Query 032493
Match_columns 139
No_of_seqs 140 out of 1042
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 14:48:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032493.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032493hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 CHL00136 rpl31 ribosomal prote 100.0 9.6E-35 2.1E-39 200.6 7.4 66 41-107 1-66 (68)
2 PRK00019 rpmE 50S ribosomal pr 100.0 8.6E-34 1.9E-38 197.7 7.7 67 42-110 1-69 (72)
3 COG0254 RpmE Ribosomal protein 100.0 1.7E-33 3.7E-38 198.0 7.9 69 42-111 1-72 (75)
4 TIGR00105 L31 ribosomal protei 100.0 2.5E-33 5.5E-38 192.8 7.5 65 42-108 1-67 (68)
5 PRK01678 rpmE2 50S ribosomal p 100.0 2.4E-33 5.3E-38 201.7 7.6 69 42-111 1-83 (87)
6 PRK01397 50S ribosomal protein 100.0 4.8E-33 1E-37 196.7 7.8 73 42-116 1-76 (78)
7 PRK00528 rpmE 50S ribosomal pr 100.0 1.2E-32 2.7E-37 190.9 7.1 66 42-109 1-71 (71)
8 PF01197 Ribosomal_L31: Riboso 100.0 6.6E-32 1.4E-36 185.9 -0.1 65 42-108 1-68 (69)
9 PF13453 zf-TFIIB: Transcripti 48.3 23 0.00049 21.4 2.6 26 60-86 5-30 (41)
10 PF04216 FdhE: Protein involve 39.5 33 0.00072 28.6 3.1 15 71-85 234-248 (290)
11 COG2139 RPL21A Ribosomal prote 36.9 33 0.00072 25.7 2.4 29 71-99 37-70 (98)
12 COG0121 Predicted glutamine am 32.8 17 0.00037 30.6 0.4 26 79-104 88-115 (252)
13 PF02661 Fic: Fic/DOC family; 29.6 22 0.00049 23.4 0.5 9 80-88 77-85 (97)
14 PRK04306 50S ribosomal protein 29.4 43 0.00094 24.8 2.0 28 71-98 39-71 (98)
15 TIGR01562 FdhE formate dehydro 28.7 51 0.0011 28.6 2.7 15 71-85 248-262 (305)
16 PRK03564 formate dehydrogenase 27.5 53 0.0012 28.6 2.6 15 71-85 248-262 (309)
17 PF06919 Phage_T4_Gp30_7: Phag 26.4 1.2E+02 0.0026 23.4 4.0 18 75-92 72-89 (121)
18 PF07591 PT-HINT: Pretoxin HIN 26.3 27 0.00059 26.1 0.5 13 77-89 57-69 (130)
19 PF12377 DuffyBP_N: Duffy bind 22.9 54 0.0012 22.8 1.4 16 73-88 26-41 (66)
20 TIGR01550 DOC_P1 death-on-curi 21.1 32 0.00069 25.5 -0.0 12 79-90 62-73 (121)
21 TIGR02613 mob_myst_B mobile my 20.9 53 0.0012 25.8 1.2 17 79-103 120-136 (186)
22 cd00352 Gn_AT_II Glutamine ami 20.3 49 0.0011 24.9 0.9 28 77-104 84-111 (220)
23 PLN02678 seryl-tRNA synthetase 20.2 55 0.0012 29.8 1.3 20 120-139 426-445 (448)
No 1
>CHL00136 rpl31 ribosomal protein L31; Validated
Probab=100.00 E-value=9.6e-35 Score=200.60 Aligned_cols=66 Identities=50% Similarity=1.028 Sum_probs=63.4
Q ss_pred cCCCCCCCCCcceeEEEeCCCeEEEEeeeeCcEEEeecCCCCCcccCceeeeeecchhHHHHHHHhc
Q 032493 41 CRKKDIHPQFYEDAKVYCNGELVMTTGGTQKEYVVDVWSGNHAFYLGGRSAVVVDADQVEKFRQKFG 107 (139)
