQVRV----NDG---PFANFTGTVEEVD 164 (193) T ss_pred CCCCCCCCCEEEE----ECC---CCCCCCEEEEEEE T ss_conf 3432357988898----038---8888514798880 No 34 >pfam05641 Agenet Agenet domain. This domain is related to the TUDOR domain pfam00567. The function of the agenet domain is unknown. This family currently only matches one of the two Agenet domains in the FMR proteins. Probab=30.46 E-value=44 Score=14.97 Aligned_cols=38 Identities=21% Similarity=0.302 Sum_probs=26.6 Q ss_pred CCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCCCCEEEEEE Q ss_conf 37899899999983588774012345354313666643388630 Q gi|254780715|r 24 FSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGINKNFTVRK 67 (141) Q Consensus 24 f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~~stftvRk 67 (141) |+.||.|.|... .+|- +-.-|.+.+|...+.. +|.|+= T Consensus 1 f~~G~~VEV~s~-~~g~--~gaWf~a~Vi~~~~~~---~~~V~Y 38 (68) T pfam05641 1 FSKGSEVEVSSE-EEGF--EGAWFRAKVLKELGED---KYKVEY 38 (68) T ss_pred CCCCCEEEEEEC-CCCC--CEEEEEEEEEEECCCC---EEEEEE T ss_conf 979999999755-8887--4078899999977998---799996 No 35 >COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis] Probab=30.03 E-value=36 Score=15.51 Aligned_cols=24 Identities=29% Similarity=0.329 Sum_probs=13.9 Q ss_pred CCCCCCCCEEEEEEEEECCCCCCC Q ss_conf 897378998999999835887740 Q gi|254780715|r 21 LPKFSPGDTLCVKTIITEGDKSRI 44 (141) Q Consensus 21 ~P~f~~GD~v~V~~~i~eg~k~R~ 44 (141) .--+.|||.|.|..+-..-+|.|+ T Consensus 44 ~i~I~~GD~V~Ve~~~~d~~kg~I 67 (75) T COG0361 44 RIRILPGDVVLVELSPYDLTKGRI 67 (75) T ss_pred EEEECCCCEEEEEECCCCCCCCCE T ss_conf 488579999999745665333558 No 36 >cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core. Probab=28.56 E-value=47 Score=14.76 Aligned_cols=42 Identities=12% Similarity=0.175 Sum_probs=25.8 Q ss_pred CCCCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCCCC Q ss_conf 7989737899899999983588774012345354313666643 Q gi|254780715|r 19 RSLPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGINK 61 (141) Q Consensus 19 ~~~P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~~s 61 (141) +.--.|+.||.|+|.+.-..-++.++ .|.-+=+..+.-|+++ T Consensus 49 r~~~~~~~GD~V~vrV~~V~~~~r~i-~~~~IgLtmrqp~lGk 90 (99) T cd04460 49 ETKRVLKVGDVVRARIVAVSLKERRP-RESKIGLTMRQPGLGK 90 (99) T ss_pred CCCCEECCCCEEEEEEEEEECCCCCC-CCCEEEECCCCCCCCC T ss_conf 27869847999999999980620676-7646650224788987 No 37 >PRK10476 multidrug resistance protein MdtN; Provisional Probab=28.28 E-value=48 Score=14.73 Aligned_cols=58 Identities=16% Similarity=0.238 Sum_probs=35.1 Q ss_pred HCCCCCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCC------C-----C---CCEEEEEEECCCCCCEEEEE Q ss_conf 02798973789989999998358877401234535431366------6-----6---43388630035613028999 Q gi|254780715|r 17 SKRSLPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGR------G-----I---NKNFTVRKISYGEGMNRLFP 79 (141) Q Consensus 17 ~k~~~P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~------G-----~---~stftvRki~~g~GVE~~fp 79 (141) ...++..+++|+-+.|++-...| +.|.|.|.++... + + ++|..-=|+.+.+.|-..|. T Consensus 254 ~Et~l~~v~~Gq~v~I~~Da~p~-----~~f~G~V~sI~~g~~~~~~~~~~~~lp~~natgn~~Kv~QRvPVrI~~d 325 (348) T PRK10476 254 RETDLKNIRVGDCATVYSMIDRG-----RPIEGKVDSIGWGVLPDDGGNVPRGLPYVPRSINWVRVAQRFPVRIMLD 325 (348) T ss_pred CHHHHCCCCCCCEEEEEEECCCC-----CEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEEEEEEC T ss_conf 27782527998989999976899-----7899999998878778100555445899799987688878985999988 No 38 >cd04455 S1_NusA S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three RNA binding domains (RBD's). The RBD's include one S1 domain and two KH domains that form an RNA binding surface. DNA transcription by RNA polymerase (RNAP) includes three phases - initiation, elongation, and termination. During initiation, sigma factors bind RNAP and target RNAP to specific promoters. During elongation, N-utilization substances (NusA, B, E, and G) replace sigma factors and regulate pausing, termination, and antitermination. NusA is cold-shock-inducible. Probab=28.15 E-value=48 Score=14.72 Aligned_cols=23 Identities=17% Similarity=0.468 Sum_probs=15.4 Q ss_pred CCCC--CCCCCCEEEEEEEEECCCC Q ss_conf 7989--7378998999999835887 Q gi|254780715|r 19 RSLP--KFSPGDTLCVKTIITEGDK 41 (141) Q Consensus 19 ~~~P--~f~~GD~v~V~~~i~eg~k 41 (141) ..