Query 025294
Match_columns 255
No_of_seqs 136 out of 809
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 04:23:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025294.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025294hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK05309 30S ribosomal protein 100.0 7.1E-43 1.5E-47 288.6 15.4 114 133-255 15-128 (128)
2 PRK09607 rps11p 30S ribosomal 100.0 3.2E-42 7E-47 286.5 15.1 113 134-255 8-129 (132)
3 PF00411 Ribosomal_S11: Riboso 100.0 1.7E-42 3.6E-47 278.8 12.7 110 136-254 1-110 (110)
4 COG0100 RpsK Ribosomal protein 100.0 8.6E-42 1.9E-46 282.6 14.5 114 133-255 16-129 (129)
5 TIGR03632 bact_S11 30S ribosom 100.0 1.9E-41 4.1E-46 272.4 14.7 108 136-252 1-108 (108)
6 PTZ00129 40S ribosomal protein 100.0 2.6E-41 5.7E-46 285.7 15.6 116 130-254 23-147 (149)
7 KOG0408 Mitochondrial/chloropl 100.0 9.6E-40 2.1E-44 280.1 14.2 137 101-255 52-190 (190)
8 CHL00041 rps11 ribosomal prote 100.0 6.1E-38 1.3E-42 255.2 14.5 106 133-247 11-116 (116)
9 TIGR03628 arch_S11P archaeal r 100.0 4.6E-37 1E-41 250.1 13.9 104 135-247 2-114 (114)
10 PTZ00090 40S ribosomal protein 100.0 5.5E-36 1.2E-40 266.0 15.7 112 134-255 117-233 (233)
11 KOG0407 40S ribosomal protein 99.9 2.4E-24 5.3E-29 175.9 12.9 121 128-254 9-135 (139)
12 cd00432 Ribosomal_L18_L5e Ribo 97.9 0.00022 4.9E-09 56.5 10.6 89 133-222 9-100 (103)
13 PRK08569 rpl18p 50S ribosomal 97.4 0.0041 8.9E-08 55.5 12.6 107 131-254 28-142 (193)
14 PF00861 Ribosomal_L18p: Ribos 97.3 0.0021 4.6E-08 52.6 9.6 88 134-222 22-114 (119)
15 TIGR00060 L18_bact ribosomal p 97.2 0.005 1.1E-07 50.8 10.5 71 135-208 24-95 (114)
16 CHL00139 rpl18 ribosomal prote 97.2 0.0058 1.2E-07 49.9 10.4 71 135-206 15-88 (109)
17 PRK05593 rplR 50S ribosomal pr 97.0 0.0077 1.7E-07 49.7 10.2 72 134-206 23-96 (117)
18 COG0256 RplR Ribosomal protein 96.4 0.056 1.2E-06 45.4 10.6 77 134-211 28-109 (125)
19 PTZ00032 60S ribosomal protein 95.7 0.09 2E-06 47.6 9.7 86 133-223 103-203 (211)
20 PTZ00069 60S ribosomal protein 77.0 19 0.00042 34.4 9.2 59 135-195 48-112 (300)
21 cd05313 NAD_bind_2_Glu_DH NAD( 58.7 17 0.00036 33.7 4.7 64 169-241 9-72 (254)
22 PF14877 mIF3: Mitochondrial t 54.3 36 0.00078 30.4 5.9 74 158-244 4-80 (181)
23 cd01076 NAD_bind_1_Glu_DH NAD( 49.1 30 0.00065 31.1 4.6 64 169-241 2-65 (227)
24 PLN02477 glutamate dehydrogena 45.2 45 0.00098 33.0 5.5 61 171-240 179-239 (410)
25 COG4782 Uncharacterized protei 35.2 1.6E+02 0.0036 29.2 7.5 52 158-209 151-202 (377)
26 PRK14030 glutamate dehydrogena 33.1 85 0.0018 31.6 5.4 73 156-243 192-264 (445)
27 cd07996 WGR_MMR_like WGR domai 31.5 1.3E+02 0.0029 21.7 5.0 45 153-198 24-72 (74)
28 PTZ00079 NADP-specific glutama 29.4 1.1E+02 0.0024 30.9 5.5 72 155-241 200-271 (454)
29 PRK09414 glutamate dehydrogena 25.9 1.1E+02 0.0024 30.6 4.8 61 171-240 205-265 (445)
30 PF00208 ELFV_dehydrog: Glutam 23.3 67 0.0015 29.3 2.6 61 173-241 6-66 (244)
31 cd05211 NAD_bind_Glu_Leu_Phe_V 23.2 1.3E+02 0.0029 26.8 4.4 39 195-241 19-57 (217)
32 PRK14031 glutamate dehydrogena 21.9 1.7E+02 0.0036 29.5 5.1 60 171-239 201-260 (444)
No 1
>PRK05309 30S ribosomal protein S11; Validated
Probab=100.00 E-value=7.1e-43 Score=288.65 Aligned_cols=114 Identities=41% Similarity=0.550 Sum_probs=109.9
Q ss_pred ccceEEEEEccCCCeEEEEEcCCCCEEEEEeccCcccccCCCCCchhHHHHHHHHHHHHHHHcCCcEEEEEEEccCCCcc
Q 025294 133 HSSEFVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGFTYFKK 212 (255)
Q Consensus 133 ~~~~IlhI~sT~NNTiITlTD~~Gnvl~~~SsGs~~GFKg~rKsT~~AAq~aae~i~~kakelGik~V~V~vKG~G~gR~ 212 (255)
...+|+||++|+|||||||||.+|+++.|.|||++ ||||++|+||||||++|+.++++|+++||+.|+|+|||+|+||
T Consensus 15 ~~~gi~hI~~t~NNTiitlTd~~G~~~~~~S~G~~-gfKg~rK~T~~Aa~~aa~~~~~~~~~~gi~~v~v~ikG~G~Gr- 92 (128)
T PRK05309 15 IPSGVAHIHATFNNTIVTITDRQGNVISWASAGGL-GFKGSRKSTPYAAQVAAEDAAKKAKEHGMKTVEVFVKGPGSGR- 92 (128)
T ss_pred cceeEEEEEccCCCEEEEEEcCCCCEEEEEecCcc-EeCCCccCCHHHHHHHHHHHHHHHHHcCCcEEEEEEECCCCcH-
Confidence 45699999999999999999999999999999999 9999999999999999999999999999999999999999997
Q ss_pred hHHHHHHHHhcccCCCCCCCeEEEEecCCCCCCCCCCCCCCCC
Q 025294 213 KRQAIMSFREGFANSRDQNPIVYIEDTTRRPHNGCRLPKKRRI 255 (255)
Q Consensus 213 k~aaIkaL~~G~~~~r~glkI~sI~D~TpiPhNGCRpkK~RRv 255 (255)
+++|++|+. .|++|++|+|+||+|||||||||+|||
T Consensus 93 -~~air~L~~------~glkI~~I~D~TpiphNGcR~~K~RRv 128 (128)
T PRK05309 93 -ESAIRALQA------AGLEVTSIKDVTPIPHNGCRPPKRRRV 128 (128)
T ss_pred -HHHHHHHHH------CCCEEEEEEEcCCCCCCCcCcCCCCCC
Confidence 799999975 689999999999999999999999997
No 2
>PRK09607 rps11p 30S ribosomal protein S11P; Reviewed
Probab=100.00 E-value=3.2e-42 Score=286.47 Aligned_cols=113 Identities=31% Similarity=0.328 Sum_probs=107.2
Q ss_pred cceEEEEEccCCCeEEEEEcCCCC-EEEEEeccCcccccCCCCCchhHHHHHHHHHHHHHHHcCCcEEEEEEEc------
Q 025294 134 SSEFVHIKLMRNNTFVTVTDSKGN-KRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGLKSVVVRVKG------ 206 (255)
Q Consensus 134 ~~~IlhI~sT~NNTiITlTD~~Gn-vl~~~SsGs~~GFKg~rKsT~~AAq~aae~i~~kakelGik~V~V~vKG------ 206 (255)
..+|+||++|+|||||||||.+|+ ++.|.|+|.+ ||||++|+||||||.||++++++|+++||+.|+|+|||
T Consensus 8 ~~gi~hI~as~NNTivtvTD~~G~~~~~~~S~G~~-g~kg~kK~TpyAAq~aae~~~~~~~~~Gi~~v~v~vkG~Ggn~~ 86 (132)
T PRK09607 8 KWGIAHIYASFNNTIITITDLTGAETIAKSSGGMV-VKADRDESSPYAAMQAAEKAAEDAKEKGITGVHIKVRAPGGNGQ 86 (132)
T ss_pred eeeEEEEEcccCCeEEEEEcCCCCEEEEEecCcce-eeCCCccCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEecCCCCC
Confidence 459999999999999999999996 9999999999 99999999999999999999999999999999999999
Q ss_pred --cCCCcchHHHHHHHHhcccCCCCCCCeEEEEecCCCCCCCCCCCCCCCC
Q 025294 207 --FTYFKKKRQAIMSFREGFANSRDQNPIVYIEDTTRRPHNGCRLPKKRRI 255 (255)
Q Consensus 207 --~G~gR~k~aaIkaL~~G~~~~r~glkI~sI~D~TpiPhNGCRpkK~RRv 255 (255)
+|+|| ++||++|+. .+++|.+|+|+||+|||||||||+||+
T Consensus 87 ~~~G~Gr--~~airal~~------~glkI~~I~DvTpiPhNGCRp~K~RR~ 129 (132)
T PRK09607 87 KSPGPGA--QAAIRALAR------AGLRIGRIEDVTPIPHDGTRPPGGRRG 129 (132)
T ss_pred cCCCCcH--HHHHHHHHH------CCCEEEEEEEcCCCCCCCCCCCCCCCC
Confidence 67775 899999975 699999999999999999999999996
No 3
>PF00411 Ribosomal_S11: Ribosomal protein S11; InterPro: IPR001971 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S11 [] plays an essential role in selecting the correct tRNA in protein biosynthesis. It is located on the large lobe of the small ribosomal subunit. On the basis of sequence similarities, S11 belongs to a family of bacterial, archaeal and eukaryotic ribosomal proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2YKR_K 3U5C_O 3O2Z_H 3IZB_K 3U5G_O 3O30_H 1S1H_K 3BBN_K 2XZN_K 2XZM_K ....