Q Consensus 41 ~MKK~IHP~y~~vv~v~cs~g~~~~~gST~~~i~vDIcS~cHPFYTGkqk~~vdt~GRVeKFnKKfg 107 (139)
+||+||||+|+.++.|.|+|+++|+++||.++|.|||||+|||||||+|+ ++|++|||||||+||+
T Consensus 1 mMKk~IHP~y~~~~~v~c~~~~~~~~~ST~~~i~vdv~s~~HPfyTG~~~-~~~~~Grv~kF~kr~~ 66 (68)
T CHL00136 1 MPKKNIHPQWFPETKVYCDGQLVMTVGSTKPELNVDIWSGNHPFYTGSQK-IIDTEGRVERFMKKYG 66 (68)
T ss_pred CCCCCCCCCceeeEEEEEcCCCEEEEeecCCCEEEEeCCCCCccCcCCee-EecccccHHHHHHHhC
Confidence 59999999998788999999999999999999999999999999999986 8999999999999998
No 2
>PRK00019 rpmE 50S ribosomal protein L31; Reviewed
Probab=100.00 E-value=8.6e-34 Score=197.70 Aligned_cols=67 Identities=40% Similarity=0.628 Sum_probs=61.0
Q ss_pred CCCCCCCCCcceeEEEeCCCeEEEEeeee--CcEEEeecCCCCCcccCceeeeeecchhHHHHHHHhcCCc
Q 032493 42 RKKDIHPQFYEDAKVYCNGELVMTTGGTQ--KEYVVDVWSGNHAFYLGGRSAVVVDADQVEKFRQKFGGLS 110 (139)
Q Consensus 42 MKK~IHP~y~~vv~v~cs~g~~~~~gST~--~~i~vDIcS~cHPFYTGkqk~~vdt~GRVeKFnKKfg~~~ 110 (139)
||+||||+|++ +.+.|+||..|+++||. ++|.|||||+|||||||+|+ ++|++|||||||+||+.+.
T Consensus 1 MKk~IHP~y~~-v~~~c~~g~~f~~~ST~~~~~i~vdi~s~~HPFyTG~q~-~~dt~GRvekF~kry~~~~ 69 (72)
T PRK00019 1 MKKDIHPKYEE-VTVTCSCGNVFETRSTLGKDEINVDVCSKCHPFYTGKQK-IVDTGGRVERFNKRFGKKG 69 (72)
T ss_pred CCCCCCCCCEE-EEEEECCCCEEEEeecCCCCcEEEEeCCCCCCcCcCCEe-EeccCCcHHHHHHHhcccc
Confidence 99999999987 56668899999999994 56999999999999999987 8999999999999999753
No 3
>COG0254 RpmE Ribosomal protein L31 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.7e-33 Score=197.99 Aligned_cols=69 Identities=39% Similarity=0.667 Sum_probs=61.3
Q ss_pred CCCCCCCCCcceeEEEeC-CCeEEEEeeee--CcEEEeecCCCCCcccCceeeeeecchhHHHHHHHhcCCcc
Q 032493 42 RKKDIHPQFYEDAKVYCN-GELVMTTGGTQ--KEYVVDVWSGNHAFYLGGRSAVVVDADQVEKFRQKFGGLSE 111 (139)
Q Consensus 42 MKK~IHP~y~~vv~v~cs-~g~~~~~gST~--~~i~vDIcS~cHPFYTGkqk~~vdt~GRVeKFnKKfg~~~~ 111 (139)
||+||||+|+..+.+.|+ |++.|+++||. ++|+|||||.|||||||+|+ ++|++|||||||+||+.+..
T Consensus 1 MKk~IHP~y~~~v~~~~~s~g~~f~~~ST~~~~~i~vdV~s~~HPFyTG~qk-~~d~~Grv~kF~kRf~~~~~ 72 (75)
T COG0254 1 MKKDIHPEYYRPVVFVCSSCGNEFTTRSTKGTDEINLDVCSKCHPFYTGKQK-IVDTEGRVEKFNKRFGGFKG 72 (75)
T ss_pred CCCCcCCCccceEEEEeCCCCCEEEEEeccCCceEEEEeCCCCCCcCcCcee-EeeccccHHHHHHHhccccc
Confidence 999999997444555564 99999999999 48999999999999999997 99999999999999998644
No 4
>TIGR00105 L31 ribosomal protein L31. This family consists exclusively of bacterial (and organellar) 50S ribosomal protein L31. In some species, such as Bacillus subtilis, this protein exists in two forms (RpmE and YtiA), one of which (RpmE) contains a pair of motifs, CXC and CXXC, for binding zinc.