+| .|++||.|++.+.-.+-.. T Consensus 34 eqip~E~~~~Gdrik~~i~~V~~~~ 58 (67) T cd04455 34 EQIPGESYRPGDRIKAYVLEVRKTS 58 (67) T ss_pred HCCCCCCCCCCCEEEEEEEEEEECC T ss_conf 9578866399998999999987469 No 39 >cd01288 FabZ FabZ is a 17kD beta-hydroxyacyl-acyl carrier protein (ACP) dehydratase that primarily catalyzes the dehydration of beta-hydroxyacyl-ACP to trans-2-acyl-ACP, the third step in the elongation phase of the bacterial/ plastid, type II, fatty-acid biosynthesis pathway. Probab=28.04 E-value=48 Score=14.71 Aligned_cols=27 Identities=22% Similarity=0.442 Sum_probs=18.6 Q ss_pred CCCCCEEEEEEEEECCCCCCCEEEEEEE Q ss_conf 3789989999998358877401234535 Q gi|254780715|r 24 FSPGDTLCVKTIITEGDKSRIQAYEGVC 51 (141) Q Consensus 24 f~~GD~v~V~~~i~eg~k~R~Q~F~Gvv 51 (141) ..|||++.+..++.. .+.++-.|.|.+ T Consensus 88 V~PGd~l~i~~~~~~-~~~~~~~~~~~~ 114 (131) T cd01288 88 VVPGDQLILEVELLK-LRRGIGKFKGKA 114 (131) T ss_pred CCCCCEEEEEEEEEE-EECCEEEEEEEE T ss_conf 899999999999999-769999999999 No 40 >PRK10559 p-hydroxybenzoic acid efflux subunit AaeA; Provisional Probab=27.83 E-value=48 Score=14.68 Aligned_cols=56 Identities=13% Similarity=0.169 Sum_probs=34.6 Q ss_pred HHCCCCCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCCCCEE---------------EEEEECCCCCCEEEE Q ss_conf 602798973789989999998358877401234535431366664338---------------863003561302899 Q gi|254780715|r 16 ESKRSLPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGINKNF---------------TVRKISYGEGMNRLF 78 (141) Q Consensus 16 ~~k~~~P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~~stf---------------tvRki~~g~GVE~~f 78 (141) ++..++..+++|+.+.|.. .+ ..+ .|.|.|.++- .|.++.| .-=|+.+-+.|-..+ T Consensus 197 fkETqL~~ir~Gq~v~I~~---~~-p~~--~f~G~V~si~-~g~~~~~s~~~~~~LP~~NatgnwvKv~QRvPVrI~l 267 (310) T PRK10559 197 MEETKLEGVRPGYRAEITP---LG-SNR--VLKGTVDSVA-AGVTNASSTRDSKGMATIDSNLEWVRLAQRVPVRIRL 267 (310) T ss_pred ECHHHCCCCCCCCEEEEEE---EC-CCC--EEEEEEEEEC-CCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEEEEEE T ss_conf 0522125389999799999---17-998--8999999887-4446632367523389968988748677874179997 No 41 >PRK08190 bifunctional enoyl-CoA hydratase/phosphate acetyltransferase; Validated Probab=27.60 E-value=49 Score=14.66 Aligned_cols=36 Identities=25% Similarity=0.384 Sum_probs=27.4 Q ss_pred CCCCCCEEEEEEEEECCCC-CCCEEEEEEEEEECCCC Q ss_conf 7378998999999835887-74012345354313666 Q gi|254780715|r 23 KFSPGDTLCVKTIITEGDK-SRIQAYEGVCIARSGRG 58 (141) Q Consensus 23 ~f~~GD~v~V~~~i~eg~k-~R~Q~F~GvvI~~~~~G 58 (141) ..++||+|.+++.+.|-.. .|.-.|.-.|....+.- T Consensus 95 PV~iGDtvtatVtV~ek~~~k~~V~L~~~~~nq~G~~ 131 (465) T PRK08190 95 PVRIGDTITVTVTVREKRPEKRIVLLDCRCTNQDGEV 131 (465) T ss_pred CCCCCCEEEEEEEEEEECCCCCEEEEEEEEECCCCCE T ss_conf 8889998999999999717889899997999069979 No 42 >pfam06940 DUF1287 Domain of unknown function (DUF1287). This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown. This family is related to pfam00877. Probab=27.02 E-value=50 Score=14.59 Aligned_cols=49 Identities=16% Similarity=0.374 Sum_probs=32.3 Q ss_pred CCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCCCCEEEEEEECCCCCCEEEE Q ss_conf 973789989999998358877401234535431366664338863003561302899 Q gi|254780715|r 22 PKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGINKNFTVRKISYGEGMNRLF 78 (141) Q Consensus 22 P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~~stftvRki~~g~GVE~~f 78 (141) -++.|||+|.- .. .|+- .--|+|..+++.. +.-+.+.|+-.|.--|-+. T Consensus 105 ~~yqpGDIV~w--~l-~~~~----~HIgIVsd~~~~~-g~p~viHNig~g~~eeD~L 153 (164) T pfam06940 105 EDYQPGDIVTW--ML-PGNL----PHIGIVSDRRRAD-GVPLVIHNIGAGPREEDIL 153 (164) T ss_pred HHCCCCCEEEE--EC-CCCC----CEEEEEECCCCCC-CCEEEEEECCCCCCHHHHH T ss_conf 66689787999--77-9997----4589983466888-9858999478885214443 No 43 >TIGR00008 infA translation initiation factor IF-1; InterPro: IPR004368 This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (IPR003029 from INTERPRO).; GO: 0003743 translation initiation factor activity, 0006413 translational initiation. Probab=26.90 E-value=47 Score=14.76 Aligned_cols=26 Identities=23% Similarity=0.298 Sum_probs=19.2 Q ss_pred CCCCCCCCCEEEEEEEEECCCCCCCE Q ss_conf 98973789989999998358877401 Q gi|254780715|r 20 SLPKFSPGDTLCVKTIITEGDKSRIQ 45 (141) Q Consensus 20 ~~P~f~~GD~v~V~~~i~eg~k~R~Q 45 (141) +.