Probab=100.00 E-value=1.7e-42 Score=278.79 Aligned_cols=110 Identities=44% Similarity=0.639 Sum_probs=102.9
Q ss_pred eEEEEEccCCCeEEEEEcCCCCEEEEEeccCcccccCCCCCchhHHHHHHHHHHHHHHHcCCcEEEEEEEccCCCcchHH
Q 025294 136 EFVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGFTYFKKKRQ 215 (255)
Q Consensus 136 ~IlhI~sT~NNTiITlTD~~Gnvl~~~SsGs~~GFKg~rKsT~~AAq~aae~i~~kakelGik~V~V~vKG~G~gR~k~a 215 (255)
+|+||++|+|||||||||.+|++++|.|||++ ||||++|+|+|||+++++.++++|+++||+.|+|+|||+|+|| ++
T Consensus 1 giihI~~s~NNt~vtlTd~~G~~~~~~S~G~~-gfK~~rk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ikG~g~gr--~~ 77 (110)
T PF00411_consen 1 GIIHIKSSFNNTIVTLTDLKGNVLFWSSAGSL-GFKGARKSTPYAAQQAAEKIAKKAKELGIKTVRVKIKGFGPGR--EA 77 (110)
T ss_dssp EEEEEEEESSEEEEEEEETTSEEEEEEETTTS-STTTTCGSSHHHHHHHHHHHHHHHHCTTEEEEEEEEESSSTTH--HH
T ss_pred CEEEEEecCCCEEEEEECCCCCEEEEEecccc-ccccccccCHHHHHHHHHHHHHHHHHcCCeEEEEEEcCCCccH--HH
Confidence 68999999999999999999999999999999 9999999999999999999999999999999999999999997 79
Q ss_pred HHHHHHhcccCCCCCCCeEEEEecCCCCCCCCCCCCCCC
Q 025294 216 AIMSFREGFANSRDQNPIVYIEDTTRRPHNGCRLPKKRR 254 (255)
Q Consensus 216 aIkaL~~G~~~~r~glkI~sI~D~TpiPhNGCRpkK~RR 254 (255)
+|++|+. .+++|++|+|+||+|||||||||+||
T Consensus 78 ~lk~l~~------~gl~I~~I~D~T~iphnGcR~kK~RR 110 (110)
T PF00411_consen 78 ALKALKK------SGLKIVSITDVTPIPHNGCRPKKKRR 110 (110)
T ss_dssp HHHHHHH------TTSEEEEEEEETT--SSSS--TTTTT
T ss_pred HHHHHHh------cCCEEEEEEeecCCCCCCCCCCCCCC
Confidence 9999975 58999999999999999999999998
No 4
>COG0100 RpsK Ribosomal protein S11 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=8.6e-42 Score=282.60 Aligned_cols=114 Identities=44% Similarity=0.566 Sum_probs=109.9
Q ss_pred ccceEEEEEccCCCeEEEEEcCCCCEEEEEeccCcccccCCCCCchhHHHHHHHHHHHHHHHcCCcEEEEEEEccCCCcc
Q 025294 133 HSSEFVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGFTYFKK 212 (255)
Q Consensus 133 ~~~~IlhI~sT~NNTiITlTD~~Gnvl~~~SsGs~~GFKg~rKsT~~AAq~aae~i~~kakelGik~V~V~vKG~G~gR~ 212 (255)
..++++||++|+||||||+||+.||++.|.|+|++ |||+.+|+||||||++|+.+++.++++||+.|+|+|||+|+||
T Consensus 16 i~~GvahI~asfNNTivtitD~~Gn~i~wassG~~-gfk~~rk~tpyAA~~aa~~aa~~a~e~Gi~~v~v~vkgpG~Gr- 93 (129)
T COG0100 16 IADGVAHIHASFNNTIVTITDLTGNVIIWASSGGM-GFKGSRKSTPYAAQLAAEDAAKKAKEHGIKSVEVKVKGPGPGR- 93 (129)
T ss_pred cccceEEEEcccCCcEEEecCCCCCEEEEEecCCc-eEcCCCCCCHHHHHHHHHHHHHHHHHhCccEEEEEEECCCCcH-
Confidence 35699999999999999999999999999999999 9999999999999999999999999999999999999999997
Q ss_pred hHHHHHHHHhcccCCCCCCCeEEEEecCCCCCCCCCCCCCCCC
Q 025294 213 KRQAIMSFREGFANSRDQNPIVYIEDTTRRPHNGCRLPKKRRI 255 (255)
Q Consensus 213 k~aaIkaL~~G~~~~r~glkI~sI~D~TpiPhNGCRpkK~RRv 255 (255)
++||++|.. .|++|.+|+|+||||||||||||+||+
T Consensus 94 -eaAiraL~~------ag~~i~~I~DvTPiphnG~Rppk~RR~ 129 (129)
T COG0100 94 -EAAIRALAA------AGLKITRIEDVTPIPHNGCRPPKRRRV 129 (129)
T ss_pred -HHHHHHHHH------ccceEEEEEEcCCCCCCCCCCCCCCCC
Confidence 899999974 699999999999999999999999996
No 5
>TIGR03632 bact_S11 30S ribosomal protein S11. This model describes the bacterial 30S ribosomal protein S11. Cutoffs are set such that the model excludes archaeal and eukaryotic ribosomal proteins, but many chloroplast and mitochondrial equivalents of S11 are detected.
Probab=100.00 E-value=1.9e-41 Score=272.45 Aligned_cols=108 Identities=40% Similarity=0.551 Sum_probs=104.4
Q ss_pred eEEEEEccCCCeEEEEEcCCCCEEEEEeccCcccccCCCCCchhHHHHHHHHHHHHHHHcCCcEEEEEEEccCCCcchHH
Q 025294 136 EFVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGFTYFKKKRQ 215 (255)
Q Consensus 136 ~IlhI~sT~NNTiITlTD~~Gnvl~~~SsGs~~GFKg~rKsT~~AAq~aae~i~~kakelGik~V~V~vKG~G~gR~k~a 215 (255)
+|+||++|+||||||+||++|+++.|.|||++ ||||++|+|+||||++|+.++++++++||+.|+|+|||+|+|| ++
T Consensus 1 gi~hI~~s~NNT~itlTd~~g~~~~~~S~G~~-gfkg~rk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~~kG~G~gr--~~ 77 (108)
T TIGR03632 1 GVAHIHATFNNTIVTITDPQGNVLSWASAGAV-GFKGSKKSTPYAAQLAAEDAAKKAKEFGMKTVDVYVKGPGAGR--ES 77 (108)
T ss_pred CEEEEEccCCCEEEEEEcCCCCEEEEEecCce-eeCCCccCCHHHHHHHHHHHHHHHHHcCCcEEEEEEECCCCcH--HH
Confidence 58999999999999999999999999999999 9999999999999999999999999999999999999999997 79
Q ss_pred HHHHHHhcccCCCCCCCeEEEEecCCCCCCCCCCCCC
Q 025294 216 AIMSFREGFANSRDQNPIVYIEDTTRRPHNGCRLPKK 252 (255)
Q Consensus 216 aIkaL~~G~~~~r~glkI~sI~D~TpiPhNGCRpkK~ 252 (255)
+|++|+. .+++|.+|+|+||+|||||||||+
T Consensus 78 ~ir~l~~------~glkI~~I~D~T~iphNGcR~~K~ 108 (108)
T TIGR03632 78 AIRALQA------AGLEVTSIKDVTPIPHNGCRPPKR 108 (108)
T ss_pred HHHHHHH------CCCEEEEEEEcCCCCCCCcCCCCC
Confidence 9999975 689999999999999999999995
No 6
>PTZ00129 40S ribosomal protein S14; Provisional
Probab=100.00 E-value=2.6e-41 Score=285.68 Aligned_cols=116 Identities=26% Similarity=0.307 Sum_probs=109.5