Probab=100.00 E-value=2.5e-33 Score=192.76 Aligned_cols=65 Identities=40% Similarity=0.640 Sum_probs=60.4
Q ss_pred CCCCCCCCCcceeEEEeCCCeEEEEeeeeCc--EEEeecCCCCCcccCceeeeeecchhHHHHHHHhcC
Q 032493 42 RKKDIHPQFYEDAKVYCNGELVMTTGGTQKE--YVVDVWSGNHAFYLGGRSAVVVDADQVEKFRQKFGG 108 (139)
Q Consensus 42 MKK~IHP~y~~vv~v~cs~g~~~~~gST~~~--i~vDIcS~cHPFYTGkqk~~vdt~GRVeKFnKKfg~ 108 (139)
||+||||+|+++.++ |+||..|+++||.++ |.|||||+|||||||+|+ ++|++|||||||+||+.
T Consensus 1 MKk~IHP~y~~v~~~-~s~g~~f~~~ST~~~~~i~vdi~s~~HPfyTG~~~-~~~~~GRv~KF~kry~~ 67 (68)
T TIGR00105 1 MKKDIHPDYHEITVT-CTCGNVFTTRSTWGKETLNLDICSKCHPFYTGKQK-IVDTGGRVDKFNKKFGG 67 (68)
T ss_pred CCCCCCCCCEEEEEE-ECCCCEEEEeeecCCceEEEEECCCCcccCCCceE-EeccCCcHHHHHHHhcC
Confidence 999999999986555 999999999999976 999999999999999886 89999999999999985
No 5
>PRK01678 rpmE2 50S ribosomal protein L31 type B; Reviewed
Probab=100.00 E-value=2.4e-33 Score=201.69 Aligned_cols=69 Identities=30% Similarity=0.464 Sum_probs=63.8
Q ss_pred CCCCCCCCCcceeEEEeCCCeEEEEeeeeC--------------cEEEeecCCCCCcccCceeeeeecchhHHHHHHHhc
Q 032493 42 RKKDIHPQFYEDAKVYCNGELVMTTGGTQK--------------EYVVDVWSGNHAFYLGGRSAVVVDADQVEKFRQKFG 107 (139)
Q Consensus 42 MKK~IHP~y~~vv~v~cs~g~~~~~gST~~--------------~i~vDIcS~cHPFYTGkqk~~vdt~GRVeKFnKKfg 107 (139)
||+||||+|++++|.+|+||..|.++||.+ +|.|||||+|||||||+|+ ++|++|||||||+||+
T Consensus 1 MKk~IHP~y~~v~~~~~t~g~~f~~~ST~~~~~t~~~~dg~~yp~i~vdi~S~~HPFyTGkq~-~vdt~GRVekF~kry~ 79 (87)
T PRK01678 1 MKKGIHPEYRPVVFHDTSTGFKFLTGSTITTDETIEWEDGKTYPLVKVEISSASHPFYTGKQK-FVDTEGRVEKFNKRFG 79 (87)
T ss_pred CCCCCCCCCEEEEEEECCCCCEEEEeeeccccceeeecCCcccceEEEEeCCCCCCcCcCCee-EeccCCcHHHHHHHHh
Confidence 999999999998888899999999999875 5999999999999999987 9999999999999999
Q ss_pred CCcc
Q 032493 108 GLSE 111 (139)
Q Consensus 108 ~~~~ 111 (139)
.+..