-.+-|||-|.|.+.-.+-.++|+- T Consensus 41 ~~iriLpGD~V~ve~SpYdl~~GRI~ 66 (69) T TIGR00008 41 NYIRILPGDKVKVELSPYDLTRGRII 66 (69) T ss_pred CEEEECCCCEEEEEECCCCCCCCCEE T ss_conf 51755479878998713648775087 No 44 >COG0231 Efp Translation elongation factor P (EF-P)/translation initiation factor 5A (eIF-5A) [Translation, ribosomal structure and biogenesis] Probab=26.45 E-value=51 Score=14.53 Aligned_cols=52 Identities=12% Similarity=0.279 Sum_probs=31.9 Q ss_pred CCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCC-CCEEEEEEECCCCCCEEEEECC Q ss_conf 97378998999999835887740123453543136666-4338863003561302899910 Q gi|254780715|r 22 PKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGI-NKNFTVRKISYGEGMNRLFPLY 81 (141) Q Consensus 22 P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~-~stftvRki~~g~GVE~~fpl~ 81 (141) -+|++|.++.. +|...++.-++= .+-|+|- -..+-++++..|.-+|.+|+-- T Consensus 7 ~~lr~G~~i~~-----dg~~~~V~~~~~---~KpGKg~a~vrvk~k~l~tG~~~e~~f~~~ 59 (131) T COG0231 7 SELRKGLYIVI-----DGEPYVVVEISH---VKPGKGGAFVRVKLKNLFTGKKVEKTFKAD 59 (131) T ss_pred HHCCCCCEEEE-----CCEEEEEEEEEE---CCCCCCCCEEEEEEEECCCCCEEEEEECCC T ss_conf 77268779998-----996899999787---269999857999999845898999997578 No 45 >cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea. Probab=26.20 E-value=52 Score=14.50 Aligned_cols=25 Identities=32% Similarity=0.405 Sum_probs=16.7 Q ss_pred CCCCCCCCEEEEEEEEECCCCCCCE Q ss_conf 8973789989999998358877401 Q gi|254780715|r 21 LPKFSPGDTLCVKTIITEGDKSRIQ 45 (141) Q Consensus 21 ~P~f~~GD~v~V~~~i~eg~k~R~Q 45 (141) ...|++||.|++.+.-.+-.+.|+. T Consensus 42 ~~~~~vGd~v~~kVi~id~e~~ri~ 66 (68) T cd05685 42 SDVVSVGDIVEVKVISIDEERGRIS 66 (68) T ss_pred HHCCCCCCEEEEEEEEEECCCCEEE T ss_conf 6857999999999999989999887 No 46 >TIGR02346 chap_CCT_theta T-complex protein 1, theta subunit; InterPro: IPR012721 Members of this eukaryotic family are part of the group II chaperonin complex called CCT (chaperonin containing TCP-1) or TRiC. The archaeal equivalent group II chaperonin is often called the thermosome. Both are somewhat related to the group I chaperonin of bacterial, GroEL/GroES. This family consists exclusively of the CCT theta chain (part of a paralogous family) from animals, plants, fungi, and other eukaryotes.; GO: 0005524 ATP binding, 0051082 unfolded protein binding, 0006457 protein folding. Probab=25.79 E-value=53 Score=14.45 Aligned_cols=56 Identities=21% Similarity=0.400 Sum_probs=39.9 Q ss_pred CHHHHHHHHHHHHHHHC----CCCCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCC Q ss_conf 35899979999997602----79897378998999999835887740123453543136666 Q gi|254780715|r 2 NIIDELDHEEMVRIESK----RSLPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGI 59 (141) Q Consensus 2 nli~~le~~~~~~~~~k----~~~P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~ 59 (141) |+|.+|-.+.+-...-+ -.+|-|.+ |.||| .++--|+=...+...|+||.+.-.|. T Consensus 170 dfL~~LvA~Ac~~v~P~~~~~GeiPyFnV-DniRV-~Ki~Ggs~~~S~v~~GmV~~reaeG~ 229 (554) T TIGR02346 170 DFLAQLVAKACITVLPKNPENGEIPYFNV-DNIRV-SKILGGSISNSEVLKGMVFKREAEGS 229 (554) T ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCCCCC-CCEEE-EEECCCCCCCCEEEECCEECCCCCCC T ss_conf 88999999887412788889886551145-60132-23207863477588511763178843 No 47 >TIGR02303 HpaG-C-term 4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase, C-terminal subunit; InterPro: IPR012684 This entry represents one of two subunits/domains of the bifunctional isomerase/decarboxylase involved in 4-hydroxyphenylacetate degradation . In Escherichia coli and some other species, this enzyme is encoded by a single polypeptide containing both this domain and the closely related N-terminal domain (IPR012686 from INTERPRO). In other species such as Pasteurella multocida, these domains are found as two separate proteins (usually as tandem genes). Together, these domains carry out the decarboxylation of 5-oxopent-3-ene-1,2,5-tricarboxylic acid (OPET) to 2-hydroxy-2,4-diene-1,7-dioate (HHDD) and the subsequent isomerization to 2-oxohept-3-ene-1,7-dioate (OHED).; GO: 0008704 5-carboxymethyl-2-hydroxymuconate delta-isomerase activity, 0018800 5-oxopent-3-ene-125-tricarboxylate decarboxylase activity. Probab=24.75 E-value=55 Score=14.33 Aligned_cols=18 Identities=22% Similarity=0.556 Sum_probs=10.9 Q ss_pred HCCCCCCCCCCCEEEEEE Q ss_conf 027989737899899999 Q gi|254780715|r 17 SKRSLPKFSPGDTLCVKT 34 (141) Q Consensus 17 ~k~~~P~f~~GD~v~V~~ 34 (141) .