Q ss_pred ccCccceEEEEEccCCCeEEEEEcCCCCEEEEEeccCcccccCCC-CCchhHHHHHHHHHHHHHHHcCCcEEEEEE----
Q 025294 130 NVEHSSEFVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGP-KMSRYAAEATAEHVGRLARNMGLKSVVVRV---- 204 (255)
Q Consensus 130 ~~e~~~~IlhI~sT~NNTiITlTD~~Gnvl~~~SsGs~~GFKg~r-KsT~~AAq~aae~i~~kakelGik~V~V~v---- 204 (255)
..+...+|+||++|+|||||||||+.|++++|.|+|.+ ||||.+ |+||||||.||+.++++|+++||+.|+|+|
T Consensus 23 ~~~~~~Gi~hI~as~NNTiItiTD~~G~~~~w~SsG~~-gfKg~r~KsTpyAAq~aa~~~a~k~~~~Gi~~v~V~vr~~g 101 (149)
T PTZ00129 23 KGELVFGVAHIFASFNDTFIHVTDLSGRETLVRVTGGM-KVKADRDESSPYAAMMAAQDVAARCKELGINALHIKLRATG 101 (149)
T ss_pred CCceeEEEEEEEcccCCeEEEEEcccCCEEEEEecCcc-eecccccCCCHHHHHHHHHHHHHHHHHcCCeEEEEEEEecC
Confidence 34456799999999999999999999999999999999 999998 999999999999999999999999999999
Q ss_pred ----EccCCCcchHHHHHHHHhcccCCCCCCCeEEEEecCCCCCCCCCCCCCCC
Q 025294 205 ----KGFTYFKKKRQAIMSFREGFANSRDQNPIVYIEDTTRRPHNGCRLPKKRR 254 (255)
Q Consensus 205 ----KG~G~gR~k~aaIkaL~~G~~~~r~glkI~sI~D~TpiPhNGCRpkK~RR 254 (255)
+|+|+|| ++||++|+. .+|+|.+|+|+||||||||||||+||
T Consensus 102 g~~~kg~GpGr--~~airaL~~------~glkI~~I~DvTPiPhNGcRppk~RR 147 (149)
T PTZ00129 102 GVRTKTPGPGA--QAALRALAR------AGLKIGRIEDVTPIPTDSTRRKGGRR 147 (149)
T ss_pred CCCCCCCCCCH--HHHHHHHHH------CCCEEEEEEecCCCCCCCCCCCCCCC
Confidence 7788886 899999975 69999999999999999999999998
No 7
>KOG0408 consensus Mitochondrial/chloroplast ribosomal protein S11 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=9.6e-40 Score=280.05 Aligned_cols=137 Identities=32% Similarity=0.380 Sum_probs=127.3
Q ss_pred CCccc-ccCccccccccc-CCCCcccCCCCcccCccceEEEEEccCCCeEEEEEcCCCCEEEEEeccCcccccCCCCCch
Q 025294 101 RPMDF-VRGIVEEDEKRF-TGPSQFGQFPRYNVEHSSEFVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSR 178 (255)
Q Consensus 101 ~~m~~-~~~~~e~d~~~~-~~g~~f~q~~~~~~e~~~~IlhI~sT~NNTiITlTD~~Gnvl~~~SsGs~~GFKg~rKsT~ 178 (255)
..|++ +-+.|++++.++ |.|++|+|+ +|+||++|+|||+|||||.+|.++.|.|||.+ ||||++|.|+
T Consensus 52 ~~i~t~I~r~p~aet~~r~~~g~~f~ei---------Pi~hIraS~NNTivtVtd~kg~vi~~~Scgte-GFrntrkgT~ 121 (190)
T KOG0408|consen 52 AGIATPINRRPGAETNTRSFSGKNFREI---------PIIHIRASFNNTIVTVTDVKGEVISWSSCGTE-GFRNTRKGTP 121 (190)
T ss_pred cccccccccCCChhhhhcccCCcccccc---------ceEEEEecCCCeEEEEEccCCcEEEEeecccc-cccccccCCc
Confidence 44444 223588777777 999999999 99999999999999999999999999999999 9999999999
Q ss_pred hHHHHHHHHHHHHHHHcCCcEEEEEEEccCCCcchHHHHHHHHhcccCCCCCCCeEEEEecCCCCCCCCCCCCCCCC
Q 025294 179 YAAEATAEHVGRLARNMGLKSVVVRVKGFTYFKKKRQAIMSFREGFANSRDQNPIVYIEDTTRRPHNGCRLPKKRRI 255 (255)
Q Consensus 179 ~AAq~aae~i~~kakelGik~V~V~vKG~G~gR~k~aaIkaL~~G~~~~r~glkI~sI~D~TpiPhNGCRpkK~RRv 255 (255)
+|||.+|..+++++.++|++.|+|+|||.|+|| ++|+++|.+ .|+.|++|+|+||+|||||||+|+|||
T Consensus 122 iAaQtaavaa~~r~v~~G~~~vrV~VkGlGpGR--msa~kgl~m------~Gl~vvsItD~Tp~~~ng~RPrK~Rrl 190 (190)
T KOG0408|consen 122 IAAQTAAVAAIRRAVDQGMQTVRVRVKGLGPGR--MSALKGLRM------GGLLVVSITDNTPMPHNGCRPRKKRRL 190 (190)
T ss_pred hhHHHHHHHHHHHHHHhcceEEEEEEecCCccH--HHHHhhhhh------cceEEEEeecCCcCCCCCCCccccccC
Confidence 999999999999999999999999999999998 899999986 599999999999999999999999996
No 8
>CHL00041 rps11 ribosomal protein S11
Probab=100.00 E-value=6.1e-38 Score=255.24 Aligned_cols=106 Identities=34% Similarity=0.441 Sum_probs=102.2
Q ss_pred ccceEEEEEccCCCeEEEEEcCCCCEEEEEeccCcccccCCCCCchhHHHHHHHHHHHHHHHcCCcEEEEEEEccCCCcc
Q 025294 133 HSSEFVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGFTYFKK 212 (255)
Q Consensus 133 ~~~~IlhI~sT~NNTiITlTD~~Gnvl~~~SsGs~~GFKg~rKsT~~AAq~aae~i~~kakelGik~V~V~vKG~G~gR~ 212 (255)
...+++||++|+|||||||||++|+++.|.|||++ ||||++|+||||||++|++++++|+++||+.|+|+|||+|+||
T Consensus 11 ~~~gi~hI~~t~NNTiiTlTd~~G~~l~~~S~G~~-gfKg~rK~T~~Aa~~~a~~~~~~~~~~gi~~v~I~ikG~G~Gr- 88 (116)
T CHL00041 11 IPKGVIHIQASFNNTIVTVTDVRGRVISWSSAGAC-GFKGARKGTPFAAQTAAENAIRTVIDQGMKRAEVMIKGPGLGR- 88 (116)
T ss_pred ceeEEEEEEcccCCEEEEEEcCCCCEEEEEecCce-eeCCCccCCHHHHHHHHHHHHHHHHHcCCcEEEEEEECCCCcH-
Confidence 45699999999999999999999999999999999 9999999999999999999999999999999999999999997
Q ss_pred hHHHHHHHHhcccCCCCCCCeEEEEecCCCCCCCC
Q 025294 213 KRQAIMSFREGFANSRDQNPIVYIEDTTRRPHNGC 247 (255)
Q Consensus 213 k~aaIkaL~~G~~~~r~glkI~sI~D~TpiPhNGC 247 (255)
+++|++|+. .+++|.+|+|+||+|||||
T Consensus 89 -~~~ir~l~~------~glkI~~I~D~TpiphNGC 116 (116)
T CHL00041 89 -DTALRAIRR------SGLKLSSIRDVTPMPHNGC 116 (116)
T ss_pred -HHHHHHHHH------CCCEEEEEEEcCCCCCCCC
Confidence 799999975 6999999999999999999
No 9
>TIGR03628 arch_S11P archaeal ribosomal protein S11P. This model describes exclusively the archaeal ribosomal protein S11P. It excludes homologous ribosomal proteins S14 from eukaryotes and S11 from bacteria.