T Consensus 80 ~~~~ 83 (87)
T PRK01678 80 RFAS 83 (87)
T ss_pred hhhh
Confidence 7643
No 6
>PRK01397 50S ribosomal protein L31; Provisional
Probab=100.00 E-value=4.8e-33 Score=196.66 Aligned_cols=73 Identities=27% Similarity=0.302 Sum_probs=62.8
Q ss_pred CCCCCCCCCcceeEEEeCCCeEEEEeeee--CcEEEeecCCCCCcccCceeeeeec-chhHHHHHHHhcCCccccccc
Q 032493 42 RKKDIHPQFYEDAKVYCNGELVMTTGGTQ--KEYVVDVWSGNHAFYLGGRSAVVVD-ADQVEKFRQKFGGLSEIMEIP 116 (139)
Q Consensus 42 MKK~IHP~y~~vv~v~cs~g~~~~~gST~--~~i~vDIcS~cHPFYTGkqk~~vdt-~GRVeKFnKKfg~~~~~~~~~ 116 (139)
||+||||+|+++++ .| ||..|.++||. ++|+|||||+|||||||+|+.++|+ +|||||||+||+.+...+.++
T Consensus 1 MKk~IHP~y~~v~~-~~-~G~~f~~~ST~~~~~i~vdi~s~~HPFyTG~q~~~vdt~~GRVeKF~kry~~~~~~~~~~ 76 (78)
T PRK01397 1 MKSGIHPEYKKFLI-KV-GSDVFETMSTHPTGEILMDVDFRKHPAWNKDSGNVVNQSNKSVSDFNKRFSGLSFGSKKE 76 (78)
T ss_pred CCCCCCCCCEEEEE-EE-CCCEEEEeECCCCCcEEEEeCCCCCCcCcCCeeEEecCCCccHHHHHHHHcCcccccccc
Confidence 99999999998665 47 79999999998 5799999999999999998645786 799999999999986544443
No 7
>PRK00528 rpmE 50S ribosomal protein L31; Reviewed
Probab=99.97 E-value=1.2e-32 Score=190.86 Aligned_cols=66 Identities=35% Similarity=0.504 Sum_probs=59.8
Q ss_pred CCCCCCCCCcceeEEEeCCCeEEEEeee----eCcEEEeecCCCCCccc-CceeeeeecchhHHHHHHHhcCC
Q 032493 42 RKKDIHPQFYEDAKVYCNGELVMTTGGT----QKEYVVDVWSGNHAFYL-GGRSAVVVDADQVEKFRQKFGGL 109 (139)
Q Consensus 42 MKK~IHP~y~~vv~v~cs~g~~~~~gST----~~~i~vDIcS~cHPFYT-Gkqk~~vdt~GRVeKFnKKfg~~ 109 (139)
||+||||+|+++++ .|+||..|++.|| +++|+|||||+|||||| |+|+ ++|++|||||||+||+.+
T Consensus 1 MKk~IHP~y~~v~~-~~~~g~~f~~~ST~g~~~~~i~vdv~s~~HPfyT~G~q~-~~d~~GRv~kF~kky~~l 71 (71)
T PRK00528 1 MKKDIHPDYHPIKV-VMTDGTEYETRSTWGKTGPELRLDIDSGNHPAWTGGTQK-LLDTGGRVAKFNKKFGGL 71 (71)
T ss_pred CCCCCCCCCEEEEE-EEeCCCEEEEEEcCCCCCCeEEEEECCCCCccEeCCcCe-EecccCcHHHHHHHHccC
Confidence 99999999998655 5889999999875 67899999999999999 9886 999999999999999864
No 8
>PF01197 Ribosomal_L31: Ribosomal protein L31; InterPro: IPR002150 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 L31 is one of the proteins from the large ribosomal subunit. L31 is a protein of 66 to 97 amino-acid residues which has only been found so far in bacteria and in some plant and algal chloroplasts.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3D5D_4 3PYO_1 3D5B_4 3PYV_1 3PYT_1 3MRZ_1 3MS1_1 3PYR_1 3F1F_4 3F1H_4 ....