-|-+-+++|||.|++.+ T Consensus 219 TPKG~~dv~pGD~v~~ei 236 (249) T TIGR02303 219 TPKGLSDVKPGDVVRLEI 236 (249) T ss_pred CCCCCCCCCCCCEEEEEE T ss_conf 888752235587899977 No 48 >TIGR01652 ATPase-Plipid phospholipid-translocating P-type ATPase, flippase; InterPro: IPR006539 These sequences represent the P-type ATPase responsible for transporting phospholipids from one leaflet of bilayer membranes to the other . These ATPases are found only in eukaryotes. ; GO: 0000287 magnesium ion binding, 0004012 phospholipid-translocating ATPase activity, 0005524 ATP binding, 0015914 phospholipid transport, 0016021 integral to membrane. Probab=24.41 E-value=32 Score=15.78 Aligned_cols=12 Identities=33% Similarity=0.470 Sum_probs=9.3 Q ss_pred CCCCCCEEEEEE Q ss_conf 737899899999 Q gi|254780715|r 23 KFSPGDTLCVKT 34 (141) Q Consensus 23 ~f~~GD~v~V~~ 34 (141) +++|||+|+|+- T Consensus 202 ~~~VGDivKv~~ 213 (1249) T TIGR01652 202 DLRVGDIVKVKK 213 (1249) T ss_pred EEEECCEEEECC T ss_conf 024155789757 No 49 >TIGR01511 ATPase-IB1_Cu copper-translocating P-type ATPase; InterPro: IPR006403 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (F-, V- and A-ATPases contain rotary motors) and in the type of ions they transport , . F-ATPases (F1F0-ATPases) in mitochondria, chloroplasts and bacterial plasma membranes are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases) are primarily found in eukaryotic vacuoles, catalysing ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases) are found in Archaea and function like F-ATPases. P-ATPases (E1E2-ATPases) are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. P-ATPases (sometime known as E1-E2 ATPases) (3.6.3.- from EC) are found in bacteria and in a number of eukaryotic plasma membranes and organelles . P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, each of which transports a specific type of ion: H^+, Na^+, K^+, Mg^2+, Ca^2+, Ag^+ and Ag^2+, Zn^2+, Co^2+, Pb^2+, Ni^2+, Cd^2+, Cu^+ and Cu^2+. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2. This entry represents P-type ATPases that specialise in cation and copper transport; those transporting copper (3.6.3.4 from EC) have been classified as belonging to the IB subfamily , , . These proteins are involved in a variety of processes in both prokaryotes and eukaryotes. Some of these P-ATPases import copper into cells, such as in Arabidopsis sp., which require copper to create functional hormone receptors for ethylene signalling. Other P-ATPases are involved in copper export out of cells, such as occurs with the efflux of hepatic copper into the bile in eukaryotes. In bacteria, some of these P-ATPases play a role in osmotic adaptation. Certain copper ATPases have been implicated in both Wilson and Menkes diseases . More information about this protein can be found at Protein of the Month: ATP Synthases .; GO: 0004008 copper-exporting ATPase activity, 0005524 ATP binding, 0046872 metal ion binding, 0046873 metal ion transmembrane transporter activity, 0030001 metal ion transport, 0016020 membrane. Probab=23.68 E-value=24 Score=16.64 Aligned_cols=31 Identities=26% Similarity=0.492 Sum_probs=21.4 Q ss_pred CCCCCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEEC Q ss_conf 27989737899899999983588774012345354313 Q gi|254780715|r 18 KRSLPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARS 55 (141) Q Consensus 18 k~~~P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~ 55 (141) .-++-++++||+|+| ..|.|- +-.|++|.=+ T Consensus 88 ~v~v~~l~~GD~~~V----~pG~k~---PvDG~v~~G~ 118 (545) T TIGR01511 88 DVPVAELQPGDIVKV----LPGEKI---PVDGTVIEGE 118 (545) T ss_pred CCCHHHCCCCCEEEE----CCCCCC---CCCCEEECCC T ss_conf 723644188888997----578956---4040785132 No 50 >TIGR03630 arch_S17P archaeal ribosomal protein S17P. This model describes exclusively the archaeal ribosomal protein S17P. It excludes homologous ribosomal proteins S11 from eukaryotes and S17 from bacteria. Probab=23.44 E-value=58 Score=14.17 Aligned_cols=21 Identities=38% Similarity=0.534 Sum_probs=16.1 Q ss_pred CCEEEEEEEEEECCCCCCCEEEEE Q ss_conf 401234535431366664338863 Q gi|254780715|r 43 RIQAYEGVCIARSGRGINKNFTVR 66 (141) Q Consensus 43 R~Q~F~GvvI~~~~~G~~stftvR 66 (141) |=|.