Probab=100.00 E-value=4.6e-37 Score=250.14 Aligned_cols=104 Identities=28% Similarity=0.299 Sum_probs=99.0
Q ss_pred ceEEEEEccCCCeEEEEEcCCCC-EEEEEeccCcccccCCCCCchhHHHHHHHHHHHHHHHcCCcEEEEEEEc-------
Q 025294 135 SEFVHIKLMRNNTFVTVTDSKGN-KRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGLKSVVVRVKG------- 206 (255)
Q Consensus 135 ~~IlhI~sT~NNTiITlTD~~Gn-vl~~~SsGs~~GFKg~rKsT~~AAq~aae~i~~kakelGik~V~V~vKG------- 206 (255)
.+|+||++|+|||||||||.+|+ ++.|.|+|++ ||||++|+||||||.|+++++++|+++||+.|+|+|||
T Consensus 2 ~gi~hI~as~NNTiitvTD~~G~~~~~~~S~G~~-g~kg~kk~TpyAAq~aa~~~~~~~~~~Gi~~v~v~ikG~gg~~~~ 80 (114)
T TIGR03628 2 WGIAHIYSSFNNTIITITDITGAETIARSSGGMV-VKADRDESSPYAAMQAAGRAAEKAKERGITGLHIKVRAPGGNGQK 80 (114)
T ss_pred cEEEEEEccCCCeEEEEEcCCCCEEEEEecCcce-EeCCCccCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEecCCCCCC
Confidence 48999999999999999999995 6999999999 99999999999999999999999999999999999999
Q ss_pred -cCCCcchHHHHHHHHhcccCCCCCCCeEEEEecCCCCCCCC
Q 025294 207 -FTYFKKKRQAIMSFREGFANSRDQNPIVYIEDTTRRPHNGC 247 (255)
Q Consensus 207 -~G~gR~k~aaIkaL~~G~~~~r~glkI~sI~D~TpiPhNGC 247 (255)
+|+|| ++||++|+. .+++|.+|+|+||+|||||
T Consensus 81 ~~G~Gr--~~air~l~~------~glkI~~I~DvTpiPhNGC 114 (114)
T TIGR03628 81 SPGPGA--QAAIRALAR------AGLRIGRIEDVTPIPHDGT 114 (114)
T ss_pred CCCCcH--HHHHHHHHH------CCCEEEEEEEcCCCCCCCC
Confidence 67776 899999975 6999999999999999999
No 10
>PTZ00090 40S ribosomal protein S11; Provisional
Probab=100.00 E-value=5.5e-36 Score=266.01 Aligned_cols=112 Identities=19% Similarity=0.294 Sum_probs=105.5
Q ss_pred cceEEEEEccCCCeEEEEEcCCCCE--EEEEeccCcccccCCCCCchhHHHHHHHHHHHHHHHcCCcEEEEEEEccCCCc
Q 025294 134 SSEFVHIKLMRNNTFVTVTDSKGNK--RIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGFTYFK 211 (255)
Q Consensus 134 ~~~IlhI~sT~NNTiITlTD~~Gnv--l~~~SsGs~~GFKg~rKsT~~AAq~aae~i~~kakelGik~V~V~vKG~G~gR 211 (255)
+.-.+-|++|+|||||||||..||+ ++|+|+|.+ ||||++|+||||||.||+.++++|+++||+.|+|+|||+| +|
T Consensus 117 ~~f~~vI~aSfNNTIVTlTD~~GNv~tl~WSSAG~~-GFKGsKKsTpfAAQ~aae~aakka~~~GIk~V~V~vKGpG-gR 194 (233)
T PTZ00090 117 DRFMLVITTSKNNVHAQVVNKSKNYKTVFGSFAGNV-GFRKKLQQSERCAYRIGENIAKKCRRLGIFAVDIKFRRIM-RV 194 (233)
T ss_pred CcEEEEEEeccCcEEEEEEeCCCCEEEEEEEccccc-CcccCccCCHHHHHHHHHHHHHHHHHcCCeEEEEEEeCCC-hH
Confidence 4567789999999999999999995 999999999 9999999999999999999999999999999999999998 44
Q ss_pred chHHHHHHHHhcccCCCCCCCeEEEEecCCCCC---CCCCCCCCCCC
Q 025294 212 KKRQAIMSFREGFANSRDQNPIVYIEDTTRRPH---NGCRLPKKRRI 255 (255)
Q Consensus 212 ~k~aaIkaL~~G~~~~r~glkI~sI~D~TpiPh---NGCRpkK~RRv 255 (255)
++||++|+. .|++|.+|.|+||+|| |||||||+|||
T Consensus 195 --EtALRaL~~------~GLkIt~I~DvTpiPHNG~NGCRPpKKRRV 233 (233)
T PTZ00090 195 --ETVLQAFYA------NGLQVTQIIHEPRLPKCGLNAVKPRKRRRV 233 (233)
T ss_pred --HHHHHHHHH------CCCEEEEEEECCCCCcCCCCCCCCCCCCCC
Confidence 899999986 6999999999999999 55999999997
No 11
>KOG0407 consensus 40S ribosomal protein S14 [Translation, ribosomal structure and biogenesis]
Probab=99.92 E-value=2.4e-24 Score=175.88 Aligned_cols=121 Identities=27% Similarity=0.310 Sum_probs=107.7
Q ss_pred CcccCccceEEEEEccCCCeEEEEEcCCCCEEEEEeccCcccccCCCCCchhHHHHHHHHHHHHHHHcCCcEEEEEEEcc
Q 025294 128 RYNVEHSSEFVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGF 207 (255)
Q Consensus 128 ~~~~e~~~~IlhI~sT~NNTiITlTD~~Gnvl~~~SsGs~~GFKg~rKsT~~AAq~aae~i~~kakelGik~V~V~vKG~ 207 (255)
.++.|+..+++||++|+|+|||++||+.|......-.|.++-...+..++||||++||++++.+|+++||+.+||++++.
T Consensus 9 ~~e~~~vfgvahi~asfndtfvhitdlsg~eti~rvtggmkvkadrdesspyaamlaaqdva~kck~~gi~alh~klrat 88 (139)
T KOG0407|consen 9 VREGEQVFGVAHIFASFNDTFVHVTDLSGKETIVRVTGGMKVKADRDESSPYAAMLAAQDVAAKCKELGITALHIKLRAT 88 (139)
T ss_pred hcccceeeeEEEEEeecccceEEEeccCCceEEEEecCCeEEecccccCChHHHHHHHHHHHHHHHhcCeeEEEEEEEec
Confidence 34567789999999999999999999999988888888773444568899999999999999999999999999999999
Q ss_pred CCCcch------HHHHHHHHhcccCCCCCCCeEEEEecCCCCCCCCCCCCCCC
Q 025294 208 TYFKKK------RQAIMSFREGFANSRDQNPIVYIEDTTRRPHNGCRLPKKRR 254 (255)
Q Consensus 208 G~gR~k------~aaIkaL~~G~~~~r~glkI~sI~D~TpiPhNGCRpkK~RR 254 (255)
|+.+.| ++||++|. |+|++|.+|+|+||||.+..|.|-.||
T Consensus 89 gg~ktktpgpgaqsalrala------r~gmrigriedvtpip~d~trrkggrr 135 (139)
T KOG0407|consen 89 GGTKTKTPGPGAQSALRALA------RSGMRIGRIEDVTPIPSDSTRRKGGRR 135 (139)
T ss_pred CCcccCCCCccHHHHHHHHH------HhcceeeeecccccCCccchhhccCcc
Confidence 988776 78999985 479999999999999999999986655
No 12
>cd00432 Ribosomal_L18_L5e Ribosomal L18/L5e: L18 (L5e) is a ribosomal protein found in the central protuberance (CP) of the large subunit. L18 binds 5S rRNA and induces a conformational change that stimulates the binding of L5 to 5S rRNA. Association of 5S rRNA with 23S rRNA depends on the binding of L18 and L5 to 5S rRNA. L18/L5e is generally described as L18 in prokaryotes and archaea, and as L5e (or L5) in eukaryotes. In bacteria, the CP proteins L5, L18, and L25 are required for the ribosome to incorporate 5S rRNA into the large subunit, one of the last steps in ribosome assembly. In archaea, both L18 and L5 bind 5S rRNA; in eukaryotes, only the L18 homolog (L5e) binds 5S rRNA but a homolog to L5 is also identified.
Probab=97.86 E-value=0.00022 Score=56.47 Aligned_cols=89 Identities=19% Similarity=0.246 Sum_probs=71.3
Q ss_pred ccceEEEEEccCCCeEEEEEcCC-CCEEEEEeccCcccccCC--CCCchhHHHHHHHHHHHHHHHcCCcEEEEEEEccCC
Q 025294 133 HSSEFVHIKLMRNNTFVTVTDSK-GNKRIGASSGCLPELKGG--PKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGFTY 209 (255)
Q Consensus 133 ~~~~IlhI~sT~NNTiITlTD~~-Gnvl~~~SsGs~~GFKg~--rKsT~~AAq~aae~i~~kakelGik~V~V~vKG~G~ 209 (255)
..++.+.|+.|.+|...+|.|.. +.++...|+-.. .+++. ......||..+++.++++|++.|+..+.+-..|.-+
T Consensus 9 ~~~~RL~v~~Sn~~i~aqvi~~~~~~vl~sast~e~-~~~~~~~~~~n~~aA~~vG~~la~r~~~~gi~~vv~D~~~~~~ 87 (103)
T cd00432 9 QERPRLVVRKSNKHIYAQIIDDSGDKTLVSASTLEL-AIKGVLGSGNNVEAAYLVGRLLAKRALEKGIKKVVFDRGGYRY 87 (103)
T ss_pred CCCCEEEEEEeCCEEEEEEEEeCcCeEEEEEecCch-hhcccccCCCcHHHHHHHHHHHHHHHHHCCCCEEEEeCCCccc
Confidence 35689999999999999999997 788999999888 87774 567788999999999999999999999888766654
Q ss_pred CcchHHHHHHHHh
Q 025294 210 FKKKRQAIMSFRE 222 (255)
Q Consensus 210 gR~k~aaIkaL~~ 222 (255)
+-.-.+++.++.+
T Consensus 88 ~grv~a~~~~~r~ 100 (103)
T cd00432 88 HGRVKALAKGARE 100 (103)
T ss_pred ccHHHHHHHHHHH
Confidence 3212344455554
No 13
>PRK08569 rpl18p 50S ribosomal protein L18P; Reviewed
Probab=97.37 E-value=0.0041 Score=55.51 Aligned_cols=107 Identities=19% Similarity=0.144 Sum_probs=77.2
Q ss_pred cCccceEEEEEccCCCeEEEEE--cCCC-CEEEEEeccCcccccCC--CCCchhHHHHHHHHHHHHHHHcCCcEEEEEEE
Q 025294 131 VEHSSEFVHIKLMRNNTFVTVT--DSKG-NKRIGASSGCLPELKGG--PKMSRYAAEATAEHVGRLARNMGLKSVVVRVK 205 (255)
Q Consensus 131 ~e~~~~IlhI~sT~NNTiITlT--D~~G-nvl~~~SsGs~~GFKg~--rKsT~~AAq~aae~i~~kakelGik~V~V~vK 205 (255)
+....+-+.|+-|.+++++.|. |..| .++.+.|+-.+ ..++- ......||+.++..++++|++.||+.+.+=.-
T Consensus 28 ~~~~kpRLvV~rSNkhIyaQiI~~dd~gd~tLaSAsS~el-~~~g~~~~~~N~~AAy~vG~llA~ral~kGi~~vvfDrG 106 (193)
T PRK08569 28 LLSGKPRLVVRKTNKHVIAQIVKYDPKGDRTLASAHSREL-AKYGWKGDTGNTPAAYLTGLLAGKKALKAGVEEAVLDIG 106 (193)
T ss_pred HhcCCCEEEEEEeCCeEEEEEEEccCCCCEEEEEEecCch-hhccccCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEecC
Confidence 3445688999999999999999 5554 57777777666 55452 35667799999999999999999999887775
Q ss_pred ccCC---CcchHHHHHHHHhcccCCCCCCCeEEEEecCCCCCCCCCCCCCCC
Q 025294 206 GFTY---FKKKRQAIMSFREGFANSRDQNPIVYIEDTTRRPHNGCRLPKKRR 254 (255)
Q Consensus 206 G~G~---gR~k~aaIkaL~~G~~~~r~glkI~sI~D~TpiPhNGCRpkK~RR 254 (255)
|.=+ || -.+++++..+ .||+ +||+..|-|---|
T Consensus 107 g~~yh~gGR-V~A~akgArd------~GL~---------fPh~~~~~p~~~r 142 (193)
T PRK08569 107 LHRPTKGSR-VFAALKGAID------AGLE---------IPHGEEVLPDEDR 142 (193)
T ss_pred CccccCCcc-HHHHHHHHHH------cCCc---------CCCCCCcCCCccc
Confidence 5443 34 2345556554 4774 6888887765433
No 14
>PF00861 Ribosomal_L18p: Ribosomal L18p/L5e family; InterPro: IPR005484 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 [, ]. This family includes L18 from bacteria and L5 from eukaryotes. The ribosomal 5S RNA is the only known rRNA species to bind a ribosomal protein before its assembly into the ribosomal subunits []. In eukaryotes, the 5S rRNA molecule binds one protein species, a 34kDa protein which has been implicated in the intracellular transport of 5 S rRNA, while in bacteria it binds two or three different protein species []. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_M 4A1C_M 4A1A_M 4A17_M 3IZR_Q 3O58_E 1S1I_E 3IZS_Q 3O5H_E 1KQS_M ....