Probab=99.96 E-value=6.6e-32 Score=185.87 Aligned_cols=65 Identities=43% Similarity=0.649 Sum_probs=57.5
Q ss_pred CCCCCCCCCcceeEEEeC-CCeEEEEeeeeCc--EEEeecCCCCCcccCceeeeeecchhHHHHHHHhcC
Q 032493 42 RKKDIHPQFYEDAKVYCN-GELVMTTGGTQKE--YVVDVWSGNHAFYLGGRSAVVVDADQVEKFRQKFGG 108 (139)
Q Consensus 42 MKK~IHP~y~~vv~v~cs-~g~~~~~gST~~~--i~vDIcS~cHPFYTGkqk~~vdt~GRVeKFnKKfg~ 108 (139)
||+||||+|++ +.|.|+ ||..|.++||.+. |.|||||+|||||||+++ ++|++|||||||+||+.
T Consensus 1 MKk~IHP~y~~-v~v~c~s~g~~~~~~St~~~~~~~vdi~s~~HPfytG~~~-~~~~~Grv~KF~kkf~~ 68 (69)
T PF01197_consen 1 MKKGIHPEYRE-VKVTCSSCGNTFETRSTKEYPVIKVDICSNCHPFYTGKQK-VVDTAGRVEKFNKKFGK 68 (69)
T ss_dssp --SSTSSSHCE-EEEEES-SSSCECECSSSSES-EEECSCSSSSCTTCSCSS-CSCCCCCCTSCCTCCCC
T ss_pred CCCCCCCCCEE-EEEEEcCCCCEEEEEECCcceEEEEeecCCCCEEEcCcEE-EEccccCHHHHHHHHcC
Confidence 89999999987 566666 9999999999865 999999999999999876 89999999999999985
No 9
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=48.34 E-value=23 Score=21.43 Aligned_cols=26 Identities=8% Similarity=0.065 Sum_probs=17.4
Q ss_pred CCeEEEEeeeeCcEEEeecCCCCCccc
Q 032493 60 GELVMTTGGTQKEYVVDVWSGNHAFYL 86 (139)
Q Consensus 60 ~g~~~~~gST~~~i~vDIcS~cHPFYT 86 (139)
|+..+.... ...+.||+|.+||=.|-
T Consensus 5 C~~~l~~~~-~~~~~id~C~~C~G~W~ 30 (41)
T PF13453_consen 5 CGTELEPVR-LGDVEIDVCPSCGGIWF 30 (41)
T ss_pred CCcccceEE-ECCEEEEECCCCCeEEc
Confidence 444443222 26799999999997764
No 10
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=39.46 E-value=33 Score=28.57 Aligned_cols=15 Identities=20% Similarity=0.386 Sum_probs=13.0
Q ss_pred CcEEEeecCCCCCcc
Q 032493 71 KEYVVDVWSGNHAFY 85 (139)
Q Consensus 71 ~~i~vDIcS~cHPFY 85 (139)
+.++||+|..||-|.
T Consensus 234 ~~~rve~C~~C~~Yl 248 (290)
T PF04216_consen 234 PAYRVEVCESCGSYL 248 (290)
T ss_dssp -SEEEEEETTTTEEE
T ss_pred CcEEEEECCcccchH
Confidence 469999999999986
No 11
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=36.89 E-value=33 Score=25.68 Aligned_cols=29 Identities=17% Similarity=0.203 Sum_probs=22.6
Q ss_pred CcEEEeecCCC-----CCcccCceeeeeecchhH
Q 032493 71 KEYVVDVWSGN-----HAFYLGGRSAVVVDADQV 99 (139)
Q Consensus 71 ~~i~vDIcS~c-----HPFYTGkqk~~vdt~GRV 99 (139)
+.+.|||+++- ||+|-|+...++...||.
T Consensus 37 d~V~I~IdpSv~kGmPh~rf~G~TG~Vvg~~g~a 70 (98)
T COG2139 37 DKVHIDIDPSVHKGMPHPRFQGKTGTVVGVRGRA 70 (98)
T ss_pred CEEEEEeCcccccCCCCccccCcceEEEeccCCE
Confidence 35888998875 799999887677777773
No 12
>COG0121 Predicted glutamine amidotransferase [General function prediction only]
Probab=32.84 E-value=17 Score=30.58 Aligned_cols=26 Identities=23% Similarity=0.314 Sum_probs=18.5
Q ss_pred CCCCCcccCceee--eeecchhHHHHHH
Q 032493 79 SGNHAFYLGGRSA--VVVDADQVEKFRQ 104 (139)
Q Consensus 79 S~cHPFYTGkqk~--~vdt~GRVeKFnK 104 (139)
++||||+-+.-.. +.-=.|.|++|..