|+|+|++-+ ++.|+++. T Consensus 26 rGril~G~VvS~K---m~KTvvV~ 46 (102) T TIGR03630 26 RGQILEGVVVSDK---MNKTVVVE 46 (102) T ss_pred EEEEEEEEEEECC---CCCEEEEE T ss_conf 6789999999787---99639999 No 51 >TIGR02278 PaaN-DH phenylacetic acid degradation protein paaN; InterPro: IPR011966 This enzyme is proposed to act in the ring-opening step of phenylacetic acid degradation which follows ligation of the acid with coenzyme A (by PaaF) and hydroxylation by a multicomponent non-heme iron hydroxylase complex (PaaGHIJK). Gene symbols have been standardised in . This enzyme is related to aldehyde dehydrogenases.. Probab=23.40 E-value=58 Score=14.17 Aligned_cols=28 Identities=18% Similarity=0.380 Sum_probs=19.8 Q ss_pred CCCCCCCCEEEEEEEEECCCCCCCEEEE Q ss_conf 8973789989999998358877401234 Q gi|254780715|r 21 LPKFSPGDTLCVKTIITEGDKSRIQAYE 48 (141) Q Consensus 21 ~P~f~~GD~v~V~~~i~eg~k~R~Q~F~ 48 (141) |-...+||+|+|.+.++.-...+...++ T Consensus 631 l~PV~~dDsi~V~LT~Krk~p~~~~~~g 658 (690) T TIGR02278 631 LEPVKPDDSIQVRLTVKRKTPRKEKEYG 658 (690) T ss_pred CCCCCCCCCEEEEEEEEECCCCCCCCCC T ss_conf 3567998845899842203777786667 No 52 >TIGR01073 pcrA ATP-dependent DNA helicase PcrA; InterPro: IPR005751 The DNA helicase PcrA is found mainly in Gram-positive bacteria and belongs to a superfamily of helicases, together with Rep and UvrD helicases from Escherichia coli. The action of the 3'5' bacterial DNA helicase is based upon two separate but coupled activities, ssDNA translocation and duplex destabilisation, and is driven by energy derived from the continuous ATP-binding and hydrolysis events that take place in the active-site cleft. The resulting conformational changes that accompany these events underpin the coupling process and allow the helicase to translocate along the DNA, destabilising the duplex and separating the two strands in an active process .; GO: 0004003 ATP-dependent DNA helicase activity, 0006268 DNA unwinding during replication, 0005737 cytoplasm. Probab=23.14 E-value=59 Score=14.14 Aligned_cols=44 Identities=20% Similarity=0.449 Sum_probs=34.7 Q ss_pred CCCCC-CEEEEEEEEEECCCCCCCEEEEEEECCC-CCCEEEEECCCCC Q ss_conf 88774-0123453543136666433886300356-1302899910786 Q gi|254780715|r 39 GDKSR-IQAYEGVCIARSGRGINKNFTVRKISYG-EGMNRLFPLYSPM 84 (141) Q Consensus 39 g~k~R-~Q~F~GvvI~~~~~G~~stftvRki~~g-~GVE~~fpl~SP~ 84 (141) |+|-. -+.=.|+|++++|+|-++...+- +.+ +||-+..+-|-|. T Consensus 765 GDrv~H~~fG~GTVv~v~G~G~~~el~i~--FP~P~gvK~Ll~~FAPi 810 (811) T TIGR01073 765 GDRVSHKKFGVGTVVSVKGKGDDAELDIA--FPSPIGVKRLLAAFAPI 810 (811) T ss_pred CCCCCCCCCCEEEEEEEEECCCCCCEEEE--CCCCCCHHHHCCCCCCC T ss_conf 86103430000589888505557512542--67885412011334889 No 53 >pfam07653 SH3_2 Variant SH3 domain. SH3 (Src homology 3) domains are often indicative of a protein involved in signal transduction related to cytoskeletal organisation. First described in the Src cytoplasmic tyrosine kinase. The structure is a partly opened beta barrel. Probab=22.99 E-value=60 Score=14.12 Aligned_cols=15 Identities=20% Similarity=0.113 Sum_probs=11.5 Q ss_pred CCCCCCCEEEEEEEE Q ss_conf 973789989999998 Q gi|254780715|r 22 PKFSPGDTLCVKTII 36 (141) Q Consensus 22 P~f~~GD~v~V~~~i 36 (141) -.|+.||+|.|.-.. T Consensus 16 L~f~~Gdii~v~~~~ 30 (53) T pfam07653 16 LTLKKGDVVKVLDKD 30 (53) T ss_pred CCCCCCCEEEEEEEC T ss_conf 789899999999954 No 54 >PRK13198 ureB urease subunit beta; Reviewed Probab=22.96 E-value=60 Score=14.11 Aligned_cols=41 Identities=24% Similarity=0.494 Sum_probs=28.7 Q ss_pred HCCCCC-----CCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCC Q ss_conf 027989-----737899899999983588774012345354313666 Q gi|254780715|r 17 SKRSLP-----KFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRG 58 (141) Q Consensus 17 ~k~~~P-----~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G 58 (141) ...++| .|-|||+..|.+ |.-|.+.++.-|-|+|=.