Probab=97.32 E-value=0.0021 Score=52.63 Aligned_cols=88 Identities=20% Similarity=0.205 Sum_probs=68.7
Q ss_pred cceEEEEEccCCCeEEEEEcCC-CCEEEEEeccCcccccCC----CCCchhHHHHHHHHHHHHHHHcCCcEEEEEEEccC
Q 025294 134 SSEFVHIKLMRNNTFVTVTDSK-GNKRIGASSGCLPELKGG----PKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGFT 208 (255)
Q Consensus 134 ~~~IlhI~sT~NNTiITlTD~~-Gnvl~~~SsGs~~GFKg~----rKsT~~AAq~aae~i~~kakelGik~V~V~vKG~G 208 (255)
..|.+-|+.|..++.+.|.|.. +.++...|+-.. .++.. ......||+.+++.++++|++.||..|.+-..|+-
T Consensus 22 ~~~RL~V~~Snk~i~aQii~~~~~~~l~~aSt~~~-~l~~~~~~~~~~n~~aa~~vG~lla~ra~~~gi~~v~fdr~~~~ 100 (119)
T PF00861_consen 22 ERPRLVVFRSNKHIYAQIIDDSKGGTLASASTLSK-ELKKYGWKGSTKNVEAAYLVGELLAKRALEKGIAKVVFDRGGYK 100 (119)
T ss_dssp SSEEEEEEEESSEEEEEEEECTTTEEEEEEEEETT-TGGGTT-SSTTSSHHHHHHHHHHHHHHHHHTTSSEEEECTSTSS
T ss_pred CCCEEEEEeccCeEEEEEEeeCCCCeEEEEEecch-hhhhhhhccCCCCEehHHHHHHHHHHHHHHcCCcEEEEcCCCCc
Confidence 4589999999999999998766 778888888777 77752 33467899999999999999999999888877776
Q ss_pred CCcchHHHHHHHHh
Q 025294 209 YFKKKRQAIMSFRE 222 (255)
Q Consensus 209 ~gR~k~aaIkaL~~ 222 (255)
++-.-.+++.++.+
T Consensus 101 y~grv~a~~~~~re 114 (119)
T PF00861_consen 101 YHGRVKALADGARE 114 (119)
T ss_dssp SSSHHHHHHHHHHH
T ss_pred ccHHHHHHHHHHHH
Confidence 65422344556665
No 15
>TIGR00060 L18_bact ribosomal protein L18, bacterial type. The archaeal and eukaryotic type rpL18 is not detectable under this model.
Probab=97.21 E-value=0.005 Score=50.76 Aligned_cols=71 Identities=20% Similarity=0.182 Sum_probs=56.7
Q ss_pred ceEEEEEccCCCeEEEEEcCCCC-EEEEEeccCcccccCCCCCchhHHHHHHHHHHHHHHHcCCcEEEEEEEccC
Q 025294 135 SEFVHIKLMRNNTFVTVTDSKGN-KRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGFT 208 (255)
Q Consensus 135 ~~IlhI~sT~NNTiITlTD~~Gn-vl~~~SsGs~~GFKg~rKsT~~AAq~aae~i~~kakelGik~V~V~vKG~G 208 (255)
.|-+.|+-|.+++.+.|.|..+. ++.+.|+=.. .++ ....-.||..+++.++++|++.||+.|..--.|+=
T Consensus 24 rpRL~V~rSnk~iyaQiIdd~~~~tlasaST~ek-~~~--~~~n~~aA~~vG~~la~ra~~~gi~~vvfDrgg~~ 95 (114)
T TIGR00060 24 RPRLVVFRSNRHIYAQVIDDSKSEVLASASTLEK-KLK--YTGNKDAAKKVGKLVAERLKEKGIKDVVFDRGGYK 95 (114)
T ss_pred CcEEEEEEeCCeEEEEEEECCCCEEEEEEecchh-hhc--CCCCHHHHHHHHHHHHHHHHHCCCCEEEEeCCCCc
Confidence 48899999999999999977665 6666665444 666 56677899999999999999999999876644433
No 16
>CHL00139 rpl18 ribosomal protein L18; Validated
Probab=97.17 E-value=0.0058 Score=49.87 Aligned_cols=71 Identities=13% Similarity=0.213 Sum_probs=57.9
Q ss_pred ceEEEEEccCCCeEEEEEc-CCCCEEEEEeccCcccccCC--CCCchhHHHHHHHHHHHHHHHcCCcEEEEEEEc
Q 025294 135 SEFVHIKLMRNNTFVTVTD-SKGNKRIGASSGCLPELKGG--PKMSRYAAEATAEHVGRLARNMGLKSVVVRVKG 206 (255)
Q Consensus 135 ~~IlhI~sT~NNTiITlTD-~~Gnvl~~~SsGs~~GFKg~--rKsT~~AAq~aae~i~~kakelGik~V~V~vKG 206 (255)
.|.+.|+.|.+++.+.|.| .+|+++.+.|+=.. .+++. ....-.||+.+++.++++|++.||..|..--.|
T Consensus 15 rpRL~V~rSnkhiyaQvidd~~g~tlasaST~ek-~~~~~~~~~~n~~aA~~vG~lla~ra~~~gi~~vvfDrgg 88 (109)
T CHL00139 15 RPRLSVFRSNKHIYAQIIDDTNGKTLVACSTLEP-DVKSSLSSTSTCDASKLVGQKLAKKSLKKGITKVVFDRGG 88 (109)
T ss_pred CCEEEEEEeCCeEEEEEEECCCCCEEEEEecCch-hhhccccCCCCHHHHHHHHHHHHHHHHHCCCCEEEEcCCC
Confidence 4789999999999998875 56789998888666 66653 456678999999999999999999998776433
No 17
>PRK05593 rplR 50S ribosomal protein L18; Reviewed
Probab=97.05 E-value=0.0077 Score=49.66 Aligned_cols=72 Identities=18% Similarity=0.204 Sum_probs=56.8
Q ss_pred cceEEEEEccCCCeEEEEEcCCCC-EEEEEeccCcccccCC-CCCchhHHHHHHHHHHHHHHHcCCcEEEEEEEc
Q 025294 134 SSEFVHIKLMRNNTFVTVTDSKGN-KRIGASSGCLPELKGG-PKMSRYAAEATAEHVGRLARNMGLKSVVVRVKG 206 (255)
Q Consensus 134 ~~~IlhI~sT~NNTiITlTD~~Gn-vl~~~SsGs~~GFKg~-rKsT~~AAq~aae~i~~kakelGik~V~V~vKG 206 (255)
..|-+.|+.|.+++.+.|.|..+. ++.+.|+=.. .++.. +...-.||+.+++.++++|++.||+.+..--.|
T Consensus 23 ~rpRL~V~~SnkhiyAQvidd~~~~tl~saST~e~-~~k~~~~~~n~~aa~~vG~~la~ra~~~gi~~vvfDrg~ 96 (117)
T PRK05593 23 ERPRLSVFRSNRHIYAQVIDDVKGKTLASASTLEK-DVRAGLKGGNKEAAKKVGKLIAERAKAKGIKQVVFDRGG 96 (117)
T ss_pred CCCEEEEEEeCCeEEEEEEECCCCEEEEEEecCcH-hHhccccCCCHHHHHHHHHHHHHHHHHCCCCEEEEcCCC
Confidence 348999999999999999987776 6666666444 55443 367778999999999999999999997666433
No 18
>COG0256 RplR Ribosomal protein L18 [Translation, ribosomal structure and biogenesis]
Probab=96.35 E-value=0.056 Score=45.38 Aligned_cols=77 Identities=17% Similarity=0.179 Sum_probs=57.1
Q ss_pred cceEEEEEccCCCeEEEEEcCCC-CEEEEEeccCcccccC--C--CCCchhHHHHHHHHHHHHHHHcCCcEEEEEEEccC
Q 025294 134 SSEFVHIKLMRNNTFVTVTDSKG-NKRIGASSGCLPELKG--G--PKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGFT 208 (255)
Q Consensus 134 ~~~IlhI~sT~NNTiITlTD~~G-nvl~~~SsGs~~GFKg--~--rKsT~~AAq~aae~i~~kakelGik~V~V~vKG~G 208 (255)
..+-+-|+-|.+|.++.|.|... .++...|+=.. ..++ . ....-.||..+++.|+++|+++||+.+.+=..|+-
T Consensus 28 ~rpRL~V~rSnkhi~aQiId~~~~~tla~aSt~~~-~l~~~g~~~~~~N~~aA~~vG~lia~ra~~kgi~~vVfdr~g~~ 106 (125)
T COG0256 28 GRPRLVVRRSNRHIYAQIIDDVKGGTLASASTLSK-ELRKYGKKGGGGNTEAAYLVGKLIAERALAKGIEEVVFDRGGYK 106 (125)