T Consensus 88 ~ntHPF~~~~~~~~~~FaHNG~l~~~~~ 115 (252)
T COG0121 88 SNTHPFTRELWGYIWLFAHNGQLDKFKL 115 (252)
T ss_pred cCCCCccccCCccceEEEecCcccCccc
Confidence 6999999875321 2344799999876
No 13
>PF02661 Fic: Fic/DOC family; InterPro: IPR003812 This entry contains the Fic (filamentation induced by cAMP) protein and doc (death on curing) protein. The Fic protein is involved in cell division and is suggested to be involved in the synthesis of PAB or folate, indicating that the Fic protein and cAMP are involved in a regulatory mechanism of cell division via folate metabolism []. This family contains a central conserved motif HPFXXGNG in most members. The exact molecular function of these proteins is uncertain. P1 lysogens of Escherichia coli carry the prophage as a stable low copy number plasmid. The frequency with which viable cells cured of prophage are produced is about 10(-5) per cell per generation []. A significant part of this remarkable stability can be attributed to a plasmid-encoded mechanism that causes death of cells that have lost P1 []. In other words, the lysogenic cells appear to be addicted to the presence of the prophage. The plasmid withdrawal response depends on a gene named doc (death on curing) that is represented by this family.; PDB: 3SHG_A 3N3V_A 3N3U_A 2F6S_B 2JK8_B 2VZA_D 2VY3_A 3LET_B 3EQX_A 3SE5_D ....
Probab=29.59 E-value=22 Score=23.43 Aligned_cols=9 Identities=33% Similarity=0.287 Sum_probs=6.5
Q ss_pred CCCCcccCc
Q 032493 80 GNHAFYLGG 88 (139)
Q Consensus 80 ~cHPFYTGk 88 (139)
.-|||+-|.
T Consensus 77 ~iHPF~dGN 85 (97)
T PF02661_consen 77 YIHPFRDGN 85 (97)
T ss_dssp HHCSSSSHH
T ss_pred hcCcccCCC
Confidence 358998774
No 14
>PRK04306 50S ribosomal protein L21e; Reviewed
Probab=29.44 E-value=43 Score=24.80 Aligned_cols=28 Identities=14% Similarity=0.156 Sum_probs=21.8
Q ss_pred CcEEEeecCCC-----CCcccCceeeeeecchh
Q 032493 71 KEYVVDVWSGN-----HAFYLGGRSAVVVDADQ 98 (139)
Q Consensus 71 ~~i~vDIcS~c-----HPFYTGkqk~~vdt~GR 98 (139)
+.+.|+|+++. ||+|-|+...+++..|+
T Consensus 39 d~V~I~~d~sv~kGmPh~~yhGkTG~V~~v~~~ 71 (98)
T PRK04306 39 DKVHIVIDPSVHKGMPHPRFHGKTGTVVGKRGR 71 (98)
T ss_pred CEEEEEecCceecCCccccccCCCEEEEeecCe
Confidence 34778888887 78999987766666776
No 15
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=28.75 E-value=51 Score=28.63 Aligned_cols=15 Identities=0% Similarity=0.084 Sum_probs=13.0
Q ss_pred CcEEEeecCCCCCcc
Q 032493 71 KEYVVDVWSGNHAFY 85 (139)
Q Consensus 71 ~~i~vDIcS~cHPFY 85 (139)
+-+++|+|..||-|.
T Consensus 248 ~~~r~e~C~~C~~Yl 262 (305)
T TIGR01562 248 AVLKAETCDSCQGYL 262 (305)
T ss_pred cceEEeeccccccch
Confidence 359999999999975
No 16
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=27.47 E-value=53 Score=28.65 Aligned_cols=15 Identities=0% Similarity=0.016 Sum_probs=13.1
Q ss_pred CcEEEeecCCCCCcc
Q 032493 71 KEYVVDVWSGNHAFY 85 (139)
Q Consensus 71 ~~i~vDIcS~cHPFY 85 (139)
+-+++|+|..||-|.