--+.| T Consensus 87 ~RLdIPAGtavRFEPG~~k~V~L-V~~gG~r~v~GfngLv~Gw~g~~ 132 (158) T PRK13198 87 KRLNISSTTAIRFEPGDETEVPL-IPFGGKQTLYGFNNLVDGWTGEG 132 (158) T ss_pred CCCCCCCCCEEEECCCCEEEEEE-EECCCCEEEEECCCCCCCCCCCC T ss_conf 53176787737528898479999-98078458982585323666886 No 55 >PRK09014 rfaH transcriptional activator RfaH; Provisional Probab=22.39 E-value=61 Score=14.04 Aligned_cols=25 Identities=20% Similarity=0.473 Sum_probs=11.6 Q ss_pred CCCCCEEEEEEEEECCCCCCCEEEEEEEEEEC Q ss_conf 37899899999983588774012345354313 Q gi|254780715|r 24 FSPGDTLCVKTIITEGDKSRIQAYEGVCIARS 55 (141) Q Consensus 24 f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~ 55 (141) |.+||.|+|. +|. .+-|+|+++..+ T Consensus 110 ~~~Gd~V~I~----~GP---f~g~~g~v~~~~ 134 (162) T PRK09014 110 PKPGDKVIIT----EGA---FEGIQAIYTEPD 134 (162) T ss_pred CCCCCEEEEE----ECC---CCCCEEEEEEEC T ss_conf 9999999994----379---998089999886 No 56 >cd05708 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea. Probab=21.98 E-value=62 Score=13.99 Aligned_cols=22 Identities=32% Similarity=0.534 Sum_probs=14.8 Q ss_pred CCCCCCEEEEEEEEECCCCCCC Q ss_conf 7378998999999835887740 Q gi|254780715|r 23 KFSPGDTLCVKTIITEGDKSRI 44 (141) Q Consensus 23 ~f~~GD~v~V~~~i~eg~k~R~ 44 (141) .|++||.|+|.+.-.+..+.|+ T Consensus 47 ~~~~Gd~V~vkVl~iD~e~~rI 68 (77) T cd05708 47 LFRVGDKVRAKVLKIDAEKKRI 68 (77) T ss_pred HCCCCCEEEEEEEEEECCCCEE T ss_conf 1689999999999998999999 No 57 >PRK03598 hypothetical protein; Provisional Probab=21.82 E-value=63 Score=13.97 Aligned_cols=45 Identities=24% Similarity=0.251 Sum_probs=30.1 Q ss_pred CCCCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCCCCEEEEEEECCC Q ss_conf 79897378998999999835887740123453543136666433886300356 Q gi|254780715|r 19 RSLPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGINKNFTVRKISYG 71 (141) Q Consensus 19 ~~~P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~~stftvRki~~g 71 (141) .+++.+++|+.+.|++.-..+ +.|.|.|-.+.- .+.||-+++..+ T Consensus 249 ~~i~~v~~Gq~v~i~~da~p~-----~~f~G~V~~Isp---~a~~tp~~~~t~ 293 (331) T PRK03598 249 RNLGQAQPGRKVLVYTDGRPD-----KPYHGQIGFVSP---TAEFTPKTVETP 293 (331) T ss_pred HHHHHCCCCCEEEEEEECCCC-----CEEEEEEEEECC---CCCCCCCCCCCC T ss_conf 999528899989999946999-----689999999856---443678755566 No 58 >cd06201 SiR_like2 Cytochrome p450- like alpha subunits of E. coli sulfite reductase (SiR) multimerize with beta subunits to catalyze the NADPH dependent reduction of sulfite to sulfide. Beta subunits have an Fe4S4 cluster and a siroheme, while the alpha subunits (cysJ gene) are of the cytochrome p450 (CyPor) family having FAD and FMN as prosthetic groups and utilizing NADPH. Cypor (including cyt -450 reductase, nitric oxide synthase, and methionine synthase reductase) are ferredoxin reductase (FNR)-like proteins with an additional N-terminal FMN domain and a connecting sub-domain inserted within the flavin binding portion of the FNR-like domain. The connecting domain orients the N-terminal FMN domain with the C-terminal FNR domain. NADPH cytochrome p450 reductase (CYPOR) serves as an electron donor in several oxygenase systems and is a component of nitric oxide synthases and methionine synthase reductases. CYPOR transfers two electrons from NADPH to the heme of cytochrome p450 via F Probab=21.78 E-value=63 Score=13.96 Aligned_cols=56 Identities=20% Similarity=0.530 Sum_probs=33.3 Q ss_pred CCCCCCCCCCEEEEEEEEECCC-CCCC--------EEEEEEEEEECCCCCCCEEEEEEECCCCCCEEEE Q ss_conf 7989737899899999983588-7740--------1234535431366664338863003561302899 Q gi|254780715|r 19 RSLPKFSPGDTLCVKTIITEGD-KSRI--------QAYEGVCIARSGRGINKNFTVRKISYGEGMNRLF 78 (141) Q Consensus 19 ~~~P~f~~GD~v~V~~~i~eg~-k~R~--------Q~F~GvvI~~~~~G~~stftvRki~~g~GVE~~f 78 (141) ..+|.|.+||.+.|. .++. ..|. .-+.-+|+.++..|+.|+++-. .--|--|.-.+ T Consensus 79 ~~~p~f~aGDLl~i~---Pp~~~~~R~YSiAs~~~dg~~~l~Vr~~~~GlcS~~L~~-L~~Gd~i~~~i 143 (289) T cd06201 79 KGLPSFEAGDLLGIL---PPGSDVPRFYSLASSSSDGFLEICVRKHPGGLCSGYLHG-LKPGDTIKAFI 143 (289) T ss_pred CCCCCCCCCCEEEEC---CCCCCCCCCCCCCCCCCCCEEEEEEEECCCCCCHHHHHC-CCCCCEEEEEE T ss_conf 668888877732334---899998752240436999979999996799743677715-99989899998 No 59 >PRK13980 NAD synthetase; Provisional Probab=21.69 E-value=15 Score=17.89 Aligned_cols=41 Identities=20% Similarity=0.312 Sum_probs=31.6 Q ss_pred EEEEEEEEEECCCCCCCEEEEEEECCCCCCEEEEECCCCCEE Q ss_conf 123453543136666433886300356130289991078610 Q gi|254780715|r 45 QAYEGVCIARSGRGINKNFTVRKISYGEGMNRLFPLYSPMIQ 86 (141) Q Consensus 45 Q~F~GvvI~~~~~G~~stftvRki~~g~GVE~~fpl~SP~i~ 86 (141) .