T ss_pred CCcEEEEEEeCCcEEEEEEEcCCCceEEEEEcchH-HHHhhcccCCCCCHHHHHHHHHHHHHHHHHcCCcEEEEcCCCCC
Confidence 44888888999999999987664 56777776553 3322 1 22346689999999999999999999997666666
Q ss_pred CCc
Q 025294 209 YFK 211 (255)
Q Consensus 209 ~gR 211 (255)
++-
T Consensus 107 yhg 109 (125)
T COG0256 107 YHG 109 (125)
T ss_pred cch
Confidence 554
No 19
>PTZ00032 60S ribosomal protein L18; Provisional
Probab=95.74 E-value=0.09 Score=47.58 Aligned_cols=86 Identities=17% Similarity=0.159 Sum_probs=63.6
Q ss_pred ccceEEEEEccCCCeEEEEEcC-CCCEEEEEeccCcccccCC--------------CCCchhHHHHHHHHHHHHHHHcCC
Q 025294 133 HSSEFVHIKLMRNNTFVTVTDS-KGNKRIGASSGCLPELKGG--------------PKMSRYAAEATAEHVGRLARNMGL 197 (255)
Q Consensus 133 ~~~~IlhI~sT~NNTiITlTD~-~Gnvl~~~SsGs~~GFKg~--------------rKsT~~AAq~aae~i~~kakelGi 197 (255)
+..+-+-|+-|.++..+++.|. .|.++.++|+=.. .+++. ...+-.||..+++.|+++|.++||
T Consensus 103 krrPRLsV~RSnkHIYAQIIDD~~~~TLasaSTlek-~l~~~~~~~~~~~~n~~~~~g~nieaA~~VGk~IAerAl~kGI 181 (211)
T PTZ00032 103 KRRPRLTLKNTNNQMYATIVDDYTRHVLCFSCTNFK-YLSHIFGTYPTKTTNRVRNNGGTIKAAYELGKLIGRKALSKGI 181 (211)
T ss_pred CCcceEEEEecCCeEEEEEEECCCCCEEEEecCCCH-HHHhhhcccccccccccccCCCcHHHHHHHHHHHHHHHHHCCC
Confidence 3568999999999999999865 6778888777544 66542 467889999999999999999999
Q ss_pred cEEEEEEEccCCCcchHHHHHHHHhc
Q 025294 198 KSVVVRVKGFTYFKKKRQAIMSFREG 223 (255)
Q Consensus 198 k~V~V~vKG~G~gR~k~aaIkaL~~G 223 (255)
+.|..==.|+=+-. -|+||.+|
T Consensus 182 ~kVvFDRgGy~YHG----RVkALAda 203 (211)
T PTZ00032 182 SKVRFDRAHYKYAG----KVEALAEG 203 (211)
T ss_pred CEEEEeCCCCeehh----HHHHHHHH
Confidence 98766533332221 35666544
No 20
>PTZ00069 60S ribosomal protein L5; Provisional
Probab=76.98 E-value=19 Score=34.44 Aligned_cols=59 Identities=17% Similarity=0.121 Sum_probs=44.3
Q ss_pred ceEEEEEccCCCeEEEEE--cCCCCEEEE-Eecc---CcccccCCCCCchhHHHHHHHHHHHHHHHc
Q 025294 135 SEFVHIKLMRNNTFVTVT--DSKGNKRIG-ASSG---CLPELKGGPKMSRYAAEATAEHVGRLARNM 195 (255)
Q Consensus 135 ~~IlhI~sT~NNTiITlT--D~~Gnvl~~-~SsG---s~~GFKg~rKsT~~AAq~aae~i~~kakel 195 (255)
.+-+.|..|..++|+.|+ ++.|..+.. ..+- -. |+|+....++ ||+.++.-+++++...
T Consensus 48 K~RlVVR~TN~~ii~Qiv~~~~~GD~vl~sA~S~eL~ky-G~k~gl~N~~-AAY~TGlL~arR~L~k 112 (300)
T PTZ00069 48 KYRLVVRITNKDIICQIVYATIVGDKVLAAAYSHELPRF-GIPVGLTNYA-AAYATGLLLARRLLKK 112 (300)
T ss_pred CceEEEEEECCcEEEEEEEeecCCCEEEEEeehhhHhhc-CcCCCCccHH-HHHHHHHHHHHHHHHh
Confidence 477888999999999987 577876554 3332 24 7887777766 7888998888888765
No 21
>cd05313 NAD_bind_2_Glu_DH NAD(P) binding domain of glutamate dehydrogenase, subgroup 2. Amino acid dehydrogenase (DH) is a widely distributed family of enzymes that catalyzes the oxidative deamination of an amino acid to its keto acid and ammonia with concomitant reduction of NADP+. Glutamate DH is a multidomain enzyme that catalyzes the reaction from glutamate to 2-oxyoglutarate and ammonia in the presence of NAD or NADP. It is present in all organisms. Enzymes involved in ammonia asimilation are typically NADP+-dependent, while those involved in glutamate catabolism are generally NAD+-dependent. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids t
Probab=58.65 E-value=17 Score=33.73 Aligned_cols=64 Identities=19% Similarity=0.105 Sum_probs=46.5
Q ss_pred cccCCCCCchhHHHHHHHHHHHHHHHcCCcEEEEEEEccCCCcchHHHHHHHHhcccCCCCCCCeEEEEecCC
Q 025294 169 ELKGGPKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGFTYFKKKRQAIMSFREGFANSRDQNPIVYIEDTTR 241 (255)
Q Consensus 169 GFKg~rKsT~~AAq~aae~i~~kakelGik~V~V~vKG~G~gR~k~aaIkaL~~G~~~~r~glkI~sI~D~Tp 241 (255)
|-.|+...|-+....+.+.+++.. +..++..+|.|.|||.-- ..+.+.|.+ .|.+|+-|.|.+-
T Consensus 9 Gs~gR~~aTg~Gv~~~~~~~~~~~-~~~l~g~~vaIqGfGnVG--~~~a~~L~e------~GakvvaVsD~~G 72 (254)
T cd05313 9 GSLIRPEATGYGLVYFVEEMLKDR-NETLKGKRVAISGSGNVA--QYAAEKLLE------LGAKVVTLSDSKG 72 (254)
T ss_pred CCCCCCchhHHHHHHHHHHHHHhc-CCCcCCCEEEEECCCHHH--HHHHHHHHH------CCCEEEEEECCCc
Confidence 446677788887777777666555 456778999999999653 456666654 4789999999553
No 22
>PF14877 mIF3: Mitochondrial translation initiation factor
Probab=54.34 E-value=36 Score=30.40 Aligned_cols=74 Identities=19% Similarity=0.113 Sum_probs=49.5
Q ss_pred EEEEEeccCcccccCCCCCchhHHHHHHHHHHHHHHHcCCcEEEEEEEccCCCcchHHHHHHHHhcccCCCCCCCeEEEE
Q 025294 158 KRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGFTYFKKKRQAIMSFREGFANSRDQNPIVYIE 237 (255)
Q Consensus 158 vl~~~SsGs~~GFKg~rKsT~~AAq~aae~i~~kakelGik~V~V~vKG~G~gR~k~aaIkaL~~G~~~~r~glkI~sI~ 237 (255)
+.+-+++|+. -|+.|+..++.++..+.-....-.| .++-++-.+.-|+-+..|+.++..|+.|+.+.
T Consensus 4 ~~~~~~tGse------------~aq~A~~svi~ki~~~n~~g~Vk~i-np~t~~Le~~~l~~~~~~lDL~~~Gl~iV~~~ 70 (181)
T PF14877_consen 4 VRFRWSTGSE------------RAQEAANSVISKIFKINPNGKVKFI-NPETNKLEESNLRDIAKGLDLSKHGLQIVNSE 70 (181)
T ss_pred eEEEeCCCCH------------HHHHHHHHHHHHHHhhCCCCeEEEE-cCCCCcceeeeHHHHHHhCCccccceEEeccc
Confidence 3445566776 6899999999999887765433333 23333322445665556667778999999999
Q ss_pred ecC---CCCC
Q 025294 238 DTT---RRPH 244 (255)
Q Consensus 238 D~T---piPh 244 (255)
+.+ ++|.