T Consensus 248 ~~~r~e~C~~C~~Yl 262 (309)
T PRK03564 248 AAVKAESCGDCGTYL 262 (309)
T ss_pred cceEeeecccccccc
Confidence 358999999999986
No 17
>PF06919 Phage_T4_Gp30_7: Phage Gp30.7 protein; InterPro: IPR009690 This family consists of several phage Gp30.7 proteins of 121 residues in length. Family members seem to be exclusively from the T4-like viruses. The function of this family is unknown.
Probab=26.38 E-value=1.2e+02 Score=23.39 Aligned_cols=18 Identities=17% Similarity=0.185 Sum_probs=14.2
Q ss_pred EeecCCCCCcccCceeee
Q 032493 75 VDVWSGNHAFYLGGRSAV 92 (139)
Q Consensus 75 vDIcS~cHPFYTGkqk~~ 92 (139)
.+-+-..||-|.|.++.+
T Consensus 72 r~RDLgTHPcwnG~nRk~ 89 (121)
T PF06919_consen 72 RERDLGTHPCWNGVNRKL 89 (121)
T ss_pred hhcccCCCcCccCcchhh
Confidence 456778999999998743
No 18
>PF07591 PT-HINT: Pretoxin HINT domain; InterPro: IPR011451 This entry represents a cluster of homologous proteins identified in Leptospira interrogans. One member (Q8EZX6 from SWISSPROT) has been predicted to be a phenazine biosynthesis family protein.; PDB: 2JNQ_A 2JMZ_A.
Probab=26.35 E-value=27 Score=26.06 Aligned_cols=13 Identities=31% Similarity=0.716 Sum_probs=0.0
Q ss_pred ecCCCCCcccCce
Q 032493 77 VWSGNHAFYLGGR 89 (139)
Q Consensus 77 IcS~cHPFYTGkq 89 (139)
.|...||||+-.+
T Consensus 57 ~~T~~HPF~~~~~ 69 (130)
T PF07591_consen 57 TTTPNHPFWVEGK 69 (130)
T ss_dssp -------------
T ss_pred ccccccccccchH
Confidence 4788999999744
No 19
>PF12377 DuffyBP_N: Duffy binding protein N terminal ; InterPro: IPR021032 This entry represents the N terminus of the Duffy-antigen binding protein and is thought to bind to the human erythrocytes Duffy blood group determinant. These domains are found in eukaryotic proteins and are approximately 70 amino acids in length [].
Probab=22.92 E-value=54 Score=22.81 Aligned_cols=16 Identities=19% Similarity=-0.108 Sum_probs=13.4
Q ss_pred EEEeecCCCCCcccCc
Q 032493 73 YVVDVWSGNHAFYLGG 88 (139)
Q Consensus 73 i~vDIcS~cHPFYTGk 88 (139)
|.-||+|+-||.||-.
T Consensus 26 ldyd~s~nghp~g~~d 41 (66)
T PF12377_consen 26 LDYDTSSNGHPAGTID 41 (66)
T ss_pred EEeeccCCCCcCchhh
Confidence 5569999999999864
No 20
>TIGR01550 DOC_P1 death-on-curing family protein. A similar region, with K replaced by G, is found in the huntingtin interacting protein (HYPE) family.