-|.|+||+.. .|++|+.+.-=.+.-.|-|+++-+..|... T Consensus 26 ~g~kg~VlGlS-GGIDSavva~La~~Alg~~~v~~v~mP~~~ 66 (264) T PRK13980 26 AGFKGVVLGLS-GGIDSAVVAYLAVKALGKENVLALLMPYRV 66 (264) T ss_pred HCCCEEEEECC-CCHHHHHHHHHHHHHCCCCCEEEEECCCCC T ss_conf 09980999798-688899999999985496606899898999 No 60 >TIGR01700 PNPH purine nucleoside phosphorylase I, inosine and guanosine-specific; InterPro: IPR011270 This entry represents a family of bacterial and metazoan purine phosphorylases acting primarily on inosine and guanosine and not acting on adenosine. PNP-I refers to the nomenclature from Bacillus stearothermophilus where PHP-II refers to the nucleotidase acting on adenosine as the primary substrate. The bacterial enzymes (PUNA) are typified by the Bacillus PupG protein which is involved in the metabolism of nucleosides as a carbon source. Several metazoan enzymes (PNPH) are well characterised including the human and bovine enzymes which have been crystallised. ; GO: 0004731 purine-nucleoside phosphorylase activity, 0006139 nucleobase nucleoside nucleotide and nucleic acid metabolic process. Probab=21.60 E-value=55 Score=14.33 Aligned_cols=13 Identities=23% Similarity=0.531 Sum_probs=7.0 Q ss_pred CCCCCCCCEEEEE Q ss_conf 8973789989999 Q gi|254780715|r 21 LPKFSPGDTLCVK 33 (141) Q Consensus 21 ~P~f~~GD~v~V~ 33 (141) .|+|++||++-|. T Consensus 97 N~~F~~GDlmlI~ 109 (259) T TIGR01700 97 NTEFKVGDLMLIR 109 (259) T ss_pred CCCCCCCCEEEEC T ss_conf 7776677778971 No 61 >cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure". Probab=21.57 E-value=64 Score=13.94 Aligned_cols=34 Identities=21% Similarity=0.435 Sum_probs=21.8 Q ss_pred HCCCCCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEE Q ss_conf 02798973789989999998358877401234535431 Q gi|254780715|r 17 SKRSLPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIAR 54 (141) Q Consensus 17 ~k~~~P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~ 54 (141) .|++.|.+++||.|=- ++...++.- --|=.|+.- T Consensus 43 TKknrP~L~~GdlVYa--RV~~a~~~~--e~EL~Cvd~ 76 (86) T cd05790 43 TKRNRPNLNVGDLVYA--RVVKANRDM--EPELSCVDS 76 (86) T ss_pred CCCCCCCCCCCCEEEE--EEEECCCCC--CEEEEEECC T ss_conf 6556887887889999--998748999--704898888 No 62 >pfam11302 DUF3104 Protein of unknown function (DUF3104). This family of proteins with unknown function appears to be restricted to Cyanobacteria. Probab=21.49 E-value=64 Score=13.93 Aligned_cols=51 Identities=27% Similarity=0.417 Sum_probs=34.5 Q ss_pred CCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCC----CCCEEEEEEECCCC Q ss_conf 9737899899999983588774012345354313666----64338863003561 Q gi|254780715|r 22 PKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRG----INKNFTVRKISYGE 72 (141) Q Consensus 22 P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G----~~stftvRki~~g~ 72 (141) ..+++||+|-|.-.-..+.+....-.-|-||...+.. ..+-|-|-++=.|+ T Consensus 4 L~Vk~Gd~ViV~~~~~~~~~~~~dWWmg~Vi~~~ggar~P~~~tlFQVadVDtG~ 58 (75) T pfam11302 4 LSVKPGDTVIVEANQENGQKDSKDWWMGQVIHCEGGARDPRVPTLFQVADVDTGE 58 (75) T ss_pred EEECCCCEEEEECCCCCCCCCCCCCEEEEEEECCCCCCCCCCCCCEEEEECCCCC T ss_conf 3627998999914844577789981789999816854489998417999837993 No 63 >PRK12442 translation initiation factor IF-1; Reviewed Probab=21.29 E-value=64 Score=13.90 Aligned_cols=10 Identities=20% Similarity=0.411 Sum_probs=3.8 Q ss_pred CCCCEEEEEE Q ss_conf 7899899999 Q gi|254780715|r 25 SPGDTLCVKT 34 (141) Q Consensus 25 ~~GD~v~V~~ 34 (141) -+||.|.|.+ T Consensus 48 l~GD~V~VEl 57 (87) T PRK12442 48 LAGDRVTLEL 57 (87) T ss_pred CCCCEEEEEE T ss_conf 6899899998 No 64 >pfam12148 DUF3590 Protein of unknown function (DUF3590). This domain is found in eukaryotes, and is typically between 83 and 97 amino acids in length. It is found in association with pfam00097, pfam02182, pfam00628, pfam00240. There are two conserved sequence motifs: RAR and NYN. The domain is part of the protein NIRF which has zinc finger and ubiquitinating domains. The function of this domain is likely to be mainly structural, however this has not been confirmed. Probab=21.11 E-value=46 Score=14.81 Aligned_cols=16 Identities=19% Similarity=0.221 Sum_probs=9.3 Q ss_pred CCCCCCEEEEEEEEEC Q ss_conf 7378998999999835 Q gi|254780715|r 23 KFSPGDTLCVKTIITE 38 (141) Q Consensus 23 ~f~~GD~v~V~~~i~e 38 (141) ++.