T Consensus 71 ~~~~~~~lPL 80 (181)
T PF14877_consen 71 KDQKGRDLPL 80 (181)
T ss_pred ccCCCCcCce
Confidence 887 6663
No 23
>cd01076 NAD_bind_1_Glu_DH NAD(P) binding domain of glutamate dehydrogenase, subgroup 1. Amino acid dehydrogenase (DH) is a widely distributed family of enzymes that catalyzes the oxidative deamination of an amino acid to its keto acid and ammonia with concomitant reduction of NADP+. Glutamate DH is a multidomain enzyme that catalyzes the reaction from glutamate to 2-oxyoglutarate and ammonia in the presence of NAD or NADP. It is present in all organisms. Enzymes involved in ammonia assimilation are typically NADP+-dependent, while those involved in glutamate catabolism are generally NAD+-dependent. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids
Probab=49.12 E-value=30 Score=31.12 Aligned_cols=64 Identities=16% Similarity=0.197 Sum_probs=45.7
Q ss_pred cccCCCCCchhHHHHHHHHHHHHHHHcCCcEEEEEEEccCCCcchHHHHHHHHhcccCCCCCCCeEEEEecCC
Q 025294 169 ELKGGPKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGFTYFKKKRQAIMSFREGFANSRDQNPIVYIEDTTR 241 (255)
Q Consensus 169 GFKg~rKsT~~AAq~aae~i~~kakelGik~V~V~vKG~G~gR~k~aaIkaL~~G~~~~r~glkI~sI~D~Tp 241 (255)
|..+....|-|....+.+.+.+... ..++..+|.|.|+|.-- ..+.+.|.+ .+.+|+.|.|.+.
T Consensus 2 G~~~~~~~Tg~Gv~~~~~~~~~~~~-~~l~~~~v~I~G~G~VG--~~~a~~L~~------~g~~vv~v~D~~g 65 (227)
T cd01076 2 GSLGREEATGRGVAYATREALKKLG-IGLAGARVAIQGFGNVG--SHAARFLHE------AGAKVVAVSDSDG 65 (227)
T ss_pred CCCCCCccchHHHHHHHHHHHHhcC-CCccCCEEEEECCCHHH--HHHHHHHHH------CCCEEEEEECCCC
Confidence 4456677787777777776666542 55788999999999643 456666654 4889999999753
No 24
>PLN02477 glutamate dehydrogenase
Probab=45.16 E-value=45 Score=32.98 Aligned_cols=61 Identities=16% Similarity=0.135 Sum_probs=43.4
Q ss_pred cCCCCCchhHHHHHHHHHHHHHHHcCCcEEEEEEEccCCCcchHHHHHHHHhcccCCCCCCCeEEEEecC
Q 025294 171 KGGPKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGFTYFKKKRQAIMSFREGFANSRDQNPIVYIEDTT 240 (255)
Q Consensus 171 Kg~rKsT~~AAq~aae~i~~kakelGik~V~V~vKG~G~gR~k~aaIkaL~~G~~~~r~glkI~sI~D~T 240 (255)
.+....|-+....+++.+++. ....++..+|.|.|||.-- ..+.+.|.+ .|.+|+.|.|.+
T Consensus 179 ~~r~~aTg~Gv~~~~~~~~~~-~g~~l~g~~VaIqGfGnVG--~~~A~~L~e------~GakVVaVsD~~ 239 (410)
T PLN02477 179 LGREAATGRGVVFATEALLAE-HGKSIAGQTFVIQGFGNVG--SWAAQLIHE------KGGKIVAVSDIT 239 (410)
T ss_pred CCCCccchHHHHHHHHHHHHH-cCCCccCCEEEEECCCHHH--HHHHHHHHH------cCCEEEEEECCC
Confidence 456677777777777666655 3334677899999999653 456666654 478999999986
No 25
>COG4782 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.19 E-value=1.6e+02 Score=29.18 Aligned_cols=52 Identities=15% Similarity=0.096 Sum_probs=42.9
Q ss_pred EEEEEeccCcccccCCCCCchhHHHHHHHHHHHHHHHcCCcEEEEEEEccCC
Q 025294 158 KRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGFTY 209 (255)
Q Consensus 158 vl~~~SsGs~~GFKg~rKsT~~AAq~aae~i~~kakelGik~V~V~vKG~G~ 209 (255)
+..|.|.|++.||--=|.++.|+.-+.+.-+-..+.+.+.+.|+|.-..-|-
T Consensus 151 vFSWPS~g~l~~Yn~DreS~~~Sr~aLe~~lr~La~~~~~~~I~ilAHSMGt 202 (377)
T COG4782 151 VFSWPSRGSLLGYNYDRESTNYSRPALERLLRYLATDKPVKRIYLLAHSMGT 202 (377)
T ss_pred EEEcCCCCeeeecccchhhhhhhHHHHHHHHHHHHhCCCCceEEEEEecchH
Confidence 6789999999899877889998888776655566677779999999998774
No 26
>PRK14030 glutamate dehydrogenase; Provisional
Probab=33.09 E-value=85 Score=31.56 Aligned_cols=73 Identities=16% Similarity=0.114 Sum_probs=48.4
Q ss_pred CCEEEEEeccCcccccCCCCCchhHHHHHHHHHHHHHHHcCCcEEEEEEEccCCCcchHHHHHHHHhcccCCCCCCCeEE
Q 025294 156 GNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGFTYFKKKRQAIMSFREGFANSRDQNPIVY 235 (255)
Q Consensus 156 Gnvl~~~SsGs~~GFKg~rKsT~~AAq~aae~i~~kakelGik~V~V~vKG~G~gR~k~aaIkaL~~G~~~~r~glkI~s 235 (255)
|+++.+ .|+ .++...|-+....+++.+++.. ...++..+|.|.|||.-- ..+.+.|.+ .|-+|+.
T Consensus 192 Gkp~~~--gGs----~gr~~ATg~Gv~~~~~~~~~~~-g~~l~g~~vaIQGfGnVG--~~aA~~L~e------~GakvVa 256 (445)
T PRK14030 192 GKGLEF--GGS----LIRPEATGFGALYFVHQMLETK-GIDIKGKTVAISGFGNVA--WGAATKATE------LGAKVVT 256 (445)
T ss_pred cccccc--CCC----CCCCCccHHHHHHHHHHHHHHc-CCCcCCCEEEEECCCHHH--HHHHHHHHH------CCCEEEE
Confidence 666644 333 4566778887777777666544 334678899999999643 345555544 4789999
Q ss_pred EEecCCCC
Q 025294 236 IEDTTRRP 243 (255)
Q Consensus 236 I~D~TpiP 243 (255)
|.|.+--=
T Consensus 257 vSD~~G~i 264 (445)
T PRK14030 257 ISGPDGYI 264 (445)
T ss_pred EEcCCceE
Confidence 98876543
No 27
>cd07996 WGR_MMR_like WGR domain of molybdate metabolism regulator and related proteins. The WGR domain is found in the putative Escherichia coli molybdate metabolism regulator and related bacterial proteins, as well as in various other bacterial proteins of unknown function. It has been called WGR after the most conserved central motif of the domain. The domain appears to occur in single-domain proteins and in a variety of domain architectures, together with ATP-dependent DNA ligase domains, WD40 repeats, leucine-rich repeats, and other domains. It has been proposed to function as a nucleic acid binding domain.
Probab=31.52 E-value=1.3e+02 Score=21.71 Aligned_cols=45 Identities=24% Similarity=0.178 Sum_probs=31.0
Q ss_pred cCCCCEEEEEeccCcccccCCCC----CchhHHHHHHHHHHHHHHHcCCc
Q 025294 153 DSKGNKRIGASSGCLPELKGGPK----MSRYAAEATAEHVGRLARNMGLK 198 (255)
Q Consensus 153 D~~Gnvl~~~SsGs~~GFKg~rK----sT~~AAq~aae~i~~kakelGik 198 (255)
|+.|....+..=|-+ |-+|..+ .++.+|..+++++.+.-...|+.