Probab=21.10 E-value=32 Score=25.48 Aligned_cols=12 Identities=17% Similarity=0.290 Sum_probs=10.2
Q ss_pred CCCCCcccCcee
Q 032493 79 SGNHAFYLGGRS 90 (139)
Q Consensus 79 S~cHPFYTGkqk 90 (139)
..+|||+.|.+|
T Consensus 62 ~~~HpF~DGNKR 73 (121)
T TIGR01550 62 IRSHPFNNANKR 73 (121)
T ss_pred HHhCCCccccHH
Confidence 468999999886
No 21
>TIGR02613 mob_myst_B mobile mystery protein B. Members of this protein family, which we designate mobile mystery protein B, are found in mobization-related contexts more often than not, including within a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and on plasmids in Agrobacterium tumefaciens and Coxiella burnetii, always together with mobile mystery protein A (TIGR02612), a member of the family of helix-turn-helix DNA binding proteins (pfam01381). This protein is encoded by the downstream member of the gene pair and belongs to the Fic protein family (pfam02661), where Fic (filamentation induced by cAMP) is a regulator of cell division. The characteristics of having a two-gene operon in a varied context and often on plasmids, with one member affecting cell division and the other able to bind DNA, suggests similarity to addiction modules.
Probab=20.93 E-value=53 Score=25.84 Aligned_cols=17 Identities=18% Similarity=0.288 Sum_probs=12.4
Q ss_pred CCCCCcccCceeeeeecchhHHHHH
Q 032493 79 SGNHAFYLGGRSAVVVDADQVEKFR 103 (139)
Q Consensus 79 S~cHPFYTGkqk~~vdt~GRVeKFn 103 (139)
-.-|||..|. ||+.|+-
T Consensus 120 ~~IHPF~DGN--------GRt~Rll 136 (186)
T TIGR02613 120 VAIHPFPNGN--------GRHARLA 136 (186)
T ss_pred heecCcCCCC--------cHHHHHH
Confidence 4579999883 7777765
No 22
>cd00352 Gn_AT_II Glutamine amidotransferases class-II (GATase). The glutaminase domain catalyzes an amide nitrogen transfer from glutamine to the appropriate substrate. In this process, glutamine is hydrolyzed to glutamic acid and ammonia. This domain is related to members of the Ntn (N-terminal nucleophile) hydrolase superfamily and is found at the N-terminus of enzymes such as glucosamine-fructose 6-phosphate synthase (GLMS or GFAT), glutamine phosphoribosylpyrophosphate (Prpp) amidotransferase (GPATase), asparagine synthetase B (AsnB), beta lactam synthetase (beta-LS) and glutamate synthase (GltS). GLMS catalyzes the formation of glucosamine 6-phosphate from fructose 6-phosphate and glutamine in amino sugar synthesis. GPATase catalyzes the first step in purine biosynthesis, an amide transfer from glutamine to PRPP, resulting in phosphoribosylamine, pyrophosphate and glutamate. Asparagine synthetase B synthesizes asparagine from aspartate and glutamine. Beta-LS catalyzes the format
Probab=20.26 E-value=49 Score=24.94 Aligned_cols=28 Identities=11% Similarity=0.213 Sum_probs=18.8
Q ss_pred ecCCCCCcccCceeeeeecchhHHHHHH
Q 032493 77 VWSGNHAFYLGGRSAVVVDADQVEKFRQ 104 (139)
Q Consensus 77 IcS~cHPFYTGkqk~~vdt~GRVeKFnK 104 (139)
-..+||||..+.....+.-.|.|+.+..
T Consensus 84 ~~~n~hPf~~~~~~~~~~hNG~i~n~~~ 111 (220)
T cd00352 84 SEANAQPFRSEDGRIALVHNGEIYNYRE 111 (220)
T ss_pred CCCCCCCcCcCCCCEEEEECcEEEcHHH
Confidence 4589999998743324455788776653
No 23
>PLN02678 seryl-tRNA synthetase
Probab=20.16 E-value=55 Score=29.77 Aligned_cols=20 Identities=50% Similarity=0.582 Sum_probs=14.8
Q ss_pred cceecCCccccccccCCCCC
Q 032493 120 GEIVLPPKRKSAAAKGGKKK 139 (139)
Q Consensus 120 ~~~~~~~~~~~~~~~~~~~~ 139 (139)
|...++..++-+++|+||||
T Consensus 426 g~~~i~~~~~~~~~~~~~~~ 445 (448)
T PLN02678 426 GIEFLPFKKKPPAKGKGKKK 445 (448)
T ss_pred CCceecCCCCcccccccccc
Confidence 43456677777899999886
Done!