+||+|.|.|.+.+ T Consensus 65 ~L~vG~~VmvNYN~d~ 80 (85) T pfam12148 65 ELEVGQVVMVNYNPDE 80 (85) T ss_pred HCCCCCEEEEECCCCC T ss_conf 8775649999758798 No 65 >cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog. Probab=21.09 E-value=65 Score=13.88 Aligned_cols=23 Identities=26% Similarity=0.439 Sum_probs=15.2 Q ss_pred CCCCCCEEEEEEEEECCCCCCCE Q ss_conf 73789989999998358877401 Q gi|254780715|r 23 KFSPGDTLCVKTIITEGDKSRIQ 45 (141) Q Consensus 23 ~f~~GD~v~V~~~i~eg~k~R~Q 45 (141) .|++||.|.+.+.-.+..+.|++ T Consensus 44 ~~k~Gd~v~~kVi~iD~~k~rIs 66 (68) T cd05688 44 VVNVGDEVEVKVLKIDKERKRIS 66 (68) T ss_pred HCCCCCEEEEEEEEEECCCCEEC T ss_conf 14799999999999999979864 No 66 >TIGR03516 ppisom_GldI peptidyl-prolyl isomerase, gliding motility-associated. Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldI is a FKBP-type peptidyl-prolyl cis-trans isomerase (pfam00254) linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. Knockout of this gene abolishes the gliding phenotype. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. This family is only found in Bacteroidetes containing the suite of genes proposed to confer the gliding motility phenotype. Probab=20.79 E-value=66 Score=13.84 Aligned_cols=69 Identities=17% Similarity=0.129 Sum_probs=37.4 Q ss_pred CCCCCEEEEEEEEECCCCC-------C--CEEEEE--EEEE-----E--CCCCCCCEEEEEEEC-CC-CCCEEEEECCCC Q ss_conf 3789989999998358877-------4--012345--3543-----1--366664338863003-56-130289991078 Q gi|254780715|r 24 FSPGDTLCVKTIITEGDKS-------R--IQAYEG--VCIA-----R--SGRGINKNFTVRKIS-YG-EGMNRLFPLYSP 83 (141) Q Consensus 24 f~~GD~v~V~~~i~eg~k~-------R--~Q~F~G--vvI~-----~--~~~G~~stftvRki~-~g-~GVE~~fpl~SP 83 (141) =..||+|.|+|.+..-+.+ + .+...| -+|. . =..|-..+|.+=-.. +| .|-.-.+|-+|| T Consensus 86 P~~gd~V~~~Y~~~~ldG~~~~ss~~~gp~~f~v~~~~vi~G~~egl~lm~~Ge~~~~~iPs~LaYG~~G~~~~I~pn~~ 165 (177) T TIGR03516 86 PEFGDLVTFEYDIRALDGDVIYSEEELGPQTYKVDQQDLFSGLRDGLKLMKEGETATFLFPSHKAYGYYGDQNKIGPNLP 165 (177) T ss_pred CCCCCEEEEEEEEEECCCCEEEEECCCCCEEEEECCCCCCHHHHHHHHHCCCCCEEEEEECCHHCCCCCCCCCCCCCCCC T ss_conf 99999899999999768988874034686569855656464899999855789789999573004466788995496985 Q ss_pred CEEEEEEEE Q ss_conf 610122200 Q gi|254780715|r 84 MIQDITVIR 92 (141) Q Consensus 84 ~i~~Iev~r 92 (141) ++-.|+++. T Consensus 166 Lif~v~Ll~ 174 (177) T TIGR03516 166 IISTVTLLN 174 (177) T ss_pred EEEEEEEEE T ss_conf 999999973 No 67 >pfam07154 DUF1392 Protein of unknown function (DUF1392). This family consists of several hypothetical cyanobacterial proteins of around 150 residues in length which seem to be specific to Anabaena species. The function of this family is unknown. Probab=20.61 E-value=67 Score=13.81 Aligned_cols=34 Identities=29% Similarity=0.514 Sum_probs=23.2 Q ss_pred CCCCCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEE Q ss_conf 2798973789989999998358877401234535431 Q gi|254780715|r 18 KRSLPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIAR 54 (141) Q Consensus 18 k~~~P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~ 54 (141) ..+-|.|.-||.|.+... .+|.|.|+ ..|+.+-. T Consensus 82 tv~kp~F~LGd~V~~~f~-~~~pkqRl--IlGv~lv~ 115 (150) T pfam07154 82 TLSKPAFALGDRVLLRFA-SHGPKQRL--ILGVSLVN 115 (150) T ss_pred ECCCCCEECCCEEEEEEC-CCCCCEEE--EEEEEEEC T ss_conf 306872224778999845-99984579--99899862 No 68 >KOG3901 consensus Probab=20.52 E-value=31 Score=15.93 Aligned_cols=27 Identities=33% Similarity=0.454 Sum_probs=21.9 Q ss_pred ECCHHH-HHHHHHHCCCCCCEEEHHHHC Q ss_conf 002046-787687508884102201200 Q gi|254780715|r 92 RRGKVR-RSKLYYLQDLRGKAARIKENT 118 (141) Q Consensus 92 r~gkvR-rakLyYLR~~~gk~arik~~~ 118 (141) ++||++ -.=+|+||.-+.|.+|+++-. T Consensus 56 ~rgk~~veD~~f~lRkDpkK~~Rv~eLL 83 (109) T KOG3901 56 KRGKVKVEDFKFLLRKDPKKLGRVKELL 83 (109) T ss_pred CCCCEEHHHHHHHHHHCHHHHHHHHHHH T ss_conf 4675008889999970858886899999 Done!