T Consensus 24 ~lfg~~~v~~~wGRi-G~~Gq~~~~~~~s~~~A~~~~~k~~~~K~~~GY~ 72 (74)
T cd07996 24 DLFGEWSLVRRWGRI-GTKGQSRTKTFDSEEEALKAAEKLIREKLKRGYR 72 (74)
T ss_pred cCCCCEEEEEEECCC-CCCCceEEEECCCHHHHHHHHHHHHHHHHhcCCC
Confidence 555777778888999 8777766 34566666666666666666764
No 28
>PTZ00079 NADP-specific glutamate dehydrogenase; Provisional
Probab=29.36 E-value=1.1e+02 Score=30.94 Aligned_cols=72 Identities=17% Similarity=0.121 Sum_probs=49.8
Q ss_pred CCCEEEEEeccCcccccCCCCCchhHHHHHHHHHHHHHHHcCCcEEEEEEEccCCCcchHHHHHHHHhcccCCCCCCCeE
Q 025294 155 KGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGFTYFKKKRQAIMSFREGFANSRDQNPIV 234 (255)
Q Consensus 155 ~Gnvl~~~SsGs~~GFKg~rKsT~~AAq~aae~i~~kakelGik~V~V~vKG~G~gR~k~aaIkaL~~G~~~~r~glkI~ 234 (255)
.|+.+.| | |-.++...|-|....+++.+++.. ...++..+|.|.|+|.-- ..+.+.|.+ .|-+|+
T Consensus 200 TGK~~~~---G---Gs~~r~eATG~Gv~~~~~~~l~~~-~~~l~Gk~VaVqG~GnVg--~~aa~~L~e------~GakVV 264 (454)
T PTZ00079 200 TGKNVKW---G---GSNIRPEATGYGLVYFVLEVLKKL-NDSLEGKTVVVSGSGNVA--QYAVEKLLQ------LGAKVL 264 (454)
T ss_pred CCCCCCC---C---CCCCCCcccHHHHHHHHHHHHHHc-CCCcCCCEEEEECCCHHH--HHHHHHHHH------CCCEEE
Confidence 4555544 3 334667788888887777776554 455788899999999542 345555544 477999
Q ss_pred EEEecCC
Q 025294 235 YIEDTTR 241 (255)
Q Consensus 235 sI~D~Tp 241 (255)
.|.|..-
T Consensus 265 avSD~~G 271 (454)
T PTZ00079 265 TMSDSDG 271 (454)
T ss_pred EEEcCCC
Confidence 9999883
No 29
>PRK09414 glutamate dehydrogenase; Provisional
Probab=25.89 E-value=1.1e+02 Score=30.64 Aligned_cols=61 Identities=16% Similarity=0.053 Sum_probs=43.4
Q ss_pred cCCCCCchhHHHHHHHHHHHHHHHcCCcEEEEEEEccCCCcchHHHHHHHHhcccCCCCCCCeEEEEecC
Q 025294 171 KGGPKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGFTYFKKKRQAIMSFREGFANSRDQNPIVYIEDTT 240 (255)
Q Consensus 171 Kg~rKsT~~AAq~aae~i~~kakelGik~V~V~vKG~G~gR~k~aaIkaL~~G~~~~r~glkI~sI~D~T 240 (255)
.++...|-+....+++.+++.. ...++..+|.|.|||.-- ..+.+.|.+ .|.+|+-|.|.+
T Consensus 205 ~gr~~aTg~Gv~~~~~~~~~~~-~~~l~g~rVaIqGfGnVG--~~~A~~L~~------~GakVVavsDs~ 265 (445)
T PRK09414 205 LIRTEATGYGLVYFAEEMLKAR-GDSFEGKRVVVSGSGNVA--IYAIEKAQQ------LGAKVVTCSDSS 265 (445)
T ss_pred CCCCCcccHHHHHHHHHHHHhc-CCCcCCCEEEEECCCHHH--HHHHHHHHH------CCCEEEEEEcCC
Confidence 4567788877777776666554 455788999999999643 345555543 478999999954
No 30
>PF00208 ELFV_dehydrog: Glutamate/Leucine/Phenylalanine/Valine dehydrogenase; InterPro: IPR006096 Glutamate, leucine, phenylalanine and valine dehydrogenases are structurally and functionally related. They contain a Gly-rich region containing a conserved Lys residue, which has been implicated in the catalytic activity, in each case a reversible oxidative deamination reaction. Glutamate dehydrogenases (1.4.1.2 from EC, 1.4.1.3 from EC, and 1.4.1.4 from EC) (GluDH) are enzymes that catalyse the NAD- and/or NADP-dependent reversible deamination of L-glutamate into alpha-ketoglutarate [, ]. GluDH isozymes are generally involved with either ammonia assimilation or glutamate catabolism. Two separate enzymes are present in yeasts: the NADP-dependent enzyme, which catalyses the amination of alpha-ketoglutarate to L-glutamate; and the NAD-dependent enzyme, which catalyses the reverse reaction [] - this form links the L-amino acids with the Krebs cycle, which provides a major pathway for metabolic interconversion of alpha-amino acids and alpha- keto acids []. Leucine dehydrogenase (1.4.1.9 from EC) (LeuDH) is a NAD-dependent enzyme that catalyses the reversible deamination of leucine and several other aliphatic amino acids to their keto analogues []. Each subunit of this octameric enzyme from Bacillus sphaericus contains 364 amino acids and folds into two domains, separated by a deep cleft. The nicotinamide ring of the NAD+ cofactor binds deep in this cleft, which is thought to close during the hydride transfer step of the catalytic cycle. Phenylalanine dehydrogenase (1.4.1.20 from EC) (PheDH) is na NAD-dependent enzyme that catalyses the reversible deamidation of L-phenylalanine into phenyl-pyruvate []. Valine dehydrogenase (1.4.1.8 from EC) (ValDH) is an NADP-dependent enzyme that catalyses the reversible deamidation of L-valine into 3-methyl-2-oxobutanoate []. This entry represents the C-terminal domain of these proteins.; GO: 0016491 oxidoreductase activity, 0006520 cellular amino acid metabolic process, 0055114 oxidation-reduction process; PDB: 1LEH_A 3AOG_D 3AOE_A 2YFQ_B 2YFH_B 1HRD_A 1K89_A 1AUP_A 1BGV_A 1B26_C ....
Probab=23.32 E-value=67 Score=29.27 Aligned_cols=61 Identities=16% Similarity=0.165 Sum_probs=38.7
Q ss_pred CCCCchhHHHHHHHHHHHHHHHcCCcEEEEEEEccCCCcchHHHHHHHHhcccCCCCCCCeEEEEecCC
Q 025294 173 GPKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGFTYFKKKRQAIMSFREGFANSRDQNPIVYIEDTTR 241 (255)
Q Consensus 173 ~rKsT~~AAq~aae~i~~kakelGik~V~V~vKG~G~gR~k~aaIkaL~~G~~~~r~glkI~sI~D~Tp 241 (255)
+...|-|....+.+.+.+......++..+|.|.|||.-- ..+.+.|.+ .|-+|+-|.|.+.
T Consensus 6 ~~~aTg~GV~~~~~~~~~~~~~~~l~g~~v~IqGfG~VG--~~~a~~l~~------~Ga~vv~vsD~~G 66 (244)
T PF00208_consen 6 RSEATGYGVAYAIEAALEHLGGDSLEGKRVAIQGFGNVG--SHAARFLAE------LGAKVVAVSDSSG 66 (244)
T ss_dssp TTTHHHHHHHHHHHHHHHHTTCHSSTTCEEEEEESSHHH--HHHHHHHHH------TTEEEEEEEESSE
T ss_pred CCcchHHHHHHHHHHHHHHcCCCCcCCCEEEEECCCHHH--HHHHHHHHH------cCCEEEEEecCce
Confidence 344555555555555555522223667899999998432 456666654 4678999999763
No 31
>cd05211 NAD_bind_Glu_Leu_Phe_Val NAD(P) binding domain of glutamate dehydrogenase, leucine dehydrogenase, phenylalanine dehydrogenase, and valine dehydrogenase. Amino acid dehydrogenase (DH) is a widely distributed family of enzymes that catalyzes the oxidative deamination of an amino acid to its keto acid and ammonia with concomitant reduction of NAD(P)+. This subfamily includes glutamate, leucine, phenylalanine, and valine DHs. Glutamate DH is a multi-domain enzyme that catalyzes the reaction from glutamate to 2-oxyoglutarate and ammonia in the presence of NAD or NADP. It is present in all organisms. Enzymes involved in ammonia assimilation are typically NADP+-dependent, while those involved in glutamate catabolism are generally NAD+-dependent. As in other NAD+-dependent DHs, monomers in this family have 2 domains separated by a deep cleft. Here the c-terminal domain contains a modified NAD-binding Rossmann fold with 7 rather than the usual 6 beta strands and one strand anti-parral
Probab=23.16 E-value=1.3e+02 Score=26.78 Aligned_cols=39 Identities=15% Similarity=0.241 Sum_probs=29.6
Q ss_pred cCCcEEEEEEEccCCCcchHHHHHHHHhcccCCCCCCCeEEEEecCC
Q 025294 195 MGLKSVVVRVKGFTYFKKKRQAIMSFREGFANSRDQNPIVYIEDTTR 241 (255)
Q Consensus 195 lGik~V~V~vKG~G~gR~k~aaIkaL~~G~~~~r~glkI~sI~D~Tp 241 (255)
..++..+|.|.|||.-- ..+.+.|.+ .|.+|+.|.|...
T Consensus 19 ~~l~g~~vaIqGfGnVG--~~~a~~L~~------~G~~vV~vsD~~g 57 (217)
T cd05211 19 DSLEGLTVAVQGLGNVG--WGLAKKLAE------EGGKVLAVSDPDG 57 (217)
T ss_pred CCcCCCEEEEECCCHHH--HHHHHHHHH------cCCEEEEEEcCCC
Confidence 45677899999999653 456666654 4789999999876
No 32
>PRK14031 glutamate dehydrogenase; Provisional
Probab=21.89 E-value=1.7e+02 Score=29.51 Aligned_cols=60 Identities=17% Similarity=0.093 Sum_probs=41.9
Q ss_pred cCCCCCchhHHHHHHHHHHHHHHHcCCcEEEEEEEccCCCcchHHHHHHHHhcccCCCCCCCeEEEEec
Q 025294 171 KGGPKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGFTYFKKKRQAIMSFREGFANSRDQNPIVYIEDT 239 (255)
Q Consensus 171 Kg~rKsT~~AAq~aae~i~~kakelGik~V~V~vKG~G~gR~k~aaIkaL~~G~~~~r~glkI~sI~D~ 239 (255)
.++...|-+....+...+++.. ...++..+|.|.|+|.-- ..+.+.|.+ .|-+|+-|.|.
T Consensus 201 ~~r~~aTg~Gv~~~~~~~~~~~-g~~l~g~rVaVQGfGNVG--~~aA~~L~e------~GAkVVaVSD~ 260 (444)
T PRK14031 201 LIRPEATGYGNIYFLMEMLKTK-GTDLKGKVCLVSGSGNVA--QYTAEKVLE------LGGKVVTMSDS 260 (444)
T ss_pred CCCCcccHHHHHHHHHHHHHhc-CCCcCCCEEEEECCCHHH--HHHHHHHHH------CCCEEEEEECC
Confidence 5667788877777776666544 345778899999999542 345555554 47799999993
Done!